diff --git a/Makefile b/Makefile
index b58113f..9354ca8 100644
--- a/Makefile
+++ b/Makefile
@@ -1,24 +1,26 @@
 # include SeqAn libraries, don't warn about MD5 deprecation
 CXXFLAGS+=-I. -Wno-deprecated-declarations
 
+#include htslib by setting -I<path_to_htslib/include> and link to the htslib library
+HTSDIR=<path_to_htsdir>
+CXXFLAGS+=-I$(HTSDIR)/include
 
-# RELEASE build 
-CXXFLAGS+= -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 
-LDLIBS=-lz -lssl -lcrypto 
-
+# RELEASE build
+CXX=g++ -std=c++11 -pthread
+CXXFLAGS+= -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1
+LDFLAGS=-L$(HTSDIR)/lib -lz -lssl -lcrypto -Wl,-rpath,$(HTSDIR)/lib -lhts
 
 TARGET = bamhash_checksum_bam bamhash_checksum_fastq bamhash_checksum_fasta
 all: $(TARGET)
 
 bamhash_checksum_bam: bamhash_checksum_common.o bamhash_checksum_bam.o
-	 $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) 
+	 $(CXX) $(LDFLAGS) -o $@ $^
 
 bamhash_checksum_fastq: bamhash_checksum_common.o bamhash_checksum_fastq.o
-	 $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS)
+	 $(CXX) $(LDFLAGS) -o $@ $^
 
 bamhash_checksum_fasta: bamhash_checksum_common.o bamhash_checksum_fasta.o
-	 $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS)
-
+	 $(CXX) $(LDFLAGS) -o $@ $^
 
 clean:
-	$(RM) *.o *~ $(TARGET)  
+	$(RM) *.o *~ $(TARGET)
diff --git a/README.md b/README.md
index df36656..e23e79e 100644
--- a/README.md
+++ b/README.md
@@ -8,6 +8,8 @@ composed of the readname, whether it is first or last in pair, sequence and qual
 All the hash values are summed up so the result is independent of the ordering within the files.
 The result can be compared to verify that the pair of FASTQ files contain the same read 
 information as the aligned BAM file.
+The program is written in C++ and uses SeqAnHTS v1.0 for parsing FASTQ, gzip compressed FASTQ and BAM files.
+SeqAnHTS is a fork of SeqAn library ( Döring etal. , 2008 ) that uses htslib to read SAM/BAM/CRAM files.
 
 ## Manuscript
 
@@ -35,6 +37,7 @@ Both multiline FASTA and FASTQ are supported and gzipped input for FASTA and FAS
 
 ~~~
 bamhash_checksum_bam [OPTIONS] <in.bam> <in2.bam> ...
+bamhash_checksum_bam [OPTIONS] -r <reference-file> <in.cram>
 ~~~
 
 processes a number of BAM files. BAM files are assumed to contain paired end reads. If you run with `--no-paired` it treats all reads as single end and displays a warning if any read is marked as "second in pair" in the BAM file.
@@ -57,4 +60,8 @@ processes a number of FASTA files. All FASTA files are assumed to be single end
 
 ## Compiling
 
-The only external dependency is on OpenSSL for the MD5 implementation.
+External dependencies are on:
+ OpenSSL for the MD5 implementation
+ htslib library (version 1.9)
+ 
+
diff --git a/bamhash_checksum_bam.cpp b/bamhash_checksum_bam.cpp
index f5fda99..e6edee0 100644
--- a/bamhash_checksum_bam.cpp
+++ b/bamhash_checksum_bam.cpp
@@ -1,6 +1,7 @@
+#include "htslib/hts.h"
+#include <seqan/bam_io.h>
 #include <iostream>
 #include <seqan/stream.h>
-#include <seqan/bam_io.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string>
@@ -9,26 +10,29 @@
 #include <stdint.h>
 #include <vector>
 #include <seqan/arg_parse.h>
+#include <seqan/hts_io.h>
 
 
-#include "bamhash_checksum_common.h"
 
+#include "bamhash_checksum_common.h"
 
-/** only needed for seqan 1.4.1 and lower
-inline bool
-hasFlagSupplementary(seqan::BamAlignmentRecord const & record)
-{
-    return (record.flag & 0x0800) == 0x0800;
-}
-*/
 struct Baminfo {
   std::vector<std::string>  bamfiles;
   bool debug;
   bool noReadNames;
   bool noQuality;
   bool paired;
+  seqan::CharString reference;
 
-  Baminfo() : debug(false), noReadNames(false), noQuality(false), paired(true) {}
+  Baminfo() : debug(false), noReadNames(false), noQuality(false), paired(true), reference("") {}
+
+};
+
+struct Counts {
+  uint64_t sum;
+  uint64_t count;
+
+  Counts() : sum(0), count(0) {}
 
 };
 
@@ -38,16 +42,15 @@ parseCommandLine(Baminfo& options, int argc, char const **argv) {
   seqan::ArgumentParser parser("bamhash_checksum_bam");
   //readlink("/proc/self/exe", options.bindir, sizeof(options.bindir)-1);
 
-  setShortDescription(parser, "Checksum of a bam file"); //TODO change description
+  setShortDescription(parser, "Checksum of a sam, bam or cram file"); //TODO change description
   setVersion(parser, BAMHASH_VERSION);
-  setDate(parser, "May 2015");
+  setDate(parser, "Oct 2018");
 
   addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fI<in.bam> <in2.bam> ...\\fP");
   addDescription(parser, "Program for checksum of sequence reads. ");
 
-  addArgument(parser, seqan::ArgParseArgument(seqan::ArgParseArgument::INPUTFILE,"bamfile", "False", 1));
-
-  setValidValues(parser, 0,"bam sam");
+  addArgument(parser, seqan::ArgParseArgument(seqan::ArgParseArgument::INPUT_FILE,"bamfile", "False", 1));
+  setValidValues(parser, 0,"sam bam cram");
 
   addSection(parser, "Options");
 
@@ -55,7 +58,11 @@ parseCommandLine(Baminfo& options, int argc, char const **argv) {
   addOption(parser, seqan::ArgParseOption("d", "debug", "Debug mode. Prints full hex for each read to stdout"));
   addOption(parser, seqan::ArgParseOption("R", "no-readnames", "Do not use read names as part of checksum"));
   addOption(parser, seqan::ArgParseOption("Q", "no-quality", "Do not use read quality as part of checksum"));
-  addOption(parser, seqan::ArgParseOption("P", "no-paired", "Bam files were not generated with paired-end reads"));
+  addOption(parser, seqan::ArgParseOption("P", "no-paired", "Cram files were not generated with paired-end reads"));
+  addOption(parser, seqan::ArgParseOption("r", "reference-file", "Path to reference-file if reference not given in header",
+                    seqan::ArgParseArgument::INPUT_FILE));
+
+  setValidValues(parser, "reference-file", "fa");
 
   // Parse command line.
   seqan::ArgumentParser::ParseResult res = seqan::parse(parser, argc, argv);
@@ -67,6 +74,7 @@ parseCommandLine(Baminfo& options, int argc, char const **argv) {
   options.noReadNames = isSet(parser, "no-readnames");
   options.noQuality = isSet(parser, "no-quality");
   options.paired = !isSet(parser, "no-paired");
+  getOptionValue(options.reference, parser, "reference-file");
 
   options.bamfiles = getArgumentValues(parser, 0);
 
@@ -74,6 +82,68 @@ parseCommandLine(Baminfo& options, int argc, char const **argv) {
 }
 
 
+// -----------------------------------------------------------------------------
+// FUNCTION getSampleIdAndLaneNames()
+// -----------------------------------------------------------------------------
+
+void getLaneNames(std::map<seqan::CharString, unsigned> & laneNames, std::string const & header)
+{
+  for (int i = 0; i < header.size(); /*empty on purpose*/)
+  {
+    auto hdr_find_it = std::find(header.begin() + i, header.end(), '\n');
+    std::string line = header.substr(i, hdr_find_it - header.begin() - i);
+
+    if (line.size() > 7 && line[0] == '@' && line[1] == 'R' && line[2] == 'G' && line[3] == '\t')
+    {
+      for (int j = 0; j < static_cast<int>(line.size()); /*empty on purpose*/)
+      {
+        auto line_find_it = std::find(line.begin() + j, line.end(), '\t');
+        std::string field = line.substr(j, line_find_it - line.begin() - j);
+
+        if (field.size() > 3 && field[0] == 'I' && field[1] == 'D' && field[2] == ':')
+        {
+          seqan::CharString read_group_name = field.substr(3);
+          int read_group_index = laneNames.size();
+          laneNames[read_group_name] = read_group_index;
+        }
+
+        j = std::distance(line.begin(), line_find_it) + 1;
+      }
+    }
+
+    i = std::distance(header.begin(), hdr_find_it) + 1;
+  }
+}
+
+// -----------------------------------------------------------------------------
+// FUNCTION getLane()
+// -----------------------------------------------------------------------------
+
+int getLane(seqan::BamAlignmentRecord & record,
+            seqan::BamTagsDict & tagsDict,
+            std::map<seqan::CharString, unsigned> & laneNames)
+{
+  unsigned tagIdx = 0;
+
+  if (!seqan::findTagKey(tagIdx, tagsDict, "RG"))
+  {
+    std::cerr << "ERROR: Found a read with a missing read group (RG) tag\n";
+    return -1;
+  }
+
+  seqan::CharString read_group;
+
+  if(!seqan::extractTagValue(read_group, tagsDict, tagIdx))
+  {
+    std::cerr << "ERROR: Failed to extract read group (RG) tag value\n";
+    return -1;
+  }
+
+  return laneNames[read_group];
+}
+
+
+
 int main(int argc, char const **argv) {
 
   Baminfo info; // Define structure variable
@@ -83,58 +153,48 @@ int main(int argc, char const **argv) {
     return res == seqan::ArgumentParser::PARSE_ERROR;
   }
 
-  uint64_t sum = 0;
-  uint64_t count = 0;
+//Moving below to struct
+//  uint64_t sum = 0;
+//  uint64_t count = 0;
   bool pairedWarning = false;
 
-  
+  //adding new stuff
+  std::map<seqan::CharString, unsigned> laneNames;
+  // Initialize all counts for each lane.
+  seqan::String<Counts> counts;
 
   for (int i = 0; i < info.bamfiles.size(); i++) {
-    // Open BGZF Stream for reading.
-    seqan::Stream<seqan::Bgzf> inStream;
 
     const char* bamfile = info.bamfiles[i].c_str();
-    
-    if (!open(inStream, bamfile, "r")) {
-      std::cerr << "ERROR: Could not open " << bamfile << " for reading.\n";
-      return 1;
-    }
+    const char* reference = toCString(info.reference);
 
-    // Setup name store, cache, and BAM I/O context.
-    typedef seqan::StringSet<seqan::CharString> TNameStore;
-    typedef seqan::NameStoreCache<TNameStore>   TNameStoreCache;
-    typedef seqan::BamIOContext<TNameStore>     TBamIOContext;
-    TNameStore      nameStore;
-    TNameStoreCache nameStoreCache(nameStore);
-    TBamIOContext   context(nameStore, nameStoreCache);
-
-    // Read header.
-    seqan::BamHeader header;
-    if (readRecord(header, context, inStream, seqan::Bam()) != 0) {
-      std::cerr << "ERROR: Could not read header from BAM file " << bamfile << "\n";
-      return 1;
-    }
-    seqan::clear(header);
+    // Open stream for reading
+    seqan::HtsFile inStream(bamfile, "r", reference);
+
+    // Initialize lane names (read groups).
+    std::string header(inStream.hdr->text, inStream.hdr->l_text);
+    getLaneNames(laneNames, header);
+    unsigned lanecount = laneNames.size();
+    resize(counts, lanecount);
 
     // Define:
     seqan::BamAlignmentRecord record;
     seqan::CharString string2hash;
-    //char hexCstr[33];
 
     // Read record
-    while (!atEnd(inStream)) {
-      if (readRecord(record, context, inStream, seqan::Bam()) != 0) {
-        std::cerr << "ERROR: Could not read record from BAM File " << bamfile << "\n";
-        return 1;
-      }
+    while (seqan::readRecord(record, inStream)){
+      seqan::BamTagsDict tagsDict(record.tags);
+      int l = getLane(record, tagsDict, laneNames);
+      if (l == -1) return 1;
+
       // Check if flag: reverse complement and change record accordingly
       if (hasFlagRC(record)) {
-        reverseComplement(record.seq);
-        reverse(record.qual);
+        seqan::reverseComplement(record.seq);
+        seqan::reverse(record.qual);
       }
       // Check if flag: supplementary and exclude those
       if (!hasFlagSupplementary(record) && !hasFlagSecondary(record)) {
-        count +=1;
+        counts[l].count +=1;
         // Construct one string from record
         if (!info.noReadNames) {
           seqan::append(string2hash, record.qName);
@@ -143,7 +203,7 @@ int main(int argc, char const **argv) {
               seqan::append(string2hash, "/2");
             } else {
               if (!pairedWarning) {
-                std::cerr << "WARNING: BamHash was run with --no-paired mode, but BAM file has reads marked as second pair" << std::endl;
+                std::cerr << "WARNING: seqread was run with --no-paired mode, but BAM file has reads marked as second pair" << std::endl;
                 pairedWarning = true;
               }
               seqan::append(string2hash, "/1");
@@ -162,26 +222,25 @@ int main(int argc, char const **argv) {
         // Get MD5 hash
         hash_t hex = str2md5(toCString(string2hash), length(string2hash));
 
-
         if (info.debug) {
           std::cout << string2hash << " " << std::hex << hex.p.low << "\n";
         } else {
-          hexSum(hex, sum);
+          hexSum(hex, counts[l].sum);
         }
 
         seqan::clear(string2hash);
       }
     }
-
-    // print result
-    
   }
 
   if (!info.debug) {
-    std::cout << std::hex << sum << "\t";
-    std::cout << std::dec << count << "\n";
+    for (std::map<seqan::CharString, unsigned>::iterator it = laneNames.begin(); it != laneNames.end(); ++it) {
+      std::cout << it->first << "\t";
+      int lid = it->second;
+      std::cout << std::hex << counts[lid].sum << "\t";
+      std::cout << std::dec << counts[lid].count << "\n";
+    }
   }
-  
+
   return 0;
 }
-
diff --git a/bamhash_checksum_common.h b/bamhash_checksum_common.h
index b3732d9..e8c6b30 100644
--- a/bamhash_checksum_common.h
+++ b/bamhash_checksum_common.h
@@ -1,7 +1,7 @@
 #ifndef BAMHASH_CHECKSUM_COMMON_H
 #define BAMHASH_CHECKSUM_COMMON_H
 
-#define BAMHASH_VERSION "1.1"
+#define BAMHASH_VERSION "1.3"
 
 #include <string>
 #include <stdint.h>
diff --git a/bamhash_checksum_fasta.cpp b/bamhash_checksum_fasta.cpp
index f6279e6..f8d1adb 100644
--- a/bamhash_checksum_fasta.cpp
+++ b/bamhash_checksum_fasta.cpp
@@ -28,12 +28,12 @@ parseCommandLine(Fastainfo& options, int argc, char const **argv) {
 
   setShortDescription(parser, "Checksum of a set of fasta files");
   setVersion(parser, BAMHASH_VERSION);
-  setDate(parser, "May 2015");
+  setDate(parser, "Okt 2018");
 
   addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fI<in1.fasta>\\fP [\\fIin2.fasta ... \\fP]");
   addDescription(parser, "Program for checksum of sequence reads. ");
 
-  addArgument(parser, seqan::ArgParseArgument(seqan::ArgParseArgument::INPUTFILE,"fastafiles", true));
+  addArgument(parser, seqan::ArgParseArgument(seqan::ArgParseArgument::INPUT_FILE,"fastafiles", true));
 
   setValidValues(parser, 0,"fa fa.gz fasta fasta.gz");
 
@@ -58,7 +58,6 @@ parseCommandLine(Fastainfo& options, int argc, char const **argv) {
   return seqan::ArgumentParser::PARSE_OK;
 }
 
-
 int main(int argc, char const **argv) {
   Fastainfo info; // Define structure variable
   seqan::ArgumentParser::ParseResult res = parseCommandLine(info, argc, argv); // Parse the command line.
@@ -77,29 +76,26 @@ int main(int argc, char const **argv) {
   seqan::CharString seq;
   hash_t hex;
 
-
-  // Open GZStream
-  seqan::Stream<seqan::GZFile> gzStream;
-
-
+  // Open stream
+  seqan::SeqFileIn seqFileIn;
 
   for (int i = 0; i < info.fastafiles.size(); i++) {
     const char* fasta = info.fastafiles[i].c_str();
     
-    if (!open(gzStream, fasta, "r")) {
+    if (!open(seqFileIn, fasta)) {
       std::cerr << "ERROR: Could not open the file: " << fasta << " for reading.\n";
       return 1;
     }
 
-    //Setup RecordReader for reading FASTA file from gzip-compressed file
-    seqan::RecordReader<seqan::Stream<seqan::GZFile>, seqan::SinglePass<> > reader(gzStream);
-
-
-
     // Read record
-    while (!atEnd(reader)) {
-      if (readRecord(id, seq, reader, seqan::Fasta()) != 0) {
-        if (atEnd(reader)) {
+    while (!seqan::atEnd(seqFileIn)) {
+      try
+      {
+        readRecord(id, seq, seqFileIn);
+      }
+      catch (seqan::Exception const & e)
+      {
+        if (seqan::atEnd(seqFileIn)) {
           std::cerr << "WARNING: Could not continue reading " << fasta <<  " at line: " << count+1 << ".\n";
           return 1;
         }
@@ -109,10 +105,8 @@ int main(int argc, char const **argv) {
 
       count +=1;
 
-
       // cut away after first space
-      seqan::strSplit(idSub, id, ' ', false, 1);
-
+      seqan::strSplit(idSub, id, seqan::EqualsChar<' '>(), false, 1);
 
       if (!info.noReadNames) {
         seqan::append(string2hash, idSub[0]);
@@ -131,8 +125,6 @@ int main(int argc, char const **argv) {
 
       seqan::clear(string2hash);
       seqan::clear(idSub);
-
-
     }
 
   }
@@ -141,7 +133,6 @@ int main(int argc, char const **argv) {
     std::cout << std::hex << sum << "\t";
     std::cout << std::dec << count << "\n";
   }
-
     
   return 0;
 }
diff --git a/bamhash_checksum_fastq.cpp b/bamhash_checksum_fastq.cpp
index 653fadf..f4d4ed2 100644
--- a/bamhash_checksum_fastq.cpp
+++ b/bamhash_checksum_fastq.cpp
@@ -31,12 +31,12 @@ parseCommandLine(Fastqinfo& options, int argc, char const **argv) {
 
   setShortDescription(parser, "Checksum of a set of fastq files");
   setVersion(parser, BAMHASH_VERSION);
-  setDate(parser, "May 2015");
+  setDate(parser, "Okt 2018");
 
   addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fI<in1.fastq.gz>\\fP [\\fIin2.fastq.gz ... \\fP]");
   addDescription(parser, "Program for checksum of sequence reads. ");
 
-  addArgument(parser, seqan::ArgParseArgument(seqan::ArgParseArgument::INPUTFILE,"fastqfiles", true));
+  addArgument(parser, seqan::ArgParseArgument(seqan::ArgParseArgument::INPUT_FILE,"fastqfiles", true));
 
   setValidValues(parser, 0,"fq fq.gz fastq fastq.gz");
 
@@ -89,10 +89,10 @@ int main(int argc, char const **argv) {
   hash_t hex1;
   hash_t hex2;
 
-  // Open GZStream
-  seqan::Stream<seqan::GZFile> gzStream1;
-  seqan::Stream<seqan::GZFile> gzStream2;
 
+  // Open Files
+  seqan::SeqFileIn seqFileIn1;
+  seqan::SeqFileIn seqFileIn2;
 
   if (info.paired && (info.fastqfiles.size() % 2 != 0)) {
     std::cerr << "ERROR: Running with paired end mode, but supplied an odd number of input files ";
@@ -109,38 +109,56 @@ int main(int argc, char const **argv) {
     if (info.paired) {
      fastq2 = info.fastqfiles[i+1].c_str();
     }
-    
-    if (!open(gzStream1, fastq1, "r")) {
-      std::cerr << "ERROR: Could not open the file: " << fastq1 << " for reading.\n";
-      return 1;
-    }
 
-    if (info.paired && !open(gzStream2, fastq2, "r")) {
-      std::cerr << "ERROR: Could not open the file: " << fastq2 << " for reading.\n";
-      return 1;
+
+    if (!open(seqFileIn1, fastq1))
+    {
+        std::cerr << "ERROR: Could not open the file: " << fastq1 << " for reading.\n";
+        return 1;
     }
 
-    //Setup RecordReader for reading FASTQ file from gzip-compressed file
-    seqan::RecordReader<seqan::Stream<seqan::GZFile>, seqan::SinglePass<> > reader1(gzStream1);
-    seqan::RecordReader<seqan::Stream<seqan::GZFile>, seqan::SinglePass<> > reader2(gzStream2);
+    if (!open(seqFileIn2, fastq2))
+    {
+        std::cerr << "ERROR: Could not open the file: " << fastq1 << " for reading.\n";
+        return 1;
+    }
 
+/*
+    StringSet<Dna5String> seqs;
+*/
 
     // Read record
-    while (!atEnd(reader1)) {
-      if(info.paired) {
-        if(atEnd(reader2)) { break; }
+    while (!atEnd(seqFileIn1)) {
+      if(info.paired)
+      {
+        if(atEnd(seqFileIn2)) { break; }
       }
-      if (readRecord(id1, seq1, qual1, reader1, seqan::Fastq()) != 0) {
-        if (atEnd(reader1)) {
-          std::cerr << "WARNING: Could not continue reading " << fastq1 <<  " at line: " << count+1 << ".\n";
+      try
+      {
+          seqan::readRecord(id1, seq1, qual1, seqFileIn1);
+      }
+      catch (seqan::Exception const & e)
+      {
+        if (atEnd(seqFileIn1))
+        {
+          std::cerr << "WARNING: Could not continue reading " << fastq1 <<  " at line: " << count+1 << ". Check if files have the same number of reads.\n";
           return 1;
         }
         std::cerr << "ERROR: Could not read from " << fastq1 << "\n";
         return 1;
       }
 
-      if (info.paired && readRecord(id2, seq2, qual2, reader2, seqan::Fastq()) != 0) {
-        if (atEnd(reader2)) {
+      try
+      {
+        if (info.paired)
+        {
+            seqan::readRecord(id2, seq2, qual2, seqFileIn2);
+        }
+      }
+      catch (seqan::Exception const & e)
+      {
+        if (atEnd(seqFileIn2))
+        {
           std::cerr << "WARNING: Could not continue reading " << fastq2 << " at line: " << count+1 << ". Check if files have the same number of reads.\n";
           return 1;
         }
@@ -153,16 +171,16 @@ int main(int argc, char const **argv) {
 
       // If include id, then cut id on first whitespace
       if (seqan::endsWith(id1,"/1") || seqan::endsWith(id1,"/2")) {
-        seqan::strSplit(idSub1, id1, '/', false, 1);
+        seqan::strSplit(idSub1, id1, seqan::EqualsChar<'/'>(), false, 1);
       } else {
-        seqan::strSplit(idSub1, id1, ' ', false, 1);
+        seqan::strSplit(idSub1, id1, seqan::EqualsChar<' '>(), false, 1);
       }
 
       if (info.paired) {
         if (seqan::endsWith(id2,"/1") || seqan::endsWith(id2,"/2")) {
-          seqan::strSplit(idSub2, id2, '/', false, 1);
+          seqan::strSplit(idSub2, id2, seqan::EqualsChar<'/'>(), false, 1);
         } else {
-          seqan::strSplit(idSub2, id2, ' ', false, 1);
+          seqan::strSplit(idSub2, id2, seqan::EqualsChar<' '>(), false, 1);
         }
       }
 
@@ -181,7 +199,6 @@ int main(int argc, char const **argv) {
         seqan::append(string2hash1, qual1);
       }
 
-
       if (info.paired) {
         if (!info.noReadNames) {
           seqan::append(string2hash2, idSub2[0]);
@@ -213,6 +230,11 @@ int main(int argc, char const **argv) {
     }
 
   }
+  if (!info.debug && count == 0)
+  {
+    std::cerr << "WARNING: Read count is : " << count << "\n";
+    return 1;
+  }
 
   if (!info.debug) {
     std::cout << std::hex << sum << "\t";
diff --git a/seqan/LICENSE b/seqan/LICENSE
index 0b7f5a9..7362ed0 100644
--- a/seqan/LICENSE
+++ b/seqan/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2006-2011, Knut Reinert, FU Berlin
+Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -9,18 +9,19 @@ modification, are permitted provided that the following conditions are met:
     * Redistributions in binary form must reproduce the above copyright
       notice, this list of conditions and the following disclaimer in the
       documentation and/or other materials provided with the distribution.
-    * Neither the name of the <organization> nor the
-      names of its contributors may be used to endorse or promote products
-      derived from this software without specific prior written permission.
+    * Neither the name of Knut Reinert or the FU Berlin nor the names of
+      its contributors may be used to endorse or promote products derived
+      from this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
-DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
 
diff --git a/seqan/align.h b/seqan/align.h
index 55f9c10..41a9399 100644
--- a/seqan/align.h
+++ b/seqan/align.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_H_
 
 // TODO(holtgrew): Usage of gapped value in align module is not consistent, need proxies in many places, reference not cleanly implemented everywhere yet.
 // TODO(holtgrew): The Author: tag at the top has to be corrected in the headers of this module.
@@ -51,6 +51,7 @@
 
 #include <seqan/basic.h>
 #include <seqan/modifier.h>  // ModifiedAlphabet<>.
+#include <seqan/align/align_metafunctions.h>
 #include <seqan/graph_align.h>  // TODO(holtgrew): We should not have to depend on this.
 
 // TODO(holtgrew): Why not use priority queue from STL?
@@ -70,6 +71,8 @@
 // Gaps & Gaps Iterator Data Structures
 // ============================================================================
 
+#include <seqan/align/fragment.h>
+
 #include <seqan/align/gaps_base.h>
 #include <seqan/align/gaps_iterator_base.h>
 
@@ -84,7 +87,6 @@
 // Alignment Data Structures and Columns
 // ============================================================================
 
-#include <seqan/align/align_metafunctions.h>
 #include <seqan/align/align_cols.h>
 #include <seqan/align/align_base.h>
 
@@ -114,6 +116,7 @@
 #include <seqan/align/dp_cell.h>
 #include <seqan/align/dp_cell_linear.h>
 #include <seqan/align/dp_cell_affine.h>
+#include <seqan/align/dp_cell_dynamic.h>
 
 // Stores the actual trace segment that was detected during traceback.
 // The trace segments can be adapted into any alignment representation
@@ -121,15 +124,11 @@
 #include <seqan/align/dp_trace_segment.h>
 #include <seqan/align/dp_traceback_adaptor.h>
 
-// Ensures the backwards compatibility for the global interfaces of the
-// alignment algorithms. Based on the called function this selects the
-// correct parameters for the new alignment module.
-#include <seqan/align/dp_setup.h>
-
 // Implements the different recursion formula of the alignment algorithms.
 #include <seqan/align/dp_formula.h>
 #include <seqan/align/dp_formula_linear.h>
 #include <seqan/align/dp_formula_affine.h>
+#include <seqan/align/dp_formula_dynamic.h>
 
 // Defines meta informations which determine how to compute a column and a
 // certain cell for different profiles.
@@ -147,6 +146,12 @@
 #include <seqan/align/dp_matrix_navigator_score_matrix_sparse.h>
 #include <seqan/align/dp_matrix_navigator_trace_matrix.h>
 
+// Ensures the backwards compatibility for the global interfaces of the
+// alignment algorithms. Based on the called function this selects the
+// correct parameters for the new alignment module.
+#include <seqan/align/dp_context.h>
+#include <seqan/align/dp_setup.h>
+
 // The actual implementations of the traceback and the dynamic programming that
 // is used by all different alignment algorithms.
 #include <seqan/align/dp_traceback_impl.h>
@@ -206,4 +211,4 @@
 #include <seqan/align/alignment_operations.h>
 #include <seqan/align/evaluate_alignment.h>
 
-#endif  // SEQAN_CORE_INCLUDE_SEQAN_ALIGN_H_
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGN_H_
diff --git a/seqan/align/INFO b/seqan/align/INFO
deleted file mode 100644
index a5a30e3..0000000
--- a/seqan/align/INFO
+++ /dev/null
@@ -1,13 +0,0 @@
-Name: seqan-align
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Author: Birte Kehr <birte.kehr@fu-berlin.de>
-Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Author: Rene Rahn <rene.rahn@fu-berlin.de>
-Maintainer: Rene Rahn <rene.rahn@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Alignment data structures.
- Definition of alignment data structures and pairwise DP alignment
- algorithms.
diff --git a/seqan/align/align_base.h b/seqan/align/align_base.h
index c26ca1c..4aa31d9 100644
--- a/seqan/align/align_base.h
+++ b/seqan/align/align_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // Gap objects, one for each row of the alignment.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_
 
 namespace seqan {
 
@@ -44,9 +44,6 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
-struct TagRaw_;
-typedef Tag<TagRaw_> Raw;
-
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
@@ -75,41 +72,17 @@ typedef Tag<TagRaw_> Raw;
  *
  * Here is an example of using an Align object with @link globalAlignment @endlink.
  *
- * @include demos/align/align.cpp
+ * @include demos/dox/align/align.cpp
  *
  * The output is as follows:
  *
- * @include demos/align/align.cpp.stdout
+ * @include demos/dox/align/align.cpp.stdout
  *
  * @see globalAlignment
  * @see localAlignment
  * @see Gaps
  */
 
-/**
-.Class.Align:
-..cat:Alignments
-..summary:An alignment of sequences.
-..signature:Align<TSource, TSpec>
-..param.TSource:Type of the ungapped sequences.
-...metafunction:Metafunction.Source
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:@Spec.ArrayGaps@
-..remarks:The default implementation of $Align$ stores the alignment in a set of @Class.Gaps|Gaps<TSource,TSpec>@ objects.
-Hence, the default implementation is row-based, so it will be faster to access the alignment row-wise than column-wise.
-..example.file:demos/align/align.cpp
-..example.text:The output is as follows:
-..example.output:
-score = -4
-align
-  0     .    :
-    AGTTTAATCA
-    ||| | |  |
-    AGTAT-ACGA
-..include:seqan/align.h
-*/
-
 template <typename TSource, typename TSpec = ArrayGaps>
 class Align
 {
@@ -154,8 +127,6 @@ class Align
  * @return Type   The resulting column type.
  */
 
-///.Metafunction.Cols.param.T.type:Class.Align
-
 template <typename TSource, typename TSpec>
 struct Cols<Align<TSource, TSpec> >
 {
@@ -183,8 +154,6 @@ struct Cols<Align<TSource, TSpec> const>
  * @return Type   The resulting value type.
  */
 
-///.Metafunction.Value.param.T.type:Class.Align
-
 template <typename TSource, typename TSpec>
 struct Value<Align<TSource, TSpec> >:
     Value<Gaps<TSource, TSpec> >
@@ -209,8 +178,6 @@ struct Value<Align<TSource, TSpec> const>:
  * @return Type   The resulting get-value type.
  */
 
-///.Metafunction.GetValue.param.T.type:Class.Align
-
 template <typename TSource, typename TSpec>
 struct GetValue<Align<TSource, TSpec> >:
     GetValue<Gaps<TSource, TSpec> >
@@ -235,8 +202,6 @@ struct GetValue<Align<TSource, TSpec> const>:
  * @return Type   The resulting reference type.
  */
 
-///.Metafunction.Reference.param.T.type:Class.Align
-
 template <typename TSource, typename TSpec>
 struct Reference<Align<TSource, TSpec> >:
     Reference<Gaps<TSource, TSpec> >
@@ -272,8 +237,6 @@ struct Reference<Align<TSource, TSpec> const>:
  * @return Type   The resulting rows type.
  */
 
-///.Metafunction.Rows.param.T.type:Class.Align
-
 template <typename TSource, typename TSpec>
 struct Rows<Align<TSource, TSpec> >
 {
@@ -293,15 +256,13 @@ struct Rows<Align<TSource, TSpec> const>
  * @mfn Align#Source
  * @brief Return the type of the underlying sequence.
  *
- * @signature Rows<TAlign>::Type
+ * @signature Rows<TAlign>::Type;
  *
  * @tparam TAlign The Align object to get the underlying sequence type for.
  *
  * @return Type   The resulting sequence type.
  */
 
-///.Metafunction.Source.param.T.type:Class.Align
-
 template <typename TSource, typename TSpec>
 struct Source<Align<TSource, TSpec> >
 {
@@ -365,23 +326,9 @@ void move(Align<TSource, TSpec> & target, Align<TSource, TSpec> & source)
  *
  * @signature TRows rows(align);
  *
- * @param align The Align object to get the rows for.
+ * @param[in] align The Align object to get the rows for.
  *
- * @signature TRows A container with the Gaps of the Align object.
- */
-
-/**
-.Function.rows:
-..cat:Alignments
-..summary:The container of rows in an alignment.
-..signature:Rows rows(align)
-..param.align:An alignment.
-...type:Class.Align
-..returns:The container of rows in $align$.
-...metafunction:Metafunction.Rows
-..see:Function.cols
-..see:Metafunction.Rows
-..include:seqan/align.h
+ * @return TRows A container with the Gaps of the Align object.
  */
 
 template <typename TSource, typename TSpec>
@@ -408,27 +355,10 @@ rows(Align<TSource, TSpec> const & me)
  *
  * @signature TRow row(align, pos);
  *
- * @param align The Align object to get the row of.
- * @param pos   The number of the row to get.
+ * @param[in] align The Align object to get the row of.
+ * @param[in] pos   The number of the row to get.
  *
- * @signature TRow Reference to the given row of align  (Type: @link Gap#Row @endlink).
- */
-
-/**
-.Function.row:
-..cat:Alignments
-..summary:A row in an alignment.
-..signature:Row & row(align, position)
-..param.align:An alignment.
-...type:Class.Align
-..param.position:A position in the @Function.rows@ container of $align$.
-..returns:The row in @Function.rows@ container of $align$ at the given $position$.
-...metafunction:Metafunction.Row
-..remarks:This function is equivalent to $value(rows(align), position)$.
-..see:Function.rows
-..see:Function.col
-..see:Metafunction.Row
-..include:seqan/align.h
+ * @return TRow Reference to the given row of align  (Metafunction: @link Align#Row @endlink).
  */
 
 template <typename TSource, typename TSpec, typename TPosition>
@@ -457,24 +387,11 @@ row(Align<TSource, TSpec> const & me,
  *
  * @signature TCols cols(align);
  *
- * @param align The Align object to get the cols of.
+ * @param[in] align The Align object to get the cols of.
  *
- * @signature TCols The columns of the Align object (type @link Align#Cols @endlink).
+ * @return TCols The columns of the Align object (Metafunction: @link Align#Cols @endlink).
  */
 
-/**
-.Function.cols:
-..cat:Alignments
-..summary:The container of columns in an alignment.
-..signature:Cols cols(align)
-..param.align:An alignment.
-...type:Class.Align
-..returns:The container of columns in $align$.
-...metafunction:Metafunction.Cols
-..see:Metafunction.Cols
-..include:seqan/align.h
-*/
-
 template <typename TSource, typename TSpec>
 inline typename Cols<Align<TSource, TSpec> >::Type
 cols(Align<TSource, TSpec> & me)
@@ -499,27 +416,11 @@ cols(Align<TSource, TSpec> const & me)
  *
  * @signature TCol col(align);
  *
- * @param align The Align object to get the cols of.
+ * @param[in] align The Align object to get the cols of.
  *
- * @signature TCol The column of the Align object (type @link Align#Col @endlink).
+ * @return TCol The column of the Align object (Metafunction: @link Align#Col @endlink).
  */
 
-/**
-.Function.col:
-..cat:Alignments
-..summary:A column in an alignment.
-..signature:Col & col(align, position)
-..param.align:An alignment.
-...type:Class.Align
-..param.position:A position in the @Function.cols@ container of $align$.
-..returns:The column in @Function.cols@ container of $align$ at the given $position$.
-...metafunction:Metafunction.Col
-..remarks:This function is equivalent to $value(cols(align), position)$.
-..see:Function.cols
-..see:Metafunction.Col
-..include:seqan/align.h
-*/
-
 template <typename TSource, typename TSpec, typename TPosition>
 inline typename Col<Align<TSource, TSpec> >::Type
 col(Align<TSource, TSpec> & me,
@@ -540,8 +441,6 @@ col(Align<TSource, TSpec> const & me,
 // Function detach()
 // ----------------------------------------------------------------------------
 
-///.Function.detach.param.object.type:Class.Align
-
 template <typename TSource, typename TSpec>
 inline void
 detach(Align<TSource, TSpec> & me)
@@ -569,21 +468,16 @@ detach(Align<TSource, TSpec> & me)
  * @deprecated Old-style I/O.
  * @brief Writing of Gaps to Streams in human-readable format.
  *
- * @signature void write(stream, align, id, Raw());
+ * @signature void write(stream, align);
  *
- * @param stream The Stream to write to.
- * @param align  The Align object to write out.
- * @param id     ID string (ignored).
+ * @param[in,out] stream The Stream to write to.
+ * @param[in]     align  The Align object to write out.
  */
 
-// TODO(holtgrew): Part of the old I/O system. Undocumented. Rename Raw() to HumanReadable() or OnScreen()?
-
-template <typename TFile, typename TSource, typename TSpec, typename TIDString>
+template <typename TFile, typename TSource, typename TSpec>
 inline void
 write(TFile & target,
-      Align<TSource, TSpec> const & source,
-      TIDString const &,
-      Raw)
+      Align<TSource, TSpec> const & source)
 {
     typedef Align<TSource, TSpec> const TAlign;
     typedef typename Row<TAlign>::Type TRow;
@@ -603,28 +497,28 @@ write(TFile & target,
             windowSize_ = end_ - begin_;
 
         // Print header line
-        char buffer[100];
-        sprintf(buffer, "%7u", (unsigned)baseCount);
-        streamPut(target, buffer);
+        char buffer[20];
+        int len = sprintf(buffer, "%7u", (unsigned)baseCount);
+        write(target, buffer, len);
         baseCount += windowSize_;
-        streamPut(target, ' ');
+        writeValue(target, ' ');
         for (TPosition i = 1; i <= windowSize_; ++i)
         {
             if ((i % 10) == 0)
-                streamPut(target, ':');
+                writeValue(target, ':');
             else if ((i % 5) == 0)
-                streamPut(target, '.');
+                writeValue(target, '.');
             else
-                streamPut(target, ' ');
+                writeValue(target, ' ');
         }
-        streamPut(target, ' ');
-        streamPut(target, '\n');
+        writeValue(target, ' ');
+        writeValue(target, '\n');
 
         // Print sequences
         for (TRowsPosition i = 0; i < 2 * row_count - 1; ++i)
         {
             for (unsigned int j = 0; j < leftSpace + 2; ++j)
-                streamPut(target, ' ');
+                writeValue(target, ' ');
             if ((i % 2) == 0)
             {
                 TRow & row_ = row(source, i / 2);
@@ -634,9 +528,9 @@ write(TFile & target,
                 for (; begin1_ != end1_; ++begin1_)
                 {
                     if (isGap(begin1_))
-                        streamPut(target, gapValue<char>());
+                        writeValue(target, gapValue<char>());
                     else
-                        streamPut(target, *begin1_);
+                        writeValue(target, getValue(begin1_));
                 }
             }
             else
@@ -647,20 +541,20 @@ write(TFile & target,
                         (!isGap(row(source, (i + 1) / 2), begin_ + j)) &&
                         (row(source, (i - 1) / 2)[begin_ + j] == row(source, (i + 1) / 2)[begin_ + j]))
                     {
-                        streamPut(target, '|');
+                        writeValue(target, '|');
                     }
                     else
                     {
-                        streamPut(target, ' ');
+                        writeValue(target, ' ');
                     }
                 }
             }
-            streamPut(target, '\n');
+            writeValue(target, '\n');
         }
-        streamPut(target, '\n');
+        writeValue(target, '\n');
         begin_ += 50;
     }
-    streamPut(target, '\n');
+    writeValue(target, '\n');
 }
 
 // ----------------------------------------------------------------------------
@@ -673,7 +567,7 @@ write(TFile & target,
  *
  * @signature void clearClipping(align);
  *
- * @param align Align object to clear clippings of.
+ * @param[in,out] align Align object to clear clippings of.
  */
 
 // TODO(holtgrew): Undocumented.
@@ -699,8 +593,8 @@ clearClipping(Align<TSource, TSpec> & align_)
  *
  * @signature TStream operator<<(stream, align);
  *
- * @param stream std::ostream to write to.
- * @param align  Align object to write out.
+ * @param[in,out] stream <tt>std::ostream</tt> to write to.
+ * @param[in]     align  Align object to write out.
  *
  * @return TStream Reference to stream after output of align.
  */
@@ -712,7 +606,8 @@ inline TStream &
 operator<<(TStream & target,
            Align<TSource, TSpec> const & source)
 {
-    write(target, source);
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
     return target;
 }
 
@@ -726,22 +621,8 @@ operator<<(TStream & target,
  *
  * @signature void setStrings(align, stringSet);
  *
- * @param align     Align object to set underlying sequence of.
- * @param stringSet The source of the data.
- */
-
-/**
-.Function.setStrings:
-..cat:Alignments
-..summary:Loads the sequences of a stringset into an alignment.
-..signature:setStrings(align, stringset)
-..param.align:An alignment.
-...type:Class.Align
-..param.stringset:A string set.
-...type:Class.StringSet
-..remarks:The function clears $align$ and creates an new global alignment between strings in $stringset$ that contains only trainling gaps.
-The alignment will be dependent from the strings in the stringset; use @Function.detach@ to make $align$ the owner of its strings.
-..include:seqan/align.h
+ * @param[in,out] align     Align object to set underlying sequence of.
+ * @param[in]     stringSet The @link StringSet @endlink with the data.
  */
 
 template <typename TSource, typename TSpec, typename TSpec2>
@@ -777,7 +658,7 @@ setStrings(Align<TSource, TSpec> & me,
  *
  * @signature void clearGaps(align);
  *
- * @param align The Align object to clear all all gaps from.
+ * @param[in] align The Align object to clear all all gaps from.
  */
 
 template <typename TSource, typename TSpec>
@@ -802,17 +683,11 @@ clearGaps(Align<TSource, TSpec> & me)
  *
  * @signature TStringSet stringSet(align);
  *
- * @param align Align object to get sequences of.
+ * @param[in] align Align object to get sequences of.
  *
- * @return TStringSet The set of ungapped sequences.  Get type with Gaps#StringSetType.
+ * @return TStringSet The set of ungapped sequences (Metafunction: @link Align#StringSetType @endlink).
  */
 
-/**
-.Function.stringSet:
-..param.g.type:Class.Align
-..include:seqan/align.h
-*/
-
 template <typename TSource, typename TSpec>
 inline typename StringSetType<Align<TSource, TSpec> >::Type
 stringSet(Align<TSource, TSpec> & me)
@@ -862,4 +737,4 @@ inline bool operator!=(Align<TSource, TSpec> const & lhs,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_
diff --git a/seqan/align/align_cols.h b/seqan/align/align_cols.h
index d140c2d..e5aafde 100644
--- a/seqan/align/align_cols.h
+++ b/seqan/align/align_cols.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // rows of an alignment.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_
 
 namespace seqan {
 
@@ -65,20 +65,6 @@ namespace seqan {
  * @tparam TAlign The Align type.
  */
 
-/**
-.Class.AlignCols:
-..cat:Alignments
-..summary:Pseudo columns container for row-based alignment classes.
-..signature:AlignCols<TAlign>
-..param.TAlign:Alignment type.
-...metafunction:Metafunction.Host
-..remarks:
-This class emulates a container of columns on alignment classes that store the alignment in a container of rows.
-Note that accessing a row-based alignment column-wise can be significantly slower than accessing the alignment row-wise.
-..see:Class.Align
-..include:seqan/align.h
- */
-
 template <typename TAlign>
 struct AlignCols
 {
@@ -112,17 +98,6 @@ struct AlignCols
 // Specialization AlignCols
 // ----------------------------------------------------------------------------
 
-/**
-.Spec.AlignColIterator:
-..cat:Iterators
-..summary:Iterator for @Class.AlignCols@ pseudo container.
-..signature:Iter< TAlign, AlignColIterator<TSpec> >
-..param.TSpec:Specialization tag.
-..general:Class.Iter
-..see:Class.AlignCols
-..include:seqan/align.h
-*/
-
 template <typename TSpec>
 struct AlignColIterator;
 
@@ -136,8 +111,6 @@ struct AlignColIterator;
 
 // TODO(holtgrew): Add HostedTypeConcept and make AlignCols object implement the concept.
 
-///.Metafunction.Host.param.T.type:Class.AlignCols
-
 template <typename TAlign>
 struct Host<AlignCols<TAlign> >
 {
@@ -153,8 +126,6 @@ struct Host<AlignCols<TAlign> const>
 // Metafunction AlignColIterator
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Iterator.param.T.type:Class.AlignCols
-
 template <typename TAlign, typename TIteratorSpec>
 struct Iterator<AlignCols<TAlign>, TIteratorSpec>
 {
@@ -172,8 +143,6 @@ struct Iterator<AlignCols<TAlign> const, TIteratorSpec>
 
 // Iterator is also used as Value
 
-///.Metafunction.Value.param.T.type:Class.AlignCols
-
 template <typename TAlign>
 struct Value<AlignCols<TAlign> >:
     Iterator<AlignCols<TAlign>, Standard>
@@ -188,8 +157,6 @@ struct Value<AlignCols<TAlign> const>:
 // Metafunction Size
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Size.param.T.type:Class.AlignCols
-
 template <typename TAlign>
 struct Size<AlignCols<TAlign> >:
     Size<typename Row<TAlign>::Type>
@@ -204,8 +171,6 @@ struct Size<AlignCols<TAlign> const>:
 // Metafunction Position
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Position.param.T.type:Class.AlignCols
-
 template <typename TAlign>
 struct Position<AlignCols<TAlign> >:
     Position<typename Row<TAlign>::Type>
@@ -224,8 +189,6 @@ struct Position<AlignCols<TAlign> const>:
 // Function host()
 // ----------------------------------------------------------------------------
 
-///.Function.host.param.object.type:Class.AlignCols
-
 template <typename TAlign>
 inline typename Host<AlignCols<TAlign> >::Type &
 host(AlignCols<TAlign> & me)
@@ -246,7 +209,25 @@ host(AlignCols<TAlign> const & me)
 // Function iter()
 // ----------------------------------------------------------------------------
 
-///.Function.iter.param.object.type:Class.AlignCols
+/*!
+ * @fn AlignCols#iter
+ * @headerfile <seqan/align.h>
+ * @brief Iterator to the item at the given position in the alignment columns.
+ *
+ * @signature TIterator iter(cols, pos[, tag]);
+ *
+ * @param[in] cols   The AlignCols object to get the iterator for.
+ * @param[in] pos    The position to get the iterator for.
+ * @param[in] tag    The tag to pick the type of the iterator.
+ *
+ * @return TIterator The resulting iterator.  If <tt>TTag</tt> is the type of <tt>tag</tt> and <tt>TAlignCols</tt> the
+ *                   type of <tt>cols</tt> then TIterator is of the type <tt>Iterator&lt;TAlignCols,
+ *                   TTag&gt;::Type</tt>.
+ *
+ * @section Remarks
+ *
+ * If <tt>pos</tt> is out of range then the iterator is invalid.
+ */
 
 template <typename TAlign, typename TPosition, typename TTag>
 inline typename Iterator<AlignCols<TAlign>, Tag<TTag> const>::Type
@@ -270,7 +251,15 @@ iter(AlignCols<TAlign> const & me,
 // Function value()
 // ----------------------------------------------------------------------------
 
-///.Function.value.param.container.type:Class.AlignCols
+/*!
+ * @fn AlignCols#value
+ * @headerfile <seqan/align.h>
+ * @brief Returns AlignCols value at a position.
+ *
+ * @signature TColumn value(alignCols, pos);
+ *
+ * @return TColumn The column, as determined by Value metafunction.
+ */
 
 template <typename TAlign, typename TPosition>
 inline typename Value<AlignCols<TAlign> >::Type
@@ -292,8 +281,6 @@ value(AlignCols<TAlign> const & me,
 // Function beginPosition()
 // ----------------------------------------------------------------------------
 
-///.Function.beginPosition.param.object.type:Class.AlignCols
-
 template <typename TAlignCols>
 inline typename Position<TAlignCols>::Type
 _beginPositionAlignCols(TAlignCols const & me)
@@ -339,8 +326,6 @@ beginPosition(AlignCols<TAlign> & me)
 // Function begin()
 // ----------------------------------------------------------------------------
 
-///.Function.begin.param.object.type:Class.AlignCols
-
 template <typename TAlign, typename TTag>
 inline typename Iterator<AlignCols<TAlign>, Tag<TTag> const>::Type
 begin(AlignCols<TAlign> & me,
@@ -361,8 +346,6 @@ begin(AlignCols<TAlign> const & me,
 // Function endPosition()
 // ----------------------------------------------------------------------------
 
-///.Function.endPosition.param.object.type:Class.AlignCols
-
 template <typename TAlignCols>
 inline typename Position<TAlignCols>::Type
 _endPositionAlignCols(TAlignCols const & me)
@@ -402,8 +385,6 @@ endPosition(AlignCols<TAlign> const & me)
 // Function end()
 // ----------------------------------------------------------------------------
 
-///.Function.end.param.object.type:Class.AlignCols
-
 template <typename TAlign, typename TTag>
 inline typename Iterator<AlignCols<TAlign>, Tag<TTag> const>::Type
 end(AlignCols<TAlign> & me,
@@ -445,4 +426,4 @@ operator==(AlignCols<TAlign> const & left,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_
diff --git a/seqan/align/align_config.h b/seqan/align/align_config.h
index 5adbade..c90c066 100644
--- a/seqan/align/align_config.h
+++ b/seqan/align/align_config.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Tobias Rausch <rausch@embl.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
 
 namespace seqan {
 
@@ -55,7 +55,7 @@ namespace seqan {
  * @brief Indication of whether begin/end gaps are free for DP alignment algorithms.
  *
  * @signature template <bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TSpec>
- *            AlignConfig;
+ *            struct AlignConfig;
  *
  * @tparam TOP    Whether or not the begin gaps in the vertical sequence are free.
  * @tparam LEFT   Whether or not the begin gaps in the horizontal sequence are free.
@@ -65,6 +65,8 @@ namespace seqan {
  *
  * Used in the DP alignment algorithms to configure the begin/end gap free-nes.
  *
+ * @see globalAlignment
+ *
  * @section Specialization List
  *
  * The following gives an (incomplete) list of useful AlignConfig specializations.
@@ -87,26 +89,6 @@ namespace seqan {
  * </dl>
  */
 
-/**
-.Class.AlignConfig:
-..cat:Alignments
-..summary:The AlignConfig class encapsulates how DP is carried out.
-It indicates at what ends gaps are free, the so-called free ends-space alignments.
-..signature:AlignConfig<bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, TSpec>
-..param.TOP:If true then 0's in top row.
-...default:$false$
-..param.LEFT:If true then 0's in the left column.
-...default:$false$
-..param.RIGHT:If true then maximum is also searched in the last column.
-...default:$false$
-..param.BOTTOM:If true then maximum is also searched in the last row.
-...default:$false$
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:$Default$, see @Tag.Default@.
-..include:seqan/align.h
-*/
-
 template <bool TOP = false, bool LEFT = false, bool RIGHT = false, bool BOTTOM = false, typename TSpec = Default>
 class AlignConfig
 {};
@@ -124,11 +106,11 @@ class AlignConfig
 template<bool TTop, bool TRight, bool TBottom, typename TSpec, typename TElement, typename TCost>
 inline void
 _initFirstColumn(AlignConfig<TTop, false, TRight, TBottom, TSpec> const,
-				 TElement& element,
-				 TCost const cost)
+                 TElement& element,
+                 TCost const cost)
 {
-	SEQAN_CHECKPOINT
-	element = cost;
+    SEQAN_CHECKPOINT
+    element = cost;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -136,11 +118,11 @@ _initFirstColumn(AlignConfig<TTop, false, TRight, TBottom, TSpec> const,
 template<bool TTop, bool TRight, bool TBottom, typename TSpec, typename TElement, typename TCost>
 inline void
 _initFirstColumn(AlignConfig<TTop, true, TRight, TBottom, TSpec> const,
-				 TElement& element,
-				 TCost const)
+                 TElement& element,
+                 TCost const)
 {
-	SEQAN_CHECKPOINT
-	element = 0;
+    SEQAN_CHECKPOINT
+    element = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -148,11 +130,11 @@ _initFirstColumn(AlignConfig<TTop, true, TRight, TBottom, TSpec> const,
 template<bool TLeft, bool TRight, bool TBottom, typename TSpec, typename TElement, typename TCost>
 inline void
 _initFirstRow(AlignConfig<false, TLeft, TRight, TBottom, TSpec> const,
-			  TElement& element,
-			  TCost const cost)
+              TElement& element,
+              TCost const cost)
 {
-	SEQAN_CHECKPOINT
-	element = cost;
+    SEQAN_CHECKPOINT
+    element = cost;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -160,11 +142,11 @@ _initFirstRow(AlignConfig<false, TLeft, TRight, TBottom, TSpec> const,
 template<bool TLeft, bool TRight, bool TBottom, typename TSpec, typename TElement, typename TCost>
 inline void
 _initFirstRow(AlignConfig<true, TLeft, TRight, TBottom, TSpec> const,
-			  TElement& element,
-			  TCost const)
+              TElement& element,
+              TCost const)
 {
-	SEQAN_CHECKPOINT
-	element = 0;
+    SEQAN_CHECKPOINT
+    element = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -175,13 +157,13 @@ _initFirstRow(AlignConfig<true, TLeft, TRight, TBottom, TSpec> const,
 template<bool TTop, bool TLeft, bool TRight, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
 inline void
 _lastRow(AlignConfig<TTop, TLeft, TRight, false, TSpec> const,
-		 TValue1&,
-		 TIndex1&,
-		 TValue2 const,
-		 TIndex2 const)
+         TValue1&,
+         TIndex1&,
+         TValue2 const,
+         TIndex2 const)
 {
-	SEQAN_CHECKPOINT
-	// Nop
+    SEQAN_CHECKPOINT
+    // Nop
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -189,16 +171,16 @@ _lastRow(AlignConfig<TTop, TLeft, TRight, false, TSpec> const,
 template<bool TTop, bool TLeft, bool TRight, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
 inline void
 _lastRow(AlignConfig<TTop, TLeft, TRight, true, TSpec> const,
-		 TValue1& maxValue,
-		 TIndex1& maxIndex,
-		 TValue2 const val,
-		 TIndex2 const index)
+         TValue1& maxValue,
+         TIndex1& maxIndex,
+         TValue2 const val,
+         TIndex2 const index)
 {
-	SEQAN_CHECKPOINT
-	if (val > maxValue[0]) {
-		maxValue[0] = val;
-		maxIndex[0] = index;
-	}
+    SEQAN_CHECKPOINT
+    if (val > maxValue[0]) {
+        maxValue[0] = val;
+        maxIndex[0] = index;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -206,12 +188,12 @@ _lastRow(AlignConfig<TTop, TLeft, TRight, true, TSpec> const,
 template<bool TTop, bool TLeft, bool TBottom, typename TSpec, typename TValue1, typename TIndex1, typename TColumn>
 inline void
 _lastColumn(AlignConfig<TTop, TLeft, false, TBottom, TSpec> const,
-			TValue1& maxValue,
-			TIndex1&,
-			TColumn const& column)
+            TValue1& maxValue,
+            TIndex1&,
+            TColumn const& column)
 {
-	SEQAN_CHECKPOINT
-	maxValue[1] = column[length(column) - 1];
+    SEQAN_CHECKPOINT
+    maxValue[1] = column[length(column) - 1];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -219,23 +201,23 @@ _lastColumn(AlignConfig<TTop, TLeft, false, TBottom, TSpec> const,
 template<bool TTop, bool TLeft, bool TBottom, typename TSpec, typename TValue1, typename TIndex1, typename TColumn>
 inline void
 _lastColumn(AlignConfig<TTop, TLeft, true, TBottom, TSpec> const,
-			TValue1& maxValue,
-			TIndex1& maxIndex,
-			TColumn const& column)
+            TValue1& maxValue,
+            TIndex1& maxIndex,
+            TColumn const& column)
 {
-	SEQAN_CHECKPOINT;
-	typedef typename Size<TColumn>::Type TSize;
-	typedef typename Iterator<TColumn, Standard>::Type TColIter;
-	TSize limit = length(column) - 1;
-	maxValue[1] = column[limit];
-	TColIter itCol = begin(column, Standard());
-	TColIter itColEnd = end(column, Standard());
-	for(TSize i = 0;itCol != itColEnd; ++i, ++itCol) {
-		if (*itCol > maxValue[1]) {
-			maxValue[1] = *itCol;
-			maxIndex[1] = i;
-		}
-	}
+    SEQAN_CHECKPOINT;
+    typedef typename Size<TColumn>::Type TSize;
+    typedef typename Iterator<TColumn, Standard>::Type TColIter;
+    TSize limit = length(column) - 1;
+    maxValue[1] = column[limit];
+    TColIter itCol = begin(column, Standard());
+    TColIter itColEnd = end(column, Standard());
+    for(TSize i = 0;itCol != itColEnd; ++i, ++itCol) {
+        if (*itCol > maxValue[1]) {
+            maxValue[1] = *itCol;
+            maxIndex[1] = i;
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -243,13 +225,13 @@ _lastColumn(AlignConfig<TTop, TLeft, true, TBottom, TSpec> const,
 template<typename TScoreValue, bool TTop, bool TLeft, typename TSpec, typename TValue, typename TIndex, typename TSize>
 inline TScoreValue
 _maxOfAlignment(AlignConfig<TTop, TLeft, false, false, TSpec> const,
-				TValue& maxValue,
-				TIndex&,
-				TSize const,
-				TSize const)
+                TValue& maxValue,
+                TIndex&,
+                TSize const,
+                TSize const)
 {
-	SEQAN_CHECKPOINT
-	return maxValue[1];
+    SEQAN_CHECKPOINT
+    return maxValue[1];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -257,14 +239,14 @@ _maxOfAlignment(AlignConfig<TTop, TLeft, false, false, TSpec> const,
 template<typename TScoreValue, bool TTop, bool TLeft, typename TSpec, typename TValue, typename TIndex, typename TSize>
 inline TScoreValue
 _maxOfAlignment(AlignConfig<TTop, TLeft, true, false, TSpec> const,
-				TValue& maxValue,
-				TIndex& maxIndex,
-				TSize const len1,
-				TSize const)
+                TValue& maxValue,
+                TIndex& maxIndex,
+                TSize const len1,
+                TSize const)
 {
-	SEQAN_CHECKPOINT
-	maxIndex[0] = len1;
-	return maxValue[1];
+    SEQAN_CHECKPOINT
+    maxIndex[0] = len1;
+    return maxValue[1];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -272,14 +254,14 @@ _maxOfAlignment(AlignConfig<TTop, TLeft, true, false, TSpec> const,
 template<typename TScoreValue, bool TTop, bool TLeft, typename TSpec, typename TValue, typename TIndex, typename TSize>
 inline TScoreValue
 _maxOfAlignment(AlignConfig<TTop, TLeft, false, true, TSpec> const,
-				TValue& maxValue,
-				TIndex& maxIndex,
-				TSize const,
-				TSize const len2)
+                TValue& maxValue,
+                TIndex& maxIndex,
+                TSize const,
+                TSize const len2)
 {
-	SEQAN_CHECKPOINT
-	maxIndex[1] = len2;
-	return maxValue[0];
+    SEQAN_CHECKPOINT
+    maxIndex[1] = len2;
+    return maxValue[0];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -287,16 +269,16 @@ _maxOfAlignment(AlignConfig<TTop, TLeft, false, true, TSpec> const,
 template<typename TScoreValue, bool TTop, bool TLeft, typename TSpec, typename TValue, typename TIndex, typename TSize>
 inline TScoreValue
 _maxOfAlignment(AlignConfig<TTop, TLeft, true, true, TSpec> const,
-				TValue& maxValue,
-				TIndex& maxIndex,
-				TSize const len1,
-				TSize const len2)
+                TValue& maxValue,
+                TIndex& maxIndex,
+                TSize const len1,
+                TSize const len2)
 {
-	SEQAN_CHECKPOINT
-	// Find the maximum
-	if (maxValue[1] > maxValue[0]) maxIndex[0] = len1;
-	else maxIndex[1] = len2;
-	return (maxValue[0] > maxValue[1]) ? maxValue[0] : maxValue[1];
+    SEQAN_CHECKPOINT
+    // Find the maximum
+    if (maxValue[1] > maxValue[0]) maxIndex[0] = len1;
+    else maxIndex[1] = len2;
+    return (maxValue[0] > maxValue[1]) ? maxValue[0] : maxValue[1];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -304,14 +286,14 @@ _maxOfAlignment(AlignConfig<TTop, TLeft, true, true, TSpec> const,
 template<bool TTop, bool TLeft, bool TBottom, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
 inline void
 _lastColumn(AlignConfig<TTop, TLeft, false, TBottom, TSpec> const,
-			TValue1& maxValue,
-			TIndex1& maxIndex,
-			TValue2 const val,	
-			TIndex2 const row,
-			TIndex2 const col)
+            TValue1& maxValue,
+            TIndex1& maxIndex,
+            TValue2 const val,
+            TIndex2 const row,
+            TIndex2 const col)
 {
-	SEQAN_CHECKPOINT
-	maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col;
+    SEQAN_CHECKPOINT
+    maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -319,29 +301,29 @@ _lastColumn(AlignConfig<TTop, TLeft, false, TBottom, TSpec> const,
 template<bool TTop, bool TLeft, bool TBottom, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
 inline void
 _lastColumn(AlignConfig<TTop, TLeft, true, TBottom, TSpec> const,
-			TValue1& maxValue,
-			TIndex1& maxIndex,
-			TValue2 const val,
-			TIndex2 const row,
-			TIndex2 const col)
+            TValue1& maxValue,
+            TIndex1& maxIndex,
+            TValue2 const val,
+            TIndex2 const row,
+            TIndex2 const col)
 {
-	SEQAN_CHECKPOINT
-	if (val > maxValue[1]) {maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col; }
+    SEQAN_CHECKPOINT
+    if (val > maxValue[1]) {maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col; }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<bool TTop, bool TLeft, bool TRight, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
 inline void
-_lastRow(AlignConfig<TTop, TLeft, TRight, false, TSpec> const,		
-		 TValue1& maxValue,
-		 TIndex1& maxIndex,
-		 TValue2 const val,
-		 TIndex2 const row,
-		 TIndex2 const col)
+_lastRow(AlignConfig<TTop, TLeft, TRight, false, TSpec> const,
+         TValue1& maxValue,
+         TIndex1& maxIndex,
+         TValue2 const val,
+         TIndex2 const row,
+         TIndex2 const col)
 {
-	SEQAN_CHECKPOINT
-	maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col;
+    SEQAN_CHECKPOINT
+    maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -349,14 +331,14 @@ _lastRow(AlignConfig<TTop, TLeft, TRight, false, TSpec> const,
 template<bool TTop, bool TLeft, bool TRight, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
 inline void
 _lastRow(AlignConfig<TTop, TLeft, TRight, true, TSpec> const,
-		 TValue1& maxValue,
-		 TIndex1& maxIndex,
-		 TValue2 const val,
-		 TIndex2 const row,
-		 TIndex2 const col)
+         TValue1& maxValue,
+         TIndex1& maxIndex,
+         TValue2 const val,
+         TIndex2 const row,
+         TIndex2 const col)
 {
-	SEQAN_CHECKPOINT
-	if (val > maxValue[0]) {maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col; }
+    SEQAN_CHECKPOINT
+    if (val > maxValue[0]) {maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col; }
 }
 
 
@@ -366,14 +348,14 @@ template<bool TLeft, bool TRight, bool TBottom, typename TSpec>
 inline bool
 _configValueTop(AlignConfig<true, TLeft, TRight, TBottom, TSpec> const)
 {
-	return true;
+    return true;
 }
 
 template<bool TLeft, bool TRight, bool TBottom, typename TSpec>
 inline bool
 _configValueTop(AlignConfig<false, TLeft, TRight, TBottom, TSpec> const)
 {
-	return false;
+    return false;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -382,14 +364,14 @@ template<bool TTop, bool TRight, bool TBottom, typename TSpec>
 inline bool
 _configValueLeft(AlignConfig<TTop, true, TRight, TBottom, TSpec> const)
 {
-	return true;
+    return true;
 }
 
 template<bool TTop, bool TRight, bool TBottom, typename TSpec>
 inline bool
 _configValueLeft(AlignConfig<TTop, false, TRight, TBottom, TSpec> const)
 {
-	return false;
+    return false;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -398,14 +380,14 @@ template<bool TTop, bool TLeft, bool TBottom, typename TSpec>
 inline bool
 _configValueRight(AlignConfig<TTop, TLeft, true, TBottom, TSpec> const)
 {
-	return true;
+    return true;
 }
 
 template<bool TTop, bool TLeft, bool TBottom, typename TSpec>
 inline bool
 _configValueRight(AlignConfig<TTop, TLeft, false, TBottom, TSpec> const)
 {
-	return false;
+    return false;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -414,16 +396,16 @@ template<bool TTop, bool TLeft, bool TRight, typename TSpec>
 inline bool
 _configValueBottom(AlignConfig<TTop, TLeft, TRight, true, TSpec> const)
 {
-	return true;
+    return true;
 }
 
 template<bool TTop, bool TLeft, bool TRight, typename TSpec>
 inline bool
 _configValueBottom(AlignConfig<TTop, TLeft, TRight, false, TSpec> const)
 {
-	return false;
+    return false;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
diff --git a/seqan/align/align_iterator_base.h b/seqan/align/align_iterator_base.h
index 26364d9..8a4f455 100644
--- a/seqan/align/align_iterator_base.h
+++ b/seqan/align/align_iterator_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,6 +45,8 @@ namespace SEQAN_NAMESPACE_MAIN
 // TODO(holtgrew): Extend class Iter?
 /*!
  * @class AlignColIterator
+ * @extends Iter
+ * @headerfile <seqan/align.h>
  * @brief Iterator for alignment columns.
  *
  * @signature template <typename TAlign, typename TSpec>
@@ -58,58 +60,58 @@ template <typename TAlign, typename TSpec>
 class Iter<TAlign, AlignColIterator<TSpec> >
 {
 public:
-	typedef typename Rows<TAlign>::Type TRows;
-	typedef typename Row<TAlign>::Type TRow;
-	typedef typename Iterator<TRow, Standard>::Type TRowIterator;
-	typedef typename Position<TRow>::Type TRowPosition;
-	typedef String<TRowIterator> TIterators;
+    typedef typename Rows<TAlign>::Type TRows;
+    typedef typename Row<TAlign>::Type TRow;
+    typedef typename Iterator<TRow, Standard>::Type TRowIterator;
+    typedef typename Position<TRow>::Type TRowPosition;
+    typedef String<TRowIterator> TIterators;
 
-	TAlign * data_host;
-	TIterators data_iterators;
+    TAlign * data_host;
+    TIterators data_iterators;
 
 public:
-	Iter()
-	{
-SEQAN_CHECKPOINT
-	}
-	Iter(TAlign & _align):
-		data_host(& _align)
-	{
-SEQAN_CHECKPOINT
-		typename Position<TRows>::Type _i = length(rows(_align));
-		resize(data_iterators, _i, Exact());
-	}
-	Iter(TAlign & _align, TRowPosition _pos):
-		data_host(& _align)
-	{
-SEQAN_CHECKPOINT
-		typename Position<TRows>::Type _i = length(rows(_align));
-		resize(data_iterators, _i, Exact());
-
-		while (_i > 0)
-		{
-			--_i;
-			data_iterators[_i] = iter(row(_align, _i), _pos);
-		}
-	}
-	Iter(Iter const & _other):
-		data_host(_other.data_host),
-		data_iterators(_other.data_iterators)
-	{
-	}
-	~Iter()
-	{
-SEQAN_CHECKPOINT
-	}
-
-	Iter const &
-	operator = (Iter const & _other)
-	{
-SEQAN_CHECKPOINT
-		data_host = _other.data_host;
-		data_iterators = _other.data_iterators;
-		return *this;
-	}
+    Iter()
+    {
+SEQAN_CHECKPOINT
+    }
+    Iter(TAlign & _align):
+        data_host(& _align)
+    {
+SEQAN_CHECKPOINT
+        typename Position<TRows>::Type _i = length(rows(_align));
+        resize(data_iterators, _i, Exact());
+    }
+    Iter(TAlign & _align, TRowPosition _pos):
+        data_host(& _align)
+    {
+SEQAN_CHECKPOINT
+        typename Position<TRows>::Type _i = length(rows(_align));
+        resize(data_iterators, _i, Exact());
+
+        while (_i > 0)
+        {
+            --_i;
+            data_iterators[_i] = iter(row(_align, _i), _pos);
+        }
+    }
+    Iter(Iter const & _other):
+        data_host(_other.data_host),
+        data_iterators(_other.data_iterators)
+    {
+    }
+    ~Iter()
+    {
+SEQAN_CHECKPOINT
+    }
+
+    Iter const &
+    operator = (Iter const & _other)
+    {
+SEQAN_CHECKPOINT
+        data_host = _other.data_host;
+        data_iterators = _other.data_iterators;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -122,14 +124,14 @@ inline TAlign &
 host(Iter<TAlign, AlignColIterator<TSpec> > & me)
 {
 SEQAN_CHECKPOINT
-	return *me.data_host;
+    return *me.data_host;
 }
 template <typename TAlign, typename TSpec>
 inline TAlign &
 host(Iter<TAlign, AlignColIterator<TSpec> > const & me)
 {
 SEQAN_CHECKPOINT
-	return *me.data_host;
+    return *me.data_host;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -139,7 +141,7 @@ inline void
 setHost(Iter<TAlign, AlignColIterator<TSpec> > & me, TAlign & _host)
 {
 SEQAN_CHECKPOINT
-	me.data_host = & _host;
+    me.data_host = & _host;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -149,14 +151,14 @@ inline typename Cols<TAlign>::Type
 container(Iter<TAlign, AlignColIterator<TSpec> > & me)
 {
 SEQAN_CHECKPOINT
-	return cols(*me.data_host);
+    return cols(*me.data_host);
 }
 template <typename TAlign, typename TSpec>
 inline typename Cols<TAlign>::Type
 container(Iter<TAlign, AlignColIterator<TSpec> > const & me)
 {
 SEQAN_CHECKPOINT
-	return cols(*me.data_host);
+    return cols(*me.data_host);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -166,40 +168,40 @@ inline void
 goNext(Iter<TAlign, AlignColIterator<TSpec> > & me)
 {
 SEQAN_CHECKPOINT
-	typedef typename Row<TAlign>::Type TRow;
-	typedef typename Iterator<TRow, Standard>::Type TRowIterator;
-	typedef String<TRowIterator> TIterators;
-	typedef typename Iterator<TIterators, Standard>::Type TIteratorsIterator;
+    typedef typename Row<TAlign>::Type TRow;
+    typedef typename Iterator<TRow, Standard>::Type TRowIterator;
+    typedef String<TRowIterator> TIterators;
+    typedef typename Iterator<TIterators, Standard>::Type TIteratorsIterator;
 
-	TIteratorsIterator _it = begin(me.data_iterators);
-	TIteratorsIterator _it_end = end(me.data_iterators);
+    TIteratorsIterator _it = begin(me.data_iterators);
+    TIteratorsIterator _it_end = end(me.data_iterators);
 
-	while (_it != _it_end)
-	{
-		goNext(*_it);
-		++_it;
-	}
+    while (_it != _it_end)
+    {
+        goNext(*_it);
+        ++_it;
+    }
 }
 //____________________________________________________________________________
 
 template <typename TAlign, typename TSpec>
-inline Iter<TAlign, AlignColIterator<TSpec> > & 
+inline Iter<TAlign, AlignColIterator<TSpec> > &
 operator ++(Iter<TAlign, AlignColIterator<TSpec> > & me)
 {
 SEQAN_CHECKPOINT
-	goNext(me);
-	return me;
+    goNext(me);
+    return me;
 }
 //____________________________________________________________________________
 
 template <typename TAlign, typename TSpec>
-inline Iter<TAlign, AlignColIterator<TSpec> > 
+inline Iter<TAlign, AlignColIterator<TSpec> >
 operator ++(Iter<TAlign, AlignColIterator<TSpec> > & me, int)
 {
 SEQAN_CHECKPOINT
-	Iter<TAlign, AlignColIterator<TSpec> > ret = me;
-	goNext(me);
-	return ret;
+    Iter<TAlign, AlignColIterator<TSpec> > ret = me;
+    goNext(me);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -209,40 +211,40 @@ inline void
 goPrevious(Iter<TAlign, AlignColIterator<TSpec> > & me)
 {
 SEQAN_CHECKPOINT
-	typedef typename Row<TAlign>::Type TRow;
-	typedef typename Iterator<TRow, Standard>::Type TRowIterator;
-	typedef String<TRowIterator> TIterators;
-	typedef typename Iterator<TIterators, Standard>::Type TIteratorsIterator;
+    typedef typename Row<TAlign>::Type TRow;
+    typedef typename Iterator<TRow, Standard>::Type TRowIterator;
+    typedef String<TRowIterator> TIterators;
+    typedef typename Iterator<TIterators, Standard>::Type TIteratorsIterator;
 
-	TIteratorsIterator _it = begin(me.data_iterators);
-	TIteratorsIterator _it_end = end(me.data_iterators);
+    TIteratorsIterator _it = begin(me.data_iterators);
+    TIteratorsIterator _it_end = end(me.data_iterators);
 
-	while (_it != _it_end)
-	{
-		goPrevious(*_it);
-		++_it;
-	}
+    while (_it != _it_end)
+    {
+        goPrevious(*_it);
+        ++_it;
+    }
 }
 //____________________________________________________________________________
 
 template <typename TAlign, typename TSpec>
-inline Iter<TAlign, AlignColIterator<TSpec> > & 
+inline Iter<TAlign, AlignColIterator<TSpec> > &
 operator --(Iter<TAlign, AlignColIterator<TSpec> > & me)
 {
 SEQAN_CHECKPOINT
-	goPrevious(me);
-	return me;
+    goPrevious(me);
+    return me;
 }
 //____________________________________________________________________________
 
 template <typename TAlign, typename TSpec>
-inline Iter<TAlign, AlignColIterator<TSpec> > 
+inline Iter<TAlign, AlignColIterator<TSpec> >
 operator --(Iter<TAlign, AlignColIterator<TSpec> > & me, int)
 {
 SEQAN_CHECKPOINT
-	Iter<TAlign, AlignColIterator<TSpec> > ret = me;
-	goPrevious(me);
-	return ret;
+    Iter<TAlign, AlignColIterator<TSpec> > ret = me;
+    goPrevious(me);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -250,34 +252,34 @@ SEQAN_CHECKPOINT
 template <typename TAlign1, typename TAlign2, typename TSpec>
 inline bool
 operator ==(Iter<TAlign1, AlignColIterator<TSpec> > & _left,
-			Iter<TAlign2, AlignColIterator<TSpec> > & _right)
+            Iter<TAlign2, AlignColIterator<TSpec> > & _right)
 {
 SEQAN_CHECKPOINT
-	return getValue(_left.data_iterators, 0) == getValue(_right.data_iterators, 0);
+    return getValue(_left.data_iterators, 0) == getValue(_right.data_iterators, 0);
 }
 template <typename TAlign1, typename TAlign2, typename TSpec>
 inline bool
 operator ==(Iter<TAlign1, AlignColIterator<TSpec> > const & _left,
-			Iter<TAlign2, AlignColIterator<TSpec> > & _right)
+            Iter<TAlign2, AlignColIterator<TSpec> > & _right)
 {
 SEQAN_CHECKPOINT
-	return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
+    return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
 }
 template <typename TAlign1, typename TAlign2, typename TSpec>
 inline bool
 operator ==(Iter<TAlign1, AlignColIterator<TSpec> > & _left,
-			Iter<TAlign2, AlignColIterator<TSpec> > const & _right)
+            Iter<TAlign2, AlignColIterator<TSpec> > const & _right)
 {
 SEQAN_CHECKPOINT
-	return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
+    return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
 }
 template <typename TAlign1, typename TAlign2, typename TSpec>
 inline bool
 operator ==(Iter<TAlign1, AlignColIterator<TSpec> > const & _left,
-			Iter<TAlign2, AlignColIterator<TSpec> > const & _right)
+            Iter<TAlign2, AlignColIterator<TSpec> > const & _right)
 {
 SEQAN_CHECKPOINT
-	return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
+    return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -285,34 +287,34 @@ SEQAN_CHECKPOINT
 template <typename TAlign1, typename TAlign2, typename TSpec>
 inline bool
 operator !=(Iter<TAlign1, AlignColIterator<TSpec> > & _left,
-			Iter<TAlign2, AlignColIterator<TSpec> > & _right)
+            Iter<TAlign2, AlignColIterator<TSpec> > & _right)
 {
 SEQAN_CHECKPOINT
-	return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
+    return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
 }
 template <typename TAlign1, typename TAlign2, typename TSpec>
 inline bool
 operator !=(Iter<TAlign1, AlignColIterator<TSpec> > const & _left,
-			Iter<TAlign2, AlignColIterator<TSpec> > & _right)
+            Iter<TAlign2, AlignColIterator<TSpec> > & _right)
 {
 SEQAN_CHECKPOINT
-	return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
+    return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
 }
 template <typename TAlign1, typename TAlign2, typename TSpec>
 inline bool
 operator !=(Iter<TAlign1, AlignColIterator<TSpec> > & _left,
-			Iter<TAlign2, AlignColIterator<TSpec> > const & _right)
+            Iter<TAlign2, AlignColIterator<TSpec> > const & _right)
 {
 SEQAN_CHECKPOINT
-	return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
+    return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
 }
 template <typename TAlign1, typename TAlign2, typename TSpec>
 inline bool
 operator !=(Iter<TAlign1, AlignColIterator<TSpec> > const & _left,
-			Iter<TAlign2, AlignColIterator<TSpec> > const & _right)
+            Iter<TAlign2, AlignColIterator<TSpec> > const & _right)
 {
 SEQAN_CHECKPOINT
-	return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
+    return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -320,36 +322,36 @@ SEQAN_CHECKPOINT
 template <typename TAlign, typename TSpec, typename TPosition>
 inline typename Reference<TAlign>::Type
 value(Iter<TAlign, AlignColIterator<TSpec> > & me,
-	  TPosition pos_)
+      TPosition pos_)
 {
 SEQAN_CHECKPOINT
-	return value(me.data_iterators[pos_]);
+    return value(me.data_iterators[pos_]);
 }
 template <typename TAlign, typename TSpec, typename TPosition>
 inline typename Reference<TAlign>::Type
 value(Iter<TAlign, AlignColIterator<TSpec> > const & me,
-	  TPosition pos_)
+      TPosition pos_)
 {
 SEQAN_CHECKPOINT
-	return value(me.data_iterators[pos_]);
+    return value(me.data_iterators[pos_]);
 }
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSpec, typename TPosition>
 inline typename GetValue<TAlign>::Type
 getValue(Iter<TAlign, AlignColIterator<TSpec> > & me,
-		 TPosition pos_)
+         TPosition pos_)
 {
 SEQAN_CHECKPOINT
-	return getValue(me.data_iterators[pos_]);
+    return getValue(me.data_iterators[pos_]);
 }
 template <typename TAlign, typename TSpec, typename TPosition>
 inline typename GetValue<TAlign>::Type
 getValue(Iter<TAlign, AlignColIterator<TSpec> > const & me,
-		 TPosition pos_)
+         TPosition pos_)
 {
 SEQAN_CHECKPOINT
-	return getValue(me.data_iterators[pos_]);
+    return getValue(me.data_iterators[pos_]);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -357,38 +359,38 @@ SEQAN_CHECKPOINT
 template <typename TAlign, typename TSpec, typename TPosition, typename TValue>
 inline void
 assignValue(Iter<TAlign, AlignColIterator<TSpec> > & me,
-			TPosition pos_,
-			TValue & val)
+            TPosition pos_,
+            TValue & val)
 {
 SEQAN_CHECKPOINT
-	return assignValue(me.data_iterators[pos_], val);
+    return assignValue(me.data_iterators[pos_], val);
 }
 template <typename TAlign, typename TSpec, typename TPosition, typename TValue>
 inline void
 assignValue(Iter<TAlign, AlignColIterator<TSpec> > & me,
-			TPosition pos_,
-			TValue const & val)
+            TPosition pos_,
+            TValue const & val)
 {
 SEQAN_CHECKPOINT
-	return assignValue(me.data_iterators[pos_], val);
+    return assignValue(me.data_iterators[pos_], val);
 }
 template <typename TAlign, typename TSpec, typename TPosition, typename TValue>
 inline void
 assignValue(Iter<TAlign, AlignColIterator<TSpec> > const & me,
-			TPosition pos_,
-			TValue & val)
+            TPosition pos_,
+            TValue & val)
 {
 SEQAN_CHECKPOINT
-	return assignValue(me.data_iterators[pos_], val);
+    return assignValue(me.data_iterators[pos_], val);
 }
 template <typename TAlign, typename TSpec, typename TPosition, typename TValue>
 inline void
 assignValue(Iter<TAlign, AlignColIterator<TSpec> > const & me,
-			TPosition pos_,
-			TValue const & val)
+            TPosition pos_,
+            TValue const & val)
 {
 SEQAN_CHECKPOINT
-	return assignValue(me.data_iterators[pos_], val);
+    return assignValue(me.data_iterators[pos_], val);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -396,38 +398,38 @@ SEQAN_CHECKPOINT
 template <typename TAlign, typename TSpec, typename TPosition, typename TValue>
 inline void
 moveValue(Iter<TAlign, AlignColIterator<TSpec> > & me,
-		  TPosition pos_,
-		  TValue & val)
+          TPosition pos_,
+          TValue & val)
 {
 SEQAN_CHECKPOINT
-	return moveValue(me.data_iterators[pos_], val);
+    return moveValue(me.data_iterators[pos_], val);
 }
 template <typename TAlign, typename TSpec, typename TPosition, typename TValue>
 inline void
 moveValue(Iter<TAlign, AlignColIterator<TSpec> > & me,
-		  TPosition pos_,
-		  TValue const & val)
+          TPosition pos_,
+          TValue const & val)
 {
 SEQAN_CHECKPOINT
-	return moveValue(me.data_iterators[pos_], val);
+    return moveValue(me.data_iterators[pos_], val);
 }
 template <typename TAlign, typename TSpec, typename TPosition, typename TValue>
 inline void
 moveValue(Iter<TAlign, AlignColIterator<TSpec> > const & me,
-		  TPosition pos_,
-		  TValue & val)
+          TPosition pos_,
+          TValue & val)
 {
 SEQAN_CHECKPOINT
-	return moveValue(me.data_iterators[pos_], val);
+    return moveValue(me.data_iterators[pos_], val);
 }
 template <typename TAlign, typename TSpec, typename TPosition, typename TValue>
 inline void
 moveValue(Iter<TAlign, AlignColIterator<TSpec> > const & me,
-		  TPosition pos_,
-		  TValue const & val)
+          TPosition pos_,
+          TValue const & val)
 {
 SEQAN_CHECKPOINT
-	return moveValue(me.data_iterators[pos_], val);
+    return moveValue(me.data_iterators[pos_], val);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -436,96 +438,96 @@ SEQAN_CHECKPOINT
 //disabled since GapsIterator has no operator - and +
 /*
 template <typename TAlign, typename TSpec, typename TSize>
-inline Iter<TAlign, AlignColIterator<TSpec> > & 
+inline Iter<TAlign, AlignColIterator<TSpec> > &
 operator +=(Iter<TAlign, AlignColIterator<TSpec> > & me,
-			TSize size)
+            TSize size)
 {
 SEQAN_CHECKPOINT
-	typedef typename Row<TAlign>::Type TRow;
-	typedef typename Iterator<TRow>::Type TRowIterator;
-	typedef String<TRowIterator> TIterators;
-	typedef typename Iterator<TIterators>::Type TIteratorsIterator;
+    typedef typename Row<TAlign>::Type TRow;
+    typedef typename Iterator<TRow>::Type TRowIterator;
+    typedef String<TRowIterator> TIterators;
+    typedef typename Iterator<TIterators>::Type TIteratorsIterator;
 
-	TIteratorsIterator _it = begin(me.data_iterators);
-	TIteratorsIterator _it_end = end(me.data_iterators);
+    TIteratorsIterator _it = begin(me.data_iterators);
+    TIteratorsIterator _it_end = end(me.data_iterators);
 
-	while (_it != _it_end)
-	{
-		*_it += size;
-		++_it;
-	}
-	return me;
+    while (_it != _it_end)
+    {
+        *_it += size;
+        ++_it;
+    }
+    return me;
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSpec, typename TSize>
-inline Iter<TAlign, AlignColIterator<TSpec> > 
+inline Iter<TAlign, AlignColIterator<TSpec> >
 operator +(Iter<TAlign, AlignColIterator<TSpec> > & me,
-		   TSize size)
+           TSize size)
 {
 SEQAN_CHECKPOINT
-	Iter<TAlign, AlignColIterator<TSpec> > ret = me;
-	me += size;
-	return me;
+    Iter<TAlign, AlignColIterator<TSpec> > ret = me;
+    me += size;
+    return me;
 }
 template <typename TAlign, typename TSpec, typename TSize>
-inline Iter<TAlign, AlignColIterator<TSpec> > 
+inline Iter<TAlign, AlignColIterator<TSpec> >
 operator +(Iter<TAlign, AlignColIterator<TSpec> > const & me,
-		   TSize size)
+           TSize size)
 {
 SEQAN_CHECKPOINT
-	Iter<TAlign, AlignColIterator<TSpec> > ret = me;
-	me += size;
-	return me;
+    Iter<TAlign, AlignColIterator<TSpec> > ret = me;
+    me += size;
+    return me;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSpec, typename TSize>
-inline Iter<TAlign, AlignColIterator<TSpec> > & 
+inline Iter<TAlign, AlignColIterator<TSpec> > &
 operator -=(Iter<TAlign, AlignColIterator<TSpec> > & me,
-			TSize size)
+            TSize size)
 {
 SEQAN_CHECKPOINT
-	typedef typename Row<TAlign>::Type TRow;
-	typedef typename Iterator<TRow>::Type TRowIterator;
-	typedef String<TRowIterator> TIterators;
-	typedef typename Iterator<TIterators>::Type TIteratorsIterator;
+    typedef typename Row<TAlign>::Type TRow;
+    typedef typename Iterator<TRow>::Type TRowIterator;
+    typedef String<TRowIterator> TIterators;
+    typedef typename Iterator<TIterators>::Type TIteratorsIterator;
 
-	TIteratorsIterator _it = begin(me.data_iterators);
-	TIteratorsIterator _it_end = end(me.data_iterators);
+    TIteratorsIterator _it = begin(me.data_iterators);
+    TIteratorsIterator _it_end = end(me.data_iterators);
 
-	while (_it != _it_end)
-	{
-		*_it -= size;
-		++_it;
-	}
-	return me;
+    while (_it != _it_end)
+    {
+        *_it -= size;
+        ++_it;
+    }
+    return me;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSpec, typename TSize>
-inline Iter<TAlign, AlignColIterator<TSpec> > 
+inline Iter<TAlign, AlignColIterator<TSpec> >
 operator -(Iter<TAlign, AlignColIterator<TSpec> > & me,
-		   TSize size)
+           TSize size)
 {
 SEQAN_CHECKPOINT
-	Iter<TAlign, AlignColIterator<TSpec> > ret = me;
-	me -= size;
-	return me;
+    Iter<TAlign, AlignColIterator<TSpec> > ret = me;
+    me -= size;
+    return me;
 }
 template <typename TAlign, typename TSpec, typename TSize>
-inline Iter<TAlign, AlignColIterator<TSpec> > 
+inline Iter<TAlign, AlignColIterator<TSpec> >
 operator -(Iter<TAlign, AlignColIterator<TSpec> > const & me,
-		   TSize size)
+           TSize size)
 {
 SEQAN_CHECKPOINT
-	Iter<TAlign, AlignColIterator<TSpec> > ret = me;
-	me -= size;
-	return me;
+    Iter<TAlign, AlignColIterator<TSpec> > ret = me;
+    me -= size;
+    return me;
 }
 
 //____________________________________________________________________________
@@ -533,13 +535,13 @@ SEQAN_CHECKPOINT
 template <typename TAlign, typename TSpec>
 inline typename Difference<TAlign>::Type
 operator -(Iter<TAlign, AlignColIterator<TSpec> > const & left,
-		   Iter<TAlign, AlignColIterator<TSpec> > const & right)
+           Iter<TAlign, AlignColIterator<TSpec> > const & right)
 {
 SEQAN_CHECKPOINT
-	SEQAN_ASSERT_GT(length(left.data_iterators), 0u);
-	SEQAN_ASSERT_GT(length(right.data_iterators), 0u);
+    SEQAN_ASSERT_GT(length(left.data_iterators), 0u);
+    SEQAN_ASSERT_GT(length(right.data_iterators), 0u);
 
-	return (left.data_iterators[0] - right.data_iterators[0]);
+    return (left.data_iterators[0] - right.data_iterators[0]);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -549,14 +551,14 @@ inline typename Position<TAlign>::Type
 position(Iter<TAlign, AlignColIterator<TSpec> > & me)
 {
 SEQAN_CHECKPOINT
-	return position(me.data_iterators[0], row(host(me), 0));
+    return position(me.data_iterators[0], row(host(me), 0));
 }
 template <typename TAlign, typename TSpec>
 inline typename Position<TAlign>::Type
 position(Iter<TAlign, AlignColIterator<TSpec> > const & me)
 {
 SEQAN_CHECKPOINT
-	return position(me.data_iterators[0], row(host(me), 0));
+    return position(me.data_iterators[0], row(host(me), 0));
 }
 */
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/align/align_metafunctions.h b/seqan/align/align_metafunctions.h
index 7cd7f67..33e76e1 100644
--- a/seqan/align/align_metafunctions.h
+++ b/seqan/align/align_metafunctions.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Align-specific metafunctions.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_
 
 namespace seqan {
 
@@ -55,17 +55,6 @@ namespace seqan {
 // Metafunction Cols
 // ----------------------------------------------------------------------------
 
-/**
-.Metafunction.Cols:
-..cat:Alignments
-..summary:Type of column container of an alignment.
-..signature:Cols<T>::Type
-..param.T:An alignment type.
-...type:Class.Align
-..returns.param.Type:The type of the container that allows access to the columns of $T$.
-..include:seqan/align.h
-*/
-
 template <typename T>
 struct Cols;
 
@@ -85,20 +74,6 @@ struct Cols;
  * @return Type   The resulting type.
  */
 
-/**
-.Metafunction.Col:
-..cat:Alignments
-..summary:Type of a column in an alignment.
-..signature:Col<T>::Type
-..param.T:An alignment type.
-...type:Class.Align
-..returns.param.Type:The column type of $T$.
-..remarks:The returned type is equivalent to $Value<Cols<T>::Type>::Type$.
-..see:Metafunction.Cols
-..see:Metafunction.Value
-..include:seqan/align.h
-*/
-
 template <typename T>
 struct Col : Value<typename Cols<T>::Type>
 {};
@@ -107,18 +82,6 @@ struct Col : Value<typename Cols<T>::Type>
 // Metafunction Rows
 // ----------------------------------------------------------------------------
 
-/**
-.Metafunction.Rows:
-..cat:Alignments
-..summary:Type of row container of an alignment.
-..signature:Rows<T>::Type
-..param.T:An alignment type.
-...type:Class.Align
-..returns.param.Type:The type of the container that allows access to the rows of $T$.
-..see:Metafunction.Cols
-..include:seqan/align.h
-*/
-
 template <typename T>
 struct Rows;
 
@@ -126,20 +89,6 @@ struct Rows;
 // Metafunction Row
 // ----------------------------------------------------------------------------
 
-/**
-.Metafunction.Row:
-..cat:Alignments
-..summary:Type of a row in an alignment.
-..signature:Row<T>::Type
-..param.T:An alignment type.
-...type:Class.Align
-..returns.param.Type:The row type of $T$.
-..remarks:The returned type is equivalent to $Value<Rows<T>::Type>::Type$.
-..see:Metafunction.Rows
-..see:Metafunction.Value
-..include:seqan/align.h
-*/
-
 template <typename T>
 struct Row : Value<typename Rows<T>::Type>
 {};
@@ -154,18 +103,6 @@ struct Row<T const>
 // Metafunction StringSetType
 // ----------------------------------------------------------------------------
 
-/**
-.Metafunction.StringSetType:
-..cat:Alignments
-..summary:Return type of @Function.stringSet@ function.
-..signature:StringSetType<T>::Type
-..param.T:Alignment data structure.
-..param.T.type:Spec.Alignment Graph
-..param.T.type:Class.Align
-..returns.param.Type:A @Class.StringSet.string set@ type of a reference to a string set type.
-..see:Function.stringSet
-..include:seqan/align.h
-*/
 template <typename T>
 struct StringSetType;
 
@@ -175,4 +112,4 @@ struct StringSetType;
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_
diff --git a/seqan/align/align_traceback.h b/seqan/align/align_traceback.h
index b6de5bf..1a5f269 100644
--- a/seqan/align/align_traceback.h
+++ b/seqan/align/align_traceback.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,8 +39,8 @@
 // defined.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
 
 namespace seqan {
 
@@ -59,15 +59,13 @@ namespace seqan {
 // TODO(holtgrew): Mark as internal with underscore?
 
 /*!
- * @tag TraceBack
+ * @typedef TraceBack
  * @headerfile <seqan/align.h>
  * @brief Traceback value.
  *
  * @signature struct TraceBack_;
  * @signature typedef SimpleType<unsigned char, TraceBack_> TraceBack.
  *
- * @section Remarks
- *
  * The ValueSize of <tt>TraceBack</tt> is 3.  The values are defined in the following way:
  *
  * <ul>
@@ -77,19 +75,6 @@ namespace seqan {
  * </ul>
  */
 
-/**
-.Spec.TraceBack:
-..cat:Alphabets
-..summary: Trace back values.
-..general:Class.SimpleType
-..signature:TraceBack
-..remarks:
-...text:The @Metafunction.ValueSize@ of $TraceBack$ is 3.
-The values are defined in the following way: 0=Diagonal Move, 1=Horizontal Move, 2=Vertical Move
-..see:Metafunction.ValueSize
-..include:seqan/align.h
-*/
-
 struct TraceBack_ {};
 typedef SimpleType<unsigned char, TraceBack_> TraceBack;
 
@@ -123,12 +108,12 @@ template <> struct BitsPerValue<TraceBack>
  */
 
 /*!
- * @var TSizes AlignTraceback#sizes
+ * @var TSizes AlignTraceback::sizes
  * @brief The traceback lengths.
  */
 
 /*!
- * @var TLengths AlignTraceback#tsv
+ * @var TLengths AlignTraceback::tsv
  * @brief The traceback lengths.
  */
 
@@ -136,9 +121,9 @@ template <typename TSize>
 struct AlignTraceback
 {
     // Run lengths in the align matrix.
-	String<TSize> sizes;
+    String<TSize> sizes;
     // Trace values: 0 = diagonal, 1 = horizontal, 2 = vertical.
-	String<TraceBack> tvs;
+    String<TraceBack> tvs;
 };
 
 // ============================================================================
@@ -167,10 +152,10 @@ _alignTracePrint(AlignTraceback<TSize> & tb,
                  TPos const segLen,
                  TTraceValue const tv)
 {
-	appendValue(tb.sizes, segLen);
-	appendValue(tb.tvs, tv);
+    appendValue(tb.sizes, segLen);
+    appendValue(tb.tvs, tv);
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
diff --git a/seqan/align/alignment_algorithm_tags.h b/seqan/align/alignment_algorithm_tags.h
index 41008f4..321cbcc 100644
--- a/seqan/align/alignment_algorithm_tags.h
+++ b/seqan/align/alignment_algorithm_tags.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // independently from the algorithms.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_
 
 namespace seqan {
 
@@ -68,21 +68,6 @@ namespace seqan {
  * @signature typedef Tag<Gotoh_> Gotoh;
  */
 
-/**
-.Tag.Pairwise Global Alignment Algorithms
-..cat:Alignments
-..summary:Tags used for selecting pairwise global alignment algorithms.
-..tag
-...Gotoh:Gotoh's for affine gap costs.
-...NeedlemanWunsch:The Needleman-Wunsch algorithm for linear gap costs.
-...Hirschberg:Hirschberg's algorithm using linear space.
-...MyersBitVector:Myer's bit-vector algorithm.
-...MyersHirschberg:Combination of Myer's and Hirschberg's algorithm.
-..see:Function.globalAlignment
-..see:Function.globalAlignmentScore
-..include:seqan/align.h
-*/
-
 struct Gotoh_;
 typedef Tag<Gotoh_> Gotoh;
 
@@ -143,18 +128,6 @@ typedef Tag<MyersHirschberg_> MyersHirschberg;
  * @brief Tags for selecting algorithms.
  */
 
-/**
-.Tag.Pairwise Local Alignment Algorithms
-..cat:Alignments
-..summary:Tags used for selecting pairwise global alignment algorithms.
-..tag
-...SmithWaterman:Smith-Waterman algorithm for local alignments.
-...WatermanEggert:Smith-Waterman algorithm with declumping to identify suboptimal local alignments.
-..see:Function.localAlignment
-..see:Class.LocalAlignmentEnumerator
-..include:seqan/align.h
-*/
-
 /*!
  * @tag PairwiseLocalAlignmentAlgorithms#SmithWaterman
  * @headerfile <seqan/align.h>
@@ -189,4 +162,4 @@ typedef Tag<WatermanEggert_> WatermanEggert;
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_
diff --git a/seqan/align/alignment_operations.h b/seqan/align/alignment_operations.h
index e2c705c..949bf33 100644
--- a/seqan/align/alignment_operations.h
+++ b/seqan/align/alignment_operations.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Operations on alignments such as integration
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
 
 namespace seqan {
 
@@ -55,6 +55,48 @@ namespace seqan {
 // Functions
 // ============================================================================
 
+template <typename TSource0, typename TGapSpec0,
+          typename TSource1, typename TGapSpec1,
+          typename TPos>
+inline void
+integrateGaps(Gaps<TSource0, TGapSpec0> & targetRow,
+              Gaps<TSource1, TGapSpec1> const & sourceRow,
+              TPos const viewPos)
+{
+    typedef typename Iterator<Gaps<TSource0, TGapSpec0>, Standard>::Type TTargetIt;
+    typedef typename Iterator<Gaps<TSource1, TGapSpec1> const, Standard>::Type TSourceIt;
+
+    // This assertion ensures that the number of sequence characters after viewPos is greater than or equal to
+    // the number of source characters in the clipped infix row.
+    SEQAN_ASSERT_GEQ(endPosition(targetRow) - toSourcePosition(targetRow, viewPos),
+                     endPosition(sourceRow) - beginPosition(sourceRow));
+
+    // init iterators
+    TTargetIt it = iter(targetRow, viewPos);
+
+    // walk through Gaps containers and copy gaps
+    for (TSourceIt sIt = begin(sourceRow, Standard()), sItEnd = end(sourceRow, Standard()); sIt != sItEnd;)
+    {
+        TPos gapSize = countGaps(sIt);
+        insertGaps(it, gapSize);
+        goFurther(it, gapSize+1);
+        goFurther(sIt, gapSize+1);
+    }
+}
+
+template <typename TSource0, typename TGapSpec0,
+          typename TSource1, typename TGapSpec1>
+inline void
+integrateGaps(Gaps<TSource0, TGapSpec0> & targetRow,
+              Gaps<TSource1, TGapSpec1> const & sourceRow)
+{
+    typename Position<TSource0>::Type viewPos = beginPosition(source(sourceRow)) // correct for infixes
+                                              - beginPosition(source(targetRow)) // ...
+                                              + beginPosition(sourceRow);        // respect source clipping
+
+    integrateGaps(targetRow, sourceRow, toViewPosition(targetRow, viewPos));
+}
+
 // ----------------------------------------------------------------------------
 // Function integrateAlign()
 // ----------------------------------------------------------------------------
@@ -66,94 +108,42 @@ namespace seqan {
  *
  * @signature void integrateAlign(align1, align2[, positions]);
  *
- * @param align1    Target Alignment object into which align2 is to be integrated.
- * @param align2    Alignment object that is to be integrated into align1.
- * @param positions The integration positions in align1 for all rows (view positions), String of positions.
+ * @param[in,out] align1    Target Alignment object into which align2 is to be integrated.
+ * @param[in]     align2    Alignment object that is to be integrated into align1.
+ * @param[in]     positions The integration positions in align1 for all rows (view positions), String of positions.
  *
  * @section Examples
  *
- * @include demos/align/integrate_align.cpp
+ * @include demos/dox/align/integrate_align.cpp
  *
  * The output is as follows:
  *
- * @include demos/align/integrate_align.cpp.stdout
- */
-
-/**
-.Function.integrateAlign
-..summary:Integrates an alignment into another by copying the gaps.
-..cat:Alignments
-...type:Class.Align
-..signature:integrateAlign(align1, align2[, positions])
-..param.align1:Alignment object into which align2 is to be integrated.
-...type:Class.Align
-..param.align2:Alignment object that is to be integrated into align1.
-...type:Class.Align
-..param.positions:The integration positions in align1 for all rows (view positions).
-...type:Class.String
-..remarks:If the integration positions are not specified, the sources of align2 have to be @Metafunction.Infix@es of the sources of align1.
-..include:seqan/align.h
+ * @include demos/dox/align/integrate_align.cpp.stdout
  */
 
-template <typename TSource1, typename TSpec1, typename TSource2, typename TSpec2, typename TPos> 
+template <typename TSource1, typename TSpec1, typename TSource2, typename TSpec2, typename TPos>
 void integrateAlign(Align<TSource1, TSpec1> & align,
                     Align<TSource2, TSpec2> const & infixAlign,
                     String<TPos> const & viewPos)
 {
-    typedef Align<TSource1, TSpec1> TAlign;
-    typedef Align<TSource2, TSpec2> TInfixAlign;
-    typedef typename Size<TAlign>::Type TSize;
-
-    typedef typename Row<TAlign>::Type TRow;
-    typedef typename Row<TInfixAlign const>::Type TInfixRow;
-
-    // Iterators on align and infixAlign.
-    typename Iterator<TRow>::Type it;
-    typedef typename Iterator<TInfixRow, Standard>::Type TInfixRowIt;
-
-
+    SEQAN_ASSERT_EQ_MSG(length(rows(infixAlign)), length(rows(align)), "Both align objects need same number of rows.");
+    typedef typename Size<Align<TSource1, TSpec1> >::Type TSize;
+    //NOTE(h-2): could be parallelized
     for (TSize i = 0; i < length(rows(align)); ++i)
-    {
-        TInfixRow const & infixRow = row(infixAlign, i);
-        // This assertion ensures that the number of sequence characters after viewPos[i] is greater than or equal to
-        // the number of source characters in the clipped infix row.
-        SEQAN_ASSERT_GEQ(endPosition(row(align, i)) - toSourcePosition(row(align, i), viewPos[i]),
-                endPosition(infixRow) - beginPosition(infixRow));
-
-        // init iterators
-        it = iter(row(align, i), value(viewPos, i));
-
-        // walk through Gaps containers and copy gaps
-        for (TInfixRowIt infixIt = begin(infixRow, Standard()); !atEnd(infixIt);)
-        {
-            TSize gapSize = countGaps(infixIt);
-            insertGaps(it, gapSize);
-            goFurther(it, gapSize+1);
-            goFurther(infixIt, gapSize+1);
-        }
-    }
+        integrateGaps(row(align, i), row(infixAlign, i), viewPos[i]);
 }
 
-template <typename TSource, typename TSpec1, typename TSpec2>
-void integrateAlign(Align<TSource, TSpec1> & align,
-                    Align<typename Infix<TSource>::Type, TSpec2> const & infixAlign) 
+template <typename TSource1, typename TSpec1, typename TSource2, typename TSpec2>
+void integrateAlign(Align<TSource1, TSpec1> & align,
+                    Align<TSource2, TSpec2> const & infixAlign)
 {
-    typedef typename Size<TSource>::Type TSize;
-    typedef typename Position<typename Row<Align<TSource, TSpec1> >::Type>::Type TPos;
-
-    String<TPos> viewPos;
-    TPos pos;
-    for (TSize i = 0; i < length(rows(infixAlign)); ++i) 
-    {
-        pos = beginPosition(source(row(infixAlign, i)))
-            - beginPosition(source(row(align, i)))
-            + beginPosition(row(infixAlign, i));
-        appendValue(viewPos, toViewPosition(row(align, i), pos));
-    }
-
-    integrateAlign(align, infixAlign, viewPos);
+    SEQAN_ASSERT_EQ_MSG(length(rows(infixAlign)), length(rows(align)), "Both align objects need same number of rows.");
+    typedef typename Size<Align<TSource1, TSpec1> >::Type TSize;
+    //NOTE(h-2): could be parallelized
+    for (TSize i = 0; i < length(rows(align)); ++i)
+        integrateGaps(row(align, i), row(infixAlign, i));
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_
diff --git a/seqan/align/dp_algorithm_impl.h b/seqan/align/dp_algorithm_impl.h
index 7b31030..32a7ba8 100644
--- a/seqan/align/dp_algorithm_impl.h
+++ b/seqan/align/dp_algorithm_impl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -130,8 +130,8 @@
 // sequence to determine there orientation within the matrix.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_
 
 namespace seqan {
 
@@ -159,7 +159,7 @@ namespace seqan {
 template <typename TSequenceH, typename TSequenceV, typename TAlignmentProfile>
 inline bool _checkBandProperties(TSequenceH const & /*seqH*/,
                                  TSequenceV const & /*seqV*/,
-                                 DPBand_<BandOff> const & /*band*/,
+                                 DPBandConfig<BandOff> const & /*band*/,
                                  TAlignmentProfile const & /*alignProfile*/)
 {
     return true;
@@ -168,7 +168,7 @@ inline bool _checkBandProperties(TSequenceH const & /*seqH*/,
 template <typename TSequenceH, typename TSequenceV, typename TAlignmentProfile>
 inline bool _checkBandProperties(TSequenceH const & seqH,
                                  TSequenceV const & seqV,
-                                 DPBand_<BandOn> const & band,
+                                 DPBandConfig<BandOn> const & band,
                                  TAlignmentProfile const & /*alignProfile*/)
 {
     typedef typename MakeSigned<typename Size<TSequenceH>::Type>::Type TSignedSize;
@@ -238,7 +238,7 @@ inline bool _isValidDPSettings(TSequenceH const & seqH,
 // Returns true if a band is selected, otherwise false.
 template <typename TBandSpec>
 inline bool
-_isBandEnabled(DPBand_<TBandSpec> const & /*band*/)
+_isBandEnabled(DPBandConfig<TBandSpec> const & /*band*/)
 {
     return IsSameType<TBandSpec, BandOn>::VALUE;
 }
@@ -270,14 +270,18 @@ _computeCell(TDPScout & scout,
                 _computeScore(activeCell, previousDiagonal, previousHorizontal, previousVertical, seqHVal, seqVVal,
                               scoringScheme, typename RecursionDirection_<TMetaColumn, TCellDescriptor>::Type(),
                               TDPProfile()));
-//	std::cout << "("<< activeCell._score << "," << previousDiagonal._score << "," << previousHorizontal._score << "," << previousVertical._score << ") ";
+
     if (TrackingEnabled_<TMetaColumn, TCellDescriptor>::VALUE)
     {
-        bool isLastColumn = IsSameType<typename TColumnDescriptor::TColumnProperty, DPFinalColumn>::VALUE;
-        bool isLastRow = And<IsSameType<TCellDescriptor, LastCell>,
-                             Or<IsSameType<typename TColumnDescriptor::TLocation, PartialColumnBottom>,
-                                IsSameType<typename TColumnDescriptor::TLocation, FullColumn> > >::VALUE;
-        _scoutBestScore(scout, activeCell, traceMatrixNavigator, isLastColumn, isLastRow);
+        typedef typename IsSameType<typename TColumnDescriptor::TColumnProperty,
+            DPFinalColumn>::Type TIsLastColumn;
+        typedef typename And<IsSameType<TCellDescriptor, LastCell>, Or<
+            IsSameType<typename TColumnDescriptor::TLocation,
+            PartialColumnBottom>,IsSameType<
+            typename TColumnDescriptor::TLocation, FullColumn> > >::Type
+            TIsLastRow;
+        _scoutBestScore(scout, activeCell, traceMatrixNavigator,
+                        TIsLastColumn(), TIsLastRow());
     }
 }
 
@@ -311,7 +315,7 @@ _computeTrack(TDPScout & scout,
                  previousCellVertical(dpScoreMatrixNavigator), seqHValue, seqVValue, scoringScheme,
                  TColumnDescriptor(), FirstCell(), TDPProfile());
 //    std::cerr << _scoreOfCell(value(dpScoreMatrixNavigator)) << " \t";
-//	std::cerr << _scoreOfCell(value(dpScoreMatrixNavigator)) << "(" << _horizontalScoreOfCell(value(dpScoreMatrixNavigator)) << "," << _verticalScoreOfCell(value(dpScoreMatrixNavigator)) << ")" << " \t";
+//    std::cerr << _scoreOfCell(value(dpScoreMatrixNavigator)) << "(" << _horizontalScoreOfCell(value(dpScoreMatrixNavigator)) << "," << _verticalScoreOfCell(value(dpScoreMatrixNavigator)) << ")" << " \t";
 
     TSeqVIterator iter = seqBegin;
     TSeqVIterator itEnd = (seqEnd - 1);
@@ -346,8 +350,8 @@ _computeTrack(TDPScout & scout,
 
 // TODO(rmaerker): Debug code!
 //template <typename TDPScout, typename TDPScoreMatrixNavigator, typename TDPTraceMatrixNavigator, typename TSeqHValue,
-//			typename TSeqVValue, typename TSeqVIterator, typename TScoringScheme, typename TDPProfile,
-//			typename TColumnDescriptor>
+//            typename TSeqVValue, typename TSeqVIterator, typename TScoringScheme, typename TDPProfile,
+//            typename TColumnDescriptor>
 //inline void
 //_computeTrack(TDPScout & scout,
 //              TDPScoreMatrixNavigator & dpScoreMatrixNavigator,
@@ -368,52 +372,52 @@ _computeTrack(TDPScout & scout,
 //    _goNextCell(dpTraceMatrixNavigator, TColumnDescriptor(), FirstCell());
 //
 //    // Compute the first cell.
-//	_computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator),
-//			previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator),
-//			previousCellVertical(dpScoreMatrixNavigator), seqHValue, seqVValue, scoringScheme,
-//			TColumnDescriptor(), FirstCell(), TDPProfile());
-//	// TODO(rmaerker): remove debug code
-////	std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\t";
-//	std::stringstream stream;
-//	stream << _scoreOfCell(value(dpScoreMatrixNavigator));
-////	stream << col + row;
-//	testMatrix[col + row] = stream.str();
-//	++row;
+//    _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator),
+//            previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator),
+//            previousCellVertical(dpScoreMatrixNavigator), seqHValue, seqVValue, scoringScheme,
+//            TColumnDescriptor(), FirstCell(), TDPProfile());
+//    // TODO(rmaerker): remove debug code
+////    std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\t";
+//    std::stringstream stream;
+//    stream << _scoreOfCell(value(dpScoreMatrixNavigator));
+////    stream << col + row;
+//    testMatrix[col + row] = stream.str();
+//    ++row;
 //
-//	TSeqVIterator iter = seqBegin;
-//	TSeqVIterator itEnd = (seqEnd - 1);
-//	// Compute the inner cells of the current track.
+//    TSeqVIterator iter = seqBegin;
+//    TSeqVIterator itEnd = (seqEnd - 1);
+//    // Compute the inner cells of the current track.
 //    for (; iter != itEnd; ++iter, ++row)  // He will out of scope....
 //    {
 //      // Set the iterator to the next cell within the track.
 //      _goNextCell(dpScoreMatrixNavigator, TColumnDescriptor(), InnerCell());
 //      _goNextCell(dpTraceMatrixNavigator, TColumnDescriptor(), InnerCell());
 //      // Compute the inner cell.
-//		_computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator),
-//				previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator),
-//				previousCellVertical(dpScoreMatrixNavigator), seqHValue, value(iter), scoringScheme,
-//				TColumnDescriptor(), InnerCell(), TDPProfile());
-//		// TODO(rmaerker): remove debug code
-////		std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\t";
-//		stream.str("");
-//		stream << _scoreOfCell(value(dpScoreMatrixNavigator));
-////		stream << col + row;
-//		testMatrix[col + row] = stream.str();
+//        _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator),
+//                previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator),
+//                previousCellVertical(dpScoreMatrixNavigator), seqHValue, value(iter), scoringScheme,
+//                TColumnDescriptor(), InnerCell(), TDPProfile());
+//        // TODO(rmaerker): remove debug code
+////        std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\t";
+//        stream.str("");
+//        stream << _scoreOfCell(value(dpScoreMatrixNavigator));
+////        stream << col + row;
+//        testMatrix[col + row] = stream.str();
 //    }
 //    // Set the iterator to the last cell of the track.
-//	_goNextCell(dpScoreMatrixNavigator, TColumnDescriptor(), LastCell());
-//	_goNextCell(dpTraceMatrixNavigator, TColumnDescriptor(), LastCell());
-//	// Compute the last cell.
-//	_computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator),
-//			previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator),
-//			previousCellVertical(dpScoreMatrixNavigator), seqHValue, value(iter), scoringScheme,
-//			TColumnDescriptor(), LastCell(), TDPProfile());
-//	// TODO(rmaerker): remove debug code
-////	std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\n";
-//	stream.str("");
-//		stream << _scoreOfCell(value(dpScoreMatrixNavigator));
-////		stream << col + row;
-//	testMatrix[col + row] = stream.str();
+//    _goNextCell(dpScoreMatrixNavigator, TColumnDescriptor(), LastCell());
+//    _goNextCell(dpTraceMatrixNavigator, TColumnDescriptor(), LastCell());
+//    // Compute the last cell.
+//    _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator),
+//            previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator),
+//            previousCellVertical(dpScoreMatrixNavigator), seqHValue, value(iter), scoringScheme,
+//            TColumnDescriptor(), LastCell(), TDPProfile());
+//    // TODO(rmaerker): remove debug code
+////    std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\n";
+//    stream.str("");
+//        stream << _scoreOfCell(value(dpScoreMatrixNavigator));
+////        stream << col + row;
+//    testMatrix[col + row] = stream.str();
 //}
 
 // ----------------------------------------------------------------------------
@@ -583,7 +587,7 @@ _computeBandedAlignment(TDPScout & scout,
                      MetaColumnDescriptor<DPInitialColumn, PartialColumnTop>(), FirstCell(), TDPProfile());
         // we might need to additionally track this point.
         if (TrackingEnabled_<DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPFinalColumn, PartialColumnTop> >, FirstCell>::VALUE)
-            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, true, false);
+            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, True(), False());
         return;
     }
     if (seqHIterEndColumnBottom == begin(seqH, Rooted()))
@@ -600,7 +604,7 @@ _computeBandedAlignment(TDPScout & scout,
                      MetaColumnDescriptor<DPInitialColumn, PartialColumnBottom>(), FirstCell(), TDPProfile());
         // We might need to additionally track this point.
         if (TrackingEnabled_<DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPInitialColumn, PartialColumnBottom> >, LastCell>::VALUE)
-            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, false, true);
+            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), True());
         return;
     }
 
@@ -635,7 +639,7 @@ _computeBandedAlignment(TDPScout & scout,
                      MetaColumnDescriptor<DPInitialColumn, PartialColumnTop>(), FirstCell(), TDPProfile());
         // we might need to additionally track this point.
         if (TrackingEnabled_<DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPInnerColumn, PartialColumnTop> >, FirstCell>::VALUE)
-            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, false, false);
+            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), False());
     }
     else  // Upper diagonal >= 0 and lower Diagonal < 0
     if (lowerDiagonal(band) <= -seqVlength)      // The band is bounded by the top and bottom of the matrix.
@@ -684,7 +688,7 @@ _computeBandedAlignment(TDPScout & scout,
         // We might want to track the current cell here, since this is the first cell that crosses the bottom but is
         // not part of the FullColumn tracks.
         if (TrackingEnabled_<DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPInnerColumn, FullColumn> >, LastCell>::VALUE)
-            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, false, true);
+            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), True());
         for (; seqHIter != seqHIterEndColumnMiddle; ++seqHIter)
         {
             _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator,
@@ -719,7 +723,7 @@ _computeBandedAlignment(TDPScout & scout,
         {
             if (lowerDiagonal(band) + seqVlength < seqHlength)
             {
-                _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, false, true);
+                _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), True());
             }
         }
 
@@ -759,7 +763,7 @@ _computeBandedAlignment(TDPScout & scout,
                      MetaColumnDescriptor<DPInnerColumn, PartialColumnBottom>(), FirstCell(), TDPProfile());
         // We might need to additionally track this point.
         if (TrackingEnabled_<DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPInnerColumn, PartialColumnBottom> >, LastCell>::VALUE)
-            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, false, true);
+            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), True());
     }
     else if (seqHIter == end(seqH, Rooted()) - 1) // Case 2: The band ends somewhere in the final column of the matrix.
     {
@@ -779,7 +783,7 @@ _computeBandedAlignment(TDPScout & scout,
                          MetaColumnDescriptor<DPFinalColumn, PartialColumnBottom>(), FirstCell(), TDPProfile());
             // we might need to additionally track this point.
             if (TrackingEnabled_<DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPFinalColumn, PartialColumnBottom> >, LastCell>::VALUE)
-                _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, true, true);
+                _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, True(), True());
         }
         else  // Case2b: At least two cells intersect between the band and the matrix in the final column of the matrix.
         {
@@ -805,7 +809,7 @@ _computeBandedAlignment(TDPScout & scout,
                                       seqVBegin, seqVEnd, scoringScheme,
                                       MetaColumnDescriptor<DPFinalColumn, PartialColumnTop>(), dpProfile);
                         if (TrackingEnabled_<DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPFinalColumn, FullColumn> >, LastCell>::VALUE)
-                            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, true, true);
+                            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, True(), True());
                     }
                     else
                         _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator,
@@ -830,7 +834,7 @@ _computeBandedAlignment(TDPScout & scout,
                                       seqVBegin, seqVEnd, scoringScheme,
                                       MetaColumnDescriptor<DPFinalColumn, PartialColumnMiddle>(), dpProfile);
                         if (TrackingEnabled_<DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPFinalColumn, PartialColumnBottom> >, LastCell>::VALUE)
-                            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, true, true);
+                            _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, True(), True());
                     }
                     else
                     {
@@ -1346,28 +1350,49 @@ _correctTraceValue(TTraceNavigator & traceNavigator,
         value(traceNavigator) &= ~TraceBitMap_::DIAGONAL;
         value(traceNavigator) |= TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
     }
+}
 
+template <typename TTraceNavigator, typename TScoreValue, typename TDPScoutSpec>
+inline void
+_correctTraceValue(TTraceNavigator & traceNavigator,
+                   DPScout_<DPCell_<TScoreValue, DynamicGaps>, TDPScoutSpec>  const & dpScout)
+{
+    _setToPosition(traceNavigator, maxHostPosition(dpScout));
+    if (isGapExtension(dpScout._maxScore, DynamicGapExtensionVertical()))
+    {
+        value(traceNavigator) &= ~TraceBitMap_::DIAGONAL;
+        value(traceNavigator) |= TraceBitMap_::MAX_FROM_VERTICAL_MATRIX;
+    }
+    else if (isGapExtension(dpScout._maxScore, DynamicGapExtensionHorizontal()))
+    {
+        value(traceNavigator) &= ~TraceBitMap_::DIAGONAL;
+        value(traceNavigator) |= TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
+    }
 }
 
 // ----------------------------------------------------------------------------
 // Function _computeAligmnment()
 // ----------------------------------------------------------------------------
 
-template <typename TTraceTarget, typename TScoutState, typename TSequenceH, typename TSequenceV, typename TScoreScheme,
-          typename TBandSwitch, typename TAlignmentAlgorithm, typename TGapCosts, typename TTraceFlag>
+template <typename TScoreValue, typename TGapScheme, typename TTraceTarget, typename TScoutState, typename TSequenceH, typename TSequenceV,
+          typename TScoreScheme, typename TBandSwitch, typename TAlignmentAlgorithm, typename TTraceFlag>
 inline typename Value<TScoreScheme>::Type
-_computeAlignment(TTraceTarget & traceSegments,
+_computeAlignment(DPContext<TScoreValue, TGapScheme> & dpContext,
+                  TTraceTarget & traceSegments,
                   TScoutState & scoutState,
                   TSequenceH const & seqH,
                   TSequenceV const & seqV,
                   TScoreScheme const & scoreScheme,
-                  DPBand_<TBandSwitch> const & band,
-                  DPProfile_<TAlignmentAlgorithm, TGapCosts, TTraceFlag> const & dpProfile)
+                  DPBandConfig<TBandSwitch> const & band,
+                  DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag> const & dpProfile)
 {
-    typedef typename Value<TScoreScheme>::Type TScoreValue;
-    typedef DPCell_<TScoreValue, TGapCosts> TDPScoreValue;
+    typedef typename GetDPScoreMatrix<DPContext<TScoreValue, TGapScheme> >::Type TDPScoreMatrixHost;
+    typedef typename Value<TDPScoreMatrixHost>::Type TDPScoreValue;
+
+    typedef typename GetDPTraceMatrix<DPContext<TScoreValue, TGapScheme> >::Type TDPTraceMatrixHost;
+    typedef typename Value<TDPTraceMatrixHost>::Type TTraceValue;
+
     typedef typename DefaultScoreMatrixSpec_<TAlignmentAlgorithm>::Type TScoreMatrixSpec;
-    typedef typename TraceBitMap_::TTraceValue TTraceValue;
 
     typedef DPMatrix_<TDPScoreValue, TScoreMatrixSpec> TDPScoreMatrix;
     typedef DPMatrix_<TTraceValue, FullDPMatrix> TDPTraceMatrix;
@@ -1401,6 +1426,10 @@ _computeAlignment(TTraceTarget & traceSegments,
         setLength(dpTraceMatrix, +DPMatrixDimension_::VERTICAL, _min(static_cast<int>(length(seqV)) + 1, bandSize));
     }
 
+    // We set the host to the score matrix and the dp matrix.
+    setHost(dpScoreMatrix, getDpScoreMatrix(dpContext));
+    setHost(dpTraceMatrix, getDpTraceMatrix(dpContext));
+
     resize(dpScoreMatrix);
     // We do not need to allocate the memory for the trace matrix if the traceback is disabled.
     if (IsTracebackEnabled_<TTraceFlag>::VALUE)
@@ -1442,20 +1471,6 @@ _computeAlignment(TTraceTarget & traceSegments,
     return maxScore(dpScout);
 }
 
-template <typename TTraceTarget, typename TSequenceH, typename TSequenceV, typename TScoreScheme, typename TBandSwitch,
-          typename TAlignmentAlgorithm, typename TGapCosts, typename TTraceFlag>
-inline typename Value<TScoreScheme>::Type
-_computeAlignment(TTraceTarget & traceSegments,
-                  TSequenceH const & seqH,
-                  TSequenceV const & seqV,
-                  TScoreScheme const & scoreScheme,
-                  DPBand_<TBandSwitch> const & band,
-                  DPProfile_<TAlignmentAlgorithm, TGapCosts, TTraceFlag> const & dpProfile)
-{
-    DPScoutState_<Default> noState;
-    return _computeAlignment(traceSegments, noState, seqH, seqV, scoreScheme, band, dpProfile);
-}
-
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_
diff --git a/seqan/align/dp_band.h b/seqan/align/dp_band.h
index 49cc73f..545a10d 100644
--- a/seqan/align/dp_band.h
+++ b/seqan/align/dp_band.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,12 +35,11 @@
 // whether a band was selected or not.
 // ==========================================================================
 
-// TODO(holtgrew): Documentation in this header necessary or internal only?
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_BAND_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_BAND_H_
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_BAND_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_BAND_H_
-
-namespace seqan {
+namespace seqan
+{
 
 // ============================================================================
 // Forwards
@@ -50,6 +49,23 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
+/*!
+ * @defgroup DPBandSwitch
+ * @brief Tags used to switch between banded and unbanded alignment.
+ *
+ * @tag DPBandSwitch#BandOn
+ * @brief Switches banded alignment on.
+ * @headerfile <seqan/align.h>
+ * @signature struct BandOn_;
+ * @signature typedef Tag<BandOn_> BandOn;
+ *
+ * @tag DPBandSwitch#BandOff
+ * @brief Switches banded alignment off.
+ * @headerfile <seqan/align.h>
+ * @signature struct BandOff_;
+ * @signature typedef Tag<BandOff_> BandOff;
+ */
+
 // ----------------------------------------------------------------------------
 // Tag BandOff
 // ----------------------------------------------------------------------------
@@ -67,76 +83,149 @@ struct BandOn_;
 typedef Tag<BandOn_> BandOn;
 
 // ----------------------------------------------------------------------------
-// Class DPBand_
+// Class DPBandConfig
 // ----------------------------------------------------------------------------
 
+/*!
+ * @class DPBandConfig
+ * @headerfile <seqan/align.h>
+ * @brief Simple class to configure banded alignments.
+ *
+ * @signature template <typename TSwitch>
+ *            class DPBandConfig<TSwitch>;
+ *
+ * @tparam TSwitch Tag to switch between banded and unbanded alignments.
+ *              One of @link DPBandSwitch @endlink. Defaults to @link DPBandSwitch#BandOff @endlink.
+ *
+ * To compute banded alignments use @link DPBand @endlink as a shortcut for the <tt>DPBandConfig</tt> with
+ * band switched on.
+ */
+
 // Simple band class.
-template <typename TSpec>
-struct DPBand_ {};
+template <typename TSpec = BandOff>
+struct DPBandConfig {};
 
 // ----------------------------------------------------------------------------
-// Class DPBand_                                                      [BandOff]
+// Class DPBandConfig                                                  [BandOff]
 // ----------------------------------------------------------------------------
 
 // The specialization when using no band.
 // Per default the member variables _lowerDiagonal and _upperDiagonal are
 // always 0.
 template <>
-struct DPBand_<BandOff>
+struct DPBandConfig<BandOff>
 {
     typedef int TPosition;
 };
 
 // ----------------------------------------------------------------------------
-// Class DPBand_                                                       [BandOn]
+// Class DPBandConfig                                                  [BandOn]
 // ----------------------------------------------------------------------------
 
 // The specialization when using a band.
 // On construction the diagonals are set to 0.
 template <>
-struct DPBand_<BandOn>
+struct DPBandConfig<BandOn>
 {
     typedef int TPosition;
 
     int _lowerDiagonal;
     int _upperDiagonal;
 
-    DPBand_() :
+/*!
+ * @fn DPBandConfig::DPBandConfig
+ * @brief Constructor.
+ *
+ * @signature DPBandConfig<TSwitch>();
+ * @signature DPBandConfig<BandOn>(lowerDiag, upperDiag);
+ *
+ * @tparam TSwitch Tag to switch between banded and unbanded alignments. One of @link DPBandSwitch @endlink.
+ *              The second constructor is only supported when @link DPBandConfig @endlink is specialized with
+ *              @link DPBandSwitch#BandOn @endlink.
+ *
+ * @param lowerDiag The value for the lower diagonal of the band.
+ * @param upperDiag The value for the upper diagonal of the band.
+ *
+ * A negative value for the diagonals indicates an intersection of the diagonal with the vertical sequence (y-axis)
+ * and a positive value indicates an intersection with the horizontal sequence (x-axis).
+ * The value of the lower diagonal has to compare less or equal to the value of the upper diagonal.
+ */
+
+    DPBandConfig() :
         _lowerDiagonal(0), _upperDiagonal(0) {}
 
-    DPBand_(int lowerDiagonal, int upperDiagonal) :
-        _lowerDiagonal(lowerDiagonal), _upperDiagonal(upperDiagonal) {}
+    DPBandConfig(int lowerDiagonal, int upperDiagonal) :
+        _lowerDiagonal(lowerDiagonal), _upperDiagonal(upperDiagonal)
+    {
+        SEQAN_ASSERT_LEQ(lowerDiagonal, upperDiagonal);
+    }
 };
 
+/*!
+ * @typedef DPBand
+ * @headerfile <seqan/align.h>
+ * @brief Global typedef used for @link DPBandConfig @endlink specialized with @link DPBandSwitch#BandOn @endlink.
+ *
+ * @signature typedef DPBandConfig<BandOn> DPBand;
+ */
+
+// Typedef for Band.
+typedef DPBandConfig<BandOn> DPBand;
+
 // ============================================================================
 // Metafunctions
 // ============================================================================
 
+/*!
+ * @mfn DPBandConfig#Position
+ * @headerfile <seqan/align.h>
+ * @brief Metafunction returning the position type.
+ *
+ * @signature typename Position<T>::Type;
+ *
+ * @tparam T The type @link DPBandConfig @endlink to query the position type for.
+ * @return TPosition The position type.
+ */
+
 // ----------------------------------------------------------------------------
 // Metafunction Position
 // ----------------------------------------------------------------------------
 
 template <typename T>
-struct Position<DPBand_<T> >
+struct Position<DPBandConfig<T> >
 {
-    typedef typename DPBand_<T>::TPosition Type;
+    typedef typename DPBandConfig<T>::TPosition Type;
 };
 
 template <typename T>
-struct Position<DPBand_<T> const>:
-    Position<DPBand_<T> >{};
+struct Position<DPBandConfig<T> const>:
+    Position<DPBandConfig<T> >{};
 
 // ----------------------------------------------------------------------------
 // Metafunction Size
 // ----------------------------------------------------------------------------
 
+/*!
+ * @mfn DPBandConfig#Size
+ * @headerfile <seqan/align.h>
+ * @brief Metafunction returning the size type.
+ *
+ * @signature typename Size<T>::Type;
+ *
+ * @tparam T The type @link DPBandConfig @endlink to query the size type for.
+ * @return TSize The size type.
+ */
+
 template <typename T>
-struct Size<DPBand_<T> >:
-    Position<DPBand_<T> >{};
+struct Size<DPBandConfig<T> >
+{
+    typedef unsigned Type;
+};
+
 
 template <typename T>
-struct Size<DPBand_<T> const>:
-    Size<DPBand_<T> >{};
+struct Size<DPBandConfig<T> const>:
+    Size<DPBandConfig<T> >{};
 
 // ============================================================================
 // Functions
@@ -146,14 +235,27 @@ struct Size<DPBand_<T> const>:
 // Function setLowerDiagonal
 // ----------------------------------------------------------------------------
 
+/*!
+ * @fn DPBandConfig#setLowerDiagonal
+ * @headerfile <seqan/align.h>
+ * @brief Sets the value of the lower diagonal.
+ *
+ * @signature setLowerDiagonal(obj, val);
+ *
+ * @param obj The object of type @link DPBandConfig @endlink to set the lower diagonal for.
+ * @param val The new value for the lower diagonal.
+ *
+ * @note If the band is switched off, this function defaults to no-op.
+ */
+
 inline void
-setLowerDiagonal(DPBand_<BandOff> & /*dpBand*/, int /*newLowerDiagonal*/)
+setLowerDiagonal(DPBandConfig<BandOff> & /*dpBand*/, int /*newLowerDiagonal*/)
 {
     //no-op
 }
 
 inline void
-setLowerDiagonal(DPBand_<BandOn> & dpBand, int newLowerDiagonal)
+setLowerDiagonal(DPBandConfig<BandOn> & dpBand, int newLowerDiagonal)
 {
     dpBand._lowerDiagonal = newLowerDiagonal;
 }
@@ -162,15 +264,28 @@ setLowerDiagonal(DPBand_<BandOn> & dpBand, int newLowerDiagonal)
 // Function lowerDiagonal
 // ----------------------------------------------------------------------------
 
-inline int
-lowerDiagonal(DPBand_<BandOff> const & /*dpBand*/)
+/*!
+ * @fn DPBandConfig#lowerDiagonal
+ * @headerfile <seqan/align.h>
+ * @brief Returns the value of the lower diagonal.
+ *
+ * @signature TPosition lowerDiagonal(obj);
+ *
+ * @param obj The object of type @link DPBandConfig @endlink to query the lower diagonal for.
+ *
+ * @note If the band is switched off this function always returns 0.
+ * @return TPosition The value of the lower diagonal.
+ */
+
+inline Position<DPBandConfig<BandOff> >::Type
+lowerDiagonal(DPBandConfig<BandOff> const & /*dpBand*/)
 {
     return 0;
 }
 
-template <typename TBandSwitch>
-inline int
-lowerDiagonal(DPBand_<TBandSwitch> const & dpBand)
+template <typename TSwitch>
+inline typename Position<DPBandConfig<BandOff> >::Type
+lowerDiagonal(DPBandConfig<TSwitch> const & dpBand)
 {
     return dpBand._lowerDiagonal;
 }
@@ -179,14 +294,27 @@ lowerDiagonal(DPBand_<TBandSwitch> const & dpBand)
 // Function setUpperDiagonal
 // ----------------------------------------------------------------------------
 
+/*!
+ * @fn DPBandConfig#setUpperDiagonal
+ * @headerfile <seqan/align.h>
+ * @brief Sets the value of the upper diagonal.
+ *
+ * @signature setUpperDiagonal(obj, val);
+ *
+ * @param obj The object of type @link DPBandConfig @endlink to set the upper diagonal for.
+ * @param val The new value for the upper diagonal.
+ *
+ * @note If the band is switched off, this function defaults to no-op.
+ */
+
 inline void
-setUpperDiagonal(DPBand_<BandOff> & /*dpBand*/, int /*newUpperDiagonal*/)
+setUpperDiagonal(DPBandConfig<BandOff> & /*dpBand*/, int /*newUpperDiagonal*/)
 {
     //no-op
 }
 
 inline void
-setUpperDiagonal(DPBand_<BandOn> & dpBand, int newUpperDiagonal)
+setUpperDiagonal(DPBandConfig<BandOn> & dpBand, int newUpperDiagonal)
 {
     dpBand._upperDiagonal = newUpperDiagonal;
 }
@@ -195,14 +323,28 @@ setUpperDiagonal(DPBand_<BandOn> & dpBand, int newUpperDiagonal)
 // Function upperDiagonal
 // ----------------------------------------------------------------------------
 
-inline int
-upperDiagonal(DPBand_<BandOff> const & /*dpBand*/)
+/*!
+ * @fn DPBandConfig#upperDiagonal
+ * @headerfile <seqan/align.h>
+ * @brief Returns the value of the upper diagonal.
+ *
+ * @signature TPosition upperDiagonal(obj);
+ *
+ * @param obj The object of type @link DPBandConfig @endlink to query the upper diagonal for.
+ *
+ * @note If the band is switched off this function always returns 0.
+ * @return TPosition The value of the upper diagonal.
+ */
+
+inline Position<DPBandConfig<BandOff> >::Type
+upperDiagonal(DPBandConfig<BandOff> const & /*dpBand*/)
 {
     return 0;
 }
 
-inline int
-upperDiagonal(DPBand_<BandOn> const & dpBand)
+template <typename TSwitch>
+inline typename Position<DPBandConfig<BandOn> >::Type
+upperDiagonal(DPBandConfig<TSwitch> const & dpBand)
 {
     return dpBand._upperDiagonal;
 }
@@ -211,18 +353,32 @@ upperDiagonal(DPBand_<BandOn> const & dpBand)
 // Function bandSize()
 // ----------------------------------------------------------------------------
 
-inline unsigned int
-bandSize(DPBand_<BandOff> const &)
+/*!
+ * @fn DPBandConfig#bandSize
+ * @headerfile <seqan/align.h>
+ * @brief Returns the size of the band.
+ *
+ * @signature TSize bandSize(obj);
+ *
+ * @param obj The object of type @link DPBandConfig @endlink to query the band size for.
+ *
+ * @note If the band is switched off this function always returns 0.
+ * @return TSize The number of diagonals covered by the band.
+ */
+
+inline Size<DPBandConfig<BandOff> >::Type
+bandSize(DPBandConfig<BandOff> const &)
 {
     return 0;
 }
 
-inline unsigned int
-bandSize(DPBand_<BandOn> const & band)
+template <typename TSwitch>
+inline typename Size<DPBandConfig<TSwitch> >::Type
+bandSize(DPBandConfig<TSwitch> const & band)
 {
     return upperDiagonal(band) - lowerDiagonal(band) + 1;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_BAND_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_BAND_H_
diff --git a/seqan/align/dp_cell.h b/seqan/align/dp_cell.h
index 41d5c7f..99e2413 100644
--- a/seqan/align/dp_cell.h
+++ b/seqan/align/dp_cell.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // scores necessary for the affine gap function.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_
 
 namespace seqan {
 
@@ -123,8 +123,8 @@ template <typename TScoreValue, typename TGapCostFunction>
 const TScoreValue DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> >::VALUE = MinValue<TScoreValue>::VALUE / 2;
 
 template <typename TScoreValue, typename TGapCostFunction>
-struct DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> const>:
-    DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> >{};
+struct DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> const> :
+    public DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> >{};
 
 // ============================================================================
 // Functions
@@ -207,7 +207,7 @@ template <typename TScoreValue, typename TGapSpec>
 inline typename  Reference<DPCell_<TScoreValue, TGapSpec> const>::Type
 _horizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> const & dpCell)
 {
-	return dpCell._score;
+    return dpCell._score;
 }
 
 // ----------------------------------------------------------------------------
@@ -222,6 +222,17 @@ _setHorizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & /*dpCell*/, TScoreVal
     // no-op
 }
 
+// ----------------------------------------------------------------------------
+// Function setGapExtension()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TGapSpec, typename TF1, typename TF2>
+inline void
+setGapExtension(DPCell_<TScoreValue, TGapSpec> & /*dpCell*/, TF1 , TF2)
+{
+    // no-op
+}
+
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_
diff --git a/seqan/align/dp_cell_affine.h b/seqan/align/dp_cell_affine.h
index 47a6c58..2165b8a 100644
--- a/seqan/align/dp_cell_affine.h
+++ b/seqan/align/dp_cell_affine.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // values for the three matrices: diagonal, vertical and horizontal.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
 
 namespace seqan {
 
@@ -183,4 +183,4 @@ _setHorizontalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell, TScoreValue
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
diff --git a/seqan/align/dp_cell_dynamic.h b/seqan/align/dp_cell_dynamic.h
new file mode 100644
index 0000000..fd9ad3c
--- /dev/null
+++ b/seqan/align/dp_cell_dynamic.h
@@ -0,0 +1,199 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements the dynamic gap model published in "Dynamic Gaps Selector:
+// A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model
+// Optimization" by Gianvito Urgese et al.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_
+#define INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct DynamicGapExtensionHorizontal_;
+typedef Tag<DynamicGapExtensionHorizontal_> DynamicGapExtensionHorizontal;
+
+struct DynamicGapExtensionVertical_;
+typedef Tag<DynamicGapExtensionVertical_> DynamicGapExtensionVertical;
+
+enum DynamicGapsMask
+{
+    MASK_VERTICAL_GAP = 1,
+    MASK_HORIZONTAL_GAP = 2
+};
+
+// ----------------------------------------------------------------------------
+// Class DPCell                                                   [DynamicGaps]
+// ----------------------------------------------------------------------------
+
+// The specialization for linear gap cost function.
+// It solely stores the maximal score.
+template <typename TScoreValue>
+class DPCell_<TScoreValue, DynamicGaps>
+{
+public:
+    TScoreValue _score;
+    char _flagMask;
+
+    // The default c'tor.
+    DPCell_() : _score(DPCellDefaultInfinity<DPCell_>::VALUE), _flagMask(0)
+    {}
+
+    // The copy c'tor.
+    DPCell_(DPCell_<TScoreValue, DynamicGaps> const & other) : _score(other._score), _flagMask(other._flagMask)
+    {}
+
+    // Implicit c'tor.
+    DPCell_(TScoreValue const & score) : _score(score), _flagMask(0)
+    {}
+
+    // The assignment operator.
+    DPCell_ &
+    operator=(DPCell_<TScoreValue, DynamicGaps> const & other)
+    {
+        if (this != &other)
+        {
+            _score = other._score;
+            _flagMask = other._flagMask;
+        }
+        return *this;
+    }
+
+    DPCell_ &
+    operator=(TScoreValue const & score)
+    {
+        _score = score;
+        return *this;
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+template <typename TCell, typename TBoolV, typename TBoolH>
+struct SetGapExtension;
+
+template <typename TScoreValue>
+struct SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, False, False>
+{
+    static const char VALUE = 0;
+};
+
+template <typename TScoreValue>
+struct SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, False, True>
+{
+    static const char VALUE = MASK_HORIZONTAL_GAP;
+};
+
+template <typename TScoreValue>
+struct SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, True, False>
+{
+    static const char VALUE = MASK_VERTICAL_GAP;
+};
+
+template <typename TScoreValue>
+struct SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, True, True>
+{
+    static const char VALUE = MASK_HORIZONTAL_GAP | MASK_VERTICAL_GAP;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TScoreValue, typename TFlag>
+inline void _setBit(DPCell_<TScoreValue, DynamicGaps> & cell,
+                    TFlag const & /*flag*/,
+                    DynamicGapExtensionVertical const & /*tag*/)
+{
+    if (IsSameType<TFlag, True>::VALUE)
+        cell._flagMask |= MASK_VERTICAL_GAP;
+    else
+        cell._flagMask &= ~MASK_VERTICAL_GAP;
+}
+
+template <typename TScoreValue, typename TFlag>
+inline void _setBit(DPCell_<TScoreValue, DynamicGaps> & cell,
+                    TFlag const & /*flag*/,
+                    DynamicGapExtensionHorizontal const & /*tag*/)
+{
+    if (IsSameType<TFlag, True>::VALUE)
+        cell._flagMask |= MASK_HORIZONTAL_GAP;
+    else
+        cell._flagMask &= ~MASK_HORIZONTAL_GAP;
+}
+
+template <typename TScoreValue, typename TSpec>
+inline bool isGapExtension(DPCell_<TScoreValue, DynamicGaps> const & cell,
+                           TSpec const & /*spec*/)
+{
+    if (IsSameType<TSpec, DynamicGapExtensionHorizontal>::VALUE)
+        return cell._flagMask & MASK_HORIZONTAL_GAP;
+    else
+        return cell._flagMask & MASK_VERTICAL_GAP;
+}
+
+template <typename TScoreValue, typename TFlagV, typename TFlagH>
+inline void
+setGapExtension(DPCell_<TScoreValue, DynamicGaps> & cell,
+                TFlagV const & /*vert*/,
+                TFlagH const & /*hori*/)
+{
+    cell._flagMask = SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, TFlagV, TFlagH>::VALUE;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator<()
+// ----------------------------------------------------------------------------
+
+// Needed for banded chain alignment for the std::set.
+template <typename TScoreValueLeft, typename TScoreValueRight>
+inline bool operator<(DPCell_<TScoreValueLeft, DynamicGaps> const & left,
+                      DPCell_<TScoreValueRight, DynamicGaps> const & right)
+{
+    return left._score < right._score;
+}
+
+}  // namespace seqan
+
+#endif  // INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_
diff --git a/seqan/align/dp_cell_linear.h b/seqan/align/dp_cell_linear.h
index 56f1572..dd43172 100644
--- a/seqan/align/dp_cell_linear.h
+++ b/seqan/align/dp_cell_linear.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 // entry.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_
 
 namespace seqan {
 
@@ -112,4 +112,4 @@ inline bool operator<(DPCell_<TScoreValueLeft, LinearGaps> const & left,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_
diff --git a/seqan/align/dp_context.h b/seqan/align/dp_context.h
new file mode 100644
index 0000000..717acec
--- /dev/null
+++ b/seqan/align/dp_context.h
@@ -0,0 +1,187 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements the context that can be passed to the dp functions in order
+// to reuse memory blocks in mutliple calls of the same function.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_
+#define INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename T>
+struct GetDPScoreMatrix
+{};
+
+template <typename T>
+struct GetDPTraceMatrix
+{};
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TScoreValue, typename TGapCosts>
+struct DPContext
+{
+    typedef typename GetDPScoreMatrix<DPContext>::Type TScoreMatrixHost;
+    typedef typename GetDPTraceMatrix<DPContext>::Type TTraceMatrixHost;
+
+    TScoreMatrixHost _scoreMatrix;
+    TTraceMatrixHost _traceMatrix;
+
+    DPContext() : _scoreMatrix(), _traceMatrix()
+    {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction GetDPScoreMatrix
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TGapCosts>
+struct GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> >
+{
+    typedef DPCell_<TScoreValue, TGapCosts> TDPScoreValue_;
+    typedef DPMatrix_<TDPScoreValue_, FullDPMatrix> TDPScoreMatrix_;
+
+    typedef typename Host<TDPScoreMatrix_>::Type Type;
+};
+
+template <typename TScoreValue, typename TGapCosts>
+struct GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> const >
+{
+    typedef DPCell_<TScoreValue, TGapCosts> TDPScoreValue_;
+    typedef DPMatrix_<TDPScoreValue_, FullDPMatrix> TDPScoreMatrix_;
+
+    typedef typename Host<TDPScoreMatrix_>::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction GetDPTraceMatrix
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TGapCosts>
+struct GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> >
+{
+    typedef typename TraceBitMap_::TTraceValue TTraceValue_;
+    typedef DPMatrix_<TTraceValue_, FullDPMatrix> TDPScoreMatrix_;
+
+    typedef typename Host<TDPScoreMatrix_>::Type Type;
+};
+
+template <typename TScoreValue, typename TGapCosts>
+struct GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> const >
+{
+    typedef typename TraceBitMap_::TTraceValue TTraceValue_;
+    typedef DPMatrix_<TTraceValue_, FullDPMatrix> TDPScoreMatrix_;
+
+    typedef typename Host<TDPScoreMatrix_>::Type const Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function dpScoreMatrix()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TGapCosts>
+inline typename GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> >::Type &
+getDpScoreMatrix(DPContext<TScoreValue, TGapCosts> & dpContext)
+{
+    return dpContext._scoreMatrix;
+}
+
+template <typename TScoreValue, typename TGapCosts>
+inline typename GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> const >::Type &
+getDpScoreMatrix(DPContext<TScoreValue, TGapCosts> const & dpContext)
+{
+    return dpContext._scoreMatrix;
+}
+
+// ----------------------------------------------------------------------------
+// Function dpTraceMatrix()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TGapCosts>
+inline typename GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> >::Type &
+getDpTraceMatrix(DPContext<TScoreValue, TGapCosts> & dpContext)
+{
+    return dpContext._traceMatrix;
+}
+
+template <typename TScoreValue, typename TGapCosts>
+inline typename GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> const >::Type &
+getDpTraceMatrix(DPContext<TScoreValue, TGapCosts> const & dpContext)
+{
+    return dpContext._traceMatrix;
+}
+
+// ----------------------------------------------------------------------------
+// Function setDpScoreMatrix()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TGapCosts>
+inline void
+setDpTraceMatrix(DPContext<TScoreValue, TGapCosts> & dpContext,
+                typename GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> >::Type const & scoreMatrix)
+{
+    dpContext._scoreMatrix = scoreMatrix;
+}
+
+// ----------------------------------------------------------------------------
+// Function setDpTraceMatrix()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TGapCosts>
+inline void
+setDpTraceMatrix(DPContext<TScoreValue, TGapCosts> & dpContext,
+                typename GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> >::Type const & traceMatrix)
+{
+    dpContext._tarceMatrix = traceMatrix;
+}
+
+}
+
+#endif // INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_
diff --git a/seqan/align/dp_formula.h b/seqan/align/dp_formula.h
index a3a9571..47a1d47 100644
--- a/seqan/align/dp_formula.h
+++ b/seqan/align/dp_formula.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 
 // TODO(holtgrew): Documentation in this header necessary or internal only?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
 
 namespace seqan {
 
@@ -173,8 +173,6 @@ _computeScore(DPCell_<TScoreValue, TGapCosts> & activeCell,
     return traceDir;
 }
 
-
-
 // ----------------------------------------------------------------------------
 // Function _doComputeScore                        [RecursionDirectionDiagonal]
 // ----------------------------------------------------------------------------
@@ -193,7 +191,7 @@ _doComputeScore(DPCell_<TScoreValue, TGapCosts> & activeCell,
                 TDPProfile const &)
 {
     activeCell._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
-
+    setGapExtension(activeCell, False(), False());
     if (!IsTracebackEnabled_<TDPProfile>::VALUE)
         return TraceBitMap_::NONE;
 
@@ -223,4 +221,4 @@ _doComputeScore(DPCell_<TScoreValue, TGapCosts> & activeCell,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
diff --git a/seqan/align/dp_formula_affine.h b/seqan/align/dp_formula_affine.h
index e5c5e09..c4e32e0 100644
--- a/seqan/align/dp_formula_affine.h
+++ b/seqan/align/dp_formula_affine.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Implements the affine gap cost functions.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
 
 namespace seqan {
 
@@ -164,9 +164,9 @@ _retrieveTraceAffine(TScoreValue const & globalMax,
 // Function _internalComputeScore      [RecursionDirectionDiagonal, AffineGaps]
 // ----------------------------------------------------------------------------
 
-template <typename TScoreValue, typename TTraceValueL, typename TTraceValueGap>
+template <typename TScoreValue, typename TAffineGaps, typename TTraceValueL, typename TTraceValueGap>
 inline typename TraceBitMap_::TTraceValue
-_internalComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
+_internalComputeScore(DPCell_<TScoreValue, TAffineGaps> & activeCell,
                       TScoreValue const & rightCompare,
                       TTraceValueL,
                       TTraceValueGap,
@@ -178,9 +178,9 @@ _internalComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     return TraceBitMap_::NONE;
 }
 
-template <typename TScoreValue, typename TTraceValueL, typename TTraceValueGap, typename TGapsPlacement>
+template <typename TScoreValue, typename TAffineGaps, typename TTraceValueL, typename TTraceValueGap, typename TGapsPlacement>
 inline typename TraceBitMap_::TTraceValue
-_internalComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
+_internalComputeScore(DPCell_<TScoreValue, TAffineGaps> & activeCell,
                       TScoreValue const & rightCompare,
                       TTraceValueL leftTrace,
                       TTraceValueGap gapTrace,
@@ -195,9 +195,9 @@ _internalComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     return leftTrace | gapTrace;
 }
 
-template <typename TScoreValue, typename TTraceValueL, typename TTraceValueGap, typename TGapsPlacement>
+template <typename TScoreValue, typename TAffineGaps, typename TTraceValueL, typename TTraceValueGap, typename TGapsPlacement>
 inline typename TraceBitMap_::TTraceValue
-_internalComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
+_internalComputeScore(DPCell_<TScoreValue, TAffineGaps> & activeCell,
                       TScoreValue const & rightCompare,
                       TTraceValueL leftTrace,
                       TTraceValueGap gapTrace,
@@ -353,10 +353,8 @@ _internalComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     {
         activeCell._score = activeCell._horizontalScore;
         return TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
-//        return traceRight;
     }
     return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX;
-//    returntraceRight;
 }
 
 template <typename TScoreValue, typename TGapsPlacement>
@@ -368,16 +366,10 @@ _internalComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     {
         activeCell._score = activeCell._horizontalScore;
         return TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
-//        return traceRight | (traceLeft & TraceBitMap_::VERTICAL_OPEN);
     }
-//    traceGap = TraceBitMap_::MAX_FROM_VERTICAL_MATRIX;
     if (activeCell._score == activeCell._horizontalScore)
-    {
         return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
-//        return traceRight | traceLeft;
-    }
     return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX;
-//    return traceLeft | (traceRight & TraceBitMap_::HORIZONTAL_OPEN);
 }
 
 // ----------------------------------------------------------------------------
@@ -406,7 +398,6 @@ _doComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     TScoreValue tmpScore = _scoreOfCell(previousHorizontal) + scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal);
 
     TTraceValue tvGap = _internalComputeScore(activeCell, tmpScore, TraceBitMap_::HORIZONTAL, TraceBitMap_::HORIZONTAL_OPEN, TTracebackConfig(), RecursionDirectionHorizontal());
-//    activeCell._score = activeCell._horizontalScore; _max(activeCell._horizontal, tmpScore)
 
     // Now we can decide for the optimal score in horizontal score or not?
     activeCell._verticalScore = _verticalScoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal);
@@ -417,32 +408,6 @@ _doComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     TTraceValue tvMax = _internalComputeScore(activeCell, TTracebackConfig());  // Stores from where the maximal score comes.
     tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
     return _internalComputeScore(activeCell, tmpScore, tvGap, tvMax, TTracebackConfig(), RecursionDirectionDiagonal());
-
-    // This should be the fastest version.
-
-//    TScoreValue tmpScoreDiagonal = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
-//    TScoreValue tmpGapExtendHorizontal = _horizontalScoreOfCell(previousHorizontal) +
-//                                         scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal);
-//    TScoreValue tmpGapOpenHorizontal = _scoreOfCell(previousHorizontal)
-//                                       + scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal);
-//    TScoreValue tmpGapExtendVertical = _verticalScoreOfCell(previousVertical)
-//                                       + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal);
-//    TScoreValue tmpGapOpenVertical = _scoreOfCell(previousVertical)
-//                                     + scoreGapOpenVertical(scoringScheme, seqHVal, seqVVal);
-//
-//    activeCell._horizontalScore = _max(tmpGapExtendHorizontal, tmpGapOpenHorizontal);
-//    activeCell._verticalScore = _max(tmpGapExtendVertical, tmpGapOpenVertical);
-//    activeCell._score = _max(tmpScoreDiagonal, _max(activeCell._horizontalScore, activeCell._verticalScore));
-//
-//    if (!IsTracebackEnabled_<TTracebackConfig>::VALUE)
-//        return TraceBitMap_::NONE;
-//
-//    TTraceValue traceGapOpen = TraceBitMap_::NONE;
-//    _conditionalOrOnInequality(traceGapOpen, _horizontalScoreOfCell(activeCell), tmpGapExtendHorizontal, TraceBitMap_::HORIZONTAL_OPEN);
-//    _conditionalOrOnInequality(traceGapOpen, _verticalScoreOfCell(activeCell), tmpGapExtendVertical, TraceBitMap_::VERTICAL_OPEN);
-//    return traceGapOpen |
-//           _retrieveTraceAffine(activeCell._score, tmpScoreDiagonal, tmpGapExtendHorizontal, tmpGapOpenHorizontal,
-//                                tmpGapExtendVertical, tmpGapOpenVertical, RecursionDirectionAll());
 }
 
 // ----------------------------------------------------------------------------
@@ -471,24 +436,6 @@ _doComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     TTraceValue tv = _internalComputeScore(activeCell, tmpScore, TraceBitMap_::HORIZONTAL, TraceBitMap_::HORIZONTAL_OPEN, TTracebackConfig(), RecursionDirectionHorizontal());
     tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
     return _internalComputeScore(activeCell, tmpScore, tv, TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, TTracebackConfig(), RecursionDirectionDiagonal());
-
-//    TScoreValue tmpScoreDiagonal = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
-//    TScoreValue tmpGapExtendHorizontal = _horizontalScoreOfCell(previousHorizontal)
-//                                         + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal);
-//    TScoreValue tmpGapOpenHorizontal = _scoreOfCell(previousHorizontal)
-//                                       + scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal);
-//
-//    activeCell._horizontalScore = _max(tmpGapExtendHorizontal, tmpGapOpenHorizontal);
-//    activeCell._score = _max(tmpScoreDiagonal, activeCell._horizontalScore);
-//
-//    if (!IsTracebackEnabled_<TTracebackConfig>::VALUE)
-//        return TraceBitMap_::NONE;
-//
-//    TTraceValue traceGapOpen = TraceBitMap_::NONE;
-//    _conditionalOrOnInequality(traceGapOpen, _horizontalScoreOfCell(activeCell), tmpGapExtendHorizontal, TraceBitMap_::HORIZONTAL_OPEN);
-//    return traceGapOpen |
-//           _retrieveTraceAffine(activeCell._score, tmpScoreDiagonal, tmpGapExtendHorizontal, tmpGapOpenHorizontal,
-//                                TScoreValue(), TScoreValue(), RecursionDirectionUpperDiagonal());
 }
 
 // ----------------------------------------------------------------------------
@@ -521,18 +468,6 @@ _doComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     // Up to here, activeCell stores the highest value of vertical or vertical open.
     tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
     return _internalComputeScore(activeCell, tmpScore, tv, TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, TTracebackConfig(), RecursionDirectionDiagonal());  // Now we have this problem. How do we determine if the max comes from the vertical distance.
-
-//    activeCell._verticalScore = _max(tmpGapExtendVertical, tmpGapOpenVertical);
-//    activeCell._score = _max(tmpScoreDiagonal, activeCell._verticalScore);
-//
-//    if (!IsTracebackEnabled_<TTracebackConfig>::VALUE)
-//        return TraceBitMap_::NONE;
-//
-//    TTraceValue traceGapOpen = TraceBitMap_::NONE;
-//    _conditionalOrOnInequality(traceGapOpen, _verticalScoreOfCell(activeCell), tmpGapExtendVertical, TraceBitMap_::VERTICAL_OPEN);
-//    return traceGapOpen |
-//           _retrieveTraceAffine(activeCell._score, tmpScoreDiagonal, TScoreValue(), TScoreValue(), tmpGapExtendVertical,
-//                                tmpGapOpenVertical, RecursionDirectionLowerDiagonal());
 }
 
 // ----------------------------------------------------------------------------
@@ -558,23 +493,6 @@ _doComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
 
     activeCell._verticalScore = DPCellDefaultInfinity<DPCell_<TScoreValue, AffineGaps> >::VALUE;
     return _internalComputeScore(activeCell, tmpGapOpenHorizontal, TraceBitMap_::HORIZONTAL, TraceBitMap_::HORIZONTAL_OPEN, TTracebackConfig(), RecursionDirectionHorizontal()) | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
-
-//    typedef typename TraceBitMap_::TTraceValue TTraceValue;
-//    TScoreValue tmpGapOpenHorizontal = _scoreOfCell(previousHorizontal) +
-//                                       scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal);
-//    TScoreValue tmpGapExtendHorizontal = _horizontalScoreOfCell(previousHorizontal) +
-//                                         scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal);
-//    activeCell._horizontalScore = _max(tmpGapOpenHorizontal, tmpGapExtendHorizontal);
-//    activeCell._score = activeCell._horizontalScore;
-//
-//    if (!IsTracebackEnabled_<TTracebackConfig>::VALUE)
-//        return TraceBitMap_::NONE;
-//
-//    TTraceValue traceGapOpen = TraceBitMap_::NONE;
-//    _conditionalOrOnInequality(traceGapOpen, _horizontalScoreOfCell(activeCell), tmpGapExtendHorizontal, TraceBitMap_::HORIZONTAL_OPEN);
-//    return traceGapOpen |
-//           _retrieveTraceAffine(activeCell._score, TScoreValue(), tmpGapExtendHorizontal, tmpGapOpenHorizontal,
-//                                TScoreValue(), TScoreValue(), RecursionDirectionHorizontal());
 }
 
 // ----------------------------------------------------------------------------
@@ -601,24 +519,8 @@ _doComputeScore(DPCell_<TScoreValue, AffineGaps> & activeCell,
     // Here we distinguish between vertical and vertical open.
     activeCell._horizontalScore = DPCellDefaultInfinity<DPCell_<TScoreValue, AffineGaps> >::VALUE;
     return _internalComputeScore(activeCell, tmpGapOpenVertical, TraceBitMap_::VERTICAL, TraceBitMap_::VERTICAL_OPEN, TTracebackConfig(), RecursionDirectionVertical()) | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX;
-//    typedef typename TraceBitMap_::TTraceValue TTraceValue;
-//    TScoreValue tmpGapOpenVertical = _scoreOfCell(previousVertical) +
-//                                     scoreGapOpenVertical(scoringScheme, seqHVal, seqVVal);
-//    TScoreValue tmpGapExtendVertical = _verticalScoreOfCell(previousVertical) +
-//                                       scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal);
-//    activeCell._verticalScore = _max(tmpGapExtendVertical, tmpGapOpenVertical);
-//    activeCell._score = activeCell._verticalScore;
-//
-//    if (!IsTracebackEnabled_<TTracebackConfig>::VALUE)
-//        return TraceBitMap_::NONE;
-//
-//    TTraceValue traceGapOpen = TraceBitMap_::NONE;
-//    _conditionalOrOnInequality(traceGapOpen, _verticalScoreOfCell(activeCell), tmpGapExtendVertical, TraceBitMap_::VERTICAL_OPEN);
-//    return traceGapOpen |
-//           _retrieveTraceAffine(activeCell._score, TScoreValue(), TScoreValue(), TScoreValue(), tmpGapExtendVertical,
-//                                tmpGapOpenVertical, RecursionDirectionVertical());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
diff --git a/seqan/align/dp_formula_dynamic.h b/seqan/align/dp_formula_dynamic.h
new file mode 100644
index 0000000..3cce01d
--- /dev/null
+++ b/seqan/align/dp_formula_dynamic.h
@@ -0,0 +1,394 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements the score function for dynamic gap costs published in
+// "Dynamic Gaps Selector: A Smith Waterman Sequence Alignment Algorithm with
+// Affine Gap Model Optimization" by Gianvito Urgese et al.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ALIGN_DP_FORMULA_DYNAMIC_H_
+#define INCLUDE_SEQAN_ALIGN_DP_FORMULA_DYNAMIC_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _internalComputeScore      [RecursionDirectionDiagonal, DynamicGaps]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TTraceValueL, typename TTraceValueGap>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      TScoreValue const & diagCompare,
+                      TTraceValueL,
+                      TTraceValueGap,
+                      TracebackOff const &,
+                      RecursionDirectionDiagonal const &)
+{
+    if(_scoreOfCell(activeCell) < diagCompare)
+    {
+        activeCell._score = diagCompare;
+        setGapExtension(activeCell, False(), False());
+        return TraceBitMap_::NONE;
+    }
+    return TraceBitMap_::NONE;
+}
+
+template <typename TScoreValue, typename TTraceValueL, typename TTraceValueGap, typename TGapsPlacement>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      TScoreValue const & diagCompare,
+                      TTraceValueL leftTrace,
+                      TTraceValueGap gapTrace,
+                      TracebackOn<TracebackConfig_<SingleTrace, TGapsPlacement> > const &,
+                      RecursionDirectionDiagonal const &)
+{
+    if(_scoreOfCell(activeCell) <= diagCompare)
+    {
+        activeCell._score = diagCompare;
+        setGapExtension(activeCell, False(), False());
+        return TraceBitMap_::DIAGONAL | leftTrace;
+    }
+    return leftTrace | gapTrace;
+}
+
+template <typename TScoreValue, typename TTraceValueL, typename TTraceValueGap, typename TGapsPlacement>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      TScoreValue const & diagCompare,
+                      TTraceValueL leftTrace,
+                      TTraceValueGap gapTrace,
+                      TracebackOn<TracebackConfig_<CompleteTrace, TGapsPlacement> >  const &,
+                      RecursionDirectionDiagonal const &)
+{
+    if(_scoreOfCell(activeCell) < diagCompare)
+    {
+        activeCell._score = diagCompare;  // Maximal score comes from diagonal.
+        setGapExtension(activeCell, False(), False());
+        return TraceBitMap_::DIAGONAL | leftTrace;  // Return trace for Diagonal.
+    }
+    if (_scoreOfCell(activeCell) == diagCompare)  // Maximal score comes from previous computed directions and diagonal.
+        return leftTrace | TraceBitMap_::DIAGONAL | gapTrace;  // Return all directions inclusively the flag indicating max from gap.
+
+    return leftTrace | gapTrace;  // Maximum comes from gap. Return gap value inclusively the flag indicating max from gap.
+}
+
+// ----------------------------------------------------------------------------
+// Function _internalComputeScore    [RecursionDirectionHorizontal, DynamicGaps]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TValueH, typename TValueV, typename TScore>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      DPCell_<TScoreValue, DynamicGaps> const & prevCell,
+                      TValueH const & valH,
+                      TValueV const & valV,
+                      TScore const & score,
+                      TracebackOff const &,
+                      RecursionDirectionHorizontal const &)
+{
+    if(!isGapExtension(prevCell, DynamicGapExtensionHorizontal()))
+        activeCell._score = _scoreOfCell(prevCell) + scoreGapOpenHorizontal(score, valH, valV);
+    return TraceBitMap_::NONE;
+}
+
+template <typename TScoreValue, typename TValueH, typename TValueV, typename TScore, typename TTraceConfig>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      DPCell_<TScoreValue, DynamicGaps> const & prevCell,
+                      TValueH const & valH,
+                      TValueV const & valV,
+                      TScore const & score,
+                      TracebackOn<TTraceConfig> const &,
+                      RecursionDirectionHorizontal const &)
+{
+    if (!isGapExtension(prevCell, DynamicGapExtensionHorizontal()))
+    {
+        activeCell._score = _scoreOfCell(prevCell) + scoreGapOpenHorizontal(score, valH, valV);
+        return TraceBitMap_::HORIZONTAL_OPEN;
+    }
+    return TraceBitMap_::HORIZONTAL;
+}
+
+// ----------------------------------------------------------------------------
+// Function _internalComputeScore      [RecursionDirectionVertical, DynamicGaps]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TValueH, typename TValueV, typename TScore>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      DPCell_<TScoreValue, DynamicGaps> const & prevCell,
+                      TValueH const & valH,
+                      TValueV const & valV,
+                      TScore const & score,
+                      TracebackOff const &,
+                      RecursionDirectionVertical const &)
+{
+    if(!isGapExtension(prevCell, DynamicGapExtensionVertical()))
+        activeCell._score = _scoreOfCell(prevCell) + scoreGapOpenVertical(score, valH, valV);
+    return TraceBitMap_::NONE;
+}
+
+template <typename TScoreValue, typename TValueH, typename TValueV, typename TScore, typename TTraceConfig>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      DPCell_<TScoreValue, DynamicGaps> const & prevCell,
+                      TValueH const & valH,
+                      TValueV const & valV,
+                      TScore const & score,
+                      TracebackOn<TTraceConfig> const &,
+                      RecursionDirectionVertical const &)
+{
+    if (!isGapExtension(prevCell, DynamicGapExtensionVertical()))
+    {
+        activeCell._score = _scoreOfCell(prevCell) + scoreGapOpenVertical(score, valH, valV);
+        return TraceBitMap_::VERTICAL_OPEN;
+    }
+    return TraceBitMap_::VERTICAL;
+}
+
+// ----------------------------------------------------------------------------
+// Function _internalComputeScore          [Vertical vs Horizontal, DynamicGaps]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      TScoreValue const & horizontalComp,
+                      TracebackOff const &)
+{
+    if(_scoreOfCell(activeCell) < horizontalComp)
+    {
+        activeCell._score = horizontalComp;
+        setGapExtension(activeCell, False(), True());
+        return TraceBitMap_::NONE;
+    }
+    setGapExtension(activeCell, True(), False());
+    return TraceBitMap_::NONE;
+}
+
+template <typename TScoreValue, typename TGapsPlacement>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      TScoreValue const & horizontalComp,
+                      TracebackOn<TracebackConfig_<SingleTrace, TGapsPlacement> >  const &)
+{
+    if(_scoreOfCell(activeCell) < horizontalComp)
+    {
+        activeCell._score = horizontalComp;
+        setGapExtension(activeCell, False(), True());
+        return TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
+    }
+    setGapExtension(activeCell, True(), False());
+    return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX;
+}
+
+template <typename TScoreValue, typename TGapsPlacement>
+inline typename TraceBitMap_::TTraceValue
+_internalComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                      TScoreValue const & horizontalComp,
+                      TracebackOn<TracebackConfig_<CompleteTrace, TGapsPlacement> >  const &)
+{
+    if(_scoreOfCell(activeCell) < horizontalComp)
+    {
+        setGapExtension(activeCell, False(), True());
+        activeCell._score = horizontalComp;
+        return TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
+    }
+    if (_scoreOfCell(activeCell) == horizontalComp)
+    {
+        setGapExtension(activeCell, True(), True());
+        return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
+    }
+    setGapExtension(activeCell, True(), False());
+    return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX;
+}
+
+// ----------------------------------------------------------------------------
+// Function _doComputeScore                 [RecursionAllDirection, DynamicGaps]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
+          typename TAlgorithm, typename TTracebackConfig>
+inline typename TraceBitMap_::TTraceValue
+_doComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                DPCell_<TScoreValue, DynamicGaps> const & previousDiagonal,
+                DPCell_<TScoreValue, DynamicGaps> const & previousHorizontal,
+                DPCell_<TScoreValue, DynamicGaps> const & previousVertical,
+                TSequenceHValue const & seqHVal,
+                TSequenceVValue const & seqVVal,
+                TScoringScheme const & scoringScheme,
+                RecursionDirectionAll const &,
+                DPProfile_<TAlgorithm, DynamicGaps, TTracebackConfig> const &)
+{
+    typedef typename TraceBitMap_::TTraceValue TTraceValue;
+
+    // Compute best alignment from either horizontal open or extension.
+    DPCell_<TScoreValue, DynamicGaps> tmpScore = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal);
+    TTraceValue tvGap = _internalComputeScore(tmpScore, previousHorizontal, seqHVal, seqVVal, scoringScheme,
+                                              TTracebackConfig(), RecursionDirectionHorizontal());
+
+    // Compute best alignment between vertical and vertical open gap.
+    activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal);
+    tvGap |= _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme,
+                                   TTracebackConfig(), RecursionDirectionVertical());
+
+    // Finds the maximum between the vertical and the horizontal matrix. Stores the flag for coming from a potential direction.
+    TTraceValue tvMax = _internalComputeScore(activeCell, tmpScore._score, TTracebackConfig());  // Stores from where the maximal score comes.
+    tmpScore._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
+    return _internalComputeScore(activeCell, tmpScore._score, tvGap, tvMax, TTracebackConfig(), RecursionDirectionDiagonal());
+}
+
+// ----------------------------------------------------------------------------
+// Function _doComputeScore       [RecursionUpperDiagonalDirection, DynamicGaps]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
+          typename TAlgorithm, typename TTracebackConfig>
+inline typename TraceBitMap_::TTraceValue
+_doComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                DPCell_<TScoreValue, DynamicGaps> const & previousDiagonal,
+                DPCell_<TScoreValue, DynamicGaps> const & previousHorizontal,
+                DPCell_<TScoreValue, DynamicGaps> const & /*previousVertical*/,
+                TSequenceHValue const & seqHVal,
+                TSequenceVValue const & seqVVal,
+                TScoringScheme const & scoringScheme,
+                RecursionDirectionUpperDiagonal const &,
+                DPProfile_<TAlgorithm, DynamicGaps, TTracebackConfig> const &)
+{
+    typedef typename TraceBitMap_::TTraceValue TTraceValue;
+
+    // This computes the difference between the horizontal extend and horizontal open.
+    activeCell._score = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal);
+    TTraceValue tv = _internalComputeScore(activeCell, previousHorizontal, seqHVal, seqVVal, scoringScheme,
+                                           TTracebackConfig(), RecursionDirectionHorizontal());
+
+    setGapExtension(activeCell, False(), True());
+    TScoreValue tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
+    return _internalComputeScore(activeCell, tmpScore, tv, TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX,
+                                 TTracebackConfig(), RecursionDirectionDiagonal());
+}
+
+// ----------------------------------------------------------------------------
+// Function _doComputeScore      [RecursionDirectionLowerDiagonal, DynamicGaps]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
+          typename TAlgorithm, typename TTracebackConfig>
+inline typename TraceBitMap_::TTraceValue
+_doComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                DPCell_<TScoreValue, DynamicGaps> const & previousDiagonal,
+                DPCell_<TScoreValue, DynamicGaps> const & /*previousHorizontal*/,
+                DPCell_<TScoreValue, DynamicGaps> const & previousVertical,
+                TSequenceHValue const & seqHVal,
+                TSequenceVValue const & seqVVal,
+                TScoringScheme const & scoringScheme,
+                RecursionDirectionLowerDiagonal const &,
+                DPProfile_<TAlgorithm, DynamicGaps, TTracebackConfig> const &)
+{
+    typedef typename TraceBitMap_::TTraceValue TTraceValue;
+
+    // This computes the difference between the vertical extend and vertical open.
+    activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal);
+    TTraceValue tv = _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme,
+                                           TTracebackConfig(), RecursionDirectionVertical());
+    setGapExtension(activeCell, True(), False());
+    TScoreValue tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
+    return _internalComputeScore(activeCell, tmpScore, tv, TraceBitMap_::MAX_FROM_VERTICAL_MATRIX,
+                                 TTracebackConfig(), RecursionDirectionDiagonal());
+}
+
+// ----------------------------------------------------------------------------
+// Function _doComputeScore                      [RecursionHorizontalDirection]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
+          typename TAlgorithm, typename TTracebackConfig>
+inline typename TraceBitMap_::TTraceValue
+_doComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                DPCell_<TScoreValue, DynamicGaps> const & /*previousDiagonal*/,
+                DPCell_<TScoreValue, DynamicGaps> const & previousHorizontal,
+                DPCell_<TScoreValue, DynamicGaps> const & /*previousVertical*/,
+                TSequenceHValue const & seqHVal,
+                TSequenceVValue const & seqVVal,
+                TScoringScheme const & scoringScheme,
+                RecursionDirectionHorizontal const & tag,
+                DPProfile_<TAlgorithm, DynamicGaps, TTracebackConfig> const &)
+{
+    activeCell._score = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal);
+    setGapExtension(activeCell, False(), True());
+    return _internalComputeScore(activeCell, previousHorizontal, seqHVal, seqVVal, scoringScheme,
+                                 TTracebackConfig(), tag) | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX;
+}
+
+// ----------------------------------------------------------------------------
+// Function _doComputeScore                        [RecursionVerticalDirection]
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
+          typename TAlgorithm, typename TTracebackConfig>
+inline typename TraceBitMap_::TTraceValue
+_doComputeScore(DPCell_<TScoreValue, DynamicGaps> & activeCell,
+                DPCell_<TScoreValue, DynamicGaps> const & /*previousDiagonal*/,
+                DPCell_<TScoreValue, DynamicGaps> const & /*previousHorizontal*/,
+                DPCell_<TScoreValue, DynamicGaps> const & previousVertical,
+                TSequenceHValue const & seqHVal,
+                TSequenceVValue const & seqVVal,
+                TScoringScheme const & scoringScheme,
+                RecursionDirectionVertical const & tag,
+                DPProfile_<TAlgorithm, DynamicGaps, TTracebackConfig> const &)
+{
+    activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal);
+    setGapExtension(activeCell, True(), False());
+    return _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme,
+                                 TTracebackConfig(), tag) | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX;
+}
+
+}  // namespace seqan
+
+#endif  // INCLUDE_SEQAN_ALIGN_DP_FORMULA_DYNAMIC_H_
diff --git a/seqan/align/dp_formula_linear.h b/seqan/align/dp_formula_linear.h
index 7b18d58..e7a2531 100644
--- a/seqan/align/dp_formula_linear.h
+++ b/seqan/align/dp_formula_linear.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Defines the methods to compute the score when using linear gap costs.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
 
 namespace seqan {
 
@@ -292,4 +292,4 @@ _doComputeScore(DPCell_<TScoreValue, LinearGaps> & activeCell,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
diff --git a/seqan/align/dp_matrix.h b/seqan/align/dp_matrix.h
index e973648..38a7350 100644
--- a/seqan/align/dp_matrix.h
+++ b/seqan/align/dp_matrix.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,8 +43,8 @@
 
 // TODO(holtgrew): Documentation in this header necessary or internal only?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_
 
 namespace seqan {
 
@@ -59,6 +59,13 @@ struct DefaultScoreMatrixSpec_;
 // Tags, Classes, Enums
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Tag MatrixMember
+// ----------------------------------------------------------------------------
+
+struct DPMatrixMember_;
+typedef Tag<DPMatrixMember_> DPMatrixMember;
+
 // ----------------------------------------------------------------------------
 // Tag SparseDPMatrix
 // ----------------------------------------------------------------------------
@@ -73,7 +80,6 @@ typedef Tag<SparseDPMatrix_> SparseDPMatrix;
 struct FullDPMatrix_;
 typedef Tag<FullDPMatrix_> FullDPMatrix;
 
-
 // ----------------------------------------------------------------------------
 // Enum DPMatrixDimension
 // ----------------------------------------------------------------------------
@@ -106,30 +112,15 @@ class DPMatrix_<TValue, FullDPMatrix>
 {
 public:
 
-    typedef Matrix<TValue, 2> THost;
+    typedef typename Member<DPMatrix_, DPMatrixMember>::Type THost;
 
-    Holder<THost>   _dataHost;  // The host containing the actual matrix.
+    Holder<THost>   data_host;  // The host containing the actual matrix.
 
     DPMatrix_() :
-        _dataHost()
+        data_host()
     {
-        create(_dataHost);
+        create(data_host);
     }
-
-    DPMatrix_(DPMatrix_ const & other) :
-        _dataHost(other._dataHost) {}
-
-    ~DPMatrix_() {}
-
-    DPMatrix_ & operator=(DPMatrix_ const & other)
-    {
-        if (this != &other)
-        {
-            _dataHost = other._dataHost;
-        }
-        return *this;
-    }
-
 };
 
 // ============================================================================
@@ -156,49 +147,44 @@ struct DefaultScoreMatrixSpec_<LocalAlignment_<WatermanEggert> >
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction _DataHost
+// Metafunction DataHost_
 // ----------------------------------------------------------------------------
 
 // Returns the type of the underlying matrix.
-template <typename TDPMatrix>
-struct _DataHost {};
-
 template <typename TValue, typename TMatrixSpec>
-struct _DataHost<DPMatrix_<TValue, TMatrixSpec> >
+struct Member<DPMatrix_<TValue, TMatrixSpec>, DPMatrixMember>
 {
-    typedef DPMatrix_<TValue, TMatrixSpec> TDPMatrix_;
-    typedef typename TDPMatrix_::THost Type;
+    typedef Matrix<TValue, 2> Type;
 };
 
 template <typename TValue, typename TMatrixSpec>
-struct _DataHost<DPMatrix_<TValue, TMatrixSpec> const>
+struct Member<DPMatrix_<TValue, TMatrixSpec> const, DPMatrixMember>
 {
-    typedef DPMatrix_<TValue, TMatrixSpec> TDPMatrix_;
-    typedef typename TDPMatrix_::THost const Type;
+    typedef Matrix<TValue, 2> const Type;
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction _SizeArr
+// Metafunction SizeArr_
 // ----------------------------------------------------------------------------
 
 // Returns the type of the containers to store the dimensions and the factors
 // in order to move properly in the matrix.
 template <typename TDPMatrix>
-struct _SizeArr {};
+struct SizeArr_ {};
 
 template <typename TValue, typename TMatrixSpec>
-struct _SizeArr<DPMatrix_<TValue, TMatrixSpec> >
+struct SizeArr_<DPMatrix_<TValue, TMatrixSpec> >
 {
     typedef DPMatrix_<TValue, TMatrixSpec> TDPMatrix_;
-    typedef typename _DataHost<TDPMatrix_>::Type TDataHost_;
+    typedef typename Member<TDPMatrix_, DPMatrixMember>::Type TDataHost_;
     typedef typename SizeArr_<TDataHost_>::Type Type;
 };
 
 template <typename TValue, typename TMatrixSpec>
-struct _SizeArr<DPMatrix_<TValue, TMatrixSpec> const>
+struct SizeArr_<DPMatrix_<TValue, TMatrixSpec> const>
 {
     typedef DPMatrix_<TValue, TMatrixSpec> TDPMatrix_;
-    typedef typename _DataHost<TDPMatrix_>::Type TDataHost_;
+    typedef typename Member<TDPMatrix_, DPMatrixMember>::Type TDataHost_;
     typedef typename SizeArr_<TDataHost_>::Type const Type;
 };
 
@@ -299,7 +285,7 @@ template <typename TValue, typename TMatrixSpec>
 struct Host<DPMatrix_<TValue, TMatrixSpec> >
 {
     typedef DPMatrix_<TValue, TMatrixSpec> TDPMatrix_;
-    typedef typename _DataHost<TDPMatrix_>::Type TDataMatrix_;
+    typedef typename Member<TDPMatrix_, DPMatrixMember>::Type TDataMatrix_;
     typedef typename Host<TDataMatrix_>::Type Type;
 };
 
@@ -307,7 +293,7 @@ template <typename TValue, typename TMatrixSpec>
 struct Host<DPMatrix_<TValue, TMatrixSpec> const>
 {
     typedef DPMatrix_<TValue, TMatrixSpec> TDPMatrix_;
-    typedef typename _DataHost<TDPMatrix_>::Type TDataMatrix_;
+    typedef typename Member<TDPMatrix_, DPMatrixMember>::Type TDataMatrix_;
     typedef typename Host<TDataMatrix_>::Type const Type;
 };
 
@@ -339,7 +325,7 @@ template <typename TValue, typename TMatrixSpec>
 struct Iterator<DPMatrix_<TValue, TMatrixSpec>, Rooted const>
 {
     typedef DPMatrix_<TValue, TMatrixSpec> TDPMatrix_;
-    typedef typename  _DataHost<TDPMatrix_>::Type TDataMatrix_;
+    typedef typename Member<TDPMatrix_, DPMatrixMember>::Type TDataMatrix_;
     typedef typename Iterator<TDataMatrix_, Rooted>::Type Type;
 };
 
@@ -347,7 +333,7 @@ template <typename TValue, typename TMatrixSpec>
 struct Iterator<DPMatrix_<TValue, TMatrixSpec> const, Rooted const>
 {
     typedef DPMatrix_<TValue, TMatrixSpec> TDPMatrix_;
-    typedef typename  _DataHost<TDPMatrix_>::Type TDataMatrix_;
+    typedef typename Member<TDPMatrix_, DPMatrixMember>::Type TDataMatrix_;
     typedef typename Iterator<TDataMatrix_ const, Rooted>::Type Type;
 };
 
@@ -371,17 +357,17 @@ inline bool _checkCorrectDimension(DPMatrixDimension_::TValue dim)
 
 // Returns a reference to the hosted matrix.
 template <typename TValue, typename TMatrixSpec>
-inline typename _DataHost<DPMatrix_<TValue, TMatrixSpec> >::Type &
-_dataHost(DPMatrix_<TValue, TMatrixSpec>&dpMatrix)
+inline Holder<typename Host<DPMatrix_<TValue, TMatrixSpec> >::Type> &
+_dataHost(DPMatrix_<TValue, TMatrixSpec>& dpMatrix)
 {
-    return value(dpMatrix._dataHost);
+    return _dataHost(value(dpMatrix.data_host));
 }
 
 template <typename TValue, typename TMatrixSpec>
-inline typename _DataHost<DPMatrix_<TValue, TMatrixSpec> const>::Type &
+inline Holder<typename Host<DPMatrix_<TValue, TMatrixSpec> >::Type> const &
 _dataHost(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix)
 {
-    return value(dpMatrix._dataHost);
+    return _dataHost(value(dpMatrix.data_host));
 }
 
 // ----------------------------------------------------------------------------
@@ -390,17 +376,17 @@ _dataHost(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix)
 
 // Returns a reference to the _dataLengths container of the hosted matrix.
 template <typename TValue, typename TMatrixSpec>
-inline typename _SizeArr<DPMatrix_<TValue, TMatrixSpec> >::Type &
+inline typename SizeArr_<DPMatrix_<TValue, TMatrixSpec> >::Type &
 _dataLengths(DPMatrix_<TValue, TMatrixSpec>&dpMatrix)
 {
-    return _dataLengths(_dataHost(dpMatrix));
+    return _dataLengths(value(dpMatrix.data_host));
 }
 
 template <typename TValue, typename TMatrixSpec>
-inline typename _SizeArr<DPMatrix_<TValue, TMatrixSpec> const>::Type &
+inline typename SizeArr_<DPMatrix_<TValue, TMatrixSpec> const>::Type &
 _dataLengths(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix)
 {
-    return _dataLengths(_dataHost(dpMatrix));
+    return _dataLengths(value(dpMatrix.data_host));
 }
 
 // ----------------------------------------------------------------------------
@@ -409,57 +395,17 @@ _dataLengths(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix)
 
 // Returns a reference to the _dataFactors container of the hosted matrix.
 template <typename TValue, typename TMatrixSpec>
-inline typename _SizeArr<DPMatrix_<TValue, TMatrixSpec> >::Type &
+inline typename SizeArr_<DPMatrix_<TValue, TMatrixSpec> >::Type &
 _dataFactors(DPMatrix_<TValue, TMatrixSpec>&dpMatrix)
 {
-    return _dataFactors(_dataHost(dpMatrix));
+    return _dataFactors(value(dpMatrix.data_host));
 }
 
 template <typename TValue, typename TMatrixSpec>
-inline typename _SizeArr<DPMatrix_<TValue, TMatrixSpec> const>::Type &
+inline typename SizeArr_<DPMatrix_<TValue, TMatrixSpec> const>::Type &
 _dataFactors(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix)
 {
-    return _dataFactors(_dataHost(dpMatrix));
-}
-
-// ----------------------------------------------------------------------------
-// Function host()
-// ----------------------------------------------------------------------------
-
-// Returns a reference to the underlying vector of the hosted matrix.
-template <typename TValue, typename TMatrixSpec>
-inline typename Host<DPMatrix_<TValue, TMatrixSpec> >::Type &
-host(DPMatrix_<TValue, TMatrixSpec>&dpMatrix)
-{
-    return host(_dataHost(dpMatrix));
-}
-
-template <typename TValue, typename TMatrixSpec>
-inline typename Host<DPMatrix_<TValue, TMatrixSpec> const>::Type &
-host(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix)
-{
-    return host(_dataHost(dpMatrix));
-}
-
-// ----------------------------------------------------------------------------
-// Function setHost()
-// ----------------------------------------------------------------------------
-
-// Sets a new value to the underlying vector of the hosted matrix.
-template <typename TValue, typename TMatrixSpec, typename THost>
-inline void
-setHost(DPMatrix_<TValue, TMatrixSpec> & dpMatrix,
-        THost & newHost)
-{
-    setHost(_dataHost(dpMatrix), newHost);
-}
-
-template <typename TValue, typename TMatrixSpec, typename THost>
-inline void
-setHost(DPMatrix_<TValue, TMatrixSpec> & dpMatrix,
-        THost const & newHost)
-{
-    setHost(_dataHost(dpMatrix), newHost);
+    return _dataFactors(value(dpMatrix.data_host));
 }
 
 // ----------------------------------------------------------------------------
@@ -472,7 +418,7 @@ inline typename Reference<DPMatrix_<TValue, TMatrixSpec> >::Type
 value(DPMatrix_<TValue, TMatrixSpec> & dpMatrix,
       TPosition const & pos)
 {
-    return value(_dataHost(dpMatrix), pos);
+    return value(value(dpMatrix.data_host), pos);
 }
 
 template <typename TValue, typename TMatrixSpec, typename TPosition>
@@ -480,7 +426,7 @@ inline typename Reference<DPMatrix_<TValue, TMatrixSpec> const>::Type
 value(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix,
       TPosition const & pos)
 {
-    return value(_dataHost(dpMatrix), pos);
+    return value(value(dpMatrix.data_host), pos);
 }
 
 // Returns the value of the matrix at the two given coordinates.
@@ -490,7 +436,7 @@ value(DPMatrix_<TValue, TMatrixSpec> & dpMatrix,
       TPositionV const & posDimV,
       TPositionH const & posDimH)
 {
-    return value(_dataHost(dpMatrix), posDimV, posDimH);
+    return value(value(dpMatrix.data_host), posDimV, posDimH);
 }
 
 template <typename TValue, typename TMatrixSpec, typename TPositionV, typename TPositionH>
@@ -499,7 +445,7 @@ value(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix,
       TPositionV const & posDimV,
       TPositionH const & posDimH)
 {
-    return value(_dataHost(dpMatrix), posDimV, posDimH);
+    return value(value(dpMatrix.data_host), posDimV, posDimH);
 }
 
 // ----------------------------------------------------------------------------
@@ -514,7 +460,7 @@ length(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix,
 {
     SEQAN_ASSERT(_checkCorrectDimension(dimension));
 
-    return length(_dataHost(dpMatrix), dimension);
+    return length(value(dpMatrix.data_host), dimension);
 }
 
 // Returns the overall length of the underlying vector of the hosted matrix.
@@ -522,7 +468,7 @@ template <typename TValue, typename TMatrixSpec>
 inline typename Size<DPMatrix_<TValue, TMatrixSpec> const>::Type
 length(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix)
 {
-    return length(_dataHost(dpMatrix));  // Note that even if the dimensional lengths are set but the matrix was not resized
+    return length(value(dpMatrix.data_host));  // Note that even if the dimensional lengths are set but the matrix was not resized
     // this function returns 0 or the previous length of the host before the resize.
 }
 
@@ -565,7 +511,26 @@ setLength(DPMatrix_<TValue, TMatrixSpec> & dpMatrix,
           TSize const & newLength)
 {
     SEQAN_ASSERT(_checkCorrectDimension(dimension));
-    setLength(_dataHost(dpMatrix), dimension, newLength);
+    setLength(value(dpMatrix.data_host), dimension, newLength);
+}
+
+// ----------------------------------------------------------------------------
+// Function updateFactors()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TMatrixSpec>
+inline typename Size<DPMatrix_<TValue, TMatrixSpec> >::Type
+updateFactors(DPMatrix_<TValue, TMatrixSpec> & dpMatrix)
+{
+    typedef typename Size<DPMatrix_<TValue, TMatrixSpec> >::Type TSize;
+
+    TSize factor_ = _dataFactors(dpMatrix)[0] * length(dpMatrix, 0);
+    for (unsigned int i = 1; (factor_ > 0) && (i < dimension(value(dpMatrix.data_host))); ++i)
+    {
+        _dataFactors(dpMatrix)[i] = factor_;
+        factor_ *= length(dpMatrix, i);
+    }
+    return factor_;
 }
 
 // ----------------------------------------------------------------------------
@@ -577,7 +542,11 @@ template <typename TValue, typename TMatrixSpec>
 inline void
 resize(DPMatrix_<TValue, TMatrixSpec> & dpMatrix)
 {
-    resize(_dataHost(dpMatrix));
+    typedef typename Size<DPMatrix_<TValue, TMatrixSpec> >::Type TSize;
+
+    TSize reqSize = updateFactors(dpMatrix);
+    if (reqSize >= length(dpMatrix))
+        resize(host(dpMatrix), reqSize, Exact());
 }
 
 template <typename TValue, typename TMatrixSpec>
@@ -585,7 +554,11 @@ inline void
 resize(DPMatrix_<TValue, TMatrixSpec> & dpMatrix,
        TValue const & fillValue)
 {
-    resize(_dataHost(dpMatrix), fillValue);
+    typedef typename Size<DPMatrix_<TValue, TMatrixSpec> >::Type TSize;
+
+    TSize reqSize = updateFactors(dpMatrix);
+    if (reqSize >= length(dpMatrix))
+        resize(host(dpMatrix), reqSize, fillValue, Exact());
 }
 
 // ----------------------------------------------------------------------------
@@ -610,14 +583,14 @@ template <typename TValue, typename TMatrixSpec>
 inline typename Iterator<DPMatrix_<TValue, TMatrixSpec>, Rooted const>::Type
 begin(DPMatrix_<TValue, TMatrixSpec> & dpMatrix, Rooted const)
 {
-    return begin(_dataHost(dpMatrix));
+    return begin(value(dpMatrix.data_host));
 }
 
 template <typename TValue, typename TMatrixSpec>
 inline typename Iterator<DPMatrix_<TValue, TMatrixSpec> const, Rooted const>::Type
 begin(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix, Rooted const)
 {
-    return begin(_dataHost(dpMatrix));
+    return begin(value(dpMatrix.data_host));
 }
 
 // ----------------------------------------------------------------------------
@@ -642,14 +615,14 @@ template <typename TValue, typename TMatrixSpec>
 inline typename Iterator<DPMatrix_<TValue, TMatrixSpec>, Rooted const>::Type
 end(DPMatrix_<TValue, TMatrixSpec> & dpMatrix, Rooted const)
 {
-    return end(_dataHost(dpMatrix));
+    return end(value(dpMatrix.data_host));
 }
 
 template <typename TValue, typename TMatrixSpec>
 inline typename Iterator<DPMatrix_<TValue, TMatrixSpec> const, Rooted const>::Type
 end(DPMatrix_<TValue, TMatrixSpec> const & dpMatrix, Rooted const)
 {
-    return end(_dataHost(dpMatrix));
+    return end(value(dpMatrix.data_host));
 }
 
 // ----------------------------------------------------------------------------
@@ -663,9 +636,9 @@ coordinate(DPMatrix_<TValue, FullDPMatrix> const & dpMatrix,
            TPosition hostPos,
            typename DPMatrixDimension_::TValue dimension)
 {
-    return coordinate(_dataHost(dpMatrix), hostPos, dimension);
+    return coordinate(value(dpMatrix.data_host), hostPos, dimension);
 }
 
 } // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_
diff --git a/seqan/align/dp_matrix_navigator.h b/seqan/align/dp_matrix_navigator.h
index 56c6725..eb45a64 100644
--- a/seqan/align/dp_matrix_navigator.h
+++ b/seqan/align/dp_matrix_navigator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,8 +45,8 @@
 
 // TODO(holtgrew): Documentation in this header necessary or internal only?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_
 
 namespace seqan {
 
@@ -227,4 +227,4 @@ container(DPMatrixNavigator_<TDPMatrix, TDPMatrixType, TNavigationSpec> const &
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_
diff --git a/seqan/align/dp_matrix_navigator_score_matrix.h b/seqan/align/dp_matrix_navigator_score_matrix.h
index 574377b..6ea4f00 100644
--- a/seqan/align/dp_matrix_navigator_score_matrix.h
+++ b/seqan/align/dp_matrix_navigator_score_matrix.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 // cells needed for the recursion formula.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
 
 namespace seqan {
 
@@ -102,12 +102,13 @@ template <typename TValue>
 inline void
 _init(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix>, DPScoreMatrix, NavigateColumnWise> & navigator,
       DPMatrix_<TValue, FullDPMatrix> & dpMatrix,
-      DPBand_<BandOff> const &)
+      DPBandConfig<BandOff> const &)
 {
     navigator._ptrDataContainer = &dpMatrix;
     navigator._activeColIterator = begin(dpMatrix, Standard());
     navigator._prevColIterator = navigator._activeColIterator - _dataFactors(dpMatrix)[DPMatrixDimension_::HORIZONTAL];
     navigator._laneLeap = 1;
+    assignValue(navigator._activeColIterator, TValue());
 }
 
 // Initializes the navigator for a banded alignment.
@@ -115,7 +116,7 @@ template <typename TValue>
 inline void
 _init(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix>, DPScoreMatrix, NavigateColumnWise> & navigator,
       DPMatrix_<TValue, FullDPMatrix> & dpMatrix,
-      DPBand_<BandOn> const & band)
+      DPBandConfig<BandOn> const & band)
 {
     typedef typename Size<DPMatrix_<TValue, FullDPMatrix> >::Type TMatrixSize;
     typedef typename MakeSigned<TMatrixSize>::Type TSignedSize;
@@ -142,6 +143,7 @@ _init(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix>, DPScoreMatrix, Navigat
     }
     // Set previous iterator to same position, one column left.
     navigator._prevColIterator = navigator._activeColIterator - _dataFactors(dpMatrix)[DPMatrixDimension_::HORIZONTAL];
+    assignValue(navigator._activeColIterator, TValue());
 }
 
 // ----------------------------------------------------------------------------
@@ -414,4 +416,4 @@ previousCellVertical(DPMatrixNavigator_<TDPMatrix, DPScoreMatrix, TNavigationSpe
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
diff --git a/seqan/align/dp_matrix_navigator_score_matrix_sparse.h b/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
index 3784961..58fa650 100644
--- a/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
+++ b/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 // cells needed for the recursion formula.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_
 
 namespace seqan {
 
@@ -101,12 +101,13 @@ template <typename TValue>
 inline void
 _init(DPMatrixNavigator_<DPMatrix_<TValue, SparseDPMatrix>, DPScoreMatrix, NavigateColumnWise> & navigator,
       DPMatrix_<TValue, SparseDPMatrix> & dpMatrix,
-      DPBand_<BandOff> const &)
+      DPBandConfig<BandOff> const &)
 {
     navigator._ptrDataContainer = &dpMatrix;
     navigator._activeColIterator = begin(dpMatrix, Standard());
     navigator._prevColIterator = navigator._activeColIterator;
     navigator._laneLeap = 1 - _dataLengths(dpMatrix)[DPMatrixDimension_::VERTICAL];
+    assignValue(navigator._activeColIterator, TValue());
 }
 
 // Initializes the navigator for banded alignments
@@ -114,7 +115,7 @@ template <typename TValue>
 inline void
 _init(DPMatrixNavigator_<DPMatrix_<TValue, SparseDPMatrix>, DPScoreMatrix, NavigateColumnWise> & navigator,
       DPMatrix_<TValue, SparseDPMatrix> & dpMatrix,
-      DPBand_<BandOn> const & band)
+      DPBandConfig<BandOn> const & band)
 {
     typedef DPMatrix_<TValue, SparseDPMatrix> TSparseDPMatrix;
     typedef typename Size<TSparseDPMatrix>::Type TSize;
@@ -138,6 +139,7 @@ _init(DPMatrixNavigator_<DPMatrix_<TValue, SparseDPMatrix>, DPScoreMatrix, Navig
         navigator._activeColIterator = begin(dpMatrix, Standard()) + length(dpMatrix, DPMatrixDimension_::VERTICAL) + navigator._laneLeap - 1;
     }
     navigator._prevColIterator = navigator._activeColIterator;
+    assignValue(navigator._activeColIterator, TValue());
 }
 
 // ----------------------------------------------------------------------------
@@ -376,4 +378,4 @@ _goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, SparseDPMatrix>, DPScoreMatrix,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_
diff --git a/seqan/align/dp_matrix_navigator_trace_matrix.h b/seqan/align/dp_matrix_navigator_trace_matrix.h
index 8b48c82..a32b7d2 100644
--- a/seqan/align/dp_matrix_navigator_trace_matrix.h
+++ b/seqan/align/dp_matrix_navigator_trace_matrix.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,8 +40,8 @@
 // is thrown.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_
 
 namespace seqan {
 
@@ -102,7 +102,7 @@ template <typename TValue, typename TTraceFlag>
 inline void
 _init(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix>, DPTraceMatrix<TTraceFlag>, NavigateColumnWise> & navigator,
       DPMatrix_<TValue, FullDPMatrix> & dpMatrix,
-      DPBand_<BandOff> const &)
+      DPBandConfig<BandOff> const &)
 {
     if (IsSameType<TTraceFlag, TracebackOff>::VALUE)
         return;  // Leave navigator uninitialized because it is never used.
@@ -110,6 +110,7 @@ _init(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix>, DPTraceMatrix<TTraceFl
     navigator._ptrDataContainer = &dpMatrix;
     navigator._activeColIterator = begin(dpMatrix, Standard());
     navigator._laneLeap = 1;
+    assignValue(navigator._activeColIterator, TValue());
 }
 
 // Initializes the navigator for banded alignments.
@@ -118,7 +119,7 @@ template <typename TValue, typename TTraceFlag>
 inline void
 _init(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix>, DPTraceMatrix<TTraceFlag>, NavigateColumnWise> & navigator,
       DPMatrix_<TValue, FullDPMatrix> & dpMatrix,
-      DPBand_<BandOn> const & band)
+      DPBandConfig<BandOn> const & band)
 {
     typedef typename Size<DPMatrix_<TValue, FullDPMatrix> >::Type TMatrixSize;
     typedef typename MakeSigned<TMatrixSize>::Type TSignedSize;
@@ -149,6 +150,7 @@ _init(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix>, DPTraceMatrix<TTraceFl
         navigator._laneLeap = lengthVertical + lastPos;
         navigator._activeColIterator = begin(dpMatrix, Standard()) + navigator._laneLeap - 1;
     }
+    assignValue(navigator._activeColIterator, TValue());
 }
 
 // ----------------------------------------------------------------------------
@@ -465,4 +467,4 @@ position(DPMatrixNavigator_<TDPMatrix, DPTraceMatrix<TTraceFlag>, TNavigationSpe
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_
diff --git a/seqan/align/dp_matrix_sparse.h b/seqan/align/dp_matrix_sparse.h
index 7fdf290..526376e 100644
--- a/seqan/align/dp_matrix_sparse.h
+++ b/seqan/align/dp_matrix_sparse.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Rene Rahn <rene.rahn@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
 
 namespace seqan {
 
@@ -54,30 +54,15 @@ class DPMatrix_<TValue, SparseDPMatrix>
 {
 public:
 
-    typedef Matrix<TValue, 2> THost;
+    typedef typename Member<DPMatrix_, DPMatrixMember>::Type THost;
 
-    Holder<THost>   _dataHost;  // The host containing the actual matrix.
+    Holder<THost>   data_host;  // The host containing the actual matrix.
 
     DPMatrix_() :
-        _dataHost()
+        data_host()
     {
-        create(_dataHost);
+        create(data_host);
     }
-
-    DPMatrix_(DPMatrix_ const & other) :
-        _dataHost(other._dataHost) {}
-
-    ~DPMatrix_() {}
-
-    DPMatrix_ & operator=(DPMatrix_ const & other)
-    {
-        if (this != &other)
-        {
-            _dataHost = other._dataHost;
-        }
-        return *this;
-    }
-
 };
 
 // ============================================================================
@@ -101,7 +86,7 @@ resize(DPMatrix_<TValue, SparseDPMatrix> & dpMatrix)
 
     TSize _dimVertical = length(dpMatrix, DPMatrixDimension_::VERTICAL);
 
-    if (_dimVertical > 0)
+    if (_dimVertical >= length(dpMatrix))
         resize(host(dpMatrix), _dimVertical, Exact());
 }
 
@@ -115,7 +100,7 @@ resize(DPMatrix_<TValue, SparseDPMatrix> & dpMatrix,
 
     TSize _dimVertical = length(dpMatrix, DPMatrixDimension_::VERTICAL);
 
-    if (_dimVertical > 0)
+    if (_dimVertical > length(dpMatrix))
         resize(host(dpMatrix), _dimVertical, fillValue, Exact());
 }
 
@@ -162,4 +147,4 @@ coordinate(DPMatrix_<TValue, SparseDPMatrix> const & /*dpMatrix*/,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
diff --git a/seqan/align/dp_meta_info.h b/seqan/align/dp_meta_info.h
index e89b423..06641a1 100644
--- a/seqan/align/dp_meta_info.h
+++ b/seqan/align/dp_meta_info.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,8 +40,8 @@
 
 // TODO(holtgrew): Documentation in this header necessary or internal only?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_
 
 namespace seqan {
 
@@ -172,7 +172,7 @@ struct DPMetaColumn_ {};
 
 
 // ----------------------------------------------------------------------------
-// Class DPMetaColumn_											   [FullColumn]
+// Class DPMetaColumn_                                               [FullColumn]
 // ----------------------------------------------------------------------------
 
 template <typename TDPProfile, typename TColumnType>
@@ -221,7 +221,7 @@ struct DPMetaColumn_<TDPProfile, MetaColumnDescriptor<TColumnType, FullColumn> >
 };
 
 // ----------------------------------------------------------------------------
-// Class DPMetaColumn_									     [PartialColumnTop]
+// Class DPMetaColumn_                                         [PartialColumnTop]
 // ----------------------------------------------------------------------------
 
 template <typename TDPProfile, typename TColumnType>
@@ -273,7 +273,7 @@ struct DPMetaColumn_<TDPProfile, MetaColumnDescriptor<TColumnType, PartialColumn
 };
 
 // ----------------------------------------------------------------------------
-// Class DPMetaColumn_									  [PartialColumnMiddle]
+// Class DPMetaColumn_                                      [PartialColumnMiddle]
 // ----------------------------------------------------------------------------
 
 template <typename TDPProfile, typename TColumnType>
@@ -322,7 +322,7 @@ struct DPMetaColumn_<TDPProfile, MetaColumnDescriptor<TColumnType, PartialColumn
 };
 
 // ----------------------------------------------------------------------------
-// Class DPMetaColumn_									  [PartialColumnBottom]
+// Class DPMetaColumn_                                      [PartialColumnBottom]
 // ----------------------------------------------------------------------------
 
 template <typename TDPProfile, typename TColumnType>
@@ -450,4 +450,4 @@ struct TrackingEnabled_<TDPMetaColumn, LastCell>:
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_
diff --git a/seqan/align/dp_profile.h b/seqan/align/dp_profile.h
index e3b0fb6..b925620 100644
--- a/seqan/align/dp_profile.h
+++ b/seqan/align/dp_profile.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,8 +41,8 @@
 
 // TODO(holtgrew): Documentation in this header necessary or internal only?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_
 
 namespace seqan {
 
@@ -82,6 +82,8 @@ typedef Tag<AlignmentSplitBreakpoint_> SplitBreakpointAlignment;
 template <typename TSpec = FreeEndGaps_<> >
 struct GlobalAlignment_;
 
+typedef GlobalAlignment_<> DPGlobal;
+
 // ----------------------------------------------------------------------------
 // Class SuboptimalAlignment
 // ----------------------------------------------------------------------------
@@ -103,6 +105,8 @@ typedef Tag<AlignmentSuboptimal_> SuboptimalAlignment;
 template <typename TSpec = Default>
 struct LocalAlignment_;
 
+typedef LocalAlignment_<> DPLocal;
+typedef LocalAlignment_<SuboptimalAlignment> DPLocalEnumerate;
 
 // ----------------------------------------------------------------------------
 // Class TraceBitMap_
@@ -189,6 +193,22 @@ typedef Tag<LinearGaps_> LinearGaps;
 struct AffineGaps_;
 typedef Tag<AffineGaps_> AffineGaps;
 
+// ----------------------------------------------------------------------------
+// Tag DynamicGaps
+// ----------------------------------------------------------------------------
+
+/*!
+ * @tag AlignmentAlgorithmTags#DynamicGaps
+ * @headerfile <seqan/align.h>
+ * @brief Tag for selecting dynamic gap cost model. This tag can be used for all standard DP algorithms.
+ *
+ * @signature struct DynamicGaps_;
+ * @signature typedef Tag<DynamicGaps_> DynamicGaps;
+ */
+
+struct DynamicGaps_;
+typedef Tag<DynamicGaps_> DynamicGaps;
+
 // ----------------------------------------------------------------------------
 // Class DPProfile
 // ----------------------------------------------------------------------------
@@ -232,6 +252,21 @@ typedef Tag<DPLastRow_> DPLastRow;
 struct DPLastColumn_;
 typedef Tag<DPLastColumn_> DPLastColumn;
 
+template <typename TDPType, typename TBand, typename TFreeEndGaps = FreeEndGaps_<False, False, False, False>,
+          typename TTraceConfig = TracebackOn<TracebackConfig_<SingleTrace, GapsLeft> > >
+class AlignConfig2
+{
+public:
+    TBand _band;
+
+    AlignConfig2() : _band()
+    {}
+
+    template <typename TPosition>
+    AlignConfig2(TPosition const & lDiag, TPosition const & uDiag) : _band(lDiag, uDiag)
+    {}
+};
+
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -453,4 +488,4 @@ struct IsFreeEndGap_<FreeEndGaps_<TFirstRow, TFirstColumn, TLastRow, True> const
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_
diff --git a/seqan/align/dp_scout.h b/seqan/align/dp_scout.h
index 1a6283c..d488df8 100644
--- a/seqan/align/dp_scout.h
+++ b/seqan/align/dp_scout.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,8 +47,8 @@
 // see dp_scout_xdrop.h for an example.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_
 
 namespace seqan {
 
@@ -198,16 +198,15 @@ struct ScoutStateSpecForScout_
 // ----------------------------------------------------------------------------
 
 // Tracks the new score, if it is the new maximum.
-template <typename TDPCell, typename TSpec, typename TTraceMatrixNavigator>
+template <typename TDPCell, typename TSpec, typename TTraceMatrixNavigator,
+          typename TIsLastColumn, typename TIsLastRow>
 inline void
 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout,
                 TDPCell const & activeCell,
                 TTraceMatrixNavigator const & navigator,
-                bool isLastColumn = false,
-                bool isLastRow = false)
+                TIsLastColumn const & /**/,
+                TIsLastRow const & /**/)
 {
-    (void)isLastColumn;
-    (void)isLastRow;
 
     if (_scoreOfCell(activeCell) > _scoreOfCell(dpScout._maxScore))
     {
@@ -216,6 +215,28 @@ _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout,
     }
 }
 
+// TODO(rmaerker): Why is this needed?
+template <typename TDPCell, typename TSpec, typename TTraceMatrixNavigator, typename TIsLastColumn>
+inline void
+_scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout,
+                TDPCell const & activeCell,
+                TTraceMatrixNavigator const & navigator,
+                TIsLastColumn const & /**/)
+{
+    return _scoutBestScore(dpScout, activeCell, navigator, TIsLastColumn(),
+                           False());
+}
+
+// TODO(rmaerker): Why is this needed?
+template <typename TDPCell, typename TSpec, typename TTraceMatrixNavigator>
+inline void
+_scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout,
+                TDPCell const & activeCell,
+                TTraceMatrixNavigator const & navigator)
+{
+    return _scoutBestScore(dpScout, activeCell, navigator, False(), False());
+}
+
 // ----------------------------------------------------------------------------
 // Function maxScore()
 // ----------------------------------------------------------------------------
@@ -266,4 +287,4 @@ terminateScout(DPScout_<TDPCell, Terminator_<TSpec> > & scout)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_
diff --git a/seqan/align/dp_setup.h b/seqan/align/dp_setup.h
index 63f802c..8e1ab28 100644
--- a/seqan/align/dp_setup.h
+++ b/seqan/align/dp_setup.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Rene Rahn <rene.rahn@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
 
 namespace seqan {
 
@@ -45,6 +45,7 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
+
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -181,38 +182,52 @@ struct SubstituteAlignConfig_<AlignConfig<true, true, true, true, TSpec> >
 };
 
 // ----------------------------------------------------------------------------
-// SetUpAlignmentProfile
+// Metafunction SubstituteAlgoTag_
 // ----------------------------------------------------------------------------
 
-template <typename TAlgoTag, typename TAlignConfig, typename TTraceSwitch, typename TGapCosts>
-struct SetupAlignmentProfile_;
+// NOTE(rmaerker): Needed to substitute the global alingment algo tags to the correct gap model.
+template <typename TTag>
+struct SubstituteAlgoTag_
+{
+    typedef TTag Type;
+};
 
-// Profile for Needleman-Wunsch algorithm.
-template <typename TAlignConfig, typename TGapCosts, typename TTraceSwitch>
-struct SetupAlignmentProfile_<NeedlemanWunsch, TAlignConfig, TGapCosts, TTraceSwitch>
+template <>
+struct SubstituteAlgoTag_<NeedlemanWunsch>
 {
-    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps_;
-    typedef DPProfile_<GlobalAlignment_<TFreeEndGaps_>, LinearGaps, TTraceSwitch> Type;
+    typedef LinearGaps Type;
 };
 
-// Profile for Gotoh algorithm.
-template <typename TAlignConfig, typename TGapCosts, typename TTraceSwitch>
-struct SetupAlignmentProfile_<Gotoh, TAlignConfig, TGapCosts, TTraceSwitch>
+template <>
+struct SubstituteAlgoTag_<Gotoh>
+{
+    typedef AffineGaps Type;
+};
+
+// ----------------------------------------------------------------------------
+// SetUpAlignmentProfile
+// ----------------------------------------------------------------------------
+
+template <typename TDPType, typename TAlignConfig, typename TTraceSwitch, typename TGapCosts>
+struct SetupAlignmentProfile_;
+
+// Profile for Needleman-Wunsch algorithm.
+template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch>
+struct SetupAlignmentProfile_<DPGlobal, TFreeEndGaps, TGapCosts, TTraceSwitch>
 {
-    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps_;
-    typedef DPProfile_<GlobalAlignment_<TFreeEndGaps_>, AffineGaps, TTraceSwitch> Type;
+    typedef DPProfile_<GlobalAlignment_<TFreeEndGaps>, TGapCosts, TTraceSwitch> Type;
 };
 
 // Profile for Smith-Waterman algorithm.
-template <typename TAlignConfig, typename TGapCosts, typename TTraceSwitch>
-struct SetupAlignmentProfile_<SmithWaterman, TAlignConfig, TGapCosts, TTraceSwitch>
+template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch>
+struct SetupAlignmentProfile_<DPLocal, TFreeEndGaps, TGapCosts, TTraceSwitch>
 {
     typedef DPProfile_<LocalAlignment_<>, TGapCosts, TTraceSwitch> Type;
 };
 
 // Profile for Waterman-Eggert algorithm
-template <typename TAlignConfig, typename TGapCosts, typename TTraceSwitch>
-struct SetupAlignmentProfile_<WatermanEggert, TAlignConfig, TGapCosts, TTraceSwitch>
+template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch>
+struct SetupAlignmentProfile_<DPLocalEnumerate, TFreeEndGaps, TGapCosts, TTraceSwitch>
 {
     typedef DPProfile_<LocalAlignment_<SuboptimalAlignment>, TGapCosts, TracebackOn<TracebackConfig_<SingleTrace, GapsLeft> > > Type;
 };
@@ -223,682 +238,137 @@ struct SetupAlignmentProfile_<WatermanEggert, TAlignConfig, TGapCosts, TTraceSwi
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function _setUpAndRunAlignment()                                  [Unbanded]
+// Function _usesAffineGaps()
 // ----------------------------------------------------------------------------
 
-// Interface without AlignConfig.
-template <typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV,
-          typename TScoreValue, typename TScoreSpec, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlgoTag const &,
-                      TGapsTag const &)
+template <typename TScoringScheme, typename TSeqH, typename TSeqV>
+inline bool
+_usesAffineGaps(TScoringScheme const & scoringScheme,
+                TSeqH const & seqH,
+                TSeqV const & seqV)
 {
-    typedef Score<TScoreValue, TScoreSpec> TScoringScheme;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceH>::Type TSequenceHEntry;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceV>::Type TSequenceVEntry;
-
-    SEQAN_ASSERT_GEQ(length(seqH), 1u);
-    SEQAN_ASSERT_GEQ(length(seqV), 1u);
+    typedef typename SequenceEntryForScore<TScoringScheme, TSeqH>::Type TSequenceHEntry;
+    typedef typename SequenceEntryForScore<TScoringScheme, TSeqV>::Type TSequenceVEntry;
 
     TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
     TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
 
-    if (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry) ||
-        scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry))
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, AlignConfig<>, AffineGaps, TracebackOn<TGapsTag> >::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOff>(), TDPProfile());
-    }
-    else
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, AlignConfig<>, LinearGaps, TracebackOn<TGapsTag> >::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOff>(), TDPProfile());
-    }
-}
-
-template <typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlgoTag const & algoTag,
-                      TGapsTag const & gapsTag)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, algoTag, gapsTag);
+    return (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
+            scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry)) ||
+           (scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
+               scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry));
 }
 
-template <typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV,
-          typename TScoreValue, typename TScoreSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlgoTag const & algoTag)
-{
-    return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-template <typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlgoTag const & algoTag)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
+// ----------------------------------------------------------------------------
+// Function _setUpAndRunAlignment()
+// ----------------------------------------------------------------------------
 
-// Interface with AlignConfig.
-template <typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV,
-          typename TScoreValue, typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec,
-          typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
+template <typename TScoreValue, typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec,
+          typename TSequenceH, typename TSequenceV, typename TScoreValue2, typename TScoreSpec, typename TDPType,
+          typename TBand, typename TFreeEndGaps, typename TTraceConfig>
+typename Value<Score<TScoreValue2, TScoreSpec> >::Type
+_setUpAndRunAlignment(DPContext<TScoreValue, AffineGaps> & dpContext,
+                      String<TTraceSegment, TSpec> & traceSegments,
                       DPScoutState_<TDPScoutStateSpec> & dpScoutState,
                       TSequenceH const & seqH,
                       TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const &,
-                      TAlgoTag const &,
-                      TGapsTag const &)
+                      Score<TScoreValue2, TScoreSpec> const & scoringScheme,
+                      AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig> const & alignConfig)
 {
-    typedef Score<TScoreValue, TScoreSpec> TScoringScheme;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceH>::Type TSequenceHEntry;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceV>::Type TSequenceVEntry;
-    typedef AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> TAlignConfig;
-
     SEQAN_ASSERT_GEQ(length(seqH), 1u);
     SEQAN_ASSERT_GEQ(length(seqV), 1u);
 
-    TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
-    TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
-
-    if (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry) ||
-        scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry))
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, TAlignConfig, AffineGaps, TracebackOn<TGapsTag> >::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOff>(), TDPProfile());
-    }
-    else
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, TAlignConfig, LinearGaps, TracebackOn<TGapsTag> >::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOff>(), TDPProfile());
-    }
+    typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, AffineGaps, TTraceConfig>::Type TDPProfile;
+    return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band,
+                             TDPProfile());
 }
 
-template <typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV,
-          typename TScoreValue, typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec,
-          typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
+template <typename TScoreValue, typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec,
+          typename TSequenceH, typename TSequenceV, typename TScoreValue2, typename TScoreSpec, typename TDPType,
+          typename TBand, typename TFreeEndGaps, typename TTraceConfig>
+typename Value<Score<TScoreValue2, TScoreSpec> >::Type
+_setUpAndRunAlignment(DPContext<TScoreValue, LinearGaps> & dpContext,
+                      String<TTraceSegment, TSpec> & traceSegments,
                       DPScoutState_<TDPScoutStateSpec> & dpScoutState,
                       TSequenceH const & seqH,
                       TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      TAlgoTag const & algoTag)
+                      Score<TScoreValue2, TScoreSpec> const & scoringScheme,
+                      AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig> const & alignConfig)
 {
-    return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, algoTag,
-                                 TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-template <typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec,
-          typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      TAlgoTag const & algoTag,
-                      TGapsTag const & gapsTag)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, algoTag, gapsTag);
-}
-
-template <typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec,
-          typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      TAlgoTag const & algoTag)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-// Interface without AlignConfig and with traceback disabled.
-template <typename TDPScoutStateSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue, 
-         typename TScoreSpec, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlgoTag const &,
-                      TGapsTag const & /*unused*/)
-{
-    typedef Score<TScoreValue, TScoreSpec> TScoringScheme;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceH>::Type TSequenceHEntry;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceV>::Type TSequenceVEntry;
-
     SEQAN_ASSERT_GEQ(length(seqH), 1u);
     SEQAN_ASSERT_GEQ(length(seqV), 1u);
 
-    String<TraceSegment_<unsigned, unsigned> > traceSegments;
-
-    TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
-    TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
-
-    if (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry) ||
-        scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry))
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, AlignConfig<>, AffineGaps, TracebackOff>::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOff>(), TDPProfile());
-    }
-    else
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, AlignConfig<>, LinearGaps, TracebackOff>::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOff>(), TDPProfile());
-    }
+    typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, LinearGaps, TTraceConfig>::Type TDPProfile;
+    return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band,
+                             TDPProfile());
 }
 
-template <typename TDPScoutStateSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-         typename TScoreSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlgoTag const & algoTag)
-{
-    return _setUpAndRunAlignment(dpScoutState, seqH, seqV, scoringScheme, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-template <typename TSequenceH, typename TSequenceV, typename TScoreValue, typename TScoreSpec, typename TAlgoTag,
-         typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlgoTag const &,
-                      TGapsTag const & gapsTag)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(noState, seqH, seqV, scoringScheme, gapsTag);
-}
-
-template <typename TSequenceH, typename TSequenceV, typename TScoreValue, typename TScoreSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlgoTag const &)
-{
-    // Note that GapsLeft could be nothing, is unused in callee without traceback.
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(noState, seqH, seqV, scoringScheme, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-// Interface with AlignConfig and with traceback disabled.
-template <typename TDPScoutStateSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-         typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec, typename TAlgoTag,
-         typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(DPScoutState_<TDPScoutStateSpec> & dpScoutState,
+template <typename TScoreValue, typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec,
+          typename TSequenceH, typename TSequenceV, typename TScoreValue2, typename TScoreSpec, typename TDPType,
+          typename TBand, typename TFreeEndGaps, typename TTraceConfig>
+typename Value<Score<TScoreValue2, TScoreSpec> >::Type
+_setUpAndRunAlignment(DPContext<TScoreValue, DynamicGaps> & dpContext,
+                      String<TTraceSegment, TSpec> & traceSegments,
+                      DPScoutState_<TDPScoutStateSpec> & dpScoutState,
                       TSequenceH const & seqH,
                       TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const &,
-                      TAlgoTag const &,
-                      TGapsTag const & /*unused*/)
+                      Score<TScoreValue2, TScoreSpec> const & scoringScheme,
+                      AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig> const & alignConfig)
 {
-    typedef AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> TAlignConfig;
-    typedef Score<TScoreValue, TScoreSpec> TScoringScheme;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceH>::Type TSequenceHEntry;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceV>::Type TSequenceVEntry;
-
     SEQAN_ASSERT_GEQ(length(seqH), 1u);
     SEQAN_ASSERT_GEQ(length(seqV), 1u);
 
-    String<TraceSegment_<unsigned, unsigned> > traceSegments;
-
-    TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
-    TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
-
-    if (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry) ||
-        scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry))
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, TAlignConfig, AffineGaps, TracebackOff>::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOff>(), TDPProfile());
-    }
-    else
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, TAlignConfig, LinearGaps, TracebackOff>::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOff>(), TDPProfile());
-    }
-}
-
-template <typename TDPScoutStateSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-         typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom,
-          typename TACSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      TAlgoTag const &)
-{
-    // Note that GapsLeft could be nothing, is unused in callee without traceback.
-    return _setUpAndRunAlignment(dpScoutState, seqH, seqV, scoringScheme, alignConfig, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-template <typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec, typename TAlgoTag,
-          typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      TAlgoTag const & algoTag,
-                      TGapsTag const & gapsTag)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(noState, seqH, seqV, scoringScheme, alignConfig, algoTag, gapsTag);
-}
-
-template <typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      TAlgoTag const & algoTag)
-{
-    DPScoutState_<Default> noState;
-    // Note that GapsLeft could be nothing, is unused in callee without traceback.
-    return _setUpAndRunAlignment(noState, seqH, seqV, scoringScheme, alignConfig, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
+    typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, DynamicGaps, TTraceConfig>::Type TDPProfile;
+    return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band,
+                             TDPProfile());
 }
 
-// ----------------------------------------------------------------------------
-// Function _setUpAndRunAlignment()                                    [Banded]
-// ----------------------------------------------------------------------------
-
-// Interface without AlignConfig.
-template <typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV,
-          typename TScoreValue, typename TScoreSpec, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
+template <typename TTraceSegment, typename TSpec, typename TDPScoutStateSpec,
+          typename TSequenceH, typename TSequenceV, typename TScoreValue2, typename TScoreSpec, typename TDPType,
+          typename TBand, typename TFreeEndGaps, typename TTraceConfig, typename TGapModel>
+typename Value<Score<TScoreValue2, TScoreSpec> >::Type
 _setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
                       DPScoutState_<TDPScoutStateSpec> & dpScoutState,
                       TSequenceH const & seqH,
                       TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const &,
-                      TGapsTag const &)
+                      Score<TScoreValue2, TScoreSpec> const & scoringScheme,
+                      AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig> const & alignConfig,
+                      TGapModel const & /**/)
 {
-    typedef Score<TScoreValue, TScoreSpec> TScoringScheme;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceH>::Type TSequenceHEntry;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceV>::Type TSequenceVEntry;
-    
-    SEQAN_ASSERT_GEQ(length(seqH), 1u);
-    SEQAN_ASSERT_GEQ(length(seqV), 1u);
-
-    TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
-    TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
-
-    if (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry) ||
-        scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry))
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, AlignConfig<>, AffineGaps, TracebackOn<TGapsTag> >::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOn>(lowerDiagonal, upperDiagonal), TDPProfile());
-    }
-    else
+    if (IsSameType<TGapModel, LinearGaps>::VALUE)
     {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, AlignConfig<>, LinearGaps, TracebackOn<TGapsTag> >::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOn>(lowerDiagonal, upperDiagonal), TDPProfile());
+        DPContext<TScoreValue2, LinearGaps> dpContext;
+        return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig);
     }
-}
-
-template <typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV,
-          typename TScoreValue, typename TScoreSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag)
-{
-    // Note that GapsLeft could be nothing, is unused in callee without traceback.
-    return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, lowerDiagonal, upperDiagonal,
-                                 algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-template <typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag,
-                      TGapsTag const & /*ignored*/)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, lowerDiagonal, upperDiagonal, algoTag);
-}
-
-template <typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag)
-{
-    // Note that GapsLeft could be nothing, is unused in callee without traceback.
-    return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, lowerDiagonal, upperDiagonal, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-// Interface with AlignConfig.
-template <typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV,
-          typename TScoreValue, typename TScoreSpec, typename TAlignConfig, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlignConfig const &,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const &,
-                      TGapsTag const &)
-{
-    typedef Score<TScoreValue, TScoreSpec> TScoringScheme;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceH>::Type TSequenceHEntry;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceV>::Type TSequenceVEntry;
-
-    SEQAN_ASSERT_GEQ(length(seqH), 1u);
-    SEQAN_ASSERT_GEQ(length(seqV), 1u);
-
-    TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
-    TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
-
-    if (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry) ||
-        scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry))
+    else if (IsSameType<TGapModel, AffineGaps>::VALUE)
     {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, TAlignConfig, AffineGaps, TracebackOn<TGapsTag> >::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOn>(lowerDiagonal, upperDiagonal), TDPProfile());
+        DPContext<TScoreValue2, AffineGaps> dpContext;
+        return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig);
     }
     else
     {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, TAlignConfig, LinearGaps, TracebackOn<TGapsTag> >::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOn>(lowerDiagonal, upperDiagonal), TDPProfile());
+        DPContext<TScoreValue2, DynamicGaps> dpContext;
+        return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig);
     }
 }
 
-template <typename TDPScoutStateSpec, typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV,
-          typename TScoreValue, typename TScoreSpec, typename TAlignConfig, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
+template <typename TTraceSegment, typename TSpec, typename TDPScoutStateSpec,
+          typename TSequenceH, typename TSequenceV, typename TScoreValue2, typename TScoreSpec, typename TDPType,
+          typename TBand, typename TFreeEndGaps, typename TTraceConfig>
+typename Value<Score<TScoreValue2, TScoreSpec> >::Type
 _setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
                       DPScoutState_<TDPScoutStateSpec> & dpScoutState,
                       TSequenceH const & seqH,
                       TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlignConfig const & alignConfig,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag)
+                      Score<TScoreValue2, TScoreSpec> const & scoringScheme,
+                      AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig> const & alignConfig)
 {
-    return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig,
-                                 lowerDiagonal, upperDiagonal, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-
-template <typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, typename TAlignConfig, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlignConfig const & alignConfig,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag,
-                      TGapsTag const & gapsTag)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(traceSegments, noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal,
-                                 upperDiagonal, algoTag, gapsTag);
-}
-
-template <typename TTraceSegment, typename TSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, typename TAlignConfig, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(String<TTraceSegment, TSpec> & traceSegments,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      TAlignConfig const & alignConfig,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag)
-{
-    return _setUpAndRunAlignment(traceSegments, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal,
-                                 algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-// Interface without AlignConfig and with traceback disabled.
-template <typename TDPScoutStateSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const &,
-                      TGapsTag const &)
-{
-//    typedef String<TAlphabetH, TSpecH> const TSequenceH;
-//    typedef String<TAlphabetV, TSpecV> const TSequenceV;
-    typedef Score<TScoreValue, TScoreSpec> TScoringScheme;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceH const>::Type TSequenceHEntry;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceV const>::Type TSequenceVEntry;
-
-    SEQAN_ASSERT_GEQ(length(seqH), 1u);
-    SEQAN_ASSERT_GEQ(length(seqV), 1u);
-
-    String<TraceSegment_<unsigned, unsigned> > traceSegments;
-
-    TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
-    TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
-
-    if (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry) ||
-        scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry))
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, AlignConfig<>, AffineGaps, TracebackOff>::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOn>(lowerDiagonal, upperDiagonal), TDPProfile());
-    }
+    if (_usesAffineGaps(scoringScheme, seqH, seqV))
+        return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, AffineGaps());
     else
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, AlignConfig<>, LinearGaps, TracebackOff>::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOn>(lowerDiagonal, upperDiagonal), TDPProfile());
-    }
-}
-
-template <typename TDPScoutStateSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag)
-{
-    // Note that GapsLeft could be nothing, is unused in callee without traceback.
-    return _setUpAndRunAlignment(dpScoutState, seqH, seqV, scoringScheme, lowerDiagonal, upperDiagonal, algoTag,
-                                 TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-template <typename TSequenceH, typename TSequenceV, typename TScoreValue, typename TScoreSpec,
-          typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(noState, seqH, seqV, scoringScheme, lowerDiagonal, upperDiagonal, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-// Interface with AlignConfig and with traceback disabled.
-template <typename TDPScoutStateSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec, typename TAlgoTag,
-          typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const &,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const &,
-                      TGapsTag const & /*ignored*/)
-{
-    typedef AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> TAlignConfig;
-//    typedef String<TAlphabetH, TSpecH> const TSequenceH;
-//    typedef String<TAlphabetV, TSpecV> const TSequenceV;
-    typedef Score<TScoreValue, TScoreSpec> TScoringScheme;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceH const>::Type TSequenceHEntry;
-    typedef typename SequenceEntryForScore<TScoringScheme, TSequenceV const>::Type TSequenceVEntry;
-
-    SEQAN_ASSERT_GEQ(length(seqH), 1u);
-    SEQAN_ASSERT_GEQ(length(seqV), 1u);
-
-    String<TraceSegment_<unsigned, unsigned> > traceSegments;
-
-    TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
-    TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
-
-    if (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry) ||
-        scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
-        scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry))
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, TAlignConfig, AffineGaps, TracebackOff>::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOn>(lowerDiagonal, upperDiagonal), TDPProfile());
-    }
-    else
-    {
-        typedef typename SetupAlignmentProfile_<TAlgoTag, TAlignConfig, LinearGaps, TracebackOff>::Type TDPProfile;
-        return _computeAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, DPBand_<BandOn>(lowerDiagonal, upperDiagonal), TDPProfile());
-    }
-}
-
-template <typename TDPScoutStateSpec, typename TSequenceH, typename TSequenceV, typename TScoreValue,
-          typename TScoreSpec, bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(DPScoutState_<TDPScoutStateSpec> & dpScoutState,
-                      TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag)
-{
-    // Note that GapsLeft could be nothing, is unused in callee without traceback.
-    return _setUpAndRunAlignment(dpScoutState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal,
-                                 algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
-}
-
-template <typename TSequenceH, typename TSequenceV, typename TScoreValue, typename TScoreSpec,
-          bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec, typename TAlgoTag, typename TGapsTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag,
-                      TGapsTag const & /*ignored*/)
-{
-    DPScoutState_<Default> noState;
-    return _setUpAndRunAlignment(noState, seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal,
-                                 algoTag);
-}
-
-template <typename TSequenceH, typename TSequenceV, typename TScoreValue, typename TScoreSpec,
-          bool TTop, bool TRight, bool TLeft, bool TBottom, typename TACSpec, typename TAlgoTag>
-typename Value<Score<TScoreValue, TScoreSpec> >::Type
-_setUpAndRunAlignment(TSequenceH const & seqH,
-                      TSequenceV const & seqV,
-                      Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                      AlignConfig<TTop, TRight, TLeft, TBottom, TACSpec> const & alignConfig,
-                      int lowerDiagonal,
-                      int upperDiagonal,
-                      TAlgoTag const & algoTag)
-{
-    // Note that GapsLeft could be nothing, is unused in callee without traceback.
-    return _setUpAndRunAlignment(seqH, seqV, scoringScheme, alignConfig, lowerDiagonal, upperDiagonal, algoTag, TracebackConfig_<SingleTrace, GapsLeft>());
+        return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, LinearGaps());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
diff --git a/seqan/align/dp_trace_segment.h b/seqan/align/dp_trace_segment.h
index c2fb366..a469ee5 100644
--- a/seqan/align/dp_trace_segment.h
+++ b/seqan/align/dp_trace_segment.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // user-defined structure, such as Align or AlignmentGraph objects.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_
 
 namespace seqan {
 
@@ -338,4 +338,4 @@ inline void _recordSegment(TTraceSegments & traceSegments,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_
diff --git a/seqan/align/dp_traceback_adaptor.h b/seqan/align/dp_traceback_adaptor.h
index e06674f..040daac 100644
--- a/seqan/align/dp_traceback_adaptor.h
+++ b/seqan/align/dp_traceback_adaptor.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // alignment representing structure.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
 
 namespace seqan {
 
@@ -47,12 +47,7 @@ namespace seqan {
 template <typename TFile, typename TSeq0Value, typename TSeq1Value>
 inline void _writeTraceSegmentToFile(TFile & file, TSeq0Value const & seq0Val, TSeq1Value const & seq1Val)
 {
-    streamPut(file, '(');
-    streamPut(file, seq0Val);
-    streamPut(file, ',');
-    streamPut(file, seq1Val);
-    streamPut(file, ')');
-    streamPut(file, '\n');
+    file << '(' << seq0Val << ',' << seq1Val << ")\n";
 }
 
 // ----------------------------------------------------------------------------
@@ -144,13 +139,9 @@ _adaptTraceSegmentsTo(Graph<Alignment<TStringSet, TCargo, TSpec> > & g,
     // insert leading gaps
     TTraceSegment traceBegin = traceSegments[length(traceSegments) - 1];
     if (_getBeginVertical(traceBegin) != 0)
-    {
         addVertex(g, seqVId, 0, _getBeginVertical(traceBegin));
-    }
     if (_getBeginHorizontal(traceBegin) != 0)
-    {
         addVertex(g, seqHId, 0, _getBeginHorizontal(traceBegin));
-    }
 
 
     for (TSize i = 0; i < length(traceSegments); ++i)
@@ -169,22 +160,19 @@ _adaptTraceSegmentsTo(Graph<Alignment<TStringSet, TCargo, TSpec> > & g,
 
         case TraceBitMap_::HORIZONTAL:
             addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length);
-            break;
         }
     }
 
     // insert trailing gaps
     TTraceSegment traceEnd = traceSegments[0];
+
     if (_getEndVertical(traceEnd) != length(value(stringSet(g), idToPosition(stringSet(g), seqVId))))
-    {
         addVertex(g, seqVId, _getEndVertical(traceEnd),
                   length(value(stringSet(g), idToPosition(stringSet(g), seqVId))) - _getEndVertical(traceEnd));
-    }
+
     if (_getEndHorizontal(traceEnd) != length(value(stringSet(g), idToPosition(stringSet(g), seqHId))))
-    {
         addVertex(g, seqHId, _getEndHorizontal(traceEnd),
                   length(value(stringSet(g), idToPosition(stringSet(g), seqHId))) - _getEndHorizontal(traceEnd));
-    }
 }
 
 // ----------------------------------------------------------------------------
@@ -203,34 +191,29 @@ _adaptTraceSegmentsTo(TFile & file,
     {
         switch (traceSegments[k - 1]._traceValue)
         {
-        case TraceBitMap_::DIAGONAL:
-        {
-            int j = traceSegments[k - 1]._verticalBeginPos;
-            for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontalBeginPos + traceSegments[k - 1]._length); ++i)
+            case TraceBitMap_::DIAGONAL:
             {
-                _writeTraceSegmentToFile(file, seqH[i], seqV[j]);
-                ++j;
+                int j = traceSegments[k - 1]._verticalBeginPos;
+                for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontalBeginPos + traceSegments[k - 1]._length); ++i)
+                {
+                    _writeTraceSegmentToFile(file, seqH[i], seqV[j]);
+                    ++j;
+                }
+                break;
             }
-            break;
-        }
 
-        case TraceBitMap_::VERTICAL:
-        {
-            for (int i = traceSegments[k - 1]._verticalBeginPos; i < (int) (traceSegments[k - 1]._verticalBeginPos + traceSegments[k - 1]._length); ++i)
+            case TraceBitMap_::VERTICAL:
             {
-                _writeTraceSegmentToFile(file, gapValue<char>(), seqV[i]);
+                for (int i = traceSegments[k - 1]._verticalBeginPos; i < (int) (traceSegments[k - 1]._verticalBeginPos + traceSegments[k - 1]._length); ++i)
+                    _writeTraceSegmentToFile(file, gapValue<char>(), seqV[i]);
+                break;
             }
-            break;
-        }
 
-        case TraceBitMap_::HORIZONTAL:
-        {
-            for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontalBeginPos + traceSegments[k - 1]._length); ++i)
+            case TraceBitMap_::HORIZONTAL:
             {
-                _writeTraceSegmentToFile(file, seqH[i], gapValue<char>());
+                for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontalBeginPos + traceSegments[k - 1]._length); ++i)
+                    _writeTraceSegmentToFile(file, seqH[i], gapValue<char>());
             }
-            break;
-        }
         }
     }
 }
@@ -250,20 +233,16 @@ _adaptTraceSegmentsTo(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & matc
     typedef Fragment<TSize, TFragmentSpec> TFragment;
 
     for (TSize2 i = 0; i < length(traceSegments); ++i)
-    {
         if (traceSegments[i]._traceValue == TraceBitMap_::DIAGONAL)
-        {
             appendValue(
                 matches,
                 TFragment(seqHId, traceSegments[i]._horizontalBeginPos, seqVId,
                           traceSegments[i]._verticalBeginPos, traceSegments[i]._length),
                 Generous());
-        }
-    }
 }
 
 // ----------------------------------------------------------------------------
-// Function _adaptTraceSegmentsTo()						     [VertexDescriptor]
+// Function _adaptTraceSegmentsTo()                             [VertexDescriptor]
 // ----------------------------------------------------------------------------
 
 //// TODO (rmaerker): Check if we really need this!
@@ -339,4 +318,4 @@ _adaptTraceSegmentsTo(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & matc
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
diff --git a/seqan/align/dp_traceback_impl.h b/seqan/align/dp_traceback_impl.h
index 5ae7587..b10e221 100644
--- a/seqan/align/dp_traceback_impl.h
+++ b/seqan/align/dp_traceback_impl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Implements the traceback algorithm.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
 
 // TODO(holtgrew): GapsRight traceback is currently untested.
 // TODO(rmaerker): Change Tracback to TraceConfig<TGapsPlacement, TPathSpec> | TraceBackOff
@@ -69,7 +69,7 @@ class TracebackCoordinator_
     template <typename TBandFlag, typename TSizeH, typename TSizeV>
     TracebackCoordinator_(TPosition currColumn,
                           TPosition currRow,
-                          DPBand_<TBandFlag> const & band,
+                          DPBandConfig<TBandFlag> const & band,
                           TSizeH seqHSize,
                           TSizeV seqVSize)
         : _currColumn(currColumn),
@@ -88,7 +88,7 @@ class TracebackCoordinator_
                           TPosition currRow,
                           TPosition endColumn,
                           TPosition endRow,
-                          DPBand_<TBandFlag> const & band,
+                          DPBandConfig<TBandFlag> const & band,
                           TSizeH seqHSize,
                           TSizeV seqVSize)
         : _currColumn(currColumn),
@@ -144,11 +144,11 @@ _hasReachedEnd(TracebackCoordinator_<TPosition> const & coordinator)
 template <typename TPosition, typename TBandFlag, typename TSizeH, typename TSizeV>
 inline void
 _initTracebackCoordinator(TracebackCoordinator_<TPosition> & coordinator,
-                          DPBand_<TBandFlag> const & band,
+                          DPBandConfig<TBandFlag> const & band,
                           TSizeH seqHSize,
                           TSizeV seqVSize)
 {
-    typedef typename Position<DPBand_<TBandFlag> >::Type TBandPosition;
+    typedef typename Position<DPBandConfig<TBandFlag> >::Type TBandPosition;
     if (IsSameType<TBandFlag, BandOn>::VALUE)
     {
         // Adapt the current column value when the lower diagonal is positive (shift right in horizontal direction).
@@ -204,7 +204,7 @@ _doTracebackGoDiagonal(TTarget & target,
     {
         _recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength,
                        lastTraceValue);
-        
+
         lastTraceValue = TraceBitMap_::DIAGONAL;
         fragmentLength = 0;
     }
@@ -469,7 +469,7 @@ _retrieveInitialTraceDirection(TTraceValue & traceValue, TDPProfile const & /*dp
             traceValue &= (TraceBitMap_::HORIZONTAL | TraceBitMap_::HORIZONTAL_OPEN | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX);
             return TraceBitMap_::HORIZONTAL;
         }
-        return TraceBitMap_::DIAGONAL;  // We set the last value to the 
+        return TraceBitMap_::DIAGONAL;  // We set the last value to the
     }
 
     if (traceValue & TraceBitMap_::DIAGONAL)
@@ -493,7 +493,7 @@ void _computeTraceback(TTarget & target,
                        unsigned  maxHostPosition,
                        TSequenceH const & seqH,
                        TSequenceV const & seqV,
-                       DPBand_<TBandFlag> const & band,
+                       DPBandConfig<TBandFlag> const & band,
                        DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec> const & dpProfile)
 {
     typedef typename Container<TDPTraceMatrixNavigator>::Type TContainer;
@@ -561,7 +561,7 @@ void _computeTraceback(TTarget & target,
                        DPScout_<TDPCell, TScoutSpec> const & dpScout,
                        TSequenceH const & seqH,
                        TSequenceV const & seqV,
-                       DPBand_<TBandFlag> const & band,
+                       DPBandConfig<TBandFlag> const & band,
                        DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec> const & dpProfile)
 {
     _computeTraceback(target, matrixNavigator, maxHostPosition(dpScout), seqH, seqV, band, dpProfile);
@@ -569,4 +569,4 @@ void _computeTraceback(TTarget & target,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_
diff --git a/seqan/align/evaluate_alignment.h b/seqan/align/evaluate_alignment.h
index 076a446..b01b89b 100644
--- a/seqan/align/evaluate_alignment.h
+++ b/seqan/align/evaluate_alignment.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Compute alignment score given a pairwise alignment.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_
-#define CORE_INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_
+#ifndef INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_
+#define INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_
 
 namespace seqan {
 
@@ -56,7 +56,19 @@ namespace seqan {
  * @headerfile <seqan/align.h>
  * @brief Statistics about a tabular alignment.
  *
- * The default constructor initializes all members to 0.
+ * @signature struct AlignmentStats;
+ *
+ * @see computeAlignmentStats
+ *
+ * @fn AlignmentStats::AlignmentStats
+ * @brief Constructor
+ *
+ * @signature AlignmentStats::AlignmentStats();
+ *
+ * All members are initialized to <tt>0</tt>.
+ *
+ * @var unsigned AlignmentStats::numGaps;
+ * @brief Number of gap characters (sum of numGapOpens and numGapExtensions)
  *
  * @var unsigned AlignmentStats::numGapOpens;
  * @brief Number of gap open events.
@@ -64,6 +76,12 @@ namespace seqan {
  * @var unsigned AlignmentStats::numGapExtensions;
  * @brief Number of gap extension events.
  *
+ * @var unsigned AlignmentStats::numInsertions;
+ * @brief Number of gaps in reference relative to query.
+ *
+ * @var unsigned AlignmentStats::numDeletions;
+ * @brief Number of gaps in query relative to reference.
+ *
  * @var unsigned AlignmentStats::numMatches;
  * @brief Number of match (identity) events.
  *
@@ -76,15 +94,28 @@ namespace seqan {
  * @var unsigned AlignmentStats::numNegativeScores;
  * @brief Number of residues aligned with negative score.
  *
+ * @var unsigned AlignmentStats::alignmentLength;
+ * @brief Length of the aligned region
+ *
+ * @var float AlignmentStats::alignmentSimilarity;
+ * @brief The resulting alignment percent similarity (positive).
+ *
+ * @var float AlignmentStats::alignmentIdentity;
+ * @brief The resulting alignment percent identity (match).
+ *
  * @var int AlignmentStats::alignmentScore;
  * @brief The resulting alignment score.
  */
 
 struct AlignmentStats
 {
-    // Number of gap opens/gap extensions.
+    // Number of gap characters/opens/gap extensions.
+    unsigned numGaps;
     unsigned numGapOpens;
     unsigned numGapExtensions;
+    // Number of insertions and deletions.
+    unsigned numInsertions;
+    unsigned numDeletions;
     // Number of matches, mismatches.
     unsigned numMatches;
     unsigned numMismatches;
@@ -92,11 +123,19 @@ struct AlignmentStats
     unsigned numPositiveScores;
     unsigned numNegativeScores;
 
+    // length of the alignment
+    unsigned alignmentLength;
+
+    // the alignment identity and similarity scores
+    float alignmentSimilarity;
+    float alignmentIdentity;
+
     // The alignment score.
     int alignmentScore;
 
-    AlignmentStats() : numGapOpens(0), numGapExtensions(0), numMatches(0), numMismatches(0),
-                       numPositiveScores(0), numNegativeScores(0), alignmentScore(0)
+    AlignmentStats() : numGaps(0), numGapOpens(0), numGapExtensions(0), numInsertions(0), numDeletions(0),
+                       numMatches(0), numMismatches(0), numPositiveScores(0), numNegativeScores(0),
+                       alignmentLength(0), alignmentSimilarity(0.0), alignmentIdentity(0.0), alignmentScore(0)
     {}
 };
 
@@ -114,7 +153,7 @@ struct AlignmentStats
 
 /*!
  * @fn AlignmentStats#clear
- * @brief Clear AlignmentStats object.
+ * @brief Resets all members to <tt>0</tt>.
  *
  * @signature void clear(stats);
  *
@@ -124,12 +163,18 @@ struct AlignmentStats
 inline
 void clear(AlignmentStats & stats)
 {
+    stats.numGaps = 0;
     stats.numGapOpens = 0;
     stats.numGapExtensions = 0;
+    stats.numInsertions = 0;
+    stats.numDeletions = 0;
     stats.numMatches = 0;
     stats.numMismatches = 0;
     stats.numPositiveScores = 0;
     stats.numNegativeScores = 0;
+    stats.alignmentLength = 0;
+    stats.alignmentSimilarity = 0.0;
+    stats.alignmentIdentity = 0.0;
     stats.alignmentScore = 0;
 }
 
@@ -142,42 +187,47 @@ void clear(AlignmentStats & stats)
  * @headerfile <seqan/align.h>
  * @brief Compute alignment statistics.
  *
- * @signature TScoreVal computeAlignmentStats([stats, ]align, scoringScheme);
+ * @signature TScoreVal computeAlignmentStats(stats, align, scoringScheme);
+ * @signature TScoreVal computeAlignmentStats(stats, row0, row1, scoringScheme);
  *
  * @param[out] stats The @link AlignmentStats @endlink object to store alignment statistics in.
  * @param[in]  align The @link Align @endlink object to score.
+ * @param[in]  row0  The first row (@link Gaps @endlink object).
+ * @param[in]  row1  The second row (@link Gaps @endlink object).
  * @param[in]  score The @link Score @endlink object to use for the scoring scheme.
  *
+ * @return TScoreVal The score value of the alignment, of the same type as the value type of <tt>scoringScheme</tt>
+ *
  * @see AlignmentStats
  *
  * @section Examples
  *
- * @include demos/align/compute_alignment_stats.cpp
+ * @include demos/dox/align/compute_alignment_stats.cpp
  *
  * The output is as follows:
  *
- * @include demos/align/compute_alignment_stats.cpp.stdout
+ * @include demos/dox/align/compute_alignment_stats.cpp.stdout
  */
 
-template <typename TSource, typename TAlignSpec, typename TScoreVal, typename TScoreSpec>
+template <typename TSource0, typename TGapsSpec0,
+          typename TSource1, typename TGapsSpec1,
+          typename TScoreVal, typename TScoreSpec>
 TScoreVal computeAlignmentStats(AlignmentStats & stats,
-                                Align<TSource, TAlignSpec> const & align,
+                                Gaps<TSource0, TGapsSpec0> const & row0,
+                                Gaps<TSource1, TGapsSpec1> const & row1,
                                 Score<TScoreVal, TScoreSpec> const & scoringScheme)
 {
-    SEQAN_ASSERT_EQ_MSG(length(rows(align)), 2u, "Only works with pairwise alignments.");
-    SEQAN_ASSERT_EQ_MSG(length(row(align, 0)), length(row(align, 1)), "Invalid alignment!");
     clear(stats);
 
-    typedef Align<TSource, TAlignSpec> const TAlign;
-    typedef typename Row<TAlign>::Type TGaps;
-    typedef typename Iterator<TGaps, Standard>::Type TGapsIter;
-    typedef typename Value<typename Source<TGaps>::Type>::Type TAlphabet;
+    typedef typename Iterator<Gaps<TSource0, TGapsSpec0> const, Standard>::Type TGapsIter0;
+    typedef typename Iterator<Gaps<TSource1, TGapsSpec1> const, Standard>::Type TGapsIter1;
+    typedef typename Value<TSource0>::Type TAlphabet;
 
     // Get iterators.
-    TGapsIter it0 = begin(row(align, 0));
-    TGapsIter itEnd0 = end(row(align, 0));
-    TGapsIter it1 = begin(row(align, 1));
-    TGapsIter itEnd1 = end(row(align, 1));
+    TGapsIter0 it0      = begin(row0);
+    TGapsIter0 itEnd0   = end(row0);
+    TGapsIter1 it1      = begin(row1);
+    TGapsIter1 itEnd1   = end(row1);
 
     // State whether we have already opened a gap.
     bool isGapOpen0 = false, isGapOpen1 = false;
@@ -186,7 +236,7 @@ TScoreVal computeAlignmentStats(AlignmentStats & stats,
     {
         if (isGap(it0))
         {
-            if (isGapOpen0)
+            if (!isGapOpen0)
             {
                 stats.numGapOpens += 1;
                 stats.alignmentScore += scoreGapOpen(scoringScheme);
@@ -196,6 +246,7 @@ TScoreVal computeAlignmentStats(AlignmentStats & stats,
                 stats.numGapExtensions += 1;
                 stats.alignmentScore += scoreGapExtend(scoringScheme);
             }
+            stats.numDeletions += 1;
             isGapOpen0 = true;
         }
         else
@@ -215,6 +266,7 @@ TScoreVal computeAlignmentStats(AlignmentStats & stats,
                 stats.numGapExtensions += 1;
                 stats.alignmentScore += scoreGapExtend(scoringScheme);
             }
+            stats.numInsertions += 1;
             isGapOpen1 = true;
         }
         else
@@ -225,12 +277,13 @@ TScoreVal computeAlignmentStats(AlignmentStats & stats,
         if (!isGap(it0) && !isGap(it1))
         {
             // Compute the alignment score and register in stats.
-            TAlphabet c0 = *it0, c1 = *it1;
+            TAlphabet c0 = *it0;
+            TAlphabet c1 = static_cast<TAlphabet>(*it1);
             TScoreVal scoreVal = score(scoringScheme, c0, c1);
             stats.alignmentScore += scoreVal;
             // Register other statistics.
             bool isMatch = (c0 == c1);
-            bool isPositive = (scoreVal >= 0);
+            bool isPositive = (scoreVal > 0);
             stats.numMatches += isMatch;
             stats.numMismatches += !isMatch;
             stats.numPositiveScores += isPositive;
@@ -240,9 +293,30 @@ TScoreVal computeAlignmentStats(AlignmentStats & stats,
     SEQAN_ASSERT(it0 == itEnd0);
     SEQAN_ASSERT(it1 == itEnd1);
 
+    stats.numGaps = stats.numGapOpens + stats.numGapExtensions;
+
+    // Finally, compute the alignment similarity from the various counts
+    stats.alignmentLength = length(row0);
+    stats.alignmentSimilarity = 100.0 * static_cast<float>(stats.numPositiveScores)
+                                / static_cast<float>(stats.alignmentLength);
+    stats.alignmentIdentity = 100.0 * static_cast<float>(stats.numMatches)
+                              / static_cast<float>(stats.alignmentLength);
+
     return stats.alignmentScore;
 }
 
+template <typename TSource, typename TAlignSpec, typename TScoreVal, typename TScoreSpec>
+TScoreVal computeAlignmentStats(AlignmentStats & stats,
+                                Align<TSource, TAlignSpec> const & align,
+                                Score<TScoreVal, TScoreSpec> const & scoringScheme)
+{
+    SEQAN_ASSERT_EQ_MSG(length(rows(align)), 2u, "Only works with pairwise alignments.");
+    SEQAN_ASSERT_EQ_MSG(length(row(align, 0)), length(row(align, 1)), "Invalid alignment!");
+
+    return computeAlignmentStats(stats, row(align, 0), row(align, 1), scoringScheme);
+}
+
+// NOTE(h-2): this interface is deprecated. Don't use it.
 template <typename TGaps, typename TAlignSpec, typename TScoreVal, typename TScoreSpec>
 TScoreVal computeAlignmentStats(Align<TGaps, TAlignSpec> const & align,
                                 Score<TScoreVal, TScoreSpec> const & scoringScheme)
@@ -254,4 +328,4 @@ TScoreVal computeAlignmentStats(Align<TGaps, TAlignSpec> const & align,
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_
+#endif  // #ifndef INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_
diff --git a/seqan/graph_types/graph_impl_fragment.h b/seqan/align/fragment.h
similarity index 62%
rename from seqan/graph_types/graph_impl_fragment.h
rename to seqan/align/fragment.h
index fa3a65c..dcdb6ac 100644
--- a/seqan/graph_types/graph_impl_fragment.h
+++ b/seqan/align/fragment.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,14 +29,15 @@
 // DAMAGE.
 //
 // ==========================================================================
+// Author: Tobias Rausch <rausch@embl.de>
+// ==========================================================================
 
-#ifndef SEQAN_HEADER_GRAPH_IMPL_FRAGMENT_H
-#define SEQAN_HEADER_GRAPH_IMPL_FRAGMENT_H
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_FRAGMENT_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_FRAGMENT_H_
 
-namespace SEQAN_NAMESPACE_MAIN
+namespace seqan
 {
 
-
 //////////////////////////////////////////////////////////////////////////////
 // Fragment Specs
 //////////////////////////////////////////////////////////////////////////////
@@ -44,7 +45,7 @@ namespace SEQAN_NAMESPACE_MAIN
 /*!
  * @class ExactFragment
  * @extends Fragment
- * @headerfile <seqan/graph_types.h>
+ * @headerfile <seqan/align.h>
  * @brief A type for ungapped, pairwise segment matches.
  *
  * @signature template <[typename TSize[, typename TSpec]]>
@@ -54,28 +55,14 @@ namespace SEQAN_NAMESPACE_MAIN
  * @tparam TSpec Specializing type.  Default: <tt>ExactFragment&lt;&gt;</tt>.
  */
 
-/**
-.Spec.ExactFragment
-..cat:Alignments
-..general:Class.Fragment
-..summary:A type for ungapped, pairwise segment matches.
-..signature:Fragment<TSize, ExactFragment<TSpec> > 
-..param.TSize: The Size type of the underlying sequences.
-...metafunction:Metafunction.Size
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-..include:seqan/graph_types.h
-..see:Spec.ExactReversableFragment
-*/
-
 template<typename TSpec = Default>
-struct ExactFragment;	
+struct ExactFragment;
 
 
 /*!
  * @class ExactReversableFragment
  * @extends Fragment
- * @headerfile <seqan/graph_types.h>
+ * @headerfile <seqan/align.h>
  * @brief A type for ungapped, pairwise segment matches that maybe in reverse orientation.
  *
  * Compared to the @link ExactFragment @endlink specialzing type of @link Fragment @endlink, a @link
@@ -89,23 +76,8 @@ struct ExactFragment;
  * @tparam TSpec Specializing type.  Default: <tt>ExactFragment&lt;&gt;</tt>.
  */
 
-/**
-.Spec.ExactReversableFragment
-..cat:Alignments
-..general:Class.Fragment
-..summary:A type for ungapped, pairwise segment matches that may be in reverse orientation.
-..signature:Fragment<TSize, ExactReversableFragment<TSpec> > 
-..param.TSize: The Size type of the underlying sequences.
-...metafunction:Metafunction.Size
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-..remarks:Compared to the @Spec.ExactFragment@ specialzing type of @Class.Fragment@, a @Spec.ExactReversableFragment@ stores an additional bool value to indicate whether a match is in reverse orientation or not.
-..include:seqan/graph_types.h
-..see:Spec.ExactFragment
-*/
-
 template<typename TSpec = Default>
-struct ExactReversableFragment;	
+struct ExactReversableFragment;
 
 
 //////////////////////////////////////////////////////////////////////////////
@@ -114,7 +86,7 @@ struct ExactReversableFragment;
 
 /*!
  * @class Fragment
- * @headerfile <seqan/graph_types.h>
+ * @headerfile <seqan/align.h>
  * @brief A type for pairwise segment matches.
  *
  * @signature template <[typename TSize[, typename TSpec]]>
@@ -129,7 +101,7 @@ struct ExactReversableFragment;
  * // Construct fragment.
  * unsigned seqId1 = 0, beg1 = 0, seqId2 = 32, beg2 = 42, len = 33;
  * Fragment<> fragment(seqId1, beg1, seqId2, beg2, len);
- * 
+ *
  * // Update fragment's properties.
  * fragmentBegin(fragment, 0) = 10;
  * fragmentBegin(fragment, 1) = 10;
@@ -139,31 +111,6 @@ struct ExactReversableFragment;
  * @endcode
  */
 
-/**
-.Class.Fragment:
-..cat:Alignments
-..summary:A type for ungapped, pairwise segment matches.
-..signature:Fragment<TSize, TSpec>
-..param.TSize:The size type of the underlying sequences.
-...metafunction:Metafunction.Size
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:@Spec.ExactFragment@
-..include:seqan/graph_types.h
-..example:A small example using fragments.
-..example.code:
-// Construct fragment.
-unsigned seqId1 = 0, beg1 = 0, seqId2 = 32, beg2 = 42, len = 33;
-Fragment<> fragment(seqId1, beg1, seqId2, beg2, len);
-
-// Update fragment's properties.
-fragmentBegin(fragment, 0) = 10;
-fragmentBegin(fragment, 1) = 10;
-sequenceId(fragment, 0) = 33;
-sequenceId(fragment, 1) = 44;
-fragmentLength(fragment) += 42;
-*/
-
 
 template<typename TSize = typename Size<String<char> >::Type, typename TSpec = ExactFragment<> >
 class Fragment;
@@ -175,20 +122,20 @@ class Fragment;
 
 template<typename TSize, typename TSpec>
 struct Size<Fragment<TSize, TSpec> > {
-	typedef TSize Type;
+    typedef TSize Type;
 };
 
 
 template<typename TSize, typename TSpec>
 struct Size<Fragment<TSize, TSpec> const> {
-	typedef TSize Type;
+    typedef TSize Type;
 };
 
 
 //////////////////////////////////////////////////////////////////////////////
 // Exact Fragment
 //////////////////////////////////////////////////////////////////////////////
-	
+
 
 template<typename TSize, typename TSpec>
 class Fragment<TSize, ExactFragment<TSpec> > {
@@ -214,26 +161,11 @@ class Fragment<TSize, ExactFragment<TSpec> > {
  * @param[in] beg2    Begin position of segment match in second sequence.  Type: <tt>TSize</tt>.
  * @param[in] l       The length of the segment match.  Type: <tt>TSize</tt>.
  */
-  
-/**
-.Memfunc.ExactFragment#Fragment:
-..class:Spec.ExactFragment
-..summary:Constructor.
-..signature:Fragment()
-..signature:Fragment(seqId1, beg1, seqId2, beg2, len)
-..param.seqId1:The id of the first sequence.
-...type:Metafunction.Id
-..param.beg1:The TSize begin position on the first sequence.
-..param.seqId2:The id of the second sequence.
-...type:Metafunction.Id
-..param.beg2:The TSize begin position on the second sequence.
-..param.len:The TSize length of the segment match.
-*/
 
     Fragment() : seqId1(0), begin1(0), seqId2(0), begin2(0), len(0) {}
 
     Fragment(TId sqId1, TSize beg1, TId sqId2, TSize beg2, TSize l) :
-            seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l) 
+            seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l)
     {}
 
 };
@@ -281,7 +213,7 @@ operator<(Fragment<TSize, ExactFragment<TSpec> > const & left,
 //////////////////////////////////////////////////////////////////////////////
 // Exact Fragment that is a forward or reverse match
 //////////////////////////////////////////////////////////////////////////////
-	
+
 
 template<typename TSize, typename TSpec>
 class Fragment<TSize, ExactReversableFragment<TSpec> > {
@@ -310,32 +242,15 @@ class Fragment<TSize, ExactReversableFragment<TSpec> > {
  * @param[in] reversed A bool; <tt>true</tt> if the segments match in reverse orientation, <tt>false</tt> otherwise.
  */
 
-/**
-.Memfunc.ExactReversableFragment#Fragment:
-..class:Spec.ExactReversableFragment
-..summary:Constructor.
-..signature:Fragment()
-..signature:Fragment(seqId1, beg1, seqId2, beg2, len[, reversed])
-..param.seqId1:The id of the first sequence.
-...type:Metafunction.Id
-..param.beg1:The TSize begin position on the first sequence.
-..param.seqId2:The id of the second sequence.
-...type:Metafunction.Id
-..param.beg2:The TSize begin position on the second sequence.
-..param.len:The TSize length of the segment match.
-..param.reversed:$true$ if the segments match in reverse orientation, $false$ otherwise.
-...default:$false$
-...type:nolink:$bool$
-*/
-    
+
     Fragment() : seqId1(0), begin1(0), seqId2(0), begin2(0), len(0), reversed(false) {}
-    
+
     Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l) :
-            seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l), reversed(false) 
+            seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l), reversed(false)
     {}
-	
+
     Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l, bool rev) :
-            seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l), reversed(rev) 
+            seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l), reversed(rev)
     {}
 };
 
@@ -397,25 +312,15 @@ operator<(Fragment<TSize, ExactReversableFragment<TSpec> > const & left,
  * @param[in] seqID     The id of the sequence for which the label should be retrieved.
  */
 
-/**
-.Function.label
-..class:Class.Fragment
-..signature:label(f,str,seqId)
-..param.f:A fragment.
-...type:Class.Fragment
-..param.str:The string set underlying the fragment.
-..param.seqId:The id of the sequence for which the label should be retrieved.
-...remarks:
-*/
 template<typename TSize, typename TSpec, typename TStringSet, typename TVal>
 inline typename Infix<typename Value<TStringSet>::Type>::Type
 label(Fragment<TSize, TSpec> const& f,
       TStringSet& str,
       TVal const seqId)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
-	return ((TId) seqId == (f.seqId1)) ? infix(getValueById(str, (TId) seqId), f.begin1, f.begin1 + f.len) : infix(getValueById(str, (TId) seqId), f.begin2, f.begin2 + f.len);
+    SEQAN_CHECKPOINT
+    typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
+    return ((TId) seqId == (f.seqId1)) ? infix(getValueById(str, (TId) seqId), f.begin1, f.begin1 + f.len) : infix(getValueById(str, (TId) seqId), f.begin2, f.begin2 + f.len);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -434,30 +339,21 @@ label(Fragment<TSize, TSpec> const& f,
  * @return TId Reference to the sequence fragment id member.
  */
 
-/**
-.Function.sequenceId
-..class:Class.Fragment
-..signature:sequenceId(f,seqNum)
-..param.f:A fragment.
-...type:Class.Fragment
-..param.seqNum:The sequence number for which the id should be retrieved.
-...remarks:Note that @Class.Fragment@ stores information about exactly two sequences which can be accessed with seqNum 0 or 1, but whose ids may differ from their seqNum.
-*/
 template<typename TSize, typename TSpec, typename TVal>
 inline typename Id<Fragment<TSize, TSpec> >::Type &
 sequenceId(Fragment<TSize, TSpec> const& f,
-		   TVal const seqId)
+           TVal const seqId)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
-	return ((TId) seqId == 0) ? const_cast<TId &>(f.seqId1) : const_cast<TId &>(f.seqId2);
+    SEQAN_CHECKPOINT
+    typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
+    return ((TId) seqId == 0) ? const_cast<TId &>(f.seqId1) : const_cast<TId &>(f.seqId2);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn Fragment#fragmentBegin
- * @label Return fragment begin.
+ * @brief Return fragment begin.
  *
  * @signature TSize fragmentBegin(frag, seqId);
  *
@@ -467,23 +363,14 @@ sequenceId(Fragment<TSize, TSpec> const& f,
  * @return TSize Reference to the fragment begin position member.
  */
 
-/**
-.Function.fragmentBegin
-..class:Class.Fragment
-..signature:fragmentBegin(f, seqId)
-..param.f:A fragment.
-...type:Class.Fragment
-..param.seqId:The sequence id for which the begin position should be retrieved.
-...remarks:Retrieve with @Function.sequenceId@.
-*/
 template<typename TSize, typename TSpec, typename TVal>
 inline TSize&
 fragmentBegin(Fragment<TSize, TSpec> const& f,
-			  TVal const seqId)
+              TVal const seqId)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
-	return ((TId) seqId == f.seqId1) ? const_cast<TSize&>(f.begin1) : const_cast<TSize&>(f.begin2);
+    SEQAN_CHECKPOINT
+    typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
+    return ((TId) seqId == f.seqId1) ? const_cast<TSize&>(f.begin1) : const_cast<TSize&>(f.begin2);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -491,10 +378,10 @@ fragmentBegin(Fragment<TSize, TSpec> const& f,
 template<typename TSize, typename TSpec, typename TVal>
 inline TSize&
 fragmentLength(Fragment<TSize, TSpec> const& f,
-			   TVal const)
+               TVal const)
 {
-	SEQAN_CHECKPOINT
-	return const_cast<TSize&>(f.len);
+    SEQAN_CHECKPOINT
+    return const_cast<TSize&>(f.len);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -510,65 +397,40 @@ fragmentLength(Fragment<TSize, TSpec> const& f,
  * @return TSize Reference to the Fragment's length.
  */
 
-/**
-.Function.fragmentLength
-..class:Class.Fragment
-..signature:fragmentBegin(f)
-..param.f:A fragment.
-...type:Class.Fragment
-*/
 template<typename TSize, typename TSpec>
 inline TSize&
 fragmentLength(Fragment<TSize, TSpec> const& f)
 {
-	SEQAN_CHECKPOINT
-	return const_cast<TSize&>(f.len);
+    SEQAN_CHECKPOINT
+    return const_cast<TSize&>(f.len);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.getProjectedPosition
-..cat:Alignments
-..class:Class.Fragment
-..signature:getProjectedPosition(f,seqId,pos,seqId2,pos2)
-..summary:Projects a position of one sequence taking part in a pairwise match onto the other sequence.
-..signature:getProjectedPosition(f,seqId1,pos1,seqId2,pos2)
-..param.f:A fragment.
-...type:Class.Fragment
-..param.seqId:The id of the sequence to project from.
-...type:Metafunction.Id
-..param.pos:The position to project.
-...type:Metafunction.Size
-..param.seqId2:The resulting id of the sequence that pos was projected onto.
-...type:Metafunction.Id
-..param.pos2:The resulting projected position.
-...type:Metafunction.Size
-*/
 template<typename TSize, typename TSpec, typename TId1, typename TPosition1, typename TId2, typename TPosition2>
 inline void
 getProjectedPosition(Fragment<TSize, ExactFragment<TSpec> > const& f,
-					 TId1 const seqId,
-					 TPosition1 const pos,
-					 TId2& seqId2,
-					 TPosition2& pos2)
+                     TId1 const seqId,
+                     TPosition1 const pos,
+                     TId2& seqId2,
+                     TPosition2& pos2)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
-	
-	if ((TId) seqId == f.seqId1) {
-		SEQAN_ASSERT((TPosition1)f.begin1<=pos);
-		SEQAN_ASSERT(pos - f.begin1 < f.len)	;
-		pos2 = f.begin2 + (pos - f.begin1);
-		seqId2 = f.seqId2;
-		return;
-	} else {
-		SEQAN_ASSERT((TPosition1)f.begin2<=pos);
-		SEQAN_ASSERT(pos - f.begin2 < f.len);
-		pos2 = f.begin1 + (pos - f.begin2);
-		seqId2 = f.seqId1;
-		return;
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
+
+    if ((TId) seqId == f.seqId1) {
+        SEQAN_ASSERT((TPosition1)f.begin1<=pos);
+        SEQAN_ASSERT(pos - f.begin1 < f.len)    ;
+        pos2 = f.begin2 + (pos - f.begin1);
+        seqId2 = f.seqId2;
+        return;
+    } else {
+        SEQAN_ASSERT((TPosition1)f.begin2<=pos);
+        SEQAN_ASSERT(pos - f.begin2 < f.len);
+        pos2 = f.begin1 + (pos - f.begin2);
+        seqId2 = f.seqId1;
+        return;
+    }
 }
 
 
@@ -577,28 +439,28 @@ getProjectedPosition(Fragment<TSize, ExactFragment<TSpec> > const& f,
 template<typename TSize, typename TSpec, typename TValue, typename TId1, typename TPosition1, typename TId2, typename TPosition2>
 inline void
 getProjectedPosition(Fragment<TSize, ExactFragment<TSpec> > const& f,
-					TValue seg_num,
-					 TId1 const seqId,
-					 TPosition1 const pos,
-					 TId2& seqId2,
-					 TPosition2& pos2)
+                    TValue seg_num,
+                     TId1 const seqId,
+                     TPosition1 const pos,
+                     TId2& seqId2,
+                     TPosition2& pos2)
 {
-	(void) seqId;  // When compiled without assertions.
-	SEQAN_ASSERT((seg_num == 0 && seqId == f.seqId1) || (seg_num == 1 && seqId == f.seqId2));
-
-	if (seg_num == 0) {
-		SEQAN_ASSERT((TPosition1)f.begin1<=pos);
-		SEQAN_ASSERT(pos - f.begin1 < f.len)	;
-		pos2 = f.begin2 + (pos - f.begin1);
-		seqId2 = f.seqId2;
-		return;
-	} else {
-		SEQAN_ASSERT((TPosition1)f.begin2<=pos);
-		SEQAN_ASSERT(pos - f.begin2 < f.len);
-		pos2 = f.begin1 + (pos - f.begin2);
-		seqId2 = f.seqId1;
-		return;
-	}
+    (void) seqId;  // When compiled without assertions.
+    SEQAN_ASSERT((seg_num == 0 && seqId == f.seqId1) || (seg_num == 1 && seqId == f.seqId2));
+
+    if (seg_num == 0) {
+        SEQAN_ASSERT((TPosition1)f.begin1<=pos);
+        SEQAN_ASSERT(pos - f.begin1 < f.len)    ;
+        pos2 = f.begin2 + (pos - f.begin1);
+        seqId2 = f.seqId2;
+        return;
+    } else {
+        SEQAN_ASSERT((TPosition1)f.begin2<=pos);
+        SEQAN_ASSERT(pos - f.begin2 < f.len);
+        pos2 = f.begin1 + (pos - f.begin2);
+        seqId2 = f.seqId1;
+        return;
+    }
 }
 
 
@@ -608,29 +470,29 @@ getProjectedPosition(Fragment<TSize, ExactFragment<TSpec> > const& f,
 template<typename TSize, typename TSpec, typename TId1, typename TPosition1, typename TId2, typename TPosition2>
 inline void
 getProjectedPosition(Fragment<TSize, ExactReversableFragment<TSpec> > const& f,
-					 TId1 const seqId,
-					 TPosition1 const pos,
-					 TId2& seqId2,
-					 TPosition2& pos2)
+                     TId1 const seqId,
+                     TPosition1 const pos,
+                     TId2& seqId2,
+                     TPosition2& pos2)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
-	
-	if ((TId) seqId == f.seqId1) {
-		SEQAN_ASSERT((TPosition1)f.begin1<=pos);
-		SEQAN_ASSERT(pos - f.begin1 < f.len)	;
-		if (f.reversed) pos2 = (f.begin2 + f.len - 1) - (pos - f.begin1);
-		else pos2 = f.begin2 + (pos - f.begin1);
-		seqId2 = f.seqId2;
-		return;
-	} else {
-		SEQAN_ASSERT((TPosition1)f.begin2<=pos);
-		SEQAN_ASSERT(pos - f.begin2 < f.len);
-		if (f.reversed) pos2 = (f.begin1 + f.len - 1) - (pos - f.begin2);
-		else pos2 = f.begin1 + (pos - f.begin2);
-		seqId2 = f.seqId1;
-		return;
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Id<Fragment<TSize, TSpec> >::Type TId;
+
+    if ((TId) seqId == f.seqId1) {
+        SEQAN_ASSERT((TPosition1)f.begin1<=pos);
+        SEQAN_ASSERT(pos - f.begin1 < f.len)    ;
+        if (f.reversed) pos2 = (f.begin2 + f.len - 1) - (pos - f.begin1);
+        else pos2 = f.begin2 + (pos - f.begin1);
+        seqId2 = f.seqId2;
+        return;
+    } else {
+        SEQAN_ASSERT((TPosition1)f.begin2<=pos);
+        SEQAN_ASSERT(pos - f.begin2 < f.len);
+        if (f.reversed) pos2 = (f.begin1 + f.len - 1) - (pos - f.begin2);
+        else pos2 = f.begin1 + (pos - f.begin2);
+        seqId2 = f.seqId1;
+        return;
+    }
 }
 
 
@@ -639,31 +501,31 @@ getProjectedPosition(Fragment<TSize, ExactReversableFragment<TSpec> > const& f,
 template<typename TSize, typename TSpec, typename TValue, typename TId1, typename TPosition1, typename TId2, typename TPosition2>
 inline void
 getProjectedPosition(Fragment<TSize, ExactReversableFragment<TSpec> > const& f,
-					 TValue seg_num,
-					 TId1 const seqId,
-					 TPosition1 const pos,
-					 TId2& seqId2,
-					 TPosition2& pos2)
+                     TValue seg_num,
+                     TId1 const seqId,
+                     TPosition1 const pos,
+                     TId2& seqId2,
+                     TPosition2& pos2)
 {
-	SEQAN_CHECKPOINT
-	(void) seqId;  // When compiled without assertions.
-	SEQAN_ASSERT((seg_num == 0 && seqId==f.seqId1) || (seg_num == 1 && seqId==f.seqId2));
-
-	if (seg_num == 0) {
-		SEQAN_ASSERT((TPosition1)f.begin1<=pos);
-		SEQAN_ASSERT(pos - f.begin1 < f.len)	;
-		if (f.reversed) pos2 = (f.begin2 + f.len - 1) - (pos - f.begin1);
-		else pos2 = f.begin2 + (pos - f.begin1);
-		seqId2 = f.seqId2;
-		return;
-	} else {
-		SEQAN_ASSERT((TPosition1)f.begin2<=pos);
-		SEQAN_ASSERT(pos - f.begin2 < f.len);
-		if (f.reversed) pos2 = (f.begin1 + f.len - 1) - (pos - f.begin2);
-		else pos2 = f.begin1 + (pos - f.begin2);
-		seqId2 = f.seqId1;
-		return;
-	}
+    SEQAN_CHECKPOINT
+    (void) seqId;  // When compiled without assertions.
+    SEQAN_ASSERT((seg_num == 0 && seqId==f.seqId1) || (seg_num == 1 && seqId==f.seqId2));
+
+    if (seg_num == 0) {
+        SEQAN_ASSERT((TPosition1)f.begin1<=pos);
+        SEQAN_ASSERT(pos - f.begin1 < f.len)    ;
+        if (f.reversed) pos2 = (f.begin2 + f.len - 1) - (pos - f.begin1);
+        else pos2 = f.begin2 + (pos - f.begin1);
+        seqId2 = f.seqId2;
+        return;
+    } else {
+        SEQAN_ASSERT((TPosition1)f.begin2<=pos);
+        SEQAN_ASSERT(pos - f.begin2 < f.len);
+        if (f.reversed) pos2 = (f.begin1 + f.len - 1) - (pos - f.begin2);
+        else pos2 = f.begin1 + (pos - f.begin2);
+        seqId2 = f.seqId1;
+        return;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -679,22 +541,12 @@ getProjectedPosition(Fragment<TSize, ExactReversableFragment<TSpec> > const& f,
  * @return bool <tt>true</tt> if the fragment is reversed and <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isReversed
-..cat:Alignments
-..class:Class.Fragment
-..signature:isReversed<Fragment<TSize,ExactReversableFragment<TSpec> >(f)
-..summary:Returns true if the segment match is in reverse orientation.
-..signature:isReversed(f)
-..param.f:A fragment.
-...type:Class.Fragment
-*/
 template<typename TSize, typename TSpec>
 inline bool
 isReversed(Fragment<TSize, ExactReversableFragment<TSpec> > const& f)
 {
-	SEQAN_CHECKPOINT
-	return f.reversed;
+    SEQAN_CHECKPOINT
+    return f.reversed;
 }
 
 // Compare lexicographically as tuple.
@@ -716,6 +568,6 @@ inline bool operator>(Fragment<TSize, ExactFragment<TSpec> > const & lhs,
     return false;
 }
 
-}// namespace SEQAN_NAMESPACE_MAIN
+}  // namespace seqan
 
-#endif //#ifndef SEQAN_HEADER_...
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_FRAGMENT_H_
diff --git a/seqan/align/gap_anchor.h b/seqan/align/gap_anchor.h
index 7e82f38..f2c9a14 100644
--- a/seqan/align/gap_anchor.h
+++ b/seqan/align/gap_anchor.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_
 
 namespace seqan {
 
@@ -62,138 +62,116 @@ typedef Tag<SortGapPos_> const SortGapPos;
 
 /*!
  * @class GapAnchor
+ * @implements ComparableConcept
  * @headerfile <seqan/align.h>
- * @brief Stores the position of an alignment character in sequence-space and in gap-space.
- * 
+ * @brief Stores the position of an alignment character in sequence-space and gap-space in @link AnchorGaps @endlink.
+ *
  * @signature template <typename TPosition>
  *            struct GapAnchor;
- * 
+ *
  * @tparam TPos Type to store gapped/ungapped positions.
- * 
+ *
  * @section Remarks
- * 
- * Value types of the <tt>gaps</tt> strings in @link ReadStoreElement @endlink and @link ContigStoreElement @endlink.
+ *
+ * Used as value type for the <tt>gaps</tt> strings in @link ReadStoreElement @endlink and @link ContigStoreElement
+ * @endlink.
+ *
+ * @see AnchorGaps
  */
 
-/**
-.Class.GapAnchor
-..summary:Stores the position of an alignment character in sequence-space and in gap-space.
-..cat:Alignments
-..signature:GapAnchor<TPos>
-..param.TPos:Type to store gapped/ungapped positions.
-..remarks:Value types of the $gaps$ strings in @Class.ReadStoreElement@ and @Class.ContigStoreElement@.
-
-.Memfunc.GapAnchor#GapAnchor
-..summary:Constructor
-..signature:GapAnchor<TPos> ()
-..signature:GapAnchor<TPos> (TPos seqPos, TPos gapPos)
-..param.seqPos:Sequence character position in the ungapped sequence.
-..param.gapPos:Sequence character position in the gapped sequence.
-..remarks:Default constructor sets both positions to $0$.
-..class:Class.GapAnchor
-.Memvar.GapAnchor#seqPos
-..summary:Sequence character position in the ungapped sequence.
-..class:Class.GapAnchor
-.Memvar.GapAnchor#gapPos
-..summary:Sequence character position in the gapped sequence.
-..class:Class.GapAnchor
-..include:seqan/store.h
-*/
-
 // We store gap anchors only for the first text character behind a gap or a clipped sequence character
 
 template <typename TPos>
 struct GapAnchor
 {
 /*!
- * @var VariableType GapAnchor::seqPos
+ * @var TPos GapAnchor::seqPos
  * @brief Sequence character position in the ungapped sequence.
  */
-	TPos	seqPos;			// sequence character position in the ungapped sequence
+    TPos    seqPos;            // sequence character position in the ungapped sequence
 
 /*!
- * @var VariableType GapAnchor::gapPos
+ * @var TPos GapAnchor::gapPos
  * @brief Sequence character position in the gapped sequence.
  */
-	TPos	gapPos;			// sequence character position in the gapped sequence
+    TPos    gapPos;            // sequence character position in the gapped sequence
 
 /*!
  * @fn GapAnchor::GapAnchor
- * 
- * @brief Constructor
- * 
- * @signature GapAnchor::GapAnchor([other])
- * @signature GapAnchor::GapAnchor(seqPos, gapPos)
+ * @brief Constructor.
+ *
+ * @signature GapAnchor::GapAnchor([other]);
+ * @signature GapAnchor::GapAnchor(seqPos, gapPos);
+ *
+ * @param[in] other  GapAnchor object to copy from.
+ * @param[in] seqPos Sequence character position in the ungapped sequence (of type <tt>TPos</tt>).
+ * @param[in] gapPos Sequence character position in the gapped sequence (of type <tt>TPos</tt>).
  *
- * @param other  GapAnchor object to copy from.
- * @param seqPos Sequence character position in the ungapped sequence.
- * @param gapPos Sequence character position in the gapped sequence.
- * 
  * @section Remarks
- * 
- * Default constructor sets both positions to <tt>0</tt>.
+ *
+ * The default constructor sets both positions to <tt>0</tt>.
  */
 
-	GapAnchor() : seqPos(0), gapPos(0) {}
-	GapAnchor(TPos sP, TPos gP) : seqPos(sP), gapPos(gP) {}
-
-	template <typename TPos_>
-	GapAnchor(GapAnchor<TPos_> const &other)
-	{
-		seqPos = other.seqPos;
-		gapPos = other.gapPos;
-	}
-
-	template <typename TPos_>
-	inline GapAnchor const &
-	operator = (GapAnchor<TPos_> const &other)
-	{
-		seqPos = other.seqPos;
-		gapPos = other.gapPos;
-		return *this;
-	} 
-
-	template <typename TOther>
-	inline bool
-	operator == (TOther const &other) const
-	{
-		return seqPos == other.seqPos && gapPos == other.gapPos;
-	} 
-
-	template <typename TOther>
-	inline bool
-	operator != (TOther const &other) const
-	{
-		return !(*this == other);
-	} 
-
-	template <typename TOther>
-	inline bool
-	operator < (TOther const &other) const
-	{
-		return seqPos < other.seqPos || gapPos < other.gapPos;
-	} 
-
-	template <typename TOther>
-	inline bool
-	operator > (TOther const &other) const
-	{
-		return seqPos > other.seqPos || gapPos > other.gapPos;
-	} 
-
-	template <typename TOther>
-	inline bool
-	operator <= (TOther const &other) const
-	{
-		return seqPos < other.seqPos || gapPos <= other.gapPos;
-	} 
-
-	template <typename TOther>
-	inline bool
-	operator >= (TOther const &other) const
-	{
-		return seqPos > other.seqPos || gapPos >= other.gapPos;
-	}
+    GapAnchor() : seqPos(0), gapPos(0) {}
+    GapAnchor(TPos sP, TPos gP) : seqPos(sP), gapPos(gP) {}
+
+    template <typename TPos_>
+    GapAnchor(GapAnchor<TPos_> const &other)
+    {
+        seqPos = other.seqPos;
+        gapPos = other.gapPos;
+    }
+
+    template <typename TPos_>
+    inline GapAnchor const &
+    operator = (GapAnchor<TPos_> const &other)
+    {
+        seqPos = other.seqPos;
+        gapPos = other.gapPos;
+        return *this;
+    }
+
+    template <typename TOther>
+    inline bool
+    operator == (TOther const &other) const
+    {
+        return seqPos == other.seqPos && gapPos == other.gapPos;
+    }
+
+    template <typename TOther>
+    inline bool
+    operator != (TOther const &other) const
+    {
+        return !(*this == other);
+    }
+
+    template <typename TOther>
+    inline bool
+    operator < (TOther const &other) const
+    {
+        return seqPos < other.seqPos || gapPos < other.gapPos;
+    }
+
+    template <typename TOther>
+    inline bool
+    operator > (TOther const &other) const
+    {
+        return seqPos > other.seqPos || gapPos > other.gapPos;
+    }
+
+    template <typename TOther>
+    inline bool
+    operator <= (TOther const &other) const
+    {
+        return seqPos < other.seqPos || gapPos <= other.gapPos;
+    }
+
+    template <typename TOther>
+    inline bool
+    operator >= (TOther const &other) const
+    {
+        return seqPos > other.seqPos || gapPos >= other.gapPos;
+    }
 };
 
 // ============================================================================
@@ -243,22 +221,22 @@ struct _LessGapAnchor;
 
 template <typename TGapAnchor>
 struct _LessGapAnchor<TGapAnchor, SortSeqPos> :
-	public ::std::binary_function<TGapAnchor, TGapAnchor, bool>
+    public std::binary_function<TGapAnchor, TGapAnchor, bool>
 {
-	inline bool 
-	operator() (TGapAnchor const& a1, TGapAnchor const& a2) const {
-		return (a1.seqPos) < (a2.seqPos);
-	}
+    inline bool
+    operator() (TGapAnchor const& a1, TGapAnchor const& a2) const {
+        return (a1.seqPos) < (a2.seqPos);
+    }
 };
 
 template <typename TGapAnchor>
 struct _LessGapAnchor<TGapAnchor, SortGapPos> :
-	public ::std::binary_function<TGapAnchor, TGapAnchor, bool>
+    public std::binary_function<TGapAnchor, TGapAnchor, bool>
 {
-	inline bool 
-	operator() (TGapAnchor const& a1, TGapAnchor const& a2) const {
-		return (a1.gapPos) < (a2.gapPos);
-	}
+    inline bool
+    operator() (TGapAnchor const& a1, TGapAnchor const& a2) const {
+        return (a1.gapPos) < (a2.gapPos);
+    }
 };
 
 // ----------------------------------------------------------------------------
@@ -267,66 +245,66 @@ struct _LessGapAnchor<TGapAnchor, SortGapPos> :
 
 template <typename TGapAnchor, typename TSearchValue>
 inline typename Iterator<TGapAnchor const, Standard>::Type
-lowerBoundGapAnchor(TGapAnchor const & gaps, 
-					TSearchValue const val,
-					SortSeqPos) 
+lowerBoundGapAnchor(TGapAnchor const & gaps,
+                    TSearchValue const val,
+                    SortSeqPos)
 {
-	typedef typename Value<TGapAnchor>::Type TGapAnchorElement;
-	TGapAnchorElement el;
-	el.seqPos = val;
-	return ::std::lower_bound(
-		begin(gaps, Standard()), 
-		end(gaps, Standard()), 
-		el,
-		_LessGapAnchor<typename Value<TGapAnchor>::Type, SortSeqPos const>() );
+    typedef typename Value<TGapAnchor>::Type TGapAnchorElement;
+    TGapAnchorElement el;
+    el.seqPos = val;
+    return std::lower_bound(
+        begin(gaps, Standard()),
+        end(gaps, Standard()),
+        el,
+        _LessGapAnchor<typename Value<TGapAnchor>::Type, SortSeqPos const>() );
 }
 
 template <typename TGapAnchor, typename TSearchValue>
 inline typename Iterator<TGapAnchor, Standard>::Type
-lowerBoundGapAnchor(TGapAnchor & gaps, 
-					TSearchValue const val,
-					SortSeqPos) 
+lowerBoundGapAnchor(TGapAnchor & gaps,
+                    TSearchValue const val,
+                    SortSeqPos)
 {
-	typedef typename Value<TGapAnchor>::Type TGapAnchorElement;
-	TGapAnchorElement el;
-	el.seqPos = val;
-	return ::std::lower_bound(
-		begin(gaps, Standard()), 
-		end(gaps, Standard()), 
-		el,
-		_LessGapAnchor<typename Value<TGapAnchor>::Type, SortSeqPos const>() );
+    typedef typename Value<TGapAnchor>::Type TGapAnchorElement;
+    TGapAnchorElement el;
+    el.seqPos = val;
+    return std::lower_bound(
+        begin(gaps, Standard()),
+        end(gaps, Standard()),
+        el,
+        _LessGapAnchor<typename Value<TGapAnchor>::Type, SortSeqPos const>() );
 }
 
 template <typename TGapAnchor, typename TSearchValue>
 inline typename Iterator<TGapAnchor const, Standard>::Type
-lowerBoundGapAnchor(TGapAnchor const & gaps, 
-					TSearchValue const val,
-					SortGapPos) 
+lowerBoundGapAnchor(TGapAnchor const & gaps,
+                    TSearchValue const val,
+                    SortGapPos)
 {
-	typedef typename Value<TGapAnchor>::Type TGapAnchorElement;
-	TGapAnchorElement el;
-	el.gapPos = val;
-	return ::std::lower_bound(
-		begin(gaps, Standard()), 
-		end(gaps, Standard()), 
-		el,
-		_LessGapAnchor<typename Value<TGapAnchor>::Type, SortGapPos const>() );
+    typedef typename Value<TGapAnchor>::Type TGapAnchorElement;
+    TGapAnchorElement el;
+    el.gapPos = val;
+    return std::lower_bound(
+        begin(gaps, Standard()),
+        end(gaps, Standard()),
+        el,
+        _LessGapAnchor<typename Value<TGapAnchor>::Type, SortGapPos const>() );
 }
 
 template <typename TGapAnchor, typename TSearchValue>
 inline typename Iterator<TGapAnchor, Standard>::Type
-lowerBoundGapAnchor(TGapAnchor & gaps, 
-					TSearchValue const val,
-					SortGapPos) 
+lowerBoundGapAnchor(TGapAnchor & gaps,
+                    TSearchValue const val,
+                    SortGapPos)
 {
-	typedef typename Value<TGapAnchor>::Type TGapAnchorElement;
-	TGapAnchorElement el;
-	el.gapPos = val;
-	return ::std::lower_bound(
-		begin(gaps, Standard()), 
-		end(gaps, Standard()), 
-		el,
-		_LessGapAnchor<typename Value<TGapAnchor>::Type, SortGapPos const>() );
+    typedef typename Value<TGapAnchor>::Type TGapAnchorElement;
+    TGapAnchorElement el;
+    el.gapPos = val;
+    return std::lower_bound(
+        begin(gaps, Standard()),
+        end(gaps, Standard()),
+        el,
+        _LessGapAnchor<typename Value<TGapAnchor>::Type, SortGapPos const>() );
 }
 
 // ----------------------------------------------------------------------------
@@ -336,67 +314,67 @@ lowerBoundGapAnchor(TGapAnchor & gaps,
 template <typename TGapAnchors, typename TSearchValue>
 inline typename Iterator<TGapAnchors const, Standard>::Type
 upperBoundGapAnchor(TGapAnchors const & gaps,
-					TSearchValue const val,
-					SortSeqPos) 
+                    TSearchValue const val,
+                    SortSeqPos)
 {
-	typedef typename Value<TGapAnchors>::Type TGapAnchorElement;
-	TGapAnchorElement el;
-	el.seqPos = val;
-	return ::std::upper_bound(
-		begin(gaps, Standard()), 
-		end(gaps, Standard()), 
-		el,
-		_LessGapAnchor<typename Value<TGapAnchors>::Type, SortSeqPos const>() );
+    typedef typename Value<TGapAnchors>::Type TGapAnchorElement;
+    TGapAnchorElement el;
+    el.seqPos = val;
+    return std::upper_bound(
+        begin(gaps, Standard()),
+        end(gaps, Standard()),
+        el,
+        _LessGapAnchor<typename Value<TGapAnchors>::Type, SortSeqPos const>() );
 }
 
 template <typename TGapAnchors, typename TSearchValue>
 inline typename Iterator<TGapAnchors, Standard>::Type
 upperBoundGapAnchor(TGapAnchors & gaps,
-					TSearchValue const val,
-					SortSeqPos) 
+                    TSearchValue const val,
+                    SortSeqPos)
 {
-	typedef typename Value<TGapAnchors>::Type TGapAnchorElement;
-	TGapAnchorElement el;
-	el.seqPos = val;
-	return ::std::upper_bound(
-		begin(gaps, Standard()), 
-		end(gaps, Standard()), 
-		el,
-		_LessGapAnchor<typename Value<TGapAnchors>::Type, SortSeqPos const>() );
+    typedef typename Value<TGapAnchors>::Type TGapAnchorElement;
+    TGapAnchorElement el;
+    el.seqPos = val;
+    return std::upper_bound(
+        begin(gaps, Standard()),
+        end(gaps, Standard()),
+        el,
+        _LessGapAnchor<typename Value<TGapAnchors>::Type, SortSeqPos const>() );
 }
 
 template <typename TGapAnchors, typename TSearchValue>
 inline typename Iterator<TGapAnchors const, Standard>::Type
-upperBoundGapAnchor(TGapAnchors const & gaps, 
-					TSearchValue const val,
-					SortGapPos) 
+upperBoundGapAnchor(TGapAnchors const & gaps,
+                    TSearchValue const val,
+                    SortGapPos)
 {
-	typedef typename Value<TGapAnchors>::Type TGapAnchorElement;
-	TGapAnchorElement el;
-	el.gapPos = val;
-	return ::std::upper_bound(
-		begin(gaps, Standard()), 
-		end(gaps, Standard()), 
-		el,
-		_LessGapAnchor<typename Value<TGapAnchors>::Type, SortGapPos const>() );
+    typedef typename Value<TGapAnchors>::Type TGapAnchorElement;
+    TGapAnchorElement el;
+    el.gapPos = val;
+    return std::upper_bound(
+        begin(gaps, Standard()),
+        end(gaps, Standard()),
+        el,
+        _LessGapAnchor<typename Value<TGapAnchors>::Type, SortGapPos const>() );
 }
 
 template <typename TGapAnchors, typename TSearchValue>
 inline typename Iterator<TGapAnchors, Standard>::Type
-upperBoundGapAnchor(TGapAnchors & gaps, 
-					TSearchValue const val,
-					SortGapPos) 
+upperBoundGapAnchor(TGapAnchors & gaps,
+                    TSearchValue const val,
+                    SortGapPos)
 {
-	typedef typename Value<TGapAnchors>::Type TGapAnchorElement;
-	TGapAnchorElement el;
-	el.gapPos = val;
-	return ::std::upper_bound(
-		begin(gaps, Standard()), 
-		end(gaps, Standard()), 
-		el,
-		_LessGapAnchor<typename Value<TGapAnchors>::Type, SortGapPos const>() );
+    typedef typename Value<TGapAnchors>::Type TGapAnchorElement;
+    TGapAnchorElement el;
+    el.gapPos = val;
+    return std::upper_bound(
+        begin(gaps, Standard()),
+        end(gaps, Standard()),
+        el,
+        _LessGapAnchor<typename Value<TGapAnchors>::Type, SortGapPos const>() );
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_
diff --git a/seqan/align/gapped_value_type.h b/seqan/align/gapped_value_type.h
index 9e98bbc..30e62b6 100644
--- a/seqan/align/gapped_value_type.h
+++ b/seqan/align/gapped_value_type.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_
 
 namespace seqan {
 
@@ -62,17 +62,6 @@ namespace seqan {
  * @return Type A type that can store the values of <tt>T</tt> and the value <tt>'-'</tt>.
  */
 
-/**
-.Metafunction.GappedValueType:
-..cat:Alignments
-..summary:Returns a value type that contains a blank value '-'.
-..signature:GappedValueType<T>::Type
-..param.T:The value type that should be expanded (if needed) by '-'.
-..returns.param.Type:A value type that can be used to store store values in $T$ and the value '-'.
-..remarks:The default implementation returns $T$.
-..include:seqan/align.h
-*/
-
 // TODO(holtgrew): Would it be enough to define it for Nothing instead of having a default implementation.
 
 // We need a default implementation since we need it for Nothing.
@@ -85,8 +74,8 @@ struct GappedValueType
 template <typename TValue, typename TSpec>
 struct GappedValueType<SimpleType<TValue, TSpec> >
 {
-	typedef SimpleType<TValue, TSpec> THost_;
-	typedef ModifiedAlphabet<THost_, ModExpand<'-'> > Type;
+    typedef SimpleType<TValue, TSpec> THost_;
+    typedef ModifiedAlphabet<THost_, ModExpand<'-'> > Type;
 };
 
 // ============================================================================
@@ -95,4 +84,4 @@ struct GappedValueType<SimpleType<TValue, TSpec> >
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_
diff --git a/seqan/align/gaps_anchor.h b/seqan/align/gaps_anchor.h
index ca25d50..ef00050 100644
--- a/seqan/align/gaps_anchor.h
+++ b/seqan/align/gaps_anchor.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,8 +38,8 @@
 // TODO(holtgrew): Clipping in leading and trailing gaps is not possible right now. Dave and I have to discuss this further.
 // TODO(holtgrew): Also, inserting gaps in the front changes the clipped begin position which is unexpected.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_
 
 namespace seqan {
 
@@ -91,34 +91,14 @@ inline void _reinitAnchorGaps(Gaps<TSequence, AnchorGaps<TGapAnchors> > & gaps);
  * @signature Gaps::Gaps(source[, anchors]);
  * @signature Gaps::Gaps(anchors);
  *
- * @param other   Another @link AnchorGaps @endlink object to copy from.
- * @param source  The underling sequence to construct the Gaps object from.
- * @param anchors The string of anchors to construct with.
+ * @param[in] other   Another @link AnchorGaps @endlink object to copy from.
+ * @param[in] source  The underling sequence to construct the Gaps object from.
+ * @param[in] anchors The string of anchors to construct with.
  *
  * An AnchorGaps object has a default constructor, can be constructed from the underlying source, and/or a string of
  * gap anchors.
  */
 
-/**
-.Spec.AnchorGaps:
-..cat:Alignments
-..general:Class.Gaps
-..summary:Stores gaps anchors of the first characters behind gaps.
-..signature:Gaps<TSource, AnchorGaps<TGapAnchors> >
-..param.TSource:Type of the ungapped sequence.
-...metafunction:Metafunction.Source
-..param.TGapAnchors:Type of the sequence of gap anchors, e.g. a string of $Class.GapAnchor$.
-..include:seqan/store.h
-
-.Memfunc.Gaps#Gaps
-..class:Class.Gaps
-..summary:Constructor
-..signature:Gaps<TSource, AnchorGaps<TGapAnchors> > ()
-..signature:Gaps<TSource, AnchorGaps<TGapAnchors> > (source[, anchors])
-..signature:Gaps<TSource, AnchorGaps<TGapAnchors> > (anchors)
-..param.source:The underlying ungapped sequence.
-..param.anchors:The sequence of gap anchors, e.g. the $gaps$ members in $Class.ReadStoreElement$ or $Class.ContigStoreElement$.
-*/
 
 template <typename TGapAnchors = String<GapAnchor<unsigned> > >
 struct AnchorGaps
@@ -137,6 +117,9 @@ class Gaps<TSource, AnchorGaps<TGapAnchors> >
     typedef typename Position<Gaps>::Type      TPosition_;
     typedef typename Value<Gaps>::Type         TValue_;
 
+    typedef typename RemoveReference<typename RemoveConst<TSource>::Type>::Type TSourceNoConstNoRef;
+    typedef TSourceNoConstNoRef const & TSourceConstRef;
+
     // -----------------------------------------------------------------------
     // Member Variables
     // -----------------------------------------------------------------------
@@ -174,7 +157,7 @@ class Gaps<TSource, AnchorGaps<TGapAnchors> >
         data_cutBegin(0),
         data_cutEnd(0),
         data_viewCutBegin(0),
-        data_viewCutEnd(0)        
+        data_viewCutEnd(0)
     {
     }
 
@@ -187,21 +170,9 @@ class Gaps<TSource, AnchorGaps<TGapAnchors> >
     {
     }
 
-    // Note: We need the variants with the first parameter "TSource const &" here because TSource can be a Segment which
-    // is often given as a temporary.
-
-    Gaps(TSource & source, TGapAnchors & anchors) :
-        data_source(source), 
-        data_gaps(anchors),
-        data_cutBegin(0),
-        data_cutEnd(0),
-        data_viewCutBegin(0),
-        data_viewCutEnd(0)        
-    {
-    }
-
-    Gaps(TSource & source, TGapAnchors const & anchors) :
-        data_source(source), 
+    // everybody has const & constructors
+    Gaps(TSourceNoConstNoRef const & source, TGapAnchors & anchors) :
+        data_source(source),
         data_gaps(anchors),
         data_cutBegin(0),
         data_cutEnd(0),
@@ -210,22 +181,8 @@ class Gaps<TSource, AnchorGaps<TGapAnchors> >
     {
     }
 
-    // TODO(holtgrew): These constructors are only here because of const-Holder issues.
-
-    template <typename TSource2>
-    Gaps(TSource2 & source, TGapAnchors & anchors) :
-        data_source(source), 
-        data_gaps(anchors), 
-        data_cutBegin(0),
-        data_cutEnd(0),
-        data_viewCutBegin(0),
-        data_viewCutEnd(0)
-    {
-    }
-
-    template <typename TSource2>
-    Gaps(TSource2 & source, TGapAnchors const & anchors) :
-        data_source(source), 
+    Gaps(TSourceNoConstNoRef const & source, TGapAnchors const & anchors) :
+        data_source(source),
         data_gaps(anchors),
         data_cutBegin(0),
         data_cutEnd(0),
@@ -234,19 +191,21 @@ class Gaps<TSource, AnchorGaps<TGapAnchors> >
     {
     }
 
-    template <typename TSource2>
-    Gaps(TSource2 const & source, TGapAnchors & anchors) :
+    // if source is not const & (but possibly const) there are also regular & constructors
+    Gaps(TSourceNoConstNoRef & source, TGapAnchors & anchors,
+         SEQAN_CTOR_DISABLE_IF(IsSameType<TSource, TSourceConstRef>)) :
         data_source(source),
-        data_gaps(anchors), 
+        data_gaps(anchors),
         data_cutBegin(0),
         data_cutEnd(0),
         data_viewCutBegin(0),
         data_viewCutEnd(0)
     {
+        ignoreUnusedVariableWarning(dummy);
     }
 
-    template <typename TSource2>
-    Gaps(TSource2 const & source, TGapAnchors const & anchors) :
+    Gaps(TSourceNoConstNoRef & source, TGapAnchors const & anchors,
+        SEQAN_CTOR_DISABLE_IF(IsSameType<TSource, TSourceConstRef>)) :
         data_source(source),
         data_gaps(anchors),
         data_cutBegin(0),
@@ -254,6 +213,7 @@ class Gaps<TSource, AnchorGaps<TGapAnchors> >
         data_viewCutBegin(0),
         data_viewCutEnd(0)
     {
+        ignoreUnusedVariableWarning(dummy);
     }
 
     // -----------------------------------------------------------------------
@@ -276,6 +236,23 @@ class Gaps<TSource, AnchorGaps<TGapAnchors> >
 // Functions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Function swap()
+// ----------------------------------------------------------------------------
+
+template <typename TSequence, typename TGapAnchors>
+void swap(Gaps<TSequence, AnchorGaps<TGapAnchors> > & lhs,
+          Gaps<TSequence, AnchorGaps<TGapAnchors> > & rhs)
+{
+    swap(lhs.data_source, rhs.data_source);
+    swap(lhs.data_gaps, rhs.data_gaps);
+
+    std::swap(lhs.data_cutBegin, rhs.data_cutBegin);
+    std::swap(lhs.data_cutEnd, rhs.data_cutEnd);
+    std::swap(lhs.data_viewCutBegin, rhs.data_viewCutBegin);
+    std::swap(lhs.data_viewCutEnd, rhs.data_viewCutEnd);
+}
+
 // ----------------------------------------------------------------------------
 // Helper Function _reinitAnchorGaps()
 // ----------------------------------------------------------------------------
@@ -438,6 +415,24 @@ clearGaps(Gaps<TSequence, AnchorGaps<TGapAnchors> > & gaps)
     _reinitAnchorGaps(gaps);
 }
 
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TSequence, typename TGapAnchors>
+inline void
+clear(Gaps<TSequence, AnchorGaps<TGapAnchors> > & gaps)
+{
+    clear(gaps.data_source); // clear source holder
+
+    // clear gaps, but on holder level
+    clear(gaps.data_gaps);
+    gaps.data_cutBegin = 0;
+    gaps.data_cutEnd = 0;
+    gaps.data_viewCutBegin = 0;
+    gaps.data_viewCutEnd = 0;
+}
+
 // ----------------------------------------------------------------------------
 // Function isGap()
 // ----------------------------------------------------------------------------
@@ -699,25 +694,6 @@ assignSource(Gaps<TSequence, AnchorGaps<TGapAnchor> > & gaps, TSequence2 const &
     value(gaps.data_source) = source;
 }
 
-// ----------------------------------------------------------------------------
-// Helper Function _helperIsNegative()
-// ----------------------------------------------------------------------------
-
-// to remove '... < 0 is always false' warning
-template <typename T>
-inline bool
-_helperIsNegative(T, False)
-{
-    return false;
-}
-
-template <typename T>
-inline bool
-_helperIsNegative(T t, True)
-{
-    return t < 0;
-}
-
 // ----------------------------------------------------------------------------
 // Function positionGapToSeq()
 // ----------------------------------------------------------------------------
@@ -730,45 +706,48 @@ _helperIsNegative(T t, True)
  *
  * @signature TPos positionGapToSeq(gaps, pos);
  *
- * @param gaps Contig AnchorGaps (e.g. from FragmentStore).
- * @param pos  Position in gap space.
+ * @param[in] gaps Contig AnchorGaps (e.g. from FragmentStore).
+ * @param[in] pos  Position in gap space.
  *
- * @return Position in sequence space.
+ * @return TPos Position in sequence space (Metafunction: @link ContainerConcept#Position @endlink).
  *
  * See the example below to construct the Gaps ojbect.  Note that this construction is fast since it ionly a thing wrapper
  * around underlying objects.
  *
- * @section Example
+ * @section Examples
  *
  * Convert from gap space to positions pace when the contig required to be loaded. * Converts position aligned read with
  * index <tt>idx</tt> in the aligned read store.
  *
- * @code
+ * @code{.cpp}
  * typedef typename TFragmentStore::TContigStore                        TContigStore;
  * typedef typename Value<TContigStore>::Type                           TContig;
  * typedef typename TFragmentStore::TContigSeq                          TContigSeq;
  * typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
- * 
+ *
  * typedef typename TFragmentStore::TAlignedReadStore                   TAlignedReadStore;
  * typedef typename Value<TAlignedReadStore>::Type                      TAlignedRead;
  * typedef typename TAlignedRead::TPos                                  TAlignedReadPos;
- * 
+ *
  * unsigned contigId = alignedReadStore[idx].contigId;
  * TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps);
  * TAlignedRead const & alignedRead = alignedReadStore[idx];
  * // Translate end position from aligned read record to sequence space in reference.
  * TAlignedReadPos endPos = positionGapToSeq(contigGaps, alignedRead.endPos);
- * ..example.text:Convert from gap space to position space when the contigs are not required.
- * ..example.text:Converts position aligned read with index $idx$ in the aligned read store.
- * ..example.code:
+ * @endcode
+ *
+ * Convert from gap space to position space when the contigs are not required.
+ * Converts position aligned read with index $idx$ in the aligned read store.
+ *
+ * @code{.cpp}
  * typedef typename TFragmentStore::TContigStore                        TContigStore;
  * typedef typename Value<TContigStore>::Type                           TContig;
  * typedef Gaps<Nothing, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
- * 
+ *
  * typedef typename TFragmentStore::TAlignedReadStore                   TAlignedReadStore;
  * typedef typename Value<TAlignedReadStore>::Type                      TAlignedRead;
  * typedef typename TAlignedRead::TPos                                  TAlignedReadPos;
- * 
+ *
  * unsigned contigId = alignedReadStore[idx].contigId;
  * TContigGaps contigGaps(Nothing(), contigStore[contigId].gaps);
  * TAlignedRead const & alignedRead = alignedReadStore[idx];
@@ -777,53 +756,6 @@ _helperIsNegative(T t, True)
  * @endcode
  */
 
-/**
-.Function.positionGapToSeq
-..cat:Fragment Store
-..signature:positionGapToSeq(gaps, pos)
-..summary:Convert from gap-space in the global alignment to the sequence-space on the reference.
-..param.gaps:Contig gaps from fragment store.
-...type:Spec.AnchorGaps
-..param.pos:Position in gap space.
-..returns:Position in sequence space.
-..remarks:See the example below to construct the gaps object. Note that this construction is fast since it is only a thin wrapper around underlying objects.
-..include:seqan/store.h
-..example.text:Convert from gap space to position space when the contigs required to be loaded.
-..example.text:Converts position aligned read with index $idx$ in the aligned read store.
-..example.code:
-typedef typename TFragmentStore::TContigStore                        TContigStore;
-typedef typename Value<TContigStore>::Type                           TContig;
-typedef typename TFragmentStore::TContigSeq                          TContigSeq;
-typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
-
-typedef typename TFragmentStore::TAlignedReadStore                   TAlignedReadStore;
-typedef typename Value<TAlignedReadStore>::Type                      TAlignedRead;
-typedef typename TAlignedRead::TPos                                  TAlignedReadPos;
-
-unsigned contigId = alignedReadStore[idx].contigId;
-TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps);
-TAlignedRead const & alignedRead = alignedReadStore[idx];
-// Translate end position from aligned read record to sequence space in reference.
-TAlignedReadPos endPos = positionGapToSeq(contigGaps, alignedRead.endPos);
-..example.text:Convert from gap space to position space when the contigs are not required.
-..example.text:Converts position aligned read with index $idx$ in the aligned read store.
-..example.code:
-typedef typename TFragmentStore::TContigStore                        TContigStore;
-typedef typename Value<TContigStore>::Type                           TContig;
-typedef Gaps<Nothing, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
-
-typedef typename TFragmentStore::TAlignedReadStore                   TAlignedReadStore;
-typedef typename Value<TAlignedReadStore>::Type                      TAlignedRead;
-typedef typename TAlignedRead::TPos                                  TAlignedReadPos;
-
-unsigned contigId = alignedReadStore[idx].contigId;
-TContigGaps contigGaps(Nothing(), contigStore[contigId].gaps);
-TAlignedRead const & alignedRead = alignedReadStore[idx];
-// Translate end position from aligned read record to sequence space in reference.
-TAlignedReadPos endPos = positionGapToSeq(contigGaps, alignedRead.endPos);
-..see:Function.positionSeqToGap
- */
-
 template <typename TSource, typename TGapAnchors, typename TPosition>
 inline TPosition
 positionGapToSeq(Gaps<TSource, AnchorGaps<TGapAnchors> > const & me, TPosition pos)
@@ -834,7 +766,7 @@ positionGapToSeq(Gaps<TSource, AnchorGaps<TGapAnchors> > const & me, TPosition p
     TPosition           seqPos;
     int                 anchorIdx;
 
-    if (_helperIsNegative(pos, typename IsSameType<TPosition, typename MakeSigned_<TPosition>::Type>::Type()))
+    if (isNegative(pos))
         anchorIdx = -1;
     else
     {
@@ -866,15 +798,15 @@ positionGapToSeq(Gaps<TSource, AnchorGaps<TGapAnchors> > const & me, TPosition p
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn Gaps#positionSeqToGap
+ * @fn AnchorGaps#positionSeqToGap
  * @brief Convert from sequence space on the reference to gap space in the global alignment.
  *
- * @signature TPosition positionSeqToGap(gaps, pos);
+ * @signature TPos positionSeqToGap(gaps, pos);
  *
- * @param gaps The AnchorGaps object to use for the translation.
- * @param pos  The gap space position to conver to sequence space.
+ * @param[in] gaps The AnchorGaps object to use for the translation.
+ * @param[in] pos  The gap space position to conver to sequence space.
  *
- * @return TPosition The resulting position in sequence space.
+ * @return TPos The resulting position in sequence space (Metafunction: @link ContainerConcept#Position @endlink).
  *
  * See the example below to construct the gaps object.  Note that this construction is fast since it is only a thin
  * wrapper around underlying objects.
@@ -883,59 +815,28 @@ positionGapToSeq(Gaps<TSource, AnchorGaps<TGapAnchors> > const & me, TPosition p
  *
  * Convert from gap space to position space on contig $contigId$ when the contigs required to be loaded.
  *
- * @code
+ * @code{.cpp}
  * typedef typename TFragmentStore::TContigStore                        TContigStore;
  * typedef typename Value<TContigStore>::Type                           TContig;
  * typedef typename TFragmentStore::TContigSeq                          TContigSeq;
  * typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
- * 
+ *
  * TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps);
  * TAlignedReadPos pos = positionGapToSeq(contigGaps, 33);
  * @endcode
  *
  * Convert from gap space to position space on contig $contigId$ when the contigs are not required.
  *
- * @code
+ * @code{.cpp}
  * typedef typename TFragmentStore::TContigStore                        TContigStore;
  * typedef typename Value<TContigStore>::Type                           TContig;
  * typedef Gaps<Nothing, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
- * 
+ *
  * TContigGaps contigGaps(Nothing(), contigStore[contigId].gaps);
  * TAlignedReadPos endPos = positionGapToSeq(contigGaps, 33);
  * @endcode
  */
 
-/**
-.Function.positionSeqToGap
-..cat:Fragment Store
-..signature:positionGapToSeq(gaps, pos)
-..summary:Convert from sequence space on the reference to gap space in the global alignment.
-..param.gaps:Contig gaps from fragment store.
-...type:Spec.AnchorGaps
-..param.pos:Position in the reference.
-..returns:Position in the gap space of the global alignment space.
-..remarks:See the example below to construct the gaps object. Note that this construction is fast since it is only a thin wrapper around underlying objects.
-..include:seqan/store.h
-..example.text:Convert from gap space to position space on contig $contigId$ when the contigs required to be loaded.
-..example.code:
-typedef typename TFragmentStore::TContigStore                        TContigStore;
-typedef typename Value<TContigStore>::Type                           TContig;
-typedef typename TFragmentStore::TContigSeq                          TContigSeq;
-typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
-
-TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps);
-TAlignedReadPos pos = positionGapToSeq(contigGaps, 33);
-..example.text:Convert from gap space to position space on contig $contigId$ when the contigs are not required.
-..example.code:
-typedef typename TFragmentStore::TContigStore                        TContigStore;
-typedef typename Value<TContigStore>::Type                           TContig;
-typedef Gaps<Nothing, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
-
-TContigGaps contigGaps(Nothing(), contigStore[contigId].gaps);
-TAlignedReadPos endPos = positionGapToSeq(contigGaps, 33);
-..see:Function.positionSeqToGap
- */
-
 template <typename TSource, typename TGapAnchors, typename TPosition>
 inline TPosition
 positionSeqToGap(Gaps<TSource, AnchorGaps<TGapAnchors> > const & me, TPosition pos)
@@ -946,7 +847,7 @@ positionSeqToGap(Gaps<TSource, AnchorGaps<TGapAnchors> > const & me, TPosition p
     TPosition           gapPos;
     int                 anchorIdx;
 
-    if (_helperIsNegative(pos, typename IsSameType<TPosition, typename MakeSigned_<TPosition>::Type>::Type()))
+    if (isNegative(pos))
         anchorIdx = -1;
     else
     {
@@ -1043,4 +944,4 @@ clippedEndPosition(Gaps<TSequence, AnchorGaps<TGapAnchors> > const & gaps)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_
diff --git a/seqan/align/gaps_array.h b/seqan/align/gaps_array.h
index af128b7..8416eea 100644
--- a/seqan/align/gaps_array.h
+++ b/seqan/align/gaps_array.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,8 +38,8 @@
 // TODO(holtgrew): Currently, operations are a function of the whole gap count, could be of clipped region only.
 // TODO(holtgrew): Problem with the gap value, getValue(), value().
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_
 
 namespace seqan {
 
@@ -77,6 +77,7 @@ typedef Tag<ArrayGaps_> ArrayGaps;
 /*!
  * @class ArrayGaps
  * @headerfile <seqan/align.h>
+ * @extends Gaps
  * @brief Stores length of gap- and non-gap runs in an array.
  *
  * @signature template <typename TSequence>
@@ -85,16 +86,17 @@ typedef Tag<ArrayGaps_> ArrayGaps;
  * @tparam TSequence The type of the underling sequence.
  */
 
-/**
-.Spec.ArrayGaps
-..cat:Alignments
-..general:Class.Gaps
-..summary:Stores length of gap- and non-gapped runs in an array.
-..signature:Gaps<TSequence, ArrayGaps>
-..param.TSequence:Type of the ungapped sequence.
-...metafunction:Metafunction.Source
-..include:seqan/align.h
-*/
+/*!
+ * @fn ArrayGaps::Gaps
+ * @headerfile <seqan/align.h>
+ * @brief Constructor.
+ *
+ * @signature Gaps::Gaps([other]);
+ * @signature Gaps::Gaps(seq);
+ *
+ * @param[in] other Other Gaps object to copy from.
+ * @param[in] seq   Sequence concept to construct the gaps for.
+ */
 
 template <typename TSequence>
 class Gaps<TSequence, ArrayGaps>
@@ -179,13 +181,29 @@ class Gaps<TSequence, ArrayGaps>
     // Array Subscript Operator
     // -----------------------------------------------------------------------
 
-	inline TValue_
-	operator[](TPosition_ clippedViewPos) const
-	{
+    inline TValue_
+    operator[](TPosition_ clippedViewPos) const
+    {
         return value(*this, clippedViewPos);
-	}
+    }
 };
 
+// ----------------------------------------------------------------------------
+// Function swap()
+// ----------------------------------------------------------------------------
+
+template <typename TSequence>
+void swap(Gaps<TSequence, ArrayGaps> & lhs, Gaps<TSequence, ArrayGaps> & rhs)
+{
+    swap(lhs._source, rhs._source);
+    swap(lhs._array, rhs._array);
+
+    std::swap(lhs._sourceBeginPos, rhs._sourceBeginPos);
+    std::swap(lhs._sourceEndPos, rhs._sourceEndPos);
+    std::swap(lhs._clippingBeginPos, rhs._clippingBeginPos);
+    std::swap(lhs._clippingEndPos, rhs._clippingEndPos);
+}
+
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -670,6 +688,24 @@ clearGaps(Gaps<TSequence, ArrayGaps> & gaps)
     _reinitArrayGaps(gaps);
 }
 
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TSequence>
+inline void
+clear(Gaps<TSequence, ArrayGaps> & gaps)
+{
+    clear(gaps._source);
+    clear(gaps._array);
+    gaps._sourceBeginPos     = 0;
+    gaps._sourceEndPos       = 0;
+    gaps._clippingBeginPos   = 0;
+    gaps._clippingEndPos     = 0;
+    // cannot use clearGaps() here, since that calls value() on _source
+    // which instates the Holder to Owner; we want it to be empty
+}
+
 // ----------------------------------------------------------------------------
 // Function isGap()
 // ----------------------------------------------------------------------------
@@ -844,4 +880,4 @@ endPosition(Gaps<TSequence, ArrayGaps> & gaps)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_
diff --git a/seqan/align/gaps_base.h b/seqan/align/gaps_base.h
index e667600..ea9af69 100644
--- a/seqan/align/gaps_base.h
+++ b/seqan/align/gaps_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 
 // TODO(holtgrew): Switch to Host interface.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_
 
 namespace seqan {
 
@@ -73,7 +73,7 @@ typedef Tag<ArrayGaps_> ArrayGaps;
 
 /*!
  * @class Gaps
- * @implements SequenceConcept
+ * @implements ContainerConcept
  * @headerfile <seqan/align.h>
  * @brief Store the gapped version of a sequence.
  *
@@ -83,12 +83,12 @@ typedef Tag<ArrayGaps_> ArrayGaps;
  * @tparam TSequence The type of the underlying sequence.
  * @tparam TSpec     Tag for specialization.
  *
- * Gaps wrap a @link SequenceConcept Sequence @endlink and allows to (1) insert gaps into the sequence and (2) select
+ * Gaps wrap a @link ContainerConcept Sequence @endlink and allows to (1) insert gaps into the sequence and (2) select
  * an infix of the gapped sequence (clipping).  The gaps are not inserted into the underlying sequence (source) but
  * stored separately.  Using the clipping is optional and meant for selecting parts of the alignment as a part of the
  * result of a local alignment algorithm.
  *
- * <img src="gaps_illustration.png" title="Illustration of Gaps object and positions with clipping. />
+ * <img src="gaps_illustration.png" title="Illustration of Gaps object and positions with clipping." />
  *
  * In the figure above, the source sequence has seven characters, the gapped sequence has four gaps and thus consists
  * of eleven characters.  The gapped sequence is clipped to start at position 0 in the gapped sequence and to end at
@@ -104,47 +104,11 @@ typedef Tag<ArrayGaps_> ArrayGaps;
  * The following example shows the construction of the gaps object from the image above together with some calls to
  * <tt>toViewPosition</tt> and <tt>toSourcePosition</tt>.
  *
- * @include demos/align/gaps_example.cpp
+ * @include demos/dox/align/gaps_example.cpp
  *
  * The output is as follows:
  *
- * @include demos/align/gaps_example.cpp.stdout
- */
-
-/**
-.Class.Gaps
-..cat:Alignments
-..implements:Concept.SequenceConcept
-..summary:Efficient storage of gaps for a sequence.
-..signature:Gaps<TSequence, TSpec>
-..description.text:
-Gaps wrap a @Concept.SequenceConcept@ and allows to (1) insert gaps into the sequence and (2) select an infix of the gapped sequence (clipping).
-The gaps are not inserted into the underlying sequence (source) but stored separately.
-Using the clipping is optional and meant for selecting parts of the alignment as a part of the result of a local alignment algorithm.
-..description.image:gaps_illustration|Illustration of Gaps object and positions with clipping.
-..description:
-In the figure above, the source sequence has seven characters, the gapped sequence has four gaps and thus consists of eleven characters.
-The gapped sequence is clipped to start at position 0 in the gapped sequence and to end at position 8 in the gapped sequence (the positions given as half-open intervals $[begin, end)$).
-..description.text:
-The figure shows the three coordinate systems that are used with Gaps objects.
-The source position is the position in the underlying sequence.
-The unclipped view position is the position in the gapped sequence without gaps.
-The view position is the position in the gapped sequence but including the clipping:
-All (clipped) view positions have the clipping begin position subtracted from them.
-..example.text:
-The following example shows the construction of the gaps object from the image above together with some calls to $toViewPosition$ and $toSourcePosition$.
-These functions allow the transformation between the source position and the clipped view position.
-..example.file:demos/align/gaps_example.cpp
-..example.text:This yields the following output:
-..example.output:Resulting gaps: GG-T-A-
-toSourcePosition(gaps, 0) == 1
-toSourcePosition(gaps, 4) == 4
-toViewPosition(gaps, 0) == -1
-toViewPosition(gaps, 5) == 9
-..param.TSequence:The type of the underlying sequence.
-...type:Concept.SequenceConcept
-..param.TSpec:Specialization tag.
-..include:seqan/align.h
+ * @include demos/dox/align/gaps_example.cpp.stdout
  */
 
 template <typename TSequence, typename TSpec = ArrayGaps>
@@ -158,9 +122,6 @@ class Gaps;
 // Metafunction Value
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Value.param.T.type:Class.Gaps
-///.Metafunction.Value.class:Class.Gaps
-
 template <typename TSequence, typename TSpec>
 struct Value<Gaps<TSequence, TSpec> >
 {
@@ -176,28 +137,22 @@ struct Value<Gaps<TSequence, TSpec> const> : Value<Gaps<TSequence, TSpec> >
 // Metafunction Iterator
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Iterator.param.T.type:Class.Gaps
-///.Metafunction.Iterator.class:Class.Gaps
-
 template <typename TSequence, typename TSpec, typename TIteratorSpec>
 struct Iterator<Gaps<TSequence, TSpec>, TIteratorSpec>
 {
-	typedef Iter<Gaps<TSequence, TSpec>, GapsIterator<TSpec> > Type;
+    typedef Iter<Gaps<TSequence, TSpec>, GapsIterator<TSpec> > Type;
 };
 
 template <typename TSequence, typename TSpec, typename TIteratorSpec>
 struct Iterator<Gaps<TSequence, TSpec> const, TIteratorSpec>
 {
-	typedef Iter<Gaps<TSequence, TSpec> const, GapsIterator<TSpec> > Type;
+    typedef Iter<Gaps<TSequence, TSpec> const, GapsIterator<TSpec> > Type;
 };
 
 // ----------------------------------------------------------------------------
 // Metafunction GetValue
 // ----------------------------------------------------------------------------
 
-///.Metafunction.GetValue.param.T.type:Class.Gaps
-///.Metafunction.GetValue.class:Class.Gaps
-
 template <typename TSequence, typename TSpec>
 struct GetValue<Gaps<TSequence, TSpec> > : Value<Gaps<TSequence, TSpec> >
 {};
@@ -210,9 +165,6 @@ struct GetValue<Gaps<TSequence, TSpec> const> : GetValue<Gaps<TSequence, TSpec>
 // Metafunction Position
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Position.param.T.type:Class.Gaps
-///.Metafunction.Position.class:Class.Gaps
-
 template <typename TSequence, typename TSpec>
 struct Position<Gaps<TSequence, TSpec> >
 {
@@ -228,30 +180,24 @@ struct Position<Gaps<TSequence, TSpec> const> : Position<Gaps<TSequence, TSpec>
 // Metafunction Reference
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Reference.param.T.type:Class.Gaps
-///.Metafunction.Reference.class:Class.Gaps
-
 template <typename TSequence, typename TSpec>
 struct Reference<Gaps<TSequence, TSpec> >
 {
-	typedef typename Iterator<Gaps<TSequence, TSpec>, Standard>::Type TIterator_;
-	typedef Proxy<IteratorProxy<TIterator_> > Type;
+    typedef typename Iterator<Gaps<TSequence, TSpec>, Standard>::Type TIterator_;
+    typedef Proxy<IteratorProxy<TIterator_> > Type;
 };
 
 template <typename TSequence, typename TSpec>
 struct Reference<Gaps<TSequence, TSpec> const>
 {
-	typedef typename Iterator<Gaps<TSequence, TSpec> const, Standard>::Type TIterator_;
-	typedef Proxy<IteratorProxy<TIterator_> > Type;
+    typedef typename Iterator<Gaps<TSequence, TSpec> const, Standard>::Type TIterator_;
+    typedef Proxy<IteratorProxy<TIterator_> > Type;
 };
 
 // ----------------------------------------------------------------------------
 // Metafunction Size
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Size.param.T.type:Class.Gaps
-///.Metafunction.Size.class:Class.Gaps
-
 template <typename TSequence, typename TSpec>
 struct Size<Gaps<TSequence, TSpec> >
 {
@@ -268,18 +214,6 @@ struct Size<Gaps<TSequence, TSpec> const> : Size<Gaps<TSequence, TSpec> >
 
 // TODO(holtgrew): Switch to Hosted Type interface
 
-/**
-.Metafunction.Source
-..cat:Alignments
-..summary:Return underlying sequence of Gaps/Alignments.
-..signature:Source<T>::Type
-..param.T:The type to query for underlying sequence.
-..include:seqan/align.h
-*/
-
-///.Metafunction.Source.param.T.type:Class.Gaps
-///.Metafunction.Source.class:Class.Gaps
-
 template <typename TSequence, typename TSpec>
 struct Source<Gaps<TSequence, TSpec> >
 {
@@ -296,9 +230,6 @@ struct Source<Gaps<TSequence, TSpec> const> : Source<Gaps<TSequence, TSpec> >
 // Metafunction IsSequence
 // ----------------------------------------------------------------------------
 
-///.Metafunction.IsSequence.param.T.type:Class.Gaps
-///.Metafunction.IsSequence.class:Class.Gaps
-
 template <typename TSequence, typename TSpec>
 struct IsSequence<Gaps<TSequence, TSpec> >
 {
@@ -319,27 +250,23 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
 // Function iter()
 // ----------------------------------------------------------------------------
 
-// From SequenceConcept, only overwriting documentation here.
+// From ContainerConcept, only overwriting documentation here.
 
 /*!
  * @fn Gaps#iter
  * @brief Return an iterator to a specific position in the current clipping.
  *
- * @signature TIterator iter(gaps, viewPos[, tag);
+ * @signature TIterator iter(gaps, viewPos[, tag]);
  *
- * @param gaps    The Gaps object to get an iterator into.
- * @param viewPos View position to get an iterator to.
- * @param tag     An optional tag for selecting the iterator type.
+ * @param[in] gaps    The Gaps object to get an iterator into.
+ * @param[in] viewPos View position to get an iterator to (Metafunction: @link ContainerConcept#Position @endlink).
+ * @param[in] tag     An optional tag for selecting the iterator type.
  *
  * @return TIterator The resulting iterator.  The type is <tt>Iterator<TGaps, TTag>::Type</tt> where <tt>TTag</tt> is
  *                   the type of <tt>tag</tt>.
  */
 
 // TODO(holtgrew): Adding links to implemented sequence. This should be cleaned up once we have better documentation with concepts.
-///.Function.begin.class:Class.Gaps
-///.Function.end.class:Class.Gaps
-///.Function.iter.class:Class.Gaps
-
 // ----------------------------------------------------------------------------
 // Function setSource()
 // ----------------------------------------------------------------------------
@@ -358,22 +285,9 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature void clearClipping(gaps);
  *
- * @param gaps Object to clear clipping from.
+ * @param[in,out] gaps Object to clear clipping from.
  */
 
-/**
-.Function.Gaps#clearClipping
-..class:Class.Gaps
-..summary:Clear clipping from @Class.Gaps@ object.
-..cat:Alignments
-..signature:void clearClipping(gaps)
-..param.gaps:The @Class.Gaps@ object to clear.
-...type:Class.Gaps
-..returns:$void$
-..see:Function.Gaps#clearGaps
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function clearGaps()
 // ----------------------------------------------------------------------------
@@ -384,27 +298,14 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature void clearGaps(gaps);
  *
- * @param gaps Object to clear gaps from.
+ * @param[in,out] gaps Object to clear gaps from.
  */
 
-/**
-.Function.Gaps#clearGaps
-..class:Class.Gaps
-..summary:Clear gaps and clipping from @Class.Gaps@ object.
-..cat:Alignments
-..signature:void clearGaps(gaps)
-..param.gaps:The @Class.Gaps@ object to clear.
-...type:Class.Gaps
-..returns:$void$
-..see:Function.Gaps#clearClipping
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function length()
 // ----------------------------------------------------------------------------
 
-// From SequenceConcept, only overwriting documentation here.
+// From ContainerConcept, only overwriting documentation here.
 
 /*!
  * @fn Gaps#length
@@ -412,24 +313,12 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature TSize length(gaps);
  *
- * @param gaps The @link Gaps @endlink object to query for its length.
+ * @param[in] gaps The @link Gaps @endlink object to query for its length.
  *
- * @return TSize The number of gaps and characters between the beginning and the end of the clipping.
+ * @return TSize The number of gaps and characters between the beginning and the end of the clipping (Metafunction:
+ *               @link ContainerConcept#Size @endlink).
  */
 
-/**
-.Function.Gaps#length
-..class:Class.Gaps
-..summary:Return length of the gapped sequence.
-..cat:Alignments
-..signature:TSize length(gaps)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..returns:Length of the gapped sequence.
-...type:Metafunction.Size
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function unclippedLength()
 // ----------------------------------------------------------------------------
@@ -440,24 +329,11 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature TSize unclippedLength(gaps);
  *
- * @param gaps The Gaps object to query.
+ * @param[in] gaps The Gaps object to query.
  *
- * @return TSize The result.
+ * @return TSize The result (Metafunction: @link ContainerConcept#Size @endlink).
  */
 
-/**
-.Function.Gaps#unclippedLength
-..class:Class.Gaps
-..summary:Return length of the gapped sequence without clipping.
-..cat:Alignments
-..signature:TSize unclippedLength(gaps)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..returns:Length of the gapped sequence, ignoring any clipping.
-...type:Metafunction.Size
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function toViewPosition()
 // ----------------------------------------------------------------------------
@@ -468,27 +344,12 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature TPos toViewPosition(gaps, sourcePos);
  *
- * @param gaps      The gaps object to use for translation.
- * @param sourcePos The source position (in the underlying sequence) to translate.
+ * @param[in] gaps      The gaps object to use for translation.
+ * @param[in] sourcePos The source position (in the underlying sequence) to translate.
  *
- * @return TPos The resulting position in the view.
+ * @return TPos The resulting position in the view (Metafunction: @link ContainerConcept#Position @endlink).
  */
 
-/**
-.Function.toViewPosition
-..class:Class.Gaps
-..summary:Transforms source to view position.
-..cat:Alignments
-..signature:toViewPosition(gaps, pos)
-..param.gap:A Gaps object, e.g. a row in the alignment.
-...type:Class.Gaps
-..param.pos:Position in the original sequence to get the view position for.
-..returns:The position in the view/gaps position.
-..remarks:If $gap$ is a clipped alignment row, gaps in the clipped part will influence the result. The position $pos$ is counted from the unclipped begin position and must be greater or equal the clipped begin position of $gap$.
-..see:Function.toSourcePosition
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function toSourcePosition()
 // ----------------------------------------------------------------------------
@@ -499,27 +360,13 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature TPos toSourcePosition(gaps, viewPos);
  *
- * @param gaps      The gaps object to use for translation.
- * @param sourcePos The view position (including gaps and clipping) to translate.
+ * @param[in] gaps      The gaps object to use for translation.
+ * @param[in] sourcePos The view position (including gaps and clipping) to translate.
  *
- * @return TPos The resulting position in the underlying sequence.
+ * @return TPos The resulting position in the underlying sequence (Metafunction: @link ContainerConcept#Position
+ *              @endlink).
  */
 
-/**
-.Function.toSourcePosition
-..class:Class.Gaps
-..summary:Transforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned.
-..cat:Alignments
-..signature:toSourcePosition(gaps, pos)
-..param.gap:A Gaps object, e.g. a row in the alignment.
-...type:Class.Gaps
-..param.pos:Position in the view sequence (this includes gaps) to get the original position for.
-..returns:The position in the source sequence.
-..remarks:If $gap$ is a clipped alignment row, gaps in the clipped part will influence the result. The position $pos$ is counted from the unclipped begin position.
-..see:Function.toViewPosition
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function isGap()
 // ----------------------------------------------------------------------------
@@ -530,29 +377,39 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature bool isGap(gaps, viewPos);
  *
- * @param gaps    The Gaps object to query.
- * @param viewPos The view position (including clipping and gaps).
+ * @param[in] gaps    The Gaps object to query.
+ * @param[in] viewPos The view position (including clipping and gaps).
+ *
+ * @return bool The query result.
+ */
+
+template <typename TSequence, typename TSpec, typename TPos>
+bool isGap(Gaps<TSequence, TSpec> const & gaps, TPos clippedViewPos)
+{
+    return isGap(iter(gaps, clippedViewPos, Standard()));
+}
+
+// ----------------------------------------------------------------------------
+// Function isCharacter()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn Gaps#isCharacer
+ * @brief Query positions in a Gaps object for being a character.
+ *
+ * @signature bool isGap(gaps, viewPos);
+ *
+ * @param[in] gaps    The Gaps object to query.
+ * @param[in] viewPos The view position (including clipping and gaps).
  *
  * @return bool The query result.
  */
 
-/**
-.Function.Gaps#isGap
-..class:Class.Gaps
-..summary:Query whether a given clipped view position is a gap.
-..cat:Alignments
-..signature:bool isGap(gaps, clippedViewPos)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..param.clippedViewPos:The position in the view to query.
-...type:Metafunction.Position
-..returns:Whether or not there is a gap at the given clipped view position.
-...type:nolink:$bool$
-..see:Function.insertGap
-..see:Function.removeGap
-..see:Function.removeGaps
-..include:seqan/align.h
-*/
+template <typename TSequence, typename TSpec, typename TPos>
+bool isCharacter(Gaps<TSequence, TSpec> const & gaps, TPos clippedViewPos)
+{
+    return isCharacter(iter(gaps, clippedViewPos, Standard()));
+}
 
 // ----------------------------------------------------------------------------
 // Function insertGaps()
@@ -564,30 +421,11 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature void insertGaps(gaps, viewPos, count);
  *
- * @param gaps    The Gaps object to insert gaps into.
- * @param viewPos The view position (including clipping and gaps) to insert gaps at.
- * @param count   The number of gaps to insert.
+ * @param[in,out] gaps    The Gaps object to insert gaps into.
+ * @param[in]     viewPos The view position (including clipping and gaps) to insert gaps at.
+ * @param[in]     count   The number of gaps to insert.
  */
 
-/**
-.Function.insertGaps
-..class:Class.Gaps
-..summary:Insert multiple gaps into a gapped sequence.
-..cat:Alignments
-..signature:void insertGaps(gaps, clippedViewPos, count)
-..param.gaps:The @Class.Gaps@ object to insert gaps into.
-...type:Class.Gaps
-..param.clippedViewPos:The position in the view to insert gaps at.
-...type:Metafunction.Position
-..param.count:The number of gaps to insert
-...type:nolink:$unsigned$
-..returns:$void$
-..see:Function.insertGap
-..see:Function.removeGap
-..see:Function.removeGaps
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function insertGap()
 // ----------------------------------------------------------------------------
@@ -598,27 +436,10 @@ struct IsSequence<Gaps<TSequence, TSpec> const> : IsSequence<Gaps<TSequence, TSp
  *
  * @signature void insertGap(gaps, viewPos);
  *
- * @param gaps    The Gaps object to insert gap into.
- * @param viewPos The view position (including clipping and gaps) to insert the gap at.
+ * @param[in,out] gaps    The Gaps object to insert gap into.
+ * @param[in]     viewPos The view position (including clipping and gaps) to insert the gap at.
  */
 
-/**
-.Function.insertGap
-..class:Class.Gaps
-..summary:Insert one gap into a gapped sequence.
-..cat:Alignments
-..signature:void insertGap(gaps, clippedViewPos)
-..param.gaps:The @Class.Gaps@ object to insert gap into.
-...type:Class.Gaps
-..param.clippedViewPos:The position in the view to insert gap at.
-...type:Metafunction.Position
-..returns:$void$
-..see:Function.insertGaps
-..see:Function.removeGap
-..see:Function.removeGaps
-..include:seqan/align.h
-*/
-
 // Forward to removeGaps() which has to be implemented in each subclass.
 
 template <typename TSequence, typename TSpec, typename TPosition>
@@ -638,33 +459,13 @@ insertGap(Gaps<TSequence, TSpec> & gaps, TPosition clippedViewPos)
  *
  * @signature TSize removeGaps(gaps, viewPos, count);
  *
- * @param gaps    The gaps object to remove gap characters from.
- * @param viewPos The view positions to remove gap characters from.
- * @param count   The number of gap characters to remove.
+ * @param[in,out] gaps    The gaps object to remove gap characters from.
+ * @param[in]     viewPos The view positions to remove gap characters from.
+ * @param[in]     count   The number of gap characters to remove.
  *
- * @return TSize The number of gap characters removed.
+ * @return TSize The number of gap characters removed (Metafunction: @link ContainerConcept#Size @endlink).
  */
 
-/**
-.Function.removeGaps
-..class:Class.Gaps
-..summary:Remove multiple gaps from a gapped sequence.
-..cat:Alignments
-..signature:TSize removeGaps(gaps, clippedViewPos, count)
-..param.gaps:The @Class.Gaps@ object to remove gaps into.
-...type:Class.Gaps
-..param.clippedViewPos:The position in the view to remove gaps from.
-...type:Metafunction.Position
-..param.count:The number of gaps to remove
-...type:nolink:$unsigned$
-..returns:The number of removed gaps.
-...type:Metafunction.Size
-..see:Function.insertGap
-..see:Function.insertGaps
-..see:Function.removeGap
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function removeGap()
 // ----------------------------------------------------------------------------
@@ -675,30 +476,12 @@ insertGap(Gaps<TSequence, TSpec> & gaps, TPosition clippedViewPos)
  *
  * @signature TSize removeGap(gaps, viewPos);
  *
- * @param gaps    The gaps object to remove one gap character from.
- * @param viewPos The view positions to remove one gap character from.
+ * @param[in,out] gaps    The gaps object to remove one gap character from.
+ * @param[in]     viewPos The view positions to remove one gap character from.
  *
- * @return TSize The number of gap characters removed.
+ * @return TSize The number of gap characters removed (Metafunction: @link ContainerConcept#Size @endlink).
  */
 
-/**
-.Function.removeGap
-..class:Class.Gaps
-..summary:Remove one gap from a gapped sequence.
-..cat:Alignments
-..signature:TSize removeGap(gaps, clippedViewPos)
-..param.gaps:The @Class.Gaps@ object to remove gap into.
-...type:Class.Gaps
-..param.clippedViewPos:The position in the view to remove gap from.
-...type:Metafunction.Position
-..returns:The number of removed gaps.
-...type:Metafunction.Size
-..see:Function.insertGap
-..see:Function.insertGaps
-..see:Function.removeGaps
-..include:seqan/align.h
-*/
-
 // Forward to removeGaps() which has to be implemented in each subclass.
 
 template <typename TSequence, typename TSpec, typename TPosition>
@@ -707,7 +490,7 @@ removeGap(Gaps<TSequence, TSpec> & gaps, TPosition clippedViewPos)
 {
     return removeGaps(gaps, clippedViewPos, 1u);
 }
-    
+
 // ----------------------------------------------------------------------------
 // Function countGaps()
 // ----------------------------------------------------------------------------
@@ -718,24 +501,63 @@ removeGap(Gaps<TSequence, TSpec> & gaps, TPosition clippedViewPos)
  *
  * @signature TSize countGaps(gaps, viewPos);
  *
- * @param gaps    The Gaps object to query.
- * @param viewPos View position (including clipping and gaps) to query at.
+ * @param[in] gaps    The Gaps object to query.
+ * @param[in] viewPos View position (including clipping and gaps) to query at.
+ *
+ * @return TSize The number of gap characters at <tt>viewPos</tt>  (Metafunction: @link ContainerConcept#Size
+ *               @endlink).
+ */
+
+template <typename TSequence, typename TSpec, typename TPos>
+typename Size<Gaps<TSequence, TSpec> >::Type
+countGaps(Gaps<TSequence, TSpec> const & gaps, TPos clippedViewPos)
+{
+    return countGaps(iter(gaps, clippedViewPos, Standard()));
+}
+
+// ----------------------------------------------------------------------------
+// Function countLeadingGaps()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn Gaps#countLeadingGaps
+ * @brief The number of leading gaps.
+ *
+ * @signature TSize countLeadingGaps(gaps);
+ *
+ * @param[in] gaps    The Gaps object to query.
+ *
+ * @return TSize The number of leading gap characters  (Metafunction: @link ContainerConcept#Size @endlink).
+ */
+
+template <typename TGaps>
+inline typename Size<TGaps>::Type
+countLeadingGaps(TGaps const & gaps)
+{
+    return toViewPosition(gaps, 0);
+}
+
+// ----------------------------------------------------------------------------
+// Function countTrailingGaps()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn Gaps#countTrailingGaps
+ * @brief The number of trailing gaps.
+ *
+ * @signature TSize countTrailingGaps(gaps);
  *
- * @return TSize The number of gap characters at <tt>viewPos</tt>.
+ * @param[in] gaps    The Gaps object to query.
+ *
+ * @return TSize The number of trailing gap characters  (Metafunction: @link ContainerConcept#Size @endlink).
  */
 
-/**
-.Function.Gaps#countGaps
-..class:Class.Gaps
-..summary:Reports number of continues gaps right of current iterator position.
-..cat:Alignments
-..signature:TSize countGaps(iter)
-..param.iter:Iterator of the  @Class.Gaps@ object to count gaps for.
-...type:Metafunction.Iterator
-..returns:The number of gaps right of the current iterator position, including the current position, or $0$ if there is no gap.
-...type:Metafunction.Size
-..include:seqan/align.h
-*/
+template <typename TGaps>
+inline typename Size<TGaps>::Type
+countTrailingGaps(TGaps const & gaps)
+{
+    return length(gaps) - toViewPosition(gaps, length(source(gaps)) - 1) - 1;
+}
 
 // ----------------------------------------------------------------------------
 // Function countCharacters()
@@ -747,12 +569,20 @@ removeGap(Gaps<TSequence, TSpec> & gaps, TPosition clippedViewPos)
  *
  * @signature TSize countCharacters(gaps, viewPos);
  *
- * @param gaps    The Gaps object to query.
- * @param viewPos View position (including clipping and gaps) to query at.
+ * @param[in] gaps    The Gaps object to query.
+ * @param[in] viewPos View position (including clipping and gaps) to query at.
  *
- * @return TSize The number of non-gaps characters characters at <tt>viewPos</tt>.
+ * @return TSize The number of non-gaps characters characters at <tt>viewPos</tt> (Metafunction: @link
+ *               ContainerConcept#Size @endlink).
  */
 
+template <typename TSequence, typename TSpec, typename TPos>
+typename Size<Gaps<TSequence, TSpec> >::Type
+countCharacters(Gaps<TSequence, TSpec> const & gaps, TPos clippedViewPos)
+{
+    return countCharacters(iter(gaps, clippedViewPos, Standard()));
+}
+
 // ----------------------------------------------------------------------------
 // Function setClippedBeginPosition()
 // ----------------------------------------------------------------------------
@@ -763,31 +593,10 @@ removeGap(Gaps<TSequence, TSpec> & gaps, TPosition clippedViewPos)
  *
  * @signature void setClippedBeginPosition(gaps, unclippedViewPos);
  *
- * @param gaps             The Gaps object to set the clipping begin position of.
- * @param unclippedViewPos View position (including gaps but excluding clipping) to set the clipping begin to.
+ * @param[in,out] gaps             The Gaps object to set the clipping begin position of.
+ * @param[in]     unclippedViewPos View position (including gaps but excluding clipping) to set the clipping begin to.
  */
 
-/**
-.Function.Gaps#setClippedBeginPosition
-..class:Class.Gaps
-..summary:Sets the begin position of the clipping.
-..signature:void setClippedBeginPosition(gaps, unclippedViewPosition)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..param.unclippedViewPosition:The position in the unclipped view to set as the clipping begin position.
-...type:Metafunction.Position
-..returns:$void$
-..remarks:Note that the position is *not* a clipped view position but an uncliped one!
-..see:Function.Gaps#beginPosition
-..see:Function.Gaps#endPosition
-..see:Function.Gaps#setBeginPosition
-..see:Function.Gaps#setEndPosition
-..see:Function.Gaps#clippedBeginPosition
-..see:Function.Gaps#clippedEndPosition
-..see:Function.Gaps#setClippedEndPosition
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function setClippedEndPosition()
 // ----------------------------------------------------------------------------
@@ -798,31 +607,10 @@ removeGap(Gaps<TSequence, TSpec> & gaps, TPosition clippedViewPos)
  *
  * @signature void setClippedEndPosition(gaps, unclippedViewPos);
  *
- * @param gaps             The Gaps object to set the clipping end position of.
- * @param unclippedViewPos View position (including gaps but excluding clipping) to set the clipping end to.
+ * @param[in,out] gaps             The Gaps object to set the clipping end position of.
+ * @param[in]     unclippedViewPos View position (including gaps but excluding clipping) to set the clipping end to.
  */
 
-/**
-.Function.Gaps#setClippedEndPosition
-..class:Class.Gaps
-..summary:Sets the end position of the clipping.
-..signature:void setClippedEndPosition(gaps, unclippedViewPosition)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..param.unclippedViewPosition:The position in the unclipped view to set as the clipping end position.
-...type:Metafunction.Position
-..returns:$void$
-..remarks:Note that the position is *not* a clipped view position but an uncliped one!
-..see:Function.Gaps#beginPosition
-..see:Function.Gaps#endPosition
-..see:Function.Gaps#setBeginPosition
-..see:Function.Gaps#setEndPosition
-..see:Function.Gaps#clippedBeginPosition
-..see:Function.Gaps#clippedEndPosition
-..see:Function.Gaps#setClippedBeginPosition
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function clippedBeginPosition()
 // ----------------------------------------------------------------------------
@@ -833,56 +621,26 @@ removeGap(Gaps<TSequence, TSpec> & gaps, TPosition clippedViewPos)
  *
  * @signature TPos clippedBeginPosition(gaps);
  *
- * @param gaps             The Gaps object to query.
+ * @param[in] gaps             The Gaps object to query.
  *
- * @return TPos The begin position of the unclipped view.
+ * @return TPos The begin position of the unclipped view  (Metafunction: @link ContainerConcept#Position @endlink).
  *
  * @section Example
  *
  * In the following gaps configuration, the result of <tt>clippedBeginPosition(gaps)</tt> is 1.
  *
- * @code
+ * @code{.txt}
  * clipping                   [     )
- *   (half-open interval)           
- * 
+ *   (half-open interval)
+ *
  * gapped sequence:          X--XXX-XX-
- * 
+ *
  * source position:          0111234456
  * unclipped view position:  0123456789
  * clipped view position:     0123456
  * @endcode
  */
 
-/**
-.Function.Gaps#clippedBeginPosition
-..class:Class.Gaps
-..summary:Return the begin position of the clipping in the unclipped gapped sequence.
-..signature:TPosition clippedBeginPosition(gaps)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..returns:The begin position of the current clipped view in the unclipped gapped sequence.
-...type:Metafunction.Position
-..see:Function.Gaps#beginPosition
-..see:Function.Gaps#endPosition
-..see:Function.Gaps#setBeginPosition
-..see:Function.Gaps#setEndPosition
-..see:Function.Gaps#clippedEndPosition
-..see:Function.Gaps#setClippedBeginPosition
-..see:Function.Gaps#setClippedEndPosition
-..example:
-In the following gaps configuration, the result of $clippedBeginPosition(gaps)$ is $1$.
-..example.code:
-clipping                   [     )
-  (half-open interval)           
-
-gapped sequence:          X--XXX-XX-
-
-source position:          0111234456
-unclipped view position:  0123456789
-clipped view position:     0123456
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function clippedEndPosition()
 // ----------------------------------------------------------------------------
@@ -893,56 +651,26 @@ clipped view position:     0123456
  *
  * @signature TPos clippedEndPosition(gaps);
  *
- * @param gaps             The Gaps object to query.
+ * @param[in] gaps             The Gaps object to query.
  *
- * @return TPos The end position of the unclipped view.
+ * @return TPos The end position of the unclipped view  (Metafunction: @link ContainerConcept#Position @endlink).
  *
  * @section Example
  *
  * In the following gaps configuration, the result of <tt>clippedEndPosition(gaps)</tt> is 7.
  *
- * @code
+ * @code{.txt}
  * clipping                   [     )
- *   (half-open interval)           
- * 
+ *   (half-open interval)
+ *
  * gapped sequence:          X--XXX-XX-
- * 
+ *
  * source position:          0111234456
  * unclipped view position:  0123456789
  * clipped view position:     0123456
  * @endcode
  */
 
-/**
-.Function.Gaps#clippedEndPosition
-..class:Class.Gaps
-..summary:Return the end position of the clipping in the unclipped gapped sequence.
-..signature:TPosition clippedEndPosition(gaps)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..returns:The end position of the current clipped view in the unclipped gapped sequence.
-...type:Metafunction.Position
-..see:Function.Gaps#beginPosition
-..see:Function.Gaps#endPosition
-..see:Function.Gaps#setBeginPosition
-..see:Function.Gaps#setEndPosition
-..see:Function.Gaps#clippedBeginPosition
-..see:Function.Gaps#setClippedBeginPosition
-..see:Function.Gaps#setClippedEndPosition
-..example:
-In the following gaps configuration, the result of $clippedEndPosition(gaps)$ is $7$.
-..example.code:
-clipping                   [     )
-  (half-open interval)           
-
-gapped sequence:          X--XXX-XX-
-
-source position:          0111234456
-unclipped view position:  0123456789
-clipped view position:     0123456
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function setBeginPosition()
 // ----------------------------------------------------------------------------
@@ -953,30 +681,10 @@ clipped view position:     0123456
  *
  * @signature void setBeginPosition(gaps, sourcePos);
  *
- * @param gaps      The Gaps object to set the begin position in.
- * @param sourcePos Position in the underlying sequence to set clipping to.
+ * @param[in,out] gaps      The Gaps object to set the begin position in.
+ * @param[in]     sourcePos Position in the underlying sequence to set clipping to.
  */
 
-/**
-.Function.Gaps#setBeginPosition
-..class:Class.Gaps
-..summary:Set the begin position of the clipped gapped sequence, given a source position.
-..signature:void setBeginPosition(gaps, sourcePosition)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..param.sourcePosition:The source position to set the clipping begin to.
-...type:Metafunction.Position
-..returns:$void$
-..see:Function.Gaps#beginPosition
-..see:Function.Gaps#endPosition
-..see:Function.Gaps#setEndPosition
-..see:Function.Gaps#clippedBeginPosition
-..see:Function.Gaps#clippedEndPosition
-..see:Function.Gaps#setClippedBeginPosition
-..see:Function.Gaps#setClippedEndPosition
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function setEndPosition()
 // ----------------------------------------------------------------------------
@@ -987,30 +695,10 @@ clipped view position:     0123456
  *
  * @signature void setEndPosition(gaps, sourcePos);
  *
- * @param gaps      The Gaps object to set the end position in.
- * @param sourcePos Position in the underlying sequence to set clipping to.
+ * @param[in,out] gaps      The Gaps object to set the end position in.
+ * @param[in]     sourcePos Position in the underlying sequence to set clipping to.
  */
 
-/**
-.Function.Gaps#setEndPosition
-..class:Class.Gaps
-..summary:Set the end position of the clipped gapped sequence, given a source position.
-..signature:void setEndPosition(gaps, sourcePosition)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..param.sourcePosition:The source position to set the clipping end to.
-...type:Metafunction.Position
-..returns:$void$
-..see:Function.Gaps#beginPosition
-..see:Function.Gaps#endPosition
-..see:Function.Gaps#setBeginPosition
-..see:Function.Gaps#clippedBeginPosition
-..see:Function.Gaps#clippedEndPosition
-..see:Function.Gaps#setClippedBeginPosition
-..see:Function.Gaps#setClippedEndPosition
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function beginPosition()
 // ----------------------------------------------------------------------------
@@ -1019,60 +707,29 @@ clipped view position:     0123456
  * @fn Gaps#beginPosition
  * @brief Return the clipping begin position as a source position.
  *
- * @signature TPosition beginPosition(gaps);
+ * @signature TPos beginPosition(gaps);
  *
- * @param gaps The Gaps object to query.
+ * @param[in] gaps The Gaps object to query.
  *
- * @return TPosition The clipping begin position in the source.
+ * @return TPos The clipping begin position in the source (Metafunction: @link ContainerConcept#Position @endlink).
  *
  * @section Example
  *
  * In the following gaps configuration, the result of <tt>beginPosition(gaps)</tt> is $1$.  The clipping starts in a
  * gap and the source position of the first non-gap character right of the clipping begin has source position 1.
  *
- * @code
+ * @code{.txt}
  * clipping                   [     )
- *   (half-open interval)           
- * 
+ *   (half-open interval)
+ *
  * gapped sequence:          X--XXX-XX-
- * 
+ *
  * source position:          0111234456
  * unclipped view position:  0123456789
  * clipped view position:     0123456
  * @endcode
  */
 
-/**
-.Function.Gaps#beginPosition
-..class:Class.Gaps
-..summary:Return the clipping begin position as a source position.
-..signature:TPosition beginPosition(gaps)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..returns:The begin position of the current clipped view in the source.
-...type:Metafunction.Position
-..see:Function.Gaps#endPosition
-..see:Function.Gaps#setBeginPosition
-..see:Function.Gaps#setEndPosition
-..see:Function.Gaps#clippedBeginPosition
-..see:Function.Gaps#clippedEndPosition
-..see:Function.Gaps#setClippedBeginPosition
-..see:Function.Gaps#setClippedEndPosition
-..example:
-In the following gaps configuration, the result of $beginPosition(gaps)$ is $1$.
-The clipping starts in a gap and the source position of the first non-gap character right of the clipping begin has source position $1$.
-..example.code:
-clipping                   [     )
-  (half-open interval)           
-
-gapped sequence:          X--XXX-XX-
-
-source position:          0111234456
-unclipped view position:  0123456789
-clipped view position:     0123456
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function endPosition()
 // ----------------------------------------------------------------------------
@@ -1081,81 +738,47 @@ clipped view position:     0123456
  * @fn Gaps#endPosition
  * @brief Return the clipping end position as a source position.
  *
- * @signature TPosition endPosition(gaps);
+ * @signature TPos endPosition(gaps);
  *
- * @param gaps The Gaps object to query for the end position as a source position.
+ * @param[in] gaps The Gaps object to query for the end position as a source position.
  *
- * @return TPosition The end position as a source position.
+ * @return TPos The end position as a source position (Metafunction: @link ContainerConcept#Position @endlink).
  *
  * @section Example
  *
  * In the following gaps configuration, the result of <tt>endPositioN(gaps)</tt> is 4.
  *
- * @code
+ * @code{.txt}
  * clipping                   [     )
- *   (half-open interval)           
- * 
+ *   (half-open interval)
+ *
  * gapped sequence:          X--XXX-XX-
- * 
+ *
  * source position:          0111234456
  * unclipped view position:  0123456789
  * clipped view position:     0123456
  * @endcode
  */
 
-/**
-.Function.Gaps#endPosition
-..class:Class.Gaps
-..summary:Return the clipping end position as a source position.
-..signature:TPosition endPosition(gaps)
-..param.gaps:The @Class.Gaps@ object to query.
-...type:Class.Gaps
-..returns:The end position of the current clipped view in the source.
-...type:Metafunction.Position
-..see:Function.Gaps#beginPosition
-..see:Function.Gaps#setBeginPosition
-..see:Function.Gaps#setEndPosition
-..see:Function.Gaps#clippedBeginPosition
-..see:Function.Gaps#clippedEndPosition
-..see:Function.Gaps#setClippedBeginPosition
-..see:Function.Gaps#setClippedEndPosition
-..example:
-In the following gaps configuration, the result of $endPosition(gaps)$ is $4$.
-..example.code:
-clipping                   [     )
-  (half-open interval)           
-
-gapped sequence:          X--XXX-XX-
-
-source position:          0111234456
-unclipped view position:  0123456789
-clipped view position:     0123456
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function write()
 // ----------------------------------------------------------------------------
 
-template <typename TFile, typename TSource, typename TIDString, typename TSpec>
+template <typename TTarget, typename TSource, typename TSpec>
 inline void
-write(TFile & target,
-	  Gaps<TSource, TSpec> const & source, 
-	  TIDString const &,
-	  Raw)
+write(TTarget & target,
+      Gaps<TSource, TSpec> const & source)
 {
-//IOREV _nodoc_ specialization not documented
-
-	// Print gaps row
-	typedef typename Iterator<Gaps<TSource, TSpec> const>::Type TIter;
-	TIter begin_ = begin(source);
-	TIter end_ = end(source);
-	for (; begin_ != end_; ++begin_) {
-		if (isGap(begin_))
-			streamPut(target, gapValue<char>());
-		else 
-			streamPut(target, convert<char>(*begin_));
-	}
+    // Print gaps row
+    typedef typename Iterator<Gaps<TSource, TSpec> const>::Type TIter;
+    TIter begin_ = begin(source);
+    TIter end_ = end(source);
+    for (; begin_ != end_; ++begin_) {
+        if (isGap(begin_))
+            writeValue(target, gapValue<char>());
+        else
+            writeValue(target, convert<char>(getValue(begin_)));
+    }
 }
 
 // ----------------------------------------------------------------------------
@@ -1164,23 +787,13 @@ write(TFile & target,
 
 // TODO(holtgrew): Document appropriately.
 
-template <typename TStream, typename TSource, typename TSpec>
-inline TStream &
-operator<<(TStream & stream, Gaps<TSource, TSpec> const & gaps)
+template <typename TTarget, typename TSource, typename TSpec>
+inline TTarget &
+operator<<(TTarget & target, Gaps<TSource, TSpec> const & gaps)
 {
-    typedef Gaps<TSource, TSpec> const             TGaps;
-    typedef typename Iterator<TGaps, Rooted>::Type TIter;
-
-    for (TIter it = begin(gaps, Rooted()); !atEnd(it); goNext(it))
-    {
-        // TODO(holtgrew): Ideally, we could simply print the expanded alphabet char but that is broken.
-        if (isGap(it))
-            stream << gapValue<char>();
-        else
-            stream << convert<char>(*it);
-    }
-
-    return stream;
+    typename DirectionIterator<TTarget, Output>::Type it = directionIterator(target, Output());
+    write(it, gaps);
+    return target;
 }
 
 // ----------------------------------------------------------------------------
@@ -1204,51 +817,39 @@ void _pumpTraceToGaps(Gaps<TSequenceH, TGapsSpecH> & gapsH,
     typedef typename Iterator<TGapsV, Standard>::Type TGapsVIter;
 
     // TODO(holtgrew): I don't understand the following.  Originally, this function used Align objects, but I did not understand it there either.
-	// TODO(rausch): Pump trace into align_ (note: this is relatively slow code here. it could be improved if specialized to the Align Specs).
+    // TODO(rausch): Pump trace into align_ (note: this is relatively slow code here. it could be improved if specialized to the Align Specs).
     clearGaps(gapsH);
     clearClipping(gapsH);
     clearGaps(gapsV);
     clearClipping(gapsV);
 
-	TSize i = length(trace.sizes);  // Scan trace backwards.
-	TGapsHIter itH = begin(gapsH);
-	TGapsVIter itV = begin(gapsV);
-	while (i > 0)
-	{
-		--i;
-		TSize size = trace.sizes[i];
-		switch ((int) trace.tvs[i])
-		{
-		case 1:  // Go horizontal.
-			insertGaps(itV, size);
-			break;
-
-		case 2:  // Go vertical.
-			insertGaps(itH, size);
-			break;
-		}
-		goFurther(itH, size);
-		goFurther(itV, size);
-	}
+    TSize i = length(trace.sizes);  // Scan trace backwards.
+    TGapsHIter itH = begin(gapsH);
+    TGapsVIter itV = begin(gapsV);
+    while (i > 0)
+    {
+        --i;
+        TSize size = trace.sizes[i];
+        switch ((int) trace.tvs[i])
+        {
+        case 1:  // Go horizontal.
+            insertGaps(itV, size);
+            break;
+
+        case 2:  // Go vertical.
+            insertGaps(itH, size);
+            break;
+        }
+        goFurther(itH, size);
+        goFurther(itV, size);
+    }
 }
 
 // ----------------------------------------------------------------------------
 // Function source()
 // ----------------------------------------------------------------------------
 
-// TODO(holtgrew): source concept in dox?
-
-/**
-.Function.source
-..summary:Return underlying object.
-..cat:Basic
-..signature:source(obj)
-..param.obj:The object to get underlying sequence of.
-...type:Class.Gaps
-..returns:The underlying object.
-...type:Metafunction.Source
-..include:seqan/align.h
-*/
+// TODO(holtgrew): Document TSource via metafunctio.
 
 /*!
  * @fn Gaps#source
@@ -1256,23 +857,11 @@ void _pumpTraceToGaps(Gaps<TSequenceH, TGapsSpecH> & gapsH,
  *
  * @signature TSource source(gaps);
  *
- * @param gaps The Gaps object to return the underling sequence for.
- * 
+ * @param[in] gaps The Gaps object to return the underling sequence for.
+ *
  * @return TSource Reference to the source of the Gaps.
  */
 
-/*
-.Function.Gaps#source
-..summary:Return underlying sequence.
-..cat:Alignments
-..signature:TSource source(gaps)
-..param.obj:The object to get underlying sequence of.
-...type:Class.Gaps
-..returns:Reference to the underlying sequence.
-...type:Metafunction.Source
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function sourceSegment()
 // ----------------------------------------------------------------------------
@@ -1313,27 +902,10 @@ sourceSegment(Gaps<TSequence, TSpec> & gaps)
  *
  * @signature void assignSource(gaps, seq);
  *
- * @param gaps The Gaps object to assign the source of.
- * @param seq  The @link SequenceConcept sequence @endlink to assign to the underlying string.:w
+ * @param[in,out] gaps The Gaps object to assign the source of.
+ * @param[in]     seq  The @link ContainerConcept sequence @endlink to assign to the underlying string.
  */
 
-/**
-.Function.Gaps#assignSource
-..class:Class.Gaps
-..summary:Assign the source of a Gaps object, copying data.
-..cat:Alignments
-..signature:void assignSource(gaps, sequence)
-..param.gaps:The @Class.Gaps@ object to assign the source of.
-...type:Class.Gaps
-..param.sequence:The @Concept.SequenceConcept@ to assign as the source.
-...type:Metafunction.Source
-..remarks:This will copy $sequence$ into the source of $gaps$.
-..returns:$void$
-..see:Function.Gaps#setSource
-..see:Function.source
-..include:seqan/align.h
-*/
-
 // TOOD(holtgrew): Switch to Hosted Type?
 
 template <typename TSequence, typename TSpec, typename TValue>
@@ -1347,23 +919,6 @@ assignSource(Gaps<TSequence, TSpec> & gaps, TValue const & value)
 // Function setSource()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.Gaps#setSource
-..class:Class.Gaps
-..summary:Set the source of a Gaps object, do not copy if possible.
-..cat:Alignments
-..signature:void setSource(gaps, sequence)
-..param.gaps:The @Class.Gaps@ object to set the source of.
-...type:Class.Gaps
-..param.sequence:The @Concept.SequenceConcept@ to set as the source.
-...type:Metafunction.Source
-..remarks:This will avoid copying if possible.
-..returns:$void$
-..see:Function.Gaps#assignSource
-..see:Function.source
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function copyGaps()
 // ----------------------------------------------------------------------------
@@ -1376,8 +931,8 @@ assignSource(Gaps<TSequence, TSpec> & gaps, TValue const & value)
  *
  * @signature void copyGaps(dest, source);
  *
- * @param[out] dest   The destination Gaps object (appropriate clipping, no gaps).
- * @param[in]  source The source Gaps object.
+ * @param[in,out] dest   The destination Gaps object (appropriate clipping, no gaps).
+ * @param[in]     source The source Gaps object.
  */
 
 template <typename TDestSource, typename TDestSpec, typename TSourceSource, typename TSourceSpec>
@@ -1419,8 +974,8 @@ void copyGaps(Gaps<TDestSource, TDestSpec> & dest, Gaps<TSourceSource, TSourceSp
  *
  * @signature void copyClipping(dest, source);
  *
- * @param[out] dest   The destination Gaps object.
- * @param[in]  source The source Gaps object.
+ * @param[in,out] dest   The destination Gaps object.
+ * @param[in]     source The source Gaps object.
  */
 
 template <typename TDestSource, typename TDestSpec, typename TSourceSource, typename TSourceSpec>
@@ -1431,10 +986,40 @@ void copyClipping(Gaps<TDestSource, TDestSpec> & dest, Gaps<TSourceSource, TSour
 }
 
 // ----------------------------------------------------------------------------
-// Function clear()
+// Function clipSemiGlobal()
 // ----------------------------------------------------------------------------
 
-///.Function.clear.class:Class.Gaps
+/*!
+ * @fn Gaps#clipSemiGlobal
+ * @brief Clip the Gaps objects to reflect a semi-global alignment.
+ *
+ * Leading and trailing gaps are clipped in the local Gaps object. The global Gaps object is updated accordingly.
+ *
+ * @signature void clipSemiGlobal(global, local);
+ *
+ * @param[in,out] global The global Gaps object.
+ * @param[in,out] local  The local Gaps object.
+ */
+
+template <typename TGlobalGaps, typename TLocalGaps>
+inline void clipSemiGlobal(TGlobalGaps & global, TLocalGaps & local)
+{
+    typedef typename Size<TLocalGaps>::Type  TGapsSize;
+
+    TGapsSize leadingGaps = countLeadingGaps(local);
+    TGapsSize trailingGaps = countTrailingGaps(local);
+    TGapsSize globalLenght = length(global);
+    TGapsSize localLength = length(local);
+
+    setClippedBeginPosition(global, leadingGaps);
+    setClippedBeginPosition(local, leadingGaps);
+    setClippedEndPosition(global, globalLenght - trailingGaps);
+    setClippedEndPosition(local, localLength - trailingGaps);
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
 
 template <typename TSequence, typename TSpec>
 inline void clearGaps(Gaps<TSequence, TSpec> & gaps);
@@ -1482,4 +1067,4 @@ inline bool operator!=(Gaps<TSequence, TSpec> const & lhs,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_
diff --git a/seqan/align/gaps_iterator_anchor.h b/seqan/align/gaps_iterator_anchor.h
index 7692a8a..fb8c87a 100644
--- a/seqan/align/gaps_iterator_anchor.h
+++ b/seqan/align/gaps_iterator_anchor.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_
 
 namespace seqan {
 
@@ -51,82 +51,82 @@ template <typename TGaps_, typename TGapAnchors_> //Gaps<TSource_, AnchorGaps<TG
 class Iter<TGaps_, GapsIterator<AnchorGaps<TGapAnchors_> > >
 {
 public:
-	typedef TGaps_											TGaps;
-	typedef typename Source<TGaps>::Type					TSource;
-	typedef TGapAnchors_									TGapAnchors;
+    typedef TGaps_                                            TGaps;
+    typedef typename Source<TGaps>::Type                    TSource;
+    typedef TGapAnchors_                                    TGapAnchors;
 
     // TODO(holtgrew): Why is the following commented out?
-//	typedef typename Value<TGapAnchors>::Type				TGapAnchor;
+//    typedef typename Value<TGapAnchors>::Type                TGapAnchor;
     typedef typename Size<typename Value<TGapAnchors>::Type>::Type          TGapAnchorSize_;
-	typedef GapAnchor<typename MakeSigned_<TGapAnchorSize_>::Type>          TGapAnchor;
-	typedef typename MakeSigned<typename Position<TGapAnchor>::Type>::Type  TGapPos;
-	typedef typename Iterator<TGapAnchors, Standard>::Type                  TAnchorIter;
-
-	TGaps *					data_container;							//the gaps object
-	TGapPos 				seqLength;
-	mutable TGapAnchor		current;
-	mutable TGapAnchor		prevAnchor;
-	mutable TGapAnchor		nextAnchor;
-	mutable TGapAnchor		viewBegin;
-	mutable TGapAnchor		viewEnd;
-	mutable int				anchorIdx;
+    typedef GapAnchor<typename MakeSigned_<TGapAnchorSize_>::Type>          TGapAnchor;
+    typedef typename MakeSigned<typename Position<TGapAnchor>::Type>::Type  TGapPos;
+    typedef typename Iterator<TGapAnchors, Standard>::Type                  TAnchorIter;
+
+    TGaps *                    data_container;                            //the gaps object
+    TGapPos                 seqLength;
+    mutable TGapAnchor        current;
+    mutable TGapAnchor        prevAnchor;
+    mutable TGapAnchor        nextAnchor;
+    mutable TGapAnchor        viewBegin;
+    mutable TGapAnchor        viewEnd;
+    mutable int                anchorIdx;
 
 public:
-	Iter() 
-	{
+    Iter()
+    {
 SEQAN_CHECKPOINT
-		data_container = NULL;
-		seqLength = 0;
-	}
-/*	Iter(Iter const & other_):
-		data_container(other_.data_container),
-		seqLength(other_.seqLength),
-		current(other_.current),
-		prevAnchor(other_.prevAnchor),
-		nextAnchor(other_.nextAnchor),
-		anchorIdx(other_.anchorIdx)
-	{
+        data_container = NULL;
+        seqLength = 0;
+    }
+/*    Iter(Iter const & other_):
+        data_container(other_.data_container),
+        seqLength(other_.seqLength),
+        current(other_.current),
+        prevAnchor(other_.prevAnchor),
+        nextAnchor(other_.nextAnchor),
+        anchorIdx(other_.anchorIdx)
+    {
 SEQAN_CHECKPOINT
-	}
-*/	Iter(TGaps & container_):
-		data_container(&container_)
-	{
+    }
+*/    Iter(TGaps & container_):
+        data_container(&container_)
+    {
 SEQAN_CHECKPOINT
-		_assignSourceLength(seqLength, container_);
-		_goToGapAnchorIterator(*this, data_container->data_viewCutBegin + data_container->data_cutBegin);
-		viewBegin = current;
-		viewEnd.gapPos   = _unclippedLength(*data_container) + data_container->data_cutBegin - data_container->data_viewCutEnd;
-		viewEnd.seqPos = positionGapToSeq(*data_container, viewEnd.gapPos);
-	}
-	Iter(TGaps & container_, TGapPos clippedViewPosition):
-		data_container(&container_)
-	{
+        _assignSourceLength(seqLength, container_);
+        _goToGapAnchorIterator(*this, data_container->data_viewCutBegin + data_container->data_cutBegin);
+        viewBegin = current;
+        viewEnd.gapPos   = _unclippedLength(*data_container) + data_container->data_cutBegin - data_container->data_viewCutEnd;
+        viewEnd.seqPos = positionGapToSeq(*data_container, viewEnd.gapPos);
+    }
+    Iter(TGaps & container_, TGapPos clippedViewPosition):
+        data_container(&container_)
+    {
 SEQAN_CHECKPOINT
-		_assignSourceLength(seqLength, container_);
-		_goToGapAnchorIterator(*this, clippedViewPosition + data_container->data_viewCutBegin + data_container->data_cutBegin);
-		viewBegin.gapPos = data_container->data_viewCutBegin + data_container->data_cutBegin;
-		viewEnd.gapPos   = _unclippedLength(*data_container) + data_container->data_cutBegin - data_container->data_viewCutEnd;
-		viewBegin.seqPos = positionGapToSeq(*data_container, viewBegin.gapPos);
-		viewEnd.seqPos   = positionGapToSeq(*data_container, viewEnd.gapPos);
-	}
-	~Iter()
-	{
+        _assignSourceLength(seqLength, container_);
+        _goToGapAnchorIterator(*this, clippedViewPosition + data_container->data_viewCutBegin + data_container->data_cutBegin);
+        viewBegin.gapPos = data_container->data_viewCutBegin + data_container->data_cutBegin;
+        viewEnd.gapPos   = _unclippedLength(*data_container) + data_container->data_cutBegin - data_container->data_viewCutEnd;
+        viewBegin.seqPos = positionGapToSeq(*data_container, viewBegin.gapPos);
+        viewEnd.seqPos   = positionGapToSeq(*data_container, viewEnd.gapPos);
+    }
+    ~Iter()
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	Iter const & operator = (Iter const & other_)
-	{
+    Iter const & operator = (Iter const & other_)
+    {
 SEQAN_CHECKPOINT
-		data_container = other_.data_container;
-		seqLength = other_.seqLength;
-		current = other_.current;
-		prevAnchor = other_.prevAnchor;
-		nextAnchor = other_.nextAnchor;
-		anchorIdx = other_.anchorIdx;
-		viewBegin = other_.viewBegin;
-		viewEnd = other_.viewEnd;
-		return *this;
-	}
+        data_container = other_.data_container;
+        seqLength = other_.seqLength;
+        current = other_.current;
+        prevAnchor = other_.prevAnchor;
+        nextAnchor = other_.nextAnchor;
+        anchorIdx = other_.anchorIdx;
+        viewBegin = other_.viewBegin;
+        viewEnd = other_.viewEnd;
+        return *this;
+    }
 };
 
 // ============================================================================
@@ -147,14 +147,14 @@ template <typename TGaps, typename TGapsArray>
 inline TGaps &
 container(Iter<TGaps, GapsIterator<AnchorGaps<TGapsArray> > > & me)
 {
-	return *me.data_container;
+    return *me.data_container;
 }
 
 template <typename TGaps, typename TGapsArray>
 inline TGaps &
 container(Iter<TGaps, GapsIterator<AnchorGaps<TGapsArray> > > const & me)
 {
-	return *me.data_container;
+    return *me.data_container;
 }
 
 // ----------------------------------------------------------------------------
@@ -165,14 +165,14 @@ template <typename TGaps, typename TGapAnchors>
 inline typename Source<Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const>::Type
 source(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me)
 {
-	return begin(source(*me.data_container), Rooted()) + me.current.seqPos;
+    return begin(source(*me.data_container), Rooted()) + me.current.seqPos;
 }
 
 template <typename TGaps, typename TGapAnchors>
 inline typename Source<Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > >::Type
 source(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 {
-	return begin(source(*me.data_container), Rooted()) + me.current.seqPos;
+    return begin(source(*me.data_container), Rooted()) + me.current.seqPos;
 }
 
 // ----------------------------------------------------------------------------
@@ -183,20 +183,20 @@ template <typename TGaps, typename TGapAnchors>
 inline typename GetValue< Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > >::Type
 getValue(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me)
 {
-	typedef typename Value<Iter<TGaps, GapsIterator<ArrayGaps> > >::Type TValue;
-	if (isGap(me)) return gapValue<TValue>();
-	else if (isUnknown(me)) return unknownValue<TValue>();
-	else return getValue(source(me));
+    typedef typename Value<Iter<TGaps, GapsIterator<ArrayGaps> > >::Type TValue;
+    if (isGap(me)) return gapValue<TValue>();
+    else if (isUnknown(me)) return unknownValue<TValue>();
+    else return getValue(source(me));
 }
 
 template <typename TGaps, typename TGapAnchors>
 inline typename GetValue< Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const>::Type
 getValue(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 {
-	typedef typename Value<Iter<TGaps, GapsIterator<ArrayGaps> > const>::Type TValue;
-	if (isGap(me)) return gapValue<TValue>();
-	else if (isUnknown(me)) return unknownValue<TValue>();
-	else return getValue(source(me));
+    typedef typename Value<Iter<TGaps, GapsIterator<ArrayGaps> > const>::Type TValue;
+    if (isGap(me)) return gapValue<TValue>();
+    else if (isUnknown(me)) return unknownValue<TValue>();
+    else return getValue(source(me));
 }
 
 // ----------------------------------------------------------------------------
@@ -227,7 +227,7 @@ template <typename TGaps, typename TGapAnchors>
 inline bool
 isGap(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 {
-	return me.current.seqPos == me.nextAnchor.seqPos;
+    return me.current.seqPos == me.nextAnchor.seqPos;
 }
 
 // ----------------------------------------------------------------------------
@@ -238,9 +238,9 @@ template <typename TGaps, typename TGapAnchors>
 inline bool
 isUnknown(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 {
-	int len;
-	_assignSourceLength(len, *me.data_container);
-	return me.current.seqPos < 0 || me.current.seqPos >= len;
+    int len;
+    _assignSourceLength(len, *me.data_container);
+    return me.current.seqPos < 0 || me.current.seqPos >= len;
 }
 
 // ----------------------------------------------------------------------------
@@ -251,7 +251,7 @@ template <typename TGaps, typename TGapAnchors>
 inline bool
 isClipped(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 {
-	return me.current.gapPos == me.nextAnchor.gapPos;
+    return me.current.gapPos == me.nextAnchor.gapPos;
 }
 
 // ----------------------------------------------------------------------------
@@ -262,8 +262,8 @@ template <typename TGaps, typename TGapAnchors>
 inline typename Size<TGaps>::Type
 countGaps(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 {
-	if (!isGap(me))
-		return 0;
+    if (!isGap(me))
+        return 0;
     if (me.nextAnchor.gapPos > me.viewEnd.gapPos)
         return me.viewEnd.gapPos - me.current.gapPos;
     return me.nextAnchor.gapPos - me.current.gapPos;
@@ -303,19 +303,19 @@ blockLength(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me)
 // ----------------------------------------------------------------------------
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 atBegin(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me)
 {
-//	return me.current.seqPos == 0 && me.current.gapPos == 0;
-	return me.current <= me.viewBegin;
+//    return me.current.seqPos == 0 && me.current.gapPos == 0;
+    return me.current <= me.viewBegin;
 }
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 atBegin(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 {
-//	return me.current.seqPos == 0 && me.current.gapPos == 0;
-	return me.current <= me.viewBegin;
+//    return me.current.seqPos == 0 && me.current.gapPos == 0;
+    return me.current <= me.viewBegin;
 }
 
 // ----------------------------------------------------------------------------
@@ -323,19 +323,19 @@ atBegin(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 // ----------------------------------------------------------------------------
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 atEnd(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me)
 {
-//	return me.current == me.nextAnchor;
-	return me.current >= me.viewEnd;
+//    return me.current == me.nextAnchor;
+    return me.current >= me.viewEnd;
 }
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 atEnd(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 {
-//	return me.current == me.nextAnchor;
-	return me.current >= me.viewEnd;
+//    return me.current == me.nextAnchor;
+    return me.current >= me.viewEnd;
 }
 
 // ----------------------------------------------------------------------------
@@ -343,12 +343,12 @@ atEnd(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me)
 // ----------------------------------------------------------------------------
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 operator == (
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
 {
-	return left.current == right.current;
+    return left.current == right.current;
 }
 
 // ----------------------------------------------------------------------------
@@ -356,12 +356,12 @@ operator == (
 // ----------------------------------------------------------------------------
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 operator != (
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
 {
-	return left.current != right.current;
+    return left.current != right.current;
 }
 
 // ----------------------------------------------------------------------------
@@ -369,12 +369,12 @@ operator != (
 // ----------------------------------------------------------------------------
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 operator < (
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
 {
-	return left.current < right.current;
+    return left.current < right.current;
 }
 
 // ----------------------------------------------------------------------------
@@ -382,12 +382,12 @@ operator < (
 // ----------------------------------------------------------------------------
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 operator<=(
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
 {
-	return !(left.current > right.current);
+    return !(left.current > right.current);
 }
 
 // ----------------------------------------------------------------------------
@@ -395,12 +395,12 @@ operator<=(
 // ----------------------------------------------------------------------------
 
 template <typename TGaps, typename TGapAnchors>
-inline bool 
+inline bool
 operator > (
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & left,
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & right)
 {
-	return left.current > right.current;
+    return left.current > right.current;
 }
 
 // ----------------------------------------------------------------------------
@@ -422,47 +422,47 @@ operator>=(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & lhs,
 template <typename TGaps, typename TGapAnchors, typename TCount>
 inline void
 insertGaps(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me,
-		   TCount size)
-{
-	TGapAnchors & anchors = _dataAnchors(*me.data_container);
-	typedef typename Iterator<TGapAnchors, Standard>::Type TIter;
-
-	if (size <= 0) return;
-
-	// insert a new anchor
-	if (!isGap(me))
-	{
-		if (me.prevAnchor.gapPos == me.current.gapPos)
-		{
-			me.nextAnchor = me.prevAnchor;
-			_getAnchor(me.prevAnchor, *me.data_container, --me.anchorIdx);
-		}
-		else
-		{
-			me.nextAnchor = me.current;
-			insertValue(anchors, me.anchorIdx, me.nextAnchor, Generous());
-		}
-	}
-	else
-	{
-		if (me.anchorIdx >= (int)length(anchors))
-		{
-			// add gap after the sequence and in (or at the right boundary of) the view
-			if (me.current.gapPos <= me.viewEnd.gapPos)
-			{
-				container(me).data_cutEnd -= size;
-				me.viewEnd.gapPos += size;				
-			}
-			return;
-		}
-		if (empty(anchors))
-			appendValue(anchors, me.nextAnchor, Generous());
-	}
-	if (me.anchorIdx < (int)length(anchors))
-	{
-		if (me.anchorIdx >= 0)
+           TCount size)
+{
+    TGapAnchors & anchors = _dataAnchors(*me.data_container);
+    typedef typename Iterator<TGapAnchors, Standard>::Type TIter;
+
+    if (size <= 0) return;
+
+    // insert a new anchor
+    if (!isGap(me))
+    {
+        if (me.prevAnchor.gapPos == me.current.gapPos)
         {
-			me.nextAnchor.gapPos += size;
+            me.nextAnchor = me.prevAnchor;
+            _getAnchor(me.prevAnchor, *me.data_container, --me.anchorIdx);
+        }
+        else
+        {
+            me.nextAnchor = me.current;
+            insertValue(anchors, me.anchorIdx, me.nextAnchor, Generous());
+        }
+    }
+    else
+    {
+        if (me.anchorIdx >= (int)length(anchors))
+        {
+            // add gap after the sequence and in (or at the right boundary of) the view
+            if (me.current.gapPos <= me.viewEnd.gapPos)
+            {
+                container(me).data_cutEnd -= size;
+                me.viewEnd.gapPos += size;
+            }
+            return;
+        }
+        if (empty(anchors))
+            appendValue(anchors, me.nextAnchor, Generous());
+    }
+    if (me.anchorIdx < (int)length(anchors))
+    {
+        if (me.anchorIdx >= 0)
+        {
+            me.nextAnchor.gapPos += size;
             TIter it = begin(anchors, Standard());
             TIter itEnd = end(anchors, Standard());
             if (me.anchorIdx >= 0)
@@ -471,22 +471,22 @@ insertGaps(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me,
                 (*it).gapPos += size;
         }
         else
-			// add gap before the sequence and in (or at the left boundary of) the view
-			if (me.current.gapPos >= me.viewBegin.gapPos)
-		    {
-		        container(me).data_cutBegin -= size;
-		        me.viewBegin.gapPos -= size;
-		        me.current.gapPos -= size;
-		        return;
-		    }
-	}
-	if (me.current.gapPos <= me.viewEnd.gapPos)
-		me.viewEnd.gapPos += size;
+            // add gap before the sequence and in (or at the left boundary of) the view
+            if (me.current.gapPos >= me.viewBegin.gapPos)
+            {
+                container(me).data_cutBegin -= size;
+                me.viewBegin.gapPos -= size;
+                me.current.gapPos -= size;
+                return;
+            }
+    }
+    if (me.current.gapPos <= me.viewEnd.gapPos)
+        me.viewEnd.gapPos += size;
 
 /*
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > it2 = begin(*me.data_container) + me.current.gapPos;
-	if (me.current != it2.current || me.prevAnchor != it2.prevAnchor || me.nextAnchor != it2.nextAnchor || me.anchorIdx != it2.anchorIdx)
-		std::cout<<"*";
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > it2 = begin(*me.data_container) + me.current.gapPos;
+    if (me.current != it2.current || me.prevAnchor != it2.prevAnchor || me.nextAnchor != it2.nextAnchor || me.anchorIdx != it2.anchorIdx)
+        std::cout<<"*";
 */
 }
 
@@ -497,40 +497,40 @@ insertGaps(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me,
 template <typename TGaps, typename TGapAnchors, typename TCount>
 inline typename Size<TGaps>::Type
 removeGaps(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & it,
-		   TCount size_)
+           TCount size_)
 {
-	TGapAnchors & anchors = _dataAnchors(*it.data_container);
-	typedef typename Iterator<TGapAnchors, Standard>::Type TAnchorsIter;
+    TGapAnchors & anchors = _dataAnchors(*it.data_container);
+    typedef typename Iterator<TGapAnchors, Standard>::Type TAnchorsIter;
 
     typedef Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > TIter;
     typedef typename TIter::TGapAnchor TGapAnchor;
-	// typedef typename Value<TGapAnchors>::Type   TGapAnchor;
+    // typedef typename Value<TGapAnchors>::Type   TGapAnchor;
     typedef typename Position<TGapAnchor>::Type TPos;
 
-	if (size_ <= 0 || !isGap(it))
+    if (size_ <= 0 || !isGap(it))
         return 0;
     TPos size = size_;
 
     // static_cast<TGapAnchor>(Nothing());
     // static_cast<TPos>(Nothing());
-	if (it.current.gapPos + size > it.nextAnchor.gapPos)
-		size = it.nextAnchor.gapPos - it.current.gapPos;
-	
-	if (it.prevAnchor.gapPos + it.current.seqPos == it.current.gapPos + it.prevAnchor.seqPos &&
-		it.current.gapPos + size == it.nextAnchor.gapPos)
-	{	
-		// remove the gap
-		if (it.anchorIdx < (int)length(anchors))
-			erase(anchors, it.anchorIdx);
-		_getAnchor(it.nextAnchor, *it.data_container, it.anchorIdx);
-	}
-
-	// shift anchors
-	if (it.anchorIdx < (int)length(anchors))
-	{
+    if (it.current.gapPos + size > it.nextAnchor.gapPos)
+        size = it.nextAnchor.gapPos - it.current.gapPos;
+
+    if (it.prevAnchor.gapPos + it.current.seqPos == it.current.gapPos + it.prevAnchor.seqPos &&
+        it.current.gapPos + size == it.nextAnchor.gapPos)
+    {
+        // remove the gap
+        if (it.anchorIdx < (int)length(anchors))
+            erase(anchors, it.anchorIdx);
+        _getAnchor(it.nextAnchor, *it.data_container, it.anchorIdx);
+    }
+
+    // shift anchors
+    if (it.anchorIdx < (int)length(anchors))
+    {
         if (it.anchorIdx >= 0)
         {
-			it.nextAnchor.gapPos -= size;
+            it.nextAnchor.gapPos -= size;
             TAnchorsIter itA = begin(anchors, Standard());
             TAnchorsIter itAEnd = end(anchors, Standard());
             if (it.anchorIdx >= 0)
@@ -539,31 +539,31 @@ removeGaps(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & it,
                 (*itA).gapPos -= size;
         }
         else
-			// remove gap before the sequence and in (or at the left boundary of) the view
-			if (it.current.gapPos >= it.viewBegin.gapPos)
-		    {
-		    	// assure that we don't remove more gaps than available
-		    	if (size > it.nextAnchor.gapPos - it.current.gapPos)
-		    		size = it.nextAnchor.gapPos - it.current.gapPos;
-		        container(it).data_cutBegin += size;
-		        it.viewBegin.gapPos += size;
-		        it.current.gapPos += size;
-		        return size;
-		    }
-	}
-	else
-	{
-		if (it.current.gapPos <= it.viewEnd.gapPos)
-			container(it).data_cutEnd += size;
-	}
-	if (it.current.gapPos <= it.viewEnd.gapPos)
-		it.viewEnd.gapPos -= size;
+            // remove gap before the sequence and in (or at the left boundary of) the view
+            if (it.current.gapPos >= it.viewBegin.gapPos)
+            {
+                // assure that we don't remove more gaps than available
+                if (size > it.nextAnchor.gapPos - it.current.gapPos)
+                    size = it.nextAnchor.gapPos - it.current.gapPos;
+                container(it).data_cutBegin += size;
+                it.viewBegin.gapPos += size;
+                it.current.gapPos += size;
+                return size;
+            }
+    }
+    else
+    {
+        if (it.current.gapPos <= it.viewEnd.gapPos)
+            container(it).data_cutEnd += size;
+    }
+    if (it.current.gapPos <= it.viewEnd.gapPos)
+        it.viewEnd.gapPos -= size;
 
     return size;
 /*
-	Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > it2 = begin(*me.data_container) + me.current.gapPos;
-	if (me.current != it2.current || me.prevAnchor != it2.prevAnchor || me.nextAnchor != it2.nextAnchor || me.anchorIdx != it2.anchorIdx)
-		std::cout<<"*";
+    Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > it2 = begin(*me.data_container) + me.current.gapPos;
+    if (me.current != it2.current || me.prevAnchor != it2.prevAnchor || me.nextAnchor != it2.nextAnchor || me.anchorIdx != it2.anchorIdx)
+        std::cout<<"*";
 */
 }
 
@@ -572,20 +572,20 @@ removeGaps(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & it,
 // ----------------------------------------------------------------------------
 
 template <typename T>
-inline void 
+inline void
 _goNextGapAnchorIterator(T & me)
 {
-	if (me.current.gapPos < me.nextAnchor.gapPos)
-	{
-		++me.current.gapPos;
-		if (me.current.seqPos < me.nextAnchor.seqPos)
-			++me.current.seqPos;
-	}
-	while (me.current.gapPos == me.nextAnchor.gapPos)
-	{
-		me.current = me.prevAnchor = me.nextAnchor;
-		_getAnchor(me.nextAnchor, *me.data_container, ++me.anchorIdx + 1);
-	}
+    if (me.current.gapPos < me.nextAnchor.gapPos)
+    {
+        ++me.current.gapPos;
+        if (me.current.seqPos < me.nextAnchor.seqPos)
+            ++me.current.seqPos;
+    }
+    while (me.current.gapPos == me.nextAnchor.gapPos)
+    {
+        me.current = me.prevAnchor = me.nextAnchor;
+        _getAnchor(me.nextAnchor, *me.data_container, ++me.anchorIdx + 1);
+    }
 }
 
 // ----------------------------------------------------------------------------
@@ -593,19 +593,19 @@ _goNextGapAnchorIterator(T & me)
 // ----------------------------------------------------------------------------
 
 template <typename T>
-inline void 
+inline void
 _goPreviousGapAnchorIterator(T & me)
-{	
-	while (me.current.gapPos == me.prevAnchor.gapPos)
-	{
-		me.current = me.nextAnchor = me.prevAnchor;
-		_getAnchor(me.prevAnchor, *me.data_container, --me.anchorIdx);
-	}
-	--me.current.gapPos;
-	if (me.nextAnchor.seqPos - me.prevAnchor.seqPos > me.current.gapPos - me.prevAnchor.gapPos)
-		me.current.seqPos = me.prevAnchor.seqPos + (me.current.gapPos - me.prevAnchor.gapPos);
-	else
-		me.current.seqPos = me.nextAnchor.seqPos;
+{
+    while (me.current.gapPos == me.prevAnchor.gapPos)
+    {
+        me.current = me.nextAnchor = me.prevAnchor;
+        _getAnchor(me.prevAnchor, *me.data_container, --me.anchorIdx);
+    }
+    --me.current.gapPos;
+    if (me.nextAnchor.seqPos - me.prevAnchor.seqPos > me.current.gapPos - me.prevAnchor.gapPos)
+        me.current.seqPos = me.prevAnchor.seqPos + (me.current.gapPos - me.prevAnchor.gapPos);
+    else
+        me.current.seqPos = me.nextAnchor.seqPos;
 }
 
 // ----------------------------------------------------------------------------
@@ -613,39 +613,39 @@ _goPreviousGapAnchorIterator(T & me)
 // ----------------------------------------------------------------------------
 
 template <typename T, typename TPos>
-inline void 
+inline void
 _goToGapAnchorIterator(T & me, TPos pos)
 {
-	typedef typename T::TGapAnchors                 TGapAnchors;
-	typedef typename Value<TGapAnchors>::Type       TGapAnchor;
-	typedef typename Position<TGapAnchor>::Type     TAnchorPos;
-	typedef typename MakeSigned<TAnchorPos>::Type   TAnchorSPos;
-
-	if (_helperIsNegative(pos, typename IsSameType<TPos, typename MakeSigned_<TPos>::Type>::Type()))
-		me.anchorIdx = -1;
-	else
-	{
-		TGapAnchors const & anchors = _dataAnchors(*me.data_container);
-		if (!empty(anchors))
-		{
-			me.anchorIdx = upperBoundGapAnchor(anchors, pos, SortGapPos()) - begin(anchors, Standard());
-			if (me.anchorIdx < (int)length(anchors))
-				if (anchors[me.anchorIdx].gapPos == (TAnchorPos)pos && anchors[me.anchorIdx].seqPos != (TAnchorPos)me.seqLength)
-					++me.anchorIdx;
-		}
-		else
+    typedef typename T::TGapAnchors                 TGapAnchors;
+    typedef typename Value<TGapAnchors>::Type       TGapAnchor;
+    typedef typename Position<TGapAnchor>::Type     TAnchorPos;
+    typedef typename MakeSigned<TAnchorPos>::Type   TAnchorSPos;
+
+    if (isNegative(pos))
+        me.anchorIdx = -1;
+    else
+    {
+        TGapAnchors const & anchors = _dataAnchors(*me.data_container);
+        if (!empty(anchors))
         {
-			me.anchorIdx = ((TAnchorSPos)pos < me.seqLength)? 0: 1;
+            me.anchorIdx = upperBoundGapAnchor(anchors, pos, SortGapPos()) - begin(anchors, Standard());
+            if (me.anchorIdx < (int)length(anchors))
+                if (anchors[me.anchorIdx].gapPos == (TAnchorPos)pos && anchors[me.anchorIdx].seqPos != (TAnchorPos)me.seqLength)
+                    ++me.anchorIdx;
         }
-	}
-	_getAnchor(me.prevAnchor, *me.data_container, me.anchorIdx);
-	_getAnchor(me.nextAnchor, *me.data_container, me.anchorIdx + 1);
+        else
+        {
+            me.anchorIdx = ((TAnchorSPos)pos < me.seqLength)? 0: 1;
+        }
+    }
+    _getAnchor(me.prevAnchor, *me.data_container, me.anchorIdx);
+    _getAnchor(me.nextAnchor, *me.data_container, me.anchorIdx + 1);
 
-	me.current.gapPos = pos;
-	if (me.nextAnchor.seqPos - me.prevAnchor.seqPos > (int)pos - me.prevAnchor.gapPos)
-		me.current.seqPos = me.prevAnchor.seqPos + ((int)pos - me.prevAnchor.gapPos);
-	else
-		me.current.seqPos = me.nextAnchor.seqPos;
+    me.current.gapPos = pos;
+    if (me.nextAnchor.seqPos - me.prevAnchor.seqPos > (int)pos - me.prevAnchor.gapPos)
+        me.current.seqPos = me.prevAnchor.seqPos + ((int)pos - me.prevAnchor.gapPos);
+    else
+        me.current.seqPos = me.nextAnchor.seqPos;
 }
 
 // ----------------------------------------------------------------------------
@@ -656,7 +656,7 @@ template <typename TGaps, typename TGapAnchors>
 inline void
 goNext(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me)
 {
-	_goNextGapAnchorIterator(me);
+    _goNextGapAnchorIterator(me);
 }
 
 // ----------------------------------------------------------------------------
@@ -667,7 +667,7 @@ template <typename TGaps, typename TGapAnchors>
 inline void
 goPrevious(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me)
 {
-	_goPreviousGapAnchorIterator(me);
+    _goPreviousGapAnchorIterator(me);
 }
 
 // ----------------------------------------------------------------------------
@@ -678,7 +678,7 @@ template <typename TGaps, typename TGapAnchors, typename TSize>
 inline void
 goFurther(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me, TSize steps)
 {
-	_goToGapAnchorIterator(me, me.current.gapPos + steps);
+    _goToGapAnchorIterator(me, me.current.gapPos + steps);
 }
 
 // ----------------------------------------------------------------------------
@@ -747,4 +747,4 @@ operator+(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & lhs, TDif
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_
diff --git a/seqan/align/gaps_iterator_array.h b/seqan/align/gaps_iterator_array.h
index 6d8da0c..5361d93 100644
--- a/seqan/align/gaps_iterator_array.h
+++ b/seqan/align/gaps_iterator_array.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_
 
 namespace seqan {
 
@@ -281,7 +281,7 @@ inline bool
 goPrevious(Iter<TGaps, GapsIterator<ArrayGaps> > & it)
 {
     typedef typename Position<TGaps>::Type TGapsPos;
-    
+
     if (atBegin(it))  // Handle case of being at the beginning of the gaps.
         return false;
 
@@ -303,7 +303,7 @@ goPrevious(Iter<TGaps, GapsIterator<ArrayGaps> > & it)
         it._sourcePosition -= 1;
     // Adjust clipped view position.
     it._unclippedViewPosition -= 1;
-    
+
     return true;
 }
 
@@ -366,7 +366,7 @@ goFurther(Iter<TGaps, GapsIterator<ArrayGaps> > & it,
     // TODO(holtgrew): Handle going backwards more efficiently.
     if (delta == TDifference(0))
         return;
-    if ((int)delta < 0)
+    if (isNegative(delta))
     {
         typedef typename MakeSigned<TDifference>::Type TSignedDifference;
         for (; -static_cast<TSignedDifference>(delta); ++delta)
@@ -487,7 +487,7 @@ insertGaps(Iter<TGaps, GapsIterator<ArrayGaps> > const & it,
 {
     if (count == TCount(0))
         return;  // Do nothing!
-    
+
     typedef typename TGaps::TArray_          TArray;
     typedef typename Position<TArray>::Type  TArrayPos;
 
@@ -738,4 +738,4 @@ operator+(Iter<TGaps, GapsIterator<ArrayGaps> > const & lhs, TDifference d)
 
 }  // namespace seqan
 
-#endif  // SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_
diff --git a/seqan/align/gaps_iterator_base.h b/seqan/align/gaps_iterator_base.h
index 1501e17..a1802b7 100644
--- a/seqan/align/gaps_iterator_base.h
+++ b/seqan/align/gaps_iterator_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 
 // TODO(holtgrew): Switch to Host interface.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
 
 namespace seqan {
 
@@ -60,6 +60,19 @@ typedef Tag<Position__> Position_;
 // Tags, Classes, Enums
 // ============================================================================
 
+/*!
+ * @class GapsIterator
+ * @implements RandomAccessIteratorConcept
+ *
+ * @brief Iterator class for @link Gaps @endlink.
+ *
+ * @signature template <typename TGaps, typename TSpec>
+ *            class Iter<TGaps, GapsIterator<TSpec> >;
+ *
+ * @tparam TGaps The @link Gaps @endlink object for the iterator.
+ * @tparam TSpec The specializing tag.
+ */
+
 template <typename TSpec>
 struct GapsIterator;
 
@@ -104,15 +117,15 @@ struct Difference<Iter<TGaps, GapsIterator<TSpec> > const> :
 template <typename TGaps, typename TSpec>
 struct Source<Iter<TGaps, GapsIterator<TSpec> > >
 {
-	typedef typename Source<TGaps>::Type TSource_;
-	typedef typename Iterator<TSource_, Rooted>::Type Type;
+    typedef typename Source<TGaps>::Type TSource_;
+    typedef typename Iterator<TSource_, Rooted>::Type Type;
 };
 
 template <typename TGaps, typename TSpec>
 struct Source<Iter<TGaps, GapsIterator<TSpec> > const>
 {
-	typedef typename Source<TGaps>::Type TSource_;
-	typedef typename Iterator<TSource_, Rooted>::Type Type;
+    typedef typename Source<TGaps>::Type TSource_;
+    typedef typename Iterator<TSource_, Rooted>::Type Type;
 };
 
 // ----------------------------------------------------------------------------
@@ -122,11 +135,11 @@ struct Source<Iter<TGaps, GapsIterator<TSpec> > const>
 template <typename TGaps, typename TSpec>
 struct Value<Iter<TGaps, GapsIterator<TSpec> > >
 {
-	typedef typename Source<Iter<TGaps, GapsIterator<TSpec> > >::Type TSource_;
-	typedef typename Value<TSource_>::Type TSourceValue_;
+    typedef typename Source<Iter<TGaps, GapsIterator<TSpec> > >::Type TSource_;
+    typedef typename Value<TSource_>::Type TSourceValue_;
     //typedef TSourceValue_ Type;
     // TODO(holtgrew): We really want gapped values here but there are issues...
-	typedef typename GappedValueType<TSourceValue_>::Type Type;
+    typedef typename GappedValueType<TSourceValue_>::Type Type;
 };
 
 template <typename TGaps, typename TSpec>
@@ -139,13 +152,13 @@ struct Value<Iter<TGaps, GapsIterator<TSpec> > const> :
 
 template <typename TGaps, typename TSpec>
 struct GetValue<Iter<TGaps, GapsIterator<TSpec> > > :
-	Value<Iter<TGaps, GapsIterator<TSpec> > >
+    Value<Iter<TGaps, GapsIterator<TSpec> > >
 {
 };
 
 template <typename TGaps, typename TSpec>
 struct GetValue<Iter<TGaps, GapsIterator<TSpec> > const> :
-	Value<Iter<TGaps, GapsIterator<TSpec> > const>
+    Value<Iter<TGaps, GapsIterator<TSpec> > const>
 {
 };
 
@@ -156,15 +169,15 @@ struct GetValue<Iter<TGaps, GapsIterator<TSpec> > const> :
 template <typename TGaps, typename TSpec>
 struct Reference<Iter<TGaps, GapsIterator<TSpec> > >
 {
-	typedef Iter<TGaps, GapsIterator<TSpec> > TIterator_;
-	typedef Proxy<IteratorProxy<TIterator_> > Type;
+    typedef Iter<TGaps, GapsIterator<TSpec> > TIterator_;
+    typedef Proxy<IteratorProxy<TIterator_> > Type;
 };
 
 template <typename TGaps, typename TSpec>
 struct Reference<Iter<TGaps, GapsIterator<TSpec> > const>
 {
-	typedef Iter<TGaps, GapsIterator<TSpec> const > TIterator_;
-	typedef Proxy<IteratorProxy<TIterator_> > Type;
+    typedef Iter<TGaps, GapsIterator<TSpec> const > TIterator_;
+    typedef Proxy<IteratorProxy<TIterator_> > Type;
 };
 
 // ============================================================================
@@ -178,20 +191,20 @@ struct Reference<Iter<TGaps, GapsIterator<TSpec> > const>
 // TODO(holtgrew): Could be general forward
 
 template <typename TGaps, typename TSpec>
-inline Iter<TGaps, GapsIterator<TSpec> > & 
+inline Iter<TGaps, GapsIterator<TSpec> > &
 operator++(Iter<TGaps, GapsIterator<TSpec> > & it)
 {
-	goNext(it);
-	return it;
+    goNext(it);
+    return it;
 }
 
 template <typename TGaps, typename TSpec>
 inline Iter<TGaps, GapsIterator<TSpec> >
 operator++(Iter<TGaps, GapsIterator<TSpec> > & it, int)
 {
-	Iter<TGaps, GapsIterator<TSpec> > ret = it;
-	goNext(it);
-	return ret;
+    Iter<TGaps, GapsIterator<TSpec> > ret = it;
+    goNext(it);
+    return ret;
 }
 
 // ----------------------------------------------------------------------------
@@ -199,26 +212,35 @@ operator++(Iter<TGaps, GapsIterator<TSpec> > & it, int)
 // ----------------------------------------------------------------------------
 
 template <typename TGaps, typename TSpec>
-inline Iter<TGaps, GapsIterator<TSpec> > & 
+inline Iter<TGaps, GapsIterator<TSpec> > &
 operator--(Iter<TGaps, GapsIterator<TSpec> > & it)
 {
-	goPrevious(it);
-	return it;
+    goPrevious(it);
+    return it;
 }
 
 template <typename TGaps, typename TSpec>
 inline Iter<TGaps, GapsIterator<TSpec> >
 operator--(Iter<TGaps, GapsIterator<TSpec> > & it, int)
 {
-	Iter<TGaps, GapsIterator<TSpec> > ret = it;
-	goPrevious(it);
-	return ret;
+    Iter<TGaps, GapsIterator<TSpec> > ret = it;
+    goPrevious(it);
+    return ret;
 }
 
 // ----------------------------------------------------------------------------
 // Function insertGap()
 // ----------------------------------------------------------------------------
 
+/*!
+ * @fn GapsIterator#insertGap
+ * @brief Insert gap at the current position.
+ *
+ * @signature void insertGap(it);
+ *
+ * @param[in,out] it The iterator to insert gaps at.
+ */
+
 // Forward to insertGaps() which has to be implemented by the specific gap
 // iterator.
 
@@ -226,13 +248,104 @@ template <typename TGaps, typename TSpec>
 inline void
 insertGap(Iter<TGaps, GapsIterator<TSpec> > & it)
 {
-	insertGaps(it, 1);
+    insertGaps(it, 1);
+}
+
+// ----------------------------------------------------------------------------
+// Function isCharacter()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn GapsIterator#isCharacter
+ * @brief Query an iterator for being at a character
+ *
+ * @signature bool isCharacter(it);
+ *
+ * @param[in] it Iterator to query for pointing at a character.
+ *
+ * @return bool <tt>true</tt> if <tt>it</tt> is at a character and <tt>false</tt> otherwise.
+ */
+
+template <typename TGaps, typename TSpec>
+bool isCharacter(Iter<TGaps, GapsIterator<TSpec> > const & it)
+{
+    return !isGap(it);
 }
 
+// ----------------------------------------------------------------------------
+// Function countCharacters()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn GapsIterator#countCharacters
+ * @brief Count characters at iterator.
+ *
+ * @signature TSize countCharacters(it);
+ *
+ * @param[in] it Iterator for counting characters at.
+ *
+ * @return TSize Number of characters.
+ */
+
+// ----------------------------------------------------------------------------
+// Function isGap()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn GapsIterator#isGap
+ * @brief Query an iterator for being at a gap
+ *
+ * @signature bool isGap(it);
+ *
+ * @param[in] it Iterator to query for pointing at a gap.
+ *
+ * @return bool <tt>true</tt> if <tt>it</tt> is at a gap and <tt>false</tt> otherwise.
+ */
+
+// ----------------------------------------------------------------------------
+// Function countGaps()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn GapsIterator#countGaps
+ * @brief Count gaps at iterator.
+ *
+ * @signature TSize countGaps(it);
+ *
+ * @param[in] it Iterator for counting gaps at.
+ *
+ * @return TSize Number of gaps.
+ */
+
+// ----------------------------------------------------------------------------
+// Function insertGaps()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn GapsIterator#insertGaps
+ * @brief Insert gaps at the current position.
+ *
+ * @signature void insertGaps(it, num);
+ *
+ * @param[in,out] it  Remove gap at the given position (if any).
+ * @param[in]     num Number of gaps to insert.
+ */
+
 // ----------------------------------------------------------------------------
 // Function removeGap()
 // ----------------------------------------------------------------------------
 
+/*!
+ * @fn GapsIterator#removeGap
+ * @brief Insert gap at the current position.
+ *
+ * @signature TSize removeGap(it);
+ *
+ * @param[in,out] it Remove gap at the given position (if any).
+ *
+ * @return TSize Number of removed gaps.
+ */
+
 // Forward to removeGaps() which has to be implemented by the specific gap
 // iterator.
 
@@ -240,9 +353,25 @@ template <typename TGaps, typename TSpec>
 inline typename Size<TGaps>::Type
 removeGap(Iter<TGaps, GapsIterator<TSpec> > & it)
 {
-	return removeGaps(it, 1);
+    return removeGaps(it, 1);
 }
 
+// ----------------------------------------------------------------------------
+// Function removeGaps()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn GapsIterator#removeGaps
+ * @brief Remove gaps from the current position.
+ *
+ * @signature TSize removeGaps(it, num);
+ *
+ * @param[in,out] it  Remove gap at the given position (if any).
+ * @param[in]     num Number of gaps to remove.
+ *
+ * @return TSize Number of removed gaps.
+ */
+
 // ----------------------------------------------------------------------------
 // Function assignValue()
 // ----------------------------------------------------------------------------
@@ -252,24 +381,24 @@ removeGap(Iter<TGaps, GapsIterator<TSpec> > & it)
 template <typename TGaps, typename TSpec, typename TValue>
 inline void
 assignValue(Iter<TGaps, GapsIterator<TSpec> > & me,
-			TValue const & val)
+            TValue const & val)
 {
-	if (!isGap(me)) 
-	{
-		assignValue(source(me), val);
-	}
+    if (!isGap(me))
+    {
+        assignValue(source(me), val);
+    }
     // TODO(holtgrew): Else, inserting gaps is problematic...
 }
 
 template <typename TGaps, typename TSpec, typename TValue>
 inline void
 assignValue(Iter<TGaps, GapsIterator<TSpec> > const & me,
-			TValue const & val)
+            TValue const & val)
 {
-	if (!isGap(me)) 
-	{
-		assignValue(source(me), val);
-	}
+    if (!isGap(me))
+    {
+        assignValue(source(me), val);
+    }
 }
 
 // ----------------------------------------------------------------------------
@@ -280,14 +409,14 @@ template <typename TGaps, typename TSpec>
 inline TGaps &
 container(Iter<TGaps, GapsIterator<TSpec> > & me)
 {
-	return *me._container;
+    return *me._container;
 }
 
 template <typename TGaps, typename TSpec>
 inline TGaps &
 container(Iter<TGaps, GapsIterator<TSpec> > const & me)
 {
-	return *me._container;
+    return *me._container;
 }
 
 // ----------------------------------------------------------------------------
@@ -345,9 +474,9 @@ operator-=(Iter<TGaps, GapsIterator<TSpec> > & it, TDiff diff)
 template <typename TGaps, typename TSpec, typename TDifference>
 inline void
 goFurther(Iter<TGaps, GapsIterator<TSpec> > & it,
-		  TDifference steps)
+          TDifference steps)
 {
-	typedef typename MakeSigned<TDifference>::Type TSignedDifference;
+    typedef typename MakeSigned<TDifference>::Type TSignedDifference;
     if (steps > TDifference(0))
         for (; steps; --steps)
             goNext(it);
@@ -369,4 +498,4 @@ isClipped(Iter<TGaps, GapsIterator<TSpec> > const &)
 
 }  // namespace seqan
 
-#endif  // SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
diff --git a/seqan/align/global_alignment_banded.h b/seqan/align/global_alignment_banded.h
index dabfcec..e705e74 100644
--- a/seqan/align/global_alignment_banded.h
+++ b/seqan/align/global_alignment_banded.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,8 +39,8 @@
 // the globalFunction() fails is actually meaningful.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
 
 namespace seqan {
 
@@ -79,28 +79,31 @@ template <typename TSequence, typename TAlignSpec,
           typename TAlgoTag>
 TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
                             Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                             int lowerDiag,
                             int upperDiag,
-                            TAlgoTag const & algoTag)
+                            TAlgoTag const & /*algoTag*/)
 {
     typedef Align<TSequence, TAlignSpec> TAlign;
     typedef typename Size<TAlign>::Type  TSize;
     typedef typename Position<TAlign>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
 
     String<TTraceSegment> trace;
 
-    // We do not need string ids for this variant and set them to 0u.  They are
-    // only required for the Fragment String and the Alignment Graph variant.
-    TScoreValue res = _setUpAndRunAlignment(trace, source(row(align, 0)), source(row(align, 1)), scoringScheme,
-                                            alignConfig, lowerDiag, upperDiag, algoTag);
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)),
+                                            scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel());
+
     _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace);
     return res;
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TSequence, typename TAlignSpec,
           typename TScoreValue, typename TScoreSpec,
           typename TAlgoTag>
@@ -115,7 +118,6 @@ TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
 }
 
 // Interface without algorithm tag.
-
 template <typename TSequence, typename TAlignSpec,
           typename TScoreValue, typename TScoreSpec,
           bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
@@ -126,13 +128,12 @@ TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
                             int upperDiag)
 {
     if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
-        return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
+        return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, LinearGaps());
     else
-        return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
+        return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, AffineGaps());
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TSequence, typename TAlignSpec,
           typename TScoreValue, typename TScoreSpec>
 TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
@@ -156,27 +157,29 @@ template <typename TSequenceH, typename TGapsSpecH,
 TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                             Gaps<TSequenceV, TGapsSpecV> & gapsV,
                             Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                             int lowerDiag,
                             int upperDiag,
-                            TAlgoTag const & algoTag)
+                            TAlgoTag const & /*algoTag*/)
 {
     typedef typename Size<TSequenceH>::Type TSize;
     typedef typename Position<TSequenceH>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
 
-    String<TTraceSegment> traceSegments;
+    String<TTraceSegment> trace;
 
-    // We do not need string ids for this variant and set them to 0u.  They are
-    // only required for the Fragment String and the Alignment Graph variant.
-    TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig,
-                                            lowerDiag, upperDiag, algoTag);
-    _adaptTraceSegmentsTo(gapsH, gapsV, traceSegments);
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme,
+                                            TAlignConfig2(lowerDiag, upperDiag), TGapModel());
+    _adaptTraceSegmentsTo(gapsH, gapsV, trace);
     return res;
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TSequenceH, typename TGapsSpecH,
           typename TSequenceV, typename TGapsSpecV,
           typename TScoreValue, typename TScoreSpec,
@@ -193,7 +196,6 @@ TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 }
 
 // Interface without algorithm tag.
-
 template <typename TSequenceH, typename TGapsSpecH,
           typename TSequenceV, typename TGapsSpecV,
           typename TScoreValue, typename TScoreSpec,
@@ -212,7 +214,6 @@ TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TSequenceH, typename TGapsSpecH,
           typename TSequenceV, typename TGapsSpecV,
           typename TScoreValue, typename TScoreSpec>
@@ -231,35 +232,39 @@ TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 // ----------------------------------------------------------------------------
 
 // Full interface.
-
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
           typename TScoreValue, typename TScoreSpec,
           bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
           typename TAlgoTag>
 TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
                             Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                             int lowerDiag,
                             int upperDiag,
-                            TAlgoTag const & algoTag)
+                            TAlgoTag const & /*algoTag*/)
 {
     typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
     typedef typename Position<TGraph>::Type TPosition;
     typedef typename Size<TGraph>::Type TSize;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
 
-    String<TTraceSegment> traceSegments;
+    String<TTraceSegment> trace;
+
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0),
+                                            value(stringSet(alignmentGraph), 1), scoringScheme,
+                                            TAlignConfig2(lowerDiag, upperDiag), TGapModel());
 
-    TScoreValue res = _setUpAndRunAlignment(traceSegments, value(stringSet(alignmentGraph), 0),
-                                            value(stringSet(alignmentGraph), 1), scoringScheme, alignConfig, lowerDiag,
-                                            upperDiag, algoTag);
     _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0),
-                          positionToId(stringSet(alignmentGraph), 1), traceSegments);
+                          positionToId(stringSet(alignmentGraph), 1), trace);
     return res;
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
           typename TScoreValue, typename TScoreSpec,
           typename TAlgoTag>
@@ -274,7 +279,6 @@ TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > &
 }
 
 // Interface without algorithm tag.
-
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
           typename TScoreValue, typename TScoreSpec,
           bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
@@ -291,7 +295,6 @@ TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > &
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
           typename TScoreValue, typename TScoreSpec>
 TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
@@ -308,7 +311,6 @@ TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > &
 // ----------------------------------------------------------------------------
 
 // Full interface.
-
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
           typename TScoreValue, typename TScoreSpec,
@@ -317,25 +319,30 @@ template <typename TSize, typename TFragmentSpec, typename TStringSpec,
 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
                             StringSet<TSequence, TStringSetSpec> const & strings,
                             Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                             int lowerDiag,
                             int upperDiag,
-                            TAlgoTag const & algoTag)
+                            TAlgoTag const & /*algoTag*/)
 {
     typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments;
     typedef typename Position<TFragments>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
+
+    String<TTraceSegment> trace;
 
-    String<TTraceSegment> traceSegments;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme,
+                                            TAlignConfig2(lowerDiag, upperDiag), TGapModel());
 
-    TScoreValue res = _setUpAndRunAlignment(traceSegments, value(strings, 0), value(strings, 1), scoringScheme,
-                                            alignConfig, lowerDiag, upperDiag, algoTag);
-    _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), traceSegments);
+    _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace);
     return res;
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
           typename TScoreValue, typename TScoreSpec,
@@ -352,7 +359,6 @@ TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec>
 }
 
 // Interface without algorithm tag.
-
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
           typename TScoreValue, typename TScoreSpec,
@@ -371,7 +377,6 @@ TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec>
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
           typename TScoreValue, typename TScoreSpec>
@@ -397,16 +402,23 @@ template <typename TSequenceH,
 TScoreValue globalAlignmentScore(TSequenceH const & seqH,
                                  TSequenceV const & seqV,
                                  Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                                 AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
+                                 AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                                  int lowerDiag,
                                  int upperDiag,
-                                 TAlgoTag const & algoTag)
+                                 TAlgoTag const & /*algoTag*/)
 {
-    return _setUpAndRunAlignment(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOff> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
+
+    DPScoutState_<Default> dpScoutState;
+    String<TraceSegment_<unsigned, unsigned> > traceSegments;  // Dummy segments.
+    return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme,
+                                 TAlignConfig2(lowerDiag, upperDiag), TGapModel());
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TSequenceH,
           typename TSequenceV,
           typename TScoreValue, typename TScoreSpec,
@@ -423,7 +435,6 @@ TScoreValue globalAlignmentScore(TSequenceH const & seqH,
 }
 
 // Interface without algorithm tag.
-
 template <typename TSequenceH,
           typename TSequenceV,
           typename TScoreValue, typename TScoreSpec,
@@ -442,7 +453,6 @@ TScoreValue globalAlignmentScore(TSequenceH const & seqH,
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TSequenceH,
           typename TSequenceV,
           typename TScoreValue, typename TScoreSpec>
@@ -466,17 +476,25 @@ template <typename TString, typename TSpec,
           typename TAlgoTag>
 TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
                                  Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                                 AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
+                                 AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                                  int lowerDiag,
                                  int upperDiag,
-                                 TAlgoTag const & algoTag)
+                                 TAlgoTag const & /*algoTag*/)
 {
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOff> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
+
     SEQAN_ASSERT_EQ(length(strings), 2u);
-    return _setUpAndRunAlignment(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
+
+    DPScoutState_<Default> dpScoutState;
+    String<TraceSegment_<unsigned, unsigned> > traceSegments;  // Dummy segments.
+    return _setUpAndRunAlignment(traceSegments, dpScoutState, strings[0], strings[1], scoringScheme,
+                                 TAlignConfig2(lowerDiag, upperDiag), TGapModel());
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TString, typename TSpec,
           typename TScoreValue, typename TScoreSpec,
           typename TAlgoTag>
@@ -493,7 +511,6 @@ TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
 }
 
 // Interface without algorithm tag.
-
 template <typename TString, typename TSpec,
           typename TScoreValue, typename TScoreSpec,
           bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
@@ -512,7 +529,6 @@ TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TString, typename TSpec,
           typename TScoreValue, typename TScoreSpec>
 TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
@@ -528,4 +544,4 @@ TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
diff --git a/seqan/align/global_alignment_hirschberg_impl.h b/seqan/align/global_alignment_hirschberg_impl.h
index 7e05496..640c18c 100644
--- a/seqan/align/global_alignment_hirschberg_impl.h
+++ b/seqan/align/global_alignment_hirschberg_impl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // TODO(holtgrew): Get rid of this?
 //#define SEQAN_HIRSCHBERG_DEBUG_CUT
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
 
 namespace seqan {
 
@@ -62,31 +62,30 @@ typedef Tag<Hirschberg_> Hirschberg;
 class HirschbergSet_
 {
 public:
-	int x1,x2,y1,y2;
-	int score;
-
-	HirschbergSet_()
-		: x1(0),x2(0),y1(0),y2(0)
-	{
-	}
-
-	HirschbergSet_(int a1,int a2,int b1,int b2,int sc)
-		: x1(a1),x2(a2),y1(b1),y2(b2),score(sc)
-	{
-		SEQAN_ASSERT_LEQ(a1, a2);
-		SEQAN_ASSERT_LEQ(b1, b2);
-	}
-
-	HirschbergSet_ & 
-	operator=(HirschbergSet_ const & other_)
-	{
-		x1 = other_.x1;
-		x2 = other_.x2;
-		y1 = other_.y1;
-		y2 = other_.y2;
-		score = other_.score;
-		return *this;
-	}
+    int x1,x2,y1,y2;
+    int score;
+
+    HirschbergSet_()
+        : x1(0), x2(0), y1(0), y2(0), score(0)
+    {}
+
+    HirschbergSet_(int a1,int a2,int b1,int b2,int sc)
+        : x1(a1), x2(a2), y1(b1), y2(b2), score(sc)
+    {
+        SEQAN_ASSERT_LEQ(a1, a2);
+        SEQAN_ASSERT_LEQ(b1, b2);
+    }
+
+    HirschbergSet_ &
+    operator=(HirschbergSet_ const & other_)
+    {
+        x1 = other_.x1;
+        x2 = other_.x2;
+        y1 = other_.y1;
+        y2 = other_.y2;
+        score = other_.score;
+        return *this;
+    }
 
 };
 
@@ -102,15 +101,15 @@ class HirschbergSet_
 // Function _begin1()
 // ----------------------------------------------------------------------------
 
-inline int& 
+inline int&
 _begin1(HirschbergSet_ & me) {
-	return me.x1;
+    return me.x1;
 }
 
 
-inline int const& 
+inline int const&
 _begin1(HirschbergSet_ const & me) {
-	return me.x1;
+    return me.x1;
 }
 
 // ----------------------------------------------------------------------------
@@ -119,7 +118,7 @@ _begin1(HirschbergSet_ const & me) {
 
 inline void
 _setBegin1(HirschbergSet_ & me, int const & new_begin) {
-	me.x1 = new_begin;
+    me.x1 = new_begin;
 }
 
 // ----------------------------------------------------------------------------
@@ -128,12 +127,12 @@ _setBegin1(HirschbergSet_ & me, int const & new_begin) {
 
 inline int&
 _end1(HirschbergSet_ & me) {
-	return me.x2;
+    return me.x2;
 }
 
-inline int const& 
+inline int const&
 _end1(HirschbergSet_ const & me) {
-	return me.x2;
+    return me.x2;
 }
 
 // ----------------------------------------------------------------------------
@@ -142,7 +141,7 @@ _end1(HirschbergSet_ const & me) {
 
 inline void
 _setEnd1(HirschbergSet_ & me, int const & new_end) {
-	me.x2 = new_end;
+    me.x2 = new_end;
 }
 
 // ----------------------------------------------------------------------------
@@ -151,12 +150,12 @@ _setEnd1(HirschbergSet_ & me, int const & new_end) {
 
 inline int&
 _begin2(HirschbergSet_ & me) {
-	return me.y1;
+    return me.y1;
 }
 
 inline int const&
 _begin2(HirschbergSet_ const & me) {
-	return me.y1;
+    return me.y1;
 }
 
 // ----------------------------------------------------------------------------
@@ -165,7 +164,7 @@ _begin2(HirschbergSet_ const & me) {
 
 inline void
 _setBegin2(HirschbergSet_ & me, int const & new_begin) {
-	me.y1 = new_begin;
+    me.y1 = new_begin;
 }
 
 // ----------------------------------------------------------------------------
@@ -174,12 +173,12 @@ _setBegin2(HirschbergSet_ & me, int const & new_begin) {
 
 inline int&
 _end2(HirschbergSet_ & me) {
-	return me.y2;
+    return me.y2;
 }
 
 inline int const&
 _end2(HirschbergSet_ const & me) {
-	return me.y2;
+    return me.y2;
 }
 
 // ----------------------------------------------------------------------------
@@ -188,7 +187,7 @@ _end2(HirschbergSet_ const & me) {
 
 inline void
 _setEnd2(HirschbergSet_ & me, int const & new_end) {
-	me.y2 = new_end;
+    me.y2 = new_end;
 }
 
 // ----------------------------------------------------------------------------
@@ -196,8 +195,8 @@ _setEnd2(HirschbergSet_ & me, int const & new_end) {
 // ----------------------------------------------------------------------------
 
 inline int&
-_score(HirschbergSet_ & me)	{
-	return me.score;
+_score(HirschbergSet_ & me)    {
+    return me.score;
 }
 
 // ----------------------------------------------------------------------------
@@ -207,7 +206,7 @@ _score(HirschbergSet_ & me)	{
 inline int const&
 _score(HirschbergSet_ const & me)
 {
-	return me.score;
+    return me.score;
 }
 
 // ----------------------------------------------------------------------------
@@ -216,7 +215,7 @@ _score(HirschbergSet_ const & me)
 
 inline void
 _setScore(HirschbergSet_ & me,int new_score) {
-	me.score = new_score;
+    me.score = new_score;
 }
 
 // ----------------------------------------------------------------------------
@@ -225,16 +224,16 @@ _setScore(HirschbergSet_ & me,int new_score) {
 
 // //////////////////////////////////////////////////////////////////////////////////////////////
 //  Debug Methods
-//		functions are only used for debugging or verbose output, therefore they
+//        functions are only used for debugging or verbose output, therefore they
 //      are only active in SEQAN_DEBUG
 // //////////////////////////////////////////////////////////////////////////////////////////////
 #ifdef SEQAN_DEBUG
-	
-inline 
+
+inline
 void
 print(HirschbergSet_ const & me)
 {
-	std::cout << me.x1 << " " << me.x2 << "\t" << me.y1 << " " << me.y2 << std::endl;
+    std::cout << me.x1 << " " << me.x2 << "\t" << me.y1 << " " << me.y2 << std::endl;
 }
 #endif
 
@@ -243,10 +242,10 @@ print(HirschbergSet_ const & me)
 // ----------------------------------------------------------------------------
 
 inline bool
-operator==(HirschbergSet_ const & lhs, 
+operator==(HirschbergSet_ const & lhs,
            HirschbergSet_ const & rhs)
 {
-	return ((_begin1(lhs) == _begin1(rhs)) && (_end1(lhs) == _end1(rhs)) &&
+    return ((_begin1(lhs) == _begin1(rhs)) && (_end1(lhs) == _end1(rhs)) &&
             (_begin2(lhs) == _begin2(rhs)) && (_end2(lhs) == _end2(rhs)));
 }
 
@@ -255,128 +254,114 @@ operator==(HirschbergSet_ const & lhs,
 // ----------------------------------------------------------------------------
 
 #ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
-	template<typename TSource>
-	void _writeDebugMatrix(TSource s1,TSource s2)
-	{
-		int l1 = length(s1);
-		int l2 = length(s2);
-	    
-		int i,j,sg,sd;
-
-		String<String<int> > fMatrix,rMatrix,tMatrix;
-
-		resize(fMatrix,l1 + 1);
-		resize(rMatrix,l1 + 1);
-		resize(tMatrix,l1 + 1);
-
-		for(i = 0;i <= l1;++i)
-		{
-			resize(fMatrix[i],l2 + 1);
-			resize(rMatrix[i],l2 + 1);
-			resize(tMatrix[i],l2 + 1);
-		}
-
-		for(i = 0;i <= l1;++i)
-			fMatrix[i][0] = i * (-1);
-
-		for(i = l1;i >= 0;--i)
-			rMatrix[i][l2] = (l1 - i) * (-1);
-
-		// calculate forward matrix
-		for(j = 1;j <= l2;++j)
-		{
-			fMatrix[0][j] = j*(-1);
-			for(i = 1;i <= l1;++i)
-			{
-				sg = -1 + ((fMatrix[i-1][j] > fMatrix[i][j-1]) ? fMatrix[i-1][j] : fMatrix[i][j-1]);
-				sd = fMatrix[i-1][j-1] + ((s1[i - 1] == s2[j-1]) ? 0 : -1 );
-		
-				fMatrix[i][j] = ((sg > sd) ? sg : sd);
-			}
-		}
-
-		// calculate reverse matrix
-		for(j = l2 - 1;j >= 0;--j)
-		{	
-			rMatrix[l1][j] = (l2 - j)*(-1);
-			for(i = l1 - 1;i >= 0;--i)
-			{
-				sg = -1 + ((rMatrix[i+1][j] > rMatrix[i][j+1]) ? rMatrix[i+1][j] : rMatrix[i][j+1]);
-				sd = rMatrix[i+1][j+1] + ((s1[i] == s2[j]) ? 0 : -1 );
-		
-				rMatrix[i][j] = ((sg > sd) ? sg : sd);
-			}
-		}
-
-		// print fMatrix
-		std::cout << ";-;";
-		for(i = 0;i < l1;++i)
-			std::cout << s1[i] << ";";
-
-		std::cout << std::endl << "-;";
-		for(j = 0;j <= l2;++j)
-		{	
-			if(j != 0) std::cout << s2[j-1] << ";";
-			for(i = 0;i <= l1;++i)
-			{
-				std::cout << fMatrix[i][j] << ";";
-			}
-			std::cout << std::endl;
-		}
-		// print rMatrix
-		std::cout << ";";
-		for(i = 0;i < l1;++i)
-			std::cout << s1[i] << ";";
-		std::cout << "-;" << std::endl;
-
-		for(j = 0;j <= l2;++j)
-		{	
-			if(j != l2) std::cout << s2[j] << ";";
-			else std::cout << "-;";
-			for(i = 0;i <= l1;++i)
-			{
-				std::cout << rMatrix[i][j] << ";";
-			}
-			std::cout << std::endl;
-		}
-
-		// fill and print target matrix
-		std::cout << ";-;";
-		for(i = 0;i < l1;++i)
-			std::cout << s1[i] << ";";
-
-		std::cout << std::endl << "-;";
-		for(j = 0;j <= l2;++j)
-		{	
-			if(j != 0) std::cout << s2[j-1] << ";";
-			for(i = 0;i <= l1;++i)
-			{
-				tMatrix[i][j] = fMatrix[i][j] + rMatrix[i][j];
-				std::cout << tMatrix[i][j] << ";";
-			}
-			std::cout << std::endl;
-		}
-	}
+    template<typename TSource>
+    void _writeDebugMatrix(TSource s1,TSource s2)
+    {
+        int l1 = length(s1);
+        int l2 = length(s2);
+
+        int i,j,sg,sd;
+
+        String<String<int> > fMatrix,rMatrix,tMatrix;
+
+        resize(fMatrix,l1 + 1);
+        resize(rMatrix,l1 + 1);
+        resize(tMatrix,l1 + 1);
+
+        for(i = 0;i <= l1;++i)
+        {
+            resize(fMatrix[i],l2 + 1);
+            resize(rMatrix[i],l2 + 1);
+            resize(tMatrix[i],l2 + 1);
+        }
+
+        for(i = 0;i <= l1;++i)
+            fMatrix[i][0] = i * (-1);
+
+        for(i = l1;i >= 0;--i)
+            rMatrix[i][l2] = (l1 - i) * (-1);
+
+        // calculate forward matrix
+        for(j = 1;j <= l2;++j)
+        {
+            fMatrix[0][j] = j*(-1);
+            for(i = 1;i <= l1;++i)
+            {
+                sg = -1 + ((fMatrix[i-1][j] > fMatrix[i][j-1]) ? fMatrix[i-1][j] : fMatrix[i][j-1]);
+                sd = fMatrix[i-1][j-1] + ((s1[i - 1] == s2[j-1]) ? 0 : -1 );
+
+                fMatrix[i][j] = ((sg > sd) ? sg : sd);
+            }
+        }
+
+        // calculate reverse matrix
+        for(j = l2 - 1;j >= 0;--j)
+        {
+            rMatrix[l1][j] = (l2 - j)*(-1);
+            for(i = l1 - 1;i >= 0;--i)
+            {
+                sg = -1 + ((rMatrix[i+1][j] > rMatrix[i][j+1]) ? rMatrix[i+1][j] : rMatrix[i][j+1]);
+                sd = rMatrix[i+1][j+1] + ((s1[i] == s2[j]) ? 0 : -1 );
+
+                rMatrix[i][j] = ((sg > sd) ? sg : sd);
+            }
+        }
+
+        // print fMatrix
+        std::cout << ";-;";
+        for(i = 0;i < l1;++i)
+            std::cout << s1[i] << ";";
+
+        std::cout << std::endl << "-;";
+        for(j = 0;j <= l2;++j)
+        {
+            if(j != 0) std::cout << s2[j-1] << ";";
+            for(i = 0;i <= l1;++i)
+            {
+                std::cout << fMatrix[i][j] << ";";
+            }
+            std::cout << std::endl;
+        }
+        // print rMatrix
+        std::cout << ";";
+        for(i = 0;i < l1;++i)
+            std::cout << s1[i] << ";";
+        std::cout << "-;" << std::endl;
+
+        for(j = 0;j <= l2;++j)
+        {
+            if(j != l2) std::cout << s2[j] << ";";
+            else std::cout << "-;";
+            for(i = 0;i <= l1;++i)
+            {
+                std::cout << rMatrix[i][j] << ";";
+            }
+            std::cout << std::endl;
+        }
+
+        // fill and print target matrix
+        std::cout << ";-;";
+        for(i = 0;i < l1;++i)
+            std::cout << s1[i] << ";";
+
+        std::cout << std::endl << "-;";
+        for(j = 0;j <= l2;++j)
+        {
+            if(j != 0) std::cout << s2[j-1] << ";";
+            for(i = 0;i <= l1;++i)
+            {
+                tMatrix[i][j] = fMatrix[i][j] + rMatrix[i][j];
+                std::cout << tMatrix[i][j] << ";";
+            }
+            std::cout << std::endl;
+        }
+    }
 
 #endif
 
-// debug flag .. define to see where Hirschberg cuts the sequences	
+// debug flag .. define to see where Hirschberg cuts the sequences
 //#define SEQAN_HIRSCHBERG_DEBUG_CUT
 
-/*DISABLED
-.Function.hirschberg:
-..cat:Alignment
-..summary:Computes a global Alignment for the passed Alignment-Container with the specified scoring scheme
-..signature:hirschberg(Align<TSource, TSpec> & align,Score<TScoreValue, Simple> const & score)
-..param.align: Reference to the Alignment-Object
-..param.score: Const Reference to the Scoring Scheme
-..remarks: The alignment is based on the algorithm proposed by Hirschberg. The general idea is to divide the DP (dynamic programming) matrix,
-to compute a global alignment in linear space. Instead of computing half of the
-DP matrix in forward direction and the other half in reverse, a pointer to the cell of the DP matrix, were the actual, optimal alignment
-passes the mid column ist saved, during the computation of the second part of the Matrix.
-..include:seqan/align.h
-*/
-
 // ----------------------------------------------------------------------------
 // Function globalAlignment()
 // ----------------------------------------------------------------------------
@@ -391,339 +376,339 @@ _globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 {
     TSequenceH const & s1 = source(gapsH);
     TSequenceV const & s2 = source(gapsV);
-	
-	TScoreValue total_score = 0;
+
+    TScoreValue total_score = 0;
 
     typedef typename Value<TSequenceV>::Type TValueV;
 
-	typedef typename Size<TSequenceH>::Type TStringSize;
-	
-	typedef typename Iterator<TSequenceH const, Standard>::Type TSequenceHIter;
-	typedef typename Iterator<TSequenceV const, Standard>::Type TSequenceVIter;
-
-	typedef typename Iterator<Gaps<TSequenceH, TGapsSpecH> >::Type TGapsHIter;
-	typedef typename Iterator<Gaps<TSequenceV, TGapsSpecV> >::Type TGapsVIter;
-
-	TGapsHIter target_0 = begin(gapsH);
-	TGapsVIter target_1 = begin(gapsV);
-
-	typedef typename Iterator<Matrix<TScoreValue> >::Type TMatrixIterator;
-
-	TValueV v;
-
-	TStringSize len1 = length(s1);
-	TStringSize len2 = length(s2);
-
-	// string to store the score values for the currently active cell
-	String<TScoreValue> c_score;
-	resize(c_score,len2 + 1);
-	// string to strore the backpointers
-	String<int> pointer;
-	resize(pointer,len2 + 1);
-
-	// scoring-scheme specific score values
-	TScoreValue score_match = scoreMatch(score_);
-	TScoreValue score_mismatch = scoreMismatch(score_);
-	TScoreValue score_gap = scoreGapExtend(score_);
-
-	TScoreValue border,s,sg,sd,sg1,sg2;
-	int dp;
-
-	std::stack<HirschbergSet_> to_process;
-	HirschbergSet_ target;
-	
-	int i,j;
-	
-	HirschbergSet_ hs_complete(0,len1,0,len2,0);
-	to_process.push(hs_complete);
-
-	while(!to_process.empty())
-	{
-		target = to_process.top();
-		to_process.pop();
-
-		if(_begin2(target) == _end2(target))
-		{
-			for(i = 0;i < (_end1(target) - _begin1(target));++i)
-			{
-				insertGap(target_1);
-				++target_0;
-				++target_1;
-			}
-		}
+    typedef typename Size<TSequenceH>::Type TStringSize;
+
+    typedef typename Iterator<TSequenceH const, Standard>::Type TSequenceHIter;
+    typedef typename Iterator<TSequenceV const, Standard>::Type TSequenceVIter;
+
+    typedef typename Iterator<Gaps<TSequenceH, TGapsSpecH> >::Type TGapsHIter;
+    typedef typename Iterator<Gaps<TSequenceV, TGapsSpecV> >::Type TGapsVIter;
+
+    TGapsHIter target_0 = begin(gapsH);
+    TGapsVIter target_1 = begin(gapsV);
+
+    typedef typename Iterator<Matrix<TScoreValue> >::Type TMatrixIterator;
+
+    TValueV v;
+
+    TStringSize len1 = length(s1);
+    TStringSize len2 = length(s2);
+
+    // string to store the score values for the currently active cell
+    String<TScoreValue> c_score;
+    resize(c_score,len2 + 1);
+    // string to strore the backpointers
+    String<int> pointer;
+    resize(pointer,len2 + 1);
+
+    // scoring-scheme specific score values
+    TScoreValue score_match = scoreMatch(score_);
+    TScoreValue score_mismatch = scoreMismatch(score_);
+    TScoreValue score_gap = scoreGapExtend(score_);
+
+    TScoreValue border,s,sg,sd,sg1,sg2;
+    int dp;
+
+    std::stack<HirschbergSet_> to_process;
+    HirschbergSet_ target;
+
+    int i,j;
+
+    HirschbergSet_ hs_complete(0,len1,0,len2,0);
+    to_process.push(hs_complete);
+
+    while(!to_process.empty())
+    {
+        target = to_process.top();
+        to_process.pop();
+
+        if(_begin2(target) == _end2(target))
+        {
+            for(i = 0;i < (_end1(target) - _begin1(target));++i)
+            {
+                insertGap(target_1);
+                ++target_0;
+                ++target_1;
+            }
+        }
         if(_begin1(target) == _end1(target))
-		{
-			for(i = 0;i < (_end2(target) - _begin2(target));++i)
-			{
-				insertGap(target_0);
-				++target_0;
-				++target_1;
-			}
-		}
-		else if(_begin1(target) + 1 == _end1(target) || _begin2(target) + 1 == _end2(target))
-		{
-			/* ALIGN */			
+        {
+            for(i = 0;i < (_end2(target) - _begin2(target));++i)
+            {
+                insertGap(target_0);
+                ++target_0;
+                ++target_1;
+            }
+        }
+        else if(_begin1(target) + 1 == _end1(target) || _begin2(target) + 1 == _end2(target))
+        {
+            /* ALIGN */
 #ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
-			std::cout << "align s1 " << _begin1(target) << " to " << _end1(target) << " and s2 " << _begin2(target) << " to " << _end2(target) << std::endl;
-			std::cout << "align " << infix(s1,_begin1(target),_end1(target)) << " and " << infix(s2,_begin2(target),_end2(target)) << std::endl << std::endl;
+            std::cout << "align s1 " << _begin1(target) << " to " << _end1(target) << " and s2 " << _begin2(target) << " to " << _end2(target) << std::endl;
+            std::cout << "align " << infix(s1,_begin1(target),_end1(target)) << " and " << infix(s2,_begin2(target),_end2(target)) << std::endl << std::endl;
 #endif
 
-			TStringSize len_1 = _end1(target) - _begin1(target);
-			TStringSize len_2 = _end2(target) - _begin2(target);
-
-			Matrix<TScoreValue> matrix_;
-
-			setDimension(matrix_, 2);
-			setLength(matrix_, 0, len_1 + 1);
-			setLength(matrix_, 1, len_2 + 1);
-			resize(matrix_);
-
-			/* init matrix */
-			TSequenceHIter x_begin = iter(s1, _begin1(target), Standard()) - 1;
-			TSequenceHIter x_end = iter(s1, _end1(target), Standard()) - 1;
-			TSequenceVIter y_begin = iter(s2, _begin2(target), Standard()) - 1;
-			TSequenceVIter y_end = iter(s2, _end2(target), Standard()) - 1;
-
-			TSequenceHIter x = x_end;
-			TSequenceVIter y;
-
-			TMatrixIterator col_ = end(matrix_) - 1;
-			TMatrixIterator finger1;
-			TMatrixIterator finger2;
-
-
-			TScoreValue h = 0;
-			TScoreValue border_ = score_gap;
-			TScoreValue v = border_;
-
-
-			//-------------------------------------------------------------------------
-			// init
-
-			finger1 = col_;
-			*finger1 = 0;
-			for (x = x_end; x != x_begin; --x)
-			{
-				goPrevious(finger1, 0);
-				*finger1 = border_;
-				border_ += score_gap;
-			}
-
-			//-------------------------------------------------------------------------
-			//fill matrix
-			border_ = 0;
-			for (y = y_end; y != y_begin; --y)
-			{
-				TValueV cy = *y;
-				h = border_;
-				border_ += score_gap;
-				v = border_;
-
-				finger2 = col_;	
-				goPrevious(col_, 1);
-				finger1 = col_;
-
-				*finger1 = v;
-
-				for (x = x_end; x != x_begin; --x)
-				{
-					goPrevious(finger1, 0);
-					goPrevious(finger2, 0);
-					if (*x == cy)
-					{
-						v = h + score_match;
-						h = *finger2;
-					}
-					else
-					{
-						TScoreValue s1 = h + score_mismatch;
-						h = *finger2;
-						TScoreValue s2 = score_gap + ((h > v) ? h : v);
-						v = (s1 > s2) ? s1 : s2;
-					}
-					*finger1 = v;
-				}
-			}
+            TStringSize len_1 = _end1(target) - _begin1(target);
+            TStringSize len_2 = _end2(target) - _begin2(target);
+
+            Matrix<TScoreValue> matrix_;
+
+            setDimension(matrix_, 2);
+            setLength(matrix_, 0, len_1 + 1);
+            setLength(matrix_, 1, len_2 + 1);
+            resize(matrix_);
+
+            /* init matrix */
+            TSequenceHIter x_begin = iter(s1, _begin1(target), Standard()) - 1;
+            TSequenceHIter x_end = iter(s1, _end1(target), Standard()) - 1;
+            TSequenceVIter y_begin = iter(s2, _begin2(target), Standard()) - 1;
+            TSequenceVIter y_end = iter(s2, _end2(target), Standard()) - 1;
+
+            TSequenceHIter x = x_end;
+            TSequenceVIter y;
+
+            TMatrixIterator col_ = end(matrix_) - 1;
+            TMatrixIterator finger1;
+            TMatrixIterator finger2;
+
+
+            TScoreValue h = 0;
+            TScoreValue border_ = score_gap;
+            TScoreValue v = border_;
+
+
+            //-------------------------------------------------------------------------
+            // init
+
+            finger1 = col_;
+            *finger1 = 0;
+            for (x = x_end; x != x_begin; --x)
+            {
+                goPrevious(finger1, 0);
+                *finger1 = border_;
+                border_ += score_gap;
+            }
+
+            //-------------------------------------------------------------------------
+            //fill matrix
+            border_ = 0;
+            for (y = y_end; y != y_begin; --y)
+            {
+                TValueV cy = *y;
+                h = border_;
+                border_ += score_gap;
+                v = border_;
+
+                finger2 = col_;
+                goPrevious(col_, 1);
+                finger1 = col_;
+
+                *finger1 = v;
+
+                for (x = x_end; x != x_begin; --x)
+                {
+                    goPrevious(finger1, 0);
+                    goPrevious(finger2, 0);
+                    if (*x == cy)
+                    {
+                        v = h + score_match;
+                        h = *finger2;
+                    }
+                    else
+                    {
+                        TScoreValue s1 = h + score_mismatch;
+                        h = *finger2;
+                        TScoreValue s2 = score_gap + ((h > v) ? h : v);
+                        v = (s1 > s2) ? s1 : s2;
+                    }
+                    *finger1 = v;
+                }
+            }
             total_score += value(matrix_, 0,0);
 #ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
             std::cout << "alignment score is " << total_score << std::endl << std::endl;
 #endif
 
-			/* TRACE BACK */
-			finger1 = begin(matrix_);
-			x = iter(s1,_begin1(target));
-			y = iter(s2,_begin2(target));
-			x_end = iter(s1,_end1(target));
-			y_end = iter(s2,_end2(target));
-
-			while ((x != x_end) && (y != y_end))
-			{
-				bool gv;
-				bool gh;
-
-				if (*x == *y)
-				{
-					gv = gh = true;
-				}
-				else
-				{
-					TMatrixIterator it_ = finger1;
-
-					goNext(it_, 0);
-					TScoreValue v = *it_;
-
-					goNext(it_, 1);
-					TScoreValue d = *it_;
-
-					it_ = finger1;
-					goNext(it_, 1);
-					TScoreValue h = *it_;
-
-					gv = (v >= h) | (d >= h);
-					gh = (h >= v) | (d >= v);
-				}
-
-				if (gv)
-				{
-					++x;
-					goNext(finger1, 0);
-				}
-				else
-				{
-					insertGap(target_0);
-				}
-
-				if (gh) 
-				{
-					++y;
-					goNext(finger1, 1);
-				}
-				else
-				{
-					insertGap(target_1);
-				}
-
-				++target_0;
-				++target_1;
-			}
-
-			// if x or y did not reached there end position, fill the rest with gaps
-			while(x != x_end)
-			{
-				insertGap(target_1);
-				++target_0;
-				++target_1;
-				++x;
-			}
-
-			while(y != y_end)
-			{
-				insertGap(target_0);
-				++target_0;
-				++target_1;
-				++y;
-			}
-			/* END ALIGN */
-		}
-		else
-		{	
-			/* 
-				Calculate cut using the algorithm as proposed in the lecture of Clemens Gröpl 
-				using a backpointer to remember the position where the optimal alignment passes
-				the mid column
-			*/
-			int mid = static_cast<int>(floor( static_cast<double>((_begin1(target) + _end1(target))/2) ));
+            /* TRACE BACK */
+            finger1 = begin(matrix_);
+            x = iter(s1,_begin1(target));
+            y = iter(s2,_begin2(target));
+            x_end = iter(s1,_end1(target));
+            y_end = iter(s2,_end2(target));
+
+            while ((x != x_end) && (y != y_end))
+            {
+                bool gv;
+                bool gh;
+
+                if (*x == *y)
+                {
+                    gv = gh = true;
+                }
+                else
+                {
+                    TMatrixIterator it_ = finger1;
+
+                    goNext(it_, 0);
+                    TScoreValue v = *it_;
+
+                    goNext(it_, 1);
+                    TScoreValue d = *it_;
+
+                    it_ = finger1;
+                    goNext(it_, 1);
+                    TScoreValue h = *it_;
+
+                    gv = (v >= h) | (d >= h);
+                    gh = (h >= v) | (d >= v);
+                }
+
+                if (gv)
+                {
+                    ++x;
+                    goNext(finger1, 0);
+                }
+                else
+                {
+                    insertGap(target_0);
+                }
+
+                if (gh)
+                {
+                    ++y;
+                    goNext(finger1, 1);
+                }
+                else
+                {
+                    insertGap(target_1);
+                }
+
+                ++target_0;
+                ++target_1;
+            }
+
+            // if x or y did not reached there end position, fill the rest with gaps
+            while(x != x_end)
+            {
+                insertGap(target_1);
+                ++target_0;
+                ++target_1;
+                ++x;
+            }
+
+            while(y != y_end)
+            {
+                insertGap(target_0);
+                ++target_0;
+                ++target_1;
+                ++y;
+            }
+            /* END ALIGN */
+        }
+        else
+        {
+            /*
+                Calculate cut using the algorithm as proposed in the lecture of Clemens Gröpl
+                using a backpointer to remember the position where the optimal alignment passes
+                the mid column
+            */
+            int mid = static_cast<int>(floor( static_cast<double>((_begin1(target) + _end1(target))/2) ));
 
 #ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
-			std::cout << "calculate cut for s1 " << _begin1(target) << " to " << _end1(target) << " and s2 " << _begin2(target) << " to " << _end2(target) << std::endl;
-			std::cout << "calculate cut for " << infix(s1,_begin1(target),_end1(target)) << " and " << infix(s2,_begin2(target),_end2(target)) << std::endl;
-			std::cout << "cut is in row " << mid << " symbol is " << getValue(s1,mid-1) << std::endl << std::endl;
+            std::cout << "calculate cut for s1 " << _begin1(target) << " to " << _end1(target) << " and s2 " << _begin2(target) << " to " << _end2(target) << std::endl;
+            std::cout << "calculate cut for " << infix(s1,_begin1(target),_end1(target)) << " and " << infix(s2,_begin2(target),_end2(target)) << std::endl;
+            std::cout << "cut is in row " << mid << " symbol is " << getValue(s1,mid-1) << std::endl << std::endl;
 
 
-			_writeDebugMatrix(infix(s1,_begin1(target),_end1(target)),infix(s2,_begin2(target),_end2(target)));
+            _writeDebugMatrix(infix(s1,_begin1(target),_end1(target)),infix(s2,_begin2(target),_end2(target)));
 #endif
 
-			border = 0;
-			for(i = _begin2(target);i <= _end2(target);++i)
-			{
-				c_score[i] = border;
-				border += score_gap; 
-				pointer[i] = i;
-			}
-
-			// iterate over s1 until the mid column is reached
-			border = score_gap;
-			for(i = _begin1(target) + 1;i <= mid;++i)
-			{
-				s = c_score[_begin2(target)];
-				c_score[_begin2(target)] = border;
-				border += score_gap;
-				v = getValue(s1,i-1);
-				for(j = _begin2(target) + 1;j <= _end2(target);++j)
-				{
-					sg = score_gap + ((c_score[j] > c_score[j - 1]) ? c_score[j] : c_score[j - 1]);
-					sd = s + ((v == getValue(s2,j-1)) ? score_match : score_mismatch);
-
-					s = c_score[j];
-					c_score[j] = (sg > sd) ? sg : sd;	
-				}
-			}
-
-			// from here, rememeber the cell of mid-column, where optimal alignment passed
-			for(i = mid + 1;i <= _end1(target);++i)
-			{
-				s = c_score[_begin2(target)];
-				c_score[_begin2(target)] = border;
-				border += score_gap;
-				v = getValue(s1,i-1);
-			
-				dp = _begin2(target);
-			
-				for(j = _begin2(target) + 1;j <= _end2(target);++j)
-				{
-					sg1 = score_gap + c_score[j];
-					sg2 = score_gap + c_score[j - 1];
-
-					sd = s + ((v == getValue(s2,j-1)) ? score_match : score_mismatch);
-
-					s = c_score[j];
-					sg = pointer[j];
-					if(sd >= _max(sg1,sg2))
-					{
-						c_score[j] = sd;
-						pointer[j] = dp;
-					}
-					else
-					{
-						if(sg2 > sg1)
-						{
-							c_score[j] = sg2;
-							pointer[j] = pointer[j-1];
-						}
-						else
-						{
-							// gap introduced from left
-							// no update for the pointer
-							c_score[j] = sg1;
-						}
-					}
-					dp = sg;
-				}
-			}
+            border = 0;
+            for(i = _begin2(target);i <= _end2(target);++i)
+            {
+                c_score[i] = border;
+                border += score_gap;
+                pointer[i] = i;
+            }
+
+            // iterate over s1 until the mid column is reached
+            border = score_gap;
+            for(i = _begin1(target) + 1;i <= mid;++i)
+            {
+                s = c_score[_begin2(target)];
+                c_score[_begin2(target)] = border;
+                border += score_gap;
+                v = getValue(s1,i-1);
+                for(j = _begin2(target) + 1;j <= _end2(target);++j)
+                {
+                    sg = score_gap + ((c_score[j] > c_score[j - 1]) ? c_score[j] : c_score[j - 1]);
+                    sd = s + ((v == getValue(s2,j-1)) ? score_match : score_mismatch);
+
+                    s = c_score[j];
+                    c_score[j] = (sg > sd) ? sg : sd;
+                }
+            }
+
+            // from here, rememeber the cell of mid-column, where optimal alignment passed
+            for(i = mid + 1;i <= _end1(target);++i)
+            {
+                s = c_score[_begin2(target)];
+                c_score[_begin2(target)] = border;
+                border += score_gap;
+                v = getValue(s1,i-1);
+
+                dp = _begin2(target);
+
+                for(j = _begin2(target) + 1;j <= _end2(target);++j)
+                {
+                    sg1 = score_gap + c_score[j];
+                    sg2 = score_gap + c_score[j - 1];
+
+                    sd = s + ((v == getValue(s2,j-1)) ? score_match : score_mismatch);
+
+                    s = c_score[j];
+                    sg = pointer[j];
+                    if(sd >= _max(sg1,sg2))
+                    {
+                        c_score[j] = sd;
+                        pointer[j] = dp;
+                    }
+                    else
+                    {
+                        if(sg2 > sg1)
+                        {
+                            c_score[j] = sg2;
+                            pointer[j] = pointer[j-1];
+                        }
+                        else
+                        {
+                            // gap introduced from left
+                            // no update for the pointer
+                            c_score[j] = sg1;
+                        }
+                    }
+                    dp = sg;
+                }
+            }
 
 #ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
-			std::cout << "hirschberg calculates cut in column " << mid << " and row " << pointer[_end2(target)] << std::endl;
-			std::cout << "requested position in c_score and pointer is " << _end2(target) << std::endl;
-			std::cout << "alignment score is " << c_score[_end2(target)] << std::endl << std::endl;
+            std::cout << "hirschberg calculates cut in column " << mid << " and row " << pointer[_end2(target)] << std::endl;
+            std::cout << "requested position in c_score and pointer is " << _end2(target) << std::endl;
+            std::cout << "alignment score is " << c_score[_end2(target)] << std::endl << std::endl;
 #endif
-			to_process.push(HirschbergSet_(mid,_end1(target),pointer[_end2(target)],_end2(target),0));
-			to_process.push(HirschbergSet_(_begin1(target),mid,_begin2(target),pointer[_end2(target)],0));
-		}
-		/* END CUT */
-	}
-	return total_score;
+            to_process.push(HirschbergSet_(mid,_end1(target),pointer[_end2(target)],_end2(target),0));
+            to_process.push(HirschbergSet_(_begin1(target),mid,_begin2(target),pointer[_end2(target)],0));
+        }
+        /* END CUT */
+    }
+    return total_score;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
diff --git a/seqan/align/global_alignment_myers_hirschberg_impl.h b/seqan/align/global_alignment_myers_hirschberg_impl.h
index c56fce7..7bc4816 100644
--- a/seqan/align/global_alignment_myers_hirschberg_impl.h
+++ b/seqan/align/global_alignment_myers_hirschberg_impl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_
 
 namespace seqan {
 
@@ -58,109 +58,109 @@ namespace seqan {
 // ----------------------------------------------------------------------------
 
 #ifdef MYERS_HIRSCHBERG_VERBOSE
-	template<typename TSource>
-	void _writeDebugMatrix(TSource s1,TSource s2)
-	{
+    template<typename TSource>
+    void _writeDebugMatrix(TSource s1,TSource s2)
+    {
 //IOREV _notio_ not relevant for iorev
-		int l1 = length(s1);
-		int l2 = length(s2);
-	    
-		int i,j,sg,sd;
-
-		String<String<int> > fMatrix,rMatrix,tMatrix;
-
-		resize(fMatrix,l1 + 1);
-		resize(rMatrix,l1 + 1);
-		resize(tMatrix,l1 + 1);
-
-		for(i = 0;i <= l1;++i)
-		{
-			resize(fMatrix[i],l2 + 1);
-			resize(rMatrix[i],l2 + 1);
-			resize(tMatrix[i],l2 + 1);
-		}
-
-		for(i = 0;i <= l1;++i)
-			fMatrix[i][0] = i * (-1);
-
-		for(i = l1;i >= 0;--i)
-			rMatrix[i][l2] = (l1 - i) * (-1);
-
-		// calculate forward matrix
-		for(j = 1;j <= l2;++j)
-		{
-			fMatrix[0][j] = j*(-1);
-			for(i = 1;i <= l1;++i)
-			{
-				sg = -1 + ((fMatrix[i-1][j] > fMatrix[i][j-1]) ? fMatrix[i-1][j] : fMatrix[i][j-1]);
-				sd = fMatrix[i-1][j-1] + ((s1[i - 1] == s2[j-1]) ? 0 : -1 );
-		
-				fMatrix[i][j] = ((sg > sd) ? sg : sd);
-			}
-		}
-
-		// calculate reverse matrix
-		for(j = l2 - 1;j >= 0;--j)
-		{	
-			rMatrix[l1][j] = (l2 - j)*(-1);
-			for(i = l1 - 1;i >= 0;--i)
-			{
-				sg = -1 + ((rMatrix[i+1][j] > rMatrix[i][j+1]) ? rMatrix[i+1][j] : rMatrix[i][j+1]);
-				sd = rMatrix[i+1][j+1] + ((s1[i] == s2[j]) ? 0 : -1 );
-		
-				rMatrix[i][j] = ((sg > sd) ? sg : sd);
-			}
-		}
-
-		// print fMatrix
-		std::cout << ";-;";
-		for(i = 0;i < l1;++i)
-			std::cout << s1[i] << ";";
-
-		std::cout << std::endl << "-;";
-		for(j = 0;j <= l2;++j)
-		{	
-			if(j != 0) std::cout << s2[j-1] << ";";
-			for(i = 0;i <= l1;++i)
-			{
-				std::cout << fMatrix[i][j] << ";";
-			}
-			std::cout << std::endl;
-		}
-		// print rMatrix
-		std::cout << ";";
-		for(i = 0;i < l1;++i)
-			std::cout << s1[i] << ";";
-		std::cout << "-;" << std::endl;
-
-		for(j = 0;j <= l2;++j)
-		{	
-			if(j != l2) std::cout << s2[j] << ";";
-			else std::cout << "-;";
-			for(i = 0;i <= l1;++i)
-			{
-				std::cout << rMatrix[i][j] << ";";
-			}
-			std::cout << std::endl;
-		}
-
-		// fill and print target matrix
-		std::cout << ";-;";
-		for(i = 0;i < l1;++i)
-			std::cout << s1[i] << ";";
-
-		std::cout << std::endl << "-;";
-		for(j = 0;j <= l2;++j)
-		{	
-			if(j != 0) std::cout << s2[j-1] << ";";
-			for(i = 0;i <= l1;++i)
-			{
-				tMatrix[i][j] = fMatrix[i][j] + rMatrix[i][j];
-				std::cout << tMatrix[i][j] << ";";
-			}
-			std::cout << std::endl;
-		}
-	}
+        int l1 = length(s1);
+        int l2 = length(s2);
+
+        int i,j,sg,sd;
+
+        String<String<int> > fMatrix,rMatrix,tMatrix;
+
+        resize(fMatrix,l1 + 1);
+        resize(rMatrix,l1 + 1);
+        resize(tMatrix,l1 + 1);
+
+        for(i = 0;i <= l1;++i)
+        {
+            resize(fMatrix[i],l2 + 1);
+            resize(rMatrix[i],l2 + 1);
+            resize(tMatrix[i],l2 + 1);
+        }
+
+        for(i = 0;i <= l1;++i)
+            fMatrix[i][0] = i * (-1);
+
+        for(i = l1;i >= 0;--i)
+            rMatrix[i][l2] = (l1 - i) * (-1);
+
+        // calculate forward matrix
+        for(j = 1;j <= l2;++j)
+        {
+            fMatrix[0][j] = j*(-1);
+            for(i = 1;i <= l1;++i)
+            {
+                sg = -1 + ((fMatrix[i-1][j] > fMatrix[i][j-1]) ? fMatrix[i-1][j] : fMatrix[i][j-1]);
+                sd = fMatrix[i-1][j-1] + ((s1[i - 1] == s2[j-1]) ? 0 : -1 );
+
+                fMatrix[i][j] = ((sg > sd) ? sg : sd);
+            }
+        }
+
+        // calculate reverse matrix
+        for(j = l2 - 1;j >= 0;--j)
+        {
+            rMatrix[l1][j] = (l2 - j)*(-1);
+            for(i = l1 - 1;i >= 0;--i)
+            {
+                sg = -1 + ((rMatrix[i+1][j] > rMatrix[i][j+1]) ? rMatrix[i+1][j] : rMatrix[i][j+1]);
+                sd = rMatrix[i+1][j+1] + ((s1[i] == s2[j]) ? 0 : -1 );
+
+                rMatrix[i][j] = ((sg > sd) ? sg : sd);
+            }
+        }
+
+        // print fMatrix
+        std::cout << ";-;";
+        for(i = 0;i < l1;++i)
+            std::cout << s1[i] << ";";
+
+        std::cout << std::endl << "-;";
+        for(j = 0;j <= l2;++j)
+        {
+            if(j != 0) std::cout << s2[j-1] << ";";
+            for(i = 0;i <= l1;++i)
+            {
+                std::cout << fMatrix[i][j] << ";";
+            }
+            std::cout << std::endl;
+        }
+        // print rMatrix
+        std::cout << ";";
+        for(i = 0;i < l1;++i)
+            std::cout << s1[i] << ";";
+        std::cout << "-;" << std::endl;
+
+        for(j = 0;j <= l2;++j)
+        {
+            if(j != l2) std::cout << s2[j] << ";";
+            else std::cout << "-;";
+            for(i = 0;i <= l1;++i)
+            {
+                std::cout << rMatrix[i][j] << ";";
+            }
+            std::cout << std::endl;
+        }
+
+        // fill and print target matrix
+        std::cout << ";-;";
+        for(i = 0;i < l1;++i)
+            std::cout << s1[i] << ";";
+
+        std::cout << std::endl << "-;";
+        for(j = 0;j <= l2;++j)
+        {
+            if(j != 0) std::cout << s2[j-1] << ";";
+            for(i = 0;i <= l1;++i)
+            {
+                tMatrix[i][j] = fMatrix[i][j] + rMatrix[i][j];
+                std::cout << tMatrix[i][j] << ";";
+            }
+            std::cout << std::endl;
+        }
+    }
 #endif
 
 // ----------------------------------------------------------------------------
@@ -181,7 +181,7 @@ _globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
     // to fit into less words.
     if (length(source(gapsH)) < length(source(gapsV)))
         return _globalAlignment(gapsV, gapsH, algorithmTag);
-    
+
     clearGaps(gapsH);
     clearGaps(gapsV);
     clearClipping(gapsH);
@@ -189,23 +189,23 @@ _globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 
     typedef int TScoreValue;
 
-	// use size of unsigned int as blocksize for bit-vectors
-	const unsigned int BLOCK_SIZE = BitsPerValue<unsigned int>::VALUE;
+    // use size of unsigned int as blocksize for bit-vectors
+    const unsigned int BLOCK_SIZE = BitsPerValue<unsigned int>::VALUE;
 
-	// saves the score value that will be returned
-	TScoreValue score,total_score = 0;
+    // saves the score value that will be returned
+    TScoreValue score,total_score = 0;
 
-	typedef typename Value<TSequenceV>::Type TPatternAlphabet;
-	typedef typename Size<TSequenceH>::Type  TStringSize;
+    typedef typename Value<TSequenceV>::Type TPatternAlphabet;
+    typedef typename Size<TSequenceH>::Type  TStringSize;
 
-	typedef typename Iterator<TSequenceH const, Rooted>::Type TSequenceHIterator;
-	typedef typename Iterator<TSequenceV const, Rooted>::Type TSequenceVIterator;
+    typedef typename Iterator<TSequenceH const, Rooted>::Type TSequenceHIterator;
+    typedef typename Iterator<TSequenceV const, Rooted>::Type TSequenceVIterator;
     typedef Gaps<TSequenceH, TGapsSpecH> TGapsH;
     typedef Gaps<TSequenceV, TGapsSpecV> TGapsV;
-	typedef typename Iterator<TGapsH, Rooted>::Type TGapsHIterator;
-	typedef typename Iterator<TGapsV, Rooted>::Type TGapsVIterator;
+    typedef typename Iterator<TGapsH, Rooted>::Type TGapsHIterator;
+    typedef typename Iterator<TGapsV, Rooted>::Type TGapsVIterator;
 
-	typedef typename Iterator<Matrix<TScoreValue>, Rooted>::Type TMatrixIterator;
+    typedef typename Iterator<Matrix<TScoreValue>, Rooted>::Type TMatrixIterator;
 
     TGapsHIterator target_0 = begin(gapsH);
     TGapsVIterator target_1 = begin(gapsV);
@@ -213,28 +213,28 @@ _globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
     TSequenceH const & x = source(gapsH);
     TSequenceV const & y = source(gapsV);
 
-	TStringSize len_x = length(x);
-	TStringSize len_y = length(y);
+    TStringSize len_x = length(x);
+    TStringSize len_y = length(y);
+
+    // string to store the score values for the currently active cell
+    String<TScoreValue> c_score;
+    resize(c_score, len_x + 1, 0);
 
-	// string to store the score values for the currently active cell
-	String<TScoreValue> c_score;
-	resize(c_score, len_x + 1, 0);
-	
-	// scoring-scheme specific score values
-	TScoreValue score_match = 0;
-	TScoreValue score_mismatch = -1;
-	TScoreValue score_gap = -1;
+    // scoring-scheme specific score values
+    TScoreValue score_match = 0;
+    TScoreValue score_mismatch = -1;
+    TScoreValue score_gap = -1;
 
-	// additional vars
-	int i;
+    // additional vars
+    int i;
 
-	// stack with parts of matrix that have to be processed
-	std::stack<HirschbergSet_> to_process;
-	HirschbergSet_ target;
+    // stack with parts of matrix that have to be processed
+    std::stack<HirschbergSet_> to_process;
+    HirschbergSet_ target;
 
-	// myers specific vars and preprocessing
-	unsigned int patternAlphabetSize = ValueSize<TPatternAlphabet>::VALUE;
-	unsigned int blockCount = (len_y + BLOCK_SIZE - 1) / BLOCK_SIZE; // maximal count of blocks
+    // myers specific vars and preprocessing
+    unsigned int patternAlphabetSize = ValueSize<TPatternAlphabet>::VALUE;
+    unsigned int blockCount = (len_y + BLOCK_SIZE - 1) / BLOCK_SIZE; // maximal count of blocks
 
     String<unsigned> VP;
     String<unsigned> VN;
@@ -244,507 +244,507 @@ _globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
     resize(VP, blockCount, maxValue<unsigned>());
     resize(VN, blockCount, 0);
 
-	// first bitMask will be constructed from the shorter sequence
+    // first bitMask will be constructed from the shorter sequence
     resize(forwardBitMask, patternAlphabetSize * blockCount, 0);
     resize(reverseBitMask, patternAlphabetSize * blockCount, 0);
 
-	// encoding the letters as bit-vectors
+    // encoding the letters as bit-vectors
     for (unsigned int j = 0; j < len_y; j++){
-		forwardBitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] = forwardBitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE);
-		reverseBitMask[blockCount * ordValue(getValue(y,len_y - j - 1)) + j/BLOCK_SIZE] = reverseBitMask[blockCount * ordValue(getValue(y,len_y - j - 1)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE);
-	}
-
-	HirschbergSet_ hs_complete(0,len_x,0,len_y,1);
-	to_process.push(hs_complete);
-
-	while(!to_process.empty())
-	{
-		target = to_process.top();
-		to_process.pop();
-		/* if score is zero, the whole part of the sequence can be simply skipped */
-		if(_score(target) == 0)
-		{
-			/* coukd work faster */
-			for(i = 0;i < (_end1(target) - _begin1(target));++i)
-			{
-				++target_0;
-				++target_1;
-			}
+        forwardBitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] = forwardBitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE);
+        reverseBitMask[blockCount * ordValue(getValue(y,len_y - j - 1)) + j/BLOCK_SIZE] = reverseBitMask[blockCount * ordValue(getValue(y,len_y - j - 1)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE);
+    }
+
+    HirschbergSet_ hs_complete(0,len_x,0,len_y,1);
+    to_process.push(hs_complete);
+
+    while(!to_process.empty())
+    {
+        target = to_process.top();
+        to_process.pop();
+        /* if score is zero, the whole part of the sequence can be simply skipped */
+        if(_score(target) == 0)
+        {
+            /* coukd work faster */
+            for(i = 0;i < (_end1(target) - _begin1(target));++i)
+            {
+                ++target_0;
+                ++target_1;
+            }
 
 #ifdef MYERS_HIRSCHBERG_VERBOSE
-			printf("skipped %i to %i in first sequence\n",_begin1(target),_end1(target));
+            printf("skipped %i to %i in first sequence\n",_begin1(target),_end1(target));
 #endif
-		}
-		else if(_begin1(target) == _end1(target))
-		{
+        }
+        else if(_begin1(target) == _end1(target))
+        {
 
 #ifdef MYERS_HIRSCHBERG_VERBOSE
-			std::cout << "align y " << _begin2(target) << " to " << _end2(target) << std::endl;
-			std::cout << "align " << infix(y,_begin2(target),_end2(target)) << std::endl << std::endl;
-#endif	
-			for(i = 0;i < (_end2(target) - _begin2(target));++i)
-			{
-				insertGap(target_0);
-				++target_0;
-				++target_1;
-			}
-		}
-		else if(_begin2(target) + 1 == _end2(target))
-		{
-			/* ALIGN */			
+            std::cout << "align y " << _begin2(target) << " to " << _end2(target) << std::endl;
+            std::cout << "align " << infix(y,_begin2(target),_end2(target)) << std::endl << std::endl;
+#endif
+            for(i = 0;i < (_end2(target) - _begin2(target));++i)
+            {
+                insertGap(target_0);
+                ++target_0;
+                ++target_1;
+            }
+        }
+        else if(_begin2(target) + 1 == _end2(target))
+        {
+            /* ALIGN */
 #ifdef MYERS_HIRSCHBERG_VERBOSE
-			std::cout << "align x " << _begin1(target) << " to " << _end1(target) << " and y " << _begin2(target) << " to " << _end2(target) << std::endl;
-			std::cout << "align " << infix(x,_begin1(target),_end1(target)) << " and " << infix(y,_begin2(target),_end2(target)) << std::endl << std::endl;
+            std::cout << "align x " << _begin1(target) << " to " << _end1(target) << " and y " << _begin2(target) << " to " << _end2(target) << std::endl;
+            std::cout << "align " << infix(x,_begin1(target),_end1(target)) << " and " << infix(y,_begin2(target),_end2(target)) << std::endl << std::endl;
 #endif
 
-			TStringSize len_1 = _end1(target) - _begin1(target);
-			TStringSize len_2 = _end2(target) - _begin2(target);
-
-			Matrix<TScoreValue> matrix_;
-
-			setDimension(matrix_, 2);
-			setLength(matrix_, 0, len_1 + 1);
-			setLength(matrix_, 1, len_2 + 1);
-			resize(matrix_);
-
-			/* init matrix */
-			TSequenceHIterator xs_begin = iter(x,_begin1(target)) - 1;
-			TSequenceHIterator xs_end = iter(x,_end1(target)) - 1;
-			TSequenceVIterator ys_begin = iter(y,_begin2(target)) - 1;
-			TSequenceVIterator ys_end = iter(y,_end2(target)) - 1;
-
-			TSequenceHIterator xs = xs_end;
-			TSequenceVIterator ys;
-
-			TMatrixIterator col_ = end(matrix_) - 1;
-			TMatrixIterator finger1;
-			TMatrixIterator finger2;
-
-
-			TScoreValue h = 0;
-			TScoreValue border_ = score_gap;
-			TScoreValue v = border_;
-
-
-			//-------------------------------------------------------------------------
-			// init
-
-			finger1 = col_;
-			*finger1 = 0;
-			for (xs = xs_end; xs != xs_begin; --xs)
-			{
-				goPrevious(finger1, 0);
-				*finger1 = border_;
-				border_ += score_gap;
-			}
-
-			//-------------------------------------------------------------------------
-			//fill matrix
-
-			border_ = 0;
-			for (ys = ys_end; ys != ys_begin; --ys)
-			{
-				TPatternAlphabet cy = *ys;
-				h = border_;
-				border_ += score_gap;
-				v = border_;
-
-				finger2 = col_;		
-				goPrevious(col_, 1);	
-				finger1 = col_;
-
-				*finger1 = v;
-
-				for (xs = xs_end; xs != xs_begin; --xs)
-				{
-					goPrevious(finger1, 0);
-					goPrevious(finger2, 0);
-					if (*xs == cy)
-					{
-						v = h + score_match;
-						h = *finger2;
-					}
-					else
-					{
-						TScoreValue s1 = h + score_mismatch;
-						h = *finger2;
-						TScoreValue s2 = score_gap + ((h > v) ? h : v);
-						v = (s1 > s2) ? s1 : s2;
-					}
-					*finger1 = v;
-				}
-			}	
-
-			// if computed the whole matrix last value of v = alignment score
-			if(target == hs_complete)   total_score = v;
-
-			/* TRACE BACK */
-			finger1 = begin(matrix_);
-			xs = iter(x,_begin1(target));
-			ys = iter(y,_begin2(target));
-			xs_end = iter(x,_end1(target));
-			ys_end = iter(y,_end2(target));
-
-			while ((xs != xs_end) && (ys != ys_end))
-			{
-				bool gv;
-				bool gh;
-
-				if (*xs == *ys)
-				{
-					gv = gh = true;
-				}
-				else
-				{
-					TMatrixIterator it_ = finger1;
-
-					goNext(it_, 0);
-					TScoreValue v = *it_;
-
-					goNext(it_, 1);
-					TScoreValue d = *it_;
-
-					it_ = finger1;
-					goNext(it_, 1);
-					TScoreValue h = *it_;
-
-					gv = (v >= h) | (d >= h);
-					gh = (h >= v) | (d >= v);
-				}
-
-				if (gv)
-				{
-					++xs;
-					goNext(finger1, 0);
-				}
-				else
-				{
-					insertGap(target_0);
-				}
-
-				if (gh) 
-				{
-					++ys;
-					goNext(finger1, 1);
-				}
-				else
-				{
-					insertGap(target_1);
-				}
-
-				++target_0;
-				++target_1;
-			}
-
-			// if x or y did not reached there end position, fill the rest with gaps
-			while(xs != xs_end)
-			{
-				insertGap(target_1);
-				++target_0;
-				++target_1;
-				++xs;
-			}
-
-			while(ys != ys_end)
-			{
-				insertGap(target_0);
-				++target_0;
-				++target_1;
-				++ys;
-			}
-			/* END ALIGN */
+            TStringSize len_1 = _end1(target) - _begin1(target);
+            TStringSize len_2 = _end2(target) - _begin2(target);
+
+            Matrix<TScoreValue> matrix_;
+
+            setDimension(matrix_, 2);
+            setLength(matrix_, 0, len_1 + 1);
+            setLength(matrix_, 1, len_2 + 1);
+            resize(matrix_);
+
+            /* init matrix */
+            TSequenceHIterator xs_begin = iter(x,_begin1(target)) - 1;
+            TSequenceHIterator xs_end = iter(x,_end1(target)) - 1;
+            TSequenceVIterator ys_begin = iter(y,_begin2(target)) - 1;
+            TSequenceVIterator ys_end = iter(y,_end2(target)) - 1;
+
+            TSequenceHIterator xs = xs_end;
+            TSequenceVIterator ys;
+
+            TMatrixIterator col_ = end(matrix_) - 1;
+            TMatrixIterator finger1;
+            TMatrixIterator finger2;
+
+
+            TScoreValue h = 0;
+            TScoreValue border_ = score_gap;
+            TScoreValue v = border_;
+
+
+            //-------------------------------------------------------------------------
+            // init
+
+            finger1 = col_;
+            *finger1 = 0;
+            for (xs = xs_end; xs != xs_begin; --xs)
+            {
+                goPrevious(finger1, 0);
+                *finger1 = border_;
+                border_ += score_gap;
+            }
+
+            //-------------------------------------------------------------------------
+            //fill matrix
+
+            border_ = 0;
+            for (ys = ys_end; ys != ys_begin; --ys)
+            {
+                TPatternAlphabet cy = *ys;
+                h = border_;
+                border_ += score_gap;
+                v = border_;
+
+                finger2 = col_;
+                goPrevious(col_, 1);
+                finger1 = col_;
+
+                *finger1 = v;
+
+                for (xs = xs_end; xs != xs_begin; --xs)
+                {
+                    goPrevious(finger1, 0);
+                    goPrevious(finger2, 0);
+                    if (*xs == cy)
+                    {
+                        v = h + score_match;
+                        h = *finger2;
+                    }
+                    else
+                    {
+                        TScoreValue s1 = h + score_mismatch;
+                        h = *finger2;
+                        TScoreValue s2 = score_gap + ((h > v) ? h : v);
+                        v = (s1 > s2) ? s1 : s2;
+                    }
+                    *finger1 = v;
+                }
+            }
+
+            // if computed the whole matrix last value of v = alignment score
+            if(target == hs_complete)   total_score = v;
+
+            /* TRACE BACK */
+            finger1 = begin(matrix_);
+            xs = iter(x,_begin1(target));
+            ys = iter(y,_begin2(target));
+            xs_end = iter(x,_end1(target));
+            ys_end = iter(y,_end2(target));
+
+            while ((xs != xs_end) && (ys != ys_end))
+            {
+                bool gv;
+                bool gh;
+
+                if (*xs == *ys)
+                {
+                    gv = gh = true;
+                }
+                else
+                {
+                    TMatrixIterator it_ = finger1;
+
+                    goNext(it_, 0);
+                    TScoreValue v = *it_;
+
+                    goNext(it_, 1);
+                    TScoreValue d = *it_;
+
+                    it_ = finger1;
+                    goNext(it_, 1);
+                    TScoreValue h = *it_;
+
+                    gv = (v >= h) | (d >= h);
+                    gh = (h >= v) | (d >= v);
+                }
+
+                if (gv)
+                {
+                    ++xs;
+                    goNext(finger1, 0);
+                }
+                else
+                {
+                    insertGap(target_0);
+                }
+
+                if (gh)
+                {
+                    ++ys;
+                    goNext(finger1, 1);
+                }
+                else
+                {
+                    insertGap(target_1);
+                }
+
+                ++target_0;
+                ++target_1;
+            }
+
+            // if x or y did not reached there end position, fill the rest with gaps
+            while(xs != xs_end)
+            {
+                insertGap(target_1);
+                ++target_0;
+                ++target_1;
+                ++xs;
+            }
+
+            while(ys != ys_end)
+            {
+                insertGap(target_0);
+                ++target_0;
+                ++target_1;
+                ++ys;
+            }
+            /* END ALIGN */
 
 
 #ifdef MYERS_HIRSCHBERG_VERBOSE
-			std::cout << std::endl << align_ << std::endl << std::endl;
+            std::cout << std::endl << align_ << std::endl << std::endl;
 #endif
 
-		}
-		else
-		{
-			/*
-				---------------------------------------------------------------
-				Calculate cut position using extended Myers-Bitvector-Algorithm
-			    --------------------------------------------------------------- 
-			*/
+        }
+        else
+        {
+            /*
+                ---------------------------------------------------------------
+                Calculate cut position using extended Myers-Bitvector-Algorithm
+                ---------------------------------------------------------------
+            */
 
-			/* declare variables */
-			unsigned int X, D0, HN, HP;
+            /* declare variables */
+            unsigned int X, D0, HN, HP;
 
-			/* compute cut position */
-			int mid = static_cast<int>(floor( static_cast<double>((_begin2(target) + _end2(target))/2) ));
+            /* compute cut position */
+            int mid = static_cast<int>(floor( static_cast<double>((_begin2(target) + _end2(target))/2) ));
 
-			/* debug infos */
+            /* debug infos */
 #ifdef MYERS_HIRSCHBERG_VERBOSE
-			std::cout << "calculate cut for x " << _begin1(target) << " to " << _end1(target) << " and y " << _begin2(target) << " to " << _end2(target) << std::endl;
-			std::cout << "calculate cut for " << infix(x,_begin1(target),_end1(target)) << " and " << infix(y,_begin2(target),_end2(target)) << std::endl;
-			std::cout << "cut is in row " << mid << " symbol is " << getValue(x,mid-1) << std::endl << std::endl;
+            std::cout << "calculate cut for x " << _begin1(target) << " to " << _end1(target) << " and y " << _begin2(target) << " to " << _end2(target) << std::endl;
+            std::cout << "calculate cut for " << infix(x,_begin1(target),_end1(target)) << " and " << infix(y,_begin2(target),_end2(target)) << std::endl;
+            std::cout << "cut is in row " << mid << " symbol is " << getValue(x,mid-1) << std::endl << std::endl;
 
-			std::cout << std::endl;
-			_writeDebugMatrix(infix(x,_begin1(target),_end1(target)),infix(y,_begin2(target),_end2(target)));
-			std::cout << std::endl;
+            std::cout << std::endl;
+            _writeDebugMatrix(infix(x,_begin1(target),_end1(target)),infix(y,_begin2(target),_end2(target)));
+            std::cout << std::endl;
 #endif
-			/* compute blocks and score masks */
-			int fStartBlock = _begin2(target) / BLOCK_SIZE;
-			int fEndBlock = (mid - 1) / BLOCK_SIZE;
-			int fSpannedBlocks = (fEndBlock - fStartBlock) + 1;
-
-			unsigned int fScoreMask = 1 << ((mid  - 1) % BLOCK_SIZE);
-			
-			unsigned int fOffSet = _begin2(target) % BLOCK_SIZE;
-			unsigned int fSilencer = ~0;
-			fSilencer <<= fOffSet;
-
-			/* reset v-bitvectors */
+            /* compute blocks and score masks */
+            int fStartBlock = _begin2(target) / BLOCK_SIZE;
+            int fEndBlock = (mid - 1) / BLOCK_SIZE;
+            int fSpannedBlocks = (fEndBlock - fStartBlock) + 1;
+
+            unsigned int fScoreMask = 1 << ((mid  - 1) % BLOCK_SIZE);
+
+            unsigned int fOffSet = _begin2(target) % BLOCK_SIZE;
+            unsigned int fSilencer = ~0;
+            fSilencer <<= fOffSet;
+
+            /* reset v-bitvectors */
             std::fill(begin(VP, Standard()) + fStartBlock, end(VP, Standard()) + fEndBlock + 1, maxValue<unsigned>());
             std::fill(begin(VN, Standard()) + fStartBlock, end(VN, Standard()) + fEndBlock + 1, 0);
 
-			/* determine start-position and start-score */
-			int pos = _begin1(target);			
-			score = (mid - _begin2(target)) * score_gap;
-			c_score[pos] = score;
-
-			/* compute with myers - forward - begin */
-			if(fSpannedBlocks == 1)
-			{
-				while (pos < _end1(target)) {
-					X = (fSilencer & forwardBitMask[(blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)))) + fStartBlock]) | VN[fStartBlock];
-
-					D0 = ((VP[fStartBlock] + (X & VP[fStartBlock])) ^ VP[fStartBlock]) | X;
-					HN = VP[fStartBlock] & D0;
-					HP = VN[fStartBlock] | ~(VP[fStartBlock] | D0);
-
-					X = (HP << 1) | (1 << fOffSet);
-					VN[fStartBlock] = X & D0;
-					VP[fStartBlock] = (HN << 1) | ~(X | D0);
-
-					if (HP & fScoreMask)
-						score--;
-					else if (HN & fScoreMask)
-						score++;
-
-					c_score[pos + 1] = score;
-
-					++pos;
-				}
-			} /* end - short patten */
-			else
-			{
-				int shift, currentBlock;
-				unsigned int temp, carryD0, carryHP, carryHN;
-
-				while (pos < _end1(target))
-				{
-					carryD0 = carryHP = carryHN = 0;
-					shift = blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)));
-
-					// computing first the top most block
-					X = (fSilencer & forwardBitMask[shift + fStartBlock]) | VN[fStartBlock];
-			
-					temp = VP[fStartBlock] + (X & VP[fStartBlock]);
-					carryD0 = temp < VP[fStartBlock];
-					
-					D0 = (temp ^ VP[fStartBlock]) | X;
-					HN = VP[fStartBlock] & D0;
-					HP = VN[fStartBlock] | ~(VP[fStartBlock] | D0);
-					
-					X = (HP << 1) | (1 << fOffSet);
-					carryHP = HP >> (BLOCK_SIZE - 1);
-					
-					VN[fStartBlock] = X & D0;
-
-					temp = (HN << 1);
-					carryHN = HN >> (BLOCK_SIZE - 1);
-										
-		 			VP[fStartBlock] = temp | ~(X | D0);
-
-					// compute the remaining blocks
-					for (currentBlock = fStartBlock + 1; currentBlock <= fEndBlock; currentBlock++) {
-						X = forwardBitMask[shift + currentBlock] | VN[currentBlock];
-				
-						temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0;
-						
-						carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]);
-					
-						D0 = (temp ^ VP[currentBlock]) | X;
-						HN = VP[currentBlock] & D0;
-						HP = VN[currentBlock] | ~(VP[currentBlock] | D0);
-						
-						X = (HP << 1) | carryHP;
-						carryHP = HP >> (BLOCK_SIZE-1);
-						
-						VN[currentBlock] = X & D0;
-
-						temp = (HN << 1) | carryHN;
-						carryHN = HN >> (BLOCK_SIZE - 1);
-											
-		 				VP[currentBlock] = temp | ~(X | D0);
-					}
-					
-					/* update score */
-					if (HP & fScoreMask)
-						score--;
-					else if (HN & fScoreMask)
-						score++;
-
-					c_score[pos + 1] = score;
-
-					++pos;
-				}
-
-			} /* end - long patten */
-			/* compute with myers - forward - end */
-			
-			/* compute blocks and score masks */
-			int rStartBlock = (len_y - _end2(target)) / BLOCK_SIZE;
-			int rEndBlock = (len_y - mid - 1) / BLOCK_SIZE;
-			int rSpannedBlocks = (rEndBlock - rStartBlock) + 1;
-
-			unsigned int rScoreMask = 1 <<  ((len_y - mid - 1) % BLOCK_SIZE);
-			unsigned int rOffSet = (len_y - _end2(target)) % BLOCK_SIZE;
-			unsigned int rSilencer = ~0;
-			rSilencer <<= rOffSet;
-
-			/* reset v-bitvectors */
+            /* determine start-position and start-score */
+            int pos = _begin1(target);
+            score = (mid - _begin2(target)) * score_gap;
+            c_score[pos] = score;
+
+            /* compute with myers - forward - begin */
+            if(fSpannedBlocks == 1)
+            {
+                while (pos < _end1(target)) {
+                    X = (fSilencer & forwardBitMask[(blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)))) + fStartBlock]) | VN[fStartBlock];
+
+                    D0 = ((VP[fStartBlock] + (X & VP[fStartBlock])) ^ VP[fStartBlock]) | X;
+                    HN = VP[fStartBlock] & D0;
+                    HP = VN[fStartBlock] | ~(VP[fStartBlock] | D0);
+
+                    X = (HP << 1) | (1 << fOffSet);
+                    VN[fStartBlock] = X & D0;
+                    VP[fStartBlock] = (HN << 1) | ~(X | D0);
+
+                    if (HP & fScoreMask)
+                        score--;
+                    else if (HN & fScoreMask)
+                        score++;
+
+                    c_score[pos + 1] = score;
+
+                    ++pos;
+                }
+            } /* end - short patten */
+            else
+            {
+                int shift, currentBlock;
+                unsigned int temp, carryD0, carryHP, carryHN;
+
+                while (pos < _end1(target))
+                {
+                    carryD0 = carryHP = carryHN = 0;
+                    shift = blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)));
+
+                    // computing first the top most block
+                    X = (fSilencer & forwardBitMask[shift + fStartBlock]) | VN[fStartBlock];
+
+                    temp = VP[fStartBlock] + (X & VP[fStartBlock]);
+                    carryD0 = temp < VP[fStartBlock];
+
+                    D0 = (temp ^ VP[fStartBlock]) | X;
+                    HN = VP[fStartBlock] & D0;
+                    HP = VN[fStartBlock] | ~(VP[fStartBlock] | D0);
+
+                    X = (HP << 1) | (1 << fOffSet);
+                    carryHP = HP >> (BLOCK_SIZE - 1);
+
+                    VN[fStartBlock] = X & D0;
+
+                    temp = (HN << 1);
+                    carryHN = HN >> (BLOCK_SIZE - 1);
+
+                     VP[fStartBlock] = temp | ~(X | D0);
+
+                    // compute the remaining blocks
+                    for (currentBlock = fStartBlock + 1; currentBlock <= fEndBlock; currentBlock++) {
+                        X = forwardBitMask[shift + currentBlock] | VN[currentBlock];
+
+                        temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0;
+
+                        carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]);
+
+                        D0 = (temp ^ VP[currentBlock]) | X;
+                        HN = VP[currentBlock] & D0;
+                        HP = VN[currentBlock] | ~(VP[currentBlock] | D0);
+
+                        X = (HP << 1) | carryHP;
+                        carryHP = HP >> (BLOCK_SIZE-1);
+
+                        VN[currentBlock] = X & D0;
+
+                        temp = (HN << 1) | carryHN;
+                        carryHN = HN >> (BLOCK_SIZE - 1);
+
+                         VP[currentBlock] = temp | ~(X | D0);
+                    }
+
+                    /* update score */
+                    if (HP & fScoreMask)
+                        score--;
+                    else if (HN & fScoreMask)
+                        score++;
+
+                    c_score[pos + 1] = score;
+
+                    ++pos;
+                }
+
+            } /* end - long patten */
+            /* compute with myers - forward - end */
+
+            /* compute blocks and score masks */
+            int rStartBlock = (len_y - _end2(target)) / BLOCK_SIZE;
+            int rEndBlock = (len_y - mid - 1) / BLOCK_SIZE;
+            int rSpannedBlocks = (rEndBlock - rStartBlock) + 1;
+
+            unsigned int rScoreMask = 1 <<  ((len_y - mid - 1) % BLOCK_SIZE);
+            unsigned int rOffSet = (len_y - _end2(target)) % BLOCK_SIZE;
+            unsigned int rSilencer = ~0;
+            rSilencer <<= rOffSet;
+
+            /* reset v-bitvectors */
             std::fill(begin(VP, Standard()) + rStartBlock, end(VP, Standard()) + rEndBlock + 1, maxValue<unsigned>());
             std::fill(begin(VN, Standard()) + rStartBlock, end(VN, Standard()) + rEndBlock + 1, 0);
 
-			/* determine start-position and start-score */
-			pos = _end1(target)-1;			
-			score = (_end2(target) - mid) * score_gap;
-
-			/* set start score */
-			c_score[_end1(target)] += score;
-
-			/* determine optimal cut position -- score extension */
-			TScoreValue max = c_score[_end1(target)];
-			TScoreValue rmax = score;
-			unsigned int pos_max = _end1(target);
-
-			/* compute with myers - reverse - begin */
-			if(rSpannedBlocks == 1)
-			{
-				while (pos >= _begin1(target)) {
-					X = (rSilencer & reverseBitMask[(blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)))) + rStartBlock]) | VN[rStartBlock];
-
-					D0 = ((VP[rStartBlock] + (X & VP[rStartBlock])) ^ VP[rStartBlock]) | X;
-					HN = VP[rStartBlock] & D0;
-					HP = VN[rStartBlock] | ~(VP[rStartBlock] | D0);
-
-					X = (HP << 1) | (1 << rOffSet);
-					VN[rStartBlock] = X & D0;
-					VP[rStartBlock] = (HN << 1) | ~(X | D0);
-
-					if (HP & rScoreMask)
-						--score;
-					else if (HN & rScoreMask)
-						++score;
-
-					c_score[pos] += score;
-
-					/* check for optimality -- score extension */
-					if(c_score[pos]> max)
-					{
-						pos_max = pos;
-						max = c_score[pos];
-						rmax =  score;
-					}
-
-					--pos;
-				}
-			} /* end - short pattern */
-			else
-			{
-				int shift, currentBlock;
-				unsigned int temp, carryD0, carryHP, carryHN;
-
-				while (pos >= _begin1(target))
-				{
-					carryD0 = carryHP = carryHN = 0;
-					shift = blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)));
-
-					// compute first the top most block
-					X = (rSilencer & reverseBitMask[shift + rStartBlock]) | VN[rStartBlock];
-			
-					temp = VP[rStartBlock] + (X & VP[rStartBlock]);
-					carryD0 = temp < VP[rStartBlock];
-					
-					D0 = (temp ^ VP[rStartBlock]) | X;
-					HN = VP[rStartBlock] & D0;
-					HP = VN[rStartBlock] | ~(VP[rStartBlock] | D0);
-					
-					X = (HP << 1) | (1 << rOffSet);
-					carryHP = HP >> (BLOCK_SIZE - 1);
-					
-					VN[rStartBlock] = X & D0;
-
-					temp = (HN << 1);
-					carryHN = HN >> (BLOCK_SIZE - 1);
-										
-		 			VP[rStartBlock] = temp | ~(X | D0);
-
-					// compute the remaining blocks
-					for (currentBlock = rStartBlock + 1; currentBlock <= rEndBlock; currentBlock++) {
-						X = reverseBitMask[shift + currentBlock] | VN[currentBlock];
-				
-						temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0;
-						
-						carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]);
-					
-						D0 = (temp ^ VP[currentBlock]) | X;
-						HN = VP[currentBlock] & D0;
-						HP = VN[currentBlock] | ~(VP[currentBlock] | D0);
-						
-						X = (HP << 1) | carryHP;
-						carryHP = HP >> (BLOCK_SIZE-1);
-						
-						VN[currentBlock] = X & D0;
-
-						temp = (HN << 1) | carryHN;
-						carryHN = HN >> (BLOCK_SIZE - 1);
-											
-		 				VP[currentBlock] = temp | ~(X | D0);
-					}
-
-					if (HP & rScoreMask)
-						--score;
-					else if (HN & rScoreMask)
-						++score;
-
-					c_score[pos] += score;
-					
-					/* check for optimality -- score extension*/
-					if(c_score[pos] > max)
-					{
-						pos_max = pos;
-						max = c_score[pos];
-						rmax = score;
-					}
-					
-					--pos;
-				}
-
-			}  /* end - long pattern */			
-			/* compute with myers - reverse - end */
-
-			// if computed the whole matrix max = alignment score
-			if(target == hs_complete)
-				total_score = max;
+            /* determine start-position and start-score */
+            pos = _end1(target)-1;
+            score = (_end2(target) - mid) * score_gap;
+
+            /* set start score */
+            c_score[_end1(target)] += score;
+
+            /* determine optimal cut position -- score extension */
+            TScoreValue max = c_score[_end1(target)];
+            TScoreValue rmax = score;
+            unsigned int pos_max = _end1(target);
+
+            /* compute with myers - reverse - begin */
+            if(rSpannedBlocks == 1)
+            {
+                while (pos >= _begin1(target)) {
+                    X = (rSilencer & reverseBitMask[(blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)))) + rStartBlock]) | VN[rStartBlock];
+
+                    D0 = ((VP[rStartBlock] + (X & VP[rStartBlock])) ^ VP[rStartBlock]) | X;
+                    HN = VP[rStartBlock] & D0;
+                    HP = VN[rStartBlock] | ~(VP[rStartBlock] | D0);
+
+                    X = (HP << 1) | (1 << rOffSet);
+                    VN[rStartBlock] = X & D0;
+                    VP[rStartBlock] = (HN << 1) | ~(X | D0);
+
+                    if (HP & rScoreMask)
+                        --score;
+                    else if (HN & rScoreMask)
+                        ++score;
+
+                    c_score[pos] += score;
+
+                    /* check for optimality -- score extension */
+                    if(c_score[pos]> max)
+                    {
+                        pos_max = pos;
+                        max = c_score[pos];
+                        rmax =  score;
+                    }
+
+                    --pos;
+                }
+            } /* end - short pattern */
+            else
+            {
+                int shift, currentBlock;
+                unsigned int temp, carryD0, carryHP, carryHN;
+
+                while (pos >= _begin1(target))
+                {
+                    carryD0 = carryHP = carryHN = 0;
+                    shift = blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)));
+
+                    // compute first the top most block
+                    X = (rSilencer & reverseBitMask[shift + rStartBlock]) | VN[rStartBlock];
+
+                    temp = VP[rStartBlock] + (X & VP[rStartBlock]);
+                    carryD0 = temp < VP[rStartBlock];
+
+                    D0 = (temp ^ VP[rStartBlock]) | X;
+                    HN = VP[rStartBlock] & D0;
+                    HP = VN[rStartBlock] | ~(VP[rStartBlock] | D0);
+
+                    X = (HP << 1) | (1 << rOffSet);
+                    carryHP = HP >> (BLOCK_SIZE - 1);
+
+                    VN[rStartBlock] = X & D0;
+
+                    temp = (HN << 1);
+                    carryHN = HN >> (BLOCK_SIZE - 1);
+
+                     VP[rStartBlock] = temp | ~(X | D0);
+
+                    // compute the remaining blocks
+                    for (currentBlock = rStartBlock + 1; currentBlock <= rEndBlock; currentBlock++) {
+                        X = reverseBitMask[shift + currentBlock] | VN[currentBlock];
+
+                        temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0;
+
+                        carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]);
+
+                        D0 = (temp ^ VP[currentBlock]) | X;
+                        HN = VP[currentBlock] & D0;
+                        HP = VN[currentBlock] | ~(VP[currentBlock] | D0);
+
+                        X = (HP << 1) | carryHP;
+                        carryHP = HP >> (BLOCK_SIZE-1);
+
+                        VN[currentBlock] = X & D0;
+
+                        temp = (HN << 1) | carryHN;
+                        carryHN = HN >> (BLOCK_SIZE - 1);
+
+                         VP[currentBlock] = temp | ~(X | D0);
+                    }
+
+                    if (HP & rScoreMask)
+                        --score;
+                    else if (HN & rScoreMask)
+                        ++score;
+
+                    c_score[pos] += score;
+
+                    /* check for optimality -- score extension*/
+                    if(c_score[pos] > max)
+                    {
+                        pos_max = pos;
+                        max = c_score[pos];
+                        rmax = score;
+                    }
+
+                    --pos;
+                }
+
+            }  /* end - long pattern */
+            /* compute with myers - reverse - end */
+
+            // if computed the whole matrix max = alignment score
+            if(target == hs_complete)
+                total_score = max;
 
 #ifdef MYERS_HIRSCHBERG_VERBOSE
-			printf("Optimal cut is at %i and %i with forward score %i and reverse score %i\n\n",mid,pos_max,(max - rmax),rmax);
+            printf("Optimal cut is at %i and %i with forward score %i and reverse score %i\n\n",mid,pos_max,(max - rmax),rmax);
 #endif
-			/* push the two computed parts of the dp-matrix on process stack */
-			to_process.push(HirschbergSet_(pos_max,_end1(target),mid,_end2(target),rmax));
-			to_process.push(HirschbergSet_(_begin1(target),pos_max,_begin2(target),mid,max - rmax));
-
-		}
-		/* END CUT */
-	}
-	
-	return total_score;
+            /* push the two computed parts of the dp-matrix on process stack */
+            to_process.push(HirschbergSet_(pos_max,_end1(target),mid,_end2(target),rmax));
+            to_process.push(HirschbergSet_(_begin1(target),pos_max,_begin2(target),mid,max - rmax));
+
+        }
+        /* END CUT */
+    }
+
+    return total_score;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_
diff --git a/seqan/align/global_alignment_myers_impl.h b/seqan/align/global_alignment_myers_impl.h
index ddf2743..2f38816 100644
--- a/seqan/align/global_alignment_myers_impl.h
+++ b/seqan/align/global_alignment_myers_impl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 
 // TODO(holtgrew): Should be called _globalAlignmentScore()!
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
 
 namespace seqan {
 
@@ -70,28 +70,28 @@ _globalAlignmentScore(String<TAlphabetH, TSpecH> const & seqH,
     if (length(seqH) < length(seqV))
         return _globalAlignmentScore(seqV, seqH, algorithmTag);
 
-	// Use size of unsigned int as blocksize for bit-vectors.
-	const unsigned int BLOCK_SIZE = BitsPerValue<unsigned int>::VALUE;
+    // Use size of unsigned int as blocksize for bit-vectors.
+    const unsigned int BLOCK_SIZE = BitsPerValue<unsigned int>::VALUE;
 
     typedef String<TAlphabetH, TSpecH> const TSequenceH;
     typedef String<TAlphabetV, TSpecV> const TSequenceV;
 
-	typedef typename Value<TSequenceV>::Type TPatternAlphabet;
-	typedef typename Size<TSequenceH>::Type  TSourceSize;
+    typedef typename Value<TSequenceV>::Type TPatternAlphabet;
+    typedef typename Size<TSequenceH>::Type  TSourceSize;
 
     TSequenceH const & x = seqH;
     TSequenceV const & y = seqV;
 
-	TSourceSize len_x = length(x);
-	unsigned int pos = 0;
+    TSourceSize len_x = length(x);
+    unsigned int pos = 0;
 
-	// init variables
-	unsigned int len_y = length(y);
-	int score = (-1)*len_y;
-	unsigned int patternAlphabetSize = ValueSize<TPatternAlphabet>::VALUE;
-	unsigned int blockCount = (len_y + BLOCK_SIZE - 1) / BLOCK_SIZE;
+    // init variables
+    unsigned int len_y = length(y);
+    int score = (-1)*len_y;
+    unsigned int patternAlphabetSize = ValueSize<TPatternAlphabet>::VALUE;
+    unsigned int blockCount = (len_y + BLOCK_SIZE - 1) / BLOCK_SIZE;
 
-	unsigned int scoreMask = 1 << ((len_y % BLOCK_SIZE) - 1);	// the mask with a bit set at the position of the last active cell
+    unsigned int scoreMask = 1 << ((len_y % BLOCK_SIZE) - 1);    // the mask with a bit set at the position of the last active cell
 
     String<unsigned> VP;
     resize(VP, blockCount, maxValue<unsigned>());
@@ -100,102 +100,102 @@ _globalAlignmentScore(String<TAlphabetH, TSpecH> const & seqH,
     String<unsigned> bitMask;
     resize(bitMask, patternAlphabetSize * blockCount, 0);
 
-	// encoding the letters as bit-vectors
+    // encoding the letters as bit-vectors
     for (unsigned int j = 0; j < len_y; j++)
-		bitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] = bitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE);
-
-	// compute score
-	unsigned int X, D0, HN, HP;
-	if(blockCount == 1)
-	{
-		while (pos < len_x) {
-			X = bitMask[ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)))] | VN[0];
-
-			D0 = ((VP[0] + (X & VP[0])) ^ VP[0]) | X;
-			HN = VP[0] & D0;
-			HP = VN[0] | ~(VP[0] | D0);
-
-			// customized to compute edit distance
-			X = (HP << 1) | 1;
-			VN[0] = X & D0;
-			VP[0] = (HN << 1) | ~(X | D0);
-
-			if (HP & scoreMask)
-				score--;
-			else if (HN & scoreMask)
-				score++;
-
-			++pos;
-		}
-	} // end compute score - short pattern
-	else
-	{
-		unsigned int temp, shift, currentBlock;
-		unsigned int carryD0, carryHP, carryHN;
-
-		while (pos < len_x) 
-		{
-			// set vars
-			carryD0 = carryHP = carryHN = 0;
-			shift = blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)));
-
-			// computing first the top most block
-			X = bitMask[shift] | VN[0];
-	
-			temp = VP[0] + (X & VP[0]);
-			carryD0 = temp < VP[0];
-			
-			D0 = (temp ^ VP[0]) | X;
-			HN = VP[0] & D0;
-			HP = VN[0] | ~(VP[0] | D0);
-			
-			// customized to compute edit distance
-			X = (HP << 1) | 1;
-			carryHP = HP >> (BLOCK_SIZE - 1);
-			
-			VN[0] = X & D0;
-
-			temp = (HN << 1);
-			carryHN = HN >> (BLOCK_SIZE - 1);
-								
-		 	VP[0] = temp | ~(X | D0);
-
-			// computing the necessary blocks, carries between blocks following one another are stored
-			for (currentBlock = 1; currentBlock < blockCount; currentBlock++) {
-				X = bitMask[shift + currentBlock] | VN[currentBlock];
-		
-				temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0;
-				
-				carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]);
-			
-				D0 = (temp ^ VP[currentBlock]) | X;
-				HN = VP[currentBlock] & D0;
-				HP = VN[currentBlock] | ~(VP[currentBlock] | D0);
-				
-				X = (HP << 1) | carryHP;
-				carryHP = HP >> (BLOCK_SIZE-1);
-				
-				VN[currentBlock] = X & D0;
-
-				temp = (HN << 1) | carryHN;
-				carryHN = HN >> (BLOCK_SIZE - 1);
-									
-		 		VP[currentBlock] = temp | ~(X | D0);
-			}
-
-			// update score with the HP and HN values of the last block the last block
-			if (HP & scoreMask)
-				score--;
-			else if (HN & scoreMask)
-				score++;
-			++pos;
-		}
-
-	}  // end compute score - long pattern
-
-	return score;
+        bitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] = bitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE);
+
+    // compute score
+    unsigned int X, D0, HN, HP;
+    if(blockCount == 1)
+    {
+        while (pos < len_x) {
+            X = bitMask[ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)))] | VN[0];
+
+            D0 = ((VP[0] + (X & VP[0])) ^ VP[0]) | X;
+            HN = VP[0] & D0;
+            HP = VN[0] | ~(VP[0] | D0);
+
+            // customized to compute edit distance
+            X = (HP << 1) | 1;
+            VN[0] = X & D0;
+            VP[0] = (HN << 1) | ~(X | D0);
+
+            if (HP & scoreMask)
+                score--;
+            else if (HN & scoreMask)
+                score++;
+
+            ++pos;
+        }
+    } // end compute score - short pattern
+    else
+    {
+        unsigned int temp, shift, currentBlock;
+        unsigned int carryD0, carryHP, carryHN;
+
+        while (pos < len_x)
+        {
+            // set vars
+            carryD0 = carryHP = carryHN = 0;
+            shift = blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)));
+
+            // computing first the top most block
+            X = bitMask[shift] | VN[0];
+
+            temp = VP[0] + (X & VP[0]);
+            carryD0 = temp < VP[0];
+
+            D0 = (temp ^ VP[0]) | X;
+            HN = VP[0] & D0;
+            HP = VN[0] | ~(VP[0] | D0);
+
+            // customized to compute edit distance
+            X = (HP << 1) | 1;
+            carryHP = HP >> (BLOCK_SIZE - 1);
+
+            VN[0] = X & D0;
+
+            temp = (HN << 1);
+            carryHN = HN >> (BLOCK_SIZE - 1);
+
+             VP[0] = temp | ~(X | D0);
+
+            // computing the necessary blocks, carries between blocks following one another are stored
+            for (currentBlock = 1; currentBlock < blockCount; currentBlock++) {
+                X = bitMask[shift + currentBlock] | VN[currentBlock];
+
+                temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0;
+
+                carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]);
+
+                D0 = (temp ^ VP[currentBlock]) | X;
+                HN = VP[currentBlock] & D0;
+                HP = VN[currentBlock] | ~(VP[currentBlock] | D0);
+
+                X = (HP << 1) | carryHP;
+                carryHP = HP >> (BLOCK_SIZE-1);
+
+                VN[currentBlock] = X & D0;
+
+                temp = (HN << 1) | carryHN;
+                carryHN = HN >> (BLOCK_SIZE - 1);
+
+                 VP[currentBlock] = temp | ~(X | D0);
+            }
+
+            // update score with the HP and HN values of the last block the last block
+            if (HP & scoreMask)
+                score--;
+            else if (HN & scoreMask)
+                score++;
+            ++pos;
+        }
+
+    }  // end compute score - long pattern
+
+    return score;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
diff --git a/seqan/align/global_alignment_specialized.h b/seqan/align/global_alignment_specialized.h
index 783e260..735eabf 100644
--- a/seqan/align/global_alignment_specialized.h
+++ b/seqan/align/global_alignment_specialized.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // MyersBitVector, MyersHirschberg.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_
 
 namespace seqan {
 
@@ -196,4 +196,4 @@ int globalAlignmentScore(StringSet<TString, TSpec> const & strings,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_
diff --git a/seqan/align/global_alignment_unbanded.h b/seqan/align/global_alignment_unbanded.h
index 190a9f8..8c4a1bd 100644
--- a/seqan/align/global_alignment_unbanded.h
+++ b/seqan/align/global_alignment_unbanded.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,8 +39,8 @@
 // the globalFunction() fails is actually meaningful.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_
 
 namespace seqan {
 
@@ -75,36 +75,34 @@ class Fragment;
 
 /*!
  * @fn globalAlignment
- * 
- * @headerfile seqan/align.h
- * 
+ * @headerfile <seqan/align.h>
  * @brief Computes the best global pairwise alignment.
- * 
+ *
  * @signature TScoreVal globalAlignment(align,          scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag]);
  * @signature TScoreVal globalAlignment(gapsH, gapsV,   scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag]);
  * @signature TScoreVal globalAlignment(frags, strings, scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag]);
  * @signature TScoreVal globalAlignment(alignGraph,     scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag]);
- * 
- * @param align        The @link Align @endlink object to use for storing the pairwise alignment.
- * @param gapsH        The @link Gaps @endlink object for the first row (horizontal in the DP matrix).
- * @param gapsV        The @link Gaps @endlink object for the second row (vertical in the DP matrix).
- * @param frags        String of @link Fragment @endlink objects to store alignment in.
- * @param strings      StringSet of length two with the strings to align.
- * @param alignGraph   Alignment Graph for the resulting alignment.  Must be initialized with two strings.
- * @param scoringScheme The @link Score scoring scheme @endlink to use for the alignment.  Note that
- *                      the user is responsible for ensuring that the scoring scheme is compatible with <tt>algorithmTag</tt>.
- * @param alignConfig  @link AlignConfig @endlink instance to use for the alignment configuration.
- * @param lowerDiag    Optional lower diagonal (<tt>int</tt>).
- * @param upperDiag    Optional upper diagonal (<tt>int</tt>).
- * @param algorithmTag Tag to select the alignment algorithm (see @link AlignmentAlgorithmTags @endlink).
  *
- * @return TScoreVal Score value of the resulting alignment.  Of type <tt>Value&lt;TScore&gt;::Type</tt> where
- *                   <tt>TScore</tt> is the type of <tt>scoringScheme</tt>.
- * 
+ * @param[in,out] align        The @link Align @endlink object to use for storing the pairwise alignment.
+ * @param[in,out] gapsH        The @link Gaps @endlink object for the first row (horizontal in the DP matrix).
+ * @param[in,out] gapsV        The @link Gaps @endlink object for the second row (vertical in the DP matrix).
+ * @param[in,out] frags        String of @link Fragment @endlink objects to store alignment in.
+ * @param[in]     strings      StringSet of length two with the strings to align.
+ * @param[in,out] alignGraph   Alignment Graph for the resulting alignment.  Must be initialized with two strings.
+ * @param[in]     scoringScheme The @link Score scoring scheme @endlink to use for the alignment.  Note that
+ *                              the user is responsible for ensuring that the scoring scheme is compatible with <tt>algorithmTag</tt>.
+ * @param[in]     alignConfig  @link AlignConfig @endlink instance to use for the alignment configuration.
+ * @param[in]     lowerDiag    Optional lower diagonal (<tt>int</tt>).
+ * @param[in]     upperDiag    Optional upper diagonal (<tt>int</tt>).
+ * @param[in]     algorithmTag Tag to select the alignment algorithm (see @link AlignmentAlgorithmTags @endlink).
+ *
+ * @return TScoreVal   Score value of the resulting alignment  (Metafunction: @link Score#Value @endlink of
+ *                     the type of <tt>scoringScheme</tt>).
+ *
  * There exist multiple overloads for this function with four configuration dimensions.
- * 
+ *
  * First, you can select whether begin and end gaps are free in either sequence using <tt>alignConfig</tt>.
- * 
+ *
  * Second, you can select the type of the target storing the alignment. This can be either an @link Align @endlink
  * object, two @link Gaps @endlink objects, a @link AlignmentGraph @endlink, or a string of @link Fragment @endlink
  * objects. @link Align @endlink objects provide an interface to tabular alignments with the restriction of all rows
@@ -113,45 +111,45 @@ class Fragment;
  * Graphs @endlink provide a graph-based representation of segment-based colinear alignments. Using @link Fragment
  * @endlink strings is useful for collecting many pairwise alignments, for example in the construction of @link
  * AlignmentGraph Alignment Graphs @endlink for multiple-sequence alignments (MSA).
- * 
+ *
  * Third, you can optionally give a band for the alignment using <tt>lowerDiag</tt> and <tt>upperDiag</tt>. The center
  * diagonal has index <tt>0</tt>, the <tt>i</tt>th diagonal below has index <tt>-i</tt>, the <tt>i</tt>th above has
  * index <tt>i</tt>.
- * 
+ *
  * Fourth, you can select the algorithm to use with <tt>algorithmTag</tt>.  This can be one of @link
  * AlignmentAlgorithmTags#NeedlemanWunsch @endlink and @link AlignmentAlgorithmTags#Gotoh @endlink.  The
  * Needleman-Wunsch algorithm supports scoring schemes with linear gap costs only while Gotoh's algorithm also allows
  * affine gap costs.
- * 
+ *
  * The available alignment algorithms all have some restrictions.  Gotoh's algorithm can handle arbitrary substitution
  * and affine gap scores.  Needleman-Wunsch is limited to linear gap scores.  The implementation of Hirschberg's
  * algorithm is further limited that it does not support <tt>alignConfig</tt> objects or banding.  The implementation of
  * the Myers-Hirschberg algorithm further limits this to only support edit distance (as scores, matches are scored with
  * 0, mismatches are scored with -1).
- * 
+ *
  * The examples below show some common use cases.
- * 
+ *
  * @section Examples
- * 
+ *
  * Global alignment of two sequences using an @link Align @endlink object and
  * the Needleman-Wunsch algorithm.
  *
- * @include demos/align/global_alignment_unbanded.cpp
+ * @include demos/dox/align/global_alignment_unbanded.cpp
  *
  * The output is as follows:
  *
- * @include demos/align/global_alignment_unbanded.cpp.stdout
+ * @include demos/dox/align/global_alignment_unbanded.cpp.stdout
  *
  * Global banded alignment of two sequences using two @link Gaps @endlink objects and the Gotoh algorithm.
  *
- * @include demos/align/global_alignment_banded.cpp
+ * @include demos/dox/align/global_alignment_banded.cpp
  *
  * The output is as follows:
  *
- * @include demos/align/global_alignment_banded.cpp.stdout
- * 
- * http://trac.seqan.de/wiki/Tutorial/PairwiseSequenceAlignment
- * 
+ * @include demos/dox/align/global_alignment_banded.cpp.stdout
+ *
+ * http://seqan.readthedocs.org/en/develop/Tutorial/PairwiseSequenceAlignment.html
+ *
  * @section References
  *
  * <ul>
@@ -159,123 +157,44 @@ class Fragment;
  *       of two proteins. J Mol Biol 1970, 48(3): 443-53.</li>
  *   <li>Gotoh O: An improved algorithm for matching biological sequences. J Mol Biol 1982, 162(3):705-8</li>
  * </ul>
- * 
+ *
  * @see localAlignment
  * @see globalAlignmentScore
  * @see AlignmentAlgorithmTags
  */
 
-/**
-.Function.globalAlignment
-..summary:Computes the best global pairwise alignment.
-..cat:Alignments
-..signature:globalAlignment(align,          scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag])
-..signature:globalAlignment(gapsH, gapsV,   scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag])
-..signature:globalAlignment(frags, strings, scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag])
-..signature:globalAlignment(alignmentGraph, scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag])
-..param.align:
-An @Class.Align@ object that stores the alignment.
-The number of rows must be 2 and the sequences must have already been set.
-$row(align, 0)$ is the horizontal one in the alignment matrix alignment, $row(align, 1)$ is the vertical one.
-...type:Class.Align
-..param.gapsH:Horizontal gapped sequence in alignment matrix.
-...type:Class.Gaps
-..param.gapsV:Vertical gapped sequence in alignment matrix.
-...type:Class.Gaps
-..param.frags:
-String of @Class.Fragment@ objects.
-The sequence with id $0$ is the horizontal one, the sequence with id $1$ is the vertical one.
-..param.alignmentGraph:
-@Spec.Alignment Graph@ object to store the alignment in.
-...type:Spec.Alignment Graph
-...remarks:The underlying @Class.StringSet@ must be an @Spec.Owner|Owner StringSet@.
-..param.strings:A @Class.StringSet@ containing two sequences.
-...type:Class.StringSet
-..param.scoringScheme:
-The scoring scheme to use for the alignment.
-Note that the user is responsible for ensuring that the scoring scheme is compatible with $algorithmTag$.
-...type:Class.Score
-..param.alignConfig:The @Class.AlignConfig@ to use for the alignment.
-...type:Class.AlignConfig
-..param.lowerDiag:Optional lower diagonal.
-...type:nolink:$int$
-..param.upperDiag:Optional upper diagonal.
-...type:nolink:$int$
-..param.algorithmTag:The Tag for picking the alignment algorithm.
-...type:Tag.Pairwise Global Alignment Algorithms.tag.Gotoh
-...type:Tag.Pairwise Global Alignment Algorithms.tag.NeedlemanWunsch
-...type:Tag.Pairwise Global Alignment Algorithms.tag.Hirschberg
-...type:Tag.Pairwise Global Alignment Algorithms.tag.MyersHirschberg
-..returns:An integer with the alignment score, as given by the @Metafunction.Value@ metafunction of the @Class.Score@ type.
-..remarks:
-There exist multiple overloads for this function with four configuration dimensions.
-..remarks:
-First, you can select whether begin and end gaps are free in either sequence using $alignConfig$.
-..remarks:
-Second, you can select the type of the target storing the alignment.
-This can be either an @Class.Align@ object, two @Class.Gaps@ objects, a @Spec.Alignment Graph@, or a string of @Class.Fragment@ objects.
-@Class.Align@ objects provide an interface to tabular alignments with the restriction of all rows having the same type.
-Using two @Class.Gaps@ objects has the advantage that you an align sequences with different types, for example @Shortcut.DnaString@ and @Shortcut.Dna5String@.
-@Spec.Alignment Graph|Alignment Graphs@ provide a graph-based representation of segment-based colinear alignments.
-Using @Class.Fragment@ strings is useful for collecting many pairwise alignments, for example in the construction of @Spec.Alignment Graph|Alignment Graphs@ for multiple-sequence alignments (MSA).
-..remarks:
-Third, you can optionally give a band for the alignment using $lowerDiag$ and $upperDiag$.
-The center diagonal has index $0$, the $i$th diagonal below has index $-i$, the $i$th above has index $i$.
-..remarks:
-Fourth, you can select the algorithm to use with $algorithmTag$.
-This can be one of @Tag.Pairwise Global Alignment Algorithms.value.NeedlemanWunsch@ and @Tag.Pairwise Global Alignment Algorithms.value.Gotoh@.
-The Needleman-Wunsch algorithm supports scoring schemes with linear gap costs only while Gotoh's algorithm also allows affine gap costs.
-..remarks:
-The available alignment algorithms all have some restrictions.
-Gotoh's algorithm can handle arbitrary substitution and affine gap scores.
-Needleman-Wunsch is limited to linear gap scores.
-The implementation of Hirschberg's algorithm is further limited that it does not support $alignConfig$ objects or banding.
-The implementation of the Myers-Hirschberg algorithm further limits this to only support edit distance (as scores, matches are scored with 0, mismatches are scored with -1).
-..remarks:
-The examples below show some common use cases.
-..example.text:Global alignment of two sequences using an @Class.Align@ object and the Needleman-Wunsch algorithm. The Needleman-Wunsch algorithm is automatically selected since the scoring scheme uses linear gap costs.
-..example.file:demos/align/global_alignment_unbanded.cpp
-..example.text:Global banded alignment of two sequences using two @Class.Gaps@ objects and the Gotoh algorithm. The Gotoh algorithm is automatically selected since the scoring scheme uses affine gap costs.
-..example.file:demos/align/global_alignment_banded.cpp
-..see:Function.localAlignment
-..see:Function.globalAlignmentScore
-..include:seqan/align.h
-..wiki:Tutorial/PairwiseSequenceAlignment
-..cite:Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48(3): 443-53.
-..cite:Gotoh O: An improved algorithm for matching biological sequences. J Mol Biol 1982, 162(3):705-8
-.
-*/
-
 // ----------------------------------------------------------------------------
 // Function globalAlignment()                                 [unbanded, Align]
 // ----------------------------------------------------------------------------
 
-template <typename TSequence, typename TAlignSpec,
-          typename TScoreValue, typename TScoreSpec,
-          bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
-          typename TAlgoTag>
+template <typename TSequence, typename TAlignSpec, typename TScoreValue, typename TScoreSpec,
+          bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec, typename TAlgoTag>
 TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
                             Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
-                            TAlgoTag const & algoTag)
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
+                            TAlgoTag const & /*algoTag*/)
 {
     typedef Align<TSequence, TAlignSpec> TAlign;
     typedef typename Size<TAlign>::Type TSize;
     typedef typename Position<TAlign>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
 
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
+
     String<TTraceSegment> trace;
+    TScoreValue res;
+    DPScoutState_<Default> dpScoutState;
+    res  = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), scoringScheme,
+                                 TAlignConfig2(), TGapModel());
 
-    // We do not need string ids for this variant and set them to 0u.  They are
-    // only required for the Fragment String and the Alignment Graph variant.
-    TScoreValue res = _setUpAndRunAlignment(trace, source(row(align, 0)), source(row(align, 1)), scoringScheme,
-                                            alignConfig, algoTag);
     _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace);
     return res;
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TSequence, typename TAlignSpec,
           typename TScoreValue, typename TScoreSpec,
           typename TAlgoTag>
@@ -288,7 +207,6 @@ TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
 }
 
 // Interface without algorithm tag.
-
 template <typename TSequence, typename TAlignSpec,
           typename TScoreValue, typename TScoreSpec,
           bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
@@ -303,7 +221,6 @@ TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TSequence, typename TAlignSpec,
           typename TScoreValue, typename TScoreSpec>
 TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
@@ -325,25 +242,26 @@ template <typename TSequenceH, typename TGapsSpecH,
 TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                             Gaps<TSequenceV, TGapsSpecV> & gapsV,
                             Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
-                            TAlgoTag const & algoTag)
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
+                            TAlgoTag const & /*algoTag*/)
 {
     typedef typename Size<TSequenceH>::Type TSize;
     typedef typename Position<TSequenceH>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
 
     String<TTraceSegment> traceSegments;
-
-    // We do not need string ids for this variant and set them to 0u.  They are
-    // only required for the Fragment String and the Alignment Graph variant.
-    TScoreValue res = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, alignConfig,
-                                            algoTag);
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, source(gapsH), source(gapsV), scoringScheme,
+                                            TAlignConfig2(), TGapModel());
     _adaptTraceSegmentsTo(gapsH, gapsV, traceSegments);
     return res;
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TSequenceH, typename TGapsSpecH,
           typename TSequenceV, typename TGapsSpecV,
           typename TScoreValue, typename TScoreSpec,
@@ -358,7 +276,6 @@ TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 }
 
 // Interface without algorithm tag.
-
 template <typename TSequenceH, typename TGapsSpecH,
           typename TSequenceV, typename TGapsSpecV,
           typename TScoreValue, typename TScoreSpec,
@@ -375,7 +292,6 @@ TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TSequenceH, typename TGapsSpecH,
           typename TSequenceV, typename TGapsSpecV,
           typename TScoreValue, typename TScoreSpec>
@@ -392,32 +308,36 @@ TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 // ----------------------------------------------------------------------------
 
 // Full interface.
-
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
           typename TScoreValue, typename TScoreSpec,
           bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
           typename TAlgoTag>
 TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
                             Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
-                            TAlgoTag const & algoTag)
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
+                            TAlgoTag const & /*algoTag*/)
 {
     typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
     typedef typename Position<TGraph>::Type TPosition;
     typedef typename Size<TGraph>::Type TSize;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
 
     String<TTraceSegment> traceSegments;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(stringSet(alignmentGraph), 0),
+                                            value(stringSet(alignmentGraph), 1), scoringScheme, TAlignConfig2(),
+                                            TGapModel());
 
-    TScoreValue res = _setUpAndRunAlignment(traceSegments, value(stringSet(alignmentGraph), 0),
-                                            value(stringSet(alignmentGraph), 1), scoringScheme, alignConfig, algoTag);
     _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0),
                           positionToId(stringSet(alignmentGraph), 1), traceSegments);
     return res;
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
           typename TScoreValue, typename TScoreSpec,
           typename TAlgoTag>
@@ -430,7 +350,6 @@ TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > &
 }
 
 // Interface without algorithm tag.
-
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
           typename TScoreValue, typename TScoreSpec,
           bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
@@ -445,7 +364,6 @@ TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > &
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
           typename TScoreValue, typename TScoreSpec>
 TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
@@ -460,7 +378,6 @@ TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > &
 // ----------------------------------------------------------------------------
 
 // Full interface.
-
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
           typename TScoreValue, typename TScoreSpec,
@@ -469,23 +386,27 @@ template <typename TSize, typename TFragmentSpec, typename TStringSpec,
 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
                             StringSet<TSequence, TStringSetSpec> const & strings,
                             Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
-                            TAlgoTag const & algoTag)
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
+                            TAlgoTag const & /*algoTag*/)
 {
     typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments;
     typedef typename Position<TFragments>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
 
     String<TTraceSegment> traceSegments;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(strings, 0), value(strings, 1),
+                                            scoringScheme, TAlignConfig2(), TGapModel());
 
-    TScoreValue res = _setUpAndRunAlignment(traceSegments, value(strings, 0), value(strings, 1), scoringScheme,
-                                            alignConfig, algoTag);
     _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), traceSegments);
     return res;
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
           typename TScoreValue, typename TScoreSpec,
@@ -500,7 +421,6 @@ TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec>
 }
 
 // Interface without algorithm tag.
-
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
           typename TScoreValue, typename TScoreSpec,
@@ -517,7 +437,6 @@ TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec>
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
           typename TScoreValue, typename TScoreSpec>
@@ -535,13 +454,14 @@ TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec>
 
 /*!
  * @fn globalAlignmentScore
+ * @headerfile <seqan/align.h>
  * @brief Computes the best global pairwise alignment score.
- * 
+ *
  * @signature TScoreVal globalAlignmentScore(seqH, seqV, scoringScheme[, alignConfig][, lowerDiag, upperDiag][, algorithmTag]);
  * @signature TScoreVal globalAlignmentScore(strings,    scoringScheme[, alignConfig][, lowerDiag, upperDiag][, algorithmTag]);
  * @signature TScoreVal globalAlignmentScore(seqH, seqV, {MyersBitVector | MyersHirschberg});
  * @signature TScoreVal globalAlignmentScore(strings,    {MyersBitVector | MyersHirschberg});
- * 
+ *
  * @param[in] seqH          Horizontal gapped sequence in alignment matrix.  Types: String
  * @param[in] seqV          Vertical gapped sequence in alignment matrix.  Types: String
  * @param[in] strings       A @link StringSet @endlink containing two sequences.  Type: StringSet.
@@ -552,64 +472,21 @@ TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec>
  * @param[in] upperDiag     Optional upper diagonal.  Types: <tt>int</tt>
  * @param[in] algorithmTag  The Tag for picking the alignment algorithm. Types: @link PairwiseLocalAlignmentAlgorithms
  *                          @endlink.
- * 
- * @return TScoreValue The score value with the alignment score, as given by the @link Score#Value @endlink metafunction
- *                     of the <tt>scoringScheme</tt> type.
- * 
- * @section Remarks
- * 
+ *
+ * @return TScoreVal   Score value of the resulting alignment  (Metafunction: @link Score#Value @endlink of
+ *                     the type of <tt>scoringScheme</tt>).
+ *
  * This function does not perform the (linear time) traceback step after the (mostly quadratic time) dynamic programming
  * step.  Note that Myers' bit-vector algorithm does not compute an alignment (only in the Myers-Hirschberg variant) but
  * scores can be computed using <tt>globalAlignmentScore</tt>.
- * 
+ *
  * The same limitations to algorithms as in @link globalAlignment @endlink apply.  Furthermore, the
  * <tt>MyersBitVector</tt> and <tt>MyersHirschberg</tt> variants can only be used without any other parameter.
- * 
- * @see http://trac.seqan.de/wiki/Tutorial/PairwiseSequenceAlignment
+ *
+ * @see http://seqan.readthedocs.org/en/develop/Tutorial/PairwiseSequenceAlignment.html
  * @see globalAlignment
  */
 
-/**
-.Function.globalAlignmentScore
-..summary:Computes the best global pairwise alignment score.
-..cat:Alignments
-..signature:globalAlignmentScore(seqH, seqV, scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag])
-..signature:globalAlignmentScore(strings,    scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag])
-..signature:globalAlignmentScore(seqH, seqV, {MyersBitVector | MyersHirschberg})
-..signature:globalAlignmentScore(strings,    {MyersBitVector | MyersHirschberg})
-..param.seqH:Horizontal gapped sequence in alignment matrix.
-...type:Class.String
-..param.seqV:Vertical gapped sequence in alignment matrix.
-...type:Class.String
-..param.strings:A @Class.StringSet@ containing two sequences.
-...type:Class.StringSet
-..param.scoringScheme:
-The scoring scheme to use for the alignment.
-Note that the user is responsible for ensuring that the scoring scheme is compatible with $algorithmTag$.
-...type:Class.Score
-..param.alignConfig:The @Class.AlignConfig@ to use for the alignment.
-...type:Class.AlignConfig
-..param.lowerDiag:Optional lower diagonal.
-...type:nolink:$int$
-..param.upperDiag:Optional upper diagonal.
-...type:nolink:$int$
-..param.algorithmTag:The Tag for picking the alignment algorithm.
-...type:Tag.Pairwise Global Alignment Algorithms.tag.Gotoh
-...type:Tag.Pairwise Global Alignment Algorithms.tag.NeedlemanWunsch
-...type:Tag.Pairwise Global Alignment Algorithms.tag.Hirschberg
-...type:Tag.Pairwise Global Alignment Algorithms.tag.MyersHirschberg
-...type:Tag.Pairwise Global Alignment Algorithms.tag.MyersBitVector
-..returns:An integer with the alignment score, as given by the @Metafunction.Value@ metafunction of the @Class.Score@ type.
-..remarks:
-This function does not perform the (linear time) traceback step after the (mostly quadratic time) dynamic programming step.
-Note that Myers' bit-vector algorithm does not compute an alignment (only in the Myers-Hirschberg variant) but scores can be computed using $globalAlignmentScore$.
-..remarks:
-The same limitations to algorithms as in @Function.globalAlignment@ apply.
-Furthermore, the $MyersBitVector$ and $MyersHirschberg$ variants can only be used without any other parameter.
-..see:Function.globalAlignment
-..wiki:Tutorial/PairwiseSequenceAlignment
-*/
-
 // ----------------------------------------------------------------------------
 // Function globalAlignmentScore()                        [unbanded, 2 Strings]
 // ----------------------------------------------------------------------------
@@ -622,14 +499,20 @@ template <typename TSequenceH,
 TScoreValue globalAlignmentScore(TSequenceH const & seqH,
                                  TSequenceV const & seqV,
                                  Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                                 AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
-                                 TAlgoTag const & algoTag)
+                                 AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
+                                 TAlgoTag const & /*algoTag*/)
 {
-    return _setUpAndRunAlignment(seqH, seqV, scoringScheme, alignConfig, algoTag);
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps, TracebackOff> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
+
+    DPScoutState_<Default> dpScoutState;
+    String<TraceSegment_<unsigned, unsigned> > traceSegments;  // Dummy segments.
+    return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, TAlignConfig2(), TGapModel());
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TSequenceH,
           typename TSequenceV,
           typename TScoreValue, typename TScoreSpec,
@@ -644,7 +527,6 @@ TScoreValue globalAlignmentScore(TSequenceH const & seqH,
 }
 
 // Interface without algorithm tag.
-
 template <typename TSequenceH,
           typename TSequenceV,
           typename TScoreValue, typename TScoreSpec,
@@ -661,7 +543,6 @@ TScoreValue globalAlignmentScore(TSequenceH const & seqH,
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TSequenceH,
           typename TSequenceV,
           typename TScoreValue, typename TScoreSpec>
@@ -683,15 +564,23 @@ template <typename TString, typename TSpec,
           typename TAlgoTag>
 TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
                                  Score<TScoreValue, TScoreSpec> const & scoringScheme,
-                                 AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
-                                 TAlgoTag const & algoTag)
+                                 AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
+                                 TAlgoTag const & /*algoTag*/)
 {
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps, TracebackOff> TAlignConfig2;
+    typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
+
     SEQAN_ASSERT_EQ(length(strings), 2u);
-    return _setUpAndRunAlignment(strings[0], strings[1], scoringScheme, alignConfig, algoTag);
+
+    DPScoutState_<Default> dpScoutState;
+    String<TraceSegment_<unsigned, unsigned> > traceSegments;  // Dummy segments.
+    return _setUpAndRunAlignment(traceSegments, dpScoutState, strings[0], strings[1], scoringScheme, TAlignConfig2(),
+                                 TGapModel());
 }
 
 // Interface without AlignConfig<>.
-
 template <typename TString, typename TSpec,
           typename TScoreValue, typename TScoreSpec,
           typename TAlgoTag>
@@ -706,7 +595,6 @@ TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
 }
 
 // Interface without algorithm tag.
-
 template <typename TString, typename TSpec,
           typename TScoreValue, typename TScoreSpec,
           bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
@@ -723,7 +611,6 @@ TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
 }
 
 // Interface without AlignConfig<> and algorithm tag.
-
 template <typename TString, typename TSpec,
           typename TScoreValue, typename TScoreSpec>
 TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
@@ -737,4 +624,4 @@ TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_
diff --git a/seqan/align/local_alignment_banded.h b/seqan/align/local_alignment_banded.h
index abdbbcf..5b5ea1a 100644
--- a/seqan/align/local_alignment_banded.h
+++ b/seqan/align/local_alignment_banded.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Interface functions for banded local alignment.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
 
 namespace seqan {
 
@@ -59,74 +59,125 @@ namespace seqan {
 // Function localAlignment()                                    [banded, Align]
 // ----------------------------------------------------------------------------
 
-template <typename TSequence, typename TAlignSpec,
-          typename TScoreValue, typename TScoreSpec>
+template <typename TSequence, typename TAlignSpec, typename TScoreValue, typename TScoreSpec, typename TTag>
 TScoreValue localAlignment(Align<TSequence, TAlignSpec> & align,
                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
                            int lowerDiag,
-                           int upperDiag)
+                           int upperDiag,
+                           TTag const & tag)
 {
     typedef Align<TSequence, TAlignSpec> TAlign;
     typedef typename Size<TAlign>::Type TSize;
     typedef typename Position<TAlign>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
 
     SEQAN_ASSERT_EQ(length(rows(align)), 2u);
 
-    String<TTraceSegment> traceSegments;
-    TScoreValue score = _setUpAndRunAlignment(traceSegments, source(row(align, 0)), source(row(align, 1)),
-                                              scoringScheme, lowerDiag, upperDiag, SmithWaterman());
-    _adaptTraceSegmentsTo(row(align, 0), row(align, 1), traceSegments);
-    return score;
+    String<TTraceSegment> trace;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)),
+                                            scoringScheme, TAlignConfig2(lowerDiag, upperDiag), tag);
+
+    _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace);
+    return res;
+}
+
+template <typename TSequence, typename TAlignSpec, typename TScoreValue, typename TScoreSpec>
+TScoreValue localAlignment(Align<TSequence, TAlignSpec> & align,
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                           int lowerDiag,
+                           int upperDiag)
+{
+    SEQAN_ASSERT(length(rows(align)) == 2u);
+    if (_usesAffineGaps(scoringScheme, source(row(align, 0)), source(row(align, 1))))
+        return localAlignment(align, scoringScheme, lowerDiag, upperDiag, AffineGaps());
+    else
+        return localAlignment(align, scoringScheme, lowerDiag, upperDiag, LinearGaps());
 }
 
 // ----------------------------------------------------------------------------
 // Function localAlignment()                                     [banded, Gaps]
 // ----------------------------------------------------------------------------
 
-template <typename TSequenceH, typename TGapsSpecH,
-          typename TSequenceV, typename TGapsSpecV,
-          typename TScoreValue, typename TScoreSpec>
+template <typename TSequenceH, typename TGapsSpecH, typename TSequenceV, typename TGapsSpecV,
+          typename TScoreValue, typename TScoreSpec, typename TTag>
 TScoreValue localAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                            Gaps<TSequenceV, TGapsSpecV> & gapsV,
                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
                            int lowerDiag,
-                           int upperDiag)
+                           int upperDiag,
+                           TTag const & tag)
 {
     typedef typename Size<TSequenceH>::Type TSize;
     typedef typename Position<TSequenceH>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
+
+    String<TTraceSegment> trace;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme,
+                                            TAlignConfig2(lowerDiag, upperDiag), tag);
+    _adaptTraceSegmentsTo(gapsH, gapsV, trace);
+    return res;
+}
 
-    String<TTraceSegment> traceSegments;
-    TScoreValue score = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme, lowerDiag,
-                                              upperDiag, SmithWaterman());
-    _adaptTraceSegmentsTo(gapsH, gapsV, traceSegments);
-    return score;
+template <typename TSequenceH, typename TGapsSpecH, typename TSequenceV, typename TGapsSpecV,
+          typename TScoreValue, typename TScoreSpec>
+TScoreValue localAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
+                           Gaps<TSequenceV, TGapsSpecV> & gapsV,
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                           int lowerDiag,
+                           int upperDiag)
+{
+    if (_usesAffineGaps(scoringScheme, source(gapsH), source(gapsV)))
+        return localAlignment(gapsH, gapsV, scoringScheme, lowerDiag, upperDiag, AffineGaps());
+    else
+        return localAlignment(gapsH, gapsV, scoringScheme, lowerDiag, upperDiag, LinearGaps());
 }
 
 // ----------------------------------------------------------------------------
 // Function localAlignment()                      [banded, Graph<Alignment<> >]
 // ----------------------------------------------------------------------------
 
-template <typename TStringSet, typename TCargo, typename TGraphSpec,
-          typename TScoreValue, typename TScoreSpec>
+template <typename TStringSet, typename TCargo, typename TGraphSpec, typename TScoreValue, typename TScoreSpec,
+          typename TTag>
 TScoreValue localAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
                            int lowerDiag,
-                           int upperDiag)
+                           int upperDiag,
+                           TTag const & tag)
 {
     typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
     typedef typename Size<TGraph>::Type TSize;
     typedef typename Position<TGraph>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
+
+    String<TTraceSegment> trace;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0),
+                                            value(stringSet(alignmentGraph), 1), scoringScheme,
+                                            TAlignConfig2(lowerDiag, upperDiag), tag);
 
-    String<TTraceSegment> traceSegments;
-    TScoreValue score = _setUpAndRunAlignment(traceSegments, value(stringSet(alignmentGraph), 0),
-                                              value(stringSet(alignmentGraph), 1), scoringScheme, lowerDiag, upperDiag,
-                                              SmithWaterman());
     _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0),
-                          positionToId(stringSet(alignmentGraph), 1), traceSegments);
-    return score;
+                          positionToId(stringSet(alignmentGraph), 1), trace);
+    return res;
+}
+
+template <typename TStringSet, typename TCargo, typename TGraphSpec,
+          typename TScoreValue, typename TScoreSpec>
+TScoreValue localAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                           int lowerDiag,
+                           int upperDiag)
+{
+    SEQAN_ASSERT(length(stringSet(alignmentGraph)) == 2u);
+
+    if (_usesAffineGaps(scoringScheme, stringSet(alignmentGraph)[0], stringSet(alignmentGraph)[1]))
+        return localAlignment(alignmentGraph, scoringScheme, lowerDiag, upperDiag, AffineGaps());
+    else
+        return localAlignment(alignmentGraph, scoringScheme, lowerDiag, upperDiag, LinearGaps());
 }
 
 // ----------------------------------------------------------------------------
@@ -134,6 +185,27 @@ TScoreValue localAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & a
 // ----------------------------------------------------------------------------
 
 // Full interface.
+template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequence, typename TStringSetSpec,
+          typename TScoreValue, typename TScoreSpec, typename TTag>
+TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
+                           StringSet<TSequence, TStringSetSpec> const & strings,
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                           int lowerDiag,
+                           int upperDiag,
+                           TTag const & tag)
+{
+    typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments;
+    typedef typename Position<TFragments>::Type TPosition;
+    typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
+
+    String<TTraceSegment> trace;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme,
+                                            TAlignConfig2(lowerDiag, upperDiag), tag);
+    _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace);
+    return res;
+}
 
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
@@ -144,18 +216,14 @@ TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> &
                            int lowerDiag,
                            int upperDiag)
 {
-    typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments;
-    typedef typename Position<TFragments>::Type TPosition;
-    typedef TraceSegment_<TPosition, TSize> TTraceSegment;
-
-    String<TTraceSegment> traceSegments;
+    SEQAN_ASSERT(length(strings) == 2u);
 
-    TScoreValue score = _setUpAndRunAlignment(traceSegments, value(strings, 0), value(strings, 1), scoringScheme,
-                                              lowerDiag, upperDiag, SmithWaterman());
-    _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), traceSegments);
-    return score;
+    if (_usesAffineGaps(scoringScheme, strings[0], strings[1]))
+        return localAlignment(fragmentString, strings, scoringScheme, lowerDiag, upperDiag, AffineGaps());
+    else
+        return localAlignment(fragmentString, strings, scoringScheme, lowerDiag, upperDiag, LinearGaps());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
diff --git a/seqan/align/local_alignment_banded_waterman_eggert_impl.h b/seqan/align/local_alignment_banded_waterman_eggert_impl.h
index 763484b..8465129 100644
--- a/seqan/align/local_alignment_banded_waterman_eggert_impl.h
+++ b/seqan/align/local_alignment_banded_waterman_eggert_impl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // Author: Birte Kehr <birte.kehr@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_
 
 namespace seqan {
 
@@ -100,7 +100,7 @@ _alignBandedSmithWaterman(LocalAlignmentFinder<TScoreValue>& finder,
     for (TSize row = 1; row < height; ++row) {
         actualRow = row + lo_row;
         hori_val = 0;
-        
+
         for (TSize col = 0; col < diagonalWidth; ++col, ++matIt) {
             // handle begin and end triangle of band
             if ((int)col + diagL + (int)actualRow < 0) {++matIt2; continue;}
@@ -153,13 +153,13 @@ _alignBandedSmithWaterman(LocalAlignmentFinder<TScoreValue>& finder,
     }
  //   // Debug code
  //   std::cerr << std::endl;
-	//for(TSize i= 0; i<height; ++i) {
-	//	for(TSize j= 0; j<diagonalWidth; ++j) {
-	//		std::cerr << value(finder.matrix, j, i) << ',';
-	//	}
-	//	if (i > 0) std::cerr << " " << str2[i-1] << std::endl;
-	//	else std::cerr << std::endl;
-	//}
+    //for(TSize i= 0; i<height; ++i) {
+    //    for(TSize j= 0; j<diagonalWidth; ++j) {
+    //        std::cerr << value(finder.matrix, j, i) << ',';
+    //    }
+    //    if (i > 0) std::cerr << " " << str2[i-1] << std::endl;
+    //    else std::cerr << std::endl;
+    //}
  //   if(length(finder.pQ) > 0) std::cerr << "Max score: " << top(finder.pQ).value_ << std::endl;
 
     if(!empty(finder.pQ)) {
@@ -177,20 +177,20 @@ _alignBandedSmithWaterman(LocalAlignmentFinder<TScoreValue>& finder,
 template<typename TSpec, typename TSize>
 inline void
 _setForbiddenCell(String<bool, TSpec>& forbidden,
-				  TSize len1,
-				  TSize len2,
-				  TSize numRows)
+                  TSize len1,
+                  TSize len2,
+                  TSize numRows)
 {
-	forbidden[(len1 - 1)*numRows + (len2 - 1)] = true;
+    forbidden[(len1 - 1)*numRows + (len2 - 1)] = true;
 }
 
 
 template<typename TSize>
 inline void
 _setForbiddenCell(Nothing&,
-				  TSize,
-				  TSize,
-				  TSize)
+                  TSize,
+                  TSize,
+                  TSize)
 {
 }
 
@@ -213,7 +213,7 @@ _alignBandedSmithWatermanDeclump(LocalAlignmentFinder<TScoreValue>& finder,
     typedef unsigned char TTraceValue;
 
     // Traceback values
-	TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2;
+    TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2;
 
     TSequenceH const& str1 = seqH;
     TSequenceV const& str2 = seqV;
@@ -279,7 +279,7 @@ _alignBandedSmithWatermanDeclump(LocalAlignmentFinder<TScoreValue>& finder,
                     maxCol = traceCol + 1;
             }
         }
- 
+
         // iterate over columns that have to be re-calculated
         if (maxCol > minCol) {
             col = minCol;
@@ -299,18 +299,18 @@ _alignBandedSmithWatermanDeclump(LocalAlignmentFinder<TScoreValue>& finder,
                 ++matIt2;
 
                 // horizontal
-				if (col > 0) {
-		            newVal = _max(newVal, *(matIt-1) +
-		                          scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, (int) actualCol-1),
-		                                                   sequenceEntryForScore(sc, str2, (int)actualRow-1)));
-				}
+                if (col > 0) {
+                    newVal = _max(newVal, *(matIt-1) +
+                                  scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, (int) actualCol-1),
+                                                           sequenceEntryForScore(sc, str2, (int)actualRow-1)));
+                }
 
                 // vertical
-				if (col+1 < maxCol) {
-					newVal = _max(newVal, *matIt2 +
-					              scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, (int)actualCol-1),
-					                                     sequenceEntryForScore(sc, str2, (int)actualRow-1)));
-				}
+                if (col+1 < maxCol) {
+                    newVal = _max(newVal, *matIt2 +
+                                  scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, (int)actualCol-1),
+                                                         sequenceEntryForScore(sc, str2, (int)actualRow-1)));
+                }
 
                 if (newVal != *matIt) {
                     // matrix entry changed
@@ -350,13 +350,13 @@ _alignBandedSmithWatermanDeclump(LocalAlignmentFinder<TScoreValue>& finder,
   //      for(TSize j = 0; j < diagonalWidth; ++j) {
   //          std::cerr << value(finder.matrix, j, i) << ',';
   //      }
-		//if (i > 0) std::cerr << " " << str2[i-1] << "    ";
-		//else std::cerr << "      ";
+        //if (i > 0) std::cerr << " " << str2[i-1] << "    ";
+        //else std::cerr << "      ";
   //      for (TSize j= 0; j<diagonalWidth; ++j) {
   //          std::cerr << value(finder.forbidden, j+i*diagonalWidth) << ',';
   //      }
   //      if (i > 0) std::cerr << " " << str2[i-1] << std::endl;
-		//else std::cerr << std::endl;
+        //else std::cerr << std::endl;
   //  }
 }
 
@@ -383,7 +383,7 @@ _alignBandedSmithWatermanTrace(LocalAlignmentFinder<TScoreValue> & finder,
     clear(finder.trace.tvs);
 
     // Traceback values
-	TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; TTraceValue Stop = 3;
+    TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; TTraceValue Stop = 3;
 
     // Initialization
     TSequenceH const& str1 = seqH;
@@ -404,18 +404,18 @@ _alignBandedSmithWatermanTrace(LocalAlignmentFinder<TScoreValue> & finder,
     TSize endRow = row + lo_row;
     TSize endCol = static_cast<TSize>(col + diagL + endRow);
 
-	TSize actualRow = row + lo_row;
+    TSize actualRow = row + lo_row;
     TSize actualCol = static_cast<TSize>(col + diagL + actualRow);
-    if ((actualCol == 0) || (actualRow == 0)) 
+    if ((actualCol == 0) || (actualRow == 0))
         return Pair<Pair<TDiagonal> >();
 
-	if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal);
-	if (actualRow < len2) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len2 - actualRow, Vertical);
-	
+    if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal);
+    if (actualRow < len2) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len2 - actualRow, Vertical);
+
     TTraceValue traceValue = Stop;
     TTraceValue nextTraceValue = Horizontal;
     TSize segLen = 0;
-	
+
     while (nextTraceValue != Stop) {
         traceValue = nextTraceValue;
         if (*matIt == 0) {
@@ -428,14 +428,14 @@ _alignBandedSmithWatermanTrace(LocalAlignmentFinder<TScoreValue> & finder,
             nextTraceValue = Diagonal;
             --actualRow; --actualCol;
             --row;
-            goPrevious(matIt, 1); 
+            goPrevious(matIt, 1);
             goPrevious(matIt2, 1);
         } else if (*matIt == *(matIt2+1) +
             scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, (int)actualCol-1),
                                    sequenceEntryForScore(sc, str2, (int)actualRow-1)))
         {
             nextTraceValue = Vertical;
-            --actualRow; 
+            --actualRow;
             --row; ++col;
             goPrevious(matIt, 1); goNext(matIt, 0);
             goPrevious(matIt2, 1); goNext(matIt2, 0);
@@ -444,7 +444,7 @@ _alignBandedSmithWatermanTrace(LocalAlignmentFinder<TScoreValue> & finder,
                             scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, (int) actualCol-1),
                                                      sequenceEntryForScore(sc, str2, (int) actualRow-1)));
             nextTraceValue = Horizontal;
-            --actualCol; 
+            --actualCol;
             --col;
             goPrevious(matIt, 0);
             goPrevious(matIt2, 0);
@@ -456,10 +456,10 @@ _alignBandedSmithWatermanTrace(LocalAlignmentFinder<TScoreValue> & finder,
             segLen = 1;
         }
     }
-    
-	// Handle the remaining sequence
-	if (actualCol != 0) _alignTracePrint(finder.trace, seqH, seqV, (TId) id1, (TSize) 0, (TId) 0, (TSize) 0, (TSize) actualCol, Horizontal);
-	if (actualRow != 0) _alignTracePrint(finder.trace, seqH, seqV, (TId) 0, (TSize) 0, (TId) id2, (TSize) 0, (TSize) actualRow, Vertical);
+
+    // Handle the remaining sequence
+    if (actualCol != 0) _alignTracePrint(finder.trace, seqH, seqV, (TId) id1, (TSize) 0, (TId) 0, (TSize) 0, (TSize) actualCol, Horizontal);
+    if (actualRow != 0) _alignTracePrint(finder.trace, seqH, seqV, (TId) 0, (TSize) 0, (TId) id2, (TSize) 0, (TSize) actualRow, Vertical);
 
     goNext(matIt, 1); // assumes that each trace ends with a diagonal
     finder.bestBeginPos = position(matIt);
@@ -488,7 +488,7 @@ _initLocalAlignmentFinder(TSequenceH const & seqH,
     TSize len0 = length(seqH);
     if (len0 - lowerDiag < hi_row) hi_row = static_cast<TSize>(len0 - lowerDiag);
     TSize height = hi_row - lo_row + 1;
-	SEQAN_ASSERT_GEQ(upperDiag, lowerDiag);
+    SEQAN_ASSERT_GEQ(upperDiag, lowerDiag);
     TSize diagonalWidth = (TSize) (upperDiag - lowerDiag + 1);
 
     setDimension(finder.matrix, 2);
@@ -498,8 +498,8 @@ _initLocalAlignmentFinder(TSequenceH const & seqH,
 
     resize(finder.forbidden, height * diagonalWidth, false);
 
-	finder.bestEndPos = minValue<typename TFinder::TMatrixPosition>();
-	finder.bestBeginPos = minValue<typename TFinder::TMatrixPosition>();
+    finder.bestEndPos = minValue<typename TFinder::TMatrixPosition>();
+    finder.bestBeginPos = minValue<typename TFinder::TMatrixPosition>();
 }
 
 // ----------------------------------------------------------------------------
@@ -524,7 +524,7 @@ _localAlignment(LocalAlignmentFinder<TScoreValue> & finder,
 
     _initLocalAlignmentFinder(source(gapsH), source(gapsV), finder, BandedWatermanEggert(), diag1, diag2);
     finder.needReinit = false;
-    
+
     // Fill the matrix
     TScoreValue maxScore = _alignBandedSmithWaterman(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2);
     if (maxScore < cutoff) return 0;
@@ -533,7 +533,7 @@ _localAlignment(LocalAlignmentFinder<TScoreValue> & finder,
     Pair<Pair<TDiagonal> > alignmentPositions = _alignBandedSmithWatermanTrace(finder, source(gapsH), source(gapsV), 0u, 0u, sc, diag1, diag2);
 
     // Fill the gaps following the trace path.
-	_pumpTraceToGaps(gapsH, gapsV, finder.trace);
+    _pumpTraceToGaps(gapsH, gapsV, finder.trace);
 
     // The following (using rightOfGaps = false) only works if the gap open cost is negative.  In this case, we can
     // assume that there are no leading or trailing gaps in either sequence.
@@ -544,10 +544,10 @@ _localAlignment(LocalAlignmentFinder<TScoreValue> & finder,
     // TODO(holtgrew): This should be done in a more robust way.  It would probably be better if alignmentPositions gave us the lengths of the local alignments!
     setClippedEndPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i2, false));
     setClippedEndPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i2, false));
-	setClippedBeginPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i1));
-	setClippedBeginPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i1));
+    setClippedBeginPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i1));
+    setClippedBeginPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i1));
 
-	pop(finder.pQ);
+    pop(finder.pQ);
 
     return maxScore;
 }
@@ -569,17 +569,17 @@ _localAlignmentNext(LocalAlignmentFinder<TScoreValue> & finder,
     // Declump the matrix and find new maximum score
     _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2);
     typename LocalAlignmentFinder<TScoreValue>::TMatrixPosition nextBestEnd;
-	nextBestEnd = _getNextBestEndPosition(finder, cutoff);
-	if(nextBestEnd==0)
-		return 0;
+    nextBestEnd = _getNextBestEndPosition(finder, cutoff);
+    if(nextBestEnd==0)
+        return 0;
     TScoreValue maxScore = getValue(finder.matrix, nextBestEnd);
-	if(maxScore == 0) return 0;
+    if(maxScore == 0) return 0;
 
     // Follow the trace matrix and create a trace path
     Pair<Pair<TDiagonal> > alignmentPositions = _alignBandedSmithWatermanTrace(finder, source(gapsH), source(gapsV), 0u, 0u, sc, diag1, diag2);
 
     // Fill the gaps following the trace path.
-	_pumpTraceToGaps(gapsH, gapsV, finder.trace);
+    _pumpTraceToGaps(gapsH, gapsV, finder.trace);
 
     // The following (using rightOfGaps = false) only works if the gap open cost is negative.  In this case, we can
     // assume that there are no leading or trailing gaps in either sequence.
@@ -590,12 +590,12 @@ _localAlignmentNext(LocalAlignmentFinder<TScoreValue> & finder,
     // TODO(holtgrew): This should be done in a more robust way.  It would probably be better if alignmentPositions gave us the lengths of the local alignments!
     setClippedEndPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i2, false));
     setClippedEndPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i2, false));
-	setClippedBeginPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i1));
-	setClippedBeginPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i1));
+    setClippedBeginPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i1));
+    setClippedBeginPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i1));
 
     return maxScore;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_
diff --git a/seqan/align/local_alignment_enumeration.h b/seqan/align/local_alignment_enumeration.h
index d797606..5af3901 100644
--- a/seqan/align/local_alignment_enumeration.h
+++ b/seqan/align/local_alignment_enumeration.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
 
 namespace seqan {
 
@@ -55,6 +55,7 @@ class LocalAlignmentEnumerator;
 /*!
  * @class LocalAlignmentEnumerator
  * @headerfile <seqan/align.h>
+ * @brief Enumeration of local alignments.
  *
  * @signature template <typename TScore, typename TSpec>
  *            class LocalAlignmentEnumerator;
@@ -83,22 +84,22 @@ class LocalAlignmentEnumerator;
  *
  * @tparam TScore The @link Score @endlink type.
  *
- * @section Example
+ * @section Examples
  *
  * Enumerate all alignments into a @link Align @endlink object.
  *
  * @code{.cpp}
  * SimpleScore scoringScheme(2, -1, -1, -2);
  * LocalAlignmentEnumerator<SimpleScore, Unbanded> enumerator(scoringScheme, 5);
- * 
+ *
  * Dna5String seqH = "CGAGAGAGACCGAGA";
  * Dna5String seqV = "TTCTGAGATCCGTTTTT";
- * 
+ *
  * Align<Dna5String> align;
- * resize(rows(align), 2);
+ * resize(rows(align), 2);@s
  * assignSource(row(align), 0, seqH);
  * assignSource(row(align), 1, seqV);
- * 
+ *
  * int i = 0;
  * while (nextLocalAlignment(align, enumerator))
  * {
@@ -115,8 +116,8 @@ class LocalAlignmentEnumerator;
  *
  * @signature LocalAlignmentEnumerator::LocalAlignmentEnumerator(scheme[, cutoff]);
  *
- * @param scheme    The @link Score @endlink object to use for the alignment score.
- * @param cutoff    Alignments with scores <tt>&lt; cutoff</tt> will be discarded (<tt>int</tt>, default 0).
+ * @param[in] scheme    The @link Score @endlink object to use for the alignment score.
+ * @param[in] cutoff    Alignments with scores <tt>&lt; cutoff</tt> will be discarded (<tt>int</tt>, default 0).
  */
 
 /*!
@@ -130,22 +131,22 @@ class LocalAlignmentEnumerator;
  *
  * @tparam TScore The @link Score @endlink type.
  *
- * @section Example
+ * @section Examples
  *
  * Enumerate all alignments in the band between -3 and 0 into an @link Align @endlink object.
  *
  * @code{.cpp}
  * SimpleScore scoringScheme(2, -1, -1, -2);
  * LocalAlignmentEnumerator<SimpleScore, Banded> enumerator(scoringScheme, -3, 0, 5);
- * 
+ *
  * Dna5String seqH = "CGAGAGAGACCGAGA";
  * Dna5String seqV = "TTCTGAGATCCGTTTTT";
- * 
+ *
  * Align<Dna5String> align;
  * resize(rows(align), 2);
  * assignSource(row(align), 0, seqH);
  * assignSource(row(align), 1, seqV);
- * 
+ *
  * int i = 0;
  * while (nextLocalAlignment(align, enumerator))
  * {
@@ -162,104 +163,12 @@ class LocalAlignmentEnumerator;
  *
  * @signature LocalAlignmentEnumerator::LocalAlignmentEnumerator(scheme, upperDiag, lowerDiag[, cutoff]);
  *
- * @param scheme    The @link Score @endlink object to use for the alignment score.
- * @param upperDiag An <tt>int</tt> with the upper diagonal.
- * @param lowerDiag An <tt>int</tt> with the lower diagonal.
- * @param cutoff    Alignments with scores <tt>&lt; cutoff</tt> will be discarded (<tt>int</tt>, default 0).
+ * @param[in] scheme    The @link Score @endlink object to use for the alignment score.
+ * @param[in] upperDiag An <tt>int</tt> with the upper diagonal.
+ * @param[in] lowerDiag An <tt>int</tt> with the lower diagonal.
+ * @param[in] cutoff    Alignments with scores <tt>&lt; cutoff</tt> will be discarded (<tt>int</tt>, default 0).
  */
 
-/**
-.Class.LocalAlignmentEnumerator
-..cat:Alignments
-..summary:Enumerate local alignments using the Waterman-Eggert algorithm.
-..description:This is an abstract base class for the alignment enumeration; the specializations provide the actual implementaiton of banded and unbanded local aligment search.
-..signature:LocalAlignmentEnumerator<TScore, TSpec>
-..param.TScore:The @Class.Score@ type to use.
-...type:Class.Score
-..param.TSpec:Specialization tag.
-..example.text:See the specializations for usage examples.
-..cite:Waterman MS, Eggert M: A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J Mol Biol 1987, 197(4):723-728.
-..include:seqan/align.h
-
-.Spec.Unbanded LocalAlignmentEnumerator
-..cat:Alignments
-..general:Class.LocalAlignmentEnumerator
-..summary:Unbanded enumeration of local alignments using the Waterman-Eggert algorithm.
-..signature:LocalAlignmentEnumerator<TScore, Unbanded>
-..example.text:Enumerate all alignments into an @Class.Align@ object.
-..example.code:
-SimpleScore scoringScheme(2, -1, -1, -2);
-LocalAlignmentEnumerator<SimpleScore, Unbanded> enumerator(scoringScheme, 5);
-
-Dna5String seqH = "CGAGAGAGACCGAGA";
-Dna5String seqV = "TTCTGAGATCCGTTTTT";
-
-Align<Dna5String> align;
-resize(rows(align), 2);
-assignSource(row(align), 0, seqH);
-assignSource(row(align), 1, seqV);
-
-int i = 0;
-while (nextLocalAlignment(align, enumerator))
-{
-    std::cout << i << "-th alignment:\n";
-    std::cout << align << "\n\n";
-    std::cout << "score == " << getScore(enumerator) << "\n";
-}
-..include:seqan/align.h
-
-.Memfunc.Unbanded LocalAlignmentEnumerator#LocalAlignmentEnumerator
-..class:Spec.Unbanded LocalAlignmentEnumerator
-..summary:Constructor
-..signature:LocalAlignmentEnumerator(score, [cutoff])
-..param.score:The scoring scheme to use for the alignments.
-...type:Class.Score
-..param.cutoff:Alignments with scores < $cutoff$ will be discarded.
-...default:0
-...type:nolink:$int$
-
-.Spec.Banded LocalAlignmentEnumerator
-..cat:Alignments
-..general:Class.LocalAlignmentEnumerator
-..signature:LocalAlignmentEnumerator<TScore, Banded>
-..summary:Banded enumeration of local alignments using the Waterman-Eggert algorithm.
-..example.text:Enumerate all alignments in the band between $-3$ and $0$ into an @Class.Align@ object.
-..example.code:
-SimpleScore scoringScheme(2, -1, -1, -2);
-LocalAlignmentEnumerator<SimpleScore, Banded> enumerator(scoringScheme, 5, -3, 0);
-
-Dna5String seqH = "CGAGAGAGACCGAGA";
-Dna5String seqV = "TTCTGAGATCCGTTTTT";
-
-Align<Dna5String> align;
-resize(rows(align), 2);
-assignSource(row(align), 0, seqH);
-assignSource(row(align), 1, seqV);
-
-int i = 0;
-while (nextLocalAlignment(align, enumerator))
-{
-    std::cout << i << "-th alignment:\n";
-    std::cout << align << "\n\n";
-    std::cout << "score == " << getScore(enumerator) << "\n";
-}
-..include:seqan/align.h
-
-.Memfunc.Banded LocalAlignmentEnumerator#LocalAlignmentEnumerator
-..class:Spec.Banded LocalAlignmentEnumerator
-..summary:Constructor
-..signature:LocalAlignmentEnumerator(score, upperDiag, lowerDiag, [cutoff])
-..param.score:The scoring scheme to use for the alignments.
-...type:Class.Score
-..param.upperDiag:Upper diagonal of the band.
-...type:nolink:$int$
-..param.lowerDiag:Lower diagonal of the band.
-...type:nolink:$int$
-..param.cutoff:Alignments with scores < $cutoff$ will be discarded.
-...type:nolink:$int$
-...default:0
-*/
-
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -279,22 +188,9 @@ while (nextLocalAlignment(align, enumerator))
  *
  * @signature TScoreVal getScore(enumerator);
  *
- * @param enumerator The LocalAlignmentEnumerator to query.
- * 
- * @return TScoreVal The current alignment score.
- */
-
-/**
-.Function.LocalAlignmentEnumerator#getScore
-..cat:Alignments
-..summary:Compute next suboptimal local alignment.
-..signature:getScore(enumerator)
-..param.enumerator:The local alignment enumerator to use.
-...type:Class.LocalAlignmentEnumerator
-..returns:
-The score of the previously computed alignment.
-(Type: @Metafunction.Value@ of $enumerator$'s class.)
-..include:seqan/align.h
+ * @param[in] enumerator The LocalAlignmentEnumerator to query.
+ *
+ * @return TScoreVal The current alignment score (@link Score#Value @endlink of <tt>TScore</tt>).
  */
 
 // ----------------------------------------------------------------------------
@@ -309,34 +205,15 @@ The score of the previously computed alignment.
  * @signature bool nextLocalAlignment(align,        enumerator);
  * @signature bool nextLocalAlignment(gapsH, gapsV, enumerator);
  *
- * @param align      @link Align @endlink object to use for the alignment representation.
- * @param gapsH      @link Gaps @endlink object to use for the first/horizontal sequence in the alignment matrix.
- * @param gapsV      @link Gaps @endlink object to use for the second/vertical sequence in the alignment matrix.
- * @param enumerator The LocalAlignmentEnumerator to advance.
- * 
+ * @param[in] align      @link Align @endlink object to use for the alignment representation.
+ * @param[in] gapsH      @link Gaps @endlink object to use for the first/horizontal sequence in the alignment matrix.
+ * @param[in] gapsV      @link Gaps @endlink object to use for the second/vertical sequence in the alignment matrix.
+ * @param[in] enumerator The LocalAlignmentEnumerator to advance.
+ *
  * @return bool <tt>true</tt> if another suboptimal alignment above the given threshold was found and <tt> false
  *              otherwise.
  */
 
-/**
-.Function.nextLocalAlignment
-..cat:Alignments
-..summary:Compute next suboptimal local alignment.
-..signature:nextLocalAlignment(align,        enumerator)
-..signature:nextLocalAlignment(gapsH, gapsV, enumerator)
-..param.align:The @Class.Align@ object to use for the alignment representation.
-...type:Class.Align
-..param.gapsH:The @Class.Gaps@ object to use for the horizontal sequence in the alignment matrix.
-...type:Class.Gaps
-..param.gapsV:The @Class.Gaps@ object to use for the vertical sequence in the alignment matrix.
-...type:Class.Gaps
-..param.enumerator:The @Class.LocalAlignmentEnumerator@ object to use.
-...type:Class.LocalAlignmentEnumerator
-..returns:$true$ if another suboptimal alignment above the given threshold was found, $false$ otherwise.
-...type:nolink:$bool$
-..include:seqan/align.h
-*/
-
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_
diff --git a/seqan/align/local_alignment_enumeration_banded.h b/seqan/align/local_alignment_enumeration_banded.h
index 2d50d72..d8a5828 100644
--- a/seqan/align/local_alignment_enumeration_banded.h
+++ b/seqan/align/local_alignment_enumeration_banded.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_
 
 namespace seqan {
 
@@ -57,13 +57,13 @@ class LocalAlignmentEnumerator<TScore, Banded>
 {
 public:
     typedef typename Value<TScore>::Type TScoreValue_;
-    
+
     TScore _score;
     int _lowerDiag;
     int _upperDiag;
     TScoreValue_ _cutoff;
     LocalAlignmentFinder<TScoreValue_> _finder;
-    
+
     LocalAlignmentEnumerator(TScore const & score, int lowerDiag, int upperDiag) :
             _score(score), _lowerDiag(lowerDiag), _upperDiag(upperDiag), _cutoff(0)
     {}
@@ -123,4 +123,4 @@ nextLocalAlignment(Align<TSequence, TAlignSpec> & align,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_
diff --git a/seqan/align/local_alignment_enumeration_unbanded.h b/seqan/align/local_alignment_enumeration_unbanded.h
index 35914ea..4df4a2b 100644
--- a/seqan/align/local_alignment_enumeration_unbanded.h
+++ b/seqan/align/local_alignment_enumeration_unbanded.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_
 
 namespace seqan {
 
@@ -57,11 +57,11 @@ class LocalAlignmentEnumerator<TScore, Unbanded>
 {
 public:
     typedef typename Value<TScore>::Type TScoreValue_;
-    
+
     TScore _scoringScheme;
     TScoreValue_ _cutoff;
     LocalAlignmentFinder<TScoreValue_> _finder;
-    
+
     LocalAlignmentEnumerator(TScore const & score) :
             _scoringScheme(score), _cutoff(0)
     {}
@@ -119,4 +119,4 @@ nextLocalAlignment(Align<TSequence, TAlignSpec> & align,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_
diff --git a/seqan/align/local_alignment_unbanded.h b/seqan/align/local_alignment_unbanded.h
index f560b1c..fe13192 100644
--- a/seqan/align/local_alignment_unbanded.h
+++ b/seqan/align/local_alignment_unbanded.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Interface functions for unbanded local alignment.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
 
 namespace seqan {
 
@@ -63,43 +63,40 @@ namespace seqan {
  * @fn localAlignment
  * @headerfile <seqan/align.h>
  * @brief Computes the best pairwise local alignment using the Smith-Waterman algorithm.
- * 
+ *
  * @signature TScoreVal localAlignment(align,          scoringScheme, [lowerDiag, upperDiag]);
  * @signature TScoreVal localAlignment(gapsH, gapsV,   scoringScheme, [lowerDiag, upperDiag]);
  * @signature TScoreVal localAlignment(fragmentString, scoringScheme, [lowerDiag, upperDiag]);
- * 
- * @param lowerDiag Optional lower diagonal (<tt>int</tt>).
- * @param lowerDiag Optional upper diagonal (<tt>int</tt>).
  *
- * @param gapsH Horizontal gapped sequence in alignment matrix. Types: Gaps
- * @param align An @link Align @endlink object that stores the alignment. The
- *              number of rows must be 2 and the sequences must have already
- *              been set. <tt>align[0]</tt> is the horizontal one in the
- *              alignment matrix alignment, <tt>align[1]</tt> is the vertical
- *              one. Types: Align
- * @param fragmentString String of @link Fragment @endlink objects. The sequence
- *                       with id <tt>0</tt> is the horizontal one, the sequence
- *                       with id <tt>1</tt> is the vertical one.
- * @param gapsV Vertical gapped sequence in alignment matrix. Types: Gaps
- * @param scoringScheme The scoring scheme to use for the alignment. Note that
- *                      the user is responsible for ensuring that the scoring
- *                      scheme is compatible with <tt>algorithmTag</tt>. Types:
- *                      Score
- * 
- * @return TScoreVal The score value of the alignmetn.
- * 
- * @section Remarks
- * 
+ * @param[in,out] gapsH Horizontal gapped sequence in alignment matrix. Types: @link Gaps @endlink
+ * @param[in,out] gapsV Vertical gapped sequence in alignment matrix. Types: @link Gaps @endlink
+ * @param[in,out] align An @link Align @endlink object that stores the alignment. The
+ *                      number of rows must be 2 and the sequences must have already
+ *                      been set. <tt>align[0]</tt> is the horizontal one in the
+ *                      alignment matrix alignment, <tt>align[1]</tt> is the vertical
+ *                      one.
+ * @param[in,out] fragmentString
+ *                      String of @link Fragment @endlink objects. The sequence
+ *                      with id <tt>0</tt> is the horizontal one, the sequence
+ *                      with id <tt>1</tt> is the vertical one.
+ * @param[in] scoringScheme
+ *                      The @link Score scoring scheme @endlink to use for the alignment.
+ * @param[in] lowerDiag Optional lower diagonal (<tt>int</tt>).
+ * @param[in] upperDiag Optional upper diagonal (<tt>int</tt>).
+ *
+ * @return TScoreVal Score value of the resulting alignment  (Metafunction @link Score#Value @endlink of the type of
+ *                   <tt>scoringScheme</tt>).
+ *
  * The Waterman-Eggert algorithm (local alignment with declumping) is available through the @link
  * LocalAlignmentEnumerator @endlink class.
- * 
+ *
  * When using @link Gaps @endlink and @link Align @endlink objects, only parts (i.e. one infix) of each sequence will be
  * aligned.  This will be presented to the user by setting the clipping begin and end position of the gaps (the rows in
  * the case of @link Align @endlink objects).  When using @link Fragment @endlink strings, these parts of the sequences
  * will not appear in any fragment.
- * 
+ *
  * There exist multiple overloads for this function with two configuration dimensions.
- * 
+ *
  * First, you can select the type of the target storing the alignment. This can be either an @link Align @endlink
  * object, two @link Gaps @endlink objects, or a string of @link Fragment @endlink objects. @link Align @endlink objects
  * provide an interface to tabular alignments with the restriction of all rows having the same type. Using two @link
@@ -107,45 +104,45 @@ namespace seqan {
  * @endlink and @link Dna5String @endlink. Using @link Fragment @endlink strings is useful for collecting many pairwise
  * alignments, for example in the construction of @link AlignmentGraph Alignment Graphs @endlink for multiple- sequence
  * alignments (MSA).
- * 
+ *
  * Second, you can optionally give a band for the alignment using <tt>lowerDiag</tt> and <tt>upperDiag</tt>. The center
  * diagonal has index <tt>0</tt>, the <tt>i</tt>th diagonal below has index <tt>-i</tt>, the <tt>i</tt>th above has
  * index <tt>i</tt>.
- * 
+ *
  * The examples below show some common use cases.
- * 
+ *
  * @section Examples
- * 
+ *
  * Local alignment of two sequences using an @link Align @endlink object.
- * 
+ *
  * @code{.cpp}
  * Dna5String seqH = "CGATT";
  * Dna5String seqV = "CGAAATT";
- *  
+ *
  * Align<Dna5String> align;
  * resize(rows(align), 2);
  * assignSource(row(align, 0), seqH);
  * assignSource(row(align, 0), seqV);
  * Score<int, Simple> scoringScheme(2, -1, -2);
- *  
+ *
  * int result = localAlignment(align, scoringScheme);
  * @endcode
  *
  * Local banded alignment of two sequences using two @link Gaps @endlink objects.
- * 
+ *
  * @code{.cpp}
  * Dna5String seqH = "CGATT";
  * Gaps<Dna5String, ArrayGaps> gapsH(seqH);
  * DnaString seqV = "CGAAATT";
  * Gaps<Dna5String, AnchorGaps<> > gapsV(seqV);
- *  
+ *
  * Score<int, Simple> scoringScheme(5, -3, -1, -5);
- *  
+ *
  * int result = localAlignment(gapsH, gapsV, scoringScheme, -2, 2);
  * @endcode
  *
- * http://trac.seqan.de/wiki/Tutorial/PairwiseSequenceAlignment
- * 
+ * http://seqan.readthedocs.org/en/develop/Tutorial/PairwiseSequenceAlignment.html
+ *
  * @section References
  *
  * <ul>
@@ -157,124 +154,78 @@ namespace seqan {
  * @see PairwiseLocalAlignmentAlgorithms
  */
 
-/**
-.Function.localAlignment
-..summary:Computes the best pairwise local alignment using the Smith-Waterman algorithm.
-..cat:Alignments
-..signature:localAlignment(align,          scoringScheme, [lowerDiag, upperDiag])
-..signature:localAlignment(gapsH, gapsV,   scoringScheme, [lowerDiag, upperDiag])
-..signature:localAlignment(fragmentString, scoringScheme, [lowerDiag, upperDiag])
-..param.align:
-An @Class.Align@ object that stores the alignment.
-The number of rows must be 2 and the sequences must have already been set.
-$align[0]$ is the horizontal one in the alignment matrix alignment, $align[1]$ is the vertical one.
-...type:Class.Align
-..param.gapsH:Horizontal gapped sequence in alignment matrix.
-...type:Class.Gaps
-..param.gapsV:Vertical gapped sequence in alignment matrix.
-...type:Class.Gaps
-..param.fragmentString:
-String of @Class.Fragment@ objects.
-The sequence with id $0$ is the horizontal one, the sequence with id $1$ is the vertical one.
-..param.scoringScheme:
-The scoring scheme to use for the alignment.
-Note that the user is responsible for ensuring that the scoring scheme is compatible with $algorithmTag$.
-...type:Class.Score
-..param.lowerDiag:Optional lower diagonal.
-...type:nolink:$int$
-..param.upperDiag:Optional upper diagonal.
-...type:nolink:$int$
-..returns:An integer with the alignment score, as given by the @Metafunction.Value@ metafunction of the @Class.Score@ type.
-..remarks:The Waterman-Eggert algorithm (local alignment with declumping) is available through the @Class.LocalAlignmentEnumerator@ class.
-..remarks:
-When using @Class.Gaps@ and @Class.Align@ objects, only parts (i.e. one infix) of each sequence will be aligned.
-This will be presented to the user by setting the clipping begin and end position of the gaps (the rows in the case of @Class.Align@ objects).
-When using @Class.Fragment@ strings, these parts of the sequences will not appear in any fragment.
-..remarks:
-There exist multiple overloads for this function with two configuration dimensions.
-..remarks:
-First, you can select the type of the target storing the alignment.
-This can be either an @Class.Align@ object, two @Class.Gaps@ objects, or a string of @Class.Fragment@ objects.
-@Class.Align@ objects provide an interface to tabular alignments with the restriction of all rows having the same type.
-Using two @Class.Gaps@ objects has the advantage that you an align sequences with different types, for example @Shortcut.DnaString@ and @Shortcut.Dna5String@.
-Using @Class.Fragment@ strings is useful for collecting many pairwise alignments, for example in the construction of @Spec.Alignment Graph|Alignment Graphs@ for multiple-sequence alignments (MSA).
-..remarks:
-Second, you can optionally give a band for the alignment using $lowerDiag$ and $upperDiag$.
-The center diagonal has index $0$, the $i$th diagonal below has index $-i$, the $i$th above has index $i$.
-..remarks:
-The examples below show some common use cases.
-..example.text:Local alignment of two sequences using an @Class.Align@ object.
-..example.code:
-Dna5String seqH = "CGATT";
-Dna5String seqV = "CGAAATT";
-
-Align<Dna5String> align;
-resize(rows(align), 2);
-assignSource(row(align, 0), seqH);
-assignSource(row(align, 0), seqV);
-Score<int, Simple> scoringScheme(2, -1, -2);
-
-int result = localAlignment(align, scoringScheme);
-..example.text:Local banded alignment of two sequences using two @Class.Gaps@ objects.
-..example.code:
-Dna5String seqH = "CGATT";
-Gaps<Dna5String, ArrayGaps> gapsH(seqH);
-DnaString seqV = "CGAAATT";
-Gaps<Dna5String, AnchorGaps<> > gapsV(seqV);
-
-Score<int, Simple> scoringScheme(5, -3, -1, -5);
-
-int result = localAlignment(gapsH, gapsV, scoringScheme, -2, 2);
-..see:Function.globalAlignment
-..see:Class.LocalAlignmentEnumerator
-..include:seqan/align.h
-..wiki:Tutorial/PairwiseSequenceAlignment
-..cite:Smith TF, Waterman, MS: Identification of Common Molecular Subsequences. J Mol Biol 1981, 147(1):195-7.
-.
-*/
-
 // ----------------------------------------------------------------------------
 // Function localAlignment()                                  [unbanded, Align]
 // ----------------------------------------------------------------------------
 
-template <typename TSequence, typename TAlignSpec,
-          typename TScoreValue, typename TScoreSpec>
+template <typename TSequence, typename TAlignSpec, typename TScoreValue, typename TScoreSpec, typename TTag>
 TScoreValue localAlignment(Align<TSequence, TAlignSpec> & align,
-                           Score<TScoreValue, TScoreSpec> const & scoringScheme)
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                           TTag const & tag)
 {
     SEQAN_ASSERT_EQ(length(rows(align)), 2u);
     typedef Align<TSequence, TAlignSpec> TAlign;
     typedef typename Size<TAlign>::Type TSize;
     typedef typename Position<TAlign>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig2<DPLocal, DPBandConfig<BandOff>, FreeEndGaps_<> > TAlignConfig2;
+
+    String<TTraceSegment> trace;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)),
+                                            scoringScheme, TAlignConfig2(), tag);
 
-    String<TTraceSegment> traceSegments;
-    TScoreValue score = _setUpAndRunAlignment(traceSegments, source(row(align, 0)), source(row(align, 1)),
-                                              scoringScheme, SmithWaterman());
-    _adaptTraceSegmentsTo(row(align, 0), row(align, 1), traceSegments);
-    return score;
+    _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace);
+    return res;
 }
 
+ template <typename TSequence, typename TAlignSpec,
+           typename TScoreValue, typename TScoreSpec>
+ TScoreValue localAlignment(Align<TSequence, TAlignSpec> & align,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme)
+ {
+     SEQAN_ASSERT(length(rows(align)) == 2u);
+     if (_usesAffineGaps(scoringScheme, source(row(align, 0)), source(row(align, 1))))
+         return localAlignment(align, scoringScheme, AffineGaps());
+     else
+         return localAlignment(align, scoringScheme, LinearGaps());
+ }
+
 // ----------------------------------------------------------------------------
 // Function localAlignment()                                   [unbanded, Gaps]
 // ----------------------------------------------------------------------------
 
-template <typename TSequenceH, typename TGapsSpecH,
+ template <typename TSequenceH, typename TGapsSpecH, typename TSequenceV, typename TGapsSpecV, typename TScoreValue,
+           typename TScoreSpec, typename TTag>
+ TScoreValue localAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
+                            Gaps<TSequenceV, TGapsSpecV> & gapsV,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                            TTag const & tag)
+ {
+     typedef typename Size<TSequenceH>::Type TSize;
+     typedef typename Position<TSequenceH>::Type TPosition;
+     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+     typedef AlignConfig2<DPLocal, DPBandConfig<BandOff>, FreeEndGaps_<> > TAlignConfig2;
+
+     String<TTraceSegment> trace;
+     DPScoutState_<Default> dpScoutState;
+     TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme,
+                                             TAlignConfig2(), tag);
+     _adaptTraceSegmentsTo(gapsH, gapsV, trace);
+     return res;
+ }
+
+ template <typename TSequenceH, typename TGapsSpecH,
           typename TSequenceV, typename TGapsSpecV,
           typename TScoreValue, typename TScoreSpec>
 TScoreValue localAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                            Gaps<TSequenceV, TGapsSpecV> & gapsV,
                            Score<TScoreValue, TScoreSpec> const & scoringScheme)
 {
-    typedef typename Size<TSequenceH>::Type TSize;
-    typedef typename Position<TSequenceH>::Type TPosition;
-    typedef TraceSegment_<TPosition, TSize> TTraceSegment;
-
-    String<TTraceSegment> traceSegments;
-    TScoreValue score = _setUpAndRunAlignment(traceSegments, source(gapsH), source(gapsV), scoringScheme,
-                                              SmithWaterman());
-    _adaptTraceSegmentsTo(gapsH, gapsV, traceSegments);
-    return score;
+     if (_usesAffineGaps(scoringScheme, source(gapsH), source(gapsV)))
+         return localAlignment(gapsH, gapsV, scoringScheme, AffineGaps());
+     else
+         return localAlignment(gapsH, gapsV, scoringScheme, LinearGaps());
 }
 
 // ----------------------------------------------------------------------------
@@ -284,21 +235,38 @@ TScoreValue localAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
 // Full interface.
 
 template <typename TStringSet, typename TCargo, typename TGraphSpec,
-          typename TScoreValue, typename TScoreSpec>
+          typename TScoreValue, typename TScoreSpec, typename TTag>
 TScoreValue localAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
-                           Score<TScoreValue, TScoreSpec> const & scoringScheme)
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                           TTag const & tag)
 {
     typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
     typedef typename Size<TGraph>::Type TSize;
     typedef typename Position<TGraph>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig2<DPLocal, DPBandConfig<BandOff>, FreeEndGaps_<> > TAlignConfig2;
+
+    String<TTraceSegment> trace;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0),
+                                            value(stringSet(alignmentGraph), 1), scoringScheme, TAlignConfig2(), tag);
 
-    String<TTraceSegment> traceSegments;
-    TScoreValue score = _setUpAndRunAlignment(traceSegments, value(stringSet(alignmentGraph), 0),
-                                              value(stringSet(alignmentGraph), 1), scoringScheme, SmithWaterman());
     _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0),
-                          positionToId(stringSet(alignmentGraph), 1), traceSegments);
-    return score;
+                          positionToId(stringSet(alignmentGraph), 1), trace);
+    return res;
+}
+
+template <typename TStringSet, typename TCargo, typename TGraphSpec,
+          typename TScoreValue, typename TScoreSpec>
+TScoreValue localAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme)
+{
+    SEQAN_ASSERT(length(stringSet(alignmentGraph)) == 2u);
+
+    if (_usesAffineGaps(scoringScheme, stringSet(alignmentGraph)[0], stringSet(alignmentGraph)[1]))
+        return localAlignment(alignmentGraph, scoringScheme, AffineGaps());
+    else
+        return localAlignment(alignmentGraph, scoringScheme, LinearGaps());
 }
 
 // ----------------------------------------------------------------------------
@@ -309,22 +277,41 @@ TScoreValue localAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & a
 
 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
           typename TSequence, typename TStringSetSpec,
-          typename TScoreValue, typename TScoreSpec>
+          typename TScoreValue, typename TScoreSpec, typename TTag>
 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
                            StringSet<TSequence, TStringSetSpec> const & strings,
-                           Score<TScoreValue, TScoreSpec> const & scoringScheme)
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                           TTag const & tag)
 {
     typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments;
     typedef typename Position<TFragments>::Type TPosition;
     typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig2<DPLocal, DPBandConfig<BandOff>, FreeEndGaps_<> > TAlignConfig2;
+
+    String<TTraceSegment> trace;
+    DPScoutState_<Default> dpScoutState;
+    TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme,
+                                            TAlignConfig2(), tag);
+
+    _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace);
+    return res;
+}
+
+template <typename TSize, typename TFragmentSpec, typename TStringSpec,
+          typename TSequence, typename TStringSetSpec,
+          typename TScoreValue, typename TScoreSpec>
+TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
+                           StringSet<TSequence, TStringSetSpec> const & strings,
+                           Score<TScoreValue, TScoreSpec> const & scoringScheme)
+{
+    SEQAN_ASSERT(length(strings) == 2u);
 
-    String<TTraceSegment> traceSegments;
-    TScoreValue score = _setUpAndRunAlignment(traceSegments, value(strings, 0), value(strings, 1), scoringScheme,
-                                              SmithWaterman());
-    _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), traceSegments);
-    return score;
+    if (_usesAffineGaps(scoringScheme, strings[0], strings[1]))
+        return localAlignment(fragmentString, strings, scoringScheme, AffineGaps());
+    else
+        return localAlignment(fragmentString, strings, scoringScheme, LinearGaps());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
diff --git a/seqan/align/local_alignment_waterman_eggert_impl.h b/seqan/align/local_alignment_waterman_eggert_impl.h
index 5723c54..a4d554f 100644
--- a/seqan/align/local_alignment_waterman_eggert_impl.h
+++ b/seqan/align/local_alignment_waterman_eggert_impl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 // Smith-Waterman algorithm with declumping.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_
 
 namespace seqan {
 
@@ -58,20 +58,20 @@ namespace seqan {
 
 // Simple class that stores a value with an ID.
 template <typename TValue, typename TID>
-class ScoreAndID 
+class ScoreAndID
 {
 public:
-	TValue value_;
-	TID id_;
+    TValue value_;
+    TID id_;
 
-	ScoreAndID() : value_(MinValue<TValue>::VALUE), id_(MaxValue<TValue>::VALUE)
-	{}
+    ScoreAndID() : value_(MinValue<TValue>::VALUE), id_(MaxValue<TValue>::VALUE)
+    {}
 
-	ScoreAndID(TValue score, TID id_pos)
-	{
-		value_ = score;
-		id_ = id_pos;
-	}
+    ScoreAndID(TValue score, TID id_pos)
+    {
+        value_ = score;
+        id_ = id_pos;
+    }
 
     inline bool operator>(ScoreAndID const & other) const
     {
@@ -82,64 +82,47 @@ class ScoreAndID
     {
         return value_ < other.value_;
     }
-}; 
+};
 
 // ----------------------------------------------------------------------------
 // Class LocalAlignmentFinder
 // ----------------------------------------------------------------------------
 
-/**
-.Class.LocalAlignmentFinder:
-..cat:Miscellaneous
-..summary:Stores the information necessary for local alignment dynamic programming.
-..signature:LocalAlignmentFinder<TScoreValue>
-..param.TScoreValue:The value type that is used for scoring the alignments.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..see:Function.localAlignment
-.Memfunc.LocalAlignmentFinder#LocalAlignmentFinder
-..class:Class.LocalAlignmentFinder
-..summary:Constructor
-..signature:LocalAlignmentFinder(align)
-..param.align:An @Class.Align@ object that is already initialized with the sequences.
-..include:seqan/align.h
-*/
-
 template <typename TScoreValue = int>
 class LocalAlignmentFinder
 {
 public:
-	typedef Matrix<TScoreValue> TMatrix;
-	typedef typename Position<TMatrix>::Type TMatrixPosition;
+    typedef Matrix<TScoreValue> TMatrix;
+    typedef typename Position<TMatrix>::Type TMatrixPosition;
     typedef typename Size<TMatrix>::Type TSize;
-	typedef ScoreAndID<TScoreValue,TMatrixPosition> TPQEntry;
-
-	typedef Iter<TMatrix,PositionIterator> TMatrixIterator;
-	typedef PriorityType<TPQEntry> TPriorityQ;
-	typedef String<bool> TBoolMatrix;
-	
-	//DP-matrix
-	TMatrix matrix;
-	//matrix that memorizes the cells from which not to go diagonal
-	TBoolMatrix forbidden;
-	//priority queue for quickly finding the maximum score in the DP-matrix
-	TPriorityQ pQ;
-	//position of maximum score (where traceback is started from) 
-	TMatrixPosition bestEndPos;
-	//position where traceback ended and where declumping begins
-	TMatrixPosition bestBeginPos;
+    typedef ScoreAndID<TScoreValue,TMatrixPosition> TPQEntry;
+
+    typedef Iter<TMatrix,PositionIterator> TMatrixIterator;
+    typedef PriorityType<TPQEntry> TPriorityQ;
+    typedef String<bool> TBoolMatrix;
+
+    //DP-matrix
+    TMatrix matrix;
+    //matrix that memorizes the cells from which not to go diagonal
+    TBoolMatrix forbidden;
+    //priority queue for quickly finding the maximum score in the DP-matrix
+    TPriorityQ pQ;
+    //position of maximum score (where traceback is started from)
+    TMatrixPosition bestEndPos;
+    //position where traceback ended and where declumping begins
+    TMatrixPosition bestBeginPos;
     //traceback path that is set to forbidden while declumping
     AlignTraceback<TSize> trace;
 
-	bool needReinit; //true: call "smithWaterman", false: call "smithWatermanGetNext" 
+    bool needReinit; //true: call "smithWaterman", false: call "smithWatermanGetNext"
 
-	LocalAlignmentFinder() : needReinit(true)
-	{}
+    LocalAlignmentFinder() : bestEndPos(0), bestBeginPos(0), needReinit(true)
+    {}
 
     // TODO(holtgrew): Remove and replace all occurrences with default constructor.
     template<typename TAlign>
-	LocalAlignmentFinder(TAlign const &)
-	    : needReinit(true)
-	{}
+    LocalAlignmentFinder(TAlign const &) : bestEndPos(0), bestBeginPos(0), needReinit(true)
+    {}
 };
 
 // ============================================================================
@@ -173,9 +156,9 @@ _initLocalAlignmentFinder(TSequenceH const & seqH,
     resize(finder.matrix);
 
     resize(finder.forbidden, (len0 + 1) * (len1 + 1), false);
- 
-	finder.bestEndPos = maxValue<typename TFinder::TMatrixPosition>();
-	finder.bestBeginPos = maxValue<typename TFinder::TMatrixPosition>();
+
+    finder.bestEndPos = maxValue<typename TFinder::TMatrixPosition>();
+    finder.bestBeginPos = maxValue<typename TFinder::TMatrixPosition>();
 }
 
 // ----------------------------------------------------------------------------
@@ -185,7 +168,7 @@ _initLocalAlignmentFinder(TSequenceH const & seqH,
 template <typename TScoreValue>
 void clear(LocalAlignmentFinder<TScoreValue> & sw_finder)
 {
-	sw_finder.needReinit = true;
+    sw_finder.needReinit = true;
 }
 
 // ----------------------------------------------------------------------------
@@ -195,10 +178,10 @@ void clear(LocalAlignmentFinder<TScoreValue> & sw_finder)
 template <typename TScoreValue>
 TScoreValue getScore(LocalAlignmentFinder<TScoreValue> const & sw)
 {
-	typedef LocalAlignmentFinder<TScoreValue> TFinder;
-	if(sw.bestEndPos !=  maxValue<typename TFinder::TMatrixPosition>())
-		return getValue(const_cast<typename TFinder::TMatrix &>(sw.matrix), sw.bestEndPos);
-	return 0;
+    typedef LocalAlignmentFinder<TScoreValue> TFinder;
+    if(sw.bestEndPos !=  maxValue<typename TFinder::TMatrixPosition>())
+        return getValue(const_cast<typename TFinder::TMatrix &>(sw.matrix), sw.bestEndPos);
+    return 0;
 }
 
 // ----------------------------------------------------------------------------
@@ -213,106 +196,106 @@ _smithWatermanGetMatrix(LocalAlignmentFinder<TScoreValue> & sw,
                         Score<TScoreValue, Simple> const & score_,
                         TScoreValue cutoff)
 {
-	// typedefs
-	typedef Matrix<TScoreValue> TMatrix;
-	typedef typename Position<TMatrix>::Type TMatrixPosition;
-	typedef Iter<TMatrix,PositionIterator> TMatrixIterator;
-
-	typedef typename Iterator<TStringH const, Rooted>::Type TStringIteratorH;
-	//typedef typename Value<TStringH const>::Type TValueH;
-	typedef typename Iterator<TStringV const, Rooted>::Type TStringIteratorV;
-	typedef typename Value<TStringV const>::Type TValueV;
-
-	//-------------------------------------------------------------------------
-	//define some variables
-
-
-//	TSize str1_length = length(strH);
-//	TSize str2_length = length(strV);
-	TStringIteratorH x_begin = begin(strH) - 1;
-	TStringIteratorH x_end = end(strH) - 1;
-	TStringIteratorV y_begin = begin(strV) - 1;
-	TStringIteratorV y_end = end(strV) - 1;
-
-	TStringIteratorH x = x_end;
-	TStringIteratorV y;
-
-	TScoreValue score_match = scoreMatch(score_);
-	TScoreValue score_mismatch = scoreMismatch(score_);
-	TScoreValue score_gap = scoreGapExtend(score_);
-
-	TScoreValue h = 0;
-	TScoreValue v = 0;
-
-	TMatrixIterator col_ = end(sw.matrix) - 1;
-	TMatrixIterator finger1;
-	TMatrixIterator finger2;
-
-	//-------------------------------------------------------------------------
-	// init
-
-	finger1 = col_;
-	*finger1 = 0;
-	//std::cout <<"  ";
-	for (x = x_end; x != x_begin; --x)
-	{
-		goPrevious(finger1, 0);
-		*finger1 = 0;
-	}
-
-	//-------------------------------------------------------------------------
-	//fill matrix
-	for (y = y_end; y != y_begin; --y)
-	{
-		TValueV cy = *y;
-
-		h = 0;
-		v = 0;
-
-		finger2 = col_;		//points to last column
-		goPrevious(col_, 1);	//points to this column
-		finger1 = col_;
-
-		*finger1 = v;
-
-		for (x = x_end; x != x_begin; --x)
-		{
-			goPrevious(finger1, 0);
-			goPrevious(finger2, 0);
-			
-			if (*x == cy)
-			{
-				v = h + score_match;
-				h = *finger2;
-			}
-			else
-			{
-				TScoreValue s1 = h + score_mismatch;
-				h = *finger2;
-				TScoreValue s2 = score_gap + ((h > v) ? h : v);
-				v = (s1 > s2) ? s1 : s2;
-				if (v < 0) v = 0;
-			
-			}
-			*finger1 = v;
-			if (v >= cutoff)
-			{
-				push(sw.pQ,ScoreAndID<TScoreValue,TMatrixPosition>(v,position(finger1)));
-			}
-		}
-	}
-
-	// check if any scores >= cutoff were found
-	if(!empty(sw.pQ))
-	{
+    // typedefs
+    typedef Matrix<TScoreValue> TMatrix;
+    typedef typename Position<TMatrix>::Type TMatrixPosition;
+    typedef Iter<TMatrix,PositionIterator> TMatrixIterator;
+
+    typedef typename Iterator<TStringH const, Rooted>::Type TStringIteratorH;
+    //typedef typename Value<TStringH const>::Type TValueH;
+    typedef typename Iterator<TStringV const, Rooted>::Type TStringIteratorV;
+    typedef typename Value<TStringV const>::Type TValueV;
+
+    //-------------------------------------------------------------------------
+    //define some variables
+
+
+//    TSize str1_length = length(strH);
+//    TSize str2_length = length(strV);
+    TStringIteratorH x_begin = begin(strH) - 1;
+    TStringIteratorH x_end = end(strH) - 1;
+    TStringIteratorV y_begin = begin(strV) - 1;
+    TStringIteratorV y_end = end(strV) - 1;
+
+    TStringIteratorH x = x_end;
+    TStringIteratorV y;
+
+    TScoreValue score_match = scoreMatch(score_);
+    TScoreValue score_mismatch = scoreMismatch(score_);
+    TScoreValue score_gap = scoreGapExtend(score_);
+
+    TScoreValue h = 0;
+    TScoreValue v = 0;
+
+    TMatrixIterator col_ = end(sw.matrix) - 1;
+    TMatrixIterator finger1;
+    TMatrixIterator finger2;
+
+    //-------------------------------------------------------------------------
+    // init
+
+    finger1 = col_;
+    *finger1 = 0;
+    //std::cout <<"  ";
+    for (x = x_end; x != x_begin; --x)
+    {
+        goPrevious(finger1, 0);
+        *finger1 = 0;
+    }
+
+    //-------------------------------------------------------------------------
+    //fill matrix
+    for (y = y_end; y != y_begin; --y)
+    {
+        TValueV cy = *y;
+
+        h = 0;
+        v = 0;
+
+        finger2 = col_;        //points to last column
+        goPrevious(col_, 1);    //points to this column
+        finger1 = col_;
+
+        *finger1 = v;
+
+        for (x = x_end; x != x_begin; --x)
+        {
+            goPrevious(finger1, 0);
+            goPrevious(finger2, 0);
+
+            if (*x == cy)
+            {
+                v = h + score_match;
+                h = *finger2;
+            }
+            else
+            {
+                TScoreValue s1 = h + score_mismatch;
+                h = *finger2;
+                TScoreValue s2 = score_gap + ((h > v) ? h : v);
+                v = (s1 > s2) ? s1 : s2;
+                if (v < 0) v = 0;
+
+            }
+            *finger1 = v;
+            if (v >= cutoff)
+            {
+                push(sw.pQ,ScoreAndID<TScoreValue,TMatrixPosition>(v,position(finger1)));
+            }
+        }
+    }
+
+    // check if any scores >= cutoff were found
+    if(!empty(sw.pQ))
+    {
         ScoreAndID<TScoreValue,TMatrixPosition> best = top(sw.pQ);
-		v = getValue(sw.matrix,best.id_);
-		sw.bestEndPos = best.id_;
-	}
-	else 
-		v=0;
+        v = getValue(sw.matrix,best.id_);
+        sw.bestEndPos = best.id_;
+    }
+    else
+        v=0;
 
-	return v;
+    return v;
 }
 
 // ----------------------------------------------------------------------------
@@ -329,9 +312,9 @@ _smithWatermanDeclump(LocalAlignmentFinder<TScoreValue> & sw ,
 {
 //-------------------------------------------------------------------------
 //typedefs
-	//typedef typename LocalAlignmentFinder<TScoreValue>::TMatrixPosition TMatrixPosition;
+    //typedef typename LocalAlignmentFinder<TScoreValue>::TMatrixPosition TMatrixPosition;
     typedef typename LocalAlignmentFinder<TScoreValue>::TMatrix         TMatrix;
-	typedef Iter<TMatrix, PositionIterator>                             TMatrixIterator;
+    typedef Iter<TMatrix, PositionIterator>                             TMatrixIterator;
 
     typedef Gaps<TSequenceH, TGapsSpecH>                TGapsH;
     typedef typename Iterator<TGapsH, Rooted>::Type     TGapsHIter;
@@ -345,193 +328,193 @@ _smithWatermanDeclump(LocalAlignmentFinder<TScoreValue> & sw ,
 
 //-------------------------------------------------------------------------
 //variables
-	// TRow row0 = row(align_,0);
-	// TRow row1 = row(align_,1);
+    // TRow row0 = row(align_,0);
+    // TRow row1 = row(align_,1);
 
     // beginPosition == # leading gaps
     // endPosition == length of clipped region without trailing gaps
     // clippedEndPosition == source position of clipping end.
 
-	// TAlignIterator ali_it0_stop = iter(row0,beginPosition(row0));
-	// TAlignIterator ali_it1_stop = iter(row1,beginPosition(row1));
-	TGapsHIter ali_it0_stop = begin(gapsH);
-	TGapsVIter ali_it1_stop = begin(gapsV);
-
-	// SEQAN_ASSERT( endPosition(row0)- beginPosition(row0) == endPosition(row1)- beginPosition(row1) );
-
-	// TAlignIterator ali_it0 = iter(row0,endPosition(row0));
-	// TAlignIterator ali_it1 = iter(row1,endPosition(row1));
-	TGapsHIter ali_it0 = end(gapsH);
-	TGapsVIter ali_it1 = end(gapsV);
-
-	// TStringIterator x_begin = begin(source(row0))-1; 
-	// TStringIterator y_begin = begin(source(row1))-1; 
-	// TStringIterator x_end = iter(source(row0),clippedEndPosition(row0))-1;
-	// TStringIterator y_end = iter(source(row1),clippedEndPosition(row1))-1;
-	TSequenceHIter x_begin = begin(source(gapsH))-1; 
-	TSequenceVIter y_begin = begin(source(gapsV))-1; 
-	TSequenceHIter x_end = iter(source(gapsH), endPosition(gapsH) - 1);
-	TSequenceVIter y_end = iter(source(gapsV), endPosition(gapsV) - 1);
-
-	// TStringIterator x = x_end;
-	// TStringIterator y = y_end;
-	// TStringIterator x_stop = x_end;
-	TSequenceHIter x = x_end;
-	TSequenceVIter y = y_end;
-	TSequenceHIter x_stop = x_end;
-
-
-	TScoreValue score_match = scoreMatch(score_);
-	TScoreValue score_mismatch = scoreMismatch(score_);
-	TScoreValue score_gap = scoreGapExtend(score_);
-	TScoreValue h,v;
-
-	TMatrixIterator finger0 = iter(sw.matrix,sw.bestBeginPos);
-	TMatrixIterator end_col = finger0;
-	TMatrixIterator finger1 = finger0;
-	TMatrixIterator forbidden = finger0;
-
-	bool different = true;
-	bool forbidden_reached = true;
-	bool end_reached = false;
-	bool skip_row = false;
-	
-
-/*	int str0_length = length(source(row(align_,0)))+1;
-	int str1_length = length(source(row(align_,1)))+1;
-	for(int i = 0; i <str1_length; ++i){
- 		for(int j=0;j<str0_length;++j){
- 			std::cout << getValue(sw.matrix,(str0_length*i)+j);
- 			if(sw.forbidden[(str0_length*i)+j]==true)
- 				std::cout <<"(1) ";
- 			else
- 				std::cout <<"(0) ";
- 		}
- 		std::cout <<"\n";
- 	}*/
+    // TAlignIterator ali_it0_stop = iter(row0,beginPosition(row0));
+    // TAlignIterator ali_it1_stop = iter(row1,beginPosition(row1));
+    TGapsHIter ali_it0_stop = begin(gapsH);
+    TGapsVIter ali_it1_stop = begin(gapsV);
+
+    // SEQAN_ASSERT( endPosition(row0)- beginPosition(row0) == endPosition(row1)- beginPosition(row1) );
+
+    // TAlignIterator ali_it0 = iter(row0,endPosition(row0));
+    // TAlignIterator ali_it1 = iter(row1,endPosition(row1));
+    TGapsHIter ali_it0 = end(gapsH);
+    TGapsVIter ali_it1 = end(gapsV);
+
+    // TStringIterator x_begin = begin(source(row0))-1;
+    // TStringIterator y_begin = begin(source(row1))-1;
+    // TStringIterator x_end = iter(source(row0),clippedEndPosition(row0))-1;
+    // TStringIterator y_end = iter(source(row1),clippedEndPosition(row1))-1;
+    TSequenceHIter x_begin = begin(source(gapsH))-1;
+    TSequenceVIter y_begin = begin(source(gapsV))-1;
+    TSequenceHIter x_end = iter(source(gapsH), endPosition(gapsH) - 1);
+    TSequenceVIter y_end = iter(source(gapsV), endPosition(gapsV) - 1);
+
+    // TStringIterator x = x_end;
+    // TStringIterator y = y_end;
+    // TStringIterator x_stop = x_end;
+    TSequenceHIter x = x_end;
+    TSequenceVIter y = y_end;
+    TSequenceHIter x_stop = x_end;
+
+
+    TScoreValue score_match = scoreMatch(score_);
+    TScoreValue score_mismatch = scoreMismatch(score_);
+    TScoreValue score_gap = scoreGapExtend(score_);
+    TScoreValue h,v;
+
+    TMatrixIterator finger0 = iter(sw.matrix,sw.bestBeginPos);
+    TMatrixIterator end_col = finger0;
+    TMatrixIterator finger1 = finger0;
+    TMatrixIterator forbidden = finger0;
+
+    bool different = true;
+    bool forbidden_reached = true;
+    bool end_reached = false;
+    bool skip_row = false;
+
+
+/*    int str0_length = length(source(row(align_,0)))+1;
+    int str1_length = length(source(row(align_,1)))+1;
+    for(int i = 0; i <str1_length; ++i){
+         for(int j=0;j<str0_length;++j){
+             std::cout << getValue(sw.matrix,(str0_length*i)+j);
+             if(sw.forbidden[(str0_length*i)+j]==true)
+                 std::cout <<"(1) ";
+             else
+                 std::cout <<"(0) ";
+         }
+         std::cout <<"\n";
+     }*/
 
     clearClipping(gapsH);
     clearClipping(gapsV);
-	// setClippedBeginPosition(row(align_, 0),0);
-	// setClippedBeginPosition(row(align_, 1),0);
-	
-
-	for (y = y_end; (y != y_begin) ; --y)
-	{
-		different = true;
-		//compute next "forbidden" cell (where you are not allowed to go diagonal)
-		if(forbidden_reached && !end_reached)
-		{
-
-			if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop)
-			{
-				end_reached = true;
-			}
-
-			if(!end_reached)
-			{
-				--ali_it0;
-				goPrevious(forbidden,1);
-				while(isGap(ali_it0)&& ali_it0!=ali_it0_stop)
-				{
-					skip_row = true;			
-					--ali_it0;
-					--ali_it1;
-					goPrevious(forbidden,1);
-				}
-
-				--ali_it1;
-				goPrevious(forbidden,0);
-				while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
-				{
-					--ali_it1;
-					--ali_it0;
-					goPrevious(forbidden,0);
-				}
-				// mark the forbidden cell 
-				sw.forbidden[position(forbidden)]=true;
-				forbidden_reached = false;
-			}
-
-		}
-
-		TValueV cy = *y;
-
-		h = *end_col;
-		
-		finger1 = end_col;		//points to last column
-		goPrevious(end_col, 1);	//points to this column
-		finger0 = end_col;
-
-		v = *finger0;
-		x = x_end;
-
-		// declump the current row until the cells in the declumped and 
-		// the cells in the original matrix are the same (or the border is reached)
-		// indicated by bool different
-		while (x != x_begin && different)
-		{
-			goPrevious(finger0, 0);
-			goPrevious(finger1, 0);
-			if (*x == cy && !(sw.forbidden[position(finger0)]))
-			{
-				v = h + score_match;
-				h = *finger1;
-			}
-			else
-			{
-				TScoreValue s1;
-			
-				if(finger0 == forbidden)
-				{
-						skip_row = false;
-						forbidden_reached = true;
-						s1 = 0;
-				}
-				else
-				{
-					if(sw.forbidden[position(finger0)]) s1 = 0;
-					else s1 = h + score_mismatch;
-				}
-
-				h = *finger1;
-				TScoreValue s2 = score_gap + ((h > v) ? h : v);
-				v = (s1 > s2) ? s1 : s2;
-				if (v < 0) v = 0;
-			
-			}
-
-			// value is the same as in the original matrix
-			if(*finger0==v)
-			{
-				//x_stop is as far as we have to go at least
-				if(x<x_stop)
-				{
-					different=false;
-			//		x_stop=x;
-				}
-				else
-				{
-					// x_end indicates where to start in the next row
-					if(x==x_end && ((!forbidden_reached && !skip_row)||end_reached))
-					{
-						--x_end;
-						goPrevious(end_col, 0);	
-					}
-				}
-			} 
-			if(x<x_stop)// && different)
-			{
-				x_stop=x;
-			}
-			*finger0 = v;
-			--x;
-		}
-		if(x_end==x_begin)
-			break;
-	}
-
-//	cout <<"...declumped.\n";
+    // setClippedBeginPosition(row(align_, 0),0);
+    // setClippedBeginPosition(row(align_, 1),0);
+
+
+    for (y = y_end; (y != y_begin) ; --y)
+    {
+        different = true;
+        //compute next "forbidden" cell (where you are not allowed to go diagonal)
+        if(forbidden_reached && !end_reached)
+        {
+
+            if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop)
+            {
+                end_reached = true;
+            }
+
+            if(!end_reached)
+            {
+                --ali_it0;
+                goPrevious(forbidden,1);
+                while(isGap(ali_it0)&& ali_it0!=ali_it0_stop)
+                {
+                    skip_row = true;
+                    --ali_it0;
+                    --ali_it1;
+                    goPrevious(forbidden,1);
+                }
+
+                --ali_it1;
+                goPrevious(forbidden,0);
+                while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
+                {
+                    --ali_it1;
+                    --ali_it0;
+                    goPrevious(forbidden,0);
+                }
+                // mark the forbidden cell
+                sw.forbidden[position(forbidden)]=true;
+                forbidden_reached = false;
+            }
+
+        }
+
+        TValueV cy = *y;
+
+        h = *end_col;
+
+        finger1 = end_col;        //points to last column
+        goPrevious(end_col, 1);    //points to this column
+        finger0 = end_col;
+
+        v = *finger0;
+        x = x_end;
+
+        // declump the current row until the cells in the declumped and
+        // the cells in the original matrix are the same (or the border is reached)
+        // indicated by bool different
+        while (x != x_begin && different)
+        {
+            goPrevious(finger0, 0);
+            goPrevious(finger1, 0);
+            if (*x == cy && !(sw.forbidden[position(finger0)]))
+            {
+                v = h + score_match;
+                h = *finger1;
+            }
+            else
+            {
+                TScoreValue s1;
+
+                if(finger0 == forbidden)
+                {
+                        skip_row = false;
+                        forbidden_reached = true;
+                        s1 = 0;
+                }
+                else
+                {
+                    if(sw.forbidden[position(finger0)]) s1 = 0;
+                    else s1 = h + score_mismatch;
+                }
+
+                h = *finger1;
+                TScoreValue s2 = score_gap + ((h > v) ? h : v);
+                v = (s1 > s2) ? s1 : s2;
+                if (v < 0) v = 0;
+
+            }
+
+            // value is the same as in the original matrix
+            if(*finger0==v)
+            {
+                //x_stop is as far as we have to go at least
+                if(x<x_stop)
+                {
+                    different=false;
+            //        x_stop=x;
+                }
+                else
+                {
+                    // x_end indicates where to start in the next row
+                    if(x==x_end && ((!forbidden_reached && !skip_row)||end_reached))
+                    {
+                        --x_end;
+                        goPrevious(end_col, 0);
+                    }
+                }
+            }
+            if(x<x_stop)// && different)
+            {
+                x_stop=x;
+            }
+            *finger0 = v;
+            --x;
+        }
+        if(x_end==x_begin)
+            break;
+    }
+
+//    cout <<"...declumped.\n";
 }
 
 // ----------------------------------------------------------------------------
@@ -543,109 +526,109 @@ template <typename TSourceH, typename TGapsSpecH, typename TSourceV, typename TG
 typename Iterator<Matrix<TScoreValue, DIMENSION>, Standard >::Type
 _smithWatermanTrace(Gaps<TSourceH, TGapsSpecH> & gapsH,
                     Gaps<TSourceV, TGapsSpecV> & gapsV,
-                    typename LocalAlignmentFinder<TScoreValue>::TBoolMatrix & fb_matrix, 
+                    typename LocalAlignmentFinder<TScoreValue>::TBoolMatrix & fb_matrix,
                     Iter< Matrix<TScoreValue, DIMENSION>, PositionIterator > source_,
                     Score<TScoreValue, Simple> const & scoring_) {
-	//typedefs
-	typedef Iter<Matrix<TScoreValue, DIMENSION>, PositionIterator > TMatrixIterator;
-	typedef typename Position<Matrix<TScoreValue, DIMENSION> >::Type TPosition;
+    //typedefs
+    typedef Iter<Matrix<TScoreValue, DIMENSION>, PositionIterator > TMatrixIterator;
+    typedef typename Position<Matrix<TScoreValue, DIMENSION> >::Type TPosition;
 
-//	typedef Segment<TTargetSource, InfixSegment> TTargetSourceSegment;
-	typedef typename Iterator<TSourceH, Standard>::Type TSourceIteratorH;
-	typedef typename Iterator<TSourceV, Standard>::Type TSourceIteratorV;
+//    typedef Segment<TTargetSource, InfixSegment> TTargetSourceSegment;
+    typedef typename Iterator<TSourceH, Standard>::Type TSourceIteratorH;
+    typedef typename Iterator<TSourceV, Standard>::Type TSourceIteratorV;
 
     typedef Gaps<TSourceH, TGapsSpecH> TGapsH;
     typedef Gaps<TSourceV, TGapsSpecV> TGapsV;
-	typedef typename Iterator<TGapsH, Rooted>::Type TTargetIteratorH;
-	typedef typename Iterator<TGapsV, Rooted>::Type TTargetIteratorV;
-
-	//-------------------------------------------------------------------------
-	//variables
-	TPosition pos_0 = coordinate(source_, 0);
-	TPosition pos_1 = coordinate(source_, 1);
-
-	TSourceH strH = source(gapsH);
-	TSourceV strV = source(gapsV);
-	
-	TTargetIteratorH target_0 = iter(gapsH, pos_0);
-	TTargetIteratorV target_1 = iter(gapsV, pos_1);
-
-	TSourceIteratorH it_0 = iter(strH, pos_0, Standard());
-	TSourceIteratorH it_0_end = end(strH);
-
-	TSourceIteratorV it_1 = iter(strV, pos_1, Standard());
-	TSourceIteratorV it_1_end = end(strV);
-
-	TScoreValue score_mismatch = scoreMismatch(scoring_);
-	TScoreValue score_gap = scoreGapExtend(scoring_);
-
-	//-------------------------------------------------------------------------
-	//follow the trace until 0 is reached
-	while ((*source_!=0) && (it_0 != it_0_end) && (it_1 != it_1_end))
-	{
-		bool gv;
-		bool gh;
-		bool forbidden = fb_matrix[position(source_)];
-
-		if (*it_0 == *it_1 && !forbidden)
-		{
-			gv = gh = true;
-		}
-		else
-		{
-			TMatrixIterator it_ = source_;
-
-			goNext(it_, 0);
-			TScoreValue v = *it_ + score_gap;
-
-			TScoreValue d;
-			if(forbidden)
-				d = 0;
-			else{
-				goNext(it_, 1);
-				d = *it_ + score_mismatch;
-			}
-
-			it_ = source_;
-			goNext(it_, 1);
-			TScoreValue h = *it_ + score_gap;
-
-			gv = (v >= h) | (d >= h);
-			gh = (h >  v) | (d >= v);
-		}
-
-		if (gv)
-		{
-			++it_0;
-			goNext(source_, 0);
-		}
-		else
-		{
-			insertGap(target_0);
-		}
-
-		if (gh) 
-		{
-			++it_1;
-			goNext(source_, 1);
-		}
-		else
-		{
-			insertGap(target_1);
-		}
-		++target_0;
-		++target_1;
-	}
+    typedef typename Iterator<TGapsH, Rooted>::Type TTargetIteratorH;
+    typedef typename Iterator<TGapsV, Rooted>::Type TTargetIteratorV;
+
+    //-------------------------------------------------------------------------
+    //variables
+    TPosition pos_0 = coordinate(source_, 0);
+    TPosition pos_1 = coordinate(source_, 1);
+
+    TSourceH strH = source(gapsH);
+    TSourceV strV = source(gapsV);
+
+    TTargetIteratorH target_0 = iter(gapsH, pos_0);
+    TTargetIteratorV target_1 = iter(gapsV, pos_1);
+
+    TSourceIteratorH it_0 = iter(strH, pos_0, Standard());
+    TSourceIteratorH it_0_end = end(strH);
+
+    TSourceIteratorV it_1 = iter(strV, pos_1, Standard());
+    TSourceIteratorV it_1_end = end(strV);
+
+    TScoreValue score_mismatch = scoreMismatch(scoring_);
+    TScoreValue score_gap = scoreGapExtend(scoring_);
+
+    //-------------------------------------------------------------------------
+    //follow the trace until 0 is reached
+    while ((*source_!=0) && (it_0 != it_0_end) && (it_1 != it_1_end))
+    {
+        bool gv;
+        bool gh;
+        bool forbidden = fb_matrix[position(source_)];
+
+        if (*it_0 == *it_1 && !forbidden)
+        {
+            gv = gh = true;
+        }
+        else
+        {
+            TMatrixIterator it_ = source_;
+
+            goNext(it_, 0);
+            TScoreValue v = *it_ + score_gap;
+
+            TScoreValue d;
+            if(forbidden)
+                d = 0;
+            else{
+                goNext(it_, 1);
+                d = *it_ + score_mismatch;
+            }
+
+            it_ = source_;
+            goNext(it_, 1);
+            TScoreValue h = *it_ + score_gap;
+
+            gv = (v >= h) | (d >= h);
+            gh = (h >  v) | (d >= v);
+        }
+
+        if (gv)
+        {
+            ++it_0;
+            goNext(source_, 0);
+        }
+        else
+        {
+            insertGap(target_0);
+        }
+
+        if (gh)
+        {
+            ++it_1;
+            goNext(source_, 1);
+        }
+        else
+        {
+            insertGap(target_1);
+        }
+        ++target_0;
+        ++target_1;
+    }
 
     // We have removed all gaps and clippings from gapsH and gapsV in the calling functions, so the following works.
     // Note that we have to set the end position first.
     // TODO(holtgrew): Use setBegin/EndPosition().
     setClippedEndPosition(gapsH, toViewPosition(gapsH, position(it_0, strH)));
     setClippedEndPosition(gapsV, toViewPosition(gapsV, position(it_1, strV)));
-	setClippedBeginPosition(gapsH, toViewPosition(gapsH, pos_0));
-	setClippedBeginPosition(gapsV, toViewPosition(gapsV, pos_1));
-	
-	return source_;
+    setClippedBeginPosition(gapsH, toViewPosition(gapsH, pos_0));
+    setClippedBeginPosition(gapsV, toViewPosition(gapsV, pos_1));
+
+    return source_;
 }
 
 // ----------------------------------------------------------------------------
@@ -659,35 +642,35 @@ _getNextBestEndPosition(LocalAlignmentFinder<TScoreValue> & sw ,
                         TScoreValue cutoff)
 {
     // get maximal score from priority queue
-	TScoreValue topScore = 0;
+    TScoreValue topScore = 0;
     if (!empty(sw.pQ))
         topScore = getValue(sw.matrix, top(sw.pQ).id_);
 
     // check if matrix entry of topScore did not change while declumping
-	if (!empty(sw.pQ)) {
-		while (top(sw.pQ).value_ != topScore) {
-			if (topScore >= cutoff) {
-				((sw.pQ).heap[0]).value_ = topScore;
-				adjustTop(sw.pQ); 
-			} else {
-				pop(sw.pQ);
-			}
-			if (!empty(sw.pQ)) topScore = getValue(sw.matrix, top(sw.pQ).id_);
-			else break;
-		}
-	}
+    if (!empty(sw.pQ)) {
+        while (top(sw.pQ).value_ != topScore) {
+            if (topScore >= cutoff) {
+                ((sw.pQ).heap[0]).value_ = topScore;
+                adjustTop(sw.pQ);
+            } else {
+                pop(sw.pQ);
+            }
+            if (!empty(sw.pQ)) topScore = getValue(sw.matrix, top(sw.pQ).id_);
+            else break;
+        }
+    }
 
     // priority queue with top scores is empty
     if(empty(sw.pQ)) {//||top(sw.pQ).value_<cutoff) {
-		sw.needReinit = true;
-		return 0;
-	}
-
-	typename LocalAlignmentFinder<TScoreValue>::TMatrixPosition ret_pos = top(sw.pQ).id_;
-	sw.bestEndPos = ret_pos;
-	pop(sw.pQ);
-	
-	return ret_pos;
+        sw.needReinit = true;
+        return 0;
+    }
+
+    typename LocalAlignmentFinder<TScoreValue>::TMatrixPosition ret_pos = top(sw.pQ).id_;
+    sw.bestEndPos = ret_pos;
+    pop(sw.pQ);
+
+    return ret_pos;
 }
 
 // ----------------------------------------------------------------------------
@@ -700,7 +683,7 @@ TScoreValue
 _smithWaterman(Gaps<TSourceH, TGapsSpecH> & gapsH,
                Gaps<TSourceV, TGapsSpecV> & gapsV,
                LocalAlignmentFinder<TScoreValue> & sw_finder,
-               Score<TScoreValue, TScoreSpec> const & score_, 
+               Score<TScoreValue, TScoreSpec> const & score_,
                TScoreValue cutoff)
 {
     // TODO(holtgrew): This sourceSegment() stuff is confusing... Do we *really* need this?
@@ -711,25 +694,25 @@ _smithWaterman(Gaps<TSourceH, TGapsSpecH> & gapsH,
     clearClipping(gapsV);
 
     _initLocalAlignmentFinder(sourceSegment(gapsH), sourceSegment(gapsV), sw_finder, WatermanEggert());
-	
-	TScoreValue ret = _smithWatermanGetMatrix(sw_finder, sourceSegment(gapsH), sourceSegment(gapsV), score_,cutoff);
-	
-	if(ret==0)
-		return ret;
-	sw_finder.needReinit = false;
 
-	typedef Iter<typename LocalAlignmentFinder<TScoreValue>::TMatrix,PositionIterator > TMatrixIterator;
-	TMatrixIterator best_begin;
+    TScoreValue ret = _smithWatermanGetMatrix(sw_finder, sourceSegment(gapsH), sourceSegment(gapsV), score_,cutoff);
+
+    if(ret==0)
+        return ret;
+    sw_finder.needReinit = false;
+
+    typedef Iter<typename LocalAlignmentFinder<TScoreValue>::TMatrix,PositionIterator > TMatrixIterator;
+    TMatrixIterator best_begin;
 
     // TODO(holtgrew): What does the following comment mean?
-	// TODO: sw_finder statt kram
-	best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_);
+    // TODO: sw_finder statt kram
+    best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_);
+
+    sw_finder.bestBeginPos = position(best_begin);
 
-	sw_finder.bestBeginPos = position(best_begin);
-	
-	pop(sw_finder.pQ);
+    pop(sw_finder.pQ);
 
-	return ret;
+    return ret;
 }
 
 // ----------------------------------------------------------------------------
@@ -742,27 +725,27 @@ TScoreValue
 _smithWatermanGetNext(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                       Gaps<TSequenceV, TGapsSpecV> & gapsV,
                       LocalAlignmentFinder<TScoreValue> & sw_finder ,
-                      Score<TScoreValue, TScoreSpec> const & score_, 
+                      Score<TScoreValue, TScoreSpec> const & score_,
                       TScoreValue cutoff)
-{	
-	_smithWatermanDeclump(sw_finder, gapsH, gapsV, score_);
+{
+    _smithWatermanDeclump(sw_finder, gapsH, gapsV, score_);
 
-	clearGaps(gapsH);
-	clearGaps(gapsV);
+    clearGaps(gapsH);
+    clearGaps(gapsV);
     clearClipping(gapsH);
     clearClipping(gapsV);
 
-	typename LocalAlignmentFinder<TScoreValue>::TMatrixPosition next_best_end;
-	next_best_end = _getNextBestEndPosition(sw_finder,cutoff);
-	if(next_best_end==0)
-		return 0;
-	typename LocalAlignmentFinder<TScoreValue>::TMatrixIterator next_best_begin;
-	next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_);
-	sw_finder.bestBeginPos = position(next_best_begin);
-	
-	return getValue(sw_finder.matrix,next_best_end);
+    typename LocalAlignmentFinder<TScoreValue>::TMatrixPosition next_best_end;
+    next_best_end = _getNextBestEndPosition(sw_finder,cutoff);
+    if(next_best_end==0)
+        return 0;
+    typename LocalAlignmentFinder<TScoreValue>::TMatrixIterator next_best_begin;
+    next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_);
+    sw_finder.bestBeginPos = position(next_best_begin);
+
+    return getValue(sw_finder.matrix,next_best_end);
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_
diff --git a/seqan/align/matrix_base.h b/seqan/align/matrix_base.h
index f1438ea..925cd24 100644
--- a/seqan/align/matrix_base.h
+++ b/seqan/align/matrix_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,9 +54,9 @@ template <typename T> struct SizeArr_;
 template <typename TValue, unsigned DIMENSION>
 struct SizeArr_<Matrix<TValue, DIMENSION> >
 {
-	typedef Matrix<TValue, DIMENSION> TMatrix_;
-	typedef typename Size<TMatrix_>::Type TSize_;
-	typedef String<TSize_> Type;
+    typedef Matrix<TValue, DIMENSION> TMatrix_;
+    typedef typename Size<TMatrix_>::Type TSize_;
+    typedef String<TSize_> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -64,7 +64,13 @@ struct SizeArr_<Matrix<TValue, DIMENSION> >
 template <typename TValue, unsigned DIMENSION>
 struct Host<Matrix<TValue, DIMENSION> >
 {
-	typedef String<TValue> Type;
+    typedef String<TValue> Type;
+};
+
+template <typename TValue, unsigned DIMENSION>
+struct Host<Matrix<TValue, DIMENSION> const>
+{
+    typedef String<TValue> const Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -77,25 +83,14 @@ struct Host<Matrix<TValue, DIMENSION> >
  * @headerfile <seqan/align.h>
  * @brief A simple n-dimensional matrix type.
  *
- * @signature template <typename TValue, unsigned DIMENSION = 0>
+ * @signature template <typename TValue[, unsigned DIMENSION]>
  *            class Matrix;
  *
  * @tparam TValue    Type of matrix entries.
  * @tparam DIMENSION Dimension of the matrix.  Use 0 for n-dimensional, values &gt; 0 for a matrix with
- *                   <tt>DIMENSION</tt> dimensions.
+ *                   <tt>DIMENSION</tt> dimensions.  Defaults to 0.
  */
 
-/**
-.Class.Matrix:
-..cat:Miscellaneous
-..summary:A simple n-dimensional matrix type.
-..signature:Matrix<TValue, unsigned DIMENSION = 0>
-..param.TValue:Type of matrix entries.
-..param.unsigned DIMENSION:The specializing type (0: NDimensional matrix; 2: two dimensional matrix).
-..remarks: The following operators and functions are supported: A*B, A*a, A+B,A-B,<<, transpose
-..include:seqan/align.h
-*/
-
 
 template <typename TValue>
 class Matrix<TValue, 0>
@@ -103,59 +98,59 @@ class Matrix<TValue, 0>
 //____________________________________________________________________________
 
 public:
-	typedef typename Size<Matrix>::Type TSize;
-	typedef String<TSize> TSizeArr;
-	typedef String<TValue> THost;
+    typedef typename Size<Matrix>::Type TSize;
+    typedef String<TSize> TSizeArr;
+    typedef String<TValue> THost;
 
-	TSizeArr data_lengths;		//Length of every dimension
-	TSizeArr data_factors;		//used for positions of dimensions in host ("size of jumps" to get to next entry of specified dimension)
+    TSizeArr data_lengths;        //Length of every dimension
+    TSizeArr data_factors;        //used for positions of dimensions in host ("size of jumps" to get to next entry of specified dimension)
 
-	Holder<THost> data_host;
+    Holder<THost> data_host;
 //____________________________________________________________________________
 
 public:
-	Matrix()
-	{
-		create(data_host);
-	}
-	Matrix(Matrix const & other_):
-		data_lengths(other_.data_lengths),
-		data_factors(other_.data_factors),
-		data_host(other_.data_host)
-	{
-	}
-	inline Matrix const &
-	operator = (Matrix const & other_)
-	{
-		data_lengths = other_.data_lengths;
-		data_factors = other_.data_factors;
-		data_host = other_.data_host;
-
-		return *this;
-	}
-	~Matrix()
-	{
-	}
+    Matrix()
+    {
+        create(data_host);
+    }
+    Matrix(Matrix const & other_):
+        data_lengths(other_.data_lengths),
+        data_factors(other_.data_factors),
+        data_host(other_.data_host)
+    {
+    }
+    inline Matrix const &
+    operator = (Matrix const & other_)
+    {
+        data_lengths = other_.data_lengths;
+        data_factors = other_.data_factors;
+        data_host = other_.data_host;
+
+        return *this;
+    }
+    ~Matrix()
+    {
+    }
 //____________________________________________________________________________
 
 
 //____________________________________________________________________________
 
-	inline TValue &
-	operator () (TSize x1, TSize x2)
-	{
-		return value(*this, x1, x2);
-	}
-	inline TValue &
-	operator () (TSize x1, TSize x2, TSize x3)
-	{
-		return value(*this, x1, x2, x3);
-	}
-	inline TValue &
-	operator () (TSize x1, TSize x2, TSize x3, TSize x4)
-	{
-		return value(*this, x1, x2, x3, x4);
-	}
+    inline TValue &
+    operator () (TSize x1, TSize x2)
+    {
+        return value(*this, x1, x2);
+    }
+    inline TValue &
+    operator () (TSize x1, TSize x2, TSize x3)
+    {
+        return value(*this, x1, x2, x3);
+    }
+    inline TValue &
+    operator () (TSize x1, TSize x2, TSize x3, TSize x4)
+    {
+        return value(*this, x1, x2, x3, x4);
+    }
 
 //____________________________________________________________________________
 };
@@ -167,57 +162,57 @@ class Matrix<TValue, 2>
 //____________________________________________________________________________
 
 public:
-	typedef typename Size<Matrix>::Type TSize;
-	typedef String<TSize> TSizeArr;
-	typedef String<TValue> THost;
+    typedef typename Size<Matrix>::Type TSize;
+    typedef String<TSize> TSizeArr;
+    typedef String<TValue> THost;
 
-	TSizeArr data_lengths;
-	TSizeArr data_factors;
+    TSizeArr data_lengths;
+    TSizeArr data_factors;
 
-	Holder<THost> data_host;
+    Holder<THost> data_host;
 
 
 //____________________________________________________________________________
 
 public:
-	Matrix()
-	{
-		create(data_host);
-
-		//setDimension to 2
-		resize(data_lengths, 2, 0);
-		resize(data_factors, 2, 0);
-		data_factors[0] = 1;
-	}
-	Matrix(Matrix const & other_):
-		data_lengths(other_.data_lengths),
-		data_factors(other_.data_factors),
-		data_host(other_.data_host)
-	{
-	}
-	inline Matrix const &
-	operator = (Matrix const & other_)
-	{
-		data_lengths = other_.data_lengths;
-		data_factors = other_.data_factors;
-		data_host = other_.data_host;
-
-		return *this;
-	}
-
-	~Matrix()
-	{
-	}
+    Matrix()
+    {
+        create(data_host);
+
+        //setDimension to 2
+        resize(data_lengths, 2, 0);
+        resize(data_factors, 2, 0);
+        data_factors[0] = 1;
+    }
+    Matrix(Matrix const & other_):
+        data_lengths(other_.data_lengths),
+        data_factors(other_.data_factors),
+        data_host(other_.data_host)
+    {
+    }
+    inline Matrix const &
+    operator = (Matrix const & other_)
+    {
+        data_lengths = other_.data_lengths;
+        data_factors = other_.data_factors;
+        data_host = other_.data_host;
+
+        return *this;
+    }
+
+    ~Matrix()
+    {
+    }
 //____________________________________________________________________________
 
 
 //____________________________________________________________________________
 
-	inline TValue &
-	operator () (TSize x1, TSize x2)
-	{
-		return value(*this, x1, x2);
-	}
+    inline TValue &
+    operator () (TSize x1, TSize x2)
+    {
+        return value(*this, x1, x2);
+    }
 
 //____________________________________________________________________________
 };
@@ -228,57 +223,57 @@ class Matrix<TValue, 3>
 //____________________________________________________________________________
 
 public:
-	typedef typename Size<Matrix>::Type TSize;
-	typedef String<TSize> TSizeArr;
-	typedef String<TValue> THost;
+    typedef typename Size<Matrix>::Type TSize;
+    typedef String<TSize> TSizeArr;
+    typedef String<TValue> THost;
 
-	TSizeArr data_lengths;
-	TSizeArr data_factors;
+    TSizeArr data_lengths;
+    TSizeArr data_factors;
 
-	Holder<THost> data_host;
+    Holder<THost> data_host;
 
 
 //____________________________________________________________________________
 
 public:
-	Matrix()
-	{
-		create(data_host);
-
-		//setDimension to 3
-		resize(data_lengths, 3, 0);
-		resize(data_factors, 3);
-		data_factors[0] = 1;
-	}
-	Matrix(Matrix const & other_):
-		data_lengths(other_.data_lengths),
-		data_factors(other_.data_factors),
-		data_host(other_.data_host)
-	{
-	}
-	inline Matrix const &
-	operator = (Matrix const & other_)
-	{
-		data_lengths = other_.data_lengths;
-		data_factors = other_.data_factors;
-		data_host = other_.data_host;
-
-		return *this;
-	}
-
-	~Matrix()
-	{
-	}
+    Matrix()
+    {
+        create(data_host);
+
+        //setDimension to 3
+        resize(data_lengths, 3, 0);
+        resize(data_factors, 3);
+        data_factors[0] = 1;
+    }
+    Matrix(Matrix const & other_):
+        data_lengths(other_.data_lengths),
+        data_factors(other_.data_factors),
+        data_host(other_.data_host)
+    {
+    }
+    inline Matrix const &
+    operator = (Matrix const & other_)
+    {
+        data_lengths = other_.data_lengths;
+        data_factors = other_.data_factors;
+        data_host = other_.data_host;
+
+        return *this;
+    }
+
+    ~Matrix()
+    {
+    }
 //____________________________________________________________________________
 
 
 //____________________________________________________________________________
 
-	inline TValue &
-	operator () (TSize x1, TSize x2, TSize x3)
-	{
-		return value(*this, x1, x2, x3);
-	}
+    inline TValue &
+    operator () (TSize x1, TSize x2, TSize x3)
+    {
+        return value(*this, x1, x2, x3);
+    }
 
 //____________________________________________________________________________
 };
@@ -287,28 +282,28 @@ template <typename TValue, unsigned DIMENSION>
 inline typename SizeArr_<Matrix<TValue, DIMENSION> >::Type &
 _dataLengths(Matrix<TValue, DIMENSION> & me)
 {
-	return me.data_lengths;
+    return me.data_lengths;
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline typename SizeArr_<Matrix<TValue, DIMENSION> >::Type const &
 _dataLengths(Matrix<TValue, DIMENSION> const & me)
 {
-	return me.data_lengths;
+    return me.data_lengths;
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline typename SizeArr_<Matrix<TValue, DIMENSION> >::Type &
 _dataFactors(Matrix<TValue, DIMENSION> & me)
 {
-	return me.data_factors;
+    return me.data_factors;
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline typename SizeArr_<Matrix<TValue, DIMENSION> >::Type const &
 _dataFactors(Matrix<TValue, DIMENSION> const & me)
 {
-	return me.data_factors;
+    return me.data_factors;
 }
 
 //____________________________________________________________________________
@@ -318,33 +313,23 @@ template <typename TValue, unsigned DIMENSION>
 inline bool
 dependent(Matrix<TValue, DIMENSION> & me)
 {
-	return dependent(me.data_host);
-}
-
-//____________________________________________________________________________
-
-template <typename TValue, unsigned DIMENSION, typename THost>
-inline void
-setHost(Matrix<TValue, DIMENSION> & me, THost & host_)
-{
-	setValue(me.data_host, host_);
+    return dependent(me.data_host);
 }
 
 //____________________________________________________________________________
 
-
 template <typename TValue, unsigned DIMENSION>
-inline typename Host<Matrix<TValue, DIMENSION> >::Type &
-host(Matrix<TValue, DIMENSION> & me)
+inline Holder<typename Host<Matrix<TValue, DIMENSION> >::Type> &
+_dataHost(Matrix<TValue, DIMENSION> & matrix)
 {
-	return value(me.data_host);
+    return matrix.data_host;
 }
 
 template <typename TValue, unsigned DIMENSION>
-inline typename Host<Matrix<TValue, DIMENSION> >::Type const &
-host(Matrix<TValue, DIMENSION> const & me)
+inline Holder<typename Host<Matrix<TValue, DIMENSION> >::Type> const &
+_dataHost(Matrix<TValue, DIMENSION> const & matrix)
 {
-	return value(me.data_host);
+    return matrix.data_host;
 }
 
 //____________________________________________________________________________
@@ -353,7 +338,7 @@ template <typename TValue, unsigned DIMENSION, typename THost>
 inline void
 assignHost(Matrix<TValue, DIMENSION> & me, THost const & value_)
 {
-	assignValue(me.data_host, value_);
+    assignValue(me.data_host, value_);
 }
 
 //____________________________________________________________________________
@@ -362,7 +347,7 @@ template <typename TValue, unsigned DIMENSION, typename THost>
 inline void
 moveHost(Matrix<TValue, DIMENSION> & me, THost const & value_)
 {
-	moveValue(me.data_host, value_);
+    moveValue(me.data_host, value_);
 }
 //////////////////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////////////////
@@ -370,7 +355,7 @@ moveHost(Matrix<TValue, DIMENSION> & me, THost const & value_)
 template <typename TValue, unsigned DIMENSION>
 struct Value< Matrix<TValue, DIMENSION> >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -378,23 +363,23 @@ struct Value< Matrix<TValue, DIMENSION> >
 template <typename TValue, unsigned DIMENSION, typename TIteratorSpec>
 struct Iterator< Matrix<TValue, DIMENSION>, TIteratorSpec >
 {
-	typedef Iter<Matrix<TValue, DIMENSION>, PositionIterator> Type;
+    typedef Iter<Matrix<TValue, DIMENSION>, PositionIterator> Type;
 };
 
 template <typename TValue, unsigned DIMENSION, typename TIteratorSpec>
 struct Iterator< Matrix<TValue, DIMENSION> const, TIteratorSpec >
 {
-	typedef Iter<Matrix<TValue, DIMENSION> const, PositionIterator> Type;
+    typedef Iter<Matrix<TValue, DIMENSION> const, PositionIterator> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, unsigned DIMENSION>
-inline unsigned int
+inline typename Size<Matrix<TValue, DIMENSION> const>::Type
 dimension(Matrix<TValue, DIMENSION> const & me)
 {
-	return length(_dataLengths(me));
+    return length(_dataLengths(me));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -402,16 +387,16 @@ dimension(Matrix<TValue, DIMENSION> const & me)
 template <typename TValue, unsigned DIMENSION>
 inline void
 setDimension(Matrix<TValue, DIMENSION> & me,
-			 unsigned int dim_)
+             unsigned int dim_)
 {
 
-	SEQAN_ASSERT_GT(dim_, 0u);
+    SEQAN_ASSERT_GT(dim_, 0u);
 //std::cout<<"\npress enter1\n";
 //std::cin.get();
-	resize(_dataLengths(me), dim_, 0);
+    resize(_dataLengths(me), dim_, 0);
 
-	resize(_dataFactors(me), dim_);
-	_dataFactors(me)[0] = 1;
+    resize(_dataFactors(me), dim_);
+    _dataFactors(me)[0] = 1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -419,22 +404,22 @@ setDimension(Matrix<TValue, DIMENSION> & me,
 template <typename TValue, unsigned DIMENSION>
 inline typename Size<Matrix<TValue, DIMENSION> >::Type
 length(Matrix<TValue, DIMENSION> const & me,
-	   unsigned int dim_)
+       unsigned int dim_)
 {
-	return me.data_lengths[dim_];
+    return me.data_lengths[dim_];
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline typename Size<Matrix <TValue, DIMENSION> >::Type
 length(Matrix<TValue, DIMENSION> const & me)
 {
-	return length(host(me));
+    return length(host(me));
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline bool empty(Matrix<TValue, DIMENSION> const & me)
 {
-	return empty(host(me));
+    return empty(host(me));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -442,65 +427,76 @@ inline bool empty(Matrix<TValue, DIMENSION> const & me)
 template <typename TValue, unsigned DIMENSION, typename TLength>
 inline void
 setLength(Matrix<TValue, DIMENSION> & me,
-		  unsigned int dim_,
-		  TLength length_)
+          unsigned int dim_,
+          TLength length_)
 {
-	SEQAN_ASSERT_GT(length_, static_cast<TLength>(0));
-	SEQAN_ASSERT_LT(dim_, dimension(me));
+    SEQAN_ASSERT_GT(length_, static_cast<TLength>(0));
+    SEQAN_ASSERT_LT(dim_, dimension(me));
 
     typedef typename SizeArr_<Matrix<TValue, DIMENSION> >::TSize_ TSize_;
 
-	_dataLengths(me)[dim_] = static_cast<TSize_>(length_);
+    _dataLengths(me)[dim_] = static_cast<TSize_>(length_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
+/*!
+ * @fn Matrix#resize
+ * @brief Resize the matrix and fill it with a given value or zeroes.
+ *
+ * @signature void resize(matrix[, val]);
+ *
+ * @param[in,out] matrix The Matrix to fill.
+ * @param[in]     val    The optional value to fill the matrix with.
+ */
+
+
 template <typename TValue, unsigned DIMENSION>
 inline void
 resize(Matrix<TValue, DIMENSION> & me)
 {
-	typedef Matrix<TValue, DIMENSION> TMatrix;
-	typedef typename Size<TMatrix>::Type TSize;
+    typedef Matrix<TValue, DIMENSION> TMatrix;
+    typedef typename Size<TMatrix>::Type TSize;
 
-	unsigned int dimension_ = dimension(me);
+    unsigned int dimension_ = dimension(me);
 
-	SEQAN_ASSERT_GT(dimension_, 0u);
+    SEQAN_ASSERT_GT(dimension_, 0u);
 
-	TSize factor_ = _dataFactors(me)[0] * length(me, 0);
-	for (unsigned int i = 1; (factor_ > 0) && (i < dimension_); ++i)
-	{
-		_dataFactors(me)[i] = factor_;
-		factor_ *= length(me, i);
-	}
+    TSize factor_ = _dataFactors(me)[0] * length(me, 0);
+    for (unsigned int i = 1; (factor_ > 0) && (i < dimension_); ++i)
+    {
+        _dataFactors(me)[i] = factor_;
+        factor_ *= length(me, i);
+    }
 
-	if (factor_ > 0)
-	{
-		resize(host(me), factor_);
-	}
+    if (factor_ > 0)
+    {
+        resize(host(me), factor_);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, unsigned DIMENSION, typename TFillValue>
 inline void
-resize(Matrix<TValue, DIMENSION> & me, TFillValue myValue)	//resize the matrix and fill with value
+resize(Matrix<TValue, DIMENSION> & me, TFillValue myValue)    //resize the matrix and fill with value
 {
-	typedef Matrix<TValue, DIMENSION> TMatrix;
-	typedef typename Size<TMatrix>::Type TSize;
+    typedef Matrix<TValue, DIMENSION> TMatrix;
+    typedef typename Size<TMatrix>::Type TSize;
 
-	unsigned int dimension_ = dimension(me);
+    unsigned int dimension_ = dimension(me);
 
-	SEQAN_ASSERT_GT(dimension_, 0u);
+    SEQAN_ASSERT_GT(dimension_, 0u);
 
-	TSize factor_ = _dataFactors(me)[0] * length(me, 0);
-	for (unsigned int i = 1; (factor_ > 0) && (i < dimension_); ++i)
-	{
-		_dataFactors(me)[i] = factor_;
-		factor_ *= length(me, i);
-	}
+    TSize factor_ = _dataFactors(me)[0] * length(me, 0);
+    for (unsigned int i = 1; (factor_ > 0) && (i < dimension_); ++i)
+    {
+        _dataFactors(me)[i] = factor_;
+        factor_ *= length(me, i);
+    }
 
-	if (factor_ > 0)
-		resize(host(me), factor_, myValue);
+    if (factor_ > 0)
+        resize(host(me), factor_, myValue);
 }
 
 
@@ -509,37 +505,37 @@ resize(Matrix<TValue, DIMENSION> & me, TFillValue myValue)	//resize the matrix a
 template <typename TValue, unsigned DIMENSION, typename TPosition>
 inline typename Position<Matrix <TValue, DIMENSION> >::Type
 nextPosition(Matrix<TValue, DIMENSION> & me,
-			 TPosition position_,
-			 unsigned int dimension_)
+             TPosition position_,
+             unsigned int dimension_)
 {
-	return position_ + _dataFactors(me)[dimension_];
+    return position_ + _dataFactors(me)[dimension_];
 }
 
 template <typename TValue, unsigned DIMENSION, typename TPosition>
 inline typename Position<Matrix <TValue, DIMENSION> >::Type
 nextPosition(Matrix<TValue, DIMENSION> const & me,
-			 TPosition position_,
-			 unsigned int dimension_)
+             TPosition position_,
+             unsigned int dimension_)
 {
-	return position_ + _dataFactors(me)[dimension_];
+    return position_ + _dataFactors(me)[dimension_];
 }
 
 template <typename TValue, unsigned DIMENSION, typename TPosition>
 inline typename Position<Matrix <TValue, DIMENSION> >::Type
 previousPosition(Matrix<TValue, DIMENSION> & me,
-				 TPosition position_,
-				 unsigned int dimension_)
+                 TPosition position_,
+                 unsigned int dimension_)
 {
-	return position_ - _dataFactors(me)[dimension_];
+    return position_ - _dataFactors(me)[dimension_];
 }
 
 template <typename TValue, unsigned DIMENSION, typename TPosition>
 inline typename Position<Matrix <TValue, DIMENSION> >::Type
 previousPosition(Matrix<TValue, DIMENSION> const & me,
-				 TPosition position_,
-				 unsigned int dimension_)
+                 TPosition position_,
+                 unsigned int dimension_)
 {
-	return position_ - _dataFactors(me)[dimension_];
+    return position_ - _dataFactors(me)[dimension_];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -547,19 +543,19 @@ previousPosition(Matrix<TValue, DIMENSION> const & me,
 template <typename TValue, unsigned DIMENSION, typename TPosition>
 inline typename Size< Matrix <TValue, DIMENSION> >::Type
 coordinate(Matrix<TValue, DIMENSION> const & me,
-		   TPosition position_,
-		   unsigned int dimension_)
-{
-	SEQAN_ASSERT_LT(dimension_, dimension(me));
-
-	if (dimension_ < dimension(me) - 1)
-	{
-		return (position_ / _dataFactors(me)[dimension_]) % _dataFactors(me)[dimension_ + 1];
-	}
-	else
-	{
-		return position_ / _dataFactors(me)[dimension_];
-	}
+           TPosition position_,
+           unsigned int dimension_)
+{
+    SEQAN_ASSERT_LT(dimension_, dimension(me));
+
+    if (dimension_ < dimension(me) - 1)
+    {
+        return (position_ / _dataFactors(me)[dimension_]) % _dataFactors(me)[dimension_ + 1];
+    }
+    else
+    {
+        return position_ / _dataFactors(me)[dimension_];
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -567,16 +563,16 @@ coordinate(Matrix<TValue, DIMENSION> const & me,
 template <typename TValue, unsigned DIMENSION, typename TTag>
 inline typename Iterator<Matrix <TValue, DIMENSION>, Tag<TTag> const>::Type
 begin(Matrix<TValue, DIMENSION> & me,
-	  Tag<TTag> const)
+      Tag<TTag> const)
 {
-	return typename Iterator<Matrix <TValue, DIMENSION>, Tag<TTag> const >::Type(me, 0);
+    return typename Iterator<Matrix <TValue, DIMENSION>, Tag<TTag> const >::Type(me, 0);
 }
 template <typename TValue, unsigned DIMENSION, typename TTag>
 inline typename Iterator<Matrix <TValue, DIMENSION> const, Tag<TTag> const>::Type
 begin(Matrix<TValue, DIMENSION> const & me,
-	  Tag<TTag> const)
+      Tag<TTag> const)
 {
-	return typename Iterator<Matrix <TValue, DIMENSION> const, Tag<TTag> const >::Type(me, 0);
+    return typename Iterator<Matrix <TValue, DIMENSION> const, Tag<TTag> const >::Type(me, 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -584,16 +580,16 @@ begin(Matrix<TValue, DIMENSION> const & me,
 template <typename TValue, unsigned DIMENSION, typename TTag>
 inline typename Iterator<Matrix <TValue, DIMENSION>, Tag<TTag> const >::Type
 end(Matrix<TValue, DIMENSION> & me,
-	  Tag<TTag> const)
+      Tag<TTag> const)
 {
-	return typename Iterator<Matrix <TValue, DIMENSION>, Tag<TTag> const >::Type(me, length(host(me)));
+    return typename Iterator<Matrix <TValue, DIMENSION>, Tag<TTag> const >::Type(me, length(host(me)));
 }
 template <typename TValue, unsigned DIMENSION, typename TTag>
 inline typename Iterator<Matrix <TValue, DIMENSION> const, Tag<TTag> const >::Type
 end(Matrix<TValue, DIMENSION> const & me,
-	  Tag<TTag> const)
+      Tag<TTag> const)
 {
-	return typename Iterator<Matrix <TValue, DIMENSION>, Tag<TTag> const >::Type(me, length(host(me)));
+    return typename Iterator<Matrix <TValue, DIMENSION>, Tag<TTag> const >::Type(me, length(host(me)));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -601,9 +597,9 @@ end(Matrix<TValue, DIMENSION> const & me,
 template <typename TValue, unsigned DIMENSION, typename TPosition>
 inline typename Reference<Matrix<TValue, DIMENSION> >::Type
 value(Matrix<TValue, DIMENSION> & me,
-	  TPosition position_)
+      TPosition position_)
 {
-	return value(host(me), position_);
+    return value(host(me), position_);
 }
 
 template <typename TValue, unsigned DIMENSION, typename TPosition>
@@ -620,10 +616,10 @@ value(Matrix<TValue, DIMENSION> const & me,
 template <typename TValue, unsigned DIMENSION, typename TOrdinate1, typename TOrdinate2>
 inline typename Reference<Matrix<TValue, DIMENSION> >::Type
 value(Matrix<TValue, DIMENSION> & me,
-	  TOrdinate1 i1,
-	  TOrdinate2 i2)
+      TOrdinate1 i1,
+      TOrdinate2 i2)
 {
-	return value(host(me), i1 + i2 * _dataFactors(me)[1]);
+    return value(host(me), i1 + i2 * _dataFactors(me)[1]);
 }
 
 template <typename TValue, unsigned DIMENSION, typename TOrdinate1, typename TOrdinate2>
@@ -642,11 +638,11 @@ value(Matrix<TValue, DIMENSION> const & me,
 template <typename TValue, unsigned DIMENSION, typename TOrdinate1, typename TOrdinate2, typename TOrdinate3>
 inline typename Reference<Matrix<TValue, DIMENSION> >::Type
 value(Matrix<TValue, DIMENSION> & me,
-	  TOrdinate1 i1,
-	  TOrdinate2 i2,
-	  TOrdinate3 i3)
+      TOrdinate1 i1,
+      TOrdinate2 i2,
+      TOrdinate3 i3)
 {
-	return value(host(me), i1 + i2 * _dataFactors(me)[1] + i3 * _dataFactors(me)[2]);
+    return value(host(me), i1 + i2 * _dataFactors(me)[1] + i3 * _dataFactors(me)[2]);
 }
 
 //____________________________________________________________________________
@@ -656,12 +652,12 @@ value(Matrix<TValue, DIMENSION> & me,
 template <typename TValue, unsigned DIMENSION, typename TOrdinate1, typename TOrdinate2, typename TOrdinate3, typename TOrdinate4>
 inline typename Reference<Matrix<TValue, DIMENSION> >::Type
 value(Matrix<TValue, DIMENSION> & me,
-	  TOrdinate1 i1,
-	  TOrdinate2 i2,
-	  TOrdinate3 i3,
-	  TOrdinate4 i4)
+      TOrdinate1 i1,
+      TOrdinate2 i2,
+      TOrdinate3 i3,
+      TOrdinate4 i4)
 {
-	return value(host(me), i1 + i2 * _dataFactors(me)[1] + i3 * _dataFactors(me)[2] + i4 * _dataFactors(me)[3]);
+    return value(host(me), i1 + i2 * _dataFactors(me)[1] + i3 * _dataFactors(me)[2] + i4 * _dataFactors(me)[3]);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -672,31 +668,31 @@ value(Matrix<TValue, DIMENSION> & me,
 template <typename TValue, unsigned DIMENSION>
 inline void
 goNext(Iter<Matrix<TValue, DIMENSION>, PositionIterator> & me,
-	   unsigned int dimension_)
+       unsigned int dimension_)
 {
-	setPosition(me, nextPosition(container(me), position(me), dimension_));
+    setPosition(me, nextPosition(container(me), position(me), dimension_));
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline void
 goNext(Iter<Matrix<TValue, DIMENSION> const, PositionIterator> & me,
-	   unsigned int dimension_)
+       unsigned int dimension_)
 {
-	setPosition(me, nextPosition(container(me), position(me), dimension_));
+    setPosition(me, nextPosition(container(me), position(me), dimension_));
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline void
 goNext(Iter<Matrix<TValue, DIMENSION>, PositionIterator> & me)
 {
-	goNext(me, 0);
+    goNext(me, 0);
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline void
 goNext(Iter<Matrix<TValue, DIMENSION> const, PositionIterator> & me)
 {
-	goNext(me, 0);
+    goNext(me, 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -706,31 +702,31 @@ goNext(Iter<Matrix<TValue, DIMENSION> const, PositionIterator> & me)
 template <typename TValue, unsigned DIMENSION>
 inline void
 goPrevious(Iter< Matrix<TValue, DIMENSION>, PositionIterator > & me,
-		   unsigned int dimension_)
+           unsigned int dimension_)
 {
-	setPosition(me, previousPosition(container(me), position(me), dimension_));
+    setPosition(me, previousPosition(container(me), position(me), dimension_));
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline void
 goPrevious(Iter< Matrix<TValue, DIMENSION> const, PositionIterator > & me,
-		   unsigned int dimension_)
+           unsigned int dimension_)
 {
-	setPosition(me, previousPosition(container(me), position(me), dimension_));
+    setPosition(me, previousPosition(container(me), position(me), dimension_));
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline void
 goPrevious(Iter< Matrix<TValue, DIMENSION>, PositionIterator > & me)
 {
-	goPrevious(me, 0);
+    goPrevious(me, 0);
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline void
 goPrevious(Iter< Matrix<TValue, DIMENSION> const, PositionIterator > & me)
 {
-	goPrevious(me, 0);
+    goPrevious(me, 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -774,102 +770,102 @@ goTo(Iter<Matrix<TValue, DIMENSION> const, PositionIterator> & me, TPosition0 po
 template <typename TValue, unsigned DIMENSION>
 inline typename Size< Matrix<TValue, DIMENSION> >::Type
 coordinate(Iter<Matrix<TValue, DIMENSION>, PositionIterator > & me,
-		   unsigned int dimension_)
+           unsigned int dimension_)
 {
-	return coordinate(container(me), position(me), dimension_);
+    return coordinate(container(me), position(me), dimension_);
 }
 
 template <typename TValue, unsigned DIMENSION>
 inline typename Size< Matrix<TValue, DIMENSION> >::Type
 coordinate(Iter<Matrix<TValue, DIMENSION> const, PositionIterator > & me,
-		   unsigned int dimension_)
+           unsigned int dimension_)
 {
-	return coordinate(container(me), position(me), dimension_);
+    return coordinate(container(me), position(me), dimension_);
 }
 
-/*
-operator +
-Computes the matricial sum between two matrices
-..signature:Matrix +(matrix1,matrix2)
-..param.matrix1:The first matrix.
-...type:Class.Matrix
-..param.matrix2:The second matrix.
-...type:Class.Matrix
-..returns:The sum of the two matrices (another nxm matrix).
-..remarks:The number of rows and columns of matrix1 must be equal to the number of rows and columns of matrix2 (length of dimensions for NDimensional matrices)
-*/
+/*!
+ * @fn Matrix::operator+
+ * @brief Sum operator for the Matrix type.
+ *
+ * @signature TMatrix Matrix::operator+(lhs, rhs);
+ *
+ * @param[in] lhs First summand.
+ * @param[in] rhs Second summand.
+ *
+ * @return TMatrix The resulting matrix of same type as <tt>lhs</tt> and <tt>rhs</tt>.
+ */
 
 template <typename TValue,unsigned DIMENSION>
 Matrix<TValue,DIMENSION>
 operator + (Matrix<TValue,DIMENSION> const & matrix1,Matrix<TValue,DIMENSION> const & matrix2)
 {
-	//the two matrices must have same dimension
-	SEQAN_ASSERT(_dataLengths(matrix1) == _dataLengths(matrix2));
-
-	Matrix<TValue,DIMENSION> result;
-	//copy the first matrix
-	setDimension(result,length(_dataLengths(matrix1)));
-	_dataLengths(result) = _dataLengths(matrix1);
-	resize(result);
-
-	//add the matrices
-	for(unsigned int i = 0;i< length(host(result));++i)
-	{
-		value(host(result), i)=value(host(matrix1), i)+value(host(matrix2), i);
-	}
-	//Return matrix sum
-	return result;
+    //the two matrices must have same dimension
+    SEQAN_ASSERT(_dataLengths(matrix1) == _dataLengths(matrix2));
+
+    Matrix<TValue,DIMENSION> result;
+    //copy the first matrix
+    setDimension(result,length(_dataLengths(matrix1)));
+    _dataLengths(result) = _dataLengths(matrix1);
+    resize(result);
+
+    //add the matrices
+    for(unsigned int i = 0;i< length(host(result));++i)
+    {
+        value(host(result), i)=value(host(matrix1), i)+value(host(matrix2), i);
+    }
+    //Return matrix sum
+    return result;
 }
 
 template <typename TValue,unsigned DIMENSION>
 Matrix<TValue,DIMENSION>
 operator - (Matrix<TValue,DIMENSION> const & matrix1,Matrix<TValue,DIMENSION> const & matrix2)
 {
-	//the two matrices must have same dimension
-	SEQAN_ASSERT(_dataLengths(matrix1) == _dataLengths(matrix2));
-
-	Matrix<TValue,DIMENSION> result;
-	//resize the matrix
-	setDimension(result,length(_dataLengths(matrix1)));
-	_dataLengths(result) = _dataLengths(matrix1);
-	resize(result);
-
-	//subtract the matrices
-	for(unsigned int i = 0;i< length(host(result));++i)
-	{
-		value(host(result), i)=value(host(matrix1), i)-value(host(matrix2), i);
-	}
-	//Return matrix difference
-	return result;
+    //the two matrices must have same dimension
+    SEQAN_ASSERT(_dataLengths(matrix1) == _dataLengths(matrix2));
+
+    Matrix<TValue,DIMENSION> result;
+    //resize the matrix
+    setDimension(result,length(_dataLengths(matrix1)));
+    _dataLengths(result) = _dataLengths(matrix1);
+    resize(result);
+
+    //subtract the matrices
+    for(unsigned int i = 0;i< length(host(result));++i)
+    {
+        value(host(result), i)=value(host(matrix1), i)-value(host(matrix2), i);
+    }
+    //Return matrix difference
+    return result;
 }
 
 template <typename TValue>
 Matrix<TValue, 2>
 operator * (Matrix<TValue, 2> const & matrix1, Matrix<TValue, 2> const & matrix2)
 {
-	SEQAN_ASSERT_EQ(length(matrix1,1), length(matrix2,0));
-
-	unsigned int nrow1=length(matrix1,0);
-	unsigned int ncol2=length(matrix2,1);
-	Matrix<TValue, 2> result;
-	//resize the matrix
-	setLength(result, 0, nrow1);
-	setLength(result, 1, ncol2);
-	resize(result,(TValue) 0);
-
-	//Matrix product
-	for(unsigned int row = 0; row < nrow1; row++)
-	{
-		for(unsigned int col = 0; col < ncol2; col++)
-		{
-			for(unsigned int colRes = 0; colRes < length(matrix1,1); colRes++)
-			{
-				value(result,row,col)+=	value(host(matrix1), row + colRes * matrix1.data_factors[1])*value(host(matrix2), colRes + col * matrix2.data_factors[1]);
-			}
-		}
-	}
-	//return the matrix product
-	return result;
+    SEQAN_ASSERT_EQ(length(matrix1,1), length(matrix2,0));
+
+    unsigned int nrow1=length(matrix1,0);
+    unsigned int ncol2=length(matrix2,1);
+    Matrix<TValue, 2> result;
+    //resize the matrix
+    setLength(result, 0, nrow1);
+    setLength(result, 1, ncol2);
+    resize(result,(TValue) 0);
+
+    //Matrix product
+    for(unsigned int row = 0; row < nrow1; row++)
+    {
+        for(unsigned int col = 0; col < ncol2; col++)
+        {
+            for(unsigned int colRes = 0; colRes < length(matrix1,1); colRes++)
+            {
+                value(result,row,col)+=    value(host(matrix1), row + colRes * matrix1.data_factors[1])*value(host(matrix2), colRes + col * matrix2.data_factors[1]);
+            }
+        }
+    }
+    //return the matrix product
+    return result;
 }
 
 
@@ -877,30 +873,30 @@ template <typename TValue>
 Matrix<TValue, 2>
 operator * (TValue const & scalar, Matrix<TValue, 2> const & matrix)
 {
-	Matrix<TValue, 2> result;
-	result= matrix;
-	//scalar multiplication
-	for(unsigned int i = 0;i< length(host(result));++i)
-	{
-		value(host(result), i)*=scalar;
-	}
-	//return the matrix product
-	return result;
+    Matrix<TValue, 2> result;
+    result= matrix;
+    //scalar multiplication
+    for(unsigned int i = 0;i< length(host(result));++i)
+    {
+        value(host(result), i)*=scalar;
+    }
+    //return the matrix product
+    return result;
 }
 
 template <typename TValue>
 Matrix<TValue, 2>
 operator * (Matrix<TValue, 2> const & matrix, TValue const & scalar)
 {
-	Matrix<TValue, 2> result;
-	result= matrix;
-	//scalar multiplication
-	for(unsigned int i = 0;i< length(host(result));++i)
-	{
-		value(host(result), i)*=scalar;
-	}
-	//return the matrix product
-	return result;
+    Matrix<TValue, 2> result;
+    result= matrix;
+    //scalar multiplication
+    for(unsigned int i = 0;i< length(host(result));++i)
+    {
+        value(host(result), i)*=scalar;
+    }
+    //return the matrix product
+    return result;
 }
 
 
@@ -908,50 +904,39 @@ template <typename TValue, unsigned DIMENSION1, unsigned DIMENSION2>
 bool
 operator == (Matrix<TValue, DIMENSION1> const & matrix1, Matrix<TValue, DIMENSION2> const & matrix2)
 {
-	bool result;
-	result= (matrix1.data_lengths==matrix2.data_lengths)&&(matrix1.data_factors==matrix2.data_factors)&&(value(matrix1.data_host)==value(matrix2.data_host))&&(DIMENSION1==DIMENSION2);
-	return result;
+    bool result;
+    result= (matrix1.data_lengths==matrix2.data_lengths)&&(matrix1.data_factors==matrix2.data_factors)&&(value(matrix1.data_host)==value(matrix2.data_host))&&(DIMENSION1==DIMENSION2);
+    return result;
 }
-/*
-.Function.matricialSum:
-..summary:Computes the matricial sum between two nxm matrixes
-..signature:matricialSum(matrix1,matrix2)
-..param.matrix1:The first matrix.
-...type:Matrix<TValue, 2>&
-..param.matrix2:The second matrix.
-...type:Matrix<TValue, 2>&
-..returns:The sum of the two matrices (another nxm matrix).
-..remarks:The number of rows and columns of matrix1 must be equal to the number of rows and columns of matrix2.
-..include:seqan/align.h
-*/
+
 /*
 template <typename TValue>
 Matrix<TValue,2>
 matricialSum(Matrix<TValue,2> &matrix1,Matrix<TValue,2> &matrix2)
 {
-	//the two matrices must have same dimension
-	if(length(matrix1,0) != length(matrix2,0)||length(matrix1,1) != length(matrix2,1))
-	{
-		fprintf(stderr,"Error: The two matrices have different dimensions");
-	}
+    //the two matrices must have same dimension
+    if(length(matrix1,0) != length(matrix2,0)||length(matrix1,1) != length(matrix2,1))
+    {
+        fprintf(stderr,"Error: The two matrices have different dimensions");
+    }
 
 
-	unsigned int nrow=length(matrix1,0);
-	unsigned int ncol=length(matrix1,1);
+    unsigned int nrow=length(matrix1,0);
+    unsigned int ncol=length(matrix1,1);
 
-	Matrix<TValue,2> result;
-	//resize the matrix
-	setLength(result, 0, nrow);
-	setLength(result, 1, ncol);
-	resize(result);
+    Matrix<TValue,2> result;
+    //resize the matrix
+    setLength(result, 0, nrow);
+    setLength(result, 1, ncol);
+    resize(result);
 
-	//add the matrices
-	for(unsigned int i = 0;i< nrow*ncol;++i)
-	{
-		value(host(result), i)=value(host(matrix1), i)+value(host(matrix2), i);
-	}
-	//Return matrix difference
-	return result;
+    //add the matrices
+    for(unsigned int i = 0;i< nrow*ncol;++i)
+    {
+        value(host(result), i)=value(host(matrix1), i)+value(host(matrix2), i);
+    }
+    //Return matrix difference
+    return result;
 
 }
 */
@@ -959,154 +944,129 @@ matricialSum(Matrix<TValue,2> &matrix1,Matrix<TValue,2> &matrix2)
 // _matricialDifference
 //////////////////////////////////////////////////////////////////////////////
 
-/*
-.Function.matricialDifference:
-..summary:Computes the matricial difference between two matrixes
-..signature:matricialDifference(matrix1,matrix2)
-..param.matrix1:The first matrix.
-...type:Matrix<TValue, 2>&
-..param.matrix2:The second matrix.
-...type:Matrix<TValue, 2>&
-..returns:The difference of the two matrices (another matrix).
-..remarks:The number of rows and columns of matrix1 must be equal to the number of rows and columns of matrix2.
-..include:seqan/align.h
-*/
 /*
 template <typename TValue>
 inline Matrix<TValue,2>
 matricialDifference(Matrix<TValue,2> & matrix1, Matrix<TValue,2> & matrix2)
 {
-	//the two matrices must have same dimension
-	if(length(matrix1,0) != length(matrix2,0)||length(matrix1,1) != length(matrix2,1))
-	{
-		fprintf(stderr,"Error: The two matrices have different dimensions");
-	}
-
-	unsigned int nrow=length(matrix1,0);
-	unsigned int ncol=length(matrix1,1);
-
-	Matrix<TValue,2> result;
-	//resize the matrix
-	//setDimension(result, 2);
-	setLength(result, 0, nrow);
-	setLength(result, 1, ncol);
-	resize(result);
-
-	//Substract the matrices
-	for(unsigned int i1 = 0;i1< nrow;++i1)
-		{
-			for(unsigned int i2 = 0;i2<ncol;++i2)
-			{
-				value(host(result), i1 + i2 * _dataFactors(result)[1])=value(host(matrix1), i1 + i2 * _dataFactors(matrix1)[1])-value(host(matrix2), i1 + i2 * _dataFactors(matrix2)[1]);
-			}
-
-		}
-	//Return matrix difference
-	return result;
+    //the two matrices must have same dimension
+    if(length(matrix1,0) != length(matrix2,0)||length(matrix1,1) != length(matrix2,1))
+    {
+        fprintf(stderr,"Error: The two matrices have different dimensions");
+    }
+
+    unsigned int nrow=length(matrix1,0);
+    unsigned int ncol=length(matrix1,1);
+
+    Matrix<TValue,2> result;
+    //resize the matrix
+    //setDimension(result, 2);
+    setLength(result, 0, nrow);
+    setLength(result, 1, ncol);
+    resize(result);
+
+    //Substract the matrices
+    for(unsigned int i1 = 0;i1< nrow;++i1)
+        {
+            for(unsigned int i2 = 0;i2<ncol;++i2)
+            {
+                value(host(result), i1 + i2 * _dataFactors(result)[1])=value(host(matrix1), i1 + i2 * _dataFactors(matrix1)[1])-value(host(matrix2), i1 + i2 * _dataFactors(matrix2)[1]);
+            }
+
+        }
+    //Return matrix difference
+    return result;
 }
 */
-/*
-.Function.matricialProduct:
-..summary:Computes the matricial product between two 2-dimensional matrixes
-..signature:matricialProduct(matrix1,matrix2)
-..param.matrix1:The first matrix (mxn).
-...type:Matrix<TValue,2>&
-..param.matrix2:The second matrix (nxp).
-...type:Matrix<TValue,2>&
-..returns:The products of the two matrices (another matrix, mxp).
-..remarks:The number of columns of matrix1 (left matrix) must be equal to the number of rows of matrix2(right matrix).
-..include:seqan/align.h
-*/
+
 /*
 template <typename TValue>
 inline Matrix<TValue, 2>
 matricialProduct(Matrix<TValue, 2> &matrix1,
-		Matrix<TValue, 2> &matrix2)
-{
-	//SEQAN_ASSERT_LT(dimension_, dimension(me));
-	if(length(matrix1,1) != length(matrix2,0))
-	{
-		fprintf(stderr,"Error: Number of columns of matrix1 is unequal to number of rows of matrix2");
-	}
-
-	unsigned int nrow1=length(matrix1,0);
-	unsigned int ncol2=length(matrix2,1);
-	Matrix<TValue, 2> result;
-	//resize the matrix
-	setLength(result, 0, nrow1);
-	setLength(result, 1, ncol2);
-	resize(result,(TValue) 0);
-
-	//Matrix product
-	for(unsigned int row = 0; row < nrow1; row++)
-	{
-		for(unsigned int col = 0; col < ncol2; col++)
-		{
-			for(unsigned int colRes = 0; colRes < length(matrix1,1); colRes++)
-			{
-				value(result,row,col)+=value(matrix1, row,colRes)*value(matrix2,colRes,col);
-			}
-		}
-	}
-	//return the matrix product
-	return result;
+        Matrix<TValue, 2> &matrix2)
+{
+    //SEQAN_ASSERT_LT(dimension_, dimension(me));
+    if(length(matrix1,1) != length(matrix2,0))
+    {
+        fprintf(stderr,"Error: Number of columns of matrix1 is unequal to number of rows of matrix2");
+    }
+
+    unsigned int nrow1=length(matrix1,0);
+    unsigned int ncol2=length(matrix2,1);
+    Matrix<TValue, 2> result;
+    //resize the matrix
+    setLength(result, 0, nrow1);
+    setLength(result, 1, ncol2);
+    resize(result,(TValue) 0);
+
+    //Matrix product
+    for(unsigned int row = 0; row < nrow1; row++)
+    {
+        for(unsigned int col = 0; col < ncol2; col++)
+        {
+            for(unsigned int colRes = 0; colRes < length(matrix1,1); colRes++)
+            {
+                value(result,row,col)+=value(matrix1, row,colRes)*value(matrix2,colRes,col);
+            }
+        }
+    }
+    //return the matrix product
+    return result;
 }
 */
-// TODO(holtgrew): Should work as the graph-transpose.
-/**
-.Function.Matrix#transpose
-..summary:Transposes matrix
-..class:Class.Matrix
-..signature:Matrix transpose(matrix)
-..param.matrix:The matrix (mxn) to transpose.
-...type:Class.Matrix
-...remarks: must be of type Matrix<TValue,2> (two dimensional)
-..returns:Transposed matrix
-..remarks:Only works on two dimensional matrices
-..include:seqan/align.h
-*/
+
+/*!
+ * @fn Matrix#transpose
+ * @brief Tranpose a 2D Matrix.
+ *
+ * @signature TMatrix transpose(matrix);
+ *
+ * @param[in] matrix The matrix to tranpose.
+ * @return TMatrix The resulting tranposed matrix.
+ */
+
 template <typename TValue>
 Matrix<TValue,2>
 transpose(Matrix<TValue,2> const & matrix)
 {
 
-	unsigned int nrow=length(matrix,0);
-	unsigned int ncol=length(matrix,1);
+    unsigned int nrow=length(matrix,0);
+    unsigned int ncol=length(matrix,1);
 
-	Matrix<TValue,2> result;
-	//resize the matrix
-	setLength(result, 0, ncol);
-	setLength(result, 1, nrow);
-	resize(result);
+    Matrix<TValue,2> result;
+    //resize the matrix
+    setLength(result, 0, ncol);
+    setLength(result, 1, nrow);
+    resize(result);
 
 
-	for(unsigned int i1 = 0;i1< nrow;++i1)
-	{
-		for(unsigned int i2 = 0;i2<ncol;++i2)
-		{
-			value(host(result), i2 + i1 * _dataFactors(result)[1])=value(host(matrix), i1 + i2 * matrix.data_factors[1]);
-		}
+    for(unsigned int i1 = 0;i1< nrow;++i1)
+    {
+        for(unsigned int i2 = 0;i2<ncol;++i2)
+        {
+            value(host(result), i2 + i1 * _dataFactors(result)[1])=value(host(matrix), i1 + i2 * matrix.data_factors[1]);
+        }
 
-	}
+    }
 
-	//Return transposed matrix
-	return result;
+    //Return transposed matrix
+    return result;
 
 }
 
 
 template < typename TValue >
-::std::ostream& operator<<(::std::ostream &out, const Matrix<TValue,2> &matrix)
-{
-	for(unsigned int i1 = 0;i1< matrix.data_lengths[0];++i1)
-	{
-			for(unsigned int i2 = 0;i2<(matrix.data_lengths[1]-1);++i2)
-			{
-				out<<value(host(matrix), i1 + i2 * matrix.data_factors[1])<<"\t";
-			}
-			//Last line is followd by \n instead of \t
-			out<<value(host(matrix), i1 + (matrix.data_lengths[1]-1) *matrix.data_factors[1])<<"\n";
-		}
+std::ostream& operator<<(std::ostream &out, const Matrix<TValue,2> &matrix)
+{
+    for(unsigned int i1 = 0;i1< matrix.data_lengths[0];++i1)
+    {
+            for(unsigned int i2 = 0;i2<(matrix.data_lengths[1]-1);++i2)
+            {
+                out<<value(host(matrix), i1 + i2 * matrix.data_factors[1])<<"\t";
+            }
+            //Last line is followd by \n instead of \t
+            out<<value(host(matrix), i1 + (matrix.data_lengths[1]-1) *matrix.data_factors[1])<<"\n";
+        }
 
     return out;
 }
@@ -1120,20 +1080,20 @@ ::std::ostream& operator<<(::std::ostream &out, const Matrix<TValue,2> &matrix)
 // template < typename TValue >
 // void read(FILE *file, Matrix<TValue,2> & matrix)
 // {
-// 	//unsigned int column_size=3;
-// 	unsigned int column_size=pow(4,5);
-// 	//read the transition matrix
-// 	setLength(matrix, 0, column_size);
-// 	setLength(matrix, 1, column_size);
+//     //unsigned int column_size=3;
+//     unsigned int column_size=pow(4,5);
+//     //read the transition matrix
+//     setLength(matrix, 0, column_size);
+//     setLength(matrix, 1, column_size);
 // resize(matrix,0.0);
-// 	for(unsigned int row=0; row<column_size; row++)
-// 	{
-// 		for(unsigned int col=0; col<column_size; col++)
-// 		{
-// 		  fscanf(file,"%lf ", & value(matrix, row,col));
-// 		}
-// 		fscanf(file,"\n");
-// 	}
+//     for(unsigned int row=0; row<column_size; row++)
+//     {
+//         for(unsigned int col=0; col<column_size; col++)
+//         {
+//           fscanf(file,"%lf ", & value(matrix, row,col));
+//         }
+//         fscanf(file,"\n");
+//     }
 // }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/align_extend.h b/seqan/align_extend.h
new file mode 100644
index 0000000..b9cc513
--- /dev/null
+++ b/seqan/align_extend.h
@@ -0,0 +1,48 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// ==========================================================================
+// Extras for the align module
+// ==========================================================================
+
+#ifndef SEQAN_ALIGN_EXTEND_H
+#define SEQAN_ALIGN_EXTEND_H
+
+#include <seqan/basic.h>
+#include <seqan/align.h>
+#include <seqan/seeds.h>
+
+#include <seqan/align_extend/align_extend_base.h>
+#include <seqan/align_extend/dp_scout_xdrop.h>
+#include <seqan/align_extend/align_extend.h>
+
+#endif
diff --git a/seqan/align_extend/align_extend.h b/seqan/align_extend/align_extend.h
new file mode 100644
index 0000000..038c28b
--- /dev/null
+++ b/seqan/align_extend/align_extend.h
@@ -0,0 +1,647 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// ==========================================================================
+// This file contains routines to extend an existing Align object
+// ==========================================================================
+
+#ifndef INCLUDE_ALIGN_ALIGN_EXTEND_H
+#define INCLUDE_ALIGN_ALIGN_EXTEND_H
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class AliExtContext_
+// ----------------------------------------------------------------------------
+
+// Context with memory holding objects for alignment extension
+// This can be reused to prevent repeated memory allocations
+template <typename TGaps0, typename TGaps1, typename TDPContext>
+struct AliExtContext_
+{
+    typedef typename Size<TGaps0>::Type TSize;
+    typedef typename Position<TGaps0>::Type TPosition;
+
+    TGaps0 leftRow0, centerRow0, rightRow0;
+    TGaps1 leftRow1, centerRow1, rightRow1;
+
+    TDPContext dpContext;
+
+    String<TraceSegment_<TPosition, TSize> > traceSegment;
+};
+
+template <typename TGaps0, typename TGaps1, typename TDPContext>
+inline void
+clear(AliExtContext_<TGaps0, TGaps1, TDPContext> & prov)
+{
+    // gaps don't need to be cleared, because they are always
+    // re-assigned before use; dpContext, too!
+
+    // trace segment always needs to be cleared
+    clear(prov.traceSegment);
+    // dpContext doesn't need to be cleared
+}
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _reverseTrace()
+// ----------------------------------------------------------------------------
+
+// Reverse a trace string and adapt internal position.
+template <typename TPosition, typename TPos2, typename TSize, typename TSpec>
+void _reversePartialTrace(String<TraceSegment_<TPosition,
+                                               TSize>, TSpec> & trace,
+                          TPos2 const lengthH,
+                          TPos2 const lengthV)
+{
+    typedef String<TraceSegment_<TPosition, TSize>, TSpec> TTrace;
+    typedef typename Iterator<TTrace, Rooted>::Type TTraceIter;
+
+    if (empty(trace))
+        return;
+
+    for (TTraceIter it = begin(trace, Rooted()); !atEnd(it); goNext(it))
+    {
+        it->_horizontalBeginPos = lengthH - _getEndHorizontal(*it);
+        it->_verticalBeginPos = lengthV - _getEndVertical(*it);
+    }
+    reverse(trace);
+}
+
+// ----------------------------------------------------------------------------
+// Function _setUpAndRunAlignImpl()
+// ----------------------------------------------------------------------------
+
+template <typename TAliExtContext_, typename TString0, typename TString1, typename TScoreValue,
+          typename TScoreSpec, typename TTracebackConfig>
+inline TScoreValue
+_setUpAndRunAlignImpl(TAliExtContext_ & alignContext,
+                      TString0 const & str0,
+                      TString1 const & str1,
+                      Score<TScoreValue, TScoreSpec> const & scoreScheme,
+                      int const /*lowerDiag*/,
+                      int const /*upperDiag*/,
+                      TScoreValue const /*xDrop*/,
+                      TTracebackConfig const & /*gapOrientation*/,
+                      False const & /*TBoolBanded*/,
+                      False const & /*TBoolXDrop*/)
+{
+    typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
+    typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOff>, TFreeEndGaps,
+                         TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
+
+    DPScoutState_<Default> scoutState;
+    return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme,
+                                 TAlignConfig());
+}
+
+template <typename TAliExtContext_, typename TString0, typename TString1, typename TScoreValue,
+          typename TScoreSpec, typename TTracebackConfig>
+inline TScoreValue
+_setUpAndRunAlignImpl(TAliExtContext_ & alignContext,
+                      TString0 const & str0,
+                      TString1 const & str1,
+                      Score<TScoreValue, TScoreSpec> const & scoreScheme,
+                      int const lowerDiag,
+                      int const upperDiag,
+                      TScoreValue const /*xDrop*/,
+                      TTracebackConfig const & /*gapOrientation*/,
+                      True const & /*TBoolBanded*/,
+                      False const & /*TBoolXDrop*/)
+{
+    typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
+    typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOn>, TFreeEndGaps,
+                         TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
+
+    DPScoutState_<Default> scoutState;
+    return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme,
+                                 TAlignConfig(lowerDiag, upperDiag));
+}
+
+template <typename TAliExtContext_, typename TString0, typename TString1, typename TScoreValue,
+          typename TScoreSpec, typename TTracebackConfig>
+inline TScoreValue
+_setUpAndRunAlignImpl(TAliExtContext_ & alignContext,
+                      TString0 const & str0,
+                      TString1 const & str1,
+                      Score<TScoreValue, TScoreSpec> const & scoreScheme,
+                      int const /*lowerDiag*/,
+                      int const /*upperDiag*/,
+                      TScoreValue const xDrop,
+                      TTracebackConfig const & /*gapOrientation*/,
+                      False const & /*TBoolBanded*/,
+                      True const & /*TBoolXDrop*/)
+{
+    typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
+    typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOff>, TFreeEndGaps,
+                         TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
+
+    DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop);
+    return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme,
+                                 TAlignConfig());
+}
+
+template <typename TAliExtContext_, typename TString0, typename TString1, typename TScoreValue,
+          typename TScoreSpec, typename TTracebackConfig>
+inline TScoreValue
+_setUpAndRunAlignImpl(TAliExtContext_ & alignContext,
+                      TString0 const & str0,
+                      TString1 const & str1,
+                      Score<TScoreValue, TScoreSpec> const & scoreScheme,
+                      int const lowerDiag,
+                      int const upperDiag,
+                      TScoreValue const xDrop,
+                      TTracebackConfig const & /*gapOrientation*/,
+                      True const & /*TBoolBanded*/,
+                      True const & /*TBoolXDrop*/)
+{
+    typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
+    typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOn>, TFreeEndGaps,
+                         TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
+
+    DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop);
+    return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme,
+                                 TAlignConfig(lowerDiag, upperDiag));
+}
+
+// ----------------------------------------------------------------------------
+// Function _extendAlignmentImpl()
+// ----------------------------------------------------------------------------
+
+template <typename TSource0, typename TSource1, typename TGapsSpec0, typename TGapsSpec1,
+          typename TString0, typename TString1, typename TPos, typename TScoreValue, typename TScoreSpec,
+          typename TBoolBanded, typename TBoolXDrop, typename TAliExtContext_>
+inline TScoreValue
+_extendAlignmentImpl(Gaps<TSource0, TGapsSpec0> & row0,
+                     Gaps<TSource1, TGapsSpec1> & row1,
+                     TScoreValue const & origScore,
+                     TString0 const & hSeq,
+                     TString1 const & vSeq,
+                     Tuple<TPos, 4> const & positions,
+                     ExtensionDirection const & direction,
+                     int const lowerDiag,
+                     int const upperDiag,
+                     TScoreValue const & xDrop,
+                     Score<TScoreValue, TScoreSpec> const & scoreScheme,
+                     TBoolBanded const & /**/,
+                     TBoolXDrop const & /**/,
+                     TAliExtContext_ & alignContext)
+{
+    typedef typename Infix<TSource0 const>::Type TInf0;
+    typedef typename Infix<TSource1 const>::Type TInf1;
+
+    TPos const hBeginPos    = positions[0];
+    TPos const vBeginPos    = positions[1];
+    TPos const hEndPos      = positions[2];
+    TPos const vEndPos      = positions[3];
+
+    SEQAN_ASSERT_EQ(infix(source(row0), beginPosition(row0), endPosition(row0)),
+                    infix(hSeq, hBeginPos, hEndPos));
+    SEQAN_ASSERT_EQ(infix(source(row1), beginPosition(row1), endPosition(row1)),
+                    infix(vSeq, vBeginPos, vEndPos));
+
+    bool extendLeft = ((direction & EXTEND_LEFT) && (hBeginPos > 0u) && (vBeginPos > 0u));
+    bool extendRight = ((direction & EXTEND_RIGHT) && (hEndPos < length(hSeq)) && (vEndPos < length(vSeq)));
+
+    clear(alignContext);
+    alignContext.centerRow0 = row0;
+    alignContext.centerRow1 = row1;
+
+    TScoreValue leftScore   = 0;
+    TScoreValue centerScore = origScore;
+    TScoreValue rightScore  = 0;
+
+    TPos newAlignLen = length(row0);
+
+    // centerScore was set to "compute yourself" by interface function without score parameter
+    if (centerScore == minValue<TScoreValue>())
+    {
+        centerScore = 0;
+
+        for (TPos i = 0; i < length(row0); ++i)
+        {
+            if ( ( isGap(row0, i)) || ( isGap(row1, i)) )
+            {
+                if (( i==0 ) ||
+                    (isGap(row0, i-1) != isGap(row0, i)) ||
+                    (isGap(row1, i-1) != isGap(row1, i)) )
+                {
+                    centerScore += scoreGapOpen(scoreScheme);
+                }
+                else
+                {
+                    centerScore += scoreGapExtend(scoreScheme);
+                }
+            }
+            else
+            {
+                centerScore += score(scoreScheme, row0[i], row1[i]);
+            }
+        }
+    }
+
+    // "reset" original alignment to full length on sequences and no gaps
+    assignSource(row0, infix(hSeq, 0, length(hSeq)));
+    assignSource(row1, infix(vSeq, 0, length(vSeq)));
+
+    // left
+    if (extendLeft)
+    {
+        TInf0 inf0 = infix(hSeq, 0, hBeginPos);
+        TInf1 inf1 = infix(vSeq, 0, vBeginPos);
+
+        // reverse input
+        ModifiedString<TInf0, ModReverse> const r_inf0(inf0);
+        ModifiedString<TInf1, ModReverse> const r_inf1(inf1);
+
+        leftScore = _setUpAndRunAlignImpl(alignContext, r_inf0, r_inf1, scoreScheme, lowerDiag, upperDiag, xDrop,
+                                          TracebackConfig_<CompleteTrace, GapsRight>(), TBoolBanded(), TBoolXDrop());
+        // un-reverve
+        _reversePartialTrace(alignContext.traceSegment, length(inf0), length(inf1));
+
+        setSource(alignContext.leftRow0, inf0);
+        setSource(alignContext.leftRow1, inf1);
+
+        _adaptTraceSegmentsTo(alignContext.leftRow0, alignContext.leftRow1, alignContext.traceSegment);
+
+        if (length(alignContext.leftRow0) > 0)
+        {
+            integrateGaps(row0, alignContext.leftRow0);
+            integrateGaps(row1, alignContext.leftRow1);
+            setClippedBeginPosition(row0, clippedBeginPosition(alignContext.leftRow0));
+            setClippedBeginPosition(row1, clippedBeginPosition(alignContext.leftRow1));
+
+            newAlignLen += length(alignContext.leftRow0);
+        }
+        else
+        {
+            extendLeft = false;
+        }
+    }
+
+    // center
+    if (extendLeft)
+    {
+        integrateGaps(row0, alignContext.centerRow0, length(alignContext.leftRow0));
+        integrateGaps(row1, alignContext.centerRow1, length(alignContext.leftRow1));
+    }
+    else
+    {
+        integrateGaps(row0, alignContext.centerRow0, hBeginPos);
+        integrateGaps(row1, alignContext.centerRow1, vBeginPos);
+        TPos leadGaps0 = countGaps(begin(alignContext.centerRow0));
+        TPos leadGaps1 = countGaps(begin(alignContext.centerRow1));
+
+        TPos sourceBeginPos0 = toSourcePosition(alignContext.centerRow0, leadGaps0) + hBeginPos -
+                               beginPosition(alignContext.centerRow0);
+        TPos sourceBeginPos1 = toSourcePosition(alignContext.centerRow1, leadGaps1) + vBeginPos -
+                               beginPosition(alignContext.centerRow1);
+
+        setClippedBeginPosition(row0, toViewPosition(row0, sourceBeginPos0) - leadGaps0);
+        setClippedBeginPosition(row1, toViewPosition(row1, sourceBeginPos1) - leadGaps1);
+    }
+
+    // right
+    if (extendRight)
+    {
+        TInf0 inf0 = infix(hSeq, hEndPos, length(hSeq));
+        TInf1 inf1 = infix(vSeq, vEndPos, length(vSeq));
+
+        clear(alignContext.traceSegment);
+        rightScore = _setUpAndRunAlignImpl(alignContext, inf0, inf1, scoreScheme, lowerDiag, upperDiag, xDrop,
+                                           TracebackConfig_<CompleteTrace, GapsLeft>(), TBoolBanded(), TBoolXDrop());
+
+        setSource(alignContext.rightRow0, inf0);
+        setSource(alignContext.rightRow1, inf1);
+        _adaptTraceSegmentsTo(alignContext.rightRow0, alignContext.rightRow1, alignContext.traceSegment);
+
+        if (length(alignContext.rightRow0) > 0)
+        {
+            integrateGaps(row0, alignContext.rightRow0);
+            integrateGaps(row1, alignContext.rightRow1);
+
+            newAlignLen += length(alignContext.rightRow0);
+        }
+    }
+
+    setClippedEndPosition(row0, clippedBeginPosition(row0) + newAlignLen);
+    setClippedEndPosition(row1, clippedBeginPosition(row1) + newAlignLen);
+
+    return leftScore + centerScore + rightScore;
+}
+
+// get rows from align object
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec,
+          typename TBoolBanded, typename TBoolXDrop, typename TAliExtContext_>
+inline TScoreValue
+_extendAlignmentImpl(Align<TStringInfix, TAlignSpec> & align,
+                     TScoreValue const & origScore,
+                     TString const & hSeq,
+                     TString const & vSeq,
+                     Tuple<TPos, 4> const & positions,
+                     ExtensionDirection const & direction,
+                     int const lowerDiag,
+                     int const upperDiag,
+                     TScoreValue const & xDrop,
+                     Score<TScoreValue, TScoreSpec> const & scoreScheme,
+                     TBoolBanded const & /**/,
+                     TBoolXDrop const & /**/,
+                     TAliExtContext_ & alignContext)
+{
+    SEQAN_ASSERT_EQ_MSG(length(rows(align)), 2u, "Only works with pairwise alignments.");
+    SEQAN_ASSERT_EQ_MSG(length(row(align, 0)), length(row(align, 1)), "Invalid alignment!");
+
+    return _extendAlignmentImpl(row(align, 0), row(align, 1), origScore, hSeq, vSeq, positions, direction, lowerDiag,
+                                upperDiag, xDrop, scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext);
+}
+
+// create AlignContext
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec,
+          typename TBoolBanded, typename TBoolXDrop>
+inline TScoreValue
+_extendAlignmentImpl(Align<TStringInfix, TAlignSpec> & align,
+                     TScoreValue const & origScore,
+                     TString const & hSeq,
+                     TString const & vSeq,
+                     Tuple<TPos, 4> const & positions,
+                     ExtensionDirection const & direction,
+                     int const lowerDiag,
+                     int const upperDiag,
+                     TScoreValue const & xDrop,
+                     Score<TScoreValue, TScoreSpec> const & scoreScheme,
+                     TBoolBanded const & /**/,
+                     TBoolXDrop const & /**/)
+{
+    if (scoreGapOpen(scoreScheme) == scoreGapExtend(scoreScheme))
+    {
+        typedef DPContext<TScoreValue, LinearGaps> TDPContext;
+        typedef AliExtContext_<Gaps<TStringInfix, TAlignSpec>,
+                               Gaps<TStringInfix, TAlignSpec>,
+                               TDPContext> TAliExtContext_;
+        TAliExtContext_ alignContext;
+        return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop,
+                                    scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext);
+    }
+    else
+    {
+        typedef DPContext<TScoreValue, AffineGaps> TDPContext;
+        typedef AliExtContext_<Gaps<TStringInfix, TAlignSpec>,
+                               Gaps<TStringInfix, TAlignSpec>,
+                               TDPContext> TAliExtContext_;
+        TAliExtContext_ alignContext;
+        return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop,
+                                    scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function extendAlignment()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn extendAlignment
+ * @headerfile <seqan/align_extend.h>
+ * @brief X-Drop extension for alignment objects.
+ * @signature TScoreValue extendAlignment(align, [origScore,] hSeq, vSeq, positions, extensionDirection,
+ *                                        [lowerDiag, upperDiag,] [xDrop,] scoreScheme);
+ *
+ * @param[in,out]  align     The @link Align @endlink object to work on.  Must be an alignment over the
+ *                           @link InfixSegment infix @endlink of the <i>const</i> type of <tt>hSeq</tt>
+ *                           and <tt>vSeq</tt>.  Also see section "Returned Alignment".
+ * @param[in]      origScore Original score value of the alignment (optional; computed if not provided).
+ * @param[in]      hSeq      Full horizontal sequence.
+ * @param[in]      vSeq      Full vertical sequence.
+ * @param[in]      positions A @link Tuple @endlink of length 4 with the begin and end position of the
+ *                           infixes in align.
+ * @param[in]      extensionDirection
+ *                           The extension direction (@link ExtensionDirection @endlink).
+ * @param[in]      lowerDiag Lower alignment diagonal to use (<tt>int</tt>).
+ * @param[in]      upperDiag Upper alignment diagonal to use (<tt>int</tt>).
+ * @param[in]      xDrop     The X-drop value to use (integral value). It only limits computation of new
+ * columns in the DP-Matrix and has no influence on the diagonals (but can be combined with them).
+ * @param[in]      scoringScheme
+ *                           The @link Score @endlink to use.
+ *
+ * @return          TScoreValue
+ *                           The score of the new alignment.  <tt>TScoreValue</tt> is the value type of
+ *                           <tt>scoringScheme</tt>.
+ *
+ * @section Returned Alignment
+ *
+ * The resulting alignment has the infixes extended to the whole underlying sequence.  The alignment
+ * is clipped to give the parts of the aligned sequences.
+ *
+ * @section Example
+ *
+ * @include demos/dox/align_extend/extend_alignment.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/align_extend/extend_alignment.cpp.stdout
+ *
+ * @section Remarks
+ *
+ * It is necessary to explicitly pass hSeq, vSeq and the positions, because the
+ * original hSeq and vSeq (that Align was created on), might have been infixes,
+ * (especially if they are members of a ConcatDirect set) in which cases their
+ * actual begin and end positions cannot be inferred from the Align object's
+ * rows' source().
+ */
+
+// NO BAND, NO XDROP
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, minValue<TScoreValue>(), hSeq, vSeq, positions, direction, 0, 0, 0, scoreScheme,
+                                False(), False());
+}
+
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TScoreValue const & origScore,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, 0, 0, 0, scoreScheme, False(),
+                                False());
+}
+
+// BAND, NO XDROP
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                int const lowerDiag,
+                int const upperDiag,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, minValue<TScoreValue>(), hSeq, vSeq, positions, direction, lowerDiag, upperDiag,
+                                0, scoreScheme, True(), False());
+}
+
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TScoreValue const & origScore,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                int const lowerDiag,
+                int const upperDiag,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, 0,
+                                scoreScheme, True(), False());
+}
+
+// NO BAND, XDROP
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                TScoreValue const & xDrop,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, minValue<TScoreValue>(), hSeq, vSeq, positions, direction, 0, 0, xDrop,
+                                scoreScheme, False(), True());
+}
+
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TScoreValue const & origScore,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                TScoreValue const & xDrop,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, 0, 0, xDrop, scoreScheme, False(),
+                                True());
+}
+
+// BAND, XDROP
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                int const lowerDiag,
+                int const upperDiag,
+                TScoreValue const & xDrop,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, minValue<TScoreValue>(), hSeq, vSeq, positions, direction, lowerDiag, upperDiag,
+                                xDrop, scoreScheme, True(), True());
+}
+
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TScoreValue const & origScore,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                int const lowerDiag,
+                int const upperDiag,
+                TScoreValue const & xDrop,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop,
+                                scoreScheme, True(), True());
+}
+
+template <typename TStringInfix, typename TAlignSpec, typename TString,
+          typename TPos, typename TScoreValue, typename TScoreSpec,
+          typename TAliExtContext>
+inline TScoreValue
+extendAlignment(Align<TStringInfix, TAlignSpec> & align,
+                TAliExtContext & alignContext,
+                TScoreValue const & origScore,
+                TString const & hSeq,
+                TString const & vSeq,
+                Tuple<TPos, 4> const & positions,
+                ExtensionDirection const & direction,
+                int const lowerDiag,
+                int const upperDiag,
+                TScoreValue const & xDrop,
+                Score<TScoreValue, TScoreSpec> const & scoreScheme)
+{
+    return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop,
+                                scoreScheme, True(), True(), alignContext);
+}
+
+}
+
+#endif  // INCLUDE_ALIGN_ALIGN_EXTEND_H
diff --git a/seqan/align_extend/align_extend_base.h b/seqan/align_extend/align_extend_base.h
new file mode 100644
index 0000000..d27d0e9
--- /dev/null
+++ b/seqan/align_extend/align_extend_base.h
@@ -0,0 +1,201 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// ==========================================================================
+// This file contains routines to extend an existing Align object
+// ==========================================================================
+
+
+#ifndef INCLUDE_ALIGN_ALIGN_EXTEND_BASE_H
+#define INCLUDE_ALIGN_ALIGN_EXTEND_BASE_H
+
+namespace seqan {
+
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TSpec = void>
+struct AlignExtend_
+{
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+
+// overrides for AligExtend general case
+template <typename TSpec, typename TAlignConfig, typename TGapCosts,
+          typename TTraceSwitch>
+struct SetupAlignmentProfile_<AlignExtend_<TSpec>, TAlignConfig, TGapCosts,
+                              TTraceSwitch>
+{
+    typedef DPProfile_<AlignExtend_<TSpec>, TGapCosts, TracebackOn<> > Type;
+};
+
+template <typename TSpec>
+struct TraceTail_<AlignExtend_<TSpec> > : False
+{};
+
+template <typename TSpec>
+struct TraceHead_<AlignExtend_<TSpec> > : True
+{};
+
+template <typename TSpec>
+struct IsFreeEndGap_<AlignExtend_<TSpec>, DPLastRow> : True
+{};
+
+template <typename TSpec>
+struct IsFreeEndGap_<AlignExtend_<TSpec>, DPLastColumn> : True
+{};
+
+
+
+// ----------------------------------------------------------------------------
+// Class DPMetaColumn_                                             [FullColumn]
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TGapCosts, typename TTraceback,
+          typename TColumnType>
+struct DPMetaColumn_<DPProfile_<AlignExtend_<TSpec>, TGapCosts,
+                                TTraceback>,
+                     MetaColumnDescriptor<TColumnType, FullColumn> >
+{
+
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionZero,
+                        RecursionDirectionHorizontal
+                       >::Type TRecursionTypeFirstCell_;
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionVertical,
+                        RecursionDirectionAll
+                       >::Type TRecursionTypeInnerCell_;
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionVertical,
+                        RecursionDirectionAll
+                       >::Type TRecursionTypeLastCell_;
+
+    typedef DPMetaCell_<TRecursionTypeFirstCell_, True> TFirstCell_;
+    typedef DPMetaCell_<TRecursionTypeInnerCell_, True> TInnerCell_;
+    typedef DPMetaCell_<TRecursionTypeLastCell_, True> TLastCell_;
+};
+
+
+// ----------------------------------------------------------------------------
+// Class DPMetaColumn_                                       [PartialColumnTop]
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TGapCosts, typename TTraceback,
+          typename TColumnType>
+struct DPMetaColumn_<DPProfile_<AlignExtend_<TSpec>, TGapCosts,
+                                TTraceback>,
+                     MetaColumnDescriptor<TColumnType, PartialColumnTop> >
+{
+
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionZero,
+                        RecursionDirectionHorizontal
+                       >::Type TRecursionTypeFirstCell_;
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionVertical,
+                        RecursionDirectionAll
+                       >::Type TRecursionTypeInnerCell_;
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionVertical,
+                        RecursionDirectionLowerDiagonal
+                       >::Type TRecursionTypeLastCell_;
+
+    typedef DPMetaCell_<TRecursionTypeFirstCell_, True> TFirstCell_;
+    typedef DPMetaCell_<TRecursionTypeInnerCell_, True> TInnerCell_;
+    typedef DPMetaCell_<TRecursionTypeLastCell_, True> TLastCell_;
+};
+
+// ----------------------------------------------------------------------------
+// Class DPMetaColumn_                                    [PartialColumnMiddle]
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TGapCosts, typename TTraceback,
+          typename TColumnType>
+struct DPMetaColumn_<DPProfile_<AlignExtend_<TSpec>, TGapCosts,
+                                TTraceback>,
+                     MetaColumnDescriptor<TColumnType, PartialColumnMiddle> >
+{
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionZero,
+                        RecursionDirectionUpperDiagonal
+                       >::Type TRecursionTypeFirstCell_;
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionVertical,
+                        RecursionDirectionAll
+                       >::Type TRecursionTypeInnerCell_;
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionVertical,
+                        RecursionDirectionLowerDiagonal
+                       >::Type TRecursionTypeLastCell_;
+
+    typedef DPMetaCell_<TRecursionTypeFirstCell_, True> TFirstCell_;
+    typedef DPMetaCell_<TRecursionTypeInnerCell_, True> TInnerCell_;
+    typedef DPMetaCell_<TRecursionTypeLastCell_, True> TLastCell_;
+};
+
+// ----------------------------------------------------------------------------
+// Class DPMetaColumn_                                    [PartialColumnBottom]
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TGapCosts, typename TTraceback,
+          typename TColumnType>
+struct DPMetaColumn_<DPProfile_<AlignExtend_<TSpec>, TGapCosts,
+                                TTraceback>,
+                     MetaColumnDescriptor<TColumnType, PartialColumnBottom> >
+{
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionZero,
+                        RecursionDirectionUpperDiagonal
+                       >::Type TRecursionTypeFirstCell_;
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionVertical,
+                        RecursionDirectionAll
+                       >::Type TRecursionTypeInnerCell_;
+    typedef typename If<IsSameType<TColumnType,
+                                   DPInitialColumn>, RecursionDirectionVertical,
+                        RecursionDirectionAll
+                       >::Type TRecursionTypeLastCell_;
+
+    typedef DPMetaCell_<TRecursionTypeFirstCell_, True> TFirstCell_;
+    typedef DPMetaCell_<TRecursionTypeInnerCell_, True> TInnerCell_;
+    typedef DPMetaCell_<TRecursionTypeLastCell_, True> TLastCell_;
+};
+
+}
+#endif
diff --git a/seqan/align_extend/dp_scout_xdrop.h b/seqan/align_extend/dp_scout_xdrop.h
new file mode 100644
index 0000000..b7d0045
--- /dev/null
+++ b/seqan/align_extend/dp_scout_xdrop.h
@@ -0,0 +1,206 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// ==========================================================================
+// This file contains routines to extend an existing Align object
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ALIGN_DP_SCOUT_EXTEND_H_
+#define INCLUDE_SEQAN_ALIGN_DP_SCOUT_EXTEND_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag XDropScout.
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+struct XDrop_
+{
+};
+
+// ----------------------------------------------------------------------------
+// Class DPScoutState_
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+class DPScoutState_<Terminator_<XDrop_<TScoreValue> > >
+{
+public:
+    TScoreValue const terminationThreshold;
+    TScoreValue columnMax;
+
+    DPScoutState_() :
+        terminationThreshold(MaxValue<TScoreValue>::VALUE),
+        columnMax(MinValue<TScoreValue>::VALUE)
+    {
+    }
+
+    DPScoutState_(TScoreValue const & _terminationThreshold) :
+        terminationThreshold(_terminationThreshold),
+        columnMax(MinValue<TScoreValue>::VALUE)
+    {
+    }
+};
+
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// overrides for AligExtend XDrop case
+template <typename TScoreValue>
+struct HasTerminationCriterium_<AlignExtend_<XDrop_<TScoreValue> > > : True {};
+
+template <typename TScoreValue>
+struct ScoutSpecForAlignmentAlgorithm_<AlignExtend_<XDrop_<TScoreValue> > >
+{
+    typedef Terminator_<XDrop_<TScoreValue> > Type;
+};
+
+template <typename TScoreValue>
+struct ScoutSpecForAlignmentAlgorithm_<AlignExtend_<XDrop_<TScoreValue> > const>
+{
+    typedef Terminator_<XDrop_<TScoreValue> > Type;
+};
+
+template <typename TDPCell>
+struct ScoutStateSpecForScout_<
+         DPScout_<
+           TDPCell, Terminator_<XDrop_< typename Value<TDPCell>::Type> > > >
+{
+    typedef Terminator_<XDrop_<typename Value<TDPCell>::Type> > Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _scoutBestScore()                                        [DPScout_]
+// ----------------------------------------------------------------------------
+
+// NOTE: The original code here used Value<TDPCell>::Type instead of TDPCellValue but this caused ambiguous call
+// errors in MSVC.
+
+template <typename TDPCell, typename TTraceMatrixNavigator, typename TDPCellValue, typename TIsLastColumn>
+inline void
+_scoutBestScore(DPScout_<TDPCell, Terminator_<XDrop_<TDPCellValue> > > & dpScout,
+                TDPCell const & activeCell,
+                TTraceMatrixNavigator const & navigator,
+                TIsLastColumn const & /**/,
+                False const & /*IsLastRow*/)
+{
+    typedef typename Value<TDPCell>::Type TScoreValue;
+    typedef XDrop_<TScoreValue> TXDrop;
+    typedef DPScout_<TDPCell, Terminator_<TXDrop> > TDPScout;
+    typedef typename TDPScout::TParent TParent;
+
+    // global maximum
+    _scoutBestScore(static_cast<TParent &>( dpScout ), activeCell, navigator);
+
+    // column maximum
+    dpScout.state->columnMax = _max(dpScout.state->columnMax, _scoreOfCell(activeCell));
+}
+
+template <typename TDPCell, typename TTraceMatrixNavigator, typename TDPCellValue, typename TIsLastColumn>
+inline void
+_scoutBestScore(DPScout_<TDPCell, Terminator_<XDrop_<TDPCellValue> > > & dpScout,
+                TDPCell const & activeCell,
+                TTraceMatrixNavigator const & navigator,
+                TIsLastColumn const & /**/,
+                True const & /*IsLastRow*/)
+{
+    typedef typename Value<TDPCell>::Type TScoreValue;
+
+    _scoutBestScore(dpScout, activeCell, navigator, TIsLastColumn(), False());
+
+    // check termination condition
+    if (_scoreOfCell(dpScout._maxScore) - dpScout.state->columnMax >= dpScout.state->terminationThreshold)
+        terminateScout(dpScout);
+    else // reset columMax at end of column
+        dpScout.state->columnMax = MinValue<TScoreValue>::VALUE;
+}
+
+// ----------------------------------------------------------------------------
+// Function _scoutBestScore()                                        [DPScout_]
+// ----------------------------------------------------------------------------
+
+// Computes the score and tracks it if enabled.
+template <typename TDPScout, typename TTraceMatrixNavigator, typename TScoreValue, typename TGapCosts,
+          typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme, typename TColumnDescriptor,
+          typename TCellDescriptor, typename TTraceback>
+inline void
+_computeCell(TDPScout & scout,
+             TTraceMatrixNavigator & traceMatrixNavigator,
+             DPCell_<TScoreValue, TGapCosts> & activeCell,
+             DPCell_<TScoreValue, TGapCosts> const & previousDiagonal,
+             DPCell_<TScoreValue, TGapCosts> const & previousHorizontal,
+             DPCell_<TScoreValue, TGapCosts> const & previousVertical,
+             TSequenceHValue const & seqHVal,
+             TSequenceVValue const & seqVVal,
+             TScoringScheme const & scoringScheme,
+             TColumnDescriptor const &,
+             TCellDescriptor const &,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             // One of FirstCell, InnerCell or LastCell.
+             DPProfile_<AlignExtend_<XDrop_<TScoreValue> >, TGapCosts,
+                        TTraceback> const &)
+{
+    typedef DPProfile_<AlignExtend_<XDrop_<TScoreValue> >, TGapCosts, TTraceback> TDPProfile;
+    typedef DPMetaColumn_<TDPProfile, TColumnDescriptor> TMetaColumn;
+
+    assignValue(traceMatrixNavigator, _computeScore(activeCell, previousDiagonal, previousHorizontal, previousVertical,
+                                                    seqHVal, seqVVal, scoringScheme,
+                                                    typename RecursionDirection_<TMetaColumn, TCellDescriptor>::Type(),
+                                                    TDPProfile()));
+    if (TrackingEnabled_<TMetaColumn, TCellDescriptor>::VALUE)
+    {
+        typedef typename IsSameType< typename TColumnDescriptor::TColumnProperty, DPFinalColumn>::Type TIsLastColumn;
+
+        // the following is the only change to the regular _computeCell:
+        // for the evaluation of the termination criterium we treat
+        // all lastCells as lastRows
+        typedef typename IsSameType<TCellDescriptor, LastCell>::Type TIsLastRow;
+        _scoutBestScore(scout, activeCell, traceMatrixNavigator, TIsLastColumn(), TIsLastRow());
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_ALIGN_DP_SCOUT_EXTEND_H_
diff --git a/seqan/align_profile.h b/seqan/align_profile.h
new file mode 100644
index 0000000..21e5317
--- /dev/null
+++ b/seqan/align_profile.h
@@ -0,0 +1,57 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for module align_profile.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ALIGN_PROFILE_H_
+#define INCLUDE_SEQAN_ALIGN_PROFILE_H_
+
+// ===========================================================================
+// Prerequisites
+// ===========================================================================
+
+#include <seqan/align.h>
+#include <seqan/basic.h>
+#include <seqan/consensus.h>
+#include <seqan/file.h>
+#include <seqan/sequence.h>
+
+// ===========================================================================
+// Module Contents
+// ===========================================================================
+
+#include <seqan/align_profile/score_profile_seq.h>
+#include <seqan/align_profile/add_to_profile.h>
+
+#endif  // INCLUDE_SEQAN_ALIGN_PROFILE_H_
diff --git a/seqan/align_profile/add_to_profile.h b/seqan/align_profile/add_to_profile.h
new file mode 100644
index 0000000..0967125
--- /dev/null
+++ b/seqan/align_profile/add_to_profile.h
@@ -0,0 +1,165 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Algorithm for profile-to-sequence alignment that then adds the resulting
+// sequence alignment to the profile.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_PROFILE_ADD_TO_PROFILE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_PROFILE_ADD_TO_PROFILE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function addToProfile()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn addToProfile
+ * @headerfile <seqan/align_profile.h>
+ * @brief Sequence-to-profile alignment with sequence integration.
+ *
+ * <tt>seq</tt> will be aligned to <tt>profile</tt> using @link globalAlignment @endlink. To compute a banded alignment
+ * <tt>lDiag</tt> and <tt>uDiag</tt> have to be given.
+ * The resulting alignment will then be integrated into <tt>profile</tt> by incrementing the <tt>count</tt> values of
+ * the <tt>profile</tt> entries that correspond to the <tt>seq</tt> row of the alignment.
+ *
+ * @signature void addToProfile(profile, seq[, lDiag, uDiag]);
+ *
+ * @param[in,out] profile The profile to add <tt>seq</tt> to. A @link String @endlink over @link ProfileChar @endlink.
+ * @param[in]     seq     @link String @endlink to align to <tt>profile</tt>.
+ * @param[in]     lDiag   Lower diagonal for alignment (@link SignedIntegerConcept @endlink).
+ * @param[in]     uDiag   Upper diagonal for alignment (@link SignedIntegerConcept @endlink).
+ */
+
+// TODO(holtgrew): Add example?
+
+template <typename TChar, typename TValue, typename TSpec, typename TSpec2>
+void addToProfile(String<ProfileChar<TChar, TValue, TSpec> > & profile,
+                  String<TChar, TSpec2> /*const*/ & seq,
+                  int lDiag = minValue<int>(),
+                  int uDiag = maxValue<int>())  // non-const because of holder issues
+{
+    typedef ProfileChar<TChar, TValue, TSpec> TProfileChar;
+
+    typedef String<TProfileChar> TProfileString;
+    typedef String<TChar, TSpec2> TSequence;
+
+    // Define gaps and scoring scheme.
+    Gaps<TProfileString> gapsH(profile);
+    Gaps<TSequence> gapsV(seq);
+    seqan::Score<int, seqan::ProfileSeqScore> sScheme(profile);
+
+    // Perform the global alignment.
+    if (lDiag == minValue<int>() || uDiag == maxValue<int>())
+        globalAlignment(gapsH, gapsV, sScheme, Gotoh());
+    else
+        globalAlignment(gapsH, gapsV, sScheme, lDiag, uDiag, Gotoh());
+
+    // Construct a new profile from the alignment into buffer and finally swap out the new profile.
+    TProfileString buffer;
+    reserve(buffer, length(gapsH));
+    typename Iterator<Gaps<TProfileString>, Standard>::Type
+            itH = begin(gapsH, Standard()),
+            itHEnd = end(gapsH, Standard());
+    typename Iterator<Gaps<TSequence>, Standard>::Type itV = begin(gapsV, Standard());
+
+    // std::cout << "--- BEFORE ----\n";
+    // std::cout << "HORIZONTAL\n";
+    // for (; itH != itHEnd; ++itH)
+    // {
+    //     if (isGap(itH))
+    //     {
+    //         std::cerr << "-\n";
+    //     }
+    //     else
+    //     {
+    //         TProfileChar c = (TProfileChar)*itH;
+    //         std::cout << "(" << c.count[0] << ", " << c.count[1] << ", " << c.count[2] << ", " << c.count[3] << ", " << c.count[4] << ")\n";
+    //     }
+    //}
+    //std::cout << "VERTICAL\n";
+    //std::cout << gapsV << "\n";
+
+    itH = begin(gapsH, Standard());
+    SEQAN_ASSERT_EQ(length(gapsH), length(gapsV));
+    for (; itH != itHEnd; ++itH, ++itV)
+    {
+        if (isGap(itH))
+        {
+            SEQAN_ASSERT_NOT_MSG(isGap(itV), "Must not generate gaps columns!");
+            appendValue(buffer, TProfileChar());
+            back(buffer).count[valueSize<TChar>()] += 1;
+            back(buffer).count[ordValue(TChar(*itV))] += 1;
+        }
+        else
+        {
+            TProfileChar c = *itH;
+            appendValue(buffer, c);
+            if (isGap(itV))
+                back(buffer).count[valueSize<TChar>()] += 1;
+            else
+                back(buffer).count[ordValue(TChar(*itV))] += 1;
+        }
+    }
+
+    //std::cout << "--- AFTER ----\n";
+    //std::cout << "HORIZONTAL\n";
+    //for (typename Iterator<TProfileString>::Type it = begin(buffer, Standard()); it != end(buffer, Standard()); ++it)
+    //{
+    //    std::cout << "(" << it->count[0] << ", " << it->count[1] << ", " << it->count[2] << ", "
+    //              << it->count[3] << ", " << it->count[4] << ")\n";
+    //}
+
+    swap(buffer, profile);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_PROFILE_ADD_TO_PROFILE_H_
diff --git a/seqan/align_profile/score_profile_seq.h b/seqan/align_profile/score_profile_seq.h
new file mode 100644
index 0000000..c557340
--- /dev/null
+++ b/seqan/align_profile/score_profile_seq.h
@@ -0,0 +1,536 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_PROFILE_SPROFILE_SEQ_H_
+#define SEQAN_INCLUDE_PROFILE_SPROFILE_SEQ_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ProfileSeqScore
+
+struct ProfileSeqScore_;
+typedef Tag<ProfileSeqScore_> ProfileSeqScore;
+
+template <typename TValue>
+class Score<TValue, ProfileSeqScore>;
+
+template <typename TValue, typename TString>
+inline void
+assignProfile(Score<TValue, ProfileSeqScore> & me, TString const & profile);
+
+// ProfileSeqFracScore
+
+struct ProfileSeqFracScore_;
+typedef Tag<ProfileSeqFracScore_> ProfileSeqFracScore;
+
+template <typename TValue>
+class Score<TValue, ProfileSeqFracScore>;
+
+template <typename TValue, typename TString>
+inline void
+assignProfile(Score<TValue, ProfileSeqFracScore> & me, TString const & profile);
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class ProfileSeq Score
+// ----------------------------------------------------------------------------
+
+struct ProfileSeqScore_;
+typedef Tag<ProfileSeqScore_> ProfileSeqScore;
+
+/*!
+ * @class ProfileSeqScore ProfileSeq Score
+ * @extends Score
+ * @headerfile <seqan/align_profile.h>
+ * @brief Score for sequence-to-profile alignments.
+ *
+ * Using this class, you can align sequences to profiles.  The profile is assumed to be in the horizontal direction
+ * (first row), the sequence in the vertical direction (second row).
+ *
+ * Scoring works as follows.
+ *
+ * The integer <tt>SEQAN_CONSENSUS_UNITY</tt> and fractions thereof are used to express scores.  Gap opens in the
+ * profile are scored proportional to the number of gaps in the profile with two times unity, gap extends with one times
+ * unity at the position.
+ *
+ * Gap opens in the sequence are scored with two times unity, gap extends in the sequence with unity.  Alignments of
+ * profile characters to sequence characters are scored with the fraction of profile characters that match the sequence
+ * characters times unity.
+ *
+ * @signature template <typename TValue>
+ *            class Score<TValue, ProfileSeqScore>;
+ *
+ * @tparam TValue The integer type to use for representing scores.
+ *
+ * @section Examples
+ *
+ * The following example uses the ProfileSeq Score to align a sequence against a profile.
+ * Note that we print the gap state for each position since profiles cannot be printed to one stdout character.
+ *
+ * @include demos/dox/align_profile/profile_seq_score.cpp
+ *
+ * The output is as follows:
+ *
+ * @code{.output}
+ * score value = -2097152
+ * gaps in profile/sequence
+ * pos G   S
+ * 0   0   0
+ * 1   1   0
+ * 2   0   0
+ * 3   1   0
+ * 4   0   0
+ * 5   0   0
+ * @endcode
+ */
+
+/*!
+ * @fn ProfileSeqScore::Score
+ * @brief Constructor
+ *
+ * @signature Score::Score();
+ * @signature Score::Score(profile);
+ *
+ * @param[in] profile The profile to copy from (@link AllocString @endlink of @link ProfileChar @endlink objects).
+ *
+ * When providing <tt>profile</tt>, the function @link ProfileSeqScore#assignProfile @endlink is automatically used to
+ * assign the profile to this class.
+ */
+
+template <typename TValue>
+class Score<TValue, ProfileSeqScore>
+{
+  public:
+    // A table of position x (ord value) giving the counts of the characters at the given positions.
+    String<int> consensusSet;
+
+    Score() {}
+
+    // Construct given a profile string.
+    template <typename TProfile>
+    explicit
+    Score(TProfile const & profile)
+    {
+        assignProfile(*this, profile);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class ProfileSeqFrac Score
+// ----------------------------------------------------------------------------
+
+struct ProfileSeqFracScore_;
+typedef Tag<ProfileSeqFracScore_> ProfileSeqFracScore;
+
+/*!
+ * @class ProfileSeqFracScore ProfileSeqFrac Score
+ * @extends Score
+ * @headerfile <seqan/align_profile.h>
+ * @brief Score for sequence-to-profile alignments.
+ *
+ * Using this class, you can align sequences to profiles.  The profile is assumed to be in the horizontal direction
+ * (first row), the sequence in the vertical direction (second row).
+ *
+ * Scoring works as follows.
+ *
+ * The integer <tt>SEQAN_CONSENSUS_UNITY</tt> and fractions thereof are used to express scores.  Gap opens in the
+ * profile are scored proportional to the number of gaps in the profile two times unity, gap extends are scored
+ * proportional to the number of gaps in the profile at the position.  Gap opens in the sequence are scored with two
+ * times unity, gap extends with one times unity.
+ *
+ * @signature template <typename TValue>
+ *            class Score<TValue, ProfileSeqFracScore>;
+ *
+ * @tparam TValue The integer type to use for representing scores.
+ *
+ * @section Examples
+ *
+ * The following example uses the ProfileSeqFrac Score to align a sequence against a profile.  Note that we print the
+ * gap state for each position since profiles cannot be printed to one stdout character.
+ *
+ * @include demos/dox/align_profile/profile_seq_frac_score.cpp
+ *
+ * The output is as follows:
+ *
+ * @code
+ * score value = -2097152
+ * gaps in profile/sequence
+ * pos G   S
+ * 0   0   0
+ * 1   1   0
+ * 2   0   0
+ * 3   1   0
+ * 4   0   0
+ * 5   0   0
+ * @endcode
+ */
+
+/*!
+ * @fn ProfileSeqFracScore::Score
+ * @brief Constructor
+ *
+ * @signature Score::Score();
+ * @signature Score::Score(profile);
+ *
+ * @param[in] profile The profile to copy from (@link AllocString @endlink of @link ProfileChar @endlink objects).
+ *
+ * When providing <tt>profile</tt>, the function @link ProfileSeqFracScore#assignProfile @endlink is automatically used to
+ * assign the profile to this class.
+ */
+
+
+template <typename TValue>
+class Score<TValue, ProfileSeqFracScore>
+{
+  public:
+    // Total number of profile characters in each column
+    String<int> sum;
+
+    Score() {}
+
+    // Construct given a profile string.
+    template <typename TProfile>
+    explicit
+    Score(TProfile const & profile)
+    {
+        assignProfile(*this, profile);
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction SequenceEntryForScore                      [ProfileSeq Score]
+// --------------------------------------------------------------------------
+
+// Returns the type that holds a sequence entry.  This is used for abstracting away the access to sequence characters.
+
+template <typename TValue, typename TSequence>
+struct SequenceEntryForScore<Score<TValue, ProfileSeqScore>, TSequence>
+{
+    typedef ConsensusScoreSequenceEntry<TSequence> Type;
+};
+
+template <typename TValue, typename TSequence>
+struct SequenceEntryForScore<Score<TValue, ProfileSeqScore> const, TSequence> :
+            SequenceEntryForScore<Score<TValue, ProfileSeqScore>, TSequence>
+{};
+
+// --------------------------------------------------------------------------
+// Metafunction SequenceEntryForScore                  [ProfileSeqFrac Score]
+// --------------------------------------------------------------------------
+
+// Returns the type that holds a sequence entry.  This is used for abstracting away the access to sequence characters.
+
+template <typename TValue, typename TSequence>
+struct SequenceEntryForScore<Score<TValue, ProfileSeqFracScore>, TSequence>
+{
+    typedef ConsensusScoreSequenceEntry<TSequence> Type;
+};
+
+template <typename TValue, typename TSequence>
+struct SequenceEntryForScore<Score<TValue, ProfileSeqFracScore> const, TSequence> :
+            SequenceEntryForScore<Score<TValue, ProfileSeqFracScore>, TSequence>
+{};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function sequenceEntryForScore()                        [ProfileSeq Score]
+// --------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSequence, typename TPosition>
+inline ConsensusScoreSequenceEntry<TSequence>
+sequenceEntryForScore(Score<TScoreValue, ProfileSeqScore> const & /*sScheme*/,
+                      TSequence const & seq, TPosition pos)
+{
+    return ConsensusScoreSequenceEntry<TSequence>(seq, pos);
+}
+
+// --------------------------------------------------------------------------
+// Function assignProfile()                                [ProfileSeq Score]
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ProfileSeqScore#assignProfile
+ * @brief Assign profile to ProfileSeqScore.
+ *
+ * @signature void assignProfile(score, profile);
+ *
+ * @param[out] score   The ProfileSeqScore object to assign the profile for.
+ * @param[in]  profile The profile to assign to the score.  @link AllocString @endlink of @link ProfileChar @endlink.
+ */
+
+template <typename TValue, typename TString>
+inline void
+assignProfile(Score<TValue, ProfileSeqScore> & me,
+              TString const & profile)
+{
+    typedef typename Size<TString>::Type TSize;
+    TSize alphSize = ValueSize<typename Value<TString>::Type>::VALUE;
+    resize(me.consensusSet, alphSize * length(profile));
+
+    typedef typename Iterator<TString const, Standard>::Type TIter;
+    typedef typename Iterator<String<TValue>, Standard>::Type TConsSetIter;
+    TConsSetIter itConsSet = begin(me.consensusSet, Standard());
+    TIter it = begin(profile, Standard());
+    TIter itEnd = end(profile, Standard());
+    TSize maxCount = 0;
+    for (;it!=itEnd;++it)
+    {
+        maxCount = 0;
+        for (TSize i = 0; i<alphSize; ++i)
+            if ((TSize)(*it).count[i] > maxCount)
+                maxCount = (*it).count[i];
+        for (TSize i = 0; i<alphSize; ++i, ++itConsSet)
+            *itConsSet = ((TSize)(*it).count[i] == maxCount)? 0 : (-SEQAN_CONSENSUS_UNITY);
+    }
+}
+
+// --------------------------------------------------------------------------
+// Function scoreGapExtendHorizontal()                     [ProfileSeq Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+scoreGapExtendHorizontal(
+        Score<TValue, ProfileSeqScore> const & me,
+        ConsensusScoreSequenceEntry<TSeq1> const & entry1,
+        ConsensusScoreSequenceEntry<TSeq2> const & entry2)
+{
+    typedef typename Value<TSeq1>::Type TValue1;
+    if ((int)position(entry2) < 0)
+        return -SEQAN_CONSENSUS_UNITY;
+    else
+        return me.consensusSet[position(entry1) * (ValueSize<TValue1>::VALUE) + (ValueSize<TValue1>::VALUE - 1)];
+}
+
+// --------------------------------------------------------------------------
+// Function scoreGapOpenHorizontal()                       [ProfileSeq Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+scoreGapOpenHorizontal(
+        Score<TValue, ProfileSeqScore> const & me,
+        ConsensusScoreSequenceEntry<TSeq1> const & entry1,
+        ConsensusScoreSequenceEntry<TSeq2> const & entry2)
+{
+    typedef typename Value<TSeq1>::Type TValue1;
+    if ((int)position(entry2) < 0)
+        return -2 * SEQAN_CONSENSUS_UNITY;
+    else
+        return 2 * me.consensusSet[position(entry1) * (ValueSize<TValue1>::VALUE) + (ValueSize<TValue1>::VALUE - 1)];
+}
+
+// --------------------------------------------------------------------------
+// Function scoreGapExtendVertical()                       [ProfileSeq Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+scoreGapOpenVertical(
+        Score<TValue, ProfileSeqScore> const &,
+        ConsensusScoreSequenceEntry<TSeq1> const & /*entry1*/,
+        ConsensusScoreSequenceEntry<TSeq2> const & /*entry2*/)
+{
+    return -2 * SEQAN_CONSENSUS_UNITY;
+}
+
+// --------------------------------------------------------------------------
+// Function scoreGapOpenVertical()                         [ProfileSeq Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+scoreGapExtendVertical(
+        Score<TValue, ProfileSeqScore> const &,
+        ConsensusScoreSequenceEntry<TSeq1> const & /*entry1*/,
+        ConsensusScoreSequenceEntry<TSeq2> const & /*entry2*/)
+{
+    return -SEQAN_CONSENSUS_UNITY;
+}
+
+// --------------------------------------------------------------------------
+// Function score()                                        [ProfileSeq Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+score(Score<TValue, ProfileSeqScore> const & me,
+      ConsensusScoreSequenceEntry<TSeq1> const & entry1,
+      ConsensusScoreSequenceEntry<TSeq2> const & entry2)
+{
+    typedef typename Value<TSeq1>::Type TValue1;
+    return me.consensusSet[position(entry1) * (ValueSize<TValue1>::VALUE) + ordValue(value(entry2))];
+}
+
+// --------------------------------------------------------------------------
+// Function sequenceEntryForScore()                    [ProfileSeqFrac Score]
+// --------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSequence, typename TPosition>
+inline ConsensusScoreSequenceEntry<TSequence>
+sequenceEntryForScore(Score<TScoreValue, ProfileSeqFracScore> const & /*sScheme*/,
+                      TSequence const & seq, TPosition pos)
+{
+    return ConsensusScoreSequenceEntry<TSequence>(seq, pos);
+}
+
+// --------------------------------------------------------------------------
+// Function assignProfile()                            [ProfileSeqFrac Score]
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ProfileSeqFracScore#assignProfile
+ * @brief Assign profile to ProfileSeqFrac Score.
+ *
+ * @signature void assignProfile(score, profile);
+ *
+ * @param[out] score   The ProfileSeqScore object to assign the profile for.
+ * @param[in]  profile The profile to assign to the score.  @link AllocString @endlink of @link ProfileChar @endlink.
+ */
+
+template <typename TValue, typename TString>
+inline void
+assignProfile(Score<TValue, ProfileSeqFracScore> & me,
+              TString const & profile)
+{
+    typedef typename Size<TString>::Type TSize;
+    resize(me.sum, length(profile));
+    typedef typename Iterator<TString const, Standard>::Type TIter;
+    typedef typename Iterator<String<int>, Standard>::Type TSumIter;
+    TSumIter itSum = begin(me.sum, Standard());
+    TIter it = begin(profile, Standard());
+    TIter itEnd = end(profile, Standard());
+    for (; it!=itEnd; ++it, ++itSum)
+    {
+        *itSum = 0;
+        for (TSize i = 0; i < (TSize) ValueSize<typename Value<TString>::Type>::VALUE; ++i)
+            *itSum += (*it).count[i];
+    }
+}
+
+// --------------------------------------------------------------------------
+// Function scoreGapExtendHorizontal()                 [ProfileSeqFrac Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+scoreGapExtendHorizontal(
+        Score<TValue, ProfileSeqFracScore> const & me,
+        ConsensusScoreSequenceEntry<TSeq1> const & entry1,
+        ConsensusScoreSequenceEntry<TSeq2> const & entry2)
+{
+    if (((int)position(entry2) < 0) || (!me.sum[position(entry1)]))
+        return -SEQAN_CONSENSUS_UNITY;
+    else
+        return ((TValue) (( (int)value(entry1).count[ValueSize<typename Value<TSeq1>::Type>::VALUE - 1] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
+}
+
+// --------------------------------------------------------------------------
+// Function scoreGapOpenHorizontal()                   [ProfileSeqFrac Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+scoreGapOpenHorizontal(
+        Score<TValue, ProfileSeqFracScore> const & me,
+        ConsensusScoreSequenceEntry<TSeq1> const & entry1,
+        ConsensusScoreSequenceEntry<TSeq2> const & entry2)
+{
+    if (((int)position(entry2) < 0) || (!me.sum[position(entry1)]))
+        return -SEQAN_CONSENSUS_UNITY;
+    else
+        return ((TValue) (((int)value(entry1).count[ValueSize<typename Value<TSeq1>::Type>::VALUE - 1] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
+}
+
+// --------------------------------------------------------------------------
+// Function scoreGapExtendVertical()                   [ProfileSeqFrac Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+scoreGapOpenVertical(
+        Score<TValue, ProfileSeqFracScore> const &,
+        ConsensusScoreSequenceEntry<TSeq1> const & /*entry1*/,
+        ConsensusScoreSequenceEntry<TSeq2> const & /*entry2*/)
+{
+    return -SEQAN_CONSENSUS_UNITY;
+}
+
+// --------------------------------------------------------------------------
+// Function scoreGapOpenVertical()                     [ProfileSeqFrac Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+scoreGapExtendVertical(
+        Score<TValue, ProfileSeqFracScore> const &,
+        ConsensusScoreSequenceEntry<TSeq1> const & /*entry1*/,
+        ConsensusScoreSequenceEntry<TSeq2> const & /*entry2*/)
+{
+    return -SEQAN_CONSENSUS_UNITY;
+}
+
+// --------------------------------------------------------------------------
+// Function score()                                    [ProfileSeqFrac Score]
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSeq1, typename TSeq2>
+inline TValue
+score(Score<TValue, ProfileSeqFracScore> const & me,
+      ConsensusScoreSequenceEntry<TSeq1> const & entry1,
+      ConsensusScoreSequenceEntry<TSeq2> const & entry2)
+{
+    if (!me.sum[position(entry1)])
+        return -SEQAN_CONSENSUS_UNITY;
+    else
+        return ((TValue) (((int)value(entry1).count[ordValue(value(entry2))] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_PROFILE_SPROFILE_SEQ_H_
diff --git a/seqan/align_split.h b/seqan/align_split.h
new file mode 100644
index 0000000..4352e2a
--- /dev/null
+++ b/seqan/align_split.h
@@ -0,0 +1,55 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for module align_split.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/align.h>
+#include <seqan/basic.h>
+#include <seqan/sequence.h>
+
+// ===========================================================================
+// Split Alignment Impelmentation.
+// ===========================================================================
+
+#include <seqan/align_split/dp_scout_split.h>
+#include <seqan/align_split/align_split_interface.h>
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_H_
diff --git a/seqan/align_split/align_split_interface.h b/seqan/align_split/align_split_interface.h
new file mode 100644
index 0000000..e0623e2
--- /dev/null
+++ b/seqan/align_split/align_split_interface.h
@@ -0,0 +1,568 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Split alignment implementation.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_ALIGN_SPLIT_INTERFACE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_ALIGN_SPLIT_INTERFACE_H_
+
+#include "dp_scout_split.h"
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// Tag for the split alignment algorithm in DPProfile_.
+
+template <typename TSpec = Default>
+struct SplitAlignment_ {};
+
+// Tag for the split alignment algorithm.
+
+struct SplitAlignmentAlgo_;
+typedef Tag<SplitAlignmentAlgo_> SplitAlignmentAlgo;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction ScoutSpecForAlignmentAlgorithm_
+// ----------------------------------------------------------------------------
+
+// For the split alignment, we will use our SplitAlignmentScout specialization of DPScout.
+
+template <typename TSpec>
+struct ScoutSpecForAlignmentAlgorithm_<SplitAlignment_<TSpec> >
+{
+    typedef SplitAlignmentScout Type;
+};
+
+template <typename TSpec>
+struct ScoutSpecForAlignmentAlgorithm_<SplitAlignment_<TSpec> const>
+{
+    typedef SplitAlignmentScout Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsSplitAlignment_
+// ----------------------------------------------------------------------------
+
+// Convenience function used in the DP configuration below.
+
+template <typename TParam>
+struct IsSplitAlignment_ : False {};
+
+template <typename TSpec>
+struct IsSplitAlignment_<SplitAlignment_<TSpec> >:
+    True {};
+
+template <typename TSpec>
+struct IsSplitAlignment_<SplitAlignment_<TSpec> const>:
+    True {};
+
+template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
+struct IsSplitAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag> >:
+    IsSplitAlignment_<TAlgoSpec> {};
+
+template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
+struct IsSplitAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag> const>:
+    IsSplitAlignment_<TAlgoSpec> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsFreeEndGap_
+// ----------------------------------------------------------------------------
+
+// We want the same free endgaps configuration as for global alignments.
+
+template <typename TSpec, typename TRow>
+struct IsFreeEndGap_<SplitAlignment_<TSpec>, TRow> :
+        IsFreeEndGap_<GlobalAlignment_<TSpec>, TRow>
+{};
+
+template <typename TSpec, typename TRow>
+struct IsFreeEndGap_<SplitAlignment_<TSpec> const, TRow> :
+        IsFreeEndGap_<GlobalAlignment_<TSpec> const, TRow>
+{};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsGlobalAlignment_
+// ----------------------------------------------------------------------------
+
+// We use similar functionality as the global alignment.
+
+template <typename TSpec>
+struct IsGlobalAlignment_<SplitAlignment_<TSpec> > :
+    True
+{};
+
+template <typename TSpec>
+struct IsGlobalAlignment_<SplitAlignment_<TSpec> const> :
+    True
+{};
+
+// ----------------------------------------------------------------------------
+// Metafunction DPMetaColumn_
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TColumnType>
+struct DPMetaColumn_<DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag>, MetaColumnDescriptor<TColumnType, FullColumn> >
+{
+    typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
+    typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
+
+    // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero  // Within the algorithm we need to define the first row as only one cell if it is no initial column
+    // If InnerColumn -> Horizontal | Zero, All, All
+    // If FinalColumn -> Horizontal | Zero, All, All
+
+    typedef typename If<Or<IsSameType<TColumnType, DPInitialColumn>,
+                           IsFreeEndGap_<TDPProfile, DPFirstRow> >, RecursionDirectionZero, RecursionDirectionHorizontal>::Type TRecursionTypeFirstCell_;
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>,
+                        typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVertical>::Type,
+                        RecursionDirectionAll>::Type TRecursionTypeInnerCell_;
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>,
+                        typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVertical>::Type,
+                        RecursionDirectionAll>::Type TRecursionTypeLastCell_;
+
+    typedef DPMetaCell_<TRecursionTypeFirstCell_, True> TFirstCell_;
+    typedef DPMetaCell_<TRecursionTypeInnerCell_, True> TInnerCell_;
+    typedef DPMetaCell_<TRecursionTypeLastCell_, True> TLastCell_;
+};
+
+
+template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TColumnType>
+struct DPMetaColumn_<DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag>, MetaColumnDescriptor<TColumnType, PartialColumnTop> >
+{
+    typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
+    typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
+
+    // How does the recursion directions look like?
+
+    // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero  // Within the algorithm we need to define the first row as only one cell if it is no initial column
+    // If InnerColumn -> Horizontal | Zero, All, LowerBand
+    // If FinalColumn -> Horizontal | Zero, All, LowerBand
+
+    typedef typename If<Or<IsSameType<TColumnType, DPInitialColumn>,
+                           IsFreeEndGap_<TDPProfile, DPFirstRow> >, RecursionDirectionZero, RecursionDirectionHorizontal>::Type TRecursionTypeFirstCell_;
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>,
+                        typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVertical>::Type,
+                        RecursionDirectionAll>::Type TRecursionTypeInnerCell_;
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>,
+                        typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVertical>::Type,
+                        RecursionDirectionLowerDiagonal>::Type TRecursionTypeLastCell_;
+
+    typedef DPMetaCell_<TRecursionTypeFirstCell_, True> TFirstCell_;
+    typedef DPMetaCell_<TRecursionTypeInnerCell_, True> TInnerCell_;
+    typedef DPMetaCell_<TRecursionTypeLastCell_, True> TLastCell_;
+};
+
+template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TColumnType>
+struct DPMetaColumn_<DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag>, MetaColumnDescriptor<TColumnType, PartialColumnMiddle> >
+{
+    typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
+    typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
+
+    // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero  // Within the algorithm we need to define the first row as only one cell if it is no initial column
+    // If InnerColumn -> UpperDiagonal, All, LowerDiagonal
+    // If FinalColumn -> UpperDiagonal, All, LowerDiagonal
+
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>, RecursionDirectionZero, RecursionDirectionUpperDiagonal>::Type TRecursionTypeFirstCell_;
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>,
+                        typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVertical>::Type,
+                        RecursionDirectionAll>::Type TRecursionTypeInnerCell_;
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>,
+                        typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVertical>::Type,
+                        RecursionDirectionLowerDiagonal>::Type TRecursionTypeLastCell_;
+
+    typedef DPMetaCell_<TRecursionTypeFirstCell_, True> TFirstCell_;
+    typedef DPMetaCell_<TRecursionTypeInnerCell_, True> TInnerCell_;
+    typedef DPMetaCell_<TRecursionTypeLastCell_, True> TLastCell_;
+};
+
+template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TColumnType>
+struct DPMetaColumn_<DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag>, MetaColumnDescriptor<TColumnType, PartialColumnBottom> >
+{
+    typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
+    typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
+
+    // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero  // Within the algorithm we need to define the first row as only one cell if it is no initial column
+    // If InnerColumn -> UpperDiagonal, All, All
+    // If FinalColumn -> UpperDiagonal, All, All
+
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>, RecursionDirectionZero, RecursionDirectionUpperDiagonal>::Type TRecursionTypeFirstCell_;
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>,
+                        typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVertical>::Type,
+                        RecursionDirectionAll>::Type TRecursionTypeInnerCell_;
+    typedef typename If<IsSameType<TColumnType, DPInitialColumn>,
+                        typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVertical>::Type,
+                        RecursionDirectionAll>::Type TRecursionTypeLastCell_;
+
+    typedef DPMetaCell_<TRecursionTypeFirstCell_, True> TFirstCell_;
+    typedef DPMetaCell_<TRecursionTypeInnerCell_, True> TInnerCell_;
+    typedef DPMetaCell_<TRecursionTypeLastCell_, True> TLastCell_;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction SetupAlignmentProfile_
+// ----------------------------------------------------------------------------
+
+template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch>
+struct SetupAlignmentProfile_<SplitAlignmentAlgo, TFreeEndGaps, TGapCosts, TTraceSwitch>
+{
+    typedef DPProfile_<SplitAlignment_<TFreeEndGaps>, TGapCosts, TTraceSwitch> Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _reverseTrace()
+// ----------------------------------------------------------------------------
+
+// Reverse a trace string and adapt internal position.
+template <typename TPosition, typename TSize, typename TSpec>
+void _reverseTrace(String<TraceSegment_<TPosition, TSize>, TSpec> & trace)
+{
+    typedef String<TraceSegment_<TPosition, TSize>, TSpec> TTrace;
+    typedef typename Iterator<TTrace, Rooted>::Type TTraceIter;
+
+    if (empty(trace))
+        return;
+    TPosition lengthH = _getEndHorizontal(front(trace));
+    TPosition lengthV = _getEndVertical(front(trace));
+
+    for (TTraceIter it = begin(trace, Rooted()); !atEnd(it); goNext(it))
+    {
+        it->_horizontalBeginPos = lengthH - _getEndHorizontal(*it);
+        it->_verticalBeginPos = lengthV - _getEndVertical(*it);
+    }
+    reverse(trace);
+}
+
+// ----------------------------------------------------------------------------
+// Function _splitAlignmentImpl()
+// ----------------------------------------------------------------------------
+
+// We call the long sequence contig and the shorter one read but could be changed roles.
+template <typename TContigSeqL, typename TReadSeqL, typename TContigSeqR, typename TReadSeqR,
+          typename TScoreValue, typename TScoreSpec>
+int _splitAlignmentImpl(Gaps<TContigSeqL> & gapsContigL,
+                        Gaps<TReadSeqL> & gapsReadL,
+                        Gaps<TContigSeqR> & gapsContigR,
+                        Gaps<TReadSeqR> & gapsReadR,
+                        int lowerDiagonal,
+                        int upperDiagonal,
+                        Score<TScoreValue, TScoreSpec> const & scoringScheme)
+{
+    typedef Gaps<TContigSeqL> TGaps;
+    typedef typename Size<TGaps>::Type TSize;
+    typedef typename Position<TGaps>::Type TPosition;
+    typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+
+    typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
+    //alignConfig;
+
+    // Check whether we need to run the banded versions.
+    bool banded = (lowerDiagonal != minValue<int>() && upperDiagonal != maxValue<int>());
+
+    // Compute trace and split score sequence for the left alignment.
+
+    DPScoutState_<SplitAlignmentScout> scoutStateL;
+    resize(scoutStateL.splitScore, length(source(gapsContigL)) + 1, minValue<TScoreValue>() / 2);
+
+    String<TTraceSegment> traceL;
+    if (!banded)
+    {
+        typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOff>, TFreeEndGaps, TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
+        _setUpAndRunAlignment(traceL, scoutStateL, source(gapsContigL), source(gapsReadL), scoringScheme, TAlignConfig());
+    }
+    else
+    {
+        typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
+        _setUpAndRunAlignment(traceL, scoutStateL, source(gapsContigL), source(gapsReadL), scoringScheme,
+                              TAlignConfig(lowerDiagonal, upperDiagonal));
+    }
+    _adaptTraceSegmentsTo(gapsContigL, gapsReadL, traceL);
+
+    // Get reversed versions of the right contig and read sequence.
+    ModifiedString<TContigSeqR, ModReverse> revContigR(source(gapsContigR));
+    ModifiedString<TReadSeqR, ModReverse> revReadR(source(gapsReadR));
+
+    // Compute trace and split score sequence for the right alignment.
+
+    DPScoutState_<SplitAlignmentScout> scoutStateR;
+    resize(scoutStateR.splitScore, length(source(gapsContigR)) + 1, minValue<TScoreValue>() / 2);
+
+    String<TTraceSegment> traceR;
+    if (!banded)
+    {
+        typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOff>, TFreeEndGaps, TracebackOn<TracebackConfig_<CompleteTrace, GapsRight> > > TAlignConfig;
+        _setUpAndRunAlignment(traceR, scoutStateR, revContigR, revReadR, scoringScheme, TAlignConfig());
+    }
+    else
+    {
+        typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOn<TracebackConfig_<CompleteTrace, GapsRight> > > TAlignConfig;
+        _setUpAndRunAlignment(traceR, scoutStateR, revContigR, revReadR, scoringScheme,
+                              TAlignConfig(lowerDiagonal, upperDiagonal));
+    }
+    // Reverse trace so it fits to the forward right sequences.  Also reverse the trace such that we can directly apply
+    // it for the right alignment.
+    _reverseTrace(traceR);
+    reverse(scoutStateR.splitScore);
+    _adaptTraceSegmentsTo(gapsContigR, gapsReadR, traceR);
+
+    SEQAN_ASSERT_EQ(length(scoutStateL.splitScore), length(scoutStateR.splitScore));
+
+    // We will split the left and right alignments into two parts such that the alignment score is optimal.  We compute
+    // the leftmost best position for a split (equivalent to the best prefix of the first left alignment).  Note that
+    // placing the breakpoint at the leftmost position is coherent with the SNPdb semantics but there are other data
+    // bases that use rightmost placement.
+
+    // TODO(holtgrew): Make selecting the left/right split position from interface possible? Maybe not necessary.
+
+    int bestScore = minValue<TScoreValue>() / 2;
+    unsigned bestPrefixLength = 0;
+    for (unsigned i = 0; i < length(scoutStateL.splitScore); ++i)
+    {
+        int s = scoutStateL.splitScore[i] + scoutStateR.splitScore[i];
+        if (s > bestScore)
+        {
+            bestScore = s;
+            bestPrefixLength = i;
+        }
+    }
+
+    // std::cerr << "bestPrefixLength = " << bestPrefixLength << "\n";
+
+    // std::cerr << "split store left ";
+    // for (unsigned i = 0; i < length(scoutStateL.splitScore); ++i)
+    //     fprintf(stderr, " %3d", scoutStateL.splitScore[i]);
+    // std::cerr << "\n";
+    // std::cerr << "split store right";
+    // for (unsigned i = 0; i < length(scoutStateR.splitScore); ++i)
+    //     fprintf(stderr, " %3d", scoutStateR.splitScore[i]);
+    // std::cerr << "\n";
+
+    // Set the clipping positions.
+    TPosition cePosR = toViewPosition(gapsContigR, bestPrefixLength);
+    setClippedBeginPosition(gapsContigR, cePosR);
+    setClippedBeginPosition(gapsReadR, cePosR);
+    // We have to correct the clipping position for the left alignment because of the to-right projection.  The
+    // insertion itself is not part of the alignment.
+    TPosition cePosL = toViewPosition(gapsContigL, bestPrefixLength);
+    if (bestPrefixLength > 0)
+        cePosL = toViewPosition(gapsContigL, bestPrefixLength - 1) + 1;
+    setClippedEndPosition(gapsContigL, cePosL);
+    setClippedEndPosition(gapsReadL, cePosL);
+
+    return bestScore;
+}
+
+// ----------------------------------------------------------------------------
+// Function splitAlignment()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn splitAlignment
+ * @headerfile <seqan/align_split.h>
+ * @brief Compute split alignments.
+ *
+ * @signature TScoreValue splitAlignment(alignL,         alignR,         scoringScheme[, lowerDiag, upperDiag]);
+ * @signature TScoreValue splitAlignment(gapsHL, gapsVL, gapsHR, gapsVR, scoringScheme[, lowerDiag, upperDiag]);
+ *
+ * @param[in,out] alignL @link Align @endlink object with two rows for the left alignment.
+ * @param[in,out] alignR @link Align @endlink object with two rows for the right alignment.
+ * @param[in,out] gapsHL @link Gaps @endlink object with the horizontal/contig row for the left alignment.
+ * @param[in,out] gapsVL @link Gaps @endlink object with the vertical/read row for the left alignment.
+ * @param[in,out] gapsHR @link Gaps @endlink object with the horizontal/contig row for the right alignment.
+ * @param[in,out] gapsVR @link Gaps @endlink object with the vertical/read row for the right alignment.
+ * @param[in]     scoringScheme The scoring scheme to use for the alignment.
+ * @param[in]     lowerDiag The lower diagonal.You have to specify the upper and lower diagonals for the left
+ *                          alignment.  For the right alignment, the corresponding diagonals are chosen for the
+ *                          lower right part of the DP matrix, <tt>int</tt>.
+ * @param[in]     upperDiag The lower diagonal.  Also see remark for <tt>lowerDiag</tt>, <tt>int</tt>.
+ *
+ * @return TScoreValue The sum of the alignment scores of both alignments (Metafunction: @link Score#Value @endlink
+ *                     of the type of <tt>scoringScheme</tt>).
+ *
+ * There are two variants of the split alignment problem.  In the first variant, we wan to align two sequences where the
+ * first (say the reference) one is shorter than the second (say a read) and the read contains an insertion with respect
+ * to the reference.  We now want to align the read agains the reference such that the left part of the read aligns well
+ * against the left part of the reference and the right part of the read aligns well against the right part of the
+ * reference.  The center gap in the reference is free.
+ *
+ * For example:
+ *
+ * @code{.console}
+ * reference  AGCATGTTAGATAAGATAGC-----------TGTGCTAGTAGGCAGTCAGCGCCAT
+ *            ||||||||||||||||||||           |||||||||||||||||||||||||
+ * read       AGCATGTTAGATAAGATAGCCCCCCCCCCCCTGTGCTAGTAGGCAGTCAGCGCCAT
+ * @endcode
+ *
+ * The second variant is to align two sequences A and B against a reference such that the left part of A aligns well to
+ * the left part of the reference and the right part of B aligns well to the right part of the reference.  Together,
+ * both reads span the whole reference and overlap with an insertion in the reference.
+ *
+ * @code{.console}
+ * reference  AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
+ *            |||||||||||||||||| | ||
+ *            AGCATGTTAGATAAGATATCCGTCC
+ *            read 1
+ *                              ||| |||||||||||||||||||||||
+ *                            CCGCTATGCTAGTAGGCAGTCAGCGCCAT
+ *                                                   read 2
+ * @endcode
+ *
+ * The resulting alignment of the left/right parts is depicted below. The square brackets indicate clipping positions.
+ *
+ * @code{.console}
+ * reference  AGCATGTTAGATAAGATA    [GCTGTGCTAGTAGGCAGTCAGCGCCAT
+ *            ||||||||||||||||||    [ | ||
+ *            AGCATGTTAGATAAGATA    [TCCGTCC
+ *            read 1
+ * reference  AGCATGTTAGATAAGATA]    GTGCTAGTAGGCAGTCAGCGCCAT
+ *                              ]     |||||||||||||||||||||||
+ *                         CCGCT]    ATGCTAGTAGGCAGTCAGCGCCAT
+ *                                                     read 2
+ * @endcode
+ *
+ * In the first case, we want to find the one breakpoint in the reference and the two breakpoints in the reads and the
+ * alignment of the left and right well-aligning read parts.  In the second case, we want to find the one breakpoint in
+ * the reference and the breakpoint/clipping position in each read.
+ *
+ * The <tt>splitAlignment()</tt> function takes as the input two alignments.  The sequence in each alignment's first row
+ * is the reference and the sequence of the second row is the read.  The sequence has to be the same sequence whereas
+ * the reads might differ.  If the reads are the same then this is the same as the first case and if the reads differ
+ * then this is the second case.
+ *
+ * The result is two alignments of the left and right contig path clipped appropriately.  The resulting score is the sum
+ * of the scores of both alignments.
+ *
+ * @section Remarks
+ *
+ * The DP algorithm is chosen automatically depending on whether the gap open and extension costs are equal.
+ *
+ * @section Example
+ *
+ * The following example demonstrates the usage of <tt>splitAlignment</tt> in the first case.  The second case
+ * works accordingly.
+ *
+ * @include demos/dox/align_split/split_alignment.cpp
+ *
+ * The output is as follows.
+ *
+ * @include demos/dox/align_split/split_alignment.cpp.stdout
+ */
+
+// Variant: unbanded, with Align objects.
+
+template <typename TSequenceL, typename TAlignSpecL, typename TSequenceR, typename TAlignSpecR,
+          typename TScoreVal, typename TScoreSpec>
+int splitAlignment(Align<TSequenceL, TAlignSpecL> & alignL,
+                   Align<TSequenceR, TAlignSpecR> & alignR,
+                   Score<TScoreVal, TScoreSpec> const & scoringScheme)
+{
+    SEQAN_ASSERT_EQ_MSG(source(row(alignL, 0)), source(row(alignR, 0)),
+                        "Contig must be the same for left and right split alignment.");
+
+    return _splitAlignmentImpl(row(alignL, 0), row(alignL, 1), row(alignR, 0), row(alignR, 1),
+                               minValue<int>(), maxValue<int>(),
+                               scoringScheme);
+}
+
+// Variant: unbanded, with Gaps objects.
+
+template <typename TSeqHL, typename TGapSpecHL, typename TSeqVL, typename TGapSpecVL,
+          typename TSeqHR, typename TGapSpecHR, typename TSeqVR, typename TGapSpecVR,
+          typename TScoreVal, typename TScoreSpec>
+int splitAlignment(Gaps<TSeqHL, TGapSpecHL> & gapsHL,
+                   Gaps<TSeqVL, TGapSpecVL> & gapsVL,
+                   Gaps<TSeqHR, TGapSpecHR> & gapsHR,
+                   Gaps<TSeqVR, TGapSpecVR> & gapsVR,
+                   Score<TScoreVal, TScoreSpec> const & scoringScheme)
+{
+    SEQAN_ASSERT_EQ_MSG(source(gapsHL), source(gapsHR),
+                        "Contig must be the same for left and right split alignment.");
+
+    return _splitAlignmentImpl(gapsHL, gapsVL, gapsHR, gapsVR, minValue<int>(), maxValue<int>(),
+                               scoringScheme);
+}
+
+// Variant: banded, with Align objects.
+
+template <typename TSequenceL, typename TAlignSpecL, typename TSequenceR, typename TAlignSpecR,
+          typename TScoreVal, typename TScoreSpec>
+int splitAlignment(Align<TSequenceL, TAlignSpecL> & alignL,
+                   Align<TSequenceR, TAlignSpecR> & alignR,
+                   Score<TScoreVal, TScoreSpec> const & scoringScheme,
+                   int lowerDiagonal,
+                   int upperDiagonal)
+{
+    SEQAN_ASSERT_EQ_MSG(source(row(alignL, 0)), source(row(alignR, 0)),
+                        "Contig must be the same for left and right split alignment.");
+
+    return _splitAlignmentImpl(row(alignL, 0), row(alignL, 1), row(alignR, 0), row(alignR, 1),
+                               lowerDiagonal, upperDiagonal, scoringScheme);
+}
+
+// Variant: banded, with Gaps objects.
+
+template <typename TSeqHL, typename TGapSpecHL, typename TSeqVL, typename TGapSpecVL,
+          typename TSeqHR, typename TGapSpecHR, typename TSeqVR, typename TGapSpecVR,
+          typename TScoreVal, typename TScoreSpec>
+int splitAlignment(Gaps<TSeqHL, TGapSpecHL> & gapsHL,
+                   Gaps<TSeqVL, TGapSpecVL> & gapsVL,
+                   Gaps<TSeqHR, TGapSpecHR> & gapsHR,
+                   Gaps<TSeqVR, TGapSpecVR> & gapsVR,
+                   Score<TScoreVal, TScoreSpec> const & scoringScheme,
+                   int lowerDiagonal,
+                   int upperDiagonal)
+{
+    SEQAN_ASSERT_EQ_MSG(source(gapsHL), source(gapsHR),
+                        "Contig must be the same for left and right split alignment.");
+
+    return _splitAlignmentImpl(gapsHL, gapsVL, gapsHR, gapsVR, lowerDiagonal, upperDiagonal,
+                               scoringScheme);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_ALIGN_SPLIT_INTERFACE_H_
diff --git a/seqan/stream/adapt_mmap.h b/seqan/align_split/dp_scout_split.h
similarity index 54%
rename from seqan/stream/adapt_mmap.h
rename to seqan/align_split/dp_scout_split.h
index c74ee3c..2eab23e 100644
--- a/seqan/stream/adapt_mmap.h
+++ b/seqan/align_split/dp_scout_split.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,15 +29,13 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
-// Adaptions for the SeqAn Strings
+// DPScout_ specialization for the split alignment implementation.
 // ==========================================================================
 
-// TODO(holtgrew): Should better be string adaption!
-
-#ifndef SEQAN_STREAM_ADAPT_MMAP_H_
-#define SEQAN_STREAM_ADAPT_MMAP_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_
 
 namespace seqan {
 
@@ -49,118 +47,85 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-/*
-.Adaption.String
-..cat:Input/Output
-..summary:Adaption from $fstream$, $ifstream$ and $ofstream$ to the @Concept.StreamConcept@ concept.
-..include:seqan/stream.h
- */
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-
-// ============================================================================
-// Functions
-// ============================================================================
-
 // ----------------------------------------------------------------------------
-// Function streamWriteChar()
+// Tag SplitAlignmentScout.
 // ----------------------------------------------------------------------------
 
-template <typename TValue, typename TSpec, typename TChar>
-inline int
-streamWriteChar(String<TValue, TSpec> & stream, TChar const & c)
-{
-    appendValue(stream, c);
-    return 0;
-}
+struct SplitAlignmentScout_;
+typedef Tag<SplitAlignmentScout_> SplitAlignmentScout;
 
 // ----------------------------------------------------------------------------
-// Function streamWriteBlock()
+// Class DPScoutState_
 // ----------------------------------------------------------------------------
 
-template <typename TValue, typename TSpec>
-inline typename Size<String<TValue, TSpec> >::Type
-streamWriteBlock(String<TValue, TSpec> & stream, char const * ptr, unsigned count)
+template <>
+class DPScoutState_<SplitAlignmentScout>
 {
-    reserve(stream, length(stream) + count);
-    for (unsigned i = 0; i < count; ++i, ++ptr)
-        appendValue(stream, *ptr);
-    return count;
-}
+public:
+    // The best score for each column.  Initialized with 0.5*minValue<TScoreVal>().
+    seqan::String<int> splitScore;
+
+    DPScoutState_()
+    {}
+};
 
 // ----------------------------------------------------------------------------
-// Function streamPut()
+// Class DPScout_
 // ----------------------------------------------------------------------------
 
-template <typename TValue, typename TSpec>
-inline int
-streamPut(String<TValue, TSpec> & stream, char const c)
-{
-    appendValue(stream, c);
-    return 0;
-}
-
-template <typename TValue1, typename TSpec1, typename TValue2, typename TSpec2>
-inline int
-streamPut(String<TValue1, TSpec1> & stream,
-          SimpleType<TValue2, TSpec2> const & c)
+template <typename TDPCell>
+class DPScout_<TDPCell, SplitAlignmentScout> : public DPScout_<TDPCell, Default>
 {
-    appendValue(stream, c);
-    return 0;
-}
+public:
+    typedef DPScout_<TDPCell, Default> TParent;
 
+    DPScoutState_<SplitAlignmentScout> * state;
 
-// template <typename TValue0, typename TSpec0,
-//           typename TValue, typename TSpec, typename TSpec2>
-// inline int
-// streamPut(String<TValue0, MMap<TSpec0> > & stream,
-//           String<SimpleType<TValue, TSpec>, TSpec2> const & source)
-// {
-//     String<char, CStyle> buf = source;
-//     append(stream, toCString(buf));
-//     return 0;
-// }
-
-template <typename TValue, typename TSpec, typename TValue2, typename TSpec2>
-inline int
-streamPut(String<TValue, TSpec> & stream,
-          String<TValue2, TSpec2> const & source)
-{
-    append(stream, source);
-    return 0;
-}
+    DPScout_() : TParent(), state(0)
+    {}
 
+    DPScout_(DPScoutState_<SplitAlignmentScout> & state) : TParent(), state(&state)
+    {}
+};
 
-template <typename TValue, typename TSpec, typename TSource>
-inline int
-_appendWithoutTrailing0(String<TValue, TSpec> & stream,
-                        TSource const & source)
-{
-    for (int i = 0; source[i] != 0; ++i)
-        appendValue(stream, source[i]);
-    return 0;
-}
+// ============================================================================
+// Metafunctions
+// ============================================================================
 
-template <typename TValue, typename TSpec>
-inline int
-streamPut(String<TValue, TSpec> & stream, char const *source)
-{
-    return _appendWithoutTrailing0(stream, source);
-}
+// ============================================================================
+// Functions
+// ============================================================================
 
+// ----------------------------------------------------------------------------
+// Function _scoutBestScore()                                        [DPScout_]
+// ----------------------------------------------------------------------------
 
-// for numerical types
-template <typename TValue, typename TSpec, typename TSource>
-inline int
-streamPut(String<TValue, TSpec> & stream, TSource const & source)
+template <typename TDPCell, typename TTraceMatrixNavigator, typename TIsLastColumn, typename TIsLastRow>
+inline void
+_scoutBestScore(DPScout_<TDPCell, SplitAlignmentScout> & dpScout,
+                TDPCell const & activeCell,
+                TTraceMatrixNavigator const & navigator,
+                TIsLastColumn /*isLastColumn*/,
+                TIsLastRow /*isLastRow*/ )
 {
-    return _streamPut(stream, source, typename IsSequence<TSource const>::Type());
+    //typedef typename Value<TDPCell>::Type TScoreValue;
+    // Note that the underlying matrix has the coordinates flipped.  We use posH/posV as we would in pairwise alignments
+    // and thus this is the reverse from the matrix representation.
+    unsigned posH = coordinate(navigator, +DPMatrixDimension_::HORIZONTAL);
+    // unsigned posV = coordinate(navigator, +DPMatrixDimension_::VERTICAL);
+
+    int & i = dpScout.state->splitScore[posH];
+    i = std::max(i, _scoreOfCell(activeCell));
+
+    // We track only the last row for the best traceback score.
+    if (TIsLastColumn::VALUE || TIsLastRow::VALUE)
+    {
+        typedef DPScout_<TDPCell, SplitAlignmentScout> TDPScout;
+        typedef typename TDPScout::TParent TParent;
+        _scoutBestScore(static_cast<TParent &>(dpScout), activeCell, navigator);
+    }
 }
 
-
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_STREAM_ADAPT_MMAP_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_
diff --git a/seqan/alignment_free.h b/seqan/alignment_free.h
new file mode 100644
index 0000000..073825a
--- /dev/null
+++ b/seqan/alignment_free.h
@@ -0,0 +1,63 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jonathan Goeke <goeke@molgen.mpg.de>
+// ==========================================================================
+// Facade header for module alignment_free.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/basic.h>
+#include <seqan/file.h>
+#include <seqan/sequence.h>
+#include <seqan/statistics.h>
+#include <seqan/misc/edit_environment.h>
+
+// ===========================================================================
+// Module's headers.
+// ===========================================================================
+
+#include <seqan/alignment_free/alignment_free_base.h>
+#include <seqan/alignment_free/kmer_functions.h>
+#include <seqan/alignment_free/af_d2.h>
+#include <seqan/alignment_free/af_d2z.h>
+#include <seqan/alignment_free/af_d2star.h>
+#include <seqan/alignment_free/af_n2.h>
+
+#include <seqan/alignment_free/alignment_free_comparison.h>
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_H_
diff --git a/seqan/alignment_free/af_d2.h b/seqan/alignment_free/af_d2.h
new file mode 100644
index 0000000..a7222d4
--- /dev/null
+++ b/seqan/alignment_free/af_d2.h
@@ -0,0 +1,124 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jonathan Goeke <goeke@molgen.mpg.de>
+// ==========================================================================
+// This header contains the implementation of the D2 score for alignment free
+// sequence comparison (inner product of kmer counts).
+//
+// These functions can be called with alignmentFreeComparison().
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_
+
+namespace seqan {
+
+/*
+ * _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h)
+ */
+template <typename TStringSet, typename TValue>
+void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix,
+                              TStringSet const & sequenceSet,
+                              AFScore<D2> const & score)
+{
+    //typedef typename Value<TStringSet>::Type                        TString;
+    //typedef typename Value<TString>::Type                           TAlphabet;
+    typedef typename Iterator<TStringSet const>::Type               TIteratorSet;
+    typedef typename Iterator<StringSet<String<unsigned> > >::Type  TIteratorSetInt;
+    //typedef Matrix<TValue, 2>                                       TMatrix;
+
+    unsigned seqNumber = length(sequenceSet);
+
+    // Resize the scoreMatrix
+    setLength(scoreMatrix, 0, seqNumber);
+    setLength(scoreMatrix, 1, seqNumber);
+    resize(scoreMatrix, (TValue) 0);
+
+    StringSet<String<unsigned> > kmerCounts;
+    resize(kmerCounts, seqNumber);
+
+    // Count all kmers
+    TIteratorSetInt itKmerCounts = begin(kmerCounts);
+    TIteratorSet itSeqSet = begin(sequenceSet);
+
+    for (; itSeqSet < end(sequenceSet); ++itSeqSet)
+    {
+        countKmers(value(itKmerCounts), value(itSeqSet), score.kmerSize);
+        ++itKmerCounts;
+    }
+    if(score.verbose)
+    {
+      std::cout << "\ncounted words";
+    }
+
+    // Calculate all pairwise scores and store them in scoreMatrix
+    for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex)
+    {
+        if(score.verbose)
+        {
+            std::cout << "\nSequence number " << rowIndex;
+        }
+        for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex)
+        {
+            _alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex], kmerCounts[colIndex], score);
+            value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex);  // Copy symmetric entries
+        }
+    }
+
+}
+
+/*
+ * Calculate pairwise score given the counts of all kmers
+ */
+template <typename TValue>
+void
+_alignmentFreeCompareCounts(TValue & result,
+                            String<unsigned> const & kmerCounts1,
+                            String<unsigned> const & kmerCounts2,
+                            AFScore<D2> const & /*score*/)
+{
+    typedef typename Iterator<String<unsigned> const>::Type TIteratorInt;
+
+    TIteratorInt it1 = begin(kmerCounts1);
+    TIteratorInt it2 = begin(kmerCounts2);
+
+    result = 0;
+    for (; it1 < end(kmerCounts1); ++it1)
+    {
+        result += value(it1) * value(it2);
+        ++it2;
+    }
+}
+
+}  // namespace seqan
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_
diff --git a/seqan/alignment_free/af_d2star.h b/seqan/alignment_free/af_d2star.h
new file mode 100644
index 0000000..2791818
--- /dev/null
+++ b/seqan/alignment_free/af_d2star.h
@@ -0,0 +1,224 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jonathan Goeke <goeke@molgen.mpg.de>
+// ==========================================================================
+// This header contains the implementation of the D2star score for alignment
+// free sequence comparison.
+//
+// See: Reinert et al. J Comput Biol. 2009 Dec;16(12):1615-34.
+//
+// These functions can be called with alignmentFreeComparison().
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2STAR_ORIGINAL_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2STAR_ORIGINAL_H_
+
+namespace seqan {
+
+/*
+ * _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h)
+ */
+template <typename TValue, typename TStringSet>
+void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix,
+                              TStringSet const & sequenceSet,
+                              AFScore<D2Star> const & score)
+{
+
+    //typedef typename Iterator<TStringSet const>::Type             TIteratorSet;
+    //typedef typename Iterator<StringSet<String<double> > >::Type  TIteratorSetDouble;
+
+    //typedef Matrix<TValue, 2> TMatrix;
+
+    unsigned seqNumber = length(sequenceSet);
+
+    // Resize the scoreMatrix
+    setLength(scoreMatrix, 0, seqNumber);
+    setLength(scoreMatrix, 1, seqNumber);
+    resize(scoreMatrix, (TValue) 0);
+    StringSet<String<double> > standardisedKmerCounts;
+    resize(standardisedKmerCounts, seqNumber);
+
+    // Calculate all pairwise scores and store them in scoreMatrix
+    for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex)
+    {
+        if(score.verbose)
+        {
+            std::cout << "\nSequence number " << rowIndex;
+        }
+        for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex)
+        {
+            _d2star(value(scoreMatrix, rowIndex, colIndex), sequenceSet[rowIndex], sequenceSet[colIndex], score);
+            value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex);  // Copy symmetric entries
+        }
+    }
+}
+
+/*
+ * _d2star calculates the pairwise score of two sequences according to the paper referenced above.
+ */
+template <typename TValue, typename TSequence>
+void _d2star(TValue & result,
+             TSequence const & sequence1,
+             TSequence const & sequence2,
+             AFScore<D2Star> const & score)
+{
+    typedef typename Value<TSequence>::Type              TAlphabet;
+    typedef typename UnmaskedAlphabet_<TAlphabet>::Type  TUnmaskedAlphabet;
+
+    TValue missing = -pow(10.0, 10);
+    TSequence seq1seq2;
+    append(seq1seq2, sequence1);
+    append(seq1seq2, sequence2);
+    result = 0.0;
+
+    // Note that there is some code below that looks like copy-and-paste.  However, pulling this out into another
+    // function is the only way to get rid of the duplicate lines since we use different types.  After some discussion,
+    // weese, goeke and holtgrew agreed that it is probably easier to read and maintain this way than to spread the code
+    // over to one more function.
+    if (score.bgModelOrder == 0)
+    {
+        // --------------------------------------------------------------------
+        // Order 0 Background Model
+        // --------------------------------------------------------------------
+
+        String<unsigned> kmerCounts1;
+        String<unsigned> kmerCounts2;
+        String<unsigned> backgroundCounts;
+        String<double> backgroundFrequencies;
+        resize(backgroundFrequencies, 4, 0);
+        countKmers(kmerCounts1, sequence1, score.kmerSize);
+        countKmers(kmerCounts2, sequence2, score.kmerSize);
+        countKmers(backgroundCounts, seq1seq2, 1);
+        int sumBG = 0;
+        for (unsigned i = 0; i < length(backgroundCounts); ++i)
+        {
+            sumBG += backgroundCounts[i];
+        }
+        for (unsigned i = 0; i < length(backgroundCounts); ++i)
+        {
+            backgroundFrequencies[i] = backgroundCounts[i] / ((double)sumBG);
+        }
+        unsigned nvals = length(kmerCounts1);  // Number of kmers
+        int len1 = 0;
+        int len2 = 0;
+
+        for (unsigned l = 0; l < nvals; l++)
+        {
+            len1 += kmerCounts1[l];
+            len2 += kmerCounts2[l];
+        }
+
+        String<TValue> probabilities;  // String of TValue to store the word probabilities p_w
+        resize(probabilities, nvals, missing);
+
+        for (unsigned i = 0; i < nvals; ++i)
+        {
+            TValue p_w = 1;  // Probability of kmer
+
+            String<TUnmaskedAlphabet> w;
+            unhash(w, i, score.kmerSize);
+            calculateProbability(p_w, w, backgroundFrequencies);
+            TValue variance1 = 0.0;
+            TValue variance2 = 0.0;
+
+            variance1 = pow(len1 * p_w, 0.5);
+            variance2 = pow(len2 * p_w, 0.5);
+
+            // Test if variance is larer than 0 and smaller than inf before dividing
+            if ((variance1 > missing) && (variance1 < pow(10.0, 10)))
+            {
+                if (p_w > 0)
+                {
+                    TValue stCount1 = (kmerCounts1[i] - p_w * len1) / variance1;
+                    TValue stCount2 = (kmerCounts2[i] - p_w * len2) / variance2;
+                    result += stCount1 * stCount2;
+                }
+            }
+        }
+    }
+    else
+    {
+        // --------------------------------------------------------------------
+        // Higher Order Background Model
+        // --------------------------------------------------------------------
+
+        String<unsigned> kmerCounts1;
+        String<unsigned> kmerCounts2;
+        StringSet<String<TUnmaskedAlphabet> > bgSequences;
+        stringToStringSet(bgSequences, seq1seq2);  // Create unmasked sequences
+        MarkovModel<TUnmaskedAlphabet, TValue> backgroundModel(score.bgModelOrder);
+        buildMarkovModel(backgroundModel, bgSequences);
+        countKmers(kmerCounts1, sequence1, score.kmerSize);
+        countKmers(kmerCounts2, sequence2, score.kmerSize);
+
+        unsigned nvals = length(kmerCounts1);  // Number of kmers
+        int len1 = 0;
+        int len2 = 0;
+
+        for (unsigned l = 0; l < nvals; l++)
+        {
+            len1 += kmerCounts1[l];
+            len2 += kmerCounts2[l];
+        }
+        String<TValue> probabilities;
+        resize(probabilities, nvals, missing);
+        for (unsigned i = 0; i < nvals; ++i)
+        {
+            TValue p_w = 1.0;  // Probability of kmer
+            TValue variance = 0.0;
+            String<TUnmaskedAlphabet> w;
+            unhash(w, i, score.kmerSize);
+            p_w = emittedProbability(backgroundModel, w);
+            variance = ((TValue) pow(((TValue) len1 * len2), 0.5)) * p_w;
+            TValue variance1 = 0.0;
+            TValue variance2 = 0.0;
+
+            variance1 = pow(len1 * p_w, 0.5);
+            variance2 = pow(len2 * p_w, 0.5);
+
+            // Calculate standardised kmer Count
+            if ((variance > pow(10.0, -10)) && (variance < pow(10.0, 10)))
+            {
+                if (p_w > 0)
+                {
+                    TValue stCount1 = (kmerCounts1[i] - p_w * len1) / variance1;
+                    TValue stCount2 = (kmerCounts2[i] - p_w * len2) / variance2;
+                    result += stCount1 * stCount2;
+                 }
+            }
+        }
+    }
+}
+
+}  // namespace seqan
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2STAR_ORIGINAL_H_
diff --git a/seqan/alignment_free/af_d2z.h b/seqan/alignment_free/af_d2z.h
new file mode 100644
index 0000000..d2a45a8
--- /dev/null
+++ b/seqan/alignment_free/af_d2z.h
@@ -0,0 +1,631 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jonathan Goeke <goeke@molgen.mpg.de>
+// ==========================================================================
+// This header contains the implementation of the D2z score for
+// alignment free sequence comparison.
+//
+// See Kantorovitz et al. Bioinformatics 2007, Volume23, Issue13,
+// Pp. i249-i255.
+//
+// These functions can be called with alignmentFreeComparison().
+// ==========================================================================
+
+// TODO(goeke): const could be added below for the input variables but the function value() in matrix_base (align) is not defined for const. Similarly, the function emittedProbabilty is not defined for const in  statistics_markov_model.h
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2Z_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2Z_H_
+
+namespace seqan {
+
+/*
+ * _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h)
+ */
+template <typename TStringSet, typename TValue>
+void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix,
+                              TStringSet const & sequenceSet,
+                              AFScore<D2z> const & score)
+{
+    typedef typename Value<TStringSet>::Type                                    TString;
+    typedef typename Value<TString>::Type                                       TAlphabet;
+    typedef typename UnmaskedAlphabet_<TAlphabet>::Type                         TUnmaskedAlphabet;
+    typedef typename Iterator<TStringSet const>::Type                           TIteratorSet;
+    typedef typename Iterator<StringSet<String<unsigned> > >::Type              TIteratorSetUnsigned;
+    typedef typename Iterator<StringSet<String<double> > >::Type                TIteratorSetDouble;
+    typedef typename Iterator<String<MarkovModel<TUnmaskedAlphabet> > >::Type   TIteratorMarkovModel;
+
+    unsigned seqNumber = length(sequenceSet);
+
+    // Resize scoreMatrix
+    setLength(scoreMatrix, 0, seqNumber);
+    setLength(scoreMatrix, 1, seqNumber);
+    resize(scoreMatrix, (TValue) 0);
+
+    StringSet<String<unsigned> > kmerCounts;
+    resize(kmerCounts, seqNumber);
+
+    // Note that there is some code below that looks like copy-and-paste.  However, pulling this out into another
+    // function is the only way to get rid of the duplicate lines since we use different types.  After some discussion,
+    // weese, goeke and holtgrew agreed that it is probably easier to read and maintain this way than to spread the code
+    // over to one more function.
+    if (score.bgModelOrder == 0)
+    {
+        // --------------------------------------------------------------------
+        // Order 0 Background Model
+        // --------------------------------------------------------------------
+
+        StringSet<String<double> > backgroundFrequencies;
+        resize(backgroundFrequencies, seqNumber);
+
+        // Count all kmers and all background nucleotide frequencies and store them in stringSets
+        TIteratorSetUnsigned itKmerCounts = begin(kmerCounts);
+        TIteratorSetDouble itBackgroundFrequencies = begin(backgroundFrequencies);
+
+        TIteratorSet itSeqSet = begin(sequenceSet);
+        for (; itSeqSet < end(sequenceSet); ++itSeqSet)
+        {
+            countKmers(*itKmerCounts, *itBackgroundFrequencies, *itSeqSet, score.kmerSize);
+            ++itKmerCounts;
+            ++itBackgroundFrequencies;
+        }
+        if(score.verbose)
+        {
+            std::cout << "\ncounted words";
+        }
+        // Calculate all pairwise scores and store them in scoreMatrix
+        for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex)
+        {
+            if(score.verbose)
+            {
+                std::cout << "\nSequence number " << rowIndex;
+            }
+            for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex)
+            {
+                _alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex],
+                                            backgroundFrequencies[rowIndex], kmerCounts[colIndex],
+                                            backgroundFrequencies[colIndex], score);
+                value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex);  // Copy symmetric entries
+            }
+        }
+    }
+    else
+    {
+        // --------------------------------------------------------------------
+        // Higher Order Background Model
+        // --------------------------------------------------------------------
+
+        String<MarkovModel<TUnmaskedAlphabet> > backgroundModels;
+        resize(backgroundModels, seqNumber, MarkovModel<TUnmaskedAlphabet>(score.bgModelOrder));
+        TIteratorMarkovModel itMM = begin(backgroundModels);
+        TIteratorSet itSeqSet = begin(sequenceSet);
+        // Count all kmers and all background nucleotide frequencies and store them in StringSets
+        TIteratorSetUnsigned itKmerCounts = begin(kmerCounts);
+
+        for (; itSeqSet < end(sequenceSet); ++itSeqSet)
+        {
+            countKmers(*itKmerCounts, *itMM, *itSeqSet, score.kmerSize);
+            ++itKmerCounts;
+            if (itMM < end(backgroundModels))
+            {
+                itMM->_computeAuxiliaryMatrices();
+                ++itMM;
+            }
+
+        }
+        if(score.verbose)
+        {
+            std::cout << "\ncounted words";
+        }
+        // Calculate all pairwise scores and store them in scoreMatrix
+        for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex)
+        {
+            if(score.verbose)
+            {
+                std::cout << "\nSequence number " << rowIndex;
+            }
+            for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex)
+            {
+                _alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex],
+                                            backgroundModels[rowIndex], kmerCounts[colIndex],
+                                            backgroundModels[colIndex], score);
+                value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex);  // Copy symmetric entries
+            }
+        }
+    }
+}
+
+/*
+ * computeExpectationD2 calculates the expected value of the D2 score given a Bernoulli model,
+ * see paper referenced above
+ */
+template <typename TValue>
+double computeExpectationD2(int const len1, int const len2, unsigned const k, TValue const * q1, TValue const * q2)
+{
+    TValue p2 = 0;
+    for (int i = 0; i < 4; i++)
+        p2 += q1[i] * q2[i];
+
+    int nbar1 = len1 - k + 1;
+    int nbar2 = len2 - k + 1;
+
+    TValue retval = nbar1;
+    retval *= nbar2;
+    retval *= pow((double)p2, (int)k);
+    return retval;
+}
+
+/*
+ * computeExpectationD2 calculates the expected value of the D2 score given a Markov model,
+ * see paper referenced above
+ */
+template <typename TAlphabet, typename TValue, typename TSpec>
+double computeExpectationD2(int const slen1,
+                            int const slen2,
+                            unsigned const k,
+                            MarkovModel<TAlphabet, TValue, TSpec> /*const*/ & bkg1,
+                            MarkovModel<TAlphabet, TValue, TSpec> /*const*/ & bkg2,
+                            TValue & indicatorexpectation)
+{
+    unsigned mo = bkg1.order;
+    if (mo >= k)
+    {
+        // Error: Can't suppport markov order greater or equal to word length
+        exit(1);
+    }
+
+    long emo  = 1 << (2 * mo);  // This is equal to pow(4, mo)
+    long ekmo = 1 << (2 * (k - mo));  // This is equal to pow(4, k - mo)
+
+    TValue mean = 0;
+    for (long i = 0; i < emo; i++)
+    {
+        TValue term = value(bkg1.stationaryDistribution, i) * value(bkg2.stationaryDistribution, i);
+        TValue subterm = 0;
+
+        for (long j = 0; j < ekmo; j++)
+        {
+            TValue subprob1 = _computeWordProbGivenPrefix(i, j, bkg1, k, mo);
+            TValue subprob2 = _computeWordProbGivenPrefix(i, j, bkg2, k, mo);
+            subterm += subprob1 * subprob2;
+        }
+        mean += term * subterm;
+    }
+
+    indicatorexpectation = mean;  // This is E[Y_ij], see paper referenced above.
+    int nbar1 = slen1 - k + 1;  // Number of kmers in sequence1
+    int nbar2 = slen2 - k + 1;  // Number of kmers in sequence2
+    return mean * ((TValue) nbar1 * nbar2);
+}
+
+/*
+ * computeVarianceD2 calculates the variance of the D2 score given a Bernoulli model,
+ * see paper referenced above
+ */
+template <typename TValue>
+double computeVarianceD2(int len1, int len2, unsigned k, TValue * q1, TValue * q2)
+{
+    int nbar1 = len1 - k + 1;  // Number of kmers in sequence 1
+    int nbar2 = len2 - k + 1;  // Number of kmers in sequence 2
+
+    int qbar1 = len1 - 2 * k + 2;  // Number of overlapping kmers in sequence 1
+    int qbar2 = len2 - 2 * k + 2;
+
+    TValue p2 = 0, p31 = 0, p32 = 0;
+    for (int i = 0; i < 4; i++)
+    {
+        p2 += q1[i] * q2[i];
+        p31 += q1[i] * q2[i] * q1[i];
+        p32 += q1[i] * q2[i] * q2[i];
+    }
+
+    TValue variance = 0;
+    // 'Crabgrass' with l = 0 (= complete overlap), see paper referenced above
+    TValue power1 = pow((double)p32, (int)k) - pow((double)p2, 2 * (int)k);
+    power1 *= TValue(nbar1) * TValue(qbar2) * TValue(qbar2 - 1);
+    TValue power2 = pow((double)p31, (int)k) - pow((double)p2, 2 * (int)k);
+    power2 *= TValue(nbar2) * TValue(qbar1) * TValue(qbar1 - 1);
+    variance += power1 + power2;
+
+    // 'Crabgrasses' with l > 0, see paper referenced above
+    for (unsigned l = 1; l <= k - 1; l++)
+        variance += 2 * TValue(nbar1 - l) * TValue(qbar2) * TValue(qbar2 - 1) * (pow((double)p2, (int)(2 * l)) * pow((double)p32, (int)(k - l)) - pow((double)p2, (int)(2 * k))) + 2 * TValue(nbar2 - l) * TValue(qbar1) * TValue(qbar1 - 1) * (pow((double)p2, (int)(2 * l)) * pow((double)p31, (int)(k - l)) - pow((double)p2, (int)(2 * k)));
+
+    // Accordion main diagonal, see paper referenced above
+    variance += TValue(nbar1) * TValue(nbar2) * (pow((double)p2, (int)(k)) - pow((double)p2, (int)(2 * k)));
+    for (unsigned l = 1; l <= k - 1; l++)
+        variance += 2 * TValue(nbar1 - l) * TValue(nbar2 - l) * (pow((double)p2, (int)(k + l)) - pow((double)p2, (int)(2 * k)));
+
+    return variance;
+}
+
+
+/*
+ * computeVarianceD2 calculates the variance of the D2 score given a Markov model,
+ * see paper referenced above
+ */
+template <typename TAlphabet, typename TValue, typename TSpec>
+double computeVarianceD2(int const slen1,
+                         int const slen2,
+                         unsigned const k,
+                         MarkovModel<TAlphabet, TValue, TSpec> /*const*/ & bkg1,
+                         MarkovModel<TAlphabet, TValue, TSpec> /*const*/ & bkg2,
+                         TValue indicatorexpectation)
+{
+    unsigned mo = bkg1.order;
+    if (mo >= k)
+    {
+        // Error: Can't support markov order greater or equal to word length
+        exit(1);
+    }
+
+    long emo  = 1 << (2 * mo);        // Equivalent to pow(4, mo);
+    long ekmo = 1 << (2 * (k - mo));  // Equivalent to pow(4, k - mo);
+
+    int q1 = slen1 - 2 * k + 2;
+    int q2 = slen2 - 2 * k + 2;
+    int nbar1 = slen1 - k + 1;
+    int nbar2 = slen2 - k + 1;
+
+    // Create matrix for Sbctilde
+    Matrix<TValue, 2> Sbctilde1;
+    setLength(Sbctilde1, 0, emo);
+    setLength(Sbctilde1, 1, emo);
+    resize(Sbctilde1);
+
+    Matrix<TValue, 2> Sbctilde2;
+    setLength(Sbctilde2, 0, emo);
+    setLength(Sbctilde2, 1, emo);
+    resize(Sbctilde2);
+
+    for (long i = 0; i < emo; i++)
+    {
+        for (long j = 0; j < emo; j++)
+        {
+            value(Sbctilde1, i, j) = (q1 * (q1 + 1) / 2) * value(bkg1.stationaryDistribution, j) - (q1 - 1) * value(bkg1._qppp, i, j) - value(bkg1._qppqpp, i, j);
+            value(Sbctilde2, i, j) = (q2 * (q2 + 1) / 2) * value(bkg2.stationaryDistribution, j) - (q2 - 1) * value(bkg2._qppp, i, j) - value(bkg2._qppqpp, i, j);
+        }
+    }
+
+    // Compute sums of word probabilities and star probabilities of x-mers (x between mo + 1 and k) conditional on last or first (resp) mo-word, see paper referenced above
+    Matrix<TValue, 2> sump;  // sump[x][wk] is the total word probability of every x-word ending with wk (which is of length mo)
+    setLength(sump, 0, k + 1);
+    setLength(sump, 1, emo);
+    resize(sump, 0.0);
+
+    Matrix<TValue, 2> sumpstar;
+    setLength(sumpstar, 0, k + 1);
+    setLength(sumpstar, 1, emo);
+    resize(sumpstar, 0.0);
+
+
+    for (unsigned x = 0; x <= k; x++)
+    {
+        if (x <= mo)
+        {
+
+            continue;
+        }
+
+        for (long wk = 0; wk < emo; wk++)
+        {
+            TValue sum = 0;
+            long exmo = 1 << (2 * (x - mo));  // Equivalent to pow(4, x - mo);
+            for (long wpre = 0; wpre < exmo; wpre++)
+            {
+                sum += _computeWordProb((wpre << (2 * mo)) + wk, bkg1, x, mo) * _computeWordProb((wpre << (2 * mo)) + wk, bkg2, x, mo);
+            }
+            value(sump, x, wk) = sum;
+        }
+
+        for (long u1 = 0; u1 < emo; u1++)
+        {
+            TValue sum = 0;
+            long exmo = 1 << (2 * (x - mo));  // Equivalent to pow(4, x - mo);
+            for (long usuf = 0; usuf < exmo; usuf++)
+            {
+                sum += _computeWordProbGivenPrefix(u1, usuf, bkg1, x, mo) * _computeWordProbGivenPrefix(u1, usuf, bkg2, x, mo);
+            }
+            value(sumpstar, x, u1) = sum;
+        }
+    }
+
+    // Handle the non overlap terms first
+    TValue covnonoverlap = 0;
+    for (long wk = 0; wk < emo; wk++)
+    {
+        for (long u1 = 0; u1 < emo; u1++)
+        {
+            TValue term = value(Sbctilde1, wk, u1) * value(Sbctilde2, wk, u1) * value(sump, k, wk) * value(sumpstar, k, u1);
+            covnonoverlap += 4 * term;
+        }
+    }
+    TValue subtractFromNonOverlap = (TValue)q1 * (q1 - 1) * q2 * (q2 - 1);
+    subtractFromNonOverlap *= pow(indicatorexpectation, 2);
+    covnonoverlap -= subtractFromNonOverlap;
+    // Compute 'crabgrass' terms, see paper referenced above
+    TValue covcrabgrass = 0;
+
+    // Case 1: overlap >= mo
+    for (unsigned m = 1; m <= k - mo; m++)
+    {
+        long ekm = 1 << (2 * (k - m)); // Equivalent to pow(4, k - m)
+        long moonesflag = (1 << (2 * mo)) - 1;
+        long kmmoonesflag = (1 << (2 * (k - m - mo))) - 1;
+        for (long v = 0; v < ekm; v++)
+        {
+            long vsuf = v & moonesflag;           // Last morder chars of v
+            long vpre = v >> (2 * (k - m - mo));  // First morder chars of v, equivalent to v / pow(4, k - m - mo)
+            long vsuf2 = v & kmmoonesflag;        // Remaining k-m-morder chars of v; equivalent to v % pow(4, k - m - mo)
+            // In the following, if m = k - mo, _computeWordProbGivenPrefix(.,.,.,k - m, mo) will return 1, as it should
+            // Overlap in A, separate in B
+            TValue term1 = value(Sbctilde2, vsuf, vpre);
+            term1 *= _computeWordProbGivenPrefix(vpre, vsuf2, bkg1, k - m, mo);
+            term1 *= pow(_computeWordProbGivenPrefix(vpre, vsuf2, bkg2, k - m, mo), 2);
+            term1 *= value(sump, m + mo, vpre);
+            term1 *= value(sumpstar, m + mo, vsuf);
+            // Overlap in B, separate in A
+            TValue term2 = value(Sbctilde1, vsuf, vpre);
+            term2 *= _computeWordProbGivenPrefix(vpre, vsuf2, bkg2, k - m, mo);
+            term2 *= pow(_computeWordProbGivenPrefix(vpre, vsuf2, bkg1, k - m, mo), 2);
+            term2 *= value(sump, m + mo, vpre);
+            term2 *= value(sumpstar, m + mo, vsuf);
+
+            covcrabgrass += 4 * q1 * term1 + 4 * q2 * term2;
+        }
+    }
+    // Case 2: overlap < morder
+    for (unsigned m = k - mo + 1; m <= k - 1; m++)
+    {
+        int tlen = 2 * mo - (k - m);
+        long et = 1 << (2 * tlen);  // Equivalent to pow(4, tlen);
+        long moonesflag = (1 << (2 * mo)) - 1;
+        long tmoonesflag = (1 << (2 * (tlen - mo))) - 1;
+        for (long t = 0; t < et; t++)
+        {
+            long tsuf = t & moonesflag;          // Last morder chars of t; equivalent to t % emo;
+            long tpre = t >> (2 * (tlen - mo));  // First morder chars of t, equivalent to t / pow(4, tlen - mo)
+            long tsuf2 = t & tmoonesflag;        // Remaining tlen-morder chars of t, equivalent to t % etmo;
+            // Overlap in A, separate in B
+            TValue term1 = value(Sbctilde2, tpre, tsuf);
+            term1 *= _computeWordProbGivenPrefix(tpre, tsuf2, bkg1, tlen, mo);
+            term1 *= value(sump, k, tpre);
+            term1 *= value(sumpstar, k, tsuf);
+            // Overlap in B, separate in A
+            TValue term2 = value(Sbctilde1, tpre, tsuf);
+            term2 *= _computeWordProbGivenPrefix(tpre, tsuf2, bkg2, tlen, mo);
+            term2 *= value(sump, k, tpre);
+            term2 *= value(sumpstar, k, tsuf);
+
+            covcrabgrass += 4 * q1 * term1 + 4 * q2 * term2;
+        }
+    }
+
+    // Case 3: m=0 (complete overlap)
+    long moonesflag = (1 << (2 * mo)) - 1;
+    for (long wpre = 0; wpre < emo; wpre++)
+    {
+        // First morder chars of w
+        TValue term1 = 0;
+        TValue term2 = 0;
+        for (long wsuf2 = 0; wsuf2 < ekmo; wsuf2++)
+        {
+            // Remaining k-morder chars of w
+            long wsuf = ((wpre << (2 * (k - mo))) + wsuf2) & moonesflag;  // Last morder chars of w
+            term1 += 2 * nbar1 * value(Sbctilde2, wsuf, wpre) * _computeWordProbGivenPrefix(wpre, wsuf2, bkg1, k, mo) * pow(_computeWordProbGivenPrefix(wpre, wsuf2, bkg2, k, mo), 2);
+            term2 += 2 * nbar2 * value(Sbctilde1, wsuf, wpre) * _computeWordProbGivenPrefix(wpre, wsuf2, bkg2, k, mo) * pow(_computeWordProbGivenPrefix(wpre, wsuf2, bkg1, k, mo), 2);
+        }
+        covcrabgrass += (term1 + term2) * value(bkg1.stationaryDistribution, wpre) * value(bkg2.stationaryDistribution, wpre);
+    }
+
+    // Ignored edge effects, see paper referened above
+    // Subtract expectations
+    TValue subtractfromcrabgrass = (((2 * q1 * k - nbar1) * (double)q2 * double(q2 - 1)) + ((2 * q2 * k - nbar2) * (double)q1 * double(q1 - 1)));
+    subtractfromcrabgrass *= pow(indicatorexpectation, 2);
+    covcrabgrass -= subtractfromcrabgrass;
+
+    // Compute the accordion main diagonal terms
+    TValue covaccordiondiag = 0;
+
+    for (unsigned m = 1; m <= k - 1; m++)
+    {
+        long tlen;
+        if (m <= mo - 1)
+            tlen = m + mo;
+        else
+            tlen = 2 * mo - 1;
+        long et = 1 << (2 * tlen);  // Equivalent to pow(4, tlen)
+        long moonesflag = (1 << (2 * mo)) - 1;
+        long tmoonesflag = (1 << (2 * (tlen - mo))) - 1;
+
+        TValue mterm = 0;
+        for (long t = 0; t < et; t++)
+        {
+            TValue term = 1;
+            long tpre = t >> (2 * (tlen - mo));  // First morder chars of t, equivalent to t / pow(4, tlen - mo)
+            long tsuf2 = t & tmoonesflag;        // The remaining tlen - morder chars of t, equivalent to t % etmo;
+            term *= _computeWordProbGivenPrefix(tpre, tsuf2, bkg1, tlen, mo) * _computeWordProbGivenPrefix(tpre, tsuf2, bkg2, tlen, mo);
+            term *= value(sump, k, tpre);
+            if (m >= mo)
+            {
+                long tsuf = t & moonesflag;  // Last morder chars of t, equivalent to t%emo;
+                term *= value(sumpstar, m + 1, tsuf);
+            }
+            mterm += term;
+        }
+        covaccordiondiag += 2 * (nbar1 - m) * (nbar2 - m) * mterm;
+    }
+    covaccordiondiag += nbar1 * nbar2 * indicatorexpectation;  // Complete overlap term
+    covaccordiondiag -= (nbar1 * nbar2 * (2 * k - 1) - (nbar1 + nbar2) * k * (k - 1) + (k - 1) * k * (2 * k - 1) / 3) * pow(indicatorexpectation, 2);
+    TValue variance = covnonoverlap + covcrabgrass + covaccordiondiag;
+    return variance;
+
+}
+
+/*
+ * Calculate pairwise score given the counts of all kmers and the background Bernoulli models
+ */
+template <typename TValue, typename TStringBG>
+void _alignmentFreeCompareCounts(TValue & result,
+                                String<unsigned> const & kmerCounts1,
+                                TStringBG const & backgroundFrequencies1,
+                                String<unsigned> const & kmerCounts2,
+                                TStringBG const & backgroundFrequencies2,
+                                AFScore<D2z> const & score)
+{
+    typedef typename Value<TStringBG>::Type TValueBG;
+    TValueBG sum = 0;
+    unsigned len1 = score.kmerSize - 1;
+    unsigned len2 = score.kmerSize - 1;
+    unsigned nvals = length(kmerCounts1);
+
+    for (unsigned l = 0; l < nvals; l++)
+    {
+        len1 += kmerCounts1[l];
+        len2 += kmerCounts2[l];
+
+        sum += kmerCounts1[l] * kmerCounts2[l];
+    }
+
+    TValueBG q1[4];
+    TValueBG q2[4];
+    for (int l = 0; l < 4; l++)
+    {
+        q1[l] = backgroundFrequencies1[l];
+        q2[l] = backgroundFrequencies2[l];
+    }
+
+    // Compute expected value and variance (IID)
+    double E = computeExpectationD2(len1, len2, score.kmerSize, q1, q2);
+    double var = computeVarianceD2(len1, len2, score.kmerSize, q1, q2);
+
+    if ((var <= 0))
+    {
+        if(score.verbose)
+        {
+            std::cout << "Error: negative variance\n";
+        }
+        result = 0;
+        return;
+    }
+    // Calculate z-score
+    result = (TValue) (sum - E) / pow(var, 0.5);
+}
+
+/*
+ * Calculate pairwise score given the counts of all kmers and the background Markov models
+ */
+template <typename TAlphabet, typename TValue, typename TSpec>
+void _alignmentFreeCompareCounts(TValue & result,
+                                String<unsigned> const & kmerCounts1,
+                                MarkovModel<TAlphabet, TValue, TSpec> /*const*/ & bgModel1,
+                                String<unsigned> const & kmerCounts2,
+                                MarkovModel<TAlphabet, TValue, TSpec> /*const*/ & bgModel2,
+                                AFScore<D2z> const & score)
+{
+    unsigned nvals = length(kmerCounts1);
+    int sum = 0;
+    int sumCounts1 = score.kmerSize - 1;
+    int sumCounts2 = score.kmerSize - 1;
+
+    for (unsigned l = 0; l < nvals; l++)
+    {
+        sumCounts1 += kmerCounts1[l];
+        sumCounts2 += kmerCounts2[l];
+        sum += value(kmerCounts1, l) * value(kmerCounts2, l);  // Calculate the inner product
+    }
+
+    TValue D2 = (TValue) sum;
+
+    // Compute mean and variance
+    TValue indicatorexpectation = 0;
+
+    double E = computeExpectationD2(sumCounts1, sumCounts2, score.kmerSize, bgModel1, bgModel2, indicatorexpectation);
+    double var = computeVarianceD2(sumCounts1, sumCounts2, score.kmerSize, bgModel1, bgModel2, indicatorexpectation);
+
+    if (var <= 0)
+    {
+        result = 0;
+        return;
+    }
+    // Return z-score of D2
+    result = (D2 - E) / pow(var, 0.5);
+}
+
+/*
+ * Compute the word probability given a Markov model
+ * see paper referenced on top
+ */
+template <typename TAlphabet, typename TValue, typename TSpec>
+double _computeWordProb(long const word, MarkovModel<TAlphabet, TValue, TSpec> /*const*/ & bkg, unsigned const k, int const mo)
+{
+    // mo needs to be passed, since that decides the prefix
+    // Similarly, this function needs to know the total length of the word k
+    long prefix = word >> (2 * (k - mo));  // Equivalent to word / pow(4, k - mo); gets the first mo chars of word
+    long suffix = word & ((1 << (2 * (k - mo))) - 1);  // Get the last (k - mo) chars of word
+    return value(bkg.stationaryDistribution, prefix) * _computeWordProbGivenPrefix(prefix, suffix, bkg, k, mo);
+}
+
+/*
+ * Compute the word probability given a Markov model
+ * see paper referenced on top
+ */
+template <typename TAlphabet, typename TValue, typename TSpec>
+double _computeWordProbGivenPrefix(long const prefix, long const suffix, MarkovModel<TAlphabet, TValue, TSpec> /*const*/ & bkg, unsigned const k, unsigned const mo)
+{
+    // Computes p_ * (prefix suffix)
+    // Calculate only if k - mo >= 1; otherwise return 1
+    if (k - mo <= 0)
+        return 1;
+
+    TValue prob = 1;
+    long pre = prefix;
+    long jcopy = suffix;
+
+    // Iterate through successive positions of the suffix
+    for (unsigned l = 0; l < k - mo; l++)
+    {
+        // Get the first char of jcopy, which is of length k - mo; equivalent to jcopy / pow(4, k - mo - 1)
+        long jcopyfirst = jcopy >> (2 * (k - mo - 1));
+        long suf = ((pre & ((1 << (2 * (mo - 1))) - 1)) << 2) + jcopyfirst;
+
+        // prob *=P[pre][suf]; P is the transition matrix
+        prob *= value(bkg.transition, pre, suf);
+        // Erase the first char of jcopy, and preserve its length at k - mo by shifting one char to the left; equivalent to (jcopy % pow(4, k - mo - 1)) * 4;
+        jcopy = (jcopy & ((1 << (2 * (k - mo - 1))) - 1)) << 2;
+        pre = suf;
+    }
+    return prob;
+}
+
+}  // namespace seqan
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2Z_H_
diff --git a/seqan/alignment_free/af_n2.h b/seqan/alignment_free/af_n2.h
new file mode 100644
index 0000000..0268992
--- /dev/null
+++ b/seqan/alignment_free/af_n2.h
@@ -0,0 +1,641 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jonathan Goeke <goeke@molgen.mpg.de>
+// ==========================================================================
+// This header contains the implementation of the N2 score for alignment free
+// sequence comparison with word neighbourhood counts
+//
+// See: Goeke et al, to appear.
+//
+// These functions can be called with alignmentFreeComparison().
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_N2_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_N2_H_
+
+namespace seqan {
+
+/*
+ * This function returns a string with indices indicating which k-mer is the
+ * reverse complement k-mer: i=revComIndex[revComIndex[i]]
+ */
+inline void _initialiseRevComIndex(String<unsigned> & revComIndex, unsigned const k)
+{
+    unsigned myLength = (unsigned)pow(4.0, (int)k);
+    resize(revComIndex, myLength, 0);
+    Shape<Dna, SimpleShape> myShape;
+    resize(myShape, k);
+    for (unsigned i = 0; i < myLength; ++i)
+    {
+        String<Dna> w;
+        unhash(w, i, k);
+        DnaStringReverseComplement wRC(w);
+        unsigned hashValue = hash(myShape, begin(wRC));
+        revComIndex[i] = hashValue;
+    }
+
+}
+
+/*
+ * This function returns a stringSet with strings of indices indicating which
+ * k-mers belong to the word neighbourhood for every k-mer (all k-mers with
+ * one mismatch)
+ */
+inline void _initialiseKmerNeighbourhood(StringSet<String<unsigned> > & kmerNeighbourhood,
+                                  unsigned const k, bool const revCom,
+                                  String<unsigned> const & revComIndex)
+{
+    unsigned myLength = (unsigned)pow(4.0, (int)k);
+    Shape<Dna, SimpleShape> myShape;
+    resize(myShape, k);
+    resize(kmerNeighbourhood, myLength);
+    for (unsigned i = 0; i < myLength; ++i)
+    {
+        resize(kmerNeighbourhood[i], 1, i);
+
+        String<Dna> w;
+        unhash(w, i, k);
+        if ((revComIndex[i] != i) && (revCom == true))
+        {
+            appendValue(kmerNeighbourhood[i], revComIndex[i]);
+        }
+        for (unsigned j = 0; j < k; ++j)
+        {
+            for (unsigned l = 0; l < 4; ++l)
+            {
+                String<Dna> wTMP;
+                wTMP = w;
+                if (wTMP[j] != l)
+                {
+                    wTMP[j] = l;
+                    unsigned hashValue = hash(myShape, begin(wTMP));
+                    // Check for double word occurrences
+                    bool duplicate = false;
+                    if (revCom == true)
+                    {
+
+                        for (unsigned n = 0; n < length(kmerNeighbourhood[i]); ++n)
+                        {
+                            if ((hashValue) == kmerNeighbourhood[i][n])
+                            {
+                                duplicate = true;
+                                break;
+                            }
+                        }
+
+                    }
+
+                    if (duplicate == false)
+                    {
+                        appendValue(kmerNeighbourhood[i], hashValue);
+                        if (revCom == true)
+                        {
+                            if (revComIndex[hashValue] != hashValue)
+                            {
+                                appendValue(kmerNeighbourhood[i], revComIndex[hashValue]);
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
+
+/*
+ * _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h)
+ */
+template <typename TValue, typename TStringSet>
+void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix,
+                              TStringSet const & sequenceSet,
+                              AFScore<N2> const & score)
+{
+
+
+
+    typedef typename Value<TStringSet>::Type                            TString;
+    typedef typename Value<TString>::Type                               TAlphabet;
+    typedef typename UnmaskedAlphabet_<TAlphabet>::Type                 TUnmaskedAlphabet;
+    typedef typename Iterator<TStringSet const>::Type                   TIteratorSet;
+    typedef typename Iterator<StringSet<String<double> > >::Type        TIteratorSetDouble;
+
+
+    // Initialise the reverse complement hash table
+    String<unsigned> revComIndex;
+    StringSet<String<unsigned> > kmerNeighbourhood;
+    _initialiseRevComIndex(revComIndex, score.kmerSize);
+    if (score.revCom == "both_strands")
+    {
+        _initialiseKmerNeighbourhood(kmerNeighbourhood, score.kmerSize, true, revComIndex);
+    }
+    else
+    {
+        _initialiseKmerNeighbourhood(kmerNeighbourhood, score.kmerSize, false, revComIndex);
+    }
+
+    unsigned seqNumber = length(sequenceSet);
+
+    setLength(scoreMatrix, 0, seqNumber);
+    setLength(scoreMatrix, 1, seqNumber);
+    resize(scoreMatrix, (TValue) 0);
+
+    StringSet<String<double> > standardisedKmerCounts;
+    resize(standardisedKmerCounts, seqNumber);
+    // Count all kmers and all background nucleotide frequencies and store them in StringSets
+    TIteratorSetDouble itStandardisedKmerCounts = begin(standardisedKmerCounts);
+    TIteratorSet itSeqSet = begin(sequenceSet);
+    for (; itSeqSet < end(sequenceSet); ++itSeqSet)
+    {
+
+        _standardiseCounts(*itStandardisedKmerCounts, revComIndex, kmerNeighbourhood, *itSeqSet, score);
+        if(score.verbose)
+        {
+            std::cout << "\n" << position(itSeqSet);
+        }
+        ++itStandardisedKmerCounts;
+    }
+
+    if (score.norm == true) // Normalise the score so that sequence-self-comparisons are always 1
+    {
+        itStandardisedKmerCounts = begin(standardisedKmerCounts);
+        for (; itStandardisedKmerCounts < end(standardisedKmerCounts); ++itStandardisedKmerCounts)
+        {
+            TValue normValue = 0.0;
+            for (unsigned i = 0; i < length(value(itStandardisedKmerCounts)); ++i)
+            {
+                normValue += value(itStandardisedKmerCounts)[i] * value(itStandardisedKmerCounts)[i];
+            }
+            for (unsigned i = 0; i < length(value(itStandardisedKmerCounts)); ++i)
+            {
+                value(itStandardisedKmerCounts)[i] /= sqrt(normValue);
+            }
+
+        }
+    }
+
+    if (!(score.outputFile == ""))
+    {
+        std::ofstream myfile;
+        myfile.open(toCString(score.outputFile));
+        for (unsigned i = 0; i < length(standardisedKmerCounts[0]); ++i)
+        {
+            String<TUnmaskedAlphabet> w;
+            unhash(w, i, score.kmerSize);
+            myfile << "\t" << w;
+        }
+        myfile << "\n";
+        for (unsigned seqIndex = 0; seqIndex < seqNumber; ++seqIndex)
+        {
+            myfile << "Seq" << seqIndex;
+            for (unsigned i = 0; i < length(standardisedKmerCounts[seqIndex]); ++i)
+            {
+                myfile << "\t" << standardisedKmerCounts[seqIndex][i];
+            }
+            myfile << "\n";
+        }
+        myfile.close();
+    }
+
+    if(score.verbose)
+    {
+        std::cout << "\ncounted words";
+    }
+
+    // Calculate all pairwise scores and store them in scoreMatrix
+    for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex)
+    {
+        if(score.verbose)
+        {
+            std::cout << "\nSequence number " << rowIndex;
+        }
+        for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex)
+        {
+            _alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), revComIndex, standardisedKmerCounts[rowIndex], standardisedKmerCounts[colIndex], score);
+            value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex);  // Copy symmetric entries
+        }
+    }
+}
+
+/*
+ * Calculate pairwise score given the counts of all kmers
+ */
+template <typename TValue, typename TString>
+void
+_alignmentFreeCompareCounts(TValue & result,
+                            String<unsigned> const revComIndex,
+                            TString const & kmerCounts1,
+                            TString const & kmerCounts2,
+                            AFScore<N2> const & score)
+{
+    typedef typename Iterator<TString const, Rooted>::Type    TIteratorTString;
+
+    TIteratorTString it1 = begin(kmerCounts1);
+    TIteratorTString it2 = begin(kmerCounts2);
+    result = 0.0;
+    TValue resultRC = 0.0;
+    for (; it1 < end(kmerCounts1); ++it1)
+    {
+        result += (TValue)(value(it1) * value(it2));
+        // Computation of the reverse complement strand score
+        if ((score.revCom != "") && (score.revCom != "both_strands"))
+        {
+            unsigned hashValue = revComIndex[position(it1)];
+            resultRC += (TValue)(value(it1) * kmerCounts2[hashValue]);
+        }
+        ++it2;
+    }
+
+    if (score.revCom == "mean")
+    {
+        result = (TValue) (resultRC + result) / 2;
+    }
+    else if (score.revCom == "max")
+    {
+        result = std::max(resultRC, result);
+    }
+    else if (score.revCom == "min")
+    {
+        result = std::min(resultRC, result);
+    }
+}
+
+/*
+ * count kmers and standardise count vectors for Dna5 and markov model background
+ */
+template <typename TString, typename TSequence>
+void _standardiseCounts(TString & standardisedCounts,
+                        String<unsigned> const & revComIndex,
+                        StringSet<String<unsigned> > const & kmerNeighbourhood,
+                        TSequence const & sequence,
+                        AFScore<N2> const & score)
+{
+    typedef typename Value<TSequence>::Type                     TAlphabet;
+    typedef typename UnmaskedAlphabet_<TAlphabet>::Type         TUnmaskedAlphabet;
+    typedef typename Value<TString>::Type                       TValue;
+    typedef typename Iterator<String<unsigned>, Rooted>::Type   TIteratorUnsigned;
+    typedef typename Iterator<TString, Rooted>::Type            TIteratorTString;
+
+    unsigned alphabetSize = ValueSize<TUnmaskedAlphabet>::VALUE;
+
+    // Save all word covariances which are computed in covariance Matrix to avoid double computations
+    Matrix<TValue, 2> covarianceMatrix;
+    TValue missing = -pow(10.0, 10);
+    if (score.mismatches > 0)
+    {
+        setLength(covarianceMatrix, 0, pow((double)alphabetSize, (int)score.kmerSize));
+        setLength(covarianceMatrix, 1, pow((double)alphabetSize, (int)score.kmerSize));
+        resize(covarianceMatrix, missing);
+    }
+
+    // Note that there is some code below that looks like copy-and-paste.  However, pulling this out into another
+    // function is the only way to get rid of the duplicate lines since we use different types.  After some discussion,
+    // weese, goeke and holtgrew agreed that it is probably easier to read and maintain this way than to spread the code
+    // over to one more function.
+    if (score.bgModelOrder == 0)
+    {
+        // ----------------------------------------------------------------------
+        // Order 0 Background Model
+        // ----------------------------------------------------------------------
+
+        String<unsigned> kmerCounts;
+        String<double> backgroundFrequencies;
+        countKmers(kmerCounts, backgroundFrequencies, sequence, score.kmerSize);
+        int nvals = length(kmerCounts);  // Number of kmers
+        int len1 = 0;
+        for (int l = 0; l < nvals; l++)
+        {
+            len1 += kmerCounts[l];
+        }
+        resize(standardisedCounts, nvals, (TValue) 0.0);
+
+        // String of TValue to store the word probabilites p_w
+        String<TValue> probabilities;
+        resize(probabilities, nvals, missing);
+
+        TIteratorUnsigned itCounts;
+        TIteratorTString itStandardisedCounts;
+
+        itCounts = begin(kmerCounts);
+        itStandardisedCounts = begin(standardisedCounts);
+
+        for (; itCounts < end(kmerCounts); ++itCounts)
+        {
+            // Temporary counter for mismatch kmer counting
+            TValue counterTMP = 0;
+            TValue p_w = 1;  // Probability of kmer
+
+            String<TUnmaskedAlphabet> w;
+            unhash(w, (unsigned)position(itCounts), score.kmerSize);
+            calculateProbability(p_w, w, backgroundFrequencies);
+            TValue variance = 0;
+            if ((score.mismatches == 1))  // Mismatch  score calculation
+            {
+                p_w = 0;
+                // The first word in the kmerNeighbourhood is the kmer itself, it is weighted normally
+                // Sum of all entries in the covariance matrix. only once computed
+                unsigned wordHash = position(itCounts);
+                unsigned wordRCHash = revComIndex[wordHash];
+
+                for (unsigned row = 0; row < length(kmerNeighbourhood[wordHash]); ++row)
+                {
+                    unsigned wordRowHash = kmerNeighbourhood[wordHash][row];
+                    // The kmer itself is weighted normally
+                    if (wordRowHash == wordHash)  // The first word in the kmerNeighbourhood is the kmer itself, it is weighted normally
+                    {
+                        counterTMP += (TValue) kmerCounts[wordRowHash];
+                    }
+                    else if ((score.revCom == "both_strands") && (wordRowHash == wordRCHash))
+                    {
+                        counterTMP += ((TValue) kmerCounts[wordRowHash]);
+                    }
+                    else
+                    {
+                        counterTMP += ((TValue) kmerCounts[wordRowHash]) * score.mismatchWeight;
+                    }
+                    String<Dna> wMM1;
+                    unhash(wMM1, wordRowHash, score.kmerSize);
+
+                    for (unsigned col = row; col < length(kmerNeighbourhood[wordHash]); ++col)
+                    {
+                        unsigned wordColHash = kmerNeighbourhood[wordHash][col];
+                        if (value(covarianceMatrix, wordColHash, wordRowHash) == missing)
+                        {
+                            String<Dna> wMM2;
+
+                            unhash(wMM2, wordColHash, score.kmerSize);
+                            calculateCovariance(value(covarianceMatrix, wordColHash, wordRowHash), wMM1, wMM2, backgroundFrequencies, (len1 + score.kmerSize - 1));
+                            value(covarianceMatrix, wordRowHash, wordColHash) = value(covarianceMatrix, wordColHash, wordRowHash);
+                        }
+                        if (row == col)  // Variance of weighted variables
+                        {
+                            if ((wordRowHash == wordHash) || (score.revCom == "both_strands" && (wordRowHash == wordRCHash)))  // The variance of the kmer is counted full
+                            {
+                                variance += value(covarianceMatrix, wordRowHash, wordColHash);
+                            }
+                            else
+                            {
+                                variance += pow(score.mismatchWeight, 2) * value(covarianceMatrix, wordRowHash, wordColHash);  // Calculate weighted variances
+                            }
+                        }
+                        // The covariance of the kmer and the reverse complement is weighted full
+                        else if ((score.revCom == "both_strands") && (((wordRowHash == wordHash) && (wordColHash == wordRCHash)) || ((wordRowHash == wordRCHash) && (wordColHash == wordHash))))
+                        {
+                            variance += (2.0) * value(covarianceMatrix, wordRowHash, wordColHash);
+                        }
+                        else if ((wordRowHash == wordHash || wordColHash == wordHash) || (score.revCom == "both_strands" && (wordRowHash == wordRCHash || wordColHash == wordRCHash)))  // The covariance is weighted half
+                        {
+                            variance += (2.0) * score.mismatchWeight * value(covarianceMatrix, wordRowHash, wordColHash);
+                        }
+                        else  // The covariance is weighted^2
+                        {
+                            variance += (2.0) * pow(score.mismatchWeight, 2) * value(covarianceMatrix, wordRowHash, wordColHash);
+                        }
+                    }
+                    if (probabilities[wordRowHash] == missing)
+                    {
+                        calculateProbability(probabilities[wordRowHash], wMM1, backgroundFrequencies);
+                    }
+                    if (wordRowHash == wordHash)  //Weight the probabilities and expected values, normal weight for the kmer itself
+                    {
+                        p_w += probabilities[wordRowHash];
+                    }
+                    else if ((score.revCom == "both_strands") && (wordRowHash == wordRCHash))  // Weight the probabiliets and expected values, normal weight for the reverse complement kmer itself
+                    {
+                        p_w += probabilities[wordRowHash];
+                    }
+                    else
+                    {
+                        p_w += score.mismatchWeight * probabilities[wordRowHash];
+                    }
+                }
+                variance = pow(variance, 0.5);
+            }  // End of mismatch calculation
+            else if (score.revCom == "both_strands")
+            {
+                TValue variance1;
+                TValue variance2;
+                TValue covariance;
+                String<Dna> wRC;
+                unhash(wRC, (unsigned)  revComIndex[(unsigned)position(itCounts)], score.kmerSize);
+                calculateVariance(variance1, w, backgroundFrequencies, (len1 + score.kmerSize - 1));
+                calculateVariance(variance2, wRC, backgroundFrequencies, (len1 + score.kmerSize - 1));
+                calculateCovariance(covariance, w, wRC, backgroundFrequencies, (len1 + score.kmerSize - 1));
+                variance = pow((variance1 + variance2 + (2.0) * covariance), 0.5);
+                TValue p_wRC = 1;  // Probability of the reverse complement kmer
+                calculateProbability(p_wRC, wRC, backgroundFrequencies);
+                p_w += p_wRC;
+            }
+            else
+            {
+                calculateVariance(variance, w, backgroundFrequencies, (len1 + score.kmerSize - 1));
+                variance = pow(variance, 0.5);
+            }
+            if ((variance > pow(10.0, -10)) && (variance < pow(10.0, 10)))
+            {
+                if (p_w > 0)
+                {
+                    if (score.mismatches > 0)
+                    {
+                        value(itStandardisedCounts) = ((TValue) ((TValue) counterTMP) - p_w * ((TValue)len1)) / variance;
+                    }
+                    else if (score.revCom == "both_strands")
+                    {
+                         value(itStandardisedCounts) = ((TValue) ((TValue) value(itCounts) + kmerCounts[revComIndex[(unsigned)position(itCounts)]]) - p_w * ((TValue)len1)) / variance;
+                    }
+                    else
+                    {
+                        value(itStandardisedCounts) = ((TValue) ((TValue) value(itCounts)) - p_w * ((TValue)len1)) / variance;
+                    }
+                }
+            }
+            ++itStandardisedCounts;
+        }
+    }
+    else
+    {
+        // ----------------------------------------------------------------------
+        // Higher Order Background Model
+        // ----------------------------------------------------------------------
+
+        String<unsigned> kmerCounts;
+        MarkovModel<TUnmaskedAlphabet, TValue> backgroundModel(score.bgModelOrder);
+        countKmers(kmerCounts, backgroundModel, sequence, score.kmerSize);
+
+        int nvals = length(kmerCounts);  // Number of kmers
+        int len1 = 0;
+        for (int l = 0; l < nvals; l++)
+        {
+            len1 += kmerCounts[l];
+        }
+        resize(standardisedCounts, nvals, (TValue) 0.0);
+        String<TValue> probabilities;
+        resize(probabilities, nvals, missing);
+        TIteratorUnsigned itCounts;
+        TIteratorTString itStandardisedCounts;
+        itCounts = begin(kmerCounts);
+        itStandardisedCounts = begin(standardisedCounts);
+
+        for (; itCounts < end(kmerCounts); ++itCounts)
+        {
+            TValue p_w = 1;  // Probability of kmer
+            TValue variance = 0;
+            String<TUnmaskedAlphabet> w;
+            unhash(w, (unsigned)position(itCounts), score.kmerSize);
+            p_w = emittedProbability(backgroundModel, w);
+
+            TValue counterTMP = 0.0;
+            if ((score.mismatches == 1))  // Start of mismatch calculations
+            {
+                p_w = 0;
+                // The first word in the kmerNeighbourhood is the kmer itself, it is weighted normally
+                // Sum of all entries in the covariance matrix, computed and stored dynamically
+                unsigned wordHash = position(itCounts);
+                unsigned wordRCHash = revComIndex[wordHash];
+
+                for (unsigned row = 0; row < length(kmerNeighbourhood[wordHash]); ++row)
+                {
+                    unsigned wordRowHash = kmerNeighbourhood[wordHash][row];
+                    // The kmer itself is weighted normally
+                    if (wordRowHash == wordHash)  // The first word in the kmerNeighbourhood is the kmer itself, it is weighted normally
+                    {
+                        counterTMP += (TValue) kmerCounts[wordRowHash];
+                    }
+                    else if ((score.revCom == "both_strands") && (wordRowHash == wordRCHash))
+                    {
+                        counterTMP += ((TValue) kmerCounts[wordRowHash]);
+                    }
+                    else
+                    {
+                        counterTMP += ((TValue) kmerCounts[wordRowHash]) * score.mismatchWeight;
+                    }
+                    String<Dna> wMM1;
+                    unhash(wMM1, wordRowHash, score.kmerSize);
+                    for (unsigned col = row; col < length(kmerNeighbourhood[wordHash]); ++col)
+                    {
+                        unsigned wordColHash = kmerNeighbourhood[wordHash][col];
+                        if (value(covarianceMatrix, wordColHash, wordRowHash) == missing)
+                        {
+                            String<Dna> wMM2;
+                            unhash(wMM2, wordColHash, score.kmerSize);
+                            calculateCovariance(value(covarianceMatrix, wordColHash, wordRowHash), wMM1, wMM2, backgroundModel, (len1 + score.kmerSize - 1));
+                            value(covarianceMatrix, wordRowHash, wordColHash) = value(covarianceMatrix, wordColHash, wordRowHash);
+                        }
+                        if (row == col)  // Variance of weighted variables
+                        {
+                            if ((wordRowHash == wordHash) || (score.revCom == "both_strands" && (wordRowHash == wordRCHash)))  // The variance of the kmer is counted full
+                            {
+                                variance += value(covarianceMatrix, wordRowHash, wordColHash);
+                            }
+                            else
+                            {
+                                variance += pow(score.mismatchWeight, 2) * value(covarianceMatrix, wordRowHash, wordColHash);
+                            }
+                        }
+                        // The covariance of the kmer and the reverse complement is weighted full
+                        else if ((score.revCom == "both_strands") && (((wordRowHash == wordHash) && (wordColHash == wordRCHash)) || ((wordRowHash == wordRCHash) && (wordColHash == wordHash))))
+                        {
+                            variance += (2.0) * value(covarianceMatrix, wordRowHash, wordColHash);
+                        }
+                        else if ((wordRowHash == wordHash || wordColHash == wordHash) || (score.revCom == "both_strands" && (wordRowHash == wordRCHash || wordColHash == wordRCHash)))  // The covariance is weighted half
+                        {
+                            variance += (2.0) * score.mismatchWeight * value(covarianceMatrix, wordRowHash, wordColHash);
+                        }
+                        else  // The covariance is weighted^2
+                        {
+                            variance += (2.0) * pow(score.mismatchWeight, 2) * value(covarianceMatrix, wordRowHash, wordColHash);
+                        }
+                    }
+                    if (probabilities[wordRowHash] == missing)
+                    {
+                        probabilities[wordRowHash] = emittedProbability(backgroundModel, wMM1);
+                    }
+                    if (wordRowHash == wordHash) //Weight the probabiliets and expected values, normal weight for the kmer itself
+                    {
+                        p_w += probabilities[wordRowHash];
+                    }
+                    else if ((score.revCom == "both_strands") && (wordRowHash == wordRCHash)) // Weight the probabiliets and expected values, normal weight for the reverse complement kmer itself
+                    {
+                        p_w += probabilities[wordRowHash];
+                    }
+                    else
+                    {
+                        p_w += score.mismatchWeight * probabilities[wordRowHash];
+                    }
+                }
+                variance = pow(variance, 0.5);  // Calculate the standard deviation
+            }  // End of mismatch calculations
+            else if (score.revCom == "both_strands")
+            {
+                TValue variance1;
+                TValue variance2;
+                TValue covariance;
+                String<Dna> wRC;
+                unhash(wRC, (unsigned)revComIndex[(unsigned)position(itCounts)], score.kmerSize);
+                calculateVariance(variance1, w, backgroundModel, (len1 + score.kmerSize - 1));
+                calculateVariance(variance2, wRC, backgroundModel, (len1 + score.kmerSize - 1));
+                calculateCovariance(covariance, w, wRC, backgroundModel, (len1 + score.kmerSize - 1));
+                variance = pow((variance1 + variance2 + (2.0) * covariance), 0.5);
+                TValue p_wRC = 1;   // Probability of the reverse complement kmer
+                p_wRC = emittedProbability(backgroundModel, wRC);
+                p_w += p_wRC;
+            }
+            else
+            {
+                calculateVariance(variance, w, backgroundModel, (len1 + score.kmerSize - 1));
+                variance = pow(variance, 0.5);
+            }
+            if ((variance > pow(10.0, -10)) && (variance < pow(10.0, 10)))
+            {
+                if (p_w > 0)
+                {
+                    if (score.mismatches > 0)
+                    {
+                        value(itStandardisedCounts) = ((TValue) ((TValue) counterTMP) - p_w * ((TValue)len1)) / variance;
+                    }
+                    else if (score.revCom == "both_strands")
+                    {
+                        value(itStandardisedCounts) = ((TValue) ((TValue) value(itCounts) + kmerCounts[revComIndex[(unsigned)position(itCounts)]]) - p_w * ((TValue)len1)) / variance;
+                    }
+                    else
+                    {
+                        value(itStandardisedCounts) = ((TValue) ((TValue) value(itCounts)) - p_w * ((TValue)len1)) / ((TValue) variance);
+                    }
+                }
+                ++itStandardisedCounts;
+            }
+        }
+    }
+}
+
+}  // namespace seqan
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_N2_H_
diff --git a/seqan/alignment_free/alignment_free_base.h b/seqan/alignment_free/alignment_free_base.h
new file mode 100644
index 0000000..490a96d
--- /dev/null
+++ b/seqan/alignment_free/alignment_free_base.h
@@ -0,0 +1,340 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jonathan Goeke <goeke@molgen.mpg.de>
+// ==========================================================================
+// Definition of all AFScore and the specialisations, D2, D2star, D2z
+// and N2.
+// ==========================================================================
+
+// TODO(holtgrew): Make struct a class here.
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_BASE_H_
+
+namespace seqan {
+
+/*!
+ * @class AFScore
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Used to specify parameters and methods for alignment-free sequence comparison.
+ *
+ * @signature template <typename TSpec>
+ *            struct AFScore;
+ *
+ * @tparam TSpec Tag for specialization.
+ *
+ * @see alignmentFreeComparison
+ */
+
+template <typename TSpec>
+struct AFScore;
+
+/*!
+ * @class D2AFScore D2 AFScore
+ * @extends AFScore
+ * @headerfile <seqan/alignment_free.h>
+ *
+ * @brief D2 computes the inner product of the kmer count vectors.
+ *
+ * @signature template <>
+ *            struct AFScore<D2>;
+ *
+ * To be used for alignment free comparison.
+ *
+ * @section References
+ *
+ * Lippert RA, et al. Distributional regimes for the number of k-word matches between two random sequences. Proc. Natl
+ * Acad. Sci. USA 2002.
+ *
+ * @see alignmentFreeComparison
+ *
+ * @var unsigned D2AFScore::kmerSize;
+ * @brief Size of the kmers.
+ *
+ * @var bool D2AFScore::verbose;
+ * @brief <tt>true</tt> to enable verbose debug output.
+ *
+ * @fn D2AFScore::AFScore
+ *
+ * @brief Constructor
+ *
+ * @signature AFScore::AFScore(kmerSize, verbose);
+ *
+ * @param[in] verbose  This option will report progress to standard output (<tt>bool</tt).
+ * @param[in] kmerSize Size of kmer (<tt>unsigned</tt>).
+ *
+ * @see alignmentFreeComparison
+ */
+
+struct D2_;     // Inner product of k-mer counts, d2 score
+typedef Tag<D2_> const D2;
+
+template <>
+struct AFScore<D2>
+{
+    unsigned kmerSize;
+    bool verbose;
+    AFScore(unsigned k, bool verbose_ = false) : kmerSize(k), verbose(verbose_)
+    {}
+};
+
+/*!
+ * @class D2StarAFScore D2Star AFSScore
+ * @extends AFScore
+ * @headerfile <seqan/alignment_free.h>
+ * @brief D2Star computes the inner product of the standardised kmer count vectors.
+ *
+ * @signature template <>
+ *            struct AFScore<D2Star>;
+ *
+ * D2Star can be used for alignment-free sequence comparison, this version calculates the background model on the
+ * concatenation of both sequences
+ *
+ * @section References
+ *
+ * Reinert, G.; Chew, D.; Sun, F.,  Waterman, M. S. Alignment-Free Sequence Comparison (I): Statistics and Power. J
+ * Comput Biol, 2009.
+ *
+ * @see alignmentFreeComparison
+ *
+ * @fn D2StarAFScore::AFScore
+ * @brief Constructor
+ * @signature AFScore::AFScore(kmerSize, bgModelOrder, verbose);
+ *
+ * @param[in] kmerSize      Size of kmer, <tt>unsigned</tt>.
+ * @param[in] bgModelOrder Order of the background Markov model, <tt>unsigned</tt>.
+ * @param[in] verbose      This option will report progress to standard output, <tt>bool</tt>.
+ *
+ * @var unsigned D2StarAFScore::kmerSize
+ * @brief Size of the kmers.
+ *
+ * @var CharString D2StarAFScore::outputFile
+ * @brief When specified, all kmerWeights will be written to this file, for every sequence, and for every sequence
+ *        comparison.
+ *
+ * @var unsigned D2StarAFScore::bgModelOrder
+ * @brief Order of the background model.
+ */
+
+struct D2Star_;        // Reinert and Waterman, D2 with centralised and standardised counts
+typedef Tag<D2Star_> const D2Star;
+
+template <>
+struct AFScore<D2Star>
+{
+    unsigned kmerSize;
+    unsigned bgModelOrder;
+    bool verbose;
+
+
+    AFScore<D2Star>(unsigned k, unsigned m, bool verbose_ = false) :
+        kmerSize(k), bgModelOrder(m), verbose(verbose_)
+    {}
+};
+
+/*!
+ * @class N2AFScore N2 AFScore
+ * @extends AFScore
+ * @headerfile <seqan/alignment_free.h>
+ * @brief N2 computes the inner product of the standardised neighbourhood kmer count vectors.
+ *
+ * @signature template <>
+ *            struct AFScore<N2>;
+ *
+ * N2 can be used for alignment-free sequence comparison.
+ *
+ * @section References
+ *
+ * Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin Vingron.
+ Estimation of Pairwise Sequence Similarity of Mammalian Enhancers with Word Neighbourhood Counts. Bioinformatics
+ (2012).
+ *
+ * @fn N2AFScore::AFScore
+ *
+ * @brief Constructor
+ *
+ * @signature AFScore::AFScore(kmerSize, bgModelOrder, outputFile, verbose);
+ * @signature AFScore::AFScore(kmerSize, bgModelOrder, revCom, outputFile, verbose);
+ * @signature AFScore::AFScore(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight, outputFile, verbose);
+ *
+ * @param[in] kmerSize       Size of kmer, <tt>unsigned</tt>.
+ * @param[in] bgModelOrder   Order of the background Markov model, <tt>unsigned</tt>.
+ * @param[in] outputFile     When specified, all normalised and standardised kmer neighbourhood counts will be written
+ *                           to this file for every sequence, @link CharString @endlink.
+ * @param[in] revCom         Scoring of reverse complements words [''/'max'/'min'/'mean'/'both_strands'/],
+ *                           @link CharString @endlink.
+ * @param[in] verbose        This option will report progress to standard output, <tt>bool</tt>, defaults to
+ *                           <tt>false</tt>.
+ * @param[in] mismatches     Includes words with one mismatch into the word neighbourhood, <tt>unsigned</tt>, 0 or 1.
+ * @param[in] mismatchWeight Weight of word counts with one mismatch, double.
+ *
+ * @see alignmentFreeComparison
+ *
+ * @var unsigned N2AFScore::kmerSize;
+ * @brief Size of the kmers.
+ *
+ * @var double N2AFScore::mismatchWeight;
+ * @brief Weight for approximate word matches
+ *
+ * @var CharString N2AFScore::revCom;
+ * @brief Scoring of reverse complements words, @link CharString @endlink [''/'max'/'min'/'mean'/'both_strands'/].
+ *
+ * @var CharString N2AFScore::outputFile;
+ * @brief When specified, all kmerWeights for every sequence will be written to this file.
+ *
+ * @var unsigned N2AFScore::bgModelOrder;
+ * @brief Order of the background model
+ *
+ * @var unsigned N2AFScore::mismatches;
+ * @brief Approximate word matches [0(exact)/1(one mismatch)]
+ *
+ * @var bool N2AFScore::verbose;
+ * @brief <tt>true</tt> to enable verbose debug output.
+ */
+
+struct N2_;     // Reinert and Waterman, D2 with centralised and standardised counts
+typedef Tag<N2_> const N2;
+
+template <>
+struct AFScore<N2>
+{
+    unsigned kmerSize;
+    unsigned bgModelOrder;
+    String<char> revCom;    // Count reverse complement words?
+                            // revCom="";"mean","max","both_strands"
+    unsigned mismatches;    // Currently 0 or 1
+    double mismatchWeight;  // Weight of words in the mismatch neighbourhood
+    bool verbose;
+    bool norm;              // Normalize score? Needed to provide a proper similarity measure
+    String<char> outputFile;  // Output of all kmer weights for every sequence into this file
+
+    // Constructor for the simple case with only exact word counts (N2*)
+    AFScore(unsigned k, unsigned m, String<char> kmerWeightsFile = "", bool verbose_ = false)
+    {
+        kmerSize = k;
+        bgModelOrder = m;
+        outputFile = kmerWeightsFile;
+        verbose = verbose_;
+        revCom = "";
+        mismatches = 0;
+        mismatchWeight = 1.0;
+        norm = true;
+
+    };
+
+    // Constructor for the case with exact word counts and reverse complement (N2rc)
+    AFScore(unsigned k, unsigned m, String<char> revCom_, String<char> kmerWeightsFile = "", bool verbose_ = false)
+    {
+        kmerSize = k;
+        bgModelOrder = m;
+        revCom = revCom_;
+        outputFile = kmerWeightsFile;
+        verbose = verbose_;
+        mismatches = 0;
+        mismatchWeight = 1.0;
+        norm = true;
+    };
+
+    // Constructor for the case with mismatch-neighbourhood word counts and reverse complement (N2mmrc)
+    AFScore(unsigned k,
+            unsigned m,
+            String<char> revCom_,
+            unsigned mm, double mmw,
+            String<char> kmerWeightsFile = "",
+            bool verbose_ = false)
+    {
+        kmerSize = k;
+        bgModelOrder = m;
+        revCom = revCom_;
+        mismatches = mm;
+        mismatchWeight = mmw;
+        outputFile = kmerWeightsFile;
+        verbose = verbose_;
+        norm = true;
+    };
+};
+
+/*!
+ * @class D2zAFScore D2zAFScore
+ * @extends AFScore
+ * @headerfile <seqan/alignment_free.h>
+ * @brief D2z computes a z-score of the inner product of kmer count vectors
+ *
+ * @signature template <>
+ *            struct AFScore<D2z>;
+ *
+ * D2z can be used for alignment-free sequence comparison. The algorithm differs from the original implementation by
+ * the way masked sequences are handled
+ *
+ * @section References
+ *
+ * Kantorovitz, M. R.; Robinson, G. E., Sinha, S. A statistical method for alignment-free comparison of regulatory
+ * sequences. Bioinformatics, 2007.
+ *
+ * @fn D2zAFScore::AFScore
+ *
+ * @brief Constructor
+ *
+ * @signature AFScore::AFScore(kmerSize, bgModelOrder[, verbose]);
+ *
+ * @param[in] kmerSize     Size of kmer, <tt>unsigned</tt>.
+ * @param[in] bgModelOrder Order of the background Markov model, <tt>unsigned</tt>.
+ * @param[in] verbose      This option will report progress to standard output; <tt>bool</tt>, defaults to
+ *                         <tt>false</tt>.
+ *
+ * @var unsigned D2zAFScore::bgModelOrder;
+ * @brief Order of the background model
+ *
+ * @var unsigned D2zAFScore::kmerSize;
+ * @brief Size of the kmers
+ *
+ * @var bool D2zAFScore::verbose;
+ * @brief <tt>true</tt> to enable verbose debug output.
+] */
+
+struct D2z_;  // Inner product of k-mer counts, d2 score with z-score
+typedef Tag<D2z_> const D2z;
+
+template <>
+struct AFScore<D2z>
+{
+    unsigned kmerSize;
+    unsigned bgModelOrder;
+    bool verbose;
+    AFScore<D2z>(unsigned k, unsigned m, bool verbose_ = false) :
+        kmerSize(k), bgModelOrder(m), verbose(verbose_)
+    {}
+};
+
+}  // namespace seqan
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_BASE_H_
diff --git a/seqan/alignment_free/alignment_free_comparison.h b/seqan/alignment_free/alignment_free_comparison.h
new file mode 100644
index 0000000..0809f09
--- /dev/null
+++ b/seqan/alignment_free/alignment_free_comparison.h
@@ -0,0 +1,106 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jonathan Goeke <goeke@molgen.mpg.de>
+// ==========================================================================
+// This file contains the function that calls alignment free sequence
+// comparisons algorithms (see AFScore):
+// alignmentFreeComparison()
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_COMPARISON_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_COMPARISON_H_
+
+namespace seqan {
+
+/*!
+ * @fn alignmentFreeComparison
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Computes the pairwise similarity scores for a set of sequences.
+ *
+ * @signature void alignmentFreeComparison(scoreMatrix, sequenceSet, score);
+ *
+ * @param[out] scoreMatrix A two-dimensional @link Matrix @endlink, used to store all pairwise scores.
+ * @param[in]  sequenceSet @link StringSet @endlink containing all sequences for which pairwise scores will be
+ *                         computed.
+ * @param[in]  score       The @link AFScore @endlink object to be used for computing the alignment.
+ *
+ * @section Examples
+ *
+ * Calculate the alignment free sequence similarity of two masked DNA sequences.
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * StringSet<Dna5String> sequences;
+ * Dna5String seq1 =
+ *     "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG"
+ *     "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG"
+ *     "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC"
+ *     "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT"
+ *     "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA"
+ *     "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT"
+ *     "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG";
+ * Dna5String seq2 =
+ *     "ACCGACGATTAGCTTTGTCCGAGTTACAACGGTTCAATAATACAAAGGATGGCATAAACCCATTTGTGTGAA"
+ *     "AGTGCCCATCACATTATGATTCTGTCTACTATGGTTAATTCCCAATATACTCTCGAAAAGAGGGTATGCTCC"
+ *     "CACGGCCATTTACGTCACTAAAAGATAAGATTGCTCAAANNNNNNNNNACTGCCAACTTGCTGGTAGCTTCA"
+ *     "GGGGTTGTCCACAGCGGGGGGTCGTATGCCTTTGTGGTATACCTTACTAGCCGCGCCATGGTGCCTAAGAAT"
+ *     "GAAGTAAAACAATTGATGTGAGACTCGACAGCCAGGCTTCGCGCTAAGGACGCAAAGAAATTCCCTACATCA"
+ *     "GACGGCCGCGNNNAACGATGCTATCGGTTAGGACATTGTGCCCTAGTATGTACATGCCTAATACAATTGGAT"
+ *     "CAAACGTTATTCCCACACACGGGTAGAAGAACNNNNATTACCCGTAGGCACTCCCCGATTCAAGTAGCCGCG";
+ *
+ * clear(sequences);
+ * appendValue(sequences, seq1);
+ * appendValue(sequences, seq2);
+ *
+ * Matrix<double, 2> myMatrix;
+ *
+ * unsigned kmerSize = 5;
+ * unsigned bgModelOrder = 1;
+ * String<char>  revCom = "both_strands";
+ * unsigned mismatches = 1;
+ * double mismatchWeight = 0.5;
+ * AFScore<N2> myScoreN2(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight);
+ *
+ * alignmentFreeComparison(myMatrix, sequences, myScoreN2);
+ * std::cout << myMatrix;
+ * @endcode
+ */
+
+template <typename TStringSet, typename TValue, typename TComparisonMethod>
+void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComparisonMethod const & comparisonMethod)
+{
+    _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod);
+}
+
+}  // namespace seqan
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_COMPARISON_H_
diff --git a/seqan/alignment_free/kmer_functions.h b/seqan/alignment_free/kmer_functions.h
new file mode 100644
index 0000000..c67935e
--- /dev/null
+++ b/seqan/alignment_free/kmer_functions.h
@@ -0,0 +1,965 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jonathan Goeke <goeke@molgen.mpg.de>
+// ==========================================================================
+// This file contains helper functions to count words in sequences and to
+// calculate probabilities and variances of word occurrences.
+// ==========================================================================
+
+// TODO (goeke) const could be added below for the input variables but the function value() in matrix_base (align) is not defined for const.  Similarly, the function emittedProbabilty is not defined for const in statistics_markov_model.h
+
+#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_KMER_FUNCTIONS_H_
+#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_KMER_FUNCTIONS_H_
+
+namespace seqan {
+
+template <typename TAlphabet>
+struct UnmaskedAlphabet_
+{
+    typedef TAlphabet Type;
+};
+
+template <>
+struct UnmaskedAlphabet_<Dna5>
+{
+    typedef Dna Type;
+};
+
+template <typename TAlphabet>
+struct UnmaskedAlphabet_<const TAlphabet>
+{
+    typedef const typename UnmaskedAlphabet_<TAlphabet>::Type Type;
+};
+
+/*!
+ * @fn countKmers
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Counts kmers in a sequence. Optionally, a background model is returned.
+ *
+ * @signature void countKmers(kmerCounts, sequence, k);
+ * @signature void countKmers(kmerCounts, bgFrequencies, sequence, k);
+ * @signature void countKmers(kmerCounts, bgModel, sequence, k);
+ *
+ * @param[out] kmerCounts    @link String @endlink of <tt>unsigned</tt> with kmer counts for every k-mer.
+ * @param[out] bgFrequencies @link String @endlink of background frequencies (<tt>double</tt>) representing the model.
+ * @param[out] bgModel       @link MarkovModel @endlink to use.
+ * @param[in]  sequence      @link String @endlink (sequence) where k-mers are counted.
+ * @param[in]  k             k-mer length (<tt>unsigned</tt>).
+ *
+ * k-mers overlapping masked (aka 'N') letters are not counted in case of Dna5Strings.  A Bernoulli or Markov Model
+ * can be choosen as a background model.
+ *
+ * @section Examples
+ *
+ * Calculate the alignment free sequence similarity o two masked DNA sequences.
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * // Masked sequence, we do not want to count words overlapping 'N'
+ * Dna5String sequenceDna5 =
+ *     "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG"
+ *     "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG"
+ *     "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC"
+ *     "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT"
+ *     "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA"
+ *     "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT"
+ *     "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG";
+ *
+ * String<unsigned> kmerCounts;
+ * unsigned k = 2;  // Count all 2-mers
+ * countKmers(kmerCounts, sequenceDna5, k);
+ *
+ * for(unsigned i = 0; i<16; ++i)       // Print the 2-mer counts
+ *     std::cout<<kmerCounts[i]<<"\n";  // 34 times AA; 30 times AC; 28 times AG; ...
+ *
+ *
+ * String<double> nucleotideFrequencies;  // Defines a Bernoulli model for DNA sequences.
+ * // Count all 2-mers and save the nucleotide frequencies
+ * countKmers(kmerCounts, nucleotideFrequencies, sequenceDna5, k);
+ *
+ * for(unsigned i = 0; i<4; ++i)          // Print the nucleotide frequencies
+ *     std::cout << nucleotideFrequencies[i] << "\n";
+ * // => p(A) = 0.238; p(C) = 0.254; p(G) = 0.238; p(T) = 0.27;
+ *
+ * MarkovModel<Dna, double>  backgroundModel(1);  // Markov model of order 1
+ * // Count all 2-mers and return a Markov model
+ * countKmers(kmerCounts, backgroundModel, sequenceDna5, k);
+ * std::cout<<backgroundModel.transition;  // Print the transition matrix of the markov model
+ * @endcode
+ *
+ * @see alignmentFreeComparison
+ * @see calculateProbability
+ * @see calculateVariance
+ * @see calculateCovariance
+ * @see stringToStringSet
+ * @see MarkovModel
+ */
+
+/*
+ * Function to count kmers, Ns are not considered
+ */
+template <typename TString>
+void countKmers(String<unsigned> & kmerCounts, TString const & sequence, unsigned const k)
+{
+    typedef typename Value<TString>::Type               TAlphabet;
+    typedef typename UnmaskedAlphabet_<TAlphabet>::Type TUnmaskedAlphabet;
+    typedef typename Iterator<TString const>::Type      TIterator;
+    typedef typename Position<TIterator>::Type          TPosition;
+    typedef Shape<TUnmaskedAlphabet, SimpleShape>       TShape;
+    // Declare variables
+    TShape myShape;  // Shape, length can be changed (kmer_length)
+    resize(myShape, k);
+    // Calculate the number of kmers, length of count vector
+    int kmerNumber = _intPow((unsigned)ValueSize<TUnmaskedAlphabet>::VALUE, weight(myShape));
+    clear(kmerCounts);
+    resize(kmerCounts, kmerNumber, 0);
+    TIterator itSequence = begin(sequence);
+    int counterN = 0;
+
+    // Check for any N that destroys the first kmers
+    unsigned j = k - 1;
+    for (TPosition i = position(itSequence); i <= j; ++i)
+    {
+        if (_repeatMaskValue(sequence[i]))
+        {
+            counterN = i + 1;
+        }
+    }
+    for (; itSequence <= (end(sequence) - k); ++itSequence)
+    {
+        // Check if there is a "N" at the end of the new kmer
+        if (_repeatMaskValue(value(itSequence + (k - 1))))
+            counterN = k;  // Do not consider any kmer covering this "N"
+
+        // If there is no "N" overlapping with the current kmer, count it
+        if (counterN <= 0)
+        {
+            unsigned hashValue = hash(myShape, itSequence);
+            ++kmerCounts[hashValue];
+        }
+        counterN--;
+    }
+}
+
+/*
+ * Function to count kmers and background nucleotide frequencies, Ns are not considered
+ * (for zero order background model)
+ */
+template <typename TValueBG, typename TString>
+void countKmers(String<unsigned> & kmerCounts, String<TValueBG> & backgroundFrequencies, TString const & sequence, unsigned const k)
+{
+    typedef typename Value<TString>::Type                    TAlphabet;
+    typedef typename UnmaskedAlphabet_<TAlphabet>::Type      TUnmaskedAlphabet;
+    typedef typename Iterator<TString const>::Type           TIterator;
+    typedef typename Iterator<String<TValueBG> >::Type       TIteratorTStringBG;
+    typedef typename Position<TIterator>::Type               TPosition;
+    typedef Shape<TUnmaskedAlphabet, SimpleShape>            TShape;
+    unsigned alphabetSize = ValueSize<TUnmaskedAlphabet>::VALUE;
+
+    // Declare variables
+    TShape myShape;         // Shape, length can be changed (kmer_length)
+    TShape myShapeBG;       // Shape for background, set to markovlen+1, here zero order only
+    resize(myShape, k);
+    resize(myShapeBG, 1);   // Markov model of zero order (count background frequencies)
+
+    // Calculate number of kmers/ length of count vector, respectively background vector
+    unsigned kmerNumber = _intPow(alphabetSize, k);
+    unsigned kmerNumberBG = alphabetSize;  // Zero order model for DNA sequences (Bernoulli model)
+    clear(kmerCounts);
+    resize(kmerCounts, kmerNumber, 0);
+    resize(backgroundFrequencies, kmerNumberBG, (TValueBG) 0);
+    TIterator itSequence = begin(sequence);
+
+    int counterN = 0;  // Counter that counts how many kmers are effected by a N
+    int counterNbg = 0;   // Counter for background model (different shape size)
+
+    // Check for any N that destroys the first kmers
+    unsigned j = k - 1;
+    for (TPosition i = position(itSequence); i <= j; ++i)
+    {
+        if (_repeatMaskValue(sequence[i]))
+            counterN = i + 1;
+    }
+
+    int sumBG = 0;  // Count the number of nucleotides for the nucleotide frequency calculation (Ns are not considered anymore).
+    for (; itSequence <= (end(sequence) - k); ++itSequence)
+    {
+        // Check if there is a "N" at the end of the new kmer
+        if (_repeatMaskValue(value(itSequence + (k - 1))))
+        {
+            counterN = k;  // Do not consider any kmer covering this "N"
+        }
+        // If there is no "N" overlapping with the current kmer, count it.
+        if (counterN <= 0)
+        {
+            unsigned hashValue = hash(myShape, itSequence);
+            ++kmerCounts[hashValue];
+        }
+        // Check if there is a "N" at the end of the new background word, here single letters only.
+        if (_repeatMaskValue(value(itSequence)))
+        {
+            counterNbg = 1;
+        }
+        if (counterNbg <= 0)
+        {
+            unsigned hashValueBG = hash(myShapeBG, itSequence);
+            backgroundFrequencies[hashValueBG] += 1.0;
+            ++sumBG;
+        }
+        counterN--;
+        counterNbg--;
+    }
+    // The background counts are updated until the last base is covered.
+    for (; itSequence < end(sequence); ++itSequence)
+    {
+        if (_repeatMaskValue(value(itSequence)))
+        {
+            counterNbg = 1;
+        }
+        if (counterNbg <= 0)
+        {
+            unsigned hashValueBG = hash(myShapeBG, itSequence);
+            ++backgroundFrequencies[hashValueBG];
+            ++sumBG;
+        }
+        counterNbg--;
+    }
+    // Normalise the background counts to obtain the nucleotide frequencies (Bernoulli model of DNA sequences).
+    TIteratorTStringBG itBackground = begin(backgroundFrequencies);
+    for (; itBackground < end(backgroundFrequencies); ++itBackground)
+        if (sumBG != 0)
+            value(itBackground) /= ((TValueBG) sumBG);
+}
+
+/*
+ * Function to count kmers and build a background markov model with masked sequences
+ */
+template <typename TString, typename TAlphabetBG, typename TValue>
+void countKmers(String<unsigned> & kmerCounts, MarkovModel<TAlphabetBG, TValue> & backgroundModel, TString const & sequence, unsigned k)
+{
+    //typedef typename Value<TString>::Type                   TAlphabet;
+    //typedef typename UnmaskedAlphabet_<TAlphabet>::Type     TUnmaskedAlphabet;
+    typedef typename Iterator<TString const, Rooted>::Type  TIterator;
+    //typedef typename Iterator<String<int>, Rooted>::Type    TIteratorInt;
+    typedef typename Position<TIterator>::Type              TPosition;
+    typedef Shape<TAlphabetBG, SimpleShape>                 TShape;
+
+    // Declare variables
+    TShape myShape;  // Shape, length can be changed (kmer_length)
+    resize(myShape, k);
+    // Only consider kmers without N
+    int kmerNumber = _intPow((unsigned)ValueSize<TAlphabetBG>::VALUE, weight(myShape));
+    clear(kmerCounts);
+    resize(kmerCounts, kmerNumber, 0);
+
+    // Create sequence set for the markov model, if Ns occur, the sequence is split and Ns are removed
+    StringSet<String<TAlphabetBG> > seqSetMM;
+
+    TIterator itSeq = begin(sequence);
+
+    // Check for any N that destroys the first kmers
+    unsigned j = (k - 1);
+    for (TPosition i = position(itSeq); i <= j; ++i)
+    {
+        if (_repeatMaskValue(sequence[i]))
+        {
+            if ((i - position(itSeq)) > 0)
+            {
+                appendValue(seqSetMM, infix(sequence, position(itSeq), i));
+            }
+            goFurther(itSeq, i + 1 - position(itSeq));
+            j = i + k - 1;
+        }
+    }
+
+    int counterN = 0;
+    TPosition startSplitSequence = position(itSeq);  // The position of possible start of a sequence after NNs is stored to split sequences.
+
+    for (; itSeq <= (end(sequence) - k); ++itSeq)
+    {
+        if (_repeatMaskValue(value(itSeq + (k - 1))))
+        {
+            counterN = k;
+
+            if (((position(itSeq) + k - 1) > startSplitSequence))
+                appendValue(seqSetMM, infix(sequence, startSplitSequence, (position(itSeq) + k - 1)));
+
+            startSplitSequence = (position(itSeq) + k);  // Position after N, possible start
+        }
+        if (counterN <= 0)
+        {
+            unsigned hashValue = hash(myShape, itSeq);
+            ++kmerCounts[hashValue];
+        }
+
+        counterN--;
+    }
+    // Create a stringSet, needed to create the Markov model
+    if ((position(itSeq) + k - 1) > startSplitSequence)
+    {
+        appendValue(seqSetMM, infix(sequence, startSplitSequence, (position(itSeq) + k - 1)));
+    }
+    // Build background Markov model
+    buildMarkovModel(backgroundModel, seqSetMM);
+}
+
+/*!
+ * @fn calculateProbability
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Calculates the probability of a sequence given a Bernoulli model.
+ *
+ * @signature void calculateProbability(probability, sequence, bgFrequencies);
+ *
+ * @param[out] probability  Probability (<tt>double</tt>) of the sequence given the model.
+ * @param[in] sequence      @link String @endlink, usually of Dna characters.
+ * @param[in] bgFrequencies @link String @endlink of background frequencies (<tt>double</tt>) representing the model.
+ *
+ * @section Examples
+ *
+ * Calculate the probability for the word CCCAAGTTT with <i>p(A) = p(T) = 0.3</i> and <i>p(C) = p(G) = 0.2</i>.
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * double p = 0.0;
+ * DnaString word = "CCCAAGTTT";
+ * String<double> model;
+ * resize(model, 4);
+ * model[0] = 0.3;  // p(A)
+ * model[1] = 0.2;  // p(C)
+ * model[2] = 0.2;  // p(G)
+ * model[3] = 0.3;  // p(T)
+ * calculateProbability(p, word, model);  // p = 3.888e-06
+ * @endcode
+ *
+ * @see calculateVariance
+ * @see alignmentFreeComparison
+ * @see calculateCovariance
+ * @see countKmers
+ */
+
+template <typename TValue, typename TString, typename TStringBG>
+void calculateProbability(TValue & probability, TString const & sequence, TStringBG const & backgroundFrequencies)
+{
+    typedef typename Iterator<TString const, Rooted>::Type  TIteratorTString;
+
+    TIteratorTString itSequence = begin(sequence);
+    probability = (TValue) 1;
+    for (; itSequence < end(sequence); ++itSequence)
+        probability *= backgroundFrequencies[ordValue(*itSequence)];
+}
+
+/*!
+ * @fn calculateVariance
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Calculates the variance for the number of word occurrences of a word in a sequence of length n given a
+ *        background model.
+ *
+ * @signature void calculateVariance(variance, word, bgFrequencies, n);
+ * @signature void calculateVariance(variance, word, bgModel, n);
+ *
+ * @param[out] variance     Variance of the number of occurrences of the word in a sequence of length n given the
+ *                          model; <tt>double</tt>.
+ * @param[in] word          @link String @endlink, usually of Dna to compute variance for.
+ * @param[in] bgFrequencies @link String @endlink of bg frequencies representing the model.
+ * @param[in] bgModel       @link MarkovModel @endlink to use.
+ * @param[in] n             Length of the sequence where the occurrences of word are counted, <tt>int</tt>.
+ *
+ * Calculates the variance for the number of word occurrences of a word in a sequence of length n given a background
+ * model (Markov model or Bernoulli model). The formula is obtained from (Robin et al., 2005).
+ *
+ * @section References
+ *
+ * Robin, S., Rodolphe, F., and Schbath, S.  (2005). DNA, Words and Models. Cambridge University Press. See Jonathan
+ * Goeke et al (to appear) for details on the implementation.
+ *
+ * @section Examples
+ *
+ * Calculate the variance for the number of occurrences of CAAGTC in a sequence of length 10000bp with
+ * <i>p(A) = p(T) = 0.3</i> and <i>p(C) = p(G) = 0.2</i>.
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * double var = 0.0;
+ * int n = 10000;
+ * DnaString word = "CAAGTC";
+ * String<double> model;
+ * resize(model, 4);
+ * model[0] = 0.3;  // p(A)
+ * model[1] = 0.2;  // p(C)
+ * model[2] = 0.2;  // p(G)
+ * model[3] = 0.3;  // p(T)
+ * calculateVariance(var, word, model, n);  // var = 2.16
+ * @endcode
+ *
+ * Estimate a Markov model on a set of sequences and calculate the variance for the number of occurrences of the word
+ * CAAGTC in a sequence of length 10000bp.
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * double var = 0.0;
+ * int n = 10000;
+ * DnaString word = "CAAGTC";
+ * StringSet<DnaString> sequences;
+ * appendValue(sequences, "CAGAAAAAAACACTGATTAACAGGAATAAGCAGTTTACTTATTTTGGGCCTGGGACCCGTGTCTCTAATTTAATTAGGTGATCCCTGCGAAGTTTCTCCA");
+ * MarkovModel<Dna, double> model(0);  // Bernoulli model
+ * model.build(sequences);
+ * calculateVariance(var, word, model, n);  // var = 2.16
+ * MarkovModel<Dna, double> model1(1);  // First order Markov model
+ * model1.build(sequences);
+ * calculateVariance(var, word, model1, n);  // var = 1.69716
+ * @endcode
+ *
+ * @see calculateProbability
+ * @see calculateCovariance
+ * @see MarkovModel
+ * @see alignmentFreeComparison
+ * @see calculatePeriodicity
+ * @see countKmers
+ * @see calculateOverlapIndicator
+ */
+
+template <typename TValue, typename TString, typename TStringBG>
+void calculateVariance(TValue & variance, TString const & word, TStringBG const & backgroundFrequencies, int const n)
+{
+    typedef typename Value<TString>::Type                       TAlphabet;
+    typedef typename Value<TStringBG>::Type                     TValueBG;
+    typedef typename Iterator<String<int>, Rooted>::Type        TIteratorInt;
+
+    int l = length(word);
+    TValueBG p_w;
+    calculateProbability(p_w, word, backgroundFrequencies);
+
+    String<int> periodicity;
+    calculatePeriodicity(periodicity, word, word);
+    variance = (TValue) (n - l + 1) * p_w;
+    for (TIteratorInt i = begin(periodicity); i < end(periodicity); ++i)
+    {
+        TValueBG p_clump;
+        TValueBG p_tmp;
+        calculateProbability(p_tmp, word, backgroundFrequencies);
+        String<TAlphabet> wordPrefix = prefix(word, value(i));
+        calculateProbability(p_clump, wordPrefix, backgroundFrequencies);
+        p_clump *= p_tmp;
+        variance += (TValue) 2 * (n - l + 1 - value(i)) * p_clump;
+    }
+    variance += (TValue) p_w * p_w * (n - 2 * n * l + 3 * l * l - 4 * l + 1);
+}
+
+
+template <typename TValue, typename TSpec, typename TAlphabet>
+void calculateVariance(TValue & variance, String<TAlphabet, TSpec> const & word, MarkovModel<TAlphabet, TValue> /*const*/ & bgModel, int const n)
+{
+    typedef typename Iterator<String<int>, Rooted>::Type        TIteratorInt;
+
+    int l = length(word);
+    TValue p_w;
+    p_w = emittedProbability(bgModel, word);
+    String<int> periodicity;
+    calculatePeriodicity(periodicity, word, word);
+    variance = (TValue) (n - l + 1) * p_w;
+    for (TIteratorInt i = begin(periodicity); i < end(periodicity); ++i)
+    {
+        TValue p_clump;
+        String<TAlphabet> clump = prefix(word, value(i));
+        append(clump, word);
+        p_clump = emittedProbability(bgModel, clump);
+        variance += (TValue) 2 * (n - l + 1 - value(i)) * p_clump;
+    }
+    variance += (TValue) p_w * p_w * (n - 2 * n * l + 3 * l * l - 4 * l + 1);
+}
+
+/*!
+ * @fn calculateCovariance
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Calculates the covariance for the number of word occurrences for two words in a sequence of length n, given a
+ *        background model.
+ *
+ * @signature void calculateCovariance(covariance, word1, word2, bgFrequencies, n);
+ * @signature void calculateCovariance(covariance, word1, word2, bgModel, n);
+ *
+ * @param[out] covariance    Variance of the number of occurrences of the word in a sequence of length n given the
+ *                           model, <tt>double</tt>.
+ * @param[in] word1          @link String @endlink, usually of Dna.
+ * @param[in] word2          @link String @endlink, usually of Dna.
+ * @param[in] bgFrequencies  @link String @endlink of <tt>double</tt> with the background frequencies representing
+ * @param[in] bgModel        @link MarkovModel @endlink to use.
+ * @param[in] n              Length of the sequence where the occurrences of word are counted, <tt>int</tt>.
+ *
+ * Calculates the covariance for the number of word occurrences for two words in a sequence of length n given a
+ * background model (Markov model or Bernoulli model). The covariance is influenced by the property of words to overlap,
+ * for example, the words ATAT and TATA have a high covariance since they are likely to overlap. The formula is based on
+ * (Robin et al., 2005).
+ *
+ * @section References
+ *
+ * Robin, S., Rodolphe, F., and Schbath, S.  (2005). DNA, Words and Models. Cambridge University Press. See Jonathan
+ * Goeke et al (to appear) for details on the implementation.
+ *
+ * @section Examples
+ *
+ * Calculate the covariance for the number of occurrences of ATATAT and TATATA in a sequence of length 10000bp with
+ * <i>p(A) = p(T) = 0.3</i> and <i>p(C) = p(G) = 0.2</i>.
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * double covar = 0.0;
+ * int n = 10000;
+ * DnaString word1 = "ATATAT";
+ * DnaString word2 = "TATATA";
+ * String<double> model;
+ * resize(model, 4);
+ * model[0] = 0.3;  // p(A)
+ * model[1] = 0.2;  // p(C)
+ * model[2] = 0.2;  // p(G)
+ * model[3] = 0.3;  // p(T)
+ * calculateCovariance(covar, word1, word2, model, n);  // covar = 4.74
+ * @endcode
+ *
+ * Estimate a Markov model on a set of sequences and calculate the covariance for the number of occurrences of ATATAT
+ * and TATATA in a sequence of length 10000bp.
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * double covar = 0.0;
+ * int n = 10000;
+ * DnaString word1 = "ATATAT";
+ * DnaString word2 = "TATATA";
+ * StringSet<DnaString> sequences;
+ * appendValue(sequences, "CAGCACTGATTAACAGGAATAAGCAGTTTACTTCTGTCAGAATATTGGGCATATATA"
+ *                        "CTGGGACCCGTGTAATACTCTAATTTAATTAGGTGATCCCTGCGAAGTCTCCA");
+ * MarkovModel<Dna, double> modelMM0(0);  // Bernoulli model
+ * modelMM0.build(sequences);
+ * calculateCovariance(covar, word1, word2, modelMM0, n);  // covar = 4.74
+ * MarkovModel<Dna, double> modelMM1(1);  // First order Markov model
+ * modelMM1.build(sequences);
+ * calculateCovariance(covar, word1, word2, modelMM1, n);  // covar = 13.1541
+ * @endcode
+ *
+ * @see calculateProbability
+ * @see calculateVariance
+ * @see MarkovModel
+ * @see alignmentFreeComparison
+ * @see calculatePeriodicity
+ * @see countKmers
+ * @see calculateOverlapIndicator
+ */
+
+template <typename TValue, typename TString, typename TStringBG>
+void calculateCovariance(TValue & covariance, TString const & word1, TString const & word2, TStringBG const & backgroundFrequencies, int const n)
+{
+    if (word1 == word2)
+    {
+        calculateVariance(covariance, word1, backgroundFrequencies, n);
+        return;
+    }
+    typedef typename Value<TString>::Type                   TAlphabet;
+    typedef typename Value<TStringBG>::Type                 TValueBG;
+    typedef typename Iterator<String<int>, Rooted>::Type    TIteratorInt;
+
+    covariance = 0;
+    int l1 = length(word1);
+    TValueBG p_w1;
+    calculateProbability(p_w1, word1, backgroundFrequencies);
+    String<int> periodicity1;
+    calculatePeriodicity(periodicity1, word1, word2);
+    for (TIteratorInt i = begin(periodicity1); i < end(periodicity1); ++i)
+    {
+        TValueBG p_clump;
+        TValueBG p_tmp;
+        calculateProbability(p_tmp, word2, backgroundFrequencies);
+        String<TAlphabet> wordPrefix = prefix(word1, value(i));
+        calculateProbability(p_clump, wordPrefix, backgroundFrequencies);
+        p_clump *= p_tmp;
+        covariance += (TValue) (n - l1 + 1 - value(i)) * p_clump;
+    }
+
+    int l2 = length(word2);
+    TValueBG p_w2;
+    calculateProbability(p_w2, word2, backgroundFrequencies);
+    String<int> periodicity2;
+    calculatePeriodicity(periodicity2, word2, word1);
+    for (TIteratorInt i = begin(periodicity2); i < end(periodicity2); ++i)
+    {
+        TValueBG p_clump;
+        TValueBG p_tmp;
+        calculateProbability(p_tmp, word1, backgroundFrequencies);
+        String<TAlphabet> wordPrefix = prefix(word2, value(i));
+        calculateProbability(p_clump, wordPrefix, backgroundFrequencies);
+        p_clump *= p_tmp;
+        covariance += (TValue) (n - l2 + 1 - value(i)) * p_clump;
+    }
+    covariance += (TValue) p_w1 * p_w2 * (n - 2 * n * l1 + 3 * l1 * l1 - 4 * l1 + 1);
+}
+
+template <typename TValue, typename TSpec, typename TAlphabet>
+void calculateCovariance(TValue & covariance, String<TAlphabet, TSpec> const & word1, String<TAlphabet, TSpec> const & word2, MarkovModel<TAlphabet, TValue> /*const*/ & bgModel, int const n)
+{
+    if (word1 == word2)
+    {
+        calculateVariance(covariance, word1, bgModel, n);
+        return;
+    }
+    typedef typename Iterator<String<int>, Rooted>::Type TIteratorInt;
+
+    covariance = 0;
+    int l1 = length(word1);
+    TValue p_w1;
+    p_w1 = emittedProbability(bgModel, word1);
+    String<int> periodicity1;
+    calculatePeriodicity(periodicity1, word1, word2);  // word2 is right
+    for (TIteratorInt i = begin(periodicity1); i < end(periodicity1); ++i)
+    {
+        TValue p_clump;
+        String<TAlphabet> clump = prefix(word1, value(i));
+        append(clump, word2);
+
+        p_clump = emittedProbability(bgModel, clump);
+
+        covariance += (TValue) (n - l1 + 1 - value(i)) * p_clump;
+    }
+    TValue p_w2;
+    p_w2 = emittedProbability(bgModel, word2);
+    String<int> periodicity2;
+    calculatePeriodicity(periodicity2, word2, word1);
+    for (TIteratorInt i = begin(periodicity2); i < end(periodicity2); ++i)
+    {
+        TValue p_clump;
+        String<TAlphabet> clump = prefix(word2, value(i));
+        append(clump, word1);
+
+        p_clump = emittedProbability(bgModel, clump);
+
+        covariance += (TValue) (n - l1 + 1 - value(i)) * p_clump;
+    }
+    covariance += (TValue) p_w1 * p_w2 * (n - 2 * n * l1 + 3 * l1 * l1 - 4 * l1 + 1);
+}
+
+/*!
+ * @fn calculatePeriodicity
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Calculate word periodicity (indicator for overlaps)
+ *
+ * @signature void calculatePeriodicity(periodicity, word1, word2);
+ *
+ * @param[out] periodicity String of <tt>int</tt> values giving the periodicity (overlap indicator) of
+ *                         <tt>word1</tt> and <tt>word2</tt>.
+ * @param[int] word1       String, usually of Dna characters.
+ * @param[int] word2       String, usually of Dna characters.
+ *
+ * Calculate word periodicity (indicator for overlaps) for two words.
+ *
+ * @section Examples
+ *
+ * Calculate the periodicity of two words (At which positions can they overlap?)
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * DnaString word1 = "ATATA";
+ * DnaString word2 = "TATAT";
+ * String<int> periodicity;
+ * calculatePeriodicity(periodicity, word1, word2);
+ * for(unsigned i = 0; i < length(periodicity); ++i)  // Print the periodicity
+ *     std::cout << periodicity[i] << "\t";
+ *
+ * // periodocity[0] = 1:
+ * // i =     01234
+ * // word1 = ATATA
+ * // word2 = -TATAT
+ *
+ * // periodocity[1] = 3:
+ * // i =     01234
+ * // word1 = ATATA
+ * // word2 = ---TATAT
+ * @endcode
+ *
+ * @see calculateVariance
+ * @see calculateCovariance
+ * @see calculateOverlapIndicator
+ * @see alignmentFreeComparison
+ */
+
+template <typename TString>
+void calculatePeriodicity(String<int> & periodicity, TString const & word1, TString const & word2)
+{
+    typedef typename Value<TString>::Type                   TAlphabet;
+    //typedef typename Iterator<TString const, Rooted>::Type  TIterator;
+    typedef typename Size<TString>::Type                    TSize;
+
+    TSize length1 = length(word1);
+    TSize length2 = length(word2);
+    for (TSize i = 1; i < length1; ++i)
+    {
+        String<TAlphabet> my_suffix = suffix(word1, i);  // Overlap of suffix of word1 with prefix of word2
+        TSize my_min = std::min(length2, (length1 - i));
+        String<TAlphabet> my_prefix = prefix(word2, my_min);
+        if (my_suffix == my_prefix)
+        {
+            appendValue(periodicity, i);
+        }
+    }
+}
+
+/*!
+ * @fn calculateOverlapIndicator
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Calculate word overlaps: <tt>epsilon(word1, word2) = 1</tt> where <tt>word2[j] = word1[j+p] for
+ *        all j = 1..(k-p)</tt>.
+ *
+ * @signature void calculateOverlapIndicator(epsilon, word1, word2);
+ *
+ * @param[out] epsilon String of int giving the periodicity (overlap indicator) of word1 and word2.
+ * @param[in]  word1   String (for example a DNA sequence).
+ * @param[in]  word2   String (for example a DNA sequence).
+ *
+ * Calculate the indicator for overlaps of two words. The formula is based on (Robin et al., 2005)
+ *
+ * @section References
+ *
+ * Robin, S., Rodolphe, F., and Schbath, S. (2005). DNA, Words and Models.  Cambridge University Press. See Jonathan
+ * Goeke et al (to appear) for details on the implementation.
+ *
+ * @section Examples
+ *
+ * Calculate the overlap indicator (epsilon) for two words
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * DnaString word1 = "ATATA";
+ * DnaString word2 = "TATAT";
+ * String<int> epsilon;
+ * calculateOverlapIndicator(epsilon, word1, word2);
+ * for(unsigned i = 0; i < length(epsilon); ++i)
+ *     std::cout << epsilon[i] << "\t";
+ * // epsilon =         01010:
+ * // word1             ATATA
+ * // word2 overlap 1:  -TATAT
+ * // word2 overlap 2:  ---TATAT
+ * @endcode
+ *
+ * @see calculateVariance
+ * @see calculateCovariance
+ * @see calculatePeriodicity
+ * @see alignmentFreeComparison
+ */
+
+template <typename TString>
+void calculateOverlapIndicator(String<int> & epsilon, TString const & word1, TString const & word2)
+{
+    typedef typename Value<TString>::Type                   TAlphabet;
+    //typedef typename Iterator<TString const, Rooted>::Type  TIterator;
+    typedef typename Size<TString>::Type                    TSize;
+
+    TSize length1 = length(word1);
+    TSize length2 = length(word2);
+    clear(epsilon);
+    resize(epsilon, length1, 0);
+    for (TSize i = 0; i < length1; ++i)
+    {
+        String<TAlphabet> my_suffix = suffix(word1, length1 - i - 1);  // Overlap of suffix of word1 with prefix of word2
+        TSize my_min = std::min(length2, i + 1);
+        String<TAlphabet> my_prefix = prefix(word2, my_min);
+        if (my_suffix == my_prefix)
+            epsilon[i] = 1;
+    }
+}
+
+/*!
+ * @fn stringToStringSet
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Transform a String into a StringSet containing this String.
+ *
+ * @signature void stringToStringSet(stringSet, string);
+ * @signature void stringToStringSet(dnaStringSet, dna5String);
+ *
+ * @param[out] stringSet    @link StringSet @endlink to create with one sequence.
+ * @param[in]  string       @link String @endlink to create the string set of.
+ * @param[out] dnaStringSet @link StringSet @endlink of @link String Strings @endlink over the alphabet @link Dna @endlink.
+ * @param[in]  dna5String   @link String @endlink over the alphabet @link Dna5 @endlink to convert.
+ *
+ * @note The second variant removes all N characters from the @link Dna5String @endlink.
+ *
+ * @section Examples
+ *
+ * Transform a masked DNA sequence into a set of sequences with all masked parts removed.
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * Dna5String sequenceDna5 =
+ *     "NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG";
+ * StringSet<DnaString> sequencesDna;
+ * stringToStringSet(sequencesDna, sequenceDna5);
+ * // Print the masked sequence
+ * std::cout<<sequenceDna5<<"\n";
+ * // Print the sequence with the masked parts removed
+ * for(unsigned i = 0; i < length(sequencesDna); ++i)
+ *     std::cout<<sequencesDna[i]<<"\n";
+ * // sequencesDna[0] = "TTTCCGAAAAGTA"
+ * // sequencesDna[1] = "GCAACTTTA"
+ * // sequencesDna[2] = "CGTGATCAAAGTTTTCCCCGTCGAAATTGGG"
+ * // sequencesDna[3] = "TG"
+ * @endcode
+ *
+ * @see MarkovModel
+ * @see alignmentFreeComparison
+ * @see cutNs
+ * @see countKmers
+ */
+
+template <typename TString>
+void
+stringToStringSet(StringSet<TString> & stringSet, TString const & sequence)
+{
+    resize(stringSet, 1);
+    stringSet[0] = sequence;
+}
+
+inline void
+stringToStringSet(StringSet<String<Dna> > & dnaStringSet, String<Dna5> const & sequence)
+{
+    typedef Iterator<String<Dna5> const, Rooted>::Type  TIterator;
+    typedef Position<TIterator>::Type                   TPosition;
+
+    TIterator itSeq = begin(sequence);
+    // Check for any N that destroys the first kmers
+    unsigned j = 0;
+    for (TPosition i = position(itSeq); i <= j; ++i)
+    {
+        if (sequence[i] == 'N')
+        {
+            if ((i - position(itSeq)) > 0)
+                appendValue(dnaStringSet, infix(sequence, position(itSeq), i));
+            goFurther(itSeq, i + 1 - position(itSeq));
+            j = i;
+        }
+    }
+    int counterN = 0;
+    TPosition startSplitSequence = position(itSeq);  // The position of possible starts of a sequence after Ns is stored to split the sequence.
+    for (; itSeq <= (end(sequence) - 1); ++itSeq)
+    {
+        if (value(itSeq) == 'N')
+        {
+            counterN = 1;
+            if (((position(itSeq)) > startSplitSequence))
+            {
+                appendValue(dnaStringSet, infix(sequence, startSplitSequence, position(itSeq)));
+            }
+            startSplitSequence = (position(itSeq) + 1);  // Position after N, possible start
+        }
+        counterN--;
+    }
+    // Create the stringSet, the stringSet can be used to create a Markov model
+    if (position(itSeq) > startSplitSequence)
+        appendValue(dnaStringSet, infix(sequence, startSplitSequence, position(itSeq)));
+}
+
+/*!
+ * @fn cutNs
+ * @headerfile <seqan/alignment_free.h>
+ * @brief Cut out all masked sequences from a Dna5String.
+ *
+ * @signature void cutNs(sequenceCut, sequence);
+ *
+ * @param[out] sequenceCut Dna5String similar to sequence with all Ns cut out.
+ * @param[in]  sequence    Masked DNA sequence.
+ *
+ * This function concatenates the nonmasked parts of the sequence, thereby changing the word content. If you want to
+ * remove the masked parts of a sequence without concatenation, use stringToStringSet.
+ *
+ * @section Examples
+ *
+ * Transform a masked DNA sequence into an unmasked sequences with all masked parts cut out
+ *
+ * @code{.cpp}
+ * using namespace seqan;
+ * Dna5String sequenceMasked =
+ *     "NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG";
+ * Dna5String sequenceMaskedPartsRemoved;
+ * cutNs(sequenceMaskedPartsRemoved, sequenceMasked);
+ * // Print the masked sequence
+ * std::cout<<sequenceMasked<<"\n";
+ * // Print the sequence with the masked parts removed
+ * std::cout<<sequenceMaskedPartsRemoved<<"\n";
+ * // sequenceMasked =
+ * // "NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG"
+ * // sequenceMaskedPartsRemoved =
+ * // "TTTCCGAAAAGGTAGCAACTTTACGTGATCAAAGTTTTCCCCGTCGAAATTGGGTG"
+ * @endcode
+ *
+ * @see MarkovModel
+ * @see stringToStringSet
+ * @see alignmentFreeComparison
+ */
+
+inline void
+cutNs(String<Dna5> & sequenceCut, String<Dna5> const & sequence)
+{
+    typedef Iterator<String<Dna5> const, Rooted>::Type  TIterator;
+    typedef Position<TIterator>::Type                   TPosition;
+
+    sequenceCut = "";
+    TIterator itSeq = begin(sequence);
+
+    // Check for any N that destroys the first kmers
+    unsigned j = 0;
+    for (TPosition i = position(itSeq); i <= j; ++i)
+    {
+        if (sequence[i] == 'N')
+        {
+            if ((i - position(itSeq)) > 0)
+                sequenceCut += infix(sequence, position(itSeq), i);
+            goFurther(itSeq, i + 1 - position(itSeq));
+            j = i;
+        }
+    }
+    int counterN = 0;
+    TPosition startSplitSequence = position(itSeq);  // The position of possible starts of a sequence after Ns is stored to split the sequence.
+    for (; itSeq <= (end(sequence) - 1); ++itSeq)
+    {
+        if (value(itSeq) == 'N')
+        {
+            counterN = 1;
+            if (((position(itSeq)) > startSplitSequence))
+                sequenceCut += infix(sequence, startSplitSequence, position(itSeq));
+            startSplitSequence = (position(itSeq) + 1);  // Position after N, possible start
+        }
+        counterN--;
+    }
+    // Create the sequence with any N cut out.
+    if (position(itSeq) > startSplitSequence)
+    {
+        sequenceCut += infix(sequence, startSplitSequence, position(itSeq));
+    }
+}
+
+}  // namespace seqan
+
+#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_KMER_FUNCTIONS_H_
diff --git a/seqan/arg_parse.h b/seqan/arg_parse.h
index b134b28..f75a094 100644
--- a/seqan/arg_parse.h
+++ b/seqan/arg_parse.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,17 +34,24 @@
 // Facade header for module arg_parse.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_H_
+#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_H_
 
 // ===========================================================================
 // Prerequisites.
 // ===========================================================================
 
 #include <seqan/basic.h>
-#include <seqan/file.h>
+//#include <seqan/file.h>
+#include <seqan/stream.h>
 #include <seqan/sequence.h>
 
+#include <sys/types.h>
+#include <sys/stat.h>
+#ifndef PLATFORM_WINDOWS
+#include <unistd.h>
+#endif
+
 // ===========================================================================
 // The ArgParse Headers.
 // ===========================================================================
@@ -64,4 +71,4 @@
 #include <seqan/arg_parse/arg_parse_parse.h>
 
 
-#endif  // SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_H_
+#endif  // SEQAN_INCLUDE_SEQAN_ARG_PARSE_H_
diff --git a/seqan/arg_parse/INFO b/seqan/arg_parse/INFO
deleted file mode 100644
index 2d19c8a..0000000
--- a/seqan/arg_parse/INFO
+++ /dev/null
@@ -1,10 +0,0 @@
-Name: arg_parse
-Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
-Maintainer: Stephan Aiche <stephan.aiche@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: under development
-Description: Command Line Parsing functionality. 
- The module arg_parse provides an argument/command line parser for SeqAn apps
- including functionality to document tools and export the documentation/command
- line information to different formats like man, html, or CTD.
diff --git a/seqan/arg_parse/arg_parse_argument.h b/seqan/arg_parse/arg_parse_argument.h
index 498d2b9..c33a1be 100644
--- a/seqan/arg_parse/arg_parse_argument.h
+++ b/seqan/arg_parse/arg_parse_argument.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_
+#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_
 
 #include <seqan/arg_parse/arg_parse_exceptions.h>
 #include <seqan/arg_parse/arg_parse_type_support.h>
@@ -62,7 +62,7 @@ inline std::string getFileExtension(ArgParseArgument const & me, unsigned pos);
 
 /*!
  * @class ArgParseArgument
- * @extends AssignableConcept
+ * @implements AssignableConcept
  * @headerfile <seqan/arg_parse.h>
  * @brief Information for a specific command line argument.
  *
@@ -75,76 +75,47 @@ inline std::string getFileExtension(ArgParseArgument const & me, unsigned pos);
  * @brief Define the type of an @link ArgParseArgument @endlink.
  *
  * @signature enum ArgParseArgument::ArgumentType;
+ *
+ * @section Examples
+ *
+ * In the following example, the types <tt>INPUT_FILE</tt>, <tt>OUTPUT_FILE</tt>, and <tt>DOUBLE</tt> are used.
+ *
+ * @include demos/dox/arg_parse/argument_parser.cpp
  */
 
 /*!
- * @var ArgParseArgument::ArgumentType ArgParseArgument::STRING
+ * @val ArgParseArgument::ArgumentType STRING
  * @brief Argument is a string.
  *
- * @var ArgParseArgument::ArgumentType ArgParseArgument::INTEGER
+ * @val ArgParseArgument::ArgumentType ArgParseArgument::INTEGER;
  * @brief Argument is a signed 32 bit integer.
  *
- * @var ArgParseArgument::ArgumentType ArgParseArgument::INT64
+ * @val ArgParseArgument::ArgumentType ArgParseArgument::INT64;
  * @brief Argument is a signed 64 bit integer.
  *
- * @var ArgParseArgument::ArgumentType ArgParseArgument::DOUBLE
+ * @val ArgParseArgument::ArgumentType ArgParseArgument::DOUBLE;
  * @brief Argument is a floating point number stored as double.
  *
- * @var ArgParseArgument::ArgumentType ArgParseArgument::INPUTFILE
+ * @val ArgParseArgument::ArgumentType ArgParseArgument::INPUT_FILE;
  * @brief Argument is an input file.
  *
- * @var ArgParseArgument::ArgumentType ArgParseArgument::OUTPUTFILE
+ * @val ArgParseArgument::ArgumentType ArgParseArgument::OUTPUT_FILE;
  * @brief Argument is an output file.
  */
 
-/**
-.Class.ArgParseArgument
-..cat:Miscellaneous
-..summary:Stores information for a specific command line argument. It can be either an argument of
-a ArgParseArgument or directly an Argument on the command line.
-..signature:ArgParseArgument
-..include:seqan/arg_parse.h
-..see:Class.ArgParseOption
-..see:Class.ArgumentParser
-*/
-
 /*!
  * @fn ArgParseArgument::ArgParseArgument
  * @brief Constructor
  *
  * @signature ArgParseArgument::ArgParseArgument(argumentType[, argumentLabel[, isListArgument[, numberOfArgument]]]);
  *
- * @param argumentType      Type of the argument (<tt>ArgParseArgument::ArgumentType</tt>).
- * @param argumentLabel     Label for the argument (<tt>char const *</tt>).
- * @param isListArgument    Whether or not this argument can be given multiple times (<tt>bool</tt>).
- * @param numberOfArguments Number of times the argument must be given.  E.g. set to 2 for the parser to always
- *                          expect two values (<tt>int</tt>, default is 1).
+ * @param[in] argumentType      Type of the argument (<tt>ArgParseArgument::ArgumentType</tt>).
+ * @param[in] argumentLabel     Label for the argument (<tt>char const *</tt>).
+ * @param[in] isListArgument    Whether or not this argument can be given multiple times (<tt>bool</tt>).
+ * @param[in] numberOfArguments Number of times the argument must be given.  E.g. set to 2 for the parser to always
+ *                              expect two values (<tt>int</tt>, default is 1).
  */
 
-/**
-.Memfunc.ArgParseArgument#ArgParseArgument
-..class:Class.ArgParseArgument
-..summary:Constructor
-..signature:ArgParseArgument (argumentType [, argumentLabel, isListArgument, numberOfArguments])
-..param.argumentType:A ArgParseArgument.ArgumentType value defining the type (e.g., String) of the
-ArgParseArgument.
-...tableheader:Flag|Description
-...table:$ArgParseArgument::STRING$|Argument is a string
-...table:$ArgParseArgument::INTEGER$|Argument is an integer
-...table:$ArgParseArgument::INT64|Argument is a 64 bit integer
-...table:$ArgParseArgument::DOUBLE$|A float
-...table:$ArgParseArgument::INPUTFILE$|An input file
-...table:$ArgParseArgument::OUTPUTFILE$|An output file
- ..param.argumentLabel:Defines a user defined argument label for the help output. If this option is
- not set, ArgParseArgument will automatically define a label based on the ArgumentType.
-..param.isListArgument:Defines if the argument can be given multiple times.
-...default:false.
-..param.numberOfArguments: Defines if the argument consists of defined number of elements (e.g., if
-you want to provide an interval you would set this option to 2, so the parser knows that he needs
-to search for exactly 2 values).
-...default:1.
-*/
-
 class ArgParseArgument
 {
 public:
@@ -155,10 +126,10 @@ class ArgParseArgument
         INTEGER,     // .. an integer
         INT64,       // .. a 64 bit integer
         DOUBLE,      // .. a float
-        INPUTFILE,   // .. an inputfile (implicitly also a string)
-        OUTPUTFILE,  // .. an outputfile (implicitly also a string)
+        INPUT_FILE,   // .. an inputfile (implicitly also a string)
+        OUTPUT_FILE,  // .. an outputfile (implicitly also a string)
         INPUTPREFIX, // .. an inputprefix (implicitly also a string)
-        OUTPUTPREFIX // .. an outoutprefix (implicitly also a string)
+        OUTPUT_PREFIX // .. an outoutprefix (implicitly also a string)
     };
 
 
@@ -250,11 +221,11 @@ inline std::string _typeToString(ArgParseArgument const & me)
         typeName = "string";
         break;
 
-    case ArgParseArgument::INPUTFILE:
+    case ArgParseArgument::INPUT_FILE:
         typeName = "inputfile";
         break;
 
-    case ArgParseArgument::OUTPUTFILE:
+    case ArgParseArgument::OUTPUT_FILE:
         typeName = "outputfile";
         break;
 
@@ -262,7 +233,7 @@ inline std::string _typeToString(ArgParseArgument const & me)
         typeName = "inputprefix";
         break;
 
-    case ArgParseArgument::OUTPUTPREFIX:
+    case ArgParseArgument::OUTPUT_PREFIX:
         typeName = "outputprefix";
         break;
 
@@ -286,24 +257,11 @@ inline std::string _typeToString(ArgParseArgument const & me)
  *
  * @signature bool isListArgument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it can be given multiple times, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isListArgument
-..class:Class.ArgParseArgument
-..summary:Returns whether the argument can be given multiple times.
-..cat:Miscellaneous
-..signature:isListArgument(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$true$ if the argument argument can be given multiple times.
-..see:Memfunc.ArgParseArgument#ArgParseArgument.param.isListArgument
-..include:seqan/arg_parse.h
-*/
-
 inline bool isListArgument(ArgParseArgument const & me)
 {
     return me._isListArgument;
@@ -319,33 +277,20 @@ inline bool isListArgument(ArgParseArgument const & me)
  *
  * @brief Returns whether the argument is a string.
  *
- * @signature bool ArgParseArgument#isStringArgument(arg);
+ * @signature bool isStringArgument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it is a string, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isStringArgument
-..class:Class.ArgParseArgument
-..summary:Returns whether the argument is a string.
-..cat:Miscellaneous
-..signature:isListArgument(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$true$ if the argument argument is a string argument.
-..see:Memfunc.ArgParseArgument#ArgParseArgument.param.argumentType
-..include:seqan/arg_parse.h
-*/
-
 inline bool isStringArgument(ArgParseArgument const & me)
 {
     return (me._argumentType == ArgParseArgument::STRING) ||
-           (me._argumentType == ArgParseArgument::INPUTFILE) ||
-           (me._argumentType == ArgParseArgument::OUTPUTFILE) ||
+           (me._argumentType == ArgParseArgument::INPUT_FILE) ||
+           (me._argumentType == ArgParseArgument::OUTPUT_FILE) ||
            (me._argumentType == ArgParseArgument::INPUTPREFIX) ||
-           (me._argumentType == ArgParseArgument::OUTPUTPREFIX) ;
+           (me._argumentType == ArgParseArgument::OUTPUT_PREFIX) ;
 }
 
 // ----------------------------------------------------------------------------
@@ -359,24 +304,11 @@ inline bool isStringArgument(ArgParseArgument const & me)
  *
  * @signature bool isIntegerArgument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it is an integer, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isIntegerArgument
-..class:Class.ArgParseArgument
-..summary:Returns whether the argument is an integer.
-..cat:Miscellaneous
-..signature:isIntegerArgument(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$true$ if the argument argument is an integer argument.
-..see:Memfunc.ArgParseArgument#ArgParseArgument.param.argumentType
-..include:seqan/arg_parse.h
-*/
-
 inline bool isIntegerArgument(ArgParseArgument const & me)
 {
     return me._argumentType == ArgParseArgument::INTEGER;
@@ -393,24 +325,11 @@ inline bool isIntegerArgument(ArgParseArgument const & me)
  *
  * @signature bool isInt64Argument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it is a 64 bit integer, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isInt64Argument
-..class:Class.ArgParseArgument
-..summary:Returns whether the argument is a 64 bit integer.
-..cat:Miscellaneous
-..signature:isInt64Argument(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$true$ if the argument argument is a 64 bit  integer argument.
-..see:Memfunc.ArgParseArgument#ArgParseArgument.param.argumentType
-..include:seqan/arg_parse.h
-*/
-
 inline bool isInt64Argument(ArgParseArgument const & me)
 {
     return me._argumentType == ArgParseArgument::INT64;
@@ -427,24 +346,11 @@ inline bool isInt64Argument(ArgParseArgument const & me)
  *
  * @signature bool isDoubleArgument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it is a double argument, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isDoubleArgument
-..class:Class.ArgParseArgument
-..summary:Returns whether the argument is a double.
-..cat:Miscellaneous
-..signature:isDoubleArgument(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$true$ if the argument argument is a double argument.
-..see:Memfunc.ArgParseArgument#ArgParseArgument.param.argumentType
-..include:seqan/arg_parse.h
-*/
-
 inline bool isDoubleArgument(ArgParseArgument const & me)
 {
     return me._argumentType == ArgParseArgument::DOUBLE;
@@ -461,27 +367,14 @@ inline bool isDoubleArgument(ArgParseArgument const & me)
  *
  * @signature bool isInputFileArgument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it is a input file argument, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isInputFileArgument
-..class:Class.ArgParseArgument
-..summary:Returns whether the argument is an input file.
-..cat:Miscellaneous
-..signature:isOutputFileArgument(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$true$ if the argument argument is an input file argument.
-..see:Memfunc.ArgParseArgument#ArgParseArgument.param.argumentType
-..include:seqan/arg_parse.h
-*/
-
 inline bool isInputFileArgument(ArgParseArgument const & me)
 {
-    return me._argumentType == ArgParseArgument::INPUTFILE;
+    return me._argumentType == ArgParseArgument::INPUT_FILE;
 }
 
 // ----------------------------------------------------------------------------
@@ -495,28 +388,14 @@ inline bool isInputFileArgument(ArgParseArgument const & me)
  *
  * @signature bool isOutputFileArgument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it is a output file argument, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isOutputFileArgument
-..class:Class.ArgParseArgument
-..summary:Returns whether the argument is an output file.
-..cat:Miscellaneous
-..signature:isOutputFileArgument(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-...type:Class.ArgParseOption
-..returns:$true$ if the argument argument is an output file argument.
-..see:Memfunc.ArgParseArgument#ArgParseArgument.param.argumentType
-..include:seqan/arg_parse.h
-*/
-
 inline bool isOutputFileArgument(ArgParseArgument const & me)
 {
-    return me._argumentType == ArgParseArgument::OUTPUTFILE;
+    return me._argumentType == ArgParseArgument::OUTPUT_FILE;
 }
 
 // ----------------------------------------------------------------------------
@@ -530,28 +409,14 @@ inline bool isOutputFileArgument(ArgParseArgument const & me)
  *
  * @signature bool isOutputPrefixArgument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it is an output prefix argument, <tt>false</tt> otherwise.
  */
 
-/**
- .Function.isOutputPrefixArgument
- ..class:Class.ArgParseArgument
- ..summary:Returns whether the argument is an output file.
- ..cat:Miscellaneous
- ..signature:isOutputPrefixArgument(argument)
- ..param.argument:The @Class.ArgParseArgument@ object.
- ...type:Class.ArgParseArgument
- ...type:Class.ArgParseOption
- ..returns:$true$ if the argument argument is an output file argument.
- ..see:Memfunc.ArgParseArgument#ArgParseArgument.param.argumentType
- ..include:seqan/arg_parse.h
- */
-
 inline bool isOutputPrefixArgument(ArgParseArgument const & me)
 {
-    return me._argumentType == ArgParseArgument::OUTPUTPREFIX;
+    return me._argumentType == ArgParseArgument::OUTPUT_PREFIX;
 }
 
 // ----------------------------------------------------------------------------
@@ -565,30 +430,16 @@ inline bool isOutputPrefixArgument(ArgParseArgument const & me)
  *
  * @signature bool isInputPrefixArgument(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if it is an input prefix argument, <tt>false</tt> otherwise.
  */
 
-/**
- .Function.isInputPrefixArgument
- ..class:Class.ArgParseArgument
- ..summary:Returns whether the argument is an output file.
- ..cat:Miscellaneous
- ..signature:isInputPrefixArgument(argument)
- ..param.argument:The @Class.ArgParseArgument@ object.
- ...type:Class.ArgParseArgument
- ...type:Class.ArgParseOption
- ..returns:$true$ if the argument argument is an input prefix argument.
- ..see:Memfunc.ArgParseArgument#ArgParseArgument.param.argumentType
- ..include:seqan/arg_parse.h
- */
-
 inline bool isInputPrefixArgument(ArgParseArgument const & me)
 {
     return me._argumentType == ArgParseArgument::INPUTPREFIX;
 }
-    
+
 // ----------------------------------------------------------------------------
 // Function getArgumentLabel()
 // ----------------------------------------------------------------------------
@@ -600,24 +451,11 @@ inline bool isInputPrefixArgument(ArgParseArgument const & me)
  *
  * @signature std::string getArgumentLabel(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return std::string The argument label as a STL string.
  */
 
-/**
-.Function.getArgumentLabel
-..class:Class.ArgParseArgument
-..summary:Returns the label for the given @Class.ArgParseArgument@. Either the user defined label
-is returned or a default label (based on the ArgumentType is used).
-..cat:Miscellaneous
-..signature:getArgumentLabel(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:A $ShortCut.std::string$ containing the label.
-..include:seqan/arg_parse.h
-*/
-
 inline std::string const getArgumentLabel(ArgParseArgument const & me)
 {
     if (me._argumentLabel != "")
@@ -661,14 +499,14 @@ inline std::string const getArgumentLabel(ArgParseArgument const & me)
 // Helper Function _intervalAssert()
 // ----------------------------------------------------------------------------
 
-// this methods ensures that the given arguments define a non emtpy value interval
+// this methods ensures that the given arguments define a valid interval
 // otherwise it will trigger a SEQAN_CHECK failure
 template <typename TIntervalBorder>
 inline void _intervalAssert(const std::string minValueAsString, const std::string maxValueAsString)
 {
     if (minValueAsString != "" && maxValueAsString != "")
-        SEQAN_CHECK(_cast<TIntervalBorder>(minValueAsString) < _cast<TIntervalBorder>(maxValueAsString),
-                    "The interval [%s:%s] is empty. Please specify a valid, non-empty interval.",
+        SEQAN_CHECK(_cast<TIntervalBorder>(minValueAsString) <= _cast<TIntervalBorder>(maxValueAsString),
+                    "The interval [%s:%s] is invalid. Please specify a valid interval.",
                     minValueAsString.c_str(),
                     maxValueAsString.c_str());
 }
@@ -684,25 +522,10 @@ inline void _intervalAssert(const std::string minValueAsString, const std::strin
  *
  * @signature void setMinValue(arg, minValue);
  *
- * @param arg      The ArgParseArgument to set the smallest value of.
- * @param minValue The smallest value to set (<tt>std::string</tt>).
- *
- * @return std::string The argument label as a STL string.
+ * @param[in,out] arg      The ArgParseArgument to set the smallest value of.
+ * @param[in]     minValue The smallest value to set (<tt>std::string</tt>).
  */
 
-/**
-.Function.setMinValue
-..class:Class.ArgParseArgument
-..summary:Sets the minimum value of a @Class.ArgParseArgument@ object.
-..cat:Miscellaneous
-..signature:setMinValue(argument,minValue)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..param.minValue:A std::string containing a string representation of the minimum value
-of the @Class.ArgParseArgument@.
-..include:seqan/arg_parse.h
-*/
-
 inline void setMinValue(ArgParseArgument & me, const std::string minValue)
 {
     if (isDoubleArgument(me))
@@ -738,25 +561,10 @@ inline void setMinValue(ArgParseArgument & me, const std::string minValue)
  *
  * @signature void setMaxValue(arg, maxValue);
  *
- * @param arg      The ArgParseArgument to set the smallest value of.
- * @param maxValue The largest value to set (<tt>std::string</tt>).
- *
- * @return std::string The argument label as a STL string.
+ * @param[in,out] arg      The ArgParseArgument to set the smallest value of.
+ * @param[in]     maxValue The largest value to set (<tt>std::string</tt>).
  */
 
-/**
-.Function.setMaxValue
-..class:Class.ArgParseArgument
-..summary:Sets the maximum value of a @Class.ArgParseArgument@ object.
-..cat:Miscellaneous
-..signature:setMaxValue(argument,maxValue)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..param.maxValue:A std::string containing a string representation of the maximum value
-of the @Class.ArgParseArgument@.
-..include:seqan/arg_parse.h
-*/
-
 inline void setMaxValue(ArgParseArgument & me, const std::string maxValue)
 {
     if (isDoubleArgument(me))
@@ -792,9 +600,9 @@ inline void setMaxValue(ArgParseArgument & me, const std::string maxValue)
  *
  * @signature void setValidValues(arg, values);
  *
- * @param arg    The ArgParseArgument to set the valid values for.
- * @param values Either a <tt>std::string</tt> containing all valid entries, separated by spaces or a
- *               <tt>std::vector&lt;std::string&gt;</tt> with the valid entries.
+ * @param[in,out] arg    The ArgParseArgument to set the valid values for.
+ * @param[in]     values Either a <tt>std::string</tt> containing all valid entries, separated by spaces or a
+ *                       <tt>std::vector&lt;std::string&gt;</tt> with the valid entries.
  *
  * If the argument is of type string then the list of valid values is the case-sensitive list of string values
  * allowed for this argument.  If it is an input or output file then the list of valid values is a list of
@@ -814,11 +622,11 @@ inline void setMaxValue(ArgParseArgument & me, const std::string maxValue)
  * setValidValues(stringArg, values);  // one of {"four", "five"}
  * @endcode
  *
- * An example for an input file option.  Note that by changing <tt>INPUTFILE</tt> to <tt>OUTPUTFILE</tt> below,
+ * An example for an input file option.  Note that by changing <tt>INPUT_FILE</tt> to <tt>OUTPUT_FILE</tt> below,
  * the example would be the same for output files.
  *
  * @code{.cpp}
- * seqan::ArgParseArgument fileArg(seqan::ArgParseArgument::INPUTFILE);
+ * seqan::ArgParseArgument fileArg(seqan::ArgParseArgument::INPUT_FILE);
  * setValidValues(fileArg, "fq fastq");  // file must end in ".fq" or ".fastq"
  *
  * std::vector<std::string> values;
@@ -828,21 +636,6 @@ inline void setMaxValue(ArgParseArgument & me, const std::string maxValue)
  * @endcode
  */
 
-/**
-.Function.setValidValues
-..class:Class.ArgParseArgument
-..summary:Sets the set of allowed values of a @Class.ArgParseArgument@ object.
-..cat:Miscellaneous
-..signature:setValidValues(argument,values)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..param.values:A std::vector<std::string> containing all valid entries for the option or a std::string
-with valid values separated by spaces.
-..remarks:If the argument or option is an in- or output file. The valid strings will be interpreted as
-file endings and the command line parser checks if the provided file has the required file ending.
-..include:seqan/arg_parse.h
-*/
-
 inline void setValidValues(ArgParseArgument & me, std::vector<std::string> const & values)
 {
     if (isDoubleArgument(me) || isIntegerArgument(me))
@@ -886,22 +679,10 @@ inline void setValidValues(ArgParseArgument & me, std::string const & valuesStri
  *
  * @signature void setHelpText(arg, text);
  *
- * @param arg  The ArgParseArgument to set the help text for.
- * @param text The text to display as the description of the argument (<tt>std::string</tt>).
+ * @param[in,out] arg  The ArgParseArgument to set the help text for.
+ * @param[in]     text The text to display as the description of the argument (<tt>std::string</tt>).
  */
 
-/**
-.Function.setHelpText
-..class:Class.ArgParseArgument
-..summary:Sets the help text for an ArgParseArgument.
-..cat:Miscellaneous
-..signature:setHelpText(argument,text)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..param.text:A std::string describing the argument.
-..include:seqan/arg_parse.h
-*/
-
 inline void setHelpText(ArgParseArgument & me, std::string const & text)
 {
     me._helpText = text;
@@ -972,7 +753,7 @@ inline bool _compareExtension(std::string const & str, std::string const & ext)
 
 // The parameter i gives the index of the value in the argument.
 
-inline void _checkStringRestrictions(ArgParseArgument const & me, std::string value,
+inline void _checkStringRestrictions(ArgParseArgument const & me, std::string const &value,
                                      unsigned i)
 {
     typedef std::vector<std::string>::const_iterator TVectorIterator;
@@ -980,6 +761,14 @@ inline void _checkStringRestrictions(ArgParseArgument const & me, std::string va
     // we only check valid values for files and string arguments, but not for prefix arguments
     if (!empty(me.validValues) && !(isInputPrefixArgument(me) || isOutputPrefixArgument(me)))
     {
+        // The file name "-" is reserved for stdin or stdout
+        if ((isInputFileArgument(me) || isOutputFileArgument(me)) && value == "-")
+            return;
+
+        // Allow the filename to be a pipe (without checking its extension)
+        if (isInputFileArgument(me) && _isPipe(value.c_str()))
+            return;
+
         bool isContained = false;
         for (TVectorIterator validValue = me.validValues.begin();
              validValue != me.validValues.end();
@@ -1059,21 +848,6 @@ inline void _checkValue(ArgParseArgument const & me)
 // Function _assignArgumentValue()
 // ----------------------------------------------------------------------------
 
-/**
-.Internal.Function._assignArgumentValue
-..class:Class.ArgParseArgument
-..summary:Assigns the given value (if applicable) to the @Class.ArgParseArgument@ object. If
-the @Class.ArgParseArgument@ is a list or can hold multiple values
-(@Memfunc.ArgParseArgument#ArgParseArgument.param.numberOfArguments@) the value will be appended.
-Otherwise the value will be overwritten.
-..cat:internal
-..signature:_assignArgumentValue(argument,value [, argNo])
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..param.value:A std::string containing the value that should be assigned.
-..include:seqan/arg_parse.h
-*/
-
 inline void _assignArgumentValue(ArgParseArgument & me, std::string const & value)
 {
     // assignment
@@ -1101,29 +875,13 @@ inline void _assignArgumentValue(ArgParseArgument & me, std::string const & valu
  *
  * @signature std::string getArgumentValue(arg[, argNo]);
  *
- * @param arg   The ArgParseArgument to query.
- * @param argNo In case that the ArgParseArgument allowed multiple values, give the index of the argument
- *              that you want to retrieve (<tt>unsigned</tt>, starts at 0).
+ * @param[in,out] arg   The ArgParseArgument to query.
+ * @param[in]     argNo In case that the ArgParseArgument allowed multiple values, give the index of the argument
+ *                      that you want to retrieve (<tt>unsigned</tt>, starts at 0).
  *
  * @return std::string Const-reference to the argument value.
  */
 
-/**
-.Function.ArgParseArgument#getArgumentValue
-..class:Class.ArgParseArgument
-..summary:Returns the value of the @Class.ArgParseArgument@ object. If
-the @Class.ArgParseArgument@ is a list or can hold multiple values
-(@Memfunc.ArgParseArgument#ArgParseArgument.param.numberOfArguments@) you can specify which value
-you want to get. If not set the first value will be returned.
-..cat:Miscellaneous
-..signature:getArgumentValue(argument [, argNo])
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..param.argNo:If the argument is a list,  the $argNo$-th list element is returned.
-..returns:The value set at position $position$.
-..include:seqan/arg_parse.h
-*/
-
 inline std::string const & getArgumentValue(ArgParseArgument const & me, unsigned argNo)
 {
     SEQAN_CHECK(argNo < me.value.size() || argNo < me.defaultValue.size(),
@@ -1151,24 +909,11 @@ inline std::string const & getArgumentValue(ArgParseArgument const & me)
  *
  * @signature std::vector<std::string> getArgumentValue(arg);
  *
- * @param arg   The ArgParseArgument to query.
+ * @param[in] arg   The ArgParseArgument to query.
  *
  * @return std::vector<std::string> Const-reference to the argument values.
  */
 
-/**
-.Function.getArgumentValues
-..class:Class.ArgParseArgument
-..summary:Returns all values of the @Class.ArgParseArgument@ object as const std::vector.
-..cat:Miscellaneous
-..signature:getArgumentValues(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$std::vector<std::string>$ containing the values. If no value was set and no
-default value exists an empty vector will be returned.
-..include:seqan/arg_parse.h
-*/
-
 inline std::vector<std::string> const & getArgumentValues(ArgParseArgument const & me)
 {
     if (!me.value.empty())
@@ -1188,24 +933,12 @@ inline std::vector<std::string> const & getArgumentValues(ArgParseArgument const
  *
  * @signature bool hasValue(arg[, pos]);
  *
- * @param arg The ArgParseArgument to query.
- * @param pos The position of the argument in case of being a list (<tt>unsigned</tt>, 0-based, default is 0).
+ * @param[in] arg The ArgParseArgument to query.
+ * @param[in] pos The position of the argument in case of being a list (<tt>unsigned</tt>, 0-based, default is 0).
  *
  * @return bool <tt>true</tt> if <tt>pos</tt> is less than the size and the argument is non-empty.
  */
 
-/**
-.Function.ArgParseArgument#hasValue
-..class:Class.ArgParseArgument
-..summary:Returns true if a value for the given position is available.
-..cat:Miscellaneous
-..signature:hasValue(argument [, position=0])
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..param.position:The position for which the availability should be tested.
-..returns: $true$ if a value is available, $false$ if not.
-..include:seqan/arg_parse.h
-*/
 inline bool hasValue(ArgParseArgument const & arg, unsigned position)
 {
     return arg.value.size() > position || arg.defaultValue.size() > position;
@@ -1227,23 +960,11 @@ inline bool hasValue(ArgParseArgument const & arg)
  *
  * @signature bool isSet(arg):
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return bool <tt>true</tt> if a value was assigned, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.ArgParseArgument#isSet
-..class:Class.ArgParseArgument
-..summary:Returns true if a value was assigned to the argument.
-..cat:Miscellaneous
-..signature:isSet(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$true$ if a value was assigned to the argument, $false$ if not.
-..include:seqan/arg_parse.h
-*/
-
 inline bool isSet(ArgParseArgument const & me)
 {
     return !me.value.empty();
@@ -1260,22 +981,11 @@ inline bool isSet(ArgParseArgument const & me)
  *
  * @signature bool hasDefault(arg);
  *
- * @param arg The argument to query.
+ * @param[in] arg The argument to query.
  *
  * @return bool <tt>true</tt> if the argument has a default value and <tt>false</tt> if not.
  */
 
-/**
-.Function.ArgParseArgument#hasDefault
-..summary:Returns true if a default value was given for that argument.
-..cat:Miscellaneous
-..signature:hasDefault(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:$true$ if a default value was given for the argument, $false$ if not.
-..include:seqan/arg_parse.h
-*/
-
 inline bool hasDefault(ArgParseArgument const & me)
 {
     return !me.defaultValue.empty();
@@ -1292,23 +1002,11 @@ inline bool hasDefault(ArgParseArgument const & me)
  *
  * @signature unsigned numberOfAllowedValues(arg);
  *
- * @param arg The ArgParseArgument to query.
+ * @param[in] arg The ArgParseArgument to query.
  *
  * @return unsigned The number of allowed values.
  */
 
-/**
-.Function.numberOfAllowedValues
-..class:Class.ArgParseArgument
-..summary:Returns the number of allowed values for this @Class.ArgParseArgument@.
-..cat:Miscellaneous
-..signature:numberOfAllowedValues(argument)
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..returns:The number of allowed values for this @Class.ArgParseArgument@.
-..include:seqan/arg_parse.h
-*/
-
 inline unsigned numberOfAllowedValues(ArgParseArgument const & me)
 {
     return me._numberOfValues;
@@ -1323,7 +1021,7 @@ inline unsigned numberOfAllowedValues(ArgParseArgument const & me)
  * @headerfile <seqan/arg_parse.h>
  * @brief Returns the file extension for the given file argument.
  *
- * Only valid when argument is an INPUTFILE or OUTPUTFILE.
+ * Only valid when argument is an INPUT_FILE or OUTPUT_FILE.
  *
  * Halts the program if not an input or output file argument.
  *
@@ -1333,33 +1031,16 @@ inline unsigned numberOfAllowedValues(ArgParseArgument const & me)
  *
  * @signature std::string getFileExtension(arg[, pos]);
  *
- * @param arg The ArgParseArgument to query.
- * @param pos The position of the value to retrieve if multiple values (<tt>unsigned</tt>).
+ * @param[in] arg The ArgParseArgument to query.
+ * @param[in] pos The position of the value to retrieve if multiple values (<tt>unsigned</tt>).
  *
  * @return std::string The file extension, empty if no extension or not set.
  */
 
-/**
-.Function.ArgParseArgument#getFileExtension
-..class:Class.ArgParseArgument
-..summary:Returns the file extension for the given file argument.
-..description:Only valid when argument is an INPUTFILE or OUTPUTFILE.
-..cat:Miscellaenous
-..signature:std::string getFileExtension(argument[, pos]);
-..param.argument:The @Class.ArgParseArgument@ object.
-...type:Class.ArgParseArgument
-..param.pos:The position of the value if multiple values are allowed.
-...type:nolink:$unsigned$
-..returns:A $std::string$ with the extension of the file, if any.  Empty if no extension.
-..remarks:Halts the program if the argument is not an input or output file argument.
-..remarks:Note that you can
-..include:seqan/arg_parse.h
-*/
-
 inline std::string getFileExtension(ArgParseArgument const & me, unsigned pos = 0)
 {
-    if (me._argumentType != ArgParseArgument::INPUTFILE &&
-        me._argumentType != ArgParseArgument::OUTPUTFILE)
+    if (me._argumentType != ArgParseArgument::INPUT_FILE &&
+        me._argumentType != ArgParseArgument::OUTPUT_FILE)
         SEQAN_FAIL("Cannot get file extension from non-file argument/option.");
 
     // Short-circuit to override file extension if set.
@@ -1399,4 +1080,4 @@ inline std::string getFileExtension(ArgParseArgument const & me, unsigned pos =
 
 } // namespace seqan
 
-#endif // SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_
+#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_
diff --git a/seqan/arg_parse/arg_parse_ctd_support.h b/seqan/arg_parse/arg_parse_ctd_support.h
index 4c46d40..3542bd9 100644
--- a/seqan/arg_parse/arg_parse_ctd_support.h
+++ b/seqan/arg_parse/arg_parse_ctd_support.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,8 @@
 // Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_
+#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_
 
 #include <seqan/sequence.h>
 
@@ -112,11 +112,6 @@ TSequence _toText(TSequence const & input)
 // Function _join()
 // ----------------------------------------------------------------------------
 
-/**
- * joins all elements of the the passed StringSet into a single CharString
- * the provided delimiter is used to separate the single entries in the
- * resulting CharString
- */
 template <typename TValue>
 inline std::string
 _join(std::vector<TValue> const & v, std::string const & delimiter)
@@ -289,6 +284,8 @@ inline std::string _getManual(ArgumentParser const & me)
 // Function writeCTD()
 // ----------------------------------------------------------------------------
 
+// TODO(holtgrew): Change argument order.
+
 /*!
  * @fn ArgumentParser#writeCTD
  * @headerfile <seqan/arg_parse.h>\
@@ -296,26 +293,13 @@ inline std::string _getManual(ArgumentParser const & me)
  *
  * @signature bool writeCTD(parser[, stream]);
  *
- * @param parser The ArgumentParser to write the CTD file for.
- * @param stream A <tt>std::ostream</tt> to write to.  If omitted an output file with the name form the "write-ctd"
- *               parameter of the parser is used.
+ * @param[in]  parser The ArgumentParser to write the CTD file for.
+ * @param[out] stream A <tt>std::ostream</tt> to write to.  If omitted an output file with the name form the
+ *                    "write-ctd" parameter of the parser is used.
  *
  * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.writeCTD
-..summary:Exports the app's interface description to a .ctd file.
-..cat:Miscellaneous
-..signature:writeCTD(parser [, ctdfile])
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.ctdfile:The stream where the ctd file will be written to. If non is given the function writes it to the file given in the write-ctd parameter.
-..param.parser:The @Class.ArgumentParser@ object.
-..returns:$true$ if the ctd file could be created correctly, $false$ otherwise.
-..include:seqan/arg_parse.h
-*/
-
 inline bool
 writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
 {
@@ -355,6 +339,11 @@ writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
          ++optionMapIterator)
     {
         ArgParseOption const & opt = *optionMapIterator;
+
+        // exclude hidden
+        if (isHidden(opt))
+            continue;
+
         std::string optionIdentifier = _getPrefixedOptionName(opt);
         std::string refName = toolname + "." + _getOptionName(opt);
 
@@ -395,6 +384,10 @@ writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
         if (!_includeInCTD(opt))
             continue;
 
+        // exclude hidden
+        if (isHidden(opt))
+            continue;
+
         // prefer short name for options
         std::string optionName = _getOptionName(opt);
 
@@ -441,7 +434,7 @@ writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
             ctdfile << "supported_formats=\"" << xmlEscape(_join(supported_formats, ",")) << "\" ";
 
         ctdfile << "required=\"" << (isRequired(opt) ? "true" : "false") << "\" ";
-        ctdfile << "advanced=\"" << (isHidden(opt) ? "true" : "false") << "\" ";
+        ctdfile << "advanced=\"" << (isAdvanced(opt) ? "true" : "false") << "\" ";
 
         // Write out tags attribute.
         if (!opt.tags.empty())
@@ -565,4 +558,4 @@ writeCTD(ArgumentParser const & me)
 
 } // namespace seqan
 
-#endif // SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_
+#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_
diff --git a/seqan/arg_parse/arg_parse_doc.h b/seqan/arg_parse/arg_parse_doc.h
index d49cb02..165a084 100644
--- a/seqan/arg_parse/arg_parse_doc.h
+++ b/seqan/arg_parse/arg_parse_doc.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_
+#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_
 
 #include <seqan/arg_parse/tool_doc.h>
 #include <seqan/arg_parse/argument_parser.h>
@@ -48,18 +48,16 @@ namespace seqan {
 // Function getAppName()
 // --------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#getAppName
-..class:Class.ArgumentParser
-..summary:Get tool name of @Class.ArgumentParser@ object.
-..cat:Miscellaneous
-..signature:getAppName(parser)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..returns:Tool name of argument parser object.
-...type:nolink:$std::string$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#getAppName
+ * @brief Return program name of ArgumentParser.
+ *
+ * @signature TCharStringRef getAppName(parser);
+ *
+ * @param[in] parser The ArgumentParser to get the app name for.
+ *
+ * @return TCharStringRef The app name, const-ref to @link CharString @endlink.
+ */
 
 inline CharString const & getAppName(ArgumentParser const & parser)
 {
@@ -86,19 +84,17 @@ inline void _parseAppName(ArgumentParser & parser, std::string const & candidate
 // Helper Function _addLine()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#addLine:
-..class:Class.ArgumentParser
-..summary:Adds a line of text to the help output of the @Class.ArgumentParser@ in the block of
-@Class.ArgParseOption@s.
-..cat:Miscellaneous
-..signature:addLine(parser, text)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.text:A line of text that will be added to the help output.
-...type:Shortcut.CharString
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#addLine
+ * @brief Adds a line of text to the help output of the ArgumentParser.
+ *
+ * The line of text will be added to the block of the options.
+ *
+ * @signature void addLine(parser, line);
+ *
+ * @param[in,out] parser The ArgumentParser to add the line to.
+ * @param[in]     line   The line of text to add, @link StringConcept @endlink of <tt>char</tt>.
+ */
 
 template <typename TString>
 inline void addLine(ArgumentParser & me, TString const & line)
@@ -110,30 +106,28 @@ inline void addLine(ArgumentParser & me, TString const & line)
 // Function addSection()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#addSection:
-..class:Class.ArgumentParser
-..summary:Begins a new section of @Class.ArgParseOption@ the help output of
-the @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:addSection(parser, text)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.text:A section header that will be added to the help output.
-...type:Shortcut.CharString
-..include:seqan/arg_parse.h
-..example.code:
-ArgumentParser parser;
-
-[...] // init parser
-
-addSection(parser, "In-/Output-Options");
-addOption("i", ... );
-addOption("o", ... );
-
-addSection(parser, "Other Options");
-addOption("x", ... );
-*/
+/*!
+ * @fn ArgumentParser#addSection
+ * @brief Begins a new section of the option block of the ArgumentParser help output.
+ *
+ * @signature void addSection(parser, title);
+ *
+ * @param[in,out] parser The ArgumentParser to add the line to.
+ * @param[in]     title  The title to add, @link StringConcept @endlink of <tt>char</tt>.
+ *
+ * @code{.cpp}
+ * ArgumentParser parser;
+ *
+ * [...] // init parser
+ *
+ * addSection(parser, "In-/Output-Options");
+ * addOption("i", ... );
+ * addOption("o", ... );
+ *
+ * addSection(parser, "Other Options");
+ * addOption("x", ... );
+ * @endcode
+ */
 
 template <typename TString>
 inline void addSection(ArgumentParser & me, TString const & line)
@@ -146,17 +140,15 @@ inline void addSection(ArgumentParser & me, TString const & line)
 // Function addUsageLine()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#addUsageLine:
-..class:Class.ArgumentParser
-..summary:Adds a line of text to the usage output of the @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:addUsageLine(parser, text)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.text:A text line that will be added to the usage output.
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#addUseLine
+ * @brief Adds a line of text to the usage output of the ArgumentParser.
+ *
+ * @signature void addUsageLine(parser, line);
+ *
+ * @param[in,out] parser The ArgumentParser to add the line to.
+ * @param[in]     line   The line to add, a <tt>std::string</tt>.
+ */
 
 inline void addUsageLine(ArgumentParser & me, std::string const & line)
 {
@@ -183,18 +175,15 @@ inline void _addUsage(ToolDoc & toolDoc, ArgumentParser const & me)
 // Function addDescription()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#addDescription
-..class:Class.ArgumentParser
-..summary:Appends a description paragraph to the @Class.ArgumentParser@ documentation.
-..cat:Miscellaneous
-..signature:addDescription(parser, text)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.text:The description paragraph.
-..returns:$void$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#addDescription
+ * @brief Appends a description paragraph to the ArgumentParser documentation.
+ *
+ * @signature void addDescription(parser, description);
+ *
+ * @param[in,out] parser      The ArgumentParser to add the line to.
+ * @param[in]     description The description text, a <tt>std::string</tt>.
+ */
 
 inline void addDescription(ArgumentParser & me, std::string const & description)
 {
@@ -205,18 +194,15 @@ inline void addDescription(ArgumentParser & me, std::string const & description)
 // Function setAppName()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#setAppName
-..class:Class.ArgumentParser
-..summary:Sets application name of @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:setAppName(parser, appName)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.appName:The name of the application.
-..returns:$void$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#setAppName
+ * @brief Sets application name of ArgumentParser.
+ *
+ * @signature void setAppName(parser, name);
+ *
+ * @param[in,out] parser The ArgumentParser to set the name of.
+ * @param[in]     name   The application name, <tt>std::string</tt>.
+ */
 
 inline void setAppName(ArgumentParser & me, std::string const & name)
 {
@@ -227,18 +213,15 @@ inline void setAppName(ArgumentParser & me, std::string const & name)
 // Function setShortDescription()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#setShortDescription
-..class:Class.ArgumentParser
-..summary:Sets short description of the @Class.ArgumentParser@ object.
-..cat:Miscellaneous
-..signature:setShortDescription(parser, text)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.text:The short description text.
-..returns:$void$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#setShortDescription
+ * @brief Sets shortDescription of ArgumentParser.
+ *
+ * @signature void setShortDescription(parser, desc);
+ *
+ * @param[in,out] parser The ArgumentParser to set the short description of.
+ * @param[in]     desc   The short description, <tt>std::string</tt>.
+ */
 
 inline void setShortDescription(ArgumentParser & me, std::string const & description)
 {
@@ -249,17 +232,16 @@ inline void setShortDescription(ArgumentParser & me, std::string const & descrip
 // Function getShortDescription()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#getShortDescription
-..class:Class.ArgumentParser
-..summary:Gets short description of @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:getShortDescription(parser)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..returns:The short description of the @Class.ArgumentParser@ object.
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#getShortDescription
+ * @brief Returns the short description.
+ *
+ * @signature CharString getShortDescription(parser);
+ *
+ * @param[in,out] parser The ArgumentParser to get short description for.
+ *
+ * @return CharString A @link CharString @endlink with the short description.
+ */
 
 inline CharString getShortDescription(ArgumentParser const & me)
 {
@@ -270,65 +252,176 @@ inline CharString getShortDescription(ArgumentParser const & me)
 // Function setVersion()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#setVersion
-..class:Class.ArgumentParser
-..summary:Sets version string of @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:setVersion(parser, versionString)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.versionString:The version string to set.
-..returns:$void$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#setVersion
+ * @brief Sets version of ArgumentParser.
+ *
+ * @signature void setVersion(parser, version);
+ *
+ * @param[in,out] parser  The ArgumentParser to set the version of.
+ * @param[in]     version The version string to set, <tt>std::string</tt>.
+ */
 
 inline void setVersion(ArgumentParser & me, std::string const & versionString)
 {
     setVersion(me._toolDoc, versionString);
     if (!hasOption(me, "version"))
-        addOption(me, ArgParseOption("", "version", "Display version information"));
+        addOption(me, ArgParseOption("", "version", "Display version information."));
 }
 
 // --------------------------------------------------------------------------
 // Function getVersion()
 // --------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#getVersion
-..class:Class.ArgumentParser
-..cat:Miscellaneous
-..summary:Get version string from @Class.ArgumentParser@ object.
-..signature:getVersion(parser)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..returns:Date string.
-...type:Shortcut.CharString
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#getVersion
+ * @brief Returns the version string.
+ *
+ * @signature TCharStringRef getVersion(parser);
+ *
+ * @param[in,out] parser The ArgumentParser to get the version string from.
+ *
+ * @return TCharString A const-ref to a @link CharString @endlink with the version string.
+ */
 
 inline CharString const & getVersion(ArgumentParser const & me)
 {
     return getVersion(me._toolDoc);
 }
 
+// ----------------------------------------------------------------------------
+// Function setShortCopyright()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ArgumentParser#setShortCopyright
+ * @brief Sets short copyright of ArgumentParser.
+ *
+ * @signature void setShortCopyright(parser, short copyright);
+ *
+ * @param[in,out] parser  The ArgumentParser to set the short copyright of.
+ * @param[in]     short copyright The short copyright string to set, <tt>std::string</tt>.
+ */
+
+inline void setShortCopyright(ArgumentParser & me, CharString const & shortCopyrightString)
+{
+    setShortCopyright(me._toolDoc, shortCopyrightString);
+}
+
+// --------------------------------------------------------------------------
+// Function getShortCopyright()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ArgumentParser#getShortCopyright
+ * @brief Returns the short copyright string.
+ *
+ * @signature TCharStringRef getShortCopyright(parser);
+ *
+ * @param[in,out] parser The ArgumentParser to get the short copyright string from.
+ *
+ * @return TCharString A const-ref to a @link CharString @endlink with the short copyright string.
+ */
+
+inline CharString const & getShortCopyright(ArgumentParser const & me)
+{
+    return getShortCopyright(me._toolDoc);
+}
+
+// ----------------------------------------------------------------------------
+// Function setLongCopyright()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ArgumentParser#setLongCopyright
+ * @brief Sets long copyright of ArgumentParser.
+ *
+ * @signature void setLongCopyright(parser, long copyright);
+ *
+ * @param[in,out] parser  The ArgumentParser to set the long copyright of.
+ * @param[in]     long copyright The long copyright string to set, <tt>std::string</tt>.
+ */
+
+inline void setLongCopyright(ArgumentParser & me, CharString const & longCopyrightString)
+{
+    setLongCopyright(me._toolDoc, longCopyrightString);
+    if (!hasOption(me, "copyright"))
+        addOption(me, ArgParseOption("", "copyright", "Display long copyright information."));
+}
+
+// --------------------------------------------------------------------------
+// Function getLongCopyright()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ArgumentParser#getLongCopyright
+ * @brief Returns the long copyright string.
+ *
+ * @signature TCharStringRef getLongCopyright(parser);
+ *
+ * @param[in,out] parser The ArgumentParser to get the long copyright string from.
+ *
+ * @return TCharString A const-ref to a @link CharString @endlink with the long copyright string.
+ */
+
+inline CharString const & getLongCopyright(ArgumentParser const & me)
+{
+    return getLongCopyright(me._toolDoc);
+}
+
+
+// ----------------------------------------------------------------------------
+// Function setCitation()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ArgumentParser#setCitation
+ * @brief Sets citation of ArgumentParser.
+ *
+ * @signature void setCitation(parser, citation);
+ *
+ * @param[in,out] parser  The ArgumentParser to set the citation of.
+ * @param[in]     citation The citation string to set, <tt>std::string</tt>.
+ */
+
+inline void setCitation(ArgumentParser & me, CharString const & citationString)
+{
+    setCitation(me._toolDoc, citationString);
+}
+
+// --------------------------------------------------------------------------
+// Function getCitation()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ArgumentParser#getCitation
+ * @brief Returns the citation string.
+ *
+ * @signature TCharStringRef getCitation(parser);
+ *
+ * @param[in,out] parser The ArgumentParser to get the citation string from.
+ *
+ * @return TCharString A const-ref to a @link CharString @endlink with the citation string.
+ */
+
+inline CharString const & getCitation(ArgumentParser const & me)
+{
+    return getCitation(me._toolDoc);
+}
+
 // --------------------------------------------------------------------------
 // Function setCategory()
 // --------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#setCategory
-..class:Class.ArgumentParser
-..summary:Set tool category for @Class.ArgumentParser@ object.
-..cat:Miscellaneous
-..signature:setCategory(parser, category)
-..param.parser:The @Class.ArgumentParser@ object to set the category.
-...type:Class.ArgumentParser
-..param.category:Category to set.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#setCategory
+ * @brief Sets category of ArgumentParser.
+ *
+ * @signature void setCategory(parser, category);
+ *
+ * @param[in,out] parser  The ArgumentParser to set the category of.
+ * @param[in]     category The category to set, <tt>std::string</tt>.
+ */
 
 inline void setCategory(ArgumentParser & parser, CharString const & category)
 {
@@ -339,18 +432,16 @@ inline void setCategory(ArgumentParser & parser, CharString const & category)
 // Function getCategory()
 // --------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#getCategory
-..class:Class.ArgumentParser
-..summary:Get tool category of @Class.ArgumentParser@ object.
-..cat:Miscellaneous
-..signature:getCategory(parser)
-..param.parser:The @Class.ArgumentParser@ object to get the tool category of.
-...type:Class.ArgumentParser
-..returns:Tool category of the @Class.ArgumentParser@ object.
-...type:Shortcut.CharString
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#getCategory
+ * @brief Returns the category.
+ *
+ * @signature TCharStringRef getCategory(parser);
+ *
+ * @param[in,out] parser The ArgumentParser to get the category from.
+ *
+ * @return TCharString A const-ref to a @link CharString @endlink with the category.
+ */
 
 inline CharString const & getCategory(ArgumentParser const & parser)
 {
@@ -361,18 +452,15 @@ inline CharString const & getCategory(ArgumentParser const & parser)
 // Function setDate()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#setDate
-..class:Class.ArgumentParser
-..summary:Sets date string of @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:setDate(parser, date)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.date:The date string.
-..returns:$void$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#setDate
+ * @brief Sets date string of ArgumentParser.
+ *
+ * @signature void setDate(parser, date);
+ *
+ * @param[in,out] parser The ArgumentParser to set the date string of.
+ * @param[in]     date   The date string to set, <tt>std::string</tt>.
+ */
 
 inline void setDate(ArgumentParser & me, std::string const & date)
 {
@@ -383,19 +471,15 @@ inline void setDate(ArgumentParser & me, std::string const & date)
 // Function addTextSection()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#addTextSection
-..class:Class.ArgumentParser
-..summary:Adds a text section to the @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:addTextSection(parser, title)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.title:The section title.
-..returns:$void$
-..remarks:This will result in an additional section heading to be printed.
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#addTextSection
+ * @brief Add a text section to the ArgumentParser.
+ *
+ * @signature void addTextSection(parser, title);
+ *
+ * @param[in,out] parser The ArgumentParser to add the text section title to.
+ * @param[in]     title  The section title to add, <tt>std::string</tt>.
+ */
 
 inline void addTextSection(ArgumentParser & me, std::string const & title)
 {
@@ -406,19 +490,15 @@ inline void addTextSection(ArgumentParser & me, std::string const & title)
 // Function addTextSubSection()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#addTextSubSection
-..class:Class.ArgumentParser
-..summary:Adds a text subsection to the @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:addTextSubSection(parser, title)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.title:The subsection title.
-..returns:$void$
-..remarks:This will result in an additional subsection heading to be printed.
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#addTextSubSection
+ * @brief Add a text sub section to the ArgumentParser.
+ *
+ * @signature void addTextSubSection(parser, title);
+ *
+ * @param[in,out] parser The ArgumentParser add the subsection title to of.
+ * @param[in]     title  The sub section title to add, <tt>std::string</tt>.
+ */
 
 inline void addTextSubSection(ArgumentParser & me, std::string const & title)
 {
@@ -429,18 +509,15 @@ inline void addTextSubSection(ArgumentParser & me, std::string const & title)
 // Function addText()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#addText
-..class:Class.ArgumentParser
-..summary:Appends a text paragraph to the @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:addText(parser, text)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.text:The content of the text.
-..returns:$void$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#addText
+ * @brief Add text to an ArgumentParser.
+ *
+ * @signature void addText(parser, text);
+ *
+ * @param[in,out] parser ArgumentParser to add text to.
+ * @param[in]     text   The <tt>std::string</tt> to add to the parser.
+ */
 
 inline void addText(ArgumentParser & me, std::string const & text)
 {
@@ -451,21 +528,16 @@ inline void addText(ArgumentParser & me, std::string const & text)
 // Function addListItem()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#addListItem
-..class:Class.ArgumentParser
-..summary:Appends a list item to the @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:addListItem(parser, item, description)
-..description:
-This method adds a list item to the parser's output.
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.item:The item text.
-..param.description:The description text.
-..returns:$void$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#addListItem
+ * @brief Appends a list item to the ArgumentParser
+ *
+ * @signature void addListItem(parser, item, description);
+ *
+ * @param[in,out] parser      The ArgumentParser to add the list item to.
+ * @param[in]     item        The item to add, <tt>std::string</tt>.
+ * @param[in]     description The item to add, <tt>std::string</tt>.
+ */
 
 inline void addListItem(ArgumentParser & me, std::string const & item, std::string const & description)
 {
@@ -476,17 +548,15 @@ inline void addListItem(ArgumentParser & me, std::string const & item, std::stri
 // Function printShortHelp()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#printShortHelp
-..class:Class.ArgumentParser
-..summary:Prints a short help message for the parser to a stream
-..cat:Miscellaneous
-..signature:printShortHelp(parser[, stream])
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.stream:Target stream (e.g. $std::cerr$).
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#printShortHelp
+ * @brief Prints a short help message for the parser to a stream.
+ *
+ * @signature void printShortHelp(parser, out);
+ *
+ * @param[in,out] parser The ArgumentParser to print help for.
+ * @param[in,out] out    The <tt>std::ostream</tt> to print help to.
+ */
 
 inline void printShortHelp(ArgumentParser const & me, std::ostream & stream)
 {
@@ -512,22 +582,24 @@ inline void printShortHelp(ArgumentParser const & me)
 // Function printVersion()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#printVersion
-..class:Class.ArgumentParser
-..summary:Prints the version information of the parser to a stream.
-..cat:Miscellaneous
-..signature:printVersion(parser[, stream])
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.stream:Target std::ostream (e.g. $std::cerr$).
-...default: $std::cerr$
-..include:seqan/arg_parse.h
-*/
+/*!
+ * @fn ArgumentParser#printVersion
+ * @brief Prints the version information of the parser to a stream.
+ *
+ * @signature void printVersion(parser, stream);
+ *
+ * @param[in,out] parser The ArgumenParser to print for.
+ * @param[in,out] stream The <tt>std::ostream</tt> to print to.
+ */
 
 inline void printVersion(ArgumentParser const & me, std::ostream & stream)
 {
-    stream << getAppName(me) << " version " << getVersion(me) << std::endl;
+    stream << getAppName(me) << " version: " << getVersion(me) << std::endl;
+    stream << "SeqAn version: " << SEQAN_VERSION_MAJOR << '.' <<  SEQAN_VERSION_MINOR << '.'
+           << SEQAN_VERSION_PATCH;
+    if (SEQAN_VERSION_PRE_RELEASE != 0)
+        stream << "-pre" << SEQAN_VERSION_PRE_RELEASE;
+    stream << "\n";
 }
 
 inline void printVersion(ArgumentParser const & me)
@@ -536,9 +608,64 @@ inline void printVersion(ArgumentParser const & me)
 }
 
 // ----------------------------------------------------------------------------
-// Function _addNumericalRestriction()
+// Function printLongCopyright()
 // ----------------------------------------------------------------------------
 
+/*!
+ * @fn ArgumentParser#printLongCopyright
+ * @brief Prints the long copyright information of the parser to a stream.
+ *
+ * @signature void printLongCopyright(parser, stream);
+ *
+ * @param[in,out] parser The ArgumenParser to print for.
+ * @param[in,out] stream The <tt>std::ostream</tt> to print to.
+ */
+
+inline void printLongCopyright(ArgumentParser const & me, std::ostream & stream)
+{
+    stream << "=============================================================================" << std::endl
+           << "Copyright information for " << getAppName(me) << ":" << std::endl
+           << "-----------------------------------------------------------------------------" << std::endl
+           << me._toolDoc._longCopyright << std::endl << std::endl
+           << "=============================================================================" << std::endl
+           << "This program contains SeqAn code licensed under the following terms:" << std::endl
+           << "-----------------------------------------------------------------------------" << std::endl
+           << " Copyright (c) 2006-2015, Knut Reinert, FU Berlin" << std::endl
+           << " All rights reserved." << std::endl
+           << "" << std::endl
+           << " Redistribution and use in source and binary forms, with or without" << std::endl
+           << " modification, are permitted provided that the following conditions are met:" << std::endl
+           << "" << std::endl
+           << "     * Redistributions of source code must retain the above copyright" << std::endl
+           << "       notice, this list of conditions and the following disclaimer." << std::endl
+           << "     * Redistributions in binary form must reproduce the above copyright" << std::endl
+           << "       notice, this list of conditions and the following disclaimer in the" << std::endl
+           << "       documentation and/or other materials provided with the distribution." << std::endl
+           << "     * Neither the name of Knut Reinert or the FU Berlin nor the names of" << std::endl
+           << "       its contributors may be used to endorse or promote products derived" << std::endl
+           << "       from this software without specific prior written permission." << std::endl
+           << "" << std::endl
+           << " THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"" << std::endl
+           << " AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE" << std::endl
+           << " IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE" << std::endl
+           << " ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE" << std::endl
+           << " FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL" << std::endl
+           << " DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR" << std::endl
+           << " SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER" << std::endl
+           << " CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT" << std::endl
+           << " LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY" << std::endl
+           << " OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH" << std::endl
+           << " DAMAGE." << std::endl;
+}
+
+inline void printLongCopyright(ArgumentParser const & me)
+{
+    printLongCopyright(me, std::cerr);
+}
+
+// ----------------------------------------------------------------------------
+// Function _addNumericalRestriction()
+// ----------------------------------------------------------------------------
 
 inline void _addNumericalRestriction(std::string & text, ArgParseOption const & opt)
 {
@@ -632,21 +759,24 @@ inline void _addValidValuesRestrictions(std::string & text, ArgParseOption const
 // Function printHelp()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.ArgumentParser#printHelp
-..class:Class.ArgumentParser
-..summary:Prints the complete help message for the parser to a stream.
-..cat:Miscellaneous
-..signature:printHelp(parser[, stream][, format])
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.stream:Target std::ostream (e.g. $std::cerr$).
-...default: $std::cerr$
-..param.format:Format to print, one of "html", "man", "txt".
-..include:seqan/arg_parse.h
-*/
-
-inline void printHelp(ArgumentParser const & me, std::ostream & stream, CharString const & format)
+// TODO(holtgrew): Parameter order.
+
+/*!
+ * @fn ArgumentParser#printHelp
+ * @brief Prints the help message for the parser.
+ *
+ * @signature void printHelp(parser, out, format, showAdvancedOptions);
+ *
+ * @param[in,out] parser                The ArgumentParser print the help for.
+ * @param[out]    out                   The output stream to print to (<tt>std::ostream</tt>).
+ * @param[in]     format                The format to print, one of "html", "man", and "txt".
+ * @param[in]     showAdvancedOptions   Also show advanced options to user (default = false).
+ */
+
+inline void printHelp(ArgumentParser const & me,
+                      std::ostream & stream,
+                      CharString const & format,
+                      bool const showAdvancedOptions)
 {
     ToolDoc toolDoc(me._toolDoc);
     clearEntries(toolDoc);  // We will append me._toolDoc later.
@@ -670,11 +800,22 @@ inline void printHelp(ArgumentParser const & me, std::ostream & stream, CharStri
                 continue;  // Skip empty lines.
 
             // Is command line parser section, maps to ToolDoc subsection.
-            std::string title = opt._helpText;
-            append(title, ":");
-            addSubSection(toolDoc, title);
+            for (unsigned j = i + 1; j < length(me.optionMap); ++j)
+            {
+                ArgParseOption const & nextopt = me.optionMap[j];
+                if (empty(nextopt.shortName) && empty(nextopt.longName))
+                    break;
+                // has visible children
+                if (!isHidden(nextopt) && (!isAdvanced(nextopt) || showAdvancedOptions))
+                {
+                    std::string title = opt._helpText;
+                    append(title, ":");
+                    addSubSection(toolDoc, title);
+                    break;
+                }
+            }
         }
-        else if (!isHidden(opt))
+        else if (!isHidden(opt) && (!isAdvanced(opt) || showAdvancedOptions))
         {
             // Build list item term.
             std::string term;
@@ -732,16 +873,21 @@ inline void printHelp(ArgumentParser const & me, std::ostream & stream, CharStri
     print(stream, toolDoc, format);
 }
 
+inline void printHelp(ArgumentParser const & me, std::ostream & stream, CharString const & format)
+{
+    printHelp(me, stream, format, false);
+}
+
 inline void printHelp(ArgumentParser const & me, std::ostream & stream)
 {
-    printHelp(me, stream, "txt");
+    printHelp(me, stream, "txt", false);
 }
 
 inline void printHelp(ArgumentParser const & me)
 {
-    printHelp(me, std::cerr, "txt");
+    printHelp(me, std::cerr, "txt", false);
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_
diff --git a/seqan/arg_parse/arg_parse_exceptions.h b/seqan/arg_parse/arg_parse_exceptions.h
index a6cde3d..ee7dde7 100644
--- a/seqan/arg_parse/arg_parse_exceptions.h
+++ b/seqan/arg_parse/arg_parse_exceptions.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                           arg_parse_exceptions.h
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_
+#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_
 
 namespace seqan {
 
@@ -45,30 +45,13 @@ namespace seqan {
 // Class ParseError
 // ----------------------------------------------------------------------------
 
-/*
-.Internal.Class.ParseError
-..cat:Miscellaneous
-..summary:General ParseError.
-*/
-
-class ParseError : public RuntimeError
-{
-public:
-    ParseError(std::string const & option) :
-        RuntimeError(option)
-    {}
-};
+// Defined in include/seqan/stream/tokenization.h
+struct ParseError;
 
 // ----------------------------------------------------------------------------
 // Class InvalidOption
 // ----------------------------------------------------------------------------
 
-/*
-.Internal.Class.InvalidOption
-..cat:Miscellaneous
-..summary:Thrown if an unknown option was set on the command line.
-*/
-
 class InvalidOption : public ParseError
 {
 public:
@@ -81,13 +64,6 @@ class InvalidOption : public ParseError
 // Class MissingArgument
 // ----------------------------------------------------------------------------
 
-/*
-.Internal.Class.MissingArgument
-..cat:Miscellaneous
-..summary:Thrown if an option was set on the command line but without giving the
-required arguments for this option.
-*/
-
 class MissingArgument : public ParseError
 {
 public:
@@ -100,13 +76,6 @@ class MissingArgument : public ParseError
 // Class NotEnoughArguments
 // ----------------------------------------------------------------------------
 
-/*
-.Internal.Class.NotEnoughArguments
-..cat:Miscellaneous
-..summary:Thrown if an option was set on the command line but not enough arguments for
-this option were provided.
-*/
-
 class NotEnoughArguments : public ParseError
 {
 public:
@@ -117,4 +86,4 @@ class NotEnoughArguments : public ParseError
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_
diff --git a/seqan/arg_parse/arg_parse_option.h b/seqan/arg_parse/arg_parse_option.h
index 5329cb4..7cfd4a3 100644
--- a/seqan/arg_parse/arg_parse_option.h
+++ b/seqan/arg_parse/arg_parse_option.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_
+#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_
 
 #include <string>
 #include <vector>
@@ -58,33 +58,21 @@ namespace seqan {
  * object.
  */
 
-/**
-.Class.ArgParseOption
-..base:Class.ArgParseArgument
-..cat:Miscellaneous
-..summary:Stores information for a specific command line option.
-..signature:ArgParseOption
-..remarks:A @Class.ArgParseOption@ object can be added to a @Class.ArgumentParser@ via @Function.ArgumentParser#addOption@.
-..include:seqan/arg_parse.h
-..see:Class.ArgParseArgument
-..see:Class.ArgumentParser
-*/
-
 /*!
  * @fn ArgParseOption::ArgParseOption
  * @brief Constructor.
  *
  * @signature ArgParseOption::ArgParseOption(shortName, longName, helpText, argumentType[, argumentLabel[, isList[, numValues]]]);
  *
- * @param shortName     The short name of the argument.
- * @param longName      The long name of the argument (<tt>std::string</tt>).
- * @param helpText      The text to display as help (<tt>std::string</tt>).
- * @param argumentType  The type of the argument (@link ArgParseArgument::ArgumentType @endlink).
- * @param argumentLabel The label for the value to use in the help display, e.g. 'INT' in '--value INT'
- *                      (<tt>std::string</tt>).
- * @param isList        Flag for whether this option can be given multiple times (<tt>bool</tt>, <tt>true</tt> for
- *                      allowing multiple values).
- * @param numValues     Number of command line arguments that each option should bind (<tt>unsigned</tt>).
+ * @param[in] shortName     The short name of the argument.
+ * @param[in] longName      The long name of the argument (<tt>std::string</tt>).
+ * @param[in] helpText      The text to display as help (<tt>std::string</tt>).
+ * @param[in] argumentType  The type of the argument (@link ArgParseArgument::ArgumentType @endlink).
+ * @param[in] argumentLabel The label for the value to use in the help display, e.g. 'INT' in '--value INT'
+ *                          (<tt>std::string</tt>).
+ * @param[in] isList        Flag for whether this option can be given multiple times (<tt>bool</tt>, <tt>true</tt> for
+ *                          allowing multiple values).
+ * @param[in] numValues     Number of command line arguments that each option should bind (<tt>unsigned</tt>).
  *
  * @section Short and Long Option Names
  *
@@ -101,27 +89,6 @@ namespace seqan {
  * </ul>
  */
 
-/**
-.Memfunc.ArgParseOption#ArgParseOption
-..class:Class.ArgParseOption
-..summary:Constructor
-..signature:ArgParseOption(shortName, longName, helpText, argumentType[, argumentLabel[, isList]])
-..param.shortName:A std::string containing the short-name option identifier (e.g. $"h"$ for the $-h/--help$ option).
-Although not suggested the short-name can contain more than 1 character.
-...remarks:Note that the leading "-" is not passed.
-..param.longName:A std::string containing the long-name option identifier (e.g. $"help"$ for the $-h/--help$ option).
-...remarks:Note that the leading "--" is not passed.
-..param.helpText:A std::string containing the help text associated with this option.
-..param.argumentType:A $ArgParseArgument::ArgumentType$ for the option (e.g., an integer argument).
-...type:Class.ArgParseArgument
-..param.argumentLabel:The label to use for the argument in the help text, e.g. $"NUMBER"$ for an integer. Optional.
-...default:$""$
-...type:nolink:$char const *$
-..param.isList:Whether or not the argument allows multiple values.
-...default:$false$
-...type:nolink:$bool$
-*/
-
 class ArgParseOption :
     public ArgParseArgument
 {
@@ -141,6 +108,8 @@ class ArgParseOption :
     bool                _isRequired;  // true if this ArgParseOption must be set
     bool                _isHidden;    // true if this ArgParseOption should not be
                                       // shown on the command line
+    bool                _isAdvanced;  // true if this ArgParseOption should only
+                                      // be shown in the full help
 
     // ----------------------------------------------------------------------------
     // Constructors
@@ -157,7 +126,8 @@ class ArgParseOption :
         longName(_longName),
         _isFlag(false),
         _isRequired(false),
-        _isHidden(false)
+        _isHidden(false),
+        _isAdvanced(false)
     {
         _helpText = _help;
     }
@@ -170,7 +140,8 @@ class ArgParseOption :
         longName(_longName),
         _isFlag(true),
         _isRequired(false),
-        _isHidden(false)
+        _isHidden(false),
+        _isAdvanced(false)
     {
         defaultValue.push_back("false");
         setValidValues(*this, "true false");
@@ -199,25 +170,13 @@ inline bool isStringArgument(ArgParseOption const & me)
  *
  * @signature bool isBooleanOption(option);
  *
- * @param option The ArgParseOption object to query.
+ * @param[in] option The ArgParseOption object to query.
  *
  * @return bool <tt>true</tt> if <tt>option</tt> is a switch and <tt>false</tt> otherwise.
  *
  * Flags are given without arguments, e.g. the <tt>-l</tt> flag in the Unix <tt>ls</tt> command.
  */
 
-/**
-.Function.ArgParseOption#isBooleanOption
-..class:Class.ArgParseOption
-..summary:Returns whether option is a switch.
-..cat:Miscellaneous
-..signature:isBooleanOption(option)
-..param.option:The @Class.ArgParseOption@ object.
-...type:Class.ArgParseOption
-..returns:$true$ if the option is a switch.
-..include:seqan/arg_parse.h
-*/
-
 inline bool isBooleanOption(ArgParseOption const & me)
 {
     return me._isFlag;
@@ -234,25 +193,13 @@ inline bool isBooleanOption(ArgParseOption const & me)
  *
  * @signature bool isHidden(option);
  *
- * @param option The ArgParseOption object to query.
+ * @param[in] option The ArgParseOption object to query.
  *
  * @return bool <tt>true</tt> if it is hidden, <tt>false</tt> otherwise.
  *
  * By default, options are not hidden.
  */
 
-/**
-.Function.ArgParseOption#isHidden
-..class:Class.ArgParseOption
-..summary:Returns whether option is hidden on the help screen. Default is false.
-..cat:Miscellaneous
-..signature:isHidden(option)
-..param.option:The @Class.ArgParseOption@ object.
-...type:Class.ArgParseOption
-..returns:$true$ if the option is hidden on the help screen.
-..include:seqan/arg_parse.h
-*/
-
 inline bool isHidden(ArgParseOption const & me)
 {
     return me._isHidden;
@@ -269,28 +216,58 @@ inline bool isHidden(ArgParseOption const & me)
  *
  * @signature void hideOption(option[, hide]);
  *
- * @param option The ArgParseOption object to set the hidden flag of.
- * @param hide   <tt>bool</tt> that indicates whether to hide the flag (default: <tt>true</tt>)
+ * @param[in,out] option The ArgParseOption object to set the hidden flag of.
+ * @param[in]     hide   <tt>bool</tt> that indicates whether to hide the flag (default: <tt>true</tt>)
  */
 
-/**
-.Function.ArgParseOption#hideOption
-..class:Class.ArgParseOption
-..summary:Hides the ArgParseOption from the help screen.
-..cat:Miscellaneous
-..signature:hideOption(option [, hide])
-..param.option:The @Class.ArgParseOption@ object.
-...type:Class.ArgParseOption
-..param.hide:The new visibility of the option. Default is false.
-...type:nolink:bool
-..include:seqan/arg_parse.h
-*/
-
 inline void hideOption(ArgParseOption & me, bool hide = true)
 {
     me._isHidden = hide;
 }
 
+// ----------------------------------------------------------------------------
+// Function isHidden()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ArgParseOption#isAdvanced
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Return whether an option is only shown in the full help screen.
+ *
+ * @signature bool isAdvanced(option);
+ *
+ * @param[in] option The ArgParseOption object to query.
+ *
+ * @return bool <tt>true</tt> if it is hidden, <tt>false</tt> otherwise.
+ *
+ * By default, options are not marked as advanced.
+ */
+
+inline bool isAdvanced(ArgParseOption const & me)
+{
+    return me._isAdvanced;
+}
+
+// ----------------------------------------------------------------------------
+// Function hideOption()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ArgParseOption#setAdvanced
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Shows the ArgParseOption only on the full help screen.
+ *
+ * @signature void setAdvanced(option[, advanced]);
+ *
+ * @param[in,out] option The ArgParseOption object to set the advanced flag of.
+ * @param[in]     advanced   <tt>bool</tt> that indicates whether to hide the flag (default: <tt>true</tt>)
+ */
+
+inline void setAdvanced(ArgParseOption & me, bool advanced = true)
+{
+    me._isAdvanced = advanced;
+}
+
 // ----------------------------------------------------------------------------
 // Function isRequired()
 // ----------------------------------------------------------------------------
@@ -302,25 +279,13 @@ inline void hideOption(ArgParseOption & me, bool hide = true)
  *
  * @signature bool isRequired(option);
  *
- * @param option The ArgParseOption object to query.
- * 
+ * @param[in] option The ArgParseOption object to query.
+ *
  * @return bool <tt>true</tt> if the option is mandatory and <tt>false</tt> if it not.
  *
  * By default, options are not mandatory.
  */
 
-/**
-.Function.ArgParseOption#isRequired
-..class:Class.ArgParseOption
-..summary:Returns whether the option is mandatory.
-..cat:Miscellaneous
-..signature:isRequired(option)
-..param.option:The @Class.ArgParseOption@ object.
-...type:Class.ArgParseOption
-..returns:$true$ if the option is mandatory.
-..include:seqan/arg_parse.h
-*/
-
 inline bool isRequired(ArgParseOption const & me)
 {
     return me._isRequired;
@@ -337,24 +302,12 @@ inline bool isRequired(ArgParseOption const & me)
  *
  * @signature void setDefaultValue(option, v);
  *
- * @param option The ArgParseOption to set the default value for.
- * @param v      The value to set, (any type that can be streamed into an <tt>std::stringstream</tt>).
+ * @param[in,out] option The ArgParseOption to set the default value for.
+ * @param[in]     v      The value to set, (any type that can be streamed into an <tt>std::stringstream</tt>).
  */
 
 // TODO(holtgrew): Deprecate in favour of string-only variant?
 
-/**
-.Function.ArgParseOption#setDefaultValue
-..summary:Sets the default value for the given option.
-..cat:Miscellaneous
-..remarks:Note that this overwrites any previously given default values.
-..signature:setDefaultValue(option, value)
-..param.option:The @Class.ArgParseOption@ object.
-...type:Class.ArgParseOption
-..param.value:The new default value.
-..include:seqan/arg_parse.h
-*/
-
 template <typename TValue>
 inline void setDefaultValue(ArgParseOption & me, const TValue & value)
 {
@@ -389,27 +342,15 @@ inline void setDefaultValue(ArgParseOption & me, const TValue & value)
  *
  * @signature void setDefaultValue(option, v);
  *
- * @param option The ArgParseOption to appen the default value for.
- * @param v      The value to append, (any type that can be streamed into an <tt>std::stringstream</tt>).
- * 
+ * @param[in,out] option The ArgParseOption to appen the default value for.
+ * @param[in]     v      The value to append, (any type that can be streamed into an <tt>std::stringstream</tt>).
+ *
  * @section Remarks
  *
  * This function does not check any length restrictions for this value.
  */
 
 
-/**
-.Function.ArgParseOption#addDefaultValue
-..summary:Adds/appends a new value to the list of default values.
-..cat:Miscellaneous
-..remarks:Note that this method does not check any length restrictions for this value.
-..signature:addDefaultValue(option, value)
-..param.option:The @Class.ArgParseOption@ object.
-...type:Class.ArgParseOption
-..param.value:The new default value.
-..include:seqan/arg_parse.h
-*/
-
 template <typename TValue>
 inline void addDefaultValue(ArgParseOption & me, const TValue & value)
 {
@@ -441,25 +382,12 @@ inline void addDefaultValue(ArgParseOption & me, const TValue & value)
  *
  * @signature void setRequired(option, required);
  *
- * @param option   The ArgParseOption to modify.
- * @param required Flag whether the option is mandatory (<tt>bool</tt>).
+ * @param[in,out] option   The ArgParseOption to modify.
+ * @param[in]     required Flag whether the option is mandatory (<tt>bool</tt>).
  *
  * By default, options are not mandatory.
  */
 
-/**
-.Function.ArgParseOption#setRequired
-..class:Class.ArgParseOption
-..summary:Sets whether or not the option is mandatory.
-..cat:Miscellaneous
-..signature:setRequired(option, required)
-..param.option:The @Class.ArgParseOption@ object.
-...type:Class.ArgParseOption
-..param.required:The new required value of the option.
-...type:nolink:bool
-..include:seqan/arg_parse.h
-*/
-
 inline void setRequired(ArgParseOption & me, bool required)
 {
     me._isRequired = required;
@@ -476,7 +404,7 @@ inline void setRequired(ArgParseOption & me, bool required)
  *
  * @signature std::string getArgumentLabel(option);
  *
- * @param option The ArgParseOption object to query.
+ * @param[in] option The ArgParseOption object to query.
  *
  * @return std::string The argument label string.
  */
@@ -500,22 +428,11 @@ inline std::string const getArgumentLabel(ArgParseOption const & me)
  *
  * @signature std::string getOptionName(option);
  *
- * @param option The ArgParseOption object to query.
+ * @param[in] option The ArgParseOption object to query.
  *
  * @return std::string The option name string.
  */
 
-/**
- .Function.ArgParseOption#getOptionName
- ..class:Class.ArgParseOption
- ..summary:Returns the name of the @Class.ArgParseOption@ in a well formated way.
- ..cat:Miscellaneous
- ..signature:getOptionName(option)
- ..param.option:The @Class.ArgParseOption@ object.
- ...type:Class.ArgParseOption
- ..include:seqan/arg_parse.h
- ..returns:The name of the option as well formated string (e.g., -h, --help).
- */
 inline std::string getOptionName(ArgParseOption const & me)
 {
     std::stringstream stream;
@@ -542,30 +459,18 @@ inline std::string getOptionName(ArgParseOption const & me)
  *
  * @signature void write(stream, option);
  *
- * @param stream The @link StreamConcept stream @endlink to write to.
- * @param option The ArgParseOption object to write to <tt>stream</tt>.
+ * @param[in,out] stream The @link StreamConcept stream @endlink to write to.
+ * @param[out]    option The ArgParseOption object to write to <tt>stream</tt>.
  */
 
-/**
-.Function.ArgParseOption#write
-..class:Class.ArgParseOption
-..summary:Writes the basic information about the @Class.ArgParseOption@ to the provided stream.
-..cat:Miscellaneous
-..signature:write(stream, option)
-..param.stream:The target stream.
-..param.option:The @Class.ArgParseOption@ object.
-...type:Class.ArgParseOption
-..include:seqan/arg_parse.h
-*/
-
 template <typename TStream>
 inline void write(TStream & target, ArgParseOption const & me)
 {
-    streamPut(target, '\t');
-    streamPut(target, getOptionName(me));
-    streamPut(target, '\t');
-    streamPut(target, '\t');
-    streamPut(target, me._helpText);
+    writeValue(target, '\t');
+    write(target, getOptionName(me));
+    writeValue(target, '\t');
+    writeValue(target, '\t');
+    write(target, me._helpText);
 }
 
 // ----------------------------------------------------------------------------
@@ -577,11 +482,11 @@ inline void write(TStream & target, ArgParseOption const & me)
 template <typename TStream>
 inline TStream & operator<<(TStream & target, ArgParseOption const & source)
 {
-
-    write(target, source);
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
     return target;
 }
 
 } // namespace seqan
 
-#endif // SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_
+#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_
diff --git a/seqan/arg_parse/arg_parse_parse.h b/seqan/arg_parse/arg_parse_parse.h
index af4941c..7ee7780 100644
--- a/seqan/arg_parse/arg_parse_parse.h
+++ b/seqan/arg_parse/arg_parse_parse.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_
+#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_
 
 #include <seqan/arg_parse/arg_parse_option.h>
 #include <seqan/arg_parse/argument_parser.h>
@@ -50,39 +50,24 @@ namespace seqan {
  * @headerfile <seqan/arg_parse.h>
  * @brief Parse command line parameters.
  *
- * @signature TResult parse(parser, argc, argv[, outStream, errStream]]);
+ * @signature TResult parse(parser, argc, argv[, outStream[, errStream]]);
  *
- * @param parser    The ArgumentParser to use for parsing and for storing parse results.
- * @param argc      The number of arguments (<tt>int</tt>).
- * @param argv      The arguments (<tt>const char * argv[]</tt>).
- * @param outStream The <tt>std::ostream</tt> to use for output.
- * @param errStream The <tt>std::ostream</tt> to use for error output.
+ * @param[in,out] parser    The ArgumentParser to use for parsing and for storing parse results.
+ * @param[in]     argc      The number of arguments (<tt>int</tt>).
+ * @param[in]     argv      The arguments (<tt>const char * argv[]</tt>).
+ * @param[in,out] outStream The <tt>std::ostream</tt> to use for output.
+ * @param[in,out] errStream The <tt>std::ostream</tt> to use for error output.
  *
  * @return TResult The parse result, of type @link ArgumentParser::ParseResult @endlink.
  *
  * This function must be called before retrieving any options or arguments from the parser.
  */
 
-/**
-.Function.ArgumentParser#parse
-..summary:Parses the command line.
-..class:Class.ArgumentParser
-..cat:Miscellaneous
-..signature:parse(parser, argc, argv[, outputStream, errorStream])
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.argc:Count of the objects on the command line.
-..param.argv:Array of the different command line arguments ($const char *argv[]$).
-..param.errorStream:A stream where error messages are sent to.
-..remarks:Must be called before retrieving options or arguments.
-..returns:$true$ if all required arguments are set and parseable and neither the help nor version argument is set.
-..include:seqan/arg_parse.h
-*/
-
 // Helper class for parsing command line arguments.
 //
 // Putting things into its a class allows us to structure the parsing in a fine way.
 
+template <typename TChar>
 class ArgumentParserHelper_
 {
 public:
@@ -92,7 +77,7 @@ class ArgumentParserHelper_
     ArgumentParser & parser;
     // The argc and argv from the main() method.
     int argc;
-    const char ** argv;
+    TChar ** argv;
 
     // The parser's state is stored in the following variables.
 
@@ -102,7 +87,7 @@ class ArgumentParserHelper_
     // The index of the current positional argument.
     TArgumentPosition currentArgument;
 
-    ArgumentParserHelper_(ArgumentParser & parser, int argc, const char * argv[])
+    ArgumentParserHelper_(ArgumentParser & parser, int argc, TChar * argv[])
             : parser(parser), argc(argc), argv(argv), seenDashDash(false), currentArgument(0)
     {}
 
@@ -123,7 +108,12 @@ class ArgumentParserHelper_
 
         for (int argi = 1; argi < argc; ++argi)
         {
-            if (seenDashDash || strlen(argv[argi]) == 0 || argv[argi][0] != '-')
+            // after "--" ever arg is treated as argument (not as option), e.g. "rm -rf -- --file-name"
+            // "-" is a treated as argument as for a filename arguments it represents stdin
+            // everything else that begins with "-" is an option
+
+            size_t argLen = strlen(argv[argi]);
+            if (seenDashDash || argLen == 0 || ((argv[argi][0] != '-') || (argLen == 1))) //
                 // Handle as position argument if we have seen "--" or does not start with dash.
                 handleArgument(argv[argi]);
             else if (strcmp(argv[argi], "--") == 0)
@@ -271,16 +261,17 @@ class ArgumentParserHelper_
 };
 
 // Parser driver function.
-inline ArgumentParser::ParseResult parse(ArgumentParser & me,
-                                         int argc,
-                                         const char * argv[],
-                                         std::ostream & outputStream,
-                                         std::ostream & errorStream)
+template <typename TChar>
+ArgumentParser::ParseResult parse(ArgumentParser & me,
+                                  int argc,
+                                  TChar * argv[],
+                                  std::ostream & outputStream,
+                                  std::ostream & errorStream)
 {
     SEQAN_TRY
     {
         // Perform the parsing without any valid value checking on the argument values.
-        ArgumentParserHelper_ parserHelper(me, argc, argv);
+        ArgumentParserHelper_<TChar> parserHelper(me, argc, argv);
         parserHelper.parseArgs();
 
         // Copy the file extensions from the "--${NAME}-file-ext" options to "--${NAME}".
@@ -322,6 +313,11 @@ inline ArgumentParser::ParseResult parse(ArgumentParser & me,
         printVersion(me, outputStream);
         return ArgumentParser::PARSE_VERSION;
     }
+    else if (hasOption(me, "copyright") && isSet(me, "copyright"))
+    {
+        printLongCopyright(me, outputStream);
+        return ArgumentParser::PARSE_COPYRIGHT;
+    }
     else if (hasOption(me, "write-ctd") && isSet(me, "write-ctd"))
     {
         if (writeCTD(me))
@@ -334,14 +330,19 @@ inline ArgumentParser::ParseResult parse(ArgumentParser & me,
         printHelp(me, outputStream);
         return ArgumentParser::PARSE_HELP;
     }
+    else if (isSet(me, "full-help"))
+    {
+        printHelp(me, outputStream, "txt", true);
+        return ArgumentParser::PARSE_HELP;
+    }
     else if (isSet(me, "export-help"))
     {
         std::string format;
         getOptionValue(format, me, "export-help");
-        printHelp(me, outputStream, format);
+        printHelp(me, outputStream, format, true);
         return ArgumentParser::PARSE_EXPORT_HELP;
     }
-    else if (argc == 1 && (me.argumentList.size() > 0 || !_allRequiredSet(me)))
+    else if (argc == 1 && !(_allRequiredSet(me) && _allArgumentsSet(me)))
     {
         // print short help and exit
         printShortHelp(me, errorStream);
@@ -364,13 +365,14 @@ inline ArgumentParser::ParseResult parse(ArgumentParser & me,
     return ArgumentParser::PARSE_ERROR;
 }
 
-inline ArgumentParser::ParseResult parse(ArgumentParser & me,
-                                         int argc,
-                                         const char * argv[])
+template <typename TChar>
+ArgumentParser::ParseResult parse(ArgumentParser & me,
+                                  int argc,
+                                  TChar * argv[])
 {
     return parse(me, argc, argv, std::cout, std::cerr);
 }
 
 } // namespace seqan
 
-#endif // SEQAN_CORE_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_
+#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_
diff --git a/seqan/arg_parse/arg_parse_type_support.h b/seqan/arg_parse/arg_parse_type_support.h
index 771bcdc..e483b9a 100644
--- a/seqan/arg_parse/arg_parse_type_support.h
+++ b/seqan/arg_parse/arg_parse_type_support.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 
 // TODO(aiche): check if parts of the functionality could be merged with lexicalCast in stream module
 
-#ifndef SEQAN_CORE_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_
-#define SEQAN_CORE_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_
+#ifndef SEQAN_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_
+#define SEQAN_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_
 
 #include <sstream>
 #include <string>
@@ -187,4 +187,4 @@ inline bool _convertArgumentValue(TObject & dst, ArgParseArgument const & opt, s
 
 } // namespace seqan
 
-#endif // SEQAN_CORE_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_
+#endif // SEQAN_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_
diff --git a/seqan/arg_parse/argument_parser.h b/seqan/arg_parse/argument_parser.h
index 674fc03..e3342cf 100644
--- a/seqan/arg_parse/argument_parser.h
+++ b/seqan/arg_parse/argument_parser.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,8 +30,8 @@
 //
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_
-#define SEQAN_CORE_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_
+#ifndef SEQAN_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_
+#define SEQAN_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_
 
 #include <seqan/map.h>
 #include <seqan/sequence.h>
@@ -91,7 +91,7 @@ inline ArgParseArgument & getArgument(ArgumentParser & me, unsigned position);
  *
  * The following gives a simple example of how to use the ArgumentParser class.
  *
- * @include demos/arg_parse/argument_parser.cpp
+ * @include demos/dox/arg_parse/argument_parser.cpp
  *
  * @code{.console}
  * $ demo_arg_parse_argument_parser in.fa out.txt --id 0
@@ -114,7 +114,7 @@ inline ArgParseArgument & getArgument(ArgumentParser & me, unsigned position);
  *
  * @signature ArgumentParser::ArgumentParser([appName]);
  *
- * @param appName The name of the application (<tt>std::string</tt>), defaults to <tt>argv[0]</tt>.
+ * @param[in] appName The name of the application (<tt>std::string</tt>), defaults to <tt>argv[0]</tt>.
  */
 
 /*!
@@ -123,73 +123,28 @@ inline ArgParseArgument & getArgument(ArgumentParser & me, unsigned position);
  *
  * @signature enum ArgumentParser::ParseResult;
  *
- * @var ArgumentParser::ParseResult ArgumentParser::PARSE_OK;
+ * @val ArgumentParser::ParseResult ArgumentParser::PARSE_OK;
  * @brief Parsing the program's arguments was successful and no builtin command was triggered.
  *
- * @var ArgumentParser::ParseResult ArgumentParser::PARSE_ERROR;
+ * @val ArgumentParser::ParseResult ArgumentParser::PARSE_ERROR;
  * @brief There were errors parsing the arguments.
  *
- * @var ArgumentParser::ParseResult ArgumentParser::PARSE_HELP;
- * @brief Parsing was successful, built-in <tt>--help</tt> option was used.
+ * @val ArgumentParser::ParseResult ArgumentParser::PARSE_HELP;
+ * @brief Parsing was successful, built-in <tt>--help</tt> or <tt>--full-help</tt> option was used.
  *
- * @var ArgumentParser::ParseResult ArgumentParser::PARSE_VERSION;
+ * @val ArgumentParser::ParseResult ArgumentParser::PARSE_VERSION;
  * @brief Parsing was successful, built-in <tt>--version</tt> option was used.
  *
- * @var ArgumentParser::ParseResult ArgumentParser::PARSE_WRITE_CTD;
+ * @val ArgumentParser::ParseResult ArgumentParser::PARSE_COPYRIGHT;
+ * @brief Parsing was successful, built-in <tt>--copyright</tt> option was used.
+ *
+ * @val ArgumentParser::ParseResult ArgumentParser::PARSE_WRITE_CTD;
  * @brief Parsing was successful, built-in <tt>--write-ctd</tt> option was used.
  *
- * @var ArgumentParser::ParseResult ArgumentParser::PARSE_EXPORT_HELP;
+ * @val ArgumentParser::ParseResult ArgumentParser::PARSE_EXPORT_HELP;
  * @brief Parsing was successful, built-in <tt>--export-help</tt> option was used.
  */
 
-/**
-.Class.ArgumentParser
-..cat:Miscellaneous
-..summary:Stores multiple @Class.ArgParseOption@ objects and parses the command line arguments for these options.
-..signature:ArgumentParser
-..include:seqan/arg_parse.h
-..remarks:
-See the documentation of @Class.ToolDoc@ on how to format text.
-Where possible, formatting is added automatically for you.
-You have to use formatting in the following places: (1) usage lines, (2) option help texts, (3) description and additional text sections.
-..example.text:
-The following gives a simple example of how to use the @Class.ArgumentParser@.
-..example.code:
-ArgumentParser parser("alf");
-setShortDescription(parser, "Alignment free sequence comparison");
-setVersion(parser, "1.0");
-setDate(parser, "Jan 2010");
-
-addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fB-i\\fP \\fIIN\\fP \\fB-o\\fP \\fIOUT\\fP");
-
-addDescription(parser,
-               "ALF can be used to calculate the pairwise similarity of sequences "
-               "using alignment-free methods. All methods which are implemented are "
-               "based on k-mer counts.");
-
-addOption(parser, ArgParseOption("i", "inputFile", "Name of the multi-FASTA input.",
-                                 ArgParseArgument(ArgParseArgument::INPUTFILE, "IN")));
-setRequired(parser, "i");
-
-addOption(parser, ArgParseOption("o", "outputFile", "Name of the multi-FASTA input.",
-                                 ArgParseArgument(ArgParseArgument::OUTPUTFILE, "OUT")));
-setRequired(parser, "o");
-
-addTextSection(parser, "See Also");
-addText(parser, "http://www.seqan.de/projects/alf");
-..see:Class.ToolDoc
-..see:Class.ArgParseArgument
-..see:Class.ArgParseOption
-
-.Memfunc.ArgumentParser#ArgumentParser
-..class:Class.ArgumentParser
-..summary:Constructor
-..signature:ArgumentParser ()
-..signature:ArgumentParser (applicationName)
-..param.applicationName:A std::string containing the name of the application.
-..remarks:If the name of the application is not passed to the constructor it will be extracted from the command line.
-*/
-
 class ArgumentParser
 {
 public:
@@ -205,6 +160,7 @@ class ArgumentParser
         PARSE_ERROR,
         PARSE_HELP,
         PARSE_VERSION,
+        PARSE_COPYRIGHT,
         PARSE_WRITE_CTD,
         PARSE_EXPORT_HELP
     };
@@ -247,13 +203,15 @@ class ArgumentParser
 
     void init()
     {
-        addOption(*this, ArgParseOption("h", "help", "Displays this help message."));
+        addOption(*this, ArgParseOption("h", "help", "Display the help message."));
+        addOption(*this, ArgParseOption("hh", "full-help", "Display the help message with advanced options."));
+        hideOption(*this, "full-help", true); // hidden by default
 
         // hidden flags used for export of man pages and ctd formats
         addOption(*this, ArgParseOption("",
                                         "write-ctd",
                                         "Exports the app's interface description to a .ctd file.",
-                                        ArgParseArgument::OUTPUTFILE));
+                                        ArgParseArgument::OUTPUT_FILE));
         hideOption(*this, "write-ctd", true);
 
         addOption(*this, ArgParseOption("",
@@ -301,25 +259,12 @@ class ArgumentParser
  *
  * @signature bool hasOption(parser, name);
  *
- * @param parser The ArgumentParser to query.
- * @param name   The name to query for (<tt>std::string</tt>).
+ * @param[in] parser The ArgumentParser to query.
+ * @param[in] name   The name to query for (<tt>std::string</tt>).
  *
  * @return bool <tt>true</tt> if there is such an option, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.ArgumentParser#hasOption
-..class:Class.ArgumentParser
-..summary:Returns whether a certain option is registered in the parser.
-..cat:Miscellaneous
-..signature:hasOption(parser, optionIdentifier)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the option.
-..returns:$true$ if the option is registered.
-..include:seqan/arg_parse.h
-*/
-
 inline bool hasOption(ArgumentParser const & me, std::string const & name)
 {
     return hasKey(me.shortNameMap, name) || hasKey(me.longNameMap, name);
@@ -336,23 +281,10 @@ inline bool hasOption(ArgumentParser const & me, std::string const & name)
  *
  * @signature void addOption(parser, option);
  *
- * @param parser The ArgumentParser to add the option to.
- * @param option The ArgParseOption to add to <tt>parser</tt>.
+ * @param[in,out] parser The ArgumentParser to add the option to.
+ * @param[in]     option The ArgParseOption to add to <tt>parser</tt>.
  */
 
-/**
-.Function.ArgumentParser#addOption
-..class:Class.ArgumentParser
-..summary:Adds a @Class.ArgParseOption@ object to the @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:addOption(parser, option)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.option:The new @Class.ArgParseOption@ object that should be added.
-...type:Class.ArgParseOption
-..include:seqan/arg_parse.h
-*/
-
 inline void _copyValidValuesToFileExt(ArgumentParser & me, std::string const & name)
 {
     // Copy valid values, remove leading dots.
@@ -414,23 +346,10 @@ inline void addOption(ArgumentParser & me, ArgParseOption const & opt)
  *
  * @signature void addArgument(parser, arg);
  *
- * @param parser The ArgumentParser to add the argument to.
- * @param arg    The ArgParseArgument to add to <tt>parser</tt>.
+ * @param[in,out] parser The ArgumentParser to add the argument to.
+ * @param[in]     arg    The ArgParseArgument to add to <tt>parser</tt>.
  */
 
-/**
-.Function.ArgumentParser#addArgument
-..class:Class.ArgumentParser
-..summary:Adds a @Class.ArgParseArgument@ object to the @Class.ArgumentParser@.
-..cat:Miscellaneous
-..signature:addArgument(parser, argument)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.arg:The new @Class.ArgParseArgument@ object that should be added.
-...type:Class.ArgParseArgument
-..include:seqan/arg_parse.h
-*/
-
 inline void _copyValidValuesToFileExt(ArgumentParser & me, unsigned no)
 {
     // Copy valid values, remove leading dots.
@@ -518,25 +437,12 @@ inline ArgumentParser::TOptionMapSize _getOptionIndex(ArgumentParser const & me,
  *
  * @signature TOption getOption(parser, name);
  *
- * @param parser The parser to query.
- * @param name   The short or long name of the option (<tt>std::string</tt>).
+ * @param[in] parser The parser to query.
+ * @param[in] name   The short or long name of the option (<tt>std::string</tt>).
  *
  * @return TOption Reference to the @link ArgParseOption @endlink with the given short or long name.
  */
 
-/**
-.Function.ArgumentParser#getOption
-..class:Class.ArgumentParser
-..summary:Returns a reference to the specified option.
-..cat:Miscellaneous
-..signature:getOption(parser, optionName)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..returns: a reference to the specified @Class.ArgParseOption@ object.
-..include:seqan/arg_parse.h
-*/
-
 inline ArgParseOption & getOption(ArgumentParser & me, std::string const & name)
 {
     SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name));
@@ -560,27 +466,11 @@ inline ArgParseOption const & getOption(ArgumentParser const & me, std::string c
  *
  * @signature void setRequired(parser, name[, required]).
  *
- * @param parser   The ArgumentParser to set the flag of.
- * @param name     The short or long name of the option (<tt>std::string</tt>).
- * @param required Whether or not the option is required (<tt>bool</tt>, default to <tt>true</tt>).
+ * @param[in,out] parser   The ArgumentParser to set the flag of.
+ * @param[in]     name     The short or long name of the option (<tt>std::string</tt>).
+ * @param[in]     required Whether or not the option is required (<tt>bool</tt>, default to <tt>true</tt>).
  */
 
-/**
-.Function.ArgumentParser#setRequired
-..class:Class.ArgumentParser
-..summary:Sets whether or not the option defined by the parameter $name$ (which can be
- either the short or the long name) is mandatory.
-..remarks: Note that the empty string is, at least for string options, also a valid string.
-Hence setting an option to required does not guarantee that the returned string is not empty.
-..cat:Miscellaneous
-..signature:setRequired(parser, optionName [, required])
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..param.required.remarks: The default value is true.
-..include:seqan/arg_parse.h
-*/
-
 inline void setRequired(ArgumentParser & me, std::string const & name, bool required = true)
 {
     SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name));
@@ -598,32 +488,42 @@ inline void setRequired(ArgumentParser & me, std::string const & name, bool requ
  *
  * @signature void hideOption(parser, name[, hide]).
  *
- * @param parser The ArgParseOption to the the hidden flag of.
- * @param name   The short or long name of the option to modify.
- * @param hide   Whether or not to hide the flag (<tt>bool</tt>, defaults to <tt>true</tt>).
+ * @param[in,out] parser The ArgParseOption to the the hidden flag of.
+ * @param[in]     name   The short or long name of the option to modify.
+ * @param[in]     hide   Whether or not to hide the flag (<tt>bool</tt>, defaults to <tt>true</tt>).
  */
 
-/**
-.Function.ArgumentParser#hideOption
-..class:Class.ArgumentParser
-..summary:Hides the ArgParseOption defined by the parameter $name$ (which can be
- either the short or the long name) from the help screen.
-..cat:Miscellaneous
-..signature:hideOption(parser, optionName [, hide])
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..param.hide:The new visibility of the option. Default is false.
-...type:nolink:bool
-..include:seqan/arg_parse.h
-*/
-
 inline void hideOption(ArgumentParser & me, std::string const & name, bool hide)
 {
     SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name));
     hideOption(getOption(me, name), hide);
 }
 
+// ----------------------------------------------------------------------------
+// Function setAdvanced()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ArgumentParser#setAdvanced
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Sets whether or not the option with the givne name is advanced.
+ *
+ * @signature void setAdvanced(parser, name[, required]).
+ *
+ * @param[in,out] parser   The ArgumentParser to set the flag of.
+ * @param[in]     name     The short or long name of the option (<tt>std::string</tt>).
+ * @param[in]     required Whether or not the option is required (<tt>bool</tt>, default to <tt>true</tt>).
+ */
+
+inline void setAdvanced(ArgumentParser & me, std::string const & name, bool advanced = true)
+{
+    SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name));
+    setAdvanced(getOption(me, name), advanced);
+    // make sure the full-help options is visible so advanced options can be shown
+    if (advanced)
+        hideOption(me, "full-help", false);
+}
+
 // ----------------------------------------------------------------------------
 // Function getArgument()
 // ----------------------------------------------------------------------------
@@ -635,25 +535,12 @@ inline void hideOption(ArgumentParser & me, std::string const & name, bool hide)
  *
  * @signature TArgument getArgument(parser, pos);
  *
- * @param parser The ArgumentParser to query.
- * @param pos    The position of the argument to return (<tt>unsigned</tt>, starting at 0).
+ * @param[in] parser The ArgumentParser to query.
+ * @param[in] pos    The position of the argument to return (<tt>unsigned</tt>, starting at 0).
  *
- * @return TArgument Reference to the argument with the given position.
+ * @return TArgument Reference to the @link ArgParseArgument @endlink with the given position.
  */
 
-/**
-.Function.ArgumentParser#getArgument
-..class:Class.ArgumentParser
-..summary:Returns a reference to the specified argument.
-..cat:Miscellaneous
-..signature:getArgument(parser, argumentPosition)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.argumentPosition:The index of the argument in the argument list.
-..returns: a reference to the specified @Class.ArgParseArgument@ object.
-..include:seqan/arg_parse.h
-*/
-
 inline ArgParseArgument & getArgument(ArgumentParser & me, unsigned position)
 {
     SEQAN_CHECK(position < me.argumentList.size(),
@@ -679,25 +566,12 @@ inline ArgParseArgument const & getArgument(ArgumentParser const & me, unsigned
  *
  * @signature bool isSet(parser, name);
  *
- * @param parser The ArgumentParser to query.
- * @param name   The short or long name of the option (<tt>std::string</tt>).
+ * @param[in] parser The ArgumentParser to query.
+ * @param[in] name   The short or long name of the option (<tt>std::string</tt>).
  *
  * @return bool Whether or not the option was set on the command line or not.
  */
 
-/**
-.Function.ArgumentParser#isSet
-..class:Class.ArgumentParser
-..summary:Returns whether an option was set on the parsed command line.
-..cat:Miscellaneous
-..signature:isSet(parser,optionIdentifier)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionIdentifier:A std::string that identifies the option (either short or long name).
-..returns:$true$ if the option was set.
-..include:seqan/arg_parse.h
-*/
-
 inline bool isSet(ArgumentParser const & me, std::string const & name)
 {
     SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name));
@@ -715,24 +589,12 @@ inline bool isSet(ArgumentParser const & me, std::string const & name)
  *
  * @signature bool hasDefault(parser, name);
  *
- * @param parser The ArgumentParser to query.
- * @param name   The short or long name of the option (<tt>std::string</tt>).
+ * @param[in] parser The ArgumentParser to query.
+ * @param[in] name   The short or long name of the option (<tt>std::string</tt>).
  *
  * @return bool Whether or not the option has a default value.
  */
 
-/**
-.Function.ArgumentParser#hasDefault
-..summary:Returns whether an option has a default value or not.
-..cat:Miscellaneous
-..signature:hasDefault(parser,optionIdentifier)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionIdentifier:A std::string that identifies the option (either short or long name).
-..returns:$true$ if the option has a default value, $false$ otherwise.
-..include:seqan/arg_parse.h
-*/
-
 inline bool hasDefault(ArgumentParser const & me, std::string const & name)
 {
     SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name));
@@ -776,33 +638,17 @@ inline bool _allArgumentsSet(ArgumentParser const & me)
  *
  * @signature bool getOptionValue(dest, parser, name[, pos]);
  *
- * @param dest   The variable to write the result to (the type is a template parameter and the value type of the option
- *               must be convertible in the type of <tt>dest</tt> for the retrieval to work, also see result value).
- * @param parser The ArgumentParser to get the value from.
- * @param name   The short or long name of the option (<tt>std::string</tt>).
- * @param pos    Optional position for multi-value options (<tt>unsigned</tt>, defaults to 0).
+ * @param[in] dest   The variable to write the result to (the type is a template parameter and the value type of the
+ *                    option must be convertible in the type of <tt>dest</tt> for the retrieval to work, also see
+ *                    result value).
+ * @param[in] parser The ArgumentParser to get the value from.
+ * @param[in] name   The short or long name of the option (<tt>std::string</tt>).
+ * @param[in] pos    Optional position for multi-value options (<tt>unsigned</tt>, defaults to 0).
  *
  * @return bool <tt>true</tt> if the requested option was given on the command line and could be coverted to the type of
  *              <tt>dest</tt>.
  */
 
-/**
-.Function.ArgumentParser#getOptionValue
-..class:Class.ArgumentParser
-..summary:Retrieves the value of an option given either the short or long name.
-..cat:Miscellaneous
-..signature:getOptionValue(value, parser, optionIdentifier[, argNo])
-..param.value:The variable where the resulting value should be stored.
-...remarks:The type of $value$ must be compatible the option type.
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionIdentifier:A std::string that is either the short or long name of the option.
-..param.argNo:If the option is list, the $argNo$-th list element is returned.
-..returns: $true$ if the requested option is set and has the requested type, $false$ otherwise.
-..remarks:The value passed to the method (value) was only updated if the method returns $true$.
-..include:seqan/arg_parse.h
-*/
-
 template <typename TValue>
 inline bool getOptionValue(TValue & val,
                            ArgumentParser const & me,
@@ -838,29 +684,27 @@ inline bool getOptionValue(TValue & val,
  *
  * @signature std::string getOptionFileExtension(parser, name[, pos]);
  *
- * Can be overridden by <tt>--${name}-file-ext</tt>.
- *
- * @param parser The ArgumentParser to get the value from.
- * @param name   The short or long name of the option (<tt>std::string</tt>).
- * @param pos    Optional position for multi-value options (<tt>unsigned</tt>, defaults to 0).
+ * @param[in] parser The ArgumentParser to get the value from.
+ * @param[in] name   The short or long name of the option (<tt>std::string</tt>).
+ * @param[in] pos    Optional position for multi-value options (<tt>unsigned</tt>, defaults to 0).
  *
  * @return std::string The extension of the option. Empty if not set or no extension.
+ *
+ * @see ArgumentParser#getArgumentFileExtension
+ *
+ * @section Overriding File Extension on the Command Line
+ *
+ * For each option with type <tt>INPUT_FILE</tt> and <tt>OUTPUT_FILE</tt>, an option with the name
+ * <tt>${name}-file-ext</tt> is automatically added to the ArgumentParser (where <tt>${name}</tt> is the name
+ * of the original option).  The extension can be overridden by specifying the argument.  Thus, the user of
+ * the program could give the value "file.ext" to the parameter "fname" and override the extension on the
+ * command line to "ext2" as follows:
+ *
+ * @code{.console}
+ * # program_name --fname file.ext --fname-file-ext ext2
+ * @endcode
  */
 
-/**
-.Function.ArgumentParser#getOptionFileExtension
-..class:Class.ArgumentParser
-..summary:Returns the extension of a file option.
-..cat:Miscellaneous
-..signature:std::string getOptionFileExtension(parser, name[, argNo]);
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParsre
-..param.name:The name of the option.
-..param.argNo:An optional index for multi-value options.
-...type:nolink:$unsigned$
-..returns:A $std::string$ with the extension. Empty if no extension or empty value.
-*/
-
 inline std::string getOptionFileExtension(ArgumentParser const & me,
                                           std::string const & name,
                                           unsigned argNo = 0)
@@ -881,23 +725,12 @@ inline std::string getOptionFileExtension(ArgumentParser const & me,
  *
  * @signature unsigned getOptionValueCount(parser, name);
  *
- * @param parser The ArgumentParser to query.
- * @param name   The short or long name of the option (<tt>string</tt>).
+ * @param[in] parser The ArgumentParser to query.
+ * @param[in] name   The short or long name of the option (<tt>string</tt>).
+ *
+ * @return unsigned The number of values for the option with the given name.
  */
 
-/**
-.Function.ArgumentParser#getOptionValueCount
-..class:Class.ArgumentParser
-..summary:Returns the number of values stored in the specified option.
-..cat:Miscellaneous
-..signature:getOptionValueCount(parser, optionIdentifier)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionIdentifier:A std::string that is either the short or long name of the option.
-..returns: The number of values stored for this option.
-..include:seqan/arg_parse.h
-*/
-
 inline unsigned getOptionValueCount(ArgumentParser const & me, std::string const & name)
 {
     SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name));
@@ -915,23 +748,12 @@ inline unsigned getOptionValueCount(ArgumentParser const & me, std::string const
  *
  * @signature unsigned getArgumentValueCount(parser, pos);
  *
- * @param parser The ArgumentParser to query.
- * @param name   The position of the argument (<tt>unsigned</tt>, 0-based).
+ * @param[in] parser The ArgumentParser to query.
+ * @param[in] name   The position of the argument (<tt>unsigned</tt>, 0-based).
+ *
+ * @return unsigned The number of values for the argument with the given position.
  */
 
-/**
-.Function.ArgumentParser#getArgumentValueCount
-..class:Class.ArgumentParser
-..summary:Returns the number of values stored in the specified option.
-..cat:Miscellaneous
-..signature:getArgumentValueCount(parser, argumentPosition)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.argumentPosition:The index of the argument in the argument list.
-..returns: The number of values stored for the specified argument.
-..include:seqan/arg_parse.h
-*/
-
 inline unsigned getArgumentValueCount(ArgumentParser const & me, unsigned argumentPosition)
 {
     SEQAN_CHECK(me.argumentList.size() > argumentPosition,
@@ -951,32 +773,16 @@ inline unsigned getArgumentValueCount(ArgumentParser const & me, unsigned argume
  *
  * @signature bool getArgumentValue(dest, parser, pos[, no]);
  *
- * @param dest   The variable to write the result to (the type is a template parameter and the value type of the
- *               argument must be convertible in the type of <tt>dest</tt> for the retrieval to work, also see result
- *               value).
- * @param parser The ArgumentParser to get the value from.
- * @param pos    The position of the argument to get the value of.
- * @param no     Optional position for multi-value arguments (<tt>unsigned</tt>, defaults to 0).
+ * @param[in] dest   The variable to write the result to (the type is a template parameter and the value type of the
+ *                   argument must be convertible in the type of <tt>dest</tt> for the retrieval to work, also see
+ *                   result value).
+ * @param[in] parser The ArgumentParser to get the value from.
+ * @param[in] pos    The position of the argument to get the value of.
+ * @param[in] no     Optional position for multi-value arguments (<tt>unsigned</tt>, defaults to 0).
  *
  * @return bool <tt>true</tt> if the retrieval was successful, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.ArgumentParser#getArgumentValue
-..class:Class.ArgumentParser
-..summary:Retrieves the value of an argument given by its position.
-..cat:Miscellaneous
-..signature:getArgumentValue(value, parser, argumentPosition[, argNo])
-..param.value:The variable where the resulting value should be stored.
-...remarks:The type of $value$ must be compatible the option type.
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.argumentPosition:The index of the argument in the argument list.
-..param.argNo:If the argument is a list, the $argNo$-th list element is returned.
-..returns: $true$ if the requested argument is set and has the requested type, $false$ otherwise.
-..include:seqan/arg_parse.h
-*/
-
 template <typename TValue>
 inline bool getArgumentValue(TValue & value,
                              ArgumentParser const & me,
@@ -1008,30 +814,27 @@ inline bool getArgumentValue(TValue & value,
  *
  * @signature std::string argumentFileExtension(parser, pos[, argNo]);
  *
- * Can be overridden by <tt>--arg-${pos}-file-ext</tt>.
- *
- * @param parser The ArgumentParser to get the value from.
- * @param pos    The position of the argument to query (<tt>unsigned</tt>).
- * @param argNo  Optional position for multi-value options (<tt>unsigned</tt>, defaults to 0).
+ * @param[in] parser The ArgumentParser to get the value from.
+ * @param[in] pos    The position of the argument to query (<tt>unsigned</tt>).
+ * @param[in] argNo  Optional position for multi-value options (<tt>unsigned</tt>, defaults to 0).
  *
  * @return std::string The extension of the argument if any.
+ *
+ * @see ArgumentParser#getOptionFileExtension
+ *
+ * @section Overriding File Extensions on the Command Line
+ *
+ * For each argument with type <tt>INPUT_FILE</tt> and <tt>OUTPUT_FILE</tt>, an option with the index
+ * <tt>arg-${idx}-file-ext</tt> is automatically added to the ArgumentParser (where <tt>${idx}</tt> is the index
+ * of the original option).  The extension can be overridden by specifying the argument.  Thus, the user of
+ * the program could give the value "file.ext" to the parameter "0" and override the extension on the
+ * command line to "ext2" as follows:
+ *
+ * @code{.console}
+ * # program_name file.ext --arg-0-file-ext ext2
+ * @endcode
  */
 
-/**
-.Function.ArgumentParser#getArgumentFileExtension
-..class:Class.ArgumentParser
-..summary:Returns the extension of a file argument.
-..cat:Miscellaneous
-..signature:std::string argumentFileExtension(parser, argPos[, argNo]);
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParsre
-..param.argPos:The position of the argument.
-...type:nolink:$unsigned$
-..param.argNo:An optional index for multi-value arguments.
-...type:nolink:$unsigned$
-..returns:A $std::string$ with the extension. Empty if no extension or empty value.
-*/
-
 inline std::string getArgumentFileExtension(ArgumentParser const & me,
                                             unsigned argumentPosition,
                                             unsigned argNo = 0)
@@ -1055,25 +858,12 @@ inline std::string getArgumentFileExtension(ArgumentParser const & me,
  *
  * @signature TVector getOptionValues(parser, name);
  *
- * @param parser The ArgumentParser to query.
- * @param name   The short or long name of the option to get (<tt>std::string</tt>).
+ * @param[in] parser The ArgumentParser to query.
+ * @param[in] name   The short or long name of the option to get (<tt>std::string</tt>).
  *
  * @return TVector The resulting values (<tt>std::vector&lt;std::string&gt;</tt>).
  */
 
-/**
-.Function.ArgumentParser#getOptionValues
-..class:Class.ArgumentParser
-..summary:Returns all values of an option given on the command line.
-..cat:Miscellaneous
-..signature:getOptionValues(parser, optionIdentifier)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionIdentifier:A std::string that is either the short or long name of the option.
-..returns: A $String<std::string>$ of option values.
-..include:seqan/arg_parse.h
-*/
-
 inline std::vector<std::string> const & getOptionValues(ArgumentParser const & me,
                                                         std::string const & name)
 {
@@ -1092,25 +882,12 @@ inline std::vector<std::string> const & getOptionValues(ArgumentParser const & m
  *
  * @signature TVector getArgumentValues(parser, pos);
  *
- * @param parser The ArgumentParser to query.
- * @param pos    The position of the argument (<tt>unsigned</tt>, 0-based).
+ * @param[in] parser The ArgumentParser to query.
+ * @param[in] pos    The position of the argument (<tt>unsigned</tt>, 0-based).
  *
  * @return TVector The resulting values (<tt>std::vector&lt;std::string&gt;</tt>).
  */
 
-/**
-.Function.ArgumentParser#getArgumentValues
-..class:Class.ArgumentParser
-..summary:Returns all values of an option given on the command line.
-..cat:Miscellaneous
-..signature:getArgumentValues(parser, argumentPosition)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.argumentPosition:The index of the argument in the argument list.
-..returns: A $String<std::string>$ of argument values.
-..include:seqan/arg_parse.h
-*/
-
 inline std::vector<std::string> const & getArgumentValues(ArgumentParser const & me,
                                                           unsigned argumentPosition)
 {
@@ -1131,23 +908,11 @@ inline std::vector<std::string> const & getArgumentValues(ArgumentParser const &
  *
  * @signature void setDefaultValue(parser, name, v);
  *
- * @param parser The ArgumentParser to set the default value to.
- * @param name   The short or long name of the argument (<tt>std::string</tt>).
- * @param v      The value to set (template parameter, must be streamable into a <tt>std::stringstream</tt>).
+ * @param[in] parser The ArgumentParser to set the default value to.
+ * @param[in] name   The short or long name of the argument (<tt>std::string</tt>).
+ * @param[in] v      The value to set (template parameter, must be streamable into a <tt>std::stringstream</tt>).
  */
 
-/**
-.Function.ArgumentParser#setDefaultValue
-..class:Class.ArgumentParser
-..summary:Set default value of an option of an ArgumentParser.
-..signature:setDefaultValue(parser, optionName, value)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..param.value:The new default value.
-..include:seqan/arg_parse.h
-*/
-
 template <typename TValue>
 inline void setDefaultValue(ArgumentParser & me,
                             std::string const & name,
@@ -1168,23 +933,11 @@ inline void setDefaultValue(ArgumentParser & me,
  *
  * @signature void addDefaultValue(parser, name, v);
  *
- * @param parser The ArgumentParser to append the default value to.
- * @param name   The short or long name of the argument (<tt>std::string</tt>).
- * @param v      The value to append (template parameter, must be streamable into a <tt>std::stringstream</tt>).
+ * @param[in,out] parser The ArgumentParser to append the default value to.
+ * @param[in]     name   The short or long name of the argument (<tt>std::string</tt>).
+ * @param[in]     v      The value to append (template parameter, must be streamable into a <tt>std::stringstream</tt>).
  */
 
-/**
-.Function.ArgumentParser#addDefaultValue
-..class:Class.ArgumentParser
-..summary:Add to the default values of an option of an ArgumentParser.
-..signature:addDefaultValue(parser, optionName, value)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..param.value:The new default value.
-..include:seqan/arg_parse.h
-*/
-
 template <typename TValue>
 inline void addDefaultValue(ArgumentParser & me,
                             std::string const & name,
@@ -1206,30 +959,16 @@ inline void addDefaultValue(ArgumentParser & me,
  * @signature void setMinValue(parser, name, v);
  * @signature void setMinValue(parser, pos, v);
  *
- * @param parser The ArgumentParser to set the minimal value for.
- * @param name   The name of the option to set the minimal value for (<tt>std::string</tt>).
- * @param pos    The position of the argument to set the minimal value for (<tt>unsigned</tt>, 0-based).
- * @param v      The minimal value to set (<tt>std::string</tt>).
+ * @param[in,out] parser The ArgumentParser to set the minimal value for.
+ * @param[in]     name   The name of the option to set the minimal value for (<tt>std::string</tt>).
+ * @param[in]     pos    The position of the argument to set the minimal value for (<tt>unsigned</tt>, 0-based).
+ * @param[in]     v      The minimal value to set (<tt>std::string</tt>).
  *
  * @section Remarks
  *
  * The option/argument must have an integer or double type.
  */
 
-/**
-.Function.ArgumentParser#setMinValue
-..class:Class.ArgumentParser
-..summary:Set smallest allowed value for an option or argument of an ArgumentParser.
-..signature:setMinValue(parser,optionName,minValue)
-..signature:setMinValue(parser,argumentPosition,minValue)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..param.argumentPosition:The index of the argument in the argument list.
-..param.minValue:A std::string containing a string representation of the minimum value of the @Class.ArgParseOption@.
-..include:seqan/arg_parse.h
-*/
-
 inline void setMinValue(ArgumentParser & me,
                         std::string const & name,
                         std::string const & _minValue)
@@ -1260,30 +999,16 @@ inline void setMinValue(ArgumentParser & me,
  * @signature void setMaxValue(parser, name, v);
  * @signature void setMaxValue(parser, pos, v);
  *
- * @param parser The ArgumentParser to set the maximal value for.
- * @param name   The name of the option to set the maximal value for (<tt>std::string</tt>).
- * @param pos    The position of the argument to set the maximal value for (<tt>unsigned</tt>, 0-based).
- * @param v      The maximal value to set (<tt>std::string</tt>).
+ * @param[in,out] parser The ArgumentParser to set the maximal value for.
+ * @param[in]     name   The name of the option to set the maximal value for (<tt>std::string</tt>).
+ * @param[in]     pos    The position of the argument to set the maximal value for (<tt>unsigned</tt>, 0-based).
+ * @param[in]     v      The maximal value to set (<tt>std::string</tt>).
  *
  * @section Remarks
  *
  * The option/argument must have an integer or double type.
  */
 
-/**
-.Function.ArgumentParser#setMaxValue
-..class:Class.ArgumentParser
-..summary:Set largest allowed value for an option or argument of an ArgumentParser.
-..signature:setMaxValue(parser,optionName,maxValue)
-..signature:setMaxValue(parser,argumentPosition,minValue)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..param.argumentPosition:The index of the argument in the argument list.
-..param.maxValue:A std::string containing a string representation of the maximum value of the @Class.ArgParseOption@.
-..include:seqan/arg_parse.h
-*/
-
 inline void setMaxValue(ArgumentParser & me,
                         std::string const & name,
                         std::string const & _maxValue)
@@ -1314,28 +1039,13 @@ inline void setMaxValue(ArgumentParser & me,
  * @signature void setValidValues(parser, name, values);
  * @signature void setValidValues(parser, pos, values);
  *
- * @param parser The ArgumentParser to set the default values to.
- * @param name   The name of the option (<tt>std::string</tt>).
- * @param pos    The position of the argument (<tt>unsigned</tt>, 0-based).
- * @param values The values to set.  Either a <tt>std::string</tt> with the values as space-separated list
- *               or a <tt>std::vector&lt;std::string&gt;</tt> with the values.
+ * @param[in,out] parser The ArgumentParser to set the default values to.
+ * @param[in]     name   The name of the option (<tt>std::string</tt>).
+ * @param[in]     pos    The position of the argument (<tt>unsigned</tt>, 0-based).
+ * @param[in]     values The values to set.  Either a <tt>std::string</tt> with the values as space-separated list
+ *                       or a <tt>std::vector&lt;std::string&gt;</tt> with the values.
  */
 
-/**
-.Function.ArgumentParser#setValidValues
-..class:Class.ArgumentParser
-..summary:Set valid values for an argument or option of an ArgumentParser.
-..signature:setValidValues(parser,optionName,values)
-..signature:setValidValues(parser,argumentPosition,values)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..param.argumentPosition:The index of the argument in the argument list.
-..param.values:A $std::string$ containing all valid entries for the option.
-Alternatively you can pass a string containing all values separated by spaces.
-..include:seqan/arg_parse.h
-*/
-
 inline void setValidValues(ArgumentParser & me,
                            std::string const & name,
                            std::vector<std::string> const & values)
@@ -1388,26 +1098,12 @@ inline void setValidValues(ArgumentParser & me,
  * @signature void setHelpText(parser, name, text);
  * @signature void setHelpText(parser, pos, text);
  *
- * @param parser The ArgumentParser object.
- * @param name   The name of the option to set the help text for (<tt>std::string</tt>).
- * @param pos    The position of the argument to set the help text for.
- * @param text   The string to use for the help text (<tt>std::string</tt>).
+ * @param[in,out] parser The ArgumentParser object.
+ * @param[in]     name   The name of the option to set the help text for (<tt>std::string</tt>).
+ * @param[in]     pos    The position of the argument to set the help text for.
+ * @param[in]     text   The string to use for the help text (<tt>std::string</tt>).
  */
 
-/**
-.Function.ArgumentParser#setHelpText
-..class:Class.ArgumentParser
-..summary:Set help text of argument parser.
-..signature:setHelpText(parser,optionName,text)
-..signature:setHelpText(parser,argumentPosition,text)
-..param.parser:The @Class.ArgumentParser@ object.
-...type:Class.ArgumentParser
-..param.optionName:The identifier of the command line option.
-..param.argumentPosition:The index of the argument in the argument list.
-..param.text:A $std::string$ describing the option or argument.
-..include:seqan/arg_parse.h
-*/
-
 inline void setHelpText(ArgumentParser & me,
                         std::string const & name,
                         std::string const & text)
@@ -1427,11 +1123,11 @@ inline void setHelpText(ArgumentParser & me,
 }
 
 // ----------------------------------------------------------------------------
-// Function getFileFormatExtensions()
+// Function getFileExtensions()
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn ArgumentParser#getFileFormatExtensions
+ * @fn ArgumentParser#getFileExtensions
  * @headerfile <seqan/arg_parse.h>
  * @brief Returns file format extension given a format tag.
  *
@@ -1439,40 +1135,23 @@ inline void setHelpText(ArgumentParser & me,
  * @signature TVector getFormatExtension(tagList);
  * @signature TVector getFormatExtension(tagSelector);
  *
- * @param tag         A single file foramt, e.g. <tt>Fastq()</tt>.
- * @param tagList     A list of file format (@link TagList @endlink).
- * @param tagSelector A file format selector (@link TagSelector @endlink).
+ * @param[in] tag         A single file foramt, e.g. <tt>Fastq()</tt>.
+ * @param[in] tagList     A list of file format (@link TagList @endlink).
+ * @param[in] tagSelector A file format selector (@link TagSelector @endlink).
  *
  * @return TVector A <tt>std::vector&lt;std::string&gt;</tt> with the allowed file format extensions.
  */
 
-/**
-.Function.ArgumentParser#getFileFormatExtensions
-..class:Class.ArgumentParser
-..summary:Returns file format extensions given a format tag.
-..signature:getFileFormatExtensions(formatTag)
-..signature:getFileFormatExtensions(formatTagList)
-..signature:getFileFormatExtensions(formatTagSelector)
-..param.format:A single file format, e.g. @Tag.File Format.tag.Fastq@ or @Tag.Sam@.
-...type:Tag.Tag
-..param.formatTagList:A list of file formats.
-...type:Tag.TagList
-..param.formatTagSelector:A file format selector.
-...type:Class.TagSelector
-..returns:A $std::vector<std::string>$ of all extensions supported by a single format or all formats of a list or selector.
-..include:seqan/arg_parse.h
-*/
-
 template <typename T>
 inline std::vector<std::string>
-getFileFormatExtensions(T const formatTag)
+getFileExtensions(T const formatTag)
 {
     std::vector<std::string> extensions;
-    _getFileFormatExtensions(extensions, formatTag);
+    _getFileExtensions(extensions, formatTag);
     return extensions;
 }
 
 
 }  // namespace seqan
 
-#endif // SEQAN_CORE_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_
+#endif // SEQAN_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_
diff --git a/seqan/arg_parse/tool_doc.h b/seqan/arg_parse/tool_doc.h
index 13447a8..902beb9 100644
--- a/seqan/arg_parse/tool_doc.h
+++ b/seqan/arg_parse/tool_doc.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,13 +32,14 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_ARG_PARSE_TOOL_DOC_H_
-#define SEQAN_CORE_INCLUDE_ARG_PARSE_TOOL_DOC_H_
+#ifndef SEQAN_INCLUDE_ARG_PARSE_TOOL_DOC_H_
+#define SEQAN_INCLUDE_ARG_PARSE_TOOL_DOC_H_
 
 #include <iterator>
 
-#include <seqan/misc/misc_terminal.h>
+#include <seqan/misc/terminal.h>
 #include <seqan/arg_parse/xml_support.h>
+#include <seqan/version.h>
 
 namespace seqan {
 
@@ -359,7 +360,7 @@ class TextToolDocPrinter_ :
     {
         std::ostream_iterator<char> out(stream);
         stream << '\n' << _toText("\\fB");
-        std::transform(begin(section._title), end(section._title), out, toupper);
+        std::transform(begin(section._title), end(section._title), out, static_cast < int(*)(int) > (toupper));
         stream << _toText("\\fP") << '\n';
     }
 
@@ -559,26 +560,27 @@ class TextToolDocPrinter_ :
 
 /*!
  * @class ToolDoc
+ * @implements AssignableConcept
  * @headerfile <seqan/arg_parse.>
  * @brief Container for string documentation on a command line tool.
- * 
+ *
  * @signature class ToolDoc;
- * 
+ *
  * @section Remarks
- * 
+ *
  * This class is generally not used directly by the user but through @link ArgumentParser @endlink. It allows to store
  * and represent all information related to a command line tool that would normally go into a man page. It can be
  * printed to STL streams in different formats, currently plain text, HTML and man pages are supported.
- * 
+ *
  * You can also use basic formatting in text. This formatting is tailored to the usage on the command line. Use
  * <tt>\fB</tt> to start bold font, <tt>\fI</tt> to start italic font and <tt>\fP</tt> to use the previous font (of
  * course, use correct escaping of the backslash in C strings, so use <tt>"\\fB"</tt>, <tt>"\\fI"</tt>, and
  * <tt>"\\fP"</tt> in your code.
- * 
+ *
  * @section Examples
- * 
+ *
  * The following shows a brief example of how to use @link ToolDoc @endlink.
- * 
+ *
  * @code{.cpp}
  * ToolDoc doc;
  * setName(doc, "RazerS");
@@ -587,13 +589,13 @@ class TextToolDocPrinter_ :
  * setVersion(doc, "1.0");
  * setCategory(doc, "Read Mapping");
  * setManTitle(doc, "SeqAn Apps Reference Manual");
- *  
+ *
  * addSection(doc, "Synopsis");
  * addText(doc, "\\fBrazers\\fP [\\fIOPTIONS\\fP] \\fIREFERENCE\\fP \\fIREADS\\fP", false);
  * addText(doc,
  *         "\\fBrazers\\fP [\\fIOPTIONS\\fP] \\fIREFERENCE\\fP \\fILEFT_READS\\fP "
  *         "\\fIRIGHT_READS\\fP", false);
- *  
+ *
  * addSection(doc, "Description");
  * addText(doc,
  *         "RazerS is a read mapper with controllable, sensitivity.  This "
@@ -602,14 +604,14 @@ class TextToolDocPrinter_ :
  *         "performance.");
  * addText(doc,
  *         "What's special about RazerS is that you can control the sensitivity.");
- *  
+ *
  * addSection(doc, "Options");
  * addSubSection(doc, "Main Options");
  * addListItem(doc, "\\fB-id\\fP, \\fB--indels\\fP",
  *             "Enable mapping with indels enabled.");
  * addListItem(doc, "\\fB-i\\fP, \\fB--identity\\fP \\fIIDENTITY\\fP",
  *             "Set minimal identity of matches to find.");
- *  
+ *
  * print(std::cout, doc, "text");
  * @endcode
  *
@@ -621,63 +623,10 @@ class TextToolDocPrinter_ :
 /*!
  * @fn ToolDoc::ToolDoc
  * @brief Constructor
- * 
+ *
  * @signature ToolDoc::ToolDoc()
  */
 
-/**
-.Class.ToolDoc
-..cat:Miscellaneous
-..summary:Container for string documentation on a command line tool.
-..signature:ToolDoc
-..remarks:
-This class is generally not used directly by the user but through @Class.ArgumentParser@.
-It allows to store and represent all information related to a command line tool that would normally go into a man page.
-It can be printed to STL streams in different formats, currently plain text, HTML and man pages are supported.
-..remarks:
-You can also use basic formatting in text. This formatting is tailored to the usage on the command line.
-Use $\fB$ to start bold font, $\fI$ to start italic font and $\fP$ to use the previous font (of course, use correct escaping of the backslash in C strings, so use $"\\fB"$, $"\\fI"$, and $"\\fP"$ in your code.
-..example.text:The following shows a brief example of how to use @Class.ToolDoc@.
-..example.code:
-ToolDoc doc;
-setName(doc, "RazerS");
-setShortDescription(doc, "Read mapping with controllable sensitivity.");
-setDate(doc, "04 March 2012");
-setVersion(doc, "1.0");
-setCategory(doc, "Read Mapping");
-setManTitle(doc, "SeqAn Apps Reference Manual");
-
-addSection(doc, "Synopsis");
-addText(doc, "\\fBrazers\\fP [\\fIOPTIONS\\fP] \\fIREFERENCE\\fP \\fIREADS\\fP", false);
-addText(doc,
-        "\\fBrazers\\fP [\\fIOPTIONS\\fP] \\fIREFERENCE\\fP \\fILEFT_READS\\fP "
-        "\\fIRIGHT_READS\\fP", false);
-
-addSection(doc, "Description");
-addText(doc,
-        "RazerS is a read mapper with controllable, sensitivity.  This "
-        "means that you can find all read matches in the reference sequence "
-        "and optionally, you can trade lower sensitivity for better "
-        "performance.");
-addText(doc,
-        "What's special about RazerS is that you can control the sensitivity.");
-
-addSection(doc, "Options");
-addSubSection(doc, "Main Options");
-addListItem(doc, "\\fB-id\\fP, \\fB--indels\\fP",
-            "Enable mapping with indels enabled.");
-addListItem(doc, "\\fB-i\\fP, \\fB--identity\\fP \\fIIDENTITY\\fP",
-            "Set minimal identity of matches to find.");
-
-print(std::cout, doc, "text");
-..include:seqan/arg_parse/tool_doc.h
-
-.Memfunc.ToolDoc#ToolDoc
-..summary:constructor
-..class:Class.ToolDoc
-..signature:ToolDoc()
-*/
-
 class ToolDoc
 {
 public:
@@ -685,6 +634,9 @@ class ToolDoc
     CharString _shortDescription;
     CharString _date;
     CharString _version;
+    CharString _shortCopyright;
+    CharString _longCopyright;
+    CharString _citation;
     CharString _manTitle;
     CharString _category;
     unsigned _manSection;
@@ -698,7 +650,8 @@ class ToolDoc
 
     ToolDoc(ToolDoc const & toolDoc) :
         _name(toolDoc._name), _shortDescription(toolDoc._shortDescription),
-        _date(toolDoc._date), _version(toolDoc._version), _manTitle(toolDoc._manTitle),
+        _date(toolDoc._date), _version(toolDoc._version), _shortCopyright(toolDoc._shortCopyright),
+        _longCopyright(toolDoc._longCopyright), _citation(toolDoc._citation), _manTitle(toolDoc._manTitle),
         _category(toolDoc._category), _manSection(1)
     {
         append(*this, toolDoc);
@@ -764,27 +717,13 @@ class ToolDoc
  * @fn ToolDoc#append
  * @headerfile <seqan/arg_parse.h>
  * @brief Append two @link ToolDoc @endlink objects.
- * 
+ *
  * @signature void append(a, b);
- * 
- * @param a This object is updated
- * @param b This object is appended to <tt>b</tt>.
+ *
+ * @param[in,out] a This object is updated
+ * @param[in]     b This object is appended to <tt>b</tt>.
  */
 
-/**
-.Function.ToolDoc#append
-..summary:Append two @Class.ToolDoc@ objects.
-..cat:Miscellaneous
-..signature:append(a, b)
-..class:Class.ToolDoc
-..param.a:This object is updated.
-...type:Class.ToolDoc
-..param.b:This object is appended to $b$.
-...type:Class.ToolDoc
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void append(ToolDoc & a, ToolDoc const & b)
 {
     for (unsigned i = 0; i < length(b._entries); ++i)
@@ -822,24 +761,10 @@ inline void append(ToolDoc & a, ToolDoc const & b)
  *
  * @signature void setName(toolDoc, name);
  *
- * @param toolDoc The ToolDoc object to the set the name for.
- * @param name    The name of the tool (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to the set the name for.
+ * @param[in]     name    The name of the tool (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#setName
-..summary:Set tool name for @Class.ToolDoc@ object.
-..cat:Miscellaneous
-..signature:setName(doc, name)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to set the name of.
-...type:Class.ToolDoc
-..param.name:Name to set.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void setName(ToolDoc & doc, CharString const & name)
 {
     doc._name = name;
@@ -856,24 +781,11 @@ inline void setName(ToolDoc & doc, CharString const & name)
  *
  * @signature CharString getName(toolDoc);
  *
- * @param toolDoc The ToolDoc object to the get the name for.
+ * @param[in] toolDoc The ToolDoc object to the get the name for.
  *
  * @return CharString Resulting name (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#getName
-..summary:Get tool name of @Class.ToolDoc@ object.
-..cat:Miscellaneous
-..signature:getName(doc)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to get the tool name of.
-...type:Class.ToolDoc
-..returns:Tool name of documentation object.
-...type:Shortcut.CharString
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline CharString const & getName(ToolDoc const & doc)
 {
     return doc._name;
@@ -890,24 +802,10 @@ inline CharString const & getName(ToolDoc const & doc)
  *
  * @signature void setName(toolDoc, name);
  *
- * @param toolDoc The ToolDoc object to the set the name for.
- * @param name    The name of the tool (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to the set the name for.
+ * @param[in]     name    The name of the tool (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#setCategory
-..summary:Set tool category for @Class.ToolDoc@ object.
-..cat:Miscellaneous
-..signature:setCategory(doc, category)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to set the name of.
-...type:Class.ToolDoc
-..param.category:Category to set.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void setCategory(ToolDoc & doc, CharString const & category)
 {
     doc._category = category;
@@ -924,24 +822,11 @@ inline void setCategory(ToolDoc & doc, CharString const & category)
  *
  * @signature CharString getCategory(toolDoc);
  *
- * @param toolDoc The ToolDoc object to the get the category for.
+ * @param[in] toolDoc The ToolDoc object to the get the category for.
  *
  * @return CharString Resulting category (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#getCategory
-..summary:Get tool category of @Class.ToolDoc@ object.
-..cat:Miscellaneous
-..signature:getCategory(doc)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to get the tool category of.
-...type:Class.ToolDoc
-..returns:Tool category of documentation object.
-...type:Shortcut.CharString
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline CharString const & getCategory(ToolDoc const & doc)
 {
     return doc._category;
@@ -958,24 +843,10 @@ inline CharString const & getCategory(ToolDoc const & doc)
  *
  * @signature void setShortDescription(toolDoc, text);
  *
- * @param toolDoc The ToolDoc object to the set the short description for.
- * @param text    The short description of the tool (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to the set the short description for.
+ * @param[in]     text    The short description of the tool (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#setShortDescription
-..summary:Set short description for @Class.ToolDoc@ object.
-..cat:Miscellaneous
-..signature:setShortDescriptioin(doc, description)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to set the short description of.
-...type:Class.ToolDoc
-..param.description:Short description to set.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void setShortDescription(ToolDoc & doc, CharString const & shortDescription)
 {
     doc._shortDescription = shortDescription;
@@ -992,24 +863,11 @@ inline void setShortDescription(ToolDoc & doc, CharString const & shortDescripti
  *
  * @signature CharString getShortDescription(toolDoc);
  *
- * @param toolDoc The ToolDoc object to the get the short description for.
+ * @param[in] toolDoc The ToolDoc object to the get the short description for.
  *
  * @return CharString Resulting short description (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#getShortDescription
-..summary:Get short description of @Class.ToolDoc@ object.
-..cat:Miscellaneous
-..signature:setName(doc)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to set the short description of.
-...type:Class.ToolDoc
-..returns:Tool description of documentation object.
-...type:Shortcut.CharString
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline CharString const & getShortDescription(ToolDoc const & doc)
 {
     return doc._shortDescription;
@@ -1026,24 +884,10 @@ inline CharString const & getShortDescription(ToolDoc const & doc)
  *
  * @signature void setName(toolDoc, str);
  *
- * @param toolDoc The ToolDoc object to the set the date string for.
- * @param str     The date string of the tool (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to the set the date string for.
+ * @param[in]     str     The date string of the tool (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#setDate
-..cat:Miscellaneous
-..summary:Set date string for @Class.ToolDoc@ object.
-..signature:setDate(doc, date)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to set the date string to.
-...type:Class.ToolDoc
-..param.date:Date string to set.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void setDate(ToolDoc & doc, CharString const & date)
 {
     doc._date = date;
@@ -1060,24 +904,11 @@ inline void setDate(ToolDoc & doc, CharString const & date)
  *
  * @signature CharString getDate(toolDoc);
  *
- * @param toolDoc The ToolDoc object to the get the date from.
+ * @param[in] toolDoc The ToolDoc object to the get the date from.
  *
  * @return CharString Resulting date string (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#getDate
-..cat:Miscellaneous
-..summary:Get date string from @Class.ToolDoc@ object.
-..signature:getDate(doc)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to get the date string of.
-...type:Class.ToolDoc
-..returns:Date string.
-...type:Shortcut.CharString
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline CharString const & getDate(ToolDoc const & doc)
 {
     return doc._date;
@@ -1092,26 +923,12 @@ inline CharString const & getDate(ToolDoc const & doc)
  * @headerfile <seqan/arg_parse.h>
  * @brief Set the tool version string.
  *
- * @signature void setName(toolDoc, str);
+ * @signature void setVersion(toolDoc, str);
  *
- * @param toolDoc The ToolDoc object to the set the version string for.
- * @param str     The version string of the tool (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to the set the version string for.
+ * @param[in]     str     The version string of the tool (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#setVersion
-..cat:Miscellaneous
-..summary:Set version string for @Class.ToolDoc@ object.
-..signature:setVersion(doc, version)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to set the version string to.
-...type:Class.ToolDoc
-..param.version:Version string to set.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void setVersion(ToolDoc & doc, CharString const & version)
 {
     doc._version = version;
@@ -1128,29 +945,140 @@ inline void setVersion(ToolDoc & doc, CharString const & version)
  *
  * @signature CharString getVersion(toolDoc);
  *
- * @param toolDoc The ToolDoc object to the get the version string.
+ * @param[in] toolDoc The ToolDoc object to the get the version string.
  *
  * @return CharString Resulting version string (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#getVersion
-..cat:Miscellaneous
-..summary:Get version string from @Class.ToolDoc@ object.
-..class:Class.ToolDoc
-..signature:CharString getVersion(doc)
-..param.doc:Tool documentation object to get the version string of.
-...type:Class.ToolDoc
-..returns:Date string.
-...type:Shortcut.CharString
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline CharString const & getVersion(ToolDoc const & doc)
 {
     return doc._version;
 }
 
+// --------------------------------------------------------------------------
+// Function setShortCopyright()                                              ToolDoc
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ToolDoc#setShortCopyright
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Set the tool short copyright string.
+ *
+ * @signature void setShortCopyright(toolDoc, str);
+ *
+ * @param[in,out] toolDoc The ToolDoc object to the set the short copyright string for.
+ * @param[in]     str     The short copyright string of the tool (@link CharString @endlink).
+ */
+
+inline void setShortCopyright(ToolDoc & doc, CharString const & shortCopyright)
+{
+    doc._shortCopyright = shortCopyright;
+}
+
+// --------------------------------------------------------------------------
+// Function getShortCopyright()                                              ToolDoc
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ToolDoc#getShortCopyright
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Get the tool short copyright string.
+ *
+ * @signature CharString getShortCopyright(toolDoc);
+ *
+ * @param[in] toolDoc The ToolDoc object to the get the short copyright string.
+ *
+ * @return CharString Resulting short copyright string (@link CharString @endlink).
+ */
+
+inline CharString const & getShortCopyright(ToolDoc const & doc)
+{
+    return doc._shortCopyright;
+}
+
+// --------------------------------------------------------------------------
+// Function setLongCopyright()                                              ToolDoc
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ToolDoc#setLongCopyright
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Set the tool long copyright string.
+ *
+ * @signature void setLongCopyright(toolDoc, str);
+ *
+ * @param[in,out] toolDoc The ToolDoc object to the set the long copyright string for.
+ * @param[in]     str     The long copyright string of the tool (@link CharString @endlink).
+ */
+
+inline void setLongCopyright(ToolDoc & doc, CharString const & longCopyright)
+{
+    doc._longCopyright = longCopyright;
+}
+
+// --------------------------------------------------------------------------
+// Function getLongCopyright()                                              ToolDoc
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ToolDoc#getLongCopyright
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Get the tool long copyright string.
+ *
+ * @signature CharString getLongCopyright(toolDoc);
+ *
+ * @param[in] toolDoc The ToolDoc object to the get the long copyright string.
+ *
+ * @return CharString Resulting long copyright string (@link CharString @endlink).
+ */
+
+inline CharString const & getLongCopyright(ToolDoc const & doc)
+{
+    return doc._longCopyright;
+}
+
+// --------------------------------------------------------------------------
+// Function setCitation()                                              ToolDoc
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ToolDoc#setCitation
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Set the tool citation string.
+ *
+ * @signature void setCitation(toolDoc, str);
+ *
+ * @param[in,out] toolDoc The ToolDoc object to the set the citation string for.
+ * @param[in]     str     The citation string of the tool (@link CharString @endlink).
+ */
+
+inline void setCitation(ToolDoc & doc, CharString const & citation)
+{
+    doc._citation = citation;
+}
+
+// --------------------------------------------------------------------------
+// Function getCitation()                                              ToolDoc
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ToolDoc#getCitation
+ * @headerfile <seqan/arg_parse.h>
+ * @brief Get the tool citation string.
+ *
+ * @signature CharString getCitation(toolDoc);
+ *
+ * @param[in] toolDoc The ToolDoc object to the get the citation string.
+ *
+ * @return CharString Resulting citation string (@link CharString @endlink).
+ */
+
+inline CharString const & getCitation(ToolDoc const & doc)
+{
+    return doc._citation;
+}
+
+
 // --------------------------------------------------------------------------
 // Function setManTitle()                                             ToolDoc
 // --------------------------------------------------------------------------
@@ -1162,24 +1090,10 @@ inline CharString const & getVersion(ToolDoc const & doc)
  *
  * @signature void setTitle(toolDoc, title);
  *
- * @param toolDoc The ToolDoc object to the set the title for.
- * @param title   The title of the tool (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to the set the title for.
+ * @param[in]     title   The title of the tool (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#setManTitle
-..cat:Miscellaneous
-..summary:Set version string for @Class.ToolDoc@ object.
-..signature:setManTitle(doc, title)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to set the man title to.
-...type:Class.ToolDoc
-..param.title:Title string to set.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void setManTitle(ToolDoc & doc, CharString const & title)
 {
     doc._manTitle = title;
@@ -1196,31 +1110,18 @@ inline void setManTitle(ToolDoc & doc, CharString const & title)
  *
  * @signature CharString getManTitle(toolDoc);
  *
- * @param toolDoc The ToolDoc object to the get the man page title.
+ * @param[in] toolDoc The ToolDoc object to the get the man page title.
  *
  * @return CharString Resulting man page title (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#getManTitle
-..cat:Miscellaneous
-..summary:Get man title from @Class.ToolDoc@ object.
-..signature:getManTitle(doc)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to get the man title of.
-...type:Class.ToolDoc
-..returns:Man title.
-...type:Shortcut.CharString
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline CharString const & getManTitle(ToolDoc & doc)
 {
     return doc._manTitle;
 }
 
 // --------------------------------------------------------------------------
-// Function addSection()                                              ToolDoc
+// Function addSection()ToolDoc
 // --------------------------------------------------------------------------
 
 /*!
@@ -1230,24 +1131,10 @@ inline CharString const & getManTitle(ToolDoc & doc)
  *
  * @signature void addSection(toolDoc, title);
  *
- * @param toolDoc The ToolDoc object to add a section for.
- * @param title   The section title (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to add a section for.
+ * @param[in]     title   The section title (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#addSection
-..cat:Miscellaneous
-..summary:Add section to @Class.ToolDoc@ object.
-..signature:addSection(doc, title)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to add section to.
-...type:Class.ToolDoc
-..param.title:Section title.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void addSection(ToolDoc & doc, CharString const & title)
 {
     appendValue(doc._entries, new ToolDocSection_(title));
@@ -1264,24 +1151,10 @@ inline void addSection(ToolDoc & doc, CharString const & title)
  *
  * @signature void addSubSection(toolDoc, title);
  *
- * @param toolDoc The ToolDoc object to add a subsection for.
- * @param title   The subsection title (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to add a subsection for.
+ * @param[in]     title   The subsection title (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#addSubSection
-..cat:Miscellaneous
-..summary:Add subsection to @Class.ToolDoc@ object.
-..signature:addSubSection(doc, title)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to add subsection to.
-...type:Class.ToolDoc
-..param.title:Subsection title.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void addSubSection(ToolDoc & doc, CharString const & title)
 {
     appendValue(doc._entries, new ToolDocSubSection_(title));
@@ -1298,29 +1171,11 @@ inline void addSubSection(ToolDoc & doc, CharString const & title)
  *
  * @signature void addText(toolDoc, text[, isParagraph]);
  *
- * @param toolDoc     The ToolDoc to add the text to.
- * @param text        The text to add (@link CharString @endlink).
- * @param isParagraph Whether to insert as paragraph or just a line (only one line break if not a paragraph).
+ * @param[in,out] toolDoc     The ToolDoc to add the text to.
+ * @param[in]     text        The text to add (@link CharString @endlink).
+ * @param[in]     isParagraph Whether to insert as paragraph or just a line (only one line break if not a paragraph).
  */
 
-/**
-.Function.ToolDoc#addText
-..cat:Miscellaneous
-..summary:Add text line/paragraph to @Class.ToolDoc@.
-..signature:addText(doc, text, [isParagraph])
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to text to.
-...type:Class.ToolDoc
-..param.text:Text to add.
-...type:Shortcut.CharString
-..param.isParagraph:Whether to insert as paragraph or just a line (only line break in the last case).
-...type:nolink:$bool$
-..returns:$void$
-..remarks:See @Class.ToolDoc@ for information on formatting of text.
-..see:Class.ToolDoc
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void addText(ToolDoc & doc, CharString const & text, bool isParagraph)
 {
     appendValue(doc._entries, new ToolDocLine_(text, isParagraph));
@@ -1342,29 +1197,11 @@ inline void addText(ToolDoc & doc, CharString const & text)
  *
  * @signature void addListItem(toolDoc, key, value);
  *
- * @param toolDoc The ToolDoc object to add the list item to.
- * @param key     The key for the list (@link CharString @endlink).
- * @param value   The value for the list (@link CharString @endlink).
+ * @param[in,out] toolDoc The ToolDoc object to add the list item to.
+ * @param[in]     key     The key for the list (@link CharString @endlink).
+ * @param[in]     value   The value for the list (@link CharString @endlink).
  */
 
-/**
-.Function.ToolDoc#addListItem
-..cat:Miscellaneous
-..summary:Add list item to @Class.ToolDoc@ object.
-..signature:addListItem(doc, key, value)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to add subsection to.
-...type:Class.ToolDoc
-..param.key:List item key.
-...type:Shortcut.CharString
-..param.key:List item value.
-...type:Shortcut.CharString
-..returns:$void$
-..remarks:You can add formatting to both $key$ and $value$. See @Class.ToolDoc@ for information on formatting of text.
-..see:Class.ToolDoc
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void addListItem(ToolDoc & doc, CharString const & key, CharString const & value)
 {
     appendValue(doc._entries, new ToolDocListItem_(key, value));
@@ -1381,27 +1218,11 @@ inline void addListItem(ToolDoc & doc, CharString const & key, CharString const
  *
  * @signature void print(stream, toolDoc, format);
  *
- * @param stream  The <tt>std::ostream</tt> to write to.
- * @param toolDoc The ToolDoc to print.
- * @param format  The format, one of {"html", "man", "txt"}.
+ * @param[in,out] stream  The <tt>std::ostream</tt> to write to.
+ * @param[in]     toolDoc The ToolDoc to print.
+ * @param[in]     format  The format, one of {"html", "man", "txt"}.
  */
 
-/**
-.Function.ToolDoc#print
-..cat:Miscellaneous
-..summary:Print @Class.ToolDoc@ object in a given format.
-..signature:print(stream, doc, format)
-..class:Class.ToolDoc
-..param.stream:List item key.
-...type:nolink:$std::ostream$
-..param.doc:Tool documentation object to print.
-...type:Class.ToolDoc
-..param.format:Format to print in. One of "html", "man", "txt".
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void print(std::ostream & stream, ToolDoc const & doc, CharString const & format)
 {
     doc.print(stream, format);
@@ -1418,21 +1239,9 @@ inline void print(std::ostream & stream, ToolDoc const & doc, CharString const &
  *
  * @signature void clearEntries(toolDoc);
  *
- * @param toolDoc The ToolDoc object to clear entries from.
+ * @param[in,out] toolDoc The ToolDoc object to clear entries from.
  */
 
-/**
-.Function.ToolDoc#clearEntries
-..cat:Miscellaneous
-..summary:Clear entries from @Class.ToolDoc@ object.
-..signature:clearEntries(doc)
-..class:Class.ToolDoc
-..param.doc:Tool documentation object to clear.
-...type:Class.ToolDoc
-..returns:$void$
-..include:seqan/arg_parse/tool_doc.h
-*/
-
 inline void clearEntries(ToolDoc & doc)
 {
     typedef Iterator<String<ToolDocEntry_ *>, Rooted>::Type TIter;
@@ -1525,8 +1334,33 @@ void HtmlToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
 
     // Print version and date.
     stream << "<h2>Version</h2>\n"
-           << "<p>Last update: " << _toHtml(doc._date) << ", " << doc._name
-           << " version: " << doc._version << "</p>\n";
+           << "<strong>Last update:</strong> " << _toHtml(doc._date) << "<br>\n<strong>"
+           << doc._name << " version:</strong> " << doc._version << "<br>\n"
+           << "<strong>SeqAn version:</strong> " << SEQAN_VERSION_MAJOR << '.' <<  SEQAN_VERSION_MINOR << '.'
+           << SEQAN_VERSION_PATCH;
+    if (SEQAN_VERSION_PRE_RELEASE != 0)
+        stream << "-pre" << SEQAN_VERSION_PRE_RELEASE;
+    stream << "<br>\n";
+
+    // Print legal stuff
+    if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation)))
+    {
+        stream << "<h2>Legal</h2>\n<strong>";
+
+        if (!empty(doc._shortCopyright))
+            stream << doc._name << " Copyright: </strong>"
+                   << doc._shortCopyright << "<br>\n<strong>";
+
+        stream << "SeqAn Copyright:</strong> 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.<br>\n<strong>";
+
+        if (!empty(doc._citation))
+            stream << "In your academic works please cite:</strong> " << doc._citation << "<br>\n";
+        else
+            stream << "</strong>";
+
+        if (!empty(doc._longCopyright))
+            stream << "For full copyright and/or warranty information see <tt>--copyright</tt>.\n";
+    }
 
     // Print HTML boilerplate footer.
     stream << "</body></html>";
@@ -1598,9 +1432,43 @@ void TextToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
     // Print version and date.
     stream << "\n" << _toText("\\fB") << "VERSION" << _toText("\\fP") << "\n";
     std::fill_n(out, _layout.leftPadding, ' ');
-    stream << doc._name << " version: " << doc._version << "\n";
+    stream << _toText("\\fB") << "Last update: " << _toText("\\fP") << doc._date << "\n";
+    std::fill_n(out, _layout.leftPadding, ' ');
+    stream << _toText("\\fB") << doc._name << " version: " << _toText("\\fP") << doc._version << "\n";
     std::fill_n(out, _layout.leftPadding, ' ');
-    stream << "Last update " << doc._date << "\n";
+    stream << _toText("\\fB") << "SeqAn version: " << _toText("\\fP") << SEQAN_VERSION_MAJOR << '.'
+           <<  SEQAN_VERSION_MINOR << '.' << SEQAN_VERSION_PATCH;
+    if (SEQAN_VERSION_PRE_RELEASE != 0)
+        stream << "-pre" << SEQAN_VERSION_PRE_RELEASE;
+    stream << "\n";
+
+    // Print legal stuff
+    if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation)))
+    {
+        stream << "\n" << _toText("\\fB") << "LEGAL" << _toText("\\fP") << "\n";
+
+        if (!empty(doc._shortCopyright))
+        {
+            std::fill_n(out, _layout.leftPadding, ' ');
+            stream << _toText("\\fB") << doc._name << " Copyright: "
+                   << _toText("\\fP") << doc._shortCopyright << "\n";
+        }
+        std::fill_n(out, _layout.leftPadding, ' ');
+        stream << _toText("\\fB") << "SeqAn Copyright: " << _toText("\\fP")
+               << "2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.\n";
+        if (!empty(doc._citation))
+        {
+            std::fill_n(out, _layout.leftPadding, ' ');
+            stream << _toText("\\fB") << "In your academic works please cite: " << _toText("\\fP")
+                   << doc._citation << "\n";
+        }
+        if (!empty(doc._longCopyright))
+        {
+            std::fill_n(out, _layout.leftPadding, ' ');
+            stream << "For full copyright and/or warranty information see " << _toText("\\fB")
+                   << "--copyright" << _toText("\\fP") << ".\n";
+        }
+    }
 }
 
 inline
@@ -1610,9 +1478,9 @@ void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
 
     // Print .TH line.
     stream << ".TH ";
-    std::transform(begin(doc._name), end(doc._name), out, toupper);
+    std::transform(begin(doc._name), end(doc._name), out, static_cast < int(*)(int) > (toupper));
     stream << " " << doc._manSection << " \"" << doc._date << "\" \"";
-    std::transform(begin(doc._name), end(doc._name), out, tolower);
+    std::transform(begin(doc._name), end(doc._name), out, static_cast < int(*)(int) > (tolower));
     stream << " " << doc._version << "\" \"" << doc._manTitle << "\"\n";
 
     // Print NAME section.
@@ -1639,7 +1507,7 @@ void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
         {
             ToolDocSection_ const * sec = static_cast<ToolDocSection_ const *>(entry);
             stream << ".SH ";
-            std::transform(begin(sec->_title), end(sec->_title), out, toupper);
+            std::transform(begin(sec->_title), end(sec->_title), out, static_cast < int(*)(int) > (toupper));
             stream << "\n";
             isFirstInSection = true;
         }
@@ -1668,8 +1536,25 @@ void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
         break;
         }
     }
+
+    // Print legal stuff
+    if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation)))
+    {
+        stream << ".SH LEGAL\n";
+
+        if (!empty(doc._shortCopyright))
+            stream << "\\fB" << doc._name << " Copyright:\\fR " << doc._shortCopyright << "\n.br\n";
+
+        stream << "\\fBSeqAn Copyright:\\fR 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.\n.br\n";
+
+        if (!empty(doc._citation))
+            stream << "\\fBIn your academic works please cite:\\fR " << doc._citation << "\n.br\n";
+
+        if (!empty(doc._longCopyright))
+            stream << "For full copyright and/or warranty information see \\fB--copyright\\fR.\n";
+    }
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_MISC_TOOL_DOC_H_
+#endif  // #ifndef SEQAN_INCLUDE_MISC_TOOL_DOC_H_
diff --git a/seqan/arg_parse/xml_support.h b/seqan/arg_parse/xml_support.h
index 14db0ce..a5120ff 100644
--- a/seqan/arg_parse/xml_support.h
+++ b/seqan/arg_parse/xml_support.h
@@ -1,7 +1,7 @@
 // ==========================================================================
-//                               xml_support.h
+//                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_
-#define CORE_INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_
+#ifndef INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_
+#define INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_
 
 namespace seqan {
 
@@ -66,15 +66,6 @@ namespace seqan {
  *  < -> &lt;
  *  > -> &gt;
  */
-/**
-.Function.xmlEscape:
-..summary:Replaces invalid XML characters in the given sequence with their valid XML equivalent.
-..cat:Miscellaneous
-..signature:xmlEscape(sequence)
-..param.sequence:The sequence to escape.
-..returns:An escaped version of the given string.
-..include:seqan/arg_parse/xml_support.h
-*/
 template <typename TSequence>
 TSequence xmlEscape(TSequence const & original)
 {
@@ -94,11 +85,11 @@ TSequence xmlEscape(TSequence const & original)
         else if (value(ch) == '>')
             append(escaped, "&gt;");
         else
-            append(escaped, *ch);
+            appendValue(escaped, *ch);
     }
     return escaped;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_
+#endif  // #ifndef INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_
diff --git a/seqan/bam_io.h b/seqan/bam_io.h
index 66ee7d1..cb4071a 100644
--- a/seqan/bam_io.h
+++ b/seqan/bam_io.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,12 +30,13 @@
 //
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 // Facade header for module bam_io.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_H_
+#define INCLUDE_SEQAN_BAM_IO_H_
 
 // ===========================================================================
 // Prerequisites.
@@ -46,7 +47,7 @@
 #include <seqan/sequence.h>
 #include <seqan/stream.h>
 #include <seqan/align.h>
-#include <seqan/misc/misc_name_store_cache.h>
+#include <seqan/misc/name_store_cache.h>
 
 // ===========================================================================
 // Data Structures & Conversion.
@@ -65,45 +66,36 @@
 
 #include <seqan/bam_io/read_sam.h>
 #include <seqan/bam_io/write_sam.h>
-
-// BAM I/O is only available when ZLIB is available (and thus the BGz Stream).
-#if SEQAN_HAS_ZLIB
 #include <seqan/bam_io/read_bam.h>
 #include <seqan/bam_io/write_bam.h>
-#endif  // #if SEQAN_HAS_ZLIB
 
 // ===========================================================================
-// BAM Index Related.
+// Easy BAM / SAM I/O.
 // ===========================================================================
 
-// BAM indices are only available when ZLIB is available.
-#if SEQAN_HAS_ZLIB
-#include <seqan/bam_io/bam_index_base.h>
-#include <seqan/bam_io/bam_index_bai.h>
-#endif  // #if SEQAN_HAS_ZLIB
+//#include <seqan/bam_io/bam_file.h>
 
 // ===========================================================================
 // Utility Routines.
 // ===========================================================================
 
-#include <seqan/bam_io/bam_alignment_record_util.h>
+#include <seqan/bam_io/bam_alignment_record_util.h> 
+
+// Not included by default, requires C++11
+// #include <seqan/bam_io/bam_scanner_cache.h>
 
 // ===========================================================================
-// Easy BAM / SAM I/O.
+// BAM Index Related.
 // ===========================================================================
 
-#include <seqan/bam_io/xam_reader.h>
-#if SEQAN_HAS_ZLIB
-#include <seqan/bam_io/bam_reader.h>
-#endif  // #if SEQAN_HAS_ZLIB
-#include <seqan/bam_io/sam_reader.h>
+#include <seqan/hts_io.h>
+
+// BAM indices are only available when ZLIB is available.
+// #if SEQAN_HAS_ZLIB
+// #include <seqan/bam_io/bam_index_bai.h>
+// #endif  // #if SEQAN_HAS_ZLIB*/
+
 
-#include <seqan/bam_io/xam_writer.h>
-#if SEQAN_HAS_ZLIB
-#include <seqan/bam_io/bam_writer.h>
-#endif  // #if SEQAN_HAS_ZLIB
-#include <seqan/bam_io/sam_writer.h>
 
-#include <seqan/bam_io/bam_stream.h>
 
-#endif  // CORE_INCLUDE_SEQAN_BAM_IO_H_
+#endif  // INCLUDE_SEQAN_BAM_IO_H_
diff --git a/seqan/bam_io/INFO b/seqan/bam_io/INFO
deleted file mode 100644
index 16e6f47..0000000
--- a/seqan/bam_io/INFO
+++ /dev/null
@@ -1,12 +0,0 @@
-Name: seqan-bam_io
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: beta
-Description: BAM and SAM record I/O code.
- This module contains code for streaming through SAM and BAM files.
- .
- It provides data structures for representing alignments, code to work with
- tags and the necessary routines for reading data from and writing data to
- streams.
diff --git a/seqan/bam_io/bam_alignment_record.h b/seqan/bam_io/bam_alignment_record.h
index fd64316..d7f9537 100644
--- a/seqan/bam_io/bam_alignment_record.h
+++ b/seqan/bam_io/bam_alignment_record.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,10 @@
 // The class BamAlignmentRecord, flag checking methods, flag constants.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_
+#define INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_
+
+#include <seqan/bam_io/cigar.h>
 
 namespace seqan {
 
@@ -57,63 +59,43 @@ inline void clear(BamAlignmentRecord & record);
  *
  * @signature enum BamFlags;
  *
- * @var BamFlags BAM_FLAG_MULTIPLE = 0x0001;
+ * @val BamFlags BAM_FLAG_MULTIPLE = 0x0001;
  * @brief Template has multiple fragments in sequencing.
  *
- * @var BamFlags BAM_FLAG_ALL_PROPER = 0x0002;
+ * @val BamFlags BAM_FLAG_ALL_PROPER = 0x0002;
  * @brief All fragments in the template are properly mapped.
  *
- * @var BamFlags BAM_FLAG_UNMAPPED = 0x0004;
+ * @val BamFlags BAM_FLAG_UNMAPPED = 0x0004;
  * @brief This fragment is unmapped.
  *
- * @var BamFlags BAM_FLAG_NEXT_UNMAPPED = 0x0008;
+ * @val BamFlags BAM_FLAG_NEXT_UNMAPPED = 0x0008;
  * @brief Next fragment in template is unmapped.
  *
- * @var BamFlags BAM_FLAG_RC = 0x0010;
+ * @val BamFlags BAM_FLAG_RC = 0x0010;
  * @brief Fragment is reverse-complemented.
  *
- * @var BamFlags BAM_FLAG_NEXT_RC = 0x0020;
+ * @val BamFlags BAM_FLAG_NEXT_RC = 0x0020;
  * @brief Next fragment in template is reverse-complemented.
  *
- * @var BamFlags BAM_FLAG_FIRST = 0x0040;
+ * @val BamFlags BAM_FLAG_FIRST = 0x0040;
  * @brief This fragment is the first one in its template.
  *
- * @var BamFlags BAM_FLAG_LAST = 0x0080;
+ * @val BamFlags BAM_FLAG_LAST = 0x0080;
  * @brief This fragment is the last one in its template (second in case of paired sequencing).
  *
- * @var BamFlags BAM_FLAG_SECONDARY = 0x0100;
+ * @val BamFlags BAM_FLAG_SECONDARY = 0x0100;
  * @brief Secondary alignment.
  *
- * @var BamFlags BAM_FLAG_QC_NO_PASS = 0x0200;
+ * @val BamFlags BAM_FLAG_QC_NO_PASS = 0x0200;
  * @brief Does not pass quality controls.
  *
- * @var BamFlags BAM_FLAG_DUPLICATE = 0x0400;
+ * @val BamFlags BAM_FLAG_DUPLICATE = 0x0400;
  * @brief PCR or optical duplicate.
  *
  * @var BamFlags BAM_FLAG_SUPPLEMENTARY = 0x0800;
  * @brief Supplementary alignment.
  */
 
-/**
-.Enum.BamFlags
-..cat:BAM I/O
-..signature:BamFlags
-..summary:Shortcuts to the bitmask flags for BAM/SAM files.
-..value.BAM_FLAG_MULTIPLE:$0x0001$ Template has multiple fragments in sequencing.
-..value.BAM_FLAG_ALL_PROPER:$0x0002$ All fragments have been aligned properly.
-..value.BAM_FLAG_UNMAPPED:$0x0004$ This fragment could not be mapped.
-..value.BAM_FLAG_NEXT_UNMAPPED:$0x0008$ Next fragment is unmapped.
-..value.BAM_FLAG_RC:$0x0010$ This fragment is reverse-complemented.
-..value.BAM_FLAG_NEXT_RC:$0x0020$ Next fragment is reverse-complemented.
-..value.BAM_FLAG_FIRST:$0x0040$ This fragment is the first one in its template.
-..value.BAM_FLAG_LAST:$0x0080$ This fragment is the last one in its template.
-..value.BAM_FLAG_SECONDARY:$0x0100$ This is a secondary alignment.
-..value.BAM_FLAG_QC_NO_PASS:$0x0200$ Does not pass quality controls.
-..value.BAM_FLAG_DUPLICATE:$0x0400$ PCR or optical duplicate.
-..remarks:Also see the SAM standard on these flags for more explanation.
-..include:seqan/bam_io.h
-*/
-
 enum BamFlags
 {
     BAM_FLAG_MULTIPLE      = 0x0001,
@@ -130,24 +112,56 @@ enum BamFlags
     BAM_FLAG_SUPPLEMENTARY = 0x0800
 };
 
+template <typename TValue>
+struct BamTypeChar
+{
+    enum
+    {
+        VALUE =
+            (IsSameType<TValue, char>::VALUE)?              'A':
+            (IsSameType<TValue, signed char>::VALUE)?       'c':
+            (IsSameType<TValue, unsigned char>::VALUE)?     'C':
+            (IsSameType<TValue, short>::VALUE)?             's':
+            (IsSameType<TValue, unsigned short>::VALUE)?    'S':
+            (IsSameType<TValue, int>::VALUE)?               'i':
+            (IsSameType<TValue, unsigned int>::VALUE)?      'I':
+            (IsSameType<TValue, float>::VALUE)?             'f':
+//          (IsSameType<TValue, double>::VALUE)?            'd':
+            (IsSequence<TValue>::VALUE)?                    'Z':
+                                                            '?'
+    };
+};
+
+// List of primitive BAM types (ordered by expected usage frequency)
+typedef TagList<int,
+        TagList<unsigned int,
+        TagList<float,
+        TagList<short,
+        TagList<unsigned short,
+        TagList<char,
+        TagList<unsigned char,
+        TagList<signed char
+//      TagList<double
+        > > > > > > > > BamTagTypes;
+
+// ----------------------------------------------------------------------------
+// Class BamAlignmentRecord
+// ----------------------------------------------------------------------------
+
 /*!
  * @class BamAlignmentRecord
  * @headerfile <seqan/bam_io.h>
- * @brief Represent a record from a BAM or SAM file.
- *
+ * @implements FormattedFileRecordConcept
  * @signature class BamAlignmentRecord;
+ * @brief Represent a record from a BAM or SAM file.
  *
  * @section Remarks
  *
  * While also used to represent SAM records, the type is called <tt>BamAlignmentRecord</tt> since the data directly
  * reflects a BAM records (0-based positions, identify references by id, and tags are stored in BAM format.
- */
-
-/*!
- * @fn BamAlignmentRecord::BamAlignmentRecord
- * @brief Default constructor.
  *
- * @signature BamAlignmentRecord::BamAlignmentRecord();
+ * @see BamFileIn
+ * @see BamFileOut
  */
 
 /*!
@@ -160,13 +174,13 @@ enum BamFlags
  * @var __uint32 BamAlignmentRecord::INVALID_LEN
  * @brief Static member with invalid/sentinel reference ids (0 as in BAM/SAM).
  *
- * @var CharString BamAlignmentRecord::qName
+ * @var CharString BamAlignmentRecord::qName;
  * @brief The query/read name.
  *
  * Note that the reads of a template all of the same query name and are differentiated by their position
  * and the <tt>BAM_FLAG_FIRST</tt>/<tt>BAM_FLAG_LAST</tt> flag values.
  *
- * @var __uint16 BamAlignmentRecord::flag
+ * @var __uint16 BamAlignmentRecord::flag;
  * @brief The flag of this mapping.
  *
  * See @link BamFlags @endlink for flag constants and also see the <tt>hasFlag*()</tt> functions.
@@ -211,131 +225,40 @@ enum BamFlags
  * @brief Raw BAM tag string, use @link BamTagsDict @endlink for comfortable access.
  */
 
-/**
-.Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Represent a record from a BAM/SAM file.
-..remarks:While also used to represent SAM records, called $BamAlignmentRecord$ since the data directly reflects a BAM record (0-based positions, identify references by ids, not names, tags stored in BAM format.)
-..include:seqan/bam_io.h
-..see:Enum.BamFlags
-
-.Memfunc.BamAlignmentRecord#BamAlignmentRecord
-..class:Class.BamAlignmentRecord
-..summary:Constructor.
-..signature:BamAlignmentRecord()
-..remarks:Only the default constructor is provided.
-
-.Memvar.BamAlignmentRecord#INVALID_POS
-..class:Class.BamAlignmentRecord
-..summary:Static member with invalid/sentinel position value (-1).
-..type:nolink:$__uint32$
-
-.Memvar.BamAlignmentRecord#INVALID_REFID
-..class:Class.BamAlignmentRecord
-..summary:Static member with invalid/sentinel reference id (-1).
-..type:nolink:$__int32$
-
-.Memvar.BamAlignmentRecord#INVALID_LEN
-..class:Class.BamAlignmentRecord
-..summary:Static member with invalid/sentinel position value (0 as in BAM/SAM).
-..type:nolink:$__int32$
-
-.Memvar.BamAlignmentRecord#qName
-..class:Class.BamAlignmentRecord
-..summary:The read/query name.
-..type:Shortcut.CharString
-
-.Memvar.BamAlignmentRecord#flag
-..class:Class.BamAlignmentRecord
-..summary:The flag of this mapping, see @Enum.BamFlags@ for flag constants and the $hasFlag*$ functions.
-..type:nolink:$__uint16$
-
-.Memvar.BamAlignmentRecord#rID
-..class:Class.BamAlignmentRecord
-..summary:ID of reference for this fragment mapping (0-based, $INVALID_REFID$ for '*' in SAM).
-..type:nolink:$__int32$
-
-.Memvar.BamAlignmentRecord#beginPos
-..class:Class.BamAlignmentRecord
-..summary:The position of this fragment mapping (0-based, $INVALID_POS$ for '*' in SAM).
-..type:nolink:$__int32$
-
-.Memvar.BamAlignmentRecord#mapQ
-..class:Class.BamAlignmentRecord
-..summary:The mapping quality (255 for '*').
-..type:nolink:$__uint8$
-
-.Memvar.BamAlignmentRecord#bin
-..class:Class.BamAlignmentRecord
-..summary:The bin of the alignment, automatically computed when writing BAM.
-..type:nolink:$__uint16$
-
-.Memvar.BamAlignmentRecord#cigar
-..class:Class.BamAlignmentRecord
-..summary:The CIGAR string as string of @Class.CigarElement@ objects (empty for '*').
-..type:nolink:$String<CigarElement<> >$
-
-.Memvar.BamAlignmentRecord#rNextId
-..class:Class.BamAlignmentRecord
-..summary:ID of reference for next fragment mapping (0-based, $INVALID_REFID$ for '*')
-..type:nolink:$__int32$
-
-.Memvar.BamAlignmentRecord#pNext
-..class:Class.BamAlignmentRecord
-..summary:Position of next fragment mapping (0-based, $INVALID_POS$ for '*')
-..type:nolink:$__uint32$
-
-.Memvar.BamAlignmentRecord#tLen
-..class:Class.BamAlignmentRecord
-..summary:The inferred template size ($INVALID_LEN$ for '*')
-..type:nolink:$__int32$
-
-.Memvar.BamAlignmentRecord#seq
-..class:Class.BamAlignmentRecord
-..summary:The sequence string (empty for '*').
-..type:Shortcut.CharString
-
-.Memvar.BamAlignmentRecord#qual
-..class:Class.BamAlignmentRecord
-..summary:String with Phred scores (as in SAM file, empty for '*').
-..type:Shortcut.CharString
-
-.Memvar.BamAlignmentRecord#tags
-..class:Class.BamAlignmentRecord
-..summary:Raw BAM tag string, use @Class.BamTagsDict@ for comfortable access.
-..type:Shortcut.CharString
-*/
-
-class BamAlignmentRecord
+struct BamAlignmentRecordCore
 {
-public:
-    static __int32 const INVALID_POS = -1;
-    static __int32 const INVALID_REFID = -1;  // TODO(holtgrew): Rename to ...REF_ID.
-    static __int32 const INVALID_LEN = 0;
-    static __uint32 const INVALID_QID = 4294967295u;  // TODO(holtgrew): Undocumented as of yet.
+            __int32 rID;
+            __int32 beginPos;
+    mutable __uint32 _l_qname:8;
+            __uint32 mapQ:8;
+    mutable __uint32 bin:16;
+    mutable __uint32 _n_cigar:16;
+            __uint32 flag:16;
+    mutable __int32 _l_qseq;  // _l_qname, _n_cigar and _l_qseq for internal usage
+            __int32 rNextId;
+            __int32 pNext;
+            __int32 tLen;
+};
 
+class BamAlignmentRecord : public BamAlignmentRecordCore
+{
+public:
     __uint32 _qID;  // TODO(holtgrew): Undocumented as of yet.
-    CharString qName;
-    __uint16 flag;
-    __int32 rID;
-    __int32 beginPos;
-    __uint8 mapQ;
-    __uint16 bin;
     String<CigarElement<> > cigar;
-    __int32 rNextId;
-    __int32 pNext;
-    __int32 tLen;
-    CharString seq;
+    CharString qName;
+    IupacString seq;
     CharString qual;
     CharString tags;  // raw tags in BAM format
+    CharString _buffer; // reusable internal buffer (used for I/O)
+
+    static __int32 const INVALID_POS = -1;
+    static __int32 const INVALID_REFID = -1;  // TODO(holtgrew): Rename to ...REF_ID.
+    static __int32 const INVALID_LEN = 0;
+    static __uint32 const INVALID_QID = 4294967295u;  // TODO(holtgrew): Undocumented as of yet.
 
     BamAlignmentRecord() : _qID(MaxValue<unsigned>::VALUE) { clear(*this); }
 };
 
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
 // ============================================================================
 // Functions
 // ============================================================================
@@ -350,18 +273,16 @@ class BamAlignmentRecord
  *
  * @signature void clear(record);
  *
- * @param record The BamAlignmentRecord to clear.
+ * @param[in,out] record The BamAlignmentRecord to clear.
  *
  * Clears all strings and resets it to default initialization state.
  */
 
-///.Function.clear.param.object.type:Class.BamAlignmentRecord
-///.Function.clear.class:Class.BamAlignmentRecord
-
 inline void
 clear(BamAlignmentRecord & record)
 {
     clear(record.qName);
+    record.flag = 0;
     record._qID = MaxValue<__uint32>::VALUE;
     record.rID = BamAlignmentRecord::INVALID_REFID;
     record.beginPos = BamAlignmentRecord::INVALID_POS;
@@ -387,39 +308,25 @@ clear(BamAlignmentRecord & record)
  *
  * @signature bool hasFlagMultiple(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagMultiple
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "multiple" flag set.
-..signature:hasFlagMultiple(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagMultiple(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_MULTIPLE) == BAM_FLAG_MULTIPLE;
 }
 
+inline void
+toggleFlagMultiple(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_MULTIPLE;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagAllProper()
 // ----------------------------------------------------------------------------
@@ -431,39 +338,25 @@ hasFlagMultiple(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagAllProper(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagAllProper
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "all properly aligned" flag set.
-..signature:hasFlagAllProper(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagAllProper(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_ALL_PROPER) == BAM_FLAG_ALL_PROPER;
 }
 
+inline void
+toggleFlagAllProper(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_ALL_PROPER;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagUnmapped()
 // ----------------------------------------------------------------------------
@@ -475,39 +368,26 @@ hasFlagAllProper(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagUnmapped(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagUnmapped
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "fragment unmapped" flag set.
-..signature:hasFlagUnmapped(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagUnmapped(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_UNMAPPED) == BAM_FLAG_UNMAPPED;
 }
 
+inline void
+toggleFlagUnmapped(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_UNMAPPED;
+}
+
+
 // ----------------------------------------------------------------------------
 // Function hasFlagNextUnmapped()
 // ----------------------------------------------------------------------------
@@ -519,39 +399,25 @@ hasFlagUnmapped(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagNextUnmapped(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagNextUnmapped
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "next fragment unmapped" flag set.
-..signature:hasFlagNextUnmapped(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagNextUnmapped(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_NEXT_UNMAPPED) == BAM_FLAG_NEXT_UNMAPPED;
 }
 
+inline void
+toggleFlagNextUnmapped(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_NEXT_UNMAPPED;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagRC()
 // ----------------------------------------------------------------------------
@@ -563,39 +429,25 @@ hasFlagNextUnmapped(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagRC(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagRC
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "reverse-complemented" flag set.
-..signature:hasFlagRC(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
 inline bool
 hasFlagRC(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_RC) == BAM_FLAG_RC;
 }
 
+inline void
+toggleFlagRC(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_RC;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagNextRC()
 // ----------------------------------------------------------------------------
@@ -607,39 +459,25 @@ hasFlagRC(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagNextRC(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagNextRC
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "next fragment reverse-complemented" flag set.
-..signature:hasFlagNextRC(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagNextRC(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_NEXT_RC) == BAM_FLAG_NEXT_RC;
 }
 
+inline void
+toggleFlagNextRC(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_NEXT_RC;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagFirst()
 // ----------------------------------------------------------------------------
@@ -651,39 +489,25 @@ hasFlagNextRC(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagFirst(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagFirst
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "first fragment of template" flag set.
-..signature:hasFlagFirst(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagFirst(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_FIRST) == BAM_FLAG_FIRST;
 }
 
+inline void
+toggleFlagFirst(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_FIRST;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagLast()
 // ----------------------------------------------------------------------------
@@ -695,39 +519,25 @@ hasFlagFirst(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagLast(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagLast
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "last fragment of template" flag set.
-..signature:hasFlagLast(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagLast(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_LAST) == BAM_FLAG_LAST;
 }
 
+inline void
+toggleFlagLast(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_LAST;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagSecondary()
 // ----------------------------------------------------------------------------
@@ -739,39 +549,25 @@ hasFlagLast(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagSecondary(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagSecondary
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "secondary alignment" flag set.
-..signature:hasFlagSecondary(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagQCNoPass
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagSecondary(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_SECONDARY) == BAM_FLAG_SECONDARY;
 }
 
+inline void
+toggleFlagSecondary(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_SECONDARY;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagQCNoPass()
 // ----------------------------------------------------------------------------
@@ -783,39 +579,25 @@ hasFlagSecondary(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagQCNoPass(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagQCNoPass
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "does not pass quality controls" flag set.
-..signature:hasFlagQCNoPass(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagDuplicate
-*/
-
 inline bool
 hasFlagQCNoPass(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_QC_NO_PASS) == BAM_FLAG_QC_NO_PASS;
 }
 
+inline void
+toggleFlagQCNoPass(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_QC_NO_PASS;
+}
+
 // ----------------------------------------------------------------------------
 // Function hasFlagDuplicate()
 // ----------------------------------------------------------------------------
@@ -827,39 +609,26 @@ hasFlagQCNoPass(BamAlignmentRecord const & record)
  *
  * @signature bool hasFlagDuplicate(record);
  *
- * @param record The BamAlignmentRecord to query.
+ * @param[in] record The BamAlignmentRecord to query.
  *
  * @return bool <tt>true</tt> if the flag is set, <tt>false</tt> otherwise.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.hasFlagDuplicate
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Return true if a @Class.BamAlignmentRecord@ has the "PCR or optical duplicate" flag set.
-..signature:hasFlagDuplicate(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$bool$, indicating the flag's status.
-..include:seqan/bam_io.h
-..see:Function.hasFlagMultiple
-..see:Function.hasFlagAllProper
-..see:Function.hasFlagUnmapped
-..see:Function.hasFlagNextUnmapped
-..see:Function.hasFlagRC
-..see:Function.hasFlagNextRC
-..see:Function.hasFlagFirst
-..see:Function.hasFlagLast
-..see:Function.hasFlagSecondary
-..see:Function.hasFlagQCNoPass
-*/
-
 inline bool
 hasFlagDuplicate(BamAlignmentRecord const & record)
 {
     return (record.flag & BAM_FLAG_DUPLICATE) == BAM_FLAG_DUPLICATE;
 }
 
+inline void
+toggleFlagDuplicate(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_DUPLICATE;
+}
+
+
 // ----------------------------------------------------------------------------
 // Function hasFlagSupplementary()
 // ----------------------------------------------------------------------------
@@ -882,6 +651,12 @@ hasFlagSupplementary(BamAlignmentRecord const & record)
     return (record.flag & BAM_FLAG_SUPPLEMENTARY) == BAM_FLAG_SUPPLEMENTARY;
 }
 
+inline void
+toggleFlagSupplementary(BamAlignmentRecord & record)
+{
+    record.flag ^= BAM_FLAG_SUPPLEMENTARY;
+}
+
 // ----------------------------------------------------------------------------
 // Function getAlignmentLengthInRef()
 // ----------------------------------------------------------------------------
@@ -893,31 +668,21 @@ hasFlagSupplementary(BamAlignmentRecord const & record)
  *
  * @signature unsigned getAlignmentLengthInRef(record);
  *
- * @param record The BamAlignmentRecord to compute length for.
+ * @param[in] record The BamAlignmentRecord to compute length for.
  *
  * @return unsigned The alignment length.
+ *
+ * @see BamFlags
  */
 
-/**
-.Function.getAlignmentLengthInRef
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Returns length of @Class.BamAlignmentRecord@'s projection in reference.
-..signature:getAlignmentLengthInRef(record)
-..param.record:The record to query.
-...type:Class.BamAlignmentRecord
-..returns:$unsigned$, the alignment length in the reference.
-..include:seqan/bam_io.h
-*/
-
 inline unsigned
 getAlignmentLengthInRef(BamAlignmentRecord const & record)
 {
     unsigned l = 0;
-    _getLengthInRef(record.cigar, l);
+    _getLengthInRef(l, record.cigar);
     return l;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_
diff --git a/seqan/bam_io/bam_alignment_record_util.h b/seqan/bam_io/bam_alignment_record_util.h
index bb9dd44..f0fc724 100644
--- a/seqan/bam_io/bam_alignment_record_util.h
+++ b/seqan/bam_io/bam_alignment_record_util.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,26 +32,64 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_
+#define INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_
 
 namespace seqan {
 
 // ============================================================================
-// Forwards
+// Functions
 // ============================================================================
 
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
+// ----------------------------------------------------------------------------
+// Function getContigName()
+// ----------------------------------------------------------------------------
 
-// ============================================================================
-// Metafunctions
-// ============================================================================
+/*!
+ * @fn BamAlignmentRecord#getContigName
+ * @brief Return the name of the reference contig of a @link BamAlignmentRecord @endlink.
+ *
+ * @signature TNameString getContigName(record, file);
+ *
+ * @param[in] record The @link BamAlignmentRecord @endlink to query.
+ * @param[in] file The @link BamFileIn @endlink or @link BamFileOut @endlink where the record belongs to.
+ *
+ * @return TNameString The name of the reference contig. <tt>TNameString</tt> is the @link Value @endlink type of the NameStore.
+ *         The NameStore type can be determined using the @link Member @endlink metafunction
+ *         for the @link BamIOContext @endlink in conjunction with the @link BamIOContextMemberTag#NameStoreMember @endlink tag.
+ */
 
-// ============================================================================
-// Functions
-// ============================================================================
+template <typename TDirection, typename TSpec>
+inline typename Value<typename Member<typename FormattedFileContext<FormattedFile<Bam, TDirection, TSpec>, Dependent<> >::Type, NameStoreMember>::Type>::Type const &
+getContigName(BamAlignmentRecord const & record, FormattedFile<Bam, TDirection, TSpec> const & file)
+{
+    return contigNames(context(file))[record.rID];
+}
+
+// ----------------------------------------------------------------------------
+// Function getContigLength()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BamAlignmentRecord#getContigLength
+ * @brief Return the length of the reference contig of a @link BamAlignmentRecord @endlink.
+ *
+ * @signature TLength getContigLength(record, file);
+ *
+ * @param[in] record The @link BamAlignmentRecord @endlink to query.
+ * @param[in] file The @link BamFileIn @endlink or @link BamFileOut @endlink where the record belongs to.
+ *
+ * @return TLength The length of the reference contig. <tt>TLength</tt> is the @link Value @endlink type of the LengthStore.
+ *         The LengthStore type can be determined using the @link Member @endlink metafunction
+ *         for the @link BamIOContext @endlink in conjunction with the @link BamIOContextMemberTag#LengthStoreMember @endlink tag.
+ */
+
+template <typename TDirection, typename TSpec>
+inline typename Value<typename Member<typename FormattedFileContext<FormattedFile<Bam, TDirection, TSpec>, Dependent<> >::Type, LengthStoreMember>::Type>::Type
+getContigLength(BamAlignmentRecord const & record, FormattedFile<Bam, TDirection, TSpec> const & file)
+{
+    return contigLengths(context(file))[record.rID];
+}
 
 // ----------------------------------------------------------------------------
 // Function getClippedPos()
@@ -98,7 +136,7 @@ getClippedPos(unsigned & posBegin, unsigned & posEnd, BamAlignmentRecord const &
 
 // Returns clipped infix of seq member.
 
-inline Infix<CharString>::Type
+inline Infix<IupacString>::Type
 clippedSeqInfix(BamAlignmentRecord & record)
 {
     unsigned begPos = 0, endPos = 0;
@@ -106,7 +144,7 @@ clippedSeqInfix(BamAlignmentRecord & record)
     return infix(record.seq, begPos, endPos);
 }
 
-inline Infix<CharString const>::Type
+inline Infix<IupacString const>::Type
 clippedSeqInfix(BamAlignmentRecord const & record)
 {
     unsigned begPos = 0, endPos = 0;
@@ -158,6 +196,8 @@ inline unsigned countPaddings(String<CigarElement<> > const & cigarString)
 // Function bamRecordToAlignment()
 // ----------------------------------------------------------------------------
 
+// TODO(holtgrew): Should rather be a global function?
+
 /*!
  * @fn BamAlignmentRecord#bamRecordToAlignment
  * @headerfile <seqan/bam_io.h>
@@ -165,9 +205,9 @@ inline unsigned countPaddings(String<CigarElement<> > const & cigarString)
  *
  * @signature void bamRecordToAlignment(align, reference, record);
  *
- * @param align     The @link Align @endlink object to create the alignment object in.
- * @param reference The string with the reference that <tt>record</tt> lies on.
- * @param record    The @link BamAlignmentRecord @endlink to construct alignment from.
+ * @param[out] align     The @link Align @endlink object to create the alignment object in.
+ * @param[in]  reference The string with the reference that <tt>record</tt> lies on.
+ * @param[in]  record    The @link BamAlignmentRecord @endlink to construct alignment from.
  *
  * The function will resize <tt>align</tt> to have two rows.  The part of the reference that the read from
  * <tt>record</tt> aligns to will be copied to the first row and the sequence from record will be copied to the second
@@ -190,29 +230,6 @@ inline unsigned countPaddings(String<CigarElement<> > const & cigarString)
 
 // TODO(holtgrew): Convert into full example.
 
-/**
-.Function.bamRecordToAlignment
-..class:Class.BamAlignmentRecord
-..cat:BAM I/O
-..summary:Convert @Class.BamAlignmentRecord@ to an @Class.Align@ object.
-..signature:bamRecordToAlignment(align, reference, record)
-..param.align:The alignment to create.
-...type:Class.Align
-..param.reference:String of Dna, Dna5, ... characters.
-...type:Class.String
-..param.record:The alignment record to convert.
-...type:Class.BamAlignmentRecord
-..returns:$void$
-..include:seqan/bam_io.h
-..example.code:
-StringSet<Dna5String> references;
-BamAlignment record;
-// Read references and record.
-Align<Dna5String> align;
-if (record.rID != BamAlignmentRecord::INVALID_REFID)
-    bamRecordToAlignment(align, references[record.refId], record);
- */
-
 template <typename TSource, typename TSpec, typename TReference>
 void
 bamRecordToAlignment(Align<TSource, TSpec> & result, TReference & reference, BamAlignmentRecord & record)
@@ -225,12 +242,12 @@ bamRecordToAlignment(Align<TSource, TSpec> & result, TReference & reference, Bam
     setSource(row(result, 0), reference);
     setClippedEndPosition(row(result, 0), record.beginPos + len);
     setClippedBeginPosition(row(result, 0), record.beginPos);
-    cigarToGapAnchorContig(record.cigar, row(result, 0));
+    cigarToGapAnchorContig(row(result, 0), record.cigar);
 
     assignSource(row(result, 1), record.seq);
-    cigarToGapAnchorRead(record.cigar, row(result, 1));
+    cigarToGapAnchorRead(row(result, 1), record.cigar);
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_
diff --git a/seqan/bam_io/bam_file.h b/seqan/bam_io/bam_file.h
new file mode 100644
index 0000000..d262943
--- /dev/null
+++ b/seqan/bam_io/bam_file.h
@@ -0,0 +1,382 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Class for reading/writing files in SAM or BAM format.
+// ==========================================================================
+
+#ifndef SEQAN_BAM_IO_BAM_FILE_H_
+#define SEQAN_BAM_IO_BAM_FILE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Typedefs
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Type BamFileIn
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BamFileIn
+ * @signature typedef FormattedFile<Bam, Input> BamFileIn;
+ * @extends FormattedFileIn
+ * @headerfile <seqan/bam_io.h>
+ * @brief Class for reading SAM and BAM files.
+ *
+ * @see BamHeader
+ * @see BamAlignmentRecord
+ *
+ * @section Example
+ *
+ * Access SAM or BAM files.
+ *
+ * @include demos/tutorial/sam_and_bam_io/solution1.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/tutorial/sam_and_bam_io/example.sam
+ */
+
+typedef FormattedFile<Bam, Input> BamFileIn;
+
+// ----------------------------------------------------------------------------
+// Type BamFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BamFileOut
+ * @signature typedef FormattedFile<Bam, Output> BamFileOut;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/bam_io.h>
+ * @brief Class for writing SAM and BAM files.
+ *
+ * @see BamHeader
+ * @see BamAlignmentRecord
+ *
+ * @section Example
+ *
+ * Access SAM or BAM files.
+ *
+ * @include demos/tutorial/sam_and_bam_io/solution1.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/tutorial/sam_and_bam_io/example.sam
+ */
+
+typedef FormattedFile<Bam, Output> BamFileOut;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<Bam, TDirection, TSpec>, TStorageSpec>
+{
+    typedef StringSet<CharString>                                   TNameStore;
+    typedef NameStoreCache<TNameStore>                              TNameStoreCache;
+    typedef BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec>
+struct FileFormat<FormattedFile<Bam, TDirection, TSpec> >
+{
+#if SEQAN_HAS_ZLIB
+    typedef TagSelector<
+                TagList<Bam,
+                TagList<Sam
+                > >
+            > Type;
+#else
+    typedef Sam Type;
+#endif
+};
+
+// --------------------------------------------------------------------------
+// Function _mapBamFormatToCompressionFormat()
+// --------------------------------------------------------------------------
+
+inline BgzfFile
+_mapFileFormatToCompressionFormat(Bam)
+{
+    return BgzfFile();
+}
+
+// ----------------------------------------------------------------------------
+// Function readHeader(); BamHeader
+// ----------------------------------------------------------------------------
+
+// support for dynamically chosen file formats
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readHeader(BamHeader & /* header */,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
+           TForwardIter & /* iter */,
+           TagSelector<> const & /* format */)
+{
+    SEQAN_FAIL("BamFileIn: File format not specified.");
+}
+
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec, typename TTagList>
+inline void
+readHeader(BamHeader & header,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        readHeader(header, context, iter, TFormat());
+    else
+        readHeader(header, context, iter, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+// convient BamFile variant
+template <typename TSpec>
+inline void
+readHeader(BamHeader & header, FormattedFile<Bam, Input, TSpec> & file)
+{
+    readHeader(header, context(file), file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(); BamAlignmentRecord
+// ----------------------------------------------------------------------------
+
+// support for dynamically chosen file formats
+template <typename TBuffer, typename TForwardIter>
+inline void
+_readBamRecord(TBuffer & /* rawRecord */, TForwardIter & /* iter */, TagSelector<> const & /* format */)
+{
+    SEQAN_FAIL("BamFileIn: File format not specified.");
+}
+
+template <typename TBuffer, typename TForwardIter, typename TTagList>
+inline void
+_readBamRecord(TBuffer & rawRecord, TForwardIter & iter, TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        _readBamRecord(rawRecord, iter, TFormat());
+    else
+        _readBamRecord(rawRecord, iter, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(); BamAlignmentRecord
+// ----------------------------------------------------------------------------
+
+// support for dynamically chosen file formats
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readRecord(BamAlignmentRecord & /* record */,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
+           TForwardIter & /* iter */,
+           TagSelector<> const & /* format */)
+{
+    SEQAN_FAIL("BamFileIn: File format not specified.");
+}
+
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec, typename TTagList>
+inline void
+readRecord(BamAlignmentRecord & record,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        readRecord(record, context, iter, TFormat());
+    else
+        readRecord(record, context, iter, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+// convient BamFile variant
+template <typename TSpec>
+inline void
+readRecord(BamAlignmentRecord & record, FormattedFile<Bam, Input, TSpec> & file)
+{
+    readRecord(record, context(file), file.iter, file.format);
+}
+
+template <typename TRecords, typename TSpec, typename TSize>
+inline SEQAN_FUNC_ENABLE_IF(And<IsSameType<typename Value<TRecords>::Type, BamAlignmentRecord>,
+                                IsInteger<TSize> >, TSize)
+readRecords(TRecords & records, FormattedFile<Bam, Input, TSpec> & file, TSize maxRecords)
+{
+    String<CharString> & buffers = context(file).buffers;
+    if (static_cast<TSize>(length(buffers)) < maxRecords)
+        resize(buffers, maxRecords, Exact());
+    if (static_cast<TSize>(length(records)) < maxRecords)
+        resize(records, maxRecords, Exact());
+
+
+    TSize numRecords = 0;
+    for (; numRecords < maxRecords && !atEnd(file.iter); ++numRecords)
+        _readBamRecord(buffers[numRecords], file.iter, file.format);
+
+//    SEQAN_OMP_PRAGMA(parallel for)
+    for (int i = 0; i < (int)numRecords; ++i)
+    {
+        CharIterator bufIter = begin(buffers[i]);
+        readRecord(records[i], context(file), bufIter, file.format);
+    }
+    return numRecords;
+}
+
+// ----------------------------------------------------------------------------
+// Function writeHeader(); BamHeader
+// ----------------------------------------------------------------------------
+
+// support for dynamically chosen file formats
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+write(TTarget & /* target */,
+      BamHeader const & /* header */,
+      BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
+      TagSelector<> const & /* format */)
+{
+    SEQAN_FAIL("BamFileOut: File format not specified.");
+}
+
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec, typename TTagList>
+inline void
+write(TTarget & target,
+      BamHeader const & header,
+      BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+      TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        write(target, header, context, TFormat());
+    else
+        write(target, header, context, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+// convient BamFile variant
+template <typename TSpec>
+inline void
+writeHeader(FormattedFile<Bam, Output, TSpec> & file, BamHeader const & header)
+{
+    write(file.iter, header, context(file), file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(); BamAlignmentRecord
+// ----------------------------------------------------------------------------
+
+// support for dynamically chosen file formats
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+write(TTarget & /* target */,
+      BamAlignmentRecord const & /* record */,
+      BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
+      TagSelector<> const & /* format */)
+{
+    SEQAN_FAIL("BamFileOut: File format not specified.");
+}
+
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec, typename TTagList>
+inline void
+write(TTarget & target,
+      BamAlignmentRecord const & record,
+      BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+      TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        write(target, record, context, TFormat());
+    else
+        write(target, record, context, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+template <typename TSpec>
+inline void
+writeRecord(FormattedFile<Bam, Output, TSpec> & file, BamAlignmentRecord const & record)
+{
+    write(file.iter, record, context(file), file.format);
+}
+
+template <typename TSpec, typename TRecords>
+inline SEQAN_FUNC_ENABLE_IF(IsSameType<typename Value<TRecords>::Type, BamAlignmentRecord>, void)
+writeRecords(FormattedFile<Bam, Output, TSpec> & file, TRecords const & records)
+{
+    String<CharString> & buffers = context(file).buffers;
+    if (length(buffers) < length(records))
+        resize(buffers, length(records));
+
+    SEQAN_OMP_PRAGMA(parallel for)
+    for (int i = 0; i < (int)length(records); ++i)
+    {
+        clear(buffers[i]);
+        write(buffers[i], records[i], context(file), file.format);
+    }
+    for (int i = 0; i < (int)length(records); ++i)
+        write(file.iter, buffers[i]);
+}
+
+// ----------------------------------------------------------------------------
+// Function getFileExtensions()
+// ----------------------------------------------------------------------------
+// NOTE(h-2): this is overloaded so we get Bgzf in addition to other
+// compressions which is crucial for Bam
+
+template <typename TDirection, typename TSpec>
+static std::vector<std::string>
+getFileExtensions(FormattedFile<Bam, TDirection, TSpec> const &)
+{
+    std::vector<std::string> extensions;
+    _getCompressionExtensions(extensions,
+                              typename FormattedFile<Bam, TDirection, TSpec>::TFileFormats(),
+                              CompressedFileTypes(),
+                              false);
+    return extensions;
+}
+
+}  // namespace seqan
+
+#endif // SEQAN_BAM_IO_BAM_FILE_H_
diff --git a/seqan/bam_io/bam_header_record.h b/seqan/bam_io/bam_header_record.h
index 466fdf3..0eeeb42 100644
--- a/seqan/bam_io/bam_header_record.h
+++ b/seqan/bam_io/bam_header_record.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,19 +35,19 @@
 // in headers.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_
+#define INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_
 
 namespace seqan {
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Enum BamHeaderRecordType
+// ----------------------------------------------------------------------------
+
 /*!
  * @enum BamHeaderRecordType
  * @headerfile <seqan/bam_io.h>
@@ -55,35 +55,22 @@ namespace seqan {
  *
  * @signature enum BamHeaderRecordType;
  *
- * @var BamHeaderRecordType BAM_HEADER_FIRST = 0;
+ * @val BamHeaderRecordType BAM_HEADER_FIRST = 0;
  * @brief Is the first header (HD).
  *
- * @var BamHeaderRecordType BAM_HEADER_REFERENCE = 1;
+ * @val BamHeaderRecordType BAM_HEADER_REFERENCE = 1;
  * @brief Is a reference (SQ) header.
  *
- * @var BamHeaderRecordType BAM_HEADER_READ_GROUP = 2;
+ * @val BamHeaderRecordType BAM_HEADER_READ_GROUP = 2;
  * @brief Is a read group (RG) header.
  *
- * @var BamHeaderRecordType BAM_HEADER_PROGRAM = 3;
+ * @val BamHeaderRecordType BAM_HEADER_PROGRAM = 3;
  * @brief Is a program (PG) header.
  *
- * @var BamHeaderRecordType BAM_HEADER_COMMENT = 4;
+ * @val BamHeaderRecordType BAM_HEADER_COMMENT = 4;
  * @brief Is a comment (CO) header.
  */
 
-/**
-.Enum.BamHeaderRecordType
-..cat:BAM I/O
-..summary:Enumeration for the header record type.
-..signature:BamHeaderRecordType
-..value.BAM_HEADER_FIRST:@Class.BamHeaderRecord@ is of type $@HD$
-..value.BAM_HEADER_REFERENCE:@Class.BamHeaderRecord@ is of type $@SQ$
-..value.BAM_HEADER_READ_GROUP:@Class.BamHeaderRecord@ is of type $@RG$
-..value.BAM_HEADER_PROGRAM:@Class.BamHeaderRecord@ is of type $@PG$
-..value.BAM_HEADER_COMMENT:@Class.BamHeaderRecord@ is of type $@CO$
-..include:seqan/bam_io.h
-*/
-
 enum BamHeaderRecordType
 {
     BAM_HEADER_FIRST       = 0,
@@ -93,6 +80,10 @@ enum BamHeaderRecordType
     BAM_HEADER_COMMENT     = 4
 };
 
+// ----------------------------------------------------------------------------
+// Enum BamSortOrder
+// ----------------------------------------------------------------------------
+
 /*!
  * @enum BamSortOrder
  * @headerfile <seqan/bam_io.h>
@@ -100,31 +91,19 @@ enum BamHeaderRecordType
  *
  * @signature enum BamSortOrder;
  *
- * @var BamSortOrder BAM_SORT_UNKNOWN = 0;
+ * @val BamSortOrder BAM_SORT_UNKNOWN = 0;
  * @brief BAM file sort order is unknown.
  *
- * @var BamSortOrder BAM_SORT_UNSORTED = 1;
+ * @val BamSortOrder BAM_SORT_UNSORTED = 1;
  * @brief BAM file is unsorted.
  *
- * @var BamSortOrder BAM_SORT_QUERYNAME = 2;
+ * @val BamSortOrder BAM_SORT_QUERYNAME = 2;
  * @brief BAM file is sorted by query name;
  *
- * @var BamSortOrder BAM_SORT_COORDINATE = 3;
+ * @val BamSortOrder BAM_SORT_COORDINATE = 3;
  * @brief BAM file is sorted by coordinate.
  */
 
-/**
-.Enum.BamSortOrder
-..cat:BAM I/O
-..summary:Enumeration for the header record type.
-..signature:BamSortOrder
-..value.BAM_SORT_UNKNOWN:BAM file sort order is unknown.
-..value.BAM_SORT_UNSORTED:BAM file is unsorted.
-..value.BAM_SORT_QUERYNAME:BAM file is sorted by query name.
-..value.BAM_SORT_COORDINATE:BAM file is sorted by coordinates.
-..include:seqan/bam_io.h
-*/
-
 enum BamSortOrder
 {
     BAM_SORT_UNKNOWN    = 0,
@@ -133,6 +112,10 @@ enum BamSortOrder
     BAM_SORT_COORDINATE = 3
 };
 
+// ----------------------------------------------------------------------------
+// Class BamHeaderRecord
+// ----------------------------------------------------------------------------
+
 /*!
  * @class BamHeaderRecord
  * @headerfile <seqan/bam_io.h>
@@ -150,167 +133,79 @@ enum BamSortOrder
  * @brief Constructor.
  * @signature BamHeaderRecord::BamRecord();
  *
- * @section Remarks
- *
  * Only the default constructor is provided.
  */
 
 /*!
  * @typedef BamHeaderRecord::TTagName
- * @brief Type of the tag keys.
+ * @brief Type of the tag keys (@link CharString @endlink).
  * @signature BamHeaderRecord::TTagName;
  *
  * @typedef BamHeaderRecord::TTagValue
- * @brief Type of the tag values.
+ * @brief Type of the tag values (@link CharString @endlink).
  * @signature BamHeaderRecord::TTagValue;
  *
  * @typedef BamHeaderRecord::TTag
- * @brief Type of the tag keys.
+ * @brief Type of the tag keys (@link Pair @endlink of <tt>TTagName</tt> and <tt>TTagValue</tt>).
  * @signature BamHeaderRecord::TTag;
  *
  * @typedef BamHeaderRecord::TTags
- * @brief Type of the string of @link Pair Pairs @endlink.
+ * @brief Type of the tags string (@link AllocString @endlink of <tt>TTag</tt>).
  * @signature BamHeaderRecord::TTags;
  *
- * @var BamHeaderRecordType BamHeaderRecord::type
+ * @var BamHeaderRecordType BamHeaderRecord::type;
  * @brief Type of the record.
  *
- * @var TRecordString BamHeaderRecord::tags
+ * @var TRecordString BamHeaderRecord::tags;
  * @brief The header record's tags, of type @link BamHeaderRecord::TTags @endlink.
  */
 
-/**
-.Class.BamHeaderRecord
-..cat:BAM I/O
-..summary:Represents a header entry in a SAM file or the header section of the BAM header.
-..signature:BamHeaderRecord
-..remarks:Comment records are stored with one tag where the key is empty and the value is the comment.
-..include:seqan/bam_io.h
-
-.Memfunc.BamHeaderRecord#BamHeaderRecord
-..class:Class.BamHeaderRecord
-..signature:BamHeaderRecord()
-..summary:Constructor.
-..remarks:Only the default constructor is provided.
-
-.Typedef.BamHeaderRecord#TTagName
-..class:Class.BamHeaderRecord
-..summary:Type of the tag keys.
-
-.Typedef.BamHeaderRecord#TTagValue
-..class:Class.BamHeaderRecord
-..summary:Type of the tag values.
-
-.Typedef.BamHeaderRecord#TTag
-..class:Class.BamHeaderRecord
-..summary:@Class.Pair@ to use for storing tags.
-
-.Typedef.BamHeaderRecord#TTags
-..class:Class.BamHeaderRecord
-..summary:Type of the string of tag @Class.Pair|Pairs@.
-
-.Memvar.BamHeaderRecord#type
-..summary:Type of the record.
-..class:Class.BamHeaderRecord
-..type:Enum.BamHeaderRecordType
-
-.Memvar.BamHeaderRecord#tags
-..summary:The header record's tags.
-..class:Class.BamHeaderRecord
-..type:Typedef.BamHeaderRecord#TTags
-*/
-
 class BamHeaderRecord
 {
 public:
-    typedef CharString TTagName;
-    typedef CharString TTagValue;
-    typedef Pair<TTagName, TTagValue> TTag;
-    typedef String<TTag> TTags;
+    typedef CharString                  TTagName;
+    typedef CharString                  TTagValue;
+    typedef Pair<TTagName, TTagValue>   TTag;
+    typedef String<TTag>                TTags;
 
     BamHeaderRecordType type;
-    String<Pair<TTagName, TTagValue> > tags;
+    TTags tags;
 
-    BamHeaderRecord() {}
+    BamHeaderRecord() : type(BAM_HEADER_FIRST) {}
 };
 
 // ----------------------------------------------------------------------------
-// Function std::swap()
+// Class BamHeader
 // ----------------------------------------------------------------------------
 
-inline void
-swap(BamHeaderRecord &a, BamHeaderRecord &b)
-{
-    std::swap(a.type, b.type);
-    swap(a.tags, b.tags);
-}
-
 /*!
  * @class BamHeader
  * @headerfile <seqan/bam_io.h>
- * @brief Stores the information of the BAM header.
- *
- * @signature class BamHeader;
- *
- * @fn BamHeader::BamHeader
- * @brief Constructor.
- *
- * @signature BamHeader::BamHeader();
- *
- * Only the the default constructor is provided.
- *
- * @var TSequenceInfos BamHeader::sequenceInfos
- * @brief String of <tt>(seqId, length)</tt> with reference name / length information.
- *
- * <tt>TSequenceInfos</tt> is a String of @link Pair @endlink objects with entries @link CharString @endlink and
- * <tt>__int32</tt>.
+ * @implements FormattedFileHeaderConcept
+ * @signature typedef String<BamHeaderRecord> BamHeader;
+ * @brief Represent the information of the BAM header.
  *
- * @var TBamHeaderRecords BamHeader::records
- * @brief String of @link BamHeaderRecord BamHeaderRecords @endlink.
+ * @see BamFileIn
+ * @see BamFileOut
  */
 
-/**
-.Class.BamHeader
-..cat:BAM I/O
-..summary:Stores the information of the BAM header.
-..signature:BamHeader
-..see:Class.BamHeaderRecord
-..include:seqan/bam_io.h
-
-.Memfunc.BamHeader#BamHeader
-..class:Class.BamHeader
-..signature:BamHeader()
-..summary:Constructor.
-..remarks:Only the default constructor is provided.
-
-.Memvar.BamHeader#sequenceInfos
-..class:Class.BamHeader
-..summary:String of $(seqid, length)$ with reference name / length information.
-..type:nolink:$String<Pair<CharString, __int32> >$
-
-.Memvar.BamHeader#records
-..class:Class.BamHeader
-..summary:String of @Class.BamHeaderRecord|BamHeaderRecords@.
-..type:nolink:$String<BamHeaderRecord>$
-*/
-
-class BamHeader
-{
-public:
-    typedef Pair<CharString, __int32> TSequenceInfo;
-
-    String<Pair<CharString, __int32> > sequenceInfos;
-    String<BamHeaderRecord> records;
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
+typedef String<BamHeaderRecord> BamHeader;
 
 // ============================================================================
 // Functions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Function std::swap()
+// ----------------------------------------------------------------------------
+
+inline void
+swap(BamHeaderRecord &a, BamHeaderRecord &b)
+{
+    std::swap(a.type, b.type);
+    swap(a.tags, b.tags);
+}
+
 // ----------------------------------------------------------------------------
 // Function clear()
 // ----------------------------------------------------------------------------
@@ -319,13 +214,11 @@ class BamHeader
  * @fn BamHeaderRecord::clear
  * @brief Clear BamHeaderRecord object.
  *
- * @signature void(record);
+ * @signature void clear(record);
  *
- * @param record The record to clear.
+ * @param[in,out] record The record to clear.
  */
 
-///.Function.clear.param.object.type:Class.BamHeaderRecord
-
 inline void
 clear(BamHeaderRecord & record)
 {
@@ -336,24 +229,6 @@ clear(BamHeaderRecord & record)
 // Function findTagKey()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.BamHeaderRecord#findTagKey
-..cat:BAM I/O
-..summary:Find a tag's key of a @Class.BamHeaderRecord@.
-..signature:findTagKey(idx, key, record)
-..param.idx:The index of the found key is stored here.
-...type:nolink:$unsigned$
-..param.key:The name of the tag key whose position is to be stored in $idx$.
-...type:Shortcut.CharString
-..param.record:The record to query.
-...type:Class.BamHeaderRecord
-..returns:$bool$, indicating whether the key could be found.
-..include:seqan/bam_io.h
-..example.code:
-unsigned myIdx = 0;
-bool keyFound = findTagKey(myIdx, "SN", record);
-*/
-
 template <typename TKeyName>
 inline bool
 findTagKey(unsigned & idx, TKeyName const & key, BamHeaderRecord const & record)
@@ -381,9 +256,9 @@ findTagKey(unsigned & idx, TKeyName const & key, BamHeaderRecord const & record)
  * @signature bool getTagValue(tagValue, idx, record);
  * @signature bool getTagValue(tagValue, key, record);
  *
- * @param tagValue The @link CharString @endlink to write the tag value to.
- * @param idx      An integer with the index of the tag in the header record.
- * @param key      A two-letter sequence with the key of the tag in the header record.
+ * @param[out] tagValue The @link CharString @endlink to write the tag value to.
+ * @param[in]  idx      An integer with the index of the tag in the header record.
+ * @param[in]  key      A two-letter sequence with the key of the tag in the header record.
  *
  * @return bool true in case the value could be retrieved, false otherwise.
  *
@@ -395,28 +270,6 @@ findTagKey(unsigned & idx, TKeyName const & key, BamHeaderRecord const & record)
  * @endcode
  */
 
-/**
-.Function.BamHeaderRecord#getTagValue
-..cat:BAM I/O
-..summary:Return tag value from a @Class.BamHeaderRecord@ or @Class.BamTagsDict@.
-..signature:getTagValue(tagValue, idx, record)
-..signature:getTagValue(tagValue, key, record)
-..param.tagValue:The tag's value is stored here.
-...type:Shortcut.CharString
-..param.idx:The index of the tag whose value is to be retrieved.
-...type:nolink:$unsigned$
-..param.key:The name of tag whose value is to be retrieved.
-...type:Shortcut.CharString
-..param.record:The record to query.
-...type:Class.BamHeaderRecord
-..returns:$bool$, indicating whether the value could be retrieved, always $true$ if $idx$ is given.
-..include:seqan/bam_io.h
-..example.code:
-CharString tagValue;
-bool keyFound = getTagValue(tagValue, "SN", record);
-..see:Function.BamHeaderRecord#findTagKey
-*/
-
 template <typename TId>
 SEQAN_FUNC_ENABLE_IF(
     IsInteger<TId>,
@@ -448,33 +301,13 @@ inline getTagValue(CharString & value, TKeyName const & key, BamHeaderRecord con
  * @signature void setTagValue(idx, value, record);
  * @signature void setTagValue(key, value, record);
  *
- * @param idx    The index of the tag in the header record to set the value for.
- * @param key    The name of the tag (two-letter sequence) to set.
- * @param record The header record to set the value for.
+ * @param[in,out] idx    The index of the tag in the header record to set the value for.
+ * @param[in]     key    The name of the tag (two-letter sequence) to set.
+ * @param[in]     record The header record to set the value for.
  */
 
 // TODO(holtgrew): Parameter order!
 
-/**
-.Function.BamHeaderRecord#setTagValue
-..cat:BAM I/O
-..summary:Set tag value of a @Class.BamHeaderRecord@.
-..signature:setTagValue(idx, tagValue, record)
-..signature:setTagValue(key, tagValue, record)
-..param.idx:The index of the tag whose value should be set.
-...type:nolink:$unsigned$
-..param.key:The name of tag whose value should be set.
-...type:Shortcut.CharString
-..param.tagValue:The new tag value.
-...type:Shortcut.CharString
-..param.record:The record to query.
-...type:Class.BamHeaderRecord
-..include:seqan/bam_io.h
-..example.code:
-setTagValue("SN", "chr1", record);
-..see:Function.BamHeaderRecord#findTagKey
-*/
-
 template <typename TId>
 SEQAN_FUNC_ENABLE_IF(
     IsInteger<TId>,
@@ -515,11 +348,9 @@ searchRecord(unsigned & recordIdx,
              BamHeaderRecordType recordType,
              unsigned startIdx)
 {
-    for (recordIdx = startIdx; recordIdx < length(header.records); ++recordIdx)
-    {
-        if (header.records[recordIdx].type == recordType)
+    for (recordIdx = startIdx; recordIdx < length(header); ++recordIdx)
+        if (header[recordIdx].type == recordType)
             return true;
-    }
     return false;
 }
 
@@ -555,22 +386,20 @@ removeDuplicates(BamHeader & header)
     BamHeaderRecordTypeLess less;
     BamHeaderRecordEqual pred;
 
-    std::stable_sort(begin(header.records, Standard()), end(header.records, Standard()), less);
+    std::stable_sort(begin(header, Standard()), end(header, Standard()), less);
 
-    for (size_t uniqueBegin = 0, uniqueEnd = 1; uniqueEnd < length(header.records);)
+    for (size_t uniqueBegin = 0, uniqueEnd = 1; uniqueEnd < length(header);)
     {
-        if (less(header.records[uniqueBegin], header.records[uniqueEnd]))
+        if (less(header[uniqueBegin], header[uniqueEnd]))
             uniqueBegin = uniqueEnd;
 
         size_t j;
         for (j = uniqueBegin; j < uniqueEnd; ++j)
-        {
-            if (pred(header.records[j], header.records[uniqueEnd]))
+            if (pred(header[j], header[uniqueEnd]))
             {
-                erase(header.records, uniqueEnd);
+                erase(header, uniqueEnd);
                 break;
             }
-        }
 
         if (j == uniqueEnd)
             ++uniqueEnd;
@@ -583,7 +412,7 @@ getSortOrder(BamHeader const & header)
     CharString soString;
     for (unsigned recIdx = 0; searchRecord(recIdx, header, BAM_HEADER_FIRST, recIdx); ++recIdx)
     {
-        if (getTagValue(soString, "SO", header.records[recIdx]))
+        if (getTagValue(soString, "SO", header[recIdx]))
         {
             if (soString == "unsorted")
                 return BAM_SORT_UNSORTED;
@@ -601,48 +430,54 @@ getSortOrder(BamHeader const & header)
 inline void
 setSortOrder(BamHeader & header, BamSortOrder sortOrder)
 {
-    for (unsigned recIdx = 0; searchRecord(recIdx, header, BAM_HEADER_FIRST, recIdx); ++recIdx)
+    char const * soString;
+    switch (sortOrder)
     {
-        unsigned idx = 0;
-        if (findTagKey(idx, "SO", header.records[recIdx]))
-        {
-            CharString soString;
-            switch (sortOrder)
-            {
-                case BAM_SORT_UNSORTED:
-                    soString = "unsorted";
-                    break;
+        case BAM_SORT_UNSORTED:
+            soString = "unsorted";
+            break;
 
-                case BAM_SORT_QUERYNAME:
-                    soString = "queryname";
-                    break;
+        case BAM_SORT_QUERYNAME:
+            soString = "queryname";
+            break;
 
-                case BAM_SORT_COORDINATE:
-                    soString = "coordinate";
-                    break;
+        case BAM_SORT_COORDINATE:
+            soString = "coordinate";
+            break;
 
-                default:
-                    soString = "unknown";
-            }
-            setTagValue(idx, soString, header.records[recIdx]);
-        }
+        default:
+            soString = "unknown";
     }
-}
-
-// ----------------------------------------------------------------------------
-// Function clear()
-// ----------------------------------------------------------------------------
 
-///.Function.clear.param.object.type:Class.BamHeader
+    bool notFound = true;
+    for (unsigned recIdx = 0; searchRecord(recIdx, header, BAM_HEADER_FIRST, recIdx); ++recIdx)
+    {
+        unsigned idx = 0;
+        if (findTagKey(idx, "SO", header[recIdx]))
+        {
+            notFound = false;
+            setTagValue(idx, soString, header[recIdx]);
+        }
+    }
 
-inline void
-clear(BamHeader & header)
-{
-    clear(header.sequenceInfos);
-    clear(header.records);
+    if (notFound)
+    {
+        unsigned recIdx = 0;
+        if (searchRecord(recIdx, header, BAM_HEADER_FIRST))
+        {
+            setTagValue("SO", soString, header[recIdx]);
+        }
+        else
+        {
+            BamHeaderRecord rec;
+            rec.type = BAM_HEADER_FIRST;
+            setTagValue("VN", "1.4", rec);
+            setTagValue("SO", soString, rec);
+            insert(header, 0, rec);
+        }
+    }
 }
 
-
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_
diff --git a/seqan/bam_io/bam_index_bai.h b/seqan/bam_io/bam_index_bai.h
index da9a27f..ea60fd5 100644
--- a/seqan/bam_io/bam_index_bai.h
+++ b/seqan/bam_io/bam_index_bai.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -58,19 +58,36 @@
    THE SOFTWARE.
 */
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_
+#define INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_
 
 namespace seqan {
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Class BamIndex
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BamIndex
+ * @headerfile <seqan/bam_io.h>
+ *
+ * @brief Access to BAM indices.
+ *
+ * @signature template <typename TSpec>
+ *            class BamIndex;
+ *
+ * This is an abstract class; don't use it itself but its specializations.
+ *
+ * @see BamFileIn
+ */
+
+template <typename TSpec>
+class BamIndex;
+
 // ----------------------------------------------------------------------------
 // Tag Bai
 // ----------------------------------------------------------------------------
@@ -95,8 +112,9 @@ struct BaiBamIndexBinData_
 
 /*!
  * @class BaiBamIndex
+ * @headerfile <seqan/bam_io.h>
  * @extends BamIndex
- * @brief Access to BAI (samtools-style)
+ * @brief Access to BAI (samtools-style).
  *
  * @signature template <>
  *            class BamIndex<Bai>;
@@ -113,21 +131,6 @@ struct BaiBamIndexBinData_
  * Only the default constructor is provided.
  */
 
-/**
-.Spec.BAI BamIndex
-..cat:BAM I/O
-..general:Class.BamIndex
-..summary:Access to BAI (samtools-style) Indices.
-..signature:BamIndex<Bai>
-..include:seqan/bam_io.h
-
-.Memfunc.BAI BamIndex#BamIndex
-..class:Spec.BAI BamIndex
-..signature:BamIndex()
-..summary:Constructor.
-..remarks:Only the default constructor is provided.
-*/
-
 template <>
 class BamIndex<Bai>
 {
@@ -147,10 +150,6 @@ class BamIndex<Bai>
     {}
 };
 
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
 // ============================================================================
 // Functions
 // ============================================================================
@@ -159,59 +158,57 @@ class BamIndex<Bai>
 // Function jumpToRegion()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.BamIndex#jumpToRegion
-..class:Class.BamIndex
-..cat:BAM I/O
-..signature:jumpToRegion(bgzfStream, hasAlignments, bamIOContext, refId, pos, posEnd, bamIndex)
-..summary:Seek in BAM BGZF stream using an index.
-..remark:Note that because of the structure of BAI indices, you cannot simply jump to a position and you have to jump to region.
-..param.bgzfStream:The BGZF Stream to seek in.
-...type:Spec.BGZF Stream
-..param.refId:Reference ID to seek to.
-...type:nolink:$__int32$
-..param.hasAlignments:Set to $true$ iff there are alignments at this position.
-...type:nolink:$bool$
-..param.bamIOContext:Context to use for loading alignments.
-...type:Class.BamIOContext
-..param.pos:Zero-based begin position in the reference.
-...type:nolink:$__int32$
-..param.pos:Zero-based (exclusive, C-style) end position in the reference.
-...type:nolink:$__int32$
-..param.bamIndex:The index to use.
-...type:Class.BamIndex
-..returns:$bool$ indicating success.
-..remarks:This function may fail if the refId/pos is invalid.
-..include:seqan/bam_io.h
-*/
+/*!
+ * @fn BamFileIn#jumpToRegion
+ * @brief Seek in BamFileIn using an index.
+ *
+ * You provide a region <tt>[pos, posEnd)</tt> on the reference <tt>refID</tt> that you want to jump to and the function
+ * jumps to the first alignment in this region, if any.
+ *
+ * @signature bool jumpToRegion(bamFileIn, hasAlignments, refID, pos, posEnd, index);
+ *
+ * @param[in,out] bamFileIn     The @link BamFileIn @endlink to jump with.
+ * @param[out]    hasAlignments A <tt>bool</tt> that is set true if the region <tt>[pos, posEnd)</tt> has any
+ *                              alignments.
+ * @param[in]     refID         The reference id to jump to (<tt>__int32</tt>).
+ * @param[in]     pos           The begin of the region to jump to (<tt>__int32</tt>).
+ * @param[in]     posEnd        The end of the region to jump to (<tt>__int32</tt>).
+ * @param[in]     index         The @link BamIndex @endlink to use for the jumping.
+ *
+ * @return bool true if seeking was successful, false if not.
+ *
+ * @section Remarks
+ *
+ * This function fails if <tt>refID</tt>/<tt>pos</tt> are invalid.
+ */
 
 static inline void
 _baiReg2bins(String<__uint16> & list, __uint32 beg, __uint32 end)
 {
-	unsigned k;
-	if (beg >= end) return;
-	if (end >= 1u<<29) end = 1u<<29;
-	--end;
-	appendValue(list, 0);
-	for (k =    1 + (beg>>26); k <=    1 + (end>>26); ++k) appendValue(list, k);
-	for (k =    9 + (beg>>23); k <=    9 + (end>>23); ++k) appendValue(list, k);
-	for (k =   73 + (beg>>20); k <=   73 + (end>>20); ++k) appendValue(list, k);
-	for (k =  585 + (beg>>17); k <=  585 + (end>>17); ++k) appendValue(list, k);
+    unsigned k;
+    if (beg >= end) return;
+    if (end >= 1u<<29) end = 1u<<29;
+    --end;
+    appendValue(list, 0);
+    for (k =    1 + (beg>>26); k <=    1 + (end>>26); ++k) appendValue(list, k);
+    for (k =    9 + (beg>>23); k <=    9 + (end>>23); ++k) appendValue(list, k);
+    for (k =   73 + (beg>>20); k <=   73 + (end>>20); ++k) appendValue(list, k);
+    for (k =  585 + (beg>>17); k <=  585 + (end>>17); ++k) appendValue(list, k);
     for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) appendValue(list, k);
 }
 
-// TODO(holtgrew): Switch order of hasAlignments and stream, stream is state.
-
-template <typename TNameStore, typename TNameStoreCache>
+template <typename TSpec>
 inline bool
-jumpToRegion(Stream<Bgzf> & stream,
+jumpToRegion(FormattedFile<Bam, Input, TSpec> & bamFile,
              bool & hasAlignments,
-             BamIOContext<TNameStore, TNameStoreCache> /*const*/ & bamIOContext,
              __int32 refId,
              __int32 pos,
              __int32 posEnd,
              BamIndex<Bai> const & index)
 {
+    if (!isEqual(format(bamFile), Bam()))
+        return false;
+
     hasAlignments = false;
     if (refId < 0)
         return false;  // Cannot seek to invalid reference.
@@ -287,7 +284,7 @@ jumpToRegion(Stream<Bgzf> & stream,
                 offsetCandidates.insert(it2->i1);
     }
 
-    // Search through candidate offsets, find smallest with a fitting alignment.
+    // Search through candidate offsets, find rightmost possible.
     //
     // Note that it is not necessarily the first.
     //
@@ -296,30 +293,28 @@ jumpToRegion(Stream<Bgzf> & stream,
     BamAlignmentRecord record;
     for (TOffsetCandidateIter candIt = offsetCandidates.begin(); candIt != offsetCandidates.end(); ++candIt)
     {
-        if (streamSeek(stream, *candIt, SEEK_SET) != 0)
-            return false;  // Error while seeking.
-        if (readRecord(record, bamIOContext, stream, Bam()) != 0)
-            return false;  // Error while reading.
+        setPosition(bamFile, *candIt);
+
+        readRecord(record, bamFile);
 
         // std::cerr << "record.beginPos == " << record.beginPos << "\n";
         // __int32 endPos = record.beginPos + getAlignmentLengthInRef(record);
         if (record.rID != refId)
             continue;  // Wrong contig.
-        if (record.beginPos >= posEnd)
-            continue;  // Cannot overlap with [pos, posEnd).
+        if (!hasAlignments || record.beginPos <= pos)
+        {
+            // Found a valid alignment.
+            hasAlignments = true;
+            offset = *candIt;
+        }
 
-        // Found an alignment.
-        hasAlignments = true;
-        offset = *candIt;
-        // std::cerr << "offset == " << offset << "\n";
-        break;
+        if (record.beginPos >= posEnd)
+            break;  // Cannot find overlapping any more.
     }
 
     if (offset != MaxValue<__uint64>::VALUE)
-    {
-        if (streamSeek(stream, offset, SEEK_SET) != 0)
-            return false;  // Error while seeking.
-    }
+        setPosition(bamFile, offset);
+
     // Finding no overlapping alignment is not an error, hasAlignments is false.
     return true;
 }
@@ -328,30 +323,25 @@ jumpToRegion(Stream<Bgzf> & stream,
 // Function jumpToOrphans()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.BamIndex#jumpToOrphans
-..class:Class.BamIndex
-..cat:BAM I/O
-..signature:jumpToOrphans(bgzfStream, bamIOContext, bamIndex)
-..summary:Seek to orphans block in BAM BGZF stream using an index.
-..param.bgzfStream:The BGZF Stream to seek in.
-...type:Spec.BGZF Stream
-..param.bamIOContext:Context to use for loading alignments.
-...type:Class.BamIOContext
-..param.bamIndex:The index to use.
-...type:Class.BamIndex
-..returns:$bool$ indicating success.
-..include:seqan/bam_io.h
-*/
-
-// TODO(holtgrew): Parameter order, see jumpToRegion()!
+/*!
+ * @fn BamFileIn#jumpToOrphans
+ * @brief Seek to orphans block in BamFileIn using an index.
+ *
+ * @signature bool jumpToOrphans(bamFileIn, hasAlignments, index);
+ *
+ * @param[in,out] bamFileIn      The @link BamFileIn @endlink object to jump with.
+ * @param[out]    hasAlignments  A <tt>bool</tt> that is set to true if there are any orphans.
+ * @param[in]     index          The @link BamIndex @endlink to use for jumping.
+ */
 
-template <typename TNameStore, typename TNameStoreCache>
-bool jumpToOrphans(Stream<Bgzf> & stream,
+template <typename TSpec>
+bool jumpToOrphans(FormattedFile<Bam, Input, TSpec> & bamFile,
                    bool & hasAlignments,
-                   BamIOContext<TNameStore, TNameStoreCache> /*const*/ & bamIOContext,
                    BamIndex<Bai> const & index)
 {
+    if (!isEqual(format(bamFile), Bam()))
+        return false;
+
     hasAlignments = false;
 
     // Search linear indices for the largest entry of all references.
@@ -369,15 +359,12 @@ bool jumpToOrphans(Stream<Bgzf> & stream,
     BamAlignmentRecord record;
     __uint64 offset = MaxValue<__uint64>::VALUE;
     __uint64 result = 0;
-    int res = streamSeek(stream, aliOffset, SEEK_SET);
-    if (res != 0)
+    if (!setPosition(bamFile, aliOffset))
         return false;  // Error while seeking.
-    while (!atEnd(stream))
+    while (!atEnd(bamFile))
     {
-        result = streamTell(stream);
-        res = readRecord(record, bamIOContext, stream, Bam());
-        if (res != 0)
-            return false;  // Error while reading.
+        result = position(bamFile);
+        readRecord(record, bamFile);
         if (record.rID == -1)
         {
             // Found alignment.
@@ -390,8 +377,7 @@ bool jumpToOrphans(Stream<Bgzf> & stream,
     // Jump back to the first alignment.
     if (offset != MaxValue<__uint64>::VALUE)
     {
-        int res = streamSeek(stream, offset, SEEK_SET);
-        if (res != 0)
+        if (!setPosition(bamFile, offset))
             return false;  // Error while seeking.
     }
 
@@ -403,17 +389,15 @@ bool jumpToOrphans(Stream<Bgzf> & stream,
 // Function getUnalignedCount()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.BamIndex#getUnalignedCount
-..class:Class.BamIndex
-..cat:BAM I/O
-..signature:getUnalignedCount(index)
-..summary:Query index for number of unaligned reads.
-..param.index:Index to query.
-...type:Class.BamIndex
-..returns:$__uint64$ with number of unaligned reads.
-..include:seqan/bam_io.h
-*/
+/*!
+ * @fn BamIndex#getUnalignedCount
+ * @brief Query index for number of unaligned reads.
+ *
+ * @signature __uint64 getUnalignedCount(index);
+ *
+ * @param[in] index     Index to query.
+ * @return    __uint64  The number of unaligned reads.
+ */
 
 inline __uint64
 getUnalignedCount(BamIndex<Bai> const & index)
@@ -422,43 +406,40 @@ getUnalignedCount(BamIndex<Bai> const & index)
 }
 
 // ----------------------------------------------------------------------------
-// Function read()
+// Function open()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.BamIndex#read
-..class:Class.BamIndex
-..cat:BAM I/O
-..signature:read(index, filename)
-..summary:Load a BAM index from a given file name.
-..param.index:Target data structure.
-...type:Class.BamIndex
-..param.filename:Path to file to load.
-...type:nolink:$char const *$
-..returns:$int$ status code, $0$ indicating success.
-..include:seqan/bam_io.h
+/*!
+ * @fn BamIndex#open
+ * @brief Load a BAM index from a given file name.
+ * @signature bool open(index, filename);
+
+ * @param[in,out] index    Target data structure.
+ * @param[in]     filename Path to file to load. Types: char const *
+ *
+ * @return        bool     Returns <tt>true</tt> on success, false otherwise.
  */
 
-inline int
-read(BamIndex<Bai> & index, char const * filename)
+inline bool
+open(BamIndex<Bai> & index, char const * filename)
 {
     std::fstream fin(filename, std::ios::binary | std::ios::in);
     if (!fin.good())
-        return 1;  // Could not open file.
+        return false;  // Could not open file.
 
     // Read magic number.
     CharString buffer;
     resize(buffer, 4);
     fin.read(&buffer[0], 4);
     if (!fin.good())
-        return 1;
+        return false;
     if (buffer != "BAI\1")
-        return 1;  // Magic number is wrong.
+        return false;  // Magic number is wrong.
 
     __int32 nRef = 0;
     fin.read(reinterpret_cast<char *>(&nRef), 4);
     if (!fin.good())
-        return 1;
+        return false;
 
     resize(index._linearIndices, nRef);
     resize(index._binIndices, nRef);
@@ -469,7 +450,7 @@ read(BamIndex<Bai> & index, char const * filename)
         __int32 nBin = 0;
         fin.read(reinterpret_cast<char *>(&nBin), 4);
         if (!fin.good())
-            return 1;
+            return false;
         index._binIndices[i].clear();
         BaiBamIndexBinData_ data;
         for (int j = 0; j < nBin; ++j)  // For each bin.
@@ -479,12 +460,12 @@ read(BamIndex<Bai> & index, char const * filename)
             __uint32 bin = 0;
             fin.read(reinterpret_cast<char *>(&bin), 4);
             if (!fin.good())
-                return 1;
+                return false;
 
             __int32 nChunk = 0;
             fin.read(reinterpret_cast<char *>(&nChunk), 4);
             if (!fin.good())
-                return 1;
+                return false;
             reserve(data.chunkBegEnds, nChunk);
             for (int k = 0; k < nChunk; ++k)  // For each chunk;
             {
@@ -493,7 +474,7 @@ read(BamIndex<Bai> & index, char const * filename)
                 fin.read(reinterpret_cast<char *>(&chunkBeg), 8);
                 fin.read(reinterpret_cast<char *>(&chunkEnd), 8);
                 if (!fin.good())
-                    return 1;
+                    return false;
                 appendValue(data.chunkBegEnds, Pair<__uint64>(chunkBeg, chunkEnd));
             }
 
@@ -505,7 +486,7 @@ read(BamIndex<Bai> & index, char const * filename)
         __int32 nIntv = 0;
         fin.read(reinterpret_cast<char *>(&nIntv), 4);
         if (!fin.good())
-            return 1;
+            return false;
         clear(index._linearIndices[i]);
         reserve(index._linearIndices[i], nIntv);
         for (int j = 0; j < nIntv; ++j)
@@ -513,13 +494,13 @@ read(BamIndex<Bai> & index, char const * filename)
             __uint64 ioffset = 0;
             fin.read(reinterpret_cast<char *>(&ioffset), 8);
             if (!fin.good())
-                return 1;
+                return false;
             appendValue(index._linearIndices[i], ioffset);
         }
     }
 
     if (!fin.good())
-        return 1;
+        return false;
 
     // Read (optional) number of alignments without coordinate.
     __uint64 nNoCoord = 0;
@@ -531,41 +512,37 @@ read(BamIndex<Bai> & index, char const * filename)
     }
     index._unalignedCount = nNoCoord;
 
-    return 0;
+    return true;
 }
 
 // TODO(holtgrew): This is only here because of the read() function with TSequence in old file.h.
 
-inline int
-read(BamIndex<Bai> & index, char * filename)
+inline bool
+open(BamIndex<Bai> & index, char * filename)
 {
-    return read(index, static_cast<char const *>(filename));
+    return open(index, static_cast<char const *>(filename));
 }
 
-// ----------------------------------------------------------------------------
-// Function buildIndex()
-// ----------------------------------------------------------------------------
+// ---------------------------------------------------------------------------
+// Function save()
+// ---------------------------------------------------------------------------
 
-/*DISABLED
-.Function.BamIndex#buildIndex
-..class:Class.BamIndex
-..cat:BAM I/O
-..signature:buildIndex(index, filename)
-..summary:Build index for BAM file with given filename.
-..remarks:This will create an index file named $filename + ".bai"$.
-..param.index:Target data structure.
-...type:Class.BamIndex
-..param.filename:Path to BAM file to load.
-...type:nolink:$char const *$
-..returns:$bool$ indicating success.
-..include:seqan/bam_io.h
+/*!
+ * @fn BamIndex#save
+ * @brief Save a BamIndex object.
+ *
+ * @signature bool save(baiIndex, baiFileName);
+ *
+ * @param[in] baiIndex    The BamIndex to write out.
+ * @param[in] baiFileName The name of the BAI file to write to.
+ *
+ * @return bool <tt>true</tt> on success, <tt>false</tt> otherwise.
  */
 
-inline int _writeIndex(BamIndex<Bai> const & index, char const * filename)
+inline bool save(BamIndex<Bai> const & index, char const * baiFilename)
 {
-    std::cerr << "WRITE INDEX TO " << filename << std::endl;
-    // Open output stream.
-    std::ofstream out(filename, std::ios::binary | std::ios::out);
+    // Open output file.
+    std::ofstream out(baiFilename, std::ios::binary | std::ios::out);
 
     SEQAN_ASSERT_EQ(length(index._binIndices), length(index._linearIndices));
 
@@ -604,7 +581,7 @@ inline int _writeIndex(BamIndex<Bai> const & index, char const * filename)
         }
 
         // Write out linear index.
-        __int32 numIntervals = length(index._linearIndices);
+        __int32 numIntervals = length(linearIndex);
         out.write(reinterpret_cast<char *>(&numIntervals), 4);
         typedef Iterator<String<__uint64> const, Rooted>::Type TLinearIndexIter;
         for (TLinearIndexIter it = begin(linearIndex, Rooted()); !atEnd(it); goNext(it))
@@ -612,13 +589,14 @@ inline int _writeIndex(BamIndex<Bai> const & index, char const * filename)
     }
 
     // Write the number of unaligned reads if set.
-    std::cerr << "UNALIGNED\t" << index._unalignedCount << std::endl;
+    //std::cerr << "UNALIGNED\t" << index._unalignedCount << std::endl;
     if (index._unalignedCount != maxValue<__uint64>())
         out.write(reinterpret_cast<char const *>(&index._unalignedCount), 8);
 
-    return !out.good();  // 1 on error, 0 on success.
+    return out.good();  // false on error, true on success.
 }
 
+
 inline void _baiAddAlignmentChunkToBin(BamIndex<Bai> & index,
                                        __uint32 currBin,
                                        __uint32 currOffset,
@@ -642,34 +620,40 @@ inline void _baiAddAlignmentChunkToBin(BamIndex<Bai> & index,
     }
 }
 
-inline bool
-buildIndex(BamIndex<Bai> & index, char const * filename)
+// ---------------------------------------------------------------------------
+// Function build()
+// ---------------------------------------------------------------------------
+// TODO(dadi): uncomment when BamIndex.build index is fixed. DOX commented out
+/*
+ * @fn BamIndex#build
+ * @brief Create a BamIndex from BAM file.
+ *
+ * @signature bool build(baiIndex, bamFileName);
+ *
+ * @param[out] baiIndex    The BamIndex to build into.
+ * @param[in]  bamFileName Path to the BAM file to build an index for.  Type: <tt>char const *</tt>.
+ *
+ * @return bool <tt>true</tt> on success, <tt>false</tt> otherwise.
+ */
+/*
+inline bool build(BamIndex<Bai> & index, char const * bamFilename)
 {
-    SEQAN_FAIL("This does not work ye!");
+    // SEQAN_FAIL("This does not work yet!");
 
     index._unalignedCount = 0;
     clear(index._binIndices);
     clear(index._linearIndices);
 
     // Open BAM file for reading.
-    Stream<Bgzf> bamStream;
-    if (!open(bamStream, filename, "r"))
+    BamFileIn bamFile;
+    if (!open(bamFile, bamFilename))
         return false;  // Could not open BAM file.
 
-    // Initialize BamIOContext.
-    typedef StringSet<CharString>      TNameStore;
-    typedef NameStoreCache<TNameStore> TNameStoreCache;
-
-    TNameStore refNameStore;
-    TNameStoreCache refNameStoreCache(refNameStore);
-    BamIOContext<TNameStore> bamIOContext(refNameStore, refNameStoreCache);
-
     // Read BAM header.
     BamHeader header;
-    int res = readRecord(header, bamIOContext, bamStream, Bam());
-    if (res != 0)
-        return false;  // Could not read BAM header.
-    __uint32 numRefSeqs = length(header.sequenceInfos);
+    readHeader(header, bamFile);
+
+    __uint32 numRefSeqs = length(contigNames(context(bamFile)));
 
     // Scan over BAM file and create index.
     BamAlignmentRecord record;
@@ -677,16 +661,14 @@ buildIndex(BamIndex<Bai> & index, char const * filename)
     __uint32 prevBin    = maxValue<__uint32>();
     __int32 currRefId   = BamAlignmentRecord::INVALID_REFID;
     __int32 prevRefId   = BamAlignmentRecord::INVALID_REFID;
-    __uint64 currOffset = streamTell(bamStream);
+    __uint64 currOffset = position(bamFile);
     __uint64 prevOffset = currOffset;
     __int32 prevPos     = minValue<__int32>();
 
-    while (!atEnd(bamStream))
+    while (!atEnd(bamFile))
     {
         // Load next record.
-        res = readRecord(record, bamIOContext, bamStream, Bam());
-        if (res != 0)
-            return false;
+        readRecord(record, bamFile);
 
         // Check ordering.
         if (prevRefId == record.rID && prevPos > record.beginPos)
@@ -770,21 +752,21 @@ buildIndex(BamIndex<Bai> & index, char const * filename)
         }
 
         // Make sure that the current file pointer is beyond prevOffset.
-        if (streamTell(bamStream) <= static_cast<__int64>(prevOffset))
+        if (position(bamFile) <= static_cast<__int64>(prevOffset))
             return false;  // Calculating offsets failed.
 
         // Update prevOffset and prevPos.
-        prevOffset = streamTell(bamStream);
+        prevOffset = position(bamFile);
         prevPos    = record.beginPos;
     }
 
     // Count remaining unaligned records.
-    while (!streamEof(bamStream))
+    while (!atEnd(bamFile))
     {
         SEQAN_ASSERT_GT(index._unalignedCount, 0u);
 
-        res = readRecord(record, bamIOContext, bamStream, Bam());
-        if (res != 0 || record.rID >= 0)
+        readRecord(record, bamFile);
+        if (record.rID >= 0)
             return false;  // Could not read record.
 
         index._unalignedCount += 1;
@@ -803,16 +785,11 @@ buildIndex(BamIndex<Bai> & index, char const * filename)
     }
 
     // Merge small bins if possible.
-    SEQAN_FAIL("TODO: Merge bins!");
-
-    // Write out index.
-    CharString baiFilename(filename);
-    append(baiFilename, ".bai");
-    res = _writeIndex(index, toCString(baiFilename));
-
-    return (res == 0);
+    // SEQAN_FAIL("TODO: Merge bins!");
+    return true;
 }
+*/
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_
diff --git a/seqan/bam_io/bam_io_context.h b/seqan/bam_io/bam_io_context.h
index a5a07c5..17c50af 100644
--- a/seqan/bam_io/bam_io_context.h
+++ b/seqan/bam_io/bam_io_context.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,17 +34,67 @@
 // Class BamIOContext, accessor functions.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_
+#define INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_
 
 namespace seqan {
 
 // ============================================================================
-// Forwards
+// Tags
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Tag NameStoreMember
+// ----------------------------------------------------------------------------
+
+/*!
+ * @defgroup BamIOContextMemberTag BamIOContext Member Tags
+ * @brief Defines standard tags used to get the type of the members of the @link BamIOContext @endlink using the @link Member @endlink metafunction.
+ */
+
+/*!
+ * @tag BamIOContextMemberTag#NameStoreMember
+ * @brief Tag used to get the type for the <tt>NameStore</tt>.
+ * @headerfile <seqan/stream.h>
+ *
+ * @signature typedef Tag<NameStoreMember_> NameStoreMember;
+ */
+
+struct NameStoreMember_;
+typedef Tag<NameStoreMember_> NameStoreMember;
+
+// ----------------------------------------------------------------------------
+// Tag NameStoreCacheMember
+// ----------------------------------------------------------------------------
+
+/*!
+ * @tag BamIOContextMemberTag#NameStoreCacheMember
+ * @brief Tag used to get the type for the <tt>NameStoreCache</tt>.
+ * @headerfile <seqan/stream.h>
+ *
+ * @signature typedef Tag<NameStoreCacheMember_> NameStoreCacheMember;
+ */
+
+struct NameStoreCacheMember_;
+typedef Tag<NameStoreCacheMember_> NameStoreCacheMember;
+
+// ----------------------------------------------------------------------------
+// Tag LengthStoreMember
+// ----------------------------------------------------------------------------
+
+/*!
+ * @tag BamIOContextMemberTag#LengthStoreMember
+ * @brief Tag used to get the type for the <tt>LengthStore</tt>.
+ * @headerfile <seqan/stream.h>
+ *
+ * @signature typedef Tag<NameStoreMember_> LengthStoreMember;
+ */
+
+struct LengthStoreMember_;
+typedef Tag<LengthStoreMember_> LengthStoreMember;
+
 // ============================================================================
-// Tags, Classes, Enums
+// Classes
 // ============================================================================
 
 /*!
@@ -52,20 +102,22 @@ namespace seqan {
  * @headerfile <seqan/bam_io.h>
  * @brief The I/O context to use for BAM I/O.
  *
- * @signature template <typename TNameStore, typename TNameStoreCache = NameStoreCache<TNameStore> >
+ * @signature template <typename TNameStore[, typename TNameStoreCache]>
  *            class BamIOContext;
  *
- * @tparam TNameStore      The name store class.
- * @tparam TNameStoreCache The name store cache class.  Defaults to @link NameStoreCache @endlink &lt;TNameStore&gtl;.
+ * @tparam TNameStore      The type used to represent the names.
+ * @tparam TNameStoreCache The type used to cache the names. Defaults to @link NameStoreCache @endlink &lt;TNameStore&gtl;.
+ *
+ * BamIOContext objects store the names of (and provide a cache for) reference contig names.
  *
  * @section Examples
  *
  * Creating a @link BamIOContext @endlink for a raw @link StringSet @endlink of @link CharString @endlink.
  *
  * @code{.cpp}
- * StringSet<CharString> nameStore;
- * NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
- * BamIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
+ * StringSet<CharString> contigNames;
+ * NameStoreCache<StringSet<CharString> > contigNamesCache(contigNames);
+ * BamIOContext<StringSet<CharString> > bamIOContext(contigNames, contigNamesCache);
  * // ...
  * @endcode
  *
@@ -88,84 +140,60 @@ namespace seqan {
  * @brief Constructor.
  *
  * @signature BamIOContext::BamIOContext();
+ * @signature BamIOContext::BamIOContext(contigNameStore, contigNamesStoreCache);
  *
- * @section Remarks
- *
- * Only the default constructor is provided.
- */
-
-/*!
- * @typedef BamIOContext::TNameStore
- *
- * @brief The name store class.
-
- * @signature typedef (...) BamIOContext::TNameStore;
- */
-
-/*!
- * @typedef BamIOContext::TNameStoreCache
- * @brief The name store cache class.
- *
- * @signature typedef (...) BamIOContext::TNameStoreCache;
+ * Default constructor or construction with references to sequence and sample names.
  */
 
-/**
-.Class.BamIOContext
-..cat:BAM I/O
-..signature:BamIOContext<TNameStore[, TNameStoreCache]>
-..summary:The I/O context to use for BAM I/O.
-..param.TNameStore:The name store class.
-..param.TNameStoreCache:The name store cache class.
-...default:@Class.NameStoreCache@<TNameStore>
-..include:bam_io.h
-..example.text:Creating a @Class.BamIOContext@ for a raw @Class.StringSet@ of @Shortcut.CharString@.
-..example.code:
-StringSet<CharString> nameStore;
-NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
-BamIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
-// ...
-..example.text:Using a @Class.BamIOContext@ with a @Class.FragmentStore@.
-..example.code:
-typedef FragmentStore<>::TContigNameStore         TNameStore;
-typedef NameStoreCache<TNameStore>                TNameStoreCache;
-FragmentStore<> store;
-// Optionally, do something with store.
-typedef BamIOContext<TNameStore, TNameStoreCache> TBamIOContext;
-TBamIOContext bamIOContext(store.contigNameStore, store.contigNameStoreCache);
-// ...
-
-.Memfunc.BamIOContext#BamIOContext
-..class:Class.BamIOContext
-..signature:BamIOContext()
-..summary:Constructor.
-..remarks:Only the default constructor is provided.
-
-.Typedef.BamIOContext#TNameStore
-..class:Class.BamIOContext
-..summary:The name store class.
-
-.Typedef.BamIOContext#TNameStoreCache
-..class:Class.BamIOContext
-..summary:The name store cache class.
-*/
-
-template <typename TNameStore_, typename TNameStoreCache_ = NameStoreCache<TNameStore_> >
+template <typename TNameStore_        = StringSet<CharString>,
+          typename TNameStoreCache_   = NameStoreCache<TNameStore_>,
+          typename TStorageSpec       = void>
 class BamIOContext
 {
 public:
-    typedef TNameStore_ TNameStore;
-    typedef TNameStoreCache_ TNameStoreCache;
+    typedef typename Member<BamIOContext, NameStoreMember>::Type            TNameStore;
+    typedef typename Member<BamIOContext, NameStoreCacheMember>::Type       TNameStoreCache;
+    typedef typename Member<BamIOContext, LengthStoreMember>::Type          TLengthStore;
+
+    typedef typename If<IsSameType<TStorageSpec, void>,
+                        Dependent<>, TStorageSpec>::Type                    TNSStorageSpec;
+    typedef typename If<IsSameType<TStorageSpec, void>,
+                        Owner<>, TStorageSpec>::Type                        TSLStorageSpec;
 
-    TNameStore * _nameStore;
-    TNameStoreCache * _nameStoreCache;
-    CharString buffer;
-    String<unsigned> translateFile2GlobalRefId;
+    typedef typename StorageSwitch<TNameStore, TNSStorageSpec>::Type        TNameStoreMember;
+    typedef typename StorageSwitch<TNameStoreCache, TNSStorageSpec>::Type   TNameStoreCacheMember;
+    typedef typename StorageSwitch<TLengthStore, TSLStorageSpec>::Type      TLengthStoreMember;
 
-    BamIOContext() : _nameStore(0), _nameStoreCache(0)
+    TNameStoreMember        _contigNames;
+    TNameStoreCacheMember   _contigNamesCache;
+    TLengthStoreMember      _contigLengths;
+    CharString              buffer;
+    String<CharString>      buffers;
+    String<unsigned>        translateFile2GlobalRefId;
+
+    BamIOContext() :
+        _contigNames(TNameStoreMember()),
+        _contigNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 (TNameStoreCache*)NULL,
+                                 _contigNames)),
+        _contigLengths(TLengthStoreMember())
+    {}
+
+    BamIOContext(TNameStore & contigNames_, TNameStoreCache & contigNamesCache_) :
+        _contigNames(_referenceCast<typename Parameter_<TNameStoreMember>::Type>(contigNames_)),
+        _contigNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 &contigNamesCache_,
+                                 _contigNames)),
+        _contigLengths(TLengthStoreMember())
     {}
 
-    BamIOContext(TNameStore & nameStore, TNameStoreCache & nameStoreCache) :
-            _nameStore(&nameStore), _nameStoreCache(&nameStoreCache)
+    template <typename TOtherStorageSpec>
+    BamIOContext(BamIOContext<TNameStore, TNameStoreCache, TOtherStorageSpec> & other) :
+        _contigNames(_referenceCast<typename Parameter_<TNameStoreMember>::Type>(contigNames(other))),
+        _contigNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 &contigNamesCache(other),
+                                 _contigNames)),
+        _contigLengths(_referenceCast<typename Parameter_<TLengthStoreMember>::Type>(contigLengths(other)))
     {}
 };
 
@@ -173,100 +201,153 @@ class BamIOContext
 // Metafunctions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Metafunction NameStore
+// ----------------------------------------------------------------------------
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
+              NameStoreMember>
+{
+    typedef TNameStore Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction NameStoreCache
+// ----------------------------------------------------------------------------
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
+              NameStoreCacheMember>
+{
+    typedef TNameStoreCache Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction LengthStore
+// ----------------------------------------------------------------------------
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
+              LengthStoreMember>
+{
+    typedef String<__int32> Type;
+};
+
 // ============================================================================
 // Functions
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function nameStore()
+// Function contigNames()
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn BamIOContext#nameStoreCache
- * @brief Return reference to name store cache from @link BamIOContext @endlink.
+ * @fn BamIOContext#contigNames
+ * @brief Return reference to contig names from @link BamIOContext @endlink.
  *
- * @signature TNameStoreRef nameStoreCache(context);
+ * @signature TNameStoreRef contigNames(context);
  *
- * @param context The @link BamIOContext @endlink to query.
+ * @param[in] context The @link BamIOContext @endlink to query.
  *
- * @return TNameStoreRef A reference to the TNameStore of the context.
+ * @return TNameStoreRef A reference to the <tt>TNameStore</tt> of the context.
  */
 
-/**
-.Function.BamIOContext#nameStore
-..class:Class.BamIOContext
-..cat:BAM I/O
-..summary:Return reference to name store from @Class.BamIOContext@.
-..signature:nameStore(context)
-..param.context:The @Class.BamIOContext@ to query.
-...type:Class.BamIOContext
-..see:Typedef.BamIOContext#TNameStore
-..include:seqan/bam_io.h
-*/
-
-// TODO(holtgrew): Rename to referenceNameStore
-template <typename TNameStore, typename TNameStoreCache>
-TNameStore &
-nameStore(BamIOContext<TNameStore, TNameStoreCache> & context)
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStore &
+contigNames(BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context)
 {
-    SEQAN_ASSERT(context._nameStore != 0);
-    return *context._nameStore;
+    return _referenceCast<TNameStore &>(context._contigNames);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStore const &
+contigNames(BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context)
+{
+    return _referenceCast<TNameStore const &>(context._contigNames);
 }
 
 template <typename TNameStore, typename TNameStoreCache>
-TNameStore const &
-nameStore(BamIOContext<TNameStore, TNameStoreCache> const & context)
+inline void
+setContigNames(BamIOContext<TNameStore, TNameStoreCache, Dependent<> > & context, TNameStore & contigNames)
 {
-    SEQAN_ASSERT(context._nameStore != 0);
-    return *context._nameStore;
+    context._contigNames = &contigNames;
 }
 
 // ----------------------------------------------------------------------------
-// Function nameStoreCache()
+// Function contigLengths()
 // ----------------------------------------------------------------------------
 
-/*
- * @fn BamIOContext#nameStore
- * @headerfile <seqan/bam_io.h>
- * @brief Return reference to name store from @link BamIOContext @endlink.
+/*!
+ * @fn BamIOContext#contigLengths
+ * @brief Return reference to contig lengths from @link BamIOContext @endlink.
  *
- * @signature TNameStoreCacheRef nameStore(context);
+ * @signature TLengthStoreRef contigLengths(context);
  *
- * @param context The @link BamIOContext @endlink to query.
+ * @param[in] context The @link BamIOContext @endlink to query.
  *
- * @return TNameStoreCacheRef A reference to the TNameStoreCache of the context.
+ * @return TLengthStoreRef A reference to the <tt>TLengthStore</tt> of the context.
  */
 
-/**
-.Function.BamIOContext#nameStoreCache
-..class:Class.BamIOContext
-..cat:BAM I/O
-..summary:Return reference to name store cache from @Class.BamIOContext@.
-..signature:nameStoreCache(context)
-..param.context:The @Class.BamIOContext@ to query.
-...type:Class.BamIOContext
-..see:Typedef.BamIOContext#TNameStoreCache
-..include:seqan/bam_io.h
-..see:Function.BamIOContext#nameStore
-*/
-
-// TODO(holtgrew): Rename to referenceNameStoreCache
-template <typename TNameStore, typename TNameStoreCache>
-TNameStoreCache &
-nameStoreCache(BamIOContext<TNameStore, TNameStoreCache> & context)
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline typename BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>::TLengthStore &
+contigLengths(BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context)
+{
+    typedef typename BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>::TLengthStore TLengthStore;
+    return _referenceCast<TLengthStore &>(context._contigLengths);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline typename BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>::TLengthStore const &
+contigLengths(BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context)
+{
+    typedef typename BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>::TLengthStore TLengthStore;
+    return _referenceCast<TLengthStore const &>(context._contigLengths);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TLengthStore>
+inline void
+setContigLengths(BamIOContext<TNameStore, TNameStoreCache, Dependent<> > & context, TLengthStore & contigLengths)
+{
+    context._contigLengths = &contigLengths;
+}
+
+// ----------------------------------------------------------------------------
+// Function contigNamesCache()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BamIOContext#contigNamesCache
+ * @brief Return reference to contig names cache from @link BamIOContext @endlink.
+ *
+ * @signature TNameStoreCacheRef contigNamesCache(context);
+ *
+ * @param[in] context The @link BamIOContext @endlink to query.
+ *
+ * @return TNameStoreCacheRef A reference to the <tt>TNameStoreCache</tt> of the context.
+ */
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStoreCache &
+contigNamesCache(BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context)
+{
+    return _referenceCast<TNameStoreCache &>(context._contigNamesCache);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStoreCache const &
+contigNamesCache(BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context)
 {
-    SEQAN_ASSERT(context._nameStoreCache != 0);
-    return *context._nameStoreCache;
+    return _referenceCast<TNameStoreCache const &>(context._contigNamesCache);
 }
 
 template <typename TNameStore, typename TNameStoreCache>
-TNameStoreCache const &
-nameStoreCache(BamIOContext<TNameStore, TNameStoreCache> const & context)
+inline void
+setContigNamesCache(BamIOContext<TNameStore, TNameStoreCache, Dependent<> > & context, TNameStoreCache & contigNamesCache)
 {
-    SEQAN_ASSERT(context._nameStoreCache != 0);
-    return *context._nameStoreCache;
+    context._contigNamesCache = &contigNamesCache;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_
diff --git a/seqan/bam_io/bam_sam_conversion.h b/seqan/bam_io/bam_sam_conversion.h
index 289abab..bd206ac 100644
--- a/seqan/bam_io/bam_sam_conversion.h
+++ b/seqan/bam_io/bam_sam_conversion.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,12 +30,13 @@
 //
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 // Code to convert between SAM and BAM format tags (textual <-> binary).
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_
+#define INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_
 
 namespace seqan {
 
@@ -59,245 +60,112 @@ namespace seqan {
 // Function assignTagsSamToBam()
 // ----------------------------------------------------------------------------
 
-template <typename TTarget, typename TRecordReader>
-void _assignTagsSamToBamOneTag(TTarget & target, TRecordReader & reader, CharString & buffer)
+template <typename TTarget, typename TBuffer>
+struct AppendTagsSamToBamOneTagHelper_
 {
-    SEQAN_ASSERT_NOT(atEnd(reader));
-    int res = readNChars(target, reader, 2);  // Read tag name.
-    (void)res;  // If run without assertions.
-    SEQAN_ASSERT_EQ(res, 0);
-    SEQAN_ASSERT_NOT(atEnd(reader));
+    TTarget     &target;
+    TBuffer     buffer;
+    char        typeC;
+
+    AppendTagsSamToBamOneTagHelper_(TTarget &target, TBuffer buffer, char typeC):
+        target(target),
+        buffer(buffer),
+        typeC(typeC)
+    {}
+
+    template <typename Type>
+    bool operator() (Type)
+    {
+        if (BamTypeChar<Type>::VALUE != typeC)
+            return false;
+
+        appendRawPod(target, lexicalCast<Type>(buffer));
+        return true;
+    }
+};
+
+template <typename TTarget, typename TForwardIter>
+void _appendTagsSamToBamOneTag(TTarget & target, TForwardIter & iter, CharString & buffer)
+{
+    write(target, iter, 2);
 
     clear(buffer);
-    res = readNChars(buffer, reader, 3);  // Read ':<type>:'.
-    SEQAN_ASSERT_EQ(res, 0);
+    write(buffer, iter, 3);
     SEQAN_ASSERT_EQ(buffer[0], ':');
     SEQAN_ASSERT_EQ(buffer[2], ':');
-    char t = buffer[1];
-    appendValue(target, t);
 
-    SEQAN_ASSERT_NOT(atEnd(reader));
+    char typeC = buffer[1];
+    appendValue(target, typeC);
 
-    switch (t)
+    switch (typeC)
     {
-    case 'A':
-        clear(buffer);
-        res = readNChars(target, reader, 1);
-        SEQAN_ASSERT_EQ(res, 0);
-        break;
-    case 'i':
-        {
-            clear(buffer);
-            res = readUntilTabOrLineBreak(buffer, reader);
-            SEQAN_ASSERT(res == 0 || res == EOF_BEFORE_SUCCESS);
-            __int32 x = 0;
-            bool b = lexicalCast2<__int32>(x, buffer);
-            (void)b;
-            SEQAN_ASSERT(b);
-            char const * ptr = reinterpret_cast<char const *>(&x);
-            for (int i = 0; i < 4; ++i, ++ptr)
-                appendValue(target, *ptr);
-        }
-        break;
-    case 'f':
-        {
-            clear(buffer);
-            res = readUntilTabOrLineBreak(buffer, reader);
-            SEQAN_ASSERT(res == 0 || res == EOF_BEFORE_SUCCESS);
-            float x = 0;
-            bool b = lexicalCast2<float>(x, buffer);
-            (void)b;
-            SEQAN_ASSERT(b);
-            char const * ptr = reinterpret_cast<char const *>(&x);
-            for (int i = 0; i < 4; ++i, ++ptr)
-                appendValue(target, *ptr);
-        }
-        break;
-    case 'H':
-    case 'Z':
-        {
+        case 'Z':
+        case 'H':
+            // BAM string
             // TODO(holtgrew): Could test on even length in case of 'H'.
-            res = readUntilTabOrLineBreak(target, reader);
-            SEQAN_ASSERT(res == 0 || res == EOF_BEFORE_SUCCESS);
+            readUntil(target, iter, OrFunctor<IsTab, IsNewline>());
             appendValue(target, '\0');
-        }
-        break;
-    case 'B':
+            break;
+
+        case 'B':
         {
-            CharString buffer2; // TODO(holtgrew): Also give from outside.
+            // BAM array
 
             // Read type.
-            clear(buffer);
-            res = readNChars(buffer, reader, 1);
-            SEQAN_ASSERT_EQ(res, 0);
-            char t2 = back(buffer);
-            appendValue(target, t2);
+            readOne(typeC, iter);
+            appendValue(target, typeC);
 
             // Read array contents.
             clear(buffer);
-            res = readUntilTabOrLineBreak(buffer, reader);
-            SEQAN_ASSERT(res == 0 || res == EOF_BEFORE_SUCCESS);
-            typename Iterator<CharString, Rooted>::Type it, it2;
-            // Search first non-comma position.
-            it = begin(buffer, Rooted());
-            for (;!atEnd(it) && *it == ','; ++it)
-                continue;
-            // Count number of entries.
-            __int32 nEntries = !atEnd(it);  // At least one if array not empty.
-            for (it2 = it; !atEnd(it2); ++it2)
-                nEntries += (*it2 == ',');
-            // Write out array length to result.
-            char const * ptr = reinterpret_cast<char const *>(&nEntries);
-            for (int i = 0; i < 4; ++i, ++ptr)
-                appendValue(target, *ptr);
-
-            // Now, write out the arrays, depending on the entry type.
-            // TODO(holtgrew): Whee, this could be a bit more compact...
-            switch (t2)
+            readUntil(buffer, iter, OrFunctor<IsTab, IsNewline>());
+
+            size_t len = length(buffer);
+
+            // Count number of entries (== number of commas after type character).
+            __uint32 nEntries = 0;
+            for (size_t i = 0; i != len; ++i)
+                if (buffer[i] == ',')
+                    ++nEntries;
+
+            // Write out array length.
+            appendRawPod(target, (__uint32)nEntries);
+
+            // Write out array values.
+            size_t startPos = 1;
+            for (unsigned i = 0; i < nEntries; ++i)
             {
-            case 'c':
-                for (int i = 0; i < nEntries; ++i)
-                {
-                    SEQAN_ASSERT_NOT(atEnd(it));
-                    clear(buffer2);
-                    for (; !atEnd(it) && *it != ',' && *it != '\t'; goNext(it))
-                        appendValue(buffer2, *it);
-                    __int16 x = 0;  // short to avoid textual interpretation in lexicalCast<> below.
-                    bool b = lexicalCast2<__int16>(x, buffer2);
-                    (void)b;
-                    SEQAN_ASSERT(b);
-                    appendValue(target, static_cast<__int8>(x));
-                    if (!atEnd(it) && *it == ',')
-                        goNext(it);  // Skip ','.
-                    else
-                        break;  // End of field or end of string.
-                }
-                break;
-            case 'C':
-                for (int i = 0; i < nEntries; ++i)
-                {
-                    SEQAN_ASSERT_NOT(atEnd(it));
-                    clear(buffer2);
-                    for (; !atEnd(it) && *it != ',' && *it != '\t'; goNext(it))
-                        appendValue(buffer2, *it);
-                    __uint16 x = 0;  // short to avoid textual interpretation in lexicalCast<> below.
-                    bool b = lexicalCast2<__uint16>(x, buffer2);
-                    (void)b;
-                    SEQAN_ASSERT(b);
-                    appendValue(target, static_cast<__int8>(x));
-                    if (!atEnd(it) && *it == ',')
-                        goNext(it);  // Skip ','.
-                    else
-                        break;  // End of field or end of string.
-                }
-                break;
-            case 's':
-                for (int i = 0; i < nEntries; ++i)
-                {
-                    SEQAN_ASSERT_NOT(atEnd(it));
-                    clear(buffer2);
-                    for (; !atEnd(it) && *it != ',' && *it != '\t'; goNext(it))
-                        appendValue(buffer2, *it);
-                    __int16 x = 0;
-                    bool b = lexicalCast2<__int16>(x, buffer2);
-                    (void)b;
-                    SEQAN_ASSERT(b);
-                    char const * ptr = reinterpret_cast<char const *>(&x);  // write out byte-wise
-                    for (int i = 0; i < 2; ++i, ++ptr)
-                        appendValue(target, *ptr);
-                    if (!atEnd(it) && *it == ',')
-                        goNext(it);  // Skip ','.
-                    else
-                        break;  // End of field or end of string.
-                }
-                break;
-            case 'S':
-                for (int i = 0; i < nEntries; ++i)
-                {
-                    SEQAN_ASSERT_NOT(atEnd(it));
-                    clear(buffer2);
-                    for (; !atEnd(it) && *it != ',' && *it != '\t'; goNext(it))
-                        appendValue(buffer2, *it);
-                    __uint16 x = 0;
-                    bool b = lexicalCast2<__uint16>(x, buffer2);
-                    (void)b;
-                    SEQAN_ASSERT(b);
-                    char const * ptr = reinterpret_cast<char const *>(&x);  // write out byte-wise
-                    for (int i = 0; i < 2; ++i, ++ptr)
-                        appendValue(target, *ptr);
-                    if (!atEnd(it) && *it == ',')
-                        goNext(it);  // Skip ','.
-                    else
-                        break;  // End of field or end of string.
-                }
-                break;
-            case 'i':
-                for (int i = 0; i < nEntries; ++i)
-                {
-                    SEQAN_ASSERT_NOT(atEnd(it));
-                    clear(buffer2);
-                    for (; !atEnd(it) && *it != ',' && *it != '\t'; goNext(it))
-                        appendValue(buffer2, *it);
-                    __int32 x = 0;
-                    bool b = lexicalCast2<__int32>(x, buffer2);
-                    (void)b;
-                    SEQAN_ASSERT(b);
-                    char const * ptr = reinterpret_cast<char const *>(&x);  // write out byte-wise
-                    for (int i = 0; i < 4; ++i, ++ptr)
-                        appendValue(target, *ptr);
-                    if (!atEnd(it) && *it == ',')
-                        goNext(it);  // Skip ','.
-                    else
-                        break;  // End of field or end of string.
-                }
-                break;
-            case 'I':
-                for (int i = 0; i < nEntries; ++i)
-                {
-                    SEQAN_ASSERT_NOT(atEnd(it));
-                    clear(buffer2);
-                    for (; !atEnd(it) && *it != ',' && *it != '\t'; goNext(it))
-                        appendValue(buffer2, *it);
-                    __uint32 x = 0;
-                    bool b = lexicalCast2<__uint32>(x, buffer2);
-                    (void)b;
-                    SEQAN_ASSERT(b);
-                    char const * ptr = reinterpret_cast<char const *>(&x);  // write out byte-wise
-                    for (int i = 0; i < 4; ++i, ++ptr)
-                        appendValue(target, *ptr);
-                    if (!atEnd(it) && *it == ',')
-                        goNext(it);  // Skip ','.
-                    else
-                        break;  // End of field or end of string.
-                }
-                break;
-            case 'f':
-                for (int i = 0; i < nEntries; ++i)
-                {
-                    SEQAN_ASSERT_NOT(atEnd(it));
-                    clear(buffer2);
-                    for (; !atEnd(it) && *it != ',' && *it != '\t'; goNext(it))
-                        appendValue(buffer2, *it);
-                    float x = 0;
-                    bool b = lexicalCast2<float>(x, buffer2);
-                    (void)b;
-                    SEQAN_ASSERT(b);
-                    char const * ptr = reinterpret_cast<char const *>(&x);  // write out byte-wise
-                    for (int i = 0; i < 4; ++i, ++ptr)
-                        appendValue(target, *ptr);
-                    if (!atEnd(it) && *it == ',')
-                        goNext(it);  // Skip ','.
-                    else
-                        break;  // End of field or end of string.
-                }
-                break;
-            default:
-                SEQAN_FAIL("Invalid array type: %c!", t2);
+                SEQAN_ASSERT_LT(startPos, len);
+
+                // search end of current entry
+                size_t endPos = startPos;
+                for (; endPos < len; ++endPos)
+                    if (buffer[endPos] == ',')
+                    {
+                        buffer[endPos] = '\0';
+                        break;
+                    }
+
+                AppendTagsSamToBamOneTagHelper_<TTarget, char*> func(target,
+                                                                     toCString(buffer) + startPos,
+                                                                     typeC);
+                if (!tagApply(func, BamTagTypes()))
+                    SEQAN_ASSERT_FAIL("Invalid tag type: %c!", typeC);
+
+                startPos = endPos + 1;
             }
+            break;
+        }
+
+        default:
+        {
+            // BAM simple value
+            clear(buffer);
+            readUntil(buffer, iter, OrFunctor<IsTab, IsNewline>());
+
+            AppendTagsSamToBamOneTagHelper_<TTarget, CharString&> func(target, buffer, typeC);
+            if (!tagApply(func, BamTagTypes()))
+                SEQAN_ASSERT_FAIL("Invalid tag type: %c!", typeC);
         }
-        break;
-    default:
-        SEQAN_ASSERT_FAIL("Invalid tag type: %c!", t);
     }
 }
 
@@ -308,323 +176,152 @@ void _assignTagsSamToBamOneTag(TTarget & target, TRecordReader & reader, CharStr
  *
  * @signature void assignTagsBamToSam(bamTags, samTags);
  *
- * @param bamTags[out] A sequence of <tt>char</tt> (e.g. @link CharString @endlink) for the target BAM tags.
- * @param samTags[in] A sequence of <tt>char</tt> (e.g. @link CharString @endlink) for the source SAM tags.
+ * @param[out] bamTags A sequence of <tt>char</tt> (e.g. @link CharString @endlink) for the target BAM tags.
+ * @param[in]  samTags A sequence of <tt>char</tt> (e.g. @link CharString @endlink) for the source SAM tags.
  *
  * @see assignTagsBamToSam
  */
 
-/**
-.Function.assignTagsSamToBam
-..cat:BAM I/O
-..summary:Assign tags in SAM format to tags in BAM format.
-..signature:assignTagsSamToBam(bamTags, samTags)
-..param.bamTags:Destination BAM tags.
-...type:Shortcut.CharString
-..param.samTags:Source SAM tags.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/bam_io.h
-*/
-
 template <typename TTarget, typename TSource>
-void assignTagsSamToBam(TTarget & target, TSource & source)
+void appendTagsSamToBam(TTarget & target, TSource const & source)
 {
     // Handle case of empty source sequence.
     if (empty(source))
-        clear(target);
-
-    typedef typename Iterator<TSource, Standard>::Type TSourceIter;
-    TSourceIter it = begin(source, Standard());
-    TSourceIter itEnd = end(source, Standard());
+        return;
 
-    typedef Stream<CharArray<char const *> > TStream;
-    typedef RecordReader<TStream, SinglePass<> > TRecordReader;
-
-    TStream stream(it, itEnd);
-    TRecordReader reader(stream);
+    typedef typename Iterator<TSource const, Rooted>::Type TSourceIter;
+    TSourceIter it = begin(source, Rooted());
 
     CharString buffer;
 
-    while (!atEnd(reader))
+    while (!atEnd(it))
     {
-        if (value(reader) == '\t')
-            goNext(reader);
-        SEQAN_ASSERT_NOT(atEnd(reader));
+        if (value(it) == '\t')
+            skipOne(it);
 
-        _assignTagsSamToBamOneTag(target, reader, buffer);
+        _appendTagsSamToBamOneTag(target, it, buffer);
     }
 }
 
+template <typename TTarget, typename TSource>
+void assignTagsSamToBam(TTarget & target, TSource const & source)
+{
+    clear(target);
+    appendTagsSamToBam(target, source);
+}
+
 // ----------------------------------------------------------------------------
 // Function assignTagsBamToSam()
 // ----------------------------------------------------------------------------
 
 template <typename TTarget, typename TSourceIter>
-void _assignTagsBamToSamOneTag(TTarget & target, TSourceIter & it)
+struct AssignTagsBamToSamOneTagHelper_
+{
+    TTarget     &target;
+    TSourceIter &it;
+    char        typeC;
+
+    AssignTagsBamToSamOneTagHelper_(TTarget &target, TSourceIter &it, char typeC):
+        target(target),
+        it(it),
+        typeC(typeC)
+    {}
+
+    template <typename Type>
+    bool operator() (Type)
+    {
+        if (BamTypeChar<Type>::VALUE != typeC)
+            return false;
+
+        appendNumber(target, reinterpret_cast<Type const &>(*it));
+        it += sizeof(Type);
+        return true;
+    }
+
+    bool operator() (char)
+    {
+        if (BamTypeChar<char>::VALUE != typeC)
+            return false;
+
+        writeValue(target, getValue(it));
+        ++it;
+        return true;
+    }
+};
+
+template <typename TTarget, typename TSourceIter>
+void _appendTagsBamToSamOneTag(TTarget & target, TSourceIter & it)
 {
     // Copy tag name.
     SEQAN_ASSERT_NOT(atEnd(it));
-    appendValue(target, *it++);
+    writeValue(target, *it++);
     SEQAN_ASSERT_NOT(atEnd(it));
-    appendValue(target, *it++);
-    unsigned char t = *it;
+    writeValue(target, *it++);
 
     // Add ':'.
-    appendValue(target, ':');
+    writeValue(target, ':');
 
-    // Add type.
-    SEQAN_ASSERT_NOT(atEnd(it));
-    if (*it == 'c' || *it == 'C' || *it == 's' || *it == 'S' || *it == 'i' || *it == 'I')
-        appendValue(target, 'i');
+    char typeC = *it++;
+    char c = FunctorLowcase<char>()(typeC);
+
+    // The only integer type supported is a 32bit signed int (SAM Format Spec, 28 Feb 2014, Section 1.5)
+    // This sucks as this projection is not identically reversible
+    if (c == 'c' || c == 's' || c == 'i')
+        writeValue(target, 'i');
     else
-        appendValue(target, *it);
-    ++it;
+        writeValue(target, typeC);
 
     // Add ':'.
-    appendValue(target, ':');
+    writeValue(target, ':');
 
-    // Convert the payload, depending on the field's type.
-
-    switch (t)
+    switch (typeC)
     {
-    case 'A':
-        appendValue(target, *it++);
-        break;
-    case 'c':
-        {
+        case 'Z':
+        case 'H':
+            // BAM string
             SEQAN_ASSERT_NOT(atEnd(it));
-            __int8 x = *it++;
-            char buffer[4];
-            snprintf(buffer, 4, "%d", x);
-            append(target, buffer);
-        }
-        break;
-    case 'C':
-        {
-            SEQAN_ASSERT_NOT(atEnd(it));
-            char buffer[4];
-            __uint8 x = *it++;
-            snprintf(buffer, 4, "%u", x);
-            append(target, buffer);
-        }
-        break;
-    case 's':
-        {
-            __int16 x = 0;
-            char * ptr = reinterpret_cast<char *>(&x);
-            for (int i = 0; i < 2; ++i)
-            {
-                SEQAN_ASSERT_NOT(atEnd(it));
-                *ptr++ = *it++;
-            }
-            char buffer[32];
-            snprintf(buffer, 32, "%d", x);
-            append(target, buffer);
-        }
-        break;
-    case 'S':
-        {
-            __uint16 x = 0;
-            char * ptr = reinterpret_cast<char *>(&x);
-            for (int i = 0; i < 2; ++i)
-            {
-                SEQAN_ASSERT_NOT(atEnd(it));
-                *ptr++ = *it++;
-            }
-            char buffer[32];
-            snprintf(buffer, 32, "%u", x);
-            append(target, buffer);
-        }
-        break;
-    case 'i':
-        {
-            int x = 0;
-            char * ptr = reinterpret_cast<char *>(&x);
-            for (int i = 0; i < 4; ++i)
-            {
-                SEQAN_ASSERT_NOT(atEnd(it));
-                *ptr++ = *it++;
-            }
-            char buffer[32];
-            snprintf(buffer, 32, "%d", x);
-            append(target, buffer);
-        }
-        break;
-    case 'I':
-        {
-            unsigned x = 0;
-            char * ptr = reinterpret_cast<char *>(&x);
-            for (int i = 0; i < 4; ++i)
-            {
-                SEQAN_ASSERT_NOT(atEnd(it));
-                *ptr++ = *it++;
-            }
-            char buffer[32];
-            snprintf(buffer, 32, "%u", x);
-            append(target, buffer);
-        }
-        break;
-    case 'f':
-        {
-            float x = 0;
-            char * ptr = reinterpret_cast<char *>(&x);
-            for (int i = 0; i < 4; ++i)
-            {
-                SEQAN_ASSERT_NOT(atEnd(it));
-                *ptr++ = *it++;
-            }
-            char buffer[32];
-            snprintf(buffer, 32, "%g", x);
-            append(target, buffer);
-        }
-        break;
-    case 'Z':
-        {
-            while (*it != '\0')
-            {
-                SEQAN_ASSERT_NOT(atEnd(it));
-                appendValue(target, *it++);
-            }
-            SEQAN_ASSERT_NOT(atEnd(it));
-            it++;
-        }
-        break;
-    case 'H':
-        {
             while (*it != '\0')
             {
+                writeValue(target, *it);
+                ++it;
                 SEQAN_ASSERT_NOT(atEnd(it));
-                appendValue(target, *it++);
             }
-            SEQAN_ASSERT_NOT(atEnd(it));
-            it++;
-        }
-        break;
-    case 'B':
+            ++it;
+            break;
+
+        case 'B':
         {
-            // Read type.
-            char t2 = *it++;
-            appendValue(target, t2);
+            // BAM array
+            typeC = *it++;
+            writeValue(target, typeC);
+            AssignTagsBamToSamOneTagHelper_<TTarget, TSourceIter> func(target, it, typeC);
+
             // Read array length.
-            __int32 x = 0;
-            char * ptr = reinterpret_cast<char *>(&x);
-            for (int i = 0; i < 4; ++i)
+            union {
+                char raw[4];
+                unsigned len;
+            } tmp;
+            for (unsigned i = 0; i < 4; ++i)
             {
                 SEQAN_ASSERT_NOT(atEnd(it));
-                *ptr++ = *it++;
+                tmp.raw[i] = *it++;
             }
-            // Depending on t2, read array.
-            // TODO(holtgrew): Whee, this could be a bit more compact...
-            switch (t2)
+            for (unsigned i = 0; i < tmp.len; ++i)
             {
-            case 'c':
-                for (__int32 i = 0; i < x; ++i)
-                {
-                    appendValue(target, ',');
-                    __int8 y = *it++;
-                    char buffer[32];
-                    snprintf(buffer, 32, "%d", y);
-                    append(target, buffer);
-                }
-                break;
-            case 'C':
-                for (__int32 i = 0; i < x; ++i)
-                {
-                    appendValue(target, ',');
-                    __uint8 y = *it++;
-                    char buffer[32];
-                    snprintf(buffer, 32, "%u", y);
-                    append(target, buffer);
-                }
-                break;
-            case 's':
-                for (__int32 i = 0; i < x; ++i)
-                {
-                    appendValue(target, ',');
-                    __int16 y = 0;
-                    char * ptr = reinterpret_cast<char *>(&y);
-                    for (int i = 0; i < 2; ++i)
-                    {
-                        SEQAN_ASSERT_NOT(atEnd(it));
-                        *ptr++ = *it++;
-                    }
-                    char buffer[32];
-                    snprintf(buffer, 32, "%d", y);
-                    append(target, buffer);
-                }
-                break;
-            case 'S':
-                for (__int32 i = 0; i < x; ++i)
-                {
-                    appendValue(target, ',');
-                    __uint16 y = 0;
-                    char * ptr = reinterpret_cast<char *>(&y);
-                    for (int i = 0; i < 2; ++i)
-                    {
-                        SEQAN_ASSERT_NOT(atEnd(it));
-                        *ptr++ = *it++;
-                    }
-                    char buffer[32];
-                    snprintf(buffer, 32, "%d", y);
-                    append(target, buffer);
-                }
-                break;
-            case 'i':
-                for (__int32 i = 0; i < x; ++i)
-                {
-                    appendValue(target, ',');
-                    int y = 0;
-                    char * ptr = reinterpret_cast<char *>(&y);
-                    for (int i = 0; i < 4; ++i)
-                    {
-                        SEQAN_ASSERT_NOT(atEnd(it));
-                        *ptr++ = *it++;
-                    }
-                    char buffer[32];
-                    snprintf(buffer, 32, "%d", y);
-                    append(target, buffer);
-                }
-                break;
-            case 'I':
-                for (__int32 i = 0; i < x; ++i)
-                {
-                    appendValue(target, ',');
-                    unsigned y = 0;
-                    char * ptr = reinterpret_cast<char *>(&y);
-                    for (int i = 0; i < 4; ++i)
-                    {
-                        SEQAN_ASSERT_NOT(atEnd(it));
-                        *ptr++ = *it++;
-                    }
-                    char buffer[32];
-                    snprintf(buffer, 32, "%u", y);
-                    append(target, buffer);
-                }
-                break;
-            case 'f':
-                for (__int32 i = 0; i < x; ++i)
-                {
-                    appendValue(target, ',');
-                    float y = 0;
-                    char * ptr = reinterpret_cast<char *>(&y);
-                    for (int i = 0; i < 4; ++i)
-                    {
-                        SEQAN_ASSERT_NOT(atEnd(it));
-                        *ptr++ = *it++;
-                    }
-                    char buffer[32];
-                    snprintf(buffer, 32, "%g", y);
-                    append(target, buffer);
-                }
-                break;
-            default:
-                SEQAN_FAIL("Invalid array type: %c!", t2);
+                writeValue(target, ',');
+                if (!tagApply(func, BamTagTypes()))
+                    SEQAN_ASSERT_FAIL("Invalid tag type: %c!", typeC);
             }
+            break;
+        }
+
+        default:
+        {
+            // BAM simple value
+            AssignTagsBamToSamOneTagHelper_<TTarget, TSourceIter> func(target, it, typeC);
+            if (!tagApply(func, BamTagTypes()))
+                SEQAN_ASSERT_FAIL("Invalid tag type: %c!", typeC);
         }
-        break;
-    default:
-        SEQAN_ASSERT_FAIL("Invalid tag type: %c!", t);
     }
 }
 
@@ -635,48 +332,38 @@ void _assignTagsBamToSamOneTag(TTarget & target, TSourceIter & it)
  *
  * @signature void assignTagsBamToSam(samTags, bamTags);
  *
- * @param samTags[out] A sequence of <tt>char</tt> (e.g. @link CharString @endlink) for the target SAM tags.
- * @param bamTags[in] A sequence of <tt>char</tt> (e.g. @link CharString @endlink) for the source BAM tags.
+ * @param[out] samTags A sequence of <tt>char</tt> (e.g. @link CharString @endlink) for the target SAM tags.
+ * @param[in]  bamTags A sequence of <tt>char</tt> (e.g. @link CharString @endlink) for the source BAM tags.
  *
  * @see assignTagsSamToBam
  */
 
-/**
-.Function.assignTagsBamToSam
-..cat:BAM I/O
-..summary:Assign tags in BAM format to tags in SAM format.
-..signature:assignTagsSamToBam(bamTags, samTags)
-..param.samTags:Destination SAM tags.
-...type:Shortcut.CharString
-..param.bamTags:Source BAM tags.
-...type:Shortcut.CharString
-..returns:$void$
-..include:seqan/bam_io.h
-..see:Function.assignTagsSamToBam
-*/
-
 template <typename TTarget, typename TSource>
-void assignTagsBamToSam(TTarget & target, TSource const & source)
+inline void
+appendTagsBamToSam(TTarget & target, TSource const & source)
 {
-    // Handle case of empty source sequence.
     if (empty(source))
-        clear(target);
-
-    clear(target);
+        return;
 
     typedef typename Iterator<TSource const, Rooted>::Type TSourceIter;
     TSourceIter it = begin(source, Rooted());
 
-    bool first = true;
-    while (!atEnd(it))
+    while (true)
     {
-        if (!first)
-            appendValue(target, '\t');
-        first = false;
-        _assignTagsBamToSamOneTag(target, it);
+        _appendTagsBamToSamOneTag(target, it);
+        if (atEnd(it))
+            return;
+        writeValue(target, '\t');
     }
 }
 
+template <typename TTarget, typename TSource>
+void assignTagsBamToSam(TTarget & target, TSource const & source)
+{
+    clear(target);
+    appendTagsBamToSam(target, source);
+}
+
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_
diff --git a/seqan/bam_io/bam_scanner_cache.h b/seqan/bam_io/bam_scanner_cache.h
new file mode 100644
index 0000000..85775e1
--- /dev/null
+++ b/seqan/bam_io/bam_scanner_cache.h
@@ -0,0 +1,318 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_BAM_IO_BAM_SCANNER_CACHE_H_
+#define INCLUDE_SEQAN_BAM_IO_BAM_SCANNER_CACHE_H_
+
+#ifdef SEQAN_CXX11_STANDARD
+#include <functional>
+#include <unordered_map>
+#else
+#include <tr1/functional>
+#include <tr1/unordered_map>
+#endif
+
+namespace seqan {
+
+#ifdef SEQAN_CXX11_STANDARD
+using namespace std;
+#else
+using namespace std::tr1;
+#endif
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct BamScannerCacheKey_
+{
+    __int32     rID;
+    __int32     beginPos;
+    __uint64    qnameHash;
+
+    bool operator== (BamScannerCacheKey_ const &other) const
+    {
+        return rID == other.rID && beginPos == other.beginPos && qnameHash == other.qnameHash;
+    }
+};
+
+struct BamScannerCacheSearchKey_
+{
+    typedef __uint16 TFlag;
+
+    BamScannerCacheKey_ cacheKey;
+    TFlag flags;
+    TFlag flagsMask;
+};
+
+struct BamScannerCacheHash_ :
+    std::unary_function<BamScannerCacheKey_, size_t>
+{
+    size_t operator()(BamScannerCacheKey_ const &v) const
+    {
+        return std::hash<__int32>()(v.rID) ^ std::hash<__int32>()(v.beginPos) ^ std::hash<__uint64>()(v.qnameHash);
+    }
+};
+
+class BamScannerCache
+{
+public:
+    // The Key is a pair of (genomic pos, name) where genomic pos is a pair of (rId, pos).
+    typedef String<BamAlignmentRecord> TRecords;
+    typedef Size<TRecords>::Type TRecordId;
+    typedef BamScannerCacheKey_ TKey;
+
+    // A mapping from the key type to the BamAlignmentRecord at this position.
+    typedef unordered_multimap<TKey, TRecordId, BamScannerCacheHash_> TMap;
+    typedef TMap::const_iterator TMapIter;
+
+    TRecords            records;
+    String<TRecordId>   unusedIds;
+    TMap                map;
+    BamAlignmentRecord  tmpRecord;
+
+    static const TRecordId INVALID_ID = (TRecordId)-1;
+};
+
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TSequence>
+__uint64 _suffixHash(TSequence const &sequence)
+{
+    typedef typename Iterator<TSequence const, Standard>::Type  TIter;
+    typedef typename Value<TSequence>::Type                     TValue;
+    typedef typename Size<TSequence>::Type                      TSize;
+
+    const __uint64 ALPH_SIZE = ValueSize<TValue>::VALUE;
+    const unsigned MAX_LEN = LogN<~(ALPH_SIZE - 1) / ALPH_SIZE, ALPH_SIZE>::VALUE + 1;
+
+    TSize len = length(sequence);
+    TIter itEnd = end(sequence, Standard());
+
+    if (len > 2 && (sequence[len - 2] == ':' || sequence[len - 2] == '/'))
+    {
+        len -= 2;
+        itEnd -= 2;
+    }
+
+    if (len > MAX_LEN)
+        len = MAX_LEN;
+
+    TIter it = itEnd - len;
+
+    __uint64 hash = 0;
+    for (; it != itEnd; ++it)
+        hash = hash * ALPH_SIZE + ordValue(*it);
+    return hash;
+}
+
+inline void
+insertRecord(BamScannerCache &cache, seqan::BamAlignmentRecord const &record)
+{
+    int _id;
+    if (empty(cache.unusedIds))
+    {
+        _id = length(cache.records);
+        appendValue(cache.records, record);
+    }
+    else
+    {
+        _id = back(cache.unusedIds);
+        eraseBack(cache.unusedIds);
+        cache.records[_id] = record;
+    }
+
+    BamScannerCache::TKey key = { record.rID, record.beginPos, _suffixHash(record.qName) };
+    cache.map.insert(std::make_pair(key, _id));
+}
+
+template <typename TQName1, typename TQName2>
+inline bool
+_qNamesEqual(TQName1 const &name1, TQName2 const &name2)
+{
+    unsigned len1 = length(name1);
+    unsigned len2 = length(name2);
+
+    if (len1 != len2)
+        return false;
+
+    if (len1 > 2 && len2 > 2)
+    {
+        if (name1[len1 - 2] == ':' || name1[len1 - 2] == '/')
+            return prefix(name1, len1 - 1) == prefix(name2, len2 - 1);
+    }
+    return name1 == name2;
+}
+
+
+// search a certain segment that might refer to lastRecord
+// if recursively search for a intermediate segments that might refer to lastRecord
+inline bool
+_recursivelyFindSegmentGraph(
+    String<BamAlignmentRecord> &records,
+    BamScannerCacheSearchKey_ &searchKey,
+    unsigned segmentNo,
+    BamScannerCache &cache)
+{
+    typedef BamScannerCache::TMapIter TMapIter;
+    typedef BamScannerCacheSearchKey_::TFlag TFlag;
+
+    // search for segment using contigId, position
+    std::pair<TMapIter, TMapIter> range = cache.map.equal_range(searchKey.cacheKey);
+    for (TMapIter iter = range.first; iter != range.second;)
+    {
+        TMapIter it = iter;
+        ++iter;
+        BamAlignmentRecord &record = cache.records[it->second];
+
+        // ... additionally check flags and qName
+        if ((record.flag & searchKey.flagsMask) == searchKey.flags &&
+            _qNamesEqual(record.qName, records[0].qName))
+        {
+            if (record.rNextId == records[0].rID && record.pNext == records[0].beginPos)
+            {
+                resize(records, segmentNo + 2);
+                records[segmentNo + 1] = records[0];
+                records[segmentNo] = record;
+                appendValue(cache.unusedIds, it->second);
+                cache.map.erase(it);
+                return true;
+            }
+        }
+    }
+
+    for (; range.first != range.second; ++range.first)
+    {
+        BamAlignmentRecord &record = cache.records[range.first->second];
+
+        // ... additionally check flags and qName
+        if ((record.flag & searchKey.flagsMask) == searchKey.flags &&
+            _qNamesEqual(record.qName, records[0].qName))
+        {
+            BamScannerCacheSearchKey_ newSearchKey = {
+                { record.rNextId, record.pNext, searchKey.cacheKey.qnameHash },
+                static_cast<TFlag>((record.flag & BAM_FLAG_MULTIPLE) | ((record.flag & BAM_FLAG_NEXT_RC) >> 1)),
+                BAM_FLAG_MULTIPLE | BAM_FLAG_RC
+            };
+            if (_recursivelyFindSegmentGraph(records, newSearchKey, segmentNo + 1, cache))
+            {
+                records[segmentNo] = record;
+                appendValue(cache.unusedIds, range.first->second);
+                cache.map.erase(range.first);
+                return true;
+            }
+        }
+    }
+
+    return false;
+}
+
+
+inline void
+readMultiRecords(String<BamAlignmentRecord> &records, BamFileIn &bamFile, BamScannerCache &cache)
+{
+    typedef BamScannerCacheSearchKey_::TFlag TFlag;
+
+    if (empty(records))
+        resize(records, 1);
+
+    while (!atEnd(bamFile))
+    {
+        // read next record
+        BamAlignmentRecord &record = records[0];
+        readRecord(record, bamFile);
+
+        // is this a single-end read or single alignment?
+        if (!hasFlagMultiple(record) ||
+            record.rID == BamAlignmentRecord::INVALID_REFID ||
+            record.beginPos == BamAlignmentRecord::INVALID_POS ||
+            record.rNextId == BamAlignmentRecord::INVALID_REFID ||
+            record.pNext == BamAlignmentRecord::INVALID_POS)
+        {
+            resize(records, 1);
+            return;
+        }
+
+        if (record.rID < record.rNextId || (record.rID == record.rNextId && record.beginPos < record.pNext))
+        {
+            // store record to retrieve it later
+            insertRecord(cache, record);
+            continue;
+        }
+
+        // search mates in case of multiple templates
+        BamScannerCacheSearchKey_ searchKey = {
+            { record.rNextId, record.pNext, _suffixHash(record.qName) },
+            static_cast<TFlag>((record.flag & BAM_FLAG_MULTIPLE) | ((record.flag & BAM_FLAG_NEXT_RC) >> 1)),
+            BAM_FLAG_MULTIPLE | BAM_FLAG_RC
+        };
+        if (_recursivelyFindSegmentGraph(records, searchKey, 0, cache))
+        {
+            // order paired-end reads by first and second segment in the template
+//            if (length(records) == 2)
+//            {
+//                if (hasFlagLast(records[0]))
+//                    std::swap(records[0], records[1]);
+//            }
+            return;
+        }
+        else
+        {
+            // we could get here if both mates align to same position and we are the first
+            // hence, insert our record to be retrieved by the second.
+            if (records[0].beginPos != records[0].pNext)
+            {
+                std::cerr << "WARNING: Mate could not be found for:\n";
+                write(std::cerr, records[0], context(bamFile), seqan::Sam());
+            }
+            insertRecord(cache, records[0]);
+        }
+    }
+    clear(records);
+}
+
+}  // namespace seqan;
+
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_SCANNER_CACHE_H_
diff --git a/seqan/bam_io/bam_stream.h b/seqan/bam_io/bam_stream.h
deleted file mode 100644
index a73fb68..0000000
--- a/seqan/bam_io/bam_stream.h
+++ /dev/null
@@ -1,851 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Simple-to-use I/O for SAM and BAM files.
-//
-// The actual implementation is done using the class hierarchies rooted in
-// XamReader and XamWriter.  We use virtual functions and native C++
-// inheritance here because the implementations requires some kind of dynamic
-// lookup, and using the built-in inheritance model is probably fast.  Also,
-// this API is on a very high level/layer and thus some loss in performance is
-// OK.
-// ==========================================================================
-
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_STREAM_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_STREAM_H_
-
-#include <fstream>
-#include <memory>
-
-#include <seqan/store.h>
-
-// TODO(holtgrew): Replace std::fstream by MMap String?
-// TODO(holtgrew): Implement BAI support?
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class BamStream
- * @headerfile <seqan/bam_io.h>
- * @brief Class that provides an easy to use interface for reading and writing SAM and BAM files.
- *
- * @signature class BamStream;
- *
- * @section Example
- *
- * Read and write SAM or BAM files.
- *
- * @include demos/bam_io/bam_stream.cpp
- *
- * The output is as follows:
- *
- * @include demos/bam_io/bam_stream.cpp.stdout
- */
-
-/*!
- * @fn BamStream::BamStream
- * @brief Constructor
- *
- * @signature BamStream::BamStream([fileName[, mode[, format]]]);
- *
- * @param[in] fileName The path to the SAM or BAM file to load, <tt>char const *</tt>.
- * @param[in] mode     The open mode, of type @link BamStream::OperationMode @endlink, defaults to <tt>READ</tt>.
- * @param[in] format   The format, of type @link BamStream::Format @endlink, defaults to <tt>AUTO</tt>.
- */
-
-/*!
- * @var THeader BamStream::header
- * @brief The @link BamHeader @endlink of the @link BamStream @endlink object.
- *
- * SAM and BAM files have a header.  When writing SAM or BAM files, you have to fill this member before writing @link
- * BamAlignmentRecord @endlinks.  Upon writing the first record, the header will be written out.
- *
- * When reading BAM files, the header will be read upon opening the file. When reading SAM files, any header will be
- * read upon opening the file.
- *
- * Note that there is a special case when reading SAM records: If there is no header, or records refer to reference
- * sequences that are previously unknown when reading SAM then a new entry is added to @link BamHeader::sequenceInfos
- * @endlink.
- */
-
-/*!
- * @var TBamIOContext BamStream::bamIOContext
- *
- * @brief The @link BamIOContext @endlink object to use for reading and writing @link BamAlignmentRecord @endlinks.
- *
- * When reading, the <tt>bamIOContext</tt> will be updated automatically.  When reading SAM, new reference sequences can
- * be introduced "on the fly" when a new sequence appears.  When writing, the <tt>bamIOContext</tt> is automatically
- * filled/reset when the first record is written.
- */
-
-/**
-.Class.BamStream
-..cat:BAM I/O
-..summary:Class that provides an easy to use interface for reading and writing SAM and BAM files.
-..signature:BamStream
-..example:Read and write SAM or BAM files.
-..example.file:demos/bam_io/bam_stream.cpp
-..example.text:The output is as follows:
-..example.output:
-@HD VN:1.3  SO:coordinate
-@SQ SN:ref  LN:45
-@SQ SN:ref2 LN:40
-r001    163 ref 7   30  8M4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG *   XX:B:S,12561,2,20,112
-r002    0   ref 9   30  1S2I6M1P1I1P1I4M2I  *   0   0   AAAAGATAAGGGATAAA   *
-r003    0   ref 9   30  5H6M    *   0   0   AGCTAA  *
-r004    0   ref 16  30  6M14N1I5M   *   0   0   ATAGCTCTCAGC    *
-r003    16  ref 29  30  6H5M    *   0   0   TAGGC   *
-r001    83  ref 37  30  9M  =   7   -39 CAGCGCCAT   *
-..include:seqan/bam_io.h
-
-.Memfunc.BamStream#BamStream:
-..class:Class.BamStream
-..description:See documentation of @Class.BamStream@ for more information.
-..summary:Constructor
-..signature:BamStream()
-..signature:BamStream(fileName[, mode[, format]])
-..param.fileName:Path to the file to open.
-...type:nolink:$char const *$
-..param.mode:The mode to use for opening the file (read/write). Optional
-...default:@Enum.BamStream\colon\colonOperationMode.value.READ@
-...type:Enum.BamStream\colon\colonOperationMode
-..param.format:Use this to enforce opening the file in the given format. Autodetected from file name or content if not specified. Optional.
-...type:Enum.BamStream\colon\colonFormat
-...default:@Enum.BamStream\colon\colonFormat.value.AUTO@
-
-.Memvar.BamStream#header:
-..class:Class.BamStream
-..type:Class.BamHeader
-..summary:The @Class.BamHeader@ of the @Class.BamStream@ object.
-..description:
-SAM and BAM files have a header.
-When writing SAM or BAM files, you have to fill this member before writing @Class.BamAlignmentRecord@s.
-Upon writing the first record, the header will be written out.
-..description:
-When reading BAM files, the header will be read upon opening the file.
-When reading SAM files, any header will be read upon opening the file.
-..description:
-Note that there is a special case when reading SAM records:
-If there is no header, or records refer to reference sequences that are previously unknown when reading SAM then a new entry is added to @Memvar.BamHeader#sequenceInfos@.\
-
-.Memvar.BamStream#bamIOContext:
-..class:Class.BamStream
-..summary:The @Class.BamIOContext@ object to use for reading and writing @Class.BamAlignmentRecord@s.
-..description:
-When reading, the $bamIOContext$ will be updated automatically.
-When reading SAM, new reference sequences can be introduced "on the fly" when a new sequence appears.
-When writing, the $bamIOContext$ is automatically filled/reset when the first record is written.
-
-.Enum.BamStream\colon\colonOperationMode:
-..cat:BAM I/O
-..summary:Select the operation mode of a @Class.BamStream@.
-..value.READ:Open stream for reading.
-..value.WRITE:Open stream for writing.
-..include:seqan/bam_io.h
-
-.Enum.BamStream\colon\colonFormat:
-..cat:BAM I/O
-..summary:Select the format to use for reading/writing.
-..value.AUTO:Auto-detect format from file content on reading and from the file name on writing. If Auto-detection fails, SAM is used.
-..value.SAM:Force reading/writing of SAM.
-..value.BAM:Force reading/writing of BAM.
-..include:seqan/bam_io.h
-*/
-
-/*!
- * @enum BamStream::OperationMode
- * @brief Selects teh operation mode of a @link BamStream @endlink.
- * @see BamStream
- *
- * @signature enum BamStream::OperationMode;
- *
- * @var BamStream::OperationMode BamStream::READ;
- * @brief Enum value for reading.
- *
- * @var BamStream::OperationMode BamStream::WRITE;
- * @brief Enum value for writing.
- */
-
-/*!
- * @enum BamStream::Format
- * @brief Select the format to use for reading/writing.
- *
- * @signature enum BamStream::Format;
- *
- * @var BamStream::Format BamStream::AUTO;
- * @brief Auto-detect the format from file content on reading and from the file name on writing.  If auto-detection
- *        fails, SAM is used.
- *
- * @var BamStream::Format BamStream::SAM;
- * @brief Force reading/writing of SAM.
- *
- * @var BamStream::Format BamStream::BAM;
- * @brief Force reading/writing of BAM.
- */
-
-class BamStream
-{
-public:
-
-    // Enum for selecting read/write mode.
-    enum OperationMode
-    {
-        READ,
-        WRITE
-    };
-
-    // Enum for selecting format.  AUTO is only used as the default, after opening, only SAM and BAM are used.
-    enum Format
-    {
-        AUTO,
-        SAM,
-        BAM
-    };
-
-    // Name of the BAM file.
-    CharString _filename;
-    // The open mode.
-    OperationMode _mode;
-    // The format.
-    Format _format;
-    // Whether or not the header was written out.
-    bool _headerWritten;
-
-    // Indicates whether stream is at end when reading.
-    bool _atEnd;
-    // Indicates whether there was an error when reading or writing.
-    bool _isGood;
-
-    // The BAM Header record.
-    BamHeader header;
-    // The BAM I/O Context and its elements.
-    StringSet<CharString>                  _nameStore;
-    NameStoreCache<StringSet<CharString> > _nameStoreCache;
-    BamIOContext<StringSet<CharString> >   bamIOContext;
-
-    // The actual implementation of writing SAM or BAM.
-    std::SEQAN_AUTO_PTR_NAME<XamWriter_> _writer;
-    // The actual implementation of reading SAM or BAM.
-    std::SEQAN_AUTO_PTR_NAME<XamReader_> _reader;
-
-    // Constructors.
-
-    BamStream() :
-        _mode(READ), _format(AUTO), _headerWritten(false), _atEnd(false), _isGood(true),
-        _nameStoreCache(_nameStore), bamIOContext(_nameStore, _nameStoreCache)
-    {}
-
-    BamStream(char const * filename, OperationMode mode = READ, Format format = AUTO);
-
-    // Write header if necessary.
-    inline int _writeHeader()
-    {
-        if (this->_headerWritten)
-            return 0;
-
-        // Rewrite name store and cache.
-        clear(_nameStore);
-        for (unsigned i = 0; i < length(header.sequenceInfos); ++i)
-            appendValue(_nameStore, header.sequenceInfos[i].i1);
-        refresh(_nameStoreCache);
-
-        // Write out header.
-        this->_headerWritten = true;
-        return this->_writer->writeHeader(header, bamIOContext);
-    }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Member Function BamStream::BamStream()
-// ----------------------------------------------------------------------------
-
-// Forward declaration is here since it refers to enum member type.
-inline int open(BamStream & bamIO,
-                char const * filename,
-                BamStream::OperationMode mode,
-                BamStream::Format format);
-
-inline BamStream::BamStream(char const * filename, OperationMode mode, Format format) :
-    _filename(filename), _mode(mode), _format(format), _headerWritten(false), _atEnd(false), _isGood(true),
-    _nameStoreCache(_nameStore), bamIOContext(_nameStore, _nameStoreCache)
-{
-    open(*this, filename, _mode, _format);
-}
-
-// ----------------------------------------------------------------------------
-// Function open()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#open
- * @brief Open a @link BamStream @endlink object for reading/writing.
- *
- * @signature int open(bamIO, fileName[, mode[, format]]);
- *
- * @param[in,out] bamIO    The @link BamStream @endlink object to open. Types: BamStream
- * @param[in]     fileName The path to the file to open, <tt>char const *</tt>.
- * @param[in]     mode     The mode to open the file in, optional, of type @link BamStream::OperationMode @endlink,
- *                         defaults to <tt>BamStream::READ</tt>.
- * @param[in]     format   The format to use, inferred from file contents (reading) or file name (writing) by default.
- *                         the path to the file to open, of type @link BamStream::Format @endlink, defaults to
- *                         <tt>AUTO</tt>.
- *
- * @return int A status code, 0 on success, a value <tt>!= 0</tt> on errors.
- */
-
-/**
-.Function.BamStream#open
-..class:Class.BamStream
-..summary:Open a @Class.BamStream@ object for reading/writing.
-..signature:open(bamIO, fileName[, mode[, format]])
-..param.bamIO:The @Class.BamStream@ object to open.
-...type:Class.BamStream
-..param.fileName:The path to the file to open.
-...type:Shortcut.CharString
-..param.mode:The mode to open the file in. Optional.
-...default:$BamStream::READ$
-...type:nolink:$BamStream::OperationMode$.
-..param.format:The format to use, inferred from file contents (reading) or file name (writing) by default.
-...default:$BamStream::AUTO$
-...type:nolink:$BamStream::Format$.
-..param.format:The path to the file to open.
-...type:Shortcut.CharString
-..returns:An $int$ status code: $0$ on success, $1$ on errors.
-..include:seqan/bam_io.h
-*/
-
-inline int open(BamStream & bamIO,
-                char const * fileName,
-                BamStream::OperationMode mode = BamStream::READ,
-                BamStream::Format format = BamStream::AUTO)
-{
-    bamIO._filename = fileName;
-    bamIO._isGood = true;
-
-    // Guess format if necessary.
-    if (format == BamStream::AUTO)
-    {
-        if (mode == BamStream::READ)
-        {
-            format = BamStream::SAM;  // SAM is default.
-
-            // Look whether the file is in BAM format.
-            std::fstream inStream(toCString(fileName), std::ios_base::binary | std::ios_base::in);
-            if (!inStream.good())
-            {
-                bamIO._isGood = false;
-                return 1;  // Error opening the file.
-            }
-            char buffer[3];
-            inStream.read(&buffer[0], 3);
-            if (buffer[0] == '\x1F' && buffer[1] == '\x8B' && buffer[2] == '\x08')
-                format = BamStream::BAM;
-        }
-        else  // mode == WRITE
-        {
-            format = BamStream::SAM;  // SAM is default.
-            if (endsWith(fileName, ".bam"))
-                format = BamStream::BAM;
-        }
-    }
-
-#if !SEQAN_HAS_ZLIB
-    // Guard against opening BAM files without zlib.
-    if (format == BamStream::BAM)
-    {
-        std::cerr << "ERROR: Trying to open BAM file and ZLIB is not available!\n";
-        bamIO._isGood = false;
-        return 1;
-    }
-#endif  // #if !SEQAN_HAS_ZLIB
-
-    if (mode == BamStream::READ)
-    {
-        if (format == BamStream::SAM)
-            bamIO._reader.reset(new SamReader_());
-#if SEQAN_HAS_ZLIB
-        // The branch above is always taken if zlib is not available, there already is a check above.
-        else
-            bamIO._reader.reset(new BamReader_());
-#endif  // #if !SEQAN_HAS_ZLIB
-        if (bamIO._reader->open(fileName) != 0)
-        {
-            bamIO._isGood = false;
-            return 1;
-        }
-    }
-    else  // (format == BamStream::WRITE)
-    {
-        if (format == BamStream::SAM)
-            bamIO._writer.reset(new SamWriter_());
-#if SEQAN_HAS_ZLIB
-        // The branch above is always taken if zlib is not available, there already is a check above.
-        else
-            bamIO._writer.reset(new BamWriter_());
-#endif  // #if !SEQAN_HAS_ZLIB
-        if (bamIO._writer->open(fileName) != 0)
-        {
-            bamIO._isGood = false;
-            return 1;
-        }
-    }
-
-    bamIO._mode = mode;
-    bamIO._format = format;
-
-    // Read header.
-    if (bamIO._isGood && bamIO._mode == BamStream::READ)
-    {
-        clear(bamIO.header);
-        if (bamIO._reader->readHeader(bamIO.header, bamIO.bamIOContext) != 0)
-        {
-            bamIO._isGood = false;
-            return 1;
-        }
-    }
-
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function reset()
-// ----------------------------------------------------------------------------
-
-/*
- * @fn BamStream#reset
- * @brief Reset @link BamStream @endlink object to status after construction.
- *
- * @signature void reset(stream);
- *
- * @param stream The @link BamStream @endlink object to reset.
- *
- * @return int A status code, 0 on success, <tt>!= 0</tt> on error.
- */
-
-/**
-.Function.BamStream#reset
-..class:Class.BamStream
-..summary:Reset @Class.BamStream@ object to status after construction.
-..signature:reset(bamIO)
-..param.bamIO:The @Class.BamStream@ object to reset.
-...type:Class.BamStream
-..returns:$int$, a status code ($0$ for success, non-$0$ for error).
-..include:seqan/bam_io.h
-*/
-
-inline int reset(BamStream & bamIO)
-{
-    return open(bamIO, toCString(bamIO._filename), bamIO._mode, bamIO._format);
-}
-
-// ----------------------------------------------------------------------------
-// Function flush()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#flush
- * @brief Flush output when writing.
- *
- * @signature int flush(stream);
- *
- * @param stream The @link BamStream @endlink object to flush.
- *
- * @return int A status code, 0 on success, <tt>!= 0</tt> on errors.
- *
- * @section Remarks
- *
- * This will write out the header if no record has been written out yet.
- */
-
-/**
-.Function.BamStream#flush
-..class:Class.BamStream
-..summary:Flush output when writing.
-..description:This will write out the header if no record has been written out yet.
-..signature:flush(bamIO)
-..param.bamIO:The @Class.BamStream@ object to flush.
-...type:Class.BamStream
-..returns:$int$ with an error code.
-..include:seqan/bam_io.h
-*/
-
-inline int flush(BamStream & bamIO)
-{
-    if (bamIO._mode == BamStream::WRITE)
-    {
-        bamIO._writeHeader();
-        return bamIO._writer->flush();
-    }
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function close()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#close
- * @brief Close BamStream object's underlying file.
- *
- * @signature int close(stream);
- *
- * @param stream[in,out] The @link BamStream @endlink object to close.
- *
- * @return int A status code, 0 on success, <tt>!= 0</tt> on error.
- */
-
-/**
-.Function.BamStream#close
-..class:Class.BamStream
-..summary:Close BamStream object's underlying file.
-..signature:close(bamIO)
-..param.bamIO:The @Class.BamStream@ object to close
-...type:Class.BamStream
-..returns:$int$ with an error code.
-..include:seqan/bam_io.h
-*/
-
-inline int close(BamStream & bamIO)
-{
-    if (bamIO._mode == BamStream::WRITE)
-    {
-        bamIO._writeHeader();
-        return bamIO._writer->close();
-    }
-    else
-    {
-        return bamIO._reader->close();
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function atEnd()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#atEnd
- * @brief Check whether a @link BamStream @endlink object is at end when reading.
- *
- * @signature bool atEnd(stream);
- *
- * @param[in] stream The @link BamStream @endlink object to query.
- *
- * @return bool true in case of the stream being at the end, false otherwise.
- *
- * @section Remarks
- *
- * The stream will only be guaranteed at the end after trying to read <b>after</b> the last character.
- */
-
-/**
-.Function.BamStream#atEnd
-..class:Class.BamStream
-..summary:Check whether a @Class.BamStream@ object is at end when reading.
-..signature:atEnd(bamIO)
-..param.bamIO:The @Class.BamStream@ object to query.
-...type:Class.BamStream
-..returns:$bool$, indicating whether the object is at the end of the file.
-..include:seqan/bam_io.h
-*/
-
-inline bool atEnd(BamStream const & bamIO)
-{
-    SEQAN_ASSERT_EQ_MSG(bamIO._mode, BamStream::READ, "You can only call atEnd() when opened the file for reading.");
-    return bamIO._reader->atEnd();
-}
-
-inline bool atEnd(BamStream & bamIO)
-{
-    SEQAN_ASSERT_EQ_MSG(bamIO._mode, BamStream::READ, "You can only call atEnd() when opened the file for reading.");
-    return bamIO._reader->atEnd();
-}
-
-// ----------------------------------------------------------------------------
-// Function isGood()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#isGood
- * @brief Check whether the @link BamStream @endlink object has is in the failure state.
- *
- * @signature bool isGood(stream);
- *
- * @param stream The @link BamStream @endlink object to query.
- *
- * @return bool true if the stream is not in an error state and false otherwise.
- */
-
-/**
-.Function.BamStream#isGood
-..class:Class.BamStream
-..summary:Check whether the @Class.BamStream@ object has is in the failure state.
-..signature:isGood(bamIO)
-..param.bamIO:The @Class.BamStream@ object to query.
-...type:Class.BamStream
-..returns:$bool$, indicating whether there was no error or not.
-..include:seqan/bam_io.h
-*/
-
-inline bool isGood(BamStream const & bamIO)
-{
-    return bamIO._isGood;
-}
-
-// ----------------------------------------------------------------------------
-// Function readRecord()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#readRecord
- * @brief Read one @link BamAlignmentRecord @endlink from a @link BamStream @endlink.
- *
- * @signature int readRecord(record, stream);
- *
- * @param[out]   record    The @link BamAlignmentRecord @endlink to read the next alignment record into.  Of type
- *                         @link BamAlignmentRecord @endlink.
- * @param[in,out] stream   The @link BamStream @endlink object to read from.
- *
- * @return int A status code, 0 on success.
- */
-
-/**
-.Function.BamStream#readRecord
-..class:Class.BamStream
-..summary:Read one @Class.BamAlignmentRecord@ from a @Class.BamStream@.
-..signature:readRecord(record, bamIO)
-..param.record:The @Class.BamAlignmentRecord@ to read the next alignment record into.
-...class:Class.BamAlignmentRecord
-..param.bamIO:The @Class.BamStream@ object to read from.
-...type:Class.BamStream
-..returns:An $int$ status code: $0$ on success, non-$0$ on failure.
-..include:seqan/bam_io.h
-*/
-
-inline int readRecord(BamAlignmentRecord & record, BamStream & bamIO)
-{
-    int res = bamIO._reader->readRecord(record, bamIO.bamIOContext);
-    bamIO._isGood = bamIO._isGood && (res == 0);
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function writeRecord()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#writeRecord
- * @brief Write one @link BamAlignmentRecord @endlink to a @link BamStream @endlink.
- *
- * @signature int writeRecord(stream, record);
- *
- * @param[in,out] bamIO  The @link BamStream @endlink object to write to.
- * @param[in]     record The @link BamAlignmentRecord @endlink to write out.
- *
- * @return int A status code, 0 on success.
- */
-
-/**
-.Function.BamStream#writeRecord
-..class:Class.BamStream
-..summary:Write one @Class.BamAlignmentRecord@ to a @Class.BamStream@.
-..signature:writeRecord(bamIO, record)
-..param.record:The @Class.BamAlignmentRecord@ to write out.
-...class:Class.BamAlignmentRecord
-..param.bamIO:The @Class.BamStream@ object to write to.
-...type:Class.BamStream
-..returns:An $int$ status code: $0$ on success, non-$0$ on failure.
-..include:seqan/bam_io.h
-*/
-
-inline int writeRecord(BamStream & bamIO, BamAlignmentRecord const & record)
-{
-    bamIO._writeHeader();  // Does nothing if head already written out.
-
-    int res = bamIO._writer->writeRecord(record, bamIO.bamIOContext);
-    bamIO._isGood = bamIO._isGood && (res == 0);
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function fileSize()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#fileSize
- * @brief Returns the size of the file in bytes as stored on the disk.
- *
- * @signature __int64 fileSize(stream);
- *
- * @param[in] stream The @link BamStream @endlink to query.
- *
- * @return __int64 The size of the file on the disk.
- *
- * @section Remarks
- *
- * This only works when reading.
- */
-
-// Returns size of file in bytes as stored on the disk.
-
-inline __int64 fileSize(BamStream const & bamIO)
-{
-    if (bamIO._mode == BamStream::WRITE)
-        return 0;
-    return bamIO._reader->fileSize();
-}
-
-// ----------------------------------------------------------------------------
-// Function positionInFile()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#positionInFile
- * @brief Approximate byte position in file, to be used for progress display, not for seeking.
- *
- * @signature __int64 positionInFile(stream);
- *
- * @param[in] stream The @link BamStream @endlink to query for its position in the file.
- *
- * @return __int64 The position in the file.
- *
- * @section Remarks
- *
- * This function returns the "approximate" position in the file and only works when the file is opened in BAM format.
- * It is meant for progress display in connection with @link BamStream#fileSize @endlink and not for jumping within the
- * file.  The position is approximate in the sense that it points between the block boundaries of the BGZ file.
- */
-
-// TODO(holtgrew): Review this functionality, extend, fix.
-
-// Returns "approximate" byte position in file.  To be used for progress display, not for seeking.  For this, we have to
-// implement streamTell() and streamSeek() for BamStream.  This works for BAM only at the moment.
-
-inline __int64 positionInFile(BamStream const & bamIO)
-{
-    if (bamIO._mode == BamStream::WRITE)
-        return 0;
-    return bamIO._reader->positionInFile();
-}
-
-// ----------------------------------------------------------------------------
-// Function jumpToRegion()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#jumpToRegion
- * @brief Seek in BamStream using an index.
- *
- * You provide a region <tt>[pos, posEnd)</tt> on the reference <tt>refID</tt> that you want to jump to and the function
- * jumps to the first alignment in this region, if any.
- *
- * @signature bool jumpToRegion(stream, hasAlignments, bamIOContext, refID, pos, posEnd, index);
- *
- * @param[in,out] stream        The @link BamStream @endlink to jump with.
- * @param[out]    hasAlignments A <tt>bool</tt> that is set true if the region <tt>[pos, posEnd)</tt> has any
- *                              alignments.
- * @param[in]     refID         The reference id to jump to (<tt>__int32</tt>).
- * @param[in]     pos           The begin of the region to jump to.
- * @param[in]     posEnd        The end of the region to jump to.
- * @param[in]     index         The @link BamIndex @endlink to use for the jumping.
- *
- * @return bool true if seeking was successful, false if not.
- *
- * @section Remarks
- *
- * This function fails if <tt>refID</tt>/<tt>pos</tt> are invalid.
- *
- * @see BamIndex#jumpToRegion
- */
-
-#if SEQAN_HAS_ZLIB
-inline bool jumpToRegion(BamStream & bamIO, bool & hasAlignments, __int32 refId, __int32 pos, __int32 posEnd, BamIndex<Bai> const & index)
-{
-    if (bamIO._format != BamStream::BAM)
-        return false;  // Can only jump in BAM files.
-    if (bamIO._mode != BamStream::READ)
-        return false;  // Can only jump when reading.
-
-    BamReader_ * s = static_cast<BamReader_ *>(bamIO._reader.get());
-    return s->jumpToRegion(hasAlignments, refId, pos, posEnd, index, bamIO.bamIOContext);
-}
-#endif  // #if SEQAN_HAS_ZLIB
-
-// ----------------------------------------------------------------------------
-// Function jumpToOrphans()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamStream#jumpToOrphans
- * @brief Seek to orphans block in BamStream using an index.
- *
- * @signature bool jumpToOrphans(stream, hasAlignments, index);
- *
- * @param[in,out] stream         The @link BgzfStream @endlink object to jump with.
- * @param[out]    hasAlignments  A <tt>bool</tt> that is set to true if there are any orphans.
- * @param[in]     index          The index to use for jumping.
- *
- * @see BamIndex#jumpToOrphans
- */
-
-#if SEQAN_HAS_ZLIB
-inline bool jumpToOrphans(BamStream & bamIO, BamIndex<Bai> const & index)
-{
-    if (bamIO._format != BamStream::BAM)
-        return false;  // Can only jump in BAM files.
-    if (bamIO._mode != BamStream::READ)
-        return false;  // Can only jump when reading.
-
-    BamReader_ * s = static_cast<BamReader_ *>(bamIO._reader.get());
-    return s->jumpToOrphans(index, bamIO.bamIOContext);
-}
-#endif  // #if SEQAN_HAS_ZLIB
-
-}  // namespace seqan;
-
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_STREAM_H_
diff --git a/seqan/bam_io/bam_tags_dict.h b/seqan/bam_io/bam_tags_dict.h
index 32f0c51..05de73c 100644
--- a/seqan/bam_io/bam_tags_dict.h
+++ b/seqan/bam_io/bam_tags_dict.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,12 +30,13 @@
 //
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 // Code for read/write access to BAM tag dicts.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_
+#define INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_
 
 namespace seqan {
 
@@ -43,6 +44,43 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
+class BamTagsDict;
+
+inline bool hasIndex(BamTagsDict const & bamTags);
+inline void buildIndex(BamTagsDict const & bamTags);
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Host
+// ----------------------------------------------------------------------------
+
+template <>
+struct Host<BamTagsDict>
+{
+    typedef CharString Type;
+};
+
+template <>
+struct Host<BamTagsDict const>
+{
+    typedef CharString const Type;
+};
+
+template <>
+struct Size<BamTagsDict>
+{
+    typedef unsigned Type;
+};
+
+template <>
+struct Position<BamTagsDict>
+{
+    typedef unsigned Type;
+};
+
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
@@ -56,33 +94,11 @@ namespace seqan {
  *
  * @section Example
  *
- * @code{.cpp}
- * CharString samStr = "AA:Z:value1\tAB:Z:value2\tAC:i:30";
- * CharString bamStr;
- * assignSamToBam(bamStr, samStr);
- * BamTagsDict tags(bamStr);
- * std::cerr << length(tags) << std::endl;  // #=> "3"
- * for (unsigned i = 0; i < length(tags); ++i)
- * {
- *     std::cerr << getTagKey(tags, i) << " -> " << getTagValue(tags, i) << std::endl;
- *     if (getTagValue(tags, i)[0] == 'i')  // is 32 bit integer
- *     {
- *         __int32 x = 0;
- *         bool res = extractTagValue(x, tags, i);
- *         SEQAN_ASSERT_MSG(res, "Not a valid integer at pos %u!", i);
- *         std::cerr << "     " << x << std::endl;
- *     }
- * }
- * @endcode
+ * @include demos/dox/bam_io/bam_tags_dict.cpp
  *
  * Output is:
  *
- * @code{.cpp}
- * "AA -> Zvalue1"
- * "AB -> Zvalue2"
- * "AC -> i<binary representation of 30>"
- *     -> "      30"
- * @endcode
+ * @include demos/dox/bam_io/bam_tags_dict.cpp.stdout
  *
  * @see getBamTypeSize
  * @see getBamTypeChar
@@ -95,72 +111,28 @@ namespace seqan {
  * @signature BamTagsDict::BamTagsDict();
  */
 
-/**
-.Class.BamTagsDict
-..cat:BAM I/O
-..cat:Fragment Store
-..signature:BamTagsDict
-..summary:Indexes start positions of BAM tags in a @Shortcut.CharString@ and provides a dict-like API.
-..example.code:
-CharString samStr = "AA:Z:value1\tAB:Z:value2\tAC:i:30";
-CharString bamStr;
-assignSamToBam(bamStr, samStr);
-BamTagsDict tags(bamStr);
-std::cerr << length(tags) << std::endl;  // #=> "3"
-for (unsigned i = 0; i < length(tags); ++i)
-{
-    std::cerr << getTagKey(tags, i) << " -> " << getTagValue(tags, i) << std::endl;
-    if (getTagValue(tags, i)[0] == 'i')  // is 32 bit integer
-    {
-        __int32 x = 0;
-        bool res = extractTagValue(x, tags, i);
-        SEQAN_ASSERT_MSG(res, "Not a valid integer at pos %u!", i);
-        std::cerr << "     " << x << std::endl;
-    }
-}
-// #=> "AA -> Zvalue1"
-// #=> "AB -> Zvalue2"
-// #-> "AC -> i<binary representation of 30>"
-#  #-> "      30"
-..include:seqan/bam_io.h
-
-.Memfunc.BamTagsDict#BamTagsDict
-..class:Class.BamTagsDict
-..signature:BamTagsDict()
-..summary:Constructor.
-..remarks:Only the default constructor is provided.
-*/
-
 class BamTagsDict
 {
 public:
-    Holder<CharString> _host;
-    String<unsigned> _positions;
+    typedef Host<BamTagsDict>::Type TBamTagsSequence;
+    typedef Position<TBamTagsSequence>::Type TPos;
+
+    Holder<TBamTagsSequence> _host;
+    mutable String<TPos> _positions;
 
     BamTagsDict() {}
 
     explicit
-    BamTagsDict(CharString & tags) : _host(tags) {}
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Host
-// ----------------------------------------------------------------------------
+    BamTagsDict(TBamTagsSequence & tags) : _host(tags) {}
 
-template <>
-struct Host<BamTagsDict>
-{
-    typedef CharString Type;
-};
-
-template <>
-struct Host<BamTagsDict const>
-{
-    typedef CharString const Type;
+    template <typename TPos>
+    inline Infix<Host<BamTagsDict const>::Type>::Type
+    operator[] (TPos pos) const
+    {
+        if (!hasIndex(*this))
+            buildIndex(*this);
+        return infix(host(*this), _positions[pos], _positions[pos + 1]);
+    }
 };
 
 // ============================================================================
@@ -193,35 +165,15 @@ host(BamTagsDict const & bamTags)
  *
  * @signature bool hasIndex(dict);
  *
- * @param dict The @link BamTagsDict @endlink to query.
+ * @param[in] dict The @link BamTagsDict @endlink to query.
  *
- * @return bool true if <tt>dict</tt> has an index and false otherwise.
+ * @return bool <tt>true</tt> if <tt>dict</tt> has an index and <tt>false</tt> otherwise.
  */
 
-/**
-.Function.BamTagsDict#hasIndex
-..class:Class.BamTagsDict
-..cat:Fragment Store
-..summary:Return $true$ if @Class.BamTagsDict@ has an index.
-..signature:hasIndex(bamTags)
-..param.bamTags:SAM Tags to query
-...type:Class.BamTagsDict
-..returns:$bool$
-..include:<seqan/store_ex.h>
-*/
-
-// TODO(holtgrew): Remove non-const variante.
-
 inline bool
 hasIndex(BamTagsDict const & bamTags)
 {
-    return length(bamTags._positions) != 0u;
-}
-
-inline bool
-hasIndex(BamTagsDict & bamTags)
-{
-    return hasIndex(const_cast<BamTagsDict const &>(bamTags));
+    return !empty(bamTags._positions) || empty(host(bamTags));
 }
 
 // ----------------------------------------------------------------------------
@@ -230,13 +182,14 @@ hasIndex(BamTagsDict & bamTags)
 
 /*!
  * @fn getBamTypeSize
+ * @headerfile <seqan/bam_io.h>
  * @brief Return size of the type identified by a type char.
  *
  * @signature int getBamTypeSize(c);
  *
- * @param c A <tt>char</tt> that identifies a type.
+ * @param[in] c A <tt>char</tt> that identifies a type.
  *
- * @return int The size of the type in bytes, -1 vor variable-sized types, -2 for invalid paramters.
+ * @return int The size of the type in bytes, -1 for variable-length types, -2 for invalid paramters.
  *
  * @see BamTagsDict
  * @see getBamTypeChar
@@ -245,41 +198,44 @@ hasIndex(BamTagsDict & bamTags)
 // Return sizeof() of the type identified with the given char.  Returns -2 if not
 // valid, -1 if of variable length.
 
-/**
-.Function.getBamTypeSize
-..class:Class.BamTagsDict
-..cat:BAM I/O
-..signature:getBamTypeSize(c)
-..summary:Return size of the type identified by $c$.
-..param.c:The BAM type identifier
-..returns:$int$ with the $sizeof()$ of the type, -1 for variable sized types, -2 for invalid parameters.
-..include:seqan/bam_io.h
-*/
+struct GetBamTypeSizeHelper_
+{
+    int     &resultSize;
+    char    typeC;
+
+    GetBamTypeSizeHelper_(int &resultSize, char typeC) :
+        resultSize(resultSize),
+        typeC(typeC)
+    {}
+
+    template <typename Type>
+    bool operator() (Type) const
+    {
+        if (BamTypeChar<Type>::VALUE != typeC)
+            return false;
+
+        resultSize = sizeof(Type);
+        return true;
+    }
+};
+
 
 inline int
 getBamTypeSize(char c)
 {
-    switch (c)
+    switch (toUpperValue(c))
     {
-        case 'A':
-            return 1;
-        case 'f':
-            return 4;
         case 'Z':
         case 'H':
         case 'B':
             return -1;
-        case 'c':
-        case 'C':
-            return 1;
-        case 's':
-        case 'S':
-            return 2;
-        case 'i':
-        case 'I':
-            return 4;
+
+        default:
+            int result = -2;
+            GetBamTypeSizeHelper_ func(result, c);
+            tagApply(func, BamTagTypes());
+            return result;
     }
-    return -2;
 }
 
 // ----------------------------------------------------------------------------
@@ -295,87 +251,106 @@ getBamTypeSize(char c)
  * @param[in,out] bamTags The BamTagsDict object to build the index for.
  */
 
-/**
-.Function.BamTagsDict#buildIndex
-..class:Class.BamTagsDict
-..cat:Fragment Store
-..summary:Build index for a @Class.BamTagsDict@ object.
-..signature:buildIndex(bamTags)
-..param.bamTags:SAM Tags to build index for.
-...type:Class.BamTagsDict
-..returns:$void$
-..include:<seqan/bam_io.h>
-*/
-
 inline void
-buildIndex(BamTagsDict & bamTags)
+buildIndex(BamTagsDict const & bamTags)
 {
-    typedef Host<BamTagsDict>::Type TCharString;
-    typedef Iterator<TCharString, Rooted>::Type TCharStringIter;
+    typedef Host<BamTagsDict>::Type TTagString;
+    typedef Iterator<TTagString const, Standard>::Type TIter;
 
     clear(bamTags._positions);
-    if (empty(value(bamTags._host)))
+    if (empty(host(bamTags)))
         return;  // Done.
 
     appendValue(bamTags._positions, 0);
-    for (TCharStringIter it = begin(host(bamTags)); !atEnd(it);)
+    TIter itBegin = begin(host(bamTags), Standard());
+    TIter itEnd = end(host(bamTags), Standard());
+    for (TIter it = itBegin; it != itEnd; )
     {
+        SEQAN_ASSERT(it < itEnd);
+        // skip tag name (e.g. "NM")
         it += 2;
-        char c = *it;
+
+        // get tag type (e.g. 'I')
+        char c = *(it++);
         if (c == 'H' || c == 'Z')
         {
-            while (!atEnd(it) && *it != '\0')
+            // skip string and its end-of-string marker
+            while (*it != '\0')
+            {
                 ++it;
+                SEQAN_ASSERT(it != itEnd);
+            }
             ++it;
         }
         else if (c == 'B')
         {
-            ++it;
-            c = *it;
-            ++it;
-            __uint32 len = 0;
-            memcpy(&len, &*it, 4);
-            it += 4;
-            it += len * getBamTypeSize(c);
+            // skip array of PODs
+            c = *(it++);
+            union {
+                char raw[4];
+                __uint32 len;
+            } tmp;
+            arrayCopyForward(it, it + 4, tmp.raw);
+            it += 4 + tmp.len * getBamTypeSize(c);
         }
         else
         {
-            ++it;
+            // skip POD type (e.g. byte, int)
             it += getBamTypeSize(c);
         }
-
-        appendValue(bamTags._positions, position(it));
+        appendValue(bamTags._positions, it - itBegin);
     }
     // if (!empty(value(bamTags._host)))
     //     appendValue(bamTags._positions, length(host(bamTags)) + 1);  // +1 since there is not tab at the end
 }
 
 // ----------------------------------------------------------------------------
-// Function setHost()
+// Function _dataHost()
 // ----------------------------------------------------------------------------
 
-inline Holder<CharString> &
+inline Holder<Host<BamTagsDict>::Type> &
 _dataHost(BamTagsDict & bamTags)
 {
     return bamTags._host;
 }
 
+inline Holder<Host<BamTagsDict>::Type> const &
+_dataHost(BamTagsDict const & bamTags)
+{
+    return bamTags._host;
+}
+
+// ----------------------------------------------------------------------------
+// Function setHost()
+// ----------------------------------------------------------------------------
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename THost>
+inline void
+setHost(BamTagsDict & me, THost && host_)
+{
+    setValue(_dataHost(me), std::forward<THost>(host_));
+    clear(me._positions);
+}
+#else
+template <typename THost>
 inline void
-setHost(BamTagsDict & me, CharString & host_)
+setHost(BamTagsDict & me, THost & host_)
 {
     SEQAN_CHECKPOINT;
-	setValue(_dataHost(me), host_);
+    setValue(_dataHost(me), host_);
     clear(me._positions);
 }
 
+template <typename THost>
 inline void
-setHost(BamTagsDict & me, CharString const & host_)
+setHost(BamTagsDict & me, THost const & host_)
 {
     SEQAN_CHECKPOINT;
-	setValue(_dataHost(me), host_);
+    setValue(_dataHost(me), host_);
     clear(me._positions);
 }
-
+#endif  // SEQAN_CXX11_STANDARD
 // ----------------------------------------------------------------------------
 // Function length()
 // ----------------------------------------------------------------------------
@@ -386,20 +361,19 @@ setHost(BamTagsDict & me, CharString const & host_)
  *
  * @signature unsigned length(tagsDict);
  *
- * @param tagsDict The BamTagsDict object to query for its length.
+ * @param[in] tagsDict The BamTagsDict object to query for its length.
  *
- * @return unsigned The number of entries in the BamTagsDict.
+ * @return TSize The number of entries in the BamTagsDict. <tt>TSize</tt> is the result of
+ *               <tt>Size&lt;BamTagsDict&gt;::Type</tt>.
  */
 
-///.Function.length.param.object.type:Class.BamTagsDict
-
-inline unsigned
+inline Size<BamTagsDict>::Type
 length(BamTagsDict const & tags)
 {
-    if (empty(value(tags._host)))
+    if (empty(host(tags)))
         return 0;
     if (!hasIndex(tags))
-        buildIndex(const_cast<BamTagsDict &>(tags));
+        buildIndex(tags);
     return length(tags._positions) - 1;
 }
 
@@ -411,31 +385,19 @@ length(BamTagsDict const & tags)
  * @fn BamTagsDict#getTagType
  * @brief Returns the tag type char for an entry of a BamTagsDict.
  *
- * @signature char getTagType(tags, idx);
+ * @signature char getTagType(tags, id);
  *
  * @param[in] tags The BamTagsDict to query.
- * @param[in] idx  The position for which to retrieve the type.
+ * @param[in] id   The id of the tag for which to determine the type. See @link BamTagsDict#findTagKey @endlink.
+ *
+ * @return char A <tt>char</tt> that identifies the tag type.
  */
 
-/**
-.Function.BamTagsDict#getTagType
-..class:Class.BamTagsDict
-..cat:BAM I/O
-..signature:getTagType(tagsDict, idx)
-..summary:Get key of a tag by index.
-..param.tagsDict:The @Class.BamTagsDict@ to retrieve data from.
-..param.idx:Index of the tag whose key to retrieve.
-..returns:$char$, the SAM/BAM identifier of the type.
-..include:seqan/bam_io.h
-*/
-
-template <typename TPos>
+template <typename TId>
 inline char
-getTagType(BamTagsDict & tags, TPos idx)
+getTagType(BamTagsDict const & tags, TId id)
 {
-    if (!hasIndex(tags))
-        buildIndex(tags);
-    return host(tags)[tags._positions[idx] + 2];
+    return tags[id][2];
 }
 
 // ----------------------------------------------------------------------------
@@ -446,42 +408,19 @@ getTagType(BamTagsDict & tags, TPos idx)
  * @fn BamTagsDict#getTagKey
  * @brief Return key of a tag by index.
  *
- * @signature TKey getTagKey(tagsDict, idx);
+ * @signature TKey getTagKey(tagsDict, id);
  *
  * @param[in] tagsDict The BamTagsDict to query.
- * @param[in] idx      The index of the dict entry.
+ * @param[in] id       The index of the dict entry.
  *
  * @return TKey An infix of a @link CharString @endlink.  Will be a two-character char sequence.
  */
 
-/**
-.Function.BamTagsDict#getTagKey
-..class:Class.BamTagsDict
-..cat:BAM I/O
-..signature:getTagKey(tagsDict, idx)
-..summary:Return key of a tag by index.
-..param.tagsDict:The @Class.BamTagsDict@ to retrieve data from.
-...type:Class.BamTagsDict
-..param.idx:Index of the tag whose key to retrieve.
-..returns:Infix of the underlying string.
-..remarks:See @Class.BamTagsDict@ for an example.
-..include:seqan/bam_io.h
-*/
-
-template <typename TPos>
-inline Infix<Host<BamTagsDict>::Type>::Type
-getTagKey(BamTagsDict & tags, TPos idx)
-{
-    if (!hasIndex(tags))
-        buildIndex(tags);
-    return infix(host(tags), tags._positions[idx], tags._positions[idx] + 2);
-}
-
-template <typename TPos>
+template <typename TId>
 inline Infix<Host<BamTagsDict const>::Type>::Type
-getTagKey(BamTagsDict const & tags, TPos idx)
+getTagKey(BamTagsDict const & tags, TId id)
 {
-    return getTagKey(const_cast<BamTagsDict &>(tags), idx);
+    return prefix(tags[id], 2);
 }
 
 // ----------------------------------------------------------------------------
@@ -492,252 +431,123 @@ getTagKey(BamTagsDict const & tags, TPos idx)
  * @fn BamTagsDict#findTagKey
  * @brief Find a tag by its key for a @link BamTagsDict @endlink object.
  *
- * @signature bool findTagKey(idx, tagsDict, name);
+ * @signature bool findTagKey(id, tagsDict, key);
  *
- * @param[out] idx      The index of the tag is stored here (<tt>unsigned</tt>).
+ * @param[out] id       The id of the found tag.
  * @param[in]  tagsDict The BamTagsDict to query.
- * @param[in]  name     The key to query for: @link CharString @endlink.
+ * @param[in]  key      The key to query for: @link CharString @endlink.
  *
- * @return bool true if the key could be found and false otherwise.
+ * @return bool <tt>true</tt> if the key could be found and <tt>false</tt> otherwise.
  */
 
-/**
-.Function.BamTagsDict#findTagKey
-..summary:Find a tag by its key for a @Class.BamTagsDict@ object.
-..class:Class.BamTagsDict
-..signature:findTagKey(idx, tagsDict, name)
-..param.idx:Index of the tag with the given key.
-...type:nolink:$unsigned$
-..param.tagsDict:The @Class.BamTagsDict@ to retrieve data from.
-..param.name:Name of the key to find.
-...type:Shortcut.CharString
-..returns:$bool$, indicating whether such a key could be found.
-..include:seqan/bam_io.h
-*/
-
+template <typename TId, typename TKey>
 inline bool
-findTagKey(unsigned & idx, BamTagsDict & tags, CharString const & name)
+findTagKey(TId & id, BamTagsDict const & tags, TKey const & key)
 {
-    for (idx = 0; idx < length(tags); ++idx)
-        if (getTagKey(tags, idx) == name)
+    for (id = 0; id < (TId)length(tags); ++id)
+        if (getTagKey(tags, id) == key)
             return true;
     return false;
 }
 
-inline bool
-findTagKey(unsigned & idx, BamTagsDict const & tags, CharString const & name)
-{
-    return findTagKey(idx, const_cast<BamTagsDict &>(tags), name);
-}
-
 // ----------------------------------------------------------------------------
-// Function getTagValue()
+// Function extractTagValue()
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn BamTagsDict#getTagValue
- * @brief The value of a tag by its key.
+ * @fn BamTagsDict#extractTagValue
+ * @brief Extract and cast "atomic" value from tags string with index <tt>id</tt>.
+ *
+ * @signature bool extractTagValue(dest, tags, id)
  *
- * @signature CharString getTagValue(tagsDict, idx);
+ * @param[out] dest The variable to write the value to.The value is first copied in a variable of the type indicated in
+ *                  the BAM file. Then it is cast into the type of <tt>dest</tt>.
  *
- * @param[in] tagsDict The tags dict to query.
- * @param[in] idx      The index of the entry to query for its value.
+ * @param[in] tags The BamTagsDict object to query.
+ * @param[in] id   The id of the tag to extract the value from. See @link BamTagsDict#findTagKey @endlink.
  *
- * @return CharString the raw tags data.
+ * @return bool <tt>true</tt> if the value could be extracted.
  *
  * @section Remarks
  *
- * Note that you will get <tt>&lt;type char&gt; + payload</tt> in the case of @link BamTagsDict @endlink.
+ * The function only works for atomic types such as <tt>int</tt>, not for <tt>char*</tt> or arrays.
  *
- * See documentation of @link BamTagsDict @endlink for an example.
+ * See @link BamTagsDict @endlink for an example.
  */
 
-
-/**
-.Function.BamTagsDict#getTagValue
-..class:Class.BamTagsDict
-..cat:BAM I/O
-..summary:Return the value of a tag by its index in the @Class.BamTagsDict@.
-..signature:getTagValue(tagsDict, idx)
-..param.tagsDict:The @Class.BamTagsDict@ to retrieve data from.
-...type:Class.BamTagsDict
-..param.idx:Index of the tag whose value to retrieve.
-..returns:@Shortcut.CharString@ with the raw tags data.
-..remarks:Note that you will get $<type char> + payload$ in case of @Class.BamTagsDict@.
-..remarks:See @Class.BamTagsDict@ for an example.
-..include:seqan/bam_io.h
-*/
-
-template <typename TIdx>
-inline CharString
-getTagValue(BamTagsDict & tags, TIdx idx)
+template <typename TResultType, typename TIter>
+struct ExtractTagValueHelper_
 {
-    if (!hasIndex(tags))
-        buildIndex(tags);
-
-    // TODO(holtgrew): Can't we use positions to speed this up?
+    TResultType &result;
+    TIter rawIter;
+    char typeC;
+
+    ExtractTagValueHelper_(TResultType &result, char typeC, TIter rawIter) :
+        result(result),
+        rawIter(rawIter),
+        typeC(typeC)
+    {}
+
+    template <typename Type>
+    bool operator() (Type) const
+    {
+        if (BamTypeChar<Type>::VALUE != typeC)
+            return false;
 
-    typedef typename Position<CharString>::Type TPos;
-    TPos beginPos = tags._positions[idx] + 2;
-    TPos endPos = beginPos + 1;
+        union {
+            char raw[sizeof(Type)];
+            Type i;
+        } tmp;
 
-    char theType = getTagType(tags, idx);
-    if (theType == 'Z' || theType == 'H')
-    {
-        typedef typename Iterator<CharString, Rooted>::Type TIterator;
-        TIterator it = begin(host(tags), Rooted()) + beginPos + 1;
-        for (; !atEnd(it) && *it != '\0'; goNext(it))
-            endPos += 1;
-        endPos += 1;
-    }
-    else if (theType == 'B')
-    {
-        __uint32 len = 0;
-        memcpy(&len, &host(tags)[tags._positions[idx]] + 4, 4);
-        char c = host(tags)[tags._positions[idx] + 3];
-        int typeSize = getBamTypeSize(c);
-        SEQAN_ASSERT_GT(typeSize, 0);
-        endPos += 5 + len * typeSize;
-    }
-    else
-    {
-        endPos += getBamTypeSize(theType);
+        arrayCopyForward(rawIter, rawIter + sizeof(Type), tmp.raw);
+        result = static_cast<TResultType>(tmp.i);
+        return true;
     }
+};
 
-    return infix(host(tags), beginPos, endPos);
-}
-
-template <typename TPos>
-inline CharString //Infix<Host<BamTagsDict const>::Type>::Type
-getTagValue(BamTagsDict const & tags, TPos idx)
+template <typename TResultValue, typename TId>
+SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TResultValue> >, bool)
+extractTagValue(TResultValue & val, BamTagsDict const & tags, TId id)
 {
-    return getValue(const_cast<BamTagsDict &>(tags), idx);
-}
+    typedef Infix<Host<BamTagsDict const>::Type>::Type TInfix;
+    typedef Iterator<TInfix, Standard>::Type TIter;
 
-// ----------------------------------------------------------------------------
-// Function extractTagValue()
-// ----------------------------------------------------------------------------
+    TInfix inf = tags[id];
+    if (length(inf) < 4 || inf[2] == 'Z')
+        return false;
 
-/*!
- * @fn BamTagsDict#extractTagValuej
- * @brief Extract and cast "atomic" value from tags string with index <tt>idx</tt>.
- *
- * @signature bool extractTagValue(dest, tags, idx)
- *
- * @param[out] dest The variable to write the value to.The value is first copied in a variable of the type indicated in
- *                  the BAM file. Then it is cast into the type of <tt>dest</tt>.
- *
- * @param[in] tags The BamTagsDict object to query.
- * @param[in] idx  The integer index in the dict to use.
- *
- * @return bool true if the value could be extracted.
- *
- * @section Remarks
- *
- * The function only works for atomic types such as <tt>int</tt>, not for <tt>char*</tt> or arrays.
- *
- * See @link BamTagsDict @endlink for an example.
- */
+    TIter it = begin(inf, Standard()) + 2;
+    char typeC = getValue(it++);
+    ExtractTagValueHelper_<TResultValue, TIter> func(val, typeC, it);
 
-/**
-.Function.BamTagsDict#extractTagValue
-..class:Class.BamTagsDict
-..cat:BAM I/O
-..signature:extractTagValue(dest, tags, idx)
-..summary:Extract and cast "atomic" value from tags string with index $idx$.
-..param.dest:The variable to write the value to.
-...remarks:The value is first copied in a variable of the type indicated in the BAM file. Then it is cast into the type of $dest$.
-..param.tags:@Class.BamTagsDict@ object.
-...type:Class.BamTagsDict
-..params.idx:Index of the tag in the tag list.
-..returns:$bool$, indicating the success.
-..remarks:The function only works for atomic types such as $int$, not for $char*$ or arrays.
-..remarks:See @Class.BamTagsDict@ for an example.
-..see:Function.BamTagsDict#getTagValue
-..include:seqan/bam_io.h
-*/
-
-template <typename TDest, typename TIdx>
-inline bool
-extractTagValue(TDest & dest, BamTagsDict & tags, TIdx idx)
+    return tagApply(func, BamTagTypes());
+}
+
+template <typename TResultValue, typename TId>
+SEQAN_FUNC_ENABLE_IF(IsSequence<TResultValue>, bool)
+extractTagValue(TResultValue & val, BamTagsDict const & tags, TId id)
 {
-    if (!hasIndex(tags))
-        buildIndex(tags);
+    typedef Infix<Host<BamTagsDict const>::Type>::Type TInfix;
 
-    char typeC = host(tags)[tags._positions[idx] + 2];
-    if (typeC == 'A')
-    {
-        char x = 0;
-        char * ptr = reinterpret_cast<char *>(&x);
-        memcpy(ptr, &host(tags)[tags._positions[idx] + 3], 1);
-        dest = static_cast<TDest>(x);
-    }
-    else if (typeC == 'c')
-    {
-        __int8 x = 0;
-        char * ptr = reinterpret_cast<char *>(&x);
-        memcpy(ptr, &host(tags)[tags._positions[idx] + 3], 1);
-        dest = static_cast<TDest>(x);
-    }
-    else if (typeC == 'C')
-    {
-        __uint8 x = 0;
-        char * ptr = reinterpret_cast<char *>(&x);
-        memcpy(ptr, &host(tags)[tags._positions[idx] + 3], 1);
-        dest = static_cast<TDest>(x);
-    }
-    else if (typeC == 's')
-    {
-        __int16 x = 0;
-        char * ptr = reinterpret_cast<char *>(&x);
-        memcpy(ptr, &host(tags)[tags._positions[idx] + 3], 2);
-        dest = static_cast<TDest>(x);
-    }
-    else if (typeC == 'S')
-    {
-        __uint16 x = 0;
-        char * ptr = reinterpret_cast<char *>(&x);
-        memcpy(ptr, &host(tags)[tags._positions[idx] + 3], 2);
-        dest = static_cast<TDest>(x);
-    }
-    else if (typeC == 'i')
-    {
-        __int32 x = 0;
-        char * ptr = reinterpret_cast<char *>(&x);
-        memcpy(ptr, &host(tags)[tags._positions[idx] + 3], 4);
-        dest = static_cast<TDest>(x);
-    }
-    else if (typeC == 'I')
-    {
-        __uint32 x = 0;
-        char * ptr = reinterpret_cast<char *>(&x);
-        memcpy(ptr, &host(tags)[tags._positions[idx] + 3], 4);
-        dest = static_cast<TDest>(x);
-    }
-    else if (typeC == 'f')
-    {
-        float x = 0;
-        char * ptr = reinterpret_cast<char *>(&x);
-        memcpy(ptr, &host(tags)[tags._positions[idx] + 3], 4);
-        dest = static_cast<TDest>(x);
-    }
-    else // variable sized type or invald
-    {
+    TInfix inf = tags[id];
+    if (length(inf) < 4 || inf[2] != 'Z')
         return false;
-    }
+
+    val = infix(inf, 3, length(inf) - 1);
     return true;
 }
 
-
 // ----------------------------------------------------------------------------
 // Function getBamTypeChar()
 // ----------------------------------------------------------------------------
 
 /*!
  * @fn getBamTypeChar
+ * @headerfile <seqan/bam_io.h>
  * @brief Return char identifying the type of the argument type.
  *
  * @signature char getBamTypeChar<T>();
+ * @signature BamTypeChar<T>::VALUE
  *
  * @tparam T The type to query for its type char.
  *
@@ -758,43 +568,14 @@ extractTagValue(TDest & dest, BamTagsDict & tags, TIdx idx)
  * @see getBamTypeSize
  */
 
-/**
-.Function.getBamTypeChar
-..class:Class.BamTagsDict
-..cat:BAM I/O
-..summary:Return char identifying the type of the atomic argument.
-..signature:getBamTypeChar<T>()
-..param.T:The type to get the BAM char for.
-..returns:$char$ describing the BAM type. One of $ACcSsIifZ$.
-..remarks:Note that this function is defined for the $__int16$, $__uint16$ etc. but not for the types $short$, $int$ etc. An exception are 8-bit characters/char, where it is defined for $__int8$, $__uint8$, and $char$ unless $char$ is equal to one of the other two types. This is important when used in @Function.BamTagsDict#setTagValue@ etc. since BAM gives type chars for printable characters, signed 8-bit numbers and unsigned 8-bit numbers.
-..remarks:If $__int8$ and $__uint8$ are not identical to $char$, we can make this decision from the type, otherwise we cannot and we will give the integer types a higher precedence.
-..remarks:In your programs, this should not make any difference, only the written SAM/BAM will differ.
-..include:seqan/bam_io.h
-*/
+template <typename TValue>
+struct BamTypeChar<TValue const> :
+    BamTypeChar<TValue> {};
 
 template <typename T>
-inline char getBamTypeChar()
+inline char getBamTypeChar(T const &)
 {
-	if (IsSameType<T, __int8>::Type::VALUE)
-		return 'C';
-	if (IsSameType<T, __uint8>::Type::VALUE)
-		return 'c';
-	if (IsSameType<T, char>::Type::VALUE)
-		return 'A';
-	if (IsSameType<T, __int16>::Type::VALUE)
-		return 's';
-	if (IsSameType<T, __uint16>::Type::VALUE)
-		return 'S';
-	if (IsSameType<T, __int32>::Type::VALUE)
-		return 'i';
-	if (IsSameType<T, __int32>::Type::VALUE)
-		return 'I';
-	if (IsSameType<T, float>::Type::VALUE)
-		return 'f';
-    if (IsSameType<T, char *>::Type::VALUE || IsSameType<T, char const *>::Type::VALUE)
-        return 'Z';
-	else
-		return '\0';
+    return BamTypeChar<T>::VALUE;
 }
 
 // ----------------------------------------------------------------------------
@@ -806,22 +587,20 @@ inline char getBamTypeChar()
 /*!
  * @fn BamTagsDict#setTagValue
  *
- * @headerfile seqan/bam_io.h
+ * @headerfile <seqan/bam_io.h>
  *
  * @brief Set the value of a tag through a @link BamTagsDict @endlink.
  *
  * @signature bool setTagValue(tags, key, val[, typeC]);
  *
  * @param[in,out] tags  The BamTagsDict to modify.
- * @param[in]     key   The key of the tag.Must be a string of length 2. Types: CharString
- * @param[in]     val   The value to set the the tag to.
-
- * @param[in]     typeC BAM type char to use.For portability (so the generated files are the same on all platforms), use
+ * @param[in]     key   The key of the tag. Must be a sequence of length 2.
+ * @param[in]     val   The value to set the tag to.
+ * @param[in]     typeC BAM type char to use. For portability (so the generated files are the same on all platforms), use
  *                      a signed/unsigned qualified type for <tt>val</tt> or give <tt>typeC</tt>. Also see the remarks
  *                      for @link getBamTypeChar @endlink. Types: getBamTypeChar@.
-
  *
- * @return bool true on success, false on failure.  This function can fail if the key is not a valid tag id (e.g. does
+ * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.  This function can fail if the key is not a valid tag id (e.g. does
  *              not have length 2) or if the type of <tt>val</tt> is not an atomic value or a string (anything but
  *              <tt>char *</tt>, <tt>char const *</tt>, a character, integer or float type is invalid).
  *
@@ -870,100 +649,73 @@ inline char getBamTypeChar()
  * @see getBamTypeChar
  */
 
-/**
-.Function.BamTagsDict#setTagValue
-..class:Class.BamTagsDict
-..cat:BAM I/O
-..summary:Set the value of a tag through a @Class.BamTagsDict@.
-..signature:setTagValue(tags, key, val[, typeC])
-..param.tags:The dict to modify.
-...type:Class.BamTagsDict
-..param.key:The key of the tag.
-...type:Shortcut.CharString
-...remarks:Must be a string of length 2.
-..param.val:The value to set the the tag to.
-..param.typeC:BAM type char to use.
-...type:nolink:By default, the type is inflected using @Function.getBamTypeChar@.
-...remarks:For portability (so the generated files are the same on all platforms), use a signed/unsigned qualified type for $val$ or give $typeC$. Also see the remarks for @Function.getBamTypeChar@.
-..returns:$bool$ indicating the success. This function can fail if the key is not a valid tag id (e.g. does not have length 2) or if the type of $val$ is not an atomic value or a string (anything but $char *$, $char const *$, a character, integer or float type is invalid).
-..see:Function.getBamTypeChar
-..remarks:Note that $setTagValue$ does not cast the type, so $typeC$ only influences the type character written out but $val$ is written out in binary without modification.
-..include:seqan/bam_io.h
-..example.text:An example setting some atomic tag values.
-..example.code:
-CharString rawTagsText;
-BamTagsDict tags(rawTagsText);
-setTagValue(tags, "XA", 9);    // int
-setTagValue(tags, "XB", 9u);   // unsigned int
-setTagValue(tags, "XC", 'X');  // char
-..example.text:If $char$ is equal to $__int8$ or $__uint8$ then the last line produces an entry with type 'c' or 'C'. To make sure that the type char 'A' (for "printable character") is written to the file, give it explicitely:
-..example.code:
-setTagValue(tags, "XC", 'X', 'A');  // Overrwrite XC, enforce type 'printable character'.
-..example.text:Note that on most systems $int$s have a width of 32 bytes, but the C++ standard leaves this open. For all types but characters, you should not give an explicit type char but use one of the types with explicit width and signed/unsigned qualifier such as $__int32$, $__uint32$ etc.
-..example.code:
-// The following is not recommended since the type of $x$ is not "unsigned 32 bit int."
-__int32 x = -1;
-setTagValue(tags, "XB", x, 'I');
-// Instead, explicitely use an unsigned type if you need one.  Note that your compiler
-// might warn you about assigning -1 to an unsigned variable so you know that you are
-// probably doing something unintended.
-__uint32 y = -1;
-setTagValue(tags, "XB", y);
-
-// Do not do this!
-setTagValue(tags, "XA", 9, 'f');    // BOGUS since 9 is not a floating point number.
-*/
+template <typename TBamValueSequence, typename TValue>
+struct ToBamTagValueHelper_
+{
+    TBamValueSequence &result;
+    TValue val;
+    char typeC;
+
+    ToBamTagValueHelper_(TBamValueSequence &result, char typeC, TValue val) :
+        result(result),
+        val(val),
+        typeC(typeC)
+    {}
+
+    template <typename Type>
+    bool operator() (Type) const
+    {
+        if (BamTypeChar<Type>::VALUE != typeC)
+            return false;
+
+        union {
+            char raw[sizeof(Type)];
+            Type i;
+        } tmp;
+
+        tmp.i = static_cast<Type>(val);
+        append(result, toRange(&tmp.raw[0], &tmp.raw[sizeof(Type)]));
+        return true;
+    }
+};
 
 // Convert "atomic" value to BAM tag.  Return whether val was atomic.
-template <typename T>
-bool _toBamTagValue(CharString & result, T const & val, char const typeC)
+template <typename TBamValueSequence, typename TValue>
+SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TValue> >, bool)
+_toBamTagValue(TBamValueSequence & result, TValue const & val, char typeC)
 {
+    if (typeC == 'Z')
+        return false;
+
     appendValue(result, typeC);
+    ToBamTagValueHelper_<TBamValueSequence, TValue> func(result, typeC, val);
+    if (tagApply(func, BamTagTypes()))
+        return true;
 
-    if (typeC == 'A' || typeC == 'c' || typeC == 'C')
-    {
-        resize(result, length(result) + 1);
-        char * dst = reinterpret_cast<char *>(&result[0]) + length(result) - 1;
-        char const * src = reinterpret_cast<char const *>(&val);
-        memcpy(dst, src, 1);
-    }
-    else if (typeC == 's' || typeC == 'S')
-    {
-        resize(result, length(result) + 2);
-        char * dst = reinterpret_cast<char *>(&result[0]) + length(result) - 2;
-        char const * src = reinterpret_cast<char const *>(&val);
-        memcpy(dst, src, 2);
-    }
-    else if (typeC == 'i' || typeC == 'I' || typeC == 'f')
-    {
-        resize(result, length(result) + 4);
-        char * dst = reinterpret_cast<char *>(&result[0]) + length(result) - 4;
-        char const * src = reinterpret_cast<char const *>(&val);
-        memcpy(dst, src, 4);
-    }
-    else if (typeC == 'Z')
-    {
-        unsigned oldSize = length(result);
-        unsigned valLen = length(val) + 1;
-        resize(result, length(result) + valLen);
-        char * dst = reinterpret_cast<char *>(&result[0] + oldSize);
-        char const * src = reinterpret_cast<char const *>(val);
-        memcpy(dst, src, valLen);
-        *(dst + valLen - 1) = '\0';
-    }
-    else // non-string and variable sized type or invald
-    {
+    resize(result, length(result) - 1);
+    return false;
+}
+
+template <typename TBamValueSequence, typename TValue>
+SEQAN_FUNC_ENABLE_IF(IsSequence<TValue>, bool)
+_toBamTagValue(TBamValueSequence & result, TValue const & val, char typeC)
+{
+    if (typeC != 'Z')
         return false;
-    }
+
+    appendValue(result, typeC);
+    append(result, val);
+    appendValue(result, '\0');
     return true;
 }
 
+
 // Sets an atomic value in a BamTagsDict.
-// Returns true successful, can fail if val not atomic or key is not a valid tag id (2 chars).
+// Returns <tt>true</tt> successful, can fail if val not atomic or key is not a valid tag id (2 chars).
 
-template <typename T>
+template <typename TKey, typename TValue>
 inline bool
-setTagValue(BamTagsDict & tags, CharString const & key, T const & val, char const typeC)
+setTagValue(BamTagsDict & tags, TKey const & key, TValue const & val, char typeC)
 {
     if (!hasIndex(tags))
         buildIndex(tags);
@@ -971,37 +723,97 @@ setTagValue(BamTagsDict & tags, CharString const & key, T const & val, char cons
     // Build value to insert/append.
     if (length(key) != 2u)
         return false;
-    CharString bamTagVal;
-    // append(bamTagVal, key);
-    if (!_toBamTagValue(bamTagVal, val, typeC))
-        return false;
 
-    unsigned idx = 0;
-    if (findTagKey(idx, tags, key))
+    Position<BamTagsDict>::Type id = 0;
+    if (findTagKey(id, tags, key))
     {
-        // TODO(holtgrew): Speed this up with positions?
-        CharString tmp;
-        tmp = getTagValue(tags, idx);
-        replace(host(tags), tags._positions[idx] + 2, tags._positions[idx] + 2 + length(tmp), bamTagVal);
+        CharString bamTagVal;
+        if (!_toBamTagValue(bamTagVal, val, typeC))
+            return false;
+
+        replace(host(tags), tags._positions[id] + 2, tags._positions[id + 1], bamTagVal);
+        clear(tags._positions);
     }
     else
     {
         append(host(tags), key);
-        append(host(tags), bamTagVal);
+        if (!_toBamTagValue(host(tags), val, typeC))
+        {
+            resize(host(tags), length(host(tags)) - length(key));
+            return false;
+        }
+        appendValue(tags._positions, length(host(tags)));
     }
 
-    // Remove index and return success.
-    clear(tags._positions);  // Also necessary when appending?
     return true;
 }
 
-template <typename T>
+template <typename TKey, typename TValue>
 inline bool
-setTagValue(BamTagsDict & tags, CharString const & key, T const & val)
+setTagValue(BamTagsDict & tags, TKey const & key, TValue const & val)
 {
-    return setTagValue(tags, key, val, getBamTypeChar<T>());
+    return setTagValue(tags, key, val, BamTypeChar<TValue>::VALUE);
 }
 
+/*!
+ * @fn BamTagsDict#appendTagValue
+ *
+ * @headerfile <seqan/bam_io.h>
+ *
+ * @brief Append a tag/value pair to a @link BamTagsDict @endlink.
+ *
+ * @signature bool appendTagValue(tags, key, val[, typeC]);
+ *
+ * @param[in,out] tags  The BamTagsDict to modify.
+ * @param[in]     key   The key of the tag. Must be a sequence of length 2.
+ * @param[in]     val   The value to set the tag to.
+ * @param[in]     typeC BAM type char to use. For portability (so the generated files are the same on all platforms), use
+ *                      a signed/unsigned qualified type for <tt>val</tt> or give <tt>typeC</tt>. Also see the remarks
+ *                      for @link getBamTypeChar @endlink. Types: getBamTypeChar@.
+ *
+ * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.  This function can fail if the key is not a valid tag id (e.g. does
+ *              not have length 2) or if the type of <tt>val</tt> is not an atomic value or a string (anything but
+ *              <tt>char *</tt>, <tt>char const *</tt>, a character, integer or float type is invalid).
+ *
+ * @section Remarks
+ *
+ * @link BamTagsDict#setTagValue @endlink behaves like <tt>appendTagValue</tt> if <tt>key</tt> was not part of <tt>tags</tt>
+ * before. However, in this case <tt>appendTagValue</tt> is faster.
+ */
+
+template <typename TSequence, typename TKey, typename TValue>
+inline bool
+appendTagValue(TSequence & tags, TKey const & key, TValue const & val, char typeC)
+{
+    // Build value to insert/append.
+    if (length(key) != 2u)
+        return false;
+
+    append(tags, key);
+    return _toBamTagValue(tags, val, typeC);
+}
+
+template <typename TKey, typename TValue>
+inline bool
+appendTagValue(BamTagsDict & tags, TKey const & key, TValue const & val, char typeC)
+{
+    if (appendTagValue(host(tags), key, val, typeC))
+    {
+        appendValue(tags._positions, length(host(tags)));
+        return true;
+    }
+    return false;
+}
+
+
+template <typename TDictOrString, typename TKey, typename TValue>
+inline bool
+appendTagValue(TDictOrString & tags, TKey const & key, TValue const & val)
+{
+    return appendTagValue(tags, key, val, BamTypeChar<TValue>::VALUE);
+}
+
+
 // ----------------------------------------------------------------------------
 // Function eraseTag()
 // ----------------------------------------------------------------------------
@@ -1013,46 +825,45 @@ setTagValue(BamTagsDict & tags, CharString const & key, T const & val)
  * @signature bool eraseTag(tagsDict, key);
  *
  * @param[in,out] tagsDict The BamTagsDict to erase the tag from.
- * @param[in]     key      The key of the tag to ersae, of type @link CharString @endlink.
+ * @param[in]     key      The key of the tag to erase.
  *
- * @return bool true if the tag was present for erasing, false if not.
+ * @return bool <tt>true</tt> if the tag could be erased, <tt>false</tt> if the key wasn't present.
  */
 
-/**
-.Function.BamTagsDict#eraseTag
-..class:Class.BamTagsDict
-..summary:Erase tag from @Class.BamTagsDict@.
-..cat:BAM I/O
-..signature:eraseTag(tagsDict, key)
-..param.tags:The dict to erase from.
-...type:Class.BamTagsDict
-..param.key:The key of the entry to remove.
-...type:Shortcut.CharString
-..returns:$bool$, indicating whether the key was present.
-..include:seqan/bam_io.h
- */
-
-inline bool
-eraseTag(BamTagsDict & tags, CharString const & key)
+template <typename TKey>
+inline SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TKey> >, bool)
+eraseTag(BamTagsDict & tags, TKey const & key)
 {
     if (!hasIndex(tags))
         buildIndex(tags);
 
-    unsigned idx = 0;
-    if (!findTagKey(idx, tags, key))
+    Position<BamTagsDict>::Type id = 0;
+    if (!findTagKey(id, tags, key))
         return false;
 
-    // TODO(holtgrew): Speed this up with positions?
-    CharString tmp;
-    tmp = getTagValue(tags, idx);
-    erase(host(tags), tags._positions[idx], tags._positions[idx + 1]);
+    erase(host(tags), tags._positions[id], tags._positions[id + 1]);
+    clear(tags._positions);
+    return true;
+}
 
-    // TODO(weese): is this really working and tested? Should _positions be updated as well?
-    // Why is tmp not used?
+template <typename TId>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TId> >, bool)
+eraseTag(BamTagsDict & tags, TId const & id)
+{
+    typedef typename Iterator<String<typename BamTagsDict::TPos>, Standard>::Type TIter;
+    if (!hasIndex(tags))
+        buildIndex(tags);
 
+    typename BamTagsDict::TPos delta = tags._positions[id + 1] - tags._positions[id];
+    erase(host(tags), tags._positions[id], tags._positions[id + 1]);
+    erase(tags._positions, id);
+    TIter it = begin(tags._positions, Standard()) + id;
+    TIter itEnd = end(tags._positions, Standard());
+    for (; it != itEnd; ++it)
+        *it -= delta;
     return true;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_
diff --git a/seqan/bam_io/cigar.h b/seqan/bam_io/cigar.h
old mode 100755
new mode 100644
index d5b8c20..c5bb34a
--- a/seqan/bam_io/cigar.h
+++ b/seqan/bam_io/cigar.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_CIGAR_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_CIGAR_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_CIGAR_H_
+#define INCLUDE_SEQAN_BAM_IO_CIGAR_H_
 
 namespace seqan {
 
@@ -54,7 +54,7 @@ namespace seqan {
  * @headerfile <seqan/bam_io.h>
  * @brief One entry of a CIGAR string.
  *
- * @signature template <typename TOperation = char, typename TCount = unsigned>
+ * @signature template <[typename TOperation[, typename TCount]]>
  *            class CigarElement;
  *
  * @tparam TOperation Type to use for storing operations, defaults to <tt>char</tt>.
@@ -78,50 +78,17 @@ namespace seqan {
  */
 
 /*!
- * @var TCount CigarElement::count
+ * @var TCount CigarElement::count;
  *
  * @brief The number of operations.
  */
 
 /*!
- * @var TOperation CigarElement::operation
+ * @var TOperation CigarElement::operation;
  *
  * @brief The described operation.
  */
 
-/**
-.Class.CigarElement
-..cat:Fragment Store
-..summary:One entry of a CIGAR string.
-..signature:CigarElement<TOperation, TCount>
-..param.TOperation:Type to use for storing operations.
-...default:nolink:$char$
-..param.TCount:Type to use for storing counts.
-...default:nolink:$unsigned$
-..include:seqan/store.h
-
-.Memfunc.CigarElement#CigarElement
-..class:Class.CigarElement
-..summary:Constructor
-..signature:CigarElement()
-..signature:CigarElement(operation, count)
-..param.operation:The operation to use.
-...type:nolink:$TOperation$, typically $char$.
-..param.count:The operation count.
-...type:nolink:$Count$, typically $unsigned$.
-..remarks:The default constructor initialized both @Memvar.CigarElement#operation@ and @Memvar.CigarElement#count@ with $0$.
-
-.Memvar.CigarElement#operation
-..class:Class.CigarElement
-..summary:The described operation.
-..type:nolink:$TOperation$
-
-.Memvar.CigarElement#count
-..class:Class.CigarElement
-..summary:The number of operations.
-..type:nolink:$TCount$
-*/
-
 template <typename TOperation_ = char, typename TCount_ = unsigned>
 struct CigarElement
 {
@@ -142,6 +109,12 @@ struct CigarElement
 // Metafunctions
 // ============================================================================
 
+template <typename TOperation, typename TCount>
+struct Size<CigarElement<TOperation, TCount> >
+{
+    typedef TCount Type;
+};
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -150,21 +123,21 @@ template <typename TOperation, typename TCount>
 inline bool operator>(CigarElement<TOperation, TCount> const & lhs,
                       CigarElement<TOperation, TCount> const & rhs)
 {
-    return lhs.operation > rhs.operation || (lhs.operation == rhs.operation && lhs.count > rhs.count);
+    return lhs.operation > rhs.operation || (lhs.operation == rhs.operation && (lhs.count) > (rhs.count));
 }
 
 template <typename TOperation, typename TCount>
 inline bool operator<(CigarElement<TOperation, TCount> const & lhs,
                       CigarElement<TOperation, TCount> const & rhs)
 {
-    return lhs.operation < rhs.operation || (lhs.operation == rhs.operation && lhs.count < rhs.count);
+    return lhs.operation < rhs.operation || (lhs.operation == rhs.operation && (lhs.count) < (rhs.count));
 }
 
 template <typename TOperation, typename TCount>
 inline bool operator==(CigarElement<TOperation, TCount> const & lhs,
                        CigarElement<TOperation, TCount> const & rhs)
 {
-    return lhs.operation == rhs.operation && lhs.count == rhs.count;
+    return lhs.operation == rhs.operation && (lhs.count) == (rhs.count);
 }
 
 // ----------------------------------------------------------------------------
@@ -197,28 +170,51 @@ template <
     typename TMDString,
     typename TGaps1,
     typename TGaps2>
-inline void
+inline unsigned
 getMDString(
     TMDString &md,
-    TGaps1 &gaps1,
-    TGaps2 &gaps2)
+    TGaps1 &gaps1,  // typically reference
+    TGaps2 &gaps2)  // typically read
 {
     typedef typename Value<TMDString>::Type TMDChar;
-	typename Iterator<TGaps1>::Type it1 = begin(gaps1);
-	typename Iterator<TGaps2>::Type it2 = begin(gaps2);
-	char op, lastOp = ' ';
-	unsigned numOps = 0;
+    typedef typename Value<typename Host<TGaps1>::Type>::Type TVal1;
+    typedef typename Value<typename Host<TGaps2>::Type>::Type TVal2;
+
+    typename Iterator<TGaps1>::Type it1 = begin(gaps1);
+    typename Iterator<TGaps2>::Type it2 = begin(gaps2);
+    char op, lastOp = ' ';
+    unsigned numOps = 0;
+    unsigned errors = 0;
 
     clear(md);
     for (; !atEnd(it1) && !atEnd(it2); goNext(it1), goNext(it2))
     {
-        if (isGap(it1)) continue;
+        if (isGap(it1))
+        {
+            if (!isGap(it2))
+                ++errors;
+            continue;       // insertion to the reference (gaps1)
+//            op = 'I';     // ignore insertions completely
+        }
         if (isGap(it2))
         {
-            op = 'D';
+            ++errors;
+//            if (op == 'I')  // ignore paddings
+//                continue;
+            op = 'D';       // deletion from the reference (gaps1)
         }
         else
-            op = (*it1 == *it2)? 'M': 'R';
+        {
+            if ((TVal1)*it1 == (TVal2)*it2)
+            {
+                op = 'M';
+            }
+            else
+            {
+                op = 'R';
+                ++errors;
+            }
+        }
 
         // append match run
         if (lastOp != op)
@@ -230,21 +226,21 @@ getMDString(
                 append(md, num.str());
             }
             numOps = 0;
-            lastOp = op;
         }
 
         // append deleted/replaced reference character
         if (op != 'M')
         {
-            // add ^ from non-deletion to deletion
+            // add ^ for deleted reference bases (from non-deletion to deletion)
             if (op == 'D' && lastOp != 'D')
                 appendValue(md, '^');
-            // add 0 from deletion to replacement
-            if (op == 'R' && lastOp == 'D')
+            // add 0 for each replaced base that doesn't follow a match (for samtools/BWA compatibility)
+            else if (op == 'R' && lastOp != 'M')
                 appendValue(md, '0');
             appendValue(md, convert<TMDChar>(*it1));
         }
 
+        lastOp = op;
         ++numOps;
     }
     SEQAN_ASSERT_EQ(atEnd(it1), atEnd(it2));
@@ -254,6 +250,7 @@ getMDString(
         num << numOps;
         append(md, num.str());
     }
+    return errors;
 }
 
 // ----------------------------------------------------------------------------
@@ -268,42 +265,46 @@ template <
 inline void
 getCigarString(
     TCigar &cigar,
-    TGaps1 &gaps1,
-    TGaps2 &gaps2,
+    TGaps1 &gaps1,  // typically reference
+    TGaps2 &gaps2,  // typically read
     TThresh splicedGapThresh)
 {
-	typename Iterator<TGaps1>::Type it1 = begin(gaps1);
-	typename Iterator<TGaps2>::Type it2 = begin(gaps2);
-	clear(cigar);
-	char op, lastOp = ' ';
-	unsigned numOps = 0;
-
-	// std::cout << "gaps1\t" << gaps1 << std::endl;
-	// std::cout << "gaps2\t" << gaps2 << "\t" << clippedBeginPosition(gaps2) << std::endl;
-	for (; !atEnd(it1) && !atEnd(it2); goNext(it1), goNext(it2))
-	{
-		if (isGap(it1))
-		{
-			if (isGap(it2))
-				op = 'P';
-			else if (isClipped(it2))
-				op = '?';
-			else
-				op = 'I';
-		}
-		else if (isClipped(it1))
-		{
-			op = '?';
-		}
-		else
-		{
-			if (isGap(it2))
-				op = 'D';
-			else if (isClipped(it2))
-				op = 'S';
-			else
-				op = 'M';
-		}
+    typename Iterator<TGaps1>::Type it1 = begin(gaps1);
+    typename Iterator<TGaps2>::Type it2 = begin(gaps2);
+//    typedef typename Value<typename Host<TGaps1>::Type>::Type TVal1;
+//    typedef typename Value<typename Host<TGaps2>::Type>::Type TVal2;
+
+    clear(cigar);
+    char op, lastOp = ' ';
+    unsigned numOps = 0;
+
+    // std::cout << "gaps1\t" << gaps1 << std::endl;
+    // std::cout << "gaps2\t" << gaps2 << "\t" << clippedBeginPosition(gaps2) << std::endl;
+    for (; !atEnd(it1) && !atEnd(it2); goNext(it1), goNext(it2))
+    {
+        if (isGap(it1))
+        {
+            if (isGap(it2))
+                op = 'P';
+            else if (isClipped(it2))
+                op = '?';
+            else
+                op = 'I';
+        }
+        else if (isClipped(it1))
+        {
+            op = '?';
+        }
+        else
+        {
+            if (isGap(it2))
+                op = 'D';
+            else if (isClipped(it2))
+                op = 'S';
+            else
+                op = 'M';
+//                op = ((TVal1)*it1 == (TVal2)*it2)? '=': 'X';
+        }
 
         // append CIGAR operation
         if (lastOp != op)
@@ -324,16 +325,16 @@ getCigarString(
     }
 //  if (atEnd(it1) != atEnd(it2))
 //        std::cerr << "Invalid pairwise alignment:" << std::endl << gaps1 << std::endl << gaps2 << std::endl;
-	SEQAN_CHECK(atEnd(it1) == atEnd(it2), "Cannot get CIGAR from invalid pairwise alignment!");
-	if (lastOp == 'D' && numOps >= (unsigned)splicedGapThresh)
-		lastOp = 'N';
-	if (numOps > 0)
-	{
-		std::stringstream num;
-		num << numOps;
-		append(cigar, num.str());
-		appendValue(cigar, lastOp);
-	}
+    SEQAN_CHECK(atEnd(it1) == atEnd(it2), "Cannot get CIGAR from invalid pairwise alignment!");
+    if (lastOp == 'D' && numOps >= (unsigned)splicedGapThresh)
+        lastOp = 'N';
+    if (numOps > 0)
+    {
+        std::stringstream num;
+        num << numOps;
+        append(cigar, num.str());
+        appendValue(cigar, lastOp);
+    }
 }
 
 template <
@@ -343,8 +344,8 @@ template <
 inline void
 getCigarString(
     TCigar &cigar,
-    TGaps1 &gaps1,
-    TGaps2 &gaps2)
+    TGaps1 &gaps1,  // typically reference
+    TGaps2 &gaps2)  // typically read
 {
     return getCigarString(cigar, gaps1, gaps2, 20);
 }
@@ -363,11 +364,14 @@ getCigarString(
         TGaps2 &gaps2,
         TThresh splicedGapThresh)
 {
-	typename Iterator<TGaps1>::Type it1 = begin(gaps1);
-	typename Iterator<TGaps2>::Type it2 = begin(gaps2);
-	clear(cigar);
-	char op = '?', lastOp = ' ';
-	unsigned numOps = 0;
+    typename Iterator<TGaps1>::Type it1 = begin(gaps1);
+    typename Iterator<TGaps2>::Type it2 = begin(gaps2);
+//    typedef typename Value<typename Host<TGaps1>::Type>::Type TVal1;
+//    typedef typename Value<typename Host<TGaps2>::Type>::Type TVal2;
+
+    clear(cigar);
+    char op = '?', lastOp = ' ';
+    unsigned numOps = 0;
 
 //  std::cout << gaps1 << std::endl;
 //  std::cout << gaps2 << std::endl;
@@ -393,6 +397,7 @@ getCigarString(
             else if (isClipped(it2))
                 op = 'S';
             else
+//                op = ((TVal1)*it1 == (TVal2)*it2)? '=': 'X';
                 op = 'M';
         }
         if (lastOp != op)
@@ -419,38 +424,129 @@ getCigarString(
 
 template <
     typename TCigar, typename TMDString, typename TContig, typename TReadSeq,
-    typename TAlignedRead, typename TErrors, typename TAlignFunctor>
+    typename TAlignedRead, typename TErrors >
 inline void
 alignAndGetCigarString(
-    TCigar &cigar, TMDString &md, TContig &contig, TReadSeq &readSeq,
-    TAlignedRead &alignedRead, TErrors &errors, TAlignFunctor const & functor)
+    TCigar &cigar, TMDString &md, TContig &, TReadSeq &,
+    TAlignedRead &, TErrors &, Nothing const &)
 {
-    typedef Align<TReadSeq, ArrayGaps> TAlign;
+    cigar = "*";
+    clear(md);
+}
 
-    TAlign align;
-    resize(rows(align), 2);
+struct BamAlignFunctorEditDistance
+{
+    typedef String<GapAnchor<int> > TGapAnchors;
 
-    if (alignedRead.beginPos <= alignedRead.endPos)
-        assignSource(row(align, 0), infix(contig.seq, alignedRead.beginPos, alignedRead.endPos));
-    else
-        assignSource(row(align, 0), infix(contig.seq, alignedRead.endPos, alignedRead.beginPos));
+    TGapAnchors contigAnchors, readAnchors;
+
+    template <typename TGaps1, typename TGaps2, typename TErrors>
+    inline int
+    align(TGaps1 &gaps1, TGaps2 &gaps2, TErrors maxErrors)
+    {
+        return -globalAlignment(
+            gaps1, gaps2,
+            Score<short, EditDistance>(),
+            -(int)maxErrors, (int)maxErrors
+        );
+    }
+};
+
+struct BamAlignFunctorSemiGlobalGotoh
+{
+    typedef String<GapAnchor<int> > TGapAnchors;
+
+    Score<int> score;
+    TGapAnchors contigAnchors, readAnchors;
+
+    BamAlignFunctorSemiGlobalGotoh(Score<int> score_) :
+        score(score_)
+    {}
+
+    template <typename TGaps1, typename TGaps2, typename TErrors>
+    inline int
+    align(TGaps1 &gaps1, TGaps2 &gaps2, TErrors maxErrors)
+    {
+        return globalAlignment(
+            gaps1, gaps2, score,
+            AlignConfig<true, false, false, true>(),
+            -(int)maxErrors, (int)maxErrors,
+            Gotoh()
+        ) / scoreMismatch(score);
+    }
+};
+
+struct BamAlignFunctorDefault
+{
+};
 
-    assignSource(row(align, 1), readSeq);
+template <
+    typename TCigar, typename TMDString, typename TContigInfix, typename TReadSeq,
+    typename TAlignedRead, typename TErrors, typename TAlignFunctor>
+inline void
+_alignAndGetCigarString(
+    TCigar &cigar, TMDString &md, TContigInfix const &contigInfix, TReadSeq const &fwdReadSeq,
+    TAlignedRead &, TErrors &errors, TAlignFunctor &functor)
+{
+    typedef Gaps<TContigInfix, AnchorGaps<typename TAlignFunctor::TGapAnchors> >    TContigGaps;
+    typedef Gaps<TReadSeq, AnchorGaps<typename TAlignFunctor::TGapAnchors> >        TReadGaps;
+
+    clear(functor.contigAnchors);
+    clear(functor.readAnchors);
+
+    TContigGaps contigGaps(contigInfix, functor.contigAnchors);
+    TReadGaps readGaps(fwdReadSeq, functor.readAnchors);
+
+    // if there is already an alignment between contigInfix and fwdReadSeq with 0 or 1 error then
+    // we don't to realign as it contains no gaps
+    if (!(errors == 0 || (errors == 1 && length(contigInfix) == length(fwdReadSeq))))
+        errors = functor.align(contigGaps, readGaps, errors);
+
+    getCigarString(cigar, contigGaps, readGaps);
+    TErrors mdErrors = getMDString(md, contigGaps, readGaps);
+
+    ignoreUnusedVariableWarning(mdErrors);
+    SEQAN_ASSERT_EQ(errors, mdErrors);
+}
+
+template <
+    typename TCigar, typename TMDString, typename TContig, typename TReadSeq,
+    typename TAlignedRead, typename TErrors, typename TAlignFunctor>
+inline void
+alignAndGetCigarString(
+    TCigar &cigar, TMDString &md, TContig const &contig, TReadSeq const &readSeq,
+    TAlignedRead &alignedRead, TErrors &errors, TAlignFunctor &functor)
+{
+    typedef typename TContig::TContigSeq            TContigSeq;
+    typedef typename Infix<TContigSeq const>::Type  TContigInfix;
 
-    if (!(errors == 0 || (errors == 1 && length(readSeq) == length(source(row(align, 0))))))
-        errors = functor.align(align);
+    TContigInfix contigInfix;
 
-    getCigarString(cigar, row(align, 0), row(align, 1));
-    getMDString(md, row(align, 0), row(align, 1));
+    if (alignedRead.beginPos <= alignedRead.endPos)
+    {
+        contigInfix = infix(contig.seq, alignedRead.beginPos, alignedRead.endPos);
+        _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor);
+    }
+    else
+    {
+        contigInfix = infix(contig.seq, alignedRead.endPos, alignedRead.beginPos);
+        _alignAndGetCigarString(cigar, md, contigInfix, reverseComplementString(readSeq), alignedRead, errors, functor);
+    }
 }
 
-template <typename TCigar, typename TMDString, typename TContig, typename TReadSeq, typename TErrors, typename TAlignedRead>
+template <
+    typename TCigar, typename TMDString, typename TContig, typename TReadSeq,
+    typename TAlignedRead, typename TErrors>
 inline void
-alignAndGetCigarString(TCigar &cigar, TMDString &md, TContig &contig, TReadSeq &readSeq, TAlignedRead &alignedRead, TErrors &, Nothing const &)
+alignAndGetCigarString(
+    TCigar &cigar, TMDString &md, TContig const &contig, TReadSeq const &readSeq,
+    TAlignedRead &alignedRead, TErrors &errors, BamAlignFunctorDefault &)
 {
-    typedef typename TContig::TContigSeq                                    TContigSeq;
-    typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> >    TContigGaps;
-    typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> > TReadGaps;
+    typedef typename TContig::TContigSeq                                            TContigSeq;
+    typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> >            TContigGaps;
+    typedef typename ReverseComplementString<TReadSeq const>::Type                  TRefCompReadSeq;
+    typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> >   TReadGaps;
+    typedef Gaps<TRefCompReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> >  TRCReadGaps;
 
     TContigGaps contigGaps(contig.seq, contig.gaps);
 
@@ -458,21 +554,22 @@ alignAndGetCigarString(TCigar &cigar, TMDString &md, TContig &contig, TReadSeq &
     {
         setClippedBeginPosition(contigGaps, alignedRead.beginPos);
         setClippedEndPosition(contigGaps, alignedRead.endPos);
-    } else
+
+        TReadGaps readGaps(readSeq, alignedRead.gaps);
+
+        getCigarString(cigar, contigGaps, readGaps);
+        errors = getMDString(md, contigGaps, readGaps);
+    }
+    else
     {
         setClippedBeginPosition(contigGaps, alignedRead.endPos);
         setClippedEndPosition(contigGaps, alignedRead.beginPos);
-    }
 
-    TReadGaps readGaps(readSeq, alignedRead.gaps);
-    // TContigGaps  contigGaps2(contig.seq, contig.gaps);
-    // if (i == 4)
-    //     printf("It's it!\n");
-    // std::cerr << "read gaps:  " << readGaps << std::endl;
-    // std::cerr << "contig gaps:" << contigGaps << std::endl;
+        TRCReadGaps readGaps(reverseComplementString(readSeq), alignedRead.gaps);
 
-    getCigarString(cigar, contigGaps, readGaps);
-    getMDString(md, contigGaps, readGaps);
+        getCigarString(cigar, contigGaps, readGaps);
+        errors = getMDString(md, contigGaps, readGaps);
+    }
 }
 
 // ----------------------------------------------------------------------------
@@ -480,9 +577,9 @@ alignAndGetCigarString(TCigar &cigar, TMDString &md, TContig &contig, TReadSeq &
 // ----------------------------------------------------------------------------
 
 template <typename TCigarString, typename TNum>
-inline void _getClippedLength(TCigarString const & cigar, TNum & sum)
+inline void _getClippedLength(TNum & sum, TCigarString const & cigar)
 {
-    typedef typename Iterator<TCigarString, Standard>::Type TCigarIter;
+    typedef typename Iterator<TCigarString const, Standard>::Type TCigarIter;
 
     TCigarIter it = begin(cigar, Standard());
     TCigarIter itEnd = end(cigar, Standard());
@@ -498,7 +595,7 @@ inline void _getClippedLength(TCigarString const & cigar, TNum & sum)
 // ----------------------------------------------------------------------------
 
 template <typename TCigarString, typename TNum>
-inline void _getLengthInRef(TCigarString const & cigar, TNum & sum)
+inline void _getLengthInRef(TNum & sum, TCigarString const & cigar)
 {
     typedef typename Iterator<TCigarString const, Standard>::Type TCigarIter;
 
@@ -511,13 +608,32 @@ inline void _getLengthInRef(TCigarString const & cigar, TNum & sum)
             sum += getValue(it).count;
 }
 
+// ----------------------------------------------------------------------------
+// _getQueryLength()
+// ----------------------------------------------------------------------------
+
+template <typename TCigarString>
+inline typename Size<typename Value<TCigarString>::Type>::Type
+_getQueryLength(TCigarString const & cigar)
+{
+    typedef typename Iterator<TCigarString const, Standard>::Type TCigarIter;
+    typedef typename Size<typename Value<TCigarString>::Type>::Type TSize;
+    TCigarIter it = begin(cigar, Standard());
+    TCigarIter itEnd = end(cigar, Standard());
+
+    TSize len = 0;
+    for (; it != itEnd; ++it)
+        if (getValue(it).operation != 'D' && getValue(it).operation != 'H' && getValue(it).operation != 'N' && getValue(it).operation != 'P')
+            len += getValue(it).count;
+    return len;
+}
+
 // ----------------------------------------------------------------------------
 // cigarToGapAnchorRead()
 // ----------------------------------------------------------------------------
 
-template<typename TCigarString, typename TGaps>
-inline unsigned
-cigarToGapAnchorRead(TCigarString const & cigar, TGaps & gaps)
+template <typename TGaps, typename TCigarString>
+unsigned cigarToGapAnchorRead(TGaps & gaps, TCigarString const & cigar)
 {
     typename Iterator<TGaps>::Type it = begin(gaps);
     bool atBegin = true;
@@ -547,8 +663,7 @@ cigarToGapAnchorRead(TCigarString const & cigar, TGaps & gaps)
 // ----------------------------------------------------------------------------
 
 template<typename TCigarString, typename TGaps>
-inline unsigned
-cigarToGapAnchorContig(TCigarString const & cigar, TGaps & gaps)
+unsigned cigarToGapAnchorContig(TGaps & gaps, TCigarString const & cigar)
 {
     typename Iterator<TGaps>::Type it = begin(gaps);
     bool atBegin = true;
@@ -575,4 +690,4 @@ cigarToGapAnchorContig(TCigarString const & cigar, TGaps & gaps)
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_CIGAR_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_CIGAR_H_
diff --git a/seqan/bam_io/read_bam.h b/seqan/bam_io/read_bam.h
index ba55fd7..3377d6c 100644
--- a/seqan/bam_io/read_bam.h
+++ b/seqan/bam_io/read_bam.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,56 +34,48 @@
 // Code for reading Bam.
 // ==========================================================================
 
-// TODO(holtgrew): Indexing.
-
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_READ_BAM_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_READ_BAM_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_READ_BAM_H_
+#define INCLUDE_SEQAN_BAM_IO_READ_BAM_H_
 
 namespace seqan {
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
 
 /*!
- * @defgroup SamBamIO SAM/BAM I/O
- * @brief Tags for identifying SAM/BAM format.
- */
-
-/*!
- * @tag SamBamIO#Bam
+ * @tag FileFormats#Bam
  * @brief Identify the BAM format.
  *
- * @tag SamBamIO#Sam
+ * @tag FileFormats#Sam
  * @brief Identify the SAM format.
  */
 
-/**
-.Tag.Bam
-..cat:BAM I/O
-..signature:Bam
-..summary:Tag for identifying the BAM format.
-..include:seqan/bam_io.h
-..see:Tag.Sam
-*/
-
 struct Bam_;
 typedef Tag<Bam_> Bam;
 
+
+template <typename T>
+struct FileExtensions<Bam, T>
+{
+    static char const * VALUE[1];    // default is one extension
+};
+
 template <typename T>
-struct FileFormatExtensions<Bam, T>
+char const * FileExtensions<Bam, T>::VALUE[1] =
 {
-    static char const * VALUE[1];
+    ".bam"     // default output extension
 };
 
+
 template <typename T>
-char const * FileFormatExtensions<Bam, T>::VALUE[1] = {
-    ".bam" };
+struct MagicHeader<Bam, T>
+{
+    static unsigned char const VALUE[4];
+};
 
+template <typename T>
+unsigned char const MagicHeader<Bam, T>::VALUE[4] = { 'B', 'A', 'M', '\1' };  // BAM's magic header
 
 // ============================================================================
 // Metafunctions
@@ -94,92 +86,46 @@ char const * FileFormatExtensions<Bam, T>::VALUE[1] = {
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function readRecord()                                              BamHeader
+// Function readHeader()                                              BamHeader
 // ----------------------------------------------------------------------------
 
-/*!
- * @fn SamBamIO#readRecord
- * @brief Read a record from a SAM/BAM file.
- *
- * @signature int readRecord(record, context, stream, tag);
- * @signature int readRecord(header, context, stream, tag);
- *
- * @param[out]    record  The @link BamAlignmentRecord @endlink object to read the information into.
- * @param[out]    header  The @link BamHeader @endlink object to read the header information into.
- * @param[in,out] context The BamIOContext object to use.
- * @param[in,out] stream  The @link StreamConcept Stream @endlink to read from.
- * @param[in]     tag     The format tag, one of <tt>Sam</tt> and <tt>Bam</tt>.
- *
- * @return int A status code, 0 on success, != 0 on failure.
- */
-
-/**
-.Function.readRecord
-..signature:readRecord(headerRecord, context, stream, tag)
-..param.header:@Class.BamHeader@ to read information into.
-...type:Class.BamHeader
-..param.context:The context to use for reading.
-...type:Class.BamIOContext
-..param.stream:The stream to read from (for BAM).
-...remarks:BAM data can be read from any stream. For the proper decompression (from compressed BAM, the default) use @Spec.BGZF Stream@.
-...type:Concept.StreamConcept
-..param.tag:Format to read @Class.BamHeader@ from.
-...type:Tag.Sam
-...type:Tag.Bam
-..include:seqan/bam_io.h
-*/
-
-template <typename TStream, typename TNameStore, typename TNameStoreCache>
-int readRecord(BamHeader & header,
-               BamIOContext<TNameStore, TNameStoreCache> & context,
-               TStream & stream,
-               Bam const & /*tag*/)
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readHeader(BamHeader & header,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           Bam const & /*tag*/)
 {
-    int res = 0;
-
+    clear(header);
     // Read BAM magic string.
-    char magic[5] = "\0\0\0\0";
-    res = streamReadBlock(&magic[0], stream, 4);
-    if (res != 4)
-        return 1;  // EOF or error while reading.
-    if (strcmp(magic, "BAM\1") != 0)
-        return 1;  // Magic was wrong.
+    String<char, Array<4> > magic;
+    read(magic, iter, 4);
+    if (magic != "BAM\1")
+        SEQAN_THROW(ParseError("Not in BAM format."));
 
     // Read header text, including null padding.
     __int32 lText;
-    res = streamReadBlock(reinterpret_cast<char *>(&lText), stream, 4);
-    if (res != 4)
-        return 1;  // Error reading the length of the header text.
+    readRawPod(lText, iter);
+
     CharString samHeader;
-    resize(samHeader, lText);
-    res = streamReadBlock(&front(samHeader), stream, lText);
+    write(samHeader, iter, lText);
+
     // Truncate to first position of '\0'.
-    typedef Iterator<CharString, Standard>::Type TIter;
-    TIter it = begin(samHeader, Standard());
-    for (; it != end(samHeader); ++it)
-        if (*it == '\0')
-            break;
-    resize(samHeader, it - begin(samHeader, Standard()));
+    cropAfterFirst(samHeader, EqualsChar<'\0'>());
 
     // Parse out header records.
-    typedef Stream<CharArray<char *> > THeaderStream;
-    THeaderStream headerStream(&samHeader[0], &samHeader[0] + length(samHeader));
-    RecordReader<THeaderStream, SinglePass<> > headerReader(headerStream);
     BamHeaderRecord headerRecord;
-    while (!atEnd(headerReader))
+    Iterator<CharString, Rooted>::Type it = begin(samHeader);
+    while (!atEnd(it))
     {
         clear(headerRecord);
-        res = readRecord(headerRecord, context, headerReader, Sam());
-        if (res != 0)
-            return 1;  // Error reading embedded SAM header.
-        appendValue(header.records, headerRecord);
+        readRecord(headerRecord, context, it, Sam());
+        appendValue(header, headerRecord);
     }
 
     // Read # reference sequences.
     __int32 nRef;
-    res = streamReadBlock(reinterpret_cast<char *>(&nRef), stream, 4);
-    if (res != 4)
-        return 1;  // Error reading the number of sequences.
+    readRawPod(nRef, iter);
     CharString name;
 
     clear(context.translateFile2GlobalRefId);
@@ -189,219 +135,145 @@ int readRecord(BamHeader & header,
     {
         // Read length of the reference name.
         __int32 nName;
-        res = streamReadBlock(reinterpret_cast<char *>(&nName), stream, 4);
-        if (res != 4)
-            return 1;  // Error reading the number of sequences.
-        // Read name of the reference sequence;
-        resize(name, nName);
-        res = streamReadBlock(&front(name), stream, nName);
-        if (res != nName)
-            return 1;  // Error reading the number of sequences.
+        readRawPod(nName, iter);
+        clear(name);
+        write(name, iter, nName);
         resize(name, nName - 1);
         // Read length of the reference sequence.
         __int32 lRef;
-        res = streamReadBlock(reinterpret_cast<char *>(&lRef), stream, 4);
-        if (res != 4)
-            return 1;  // Error reading the number of sequences.
-
-        // Store sequence info.
-        typedef typename BamHeader::TSequenceInfo TSequenceInfo;
-        appendValue(header.sequenceInfos, TSequenceInfo(name, lRef));
-        // Append contig name to name store, if not known already.
-        typename Size<TNameStore>::Type globalRId = 0;
-        if (!getIdByName(nameStore(context), name, globalRId, nameStoreCache(context)))
-        {
-            globalRId = length(nameStore(context));
-            appendName(nameStore(context), name, nameStoreCache(context));
-        }
-        context.translateFile2GlobalRefId[i] = globalRId;
+        readRawPod(lRef, iter);
+
+        // Add entry to name store and sequenceInfos if necessary.
+        // Compute translation from local ids (used in the BAM file) to corresponding ids in the name store
+        size_t globalRefId = nameToId(contigNamesCache(context), name);
+        context.translateFile2GlobalRefId[i] = globalRefId;
+        if (length(contigLengths(context)) <= globalRefId)
+            resize(contigLengths(context), globalRefId + 1, 0);
+        contigLengths(context)[globalRefId] = lRef;
     }
-
-    return 0;
 }
 
 // ----------------------------------------------------------------------------
 // Function readRecord()                                     BamAlignmentRecord
 // ----------------------------------------------------------------------------
 
-/**
-.Function.readRecord
-..signature:readRecord(alignmentRecord, context, stream, tag)
-..param.alignmentRecord.type:Class.BamAlignmentRecord
-*/
-
-template <typename TStream, typename TNameStore, typename TNameStoreCache>
-int readRecord(BamAlignmentRecord & record,
-               BamIOContext<TNameStore, TNameStoreCache> & context,
-               TStream & stream,
-               Bam const & /*tag*/)
+template <typename TBuffer, typename TForwardIter>
+inline __int32
+_readBamRecordWithoutSize(TBuffer & rawRecord, TForwardIter & iter)
 {
-    int res = 0;
-    (void)context;  // Only used for assertions.
-
-    // Read size of the remaining block.
-    __int32 remainingBytes = 0;
-    res = streamReadBlock(reinterpret_cast<char *>(&remainingBytes), stream, 4);
-    if (res != 4)
-        return 1;  // Error reading the number of sequences.
-
-    // Reference sequence id.
-    SEQAN_ASSERT_GT(remainingBytes, 4);
-    record.rID = 0;
-    res = streamReadBlock(reinterpret_cast<char *>(&record.rID), stream, 4);
-    if (res != 4)
-        return res;
-    SEQAN_ASSERT_GEQ(record.rID, -1);
-
-    // Translate file local rID into a global rID that is compatible with the context nameStore.
+    __int32 recordLen = 0;
+    readRawPod(recordLen, iter);
+
+    // fail, if we read "BAM\1" (did you miss to call readRecord(header, bamFile) first?)
+    if (recordLen == 0x014D4142)
+        SEQAN_THROW(ParseError("Unexpected BAM header encountered."));
+
+    clear(rawRecord);
+    write(rawRecord, iter, (size_t)recordLen);
+    return recordLen;
+}
+
+template <typename TBuffer, typename TForwardIter>
+inline void
+_readBamRecord(TBuffer & rawRecord, TForwardIter & iter, Bam)
+{
+    __int32 recordLen = 0;
+    readRawPod(recordLen, iter);
+
+    // fail, if we read "BAM\1" (did you miss to call readRecord(header, bamFile) first?)
+    if (recordLen == 0x014D4142)
+        SEQAN_THROW(ParseError("Unexpected BAM header encountered."));
+
+    clear(rawRecord);
+    appendRawPod(rawRecord, recordLen);
+    write(rawRecord, iter, (size_t)recordLen);
+}
+
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readRecord(BamAlignmentRecord & record,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           Bam const & /* tag */)
+{
+    typedef typename Iterator<CharString, Standard>::Type                             TCharIter;
+    typedef typename Iterator<String<CigarElement<> >, Standard>::Type SEQAN_RESTRICT TCigarIter;
+    typedef typename Iterator<IupacString, Standard>::Type SEQAN_RESTRICT             TSeqIter;
+    typedef typename Iterator<CharString, Standard>::Type SEQAN_RESTRICT              TQualIter;
+
+    // Read size and data of the remaining block in one chunk (fastest).
+    __int32 remainingBytes = _readBamRecordWithoutSize(context.buffer, iter);
+    TCharIter it = begin(context.buffer, Standard());
+
+    // BamAlignmentRecordCore.
+    arrayCopyForward(it, it + sizeof(BamAlignmentRecordCore), reinterpret_cast<char*>(&record));
+    it += sizeof(BamAlignmentRecordCore);
+
+    remainingBytes -= sizeof(BamAlignmentRecordCore) + record._l_qname +
+                      record._n_cigar * 4 + (record._l_qseq + 1) / 2 + record._l_qseq;
+    SEQAN_ASSERT_GEQ(remainingBytes, 0);
+
+    // Translate file local rID into a global rID that is compatible with the context contigNames.
     if (record.rID >= 0 && !empty(context.translateFile2GlobalRefId))
         record.rID = context.translateFile2GlobalRefId[record.rID];
-
     if (record.rID >= 0)
-        SEQAN_ASSERT_LT(static_cast<__uint64>(record.rID), length(nameStore(context)));
-    remainingBytes -= 4;
-
-    // 0-based position.
-    SEQAN_ASSERT_GT(remainingBytes, 4);
-    record.beginPos = 0;
-    res = streamReadBlock(reinterpret_cast<char *>(&record.beginPos), stream, 4);
-    if (res != 4)
-        return res;
-    remainingBytes -= 4;
-
-    // Bin, mapping quality, read name length.
-    SEQAN_ASSERT_GT(remainingBytes, 4);
-    __uint32 binMqNl = 0;
-    res = streamReadBlock(reinterpret_cast<char *>(&binMqNl), stream, 4);
-    if (res != 4)
-        return res;
-    remainingBytes -= 4;
-    record.bin = binMqNl >> 16;
-    record.mapQ = (binMqNl >> 8) & 0x000000ff;
-    __uint16 lReadName = binMqNl & 0x000000ff;
-
-    // flag, cigar string length.
-    SEQAN_ASSERT_GT(remainingBytes, 4);
-    __uint32 flagNc = 0;
-    res = streamReadBlock(reinterpret_cast<char *>(&flagNc), stream, 4);
-    if (res != 4)
-        return res;
-    remainingBytes -= 4;
-    record.flag = flagNc >> 16;
-    __uint16 nCigarOp = flagNc & 0x0000FFFF;
-
-    // sequence length.
-    SEQAN_ASSERT_GT(remainingBytes, 4);
-    __int32 lSeq = 0;
-    res = streamReadBlock(reinterpret_cast<char *>(&lSeq), stream, 4);
-    if (res != 4)
-        return res;
-    remainingBytes -= 4;
-
-    // reference id of the next fragment.
-    SEQAN_ASSERT_GT(remainingBytes, 4);
-    record.rNextId = 0;
-    res = streamReadBlock(reinterpret_cast<char *>(&record.rNextId), stream, 4);
-    if (res != 4)
-        return res;
-    remainingBytes -= 4;
-
-    // 0-based position of the next fragment.
-    SEQAN_ASSERT_GT(remainingBytes, 4);
-    res = streamReadBlock(reinterpret_cast<char *>(&record.pNext), stream, 4);
-    if (res != 4)
-        return res;
-    remainingBytes -= 4;
-
-    // template length.
-    SEQAN_ASSERT_GT(remainingBytes, 4);
-    res = streamReadBlock(reinterpret_cast<char *>(&record.tLen), stream, 4);
-    if (res != 4)
-        return res;
-    remainingBytes -= 4;
-
-    // read name.
-    SEQAN_ASSERT_GT(remainingBytes, lReadName);
-    resize(record.qName, lReadName);
-    res = streamReadBlock(reinterpret_cast<char *>(&record.qName[0]), stream, lReadName);
-    if (res != lReadName)
-        return res;
-    resize(record.qName, lReadName - 1);
-    remainingBytes -= lReadName;
+        SEQAN_ASSERT_LT(static_cast<__uint64>(record.rID), length(contigNames(context)));
+
+    // ... the same for rNextId
+    if (record.rNextId >= 0 && !empty(context.translateFile2GlobalRefId))
+        record.rNextId = context.translateFile2GlobalRefId[record.rNextId];
+    if (record.rNextId >= 0)
+        SEQAN_ASSERT_LT(static_cast<__uint64>(record.rNextId), length(contigNames(context)));
+
+    // query name.
+    resize(record.qName, record._l_qname - 1, Exact());
+    arrayCopyForward(it, it + record._l_qname - 1, begin(record.qName, Standard()));
+    it += record._l_qname;
 
     // cigar string.
-    SEQAN_ASSERT_GT(remainingBytes, nCigarOp * 4);
-    resize(record.cigar, nCigarOp, Exact());
-    static char const * CIGAR_MAPPING = "MIDNSHP=";
-    typedef typename Iterator<String<CigarElement<> >, Rooted>::Type TCigarIter;
-    for (TCigarIter it = begin(record.cigar, Rooted()); !atEnd(it); goNext(it))
+    resize(record.cigar, record._n_cigar, Exact());
+    static char const * CIGAR_MAPPING = "MIDNSHP=X*******";
+    TCigarIter cigEnd = end(record.cigar, Standard());
+    for (TCigarIter cig = begin(record.cigar, Standard()); cig != cigEnd; ++cig)
     {
-        __uint32 ui = 0;
-        res = streamReadBlock(reinterpret_cast<char *>(&ui), stream, 4);
-        if (res != 4)
-            return res;
-        it->operation = CIGAR_MAPPING[ui & 0x0007];
-        it->count = ui >> 4;
+        unsigned opAndCnt;
+        readRawPod(opAndCnt, it);
+        SEQAN_ASSERT_LEQ(opAndCnt & 15, 8u);
+        cig->operation = CIGAR_MAPPING[opAndCnt & 15];
+        cig->count = opAndCnt >> 4;
     }
-    remainingBytes -= nCigarOp * 4;
-
-    // sequence, 4-bit encoded "=ACMGRSVTWYHKDBN".
-    SEQAN_ASSERT_GT(remainingBytes, (lSeq + 2) / 2);
-    resize(record.seq, lSeq + 1, Exact());
-    static char const * SEQ_MAPPING = "=ACMGRSVTWYHKDBN";
 
-    typedef typename Iterator<CharString, Rooted>::Type TSeqIter;
+    // query sequence.
+    resize(record.seq, record._l_qseq, Exact());
+    TSeqIter sit = begin(record.seq, Standard());
+    TSeqIter sitEnd = sit + (record._l_qseq & ~1);
+    while (sit != sitEnd)
     {
-        // Note: Yes, we need separate index i and iterator.  The iterator allows the fast iteration and i is for
-        // book-keeping since we potentially create too long seq records.
-        TSeqIter it = begin(record.seq, Rooted());
-        for (__int32 i = 0; i < lSeq; i += 2)
-        {
-            __uint8 ui;
-            res = streamReadChar(reinterpret_cast<char &>(ui), stream);
-            if (res != 0)
-                return res;
-            *it++ = SEQ_MAPPING[ui >> 4];
-            *it++ = SEQ_MAPPING[ui & 0x0f];
-        }
+        unsigned char ui = getValue(it);
+        ++it;
+        assignValue(sit, Iupac(ui >> 4));
+        ++sit;
+        assignValue(sit, Iupac(ui & 0x0f));
+        ++sit;
     }
-    resize(record.seq, lSeq);  // Possibly trim last, overlap base.
-    remainingBytes -= (lSeq + 1) / 2;
+    if (record._l_qseq & 1)
+        *sit++ = Iupac((__uint8)*it++ >> 4);
 
     // phred quality
-    SEQAN_ASSERT_GEQ(remainingBytes, lSeq);
-    resize(record.qual, lSeq, Exact());
-    if (lSeq > 0)
-    {
-        res = streamReadBlock(&(record.qual[0]), stream, lSeq);
-        if (res != lSeq)
-            return res;
-    }
+    resize(record.qual, record._l_qseq, Exact());
     // If qual is a sequence of 0xff (heuristic same as samtools: Only look at first byte) then we clear it, to get the
     // representation of '*';
-    if (!empty(record.qual) && record.qual[0] == '\xFF')
+    TQualIter qitEnd = end(record.qual, Standard());
+    for (TQualIter qit = begin(record.qual, Standard()); qit != qitEnd;)
+        *qit++ = '!' + *it++;
+    if (!empty(record.qual) && record.qual[0] == '\xff')
         clear(record.qual);
-    typedef typename Iterator<CharString, Rooted>::Type TQualIter;
-    for (TQualIter it = begin(record.qual, Rooted()); !atEnd(it); goNext(it))
-        *it += '!';
-    remainingBytes -= lSeq;
 
     // tags
-    if (remainingBytes > 0)
-    {
-        resize(record.tags, remainingBytes);
-        res = streamReadBlock(&record.tags[0], stream, remainingBytes);
-        if (res != remainingBytes)
-            return 1;
-    }
-    else
-    {
-        clear(record.tags);
-    }
-
-    return 0;
+    resize(record.tags, remainingBytes, Exact());
+    arrayCopyForward(it, it + remainingBytes, begin(record.tags, Standard()));
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_READ_BAM_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_READ_BAM_H_
diff --git a/seqan/bam_io/read_sam.h b/seqan/bam_io/read_sam.h
index c822a8e..acf91d1 100644
--- a/seqan/bam_io/read_sam.h
+++ b/seqan/bam_io/read_sam.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,30 +34,41 @@
 // Code for reading SAM.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_READ_SAM_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_READ_SAM_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_READ_SAM_H_
+#define INCLUDE_SEQAN_BAM_IO_READ_SAM_H_
 
 namespace seqan {
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
 
-/**
-.Tag.Sam
-..cat:BAM I/O
-..signature:Sam
-..summary:Tag for identifying the SAM format.
-..include:seqan/bam_io.h
-..see:Tag.Bam
-*/
-
 struct Sam_;
-typedef Tag<Sam_> const Sam;
+typedef Tag<Sam_> Sam;
+
+
+template <typename T>
+struct FileExtensions<Sam, T>
+{
+    static char const * VALUE[1];    // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<Sam, T>::VALUE[1] =
+{
+    ".sam"     // default output extension
+};
+
+
+template <typename T>
+struct MagicHeader<Sam, T>
+{
+    static unsigned char const * VALUE;
+};
+
+template <typename T>
+unsigned char const * MagicHeader<Sam, T>::VALUE = NULL;  // SAM has no magic header
+
 
 enum SamTokenizeErrors_
 {
@@ -70,10 +81,6 @@ typedef Tag<SamHeader_> SamHeader;
 struct SamAlignment_;
 typedef Tag<SamAlignment_> SamAlignment;
 
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
 // ============================================================================
 // Functions
 // ============================================================================
@@ -82,90 +89,61 @@ typedef Tag<SamAlignment_> SamAlignment;
 // Function nextIs()                                                  SamHeader
 // ----------------------------------------------------------------------------
 
-template <typename TStream, typename TPass>
-inline bool nextIs(RecordReader<TStream, TPass> & reader, SamHeader const & /*tag*/)
-{
-    if (atEnd(reader))
-        return false;
-    return value(reader) == '@';
-}
-
-// ----------------------------------------------------------------------------
-// Function nextIs()                                               SamAlignment
-// ----------------------------------------------------------------------------
-
-template <typename TStream, typename TPass>
-inline bool nextIs(RecordReader<TStream, TPass> & reader, SamAlignment const & /*tag*/)
+template <typename TForwardIter>
+inline bool nextIs(TForwardIter & iter, SamHeader const & /*tag*/)
 {
-    if (atEnd(reader))
+    if (atEnd(iter))
         return false;
-    return value(reader) != '@';
-}
-
-// ----------------------------------------------------------------------------
-// Function skipRecord()                                              SamHeader
-// ----------------------------------------------------------------------------
-
-template <typename TStream, typename TPass>
-inline int skipRecord(RecordReader<TStream, TPass> & reader,
-                      SamHeader const & tag)
-{
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (!nextIs(reader, tag))
-        return SAM_INVALID_RECORD;
-    int res = skipLine(reader);
-    if (res == 0 || res == EOF_BEFORE_SUCCESS)
-        return 0;
-    else
-        return res;
+    return value(iter) == '@';
 }
 
-// ----------------------------------------------------------------------------
-// Function skipRecord()                                           SamAlignment
-// ----------------------------------------------------------------------------
-
-template <typename TStream, typename TPass>
-inline int skipRecord(RecordReader<TStream, TPass> & reader,
-                      SamAlignment const & tag)
-{
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (!nextIs(reader, tag))
-        return SAM_INVALID_RECORD;
-    int res = skipLine(reader);
-    if (res == 0 || res == EOF_BEFORE_SUCCESS)
-        return 0;
-    else
-        return res;
-}
+//// ----------------------------------------------------------------------------
+//// Function skipRecord()                                              SamHeader
+//// ----------------------------------------------------------------------------
+//
+//template <typename TForwardIter, typename TPass>
+//inline void skipRecord(TForwardIter & iter,
+//                      SamHeader const & /*tag*/)
+//{
+//    skipOne(iter, EqualsChar<'@'>());
+//    skipLine(iter);
+//    return 0;
+//}
+//
+//// ----------------------------------------------------------------------------
+//// Function skipRecord()                                           SamAlignment
+//// ----------------------------------------------------------------------------
+//
+//template <typename TForwardIter, typename TPass>
+//inline void skipRecord(TForwardIter & iter,
+//                      SamAlignment const & /*tag*/)
+//{
+//    skipOne(iter, EqualsChar<'@'>());
+//    skipLine(iter);
+//    return 0;
+//}
 
 // ----------------------------------------------------------------------------
 // Function readRecord()                                        BamHeaderRecord
 // ----------------------------------------------------------------------------
 
-template <typename TStream, typename TSpec, typename TNameStore, typename TNameStoreCache>
-int readRecord(BamHeaderRecord & record,
-               BamIOContext<TNameStore, TNameStoreCache> & context,
-               RecordReader<TStream, SinglePass<TSpec> > & reader,
-               Sam const & /*tag*/)
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readRecord(BamHeaderRecord & record,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           Sam const & /*tag*/)
 {
     clear(record);
 
     // Make sure the first character is '@'.
-    char c = value(reader);
-    if (c != '@')
-        return SAM_INVALID_RECORD;
-    if (goNext(reader))
-        return SAM_INVALID_RECORD;
+    skipOne(iter, EqualsChar<'@'>());
 
     // Read the header tag.
-    char c1 = value(reader);
-    if (goNext(reader))
-        return SAM_INVALID_RECORD;
-    char c2 = value(reader);
-    if (goNext(reader))
-        return SAM_INVALID_RECORD;
+    char c1, c2;
+    readOne(c1, iter);
+    readOne(c2, iter);
+
     // Determine header type.
     if (c1 == 'H' && c2 == 'D')
         record.type = BAM_HEADER_FIRST;
@@ -178,333 +156,245 @@ int readRecord(BamHeaderRecord & record,
     else if (c1 == 'C' && c2 == 'O')
         record.type = BAM_HEADER_COMMENT;
     else
-        return SAM_INVALID_RECORD;
+        SEQAN_THROW(ParseError("Unknown SAM header type!"));
+
+    CharString &buffer = context.buffer;
 
     if (record.type == BAM_HEADER_COMMENT)
     {
-        int res = skipChar(reader, '\t');
-        if (res != 0)
-            return res;
-        CharString &buffer = context.buffer;
+        skipOne(iter, IsTab());
+
+        appendValue(record.tags, Pair<CharString>());
+
         clear(buffer);
-        res = readLine(buffer, reader);
-        if (res != 0)
-            return res;
-        appendValue(record.tags, Pair<CharString>(CharString(), buffer));
-        return 0;  // done, do not skip line a second time below
+        readLine(buffer, iter);
+        assign(back(record.tags).i2, buffer, Exact());
     }
     else
     {
         // Read the rest of the line into the tag field of record.
-        int res = 0;
-        CharString key, val;
-        while (!atEnd(reader) && value(reader) == '\t')
+        while (!atEnd(iter) && value(iter) == '\t')
         {
-            clear(key);
-            clear(val);
-
-            res = skipChar(reader, '\t');
-            if (res != 0)
-                return res;
-            res = readUntilChar(key, reader, ':');
-            if (res != 0)
-                return res;
-            if (goNext(reader))
-                return SAM_INVALID_RECORD;
-            res = readUntilOneOf(val, reader, '\t', '\r', '\n');
-            if (res != 0 && res != EOF_BEFORE_SUCCESS)
-                return res;
-
-            appendValue(record.tags, Pair<CharString>(key, val));
+            skipOne(iter, IsTab());
+
+            appendValue(record.tags, Pair<CharString>());
+
+            clear(buffer);
+            readUntil(buffer, iter, EqualsChar<':'>());
+            assign(back(record.tags).i1, buffer, Exact());
+
+            skipOne(iter, EqualsChar<':'>());
+
+            clear(buffer);
+            readUntil(buffer, iter, OrFunctor<IsTab, IsNewline>());
+            assign(back(record.tags).i2, buffer, Exact());
         }
+        // Skip remaining line break
+        skipLine(iter);
     }
-
-    // Skip remaining line break.
-    int res = skipLine(reader);
-    if (res != 0 && res != EOF_BEFORE_SUCCESS)
-        return res;
-    return 0;
 }
 
 // ----------------------------------------------------------------------------
 // Function readRecord()                                              BamHeader
 // ----------------------------------------------------------------------------
 
-/**
-.Function.readRecord
-..signature:readRecord(headerRecord, context, recordReader, tag)
-..param.recordReader:The RecordReader to read from.
-...type:Class.RecordReader
-...remarks:Use for SAM.
-*/
-
-template <typename TStream, typename TSpec, typename TNameStore, typename TNameStoreCache>
-int readRecord(BamHeader & header,
-               BamIOContext<TNameStore, TNameStoreCache> & context,
-               RecordReader<TStream, SinglePass<TSpec> > & reader,
-               Sam const & tag)
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readHeader(BamHeader & header,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           Sam const & tag)
 {
-    typedef typename BamHeader::TSequenceInfo TSequenceInfo;
-
     BamHeaderRecord record;
-    while (nextIs(reader, SamHeader()))
+    while (nextIs(iter, SamHeader()))
     {
         clear(record);
-        int res = readRecord(record, context, reader, tag);
-        if (res != 0)
-            return res;
-        appendValue(header.records, record);
+        readRecord(record, context, iter, tag);
+        appendValue(header, record);
 
         // Get sequence information from @SQ header.
         if (record.type == BAM_HEADER_REFERENCE)
         {
-            CharString sn = "unknown";
-            unsigned ln = 0;
+            CharString name;
+            unsigned lRef = 0;
             for (unsigned i = 0; i < length(record.tags); ++i)
             {
                 if (record.tags[i].i1 == "SN")
-                {
-                    sn = record.tags[i].i2;
-                }
+                    name = record.tags[i].i2;
                 else if (record.tags[i].i1 == "LN")
-                {
-                    if (!lexicalCast2<unsigned>(ln, record.tags[i].i2))
-                        ln = 0;
-                }
+                    lexicalCast(lRef, record.tags[i].i2);
             }
 
-            // Add name to name store cache if necessary.
-            unsigned contigId = 0;
-            if (!getIdByName(nameStore(context), sn, contigId, nameStoreCache(context)))
-            {
-                contigId = length(nameStore(context));
-                appendName(nameStore(context), sn, nameStoreCache(context));
-            }
-
-            if (length(header.sequenceInfos) <= contigId)
-                resize(header.sequenceInfos, contigId + 1);
-            header.sequenceInfos[contigId] = TSequenceInfo(sn, ln);
+            // Add entry to name store and sequenceInfos if necessary.
+            size_t globalRefId = nameToId(contigNamesCache(context), name);
+            if (length(contigLengths(context)) <= globalRefId)
+                resize(contigLengths(context), globalRefId + 1, 0);
+            contigLengths(context)[globalRefId] = lRef;
         }
     }
+}
+
+// ----------------------------------------------------------------------------
+// Function _readBamRecord()
+// ----------------------------------------------------------------------------
 
-    return 0;
+template <typename TBuffer, typename TForwardIter>
+inline void
+_readBamRecord(TBuffer & rawRecord, TForwardIter & iter, Sam)
+{
+    clear(rawRecord);
+    readLine(rawRecord, iter);
 }
 
 // ----------------------------------------------------------------------------
 // Function readRecord()                                     BamAlignmentRecord
 // ----------------------------------------------------------------------------
 
-/**
-.Function.readRecord
-..signature:readRecord(alignmentRecord, context, recordReader, tag)
-*/
-
-template <typename TStream, typename TSpec, typename TNameStore, typename TNameStoreCache>
-int readRecord(BamAlignmentRecord & record,
-               BamIOContext<TNameStore, TNameStoreCache> & context,
-               RecordReader<TStream, SinglePass<TSpec> > & reader,
-               Sam const & /*tag*/)
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readRecord(BamAlignmentRecord & record,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           Sam const & /*tag*/)
 {
-    clear(record);
-    CharString &buffer = context.buffer;
+    // fail, if we read "@" (did you miss to call readRecord(header, bamFile) first?)
+    if (nextIs(iter, SamHeader()))
+        SEQAN_THROW(ParseError("Unexpected SAM header encountered."));
 
-#define SEQAN_SKIP_TAB                              \
-    do                                              \
-    {                                               \
-        res = skipChar(reader, '\t');               \
-        if (res != 0)                               \
-            return res;                             \
-    }                                               \
-    while (false)
+    OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Sam> > nextEntry;
 
-    int res = 0;
+    clear(record);
+    CharString &buffer = context.buffer;
 
     // QNAME
-    res = readUntilTabOrLineBreak(record.qName, reader);
-    if (res != 0)
-        return res;
-    SEQAN_SKIP_TAB;
+    readUntil(record.qName, iter, nextEntry);
+    skipOne(iter, IsTab());
 
     // FLAG
     // TODO(holtgrew): Interpret hex and char as c-samtools -X does?
     clear(buffer);
-    res = readDigits(buffer, reader);
-    if (res != 0)
-        return res;
+    readUntil(buffer, iter, nextEntry);
     record.flag = lexicalCast<__uint16>(buffer);
-    SEQAN_SKIP_TAB;
+    skipOne(iter, IsTab());
 
     // RNAME
     clear(buffer);
-    res = readUntilTabOrLineBreak(buffer, reader);
-    if (res != 0)
-        return res;
+    readUntil(buffer, iter, nextEntry);
     if (buffer == "*")
-    {
         record.rID = BamAlignmentRecord::INVALID_REFID;
-    }
-    else if (!getIdByName(nameStore(context), buffer, record.rID, nameStoreCache(context)))
-    {
-        record.rID = length(nameStore(context));
-        appendName(nameStore(context), buffer, nameStoreCache(context));
-    }
-    SEQAN_SKIP_TAB;
+    else
+        record.rID = nameToId(contigNamesCache(context), buffer);
+    skipOne(iter, IsTab());
 
     // POS
     clear(buffer);
-    res = readUntilChar(buffer, reader, '\t');
-    if (res != 0)
-        return res;
-    if (buffer == "*")
-        record.beginPos = BamAlignmentRecord::INVALID_POS;
-    else
-        record.beginPos = lexicalCast<__uint32>(buffer) - 1;
-    SEQAN_SKIP_TAB;
+    SEQAN_ASSERT_EQ((__int32)0 - 1, (__int32)BamAlignmentRecord::INVALID_POS);
+    readUntil(buffer, iter, nextEntry);
+    record.beginPos = (__int32)lexicalCast<__uint32>(buffer) - 1;
+    skipOne(iter, IsTab());
 
     // MAPQ
     clear(buffer);
-    if (value(reader) == '*')
+    if (value(iter) == '*')
     {
         record.mapQ = 255;
-        goNext(reader);
+        skipOne(iter);
     }
     else
     {
-        res = readDigits(buffer, reader);
-        if (res != 0)
-            return res;
+        readUntil(buffer, iter, nextEntry);
         record.mapQ = lexicalCast<__uint16>(buffer);
     }
-    SEQAN_SKIP_TAB;
+    skipOne(iter, IsTab());
 
     // CIGAR
     CigarElement<> element;
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (value(reader) == '*')
-    {
-        goNext(reader);
-    }
+    if (value(iter) == '*')
+        skipOne(iter);
     else
     {
         do
         {
             clear(buffer);
-            res = readDigits(buffer, reader);
-            if (res != 0)
-                return res;
+            readUntil(buffer, iter, OrFunctor<IsAlpha, AssertFunctor<NotFunctor<IsNewline>, ParseError, Sam> >());
             element.count = lexicalCast<__uint32>(buffer);
-            element.operation = value(reader);
-            if (goNext(reader))
-                return EOF_BEFORE_SUCCESS;
+            element.operation = value(iter);
+            skipOne(iter);
             appendValue(record.cigar, element);
-        } while (value(reader) != '\t');
+        } while (value(iter) != '\t');
     }
-    SEQAN_SKIP_TAB;
+    skipOne(iter, IsTab());
 
     // RNEXT
     clear(buffer);
-    res = readUntilChar(buffer, reader, '\t');
-    if (res != 0)
-        return res;
+    readUntil(buffer, iter, nextEntry);
     if (buffer == "*")
-    {
         record.rNextId = BamAlignmentRecord::INVALID_REFID;
-    }
     else if (buffer == "=")
-    {
         record.rNextId = record.rID;
-    }
-    else if (!getIdByName(nameStore(context), buffer, record.rNextId, nameStoreCache(context)))
-    {
-        record.rNextId = length(nameStore(context));
-        appendName(nameStore(context), buffer, nameStoreCache(context));
-    }
-    SEQAN_SKIP_TAB;
+    else
+        record.rNextId = nameToId(contigNamesCache(context), buffer);
+    skipOne(iter, IsTab());
 
     // PNEXT
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (value(reader) == '*')
+    if (value(iter) == '*')
     {
         record.pNext = BamAlignmentRecord::INVALID_POS;
-        goNext(reader);
+        skipOne(iter);
     }
     else
     {
         clear(buffer);
-        res = readDigits(buffer, reader);
-        if (res != 0)
-            return res;
-        record.pNext = lexicalCast<__uint32>(buffer) - 1;
+        readUntil(buffer, iter, nextEntry);
+        record.pNext = (__int32)lexicalCast<__uint32>(buffer) - 1;
     }
-    SEQAN_SKIP_TAB;
+    skipOne(iter, IsTab());
 
     // TLEN
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (value(reader) == '*')
+    if (value(iter) == '*')
     {
         record.tLen = MaxValue<__int32>::VALUE;
-        goNext(reader);
+        skipOne(iter);
     }
     else
     {
         clear(buffer);
-        if (value(reader) == '-')
-        {
-            appendValue(buffer, value(reader));
-            if (goNext(reader))
-                return SAM_INVALID_RECORD;
-        }
-        res = readDigits(buffer, reader);
-        if (res != 0)
-            return res;
+        readUntil(buffer, iter, nextEntry);
         record.tLen = lexicalCast<__int32>(buffer);
     }
-    SEQAN_SKIP_TAB;
+    skipOne(iter, IsTab());
 
     // SEQ
-    res = readUntilTabOrLineBreak(record.seq, reader);
-    if (res != 0)
-        return res;
+    readUntil(record.seq, iter, nextEntry);
     // Handle case of missing sequence:  Clear seq string as documented.
     if (record.seq == "*")
         clear(record.seq);
-    SEQAN_SKIP_TAB;
+    skipOne(iter, IsTab());
 
     // QUAL
-    res = readUntilTabOrLineBreak(record.qual, reader);
-    if (res == EOF_BEFORE_SUCCESS)  // The record ends on EOF.
-        return 0;
-    if (res != 0)
-        return res;
+    readUntil(record.qual, iter, OrFunctor<IsTab, IsNewline>());
+
     // Handle case of missing quality:  Clear qual string as documented.
     if (record.qual == "*")
         clear(record.qual);
 
     // The following list of tags is optional.  A line break or EOF could also follow.
-    if (atEnd(reader))
-        return 0;
-    if (value(reader) != '\t')
+    if (atEnd(iter))
+        return;
+    if (value(iter) != '\t')
     {
-        res = skipLine(reader);
-        return res;
+        skipLine(iter);
+        return;
     }
-    SEQAN_SKIP_TAB;
+    skipOne(iter, IsTab());
 
     // TAGS
     clear(buffer);
-    res = readLine(buffer, reader);
-    if (res != 0 && res != EOF_BEFORE_SUCCESS)
-        return res;
-    assignTagsSamToBam(record.tags, buffer);
-
-    return 0;
-
-#undef SEQAN_SKIP_TAB
+    readLine(buffer, iter);
+    appendTagsSamToBam(record.tags, buffer);
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_READ_SAM_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_READ_SAM_H_
+
diff --git a/seqan/bam_io/write_bam.h b/seqan/bam_io/write_bam.h
index 4f6c5c7..3fd7ca1 100644
--- a/seqan/bam_io/write_bam.h
+++ b/seqan/bam_io/write_bam.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,30 +30,16 @@
 //
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 // Code for writing BAM.
 // ==========================================================================
 
-// TODO(holtgrew): Add buffer to context?
-// TODO(holtgrew): Rename to writeRecord from write2! Go over deprecated alias!
-
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
+#define INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
 
 namespace seqan {
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
 // ============================================================================
 // Functions
 // ============================================================================
@@ -62,82 +48,48 @@ namespace seqan {
 // Function writeRecord()                                             BamHeader
 // ----------------------------------------------------------------------------
 
-/*!
- * @fn SamBamIO#write2
- * @brief Write a record to a SAM/BAM file.
- *
- * @signature int writeRecord(stream, record, context, tag);
- * @signature int writeRecord(stream, header, context, tag);
- *
- * @param[in,out] stream  The @link StreamConcept Stream @endlink to write to.
- * @param[out]    record  The @link BamAlignmentRecord @endlink object to write out.
- * @param[out]    header  The @link BamHeader @endlink object to write out.
- * @param[in,out] context The BamIOContext object to use.
- * @param[in]     tag     The format tag, one of <tt>Sam</tt> and <tt>Bam</tt>.
- *
- * @return int A status code, 0 on success, != 0 on failure.
- */
-
-
-template <typename TStream, typename TNameStore, typename TNameStoreCache>
-int write2(TStream & stream,
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+void write(TTarget & target,
            BamHeader const & header,
-           BamIOContext<TNameStore, TNameStoreCache> const & context,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
            Bam const & /*tag*/)
 {
-    int res = streamWriteBlock(stream, "BAM\1", 4);
-    if (res != 4)
-        return 1;  // Could not write magic.
+    write(target, "BAM\1");
+    clear(context.buffer);
 
     // Create text of header.
-    CharString headerBuffer;
-    for (unsigned i = 0; i < length(header.records); ++i)
-    {
-        res = write2(headerBuffer, header.records[i], context, Sam());
-        if (res != 0)
-            return 1;  // Error writing header to buffer.
-    }
+    for (unsigned i = 0; i < length(header); ++i)
+        write(context.buffer, header[i], context, Sam());
+
     // Note that we do not write out a null-character to terminate the header.  This would be valid by the SAM standard
     // but the samtools do not expect this and write out the '\0' when converting from BAM to SAM.
-    // appendValue(headerBuffer, '\0');
+    // appendValue(context.buffer, '\0');
 
     // Write text header.
-    __int32 lText = length(headerBuffer);
-    res = streamWriteBlock(stream, reinterpret_cast<char const *>(&lText), 4);
-    if (res != 4)
-        return 1;  // Error writing l_text.
-
-    res = streamWriteBlock(stream, &headerBuffer[0], lText);
+    appendRawPod(target, (__int32)length(context.buffer));
+    write(target, context.buffer);
 
     // Write references.
-    __int32 nRef = _max(length(header.sequenceInfos), length(nameStore(context)));
-    res = streamWriteBlock(stream, reinterpret_cast<char const *>(&nRef), 4);
-    if (res != 4)
-        return 1;  // Error writing n_ref;
+    __int32 nRef = _max(length(contigNames(context)), length(contigLengths(context)));
+    appendRawPod(target, nRef);
 
-    for (unsigned i = 0; i < length(header.sequenceInfos); ++i)
+    for (__int32 i = 0; i < nRef; ++i)
     {
-        __int32 lName = length(header.sequenceInfos[i].i1) + 1;
-        res = streamWriteBlock(stream, reinterpret_cast<char const *>(&lName), 4);
-        if (res != 4)
-            return 1;  // Error writing l_name;
-
-        res = streamWriteBlock(stream, &header.sequenceInfos[i].i1[0], lName - 1);
-        if (res != lName - 1)
-            return 1;  // Error writing name;
-
-        char const n = '\0';
-        res = streamWriteBlock(stream, &n, 1);
-        if (res != 1)
-            return 1;  // Error writing trailing '\0'.
-
-        __int32 lRef = header.sequenceInfos[i].i2;
-        res = streamWriteBlock(stream, reinterpret_cast<char const *>(&lRef), 4);
-        if (res != 4)
-            return 1;  // Error writing l_ref;
+        if (i < (__int32)length(contigNames(context)))
+        {
+            appendRawPod(target, (__int32)(length(contigNames(context)[i]) + 1));
+            write(target, contigNames(context)[i]);
+        }
+        else
+        {
+            appendRawPod(target, (__int32)1);
+        }
+        writeValue(target, '\0');
+        __int32 lRef = 0;
+        if (i < (__int32)length(contigLengths(context)))
+            lRef = contigLengths(context)[i];
+        appendRawPod(target, lRef);
     }
-
-    return 0;
 }
 
 // ----------------------------------------------------------------------------
@@ -165,55 +117,44 @@ static inline int _reg2Bin(uint32_t beg, uint32_t end)
     return 0;
 }
 
-template <typename TStream, typename TNameStore, typename TNameStoreCache>
-int write2(TStream & stream,
-           BamAlignmentRecord const & record,
-           BamIOContext<TNameStore, TNameStoreCache> const & /*context*/,
-           Bam const & /*tag*/)
+inline __uint32
+updateLengths(BamAlignmentRecord const & record)
 {
-    CharString buffer;
-
-    // First, write record to buffer.
+    // update internal lengths.
+    record._l_qname = length(record.qName) + 1;
+    record._n_cigar = length(record.cigar);
+    record._l_qseq = length(record.seq);
+
+    return sizeof(BamAlignmentRecordCore) + record._l_qname +
+           record._n_cigar * 4 + (record._l_qseq + 1) / 2 + record._l_qseq +
+           length(record.tags);
+}
 
-    // refID
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&record.rID), 4);
 
-    // pos
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&record.beginPos), 4);
+template <typename TTarget>
+inline void
+_writeBamRecord(TTarget & target,
+                BamAlignmentRecord const & record,
+                Bam const & /*tag*/)
+{
+    typedef typename Iterator<String<CigarElement<> > const, Standard>::Type SEQAN_RESTRICT TCigarIter;
+    typedef typename Iterator<IupacString const, Standard>::Type SEQAN_RESTRICT             TSeqIter;
+    typedef typename Iterator<CharString const, Standard>::Type SEQAN_RESTRICT              TQualIter;
 
     // bin_mq_nl
-    SEQAN_ASSERT_LT(length(record.qName) + 1u, 255u);
-    __uint8 lReadName = length(record.qName) + 1;
     unsigned l = 0;
-    _getLengthInRef(record.cigar, l);
-    __uint32 bin = _reg2Bin(record.beginPos, record.beginPos + l);
-    __uint32 binMqNl = (bin << 16) | (record.mapQ << 8) | lReadName;
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&binMqNl), 4);
-
-    // flag_nc
-    __uint16 nCigarOp = length(record.cigar);
-    __uint32 flagNc = (record.flag << 16) | nCigarOp;
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&flagNc), 4);
-
-    // l_seq
-    __int32 lSeq = length(record.seq);
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&lSeq), 4);
+    _getLengthInRef(l, record.cigar);
+    record.bin =_reg2Bin(record.beginPos, record.beginPos + std::max(1u, l));
 
-    // next_refID
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&record.rNextId), 4);
-
-    // next_pos
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&record.pNext), 4);
-
-    // tlen
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&record.tLen), 4);
+    // Write fixed-size BamAlignmentRecordCore.
+    appendRawPod(target, (BamAlignmentRecordCore &)record);
 
     // read_name
-    streamWriteBlock(buffer, reinterpret_cast<char const *>(&record.qName[0]), lReadName - 1);
-    streamWriteChar(buffer, '\0');
+    write(target, record.qName);
+    writeValue(target, '\0');
 
     // cigar
-    static __uint8 const MAP[256] =
+    static unsigned char const MAP[256] =
     {
         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
@@ -232,72 +173,91 @@ int write2(TStream & stream,
         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
     };
-    for (unsigned i = 0; i < length(record.cigar); ++i)
-    {
-        __uint32 x = record.cigar[i].count;
-        x <<= 4;
-        x |= MAP[static_cast<int>(record.cigar[i].operation)];
-        streamWriteBlock(buffer, reinterpret_cast<char const *>(&x), 4);
-    }
+    TCigarIter citEnd = end(record.cigar, Standard());
+    for (TCigarIter cit = begin(record.cigar, Standard()); cit != citEnd; ++cit)
+        appendRawPod(target, ((__uint32)cit->count << 4) | MAP[(unsigned char)cit->operation]);
 
     // seq
-    static __uint8 const MAP2[256] =
-    {
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, 15, 15,
-        15, 1, 14, 2, 13, 15, 15, 4, 11, 15, 15, 12, 15, 3, 15, 15,
-        15, 15, 5, 6, 8, 15, 7, 9, 15, 10, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-        15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15
-    };
-    __uint8 c = 0;
-    for (int i = 0; i < lSeq; ++i)
+    TSeqIter sit = begin(record.seq, Standard());
+    TSeqIter sitEnd = sit + (record._l_qseq & ~1);
+    while (sit != sitEnd)
     {
-        c <<= 4;
-        c &= 0xf0;
-        c |= MAP2[static_cast<int>(record.seq[i])];
-        if (i % 2 == 1)
-            streamWriteChar(buffer, c);
-    }
-    if (lSeq % 2 == 1)
-    {
-        c <<= 4;
-        c &= 0xf0;
-        streamWriteChar(buffer, c);
+        unsigned char x = (ordValue(getValue(sit++)) << 4);
+        writeValue(target, x | ordValue(getValue(sit++)));
     }
+    if (record._l_qseq & 1)
+        writeValue(target, ordValue(getValue(sit++)) << 4);
 
     // qual
-    if (empty(record.qual))
+    SEQAN_ASSERT_LEQ(length(record.qual), length(record.seq));
+    TQualIter qit = begin(record.qual, Standard());
+    TQualIter qitEnd = end(record.qual, Standard());
+    TQualIter qitVirtEnd = qit + record._l_qseq;
+    while (qit != qitEnd)
+        writeValue(target, *qit++ - '!');
+    for (; qit != qitVirtEnd; ++qit)
+        writeValue(target, '\xff');     // fill with zero qualities
+
+    // tags
+    write(target, record.tags);
+}
+
+template <typename TTarget>
+inline void
+_writeBamRecordWrapper(TTarget & target,
+                       BamAlignmentRecord const & record,
+                       Nothing & /* range */,
+                       __uint32 size,
+                       Bam const & tag)
+{
+    appendRawPod(target, size);
+    _writeBamRecord(target, record, tag);
+}
+
+template <typename TTarget, typename TOValue>
+inline void
+_writeBamRecordWrapper(TTarget & target,
+                       BamAlignmentRecord const & record,
+                       Range<TOValue*> & range,
+                       __uint32 size,
+                       Bam const & tag)
+{
+    if (SEQAN_LIKELY(size + 4 <= length(range)))
     {
-        for (unsigned i = 0; i < length(record.qual); ++i)
-            streamWriteChar(buffer, static_cast<unsigned char>(0xff));
+        appendRawPod(range.begin, size);
+        _writeBamRecord(range.begin, record, tag);
+        advanceChunk(target, size + 4);
     }
     else
     {
-        for (unsigned i = 0; i < length(record.qual); ++i)
-            streamWriteChar(buffer, static_cast<char>(record.qual[i] - '!'));
+        appendRawPod(target, size);
+        _writeBamRecord(target, record, tag);
     }
+}
 
-    // tags
-    if (length(record.tags) > 0u)
-        streamWriteBlock(buffer, reinterpret_cast<char const *>(&record.tags[0]), length(record.tags));
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+void write(TTarget & target,
+           BamAlignmentRecord const & record,
+           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           Bam const & tag)
+{
+    // Check for valid IO Context.
+    SEQAN_ASSERT_LT_MSG(record.rID, static_cast<__int32>(length(contigNames(context))), "BAM IO Assertion: Unknown REF ID!");
+    SEQAN_ASSERT_LT_MSG(record.rNextId, static_cast<__int32>(length(contigNames(context))), "BAM IO Assertion: Unknown NEXT REF ID!");
+    ignoreUnusedVariableWarning(context);
+
+    // Update internal lengths
+    __uint32 size = updateLengths(record);
+
+    // Reserve chunk memory
+    reserveChunk(target, 4 + size, Output());
 
-    // buffer to stream
-    __uint32 blockSize = length(buffer);
-    streamWriteBlock(stream, reinterpret_cast<char const *>(&blockSize), 4);
-    return streamWriteBlock(stream, &buffer[0], blockSize) != blockSize;
+    // Write length and record
+    typename Chunk<TTarget>::Type ochunk;
+    getChunk(ochunk, target, Output());
+    _writeBamRecordWrapper(target, record, ochunk, size, tag);
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_
diff --git a/seqan/bam_io/write_sam.h b/seqan/bam_io/write_sam.h
index dfc2a74..bb101e1 100644
--- a/seqan/bam_io/write_sam.h
+++ b/seqan/bam_io/write_sam.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,254 +34,178 @@
 // Code for writing SAM.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_
+#ifndef INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_
+#define INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_
 
 namespace seqan {
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
 // ============================================================================
 // Functions
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function write2()                                            BamHeaderRecord
+// Function write()                                             BamHeaderRecord
 // ----------------------------------------------------------------------------
 
-template <typename TStream, typename TNameStore, typename TNameStoreCache>
-int write2(TStream & stream,
-           BamHeaderRecord const & header,
-           BamIOContext<TNameStore, TNameStoreCache> const & /*context*/,
-           Sam const & /*tag*/)
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void write(TTarget & target,
+                  BamHeaderRecord const & header,
+                  BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & /*context*/,
+                  Sam const & /*tag*/)
 {
     char const * headerTypes[] = {"@HD", "@SQ", "@RG", "@PG", "@CO"};
-    streamPut(stream, headerTypes[header.type]);
-    if (header.type == BAM_HEADER_COMMENT)
+    write(target, headerTypes[header.type]);
+
+    if (header.type == BAM_HEADER_COMMENT && !empty(header.tags))
     {
-        streamPut(stream, '\t');
-        streamPut(stream, header.tags[0].i2);
+        writeValue(target, '\t');
+        write(target, header.tags[0].i2);
     }
     else
     {
         for (unsigned i = 0; i < length(header.tags); ++i)
         {
-            streamPut(stream, '\t');
-            streamPut(stream, header.tags[i].i1);
-            streamPut(stream, ':');
-            streamPut(stream, header.tags[i].i2);
+            writeValue(target, '\t');
+            write(target, header.tags[i].i1);
+            writeValue(target, ':');
+            write(target, header.tags[i].i2);
         }
     }
 
-    int res = streamPut(stream, '\n');
-    if (res != 0)
-        return res;
-
-    return 0;
+    writeValue(target, '\n');
 }
 
 // ----------------------------------------------------------------------------
-// Function write2()                                                  BamHeader
+// Function write()                                                   BamHeader
 // ----------------------------------------------------------------------------
 
-template <typename TStream, typename TNameStore, typename TNameStoreCache>
-int write2(TStream & stream,
-           BamHeader const & header,
-           BamIOContext<TNameStore, TNameStoreCache> const & context,
-           Sam const & tag)
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void write(TTarget & target,
+                  BamHeader const & header,
+                  BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context,
+                  Sam const & tag)
 {
-    std::set<CharString> writtenSeqInfos;
+    String<bool> writtenSeqInfos;
+    resize(writtenSeqInfos, length(contigNames(context)), false);
 
-    for (unsigned i = 0; i < length(header.records); ++i)
+    size_t globalRefId = 0;
+    for (unsigned i = 0; i < length(header); ++i)
     {
-        BamHeaderRecord const & record = header.records[i];
+        BamHeaderRecord const & record = header[i];
         if (record.type == BAM_HEADER_REFERENCE)
-        {
-            for (unsigned i = 0; i < length(record.tags); ++i)
-            {
-                if (record.tags[i].i1 == "SN")
+            for (unsigned j = 0; j < length(record.tags); ++j)
+                if (record.tags[j].i1 == "SN")
                 {
-                    writtenSeqInfos.insert(record.tags[i].i2);
+                    if (getIdByName(globalRefId, contigNamesCache(context), record.tags[j].i2))
+                        writtenSeqInfos[globalRefId] = true;
                     break;
                 }
-            }
-        }
 
-        int res = write2(stream, record, context, tag);
-        if (res != 0)
-            return res;
+        write(target, record, context, tag);
     }
 
     // Write missing @SQ header records.
-    for (unsigned i = 0; i < length(header.sequenceInfos); ++i)
+    SEQAN_ASSERT_LEQ(length(contigLengths(context)), length(contigNames(context)));
+    for (unsigned i = 0; i < length(contigLengths(context)); ++i)
     {
-        if (writtenSeqInfos.find(header.sequenceInfos[i].i1) != writtenSeqInfos.end())
+        if (writtenSeqInfos[i])
             continue;
-        int res = streamPut(stream, "@SQ\tSN:");
-        if (res != 0)
-            return res;
-
-        res = streamPut(stream, header.sequenceInfos[i].i1);
-        if (res != 0)
-            return res;
-
-        res = streamPut(stream, "\tLN:");
-        if (res != 0)
-            return res;
-
-        res = streamPut(stream, header.sequenceInfos[i].i2);
-        if (res != 0)
-            return res;
-
-        res = streamPut(stream, '\n');
-        if (res != 0)
-            return res;
+        write(target, "@SQ\tSN:");
+        write(target, contigNames(context)[i]);
+        write(target, "\tLN:");
+        appendNumber(target, contigLengths(context)[i]);
+        writeValue(target, '\n');
     }
-
-    return 0;
 }
 
 // ----------------------------------------------------------------------------
-// Function write2()                                         BamAlignmentRecord
+// Function write()                                          BamAlignmentRecord
 // ----------------------------------------------------------------------------
 
-template <typename TStream, typename TNameStore, typename TNameStoreCache>
-int write2(TStream & stream,
-           BamAlignmentRecord const & record,
-           BamIOContext<TNameStore, TNameStoreCache> const & context,
-           Sam const & /*tag*/)
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void write(TTarget & target,
+                  BamAlignmentRecord const & record,
+                  BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context,
+                  Sam const & /*tag*/)
 {
-    int res = 0;
-
-#define SEQAN_PUT_TAB                           \
-    do {                                        \
-        res = streamPut(stream, '\t');      \
-        if (res != 0)                       \
-            return res;                     \
-    } \
-    while (false)
-
-    res = streamPut(stream, record.qName);
-    if (res != 0)
-        return res;
-
-    SEQAN_PUT_TAB;
+    // Check for valid IO Context.
+    SEQAN_ASSERT_LT_MSG(record.rID, static_cast<__int32>(length(contigNames(context))), "SAM IO Assertion: Unknown REF ID!");
+    SEQAN_ASSERT_LT_MSG(record.rNextId, static_cast<__int32>(length(contigNames(context))), "SAM IO Assertion: Unknown NEXT REF ID!");
 
-    res = streamPut(stream, record.flag);
-    if (res != 0)
-        return res;
+    write(target, record.qName);
+    writeValue(target, '\t');
 
-    SEQAN_PUT_TAB;
+    appendNumber(target, record.flag);
+    writeValue(target, '\t');
 
     if (record.rID == BamAlignmentRecord::INVALID_REFID)
-        res = streamPut(stream, '*');
+        writeValue(target, '*');
     else
-        res = streamPut(stream, nameStore(context)[record.rID]);
-    if (res != 0)
-        return res;
+        write(target, contigNames(context)[record.rID]);
 
-    SEQAN_PUT_TAB;
+    writeValue(target, '\t');
 
-    res = streamPut(stream, record.beginPos + 1);
-    if (res != 0)
-        return res;
+    SEQAN_ASSERT_EQ((__int32)BamAlignmentRecord::INVALID_POS + 1, (__int32)0);
+    appendNumber(target, record.beginPos + 1);
 
-    SEQAN_PUT_TAB;
+    writeValue(target, '\t');
 
-    res = streamPut(stream, static_cast<__uint16>(record.mapQ));
-    if (res != 0)
-        return res;
-
-    SEQAN_PUT_TAB;
+    appendNumber(target, static_cast<__uint16>(record.mapQ));
+    writeValue(target, '\t');
 
     if (empty(record.cigar))
-    {
-        res = streamPut(stream, '*');
-        if (res != 0)
-            return res;
-    }
+        writeValue(target, '*');
     else
-    {
         for (unsigned i = 0; i < length(record.cigar); ++i)
         {
-            res = streamPut(stream, record.cigar[i].count);
-            if (res != 0)
-                return res;
-
-            res = streamPut(stream, record.cigar[i].operation);
-            if (res != 0)
-                return res;
+            appendNumber(target, record.cigar[i].count);
+            writeValue(target, record.cigar[i].operation);
         }
-    }
 
-    SEQAN_PUT_TAB;
+    writeValue(target, '\t');
 
     if (record.rNextId == BamAlignmentRecord::INVALID_REFID)
-        res = streamPut(stream, '*');
+        writeValue(target, '*');
     else if (record.rID == record.rNextId)
-        res = streamPut(stream, '=');
+        writeValue(target, '=');
     else
-        res = streamPut(stream, nameStore(context)[record.rNextId]);
-    if (res != 0)
-        return res;
+        write(target, contigNames(context)[record.rNextId]);
 
-    SEQAN_PUT_TAB;
+    writeValue(target, '\t');
 
-    res = streamPut(stream, record.pNext + 1);
-    if (res != 0)
-        return res;
+    appendNumber(target, record.pNext + 1);
 
-    SEQAN_PUT_TAB;
+    writeValue(target, '\t');
 
     if (record.tLen == BamAlignmentRecord::INVALID_LEN)
-        res = streamPut(stream, '0');
+        writeValue(target, '0');
     else
-        res = streamPut(stream, record.tLen);
-    if (res != 0)
-        return res;
+        appendNumber(target, record.tLen);
 
-    SEQAN_PUT_TAB;
+    writeValue(target, '\t');
 
     if (empty(record.seq))
-        res = streamPut(stream, '*');  // Case of empty seq string / "*".
+        writeValue(target, '*');  // Case of empty seq string / "*".
     else
-        res = streamPut(stream, record.seq);
-    if (res != 0)
-        return res;
+        write(target, record.seq);
 
-    SEQAN_PUT_TAB;
+    writeValue(target, '\t');
 
 
     if (empty(record.qual))  // Case of empty quality string / "*".
-        res = streamPut(stream, '*');
+        writeValue(target, '*');
     else
-        res = streamPut(stream, record.qual);
-    if (res != 0)
-        return res;
+        write(target, record.qual);
 
     if (!empty(record.tags))
     {
-        SEQAN_PUT_TAB;
-        CharString buffer;
-        assignTagsBamToSam(buffer, record.tags);
-        streamPut(stream, buffer);
+        writeValue(target, '\t');
+        appendTagsBamToSam(target, record.tags);
     }
 
-    return streamPut(stream, '\n');
-
-#undef SEQAN_PUT_TAB
+    writeValue(target, '\n');
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_
+#endif  // #ifndef INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_
diff --git a/seqan/basic.h b/seqan/basic.h
index 9580594..4409c8b 100644
--- a/seqan/basic.h
+++ b/seqan/basic.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Umbrella header for the basic module.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_H_
 
 // --------------------------------------------------------------------------
 // Prerequisites
@@ -48,15 +48,18 @@
 // Code for debugging and testing (assertions, test system) and profiling.
 #include <seqan/basic/basic_debug.h>
 
-// Basic exceptions.
-#include <seqan/basic/basic_exception.h>
-
 // C++ Metaprogramming Support Code, generally independent of SeqAn.
 #include <seqan/basic/basic_metaprogramming.h>
 
+// Basic functors.
+#include <seqan/basic/basic_functors.h>
+
 // Fundamental meta and global functions.  This is what makes SeqAn SeqAn.
 #include <seqan/basic/basic_fundamental.h>
 
+// Basic exceptions.
+#include <seqan/basic/basic_exception.h>
+
 // More advanced debug system constructs.
 // TODO(holtgrew): Move into basic_debug subsystem, some stuff from metaprogramming and fundamental required, those should not depend on debug system.
 #include <seqan/basic/test_system.h>
@@ -64,11 +67,8 @@
 // SeqAn Concept Checking Library (ported from Boost).
 #include <seqan/basic/basic_concept.h>
 
-// Alphabet concept and biological implementations.
-#include <seqan/basic/basic_alphabet.h>
-
-// Aggregate data types (pairs, triples, tuples).
-#include <seqan/basic/basic_aggregate.h>
+// Container concept and supporting code.
+#include <seqan/basic/basic_container.h>
 
 // Memory allocation code.
 #include <seqan/basic/basic_allocator.h>
@@ -85,13 +85,28 @@
 // Iterator concept and implementation.
 #include <seqan/basic/basic_iterator.h>
 
+// Functions to efficiently move data between containers/iterators/streams
+#include <seqan/basic/basic_stream.h>
+
+// Alphabet concept and biological implementations.
+#include <seqan/basic/basic_alphabet.h>
+
 // Proxy class and supporting code.
 #include <seqan/basic/basic_proxy.h>
 
-// Container concept and supporting code.
-#include <seqan/basic/basic_container.h>
+// Aggregate data types (pairs, triples, tuples).
+#include <seqan/basic/basic_aggregate.h>
 
 // Remaining code with cyclic dependencies.
 #include <seqan/basic/basic_tangle.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_H_
+// Basic views functions and metafunctions.
+#include <seqan/basic/basic_view.h>
+
+// Basic device metafunctions.
+#include <seqan/basic/basic_device.h>
+
+// Basic SIMD vector (not included by default on purpose)
+//#include <seqan/basic/basic_simd_vector.h>
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_H_
diff --git a/seqan/basic/INFO b/seqan/basic/INFO
deleted file mode 100644
index 6506f01..0000000
--- a/seqan/basic/INFO
+++ /dev/null
@@ -1,14 +0,0 @@
-Name: seqan-basic
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Author: Tobias Rausch <rausch@embl.de>
-Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: SeqAn core module with fundamental infrastructure.
- The basic module contains the infrastructure for testing, allocators, the SeqAn
- types and concepts, iterators, the Holder classes, aggregats (Pairs, Triples,
- Tuples, ...) and other fundamentals.
diff --git a/seqan/basic/aggregate_concept.h b/seqan/basic/aggregate_concept.h
index 15cfa1b..206530a 100644
--- a/seqan/basic/aggregate_concept.h
+++ b/seqan/basic/aggregate_concept.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_
 
 namespace seqan {
 
@@ -47,13 +47,11 @@ namespace seqan {
 
 /*!
  * @concept AggregateConcept
- * 
+ *
  * @brief Aggregate types contain a fixed number of fixed-size values (pairs, triples, tuples).
- * 
- * @section Remarks
- * 
+ *
  * Stream output operators are not shown in the function list below, but required.
- * 
+ *
  * Comparison operators are not shown in the function list below, but required.
  */
 
@@ -63,26 +61,12 @@ namespace seqan {
  *
  * @signature TStream AggregateConcept::operator<<(stream, aggregate);
  *
- * @param stream    The <tt>std::ostream</tt> to write to.
- * @param aggregate The aggregate type to write to the stream.
+ * @param[in,out] stream    The <tt>std::ostream</tt> to write to.
+ * @param[in]     aggregate The aggregate type to write to the stream.
  *
  * @return TStream Reference to <tt>stream</tt> after writing <tt>aggregate</tt> to it.
  */
 
-/**
-.Concept.AggregateConcept
-..summary:Aggregate types contain a fixed number of fixed-size values.
-..remarks:Stream output operators are not shown in the function list below, but required.
-..remarks:Comparison operators are not shown in the function list below, but required.
-
-.Function.clear.concept:Concept.AggregateConcept
-.Function.value.concept:Concept.AggregateConcept
-.Function.assignValue.concept:Concept.AggregateConcept
-
-.Metafunction.LENGTH.concept:Concept.AggregateConcept
-.Metafunction.Value.concept:Concept.AggregateConcept
- */
-
 /*!
  * @defgroup AggregateTags Aggregate Tags
  * @brief Tags to use in aggregate (e.g. Pair, Triple, and Tuple) types.
@@ -96,14 +80,6 @@ namespace seqan {
  * @signature typedef Tag<Pack_> Pack;
  */
 
-/**
-.Tag.Pack
-..cat:Aggregates
-..summary:Tag to mark a packed specialization that disables address alignment for members.
-..signature:Pack
-..include:seqan/basic.h
- */
-
 struct Pack_;
 typedef Tag<Pack_> Pack;
 
@@ -122,18 +98,6 @@ typedef Tag<Pack_> Pack;
  * BITSIZE2 The number of bits for the second entry.
  */
 
-/**
-.Tag.BitPacked
-..cat:Aggregates
-..summary:Tag to mark a bit-packed specialization that avoids to waste bits.
-..signature:BitPacked<BITSIZE1, BITSIZE2>
-..param.BITSIZE1:Number of bits used for first element.
-...type:nolink:$unsigned$
-..param.BITSIZE2:Number of bits used for second element.
-...type:nolink:$unsigned$
-..include:seqan/basic.h
- */
-
 template <unsigned BITSIZE1 = 16, unsigned BITSIZE2 = 16>
 struct BitPacked;
 
@@ -153,16 +117,6 @@ struct BitPacked;
  * @return Type The resulting packed type.
  */
 
-/**
-.Metafunction.MakePacked
-..cat:Aggregates
-..summary:Return the corresponding packed type of a type.
-..signature:MakePacked<TAggregate>
-..param.TAggregate:An aggregate type.
-..returns:The corresponding packed aggregate.
-..include:seqan/basic.h
- */
-
 template <typename T>
 struct MakePacked
 {
@@ -175,4 +129,4 @@ struct MakePacked
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_
diff --git a/seqan/basic/allocator_chunkpool.h b/seqan/basic/allocator_chunkpool.h
index b40a1ff..1308a61 100644
--- a/seqan/basic/allocator_chunkpool.h
+++ b/seqan/basic/allocator_chunkpool.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // size.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_
 
 #include <seqan/basic/allocator_interface.h>
 
@@ -50,31 +50,9 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-/**
-.Spec.Chunk Pool Allocator:
-..cat:Allocators
-..general:Class.Allocator
-..summary:Allocator that pools one or more consecutive memory blocks of a specific size.
-..signature:Allocator< ChunkPool<SIZE, MAX_COUNT, ParentAllocator> >
-..param.SIZE:Size of memory blocks that are pooled.
-...value:An unsigned integer with $SIZE >= sizeof(void *)$.
-..param.MAX_COUNT:Maximum number of consecutive memory blocks that are pooled.
-...default:26
-...remarks:Longer "chunks" are allocated and deallocated without pooling.
-..param.ParentAllocator:An allocator that is by the pool allocator used to allocate memory.
-...default:@Spec.Simple Allocator@
-...note:The multi pool allocator only supports @Function.clear@ if this function is also implemented for $ParentAllocator$.
-..remarks:A pool allocator allocates several memory blocks at once. 
-Freed blocks are not immediately deallocated but recycled in subsequential allocations.
-This way, the number of calls to the heap manager is reduced, and that speeds up memory management.
-...text:Note that memory blocks of size different than $SIZE$, $2*SIZE$, $3*SIZE$, ..., $MAX_COUNT * SIZE$ 
-are not pooled but immediately allocated and deallocated using $ParentAllocator$.
-..include:seqan/basic.h
-*/
-
 template <
-    size_t SIZE, 
-    size_t MAX_COUNT = 26, 
+    size_t SIZE,
+    size_t MAX_COUNT = 26,
     typename TParentAllocator = Allocator<SimpleAlloc<Default> > >
 struct ChunkPool;
 
@@ -101,7 +79,7 @@ struct Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >
     Allocator()
     {
         SEQAN_CHECKPOINT;
-        ::std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
         data_current_end = data_current_free = 0;
         //dont need to initialize data_current_begin
     }
@@ -109,7 +87,7 @@ struct Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >
     Allocator(size_t reserve_item_count)
     {
         SEQAN_CHECKPOINT;
-        ::std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
 
         size_t storage_size = (reserve_item_count * SIZE > STORAGE_SIZE_MIN) ? reserve_item_count * SIZE : STORAGE_SIZE_MIN;
         allocate( parentAllocator( *this ), data_current_begin, storage_size );
@@ -120,7 +98,7 @@ struct Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >
     Allocator(TParentAllocator & parent_alloc)
     {
         SEQAN_CHECKPOINT;
-        ::std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
         data_current_end = data_current_free = 0;
         //dont need to initialize data_current_begin
 
@@ -130,7 +108,7 @@ struct Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >
     Allocator(size_t reserve_item_count, TParentAllocator & parent_alloc)
     {
         SEQAN_CHECKPOINT;
-        ::std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
 
         setValue(data_parent_allocator, parent_alloc);
 
@@ -143,7 +121,7 @@ struct Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >
     //Dummy copy
     Allocator(Allocator const &)
     {
-        ::std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
         data_current_end = data_current_free = 0;
         //dont need to initialize data_current_begin
     }
@@ -190,7 +168,7 @@ void
 clear(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me)
 {
     SEQAN_CHECKPOINT;
-    ::std::memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks));
+    std::memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks));
     me.data_current_end = me.data_current_free = 0;
 
     clear(parentAllocator(me));
@@ -202,7 +180,7 @@ clear(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me)
 
 template <size_t SIZE, size_t MAX_COUNT, typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
 inline void
-allocate(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me, 
+allocate(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me,
          TValue * & data,
          TSize count,
          Tag<TUsage> const tag_)
@@ -273,4 +251,4 @@ deallocate(Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > & me,
 
 }  // namespace seqan
 
-#endif  // SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_
+#endif  // SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_
diff --git a/seqan/basic/allocator_interface.h b/seqan/basic/allocator_interface.h
index 851fdef..c9917bd 100644
--- a/seqan/basic/allocator_interface.h
+++ b/seqan/basic/allocator_interface.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // TODO(holtgrew): Perform some benchmarks and use a better malloc, e.g. tcmalloc and see whether our allocator infrastructure is worth keeping around.
 // TODO(holtgrew): Rename to allocator_base.h?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_
 
 namespace seqan {
 
@@ -55,34 +55,22 @@ template <typename TValue, typename TSpec> struct Holder;
 // ============================================================================
 
 /*!
- * @defgroup AllocatorUsageTags Allocator Usage
+ * @defgroup AllocatorUsageTags Allocator Usage Tags
  * @brief The purpose of an allocated memory block.
- * 
+ *
  * @tag AllocatorUsageTags#TagAllocateUnspecified
  * @headerfile <seqan/basic.h>
  * @brief Not specified.
- * 
+ *
  * @tag AllocatorUsageTags#TagAllocateTemp
  * @headerfile <seqan/basic.h>
  * @brief Temporary memory.
- * 
+ *
  * @tag AllocatorUsageTags#TagAllocateStorage
  * @headerfile <seqan/basic.h>
  * @brief Memory for storing container content.
  */
 
-/**
-.Tag.Allocator Usage:
-..cat:Memory
-..summary:The purpose of an allocated memory block.
-..tag.TagAllocateUnspecified:Not specified.
-..tag.TagAllocateTemp:Temporary memory. 
-..tag.TagAllocateStorage:Memory for storing container content. 
-..see:Function.allocate
-..see:Function.deallocate
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): ANY use/difference?
 
 struct AllocateUnspecified_;
@@ -98,14 +86,14 @@ typedef Tag<AllocateStorage_> TagAllocateStorage;
  * @class Allocator
  * @headerfile <seqan/basic.h>
  * @brief Manager for allocated memory.
- * 
+ *
  * @signature template <typename TSpec>
  *            class Allocator;
- * 
+ *
  * @tparam TSpec The specializing type.
- * 
+ *
  * @section Remarks
- * 
+ *
  * There are two reasons for using non-trivial allocators:
  *
  * <ol>
@@ -118,32 +106,9 @@ typedef Tag<AllocateStorage_> TagAllocateStorage;
  * </ol>
  */
 
-/**
-.Class.Allocator:
-..cat:Basic
-..summary:Manager for allocated memory.
-..signature:Allocator<TSpec>
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-..include:basic.h
-..remarks:There are two reasons for using non-trivial allocators:
-...text:1. Allocators support the function @Function.Allocator#clear@ for a fast deallocation of all 
-allocated memory blocks. 
-...text:2. Some allocators are faster in allocating an deallocating memory.
-Pool allocators like e.g. @Spec.Single Pool Allocator@ or @Spec.Multi Pool Allocator@
-speed up @Function.allocate@, @Function.deallocate@, and @Function.Allocator#clear@ for
-pooled memory blocks.
-..include:seqan/basic.h
-*/
-
 template <typename TSpec>
 struct Allocator;
 
-///.Function.allocate.param.object.type:Class.Allocator
-///.Function.allocate.class:Class.Allocator
-///.Function.deallocate.param.object.type:Class.Allocator
-///.Function.deallocate.class:Class.Allocator
-
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -168,9 +133,9 @@ struct Spec<Allocator<TSpec> >
  * @fn Allocator#allocate
  * @headerfile <seqan/basic.h>
  * @brief Allocates memory from heap.
- * 
+ *
  * @signature void allocate(allocator, data, count[, usageTag]);
- * 
+ *
  * @param[in]     count     Number of items that could be stored in the allocated memory.  The type of the allocated
  *                          items is given by the type of <tt>data</tt>.
  * @param[in]     usageTag  A tag the specifies the purpose for the allocated memory.  Values:
@@ -179,58 +144,23 @@ struct Spec<Allocator<TSpec> >
  *                          memory.  Objects of all types can be used as allocators.  If no special behavior is
  *                          implemented,  default functions allocation/deallocation are applied that uses standard
  *                          <tt>new</tt> and <tt>delete</tt> operators. Types: Allocator
- * 
+ *
  * @section Remarks
- * 
+ *
  * The function allocates at least <tt>count*sizeof(data)</tt> bytes.  The allocated memory is large enough  to hold
  * <tt>count</tt> objects of type <tt>T</tt>, where <tt>T *</tt> is type of <tt>data</tt>.
- * 
+ *
  * These objects are not constructed by <tt>allocate</tt>.
- * 
+ *
  * Use e.g. one of the functions @link valueConstruct @endlink, @link arrayConstruct @endlink, @link arrayConstructCopy
  * @endlink or @link arrayFill @endlink to construct the objects. A <tt>new</tt> operator which is part of the C++
  * standard (defined in <tt>&lt;new&gt;</tt>)  can also be used to construct objects at a given memory address.
- * 
+ *
  * @section Remarks
- * 
+ *
  * All allocated memory blocks should be deallocated by the corresponding function @link Allocator#deallocate @endlink.
  */
 
-/**
-.Function.allocate
-..class:Class.Allocator
-..cat:Memory
-..summary:Allocates memory from heap.
-..signature:allocate(object, data, count [, usage_tag])
-..param.object:Allocator object.
-...remarks:$object$ is conceptually the "owner" of the allocated memory.
- Objects of all types can be used as allocators. If no special behavior is implemented,
- default functions allocation/deallocation are applied that uses standard
- $new$ and $delete$ operators.
-..param.count:Number of items that could be stored in the allocated memory.
-...text:The type of the allocated items is given by the type of $data$.
-..param.usage_tag:A tag the specifies the purpose for the allocated memory.
-...value:@Tag.Allocator Usage@
-..returns.param.data:Pointer to allocated memory.
-...remarks:The value of this pointer is overwritten by the function.
-..remarks:
-...text:The function allocates at least $count*sizeof(data)$ bytes. 
- The allocated memory is large enough 
- to hold $count$ objects of type $T$, where $T *$ is type of $data$.
-...note:These objects are not constructed by $allocate$.
-...text:Use e.g. one of the functions @Function.valueConstruct@, @Function.arrayConstruct@, @Function.arrayConstructCopy@ or @Function.arrayFill@
-to construct the objects.
-A $new$ operator which is part of the C++ standard (defined in $<new>$)
- can also be used to construct objects at a given memory address.
-..note:All allocated memory blocks should be deallocated by the corresponding function @Function.deallocate@.
-..see:Function.deallocate
-..see:Function.valueConstruct
-..see:Function.arrayFill
-..see:Function.arrayConstruct
-..see:Function.arrayConstructCopy
-..include:seqan/basic.h
-*/
-
 template <typename T, typename TValue, typename TSize>
 inline void
 allocate(T const & me,
@@ -251,7 +181,7 @@ allocate(T & me,
 
 template <typename T, typename TValue, typename TSize, typename TUsage>
 inline void
-allocate(T const &, 
+allocate(T const &,
          TValue * & data,
          TSize count,
          Tag<TUsage> const &)
@@ -278,7 +208,7 @@ allocate(T const &,
 
 template <typename T, typename TValue, typename TSize, typename TUsage>
 inline void
-allocate(T &, 
+allocate(T &,
          TValue * & data,
          TSize count,
          Tag<TUsage> const &)
@@ -311,71 +241,41 @@ allocate(T &,
  * @fn Allocator#deallocate
  * @headerfile <seqan/basic.h>
  * @brief Deallocates memory.
- * 
+ *
  * @signature void deallocate(object, data, count[, usageTag])
- * 
- * @param count    Number of items that could be stored in the allocated memory.
- * @param usageTag A tag the specifies the purpose for the allocated memory.
- *                 Values: @link AllocatorUsageTags @endlink.
- * @param object   Allocator object.<tt>object</tt> is conceptually the "owner" of the allocated memory.  Objects of
- *                 all types can be used as allocators.  If no special behavior is implemented,  default
- *                 functions allocation/deallocation are applied that uses standard  <tt>new</tt> and <tt>delete</tt>
- *                 operators. Types: Allocator
- * @param data     Pointer to allocated memory that was allocated by <tt>allocate</tt>.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] object Allocator object.<tt>object</tt> is conceptually the "owner" of the allocated memory.
+ *                       Objects of all types can be used as allocators.  If no special behavior is implemented,
+ *                       default functions allocation/deallocation are applied that uses standard  <tt>new</tt>
+ *                       and <tt>delete</tt> operators.  Types: Allocator
+ * @param[out]     data  Pointer to allocated memory that was allocated by <tt>allocate</tt>.
+ * @param[in]     count    Number of items that could be stored in the allocated memory.
+ * @param[in]     usageTag A tag the specifies the purpose for the allocated memory.
+ *                         Values: @link AllocatorUsageTags @endlink.
+ *
  * The values for <tt>object</tt>, <tt>count</tt> and <tt>usageTag</tt> should be the same that was used when
  * <tt>allocate</tt> was called. The value of <tt>data</tt> should be the same that was returned by <tt>allocate</tt>.
- * 
+ *
  * <tt>deallocate</tt> does not destruct objects.
- * 
+ *
  * Use e.g. one of the functions @link valueDestruct @endlink or @link arrayDestruct @endlink to destruct the objects.
  * <tt>delete</tt> and <tt>delete []</tt> operators which are part of the C++ standard (defined in <tt>&lt;new&gt;</tt>)
  * can also be used to destruct objects at a given memory address.
  */
 
-/**
-.Function.deallocate
-..class:Class.Allocator
-..cat:Memory
-..summary:Deallocates memory.
-..signature:deallocate(object, data, count [, usage_tag])
-..param.object:Allocator object.
-...remarks:$object$ is conceptually the "owner" of the allocated memory.
- Objects of all types can be used as allocators. If no special behavior is implemented,
- default functions allocation/deallocation are applied that uses standard
- $new$ and $delete$ operators.
-..param.data:Pointer to allocated memory that was allocated by $allocate$.
-..param.count:Number of items that could be stored in the allocated memory.
-..param.usage_tag:A tag the specifies the purpose for the allocated memory.
-...value:@Tag.Allocator Usage@
-..remarks:
-...text:The values for $object$, $count$ and $usage_tag$ should be the same that was 
-used when $allocate$ was called. The value of $data$ should be the same that was
-returned by $allocate$.
-...note:$deallocate$ does not destruct objects.
-...text:Use e.g. one of the functions @Function.valueDestruct@ or @Function.arrayDestruct@ to destruct the objects.
-$delete$ and $delete []$ operators which are part of the C++ standard (defined in $<new>$)
- can also be used to destruct objects at a given memory address.
-..see:Function.valueDestruct
-..see:Function.arrayDestruct
-..include:seqan/basic.h
-*/
-
 template <typename T, typename TValue, typename TSize>
-inline void 
-deallocate(T const & me, 
-           TValue * data, 
+inline void
+deallocate(T const & me,
+           TValue * data,
            TSize const count)
 {
     deallocate(me, data, count, TagAllocateUnspecified());
 }
 
 template <typename T, typename TValue, typename TSize>
-inline void 
-deallocate(T & me, 
-           TValue * data, 
+inline void
+deallocate(T & me,
+           TValue * data,
            TSize const count)
 {
     deallocate(me, data, count, TagAllocateUnspecified());
@@ -386,7 +286,7 @@ inline void
 deallocate(
     T const & /*me*/,
     TValue * data,
-#ifdef SEQAN_PROFILE 
+#ifdef SEQAN_PROFILE
     TSize count,
 #else
     TSize,
@@ -407,11 +307,11 @@ deallocate(
 }
 
 template <typename T, typename TValue, typename TSize, typename TUsage>
-inline void 
+inline void
 deallocate(
     T & /*me*/,
     TValue * data,
-#ifdef SEQAN_PROFILE 
+#ifdef SEQAN_PROFILE
     TSize count,
 #else
     TSize,
@@ -433,4 +333,4 @@ deallocate(
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_
diff --git a/seqan/basic/allocator_multipool.h b/seqan/basic/allocator_multipool.h
index 7fdbb39..36b17c8 100644
--- a/seqan/basic/allocator_multipool.h
+++ b/seqan/basic/allocator_multipool.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -51,41 +51,23 @@ namespace seqan {
 
 /*!
  * @class MultiPoolAllocator
+ * @extends Allocator
  * @headerfile <seqan/basic.h>
  * @brief Allocator that pools memory blocks.
  *
- * @signature template <typename TParentAllocator, unsigned BLOCKING_LIMIT>
+ * @signature template <typename TParentAllocator[, unsigned BLOCKING_LIMIT]>
  *            class Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> >;
  *
- * @tparam TParentAllocator Th eparent allocator.
+ * @tparam TParentAllocator The parent allocator.
  * @tparam BLOCKING_LIMIT The maximum size for memory blocks to be pooled (default is 256).
  *
- * Freed blocks are not immediately deallocated but recycled in subsequential allocations.  This way, th enumber of
+ * Freed blocks are not immediately deallocated but recycled in subsequential allocations.  This way, the number of
  * calls to the heap manager is reduced and that might speed up memory management.
  *
  * Note that memory block larger than <tt>BLOCKING_LIMIT</tt> are not pooled but immediately allocated and deallocated
  * using <tt>ParentAllocator</tt>.
  */
 
-/**
-.Spec.Multi Pool Allocator:
-..cat:Allocators
-..general:Class.Allocator
-..summary:Allocator that pools memory blocks.
-..signature:Allocator MultiPool<ParentAllocator, BLOCKING_LIMIT> >
-..param.ParentAllocator:An allocator that is by the pool allocator used to allocate memory.
-...default:@Spec.Simple Allocator@
-...note:The multi pool allocator only supports @Function.clear@ if this function is also implemented for $ParentAllocator$.
-..remarks:A pool allocator allocates several memory blocks at once. 
-..param.BLOCKING_LIMIT:The maximum size for memory blocks to be pooled.
-...default:256
-Freed blocks are not immediately deallocated but recycled in subsequential allocations.
-This way, the number of calls to the heap manager is reduced, and that speeds up memory management.
-...text:Note that memory blocks larger than $BLOCKING_LIMIT$ are not pooled 
-but immediately allocated and deallocated using $ParentAllocator$.
-..include:seqan/basic.h
-*/
-
 template <typename TParentAllocator = Allocator<SimpleAlloc<Default> >, unsigned int BLOCKING_LIMIT = 0x100>
 struct MultiPool;
 
@@ -111,18 +93,18 @@ struct Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT_> >
     {
         SEQAN_CHECKPOINT;
         // TODO(holtrew): Why not SeqAn's memset? or use using?
-        ::std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
-        ::std::memset(data_current_begin, 0, sizeof(data_current_begin));
-        ::std::memset(data_current_free, 0, sizeof(data_current_free));
+        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+        std::memset(data_current_begin, 0, sizeof(data_current_begin));
+        std::memset(data_current_free, 0, sizeof(data_current_free));
     }
 
     Allocator(TParentAllocator & parent_alloc)
     {
         SEQAN_CHECKPOINT;
         // TODO(holtrew): Why not SeqAn's memset? or use using?
-        ::std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
-        ::std::memset(data_current_begin, 0, sizeof(data_current_begin));
-        ::std::memset(data_current_free, 0, sizeof(data_current_free));
+        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+        std::memset(data_current_begin, 0, sizeof(data_current_begin));
+        std::memset(data_current_free, 0, sizeof(data_current_free));
 
         setValue(data_parent_allocator, parent_alloc);
     }
@@ -131,9 +113,9 @@ struct Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT_> >
     Allocator(Allocator const &)
     {
         // TODO(holtrew): Why not SeqAn's memset? or use using?
-        ::std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
-        ::std::memset(data_current_begin, 0, sizeof(data_current_begin));
-        ::std::memset(data_current_free, 0, sizeof(data_current_free));
+        std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
+        std::memset(data_current_begin, 0, sizeof(data_current_begin));
+        std::memset(data_current_free, 0, sizeof(data_current_free));
     }
 
     inline Allocator &
@@ -179,9 +161,9 @@ void
 clear(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me)
 {
     SEQAN_CHECKPOINT;
-    ::std::memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks));
-    ::std::memset(me.data_current_begin, 0, sizeof(me.data_current_begin));
-    ::std::memset(me.data_current_free, 0, sizeof(me.data_current_free));
+    std::memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks));
+    std::memset(me.data_current_begin, 0, sizeof(me.data_current_begin));
+    std::memset(me.data_current_free, 0, sizeof(me.data_current_free));
 
     clear(parentAllocator(me));
 }
@@ -216,7 +198,7 @@ _allocatorBlockNumber(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > &,
 
 template <typename TParentAllocator, unsigned int BLOCKING_LIMIT, typename TValue, typename TSize, typename TUsage>
 inline void
-allocate(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me, 
+allocate(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me,
          TValue * & data,
          TSize count,
          Tag<TUsage> const & tag_)
@@ -259,9 +241,9 @@ allocate(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me,
 // ----------------------------------------------------------------------------
 
 template <typename TParentAllocator, unsigned int BLOCKING_LIMIT, typename TValue, typename TSize, typename TUsage>
-inline void 
+inline void
 deallocate(Allocator<MultiPool<TParentAllocator, BLOCKING_LIMIT> > & me,
-           TValue * data, 
+           TValue * data,
            TSize count,
            Tag<TUsage> const tag_)
 {
diff --git a/seqan/basic/allocator_simple.h b/seqan/basic/allocator_simple.h
index 52937bd..b60aec7 100644
--- a/seqan/basic/allocator_simple.h
+++ b/seqan/basic/allocator_simple.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // General purpose allocator.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_
 
 #include <seqan/basic/allocator_interface.h>
 
@@ -51,6 +51,7 @@ namespace seqan {
 
 /*!
  * @class SimpleAllocator
+ * @extends Allocator
  * @headerfile <seqan/basic.h>
  * @brief General purpose allocator.
  *
@@ -59,25 +60,10 @@ namespace seqan {
  *
  * @tparam TParentAllocator An allocator that is used by the simple allocator to allocate memory.
  *
- * @section Remarks
- *
  * The tag Default used as TparentAllocator means that the default implementations of <tt>allocate</tt> and
  * <tt>deallocate</tt> are used.
  */
 
-/**
-.Spec.Simple Allocator:
-..cat:Allocators
-..general:Class.Allocator
-..summary:General purpose allocator.
-..signature:Allocator< SimpleAlloc<ParentAllocator> >
-..param.ParentAllocator:An allocator that is by the simple allocator used to allocate memory.
-...default:@Tag.Default@
-...remarks:@Tag.Default@ used as allocator means that the default implementations
-of @Function.allocate@ and @Function.deallocate@ are used.
-..include:seqan/basic.h
-*/
-
 template <typename TParentAllocator = Default>
 struct SimpleAlloc;
 
@@ -168,21 +154,6 @@ parentAllocator(Allocator<SimpleAlloc<TParentAllocator> > & me)
  */
 
 // TODO(holtgrew): Using #-functions messes up search results.
-/**
-.Function.Allocator#clear
-..class:Class.Allocator
-..cat:Memory
-..summary:Deallocates all memory blocks.
-..signature:clear(allocator)
-..param.allocator:Allocator object.
-...type:Class.Allocator
-..remarks:This function deallocates all memory blocks 
-that was allocated using @Function.allocate@ for $allocator$.
-The memory is not pooled but directly passed back to the heap manager.
-..see:Function.allocate
-..see:Function.deallocate
-..include:seqan/basic.h
-*/
 template <typename TParentAllocator>
 void
 clear(Allocator<SimpleAlloc<TParentAllocator> > & me)
@@ -204,7 +175,7 @@ clear(Allocator<SimpleAlloc<TParentAllocator> > & me)
 
 template <typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
 inline void
-allocate(Allocator<SimpleAlloc<TParentAllocator> > & me, 
+allocate(Allocator<SimpleAlloc<TParentAllocator> > & me,
          TValue * & data,
          TSize count,
          Tag<TUsage> const &)
@@ -240,9 +211,9 @@ allocate(Allocator<SimpleAlloc<TParentAllocator> > & me,
 // ----------------------------------------------------------------------------
 
 template <typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
-inline void 
+inline void
 deallocate(Allocator<SimpleAlloc<TParentAllocator> > & me,
-           TValue * data, 
+           TValue * data,
            TSize,
            Tag<TUsage> const &)
 {
@@ -272,4 +243,4 @@ deallocate(Allocator<SimpleAlloc<TParentAllocator> > & me,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_
diff --git a/seqan/basic/allocator_singlepool.h b/seqan/basic/allocator_singlepool.h
index 1d5b244..da290d4 100644
--- a/seqan/basic/allocator_singlepool.h
+++ b/seqan/basic/allocator_singlepool.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -62,8 +62,6 @@ namespace seqan {
  * @tparam SIZE             The size of the blocks.
  * @tparam TParentAllocator The parent allocator to use.
  *
- * @section Remarks
- *
  * A pool allocator allocates several memory blocks at once.  Freed blocks are not immediately deallocated but
  * recycled in subsequential allocations.  This way, the number of calls to the heap manager is reduced, and that
  * might speed up memory management.
@@ -73,25 +71,6 @@ namespace seqan {
  * than a few KB is not advised.
  */
 
-/**
-.Spec.Single Pool Allocator:
-..cat:Allocators
-..general:Class.Allocator
-..summary:Allocator that pools memory blocks of specific size.
-..signature:Allocator< SinglePool<SIZE, ParentAllocator> >
-..param.SIZE:Size of memory blocks that are pooled.
-..param.ParentAllocator:An allocator that is by the pool allocator used to allocate memory.
-...default:@Spec.Simple Allocator@
-...note:The single pool allocator only supports @Function.clear@ if this function is also implemented for $ParentAllocator$.
-..remarks:A pool allocator allocates several memory blocks at once. 
-Freed blocks are not immediately deallocated but recycled in subsequential allocations.
-This way, the number of calls to the heap manager is reduced, and that speeds up memory management.
-...text:The single pool allocator only pools memory blocks of size at most $SIZE$.
-Blocks of other sizes are allocated and deallocated using an allocator of type $ParentAllocator$.
-...text:Using the single pool allocator for blocksizes larger than some KB is not advised.
-..include:seqan/basic.h
-*/
-
 template <size_t SIZE, typename TParentAllocator = SimpleAllocator>
 struct SinglePool;
 
@@ -113,16 +92,11 @@ struct Allocator<SinglePool<SIZE, TParentAllocator> >
     char * data_current_free;
     Holder<TParentAllocator, Tristate> data_parent_allocator;
 
-    Allocator()
-    {
-        data_recycled_blocks = data_current_end = data_current_free = 0;
-        //dont need to initialize data_current_begin
-    }
+    Allocator() : data_recycled_blocks(), data_current_begin(), data_current_end(), data_current_free()
+    {}
 
-    Allocator(size_t reserve_item_count)
+    Allocator(size_t reserve_item_count) : data_recycled_blocks()
     {
-        data_recycled_blocks = 0;
-
         size_t storage_size = std::max(reserve_item_count * SIZE_PER_ITEM, STORAGE_SIZE_MIN);
         allocate(parentAllocator(*this), data_current_begin, storage_size);
         data_current_end = data_current_begin + storage_size;
@@ -149,11 +123,12 @@ struct Allocator<SinglePool<SIZE, TParentAllocator> >
         data_current_free = data_current_begin;
     }
 
-    //Dummy copy
-    Allocator(Allocator const &)
+    // Dummy copy
+    Allocator(Allocator const &) :
+        data_recycled_blocks(), data_current_begin(), data_current_end(),
+        data_current_free()
     {
         data_recycled_blocks = data_current_end = data_current_free = 0;
-        //dont need to initialize data_current_begin
     }
 
     inline Allocator &
@@ -206,7 +181,7 @@ clear(Allocator<SinglePool<SIZE, TParentAllocator> > & me)
 
 template <size_t SIZE, typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
 inline void
-allocate(Allocator<SinglePool<SIZE, TParentAllocator> > & me, 
+allocate(Allocator<SinglePool<SIZE, TParentAllocator> > & me,
          TValue * & data,
          TSize count,
          Tag<TUsage> const tag_)
@@ -249,9 +224,9 @@ allocate(Allocator<SinglePool<SIZE, TParentAllocator> > & me,
 // ----------------------------------------------------------------------------
 
 template <size_t SIZE, typename TParentAllocator, typename TValue, typename TSize, typename TUsage>
-inline void 
+inline void
 deallocate(Allocator<SinglePool<SIZE, TParentAllocator> > & me,
-           TValue * data, 
+           TValue * data,
            TSize count,
            Tag<TUsage> const tag_)
 {
diff --git a/seqan/basic/allocator_to_std.h b/seqan/basic/allocator_to_std.h
index d065c97..2a755e8 100644
--- a/seqan/basic/allocator_to_std.h
+++ b/seqan/basic/allocator_to_std.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // TODO(holtgrew): Rename STD to STL?
 // TODO(holtgrew): Rename to allocator_to_stl.h, remove basic_ prefix of all other allocator headers.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_
 
 namespace seqan {
 
@@ -54,55 +54,28 @@ namespace seqan {
  * @class ToStdAllocator
  * @headerfile <seqan/basic.h>
  * @brief Emulates standard conform allocator.
- * 
+ *
  * @signature template <typename THost, typename TValue>
  *            class ToStdAllocator;
- * 
+ *
  * @tparam TValue Type of allocated items.
- * @tparam THost  Type of the host allocator object.This object is used to call @link allocate @endlink and
- *                @link deallocate @endlink.
- * 
- * @section Remarks
- * 
+ * @tparam THost  Type of the host allocator object.This object is used to call @link Allocator#allocate @endlink and
+ *                @link Allocator#deallocate @endlink.
+ *
  * The member functions <tt>allocate</tt> and <tt>deallocate</tt> of <tt>ToStdAllocator</tt> call the (globale)
  * functions @link Allocator#allocate @endlink and @link Allocator#deallocate @endlink, respectively. The globale
  * functions get an allocator object as their first arguments. This allocator object is not the <tt>ToStdAllocator</tt>
  * object itself, but the host object that was given to the constructor.
- * 
+ *
  * @fn ToStdAllocator#ToStdAllocator
- * 
  * @brief Constructor
- * 
+ *
  * @signature ToStdAllocator::ToStdAllocator(host);
- * 
- * @param host The host object that is used as allocator for @link Allocator#allocate @endlink and @link
- * Allocator#deallocate @endlink.
+ *
+ * @param[in] host The host object that is used as allocator for @link Allocator#allocate @endlink and @link
+ *                 Allocator#deallocate @endlink.
  */
 
-/**
-.Class.ToStdAllocator:
-..summary:Emulates standard conform allocator.
-..signature:ToStdAllocator<THost, TValue>
-..param.THost:Type of the host allocator object.
-...text:This object is used to call @Function.allocate@ and @Function.deallocate@.
-..param.TValue:Type of allocated items.
-..remarks:The member functions $allocate$ and $deallocate$ of $ToStdAllocator$ call
-the (globale) functions @Function.allocate@ and @Function.deallocate@, respectively. The globale functions
-get an allocator object as their first arguments. This allocator object is not the $ToStdAllocator$ object itself,
-but the host object that was given to the constructor.
-..cat:Basic
-..remarks:
-..see:Function.allocate
-..see:Function.deallocate
-..include:seqan/basic.h
-
-.Memfunc.ToStdAllocator:
-..summary:Constructor
-..signature:ToStdAllocator(host)
-..class:Class.ToStdAllocator
-..param.host:The host object that is used as allocator for @Function.allocate@ and @Function.deallocate@.
-*/
-
 template <typename THost, typename TValue>
 struct ToStdAllocator
 {
@@ -213,26 +186,14 @@ struct StdAllocator
  * @fn ToStdAllocator#host
  * @headerfile <seqan/basic.h>
  * @brief The object a given object depends on.
- * 
+ *
  * @signature THost host(allocator);
- * 
- * @param allocator The allocator to query.
- * 
+ *
+ * @param[in] allocator The allocator to query.
+ *
  * @return THost The host object.
  */
 
-/**
-.Function.host
-..class:Class.ToStdAllocator
-..summary:The object a given object depends on.
-..cat:Dependent Objects
-..signature:host(object)
-..param.object:An object.
-...type:Class.ToStdAllocator
-..returns:The host object.
-..include:seqan/basic.h
-*/
-
 template <typename THost, typename TValue>
 THost &
 host(ToStdAllocator<THost, TValue> & me)
@@ -242,4 +203,4 @@ host(ToStdAllocator<THost, TValue> & me)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_
diff --git a/seqan/basic/alphabet_adapt_builtins.h b/seqan/basic/alphabet_adapt_builtins.h
index b22c783..fba40f7 100644
--- a/seqan/basic/alphabet_adapt_builtins.h
+++ b/seqan/basic/alphabet_adapt_builtins.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 // concepts they are in.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_
-#define SEQAN_CORE_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_
+#ifndef SEQAN_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_
+#define SEQAN_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_
 
 #include <limits>
 
@@ -82,36 +82,22 @@ struct BitsPerValue<bool>
 /*!
  * @mfn IsCharType
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief Return whether the argument is <tt>char</tt>, <tt>wchar_t</tt>, <tt>char const</tt>, or <tt>wchar_t
  *               const</tt>.
- * 
+ *
  * @signature IsCharType<T>::Type;
  * @signature IsCharType<T>::VALUE;
- * 
+ *
  * @tparam T Type to check type of.
- * 
- * @section Remarks
- * 
+ *
  * This metafunction is used to enable and disable templated adaptions of arrays to sequences for builtin character
  * types only.
- * 
+ *
  * The return value is <tt>True</tt>/<tt>true</tt> for <tt>char</tt>, <tt>wchar_t</tt>, <tt>char const</tt>, and
  * <tt>wchar_t const</tt>.
  */
 
-/**
-.Metafunction.IsCharType
-..cat:Alphabets
-..summary:Return whether the argument is $char$, $wchar_t$, $char const$, or $wchar_t const$.
-..signature:IsCharType<T>::Type
-..signature:IsCharType<T>::VALUE
-..param.T:Type to check type of.
-..remarks:This metafunction is used to enable and disable templated adaptions of arrays to sequences for builtin character types only.
-..remarks:The return value is $True$/$true$ for $char$, $wchar_t$, $char const$, and $wchar_t const$.
-..include:seqan/sequence.h
-*/
-
 template <typename T>
 struct IsCharType;
 
@@ -196,7 +182,7 @@ inline long double const &
 supremumValueImpl(long double *)
 {
 #ifdef PLATFORM_WINDOWS
-    static long double const _value = ::std::numeric_limits<long double>::infinity( );
+    static long double const _value = std::numeric_limits<long double>::infinity( );
 #else
     static long double const _value = 1.7976931348623157e+308;
 #endif
@@ -207,7 +193,7 @@ inline double const &
 supremumValueImpl(double *)
 {
 #ifdef PLATFORM_WINDOWS
-    static double const _value = ::std::numeric_limits<double>::infinity( );
+    static double const _value = std::numeric_limits<double>::infinity( );
 #else
     static double const _value = 1.7976931348623157e+308;
 #endif
@@ -217,7 +203,7 @@ inline float const &
 supremumValueImpl(float *)
 {
 #ifdef PLATFORM_WINDOWS
-    static float const _value = ::std::numeric_limits<float>::infinity( );
+    static float const _value = std::numeric_limits<float>::infinity( );
 #else
     static float const _value = 3.40282347e+38F;
 #endif
@@ -240,7 +226,7 @@ inline float const &
 infimumValueImpl(float *)
 {
 #ifdef PLATFORM_WINDOWS
-    static float const _value = -::std::numeric_limits<float>::infinity( );
+    static float const _value = -std::numeric_limits<float>::infinity( );
 #else
     static float const _value = -3.40282347e+38F;
 #endif
@@ -251,7 +237,7 @@ inline double const &
 infimumValueImpl(double *)
 {
 #ifdef PLATFORM_WINDOWS
-    static double const _value = -::std::numeric_limits<double>::infinity( );
+    static double const _value = -std::numeric_limits<double>::infinity( );
 #else
     static double const _value = -1.7976931348623157e+308;
 #endif
@@ -262,7 +248,7 @@ inline long double const &
 infimumValueImpl(long double *)
 {
 #ifdef PLATFORM_WINDOWS
-    static long double const _value = -::std::numeric_limits<long double>::infinity( );
+    static long double const _value = -std::numeric_limits<long double>::infinity( );
 #else
     static long double const _value = -1.7976931348623157e+308;
 #endif
@@ -271,4 +257,4 @@ infimumValueImpl(long double *)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_
+#endif  // #ifndef SEQAN_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_
diff --git a/seqan/basic/alphabet_bio.h b/seqan/basic/alphabet_bio.h
index b333b30..c6ca89b 100644
--- a/seqan/basic/alphabet_bio.h
+++ b/seqan/basic/alphabet_bio.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 
 // TODO(holtgrew): Where is the documentation, shouldnt it be here?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_
 
 namespace seqan {
 
@@ -98,4 +98,4 @@ unknownValue()
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_
diff --git a/seqan/basic/alphabet_concept.h b/seqan/basic/alphabet_concept.h
index 459ee88..10c22b4 100644
--- a/seqan/basic/alphabet_concept.h
+++ b/seqan/basic/alphabet_concept.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 
 // SEQAN_NO_GENERATED_FORWARDS
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_
 
 namespace seqan {
 
@@ -55,11 +55,11 @@ namespace seqan {
  * @brief Natural container value.
  *
  * @signature concept AlphabetConcept;
- * 
+ *
  * @section Examples
- * 
+ *
  * Valid expressions (<tt>v</tt> is of type <tt>T</tt>):
- * 
+ *
  * @code{.cpp}
  * unsigned bpv = BitsPerValue<T>::VALUE;
  * @endcode
@@ -69,37 +69,12 @@ namespace seqan {
  * @mfn AlphabetConcept#BitsPerValue
  * @headerfile <seqan/basic.h>
  * @brief Number of bits needed to store a value.
- * 
+ *
  * @signature BitsPerValue<T>::VALUE
- * 
+ *
  * @tparam T A class.
- * 
- * @return TReturn 
- */
-
-/**
-.Concept.AlphabetConcept
-..cat:Alphabets
-..baseconcept:Concept.AssignableConcept
-..baseconcept:Concept.DefaultConstructibleConcept
-..baseconcept:Concept.CopyConstructibleConcept
-..summary:Natural container value.
-..include:seqan/basic.h
-..example.text:Valid expressions ($v$ is of type $T$):
-..example.code:
-unsigned bpv = BitsPerValue<T>::VALUE;
-
-.Metafunction.BitsPerValue
-..concept:Concept.AlphabetConcept
-..cat:Basic
-..summary:Number of bits needed to store a value.
-..signature:BitsPerValue<T>::VALUE
-..param.T:A class.
-...type:Concept.AlphabetConcept
-..returns.param.VALUE:Number of bits needed to store $T$.
-...default:$sizeof<T> * 8$
-..see:Metafunction.ValueSize
-..include:seqan/basic.h
+ *
+ * @return VALUE The number of bits needed to store a value.
  */
 
 // Forwards for Metafunctions and Functions.
@@ -109,7 +84,7 @@ template <typename T> struct BitsPerValue;
 SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructible)(CopyConstructible))
 {
     typedef typename BitsPerValue<TValue>::Type TBitsPerValue;
-    
+
     TValue val, val2;
 
     SEQAN_CONCEPT_USAGE(AlphabetConcept)
@@ -121,7 +96,7 @@ SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructibl
 //      swap(val, val2);
 
         TBitsPerValue b = BitsPerValue<TValue>::VALUE;
-        
+
         ignoreUnusedVariableWarning(b);
     }
 };
@@ -135,7 +110,7 @@ SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructibl
  * @extends AlphabetConcept
  * @extends ComparableConcept
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief Totally strict ordered alphabet.
  *
  * @signature concept OrderedAlphabetConcept;
@@ -156,13 +131,13 @@ SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructibl
  * @mfn OrderedAlphabetConcept#MaxValue
  * @headerfile <seqan/basic.h>
  * @brief Supremum for a given type.
- * 
+ *
  * @signature MaxValue<T>::VALUE
  *
  * @tparam T An ordered type.
- * 
+ *
  * @return VALUE The largest value that <tt>T</tt> can represent.
- * 
+ *
  * @see OrderedAlphabetConcept#maxValue
  */
 
@@ -170,59 +145,54 @@ SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructibl
  * @mfn OrderedAlphabetConcept#MinValue
  * @headerfile <seqan/basic.h>
  * @brief Infimum for a given type.
- * 
+ *
  * @signature MinValue<T>::VALUE
  *
  * @tparam T An ordered type.
- * 
+ *
  * @return VALUE The smallest value that <tt>T</tt> can represent.
- * 
+ *
  * @see OrderedAlphabetConcept#minValue
  */
 
 /*!
  * @fn OrderedAlphabetConcept#supremumValueImpl
  * @brief Implements maxValue.
- * 
+ *
  * @signature T supremumValueImpl(valuePointerTag);
- * 
+ *
  * @param[in] valuePointerTag A pointer that is used as a tag to specify the value type.  The pointer needs not to point
  *                            to a valid object, so it is possible to use a null pointer here.
- * 
+ *
  * @return T A value <tt>inf</tt> that holds: <tt>inf &gt;= i</tt> for all values <tt>i</tt>.
- * 
- * @section Remarks
- * 
+ *
  * This function implements OrderedAlphabetConcept#maxValue.  It is recommended to use OrderedAlphabetConcept#maxValue
  * rather than <tt>supremumValueImpl</tt>.
- * 
+ *
  * @section Status
  *
  * Deprecated, will be removed in favour of OrderedAlphabetConcept#MaxValue.
- * 
+ *
  * @see OrderedAlphabetConcept#maxValue
  */
 
 /*!
  * @fn OrderedAlphabetConcept#maxValue
  * @brief Supremum for a given type.
- * 
- * @signature template <typename T>
- *            T maxValue<T>();
- * 
+ *
+ * @signature T maxValue<T>();
+ *
  * @tparam T The type to get the max value of.
  *
  * @return T A value <tt>inf</tt> that holds: <tt>inf >= i</tt> for all values <tt>i</tt> of type <tt>T</tt>.
- * 
- * @section Remarks
- * 
+ *
  * The function is implemented in supremumValueImpl.  Do not specialize <tt>maxValue</tt>, specialize supremumValueImpl
  * instead!
- * 
+ *
  * @section Status
  *
  * Deprecated, will be removed in favour of MaxValue.
- * 
+ *
  * @see OrderedAlphabetConcept#supremumValueImpl
  * @see OrderedAlphabetConcept#minValue
  * @see OrderedAlphabetConcept#MaxValue
@@ -231,148 +201,45 @@ SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructibl
 /*!
  * @fn OrderedAlphabetConcept#infimumValueImpl
  * @brief Implements minValue.
- * 
+ *
  * @signature T infimumValueImpl(valuePointerTag);
- * 
+ *
  * @param[in] valuePointerTag A pointer that is used as a tag to specify the value type.  The pointer needs not to point
  *                            to a valid object, so it is possible to use a null pointer here.
- * 
+ *
  * @return T A value <tt>inf</tt> that holds: <tt>inf &lt;= i</tt> for all values <tt>i</tt>.
- * 
- * @section Remarks
- * 
+ *
  * This function implements minValue.  It is recommended to use minValue rather than <tt>infimumValueImpl</tt>.
  *
  * @section Status
  *
  * Deprecated, will be removed in favour of MinValue.
- * 
+ *
  * @see OrderedAlphabetConcept#minValue
  */
 
 /*!
  * @fn OrderedAlphabetConcept#minValue
  * @brief Infimum for a given type.
- * 
- * @signature template <typename T>
- *            T minValue<T>();
- * 
+ *
+ * @signature T minValue<T>();
+ *
  * @tparam T An ordered type.
- * 
+ *
  * @return T A value <tt>inf</tt> that holds: <tt>inf &lt;= i</tt> for all values <tt>i</tt> of type <tt>T</tt>.
- * 
- * @section Remarks
- * 
+ *
  * The function is implemented in infimumValueImpl.  Do not specialize <tt>minValue</tt>, specialize infimumValueImpl
  * instead!
  *
  * @section Status
  *
  * Deprecated, will be removed in favour of MinValue.
- * 
+ *
  * @see OrderedAlphabetConcept#infimumValueImpl
  * @see OrderedAlphabetConcept#maxValue
  * @see OrderedAlphabetConcept#MinValue
  */
 
-/**
-.Concept.OrderedAlphabetConcept
-..concept:Concept.OrderedAlphabetConcept
-..cat:Alphabets
-..summary:Totally strict ordered alphabet.
-..baseconcept:Concept.AlphabetConcept
-..baseconcept:Concept.ComparableConcept
-..include:seqan/basic.h
-
-.Function.operator<.concept:Concept.OrderedAlphabetConcept
-
-.Metafunction.MaxValue
-..concept:Concept.OrderedAlphabetConcept
-..cat:Miscellaneous
-..summary:Supremum for a given type.
-..signature:MaxValue<T>::VALUE
-..param.T:An ordered type.
-...type:Concept.OrderedAlphabetConcept
-..returns.param.VALUE:A value $sup$ for which holds: $sup >= i$ for all values $i$ of type $T$.
-..remarks:Note tat
-..see:Function.maxValue
-..include:seqan/basic.h
-
-.Metafunction.MinValue
-..concept:Concept.OrderedAlphabetConcept
-..cat:Miscellaneous
-..summary:Infimum for a given type.
-..signature:MinValue<T>::VALUE
-..param.T:An ordered type.
-...type:Concept.OrderedAlphabetConcept
-..returns.param.VALUE:A value $inf$ for which holds: $inf <= i$ for all values $i$ of type $T$.
-..remarks:Note tat
-..see:Function.minValue
-..include:seqan/basic.h
-
-.Function.supremumValueImpl
-..concept:Concept.OrderedAlphabetConcept
-..hidefromindex
-..cat:Alphabets
-..summary:Implements @Function.maxValue@.
-..signature:supremumValueImpl(value_pointer_tag)
-..param.value_pointer_tag:A pointer that is used as a tag to specify the value type.
-...type:Concept.OrderedAlphabetConcept
-...remarks:The pointer needs not to point to a valid object, so it is possible to use a null pointer here.
-..returns:A value $inf$ that holds: $inf >= i$ for all values $i$.
-..remarks.text:This function implements @Function.maxValue@. 
-It is recommended to use @Function.maxValue@ rather than $supremumValueImpl$.
-..status:deprecated, will be removed in favour of @Metafunction.MaxValue@
-..include:seqan/basic.h
-
-.Function.maxValue
-..concept:Concept.OrderedAlphabetConcept
-..cat:Alphabets
-..summary:Supremum for a given type.
-..signature:maxValue<T>()
-..param.T:An ordered type.
-...type:Concept.OrderedAlphabetConcept
-..returns:A value $inf$ that holds: $inf >= i$ for all values $i$ of type $T$.
-..remarks:
-The function is implemented in @Function.supremumValueImpl@. 
-Do not specialize $maxValue$, specialize @Function.supremumValueImpl@ instead!
-..see:Function.supremumValueImpl
-..status:deprecated, will be removed in favour of @Metafunction.MaxValue@
-..include:seqan/basic.h
-
-// TODO(holtgrew): Rename to minValueImpl?
-
-.Function.infimumValueImpl
-..concept:Concept.OrderedAlphabetConcept
-..hidefromindex
-..cat:Alphabets
-..summary:Implements @Function.minValue@.
-..signature:infimumValueImpl(value_pointer_tag)
-..param.value_pointer_tag:A pointer that is used as a tag to specify the value type.
-...type:Concept.OrderedAlphabetConcept
-...remarks:The pointer needs not to point to a valid object, so it is possible to use a null pointer here.
-..returns:A value $inf$ that holds: $inf <= i$ for all values $i$.
-..remarks.text:This function implements @Function.minValue@. 
-It is recommended to use @Function.minValue@ rather than $infimumValueImpl$.
-..status:deprecated, will be removed in favour of @Metafunction.MinValue@
-..include:seqan/basic.h
-
-.Function.minValue
-..concept:Concept.OrderedAlphabetConcept
-..cat:Alphabets
-..summary:Infimum for a given type.
-..signature:minValue<T>()
-..param.T:An ordered type.
-...type:Concept.OrderedAlphabetConcept
-..returns:A value $inf$ that holds: $inf <= i$ for all values $i$ of type $T$.
-..remarks.text:The function is implemented in @Function.infimumValueImpl@. 
-Do not specialize $minValue$, specialize @Function.infimumValueImpl@ instead!
-..see:Function.infimumValueImpl
-..see:Function.maxValue
-..status:deprecated, will be removed in favour of @Metafunction.MinValue@
-..include:seqan/basic.h
-*/
-
 // Forwards for Metafunctions and Functions.
 template <typename T> struct MinValue;
 template <typename T> struct MaxValue;
@@ -418,27 +285,27 @@ SEQAN_CONCEPT_REFINE(OrderedAlphabetConcept, (TValue), (AlphabetConcept)(Compara
 /*!
  * @mfn FiniteOrderedAlphabetConcept#ValueSize
  * @brief Number of different values a value type object can have.
- * 
- * @signature ValueSize<T>::VALUE
- * 
- * @tparam T A class.
- * 
- * @return VALUE The number of different values the value can have.
- * 
- * @section Remarks
- * 
+ *
+ * @signature ValueSize<T>::Type;
+ * @signature ValueSize<T>::VALUE;
+ *
+ * @tparam T A type to query for its value size.
+ *
+ * @return VALUE The number of different values a value of type T can have.  The type is <tt>Type</tt>.
+ * @return Type  The type of the result <tt>VALUE</tt>.
+ *
  * This function is only defined for integral types like <tt>unsigned</tt>, <tt>int</tt>, or Dna.  For floating point
  * numbers and the 64 bit types <tt>__int64</tt> and <tt>__uint64</tt>, it returns 0 since there is no standard
  * compliant way to return the number of values for these types.
- * 
+ *
  * Note that you cannot get pointers or references to <tt>ValueSize&lt;T&gt;::VALUE</tt> in your program.  You can use
- * @link FiniteOrderedAlphabetConcept#valueSize @endlink in your programs without problems, though.  When you get problems in your tests, use the
- * "unary plus" workaround from the examples section.
- * 
+ * @link FiniteOrderedAlphabetConcept#valueSize @endlink in your programs without problems, though.  When you get
+ * problems in your tests, use the "unary plus" workaround from the examples section.
+ *
  * @section Examples
- * 
+ *
  * The temporary assignment workaround.
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_EQ(ValueSize<bool>::VALUE, 2u);    // Linker error.
  * SEQAN_ASSERT_EQ(+ValueSize<bool>::VALUE, 2u);   // OK
@@ -448,17 +315,15 @@ SEQAN_CONCEPT_REFINE(OrderedAlphabetConcept, (TValue), (AlphabetConcept)(Compara
 
 /*!
  * @fn FiniteOrderedAlphabetConcept#ordValue
- * @headerfile seqan/sequence.h
+ * @headerfile <seqan/sequence.h>
  * @brief Maps an alphabet 1-to-1 to the interval [0..ValueSize).
- * 
+ *
  * @signature T ordValue(value);
- * 
- * @param value Arbitrary character value. Types: SimpleType
- * 
+ *
+ * @param[in] value Arbitrary character value. Types: SimpleType
+ *
  * @return T An unsigned value (result of Size<tt>&lt;typeof(value)&gt;</tt> between 0 and ValueSize of the type of value.
- * 
- * @section Remarks
- * 
+ *
  * This function first converts value to its unsigned value type and after that to an <tt>unsigned int</tt>. You can't
  * use <tt>(unsigned int)c</tt> for a character <tt>c</tt> as on some systems <tt>char</tt> is signed and a <tt>-1</tt>
  * would be mapped to <tt>0xffffffff</tt> instead of <tt>0x000000ff</tt>.
@@ -467,72 +332,16 @@ SEQAN_CONCEPT_REFINE(OrderedAlphabetConcept, (TValue), (AlphabetConcept)(Compara
 /*!
  * @fn FiniteOrderedAlphabetConcept#valueSize
  * @brief Returns size of an alphabet.
- * 
- * @signature template <typename T>
- *            T valueSize<T>();
- * 
- * @tparam T Type to query for value size.
- * 
- * @return T Number of values in type <tt>T</tt>.
- * 
+ *
+ * @signature T1 valueSize<T2>();
+ *
+ * @tparam T2 Type to query for value size.
+ *
+ * @return T1 Number of values in type <tt>T2</tt>.
+ *
  * @see FiniteOrderedAlphabetConcept#ValueSize
  */
 
-/**
-.Concept.FiniteOrderedAlphabetConcept
-..cat:Alphabets
-..summary:An type that is of finite domain and totally ordered and thus has a minimum and maximum value.
-..baseconcept:Concept.OrderedAlphabetConcept
-..include:seqan/basic.h
-
-.Function.ordValue
-..concept:Concept.FiniteOrderedAlphabetConcept
-..summary:Maps an alphabet 1-to-1 to the interval [0..ValueSize).
-..cat:Alphabets
-..signature:ordValue(value)
-..param.value:Arbitrary character value.
-...type:Class.SimpleType
-..returns:An unsigned value (result of @Metafunction.Size@$<typeof(value)>$ between 0 and @Metafunction.ValueSize@ of the type of value.
-..note:This function first converts value to its unsigned value type and after that to an $unsigned int$.
-You can't use $(unsigned int)c$ for a character $c$ as on some systems $char$ is signed and a $-1$ would be mapped to $0xffffffff$ instead of $0x000000ff$.
-..include:seqan/sequence.h
-
-.Function.valueSize
-..concept:Concept.FiniteOrderedAlphabetConcept
-..cat:Alphabets
-..summary:Returns size of an alphabet.
-..signature:valueSize<T>()
-..param.T:Type to query for value size.
-..returns:Number of values in type $T$.
-...type:Metafunction.ValueSize
-..include:seqan/basic.h
-..see:Metafunction.ValueSize
-
-.Metafunction.ValueSize:
-..concept:Concept.FiniteOrderedAlphabetConcept
-..cat:Basic
-..summary:Number of different values a value type object can have.
-..signature:ValueSize<T>::VALUE
-..param.T:A class.
-...type:Concept.FiniteOrderedAlphabetConcept
-..returns.param.VALUE:Value size of $T$.
-..remarks:
-This function is only defined for integral types like $unsigned$, $int$, or @Spec.Dna@.
-For floating point numbers and the 64 bit types $__int64$ and $__uint64$, it returns 0 since there is no standard compliant way to return the number of values for these types.
-..remarks:
-Note that you cannot get pointers or references to $ValueSize<T>::VALUE$ in your program.
-You can use @Function.valueSize@ in your programs without problems, though.
-When you get problems in your tests, use the "unary plus" workaround from the examples section.
-..example.text:The temporary assignment workaround.
-..example.code:
-SEQAN_ASSERT_EQ(ValueSize<bool>::VALUE, 2u);    // Linker error.
-SEQAN_ASSERT_EQ(+ValueSize<bool>::VALUE, 2u);  // OK
-SEQAN_ASSERT_EQ(valueSize<bool>(), 2u);         // OK
-..see:Function.valueSize
-..see:Metafunction.Value
-..include:seqan/basic.h
- */
-
 // Forwards for Metafunctions and Functions.
 template <typename T> struct ValueSize;
 template <typename T> typename ValueSize<T>::Type valueSize();
@@ -557,7 +366,7 @@ SEQAN_CONCEPT_REFINE(FiniteOrderedAlphabetConcept, (TValue), (OrderedAlphabetCon
 
         // alphabet must be non-empty
         SEQAN_STATIC_ASSERT_MSG(static_cast<TSize>(0) < ValueSize<TValue>::VALUE, "Alphabet size be greater than zero.");
-        
+
         // convert integer to alphabet value
         val = 0;
         val = size;
@@ -576,85 +385,42 @@ SEQAN_CONCEPT_REFINE(FiniteOrderedAlphabetConcept, (TValue), (OrderedAlphabetCon
  * @concept AlphabetWithGapsConcept
  * @extends AlphabetConcept
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief An alphabet that includes a specific gap character.
  */
 
 /*!
  * @fn AlphabetWithGapsConcept#gapValueImpl
  * @brief Implements gapValue.
- * 
+ *
  * @signature T gapValueImpl(valuePointerTag);
- * 
- * @param valuePointerTag A pointer that is used as a tag to specify the value type.  The pointer needs not to point
- *                        to a valid object, so it is possible to use a null pointer here.
- * 
+ *
+ * @param[in] valuePointerTag A pointer that is used as a tag to specify the value type.  The pointer needs not to
+ *                            point to a valid object, so it is possible to use a null pointer here.
+ *
  * @return T A gap character.
- * 
- * @section Remarks
- * 
+ *
  * This function implements gapValue.  It is recommended to use gapValue rather than <tt>gapValueImpl</tt>.
- * 
+ *
  * @see AlphabetWithGapsConcept#gapValue
  */
 
 /*!
  * @fn AlphabetWithGapsConcept#gapValue
  * @brief Return the "gap" value from an alphabet.
- * 
- * @signature template <typename T>
- *            T gapValue<T>();
- * 
+ *
+ * @signature T gapValue<T>();
+ *
  * @tparam T The alphabet type to query the gap value from.
- * 
+ *
  * @return T The gap character.
- * 
- * @section Remarks
- * 
+ *
  * The function is implemented in gapValueImpl.  Do not specialize <tt>gapValue</tt>, specialize link gapValueImpl
  * instead!
- * 
+ *
  * @see AlphabetWithGapsConcept#gapValueImpl
  */
 
-/**
-.Concept.AlphabetWithGapsConcept
-..cat:Alphabets
-..baseconcept:Concept.AlphabetConcept
-..summary:An alphabet that includes a specific gap character.
-..include:seqan/basic.h
-
-.Function.gapValue
-..concept:Concept.AlphabetWithGapsConcept
-..cat:Alphabets
-..cat:Alignments
-..summary:Return the "gap" value from an alphabet.
-..signature:gapValue<T>()
-..param.T:The alphabet type to query the "gap" value from.
-...type:Concept.AlphabetWithGapsConcept
-..returns:The gap character.
-..remarks.text:The function is implemented in @Function.gapValueImpl@.
-Do not specialize $gapValue$, specialize @Function.gapValueImpl@ instead!
-..see:Function.gapValueImpl
-..include:seqan/basic.h
-
-.Function.gapValueImpl
-..concept:Concept.AlphabetWithGapsConcept
-..hidefromindex
-..cat:Alphabets
-..cat:Alignments
-..summary:Implements @Function.gapValue@.
-..signature:gapValueImpl(valuePointerTag)
-..param.valuePointerTag:A pointer that is used as a tag to specify the value type.
-....type:Concept.AlphabetWithGapsConcept
-...remarks:The pointer needs not to point to a valid object, so it is possible to use a null pointer here.
-..returns:A gap character.
-..see:Function.gapValue
-..remarks.text:This function implements @Function.gapValue@.
-It is recommended to use @Function.gapValue@ rather than $gapValueImpl$.
-..include:seqan/basic.h
-*/
-
 // Forwards for Metafunctions and Functions.
 template <typename T> T gapValue();
 template <typename T> T gapValueImpl(T *);
@@ -675,75 +441,40 @@ SEQAN_CONCEPT_REFINE(AlphabetWithGapsConcept, (TValue), (AlphabetConcept))
  * @concept AlphabetWithUnknownValueConcept
  * @extends AlphabetConcept
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief An alphabet which includes a specific "unknown" character.
  */
 
 /*!
  * @fn AlphabetWithUnknownValueConcept#unknownValue
- * 
+ *
  * @brief Return the "unknown" value from an alphabet.
- * 
- * @signature template <typename T>
- *            T unknownValue<T>();
- * 
+ *
+ * @signature T unknownValue<T>();
+ *
  * @tparam T The alphabet type to query the unknown value from.
- * 
+ *
  * @return TReturn The "unknown" value.
- * 
+ *
  * @see AlphabetWithUnknownValueConcept#unknownValueImpl
  */
 
 /*!
  * @fn AlphabetWithUnknownValueConcept#unknownValueImpl
  * @brief Implements unknownValue.
- * 
+ *
  * @signature T gapValueImpl(valuePointerTag)
- * 
- * @param valuePointerTag A pointer that is used as a tag to specify the value type.  The pointer needs not to point
- *                        to a valid object, so it is possible to use a null pointer here.
- * 
+ *
+ * @param[in] valuePointerTag A pointer that is used as a tag to specify the value type.  The pointer needs not to
+ *                            point to a valid object, so it is possible to use a null pointer here.
+ *
  * @return TReturn A "unknown" character.
- * 
- * @section Remarks
- * 
+ *
  * This function implements unknownValue.  It is recommended to use gapValue rather than <tt>gapValueImpl</tt>.
- * 
+ *
  * @see AlphabetWithUnknownValueConcept#unknownValue
  */
 
-/**
-.Concept.AlphabetWithUnknownValueConcept
-..cat:Alphabets
-..baseconcept:Concept.AlphabetConcept
-..summary:An alphabet which includes a specific "unknown" character.
-..include:seqan/basic.h
-
-.Function.unknownValueImpl
-..concept:Concept.AlphabetWithUnknownValueConcept
-..hidefromindex
-..cat:Alphabets
-..summary:Implements @Function.unknownValue@.
-..signature:gapValueImpl(valuePointerTag)
-..param.valuePointerTag:A pointer that is used as a tag to specify the value type.
-...type:Concept.AlphabetWithUnknownValueConcept
-...remarks:The pointer needs not to point to a valid object, so it is possible to use a null pointer here.
-..returns:A "unknown" character.
-..see:Function.unknownValue
-..remarks.text:This function implements @Function.unknownValue@.
-It is recommended to use @Function.gapValue@ rather than $gapValueImpl$.
-..include:seqan/basic.h
-
-.Function.unknownValue
-..concept:Concept.AlphabetWithUnknownValueConcept
-..cat:Alphabets
-..summary:Return the "unknown" value from an alphabet.
-..signature:unknownValue<T>()
-..param.T:The alphabet type to query the "unknown" value from.
-...type:Concept.AlphabetWithUnknownValueConcept
-..returns:The "unknown" value.
- */
-
 // Forwards for Metafunctions and Functions.
 template <typename T> T unknownValue();
 template <typename T> T unknownValueImpl(T *);
@@ -764,7 +495,7 @@ SEQAN_CONCEPT_REFINE(AlphabetWithUnknownValueConcept, (TValue), (AlphabetConcept
  * @concept AlphabetWithQualitiesConcept
  * @extends AlphabetConcept
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief An alphabet where qualities can be attached to the characters.
  */
 
@@ -772,12 +503,12 @@ SEQAN_CONCEPT_REFINE(AlphabetWithUnknownValueConcept, (TValue), (AlphabetConcept
  * @mfn AlphabetWithQualitiesConcept#HasQualities
  * @headerfile <seqan/basic.h>
  * @brief Return whether the given type stores qualities besides the alphabet.
- * 
+ *
  * @signature HasQualities<TAlphabet>::VALUE;
  * @signature HasQualities<TAlphabet>::Type;
- * 
+ *
  * @tparam TAlphabet The alphabe to query.
- * 
+ *
  * @return VALUE <tt>true</tt> or <tt>false</tt>
  * @return Type  <tt>True</tt> or <tt>False</tt>
  */
@@ -785,11 +516,11 @@ SEQAN_CONCEPT_REFINE(AlphabetWithUnknownValueConcept, (TValue), (AlphabetConcept
 /*!
  * @mfn AlphabetWithQualitiesConcept#QualityValueSize
  * @brief Return the number of quality values in characters from alphabet with qualities.
- * 
+ *
  * @signature QualityValueSize<TAlphabet>::VALUE;
- * 
+ *
  * @tparam TAlphabet The alphabet to query for its value size.
- * 
+ *
  * @return VALUE The cardinality of the set of qualities.
  */
 
@@ -798,13 +529,13 @@ SEQAN_CONCEPT_REFINE(AlphabetWithUnknownValueConcept, (TValue), (AlphabetConcept
  * @brief Returns the quality of a character from an alphabet with integrated quality, e.g. the quality associated with
  *        a specified element from a sequence.
  * @signature int getQualityValue(c);
- * 
+ *
  * @param[in] c Character to retrieve the quality from.
- * 
+ *
  * @return int Quality value of <tt>c</tt>.  The quality value is an <tt>int</tt> value between 0 and 62 (inclusive).
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * String<Dna5Q> seq = "TATA";
  * // Assign quality value to first 'T' in sequence seq
@@ -822,89 +553,21 @@ SEQAN_CONCEPT_REFINE(AlphabetWithUnknownValueConcept, (TValue), (AlphabetConcept
  * @fn AlphabetWithQualitiesConcept#assignQualityValue
  * @brief Assigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a
  *        sequence.
- * 
+ *
  * @signature void assignQualityValue(c, q);
- * 
+ *
  * @param[out] c Target character to assign quality to.
  * @param[in] q  Quality to assign to the character.  The quality value is an integral value between 0 and 62
  *               (inclusive).
- * 
- * @section Remarks
- * 
+ *
  * If <tt>q</tt> is a <tt>char</tt> then <tt>'!'</tt> is subtracted from <tt>q</tt>.  This is useful for ASCII encoded
  * PHRED scores.
- * 
+ *
  * @see AlphabetWithQualitiesConcept#getQualityValue
  * @see convertQuality
  * @see assignQualities
  */
 
-/**
-.Concept.AlphabetWithQualitiesConcept
-..cat:Alphabets
-..baseconcept:Concept.AlphabetConcept
-..summary:An alphabet where qualities can be attached to the characters.
-..include:seqan/basic.h
-
-.Metafunction.QualityValueSize
-..concept:Concept.AlphabetWithQualitiesConcept
-..cat:Alphabets
-..summary:Return the number of quality values in characters from alphabet with qualities.
-..signature:QualityValueSize<TAlphabet>::VALUE
-..param.TAlphabet:The alphabet to query for its value size.
-...type:Concept.AlphabetWithQualitiesConcept
-..returns:The cardinality of the set of qualities.
-..include:seqan/basic.h
-
-.Metafunction.HasQualities
-..concept:Concept.AlphabetWithQualitiesConcept
-..cat:Alphabets
-..summary:Return whether the given type stores qualities besides the alphabet.
-..signature:HasQualities<TAlphabet>::VALUE
-..signature:HasQualities<TAlphabet>::Type
-..param.TAlphabet:The alphabe to query.
-..returns:$true$, $false$, $True$, or $False$.
-..include:seqan/basic.h
-
-.Function.getQualityValue
-..concept:Concept.AlphabetWithQualitiesConcept
-..cat:Alphabets
-..signature:getQualityValue(c)
-..summary:Returns the quality of a character from an alphabet with integrated quality, e.g. the quality associated with a specified element from a sequence.
-..param.c:Character to retrieve the quality from.
-...type:Concept.AlphabetWithQualitiesConcept
-..returns:Quality value of $c$.
-...type:nolink:int
-...remarks:The quality value is an integral value between 0 and 62 (inclusive).
-..see:Function.assignQualityValue
-..see:Function.convertQuality
-..include:seqan/basic.h
-..example.code:
-    String<Dna5Q> seq = "TATA";
-    // Assign quality value to first 'T' in sequence seq
-    assignQualityValue(seq[0], 35);
-    // Print quality value of first 'T', and default quality value of first 'A'
-    std::cout << getQualityValue(seq[0]) << std::endl; // Defined as 35
-    std::cout << getQualityValue(seq[1]) << std::endl; // Default value 60
-
-
-.Function.assignQualityValue
-..concept:Concept.AlphabetWithQualitiesConcept
-..cat:Alphabets
-..signature:assignQualityValue(c, q)
-..summary:Assigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a sequence.
-..param.c:Target character to assign quality to.
-...type:Concept.AlphabetWithQualitiesConcept
-..param.q:Quality to assign to the character.
-...type:nolink:int
-...type:nolink:char
-...remarks:The quality value is an integral value between 0 and 62 (inclusive).
-..remarks:If $q$ is a $char$ then $'!'$ is subtracted from $q$. This is useful for ASCII encoded PHRED scores.
-..see:Function.getQualityValue
-..see:Function.convertQuality
-..include:seqan/basic.h
- */
-
 // TODO(holtgrew): What about different quality types? Guess scaling? Look at how other packages do this.
 
 SEQAN_CONCEPT_REFINE(AlphabetWithQualitiesConcept, (TValue), (AlphabetConcept))
@@ -920,4 +583,4 @@ SEQAN_CONCEPT_REFINE(AlphabetWithQualitiesConcept, (TValue), (AlphabetConcept))
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_
diff --git a/seqan/basic/alphabet_math.h b/seqan/basic/alphabet_math.h
index 61736a2..ec9d28c 100644
--- a/seqan/basic/alphabet_math.h
+++ b/seqan/basic/alphabet_math.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -272,6 +272,32 @@ minValue(T /*tag*/)
     return infimumValueImpl(_tag);
 }
 
+// ----------------------------------------------------------------------------
+// Function isNegative()
+// ----------------------------------------------------------------------------
+
+// to remove '... < 0 is always false' warning
+template <typename T>
+inline bool
+isNegative(T, False)
+{
+    return false;
+}
+
+template <typename T>
+inline bool
+isNegative(T t, True)
+{
+    return t < 0;
+}
+
+template <typename T>
+inline bool
+isNegative(T t)
+{
+    return isNegative(t, typename IsSameType<T, typename MakeSigned_<T>::Type>::Type());
+}
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_BASIC_ALPHABET_MATH_H_
diff --git a/seqan/basic/alphabet_profile.h b/seqan/basic/alphabet_profile.h
index cebb8d2..74103c5 100644
--- a/seqan/basic/alphabet_profile.h
+++ b/seqan/basic/alphabet_profile.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,10 +34,10 @@
 // Profile alphabet character code.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_
 
-#include <seqan/misc/misc_memset.h>
+#include <seqan/misc/memset.h>
 
 namespace seqan {
 
@@ -57,14 +57,14 @@ struct IteratorProxy;
 
 /*!
  * @class ProfileChar
- * 
- * @headerfile seqan/basic.h
- * 
+ *
+ * @headerfile <seqan/basic.h>
+ *
  * @brief Alphabet type for profiles over another alphabet.
- * 
+ *
  * @signature template <typename TValue[, typename TCount[, typename TSpec]]>
  *            class ProfileChar;
- * 
+ *
  * @tparam TValue The underlying alphabet type.
  * @tparam TCount The type to use for counting, default: <tt>unsigned int</tt>.
  * @tparam TSpec  Specialization tag, default: <tt>void</tt>
@@ -72,27 +72,10 @@ struct IteratorProxy;
 
 /*!
  * @var VariableType ProfileChar::count[]
- * 
+ *
  * @brief Array of ValueSize elements, giving counts in profile.
  */
 
-/**
-.Class.ProfileChar
-..summary:Alphabet type for profiles over another alphabet.
-..cat:Alphabets
-..signature:ProfileChar<TValue, TCount[, TSpec=void]>
-..param.TValue:The underlying alphabet type.
-..param.TCount:The type to use for counting.
-...default:nolink:$unsigned int$
-..param.TSpec:Specialization tag.
-...default:nolink:$void$
-..include:seqan/basic.h
-
-.Memvar.ProfileChar#count[]
-..class:Class.ProfileChar
-..summary:Array of @Metafunction.ValueSize@ elements, giving counts in profile.
- */
-
 template <typename TValue, typename TCount = unsigned, typename TSpec = void>
 class ProfileChar;
 
@@ -163,7 +146,7 @@ class ProfileChar
 
     operator char()
     {
-        typename Size<ProfileChar>::Type maxIndex = _getMaxIndex(*this);
+        typename Size<ProfileChar>::Type maxIndex = getMaxIndex(*this);
         return (maxIndex == ValueSize<ProfileChar>::VALUE - 1) ? gapValue<char>() : (char) TValue(maxIndex);
     }
 };
@@ -179,17 +162,14 @@ class ProfileChar
 /*!
  * @mfn ProfileChar#ValueSize
  * @brief Number of different values a value type object can have.
- * 
+ *
  * @signature ValueSize<T>::VALUE;
- * 
+ *
  * @tparam T The type to query.
- * 
+ *
  * @return VALUE Number of different values T can have.
  */
 
-///.Metafunction.ValueSize.param.T.type:Class.ProfileChar
-///.Metafunction.ValueSize.class:Class.ProfileChar
-
 template <typename TValue, typename TCount, typename TSpec>
 struct ValueSize<ProfileChar<TValue, TCount, TSpec> >
 {
@@ -204,36 +184,21 @@ struct ValueSize<ProfileChar<TValue, TCount, TSpec> >
 /*!
  * @mfn ProfileChar#SourceValue
  * @brief Returns underlying value for ProfileChar.
- * 
+ *
  * @signature SourceValue<T>::Type
- * 
+ *
  * @tparam T Type to query.
- * 
+ *
  * @return Type The type of the underlying character.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * typedef ProfileChar<Dna5>               TProfileChar;
  * typedef SourceValue<TProfileChar>::Type TType;  // Is Dna.
  * @endcode
  */
 
-/**
-.Metafunction.SourceValue
-..class:Class.ProfileChar
-..cat:Alphabets
-..summary:Returns underlying value for @Class.ProfileChar@.
-..signature:SourceValue<T>::Type
-..param.T:Type to query.
-...type:Class.ProfileChar
-..returns:The type of the underlying character.
-..example.code:
-typedef ProfileChar<Dna5>               TProfileChar;
-typedef SourceValue<TProfileChar>::Type TType;  // Is Dna.
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct SourceValue;
 
@@ -293,13 +258,17 @@ operator!=(ProfileChar<TValue, TCount, TSpec> const & lhs,
 // Function empty()
 // ----------------------------------------------------------------------------
 
-// TODO(holtgrew): Document.
-
-// Check if there are only gaps.
-
+/*!
+ * @fn ProfileChar#empty
+ * @brief Check whether there are only gaps in the representation of the ProfileChar.
+ *
+ * @signature bool empty(c);
+ *
+ * @param  c    ProfileChar to query.
+ * @return bool Whether or not the ProfileChar only contains gaps.
+ */
 template <typename TSourceValue, typename TSourceCount, typename TSourceSpec>
-inline bool
-empty(ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
+bool empty(ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
 {
     typedef typename ValueSize<ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const>::Type TSize;
 
@@ -310,12 +279,22 @@ empty(ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
 }
 
 // ----------------------------------------------------------------------------
-// Helper Function _getMaxIndex()
+// Helper Function getMaxIndex()
 // ----------------------------------------------------------------------------
 
+/*!
+ * @fn ProfileChar#getMaxIndex
+ * @brief Return number of dominating entry in ProfileChar.
+ *
+ * @signature TSize getMaxIndex(c);
+ *
+ * @param[in] c     ProfileChar to query for its dominating entry.
+ * @return    TSize index (with the @link FiniteOrderedAlphabetConcept#ordValue @endlink) of the dominating character
+ *                  in <tt>c</tt>
+ */
 template <typename TSourceValue, typename TSourceCount, typename TSourceSpec>
-inline typename Size<ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const>::Type
-_getMaxIndex(ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
+typename Size<ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const>::Type
+getMaxIndex(ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
 {
     typedef ProfileChar<TSourceValue, TSourceCount, TSourceSpec> TProfileChar;
     typedef typename Size<TProfileChar>::Type TSize;
@@ -333,12 +312,20 @@ _getMaxIndex(ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source
 }
 
 // ----------------------------------------------------------------------------
-// Helper Function _totalCount()
+// Helper Function totalCount()
 // ----------------------------------------------------------------------------
 
+/*!
+ * @fn ProfileChar#totalCount
+ * @brief Return sum of counts in ProfileChar.
+ *
+ * @signature TCount totalCount(c);
+ *
+ * @param[in] c      ProfileChar to query.
+ * @return    TCount Total number of characters represented by <tt>c</tt>.
+ */
 template <typename TSourceValue, typename TSourceCount, typename TSourceSpec>
-inline TSourceCount
-_totalCount(ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
+TSourceCount totalCount(ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
 {
     typedef ProfileChar<TSourceValue, TSourceCount, TSourceSpec> TProfileChar;
     typedef typename Size<TProfileChar>::Type TSize;
@@ -360,7 +347,7 @@ inline void
 assign(SimpleType<TTargetValue, TTargetSpec> & target,
        ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
 {
-    target.value = _getMaxIndex(source);
+    target.value = getMaxIndex(source);
 }
 
 // ----------------------------------------------------------------------------
@@ -372,7 +359,7 @@ inline typename Convert<TTarget, ProfileChar<TSourceValue, TSourceCount, TSource
 convertImpl(Convert<TTarget, T> const &,
             ProfileChar<TSourceValue, TSourceCount, TSourceSpec> const & source)
 {
-    return (_getMaxIndex(source) == ValueSize<TSourceValue>::VALUE) ? convertImpl(Convert<TTarget, T>(), '-') : convertImpl(Convert<TTarget, T>(), TSourceValue(_getMaxIndex(source)));
+    return (getMaxIndex(source) == ValueSize<TSourceValue>::VALUE) ? convertImpl(Convert<TTarget, T>(), '-') : convertImpl(Convert<TTarget, T>(), TSourceValue(getMaxIndex(source)));
 }
 
 // ----------------------------------------------------------------------------
@@ -392,4 +379,4 @@ operator<<(TStream & os, ProfileChar<TValue, TCount, TSpec> const & rhs)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_
diff --git a/seqan/basic/alphabet_qualities.h b/seqan/basic/alphabet_qualities.h
index e84a635..6112dd5 100644
--- a/seqan/basic/alphabet_qualities.h
+++ b/seqan/basic/alphabet_qualities.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // Definitions for piggybacking qualities in free bits of bytes.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
 
 // TODO(holtgrew): Should the documentation be here?
 
@@ -76,8 +76,8 @@ struct QualityValueSize<TValue const> : QualityValueSize<TValue>
 template <typename TValue>
 struct HasQualities
 {
-    enum { VALUE = false };
     typedef False Type;
+    static const bool VALUE = false;
 };
 
 // ============================================================================
@@ -105,39 +105,25 @@ struct HasQualities
 /*!
  * @fn convertQuality
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief Convert an integer quality value into its ASCII representation for FASTQ (Phred scale).
- * 
+ *
  * @signature void convertQuality(c, q);
- * 
+ *
  * @param[in]  q Value of the quality to convert.  The quality value is an integral value between 0 and 62
  *               (inclusive), <tt>int</tt>.
  * @param[out] c Character to store the quality in, <tt>char</tt>.
- * 
+ *
  * @see AlphabetWithQualitiesConcept#getQualityValue
  * @see AlphabetWithQualitiesConcept#assignQualityValue
  */
 
-/**
-.Function.convertQuality
-..cat:Alphabets
-..signature:convertQuality(c, q)
-..summary:Convert an integer quality value into its ASCII representation for FASTQ (Phred scale).
-..param.c:Character to store the quality in.
-...type:nolink:$char$
-..param.q:Value of the quality to convert.
-...remarks:The quality value is an integral value between 0 and 62 (inclusive).
-...type:nolink:$int$
-..see:Function.getQualityValue
-..include:seqan/basic.h
- */
-
-inline 
-void convertQuality(char & c, int q) 
+inline
+void convertQuality(char & c, int q)
 {
     c = '!' + char(q);
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
diff --git a/seqan/basic/alphabet_residue.h b/seqan/basic/alphabet_residue.h
index 4aa1ac2..c05d254 100644
--- a/seqan/basic/alphabet_residue.h
+++ b/seqan/basic/alphabet_residue.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,8 +45,8 @@
 
 // TODO(holtgrew): Add RnaQ and Rna5Q? Can we create a tag/type for Dna and Rna that is then differentiated with one additional tag?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_
 
 namespace seqan {
 
@@ -76,40 +76,20 @@ template <typename T> struct BaseAlphabet;
  * @extends SimpleType
  * @headerfile <seqan/basic.h>
  * @brief Alphabet for DNA.
- * 
+ *
  * @signature typedef SimpleType<unsigned char, Dna_> Dna;
- * 
- * @section Remarks
- * 
+ *
  * The ValueSize of <tt>Dna</tt> is 4.  The nucleotides are enumerated this way: <tt>'A' = 0, 'C' = 1, 'G' = 2, 'T' =
  * 3</tt>.
- * 
+ *
  * Objects of type <tt>Dna</tt> can be converted to various other types and vice versa.  An object that has a value not
  * in <tt>{'A', 'C', 'G', 'T'}</tt> is converted to <tt>'A'</tt>.
- * 
+ *
  * @see Dna5
  * @see DnaString
  * @see DnaIterator
  */
 
-/**
-.Spec.Dna
-..cat:Alphabets
-..summary:Alphabet for DNA.
-..general:Class.SimpleType
-..signature:Dna
-..remarks:
-...text:The @Metafunction.ValueSize@ of $Dna$ is 4. 
-The nucleotides are enumerated this way: $'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3$.
-...text:Objects of type $Dna$ can be converted to various other types and vice versa. 
-An object that has a value not in ${'A', 'C', 'G', 'T'}$ is converted to $'A'$.
-...text:$Dna$ is typedef for $SimpleType<char,Dna_>$, while $Dna_$ is a helper
-specialization tag class.
-..see:Metafunction.ValueSize
-..see:Spec.Dna5
-..include:seqan/basic.h
-*/
-
 struct Dna_ {};
 typedef SimpleType<unsigned char, Dna_> Dna;
 
@@ -136,40 +116,20 @@ struct BitsPerValue< Dna >
  * @extends SimpleType
  * @headerfile <seqan/basic.h>
  * @brief Alphabet for DNA including 'N' character.
- * 
+ *
  * @signature typedef SimpleType<unsigned char, Dna5_> Dna5;
- * 
- * @section Remarks
- * 
+ *
  * The @link FiniteOrderedAlphabetConcept#ValueSize @endlink of <tt>Dna5</tt> is 5.  The nucleotides are enumerated this
  * way: <tt>'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3</tt>.  The 'N' character ("unkown nucleotide") is encoded by 4.
- * 
+ *
  * Objects of type <tt>Dna5</tt> can be converted to various other types and vice versa.  An object that has a value not
  * in <tt>{'A', 'C', 'G', 'T'}</tt> is converted to <tt>'N'</tt>.
- * 
+ *
  * @see Dna5Iterator
  * @see Dna5String
  * @see Dna
  */
 
-/**
-.Spec.Dna5:
-..cat:Alphabets
-..summary:Alphabet for DNA including 'N' character.
-..general:Class.SimpleType
-..signature:Dna5
-..remarks:
-...text:The @Metafunction.ValueSize@ of $Dna5$ is 5. 
-The nucleotides are enumerated this way: $'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3$. 
-The 'N' character ("unkown nucleotide") is encoded by 4.
-...text:Objects of type $Dna5$ can be converted to various other types and vice versa. 
-An object that has a value not in ${'A', 'C', 'G', 'T'}$ is converted to $'N'$.
-...text:$Dna5$ is typedef for $SimpleType<char,Dna5_>$, while $Dna5_$ is a helper
-specialization tag class.
-..see:Metafunction.ValueSize
-..include:seqan/basic.h
-*/
-
 struct Dna5_ {};
 typedef SimpleType<unsigned char, Dna5_> Dna5;
 
@@ -204,39 +164,23 @@ unknownValueImpl(Dna5 *)
  * @headerfile <seqan/basic.h>
  * @implements AlphabetWithQualitiesConcept
  * @brief Alphabet for DNA plus PHRED quality.
- * 
+ *
  * @signature typedef SimpleType<unsigned char, DnaQ_> DnaQ;
- * 
- * @section Remarks
- * 
+ *
  * The ValueSize of <tt>DnaQ</tt> is 4.  The nucleotides are enumerated this way: <tt>'A' = 0, 'C' = 1, 'G' = 2, 'T' =
  * 3</tt>.
- * 
+ *
  * Objects of type <tt>DnaQ</tt> can be converted to various other types and vice versa.
- * 
+ *
  * Note that the default quality value is set to 60.
- * 
+ *
  * @see Dna5Q
  * @see Dna
  */
 
-/**
-.Spec.DnaQ:
-..implements:Concept.AlphabetWithQualitiesConcept
-..cat:Alphabets
-..summary:Alphabet for DNA plus PHRED quality.
-..general:Class.SimpleType
-..signature:DnaQ
-..remarks:
-...text:The @Metafunction.ValueSize@ of $DnaQ$ is 4. 
-The nucleotides are enumerated this way: $'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3$.
-...text:Objects of type $DnaQ$ can be converted to various other types and vice versa. 
-...text:$DnaQ$ is typedef for $SimpleType<char,DnaQ_>$, while $DnaQ_$ is a helper
-specialization tag class.
-...text:Note that the default quality value is set to 60.
-..see:Metafunction.ValueSize
-..see:Spec.Dna5Q
-*/
+#ifndef SEQAN_DEFAULT_QUALITY
+#define SEQAN_DEFAULT_QUALITY 40
+#endif
 
 struct DnaQ_ {};
 typedef SimpleType <unsigned char, DnaQ_> DnaQ;
@@ -260,8 +204,8 @@ template <> struct BitsPerValue<DnaQ>
 
 template <> struct HasQualities<DnaQ>
 {
-    enum { VALUE = true };
     typedef True Type;
+    static const bool VALUE = true;
 };
 
 template <>
@@ -276,17 +220,17 @@ struct QualityValueSize<DnaQ>
     enum { VALUE = 63 }; // 64 - 1 (N)
 };
 
-///.Function.getQualityValue.param.c.type:Spec.DnaQ
-///.Function.getQualityValue.class:Spec.DnaQ
+template <typename TValue>
+inline int getQualityValue(TValue const &)
+{
+    return 0;
+}
 
-inline int getQualityValue(DnaQ const & c) 
+inline int getQualityValue(DnaQ const & c)
 {
     return c.value >> 2;
 }
 
-///.Function.assignQualityValue.param.c.type:Spec.DnaQ
-///.Function.assignQualityValue.class:Spec.DnaQ
-
 inline
 void assignQualityValue(DnaQ & c, int q)
 {
@@ -323,40 +267,20 @@ void assignQualityValue(char & q, DnaQ c)
  * @headerfile <seqan/basic.h>
  * @implements AlphabetWithQualitiesConcept
  * @brief Alphabet for DNA plus PHRED quality including 'N' character.
- * 
+ *
  * @signature typedef SimpleType<unsigned char, Dna5Q_> Dna5Q;
- * 
- * @section Remarks
- * 
+ *
  * The ValueSize of <tt>Dna5Q</tt> is 5.  The nucleotides are enumerated this way: <tt>'A' = 0, 'C' = 1, 'G' = 2, 'T' =
  * 3</tt>. The 'N' character ("unknown nucleotide") is encoded by 4.
- * 
+ *
  * Objects of type <tt>Dna5</tt> can be converted to various other types and vice versa.
- * 
- * Note that the default quality value is set to 60.
- * 
+ *
+ * Note that the default quality value is set to 40.
+ *
  * @see Dna5
  * @see DnaQ
  */
 
-/**
-.Spec.Dna5Q
-..implements:Concept.AlphabetWithQualitiesConcept
-..cat:Alphabets
-..summary:Alphabet for DNA plus PHRED quality including 'N' character.
-..general:Class.SimpleType
-..signature:Dna5Q
-..remarks:
-...text:The @Metafunction.ValueSize@ of $Dna5Q$ is 5. 
-The nucleotides are enumerated this way: $'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3$. 
-The 'N' character ("unkown nucleotide") is encoded by 4.
-...text:Objects of type $Dna5$ can be converted to various other types and vice versa. 
-...text:$Dna5Q$ is typedef for $SimpleType<char,Dna5Q_>$, while $Dna5Q_$ is a helper
-specialization tag class.
-...text:Note that the default quality value is set to 60.
-..see:Metafunction.ValueSize
-*/
-
 struct Dna5Q_ {};
 typedef SimpleType <unsigned char, Dna5Q_> Dna5Q;
 
@@ -381,8 +305,8 @@ template <> struct BitsPerValue<Dna5Q>
 
 template <> struct HasQualities<Dna5Q>
 {
-    enum { VALUE = true };
     typedef True Type;
+    static const bool VALUE = true;
 };
 
 template <>
@@ -404,10 +328,7 @@ unknownValueImpl(Dna5Q *)
     return _result;
 }
 
-///.Function.getQualityValue.param.c.type:Spec.Dna5Q
-///.Function.getQualityValue.class.Spec.Dna5Q
-
-inline int getQualityValue(Dna5Q const &c) 
+inline int getQualityValue(Dna5Q const &c)
 {
     // We use a lookup table to extract the qualities from DNA5Q.  The lookup
     // table based code is equivalent to the following line:
@@ -433,9 +354,6 @@ inline int getQualityValue(Dna5Q const &c)
     return table[c.value];
 }
 
-///.Function.assignQualityValue.param.c.type:Spec.Dna5Q
-///.Function.assignQualityValue.class:Spec.Dna5Q
-
 inline
 void assignQualityValue(Dna5Q &c, int q)
 {
@@ -446,8 +364,8 @@ void assignQualityValue(Dna5Q &c, int q)
         c.value = (c.value & 3) | (q << 2);
 }
 
-inline 
-void assignQualityValue(Dna5Q &c, char q) 
+inline
+void assignQualityValue(Dna5Q &c, char q)
 {
     int q1 = static_cast<int>(q - '!');
     if (q1 < 0) q1 = 0;
@@ -456,7 +374,7 @@ void assignQualityValue(Dna5Q &c, char q)
     assignQualityValue(c, q1);
 }
 
-inline 
+inline
 void assignQualityValue(char & q, Dna5Q c)
 {
     q = '!' + getQualityValue(c);
@@ -471,42 +389,22 @@ void assignQualityValue(char & q, Dna5Q c)
  * @extends SimpleType
  * @headerfile <seqan/basic.h>
  * @brief Alphabet for RNA.
- * 
+ *
  * @signature typedef SimpleType<unsigned char, Rna_> Rna;
- * 
- * @section Remarks
- * 
+ *
  * The ValueSize of <tt>Rna</tt> is 4.  The nucleotides are enumerated this way: <tt>'A' = 0, 'C' = 1, 'G' = 2, 'U' =
  * 3</tt>.
- * 
+ *
  * Objects of type <tt>Rna</tt> can be converted to various other types and vice versa.  An object that has a value not
  * in <tt>{'A', 'C', 'G', 'U'}</tt> is converted to <tt>'A'</tt>.
- * 
+ *
  * <tt>Rna</tt> is typedef for <tt>SimpleType<char,Rna_></tt>, while <tt>Rna_</tt> is a helper specialization tag class.
- * 
+ *
  * @see Rna5
  * @see RnaString
  * @see RnaIterator
  */
 
-/**
-.Spec.Rna:
-..cat:Alphabets
-..summary:Alphabet for RNA.
-..general:Class.SimpleType
-..signature:Rna
-..remarks:
-...text:The @Metafunction.ValueSize@ of $Rna$ is 4. 
-The nucleotides are enumerated this way: $'A' = 0, 'C' = 1, 'G' = 2, 'U' = 3$.
-...text:Objects of type $Rna$ can be converted to various other types and vice versa. 
-An object that has a value not in ${'A', 'C', 'G', 'U'}$ is converted to $'A'$.
-...text:$Rna$ is typedef for $SimpleType<char,Rna_>$, while $Rna_$ is a helper
-specialization tag class.
-..see:Metafunction.ValueSize
-..see:Spec.Rna5
-..include:seqan/basic.h
-*/
-
 struct Rna_ {};
 typedef SimpleType<unsigned char, Rna_> Rna;
 
@@ -533,40 +431,20 @@ struct BitsPerValue<Rna>
  * @extends SimpleType
  * @headerfile <seqan/basic.h>
  * @brief Alphabet for RNA including 'N' character.
- * 
+ *
  * @signature typedef SimpleType<unsigned char, Rna5_> Rna5;
- * 
- * @section Remarks
- * 
+ *
  * The ValueSize of <tt>Rna5</tt> is 5.  The nucleotides are enumerated this way: <tt>'A' = 0, 'C' = 1, 'G' = 2, 'U' =
  * 3</tt>.  The 'N' character ("unkown nucleotide") is encoded by 4.
- * 
+ *
  * Objects of type <tt>Rna5</tt> can be converted to various other types and vice versa.  An object that has a value not
  * in <tt>{'A', 'C', 'G', 'U'}</tt> is converted to <tt>'N'</tt>.
- * 
+ *
  * @see Rna5Iterator
  * @see Rna5String
  * @see Rna
  */
 
-/**
-.Spec.Rna5:
-..cat:Alphabets
-..summary:Alphabet for RNA including 'N' character.
-..general:Class.SimpleType
-..signature:Rna5
-..remarks:
-...text:The @Metafunction.ValueSize@ of $Rna5$ is 5. 
-The nucleotides are enumerated this way: $'A' = 0, 'C' = 1, 'G' = 2, 'U' = 3$. 
-The 'N' character ("unkown nucleotide") is encoded by 4.
-...text:Objects of type $Rna5$ can be converted to various other types and vice versa. 
-An object that has a value not in ${'A', 'C', 'G', 'U'}$ is converted to $'N'$.
-...text:$Rna5$ is typedef for $SimpleType<char,Rna5_>$, while $Rna5_$ is a helper
-specialization tag class.
-..see:Metafunction.ValueSize
-..include:seqan/basic.h
-*/
-
 struct Rna5_ {};
 typedef SimpleType<unsigned char, Rna5_> Rna5;
 
@@ -601,14 +479,12 @@ unknownValueImpl(Rna5 *)
  * @extends SimpleType
  * @headerfile <seqan/basic.h>
  * @brief Iupac code for DNA.
- * 
+ *
  * @signature typedef SimpleType<unsigned char, Iupac_> Iupac;
- * 
- * @section Remarks
- * 
+ *
  * The ValueSize of <tt>Iupac</tt> is 16.  The nucleotides are enumerated from 0 to 19 in this order: 'U'=0, 'T', 'A',
  * 'W', 'C', 'Y', 'M', 'H', 'G', 'K', 'R', 'D', 'S', 'B', 'V', 'N'=15.
- * 
+ *
  * Objects of type <tt>Iupac</tt> can be converted to various other types and vice versa.  Unknown values are converted
  * to <tt>'N'</tt>.
  *
@@ -616,24 +492,6 @@ unknownValueImpl(Rna5 *)
  * @see IupacIterator
  */
 
-/**
-.Spec.Iupac:
-..cat:Alphabets
-..summary:Iupac code for DNA.
-..general:Class.SimpleType
-..signature:Iupac
-..remarks:
-...text:The @Metafunction.ValueSize@ of $Iupac$ is 16. 
-The nucleotides are enumerated from 0 to 19 in this order: 
-'U'=0, 'T', 'A', 'W', 'C', 'Y', 'M', 'H', 'G', 'K', 'R', 'D', 'S', 'B', 'V', 'N'=15. 
-...text:Objects of type $Iupac$ can be converted to various other types and vice versa. 
-Unkown values are converted to $'N'$.
-...text:$Iupac$ is typedef for $SimpleType<char,Iupac_>$, while $Iupac_$ is a helper
-specialization tag class.
-..see:Metafunction.ValueSize
-..include:seqan/basic.h
-*/
-
 struct Iupac_ {};
 typedef SimpleType<unsigned char, Iupac_> Iupac;
 
@@ -666,54 +524,35 @@ unknownValueImpl(Iupac *)
  * @headerfile <seqan/basic.h>
  * @brief IUPAC code for amino acids.
  * @signature typedef SingleType<unsigned char, AminoAcid_> AminoAcid;
- * 
- * @section Remarks
- * 
- * The ValueSize of <tt>AminoAcid</tt> is 24.
- * 
- * The amino acids are enumerated from 0 to 15 in this order:
- * 
- * 'A'=0, 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'=19.
- * 
- * The remaining 4 symbols are:
- * 
- * 'B'=20 (Aspartic Acid, Asparagine), 'Z'=21 (Glutamic Acid, Glutamine), 'X'=22 (unknown), '*'=23 (terminator)
- * 
+ *
+ * The ValueSize of <tt>AminoAcid</tt> is 27.
+ *
+ * The amino acid symbols are as follows, i.e. they are sorted alphabetically
+ * up until the last two symbols:
+ *
+ * 'A' = 0, 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'Y', 'Z', 'X'. '*'
+ *
+ * Of these 'B' is a wildcard for (Aspartic Acid, Asparagine),
+ * 'J' for (Leucine, Isoleucine), 'Z' for (Glutamic Acid, Glutamine) and
+ * 'X' for "any amino acid".
+ *
+ * 'O' refers to the rare Pyrrolysine, 'U' refers to the rare Selenocysteine and '*' to the terminator tRNA.
+ *
  * Objects of type <tt>AminoAcid</tt> can be converted to <tt>char</tt> and vice versa.  Unknown values are converted to
  * <tt>'X'</tt>.
- * 
+ *
  * @see FiniteOrderedAlphabetConcept#ValueSize
  * @see PeptideIterator
  * @see Peptide
  */
 
-/**
-.Spec.AminoAcid:
-..cat:Alphabets
-..summary:Iupac code for amino acids.
-..general:Class.SimpleType
-..signature:AminoAcid
-..remarks:
-...text:The @Metafunction.ValueSize@ of $AminoAcid$ is 24. 
-...text:The amino acids are enumerated from 0 to 15 in this order: 
-...text:'A'=0, 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'=19.
-...text:The remaining 4 symbols are:
-...text: 'B'=20 (Aspartic Acid, Asparagine), 'Z'=21 (Glutamic Acid, Glutamine), 'X'=22 (unknown), '*'=23 (terminator)
-...text:Objects of type $AminoAcid$ can be converted to $char$ and vice versa. 
-Unkown values are converted to $'X'$.
-...text:$AminoAcid$ is typedef for $SimpleType<char,AminoAcid_>$, while $AminoAcid_$ is a helper
-specialization tag class.
-..see:Metafunction.ValueSize
-..include:seqan/basic.h
-*/
-
 struct AminoAcid_ {};
 typedef SimpleType<unsigned char, AminoAcid_> AminoAcid;
 
 template <> struct ValueSize<AminoAcid>
 {
     typedef __uint8 Type;
-    static const Type VALUE = 24;
+    static const Type VALUE = 27;
 };
 
 template <> struct BitsPerValue<AminoAcid>
@@ -737,40 +576,27 @@ unknownValueImpl(AminoAcid *)
  * @class Finite
  * @extends SimpleType
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief A finite alphabet of a fixed size.
- * 
+ *
  * @signature template <typename TValue, unsigned SIZE>
  *            class SimpleType<TValue, Finite<SIZE> >;
- * 
+ *
  * @tparam TValue The type that is use to store the values.
  * @tparam SIZE   The ValueSize of the alphabet.
  */
 
-/**
-.Spec.Finite:
-..cat:Alphabets
-..summary:A finite alphabet of a fixed size.
-..general:Class.SimpleType
-..signature:SimpleType<TValue, Finite<SIZE> >
-..param.TValue:The type that is use to store the values.
-...default:$char$
-..param.SIZE:The @Metafunction.ValueSize@ of the alphabet.
-..see:Metafunction.ValueSize
-..include:seqan/basic.h
-*/
-
 template <unsigned SIZE>
 struct Finite;
 
-template <typename TValue, unsigned SIZE> 
+template <typename TValue, unsigned SIZE>
 struct ValueSize<SimpleType<TValue, Finite<SIZE> > >
 {
-    typedef __uint8 Type;
+    typedef unsigned Type;
     static const Type VALUE = SIZE;
 };
 
-template <typename TValue, unsigned SIZE> 
+template <typename TValue, unsigned SIZE>
 struct BitsPerValue<SimpleType<TValue, Finite<SIZE> > >
 {
     typedef __uint8 Type;
@@ -785,38 +611,38 @@ struct BitsPerValue<SimpleType<TValue, Finite<SIZE> > >
 // char
 // ----------------------------------------------------------------------------
 
-inline void assign(char & c_target, 
+inline void assign(char & c_target,
                    Dna const & source)
 {
-    c_target = TranslateTableDna5ToAscii_<>::VALUE[source.value];
+    c_target = TranslateTableDna5ToChar_<>::VALUE[source.value];
 }
 
-inline void assign(char & c_target, 
+inline void assign(char & c_target,
                    Dna5 const & source)
 {
-    c_target = TranslateTableDna5ToAscii_<>::VALUE[source.value];
+    c_target = TranslateTableDna5ToChar_<>::VALUE[source.value];
 }
 
-inline void assign(char& target,
+inline void assign(char & c_target,
                    Rna const & source)
 {
-        target = TranslateTableRna5ToAscii_<>::VALUE[source.value];
+    c_target = TranslateTableRna5ToChar_<>::VALUE[source.value];
 }
 
-inline void assign(char& target,
+inline void assign(char & c_target,
                    Rna5 const & source)
 {
-        target = TranslateTableRna5ToAscii_<>::VALUE[source.value];
+    c_target = TranslateTableRna5ToChar_<>::VALUE[source.value];
 }
 
 inline void assign(char & c_target, Iupac const & source)
 {
-    c_target = TranslateTableIupacToAscii_<>::VALUE[source.value];
+    c_target = TranslateTableIupacToChar_<>::VALUE[source.value];
 }
 
 inline void assign(char & c_target, AminoAcid const & source)
 {
-    c_target = TranslateTableAAToAscii_<>::VALUE[source.value];
+    c_target = TranslateTableAAToChar_<>::VALUE[source.value];
 }
 
 // ----------------------------------------------------------------------------
@@ -824,7 +650,7 @@ inline void assign(char & c_target, AminoAcid const & source)
 // ----------------------------------------------------------------------------
 
 template <>
-struct CompareType<Dna, __uint8>
+struct CompareTypeImpl<Dna, __uint8>
 {
     typedef Dna Type;
 };
@@ -835,7 +661,7 @@ inline void assign(Dna & target, __uint8 c_source)
 }
 
 template <>
-struct CompareType<Dna, char>
+struct CompareTypeImpl<Dna, char>
 {
     typedef Dna Type;
 };
@@ -843,29 +669,14 @@ struct CompareType<Dna, char>
 inline void assign(Dna & target, char c_source)
 {
 #ifdef __CUDA_ARCH__
-    target.value = _translateAsciiToDna<void>((unsigned char)c_source);
-#else
-    target.value = TranslateTableAsciiToDna_<>::VALUE[(unsigned char) c_source];
-#endif
-}
-
-template <>
-struct CompareType<Dna, Unicode>
-{
-    typedef Dna Type;
-};
-
-inline void assign(Dna & target, Unicode c_source)
-{
-#ifdef __CUDA_ARCH__
-    target.value = _translateAsciiToDna<void>((unsigned char)c_source);
+    target.value = _translateCharToDna<void>((unsigned char)c_source);
 #else
-    target.value = TranslateTableAsciiToDna_<>::VALUE[(unsigned char) c_source];
+    target.value = TranslateTableCharToDna_<>::VALUE[(unsigned char) c_source];
 #endif
 }
 
 template <>
-struct CompareType<Dna, Dna5>
+struct CompareTypeImpl<Dna, Dna5>
 {
     typedef Dna Type;
 };
@@ -876,7 +687,7 @@ inline void assign(Dna & target, Dna5 const & c_source)
 }
 
 template <>
-struct CompareType<Dna, Iupac>
+struct CompareTypeImpl<Dna, Iupac>
 {
     typedef Dna Type;
 };
@@ -891,7 +702,7 @@ inline void assign(Dna & target, Iupac const & source)
 // ----------------------------------------------------------------------------
 
 template <>
-struct CompareType<Dna5, __uint8>
+struct CompareTypeImpl<Dna5, __uint8>
 {
     typedef Dna5 Type;
 };
@@ -902,29 +713,22 @@ inline void assign(Dna5 & target, __uint8 c_source)
 }
 
 template <>
-struct CompareType<Dna5, char>
+struct CompareTypeImpl<Dna5, char>
 {
     typedef Dna5 Type;
 };
 
 inline void assign(Dna5 & target, char c_source)
 {
-    target.value = TranslateTableAsciiToDna5_<>::VALUE[(unsigned char) c_source];
-}
-
-template <>
-struct CompareType<Dna5, Unicode>
-{
-    typedef Dna5 Type;
-};
-
-inline void assign(Dna5 & target, Unicode c_source)
-{
-    target.value = TranslateTableAsciiToDna5_<>::VALUE[(unsigned char) c_source];
+#ifdef __CUDA_ARCH__
+    target.value = _translateCharToDna5<void>((unsigned char)c_source);
+#else
+    target.value = TranslateTableCharToDna5_<>::VALUE[(unsigned char) c_source];
+#endif
 }
 
 template <>
-struct CompareType<Dna5, Iupac>
+struct CompareTypeImpl<Dna5, Iupac>
 {
     typedef Dna5 Type;
 };
@@ -935,7 +739,7 @@ inline void assign(Dna5 & target, Iupac const & source)
 }
 
 template <>
-struct CompareType<Dna5, Dna>
+struct CompareTypeImpl<Dna5, Dna>
 {
     typedef Dna Type;
 };
@@ -950,40 +754,29 @@ inline void assign(Dna5 & target, Dna const & c_source)
 // ----------------------------------------------------------------------------
 
 template <>
-struct CompareType<Rna, __uint8>
+struct CompareTypeImpl<Rna, __uint8>
 {
     typedef Rna Type;
 };
 
 inline void assign(Rna & target, __uint8 c_source)
 {
-        target.value = TranslateTableByteToRna_<>::VALUE[c_source];
+    target.value = TranslateTableByteToDna_<>::VALUE[c_source];
 }
 
 template <>
-struct CompareType<Rna, char>
+struct CompareTypeImpl<Rna, char>
 {
     typedef Rna Type;
 };
 
 inline void assign(Rna & target, char c_source)
 {
-        target.value = TranslateTableAsciiToRna_<>::VALUE[(unsigned char)c_source];
-}
-
-template <>
-struct CompareType<Rna, Unicode>
-{
-    typedef Rna Type;
-};
-
-inline void assign(Rna & target, Unicode c_source)
-{
-        target.value = TranslateTableAsciiToRna_<>::VALUE[(unsigned char) c_source];
+    target.value = TranslateTableCharToDna_<>::VALUE[(unsigned char)c_source];
 }
 
 template <>
-struct CompareType<Rna, Rna5>
+struct CompareTypeImpl<Rna, Rna5>
 {
     typedef Rna Type;
 };
@@ -998,40 +791,29 @@ inline void assign(Rna & target, Rna5 const & c_source)
 // ---------------------------------------------------------------------------
 
 template <>
-struct CompareType<Rna5, __uint8>
+struct CompareTypeImpl<Rna5, __uint8>
 {
     typedef Rna5 Type;
 };
 
 inline void assign(Rna5 & target, __uint8 c_source)
 {
-        target.value = TranslateTableByteToRna5_<>::VALUE[c_source];
+    target.value = TranslateTableByteToDna5_<>::VALUE[c_source];
 }
 
 template <>
-struct CompareType<Rna5, char>
+struct CompareTypeImpl<Rna5, char>
 {
     typedef Rna5 Type;
 };
 
 inline void assign(Rna5 & target, char c_source)
 {
-        target.value = TranslateTableAsciiToRna5_<>::VALUE[(unsigned char)c_source];
+    target.value = TranslateTableCharToDna5_<>::VALUE[(unsigned char)c_source];
 }
 
 template <>
-struct CompareType<Rna5, Unicode>
-{
-    typedef Rna5 Type;
-};
-
-inline void assign(Rna5 & target, Unicode c_source)
-{
-        target.value = TranslateTableAsciiToRna5_<>::VALUE[(unsigned char) c_source];
-}
-
-template <>
-struct CompareType<Rna5, Rna>
+struct CompareTypeImpl<Rna5, Rna>
 {
     typedef Dna Type;
 };
@@ -1046,7 +828,7 @@ inline void assign(Rna5 & target, Rna const & c_source)
 // ---------------------------------------------------------------------------
 
 template <>
-struct CompareType<Iupac, __uint8>
+struct CompareTypeImpl<Iupac, __uint8>
 {
     typedef Iupac Type;
 };
@@ -1057,25 +839,14 @@ inline void assign(Iupac & target, __uint8 c_source)
 }
 
 template <>
-struct CompareType<Iupac, char>
+struct CompareTypeImpl<Iupac, char>
 {
     typedef Iupac Type;
 };
 
 inline void assign(Iupac & target, char c_source)
 {
-    target.value = TranslateTableAsciiToIupac_<>::VALUE[(unsigned char) c_source];
-}
-
-template <>
-struct CompareType<Iupac, Unicode>
-{
-    typedef Iupac Type;
-};
-
-inline void assign(Iupac & target, Unicode c_source)
-{
-    target.value = TranslateTableAsciiToIupac_<>::VALUE[(unsigned char) c_source];
+    target.value = TranslateTableCharToIupac_<>::VALUE[(unsigned char) c_source];
 }
 
 inline void assign(Iupac & target, Dna const & source)
@@ -1093,7 +864,7 @@ inline void assign(Iupac & target, Dna5 const & source)
 // ---------------------------------------------------------------------------
 
 template <>
-struct CompareType<AminoAcid, __uint8>
+struct CompareTypeImpl<AminoAcid, __uint8>
 {
     typedef AminoAcid Type;
 };
@@ -1104,25 +875,14 @@ inline void assign(AminoAcid & target, __uint8 c_source)
 }
 
 template <>
-struct CompareType<AminoAcid, char>
+struct CompareTypeImpl<AminoAcid, char>
 {
     typedef AminoAcid Type;
 };
 
 inline void assign(AminoAcid & target, char c_source)
 {
-    target.value = TranslateTableAsciiToAA_<>::VALUE[(unsigned char) c_source];
-}
-
-template <>
-struct CompareType<AminoAcid, Unicode>
-{
-    typedef AminoAcid Type;
-};
-
-inline void assign(AminoAcid & target, Unicode c_source)
-{
-    target.value = TranslateTableAsciiToAA_<>::VALUE[(unsigned char) c_source];
+    target.value = TranslateTableCharToAA_<>::VALUE[(unsigned char) c_source];
 }
 
 // ---------------------------------------------------------------------------
@@ -1130,36 +890,36 @@ inline void assign(AminoAcid & target, Unicode c_source)
 // ---------------------------------------------------------------------------
 
 // template <typename TValue, typename TValue2>
-// struct CompareType<SimpleType<TValue,DnaQ_>, SimpleType<TValue2,Dna_> >
+// struct CompareTypeImpl<SimpleType<TValue,DnaQ_>, SimpleType<TValue2,Dna_> >
 // {
 //  typedef SimpleType<TValue2,Dna_> Type;
 // };
-// 
+//
 // template <typename TValue, typename TValue2>
-// struct CompareType<SimpleType<TValue,Dna_>, SimpleType<TValue2,DnaQ_> >
+// struct CompareTypeImpl<SimpleType<TValue,Dna_>, SimpleType<TValue2,DnaQ_> >
 // {
 //  typedef SimpleType<TValue,Dna_> Type;
 // };
 
 template <>
-struct CompareType<DnaQ, DnaQ>
+struct CompareTypeImpl<DnaQ, DnaQ>
 {
     typedef Dna Type;
 };
 
 template <>
-struct CompareType<DnaQ, Dna>
+struct CompareTypeImpl<DnaQ, Dna>
 {
     typedef Dna Type;
 };
 
 inline void assign(DnaQ & target, Dna const & source)
 {
-    target.value = source.value | (60 << 2);
+    target.value = source.value | (SEQAN_DEFAULT_QUALITY << 2);
 }
 
 template <>
-struct CompareType<Dna, DnaQ>
+struct CompareTypeImpl<Dna, DnaQ>
 {
     typedef Dna Type;
 };
@@ -1170,9 +930,9 @@ inline void assign(Dna & target, DnaQ const & source)
 }
 
 template <>
-struct CompareType<DnaQ, Iupac>
+struct CompareTypeImpl<DnaQ, Iupac>
 {
-    typedef Dna Type;
+    typedef Iupac Type;
 };
 
 inline void assign(DnaQ & target, Iupac const & source)
@@ -1181,71 +941,71 @@ inline void assign(DnaQ & target, Iupac const & source)
 }
 
 template <>
-struct CompareType<DnaQ, Dna5>
+struct CompareTypeImpl<Iupac, DnaQ>
 {
-    typedef Dna Type;
+    typedef Iupac Type;
 };
 
-inline void assign(DnaQ & target, Dna5 const & source)
+inline void assign(Iupac & target, DnaQ const & source)
 {
     assign(target, (Dna) source);
 }
 
 template <>
-struct CompareType<DnaQ, __uint8>
+struct CompareTypeImpl<DnaQ, Dna5>
 {
     typedef Dna Type;
 };
 
-inline void assign(DnaQ & target, __uint8 c_source)
+inline void assign(DnaQ & target, Dna5 const & source)
 {
-    assign(target, (Dna) c_source);
+    assign(target, (Dna) source);
 }
 
 template <>
-struct CompareType<DnaQ, char>
+struct CompareTypeImpl<DnaQ, __uint8>
 {
     typedef Dna Type;
 };
 
-inline void assign(DnaQ & target, char c_source)
+inline void assign(DnaQ & target, __uint8 c_source)
 {
     assign(target, (Dna) c_source);
 }
 
 template <>
-struct CompareType<DnaQ, Unicode>
+struct CompareTypeImpl<DnaQ, char>
 {
     typedef Dna Type;
 };
 
-inline void assign(DnaQ & target, Unicode c_source)
+inline void assign(DnaQ & target, char c_source)
 {
     assign(target, (Dna) c_source);
 }
 
-inline void 
+inline void
 assign(DnaQ & target, DnaQ const & source)
 {
     target.value = source.value;
 }
 
 template <typename TSource>
-inline void 
+inline void
 assign(DnaQ & target, TSource const & source)
 {
     target.value = (Dna)source;
 }
 
-inline void 
-assign(__int64 & c_target, 
+inline void
+assign(__int64 & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(__int64 & c_target, 
+inline void
+assign(__int64 & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1253,15 +1013,15 @@ assign(__int64 & c_target,
 
 // __uint64
 
-inline void 
-assign(__uint64 & c_target, 
+inline void
+assign(__uint64 & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(__uint64 & c_target, 
+inline void
+assign(__uint64 & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1269,15 +1029,15 @@ assign(__uint64 & c_target,
 
 // int
 
-inline void 
-assign(int & c_target, 
+inline void
+assign(int & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(int & c_target, 
+inline void
+assign(int & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1285,15 +1045,15 @@ assign(int & c_target,
 
 // unsigned int
 
-inline void 
-assign(unsigned int & c_target, 
+inline void
+assign(unsigned int & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(unsigned int & c_target, 
+inline void
+assign(unsigned int & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1301,15 +1061,15 @@ assign(unsigned int & c_target,
 
 // short
 
-inline void 
-assign(short & c_target, 
+inline void
+assign(short & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(short & c_target, 
+inline void
+assign(short & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1317,15 +1077,15 @@ assign(short & c_target,
 
 // unsigned short
 
-inline void 
-assign(unsigned short & c_target, 
+inline void
+assign(unsigned short & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(unsigned short & c_target, 
+inline void
+assign(unsigned short & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1333,15 +1093,15 @@ assign(unsigned short & c_target,
 
 // char
 
-inline void 
-assign(char & c_target, 
+inline void
+assign(char & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(char & c_target, 
+inline void
+assign(char & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1349,15 +1109,15 @@ assign(char & c_target,
 
 // signed char
 
-inline void 
-assign(signed char & c_target, 
+inline void
+assign(signed char & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(signed char & c_target, 
+inline void
+assign(signed char & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1365,15 +1125,15 @@ assign(signed char & c_target,
 
 // unsigned char
 
-inline void 
-assign(unsigned char & c_target, 
+inline void
+assign(unsigned char & c_target,
        DnaQ & source)
 {
     c_target = Dna(source);
 }
 
-inline void 
-assign(unsigned char & c_target, 
+inline void
+assign(unsigned char & c_target,
        DnaQ const & source)
 {
     c_target = Dna(source);
@@ -1384,26 +1144,26 @@ assign(unsigned char & c_target,
 // ---------------------------------------------------------------------------
 
 // template <typename TValue, typename TValue2>
-// struct CompareType<SimpleType<TValue,Dna5Q_>, SimpleType<TValue2,Dna5_> >
+// struct CompareTypeImpl<SimpleType<TValue,Dna5Q_>, SimpleType<TValue2,Dna5_> >
 // {
 //  typedef SimpleType<TValue2,Dna5_> Type;
 // };
-// 
+//
 // template <typename TValue, typename TValue2>
-// struct CompareType<SimpleType<TValue,Dna5_>, SimpleType<TValue2,Dna5Q_> >
+// struct CompareTypeImpl<SimpleType<TValue,Dna5_>, SimpleType<TValue2,Dna5Q_> >
 // {
 //  typedef SimpleType<TValue,Dna5_> Type;
 // };
 
 
 template <>
-struct CompareType<Dna5Q, Dna5Q>
+struct CompareTypeImpl<Dna5Q, Dna5Q>
 {
     typedef Dna5 Type;
 };
 
 template <>
-struct CompareType<DnaQ, Dna5Q>
+struct CompareTypeImpl<DnaQ, Dna5Q>
 {
     typedef Dna Type;
 };
@@ -1437,7 +1197,7 @@ inline void assign(DnaQ & target, Dna5Q const & source)
 }
 
 template <>
-struct CompareType<Dna5Q, DnaQ>
+struct CompareTypeImpl<Dna5Q, DnaQ>
 {
     typedef Dna Type;
 };
@@ -1449,7 +1209,7 @@ inline void assign(Dna5Q & target, DnaQ const & source)
 
 
 template <>
-struct CompareType<Dna5, Dna5Q>
+struct CompareTypeImpl<Dna5, Dna5Q>
 {
     typedef Dna5 Type;
 };
@@ -1482,7 +1242,7 @@ inline void assign(Dna5 & target, Dna5Q const & source)
 }
 
 template <>
-struct CompareType<Dna5Q, Dna5>
+struct CompareTypeImpl<Dna5Q, Dna5>
 {
     typedef Dna5 Type;
 };
@@ -1493,16 +1253,17 @@ inline void assign(Dna5Q & target, Dna5 const & source)
     // We perform the conversion from DNA5 with qualities to DNA5 by a simple
     // table lookup.  The lookup below is equivalent to the following line:
     //
-    // target.value = (source.value == 4)? Dna5QValueN_ : source.value | (60 << 2);
+    // target.value = (source.value == 4)? Dna5QValueN_ : source.value | (40 << 2);
 
     static const unsigned table[] = {
-        (60 << 2) + 0, (60 << 2) + 1, (60 << 2) + 2, (60 << 2) + 3, Dna5QValueN_
+        (SEQAN_DEFAULT_QUALITY << 2) + 0, (SEQAN_DEFAULT_QUALITY << 2) + 1,
+        (SEQAN_DEFAULT_QUALITY << 2) + 2, (SEQAN_DEFAULT_QUALITY << 2) + 3, Dna5QValueN_
     };
     target.value = table[source.value];
 }
 
 template <>
-struct CompareType<Dna5Q, Dna>
+struct CompareTypeImpl<Dna5Q, Dna>
 {
     typedef Dna Type;
 };
@@ -1513,7 +1274,7 @@ inline void assign(Dna5Q & target, Dna const & source)
 }
 
 template <>
-struct CompareType<Dna, Dna5Q>
+struct CompareTypeImpl<Dna, Dna5Q>
 {
     typedef Dna Type;
 };
@@ -1524,7 +1285,7 @@ inline void assign(Dna & target, Dna5Q const & source)
 }
 
 template <>
-struct CompareType<Dna5, DnaQ>
+struct CompareTypeImpl<Dna5, DnaQ>
 {
     typedef Dna5 Type;
 };
@@ -1535,7 +1296,7 @@ inline void assign(Dna5 & target, DnaQ const & source)
 }
 
 template <>
-struct CompareType<Dna5Q, __uint8>
+struct CompareTypeImpl<Dna5Q, __uint8>
 {
     typedef Dna5 Type;
 };
@@ -1546,7 +1307,7 @@ inline void assign(Dna5Q & target, __uint8 c_source)
 }
 
 template <>
-struct CompareType<Dna5Q, char>
+struct CompareTypeImpl<Dna5Q, char>
 {
     typedef Dna5 Type;
 };
@@ -1557,35 +1318,35 @@ inline void assign(Dna5Q & target, char c_source)
 }
 
 template <>
-struct CompareType<Dna5Q, Unicode>
+struct CompareTypeImpl<Dna5Q, Iupac>
 {
-    typedef Dna5 Type;
+    typedef Iupac Type;
 };
 
-inline void assign(Dna5Q & target, Unicode c_source)
+inline void assign(Dna5Q & target, Iupac const & source)
 {
-    assign(target, (Dna5)c_source);
+    assign(target, (Dna5)source);
 }
 
 template <>
-struct CompareType<Dna5Q, Iupac>
+struct CompareTypeImpl<Iupac, Dna5Q>
 {
-    typedef Dna5 Type;
+    typedef Iupac Type;
 };
 
-inline void assign(Dna5Q & target, Iupac const & source)
+inline void assign(Iupac & target, Dna5Q const & source)
 {
     assign(target, (Dna5)source);
 }
 
-inline void 
+inline void
 assign(Dna5Q & target, Dna5Q const & source)
 {
     target.value = source.value;
 }
 
 template <typename TSource>
-inline void 
+inline void
 assign(Dna5Q & target, TSource const & source)
 {
     assign(target, (Dna5)source);
@@ -1593,15 +1354,15 @@ assign(Dna5Q & target, TSource const & source)
 
 // __int64
 
-inline void 
-assign(__int64 & c_target, 
+inline void
+assign(__int64 & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(__int64 & c_target, 
+inline void
+assign(__int64 & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1609,15 +1370,15 @@ assign(__int64 & c_target,
 
 // __uint64
 
-inline void 
-assign(__uint64 & c_target, 
+inline void
+assign(__uint64 & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(__uint64 & c_target, 
+inline void
+assign(__uint64 & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1625,15 +1386,15 @@ assign(__uint64 & c_target,
 
 // int
 
-inline void 
-assign(int & c_target, 
+inline void
+assign(int & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(int & c_target, 
+inline void
+assign(int & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1641,15 +1402,15 @@ assign(int & c_target,
 
 // unsigned int
 
-inline void 
-assign(unsigned int & c_target, 
+inline void
+assign(unsigned int & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(unsigned int & c_target, 
+inline void
+assign(unsigned int & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1658,15 +1419,15 @@ assign(unsigned int & c_target,
 
 //short
 
-inline void 
-assign(short & c_target, 
+inline void
+assign(short & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(short & c_target, 
+inline void
+assign(short & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1674,15 +1435,15 @@ assign(short & c_target,
 
 //unsigned short
 
-inline void 
-assign(unsigned short & c_target, 
+inline void
+assign(unsigned short & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(unsigned short & c_target, 
+inline void
+assign(unsigned short & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1690,15 +1451,15 @@ assign(unsigned short & c_target,
 
 // char
 
-inline void 
-assign(char & c_target, 
+inline void
+assign(char & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(char & c_target, 
+inline void
+assign(char & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1706,15 +1467,15 @@ assign(char & c_target,
 
 // signed char
 
-inline void 
-assign(signed char & c_target, 
+inline void
+assign(signed char & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(signed char & c_target, 
+inline void
+assign(signed char & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1722,15 +1483,15 @@ assign(signed char & c_target,
 
 // unsigned char
 
-inline void 
-assign(unsigned char & c_target, 
+inline void
+assign(unsigned char & c_target,
        Dna5Q & source)
 {
     c_target = Dna5(source);
 }
 
-inline void 
-assign(unsigned char & c_target, 
+inline void
+assign(unsigned char & c_target,
        Dna5Q const & source)
 {
     c_target = Dna5(source);
@@ -1738,4 +1499,4 @@ assign(unsigned char & c_target,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_
diff --git a/seqan/basic/alphabet_residue_funcs.h b/seqan/basic/alphabet_residue_funcs.h
index 847437c..12fa686 100644
--- a/seqan/basic/alphabet_residue_funcs.h
+++ b/seqan/basic/alphabet_residue_funcs.h
@@ -32,8 +32,8 @@
 // Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
 
 
 namespace seqan {
@@ -44,7 +44,7 @@ namespace seqan {
 
 template <typename T>
 SEQAN_HOST_DEVICE inline unsigned char
-_translateAsciiToDna(unsigned char c)
+_translateCharToDna(unsigned char c)
 {
     switch (toUpperValue(c))
     {
@@ -58,6 +58,30 @@ _translateAsciiToDna(unsigned char c)
             return 0;
     };
 }
+
+// --------------------------------------------------------------------------
+// Dna5
+// --------------------------------------------------------------------------
+
+template <typename T>
+SEQAN_HOST_DEVICE inline unsigned char
+_translateCharToDna5(unsigned char c)
+{
+    switch (toUpperValue(c))
+    {
+        case 'A':
+            return 0;
+        case 'C':
+            return 1;
+        case 'G':
+            return 2;
+        case 'T':
+            return 3;
+        default:
+            return 4;
+    };
+}
+
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
diff --git a/seqan/basic/alphabet_residue_tabs.h b/seqan/basic/alphabet_residue_tabs.h
index e30fd43..7805607 100644
--- a/seqan/basic/alphabet_residue_tabs.h
+++ b/seqan/basic/alphabet_residue_tabs.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // Rna5.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_
 
 
 namespace seqan {
@@ -48,13 +48,13 @@ namespace seqan {
 // --------------------------------------------------------------------------
 
 template <typename T = void>
-struct TranslateTableDna5ToAscii_
+struct TranslateTableDna5ToChar_
 {
     static char const VALUE[5];
 };
 
 template <typename T>
-char const TranslateTableDna5ToAscii_<T>::VALUE[5] = {'A', 'C', 'G', 'T', 'N'};
+char const TranslateTableDna5ToChar_<T>::VALUE[5] = {'A', 'C', 'G', 'T', 'N'};
 
 
 template <typename T = void>
@@ -64,16 +64,16 @@ struct TranslateTableDna5ToIupac_
 };
 
 template <typename T>
-char const TranslateTableDna5ToIupac_<T>::VALUE[5] = {0x02, 0x04, 0x08, 0x01, 0x0f};
+char const TranslateTableDna5ToIupac_<T>::VALUE[5] = {0x01, 0x02, 0x04, 0x08, 0x0f};
 
 template <typename T = void>
-struct TranslateTableAsciiToDna_
+struct TranslateTableCharToDna_
 {
     static char const VALUE[256];
 };
 
 template <typename T>
-char const TranslateTableAsciiToDna_<T>::VALUE[256] = 
+char const TranslateTableCharToDna_<T>::VALUE[256] =
 {
     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //0
     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //1
@@ -84,13 +84,13 @@ char const TranslateTableAsciiToDna_<T>::VALUE[256] =
 //   ,   A,   B,   C,   D,   E,   D,   G,   H,   I,   J,   K,   L,   M,   N,   O,
 
     0,   0,   0,   0,   3,   3,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //5
-//  P,   Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z,    ,    ,    ,    ,    
+//  P,   Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z,    ,    ,    ,    ,
 
     0,   0,   0,   1,   0,   0,   0,   2,   0,   0,   0,   0,   0,   0,   0,   0, //6
 //   ,   a,   b,   c,   d,   e,   f,   g,   h,   i,   j,   k,   l,   m,   n,   o,
 
     0,   0,   0,   0,   3,   3,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //7
-//  p,   q,   r,   s,   t,   u,   v,   w,   x,   y,   z,    ,    ,    ,    ,   
+//  p,   q,   r,   s,   t,   u,   v,   w,   x,   y,   z,    ,    ,    ,    ,
 
     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //8
     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //9
@@ -104,13 +104,13 @@ char const TranslateTableAsciiToDna_<T>::VALUE[256] =
 
 
 template <typename T = void>
-struct TranslateTableAsciiToDna5_
+struct TranslateTableCharToDna5_
 {
     static char const VALUE[256];
 };
 
 template <typename T>
-char const TranslateTableAsciiToDna5_<T>::VALUE[256] = 
+char const TranslateTableCharToDna5_<T>::VALUE[256] =
 {
     4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //0
     4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //1
@@ -121,13 +121,13 @@ char const TranslateTableAsciiToDna5_<T>::VALUE[256] =
 //   ,   A,   B,   C,   D,   E,   D,   G,   H,   I,   J,   K,   L,   M,   N,   O,
 
     4,   4,   4,   4,   3,   3,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //5
-//  P,   Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z,    ,    ,    ,    ,    
+//  P,   Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z,    ,    ,    ,    ,
 
     4,   0,   4,   1,   4,   4,   4,   2,   4,   4,   4,   4,   4,   4,   4,   4, //6
 //   ,   a,   b,   c,   d,   e,   f,   g,   h,   i,   j,   k,   l,   m,   n,   o,
 
     4,   4,   4,   4,   3,   3,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //7
-//  p,   q,   r,   s,   t,   u,   v,   w,   x,   y,   z,    ,    ,    ,    ,   
+//  p,   q,   r,   s,   t,   u,   v,   w,   x,   y,   z,    ,    ,    ,    ,
 
     4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //8
     4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //9
@@ -146,7 +146,7 @@ struct TranslateTableByteToDna_
 };
 
 template <typename T>
-char const TranslateTableByteToDna_<T>::VALUE[256] = 
+char const TranslateTableByteToDna_<T>::VALUE[256] =
 {
     0,   1,   2,   3,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //0
     0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //1
@@ -198,168 +198,44 @@ char const TranslateTableByteToDna5_<T>::VALUE[256] =
 // --------------------------------------------------------------------------
 
 template <typename T = void>
-struct TranslateTableRna5ToAscii_
+struct TranslateTableRna5ToChar_
 {
     static char const VALUE[5];
 };
 
 template <typename T>
-char const TranslateTableRna5ToAscii_<T>::VALUE[5] = {'A', 'C', 'G', 'U', 'N'}; 
+char const TranslateTableRna5ToChar_<T>::VALUE[5] = {'A', 'C', 'G', 'U', 'N'};
 
-template <typename T = void>
-struct TranslateTableAsciiToRna_
-{
-    static char const VALUE[256];
-};
-
-template <typename T>
-char const TranslateTableAsciiToRna_<T>::VALUE[256] = 
-{
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //0
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //1
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //2
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //3
-
-    0,   0,   0,   1,   0,   0,   0,   2,   0,   0,   0,   0,   0,   0,   0,   0, //4
-//   ,   A,   B,   C,   D,   E,   D,   G,   H,   I,   J,   K,   L,   M,   N,   O,
-
-    0,   0,   0,   0,   0,   3,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //5
-//  P,   Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z,    ,    ,    ,    ,    
-
-    0,   0,   0,   1,   0,   0,   0,   2,   0,   0,   0,   0,   0,   0,   0,   0, //6
-//   ,   a,   b,   c,   d,   e,   f,   g,   h,   i,   j,   k,   l,   m,   n,   o,
-
-    0,   0,   0,   0,   0,   3,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //7
-//  p,   q,   r,   s,   t,   u,   v,   w,   x,   y,   z,    ,    ,    ,    ,   
-
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //8
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //9
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //10
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //11
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //12
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //13
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //14
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0  //15
-};
-
-template <typename T = void>
-struct TranslateTableAsciiToRna5_
-{
-    static char const VALUE[256];
-};
-template <typename T>
-char const TranslateTableAsciiToRna5_<T>::VALUE[256] = 
-{
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //0
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //1
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //2
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //3
-
-    4,   0,   4,   1,   4,   4,   4,   2,   4,   4,   4,   4,   4,   4,   4,   4, //4
-//   ,   A,   B,   C,   D,   E,   D,   G,   H,   I,   J,   K,   L,   M,   N,   O,
-
-    4,   4,   4,   4,   4,   3,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //5
-//  P,   Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z,    ,    ,    ,    ,    
-
-    4,   0,   4,   1,   4,   4,   4,   2,   4,   4,   4,   4,   4,   4,   4,   4, //6
-//   ,   a,   b,   c,   d,   e,   f,   g,   h,   i,   j,   k,   l,   m,   n,   o,
-
-    4,   4,   4,   4,   4,   3,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //7
-//  p,   q,   r,   s,   t,   u,   v,   w,   x,   y,   z,    ,    ,    ,    ,   
-
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //8
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //9
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //10
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //11
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //12
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //13
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4, //14
-    4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4,   4  //15
-};
-
-
-template <typename T = void>
-struct TranslateTableByteToRna_
-{
-    static char const VALUE[256];
-};
-
-template <typename T>
-char const TranslateTableByteToRna_<T>::VALUE[256] = 
-{
-    0,   1,   2,   3,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //0
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //1
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //2
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //3
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //4
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //5
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //6
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //7
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //8
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //9
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //10
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //11
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //12
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //13
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //14
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0  //15
-};
-
-template <typename T = void>
-struct TranslateTableByteToRna5_
-{
-    static char const VALUE[256];
-};
-
-template <typename T>
-char const TranslateTableByteToRna5_<T>::VALUE[256] = 
-{
-    0,   1,   2,   3,   4,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //0
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //1
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //2
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //3
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //4
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //5
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //6
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //7
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //8
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //9
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //10
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //11
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //12
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //13
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0, //14
-    0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0  //15
-};
+// other tables identical to Dna(5)
 
 // --------------------------------------------------------------------------
 // Iupac
 // --------------------------------------------------------------------------
 
 template <typename T = void>
-struct TranslateTableIupacToAscii_
+struct TranslateTableIupacToChar_
 {
     static char const VALUE[16];
 };
 
 template <typename T>
-char const TranslateTableIupacToAscii_<T>::VALUE[16] = 
-{
-    'U', //0000=0
-    'T', //0001=1 //T=1: change between U and T is just inc/dec
-    'A', //0010=2
-    'W', //0011=3 TA
-    'C', //0100=4 
-    'Y', //0101=5 TC (pyrimidine)
-    'M', //0110=6 AC
-    'H', //0111=7 not-G
-    'G', //1000=8
-    'K', //1001=9 TG
-    'R', //1010=A AG (purine)
-    'D', //1011=B not-C
-    'S', //1100=C CG
-    'B', //1101=D non-A
-    'V', //1110=E non-T
+char const TranslateTableIupacToChar_<T>::VALUE[16] =
+{        //TGCA
+    'U', //0000=0 = or U
+    'A', //0001=1
+    'C', //0010=2
+    'M', //0011=3 AC
+    'G', //0100=4
+    'R', //0101=5 AG (purine)
+    'S', //0110=6 CG
+    'V', //0111=7 non-T
+    'T', //1000=8
+    'W', //1001=9 TA
+    'Y', //1010=A TC (pyrimidine)
+    'H', //1011=B not-G
+    'K', //1100=C TG
+    'D', //1101=D not-C
+    'B', //1110=E non-A
     'N'  //1111=F any
 };
 
@@ -370,24 +246,24 @@ struct TranslateTableIupacToDna_
 };
 
 template <typename T>
-char const TranslateTableIupacToDna_<T>::VALUE[16] = 
-{
-    3, //'U'
-    3, //'T'
-    0, //'A'
-    0, //'W' = TA
-    1, //'C' 
-    1, //'Y' = TC
-    0, //'M' = AC
-    0, //'H' = not-G
-    2, //'G'
-    2, //'K' = TG
-    0, //'R' = AG
-    0, //'D' = not-C
-    1, //'S' = CG
-    1, //'B' = non-A
-    0, //'V' = non-T
-    0  //'N' = any
+char const TranslateTableIupacToDna_<T>::VALUE[16] =
+{      //TGCA
+    3, //0000=0 = or U
+    0, //0001=1
+    1, //0010=2
+    0, //0011=3 AC
+    2, //0100=4
+    0, //0101=5 AG (purine)
+    1, //0110=6 CG
+    0, //0111=7 non-T
+    3, //1000=8
+    0, //1001=9 TA
+    1, //1010=A TC (pyrimidine)
+    0, //1011=B not-G
+    2, //1100=C TG
+    0, //1101=D not-C
+    1, //1110=E non-A
+    0  //1111=F any
 };
 
 template <typename T = void>
@@ -397,60 +273,56 @@ struct TranslateTableIupacToDna5_
 };
 
 template <typename T>
-char const TranslateTableIupacToDna5_<T>::VALUE[16] = 
-{
-    3, //'U'
-    3, //'T'
-    0, //'A'
-    4, //'W' = TA
-    1, //'C' 
-    4, //'Y' = TC
-    4, //'M' = AC
-    4, //'H' = not-G
-    2, //'G'
-    4, //'K' = TG
-    4, //'R' = AG
-    4, //'D' = not-C
-    4, //'S' = CG
-    4, //'B' = non-A
-    4, //'V' = non-T
-    4  //'N' = any
+char const TranslateTableIupacToDna5_<T>::VALUE[16] =
+{      //TGCA
+    3, //0000=0 = or U
+    0, //0001=1
+    1, //0010=2
+    4, //0011=3 AC
+    2, //0100=4
+    4, //0101=5 AG (purine)
+    4, //0110=6 CG
+    4, //0111=7 non-T
+    3, //1000=8
+    4, //1001=9 TA
+    4, //1010=A TC (pyrimidine)
+    4, //1011=B not-G
+    4, //1100=C TG
+    4, //1101=D not-C
+    4, //1110=E non-A
+    4  //1111=F any
 };
 
 template <typename T = void>
-struct TranslateTableAsciiToIupac_
+struct TranslateTableCharToIupac_
 {
     static char const VALUE[256];
 };
 
 template <typename T>
-char const TranslateTableAsciiToIupac_<T>::VALUE[256] = 
-{
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //0
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //1
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //2
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //3
-
-    15,   2,  13,   4,  11,  15,  15,   8,   7,  15,  15,   9,  15,   6,  15,  15, //4
-    //   ,   A,   B,   C,   D,   E,   F,   G,   H,   I,   J,   K,   L,   M,   N,   O,
-
-    15,  15,  10,  12,   1,   0,  14,   3,  15,   5,  15,  15,  15,  15,  15,  15, //5
-    //  P,   Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z,    ,    ,    ,    ,   
-
-    15,   2,  13,   4,  11,  15,  15,   8,   7,  15,  15,   9,  15,   6,  15,  15, //6
-    //   ,   a,   b,   c,   d,   e,   f,   g,   h,   i,   j,   k,   l,   m,   n,   o,
-
-    15,  15,  10,  12,   1,   0,  14,   3,  15,   5,  15,  15,  15,  15,  15,  15, //7
-    //  p,   q,   r,   s,   t,   u,   v,   w,   x,   y,   z,    ,    ,    ,    ,   
-
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //8
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //9
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //10
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //11
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //12
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //13
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //14
-    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15  //15
+char const TranslateTableCharToIupac_<T>::VALUE[256] =
+{
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    //                                                                =
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,   0,  15,  15,
+    //    A,   B,   C,   D,   E,   F,   G,   H,   I,   J,   K,   L,   M,   N,   O,
+    15,   1,  14,   2,  13,  15,  15,   4,  11,  15,  15,  12,  15,   3,  15,  15,
+    //    Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z
+    15,  15,   5,   6,   8,   0,   7,   9,  15,  10,  15,  15,  15,  15,  15,  15,
+    //    a,   b,   c,   d,   e,   f,   g,   h,   i,   j,   k,   l,   m,   n,   o,
+    15,   1,  14,   2,  13,  15,  15,   4,  11,  15,  15,  12,  15,   3,  15,  15,
+    //    q,   r,   s,   t,   u,   v,   w,   x,   y,   z
+    15,  15,   5,   6,   8,   0,   7,   9,  15,  10,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,
+    15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15
 };
 
 template <typename T = void>
@@ -460,9 +332,9 @@ struct TranslateTableByteToIupac_
 };
 
 template <typename T>
-char const TranslateTableByteToIupac_<T>::VALUE[256] = 
+char const TranslateTableByteToIupac_<T>::VALUE[256] =
 {
-    0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,  14,  15, //0
+    0,   1,   2,   3,   4,   5,   6,   7,   8,   9,   10,  11,  12,  13,  14,  15, //0
     15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //1
     15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //2
     15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15,  15, //3
@@ -485,73 +357,76 @@ char const TranslateTableByteToIupac_<T>::VALUE[256] =
 // --------------------------------------------------------------------------
 
 template <typename T = void>
-struct TranslateTableAAToAscii_
+struct TranslateTableAAToChar_
 {
-    static char const VALUE[24];
+    static char const VALUE[27];
 };
 template <typename T>
-char const TranslateTableAAToAscii_<T>::VALUE[24] = 
-{
-    'A', // 0 Ala Alanine                 
-    'R', // 1 Arg Arginine                
-    'N', // 2 Asn Asparagine              
-    'D', // 3 Asp Aspartic Acid           
-    'C', // 4 Cys Cystine                 
-    'Q', // 5 Gln Glutamine               
-    'E', // 6 Glu Glutamic Acid           
-    'G', // 7 Gly Glycine                 
-    'H', // 8 His Histidine               
-    'I', // 9 Ile Isoleucine              
-    'L', //10 Leu Leucine                 
-    'K', //11 Lys Lysine                  
-    'M', //12 Met Methionine              
-    'F', //13 Phe Phenylalanine           
-    'P', //14 Pro Proline                 
-    'S', //15 Ser Serine                  
-    'T', //16 Thr Threonine               
-    'W', //17 Trp Tryptophan              
-    'Y', //18 Tyr Tyrosine                
-    'V', //19 Val Valine                  
-    'B', //20 Aspartic Acid, Asparagine   
-    'Z', //21 Glutamic Acid, Glutamine    
-    'X', //22 Unknown                     
-    '*'  //23 Terminator                  
+char const TranslateTableAAToChar_<T>::VALUE[27] =
+{
+    'A', // Ala Alanine
+    'B', // Aspartic Acid, Asparagine
+    'C', // Cys Cystine
+    'D', // Asp Aspartic Acid
+    'E', // Glu Glutamic Acid
+    'F', // Phe Phenylalanine
+    'G', // Gly Glycine
+    'H', // His Histidine
+    'I', // Ile Isoleucine
+    'J', // Leucine, Isoleucine
+    'K', // Lys Lysine
+    'L', // Leu Leucine
+    'M', // Met Methionine
+    'N', // Asn Asparagine
+    'O', // Pyl Pyrrolysine
+    'P', // Pro Proline
+    'Q', // Gln Glutamine
+    'R', // Arg Arginine
+    'S', // Ser Serine
+    'T', // Thr Threonine
+    'U', // Selenocystein
+    'V', // Val Valine
+    'W', // Trp Tryptophan
+    'Y', // Tyr Tyrosine
+    'Z', // Glutamic Acid, Glutamine
+    'X', // Unknown
+    '*'  // Terminator
 };
 
 template <typename T = void>
-struct TranslateTableAsciiToAA_
+struct TranslateTableCharToAA_
 {
     static char const VALUE[256];
 };
 
 template <typename T>
-char const TranslateTableAsciiToAA_<T>::VALUE[256] = 
-{
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //0
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //1
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  23,  22,  22,  22,  22,  22, //2
-//                                                     *    
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //3
-    22,   0,  20,   4,   3,   6,  13,   7,   8,   9,  22,  11,  10,  12,   2,  22, //4
+char const TranslateTableCharToAA_<T>::VALUE[256] =
+{
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //0
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //1
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  26,  25,  25,  25,  25,  25, //2
+//                                                     *
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //3
+    25,   0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,  14, //4
 //    ,   A,   B,   C,   D,   E,   F,   G,   H,   I,   J,   K,   L,   M,   N,   O,
 
-    14,   5,   1,  15,  16,  22,  19,  17,  22,  18,  21,  22,  22,  22,  22,  22, //5
+    15,  16,  17,  18,  19,  20,  21,  22,  25,  23,  24,  25,  25,  25,  25,  25, //5
 //   P,   Q,   R,   S,   T,   U,   V,   W,   X,   Y,   Z,    ,    ,    ,    ,    ,
 
-    22,   0,  20,   4,   3,   6,  13,   7,   8,   9,  22,  11,  10,  12,   2,  22, //6
+    25,   0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,  14, //6
 //    ,   a,   b,   c,   d,   e,   f,   g,   h,   i,   j,   k,   l,   m,   n,   o,
 
-    14,   5,   1,  15,  16,  22,  19,  17,  22,  18,  21,  22,  22,  22,  22,  22, //7
+    15,  16,  17,  18,  19,  20,  21,  22,  25,  23,  24,  25,  25,  25,  25, //7
 //   p,   q,   r,   s,   t,   u,   v,   w,   x,   y,   z,    ,    ,    ,    ,    ,
 
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //8
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //9
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //10
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //11
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //12
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //13
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //14
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22  //15
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //8
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //9
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //10
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //11
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //12
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //13
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //14
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25  //15
 };
 
 template <typename T = void>
@@ -561,26 +436,26 @@ struct TranslateTableByteToAA_
 };
 
 template <typename T>
-char const TranslateTableByteToAA_<T>::VALUE[256] = 
+char const TranslateTableByteToAA_<T>::VALUE[256] =
 {
     0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,  14,  15, //0
-    16,  17,  18,  19,  20,  21,  22,  23,  22,  22,  22,  22,  22,  22,  22,  22, //1
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //2
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //3
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //4
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //5
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //6
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //7
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //8
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //9
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //10
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //11
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //12
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //13
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22, //14
-    22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22,  22  //15
+    16,  17,  18,  19,  20,  21,  22,  23,  24,  25,  25,  25,  25,  25,  25,  25, //1
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //2
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //3
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //4
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //5
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //6
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //7
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //8
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //9
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //10
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //11
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //12
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //13
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25, //14
+    25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25,  25  //15
 };
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_
diff --git a/seqan/basic/alphabet_simple_type.h b/seqan/basic/alphabet_simple_type.h
index 2d392c6..535ea52 100644
--- a/seqan/basic/alphabet_simple_type.h
+++ b/seqan/basic/alphabet_simple_type.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // The SimpleType alphabet type is the base class for all residue types.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_
 
 namespace seqan {
 
@@ -56,58 +56,75 @@ namespace seqan {
  * @class SimpleType
  * @implements FiniteOrderedAlphabetConcept
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief Implementation for "simple" types.
- * 
+ *
  * @signature template <typename TValue, typename TSpec>
  *            class SimpleType;
- * 
+ *
  * @tparam TSpec  Specialization tag.
  * @tparam TValue Type that stores the values of an instance.  TValue must be a simple type.
- * 
- * @section Remarks
- * 
+ *
  * A "simple type" is a C++ type that can be constructed without constructor, destructed without destructor and copied
  * without copy constructor or assignment operator.  All basic types (like <tt>char</tt>, <tt>int</tt> or
  * <tt>float</tt>) are simple. Pointers, references and arrays of simple types are simple.  POD types ("plain old data
  * types"), that are - simplified spoken - C++-types that already existed in C, are simple too.
- * 
+ *
  * Arrays of simple types can be copied very fast by memory manipulation routines, but the default implementation of
  * functions like arrayCopyForward and arrayCopy are not optimized for simple types this way.  But for classes derived
  * from <tt>SimpleType</tt>, optimized variants of array manipulation functions are applied.
- * 
+ *
  * Note that simple types need not to be derived or specialized from <tt>SimpleType</tt>, but it could be convenient to
  * do so.
- * 
+ *
  * @see IsSimple
  */
 
-/**
-.Class.SimpleType:
-..cat:Basic
-..implements:Concept.FiniteOrderedAlphabetConcept
-..summary:Implementation for "simple" types.
-..signature:SimpleType<TValue, TSpec>
-..param.TValue:Type that stores the values of an instance.
-...remarks:TValue must be a simple type.
-...metafunction:Metafunction.Value
-..param.TSpec:Specialization tag.
-...metafunction:Metafunction.Spec
-..remarks:
-...text:A "simple type" is a C++ type that can be constructed without constructor,
-destructed without destructor and copied without copy constructor or assignment operator.
-All basic types (like $char$, $int$ or $float$) are simple. Pointers, references and arrays of
-simple types are simple.
-POD types ("plain old data types"), that are - simplified spoken - C++-types that already existed in C,
-are simple too. 
-...text:Arrays of simple types can be copied very fast by memory manipulation routines, 
-but the default implementation of functions like @Function.arrayCopyForward@ and @Function.arrayCopy@
-are not optimized for simple types this way.
-But for classes derived from $SimpleType$, optimized variants of array manipulation functions are applied. 
-...text:Note that simple types need not to be derived or specialized from $SimpleType$, but
-it could be convenient to do so.
-..include:seqan/basic.h
-*/
+/*!
+ * @var TValue SimpleType::value
+ * @brief The internal value storage of the SimpleType object.
+ *
+ * @important Do not modify this value directly.  SimpleType implements conversion operators for all numeric types, so
+ *            you can simply assign and cast the SimpleType to all built-in numeric types.
+ *
+ * Stores the value of the SimpleType, is of type <tt>TValue</tt>.  Valid values are from <tt>0</tt> to @link
+ * FiniteOrderedAlphabetConcept#ValueSize @endlink minus one.
+ */
+
+/*!
+ * @fn SimpleType::SimpleType
+ * @brief Constructor of SimpleType type.
+ *
+ * @signature SimpleType::SimpleType();
+ * @signature SimpleType::SimpleType(other);
+ * @signature template <typename TParam> SimpleType::SimpleType(param);
+ *
+ * @param[in] other Other SimpleType to copy construct with.
+ * @param[in] param Any value of type <tt>TParam</tt> that can be assigned to the SimpleType object.
+ *
+ * The default constructor initializes the SimpleType object with the value <tt>0</tt> and the copy constructor copies
+ * over the value of the SimpleType.
+ *
+ * When constructing with a <tt>param</tt> that is not a SimpleType then <tt>param</tt> is assigned to the SimpleType
+ * object, using @link AssignableConcept#assign assign @endlink.  This function can be overloaded differently for each
+ * type.  You can expect the following behaviour for all SimpleType objects, however:
+ *
+ * <ul>
+ * <li>If <tt>param</tt> is a builtin integer then this value is directly assigned to the @link SimpleType::value value
+ *     @endlink member of the SimpleType object.  Note that this can allow an invalid assignment, e.g., when assigning
+ *     <tt>42</tt> to a @link Dna @endlink object.</li>
+ * <li>If <tt>param</tt> is a <tt>char</tt> then this character value is converted to the appropriate value and written
+ *     to the @link SimpleType::value value @endlink member.  For example, assigning <tt>'A'</tt> or <tt>'a'</tt> to
+ *     a SimpleType object assigns <tt>0</tt> to the @link SimpleType::value value @endlink member.</li>
+ * </ul>
+ *
+ * @section Example
+ *
+ * The following example shows construction of a @link Dna @endlink (specialization of SimpleType) object with from
+ * <tt>char</tt> and integer values.
+ *
+ * @snippet demos/dox/basic/simple_type_construction.cpp simple type construction and assignment
+ */
 
 #ifdef PLATFORM_WINDOWS
     #pragma pack(push,1)
@@ -150,16 +167,16 @@ class SimpleType
     // ------------------------------------------------------------------------
 
     SEQAN_HOST_DEVICE
-    SimpleType & operator=(SimpleType const & other) 
-    { 
+    SimpleType & operator=(SimpleType const & other)
+    {
         assign(*this, other);
         return *this;
     }
 
     template <typename T>
     SEQAN_HOST_DEVICE inline SimpleType &
-    operator=(T const & other) 
-    { 
+    operator=(T const & other)
+    {
         assign(*this, other);
         return *this;
     }
@@ -263,22 +280,30 @@ class SimpleType
 // Metafunction IsSimple
 // ----------------------------------------------------------------------------
 
-///.Metafunction.IsSimple.param.T.type:Class.SimpleType
-
 template <typename TValue, typename TSpec>
 struct IsSimple<SimpleType<TValue, TSpec> >
 {
     typedef True Type;
 };
 
+// ----------------------------------------------------------------------------
+// Concept Convertible
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TSource>
+struct Is< Convertible<SimpleType<TValue, TSpec>, TSource> > :
+    Is< FundamentalConcept<TSource> > {};
+
+template <typename TTarget, typename TValue, typename TSpec>
+struct Is< Convertible<TTarget, SimpleType<TValue, TSpec> > > :
+    Is< FundamentalConcept<TTarget> > {};
+
 // ----------------------------------------------------------------------------
 // Metafunction Value
 // ----------------------------------------------------------------------------
 
 // TODO(holtgrew): Rename? SimpleType is no container!
 
-///.Metafunction.Value.param.T.type:Class.SimpleType
-
 template <typename TValue, typename TSpec>
 struct Value<SimpleType<TValue, TSpec> >
 {
@@ -335,8 +360,6 @@ supremumValueImpl(SimpleType<TValue, TSpec> *)
 // Metafunction Spec
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Spec.param.T.type:Class.SimpleType
-
 template <typename TValue, typename TSpec>
 struct Spec<SimpleType<TValue, TSpec> >
 {
@@ -359,7 +382,7 @@ struct Spec<SimpleType<TValue, TSpec> const>
 // TODO(holtgrew): Is some of the code below redundant, can we lose some copy and paste here?
 
 template <typename TValue, typename TSpec, typename TRight>
-struct CompareType<SimpleType<TValue, TSpec>, TRight>
+struct CompareTypeImpl<SimpleType<TValue, TSpec>, TRight>
 {
     typedef TRight Type;
 };
@@ -392,7 +415,7 @@ convertImpl(Convert<TTarget, T> const,
 
 template <typename TStream, typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline TStream &
-operator<<(TStream & stream, 
+operator<<(TStream & stream,
            SimpleType<TValue, TSpec> const & data)
 {
     stream << convert<char>(data);
@@ -405,7 +428,7 @@ operator<<(TStream & stream,
 
 template <typename TStream, typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline TStream &
-operator>>(TStream & stream, 
+operator>>(TStream & stream,
            SimpleType<TValue, TSpec> & data)
 {
     char c;
@@ -418,13 +441,9 @@ operator>>(TStream & stream,
 // Function assign()
 // ----------------------------------------------------------------------------
 
-///.Function.assign.param.target.type:Class.SimpleType
-///.Function.assign.param.target.type:Class.SimpleType
-///.Function.assign.class:Class.SimpleType
-
 template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSourceSpec>
 SEQAN_HOST_DEVICE inline void
-assign(SimpleType<TTargetValue, TTargetSpec> & target, 
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
        SimpleType<TSourceValue, TSourceSpec> & source)
 {
     target.value = source.value;
@@ -432,15 +451,15 @@ assign(SimpleType<TTargetValue, TTargetSpec> & target,
 
 template <typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSourceSpec>
 SEQAN_HOST_DEVICE inline void
-assign(SimpleType<TTargetValue, TTargetSpec> & target, 
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
        SimpleType<TSourceValue, TSourceSpec> const & source)
 {
     target.value = source.value;
 }
 
 template <typename TTargetValue, typename TTargetSpec, typename TSource>
-SEQAN_HOST_DEVICE inline void 
-assign(SimpleType<TTargetValue, TTargetSpec> & target, 
+SEQAN_HOST_DEVICE inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
        TSource & source)
 {
     target.value = source;
@@ -448,27 +467,27 @@ assign(SimpleType<TTargetValue, TTargetSpec> & target,
 
 template <typename TTargetValue, typename TTargetSpec, typename TSource>
 SEQAN_HOST_DEVICE inline void
-assign(SimpleType<TTargetValue, TTargetSpec> & target, 
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
        TSource const & source)
 {
     target.value = source;
 }
 
-// Assign Proxy to SimpleType 
+// Assign Proxy to SimpleType
 // NOTE(doering): Diese Funktionen wurden noetig wegen eines seltsamen VC++-Verhaltens
 // TODO(holtgrew): Still necessary with dropped 2003 support?
 
 template <typename TTargetValue, typename TTargetSpec, typename TSourceSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(SimpleType<TTargetValue, TTargetSpec> & target, 
+SEQAN_HOST_DEVICE inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
        Proxy<TSourceSpec> & source)
 {
     target.value = getValue(source);
 }
 
 template <typename TTargetValue, typename TTargetSpec, typename TSourceSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(SimpleType<TTargetValue, TTargetSpec> & target, 
+SEQAN_HOST_DEVICE inline void
+assign(SimpleType<TTargetValue, TTargetSpec> & target,
        Proxy<TSourceSpec> const & source)
 {
     target.value = getValue(source);
@@ -478,144 +497,144 @@ assign(SimpleType<TTargetValue, TTargetSpec> & target,
 // NOTE(doering): It is not possible to write a single function here since "assign" must be specialized for the first argument at the first place
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(__int64 & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(__int64 & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(__int64 & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(__int64 & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(__uint64 & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(__uint64 & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(__uint64 & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(__uint64 & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(int & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(int & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(int & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(int & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(unsigned int & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(unsigned int & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(unsigned int & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(unsigned int & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(short & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(short & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(short & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(short & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(unsigned short & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(unsigned short & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(unsigned short & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(unsigned short & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(char & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(char & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(char & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(char & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(signed char & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(signed char & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(signed char & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(signed char & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(unsigned char & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(unsigned char & c_target,
        SimpleType<TValue, TSpec> & source)
 {
     c_target = source.value;
 }
 
 template <typename TValue, typename TSpec>
-SEQAN_HOST_DEVICE inline void 
-assign(unsigned char & c_target, 
+SEQAN_HOST_DEVICE inline void
+assign(unsigned char & c_target,
        SimpleType<TValue, TSpec> const & source)
 {
     c_target = source.value;
@@ -627,7 +646,7 @@ assign(unsigned char & c_target,
 
 template <typename TValue, typename TSpec, typename TRight>
 SEQAN_HOST_DEVICE inline bool
-operator==(SimpleType<TValue, TSpec> const & left_, 
+operator==(SimpleType<TValue, TSpec> const & left_,
            TRight const & right_)
 {
     typedef SimpleType<TValue, TSpec> TLeft;
@@ -637,7 +656,7 @@ operator==(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TLeft, typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator==(TLeft const & left_, 
+operator==(TLeft const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     typedef SimpleType<TValue, TSpec> TRight;
@@ -647,7 +666,7 @@ operator==(TLeft const & left_,
 
 template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
 SEQAN_HOST_DEVICE inline bool
-operator==(SimpleType<TLeftValue, TLeftSpec> const & left_, 
+operator==(SimpleType<TLeftValue, TLeftSpec> const & left_,
            SimpleType<TRightValue, TRightSpec> const & right_)
 {
     typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
@@ -658,7 +677,7 @@ operator==(SimpleType<TLeftValue, TLeftSpec> const & left_,
 
 template <typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator==(SimpleType<TValue, TSpec> const & left_, 
+operator==(SimpleType<TValue, TSpec> const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     return convert<TValue>(left_) == convert<TValue>(right_);
@@ -666,7 +685,7 @@ operator==(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TSpec, typename TValue, typename TSpec2>
 SEQAN_HOST_DEVICE inline bool
-operator==(Proxy<TSpec> const & left_, 
+operator==(Proxy<TSpec> const & left_,
            SimpleType<TValue, TSpec2> const & right_)
 {
     typedef Proxy<TSpec> TLeft;
@@ -692,7 +711,7 @@ operator==(SimpleType<TValue, TSpec2> const & left_,
 
 template <typename TValue, typename TSpec, typename TRight>
 SEQAN_HOST_DEVICE inline bool
-operator!=(SimpleType<TValue, TSpec> const & left_, 
+operator!=(SimpleType<TValue, TSpec> const & left_,
            TRight const & right_)
 {
     typedef SimpleType<TValue, TSpec> TLeft;
@@ -702,7 +721,7 @@ operator!=(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TLeft, typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator!=(TLeft const & left_, 
+operator!=(TLeft const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     typedef SimpleType<TValue, TSpec> TRight;
@@ -712,7 +731,7 @@ operator!=(TLeft const & left_,
 
 template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
 SEQAN_HOST_DEVICE inline bool
-operator!=(SimpleType<TLeftValue, TLeftSpec> const & left_, 
+operator!=(SimpleType<TLeftValue, TLeftSpec> const & left_,
            SimpleType<TRightValue, TRightSpec> const & right_)
 {
     typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
@@ -723,7 +742,7 @@ operator!=(SimpleType<TLeftValue, TLeftSpec> const & left_,
 
 template <typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator!=(SimpleType<TValue, TSpec> const & left_, 
+operator!=(SimpleType<TValue, TSpec> const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     return convert<TValue>(left_) != convert<TValue>(right_);
@@ -731,7 +750,7 @@ operator!=(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TSpec, typename TValue, typename TSpec2>
 SEQAN_HOST_DEVICE inline bool
-operator!=(Proxy<TSpec> const & left_, 
+operator!=(Proxy<TSpec> const & left_,
            SimpleType<TValue, TSpec2> const & right_)
 {
     typedef Proxy<TSpec> TLeft;
@@ -757,7 +776,7 @@ operator!=(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TValue, typename TSpec, typename TRight>
 SEQAN_HOST_DEVICE inline bool
-operator<(SimpleType<TValue, TSpec> const & left_, 
+operator<(SimpleType<TValue, TSpec> const & left_,
           TRight const & right_)
 {
     typedef SimpleType<TValue, TSpec> TLeft;
@@ -767,7 +786,7 @@ operator<(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TLeft, typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator<(TLeft const & left_, 
+operator<(TLeft const & left_,
           SimpleType<TValue, TSpec> const & right_)
 {
     typedef SimpleType<TValue, TSpec> TRight;
@@ -777,7 +796,7 @@ operator<(TLeft const & left_,
 
 template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
 SEQAN_HOST_DEVICE inline bool
-operator<(SimpleType<TLeftValue, TLeftSpec> const & left_, 
+operator<(SimpleType<TLeftValue, TLeftSpec> const & left_,
           SimpleType<TRightValue, TRightSpec> const & right_)
 {
     typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
@@ -788,7 +807,7 @@ operator<(SimpleType<TLeftValue, TLeftSpec> const & left_,
 
 template <typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator<(SimpleType<TValue, TSpec> const & left_, 
+operator<(SimpleType<TValue, TSpec> const & left_,
           SimpleType<TValue, TSpec> const & right_)
 {
     return convert<TValue>(left_) < convert<TValue>(right_);
@@ -796,7 +815,7 @@ operator<(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TSpec, typename TValue, typename TSpec2>
 SEQAN_HOST_DEVICE inline bool
-operator<(Proxy<TSpec> const & left_, 
+operator<(Proxy<TSpec> const & left_,
           SimpleType<TValue, TSpec2> const & right_)
 {
     typedef Proxy<TSpec> TLeft;
@@ -822,7 +841,7 @@ operator<(SimpleType<TValue, TSpec2> const & left_,
 
 template <typename TValue, typename TSpec, typename TRight>
 SEQAN_HOST_DEVICE inline bool
-operator<=(SimpleType<TValue, TSpec> const & left_, 
+operator<=(SimpleType<TValue, TSpec> const & left_,
            TRight const & right_)
 {
     typedef SimpleType<TValue, TSpec> TLeft;
@@ -832,7 +851,7 @@ operator<=(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TLeft, typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator<=(TLeft const & left_, 
+operator<=(TLeft const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     typedef SimpleType<TValue, TSpec> TRight;
@@ -842,7 +861,7 @@ operator<=(TLeft const & left_,
 
 template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
 SEQAN_HOST_DEVICE inline bool
-operator<=(SimpleType<TLeftValue, TLeftSpec> const & left_, 
+operator<=(SimpleType<TLeftValue, TLeftSpec> const & left_,
            SimpleType<TRightValue, TRightSpec> const & right_)
 {
     typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
@@ -853,7 +872,7 @@ operator<=(SimpleType<TLeftValue, TLeftSpec> const & left_,
 
 template <typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator<=(SimpleType<TValue, TSpec> const & left_, 
+operator<=(SimpleType<TValue, TSpec> const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     return convert<TValue>(left_) <= convert<TValue>(right_);
@@ -861,7 +880,7 @@ operator<=(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TSpec, typename TValue, typename TSpec2>
 SEQAN_HOST_DEVICE inline bool
-operator<=(Proxy<TSpec> const & left_, 
+operator<=(Proxy<TSpec> const & left_,
            SimpleType<TValue, TSpec2> const & right_)
 {
     typedef Proxy<TSpec> TLeft;
@@ -886,7 +905,7 @@ operator<=(SimpleType<TValue, TSpec2> const & left_,
 
 template <typename TValue, typename TSpec, typename TRight>
 SEQAN_HOST_DEVICE inline bool
-operator>(SimpleType<TValue, TSpec> const & left_, 
+operator>(SimpleType<TValue, TSpec> const & left_,
           TRight const & right_)
 {
             typedef SimpleType<TValue, TSpec> TLeft;
@@ -896,7 +915,7 @@ operator>(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TLeft, typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator>(TLeft const & left_, 
+operator>(TLeft const & left_,
           SimpleType<TValue, TSpec> const & right_)
 {
     typedef SimpleType<TValue, TSpec> TRight;
@@ -906,7 +925,7 @@ operator>(TLeft const & left_,
 
 template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
 SEQAN_HOST_DEVICE inline bool
-operator>(SimpleType<TLeftValue, TLeftSpec> const & left_, 
+operator>(SimpleType<TLeftValue, TLeftSpec> const & left_,
           SimpleType<TRightValue, TRightSpec> const & right_)
 {
     typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
@@ -917,7 +936,7 @@ operator>(SimpleType<TLeftValue, TLeftSpec> const & left_,
 
 template <typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator>(SimpleType<TValue, TSpec> const & left_, 
+operator>(SimpleType<TValue, TSpec> const & left_,
           SimpleType<TValue, TSpec> const & right_)
 {
     return convert<TValue>(left_) > convert<TValue>(right_);
@@ -925,7 +944,7 @@ operator>(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TSpec, typename TValue, typename TSpec2>
 SEQAN_HOST_DEVICE inline bool
-operator>(Proxy<TSpec> const & left_, 
+operator>(Proxy<TSpec> const & left_,
           SimpleType<TValue, TSpec2> const & right_)
 {
     typedef Proxy<TSpec> TLeft;
@@ -951,7 +970,7 @@ operator>(SimpleType<TValue, TSpec2> const & left_,
 
 template <typename TValue, typename TSpec, typename TRight>
 SEQAN_HOST_DEVICE inline bool
-operator>=(SimpleType<TValue, TSpec> const & left_, 
+operator>=(SimpleType<TValue, TSpec> const & left_,
            TRight const & right_)
 {
     typedef SimpleType<TValue, TSpec> TLeft;
@@ -961,7 +980,7 @@ operator>=(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TLeft, typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator>=(TLeft const & left_, 
+operator>=(TLeft const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     typedef SimpleType<TValue, TSpec> TRight;
@@ -971,7 +990,7 @@ operator>=(TLeft const & left_,
 
 template <typename TLeftValue, typename TLeftSpec, typename TRightValue, typename TRightSpec>
 SEQAN_HOST_DEVICE inline bool
-operator>=(SimpleType<TLeftValue, TLeftSpec> const & left_, 
+operator>=(SimpleType<TLeftValue, TLeftSpec> const & left_,
            SimpleType<TRightValue, TRightSpec> const & right_)
 {
     typedef SimpleType<TLeftValue, TLeftSpec> TLeft;
@@ -982,7 +1001,7 @@ operator>=(SimpleType<TLeftValue, TLeftSpec> const & left_,
 
 template <typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
-operator>=(SimpleType<TValue, TSpec> const & left_, 
+operator>=(SimpleType<TValue, TSpec> const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     return convert<TValue>(left_) >= convert<TValue>(right_);
@@ -990,7 +1009,7 @@ operator>=(SimpleType<TValue, TSpec> const & left_,
 
 template <typename TSpec, typename TValue, typename TSpec2>
 SEQAN_HOST_DEVICE inline bool
-operator>=(Proxy<TSpec> const & left_, 
+operator>=(Proxy<TSpec> const & left_,
            SimpleType<TValue, TSpec2> const & right_)
 {
     typedef Proxy<TSpec> TLeft;
@@ -1078,4 +1097,4 @@ ordValue(SimpleType<TValue, TSpec> const & c)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_
diff --git a/seqan/basic/alphabet_storage.h b/seqan/basic/alphabet_storage.h
index a2e7ba9..aa4fc48 100644
--- a/seqan/basic/alphabet_storage.h
+++ b/seqan/basic/alphabet_storage.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 // construction type (simple, non-simple) and storage size.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_
 
 #include <float.h>
 
@@ -54,11 +54,6 @@ class SimpleType;
 // Tags, Classes, Enums
 // ============================================================================
 
-// TODO(holtgrew): Remove Ascii and Unicode alias. Also see #849.
-typedef char Ascii;
-//typedef unsigned char Byte;  // TODO(holtgrew): Disabling, remove together with Ascii and Unicode with #849
-typedef wchar_t Unicode;
-
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -131,9 +126,9 @@ struct ValueSize<float>
 
 // The internal value size is used for alphabets with piggyback qualities,
 // for example Dna5Q.  Here, the public value size is 5 but the internal
-// value size is 256.  
+// value size is 256.
 
-template <typename TValue> 
+template <typename TValue>
 struct InternalValueSize_
         : public ValueSize<TValue>
 {};
@@ -146,36 +141,21 @@ struct InternalValueSize_
  * @mfn BytesPerValue
  * @headerfile <seqan/basic.h>
  * @brief Number of bytes needed to store a value.
- * 
+ *
  * @signature BytesPerValue<T>::VALUE
- * 
+ *
  * @tparam T The type to query.
- * 
- * @return VALUE The number of bytes to store on T object.
  *
- * @section Remarks
+ * @return VALUE The number of bytes to store on T object.
  *
  * By default, this function returns <tt>ceil(BitsPerValue&lt;T&gt;::VALUE)</tt>.  For built-in types, this is the same
  * as <tt>sizeof(T)</tt>.
- * 
+ *
  * @see FiniteOrderedAlphabetConcept#ValueSize
  * @see AlphabetConcept#BitsPerValue
  * @see IntegralForValue
  */
 
-/**
-.Metafunction.BytesPerValue:
-..cat:Basic
-..summary:Number of bytes needed to store a value.
-..signature:BytesPerValue<T>::VALUE
-..param.T:A class.
-..returns.param.VALUE:Number of bytes needed to store $T$.
-...default:$BitsPerValue / 8$, rounded up. For built-in types, this is the same as $sizeof(T)$.
-..see:Metafunction.ValueSize
-..see:Metafunction.BitsPerValue
-..include:seqan/basic.h
-*/
-
 template <typename TValue>
 struct BytesPerValue
 {
@@ -190,15 +170,13 @@ struct BytesPerValue
  * @mfn IntegralForValue
  * @headerfile <seqan/basic.h>
  * @brief Returns an itegral type that provides sufficient space to store a value.
- * 
- * @signature IntegralForValue<T>::Type
- * 
+ *
+ * @signature IntegralForValue<T>::Type;
+ *
  * @tparam T The type to query.
- * 
+ *
  * @return Type An integral type.
- * 
- * @section Remarks
- * 
+ *
  * The type is the smallest unsigned integral type that has a size of at least BytesPerValue bytes.
  *
  * <table>
@@ -227,37 +205,15 @@ struct BytesPerValue
  *     <td><tt>__int64</tt></td>
  *   </tr>
  * </table>
- * 
+ *
  * Note that the returned integral type cannot store <tt>T</tt> values, if <tt>T</tt> takes more than 8 bytes, since
  * there exists no integral type that provides sufficient space to store types of this size.
- * 
+ *
  * @see FiniteOrderedAlphabetConcept#ValueSize
  * @see AlphabetConcept#BitsPerValue
  * @see BytesPerValue
  */
 
-/**
-.Metafunction.IntegralForValue:
-..cat:Basic
-..summary:Returns an itegral type that provides sufficient space to store a value.
-..signature:IntegralForValue<T>::Type
-..param.T:A class.
-..returns.param.Type:An integral type that can store $T$ values.
-..remarks:The type is the smallest unsigned integral type that has a size of at least @Metafunction.BytesPerValue@ bytes.
-...tableheader:bytes|integral type
-...table:1|$unsigned char$
-...table:2|$unsigned short$
-...table:3|$unsigned int$
-...table:4|$unsigned int$
-...table:5 and above|$__int64$
-..remarks:Note that the returned integral type cannot store $T$ values, if $T$ takes more than 8 bytes, 
-    since there exists no integral type that provides sufficient space to store types of this size.
-..see:Metafunction.ValueSize
-..see:Metafunction.BitsPerValue
-..see:Metafunction.BytesPerValue
-..include:seqan/basic.h
-*/
-
 template <int SIZE>
 struct IntegralForValueImpl_
 {
@@ -307,7 +263,7 @@ template <typename TValue>
 SEQAN_HOST_DEVICE inline typename ValueSize<TValue>::Type
 ordValue(TValue const & c)
 {
-	return convert<unsigned>(static_cast<typename MakeUnsigned_<TValue>::Type const &>(c));
+    return convert<unsigned>(static_cast<typename MakeUnsigned_<TValue>::Type const &>(c));
 }
 
 // The internal ord value is used for alphabets with piggyback qualities.
@@ -316,7 +272,7 @@ template <typename TValue>
 SEQAN_HOST_DEVICE inline typename ValueSize<TValue>::Type
 _internalOrdValue(TValue const & c)
 {
-	return ordValue(c);
+    return ordValue(c);
 }
 
 // ----------------------------------------------------------------------------
@@ -332,4 +288,4 @@ valueSize()
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_
diff --git a/seqan/basic/array_construct_destruct.h b/seqan/basic/array_construct_destruct.h
index 3e983f2..5e192bc 100644
--- a/seqan/basic/array_construct_destruct.h
+++ b/seqan/basic/array_construct_destruct.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,8 +41,8 @@
 
 #include <new>
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_
 
 namespace seqan {
 
@@ -68,38 +68,20 @@ namespace seqan {
  * @mfn IsSimple
  * @headerfile <seqan/basic.h>
  * @brief Tests type to be simple.
- * 
+ *
  * @signature IsSimple<T>::Type;
- * 
+ *
  * @tparam T Type that is tested.
- * 
+ *
  * @return Type Either True or False, depending on T being a "POD" type.
- * 
- * @section Remarks
- * 
+ *
  * A simple type is a type that does not need constructors to be created, a destructor to be destroyed, and copy
  * assignment operators or copy constructors to be copied.  All POD ("plain old data") types are simple, but some
  * non-POD types could be simple too, e.g. some specializations of SimpleType.
- * 
+ *
  * @see SimpleType
  */
 
-/**
-.Metafunction.IsSimple
-..cat:Basic
-..summary:Tests type to be simple.
-..signature:IsSimple<T>::Type
-..param.T:Type that is tested.
-..returns.param.Type:@Tag.Logical Values.True@, if $T$ is a simple type, @Tag.Logical Values.False@ otherwise.
-...default:@Tag.Logical Values.False@
-..remarks:A simple type is a type that does not need constructors to be created,
-a destructor to be destroyed, and copy assignment operators or copy constructors
-to be copied. All POD ("plain old data") types are simple, but some
-non-POD types could be simple too, e.g. some specializations of @Class.SimpleType@.
-..see:Class.SimpleType
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct IsSimple_
 {
@@ -149,9 +131,6 @@ struct IsSimple<T const> : public IsSimple<T> {};
 
 // TODO(holtgrew): This should probably to into sequence module along with this header.
 
-///.Metafunction.Value.param.T.type:Adaption.char array
-///.Metafunction.Value.class:Adaption.char array
-
 template <typename TValue>
 struct Value<TValue *>
 {
@@ -187,9 +166,6 @@ struct Value<TValue const [SIZE]>
 
 // TODO(holtgrew): This should probably to into sequence module along with this header.
 
-///.Metafunction.Reference.param.T.type:Adaption.char array
-///.Metafunction.Reference.class:Adaption.char array
-
 template <typename TValue>
 struct Reference<TValue *>
 {
@@ -216,7 +192,6 @@ template <typename T>
 SEQAN_HOST_DEVICE inline T &
 value(T * me)
 {
-    SEQAN_CHECKPOINT;
     return *me;
 }
 
@@ -230,7 +205,6 @@ template <typename T>
 SEQAN_HOST_DEVICE inline T &
 getValue(T * me)
 {
-    SEQAN_CHECKPOINT;
     return value(me);
 }
 
@@ -246,36 +220,20 @@ getValue(T * me)
  * @fn valueConstruct
  * @headerfile <seqan/basic.h>
  * @brief Constructs an object at specified position.
- * 
+ *
  * @signature void valueConstruct(iterator [, param [, move_tag]]);
- * 
- * @param iterator Pointer or iterator to position where the object should be constructed.
- * @param param    Parameter that is forwarded to constructor.
- * @param moveTag  Instance of the move tag.  If the tag is specified, it is forwarded to the constructor, so the
- *                 constructed object must support move construction.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] iterator Pointer or iterator to position where the object should be constructed.
+ * @param[in]     param    Parameter that is forwarded to constructor.
+ * @param[in]     moveTag  Instance of the move tag.  If the tag is specified, it is forwarded to the constructor,
+ *                         so the constructed object must support move construction.
+ *
  * The type of the destructed object is the value type of <tt>iterator</tt>.
  */
 
-/**
-.Function.valueConstruct
-..cat:Content Manipulation
-..summary:Constructs an object at specified position.
-..signature:valueConstruct(iterator [, param [, move_tag] ])
-..param.iterator:Pointer or iterator to position where the object should be constructed.
-..param.param:Parameter that is forwarded to constructor. (optional)
-..param.move_tag:Instance of the @Tag.Move Switch.move switch tag@. (optional)
-...remarks:If the @Tag.Move Switch.move switch tag@ is specified, it is forwarded to the constructor,
-so the constructed object must support move construction.
-..remarks:The type of the destructed object is the @Metafunction.Value.value type@ of $iterator$.
-..include:seqan/basic.h
-*/
-
 // Helper code for constructing values behind iterators that do not return
 // proxies from their value() functions but references.
-struct ValueConstructor_ 
+struct ValueConstructor_
 {
     template <typename TIterator>
     static inline void
@@ -289,7 +247,32 @@ struct ValueConstructor_
     template <typename TIterator, typename TParam>
     static inline void
     construct(TIterator it,
-              TParam const & param_)
+              TParam SEQAN_FORWARD_CARG param_)
+    {
+        typedef typename Value<TIterator>::Type    TValue;
+        typedef typename RemoveConst<TValue>::Type TNonConstValue;
+        new( (void*) & value(it) ) TNonConstValue(SEQAN_FORWARD(TParam, param_));
+    }
+
+#ifndef SEQAN_CXX11_STANDARD
+    template <typename TIterator, typename TParam>
+    static inline void
+    construct(TIterator it,
+              TParam & param_,
+              Move const & tag,
+              True)
+    {
+        typedef typename Value<TIterator>::Type    TValue;
+        typedef typename RemoveConst<TValue>::Type TNonConstValue;
+        new( (void*) & value(it) ) TNonConstValue(param_, tag);
+    }
+
+    template <typename TIterator, typename TParam>
+    static inline void
+    construct(TIterator it,
+              TParam & param_,
+              Move const &,
+              False)
     {
         typedef typename Value<TIterator>::Type    TValue;
         typedef typename RemoveConst<TValue>::Type TNonConstValue;
@@ -304,31 +287,33 @@ struct ValueConstructor_
     {
         typedef typename Value<TIterator>::Type    TValue;
         typedef typename RemoveConst<TValue>::Type TNonConstValue;
-        new( (void*) & value(it) ) TNonConstValue(param_, tag);
+        construct(it, param_, tag, typename HasMoveConstructor<TNonConstValue>::Type());
     }
+#endif
 };
 
 // Helper code for constructing values behind iterators that return proxies
 // from their value() function.
 //
 // TODO(holtgrew): These implementations are empty and to be overwritten. Should we have dynamic/static asserstions here?
-struct ValueConstructorProxy_ 
+struct ValueConstructorProxy_
 {
     template <typename TIterator>
     static inline void construct(TIterator) {}
 
     template <typename TIterator, typename TParam>
-    static inline void construct(TIterator, TParam const &) {}
+    static inline void construct(TIterator, TParam SEQAN_FORWARD_CARG) {}
 
+#ifndef SEQAN_CXX11_STANDARD
     template <typename TIterator, typename TParam>
     static inline void construct(TIterator, TParam &, Move const & ) {}
+#endif
 };
 
 template <typename TIterator>
 inline void
 valueConstruct(TIterator it)
 {
-    SEQAN_CHECKPOINT;
     typedef typename IfC<
         IsSameType<
             typename Value<TIterator>::Type &,
@@ -346,9 +331,8 @@ valueConstruct(TIterator it)
 template <typename TIterator, typename TParam>
 inline void
 valueConstruct(TIterator it,
-               TParam const & param_)
+               TParam SEQAN_FORWARD_CARG param_)
 {
-    SEQAN_CHECKPOINT;
     typedef typename IfC<
         IsSameType<
             typename Value<TIterator>::Type &,
@@ -360,16 +344,16 @@ valueConstruct(TIterator it,
         ValueConstructorProxy_      // false, types differ -> value() returns a proxy
     >::Type TConstructor;
 
-    TConstructor::construct(it, param_);
+    TConstructor::construct(it, SEQAN_FORWARD(TParam, param_));
 }
 
+#ifndef SEQAN_CXX11_STANDARD
 template <typename TIterator, typename TParam>
 inline void
 valueConstruct(TIterator it,
                TParam & param_,
                Move const & tag)
 {
-    SEQAN_CHECKPOINT;
     typedef typename IfC<
         IsSameType<
             typename Value<TIterator>::Type &,
@@ -383,6 +367,7 @@ valueConstruct(TIterator it,
 
     TConstructor::construct(it, param_, tag);
 }
+#endif
 
 // ----------------------------------------------------------------------------
 // Function valueDestruct() using iterators
@@ -390,7 +375,7 @@ valueConstruct(TIterator it,
 
 // Helper code for destructing values behind iterators that do not return
 // proxies from their value() function but references.
-struct ValueDestructor_ 
+struct ValueDestructor_
 {
     template <typename TValue>
     static inline void
@@ -411,7 +396,7 @@ struct ValueDestructor_
 // from their value() function.
 //
 // TODO(holtgrew): These implementations are empty and to be overwritten. Should we have dynamic/static asserstions here?
-struct ValueDestructorProxy_ 
+struct ValueDestructorProxy_
 {
     template <typename TIterator>
     static inline void destruct(TIterator) {}
@@ -420,33 +405,19 @@ struct ValueDestructorProxy_
 /*!
  * @fn valueDestruct
  * @headerfile <seqan/basic.h>
- * @brief Destoys an object at specified position.
- * 
+ * @brief Destroys an object at specified position.
+ *
  * @signature void valueDestruct(iterator);
- * 
- * @param iterator Pointer or iterator to position where the object should be destructed.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] iterator Pointer or iterator to position where the object should be destructed.
+ *
  * The type of the constructed object is the value type of <tt>iterator</tt>.
  */
 
-/**
-.Function.valueDestruct
-..cat:Content Manipulation
-..summary:Destoys an object at specified position.
-..signature:valueDestruct(iterator)
-..param.iterator:Pointer or iterator to position where the object should be destructed.
-..remarks:The type of the constructed object is the @Metafunction.Value.value type@ of $iterator$.
-..see:Function.valueConstruct
-..include:seqan/basic.h
-*/
-
 template <typename TIterator>
 inline void
 valueDestruct(TIterator it)
 {
-    SEQAN_CHECKPOINT;
     typedef typename IfC<
         IsSameType<
             typename Value<TIterator>::Type &,
@@ -469,47 +440,24 @@ valueDestruct(TIterator it)
  * @fn arrayConstruct
  * @headerfile <seqan/basic.h>
  * @brief Construct objects in a given memory buffer.
- * 
+ *
  * @signature void arrayConstruct(begin, end[, value]);
- * 
- * @param begin Iterator to the begin of the range that is to be constructed.
- * @param end   Iterator behind the end of the range.
- * @param value Argument that is forwarded to the constructor.  An appropriate constructor is required.  If
- *              <tt>value</tt> is not specified, the default constructor is used.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] begin Iterator to the begin of the range that is to be constructed.
+ * @param[in] end   Iterator behind the end of the range.
+ * @param[in] value Argument that is forwarded to the constructor.  An appropriate constructor is required.  If
+ *                 <tt>value</tt> is not specified, the default constructor is used.
+ *
  * The type of the constructed Objects is the value type of <tt>begin</tt> and <tt>end</tt>.
  */
 
-/**
-.Function.arrayConstruct
-..cat:Array Handling
-..summary:Construct objects in a given memory buffer.
-..signature:arrayConstruct(begin, end [, value])
-..param.begin:Iterator to the begin of the range that is to be constructed.
-..param.end:Iterator behind the end of the range.
-..param.value:Argument that is forwarded to the constructor. (optional)
-...text:An appropriate constructor is required. 
-If $value$ is not specified, the default constructor is used. 
-..remarks:The type of the constructed Objects is the @Metafunction.Value.value type@
-of $begin$ and $end$.
-..see:Function.arrayDestruct
-..see:Function.arrayConstructCopy
-..see:Function.arrayFill
-..see:Class.SimpleType
-..see:Function.valueConstruct
-..include:seqan/basic.h
-*/
-
 // NOTE(holtgrew): Of course, it does not make sense to declare this in a move version!
 
 template<typename TIterator1, typename TIterator2>
-inline void 
-_arrayConstructDefault(TIterator1 begin_, 
+inline void
+_arrayConstructDefault(TIterator1 begin_,
                        TIterator2 end_)
 {
-    SEQAN_CHECKPOINT;
     while (begin_ != end_)
     {
         valueConstruct(begin_);
@@ -518,21 +466,19 @@ _arrayConstructDefault(TIterator1 begin_,
 }
 
 template<typename TIterator1, typename TIterator2>
-inline void 
-arrayConstruct(TIterator1 begin_, 
+inline void
+arrayConstruct(TIterator1 begin_,
                TIterator2 end_)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructDefault(begin_, end_);
 }
 
 template<typename TIterator1, typename TIterator2, typename TParam>
-inline void 
-_arrayConstructDefault(TIterator1 begin_, 
-                       TIterator2 end_, 
+inline void
+_arrayConstructDefault(TIterator1 begin_,
+                       TIterator2 end_,
                        TParam const & param_)
 {
-    SEQAN_CHECKPOINT;
     while (begin_ != end_)
     {
         valueConstruct(begin_, param_);
@@ -541,12 +487,11 @@ _arrayConstructDefault(TIterator1 begin_,
 }
 
 template<typename TIterator1, typename TIterator2, typename TParam>
-inline void 
-arrayConstruct(TIterator1 begin_, 
-               TIterator2 end_, 
+inline void
+arrayConstruct(TIterator1 begin_,
+               TIterator2 end_,
                TParam const & param_)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructDefault(begin_, end_, param_);
 }
 
@@ -558,46 +503,25 @@ arrayConstruct(TIterator1 begin_,
  * @fn arrayConstructCopy
  * @headerfile <seqan/basic.h>
  * @brief Copy constructs an array of objects into in a given memory buffer.
- * 
+ *
  * @signature void arrayConstructCopy(sourceBegin, sourceEnd, target);
- * 
- * @param sourceBegin Iterator to the first element of the source range.
- * @param sourceEnd   Iterator behind the last element of the source range.  <tt>sourceEnd</tt> should have the same
- *                    type as <tt>sourceBegin</tt>.
- * @param target      Pointer to the memory block the new objects will be constructed in.  The type of <tt>target</tt>
- *                    specifies the type of the constructed objects: If <tt>T*</tt> is the type of <tt>target</tt>, then
- *                    the function constructs objects of type <tt>T</tt>.  The memory buffer should be large enough to
- *                    store <tt>sourceEnd</tt> - <tt>sourceBegin</tt> objects.  An appropriate (copy-) constructor that
- *                    constructs an target objects given a source object is required.
+ *
+ * @param[in] sourceBegin Iterator to the first element of the source range.
+ * @param[in] sourceEnd   Iterator behind the last element of the source range.  <tt>sourceEnd</tt> should have the same
+ *                        type as <tt>sourceBegin</tt>.
+ * @param[in] target      Pointer to the memory block the new objects will be constructed in.  The type of <tt>target</tt>
+ *                        specifies the type of the constructed objects: If <tt>T*</tt> is the type of <tt>target</tt>, then
+ *                        the function constructs objects of type <tt>T</tt>.  The memory buffer should be large enough to
+ *                        store <tt>sourceEnd</tt> - <tt>sourceBegin</tt> objects.  An appropriate (copy-) constructor that
+ *                        constructs an target objects given a source object is required.
  */
 
-/**
-.Function.arrayConstructCopy
-..cat:Array Handling
-..summary:Copy constructs an array of objects into in a given memory buffer.
-..signature:arrayConstructCopy(source_begin, source_end, target)
-..param.source_begin:Iterator to the first element of the source range.
-..param.source_end:Iterator behind the last element of the source range.
-...text:$source_end$ should have the same type as $source_begin$.
-..param.target:Pointer to the memory block the new objects will be constructed in.
-...text:The type of $target$ specifies the type of the constructed objects:
-If $T*$ is the type of $target$, then the function constructs objects of type $T$. 
-...text:The memory buffer should be large enough to store $source_end$ - $source_begin$ objects.
-An appropriate (copy-) constructor that constructs an target objects given a source object is required.
-..see:Function.arrayDestruct
-..see:Function.arrayCopyForward
-..see:Function.arrayCopy
-..see:Function.valueConstruct
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-_arrayConstructCopyDefault(TSource1 source_begin, 
-                           TSource2 source_end, 
+inline void
+_arrayConstructCopyDefault(TSource1 source_begin,
+                           TSource2 source_end,
                            TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
     while (source_begin != source_end)
     {
         // NOTE(holtgrew): getValue() is used here since value() could return
@@ -609,12 +533,11 @@ _arrayConstructCopyDefault(TSource1 source_begin,
 }
 
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-arrayConstructCopy(TSource1 source_begin, 
-                   TSource2 source_end, 
+inline void
+arrayConstructCopy(TSource1 source_begin,
+                   TSource2 source_end,
                    TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructCopyDefault(source_begin, source_end, target_begin);
 }
 
@@ -626,66 +549,47 @@ arrayConstructCopy(TSource1 source_begin,
  * @fn arrayConstructMove
  * @headerfile <seqan/basic.h>
  * @brief Move constructs an array of objects into in a given memory buffer.
- * 
+ *
  * @signature void arrayConstructMove(sourceBegin, sourceEnd, target);
- * 
- * @param sourceEnd   Iterator behind the last element of the source range.  <tt>sourceEnd</tt> should have the same
- *                    type as <tt>sourceBegin</tt>.
- * @param sourceBegin Iterator to the first element of the source range.
- * @param target      Pointer to the memory block the new objects will be constructed in.  The type of <tt>target</tt>
- *                    specifies the type of the constructed objects: If <tt>T*</tt> is the type of <tt>target</tt>, then
- *                    the function constructs objects of type <tt>T</tt>.  The memory buffer should be large enough to
- *                    store <tt>sourceEnd</tt> - <tt>sourceBegin</tt> objects.  An appropriate move constructor that
- *                    constructs an target objects given a source object is required.
+ *
+ * @param[in] sourceEnd   Iterator behind the last element of the source range.  <tt>sourceEnd</tt> should have the same
+ *                        type as <tt>sourceBegin</tt>.
+ * @param[in] sourceBegin Iterator to the first element of the source range.
+ * @param[in] target      Pointer to the memory block the new objects will be constructed in.  The type of <tt>target</tt>
+ *                        specifies the type of the constructed objects: If <tt>T*</tt> is the type of <tt>target</tt>, then
+ *                        the function constructs objects of type <tt>T</tt>.  The memory buffer should be large enough to
+ *                        store <tt>sourceEnd</tt> - <tt>sourceBegin</tt> objects.  An appropriate move constructor that
+ *                        constructs an target objects given a source object is required.
  */
 
-/**
-.Function.arrayConstructMove
-..cat:Array Handling
-..summary:Move constructs an array of objects into in a given memory buffer.
-..signature:arrayConstructMove(source_begin, source_end, target)
-..param.source_begin:Iterator to the first element of the source range.
-..param.source_end:Iterator behind the last element of the source range.
-...text:$source_end$ should have the same type as $source_begin$.
-..param.target:Pointer to the memory block the new objects will be constructed in.
-...text:The type of $target$ specifies the type of the constructed objects:
-If $T*$ is the type of $target$, then the function constructs objects of type $T$. 
-...text:The memory buffer should be large enough to store $source_end$ - $source_begin$ objects.
-An appropriate move constructor that constructs an target objects given a source object is required.
-..see:Function.arrayDestruct
-..see:Function.arrayConstructCopy
-..see:Function.arrayMoveForward
-..see:Function.arrayMove
-..see:Function.valueConstruct
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-_arrayConstructMoveDefault(TSource1 source_begin, 
-                           TSource2 source_end, 
+inline void
+_arrayConstructMoveDefault(TSource1 source_begin,
+                           TSource2 source_end,
                            TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
     while (source_begin < source_end)
     {
         // NOTE(holtgrew): Using value() here, used to be getValue() but
         // cannot move from const reference or proxy.
         // valueConstruct(target_begin, value(source_begin), Move());
         // TODO(holtgrew): We need a "has move constructor" metafunction to switch between move/copy constructing before we can use the line here.
-        valueConstruct(target_begin, value(source_begin));
+#ifdef SEQAN_CXX11_STANDARD
+        valueConstruct(target_begin, std::move<decltype(*source_begin)>(*source_begin));
+#else
+        valueConstruct(target_begin, value(source_begin), Move());
+#endif
         ++source_begin;
         ++target_begin;
     }
 }
 
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-arrayConstructMove(TSource1 source_begin, 
-                   TSource2 source_end, 
+inline void
+arrayConstructMove(TSource1 source_begin,
+                   TSource2 source_end,
                    TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructMoveDefault(source_begin, source_end, target_begin);
 }
 
@@ -697,36 +601,20 @@ arrayConstructMove(TSource1 source_begin,
  * @fn arrayDestruct
  * @headerfile <seqan/basic.h>
  * @brief Destroys an array of objects.
- * 
+ *
  * @signature void arrayDestruct(begin, end);
- * 
- * @param begin Iterator to the begin of the range that is to be destructed.
- * @param end   Iterator behind the end of the range.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] begin Iterator to the begin of the range that is to be destructed.
+ * @param[in] end   Iterator behind the end of the range.
+ *
  * This function does not deallocates the memory.
  */
 
-/**
-.Function.arrayDestruct
-..cat:Array Handling
-..summary:Destroys an array of objects.
-..signature:arrayDestruct(begin, end)
-..param.begin:Iterator to the begin of the range that is to be destructed.
-..param.end:Iterator behind the end of the range.
-..remarks:This function does not deallocates the memory.
-..see:Class.SimpleType
-..see:Function.valueDestruct
-..include:seqan/basic.h
-*/
-
 template<typename TIterator1, typename TIterator2>
-inline void 
-_arrayDestructDefault(TIterator1 begin_, 
+inline void
+_arrayDestructDefault(TIterator1 begin_,
                       TIterator2 end_)
 {
-    SEQAN_CHECKPOINT;
     while (begin_ != end_)
     {
         valueDestruct(begin_);
@@ -735,11 +623,10 @@ _arrayDestructDefault(TIterator1 begin_,
 }
 
 template<typename TIterator1, typename TIterator2>
-inline void 
-arrayDestruct(TIterator1 begin_, 
+inline void
+arrayDestruct(TIterator1 begin_,
               TIterator2 end_)
 {
-    SEQAN_CHECKPOINT;
     _arrayDestructDefault(begin_, end_);
 }
 
@@ -753,49 +640,32 @@ arrayDestruct(TIterator1 begin_,
  * @fn arrayFill
  * @headerfile <seqan/basic.h>
  * @brief Assigns one object to each element of a range.
- * 
+ *
  * @signature void arrayFill(begin, end, value[, parallelTag]);
- * 
- * @param begin       Iterator to the begin of the range that is to be filled.
- * @param end         Iterator behind the end of the range.
- * @param value       Argument that is assigned to all <tt>count</tt> objects in <tt>array</tt>.
- * @param parallelTag Tag to enable/disable parallelism. Types: Serial, Parallel
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] begin       Iterator to the begin of the range that is to be filled.
+ * @param[in] end         Iterator behind the end of the range.
+ * @param[in] value       Argument that is assigned to all <tt>count</tt> objects in <tt>array</tt>.
+ * @param[in] parallelTag Tag to enable/disable parallelism. Types: Serial, Parallel
+ *
  * All objects <tt>target_begin[0]</tt> to <tt>target_begin[count-1]</tt> are set to <tt>value</tt>.
  */
 
-/**
-.Function.arrayFill
-..cat:Array Handling
-..summary:Assigns one object to each element of a range.
-..signature:arrayFill(begin, end, value)
-..param.begin:Iterator to the begin of the range that is to be filled.
-..param.end:Iterator behind the end of the range.
-..param.value:Argument that is assigned to all $count$ objects in $array$.
-..remarks:All objects $target_begin[0]$ to $target_begin[count-1]$ are set to $value$.
-..see:Function.arrayCopy
-..see:Function.arrayCopyForward
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Redirects to fill_n. What are the exact semantics here? Do the array elements have to be initialized already? fill_n uses assignment, not copy construction!
 
 template <typename TIterator, typename TValue>
-inline void 
+inline void
 arrayFill(TIterator begin_,
           TIterator end_,
           TValue const & value)
 {
-    SEQAN_CHECKPOINT;
-    ::std::fill_n(begin_, end_ - begin_, value);
+    std::fill_n(begin_, end_ - begin_, value);
 }
 
 template <typename TIterator, typename TValue>
-inline void 
+inline void
 arrayFill(TIterator begin_,
-          TIterator end_, 
+          TIterator end_,
           TValue const & value,
           Serial)
 {
@@ -810,59 +680,38 @@ arrayFill(TIterator begin_,
  * @fn arrayCopyForward
  * @headerfile <seqan/basic.h>
  * @brief Copies a range of objects into another range of objects starting from the first element.
- * 
+ *
  * @signature void arrayCopyForward(sourceBegin, sourceEnd, target);
- * 
- * @param sourceEnd   Iterator behind the last element of the source array.  <tt>sourceEnd</tt> must have the same type
- *                    as <tt>sourceBegin</tt>.
- * @param sourceBegin Iterator to the first element of the source array.
- * @param target      Iterator to the first element of the target array.  The target capacity should be at least as
- *                    long as the source range.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] sourceEnd   Iterator behind the last element of the source array.  <tt>sourceEnd</tt> must have the same type
+ *                        as <tt>sourceBegin</tt>.
+ * @param[in] sourceBegin Iterator to the first element of the source array.
+ * @param[in] target      Iterator to the first element of the target array.  The target capacity should be at least as
+ *                        long as the source range.
+ *
  * Be careful if source and target range overlap, because in this case some source elements could be accidently
  * overwritten before they are copied.
- * 
+ *
  * If there is no need for the source elements to persist, consider to use arrayMoveForward instead to improve
  * performance.
  */
 
-/**
-.Function.arrayCopyForward
-..cat:Array Handling
-..summary:Copies a range of objects into another range of objects starting from the first element.
-..signature:arrayCopyForward(source_begin, source_end, target)
-..param.source_begin:Iterator to the first element of the source array.
-..param.source_end:Iterator behind the last element of the source array.
-...text:$source_end$ must have the same type as $source_begin$.
-..param.target:Iterator to the first element of the target array.
-...text:The target capacity should be at least as long as the source range.
-..remarks.note:Be careful if source and target range overlap, because in this case some source elements could be accidently overwritten before they are copied.
-..remarks:If there is no need for the source elements to persist, consider to use 
-@Function.arrayMoveForward@ instead to improve performance.
-..see:Class.SimpleType
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-_arrayCopyForwardDefault(TSource1 source_begin, 
-                         TSource2 source_end, 
+inline void
+_arrayCopyForwardDefault(TSource1 source_begin,
+                         TSource2 source_end,
                          TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
-    ::std::copy(source_begin, source_end, target_begin);
+    std::copy(source_begin, source_end, target_begin);
 }
 
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-arrayCopyForward(TSource1 source_begin, 
-                 TSource2 source_end, 
+inline void
+arrayCopyForward(TSource1 source_begin,
+                 TSource2 source_end,
                  TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
-    _arrayCopyForwardDefault(source_begin, source_end, target_begin);   
+    _arrayCopyForwardDefault(source_begin, source_end, target_begin);
 }
 
 // ----------------------------------------------------------------------------
@@ -873,68 +722,42 @@ arrayCopyForward(TSource1 source_begin,
  * @fn arrayCopyBackward
  * @headerfile <seqan/basic.h>
  * @brief Copies a range of objects into another range of objects starting from the last element.
- * 
+ *
  * @signature void arrayCopyBackward(source_begin, source_end, target);
- * 
- * @param sourceBegin Iterator to the first element of the source array.
- * @param sourceEnd   Iterator behind the last element of the source array.  <tt>sourceEnd</tt> must have the same type
- *                    as <tt>source_begin</tt>.
- * @param target      Iterator to the first element of the target array.  The target capacity should be at least as
- *                    long as the source range.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] sourceBegin Iterator to the first element of the source array.
+ * @param[in] sourceEnd   Iterator behind the last element of the source array.  <tt>sourceEnd</tt> must have the same type
+ *                        as <tt>source_begin</tt>.
+ * @param[in] target      Iterator to the first element of the target array.  The target capacity should be at least as
+ *                        long as the source range.
+ *
  * Be careful if source and target range overlap, because in this case some source elements could be accidently
  * overwritten before they are moved.
- * 
+ *
  * If source and target do not overlap, consider to use the function arrayCopyForward instead that is faster in some
  * cases.
- * 
+ *
  * If there is no need for the source elements to persist, consider to use arrayMoveBackward instead to improve
  * performance.
- * 
- * The semantic of this function's argument <tt>target</tt> differ from the arguments of <tt>::std::copy_backward</tt>.
+ *
+ * The semantic of this function's argument <tt>target</tt> differ from the arguments of <tt>std::copy_backward</tt>.
  */
 
-/**
-.Function.arrayCopyBackward
-..cat:Array Handling
-..summary:Copies a range of objects into another range of objects starting from the last element.
-..signature:arrayCopyBackward(source_begin, source_end, target)
-..param.source_begin:Iterator to the first element of the source array.
-..param.source_end:Iterator behind the last element of the source array.
-...text:$source_end$ must have the same type as $source_begin$.
-..param.target:Iterator to the first element of the target array.
-...text:The target capacity should be at least as long as the source range.
-..remarks.note:Be careful if source and target range overlap, because in this case
-    some source elements could be accidently overwritten before they are moved.
-..remarks.text:If source and target do not overlap, consider to use the function
-@Function.arrayCopyForward@ instead that is faster in some cases.
-..remarks:If there is no need for the source elements to persist, consider to use 
-@Function.arrayMoveBackward@ instead to improve performance.
-..remarks.note:The semantic of this function's argument $target$ differ from the arguments of $::std::copy_backward$.
-..see:Function.arrayCopyForward
-..see:Class.SimpleType
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-_arrayCopyBackwardDefault(TSource1 source_begin, 
+inline void
+_arrayCopyBackwardDefault(TSource1 source_begin,
                           TSource2 source_end,
                           TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
-    ::std::copy_backward(source_begin, source_end, target_begin + (source_end - source_begin));
+    std::copy_backward(source_begin, source_end, target_begin + (source_end - source_begin));
 }
 
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-arrayCopyBackward(TSource1 source_begin, 
-                  TSource2 source_end, 
+inline void
+arrayCopyBackward(TSource1 source_begin,
+                  TSource2 source_end,
                   TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayCopyBackwardDefault(source_begin, source_end, target_begin);
 }
 
@@ -944,53 +767,28 @@ arrayCopyBackward(TSource1 source_begin,
 
 /*!
  * @fn arrayCopy
- * 
- * @headerfile seqan/basic.h
- * 
+ *
+ * @headerfile <seqan/basic.h>
+ *
  * @brief Copies a range of objects into another range of objects.
- * 
+ *
  * @signature void arrayCopy(sourceBegin, sourceEnd, target);
- * 
- * @param sourceEnd   Iterator behind the last element of the source range.  <tt>sourceEnd</tt> must have the same type
- *                    as <tt>sourceBegin</tt>.
- * @param sourceBegin Iterator to the first element of the source range.
- * @param target      Iterator to the first element of the target range.The target capacity should be at least as long
- *                    as the source range.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] sourceEnd   Iterator behind the last element of the source range.  <tt>sourceEnd</tt> must have the same type
+ *                        as <tt>sourceBegin</tt>.
+ * @param[in] sourceBegin Iterator to the first element of the source range.
+ * @param[in] target      Iterator to the first element of the target range.The target capacity should be at least as long
+ *                        as the source range.
+ *
  * If source and target range do not overlap, consider to use arrayCopyForward instead to improve performance.
- * 
+ *
  * If there is no need for the source elements to persist, consider to use arrayMoveForward instead to improve
  * performance.
  */
 
-/**
-.Function.arrayCopy
-..cat:Array Handling
-..summary:Copies a range of objects into another range of objects.
-..signature:arrayCopy(source_begin, source_end, target)
-..param.source_begin:Iterator to the first element of the source range.
-..param.source_end:Iterator behind the last element of the source range.
-...text:$source_end$ must have the same type as $source_begin$.
-..param.target:Iterator to the first element of the target range.
-...text:The target capacity should be at least as long as the source range.
-..remarks.text:If source and target range do not overlap, consider to use
-    @Function.arrayCopyForward@ instead to improve performance.
-..remarks:If there is no need for the source elements to persist, consider to use 
-    @Function.arrayMoveForward@ instead to improve performance.
-..DISABLED.remarks.note:Be careful if source and target range overlap and the size of the
-    source elements differ from the size of target elements, because in this case
-    some source elements could be accidently overwritten before they are moved.
-..see:Function.arrayCopyForward
-..see:Function.arrayCopyBackward
-..see:Class.SimpleType
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void arrayCopy(TSource1 source_begin, 
-                      TSource2 source_end, 
+inline void arrayCopy(TSource1 source_begin,
+                      TSource2 source_end,
                       TTarget target_begin)
 {
     if (target_begin <= source_begin)
@@ -1007,66 +805,47 @@ inline void arrayCopy(TSource1 source_begin,
  * @fn arrayMoveForward
  * @headerfile <seqan/basic.h>
  * @brief Moves a range of objects into another range of objects starting from the first element.
- * 
+ *
  * @signature void arrayMoveForward(sourceBegin, sourceEnd, target);
- * 
- * @param sourceEnd   Iterator behind the last element of the source array.  <tt>sourceEnd</tt> must have the same type
- *                    as <tt>sourceBegin</tt>.
- * @param sourceBegin Iterator to the first element of the source array.
- * @param target      Iterator to the first element of the target array.  The target capacity should be at least as
- *                    long as the source range.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] sourceEnd   Iterator behind the last element of the source array.  <tt>sourceEnd</tt> must have the same type
+ *                        as <tt>sourceBegin</tt>.
+ * @param[in] sourceBegin Iterator to the first element of the source array.
+ * @param[in] target      Iterator to the first element of the target array.  The target capacity should be at least as
+ *                        long as the source range.
+ *
  * The function possibly clears (but does not destroy) the source elements.  If source elements must persist, consider
  * to use arrayCopyForward instead.
- * 
+ *
  * Be careful if source and target range overlap, because in this case some source elements could be accidently
  * overwritten before they are moved.
  */
 
-/**
-.Function.arrayMoveForward
-..cat:Array Handling
-..summary:Moves a range of objects into another range of objects starting from the first element.
-..signature:arrayMoveForward(source_begin, source_end, target)
-..param.source_begin:Iterator to the first element of the source array.
-..param.source_end:Iterator behind the last element of the source array.
-...text:$source_end$ must have the same type as $source_begin$.
-..param.target:Iterator to the first element of the target array.
-...text:The target capacity should be at least as long as the source range.
-..remarks:The function possibly clears (but does not destroy) the source elements.
-    If source elements must persist, consider to use @Function.arrayCopyForward@ instead.
-..remarks.note:Be careful if source and target range overlap, because in this case
-    some source elements could be accidently overwritten before they are moved.
-..see:Function.arrayCopyForward
-..see:Class.SimpleType
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-_arrayMoveForwardDefault(TSource1 source_begin, 
-                          TSource2 source_end, 
+inline void
+_arrayMoveForwardDefault(TSource1 source_begin,
+                          TSource2 source_end,
                           TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
+#ifdef SEQAN_CXX11_STANDARD
+    std::move(source_begin, source_end, target_begin);
+#else
     while (source_begin != source_end)
     {
         move(*target_begin, *source_begin);
         ++source_begin;
         ++target_begin;
     }
+#endif
 }
 
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-arrayMoveForward(TSource1 source_begin, 
-                 TSource2 source_end, 
+inline void
+arrayMoveForward(TSource1 source_begin,
+                 TSource2 source_end,
                  TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
-    _arrayMoveForwardDefault(source_begin, source_end, target_begin);   
+    _arrayMoveForwardDefault(source_begin, source_end, target_begin);
 }
 
 // ----------------------------------------------------------------------------
@@ -1077,74 +856,51 @@ arrayMoveForward(TSource1 source_begin,
  * @fn arrayMoveBackward
  * @headerfile <seqan/basic.h>
  * @brief Moves a range of objects into another range of objects starting from the last element.
- * 
+ *
  * @signature void arrayMoveBackward(sourceBegin, sourceEnd, target);
- * 
- * @param sourceEnd   Iterator behind the last element of the source array.  <tt>sourceEnd</tt> must have the same type
- *                    as <tt>sourceBegin</tt>.
- * @param sourceBegin Iterator to the first element of the source array.
- * @param target      Iterator to the first element of the target array.The target capacity should be at least as long
- *                    as the source range.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] sourceEnd   Iterator behind the last element of the source array.  <tt>sourceEnd</tt> must have the same type
+ *                        as <tt>sourceBegin</tt>.
+ * @param[in] sourceBegin Iterator to the first element of the source array.
+ * @param[in] target      Iterator to the first element of the target array.The target capacity should be at least as long
+ *                        as the source range.
+ *
  * The function possibly clears (but does not destroy) the source elements.  If source elements must persist, consider
  * to use arrayCopyBackward instead.
- * 
+ *
  * Be careful if source and target range overlap, because in this case some source elements could be accidently
  * overwritten before they are moved.
- * 
+ *
  * If source and target do not overlap, consider to use the function arrayMoveForward instead that is faster in some
  * cases.
- * 
- * The semantic of this function's argument <tt>target</tt> differ from the arguments of <tt>::std::copy_backward</tt>.
+ *
+ * The semantic of this function's argument <tt>target</tt> differ from the arguments of <tt>std::copy_backward</tt>.
  */
 
-/**
-.Function.arrayMoveBackward
-..cat:Array Handling
-..summary:Moves a range of objects into another range of objects starting from the last element.
-..signature:arrayMoveBackward(source_begin, source_end, target)
-..param.source_begin:Iterator to the first element of the source array.
-..param.source_end:Iterator behind the last element of the source array.
-...text:$source_end$ must have the same type as $source_begin$.
-..param.target:Iterator to the first element of the target array.
-...text:The target capacity should be at least as long as the source range.
-..remarks:The function possibly clears (but does not destroy) the source elements.
-    If source elements must persist, consider to use @Function.arrayCopyBackward@ instead.
-..remarks.note:Be careful if source and target range overlap, because in this case
-    some source elements could be accidently overwritten before they are moved.
-..remarks.text:If source and target do not overlap, consider to use the function
-@Function.arrayMoveForward@ instead that is faster in some cases.
-..remarks.note:The semantic of this function's argument $target$ differ from the arguments of $::std::copy_backward$.
-..see:Function.arrayMoveForward
-..see:Function.arrayCopyBackward
-..see:Class.SimpleType
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-_arrayMoveBackwardDefault(TSource1 source_begin, 
-                          TSource2 source_end, 
+inline void
+_arrayMoveBackwardDefault(TSource1 source_begin,
+                          TSource2 source_end,
                           TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
+#ifdef SEQAN_CXX11_STANDARD
+    std::move_backward(source_begin, source_end, target_begin + (source_end - source_begin));
+#else
     target_begin += (source_end - source_begin);
     while (source_end != source_begin) {
         --source_end;
         --target_begin;
         move(*target_begin, *source_end);
     }
+#endif
 }
 
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-arrayMoveBackward(TSource1 source_begin, 
-                  TSource2 source_end, 
+inline void
+arrayMoveBackward(TSource1 source_begin,
+                  TSource2 source_end,
                   TTarget target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayMoveBackwardDefault(source_begin, source_end, target_begin);
 }
 
@@ -1158,52 +914,24 @@ arrayMoveBackward(TSource1 source_begin,
  * @brief Moves a range of objects into another range of objects.
  *
  * @signature void arrayMove(sourceBegin, sourceEnd, target);
- * 
- * @param sourceBegin Iterator to the first element of the source range.
- * @param sourceEnd   Iterator behind the last element of the source range.  <tt>sourceEnd</tt> must have the same type
- *                    as <tt>sourceBegin</tt>.
- * @param target      Iterator to the first element of the target range.  The target capacity should be at least as
- *                    long as the source range.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] sourceBegin Iterator to the first element of the source range.
+ * @param[in] sourceEnd   Iterator behind the last element of the source range.  <tt>sourceEnd</tt> must have the same type
+ *                        as <tt>sourceBegin</tt>.
+ * @param[in] target      Iterator to the first element of the target range.  The target capacity should be at least as
+ *                        long as the source range.
+ *
  * The function possibly clears (but does not destroy) the source elements.  If source elements must persist, consider
  * to use arrayCopy instead.
- * 
+ *
  * If source and target range do not overlap, consider to use arrayMoveForward instead to improve performance.
- * 
+ *
  * Don't confuse this function with the standard <tt>move</tt> function that resembles arrayCopy.
  */
 
-/**
-.Function.arrayMove
-..cat:Array Handling
-..summary:Moves a range of objects into another range of objects.
-..signature:arrayMove(source_begin, source_end, target)
-..param.source_begin:Iterator to the first element of the source range.
-..param.source_end:Iterator behind the last element of the source range.
-...text:$source_end$ must have the same type as $source_begin$.
-..param.target:Iterator to the first element of the target range.
-...text:The target capacity should be at least as long as the source range.
-..remarks:The function possibly clears (but does not destroy) the source elements.
-    If source elements must persist, consider to use @Function.arrayCopy@ instead.
-..remarks.text:If source and target range do not overlap, consider to use
-    @Function.arrayMoveForward@ instead to improve performance.
-..DISABLED.remarks.note:Be careful if source and target range overlap and the size of the
-    source elements differ from the size of target elements, because in this case
-    some source elements could be accidently overwritten before they are moved.
-..remarks.note:Don't confuse this function with the standard $move$ function that
-resembles @Function.arrayCopy@.
-..see:Function.arrayMoveForward
-..see:Function.arrayMoveBackward
-..see:Function.arrayCopy
-..see:Class.SimpleType
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource1, typename TSource2>
-inline void 
-arrayMove(TSource1 source_begin, 
+inline void
+arrayMove(TSource1 source_begin,
           TSource2 source_end,
           TTarget target_begin)
 {
@@ -1221,55 +949,30 @@ arrayMove(TSource1 source_begin,
  * @fn arrayClearSpace
  * @headerfile <seqan/basic.h>
  * @brief Destroys the begin of an array and keeps the rest.
- * 
+ *
  * @signature void arrayClearSpace(arrBegin, arrLength, keepFrom, moveTo);
- * 
- * @param arrBegin  Pointer to the first element of the array.
- * @param keepFrom  Offset of the first object that will be kept.
- * @param arrLength Length of the array.
- * @param moveTo    Offset the first kept object will get at the end of the function.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] arrBegin  Pointer to the first element of the array.
+ * @param[in] keepFrom  Offset of the first object that will be kept.
+ * @param[in] arrLength Length of the array.
+ * @param[in] moveTo    Offset the first kept object will get at the end of the function.
+ *
  * The objects <tt>arr[keep_from]</tt> to <tt>arr[arr_length-1]</tt> are moved to the area beginning at positions
  * <tt>move_to</tt>. All objects in <tt>arr[0]</tt> to <tt>arr[keep_from-1]</tt> are destroyed. After this function, the
  * first <tt>move_to</tt> positions of the array are free and dont contain objects.
- * 
+ *
  * The array must have at least enough space to store <tt>arr_length + move_to - keep_from</tt> objects.
- * 
+ *
  * The objects from <tt>arr[0]</tt> to <tt>arr[array_length-1]</tt> have to be initialized/constructed, arrays beyond
  * <tt>arr[array_length-1]</tt> are assumed not to be constructed. If this assumption is violated, memory might leak.
  */
 
-/**
-.Function.arrayClearSpace
-..cat:Array Handling
-..summary:Destroys the begin of an array and keeps the rest.
-..signature:arrayClearSpace(arr_begin, arr_length, keep_from, move_to)
-..param.arr_begin:Pointer to the first element of the array.
-..param.arr_length:Length of the array.
-..param.keep_from:Offset of the first object that will be kept.
-..param.move_to:Offset the first kept object will get at the end of the function. 
-..remarks.text:The objects $arr[keep_from]$ to $arr[arr_length-1]$
-are moved to the area beginning at positions $move_to$. 
-All objects in $arr[0]$ to $arr[keep_from-1]$ are destroyed.
-After this function, the first $move_to$ positions of the array
-are free and dont contain objects. 
-..remarks.text:The array must have at least enough space to store $arr_length + move_to - keep_from$ objects.
-..remarks.text:The objects from $arr[0]$ to $arr[array_length-1]$ have to be initialized/constructed, arrays beyond $arr[array_length-1]$ are assumed not to be constructed. If this assumption is violated, memory might leak.
-..see:Function.arrayCopy
-..see:Function.arrayDestruct
-..see:Function.arrayCopyForward
-..see:Class.SimpleType
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): The feature that the range [0, array_begin) is deleted is used nowhere. Can this be removed to simplify behaviour?
 
 template <typename TIterator>
-void _arrayClearSpaceDefault(TIterator array_begin, 
-                             size_t array_length, 
-                             size_t keep_from, 
+void _arrayClearSpaceDefault(TIterator array_begin,
+                             size_t array_length,
+                             size_t keep_from,
                              size_t move_to)
 {
     if (keep_from == array_length) {
@@ -1289,20 +992,17 @@ void _arrayClearSpaceDefault(TIterator array_begin,
         if (array_length > move_to) {
             // Case 2a: Moving right of array_length, i.e. we can move a part
             // of the objects and have to move-construct the rest.
-            SEQAN_CHECKPOINT;
             size_t middle = array_length - (move_to - keep_from);
             arrayConstructMove(array_begin + middle, array_begin + array_length, array_begin + array_length);
             arrayMove(array_begin + keep_from, array_begin + middle, array_begin + move_to);
             arrayDestruct(array_begin, array_begin + move_to);
         } else {
             // Case 2b: We have to move-construct all target objects.
-            SEQAN_CHECKPOINT;
             arrayConstructMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to);
             arrayDestruct(array_begin, array_begin + array_length);
         }
     } else {
         // Case 3: Move to the left.
-        SEQAN_CHECKPOINT;
         arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to);
         arrayDestruct(array_begin, array_begin + move_to);
         arrayDestruct(array_begin + array_length - (keep_from - move_to), array_begin + array_length);
@@ -1310,9 +1010,9 @@ void _arrayClearSpaceDefault(TIterator array_begin,
 }
 
 template <typename TIterator>
-void arrayClearSpace(TIterator array_begin, 
-                     size_t array_length, 
-                     size_t keep_from, 
+void arrayClearSpace(TIterator array_begin,
+                     size_t array_length,
+                     size_t keep_from,
                      size_t move_to)
 {
     _arrayClearSpaceDefault(array_begin, array_length, keep_from, move_to);
@@ -1323,63 +1023,57 @@ void arrayClearSpace(TIterator array_begin,
 // ----------------------------------------------------------------------------
 
 template<typename TIterator>
-inline void 
-_arrayConstructPointer(TIterator, 
+inline void
+_arrayConstructPointer(TIterator,
                        TIterator,
                        True)
 {
-    SEQAN_CHECKPOINT;
     //nothing to do
 }
 
 template<typename TIterator>
-inline void 
-_arrayConstructPointer(TIterator begin_, 
+inline void
+_arrayConstructPointer(TIterator begin_,
                        TIterator end_,
                        False)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructDefault(begin_, end_);
 }
 
 template <typename TValue>
-inline void 
-arrayConstruct(TValue * begin_, 
+inline void
+arrayConstruct(TValue * begin_,
                TValue * end_)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructPointer(begin_, end_, typename IsSimple<TValue>::Type() );
 }
 
 template <typename TValue, typename TParam>
-inline void 
+inline void
 _arrayConstructPointer(TValue * begin_,
                        TValue * end_,
                        TParam const & param_,
                        True)
 {
-    SEQAN_CHECKPOINT;
     arrayFill(begin_, end_, static_cast<TValue>(param_));
 }
 
 template <typename TValue, typename TParam>
-inline void 
+inline void
 _arrayConstructPointer(TValue * begin_,
                        TValue * end_,
                        TParam const & param_,
                        False)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructDefault(begin_, end_, param_);
 }
 
 template<typename TValue, typename TParam>
-inline void 
-arrayConstruct(TValue * begin_, 
-               TValue * end_, 
+inline void
+arrayConstruct(TValue * begin_,
+               TValue * end_,
                TParam const & param_)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructPointer(begin_, end_, param_, typename IsSimple<TValue>::Type());
 }
 
@@ -1388,44 +1082,40 @@ arrayConstruct(TValue * begin_,
 // ----------------------------------------------------------------------------
 
 template<typename TValueSource, typename TValueTarget>
-inline void 
-_arrayConstructCopyPointer(TValueSource * source_begin, 
-                            TValueSource * source_end, 
+inline void
+_arrayConstructCopyPointer(TValueSource * source_begin,
+                            TValueSource * source_end,
                             TValueTarget * target_begin,
                             True)
 {
-    SEQAN_CHECKPOINT;
     arrayCopyForward(source_begin, source_end, target_begin);
 }
 
 template<typename TValueSource, typename TValueTarget>
-inline void 
-_arrayConstructCopyPointer(TValueSource * source_begin, 
-                            TValueSource * source_end, 
+inline void
+_arrayConstructCopyPointer(TValueSource * source_begin,
+                            TValueSource * source_end,
                             TValueTarget const* target_begin,
                             True)
 {
-    SEQAN_CHECKPOINT;
     arrayCopyForward(source_begin, source_end, const_cast<TValueTarget *>(target_begin));
 }
 
 template<typename TValueSource, typename TValueTarget>
-inline void 
-_arrayConstructCopyPointer(TValueSource * source_begin, 
-                            TValueSource * source_end, 
+inline void
+_arrayConstructCopyPointer(TValueSource * source_begin,
+                            TValueSource * source_end,
                             TValueTarget * target_begin,
                             False)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructCopyDefault(source_begin, source_end, target_begin);
 }
 template<typename TValueSource, typename TValueTarget>
-inline void 
-arrayConstructCopy(TValueSource * source_begin, 
-                   TValueSource * source_end, 
+inline void
+arrayConstructCopy(TValueSource * source_begin,
+                   TValueSource * source_end,
                    TValueTarget * target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple<TValueTarget>::Type() );
 }
 
@@ -1434,34 +1124,31 @@ arrayConstructCopy(TValueSource * source_begin,
 // ----------------------------------------------------------------------------
 
 template<typename TValue>
-inline void 
-_arrayConstructMovePointer(TValue * source_begin, 
-                            TValue * source_end, 
+inline void
+_arrayConstructMovePointer(TValue * source_begin,
+                            TValue * source_end,
                             TValue * target_begin,
                             True)
 {
-    SEQAN_CHECKPOINT;
     arrayMoveForward(source_begin, source_end, target_begin);
 }
 
 template<typename TValue>
-inline void 
-_arrayConstructMovePointer(TValue * source_begin, 
-                            TValue * source_end, 
+inline void
+_arrayConstructMovePointer(TValue * source_begin,
+                            TValue * source_end,
                             TValue * target_begin,
                             False)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructMoveDefault(source_begin, source_end, target_begin);
 }
 
 template<typename TValue>
-inline void 
-arrayConstructMove(TValue * source_begin, 
-                   TValue * source_end, 
+inline void
+arrayConstructMove(TValue * source_begin,
+                   TValue * source_end,
                    TValue * target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
 }
 
@@ -1470,31 +1157,28 @@ arrayConstructMove(TValue * source_begin,
 // ----------------------------------------------------------------------------
 
 template<typename TValue>
-inline void 
-_arrayDestructPointer(TValue * /*begin_*/, 
+inline void
+_arrayDestructPointer(TValue * /*begin_*/,
                        TValue * /*end_*/,
                        True)
 {
-    SEQAN_CHECKPOINT;
     //do nothing
 }
 
 template<typename TValue>
-inline void 
-_arrayDestructPointer(TValue * begin_, 
+inline void
+_arrayDestructPointer(TValue * begin_,
                        TValue * end_,
                        False)
 {
-    SEQAN_CHECKPOINT;
     _arrayDestructDefault(begin_, end_);
 }
 
 template<typename TValue>
-inline void 
-arrayDestruct(TValue * begin_, 
+inline void
+arrayDestruct(TValue * begin_,
               TValue * end_)
 {
-    SEQAN_CHECKPOINT;
     _arrayDestructPointer(begin_, end_, typename IsSimple<TValue>::Type() );
 }
 
@@ -1511,66 +1195,60 @@ arrayDestruct(TValue * begin_,
 // ----------------------------------------------------------------------------
 
 template<typename TValue>
-inline void 
-_arrayCopyForwardPointer(TValue * source_begin, 
-                          TValue * source_end, 
+inline void
+_arrayCopyForwardPointer(TValue * source_begin,
+                          TValue * source_end,
                           TValue * target_begin,
                           True)
 {
-    SEQAN_CHECKPOINT;
-    ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
+    std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
 }
 
 template<typename TValue>
-inline void 
-_arrayCopyForwardPointer(TValue * source_begin, 
-                          TValue * source_end, 
+inline void
+_arrayCopyForwardPointer(TValue * source_begin,
+                          TValue * source_end,
                           TValue * target_begin,
                           False)
 {
-    SEQAN_CHECKPOINT;
     _arrayCopyForwardDefault(source_begin, source_end, target_begin);
 }
 
 template<typename TValue>
-inline void 
-arrayCopyForward(TValue * source_begin, 
-                 TValue * source_end, 
+inline void
+arrayCopyForward(TValue * source_begin,
+                 TValue * source_end,
                  TValue * target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
 }
 
 template <typename TValue>
-inline void 
-_arrayCopyBackwardPointer(TValue * source_begin, 
-                           TValue * source_end, 
+inline void
+_arrayCopyBackwardPointer(TValue * source_begin,
+                           TValue * source_end,
                            TValue * target_begin,
                            True)
 {
-    SEQAN_CHECKPOINT;
-    ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
+    std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
 }
 
 template <typename TValue>
-inline void 
-_arrayCopyBackwardPointer(TValue * source_begin, 
-                           TValue * source_end, 
+inline void
+_arrayCopyBackwardPointer(TValue * source_begin,
+                           TValue * source_end,
                            TValue * target_begin,
                            False)
 {
-    SEQAN_CHECKPOINT;
-    _arrayCopyBackwardDefault(source_begin, source_end, target_begin); 
+    _arrayCopyBackwardDefault(source_begin, source_end, target_begin);
 }
 
 template<typename TValue>
-inline void 
-arrayCopyBackward(TValue * source_begin, 
-                  TValue * source_end, 
+inline void
+arrayCopyBackward(TValue * source_begin,
+                  TValue * source_end,
                   TValue * target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayCopyBackwardPointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
 }
 
@@ -1579,65 +1257,59 @@ arrayCopyBackward(TValue * source_begin,
 // ----------------------------------------------------------------------------
 
 template<typename TValue>
-inline void 
-_arrayMoveForwardPointer(TValue * source_begin, 
-                          TValue * source_end, 
+inline void
+_arrayMoveForwardPointer(TValue * source_begin,
+                          TValue * source_end,
                           TValue * target_begin,
                           True)
 {
-    SEQAN_CHECKPOINT;
-    ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
+    std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
 }
 
 template<typename TValue>
-inline void 
-_arrayMoveForwardPointer(TValue * source_begin, 
-                          TValue * source_end, 
+inline void
+_arrayMoveForwardPointer(TValue * source_begin,
+                          TValue * source_end,
                           TValue * target_begin,
                           False)
 {
-    SEQAN_CHECKPOINT;
     _arrayMoveForwardDefault(source_begin, source_end, target_begin);
 }
 
 template<typename TValue>
-inline void 
-arrayMoveForward(TValue * source_begin, 
-                 TValue * source_end, 
+inline void
+arrayMoveForward(TValue * source_begin,
+                 TValue * source_end,
                  TValue * target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
 }
 
 template <typename TValue>
-inline void 
-_arrayMoveBackwardPointer(TValue * source_begin, 
-                           TValue * source_end, 
+inline void
+_arrayMoveBackwardPointer(TValue * source_begin,
+                           TValue * source_end,
                            TValue * target_begin,
                            True)
 {
-    SEQAN_CHECKPOINT;
-    ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
+    std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
 }
 template <typename TValue>
-inline void 
-_arrayMoveBackwardPointer(TValue * source_begin, 
-                           TValue * source_end, 
+inline void
+_arrayMoveBackwardPointer(TValue * source_begin,
+                           TValue * source_end,
                            TValue * target_begin,
                            False)
 {
-    SEQAN_CHECKPOINT;
-    _arrayMoveBackwardDefault(source_begin, source_end, target_begin); 
+    _arrayMoveBackwardDefault(source_begin, source_end, target_begin);
 }
 
 template<typename TValue>
-inline void 
-arrayMoveBackward(TValue * source_begin, 
-                  TValue * source_end, 
+inline void
+arrayMoveBackward(TValue * source_begin,
+                  TValue * source_end,
                   TValue * target_begin)
 {
-    SEQAN_CHECKPOINT;
     _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple<TValue>::Type() );
 }
 
@@ -1647,25 +1319,24 @@ arrayMoveBackward(TValue * source_begin,
 
 // clearSpace() on simple type using pointers.
 template <typename TValue>
-inline void 
-_arrayClearSpacePointer(TValue * array_begin, 
-                        size_t array_length, 
-                        size_t keep_from, 
+inline void
+_arrayClearSpacePointer(TValue * array_begin,
+                        size_t array_length,
+                        size_t keep_from,
                         size_t move_to,
                         True const & /*isSimple*/)
 {
     if (keep_from == move_to) return;
-    SEQAN_CHECKPOINT;
     // TODO(holtgrew): arrayCopy is more appropriate here since we are dealing with the IsSimple case.
     arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to);
 }
 
 // clearSpace() on non-simple type using pointers.
 template <typename TValue>
-inline void 
-_arrayClearSpacePointer(TValue * array_begin, 
-                        size_t array_length, 
-                        size_t keep_from, 
+inline void
+_arrayClearSpacePointer(TValue * array_begin,
+                        size_t array_length,
+                        size_t keep_from,
                         size_t move_to,
                         False const & /*isSimple*/)
 {
@@ -1673,9 +1344,9 @@ _arrayClearSpacePointer(TValue * array_begin,
 }
 
 template <typename TValue>
-void arrayClearSpace(TValue * array_begin, 
-                     size_t array_length, 
-                     size_t keep_from, 
+void arrayClearSpace(TValue * array_begin,
+                     size_t array_length,
+                     size_t keep_from,
                      size_t move_to)
 {
     _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple<TValue>::Type());
@@ -1684,4 +1355,4 @@ void arrayClearSpace(TValue * array_begin,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_
diff --git a/seqan/basic/basic_aggregate.h b/seqan/basic/basic_aggregate.h
index 2945299..18bc52a 100644
--- a/seqan/basic/basic_aggregate.h
+++ b/seqan/basic/basic_aggregate.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for basic/aggregate submodule.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_
 
 // --------------------------------------------------------------------------
 // Prerequisites
@@ -59,4 +59,4 @@
 #include <seqan/basic/tuple_base.h>
 #include <seqan/basic/tuple_bit_compressed.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_
diff --git a/seqan/basic/basic_allocator.h b/seqan/basic/basic_allocator.h
index 70c238f..d632f69 100644
--- a/seqan/basic/basic_allocator.h
+++ b/seqan/basic/basic_allocator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                             basic_allocator.h
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for basic/allocator submodule.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_
 
 // --------------------------------------------------------------------------
 // Dependencies
@@ -61,4 +61,4 @@
 // Adaption from SeqAn allocator to STL allocator.
 #include <seqan/basic/allocator_to_std.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_
diff --git a/seqan/basic/basic_alphabet.h b/seqan/basic/basic_alphabet.h
index f52a467..4da25b0 100644
--- a/seqan/basic/basic_alphabet.h
+++ b/seqan/basic/basic_alphabet.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for the basic/alphabet sub module.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_
 
 // --------------------------------------------------------------------------
 // Dependencies
@@ -95,4 +95,4 @@
 // The profile character implementation.
 #include <seqan/basic/alphabet_profile.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_
diff --git a/seqan/basic/basic_concept.h b/seqan/basic/basic_concept.h
index c841da3..a89db30 100644
--- a/seqan/basic/basic_concept.h
+++ b/seqan/basic/basic_concept.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,6 +29,7 @@
 // DAMAGE.
 //
 // ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 // Facade header for sub module basic_concept.
@@ -38,8 +39,8 @@
 // Boost concepts and ConceptC++ concepts).
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_
 
 // --------------------------------------------------------------------------
 // Prerequisites
@@ -63,4 +64,4 @@
 // Fundamental concepts such as Assignable.
 #include <seqan/basic/fundamental_concepts.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_
diff --git a/seqan/basic/basic_container.h b/seqan/basic/basic_container.h
index e8a4b06..53a2e58 100644
--- a/seqan/basic/basic_container.h
+++ b/seqan/basic/basic_container.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for the basic_container submodule.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_
 
 // --------------------------------------------------------------------------
 // Dependencies
@@ -50,7 +50,10 @@
 // Sub Module Headers
 // --------------------------------------------------------------------------
 
-// The container concept.
+// PropertyMap concept.
+#include <seqan/basic/property_map_concept.h>
+
+// Container concept.
 #include <seqan/basic/container_concept.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_
diff --git a/seqan/basic/basic_debug.h b/seqan/basic/basic_debug.h
index abe12ab..b16d926 100644
--- a/seqan/basic/basic_debug.h
+++ b/seqan/basic/basic_debug.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // assert macros double for test checks.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_
 
 // --------------------------------------------------------------------------
 // Prerequisites
@@ -57,4 +57,4 @@
 // Code for profiling.
 #include <seqan/basic/profiling.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_
diff --git a/seqan/basic/basic_device.h b/seqan/basic/basic_device.h
new file mode 100644
index 0000000..c20f412
--- /dev/null
+++ b/seqan/basic/basic_device.h
@@ -0,0 +1,152 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_BASIC_DEVICE_H
+#define SEQAN_BASIC_DEVICE_H
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Execution space tags
+// ----------------------------------------------------------------------------
+
+struct ExecHost_;
+struct ExecDevice_;
+
+typedef Tag<ExecHost_>   ExecHost;
+typedef Tag<ExecDevice_> ExecDevice;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Device
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn Device
+ * @headerfile <seqan/basic.h>
+ * @brief Converts a given type into one that lives on a device.
+ *
+ * @signature Device<TObject>::Type;
+ * @tparam TObject The type to be converted into a device type.
+ * @return Type The resulting device type.
+ *
+ * This metafunction is used to convert host containers into device containers.
+ *
+ * @see View
+ */
+
+template <typename TObject = void>
+struct Device
+{
+    typedef TObject Type;
+};
+
+template <typename TObject>
+struct Device<TObject const>
+{
+    typedef typename Device<TObject>::Type const    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsDevice
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn IsDevice
+ * @headerfile <seqan/basic.h>
+ * @brief Tests if a given type is a device type.
+ *
+ * @signature IsDevice<TObject>::Type;
+ * @tparam TObject The type to be tested for being a device type.
+ * @return Type @link LogicalValuesTags#True @endlink or @link LogicalValuesTags#False @endlink.
+ *
+ * @see Device
+ */
+
+template <typename TObject>
+struct IsDevice : public False {};
+
+template <typename TObject>
+struct IsDevice<TObject const> : public IsDevice<TObject> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction IfDevice
+// ----------------------------------------------------------------------------
+
+template <typename TObject, typename T1, typename T2>
+struct IfDevice
+{
+    typedef typename If<IsDevice<TObject>, T1, T2>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction ExecSpace
+// ----------------------------------------------------------------------------
+
+template <typename TObject>
+struct ExecSpace
+{
+    typedef typename If<IsDevice<TObject>, ExecDevice, ExecHost>::Type   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction ExecSpec
+// ----------------------------------------------------------------------------
+
+template <typename TObject, typename TSpec = void>
+struct ExecSpec
+{
+    typedef typename IfDevice<TObject, Device<TSpec>, TSpec>::Type   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction CtaSize
+// ----------------------------------------------------------------------------
+
+template <typename TObject, typename TSpec = void>
+struct CtaSize
+{
+    static const unsigned VALUE = 256;
+};
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_BASIC_DEVICE_H
diff --git a/seqan/basic/basic_exception.h b/seqan/basic/basic_exception.h
index 8d84db9..4e84e41 100644
--- a/seqan/basic/basic_exception.h
+++ b/seqan/basic/basic_exception.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,38 +45,57 @@
 #include <exception>
 #include <stdexcept>
 
+#ifdef PLATFORM_GCC
+#include <cxxabi.h>
+#endif
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename T>
+struct Tag;
+
+//struct Nothing_;
+//typedef Tag<Nothing_> Nothing;
+
 // ============================================================================
 // Macros
 // ============================================================================
 
 /*!
- * @macro SEQAN_EXCEPTIONS
+ * @defgroup ExceptionHandling SeqAn Exception Handling
+ * @brief Macros supporting exception handling on various platforms.
+ */
+
+/*!
+ * @macro ExceptionHandling#SEQAN_EXCEPTIONS
  * @headerfile <seqan/basic.h>
  * @brief Determines whether exceptions are enabled or not.
- * 
- * @signature SEQAN_EXCEPTIONS
  *
- * @see SEQAN_TRY
- * @see SEQAN_CATCH
- * @see SEQAN_THROW
+ * @signature #define SEQAN_EXCEPTIONS
+ *
+ * @see ExceptionHandling#SEQAN_TRY
+ * @see ExceptionHandling#SEQAN_CATCH
+ * @see ExceptionHandling#SEQAN_THROW
  * @see Exception
  */
 
 #define SEQAN_EXCEPTIONS    __EXCEPTIONS
 
 /*!
- * @macro SEQAN_TRY
+ * @macro ExceptionHandling#SEQAN_TRY
  * @headerfile <seqan/basic.h>
  * @brief Replaces the C++ try keyword.
- * 
+ *
  * @signature SEQAN_TRY {} SEQAN_CATCH() {}
  *
- * @section Remarks
- * 
- * When exceptions are disabled, i.e. SEQAN_EXCEPTIONS is set to false, the code inside the try block is always executed".
- * 
- * @see SEQAN_CATCH
- * @see SEQAN_THROW
+ * When exceptions are disabled, i.e. SEQAN_EXCEPTIONS is set to false, the code inside the try block is always executed.
+ *
+ * @see ExceptionHandling#SEQAN_CATCH
+ * @see ExceptionHandling#SEQAN_THROW
  * @see Exception
  *
  * @section Examples
@@ -96,44 +115,40 @@
  */
 
 /*!
- * @macro SEQAN_CATCH
+ * @macro ExceptionHandling#SEQAN_CATCH
  * @headerfile <seqan/basic.h>
  * @brief Replaces the C++ catch keyword.
  *
  * @signature SEQAN_TRY {} SEQAN_CATCH() {}
  *
- * @section Remarks
+ * When exceptions are disabled, i.e. SEQAN_EXCEPTIONS is set to false, the code inside the catch block is never executed.
  *
- * When exceptions are disabled, i.e. SEQAN_EXCEPTIONS is set to false, the code inside the catch block is never executed".
- *
- * @see SEQAN_TRY
- * @see SEQAN_THROW
+ * @see ExceptionHandling#SEQAN_TRY
+ * @see ExceptionHandling#SEQAN_THROW
  * @see Exception
  *
  * @section Examples
  *
- * See @link SEQAN_TRY @endlink for a full example.
+ * See @link ExceptionHandling#SEQAN_TRY @endlink for a full example.
  */
 
 /*!
- * @macro SEQAN_THROW
+ * @macro ExceptionHandling#SEQAN_THROW
  * @headerfile <seqan/basic.h>
  * @brief Replaces the C++ throw keyword.
  *
  * @signature SEQAN_THROW(Exception);
  *
- * @section Remarks
- *
- * When exceptions are disabled, i.e. SEQAN_EXCEPTIONS is set to false, the macro turns into SEQAN_FAIL".
+ * When exceptions are disabled, i.e. AssertMacros#SEQAN_EXCEPTIONS is set to false, the macro turns into SEQAN_FAIL.
  *
- * @see SEQAN_TRY
- * @see SEQAN_CATCH
- * @see SEQAN_FAIL
+ * @see ExceptionHandling#SEQAN_TRY
+ * @see ExceptionHandling#SEQAN_CATCH
+ * @see AssertMacros#SEQAN_FAIL
  * @see Exception
  *
  * @section Examples
  *
- * See @link SEQAN_TRY @endlink for a full example.
+ * See @link ExceptionHandling#SEQAN_TRY @endlink for a full example.
  */
 
 #ifdef SEQAN_EXCEPTIONS
@@ -153,69 +168,180 @@
 
 #endif // #ifdef SEQAN_EXCEPTIONS
 
-namespace seqan {
-
 // ============================================================================
-// Classes
+// Exceptions
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Class Exception
+// Basic Exception
 // ----------------------------------------------------------------------------
 
 /*!
  * @class Exception
  * @headerfile <seqan/basic.h>
  * @brief Generic SeqAn exception.
- * @signature Exception;
+ * @signature typedef std::exception Exception;
+ *
+ * @fn Exception::Exception
+ * @brief Constructor.
+ *
+ * @signature Exception::Exception(msg);
+ * @param[in] msg The message as a <tt>std::string</tt>.
  */
 
 typedef std::exception          Exception;
 
 // ----------------------------------------------------------------------------
-// Class BadAlloc
+// Exception BadAlloc
 // ----------------------------------------------------------------------------
 
 /*!
  * @class BadAlloc
  * @headerfile <seqan/basic.h>
- * @brief Bad memory allocation exception.
- * @signature BadAlloc;
+ * @brief Generic SeqAn exception.
+ * @signature typedef std::bad_alloc BadAlloc;
+ *
+ * @fn BadAlloc::BadAlloc
+ * @brief Constructor.
+ *
+ * @signature BadAlloc::BadAlloc(msg);
+ * @param[in] msg The message as a <tt>std::string</tt>.
  */
 
 typedef std::bad_alloc          BadAlloc;
 
 // ----------------------------------------------------------------------------
-// Classes Bad*
+// Exception BadCast
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BadCast
+ * @headerfile <seqan/basic.h>
+ * @brief Generic SeqAn exception.
+ * @signature typedef std::bad_cast BadCast;
+ *
+ * @fn BadCast::BadCast
+ * @brief Constructor.
+ *
+ * @signature BadCast::BadCast(msg);
+ * @param[in] msg The message as a <tt>std::string</tt>.
+ */
+
+typedef std::bad_cast           BadCast;
+
+// ----------------------------------------------------------------------------
+// Exceptions Bad*
 // ----------------------------------------------------------------------------
 // NOTE(esiragusa): These exceptions can be introduced as long as we need them.
 
 //typedef std::bad_exception      BadException;
-//typedef std::bad_cast           BadCast;
 //typedef std::bad_typeid         BadTypeId;
 //typedef std::bad_function_call  BadFunctionCall;
 //typedef std::bad_weak_ptr       BadWeakPtr;
 
 // ----------------------------------------------------------------------------
-// Class RuntimeError
+// Exception RuntimeError
 // ----------------------------------------------------------------------------
 
 /*!
  * @class RuntimeError
  * @headerfile <seqan/basic.h>
  * @brief Runtime error exception.
- * @signature RuntimeError("Message");
+ * @signature typedef std::runtime_error RuntimeError;
+ *
+ *
+ * @fn RuntimeError::RuntimeError
+ * @brief Constructor.
+ *
+ * @signature RuntimeError::RuntimeError(msg);
+ * @param[in] msg The message as a <tt>std::string</tt>.
  */
 
 typedef std::runtime_error      RuntimeError;
 
 // ----------------------------------------------------------------------------
-// Class LogicError
+// Exception LogicError
 // ----------------------------------------------------------------------------
 // NOTE(esiragusa): Always prefer SEQAN_ASSERT to logic error exceptions.
 
 //typedef std::logic_error        LogicError;
 
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction ExceptionMessage
+// ----------------------------------------------------------------------------
+
+template <typename T, typename TSpec = void>
+struct ExceptionMessage
+{
+    static const std::string VALUE;
+};
+
+template <typename T, typename TSpec>
+const std::string ExceptionMessage<T, TSpec>::VALUE;
+
+// ----------------------------------------------------------------------------
+// Function getExceptionMessage()
+// ----------------------------------------------------------------------------
+
+template <typename TFunctor, typename TContext>
+inline std::string const &
+getExceptionMessage(TFunctor const &, TContext const &)
+{
+    return ExceptionMessage<TFunctor, TContext>::VALUE;
+}
+
+// ============================================================================
+// Functors
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Functor AssertFunctor
+// ----------------------------------------------------------------------------
+
+template <typename TFunctor, typename TException, typename TContext = Nothing, bool RETURN_VALUE = false>
+struct AssertFunctor
+{
+    TFunctor func;
+
+    AssertFunctor() {}
+
+    AssertFunctor(TFunctor & func) :
+        func(func)
+    {}
+
+    std::string escapeChar(unsigned char val)
+    {
+        if (val <= '\r')
+        {
+            static const char * const escapeCodes[14] = {
+                "\\0",  "\\1",  "\\2",  "\\3",  "\\4",  "\\5",  "\\6",  "\\a",
+                "\\b",  "\\t",  "\\n",  "\\v",  "\\f",  "\\r" };
+            return std::string(escapeCodes[val]);
+        }
+        else if (' ' <= val && val < 128u)
+            return std::string() + (char)val;
+        else
+        {
+            char buffer[6]; // 5 + 1, e.g. "\0xff" + trailing zero
+            sprintf(buffer, "\\%#2x", (unsigned)val);
+            return std::string(buffer);
+        }
+    }
+
+    template <typename TValue>
+    bool operator() (TValue const & val)
+    {
+        if (SEQAN_UNLIKELY(!func(val)))
+            throw TException(std::string("Unexpected character '") + escapeChar(val) + "' found. " +
+                             getExceptionMessage(func, TContext()));
+        return RETURN_VALUE;
+    }
+};
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -224,8 +350,9 @@ typedef std::runtime_error      RuntimeError;
 // Function globalExceptionHandler()
 // ----------------------------------------------------------------------------
 
-#ifdef SEQAN_EXCEPTIONS
-static void globalExceptionHandler()
+#if defined(SEQAN_EXCEPTIONS) && defined(SEQAN_GLOBAL_EXCEPTION_HANDLER)
+// Declare global exception handler.
+inline static void globalExceptionHandler()
 {
     SEQAN_TRY
     {
@@ -233,13 +360,18 @@ static void globalExceptionHandler()
     }
     SEQAN_CATCH(Exception & e)
     {
-        SEQAN_FAIL("Uncaught exception of type %s: %s", typeid(e).name(), e.what());
+        SEQAN_FAIL("Uncaught exception of type %s: %s", toCString(Demangler<Exception>(e)), e.what());
+    }
+    SEQAN_CATCH(...)
+    {
+        SEQAN_FAIL("Uncaught exception of unknown type.\n");
     }
 }
 
 // Install global exception handler.
-static const std::terminate_handler _globalExceptionHandler = std::set_terminate(globalExceptionHandler);
-#endif
+static const std::terminate_handler SEQAN_UNUSED _globalExceptionHandler = std::set_terminate(globalExceptionHandler);
+
+#endif  // #if defined(SEQAN_EXCEPTIONS) && defined(SEQAN_GLOBAL_EXCEPTION_HANDLER)
 
 }  // namespace seqan
 
diff --git a/seqan/basic/basic_functors.h b/seqan/basic/basic_functors.h
new file mode 100644
index 0000000..076127d
--- /dev/null
+++ b/seqan/basic/basic_functors.h
@@ -0,0 +1,214 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_BASIC_FUNCTORS_H_
+#define SEQAN_BASIC_FUNCTORS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Functors
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Functor OrFunctor
+// ----------------------------------------------------------------------------
+
+template <typename TFunctor1, typename TFunctor2>
+struct OrFunctor
+{
+    TFunctor1 func1;
+    TFunctor2 func2;
+
+    OrFunctor()
+    {}
+
+    OrFunctor(TFunctor1 const &func1, TFunctor2 const &func2):
+        func1(func1), func2(func2)
+    {}
+
+    template <typename TValue>
+    bool operator() (TValue const & val)
+    {
+        return func1(val) || func2(val);
+    }
+
+    template <typename TValue>
+    bool operator() (TValue const & val) const
+    {
+        return func1(val) || func2(val);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Functor AndFunctor
+// ----------------------------------------------------------------------------
+
+template <typename TFunctor1, typename TFunctor2>
+struct AndFunctor
+{
+    TFunctor1 func1;
+    TFunctor2 func2;
+
+    AndFunctor()
+    {}
+
+    AndFunctor(TFunctor1 const &func1, TFunctor2 const &func2):
+        func1(func1), func2(func2)
+    {}
+
+    template <typename TValue>
+    bool operator() (TValue const & val)
+    {
+        return func1(val) && func2(val);
+    }
+
+    template <typename TValue>
+    bool operator() (TValue const & val) const
+    {
+        return func1(val) && func2(val);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Functor NotFunctor
+// ----------------------------------------------------------------------------
+
+template <typename TFunctor>
+struct NotFunctor
+{
+    TFunctor func;
+
+    NotFunctor()
+    {}
+
+    NotFunctor(TFunctor const &func):
+        func(func)
+    {}
+
+    template <typename TValue>
+    bool operator() (TValue const & val)
+    {
+        return !func(val);
+    }
+
+
+    template <typename TValue>
+    bool operator() (TValue const & val) const
+    {
+        return !func(val);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Functor CountDownFunctor
+// ----------------------------------------------------------------------------
+
+template <typename TFunctor = True, __uint64 REMAINING = 0>
+struct CountDownFunctor
+{
+    __uint64 remaining;
+    TFunctor func;
+
+    CountDownFunctor(__uint64 remaining = REMAINING):
+        remaining(remaining)
+    {}
+
+    CountDownFunctor(__uint64 remaining, TFunctor const &func):
+        remaining(remaining),
+        func(func)
+    {}
+
+    template <typename TValue>
+    bool operator() (TValue const & val)
+    {
+        if (remaining == 0)
+            return true;
+        if (func(val))
+            --remaining;
+        return false;
+    }
+
+    operator bool()
+    {
+        return remaining == 0;
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Functor CountFunctor
+// ----------------------------------------------------------------------------
+
+template <typename TFunctor = True>
+struct CountFunctor
+{
+    __uint64 count;
+    TFunctor func;
+
+    CountFunctor() : count(0)
+    {}
+
+    CountFunctor(TFunctor const & func) : count(0), func(func)
+    {}
+
+    template <typename TValue>
+    bool operator() (TValue const & val)
+    {
+        if (func(val))
+            ++count;
+        return false;
+    }
+
+    operator __uint64() const
+    {
+        return count;
+    }
+};
+
+template <typename TFunctor>
+inline void clear(CountFunctor<TFunctor> &func)
+{
+    func.count = 0;
+}
+
+template <typename TFunctor>
+inline __uint64 & value(CountFunctor<TFunctor> &func)
+{
+    return func.count;
+}
+
+}   // namespace seqan
+
+#endif // SEQAN_BASIC_FUNCTORS_H_
diff --git a/seqan/basic/basic_fundamental.h b/seqan/basic/basic_fundamental.h
index 2296de3..ecfbda1 100644
--- a/seqan/basic/basic_fundamental.h
+++ b/seqan/basic/basic_fundamental.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // prototypes for common metafunctions like Value<>, functions assign() etc.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_FUNDAMENTAL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_FUNDAMENTAL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_FUNDAMENTAL_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_FUNDAMENTAL_H_
 
 // --------------------------------------------------------------------------
 // Prerequisites
@@ -65,6 +65,9 @@
 // Basic tag-related code.
 #include <seqan/basic/fundamental_tags.h>
 
+// Functions and metafunctions to use contiguous chunks of memory
+#include <seqan/basic/fundamental_chunking.h>
+
 // Definition of assign(), set(), move().
 #include <seqan/basic/fundamental_transport.h>
 
@@ -82,4 +85,4 @@
 // Hosted type.
 #include <seqan/basic/hosted_type_interface.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_
diff --git a/seqan/basic/basic_iterator.h b/seqan/basic/basic_iterator.h
index ca6e41f..2de7c10 100644
--- a/seqan/basic/basic_iterator.h
+++ b/seqan/basic/basic_iterator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for basic_iterator submodule.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_
 
 // --------------------------------------------------------------------------
 // Dependencies
@@ -61,12 +61,24 @@
 // Iterator concept.
 #include <seqan/basic/iterator_concept.h>
 
-// Iterator for adapting iterators to Rooted Iterators.
-#include <seqan/basic/iterator_adaptor.h>
+// PropertyMap concept.
+#include <seqan/basic/property_map_concept.h>
+
+// Container concept.
+#include <seqan/basic/container_concept.h>
+
+// Counting iterator.
+#include <seqan/basic/iterator_counting.h>
 
 // Positional iterator.
 #include <seqan/basic/iterator_position.h>
 
+// Makes a container out of begin/end iterators
+#include <seqan/basic/iterator_range.h>
+
+// Iterator for adapting iterators to Rooted Iterators.
+#include <seqan/basic/iterator_adaptor.h>
+
 // Adaption between STL iterators and SeqAn iterators.
 #include <seqan/basic/iterator_adapt_std.h>
 
@@ -74,4 +86,4 @@
 #include <seqan/basic/proxy_base.h>
 #include <seqan/basic/proxy_iterator.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_
diff --git a/seqan/basic/basic_math.h b/seqan/basic/basic_math.h
index 30ae4df..8b8097d 100644
--- a/seqan/basic/basic_math.h
+++ b/seqan/basic/basic_math.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for the basic/math sub module.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_
 
 // --------------------------------------------------------------------------
 // Dependencies
@@ -54,5 +54,5 @@
 #include <seqan/basic/math_functions.h>
 #include <seqan/basic/math_log_space_value.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_
 
diff --git a/seqan/basic/basic_metaprogramming.h b/seqan/basic/basic_metaprogramming.h
index b43cee5..44b6337 100644
--- a/seqan/basic/basic_metaprogramming.h
+++ b/seqan/basic/basic_metaprogramming.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,11 +34,15 @@
 // Facade header for the basic/metaprogramming submodule.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_METAPROGRAMMING_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_METAPROGRAMMING_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_METAPROGRAMMING_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_METAPROGRAMMING_H_
 
 #include <cstdlib>
 
+#ifdef SEQAN_CXX11_STANDARD
+#include <type_traits>
+#endif
+
 #include <seqan/platform.h>
 
 // Metaprogramming logical operations.
@@ -53,7 +57,10 @@
 // Metaprogramming for querying and modifying types.
 #include <seqan/basic/metaprogramming_type.h>
 
+// Metaprogramming for type algebra.
+#include <seqan/basic/metaprogramming_type_algebra.h>
+
 // Metaprogramming for conditional enabling/disabling of code.
 #include <seqan/basic/metaprogramming_enable_if.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_H_
diff --git a/seqan/basic/basic_parallelism.h b/seqan/basic/basic_parallelism.h
index db7761a..11ef6ac 100644
--- a/seqan/basic/basic_parallelism.h
+++ b/seqan/basic/basic_parallelism.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // It mainly defines the macro SEQAN_ENABLE_PARALLELISM.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_
 
 /*!
  * @macro SEQAN_ENABLE_PARALLELISM
@@ -65,24 +65,6 @@
  * @endcode
  */
 
-/**
-.Macro.SEQAN_ENABLE_PARALLELISM
-..summary:Indicates whether parallelism is enabled with value 0/1.
-..cat:Parallelism
-..signature:SEQAN_ENABLE_PARALLELISM
-..remarks:By default, set to 1 if $_OPENMP$ is defined and set to 0 otherwise.
-..example:If you want to change this value, you have to define this value before including any SeqAn header.
-...code:#define SEQAN_ENABLE_PARALLELISM 0  // ALWAYS switch off parallelism!
-
-#include <seqan/basic.h>
-
-int main(int argc, char ** argv)
-{
-  return 0;
-}
-..include:seqan/basic.h
- */
-
 #if !defined(SEQAN_ENABLE_PARALLELISM)
 #if defined(_OPENMP)
 #define SEQAN_ENABLE_PARALLELISM 1
@@ -91,4 +73,4 @@ int main(int argc, char ** argv)
 #endif  // defined(_OPENMP)
 #endif  // !defined(SEQAN_ENABLE_PARALLELISM)
 
-#endif  // SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_
+#endif  // SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_
diff --git a/seqan/basic/basic_proxy.h b/seqan/basic/basic_proxy.h
index eda6402..ee6fd97 100644
--- a/seqan/basic/basic_proxy.h
+++ b/seqan/basic/basic_proxy.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Proxy definition.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_
 
 // --------------------------------------------------------------------------
 // Dependencies
@@ -56,4 +56,4 @@
 // assignValue() and setValue()).
 #include <seqan/basic/proxy_iterator.h>
 
-#endif  // SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_
+#endif  // SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_
diff --git a/seqan/basic/basic_simd_vector.h b/seqan/basic/basic_simd_vector.h
new file mode 100644
index 0000000..ee28655
--- /dev/null
+++ b/seqan/basic/basic_simd_vector.h
@@ -0,0 +1,662 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// generic SIMD interface for SSE4/AVX
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_SIMD_VECTOR_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_SIMD_VECTOR_H_
+
+#ifdef __SSE4_1__
+ #include <immintrin.h>
+#else
+// SSE4.1 or greater required
+ #warning "SSE4.1 instruction set not enabled"
+#endif
+
+
+namespace seqan {
+
+// ============================================================================
+// Useful Macros
+// ============================================================================
+
+#define SEQAN_DEFINE_SIMD_VECTOR_GETVALUE_(TSimdVector)                                                 \
+template <typename TPosition>                                                                           \
+inline typename Value<TSimdVector>::Type                                                                \
+getValue(TSimdVector &vector, TPosition pos)                                                            \
+{                                                                                                       \
+/*                                                                                                      \
+    typedef typename Value<TSimdVector>::Type TValue;                                                   \
+    TValue val = (reinterpret_cast<TValue*>(&vector))[pos];                                    \
+    return val;                                                                                         \
+*/                                                                                                      \
+    return vector[pos];                                                                                 \
+}
+
+
+#define SEQAN_DEFINE_SIMD_VECTOR_VALUE_(TSimdVector)                                                    \
+template <typename TPosition>                                                                           \
+inline typename Value<TSimdVector>::Type                                                                \
+value(TSimdVector &vector, TPosition pos)                                                               \
+{                                                                                                       \
+    return getValue(vector, pos);                                                                       \
+}
+
+#define SEQAN_DEFINE_SIMD_VECTOR_ASSIGNVALUE_(TSimdVector)                                              \
+template <typename TPosition, typename TValue2>                                                         \
+inline void                                                                                             \
+assignValue(TSimdVector &vector, TPosition pos, TValue2 value)                                          \
+{                                                                                                       \
+/*                                                                                                      \
+    typedef typename Value<TSimdVector>::Type TValue;                                                   \
+    (reinterpret_cast<TValue*>(&vector))[pos] = value;                                                  \
+*/                                                                                                      \
+    vector[pos] = value;                                                                                \
+}
+
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// define a concept and its models
+// they allow us to define generic vector functions
+SEQAN_CONCEPT(SimdVectorConcept, (T)) {};
+
+#if defined(__AVX2__)
+#define SEQAN_SIZEOF_MAX_VECTOR 32
+#elif defined(__SSE3__)
+#define SEQAN_SIZEOF_MAX_VECTOR 16
+#else
+#define SEQAN_SIZEOF_MAX_VECTOR 8
+#endif
+
+// a metafunction returning the biggest supported SIMD vector
+template <typename TValue, int LENGTH = SEQAN_SIZEOF_MAX_VECTOR / sizeof(TValue)>
+struct SimdVector;
+
+// internal struct to specialize for vector parameters (SIZEOF=sizeof(TVector), LENGTH=LENGTH<TVector>::VALUE)
+template <int SIZEOF, int LENGTH = 0>
+struct SimdParams_ {};
+
+// internal struct to specialize for matrix parameters
+template <int ROWS, int COLS, int BITS_PER_VALUE>
+struct SimdMatrixParams_
+{
+};
+
+
+#define SEQAN_DEFINE_SIMD_VECTOR_(TSimdVector, TValue, SIZEOF_VECTOR)                                       \
+    typedef TValue TSimdVector __attribute__ ((__vector_size__ (SIZEOF_VECTOR)));                           \
+    template <> struct SimdVector<TValue, SIZEOF_VECTOR / sizeof(TValue)> { typedef TSimdVector Type; };    \
+    template <> struct Value<TSimdVector>           { typedef TValue Type; };                               \
+    template <> struct LENGTH<TSimdVector>          { enum { VALUE = SIZEOF_VECTOR / sizeof(TValue) }; };   \
+    template <> struct Value<TSimdVector const>:  public Value<TSimdVector> {};                             \
+    template <> struct LENGTH<TSimdVector const>: public LENGTH<TSimdVector> {};                            \
+    SEQAN_DEFINE_SIMD_VECTOR_GETVALUE_(TSimdVector const)                                                   \
+    SEQAN_DEFINE_SIMD_VECTOR_VALUE_(TSimdVector)                                                            \
+    SEQAN_DEFINE_SIMD_VECTOR_VALUE_(TSimdVector const)                                                      \
+    SEQAN_DEFINE_SIMD_VECTOR_ASSIGNVALUE_(TSimdVector)                                                      \
+    template <>                                                                                             \
+    SEQAN_CONCEPT_IMPL((TSimdVector),       (SimdVectorConcept));                                           \
+    template <>                                                                                             \
+    SEQAN_CONCEPT_IMPL((TSimdVector const), (SimdVectorConcept));
+
+#ifdef __AVX__
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector32Char,     char,           32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector32SChar,    signed char,    32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector32UChar,    unsigned char,  32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16Short,    short,          32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16UShort,   unsigned short, 32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8Int,       int,            32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8UInt,      unsigned int,   32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Int64,     __int64,        32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4UInt64,    __uint64,       32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8Float,     float,          32)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Double,    double,         32)
+#endif
+
+#ifdef __SSE3__
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8Char,      char,           8)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8SChar,     signed char,    8)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8UChar,     unsigned char,  8)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Short,     short,          8)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4UShort,    unsigned short, 8)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2Int,       int,            8)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2UInt,      unsigned int,   8)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2Float,     float,          8)
+
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16Char,     char,           16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16SChar,    signed char,    16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16UChar,    unsigned char,  16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8Short,     short,          16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8UShort,    unsigned short, 16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Int,       int,            16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4UInt,      unsigned int,   16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2Int64,     __int64,        16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2UInt64,    __uint64,       16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Float,     float,          16)
+SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2Double,    double,         16)
+#endif
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// AVX/AVX2 wrappers
+// --------------------------------------------------------------------------
+
+#ifdef __AVX__
+
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, TValue x, SimdParams_<32, 32>) { reinterpret_cast<__m256i&>(vector) = _mm256_set1_epi8(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, TValue x, SimdParams_<32, 16>) { reinterpret_cast<__m256i&>(vector) = _mm256_set1_epi16(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, TValue x, SimdParams_<32, 8>)  { reinterpret_cast<__m256i&>(vector) = _mm256_set1_epi32(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, TValue x, SimdParams_<32, 4>)  { reinterpret_cast<__m256i&>(vector) = _mm256_set1_epi64x(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, float x,  SimdParams_<32, 8>)  { reinterpret_cast<__m256i&>(vector) = _mm256_set1_ps(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, double x, SimdParams_<32, 4>)  { reinterpret_cast<__m256i&>(vector) = _mm256_set1_pd(x); }
+
+template <typename TSimdVector, int L>
+inline void _clearVector(TSimdVector &vector, SimdParams_<32, L>) { reinterpret_cast<__m256i&>(vector) = _mm256_setzero_si256(); }
+template <typename TSimdVector>
+inline void _clearVector(TSimdVector &vector, SimdParams_<32, 8>) { reinterpret_cast<__m256&>(vector) = _mm256_setzero_ps(); }
+template <typename TSimdVector>
+inline void _clearVector(TSimdVector &vector, SimdParams_<32, 4>) { reinterpret_cast<__m256d&>(vector) = _mm256_setzero_pd(); }
+
+#ifdef __AVX2__
+
+template <typename TSimdVector, int L>
+inline TSimdVector _blend(TSimdVector const &a, TSimdVector const &b, TSimdVector const &mask, SimdParams_<32, L>)
+{
+    return reinterpret_cast<TSimdVector>(_mm256_blendv_epi8(
+        reinterpret_cast<const __m256i &>(a),
+        reinterpret_cast<const __m256i &>(b),
+        reinterpret_cast<const __m256i &>(mask)));
+}
+
+template <typename TSimdVector1, typename TSimdVector2>
+inline TSimdVector1
+_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<32, 32>, SimdParams_<32, 32>)
+{
+    return reinterpret_cast<TSimdVector1>(_mm256_shuffle_epi8(
+        reinterpret_cast<const __m256i &>(vector),
+        reinterpret_cast<const __m256i &>(indices)));
+}
+template <typename TSimdVector1, typename TSimdVector2>
+inline TSimdVector1
+_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<32, 16>, SimdParams_<16, 16>)
+{
+    // copy 2nd 64bit word to 3rd, compute 2*idx
+    __m256i idx = _mm256_slli_epi16(_mm256_permute4x64_epi64(_mm256_castsi128_si256(reinterpret_cast<const __m128i &>(indices)), 0x50), 1);
+    // interleave with 2*idx+1 and call shuffle
+    return reinterpret_cast<TSimdVector1>(_mm256_shuffle_epi8(
+        reinterpret_cast<const __m256i &>(vector),
+         _mm256_unpacklo_epi8(idx, _mm256_add_epi8(idx, _mm256_set1_epi8(1)))));
+}
+
+template <typename TSimdVector>
+inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<32, 32>)
+{
+    return reinterpret_cast<TSimdVector>(_mm256_srli_epi16(reinterpret_cast<const __m256i &>(vector), imm) & _mm256_set1_epi8(0xff >> imm));
+}
+template <typename TSimdVector>
+inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<32, 16>)
+{
+    return reinterpret_cast<TSimdVector>(_mm256_srli_epi16(reinterpret_cast<const __m256i &>(vector), imm));
+}
+template <typename TSimdVector>
+inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<32, 8>)
+{
+    return reinterpret_cast<TSimdVector>(_mm256_srli_epi32(reinterpret_cast<const __m256i &>(vector), imm));
+}
+template <typename TSimdVector>
+inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<32, 4>)
+{
+    return reinterpret_cast<TSimdVector>(_mm256_srli_epi64(reinterpret_cast<const __m256i &>(vector), imm));
+}
+
+// emulate missing _mm256_unpacklo_epi128/_mm256_unpackhi_epi128 instructions
+inline __m256i _mm256_unpacklo_epi128(__m256i const &a, __m256i const &b)
+{
+    return _mm256_permute2x128_si256(a, b, 0x20);
+//    return _mm256_inserti128_si256(a, _mm256_extracti128_si256(b, 0), 1);
+}
+
+inline __m256i _mm256_unpackhi_epi128(__m256i const &a, __m256i const &b)
+{
+    return _mm256_permute2x128_si256(a, b, 0x31);
+//    return _mm256_inserti128_si256(b, _mm256_extracti128_si256(a, 1), 0);
+}
+
+template <typename TSimdVector>
+inline void
+_transposeMatrix(TSimdVector matrix[], SimdMatrixParams_<32, 32, 8>)
+{
+    // we need a look-up table to reverse the lowest 4 bits
+    // in order to place the permute the transposed rows
+    static const unsigned char bitRev[] = { 0, 8, 4,12, 2,10, 6,14, 1, 9, 5,13, 3,11, 7,15,
+                                           16,24,20,28,18,26,22,30,17,25,21,29,19,27,23,31};
+
+    // transpose a 32x32 byte matrix
+    __m256i tmp1[32];
+    for (int i = 0; i < 16; ++i)
+    {
+        tmp1[i]    = _mm256_unpacklo_epi8(reinterpret_cast<const __m256i &>(matrix[2*i]), reinterpret_cast<const __m256i &>(matrix[2*i+1]));
+        tmp1[i+16] = _mm256_unpackhi_epi8(reinterpret_cast<const __m256i &>(matrix[2*i]), reinterpret_cast<const __m256i &>(matrix[2*i+1]));
+    }
+    __m256i  tmp2[32];
+    for (int i = 0; i < 16; ++i)
+    {
+        tmp2[i]    = _mm256_unpacklo_epi16(tmp1[2*i], tmp1[2*i+1]);
+        tmp2[i+16] = _mm256_unpackhi_epi16(tmp1[2*i], tmp1[2*i+1]);
+    }
+    for (int i = 0; i < 16; ++i)
+    {
+        tmp1[i]    = _mm256_unpacklo_epi32(tmp2[2*i], tmp2[2*i+1]);
+        tmp1[i+16] = _mm256_unpackhi_epi32(tmp2[2*i], tmp2[2*i+1]);
+    }
+    for (int i = 0; i < 16; ++i)
+    {
+        tmp2[i]    = _mm256_unpacklo_epi64(tmp1[2*i], tmp1[2*i+1]);
+        tmp2[i+16] = _mm256_unpackhi_epi64(tmp1[2*i], tmp1[2*i+1]);
+    }
+    for (int i = 0; i < 16; ++i)
+    {
+        matrix[bitRev[i]]    = reinterpret_cast<TSimdVector>(_mm256_unpacklo_epi128(tmp2[2*i],tmp2[2*i+1]));
+        matrix[bitRev[i+16]] = reinterpret_cast<TSimdVector>(_mm256_unpackhi_epi128(tmp2[2*i],tmp2[2*i+1]));
+    }
+}
+
+#else   // #ifdef __AVX2__
+template <typename TSimdVector1, typename TSimdVector2>
+inline TSimdVector1
+_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<32, 32>, SimdParams_<32, 32>)
+{
+    return reinterpret_cast<TSimdVector1>(_mm256_permute2f128_si256(
+        _mm256_castsi128_si256 (_mm_shuffle_epi8(
+                                    _mm256_castsi256_si128(reinterpret_cast<const __m256i &>(vector)),
+                                    _mm256_castsi256_si128(reinterpret_cast<const __m256i &>(indices)))),
+        _mm256_castsi128_si256 (_mm_shuffle_epi8(
+                                    _mm256_castsi256_si128(reinterpret_cast<const __m256i &>(vector)),
+                                    _mm256_extractf128_si256(reinterpret_cast<const __m256i &>(indices), 1))),
+        0x20));
+}
+
+inline SimdVector32Char   shiftRightLogical(SimdVector32Char   const &vector, const int imm)
+{
+    return reinterpret_cast<SimdVector32Char>(_mm256_permute2f128_si256(
+        _mm256_castsi128_si256 (_mm_srli_epi16(
+                                    _mm256_castsi256_si128(reinterpret_cast<const __m256i &>(vector)),
+                                    imm)),
+        _mm256_castsi128_si256 (_mm_srli_epi16(
+                                    _mm256_extractf128_si256(reinterpret_cast<const __m256i &>(vector), 1),
+                                    imm)),
+        0x20) & _mm256_set1_epi8(0xff >> imm));
+}
+
+#endif  // #ifdef __AVX2__
+
+
+template <typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    int)
+inline _testAllZeros(TSimdVector const &vector, TSimdVector const &mask, SimdParams_<32>)
+{
+#ifdef __AVX2__
+    return _mm256_testz_si256(vector, mask);
+#else   // #ifdef __AVX2__
+    return
+        _mm_testz_si128(_mm256_castsi256_si128(vector), _mm256_castsi256_si128(mask)) &
+        _mm_testz_si128(_mm256_extractf128_si256(vector, 1), _mm256_extractf128_si256(mask, 1));
+#endif  // #ifdef __AVX2__
+}
+
+template <typename TSimdVector>
+inline int _testAllOnes(TSimdVector const &vector, SimdParams_<32>)
+{
+    __m256i vec = reinterpret_cast<const __m256i &>(vector);
+#ifdef __AVX2__
+    return _mm256_testc_si256(vec, _mm256_cmpeq_epi32(vec, vec));
+#else   // #ifdef __AVX2__
+    return
+        _mm_test_all_ones(_mm256_castsi256_si128(vec)) &
+        _mm_test_all_ones(_mm256_extractf128_si256(vec, 1));
+#endif  // #ifdef __AVX2__
+}
+
+#endif  // #ifdef __AVX__
+
+
+// --------------------------------------------------------------------------
+// SSE3 wrappers
+// --------------------------------------------------------------------------
+
+#ifdef __SSE3__
+
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, TValue x, SimdParams_<16, 16>) { reinterpret_cast<__m128i&>(vector) = _mm_set1_epi8(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, TValue x, SimdParams_<16, 8>)  { reinterpret_cast<__m128i&>(vector) = _mm_set1_epi16(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, TValue x, SimdParams_<16, 4>)  { reinterpret_cast<__m128i&>(vector) = _mm_set1_epi32(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, TValue x, SimdParams_<16, 2>)  { reinterpret_cast<__m128i&>(vector) = _mm_set1_epi64x(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, float x,  SimdParams_<16, 4>)   { reinterpret_cast<__m128i&>(vector) = _mm_set1_ps(x); }
+template <typename TSimdVector, typename TValue>
+inline void _fillVector(TSimdVector &vector, double x, SimdParams_<16, 2>)  { reinterpret_cast<__m128i&>(vector) = _mm_set1_pd(x); }
+
+template <typename TSimdVector, int L>
+inline void _clearVector(TSimdVector &vector, SimdParams_<16, L>) { reinterpret_cast<__m128i&>(vector) = _mm_setzero_si128(); }
+template <typename TSimdVector>
+inline void _clearVector(TSimdVector &vector, SimdParams_<16, 4>)  { reinterpret_cast<__m128&>(vector) = _mm_setzero_ps(); }
+template <typename TSimdVector>
+inline void _clearVector(TSimdVector &vector, SimdParams_<16, 2>)  { reinterpret_cast<__m128d&>(vector) = _mm_setzero_pd(); }
+
+
+template <typename TSimdVector, int L>
+inline TSimdVector _blend(TSimdVector const &a, TSimdVector const &b, TSimdVector const &mask, SimdParams_<16, L>)
+{
+    return reinterpret_cast<TSimdVector>(_mm_blendv_epi8(
+        reinterpret_cast<const __m128i &>(a),
+        reinterpret_cast<const __m128i &>(b),
+        reinterpret_cast<const __m128i &>(mask)));
+}
+
+template <typename TSimdVector1, typename TSimdVector2>
+inline TSimdVector1
+_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<16, 16>, SimdParams_<16, 16>)
+{
+    return reinterpret_cast<TSimdVector1>(_mm_shuffle_epi8(
+        reinterpret_cast<const __m128i &>(vector),
+        reinterpret_cast<const __m128i &>(indices)));
+}
+template <typename TSimdVector1, typename TSimdVector2>
+inline TSimdVector1
+_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<16, 8>, SimdParams_<8, 8>)
+{
+    __m128i idx = _mm_slli_epi16(_mm_cvtsi64_si128(reinterpret_cast<const __uint64 &>(indices)), 1);
+    return reinterpret_cast<TSimdVector1>(_mm_shuffle_epi8(
+        reinterpret_cast<const __m128i &>(vector),
+        _mm_unpacklo_epi8(idx, _mm_add_epi8(idx, _mm_set1_epi8(1)))));
+}
+
+template <typename TSimdVector>
+inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<16, 16>)
+{
+    return reinterpret_cast<TSimdVector>(_mm_srli_epi16(reinterpret_cast<const __m128i &>(vector), imm) & _mm_set1_epi8(0xff >> imm));
+}
+template <typename TSimdVector>
+inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<16, 8>)
+{
+    return reinterpret_cast<TSimdVector>(_mm_srli_epi16(reinterpret_cast<const __m128i &>(vector), imm));
+}
+template <typename TSimdVector>
+inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<16, 4>)
+{
+    return reinterpret_cast<TSimdVector>(_mm_srli_epi32(reinterpret_cast<const __m128i &>(vector), imm));
+}
+template <typename TSimdVector>
+inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<16, 2>)
+{
+    return reinterpret_cast<TSimdVector>(_mm_srli_epi64(reinterpret_cast<const __m128i &>(vector), imm));
+}
+
+
+
+template <typename TSimdVector>
+inline void
+_transposeMatrix(TSimdVector matrix[], SimdMatrixParams_<8, 8, 8>)
+{
+    // we need a look-up table to reverse the lowest 4 bits
+    // in order to place the permute the transposed rows
+    static const unsigned char bitRev[] = {0,4,2,6,1,5,3,7};
+
+    // transpose a 8x8 byte matrix
+    __m64 tmp1[8];
+    for (int i = 0; i < 4; ++i)
+    {
+        tmp1[i]   = _mm_unpacklo_pi8(reinterpret_cast<const __m64 &>(matrix[2*i]), reinterpret_cast<const __m64 &>(matrix[2*i+1]));
+        tmp1[i+4] = _mm_unpackhi_pi8(reinterpret_cast<const __m64 &>(matrix[2*i]), reinterpret_cast<const __m64 &>(matrix[2*i+1]));
+    }
+    __m64 tmp2[8];
+    for (int i = 0; i < 4; ++i)
+    {
+        tmp2[i]   = _mm_unpacklo_pi16(tmp1[2*i], tmp1[2*i+1]);
+        tmp2[i+4] = _mm_unpackhi_pi16(tmp1[2*i], tmp1[2*i+1]);
+    }
+    for (int i = 0; i < 4; ++i)
+    {
+        matrix[bitRev[i]]   = reinterpret_cast<TSimdVector>(_mm_unpacklo_pi32(tmp2[2*i], tmp2[2*i+1]));
+        matrix[bitRev[i+4]] = reinterpret_cast<TSimdVector>(_mm_unpackhi_pi32(tmp2[2*i], tmp2[2*i+1]));
+    }
+}
+
+template <typename TSimdVector>
+inline void
+_transposeMatrix(TSimdVector matrix[], SimdMatrixParams_<16, 16, 8>)
+{
+    // we need a look-up table to reverse the lowest 4 bits
+    // in order to place the permute the transposed rows
+    static const unsigned char bitRev[] = {0,8,4,12,2,10,6,14,1,9,5,13,3,11,7,15};
+
+    // transpose a 16x16 byte matrix
+    //
+    // matrix =
+    // A0 A1 A2 ... Ae Af
+    // B0 B1 B2 ... Be Bf
+    // ...
+    // P0 P1 P2 ... Pe Pf
+    __m128i tmp1[16];
+    for (int i = 0; i < 8; ++i)
+    {
+        tmp1[i]   = _mm_unpacklo_epi8(reinterpret_cast<const __m128i &>(matrix[2*i]), reinterpret_cast<const __m128i &>(matrix[2*i+1]));
+        tmp1[i+8] = _mm_unpackhi_epi8(reinterpret_cast<const __m128i &>(matrix[2*i]), reinterpret_cast<const __m128i &>(matrix[2*i+1]));
+    }
+    // tmp1[0]  = A0 B0 A1 B1 ... A7 B7
+    // tmp1[1]  = C0 D0 C1 D1 ... C7 D7
+    // ...
+    // tmp1[7]  = O0 P0 O1 P1 ... O7 P7
+    // tmp1[8]  = A8 B8 A9 B9 ... Af Bf
+    // ...
+    // tmp1[15] = O8 P8 O9 P9 ... Of Pf
+    __m128i tmp2[16];
+    for (int i = 0; i < 8; ++i)
+    {
+        tmp2[i]   = _mm_unpacklo_epi16(tmp1[2*i], tmp1[2*i+1]);
+        tmp2[i+8] = _mm_unpackhi_epi16(tmp1[2*i], tmp1[2*i+1]);
+    }
+    // tmp2[0]  = A0 B0 C0 D0 ... A3 B3 C3 D3
+    // tmp2[1]  = E0 F0 G0 H0 ... E3 F3 G3 H3
+    // ...
+    // tmp2[3]  = M0 N0 O0 P0 ... M3 N3 O3 P3
+    // tmp2[4]  = A8 B8 C8 D8 ... Ab Bb Cb Db
+    // ...
+    // tmp2[7]  = M8 N8 O8 P8 ... Mb Nb Ob Pb
+    // tmp2[8]  = A4 B4 C4 D4 ... A7 B7 C7 D7
+    // ..
+    // tmp2[12] = Ac Bc Cc Dc ... Af Bf Cf Df
+    // ...
+    // tmp2[15] = Mc Nc Oc Pc ... Mf Nf Of Pf
+    for (int i = 0; i < 8; ++i)
+    {
+        tmp1[i]   = _mm_unpacklo_epi32(tmp2[2*i], tmp2[2*i+1]);
+        tmp1[i+8] = _mm_unpackhi_epi32(tmp2[2*i], tmp2[2*i+1]);
+    }
+    // tmp1[0]  = A0 B0 .... H0 A1 B1 .... H1
+    // tmp1[1]  = I0 J0 .... P0 I1 J1 .... P1
+    // ...
+    // tmp1[4]  = A0 B0 .... H0 A1 B1 .... H1
+    // tmp1[1]  = I0 J0 .... P0 I1 J1 .... P1
+    for (int i = 0; i < 8; ++i)
+    {
+        matrix[bitRev[i]]   = reinterpret_cast<TSimdVector>(_mm_unpacklo_epi64(tmp1[2*i], tmp1[2*i+1]));
+        matrix[bitRev[i+8]] = reinterpret_cast<TSimdVector>(_mm_unpackhi_epi64(tmp1[2*i], tmp1[2*i+1]));
+    }
+}
+
+#ifdef __SSE4_1__
+template <typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    int)
+inline _testAllZeros(TSimdVector const &vector, TSimdVector const &mask, SimdParams_<16>)
+{
+    return _mm_testz_si128(vector, mask);
+}
+
+template <typename TSimdVector>
+inline int _testAllOnes(TSimdVector const &vector, SimdParams_<16>)
+{
+    return _mm_test_all_ones(reinterpret_cast<const __m128i &>(vector));
+}
+
+
+#endif  // #ifdef __SSE3__
+//#endif  // #ifdef __AVX__
+#endif
+
+
+template <typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    int)
+inline testAllZeros(TSimdVector const &vector, TSimdVector const &mask)
+{
+    return _testAllZeros(vector, mask, SimdParams_<sizeof(TSimdVector)>());
+}
+
+template <typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    int)
+inline testAllZeros(TSimdVector const &vector)
+{
+    return _testAllZeros(vector, vector, SimdParams_<sizeof(TSimdVector)>());
+}
+
+template <typename TSimdVector>
+inline int _testAllOnes(TSimdVector const &vector, True)
+{
+    return _testAllOnes(vector, SimdParams_<sizeof(vector)>());
+}
+
+template <int ROWS, typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    void)
+inline transpose(TSimdVector matrix[ROWS])
+{
+    typedef typename Value<TSimdVector>::Type TValue;
+    _transposeMatrix(matrix, SimdMatrixParams_<
+                                    ROWS,
+                                    LENGTH<TSimdVector>::VALUE,
+                                    BitsPerValue<TValue>::VALUE>());
+}
+
+
+template <typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    void)
+inline clearVector(TSimdVector &vector)
+{
+    _clearVector(vector, SimdParams_<sizeof(TSimdVector), LENGTH<TSimdVector>::VALUE>());
+}
+
+
+template <typename TSimdVector, typename TValue>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    void)
+inline fillVector(TSimdVector &vector, TValue x)
+{
+    _fillVector(vector, x, SimdParams_<sizeof(TSimdVector), LENGTH<TSimdVector>::VALUE>());
+}
+
+template <typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    TSimdVector)
+inline blend(TSimdVector const &a, TSimdVector const &b, TSimdVector const &mask)
+{
+    return _blend(a, b, mask, SimdParams_<sizeof(TSimdVector), LENGTH<TSimdVector>::VALUE>());
+}
+
+template <typename TSimdVector1, typename TSimdVector2>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector1> >,
+    TSimdVector1)
+inline shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices)
+{
+    return _shuffleVector(
+                vector,
+                indices,
+                SimdParams_<sizeof(TSimdVector1), LENGTH<TSimdVector1>::VALUE>(),
+                SimdParams_<sizeof(TSimdVector2), LENGTH<TSimdVector2>::VALUE>());
+}
+
+template <typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    TSimdVector)
+inline shiftRightLogical(TSimdVector const &vector, const int imm)
+{
+    return _shiftRightLogical(vector, imm, SimdParams_<sizeof(TSimdVector), LENGTH<TSimdVector>::VALUE>());
+}
+
+
+template <typename TSimdVector>
+SEQAN_FUNC_ENABLE_IF(
+    Is<SimdVectorConcept<TSimdVector> >,
+    std::ostream &)
+inline print(std::ostream &stream, TSimdVector const &vector)
+{
+    stream << '<';
+    for (int i = 0; i < LENGTH<TSimdVector>::VALUE; ++i)
+        stream << '\t' << (unsigned)vector[i];
+    stream << "\t>";
+    return stream;
+}
+
+} // namespace seqan
+
+#endif // SEQAN_INCLUDE_SEQAN_BASIC_SIMD_VECTOR_H_
diff --git a/seqan/basic/basic_smart_pointer.h b/seqan/basic/basic_smart_pointer.h
index bc020e1..9c3ba38 100644
--- a/seqan/basic/basic_smart_pointer.h
+++ b/seqan/basic/basic_smart_pointer.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for the basic/smart_pointer sub module.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_
 
 // --------------------------------------------------------------------------
 // Dependencies
@@ -56,4 +56,4 @@
 
 #include <seqan/basic/volatile_ptr.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_
diff --git a/seqan/basic/basic_stream.h b/seqan/basic/basic_stream.h
new file mode 100644
index 0000000..ac25b8a
--- /dev/null
+++ b/seqan/basic/basic_stream.h
@@ -0,0 +1,1303 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Basic definitions for the stream module.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_STREAM_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_STREAM_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TDirection>
+struct StreamIterator;
+
+template <typename TValue, typename TTraits, typename TValue2>
+inline void writeValue(std::basic_ostream<TValue, TTraits> &ostream, TValue2 val);
+
+template <typename TValue, typename TTraits, typename TValue2>
+inline void writeValue(std::ostreambuf_iterator<TValue, TTraits> &iter, TValue2 val);
+
+template <typename TContainer, typename TValue>
+inline void writeValue(Iter<TContainer, StreamIterator<Output> > &iter, TValue val);
+
+template <typename TValue, typename TTraits>
+inline bool atEnd(std::istreambuf_iterator<TValue, TTraits> const &it);
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Size<TContainer>::Type)
+length(TContainer const & me);
+
+template <typename TContainer, typename TSource>
+inline void
+appendValue(TContainer SEQAN_FORWARD_ARG me, TSource SEQAN_FORWARD_CARG source);
+
+/*!
+ * @macro SEQAN_HAS_ZLIB
+ * @headerfile <seqan/stream.h>
+ * @brief Defined as 0 or 1, depending on zlib being available.
+ *
+ * @signature #define SEQAN_HAS_ZLIB 0  // or 1
+ */
+
+/*!
+ * @macro SEQAN_HAS_BZIP2
+ * @headerfile <seqan/stream.h>
+ * @brief Defined as 0 or 1, depending on bzlib being available.
+ *
+ * @signature #define SEQAN_HAS_BZIP 0  // or 1
+ */
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// ============================================================================
+// Concepts
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Concept StreamConcept
+// --------------------------------------------------------------------------
+
+/*!
+ * @concept StreamConcept
+ * @headerfile <seqan/basic.h>
+ *
+ * @brief Base concept for streams.
+ *
+ * @signature concept StreamConcept;
+ */
+
+/*!
+ * @mfn StreamConcept#Value
+ * @brief Metafunction for retrieving the value type of a stream.
+ *
+ * @signature Value<TStream>::Type;
+ *
+ * @tparam TStream The stream type to query for its value type.
+ * @return Type    The resulting value type.
+ */
+
+/*!
+ * @mfn StreamConcept#Size
+ * @brief Metafunction for retrieving the type of a stream.
+ *
+ * @signature Size<TStream>::Type;
+ *
+ * @tparam TStream The stream type to query for its size type.
+ * @return Type    The resulting size type.
+ */
+
+/*!
+ * @mfn StreamConcept#Position
+ * @brief Metafunction for retrieving the position type of a stream.
+ *
+ * @signature Position<TStream>::Type;
+ *
+ * @tparam TStream The stream type to query for its position type.
+ * @return Type    The resulting position type.
+ */
+
+/*!
+ * @fn StreamConcept#position
+ * @brief Return current stream position.
+ *
+ * @signature TPosition position(stream);
+ *
+ * @param[in] stream The stream to query.
+ * @return TPosition Current position in stream, see @link StreamConcept#Position Position @endlink.
+ */
+
+/*!
+ * @fn StreamConcept#setPosition
+ * @brief Set stream position.
+ *
+ * @signature void setPosition(stream, pos);
+ *
+ * @param[in,out] stream The stream to update
+ * @param[in]     pos    The positoin to set.
+ */
+
+/*!
+ * @fn StreamConcept#atEnd
+ * @brief Return whether stream is at the end.
+ *
+ * @signature bool atEnd(stream);
+ *
+ * @param[in] stream The stream to check.
+ * @return bool <tt>true</tt> if the file at EOF, <tt>false</tt> otherwise.
+ */
+
+SEQAN_CONCEPT(StreamConcept, (TStream))
+{};
+
+// --------------------------------------------------------------------------
+// Concept InputStreamConcept
+// --------------------------------------------------------------------------
+
+/*!
+ * @concept InputStreamConcept Input StreamConcept
+ * @extends StreamConcept
+ * @headerfile <seqan/basic.h>
+ *
+ * @signature concept InputStreamConcept : StreamConcept;
+ *
+ * @brief Concept for input streams (for reading).
+ */
+
+SEQAN_CONCEPT_REFINE(InputStreamConcept, (TStream), (StreamConcept))
+{
+    typedef typename Value<TStream>::Type       TValue;
+    typedef typename Size<TStream>::Type        TSize;
+    typedef typename Position<TStream>::Type    TPosition;
+
+    SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<TPosition>));
+
+    SEQAN_CONCEPT_USAGE(InputStreamConcept)
+    {}
+};
+
+// --------------------------------------------------------------------------
+// Concept OutputStreamConcept
+// --------------------------------------------------------------------------
+
+/*!
+ * @concept OutputStreamConcept Output StreamConcept
+ * @extends StreamConcept
+ * @headerfile <seqan/basic.h>
+ *
+ * @signature concept OutputStreamConcept : StreamConcept;
+ *
+ * @brief Concept for output streams (for writing).
+ */
+
+SEQAN_CONCEPT_REFINE(OutputStreamConcept, (TStream), (StreamConcept))
+{
+    typedef typename Value<TStream>::Type       TValue;
+    typedef typename Size<TStream>::Type        TSize;
+    typedef typename Position<TStream>::Type    TPosition;
+
+    SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<TPosition>));
+
+    SEQAN_CONCEPT_USAGE(OutputStreamConcept)
+    {}
+};
+
+// --------------------------------------------------------------------------
+// Concept BidirectionalStreamConcept
+// --------------------------------------------------------------------------
+
+/*!
+ * @concept BidirectionalStreamConcept Bidirectional StreamConcept
+ * @extends StreamConcept
+ * @headerfile <seqan/basic.h>
+ *
+ * @signature concept BidirectionalStreamConcept : StreamConcept;
+ *
+ * @brief Concept for bidirectional streams (both for reading and writing).
+ */
+
+SEQAN_CONCEPT_REFINE(BidirectionalStreamConcept, (TStream), (InputStreamConcept)(OutputStreamConcept))
+{};
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Struct FormattedNumber
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class FormattedNumber
+ * @implements NumberConcept
+ * @headerfile <seqan/basic.h>
+ *
+ * @brief Helper class for storing a numeric value together with a
+ *        <a href="http://www.cplusplus.com/reference/cstdio/printf/">printf format string</a>.
+ *
+ * @signature template <typename TValue>
+ *            struct FormattedNumber;
+ *
+ * @tparam The numeric value type.
+ */
+
+template <typename TValue>
+struct FormattedNumber
+{
+    char const * format;
+    TValue value;
+
+    /*!
+     * @fn FormattedNumber::FormattedNumber
+     * @brief Constructor.
+     *
+     * @signature FormattedNumber::FormattedNumber(format, value);
+     *
+     * @param[in] format A <tt>char const *</tt> for the format string.
+     * @param[in] value  The <tt>TValue</tt> to store.
+     *
+     * The constructed FormattedNumber object store the <tt>format</tt> pointer "as is".  This means that you are
+     * responsible for keeping this pointer valid until the object is deconstructed.  Passing in a C string literal
+     * (as in <tt>FormattedNumber&lt;double&gt;("%.2f", 1.234)</tt> is fine.
+     */
+
+    FormattedNumber(char const * format, TValue const & value) :
+        format(format), value(value)
+    {}
+
+    operator TValue() const
+    {
+        return value;
+    }
+};
+
+template <typename TValue>
+struct Is< NumberConcept< FormattedNumber<TValue> > > :
+    Is< NumberConcept<TValue> > {};
+
+// ============================================================================
+// Exceptions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Exception ParseError
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class ParseError
+ * @extends RuntimeError
+ * @headerfile <seqan/basic.h>
+ *
+ * @brief Exception class for parser errors.
+ *
+ * @signature struct ParseError : RuntimeError;
+ */
+
+struct ParseError : RuntimeError
+{
+    /*!
+     * @fn ParseError::ParseError
+     * @headerfile <seqan/basic.h>
+     *
+     * @brief Constructor.
+     *
+     * @signature ParseError::ParseError(message);
+     *
+     * @param[in] message The error message to use, <tt>std::string</tt> or <tt>char const * </tt>.
+     */
+
+    template <typename TString>
+    ParseError(TString const & message) :
+        RuntimeError(message)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Exception UnexpectedEnd
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class UnexpectedEnd
+ * @extends ParseError
+ * @headerfile <seqan/basic.h>
+ *
+ * @brief Exception class for "unexpected end of input" errors.
+ *
+ * @signature struct UnexpectedEnd : RuntimeError;
+ */
+
+struct UnexpectedEnd : ParseError
+{
+    /*!
+     * @fn UnexpectedEnd::UnexpectedEnd
+     * @headerfile <seqan/basic.h>
+     *
+     * @brief Default constructor, makes the object use a default message.
+     *
+     * @signature UnexpectedEnd::UnexpectedEnd();
+     */
+
+    UnexpectedEnd() :
+        ParseError("Unexpected end of input.")
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Exception EmptyFieldError
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class EmptyFieldError
+ * @extends ParseError
+ * @headerfile <seqan/basic.h>
+ *
+ * @brief Exception class for "empty field" errors.
+ *
+ * @signature struct EmptyFieldError : RuntimeError;
+ */
+
+struct EmptyFieldError : ParseError
+{
+    /*!
+     * @fn EmptyFieldError::EmptyFieldError
+     * @headerfile <seqan/basic.h>
+     *
+     * @brief Construct the exception with <tt>fieldName + " field was empty."</tt>.
+     *
+     * @signature EmptyFieldEror::EmptyFieldError(fieldName);
+     *
+     * @param[in] fieldName The field name to use for the message, <tt>std::string</tt>.
+     */
+
+    EmptyFieldError(std::string fieldName):
+        ParseError(fieldName + " field was empty.")
+    {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn StreamConcept#DirectionIterator
+ * @brief Return the direction iterator for the given direction.
+ *
+ * @signature DirectionIterator<TStream>::Type;
+ *
+ * @tparam TStream The stream to query for its direction iterator.
+ * @return Type    The resulting direction iterator.
+ */
+
+/*!
+ * @mfn ContainerConcept#DirectionIterator
+ * @brief Return the direction iterator for the given direction.
+ *
+ * @signature DirectionIterator<TContainer>::Type;
+ *
+ * @tparam TContainer The container to query for its direction iterator.
+ * @return Type       The resulting direction iterator.
+ */
+
+template <typename TObject, typename TDirection>
+struct DirectionIterator :
+    If<Is<StreamConcept<TObject> >,
+       Iter<TObject, StreamIterator<TDirection> >,
+       typename Iterator<TObject, Rooted>::Type>
+{};
+
+// --------------------------------------------------------------------------
+// Metafunction BasicStream
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn BasicStream
+ * @headerfile <seqan/basic.h>
+ * @brief Return the stream type to read or write values.
+ *
+ * @signature BasicStream<TValue, TDirection[, TTraits]>::Type;
+ *
+ * @tparam TValue     The value type of the stream.
+ * @tparam TDirection The direction of the stream, one of the @link DirectionTags @endlink.
+ * @tparam TTraits    The traits to use for the values, defaults to <tt>std::char_traits&lt;TValue&gt;</tt>.
+ *
+ */
+
+template <typename TValue, typename TDirection, typename TTraits = std::char_traits<TValue> >
+struct BasicStream :
+    If<
+        IsSameType<TDirection, Input>,
+        std::basic_istream<TValue, TTraits>,
+        typename If<
+            IsSameType<TDirection, Output>,
+            std::basic_ostream<TValue, TTraits>,
+            std::basic_iostream<TValue, TTraits>
+            >::Type
+        >
+{};
+
+// --------------------------------------------------------------------------
+// Metafunction IosOpenMode
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn IosOpenMode
+ * @headerfile <seqan/basic.h>
+ * @brief Return the <tt>std::ios</tt> open mode for a direction.
+ *
+ * @signature IosOpenMode<TDirection[, TDummy]>::Type;
+ *
+ * @tparam TDirection The direction to query for the open mode, one of the @link DirectionTags @endlink.
+ * @tparam TDummy     Implementation detail, defaults to <tt>void</tt> and is ignored.
+ * @return Type       The resulting open mode of type <tt>const int</tt>.
+ */
+
+template <typename TDirection, typename TDummy = void>
+struct IosOpenMode;
+
+
+template <typename TDummy>
+struct IosOpenMode<Input, TDummy>
+{
+    static const int VALUE;
+};
+
+template <typename TDummy>
+struct IosOpenMode<Output, TDummy>
+{
+    static const int VALUE;
+};
+
+template <typename TDummy>
+struct IosOpenMode<Bidirectional, TDummy>
+{
+    static const int VALUE;
+};
+
+template <typename TDummy>
+const int IosOpenMode<Input, TDummy>::VALUE = std::ios::in | std::ios::binary;
+
+template <typename TDummy>
+const int IosOpenMode<Output, TDummy>::VALUE = std::ios::out | std::ios::binary;
+
+template <typename TDummy>
+const int IosOpenMode<Bidirectional, TDummy>::VALUE = std::ios::in | std::ios::out | std::ios::binary;
+
+
+// --------------------------------------------------------------------------
+// Metafunction MagicHeader
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn MagicHeader
+ * @headerfile <seqan/basic.h>
+ * @brief Returns the magic header for a file format tag.
+ *
+ * The magic header is used for recognizing files from the first few bytes.
+ *
+ * @signature MagicHeader<TTag[, TDummy]>::VALUE;
+ *
+ * @tparam TTag   The file format tag to use for the query.
+ * @tparam TDummy Implementation detail, defaults to <tt>void</tt> and is ignored.
+ * @return VALUE  The magic header string, of type <tt>char const *</tt>.
+ *
+ * This metafunction must be implemented in the modules implementing the file I/O.  The metafunction is predefined when
+ * <tt>TTag</tt> is @link Nothing @endlink.  In this case, <tt>VALUE</tt> is <tt>NULL</tt>.
+ */
+
+template <typename TTag, typename T = void>
+struct MagicHeader;
+
+template <typename T>
+struct MagicHeader<Nothing, T>
+{
+    static char const * VALUE;
+};
+
+template <typename T>
+char const * MagicHeader<Nothing, T>::VALUE = NULL;
+
+// --------------------------------------------------------------------------
+// Metafunction FileExtensions
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn FileExtensions
+ * @headerfile <seqan/basic.h>
+ * @brief Returns an array of file format extension strings for file foramt tag.
+ *
+ * @signature FileExtensions<TFormat[, TDummy]>::VALUE;
+ *
+ * @tparam TTag   The file format tag to use for the query.
+ * @tparam TDummy Implementation detail, defaults to <tt>void</tt> and is ignored.
+ * @return VALUE  The array of file format extension, of type <tt>char const *[]</tt>.
+ *
+ * This metafunction must be implemented in the modules implementing the file I/O.  The metafunction is predefined when
+ * <tt>TTag</tt> is @link Nothing @endlink.  In this case, <tt>VALUE</tt> is <tt>{""}</tt>.
+ */
+
+template <typename TFormat, typename T = void>
+struct FileExtensions;
+
+template <typename T>
+struct FileExtensions<Nothing, T>
+{
+    static char const * VALUE[1];
+};
+
+template <typename T>
+char const * FileExtensions<Nothing, T>::VALUE[1] =
+{
+    ""  // default output extension
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IntegerFormatString_
+// ----------------------------------------------------------------------------
+// Return the format string for numbers.
+
+template <typename TUnsigned, unsigned SIZE, typename T = void>
+struct IntegerFormatString_;
+
+
+template <typename TUnsigned, typename T>
+struct IntegerFormatString_<TUnsigned, 1, T> :
+    IntegerFormatString_<TUnsigned, 2, T> {};
+
+
+template <typename T>
+struct IntegerFormatString_<False, 2, T>
+{
+    static const char VALUE[];
+    typedef short Type;
+};
+template <typename T>
+const char IntegerFormatString_<False, 2, T>::VALUE[] = "%hi";
+
+
+template <typename T>
+struct IntegerFormatString_<True, 2, T>
+{
+    static const char VALUE[];
+    typedef unsigned short Type;
+};
+template <typename T>
+const char IntegerFormatString_<True, 2, T>::VALUE[] = "%hu";
+
+
+template <typename T>
+struct IntegerFormatString_<False, 4, T>
+{
+    static const char VALUE[];
+    typedef int Type;
+};
+template <typename T>
+const char IntegerFormatString_<False, 4, T>::VALUE[] = "%i";
+
+
+template <typename T>
+struct IntegerFormatString_<True, 4, T>
+{
+    static const char VALUE[];
+    typedef unsigned Type;
+};
+template <typename T>
+const char IntegerFormatString_<True, 4, T>::VALUE[] = "%u";
+
+
+// helper for the case: typedef long __int64;
+template <typename TIsUnsigned, typename T>
+struct LongFormatString_;
+
+template <typename T>
+struct LongFormatString_<False, T>
+{
+    static const char VALUE[];
+    typedef long Type;
+};
+template <typename T>
+const char LongFormatString_<False, T>::VALUE[] = "%li";
+
+template <typename T>
+struct LongFormatString_<True, T>
+{
+    static const char VALUE[];
+    typedef unsigned long Type;
+};
+template <typename T>
+const char LongFormatString_<True, T>::VALUE[] = "%lu";
+
+// helper for the case: typedef long long __int64;
+template <typename TIsUnsigned, typename T>
+struct Int64FormatString_;
+
+template <typename T>
+struct Int64FormatString_<False, T>
+{
+    static const char VALUE[];
+    typedef __int64 Type;
+};
+template <typename T>
+const char Int64FormatString_<False, T>::VALUE[] = "%lli";
+
+template <typename T>
+struct Int64FormatString_<True, T>
+{
+    static const char VALUE[];
+    typedef __uint64 Type;
+};
+template <typename T>
+const char Int64FormatString_<True, T>::VALUE[] = "%llu";
+
+
+template <typename TIsUnsigned, typename T>
+struct IntegerFormatString_<TIsUnsigned, 8, T> :
+    If<IsSameType<__uint64, unsigned long>,
+       LongFormatString_<TIsUnsigned, T>,
+       Int64FormatString_<TIsUnsigned, T> >::Type {};
+
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function writeValue()                                     [ContainerConcept]
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ContainerConcept#writeValue
+ * @brief Write a value at the end of a container.
+ *
+ * @signature void writeValue(container, val);
+ *
+ * @param[in,out] container to append to.
+ * @param[in]     val       The value to append.
+ *
+ * @see ContainerConcept#appendValue
+ */
+
+// resizable containers
+template <typename TSequence, typename TValue>
+inline SEQAN_FUNC_ENABLE_IF(Is<ContainerConcept<TSequence> >, void)
+writeValue(TSequence &cont, TValue val)
+{
+    appendValue(cont, val);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeValue()                                                [Range]
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn Range#writeValue
+ * @brief Write a value to a @link Range @endlink.
+ *
+ * @signature void writeValue(range, val);
+ *
+ * <tt>val</tt> will be assigned to the first element of the range.  Then, the beginning of the range will be advanced
+ * by one.
+ *
+ * @param[in,out] range to append to.
+ * @param[in]     val   The value to append.
+ */
+
+// Range
+template <typename TIterator, typename TValue>
+inline void
+writeValue(Range<TIterator> &range, TValue val)
+{
+    assignValue(range.begin, val);
+    ++range.begin;
+}
+
+// ----------------------------------------------------------------------------
+// Function writeValue()                                                 [Iter]
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn OutputIteratorConcept#writeValue
+ * @brief Write a single value to a container by dereferencing its iterator.
+ *
+ * @signature void writeValue(iter, val);
+ *
+ * @param[in,out] iter The iterator to use for dereferenced writing.
+ * @param[in]     val  The value to write into the container.
+ *
+ * If the host of <tt>iter</tt> is a @link ContainerConcept @endlink then container is resized to make space for the
+ * item.
+ */
+
+// resizable containers
+template <typename TSequence, typename TSpec, typename TValue>
+inline SEQAN_FUNC_ENABLE_IF(Is<ContainerConcept<TSequence> >, void)
+writeValue(Iter<TSequence, TSpec> & iter, TValue val)
+{
+    typedef Iter<TSequence, TSpec> TIter;
+
+    TSequence &cont = container(iter);
+    typename Position<TIter>::Type pos = position(iter);
+    typename Size<TIter>::Type len = length(cont);
+
+    if (pos < len)
+    {
+        assignValue(iter, val);
+        ++iter;
+    }
+    else
+    {
+        if (pos > len)
+            resize(cont, pos - 1);
+        appendValue(cont, val);
+        setPosition(iter, pos + 1);
+    }
+}
+
+// non-resizable containers
+template <typename TNoSequence, typename TSpec, typename TValue>
+inline SEQAN_FUNC_DISABLE_IF(Is<ContainerConcept<TNoSequence> >, void)
+writeValue(Iter<TNoSequence, TSpec> & iter, TValue val)
+{
+    SEQAN_ASSERT_LT(position(iter), length(container(iter)));
+
+    assignValue(iter, val);
+    ++iter;
+}
+
+// ----------------------------------------------------------------------------
+// Function writeValue()                                              [pointer]
+// ----------------------------------------------------------------------------
+
+///*!
+// * @fn ContainerConcept#writeValue
+// * @brief Write a value by dereferencing a pointer and incrementing its position by one.
+// *
+// * @signature void writeValue(pointer, val);
+// *
+// * @param[in,out] iter The pointer to dereference, usually a <tt>char *</tt>.
+// * @param[in]     val  The value to write to the dereferenced pointer.
+// *
+// * This function is equivalent to <tt>*iter++ = val</tt>.
+// */
+
+template <typename TTargetValue, typename TValue>
+inline void
+writeValue(TTargetValue * & iter, TValue val)
+{
+    *iter++ = val;
+}
+
+// ----------------------------------------------------------------------------
+// Function _write(); Element-wise
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator, typename TSize, typename TIChunk, typename TOChunk>
+inline void _write(TTarget &target, TFwdIterator &iter, TSize n, TIChunk, TOChunk)
+{
+    for (; n > (TSize)0; --n, ++iter)
+        writeValue(target, getValue(iter));
+}
+
+// ----------------------------------------------------------------------------
+// Function _write(); Chunked
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator, typename TSize, typename TIValue, typename TOValue>
+inline void _write(TTarget &target, TFwdIterator &iter, TSize n, Range<TIValue*> *, Range<TOValue*> *)
+{
+    typedef Nothing* TNoChunking;
+    typedef typename Size<TTarget>::Type TTargetSize;
+
+    Range<TIValue*> ichunk;
+    Range<TOValue*> ochunk;
+
+    while (n != (TSize)0)
+    {
+        getChunk(ichunk, iter, Input());
+        getChunk(ochunk, target, Output());
+
+        TTargetSize minChunkSize = std::min((TTargetSize)length(ichunk), (TTargetSize)length(ochunk));
+
+        if (SEQAN_UNLIKELY(minChunkSize == 0u))
+        {
+            reserveChunk(target, n, Output());
+            reserveChunk(iter, n, Input());
+            getChunk(ochunk, target, Output());
+            getChunk(ichunk, iter, Input());
+            minChunkSize = std::min((TTargetSize)length(ichunk), (TTargetSize)length(ochunk));
+            if (SEQAN_UNLIKELY(minChunkSize == 0u))
+            {
+                _write(target, iter, n, TNoChunking(), TNoChunking());
+                return;
+            }
+        }
+
+        if (minChunkSize > (TTargetSize)n)
+            minChunkSize = (TTargetSize)n;
+
+        arrayCopyForward(ichunk.begin, ichunk.begin + minChunkSize, ochunk.begin);
+
+        iter += minChunkSize;                      // advance input iterator
+        advanceChunk(target, minChunkSize);
+        n -= minChunkSize;
+    }
+}
+
+// chunked, target is pointer (e.g. readRawPod)
+template <typename TOValue, typename TFwdIterator, typename TSize>
+inline SEQAN_FUNC_DISABLE_IF(IsSameType<typename Chunk<TFwdIterator>::Type, Nothing>, void)
+write(TOValue *ptr, TFwdIterator &iter, TSize n)
+{
+    typedef Nothing* TNoChunking;
+    typedef typename Size<TFwdIterator>::Type TSourceSize;
+    typedef typename Chunk<TFwdIterator>::Type TIChunk;
+
+    TIChunk ichunk;
+
+    while (n != (TSize)0)
+    {
+        getChunk(ichunk, iter, Input());
+        TSourceSize chunkSize = length(ichunk);
+
+        if (SEQAN_UNLIKELY(chunkSize == 0u))
+        {
+            reserveChunk(iter, n, Input());
+            getChunk(ichunk, iter, Input());
+            TSourceSize chunkSize = length(ichunk);
+            if (SEQAN_UNLIKELY(chunkSize == 0u))
+            {
+                _write(ptr, iter, n, TNoChunking(), TNoChunking());
+                return;
+            }
+        }
+
+        if (chunkSize > (TSourceSize)n)
+            chunkSize = (TSourceSize)n;
+
+        arrayCopyForward(ichunk.begin, ichunk.begin + chunkSize, ptr);
+
+        iter += chunkSize;                          // advance input iterator
+        ptr += chunkSize;
+        n -= chunkSize;
+    }
+}
+
+// non-chunked fallback
+template <typename TTarget, typename TIValue, typename TSize>
+inline SEQAN_FUNC_ENABLE_IF(And< IsSameType<typename Chunk<TTarget>::Type, Nothing>,
+                                 Is<Convertible<typename Value<TTarget>::Type, TIValue> > >, void)
+write(TTarget &target, TIValue *ptr, TSize n)
+{
+    _write(target, ptr, n, Nothing(), Nothing());
+}
+
+// ostream shortcut, source is pointer (e.g. readRawPod)
+template <typename TTarget, typename TSize>
+inline SEQAN_FUNC_ENABLE_IF(Is< OutputStreamConcept<TTarget> >, void)
+write(TTarget &target, const char *ptr, TSize n)
+{
+    target.write(ptr, n);
+}
+
+// ostream shortcut, source is pointer (e.g. readRawPod)
+template <typename TTarget, typename TSize>
+inline SEQAN_FUNC_ENABLE_IF(Is< OutputStreamConcept<TTarget> >, void)
+write(TTarget &target, char *ptr, TSize n)
+{
+    target.write(ptr, n);
+}
+
+// chunked, source is pointer (e.g. readRawPod)
+template <typename TTarget, typename TIValue, typename TSize>
+inline SEQAN_FUNC_ENABLE_IF(And< Not<IsSameType<typename Chunk<TTarget>::Type, Nothing> >,
+                                 Is<Convertible<typename Value<TTarget>::Type, TIValue> > >, void)
+write(TTarget &target, TIValue *ptr, TSize n)
+{
+    typedef Nothing* TNoChunking;
+    typedef typename Size<TTarget>::Type TTargetSize;
+    typedef typename Chunk<TTarget>::Type TOChunk;
+
+    TOChunk ochunk;
+
+    while (n != (TSize)0)
+    {
+        getChunk(ochunk, target, Output());
+        TTargetSize chunkSize = length(ochunk);
+
+        if (SEQAN_UNLIKELY(chunkSize == 0u))
+        {
+            reserveChunk(target, n, Output());
+            getChunk(ochunk, target, Output());
+            chunkSize = length(ochunk);
+            if (SEQAN_UNLIKELY(chunkSize == 0u))
+            {
+                _write(target, ptr, n, TNoChunking(), TNoChunking());
+                return;
+            }
+        }
+
+        if (chunkSize > (TTargetSize)n)
+            chunkSize = (TTargetSize)n;
+
+        arrayCopyForward(ptr, ptr + chunkSize, ochunk.begin);
+
+        ptr += chunkSize;                      // advance input iterator
+        advanceChunk(target, chunkSize);
+        n -= chunkSize;
+    }
+}
+
+template <typename TOValue, typename TIValue, typename TSize>
+inline SEQAN_FUNC_ENABLE_IF(And< Is<CharConcept<TOValue> >,
+                                 Is<CharConcept<TIValue> > >, void)
+write(TOValue * &optr, TIValue *iptr, TSize n)
+{
+    std::memcpy(optr, iptr, n);
+    optr += n;
+}
+
+template <typename TOValue, typename TIValue, typename TSize>
+inline SEQAN_FUNC_ENABLE_IF(And< Is<CharConcept<TOValue> >,
+                                 Is<CharConcept<TIValue> > >, void)
+write(TOValue * optr, TIValue * &iptr, TSize n)
+{
+    std::memcpy(optr, iptr, n);
+    iptr += n;
+}
+
+// ----------------------------------------------------------------------------
+// Function write(TValue *)
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): should it be defined for Streams and Containers?
+
+//template <typename TTarget, typename TValue, typename TSize>
+//inline SEQAN_FUNC_ENABLE_IF(Or<Is<OutputStreamConcept<TTarget> >, Is<ContainerConcept<TTarget> > >, void)
+//write(TTarget &target, TValue *ptr, TSize n)
+//{
+//    typedef Range<TValue*>                          TRange;
+//    typedef typename Iterator<TRange, Rooted>::Type TIterator;
+//    typedef typename Chunk<TIterator>::Type*        TIChunk;
+//    typedef typename Chunk<TTarget>::Type*          TOChunk;
+//
+//    TRange range(ptr, ptr + n);
+//    TIterator iter = begin(range, Rooted());
+//    _write(target, iter, n, TIChunk(), TOChunk());
+//}
+
+// ----------------------------------------------------------------------------
+// Function write(Iterator<Input>)
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ContainerConcept#write
+ * @brief Write to a container.
+ *
+ * @signature void write(container, iter, n);
+ *
+ * @param[in,out] container The container to append to.
+ * @param[in,out] iter      The @link ForwardIteratorConcept forward iterator @endlink to take the values from.
+ * @param[in]     n         Number of elements to write from <tt>iter</tt>.
+ *
+ * This function reads <tt>n</tt> values from <tt>iter</tt> and appends them to the back of <tt>container</tt>.
+ */
+
+//TODO(singer): Enable this!
+template <typename TTarget, typename TFwdIterator, typename TSize>
+//inline SEQAN_FUNC_ENABLE_IF(Or<Is<OutputStreamConcept<TTarget> >, Is<ContainerConcept<TTarget> > >, void)
+inline SEQAN_FUNC_ENABLE_IF(And< Is<IntegerConcept<TSize> >,
+                                 Is<Convertible<typename Value<TTarget>::Type,
+                                                typename Value<TFwdIterator>::Type> > >, void)
+write(TTarget &target, TFwdIterator &iter, TSize n)
+{
+    typedef typename Chunk<TFwdIterator>::Type* TIChunk;
+    typedef typename Chunk<TTarget>::Type*      TOChunk;
+
+    _write(target, iter, n, TIChunk(), TOChunk());
+}
+
+// write for more complex values (defer to write of iterator value)
+// used for Strings of Pairs
+template <typename TTarget, typename TFwdIterator, typename TSize>
+//inline SEQAN_FUNC_ENABLE_IF(Or<Is<OutputStreamConcept<TTarget> >, Is<ContainerConcept<TTarget> > >, void)
+inline SEQAN_FUNC_ENABLE_IF(And<
+    Is<IntegerConcept<TSize> >,
+    Not< Is<Convertible<typename Value<TTarget>::Type,
+                        typename Value<TFwdIterator>::Type> > > >, void)
+write(TTarget &target, TFwdIterator &iter, TSize n)
+{
+    for (; n > (TSize)0; --n, ++iter)
+    {
+        write(target, *iter);
+        writeValue(target, ' ');
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function write(TContainer) but not container of container
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And< Not<IsContiguous<TContainer> >,
+                                 And< Is<ContainerConcept<TContainer> >,
+                                      Not<Is<ContainerConcept<typename Value<TContainer>::Type> > > > >, void)
+write(TTarget &target, TContainer &cont)
+{
+    typename DirectionIterator<TContainer, Input>::Type iter = directionIterator(cont, Input());
+    write(target, iter, length(cont));
+}
+
+template <typename TTarget, typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And< IsContiguous<TContainer>,
+                                 And< Is<ContainerConcept<TContainer> >,
+                                      Not<Is<ContainerConcept<typename Value<TContainer>::Type> > > > >, void)
+write(TTarget &target, TContainer &cont)
+{
+    typename Iterator<TContainer, Standard>::Type iter = begin(cont, Standard());
+    write(target, iter, length(cont));
+}
+
+template <typename TTarget, typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And< Not<IsContiguous<TContainer> >,
+                                 And< Is<ContainerConcept<TContainer> >,
+                                      Not<Is<ContainerConcept<typename Value<TContainer>::Type> > > > >, void)
+write(TTarget &target, TContainer const &cont)
+{
+    typename DirectionIterator<TContainer const, Input>::Type iter = directionIterator(cont, Input());
+    write(target, iter, length(cont));
+}
+
+template <typename TTarget, typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And< IsContiguous<TContainer>,
+                                 And< Is<ContainerConcept<TContainer> >,
+                                      Not<Is<ContainerConcept<typename Value<TContainer>::Type> > > > >, void)
+write(TTarget &target, TContainer const &cont)
+{
+    typename Iterator<TContainer const, Standard>::Type iter = begin(cont, Standard());
+    write(target, iter, length(cont));
+}
+
+template <typename TTarget, typename TValue>
+inline void
+write(TTarget &target, TValue * ptr)
+{
+    write(target, ptr, length(ptr));
+}
+
+// ----------------------------------------------------------------------------
+// Function appendNumber()
+// ----------------------------------------------------------------------------
+// Generic version for integers.
+
+template <typename TTarget, typename TInteger>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TInteger> >, typename Size<TTarget>::Type)
+appendNumber(TTarget & target, TInteger i)
+{
+    typedef IntegerFormatString_<typename Is<UnsignedIntegerConcept<TInteger> >::Type,
+                                 sizeof(TInteger)> TInt;
+
+    // 1 byte has at most 3 decimal digits (plus 2 for '-' and the NULL character)
+    char buffer[sizeof(TInteger) * 3 + 2];
+    size_t len = snprintf(buffer, sizeof(buffer),
+                          TInt::VALUE, static_cast<typename TInt::Type>(i));
+    char *bufPtr = buffer;
+    write(target, bufPtr, len);
+    return len;
+}
+
+// ----------------------------------------------------------------------------
+// Function appendNumber(bool)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget>
+inline typename Size<TTarget>::Type
+appendNumber(TTarget & target, bool source)
+{
+    writeValue(target, '0' + source);
+    return 1;
+}
+
+// ----------------------------------------------------------------------------
+// Function appendNumber(float)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget>
+inline typename Size<TTarget>::Type
+appendNumber(TTarget & target, float source)
+{
+    char buffer[32];
+    size_t len = snprintf(buffer, sizeof(buffer), "%g", source);
+    write(target, (char *)buffer, len);
+    return len;
+}
+
+// ----------------------------------------------------------------------------
+// Function appendNumber(double)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget>
+inline typename Size<TTarget>::Type
+appendNumber(TTarget & target, double source)
+{
+    char buffer[32];
+    size_t len = snprintf(buffer, sizeof(buffer), "%g", source);
+    write(target, (char *)buffer, len);
+    return len;
+}
+
+// ----------------------------------------------------------------------------
+// Function appendNumber(double)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TValue>
+inline typename Size<TTarget>::Type
+appendNumber(TTarget & target, FormattedNumber<TValue> const & source)
+{
+    char buffer[100];
+    size_t len = snprintf(buffer, sizeof(buffer), source.format, source.value);
+    write(target, (char *)buffer, len);
+    return len;
+}
+
+template <typename TValue>
+inline FormattedNumber<TValue>
+formattedNumber(const char *format, TValue const & val)
+{
+    return FormattedNumber<TValue>(format, val);
+}
+
+// ----------------------------------------------------------------------------
+// Function appendRawPod()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TValue>
+inline void
+appendRawPod(TTarget & target, TValue const & val)
+{
+    write(target, (unsigned char*)&val, sizeof(TValue));
+}
+
+template <typename TTargetValue, typename TValue>
+inline void
+appendRawPod(TTargetValue * &ptr, TValue const & val)
+{
+    *reinterpret_cast<TValue* &>(ptr)++ = val;
+}
+
+// ----------------------------------------------------------------------------
+// Function write(TNumber); write fundamental type
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TValue>
+inline SEQAN_FUNC_ENABLE_IF(And< Is<Convertible<typename Value<TTarget>::Type, TValue> >,
+                                 Is<FundamentalConcept<TValue> > >, void)
+write(TTarget &target, TValue &number)
+{
+    if (sizeof(TValue) == 1)
+        writeValue(target, number);     // write chars as chars
+    else
+        appendNumber(target, number);
+}
+
+template <typename TTarget, typename TValue>
+inline SEQAN_FUNC_ENABLE_IF(And< Is<Convertible<typename Value<TTarget>::Type, TValue> >,
+                                 Is<FundamentalConcept<TValue> > >, void)
+write(TTarget &target, TValue const &number)
+{
+    if (sizeof(TValue) == 1)
+        writeValue(target, number);     // write chars as chars
+    else
+        appendNumber(target, number);
+}
+
+// ----------------------------------------------------------------------------
+// Function write(TNumber); write non-fundamental, convertible type
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TValue>
+inline SEQAN_FUNC_ENABLE_IF(And< Is<Convertible<typename Value<TTarget>::Type, TValue> >,
+                                 Not<Is<FundamentalConcept<TValue> > > >, void)
+write(TTarget &target, TValue &number)
+{
+    writeValue(target, number);
+}
+
+template <typename TTarget, typename TValue>
+inline SEQAN_FUNC_ENABLE_IF(And< Is<Convertible<typename Value<TTarget>::Type, TValue const> >,
+                                 Not<Is<FundamentalConcept<TValue const> > > >, void)
+write(TTarget &target, TValue const &number)
+{
+    writeValue(target, number);
+}
+
+// ----------------------------------------------------------------------------
+// Function read(Iterator<Input>)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator, typename TSize>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TSize> >, TSize)
+read(TTarget &target, TFwdIterator &iter, TSize n)
+{
+    TSize i;
+    for (i = 0; !atEnd(iter) && i < n; ++i, ++iter)
+        writeValue(target, value(iter));
+    return i;
+}
+
+// ----------------------------------------------------------------------------
+// Function read(TContainer)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TContainer>
+inline typename Size<TTarget>::Type
+read(TTarget &target, TContainer &cont)
+{
+    typename DirectionIterator<TContainer, Input>::Type iter = directionIterator(cont, Input());
+    return read(target, iter, length(cont));
+}
+
+// ----------------------------------------------------------------------------
+// operator<<
+// ----------------------------------------------------------------------------
+
+template <typename TStream, typename TIterator>
+inline TStream &
+operator<<(TStream & target,
+           Range<TIterator> const & source)
+{
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
+    return target;
+}
+
+template <typename TStream, typename TValue>
+inline TStream &
+operator<<(TStream & target,
+           FormattedNumber<TValue> const & source)
+{
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
+    return target;
+}
+
+}  // namespace seqean
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_STREAM_H_
diff --git a/seqan/basic/basic_tangle.h b/seqan/basic/basic_tangle.h
index 393a7a9..e6b2b0d 100644
--- a/seqan/basic/basic_tangle.h
+++ b/seqan/basic/basic_tangle.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                               basic_tangle.h
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 
 // TODO(holtgrew): This header contains code that does not clearly belongs somewhere else.
 
-#ifndef CORE_INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
-#define CORE_INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
+#ifndef INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
+#define INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
 
 namespace seqan {
 
@@ -75,10 +75,8 @@ struct Iterator<SimpleType<TValue, TSpec> const, Standard>
 
 // TODO(holtgrew): Is this part of some adaption?
 
-///.Metafunction.Key.param.T.type:Class.Pair
-
 template <typename TKey, typename TObject, typename TSpec>
-struct Key<Pair<TKey, TObject, TSpec> > 
+struct Key<Pair<TKey, TObject, TSpec> >
 {
     typedef TKey Type;
 };
@@ -89,10 +87,8 @@ struct Key<Pair<TKey, TObject, TSpec> >
 
 // TODO(holtgrew): Is this part of some adaption?
 
-///.Metafunction.Cargo.param.T.type:Class.Pair
-
 template <typename TKey, typename TCargo, typename TSpec>
-struct Cargo<Pair<TKey, TCargo, TSpec> > 
+struct Cargo<Pair<TKey, TCargo, TSpec> >
 {
     typedef TCargo Type;
 };
@@ -110,49 +106,31 @@ struct Cargo<Pair<TKey, TCargo, TSpec> >
  * @fn assignQualities
  * @headerfile <seqan/basic.h>
  * @brief Assign quality values between strings.
- * 
+ *
  * @signature void assignQualities(target, source);
- * 
+ *
  * @param[out] target Target string, can be a String of DnaQ or Dna5Q characters.
  * @param[in]  source Source string.  Can be a String of int or char.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The target is resized to the length of source.  This function calls assignQualityValue for all entries of
  * <tt>target</tt> and <tt>source</tt>, look at the documentation of assignQualityValue on how the values of
  * <tt>source</tt> are interpreted.
- * 
+ *
  * Note that qualities are expected to be in PHRED scale.
- * 
+ *
  * @see AlphabetWithQualitiesConcept#assignQualityValue
  */
 
-/**
-.Function.assignQualities
-..cat:Alphabets
-..summary:Assign quality values between strings.
-..signature:assignQualities(target, source)
-..param.target:Target string
-...type:nolink:@Class.String@ of any alphabet with qualities, e.g. @Spec.DnaQ@, @Spec.Dna5Q@
-..param.source:Source string.
-...type:nolink:@Class.String@ of $int$ or $char$.
-..remarks:
-The target is resized to the length of source.
-This function calls @Function.assignQualityValue@ for all entries of $target$ and $source$, look at the documentation of @Function.assignQualityValue@ on how the values of $source$ are interpreted.
-..remarks:
-Note that qualities are expected to be in PHRED scale.
-..see:Function.assignQualityValue
-..include:seqan/basic.h
-*/
-
-// TODO(holtgrew): Uncomment, place somewhere that knows both iterators and assignQualityValue, maybe in module sequence?
 template <typename TDest, typename TSource>
-void assignQualities(TDest &dst, TSource const &src)
+inline void
+_assignQualities(TDest &dst, TSource const &src, True)
 {
     typedef typename Iterator<TDest>::Type TDestIter;
     typedef typename Iterator<TSource const>::Type TSourceIter;
 
-	if (length(dst) < length(src))
+    if (length(dst) < length(src))
         resize(dst, length(src));
 
     TDestIter itDst = begin(dst, Standard());
@@ -162,6 +140,20 @@ void assignQualities(TDest &dst, TSource const &src)
         assignQualityValue(*itDst, *itSrc);
 }
 
+template <typename TDest, typename TSource>
+inline void
+_assignQualities(TDest &, TSource const &, False)
+{}
+
+// TODO(holtgrew): Uncomment, place somewhere that knows both iterators and assignQualityValue, maybe in module sequence?
+template <typename TDest, typename TSource>
+inline void
+assignQualities(TDest &dst, TSource const &src)
+{
+    typedef typename Value<TDest>::Type TValue;
+    _assignQualities(dst, src, typename Or<IsSameType<TValue, DnaQ>, IsSameType<TValue, Dna5Q> >::Type());
+}
+
 template <typename T>
 inline T
 unknownValueImpl(T *)
@@ -172,4 +164,4 @@ unknownValueImpl(T *)
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
+#endif  // #ifndef INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
diff --git a/seqan/basic/basic_type.h b/seqan/basic/basic_type.h
index b23f7f5..995a516 100644
--- a/seqan/basic/basic_type.h
+++ b/seqan/basic/basic_type.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -158,30 +158,18 @@ struct Host
 
 /*!
  * @mfn Cargo
+ * @headerfile <seqan/basic.h>
  * @brief Type of additional data stored in an object.
- * 
- * @signature Cargo<T>::Type
+ *
+ * @signature Cargo<T>::Type;
  *
  * @tparam T Type for which the cargo tpye is queried.
  *
  * @return Type  The cargo type of <tt>T</tt>.
  *
- * @section Remarks
- *
  * The definition of Cargo allows the addition of user-specified data into existing data structures.
  */
 
-/**
-.Metafunction.Cargo:
-..cat:Basic
-..summary:Type of additional data stored in an object. 
-..signature:Cargo<T>::Type
-..param.T:Type for which the cargo tyoe is determined.
-..returns.param.Type:Cargo of $T$.
-..remarks:The definition of Cargo allows the addition of user specific data to existing data structures.
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Should this have a default implementation?
 
 template <typename T>
@@ -207,20 +195,6 @@ struct Cargo<T const> {
  * @return Type The resulting vertex descriptor type.
  */
 
-/**
-.Metafunction.VertexDescriptor:
-..cat:Graph
-..summary:Type of an object that represents a vertex descriptor.
-..signature:VertexDescriptor<T>::Type
-..param.T:Type T must be a graph. All graphs currently use ids as vertex descriptors.
-..returns.param.Type:VertexDescriptor type.
-..remarks.text:The vertex descriptor is a unique handle to a vertex in a graph.
-It is used in various graph functions, e.g., to add edges, to create OutEdge Iterators or to remove a vertex.
-It is also used to attach properties to vertices.
-..example.code:VertexDescriptor<Graph<> >::Type vD; //vD is a vertex descriptor
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Should this have a default implementation? For all graphs -- OK but for all types?
 
 template <typename T>
@@ -245,19 +219,6 @@ struct VertexDescriptor<T const>:
  *
  * @return Type The resulting identifier type.
  */
-    
-/**
-.Metafunction.Id:
-..cat:Graph
-..summary:Type of an object that represents an id.
-..signature:Id<T>::Type
-..param.T:Type for which a suitable id type is determined.
-..returns.param.Type:Id type.
-..remarks.text:The id type of a container is the type that is used to uniquely identify its elements.
-In most cases this type is unsigned int.
-..example.code:Id<Graph<> >::Type id; //id has type unsigned int
-..include:seqan/basic.h
-*/
 
 // TODO(holtgrew): Should this have a default implementation?
 
@@ -283,17 +244,6 @@ struct Id<T const> : Id<T> {};
  * @return Type The key type.
  */
 
-/**
-.Metafunction.Key:
-..cat:Graph
-..summary:Key type of a key to cargo mapping.
-..signature:Key<T>::Type
-..param.T:Type for which a key type is determined.
-..returns.param.Type:Key type.
-...default:The type $T$ itself.
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Should this have a default implementation?
 
 template< typename T >
@@ -308,17 +258,8 @@ struct Key<T const>:
 
 //____________________________________________________________________________
 
-/*VERALTET
-.Metafunction.Object:
-..summary:Object type of a key to object mapping.
-..signature:Object<T>::Type
-..param.T:Type for which a object type is determined.
-..returns.param.Type:Object type.
-..include:seqan/basic.h
-*/
-
 template<typename T>
-struct Object; 
+struct Object;
 
 template <typename T>
 struct Object<T const>:
@@ -330,11 +271,6 @@ struct Object<T const>:
 // TODO(holtgrew): Move to alignments?
 // TODO(holtgrew): Is this default implementation what we want?
 
-/**
-.Metafunction.Source
-..cat:Alignments
-*/
-
 template < typename TSpec = void >
 struct Source
 {
@@ -362,32 +298,12 @@ struct Source<T const>:
  * @return Type Either True or False.  True if the object can efficiently be copied.
  */
 
-/**
-.Metafunction.IsLightWeight:
-..cat:Metafunctions
-..summary:Determines whether an object can efficiently be passed by copy.
-..signature:IsLightWeight<T>::Type
-..param.T:A type.
-..returns.param.Type:@Tag.Logical Values.tag.True@ if the object is light-weight and can efficiently be copied, e.g. @Class.Segment@, otherwise @Tag.Logical Values.tag.False@.
-*/
-
 template <typename T>
 struct IsLightWeight:
     False {};
 
 //____________________________________________________________________________
 
-/**
-.Internal.Parameter_:
-..cat:Metafunctions
-..summary:Type for function parameters and return values.
-..signature:Parameter_<T>::Type
-..param.T:A type.
-..returns.param.Type:The parameter type for arguments of type $T$.
-...text:If $T$ is a pointer or array type, then $Parameter_<T>::Type$ is $T$, 
-otherwise $Parameter_<T>::Type$ is $T &$.
-*/
-
 // TODO(holtgrew): Really required?
 
 template <typename T>
@@ -396,30 +312,35 @@ struct Parameter_
     typedef T & Type;
 };
 
+template <typename T>
+struct Parameter_<T const>
+{
+    typedef T const & Type;
+};
+
 template <typename T>
 struct Parameter_<T *>
 {
     typedef T * Type;
 };
 
+template <typename T>
+struct Parameter_<T const *>
+{
+    typedef T const * Type;
+};
+
 template <typename T, size_t I>
 struct Parameter_<T [I]>
 {
     typedef T * Type;
 };
 
-/**
-.Internal._toParameter:
-..cat:Functions
-..summary:Transforms pointers to parameter types.
-..signature:_toParameter<T>(pointer)
-..param.pointer:A pointer.
-..param.T:A Type.
-...text:$object$ is transformed into the parameter type of $T$ that is given by @Internal.Parameter_@.
-...note:This type must be explicitely specified.
-..returns:To $TParameter$ transformed $object$.
-..see:Internal.Parameter_
-*/
+template <typename T, size_t I>
+struct Parameter_<T const [I]>
+{
+    typedef T const * Type;
+};
 
 // TODO(holtgrew): Really required?
 
@@ -446,56 +367,6 @@ SEQAN_HOST_DEVICE inline _toParameter(T const & _object)
 
 //____________________________________________________________________________
 
-/**
-.Internal.ConstParameter_:
-..cat:Metafunctions
-..summary:Type for constant function parameters and return values.
-..signature:ConstParameter_<T>::Type
-..param.T:A type.
-..returns.param.Type:The const parameter type for arguments of type $T$.
-...text:If $T$ is a pointer or array type, then $Parameter_<T>::Type$ is a pointer to a const array, 
-otherwise $Parameter_<T>::Type$ is $T const &$.
-..see:Internal.Parameter_
-*/
-
-// TODO(holtgrew): Really required?
-
-template <typename T>
-struct ConstParameter_
-{
-    typedef T const & Type;
-};
-
-template <typename T>
-struct ConstParameter_<T const>:
-    public ConstParameter_<T> {};
-
-template <typename T>
-struct ConstParameter_<T *>
-{
-    typedef T const * Type;
-};
-
-template <typename T>
-struct ConstParameter_<T const *>
-{
-    typedef T const * Type;
-};
-
-template <typename T, size_t I>
-struct ConstParameter_<T [I]>
-{
-    typedef T const * Type;
-};
-
-template <typename T, size_t I>
-struct ConstParameter_<T const [I]>
-{
-    typedef T const * Type;
-};
-
-//____________________________________________________________________________
-
 /*!
  * @mfn Member
  * @headerfile <seqan/basic.h>
@@ -506,14 +377,12 @@ struct ConstParameter_<T const [I]>
  * @tparam TSpec A tag to identify the object's member.
  * @return Type The resulting object's member type.
  *
- * @section Remarks
- *
- * This metafunction is used to control the type of a member of a given object. It works analogously to @link Index#Fibre @endlink.
+ * This metafunction is used to control the type of a member of a given object. It works analogously to @link Fibre @endlink.
  * For instance, it is used to change the relationship between two objects from aggregation to composition and vice versa.
  *
- * @see Index#Fibre
+ * @see Fibre
  */
- 
+
 template <typename TObject, typename TSpec>
 struct Member;
 
@@ -523,19 +392,6 @@ struct Member<TObject const, TSpec> :
 
 //____________________________________________________________________________
 
-/**
-.Internal.Pointer_:
-..cat:Metafunctions
-..summary:The associated pointer type.
-..signature:Pointer_<T>::Type
-..param.T:A type.
-..returns.param.Type:A pointer type for $T$.
-...text:if $T$ is already a pointer type, then $Pointer_<T>::Type$ is $T$,
-otherwise $Pointer_<T>::Type$ is $T *$.
-..see:Internal.Parameter_
-..see:Internal._toParameter
-*/
-
 // TODO(holtgrew): Really required?
 
 template <typename T>
@@ -574,17 +430,6 @@ struct NonConstPointer_<T * const>
     typedef T * Type;
 };
 
-/**
-.Internal._toPointer:
-..cat:Functions
-..summary:Transforms types into pointers.
-..signature:_toPointer(object)
-..param.object:An object.
-..returns:$object$, transformed to a pointer. 
-...text:The type of the returned pointer is given by @Internal.Pointer_@.
-..see:Internal.Pointer_
-*/
-
 // TODO(holtgrew): Really required?
 
 template <typename T>
@@ -611,25 +456,32 @@ SEQAN_CHECKPOINT
 }
 
 // --------------------------------------------------------------------------
-// Function _dereference()
+// Function _referenceCast()
 // --------------------------------------------------------------------------
 
 // explicitly give desired dereferenced type as first argument,
 // e.g. _dereference<int>(int*) or _dereference<Segment<..> &>(Segment<..> &)
 template <typename T>
 inline T
-_dereference(typename RemoveReference<T>::Type & ptr)
+_referenceCast(typename RemoveReference<T>::Type & ptr)
 {
     return ptr;
 }
 
 template <typename T>
-inline T
-_dereference(typename RemoveReference<T>::Type * ptr)
+inline SEQAN_FUNC_DISABLE_IF(IsSameType<T, typename RemoveReference<T>::Type>, T)
+_referenceCast(typename RemoveReference<T>::Type * ptr)
 {
     return *ptr;
 }
 
+template <typename T>
+inline SEQAN_FUNC_DISABLE_IF(IsSameType<T, typename RemovePointer<T>::Type>, T)
+_referenceCast(typename RemovePointer<T>::Type & ptr)
+{
+    return &ptr;
+}
+
 
 //____________________________________________________________________________
 
@@ -640,21 +492,10 @@ _dereference(typename RemoveReference<T>::Type * ptr)
  * @signature LENGTH<T>::VALUE;
  *
  * @tparam T The type to query for its length.
- * 
+ *
  * @return VALUE The length of <tt>T</tt>.
  */
 
-/**
-.Metafunction.LENGTH:
-..cat:Basic
-..summary:Number of elements in a fixed-size container.
-..signature:LENGTH<T>::VALUE
-..param.T:Type for which the number of elements is determined.
-..returns.param.VALUE:Number of elements.
-..remarks.text:The default return value is 1 for dynamic-size containers.
-..include:seqan/basic.h
-*/
-
 // SEQREV: elements-are-containers should probably not have a default implementation
 // TODO(holtgrew): Rather switch to static const unsigned VALUE = ?
 
@@ -673,26 +514,13 @@ struct LENGTH<T const>:
 /*!
  * @mfn WEIGHT
  * @brief Number of relevant positions in a shape.
- * 
+ *
  * @signature WEIGHT<T>::VALUE;
  *
  * @tparam T     The Shape type to query.
  * @return VALUE The number of relevant positions in a shape.
  */
 
-/**
-.Metafunction.WEIGHT:
-..cat:Index
-..summary:Number of relevant positions in a shape.
-..signature:WEIGHT<T>::Type
-..param.T:Shape type for which the number of relevant positions is determined.
-...type:Class.Shape
-..returns.param.VALUE:Number of relevant positions.
-..remarks.text:The default return value is the result of the @Metafunction.LENGTH@ function.
-For gapped shapes this is the number of '1's.
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Should probably go to wherever shapes are defined.
 
 template <typename T>
diff --git a/seqan/basic/basic_view.h b/seqan/basic/basic_view.h
new file mode 100644
index 0000000..debdcfc
--- /dev/null
+++ b/seqan/basic/basic_view.h
@@ -0,0 +1,190 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_BASIC_VIEW_H
+#define SEQAN_BASIC_VIEW_H
+
+namespace seqan {
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction View
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn View
+ * @headerfile <seqan/basic.h>
+ * @brief Converts a given type into its view type.
+ *
+ * @signature View<TObject>::Type;
+ *
+ * @tparam TObject The type to be converted into a view type.
+ * @return Type The resulting view type.
+ *
+ * This metafunction is used to convert device containers into views of device containers.
+ * Subsequently, the view of a device container can be safely passed to and used in device space.
+ * On the host, a view of a @link String @endlink is equivalent to an @link SegmentableConcept#Infix @endlink of the complete string.
+ * @link RemoveView @endlink is the inverse of this metafunction.
+ *
+ * @see RemoveView
+ * @see Device
+ * @see SegmentableConcept#Infix
+ */
+
+template <typename TObject>
+struct View
+{
+    typedef TObject Type;
+};
+
+template <typename TObject>
+struct View<TObject const>
+{
+    typedef typename View<TObject>::Type const  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RemoveView
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn RemoveView
+ * @headerfile <seqan/basic.h>
+ * @brief Converts a given view type into its original type.
+ *
+ * @signature RemoveView<TObject>::Type;
+ *
+ * @tparam TObject The view type to be converted into its original type.
+ * @return Type The resulting original type.
+ *
+ * @link View @endlink is the inverse of this metafunction.
+ *
+ * @see View
+ */
+
+template <typename TObject>
+struct RemoveView
+{
+    typedef TObject Type;
+};
+
+template <typename TObject>
+struct RemoveView<TObject const>
+{
+    typedef typename RemoveView<TObject>::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn IsView
+ * @headerfile <seqan/basic.h>
+ * @brief Tests if a given type is a view type.
+ *
+ * @signature IsView<TObject>::Type;
+ *
+ * @tparam TObject The type to be tested for being a view type.
+ * @return Type @link LogicalValuesTags#True @endlink or @link LogicalValuesTags#False @endlink.
+ *
+ * @see View
+ * @see RemoveView
+ */
+
+template <typename TObject>
+struct IsView : public False {};
+
+template <typename TObject>
+struct IsView<TObject const> : public IsView<TObject> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction IfView
+// ----------------------------------------------------------------------------
+
+template <typename TObject, typename T1, typename T2>
+struct IfView
+{
+    typedef typename If<IsView<TObject>, T1, T2>::Type  Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function view()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn TView view
+ * @headerfile <seqan/basic.h>
+ * @brief Returns the view of a given object.
+ *
+ * @signature TView view(object);
+ *
+ * @param[in] object A generic object.
+ * @return TView The @link View @endlink type of the given object.
+ *
+ * @see View
+ * @see IsView
+ */
+
+template <typename TObject>
+inline typename View<TObject>::Type
+view(TObject & object)
+{
+    return typename View<TObject>::Type(object);
+}
+
+template <typename TObject>
+inline typename View<TObject const>::Type
+view(TObject const & object)
+{
+    return typename View<TObject const>::Type(object);
+}
+
+template <typename TObject>
+inline typename View<TObject>::Type
+view(TObject * object)
+{
+    return typename View<TObject>::Type(value(object));
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_BASIC_VIEW_H
diff --git a/seqan/basic/boost_preprocessor_subset.h b/seqan/basic/boost_preprocessor_subset.h
index bef6d2b..7e0df98 100644
--- a/seqan/basic/boost_preprocessor_subset.h
+++ b/seqan/basic/boost_preprocessor_subset.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,8 +39,8 @@
 // probably a bad idea to repeat this.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_
 
 // --------------------------------------------------------------------------
 // ==> boost/preprocessor/tuple/rem.hpp <==
@@ -5112,7 +5112,7 @@
 //  Copyright (c) 2001-2003 John Maddock
 //  Copyright (c) 2001 Darin Adler
 //  Copyright (c) 2001 Peter Dimov
-//  Copyright (c) 2002 Bill Kempf 
+//  Copyright (c) 2002 Bill Kempf
 //  Copyright (c) 2002 Jens Maurer
 //  Copyright (c) 2002-2003 David Abrahams
 //  Copyright (c) 2003 Gennaro Prota
@@ -5135,4 +5135,4 @@
 #define SEQAN_DO_JOIN2( X, Y ) X##Y
 
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_
diff --git a/seqan/basic/builtin_functions.h b/seqan/basic/builtin_functions.h
index 55f849f..e3652d3 100644
--- a/seqan/basic/builtin_functions.h
+++ b/seqan/basic/builtin_functions.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                            builtin_functions.h
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // are overridden for some classes.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_
 
 namespace seqan {
 
@@ -58,212 +58,6 @@ namespace seqan {
 // Functions
 // ============================================================================
 
-/**
-.Function.operator=
-..cat:C++ built-in
-..summary:C++ built-in Assignment operator.
-
-.Function.operator+
-..cat:C++ built-in
-..summary:C++ built-in addition operator.
-
-.Function.operator+ (unary)
-..cat:C++ built-in
-..summary:C++ built-in unary plus (integer promotion) operator.
-
-.Function.operator-
-..cat:C++ built-in
-..summary:C++ built-in subtraction operator.
-
-.Function.operator- (unary)
-..cat:C++ built-in
-..summary:C++ built-in unary minus (additive inverse) operator.
-
-.Function.operator*
-..cat:C++ built-in
-..summary:C++ built-in multiplication operator.
-
-.Function.operator/
-..cat:C++ built-in
-..summary:C++ built-in division operator.
-
-.Function.operator%
-..cat:C++ built-in
-..summary:C++ built-in modulo operator.
-
-.Function.operator++ (prefix)
-..cat:C++ built-in
-..summary:C++ built-in prefix increment operator.
-
-.Function.operator++ (suffix)
-..cat:C++ built-in
-..summary:C++ built-in suffix increment operator.
-
-.Function.operator-- (prefix)
-..cat:C++ built-in
-..summary:C++ built-in prefix decrement operator.
-
-.Function.operator-- (suffix)
-..cat:C++ built-in
-..summary:C++ built-in suffix decrement operator.
-
-.Function.operator==
-..cat:C++ built-in
-..summary:C++ built-in equal comparison operator.
-
-.Function.operator!=
-..cat:C++ built-in
-..summary:C++ built-in inequal comparison operator.
-
-.Function.operator>
-..cat:C++ built-in
-..summary:C++ built-in greater-than comparison operator.
-
-.Function.operator<
-..cat:C++ built-in
-..summary:C++ built-in less-than comparison operator.
-
-.Function.operator>=
-..cat:C++ built-in
-..summary:C++ built-in greather-than-or-equal comparison operator.
-
-.Function.operator<=
-..cat:C++ built-in
-..summary:C++ built-in less-than-or-equal comparison operator.
-
-.Function.operator!
-..cat:C++ built-in
-..summary:C++ built-in logical negation operator.
-
-.Function.operator&&
-..cat:C++ built-in
-..summary:C++ built-in logical AND operator.
-
-.DISABLED.Function.operator\pipe\pipe|operator||
-..cat:C++ built-in
-..summary:C++ built-in logical OR operator.
-
-.Function.operator~
-..cat:C++ built-in
-..summary:C++ built-in bitwise NOT operator.
-
-.Function.operator&
-..cat:C++ built-in
-..summary:C++ built-in bitwise AND operator.
-
-.DISABLED.Function.operator\pipe|operator\pipe
-..cat:C++ built-in
-..summary:C++ built-in bitwise OR operator.
-
-.Function.operator^
-..cat:C++ built-in
-..summary:C++ built-in bitwise XOR operator.
-
-.Function.operator<<
-..cat:C++ built-in
-..summary:C++ built-in bitwise left shift operator.
-
-.Function.operator<< (Stream)
-..cat:C++ built-in
-..summary:C++ built-in bitwise put-to/stream insertion operator.
-
-.Function.operator>>
-..cat:C++ built-in
-..summary:C++ built-in bitwise right shift operator.
-
-.Function.operator>> (Stream)
-..cat:C++ built-in
-..summary:C++ built-in bitwise get-from/stream extraction operator.
-
-.Function.operator+=
-..cat:C++ built-in
-..summary:C++ built-in addition assignment operator.
-
-.Function.operator-=
-..cat:C++ built-in
-..summary:C++ built-in subtraction assignment operator.
-
-.Function.operator*=
-..cat:C++ built-in
-..summary:C++ built-in multiplication assignment operator.
-
-.Function.operator/=
-..cat:C++ built-in
-..summary:C++ built-in division assignment operator.
-
-.Function.operator%=
-..cat:C++ built-in
-..summary:C++ built-in modulo assignment operator.
-
-.Function.operator&=
-..cat:C++ built-in
-..summary:C++ built-in bitwise AND assignment operator.
-
-.DISABLED.Function.operator\pipe=|operator|=
-..cat:C++ built-in
-..summary:C++ built-in bitwise OR assignment operator.
-
-.Function.operator^=
-..cat:C++ built-in
-..summary:C++ built-in bitwise XOR assignment operator.
-
-.Function.operator<<=
-..cat:C++ built-in
-..summary:C++ built-in bitwise left shift assignment operator.
-
-.Function.operator>>=
-..cat:C++ built-in
-..summary:C++ built-in bitwise right shift assignment operator.
-
-.Function.operator[]
-..cat:C++ built-in
-..summary:C++ built-in array subscript operator.
-
-.Function.operator* (indirection)
-..cat:C++ built-in
-..summary:C++ built-in indirection/object-pointed-to-by operator.
-
-.Function.operator& (reference)
-..cat:C++ built-in
-..summary:C++ built-in reference/address-of operator.
-
-.Function.operator->
-..cat:C++ built-in
-..summary:C++ built-in structure dereference operator.
-
-.Function.operator->*
-..cat:C++ built-in
-..summary:C++ built-in member-pointed-to-by-b-of-object-pointed-to-by-a operator.
-
-.Function.operator()
-..cat:C++ built-in
-..summary:C++ built-in function call operator.
-
-.Function.operator,
-..cat:C++ built-in
-..summary:C++ built-in comma operator.
-
-.Function.cast operator
-..cat:C++ built-in
-..summary:C++ built-in cast operator.
-
-.Function.operator new
-..cat:C++ built-in
-..summary:C++ built-in allocation operator.
-
-.Function.operator new[]
-..cat:C++ built-in
-..summary:C++ built-in array allocation operator operator.
-
-.Function.operator delete
-..cat:C++ built-in
-..summary:C++ built-in deallocation operator.
-
-.Function.operator delete[]
-..cat:C++ built-in
-..summary:C++ built-in array deallocation operator.
- */
-
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_
diff --git a/seqan/basic/concept_checking.h b/seqan/basic/concept_checking.h
index 52c4c55..d7512fa 100644
--- a/seqan/basic/concept_checking.h
+++ b/seqan/basic/concept_checking.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,6 +29,7 @@
 // DAMAGE.
 //
 // ==========================================================================
+// Author: David Weese <davod.weese@fu-berlin.de>
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 // A minimal subset of the Boost Concept Checking Library.  A lot of the code
@@ -40,8 +41,8 @@
 
 // SEQAN_NO_GENERATED_FORWARDS
 
-#ifndef CORE_INCLUDE_SEQAN_BASIC_CONCEPT_CHECKING_H_
-#define CORE_INCLUDE_SEQAN_BASIC_CONCEPT_CHECKING_H_
+#ifndef INCLUDE_SEQAN_BASIC_CONCEPT_CHECKING_H_
+#define INCLUDE_SEQAN_BASIC_CONCEPT_CHECKING_H_
 
 namespace seqan {
 
@@ -50,8 +51,8 @@ namespace seqan {
 // ---------------------------------------------------------------------------
 
 //  (C) Copyright John Maddock 2000.
-//  Use, modification and distribution are subject to the 
-//  Boost Software License, Version 1.0. (See accompanying file 
+//  Use, modification and distribution are subject to the
+//  Boost Software License, Version 1.0. (See accompanying file
 //  LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
 
 //  See http://www.boost.org/libs/static_assert for documentation.
@@ -72,15 +73,6 @@ namespace seqan {
 #  define SEQAN_STATIC_ASSERT_BOOL_CAST(x) (bool)(x)
 //#endif
 
-//
-// If the compiler warns about unused typedefs then enable this:
-//
-#if defined(__GNUC__) && ((__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)))
-#  define SEQAN_STATIC_ASSERT_UNUSED_ATTRIBUTE __attribute__((unused))
-#else
-#  define SEQAN_STATIC_ASSERT_UNUSED_ATTRIBUTE
-#endif
-
 #ifdef SEQAN_CXX11_STANDARD
 #  define SEQAN_STATIC_ASSERT( B ) static_assert(B, #B)
 #else
@@ -133,7 +125,7 @@ template<int x> struct static_assert_test{};
          SEQAN_JOIN(seqan_static_assert_typedef_, __COUNTER__)
 /*
 #elif defined(SEQAN_INTEL_CXX_VERSION) || defined(SEQAN_SA_GCC_WORKAROUND)
-// agurt 15/sep/02: a special care is needed to force Intel C++ issue an error 
+// agurt 15/sep/02: a special care is needed to force Intel C++ issue an error
 // instead of warning in case of failure
 # define SEQAN_STATIC_ASSERT( B ) \
     typedef char SEQAN_JOIN(seqan_static_assert_typedef_, __LINE__) \
@@ -159,7 +151,7 @@ template<int x> struct static_assert_test{};
 #define SEQAN_STATIC_ASSERT( B ) \
    typedef static_assert_test<\
       sizeof(STATIC_ASSERTION_FAILURE< SEQAN_STATIC_ASSERT_BOOL_CAST( B ) >)>\
-         SEQAN_JOIN(seqan_static_assert_typedef_, __LINE__) SEQAN_STATIC_ASSERT_UNUSED_ATTRIBUTE
+         SEQAN_JOIN(seqan_static_assert_typedef_, __LINE__) SEQAN_UNUSED
 #endif
 /*
 #else
@@ -185,7 +177,7 @@ struct unaryfunptr_arg_type;
 template <class Arg>
 struct unaryfunptr_arg_type<void(*)(Arg)>
 {
-    typedef Arg type; 
+    typedef Arg type;
 };
 
 template <>
@@ -212,7 +204,8 @@ template <class ModelFn> struct concept_check_;
 template <class Model>
 void concept_check_failed()
 {
-    ((Model*)0)->~Model();
+    Model *p = static_cast<Model*>(NULL);
+    p->~Model();
 }
 
 template <class Model>
@@ -228,9 +221,9 @@ struct concept_check_<void(*)(Model)>
 {};
 
 #  define SEQAN_CONCEPT_ASSERT_FN( ModelFnPtr )             \
-    typedef ::seqan::detail::instantiate<          \
-    &::seqan::requirement_<ModelFnPtr>::failed>    \
-      SEQAN_PP_CAT(seqan_concept_check,__LINE__) SEQAN_STATIC_ASSERT_UNUSED_ATTRIBUTE
+    typedef seqan::detail::instantiate<          \
+    &seqan::requirement_<ModelFnPtr>::failed>    \
+      SEQAN_PP_CAT(seqan_concept_check,__LINE__) SEQAN_UNUSED
 
 // ---------------------------------------------------------------------------
 // ==> boost/concept/assert.hpp <==
@@ -241,30 +234,41 @@ struct concept_check_<void(*)(Model)>
 // http://www.boost.org/LICENSE_1_0.txt).
 
 /*!
- * @macro SEQAN_CONCEPT_ASSERT
+ * @defgroup ConceptChecking Concept Checking
+ * @brief Macros for the concept checking system in SeqAn.
+ *
+ * SeqAn's concept checking system is copied from Boost.  The license for the library is as follows:
+ *
+ * @code{.cpp}
+ * // Copyright David Abrahams 2006. Distributed under the Boost Software
+ * // License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at
+ * // http://www.boost.org/LICENSE_1_0.txt).
+ * @endcode
+ */
+
+/*!
+ * @macro ConceptChecking#SEQAN_CONCEPT_ASSERT
  * @brief Perform a concept check.
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature SEQAN_CONCEPT_ASSERT((concept))
- * 
+ *
  * @param concept Concept specialized with a the type that should be checked.
- * 
- * @section Remarks
- * 
+ *
  * This macro is a compile-time assertion and requires the concept specialized
  * with the tested types to compile. The check neither consumes memory nor
  * running time. The macro can be used at the beginning of a function or within
  * a struct/class definition. The checked concepts should be as restrictive and
  * generic as possible to on the one hand cover all used functionality and on
  * the other hand not limit the applicability of a function/class.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * typedef typename Value<TContainer>::Type                TValue;
  * typedef typename Position<TContainer>::Type             TPosition;
  * typedef typename Difference<TContainer>::Type           TDifference;
- *  
+ *
  * SEQAN_CONCEPT_ASSERT((AlphabetConcept<TValue>));
  * SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<TDifference>));
  * SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept<TSize>));
@@ -272,28 +276,6 @@ struct concept_check_<void(*)(Model)>
  * @see Is
  */
 
-/**
-.Macro.SEQAN_CONCEPT_ASSERT
-..cat:Concepts
-..summary:Perform a concept check.
-..signature:SEQAN_CONCEPT_ASSERT((concept))
-..param.concept:Concept specialized with a the type that should be checked.
-..remarks:This macro is a compile-time assertion and requires the concept specialized with the tested types to compile.
-The check neither consumes memory nor running time.
-The macro can be used at the beginning of a function or within a struct/class definition.
-The checked concepts should be as restrictive and generic as possible to on the one hand 
-cover all used functionality and on the other hand not limit the applicability of a function/class.
-..example.code:
-typedef typename Value<TContainer>::Type                TValue;
-typedef typename Position<TContainer>::Type             TPosition;
-typedef typename Difference<TContainer>::Type           TDifference;
-
-SEQAN_CONCEPT_ASSERT((AlphabetConcept<TValue>));
-SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<TDifference>));
-SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept<TSize>));
-..include:seqan/basic.h
- */
-
 // Usage, in class or function context:
 //     SEQAN_CONCEPT_ASSERT((UnaryFunctionConcept<F,bool,int>));
 # define SEQAN_CONCEPT_ASSERT(ModelInParens) \
@@ -304,30 +286,34 @@ SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept<TSize>));
 template <class Model>
 struct usage_requirements
 {
-    ~usage_requirements() { ((Model*)0)->~Model(); }
+    ~usage_requirements()
+    {
+        Model *p = static_cast<Model*>(NULL);
+        p->~Model();
+    }
 };
 
 /*!
- * @macro SEQAN_CONCEPT_USAGE
+ * @macro ConceptChecking#SEQAN_CONCEPT_USAGE
  * @headerfile <seqan/basic.h>
  * @brief Defines valid expressions.
  *
  * @signature SEQAN_CONCEPT_USAGE(name)
  *
- * @param[in] name Identifier of the concept defined with @link SEQAN_CONCEPT @endlink or @link SEQAN_CONCEPT_REFINE
- *                 @endlink.
+ * @param[in] name Identifier of the concept defined with @link ConceptChecking#SEQAN_CONCEPT @endlink or
+ *                 @link ConceptChecking#SEQAN_CONCEPT_REFINE @endlink.
  *
  * This macro should be used to introduce a block (enclosed with curly braces) of valid expressions within a newly
  * defined concept.  Valid expressions should test for available functions, operators and the correctness of return
- * types.  Use helper functions, e.g. @link ignoreUnusedVariableWarning @endlink, @link requireBooleanExpr @endlink and
- * @link sameType @endlink.
+ * types.  Use helper functions, e.g. @link ignoreUnusedVariableWarning @endlink,
+ * @link ConceptChecking#requireBooleanExpr @endlink and @link ConceptChecking#sameType @endlink.
  *
  * @section Examples
  *
  * @code{.cpp}
  * SEQAN_CONCEPT(EqualityComparable,(T))
  * {
- *     SEQAN_CONCEPT_USAGE(EqualityComparable) 
+ *     SEQAN_CONCEPT_USAGE(EqualityComparable)
  *     {
  *         requireBooleanExpr(a == b);
  *         requireBooleanExpr(a != b);
@@ -337,37 +323,11 @@ struct usage_requirements
  * };
  * @endcode
  *
- * @see requireBooleanExpr
- * @see SEQAN_CONCEPT
- * @see SEQAN_CONCEPT_REFINE
+ * @see ConceptChecking#requireBooleanExpr
+ * @see ConceptChecking#SEQAN_CONCEPT
+ * @see ConceptChecking#SEQAN_CONCEPT_REFINE
  */
 
-/**
-.Macro.SEQAN_CONCEPT_USAGE
-..cat:Concepts
-..summary:Define valid expressions.
-..signature:SEQAN_CONCEPT_USAGE(name)
-..param.name:Identifier of the concept defined with @Macro.SEQAN_CONCEPT@ or @Macro.SEQAN_CONCEPT_REFINE@.
-..remarks:This macro should be used to introduce a block (enclosed with curly braces) of valid expressions within
-a newly defined concept.
-Valid expressions should test for available functions, operators and the correctness of return types.
-Use helper functions, e.g. @Function.ignoreUnusedVariableWarning@, @Function.requireBooleanExpr@ and @Function.sameType@.
-..example.code:
-SEQAN_CONCEPT(EqualityComparable,(T))
-{
-    SEQAN_CONCEPT_USAGE(EqualityComparable) 
-    {
-        requireBooleanExpr(a == b);
-        requireBooleanExpr(a != b);
-    }
-private:
-    T a, b;
-};
-..see:Function.requireBooleanExpr
-..see:Macro.SEQAN_CONCEPT
-..see:Macro.SEQAN_CONCEPT_REFINE
-..include:seqan/basic.h
- */
 #define SEQAN_CONCEPT_USAGE(model)                                      \
     SEQAN_CONCEPT_ASSERT((seqan::usage_requirements<model>));           \
     ~model()
@@ -386,7 +346,7 @@ namespace detail {
 
   template <class Model, void (Model::*)()>
   struct wrap_constraints {};
-    
+
   template <class Model>
   inline yes has_constraints_(Model*, wrap_constraints<Model,&Model::constraints>* = 0);
   inline no has_constraints_(...);
@@ -420,7 +380,11 @@ namespace detail
 template <class Model>
 struct requirement
 {
-    static void failed() { ((Model*)0)->~Model(); }
+    static void failed()
+    {
+        Model *p = static_cast<Model*>(NULL);
+        p->~Model();
+    }
 };
 
 struct failed {};
@@ -428,15 +392,23 @@ struct failed {};
 template <class Model>
 struct requirement<failed ************ Model::************>
 {
-    static void failed() { ((Model*)0)->~Model(); }
+    static void failed()
+    {
+        Model *p = static_cast<Model*>(NULL);
+        p->~Model();
+    }
 };
 
 template <class Model>
 struct constraint
 {
-    static void failed() { ((Model*)0)->constraints(); }
+    static void failed()
+    {
+        Model *p = static_cast<Model*>(NULL);
+        p->constraints();
+    }
 };
-  
+
 template <class Model>
 struct requirement_<void(*)(Model)>
         : IfC<not_satisfied<Model>::Type::VALUE, /* should be called "has_constraints", see above */
@@ -446,9 +418,9 @@ struct requirement_<void(*)(Model)>
 {};
 
 #  define SEQAN_CONCEPT_ASSERT_FN( ModelFnPtr )             \
-    typedef ::seqan::detail::instantiate<          \
-    &::seqan::requirement_<ModelFnPtr>::failed>    \
-      SEQAN_PP_CAT(seqan_concept_check,__LINE__) SEQAN_STATIC_ASSERT_UNUSED_ATTRIBUTE
+    typedef seqan::detail::instantiate<          \
+    &seqan::requirement_<ModelFnPtr>::failed>    \
+      SEQAN_PP_CAT(seqan_concept_check,__LINE__) SEQAN_UNUSED
 
 // ---------------------------------------------------------------------------
 // ==> boost/concept_check/detail/requires.hpp <==
@@ -480,7 +452,7 @@ template <int check, class Result>
 struct Requires_ : unaryfunptr_arg_type<Result>
 {};
 
-#  define SEQAN_CONCEPT_REQUIRES_(r,data,t) + (::seqan::_requires_<void(*)t>::value)
+#  define SEQAN_CONCEPT_REQUIRES_(r,data,t) + (seqan::_requires_<void(*)t>::value)
 
 #if defined(NDEBUG)
 
@@ -490,7 +462,7 @@ struct Requires_ : unaryfunptr_arg_type<Result>
 #else  // #if defined(NDEBUG)
 
 # define SEQAN_CONCEPT_REQUIRES(models, result)                                        \
-    typename ::seqan::Requires_<                                                       \
+    typename seqan::Requires_<                                                       \
       (0 SEQAN_PP_SEQ_FOR_EACH(SEQAN_CONCEPT_REQUIRES_, ~, models)),                   \
       void(*)result                                                                 \
     >::type
@@ -519,7 +491,7 @@ inline void functionRequires(Model* = 0)
 
 /*!
  * @fn ignoreUnusedVariableWarning
- * @headefile <seqan/basic.h>
+ * @headerfile <seqan/basic.h>
  * @brief Removes unused variable warning.
  *
  * @signature void ignoreUnusedVariableWarning(x);
@@ -530,17 +502,6 @@ inline void functionRequires(Model* = 0)
  * operators.  Use this functions to remove a compile warning that otherwise would be raised in this case.
  */
 
-/**
-.Function.ignoreUnusedVariableWarning
-..summary:Removes unused variable warning.
-..cat:Concepts
-..signature:ignoreUnusedVariableWarning(x)
-..param.x: Variable that causes the unused variable warning.
-..remarks:It sometimes is necessary to define variables which are not further used, e.g. to check available assignment operators.
-Use this functions to remove a compile warning that otherwise would be raised in this case.
-..see:Macro.SEQAN_CONCEPT_USAGE
-..include:seqan/basic.h
- */
 template <class T> SEQAN_HOST_DEVICE inline void ignoreUnusedVariableWarning(T const&) {}
 
 // ---------------------------------------------------------------------------
@@ -554,12 +515,12 @@ template <class T> SEQAN_HOST_DEVICE inline void ignoreUnusedVariableWarning(T c
 // SEQAN_CONCEPT_REFINE added by David Weese
 
 /*!
- * @macro SEQAN_CONCEPT
+ * @macro ConceptChecking#SEQAN_CONCEPT
  * @brief Defines a new concept.
- * @headerfile seqan/basic.h
- * 
+ * @headerfile <seqan/basic.h>
+ *
  * @signature SEQAN_CONCEPT(name, params)
- * 
+ *
  * @param params Template paramter list in parantheses, e.g. (T) or (T1)(T2).
  *               Typically, template parameters are models, i.e. one or multiple
  *               classes that should be checked for fulfilling a concept.This is
@@ -567,19 +528,17 @@ template <class T> SEQAN_HOST_DEVICE inline void ignoreUnusedVariableWarning(T c
  *               href="http://www.boost.org/doc/libs/1_47_0/libs/preprocessor/doc/index.html">more</a>.
  * @param name Concept identifier. Non-trivial concepts should have an
  *             identifier with a Concept-suffix.
- * 
- * @section Remarks
- * 
+ *
  * A concept is implemented as a template struct with name <tt>name</tt> and
  * arguments <tt>params</tt>. The concept checking should be part of the struct
- * definition. Associated types should be checked via @link SEQAN_CONCEPT_ASSERT
- * @endlink and valid expressions in a function @link SEQAN_CONCEPT_USAGE
+ * definition. Associated types should be checked via @link ConceptChecking#SEQAN_CONCEPT_ASSERT
+ * @endlink and valid expressions in a function @link ConceptChecking#SEQAN_CONCEPT_USAGE
  * @endlink, see below. Variables used in valid expressions should be (private)
  * struct members instead of local variables in member functions (read <a
  * href="http://www.boost.org/doc/libs/1_47_0/libs/concept_check/creating_concepts.htm">more</a>.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_CONCEPT(Assignable,(T))
  * {
@@ -598,7 +557,7 @@ template <class T> SEQAN_HOST_DEVICE inline void ignoreUnusedVariableWarning(T c
  *     T a;
  *     T b;
  * };
- *  
+ *
  * SEQAN_CONCEPT(EqualityComparable,(T))
  * {
  *     SEQAN_CONCEPT_USAGE(EqualityComparable)
@@ -611,52 +570,7 @@ template <class T> SEQAN_HOST_DEVICE inline void ignoreUnusedVariableWarning(T c
  * };
  * @endcode
  *
- * @see SEQAN_CONCEPT_USAGE
- */
-
-/**
-.Macro.SEQAN_CONCEPT
-..cat:Concepts
-..summary:Defines a new concept.
-..signature:SEQAN_CONCEPT(name, params)
-..param.name:Concept identifier. Non-trivial concepts should have an identifier with a "Concept"-suffix.
-..param.params:Template paramter list in parantheses, e.g. (T) or (T1)(T2).
-Typically, template parameters are models, i.e. one or multiple classes that should be checked for fulfilling a concept.
-...remarks:This is a sequence of the Boost Preprocessor Library, read @http://www.boost.org/doc/libs/1_47_0/libs/preprocessor/doc/index.html|more@.
-..remarks:A concept is implemented as a template struct with name $name$ and arguments $params$.
-The concept checking should be part of the struct definition.
-Associated types should be checked via @Macro.SEQAN_CONCEPT_ASSERT@ and valid expressions in a function @Macro.SEQAN_CONCEPT_USAGE@, see below.
-Variables used in valid expressions should be (private) struct members instead of local variables in member functions (read @http://www.boost.org/doc/libs/1_47_0/libs/concept_check/creating_concepts.htm|more@).
-..example.code:
-SEQAN_CONCEPT(Assignable,(T))
-{
-    SEQAN_CONCEPT_USAGE(Assignable) 
-    {
-        a = b;              // require assignment operator
-        constConstraints(b);
-    }
-private:
-    void constConstraints(const T& x) 
-    {
-        a = x;              // const required for argument to assignment
-        ignoreUnusedVariableWarning(x);
-    }
-private:
-    T a;
-    T b;
-};
-
-SEQAN_CONCEPT(EqualityComparable,(T))
-{
-    SEQAN_CONCEPT_USAGE(EqualityComparable) 
-    {
-        requireBooleanExpr(a == b);
-        requireBooleanExpr(a != b);
-    }
-private:
-    T a, b;
-};
-..include:seqan/basic.h
+ * @see ConceptChecking#SEQAN_CONCEPT_USAGE
  */
 
 # define SEQAN_CONCEPT(name, params)                                            \
@@ -664,12 +578,12 @@ SEQAN_CONCEPT(EqualityComparable,(T))
     struct name
 
 /*!
- * @macro SEQAN_CONCEPT_REFINE
+ * @macro ConceptChecking#SEQAN_CONCEPT_REFINE
  * @brief Defines a new concept as a refinement of existing concepts.
- * @headerfile seqan/basic.h
- * 
+ * @headerfile <seqan/basic.h>
+ *
  * @signature SEQAN_CONCEPT_REFINE(name, params, refinedConcepts)
- * 
+ *
  * @param params Template paramter list in parantheses, e.g. (T) or (T1)(T2).
  *               Typically, template parameters are models, i.e. one or multiple
  *               classes that should be checked for fulfilling a concept.This is
@@ -682,57 +596,26 @@ SEQAN_CONCEPT(EqualityComparable,(T))
  *                        into the requirements of the new concept.This is a
  *                        sequence of the Boost Preprocessor Library, read
  *                        <a href="http://boost.org/doc/libs/1_47_0/libs/preprocessor/doc/index.html">more</a>
- * 
- * @section Remarks
- * 
+ *
  * A concept is implemented as a template struct with name <tt>name</tt> and
  * arguments <tt>params</tt>. The struct inherits all refined concept structs.
  * The concept checking should be part of the struct definition. For more
- * information, see @link SEQAN_CONCEPT @endlink.
- * 
+ * information, see @link ConceptChecking#SEQAN_CONCEPT @endlink.
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructible)(CopyConstructible))
  * {
  *     TValue val, val2;
- *  
+ *
  *     SEQAN_CONCEPT_USAGE(AlphabetConcept)
  *     {
  *         assign(val, val2);
  *     }
  * };
  * @endcode
- * @see SEQAN_CONCEPT_USAGE
- */
-
-/**
-.Macro.SEQAN_CONCEPT_REFINE
-..cat:Concepts
-..summary:Defines a new concept as a refinement of existing concepts.
-..signature:SEQAN_CONCEPT_REFINE(name, params, refinedConcepts)
-..param.name:Concept identifier. Non-trivial concepts should have an identifier with a "Concept"-suffix.
-..param.params:Template paramter list in parantheses, e.g. (T) or (T1)(T2).
-Typically, template parameters are models, i.e. one or multiple classes that should be checked for fulfilling a concept.
-...remarks:This is a sequence of the Boost Preprocessor Library, read @http://www.boost.org/doc/libs/1_47_0/libs/preprocessor/doc/index.html|more@.
-..param.refinedConcepts:Identifiers of concepts that are refined by the new concept.
-...remarks:Refined concepts are implicitly integrated into the requirements of the new concept.
-...remarks:This is a sequence of the Boost Preprocessor Library, read @http://www.boost.org/doc/libs/1_47_0/libs/preprocessor/doc/index.html|more@.
-..remarks:A concept is implemented as a template struct with name $name$ and arguments $params$.
-The struct inherits all refined concept structs.
-The concept checking should be part of the struct definition.
-For more information, see @Macro.SEQAN_CONCEPT@.
-..example.code:
-SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructible)(CopyConstructible))
-{
-    TValue val, val2;
-
-    SEQAN_CONCEPT_USAGE(AlphabetConcept)
-    {
-        assign(val, val2); 
-    }
-};
-..include:seqan/basic.h
+ * @see ConceptChecking#SEQAN_CONCEPT_USAGE
  */
 
 # define SEQAN_CONCEPT_REFINE(name, params, refinedConcepts)                                        \
@@ -752,65 +635,59 @@ SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructibl
         SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_REFINE_superclass,params,refinedConcepts)
 
 /*!
- * @macro SEQAN_CONCEPT_IMPL
+ * @macro ConceptChecking#SEQAN_CONCEPT_IMPL
  * @brief Defines which concepts a model fulfills.
- * @headerfile seqan/basic.h
- * 
- * 
- * @signature template<> SEQAN_CONCEPT_IMPL(name, implementedConcepts)
- *            template<typename T, int I> SEQAN_CONCEPT_IMPL(name<T,I>, implementedConcepts)
- * 
+ * @headerfile <seqan/basic.h>
+ *
+ *
+ * @signature template<>    // required, even if name has no template arguments
+ *            SEQAN_CONCEPT_IMPL((name), implementedConcepts)
+ *
+ *            template<typename T, int I>
+ *            SEQAN_CONCEPT_IMPL((name<T,I>), implementedConcepts)
+ *
  * @param implementedConcepts Identifiers of concepts that are fulfilled by the model.  This is a sequence of the
  *                            Boost Preprocessor Library, read <a
  *                            href="http://www.boost.org/doc/libs/1_47_0/libs/preprocessor/doc/index.html">more</a>.
  * @param name Model type, i.e. an identifier or an identifier with template
  *             arguments.
- * 
- * @section Remarks
- * 
+ *
  * The metafunction @link Is @endlink can be used to determine whether a class
  * models (fulfills) a concepts. A model of a concept must pass the concept
- * check via @link SEQAN_CONCEPT_ASSERT @endlink.
- * 
+ * check via @link ConceptChecking#SEQAN_CONCEPT_ASSERT @endlink.
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * template <typename TValue, typename TSpec>
- * SEQAN_CONCEPT_IMPL(String<TValue, TSpec>, (StringConcept));
+ * SEQAN_CONCEPT_IMPL((String<TValue, TSpec>), (StringConcept));
  * @endcode
  */
 
-/**
-.Macro.SEQAN_CONCEPT_IMPL
-..cat:Concepts
-..summary:Defines which concepts a model fulfills.
-..signature:
-template<> 
-SEQAN_CONCEPT_IMPL(name, implementedConcepts)
-
-template<typename T, int I>
-SEQAN_CONCEPT_IMPL(name<T,I>, implementedConcepts)
-..param.name:Model type, i.e. an identifier or an identifier with template arguments.
-..param.implementedConcepts:Identifiers of concepts that are fulfilled by the model.
-...remarks:This is a sequence of the Boost Preprocessor Library, read @http://www.boost.org/doc/libs/1_47_0/libs/preprocessor/doc/index.html|more@.
-..remarks:The metafunction @Metafunction.Is@ can be used to determine whether a class models (fulfills) a concepts.
-A model of a concept must pass the concept check via @Macro.SEQAN_CONCEPT_ASSERT@.
-..example.code:
-template <typename TValue, typename TSpec>
-SEQAN_CONCEPT_IMPL(String<TValue, TSpec>, (StringConcept));
-..include:seqan/basic.h
- */
+
+// STRIP_PARENS macro by Steven Watanabe (http://lists.boost.org/boost-users/2010/08/61429.php)
+#define SEQAN_APPLY(macro, args) SEQAN_APPLY_I(macro, args)
+#define SEQAN_APPLY_I(macro, args) macro args
+#define SEQAN_STRIP_PARENS(x) SEQAN_EVAL((SEQAN_STRIP_PARENS_I x), x)
+#define SEQAN_STRIP_PARENS_I(...) 1,1
+#define SEQAN_EVAL(test, x) SEQAN_EVAL_I(test, x)
+#define SEQAN_EVAL_I(test, x) SEQAN_MAYBE_STRIP_PARENS(SEQAN_TEST_ARITY test, x)
+#define SEQAN_TEST_ARITY(...) SEQAN_APPLY(SEQAN_TEST_ARITY_I, (__VA_ARGS__, 2, 1))
+#define SEQAN_TEST_ARITY_I(a,b,c,...) c
+#define SEQAN_MAYBE_STRIP_PARENS(cond, x) SEQAN_MAYBE_STRIP_PARENS_I(cond, x)
+#define SEQAN_MAYBE_STRIP_PARENS_I(cond, x) SEQAN_PP_CAT(SEQAN_MAYBE_STRIP_PARENS_, cond)(x)
+#define SEQAN_MAYBE_STRIP_PARENS_1(x) x
+#define SEQAN_MAYBE_STRIP_PARENS_2(x) SEQAN_APPLY(SEQAN_MAYBE_STRIP_PARENS_2_I, x)
+#define SEQAN_MAYBE_STRIP_PARENS_2_I(...) __VA_ARGS__
 
 # define SEQAN_CONCEPT_IMPL(model, implementedConcepts)                                                 \
-    template <>                                                                                         \
-    struct Implements<model>                                                                            \
+    struct Implements<SEQAN_STRIP_PARENS(model)>                                                        \
     {                                                                                                   \
         typedef                                                                                         \
-            SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_LIST_prefix,(model),implementedConcepts)              \
+            SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_LIST_prefix,model,implementedConcepts)                \
             SEQAN_PP_REPEAT(SEQAN_PP_SEQ_SIZE(implementedConcepts),SEQAN_CONCEPT_LIST_suffix,~) Type;   \
     }
 
-    
 // helper for the SEQAN_CONCEPT, above.
 # define SEQAN_CONCEPT_typename(r, ignored, index, t) \
     SEQAN_PP_COMMA_IF(index) typename t
@@ -819,15 +696,15 @@ SEQAN_CONCEPT_IMPL(String<TValue, TSpec>, (StringConcept));
 # define SEQAN_CONCEPT_REFINE_superclass(r, params, index, t) \
     SEQAN_PP_COMMA_IF(index) t<SEQAN_PP_SEQ_ENUM(params)>
 # define SEQAN_CONCEPT_LIST_prefix(r, params, index, t) \
-    SEQAN_PP_COMMA_IF(index) TagList<t<SEQAN_PP_SEQ_ENUM(params)>
-# define SEQAN_CONCEPT_LIST_suffix(z, n, text) > 
+    SEQAN_PP_COMMA_IF(index) TagList<t<SEQAN_STRIP_PARENS(params)>
+# define SEQAN_CONCEPT_LIST_suffix(z, n, text) >
 
 // ============================================================================
 // Functions
 // ============================================================================
 
 /*!
- * @fn sameType
+ * @fn ConceptChecking#sameType
  * @brief Tests for equality of types.
  *
  * @signature void sameType(x, y);
@@ -838,19 +715,7 @@ SEQAN_CONCEPT_IMPL(String<TValue, TSpec>, (StringConcept));
  * This function can be used to test for the correctness of function return types or the type of an expression in
  * concept tests.
  *
- * @see SEQAN_CONCEPT_USAGE
- */
-
-/**
-.Function.sameType
-..summary:Tests for equality of types.
-..cat:Concepts
-..signature:sameType(x, y)
-..param.x: Object of a certain type.
-..param.y: Object that must be of the same type.
-..remarks:This function can be used to test for the correctness of function return types or the type of an expression.
-..see:Macro.SEQAN_CONCEPT_USAGE
-..include:seqan/basic.h
+ * @see ConceptChecking#SEQAN_CONCEPT_USAGE
  */
 
 template <typename T>
@@ -864,56 +729,57 @@ void sameType(T, T) { }
 /*!
  * @mfn Is
  * @brief Returns whether a concept is fulfilled.
- * @headerfile seqan/basic.h
- * 
+ * @headerfile <seqan/basic.h>
+ *
  * @signature Is<TConcept>::Type
  * @signature Is<TConcept>::VALUE
- * 
+ *
  * @tparam TConcept A concept that is specialized with type(s) that should be
  *                  tested for fulfilling the concept.
- * 
- * @return Type @link Logical Values.tag.True @endlink/<tt>true</tt> if
+ *
+ * @return Type @link LogicalValuesTags#True @endlink/<tt>true</tt> if
  *              <tt>TConcept</tt> is a fulfilled concept, otherwise @link
- *              Logical Values.tag.False @endlink/<tt>false</tt>.
- * 
- * @section Remarks
- * 
+ *              LogicalValuesTags#False @endlink/<tt>false</tt>.
+ *
  * The @link Is @endlink-metafunction can be used to test types for fulfilling a concept without causing compilation
  * errors.  If <tt>True</tt> or <tt>true</tt> is returned, <tt>TConcept</tt> must pass the concept test via @link
- * SEQAN_CONCEPT_ASSERT @endlink.  It can be used to switch between different implementations depending on the concept
- * of a type, or in combination with @link EnableIfFunctionality#SEQAN_FUNC_ENABLE_IF @endlink to make a function only
- * visible to types of certain concepts.
- * 
+ * ConceptChecking#SEQAN_CONCEPT_ASSERT @endlink.  It can be used to switch between different implementations
+ * depending on the concept of a type, or in combination with @link EnableIfFunctionality#SEQAN_FUNC_ENABLE_IF
+ * @endlink to make a function only visible to types of certain concepts.
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
- * Is<SequenceConcept<TSeq> >::Type
+ * Is<StringConcept<TSeq> >::Type
  * IfC<Is<ContainerConcept<TSeq> >::VALUE, T1, T2>::Type
- *  
+ *
  * std::cout << Is<IntegerConcept<int> >::VALUE << std::endl;     // 1
  * std::cout << Is<IntegerConcept<double> >::VALUE << std::endl;  // 0
  * @endcode
  * Define a hierarchy of concepts and two models <tt>Alice</tt> and <tt>Bob</tt>
  * that implements some of them. @link Is @endlink determines which concepts are
  * explicitly or implicitly fulfilled.
- * 
+ *
  * @code{.cpp}
  * struct Alice {};
  * struct Bob {};
- *  
+ *
  * SEQAN_CONCEPT(ConceptA, (T)) {};
  * SEQAN_CONCEPT(ConceptB, (T)) {};
  * SEQAN_CONCEPT_REFINE(ConceptC, (T), (ConceptA)(ConceptB)) {};
  * SEQAN_CONCEPT_REFINE(ConceptD, (T), (ConceptC)) {};
- *  
+ *
+ * template<>   // Alice has no template arguments
  * SEQAN_CONCEPT_IMPL(Alice, (ConceptA)(ConceptB));
+ *
+ * template<>   // Bob has no template arguments
  * SEQAN_CONCEPT_IMPL(Bob, (ConceptC));
- *  
+ *
  * std::cout << Is< ConceptA<Alice> >::VALUE << std::endl; // 1
  * std::cout << Is< ConceptB<Alice> >::VALUE << std::endl; // 1
  * std::cout << Is< ConceptC<Alice> >::VALUE << std::endl; // 0
  * std::cout << Is< ConceptD<Alice> >::VALUE << std::endl; // 0
- *  
+ *
  * std::cout << Is< ConceptA<Bob> >::VALUE << std::endl;   // 1
  * std::cout << Is< ConceptB<Bob> >::VALUE << std::endl;   // 1
  * std::cout << Is< ConceptC<Bob> >::VALUE << std::endl;   // 1
@@ -921,55 +787,9 @@ void sameType(T, T) { }
  * @endcode
  *
  * @see EnableIfFunctionality#SEQAN_FUNC_ENABLE_IF
- * @see SEQAN_CONCEPT_ASSERT
+ * @see ConceptChecking#SEQAN_CONCEPT_ASSERT
  */
 
-/**
-.Metafunction.Is
-..cat:Concepts
-..summary:Returns whether a concept is fulfilled.
-..signature:Is<TConcept>::Type
-..signature:Is<TConcept>::VALUE
-..param.TConcept:A concept that is specialized with type(s) that should be tested for fulfilling the concept.
-..returns:@Tag.Logical Values.tag.True@/$true$ if $TConcept$ is a fulfilled concept, otherwise @Tag.Logical Values.tag.False@/$false$.
-..remarks:
-...text:The @Metafunction.Is@-metafunction can be used to test types for fulfilling a concept without causing compilation errors.
-If @Tag.Logical Values.tag.True@/$true$ is returned, $TConcept$ must pass the concept test via @Macro.SEQAN_CONCEPT_ASSERT@.
-It can be used to switch between different implementations depending on the concept of a type, or in combination with @Macro.SEQAN_FUNC_ENABLE_IF@ to make a function only visible to types of certain concepts.
-..example.code:
-Is<SequenceConcept<TSeq> >::Type
-IfC<Is<ContainerConcept<TSeq> >::VALUE, T1, T2>::Type
-
-std::cout << Is<IntegerConcept<int> >::VALUE << std::endl;     // 1
-std::cout << Is<IntegerConcept<double> >::VALUE << std::endl;  // 0
-..example.text:Define a hierarchy of concepts and two models $Alice$ and $Bob$ that implements some of them.
-@Metafunction.Is@ determines which concepts are explicitly or implicitly fulfilled.
-..example.code:
-struct Alice {};
-struct Bob {};
-
-SEQAN_CONCEPT(ConceptA, (T)) {};
-SEQAN_CONCEPT(ConceptB, (T)) {};
-SEQAN_CONCEPT_REFINE(ConceptC, (T), (ConceptA)(ConceptB)) {};
-SEQAN_CONCEPT_REFINE(ConceptD, (T), (ConceptC)) {};
-
-SEQAN_CONCEPT_IMPL(Alice, (ConceptA)(ConceptB));
-SEQAN_CONCEPT_IMPL(Bob, (ConceptC));
-
-std::cout << Is< ConceptA<Alice> >::VALUE << std::endl; // 1
-std::cout << Is< ConceptB<Alice> >::VALUE << std::endl; // 1
-std::cout << Is< ConceptC<Alice> >::VALUE << std::endl; // 0
-std::cout << Is< ConceptD<Alice> >::VALUE << std::endl; // 0
-
-std::cout << Is< ConceptA<Bob> >::VALUE << std::endl;   // 1
-std::cout << Is< ConceptB<Bob> >::VALUE << std::endl;   // 1
-std::cout << Is< ConceptC<Bob> >::VALUE << std::endl;   // 1
-std::cout << Is< ConceptD<Bob> >::VALUE << std::endl;   // 0
-..include:seqan/basic.h
-..see:Macro.SEQAN_FUNC_ENABLE_IF
-..see:Macro.SEQAN_CONCEPT_ASSERT
-*/
-
 // test whether a concept is fulfilled (without concept checking)
 template <typename T>
 struct Implements: False {};
@@ -988,8 +808,8 @@ template <typename TConceptWithModel, typename TTail>
 struct IsRecurse_<TConceptWithModel, TagList<TConceptWithModel, TTail> >: True {};
 
 template <typename TConceptModel, typename THead, typename TTail>
-struct IsRecurse_< TConceptModel, TagList<THead, TTail>  >:     
-    Or< 
+struct IsRecurse_< TConceptModel, TagList<THead, TTail>  >:
+    Or<
         IsRecurse_<TConceptModel, typename Refines<THead>::Type >,
         IsRecurse_<TConceptModel, TTail>
     > {};
@@ -998,10 +818,10 @@ template <typename TConceptWithModel>
 struct Is;
 
 template <template <typename> class TConcept, typename TModel>
-struct Is< TConcept<TModel> >: 
+struct Is< TConcept<TModel> >:
     IsRecurse_<TConcept<TModel>, typename Implements<TModel>::Type> {};
 
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BASIC_CONCEPT_CHECKING_H_
+#endif  // #ifndef INCLUDE_SEQAN_BASIC_CONCEPT_CHECKING_H_
diff --git a/seqan/basic/container_concept.h b/seqan/basic/container_concept.h
index cb17577..62b8d8e 100644
--- a/seqan/basic/container_concept.h
+++ b/seqan/basic/container_concept.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 
 // SEQAN_NO_GENERATED_FORWARDS
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_CONTAINER_CONCEPT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_CONTAINER_CONCEPT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_CONTAINER_CONCEPT_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_CONTAINER_CONCEPT_H_
 
 namespace seqan {
 
@@ -212,9 +212,9 @@ template <typename TContainer, typename TSpec> struct Iterator;
  *
  * @signature TIterator begin(c[, tag]);
  *
- * @param c   The container to get the begin iterator for (type <tt>TContainer</tt>).
- * @param tag An optional tag for selecting the type of the iterator.  One of <tt>Standard</tt> and <tt>Rooted</tt>.
- *            When left out, @link ContainerConcept#DefaultGetIteratorSpec @endlink of <tt>TContainer</tt> is used.
+ * @param[in] c   The container to get the begin iterator for (type <tt>TContainer</tt>).
+ * @param[in] tag An optional tag for selecting the type of the iterator.  One of <tt>Standard</tt> and <tt>Rooted</tt>.
+ *                When left out, @link ContainerConcept#DefaultGetIteratorSpec @endlink of <tt>TContainer</tt> is used.
  *
  * @return TIterator Iterator to the beginning of the container, the type is selected by @link ContainerConcept#Iterator @endlink with
  *                   the given (or default) tag.
@@ -228,9 +228,9 @@ template <typename TContainer, typename TSpec> struct Iterator;
  *
  * @signature TIterator end(c[, tag]);
  *
- * @param c   The container to get the end iterator for (type <tt>TContainer</tt>).
- * @param tag An optional tag for selecting the type of the iterator.  One of <tt>Standard</tt> and <tt>Rooted</tt>.
- *            When left out, @link ContainerConcept#DefaultGetIteratorSpec @endlink of <tt>TContainer</tt> is used.
+ * @param[in] c   The container to get the end iterator for (type <tt>TContainer</tt>).
+ * @param[in] tag An optional tag for selecting the type of the iterator.  One of <tt>Standard</tt> and <tt>Rooted</tt>.
+ *                When left out, @link ContainerConcept#DefaultGetIteratorSpec @endlink of <tt>TContainer</tt> is used.
  *
  * @return TIterator Iterator to the end of the container, the type is selected by @link ContainerConcept#Iterator @endlink with
  *                   the given (or default) tag.
@@ -242,9 +242,9 @@ template <typename TContainer, typename TSpec> struct Iterator;
  * @fn ContainerConcept#length
  * @brief Returns the size of the container.
  *
- * @signature TSize size(c);
+ * @signature TSize length(c);
  *
- * @param c The container to query for its size.
+ * @param[in] c The container to query for its size.
  *
  * @return TSize The number of elements in the container.
  */
@@ -255,7 +255,7 @@ template <typename TContainer, typename TSpec> struct Iterator;
  *
  * @signature bool empty(c);
  *
- * @param c The container to query.
+ * @param[in] c The container to query.
  *
  * @return bool Whether or not the container is empty.
  */
@@ -266,8 +266,8 @@ template <typename TContainer, typename TSpec> struct Iterator;
  *
  * @signature void swap(c1, c2);
  *
- * @param c1 The first container.
- * @param c2 The second container.
+ * @param[in,out] c1 The first container.
+ * @param[in,out] c2 The second container.
  *
  * Swaps the contents of <tt>c1</tt> and <tt>c2</tt>.  The <tt>swap</tt> function must be defined in the same
  * namespace as the container for Koenig lookup to work.  In the heart of sorting algorithms, for example,
@@ -281,16 +281,6 @@ template <typename TContainer, typename TSpec> struct Iterator;
  * @endcode
  */
 
-/**
-.Concept.ContainerConcept
-..baseconcept:Concept.AssignableConcept
-..baseconcept:Concept.DefaultConstructibleConcept
-..baseconcept:Concept.CopyConstructibleConcept
-..signature:ContainerConcept
-..summary:Concept for mutable containers.
-..include:seqan/basic.h
-*/
-
 // mutable container concept
 template <typename TContainer>
 struct ContainerConcept :
@@ -342,25 +332,14 @@ struct ContainerConcept :
         sameType(size, length(c));
         sameType(true, empty(c));
 
-        // clear
-        clear(c);
-
         // TODO: infix/suffix/prefix
-        // maybe we need a SequenceConcept between Container and String
 
         // swap containers
 //        swap(c, c2);          // swap is not yet supported by every string
     }
 };
 
-/**
-.Concept.SequenceConcept
-..baseconcept:Concept.ContainerConcept
-..summary:Concept for sequences.
-..include:seqan/basic.h
-*/
-
-SEQAN_CONCEPT_REFINE(SequenceConcept, (TString), (ContainerConcept))
+SEQAN_CONCEPT_REFINE(StringConcept, (TString), (ContainerConcept)(PropertyMapConcept))
 {
     typedef typename Value<TString>::Type                 TValue;
     typedef typename Size<TString>::Type                  TSize;
@@ -374,10 +353,13 @@ SEQAN_CONCEPT_REFINE(SequenceConcept, (TString), (ContainerConcept))
 
     TString     str, str2;
 
-    SEQAN_CONCEPT_USAGE(SequenceConcept)
+    SEQAN_CONCEPT_USAGE(StringConcept)
     {
         pos = 0u;
 
+        // clear
+        clear(str);
+
         // append
         append(str, str2);
         appendValue(str, val);
@@ -387,14 +369,59 @@ SEQAN_CONCEPT_REFINE(SequenceConcept, (TString), (ContainerConcept))
     }
 };
 
-//void testStringConcepts()
-//{
-//    SEQAN_CONCEPT_ASSERT((StringConcept<String<char, Alloc<> > >));
-//    SEQAN_CONCEPT_ASSERT((StringConcept<String<Pair<int, double>, Alloc<> > >));
-////    SEQAN_CONCEPT_ASSERT((StringConcept<String<bool, Packed<> > >));  // doesn't compile yet
-////    SEQAN_CONCEPT_ASSERT((StringConcept<String<Dna5, Packed<> > >));
-//    SEQAN_CONCEPT_ASSERT((StringConcept<String<int, Array<50> > >));
-//}
+
+// ----------------------------------------------------------------------------
+// Concept StlContainerConcept
+// ----------------------------------------------------------------------------
+
+// template <typename TContainer>
+// struct StlContainerConcept :
+//     ContainerConcept<TContainer>
+    
+
+SEQAN_CONCEPT_REFINE(StlContainerConcept, (TContainer), (ContainerConcept))
+{
+    SEQAN_CONCEPT_USAGE(StlContainerConcept)
+    {}
+};
+
+// --------------------------------------------------------------------------
+// Metafunction IsContiguous
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn IsContiguous
+ * @headerfile <seqan/sequence.h>
+ * @brief Determines whether a container stores its elements contiguously in memory.
+ *
+ * @signature IsContiguous<T>::Type;
+ * @signature IsContiguous<T>::VALUE;
+ *
+ * @tparam T The type that is tested for being a string.
+ *
+ * @return Type  Either <tt>True</tt> or <tt>False</tt>, depending on whether <tt>T</tt> is stored contiguously.
+ * @return VALUE Either <tt>true</tt> or <tt>false</tt>, depending on whether <tt>T</tt> is stored contiguously.
+ *
+ * A sequence container is "contiguous", if its elements are stored in a single contiguous array.  Examples for
+ * contiguous sequences are AllocString or char arrays.
+ *
+ * If an object <tt>obj</tt> is a contiguous sequence, then <tt>begin(obj)</tt> can be converted to a pointer to the
+ * first element of the content array.
+ */
+
+template <typename T>
+struct IsContiguous
+    : public False
+{};
+
+// ----------------------------------------------------------------------------
+// Mfn HasSubscriptOperator (different for e.g. std::deque)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+struct HasSubscriptOperator :
+    public IsContiguous<TContainer>
+{};
 
 /*!
  * @concept ForwardContainerConcept
@@ -433,9 +460,9 @@ SEQAN_CONCEPT_REFINE(SequenceConcept, (TString), (ContainerConcept))
  * @fn RandomAccessContainerConcept::operator[]
  * @brief Returns a reference to an arbitrary element in the sequence.
  *
- * @signature TReference SequenceConcept::operator[](pos);
+ * @signature TReference T::operator[](pos);
  *
- * @param pos Position in the sequence (convertible to @link ContainerConcept#Position position @endlink type).
+ * @param[in] pos Position in the sequence (convertible to @link ContainerConcept#Position position @endlink type).
  *
  * @return TReference A reference to into the container with position <tt>pos</tt>.
  */
@@ -448,12 +475,23 @@ SEQAN_CONCEPT_REFINE(SequenceConcept, (TString), (ContainerConcept))
  *
  * @signature TReference value(seq, pos);
  *
- * @param seq The sequence to get value in.
- * @param pos Position in the sequence (convertible to @link ContainerConcept#Position position @endlink type).
+ * @param[in] seq The sequence to get value in.
+ * @param[in] pos Position in the sequence (convertible to @link ContainerConcept#Position position @endlink type).
  *
  * @return TReference A reference to into the container with position <tt>pos</tt>.
  */
 
+/*!
+ * @fn RandomAccessContainerConcept#assignValue
+ * @brief Assign value in RandomAccessContainer.
+ *
+ * @signature void assignValue(cont, pos, val);
+ *
+ * @param[in,out] seq The RandomAccessContainer to modify.
+ * @param[in]     pos The position to modify value at.
+ * @param[in]     val The value to assign to the given position.
+ */
+
 // TODO(holtgrew): Really deprecated?
 /*!
  * @fn RandomAccessContainerConcept#getValue
@@ -462,171 +500,134 @@ SEQAN_CONCEPT_REFINE(SequenceConcept, (TString), (ContainerConcept))
  *
  * @signature TGetValue getValue(seq, pos);
  *
- * @param seq The sequence to get value in.
- * @param pos Position in the sequence (convertible to @link ContainerConcept#Position position @endlink type).
+ * @param[in] seq The sequence to get value in.
+ * @param[in] pos Position in the sequence (convertible to @link ContainerConcept#Position position @endlink type).
  *
  * @return TGetValue The get-value (type is @link ContainerConcept#GetValue @endlink of the sequence type).
  */
 
 /*!
- * @concept SequenceConcept
+ * @concept StringConcept
+ * @brief Sequences are dense linear containers that have positions.
  * @extends RandomAccessContainerConcept
  * @headerfile <seqan/basic.h>
  *
- * @signature SequenceConcept<T>
+ * @signature StringConcept<T>
  */
 
 /*!
- * @fn SequenceConcept#iter
- * @brief Return iterator to given position.
+ * @fn StringConcept#iter
+ * @headerfile <seqan/sequence.h>
+ * @brief Iterator to the item at the given position in a container.
+ *
+ * @signature TIterator iter(seq, pos[, tag]);
+ *
+ * @param[in] seq    The sequence to get the iterator for.
+ * @param[in] pos    The position to get the iterator for.
+ * @param[in] tag    The tag to pick the type of the iterator.
  *
- * @signature TIter iter(seq, pos[, tag]);
+ * @return TIterator The resulting iterator.  If <tt>TTag</tt> is the type of <tt>tag</tt> and <tt>TSequence</tt> the
+ *                   type of <tt>seq</tt> then TIterator is of the type <tt>Iterator&lt;TSequence,
+ *                   TTag&gt;::Type</tt>.
  *
- * @param seq The sequence to get an iterator into.
- * @param pos The position to generate the iterator at.
- * @param tag The tag to use for selecting the ierator type.    One of <tt>Standard</tt> and <tt>Rooted</tt>.
+ * @section Remarks
  *
- * @return TIter The resulting iterator.
+ * If <tt>pos</tt> is out of range then the iterator is invalid.
  */
 
 /*!
- * @fn SequenceConcept#append
+ * @fn StringConcept#append
  * @brief Append a sequence to another one.
  *
  * @signature void append(seq, other);
  *
- * @param seq   The sequence to append the other sequence to.
- * @param other The other sequence to append to <tt>seq</tt>.  Of same type as <tt>seq</tt>.
+ * @param[in,out] seq   The sequence to append the other sequence to.
+ * @param[in]     other The other sequence to append to <tt>seq</tt>.  Of same type as <tt>seq</tt>.
  */
 
 /*!
- * @fn SequenceConcept#appendValue
+ * @fn StringConcept#appendValue
  * @brief Append a value to a sequence.
  *
  * @signature void appendValue(seq, val);
  *
- * @param seq The sequence to append a value to (type <tt>TSequence</tt>).
- * @param val A value to append to the sequence.  Convertible to <tt>Value&lt;TSequence&gt;::Type</tt>.
+ * @param[in,out] seq The sequence to append a value to (type <tt>TSequence</tt>).
+ * @param[in]     val A value to append to the sequence.  Convertible to <tt>Value&lt;TSequence&gt;::Type</tt>.
  */
 
 /*!
- * @fn SequenceConcept#front
+ * @fn StringConcept#front
  * @brief Return reference to the first element.
  *
  * @signature TReference front(seq);
  *
- * @param seq The sequence to get the first element of.
+ * @param[in] seq The sequence to get the first element of.
  *
  * @return TReference A reference to the first element of <tt>seq</tt>.
  */
 
 /*!
- * @fn SequenceConcept#back
+ * @fn StringConcept#back
  * @brief Return reference to the last element.
  *
  * @signature TReference back(seq);
  *
- * @param seq The sequence to get the last element of.
+ * @param[in] seq The sequence to get the last element of.
  *
  * @return TReference A reference to the last element of <tt>seq</tt>.
  */
 
 /*!
- * @fn SequenceConcept#resize
+ * @fn StringConcept#resize
  * @brief Resize a sequence.
  *
  * @signature void resize(seq, len[, val]);
  *
- * @param seq Sequence to resize.
- * @param len Length to resize <tt>seq</tt> to.
- * @param val When increasing the size, <tt>val</tt> is used to fill new entries.  When omitted,
- *            <tt>TValue()</tt> is used where <tt>TValue</tt> is the @link ContainerConcept#Value @endlink
- *            type of the sequence.
+ * @param[in,out] seq Sequence to resize.
+ * @param[in]     len Length to resize <tt>seq</tt> to.
+ * @param[in]     val When increasing the size, <tt>val</tt> is used to fill new entries.  When omitted,
+ *                    <tt>TValue()</tt> is used where <tt>TValue</tt> is the @link ContainerConcept#Value @endlink
+ *                    type of the sequence.
  */
 
 /*!
- * @fn SequenceConcept#clear
+ * @fn StringConcept#clear
  * @brief Remove all elements from the sequences.
  *
  * @signature void clear(seq);
  *
- * @param seq Sequence to clear.
+ * @param[in,out] seq Sequence to clear.
  */
 
 /*!
- * @fn SequenceConcept#erase
+ * @fn StringConcept#erase
  * @brief Erase an element or a range of elements from a sequence.
  *
  * @signature void erase(seq, pos[, posEnd)
  *
- * @param seq    Sequence to remove range from.
- * @param pos    Begin position of the range to remove.
- * @param posEnd Optional end position of the range to remove.  If omitted, <tt>pos + 1</tt> is used.
+ * @param[in,out] seq    Sequence to remove range from.
+ * @param[in]     pos    Begin position of the range to remove.
+ * @param[in]     posEnd Optional end position of the range to remove.  If omitted, <tt>pos + 1</tt> is used.
  */
 
 /*!
- * @fn SequenceConcept#eraseFront
+ * @fn StringConcept#eraseFront
  * @brief Erase first element in a sequence.
  *
  * @signature void eraseFront(seq);
  *
- * @param seq The sequence to remove the first element from.
+ * @param[in,out] seq The sequence to remove the first element from.
  */
 
 /*!
- * @fn SequenceConcept#eraseBack
+ * @fn StringConcept#eraseBack
  * @brief Erase last element in a sequence.
  *
  * @signature void eraseBack(seq);
  *
- * @param seq The sequence to remove the last element from.
- */
-
-/*!
- * @fn SequenceConcept#replace
- * @brief Replace part of a sequence.
- *
- * @signature void replace(seq, posBegin, posEnd, source)
- *
- * @param seq      The sequence to replace infix of.
- * @param posBegin Begin position in the sequence of the infix to replace.
- * @param posEnd   End position in the sequence of the infix to replace.
- * @param source   A sequence with the same value type as <tt>seq</tt>.
- */
-
-/*!
- * @mfn SequenceConcept#Infix
- * @brief Returns the infix type for a sequence.
- *
- * @signature Infix<TSequence>::Type
- *
- * @tparam TSequence The type for getting the infix type of.
- *
- * @return Type The infix type for <tt>TSequence</tt>.
- */
-
-/*!
- * @mfn SequenceConcept#Suffix
- * @brief Returns the suffix type for a sequence.
- *
- * @signature Suffix<TSequence>::Type
- *
- * @tparam TSequence The type for getting the suffix type of.
- *
- * @return Type The suffix type for <tt>TSequence</tt>.
- */
-
-/*!
- * @mfn SequenceConcept#Prefix
- * @brief Returns the prefix type for a sequence.
- *
- * @signature Prefix<TSequence>::Type
- *
- * @tparam TSequence The type for getting the prefix type of.
- *
- * @return Type The prefix type for <tt>TSequence</tt>.
+ * @param[in,out] seq The sequence to remove the last element from.
  */
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_CONTAINER_CONCEPT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_CONTAINER_CONCEPT_H_
diff --git a/seqan/basic/debug_helper.h b/seqan/basic/debug_helper.h
index 3814344..1534ed3 100644
--- a/seqan/basic/debug_helper.h
+++ b/seqan/basic/debug_helper.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Helper code for debugging and testing.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_DEBUG_HELPER_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_DEBUG_HELPER_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_DEBUG_HELPER_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_DEBUG_HELPER_H_
 
 #include <cstdio>
 #include <fstream>
@@ -61,7 +61,7 @@ namespace seqan {
 // TODO(holtgrew): Document, make public.
 
 // compare two files, do not translate linebreaks
-inline bool 
+inline bool
 _compareBinaryFiles(const char * file1, const char * file2)
 {
 //IOREV see above
@@ -97,7 +97,7 @@ _compareBinaryFiles(const char * file1, const char * file2)
 //one line break is either \r, \n, or \r\n.
 //a single line break is skipped.
 //the second line break is transformed into \n
-inline void 
+inline void
 _compareTextFilesReadChar(FILE * fl, char & c, int & num_lb, bool & is_eof)
 {
 //IOREV see above
@@ -130,7 +130,7 @@ _compareTextFilesReadChar(FILE * fl, char & c, int & num_lb, bool & is_eof)
 }
 
 // compare two files, translate linebreaks
-inline bool 
+inline bool
 _compareTextFiles(const char * file1, const char * file2)
 {
 //IOREV see above
@@ -221,6 +221,9 @@ _compareTextFilesAlt(const char * file1, const char * file2)
 
         if (line1 != line2)
         {
+            std::cerr << "The following files are different:" << std::endl;
+            std::cerr << '\t' << file1 << std::endl;
+            std::cerr << '\t' << file2 << std::endl;
             std::cerr << "Line " << lineNo << " of the text files differ:" << std::endl;
             std::cerr << line1 << std::endl;
             std::cerr << line2 << std::endl;
@@ -237,4 +240,4 @@ _compareTextFilesAlt(const char * file1, const char * file2)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_DEBUG_HELPER_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_DEBUG_HELPER_H_
diff --git a/seqan/basic/debug_test_system.h b/seqan/basic/debug_test_system.h
index 79319ba..b4a17bf 100644
--- a/seqan/basic/debug_test_system.h
+++ b/seqan/basic/debug_test_system.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -40,8 +40,8 @@
 
 // SEQAN_NO_GENERATED_FORWARDS
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_DEBUG_TEST_SYSTEM_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_DEBUG_TEST_SYSTEM_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_DEBUG_TEST_SYSTEM_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_DEBUG_TEST_SYSTEM_H_
 
 #include <iostream>  // stdout, stderr
 #include <iomanip>
@@ -53,6 +53,7 @@
 #include <set>
 #include <vector>
 #include <string>
+#include <typeinfo>
 
 #ifdef PLATFORM_WINDOWS
 #include <Windows.h>    // DeleteFile()
@@ -67,6 +68,78 @@
 #include <signal.h>
 #endif  // #ifdef PLATFORM_WINDOWS
 
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class Demangler
+// ----------------------------------------------------------------------------
+// Holds the name of a given C++ type T.
+// NOTE(esiragusa): this class could become a subclass of CStyle String...
+
+namespace seqan {
+
+template <typename T>
+struct Demangler
+{
+#ifdef PLATFORM_GCC
+    char *data_begin;
+#else
+    const char *data_begin;
+#endif
+
+    Demangler()
+    {
+        T t;
+        _demangle(*this, t);
+    }
+
+    Demangler(T const & t)
+    {
+        _demangle(*this, t);
+    }
+
+    ~Demangler()
+    {
+#ifdef PLATFORM_GCC
+        free(data_begin);
+#endif
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _demangle(Demangler)
+// ----------------------------------------------------------------------------
+
+template <typename T>
+inline void _demangle(Demangler<T> & me, T const & t)
+{
+#ifdef PLATFORM_GCC
+    int status;
+    me.data_begin = abi::__cxa_demangle(typeid(t).name(), NULL, NULL, &status);
+#else
+    me.data_begin = typeid(t).name();
+#endif
+}
+
+// ----------------------------------------------------------------------------
+// Function toCString(Demangler)
+// ----------------------------------------------------------------------------
+
+template <typename T>
+inline const char * toCString(Demangler<T> const & me)
+{
+
+    return me.data_begin;
+}
+
+}
+
 /*!
  * @defgroup AssertMacros Assertion and Check Macros
  * @brief The assertion and check macros provided by SeqAn.
@@ -83,29 +156,29 @@
  * @macro AssertMacros#SEQAN_FAIL
  * @headerfile <seqan/basic.h>
  * @brief Force abortion of program, regardless of debugging settings.
- * 
+ *
  * @signature SEQAN_FAIL(msg[, args]);
- * 
+ *
  * @param[in] msg  A format string.
  * @param[in] args An optional list of arguments that are used for filling msg.
- * 
+ *
  * @section Remarks
- * 
+ *
  * Use this if something really unexpected happens inside your functions and there is no way to report this through the
  * API.  A good example would be logic errors, e.g. invalid values.
- * 
+ *
  * @section Examples
- * 
+ *
  * In the following example, the <tt>SEQAN_FAIL</tt> is there if a possible value is added to <tt>MyEnum</tt> but the
  * function <tt>foo</tt> is not updated accordingly.
- * 
+ *
  * @code{.cpp}
  * enum MyEnum
  * {
  *   VALUE_ONE,
  *   VALUE_TWO
  * };
- *  
+ *
  * bool foo(MyEnum x)
  * {
  *     switch (x)
@@ -117,45 +190,13 @@
  *         // do something
  *         return true;
  *     }
- *  
+ *
  *     SEQAN_FAIL("Logic error. Should never reach here. x == %d.", x);
  *     return false;
  * }
  * @endcode
  */
 
-/**
-.Macro.SEQAN_FAIL
-..cat:Assertions
-..summary:Force abortion of program, regardless of debugging settings.
-..signature:SEQAN_FAIL(msg[, args])
-..param.msg:A format string.
-..param.args:An optional list of arguments.
-..remarks:Use this if something really unexpected happens inside your functions and there is no way to report this through the API. A good example would be logic errors, e.g. invalid values.
-..example.text:In the following example, the $SEQAN_FAIL$ is there if a possible value is added to $MyEnum$ but the function $foo$ is not updated accordingly.
-..example.code:
-enum MyEnum {
-  VALUE_ONE,
-  VALUE_TWO
-};
-
-bool foo(MyEnum x) {
-    switch (x) {
-    case VALUE_ONE:
-        // do something
-        return true;
-    case VALUE_TWO:
-        // do something
-        return true;
-    }
-
-    SEQAN_FAIL("Logic error. Should never reach here. x == %d.", x);
-    return false;
-}
-..include:seqan/basic.h
-..see:Macro.SEQAN_CHECK
- */
-
 #define SEQAN_FAIL(...)                                                 \
     do {                                                                \
         ::seqan::ClassTest::forceFail(__FILE__, __LINE__,               \
@@ -164,37 +205,37 @@ bool foo(MyEnum x) {
     } while (false)
 
 /*!
- * @macro SEQAN_CHECK
+ * @macro AssertMacros#SEQAN_CHECK
  * @headerfile <seqan/basic.h>
  * @brief Force abortion of program if a condition is not met, regardless of debugging settings.
- * 
+ *
  * @signature SEQAN_CHECK(condition, msg[, args]);
  *
  * @param[in] condition An expression that is checked.
  * @param[in] msg       A format string.
  * @param[in] args      An optional list of arguments.
- * 
+ *
  * @section Remarks
- * 
+ *
  * Use this if something really unexpected happens inside your functions and there is no way to report this through the
  * API.  A good example would be logic errors, e.g. invalid values.
- * 
+ *
  * @section Examples
- * 
+ *
  * In the following example, the <tt>SEQAN_CHECK</tt> stops program execution if a value is added to <tt>MyEnum</tt> but
  * the function <tt>foo</tt> is not updated accordingly.
- * 
+ *
  * @code{.cpp}
  * enum MyEnum
  * {
  *   VALUE_ONE,
  *   VALUE_TWO
  * };
- *  
+ *
  * bool foo(MyEnum x)
  * {
  *     SEQAN_CHECK((x == VALUE_ONE || x == VALUE_TWO), "Invalid value for x == %d.", x);
- *  
+ *
  *     switch (x)
  *     {
  *     case VALUE_ONE:
@@ -204,45 +245,12 @@ bool foo(MyEnum x) {
  *         // do something
  *         return true;
  *     }
- *  
+ *
  *     return false;  // Should never reach here, checked above with SEQAN_CHECK.
  * }
  * @endcode
  */
 
-/**
-.Macro.SEQAN_CHECK
-..cat:Assertions
-..summary:Force abortion of program if a condition is not met, regardless of debugging settings.
-..signature:SEQAN_CHECK(condition, msg[, args])
-..param.msg:A format string.
-..param.args:An optional list of arguments.
-..remarks:Use this if something really unexpected happens inside your functions and there is no way to report this through the API. A good example would be logic errors, e.g. invalid values.
-..example.text:In the following example, the $SEQAN_CHECK$ stops program execution if a value is added to $MyEnum$ but the function $foo$ is not updated accordingly.
-..example.code:
-enum MyEnum {
-  VALUE_ONE,
-  VALUE_TWO
-};
-
-bool foo(MyEnum x) {
-    SEQAN_CHECK((x == VALUE_ONE || x == VALUE_TWO), "Invalid value for x == %d.", x);
-
-    switch (x) {
-    case VALUE_ONE:
-        // do something
-        return true;
-    case VALUE_TWO:
-        // do something
-        return true;
-    }
-
-    return false;  // Should never reach here, checked above with SEQAN_CHECK.
-}
-..include:seqan/basic.h
-..see:Macro.SEQAN_FAIL
- */
-
 #define SEQAN_CHECK(_arg1, ...)                                         \
     do {                                                                \
         if (!::seqan::ClassTest::testTrue(__FILE__, __LINE__,           \
@@ -275,11 +283,11 @@ bool foo(MyEnum x) {
 // You can print the current level using the function seqan::printDebugLevel().
 
 /*!
- * @macro SEQAN_ENABLE_TESTING
+ * @macro TestSystemMacros#SEQAN_ENABLE_TESTING
  * @headerfile <seqan/basic.h>
  * @brief Indicates whether testing is enabled.
  *
- * @signature SEQAN_ENABLE_DEBUG
+ * @signature SEQAN_ENABLE_TESTING
  *
  * When set to 1, testing is enabled.  If it is undefined or set to 0, testing is disabled.  This means the macros for
  * the tests (SEQAN_BEGIN_TESTSUITE, SEQAN_DEFINE_TEST, SEQAN_CALL_TEST, and SEQAN_END_TESTSUITE) will be enabled.  This
@@ -289,24 +297,9 @@ bool foo(MyEnum x) {
  *
  * If you want to change this value in your C++ program code you have to define this value before including any SeqAn header!
  *
- * If set to 1 then SEQAN_ENABLE_DEBUG is forced to 1 as well.
+ * If set to 1 then @link TestSystemMacros#SEQAN_ENABLE_DEBUG @endlink is forced to 1 as well.
  *
- * @see SEQAN_ENABLE_DEBUG
- */
-
-/**
-.Macro.SEQAN_ENABLE_TESTING
-..cat:Testing & Debugging
-..summary:Indicates whether testing is enabled.
-..signature:SEQAN_ENABLE_DEBUG
-..remarks:When enabled (set to 1), testing is enabled. This means the macros for the tests (@Macro.SEQAN_BEGIN_TESTSUITE@, @Macro.SEQAN_DEFINE_TEST@, @Macro.SEQAN_CALL_TEST@, and @Macro.SEQAN_END_TESTSUITE@) will be enabled. This makes failing assertions raise
- exceptions instead of call $abort()$ and enables checkpoints.
-..remarks:By default, this is set to 0.
-..remarks:If @Macro.SEQAN_ENABLE_CHECKPOINTS@ is not defined before including $<seqan/basic.h>$, then @Macro.SEQAN_ENABLE_CHECKPOINTS@ will be set to the value of @Macro.SEQAN_ENABLE_TESTING@ (after the default initialization to 0).
-..remarks:If you want to change this value, you have to define this value before including any SeqAn header.
-..remarks:If set to 1 then @Macro.SEQAN_ENABLE_TESTING@ is force-set to 0 as well.
-..see:Macro.SEQAN_ENABLE_DEBUG
-..see:Macro.SEQAN_ENABLE_CHECKPOINTS
+ * @see TestSystemMacros#SEQAN_ENABLE_DEBUG
  */
 
 // Set default for SEQAN_ENABLE_TESTING.
@@ -315,7 +308,7 @@ bool foo(MyEnum x) {
 #endif  // #ifndef SEQAN_ENABLE_TESTING
 
 /*!
- * @macro SEQAN_ENABLE_DEBUG
+ * @macro TestSystemMacros#SEQAN_ENABLE_DEBUG
  * @headerfile <seqan/basic.h>
  * @brief Indicates whether debugging is enabled.
  *
@@ -330,20 +323,7 @@ bool foo(MyEnum x) {
  *
  * Force-enabled if SEQAN_ENABLE_TESTING is set to 1.
  *
- * @see SEQAN_ENABLE_TESTING
- */
-
-/**
-.Macro.SEQAN_ENABLE_DEBUG
-..cat:Testing & Debugging
-..summary:Indicates whether debugging is enabled.
-..signature:SEQAN_ENABLE_DEBUG
-..remarks:When enabled (set to 1), debugging is enabled. This means the assertion macros are expanded to actual code and not to nothing.
-..remarks:By default, this is set to 0 if $NDEBUG$ is defined and to 1 if $NDEBUG$ is not defined.
-..remarks:If you want to change this value, you have to define this value before including any SeqAn header.
-..remarks:Force-enabled if @Macro.SEQAN_ENABLE_TESTING@ is set to 1.
-..see:Macro.SEQAN_ENABLE_TESTING
-..see:Macro.SEQAN_ENABLE_CHECKPOINTS
+ * @see TestSystemMacros#SEQAN_ENABLE_TESTING
  */
 
 // Set default for SEQAN_ENABLE_DEBUG.
@@ -361,40 +341,13 @@ bool foo(MyEnum x) {
 #define SEQAN_ENABLE_DEBUG 1
 #endif  // #if SEQAN_ENABLE_TESTING
 
-/**
-.Macro.SEQAN_ENABLE_CHECKPOINTS
-..cat:Testing & Debugging
-..summary:Indicates whether checkpoints are enabled.
-..signature:SEQAN_ENABLE_CHECKPOINTS
-..remarks:When enabled (set to 1), checkpoints are enabled. This means the $SEQAN_CHECKPOINT$ macros are expanded to actual code and not to nothing.
-..remarks:By default, this is set to $SEQAN_ENABLE_TESTING$.
-..remarks:Checkpoints can come at large increases of running time in your tests. Disable them when your test run too slow.
-..remarks:If you want to change this value, you have to define this value before including any SeqAn header.
-..example.text:Disable checkpoints in a program.
-..example.code:
-// Disable SeqAn checkpoints in this program.
-#define SEQAN_ENABLE_CHECKPOINTS 0
-
-// Any SeqAn headers or headers including SeqAn headers have to come AFTER the
-// definition of SEQAN_ENABLE_CHECKPOINT above.
-#include <seqan/base.h>
-
-int main(int argc, char const ** argv)
-{
-    // Any call to SeqAn functions will NOT log any checkpoints.
-    return 0;
-}
-..see:Macro.SEQAN_ENABLE_DEBUG
-..see:Macro.SEQAN_ENABLE_TESTING
- */
-
 // Allow disabling checkpoints independent of testing.
 #ifndef SEQAN_ENABLE_CHECKPOINTS
 #define SEQAN_ENABLE_CHECKPOINTS 0 // SEQAN_ENABLE_TESTING
 #endif  // #ifndef SEQAN_ENABLE_CHECKPOINTS
 
 /*!
- * @macro SEQAN_TYPEDEF_FOR_DEBUG
+ * @macro TestSystemMacros#SEQAN_TYPEDEF_FOR_DEBUG
  * @headerfile <seqan/basic.h>
  * @brief When using typedefs that are only used in debug mode then they have to be marked with macro.
  *
@@ -407,29 +360,10 @@ int main(int argc, char const ** argv)
  * @endcode
  */
 
-/**
-.Macro.SEQAN_TYPEDEF_FOR_DEBUG
-..cat:Testing & Debugging
-..summary: When using typedefs that are only used in debug mode then they have to be marked with macro.
-..signature:SEQAN_TYPEDEF_FOR_DEBUG
-..example.code:
-typedef int TInt SEQAN_TYPEDEF_FOR_DEBUG;
-*/
 #if !SEQAN_ENABLE_DEBUG
-#  if defined(__GNUC__) && ((__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)))
-#    define SEQAN_TYPEDEF_FOR_DEBUG __attribute__((unused))
-#  else
-#    define SEQAN_TYPEDEF_FOR_DEBUG
-#  endif
+#define SEQAN_TYPEDEF_FOR_DEBUG SEQAN_UNUSED
 #else
-#  define SEQAN_TYPEDEF_FOR_DEBUG
-#endif
-
-// TODO(holtgrew): This one is for profiling and in tests.
-#if defined(__GNUC__) && ((__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)))
-#  define SEQAN_UNUSED_TYPEDEF __attribute__((unused))
-#else
-#  define SEQAN_UNUSED_TYPEDEF
+#define SEQAN_TYPEDEF_FOR_DEBUG
 #endif
 
 namespace seqan {
@@ -455,14 +389,6 @@ namespace seqan {
  * @param[in,out] stream A std::ostream where the information about the levels are streamed to.
  */
 
-/**
-.Function.printDebugLevel
-..cat:Testing & Debugging
-..summary:Print the current SeqAn debug level and the compiler flags to the given stream.
-..signature:printDebugLevel(stream)
-..param.stream:The stream to print to, e.g. $std::cout$.
-..include:seqan/basic.h
- */
 template <typename TStream>
 void printDebugLevel(TStream & stream)
 {
@@ -481,6 +407,7 @@ void printStackTrace(TSize /*maxFrames*/)
 #else
 
 // print a demangled stack backtrace of the caller function
+// TODO(esiragusa): use Demangler.
 template <typename TSize>
 void printStackTrace(TSize maxFrames)
 {
@@ -671,12 +598,12 @@ struct StaticData
 
     static char const * _computePathToRoot()
     {
-        // Get path to core (this file resides in core/include/seqan/basic).
+        // Get path to include.
         const char * file = __FILE__;
         int pos = -1;
-        for (size_t i = 0; i < strlen(file) - strlen("core"); ++i)
+        for (size_t i = 0; i < strlen(file) - strlen("include"); ++i)
         {
-            if (strncmp(file + i, "core", strlen("core")) == 0)
+            if (strncmp(file + i, "include", strlen("include")) == 0)
             {
                 pos = i;
             }
@@ -689,7 +616,7 @@ struct StaticData
                       << __FILE__ << "\"" << std::endl;
             exit(1);
         }
-        
+
         static char buffer[1024];
         strncpy(&buffer[0], file, pos);
         buffer[pos - 1] = '\0';
@@ -792,8 +719,10 @@ const char * tempFileName()
 
 #else  // ifdef PLATFORM_WINDOWS_VS
     strcpy(fileNameBuffer, "/tmp/SEQAN.XXXXXXXXXXXXXXXXXXXX");
+    mode_t cur_umask = umask(S_IRWXO | S_IRWXG);  // to silence Coverity warning
     int _tmp = mkstemp(fileNameBuffer);
     (void) _tmp;
+    umask(cur_umask);
     unlink(fileNameBuffer);
     mkdir(fileNameBuffer, 0777);
 
@@ -916,6 +845,8 @@ int endTestSuite()
         }
 
         rmdir(StaticData::tempFileNames()[i].c_str());
+        if (closedir(dpdf) != 0)
+            std::cerr << "WARNING: Could not delete directory " << StaticData::tempFileNames()[i] << "\n";
 #endif  // #ifdef PLATFORM_WINDOWS
     }
 
@@ -1778,7 +1709,7 @@ inline void fail()
 }  // namespace ClassTest
 
 /*!
- * @macro SEQAN_DEFINE_TEST
+ * @macro TestSystemMacros#SEQAN_DEFINE_TEST
  * @headerfile <seqan/basic.h>
  * @brief Expand to test definition.
  *
@@ -1796,31 +1727,18 @@ inline void fail()
  * @endcode
  */
 
-/**
-.Macro.SEQAN_DEFINE_TEST
-..summary:Expand to test definition.
-..cat:Testing & Debugging
-..signature:SEQAN_DEFINE_TEST(test_name)
-..param.test_name:The name of the test.
-..remarks:This macro expands to the definition of a $void$ function with $SEQAN_TEST_ + test_name$ as its name.
-..example.code:
-SEQAN_DEFINE_TEST(test_name)
-{
-   SEQAN_ASSERT_LT(0, 3);
-}
-..see:Macro.SEQAN_SKIP_TEST
-..see:Macro.SEQAN_CALL_TEST
-..see:Macro.SEQAN_BEGIN_TESTSUITE
-..see:Macro.SEQAN_END_TESTSUITE
- */
-
 // This macro expands to function header for one test.
 #define SEQAN_DEFINE_TEST(test_name)                    \
     template <bool speed_up_dummy_to_prevent_compilation_of_unused_tests_> \
     void SEQAN_TEST_ ## test_name()
 
 /*!
- * @macro SEQAN_BEGIN_TESTSUITE
+ * @defgroup TestSystemMacros Test System Macros
+ * @brief Macros for the test system.
+ */
+
+/*!
+ * @macro TestSystemMacros#SEQAN_BEGIN_TESTSUITE
  * @headerfile <seqan/basic.h>
  * @brief Expand to a test suite beginning.
  *
@@ -1843,27 +1761,6 @@ SEQAN_DEFINE_TEST(test_name)
  * @endcode
  */
 
-/**
-.Macro.SEQAN_BEGIN_TESTSUITE
-..summary:Expand to a test suite beginning.
-..cat:Testing & Debugging
-..signature:SEQAN_BEGIN_TESTSUITE(name)
-..param.name:The name of the test suite.
-..remarks:This macro expands to a $main()$ function and some initialization code that sets up the test system.
-..example.code:
-#include <seqan/basic.h>
-
-SEQAN_BEGIN_TESTSUITE(test_foo)
-{
-    SEQAN_CALL_TEST(test_foo_my_test);
-}
-SEQAN_END_TESTSUITE
-..see:Macro.SEQAN_SKIP_TEST
-..see:Macro.SEQAN_DEFINE_TEST
-..see:Macro.SEQAN_CALL_TEST
-..see:Macro.SEQAN_END_TESTSUITE
- */
-
 #if SEQAN_ENABLE_TESTING
 // This macro expands to startup code for a test file.
 #define SEQAN_BEGIN_TESTSUITE(suite_name)                       \
@@ -1872,7 +1769,7 @@ SEQAN_END_TESTSUITE
         ::seqan::ClassTest::beginTestSuite(# suite_name, argv[0]);
 
 /*!
- * @macro SEQAN_END_TESTSUITE
+ * @macro TestSystemMacros#SEQAN_END_TESTSUITE
  * @headerfile <seqan/basic.h>
  * @brief Expand to test suite ending.
  *
@@ -1893,33 +1790,13 @@ SEQAN_END_TESTSUITE
  * @endcode
  */
 
-/**
-.Macro.SEQAN_END_TESTSUITE
-..summary:Expand to a test suite ending.
-..cat:Testing & Debugging
-..signature:SEQAN_END_TESTSUITE
-..remarks:This macro expands to finalization code for a test suite.
-..example.code:
-#include <seqan/basic.h>
-
-SEQAN_BEGIN_TESTSUITE(test_foo)
-{
-    SEQAN_CALL_TEST(test_foo_my_test);
-}
-SEQAN_END_TESTSUITE
-..see:Macro.SEQAN_SKIP_TEST
-..see:Macro.SEQAN_DEFINE_TEST
-..see:Macro.SEQAN_CALL_TEST
-..see:Macro.SEQAN_BEGIN_TESTSUITE
- */
-
 // This macro expands to shutdown code for a test file.
 #define SEQAN_END_TESTSUITE                     \
     return ::seqan::ClassTest::endTestSuite();  \
     }
 
 /*!
- * @macro SEQAN_CALL_TESTS
+ * @macro TestSystemMacros#SEQAN_CALL_TEST
  * @headerfile <seqan/basic.h>
  * @brief Expand to calling a test.
  *
@@ -1936,37 +1813,31 @@ SEQAN_END_TESTSUITE
  * @endcode
  */
 
-/**
-.Macro.SEQAN_CALL_TEST
-..summary:Expand to calling a test.
-..cat:Testing & Debugging
-..signature:SEQAN_CALL_TEST(test_name)
-..param.test_name:The name of the test.
-..remarks:This expects the test to be defined with @Macro.SEQAN_DEFINE_TEST@. This macro will expand to code that calls the code inside a try/catch block. Use this macro within a test suite, only.
-..example.code:
-// Within a test suite.
-SEQAN_CALL_TEST(test_name);
-..see:Macro.SEQAN_SKIP_TEST
-..see:Macro.SEQAN_DEFINE_TEST
-..see:Macro.SEQAN_BEGIN_TESTSUITE
-..see:Macro.SEQAN_END_TESTSUITE
- */
-
 // This macro expands to code to call a given test.
 #define SEQAN_CALL_TEST(test_name)                                      \
     do {                                                                \
-        ::seqan::ClassTest::beginTest(# test_name);                      \
+        seqan::ClassTest::beginTest(# test_name);                       \
         try {                                                           \
             SEQAN_TEST_ ## test_name<true>();                           \
-        } catch (::seqan::ClassTest::AssertionFailedException e) {       \
+        } catch (seqan::ClassTest::AssertionFailedException e) {        \
             /* Swallow exception, go on with next test. */              \
             (void) e;  /* Get rid of unused variable warning. */        \
+        } catch (std::exception const & e) {                            \
+            std::cerr << "Unexpected exception of type "                \
+                      << toCString(seqan::Demangler<std::exception>(e)) \
+                      << "; message: " << e.what() << "\n";             \
+            seqan::ClassTest::StaticData::thisTestOk() = false;         \
+            seqan::ClassTest::StaticData::errorCount() += 1;            \
+        } catch (...) {                                                 \
+            std::cerr << "Unexpected exception of unknown type\n";      \
+            seqan::ClassTest::StaticData::thisTestOk() = false;         \
+            seqan::ClassTest::StaticData::errorCount() += 1;            \
         }                                                               \
-        ::seqan::ClassTest::endTest();                                  \
+        seqan::ClassTest::endTest();                                    \
     } while (false)
 
 /*!
- * @mfn SEQAN_SKIP_TEST
+ * @macro TestSystemMacros#SEQAN_SKIP_TEST
  * @headerfile <seqan/basic.h>
  * @brief Force the test to return without failing and mark it as skipped.
  *
@@ -1982,22 +1853,6 @@ SEQAN_CALL_TEST(test_name);
  * @endcode
  */
 
-/**
-.Macro.SEQAN_SKIP_TEST
-..cat:Testing & Debugging
-..summary:Force the test to return without failing and mark it as skipped.
-..signature:SEQAN_SKIP_TEST
-..example.code:
-SEQAN_DEFINE_TEST(test_skipped)
-{
-    SEQAN_SKIP_TEST;
-}
-..see:Macro.SEQAN_DEFINE_TEST
-..see:Macro.SEQAN_CALL_TEST
-..see:Macro.SEQAN_BEGIN_TESTSUITE
-..see:Macro.SEQAN_END_TESTSUITE
- */
-
 // This macro returns from the current function and logs a "skipped"
 // event for the current test.
 #define SEQAN_SKIP_TEST                         \
@@ -2016,24 +1871,24 @@ SEQAN_DEFINE_TEST(test_skipped)
  * @macro AssertMacros#SEQAN_ASSERT
  * @headerfile <seqan/basic.h>
  * @brief Test that the given expression can be coerced to <tt>true</tt>.
- * 
+ *
  * @signature SEQAN_ASSERT(expression);
  * @signature SEQAN_ASSERT_MSG(expression, message[, parameters]);
  *
  * @param[in] expression An expression to check for being true.
  * @param[in] message    A format string.
  * @param[in] parameters An optional list of parameters.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The main advantage of this macro is that it prints the values of its argument on failures.  Note that the
  * <tt>operator&lt;&lt;</tt> to the type of <tt>std::cerr</tt> has to be defined for the type of both expression
  * parameters. Otherwise, simply use the equivalent SEQAN_ASSERT @call.
- * 
+ *
  * See SEQAN_CHECK and SEQAN_FAIL for (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT(0);  // will fail
  * SEQAN_ASSERT(1);  // will run through
@@ -2042,27 +1897,27 @@ SEQAN_DEFINE_TEST(test_skipped)
  */
 
 /*!
- * @macro SEQAN_ASSERT_NOT
+ * @macro AssertMacros#SEQAN_ASSERT_NOT
  * @headerfile <seqan/basic.h>
  * @brief Test that the given expression can be coerced to <tt>false</tt>.
- * 
+ *
  * @signature SEQAN_ASSERT_NOT(expression)
  * @signature SEQAN_ASSERT_NOT_MSG(expression, message[, parameters])
- * 
+ *
  * @param[in] expression An expression to check for being false.
  * @param[in] message    A format string.
  * @param[in] parameters An optional list of parameters.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The main advantage of this macro is that it prints the values of its argument on failures.  Note that the
  * <tt>operator&lt;&lt;</tt> to the type of <tt>std::cerr</tt> has to be defined for the type of both expression
  * parameters.  Otherwise, simply use the equivalent SEQAN_ASSERT call.
- * 
+ *
  * See SEQAN_CHECK and SEQAN_FAIL for (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_NOT(0);  // will run through
  * SEQAN_ASSERT_NOT(1);  // will fail
@@ -2071,23 +1926,28 @@ SEQAN_DEFINE_TEST(test_skipped)
  */
 
 /*!
- * @macro SEQAN_ASSERT_EQ
+ * @macro AssertMacros#SEQAN_ASSERT_EQ
  * @headerfile <seqan/basic.h>
  * @brief Test that two given expressions are equal, as defined by the matching call to the <tt>operator=(,)</tt>.
- 
+
  * @signature SEQAN_ASSERT_EQ(expression1, expression2);
  * @signature SEQAN_ASSERT_EQ_MSG(expression1, expression2, comment[, parameters]);
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] expression1 The first expression.
+ * @param[in] expression2 The second expression.
+ * @param[in] comment     A C-string (<tt>char const *</tt>) to use as a format string for printing a message
+ *                        on failure.
+ * @param[in] parameters  An optional parameter that is put into <tt>printf()</tt> with format string
+ *                        <tt>comment</tt>.
+ *
  * The main advantage of this macro is that it prints the values of its argument on failures.  Note that the
  * <tt>operator&lt;&lt;</tt> to the type of <tt>std::cerr</tt> has to be defined for the type of both expression
  * parameters.  Otherwise, simply use the equivalent SEQAN_ASSERT call.
- * 
+ *
  * See SEQAN_CHECK and SEQAN_FAIL for (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_EQ(0, false);  // will run through
  * SEQAN_ASSERT_EQ(1, false);  // will fail
@@ -2097,23 +1957,28 @@ SEQAN_DEFINE_TEST(test_skipped)
  */
 
 /*!
- * @macro SEQAN_ASSERT_NEQ
+ * @macro AssertMacros#SEQAN_ASSERT_NEQ
  * @headerfile <seqan/basic.h>
  * @brief Test that two given expressions are not equal, as defined by the matching call to the <tt>operator!=(,)</tt>.
- * 
- * @signature SEQAN_ASSERT_NEQ(expression);
- * @signature SEQAN_ASSERT_NEQ_MSG(expression, message[, parameters]);
- * 
- * @section Remarks
- * 
+ *
+ * @signature SEQAN_ASSERT_NEQ(expression1, expression2);
+ * @signature SEQAN_ASSERT_NEQ_MSG(expression1, expression2, comment[, parameters]);
+ *
+ * @param[in] expression1 The first expression.
+ * @param[in] expression2 The second expression.
+ * @param[in] comment     A C-string (<tt>char const *</tt>) to use as a format string for printing a message
+ *                        on failure.
+ * @param[in] parameters  An optional parameter that is put into <tt>printf()</tt> with format string
+ *                        <tt>comment</tt>.
+ *
  * The main advantage of this macro is that it prints the values of its argument on failures.  Note that the
  * <tt>operator&lt;&lt;</tt> to the type of <tt>std::cerr</tt> has to be defined for the type of both expression
  * parameters.  Otherwise, simply use the equivalent SEQAN_ASSERT call.
- * 
+ *
  * See SEQAN_CHECK and SEQAN_FAIL for (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_NEQ(0, false);  // will fail
  * SEQAN_ASSERT_NEQ(1, false);  // will run through
@@ -2123,24 +1988,29 @@ SEQAN_DEFINE_TEST(test_skipped)
  */
 
 /*!
- * @macro SEQAN_ASSERT_LT
+ * @macro AssertMacros#SEQAN_ASSERT_LT
  * @headerfile <seqan/basic.h>
  * @brief Test that the two given expressions are in the less-than relation as defined by the matching call to
  *        operator<(,).
- * 
+ *
  * @signature SEQAN_ASSERT_LT(expression1, expression2);
  * @signature SEQAN_ASSERT_LT(expression1, expression2, comment[, parameters]);
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] expression1 The first expression.
+ * @param[in] expression2 The second expression.
+ * @param[in] comment     A C-string (<tt>char const *</tt>) to use as a format string for printing a message
+ *                        on failure.
+ * @param[in] parameters  An optional parameter that is put into <tt>printf()</tt> with format string
+ *                        <tt>comment</tt>.
+ *
  * The main advantage of this macro is that it prints the values of its argument on failures.  Note that the
  * <tt>operator&lt;&lt;</tt> to the type of <tt>std::cerr</tt> has to be defined for the type of both expression
  * parameters.  Otherwise, simply use the equivalent SEQAN_ASSERT call.
- * 
+ *
  * See SEQAN_CHECK and SEQAN_FAIL for (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_LT(0, 1);  // will run through
  * SEQAN_ASSERT_LT(1, 1);  // will not run through
@@ -2149,28 +2019,33 @@ SEQAN_DEFINE_TEST(test_skipped)
  */
 
 /*!
- * @macro SEQAN_ASSERT_LEQ
- * 
+ * @macro AssertMacros#SEQAN_ASSERT_LEQ
+ *
  * @brief Test that the two given expressions are in the less-than-or-equal
  *        relation as defined by the matching call to operator<=(,).
- * 
+ *
  * @signature SEQAN_ASSERT_LEQ(expression1, expression2)
  * @signature SEQAN_ASSERT_LEQ_MSG(expression1, expression2, comment[,
  *            parameters])
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] expression1 The first expression.
+ * @param[in] expression2 The second expression.
+ * @param[in] comment     A C-string (<tt>char const *</tt>) to use as a format string for printing a message
+ *                        on failure.
+ * @param[in] parameters  An optional parameter that is put into <tt>printf()</tt> with format string
+ *                        <tt>comment</tt>.
+ *
  * The main advantage of this macro is that it prints the values of its argument
  * on failures. Note that the <tt>operator&lt;&lt;</tt> to the type of
  * <tt>std::cerr</tt> has to be defined for the type of both expression
- * parameters. Otherwise, simply use the equivalent  SEQAN_ASSERT 
+ * parameters. Otherwise, simply use the equivalent  SEQAN_ASSERT
  * call.
- * 
+ *
  * See  SEQAN_CHECK  and  SEQAN_FAIL  for
  * (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_LEQ(1, 1);  // will run through
  * SEQAN_ASSERT_LEQ(1, 2);  // will not run through
@@ -2179,27 +2054,32 @@ SEQAN_DEFINE_TEST(test_skipped)
  */
 
 /*!
- * @macro SEQAN_ASSERT_GT
- * 
+ * @macro AssertMacros#SEQAN_ASSERT_GT
+ *
  * @brief Test that the two given expressions are in the greather-than relation
  *        as defined by the matching call to operator>(,).
- * 
+ *
  * @signature SEQAN_ASSERT_GT(expression1, expression2);
  * @signature SEQAN_ASSERT_GT_MSG(expression1, expression2, comment[, parameters]);
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] expression1 The first expression.
+ * @param[in] expression2 The second expression.
+ * @param[in] comment     A C-string (<tt>char const *</tt>) to use as a format string for printing a message
+ *                        on failure.
+ * @param[in] parameters  An optional parameter that is put into <tt>printf()</tt> with format string
+ *                        <tt>comment</tt>.
+ *
  * The main advantage of this macro is that it prints the values of its argument
  * on failures. Note that the <tt>operator&lt;&lt;</tt> to the type of
  * <tt>std::cerr</tt> has to be defined for the type of both expression
- * parameters. Otherwise, simply use the equivalent  SEQAN_ASSERT 
+ * parameters. Otherwise, simply use the equivalent  SEQAN_ASSERT
  * call.
- * 
+ *
  * See  SEQAN_CHECK  and  SEQAN_FAIL  for
  * (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_GT(2, 1);  // will run through
  * SEQAN_ASSERT_GT(1, 1);  // will not run through
@@ -2208,24 +2088,29 @@ SEQAN_DEFINE_TEST(test_skipped)
  */
 
 /*!
- * @macro SEQAN_ASSERT_GEQ
- * 
+ * @macro AssertMacros#SEQAN_ASSERT_GEQ
+ *
  * @brief Test that the two given expressions are in the greater-than-or-equal
  *        relation as defined by the matching call to operator>=(,).
- * 
+ *
  * @signature SEQAN_ASSERT_GEQ(expression1, expression2);
  * @signature SEQAN_ASSERT_GEQ_MSG(expression1, expression2, comment[, parameters]);
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] expression1 The first expression.
+ * @param[in] expression2 The second expression.
+ * @param[in] comment     A C-string (<tt>char const *</tt>) to use as a format string for printing a message
+ *                        on failure.
+ * @param[in] parameters  An optional parameter that is put into <tt>printf()</tt> with format string
+ *                        <tt>comment</tt>.
+ *
  * The main advantage of this macro is that it prints the values of its argument on failures.  Note that the
  * <tt>operator&lt;&lt;</tt> to the type of <tt>std::cerr</tt> has to be defined for the type of both expression
  * parameters.  Otherwise, simply use the equivalent SEQAN_ASSERT call.
- * 
+ *
  * See SEQAN_CHECK and SEQAN_FAIL for (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_GEQ(1, 1);  // will run through
  * SEQAN_ASSERT_GEQ(0, 1);  // will not run through
@@ -2234,23 +2119,29 @@ SEQAN_DEFINE_TEST(test_skipped)
  */
 
 /*!
- * @macro SEQAN_ASSERT_IN_DELTA
- * 
- * @brief Test that the given expression can be coerced to <tt>true</tt>.
- * 
+ * @macro AssertMacros#SEQAN_ASSERT_IN_DELTA
+ *
+ * @brief Test that a value <tt>y</tt> lies within an <tt>delta</tt> environment of a value <tt>x</tt>.
+ *
  * @signature SEQAN_ASSERT_IN_DELTA(x, y, delta);
  * @signature SEQAN_ASSERT_IN_DELTA_MSG(x, y, delta, comment[, parameters]);
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] x           The value to center the environment in.
+ * @param[in] y           The value to check whether it falls within the environment.
+ * @param[in] delta       The environment size.
+ * @param[in] comment     A C-string (<tt>char const *</tt>) to use as a format string for printing a message
+ *                        on failure.
+ * @param[in] parameters  An optional parameter that is put into <tt>printf()</tt> with format string
+ *                        <tt>comment</tt>.
+ *
  * The main advantage of this macro is that it prints the values of its argument on failures.  Note that the
  * <tt>operator&lt;&lt;</tt> to the type of <tt>std::cerr</tt> has to be defined for the type of both expression
  * parameters.  Otherwise, simply use the equivalent SEQAN_ASSERT call.
- * 
+ *
  * See SEQAN_CHECK and SEQAN_FAIL for (conditionally) aborting your program regardless of debug settings.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_ASSERT_IN_DELTA(0, 0, 0.1);  // will run through
  * SEQAN_ASSERT_IN_DELTA(1, -2, 1);  // will fail
@@ -2259,209 +2150,6 @@ SEQAN_DEFINE_TEST(test_skipped)
  * @endcode
  */
 
-/**
-.Macro.SEQAN_ASSERT
-..cat:Assertions
-..summary:Test that the given expression can be coerced to $true$.
-..signature:SEQAN_ASSERT(expression)
-..signature:SEQAN_ASSERT_MSG(expression, message[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT(0);  // will fail
-SEQAN_ASSERT(1);  // will run through
-SEQAN_ASSERT_MSG(0, "message %d", 2);  // Will fail with message.
-..see:Macro.SEQAN_ASSERT_NOT
-..see:Macro.SEQAN_ASSERT_EQ
-..see:Macro.SEQAN_ASSERT_NEQ
-..see:Macro.SEQAN_ASSERT_LEQ
-..see:Macro.SEQAN_ASSERT_GEQ
-..see:Macro.SEQAN_ASSERT_LT
-..see:Macro.SEQAN_ASSERT_GT
-..see:Macro.SEQAN_ASSERT_IN_DELTA
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
-
-.Macro.SEQAN_ASSERT_NOT
-..cat:Assertions
-..summary:Test that the given expression can be coerced to $false$.
-..signature:SEQAN_ASSERT(expression)
-..signature:SEQAN_ASSERT_MSG(expression, message[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT_NOT(0);  // will run through
-SEQAN_ASSERT_NOT(1);  // will fail
-SEQAN_ASSERT_NOT_MSG(0, "msg %s", "test");  // will fail with message
-..see:Macro.SEQAN_ASSERT
-..see:Macro.SEQAN_ASSERT_EQ
-..see:Macro.SEQAN_ASSERT_NEQ
-..see:Macro.SEQAN_ASSERT_LEQ
-..see:Macro.SEQAN_ASSERT_GEQ
-..see:Macro.SEQAN_ASSERT_LT
-..see:Macro.SEQAN_ASSERT_GT
-..see:Macro.SEQAN_ASSERT_IN_DELTA
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
-
-.Macro.SEQAN_ASSERT_EQ
-..cat:Assertions
-..summary:Test that two given expressions are equal, as defined by the matching call to the $operator=(,)$.
-..signature:SEQAN_ASSERT_EQ(expression1, expression2)
-..signature:SEQAN_ASSERT_EQ_MSG(expression1, expression2, comment[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT_EQ(0, false);  // will run through
-SEQAN_ASSERT_EQ(1, false);  // will fail
-SEQAN_ASSERT_EQ(1, "foo");  // will not compile
-SEQAN_ASSERT_EQ_MSG(1, false, "msg");  // will fail with message
-..see:Macro.SEQAN_ASSERT
-..see:Macro.SEQAN_ASSERT_NOT
-..see:Macro.SEQAN_ASSERT_NEQ
-..see:Macro.SEQAN_ASSERT_LEQ
-..see:Macro.SEQAN_ASSERT_GEQ
-..see:Macro.SEQAN_ASSERT_LT
-..see:Macro.SEQAN_ASSERT_GT
-..see:Macro.SEQAN_ASSERT_IN_DELTA
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
-
-.Macro.SEQAN_ASSERT_NEQ
-..cat:Assertions
-..summary:Test that two given expressions are not equal, as defined by the matching call to the $operator!=(,)$.
-..signature:SEQAN_ASSERT_NEQ(expression)
-..signature:SEQAN_ASSERT_NEQ_MSG(expression, message[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT_NEQ(0, false);  // will fail
-SEQAN_ASSERT_NEQ(1, false);  // will run through
-SEQAN_ASSERT_NEQ(1, "foo");  // will not compile
-SEQAN_ASSERT_NEQ_MSG(1, false, "msg");  // will fail with message
-..see:Macro.SEQAN_ASSERT
-..see:Macro.SEQAN_ASSERT_NOT
-..see:Macro.SEQAN_ASSERT_EQ
-..see:Macro.SEQAN_ASSERT_LEQ
-..see:Macro.SEQAN_ASSERT_GEQ
-..see:Macro.SEQAN_ASSERT_LT
-..see:Macro.SEQAN_ASSERT_GT
-..see:Macro.SEQAN_ASSERT_IN_DELTA
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
-
-.Macro.SEQAN_ASSERT_LT
-..cat:Assertions
-..summary:Test that the two given expressions are in the less-than relation as defined by the matching call to operator<(,).
-..signature:SEQAN_ASSERT_LT(expression1, expression2)
-..signature:SEQAN_ASSERT_LT(expression1, expression2, comment[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT_LT(0, 1);  // will run through
-SEQAN_ASSERT_LT(1, 1);  // will not run through
-SEQAN_ASSERT_LT_MSG(1, 1, "msg");  // will fail with message
-..see:Macro.SEQAN_ASSERT
-..see:Macro.SEQAN_ASSERT_NOT
-..see:Macro.SEQAN_ASSERT_EQ
-..see:Macro.SEQAN_ASSERT_NEQ
-..see:Macro.SEQAN_ASSERT_LEQ
-..see:Macro.SEQAN_ASSERT_GEQ
-..see:Macro.SEQAN_ASSERT_GT
-..see:Macro.SEQAN_ASSERT_IN_DELTA
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
-
-.Macro.SEQAN_ASSERT_LEQ
-..cat:Assertions
-..summary:Test that the two given expressions are in the less-than-or-equal relation as defined by the matching call to operator<=(,).
-..signature:SEQAN_ASSERT_LEQ(expression1, expression2)
-..signature:SEQAN_ASSERT_LEQ_MSG(expression1, expression2, comment[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT_LEQ(1, 1);  // will run through
-SEQAN_ASSERT_LEQ(1, 2);  // will not run through
-SEQAN_ASSERT_LEQ_MSG(1, 2, "msg");  // will fail with message
-..see:Macro.SEQAN_ASSERT
-..see:Macro.SEQAN_ASSERT_NOT
-..see:Macro.SEQAN_ASSERT_EQ
-..see:Macro.SEQAN_ASSERT_NEQ
-..see:Macro.SEQAN_ASSERT_GEQ
-..see:Macro.SEQAN_ASSERT_LT
-..see:Macro.SEQAN_ASSERT_GT
-..see:Macro.SEQAN_ASSERT_IN_DELTA
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
-
-.Macro.SEQAN_ASSERT_GT
-..cat:Assertions
-..summary:Test that the two given expressions are in the greather-than relation as defined by the matching call to operator>(,).
-..signature:SEQAN_ASSERT_GT(expression1, expression2)
-..signature:SEQAN_ASSERT_GT_MSG(expression1, expression2, comment[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT_GT(2, 1);  // will run through
-SEQAN_ASSERT_GT(1, 1);  // will not run through
-SEQAN_ASSERT_GT_MSG(1, 1, "msg");  // will fail with message
-..see:Macro.SEQAN_ASSERT
-..see:Macro.SEQAN_ASSERT_NOT
-..see:Macro.SEQAN_ASSERT_EQ
-..see:Macro.SEQAN_ASSERT_NEQ
-..see:Macro.SEQAN_ASSERT_LEQ
-..see:Macro.SEQAN_ASSERT_GEQ
-..see:Macro.SEQAN_ASSERT_LT
-..see:Macro.SEQAN_ASSERT_IN_DELTA
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
-
-.Macro.SEQAN_ASSERT_GEQ
-..cat:Assertions
-..summary:Test that the two given expressions are in the greater-than-or-equal relation as defined by the matching call to operator>=(,).
-..signature:SEQAN_ASSERT_GEQ(expression1, expression2)
-..signature:SEQAN_ASSERT_GEQ_MSG(expression1, expression2, comment[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT_GEQ(1, 1);  // will run through
-SEQAN_ASSERT_GEQ(0, 1);  // will not run through
-SEQAN_ASSERT_GEQ_MSG(0, 1, "msg");  // will fail with message
-..see:Macro.SEQAN_ASSERT
-..see:Macro.SEQAN_ASSERT_NOT
-..see:Macro.SEQAN_ASSERT_EQ
-..see:Macro.SEQAN_ASSERT_NEQ
-..see:Macro.SEQAN_ASSERT_LEQ
-..see:Macro.SEQAN_ASSERT_LT
-..see:Macro.SEQAN_ASSERT_GT
-..see:Macro.SEQAN_ASSERT_IN_DELTA
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
-
-.Macro.SEQAN_ASSERT_IN_DELTA
-..cat:Assertions
-..summary:Test that the given expression can be coerced to $true$.
-..signature:SEQAN_ASSERT_IN_DELTA(x, y, delta)
-..signature:SEQAN_ASSERT_IN_DELTA_MSG(x, y, delta, comment[, parameters])
-..remarks:The main advantage of this macro is that it prints the values of its argument on failures. Note that the $operator<<$ to the type of $std::cerr$ has to be defined for the type of both expression parameters. Otherwise, simply use the equivalent @Macro.SEQAN_ASSERT@ call.
-..remarks:See @Macro.SEQAN_CHECK@ and @Macro.SEQAN_FAIL@ for (conditionally) aborting your program regardless of debug settings.
-..example.code:
-SEQAN_ASSERT_IN_DELTA(0, 0, 0.1);  // will run through
-SEQAN_ASSERT_IN_DELTA(1, -2, 1);  // will fail
-SEQAN_ASSERT_IN_DELTA(1, "foo");  // will not compile
-SEQAN_ASSERT_IN_DELTA_MSG(1, 0, 0.1, "msg");  // will fail with message
-..see:Macro.SEQAN_ASSERT
-..see:Macro.SEQAN_ASSERT_NOT
-..see:Macro.SEQAN_ASSERT_EQ
-..see:Macro.SEQAN_ASSERT_NEQ
-..see:Macro.SEQAN_ASSERT_LEQ
-..see:Macro.SEQAN_ASSERT_GEQ
-..see:Macro.SEQAN_ASSERT_LT
-..see:Macro.SEQAN_ASSERT_GT
-..see:Macro.SEQAN_CHECK
-..see:Macro.SEQAN_FAIL
- */
-
 // Force a test failure.
 //
 // Usage:  SEQAN_ASSERT_FAIL("Failed at position %d", pos);
@@ -2956,53 +2644,30 @@ void SEQAN_ASSERT_NOT_MSG(T1 const & _arg1, const char * comment, ...) {}
 /*!
  * @macro SEQAN_PATH_TO_ROOT
  * @headerfile <seqan/basic.h>
- * @brief Return path to the checkout root directory (i.e. containing core/extras).
- * 
+ * @brief Return path to the checkout root directory.
+ *
  * @signature TCharPtr SEQAN_PATH_TO_ROOT()
- * 
+ *
  * @return TCharPtr <tt>char const *</tt>, string with the path to the parent directory of the tests directory.
- * 
- * This only works when using the SeqAn SVN checkout!
- * 
- * @section Remarks
- * 
- * The pointed to string is initialized on program startup by the code generated by SEQAN_BEGIN_TESTSUITE.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
- * const char *p = SEQAN_PATH_TO_ROOT);
- * char buffer[1000];
- * strcpy(buffer, p);
- * strcat(buffer, "/tests/files/example.txt");
- * FILE *f = fopen(buffer, "w");
+ * CharString buffer = SEQAN_PATH_TO_ROOT();
+ * append(buffer, "/tests/files/example.txt");
+ *
+ * FILE *f = fopen(toCString(buffer), "w");
  * fprintf(f, "Test Data");
  * fclose(f);
  * @endcode
  *
+ * @deprecated Unsafe.
+ * @see getAbsolutePath
+
  * @see SEQAN_TEMP_FILENAME
  */
 
 // TODO(holtgrew): Subject to change wiht restructuring.
-/**
-.Macro.SEQAN_PATH_TO_ROOT
-..cat:Testing & Debugging
-..summary:Return path to the checkout root directory (i.e. containing core/extras).
-..description.note:This only works when using the SeqAn SVN checkout!
-..returns:$char const *$, string with the path to the parent directory of the tests directory.
-..signature:SEQAN_PATH_TO_ROOT()
-..remarks:The pointed to string is initialized on program startup by the code generated by @Macro.SEQAN_BEGIN_TESTSUITE@.
-..example.code:
-const char *p = SEQAN_PATH_TO_ROOT);
-char buffer[1000];
-strcpy(buffer, p);
-strcat(buffer, "/tests/files/example.txt");
-FILE *f = fopen(buffer, "w");
-fprintf(f, "Test Data");
-fclose(f);
-..see:Macro.SEQAN_TEMP_FILENAME
- */
-
 // Returns a const char * string with the path to the projects directory.
 #define SEQAN_PATH_TO_ROOT()                      \
     ::seqan::ClassTest::StaticData::pathToRoot()
@@ -3016,18 +2681,18 @@ fclose(f);
  * @macro SEQAN_TEMP_FILENAME
  * @headerfile <seqan/basic.h>
  * @brief Generates the name to a temporary file.
- * 
+ *
  * @signature TCharType SEQAN_TEMP_FILENAME();
- * 
+ *
  * @return TCharType <tt>char const *</tt>, string with the path to a temporary file.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The pointed to string is stored in a buffer and is overwritten by the next call to this macro. Copy it out if you
  * need it.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * const char *p = SEQAN_TEMP_FILENAME();
  * buffer char tempFilename[1000];
@@ -3039,46 +2704,10 @@ fclose(f);
  * @see SEQAN_PATH_TO_ROOT
  */
 
-/**
-.Macro.SEQAN_TEMP_FILENAME
-..cat:Testing & Debugging
-..summary:Generates the name to a temporary file.
-..returns:$char const *$, string with the path to a temporary file.
-..signature:SEQAN_TEMP_FILENAME()
-..remarks:The pointed to string is stored in a buffer and is overwritten by the next call to this macro. Copy it out if you need it.
-..example.code:
-const char *p = SEQAN_TEMP_FILENAME();
-buffer char tempFilename[1000];
-strcpy(tempFilename, p);
-FILE *f = fopen(tempFilename, "w");
-fprintf(f, "Test Data");
-fclose(f);
-..see:Macro.SEQAN_PATH_TO_ROOT
- */
-
 // Returns a temporary filename.
 #define SEQAN_TEMP_FILENAME() (::seqan::ClassTest::tempFileName())
 
 
-/**
-.Macro.SEQAN_VERIFY_CHECKPOINTS
-..cat:Testing & Debugging
-..summary:Verify check points for the given file name.
-..signature:SEQAN_VERIFY_CHECKPOINTS(path)
-..param.path:Path to the file to verify check points for. Relative to parent directory of tests.
-..example.code:
-SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/basic_alphabet.h");
-..see:Macro.SEQAN_CHECKPOINT
-
-.Macro.SEQAN_CHECKPOINT
-..cat:Testing & Debugging
-..summary:Generate a check point.
-..signature:SEQAN_CHECKPOINT
-..remarks:Whever the code executes the instructions generated by this macro, the check point for this line will be set in global testing state. Use @Macro.SEQAN_VERIFY_CHECKPOINTS@ to verify whether all checkpoints have been reached in a file up to this point.
-SEQAN_CHECKPOINT;
-..see:Macro.SEQAN_VERIFY_CHECKPOINTS
- */
-
 #if SEQAN_ENABLE_CHECKPOINTS
 
 // Create a check point at the point where the macro is placed.
@@ -3120,6 +2749,26 @@ SEQAN_CHECKPOINT;
 
 #endif  // #if !SEQAN_ENABLE_TESTING
 
+
+// ----------------------------------------------------------------------------
+// Function getAbsolutePath()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn getAbsolutePath
+ * @headerfile <seqan/basic.h>
+ * @brief Returns absolute path for a filename within the source repository.
+ *
+ * @signature std::string getAbsolutePath(const char * filename)
+ *
+ * @return <tt>std::string</tt>, absolute path for a filename within the source repository.
+ */
+
+inline std::string getAbsolutePath(const char * path)
+{
+    return std::string(SEQAN_PATH_TO_ROOT()) + path;
+}
+
 }  // namespace seqan
 
-#endif  // SEQAN_CORE_INCLUDE_SEQAN_BASIC_DEBUG_TEST_SYSTEM_H_
+#endif  // SEQAN_INCLUDE_SEQAN_BASIC_DEBUG_TEST_SYSTEM_H_
diff --git a/seqan/basic/fundamental_chunking.h b/seqan/basic/fundamental_chunking.h
new file mode 100644
index 0000000..976d0bf
--- /dev/null
+++ b/seqan/basic/fundamental_chunking.h
@@ -0,0 +1,148 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CHUNKING_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CHUNKING_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Direction Tags
+// --------------------------------------------------------------------------
+
+/*!
+ * @defgroup DirectionTags Direction Tags
+ * @brief Tags for selecting a direction.
+ */
+
+/*!
+ * @tag DirectionTags#Input
+ * @headerfile <seqan/basic.h>
+ * @brief Tag for selecting the input direction.
+ *
+ * @signature typedef Tag<Input_> Input;
+ */
+
+struct Input_;
+typedef Tag<Input_> Input;
+
+/*!
+ * @tag DirectionTags#Output
+ * @headerfile <seqan/basic.h>
+ * @brief Tag for selecting the output direction.
+ *
+ * @signature typedef Tag<Output_> Output;
+ */
+
+struct Output_;
+typedef Tag<Output_> Output;
+
+/*!
+ * @tag DirectionTags#Bidirectional
+ * @headerfile <seqan/basic.h>
+ * @brief Tag for allowing both input and output.
+ *
+ * @signature typedef Tag<Bidirectional_> Bidirectional;
+ */
+
+struct Bidirectional_;
+typedef Tag<Bidirectional_> Bidirectional;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction Chunk
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn Chunk
+ * @headerfile <seqan/basic.h>
+ * @brief Return the chunk type for an object.
+ *
+ * @signature Chunk<TObject>::Type;
+ *
+ * @tparam TObject The object to query for its chunk type.
+ * @return Type    The chunk type of <tt>TObject</tt>.
+ *
+ * The default result type (if not overloaded) is @link Nothing @endlink.
+ */
+
+// Chunking is only supported for selected objects
+template <typename TObject>
+struct Chunk
+{
+    typedef Nothing Type;   // disabled by default
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function reserveChunk()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator, typename TSize, typename TDirection>
+inline void reserveChunk(TIterator &, TSize, TDirection)
+{}
+
+// ----------------------------------------------------------------------------
+// Function getChunk()
+// ----------------------------------------------------------------------------
+
+template <typename TChunk, typename TIterator, typename TDirection>
+inline Nothing getChunk(TChunk &, TIterator &, TDirection)
+{
+    return Nothing();
+}
+
+// ----------------------------------------------------------------------------
+// Function advanceChunk()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator, typename TSize>
+inline void advanceChunk(TIterator &iter, TSize size)
+{
+    iter += size;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CHUNKING_H_
diff --git a/seqan/basic/fundamental_comparison.h b/seqan/basic/fundamental_comparison.h
index 4e20a2c..eeccdb5 100644
--- a/seqan/basic/fundamental_comparison.h
+++ b/seqan/basic/fundamental_comparison.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Basic comparison code.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_FUNDAMENTAL_COMPARISON_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_FUNDAMENTAL_COMPARISON_H_
+#ifndef SEQAN_INCLUDE_SEQAN_FUNDAMENTAL_COMPARISON_H_
+#define SEQAN_INCLUDE_SEQAN_FUNDAMENTAL_COMPARISON_H_
 
 namespace seqan {
 
@@ -61,25 +61,23 @@ template <typename TValue> SEQAN_HOST_DEVICE inline typename ValueSize<TValue>::
  * @mfn CompareType
  * @headerfile <seqan/basic.h>
  * @brief Type to convert other types for comparisons.
- * 
+ *
  * @signature CompareType<T1, T2>::Type;
- * 
+ *
  * @tparam T2 Type of the right operand of a comparison.
  * @tparam T1 Type of the left operand of a comparison.
- * 
+ *
  * @return Type The resulting type to convert other type to.
- * 
- * @section Remarks
- * 
- * Comparisons are for example operators like <tt>==</tt> or <tt><</tt>.
- * 
+ *
+ * Comparisons are for example operators like <tt>==</tt> or <tt>&lt;</tt>.
+ *
  * Do not implement, implement CompareTypeImpl instead.
- * 
+ *
  * Note that there is no rule that guarantees that <tt>CompareType&lt;T1, T2&gt;::Type</tt> is the same as
  * <tt>CompareType&lt;T2, T1&gt;::Type</tt>.  It is also possible, that only one of these two types is defined.
- * 
+ *
  * This metafunction is used for the implementation of comparisons that involve SimpleType.
- * 
+ *
  * @see CompareTypeImpl
  */
 
@@ -87,52 +85,21 @@ template <typename TValue> SEQAN_HOST_DEVICE inline typename ValueSize<TValue>::
  * @mfn CompareTypeImpl
  * @headerfile <seqan/basic.h>
  * @brief Implementation of CompareType.
- * 
+ *
  * @signature CompareTypeImpl<T1, T2>::Type;
- * 
+ *
  * @tparam T2 Type of the right operand of a comparison.
  * @tparam T1 Type of the left operand of a comparison.
- * 
+ *
  * @return Type The type to use for the comparison.
- * 
+ *
  * @see CompareType
  */
 
-/**
-.Metafunction.CompareType
-..cat:Basic
-..summary:Type to convert other types for comparisons.
-..signature:CompareType<T1, T2>::Type
-..param.T1:Type of the left operand of a comparison.
-..param.T2:Type of the right operand of a comparison.
-..return.type:The Type in which the arguments are converted in order to compare them.
-..remarks:Comparisons are for example operators like $==$ or $<$.
-..remarks:Do not implement, implement @Metafunction.CompareTypeImpl@ instead.
-..remarks.text:Note that there is no rule that guarantees that $CompareType<T1, T2>::Type$
-is the same as $CompareType<T2, T1>::Type$. It is also possible, that only one of these
-two types is defined.
-..see:Metafunction.CompareTypeImpl
-..remarks.text:This metafunction is used for the implementation of
-comparisons that involve @Class.SimpleType@.
-..include:seqan/basic.h
-
-.Metafunction.CompareTypeImpl
-..cat:Basic
-..summary:Implementation of @Metafunction.CompareType@.
-..signature:CompareType<T1, T2>::Type
-..param.T1:Type of the left operand of a comparison.
-..param.T2:Type of the right operand of a comparison.
-..return.type:The Type in which the arguments are converted in order to compare them.
-..see:Metafunction.CompareType
-..include:seqan/basic.h
-*/
-
 // Given two types, the CompareType is a type that both types can be cast to
 // and where the results are then used to compare two values.
 
-template <typename T1, typename T2>
-struct CompareType;
-
+// step 3: choose the actual comparison type
 template <typename T1, typename T2>
 struct CompareTypeImpl;
 
@@ -142,13 +109,15 @@ struct CompareTypeImpl<T, T>
     typedef T Type;
 };
 
+// step 2: disolve all iterator proxies (see proxy_iterator.h)
 template <typename T1, typename T2>
-struct CompareType
-{
-    typedef typename RemoveConst<T1>::Type T1_;
-    typedef typename RemoveConst<T2>::Type T2_;
-    typedef typename CompareTypeImpl<T1_, T2_>::Type Type;
-};
+struct CompareTypeRemoveProxy:
+    CompareTypeImpl<T1, T2> {};
+
+// step 1: remove const from types
+template <typename T1, typename T2>
+struct CompareType:
+    CompareTypeRemoveProxy<typename RemoveConst<T1>::Type, typename RemoveConst<T2>::Type> {};
 
 // ============================================================================
 // Functions
@@ -177,4 +146,4 @@ SEQAN_HOST_DEVICE inline bool ordGreater(TValue1 const & left, TValue2 const & r
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_FUNDAMENTAL_COMPARISON_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_FUNDAMENTAL_COMPARISON_H_
diff --git a/seqan/basic/fundamental_concepts.h b/seqan/basic/fundamental_concepts.h
index eaa7ba7..c9984ff 100644
--- a/seqan/basic/fundamental_concepts.h
+++ b/seqan/basic/fundamental_concepts.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,11 +36,31 @@
 
 // SEQAN_NO_GENERATED_FORWARDS
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONCEPTS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONCEPTS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONCEPTS_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONCEPTS_H_
 
 namespace seqan {
 
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// TODO(holtgrew): Document all the other concepts as well.
+
+/*!
+ * @concept NumberConcept
+ * @headerfile <seqan/basic.h>
+ * @brief Concept for numbers.
+ */
+
+SEQAN_CONCEPT(FundamentalConcept, (T));
+SEQAN_CONCEPT(IntegralConcept, (T));
+SEQAN_CONCEPT(NumberConcept, (T));
+SEQAN_CONCEPT(CharConcept, (T));
+SEQAN_CONCEPT(IntegerConcept, (T));
+SEQAN_CONCEPT(SignedIntegerConcept, (T));
+SEQAN_CONCEPT(UnsignedIntegerConcept, (T));
+
 // ---------------------------------------------------------------------------
 // ==> boost/concept_check.hpp <==
 // ---------------------------------------------------------------------------
@@ -62,13 +82,13 @@ namespace seqan {
  * @brief A type with a default constructor.
  *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature DefaultConstructible<T>
- * 
+ *
  * Expects an instance of type <tt>T</tt> to be default constructible.
- * 
+ *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * T()
  * T a;
@@ -79,25 +99,9 @@ namespace seqan {
  * @see DestructibleConcept
  */
 
-/**
-.Concept.DefaultConstructibleConcept
-..cat:Basic
-..summary:A type with a default constructor.
-..signature:DefaultConstructible<T>
-..remarks:
-...text:Expects an instance of type $T$ to be default constructible.
-..example.text:Valid expressions:
-..example.code:
-T()
-T a;
-..include:seqan/basic.h
-..see:Concept.AssignableConcept
-..see:Concept.CopyConstructibleConcept
-*/
-
 SEQAN_CONCEPT(DefaultConstructible,(T))
 {
-    SEQAN_CONCEPT_USAGE(DefaultConstructible) 
+    SEQAN_CONCEPT_USAGE(DefaultConstructible)
     {
         T a;                // require default constructor
         ignoreUnusedVariableWarning(a);
@@ -107,15 +111,15 @@ SEQAN_CONCEPT(DefaultConstructible,(T))
 /*!
  * @concept DestructibleConcept
  * @brief A type with a destructor.
- * 
+ *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature Destructible<T>
- * 
+ *
  * Expects an instance of type <tt>T</tt> to be destructible.
- * 
+ *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * T()
  * T a;
@@ -124,24 +128,9 @@ SEQAN_CONCEPT(DefaultConstructible,(T))
  * @see DefaultConstructibleConcept
  */
 
-/**
-.Concept.DestructibleConcept
-..cat:Basic
-..summary:A type with a destructor.
-..signature:Destructible<T>
-..remarks:
-...text:Expects an instance of type $T$ to be destructible.
-..example.text:Valid expressions:
-..example.code:
-T()
-T a;
-..include:seqan/basic.h
-..see:Concept.DefaultConstructibleConcept
-*/
-
 SEQAN_CONCEPT(Destructible, (T))
 {
-    SEQAN_CONCEPT_USAGE(Destructible) 
+    SEQAN_CONCEPT_USAGE(Destructible)
     {
         // It is hard to test this.
     }
@@ -152,13 +141,13 @@ SEQAN_CONCEPT(Destructible, (T))
  * @brief A type with an assignment operator.
  *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature Assignable<T>
- * 
+ *
  * Expects instances of type <tt>T</tt> to be assignable into each other.
- * 
+ *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * a = b;  // a, b are of type T
  * @endcode
@@ -175,27 +164,11 @@ SEQAN_CONCEPT(Destructible, (T))
  * @signature T & T::operator=(T const & other);
  */
 
-/**
-.Concept.AssignableConcept
-..cat:Basic
-..summary:A type with an assignment operator.
-..signature:Assignable<T>
-..remarks:
-...text:Expects instances of type $T$ to be assignable into each other.
-..example.text:Valid expressions:
-..example.code:
-a = b;  // a, b are of type T
-..include:seqan/basic.h
-
-.Function.assign.concept:Concept.AssignableConcept
-.Function.operator=.concept:Concept.AssignableConcept
-*/
-
 // TODO(holtgrew): Test availability of assign() function?
 
 SEQAN_CONCEPT(Assignable,(T))
 {
-    SEQAN_CONCEPT_USAGE(Assignable) 
+    SEQAN_CONCEPT_USAGE(Assignable)
     {
 #if !defined(_ITERATOR_)    // back_insert_iterator broken for VC++ STL
         a = b;              // require assignment operator
@@ -203,7 +176,7 @@ SEQAN_CONCEPT(Assignable,(T))
         constConstraints(b);
     }
 private:
-    void constConstraints(const T& x) 
+    void constConstraints(const T& x)
     {
 #if !defined(_ITERATOR_)    // back_insert_iterator broken for VC++ STL
         a = x;              // const required for argument to assignment
@@ -216,37 +189,99 @@ SEQAN_CONCEPT(Assignable,(T))
     T b;
 };
 
+template <typename T>
+struct Is<Assignable<T> > :
+    Is<FundamentalConcept<T> > {};
+
+
+/*!
+ * @concept ConvertibleConcept
+ * @brief A type that can be converted into another.
+ *
+ * @headerfile <seqan/basic.h>
+ *
+ * @signature Convertible<T, S>
+ *
+ * Expects instances of type <tt>S</tt> to be assignable to instances of type <tt>T</tt>.
+ *
+ * @section Valid Expressions
+ *
+ * @code{.cpp}
+ * t = s;  // t, s are of type T, S
+ * @endcode
+ *
+ * @see AssignableConcept
+ */
+
+/*!
+ * @fn ConvertibleConcept::operator=
+ * @brief C++ built-in assignment operator.
+ *
+ * The C++ standard requires the assignment operator to be a member function.
+ *
+ * @signature T & T::operator=(S const & other);
+ */
+
+SEQAN_CONCEPT(Convertible,(T)(S))
+{
+    SEQAN_CONCEPT_USAGE(Convertible)
+    {
+#if !defined(_ITERATOR_)    // back_insert_iterator broken for VC++ STL
+        t = s;              // require assignment operator
+#endif
+        constConstraints(s);
+    }
+private:
+    void constConstraints(const S& x)
+    {
+#if !defined(_ITERATOR_)    // back_insert_iterator broken for VC++ STL
+        t = x;              // const required for argument to assignment
+#else
+        ignoreUnusedVariableWarning(x);
+#endif
+    }
+private:
+    T t;
+    S s;
+};
+
+template <typename T>
+struct Is<Convertible<T, T> > :
+    Is<Assignable<T> > {};
+
+template <typename T>
+struct Is<Convertible<T, T const> > :
+    Is<Assignable<typename RemoveConst<T>::Type> > {};
+
+template <typename T, typename S>
+struct Is<Convertible<T, S> > :
+    And< Is< FundamentalConcept<T> >,
+         Is< FundamentalConcept<S> > > {};
+
+template <typename T, typename S>
+struct Is<Convertible<T, S const> > :
+    Is<Convertible<T, typename RemoveConst<S>::Type> > {};
+
 /*!
  * @concept CopyConstructibleConcept
  * @brief A type with a copy-constructor.
- * 
+ *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature CopyConstructible<T>
- * 
+ *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * T a(b);  // b is of type T
  * @endcode
- * 
+ *
  * @see DefaultConstructibleConcept
  */
 
-/**
-.Concept.CopyConstructibleConcept
-..cat:Basic
-..summary:A type with a copy-constructor.
-..signature:CopyConstructible<T>
-..example.text:Valid expressions:
-..example.code:
-T a(b);  // b is of type T
-..include:seqan/basic.h
-*/
-
 SEQAN_CONCEPT(CopyConstructible,(T))
 {
-    SEQAN_CONCEPT_USAGE(CopyConstructible) 
+    SEQAN_CONCEPT_USAGE(CopyConstructible)
     {
         T a(b);            // require copy constructor
         T* ptr = &a;       // require address of operator
@@ -254,7 +289,7 @@ SEQAN_CONCEPT(CopyConstructible,(T))
         ignoreUnusedVariableWarning(ptr);
     }
 private:
-    void constConstraints(const T& a) 
+    void constConstraints(const T& a)
     {
         T c(a);            // require const copy constructor
         const T* ptr = &a; // require const address of operator
@@ -280,7 +315,7 @@ SEQAN_CONCEPT(CopyConstructible,(T))
 // For now we just test for convertible to bool.
 
 /*!
- * @fn requireBooleanExpr
+ * @fn ConceptChecking#requireBooleanExpr
  * @headerfile <seqan/basic.h>
  * @brief Tests for a boolean expression.
  *
@@ -290,21 +325,11 @@ SEQAN_CONCEPT(CopyConstructible,(T))
  *
  * This function can be used to test for functions returning bools, e.g. less operators.
  *
- * @see SEQAN_CONCEPT_USAGE
+ * @see ConceptChecking#SEQAN_CONCEPT_USAGE
  */
 
-/**
-.Function.requireBooleanExpr
-..summary:Tests for a boolean expression.
-..cat:Concepts
-..signature:requireBooleanExpr(x)
-..param.x: Object that must be convertible to $bool$.
-..remarks:This function can be used to test for available boolean functions, e.g. less operators.
-..include:seqan/basic.h
-..see:Macro.SEQAN_CONCEPT_USAGE
- */
 template <class T>
-void requireBooleanExpr(const T& t) 
+void requireBooleanExpr(const T& t)
 {
     bool x = t;
     ignoreUnusedVariableWarning(x);
@@ -314,21 +339,21 @@ void requireBooleanExpr(const T& t)
 /*!
  * @concept EqualityComparableConcept
  * @brief A type that can be equality compared.
- * 
+ *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature EqualityComparable<T>
- * 
+ *
  * @section Remarks
- * 
+ *
  * Expects instances of type <tt>T</tt> to be comparable via <tt>operator==</tt>
  * and <tt>operator!=</tt>. Comparison operators must return boolean convertible
  * values. <tt>operator==</tt> must be an equivalence relation.
- * 
+ *
  * @section Examples
- * 
+ *
  * Valid expressions:
- * 
+ *
  * @code{.cpp}
  * a == b;
  * a != b;
@@ -341,7 +366,7 @@ void requireBooleanExpr(const T& t)
  *  <li><tt>(a == b)</tt> => <tt> (b == a)</tt> (symmetry)</li>
  *  <li> <tt>(a == b) &amp;&amp;(b == c)</tt> => <tt>(a == c)</tt> (transitivity)</li>
  * </ul>
- * 
+ *
  * @see ComparableConcept
  */
 
@@ -372,29 +397,9 @@ void requireBooleanExpr(const T& t)
  * @see EqualityComparableConcept::operator==
  */
 
-/**
-.Concept.EqualityComparableConcept
-..cat:Comparisons
-..summary:A type that can be equality compared.
-..signature:EqualityComparable<T>
-..remarks:
-...text:Expects instances of type $T$ to be comparable via $operator==$ and $operator!=$. 
-Comparison operators must return boolean convertible values.
-$operator==$ must be an equivalence relation.
-..example.text:Valid expressions:
-..example.code:
-a == b;
-a != b;
-..example.text:Invariants:\br
-$a==a$ (reflexivity)\nl
-$a==b$ \Rightarrow $b==a$ (symmetry)\nl
-$a==b$ and $b==c$ \Rightarrow $a==c$ (transitivity)
-..include:seqan/basic.h
-*/
-
 SEQAN_CONCEPT(EqualityComparable,(T))
 {
-    SEQAN_CONCEPT_USAGE(EqualityComparable) 
+    SEQAN_CONCEPT_USAGE(EqualityComparable)
     {
         requireBooleanExpr(a == b);
         requireBooleanExpr(a != b);
@@ -406,17 +411,17 @@ SEQAN_CONCEPT(EqualityComparable,(T))
 /*!
  * @concept LessThanComparableConcept
  * @brief A type that can be less-than compared.
- * 
+ *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature LessThanComparable<T>
- * 
+ *
  * Expects instances of type <tt>T</tt> to be comparable via <tt>operator<</tt>.
  * Comparison operator must return a boolean convertible value.
  * <tt>operator&lt;<tt> must be a partial ordering.
- * 
+ *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * a < b;
  * @endcode
@@ -427,7 +432,7 @@ SEQAN_CONCEPT(EqualityComparable,(T))
  *   <li><tt>!(b &lt; a)</tt> => <tt>a < b</tt> (antisymmetry)</li>
  *   <li><tt>(a &lt; b) &amp;&amp; (b < c)</tt> =&gt; <tt>a &lt; c</tt> (transitivity)</li>
  * </ul>
- * 
+ *
  * @see ComparableConcept
  */
 
@@ -438,30 +443,9 @@ SEQAN_CONCEPT(EqualityComparable,(T))
  * @signature bool T::operator<(T const & other) const;
  */
 
-/**
-.Concept.LessThanComparableConcept
-..cat:Comparisons
-..summary:A type that can be less-than compared.
-..signature:LessThanComparable<T>
-..remarks:
-...text:Expects instances of type $T$ to be comparable via $operator<$. 
-Comparison operator must return a boolean convertible value.
-$operator<$ must be a partial ordering.
-..example.text:Valid expressions:
-..example.code:
-a < b;
-..example.text:Invariants:\br
-$\not a<a$ (irreflexivity)\nl
-$a<b$ \Rightarrow $\not b<a$ (antisymmetry)\nl
-$a<b$ and $b<c$ \Rightarrow $a<c$ (transitivity)
-..include:seqan/basic.h
-
-.Function.operator<.concept:Concept.LessThanComparableConcept
-*/
-
 SEQAN_CONCEPT(LessThanComparable,(T))
 {
-    SEQAN_CONCEPT_USAGE(LessThanComparable) 
+    SEQAN_CONCEPT_USAGE(LessThanComparable)
     {
         requireBooleanExpr(a < b);
     }
@@ -474,16 +458,16 @@ SEQAN_CONCEPT(LessThanComparable,(T))
  * @extends EqualityComparableConcept
  * @extends LessThanComparableConcept
  * @brief A type that can be compared.
- * 
+ *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature Comparable<T>
- * 
+ *
  * Expects instances of type <tt>T</tt> to be comparable. Comparison operators
  * must return boolean convertible values.
- * 
+ *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * a < b;
  * a > b;
@@ -498,7 +482,7 @@ SEQAN_CONCEPT(LessThanComparable,(T))
  *   <li><tt>(a &lt;= b)</tt> <=> <tt>b &gt;= a</tt></li>
  *   <li><tt>(a == b)</tt> <=> <tt>(a &gt;= b) &amp;&amp; (b &gt;= a)</tt></li>
  * </ul>
- * 
+ *
  * @see EqualityComparableConcept
  * @see LessThanComparableConcept
  */
@@ -530,37 +514,10 @@ SEQAN_CONCEPT(LessThanComparable,(T))
  * This operator can be implemented as a member or a global function.
  */
 
-/**
-.Concept.ComparableConcept
-..cat:Comparisons
-..summary:A type that can be compared.
-..signature:Comparable<T>
-..baseconcept:Concept.LessThanComparableConcept
-..remarks:
-...text:Expects instances of type $T$ to be comparable. Comparison operators must return boolean convertible values.
-..example.text:Valid expressions:
-..example.code:
-a < b;
-a > b;
-a <= b;
-a >= b;
-..example.text:Invariants:\br
-$a<b$ \Leftrightarrow $b>a$\nl
-$a<=b$ \Leftrightarrow $b>=a$\nl
-$a<=b$ \Leftrightarrow $a<b$ or ($a<=b$ and $a>=b$)
-..include:seqan/basic.h
-..see:Concept.EqualityComparableConcept
-..see:Concept.LessThanComparableConcept
-
-.Function.operator<=.concept:Concept.ComparableConcept
-.Function.operator>.concept:Concept.ComparableConcept
-.Function.operator>=.concept:Concept.ComparableConcept
-*/
-
 // This is equiaent to SGI STL's LessThanComparable.
 SEQAN_CONCEPT(Comparable,(T))
 {
-    SEQAN_CONCEPT_USAGE(Comparable) 
+    SEQAN_CONCEPT_USAGE(Comparable)
     {
         requireBooleanExpr(a < b);
         requireBooleanExpr(a > b);
@@ -572,30 +529,36 @@ SEQAN_CONCEPT(Comparable,(T))
 };
 
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
-SEQAN_CONCEPT(IntegerConcept, (T));
-SEQAN_CONCEPT(SignedIntegerConcept, (T));
-SEQAN_CONCEPT(UnsignedIntegerConcept, (T));
-
 // ============================================================================
 // Test fulfilled concepts
 // ============================================================================
 
+template <typename T>
+struct Is< CharConcept<T> >
+{
+    typedef
+        // Explicitely unsigned.
+        typename IfC< IsSameType<T, char>::VALUE,           True,
+        typename IfC< IsSameType<T, signed char>::VALUE,    True,
+        typename IfC< IsSameType<T, unsigned short>::VALUE, True,
+        False
+        >::Type>::Type>::Type Type;
+        enum { VALUE = Type::VALUE };
+};
+
 template <typename T>
 struct Is< SignedIntegerConcept<T> >
 {
     typedef
         // Explicitely unsigned.
-        typename IfC< IsSameType<T, signed char>::VALUE,     True,
-        typename IfC< IsSameType<T, short>::VALUE,           True,
-        typename IfC< IsSameType<T, int>::VALUE,             True,
-        typename IfC< IsSameType<T, long>::VALUE,            True,
-        typename IfC< IsSameType<T, __int64>::VALUE,         True,
+        typename IfC< IsSameType<T, signed char>::VALUE,        True,
+        typename IfC< IsSameType<T, short>::VALUE,              True,
+        typename IfC< IsSameType<T, int>::VALUE,                True,
+        typename IfC< IsSameType<T, long>::VALUE,               True,
+        typename IfC< IsSameType<T, long long>::VALUE,          True,   // for the __int64 != long long
+        typename IfC< IsSameType<T, __int64>::VALUE,            True,
         False
-        >::Type>::Type>::Type>::Type>::Type Type;
+        >::Type>::Type>::Type>::Type>::Type>::Type Type;
         enum { VALUE = Type::VALUE };
 };
 
@@ -604,13 +567,14 @@ struct Is< UnsignedIntegerConcept<T> >
 {
     typedef
         // Explicitely unsigned.
-        typename IfC< IsSameType<T, unsigned char>::VALUE,   True,
-        typename IfC< IsSameType<T, unsigned short>::VALUE,  True,
-        typename IfC< IsSameType<T, unsigned int>::VALUE,    True,
-        typename IfC< IsSameType<T, unsigned long>::VALUE,   True,
-        typename IfC< IsSameType<T, __uint64>::VALUE,        True,
+        typename IfC< IsSameType<T, unsigned char>::VALUE,      True,
+        typename IfC< IsSameType<T, unsigned short>::VALUE,     True,
+        typename IfC< IsSameType<T, unsigned int>::VALUE,       True,
+        typename IfC< IsSameType<T, unsigned long>::VALUE,      True,
+        typename IfC< IsSameType<T, unsigned long long>::VALUE, True,   // for the __uint64 != unsigned long long
+        typename IfC< IsSameType<T, __uint64>::VALUE,           True,
         False
-        >::Type>::Type>::Type>::Type>::Type Type;
+        >::Type>::Type>::Type>::Type>::Type>::Type Type;
         enum { VALUE = Type::VALUE };
 };
 
@@ -629,6 +593,41 @@ struct Is< IntegerConcept<T> >
         enum { VALUE = Type::VALUE };
 };
 
+template <typename T>
+struct Is< NumberConcept<T> >
+{
+    typedef
+        typename IfC< IsSameType<T, float>::VALUE,              True,
+        typename IfC< IsSameType<T, double>::VALUE,             True,
+        typename IfC< IsSameType<T, long double>::VALUE,        True,
+        typename IfC< Is< IntegerConcept<T> >::VALUE,           True,
+        False
+        >::Type>::Type>::Type>::Type Type;
+        enum { VALUE = Type::VALUE };
+};
+
+template <typename T>
+struct Is< IntegralConcept<T> >
+{
+    typedef
+        typename IfC< IsSameType<T, bool>::VALUE,               True,
+        typename IfC< Is< IntegerConcept<T> >::VALUE,           True,
+        False
+        >::Type>::Type Type;
+        enum { VALUE = Type::VALUE };
+};
+
+template <typename T>
+struct Is< FundamentalConcept<T> >
+{
+    typedef
+        typename IfC< IsSameType<T, bool>::VALUE,               True,
+        typename IfC< Is< NumberConcept<T> >::VALUE,            True,
+        False
+        >::Type>::Type Type;
+        enum { VALUE = Type::VALUE };
+};
+
 template <typename T>
 struct Is< SignedIntegerConcept<T const> > : Is< SignedIntegerConcept<typename RemoveConst<T>::Type> > {};
 
@@ -638,88 +637,43 @@ struct Is< UnsignedIntegerConcept<T const> > : Is< UnsignedIntegerConcept<typena
 template <typename T>
 struct Is< IntegerConcept<T const> > : Is< IntegerConcept<typename RemoveConst<T>::Type> > {};
 
+template <typename T>
+struct Is< NumberConcept<T const> > : Is< NumberConcept<typename RemoveConst<T>::Type> > {};
 
-/**
-.Metafunction.IsSignedInteger:
-..cat:Basic
-..summary:Tests for a type to be of signed integral aue.
-..signature:IsSignedInteger<T>::Type
-..param.T:Type that is tested.
-..returns.param.Type:@Tag.Logical Values.True@, if $T$ is a signed integral type, @Tag.Logical Values.False@ otherwise.
-...default:@Tag.Logical Values.False@
-..status:deprecated, please use $Is<SignedIntegerConcept<T> >::Type$
-..include:seqan/basic.h
-..see:Metafunction.IsUnsignedInteger
- */
+template <typename T>
+struct Is< FundamentalConcept<T const> > : Is< FundamentalConcept<typename RemoveConst<T>::Type> > {};
 
-/**
-.Metafunction.IsUnsignedInteger:
-..cat:Basic
-..summary:Tests for a type to be of unsigned integral aue.
-..signature:IsUnsignedInteger<T>::Type
-..param.T:Type that is tested.
-..returns.param.Type:@Tag.Logical Values.True@, if $T$ is an unsigned integral type, @Tag.Logical Values.False@ otherwise.
-...default:@Tag.Logical Values.False@
-..status:deprecated, please use $Is<UnsignedIntegerConcept<T> >::Type$
-..include:seqan/basic.h
- */
 
 /*!
  * @mfn IsInteger
  * @brief Tests for a type to be of integral value.
- * @headerfile seqan/basic.h
- * 
+ * @headerfile <seqan/basic.h>
+ *
  * @signature IsInteger<T>::Type
- * 
+ *
  * @tparam T Type that is tested.
- * 
- * @return TReturn 
- * 
+ *
+ * @return Type Either True or False.
+ *
  * @deprecated Please use <tt>Is&lt;IntegerConcept&lt;T&gt; &gt;::Type</tt>.
- * 
+ *
  * @see IsIntegral
  */
 
-/**
-.Metafunction.IsInteger:
-..cat:Basic
-..summary:Tests for a type to be of integral aue.
-..signature:IsInteger<T>::Type
-..param.T:Type that is tested.
-..returns.param.Type:@Tag.Logical Values.True@, if $T$ is an ingegral type, @Tag.Logical Values.False@ otherwise.
-...default:@Tag.Logical Values.False@
-..status:deprecated, please use $Is<IntegerConcept<T> >::Type$
-..include:seqan/basic.h
-..see:Metafunction.IsSignedInteger
-..see:Metafunction.IsUnsignedInteger
- */
-
 /*!
  * @mfn IsIntegral
  * @brief Tests for a type to be of integral vaule.
- * @headerfile seqan/basic.h
- * 
+ * @headerfile <seqan/basic.h>
+ *
  * @signature IsIntegral<T>::Type
- * 
+ *
  * @tparam T Type that is tested.
- * 
- * @return TReturn 
- * 
+ *
+ * @return Type Either True or False.
+ *
  * @deprecated Please use <tt>Is&lt;IntegerConcept&lt;T&gt; &gt;::Type</tt>.
  */
 
-/**
-.Metafunction.IsIntegral:
-..cat:Basic
-..summary:Tests for a type to be of integral aue.
-..signature:IsIntegral<T>::Type
-..param.T:Type that is tested.
-..returns.param.Type:@Tag.Logical Values.True@, if $T$ is an ingegral type, @Tag.Logical Values.False@ otherwise.
-...default:@Tag.Logical Values.False@
-..status:deprecated, please use $Is<IntegerConcept<T> >::Type$
-..include:seqan/basic.h
- */
-
 // deprecation wrappers
 template <typename T>
 struct IsSignedInteger : Is< SignedIntegerConcept<T> > {};
@@ -753,24 +707,24 @@ struct IsIntegral : IsInteger<T> {};
  * @extends DefaultConstructibleConcept
  * @extends DestructibleConcept
  * @brief An integral type.
- * 
+ *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature IntegerConcept<T>
- * 
+ *
  * Expects an instance of type <tt>T</tt> to be of integral value and to provide
  * the same operations as <tt>int</tt>. The integer concept imposes no
  * restrictions on an available sign. Every type <tt>T</tt> that fulfills the
  * @link IntegerConcept @endlink fulfills either the @link SignedIntegerConcept
  * @endlink or the @link UnsignedIntegerConcept @endlink.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_CONCEPT_ASSERT((IntegerConcept<int>));
  * SEQAN_CONCEPT_ASSERT((IntegerConcept<char>));
  * //SEQAN_CONCEPT_ASSERT((IntegerConcept<double>));                       // fails to compile
- *  
+ *
  * std::cout << Is<IntegerConcept<char> >::VALUE << std::endl;             // 1
  * std::cout << Is<IntegerConcept<int> >::VALUE << std::endl;              // 1
  * std::cout << Is<IntegerConcept<unsigned short> >::VALUE << std::endl;   // 1
@@ -778,44 +732,44 @@ struct IsIntegral : IsInteger<T> {};
  * @endcode
  *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * T a, b;
  * int c;
- *  
+ *
  * a = 0u;
  * b = 1u;
  * c = a;
- *  
+ *
  * b = a + 1u;
  * b = a + a;
  * b += a;
  * b += 1u;
  * b = a++;
  * b = ++a;
- *  
+ *
  * b = a - a;
  * b = a - 1u;
  * b -= a;
  * b -= 1u;
  * b = a--;
  * b = --a;
- *  
+ *
  * b = a * a;
  * b = a * 1u;
  * b *= a;
  * b *= 1u;
- *  
+ *
  * b = a / a;
  * b = a / 1u;
  * b /= a;
  * b /= 1u;
- *  
+ *
  * b = a << a;
  * b = a << 1;
  * b <<= a;
  * b <<= 1;
- *  
+ *
  * b = a >> a;
  * b = a >> 1;
  * b >>= a;
@@ -823,85 +777,18 @@ struct IsIntegral : IsInteger<T> {};
  * @endcode
  */
 
-/**
-.Concept.IntegerConcept
-..cat:Basic
-..baseconcept:Concept.ComparableConcept
-..baseconcept:Concept.EqualityComparableConcept
-..summary:An integral type.
-..signature:IntegerConcept<T>
-..remarks:
-...text:Expects an instance of type $T$ to be of integral value and to provide the same operations as $int$.
-The integer concept imposes no restrictions on an available sign.
-Every type $T$ that fulfills the @Concept.IntegerConcept@ fulfills either the @Concept.SignedIntegerConcept@ or the @Concept.UnsignedIntegerConcept@.
-..example.code:
-SEQAN_CONCEPT_ASSERT((IntegerConcept<int>));
-SEQAN_CONCEPT_ASSERT((IntegerConcept<char>));
-//SEQAN_CONCEPT_ASSERT((IntegerConcept<double>));                       // fails to compile
-
-std::cout << Is<IntegerConcept<char> >::VALUE << std::endl;             // 1
-std::cout << Is<IntegerConcept<int> >::VALUE << std::endl;              // 1
-std::cout << Is<IntegerConcept<unsigned short> >::VALUE << std::endl;   // 1
-std::cout << Is<IntegerConcept<double> >::VALUE << std::endl;           // 0
-..example.text:Valid expressions:
-..example.code:
-T a, b;
-int c;
-
-a = 0u;
-b = 1u;
-c = a;
-
-b = a + 1u;
-b = a + a;
-b += a;
-b += 1u;
-b = a++;
-b = ++a;
-
-b = a - a;
-b = a - 1u;
-b -= a;
-b -= 1u;
-b = a--;
-b = --a;
-
-b = a * a;
-b = a * 1u;
-b *= a;
-b *= 1u;
-
-b = a / a;
-b = a / 1u;
-b /= a;
-b /= 1u;
-
-b = a << a;
-b = a << 1;
-b <<= a;
-b <<= 1;
-
-b = a >> a;
-b = a >> 1;
-b >>= a;
-b >>= 1;
-..include:seqan/basic.h
-..see:Concept.SignedIntegerConcept
-..see:Concept.UnsignedIntegerConcept
-*/
-
 SEQAN_CONCEPT(IntegerConcept, (TValue)) :
     Comparable<TValue>
 {
     TValue a, b;
     int c;
-    
+
     SEQAN_CONCEPT_USAGE(IntegerConcept)
     {
         a = 0u;
         b = 1u;
         c = a;
-        
+
         b = a + 1u;
         b = a + a;
         b += a;
@@ -915,7 +802,7 @@ SEQAN_CONCEPT(IntegerConcept, (TValue)) :
         b -= 1u;
         b = a--;
         b = --a;
-        
+
         b = a * a;
         b = a * 1u;
         b *= a;
@@ -925,7 +812,7 @@ SEQAN_CONCEPT(IntegerConcept, (TValue)) :
         b = a / 1u;
         b /= a;
         b /= 1u;
-        
+
         b = a << a;
         b = a << 1;
         b <<= a;
@@ -935,7 +822,7 @@ SEQAN_CONCEPT(IntegerConcept, (TValue)) :
         b = a >> 1;
         b >>= a;
         b >>= 1;
-                
+
         SEQAN_STATIC_ASSERT_MSG(static_cast<TValue>(0u) < static_cast<TValue>(1u), "Integer has wrong order.");
     }
 };
@@ -944,23 +831,23 @@ SEQAN_CONCEPT(IntegerConcept, (TValue)) :
  * @concept SignedIntegerConcept
  * @extends IntegerConcept
  * @brief An integral type with a sign.
- * 
+ *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature SignedIntegerConcept<T>
- * 
+ *
  * Expects an instance of type <tt>T</tt> to represent (possibly negative)
  * integral values and to provide the same operations as <tt>int</tt>. Every
  * type <tt>T</tt> that fulfills the @link IntegerConcept @endlink fulfills
  * either the @link SignedIntegerConcept @endlink or the @link
  * UnsignedIntegerConcept @endlink.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<int>));
  * //SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<unsigned short>));             // fails to compile
- *  
+ *
  * std::cout << Is<SignedIntegerConcept<char> >::VALUE << std::endl;           // 0
  * std::cout << Is<SignedIntegerConcept<int> >::VALUE << std::endl;            // 0
  * std::cout << Is<SignedIntegerConcept<unsigned short> >::VALUE << std::endl; // 1
@@ -968,77 +855,42 @@ SEQAN_CONCEPT(IntegerConcept, (TValue)) :
  * @endcode
  *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * T a;
  * int b;
- *  
+ *
  * a = -1;
  * b = a;
- *  
+ *
  * a = a - a;
  * a = a + 1;
  * a = a - 1;
- *  
+ *
  * a = a / 2;
- *  
+ *
  * static_cast<T>(-1) < static_cast<T>(0);
  * @endcode
  */
 
-/**
-.Concept.SignedIntegerConcept
-..cat:Basic
-..baseconcept:Concept.IntegerConcept
-..summary:An integral type with a sign.
-..signature:SignedIntegerConcept<T>
-..remarks:
-...text:Expects an instance of type $T$ to represent (possibly negative) integral values and to provide the same operations as $int$.
-Every type $T$ that fulfills the @Concept.IntegerConcept@ fulfills either the @Concept.SignedIntegerConcept@ or the @Concept.UnsignedIntegerConcept@.
-..example.code:
-SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<int>));
-//SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<unsigned short>));             // fails to compile
-
-std::cout << Is<SignedIntegerConcept<char> >::VALUE << std::endl;           // 0
-std::cout << Is<SignedIntegerConcept<int> >::VALUE << std::endl;            // 0
-std::cout << Is<SignedIntegerConcept<unsigned short> >::VALUE << std::endl; // 1
-std::cout << Is<SignedIntegerConcept<double> >::VALUE << std::endl;         // 0
-..example.text:Valid expressions:
-..example.code:
-T a;
-int b;
-
-a = -1;
-b = a;
-
-a = a - a;
-a = a + 1;
-a = a - 1;
-
-a = a / 2;
-
-static_cast<T>(-1) < static_cast<T>(0);
-..include:seqan/basic.h
-*/
-
 // an integer that must have a sign
 SEQAN_CONCEPT(SignedIntegerConcept, (TValue)) :
     IntegerConcept<TValue>
 {
     TValue a;
     int b;
-    
+
     SEQAN_CONCEPT_USAGE(SignedIntegerConcept)
     {
         a = -1;
         b = a;
-        
+
         a = a - a;
         a = a + 1;
         a = a - 1;
 
         a = a / 2;
-        
+
         SEQAN_STATIC_ASSERT_MSG(static_cast<TValue>(-1) < static_cast<TValue>(0), "Signed integer is either not signed or has wrong order.");
     }
 };
@@ -1047,23 +899,23 @@ SEQAN_CONCEPT(SignedIntegerConcept, (TValue)) :
  * @concept UnsignedIntegerConcept
  * @extends IntegerConcept
  * @brief An integral type without a sign.
- * 
+ *
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @signature UnsignedIntegerConcept<T>
- * 
+ *
  * Expects an instance of type <tt>T</tt> to represent non-negative integral
  * values and to provide the same operations as <tt>unsigned int</tt>. Every
  * type <tt>T</tt> that fulfills the @link IntegerConcept @endlink fulfills
  * either the @link SignedIntegerConcept @endlink or the @link
  * UnsignedIntegerConcept @endlink.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * //SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept<int>));                          // fails to compile
  * SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept<unsigned short>));
- *  
+ *
  * std::cout << Is<UnsignedIntegerConcept<char> >::VALUE << std::endl;             // 0
  * std::cout << Is<UnsignedIntegerConcept<int> >::VALUE << std::endl;              // 0
  * std::cout << Is<UnsignedIntegerConcept<unsigned short> >::VALUE << std::endl;   // 1
@@ -1071,47 +923,18 @@ SEQAN_CONCEPT(SignedIntegerConcept, (TValue)) :
  * @endcode
  *
  * @section Valid Expressions
- * 
+ *
  * @code{.cpp}
  * T a;
  * unsigned int b;
- *  
+ *
  * a = 1u;
  * b = a;
- *  
+ *
  * std::cout << static_cast<T>(0) < static_cast<T>(-1) << std::endl;  // 1
  * @endcode
  */
 
-/**
-.Concept.UnsignedIntegerConcept
-..cat:Basic
-..baseconcept:Concept.IntegerConcept
-..summary:An integral type without a sign.
-..signature:UnsignedIntegerConcept<T>
-..remarks:
-...text:Expects an instance of type $T$ to represent non-negative integral values and to provide the same operations as $unsigned int$.
-Every type $T$ that fulfills the @Concept.IntegerConcept@ fulfills either the @Concept.SignedIntegerConcept@ or the @Concept.UnsignedIntegerConcept@.
-..example.code:
-//SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept<int>));                          // fails to compile
-SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept<unsigned short>));
-
-std::cout << Is<UnsignedIntegerConcept<char> >::VALUE << std::endl;             // 0
-std::cout << Is<UnsignedIntegerConcept<int> >::VALUE << std::endl;              // 0
-std::cout << Is<UnsignedIntegerConcept<unsigned short> >::VALUE << std::endl;   // 1
-std::cout << Is<UnsignedIntegerConcept<double> >::VALUE << std::endl;           // 0
-..example.text:Valid expressions:
-..example.code:
-T a;
-unsigned int b;
-
-a = 1u;
-b = a;
-
-std::cout << static_cast<T>(0) < static_cast<T>(-1) << std::endl;  // 1
-..include:seqan/basic.h
-*/
-
 
 // an integer that mustn't have a sign
 SEQAN_CONCEPT(UnsignedIntegerConcept, (TValue)) :
@@ -1119,7 +942,7 @@ SEQAN_CONCEPT(UnsignedIntegerConcept, (TValue)) :
 {
     TValue a;
     unsigned b;
-    
+
     SEQAN_CONCEPT_USAGE(UnsignedIntegerConcept)
     {
         a = 1u;
@@ -1192,4 +1015,4 @@ template <> struct UnignedIntegerConcept<unsigned long> {};
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONCEPTS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONCEPTS_H_
diff --git a/seqan/basic/fundamental_conversion.h b/seqan/basic/fundamental_conversion.h
index 25b1f7a..ee7146c 100644
--- a/seqan/basic/fundamental_conversion.h
+++ b/seqan/basic/fundamental_conversion.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 
 // TODO(holtgrew): Move to alphabet submodule?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONVERSION_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONVERSION_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONVERSION_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONVERSION_H_
 
 namespace seqan {
 
@@ -57,36 +57,20 @@ namespace seqan {
  * @mfn Convert
  * @headerfile <seqan/basic.h>
  * @brief Return type of a conversion.
- * 
+ *
  * @signature Convert<TTarget, TSource>::Type;
- * 
+ *
  * @tparam TSource Type of the object that should be converted to <tt>Target</tt>.
  * @tparam TTarget Type the object should be converted to.
  *
  * If instances of <tt>Source</tt> can be re-interpreted as instances of <tt>Target</tt>, than this metafunction returns
  * a reference, otherwise it returns <tt>Target</tt>, that is convert returns a temporary.
- * 
+ *
  * @section Remarks
- * 
+ *
  * A constant instance of <tt>Convert</tt> is (ab)used as tag argument of convertImpl.
  */
 
-/**
-.Metafunction.Convert:
-..cat:Alphabets
-..summary:Return type of a conversion. 
-..signature:Convert<Target, Source>::Type
-..param.Target:Type the object should be converted to.
-..param.Source:Type of the object that should be converted to $Target$.
-..returns.param.Type:Type that is returned by @Function.convert@.
-...remarks:This is either $Target$ or $Target &$:
-If instances of $Source$ can be re-interpreted as instances of $Target$,
-than this metafunction returns a reference, otherwise it returns $Target$, 
-that is @Function.convert@ returns a temporary.
-..remarks:A constant instance of $Convert$ is (ab)used as tag argument of @Function.convertImpl@.
-..include:seqan/basic.h
-*/
-
 template <typename TTarget, typename TSource = void>
 struct Convert
 {
@@ -105,39 +89,22 @@ struct Convert
  * @fn convertImpl
  * @headerfile <seqan/basic.h>
  * @brief Implements convert.
- * 
+ *
  * @signature T convertImpl(convert, source);
- * 
- * @param convert Object that specifies the conversion.  A constant instance of Convert is used to specify the
- *                conversion target.
- * @param source  An object that should be converted.
- * 
+ *
+ * @param[in] convert Object that specifies the conversion.  A constant instance of Convert is used to specify the
+ *                    conversion target.
+ * @param[in] source  An object that should be converted.
+ *
  * @return T <tt>source</tt> converted to the type specified by convert.
- * 
+ *
  * @section Remarks
- * 
+ *
  * This function implements convert.  It is recommended to use convert rather than <tt>convertImpl</tt>.
- * 
+ *
  * @see convert
  */
 
-/**
-.Function.convertImpl
-..hidefromindex
-..cat:Alphabets
-..summary:Implements @Function.convert@.
-..signature:Convert convertImpl(convert, source)
-..param.convert:Object that specifies the conversion.
-...type:Metafunction.Convert
-...remarks:A constant instance of @Metafunction.Convert@ is used to specify the conversion target.
-..param.source:An object that should be converted.
-..returns:$source$ converted to the type specified by convert.
-...metafunction:Metafunction.Convert
-..remarks:This function implements @Function.convert@. 
-It is recommended to use @Function.convert@ rather than $convertImpl$.
-..include:seqan/basic.h
-*/
-
 // NOTE(doering): Specialize convertImpl, use convert.
 // NOTE(doering): Conversion of one char into another char happes at another place.
 // NOTE(doering): Conversion of sequences happens at another place.
@@ -159,41 +126,22 @@ convertImpl(Convert<TTarget, T> const,
  * @fn convert
  * @headerfile <seqan/basic.h>
  * @brief Converts a value into another value.
- * 
+ *
  * @signature T convert<Target>(source);
  *
  * @tparam Target The type <tt>source</tt> is converted to.
- * 
- * @param source An object that is converted to <tt>Target</tt>.
- * 
+ *
+ * @param[in] source An object that is converted to <tt>Target</tt>.
+ *
  * @return TReturn <tt>source</tt> converted to <tt>Target</tt>.  If <tt>source</tt> can be re-interpreted as instance
  *                 of <tt>Target</tt>, then a reference is returned.  Otherwise the function returns a temporary
  *                 object.
- * 
- * @section Remarks
- * 
+ *
  * This function is implemented in convertImpl. Do not specialize <tt>convert</tt>, specialize convertImpl instead.
- * 
+ *
  * @see convertImpl
  */
 
-/**
-.Function.convert
-..cat:Alphabets
-..summary:Converts a value into another value.
-..signature:Convert convert<Target>(source)
-..param.Target:The type $source$ is converted to.
-..param.source:An object that is converted to $Target$.
-..returns:$source$ converted to $Target$.
-...remarks:If $source$ can be re-interpreted as instance of $Target$, then a reference is returned.
-Otherwise the function returns a temporary object. 
-...metafunction:Metafunction.Convert
-..remarks:This function is implemented in @Function.convertImpl@. 
-Do not specialize $convert$, specialize @Function.convertImpl@ instead.
-..see:Function.convertImpl
-..include:seqan/basic.h
-*/
-
 template <typename TTarget, typename TSource>
 SEQAN_HOST_DEVICE inline typename Convert<TTarget, TSource>::Type
 convert(TSource const & source)
@@ -203,4 +151,4 @@ convert(TSource const & source)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONVERSION_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_CONVERSION_H_
diff --git a/seqan/basic/fundamental_metafunctions.h b/seqan/basic/fundamental_metafunctions.h
index cf8c81c..e34ae2f 100644
--- a/seqan/basic/fundamental_metafunctions.h
+++ b/seqan/basic/fundamental_metafunctions.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // defined for many types.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_METAFUNCTIONS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_METAFUNCTIONS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_METAFUNCTIONS_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_METAFUNCTIONS_H_
 
 #include <seqan/basic/basic_metaprogramming.h>
 
@@ -74,23 +74,6 @@ namespace seqan {
  * is int.
  */
 
-/**
-.Metafunction.Value:
-..cat:Fundamental
-..summary:Type of the items in the container or behind an iterator.
-..signature:Value<T[, I]>::Type
-..param.T:Type for which the value type is determined.
-..param.I:Index of the entry for which to retrieve the type.
-...remarks:This is only used for static-sized containers and aggregates.
-...type:nolink:$int$
-..returns.param.Type:Value type of $T$.
-..remarks.text:
-The value type of a container $T$ is the type of the elements in $T$.
-For example, the value type of a sequence of $int$ is $int$.
-..example.code:Value<String<char> >::Type c;  // c has type char
-..include:seqan/basic.h
-*/
-
 template <typename T, const int I = 0>
 struct Value;
 
@@ -115,21 +98,6 @@ struct Value;
  * confuse it with value that returns a reference to the value.
  */
 
-/**
-.Metafunction.GetValue:
-..cat:Fundamental
-..summary:Type for reading values. 
-..signature:GetValue<T>::Type
-..param.T:Type of container that holds a value.
-..returns.param.Type:GetValue type of $T$.
-..remarks.text:Depending on $T$, the $GetValue$-type can either be $Value<T>::Type &$ or $Value<T>::Type$.
-..text:$GetValue$ is the return type of @Function.getValue@ that allows a (read-only) access to objects.
-Do not confuse it with @Function.value@ that returns a @Metafunction.Reference.reference@ to the value.
-..see:Metafunction.Value
-..see:Function.getValue
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct GetValue;
 
@@ -149,18 +117,6 @@ struct GetValue;
  * @return Type Either <tt>Value&lt;T&gt;Type &amp;</tt> or a proxy object Proxy for <tt>T</tt>.
  */
 
-/**
-.Metafunction.Reference:
-..cat:Fundamental
-..summary:Reference type.
-..signature:Reference<T>::Type
-..param.T:A Type.
-..returns.param.Type:Either $Value<T>::Type &$ or a proxy object @Class.Proxy@ for $T$.
-..see:Metafunction.Value
-..see:Metafunction.GetValue
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct Reference;
 
@@ -180,17 +136,6 @@ struct Reference;
  * @returns Type Size type of <tt>T</tt>.
  */
 
-/**
-.Metafunction.Size:
-..cat:Fundamental
-..summary:Type of an object that is suitable to hold size information.
-..signature:Size<T>::Type
-..param.T:Type for which the size type is determined.
-..returns.param.Type:Size type of $T$.
-..remarks.text:In most cases this type is $size_t$.
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct Size;
 
@@ -210,19 +155,6 @@ struct Size;
  * @returns Type Difference type of <tt>T</tt>.
  */
 
-/**
-.Metafunction.Difference:
-..cat:Fundamental
-..summary:Type of an object that stores the difference between two iterators.
-..signature:Difference<T>::Type
-..param.T:Type for which the difference type is determined.
-...type:Class.Iter
-..returns.param.Type:Difference type of $T$.
-..remarks.text:In most cases this type is $ptrdiff_t$.
-..see:Metafunction.Size
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct Difference;
 
@@ -242,19 +174,6 @@ struct Difference;
  * @returns Type position type of <tt>T</tt>.
  */
 
-/**
-.Metafunction.Position
-..cat:Fundamental
-..summary:Type of an object that represents a position in a container.
-..signature:Position<T>::Type
-..param.T:Type for which the position type is determined.
-...type:Class.Iter
-...type:Class.String
-..returns.param.Type:Position type of $T$.
-..see:Metafunction.Iterator
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct Position;
 
@@ -266,7 +185,7 @@ struct Position;
 /*!
  * @mfn Spec
  * @headerfile <seqan/basic.h>
- * @brief The spec of a class. 
+ * @brief The spec of a class.
  *
  * @signature Spec<T>::Type;
  *
@@ -275,22 +194,6 @@ struct Position;
  * @returns Type Spec type of <tt>T</tt>.
  */
 
-/**
-.Metafunction.Spec
-..cat:Fundamental
-..summary:The spec of a class. 
-..signature:Spec<T>::Type
-..param.T:Type for which the spec is determined.
-..returns.param.Type:Spec of $T$.
-..remarks:
-The spec of a SeqAn type is the class that is used in template subclassing to specify the specialization. 
-For example, the spec of $String<char, Alloc<> >$ is $Alloc<>$.
-..remarks:
-There is a default specialization for this metafunction that returns $void$.
-Also, there is an implementation of Metafunction Spec for templates with one argument that returns this argument.
-..include:seqan/basic.h
-*/
-
 // Default case for types without Spec<>::Type specialization.
 
 template <typename T>
@@ -327,18 +230,6 @@ struct Spec<T const> : Spec<T>
  * @returns Type Size type of <tt>T</tt>.
  */
 
-/**
-.Metafunction.DeepestSpec:
-..cat:Fundamental
-..summary:The deepest spec of a class with nested template arguments.
-..signature:DeepestSpec<T>::Type
-..param.T:Type for which the deepest spec is determined.
-..returns.param.Type:Deepest spec of $T$.
-..remarks:The spec of a SeqAn type is the innermost class that is used in nested subclassing.
-For example, the deepest spec of $Iter<..., VSTree<BottomUp<Mums> > >$ is $Mums$.
-..include:seqan/basic.h
-*/
-
 // Default case if not specialized for T.
 
 template <typename T>
@@ -361,7 +252,7 @@ template <template <typename> class T,
           typename T1>
 struct DeepestSpec<T<T1> >
 {
-    typedef typename 
+    typedef typename
         IfC<IsSameType<T1, void>::VALUE,                                  // is T1 void?
             T<T1>,                                                        // yes, end of recursion
             typename DeepestSpec<typename Spec<T<T1> >::Type >::Type      // no,  recurse
@@ -377,21 +268,21 @@ struct DeepestSpec<T<T1, T2> > : DeepestSpec<typename Spec<T<T1,T2> >::Type>
 
 // Recursion for 3 arguments.
 
-template <template <typename, typename, typename> class T, 
+template <template <typename, typename, typename> class T,
           typename T1, typename T2, typename T3>
 struct DeepestSpec<T<T1, T2, T3> >:
     DeepestSpec<typename Spec<T<T1, T2, T3> >::Type> {};
 
 // Recursion for 4 arguments.
 
-template <template <typename, typename, typename, typename> class T, 
+template <template <typename, typename, typename, typename> class T,
           typename T1, typename T2, typename T3, typename T4>
 struct DeepestSpec<T<T1, T2, T3, T4> >:
     DeepestSpec<typename Spec<T<T1, T2, T3, T4> >::Type> {};
 
 // Recursion for 5 arguments.
 
-template <template <typename, typename, typename, typename, typename> class T, 
+template <template <typename, typename, typename, typename, typename> class T,
           typename T1, typename T2, typename T3, typename T4, typename T5>
 struct DeepestSpec<T<T1, T2, T3, T4, T5> > :
     DeepestSpec<typename Spec<T<T1, T2, T3, T4, T5> >::Type>
@@ -404,10 +295,20 @@ struct DeepestSpec<T<T1, T2, T3, T4, T5> > :
 template <typename T>
 struct LENGTH;
 
+// ----------------------------------------------------------------------------
+// Metafunction MinLength
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct MinLength
+{
+    static const unsigned VALUE = 0;
+};
+
 // ============================================================================
 // Functions
 // ============================================================================
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_METAFUNCTIONS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_METAFUNCTIONS_H_
diff --git a/seqan/basic/fundamental_tags.h b/seqan/basic/fundamental_tags.h
index 263db16..66713ee 100644
--- a/seqan/basic/fundamental_tags.h
+++ b/seqan/basic/fundamental_tags.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -58,35 +58,33 @@ namespace seqan {
  * @class Tag
  * @headerfile <seqan/basic.h>
  * @brief Template for tag definition.
- * 
+ *
  * @signature template <typename T>
  *            struct Tag;
  *
- * @tparam T Any parameter less types.
- * 
- * @section Remarks
- * 
+ * @tparam T Any parameterless types.
+ *
  * This <tt>struct</tt> is defined such that parameter less tags are easier recognizeable.  This is best explained with
  * the example below.
- * 
+ *
  * @section Examples
- * 
+ *
  * Usually, tags are defined in the following way.
- * 
+ *
  * @code{.cpp}
  * struct SomeTag_;
  * typedef Tag<SomeTag_> SomeTag;
  * @endcode
  *
  * They are then used as follows.
- * 
+ *
  * @code{.cpp}
  * template <typename T>
  * void f(T const & x, SomeTag const & tag)
  * {
  *     // ...
  * }
- *  
+ *
  * // Somewhere else:
  * f(3, SomeTag());
  * @endcode
@@ -97,36 +95,6 @@ namespace seqan {
  * (<tt>struct SomeTag;</tt>) or full declarations (<tt>struct SomeTag {};</tt>) everywhere.
  */
 
-/**
-.Tag.Tag
-..cat:Fundamental
-..signature:Tag<T>
-..param.T:Any parameter less types.
-..summary:Template for tag definition.
-..remarks:
-This $struct$ is defined such that parameter less tags are easier recognizeable.
-This is best explained with the example below.
-..example.text:Usually, tags are defined in the following way.
-..example.code:
-struct SomeTag_;
-typedef Tag<SomeTag_> SomeTag;
-..example.text:They are then used as follows.
-..example.code:
-template <typename T>
-void f(T const & x, SomeTag const & tag)
-{
-    // ...
-}
-
-// Somewhere else:
-f(3, SomeTag());
-..example.text:
-This has the advantages that (1) the type of tag parameters is printed as $Tag<SomeTag_>$ in compiler error traces.
-Furthermore, (2) parameter less tags can be defined redundantly in multiple headers and we can still instantiate them anywhere where they are declared.
-The latter (2) cannot be achieved with only forward declaration ($struct SomeTag;$) or full declarations ($struct SomeTag {};$) everywhere.
-..include:seqan/basic.h
- */
-
 template <typename T>
 struct Tag {};
 
@@ -142,13 +110,6 @@ struct Tag {};
  * @signature typedef Tag<Default_> Default;
  */
 
-/**
-.Tag.Default:
-..cat:Basic
-..summary:Tag that specifies default behavior.
-..tag.Default:Use default behavior. 
-..include:seqan/basic.h
-*/
 struct Default_;
 typedef Tag<Default_> Default;
 
@@ -166,15 +127,15 @@ typedef Tag<Default_> Default;
  * @signature struct Nothing {};
  */
 
-/**
-.Tag.Nothing:
-..cat:Basic
-..summary:Tag that represents an absent parameter or an absent type.
-..tag.Nothing:Omit parameter.
-..include:seqan/basic.h
-*/
+struct Nothing_;
+typedef Tag<Nothing_> Nothing;
+
+// --------------------------------------------------------------------------
+// Tag Raw
+// --------------------------------------------------------------------------
 
-struct Nothing {};
+struct Raw_;
+typedef Tag<Raw_> Raw;
 
 // ----------------------------------------------------------------------------
 // Tag Move
@@ -188,15 +149,13 @@ struct Nothing {};
  * @brief Switch to force move.
  *
  * @signature typedef Tag<Move_> Move;
- * 
- * @section Remarks
- * 
+ *
  * The difference between move constructor and copy constructor is that the source object is not copied but moved into
  * the target object.  The source object can lose its content and will be empty after this operation in this case.  A
  * move constructor can sigificantly faster than a copy constructor.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * String source("hello");
  * String target(source, Move()); // source is moved to target
@@ -205,55 +164,24 @@ struct Nothing {};
  * @endcode
  *
  * Move constructors are like copy-constructors.  However, their argument is not const.
- * 
+ *
  * @code{.cpp}
  * class Klass
  * {
  * public:
  *     seqan::String m;
- *  
+ *
  *     // Copy constructor, other is left untouched.
  *     Klass(Klass const & other) { ... }
- *  
+ *
  *     // Move constructor, leaves other and its members in an "empty" state.
  *     Klass(Klass & other, seqan::Move const &) { ... }
  * };
  * @endcode
  *
- * @see move
+ * @see AssignableConcept#move
  */
 
-/**
-.Tag.Move Switch:
-..cat:Basic
-..summary:Switch to force move.
-..tag.Move:Move instead of assign. 
-..remarks.text:The difference between move constructor and copy constructor
-is that the source object is not copied but moved into the target object.
-The source object can lose its content and will be empty after
-this operation in this case.
-A move constructor can sigificantly faster than a copy constructor.
-..example.code:String source("hello");
-String target(source, Move()); // source is moved to target
-std::cout << source; //nothing printed since source lost content
-std::cout << target; //"hello"
-..see:Function.move
-..example.text:Move constructors are like copy-constructors. However, their argument is not const.
-..example.code:
-class Klass
-{
-public:
-    seqan::String m;
-
-    // Copy constructor, other is left untouched.
-    Klass(Klass const & other) { ... }
-
-    // Move constructor, leaves other and its members in an "empty" state.
-    Klass(Klass & other, seqan::Move const &) { ... }
-};
-..include:seqan/basic.h
-*/
-
 struct Move_;
 typedef Tag<Move_> Move;
 
@@ -291,22 +219,6 @@ typedef Tag<GoEnd_> GoEnd;
 // Tag Serial
 // ----------------------------------------------------------------------------
 
-/*!
- * @tag Serial
- * @headerfile <seqan/basic.h>
- * @brief Tag to select a non-parallel implementation of an algorithm.
- *
- * @signature typedef<Serial_> Serial;
- */
-
-/**
-.Tag.Serial:
-..cat:Parallelism
-..summary:Tag to select a non-parallel implementation of an algorithm.
-..tag.Serial:Select serial implementation of an algorithm.
-..include:seqan/parallel.h
-*/
-
 struct Serial_;
 typedef Tag<Serial_> Serial;
 
@@ -326,19 +238,6 @@ typedef Tag<Serial_> Serial;
  * @tparam TSubList Nested list.
  */
 
-/**
-.Tag.TagList:
-..cat:Basic
-..summary:A structure to represent a list of tags.
-..signature:TagList<TTag1>
-..signature:TagList<TTag1, TagList<TTag2> >
-..signature:TagList<TTag1, TagList<TTag2, TagList<TTag3[...]> > >
-..param.TTag1:The first tag of the list.
-..param.TTag2:The second tag of the list.
-..param.TTag3:The third tag of the list.
-..include:seqan/basic.h
-*/
-
 template <typename TTag = void, typename TSubList = void>
 struct TagList
 {
@@ -353,10 +252,10 @@ struct TagList
  * @class TagSelector
  * @headerfile <seqan/basic.h>
  * @brief A structure to select a tag from a @link TagList @endlink.
- * 
+ *
  * @signature template <typename TTagList>
  *            struct TagSelector;
- * 
+ *
  * @tparam TTagList A tag list.
  */
 
@@ -366,21 +265,6 @@ struct TagList
  * @brief Stores the index of a Tag in the tag list.
  */
 
-/**
-.Class.TagSelector:
-..cat:Basic
-..summary:A structure to select a tag from a @Tag.TagList@.
-..signature:TagSelector<TTagList>
-..param.TTagList:A tag list.
-...type:Tag.TagList
-.Memvar.TagSelector#tagId:
-..class:Class.TagSelector
-..type:nolink:int
-..cat:Basic
-..summary:Stores the index of a @Page.Glossary.Tag@ in the tag list.
-..include:seqan/basic.h
-*/
-
 template <typename TTagList = void>
 struct TagSelector
 {
@@ -439,14 +323,6 @@ value(TagSelector<TTagList> const &selector)
  * @signature typedef Tag<DotDrawing_> DotDrawing;
  */
 
-/**
-.Tag.DotDrawing
-..cat:Input/Output
-..summary:Switch to trigger drawing in dot format.
-..value.DotDrawing:Graphs in dot format.
-..include:seqan/basic.h
-*/
-
 struct DotDrawing_;
 typedef Tag<DotDrawing_> DotDrawing;
 
@@ -461,13 +337,6 @@ typedef Tag<DotDrawing_> DotDrawing;
  * @signature typedef Tag<HammingDistance_> HammingDistance;
  */
 
-/**
-.Tag.HammingDistance
-..cat:Basic
-..summary:Switch to trigger Hamming distance, which is a measure of character substitutions.
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Why ambiguous here? Edit distance is the more common name.
 
 /*!
@@ -486,21 +355,12 @@ typedef Tag<DotDrawing_> DotDrawing;
  * @signature typedef Tag<LevenshteinDistance_> EditDistance;
  */
 
-/**
-.Tag.LevenshteinDistance
-..cat:Basic
-..summary:Switch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions).
-..remarks:$EditDistance$ is a synonym for $LevenshteinDistance$.
-..see:Spec.EditDistance
-..include:seqan/basic.h
-*/
-
 struct HammingDistance_;
 struct LevenshteinDistance_;
 
 typedef Tag<HammingDistance_>       HammingDistance;
 typedef Tag<LevenshteinDistance_>   LevenshteinDistance;
-typedef Tag<LevenshteinDistance_>   EditDistance; 
+typedef Tag<LevenshteinDistance_>   EditDistance;
 
 
 // ----------------------------------------------------------------------------
@@ -531,8 +391,6 @@ typedef Tag<Blat_> Blat;
  * @return VALUE The length of the TagList.
  */
 
-///.Metafunction.LENGTH.param.T.type:Tag.TagList
-
 template <>
 struct LENGTH<void>
 {
@@ -566,19 +424,6 @@ struct LENGTH<TagList<TTag, TSubList> >
  *                 <tt>0..LENGTH&lt;TTagList&gt;::VALUE -1</tt>.
  */
 
-/**
-.Metafunction.TagListValue:
-..cat:Basic
-..summary:A metafunction to retrieve a tag from a @Tag.TagList@.
-..signature:TagListValue<TTagList, tagId>
-..param.TTagList:A tag list.
-...type:Tag.TagList
-..param.tagId:An index of a @Page.Glossary.Tag@ in the tag list. This value must in 0..@Metafunction.LENGTH@$<TTagList>::VALUE-1$.
-...type:nolink:int
-..cat:Basic
-..include:seqan/basic.h
-*/
-
 template <typename TList, int I>
 struct TagListValue
 {
@@ -600,32 +445,32 @@ struct TagListValue<TagList<TTag, TSubList>, I>:
 //    public typename TagListValue<TTagList, I> {};
 
 // ----------------------------------------------------------------------------
-// Metafunction TagListGetIndex
+// Metafunction Find
 // ----------------------------------------------------------------------------
 
 /*!
  * @mfn Find
  * @headerfile <seqan/basic.h>
  * @brief A metafunction to retrieve the index of a tag in the TagList.
- * 
+ *
  * @signature Find<TTagList, TSearchTag>::VALUE;
- * 
+ *
  * @tparam TSearchTag A tag to retrieve the index of.
  * @tparam TTagList   A tag list.
- * 
+ *
  * @return VALUE This meta-function can be used to test whether the value of a TagSelector equals a specific tag.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
- * AutoSeqStreamFormat format;
- * if (format.tagId == TagListGetIndex<AutoSeqStreamFormat, Fasta>::VALUE)
+ * AutoSeqFormat format;
+ * if (format.tagId == Find<AutoSeqFormat, Fasta>::VALUE)
  * {
  *     // do something specific to Fasta format
  * }
- *  
+ *
  * // or even shorter:
- *  
+ *
  * if (isEqual(format.tagId, Fasta()))
  * {
  *     // do something specific to Fasta format
@@ -633,37 +478,6 @@ struct TagListValue<TagList<TTag, TSubList>, I>:
  * @endcode
  */
 
-/**
-.Metafunction.Find:
-..cat:Basic
-..summary:A metafunction to retrieve the index of a tag in the @Tag.TagList@.
-..signature:Find<TTagList, TSearchTag>
-..param.TTagList:A tag list.
-...remarks:For a @Class.TagSelector@ the underlying @Tag.TagList@ is used.
-...type:Tag.TagList
-...type:Class.TagSelector
-..param.TSearchTag:A tag to retrieve the index of.
-...type:Tag.Tag
-..return:The index of $TSearchTag$ in the tag list $TTagList$. If $TSearchTag$ is not contained $-1$ is returned.
-...remarks:This meta-function can be used to test whether the value of a @Class.TagSelector@ equals a specific tag.
-...type:nolink:int
-..cat:Basic
-..include:seqan/basic.h
-..example.code:
-AutoSeqStreamFormat format;
-if (format.tagId == TagListGetIndex<AutoSeqStreamFormat, Fasta>::VALUE)
-{
-    // do something specific to Fasta format
-}
-
-// or even shorter:
-
-if (isEqual(format.tagId, Fasta()))
-{
-    // do something specific to Fasta format
-}
-*/
-
 template <typename TList, typename TSearchTag>
 struct Find;
 
@@ -705,18 +519,84 @@ inline int find(TagSelector<TTagList> const &, TSearchTag const &)
 // Functions
 // ============================================================================
 
+// isEqual()
 template <typename TTagList, typename TTag>
 inline bool isEqual(TagSelector<TTagList> const &selector, TTag const &)
 {
     return selector.tagId == Find<TTagList, TTag>::VALUE;
 }
 
+// assign()
+template <typename TTagList, typename TTag>
+inline void assign(TagSelector<TTagList> &selector, TTag &)
+{
+    SEQAN_ASSERT_NEQ(int(Find<TTagList, TTag>::VALUE), -1);
+    selector.tagId = Find<TTagList, TTag>::VALUE;
+}
+
 template <typename TTagList, typename TTag>
 inline void assign(TagSelector<TTagList> &selector, TTag const &)
 {
+    SEQAN_ASSERT_NEQ(int(Find<TTagList, TTag>::VALUE), -1);
     selector.tagId = Find<TTagList, TTag>::VALUE;
 }
 
+template <typename TTagList>
+inline void assign(TagSelector<TTagList> &selector, TagSelector<TTagList> &other)
+{
+    selector.tagId = other.tagId;
+}
+
+template <typename TTagList>
+inline void assign(TagSelector<TTagList> &selector, TagSelector<TTagList> const &other)
+{
+    selector.tagId = other.tagId;
+}
+
+// --------------------------------------------------------------------------
+// Function tagApply()
+// --------------------------------------------------------------------------
+
+template <typename TFunctor, typename TTag>
+inline bool
+tagApply(TFunctor &func, TagList<TTag>)
+{
+    return func(TTag());
+}
+
+template <typename TFunctor, typename TTag, typename TSubList>
+inline bool
+tagApply(TFunctor &func, TagList<TTag, TSubList>)
+{
+    if (func(TTag()))
+        return true;
+    return tagApply(func, TSubList());
+}
+
+// --------------------------------------------------------------------------
+// Function tagApply()
+// --------------------------------------------------------------------------
+
+template <typename TContext>
+inline typename Value<TContext>::Type
+tagApply(TContext &, TagSelector<>)
+{
+    return typename Value<TContext>::Type();
+}
+
+template <typename TContext, typename TTagList>
+inline typename Value<TContext>::Type
+tagApply(TContext &ctx, TagSelector<TTagList> &format)
+{
+    typedef typename TTagList::Type TFormatTag;
+
+    if (isEqual(format, TFormatTag()))
+        return tagApply(ctx, TFormatTag());
+
+    return tagApply(ctx, static_cast<typename TagSelector<TTagList>::Base &>(format));
+}
+
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_BASIC_BASIC_TAGS_H_
diff --git a/seqan/basic/fundamental_transport.h b/seqan/basic/fundamental_transport.h
index e8fb2bf..656e508 100644
--- a/seqan/basic/fundamental_transport.h
+++ b/seqan/basic/fundamental_transport.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 
 // TODO(holtgrew): Do we want to get rid of move() and HasMoveConstructor<>? Will get rrvalues in C++11 and for everything else, swap() would be better.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_TRANSPORT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_TRANSPORT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_TRANSPORT_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_TRANSPORT_H_
 
 namespace seqan {
 
@@ -46,6 +46,12 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
+template <typename T>
+struct Is;
+
+template <typename T>
+struct StlContainerConcept;
+
 template <typename TDest, typename TSource>
 void assignValue(TDest &, TSource const &);
 
@@ -61,23 +67,13 @@ void assignValue(TDest &, TSource const &);
  * @mfn HasMoveConstructor
  * @headerfile <seqan/basic.h>
  * @brief Query whether a class has a move constructor.
- * 
+ *
  * @signature HasMoveConstructor<T>::Type;
  * @signature HasMoveConstructor<T>::VALUE;
- * 
+ *
  * @tparam T Type to query for availability of move constructor.
  */
 
-/**
-.Metafunction.HasMoveConstructor
-..summary:Query whether a class has a move constructor.
-..cat:Content Manipulation
-..signature:HasMoveConstructor<T>::Type
-..signature:HasMoveConstructor<T>::VALUE
-..param.T:Type to query for availability of move constructor.
-..include:seqan/basic.h
- */
-
 template <typename T>
 struct HasMoveConstructor
 {
@@ -94,7 +90,7 @@ struct HasMoveConstructor
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn assign
+ * @fn AssignableConcept#assign
  * @headerfile <seqan/basic.h>
  * @brief Assigns one object to another object.
  *
@@ -106,26 +102,8 @@ struct HasMoveConstructor
  * Assign value of source to target.
  */
 
-/**
-.Function.assign
-..summary:Assigns one object to another object.
-..cat:Content Manipulation
-..signature:assign(target, source)
-..signature:assign(target, source [, limit] [,resize_tag])
-..param.target: Gets the content of $source$.
-..param.source: Is copied to $target$.
-..param.limit: The maximal length of $target$ after the operation. (optional)
-...remarks:This arguments can be applied if $target$ is a container.
-..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
-...remarks:This arguments can be applied if $target$ is a container.
-..remarks:$assign(target, source)$ is semantically equivalent to $target = source$.
-..include:seqan/basic.h
-*/
-
 template <typename TTarget, typename TSource>
-inline void
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<TTarget> >)
 assign(TTarget & target,
        TSource & source)
 {
@@ -134,7 +112,7 @@ assign(TTarget & target,
 }
 
 template <typename TTarget, typename TSource>
-inline void
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<TTarget> >)
 assign(TTarget & target,
        TSource const & source)
 {
@@ -169,7 +147,7 @@ assign(Proxy<TTargetSpec> & target,
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn set
+ * @fn AssignableConcept#set
  * @headerfile <seqan/basic.h>
  * @brief Assigns one object to another object avoiding to copy contents.
  *
@@ -177,21 +155,10 @@ assign(Proxy<TTargetSpec> & target,
  *
  * @param[out] target Reference to the set to source.
  * @param[in]  source Value to set to target.
+ *
+ * The default implementation copies.  Types implementing AssignableConcept can implement more efficient variants.
  */
 
-/**
-.Function.set
-..summary:Assigns one object to another object avoiding to copy contents.
-..cat:Content Manipulation
-..signature:set(target, source)
-..signature:set(target, source)
-..param.target: Gets the content of $source$.
-..param.source: Content source.
-..remarks:$set(target, source)$ is semantically equivalent to $target = source$.
-If possible, $set$ copies content references instead of the content itself.
-..include:seqan/basic.h
-*/
-
 template<typename TTarget, typename TSource>
 inline void
 set(TTarget & target,
@@ -233,30 +200,19 @@ set(TTarget const & target,
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn move
+ * @fn AssignableConcept#move
  * @headerfile <seqan/basic.h>
  * @brief Hands over content from one object to another object.
  *
  * @signature void move(target, source);
  *
- * @param[out] target Where to move source to.
- * @param[in]  source What to move to target.
+ * @param[out]     target Where to move source to.
+ * @param[in,out]  source What to move to target.
+ *
+ * The default implementation will call @link AssignableConcept#assign @endlink and classes implementing
+ * AssignableConcept can override move to provide a more efficient implementation.
  */
 
-/**
-.Function.move
-..summary:Hands over content from one container to another container.
-..cat:Content Manipulation
-..signature:move(target, source)
-..param.target:A container $source$ is moved to.
-..param.source:A container that is moved to $target$.
-..remarks:The function tries to hand over the contents of $source$ to $target$.
-If this is possible, $source$ loses its content and will therefore be empty after this operation.
-Otherwise, the function behaves like @Function.assign@ and $source$ is copied to $target$.
-..see:Function.assign
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Are all specializations necessary?
 
 template<typename TTarget, typename TSource>
@@ -297,4 +253,4 @@ move(TTarget const & target,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_TRANSPORT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_FUNDAMENTAL_TRANSPORT_H_
diff --git a/seqan/basic/holder_base.h b/seqan/basic/holder_base.h
index 20a4532..14ca045 100644
--- a/seqan/basic/holder_base.h
+++ b/seqan/basic/holder_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -60,20 +60,20 @@ namespace seqan {
  * @class Holder
  * @headerfile <seqan/basic.h>
  * @brief Manages relationship to another object.
- * 
+ *
  * @signature template <typename TValue[, typename TSpec>
  *            class Holder;
- * 
+ *
  * @tparam TSpec  The specializing type. Default: <tt>Tristate</tt>
  * @tparam TValue Type of the managed object.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The main purpose of this class is to facilitate the handling of member objects. If we want class <tt>A</tt> to be
  * dependent on or the owner of another object of class <tt>B</tt>, then we add a data member of type <tt>Holder&lt;B&gt;</tt>
  * to <tt>A</tt>.  <tt>Holder</tt> offers some useful access functions and stores the kind of relationship between
  * <tt>A</tt> and <tt>B</tt>.
- * 
+ *
  * @see Holder#create
  * @see Holder#setValue
  */
@@ -91,43 +91,12 @@ namespace seqan {
  * @param[in] other Other Holder to copy from.
  * @param[in] value The value to hold.
  *
- * @section Remarks
- *
  * The main purpose of this class is to facilitate the handling of member objects.  If we want a class <tt>A</tt> to be
  * dependent on or the owner or another object of class <tt>B</tt> then we add a data member of type
  * <tt>Holder&lt;B&gt;</tt> to <tt>A</tt>.  Holder offers some useful access functions and stores the kind of
  * relationship between <tt>A</tt> and <tt>B</tt>.
  */
 
-/**
-.Class.Holder:
-..cat:Basic
-..summary:Manages relationship to another object.
-..signature:Holder<TValue, TSpec>
-..param.TValue:Type of the managed object.
-...metafunction:Metafunction.Value
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:$Tristate$
-..remarks.text:The main purpose of this class is to facilitate the handling of
-member objects. If we want class $A$ to be dependent on or the owner of another object of class $B$, 
-then we add a data member of type $Holder<B>$ to $A$. 
-$Holder$ offers some useful access functions and stores the kind of relationship between $A$ and $B$.
-..include:seqan/basic.h
-
-.Memfunc.Holder:
-..class:Class.Holder
-..summary:Constructor
-..signature:Holder<TValue, TSpec>()
-..signature:Holder<TValue, TSpec>(holder)
-..signature:Holder<TValue, TSpec>(value)
-..param.holder:Another holder object.
-..param.value:An object of type $TValue$.
-..remarks.text:
-The default constructor creates a holder that is in state 'empty'.
-If a $value$ is passed to the constructor, the holder will be in state 'dependent'.
- */
-
 // Tag for default Holder specialization.
 struct Tristate_;
 typedef Tag<Tristate_> Tristate;
@@ -169,8 +138,6 @@ struct Holder;
  * @return Type The value type for its holder.
  */
 
-///.Metafunction.Value.param.T.type:Class.Holder
-
 template <typename TValue, typename TSpec>
 struct Value<Holder<TValue, TSpec> >
 {
@@ -207,9 +174,6 @@ struct Value<Holder<TValue * const, TSpec> >
  * @return Type The resulting specialization tag.
  */
 
-///.Metafunction.Spec.param.T.type:Class.Holder
-///.Metafunction.Spec.class:Class.Holder
-
 template <typename TValue, typename TSpec>
 struct Spec<Holder<TValue, TSpec> >
 {
@@ -237,9 +201,6 @@ struct Spec<Holder<TValue, TSpec> const>
  * @return Type The resulting reference type.
  */
 
-///.Metafunction.Reference.param.T.type:Class.Holder
-///.Metafunction.Reference.class:Class.Holder
-
 template <typename TValue, typename TSpec>
 struct Reference<Holder<TValue, TSpec> >
 {
@@ -271,14 +232,12 @@ struct Reference<Holder<TValue *, TSpec> const>
 /*!
  * @fn Holder#create
  * @brief Makes an object to owner of its content.
- * 
+ *
  * @signature void create(holder[, object]);
- * 
- * @param holder The Holder to create the object of.
- * @param object Object from which a copy is made and stored in <tt>holder</tt>.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] holder The Holder to create the object of.
+ * @param[in]     object Object from which a copy is made and stored in <tt>holder</tt>.
+ *
  * After this operation, <tt>holder</tt> will be in state 'owner'.  If <tt>object</tt> is specified, <tt>holder</tt>
  * will hold a copy of <tt>object</tt> at the end of this function.  If <tt>object</tt> is not specified, the action
  * depends on the former state of <tt>holder</tt>:
@@ -290,7 +249,7 @@ struct Reference<Holder<TValue *, TSpec> const>
  *       <tt>holder</tt>.</li>
  *   <li>If the state of <tt>holder</tt> was already 'owner', nothing happens.</li>
  * </ul>
- * 
+ *
  * It is guaranteed, that after calling this function <tt>source</tt> and <tt>target</tt> can be used independently.
  */
 
@@ -303,11 +262,11 @@ struct Reference<Holder<TValue *, TSpec> const>
  * @brief Makes an object independent from other objects.
 
  * @signature void detach(holder);
- * 
+ *
  * @param[in,out] holder The Holder to detach.
- * 
+ *
  * @section Remarks
- * 
+ *
  * After this function, <tt>holder</tt> does not depends from any other entity outside of <tt>holder</tt>, like a source
  * or a host, and dependent(holer) returns <tt>false</tt>
  */
@@ -319,14 +278,12 @@ struct Reference<Holder<TValue *, TSpec> const>
 /*!
  * @fn Holder#setValue
  * @brief Makes holder dependent.
- * 
+ *
  * @signature void setValue(holder, object);
- * 
- * @param holder A holder object. Types: Holder
- * @param object Object from which <tt>holder</tt> will be dependent.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] holder A holder object. Types: Holder
+ * @param[in]     object Object from which <tt>holder</tt> will be dependent.
+ *
  * After this operation, <tt>holder</tt> will be dependent in state 'dependent'.
  */
 
@@ -337,18 +294,18 @@ struct Reference<Holder<TValue *, TSpec> const>
 /*!
  * @fn Holder#empty
  * @brief Test a Holder for being empty.
- * 
+ *
  * @signature bool empty(holder);
- * 
- * @param holder A Holder.
+ *
+ * @param[in] holder A Holder.
+ *
  * @return bool <tt>true</tt> if <tt>holder</tt> contains no elements, otherwise <tt>false</tt>.
- * 
+ *
  * @section Remarks
- * 
+ *
  * <tt>empty(x)</tt> is guaranteed to be at least as fast as <tt>length(me) == 0</tt>, but can be significantly faster
  * in some cases.
- * 
- * @see length
+ *
  * @see HostedConcept#emptyHost
  */
 
@@ -358,40 +315,32 @@ struct Reference<Holder<TValue *, TSpec> const>
 
 /*!
  * @fn Holder#assignValue
- * 
- * @headerfile seqan/basic.h
- * @headerfile seqan/sequence.h
- * 
+ *
+ * @headerfile <seqan/basic.h>
+ * @headerfile <seqan/sequence.h>
+ *
  * @brief Assigns value to item.
- * 
- * @signature assignValue(object, value)
- * @signature assignValue(container, pos, value)
- * 
- * @param object An object that holds a value or points to a value. Types:
- *               Holder, Iter Concepts: Concept.BasicOutputIteratorConcept
- * @param container A container. Types: SparseString, char array Concepts:
- *                  Concept.ContainerConcept
- * @param pos Position of the item in <tt>container</tt> to that <tt>value</tt>
- *            is assigned.
- * @param value A value that is assigned to the item <tt>object</tt> holds or
- *              points to.
- * 
- * @section Remarks
- * 
- * This function is similar to @link assign @endlink. The difference is, that
+ *
+ * @signature void assignValue(object, value);
+ *
+ * @param[in,out] object An object that holds a value or points to a value. Types:
+ *                       Holder, Iter Concepts: Concept.BasicOutputIteratorConcept
+ * @param[in]     value  A value that is assigned to the item <tt>object</tt> holds or points to.
+ *
+ * This function is similar to @link AssignableConcept#assign @endlink. The difference is, that
  * <tt>assignValue</tt> just changes a value stored in <tt>object</tt> or the
- * value <tt>object</tt> points to, while @link assign @endlink changes the
+ * value <tt>object</tt> points to, while @link AssignableConcept#assign @endlink changes the
  * whole object.
- * 
+ *
  * If <tt>object</tt> is a container (that is <tt>pos</tt> is not specified),
  * the whole content of <tt>object</tt> is replaced by <tt>value</tt>.
- * 
+ *
  * If <tt>value</tt> is not used again after calling this function,     then
- * consider to use @link moveValue @endlink that could be faster in some cases
+ * consider to use @link Holder#moveValue @endlink that could be faster in some cases
  * instead.
- * 
- * @see assign
- * @see moveValue
+ *
+ * @see AssignableConcept#assign
+ * @see Holder#moveValue
  */
 
 // ----------------------------------------------------------------------------
@@ -402,15 +351,13 @@ struct Reference<Holder<TValue *, TSpec> const>
  * @fn Holder#dependent
  * @headerfile <seqan/basic.h>
  * @brief Test whether Holder depends on other objects.
- * 
+ *
  * @signature bool dependent(holder);
- * 
- * @param holder The Holder to query;
- * 
+ *
+ * @param[in] holder The Holder to query;
+ *
  * @return bool <tt>true</tt> if <tt>object</tt> depends one some other object, <tt>false</tt> otherwise.
- * 
- * @section Remarks
- * 
+ *
  * An object "<tt>a</tt>" depends on another object "<tt>b</tt>", if changing "<tt>b</tt>" can invalidate "<tt>a</tt>";
  * especially the destruction of "<tt>b</tt>" invalidates "<tt>a</tt>".
  */
@@ -425,7 +372,7 @@ struct Reference<Holder<TValue *, TSpec> const>
  *
  * @signature void clear(holder);
  *
- * @param[in] holder The Holder to clear.
+ * @param[in,out] holder The Holder to clear.
  */
 
 // ----------------------------------------------------------------------------
@@ -443,6 +390,23 @@ struct Reference<Holder<TValue *, TSpec> const>
  * @return TReference The reference of the Holder's value.
  */
 
+// ----------------------------------------------------------------------------
+// Function moveValue()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn Holder#moveValue
+ *
+ * @headerfile <seqan/sequence.h>
+ *
+ * @brief Move a value of into a holder.
+ *
+ * @signature void moveValue(holder, value);
+ *
+ * @param[in,out] holder  The Holder to manipulate.
+ * @param[in,out] value   The value to move into <tt>holder</tt>.
+ */
+
 // ----------------------------------------------------------------------------
 // Function getValue()
 // ----------------------------------------------------------------------------
diff --git a/seqan/basic/holder_simple.h b/seqan/basic/holder_simple.h
index defac04..f319c50 100644
--- a/seqan/basic/holder_simple.h
+++ b/seqan/basic/holder_simple.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -58,28 +58,17 @@ namespace seqan {
  * @extends Holder
  * @headerfile <seqan/basic.h>
  * @brief Simple copying wrapper without any additional state.
- * 
+ *
  * @signature template <typename TValue>
  *            class Holder<TValue, Simple>;
- * 
+ *
  * @tparam TValue Type of the managed object.
- * 
+ *
  * @section Remarks
- * 
+ *
  * This holder stores a copy of the value.
  */
 
-/**
-.Spec.Simple Holder
-..cat:Holders
-..summary:Simple copying wrapper without any additional state.
-..signature:Holder<TValue, Simple>
-..param.TValue:Type of the managed object.
-..general:Class.Holder
-..remarks.text:This holder stores a copy of the value.
-..include:seqan/basic.h
- */
-
 template <typename TValue>
 struct Holder<TValue, Simple>
 {
diff --git a/seqan/basic/holder_tristate.h b/seqan/basic/holder_tristate.h
index ad3eb1b..3b504c8 100644
--- a/seqan/basic/holder_tristate.h
+++ b/seqan/basic/holder_tristate.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,6 +46,10 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >, void)
+assign(TContainer SEQAN_FORWARD_ARG me, typename RemoveReference<TContainer>::Type source);
+
 #if SEQAN_ENABLE_POINTER_HOLDER
 template <typename T> struct IsSimple;
 
@@ -64,14 +68,12 @@ template <typename TValue> inline size_t length(TValue * me);
  * @extends Holder
  * @headerfile <seqan/basic.h>
  * @brief Holder that can be empty, dependent, or owner.
- * 
+ *
  * @signature template <typename TValue>
  *            class Holder<TValue, Tristate>;
- * 
+ *
  * @tparam TValue Type of the managed object.
- * 
- * @section Remarks
- * 
+ *
  * A tristate holder <tt>A</tt> that holds an object <tt>B</tt> has one of the following states:
  *
  * <ul>
@@ -81,28 +83,12 @@ template <typename TValue> inline size_t length(TValue * me);
  *       used.</li>
  *   <li>empty: there is currently no object reference stored in the holder <tt>A</tt>.</li>
  * </ul>
- * 
+ *
  * The state of the holder can be determined by empty and dependent.
- * 
+ *
  * If a holder object is in owner state when destructed, the owned object is destructed as well.
  */
 
-/**
-.Spec.Tristate Holder
-..cat:Holders
-..summary:Holder that can be empty, dependent, or owner.
-..signature:Holder<TValue, Tristate>
-..param.TValue:Type of the managed object.
-..general:Class.Holder
-..remarks.text:A tristate holder $A$ that holds an object $B$ has one of the following states:
-..remarks.text:- owner: $A$ is the owner of $B$. If $A$ is destroyed, $B$ will be destroyed automatically.
-..remarks.text:- dependent: $A$ depends on $B$. $B$ should not be destroyed as long as $A$ is used.
-..remarks.text:- empty: there is currently no object reference stored in the holder $A$.
-..remarks.text:The state of the holder can be determined by @Function.empty@ and @Function.dependent@.
-..remarks.text:If a holder object is in owner state when destructed, the owned object is destructed as well.
-..include:seqan/basic.h
- */
-
 // TODO(holtgrew): This is broken for const TValue since we use Value<Holder>::Type below.
 
 template <typename TValue>
@@ -214,32 +200,26 @@ struct Holder<TValue const, Tristate>
     // Constructors; Destructor
     // ------------------------------------------------------------------------
 
-    Holder() : data_state(EMPTY)
-    {
-        SEQAN_CHECKPOINT;
-    }
+    Holder() : data_value(), data_state(EMPTY)
+    {}
 
-    Holder(Holder const & source_) : data_state(EMPTY)
+    Holder(Holder const & source_) : data_value(), data_state(EMPTY)
     {
-        SEQAN_CHECKPOINT;
         assign(*this, source_);
     }
 
-    Holder(TValue & value_) : data_state(EMPTY)
+    Holder(TValue & value_) : data_value(), data_state(EMPTY)
     {
-        SEQAN_CHECKPOINT;
         setValue(*this, value_);
     }
 
-    Holder(TValue const & value_): data_state(EMPTY)
+    Holder(TValue const & value_) : data_value(), data_state(EMPTY)
     {
-        SEQAN_CHECKPOINT;
         setValue(*this, value_);
     }
 
     ~Holder()
     {
-        SEQAN_CHECKPOINT;
         clear(*this);
     }
 
@@ -509,9 +489,6 @@ _dataValue(Holder<TValue * const, Tristate> const & me)
 // Function empty()
 // ----------------------------------------------------------------------------
 
-///.Function.empty.param.object.type:Class.Holder
-///.Function.empty.class:Class.Holder
-
 template <typename TValue>
 inline bool
 empty(Holder<TValue, Tristate> const & me)
@@ -524,9 +501,6 @@ SEQAN_CHECKPOINT
 // Function dependent()
 // ----------------------------------------------------------------------------
 
-///.Function.dependent.param.object.type:Class.Holder
-///.Function.dependent.class:Class.Holder
-
 template <typename TValue>
 inline bool
 dependent(Holder<TValue, Tristate> const & me)
@@ -542,7 +516,7 @@ dependent(Holder<TValue, Tristate> const & me)
 template <typename THolder, typename TValue>
 inline void
 _holderDeallocate(THolder & me, TValue const & data)
-{   
+{
     valueDestruct(& data);
     deallocate(me, & data, 1);
 }
@@ -569,9 +543,6 @@ _holderDeallocate(THolder & me, TValue * data)
     return _holderDeallocate(me, data, IsSimple<TValue>());         // try to distinguish between a pointer to one/array of object(s)
 }
 
-///.Function.clear.class:Class.Holder
-///.Function.clear.param.object.type:Class.Holder
-///.Function.clear.remarks.text:If $clear$ is applied on a @Class.Holder@ object,
 ///the state of this object is set to 'empty'.
 
 template <typename TValue>
@@ -600,7 +571,7 @@ clear(Holder<TValue, Tristate> & me)
 template <typename THolder, typename TValue>
 inline typename Value<THolder, 0>::Type *
 _holderAllocateObject(THolder & me, TValue const & data)
-{   
+{
     typename Value<THolder>::Type * ret;
     allocate(me, ret, 1);
     valueConstruct(ret, data);
@@ -634,26 +605,6 @@ _holderAllocatePointer(THolder & me, TValue * data)
 }
 #endif  // #if SEQAN_ENABLE_POINTER_HOLDER
 
-/**
-.Function.create
-..class:Class.Holder
-..summary:Makes an object to owner of its content.
-..cat:Dependent Objects
-..signature:create(holder [, object])
-..param.holder:A holder object.
-...type:Class.Holder
-..param.object:Object from which a copy is made and stored in $holder$. (optional)
-...type:Metafunction.Value.Value<Holder>::Type
-..remarks.text:After this operation, $holder$ will be in state 'owner'.
-If $object$ is specified, $holder$ will hold a copy of $object$ at the end of this function.
-If $object$ is not specified, the action depends on the former state of $holder$:
-..remarks.text:- If the state of $holder$ was 'empty', a new object is default constructed and stored into $holder$.
-..remarks.text:- If the state of $holder$ was 'dependent', a copy of the former object is made and stored into $holder$. 
-..remarks.text:- If the state of $holder$ was already 'owner', nothing happens.
-..see:Class.Holder
-..include:seqan/basic.h
-*/
-
 template <typename TValue>
 inline void
 create(Holder<TValue, Tristate> & me)
@@ -668,7 +619,7 @@ create(Holder<TValue, Tristate> & me)
             valueConstruct(me.data_value);
             me.data_state = THolder::OWNER;
             break;
-            
+
         case THolder::DEPENDENT:
             SEQAN_CHECKPOINT;
             create(me, _dataValue(me));
@@ -797,23 +748,6 @@ create(Holder<TValue, Tristate> & me,
 }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.detach
-..class:Class.Holder
-..summary:Makes an object independent from other objects.
-..cat:Dependent Objects
-..signature:detach(object)
-..param.object:An object.
-...type:Class.Holder
-..remarks:
-After this function, $object$ does not depends from any other entity outside of $object$,
-like a @Function.source@ or a @Function.host@, and @Function.dependent.dependent(object)@ returns $false$ 
-..see:Function.source
-..see:Function.host
-..see:Function.create
-..include:seqan/basic.h
-*/
-
 template <typename TValue>
 inline void
 detach(Holder<TValue, Tristate> & me)
@@ -826,21 +760,6 @@ detach(Holder<TValue, Tristate> & me)
 // Function setValue()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.setValue
-..class:Class.Holder
-..cat:Content Manipulation
-..summary:Makes holder dependent.
-..signature:setValue(holder, object)
-..param.holder:A holder object.
-...type:Class.Holder
-..param.object:Object from which $holder$ will be dependent.
-...type:Metafunction.Value.Value<Holder>::Type
-..remarks.text:After this operation, $holder$ will be dependent in state 'dependent'.
-..see:Class.Holder
-..include:seqan/basic.h
-*/
-
 template <typename TValue>
 inline void
 setValue(Holder<TValue, Tristate> & me,
@@ -976,11 +895,19 @@ setValue(Holder<TValue, Tristate> & me,
 }
 
 // ----------------------------------------------------------------------------
-// Function value()
+// Function swap()
 // ----------------------------------------------------------------------------
 
-///.Function.value.param.object.type:Class.Holder
-///.Function.value.class:Class.Holder
+template <typename TValue>
+void swap(Holder<TValue, Tristate> & lhs, Holder<TValue, Tristate> & rhs)
+{
+    std::swap(lhs.data_value, rhs.data_value);
+    std::swap(lhs.data_state, rhs.data_state);
+}
+
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
 
 template <typename TValue>
 inline typename Reference<Holder<TValue, Tristate> >::Type
@@ -1006,9 +933,6 @@ value(Holder<TValue, Tristate> const & me)
 // Function assignValue()
 // ----------------------------------------------------------------------------
 
-///.Function.assignValue.param.object.type:Class.Holder
-///.Function.assignValue.class:Class.Holder
-
 template <typename TValue, typename TSource>
 inline void
 assignValue(Holder<TValue, Tristate> & me,
@@ -1025,9 +949,6 @@ assignValue(Holder<TValue, Tristate> & me,
 // Function moveValue()
 // ----------------------------------------------------------------------------
 
-///.Function.moveValue.param.object.type:Class.Holder
-///.Function.moveValue.class:Class.Holder
-
 template <typename TValue, typename TSource>
 inline void
 moveValue(Holder<TValue, Tristate> & me,
@@ -1045,11 +966,6 @@ moveValue(Holder<TValue, Tristate> & me,
 // Function assign()
 // ----------------------------------------------------------------------------
 
-///.Function.assign.param.target.type:Class.Holder
-///.Function.assign.class:Class.Holder
-///.Function.assign.param.source.type:Class.Holder
-///.Function.assign.class:Class.Holder
-
 template <typename TValue>
 inline void
 assign(Holder<TValue, Tristate> & target_,
@@ -1060,7 +976,7 @@ assign(Holder<TValue, Tristate> & target_,
         case Holder<TValue, Tristate>::EMPTY:
             clear(target_);
             break;
-            
+
         case Holder<TValue, Tristate>::OWNER:
             assignValue(target_, value(source_));
             break;
@@ -1071,6 +987,27 @@ assign(Holder<TValue, Tristate> & target_,
     }
 }
 
+template <typename TValue>
+inline void
+assign(Holder<TValue const, Tristate> & target_,
+       Holder<TValue const, Tristate> const & source_)
+{
+    SEQAN_CHECKPOINT;
+    switch(source_.data_state) {
+        case Holder<TValue, Tristate>::EMPTY:
+            clear(target_);
+            break;
+
+        case Holder<TValue, Tristate>::OWNER:
+            create(target_, value(source_));
+            break;
+
+        default:  // case Holder<TValue, Tristate>::DEPENDENT
+            setValue(target_, value(source_));
+            break;
+    }
+}
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_BASIC_HOLDER_TRISTATE_H_
diff --git a/seqan/basic/hosted_type_interface.h b/seqan/basic/hosted_type_interface.h
index 695104e..e1728e1 100644
--- a/seqan/basic/hosted_type_interface.h
+++ b/seqan/basic/hosted_type_interface.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // TODO(holtgrew): We could add a HostedTypeConcept and make this a submodule of basic, e.g. basic/hosted.
 // TODO(holtgrew): This looks a bit unused/underused.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_
 
 namespace seqan {
 
@@ -55,21 +55,13 @@ namespace seqan {
  * @brief Concept for types that have a host.
  *
  * @signature concept HostedConcept;
- * 
+ *
  * @section Remarks
- * 
+ *
  * The functions of this concept assume that the hosted object exports a function <tt>_dataHost</tt> that returns a
  * reference to a holder type of <tt>Host&lt;T&gt;::Type &amp;</tt>.
  */
 
-/**
-.Concept.HostedConcept Type
-..summary:Concept for types that have a host.
-..remarks:The functions of this concept assume that the hosted object exports a function $_dataHost$ that returns a reference to a holder type of $Host<T>::Type &$.
-
-.Metafunction.Host.concept:Concept.HostedConcept Type
-*/
-
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -77,23 +69,13 @@ namespace seqan {
 /*!
  * @mfn HostedConcept#Host
  * @brief Type of the object a given object depends on.
- * 
+ *
  * @signature Host<T>::Type
- * 
+ *
  * @tparam T Type for which the host type is determined.
  * @return Type The Host type.
  */
 
-/**
-.Metafunction.Host
-..cat:Basic
-..summary:Type of the object a given object depends on.
-..signature:Host<T>::Type
-..param.T:Type for which the host type is determined.
-..returns.param.Type:Host type of $T$.
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct Host;
 
@@ -108,26 +90,14 @@ struct Host;
 /*!
  * @fn HostedConcept#emptyHost
  * @brief Query emptiness state of a hosted object.
- * 
+ *
  * @signature bool emptyHost(object);
- * 
- * @param object The object query state of host of.
- * 
+ *
+ * @param[in] object The object query state of host of.
+ *
  * @return bool <tt>true</tt> if the host is empty, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.emptyHost
-..cat:Dependent Object
-..summary:Query emptiness state of a hosted object.
-..signature:emptyHost(object)
-..param.object:The object query state of host of.
-..returns:$bool$, $true$ if the host is empty, $false$ otherwise.
-..see:Function.empty
-..concept:Concept.HostedConcept Type
-..include:seqan/basic.h
- */
-
 template <typename T>
 inline bool
 emptyHost(T const & me)
@@ -143,26 +113,14 @@ emptyHost(T const & me)
 /*!
  * @fn HostedConcept#dependentHost
  * @brief Query dependent state of a hosted object.
- * 
+ *
  * @signature void clearHost(object);
- * 
- * @param object The object query state of host of.
- * 
+ *
+ * @param[in] object The object query state of host of.
+ *
  * @return bool <tt>true</tt> if the host is dependent, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.dependentHost
-..cat:Dependent Object
-..summary:Query dependent state of a hosted object.
-..signature:clearHost(object)
-..param.object:The object query state of host of.
-..returns:$bool$, $true$ if the host is dependent, $false$ otherwise.
-..see:Function.dependent
-..concept:Concept.HostedConcept Type
-..include:seqan/basic.h
- */
-
 template <typename T>
 inline bool
 dependentHost(T const & me)
@@ -178,23 +136,12 @@ dependentHost(T const & me)
 /*!
  * @fn HostedConcept#clearHost
  * @brief Clear the host of the given object.
- * 
+ *
  * @signature void clearHost(object);
- * 
+ *
  * @param[in,out] object The object to clear the host of.
  */
 
-/**
-.Function.clearHost
-..cat:Dependent Object
-..summary:Clear the host of the given object.
-..signature:clearHost(object)
-..param.object:The object to clear the host of.
-..see:Function.clear
-..concept:Concept.HostedConcept Type
-..include:seqan/basic.h
- */
-
 template <typename T>
 inline void
 clearHost(T & me)
@@ -210,31 +157,17 @@ clearHost(T & me)
 /*!
  * @fn HostedConcept#createHost
  * @brief Construct the host of the given object.
- * 
+ *
  * @signature void createHost(object[, host]);
- * 
- * @param object The object to copy construct the host of.
- * @param host   The object to copy in host creation.
- * 
+ *
+ * @param[in,out] object The object to copy construct the host of.
+ * @param[in]     host   The object to copy in host creation.
+ *
  * @section Remarks
- * 
+ *
  * If <tt>host</tt> is given then it is used for copy creation.  Otherwise, the default constructor is used.
  */
 
-/**
-.Function.createHost
-..cat:Dependent Object
-..summary:Construct the host of the given object.
-..signature:createHost(object[, host])
-..param.object:The object to copy construct the host of.
-..param.host:The object to copy in host creation.
-...type:nolink:$Host<T>::Type const &$
-..remarks:If $host$ is given then it is used for copy creation.  Otherwise, the default constructor is used.
-..see:Function.create
-..concept:Concept.HostedConcept Type
-..include:seqan/basic.h
- */
-
 template <typename T>
 inline void
 createHost(T & me)
@@ -259,18 +192,16 @@ createHost(T & me,
 /*!
  * @fn HostedConcept#host
  * @brief The object a given object depends on.
- * 
+ *
  * @signature THostRef host(object);
- * 
- * @param object An object.
+ *
+ * @param[in] object An object.
  *
  * @return THostRef Reference to the host object.
  */
 
 /// TODO(holtgrew): Move documentation here?
 
-///.Function.host.concept:Concept.HostedConcept Type
-
 template <typename T>
 inline typename Host<T>::Type &
 host(T & me)
@@ -296,24 +227,32 @@ host(T const & me)
 /*!
  * @fn HostedConcept#setHost
  * @brief Sets the host of an object.
- * 
+ *
  * @signature void setHost(object, host);
- * 
- * @param host   The new host. Types: String
- * @param object The object that will get a new host.
- * 
+ *
+ * @param[in,out] host   The new host. Types: String
+ * @param[in]     object The object that will get a new host.
+ *
  * @section Remarks
- * 
+ *
  * After this operation, <tt>object</tt> depends on <tt>host</tt>.
- * 
+ *
  * Note that setting the host can invalidate <tt>object</tt>.  For example, if one changes the host of a Segment object,
  * it is possible that begin- and end-position of the segment does not fit into the new host sequence.
  */
 
-/// TODO(holtgrew): Move documentation here?
+#ifdef SEQAN_CXX11_STANDARD
+
+template <typename T, typename THost>
+inline void
+setHost(T & me,
+        THost && host_)
+{
+    SEQAN_CHECKPOINT;
+    setValue(_dataHost(me), std::forward<THost>(host_));
+}
 
-///.Function.setHost.param.object.type:nolink:$Host<T>::Type &$
-///.Function.setHost.concept:Concept.HostedConcept Type
+#else  // SEQAN_CXX11_STANDARD
 
 template <typename T, typename THost>
 inline void
@@ -333,6 +272,8 @@ setHost(T & me,
     setValue(_dataHost(me), host_);
 }
 
+#endif  // SEQAN_CXX11_STANDARD
+
 // ----------------------------------------------------------------------------
 // Function assignHost()
 // ----------------------------------------------------------------------------
@@ -340,24 +281,11 @@ setHost(T & me,
 /*!
  * @fn HostedConcept#assignHost
  * @brief Assign to the host of a given value.
- * 
+ *
  * @signature void assignHost(object, host);
- * 
- * @param host   The object to assign as host.
- * @param object The object to assign the host of.
- */
-
-/**
-.Function.assignHost
-..cat:Dependent Object
-..summary:Assign to the host of a given value.
-..signature:assignHost(object, host)
-..param.object:The object to assign the host of.
-..param.host:The object to assign as host.
-...type:nolink:$Host<T>::Type const &$
-..see:Function.assign
-..concept:Concept.HostedConcept Type
-..include:seqan/basic.h
+ *
+ * @param[in,out] host   The object to assign as host.
+ * @param[in]     object The object to assign the host of.
  */
 
 template <typename T, typename THost>
@@ -375,25 +303,12 @@ assignHost(T & me,
 
 /*!
  * @fn HostedConcept#moveHost
- * @brief Assign to the host of a given value.
- * 
+ * @brief Move to the host of a given value.
+ *
  * @signature void moveHost(object, host);
- * 
- * @param host The object to move-assign as host.
- * @param object The object to move-assign the host of.
- */
-
-/**
-.Function.moveHost
-..cat:Dependent Object
-..summary:Assign to the host of a given value.
-..signature:assignHost(object, host)
-..param.object:The object to move-assign the host of.
-..param.host:The object to move-assign as host.
-...type:nolink:$Host<T>::Type &$
-..see:Function.move
-..concept:Concept.HostedConcept Type
-..include:seqan/basic.h
+ *
+ * @param[in,out] host   The object to move-assign as host.
+ * @param[in,out] object The object to move-assign the host of.
  */
 
 template <typename T, typename THost>
@@ -407,4 +322,4 @@ moveHost(T & me,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_
diff --git a/seqan/basic/iterator_adapt_pointer.h b/seqan/basic/iterator_adapt_pointer.h
index f86eff1..7fb67fb 100644
--- a/seqan/basic/iterator_adapt_pointer.h
+++ b/seqan/basic/iterator_adapt_pointer.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 // TODO(holtgrew): Break out into adapt_pointer.h and adapt_array.h? The important main distinction is the fixed size at compile time.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_POINTER_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_POINTER_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_POINTER_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_POINTER_H_
 
 // ===========================================================================
 // Forwards
@@ -93,4 +93,4 @@ struct Value<TValue * const> : Value<TValue *>
 // Functions
 // ===========================================================================
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_POINTER_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_POINTER_H_
diff --git a/seqan/basic/iterator_adapt_std.h b/seqan/basic/iterator_adapt_std.h
index 1f6caba..3abb8a7 100644
--- a/seqan/basic/iterator_adapt_std.h
+++ b/seqan/basic/iterator_adapt_std.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // iterator traits.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_STD_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_STD_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_STD_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_STD_H_
 
 // ============================================================================
 // Adaption of SeqAn Iterators to STL Iterators.
@@ -47,14 +47,25 @@ namespace std
     template<typename TContainer, typename TSpec>
     struct iterator_traits<seqan::Iter<TContainer, TSpec> > // nolint
     {
-        typedef ::seqan::Iter<TContainer, TSpec> TIter; // nolint
+        typedef seqan::Iter<TContainer, TSpec> TIter; // nolint
 
         typedef random_access_iterator_tag iterator_category; // nolint
-        typedef typename ::seqan::Value<TIter>::Type value_type; // nolint
-        typedef typename ::seqan::Difference<TIter>::Type difference_type; // nolint
-        typedef typename ::seqan::Value<TIter>::Type * pointer; // nolint
-        typedef typename ::seqan::Reference<TIter>::Type reference; // nolint
+        typedef typename seqan::Value<TIter>::Type value_type; // nolint
+        typedef typename seqan::Difference<TIter>::Type difference_type; // nolint
+        typedef typename seqan::Value<TIter>::Type * pointer; // nolint
+        typedef typename seqan::Reference<TIter>::Type reference; // nolint
     };
+
+	// there is a bug in vc2015 stl, it doesnt check the iterator_traits correctly
+	// I have reported this bug to microsoft already (filed as DevDiv#1208117). 
+	// For now, this is a workaround.
+#if _MSC_VER == 1900
+	template<class _Ty, class Tag>
+	struct _Is_iterator<typename seqan::Iter<_Ty, Tag> >
+		: true_type
+	{
+	};
+#endif
 }
 
 namespace seqan {
@@ -85,21 +96,9 @@ struct StdContainerIterator;
  *
  * @tparam TContainer The container to iterate over.
  *
- * @section Remarks
- *
  * This type is a wrapper around STL iterators that has a conversion operator back to the underlying iterator.
  */
 
-/**
-.Spec.STD Adaptor Iterator
-..general:Class.Iter
-..cat:Iterators
-..summary:Adapt STL iterators to SeqAn iterators.
-..signature:Iter<TContainer, StdIteratorAdaptor>
-..param.TContainer:The STL container to iterate over.
-..remarks:This type is a wrapper around STL iterators that has a conversion operator back to the underlying iterator.
- */
-
 struct StdIteratorAdaptor_;
 typedef Tag<StdIteratorAdaptor_> StdIteratorAdaptor;
 
@@ -158,14 +157,14 @@ class Iter<TContainer, StdIteratorAdaptor>
     // ------------------------------------------------------------------------
     // Pointer Operators;  Have to be defined within class.
     // ------------------------------------------------------------------------
-    
-    typename Value<Iter>::Type *
+
+    typename std::iterator_traits<TIterator>::pointer
     operator->()
     {
         return &*data_iterator;
     }
 
-    typename Value<Iter>::Type const *
+    typename std::iterator_traits<TIterator>::pointer const
     operator->() const
     {
         return &*data_iterator;
@@ -254,18 +253,6 @@ struct Reference<Iter<TContainer const, StdIteratorAdaptor> const> :
 // Metafunction StdContainerIterator
 // ----------------------------------------------------------------------------
 
-// TODO(holtgrew): This is a candidate for not beging publically documented
-
-/**
-.Metafunction.StdContainerIterator
-..cat:Sequences
-..summary:Returns type of the STL container iterator.
-..signature:StdContainerIterator<T>::Type
-..param.T.type:Adaption.std::list
-..include:seqan/sequence.h
-..remarks:This is used in @Spec.STD Adaptor Iterator@.
- */
-
 template <typename TStdContainer>
 struct StdContainerIterator;
 
@@ -308,14 +295,14 @@ hostIterator(Iter<TContainer, StdIteratorAdaptor> const & me)
 // ----------------------------------------------------------------------------
 
 template <typename TContainer>
-inline typename Reference<Iter<TContainer, StdIteratorAdaptor> >::Type 
+inline typename Reference<Iter<TContainer, StdIteratorAdaptor> >::Type
 value(Iter<TContainer, StdIteratorAdaptor> & me)
 {
     return *(me.data_iterator);
 }
 
 template <typename TContainer>
-inline typename Reference<Iter<TContainer, StdIteratorAdaptor> const>::Type 
+inline typename Reference<Iter<TContainer, StdIteratorAdaptor> const>::Type
 value(Iter<TContainer, StdIteratorAdaptor> const & me)
 {
     return *(me.data_iterator);
@@ -326,14 +313,14 @@ value(Iter<TContainer, StdIteratorAdaptor> const & me)
 // ----------------------------------------------------------------------------
 
 template <typename TContainer>
-inline typename Reference<Iter<TContainer, StdIteratorAdaptor> >::Type 
+inline typename Reference<Iter<TContainer, StdIteratorAdaptor> >::Type
 operator*(Iter<TContainer, StdIteratorAdaptor> & me)
 {
     return *(me.data_iterator);
 }
 
 template <typename TContainer>
-inline typename Reference<Iter<TContainer, StdIteratorAdaptor> const>::Type 
+inline typename Reference<Iter<TContainer, StdIteratorAdaptor> const>::Type
 operator*(Iter<TContainer, StdIteratorAdaptor> const & me)
 {
     return *(me.data_iterator);
@@ -344,7 +331,7 @@ operator*(Iter<TContainer, StdIteratorAdaptor> const & me)
 // ----------------------------------------------------------------------------
 
 template <typename TContainer, typename TValue>
-inline void 
+inline void
 assignValue(Iter<TContainer, StdIteratorAdaptor> & me,
             TValue & val)
 {
@@ -352,7 +339,7 @@ assignValue(Iter<TContainer, StdIteratorAdaptor> & me,
 }
 
 template <typename TContainer, typename TValue>
-inline void 
+inline void
 assignValue(Iter<TContainer, StdIteratorAdaptor> & me,
             TValue const & val)
 {
@@ -364,14 +351,14 @@ assignValue(Iter<TContainer, StdIteratorAdaptor> & me,
 // ----------------------------------------------------------------------------
 
 template <typename TContainer, typename TValue>
-inline void 
+inline void
 moveValue(Iter<TContainer, StdIteratorAdaptor> & me,
           TValue & val)
 {
     move(*(me.data_iterator), val);
 }
 template <typename TContainer, typename TValue>
-inline void 
+inline void
 moveValue(Iter<TContainer, StdIteratorAdaptor> & me,
           TValue const & val)
 {
@@ -382,12 +369,11 @@ moveValue(Iter<TContainer, StdIteratorAdaptor> & me,
 // Function operator==()
 // ----------------------------------------------------------------------------
 
-template <typename TContainer>
-inline bool 
+template <typename TContainer, typename TContainer2>
+inline SEQAN_FUNC_ENABLE_IF(IsSameType<TContainer const &, TContainer2 const &>, bool)
 operator==(Iter<TContainer, StdIteratorAdaptor> const & left,
-           Iter<TContainer, StdIteratorAdaptor> const & right)
+           Iter<TContainer2, StdIteratorAdaptor> const & right)
 {
-    SEQAN_CHECKPOINT;
     return hostIterator(left) == hostIterator(right);
 }
 
@@ -395,12 +381,11 @@ operator==(Iter<TContainer, StdIteratorAdaptor> const & left,
 // Function operator!=()
 // ----------------------------------------------------------------------------
 
-template <typename TContainer>
-inline bool 
+template <typename TContainer, typename TContainer2>
+inline SEQAN_FUNC_ENABLE_IF(IsSameType<TContainer const &, TContainer2 const &>, bool)
 operator!=(Iter<TContainer, StdIteratorAdaptor> const & left,
-           Iter<TContainer, StdIteratorAdaptor> const & right)
+           Iter<TContainer2, StdIteratorAdaptor> const & right)
 {
-    SEQAN_CHECKPOINT;
     return hostIterator(left) != hostIterator(right);
 }
 
@@ -408,12 +393,11 @@ operator!=(Iter<TContainer, StdIteratorAdaptor> const & left,
 // Function operator<()
 // ----------------------------------------------------------------------------
 
-template <typename TContainer>
-inline bool 
+template <typename TContainer, typename TContainer2>
+inline SEQAN_FUNC_ENABLE_IF(IsSameType<TContainer const &, TContainer2 const &>, bool)
 operator<(Iter<TContainer, StdIteratorAdaptor> const & left,
-          Iter<TContainer, StdIteratorAdaptor> const & right)
+          Iter<TContainer2, StdIteratorAdaptor> const & right)
 {
-    SEQAN_CHECKPOINT;
     return hostIterator(left) < hostIterator(right);
 }
 
@@ -421,12 +405,11 @@ operator<(Iter<TContainer, StdIteratorAdaptor> const & left,
 // Function operator>()
 // ----------------------------------------------------------------------------
 
-template <typename TContainer>
-inline bool 
+template <typename TContainer, typename TContainer2>
+inline SEQAN_FUNC_ENABLE_IF(IsSameType<TContainer const &, TContainer2 const &>, bool)
 operator>(Iter<TContainer, StdIteratorAdaptor> const & left,
-          Iter<TContainer, StdIteratorAdaptor> const & right)
+          Iter<TContainer2, StdIteratorAdaptor> const & right)
 {
-    SEQAN_CHECKPOINT;
     return hostIterator(left) > hostIterator(right);
 }
 
@@ -434,10 +417,10 @@ operator>(Iter<TContainer, StdIteratorAdaptor> const & left,
 // Function operator<=()
 // ----------------------------------------------------------------------------
 
-template <typename TContainer>
-inline bool 
+template <typename TContainer, typename TContainer2>
+inline SEQAN_FUNC_ENABLE_IF(IsSameType<TContainer const &, TContainer2 const &>, bool)
 operator<=(Iter<TContainer, StdIteratorAdaptor> const & left,
-           Iter<TContainer, StdIteratorAdaptor> const & right)
+           Iter<TContainer2, StdIteratorAdaptor> const & right)
 {
     return hostIterator(left) <= hostIterator(right);
 }
@@ -446,12 +429,11 @@ operator<=(Iter<TContainer, StdIteratorAdaptor> const & left,
 // Function operator>=()
 // ----------------------------------------------------------------------------
 
-template <typename TContainer>
-inline bool 
+template <typename TContainer, typename TContainer2>
+inline SEQAN_FUNC_ENABLE_IF(IsSameType<TContainer const &, TContainer2 const &>, bool)
 operator>=(Iter<TContainer, StdIteratorAdaptor> const & left,
-           Iter<TContainer, StdIteratorAdaptor> const & right)
+           Iter<TContainer2, StdIteratorAdaptor> const & right)
 {
-    SEQAN_CHECKPOINT;
     return hostIterator(left) >= hostIterator(right);
 }
 
@@ -484,41 +466,45 @@ goPrevious(Iter<TContainer, StdIteratorAdaptor> & me)
 // ----------------------------------------------------------------------------
 
 template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, StdIteratorAdaptor>  
-operator+(Iter<TContainer, StdIteratorAdaptor> const & left,
+inline Iter<TContainer, StdIteratorAdaptor>
+operator+(Iter<TContainer, StdIteratorAdaptor> left,
           TIntegral right)
 {
     SEQAN_CHECKPOINT;
-    return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
+    std::advance(hostIterator(left), right);
+    return left;
 }
 
 // for <anonymous enum> types
 template <typename TContainer>
-inline Iter<TContainer, StdIteratorAdaptor>  
-operator+(Iter<TContainer, StdIteratorAdaptor> const & left,
+inline Iter<TContainer, StdIteratorAdaptor>
+operator+(Iter<TContainer, StdIteratorAdaptor> left,
           int right)
 {
     SEQAN_CHECKPOINT;
-    return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) + right);
+    std::advance(hostIterator(left), right);
+    return left;
 }
 
 template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, StdIteratorAdaptor>  
+inline Iter<TContainer, StdIteratorAdaptor>
 operator+(TIntegral left,
-          Iter<TContainer, StdIteratorAdaptor> const & right)
+          Iter<TContainer, StdIteratorAdaptor> right)
 {
     SEQAN_CHECKPOINT;
-    return Iter<TContainer, StdIteratorAdaptor>(hostIterator(right) + left);
+    std::advance(hostIterator(right), left);
+    return right;
 }
 
 // for <anonymous enum> types
 template <typename TContainer>
-inline Iter<TContainer, StdIteratorAdaptor>  
+inline Iter<TContainer, StdIteratorAdaptor>
 operator+(int left,
-          Iter<TContainer, StdIteratorAdaptor> const & right)
+          Iter<TContainer, StdIteratorAdaptor> right)
 {
     SEQAN_CHECKPOINT;
-    return Iter<TContainer, StdIteratorAdaptor>(hostIterator(right) + left);
+    std::advance(hostIterator(right), left);
+    return right;
 }
 
 // ----------------------------------------------------------------------------
@@ -531,7 +517,7 @@ operator+=(Iter<TContainer, StdIteratorAdaptor> & left,
            TIntegral right)
 {
     SEQAN_CHECKPOINT;
-    hostIterator(left) += right;
+    std::advance(hostIterator(left), right);
     return left;
 }
 
@@ -542,7 +528,7 @@ operator+=(Iter<TContainer, StdIteratorAdaptor> & left,
            int right)
 {
     SEQAN_CHECKPOINT;
-    hostIterator(left) += right;
+    std::advance(hostIterator(left), right);
     return left;
 }
 
@@ -551,26 +537,28 @@ operator+=(Iter<TContainer, StdIteratorAdaptor> & left,
 // ----------------------------------------------------------------------------
 
 template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, StdIteratorAdaptor>  
-operator-(Iter<TContainer, StdIteratorAdaptor> const & left,
+inline Iter<TContainer, StdIteratorAdaptor>
+operator-(Iter<TContainer, StdIteratorAdaptor> left,
           TIntegral right)
 {
     SEQAN_CHECKPOINT;
-    return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) - right);
+    std::advance(hostIterator(left), -right);
+    return left;
 }
 
 // for <anonymous enum> types
 template <typename TContainer>
-inline Iter<TContainer, StdIteratorAdaptor>  
-operator-(Iter<TContainer, StdIteratorAdaptor> const & left,
+inline Iter<TContainer, StdIteratorAdaptor>
+operator-(Iter<TContainer, StdIteratorAdaptor> left,
           int right)
 {
-SEQAN_CHECKPOINT
-    return Iter<TContainer, StdIteratorAdaptor>(hostIterator(left) - right);
+    SEQAN_CHECKPOINT
+    std::advance(hostIterator(left), -right);
+    return left;
 }
 
 template <typename TContainer>
-inline typename Difference<Iter<TContainer, StdIteratorAdaptor> >::Type  
+inline typename Difference<Iter<TContainer, StdIteratorAdaptor> >::Type
 operator-(Iter<TContainer, StdIteratorAdaptor> const & left,
           Iter<TContainer, StdIteratorAdaptor> const & right)
 {
@@ -588,7 +576,7 @@ operator-=(Iter<TContainer, StdIteratorAdaptor> & left,
            TIntegral right)
 {
     SEQAN_CHECKPOINT;
-    hostIterator(left) -= right;
+    std::advance(hostIterator(left), -right);
     return left;
 }
 
@@ -599,7 +587,7 @@ operator -= (Iter<TContainer, StdIteratorAdaptor> & left,
              int right)
 {
     SEQAN_CHECKPOINT;
-    hostIterator(left) -= right;
+    std::advance(hostIterator(left), -right);
     return left;
 }
 
@@ -619,4 +607,4 @@ assign(Iter<TTargetContainer, StdIteratorAdaptor> & target,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_STD_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPT_STD_H_
diff --git a/seqan/basic/iterator_adaptor.h b/seqan/basic/iterator_adaptor.h
index fe5eccb..61bf347 100644
--- a/seqan/basic/iterator_adaptor.h
+++ b/seqan/basic/iterator_adaptor.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // rooted by adding a pointer to the original container.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPTOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPTOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPTOR_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPTOR_H_
 
 namespace seqan {
 
@@ -44,6 +44,9 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
+template <typename TValue>
+inline size_t length(TValue const * me);
+
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
@@ -82,30 +85,6 @@ struct AdaptorIterator;
  * @param[in] iterator  The <tt>Standard</tt> iterator to wrap, defaults to beginning of <tt>container</tt>.
  */
 
-/**
-.Spec.Adaptor Iterator:
-..cat:Iterators
-..general:Class.Iter
-..summary:Adapts iterators to @Concept.RootedIteratorConcept@.
-..signature:Iter<TContainer, AdaptorIterator<TIterator [, TSpec]> >
-..param.TContainer:Type of the container that can be iterated by $TIterator$.
-...remarks:Use @Metafunction.Container@ to get the container type for a given iterator.
-..param.TIterator:Type of the iterator that is adapted to @Concept.RootedIteratorConcept@.
-..remarks.text:Adaptor iterators can implicitly converted to $TIterator$.
-..include:seqan/basic.h
-
-.Memfunc.Adaptor Iterator#Iter:
-..class:Spec.Adaptor Iterator
-..summary:Constructor
-..signature:Iter()
-..signature:Iter(iter)
-..signature:Iter(container [, iterator])
-..param.iter:Another adaptor iterator object.
-..param.container:The corresponding container object.
-..param.iterator:A iterator of $container$. (optional)
-...remarks.text:If this argument is omitted, the adaptor iterator is initialized to the @Function.begin.begin iterator@ of $container$.
-*/
-
 template <typename TContainer, typename TIterator, typename TSpec>
 class Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
 {
@@ -175,7 +154,7 @@ class Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
 
     template <typename TContainer_>
     SEQAN_FUNC_ENABLE_IF(IsSameType<TContainer, TContainer_ const>, Iter &)
-    SEQAN_HOST_DEVICE 
+    SEQAN_HOST_DEVICE
     operator=(Iter<TContainer_, AdaptorIterator<TIterator, TSpec> > const & other_)
     {
         data_container = other_.data_container;
@@ -188,7 +167,7 @@ class Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
     // ------------------------------------------------------------------------
 
     // For chaining behaviour of operator->(), see http://stackoverflow.com/a/8782794/84349
-    
+
     SEQAN_HOST_DEVICE
     TIterator &
     operator->()
@@ -219,6 +198,30 @@ class Iter<TContainer, AdaptorIterator<TIterator, TSpec> >
 // Metafunctions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Metafunction GetValue
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TIterator, typename TSpec>
+struct GetValue<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > > :
+    GetValue<TIterator> {};
+
+//template <typename TContainer, typename TIterator, typename TSpec>
+//struct GetValue<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const> :
+//    GetValue<TIterator const> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+//template <typename TContainer, typename TIterator, typename TSpec>
+//struct Value<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > > :
+//    GetValue<TIterator> {};
+//
+//template <typename TContainer, typename TIterator, typename TSpec>
+//struct Value<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const> :
+//    GetValue<TIterator const> {};
+
 // ----------------------------------------------------------------------------
 // Metafunction IteratorDefaultImp_
 // ----------------------------------------------------------------------------
@@ -230,6 +233,17 @@ struct IteratorDefaultImp_<T, Rooted>
     typedef Iter<T, AdaptorIterator<TStandardIterator> > Type;
 };
 
+// ----------------------------------------------------------------------------
+// Metafunction Chunk
+// ----------------------------------------------------------------------------
+
+// Chunk interface for rooted iterators
+template <typename TContainer, typename TValue, typename TSpec>
+struct Chunk<Iter<TContainer, AdaptorIterator<TValue*, TSpec> > >
+{
+    typedef Range<TValue*> Type;
+};
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -258,7 +272,7 @@ template <typename TContainer, typename TIterator, typename TSpec>
 inline SEQAN_HOST_DEVICE TContainer &
 container(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me)
 {
-    return _dereference<TContainer &>(me.data_container);
+    return _referenceCast<TContainer &>(me.data_container);
 }
 
 template <typename TContainer, typename TIterator, typename TSpec>
@@ -283,18 +297,6 @@ container(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me)
  */
 
 // TODO(holtgrew): Also defined in index module, change documentation?
-/**
-.Function.setContainer
-..class:Spec.Adaptor Iterator
-..summary:Set container of an adaptor iterator.
-..description:After setting the pointer to the container, the position will be set to 0.
-..cat:Dependent Objects
-..signature:setContainer(object, container)
-..param.object:Object to set the container for.
-...type:Spec.Adaptor Iterator
-..param.container:The container to "root" the iterator in.
- */
-
 template <typename TContainer, typename TIterator, typename TSpec>
 inline SEQAN_HOST_DEVICE void
 setContainer(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me,
@@ -319,17 +321,6 @@ setContainer(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me,
  * @return TIter The wrapped iterator.
  */
 
-/**
-.Function.hostIterator
-..class:Spec.Adaptor Iterator
-..cat:Dependent Objects
-..summary:Return host iterator.
-..signature:hostIterator(object)
-..param.object:Object to return host iterator for.
-...type:Spec.Adaptor Iterator
-..returns:Container of the given object.
- */
-
 template <typename TContainer, typename TIterator, typename TSpec>
 inline SEQAN_HOST_DEVICE TIterator &
 hostIterator(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me)
@@ -350,8 +341,6 @@ hostIterator(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me)
 // Function position()
 // ----------------------------------------------------------------------------
 
-///.Function.position.param.iter.type:Spec.Adaptor Iterator
-
 template <typename TContainer, typename TIterator, typename TSpec>
 inline SEQAN_HOST_DEVICE typename Position<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>::Type
 position(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me)
@@ -383,15 +372,6 @@ position(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me,
  * @param[in]     pos  The position to set.
  */
 
-/**
-.Function.setPosition
-..class:Spec.Adaptor Iterator
-..cat:Dependent Objects
-..signature:setPosition(iterator, pos)
-..param.iterator:The iterator to set the position of.
-...type:Spec.Adaptor Iterator
- */
-
 template <typename TContainer, typename TIterator, typename TSpec, typename TPosition>
 inline SEQAN_HOST_DEVICE void
 setPosition(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me,
@@ -421,6 +401,26 @@ value(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me)
     return value(hostIterator(me));
 }
 
+// ----------------------------------------------------------------------------
+// Function getValue()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline SEQAN_HOST_DEVICE typename GetValue<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > >::Type
+getValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me)
+{
+    SEQAN_CHECKPOINT;
+    return getValue(hostIterator(me));
+}
+
+template <typename TContainer, typename TIterator, typename TSpec>
+inline SEQAN_HOST_DEVICE typename GetValue<Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const>::Type
+getValue(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me)
+{
+    SEQAN_CHECKPOINT;
+    return getValue(hostIterator(me));
+}
+
 // ----------------------------------------------------------------------------
 // Function assignValue()
 // ----------------------------------------------------------------------------
@@ -725,20 +725,12 @@ operator-=(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & left,
 // Function atEnd()
 // ----------------------------------------------------------------------------
 
-template <typename TContainer, typename TIterator, typename TSpec>
-inline SEQAN_HOST_DEVICE bool
-atEnd(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > & me)
-{
-    SEQAN_CHECKPOINT;
-    return atEnd(me, container(me));
-}
-
 template <typename TContainer, typename TIterator, typename TSpec>
 inline SEQAN_HOST_DEVICE bool
 atEnd(Iter<TContainer, AdaptorIterator<TIterator, TSpec> > const & me)
 {
     SEQAN_CHECKPOINT;
-    return atEnd(me, container(me));
+    return atEnd(hostIterator(me), container(me));
 }
 
 // ----------------------------------------------------------------------------
@@ -758,6 +750,54 @@ assign(Iter<TTargetContainer, AdaptorIterator<TIterator, TSpec> > & target,
     target.data_iterator = begin(container(source)) + position(source);
 }
 
+// ----------------------------------------------------------------------------
+// Function reserveChunk()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TSize>
+inline void reserveChunk(Iter<TContainer, TSpec> &iter, TSize size, Output)
+{
+    typedef Iter<TContainer, TSpec> TIter;
+
+    TContainer &cont = container(iter);
+    typename Position<TIter>::Type pos = position(iter);
+    typename Size<TIter>::Type len = length(cont);
+
+    if (pos < len)
+        return;
+
+    len += size;
+    if (len <= capacity(cont))
+        return;
+
+    reserve(cont, len);
+    setPosition(iter, pos);
+}
+
+template <typename TContainer, typename TSpec, typename TSize>
+inline void reserveChunk(Iter<TContainer, TSpec> &, TSize, Input)
+{}
+
+// ----------------------------------------------------------------------------
+// Function getChunk()
+// ----------------------------------------------------------------------------
+
+// AdaptorIterator
+template <typename TChunk, typename TContainer, typename TValue, typename TSpec>
+inline void
+getChunk(TChunk &result, Iter<TContainer, AdaptorIterator<TValue*, TSpec> > &rootedIter, Input)
+{
+    return assignRange(result, hostIterator(rootedIter), end(container(rootedIter), Standard()));
+}
+
+template <typename TChunk, typename TContainer, typename TValue, typename TSpec>
+inline void
+getChunk(TChunk &result, Iter<TContainer, AdaptorIterator<TValue*, TSpec> > &rootedIter, Output)
+{
+    TContainer &cont = container(rootedIter);
+    return assignRange(result, hostIterator(rootedIter), begin(cont, Standard()) + capacity(cont));
+}
+
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPTOR_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_ADAPTOR_H_
diff --git a/seqan/basic/iterator_base.h b/seqan/basic/iterator_base.h
index 5460ff0..438e69c 100644
--- a/seqan/basic/iterator_base.h
+++ b/seqan/basic/iterator_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 
 // TODO(holtgrew): I think the interface is not completely specified here. Also, we could maybe have more generic implementations for operators?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_BASE_H_
 
 namespace seqan {
 
@@ -51,7 +51,7 @@ namespace seqan {
 
 /*!
  * @class Iter
- * @extends IteratorAssociatedTypesConcept
+ * @implements IteratorAssociatedTypesConcept
  * @headerfile <seqan/basic.h>
  * @brief Base class for iterators to traverse containers.
  *
@@ -62,19 +62,6 @@ namespace seqan {
  * @tparam TSpec      Type to use for specializing the <tt>Iter</tt> class.
  */
 
-/**
-.Class.Iter:
-..cat:Basic
-..summary:Iterator that is used to traverse containers.
-..signature:Iter<TContainer, TSpec>
-..param.TContainer:Type of the container that can be iterated by $Iter$.
-...metafunction:Metafunction.Container
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-..implements:Concept.IteratorAssociatedTypesConcept
-..include:seqan/basic.h
-*/
-
 template <typename TContainer, typename TSpec>
 class Iter;
 
@@ -98,15 +85,6 @@ class Iter;
  *              container is complemented.
  */
 
-/**
-.Metafunction.IterComplementConst:
-..cat:Basic
-..summary:Complement the "constness" of the container of an iterator.
-..signature:IterComplementConst<TIterator>
-..param.TIterator:The iterator to toggle the constness of its container for.
-..include:seqan/basic.h
-*/
-
 template <typename TIterator>
 struct IterComplementConst;
 
@@ -140,15 +118,6 @@ struct IterComplementConst<Iter<TContainer, TSpec> const>
  * @return Type The resulting Iter type with a const container.
  */
 
-/**
-.Metafunction.IterMakeConst:
-..cat:Basic
-..summary:Make the container of an Iter const.
-..signature:IterMakeConst<TIterator>
-..param.TIterator:The iterator make the container const for.
-..include:seqan/basic.h
-*/
-
 template <typename TIterator>
 struct IterMakeConst;
 
@@ -177,9 +146,6 @@ struct IterMakeConst<Iter<TContainer, TSpec> const>
  * @return Type The specialization tag used for the <tt>Iter</tt>.
  */
 
-///.Metafunction.Spec.param.T.type:Class.Iter
-///.Metafunction.Spec.class:Class.Iter
-
 template <typename TContainer, typename TSpec>
 struct Spec<Iter<TContainer, TSpec> >
 {
@@ -196,9 +162,6 @@ struct Spec<Iter<TContainer, TSpec> const>
 // Metafunction Value
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Value.param.T.type:Class.Iter
-///.Metafunction.Value.class:Class.Iter
-
 template <typename TContainer, typename TSpec>
 struct Value<Iter<TContainer, TSpec> >:
     Value<TContainer>
@@ -215,9 +178,6 @@ struct Value<Iter<TContainer, TSpec> const>:
 // Metafunction GetValue
 // ----------------------------------------------------------------------------
 
-///.Metafunction.GetValue.param.T.type:Class.Iter
-///.Metafunction.GetValue.class:Class.Iter
-
 template <typename TContainer, typename TSpec>
 struct GetValue<Iter<TContainer, TSpec> >:
     GetValue<TContainer>
@@ -234,9 +194,6 @@ struct GetValue<Iter<TContainer, TSpec> const>:
 // Metafunction Reference
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Reference.param.T.type:Class.Iter
-///.Metafunction.Reference.class:Class.Iter
-
 template <typename TContainer, typename TSpec>
 struct Reference<Iter<TContainer, TSpec> >:
     Reference<TContainer>
@@ -264,9 +221,6 @@ struct Reference<Iter<TContainer, TSpec> const>:
  * @return Type The container type of <tt>TIter</tt>
  */
 
-///.Metafunction.Container.param.T.type:Class.Iter
-///.Metafunction.Container.class:Class.Iter
-
 template <typename T> struct Container;
 
 template <typename TContainer, typename TSpec>
@@ -430,4 +384,4 @@ position(Iter<TContainer, TSpec> const & me,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_BASE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_BASE_H_
diff --git a/seqan/basic/iterator_concept.h b/seqan/basic/iterator_concept.h
index 691561b..697d312 100644
--- a/seqan/basic/iterator_concept.h
+++ b/seqan/basic/iterator_concept.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,21 +34,11 @@
 
 // SEQAN_NO_GENERATED_FORWARDS
 
-#ifndef CORE_INCLUDE_SEQAN_BASIC_ITERATOR_CONCEPT_H_
-#define CORE_INCLUDE_SEQAN_BASIC_ITERATOR_CONCEPT_H_
+#ifndef INCLUDE_SEQAN_BASIC_ITERATOR_CONCEPT_H_
+#define INCLUDE_SEQAN_BASIC_ITERATOR_CONCEPT_H_
 
 namespace seqan {
 
-/**
-.Metafunction.Pointer
-..cat:Basic
-..summary:Returns pointer to an object, required for @Function.operator->@, for example.
-..signature:Pointer<T>::Type
-..param.T:The type to query.
-..returns:Pointer type.
-..include:seqan/basic.h
- */
-
 // Forward Declaration / Prototype.
 template <typename T> struct Pointer;
 
@@ -56,11 +46,9 @@ template <typename T> struct Pointer;
  * @concept IteratorAssociatedTypesConcept
  * @headerfile <seqan/basic.h>
  * @brief Requires metafunctions for the associated types used in the iterator concepts.
- * 
+ *
  * @signature IteratorAssociatedTypesConcept<T>
- * 
- * @section Remarks
- * 
+ *
  * The SeqAn iterators mirror the definitions from <a href="http://generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator">ConceptC++</a>.
  */
 
@@ -112,22 +100,22 @@ template <typename T> struct Pointer;
 /*!
  * @mfn IteratorAssociatedTypesConcept#Pointer
  * @brief Returns pointer to an object, required for <tt>operator-></tt>, for example.
- * 
+ *
  * @signature Pointer<TIter>::Type
- * 
+ *
  * @tparam TIter The type to query.
- * 
+ *
  * @return Type Pointer type.
  */
 
 /*!
  * @fn IteratorAssociatedTypesConcept#operator*
  * @brief Returns reference to the pointed-to value.
- * 
+ *
  * @signature TReference operator*(it);
- * 
- * @param it The iterator to dereference.
- * 
+ *
+ * @param[in] it The iterator to dereference.
+ *
  * @return TReference The reference type.
  */
 
@@ -135,11 +123,11 @@ template <typename T> struct Pointer;
  * @fn IteratorAssociatedTypesConcept#value
  * @brief Returns reference to the pointed-to value.
  * @deprecated Use <tt>operator*()</tt> instead.
- * 
+ *
  * @signature TReference value(it);
- * 
- * @param it The iterator to dereference.
- * 
+ *
+ * @param[in] it The iterator to dereference.
+ *
  * @return TReference The reference type.
  */
 
@@ -147,29 +135,14 @@ template <typename T> struct Pointer;
  * @fn IteratorAssociatedTypesConcept#getValue
  * @brief Returns get-value of pointed-to character.
  * @deprecated Use <tt>operator*()</tt> instead.
- * 
+ *
  * @signature TGetValue getValue(it);
- * 
- * @param it The iterator to get get-value from.
- * 
+ *
+ * @param[in] it The iterator to get get-value from.
+ *
  * @return TGetValue The get-value that is pointed to.
  */
 
-/**
-.Concept.IteratorAssociatedTypesConcept
-..cat:Iterators
-..summary:Requires metafunctions for the associated types used in the iterator concepts.
-..signature:IteratorAssociatedTypesConcept<T>
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
-
-.Metafunction.Value.concept:Concept.IteratorAssociatedTypesConcept
-.Metafunction.GetValue.concept:Concept.IteratorAssociatedTypesConcept
-.Metafunction.Difference.concept:Concept.IteratorAssociatedTypesConcept
-.Metafunction.Reference.concept:Concept.IteratorAssociatedTypesConcept
-.Metafunction.Pointer.concept:Concept.IteratorAssociatedTypesConcept
- */
-
 SEQAN_CONCEPT(IteratorAssociatedTypesConcept, (T))
 {
     typedef typename Value<T>::Type      TValue;
@@ -177,7 +150,7 @@ SEQAN_CONCEPT(IteratorAssociatedTypesConcept, (T))
     typedef typename Difference<T>::Type TDifference;
     typedef typename Reference<T>::Type  TReference;
     typedef typename Pointer<T>::Type    TPointer;
-    
+
     SEQAN_CONCEPT_ASSERT((SignedIntegerConcept<TDifference>));
 
     SEQAN_CONCEPT_USAGE(IteratorAssociatedTypesConcept)
@@ -190,26 +163,24 @@ SEQAN_CONCEPT(IteratorAssociatedTypesConcept, (T))
  * @extends IteratorAssociatedTypesConcept
  * @extends CopyConstructibleConcept
  * @extends EqualityComparableConcept
- * @headerfile seqan/basic.h
+ * @headerfile <seqan/basic.h>
  * @brief Iterator that allows dereferenced reading.
- * 
+ *
  * @signature InputIteratorConcept<T>
- * 
- * @section Remarks
- * 
+ *
  * The SeqAn iterators mirror the definitions from <a href="http://generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator">ConceptC++</a>.
- * 
- * @see BasicOutputIteratorConcept
+ *
+ * @see OutputIteratorConcept
  */
 
 /*!
  * @fn InputIteratorConcept#operator++(suffix)
  * @brief C++ built-in suffix increment operator.
  *
- * @signature TIterator operator++(it, i)
+ * @signature TIterator operator++(it, i);
  *
- * @param it The iterator to increment.
- * @param i  An integer, used to mark suffix decrement.
+ * @param[in,out] it The iterator to increment.
+ * @param[in]     i  An integer, used to mark suffix decrement.
  *
  * @return TIterator A copy of the original iterator.
  */
@@ -218,9 +189,9 @@ SEQAN_CONCEPT(IteratorAssociatedTypesConcept, (T))
  * @fn InputIteratorConcept#operator++(prefix)
  * @brief C++ built-in prefix increment operator.
  *
- * @signature TIterator operator++(it)
+ * @signature TIterator operator++(it);
  *
- * @param it The iterator to increment.
+ * @param[in] it The iterator to increment.
  *
  * @return TIterator A copy of the original iterator.
  */
@@ -229,9 +200,9 @@ SEQAN_CONCEPT(IteratorAssociatedTypesConcept, (T))
  * @fn InputIteratorConcept#operator->
  * @brief C++ built-in structure dereference operator.
  *
- * @signature TResult operator->(it)
+ * @signature TResult operator->(it);
  *
- * @param it The iterator to structure-dereference.
+ * @param[in] it The iterator to structure-dereference.
  *
  * @return TResult Either a pointer or another type.  If it is another type, the <tt>operator-></tt> is called
  *                 recursively.
@@ -242,34 +213,12 @@ SEQAN_CONCEPT(IteratorAssociatedTypesConcept, (T))
  * @brief Iterates to next position.
  *
  * @signature void goNext(it);
- * 
- * @param it The iterator to increment.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] it The iterator to increment.
+ *
  * This function is equivalent to <tt>++iterator</tt>.
  */
 
-/**
-.Concept.InputIteratorConcept
-..cat:Iterators
-..summary:Iterator that allows dereferenced reading.
-..baseconcept:Concept.IteratorAssociatedTypesConcept
-..baseconcept:Concept.CopyConstructibleConcept
-..baseconcept:Concept.EqualityComparableConcept
-..signature:InputIteratorConcept<T>
-..see:Concept.BasicOutputIteratorConcept
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
-
-.Function.operator->.concept:Concept.InputIteratorConcept
-.Function.operator++ (prefix).concept:Concept.InputIteratorConcept
-.Function.operator++ (suffix).concept:Concept.InputIteratorConcept
-.Function.goNext.concept:Concept.InputIteratorConcept
-.Function.operator*.concept:Concept.InputIteratorConcept
-.Function.operator!=.concept.Concept.InputIteratorConcept
- */
-
 SEQAN_CONCEPT_REFINE(InputIteratorConcept, (T), (IteratorAssociatedTypesConcept)(CopyConstructible)(EqualityComparable))
 {
     typedef typename Value<T>::Type      TValue;
@@ -294,7 +243,7 @@ SEQAN_CONCEPT_REFINE(InputIteratorConcept, (T), (IteratorAssociatedTypesConcept)
         // TODO(holtgrew): requires requires Dereferenceable<postincrement_result>;
 
         // operator->: Cannot check this, need to know member for this.
-        
+
         sameType(++x, rx);
         sameType(x++, y);
         goNext(x);
@@ -306,32 +255,30 @@ SEQAN_CONCEPT_REFINE(InputIteratorConcept, (T), (IteratorAssociatedTypesConcept)
 };
 
 /*!
- * @concept BasicOutputIteratorConcept
+ * @concept OutputIteratorConcept
  * @extends IteratorAssociatedTypesConcept
  * @extends CopyConstructibleConcept
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief Iterator that allows dereferenced writing.
- * 
+ *
  * @signature OutputIteratorConcept<T>
- * 
- * @section Remarks
- * 
- * The SeqAn iterators mirror the definitions from <a href="http://generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator">ConceptC++</a>. * 
+ *
+ * The SeqAn iterators mirror the definitions from <a href="http://generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator">ConceptC++</a>. *
  *
  * @section Examples
- * 
+ *
  * In the following, <tt>x</tt> is an iterator to type <tt>X</tt>, <tt>t</tt> is
  * a valid rvalue of type <tt>X</tt>.
- * 
+ *
  * The following expressions must be valid.
- * 
+ *
  * @code{.cpp}
  * *x = t     // Dereference assignment.
  * ++x        // Preincrement.
  * (void)x++  // Postincrement.
  * *x++ = t   // Postincrement and assign.
- *  
+ *
  * assignValue(x, t);
  * @endcode
  *
@@ -339,89 +286,60 @@ SEQAN_CONCEPT_REFINE(InputIteratorConcept, (T), (IteratorAssociatedTypesConcept)
  */
 
 /*!
- * @fn BasicOutputIteratorConcept#assignValue
+ * @fn OutputIteratorConcept#assignValue
  * @brief Assigns value to iterator.
  * @deprecated Use dereferencement and assignment instead.
- * 
+ *
  * @signature void assignValue(it, value);
- * @signature assignValue(container, pos, value)
- * 
- * @param it The iterator to assign value to.
- * @param value A value that is assigned to the item <tt>it</tt> points to.
+ *
+ * @param[in,out] it    The iterator to assign value to.
+ * @param[in]     value A value that is assigned to the item <tt>it</tt> points to.
  */
 
 /*!
- * @fn BasicOutputIteratorConcept#operator++(suffix)
+ * @fn OutputIteratorConcept#operator++(suffix)
  * @brief C++ built-in suffix increment operator.
- * 
+ *
  * @signature TIterator operator++(it, i)
- * 
- * @param it The iterator to increment.
- * @param i An integer, used to mark suffix decrement.
- * 
+ *
+ * @param[in,out] it The iterator to increment.
+ * @param[in]     i  An integer, used to mark suffix decrement.
+ *
  * @return TIterator A copy of the original iterator.
  */
 
 /*!
- * @fn BasicOutputIteratorConcept#operator++(prefix)
+ * @fn OutputIteratorConcept#operator++(prefix)
  * @brief C++ built-in prefix increment operator.
- * 
+ *
  * @signature TIterator operator++(it)
- * 
- * @param it The iterator to increment.
- * 
+ *
+ * @param[in,out] it The iterator to increment.
+ *
  * @return TIterator A copy of the original iterator.
  */
 
 /*!
- * @fn BasicOutputIteratorConcept#goNext
+ * @fn OutputIteratorConcept#goNext
  * @brief Iterates to next position.
- * 
+ *
  * @signature void goNext(it);
- * 
- * @param it The iterator to increment.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] it The iterator to increment.
+ *
  * This function is equivalent to <tt>++iterator</tt>.
  */
 
-/**
-.Concept.BasicOutputIteratorConcept
-..cat:Iterators
-..summary:Iterator that allows dereferenced writing.
-..baseconcept:Concept.IteratorAssociatedTypesConcept
-..baseconcept:Concept.CopyConstructibleConcept
-..signature:OutputIteratorConcept<T>
-..see:Concept.InputIteratorConcept
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
-..example.text:In the following, $x$ is an iterator to type $X$, $t$ is a valid rvalue of type $X$.
-..example.text:The following expressions must be valid.
-..example.code:
-*x = t     // Dereference assignment.
-++x        // Preincrement.
-(void)x++  // Postincrement.
-*x++ = t   // Postincrement and assign.
-
-assignValue(x, t);
-
-.Function.assignValue.concept:Concept.BasicOutputIteratorConcept
-.Function.operator++ (prefix).concept:Concept.BasicOutputIteratorConcept
-.Function.operator++ (suffix).concept:Concept.BasicOutputIteratorConcept
-.Function.goNext.concept:Concept.BasicOutputIteratorConcept
- */
-
-SEQAN_CONCEPT_REFINE(BasicOutputIteratorConcept, (T), (CopyConstructible))
+SEQAN_CONCEPT_REFINE(OutputIteratorConcept, (T), (CopyConstructible))
 {
     typedef typename Value<T>::Type TValue;
 
     SEQAN_CONCEPT_ASSERT((Is<Assignable<TValue> >));
-    
+
     T      x;
     TValue v;
 
-    SEQAN_CONCEPT_USAGE(BasicOutputIteratorConcept)
+    SEQAN_CONCEPT_USAGE(OutputIteratorConcept)
     {
         *x = v;
         assignValue(x, v);
@@ -442,41 +360,23 @@ SEQAN_CONCEPT_REFINE(BasicOutputIteratorConcept, (T), (CopyConstructible))
  * @extends DefaultConstructibleConcept
  * @headerfile <seqan/basic.h>
  * @brief Iterator that allows passing over a linear sequence multiple times.
- * 
+ *
  * @signature ForwardIteratorConcept<T>
- * 
- * @section Remarks
- * 
+ *
  * The SeqAn iterators mirror the definitions from <a href="http://generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator">ConceptC++</a>.
- * 
+ *
  * @section Examples
- * 
+ *
  * In the following, <tt>x</tt> is an iterator to type <tt>X</tt>.
- * 
+ *
  * The following expressions must be valid.
- * 
+ *
  * @code{.cpp}
  * ++x  // Preincrement.
  * x++  // Postincrement.
  * @endcode
  */
 
-/**
-.Concept.ForwardIteratorConcept
-..cat:Iterators
-..summary:Iterator that allows passing over a linear sequence multiple times.
-..baseconcept:Concept.InputIteratorConcept
-..baseconcept:Concept.DefaultConstructibleConcept
-..signature:ForwardIteratorConcept<T>
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
-..example.text:In the following, $x$ is an iterator to type $X$.
-..example.text:The following expressions must be valid.
-..example.code:
-++x  // Preincrement.
-x++  // Postincrement.
- */
-
 SEQAN_CONCEPT_REFINE(ForwardIteratorConcept, (T), (InputIteratorConcept)(DefaultConstructible))
 {
     typedef typename Value<T>::Type TValue;
@@ -493,27 +393,15 @@ SEQAN_CONCEPT_REFINE(ForwardIteratorConcept, (T), (InputIteratorConcept)(Default
 /*!
  * @concept MutableForwardIteratorConcept
  * @extends ForwardIteratorConcept
- * @extends BasicOutputIteratorConcept
+ * @extends OutputIteratorConcept
  * @headerfile <seqan/basic.h>
- * 
+ *
  * @brief A @link ForwardIteratorConcept Forward Iterator @endlink that allows dereferenced assignment.
- * 
- * @section Remarks
- * 
+ *
  * The SeqAn iterators mirror the definitions from <a href="http://generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator">ConceptC++</a>.
  */
 
-/**
-.Concept.MutableForwardIteratorConcept
-..cat:Iterators
-..summary:A @Concept.ForwardIteratorConcept|Forward Iterator@ that allows dereferenced assignment.
-..baseconcept:Concept.ForwardIteratorConcept
-..baseconcept:Concept.BasicOutputIteratorConcept
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
- */
-
-SEQAN_CONCEPT_REFINE(MutableForwardIteratorConcept, (T), (ForwardIteratorConcept)(BasicOutputIteratorConcept))
+SEQAN_CONCEPT_REFINE(MutableForwardIteratorConcept, (T), (ForwardIteratorConcept)(OutputIteratorConcept))
 {
     typedef typename Value<T>::Type      TValue;
 
@@ -528,25 +416,23 @@ SEQAN_CONCEPT_REFINE(MutableForwardIteratorConcept, (T), (ForwardIteratorConcept
 
 /*!
  * @concept BidirectionalIteratorConcept
- * 
- * @headerfile seqan/basic.h
- * 
+ *
+ * @headerfile <seqan/basic.h>
+ *
  * @extends ForwardIteratorConcept
- * 
+ *
  * @brief Iterator that can be both incremented and decremented.
- * 
+ *
  * @signature BidirectionalIteratorConcept<T>
- * 
- * @section Remarks
- * 
+ *
  * The SeqAn iterators mirror the definitions from <a href="http://generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator">ConceptC++</a>.
- * 
+ *
  * @section Examples
- * 
+ *
  * In the following, <tt>x</tt> is an iterator to type <tt>X</tt>.
- * 
+ *
  * The following expressions must be valid.
- * 
+ *
  * @code{.cpp}
  * --x  // Predecrement.
  * x--  // Postdecrement.
@@ -559,7 +445,7 @@ SEQAN_CONCEPT_REFINE(MutableForwardIteratorConcept, (T), (ForwardIteratorConcept
  *
  * @signature TIterator operator--(it);
  *
- * @param it The iterator to increment.
+ * @param[in,out] it The iterator to increment.
  *
  * @return TIterator Reference to the incremented iterator.
  */
@@ -570,8 +456,8 @@ SEQAN_CONCEPT_REFINE(MutableForwardIteratorConcept, (T), (ForwardIteratorConcept
  *
  * @signature TIterator operator--(it, i);
  *
- * @param it The iterator to increment.
- * @param i  An int value to mark the operator as suffix decrement.
+ * @param[in,out] it The iterator to increment.
+ * @param[in]     i  An int value to mark the operator as suffix decrement.
  *
  * @return TIterator Reference to the incremented iterator.
  */
@@ -579,35 +465,14 @@ SEQAN_CONCEPT_REFINE(MutableForwardIteratorConcept, (T), (ForwardIteratorConcept
 /*!
  * @fn BidirectionalIteratorConcept#goPrevious
  * @brief Iterates to pevious position.
- * 
+ *
  * @signature void goPrevious(it);
- * 
- * @param it Iterator to move to previous position.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] it Iterator to move to previous position.
+ *
  * This function is equivalent to <tt>--iterator</tt>.
  */
 
-/**
-.Concept.BidirectionalIteratorConcept
-..cat:Iterators
-..summary:Iterator that can be both incremented and decremented.
-..baseconcept:Concept.ForwardIteratorConcept
-..signature:BidirectionalIteratorConcept<T>
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
-..example.text:In the following, $x$ is an iterator to type $X$.
-..example.text:The following expressions must be valid.
-..example.code:
---x  // Predecrement.
-x--  // Postdecrement.
-
-.Function.operator-- (prefix).concept:Concept.BidirectionalIteratorConcept
-.Function.operator-- (suffix).concept:Concept.BidirectionalIteratorConcept
-.Function.goPrevious.concept:Concept.BidirectionalIteratorConcept
- */
-
 SEQAN_CONCEPT_REFINE(BidirectionalIteratorConcept, (T), (ForwardIteratorConcept))
 {
     T x;
@@ -629,15 +494,6 @@ SEQAN_CONCEPT_REFINE(BidirectionalIteratorConcept, (T), (ForwardIteratorConcept)
  * @signature MutableBidirectionalIteratorConcept<T>
  */
 
-/**
-.Concept.MutableBidirectionalIteratorConcept
-..cat:Iterators
-..summary:A @Concept.BidirectionalIteratorConcept|Bidirectional Iterator@ that allows dereferenced assignment
-..baseconcept:Concept.ForwardIteratorConcept
-..signature:MutableBidirectionalIteratorConcept<T>
-..include:seqan/basic.h
- */
-
 SEQAN_CONCEPT_REFINE(MutableBidirectionalIteratorConcept, (T), (BidirectionalIteratorConcept)(MutableForwardIteratorConcept))
 {
     typedef typename Value<T>::Type TValue;
@@ -660,17 +516,15 @@ SEQAN_CONCEPT_REFINE(MutableBidirectionalIteratorConcept, (T), (BidirectionalIte
  *
  * @signature RandomAccessIteratorConcept<T>
  *
- * @section Remarks
- * 
  * This function is equivalent to <tt>--iterator</tt>.
  *
  * @section Examples
- * 
+ *
  * In the following, <tt>x</tt> is an iterator to type <tt>X</tt>, <tt>t</tt> is
  * a valid rvalue of type <tt>X</tt>, <tt>n</tt> is a distance type.
- * 
+ *
  * The following expressions must be valid.
- * 
+ *
  * @code{.cpp}
  * x += n    // Iterator addition assignment.
  * x + n     // Iterator addition.
@@ -685,33 +539,29 @@ SEQAN_CONCEPT_REFINE(MutableBidirectionalIteratorConcept, (T), (BidirectionalIte
 /*!
  * @mfn RandomAccessIteratorConcept#Difference
  * @brief Type of an object that stores the difference between two iterators.
- * 
+ *
  * @signature Difference<T>::Type
- * 
+ *
  * @tparam T Type for which the difference type is determined.
- * 
+ *
  * @return Type The difference type.
- * 
- * @section Remarks
- * 
+ *
  * In most cases this type is <tt>ptrdiff_t</tt>.
  */
 
 /*!
  * @fn RandomAccessIteratorConcept#difference
  * @brief The difference between two iterators.
- * 
+ *
  * @signature TDifference difference(begin, end);
- * 
- * @param begin Iterator to the first position of a range.
- * @param end  Iterator behind the last position of a range.
- * 
- * @return TDifference Length of the range between <tt>begin</tt> and <tt>end</tt>, type from 
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] begin Iterator to the first position of a range.
+ * @param[in] end   Iterator behind the last position of a range.
+ *
+ * @return TDifference Length of the range between <tt>begin</tt> and <tt>end</tt>, type from
+ *
  * This function is equivalent to <tt>end - begin</tt>.
- * 
+ *
  * Usually, <tt>begin</tt> and <tt>end</tt> have the same type.
  */
 
@@ -739,28 +589,23 @@ SEQAN_CONCEPT_REFINE(MutableBidirectionalIteratorConcept, (T), (BidirectionalIte
 /*!
  * @fn RandomAccessIteratorConcept#goNil
  * @brief Moves iterator to nil position.
- * 
+ *
  * @signature void goNil(it);
- * 
- * @param it The iterator that will be moved.
  *
- * 
- * @section Remarks
- * 
+ * @param[in,out] it The iterator that will be moved.
+ *
  * <tt>it</tt> is set to an invalid position, e.g. <tt>NULL</tt> for pointer types.
  */
 
 /*!
  * @fn RandomAccessIteratorConcept#goFurther
  * @brief Iterates some steps further.
- * 
+ *
  * @signature void goFurther(iterator, steps);
- * 
- * @param it    The iterator to move.
- * @param steps Number of steps <tt>iterator</tt> should be moved further.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] it    The iterator to move.
+ * @param[in]     steps Number of steps <tt>iterator</tt> should be moved further.
+ *
  * This function is equivalent to <tt>iterator += steps</tt>.
  */
 
@@ -771,56 +616,21 @@ SEQAN_CONCEPT_REFINE(MutableBidirectionalIteratorConcept, (T), (BidirectionalIte
  * @signature TReference TIterator::operator[](pos);
  *
  * @tparam TReference The referenced element.
- * @tparam TIterator  The iterator to subscript.
  *
- * @param pos Position to get element at.
+ * @param[in] pos Position to get element at.
  */
 
 /*!
  * @fn RandomAccessIteratorConcept#atNil
  * @brief Tests whether iterator is at nil position.
- * 
+ *
  * @signature bool atNil(it);
- * 
- * @param it The iterator to query.
+ *
+ * @param[in] it The iterator to query.
  *
  * @return bool Whether or not the iterator is at the nil positions (NULL for pointers).
  */
 
-/**
-.Concept.RandomAccessIteratorConcept
-..cat:Iterators
-..summary:An iterator allowing random access.
-..baseconcept:Concept.BidirectionalIteratorConcept
-..baseconcept:Concept.LessThanComparableConcept
-..signature:RandomAccessIteratorConcept<T>
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
-..example.text:In the following, $x$ is an iterator to type $X$, $t$ is a valid rvalue of type $X$, $n$ is a distance type.
-..example.text:The following expressions must be valid.
-..example.code:
-x += n    // Iterator addition assignment.
-x + n     // Iterator addition.
-n + i     // Iterator addition.
-x -= n    // Iterator subtraction assignment.
-x - n     // Iterator subtraction.
-x - a     // Difference.
-x[n]      // Element operator.
-
-.Metafunction.Difference.concept:Concept.RandomAccessIteratorConcept
-.Function.operator+=.concept:Concept.RandomAccessIteratorConcept
-.Function.operator+.concept:Concept.RandomAccessIteratorConcept
-.Function.operator-=.concept:Concept.RandomAccessIteratorConcept
-.Function.operator-.concept:Concept.RandomAccessIteratorConcept
-.Function.difference.concept:Concept.RandomAccessIteratorConcept
-.Function.operator[].concept:Concept.RandomAccessIteratorConcept
-.Function.goFurther.concept:Concept.RandomAccessIteratorConcept
-
-.Function.operator>=.concept:Concept.RandomAccessIteratorConcept
-.Function.operator>.concept:Concept.RandomAccessIteratorConcept
-.Function.operator<=.concept:Concept.RandomAccessIteratorConcept
- */
-
 SEQAN_CONCEPT_REFINE(RandomAccessIteratorConcept, (T), (BidirectionalIteratorConcept)(LessThanComparable))
 {
     typedef typename Difference<T>::Type TDifference;
@@ -834,7 +644,7 @@ SEQAN_CONCEPT_REFINE(RandomAccessIteratorConcept, (T), (BidirectionalIteratorCon
     {
 
         x += n;
-        goFurther(x, n);        
+        goFurther(x, n);
         ignoreUnusedVariableWarning(x + n);
         ignoreUnusedVariableWarning(n + x);
         x -= n;
@@ -857,21 +667,6 @@ SEQAN_CONCEPT_REFINE(RandomAccessIteratorConcept, (T), (BidirectionalIteratorCon
  * @signature MutableRandomAccessIteratorConcept<T>
  */
 
-/**
-.Concept.MutableRandomAccessIteratorConcept
-..cat:Iterators
-..summary:A @Concept.RandomAccessIteratorConcept@ that allows assignable derefentiation.
-..baseconcept:Concept.BidirectionalIteratorConcept
-..baseconcept:Concept.LessThanComparableConcept
-..signature:RandomAccessIteratorConcept<T>
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..example.text:The following expressions should be valid.
-..example.code:
-value(x, n) = t
-x[n] = t
-..include:seqan/basic.h
- */
-
 SEQAN_CONCEPT_REFINE(MutableRandomAccessIteratorConcept, (T), (RandomAccessIteratorConcept)(MutableBidirectionalIteratorConcept))
 {
     typedef typename Difference<T>::Type TDifference;
@@ -913,12 +708,11 @@ SEQAN_CONCEPT_REFINE(MutableRandomAccessIteratorConcept, (T), (RandomAccessItera
  *
  * @signature TContainer container(it);
  *
- * @param it The iterator to get the container of.
+ * @param[in] it The iterator to get the container of.
  *
  * @return TContainer The container of the iterat.r
- *
- * TODO(holtgrew): Need to document Reference_ and Parameter_.
  */
+// TODO(holtgrew): Need to document Reference_ and Parameter_.
 
 /*!
  * @fn RootedIteratorConcept#atBegin
@@ -926,7 +720,7 @@ SEQAN_CONCEPT_REFINE(MutableRandomAccessIteratorConcept, (T), (RandomAccessItera
  *
  * @signature bool atBegin(it);
  *
- * @param it The rooted iterator to query.
+ * @param[in] it The rooted iterator to query.
  *
  * @return bool Whether or not the iterator is at the beginning.
  */
@@ -937,26 +731,11 @@ SEQAN_CONCEPT_REFINE(MutableRandomAccessIteratorConcept, (T), (RandomAccessItera
  *
  * @signature bool atEnd(it);
  *
- * @param it The rooted iterator to query.
+ * @param[in] it The rooted iterator to query.
  *
  * @return bool Whether or not the iterator is at the end.
  */
 
-/**
-.Concept.RootedIteratorConcept
-..cat:Iterators
-..summary:Iterator that knows its container.
-..baseconcept:Concept.ForwardIteratorConcept
-..signature:RootedIteratorConcept<T>
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
-
-.Metafunction.Container.concept:Concept.RootedIteratorConcept
-.Function.container.concept:Concept.RootedIteratorConcept
-.Function.atBegin.concept:Concept.RootedIteratorConcept
-.Function.atEnd.concept:Concept.RootedIteratorConcept
- */
-
 SEQAN_CONCEPT_REFINE(RootedIteratorConcept, (T), (IteratorAssociatedTypesConcept))
 {
     typedef typename Container<T>::Type TContainer;
@@ -985,16 +764,6 @@ SEQAN_CONCEPT_REFINE(RootedIteratorConcept, (T), (IteratorAssociatedTypesConcept
  * @signature MutableRootedIteratorConcept<T>
  */
 
-/**
-.Concept.MutableRootedIteratorConcept
-..cat:Iterators
-..summary:A @Concept.RootedIteratorConcept|Rooted Iterator@ that allows dereferenced assignment.
-..baseconcept:Concept.ForwardIteratorConcept
-..signature:RootedIteratorConcept<T>
-..remarks:The SeqAn iterators mirror the definitions from @http://www.generic-programming.org/languages/conceptcpp/concept_web.php?header=iterator|ConceptC++@.
-..include:seqan/basic.h
- */
-
 SEQAN_CONCEPT_REFINE(MutableRootedIteratorConcept, (T), (RootedIteratorConcept)(MutableForwardIteratorConcept))
 {
     SEQAN_CONCEPT_USAGE(MutableRootedIteratorConcept)
@@ -1028,7 +797,7 @@ SEQAN_CONCEPT_REFINE(MutableRootedIteratorConcept, (T), (RootedIteratorConcept)(
  *
  * @signature TPosition position(it);
  *
- * @param it The iterator to query for its position.
+ * @param[in] it The iterator to query for its position.
  *
  * @return TPosition The position of <tt>it</tt>
  */
@@ -1039,8 +808,8 @@ SEQAN_CONCEPT_REFINE(MutableRootedIteratorConcept, (T), (RootedIteratorConcept)(
  *
  * @signature void setPosition(it, pos);
  *
- * @param it  The iterator to set the position of.
- * @param pos The position to set <tt>it</tt> to.
+ * @param[in,out] it  The iterator to set the position of.
+ * @param[in]     pos The position to set <tt>it</tt> to.
  */
 
 /*!
@@ -1049,7 +818,7 @@ SEQAN_CONCEPT_REFINE(MutableRootedIteratorConcept, (T), (RootedIteratorConcept)(
  *
  * @signature void goBegin(it);
  *
- * @param it  The iterator to set the position of.
+ * @param[in,out] it  The iterator to set the position of.
  */
 
 /*!
@@ -1058,22 +827,7 @@ SEQAN_CONCEPT_REFINE(MutableRootedIteratorConcept, (T), (RootedIteratorConcept)(
  *
  * @signature void goEnd(it, pos);
  *
- * @param it  The iterator to set the position of.
- */
-
-/**
-.Concept.RootedRandomAccessIteratorConcept
-..cat:Iterators
-..summary:An iterator that is both rooted and random access, allowing to implement @Function.position@.
-..signature:RootedRandomAccessIteratorConcept<T>
-..baseconcept:Concept.RandomAccessIteratorConcept
-..baseconcept:Concept.RootedIteratorConcept
-
-.Metafunction.Position.concept:Concept.RootedRandomAccessIteratorConcept
-.Function.position.concept:Concept.RootedRandomAccessIteratorConcept
-.Function.setPosition.concept:Concept.RootedRandomAccessIteratorConcept
-.Function.goBegin.concept:Concept.RootedRandomAccessIteratorConcept
-.Function.goEnd.concept:Concept.RootedRandomAccessIteratorConcept
+ * @param[in,out] it  The iterator to set the position of.
  */
 
 SEQAN_CONCEPT_REFINE(RootedRandomAccessIteratorConcept, (T), (RootedIteratorConcept)(RandomAccessIteratorConcept))
@@ -1100,16 +854,6 @@ SEQAN_CONCEPT_REFINE(RootedRandomAccessIteratorConcept, (T), (RootedIteratorConc
  * @signature RootedRandomAccessIteratorConcept<T>
  */
 
-/**
-.Concept.MutableRootedRandomAccessIteratorConcept
-..cat:Iterators
-..baseconcept:Concept.RootedRandomAccessIteratorConcept
-..baseconcept:Concept.MutableBidirectionalIteratorConcept
-..summary:A @Concept.RootedIteratorConcept|Rooted Iterator@ that allows dereferenced assignment.
-..signature:MutableRootedRandomAccessIteratorConcept<T>
-..include:seqan/basic.h
- */
-
 SEQAN_CONCEPT_REFINE(MutableRootedRandomAccessIteratorConcept, (T), (RootedRandomAccessIteratorConcept)(MutableBidirectionalIteratorConcept))
 {
     SEQAN_CONCEPT_USAGE(MutableRootedRandomAccessIteratorConcept)
@@ -1119,4 +863,4 @@ SEQAN_CONCEPT_REFINE(MutableRootedRandomAccessIteratorConcept, (T), (RootedRando
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BASIC_ITERATOR_CONCEPT_H_
+#endif  // #ifndef INCLUDE_SEQAN_BASIC_ITERATOR_CONCEPT_H_
diff --git a/seqan/basic/iterator_counting.h b/seqan/basic/iterator_counting.h
new file mode 100644
index 0000000..fbe9a45
--- /dev/null
+++ b/seqan/basic/iterator_counting.h
@@ -0,0 +1,359 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Counting iterator implementation.
+// ==========================================================================
+
+#ifndef SEQAN_BASIC_ITERATOR_COUNTING_H_
+#define SEQAN_BASIC_ITERATOR_COUNTING_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+template <typename TSpec = void>
+struct CountingIteratorImpl_;
+
+typedef CountingIteratorImpl_<void> CountingIterator;
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+template <typename TSpec, typename TIncrementable>
+class Iter<TIncrementable, CountingIteratorImpl_<TSpec> >
+{
+public:
+    TIncrementable data_position;
+
+    // ------------------------------------------------------------------------
+    // Constructors
+    // ------------------------------------------------------------------------
+
+    Iter(TIncrementable position = 0) :
+        data_position(position)
+    {}
+
+    template <typename TOther>
+    Iter(TOther position) :
+        data_position(position)
+    {}
+
+    Iter(Iter const & other) :
+        data_position(other.data_position)
+    {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+template <typename TSpec, typename TIncrementable>
+struct Size<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >
+{
+    typedef TIncrementable Type;
+};
+
+template <typename TSpec, typename TIncrementable>
+struct Position<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >
+{
+    typedef TIncrementable Type;
+};
+
+template <typename TSpec, typename TIncrementable>
+struct Difference<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >
+{
+    typedef typename MakeSigned<TIncrementable>::Type Type;
+};
+
+template <typename TSpec, typename TIncrementable>
+struct Value<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >
+{
+    typedef TIncrementable Type;
+};
+
+template <typename TSpec, typename TIncrementable>
+struct GetValue<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >
+{
+    typedef TIncrementable Type;
+};
+
+template <typename TSpec, typename TIncrementable>
+struct Reference<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >
+{
+    typedef TIncrementable Type;
+};
+
+template <typename TSpec, typename TIncrementable>
+struct Reference<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const>
+{
+    typedef TIncrementable const Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function position()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIncrementable>
+inline typename Position<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >::Type
+position(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & me)
+{
+    return me.data_position;
+}
+
+template <typename TSpec, typename TIncrementable>
+inline typename Position<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const>::Type
+position(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & me)
+{
+    return me.data_position;
+}
+
+// ----------------------------------------------------------------------------
+// Function setPosition()
+// ----------------------------------------------------------------------------
+
+template <typename TIncrementable, typename TSpec, typename TPosition>
+inline void
+setPosition(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & me, TPosition position_)
+{
+    me.data_position = position_;
+}
+
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIncrementable>
+inline typename Reference<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >::Type
+value(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & me)
+{
+    return position(me);
+}
+
+template <typename TSpec, typename TIncrementable>
+inline typename Reference<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const>::Type
+value(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & me)
+{
+    return position(me);
+}
+
+// ----------------------------------------------------------------------------
+// Function assignValue()
+// ----------------------------------------------------------------------------
+
+template <typename TIncrementable, typename TSpec, typename TValue>
+inline void
+assignValue(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & me, TValue _value)
+{
+    setPosition(me, _value);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator==()
+// ----------------------------------------------------------------------------
+
+//NOTE(h-2): the other operators should get a similar const-container-tolerant interface
+template <typename TSpec, typename TIncrementable, typename TIncrementable2>
+inline SEQAN_FUNC_ENABLE_IF(IsSameType<TIncrementable const &, TIncrementable2 const &>, bool)
+operator==(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left,
+           Iter<TIncrementable2, CountingIteratorImpl_<TSpec> > const & right)
+{
+    return position(left) == position(right);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator!=()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIncrementable>
+inline bool
+operator!=(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left,
+           Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & right)
+{
+    return position(left) != position(right);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator<()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIncrementable>
+inline bool
+operator<(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left,
+          Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & right)
+{
+    return position(left) < position(right);
+}
+
+template <typename TSpec, typename TIncrementable>
+inline bool
+operator>(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left,
+          Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & right)
+{
+    return position(left) > position(right);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator<=()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIncrementable>
+inline bool
+operator<=(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left,
+           Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & right)
+{
+    return position(left) <= position(right);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator>=()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIncrementable>
+inline bool
+operator>=(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left,
+           Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & right)
+{
+    return position(left) >= position(right);
+}
+
+// ----------------------------------------------------------------------------
+// Function goNext()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIncrementable>
+inline void
+goNext(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & me)
+{
+    setPosition(me, position(me) + 1);
+}
+
+// ----------------------------------------------------------------------------
+// Function goPrevious()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIncrementable>
+inline void
+goPrevious(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & me)
+{
+    setPosition(me, position(me) - 1);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator+()
+// ----------------------------------------------------------------------------
+
+template <typename TIncrementable, typename TSpec, typename TIntegral>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TIntegral> >, Iter<TIncrementable, CountingIteratorImpl_<TSpec> >)
+operator+(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left, TIntegral right)
+{
+    Iter<TIncrementable, CountingIteratorImpl_<TSpec> > tmp(left);
+    setPosition(tmp, position(left) + right);
+    return tmp;
+}
+
+template <typename TIncrementable, typename TSpec, typename TIntegral>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TIntegral> >, Iter<TIncrementable, CountingIteratorImpl_<TSpec> >)
+operator+(TIntegral left, Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & right)
+{
+    Iter<TIncrementable, CountingIteratorImpl_<TSpec> > tmp(right);
+    setPosition(tmp, position(right) + left);
+    return tmp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator+=()
+// ----------------------------------------------------------------------------
+
+template <typename TIncrementable, typename TSpec, typename TIntegral>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TIntegral> >, Iter<TIncrementable, CountingIteratorImpl_<TSpec> > &)
+operator+=(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & left, TIntegral right)
+{
+    setPosition(left, position(left) + right);
+    return left;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator-()
+// ----------------------------------------------------------------------------
+
+template <typename TIncrementable, typename TSpec, typename TIntegral>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TIntegral> >, Iter<TIncrementable, CountingIteratorImpl_<TSpec> >)
+operator-(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left, TIntegral right)
+{
+    Iter<TIncrementable, CountingIteratorImpl_<TSpec> > tmp(left);
+    setPosition(tmp, position(left) - right);
+    return tmp;
+}
+
+template <typename TSpec, typename TIncrementable>
+inline typename Difference<Iter<TIncrementable, CountingIteratorImpl_<TSpec> > >::Type
+operator-(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & left,
+          Iter<TIncrementable, CountingIteratorImpl_<TSpec> > const & right)
+{
+    return position(left) - position(right);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator-=()
+// ----------------------------------------------------------------------------
+
+template <typename TIncrementable, typename TSpec, typename TIntegral>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TIntegral> >, Iter<TIncrementable, CountingIteratorImpl_<TSpec> > &)
+operator-=(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & left, TIntegral right)
+{
+    setPosition(left, position(left) - right);
+    return left;
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()
+// ----------------------------------------------------------------------------
+
+// Conversion assignment.
+template <typename TIncrementable, typename TSpec, typename TSource>
+inline void
+assign(Iter<TIncrementable, CountingIteratorImpl_<TSpec> > & target, TSource const & source)
+{
+    setPosition(target, position(source));
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_BASIC_ITERATOR_COUNTING_H_
diff --git a/seqan/basic/iterator_interface.h b/seqan/basic/iterator_interface.h
index 540d883..bee86c9 100644
--- a/seqan/basic/iterator_interface.h
+++ b/seqan/basic/iterator_interface.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 
 // TODO(holtgrew): Split into iterator_interface.h and iterator_adapt_pointer.h.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_INTERFACE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_INTERFACE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_INTERFACE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_INTERFACE_H_
 
 namespace seqan {
 
@@ -51,6 +51,7 @@ namespace seqan {
 
 /*!
  * @defgroup ContainerIteratorTags Container Iterator Tags
+ * @brief Tags for container iterators.
  *
  * The tags <tt>Standard</tt> and <tt>Rooted</tt> can be used for selecting specific iterator types with the
  * @link ContainerConcept#Iterator @endlink metafunction.  Rooted iterators also carry a pointer to the container
@@ -69,25 +70,6 @@ namespace seqan {
  *            typedef Tag<Rooted_> Rooted;
  */
 
-/**
-.Tag.Iterator Spec:
-..cat:Iteration
-..summary:Specifies the kind of an iterator.
-..tag.Rooted:Rooted iterator.
-...remarks
-....text:This iterator implements some more advanced functions like
-@Function.container@ and @Function.position@.
-....concept:Concept.RootedIteratorConcept
-..tag.Standard:Standard conform iterator.
-...remarks
-....text:Note that standard iterators need not to implement all functions
-that are available for rooted iterators.
-..remarks.text:The default iterator spec is given by @Metafunction.DefaultIteratorSpec@.
-..see:Metafunction.DefaultIteratorSpec
-..see:Concept.IteratorAssociatedTypesConcept
-..include:seqan/basic.h
-*/
-
 struct Rooted_;
 typedef Tag<Rooted_> const Rooted;
 
@@ -116,19 +98,6 @@ typedef Tag<Standard_> const Standard;
  * @see ContainerConcept#Iterator
  */
 
-/**
-.Metafunction.DefaultIteratorSpec:
-..hidefromindex
-..concept:Concept.ContainerConcept
-..summary:Specifies default kind of iterator.
-..signature:DefaultIteratorSpec<T>::Type
-..param.T:Container type for which the default iterator spec is determined.
-...type:Concept.ContainerConcept
-..returns.param.Type:Iterator spec of $T$.
-..see:Metafunction.Iterator
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct DefaultIteratorSpec
 {
@@ -154,22 +123,6 @@ struct DefaultIteratorSpec
  * @see ContainerConcept#Iterator
  */
 
-/**
-.Metafunction.DefaultGetIteratorSpec:
-..hidefromindex
-..concept:Concept.ContainerConcept
-..summary:Specifies default kind of iterator returned by functions.
-..signature:DefaultGetIteratorSpec<T>::Type
-..param.T:Container type for which the spec is determined.
-...concept:Concept.ContainerConcept
-..returns.param.Type:Iterator spec of $T$.
-..remarks:This metafunction returns the iterator spec of iterators that are returned by functions like
-@Function.begin@, @Function.end@, or @Function.iter@.
-..see:Metafunction.Iterator
-..see:Metafunction.DefaultIteratorSpec
-..include:seqan/basic.h
-*/
-
 template <typename T>
 struct DefaultGetIteratorSpec
 {
@@ -180,25 +133,6 @@ struct DefaultGetIteratorSpec
 // Metafunction Iterator
 // ----------------------------------------------------------------------------
 
-/**
-.Metafunction.Iterator:
-..concept:Concept.ContainerConcept
-..cat:Iteration
-..summary:Type of iterator objects that are used to traverse the container.
-..signature:Iterator<T, TSpec>::Type
-..param.T:Type for which the iterator type is determined.
-...concept:Concept.ContainerConcept
-...type:Class.Iter
-..param.TSpec:Specifies an @Tag.Iterator Spec.iterator spec@.
-...default:The default iterator spec is given by @Metafunction.DefaultIteratorSpec@.
-..returns.param.Type:Iterator type of $T$.
-..remarks.text:Iterators behave like pointers in some respects.
- For example, you can use $*it$ to access the value object the iterator $it$ points to.
- But note that $Iterator<T>::Type$ can differ from $T *$, depending on $T$.
-..see:Metafunction.Position
-..include:seqan/basic.h
-*/
-
 template <typename T, typename TSpec>
 struct IteratorDefaultImp_;
 
@@ -232,19 +166,6 @@ struct Iterator : IteratorDefaultImp_<T, TSpec>
 // Metafunction Container
 // ----------------------------------------------------------------------------
 
-/**
-.Metafunction.Container:
-..class:Class.Iter
-..cat:Iteration
-..summary:Type of the container given an iterator.
-..signature:Container<T>::Type
-..param.T:Iterator type.
-...type:Class.Iter
-...concept:Concept.RootedIteratorConcept
-..returns.param.Type:The container type to $T$.
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Remove the default implementation; anti-auto-sequence. Also, using plain pointers for strings does not work any more. Will probably only work for rooted/adaptor/positional iterators. Same below.
 
 template <typename T>
@@ -261,16 +182,6 @@ struct Container
 // Function value()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.value
-..class:Class.Iter
-..signature:Reference value(object)
-..param.object:An object that holds a value or an iterator that points to a value.
-...type:Class.Iter
-...concept:Concept.IteratorAssociatedTypesConcept
-..include:seqan/basic.h
-*/
-
 template <typename T>
 inline typename Reference<T>::Type
 value(T & me)
@@ -291,18 +202,6 @@ value(T const & me)
 // Function getValue()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.getValue
-..class:Class.Iter
-..cat:Iteration
-..signature:GetValue getValue(object)
-..param.object:An object that holds a value or points to a value.
-...type:Class.Iter
-...concept:Concept.IteratorAssociatedTypesConcept
-..see:Metafunction.GetValue
-..include:seqan/basic.h
-*/
-
 template <typename T>
 inline typename GetValue<T>::Type
 getValue(T & me)
@@ -330,23 +229,6 @@ getValue(T const & me)
 // Function assignValue()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.assignValue
-..class:Class.Iter
-..cat:Iteration
-..summary:Assigns value to item.
-..signature:assignValue(object, value)
-..param.object:An object that holds a value or points to a value.
-...type:Class.Iter
-...concept:Concept.BasicOutputIteratorConcept
-..param.value:A value that is assigned to the item $object$ holds or points to.
-..remarks.text:This function is similar to @Function.assign@.
-The difference is, that $assignValue$ just changes a value stored in $object$ or the value $object$ points to,
-while @Function.assign@ changes the whole object.
-..see:Function.assign
-..include:seqan/basic.h
-*/
-
 template <typename T, typename TValue>
 inline void
 assignValue(T & me,
@@ -370,23 +252,17 @@ assignValue(T const & me,
 // Function moveValue()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.moveValue
-..class:Class.Iter
-..cat:Iteration
-..summary:Assigns value to item.
-..signature:moveValue(object, value)
-..param.object:An object that holds a value or points to a value.
-...type:Class.Iter
-...concept:Concept.BasicOutputIteratorConcept
-..param.value:A value that is handed over to the item $object$ holds or points to.
-..remarks.text:This function is similar to @Function.move@.
-The difference is, that $moveValue$ just changes a value stored in $object$ or the value $object$ points to,
-while @Function.move@ changes the whole object.
-..see:Function.move
-..see:Function.assignValue
-..include:seqan/basic.h
-*/
+/*!
+ * @fn OutputIteratorConcept#moveValue
+ * @headerfile <seqan/sequence.h>
+ * @brief Move a value of a container to a given position.
+ *
+ * @signature void moveValue(container, pos, value);
+ *
+ * @param[in,out] container The container to manipulate.
+ * @param[in]     pos       The position of the item in the container to manipulate.
+ * @param[in,out] value     The value to move to <tt>container[pos]</tt>.
+ */
 
 template <typename T, typename TValue>
 inline void
@@ -411,9 +287,6 @@ moveValue(T const & me,
 // Function setValue()
 // ---------------------------------------------------------------------------
 
-///.Function.setValue.param.object.type:Concept.BasicOutputIteratorConcept
-///.Function.setValue.concept:Concept.BasicOutputIteratorConcept
-
 template <typename T, typename TValue>
 inline void
 setValue(T * & ptr,
@@ -437,20 +310,6 @@ setValue(T const * & ptr,
 // Function container()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.container
-..concept:Concept.RootedIteratorConcept
-..cat:Iteration
-..summary:Container of an iterator.
-..signature:Container container(iterator)
-..param.iterator:An iterator.
-...type:Class.Iter
-...concept:Concept.RootedIteratorConcept
-..returns:The container that $iterator$ traverses.
-...metafunction:Metafunction.Container
-..include:seqan/basic.h
-*/
-
 template <typename T>
 inline
 typename Container<T>::Type &
@@ -465,25 +324,6 @@ container(T me)
 // Function position()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.position
-..class:Class.Iter
-..concept:Concept.ContainerConcept
-..summary:Position of an iterator.
-..cat:Iteration
-..signature:Position position(iterator [, container])
-..param.iterator:An iterator.
-...type:Class.Iter
-...concept:Concept.RootedRandomAccessIteratorConcept
-..param.container:A container.
-...concept:Concept.ContainerConcept
-...remarks:If $iterator$ implements @Concept.RootedIteratorConcept@, then $container$ is optional.
-...remarks:If $container$ is specified, $iterator$ must be a container of $container$.
-..returns:The position of the value in the container $iterator$ points to.
-...metafunction:Metafunction.Position
-..include:seqan/basic.h
-*/
-
 template <typename T>
 inline typename Position<T>::Type
 position(T * /*me*/)
@@ -498,7 +338,6 @@ inline SEQAN_HOST_DEVICE typename Position<TContainer>::Type
 position(TIterator const & it,
          TContainer const & me)
 {
-    SEQAN_CHECKPOINT;
     return it - begin(me, Standard());
 }
 
@@ -506,65 +345,16 @@ position(TIterator const & it,
 // Function atBegin()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.atBegin
-..class:Class.Iter
-..concept:Concept.ContainerConcept
-..concept:Concept.RootedIteratorConcept
-..cat:Iteration
-..summary:Determines whether an iterator is at the beginning position.
-..signature:bool atBegin(iterator [, container])
-..param.iterator:An iterator.
-...type:Class.Iter
-...concept:Concept.RootedIteratorConcept
-..param.container:Container of $iterator$. (optional)
-...remarks.text:If $iterator$ implements @Concept.RootedIteratorConcept@ then $container$ is optional otherwise $container$ is required.
-..returns:$true$ if $iterator$ points to the fist item of the container, otherwise $false$.
-..see:Function.begin
-..include:seqan/basic.h
-*/
-
 // TODO(doering): Was, wenn der Container leer ist?
 
 template <typename T, typename TContainer>
 inline SEQAN_HOST_DEVICE bool
-atBegin(T const & it, TContainer const & cont)
-{
-    SEQAN_CHECKPOINT;
-    return it == begin(cont, Standard());
-}
-
-template <typename T, typename TContainer>
-inline SEQAN_HOST_DEVICE bool
-atBegin(T const & it, TContainer & cont)
+atBegin(T const & it,
+        TContainer const & cont)
 {
-    SEQAN_CHECKPOINT;
-    return it == begin(cont, Standard());
-}
-
-template <typename T, typename TContainer>
-inline SEQAN_HOST_DEVICE bool
-atBegin(T & it, TContainer & cont)
-{
-    SEQAN_CHECKPOINT;
     return it == begin(cont, Standard());
 }
 
-template <typename T, typename TContainer>
-inline SEQAN_HOST_DEVICE bool
-atBegin(T & it, TContainer const & cont)
-{
-    SEQAN_CHECKPOINT;
-    return it == begin(cont, Standard());
-}
-
-template <typename T>
-inline SEQAN_HOST_DEVICE bool
-atBegin(T & it)
-{
-    return atBegin(it, container(it));
-}
-
 template <typename T>
 inline SEQAN_HOST_DEVICE bool
 atBegin(T const & it)
@@ -576,71 +366,14 @@ atBegin(T const & it)
 // Function atEnd()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.atEnd
-..class:Class.Iter
-..concept:Concept.ContainerConcept
-..concept:Concept.RootedIteratorConcept
-..cat:Iteration
-..summary:Determines whether an iterator is at the end position.
-..signature:bool atEnd(iterator [, container])
-..param.iterator:An iterator.
-...type:Class.Iter
-...concept:Concept.RootedIteratorConcept
-..param.container:Container of $iterator$.
-...remarks.text:If $iterator$ implements @Concept.RootedIteratorConcept@ then $container$ is optional.
-....text:$container$ is also optional for iterators to @Adaption.char array.char arrays@.
-....text:Otherwise, $container$ is required.
-..returns:$true$ if $iterator$ points behind the last item of the container, otherwise $false$.
-..see:Function.atBegin
-..see:Function.end
-..include:seqan/basic.h
-*/
-
-template <typename T, typename TContainer>
-inline SEQAN_HOST_DEVICE bool
-atEnd(T & it,
-      TContainer const & cont)
-{
-    SEQAN_CHECKPOINT;
-    return it == end(cont, Standard());
-}
-
 template <typename T, typename TContainer>
 inline SEQAN_HOST_DEVICE bool
 atEnd(T const & it,
       TContainer const & cont)
 {
-    SEQAN_CHECKPOINT;
-    return it == end(cont, Standard());
-}
-
-template <typename T, typename TContainer>
-inline SEQAN_HOST_DEVICE bool
-atEnd(T & it,
-      TContainer & cont)
-{
-    SEQAN_CHECKPOINT;
-    return it == end(cont, Standard());
-}
-
-template <typename T, typename TContainer>
-inline SEQAN_HOST_DEVICE bool
-atEnd(T const & it,
-      TContainer & cont)
-{
-    SEQAN_CHECKPOINT;
     return it == end(cont, Standard());
 }
 
-template <typename T>
-inline SEQAN_HOST_DEVICE bool
-atEnd(T & it)
-{
-    SEQAN_CHECKPOINT;
-    return atEnd(it, container(it));
-}
-
 template <typename T>
 inline SEQAN_HOST_DEVICE bool
 atEnd(T const & it)
@@ -653,28 +386,6 @@ atEnd(T const & it)
 // Function goBegin()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.goBegin
-..class:Class.Iter
-..concept:Concept.RootedIteratorConcept
-..cat:Iteration
-..summary:Iterates to the first position of a container.
-..signature:goBegin(iterator [, container])
-..param.iterator:Object that iterates through $container$.
-...type:Class.Iter
-...concept:Concept.RootedIteratorConcept
-...text:$iterator$ is set to the position of the first item in $container$.
-..param.container:Container of $iterator$.
-...type:Concept.ContainerConcept
-...remarks.text:If $iterator$ implements @Concept.RootedIteratorConcept@ then $container$ is optional,
-otherwise $container$ is required.
-..remarks:This function is equivalent to $iterator = begin(container)$.
-..see:Function.begin
-..see:Function.atBegin
-..see:Function.goEnd
-..include:seqan/basic.h
-*/
-
 template <typename TIterator, typename TContainer>
 inline SEQAN_HOST_DEVICE void
 goBegin(TIterator & it,
@@ -703,29 +414,6 @@ goBegin(TIterator & it)
 // Function goEnd()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.goEnd
-..class:Class.Iter
-..concept:Concept.RootedIteratorConcept
-..cat:Iteration
-..summary:Iterates to the last position of a container.
-..signature:goEnd(iterator [, container])
-..param.iterator:Object that iterates through $container$.
-...type:Class.Iter
-...concept:Concept.RootedIteratorConcept
-...text:$iterator$ is set to the position behin the last item in $container$.
-..param.container:Container of $iterator$.
-...type:Concept.ContainerConcept
-...remarks.text:If $iterator$ implements @Concept.RootedIteratorConcept@ then $container$ is optional,
-otherwise $container$ is required.
-..remarks:This function is equivalent to $iterator = end(container)$.
-..see:Function.end
-..see:Function.atEnd
-..see:Function.goBegin
-..see:Function.goEnd
-..include:seqan/basic.h
-*/
-
 template <typename TIterator, typename TContainer>
 inline SEQAN_HOST_DEVICE void
 goEnd(TIterator & it,
@@ -756,22 +444,6 @@ goEnd(TIterator & it)
 // Function goNext()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.goNext
-..concept:Concept.ForwardIteratorConcept
-..cat:Iteration
-..summary:Iterates to next position.
-..signature:goNext(iterator)
-..param.iterator:An iterator.
-...type:Class.Iter
-...concept:Concept.ForwardIteratorConcept
-...text:$iterator$ is set to the next position of an iteration through its container.
-..remarks:This function is equivalent to $++iterator$.
-..see:Function.goBegin
-..see:Function.goEnd
-..include:seqan/basic.h
-*/
-
 template <typename TIterator>
 inline SEQAN_HOST_DEVICE void
 goNext(TIterator & it)
@@ -784,24 +456,6 @@ goNext(TIterator & it)
 // Function goFurther()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.goFurther
-..concept:Concept.RandomAccessIteratorConcept
-..cat:Iteration
-..summary:Iterates some steps further.
-..signature:goFurther(iterator, steps)
-..param.iterator:An iterator.
-...type:Class.Iter
-...concept:Concept.RandomAccessIteratorConcept
-...text:$iterator$ is set $steps$ positions further in the iteration through the container.
-..param.steps:Number of steps $iterator$ should be moved further.
-...remarks:If $iterator$ supports bidirectional iteration, $steps$ could also be negativ.
-..remarks:This function is equivalent to $iterator += steps$ for random access iterators.
-..see:Function.goNext
-..see:Function.goPrevious
-..include:seqan/basic.h
-*/
-
 template <typename TIterator, typename TDiff>
 inline SEQAN_HOST_DEVICE void
 goFurther(TIterator & it,
@@ -814,22 +468,6 @@ goFurther(TIterator & it,
 // Function goPrevious()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.goPrevious
-..concept:Concept.BidirectionalIteratorConcept
-..cat:Iteration
-..summary:Iterates to pevious position.
-..signature:goPrevious(iterator)
-..param.iterator:An iterator.
-...type:Class.Iter
-...concept:Concept.BidirectionalIteratorConcept
-...text:$iterator$ is set to the pevious position of an iteration through its container.
-..remarks:This function is equivalent to $--iterator$.
-..see:Function.goBegin
-..see:Function.goEnd
-..see:Function.goNext
-..include:seqan/basic.h
-*/
 template <typename TIterator>
 inline SEQAN_HOST_DEVICE void
 goPrevious(TIterator & it)
@@ -842,27 +480,6 @@ goPrevious(TIterator & it)
 // Function difference()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.difference
-..concept:Concept.RandomAccessIteratorConcept
-..cat:Iteration
-..summary:The difference between two iterators.
-..signature:difference(begin, end)
-..param.begin:Iterator to the first position of a range.
-...type:Class.Iter
-...concept:Concept.RandomAccessIteratorConcept
-..param.end:Iterator behind the last position of a range.
-...type:Class.Iter
-...concept:Concept.RandomAccessIteratorConcept
-..returns:Length of the range between $begin$ and $end$.
-..remarks:This function is equivalent to $end - begin$.
-...text:Usually, $begin$ and $end$ have the same type.
-..see:Function.begin
-..see:Function.end
-..see:Function.length
-..include:seqan/basic.h
-*/
-
 template <typename TIterator>
 inline SEQAN_HOST_DEVICE
 typename Difference<TIterator>::Type
@@ -877,19 +494,6 @@ difference(TIterator const & begin,
 // Function goNil()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.goNil
-..concept:Concept.RandomAccessIteratorConcept
-..cat:Iteration
-..summary:Moves iterator to nil position.
-..signature:goNil(iterator)
-..param.iterator:The iterator that will be moved.
-...type:Concept.RandomAccessIteratorConcept
-..remarks:$iterator$ is set to an invalid position, e.g. $NULL$ for pointer types.
-..see:Function.clear
-..include:seqan/basic.h
-*/
-
 template <typename TIterator>
 inline void
 goNil(TIterator & me)
@@ -910,20 +514,6 @@ goNil(TIterator * & me)
 // Function atNil()
 // ---------------------------------------------------------------------------
 
-/**
-.Function.atNil
-..concept:Concept.RandomAccessIteratorConcept
-..cat:Iteration
-..summary:Tests whether iterator is at nil position.
-..signature:bool atNil(iterator)
-..param.iterator:An iterator.
-...type:Concept.RandomAccessIteratorConcept
-..returns:$true$ if $iterator$ points to an ivalid position, e.g. $iterator$ is a $NULL$ pointer.
-$false$ otherwise.
-..see:Function.goNil
-..include:seqan/basic.h
-*/
-
 template <typename TIterator>
 inline bool
 atNil(TIterator & me)
@@ -942,4 +532,4 @@ atNil(TIterator * me)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_INTERFACE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_INTERFACE_H_
diff --git a/seqan/basic/iterator_position.h b/seqan/basic/iterator_position.h
index 06836ea..472a140 100644
--- a/seqan/basic/iterator_position.h
+++ b/seqan/basic/iterator_position.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Positional iterator implementation.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_POSITION_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_POSITION_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_POSITION_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_POSITION_H_
 
 namespace seqan {
 
@@ -47,7 +47,7 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-struct PositionIterator;
+typedef CountingIteratorImpl_<Nothing> PositionIterator;
 
 /*!
  * @class PositionIterator
@@ -77,101 +77,56 @@ struct PositionIterator;
  * @param[in] position  The position to create the iterator at, defauls to 0.
  */
 
-/**
-.Spec.Position Iterator
-..cat:Iterators
-..general:Class.Iter
-..summary:Adapts @Metafunction.Position|Position Iterator@ to @Concept.RootedIteratorConcept|Rooted Iterator@.
-..signature:Iter<TContainer, PositionIterator>
-..param.TContainer:Type of the container.
-...metafunction:Metafunction.Container
-..remarks
-...text:Position Iterators provide the concept @Concept.RootedIteratorConcept|Rooted Iterator@.
-..see:Metafunction.Position
-..include:seqan/basic.h
-
-.Memfunc.Position Iterator#Iter:
-..class:Spec.Position Iterator
-..summary:Constructor
-..signature:Iter()
-..signature:Iter(iter)
-..signature:Iter(container [, position])
-..param.iter:Another position iterator object.
-..param.container:The corresponding container object.
-...metafunction:Metafunction.Container
-..param.position:A position in $container$. (optional)
-...metafunction:Metafunction.Position
-...remarks.text:If this argument is omitted, the adaptor iterator is initialized to the @Function.beginPosition.begin position@ of $container$.
-*/
-
 template <typename TContainer>
-class Iter<TContainer, PositionIterator>
+class Iter<TContainer, PositionIterator> :
+    public Iter<typename Position<TContainer>::Type, CountingIterator>
 {
 public:
-    typedef typename Position<TContainer>::Type TPosition;
-    typedef typename Pointer_<TContainer>::Type TContainerPointer_;
+    typedef Iter<typename Position<TContainer>::Type, CountingIterator> TBase;
+    typedef typename Position<TContainer>::Type                         TPosition;
+    typedef typename Pointer_<TContainer>::Type                         TContainerPointer_;
 
     TContainerPointer_ data_container;
-    TPosition data_position;
 
     // ------------------------------------------------------------------------
     // Constructors
     // ------------------------------------------------------------------------
 
-    Iter() : data_container(TContainerPointer_(0)), data_position(0)
-    {
-        SEQAN_CHECKPOINT;
-    }
+    Iter() :
+        TBase(),
+        data_container(TContainerPointer_())
+    {}
 
-    Iter(typename Parameter_<TContainer>::Type container_, TPosition position_ = 0)
-        : data_container(_toPointer(container_)),
-          data_position(position_)
-    {
-        SEQAN_CHECKPOINT;
-    }
+    Iter(typename Parameter_<TContainer>::Type container_, TPosition position_ = 0) :
+        TBase(position_),
+        data_container(_toPointer(container_))
+    {}
 
-    Iter(Iter const & other_)
-        : data_container(other_.data_container),
-          data_position(other_.data_position)
-    {
-        SEQAN_CHECKPOINT;
-    }
+    Iter(Iter const & other_) :
+        TBase(static_cast<TBase const &>(other_)),
+        data_container(other_.data_container)
+    {}
 
     template <typename TContainer2, typename TSpec2>
-    Iter(Iter<TContainer2, TSpec2> const & other_)
-            : data_container(_toPointer(container(other_))),
-              data_position(position(other_))
-    {
-        SEQAN_CHECKPOINT;
-    }
-
-    // ------------------------------------------------------------------------
-    // Assignment Operators;  Have to be defined in class.
-    // ------------------------------------------------------------------------
-
-    Iter const &
-    operator=(Iter const & other_)
-    {
-        SEQAN_CHECKPOINT;
-        data_container = other_.data_container;
-        data_position = other_.data_position;
-        return *this;
-    }
+    Iter(Iter<TContainer2, TSpec2> const & other_) :
+        TBase(position(other_)),
+        data_container(_toPointer(container(other_)))
+    {}
 
     // ------------------------------------------------------------------------
     // Pointer Operators;  Have to be defined within class.
     // ------------------------------------------------------------------------
-    
+
     typename Value<Iter>::Type *
     operator->()
     {
-        return &data_container[data_position];
+        return &data_container[position(*this)];
     }
 
     typename Value<Iter>::Type const *
     operator->() const
     {
-        return &data_container[data_position];
+        return &data_container[position(*this)];
     }
 
     // ------------------------------------------------------------------------
@@ -185,6 +140,27 @@ class Iter<TContainer, PositionIterator>
 // Metafunctions
 // ============================================================================
 
+template <typename TContainer>
+struct Size<Iter<TContainer, PositionIterator> > : Size<TContainer> {};
+
+template <typename TContainer>
+struct Position<Iter<TContainer, PositionIterator> > : Position<TContainer> {};
+
+template <typename TContainer>
+struct Difference<Iter<TContainer, PositionIterator> > : Difference<TContainer> {};
+
+template <typename TContainer>
+struct Value<Iter<TContainer, PositionIterator> > : Value<TContainer> {};
+
+template <typename TContainer>
+struct GetValue<Iter<TContainer, PositionIterator> > : GetValue<TContainer> {};
+
+template <typename TContainer>
+struct Reference<Iter<TContainer, PositionIterator> > : Reference<TContainer> {};
+
+template <typename TContainer>
+struct Reference<Iter<TContainer, PositionIterator> const> : Reference<TContainer> {};
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -197,7 +173,6 @@ template <typename TContainer>
 inline typename Parameter_<TContainer>::Type
 container(Iter<TContainer, PositionIterator> & me)
 {
-    SEQAN_CHECKPOINT;
     return _toParameter<TContainer>(me.data_container);
 }
 
@@ -205,7 +180,6 @@ template <typename TContainer>
 inline typename Parameter_<TContainer>::Type
 container(Iter<TContainer, PositionIterator> const & me)
 {
-    SEQAN_CHECKPOINT;
     return _toParameter<TContainer>(me.data_container);
 }
 
@@ -213,58 +187,16 @@ container(Iter<TContainer, PositionIterator> const & me)
 // Function setContainer()
 // ----------------------------------------------------------------------------
 
-///.Function.setContainer.param.object.type:Spec.Position Iterator
-///.Function.setContainer.class:Spec.Position Iterator
-
 template <typename TContainer>
 inline void
 setContainer(Iter<TContainer, PositionIterator> & me, typename Parameter_<TContainer>::Type container_)
 {
-    SEQAN_CHECKPOINT;
     typedef Iter<TContainer, PositionIterator> TIter;
     typename Position<TIter>::Type pos = position(me);
     me.data_container = _toPointer(container_);
     setPosition(me, pos);
 }
 
-// ----------------------------------------------------------------------------
-// Function position()
-// ----------------------------------------------------------------------------
-
-///.Function.position.param.iterator.type:Spec.Position Iterator
-///.Function.position.class:Spec.Position Iterator
-
-template <typename TContainer>
-inline typename Position<TContainer>::Type &
-position(Iter<TContainer, PositionIterator> & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.data_position;
-}
-
-template <typename TContainer>
-inline typename Position<TContainer>::Type const &
-position(Iter<TContainer, PositionIterator> const & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.data_position;
-}
-
-// ----------------------------------------------------------------------------
-// Function setPosition()
-// ----------------------------------------------------------------------------
-
-///.Function.setPosition.param.iterator.type:Spec.Position Iterator
-///.Function.setPosition.class:Spec.Position Iterator
-
-template <typename TContainer, typename TPosition>
-inline void
-setPosition(Iter<TContainer, PositionIterator> & me, TPosition position_)
-{
-    SEQAN_CHECKPOINT;
-    me.data_position = position_;
-}
-
 // ----------------------------------------------------------------------------
 // Function value()
 // ----------------------------------------------------------------------------
@@ -273,15 +205,13 @@ template <typename TContainer>
 inline typename Reference<Iter<TContainer, PositionIterator> >::Type
 value(Iter<TContainer, PositionIterator> & me)
 {
-    SEQAN_CHECKPOINT;
     return value(container(me), position(me));
 }
 
 template <typename TContainer>
-inline typename Reference<Iter<TContainer, PositionIterator> >::Type
+inline typename Reference<Iter<TContainer, PositionIterator> const>::Type
 value(Iter<TContainer, PositionIterator> const & me)
 {
-    SEQAN_CHECKPOINT;
     return value(container(me), position(me));
 }
 
@@ -291,19 +221,15 @@ value(Iter<TContainer, PositionIterator> const & me)
 
 template <typename TContainer, typename TValue>
 inline void
-assignValue(Iter<TContainer, PositionIterator> & me,
-            TValue const & _value)
+assignValue(Iter<TContainer, PositionIterator> & me, TValue const & _value)
 {
-    SEQAN_CHECKPOINT;
     assignValue(container(me), position(me), _value);
 }
 
 template <typename TContainer, typename TValue>
 inline void
-assignValue(Iter<TContainer, PositionIterator> const & me,
-            TValue const & _value)
+assignValue(Iter<TContainer, PositionIterator> const & me, TValue const & _value)
 {
-    SEQAN_CHECKPOINT;
     assignValue(container(me), position(me), _value);
 }
 
@@ -320,244 +246,18 @@ inline void moveValue(T const & me, TPos pos, TValue const & _value);
 
 template <typename TContainer, typename TValue>
 inline void
-moveValue(Iter<TContainer, PositionIterator> & me,
-          TValue const & _value)
+moveValue(Iter<TContainer, PositionIterator> & me, TValue const & _value)
 {
-    SEQAN_CHECKPOINT;
     moveValue(container(me), position(me), _value);
 }
 
 template <typename TContainer, typename TValue>
 inline void
-moveValue(Iter<TContainer, PositionIterator> const & me,
-          TValue const & _value)
+moveValue(Iter<TContainer, PositionIterator> const & me, TValue const & _value)
 {
-    SEQAN_CHECKPOINT;
     moveValue(container(me), position(me), _value);
 }
 
-// ----------------------------------------------------------------------------
-// Function operator==()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer>
-inline bool
-operator==(Iter<TContainer, PositionIterator> const & left,
-           Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return position(left) == position(right);
-}
-
-// ----------------------------------------------------------------------------
-// Function operator!=()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer>
-inline bool
-operator!=(Iter<TContainer, PositionIterator> const & left,
-           Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return position(left) != position(right);
-}
-
-// ----------------------------------------------------------------------------
-// Function operator<()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer>
-inline bool
-operator<(Iter<TContainer, PositionIterator> const & left,
-          Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return position(left) < position(right);
-}
-
-template <typename TContainer>
-inline bool
-operator>(Iter<TContainer, PositionIterator> const & left,
-          Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return position(left) > position(right);
-}
-
-// ----------------------------------------------------------------------------
-// Function operator<=()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer>
-inline bool
-operator<=(Iter<TContainer, PositionIterator> const & left,
-           Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return position(left) <= position(right);
-}
-
-// ----------------------------------------------------------------------------
-// Function operator>=()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer>
-inline bool
-operator>=(Iter<TContainer, PositionIterator> const & left,
-           Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return position(left) >= position(right);
-}
-
-// ----------------------------------------------------------------------------
-// Function goNext()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer>
-inline void
-goNext(Iter<TContainer, PositionIterator> & me)
-{
-    SEQAN_CHECKPOINT;
-    setPosition(me, position(me) + 1);
-}
-
-// ----------------------------------------------------------------------------
-// Function goPrevious()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer>
-inline void
-goPrevious(Iter<TContainer, PositionIterator> & me)
-{
-    SEQAN_CHECKPOINT;
-    setPosition(me, position(me) - 1);
-}
-
-// ----------------------------------------------------------------------------
-// Function operator+()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, PositionIterator>
-operator+(Iter<TContainer, PositionIterator> const & left,
-          TIntegral right)
-{
-    SEQAN_CHECKPOINT;
-    return Iter<TContainer, PositionIterator>(container(left), position(left) + right);
-}
-
-// for <anonymous enum> types
-template <typename TContainer>
-inline Iter<TContainer, PositionIterator>
-operator+(Iter<TContainer, PositionIterator> const & left,
-          int right)
-{
-    SEQAN_CHECKPOINT;
-    return Iter<TContainer, PositionIterator>(container(left), position(left) + right);
-}
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, PositionIterator>
-operator+(TIntegral left,
-          Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return Iter<TContainer, PositionIterator>(container(right), position(right) + left);
-}
-
-// for <anonymous enum> types
-template <typename TContainer>
-inline Iter<TContainer, PositionIterator>
-operator+(int left,
-          Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return Iter<TContainer, PositionIterator>(container(right), position(right) + left);
-}
-
-// ----------------------------------------------------------------------------
-// Function operator+=()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, PositionIterator> &
-operator+=(Iter<TContainer, PositionIterator> & left,
-           TIntegral right)
-{
-    SEQAN_CHECKPOINT;
-    setPosition(left, position(left) + right);
-    return left;
-}
-
-// for <anonymous enum> types
-template <typename TContainer>
-inline Iter<TContainer, PositionIterator> &
-operator+=(Iter<TContainer, PositionIterator> & left,
-           int right)
-{
-    SEQAN_CHECKPOINT;
-    setPosition(left, position(left) + right);
-    return left;
-}
-
-// ----------------------------------------------------------------------------
-// Function operator-()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, PositionIterator>
-operator-(Iter<TContainer, PositionIterator> const & left,
-          TIntegral right)
-{
-    SEQAN_CHECKPOINT;
-    return Iter<TContainer, PositionIterator>(container(left), position(left) - right);
-}
-
-// for <anonymous enum> types
-template <typename TContainer>
-inline Iter<TContainer, PositionIterator>
-operator-(Iter<TContainer, PositionIterator> const & left,
-          int right)
-{
-    SEQAN_CHECKPOINT;
-    return Iter<TContainer, PositionIterator>(container(left), position(left) - right);
-}
-
-template <typename TContainer>
-inline typename Difference<TContainer>::Type
-operator-(Iter<TContainer, PositionIterator> const & left,
-          Iter<TContainer, PositionIterator> const & right)
-{
-    SEQAN_CHECKPOINT;
-    return position(left) - position(right);
-}
-
-// ----------------------------------------------------------------------------
-// Function operator-=()
-// ----------------------------------------------------------------------------
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, PositionIterator> &
-operator-=(Iter<TContainer, PositionIterator> & left,
-           TIntegral right)
-{
-    SEQAN_CHECKPOINT;
-    setPosition(left, position(left) - right);
-    return left;
-}
-
-// for <anonymous enum> types
-template <typename TContainer>
-inline Iter<TContainer, PositionIterator> &
-operator-=(Iter<TContainer, PositionIterator> & left,
-           int right)
-{
-    SEQAN_CHECKPOINT;
-    setPosition(left, position(left) - right);
-    return left;
-}
-
 // ----------------------------------------------------------------------------
 // Function assign()
 // ----------------------------------------------------------------------------
@@ -565,14 +265,12 @@ operator-=(Iter<TContainer, PositionIterator> & left,
 // Conversion assignment.
 template <typename TTargetContainer, typename TSource>
 inline void
-assign(Iter<TTargetContainer, PositionIterator> & target,
-       TSource const & source)
+assign(Iter<TTargetContainer, PositionIterator> & target, TSource const & source)
 {
-    SEQAN_CHECKPOINT;
-    target.data_container = _toPointer(container(source));
-    target.data_position = position(source);
+    setContainer(target, container(source));
+    setPosition(target, position(source));
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_ITERATOR_POSITION_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_POSITION_H_
diff --git a/seqan/basic/iterator_range.h b/seqan/basic/iterator_range.h
new file mode 100644
index 0000000..b227f30
--- /dev/null
+++ b/seqan/basic/iterator_range.h
@@ -0,0 +1,398 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_RANGE_H
+#define SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_RANGE_H
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TInput, typename TPipeSpec>
+struct Pipe;
+
+template <typename TObject>
+struct IsView;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// class Range
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class Range
+ * @headerfile <seqan/basic.h>
+ * @brief A range between two iterators.
+ *
+ * @signature template <typename TIterator>
+ *            class Range;
+ *
+ * @tparam The type of the iterator to use.
+ */
+
+// TODO(holtgrew): Completely missing documentation.
+
+template <typename TIterator>
+class Range
+{
+public:
+
+    TIterator begin;
+    TIterator end;
+
+    // ------------------------------------------------------------------------
+    // Range Constructors
+    // ------------------------------------------------------------------------
+
+    SEQAN_HOST_DEVICE
+    Range():
+        begin(),
+        end()
+    {}
+
+    SEQAN_HOST_DEVICE
+    Range(Range const & range) :
+        begin(range.begin),
+        end(range.end)
+    {}
+
+    SEQAN_HOST_DEVICE
+    Range(TIterator const & begin, TIterator const & end):
+        begin(begin),
+        end(end)
+    {}
+
+    // ------------------------------------------------------------------------
+    // Operator =
+    // ------------------------------------------------------------------------
+
+    template <typename TOtherContainer>
+    SEQAN_HOST_DEVICE
+    Range &
+    operator= (TOtherContainer &other)
+    {
+        assign(*this, other);
+        return *this;
+    }
+
+    // ------------------------------------------------------------------------
+    // Operator []
+    // ------------------------------------------------------------------------
+
+    template <typename TPos>
+    SEQAN_HOST_DEVICE
+    typename Reference<Range>::Type
+    operator[] (TPos pos)
+    {
+        return value(*this, pos);
+    }
+
+    template <typename TPos>
+    SEQAN_HOST_DEVICE
+    typename GetValue<Range>::Type
+    operator[] (TPos pos) const
+    {
+        return getValue(*this, pos);
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Concept ContainerConcept
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+SEQAN_CONCEPT_IMPL((Range<TIterator>), (ContainerConcept));
+
+template <typename TIterator>
+SEQAN_CONCEPT_IMPL((Range<TIterator> const), (ContainerConcept));
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+struct IsView<Range<TIterator> > : True {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+struct Value<Range<TIterator> >:
+    Value<TIterator> {};
+
+template <typename TIterator>
+struct Value<Range<TIterator> const>:
+    Value<TIterator> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction GetValue
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+struct GetValue<Range<TIterator> >:
+    GetValue<TIterator> {};
+
+template <typename TIterator>
+struct GetValue<Range<TIterator> const>:
+    GetValue<TIterator const> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Reference
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+struct Reference<Range<TIterator> > :
+    Reference<TIterator> {};
+
+template <typename TIterator>
+struct Reference<Range<TIterator> const>:
+    Reference<TIterator const> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+struct Iterator<Range<TIterator>, Standard>
+{
+    typedef typename If< Is< IntegerConcept<TIterator> >, Iter<TIterator, CountingIterator>, TIterator>::Type Type;
+};
+
+template <typename TIterator>
+struct Iterator<Range<TIterator> const, Standard> : Iterator<Range<TIterator>, Standard> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Difference
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+struct Difference<Range<TIterator> >
+{
+    typedef typename Difference<TIterator>::Type Type;
+};
+
+template <typename TIterator>
+struct Size<Range<TIterator> >
+{
+    typedef typename Difference<TIterator>::Type        TDifference;
+    typedef typename MakeUnsigned<TDifference>::Type    Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// begin()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+SEQAN_HOST_DEVICE inline typename Iterator<Range<TIterator>, Standard>::Type
+begin(Range<TIterator> & range, Standard)
+{
+    return range.begin;
+}
+
+template <typename TIterator>
+SEQAN_HOST_DEVICE inline typename Iterator<Range<TIterator>, Standard>::Type
+begin(Range<TIterator> const & range, Standard)
+{
+    return range.begin;
+}
+
+// ----------------------------------------------------------------------------
+// end()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+SEQAN_HOST_DEVICE inline typename Iterator<Range<TIterator>, Standard>::Type
+end(Range<TIterator> & range, Standard)
+{
+    return range.end;
+}
+
+template <typename TIterator>
+SEQAN_HOST_DEVICE inline typename Iterator<Range<TIterator>, Standard>::Type
+end(Range<TIterator> const & range, Standard)
+{
+    return range.end;
+}
+
+// ----------------------------------------------------------------------------
+// value()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator, typename TPos>
+SEQAN_HOST_DEVICE inline typename Reference<Range<TIterator> >::Type
+value(Range<TIterator> & range, TPos pos)
+{
+    return *(range.begin + pos);
+}
+
+template <typename TIterator, typename TPos>
+SEQAN_HOST_DEVICE inline typename Reference<Range<TIterator> const>::Type
+value(Range<TIterator> const & range, TPos pos)
+{
+    return *(range.begin + pos);
+}
+
+// ----------------------------------------------------------------------------
+// length()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+SEQAN_HOST_DEVICE inline typename Size<Range<TIterator> >::Type
+length(Range<TIterator> const & range)
+{
+    return range.end - range.begin;
+}
+
+// ----------------------------------------------------------------------------
+// resize()
+// ----------------------------------------------------------------------------
+
+// this function doesn't do anything as we are not allowed to change the host (only its elements)
+// it is, however, implemented for algorithms that get a sequence to work on
+// and need to make sure that it has a certain length
+
+template <typename TIterator, typename TSize, typename TExpand>
+SEQAN_HOST_DEVICE inline typename Size< Range<TIterator> >::Type
+resize(
+    Range<TIterator> & me,
+    TSize new_length,
+    Tag<TExpand>)
+{
+    ignoreUnusedVariableWarning(new_length);
+
+    SEQAN_ASSERT_EQ(new_length, (TSize)length(me));
+    return length(me);
+}
+
+// ----------------------------------------------------------------------------
+// assign()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator, typename TContainer>
+SEQAN_HOST_DEVICE inline void
+assign(Range<TIterator> &range, TContainer &cont)
+{
+    range.begin = begin(cont, Standard());
+    range.end = end(cont, Standard());
+}
+
+// ----------------------------------------------------------------------------
+// toRange()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator, typename TIterator2, typename TIterator3>
+SEQAN_HOST_DEVICE inline void
+assignRange(Range<TIterator> &result, TIterator2 const &begin, TIterator3 const &end)
+{
+    result.begin = begin;
+    result.end = end;
+}
+
+template <typename TIterator>
+SEQAN_HOST_DEVICE inline
+Range<TIterator>
+toRange(TIterator const &begin, TIterator const &end)
+{
+    return Range<TIterator>(begin, end);
+}
+
+template <typename TContainer>
+SEQAN_HOST_DEVICE inline
+Range<typename Iterator<TContainer, Standard>::Type>
+toRange(TContainer &cont)
+{
+    return Range<typename Iterator<TContainer, Standard>::Type >(begin(cont, Standard()), end(cont, Standard()));
+}
+
+template <typename TContainer>
+SEQAN_HOST_DEVICE inline
+Range<typename Iterator<TContainer const, Standard>::Type>
+toRange(TContainer const &cont)
+{
+    return Range<typename Iterator<TContainer const, Standard>::Type >(begin(cont, Standard()), end(cont, Standard()));
+}
+
+// ----------------------------------------------------------------------------
+// getObjectId()
+// ----------------------------------------------------------------------------
+
+template <typename TIterator>
+inline void const *
+getObjectId(Range<TIterator> const & /* me */)
+{
+    return NULL;
+}
+
+// ----------------------------------------------------------------------------
+// pipe interface
+// ----------------------------------------------------------------------------
+
+template < typename TIterator,
+           typename TInput,
+           typename TPipeSpec >
+inline void assign(Range<TIterator> &dest, Pipe<TInput, TPipeSpec> &src)
+{
+    typedef typename Iterator<Range<TIterator>, Standard>::Type TDestIter;
+    resize(dest, length(src));
+    beginRead(src);
+    for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src)
+        *_cur = *src;
+    endRead(src);
+}
+
+template < typename TIterator,
+           typename TInput,
+           typename TPipeSpec >
+inline void operator << (Range<TIterator> &dest, Pipe<TInput, TPipeSpec> &src)
+{
+    assign(dest, src);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ITERATOR_RANGE_H
diff --git a/seqan/basic/macro_deprecated.h b/seqan/basic/macro_deprecated.h
index 85c89ff..1fbcc73 100644
--- a/seqan/basic/macro_deprecated.h
+++ b/seqan/basic/macro_deprecated.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Macro for deprecating code.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BASIC_MACRO_DEPRECATED_H_
-#define CORE_INCLUDE_SEQAN_BASIC_MACRO_DEPRECATED_H_
+#ifndef INCLUDE_SEQAN_BASIC_MACRO_DEPRECATED_H_
+#define INCLUDE_SEQAN_BASIC_MACRO_DEPRECATED_H_
 
 namespace seqan {
 
@@ -75,4 +75,4 @@ namespace seqan {
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BASIC_MACRO_DEPRECATED_H_
+#endif  // #ifndef INCLUDE_SEQAN_BASIC_MACRO_DEPRECATED_H_
diff --git a/seqan/basic/math_functions.h b/seqan/basic/math_functions.h
index 52841a2..48cc530 100644
--- a/seqan/basic/math_functions.h
+++ b/seqan/basic/math_functions.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Math-related utility routines.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_MATH_FUNCTIONS_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_MATH_FUNCTIONS_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_MATH_FUNCTIONS_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_MATH_FUNCTIONS_H_
 
 namespace seqan {
 
@@ -70,7 +70,7 @@ inline TValue _intPow(TValue a, TExponent b)
         if (b & 1) ret *= a;
         a *= a;
         b >>= 1;
-    }   
+    }
     return ret;
 }
 
@@ -82,25 +82,14 @@ inline TValue _intPow(TValue a, TExponent b)
  * @fn log2
  * @headerfile <seqan/basic.h>
  * @brief Computes floored logarithm of base 2 for integer types
- * 
+ *
  * @signature unsigned log2(i);
- * 
- * @param i An integer type.
- * 
+ *
+ * @param[in] i An integer type.
+ *
  * @return unsigned The largest integer smaller or equal than the logarithm of <tt>i</tt>.
  */
 
-/**
-.Function.log2
-..cat:Miscellaneous
-..summary:Computes floored logarithm of base 2 for integer types
-..signature:unsigned int log2(i)
-..param.i:An integer type.
-..returns:The largest integer smaller or equal than
-the logarithm of $i$.
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Should this maybe called log2floor for consistency with Log2Floor<>::VALUE?
 
 template <int BITS_MAX>
@@ -214,5 +203,5 @@ T _abs(T const & x)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_MATH_FUNCTIONS_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_MATH_FUNCTIONS_H_
 
diff --git a/seqan/basic/math_log_space_value.h b/seqan/basic/math_log_space_value.h
index d195cb2..0fb6ac1 100644
--- a/seqan/basic/math_log_space_value.h
+++ b/seqan/basic/math_log_space_value.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,8 +39,8 @@
 
 // TODO(holtgrew): Rename to "LogSpaceValue"?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_MATH_LOG_SPACE_VALUE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_MATH_LOG_SPACE_VALUE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_MATH_LOG_SPACE_VALUE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_MATH_LOG_SPACE_VALUE_H_
 
 namespace seqan {
 
@@ -56,21 +56,21 @@ namespace seqan {
  * @class LogProb
  * @headerfile <seqan/basic.h>
  * @brief Value type for computation in log-space.
- * 
+ *
  * @signature template <[typename T]>
  *            class LogProb;
- * 
+ *
  * @tparam T Floating number type to use as the basic, defaults to <tt>double</tt>.
- * 
+ *
  * @section Remarks
- * 
+ *
  * Internally, the logarithms of the original values are stored.  This is numerically more stable for multiplications
  * and large numbers.
- * 
+ *
  * This type can be used like an ordinary <tt>double</tt> or <tt>float</tt> value.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * LogProb<double> x = 10;
  * x *= 3;
@@ -79,23 +79,6 @@ namespace seqan {
  * @endcode
  */
 
-/**
-.Class.LogProb
-..summary:Value type for computation in log-space.
-..signature:LogProb<T>
-..param.T:Floating number type to use as the basic.
-...default:$double$
-..remarks:Internally, the logarithms of the original values are stored.  This is numerically more stable for multiplications and large numbers.
-..remarks:This type can be used like an ordinary $double$ or $float$ value.
-..example.code:
-LogProb<double> x = 10;
-x *= 3;
-x += 4;
-int y = x;
-..cat:Basic
-..include:seqan/basic.h
-*/
-
 template<typename TValue = double, typename TSpec = Default>
 class LogProb;
 
@@ -115,21 +98,21 @@ template <typename TValue>
 inline double
 log(TValue const & value)
 {
-    return ::std::log((double)value);
+    return std::log((double)value);
 }
 
 
 template<typename TValue, typename TSpec>
 class LogProb
 {
-  public:   
+  public:
     TValue data_value;
 
     // ------------------------------------------------------------------------
     // Constructors
     // ------------------------------------------------------------------------
-    
-    LogProb() : data_value(::std::log(0.0)) {}
+
+    LogProb() : data_value(std::log(0.0)) {}
 
     template <typename TValue2>
     LogProb(TValue2 const & _other)
@@ -140,17 +123,17 @@ class LogProb
     // ------------------------------------------------------------------------
     // Type conversion operators;  Have to be defined in class.
     // ------------------------------------------------------------------------
-    
+
     template <typename TResult>
     inline TResult _convert(False) const
     {
-        return (TResult)::std::exp(data_value);
+        return (TResult)std::exp(data_value);
     }
 
     template <typename TResult>
     inline TResult _convert(True) const
     {
-        return (TResult)round(::std::exp(data_value));
+        return (TResult)round(std::exp(data_value));
     }
 
     template <typename TValue2>
@@ -163,13 +146,13 @@ class LogProb
     inline
     operator float() const
     {
-        return (float) ::std::exp(data_value);
+        return (float) std::exp(data_value);
     }
 
     inline
     operator double() const
     {
-        return (double) ::std::exp(data_value);
+        return (double) std::exp(data_value);
     }
 */
     // ------------------------------------------------------------------------
@@ -181,7 +164,7 @@ class LogProb
     LogProb &
     operator=(TRhs const& rhs)
     {
-        data_value = ::std::log(rhs);
+        data_value = std::log(rhs);
         return *this;
     }
 
@@ -293,7 +276,7 @@ inline
 LogProb<TValue, TSpec> &
 operator+=(LogProb<TValue, TSpec> & lhs,
            TRhs const & rhs) {
-    lhs.data_value = ::std::log(::std::exp(lhs.data_value) + rhs);
+    lhs.data_value = std::log(std::exp(lhs.data_value) + rhs);
     return lhs;
 }
 
@@ -304,15 +287,15 @@ operator+=(LogProb<TValue, TSpec> & lhs,
            LogProb<TValue2, TSpec2> const & rhs)
 {
     if (lhs.data_value > rhs.data_value) {
-        if ((rhs.data_value == ::std::log(0.0)) || (lhs.data_value - rhs.data_value > 100))
+        if ((rhs.data_value == std::log(0.0)) || (lhs.data_value - rhs.data_value > 100))
             return lhs;
-        lhs.data_value = lhs.data_value + ::std::log(1 + ::std::exp(rhs.data_value - lhs.data_value));
+        lhs.data_value = lhs.data_value + std::log(1 + std::exp(rhs.data_value - lhs.data_value));
     } else {
-        if ((lhs.data_value == ::std::log(0.0)) || (rhs.data_value - lhs.data_value > 100)) {
+        if ((lhs.data_value == std::log(0.0)) || (rhs.data_value - lhs.data_value > 100)) {
             lhs.data_value = rhs.data_value;
             return lhs;
         }
-        lhs.data_value = rhs.data_value + ::std::log(1 + ::std::exp(lhs.data_value - rhs.data_value));
+        lhs.data_value = rhs.data_value + std::log(1 + std::exp(lhs.data_value - rhs.data_value));
     }
     return lhs;
 }
@@ -352,7 +335,7 @@ LogProb<TValue, TSpec> &
 operator-=(LogProb<TValue, TSpec> & lhs,
            TRhs const & rhs)
 {
-    lhs.data_value = ::std::log(::std::exp(lhs.data_value) - rhs);
+    lhs.data_value = std::log(std::exp(lhs.data_value) - rhs);
     return lhs;
 }
 
@@ -363,15 +346,15 @@ operator-=(LogProb<TValue, TSpec> & lhs,
            LogProb<TValue2, TSpec2> const & rhs)
 {
     if (lhs.data_value > rhs.data_value) {
-        if ((rhs.data_value == ::std::log(0.0)) || (lhs.data_value - rhs.data_value > 100))
+        if ((rhs.data_value == std::log(0.0)) || (lhs.data_value - rhs.data_value > 100))
             return lhs;
-        lhs.data_value = lhs.data_value + ::std::log(1 - ::std::exp(rhs.data_value - lhs.data_value));
+        lhs.data_value = lhs.data_value + std::log(1 - std::exp(rhs.data_value - lhs.data_value));
     } else {
-        if ((lhs.data_value == ::std::log(0.0)) || (rhs.data_value - lhs.data_value > 100)) {
+        if ((lhs.data_value == std::log(0.0)) || (rhs.data_value - lhs.data_value > 100)) {
             lhs.data_value = rhs.data_value;
             return lhs;
         }
-        lhs.data_value = rhs.data_value + ::std::log(1 - ::std::exp(lhs.data_value - rhs.data_value));
+        lhs.data_value = rhs.data_value + std::log(1 - std::exp(lhs.data_value - rhs.data_value));
     }
     return lhs;
 }
@@ -406,7 +389,7 @@ operator-(LogProb<TValue, TSpec> const & lhs,
 // ----------------------------------------------------------------------------
 
 template <typename TValue, typename TSpec, typename TRhs>
-inline 
+inline
 bool
 operator==(LogProb<TValue, TSpec> const & lhs,
            TRhs const & rhs)
@@ -490,9 +473,9 @@ inline
 TStream &
 operator<<(TStream & stream, LogProb<TValue, TSpec> const & rhs)
 {
-    return stream << ::std::exp(rhs.data_value);
+    return stream << std::exp(rhs.data_value);
 }
-    
+
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_MATH_LOG_SPACE_VALUE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_MATH_LOG_SPACE_VALUE_H_
diff --git a/seqan/basic/metaprogramming_control.h b/seqan/basic/metaprogramming_control.h
index 6b726c5..e4b5119 100644
--- a/seqan/basic/metaprogramming_control.h
+++ b/seqan/basic/metaprogramming_control.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // and loops.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_CONTROL_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_CONTROL_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_CONTROL_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_CONTROL_H_
 
 namespace seqan {
 
@@ -66,7 +66,7 @@ namespace seqan {
  *
  * The following shows a complete example of using the Switch statement.
  *
- * @snippet demos/basic/metaprogramming_switch.cpp switch demo
+ * @snippet demos/dox/basic/metaprogramming_switch.cpp switch demo
  */
 
 // TODO(holtgrew): Use Tag<>?
@@ -101,74 +101,6 @@ namespace seqan {
  * @return Type The selected type.
  */
 
-/**
-.Tag.NilCase
-..cat:Metaprogramming
-..summary:Metaprogramming $default:$ case expression.
-..signature:NilCase
-..remarks:$NilCase$ is returned by metafunction @Metafunction.Switch@ if no case matched.
-..include:seqan/basic.h
-..remarks:The documentation of @Metafunction.Switch@ gives an example.
-..see:Tag.Case
-..see:Metafunction.Switch
-
-.Tag.Case
-..cat:Metaprogramming
-..summary:Metaprogramming $case$ expression.
-..signature:Case<TAG[, NextCase]>
-..param.TAG:
-..param.NextCase:Optional next case of type @Tag.Case@, defaults to @Tag.NilCase@.
-...type:Tag.NilCase
-...type:Tag.Case
-..include:seqan/basic.h
-..remarks:The documentation of @Metafunction.Switch@ gives an example.
-..see:Tag.NilCase
-..see:Metafunction.Switch
-
-.Metafunction.Switch
-..cat:Metaprogramming
-..summary:Metaprogramming $switch$ expression.
-..signature:Switch<TAG, Case>::Type
-..param.TAG:The case label.
-...type:nolink:$int$
-..param.Case:Cascade of $Case$ tags.
-...type:Tag.Case
-...type:Tag.NilCase
-..returns:The selected type from the @Tag.Case@ cascade or @Tag.NilCase@.
-..include:seqan/basic.h
-..see:Tag.NilCase
-..see:Tag.Case
-..example.code:
-int switchTest(Nothing const &) { return -1; }
-int switchTest(False const &) { return 0; }
-int switchTest(True const &) { return 1; }
-int switchTest(NilCase const &) { return 2; }
-
-template <int X>
-struct SwitchTest
-{
-    typedef typename Switch<
-        X,
-        Case<-1, Nothing,
-        Case<0, False,
-        Case<1, True
-        > > > >::Type Type;
-};
-
-SEQAN_DEFINE_TEST(test_metaprogramming_switch)
-{
-    typedef typename SwitchTest<-1>::Type T1;
-    typedef typename SwitchTest< 0>::Type T2;
-    typedef typename SwitchTest< 1>::Type T3;
-    typedef typename SwitchTest< 2>::Type T4;
-
-    std::cout << switchTest(T1()) << std::endl;  // => -1
-    std::cout << switchTest(T2()) << std::endl;  // =>  0
-    std::cout << switchTest(T3()) << std::endl;  // =>  1
-    std::cout << switchTest(T4()) << std::endl;  // =>  2
- }
- */
-
 const int DEFAULT_ = ~(~0u >> 1); // initialize with the smallest int
 
 struct NilCase {};
@@ -207,60 +139,42 @@ struct Switch<TAG, NilCase>
 // Metafunction Loop
 // ----------------------------------------------------------------------------
 
-// TODO(holtgrew): This is more of a class than a function or metafunction.
-
 /*!
- * @fn Loop
+ * @class Loop
  * @headerfile <seqan/basic.h>
+ * @brief Helper for loops.
  *
- * @signature void Loop<TWorker, COUNT>::run(args);
+ * @signature template <typename TWorker, unsigned COUNT>
+ *            struct Loop;
  *
  * @tparam TWorker A struct with a static inline void function called <tt>body</tt>.  <tt>body</tt> should have two
  *                 parameters, one for passing in values and state from the outside and the second is an int.  The
  *                 function will be called <tt>COUNT</tt> times with the same reference for the first one and the values
  *                 <tt>COUNT</tt>, <tt>COUNT - 1</tt>, ..., <tt>1</tt> for the second parameter.
- * @param COUNT    An <tt>int</tt> constant.
+ * @tparam COUNT   An <tt>int</tt> constant.
  *
  * @section Example
  *
  * We define the following worker to print an integer.  The first argument is of <tt>Nothing</tt> as a dummy.  Note that
  * the parameter is not const.
  *
- * @snippet demos/basic/metaprogramming_control.cpp print worker
+ * @snippet demos/dox/basic/metaprogramming_control.cpp print worker
  *
  * The following shows an example calling <tt>PrintWorker::body()</tt> through Loop.  We have to create a local variable
  * since the first parameter is not const.  The reason for this is that the parameter can also be used for a mutable
  * object that holds some state.
  *
- * @snippet demos/basic/metaprogramming_control.cpp print worker call loop reverse
+ * @snippet demos/dox/basic/metaprogramming_control.cpp print worker call loop reverse
  *
  * @see LoopReverse
- */
-
-/**
-.Metafunction.Loop:
-..cat:Metaprogramming
-..summary:Metafunction returning a function that iterates over a static integer range.
-..signature:Loop<Worker, I>::run(Arg & arg)
-..param.Worker:A worker $struct$. It has to implement the static (and preferably finline/inline) function $body$ that accepts two parameters. The first one will be a reference to $arg$, as given to $run()$.  The second will be the current value of the iterating variable.
-..param.I:The upper limit for the iteration.
-..param.arg:The argument to be passed into the workers' $body()$ function.
-..remarks:The loop will go from 1 up to and including $I$.
-..see:Metafunction.LoopReverse
-..include:seqan/basic.h
-..example.text:Print the values 1, 2, ..., $I-1$, $I$.
-..example.code:
-struct PrintWorker
-{
-    static inline void body(Nothing & arg, int I)
-    {
-        (void)arg;  // ignored
-        printf("%d\n", I);
-    }
-};
-
-Loop<PrintWorker, 10>::run(Nothing());
-// This will print the numbers 1, 2, ..., 9, 10.
+ *
+ * @fn Loop::run
+ * @brief Run the loop body.
+ *
+ * @signature Loop::run(arg, i);
+ *
+ * @param[in,out] arg The argument to pass to the worker's <tt>body()</tt> function.
+ * @param[in]     i   The <tt>int</tt> passed to the <tt>body()</tt> function.
  */
 
 // Example of a loop Worker class.  Could be removed, serves no
@@ -297,60 +211,43 @@ class Loop<Worker, 0>
 // Metafunction LoopReverse
 // ----------------------------------------------------------------------------
 
-// TODO(holtgrew): This is more of a class than a function or metafunction.
-
 /*!
- * @fn LoopReverse
+ * @class LoopReverse
+ * @brief Helper for reverse loops.
+ *
  * @headerfile <seqan/basic.h>
  *
- * @signature void LoopReverse<TWorker, COUNT>::run(args);
+ * @signature template <typename TWorker, unsigned COUNT>
+ *            struct LoopReverse;
  *
  * @tparam TWorker A struct with a static inline void function called <tt>body</tt>.  <tt>body</tt> should have two
  *                 parameters, one for passing in values and state from the outside and the second is an int.  The
  *                 function will be called <tt>COUNT</tt> times with the same reference for the first one and the values
  *                 <tt>COUNT</tt>, <tt>COUNT - 1</tt>, ..., <tt>1</tt> for the second parameter.
- * @param COUNT    An <tt>int</tt> constant.
+ * @tparam COUNT   An <tt>int</tt> constant.
  *
  * @section Example
  *
  * We define the following worker to print an integer.  The first argument is of <tt>Nothing</tt> as a dummy.  Note that
  * the parameter is not const.
  *
- * @snippet demos/basic/metaprogramming_control.cpp print worker
+ * @snippet demos/dox/basic/metaprogramming_control.cpp print worker
  *
  * The following shows an example calling <tt>PrintWorker::body()</tt> through LoopReverse.  We have to create a local
  * variable since the first parameter is not const.  The reason for this is that the parameter can also be used for a
  * mutable object that holds some state.
  *
- * @snippet demos/basic/metaprogramming_control.cpp print worker call loop
+ * @snippet demos/dox/basic/metaprogramming_control.cpp print worker call loop
  *
  * @see Loop
- */
-
-/**
-.Metafunction.LoopReverse:
-..cat:Metaprogramming
-..summary:Metafunction returning a function that iterates over a static integer range in reverse order.
-..signature:LoopReverse<Worker, I>::run(Arg & arg)
-..param.Worker:A worker $struct$. It has to implement the static (and preferably finline/inline) function $body$ that accepts two parameters. The first one will be a reference to $arg$, as given to $run()$.  The second will be the current value of the iterating variable.
-..param.I:The upper limit for the iteration.
-..param.arg:The argument to be passed into the workers' $body()$ function.
-..remarks:The loop will go from $I$ down to and including 1.
-..include:seqan/basic.h
-..see:Metafunction.Loop
-..example.text:Print the values $I$, $I - 1$, ..., 2, 1.
-..example.code:
-struct PrintWorker
-{
-    static inline body(Nothing & arg, int I)
-    {
-        (void)arg;  // ignored
-        printf("%d\n", I);
-    }
-};
-
-Loop<PrintWorker, 10>::run(Nothing());
-// This will print the numbers 1, 2, ..., 9, 10.
+ *
+ * @fn LoopReverse::run
+ * @brief Run the loop body.
+ *
+ * @signature LoopReverse::run(arg, i);
+ *
+ * @param[in,out] arg The argument to pass to the worker's <tt>body()</tt> function.
+ * @param[in]     i   The <tt>int</tt> passed to the <tt>body()</tt> function.
  */
 
 template <typename Worker, int I>
@@ -380,4 +277,4 @@ class LoopReverse<Worker, 0>
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_CONTROL_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_CONTROL_H_
diff --git a/seqan/basic/metaprogramming_enable_if.h b/seqan/basic/metaprogramming_enable_if.h
index 8239395..513d54d 100644
--- a/seqan/basic/metaprogramming_enable_if.h
+++ b/seqan/basic/metaprogramming_enable_if.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,8 +39,8 @@
 // TODO(holtgrew): Rename *2 Metafunctions to *C metafunctions.
 // TODO(holtgrew): Document properly.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_ENABLE_IF_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_ENABLE_IF_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_ENABLE_IF_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_ENABLE_IF_H_
 
 namespace seqan {
 
@@ -157,7 +157,7 @@ struct DisableIf<False, T>
  * @deprecated Will be renamed to EnableIfC.
  * @brief Metafunction to use for conditionally enabling code, bool version.
  *
- * @signature EnableIf<BOOL, T = void>::Type
+ * @signature EnableIf2<BOOL, T = void>::Type
  *
  * @tparam BOOL The <tt>bool</tt> constant to evaluate for enabling/disabling.
  * @tparam T    Dummy, do not set.
@@ -174,18 +174,18 @@ struct DisableIf<False, T>
  */
 
 //
-// Example for enable-if function: 
+// Example for enable-if function:
 //
 //    template <typename TContainer>
 //    typename EnableIf<
 //        IsContainer<TContainer>,                  // 1st arg: enable-if condition
 //        typename Size<TContainer>::Type >::Type   // 2nd arg: return type
-//    length(TContainer & cont) 
+//    length(TContainer & cont)
 //    {
 //        SEQAN_CONCEPT_ASSERT((ContainerConcept<TContainer>));
 //        return end(cont) - begin(cont);
 //    }
-    
+
 template <bool b, typename T>
 struct EnableIf2;
 
@@ -208,7 +208,7 @@ struct EnableIf2<false, T> {};
  * @deprecated Will be renamed to DisableIfC.
  * @brief Metafunction to use for conditionally disabling code, bool version.
  *
- * @signature DisableIf<BOOL, T = void>::Type
+ * @signature DisableIf2<BOOL, T = void>::Type
  *
  * @tparam BOOL The <tt>bool</tt> constant to evaluate for enabling/disabling.
  * @tparam T    Dummy, do not set.
@@ -265,26 +265,10 @@ struct DisableIf2<true, T> {};
  * The following shows an example on how to properly use <tt>SEQAN_CTOR_ENABLE_IF</tt> as the last argument to the
  * constructor and suppressing the unused variable warning for the dummy parameter.
  *
- * @snippet demos/basic/enable_if.cpp enable if example constructor
- */
-
-/**
-.Macro.SEQAN_CTOR_ENABLE_IF
-..cat:Concepts
-..summary:Bind the visibility of a constructor to an expression.
-..signature:SEQAN_CTOR_ENABLE_IF(cond)
-..param.cond:Boolean type. If @Tag.Logical Values.tag.True@ or a metafunction that returns @Tag.Logical Values.tag.True@, the following function is visible, otherwise not.
-...remarks:The boolean value must be available at compile-time, e.g. $sizeof(T)>4$.
-..remarks:This macro allows to bind the visibility of a constructor to a boolean expression
-by using the SFINAE principle for an optional argument with default value.
-It can be used as the last dummy-argument of a constructor.
-To avoid an unused argument warning, call $ignoreUnusedVariableWarning(dummy)$ in the constructor's body.
-..example.text:Here is an example on how to use the macro:
-..example.snippet:demos/basic/enable_if.cpp|enable if example constructor
-..include:seqan/basic.h
+ * @snippet demos/dox/basic/enable_if.cpp enable if example constructor
  */
 
-#define SEQAN_CTOR_ENABLE_IF(...) typename ::seqan::EnableIf<__VA_ARGS__>::Type * dummy = 0
+#define SEQAN_CTOR_ENABLE_IF(...) typename seqan::EnableIf<__VA_ARGS__>::Type * dummy = 0
 
 /*!
  * @macro EnableIfFunctionality#SEQAN_CTOR_DISABLE_IF
@@ -309,30 +293,10 @@ To avoid an unused argument warning, call $ignoreUnusedVariableWarning(dummy)$ i
  * The following shows an example on how to properly use <tt>SEQAN_CTOR_DISABLE_IF</tt> as the last argument to the
  * constructor and suppressing the unused variable warning for the dummy parameter.
  *
- * @snippet demos/basic/enable_if.cpp disable if example constructor
- */
-
-/**
-.Macro.SEQAN_CTOR_DISABLE_IF
-..cat:Concepts
-..summary:Bind the visibility of a constructor to an expression.
-..signature:SEQAN_CTOR_DISABLE_IF(cond)
-..param.cond:Boolean type. If @Tag.Logical Values.tag.False@ or a metafunction that returns @Tag.Logical Values.tag.False@, the following function is visible, otherwise not.
-...remarks:The boolean value must be available at compile-time, e.g. $sizeof(T)>4$.
-..remarks:This macro allows to bind the visibility of a constructor to a boolean expression
-by using the @http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error|SFINAE@ principle for an optional argument with default value.
-It can be used as the last dummy-argument of a constructor.
-To avoid an unused argument warning, call $ignoreUnusedVariableWarning(dummy)$ in the constructor's body.
-..example.code:
-String(T const & s, SEQAN_CTOR_DISABLE_IF(IsProxy<T> >)) :  // macro must be extra c'tor argument
-    str(s)
-{
-    ignoreUnusedVariableWarning(dummy);     // necessary to avoid unused warning
-}
-..include:seqan/basic.h
+ * @snippet demos/dox/basic/enable_if.cpp disable if example constructor
  */
 
-#define SEQAN_CTOR_DISABLE_IF(...) typename ::seqan::DisableIf<__VA_ARGS__>::Type * dummy = 0
+#define SEQAN_CTOR_DISABLE_IF(...) typename seqan::DisableIf<__VA_ARGS__>::Type * dummy = 0
 
 /*!
  * @macro EnableIfFunctionality#SEQAN_FUNC_ENABLE_IF
@@ -358,35 +322,10 @@ String(T const & s, SEQAN_CTOR_DISABLE_IF(IsProxy<T> >)) :  // macro must be ext
  * The following shows an example on how to properly use <tt>SEQAN_FUNC_ENABLE_IF</tt> as the last argument to the
  * constructor and suppressing the unused variable warning for the dummy parameter.
  *
- * @snippet demos/basic/enable_if.cpp enable if example function
+ * @snippet demos/dox/basic/enable_if.cpp enable if example function
  */
 
-/**
-.Macro.SEQAN_FUNC_ENABLE_IF
-..cat:Concepts
-..summary:Bind the visibility of a function to an expression.
-..signature:SEQAN_FUNC_ENABLE_IF(cond, retType)
-..param.cond:Boolean type. If @Tag.Logical Values.tag.True@ or a metafunction that returns @Tag.Logical Values.tag.True@, the following function is visible, otherwise not.
-...remarks:The boolean value must be available at compile-time, e.g. $sizeof(T)>4$.
-..param.retType:Function return type, e.g. $typename Size<T>::Type$ or $void$.
-..remarks:This macro allows to bind the visibility of a function to a boolean expression
-by using the @http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error|SFINAE@ principle.
-It can be used in a function declaration/definition instead of its return type.
-As constructors have no return types, they must be disabled with @Macro.SEQAN_CTOR_ENABLE_IF@.
-..example.code:
-template <typename TContainer>
-SEQAN_FUNC_ENABLE_IF(
-    IsContainer<TContainer>, 
-    typename Size<TContainer>::Type)
-length(TContainer & cont) 
-{
-    SEQAN_CONCEPT_ASSERT((ContainerConcept<TContainer>));
-    return end(cont) - begin(cont);
-}
-..include:seqan/basic.h
- */
-
-#define SEQAN_FUNC_ENABLE_IF(...) typename ::seqan::EnableIf<__VA_ARGS__>::Type
+#define SEQAN_FUNC_ENABLE_IF(...) typename seqan::EnableIf<__VA_ARGS__>::Type
 
 /*!
  * @macro EnableIfFunctionality#SEQAN_FUNC_DISABLE_IF
@@ -412,38 +351,13 @@ length(TContainer & cont)
  * The following shows an example on how to properly use <tt>SEQAN_FUNC_DISABLE_IF</tt> as the last argument to the
  * constructor and suppressing the unused variable warning for the dummy parameter.
  *
- * @snippet demos/basic/enable_if.cpp disable if example function
- */
-
-/**
-.Macro.SEQAN_FUNC_DISABLE_IF
-..cat:Concepts
-..summary:Bind the visibility of a function to an expression.
-..signature:SEQAN_FUNC_DISABLE_IF(cond, retType)
-..param.cond:Boolean type. If @Tag.Logical Values.tag.False@ or a metafunction that returns @Tag.Logical Values.tag.False@, the following function is visible, otherwise not.
-...remarks:The boolean value must be available at compile-time, e.g. $sizeof(T)>4$.
-..param.retType:Function return type, e.g. $typename Size<T>::Type$ or $void$.
-..remarks:This macro allows to bind the visibility of a function to a boolean expression
-by using the @http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error|SFINAE@ principle.
-It can be used in a function declaration/definition instead of its return type.
-As constructors have no return types, they must be disabled with @Macro.SEQAN_CTOR_DISABLE_IF@.
-..example.code:
-template <typename TContainer>
-SEQAN_FUNC_DISABLE_IF(
-    IsIntergral<TContainer>,
-    typename Size<TContainer>::Type)
-length(TContainer & cont)
-{
-    SEQAN_CONCEPT_ASSERT((ContainerConcept<TContainer>));
-    return end(cont) - begin(cont);
-}
-..include:seqan/basic.h
+ * @snippet demos/dox/basic/enable_if.cpp disable if example function
  */
 
-#define SEQAN_FUNC_DISABLE_IF(...) typename ::seqan::DisableIf<__VA_ARGS__>::Type
+#define SEQAN_FUNC_DISABLE_IF(...) typename seqan::DisableIf<__VA_ARGS__>::Type
 
 // ============================================================================
 // Functions
 // ============================================================================
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_ENABLE_IF_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_ENABLE_IF_H_
diff --git a/seqan/basic/metaprogramming_logic.h b/seqan/basic/metaprogramming_logic.h
index bb2b8b2..824a06e 100644
--- a/seqan/basic/metaprogramming_logic.h
+++ b/seqan/basic/metaprogramming_logic.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,7 +29,7 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 // Logic types and operations for metaprogramming.
 //
@@ -42,8 +42,8 @@
 // TODO(holtgrew): Group all these metafunctions?
 // TODO(holtgrew): Make a comment on the C prefix and the auto-evaluation to TParam::Type in the group?
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_LOGIC_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_LOGIC_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_LOGIC_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_LOGIC_H_
 
 namespace seqan {
 
@@ -67,18 +67,18 @@ namespace seqan {
  *
  * Print the values of the tags/metafunctions <tt>True</tt> and <tt>False</tt>.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp tags true false
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp tags true false
  *
  * @section Inheriting from True and False
  *
  * The two tags True and False have the special property that they can also be used as metafunctions and both have a
  * <tt>VALUE</tt> as well as a <tt>TYPE</tt>.  This property makes it very convenient to define metafunctions by inheriting from the <tt>True</tt> or <tt>False</tt>.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp inheriting from true false
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp inheriting from true false
  *
  * The metafunction <tt>IsInt32</tt> can now be used as follows.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp using isint32
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp using isint32
  */
 
 /*!
@@ -101,33 +101,38 @@ namespace seqan {
  * @signature bool False::VALUE = false;
  */
 
-/**
-.Tag.Logical Values:
-..cat:Metaprogramming
-..summary:Tag that represents true and false.
-..tag.True:The logical value "true".
-..tag.False:The logical value "false".
-..remarks:These tags also function as Metafunctions that return a boolean value $VALUE$ and themselves ($True$/$False$) as $Type$.
-..example.text:Print the values of these tags/metafunctions.
-..example.code:
-std::cout << False::VALUE << std::endl;                         // 0
-std::cout << True::VALUE << std::endl;                          // 1
-std::cout << IsSameType<False,False::Type>::VALUE << std::endl; // 1
-..include:seqan/basic.h
-..see:Metafunction.Eval
-..see:Metafunction.IsSameType
-*/
-
 struct True
 {
     typedef True Type;
-	static const bool VALUE = true;
+    static const bool VALUE = true;
+
+    operator bool () const
+    {
+        return true;
+    }
+
+    template <typename TValue>
+    bool operator() (TValue const &) const
+    {
+        return true;
+    }
 };
 
 struct False
 {
     typedef False Type;
-	static const bool VALUE = false;
+    static const bool VALUE = false;
+
+    operator bool () const
+    {
+        return false;
+    }
+
+    template <typename TValue>
+    bool operator() (TValue const &) const
+    {
+        return false;
+    }
 };
 
 // ============================================================================
@@ -153,7 +158,7 @@ struct False
  *
  * Here is an example for this:
  *
- * @snippet demos/basic/metaprogramming_logic.cpp shortcut to type feature
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp shortcut to type feature
  *
  * @see LogicalValuesTags#True
  * @see LogicalValuesTags#False
@@ -174,44 +179,13 @@ struct False
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code and achieve the following output:
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type eval
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type eval
  */
 
-/**
-.Metafunction.Eval
-..cat:Metaprogramming
-..summary:Convert from $bool$ values to types ($True$ and $False$).
-..signature:Eval<b>::Type
-..param.b:The boolean to evaluate.
-...type:nolink:$bool$
-..returns:Either @Tag.Logical Values.tag.True@ or @Tag.Logical Values.tag.False@, depending on $b$.
-..include:seqan/basic.h
-..example.text:Demonstrate the usage of $Eval$ to bridge between $bool$ values and the logical tags.
-..example.code:
-void printBoolType(True const &)
-{
-    std::cout << "true" << std::endl;
-}
-
-void printBoolType(False const &)
-{
-    std::cout << "false" << std::endl;
-}
-
-int main(int argc, char ** argv)
-{
-    using namespace seqan;
-
-    printBoolType(Eval<true>::Type());   // => "true\n"
-    printBoolType(Eval<false>::Type());  // => "false\n"
-    return 0;
-}
-*/
-
 template <bool B>
 struct Eval : False {};
 
@@ -239,32 +213,15 @@ struct Eval<true> : True {};
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code using Not.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type not
- */ 
-
-/**
-.Metafunction.Not
-..cat:Metaprogramming
-..summary:Metaprogramming boolean "not" operator.
-..signature:Not<B>::Type
-..param.B:Argument to invert.
-...type:Tag.Logical Values.tag.True
-...type:Tag.Logical Values.tag.False
-..returns:One of @Tag.Logical Values.tag.True@ and @Tag.Logical Values.tag.False@, the result of logical not.
-The arguments $B$ can either be @Tag.Logical Values.tag.True@/@Tag.Logical Values.tag.False@
-or boolean metafunctions that return @Tag.Logical Values.tag.True@/@Tag.Logical Values.tag.False@.
-..example.code:
-Not<False>::Type
-Not<True>::Type
-..include:seqan/basic.h
-*/
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type not
+ */
 
 template <typename TBool1>
-struct Not : Not<typename TBool1::Type> {}; 
+struct Not : Not<typename TBool1::Type> {};
 
 template <>
 struct Not<False> : True {};
@@ -292,31 +249,12 @@ struct Not<True> : False {};
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code using NotC.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type notc
- */ 
-
-/**
-.Metafunction.NotC
-..cat:Metaprogramming
-..summary:Metaprogramming boolean "not" operator, value variant.
-..signature:NotC<B>::Type
-..param.B:Argument
-...type:nolink:$bool$
-..returns:$!B1$.
-..example.code:
-NotC<false, true>::Type
-NotC<false, false>::VALUE
-NotC<AndC<false, true>::VALUE, false>::Type
-NotC<AndC<false, true>, true>::Type
-..see:Metafunction.Or
-..see:Metafunction.And
-..see:Metafunction.AndC
-..include:seqan/basic.h
-*/
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type notc
+ */
 
 template <bool B>
 struct NotC;
@@ -348,41 +286,15 @@ struct NotC<true> : False {};
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code using Or.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type or
- */ 
-
-/**
-.Metafunction.Or
-..cat:Metaprogramming
-..summary:Metaprogramming boolean "or" operator.
-..signature:Or<B1, B2>::Type
-..signature:Or<B1, B2>::VALUE
-..param.B1:Left-hand argument.
-...type:Tag.Logical Values.tag.True
-...type:Tag.Logical Values.tag.False
-..param.B2:Right-hand argument.
-...type:Tag.Logical Values.tag.True
-...type:Tag.Logical Values.tag.False
-..returns:One of @Tag.Logical Values.tag.True@ and @Tag.Logical Values.tag.False@, the result of logical or.
-The arguments $B1$/$B2$ can either be @Tag.Logical Values.tag.True@/@Tag.Logical Values.tag.False@
-or boolean metafunctions that return @Tag.Logical Values.tag.True@/@Tag.Logical Values.tag.False@.
-..example.code:
-Or<False,False>::Type
-Or<False,True>::Type
-Or<typename And<T1,T2>::Type,T3>::Type
-Or<And<T1,T2>,T3>::Type
-..see:Metafunction.And
-..see:Metafunction.AndC
-..see:Metafunction.OrC
-..include:seqan/basic.h
-*/
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type or
+ */
 
 template <typename TBool1, typename TBool2>
-struct Or : Or<typename TBool1::Type, typename TBool2::Type> {}; 
+struct Or : Or<typename TBool1::Type, typename TBool2::Type> {};
 
 template <>
 struct Or<False, False> : False {};
@@ -415,35 +327,13 @@ struct Or<True, True> : True {};
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code using OrC.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type orc
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type orc
  */
 
-/**
-.Metafunction.OrC
-..cat:Metaprogramming
-..summary:Metaprogramming boolean "or" operator, value variant.
-..signature:OrC<B1, B2>::Type
-..signature:OrC<B1, B2>::VALUE
-..param.B1:Left-hand argument.
-...type:nolink:$bool$
-..param.B2:Right-hand argument.
-...type:nolink:$bool$
-..returns:$B1 || B2$.
-..example.code:
-OrC<false, true>::Type
-OrC<false, false>::VALUE
-OrC<AndC<false, true>::VALUE, false>::Type
-OrC<AndC<false, true>, true>::Type
-..see:Metafunction.Or
-..see:Metafunction.And
-..see:Metafunction.AndC
-..include:seqan/basic.h
-*/
-
 template <bool B1, bool B2>
 struct OrC;
 
@@ -478,30 +368,15 @@ struct OrC<true, true> : True {};
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code using And.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type and
- */ 
-
-/**
-.Metafunction.And
-..cat:Metaprogramming
-..summary:Metaprogramming "and" operator.
-..signature:Or<B1, B2>::Type
-..param.B1:Left-hand argument.
-...type:Tag.Logical Values.tag.True
-...type:Tag.Logical Values.tag.False
-..param.B2:Right-hand argument.
-...type:Tag.Logical Values.tag.True
-...type:Tag.Logical Values.tag.False
-..returns:One of @Tag.Logical Values.tag.True@ and @Tag.Logical Values.tag.False@, the result of logical and.
-..include:seqan/basic.h
-*/
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type and
+ */
 
 template <typename TBool1, typename TBool2>
-struct And : And<typename TBool1::Type, typename TBool2::Type> {}; 
+struct And : And<typename TBool1::Type, typename TBool2::Type> {};
 
 template <>
 struct And<False, False> : False {};
@@ -534,35 +409,13 @@ struct And<True, True> : True {};
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code using AndC.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type andc
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type andc
  */
 
-/**
-.Metafunction.AndC
-..cat:Metaprogramming
-..summary:Metaprogramming boolean "and" operatand, value variant.
-..signature:AndC<B1, B2>::Type
-..signature:AndC<B1, B2>::VALUE
-..param.B1:Left-hand argument.
-...type:nolink:$bool$
-..param.B2:Right-hand argument.
-...type:nolink:$bool$
-..returns:$B1 && B2$.
-..example.code:
-AndC<false, true>::Type
-AndC<false, false>::VALUE
-AndC<AndC<false, true>::VALUE, false>::Type
-AndC<AndC<false, true>, true>::Type
-..see:Metafunction.And
-..see:Metafunction.And
-..see:Metafunction.AndC
-..include:seqan/basic.h
-*/
-
 template <bool B1, bool B2>
 struct AndC;
 
@@ -596,27 +449,13 @@ struct AndC<true, true> : True {};
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code using If.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type if
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type if
  */
 
-/**
-.Metafunction.If
-..cat:Metaprogramming
-..summary:Metaprogramming "if".
-..signature:If<T, T1, T2>::Type
-..param.T:The condition.
-..param.T1:Result if $b$.
-..param.T2:Result if not $b$.
-..see:Metafunction.IfC
-..returns:If $T$ is $True$ then $T1$, otherwise $T2$.
-..include:seqan/basic.h
-*/
-
-// TODO(holtgrew): Inherit from T1/T2 to follow pattern for Or<>, And<>?
 template <typename TCondition, typename T1, typename T2>
 struct If : If<typename TCondition::Type, T1, T2>{};
 
@@ -632,6 +471,40 @@ struct If<False, T1, T2>
     typedef T2 Type;
 };
 
+
+
+template <typename TArgT, typename TArgF>
+inline TArgT SEQAN_FORWARD_ARG
+ifSwitch(True, TArgT SEQAN_FORWARD_ARG argTrue, TArgF const &)
+{
+    return SEQAN_FORWARD(TArgT, argTrue);
+}
+
+template <typename TArgT, typename TArgF>
+inline TArgF SEQAN_FORWARD_ARG
+ifSwitch(False, TArgT const &, TArgF SEQAN_FORWARD_ARG argFalse)
+{
+    return SEQAN_FORWARD(TArgF, argFalse);
+}
+
+#ifndef SEQAN_CXX11_STANDARD
+
+template <typename TArgT, typename TArgF>
+inline TArgT const &
+ifSwitch(True, TArgT const & argTrue, TArgF const &)
+{
+    return SEQAN_FORWARD(TArgT, argTrue);
+}
+
+template <typename TArgT, typename TArgF>
+inline TArgF const &
+ifSwitch(False, TArgT const &, TArgF const & argFalse)
+{
+    return SEQAN_FORWARD(TArgF, argFalse);
+}
+
+#endif
+
 // ----------------------------------------------------------------------------
 // Metafunction IfC
 // ----------------------------------------------------------------------------
@@ -653,28 +526,13 @@ struct If<False, T1, T2>
  *
  * We define the following two helper functions.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp true false print helpers
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp true false print helpers
  *
  * Now, we can write the following code using If.
  *
- * @snippet demos/basic/metaprogramming_logic.cpp print bool type if
+ * @snippet demos/dox/basic/metaprogramming_logic.cpp print bool type if
  */
 
-/**
-.Metafunction.IfC
-..cat:Metaprogramming
-..summary:Metaprogramming "if", value based version.
-..signature:If<b, T1, T2>::Type
-..param.b:The condition to evaluate.
-...type:nolink:$bool$
-..param.T1:Result if $b$.
-..param.T2:Result if not $b$.
-..returns:If $b$ is $true$ then $T1$, otherwise $T2$.
-..see:Metafunction.If
-..include:seqan/basic.h
-*/
-
-// TODO(holtgrew): Inherit from T1/T2 to follow pattern for Or<>, And<>?
 template <bool FLAG, typename T1, typename T2>
 struct IfC
 {
@@ -693,4 +551,4 @@ struct IfC<false, T1, T2>
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_LOGIC_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_LOGIC_H_
diff --git a/seqan/basic/metaprogramming_math.h b/seqan/basic/metaprogramming_math.h
index 8f56b90..78348fd 100644
--- a/seqan/basic/metaprogramming_math.h
+++ b/seqan/basic/metaprogramming_math.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -35,8 +35,8 @@
 // Mathematical Metafunctions.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_MATH_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_MATH_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_MATH_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_MATH_H_
 
 #include <seqan/platform.h>
 
@@ -81,29 +81,21 @@ struct ConstUInt {};
  *
  * @section Example
  *
- * @snippet demos/basic/metaprogramming_math.cpp log2 call
+ * @snippet demos/dox/basic/metaprogramming_math.cpp log2 call
  */
 
-/**
-.Metafunction.Log2
-..cat:Metaprogramming
-..summary:Compute ceiled logarithm to base 2 using metaprogramming.
-..signature:Log2<x>::VALUE
-..param.x:The value to take the logarithm of.
-...type:nolink:$__int64$
-..returns:$ceil(log2(x))$.
-..include:seqan/basic.h
- */
-
-template <__int64 numerus>
-struct Log2
+template <__uint64 numerus, __uint64 base>
+struct LogN
 {
-    static const __uint64 VALUE = Log2<(numerus + 1) / 2>::VALUE + 1; // ceil(log_2(n))
+    static const __uint64 VALUE = LogN<(numerus + 1) / base, base>::VALUE + 1; // ceil(log(numerus) / log(base))
 };
 
+template <__uint64 numerus>
+struct Log2: LogN<numerus, 2> {};
+
 // Base cases.
-template <> struct Log2<1> { static const __uint64 VALUE = 0; };
-template <> struct Log2<0> { static const __uint64 VALUE = 0; };
+template <__uint64 base> struct LogN<1, base> { static const __uint64 VALUE = 0; };
+template <__uint64 base> struct LogN<0, base> { static const __uint64 VALUE = 0; };
 
 // ----------------------------------------------------------------------------
 // Metafunction Log2Floor
@@ -121,29 +113,21 @@ template <> struct Log2<0> { static const __uint64 VALUE = 0; };
  *
  * @section Example
  *
- * @snippet demos/basic/metaprogramming_math.cpp log2floor call
- */
-
-/**
-.Metafunction.Log2Floor
-..cat:Metaprogramming
-..summary:Compute floored logarithm to base 2 using metaprogramming.
-..signature:Log2<x>::VALUE
-..param.x:The value to take the logarithm of.
-...type:nolink:$__int64$
-..returns:$floor(log2(x))$.
-..include:seqan/basic.h
+ * @snippet demos/dox/basic/metaprogramming_math.cpp log2floor call
  */
 
-template <__int64 numerus>
-struct Log2Floor
+template <__uint64 numerus, __uint64 base>
+struct LogNFloor
 {
-    static const __uint64 VALUE = Log2Floor<numerus / 2>::VALUE + 1;  // floor(log_2(n))
+    static const __uint64 VALUE = LogNFloor<numerus / base, base>::VALUE + 1; // floor(log(numerus) / log(base))
 };
 
+template <__uint64 numerus>
+struct Log2Floor: LogNFloor<numerus, 2> {};
+
 // Base cases.
-template <> struct Log2Floor<1> { static const __uint64 VALUE = 0; };
-template <> struct Log2Floor<0> { static const __uint64 VALUE = 0; };
+template <__uint64 base> struct LogNFloor<1, base> { static const __uint64 VALUE = 0; };
+template <__uint64 base> struct LogNFloor<0, base> { static const __uint64 VALUE = 0; };
 
 // ----------------------------------------------------------------------------
 // Metafunction Power
@@ -160,20 +144,7 @@ template <> struct Log2Floor<0> { static const __uint64 VALUE = 0; };
  *
  * @return __uint64 b<sup>e</sup
  *
- * @snippet demos/basic/metaprogramming_math.cpp power call
- */
-
-/**
-.Metafunction.Power
-..cat:Metaprogramming
-..summary:Compute power of a number.
-..signature:Power<b, e>::VALUE
-..param.b:The base.
-...type:nolink:$__int64$
-..param.e:The exponent.
-...type:nolink:$__int64$
-..returns:$b^e$
-..include:seqan/basic.h
+ * @snippet demos/dox/basic/metaprogramming_math.cpp power call
  */
 
 template <__int64 base, __int64 exponent>
@@ -213,4 +184,4 @@ struct Max
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_MATH_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_MATH_H_
diff --git a/seqan/basic/metaprogramming_type.h b/seqan/basic/metaprogramming_type.h
index 1d0ee70..3e9fabd 100644
--- a/seqan/basic/metaprogramming_type.h
+++ b/seqan/basic/metaprogramming_type.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,8 +38,8 @@
 // and modifying it, such as querying for const-ness.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_H_
 
 namespace seqan {
 
@@ -60,7 +60,7 @@ namespace seqan {
 // ----------------------------------------------------------------------------
 
 /*!
- * @mfn IsSamEtype
+ * @mfn IsSameType
  * @headerfile <seqan/basic.h>
  * @brief Metaprogramming type comparison.
  *
@@ -72,19 +72,7 @@ namespace seqan {
  *
  * @return Type  Either True or False, depending on whether T1 is the same type as T2.
  * @return VALUE The same as <tt>Type::VALUE</tt>.
- */ 
-
-/**
-.Metafunction.IsSameType
-..cat:Metaprogramming
-..summary:Metaprogramming type comparison.
-..signature:IsSameType<T1, T2>::Type
-..signature:IsSameType<T1, T2>::VALUE
-..param.T1:Left-hand argument.
-..param.T2:Right-hand argument.
-..returns:@Tag.Logical Values.tag.True@/$true$ if $T1$ is the same as $T2$, otherwise @Tag.Logical Values.tag.False@/$false$.
-..include:seqan/basic.h
-*/
+ */
 
 template <typename Type1, typename Type2>
 struct IsSameType : False {};
@@ -115,44 +103,28 @@ struct IsSameType<Type1, Type1> : True {};
  * integral value.  You can specialize the metafunction for your custom types.
  */
 
-/**
-.Metafunction.MakeUnsigned:
-..cat:Basic
-..summary:Converts an integral value into an unsigned integral value.
-..signature:MakeUnsigned<T>::Type
-..param.T:Input integral type.
-..returns.param.Type:A type without a sign of the same domain, e.g. $unsigned int$ for $T$ = $int$.
-...default:$T$
-..include:seqan/basic.h
- */
-
 template <typename T>
 struct MakeUnsigned
 {
-	typedef
-		typename If<typename IsSameType<T, __int8>::Type,       __uint8,
-		typename If<typename IsSameType<T, char>::Type,         unsigned char,
-		typename If<typename IsSameType<T, signed char>::Type,  unsigned char,
-		typename If<typename IsSameType<T, signed short>::Type, unsigned short,
-		typename If<typename IsSameType<T, signed int>::Type,   unsigned int,
-		typename If<typename IsSameType<T, signed long>::Type,  unsigned long,
-		typename If<typename IsSameType<T, __int64>::Type,      __uint64, T
-		>::Type>::Type>::Type>::Type>::Type>::Type>::Type Type;
+    typedef
+        typename If<typename IsSameType<T, __int8>::Type,       __uint8,
+        typename If<typename IsSameType<T, char>::Type,         unsigned char,
+        typename If<typename IsSameType<T, signed char>::Type,  unsigned char,
+        typename If<typename IsSameType<T, signed short>::Type, unsigned short,
+        typename If<typename IsSameType<T, signed int>::Type,   unsigned int,
+        typename If<typename IsSameType<T, signed long>::Type,  unsigned long,
+        typename If<typename IsSameType<T, __int64>::Type,      __uint64, T
+        >::Type>::Type>::Type>::Type>::Type>::Type>::Type Type;
 };
 
 template <typename T>
 struct MakeUnsigned<T const>
 {
-	typedef typename MakeUnsigned<T>::Type const Type;
+    typedef typename MakeUnsigned<T>::Type const Type;
 };
 
 // TODO(holtgrew): Internal metafunction unnecessary now?
-/*
-.Internal.MakeUnsigned_:
-..signature:MakeUnsigned_<T>
-..status:deprecated, please use @Metafunction.MakeUnsigned@
-..returns:$unsigned t$ if $T$ is not $unsigned t$, otherwise $T$.
-*/
+
 template <typename T>
 struct MakeUnsigned_ : MakeUnsigned<T> {};
 
@@ -179,45 +151,28 @@ struct MakeUnsigned_ : MakeUnsigned<T> {};
  * integral value.  You can specialize the metafunction for your custom types.
  */
 
-/**
-.Metafunction.MakeSigned:
-..cat:Basic
-..summary:Converts an integral value into a signed integral value.
-..signature:MakeSigned<T>::Type
-..param.T:Input integral type.
-..returns.param.Type:A type with a sign of the same domain, e.g. $int$ for $T$ = $unsigned int$.
-...default:$T$
-..include:seqan/basic.h
-..see:Metafunction.MakeUnsigned
- */
-
 template <typename T>
 struct MakeSigned
 {
-	typedef
-		typename If<typename IsSameType<T, char>::Type,           signed char,
-		typename If<typename IsSameType<T, __int8>::Type,         __int8,
-		typename If<typename IsSameType<T, unsigned char>::Type,  signed char,
-		typename If<typename IsSameType<T, unsigned short>::Type, signed short,
-		typename If<typename IsSameType<T, unsigned int>::Type,   signed int,
-		typename If<typename IsSameType<T, unsigned long>::Type,  signed long,
-		typename If<typename IsSameType<T, __uint64>::Type,       __int64, T
-		>::Type>::Type>::Type>::Type>::Type>::Type>::Type Type;
+    typedef
+        typename If<typename IsSameType<T, char>::Type,           signed char,
+        typename If<typename IsSameType<T, __int8>::Type,         __int8,
+        typename If<typename IsSameType<T, unsigned char>::Type,  signed char,
+        typename If<typename IsSameType<T, unsigned short>::Type, signed short,
+        typename If<typename IsSameType<T, unsigned int>::Type,   signed int,
+        typename If<typename IsSameType<T, unsigned long>::Type,  signed long,
+        typename If<typename IsSameType<T, __uint64>::Type,       __int64, T
+        >::Type>::Type>::Type>::Type>::Type>::Type>::Type Type;
 };
 
 template <typename T>
 struct MakeSigned<T const>
 {
-	typedef typename MakeSigned<T>::Type const Type;
+    typedef typename MakeSigned<T>::Type const Type;
 };
 
 // TODO(holtgrew): Internal metafunction unnecessary now?
-/*
-.Internal.MakeSigned_:
-..signature:MakeSigned_<T>
-..status:deprecated, please use @Metafunction.MakeSigned@
-..returns:$signed t$ if $T$ is not $signed t$, otherwise $T$.
-*/
+
 template <typename T>
 struct MakeSigned_ : MakeSigned<T> {};
 
@@ -237,24 +192,12 @@ struct MakeSigned_ : MakeSigned<T> {};
  * @return Type A corresponding non-reference type, e.g. <tt>int</tt> for <tt>T = &amp; int</tt>.
  */
 
-/**
-.Metafunction.RemoveReference:
-..cat:Basic
-..summary:Converts a (reference) type into the same type without reference.
-..signature:RemoveReference<T>::Type
-..param.T:Input type.
-..returns.param.Type:A corresponding non-reference type, e.g. $int$ for $T$ = $int &$.
-...default:$T$
-..include:seqan/basic.h
-..see:Metafunction.RemoveConst
-*/
-
 #ifdef SEQAN_CXX11_STANDARD
 
 template <typename T>
 struct RemoveReference
 {
-	typedef typename std::remove_reference<T>::type Type;
+    typedef typename std::remove_reference<T>::type Type;
 };
 
 #else
@@ -262,7 +205,7 @@ struct RemoveReference
 template <typename T>
 struct RemoveReference
 {
-	typedef T Type;
+    typedef T Type;
 };
 
 template <typename T>
@@ -270,6 +213,61 @@ struct RemoveReference<T &> : RemoveReference<T> {};
 
 #endif
 
+// ----------------------------------------------------------------------------
+// Metafunction RemoveReference
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn RemovePointer
+ * @headerfile <seqan/basic.h>
+ * @brief Converts a (pointer) type into the same type without a pointer.
+ *
+ * @signature RemovePointer<T>::Type;
+ *
+ * @tparam T The input type.
+ *
+ * @return Type A corresponding non-pointer type, e.g. <tt>int</tt> for <tt>T = *int</tt>.
+ */
+
+#ifdef SEQAN_CXX11_STANDARD
+
+template <typename T>
+struct RemovePointer
+{
+    typedef typename std::remove_pointer<T>::type Type;
+};
+
+#else
+
+template <typename T>
+struct RemovePointer
+{
+    typedef T Type;
+};
+
+template <typename T>
+struct RemovePointer<T *>
+{
+    typedef T Type;
+};
+
+template <typename T>
+struct RemovePointer<T * const>
+{
+    typedef T Type;
+};
+
+#endif
+
+template <typename T>
+struct IsPointer : False {};
+
+template <typename T>
+struct IsPointer<T *> : True {};
+
+template <typename T>
+struct IsPointer<T * const> : True {};
+
 // ----------------------------------------------------------------------------
 // Metafunction RemoveConst
 // ----------------------------------------------------------------------------
@@ -286,28 +284,10 @@ struct RemoveReference<T &> : RemoveReference<T> {};
  * @return Type A corresponding non-const type, e.g. <tt>int</tt> for <tt>T = const int</tt>.
  */
 
-/**
-.Metafunction.RemoveConst:
-..cat:Basic
-..summary:Converts a (const) type into the corresponding non-const type.
-..signature:RemoveConst<T>::Type
-..param.T:Input type.
-..returns.param.Type:A corresponding non-const type, e.g. $int$ for $T$ = $const int$.
-...default:$T$
-..include:seqan/basic.h
-*/
-
-/*
-.Internal.RemoveConst_:
-..signature:RemoveConst_<T>
-..status:deprecated, please use @Metafunction.RemoveConst@
-..returns:$t$ if $T$ is $t const$, otherwise $T$.
-*/
-
 template <typename T>
 struct RemoveConst
 {
-	typedef T Type;
+    typedef T Type;
 };
 
 template <typename T>
@@ -316,21 +296,21 @@ struct RemoveConst<T const> : public RemoveConst<T> {};
 template <typename T>
 struct RemoveConst<T &>
 {
-	typedef typename RemoveConst<T>::Type & Type;
+    typedef typename RemoveConst<T>::Type & Type;
 };
 
 /*
 template <typename T>
 struct RemoveConst<T const *>
 {
-	typedef typename RemoveConst<T>::Type * Type;
+    typedef typename RemoveConst<T>::Type * Type;
 };
 */
 
 template <typename T, size_t I>
 struct RemoveConst<T const [I]>
 {
-	typedef T Type[I];
+    typedef T Type[I];
 };
 
 // TODO(holtgrew): Internal metafunction superflous?
@@ -348,13 +328,13 @@ struct RemoveConst_ : RemoveConst<T> {};
 template <typename TFrom, typename TTo>
 struct CopyConst_
 {
-	typedef TTo Type;
+    typedef TTo Type;
 };
 
 template <typename TFrom, typename TTo>
 struct CopyConst_<TFrom const, TTo>
 {
-	typedef TTo const Type;
+    typedef TTo const Type;
 };
 
 // ----------------------------------------------------------------------------
@@ -363,12 +343,6 @@ struct CopyConst_<TFrom const, TTo>
 
 // TODO(holtgrew): Make public, complete documentation.
 
-/*
-.Internal.IsConst_:
-..signature:IsConst_<T>
-..returns:@Tag.Logical Values.tag.True@ if $T$ is $t const$, otherwise @Tag.Logical Values.tag.False@.
-*/
-
 template <typename T>
 struct IsConst_ : False
 {};
@@ -383,23 +357,15 @@ struct IsConst_<T const> : True
 
 // TODO(holtgrew): Make public, complete documentation or deletion candidate.
 
-/*
-.Internal.ClassIdentifier_:
-..signature:void * ClassIdentifier_<T>::getID()
-..returns:A void * that identifies $T$.
-...text:The returned values of two calls of $getID$ are equal if and only if
-the used type $T$ was the same.
- */
-
 template <typename T>
 struct ClassIdentifier_
 {
-	static inline void *
-	getID()
-	{
-		static bool _id_dummy;
-		return &_id_dummy;
-	}
+    static inline void *
+    getID()
+    {
+        static bool _id_dummy;
+        return &_id_dummy;
+    }
 };
 
 // ============================================================================
@@ -408,4 +374,4 @@ struct ClassIdentifier_
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_H_
diff --git a/seqan/stream/adapt_cstdio.h b/seqan/basic/metaprogramming_type_algebra.h
similarity index 50%
rename from seqan/stream/adapt_cstdio.h
rename to seqan/basic/metaprogramming_type_algebra.h
index 96ad6e5..7f9b244 100644
--- a/seqan/stream/adapt_cstdio.h
+++ b/seqan/basic/metaprogramming_type_algebra.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,16 +29,13 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
 // ==========================================================================
-// Adaption for <cstdio> streams: std::FILE * to the stream concept.
+// Metaprogramming for types algebra.
 // ==========================================================================
 
-#include <cstdio>
-#include <sstream>
-
-#ifndef SEQAN_STREAM_ADAPT_CSTIO_H_
-#define SEQAN_STREAM_ADAPT_CSTIO_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_ALGEBRA_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_ALGEBRA_H_
 
 namespace seqan {
 
@@ -46,337 +43,232 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/**
-.Adaption."FILE *"
-..cat:Input/Output
-..summary:Adaption from $FILE *$ of $<cstdio>$ to streams.
-..include:seqan/stream.h
- */
+template <typename T1, typename T2, typename TSpec> struct Pair;
+template <typename TTag, typename TSubList> struct TagList;
 
-// ============================================================================
+// ==========================================================================
 // Metafunctions
-// ============================================================================
+// ==========================================================================
 
-/* // Clashes with definition of these metafunctions in file module.
 // ----------------------------------------------------------------------------
-// Metafunction Difference
+// Metafunction Sum<T1, T2>
 // ----------------------------------------------------------------------------
+// T1 + T2
 
-template <>
-struct Difference<FILE *>
+template <typename T1 = void, typename T2 = void>
+struct Sum
 {
-    typedef long int Type;
+    typedef TagList<T1, TagList<T2, void> >   Type;
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction Position
+// Metafunction Sum<T1, void>
 // ----------------------------------------------------------------------------
 
-template <>
-struct Position<FILE *>
+template <typename T1>
+struct Sum<T1, void>
 {
-    typedef long int Type;
+    typedef T1 Type;
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction Size
+// Metafunction Sum<void, T2>
 // ----------------------------------------------------------------------------
 
-template <>
-struct Size<FILE *>
+template <typename T2>
+struct Sum<void, T2>
 {
-    typedef long int Type;
+    typedef T2 Type;
 };
-*/
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
+// Metafunction Sum<void, void>
 // ----------------------------------------------------------------------------
 
-template <>
-struct HasStreamFeature<FILE *, IsInput>
-{
-    typedef True Type;
-};
+//template <>
+//struct Sum<void, void>
+//{
+//    typedef void Type;
+//};
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsOutput>
+// Metafunction Sum<TTag1, TTagList2>
 // ----------------------------------------------------------------------------
+// T1 + L2[0..0] = T1 + L2[0]
 
-template <>
-struct HasStreamFeature<FILE *, IsOutput>
+template <typename TTag1, typename TTag2>
+struct Sum<TTag1, TagList<TTag2, void> >
 {
-    typedef True Type;
+    typedef typename Sum<TTag1, TTag2>::Type    Type;
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasPeek>
+// Metafunction Sum<TTag1, TTagList2>
 // ----------------------------------------------------------------------------
+// T1 + L2[0..m] = T1 + (L2[0] + .. + L2[m])
 
-template <>
-struct HasStreamFeature<FILE *, HasPeek>
+template <typename TTag1, typename TTag2, typename TSubList2>
+struct Sum<TTag1, TagList<TTag2, TSubList2> >
 {
-    typedef True Type;
+    typedef TagList<TTag1, TagList<TTag2, TSubList2> >  Type;
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasFilename>
+// Metafunction Sum<TTagList1, TTagList2>
 // ----------------------------------------------------------------------------
+// L1[0..0] + L2[0..m] = L1[0] + (L2[0] + .. + L2[m])
 
-template <>
-struct HasStreamFeature<FILE *, HasFilename>
+template <typename TTag1, typename TTag2, typename TSubList2>
+struct Sum<TagList<TTag1, void>, TagList<TTag2, TSubList2> >
 {
-    typedef False Type;
+    typedef TagList<TTag1, TagList<TTag2, TSubList2> >  Type;
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Seek<TSpec> >
+// Metafunction Sum<TTagList1, TTagList2>
 // ----------------------------------------------------------------------------
+// L1[0..n] + L2[0..m] = L1[0] + (L1[1..n] + (L2[0] + .. + L2[m]))
 
-template <typename TSpec>
-struct HasStreamFeature<FILE *, Seek<TSpec> >
+template <typename TTag1, typename TSubList1, typename TTag2, typename TSubList2>
+struct Sum<TagList<TTag1, TSubList1>, TagList<TTag2, TSubList2> >
 {
-    typedef True Type;
+    typedef TagList<TTag1, typename Sum<TSubList1, TagList<TTag2, TSubList2> >::Type> Type;
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Tell>
+// Metafunction Product<T1, T2>
 // ----------------------------------------------------------------------------
+// T1 x T2
 
-template <>
-struct HasStreamFeature<FILE *, Tell>
+template <typename T1 = void, typename T2 = void>
+struct Product
 {
-    typedef True Type;
+    typedef Pair<T1, T2, void>  Type;
 };
 
-// ============================================================================
-// Functions
-// ============================================================================
-
 // ----------------------------------------------------------------------------
-// Function streamPeek()
+// Metafunction Product<T1, void>
 // ----------------------------------------------------------------------------
 
-inline int
-streamPeek(char & c, FILE * stream)
-{
-    c = fgetc(stream);
-    ungetc(c, stream);
-    if (c == EOF)
-        return EOF;
-    return 0;
-}
+//template <typename T1>
+//struct Product<T1, void>
+//{
+//    typedef void    Type;
+//};
 
 // ----------------------------------------------------------------------------
-// Function streamReadChar()
+// Metafunction Product<void, T2>
 // ----------------------------------------------------------------------------
 
-inline int
-streamReadChar(char & c, FILE * stream)
-{
-    c = fgetc(stream);
-    if (c == EOF)
-        return EOF;
-    return 0;
-}
+//template <typename T2>
+//struct Product<void, T2>
+//{
+//    typedef void    Type;
+//};
 
 // ----------------------------------------------------------------------------
-// Function streamEof()
+// Metafunction Product<void, void>
 // ----------------------------------------------------------------------------
 
-inline bool
-streamEof(FILE * stream)
-{
-    return ::std::feof(stream) != 0;
-}
+//template <>
+//struct Product<void, void>
+//{
+//    typedef void    Type;
+//};
 
 // ----------------------------------------------------------------------------
-// Function streamError
+// Metafunction Product<TTag1, TTagList2>
 // ----------------------------------------------------------------------------
+// T1 x L2[0..0] = T1 x L2[0]
 
-inline int
-streamError(FILE * stream)
+template <typename TTag1, typename TTag2>
+struct Product<TTag1, TagList<TTag2, void> >
 {
-    return ::std::ferror(stream);
-}
+    typedef TagList<typename Product<TTag1, TTag2>::Type, void> Type;
+};
 
 // ----------------------------------------------------------------------------
-// Function streamReadBlock()
+// Metafunction Product<TTagList1, TTag2>
 // ----------------------------------------------------------------------------
+// L1[0..0] x T2 = L1[0] x T2
 
-inline size_t
-streamReadBlock(char * target, FILE * stream, size_t maxLen)
-{
-    return ::std::fread(target, sizeof(char), maxLen, stream);
-}
+//template <typename TTag1, typename TTag2>
+//struct Product<TagList<TTag1, void>, TTag2>
+//{
+//    typedef TagList<typename Product<TTag1, TTag2>::Type>   Type;
+//};
 
 // ----------------------------------------------------------------------------
-// Function streamWriteChar
+// Metafunction Product<TTagList1, TTagList2>
 // ----------------------------------------------------------------------------
+// L1[0..0] x L2[0..0] = L1[0] x L2[0]
 
-inline int
-streamWriteChar(FILE * stream, char const c)
-{
-    int x = ::std::fputc(c, stream);
-    if (x == EOF)
-        return EOF;
-    return c != x;
-}
+//template <typename TTag1, typename TTag2>
+//struct Product<TagList<TTag1, void>, TagList<TTag2, void> >
+//{
+//    typedef TagList<typename Product<TTag1, TTag2>::Type>   Type;
+//};
 
 // ----------------------------------------------------------------------------
-// Function streamWriteBlock()
+// Metafunction Product<TTag1, TTagList2>
 // ----------------------------------------------------------------------------
+// T1 x L2[0..m] = T1 x L2[0] + T1 x L2[1..m]
 
-inline size_t
-streamWriteBlock(FILE * stream, char const * source, size_t count)
+template <typename TTag1, typename TTag2, typename TSubList2>
+struct Product<TTag1, TagList<TTag2, TSubList2> >
 {
-    return ::std::fwrite(source, sizeof(char), count, stream);
-}
+    typedef TagList<typename Product<TTag1, TTag2>::Type,
+                    typename Product<TTag1, TSubList2>::Type>   Type;
+};
 
 // ----------------------------------------------------------------------------
-// Function streamPut()
+// Metafunction Product<TTagList1, TTag2>
 // ----------------------------------------------------------------------------
+// L1[0..n] x T2 = L1[0] x T2 + L1[1..n] x T2
 
-// --- strings
-
-inline int
-streamPut(FILE * stream, char const * source)
-{
-    return (streamWriteBlock(stream, source, strlen(source))
-                == strlen(source) )  ?   0 : 1;
-}
-
-template <typename TSpec>
-inline int
-streamPut(FILE * stream, String<char, TSpec> const & source)
-{
-    return (streamWriteBlock(stream, toCString(source), length(source))
-                == length(source))  ?   0 : 1;
-}
-
-template <typename TSpec, typename TSpec2>
-inline int
-streamPut(FILE * stream,
-          String<SimpleType<unsigned char, TSpec>, TSpec2> const & source)
-{
-    String<char, CStyle> buf = source;
-    return (streamWriteBlock(stream, toCString(buf), length(buf))
-                == length(buf))  ?   0 : 1;
-}
-
-// --- characters
-
-inline int
-streamPut(FILE * stream, char const c)
-{
-    return streamWriteChar(stream, c);
-}
-
-template <typename TValue, typename TSpec>
-inline int
-streamPut(FILE * stream, SimpleType<TValue, TSpec> const & c)
-{
-    return streamPut(stream, convert<char>(c));
-}
-
-// --- numbers
-
-inline char const *
-_streamPutChar(char const * /*tag*/)
-{
-    return "%s";
-}
-
-inline char const *
-_streamPutChar(int const /*tag*/)
-{
-    return "%d";
-}
-
-inline char const *
-_streamPutChar(unsigned int const /*tag*/)
-{
-    return "%u";
-}
-
-inline char const *
-_streamPutChar(long const /*tag*/)
-{
-    return "%ld";
-}
-
-inline char const *
-_streamPutChar(unsigned long const /*tag*/)
-{
-    return "%lu";
-}
-
-inline char const *
-_streamPutChar(float const /*tag*/)
-{
-    return "%.2f"; 
-}
-
-inline char const *
-_streamPutChar(double const /*tag*/)
-{
-    return "%.2lf";
-}
-
-// template <typename TValue, typename TSpec>
-// inline char const *
-// _streamPutChar(SimpleType<TValue, TSpec> const & /*tag*/)
-// {
-//     return _streamPutChar(TValue());
-// }
-
-
-// TODO(h4nn3s) according to man fprintf's point character is locale dependent,
-// maybe overload for doubles and floats to avoid that?
-template <typename TSource>
-inline int
-streamPut(FILE * stream, TSource const & source)
-{
-    std::stringstream tmp;
-    tmp << source;
-    return streamWriteBlock(stream, tmp.str().c_str(), tmp.str().size()) != tmp.str().size();
-}
-
+//template <typename TTag1, typename TSubList1, typename TTag2>
+//struct Product<TagList<TTag1, TSubList1>, TTag2>
+//{
+//    typedef TagList<typename Product<TTag1, TTag2>::Type,
+//                    typename Product<TSubList1, TTag2>::Type>   Type;
+//};
 
 // ----------------------------------------------------------------------------
-// Function streamFlush()
+// Metafunction Product<TTagList1, TTagList2>
 // ----------------------------------------------------------------------------
+// L1[0..0] x L2[0..m] = L1[0] x L2[0] + L1[0] x L2[1..m]
 
-inline int
-streamFlush(FILE * stream)
+template <typename TTag1, typename TTag2, typename TSubList2>
+struct Product<TagList<TTag1, void>, TagList<TTag2, TSubList2> >
 {
-    return ::std::fflush(stream);
-}
+    typedef TagList<typename Product<TTag1, TTag2>::Type,
+                    typename Product<TTag1, TSubList2>::Type> Type;
+};
 
 // ----------------------------------------------------------------------------
-// Function streamSeek()
+// Metafunction Product<TTagList1, TTagList2>
 // ----------------------------------------------------------------------------
+// L1[0..n] x L2[0..0] = L1[0] x L2[0] + L1[1..n] x L2[0]
 
-inline int
-streamSeek(FILE * stream, long int delta, int origin)
-{
-    return ::std::fseek(stream, delta, origin);
-}
+//template <typename TTag1, typename TSubList1, typename TTag2>
+//struct Product<TagList<TTag1, TSubList1>, TagList<TTag2, void> >
+//{
+//    typedef TagList<typename Product<TTag1, TTag2>::Type,
+//                    typename Product<TSubList1, TTag2>::Type> Type;
+//};
 
 // ----------------------------------------------------------------------------
-// Function streamTell()
+// Metafunction Product<TTagList1, TTagList2>
 // ----------------------------------------------------------------------------
+// L1[0..n] x L2[0..m] = L1[0] x L2[0..m] + L1[1..n] x L2[0..m]
 
-inline Position<FILE *>::Type
-streamTell(FILE * stream)
+template <typename TTag1, typename TSubList1, typename TTag2, typename TSubList2>
+struct Product<TagList<TTag1, TSubList1>, TagList<TTag2, TSubList2> >
 {
-    return ::std::ftell(stream);
-}
+    typedef typename Sum<typename Product<TTag1, TagList<TTag2, TSubList2> >::Type,
+                         typename Product<TSubList1, TagList<TTag2, TSubList2> >::Type>::Type Type;
+};
 
-}  // namespace seqean
+}  // namespace seqan
 
-#endif  // #ifndef SEQAN_STREAM_ADAPT_CSTIO_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_TYPE_ALGEBRA_H_
diff --git a/seqan/basic/pair_base.h b/seqan/basic/pair_base.h
index 2893efb..4d66cbe 100644
--- a/seqan/basic/pair_base.h
+++ b/seqan/basic/pair_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 
 // TODO(holtgrew): What about move construction? Useful for pairs of strings and such. Tricky to implement since ints have no move constructor, for example.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_PAIR_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_PAIR_BASE_H_
 
 namespace seqan {
 
@@ -45,13 +45,19 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
+template <typename TObject, typename TDirection>
+struct DirectionIterator;
+
+struct Output_;
+typedef Tag<Output_> Output;
+
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
 
 /*!
  * @class Pair
- * @extends ComparableConcept
+ * @implements ComparableConcept
  * @headerfile <seqan/basic.h>
  * @brief Store two arbitrary objects.
  *
@@ -71,9 +77,9 @@ namespace seqan {
  * @signature Pair::Pair(other);
  * @signature Pair::Pair(x1, x2);
  *
- * @param other The other Pair object to copy from.
- * @param x1    Copied to first member.
- * @param x2    Copied to second member
+ * @param[in] other The other Pair object to copy from.
+ * @param[in] x1    Copied to first member.
+ * @param[in] x2    Copied to second member
  */
 
 /*!
@@ -86,35 +92,6 @@ namespace seqan {
  * @brief Second member
  */
 
-/**
-.Class.Pair:
-..cat:Aggregates
-..concept:Concept.AggregateConcept
-..summary:Stores two arbitrary objects.
-..signature:Pair<T1[, T2[, TSpec]]>
-..param.T1:The type of the first object.
-..param.T2:The type of the second object.
-...default:$T1$
-..param.TSpec:The specializing type.
-...default:$void$, no packing (faster access).
-.Memfunc.Pair#Pair:
-..class:Class.Pair
-..summary:Constructor
-..signature:Pair<T1, T2[, TSpec]> ()    
-..signature:Pair<T1, T2[, TSpec]> (pair)
-..signature:Pair<T1, T2[, TSpec]> (i1, i2)
-..param.pair:Other Pair object. (copy constructor)
-..param.i1:T1 object.
-..param.i2:T2 object.
-.Memvar.Pair#i1:
-..class:Class.Pair
-..summary:T1 object
-.Memvar.Pair#i2:
-..class:Class.Pair
-..summary:T2 object
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Should default specs be specialized with void or Default?
 // TODO(holtgrew): Move construction, will be a bit tricky, either with enable_if or with 4 base classes and all constructors are forwarded there.
 
@@ -169,9 +146,6 @@ struct Pair
  * @return VALUE The number of element in a Pair (2).
  */
 
-///.Metafunction.LENGTH.param.T.type:Class.Pair
-///.Metafunction.LENGTH.class:Class.Pair
-
 template <typename T1, typename T2, typename TSpec>
 struct LENGTH<Pair<T1, T2, TSpec> >
 {
@@ -196,20 +170,6 @@ struct LENGTH<Pair<T1, T2, TSpec> >
  * @return Type Result type.
  */
 
-/**
-.Metafunction.Value
-..class:Class.Pair
-..class:Class.Triple
-..class:Class.Tuple
-..signature:Value<TTuple, POSITION>::Type
-..param.TTuple:@Class.Pair@, @Class.Triple@, or @Class.Tuple@ to return value from.
-...type:Class.Pair
-...type:Class.Triple
-...type:Class.Tuple
-..param.POSITION:Position of the type to query.
-...type:nolink:$int$
- */
-
 template <typename T1, typename T2, typename TSpec>
 struct Value<Pair<T1, T2, TSpec>, 1>
 {
@@ -237,9 +197,6 @@ struct Value<Pair<T1, T2, TSpec>, 2>
  * @return Type The resulting type.
  */
 
-///.Metafunction.Spec.param.T.type:Class.Pair
-///.Metafunction.Spec.class:Class.Pair
-
 template <typename T1, typename T2, typename TSpec>
 struct Spec<Pair<T1, T2, TSpec> >
 {
@@ -278,13 +235,25 @@ move(Pair<T1, T2, TSpec> & p1, Pair<T1, T2, TSpec> & p2)
 // Function operator<<();  Stream Output.
 // ----------------------------------------------------------------------------
 
-template <typename T1, typename T2, typename TSpec>
-inline
-std::ostream & operator<<(std::ostream & out, Pair<T1, T2, TSpec> const & p)
+template <typename TTarget, typename T1, typename T2, typename TSpec>
+inline void
+write(TTarget &target, Pair<T1, T2, TSpec> const & p)
 {
-    // TODO(holtgrew): Incorporate this into new stream concept? Adapt from stream module?
-    out << "< " << getValueI1(p) << " , " << getValueI2(p) << " >";
-    return out;
+    write(target, "< ");
+    write(target, getValueI1(p));
+    write(target, " , ");
+    write(target, getValueI2(p));
+    write(target, " >");
+}
+
+template <typename TStream, typename T1, typename T2, typename TSpec>
+inline TStream &
+operator<<(TStream & target,
+           Pair<T1, T2, TSpec> const & source)
+{
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
+    return target;
 }
 
 // -----------------------------------------------------------------------
@@ -295,9 +264,9 @@ std::ostream & operator<<(std::ostream & out, Pair<T1, T2, TSpec> const & p)
  * @fn Pair#getValueI1
  * @brief The get-value of the Pair's first entry.
  *
- * @signature T1 getValue(pair);
+ * @signature T1 getValueI1(pair);
  *
- * @param pair The pair to get entry from.
+ * @param[in] pair The pair to get entry from.
  *
  * @return T1 The first entry of the Pair.
  */
@@ -315,9 +284,9 @@ T1 getValueI1(Pair<T1, T2, TSpec> const & pair)
  * @fn Pair#getValueI2
  * @brief The get-value of the Pair's second entry.
  *
- * @signature T2 getValue(pair);
+ * @signature T2 getValueI2(pair);
  *
- * @param pair The pair to get entry from.
+ * @param[in] pair The pair to get entry from.
  *
  * @return T2 The second entry of the Pair.
  */
@@ -339,8 +308,8 @@ T2 getValueI2(Pair<T1, T2, TSpec> const & pair)
  *
  * @signature void assignValueI1(pair, val);
  *
- * @param pair The pair to get entry from.
- * @param val  Set the value of the Pair's first entry.
+ * @param[in] pair The pair to get entry from.
+ * @param[in] val  Set the value of the Pair's first entry.
  */
 
 // Cannot be assignValue with index since T1 can be != T2.
@@ -355,10 +324,10 @@ inline void assignValueI1(Pair<T1, T2, TSpec> & pair, T const & _i)
  * @fn Pair#assignValueI2
  * @brief Set second entry of a pair.
  *
- * @signature void assignValueI1(pair, val);
+ * @signature void assignValueI2(pair, val);
  *
- * @param pair The pair to get entry from.
- * @param val  Set the value of the Pair's second entry.
+ * @param[in] pair The pair to get entry from.
+ * @param[in] val  Set the value of the Pair's second entry.
  */
 
 template <typename T1, typename T2, typename TSpec, typename T>
@@ -377,8 +346,8 @@ inline void assignValueI2(Pair<T1, T2, TSpec> & pair, T const & _i)
  *
  * @signature void setValueI1(pair, val);
  *
- * @param pair The pair to get entry from.
- * @param val  Set the value of the Pair's first entry.
+ * @param[in] pair The pair to get entry from.
+ * @param[in] val  Set the value of the Pair's first entry.
  */
 
 // Cannot be setValue with index since T1 can be != T2.
@@ -393,10 +362,10 @@ inline void setValueI1(Pair<T1, T2, TSpec> & pair, T const & _i)
  * @fn Pair#setValueI2
  * @brief Set second entry of a pair.
  *
- * @signature void setValueI1(pair, val);
+ * @signature void setValueI2(pair, val);
  *
- * @param pair The pair to get entry from.
- * @param val  Set the value of the Pair's second entry.
+ * @param[in] pair The pair to get entry from.
+ * @param[in] val  Set the value of the Pair's second entry.
  */
 
 template <typename T1, typename T2, typename TSpec, typename T>
@@ -510,4 +479,4 @@ swap(Pair<L1, L2, LPack> const & a,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_BASE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_PAIR_BASE_H_
diff --git a/seqan/basic/pair_bit_compressed.h b/seqan/basic/pair_bit_compressed.h
index 6b70841..d93f853 100644
--- a/seqan/basic/pair_bit_compressed.h
+++ b/seqan/basic/pair_bit_compressed.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Bit-packed pair specialization.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_BIT_PACKED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_BIT_PACKED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_PAIR_BIT_PACKED_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_PAIR_BIT_PACKED_H_
 
 namespace seqan {
 
@@ -71,25 +71,6 @@ namespace seqan {
  * <tt>getValue()</tt>, <tt>assignValue()</tt>, <tt>moveValue()</tt>, <tt>setValue()</tt> instead.
  */
 
-/**
-.Spec.Bit Packed Pair:
-..cat:Aggregates
-..general:Class.Pair
-..summary:Stores two arbitrary objects. Saves memory by packing bits with bit fields.
-..signature:Pair<T1, T2, BitPacked<BITSIZE1, BITSIZE2> >
-..param.T1:The type of the first object.
-..param.T2:The type of the second object.
-..param.BITSIZE1:Number of bits to store $T1$.
-..param.BITSIZE2:Number of bits to store $T2$.
-..notes:Useful for external storage.
-..remarks:Memory access could be slower. Direct access to members by pointers is not allowed.
-..remarks:Functions $value()$ is not implemented yet since there it would require using a proxy. Use $getValue()$, $assignValue()$, $moveValue()$, $setValue()$ instead.
-..include:seqan/basic.h
-.Memfunc.Pair#Pair.class:Spec.Bit Packed Pair
-.Memvar.Pair#i1.class:Spec.Bit Packed Pair
-.Memvar.Pair#i2.class:Spec.Bit Packed Pair
-*/
-
 #ifdef PLATFORM_WINDOWS
     #pragma pack(push,1)
 #endif
@@ -198,4 +179,4 @@ inline void moveValueI2(Pair<T1, T2, BitPacked<BITSIZE1, BITSIZE2> > & pair, T &
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_BIT_PACKED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_PAIR_BIT_PACKED_H_
diff --git a/seqan/basic/pair_packed.h b/seqan/basic/pair_packed.h
index 4f9ff6e..b16e362 100644
--- a/seqan/basic/pair_packed.h
+++ b/seqan/basic/pair_packed.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Packed pair specialization.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_PACKED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_PACKED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_PAIR_PACKED_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_PAIR_PACKED_H_
 
 namespace seqan {
 
@@ -71,23 +71,6 @@ namespace seqan {
  * <tt>getValue()</tt>, <tt>assignValue()</tt>, <tt>moveValue()</tt>, <tt>setValue()</tt> instead.
  */
 
-/**
-.Spec.Packed Pair:
-..cat:Aggregates
-..general:Class.Pair
-..summary:Stores two arbitrary objects. Saves memory by disabling memory alignment.
-..signature:Pair<T1, T2, Pack>
-..param.T1:The type of the first object.
-..param.T2:The type of the second object.
-..notes:Useful for external storage.
-..remarks:Memory access could be slower. Direct access to members by pointers is not allowed on all platforms.
-..remarks:Functions $value()$ is not implemented yet since there it would require using a proxy. Use $getValue()$, $assignValue()$, $moveValue()$, $setValue()$ instead.
-..include:seqan/basic.h
-.Memfunc.Pair#Pair.class:Spec.Packed Pair
-.Memvar.Pair#i1.class:Spec.Packed Pair
-.Memvar.Pair#i2.class:Spec.Packed Pair
-*/
-
 #ifdef PLATFORM_WINDOWS
     #pragma pack(push,1)
 #endif
@@ -202,4 +185,4 @@ inline void moveValueI2(Pair<T1, T2, Pack> & pair, T & _i)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PAIR_PACKED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_PAIR_PACKED_H_
diff --git a/seqan/basic/profiling.h b/seqan/basic/profiling.h
index 1c05f39..f7d4542 100644
--- a/seqan/basic/profiling.h
+++ b/seqan/basic/profiling.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,8 +40,8 @@
 
 //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROFILING_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROFILING_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_PROFILING_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_PROFILING_H_
 
 namespace seqan
 {
@@ -125,14 +125,14 @@ namespace seqan
     };
 
     const char ProfileValueType_[] = {
-        SEQAN_PROTIME, 
-        SEQAN_PROTIME, 
-        SEQAN_PROINT + SEQAN_PROSTATE, 
+        SEQAN_PROTIME,
+        SEQAN_PROTIME,
+        SEQAN_PROINT + SEQAN_PROSTATE,
         SEQAN_PROINT,
         SEQAN_PROINT,
-        SEQAN_PROINT + SEQAN_PROSTATE, 
-        SEQAN_PROINT + SEQAN_PROSTATE, 
-        SEQAN_PROINT + SEQAN_PROSTATE, 
+        SEQAN_PROINT + SEQAN_PROSTATE,
+        SEQAN_PROINT + SEQAN_PROSTATE,
+        SEQAN_PROINT + SEQAN_PROSTATE,
         SEQAN_PROFLOAT,
         SEQAN_PROFLOAT,
         SEQAN_PROFLOAT + SEQAN_PROSTATE,
@@ -155,7 +155,7 @@ namespace seqan
         static ProfileTStates_  _proValue;
         static ProfileTTimes    _proLastUpdate;
         static int          _proExtraCount;
-        
+
         static clock_t      _proCpuTimeLast;            // clock_t wraps around every 72mins
         static ProfileInt_      _proCpuTimeOffset;          // we have to work around this
 
@@ -181,36 +181,18 @@ namespace seqan
  * @fn cpuTime
  * @headerfile <seqan/basic.h>
  * @brief Returns the cpu time in seconds.
- * 
+ *
  * @signature double cpuTime();
- * 
+ *
  * @return double CPU time stamp in seconds.
- * 
- * @section Remarks
- * 
+ *
  * Calls <tt>clock</tt> to retrieve the processor time used by the running thread. This implies that the thread's
  * processor time does not tick if the thread is suspended. While this has its advantages, benchmarks should generally
  * focus on wall clock time, not processor time. Wall clock time is returned by sysTime.
- * 
+ *
  * @see sysTime
  */
 
-/**
-.Function.cpuTime
-..cat:Miscellaneous
-..summary:Returns the cpu time in seconds.
-..signature:cpuTime()
-..returns:A $double$, cpu time stamp in seconds.
-...type:nolink:double
-..remarks:
-Calls $clock$ to retrieve the processor time used by the running thread.
-This implies that the thread's processor time does not tick if the thread is suspended.
-While this has its advantages, benchmarks should generally focus on wall clock time, not processor time.
-Wall clock time is returned by @Function.sysTime@.
-..see:Function.sysTime
-..include:seqan/basic.h
-*/
-
 
 // HINT: The unit of all time functions is second.
     inline _proFloat cpuTime() {
@@ -228,30 +210,28 @@ Wall clock time is returned by @Function.sysTime@.
  * @fn sysTime
  * @headerfile <seqan/basic.h>
  * @brief Returns the system time in seconds.
- * 
+ *
  * @signature double sysTime();
- * 
+ *
  * @return double A <tt>double</tt>, system time stamp in seconds. Types: nolink:double
- * 
- * @section Remarks
- * 
- * In contrast to cpuTime, the system time corresponds to the wall clock time under Linux and Mac OS X.  Under Windows
- * sysTime returns the result of cpuTime.
- * 
+ *
+ * In contrast to @link cpuTime @endlink, the system time corresponds to the wall clock time under Linux and Mac OS X.
+ * Under Windows sysTime returns the result of cpuTime.
+ *
  * Use this for benchmarking uner Linux and Mac Os X.
- * 
+ *
  * Calls <tt>clock_gettime</tt> under Linux and <tt>gettimeofday</tt> under Mac OS X.
- * 
+ *
  * @section Examples
- * 
+ *
  * We can use sysTime to instrument our code for profiling/timing information quite robustly. The following demonstrates
  * how the Function.sysTime is used in many SeqAn apps for collecting timing information.
- * 
+ *
  * @code{.cpp}
  * bool printTiming = true;
- *  
+ *
  * // ...
- *  
+ *
  * double startTime = sysTime();
  * // Do some complex calculation.
  * if (printTiming)
@@ -261,33 +241,6 @@ Wall clock time is returned by @Function.sysTime@.
  * @see cpuTime
  */
 
-/**
-.Function.sysTime
-..cat:Miscellaneous
-..summary:Returns the system time in seconds.
-..signature:sysTime()
-..returns:A $double$, system time stamp in seconds.
-...type:nolink:double
-..remarks:In contrast to @Function.cpuTime@, the system time corresponds to the wall clock time under Linux and Mac OS X.
-Under Windows @Function.sysTime@ returns the result of @Function.cpuTime@.
-..remarks:Use this for benchmarking uner Linux and Mac Os X.
-..remarks:Calls $clock_gettime$ under Linux and $gettimeofday$ under Mac OS X.
-..see:Function.cpuTime
-..example.text:
-We can use @Function.sysTime@ to instrument our code for profiling/timing information quite robustly.
-The following demonstrates how the Function.sysTime is used in many SeqAn apps for collecting timing information.
-..example.code:
-bool printTiming = true;
-
-// ...
-
-double startTime = sysTime();
-// Do some complex calculation.
-if (printTiming)
-    std::cerr << "Some complex calculation too " << sysTime() - startTime << " s." << std::endl;
-..include:seqan/basic.h
-*/
-
     #ifdef PLATFORM_WINDOWS
 //        inline _proFloat sysTime() { return GetTickCount() * 1e-3; }
         inline _proFloat sysTime() { return ( (_proFloat) clock() ) / CLOCKS_PER_SEC; }
@@ -299,12 +252,12 @@ if (printTiming)
             #define SEQAN_USE_CLOCKGETTIME
             #endif
         #endif
-        
+
         #ifndef SEQAN_USE_CLOCKGETTIME
         /* some systems e.g. darwin have no clock_gettime */
-        
+
             #include <sys/time.h>
-            
+
             inline _proFloat sysTime() {
                 struct timeval tp;
                 gettimeofday(&tp, NULL);
@@ -323,7 +276,7 @@ if (printTiming)
 
     #endif
 
-    
+
     struct ProfileFile_ {
 //IOREV not generic, uses FILE* instead of File() and custom IO
 
@@ -331,10 +284,10 @@ if (printTiming)
         bool   running;
 
         _proFloat dumpStep;            // 0 .. manual dump mode, >0 .. live stream
-        _proFloat dumpNext;        
+        _proFloat dumpNext;
 
         ProfileTStates_ all, last;
-        ::std::string mark;
+        std::string mark;
         unsigned    lines;
 
         ProfileFile_() {
@@ -382,15 +335,15 @@ if (printTiming)
         }
 
         inline void syncTime(ProfileTStates_ &dst) {
-            ::std::memcpy(dst, ProfileData_<>::_proValue, 2 * sizeof(ProfileTimeValue_));
+            std::memcpy(dst, ProfileData_<>::_proValue, 2 * sizeof(ProfileTimeValue_));
         }
 
         inline void sync(ProfileTStates_ &dst) {
-            ::std::memcpy(&(dst[2]), &(ProfileData_<>::_proValue[2]), sizeof(ProfileTStates_) - 2 * sizeof(ProfileTimeValue_));
+            std::memcpy(&(dst[2]), &(ProfileData_<>::_proValue[2]), sizeof(ProfileTStates_) - 2 * sizeof(ProfileTimeValue_));
         }
 
         inline void syncAll(ProfileTStates_ &dst) {
-            ::std::memcpy(dst, ProfileData_<>::_proValue, sizeof(ProfileTStates_));
+            std::memcpy(dst, ProfileData_<>::_proValue, sizeof(ProfileTStates_));
         }
 
         inline static void setTime(ProfileTStates_ &dst) {
@@ -468,7 +421,7 @@ if (printTiming)
                 dumpValue(stat, SEQAN_PROINDEXCOUNT - SEQAN_PROEXTRACOUNT + i);
             }
     }
-    
+
         inline void dumpMark() {
             if (!mark.empty()) {
                 dumpTab();
@@ -515,7 +468,7 @@ if (printTiming)
                 }
             }
         }
-        
+
         inline void reset() {
             syncTime(last);
         }
@@ -528,7 +481,7 @@ if (printTiming)
         }
 
     private:
-        
+
         bool bol;   // begin of line
     };
 
@@ -544,7 +497,7 @@ if (printTiming)
     inline void _profileSet(int valNum, _proFloat value);
     inline void _profileAdd(int valNum, _proFloat value);
     inline void _profileSub(int valNum, _proFloat value);
-    
+
     // simple interface for external programs
     inline void *_profileMalloc(size_t size);
     inline void _profileFree(void *_ptr);
@@ -616,7 +569,7 @@ if (printTiming)
         ProfileData_<>::_proLastUpdate[valNum] = now;
         _profileSignalDumpTest(now);
     }
-    
+
     // simple interface for external programs
     inline void *_profileMalloc(size_t size) {
 //IOREV _notio_
@@ -648,4 +601,4 @@ if (printTiming)
     }
 }
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROFILING_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_PROFILING_H_
diff --git a/seqan/basic/property_map_concept.h b/seqan/basic/property_map_concept.h
new file mode 100644
index 0000000..21aec55
--- /dev/null
+++ b/seqan/basic/property_map_concept.h
@@ -0,0 +1,169 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_BASIC_PROPERTY_MAP_CONCEPT_H_
+#define INCLUDE_SEQAN_BASIC_PROPERTY_MAP_CONCEPT_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Concept PropertyMapConcept
+// ----------------------------------------------------------------------------
+
+/*!
+ * @concept PropertyMapConcept
+ * @headerfile <seqan/graph_types.h>
+ * @brief Concept for maps from contained elements (such as graph vertices or index nodes) to values.
+ *
+ * @signature concept PropertyMapConcept;
+ */
+
+/*!
+ * @mfn PropertyMapConcept#Value
+ * @brief Returns the value type of the property map.
+ *
+ * @signature Value<TPropertyMap>::Type
+ *
+ * @tparam TPropertyMap The property map to query.
+ *
+ * @return Type The element type of the container.
+ *
+ * @see PropertyMapConcept#Value
+ */
+
+/*!
+ * @mfn PropertyMapConcept#GetValue
+ * @brief Returns the get-value type of the property map.
+ *
+ * @signature GetValue<TPropertyMap>::Type
+ *
+ * @tparam TPropertyMap The property map to query.
+ *
+ * @return Type The get-value type of the container.
+ *
+ * @see PropertyMapConcept#GetValue
+ */
+
+/*!
+ * @mfn PropertyMapConcept#Reference
+ * @brief Returns the reference type of the property map.
+ *
+ * @signature Reference<TPropertyMap>::Type
+ *
+ * @tparam TPropertyMap The property map to query.
+ *
+ * @see PropertyMapConcept#Reference
+ */
+
+/*!
+ * @fn PropertyMapConcept#assignProperty
+ * @brief Assigns a property to an item in the property map.
+ *
+ * @signature void assignProperty(pm, d, val);
+ *
+ * @param[in,out] pm  The property map
+ * @param[in]     d   A vertex or edge descriptor that identifies the item in the property map.
+ * @param[in]     val The new value, where the type of the new value must match the value type of the property map.
+ */
+
+/*!
+ * @fn PropertyMapConcept#property
+ * @brief Accesses the property of an item in the property map.
+ *
+ * @signature TReference property(pm, d);
+ *
+ * @param[in,out] pm  The property map.
+ * @param[in]     d   A vertex or edge descriptor that identifies the item in the property map.
+ *
+ * @return TReference Reference to the item in the property map of type @link Reference @endlink.
+ */
+
+/*!
+ * @fn PropertyMapConcept#getProperty
+ * @brief Get method for an item's property.
+ *
+ * @signature TGetValue getProperty(pm, d);
+ *
+ * @param[in,out] pm  The property map.
+ * @param[in]     d   A vertex or edge descriptor that identifies the item in the property map.
+ *
+ * @return TGetValue Get-value to the item in the property map of type @link PropertyMapConcept#GetValue
+ *                   GetValue @endlink.
+ */
+
+/*!
+ * @fn PropertyMapConcept#resize
+ * @brief Resize a sequence.
+ *
+ * @signature void resize(pm, len[, val]);
+ *
+ * @param[in,out] seq Sequence to resize.
+ * @param[in]     len Length to resize <tt>seq</tt> to.
+ * @param[in]     val When increasing the size, <tt>val</tt> is used to fill new entries.  When omitted,
+ *                    <tt>TValue()</tt> is used where <tt>TValue</tt> is the @link ContainerConcept#Value @endlink
+ *                    type of the sequence.
+ *
+ * @see StringConcept#resize
+ */
+
+SEQAN_CONCEPT(PropertyMapConcept, (TPropertyMap))
+{
+public:
+    typedef typename Value<TPropertyMap>::Type                TValue;
+    typedef typename GetValue<TPropertyMap>::Type             TGetValue;
+    typedef typename Reference<TPropertyMap>::Type            TReference;
+
+    SEQAN_CONCEPT_USAGE(PropertyMapConcept)
+    {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_BASIC_PROPERTY_MAP_CONCEPT_H_
diff --git a/seqan/basic/proxy_base.h b/seqan/basic/proxy_base.h
index 05c6574..529c028 100644
--- a/seqan/basic/proxy_base.h
+++ b/seqan/basic/proxy_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Proxy base class definition.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROXY_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROXY_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_PROXY_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_PROXY_BASE_H_
 
 namespace seqan {
 
@@ -57,31 +57,13 @@ namespace seqan {
  *
  * @tparam TSpec The specializing types.
  *
- * @section Remarks
- *
  * Use Value to get the emulated type. An instance of <tt>Proxy</tt> behaves like an object of its value
- * type. <tt>Proxy</tt> can be used as reference type (see Reference).
- * 
+ * type.  <tt>Proxy</tt> can be used as reference type (see Reference).
+ *
  * Note that functions that are both general and specialized for the value type should be specialized for
  * <tt>Proxy&lt;TSpec&gt;</tt> too, since otherwise the general version will be called.
  */
 
-/**
-.Class.Proxy:
-..cat:Basic
-..summary:Emulates object of another class.
-..signature:Proxy<TSpec>
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-..remarks.text:Use @Metafunction.Value@ to get the emulated type.
-An instance of $Proxy$ behaves like an object of its value type.
-$Proxy$ can be used as reference type (see @Metafunction.Reference@).
-..remarks.text:Note that functions that are both general and specialized for
-the value type should be specialized for $Proxy<TSpec>$ too,
-since otherwise the general version will be called.
-..include:seqan/basic.h
-*/
-
 template <typename TSpec>
 class Proxy;
 
@@ -89,6 +71,21 @@ class Proxy;
 // Metafunctions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn Proxy#Value
+ * @brief Return emulated type.
+ *
+ * @signature Value<TProxy>::Type;
+ *
+ * @tparam TProxy The proxy type to query.
+ *
+ * @return Type The emulated type.
+ */
+
 // ----------------------------------------------------------------------------
 // Metafunction Spec
 // ----------------------------------------------------------------------------
@@ -104,9 +101,6 @@ class Proxy;
  * @return Type The specializing tag.
  */
 
-///.Metafunction.Spec.param.T.type:Class.Proxy
-///.Metafunction.Spec.class:Class.Proxy
-
 template <typename TSpec>
 struct Spec<Proxy<TSpec> >
 {
@@ -502,4 +496,4 @@ operator<<(TStream & strm,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROXY_BASE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_PROXY_BASE_H_
diff --git a/seqan/basic/proxy_iterator.h b/seqan/basic/proxy_iterator.h
index 644d506..ee65aef 100644
--- a/seqan/basic/proxy_iterator.h
+++ b/seqan/basic/proxy_iterator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,8 +37,8 @@
 // using assignValue() on the iterator, reading via getValue().
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROXY_ITERATOR_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROXY_ITERATOR_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_PROXY_ITERATOR_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_PROXY_ITERATOR_H_
 
 namespace seqan {
 
@@ -62,17 +62,6 @@ namespace seqan {
  * @tparam TIterator The iterator to store internally.
  */
 
-/**
-.Spec.Iterator Proxy
-..cat:Proxies
-..general:Class.Proxy
-..summary:Proxy that is implemented by an iterator.
-..signature:Proxy<IteratorProxy<TIterator> >
-..param.TIterator:Iterator type.
-..remarks.text:The value type of an iterator proxy is the value type of the iterator $TIterator$.
-..include:seqan/basic.h
-*/
-
 // TODO(holtgrew): Assignment works through operator=() but we also need set() and move()!
 // TODO(holtgrew): Proxy cannot work correctly for const containers, but should! RemoveConst_ removes the const of the values inside pointers and references.
 
@@ -138,10 +127,15 @@ class Proxy<IteratorProxy<TIterator> >
         return getValue(data_iterator);
     }
 
-    operator unsigned int() const
-    {
-        return static_cast<unsigned int>(getValue(data_iterator));
-    }
+//    operator TAccessor_() const
+//    {
+//        return getValue(data_iterator);
+//    }
+
+//    operator unsigned int() const
+//    {
+//        return static_cast<unsigned int>(getValue(data_iterator));
+//    }
 };
 
 // ============================================================================
@@ -152,9 +146,6 @@ class Proxy<IteratorProxy<TIterator> >
 // Metafunction Value
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Value.param.T.type:Class.Proxy
-///.Metafunction.Value.class:Class.Proxy
-
 template <typename TIterator>
 struct Value<Proxy<IteratorProxy<TIterator> > >
         : Value<TIterator>
@@ -171,9 +162,6 @@ struct Value<Proxy<IteratorProxy<TIterator> > const>
 // Metafunction GetValue
 // ----------------------------------------------------------------------------
 
-///.Metafunction.GetValue.param.T.type:Class.Proxy
-///.Metafunction.GetValue.class:Class.Proxy
-
 template <typename TIterator>
 struct GetValue<Proxy<IteratorProxy<TIterator> > >
         : GetValue<TIterator>
@@ -190,9 +178,6 @@ struct GetValue<Proxy<IteratorProxy<TIterator> > const>
 // Metafunction Reference
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Reference.param.T.type:Class.Proxy
-///.Metafunction.Reference.class:Class.Proxy
-
 template <typename TIterator>
 struct Reference<Proxy<IteratorProxy<TIterator> > >
 {
@@ -209,9 +194,6 @@ struct Reference<Proxy<IteratorProxy<TIterator> > const>
 // Metafunction Size
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Size.param.T.type:Class.Proxy
-///.Metafunction.Size.class:Class.Proxy
-
 template <typename TIterator>
 struct Size<Proxy<IteratorProxy<TIterator> > >
         : Size<TIterator>
@@ -228,9 +210,6 @@ struct Size<Proxy<IteratorProxy<TIterator> > const>
 // Metafunction Difference
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Difference.param.T.type:Class.Proxy
-///.Metafunction.Difference.class:Class.Proxy
-
 template <typename TIterator>
 struct Difference<Proxy<IteratorProxy<TIterator> > >
         : Difference<TIterator>
@@ -243,6 +222,22 @@ struct Difference<Proxy<IteratorProxy<TIterator> > const>
 {
 };
 
+// ----------------------------------------------------------------------------
+// Metafunction CompareType
+// ----------------------------------------------------------------------------
+
+template <typename TIterator, typename T>
+struct CompareTypeRemoveProxy<Proxy<IteratorProxy<TIterator> >, T>:
+    CompareTypeRemoveProxy<typename Value<TIterator>::Type, T> {};
+
+template <typename TIterator, typename T>
+struct CompareTypeRemoveProxy<T, Proxy<IteratorProxy<TIterator> > >:
+    CompareTypeRemoveProxy<T, typename Value<TIterator>::Type> {};
+
+template <typename TIterator1, typename TIterator2>
+struct CompareTypeRemoveProxy<Proxy<IteratorProxy<TIterator1> >, Proxy<IteratorProxy<TIterator2> > >:
+    CompareTypeRemoveProxy<typename Value<TIterator1>::Type, typename Value<TIterator2>::Type> {};
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -251,9 +246,6 @@ struct Difference<Proxy<IteratorProxy<TIterator> > const>
 // Function iter()
 // ----------------------------------------------------------------------------
 
-///.Function.iter.param.object.type:Spec.Iterator Proxy
-///.Function.iter.class:Spec.Iterator Proxy
-
 template <typename TIterator>
 inline TIterator &
 iter(Proxy<IteratorProxy<TIterator> > & me)
@@ -321,5 +313,28 @@ operator<<(TStream & stream, Proxy<IteratorProxy<TIterator> > const & it)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_PROXY_ITERATOR_H_
+
+
+namespace std {
+
+// ------------------------------------------------------------------------
+// Function swap()
+// ------------------------------------------------------------------------
+
+// std::swap doesn't cover the case of const-ref proxies, so we provide it here
+template <typename TIterator>
+inline void
+swap(seqan::Proxy<seqan::IteratorProxy<TIterator> > const & left, seqan::Proxy<seqan::IteratorProxy<TIterator> > const & right)
+{
+    typedef seqan::Proxy<seqan::IteratorProxy<TIterator> >  TProxy;
+    typedef typename seqan::GetValue<TProxy>::Type          TGetValue;
+
+    TGetValue tmp = getValue(iter(left));
+    assignValue(iter(left), getValue(iter(right)));
+    assignValue(iter(right), tmp);
+}
+
+}  // namespace std
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_PROXY_ITERATOR_H_
 
diff --git a/seqan/basic/test_system.h b/seqan/basic/test_system.h
index 7ae1018..811eba5 100644
--- a/seqan/basic/test_system.h
+++ b/seqan/basic/test_system.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,8 +41,8 @@
 // TODO(holtgrew): Add DDDoc documentation.
 // TODO(holtgrew): Port all tests over to new system?
 
-#ifndef CORE_INCLUDE_SEQAN_BASIC_TEST_SYSTEM_H_
-#define CORE_INCLUDE_SEQAN_BASIC_TEST_SYSTEM_H_
+#ifndef INCLUDE_SEQAN_BASIC_TEST_SYSTEM_H_
+#define INCLUDE_SEQAN_BASIC_TEST_SYSTEM_H_
 
 #ifdef PLATFORM_WINDOWS
 #include <typeinfo>
@@ -75,6 +75,8 @@ class Test
     virtual void setUp() {}
     virtual void runTest() = 0;
     virtual void tearDown() {}
+
+    virtual ~Test() {}
 };
 
 // --------------------------------------------------------------------------
@@ -122,7 +124,7 @@ class TestSystem
     static void init(int argc, char const ** argv)
     {
         (void)argc;
-        ::seqan::ClassTest::beginTestSuite("tests", argv[0]);
+        seqan::ClassTest::beginTestSuite("tests", argv[0]);
     }
 
     static TestSystem * getInstance()
@@ -150,18 +152,28 @@ class TestSystem
                 testName += " type parameter ";
                 testName += (*it)->typeName;
             }
-            ::seqan::ClassTest::beginTest(testName.c_str());
+            seqan::ClassTest::beginTest(testName.c_str());
             try {
                 (*it)->instance->setUp();
                 (*it)->instance->runTest();
                 (*it)->instance->tearDown();
-            } catch(::seqan::ClassTest::AssertionFailedException e) {
-                /* Swallow exception, go on with next test. */       
+            } catch(seqan::ClassTest::AssertionFailedException e) {
+                /* Swallow exception, go on with next test. */
                 (void) e;  /* Get rid of unused variable warning. */
+            } catch (seqan::Exception const & e) {
+                std::cerr << "Unexpected exception of type "
+                            << toCString(seqan::Demangler< seqan::Exception>(e))
+                            << "; message: " << e.what() << "\n";
+                seqan::ClassTest::StaticData::thisTestOk() = false;
+                seqan::ClassTest::StaticData::errorCount() += 1;
+            } catch (...) {
+                std::cerr << "Unexpected exception of unknown type\n";
+                seqan::ClassTest::StaticData::thisTestOk() = false;
+                seqan::ClassTest::StaticData::errorCount() += 1;
             }
-            ::seqan::ClassTest::endTest();
+            seqan::ClassTest::endTest();
         }
-        return ::seqan::ClassTest::endTestSuite();
+        return seqan::ClassTest::endTestSuite();
     }
 };
 
@@ -208,6 +220,7 @@ template <template <typename> class TTestCase, typename TType, typename TSubList
 class TypedTestFactory_<TTestCase, TagList<TType, TSubList> >
 {
 public:
+    // TODO(esiragusa): use Demangler.
     template <typename T>
     static std::string getTypeName()
     {
@@ -261,19 +274,19 @@ class TypedTestFactory_<TTestCase, TagList<TType, TSubList> >
 // Macro for defining a test.
 
 #define SEQAN_TEST(testCaseName, testName)                                    \
-    class SEQAN_TEST_NAME_(testCaseName, testName) : public ::seqan::Test     \
+    class SEQAN_TEST_NAME_(testCaseName, testName) : public seqan::Test     \
     {                                                                         \
     public:                                                                   \
         SEQAN_TEST_NAME_(testCaseName, testName)() {}                         \
                                                                               \
         virtual void runTest();                                               \
                                                                               \
-        static ::seqan::TestDescription_ * description;                       \
+        static seqan::TestDescription_ * description;                       \
     };                                                                        \
                                                                               \
-    ::seqan::TestDescription_ *                                               \
+    seqan::TestDescription_ *                                               \
     SEQAN_TEST_NAME_(testCaseName, testName)::description =                   \
-    ::seqan::TestCaseFactory_<SEQAN_TEST_NAME_(testCaseName, testName)>::make(\
+    seqan::TestCaseFactory_<SEQAN_TEST_NAME_(testCaseName, testName)>::make(\
             SEQAN_MKSTRING(testCaseName),                                     \
             SEQAN_MKSTRING(testName));                                        \
                                                                               \
@@ -293,12 +306,12 @@ class TypedTestFactory_<TTestCase, TagList<TType, TSubList> >
                                                                               \
         virtual void runTest();                                               \
                                                                               \
-        static ::seqan::TestDescription_ * description;                       \
+        static seqan::TestDescription_ * description;                       \
     };                                                                        \
                                                                               \
-    ::seqan::TestDescription_ *                                               \
+    seqan::TestDescription_ *                                               \
     SEQAN_TEST_NAME_(testCaseName, testName)::description =                   \
-    ::seqan::TestCaseFactory_<SEQAN_TEST_NAME_(testCaseName, testName)>::make(\
+    seqan::TestCaseFactory_<SEQAN_TEST_NAME_(testCaseName, testName)>::make(\
             SEQAN_MKSTRING(testCaseName),                                     \
             SEQAN_MKSTRING(testName));                                        \
                                                                               \
@@ -341,13 +354,61 @@ class TypedTestFactory_<TTestCase, TagList<TType, TSubList> >
     };                                                                  \
                                                                         \
     bool SEQAN_ ## testCaseName ## __ ## testName ## _registered_ =     \
-            ::seqan::TypedTestFactory_<SEQAN_TEST_NAME_(testCaseName, testName), \
+            seqan::TypedTestFactory_<SEQAN_TEST_NAME_(testCaseName, testName), \
                                SEQAN_TYPED_TEST_CASE_TYPES_NAME_(testCaseName, types) \
                                >::make(SEQAN_MKSTRING(testCaseName), SEQAN_MKSTRING(testName)); \
                                                                         \
     template <typename SEQAN_TParam>                                    \
     void SEQAN_TEST_NAME_(testCaseName, testName)<SEQAN_TParam>::runTest()
 
+// --------------------------------------------------------------------------
+// Macro SEQAN_TEST_EXCEPTION()
+// --------------------------------------------------------------------------
+
+#define SEQAN_TEST_EXCEPTION(_exception_type, command)                              \
+    do                                                                              \
+    {                                                                               \
+        bool caughtException = false;                                               \
+        try                                                                         \
+        {                                                                           \
+            command;                                                                \
+        }                                                                           \
+        catch(_exception_type& ex)                                                  \
+        {                                                                           \
+            caughtException = true;                                                 \
+        }                                                                           \
+        catch(...)                                                                  \
+        {                                                                           \
+            SEQAN_FAIL("Wrong exception thrown: %s", #_exception_type);             \
+        }                                                                           \
+        if (!caughtException)                                                       \
+            SEQAN_FAIL("No exception thrown!");                                     \
+    } while(false)
+
+#define SEQAN_TEST_EXCEPTION_WITH_MESSAGE(_exception_type, command, _message)       \
+    do                                                                              \
+    {                                                                               \
+        bool caughtException = false;                                               \
+        try                                                                         \
+        {                                                                           \
+            command;                                                                \
+        }                                                                           \
+        catch(_exception_type& ex)                                                  \
+        {                                                                           \
+            if(std::string(ex.what()) != _message)                                  \
+                SEQAN_FAIL("Got correct exception but wrong message: '%s' != '%s'", \
+                           ex.what(), _message);                                    \
+            caughtException = true;                                                 \
+        }                                                                           \
+        catch(...)                                                                  \
+        {                                                                           \
+            SEQAN_FAIL("Wrong exception thrown: %s", #_exception_type);             \
+        }                                                                           \
+        if (!caughtException)                                                       \
+            SEQAN_FAIL("No exception thrown!");                                     \
+    } while(false)
+
+
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BASIC_TEST_SYSTEM_H_
+#endif  // #ifndef INCLUDE_SEQAN_BASIC_TEST_SYSTEM_H_
diff --git a/seqan/basic/triple_base.h b/seqan/basic/triple_base.h
index 0536b62..a91fc81 100644
--- a/seqan/basic/triple_base.h
+++ b/seqan/basic/triple_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 
 // TODO(holtgrew): What about move construction? Useful for pairs of strings and such. Tricky to implement since ints have no move constructor, for example.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_TRIPLE_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_TRIPLE_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_TRIPLE_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_TRIPLE_BASE_H_
 
 namespace seqan {
 
@@ -73,10 +73,10 @@ namespace seqan {
  * @signature Triple::Triple(other)
  * @signature Triple::Triple(x1, x2, x3)
  *
- * @param other Other Triple object to copy from.
- * @param x1 First object.
- * @param x2 Second object.
- * @param x3 Third object.
+ * @param[in] other Other Triple object to copy from.
+ * @param[in] x1 First object.
+ * @param[in] x2 Second object.
+ * @param[in] x3 Third object.
  *
  * <tt>x1</tt> must be convertible to T1, <tt>x2</tt> to T2, <tt>x3</tt> to T3.  For example, a Triple of three
  * <tt>int</tt> values can be constructed with three <tt>double</tt> values.
@@ -96,52 +96,13 @@ namespace seqan {
  * signature T2 Triple::i2;
  */
 
-/*
+/*!
  * @var T3 Triple::i3
  * @brief Third value of triple.
  *
  * signature T3 Triple::i3;
  */
 
-/**
-.Class.Triple:
-..cat:Aggregates
-..concept:Concept.AggregateConcept
-..summary:Stores three arbitrary objects.
-..signature:Triple<T1[, T2[, T3[, TSpec]]]>
-..param.T1:The type of the first object.
-..param.T2:The type of the second object.
-...default:$T1$
-..param.T3:The type of the third object.
-...default:$T1$
-..param.TSpec:The specializing type.
-...default:$void$, no packing (faster access).
-
-.Memfunc.Triple#Triple:
-..class:Class.Triple
-..summary:Constructor
-..signature:Triple<T1, T2, T3[, TSpec]> ()
-..signature:Triple<T1, T2, T3[, TSpec]> (triple)
-..signature:Triple<T1, T2, T3[, TSpec]> (i1, i2, i3)
-..param.triple:Other Triple object. (copy constructor)
-..param.i1:T1 object.
-..param.i2:T2 object.
-..param.i3:T3 object.
-
-.Memvar.Triple#i1:
-..class:Class.Triple
-..summary:T1 object
-
-.Memvar.Triple#i2:
-..class:Class.Triple
-..summary:T2 object
-
-.Memvar.Triple#i3:
-..class:Class.Triple
-..summary:T3 object
-..include:seqan/basic.h
-*/
-
 template <typename T1, typename T2 = T1, typename T3 = T1, typename TSpec = void>
 struct Triple
 {
@@ -158,13 +119,13 @@ struct Triple
     // ------------------------------------------------------------------------
 
     inline Triple() : i1(T1()), i2(T2()), i3(T3()) {}
-    
+
     inline Triple(Triple const & _p)
             : i1(_p.i1), i2(_p.i2), i3(_p.i3) {}
-    
+
     inline Triple(T1 const & _i1, T2 const & _i2, T3 const & _i3)
             : i1(_i1), i2(_i2), i3(_i3) {}
-    
+
     template <typename T1_, typename T2_, typename T3_, typename TSpec__>
     inline Triple(Triple<T1_, T2_, T3_, TSpec__> const & _p)
             : i1(getValueI1(_p)), i2(getValueI2(_p)), i3(getValueI3(_p)) {}
@@ -175,7 +136,7 @@ struct Triple
     {
         return i1 == other.i1 && i2 == other.i2 && i3 == other.i3;
     }
-    
+
     inline bool
     operator<(Triple const & other) const
     {
@@ -208,9 +169,6 @@ struct Triple
  * @return VALUE Length of the triple (always 3).
  */
 
-///.Metafunction.LENGTH.param.T.type:Class.Triple
-///.Metafunction.LENGTH.class:Class.Triple
-
 template <typename T1, typename T2, typename T3, typename TSpec>
 struct LENGTH<Triple<T1, T2, T3, TSpec> >
 {
@@ -225,7 +183,7 @@ struct LENGTH<Triple<T1, T2, T3, TSpec> >
 
 /*!
  * @mfn Triple#Value
- * @brief Return i<sup>th type of the triple.
+ * @brief Return i<sup>th</sup> type of the triple.
  *
  * @signature Value<TTriple, I>::Type;
  *
@@ -233,9 +191,6 @@ struct LENGTH<Triple<T1, T2, T3, TSpec> >
  * @tparam I       The index of the value to return, one of 1, 2, or 3.
  */
 
-///.Metafunction.Value.param.T.type:Class.Triple
-///.Metafunction.Value.class:Class.Triple
-
 template <typename T1, typename T2, typename T3, typename TSpec>
 struct Value<Triple<T1, T2, T3, TSpec>, 1>
 {
@@ -269,9 +224,6 @@ struct Value<Triple<T1, T2, T3, TSpec>, 3 >
  * @return Type The specialization type.
  */
 
-///.Metafunction.Spec.param.T.type:Class.Triple
-///.Metafunction.Spec.class:Class.Triple
-
 template <typename T1, typename T2, typename T3, typename TSpec>
 struct Spec<Triple<T1, T2, T3, TSpec> >
 {
@@ -286,13 +238,27 @@ struct Spec<Triple<T1, T2, T3, TSpec> >
 // Function operator<<();  Stream Output.
 // -----------------------------------------------------------------------
 
-// TODO(holtgrew): Document?
+template <typename TTarget, typename T1, typename T2, typename T3, typename TSpec>
+inline void
+write(TTarget &target, Triple<T1, T2, T3, TSpec> const & p)
+{
+    write(target, "< ");
+    write(target, getValueI1(p));
+    write(target, " , ");
+    write(target, getValueI2(p));
+    write(target, " , ");
+    write(target, getValueI3(p));
+    write(target, " >");
+}
 
-template <typename T1, typename T2, typename T3, typename TSpec>
-std::ostream & operator<<(std::ostream & out, Triple<T1,T2,T3,TSpec> const & t)
+template <typename TStream, typename T1, typename T2, typename T3, typename TSpec>
+inline TStream &
+operator<<(TStream & target,
+           Triple<T1, T2, T3, TSpec> const & source)
 {
-    out << "< " << getValueI1(t) << " , " << getValueI2(t) << " , " << getValueI3(t) << " >";
-    return out;
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
+    return target;
 }
 
 // -----------------------------------------------------------------------
@@ -305,7 +271,7 @@ std::ostream & operator<<(std::ostream & out, Triple<T1,T2,T3,TSpec> const & t)
  *
  * @signature T1 getValue(triple);
  *
- * @param triple The triple to get entry from.
+ * @param[in] triple The triple to get entry from.
  *
  * @return T1 The first entry of the Triple.
  */
@@ -323,7 +289,7 @@ getValueI1(Triple<T1, T2, T3, TSpec> const & triple)
  *
  * @signature T2 getValue(triple);
  *
- * @param triple The triple to get entry from.
+ * @param[in] triple The triple to get entry from.
  *
  * @return T2 The second entry of the Triple.
  */
@@ -341,7 +307,7 @@ getValueI2(Triple<T1, T2, T3, TSpec> const & triple)
  *
  * @signature T3 getValue(triple);
  *
- * @param triple The triple to get entry from.
+ * @param[in] triple The triple to get entry from.
  *
  * @return T3 The third entry of the Triple.
  */
@@ -363,8 +329,8 @@ getValueI3(Triple<T1, T2, T3, TSpec> const & triple)
  *
  * @signature void assignValueI1(triple, val);
  *
- * @param triple The triple to get entry from.
- * @param val    Set the value of the Triple's first entry.
+ * @param[in] triple The triple to get entry from.
+ * @param[in] val    Set the value of the Triple's first entry.
  */
 
 template <typename T1, typename T2, typename T3, typename TSpec, typename T>
@@ -379,8 +345,8 @@ inline void assignValueI1(Triple<T1, T2, T3, TSpec> & triple, T const & _i)
  *
  * @signature void assignValueI2(triple, val);
  *
- * @param triple The triple to get entry from.
- * @param val    Set the value of the Triple's second entry.
+ * @param[in] triple The triple to get entry from.
+ * @param[in] val    Set the value of the Triple's second entry.
  */
 
 template <typename T1, typename T2, typename T3, typename TSpec, typename T>
@@ -395,8 +361,8 @@ inline void assignValueI2(Triple<T1, T2, T3, TSpec> & triple, T const & _i)
  *
  * @signature void assignValueI3(triple, val);
  *
- * @param triple The triple to get entry from.
- * @param val    Set the value of the Triple's third entry.
+ * @param[in] triple The triple to get entry from.
+ * @param[in] val    Set the value of the Triple's third entry.
  */
 
 template <typename T1, typename T2, typename T3, typename TSpec, typename T>
@@ -415,8 +381,8 @@ inline void assignValueI3(Triple<T1, T2, T3, TSpec> & triple, T const & _i)
  *
  * @signature void setValueI1(triple, val);
  *
- * @param triple The triple to get entry from.
- * @param val    Set the value of the Triple's first entry.
+ * @param[in] triple The triple to get entry from.
+ * @param[in] val    Set the value of the Triple's first entry.
  */
 
 template <typename T1, typename T2, typename T3, typename TSpec, typename T>
@@ -431,8 +397,8 @@ inline void setValueI1(Triple<T1, T2, T3, TSpec> & triple, T const & _i)
  *
  * @signature void setValueI2(triple, val);
  *
- * @param triple The triple to get entry from.
- * @param val    Set the value of the Triple's second entry.
+ * @param[in] triple The triple to get entry from.
+ * @param[in] val    Set the value of the Triple's second entry.
  */
 
 template <typename T1, typename T2, typename T3, typename TSpec, typename T>
@@ -447,8 +413,8 @@ inline void setValueI2(Triple<T1, T2, T3, TSpec> & triple, T const & _i)
  *
  * @signature void setValueI3(triple, val);
  *
- * @param triple The triple to get entry from.
- * @param val    Set the value of the Triple's third entry.
+ * @param[in] triple The triple to get entry from.
+ * @param[in] val    Set the value of the Triple's third entry.
  */
 
 template <typename T1, typename T2, typename T3, typename TSpec, typename T>
@@ -484,7 +450,7 @@ inline void moveValueI3(Triple<T1, T2, T3, TSpec> & triple, T const & _i)
 // -----------------------------------------------------------------------
 
 template <
-    typename L1, typename L2, typename L3, typename LPack, 
+    typename L1, typename L2, typename L3, typename LPack,
     typename R1, typename R2, typename R3, typename RPack>
 inline bool
 operator<(Triple<L1, L2, L3, LPack> const & _left,
@@ -498,7 +464,7 @@ operator<(Triple<L1, L2, L3, LPack> const & _left,
 // -----------------------------------------------------------------------
 
 template <
-    typename L1, typename L2, typename L3, typename LPack, 
+    typename L1, typename L2, typename L3, typename LPack,
     typename R1, typename R2, typename R3, typename RPack>
 inline bool
 operator>(Triple<L1, L2, L3, LPack> const & _left,
@@ -512,7 +478,7 @@ operator>(Triple<L1, L2, L3, LPack> const & _left,
 // -----------------------------------------------------------------------
 
 template <
-    typename L1, typename L2, typename L3, typename LPack, 
+    typename L1, typename L2, typename L3, typename LPack,
     typename R1, typename R2, typename R3, typename RPack>
 inline bool
 operator<=(Triple<L1, L2, L3, LPack> const & _left,
@@ -526,7 +492,7 @@ operator<=(Triple<L1, L2, L3, LPack> const & _left,
 // -----------------------------------------------------------------------
 
 template <
-    typename L1, typename L2, typename L3, typename LPack, 
+    typename L1, typename L2, typename L3, typename LPack,
     typename R1, typename R2, typename R3, typename RPack>
 inline bool
 operator==(Triple<L1, L2, L3, LPack> const & _left,
@@ -540,7 +506,7 @@ operator==(Triple<L1, L2, L3, LPack> const & _left,
 // -----------------------------------------------------------------------
 
 template <
-    typename L1, typename L2, typename L3, typename LPack, 
+    typename L1, typename L2, typename L3, typename LPack,
     typename R1, typename R2, typename R3, typename RPack>
 inline bool
 operator>=(Triple<L1, L2, L3, LPack> const & _left,
@@ -554,7 +520,7 @@ operator>=(Triple<L1, L2, L3, LPack> const & _left,
 // -----------------------------------------------------------------------
 
 template <
-    typename L1, typename L2, typename L3, typename LPack, 
+    typename L1, typename L2, typename L3, typename LPack,
     typename R1, typename R2, typename R3, typename RPack>
 inline bool
 operator!=(Triple<L1, L2, L3, LPack> const & _left,
@@ -564,4 +530,4 @@ operator!=(Triple<L1, L2, L3, LPack> const & _left,
 }
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_TRIPLE_BASE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_TRIPLE_BASE_H_
diff --git a/seqan/basic/triple_packed.h b/seqan/basic/triple_packed.h
index 6687f2f..55c16f1 100644
--- a/seqan/basic/triple_packed.h
+++ b/seqan/basic/triple_packed.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Packed triple specialization.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_TRIPLE_PACKED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_TRIPLE_PACKED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_TRIPLE_PACKED_H_
+#define SEQAN_INCLUDE_SEQAN_TRIPLE_PACKED_H_
 
 namespace seqan {
 
@@ -61,25 +61,6 @@ namespace seqan {
  * @tparam T3 The third type of the Triple.
  */
 
-/**
-.Spec.Packed Triple:
-..cat:Aggregates
-..general:Class.Triple
-..summary:Stores three arbitrary objects. Saves memory by disabling memory alignment.
-..signature:Triple<T1, T2, T3, Pack>
-..param.T1:The type of the first object.
-..param.T2:The type of the second object.
-..param.T3:The type of the third object.
-..notes:Useful for external storage.
-..remarks:Memory access could be slower. Direct access to members by pointers is not allowed on all platforms.
-..include:seqan/basic.h
-
-.Memfunc.Triple#Triple.class:Spec.Packed Triple
-.Memvar.Triple#i1.class:Spec.Packed Triple
-.Memvar.Triple#i2.class:Spec.Packed Triple
-.Memvar.Triple#i3.class:Spec.Packed Triple
-*/
-
 #ifdef PLATFORM_WINDOWS
     #pragma pack(push,1)
 #endif
@@ -99,13 +80,13 @@ struct Triple<T1, T2, T3, Pack>
     // -----------------------------------------------------------------------
 
     inline Triple() : i1(T1()), i2(T2()), i3(T3()) {}
-    
+
     inline Triple(Triple const &_p)
             : i1(_p.i1), i2(_p.i2), i3(_p.i3) {}
-    
+
     inline Triple(T1 const &_i1, T2 const &_i2, T3 const &_i3)
             : i1(_i1), i2(_i2), i3(_i3) {}
-    
+
     template <typename T1_, typename T2_, typename T3_, typename TSpec__>
     inline Triple(Triple<T1_, T2_, T3_, TSpec__> const & _p)
             : i1(getValueI1(_p)), i2(getValueI2(_p)), i3(getValueI3(_p)) {}
@@ -208,4 +189,4 @@ inline void moveValueI3(Triple<T1, T2, T3, Pack> & triple, T const & _i)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_TRIPLE_PACKED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_TRIPLE_PACKED_H_
diff --git a/seqan/basic/tuple_base.h b/seqan/basic/tuple_base.h
index 2531d1f..7a8d998 100644
--- a/seqan/basic/tuple_base.h
+++ b/seqan/basic/tuple_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -37,8 +37,8 @@
 
 // TODO(holtgrew): What about move construction? Useful for pairs of strings and such. Tricky to implement since ints have no move constructor, for example.
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_TUPLE_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_TUPLE_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_TUPLE_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_TUPLE_BASE_H_
 
 namespace seqan {
 
@@ -75,19 +75,14 @@ struct StoredTupleValue_< SimpleType<TValue, TSpec> >
  * @tparam TSpec  Specialization tag, optional;  defaults to void.
  */
 
-/**
-.Class.Tuple:
-..cat:Aggregates
-..concept:Concept.AggregateConcept
-..summary:A plain fixed-length string.
-..signature:Tuple<T, SIZE[, TSpec]>
-..param.T:The value type, that is the type of characters stored in the tuple.
-..param.SIZE:The size/length of the tuple.
-...remarks:In contrast to @Class.String@ the length of Tuple is fixed.
-..param.TSpec:The specializing type.
-...default:$void$, no packing (faster access).
-..include:seqan/basic.h
-*/
+/*!
+ * @fn Tuple::i
+ * @brief Array of tuple value.
+ *
+ * @signature TValue Tuple::i[SIZE];
+ *
+ * The array of the tuple's values.
+ */
 
 template <typename TValue, unsigned SIZE, typename TSpec = void>
 struct Tuple
@@ -146,7 +141,7 @@ struct Tuple<TValue, SIZE, Pack>
     // -----------------------------------------------------------------------
 
     typename StoredTupleValue_<TValue>::Type i[SIZE];
-    
+
     // -----------------------------------------------------------------------
     // Subscription Operators;  Have to be declared in class.
     // -----------------------------------------------------------------------
@@ -210,9 +205,6 @@ struct Tuple<TValue, SIZE, Pack>
  * @return VALUE The length of the tuple.
  */
 
-///.Metafunction.LENGTH.param.T.type:Class.Tuple
-///.Metafunction.LENGTH.class:Class.Tuple
-
 template <typename TValue, unsigned SIZE, typename TSpec>
 struct LENGTH<Tuple<TValue, SIZE, TSpec> >
 {
@@ -234,9 +226,6 @@ struct LENGTH<Tuple<TValue, SIZE, TSpec> >
  * @return Type The resulting value type.
  */
 
-///.Metafunction.Value.param.T.type:Class.Tuple
-///.Metafunction.Value.class:Class.Tuple
-
 template <typename TValue, unsigned SIZE, typename TSpec>
 struct Value<Tuple<TValue, SIZE, TSpec> >
 {
@@ -247,9 +236,6 @@ struct Value<Tuple<TValue, SIZE, TSpec> >
 // Metafunction Spec
 // -----------------------------------------------------------------------
 
-///.Metafunction.Spec.param.T.type:Class.Tuple
-///.Metafunction.Spec.class:Class.Tuple
-
 template <typename TValue, unsigned SIZE, typename TSpec>
 struct Spec<Tuple<TValue, SIZE, TSpec> >
 {
@@ -264,17 +250,29 @@ struct Spec<Tuple<TValue, SIZE, TSpec> >
 // Function operator<<();  Stream Output.
 // -----------------------------------------------------------------------
 
-template <typename TValue, unsigned SIZE, typename TSpec>
-inline std::ostream &
-operator<< (std::ostream & out, Tuple<TValue, SIZE, TSpec> const &a)
+template <typename TTarget, typename TValue, unsigned SIZE, typename TSpec>
+inline void
+write(TTarget &target, Tuple<TValue, SIZE, TSpec> const &a)
 {
-    out << '[';
+    writeValue(target, '[');
     if (SIZE > 0)
-        out << a[0];
-    for(unsigned j = 1; j < SIZE; ++j)
-        out << ' ' << a[j];
-    out << ']';
-    return out;
+        write(target, (TValue)a[0]);
+    for (unsigned j = 1; j < SIZE; ++j)
+    {
+        writeValue(target, ' ');
+        write(target, (TValue)a[j]);
+    }
+    writeValue(target, ']');
+}
+
+template <typename TStream, typename TValue, unsigned SIZE, typename TSpec>
+inline TStream &
+operator<<(TStream & target,
+           Tuple<TValue, SIZE, TSpec> const & source)
+{
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
+    return target;
 }
 
 // ----------------------------------------------------------------------------
@@ -357,6 +355,14 @@ assignValue(Tuple<TValue, SIZE, TSpec> & me, TPos k, TValue2 const source)
 // Function getValue()
 // -----------------------------------------------------------------------
 
+template <typename TValue, unsigned SIZE, typename TSpec, typename TPos>
+inline TValue
+getValue(Tuple<TValue, SIZE, TSpec> & me, TPos k)
+{
+    SEQAN_CHECK((unsigned(k) < SIZE), "Invalid position, k = %u, SIZE = %u.", unsigned(k), unsigned(SIZE));
+    return me.i[k];
+}
+
 template <typename TValue, unsigned SIZE, typename TSpec, typename TPos>
 inline TValue
 getValue(Tuple<TValue, SIZE, TSpec> const & me, TPos k)
@@ -455,14 +461,14 @@ inline void clear(Tuple<TValue, SIZE, TSpec> & me)
 // Function operator==()
 // -----------------------------------------------------------------------
 
-template <typename TTuple>
+template <typename TTupleL, typename TTupleR>
 struct ComparisonWorkerContext_
 {
     int result;
-    TTuple const & left;
-    TTuple const & right;
+    TTupleL const & left;
+    TTupleR const & right;
 
-    ComparisonWorkerContext_(int b, TTuple const & l, TTuple const & r)
+    ComparisonWorkerContext_(int b, TTupleL const & l, TTupleR const & r)
             : result(b), left(l), right(r)
     {}
 };
@@ -474,18 +480,19 @@ struct TupleComparisonWorkerEq_
     {
         if (arg.result != 1)
             return;
-        if (arg.left.i[I - 1] != arg.right.i[I - 1])
+        if (getValue(arg.left, I - 1) != getValue(arg.right, I - 1))
             arg.result = 0;
     }
 };
 
-template <typename TValue, unsigned SIZE, typename TSpec>
+template <typename TValue, unsigned SIZE, typename TSpecL, typename TSpecR>
 inline bool
-operator==(Tuple<TValue, SIZE, TSpec> const & left,
-           Tuple<TValue, SIZE, TSpec> const & right)
+operator==(Tuple<TValue, SIZE, TSpecL> const & left,
+           Tuple<TValue, SIZE, TSpecR> const & right)
 {
-    typedef Tuple<TValue, SIZE, TSpec> TTuple;
-    ComparisonWorkerContext_<TTuple> context(1, left, right);
+    typedef Tuple<TValue, SIZE, TSpecL> TTupleL;
+    typedef Tuple<TValue, SIZE, TSpecR> TTupleR;
+    ComparisonWorkerContext_<TTupleL, TTupleR> context(1, left, right);
     Loop<TupleComparisonWorkerEq_, SIZE>::run(context);
     return context.result == 1;
 }
@@ -495,10 +502,10 @@ operator==(Tuple<TValue, SIZE, TSpec> const & left,
 // -----------------------------------------------------------------------
 
 
-template <typename TValue, unsigned SIZE, typename TSpec>
+template <typename TValue, unsigned SIZE, typename TSpecL, typename TSpecR>
 inline bool
-operator!=(Tuple<TValue, SIZE, TSpec> const & left,
-           Tuple<TValue, SIZE, TSpec> const & right)
+operator!=(Tuple<TValue, SIZE, TSpecL> const & left,
+           Tuple<TValue, SIZE, TSpecR> const & right)
 {
     return !operator==(left, right);
 }
@@ -523,13 +530,14 @@ struct TupleComparisonWorkerLt_
     }
 };
 
-template <typename TValue, unsigned SIZE, typename TSpec>
+template <typename TValue, unsigned SIZE, typename TSpecL, typename TSpecR>
 inline bool
-operator<(Tuple<TValue, SIZE, TSpec> const & left,
-          Tuple<TValue, SIZE, TSpec> const & right)
+operator<(Tuple<TValue, SIZE, TSpecL> const & left,
+          Tuple<TValue, SIZE, TSpecR> const & right)
 {
-    typedef Tuple<TValue, SIZE, TSpec> TTuple;
-    ComparisonWorkerContext_<TTuple> context(-1, left, right);
+    typedef Tuple<TValue, SIZE, TSpecL> TTupleL;
+    typedef Tuple<TValue, SIZE, TSpecR> TTupleR;
+    ComparisonWorkerContext_<TTupleL, TTupleR> context(-1, left, right);
     Loop<TupleComparisonWorkerLt_, SIZE>::run(context);
     return context.result == 1;
 }
@@ -554,13 +562,14 @@ struct TupleComparisonWorkerGt_
     }
 };
 
-template <typename TValue, unsigned SIZE, typename TSpec>
+template <typename TValue, unsigned SIZE, typename TSpecL, typename TSpecR>
 inline bool
-operator>(Tuple<TValue, SIZE, TSpec> const & left,
-          Tuple<TValue, SIZE, TSpec> const & right)
+operator>(Tuple<TValue, SIZE, TSpecL> const & left,
+          Tuple<TValue, SIZE, TSpecR> const & right)
 {
-    typedef Tuple<TValue, SIZE, TSpec> TTuple;
-    ComparisonWorkerContext_<TTuple> context(-1, left, right);
+    typedef Tuple<TValue, SIZE, TSpecL> TTupleL;
+    typedef Tuple<TValue, SIZE, TSpecR> TTupleR;
+    ComparisonWorkerContext_<TTupleL, TTupleR> context(-1, left, right);
     Loop<TupleComparisonWorkerGt_, SIZE>::run(context);
     return context.result == 1;
 }
@@ -569,10 +578,10 @@ operator>(Tuple<TValue, SIZE, TSpec> const & left,
 // Function operator<=()
 // -----------------------------------------------------------------------
 
-template <typename TValue, unsigned SIZE, typename TSpec>
+template <typename TValue, unsigned SIZE, typename TSpecL, typename TSpecR>
 inline bool
-operator<=(Tuple<TValue, SIZE, TSpec> const & left,
-           Tuple<TValue, SIZE, TSpec> const & right)
+operator<=(Tuple<TValue, SIZE, TSpecL> const & left,
+           Tuple<TValue, SIZE, TSpecR> const & right)
 {
     return !operator>(left, right);
 }
@@ -581,10 +590,10 @@ operator<=(Tuple<TValue, SIZE, TSpec> const & left,
 // Function operator>=()
 // -----------------------------------------------------------------------
 
-template <typename TValue, unsigned SIZE, typename TSpec>
+template <typename TValue, unsigned SIZE, typename TSpecL, typename TSpecR>
 inline bool
-operator>=(Tuple<TValue, SIZE, TSpec> const & left,
-           Tuple<TValue, SIZE, TSpec> const & right)
+operator>=(Tuple<TValue, SIZE, TSpecL> const & left,
+           Tuple<TValue, SIZE, TSpecR> const & right)
 {
     return !operator<(left, right);
 }
@@ -593,12 +602,12 @@ operator>=(Tuple<TValue, SIZE, TSpec> const & left,
 // Function operator+()
 // -----------------------------------------------------------------------
 
-template <typename TValue, unsigned SIZE, typename TSpec>
-inline Tuple<TValue, SIZE, TSpec>
-operator+(Tuple<TValue, SIZE, TSpec> const & left,
-          Tuple<TValue, SIZE, TSpec> const & right)
+template <typename TValue, unsigned SIZE, typename TSpecL, typename TSpecR>
+inline Tuple<TValue, SIZE, TSpecL>
+operator+(Tuple<TValue, SIZE, TSpecL> const & left,
+          Tuple<TValue, SIZE, TSpecR> const & right)
 {
-    Tuple<TValue, SIZE, TSpec>  tuple;
+    Tuple<TValue, SIZE, TSpecL>  tuple;
 
     for (unsigned j = 0; j < SIZE; ++j)
         tuple[j] = left[j] + right[j];
@@ -608,4 +617,4 @@ operator+(Tuple<TValue, SIZE, TSpec> const & left,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_TUPLE_BASE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_TUPLE_BASE_H_
diff --git a/seqan/basic/tuple_bit_compressed.h b/seqan/basic/tuple_bit_compressed.h
index aff0d8d..b1a5b85 100644
--- a/seqan/basic/tuple_bit_compressed.h
+++ b/seqan/basic/tuple_bit_compressed.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Bit-packed tuple specialization.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_TUPLE_BIT_PACKED_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_BASIC_TUPLE_BIT_PACKED_H_
+#ifndef SEQAN_INCLUDE_SEQAN_BASIC_TUPLE_BIT_PACKED_H_
+#define SEQAN_INCLUDE_SEQAN_BASIC_TUPLE_BIT_PACKED_H_
 
 namespace seqan {
 
@@ -43,6 +43,12 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
+template <typename TValue>
+inline bool testAllZeros(TValue const & val);
+
+template <typename TValue>
+inline bool testAllOnes(TValue const & val);
+
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
@@ -66,21 +72,6 @@ namespace seqan {
  * Only useful for small alphabets as small tuple sizes (|Sigma|^size &lt;= 2^64 as for Dna or AminoAcid m-grams).
  */
 
-/**
-.Spec.Bit Packed Tuple:
-..cat:Aggregates
-..general:Class.Tuple
-..summary:A plain fixed-length string. Saves memory by packing bits.
-..signature:Tuple<T, SIZE, BitPacked<> >
-..param.T:The value type, that is the type of characters stored in the tuple.
-..param.SIZE:The size/length of the tuple.
-...remarks:In contrast to @Class.String@ the length of Tuple is fixed.
-..notes:The characters are stored as a bit sequence in an ordinal type (char, ..., __int64).
-..remarks:Only useful for small alphabets and small tuple sizes (|Sigma|^size <= 2^64) as for @Spec.Dna@ or @Spec.AminoAcid@ m-grams)
-..see:Spec.Sampler
-..include:seqan/basic.h
- */
-
 template <unsigned char SIZE>
 struct BitVector_
 {
@@ -199,7 +190,7 @@ struct Tuple<TValue, SIZE, BitPacked<> >
         SEQAN_ASSERT_GEQ(static_cast<__int64>(k), 0);
         SEQAN_ASSERT_LT(static_cast<__int64>(k), static_cast<__int64>(SIZE));
 
-        register unsigned shift = ((SIZE - 1 - k) * BitsPerValue<TValue>::VALUE);
+        unsigned shift = ((SIZE - 1 - k) * BitsPerValue<TValue>::VALUE);
         i = (i & ~(BIT_MASK << shift)) | (TBitVector)ordValue(source) << shift;
         return source;
     }
@@ -231,19 +222,21 @@ getValue(Tuple<TValue, SIZE, BitPacked<> > const & me,
 {
     SEQAN_ASSERT_GEQ(static_cast<__int64>(k), 0);
     SEQAN_ASSERT_LT(static_cast<__int64>(k), static_cast<__int64>(SIZE));
-    
+
     return (me.i >> (SIZE - 1 - k) * BitsPerValue<TValue>::VALUE) & me.BIT_MASK;
 }
 
-/*
 template <typename TValue, unsigned SIZE, typename TPos>
 TValue
 getValue(Tuple<TValue, SIZE, BitPacked<> > & me,
          TPos k)
 {
-    return getValue(const_cast<Tuple<TValue, SIZE, BitPacked<> > const &>(me), k);
+    SEQAN_ASSERT_GEQ(static_cast<__int64>(k), 0);
+    SEQAN_ASSERT_LT(static_cast<__int64>(k), static_cast<__int64>(SIZE));
+
+    return (me.i >> (SIZE - 1 - k) * BitsPerValue<TValue>::VALUE) & me.BIT_MASK;
 }
-*/
+
 // -----------------------------------------------------------------------
 // Function assignValue()
 // -----------------------------------------------------------------------
@@ -259,7 +252,7 @@ assignValue(Tuple<TValue, SIZE, BitPacked<> > & me,
     SEQAN_ASSERT_GEQ(static_cast<__int64>(k), 0);
     SEQAN_ASSERT_LT(static_cast<__int64>(k), static_cast<__int64>(SIZE));
 
-    register unsigned shift = ((SIZE - 1 - k) * BitsPerValue<TValue>::VALUE);
+    unsigned shift = ((SIZE - 1 - k) * BitsPerValue<TValue>::VALUE);
     me.i = (me.i & ~(me.BIT_MASK << shift)) | (TBitVector)ordValue(source) << shift;
     return source;
 }
@@ -336,14 +329,113 @@ inline void shiftRight(Tuple<TValue, SIZE, BitPacked<> > & me)
     me >>= 1;
 }
 
+// ----------------------------------------------------------------------------
+// Function testAllZeros()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned SIZE>
+inline bool testAllZeros(Tuple<TValue, SIZE, BitPacked<> > const & me)
+{
+    return testAllZeros(me.i);
+}
+
+// ----------------------------------------------------------------------------
+// Function testAllOnes()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned SIZE>
+inline bool testAllOnes(Tuple<TValue, SIZE, BitPacked<> > const & me)
+{
+    return testAllOnes(me.i);
+}
+
 // -----------------------------------------------------------------------
 // Function clear()
 // -----------------------------------------------------------------------
- 
+
 template <typename TValue, unsigned SIZE>
 inline void clear(Tuple<TValue, SIZE, BitPacked<> > & me)
 {
-    me.i = 0; 
+    me.i = 0;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator&()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned SIZE>
+inline Tuple<TValue, SIZE, BitPacked<> >
+operator&(Tuple<TValue, SIZE, BitPacked<> > const & left,
+          Tuple<TValue, SIZE, BitPacked<> > const & right)
+{
+    Tuple<TValue, SIZE, BitPacked<> > tmp;
+    tmp.i = left.i & right.i;
+    return tmp;
+}
+
+template <typename TValue, unsigned SIZE, typename T>
+inline typename Tuple<TValue, SIZE, BitPacked<> >::TBitVector
+operator&(Tuple<TValue, SIZE, BitPacked<> > const & left,
+          T const & right)
+{
+    return left.i & right;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator|()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned SIZE>
+inline Tuple<TValue, SIZE, BitPacked<> >
+operator|(Tuple<TValue, SIZE, BitPacked<> > const & left,
+          Tuple<TValue, SIZE, BitPacked<> > const & right)
+{
+    Tuple<TValue, SIZE, BitPacked<> > tmp;
+    tmp.i = left.i | right.i;
+    return tmp;
+}
+
+template <typename TValue, unsigned SIZE, typename T>
+inline typename Tuple<TValue, SIZE, BitPacked<> >::TBitVector
+operator|(Tuple<TValue, SIZE, BitPacked<> > const & left,
+          T const & right)
+{
+    return left.i | right;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator^()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned SIZE>
+inline Tuple<TValue, SIZE, BitPacked<> >
+operator^(Tuple<TValue, SIZE, BitPacked<> > const & left,
+          Tuple<TValue, SIZE, BitPacked<> > const & right)
+{
+    Tuple<TValue, SIZE, BitPacked<> > tmp;
+    tmp.i = left.i ^ right.i;
+    return tmp;
+}
+
+template <typename TValue, unsigned SIZE, typename T>
+inline typename Tuple<TValue, SIZE, BitPacked<> >::TBitVector
+operator^(Tuple<TValue, SIZE, BitPacked<> > const & left,
+          T const & right)
+{
+    return left.i ^ right;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator~()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned SIZE>
+inline Tuple<TValue, SIZE, BitPacked<> >
+operator~(Tuple<TValue, SIZE, BitPacked<> > const & val)
+{
+    Tuple<TValue, SIZE, BitPacked<> > tmp;
+    tmp.i = ~val.i;
+    return tmp;
 }
 
 // -----------------------------------------------------------------------
@@ -462,4 +554,4 @@ inline bool operator!=(Tuple<TValue, SIZE, BitPacked<> > & left,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_BASIC_TUPLE_BIT_PACKED_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_TUPLE_BIT_PACKED_H_
diff --git a/seqan/basic/volatile_ptr.h b/seqan/basic/volatile_ptr.h
index 72122ce..c89bb97 100644
--- a/seqan/basic/volatile_ptr.h
+++ b/seqan/basic/volatile_ptr.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -70,17 +70,6 @@ namespace seqan {
  * the component and set all pointers to <tt>NULL</tt>.
  */
 
-/**
-.Class.VolatilePtr
-..summary:Helper data structure for handling volatile data.
-..cat:Basic
-..signature:VolatilePtr<T>
-..param.T:The pointed-to type.
-..remarks:Allows you to handle volatile data (used by ext. string during swapping).
-..remarks:Imagine volatile pointers as nodes in an undirected graph.  When you assign one to another then they are connected.  All pointers in a connection component points to the same value.  By calling @Function.nukeCopies@ you can destroy the component and set all pointers to $NULL$.
-..include:seqan/basic.h
- */
-
 template < typename Type >
 struct VolatilePtr
 {
@@ -216,17 +205,7 @@ struct VolatilePtr
  *
  * @signature void nukeCopies(ptr);
  *
- * @param ptr One pointer of the connected component to reset.
- */
- 
-/**
-.Function.nukeCopies
-..class:Class.VolatilePtr
-..cat:Basic
-..summary:Reset all pointers connected to a given one.
-..signature:nukeCopies(ptr)
-..param.ptr:One pointer of the connected component to reset.
-...type:Class.VolatilePtr
+ * @param[in] ptr One pointer of the connected component to reset.
  */
 
 // TODO(holtgrew): Remove this version?
diff --git a/seqan/bed_io.h b/seqan/bed_io.h
new file mode 100644
index 0000000..ca53fdd
--- /dev/null
+++ b/seqan/bed_io.h
@@ -0,0 +1,59 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for module bed_io.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_BED_IO_H_
+#define INCLUDE_SEQAN_BED_IO_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/basic.h>
+#include <seqan/stream.h>
+#include <seqan/sequence.h>
+
+// ===========================================================================
+// First Header Group.
+// ===========================================================================
+
+#include <seqan/bed_io/bed_record.h>
+
+#include <seqan/bed_io/read_bed.h>
+#include <seqan/bed_io/write_bed.h>
+
+#include <seqan/bed_io/bed_file.h>
+
+#endif  // INCLUDE_SEQAN_BED_IO_H_
diff --git a/seqan/bed_io/bed_file.h b/seqan/bed_io/bed_file.h
new file mode 100644
index 0000000..b1d8cf8
--- /dev/null
+++ b/seqan/bed_io/bed_file.h
@@ -0,0 +1,127 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Class for reading/writing files in BED format.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_BED_IO_BED_FILE_H_
+#define SEQAN_INCLUDE_SEQAN_BED_IO_BED_FILE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Typedefs
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Type BedFileIn
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BedFileIn
+ * @signature typedef FormattedFile<Bed, Input> BedFileIn;
+ * @extends FormattedFileIn
+ * @headerfile <seqan/bed_io.h>
+ * @brief Class for reading BED files.
+ *
+ * @see BedRecord
+ */
+
+typedef FormattedFile<Bed, Input>   BedFileIn;
+
+// ----------------------------------------------------------------------------
+// Type BedFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BedFileOut
+ * @signature typedef FormattedFile<Bed, Output> BedFileOut;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/bed_io.h>
+ * @brief Class for writing BED files.
+ *
+ * @see BedRecord
+ */
+
+typedef FormattedFile<Bed, Output>  BedFileOut;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<Bed, TDirection, TSpec>, TStorageSpec>
+{
+    typedef CharString Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec>
+struct FileFormat<FormattedFile<Bed, TDirection, TSpec> >
+{
+    typedef Bed Type;
+};
+
+// ----------------------------------------------------------------------------
+// Function readRecord(); BedRecord
+// ----------------------------------------------------------------------------
+
+// convient BedFile variant
+template <typename TRecordSpec, typename TSpec>
+inline void
+readRecord(BedRecord<TRecordSpec> & record, FormattedFile<Bed, Input, TSpec> & file)
+{
+    readRecord(record, context(file), file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function write(); BedRecord
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TRecordSpec>
+inline void
+writeRecord(FormattedFile<Bed, Output, TSpec> & file, BedRecord<TRecordSpec> & record)
+{
+    writeRecord(file.iter, record, file.format);
+}
+
+}  // namespace seqan
+
+#endif // SEQAN_INCLUDE_SEQAN_BED_IO_BED_FILE_H_
diff --git a/seqan/bed_io/bed_record.h b/seqan/bed_io/bed_record.h
new file mode 100644
index 0000000..a5f4676
--- /dev/null
+++ b/seqan/bed_io/bed_record.h
@@ -0,0 +1,432 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_BED_IO_BED_RECORD_H_
+#define INCLUDE_SEQAN_BED_IO_BED_RECORD_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct Bed3_;
+typedef Tag<Bed3_> Bed3;
+
+struct Bed4_;
+typedef Tag<Bed4_> Bed4;
+
+struct Bed5_;
+typedef Tag<Bed5_> Bed5;
+
+struct Bed6_;
+typedef Tag<Bed6_> Bed6;
+
+struct Bed12_;
+typedef Tag<Bed12_> Bed12;
+
+// ----------------------------------------------------------------------------
+// Class BedRecord
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BedRecord
+ * @implements FormattedFileRecordConcept
+ * @headerfile <seqan/bed_io.h>
+ * @brief Data structure for storing BED records.
+ *
+ * @signature template <typename TSpec>
+ *            class BedRecord;
+ *
+ * @tparam TSpec The specialization to use.  Default: <tt>Bed12</tt>.
+ *
+ * BED files allow the easy representation of intervals on the genome.  Originally, they were designed for tracks in the
+ * UCSC genome browser. The original format has 12 columns but often variants using fewer columns with interpreted data
+ * are used and the rest is kept as application dependent data.
+ *
+ * The BedRecord class allows for storing BED records. The various subclasses provide access to 3, 4, 5, 6, or 12 fields
+ * of the BED format. For example, a <tt>BedRecord&lt;Bed&gt;></tt> has members variables for the first 5 columns of a BED
+ * file. The remaining data is stored as the @link CharString @endlink member variable <tt>data</tt>.
+ *
+ * @section Remarks
+ *
+ * The <tt>ref</tt> field is the name of the reference as loaded from the BED file. The <tt>rID</tt> field can be used
+ * to store a numeric reference id.
+ *
+ * Note that while the BED file format is 1-based, the coordinates in the BedRecord are 0-based.
+ *
+ * @var CharString BedRecord::ref;
+ * @brief Name of the interval's reference name.
+ *
+ * @var __int32 BedRecord::beginPosition;
+ * @brief Begin position on the reference.
+ *
+ * @var __int32 BedRecord::rID;
+ * @brief Numeric id of the interval's reference (<tt>__int32</tt>, defaults to <tt>INVALID_REFID</tt>).
+ *
+ * @var __int32 BedRecord::INVALID_REFID;
+ * @brief Constant for invalid references.
+ * @signature static const __int32 BedRecord::INVALID_REFID = -1;
+ *
+ * @var __int32 BedRecord::endPosition;
+ * @brief End position on the reference.
+ *
+ * @var __int32 BedRecord::INVALID_POS;
+ * @brief Constant for invalid positions.
+ * @signature static const __int32 BedRecord::INVALID_POS = -1;
+ *
+ * @var CharString BedRecord::data;
+ * @brief Any data after the last position.
+ */
+
+/*!
+ * @fn BedRecord::BedRecord
+ * @brief Constructor.
+ *
+ * @signature BedRecord::BedRecord();
+ */
+
+template <typename TSpec = Bed12>
+class BedRecord;
+
+// ----------------------------------------------------------------------------
+// Class Bed3 BedRecord
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class Bed3Record
+ * @extends BedRecord
+ * @headerfile <seqan/bed_io.h>
+ * @brief BedRecord with 3 fields.
+ *
+ * @signature template <>
+ *            class BedRecord<Bed3>;
+ *
+ * This BedRecord specialization stores the first three fields (ref, beginPos, endPos) of a BED file.
+ */
+
+template <>
+class BedRecord<Bed3>
+{
+public:
+    static const int INVALID_REFID = -1;
+    static const int INVALID_POS = -1;
+
+    // The chromosome name.
+    CharString ref;
+    // The id of the chromosome, -1 if not translated.
+    __int32 rID;
+    // The start position.
+    __int32 beginPos;
+    // The end position;
+    __int32 endPos;
+    // The remaining data from the file, unparsed.
+    CharString data;
+
+    BedRecord() : rID(INVALID_REFID), beginPos(INVALID_POS), endPos(INVALID_POS)
+    {}
+
+    void _clear()
+    {
+        rID = INVALID_REFID;
+        beginPos = INVALID_POS;
+        endPos = INVALID_POS;
+        clear(ref);
+        clear(data);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class Bed4 BedRecord
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class Bed4Record
+ * @extends Bed3Record
+ * @headerfile <seqan/bed_io.h>
+ * @brief BedRecord with 4 fields.
+ *
+ * @signature template <>
+ *            class BedRecord<Bed3>;
+ *
+ * This BedRecord specialization stores the first four fields (ref, beginPos, endPos, name) of a BED file.
+ *
+ * @var CharString Bed4Record::name;
+ * @brief The name of the interval (@link CharString @endlink).
+ */
+
+template <>
+class BedRecord<Bed4> : public BedRecord<Bed3>
+{
+public:
+    // The name of the feature.
+    CharString name;
+
+    BedRecord() : BedRecord<Bed3>()
+    {}
+
+    void _clear()
+    {
+        BedRecord<Bed3>::_clear();
+        clear(name);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class Bed5 BedRecord
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class Bed5Record
+ * @extends Bed4Record
+ * @headerfile <seqan/bed_io.h>
+ *
+ * @brief BedRecord with 5 fields.
+ *
+ * @signature template <>
+ *            class BedRecord<Bed5>;
+ *
+ * This BedRecord specialization stores the first five fields (ref, beginPos, endPos, name, score) of a BED file.
+ *
+ * @var CharString Bed5Record::score;
+ * @brief The score of the interval (stored as @link CharString @endlink to allow more flexible annotation).
+ *
+ * @section Remarks
+ *
+ * Storing the score as a @link CharString @endlink is provided for compatibility with bedtools.
+ */
+
+template <>
+class BedRecord<Bed5> : public BedRecord<Bed4>
+{
+public:
+    // The score of the feature, stored as CharString for compatibility with bedtools.
+    CharString score;
+
+    BedRecord() : BedRecord<Bed4>()
+    {}
+
+    void _clear()
+    {
+        BedRecord<Bed4>::_clear();
+        clear(score);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class Bed6 BedRecord
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class Bed6Record
+ * @extends Bed5Record
+ * @headerfile <seqan/bed_io.h>
+ *
+ * @brief BedRecord with 6 fields.
+ *
+ * @signature template <>
+ *            class BedRecord<Bed6>;
+ *
+ * This BedRecord specialization stores the first six fields (ref, beginPos, endPos, name, score, strand) of a BED file.
+ *
+ * @var char Bed6Record::strand;
+ * @brief The strand of the interval (stored as <tt>char</tt>, one of <tt>.</tt>, '-', and <tt>+</tt>).
+ *
+ * Defaults to '.'.
+ */
+
+template <>
+class BedRecord<Bed6> : public BedRecord<Bed5>
+{
+public:
+    // The strand of the feature.  One of '.', '-', and '+'.
+    char strand;
+
+    BedRecord() : BedRecord<Bed5>(), strand('.')
+    {}
+
+    void _clear()
+    {
+        BedRecord<Bed5>::_clear();
+        strand = '.';
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class BedRgb
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BedRgb
+ * @headerfile <seqan/bed_io.h>
+ * @brief RGB color for @link Bed12Record @endlink.
+ *
+ * @signature class BedRgb;
+ *
+ * @var __int32 BedRgb::red;
+ * @brief Red value of RGB color (default is <tt>0</tt>).
+ *
+ * @var __int32 BedRgb::green;
+ * @brief Green value of RGB color (default is <tt>0</tt>).
+ *
+ * @var __int32 BedRgb::blue;
+ * @brief Blue value of RGB color (default is <tt>0</tt>).
+ */
+
+/*!
+ * @fn BedRgb::BedRgb
+ * @brief Default constructor and initialization of integer RGB values.
+ *
+ * @signature BedRgb::BedRgb();
+ * @signature BedRgb::BedRgb(red, green, blue);
+ *
+ * @param[in] blue  __int32 blue value <tt>0-255</tt> (defaults to <tt>0</tt>).
+ * @param[in] green __int32 green value <tt>0-255</tt> (defaults to <tt>0</tt>).
+ * @param[in] red   __int32 red value <tt>0-255</tt> (defaults to <tt>0</tt>).
+ */
+
+class BedRgb
+{
+public:
+    __int32 red, green, blue;
+
+    BedRgb() : red(0), green(0), blue(0)
+    {}
+
+    BedRgb(int red, int green, int blue) : red(red), green(green), blue(blue)
+    {}
+
+    bool operator==(BedRgb const & other) const
+    {
+        return red == other.red && green == other.green && blue == other.blue;
+    }
+
+    bool operator!=(BedRgb const & other) const
+    {
+        return !(*this == other);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class Bed12 BedRecord
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class Bed12Record
+ * @extends BedRecord
+ * @headerfile <seqan/bed_io.h>
+ * @brief BedRecord with 12 fields.
+ *
+ * @signature template <>
+ *            class BedRecord<Bed12>;
+ *
+ * This @link BedRecord @endlink specialization stores all fields of a BED file.
+ *
+ * @var __int32 Bed12Record::itemRgb;
+ * @brief RGB color of item (@link BedRgb @endlink).
+ *
+ * @var __int32 Bed12Record::blockCount;
+ * @brief The number of blocks.
+ *
+ * @var TIntString Bed12Record::blockBegins;
+ * @brief The begin positions of the blocks (@link AllocString @endlink of <tt>__int32</tt>).
+ *
+ * @var TIntString Bed12Record::blockSizes;
+ * @brief The sizes of the blocks (@link AllocString @endlink of <tt>__int32</tt>).
+ *
+ * @var __int32 Bed12Record::thickBegin;
+ * @brief The begin position of thick drawing.
+ *
+ * @var __int32 Bed12Record::thickEnd;
+ * @brief The end position of thick drawing.
+ */
+
+template <>
+class BedRecord<Bed12> : public BedRecord<Bed6>
+{
+public:
+    // The starting position of thick line for feature.
+    __int32 thickBegin;
+    // The end position of thick line for feature.
+    __int32 thickEnd;
+    // The color of the item.
+    BedRgb itemRgb;
+    // The number of blocks/exons for the feature.
+    __int32 blockCount;
+    // The list of block size.
+    String<__int32> blockSizes;
+    // List of block starts.
+    String<__int32> blockBegins;
+
+    BedRecord() : BedRecord<Bed6>(), thickBegin(INVALID_POS), thickEnd(INVALID_POS), blockCount(0)
+    {}
+
+    void _clear()
+    {
+        BedRecord<Bed6>::_clear();
+        thickBegin = INVALID_POS;
+        thickEnd = INVALID_POS;
+        blockCount = 0;
+        itemRgb = BedRgb();
+        clear(blockSizes);
+        clear(blockBegins);
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BedRecord#clear
+ * @brief Reset BED record to state after default initialization.
+ *
+ * @signature void clear(record);
+ *
+ * @param[in,out] record BedRecord to reset.
+ */
+
+template <typename TSpec>
+void clear(BedRecord<TSpec> & record)
+{
+    record._clear();
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_BED_IO_BED_RECORD_H_
diff --git a/seqan/bed_io/read_bed.h b/seqan/bed_io/read_bed.h
new file mode 100644
index 0000000..4ba33d7
--- /dev/null
+++ b/seqan/bed_io/read_bed.h
@@ -0,0 +1,279 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Reading of BED from files.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_BED_IO_READ_BED_H_
+#define INCLUDE_SEQAN_BED_IO_READ_BED_H_
+
+#include <seqan/stream.h>
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct Bed_;
+typedef Tag<Bed_> Bed;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class MagicHeader
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<Bed, T> :
+    public MagicHeader<Nothing, T> {};
+
+// ----------------------------------------------------------------------------
+// Class FileExtensions
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<Bed, T>
+{
+    static char const * VALUE[1];    // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<Bed, T>::VALUE[1] =
+{
+    ".bed"     // default output extension
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord()                                            [BedRecord]
+// ----------------------------------------------------------------------------
+
+// We have a helper function _readBedRecordNoData() that has various
+// overloads.  The one for Bed$N$ calls the one with Bed$N-1$.
+
+// Helper function that reads first three fields of BED record.
+// NoData means the the member data (for the columns not read) is not
+// filled.
+template <typename TForwardIter>
+inline void
+_readBedRecordNoData(BedRecord<Bed3> & record,
+                     TForwardIter & iter,
+                     CharString & buffer)
+{
+    // Read CHROM.
+    readUntil(record.ref, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    if (record.ref == "track")
+    {
+        skipLine(iter);
+        return;
+    }
+    skipOne(iter);
+
+    // Read START.
+    // TODO(singer): Realy __int32 for a position ???
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    // NB: in contrast to many other text-based formats, UCSC BED uses 0-based and not 1-based coordinates.
+    record.beginPos = lexicalCast<__int32>(buffer);
+    skipOne(iter);
+
+    // Read END.
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, IsNewline>());
+    record.endPos = lexicalCast<__int32>(buffer);
+
+    // Go over tab if any.
+    if (!atEnd(iter) && IsTab()(value(iter)))
+        skipOne(iter);
+}
+
+// Read first four fields without data.
+
+template <typename TForwardIter>
+inline void
+_readBedRecordNoData(BedRecord<Bed4> & record,
+                     TForwardIter & iter,
+                     CharString & buffer)
+{
+    // Read first three fields.
+    _readBedRecordNoData(static_cast<BedRecord<Bed3> &>(record), iter, buffer);
+
+    // Read NAME.
+    readUntil(record.name, iter, OrFunctor<IsTab, IsNewline>());
+
+    // Go over tab if any.
+    if (!atEnd(iter) && IsTab()(value(iter)))
+        skipOne(iter);
+}
+
+// Read first five fields without data.
+
+template <typename TForwardIter>
+inline void
+_readBedRecordNoData(BedRecord<Bed5> & record,
+                     TForwardIter & iter,
+                     CharString & buffer)
+{
+    // Read first four fields.
+    _readBedRecordNoData(static_cast<BedRecord<Bed4 > &>(record), iter, buffer);
+
+    // Read SCORE.
+    readUntil(record.score, iter, OrFunctor<IsTab, IsNewline>());
+
+    // Go over tab if any.
+    if (!atEnd(iter) && IsTab()(value(iter)))
+        skipOne(iter);
+}
+
+// Read first six fields without data.
+
+template <typename TForwardIter>
+inline void
+_readBedRecordNoData(BedRecord<Bed6> & record,
+                     TForwardIter & iter,
+                     CharString & buffer)
+{
+    // Read first three fields.
+    _readBedRecordNoData(static_cast<BedRecord<Bed5 > &>(record), iter, buffer);
+
+    // Read STRAND.
+    record.strand = value(iter);
+    skipOne(iter, OrFunctor<OrFunctor<EqualsChar<'.'>, EqualsChar<'+'> >, EqualsChar<'-'> >());
+
+    // Go over tab if any.
+    if (!atEnd(iter) && !IsNewline()(value(iter)))
+        skipOne(iter);
+}
+
+// Read first twelve fields without data.
+
+template <typename TForwardIter>
+inline void
+_readBedRecordNoData(BedRecord<Bed12> & record,
+                     TForwardIter & iter,
+                     CharString & buffer)
+{
+    IsNewline isNewline;
+    // Read first three fields.
+    _readBedRecordNoData(static_cast<BedRecord<Bed6 > &>(record), iter, buffer);
+
+    // Read THICK BEGIN
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    record.thickBegin = lexicalCast<__int32>(buffer);
+    skipOne(iter);
+
+    // Read THICK END
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    record.thickEnd = lexicalCast<__int32>(buffer);
+    skipOne(iter);
+
+    // Read ITEM RGB
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<EqualsChar<','>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    record.itemRgb.red = lexicalCast<__int32>(buffer);
+    skipOne(iter);
+
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<EqualsChar<','>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    record.itemRgb.green = lexicalCast<__int32>(buffer);
+    skipOne(iter);
+
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    record.itemRgb.blue = lexicalCast<__int32>(buffer);
+    skipOne(iter);
+
+    // Read BLOCK COUNT
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    record.blockCount = lexicalCast<__int32>(buffer);
+    skipOne(iter);
+
+    // READ BLOCK SIZES
+    for (int i = 0; i < record.blockCount - 1; ++i)
+    {
+        clear(buffer);
+        readUntil(buffer, iter, OrFunctor<EqualsChar<','>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+        appendValue(record.blockSizes, lexicalCast<int>(buffer));
+        skipOne(iter);
+    }
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+    appendValue(record.blockSizes, lexicalCast<int>(buffer));
+    skipOne(iter);
+
+    // READ BLOCK STARTS
+    for (int i = 0; i < record.blockCount - 1; ++i)
+    {
+        clear(buffer);
+        readUntil(buffer, iter, OrFunctor<EqualsChar<','>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Bed> >());
+        appendValue(record.blockBegins, lexicalCast<int>(buffer));
+        skipOne(iter);
+    }
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, IsNewline>());
+    appendValue(record.blockBegins, lexicalCast<int>(buffer));
+    if (isNewline(value(iter)))
+    {
+        skipLine(iter);
+        return;
+    }
+    skipOne(iter);
+}
+
+// The front-end function automatically calls the correct overload of
+// _readBedRecordNoData through the type of record.
+
+template <typename TSpec, typename TForwardIter>
+inline void
+readRecord(BedRecord<TSpec> & record,
+           CharString & buffer,
+           TForwardIter & iter,
+           Bed const & /*tag*/)
+{
+    clear(record);
+    _readBedRecordNoData(record, iter, buffer);
+    readLine(record.data, iter);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_BED_IO_READ_BED_H_
diff --git a/seqan/bed_io/write_bed.h b/seqan/bed_io/write_bed.h
new file mode 100644
index 0000000..15891fa
--- /dev/null
+++ b/seqan/bed_io/write_bed.h
@@ -0,0 +1,148 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Writing of BED to files.
+// ==========================================================================
+
+// TODO(holtgrew): Add overload with BedIOContext.
+
+#ifndef INCLUDE_SEQAN_BED_IO_WRITE_BED_H_
+#define INCLUDE_SEQAN_BED_IO_WRITE_BED_H_
+
+namespace seqan {
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()                                      [Bed3 BedRecord]
+// ----------------------------------------------------------------------------
+
+// Similar to readRecord() for BedRecord, we have various overloads of _writeBedRecord().
+
+template <typename TTarget>
+inline void
+_writeBedRecord(TTarget & target, BedRecord<Bed3> const & record, CharString const & ref)
+{
+    write(target, ref);
+    writeValue(target, '\t');
+    // NB: in contrast to many other text-based formats, UCSC BED uses 0-based and not 1-based coordinates.
+    appendNumber(target, record.beginPos);
+    writeValue(target, '\t');
+    appendNumber(target, record.endPos);
+}
+
+template <typename TTarget>
+inline void
+_writeBedRecord(TTarget & target, BedRecord<Bed4> const & record, CharString const & ref)
+{
+    _writeBedRecord(target, static_cast<BedRecord<Bed3> const &>(record), ref);
+    writeValue(target, '\t');
+    write(target, record.name);
+}
+
+template <typename TTarget>
+inline void
+_writeBedRecord(TTarget & target, BedRecord<Bed5> const & record, CharString const & ref)
+{
+    _writeBedRecord(target, static_cast<BedRecord<Bed4> const &>(record), ref);
+    writeValue(target, '\t');
+    write(target, record.score);
+}
+
+template <typename TTarget>
+inline void
+_writeBedRecord(TTarget & target, BedRecord<Bed6> const & record, CharString const & ref)
+{
+    _writeBedRecord(target, static_cast<BedRecord<Bed5> const &>(record), ref);
+    writeValue(target, '\t');
+    writeValue(target, record.strand);
+}
+
+template <typename TTarget>
+inline void
+_writeBedRecord(TTarget & target, BedRecord<Bed12> const & record, CharString const & ref)
+{
+    _writeBedRecord(target, static_cast<BedRecord<Bed6> const &>(record), ref);
+    writeValue(target, '\t');
+
+    appendNumber(target, record.thickBegin);
+    writeValue(target, '\t');
+
+    appendNumber(target, record.thickEnd);
+    writeValue(target, '\t');
+
+    appendNumber(target, record.itemRgb.red);
+    writeValue(target, ',');
+    appendNumber(target, record.itemRgb.green);
+    writeValue(target, ',');
+    appendNumber(target, record.itemRgb.blue);
+    writeValue(target, '\t');
+
+    appendNumber(target, record.blockCount);
+    writeValue(target, '\t');
+
+    for (unsigned i = 0; i < length(record.blockSizes); ++i)
+    {
+        if (i > 0)
+            writeValue(target, ',');
+        appendNumber(target, record.blockSizes[i]);
+    }
+
+    writeValue(target, '\t');
+
+    for (unsigned i = 0; i < length(record.blockBegins); ++i)
+    {
+        if (i > 0)
+            writeValue(target, ',');
+        appendNumber(target, record.blockBegins[i]);
+    }
+}
+
+template <typename TTarget, typename TRecordSpec>
+inline void
+writeRecord(TTarget & target, BedRecord<TRecordSpec> const & record, Bed const & /*tag*/)
+{
+    _writeBedRecord(target, record, record.ref);
+    if (!empty(record.data))
+    {
+        writeValue(target, '\t');
+        write(target, record.data);
+    }
+    writeValue(target, '\n');
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_BED_IO_WRITE_BED_H_
diff --git a/seqan/blast.h b/seqan/blast.h
new file mode 100644
index 0000000..aebf652
--- /dev/null
+++ b/seqan/blast.h
@@ -0,0 +1,76 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Module for handling NCBI Blast I/O and E-Value computation
+// ==========================================================================
+
+#ifndef SEQAN_BLAST_H
+#define SEQAN_BLAST_H
+
+#include <seqan/platform.h>
+
+#ifdef SEQAN_CXX11_COMPLETE
+
+#include <cinttypes>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <sstream>
+#include <type_traits>
+#include <unordered_map>
+#include <regex>
+
+#include <seqan/basic.h>
+#include <seqan/sequence.h>
+#include <seqan/version.h>
+#include <seqan/align.h>
+#include <seqan/score.h>
+
+#include "blast/blast_base.h"
+#include "blast/blast_tabular_lowlevel.h"
+#include "blast/blast_record.h"
+#include "blast/blast_tabular.h"
+#include "blast/blast_io_context.h"
+#include "blast/blast_statistics.h"
+#include "blast/blast_tabular_in.h"
+#include "blast/blast_tabular_out.h"
+#include "blast/blast_report_out.h"
+
+#else //SEQAN_CXX11_COMPLETE
+
+#error The blast module requires C++11 support. \
+If your compiler supports C++11, please define SEQAN_CXX11_STANDARD
+
+#endif //SEQAN_CXX11_COMPLETE
+
+#endif
diff --git a/seqan/blast/blast_base.h b/seqan/blast/blast_base.h
new file mode 100644
index 0000000..14ed4fe
--- /dev/null
+++ b/seqan/blast/blast_base.h
@@ -0,0 +1,426 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Module for handling NCBI Blast I/O and E-Value computation
+// ==========================================================================
+
+#ifndef SEQAN_EXTRAS_BLAST_BLAST_BASE_H_
+#define SEQAN_EXTRAS_BLAST_BLAST_BASE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Enum BlastProgram
+// ----------------------------------------------------------------------------
+
+/*!
+ * @enum BlastProgram
+ * @brief Enum with BLAST program spec
+ * @signature enum class BlastProgram : __uint8 { ... };
+ *
+ * @headerfile <seqan/blast.h>
+ * @see BlastProgramSelector
+ *
+ * @val BlastProgram BlastProgram::BLASTN
+ * @brief Nucleotide Query VS Nucleotide Subject
+ *
+ * @val BlastProgram BlastProgram::BLASTP
+ * @brief Protein Query VS Protein Subject
+ *
+ * @val BlastProgram BlastProgram::BLASTX
+ * @brief translated Nucleotide Query VS Protein Subject
+ *
+ * @val BlastProgram BlastProgram::TBLASTN
+ * @brief Protein Query VS translated Nucleotide Subject
+ *
+ * @val BlastProgram BlastProgram::TBLASTX
+ * @brief translated Nucleotide Query VS translated Nucleotide Subject
+ *
+ * @val BlastProgram BlastProgram::UNKNOWN
+ * @brief Unkown type. Used to signify that the type could not be inferred from the file.
+ *
+ * @val BlastProgram BlastProgram::DYNAMIC
+ * @brief This can only be used when defining a @link BlastProgramSelector @endlink
+ *
+ */
+enum class BlastProgram : __uint8
+{
+    BLASTN,         //              NUCL VS             NUCL
+    BLASTP,         //              PROT VS             PROT
+    BLASTX,         // TRANSLATED   NUCL VS             PROT
+    TBLASTN,        //              PROT VS TRANSLATED  NUCL
+    TBLASTX,        // TRANSLATED   NUCL VS TRANSLATED  NUCL
+    UNKNOWN=254,
+    DYNAMIC=255
+};
+
+/*!
+ * @class BlastProgramSelector
+ * @brief A datatype that can act as either a @link BlastProgram @endlink or as an constexpr integral constant
+ * thereof.
+ *
+ * @signature template <BlastProgram p> struct BlastProgramSelector { ... };
+ * @headerfile <seqan/blast.h>
+ *
+ * This is a proxy datatype that enables compile-time optimizations through constexpressions iff the value
+ * is known at compile time. You will rarely need to instantiate objects of this type yourself, but they
+ * are used in the @link BlastIOContext @endlink.
+ *
+ * The interface functions work on regular enum values of @link BlastProgram @endlink, as well, but are
+ * gathered here for convenience.
+ *
+ * Please note that the default value for <tt>BlastProgramSelector<BlastProgram::DYNAMIC></tt> is
+ * <tt>BlastProgram::UNKNOWN</tt>, not <tt>BlastProgram::DYNAMIC</tt>.
+ *
+ * @subsection Example
+ *
+ * mutable variable:
+ * @code{.cpp}
+ * BlastProgramSelector<BlastProgram::DYNAMIC> myProgram = BlastProgram::BLASTN;
+ * // same as:
+ * // BlastProgram myProgram = BlastProgram::BLASTN;
+ *
+ * SEQAN_ASSERT(myProgram == BlastProgram::BLASTN); // assertion is checked at run-time
+ * myProgram = BlastProgram::BLASTP; // works without problems
+ * @endcode
+ *
+ * compile time integral constant:
+ * @code{.cpp}
+ * BlastProgramSelector<BlastProgram::BLASTN> myProgram;
+ * static_assert(myProgram == BlastProgram::BLASTN, ""); // assertion is checked at compile time
+ * myProgram = BlastProgram::BLASTP; // would fail, because value is fixed (and different)
+ * @endcode
+ */
+template <BlastProgram _p>
+struct BlastProgramSelector
+{
+    constexpr operator BlastProgram() const
+    {
+        return _p;
+    }
+
+    BlastProgramSelector operator=(BlastProgram const p)
+    {
+        if (p != _p)
+            SEQAN_FAIL("ERROR: Tried to set blastProgram on context, but was already defined at compile time (and set to a "
+                       "different value)!");
+        return *this;
+    }
+};
+
+template <>
+struct BlastProgramSelector<BlastProgram::DYNAMIC>
+{
+    BlastProgram _runtimeValue = BlastProgram::UNKNOWN;
+
+    operator BlastProgram() const
+    {
+        return _runtimeValue;
+    }
+
+    BlastProgramSelector operator=(BlastProgram const p)
+    {
+        _runtimeValue = p;
+        return *this;
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// qHasRevComp()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastProgramSelector#qHasRevComp
+ * @brief Whether the reverse complement of the <b>query</b> sequence(s) is searched with the given BlastProgram
+ * @signature constexpr bool qHasRevComp(BlastProgram const p);
+ *
+ * @return false for @link BlastProgram::BLASTP @endlink and @link BlastProgram::TBLASTN @endlink
+ * @return true otherwise
+ * @headerfile <seqan/blast.h>
+ */
+
+constexpr bool
+qHasRevComp(BlastProgram const p)
+{
+    return (!(p==BlastProgram::BLASTP) || (p==BlastProgram::TBLASTN));
+}
+
+// ----------------------------------------------------------------------------
+// qIsTranslated()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastProgramSelector#qIsTranslated
+ * @brief Whether the <b>query</b> sequence is translated in the given BlastProgram
+ * @signature constexpr bool qIsTranslated(BlastProgram const p);
+ *
+ * @return true for @link BlastProgram::BLASTX @endlink and @link BlastProgram::TBLASTX @endlink
+ * @return false otherwise
+ * @headerfile <seqan/blast.h>
+ */
+
+constexpr bool
+qIsTranslated(BlastProgram const p)
+{
+    return ((p==BlastProgram::BLASTX) || (p==BlastProgram::TBLASTX));
+}
+
+// ----------------------------------------------------------------------------
+// qNumFrames()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastProgramSelector#qNumFrames
+ * @brief The number of frames per <b>query</b> sequence implied by the given BlastProgram
+ * @signature constexpr __uint8 qNumFrames(BlastProgram const p);
+ *
+ * @return 6 for @link BlastProgram::BLASTX @endlink and @link BlastProgram::TBLASTX @endlink
+ * @return 2 for @link BlastProgram::BLASTN @endlink
+ * @return 1 for @link BlastProgram::BLASTP @endlink and @link BlastProgram::TBLASTN @endlink
+ * @headerfile <seqan/blast.h>
+ */
+
+constexpr __uint8
+qNumFrames(BlastProgram p)
+{
+    return (qIsTranslated(p) ? 6 : (qHasRevComp(p) ? 2 : 1));
+}
+
+// ----------------------------------------------------------------------------
+// sHasRevComp()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastProgramSelector#sHasRevComp
+ * @brief Whether the reverse complement of the <b>subject</b> sequence(s) is searched with the given BlastProgram
+ * @signature constexpr bool sHasRevComp(BlastProgram const p);
+ *
+ * @return true for @link BlastProgram::TBLASTX @endlink and @link BlastProgram::TBLASTN @endlink
+ * @return false otherwise
+ * @headerfile <seqan/blast.h>
+ */
+
+constexpr bool
+sHasRevComp(BlastProgram const p)
+{
+    return ((p==BlastProgram::TBLASTX) || (p==BlastProgram::TBLASTN));
+}
+
+// ----------------------------------------------------------------------------
+// sIsTranslated()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastProgramSelector#sIsTranslated
+ * @brief Whether the <b>subject</b> sequence is translated in the given BlastProgram
+ * @signature constexpr bool sIsTranslated(BlastProgram const p);
+ *
+ * @return true for @link BlastProgram::TBLASTX @endlink and @link BlastProgram::TBLASTN @endlink
+ * @return false otherwise
+ * @headerfile <seqan/blast.h>
+ */
+
+constexpr bool
+sIsTranslated(BlastProgram const p)
+{
+    return ((p==BlastProgram::TBLASTX) || (p==BlastProgram::TBLASTN));
+}
+
+// ----------------------------------------------------------------------------
+// sNumFrames()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastProgramSelector#sNumFrames
+ * @brief The number of frames per <b>query</b> sequence implied by the given BlastProgram
+ * @signature constexpr __uint8 sNumFrames(BlastProgram const p);
+ *
+ * @return 6 for @link BlastProgram::TBLASTX @endlink and @link BlastProgram::TBLASTN @endlink
+ * @return 1 otherwise
+ * @headerfile <seqan/blast.h>
+ */
+
+constexpr __uint8
+sNumFrames(BlastProgram p)
+{
+    return (sIsTranslated(p) ? 6 : (sHasRevComp(p) ? 2 : 1));
+}
+
+// ----------------------------------------------------------------------------
+// _programTagToString()
+// ----------------------------------------------------------------------------
+
+template <typename TVoidSpec = void>
+struct BlastProgramStrings_
+{
+    static constexpr char const * const VALUE [] =
+    {
+        "BLASTN",
+        "BLASTP",
+        "BLASTX",
+        "TBLASTN",
+        "TBLASTX",
+        "UNKOWN BLAST PROGRAM"
+    };
+};
+
+template <typename TVoidSpec>
+constexpr char const * const BlastProgramStrings_<TVoidSpec>::VALUE[6];
+
+constexpr const char *
+_programTagToString(BlastProgram const _p)
+{
+    return (__uint8(_p) < 5) ? BlastProgramStrings_<>::VALUE[__uint8(_p)] : BlastProgramStrings_<>::VALUE[5];
+}
+
+// ----------------------------------------------------------------------------
+// _programStringToTag()
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+inline BlastProgram
+_programStringToTag(TString const & str)
+{
+    for (__uint8 i = 0; i < 5; ++i)
+        if (str == BlastProgramStrings_<>::VALUE[i])
+            return BlastProgram(i);
+
+    return BlastProgram::UNKNOWN;
+}
+
+// ----------------------------------------------------------------------------
+// Function _untranslatePositions() -- retransform positions
+// ----------------------------------------------------------------------------
+
+template <typename TPos>
+inline void
+_untranslatePositions(TPos & effectiveStart,
+                      TPos & /**/,
+                      signed char const /**/,
+                      TPos const & /**/,
+                      False const & /*hasReverseComplement*/,
+                      False const & /*hasFrames*/)
+{
+    // BLAST is 1-indexed, but end positions are "on" instead of behind
+    // so only the begin positions need adapting
+    ++effectiveStart;
+}
+
+template <typename TPos>
+inline void
+_untranslatePositions(TPos & effectiveStart,
+                      TPos & effectiveEnd,
+                      signed char const frameShift,
+                      TPos const & length,
+                      True const & /*hasReverseComplement*/,
+                      False const & /*hasFrames*/)
+{
+    if (frameShift > 0)
+    {
+        // BLAST is 1-indexed, but end positions are "on" instead of behind
+        // so only the begin positions need adapting
+        ++effectiveStart;
+    } else
+    {
+        // reverse strand coordinates have to be transformed
+        effectiveStart = length - effectiveStart;
+        effectiveEnd = length - effectiveEnd + 1;
+        // end is incremented instead of start
+    }
+}
+
+template <typename TPos>
+inline void
+_untranslatePositions(TPos & effectiveStart,
+                      TPos & effectiveEnd,
+                      signed char const frameShift,
+                      TPos const & length,
+                      True const & /*hasReverseComplement*/,
+                      True const & /*hasFrames*/)
+{
+    // correct for codon translation and frameshift
+    // subtract 1 because frameshift is 1-indexed
+    effectiveStart = effectiveStart * 3 + std::abs(frameShift) - 1;
+    effectiveEnd = effectiveEnd * 3 + std::abs(frameShift) - 1;
+
+    _untranslatePositions(effectiveStart, effectiveEnd, frameShift,
+                          length, True(), False());
+}
+
+template <typename TPos, BlastProgram p>
+inline void
+_untranslateQPositions(TPos & effectiveStart,
+                      TPos & effectiveEnd,
+                      int8_t const frameShift,
+                      TPos const & length,
+                      BlastProgramSelector<p> const & selector)
+{
+     if (qIsTranslated(selector))
+         _untranslatePositions(effectiveStart, effectiveEnd, frameShift, length, True(), True());
+     else if (qHasRevComp(selector))
+         _untranslatePositions(effectiveStart, effectiveEnd, frameShift, length, True(), False());
+     else
+        _untranslatePositions(effectiveStart, effectiveEnd, frameShift, length, False(), False());
+}
+
+template <typename TPos, BlastProgram p>
+inline void
+_untranslateSPositions(TPos & effectiveStart,
+                      TPos & effectiveEnd,
+                      int8_t const frameShift,
+                      TPos const & length,
+                      BlastProgramSelector<p> const & selector)
+{
+     if (sIsTranslated(selector))
+         _untranslatePositions(effectiveStart, effectiveEnd, frameShift, length, True(), True());
+     else if (sHasRevComp(selector))
+         _untranslatePositions(effectiveStart, effectiveEnd, frameShift, length, True(), False());
+     else
+        _untranslatePositions(effectiveStart, effectiveEnd, frameShift, length, False(), False());
+}
+
+} // namespace seqan
+
+#endif // header guard
diff --git a/seqan/blast/blast_io_context.h b/seqan/blast/blast_io_context.h
new file mode 100644
index 0000000..0f91784
--- /dev/null
+++ b/seqan/blast/blast_io_context.h
@@ -0,0 +1,286 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// This file contains the BlastIOContext's code
+// ==========================================================================
+
+#ifndef SEQAN_BLAST_BLAST_IO_CONTEXT_H__
+#define SEQAN_BLAST_BLAST_IO_CONTEXT_H__
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TScore>
+struct BlastScoringScheme;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Mfn BlastIOContextStringType_
+// ----------------------------------------------------------------------------
+
+template <typename TContext>
+struct BlastIOContextStringType_
+{
+    typedef std::string Type;
+};
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class BlastIOContext
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastIOContext
+ * @headerfile <seqan/blast.h>
+ * @signature template <typename TScore_ = Blosum62,
+ * BlastProgram p = BlastProgram::UNKNOWN, BlastTabularSpec h = BlastTabularSpec::UNKNOWN>
+ * struct BlastIOContext { ... };
+ *
+ * @brief An object that holds file global information and buffers for BlastIO
+ *
+ * @tparam TScore   Type of the @link Score @endlink object used.
+ * @tparam p        @link BlastProgram @endlink as compile-time parameter.
+ * @tparam h        @link BlastTabularSpec @endlink as compile-time parameter.
+ *
+ * This is a part of the Blast formatted files. Before writing, some of the context's members should be set; after
+ * reading it will contain
+ * all information from the file that did not belong to a @link BlastRecord @endlink, e.g. the name of the database.
+ * It also contains buffers for internal use.
+ *
+ * You should re-use this object (i.e. only create it once for
+ * every file that you read/write). And you don't need to and should not clear()
+ * this, except when restarting IO on a different file.
+ *
+ * To speed-up file writing slightly you can set the value template parameters <tt>p</tt> and/or <tt>h</tt> to something
+ * other than ::DYNAMIC at compile-time (e.g. if you know that you will be printing only BLASTX), but then you won't
+ * be able to modify these values at run-time. For file reading this is also possible, but usually the
+ * added flexibility of automatically detecting these values is prefferable.
+ *
+ * If not explicitly stated otherwise, the member variables are <i>out-parameters</i> of <tt>readHeader()</tt>,
+ * <tt>readRecord()</tt> and <tt>readFooter()</tt>, i.e. they are set by these functions; and they are
+ * <i>in-parameters</i> to  <tt>writeHeader()</tt>, <tt>writeRecord()</tt> and <tt>writeFooter()</tt>, i.e. they
+ * influence these functions' output.
+ *
+ * See @link BlastTabularFileOut @endlink and @link BlastReportFileOut @endlink for more complete examples of usage.
+ */
+
+template <typename TScore_ = Blosum62,
+          BlastProgram p = BlastProgram::DYNAMIC,
+          BlastTabularSpec h = BlastTabularSpec::DYNAMIC>
+struct BlastIOContext
+{
+    typedef TScore_ TScore;
+    typedef typename BlastIOContextStringType_<BlastIOContext>::Type TString;
+
+    /*!
+     * @var BlastProgramSelector BlastIOContext::blastProgram;
+     * @brief The @link BlastProgram @endlink.
+     *
+     * @section Remarks
+     *
+     * Behaves exactly like an enum of type @link BlastProgram @endlink, unless the second template parameter was
+     * specified to make this a compile-time constant. See @link BlastProgramSelector @endlink for more information.
+     */
+    BlastProgramSelector<p> blastProgram;
+
+    /*!
+     * @var BlastTabularSpecSelector BlastIOContext::tabularSpec;
+     * @brief The @link BlastTabularSpec @endlink.
+     *
+     * @section Remarks
+     *
+     * Behaves exactly like an enum of type @link BlastTabularSpec @endlink, unless the third template parameter was
+     * specified to make this a compile-time constant. See @link BlastTabularSpecSelector @endlink for more information.
+     */
+    BlastTabularSpecSelector<h> tabularSpec;
+
+    /*!
+     * @var BlastScoringScheme<TScore> BlastIOContext::scoringScheme;
+     * @brief The @link BlastScoringScheme @endlink.
+     */
+    BlastScoringScheme<TScore> scoringScheme;
+
+    /*!
+     * @var TString BlastIOContext::versionString;
+     * @brief The blast version string.
+     *
+     * @section Remarks
+     *
+     * Used when writing @link BlastReportFileOut @endlink and @link BlastTabularFileOut @endlink if the context's tabularSpec
+     * is set to BlastTabularSpec::COMMENTS. Defaults to a version string based on the emulated
+     * blast version and the current SeqAn version.
+     * When reading from @link BlastTabularFileOut @endlink the corresponding line is extracted from the comment lines
+     * (if present).
+     */
+    TString versionString;
+    void _setDefaultVersionString()
+    {
+        clear(versionString);
+        append(versionString, _programTagToString(blastProgram));
+        append(versionString, " 2.2.26");
+        if (!legacyFormat)
+            append(versionString, "+");
+        append(versionString, " [I/O Module of SeqAn-");
+        append(versionString, std::to_string(SEQAN_VERSION_MAJOR));
+        append(versionString, '.');
+        append(versionString, std::to_string(SEQAN_VERSION_MINOR));
+        append(versionString, '.');
+        append(versionString, std::to_string(SEQAN_VERSION_PATCH));
+        append(versionString, ", http://www.seqan.de]");
+    }
+
+    /*!
+     * @var bool BlastIOContext::legacyFormat;
+     * @brief Whether to use the legacy format (only @link BlastTabular @endlink).
+     *
+     * @section Remarks
+     *
+     * Setting this flag when writing to a @link BlastTabularFileOut @endlink (that has BlastTabularSpec::COMMENTS set)
+     * will result in the legacy version of the comments being written. In the legacy format the mismatches column
+     * also includes all gaps in addition to mismatches.
+     * Note that many other features like custom fields are not supported in this format.
+     *
+     * When reading @link BlastTabularFileOut @endlink this flag will automatically be set based on the comments (if a
+     * they exist).
+     */
+    bool legacyFormat = false;
+
+    /*!
+     * @var TString BlastIOContext::dbName;
+     * @brief Name of the dabase or path to the file.
+     */
+    TString         dbName;
+
+    /*!
+     * @var __uint64 BlastIOContext::dbTotalLength;
+     * @brief Summed up sequence length of the database.
+     */
+    __uint64        dbTotalLength = 0u;
+
+    /*!
+     * @var __uint64 BlastIOContext::dbNumberOfSeqs;
+     * @brief Number of sequences in the database.
+     */
+    __uint64        dbNumberOfSeqs = 0u;
+
+    /*!
+     * @var StringSet<TString> BlastIOContext::otherLines;
+     * @brief A StringSet that will contain all comment lines that
+     * could not be interpreted in another way (only @link BlastTabularFileIn @endlink).
+     */
+    StringSet<TString, Owner<ConcatDirect<>>> otherLines;
+
+    /*!
+     * @var std::vector<BlastMatchField::Enum> BlastIOContext::fields;
+     * @brief The fields (types of columns) in @link BlastTabular @endlink-formats.
+     *
+     * @section Remarks
+     *
+     * This is an <i>out-parameter</i> for:
+     * <li> @link BlastTabularFileIn#readRecord @endlink iff tabularSpec == COMMENTS (otherwise it can't be deduced)</li>
+     *
+     * This is an <i>in-parameter</i> for:
+     * <li> @link BlastTabularFileIn#readRecord @endlink if tabularSpec != COMMENTS (specified fields will be expected)</li>
+     * <li> @link BlastTabularFileOut#writeRecord @endlink (specified fields will written)
+     *
+     * Setting @link BlastIOContext::ignoreFieldsInComments @endlink will make this variable be an <i>in-parameter</i> for
+     * the first case, as well. This variable is ignored in the legacy formats and for non-tabular formats.
+     */
+    std::vector<typename BlastMatchField<>::Enum> fields = { BlastMatchField<>::Enum::STD };
+
+    /*!
+     * @var StringSet<TString> BlastIOContext::fieldsAsStrings;
+     * @brief The fields (types of columns) in @link BlastTabular @endlink-formats, but as uninterpreted strings.
+     *
+     * @section Remarks
+     *
+     * Useful when the comment lines do not conform to standards and you want to extract the verbatim column labels or
+     * if you wish to print non-standard column labels (which you shouldn't!).
+     */
+    StringSet<TString, Owner<ConcatDirect<>>> fieldsAsStrings;
+
+    /*!
+     * @var bool BlastIOContext::ignoreFieldsInComments;
+     * @brief Use fields as in-parameter for readRecord as well (only @link BlastTabularFileIn @endlink).
+     *
+     * @section Remarks
+     *
+     * See @link BlastTabularFileIn#readRecord @endlink. Use this when the comment lines do not
+     * conform to standards (and the fields can't be read), but you know that
+     * the matches are in the given, e.g. default format.
+     */
+    bool ignoreFieldsInComments = false;
+
+    /*!
+     * @var StringSet<TString> BlastIOContext::conformancyErrors;
+     * @brief Holds non fatal error messages when reading from @link BlastTabularFileIn @endlink.
+     *
+     * @section Remarks
+     *
+     * After doing a @link BlastTabularFileIn#readRecord @endlink this will indicate whether the
+     * comment lines contained non-fatal parse errors, usually the result
+     * of a file written by a sloppy blast implementation or possibly a bug in SeqAn.
+     * An empty StringSet indicates that all is good.
+     */
+    StringSet<TString, Owner<ConcatDirect<>>> conformancyErrors;
+
+    // ------- CACHES, BUFFERS and INTERNALS --------- //
+
+    // counted internally for TabularFooter
+    __uint64 _numberOfRecords = 0;
+
+    // cache for length adjustments in blast statistics
+    std::unordered_map<__uint64, __uint64> _cachedLengthAdjustments;
+
+    // io-buffers
+    TString _lineBuffer; // holds the current line
+    TString _stringBuffer;
+    StringSet<TString, Owner<ConcatDirect<>>> _setBuffer1;
+    StringSet<TString, Owner<ConcatDirect<>>> _setBuffer2;
+    BlastMatch<> bufMatch;
+    BlastRecord<> bufRecord;
+};
+
+}
+
+#endif
diff --git a/seqan/blast/blast_record.h b/seqan/blast/blast_record.h
new file mode 100644
index 0000000..e76beaa
--- /dev/null
+++ b/seqan/blast/blast_record.h
@@ -0,0 +1,395 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Module for handling NCBI Blast I/O and E-Value computation
+// ==========================================================================
+
+#ifndef SEQAN_EXTRAS_BLAST_BLAST_RECORD_H_
+#define SEQAN_EXTRAS_BLAST_BLAST_RECORD_H_
+
+namespace seqan
+{
+
+/*!
+ * @class BlastMatch
+ * @implements AssignableConcept
+ * @implements CopyConstructibleConcept
+ * @implements DefaultConstructibleConcept
+ * @implements EqualityComparableConcept
+ * @implements LessThanComparableConcept
+ * @headerfile <seqan/blast.h>
+ * @signature struct BlastMatch<TAlign, TPos, TQId, TSId> { ... };
+ * @brief An data structure to hold a blast match, also known as high-scoring segment pair (HSP)
+ *
+ * You should set the following members manually: @link BlastMatch::qId @endlink, @link BlastMatch::sId @endlink,
+ * @link BlastMatch::qLength @endlink, @link BlastMatch::sLength @endlink,
+ * @link BlastMatch::qFrameShift @endlink and @link BlastMatch::sFrameShift @endlink.
+ *
+ * If you then also set valid alignRow-members (@link BlastMatch::alignRow0 @endlink, 
+ * @link BlastMatch::alignRow1 @endlink), you can let the other members be computed by
+ * @link BlastMatch#computeAlignmentStats @endlink and
+ * @link BlastMatch#computeBitScore @endlink, @link BlastMatch#computeEValue @endlink.
+ *
+ * @tparam TAlignRow0 Type of the first alignment row, usually @link Gaps @endlink
+ * @tparam TAlignRow1 Type of the second alignment row, usually @link Gaps @endlink
+ * @tparam TPos   Position type of the sequences, defaults to <tt>__uint32</tt>
+ * @tparam TQId   Type of qId, defaults to std::string
+ * @tparam TSId   Type of sId, defaults to std::string
+ */
+
+template <typename TAlignRow0_ = Gaps<CharString, ArrayGaps>,
+          typename TAlignRow1_ = Gaps<CharString, ArrayGaps>,
+          typename TPos_ = __uint32,
+          typename TQId_ = std::string,
+          typename TSId_ = std::string>
+struct BlastMatch
+{
+    typedef TAlignRow0_ TAlignRow0;
+    typedef TAlignRow1_ TAlignRow1;
+    typedef TPos_ TPos;
+    typedef TQId_ TQId;
+    typedef TSId_ TSId;
+
+    // internal use numerical ids
+    __uint32 _n_qId;
+    __uint32 _n_sId;
+
+    /*!
+     * @var TQId BlastMatch::qId;
+     * @brief The verbose Id of the query.
+     *
+     * @var TSId BlastMatch::sId;
+     * @brief The verbose Id of the subject.
+     */
+    TQId            qId;
+    TSId            sId;
+
+    /*!
+     * @var TPos BlastMatch::qStart;
+     * @brief The start of the alignment on the (possibly translated) query sequence.
+     *
+     * @var TPos BlastMatch::qEnd;
+     * @brief The end of the alignment on the (possibly translated) query sequence.
+     *
+     * @var TPos BlastMatch::sStart;
+     * @brief The start of the alignment on the (possibly translated) subject sequence.
+     *
+     * @var TPos BlastMatch::sEnd;
+     * @brief The end of the alignment on the (possibly translated) subject sequence.
+     */
+    TPos            qStart        = 0;
+    TPos            qEnd          = 0;
+    TPos            sStart        = 0;
+    TPos            sEnd          = 0;
+
+    /*!
+     * @var TPos BlastMatch::qLength;
+     * @brief The length of the original query sequence (possibly before translation).
+     *
+     * @var TPos BlastMatch::sLength;
+     * @brief The length of the original subject sequence (possibly before translation).
+     */
+    TPos            qLength       = 0;
+    TPos            sLength       = 0;
+    /*!
+     * @var char BlastMatch::qFrameShift;
+     * @brief An indicator for query frame and query strand.
+     *
+     * one out of { -3, -2, -1, +1, +2, +3 } where the <tt>absolute value - 1</tt> is
+     * the shift of the translation frame and a negative sign indicates the reverse
+     * complement strand [query sequence, only applies for BlastFormatProgram ==
+     * BLASTX | TBLASTX]; -1 implies reverse complement for BLASTN.
+     *
+     * @var char BlastMatch::sFrameShift;
+     * @brief An indicator for subject frame and subject strand.
+     *
+     * one out of { -3, -2, -1, +1, +2, +3 } where the <tt>absolute value - 1</tt> is
+     * the shift of the translation frame and a negative sign indicates the reverse
+     * complement strand [subject sequence, only applies for BlastFormatProgram ==
+     * TBLASTN | TBLASTX].
+     */
+    __int8          qFrameShift   = 1;
+    __int8          sFrameShift   = 1;
+
+    /*!
+     * @var double BlastMatch::eValue;
+     * @brief The e-value of the alignment.
+     *
+     * @var double BlastMatch::bitScore;
+     * @brief The bit-score of the alignment.
+     */
+    double          eValue        = 0;
+    double          bitScore      = 0;
+
+    /*!
+     * @var AlignmentStats BlastMatch::alignStats
+     * @brief An @link AlignmentStats @endlink object holding further stats of the alignment.
+     */
+    AlignmentStats  alignStats;
+
+    /*!
+     * @var TAlign BlastMatch::alignRow0;
+     * @brief First alignment row (@link Gaps @endlink object).
+     *
+     * @var TAlign BlastMatch::alignRow1;
+     * @brief Second alignment row (@link Gaps @endlink object).
+     */
+    TAlignRow0      alignRow0;
+    TAlignRow1      alignRow1;
+
+    /*!
+     * @fn BlastMatch::BlastMatch()
+     * @brief Constructor, can be called with arguments for qId and sId.
+     * @signature BlastMatch::BlastMatch()
+     * BlastMatch::BlastMatch(qId, sId)
+     */
+    BlastMatch() :
+        qId(TQId()), sId(TSId())
+    {}
+
+    BlastMatch(TQId const & _qId, TSId const & _sId) :
+        qId(_qId), sId(_sId)
+    {}
+
+    BlastMatch(TQId && _qId, TSId && _sId) :
+        qId(std::move(_qId)), sId(std::move(_sId))
+    {}
+
+    inline bool operator==(BlastMatch const & bm2) const
+    {
+        return std::tie(qId,
+                        sId,
+                        qStart,
+                        qEnd,
+                        sStart,
+                        sEnd,
+                        qLength,
+                        sLength,
+// gaps too expensive too to compare
+                        qFrameShift,
+                        sFrameShift
+//                         alignStats
+// scores have rounding errors
+//                         eValue,
+//                         bitScore
+                       )
+            == std::tie(bm2.qId,
+                        bm2.sId,
+                        bm2.qStart,
+                        bm2.qEnd,
+                        bm2.sStart,
+                        bm2.sEnd,
+                        bm2.qLength,
+                        bm2.sLength,
+// gaps too expensive too to compare
+                        bm2.qFrameShift,
+                        bm2.sFrameShift
+//                         bm2.alignStats
+// scores have rounding errors
+//                         bm2.eValue,
+//                         bm2.bitScore
+                       );
+    }
+
+    // copy, move and assign implicitly
+
+    /*!
+     * @fn BlastMatch::operator<
+     * @brief The comparison operator (for sorting by bit-score).
+     * @signature bool BlastMatch::operator< (BlastMatch const & bm2) const
+     *
+     * To facilitate fast sorting of matches in a @link BlastRecord @endlink, only the bit-score is compared. Also
+     * large bit-score are sorted to front (i.e. operator< on BlastMatch checks operator>= on the bitScores).
+     */
+
+    inline bool operator< (BlastMatch const & bm2) const
+    {
+        return (bitScore >= bm2.bitScore);
+    }
+
+    inline void _clear()
+    {
+        clear(qId);
+        clear(sId);
+
+        qStart        = 0;
+        qEnd          = 0;
+        sStart        = 0;
+        sEnd          = 0;
+        qLength       = 0;
+        sLength       = 0;
+
+        eValue        = 0;
+        bitScore      = 0;
+        qFrameShift   = 1;
+        sFrameShift   = 1;
+        clear(alignStats);
+        clear(alignRow0);
+        clear(alignRow1);
+    }
+
+    inline void _maxInitialize()
+    {
+        qId           = "not init";
+        sId           = "not init";
+
+        qStart        = std::numeric_limits<TPos>::max();
+        qEnd          = std::numeric_limits<TPos>::max();
+        sStart        = std::numeric_limits<TPos>::max();
+        sEnd          = std::numeric_limits<TPos>::max();
+
+        qLength       = std::numeric_limits<TPos>::max();
+        sLength       = std::numeric_limits<TPos>::max();
+
+        eValue        = std::numeric_limits<double>::max();
+        bitScore      = std::numeric_limits<double>::max();
+
+        qFrameShift   = std::numeric_limits<int8_t>::max();
+        sFrameShift   = std::numeric_limits<int8_t>::max();
+
+        alignStats.numGaps              = std::numeric_limits<unsigned>::max();
+        alignStats.numGapOpens          = std::numeric_limits<unsigned>::max();
+        alignStats.numGapExtensions     = std::numeric_limits<unsigned>::max();
+        alignStats.numInsertions        = std::numeric_limits<unsigned>::max();
+        alignStats.numDeletions         = std::numeric_limits<unsigned>::max();
+        alignStats.numMatches           = std::numeric_limits<unsigned>::max();
+        alignStats.numMismatches        = std::numeric_limits<unsigned>::max();
+        alignStats.numPositiveScores    = std::numeric_limits<unsigned>::max();
+        alignStats.numNegativeScores    = std::numeric_limits<unsigned>::max();
+        alignStats.alignmentLength      = std::numeric_limits<unsigned>::max();
+        alignStats.alignmentSimilarity  = std::numeric_limits<float>::max();
+        alignStats.alignmentIdentity    = std::numeric_limits<float>::max();
+        alignStats.alignmentScore       = std::numeric_limits<unsigned>::max();
+
+        clear(alignRow0);
+        clear(alignRow1);
+    }
+};
+
+inline bool
+_memberIsSet(CharString const & in)
+{
+    return (in != "not init");
+}
+
+template <typename TNumber>
+inline SEQAN_FUNC_ENABLE_IF(Is<NumberConcept<TNumber> >, bool)
+_memberIsSet(TNumber const & in)
+{
+    return (in != std::numeric_limits<TNumber>::max());
+}
+
+template <typename TAlignRow0,
+          typename TAlignRow1,
+          typename TPos,
+          typename TQId,
+          typename TSId>
+inline void
+clear(BlastMatch<TAlignRow0, TAlignRow1, TPos, TQId, TSId> & match)
+{
+    match._clear();
+}
+
+/*!
+ * @class BlastRecord
+ * @implements FormattedFileRecordConcept
+ * @headerfile <seqan/blast.h>
+ * @signature struct BlastRecord<TMatch> { ... };
+ * @brief A record of blast-matches (belonging to one query).
+ *
+ * @tparam TMatch Specialization of @link BlastMatch @endlink
+ */
+
+template <typename TBlastMatch_ = BlastMatch<>>
+struct BlastRecord
+{
+    /*!
+     * @typedef BlastRecord::TBlastMatch
+     * @signature typedef TBlastMatch_ TBlastMatch;
+     * @brief type of the contained matches
+     */
+    typedef TBlastMatch_                TBlastMatch;
+    typedef typename TBlastMatch::TQId  TQId;
+    typedef typename TBlastMatch::TPos  TPos;
+
+    /*!
+     * @var TQId BlastRecord::qId;
+     * @brief verbose Id of the query
+     */
+    TQId            qId;
+
+    /*!
+     * @var TPos BlastRecord::qLength;
+     * @brief length of the query sequence
+     */
+    TPos            qLength;
+
+    /*!
+     * @var std::list<TBlastMatch> BlastRecord::matches;
+     * @brief list of the contained matches
+     */
+    std::list<TBlastMatch>  matches;
+
+    /*!
+     * @fn BlastRecord::BlastRecord()
+     * @brief constructor, can be passed the qId
+     * @signature BlastRecord::BlastRecord()
+     * BlastRecord::BlastRecord(qid)
+     */
+    BlastRecord() :
+        qId(TQId()), qLength(0), matches()
+    {}
+
+    BlastRecord(TQId const & _qId) :
+        qId(_qId), qLength(0), matches()
+    {}
+
+    BlastRecord(TQId && _qId) :
+        qId(std::move(_qId)), qLength(0), matches()
+    {}
+
+    // copy, move and assign implicitly
+};
+
+template <typename TMatch>
+inline void
+clear(BlastRecord<TMatch> & blastRecord)
+{
+    clear(blastRecord.qId);
+    blastRecord.qLength = 0;
+    clear(blastRecord.matches);
+}
+
+}
+
+#endif // SEQAN_EXTRAS_BLAST_BLAST_RECORD_H_
diff --git a/seqan/blast/blast_report_out.h b/seqan/blast/blast_report_out.h
new file mode 100644
index 0000000..56ce3f7
--- /dev/null
+++ b/seqan/blast/blast_report_out.h
@@ -0,0 +1,835 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// This file contains routines to generate BLAST default output
+// ==========================================================================
+
+#ifndef SEQAN_EXTRAS_BLAST_WRITE_BLAST_REPORT_H_
+#define SEQAN_EXTRAS_BLAST_WRITE_BLAST_REPORT_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag BlastReport
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastReport
+ * @signature typedef Tag<BlastReport_> BlastReport;
+ * @headerfile <seqan/blast.h>
+ * @brief Support for Blast default file format
+ *
+ * There are three blast format related tags in SeqAn:
+ *
+ * <li> @link BlastReport @endlink with the FormattedFile output specialization @link BlastReportFileOut @endlink</li>
+ * <li> @link BlastTabular @endlink with the FormattedFile output and input specializations
+ * @link BlastTabularFileOut @endlink and @link BlastTabularFileIn @endlink</li>
+ * <li> @link BlastTabularLL @endlink which provides light-weight, but very basic tabular IO </li>
+ *
+ * This is the first tag, it represents support for Blast's default file format (<tt>blastall -m 0</tt> / <tt>blast*
+ * -outfmt 0</tt>).
+ * Only support for writing is available, see the example below.
+ *
+ * The reference Blast implementation used for developing the SeqAn support is NCBI Blast+ 2.2.26. In contrast to the
+ * tabular format there is no support for writing legacy files (without the +).
+ *
+ * See @link BlastReportFileOut @endlink for more details.
+ */
+
+struct BlastReport_;
+typedef Tag<BlastReport_> BlastReport;
+
+// ----------------------------------------------------------------------------
+// Tag BlastReportFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastReportFileOut
+ * @signature template <typename TBlastIOContext = BlastIOContext<>>
+ * using BlastReportFileOut = FormattedFile<BlastReport, Output, TBlastIOContext>;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/blast.h>
+ * @brief FormattedFileOut abstraction for @link BlastReport @endlink
+ *
+ * This is a @link FormattedFile @endlink specialization for writing @link BlastReport @endlink formats. For details
+ * on how to influence the writing of files, see @link BlastIOContext @endlink.
+ * Please note that you have to specify the type of the context as a template parameter to BlastReportFileOut.
+ *
+ * @section Overview
+ *
+ * <ul>
+ * <li> open @link BlastReportFileOut @endlink,</li>
+ * <li> configure the @link BlastIOContext @endlink </li>
+ * <li> @link BlastReportFileOut#writeHeader @endlink </li>
+ * <li> @link BlastReportFileOut#writeRecord @endlink repeated up to n times</li>
+ * <li> @link BlastReportFileOut#writeFooter @endlink </li>
+ * </ul>
+ *
+ * The following members of the context have to be defined before writing:
+ * <ul>
+ * <li> @link BlastIOContext::blastProgram @endlink (unless fixed at compile-time)</li>
+ * <li> @link BlastIOContext::scoringScheme @endlink</li>
+ * <li> @link BlastIOContext::dbName @endlink</li>
+ * <li> @link BlastIOContext::dbTotalLength @endlink</li>
+ * <li> @link BlastIOContext::dbNumberOfSeqs @endlink</li>
+ * </ul>
+ *
+ * For a detailed example have a look at the
+ * <a href="http://seqan.readthedocs.org/en/develop/Tutorial/BlastIO.html">Blast IO tutorial</a>.
+ *
+ * @see BlastRecord
+ */
+
+template <typename TBlastIOContext = BlastIOContext<> >
+using BlastReportFileOut = FormattedFile<BlastReport, Output, TBlastIOContext>;
+
+// ----------------------------------------------------------------------------
+// Class MagicHeader
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<BlastReport, T> :
+    public MagicHeader<Nothing, T> {};
+
+// ----------------------------------------------------------------------------
+// Class FileExtensions
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<BlastReport, T>
+{
+    static constexpr char const * VALUE[1] =
+    {
+        ".m0"
+    };
+};
+
+template <typename T>
+constexpr char const * FileExtensions<BlastReport, T>::VALUE[1];
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TContext, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<BlastReport, Output, TContext>, TStorageSpec>
+{
+    typedef TContext Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+struct FileFormat<FormattedFile<BlastReport, Output, TSpec> >
+{
+    typedef BlastReport Type;
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function guessFormat()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+inline bool guessFormat(FormattedFile<BlastReport, Output, TSpec> &)
+{
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function _numberOfDigits
+// ----------------------------------------------------------------------------
+
+template <typename T>
+constexpr typename std::enable_if<std::is_integral<T>::value, T>::type
+_numberOfDigits(T const number)
+{
+    return (number == 0) ? 1 : static_cast<T>(std::floor(std::log10(number))+1);
+}
+
+// ----------------------------------------------------------------------------
+// some string constants
+// ----------------------------------------------------------------------------
+
+constexpr const char *
+_blastReference()
+{
+    return "Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro "
+    "A. Schaffer,\nJinghui Zhang, Zheng Zhang, Webb Miller, and David J. "
+    "Lipman (1997),\n\"Gapped BLAST and PSI-BLAST: a new generation of protein "
+    "database search\nprograms\",  Nucleic Acids Res. 25:3389-3402.\n";
+}
+
+constexpr const char *
+_seqanReference()
+{
+    return "Reference for SeqAn: Doering, A., D. Weese, T. Rausch, K. Reinert (2008): "
+    "SeqAn --\nAn efficient, generic C++ library for sequence analysis. BMC "
+    "Bioinformatics,\n9(1), 11. BioMed Central Ltd."
+    " doi:10.1186/1471-2105-9-11\n";
+}
+
+template <typename T>
+constexpr const char *
+_matrixName(T const & /**/)
+{
+    return "'_matrixName not implemented for this matrix'";
+}
+
+constexpr const char *
+_matrixName(Blosum45 const & /**/)
+{
+    return "BLOSUM45";
+}
+
+constexpr const char *
+_matrixName(Blosum62 const & /**/)
+{
+    return "BLOSUM62";
+}
+
+constexpr const char *
+_matrixName(Blosum80 const & /**/)
+{
+    return "BLOSUM80";
+}
+
+constexpr const char *
+_matrixName(Pam250 const & /**/)
+{
+    return "PAM250";
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeStatsBlock
+// ----------------------------------------------------------------------------
+
+template <typename TStream,
+          typename TScore,
+          typename TMatch,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeStatsBlock(TStream & stream,
+                 BlastIOContext<TScore, p, h> const &,
+                 TMatch const & m,
+                 BlastReport const &)
+{
+    write(stream, " Score =  ");
+    write(stream, FormattedNumber<double>("%.1f", m.bitScore));
+    write(stream, " bits (");
+    write(stream, unsigned(m.alignStats.alignmentScore));
+    write(stream, "), Expect =  ");
+    write(stream, FormattedNumber<double>("%.1g", m.eValue));
+    write(stream, "\n Identities = ");
+    write(stream, m.alignStats.numMatches);
+    write(stream, '/');
+    write(stream, m.alignStats.alignmentLength);
+    write(stream, " (");
+    write(stream, int(std::lround(m.alignStats.alignmentIdentity)));
+    write(stream, "%), Gaps = ");
+    write(stream, m.alignStats.numGaps);
+    write(stream, '/');
+    write(stream, m.alignStats.alignmentLength);
+    write(stream, " (");
+    write(stream, int(std::lround(double(m.alignStats.numGaps) * 100 / m.alignStats.alignmentLength)));
+    write(stream, "%)\n Strand=");
+
+    if (m.qFrameShift == 1)
+        write(stream, "Plus/");
+    else
+        write(stream, "Minus/");
+
+    if (m.sFrameShift == 1)
+        write(stream, "Plus\n\n");
+    else
+        write(stream, "Minus\n\n");
+}
+
+template <typename TStream,
+          typename TScoreSpec,
+          typename TMatch,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeStatsBlock(TStream & stream,
+                 BlastIOContext<Score<int, ScoreMatrix<AminoAcid, TScoreSpec> >, p, h> const & context,
+                 TMatch const & m,
+                 BlastReport const &)
+{
+    write(stream, " Score =  ");
+    write(stream, FormattedNumber<double>("%.1f", m.bitScore));
+    write(stream, " bits (");
+    write(stream, unsigned(m.alignStats.alignmentScore));
+    write(stream, "), Expect =  ");
+    write(stream, FormattedNumber<double>("%.1g", m.eValue));
+    write(stream, "\n Identities = ");
+    write(stream, m.alignStats.numMatches);
+    write(stream, '/');
+    write(stream, m.alignStats.alignmentLength);
+    write(stream, " (");
+    write(stream, int(std::lround(m.alignStats.alignmentIdentity)));
+    write(stream, "%), Positives = ");
+    write(stream, m.alignStats.numPositiveScores);
+    write(stream, '/');
+    write(stream, m.alignStats.alignmentLength);
+    write(stream, " (");
+    write(stream, int(std::lround(m.alignStats.alignmentSimilarity)));
+    write(stream, "%), Gaps = ");
+    write(stream, m.alignStats.numGaps);
+    write(stream, '/');
+    write(stream, m.alignStats.alignmentLength);
+    write(stream, " (");
+    write(stream, int(std::lround(double(m.alignStats.numGaps) * 100 / m.alignStats.alignmentLength)));
+    write(stream, "%)");
+
+    if (context.blastProgram != BlastProgram::BLASTP)
+        write(stream, "\n Frame = ");
+
+    if (context.blastProgram == BlastProgram::BLASTX)
+    {
+        write(stream, FormattedNumber<int8_t>("%+d", m.qFrameShift));
+    }
+    else if (context.blastProgram == BlastProgram::TBLASTN)
+    {
+        write(stream, FormattedNumber<int8_t>("%+d", m.sFrameShift));
+    }
+    else if (context.blastProgram == BlastProgram::TBLASTX)
+    {
+        write(stream, FormattedNumber<int8_t>("%+d", m.qFrameShift));
+        write(stream, "/");
+        write(stream, FormattedNumber<int8_t>("%+d", m.sFrameShift));
+    }
+    write(stream, "\n\n");
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeAlignmentBlockIntermediateChar
+// ----------------------------------------------------------------------------
+
+template <typename TStream,
+          typename TScore,
+          typename TChar1,
+          typename TChar2,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeAlignmentBlockIntermediateChar(TStream & stream,
+                                     BlastIOContext<TScore, p, h> const &,
+                                     TChar1 const & char1,
+                                     TChar2 const & char2,
+                                     BlastReport const & /*tag*/)
+{
+    if (char1 == char2)
+        write(stream, '|');
+    else
+        write(stream, ' ');
+}
+
+template <typename TStream,
+          typename TScoreSpec,
+          typename TChar1,
+          typename TChar2,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeAlignmentBlockIntermediateChar(TStream & stream,
+                                     BlastIOContext<Score<int, ScoreMatrix<AminoAcid, TScoreSpec> >,
+                                                    p,
+                                                    h> const & context,
+                                     TChar1 const & char1,
+                                     TChar2 const & char2,
+                                     BlastReport const & /*tag*/)
+{
+    // TODO(h4nn3s): this function could be replaced by a matrix, which would be a lot faster
+    // but it would also require a matrix for every scoringScheme
+
+    if (char1 == char2)
+        write(stream, char1);
+    else if ((char1 == '-') || (char2 == '-'))
+        write(stream, ' ');
+    else if (score(seqanScheme(context.scoringScheme), char1, char2) > 0)
+        write(stream, '+');
+    else
+        write(stream, ' ');
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeAlignmentBlock
+// ----------------------------------------------------------------------------
+
+template <typename TStream,
+          typename TScore,
+          typename TQId,
+          typename TSId,
+          typename TPos,
+          typename TAlignRow0,
+          typename TAlignRow1,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeAlignmentBlock(TStream & stream,
+                     BlastIOContext<TScore, p, h> & context,
+                     BlastMatch<TAlignRow0, TAlignRow1, TPos, TQId, TSId> const & m,
+                     BlastReport const & /*tag*/)
+{
+    TPos const   windowSize  = 60;
+
+    char            buffer[40]  = "";
+
+    TPos            aPos        = 0; // position in alignment
+    TPos            qPos        = 0; // position in query (without gaps)
+    TPos            sPos        = 0; // position in subject (without gaps)
+    // the latter two might become negative in below calculation, but it is safe even for unsigned types
+
+    TPos            effQStart   = m.qStart;
+    TPos            effQEnd     = m.qEnd;
+    TPos            effSStart   = m.sStart;
+    TPos            effSEnd     = m.sEnd;
+
+    _untranslateQPositions(effQStart, effQEnd, m.qFrameShift, m.qLength, context.blastProgram);
+    _untranslateSPositions(effSStart, effSEnd, m.sFrameShift, m.sLength, context.blastProgram);
+
+    int8_t const  qStepOne = (m.qFrameShift < 0) ?  -1 : 1;
+    int8_t const  sStepOne = (m.sFrameShift < 0) ?  -1 : 1;
+    int8_t const     qStep = qIsTranslated(context.blastProgram) ? qStepOne * 3 : qStepOne;
+    int8_t const     sStep = sIsTranslated(context.blastProgram) ? sStepOne * 3 : sStepOne;
+
+    TPos const   maxPos      = std::max({effQStart, effQEnd, effSStart, effSEnd});
+    // max # digits in pos's
+    unsigned char const numberWidth = _numberOfDigits(maxPos);
+
+    while (aPos < m.alignStats.alignmentLength)
+    {
+        // Query line
+        sprintf(buffer, "Query  %-*d  ", numberWidth, qPos + effQStart);
+        write(stream, buffer);
+
+        TPos const end = std::min(static_cast<TPos>(aPos + windowSize), m.alignStats.alignmentLength);
+        for (TPos i = aPos; i < end; ++i)
+        {
+            if (!isGap(m.alignRow0, i))
+                qPos += qStep;
+            write(stream, value(m.alignRow0, i));
+        }
+        sprintf(buffer, "  %-*d", numberWidth, (qPos + effQStart) - qStepOne);
+        write(stream, buffer);
+
+        // intermediate line
+        write(stream, "\n         ");
+        for (unsigned i = 0; i < numberWidth; ++i)
+            write(stream, ' ');
+
+        for (TPos i = aPos; i < end; ++i)
+            _writeAlignmentBlockIntermediateChar(stream, context, value(m.alignRow0,i), value(m.alignRow1,i), BlastReport());
+
+        // Subject line
+        sprintf(buffer, "\nSbjct  %-*d  ", numberWidth, sPos + effSStart);
+        write(stream, buffer);
+
+        for (TPos i = aPos; i < end; ++i)
+        {
+            if (!isGap(m.alignRow1, i))
+                sPos += sStep;
+            write(stream, value(m.alignRow1, i));
+        }
+        sprintf(buffer, "  %-*d\n\n", numberWidth, (sPos + effSStart) - sStepOne);
+        write(stream, buffer);
+
+        aPos = end;
+    }
+    write(stream, '\n');
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeFullMatch
+// ----------------------------------------------------------------------------
+
+template <typename TStream,
+          typename TScore,
+          typename TQId,
+          typename TSId,
+          typename TPos,
+          typename TAlignRow0,
+          typename TAlignRow1,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeFullMatch(TStream & stream,
+                BlastIOContext<TScore, p, h> & context,
+                BlastMatch<TAlignRow0, TAlignRow1, TPos, TQId, TSId> const & m,
+                BlastReport const & /*tag*/)
+{
+    write(stream, "> ");
+    for (unsigned beg = 0, end = 0; end < length(m.sId);)
+    {
+        if (beg == 0)
+            end += 64;
+        else
+            end += 60;
+
+        if (end >= length(m.sId))
+            end = length(m.sId);
+
+        write(stream, infix(m.sId, beg, end));
+        write(stream, '\n');//            ");
+
+        beg = end;
+    }
+    write(stream, "Length=");
+    write(stream, m.sLength);
+    write(stream, "\n\n");
+
+    _writeStatsBlock(stream, context, m, BlastReport());
+
+    _writeAlignmentBlock(stream, context, m, BlastReport());
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeMatchOneLiner
+// ----------------------------------------------------------------------------
+
+template <typename TStream,
+          typename TScore,
+          typename TQId,
+          typename TSId,
+          typename TPos,
+          typename TAlignRow0,
+          typename TAlignRow1,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeMatchOneLiner(TStream & stream,
+                    BlastIOContext<TScore, p, h> &,
+                    BlastMatch<TAlignRow0, TAlignRow1, TPos, TQId, TSId> const & m,
+                    BlastReport const & /*tag*/)
+{
+    if (length(m.sId) == 66) // it fits
+    {
+        write(stream, m.sId);
+    }
+    else if (length(m.sId) < 66) // needs to be padded with ' '
+    {
+        write(stream, m.sId);
+        for (unsigned char i = 0; i < 66 - length(m.sId); ++i)
+            write(stream, ' ');
+    }
+    else // needs to be truncated
+    {
+        write(stream, prefix(m.sId, 63));
+        write(stream, "...");
+    }
+    write(stream, ' ');
+
+    write(stream, FormattedNumber<long>("%4li", m.bitScore));
+    write(stream, "  ");
+    write(stream, FormattedNumber<double>("%.1g", m.eValue));
+    write(stream, '\n');
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()
+// ----------------------------------------------------------------------------
+
+template <typename TStream,
+          typename TScore,
+          typename TMatch,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeRecordTop(TStream & stream,
+                   BlastIOContext<TScore, p, h> &,
+                   BlastRecord<TMatch> const & record,
+                   BlastReport const & /*tag*/)
+{
+    // write query header
+    write(stream, "\nQuery= ");
+    write(stream, record.qId);
+    write(stream, "\n\nLength=");
+    write(stream, record.qLength);
+    write(stream, "\n");
+}
+
+template <typename TStream,
+          typename TScore,
+          typename TMatch,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeRecordFooter(TStream & stream,
+                   BlastIOContext<TScore, p, h> & context,
+                   BlastRecord<TMatch> const & record,
+                   BlastReport const & /*tag*/)
+{
+    write(stream, "\n"
+                  "Lambda     K      H\n"
+                  "   ");
+    write(stream, FormattedNumber<double>("%-4.3f", getLambda(context.scoringScheme)));
+    write(stream, "   ");
+    write(stream, FormattedNumber<double>("%-5.4f", getKappa(context.scoringScheme)));
+    write(stream, "   ");
+    write(stream, FormattedNumber<double>("%-5.4f", getH(context.scoringScheme)));
+    write(stream, "\n\n"
+                  "Gapped\n"
+                  "Lambda     K      H\n");
+    write(stream, "   ");
+    write(stream, FormattedNumber<double>("%-4.3f", getLambda(context.scoringScheme)));
+    write(stream, "   ");
+    write(stream, FormattedNumber<double>("%-5.4f", getKappa(context.scoringScheme)));
+    write(stream, "   ");
+    write(stream, FormattedNumber<double>("%-5.4f", getH(context.scoringScheme)));
+    write(stream, "\n\n"
+                  "Effective search space used: ");
+    write(stream, record.qLength * context.dbTotalLength);
+    write(stream, "\n\n");
+}
+
+/*!
+ * @fn BlastReportFileOut#writeRecord
+ * @headerfile seqan/blast.h
+ * @brief write a @link BlastRecord @endlink including it's @link BlastMatch @endlinkes and possibly comment lines to a file.
+ * @signature void writeRecord(blastReportOut, blastRecord);
+ *
+ * @param[in,out] blastReportOut A @link BlastReportFileOut @endlink formattedFile.
+ * @param[in]     blastRecord     The @link BlastRecord @endlink you wish to print.
+ *
+ * @section Remarks
+ *
+ * Modifiy the formattedFile's @link BlastIOContext @endlink to set some properties of the output, like the
+ * @link BlastIOContext::versionString @endlink or @link BlastIOContext::dbName @endlink.
+ *
+ * @throw IOError On low-level I/O errors.
+ *
+ * @see BlastRecord
+ * @see BlastIOContext
+ */
+
+template <typename TStream,
+          typename TScore,
+          typename TMatch,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+writeRecord(TStream & stream,
+            BlastIOContext<TScore, p, h> & context,
+            BlastRecord<TMatch> const & record,
+            BlastReport const & /*tag*/)
+{
+
+    #ifdef DEBUG
+    {
+        CharString str1(record.qId);
+        for (auto const & m : record.matches)
+        {
+            CharString str2(m.qId);
+            SEQAN_ASSERT(startsWith(str1, str2));
+        }
+    }
+    #endif// DEBUG
+
+    _writeRecordTop(stream, context, record, BlastReport());
+
+    if (!empty(record.matches))
+    {
+        write(stream, "                                                                   Score     E\n"
+                      "Sequences producing significant alignments:                       (Bits)  Value\n\n");
+        // match one-liners
+        for (auto const & m : record.matches)
+            _writeMatchOneLiner(stream, context, m, BlastReport());
+
+        write(stream, "\nALIGNMENTS\n");
+        // full matches
+        for (auto const & m : record.matches)
+            _writeFullMatch(stream, context, m, BlastReport());
+    }
+    else
+    {
+        write(stream, "\n\n***** No hits found *****\n\n\n");
+    }
+
+    _writeRecordFooter(stream, context, record, BlastReport());
+}
+
+template <typename TContext,
+          typename TMatch>
+inline void
+writeRecord(BlastReportFileOut<TContext> & formattedFile,
+            BlastRecord<TMatch> const & r)
+{
+    writeRecord(formattedFile.iter, context(formattedFile), r, BlastReport());
+}
+
+// ----------------------------------------------------------------------------
+// Function writeHeader()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastReportFileOut#writeHeader
+ * @headerfile seqan/blast.h
+ * @brief Write the header (top-most section) of a BlastReport file.
+ * @signature void writeHeader(blastReportOut);
+ *
+ * @param[in,out] blastReportOut A @link BlastReportFileOut @endlink formattedFile.
+ *
+ * @throw IOError On low-level I/O errors.
+ *
+ * @see BlastRecord
+ * @see BlastIOContext
+ */
+
+template <typename TStream,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+writeHeader(TStream & stream,
+            BlastIOContext<TScore, p, h> & context,
+            BlastReport const & /*tag*/)
+{
+
+    if (empty(context.versionString))
+        context._setDefaultVersionString();
+    write(stream, context.versionString);
+    write(stream, "\n\n\n");
+
+    // write references
+    write(stream, _blastReference());
+    write(stream, "\n\n\n");
+    write(stream, _seqanReference());
+
+    write(stream, "\n\n\nDatabase: ");
+    write(stream, context.dbName);
+    write(stream, "\n           ");
+    write(stream, context.dbNumberOfSeqs); //TODO insert commata
+    write(stream, " sequences; ");
+    write(stream, context.dbTotalLength); //TODO insert commata
+    write(stream, " total letters\n\n");
+}
+
+template <typename TContext>
+inline void
+writeHeader(BlastReportFileOut<TContext> & formattedFile)
+{
+    writeHeader(formattedFile.iter, context(formattedFile), BlastReport());
+}
+
+// ----------------------------------------------------------------------------
+// Function writeFooter()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastReportFileOut#writeFooter
+ * @headerfile seqan/blast.h
+ * @brief Write the footer of a BlastReport.
+ * @signature void writeFooter(blastReportOut);
+ *
+ * @param[in,out] blastReportOut A @link BlastReportFileOut @endlink formattedFile.
+ *
+ * @throw IOError On low-level I/O errors.
+ *
+ * @see BlastRecord
+ * @see BlastIOContext
+ */
+
+template <typename TStream>
+inline void
+writeMatrixName(TStream & stream, SimpleScore const & scheme)
+{
+    write(stream, " blastn matrix:");
+    write(stream, scoreMatch(scheme));
+    write(stream, ' ');
+    write(stream, scoreMismatch(scheme));
+}
+
+template <typename TStream, typename TScheme>
+inline void
+writeMatrixName(TStream & stream, TScheme const &)
+{
+    // see top of file
+    write(stream, _matrixName(TScheme()));
+}
+
+template <typename TStream,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+writeFooter(TStream & stream,
+            BlastIOContext<TScore, p, h> & context,
+            BlastReport const & /*tag*/)
+{
+    write(stream, "\n  Database: ");
+    write(stream, context.dbName);
+    write(stream, "\n  Number of letters in database: ");
+    write(stream, context.dbTotalLength);
+    write(stream, "\n  Number of sequences in database:  ");
+    write(stream, context.dbNumberOfSeqs);
+    write(stream, "\n\n\n\n");
+
+    write(stream, "Matrix: ");
+    writeMatrixName(stream, seqanScheme(context.scoringScheme));
+    write(stream, "\nGap Penalties: Existence: ");
+    write(stream, -scoreGapOpenBlast(context.scoringScheme)); // convert scores to penalties
+    write(stream, ", Extension: ");
+    write(stream, -scoreGapExtend(context.scoringScheme)); // convert scores to penalties
+    //TODO possibly add more parameter information
+    write(stream, "\n\n");
+}
+
+template <typename TContext>
+inline void
+writeFooter(BlastReportFileOut<TContext> & formattedFile)
+{
+    writeFooter(formattedFile.iter, context(formattedFile), BlastReport());
+}
+
+} // namespace seqan
+
+#endif // header guard
diff --git a/seqan/blast/blast_statistics.h b/seqan/blast/blast_statistics.h
new file mode 100644
index 0000000..7f73e4b
--- /dev/null
+++ b/seqan/blast/blast_statistics.h
@@ -0,0 +1,1072 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// bitScore and e-Value calculation
+// ==========================================================================
+// contains empiric values from blast_stat.c as well as small portions of
+// code from blast_stat.c written by Tom Madden and released into the public
+// domain by the NCBI.
+// ==========================================================================
+
+#ifndef __BLAST_STATISTICS_H__
+#define __BLAST_STATISTICS_H__
+
+#ifndef NCBI_INT2_MAX
+#define NCBI_INT2_MAX    32767
+#endif
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class KarlinAltschulValues
+// ----------------------------------------------------------------------------
+
+//NOTE(h-2): removed to clean up interface
+/*
+ * @class KarlinAltschulValues
+ * @headerfile <seqan/blast.h>
+ * @brief An object that holds Statistical parameters
+ * @signature struct KarlinAltschulValues<TScore, TSpec> { ... };
+ *
+ * This is an adapter around the SeqAn scoring scheme, for use with BLAST and
+ * other e-value statistics. If you only use high-level Blast IO, you do not
+ * have to worry about this, except that you have to know that not every scoring
+ * scheme supported by SeqAn and not every combination of gap scores is supported.
+ * [@link BlastIOContext#setBlastScoringScheme @endlink/@link BlastIOContext#setScoringScheme @endlink will fail if
+ * a non-supported scoringScheme is passed]
+ *
+ * @section Details
+ *
+ * This data structure holds Karlin-Altschul statistical scoring
+ * parameters (&lambda;, &Kappa;, H, &alpha;, &beta;, &theta;) for the given
+ * scoring scheme. These values are empirically derived. The ones in
+ * SeqAn are imported from the NCBI blast source code (blast-2.2.26).
+ * For an explanation of the role of &lambda; and &Kappa; please see these
+ * slides: <a href="https://www.cs.umd.edu/class/fall2011/cmsc858s/Local_Alignment_Statistics.pdf">
+ * https://www.cs.umd.edu/class/fall2011/cmsc858s/Local_Alignment_Statistics.pdf</a>.
+ *
+ * <b>Warning</b>, not every scoring scheme supported by SeqAn and not every
+ * combination of gap scores is supported.
+ */
+
+/// GENERIC
+template <typename TScore, typename TSpec = void>
+struct KarlinAltschulValues;
+
+/// BLOSUM30
+// not implemented in BLAST
+
+/// BLOSUM45
+template <typename TSpec>
+struct KarlinAltschulValues<Blosum45, TSpec>
+{
+    typedef uint8_t TSize;
+
+    /* statics */
+    static constexpr TSize nParams = 8;
+    static constexpr TSize nParamSets = 16;
+    static double const VALUE[nParamSets][nParams];
+};
+
+template <typename TSpec>
+double const KarlinAltschulValues<Blosum45, TSpec>::VALUE
+  [KarlinAltschulValues<Blosum45, TSpec>::nParamSets]
+  [KarlinAltschulValues<Blosum45, TSpec>::nParams] =
+{
+    {(double) NCBI_INT2_MAX, (double) NCBI_INT2_MAX,
+            (double) NCBI_INT2_MAX, 0.2291, 0.0924, 0.2514, 0.9113, -5.7},
+    {13, 3, (double) NCBI_INT2_MAX, 0.207,  0.049,  0.14,   1.5, -22},
+    {12, 3, (double) NCBI_INT2_MAX, 0.199,  0.039,  0.11,   1.8, -34},
+    {11, 3, (double) NCBI_INT2_MAX, 0.190,  0.031,  0.095,  2.0, -38},
+    {10, 3, (double) NCBI_INT2_MAX, 0.179,  0.023,  0.075,  2.4, -51},
+    {16, 2, (double) NCBI_INT2_MAX, 0.210,  0.051,  0.14,   1.5, -24},
+    {15, 2, (double) NCBI_INT2_MAX, 0.203,  0.041,  0.12,   1.7, -31},
+    {14, 2, (double) NCBI_INT2_MAX, 0.195,  0.032,  0.10,   1.9, -36},
+    {13, 2, (double) NCBI_INT2_MAX, 0.185,  0.024,  0.084,  2.2, -45},
+    {12, 2, (double) NCBI_INT2_MAX, 0.171,  0.016,  0.061,  2.8, -65},
+    {19, 1, (double) NCBI_INT2_MAX, 0.205,  0.040,  0.11,   1.9, -43},
+    {18, 1, (double) NCBI_INT2_MAX, 0.198,  0.032,  0.10,   2.0, -43},
+    {17, 1, (double) NCBI_INT2_MAX, 0.189,  0.024,  0.079,  2.4, -57},
+    {16, 1, (double) NCBI_INT2_MAX, 0.176,  0.016,  0.063,  2.8, -67},
+};
+
+
+/// BLOSUM50
+// not implemented in seqan
+
+/// BLOSUM62
+template <typename TSpec>
+struct KarlinAltschulValues<Blosum62, TSpec>
+{
+    typedef uint8_t TSize;
+
+    /* statics */
+    static constexpr TSize nParams = 8;
+    static constexpr TSize nParamSets = 12;
+    static double const VALUE[nParamSets][nParams];
+};
+
+template <typename TSpec>
+double const KarlinAltschulValues<Blosum62, TSpec>::VALUE
+  [KarlinAltschulValues<Blosum62, TSpec>::nParamSets]
+  [KarlinAltschulValues<Blosum62, TSpec>::nParams] =
+{
+        {(double) NCBI_INT2_MAX, (double) NCBI_INT2_MAX,
+                (double) NCBI_INT2_MAX, 0.3176, 0.134, 0.4012, 0.7916, -3.2},
+        {11, 2, (double) NCBI_INT2_MAX, 0.297,  0.082, 0.27,   1.1,    -10} ,
+        {10, 2, (double) NCBI_INT2_MAX, 0.291,  0.075, 0.23,   1.3,    -15} ,
+        { 9, 2, (double) NCBI_INT2_MAX, 0.279,  0.058, 0.19,   1.5,    -19} ,
+        { 8, 2, (double) NCBI_INT2_MAX, 0.264,  0.045, 0.15,   1.8,    -26} ,
+        { 7, 2, (double) NCBI_INT2_MAX, 0.239,  0.027, 0.10,   2.5,    -46} ,
+        { 6, 2, (double) NCBI_INT2_MAX, 0.201,  0.012, 0.061,  3.3,    -58} ,
+        {13, 1, (double) NCBI_INT2_MAX, 0.292,  0.071, 0.23,   1.2,    -11} ,
+        {12, 1, (double) NCBI_INT2_MAX, 0.283,  0.059, 0.19,   1.5,    -19} ,
+        {11, 1, (double) NCBI_INT2_MAX, 0.267,  0.041, 0.14,   1.9,    -30} ,
+        {10, 1, (double) NCBI_INT2_MAX, 0.243,  0.024, 0.10,   2.5,    -44} ,
+        { 9, 1, (double) NCBI_INT2_MAX, 0.206,  0.010, 0.052,  4.0,    -87} ,
+};
+/// BLOSUM80
+template <typename TSpec>
+struct KarlinAltschulValues<Blosum80, TSpec>
+{
+    typedef uint8_t TSize;
+
+    /* statics */
+    static constexpr TSize nParams = 8;
+    static constexpr TSize nParamSets = 10;
+    static double const VALUE[nParamSets][nParams];
+};
+
+template <typename TSpec>
+double const KarlinAltschulValues<Blosum80, TSpec>::VALUE
+ [KarlinAltschulValues<Blosum80, TSpec>::nParamSets]
+ [KarlinAltschulValues<Blosum80, TSpec>::nParams] =
+{
+    {(double) NCBI_INT2_MAX, (double) NCBI_INT2_MAX,
+            (double) NCBI_INT2_MAX, 0.3430,  0.177, 0.6568, 0.5222, -1.6},
+    {25, 2, (double) NCBI_INT2_MAX, 0.342,   0.17,  0.66,   0.52,   -1.6},
+    {13, 2, (double) NCBI_INT2_MAX, 0.336,   0.15,  0.57,   0.59,   -3},
+    { 9, 2, (double) NCBI_INT2_MAX, 0.319,   0.11,  0.42,   0.76,   -6},
+    { 8, 2, (double) NCBI_INT2_MAX, 0.308,   0.090, 0.35,   0.89,   -9},
+    { 7, 2, (double) NCBI_INT2_MAX, 0.293,   0.070, 0.27,   1.1,   -14},
+    { 6, 2, (double) NCBI_INT2_MAX, 0.268,   0.045, 0.19,   1.4,   -19},
+    {11, 1, (double) NCBI_INT2_MAX, 0.314,   0.095, 0.35,   0.90,   -9},
+    {10, 1, (double) NCBI_INT2_MAX, 0.299,   0.071, 0.27,   1.1,   -14},
+    { 9, 1, (double) NCBI_INT2_MAX, 0.279,   0.048, 0.20,   1.4,   -19},
+};
+
+/// BLOSUM90
+// not implemented in seqan
+
+/// PAM30
+// not implemented in seqan
+
+/// PAM40
+// not implemented in blast
+
+/// PAM70
+// not implemented in seqan
+
+/// PAM120
+// not implemented in blast
+
+/// PAM200
+// not implemented in blast
+
+/// PAM250
+template <typename TSpec>
+struct KarlinAltschulValues<Pam250, TSpec>
+{
+    typedef uint8_t TSize;
+
+    /* statics */
+    static constexpr TSize nParams = 8;
+    static constexpr TSize nParamSets = 16;
+    static double const VALUE[nParamSets][nParams];
+};
+
+template <typename TSpec>
+double const KarlinAltschulValues<Pam250, TSpec>::VALUE
+  [KarlinAltschulValues<Pam250, TSpec>::nParamSets]
+  [KarlinAltschulValues<Pam250, TSpec>::nParams] =
+{
+    {(double) NCBI_INT2_MAX, (double) NCBI_INT2_MAX,
+            (double) NCBI_INT2_MAX, 0.2252, 0.0868, 0.2223, 0.98,  -5.0},
+    {15, 3, (double) NCBI_INT2_MAX, 0.205,  0.049,  0.13,   1.6,  -23},
+    {14, 3, (double) NCBI_INT2_MAX, 0.200,  0.043,  0.12,   1.7,  -26},
+    {13, 3, (double) NCBI_INT2_MAX, 0.194,  0.036,  0.10,   1.9,  -31},
+    {12, 3, (double) NCBI_INT2_MAX, 0.186,  0.029,  0.085,  2.2,  -41},
+    {11, 3, (double) NCBI_INT2_MAX, 0.174,  0.020,  0.070,  2.5,  -48},
+    {17, 2, (double) NCBI_INT2_MAX, 0.204,  0.047,  0.12,   1.7,  -28},
+    {16, 2, (double) NCBI_INT2_MAX, 0.198,  0.038,  0.11,   1.8,  -29},
+    {15, 2, (double) NCBI_INT2_MAX, 0.191,  0.031,  0.087,  2.2,  -44},
+    {14, 2, (double) NCBI_INT2_MAX, 0.182,  0.024,  0.073,  2.5,  -53},
+    {13, 2, (double) NCBI_INT2_MAX, 0.171,  0.017,  0.059,  2.9,  -64},
+    {21, 1, (double) NCBI_INT2_MAX, 0.205,  0.045,  0.11,   1.8,  -34},
+    {20, 1, (double) NCBI_INT2_MAX, 0.199,  0.037,  0.10,   1.9,  -35},
+    {19, 1, (double) NCBI_INT2_MAX, 0.192,  0.029,  0.083,  2.3,  -52},
+    {18, 1, (double) NCBI_INT2_MAX, 0.183,  0.021,  0.070,  2.6,  -60},
+    {17, 1, (double) NCBI_INT2_MAX, 0.171,  0.014,  0.052,  3.3,  -86},
+};
+
+/// VTML200
+// not implemented in blast
+
+/// NUCLEOTIDES
+template <typename TSpec>
+struct KarlinAltschulValues<Score<int, Simple>, TSpec>
+{
+    typedef uint8_t TSize;
+
+    /* statics */
+    static constexpr TSize nParams = 11;
+    static constexpr TSize nParamSets = 60;
+    /*  0 = matchScore
+        1 = mismatch cost
+        2 = Gap opening cost,
+        3 = Gap extension cost,
+        4 = Lambda,
+        5 = K,
+        6 = H,
+        7 = Alpha,
+        8 = Beta,
+        9 = Theta
+        10 = only applicable to even score, uneven need to be rounded down */
+    static double const VALUE[nParamSets][nParams];
+};
+
+template <typename TSpec>
+double const KarlinAltschulValues<Score<int, Simple>, TSpec>::VALUE
+ [KarlinAltschulValues<Score<int, Simple>, TSpec>::nParamSets]
+ [KarlinAltschulValues<Score<int, Simple>, TSpec>::nParams] =
+{
+    { 1, 5, 0, 0, 1.39, 0.747, 1.38, 1.00,  0, 100, 0 } ,
+    { 1, 5, 3, 3, 1.39, 0.747, 1.38, 1.00,  0, 100, 0 } ,
+
+    { 1, 4, 0, 0, 1.383, 0.738, 1.36, 1.02,  0, 100, 0 } ,
+    { 1, 4, 1, 2,  1.36,  0.67,  1.2,  1.1,  0,  98, 0 } ,
+    { 1, 4, 0, 2,  1.26,  0.43, 0.90,  1.4, -1,  91, 0 } ,
+    { 1, 4, 2, 1,  1.35,  0.61,  1.1,  1.2, -1,  98, 0 } ,
+    { 1, 4, 1, 1,  1.22,  0.35, 0.72,  1.7, -3,  88, 0 } ,
+
+    { 2, 7, 0, 0,  0.69, 0.73, 1.34, 0.515,  0, 100, 1 } ,
+    { 2, 7, 2, 4,  0.68, 0.67,  1.2,  0.55,  0,  99, 1 } ,
+    { 2, 7, 0, 4,  0.63, 0.43, 0.90,   0.7, -1,  91, 1 } ,
+    { 2, 7, 4, 2, 0.675, 0.62,  1.1,   0.6, -1,  98, 1 } ,
+    { 2, 7, 2, 2,  0.61, 0.35, 0.72,   1.7, -3,  88, 1 } ,
+
+    { 1, 3, 0, 0, 1.374, 0.711, 1.31, 1.05,  0, 100, 0 } ,
+    { 1, 3, 2, 2,  1.37,  0.70,  1.2,  1.1,  0,  99, 0 } ,
+    { 1, 3, 1, 2,  1.35,  0.64,  1.1,  1.2, -1,  98, 0 } ,
+    { 1, 3, 0, 2,  1.25,  0.42, 0.83,  1.5, -2,  91, 0 } ,
+    { 1, 3, 2, 1,  1.34,  0.60,  1.1,  1.2, -1,  97, 0 } ,
+    { 1, 3, 1, 1,  1.21,  0.34, 0.71,  1.7, -2,  88, 0 } ,
+
+    { 2, 5, 0, 0, 0.675, 0.65,  1.1,  0.6, -1, 99, 1 },
+    { 2, 5, 2, 4,  0.67, 0.59,  1.1,  0.6, -1, 98, 1 },
+    { 2, 5, 0, 4,  0.62, 0.39, 0.78,  0.8, -2, 91, 1 },
+    { 2, 5, 4, 2,  0.67, 0.61,  1.0, 0.65, -2, 98, 1 },
+    { 2, 5, 2, 2,  0.56, 0.32, 0.59, 0.95, -4, 82, 1 },
+
+    { 1, 2, 0, 0, 1.28, 0.46, 0.85, 1.5, -2, 96, 0 },
+    { 1, 2, 2, 2, 1.33, 0.62,  1.1, 1.2,  0, 99, 0 },
+    { 1, 2, 1, 2, 1.30, 0.52, 0.93, 1.4, -2, 97, 0 },
+    { 1, 2, 0, 2, 1.19, 0.34, 0.66, 1.8, -3, 89, 0 },
+    { 1, 2, 3, 1, 1.32, 0.57,  1.0, 1.3, -1, 99, 0 },
+    { 1, 2, 2, 1, 1.29, 0.49, 0.92, 1.4, -1, 96, 0 },
+    { 1, 2, 1, 1, 1.14, 0.26, 0.52, 2.2, -5, 85, 0 },
+
+    { 2, 3, 0, 0,  0.55, 0.21, 0.46,  1.2, -5, 87, 1 },
+    { 2, 3, 4, 4,  0.63, 0.42, 0.84, 0.75, -2, 99, 1 },
+    { 2, 3, 2, 4, 0.615, 0.37, 0.72, 0.85, -3, 97, 1 },
+    { 2, 3, 0, 4,  0.55, 0.21, 0.46,  1.2, -5, 87, 1 },
+    { 2, 3, 3, 3, 0.615, 0.37, 0.68,  0.9, -3, 97, 1 },
+    { 2, 3, 6, 2,  0.63, 0.42, 0.84, 0.75, -2, 99, 1 },
+    { 2, 3, 5, 2, 0.625, 0.41, 0.78,  0.8, -2, 99, 1 },
+    { 2, 3, 4, 2,  0.61, 0.35, 0.68,  0.9, -3, 96, 1 },
+    { 2, 3, 2, 2, 0.515, 0.14, 0.33, 1.55, -9, 81, 1 },
+
+    { 3, 4, 6, 3, 0.389, 0.25, 0.56, 0.7, -5, 95, 0},
+    { 3, 4, 5, 3, 0.375, 0.21, 0.47, 0.8, -6, 92, 0},
+    { 3, 4, 4, 3, 0.351, 0.14, 0.35, 1.0, -9, 86, 0},
+    { 3, 4, 6, 2, 0.362, 0.16, 0.45, 0.8, -4, 88, 0},
+    { 3, 4, 5, 2, 0.330, 0.092, 0.28, 1.2, -13, 81, 0},
+    { 3, 4, 4, 2, 0.281, 0.046, 0.16, 1.8, -23, 69, 0},
+
+    { 4, 5, 0, 0, 0.22, 0.061, 0.22, 1.0, -15, 74, 0 },
+    { 4, 5, 6, 5, 0.28,  0.21, 0.47, 0.6 , -7, 93, 0 },
+    { 4, 5, 5, 5, 0.27,  0.17, 0.39, 0.7,  -9, 90, 0 },
+    { 4, 5, 4, 5, 0.25,  0.10, 0.31, 0.8, -10, 83, 0 },
+    { 4, 5, 3, 5, 0.23, 0.065, 0.25, 0.9, -11, 76, 0 },
+
+    { 1, 1, 3,  2, 1.09,  0.31, 0.55, 2.0,  -2, 99, 0 },
+    { 1, 1, 2,  2, 1.07,  0.27, 0.49, 2.2,  -3, 97, 0 },
+    { 1, 1, 1,  2, 1.02,  0.21, 0.36, 2.8,  -6, 92, 0 },
+    { 1, 1, 0,  2, 0.80, 0.064, 0.17, 4.8, -16, 72, 0 },
+    { 1, 1, 4,  1, 1.08,  0.28, 0.54, 2.0,  -2, 98, 0 },
+    { 1, 1, 3,  1, 1.06,  0.25, 0.46, 2.3,  -4, 96, 0 },
+    { 1, 1, 2,  1, 0.99,  0.17, 0.30, 3.3, -10, 90, 0 },
+
+    { 3, 2,  5, 5, 0.208, 0.030, 0.072, 2.9, -47, 77, 0},
+    { 5, 4, 10, 6, 0.163, 0.068, 0.16,  1.0, -19, 85, 0 },
+    { 5, 4,  8, 6, 0.146, 0.039, 0.11,  1.3, -29, 76, 0 }
+
+};
+
+// ----------------------------------------------------------------------------
+// Class BlastScoringScheme
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastScoringScheme
+ * @brief Wrapper around a SeqAn scoring scheme
+ * @signature struct BlastScoringScheme<TScoringScheme> { ... };
+ * @headerfile <seqan/blast.h>
+ *
+ * This class wraps around a SeqAn scoring scheme and add functions for the retrievel of pre-computed
+ * Karlin-Altschul-Values (required for e-value statistics) and it modifies the gap-scoring slightly.
+ * If you use high-level IO (@link BlastReport @endlink, @link BlastTabular @endlink) you need not worry about the
+ * specifics, however you should always make sure that the scoring scheme @link BlastScoringScheme#isValid @endlink
+ * after you modify it (or check the return values of the set* functions).
+ *
+ * To retrieve a score-object compatible with regular SeqAn-functions, call
+ * @link BlastScoringScheme#seqanScheme @endlink.
+ *
+ * @section Gap cost computation
+ *
+ * Gap-costs are computed differently in SeqAn and in BLAST.
+ * Blast (and many other tools) compute scores of a stretch of gaps as
+ * <tt>s = gO + n * gE</tt>
+ * where gO is the gapOpen score, gE is the gap extend score and n ist the
+ * total number of gap characters.
+ *
+ * SeqAn, however, normally computes them as as <tt>s = gO + (n-1) * gE</tt>.
+ *
+ * Effectively this results only in a different gap open score. To make dealing with this easier, there are
+ * convenience functions for setting and getting the gap open score in blast convention:
+ * @link BlastScoringScheme#scoreGapOpenBlast @endlink and @link BlastScoringScheme#setScoreGapOpenBlast @endlink.
+ *
+ * @section Karlin-Altschul values
+ *
+ * E-Value statistics require certain pre-computed constants. The BlastScoringScheme picks these automatically
+ * whenever you modify it. Unfortunately there aren't parameters for all combinations of scoring schemes and gap
+ * costs, so you have to check @link BlastScoringScheme#isValid @endlink after modifying it or verify the return
+ * value of the set* functions which is bool here (instead of void).
+ *
+ * More details on the scoring parameters is in these slides:
+ * <a href="https://www.cs.umd.edu/class/fall2011/cmsc858s/Local_Alignment_Statistics.pdf">
+ * https://www.cs.umd.edu/class/fall2011/cmsc858s/Local_Alignment_Statistics.pdf</a>.
+ *
+ * The constants used in SeqAn were imported from the NCBI blast source code (blast-2.2.26)
+ *
+ * @tparam TScoringScheme A SeqAn Score type
+ */
+
+/* NOTE(h-2): Maybe this should specialize Score<> instead of being a wrapper.
+ * This would however involve adding a new template parameter to score and
+ * changing lots of code. Also it would become confusing as the shortcuts
+ * like Blosum62 would no longer work...
+ */
+template <typename TScore>
+struct BlastScoringScheme
+{
+    typedef typename Value<TScore>::Type TValue;
+    typedef typename KarlinAltschulValues<TScore, void>::TSize TNumValues;
+
+    /* related to ScoringScheme conversion */
+    TValue _gapOpenBlast = 0;
+    TScore _internalScheme;
+
+    /* parameter selection */
+    TNumValues parameterIndex = std::numeric_limits<TNumValues>::max();
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+/*!
+ * @fn BlastScoringScheme#seqanScheme
+ * @headerfile <seqan/blast.h>
+ * @brief Retrieve a @link Score @endlink object for use with e.g. @link localAlignment @endlink.
+ * @signature TScoringScheme const & seqanScheme(blastScoringScheme);
+ * @return TScoringScheme_const_& the internal scoring object for use with other SeqAn functions.
+ *
+ * @section Remarks
+ *
+ * The reference returned is always const, because you should not modify the internal score object
+ * directly. Use @link BlastScoringScheme @endlink's interface instead.
+ */
+
+template <typename TScore>
+inline TScore const &
+seqanScheme(BlastScoringScheme<TScore> const & bscheme)
+{
+    return bscheme._internalScheme;
+}
+
+// ----------------------------------------------------------------------------
+// Function overloads for getScore*
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#scoreMatch
+ * @headerfile <seqan/blast.h>
+ * @brief The Match score (only for SimpleScore specialization).
+ * @signature int scoreMatch(blastScoringScheme);
+ */
+
+inline int
+scoreMatch(BlastScoringScheme<Score<int, Simple>> & scheme)
+{
+    return scoreMatch(scheme._internalScheme);
+}
+
+/*!
+ * @fn BlastScoringScheme#scoreMismatch
+ * @headerfile <seqan/blast.h>
+ * @brief The Mismatch score (only for SimpleScore specialization).
+ * @signature int scoreMismatch(blastScoringScheme);
+ */
+
+inline int
+scoreMismatch(BlastScoringScheme<Score<int, Simple>> & scheme)
+{
+    return scoreMismatch(scheme._internalScheme);
+}
+
+/*!
+ * @fn BlastScoringScheme#scoreGapOpen
+ * @headerfile <seqan/blast.h>
+ * @brief The Gap Open score in SeqAn convention.
+ * @signature TValue scoreGapOpen(blastScoringScheme);
+ */
+
+template <typename TScore>
+inline typename Value<TScore>::Type
+scoreGapOpen(BlastScoringScheme<TScore> const & scheme)
+{
+    return scoreGapOpen(scheme._internalScheme);
+}
+
+/*!
+ * @fn BlastScoringScheme#scoreGapOpenBlast
+ * @headerfile <seqan/blast.h>
+ * @brief The Gap Open score in Blast convention.
+ * @signature TValue scoreGapOpenBlast(blastScoringScheme);
+ */
+
+template <typename TScore>
+inline typename Value<TScore>::Type
+scoreGapOpenBlast(BlastScoringScheme<TScore> const & scheme)
+{
+    return scheme._gapOpenBlast;
+}
+
+/*!
+ * @fn BlastScoringScheme#scoreGapExtend
+ * @headerfile <seqan/blast.h>
+ * @brief The Gap Extend score.
+ * @signature TValue scoreGapExtend(blastScoringScheme);
+ */
+
+template <typename TScore>
+inline typename Value<TScore>::Type
+scoreGapExtend(BlastScoringScheme<TScore> const & scheme)
+{
+    return scoreGapExtend(scheme._internalScheme);
+}
+
+// ----------------------------------------------------------------------------
+// Function isValid
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#isValid
+ * @headerfile <seqan/blast.h>
+ * @brief check whether valid KarlinAltschulValues are selected
+ * @signature bool isValid(blastScoringScheme);
+ */
+
+template <typename TScore>
+inline bool
+isValid(BlastScoringScheme<TScore> const & scheme)
+{
+    typedef KarlinAltschulValues<TScore> TKAValues;
+    return scheme.parameterIndex < TKAValues::nParamSets;
+}
+
+// ----------------------------------------------------------------------------
+// Function _selectSet
+// ----------------------------------------------------------------------------
+
+template <typename TScore>
+inline bool
+_selectSet(BlastScoringScheme<TScore> & scheme)
+{
+    typedef KarlinAltschulValues<TScore> TKAValues;
+
+    for (typename TKAValues::TSize i = 0; i < TKAValues::nParamSets; ++i)
+    {
+        if ((TKAValues::VALUE[i][0] == -scoreGapOpenBlast(scheme)) &&
+            (TKAValues::VALUE[i][1] == -scoreGapExtend(scheme)))
+        {
+            scheme.parameterIndex = i;
+            return true;
+        }
+    }
+    // no suitable adapter
+    scheme.parameterIndex = std::numeric_limits<typename TKAValues::TSize>::max();
+    return false;
+}
+
+inline bool
+_selectSet(BlastScoringScheme<Score<int, Simple>> & scheme)
+{
+    typedef KarlinAltschulValues<Score<int, Simple>> TKAValues;
+
+    for (typename TKAValues::TSize i = 0; i < TKAValues::nParamSets; ++i)
+    {
+        if ((TKAValues::VALUE[i][0] ==  scoreMatch(scheme))  &&
+            (TKAValues::VALUE[i][1] == -scoreMismatch(scheme)) &&
+            (TKAValues::VALUE[i][2] == -scoreGapOpenBlast(scheme)) &&
+            (TKAValues::VALUE[i][3] == -scoreGapExtend(scheme)))
+        {
+            scheme.parameterIndex = i;
+            return true;
+        }
+    }
+    // no suitable adapter
+    scheme.parameterIndex = std::numeric_limits<typename TKAValues::TSize>::max();
+    return false;
+}
+
+// ----------------------------------------------------------------------------
+// Function overloads for setScore*
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#setScoreMatch
+ * @brief Set match score.
+ * @signature bool setScoreMatch(blastScoringScheme, value);
+ * @param[in,out] blastScoringScheme The @link BlastScoringScheme @endlink to modify.
+ * @param[in]     value              The new value.
+ * @return isValid(blastScoringScheme) whether Karlin-Altschul values for the new scheme exist.
+ */
+
+inline bool
+setScoreMatch(BlastScoringScheme<Score<int, Simple>> & scheme, int const val)
+{
+    setScoreMatch(scheme._internalScheme, val);
+    return _selectSet(scheme);
+}
+
+/*!
+ * @fn BlastScoringScheme#setScoreMismatch
+ * @brief Set mismatch score.
+ * @signature bool setScoreMismatch(blastScoringScheme, value);
+ * @param[in,out] blastScoringScheme The @link BlastScoringScheme @endlink to modify.
+ * @param[in]     value              The new value.
+ * @return isValid(blastScoringScheme) whether Karlin-Altschul values for the new scheme exist.
+ */
+
+inline bool
+setScoreMismatch(BlastScoringScheme<Score<int, Simple>> & scheme, int const val)
+{
+    setScoreMismatch(scheme._internalScheme, val);
+    return _selectSet(scheme);
+}
+
+/*!
+ * @fn BlastScoringScheme#setScoreGapOpenBlast
+ * @headerfile <seqan/blast.h>
+ * @brief Set gap open score in BLAST convention.
+ * @signature bool setScoreGapOpenBlast(blastScoringScheme, value);
+ * @param[in,out] blastScoringScheme The @link BlastScoringScheme @endlink to modify.
+ * @param[in]     value              The new value.
+ * @return isValid(blastScoringScheme) whether Karlin-Altschul values for the new scheme exist.
+ */
+
+template <typename TScore>
+inline bool
+setScoreGapOpenBlast(BlastScoringScheme<TScore> & scheme, typename Value<TScore>::Type const val)
+{
+    scheme._gapOpenBlast = val;
+    setScoreGapOpen(scheme._internalScheme, scoreGapOpenBlast(scheme) + scoreGapExtend(scheme));
+
+    return _selectSet(scheme);
+}
+
+/*!
+ * @fn BlastScoringScheme#setScoreGapOpen
+ * @brief Set gap open score in SeqAn convention.
+ * @signature bool setScoreGapOpen(blastScoringScheme, value);
+ * @param[in,out] blastScoringScheme The @link BlastScoringScheme @endlink to modify.
+ * @param[in]     value              The new value.
+ * @return isValid(blastScoringScheme) whether Karlin-Altschul values for the new scheme exist.
+ */
+
+template <typename TScore>
+inline bool
+setScoreGapOpen(BlastScoringScheme<TScore> & scheme, typename Value<TScore>::Type const val)
+{
+    return setScoreGapOpenBlast(scheme, val - scoreGapExtend(scheme));
+}
+
+/*!
+ * @fn BlastScoringScheme#setScoreGapExtend
+ * @brief Set gap extend score.
+ * @signature bool setScoreGapExtend(blastScoringScheme, value);
+ * @param[in,out] blastScoringScheme The @link BlastScoringScheme @endlink to modify.
+ * @param[in]     value              The new value.
+ * @return isValid(blastScoringScheme) whether Karlin-Altschul values for the new scheme exist.
+ */
+
+template <typename TScore>
+inline bool
+setScoreGapExtend(BlastScoringScheme<TScore> & scheme, typename Value<TScore>::Type const val)
+{
+    setScoreGapExtend(scheme._internalScheme, val);
+    setScoreGapOpen(scheme._internalScheme, scoreGapOpenBlast(scheme) + scoreGapExtend(scheme));
+
+    return _selectSet(scheme);
+}
+
+// ----------------------------------------------------------------------------
+// Function getLambda
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#getLambda
+ * @headerfile <seqan/blast.h>
+ * @brief Get the &lambda; value of the Karlin-Altschul parameters.
+ * @signature double getLambda(blastScoringScheme);
+ */
+
+template <typename TMatrixSpec>
+inline double
+getLambda(BlastScoringScheme<Score<int, ScoreMatrix<AminoAcid, TMatrixSpec>>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int, ScoreMatrix<AminoAcid, TMatrixSpec>>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][3];
+}
+
+inline double
+getLambda(BlastScoringScheme<Score<int, Simple>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int, Simple>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][4];
+}
+
+// ----------------------------------------------------------------------------
+// Function getKappa
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#getKappa
+ * @headerfile <seqan/blast.h>
+ * @brief Get the &Kappa; value of the Karlin-Altschul parameters.
+ * @signature double getKappa(blastScoringScheme);
+ */
+
+template <typename TMatrixSpec>
+inline double
+getKappa(BlastScoringScheme<Score<int, ScoreMatrix<AminoAcid, TMatrixSpec>>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int,
+        ScoreMatrix< AminoAcid, TMatrixSpec>>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][4];
+}
+
+inline double
+getKappa(BlastScoringScheme<Score<int, Simple>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int, Simple>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][5];
+}
+
+// ----------------------------------------------------------------------------
+// Function getH
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#getH
+ * @headerfile <seqan/blast.h>
+ * @brief Get the H value of the Karlin-Altschul parameters.
+ * @signature double getH(blastScoringScheme);
+ */
+
+template <typename TMatrixSpec>
+inline double
+getH(BlastScoringScheme<Score<int, ScoreMatrix<AminoAcid, TMatrixSpec>>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int,
+        ScoreMatrix< AminoAcid, TMatrixSpec>>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][5];
+}
+
+inline double
+getH(BlastScoringScheme<Score<int, Simple>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int, Simple>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][6];
+}
+
+// ----------------------------------------------------------------------------
+// Function getAlpha
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#getAlpha
+ * @headerfile <seqan/blast.h>
+ * @brief Get the &alpha; value of the Karlin-Altschul parameters.
+ * @signature double getAlpha(blastScoringScheme);
+ */
+
+template <typename TMatrixSpec>
+inline double
+getAlpha(BlastScoringScheme<Score<int, ScoreMatrix<AminoAcid, TMatrixSpec>>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int, ScoreMatrix<AminoAcid, TMatrixSpec>>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][6];
+}
+
+inline double
+getAlpha(BlastScoringScheme<Score<int, Simple>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int, Simple>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][7];
+}
+
+// ----------------------------------------------------------------------------
+// Function getBeta
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#getBeta
+ * @headerfile <seqan/blast.h>
+ * @brief Get the &beta; value of the Karlin-Altschul parameters.
+ * @signature double getBeta(blastScoringScheme);
+ */
+
+template <typename TMatrixSpec>
+inline double
+getBeta(BlastScoringScheme<Score<int, ScoreMatrix<AminoAcid, TMatrixSpec>>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int, ScoreMatrix<AminoAcid, TMatrixSpec>>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][7];
+}
+
+inline double
+getBeta(BlastScoringScheme<Score<int, Simple>> const & scoringScheme)
+{
+    typedef KarlinAltschulValues<Score<int, Simple>> TKAValues;
+    SEQAN_ASSERT(isValid(scoringScheme));
+    return TKAValues::VALUE[scoringScheme.parameterIndex][8];
+}
+
+// ----------------------------------------------------------------------------
+// Function _lengthAdjustment
+// ----------------------------------------------------------------------------
+
+// Computes the length adjustment for E-value computation
+// Based on the public domain NCBI BLAST code by Tom Madden.
+template <typename TSize, typename TSize2, typename TScore>
+inline TSize
+_lengthAdjustment(TSize     const & dbLength,
+                  TSize2    const & queryLength,
+                  BlastScoringScheme<TScore> const & scheme)
+{
+    const double lambda = getLambda(scheme);
+    const double K      = getKappa(scheme);
+    const double logK   = std::log(K);
+    const double alpha  = getAlpha(scheme);
+    const double alphaByLambda = alpha/lambda;
+    const double beta   = getBeta(scheme);
+    const TSize maxIterations = 20;
+
+    double n = (double)dbLength;
+    double m = (double)queryLength;
+    double totalLen;
+
+    double val = 0, val_min = 0, val_max;
+    bool converged = false;
+
+     /* Choose val_max to be the largest nonnegative value that satisfies
+      *    K * (m - val) * (n - N * val) > max(m,n)
+      * Use quadratic formula: 2 c /( - b + sqrt( b*b - 4 * a * c )) */
+
+    { // scope of mb, and c, the coefficients in the quadratic formula (the variable mb is -b, a=1 ommited)
+        double mb = m + n;
+        double c  = n * m - std::max(m, n) / K;
+
+        if(c < 0) {
+            return 0;
+        } else {
+            val_max = 2 * c / (mb + std::sqrt(mb * mb - 4 * c));
+        }
+    } // end scope of mb and c
+
+    for(TSize i = 1; i <= maxIterations; i++) {
+        totalLen = (m - val) * (n - val);
+        double val_new  = alphaByLambda * (logK + std::log(totalLen)) + beta;  // proposed next value of val
+        if(val_new >= val) { // val is no bigger than the true fixed point
+            val_min = val;
+            if(val_new - val_min <= 1.0) {
+                converged = true;
+                break;
+            }
+            if(val_min == val_max) { // There are no more points to check
+                break;
+            }
+        } else { // val is greater than the true fixed point
+            val_max = val;
+        }
+        if(val_min <= val_new && val_new <= val_max) { // ell_new is in range. Accept it.
+            val = val_new;
+        } else { // else val_new is not in range. Reject it.
+            val = (i == 1) ? val_max : (val_min + val_max) / 2;
+        }
+    }
+
+    if(converged) { // the iteration converged
+        // If val_fixed is the (unknown) true fixed point, then we wish to set lengthAdjustment to floor(val_fixed).
+        // We assume that floor(val_min) = floor(val_fixed)
+        return (TSize) val_min;
+
+        // But verify that ceil(val_min) != floor(val_fixed)
+        val = std::ceil(val_min);
+        if( val <= val_max ) {
+          totalLen = (m - val) * (n - val);
+          if(alphaByLambda * (logK + std::log(totalLen)) + beta >= val) {
+            // ceil(val_min) == floor(val_fixed)
+            return (TSize) val;
+          }
+        }
+    } else { // the iteration did not converge
+        // Use the best value seen so far.
+        return (TSize) val_min;
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function computeAlignmentStats
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastMatch#computeAlignmentStats
+ * @headerfile <seqan/blast.h>
+ * @brief Compute the @link BlastMatch::alignStats @endlink member of a @link BlastMatch @endlink.
+ * @signature void computeAlignmentStats(blastMatch, context);
+ *
+ * @param[in,out]   blastMatch  A @link BlastMatch @endlink that has a valid align member.
+ * @param[in]       context     A @link BlastIOContext @endlink with parameters and buffers.
+ *
+ * The alignRow-members (@link BlastMatch::alignRow0 @endlink, @link BlastMatch::alignRow1 @endlink) are used as 
+ * in-parameter to compute the @link BlastMatch::alignStats @endlink member. This includes the raw
+ * score, amount of gaps, mismatches et cetera. This is a prerequisite for printing a match to file or computing it's
+ * e-value.
+ */
+
+template <typename TBlastMatch,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+computeAlignmentStats(TBlastMatch & match,
+                      BlastIOContext<TScore, p, h> const & context)
+{
+    computeAlignmentStats(match.alignStats, match.alignRow0, match.alignRow1, seqanScheme(context.scoringScheme));
+}
+
+// ----------------------------------------------------------------------------
+// Function computeBitScore
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastScoringScheme#computeBitScore
+ * @brief Compute the bit-score for a given raw score.
+ * @signature double computeBitScore(rawScore, blastScoringScheme);
+ *
+ * @param[in]   rawScore            The raw score of the alignment.
+ * @param[in]   blastScoringScheme The @link BlastScoringScheme @endlink.
+ *
+ * @return double The bit-score computed.
+ * @headerfile <seqan/blast.h>
+ */
+
+template <typename TScore>
+inline double
+computeBitScore(double const rawScore, BlastScoringScheme<TScore> const & scheme)
+{
+    return (getLambda(scheme) * rawScore - std::log(getKappa(scheme))) / std::log(2);
+}
+
+/*!
+ * @fn BlastMatch#computeBitScore
+ * @brief Compute the bit-score for a @link BlastMatch @endlink.
+ * @signature double computeBitScore(blastMatch, context);
+ *
+ * @param[in,out]   blastMatch  A @link BlastMatch @endlink that has a valid align member.
+ * @param[in]       context     A @link BlastIOContext @endlink with parameters and buffers.
+ *
+ * @return double blastMatch.@link BlastMatch::bitScore @endlink after computation
+ * @headerfile <seqan/blast.h>
+ *
+ * @section Remarks
+ *
+ * This  will compute the bit-score for a @link BlastMatch @endlink. At least the following
+ * members need to be set before calling this function:
+ * <li> blastMatch.@link BlastMatch::alignStats @endlink.@link AlignmentStats::alignmentScore @endlink (if you have valid
+ * alignRow-members (@link BlastMatch::alignRow0 @endlink, @link BlastMatch::alignRow1 @endlink), you can call
+ * @link BlastMatch#computeAlignmentStats @endlink to compute the stats member). </li>
+ */
+
+template <typename TBlastMatch,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline double
+computeBitScore(TBlastMatch & match,
+                BlastIOContext<TScore, p, h> const & context)
+{
+    match.bitScore = computeBitScore(match.alignStats.alignmentScore, context.scoringScheme);
+    return match.bitScore;
+}
+
+/*!
+ * @fn BlastScoringScheme#computeEValue
+ * @brief Compute the E-Value for a given raw score and sequence lengths.
+ * @signature double computeEValue(rawScore, queryLength, dbLength, blastScoringScheme);
+ *
+ * @param[in]   rawScore            The raw score of the alignment.
+ * @param[in]   queryLength         The length of the query sequence.
+ * @param[in]   dbLength            The length of the database in case of many subject sequences, otherwise the
+ * length of the subject sequence.
+ * @param[in]   blastScoringScheme The @link BlastScoringScheme @endlink.
+ *
+ * @return double The e-value computed.
+ * @headerfile <seqan/blast.h>
+ */
+
+template <typename TScore>
+inline double
+_computeEValue(double const rawScore,
+               double const adjustedQueryLength,
+               double const adjustedDbLength,
+               BlastScoringScheme<TScore> const & scheme)
+{
+    return getKappa(scheme) * adjustedQueryLength * adjustedDbLength * std::exp(-getLambda(scheme) * rawScore);
+}
+
+template <typename TScore>
+inline double
+computeEValue(__uint64 rawScore,
+              __uint64 const queryLength,
+              __uint64 const dbLength,
+              BlastScoringScheme<TScore> const & scheme)
+{
+    typedef KarlinAltschulValues<TScore> TKAValues;
+    // for some parameters the score has to be "rounded down" to being even
+    if ((TKAValues::nParams >= 11) && (TKAValues::VALUE[scheme.parameterIndex][10]))
+        --rawScore;
+
+    __uint64 adj = _lengthAdjustment(dbLength, queryLength, scheme);
+    return _computeEValue(rawScore, queryLength - adj, dbLength - adj, scheme);
+}
+
+/*!
+ * @fn BlastMatch#computeEValue
+ * @brief Compute the E-Value for a @link BlastMatch @endlink.
+ * @signature double computeEValue(blastMatch, context);
+ *
+ * @param[in,out]   blastMatch  A @link BlastMatch @endlink that has a valid align member.
+ * @param[in,out]   context     A @link BlastIOContext @endlink with parameters and buffers.
+ *
+ * @return double blastMatch.@link BlastMatch::eValue @endlink after computation
+ * @headerfile <seqan/blast.h>
+ *
+ * @section Remarks
+ *
+ * This  will compute the e-value for a @link BlastMatch @endlink. At least the following
+ * members need to be set before calling this function:
+ * <li> blastMatch.@link BlastMatch::alignStats @endlink.@link AlignmentStats::alignmentScore @endlink (if you have valid
+ * alignRow-members (@link BlastMatch::alignRow0 @endlink, @link BlastMatch::alignRow1 @endlink), you can call
+ * @link BlastMatch#computeAlignmentStats @endlink to compute the stats member). </li>
+ * <li> blastMatch.@link BlastMatch::qLength @endlink </li>
+ * <li> context.@link BlastIOContext::dbTotalLength @endlink </li>
+ *
+ * Note, that in contrast to the general interface (@link BlastScoringScheme#computeEValue @endlink), this interface
+ * caches some computation steps in the context and is therefore faster.
+ */
+
+template <typename TBlastMatch,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline double
+computeEValue(TBlastMatch & match,
+              BlastIOContext<TScore, p, h> & context)
+{
+    // convert to 64bit and divide for translated sequences
+    __uint64 ql = match.qLength / (qIsTranslated(context.blastProgram) ? 3 : 1);
+    // length adjustment not yet computed
+    if (context._cachedLengthAdjustments.find(ql) == context._cachedLengthAdjustments.end())
+        context._cachedLengthAdjustments[ql] = _lengthAdjustment(context.dbTotalLength, ql, context.scoringScheme);
+
+    __uint64 adj = context._cachedLengthAdjustments[ql];
+
+    match.eValue = _computeEValue(match.alignStats.alignmentScore,
+                                  ql - adj,
+                                  context.dbTotalLength - adj,
+                                  context.scoringScheme);
+    return match.eValue;
+}
+
+}
+
+#endif // ndef __BLAST_STATISTICS_H__
diff --git a/seqan/blast/blast_tabular.h b/seqan/blast/blast_tabular.h
new file mode 100644
index 0000000..c42e0ef
--- /dev/null
+++ b/seqan/blast/blast_tabular.h
@@ -0,0 +1,677 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// This file contains routines to generate BLAST tab-seperated output
+// ==========================================================================
+
+#ifndef SEQAN_BLAST_BLAST_TABULAR_H_
+#define SEQAN_BLAST_BLAST_TABULAR_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class BlastTabular
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastTabular
+ * @signature typedef Tag<BlastTabular_> BlastTabular;
+ * @headerfile <seqan/blast.h>
+ * @brief Support for Blast Tabular file formats (with and without comment lines)
+ *
+ * There are three blast format related tags in SeqAn:
+ *
+ * <li> @link BlastReport @endlink with the FormattedFile output specialization @link BlastReportFileOut @endlink</li>
+ * <li> @link BlastTabular @endlink with the FormattedFile output and input specializations
+ * @link BlastTabularFileOut @endlink and @link BlastTabularFileIn @endlink</li>
+ * <li> @link BlastTabularLL @endlink which provides light-weight, but very basic tabular IO </li>
+ *
+ * This is the second tag, it offers <b>high-level</b> support for reading and writing NCBI Blast compatible
+ * <b>tabular</b> files, both with and without comment lines. These are the formats that are available in legacy Blast
+ * (<tt>blastall</tt> executable) with the parameters <tt>-m 8</tt> and <tt>-m 9</tt> (with comment lines)
+ * and in BLAST+ (<tt>blastx</tt>, <tt>blastn</tt>...) with
+ * the parameters <tt>-outfmt 6</tt> and <tt>-outfmt 7</tt> respectively.
+ *
+ * Please consult the documentation for @link BlastIOContext @endlink to understand
+ * the different options you have with this format.
+ *
+ * For very basic tabular IO there is the third tag, @link BlastTabularLL @endlink.
+ *
+ * The reference Blast implementation used for developing the SeqAn support is NCBI Blast+ 2.2.26 and
+ * NCBI Blast 2.2.26 for the legacy support.
+ *
+ * See @link BlastTabularFileIn @endlink for more information on file reading and @link BlastTabularFileOut @endlink
+ * for more information on file writing.
+ */
+struct BlastTabular_;
+typedef Tag<BlastTabular_> BlastTabular;
+
+// ----------------------------------------------------------------------------
+// Class BlastTabularSpec
+// ----------------------------------------------------------------------------
+
+/*!
+ * @enum BlastTabularSpec
+ * @headerfile <seqan/blast.h>
+ * @signature enum class BlastTabularSpec : uint8_t { ... };
+ * @brief Spec for @link BlastIOContext @endlink
+ *
+ * @val BlastTabularSpec BlastTabularSpec::NO_COMMENTS
+ * @brief Tabular format without comment lines
+ *
+ * @val BlastTabularSpec BlastTabularSpec::COMMENTS
+ * @brief Tabular format with comment lines
+ *
+ * @val BlastTabularSpec BlastTabularSpec::UNKNOWN
+ * @brief not defined or not known
+ *
+ * @val BlastTabularSpec BlastTabularSpec::DYNAMIC
+ * @brief This can only be used when defining a @link BlastTabularSpecSelector @endlink
+ *
+ */
+enum class BlastTabularSpec : uint8_t
+{
+    NO_COMMENTS = 0,
+    COMMENTS = 1,
+    UNKNOWN = 254,
+    DYNAMIC = 255
+};
+
+// ----------------------------------------------------------------------------
+// Class BlastTabularSpecSelector
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastTabularSpecSelector
+ * @brief A datatype that can act as either a @link BlastTabularSpec @endlink or as an constexpr integral constant
+ * thereof.
+ *
+ * @signature template <BlastTabularSpec h> struct BlastTabularSpecSelector { ... };
+ * @headerfile <seqan/blast.h>
+ *
+ * This is a proxy datatype that enables compile-time optimizations through constexpressions iff the value
+ * is known at compile time. You will rarely need to instantiate objects of this type yourself, but they
+ * are used in the @link BlastIOContext @endlink.
+ *
+ * @subsection Example
+ *
+ * mutable variable:
+ * @code{.cpp}
+ * BlastTabularSpecSelector<BlastTabularSpec::DYNAMIC> myProgram = BlastTabularSpec::COMMENTS;
+ * // same as
+ * // BlastTabularSpec myProgram = BlastTabularSpec::COMMENTS;
+ *
+ * SEQAN_ASSERT(myProgram == BlastTabularSpec::COMMENTS); // assertion is checked at run-time
+ * myProgram = BlastTabularSpec::NO_COMMENTS; // works without problems
+ * @endcode
+ *
+ * compile time integral constant:
+ * @code{.cpp}
+ * BlastTabularSpecSelector<BlastTabularSpec::COMMENTS> myProgram;
+ * static_assert(myProgram == BlastTabularSpec::COMMENTS, ""); // assertion is checked at compile time
+ * myProgram = BlastTabularSpec::NO_COMMENTS; // would fail, because value is fixed
+ * @endcode
+ */
+
+template <BlastTabularSpec _h>
+struct BlastTabularSpecSelector
+{
+    constexpr operator BlastTabularSpec() const
+    {
+        return _h;
+    }
+
+    BlastTabularSpecSelector operator=(BlastTabularSpec const h)
+    {
+        if (h != _h)
+            SEQAN_FAIL("ERROR: Tried to set tabularSpec on context, but was already defined at compile time (and set "
+                       "to a different value)!");
+        return *this;
+    }
+};
+
+template <>
+struct BlastTabularSpecSelector<BlastTabularSpec::DYNAMIC>
+{
+    BlastTabularSpec _runtimeValue = BlastTabularSpec::UNKNOWN;
+
+    operator BlastTabularSpec() const
+    {
+        return _runtimeValue;
+    }
+
+    BlastTabularSpecSelector operator=(BlastTabularSpec const h)
+    {
+        _runtimeValue = h;
+        return *this;
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class MagicHeader
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<BlastTabular, T> :
+    public MagicHeader<Nothing, T> {};
+
+// ----------------------------------------------------------------------------
+// Class FileExtensions
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<BlastTabular, T>
+{
+    static constexpr char const * VALUE[2] =
+    {
+        ".m8",
+        ".m9"
+    };
+};
+
+template <typename T>
+constexpr char const * FileExtensions<BlastTabular, T>::VALUE[2];
+
+// ----------------------------------------------------------------------------
+// Class BlastMatchField
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastMatchField BlastMatchField
+ * @brief A "meta" datastructure that contains information about members of @link BlastMatch @endlinkes
+ * @headerfile seqan/blast.h
+ *
+ * @signature template <typename TVoidSpec = void> struct BlastMatchField;
+ * @tparam TVoidSpec An extra spec to prevent global inclusion of statics members (you can safely ignore this)
+ *
+ * This data structure conveniently gives access to all possible fields used in
+ * BLAST-compatabile tabular output formats. @link BlastMatchField::Enum @endlink is needed to
+ * specify a custom field composition for a @link BlastIOContext @endlink.
+ *
+ * The member variables offer the correct labels for the tabular formats' I/O and strings
+ * to interact with the user on the command line.
+ *
+ * Please note that for the legacyFormat (@link BlastIOContext::legacyFormat @endlink) specifying or reading custom
+ * fields is not supported and the columnsLabels will always be printed as
+ * @link BlastMatchField::legacyColumnLabels @endlink.
+ *
+ * <h3>Table overview</h3>
+ * @htmlonly
+ * <span style="font-size:90%"><table>
+ * <tr><th>#</th><th>Enum</th><th>optionLabels</th><th>columnLabels</th><th>descriptions</th><th>implemented</th></tr>
+ * <tr><td>0</td><td>STD</td><td>std</td><td>query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score</td><td>Default 12 columns (Query Seq-id, Subject Seq-id, Percentage of identical matches, Alignment length, Number of mismatches, Number of gap openings, Start of alignment in query, End of alignment in query, Start of alignment in subject, End of alignment in subject, Expect value, Bit score)</td><td>&#9745;</td></tr>
+ * <tr><td>1</td><td>Q_SEQ_ID</td><td>qseqid</td><td>query id</td><td>Query Seq-id</td><td>&#9745;</td></tr>
+ * <tr><td>2</td><td>Q_GI</td><td>qgi</td><td>query gi</td><td>Query GI</td><td>&#9744;</td></tr>
+ * <tr><td>3</td><td>Q_ACC</td><td>qacc</td><td>query acc.</td><td>Query accesion</td><td>&#9744;</td></tr>
+ * <tr><td>4</td><td>Q_ACCVER</td><td>qaccver</td><td>query acc.ver</td><td>Query accesion.version</td><td>&#9744;</td></tr>
+ * <tr><td>5</td><td>Q_LEN</td><td>qlen</td><td>query length</td><td>Query sequence length</td><td>&#9745;</td></tr>
+ * <tr><td>6</td><td>S_SEQ_ID</td><td>sseqid</td><td>subject id</td><td>Subject Seq-id</td><td>&#9745;</td></tr>
+ * <tr><td>7</td><td>S_ALL_SEQ_ID</td><td>sallseqid</td><td>subject ids</td><td>All subject Seq-id(s), separated by a ';'</td><td>&#9744;</td></tr>
+ * <tr><td>8</td><td>S_GI</td><td>sgi</td><td>subject gi</td><td>Subject GI</td><td>&#9744;</td></tr>
+ * <tr><td>9</td><td>S_ALL_GI</td><td>sallgi</td><td>subject gis</td><td>All subject GIs</td><td>&#9744;</td></tr>
+ * <tr><td>10</td><td>S_ACC</td><td>sacc</td><td>subject acc.</td><td>Subject accession</td><td>&#9744;</td></tr>
+ * <tr><td>11</td><td>S_ACCVER</td><td>saccver</td><td>subject acc.ver</td><td>Subject accession.version</td><td>&#9744;</td></tr>
+ * <tr><td>12</td><td>S_ALLACC</td><td>sallacc</td><td>subject accs.</td><td>All subject accessions</td><td>&#9744;</td></tr>
+ * <tr><td>13</td><td>S_LEN</td><td>slen</td><td>subject length</td><td>Subject sequence length</td><td>&#9745;</td></tr>
+ * <tr><td>14</td><td>Q_START</td><td>qstart</td><td>q. start</td><td>Start of alignment in query</td><td>&#9745;</td></tr>
+ * <tr><td>15</td><td>Q_END</td><td>qend</td><td>q. end</td><td>End of alignment in query</td><td>&#9745;</td></tr>
+ * <tr><td>16</td><td>S_START</td><td>sstart</td><td>s. start</td><td>Start of alignment in subject</td><td>&#9745;</td></tr>
+ * <tr><td>17</td><td>S_END</td><td>send</td><td>s. end</td><td>End of alignment in subject</td><td>&#9745;</td></tr>
+ * <tr><td>18</td><td>Q_SEQ</td><td>qseq</td><td>query seq</td><td>Aligned part of query sequence</td><td>&#9744;</td></tr>
+ * <tr><td>19</td><td>S_SEQ</td><td>sseq</td><td>subject seq</td><td>Aligned part of subject sequence</td><td>&#9744;</td></tr>
+ * <tr><td>20</td><td>E_VALUE</td><td>evalue</td><td>evalue</td><td>Expect value</td><td>&#9745;</td></tr>
+ * <tr><td>21</td><td>BIT_SCORE</td><td>bitscore</td><td>bit score</td><td>Bit score</td><td>&#9745;</td></tr>
+ * <tr><td>22</td><td>SCORE</td><td>score</td><td>score</td><td>Raw score</td><td>&#9745;</td></tr>
+ * <tr><td>23</td><td>LENGTH</td><td>length</td><td>alignment length</td><td>Alignment length</td><td>&#9745;</td></tr>
+ * <tr><td>24</td><td>P_IDENT</td><td>pident</td><td>% identity</td><td>Percentage of identical matches</td><td>&#9745;</td></tr>
+ * <tr><td>25</td><td>N_IDENT</td><td>nident</td><td>identical</td><td>Number of identical matches</td><td>&#9745;</td></tr>
+ * <tr><td>26</td><td>MISMATCH</td><td>mismatch</td><td>mismatches</td><td>Number of mismatches</td><td>&#9745;</td></tr>
+ * <tr><td>27</td><td>POSITIVE</td><td>positive</td><td>positives</td><td>Number of positive-scoring matches</td><td>&#9745;</td></tr>
+ * <tr><td>28</td><td>GAP_OPEN</td><td>gapopen</td><td>gap opens</td><td>Number of gap openings</td><td>&#9745;</td></tr>
+ * <tr><td>29</td><td>GAPS</td><td>gaps</td><td>gaps</td><td>Total number of gaps</td><td>&#9745;</td></tr>
+ * <tr><td>30</td><td>P_POS</td><td>ppos</td><td>% positives</td><td>Percentage of positive-scoring matches</td><td>&#9745;</td></tr>
+ * <tr><td>31</td><td>FRAMES</td><td>frames</td><td>query/sbjct frames</td><td>Query and subject frames separated by a '/'</td><td>&#9745;</td></tr>
+ * <tr><td>32</td><td>Q_FRAME</td><td>qframe</td><td>query frame</td><td>Query frame</td><td>&#9745;</td></tr>
+ * <tr><td>33</td><td>S_FRAME</td><td>sframe</td><td>sbjct frame</td><td>Subject frame</td><td>&#9745;</td></tr>
+ * <tr><td>34</td><td>BTOP</td><td>btop</td><td>BTOP</td><td>Blast traceback operations (BTOP)</td><td>&#9744;</td></tr>
+ * <tr><td>35</td><td>S_TAX_IDS</td><td>staxids</td><td>subject tax ids</td><td>unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</td><td>&#9744;</td></tr>
+ * <tr><td>36</td><td>S_SCI_NAMES</td><td>sscinames</td><td>subject sci names</td><td>unique Subject Scientific Name(s), separated by a ';'</td><td>&#9744;</td></tr>
+ * <tr><td>37</td><td>S_COM_NAMES</td><td>scomnames</td><td>subject com names</td><td>unique Subject Common Name(s), separated by a ';'</td><td>&#9744;</td></tr>
+ * <tr><td>38</td><td>S_BLAST_NAMES</td><td>sblastnames</td><td>subject blast names</td><td>unique Subject Blast Name(s), separated by a ';' (in alphabetical order)</td><td>&#9744;</td></tr>
+ * <tr><td>39</td><td>S_S_KINGDOMS</td><td>sskingdoms</td><td>subject super kingdoms</td><td>unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)</td><td>&#9744;</td></tr>
+ * <tr><td>40</td><td>S_TITLE</td><td>stitle</td><td>subject title</td><td>Subject Title</td><td>&#9744;</td></tr>
+ * <tr><td>41</td><td>S_ALL_TITLES</td><td>salltitles</td><td>subject titles</td><td>All Subject Title(s), separated by a '<>'</td><td>&#9744;</td></tr>
+ * <tr><td>42</td><td>S_STRAND</td><td>sstrand</td><td>subject strand</td><td>Subject Strand</td><td>&#9744;</td></tr>
+ * <tr><td>43</td><td>Q_COV_S</td><td>qcovs</td><td>% subject coverage</td><td>Query Coverage Per Subject</td><td>&#9744;</td></tr>
+ * <tr><td>45</td><td>Q_COV_HSP</td><td>qcovhsp</td><td>% hsp coverage</td><td>Query Coverage Per HSP</td><td>&#9744;</td></tr>
+ * </table></span>
+ * @endhtmlonly
+ *
+ * More fields will likely be implemented in the future.
+ */
+
+template <typename TVoidSpec = void>
+struct BlastMatchField
+{
+    /*!
+     * @enum BlastMatchField::Enum
+     * @headerfile seqan/blast.h
+     * @signature enum class BlastMatchField<TVoidSpec>::Enum : uint8_t { ... };
+     * @brief A strongly typed enum mapping all fields supported by NCBI Blast to an integer
+     *
+     * The available values are visible in detailed description of @link BlastMatchField @endlink.
+     */
+    enum class Enum : uint8_t
+    {
+        STD,
+        Q_SEQ_ID,
+        Q_GI,
+        Q_ACC,
+        Q_ACCVER,
+        Q_LEN,
+        S_SEQ_ID,
+        S_ALL_SEQ_ID,
+        S_GI,
+        S_ALL_GI,
+        S_ACC,
+        S_ACCVER,
+        S_ALLACC,
+        S_LEN,
+        Q_START,
+        Q_END,
+        S_START,
+        S_END,
+        Q_SEQ,
+        S_SEQ,
+        E_VALUE,
+        BIT_SCORE,
+        SCORE,
+        LENGTH,
+        P_IDENT,
+        N_IDENT,
+        MISMATCH,
+        POSITIVE,
+        GAP_OPEN,
+        GAPS,
+        P_POS,
+        FRAMES,
+        Q_FRAME,
+        S_FRAME,
+        BTOP,
+        S_TAX_IDS,
+        S_SCI_NAMES,
+        S_COM_NAMES,
+        S_BLAST_NAMES,
+        S_S_KINGDOMS,
+        S_TITLE,
+        S_ALL_TITLES,
+        S_STRAND,
+        Q_COV_S,
+        Q_COV_HSP
+    };
+
+    /*!
+     * @var static_constexpr_std::array<Enum_const,12> BlastMatchField::defaults
+     * @brief An std::array of @link BlastMatchField::Enum @endlink indicating the fields that are default
+     *
+     * @code{.cpp}
+     * static constexpr std::array<Enum const, 12> defaults
+     * {
+     *     {
+     *         Enum::Q_SEQ_ID,
+     *         Enum::S_SEQ_ID,
+     *         Enum::P_IDENT,
+     *         Enum::LENGTH,
+     *         Enum::MISMATCH,
+     *         Enum::GAP_OPEN,
+     *         Enum::Q_START,
+     *         Enum::Q_END,
+     *         Enum::S_START,
+     *         Enum::S_END,
+     *         Enum::E_VALUE,
+     *         Enum::BIT_SCORE
+     *     }
+     * };
+     * @endcode
+     */
+    // this is what Enum::STD stands for
+    static constexpr std::array<Enum const, 12> defaults
+    {
+        {
+            Enum::Q_SEQ_ID,
+            Enum::S_SEQ_ID,
+            Enum::P_IDENT,
+            Enum::LENGTH,
+            Enum::MISMATCH,
+            Enum::GAP_OPEN,
+            Enum::Q_START,
+            Enum::Q_END,
+            Enum::S_START,
+            Enum::S_END,
+            Enum::E_VALUE,
+            Enum::BIT_SCORE
+        }
+    };
+
+    /*!
+     * @var static_constexpr_const_std::array<char_const*,45> BlastMatchField::optionLabels[]
+     * @brief An array of CStrings representing the command line parameter name of each field
+     */
+    static constexpr const std::array<char const *, 45> optionLabels
+    {
+      {
+        "std",
+        "qseqid",
+        "qgi",
+        "qacc",
+        "qaccver",
+        "qlen",
+        "sseqid",
+        "sallseqid",
+        "sgi",
+        "sallgi",
+        "sacc",
+        "saccver",
+        "sallacc",
+        "slen",
+        "qstart",
+        "qend",
+        "sstart",
+        "send",
+        "qseq",
+        "sseq",
+        "evalue",
+        "bitscore",
+        "score",
+        "length",
+        "pident",
+        "nident",
+        "mismatch",
+        "positive",
+        "gapopen",
+        "gaps",
+        "ppos",
+        "frames",
+        "qframe",
+        "sframe",
+        "btop",
+        "staxids",
+        "sscinames",
+        "scomnames",
+        "sblastnames",
+        "sskingdoms",
+        "stitle",
+        "salltitles",
+        "sstrand",
+        "qcovs",
+        "qcovhsp"
+      }
+    };
+
+    /*!
+     * @var static_constexpr_char_const_*_const BlastMatchField::legacyColumnLabels
+     * @brief A single CString representing the <b>column labels</b> of the @link BlastIOContext::legacyFormat @endlink.
+     */
+    static constexpr char const * const legacyColumnLabels =
+    {
+        "Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s."
+         " end, e-value, bit score"
+    };
+
+    /*!
+     * @var static_constexpr_const_std::array<char_const*,45> BlastMatchField::columnLabels[]
+     * @brief An array of CStrings representing the <b>column label</b> of each possible field; for the
+     * @link BlastIOContext::legacyFormat @endlink, use @link BlastMatchField::legacyColumnLabels @endlink instead.
+     */
+    static constexpr const std::array<char const *, 45> columnLabels
+    {
+      {
+        "query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. "
+        "end, evalue, bit score",
+        "query id",
+        "query gi",
+        "query acc.",
+        "query acc.ver",
+        "query length",
+        "subject id",
+        "subject ids",
+        "subject gi",
+        "subject gis",
+        "subject acc.",
+        "subject acc.ver",
+        "subject accs.",
+        "subject length",
+        "q. start",
+        "q. end",
+        "s. start",
+        "s. end",
+        "query seq",
+        "subject seq",
+        "evalue",
+        "bit score",
+        "score",
+        "alignment length",
+        "% identity",
+        "identical",
+        "mismatches",
+        "positives",
+        "gap opens",
+        "gaps",
+        "% positives",
+        "query/sbjct frames",
+        "query frame",
+        "sbjct frame",
+        "BTOP",
+        "subject tax ids",
+        "subject sci names",
+        "subject com names",
+        "subject blast names",
+        "subject super kingdoms",
+        "subject title",
+        "subject titles",
+        "subject strand",
+        "% subject coverage",
+        "% hsp coverage"
+      }
+    };
+
+    /*!
+     * @var static_constexpr_const_std::array<char_const*,45> BlastMatchField::descriptions[]
+     * @brief An array of CStrings representing the human-readable descriptions of each field
+     */
+    static constexpr const std::array<char const *, 45> descriptions
+    {
+      {
+        "Default 12 columns (Query Seq-id, Subject Seq-id, Percentage of "
+         "identical matches, Alignment length, Number of mismatches, Number of "
+         "gap openings, Start of alignment in query, End of alignment in query,"
+         " Start of alignment in subject, End of alignment in subject, Expect "
+         "value, Bit score",
+        "Query Seq-id",
+        "Query GI",
+        "Query accesion",
+        "Query accesion.version",
+        "Query sequence length",
+        "Subject Seq-id",
+        "All subject Seq-id(s), separated by a ';'",
+        "Subject GI",
+        "All subject GIs",
+        "Subject accession",
+        "Subject accession.version",
+        "All subject accessions",
+        "Subject sequence length",
+        "Start of alignment in query",
+        "End of alignment in query",
+        "Start of alignment in subject",
+        "End of alignment in subject",
+        "Aligned part of query sequence",
+        "Aligned part of subject sequence",
+        "Expect value",
+        "Bit score",
+        "Raw score",
+        "Alignment length",
+        "Percentage of identical matches",
+        "Number of identical matches",
+        "Number of mismatches",
+        "Number of positive-scoring matches",
+        "Number of gap openings",
+        "Total number of gaps",
+        "Percentage of positive-scoring matches",
+        "Query and subject frames separated by a '/'",
+        "Query frame",
+        "Subject frame",
+        "Blast traceback operations (BTOP)",
+        "unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)",
+        "unique Subject Scientific Name(s), separated by a ';'",
+        "unique Subject Common Name(s), separated by a ';'",
+        "unique Subject Blast Name(s), separated by a ';' (in alphabetical order)",
+        "unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)",
+        "Subject Title",
+        "All Subject Title(s), separated by a '<>'",
+        "Subject Strand",
+        "Query Coverage Per Subject",
+        "Query Coverage Per HSP"
+      }
+    };
+
+    /*!
+     * @var static_constexpr_const_std::array<bool,45> BlastMatchField::implemented[]
+     * @brief An array of bools revealing whether the Blast I/O module supports printing this field
+     */
+    //TODO(c++14): change to std::bitset that is initialized with binary literal
+    static constexpr const std::array<bool, 45> implemented
+    {
+      {
+        true,
+        true,
+        false,
+        false,
+        false,
+        true,
+        true,
+        false,
+        false,
+        false,
+        false,
+        false,
+        false,
+        true,
+        true,
+        true,
+        true,
+        true,
+        false,
+        false,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        true,
+        false,
+        false,
+        false,
+        false,
+        false,
+        false,
+        false,
+        false,
+        false,
+        false,
+        false
+      }
+    };
+};
+
+template <typename TVoidSpec>
+constexpr const std::array<char const *, 45> BlastMatchField<TVoidSpec>::optionLabels;
+
+template <typename TVoidSpec>
+constexpr char const * const BlastMatchField<TVoidSpec>::legacyColumnLabels;
+
+template <typename TVoidSpec>
+constexpr const std::array<char const *, 45> BlastMatchField<TVoidSpec>::columnLabels;
+
+template <typename TVoidSpec>
+constexpr const std::array<char const *, 45> BlastMatchField<TVoidSpec>::descriptions;
+
+template <typename TVoidSpec>
+constexpr const std::array<bool, 45> BlastMatchField<TVoidSpec>::implemented;
+
+template <typename TVoidSpec>
+constexpr const std::array<typename BlastMatchField<TVoidSpec>::Enum const, 12> BlastMatchField<TVoidSpec>::defaults;
+
+// ============================================================================
+// Metafunctions and global const-expressions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TContext, typename TDirection, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<BlastTabular, TDirection, TContext>, TStorageSpec>
+{
+    typedef TContext Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec>
+struct FileFormat<FormattedFile<BlastTabular, TDirection, TSpec> >
+{
+    typedef BlastTabular Type;
+};
+
+}
+
+#endif
diff --git a/seqan/blast/blast_tabular_in.h b/seqan/blast/blast_tabular_in.h
new file mode 100644
index 0000000..5f01550
--- /dev/null
+++ b/seqan/blast/blast_tabular_in.h
@@ -0,0 +1,986 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// This file contains routines to read BLAST tab-seperated output
+// ==========================================================================
+
+#ifndef SEQAN_BLAST_BLAST_TABULAR_READ_H_
+#define SEQAN_BLAST_BLAST_TABULAR_READ_H_
+
+/* IMPLEMENTATION NOTES
+
+BLAST TABULAR example:
+
+The format of a blast tabular output file is less simple than it looks, here's
+the general form
+
+COMMENTLINES
+ MATCH
+ MATCH
+ MATCH
+ MATCH
+COMMENTLINES
+ MATCH
+COMMENTLINES
+COMMENTLINES
+...
+
+=> COMMENTLINES for each sequence, 0-n Matchs for each sequence
+=> Each record is one-line, each COMMENTLINES is multiline
+
+COMMENTLINES usually consists of:
+
+# Program Tag [e.g BLASTX 2.2.27+ ]
+# Query Id [ID of the query *sequence*]
+# Database Id [note that this is not the name of the sequence in the db, but of
+  the database itself, e.g. "nr" -> usually the same for each file]
+# Fields: [Headers of columns]
+# n "hits found"
+
+The first three lines are always written.
+The Fields line is always writen by NCBI Blast, but only when hits > 0 by NCBI Blast+.
+The "number of hits"-line is always printed by NCBI Blast+, and never by NCBI Blast.
+
+Possibly other lines can be written as comments.
+
+Because 0 matches are allowed, multiple COMMENTLINES can succeed each other, the
+criterium for seperation employed by this implementation is that an NCBI Blast
+COMMENTLINES always ends after the "Fields" line and NCBI Blast+ COMMENTLINES end after
+the "number of hits"-line.
+*/
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Type BlastFileIn
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastTabularFileIn
+ * @signature template <typename TBlastIOContext>
+ * using BlastTabularFileIn = FormattedFile<BlastTabular, Input, TBlastIOContext>;
+ * @extends FormattedFileIn
+ * @headerfile <seqan/blast.h>
+ * @brief FormattedFileIn abstraction for @link BlastTabular @endlink
+ *
+ * This is a @link FormattedFile @endlink specialization for reading @link BlastTabular @endlink formats. For details
+ * on how to influence the reading of files and how to differentiate between the tabular format without comment lines
+ * and the one with comment lines, see @link BlastIOContext @endlink.
+ * Please note that you have specify the type of the context as a template parameter to BlastTabularFileIn.
+ *
+ * @section Overview
+ *
+ * <ul>
+ * <li> open @link BlastTabularFileIn @endlink</li>
+ * <li> @link BlastTabularFileIn#readHeader @endlink </li>
+ * <li> while @link BlastTabularFileIn#onRecord @endlink </li>
+ * <ul><li> @link BlastTabularFileIn#readRecord @endlink</li></ul>
+ * <li> @link BlastTabularFileIn#readFooter @endlink </li>
+ * </ul>
+ *
+ * For a detailed example have a look at the
+ * <a href="http://seqan.readthedocs.org/en/develop/Tutorial/BlastIO.html">Blast IO tutorial</a>.
+ *
+ * @see BlastRecord
+ */
+
+template <typename TBlastIOContext = BlastIOContext<>>
+using BlastTabularFileIn = FormattedFile<BlastTabular, Input, TBlastIOContext>;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function atEnd()
+// ----------------------------------------------------------------------------
+
+template <typename TScore,
+          typename TFwdIterator,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline bool
+atEnd(BlastIOContext<TScore, p, h> const & context,
+      TFwdIterator const & iter,
+      BlastTabular const &)
+{
+    return (atEnd(iter) && empty(context._lineBuffer));
+}
+
+template <typename TContext>
+inline bool
+atEnd(BlastTabularFileIn<TContext> & formattedFile)
+{
+    return atEnd(context(formattedFile), formattedFile.iter, BlastTabular());
+}
+
+// ----------------------------------------------------------------------------
+// Function guessFormat()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+inline bool guessFormat(FormattedFile<BlastTabular, Input, TSpec> & file)
+{
+    if (value(file.iter) == '#')
+        context(file).tabularSpec = BlastTabularSpec::COMMENTS;
+    else
+        context(file).tabularSpec = BlastTabularSpec::NO_COMMENTS;
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function _onMatch()
+// ----------------------------------------------------------------------------
+
+template <typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline bool
+_onMatch(BlastIOContext<TScore, p, h> & context,
+        BlastTabular const &)
+{
+    return (!startsWith(context._lineBuffer, "#") && !empty(context._lineBuffer));
+}
+
+// ----------------------------------------------------------------------------
+// Function onRecord()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularFileIn#onRecord
+ * @brief Returns whether the currently buffered line looks like the start of a record.
+ * @signature bool onRecord(blastTabularIn);
+ * @headerfile seqan/blast.h
+ *
+ * @param[in,out] blastTabularIn A @link BlastTabularFileIn @endlink formattedFile.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ *
+ * @return bool true or false
+ */
+
+template <typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline bool
+onRecord(BlastIOContext<TScore, p, h> & context,
+         BlastTabular const &)
+{
+    if (context.tabularSpec == BlastTabularSpec::NO_COMMENTS)
+        return _onMatch(context, BlastTabular());
+
+    //      comment lines                                  Footer
+    return (startsWith(context._lineBuffer, "#") && (!startsWith(context._lineBuffer, "# BLAST processed ")));
+}
+
+template <typename TContext>
+inline bool
+onRecord(BlastTabularFileIn<TContext> & formattedFile)
+{
+    return onRecord(context(formattedFile), BlastTabular());
+}
+
+// ----------------------------------------------------------------------------
+// Function _goNextLine()
+// ----------------------------------------------------------------------------
+
+template <typename TScore,
+          typename TFwdIterator,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_goNextLine(BlastIOContext<TScore, p, h> & context,
+           TFwdIterator & iter,
+           BlastTabular const &)
+{
+    clear(context._lineBuffer);
+    if (!atEnd(iter))
+        readLine(context._lineBuffer, iter);
+}
+
+// ----------------------------------------------------------------------------
+// Function _readCommentLines()
+// ----------------------------------------------------------------------------
+
+template <typename TMatch,
+          typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_readCommentLinesImpl(BlastRecord<TMatch> & r,
+                      TFwdIterator & iter,
+                      BlastIOContext<TScore, p, h> & context,
+                      BlastTabular const &)
+{
+    // this is a match instead of comment lines
+    if (_onMatch(context, BlastTabular()))
+        SEQAN_THROW(ParseError("Commen lines expected, but not found."));
+    else
+        context.tabularSpec = BlastTabularSpec::COMMENTS;
+
+    int queryLinePresent = 0;
+    int dbLinePresent = 0;
+    int fieldsLinePresent = 0;
+    int hitsLinePresent = 0;
+
+    do
+    {
+        if (std::regex_search(begin(context._lineBuffer, Standard()),
+                              end(context._lineBuffer, Standard()),
+                              std::regex("^# T?BLAST")))
+        {
+            // last line of file
+            if (SEQAN_UNLIKELY(startsWith(context._lineBuffer, "# BLAST processed ") && !context.legacyFormat))
+            {
+                SEQAN_FAIL("ERROR: You called readRecord() when you should have called readFooter()."
+                           "Always check onRecord() before calling readRecord().");
+            }
+            else // first line of the comments
+            {
+                assign(context.versionString, suffix(context._lineBuffer, 2));
+                context.blastProgram = _programStringToTag(prefix(context.versionString,
+                                                                  std::find(begin(context.versionString, Standard()),
+                                                                            end(context.versionString, Standard()),
+                                                                            ' ')
+                                                                  - begin(context.versionString, Standard())));
+
+                context.legacyFormat = !std::regex_search(begin(context.versionString, Standard()),
+                                                          end(context.versionString, Standard()),
+                                                          std::regex("\\d\\.\\d\\.\\d{1,2}\\+"));
+            }
+        }
+        else if (startsWith(context._lineBuffer, "# Query:"))
+        {
+            ++queryLinePresent;
+            assign(r.qId, suffix(context._lineBuffer, 9));
+
+        }
+        else if (startsWith(context._lineBuffer, "# Database:"))
+        {
+            ++dbLinePresent;
+            assign(context.dbName, suffix(context._lineBuffer, 12));
+        }
+        else if (startsWith(context._lineBuffer, "# Fields:"))
+        {
+            ++fieldsLinePresent;
+            clear(context._stringBuffer);
+            // make sure target is big enough
+            resize(context._stringBuffer, length(context._lineBuffer) - 10);
+            // use escape character as placeholder for replacement since strSplit only handles single characters
+            std::regex_replace(begin(context._stringBuffer, Standard()),
+                               begin(context._lineBuffer, Standard()) + 10, // skip "# Fields:"
+                               end(context._lineBuffer, Standard()),
+                               std::regex(", "),
+                               "\x7F");
+            // shrink back down to actual size (replacing two letters with one makes string shorter!)
+            resize(context._stringBuffer, length(context._stringBuffer.c_str()));
+            strSplit(context.fieldsAsStrings, context._stringBuffer, EqualsChar<'\x7F'>(), true);
+
+            if (context.legacyFormat)
+            {
+                // assume defaults for LEGACY
+                if (!context.ignoreFieldsInComments)
+                    appendValue(context.fields, BlastMatchField<>::Enum::STD);
+            }
+            else if (!context.ignoreFieldsInComments)
+            {
+                bool defaults = true;
+                resize(context.fields, length(context.fieldsAsStrings));
+                for (uint8_t j = 0; j < length(context.fieldsAsStrings); ++j)
+                {
+                    for (uint8_t i = 0; i < length(BlastMatchField<>::columnLabels); ++i)
+                    {
+                        if (context.fieldsAsStrings[j] ==
+                            BlastMatchField<>::columnLabels[i])
+                        {
+                            context.fields[j] =
+                                static_cast<BlastMatchField<>::Enum>(i);
+
+                            if ((j >= length(BlastMatchField<>::defaults)) &&
+                                (static_cast<BlastMatchField<>::Enum>(i) !=
+                                BlastMatchField<>::defaults[j]))
+                                defaults = false;
+                            break;
+                        }
+                    }
+                }
+                if (defaults) // replace multiple fields with the default meta field
+                {
+                    clear(context.fields);
+                    appendValue(context.fields, BlastMatchField<>::Enum::STD);
+                }
+            }
+        }
+        else
+        {
+            if (!context.legacyFormat)
+            {
+                // is hits counter?
+                if (endsWith(context._lineBuffer, "hits found"))
+                {
+                    clear(context._stringBuffer);
+                    for (unsigned i = 2; (i < length(context._lineBuffer) && isdigit(context._lineBuffer[i])); ++i)
+                        appendValue(context._stringBuffer, context._lineBuffer[i], Generous());
+
+                    __uint64 hits = lexicalCast<__uint64>(context._stringBuffer);
+
+                    if (hits)
+                    {
+                        resize(r.matches, hits);
+                    }
+                    else  // hits = 0 means no fieldList, restore default
+                    {
+                        appendValue(context.fields, BlastMatchField<>::Enum::STD);
+
+                        context._stringBuffer = std::regex_replace(BlastMatchField<>::columnLabels[0],
+                                                                   std::regex(", "),
+                                                                   "\x7F");
+                        strSplit(context.fieldsAsStrings, context._stringBuffer, EqualsChar<'\x7F'>(), true);
+                    }
+
+                    ++hitsLinePresent;
+//                     break; // comments are finished
+                }
+                else
+                {
+                    appendValue(context.otherLines, suffix(context._lineBuffer, 1), Generous());
+                }
+            }
+            else
+            {
+                appendValue(context.otherLines, suffix(context._lineBuffer, 1), Generous());
+            }
+        }
+
+        _goNextLine(context, iter, BlastTabular());
+
+    } while (startsWith(context._lineBuffer, "#") &&                   // still on comments
+             !std::regex_search(begin(context._lineBuffer, Standard()),// start of next record
+                                end(context._lineBuffer, Standard()),
+                                std::regex("^# T?BLAST")));
+
+    if (context.blastProgram == BlastProgram::UNKNOWN)
+        appendValue(context.conformancyErrors,
+                    "Type of BlastProgram could not be determined from comments, you are advised to look "
+                    "at context.versionString and context.otherLines.");
+
+    if (queryLinePresent != 1)
+        appendValue(context.conformancyErrors, "No or multiple query lines present.");
+
+    if (dbLinePresent != 1)
+        appendValue(context.conformancyErrors, "No or multiple database lines present.");
+
+    if (context.legacyFormat)
+    {
+        if (fieldsLinePresent != 1)
+            appendValue(context.conformancyErrors, "No or multiple fields lines present.");
+    }
+    else
+    {
+        // is ommitted in BLAST_PLUS when there are no hits
+        if ((fieldsLinePresent != 1) && (length(r.matches) > 0))
+            appendValue(context.conformancyErrors, "No or multiple fields lines present.");
+    }
+
+    if (!empty(context.otherLines))
+        appendValue(context.conformancyErrors, "Unexpected lines present, see context.otherLines.");
+}
+
+template <typename TMatch,
+          typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_readCommentLines(BlastRecord<TMatch> & r,
+                  TFwdIterator & iter,
+                  BlastIOContext<TScore, p, h> & context,
+                  BlastTabular const &)
+{
+    ++context._numberOfRecords;
+
+    if (context.tabularSpec == BlastTabularSpec::NO_COMMENTS)
+        return;
+
+    clear(r);
+    clear(context.versionString);
+    clear(context.dbName);
+    clear(context.otherLines);
+    clear(context.conformancyErrors);
+    clear(context.fieldsAsStrings);
+
+    if (!context.ignoreFieldsInComments)
+        clear(context.fields);
+
+    _readCommentLinesImpl(r, iter, context, BlastTabular());
+}
+
+// ----------------------------------------------------------------------------
+// Function _readField()
+// ----------------------------------------------------------------------------
+
+template <typename TAlignRow0,
+          typename TAlignRow1,
+          typename TPos,
+          typename TQId,
+          typename TSId,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_readField(BlastMatch<TAlignRow0, TAlignRow1, TPos, TQId, TSId> & match,
+           BlastIOContext<TScore, p, h> & context,
+           typename BlastMatchField<>::Enum const fieldId)
+{
+    switch (fieldId)
+    {
+        case BlastMatchField<>::Enum::STD: // this is cought in the calling function
+            break;
+        case BlastMatchField<>::Enum::Q_SEQ_ID:
+            match.qId = context._stringBuffer;
+            break;
+//         case ENUM::Q_GI: write(s,  * ); break;
+//         case ENUM::Q_ACC: write(s,  * ); break;
+//         case ENUM::Q_ACCVER: write(s,  * ); break;
+        case BlastMatchField<>::Enum::Q_LEN:
+            match.qLength = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::S_SEQ_ID:
+            match.sId = context._stringBuffer;
+            break;
+//         case ENUM::S_ALL_SEQ_ID: write(s,  * ); break;
+//         case ENUM::S_GI: write(s,  * ); break;
+//         case ENUM::S_ALL_GI: write(s,  * ); break;
+//         case ENUM::S_ACC: write(s,  * ); break;
+//         case ENUM::S_ACCVER: write(s,  * ); break;
+//         case ENUM::S_ALLACC: write(s,  * ); break;
+        case BlastMatchField<>::Enum::S_LEN:
+            match.sLength = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::Q_START:
+            match.qStart = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::Q_END:
+            match.qEnd = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::S_START:
+            match.sStart = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::S_END:
+            match.sEnd = lexicalCast<TPos>(context._stringBuffer);
+            break;
+//         case ENUM::Q_SEQ: write(s,  * ); break;
+//         case ENUM::S_SEQ: write(s,  * ); break;
+        case BlastMatchField<>::Enum::E_VALUE:
+            match.eValue = lexicalCast<double>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::BIT_SCORE:
+            match.bitScore = lexicalCast<double>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::SCORE:
+            match.alignStats.alignmentScore = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::LENGTH:
+            match.alignStats.alignmentLength = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::P_IDENT:
+            match.alignStats.alignmentIdentity = lexicalCast<double>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::N_IDENT:
+            match.alignStats.numMatches = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::MISMATCH:
+            match.alignStats.numMismatches = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::POSITIVE:
+            match.alignStats.numPositiveScores = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::GAP_OPEN:
+            match.alignStats.numGapOpens = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::GAPS:
+            match.alignStats.numGaps = lexicalCast<TPos>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::P_POS:
+            match.alignStats.alignmentSimilarity = lexicalCast<double>(context._stringBuffer);
+        case BlastMatchField<>::Enum::FRAMES:
+        {
+            clear(context._setBuffer2);
+            strSplit(context._setBuffer2, context._stringBuffer, EqualsChar<'/'>());
+            if (length(context._setBuffer2) != 2)
+                SEQAN_THROW(ParseError("Could not process frame string."));
+            match.qFrameShift = lexicalCast<int8_t>(context._setBuffer2[0]);
+            match.sFrameShift = lexicalCast<int8_t>(context._setBuffer2[1]);
+        } break;
+        case BlastMatchField<>::Enum::Q_FRAME:
+            match.qFrameShift = lexicalCast<int8_t>(context._stringBuffer);
+            break;
+        case BlastMatchField<>::Enum::S_FRAME:
+            match.sFrameShift = lexicalCast<int8_t>(context._stringBuffer);
+            break;
+//         case ENUM::BTOP: write( * ); break;
+//         case ENUM::S_TAX_IDS: write( * ); break;
+//         case ENUM::S_SCI_NAMES: write( * ); break;
+//         case ENUM::S_COM_NAMES: write( * ); break;
+//         case ENUM::S_BLAST_NAMES: write( * ); break;
+//         case ENUM::S_S_KINGDOMS: write( * ); break;
+//         case ENUM::S_TITLE: write( * ); break;
+//         case ENUM::S_ALL_TITLES: write( * ); break;
+//         case ENUM::S_STRAND: write( * ); break;
+//         case ENUM::Q_COV_S: write( * ); break;
+//         case ENUM::Q_COV_HSP:
+        default:
+            SEQAN_THROW(ParseError("The requested column type is not yet "
+                                   "implemented."));
+    };
+}
+
+// ----------------------------------------------------------------------------
+// Function _readMatch()
+// ----------------------------------------------------------------------------
+
+template <typename TAlignRow0,
+          typename TAlignRow1,
+          typename TPos,
+          typename TQId,
+          typename TSId,
+          typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_readMatch(BlastMatch<TAlignRow0, TAlignRow1, TPos, TQId, TSId> & match,
+           TFwdIterator & iter,
+           BlastIOContext<TScore, p, h> & context,
+           BlastTabular const &)
+{
+    if (context.legacyFormat)
+    {
+        #if SEQAN_ENABLE_DEBUG
+        if ((length(context.fields) != 1) || (context.fields[0] != BlastMatchField<>::Enum::STD))
+            std::cerr << "Warning: custom fields set, but will be reset, because legacyFormat is also set.\n";
+        #endif
+        // set defaults
+        clear(context.fields);
+        appendValue(context.fields,  BlastMatchField<>::Enum::STD);
+    }
+
+    // comments should have been read or skipped
+    if (SEQAN_UNLIKELY(!_onMatch(context, BlastTabular())))
+        SEQAN_THROW(ParseError("Not on beginning of Match (you should have skipped comments)."));
+
+    match._maxInitialize(); // mark all members as "not set"
+
+    clear(context._setBuffer1);
+
+    auto & fields = context._setBuffer1;
+    strSplit(fields, context._lineBuffer, IsTab());
+
+    // line in buffer was processed so new line is read from iter into buffer
+    _goNextLine(context, iter, BlastTabular());
+
+    unsigned n = 0u;
+    for (BlastMatchField<>::Enum const f : context.fields)
+    {
+        // this field represents multiple fields
+        if (f == BlastMatchField<>::Enum::STD)
+        {
+            for (typename BlastMatchField<>::Enum const f2 : BlastMatchField<>::defaults)
+            {
+                if (SEQAN_UNLIKELY(n >= length(fields)))
+                    SEQAN_THROW(ParseError("More columns expected than were present in file."));
+
+                context._stringBuffer = static_cast<decltype(context._stringBuffer)>(fields[n++]);
+                _readField(match, context, f2);
+            }
+        } else
+        {
+            if (SEQAN_UNLIKELY(n >= length(fields)))
+                SEQAN_THROW(ParseError("More columns expected than were present in file."));
+
+            context._stringBuffer = static_cast<decltype(context._stringBuffer)>(fields[n++]);
+            _readField(match, context, f);
+        }
+    }
+
+    // retransform the percentages to real numbers
+    if (!_memberIsSet(match.alignStats.numMatches) &&
+        _memberIsSet(match.alignStats.alignmentLength) &&
+        _memberIsSet(match.alignStats.alignmentIdentity))
+        match.alignStats.numMatches = std::lround(double(match.alignStats.alignmentLength) *
+                                            match.alignStats.alignmentIdentity / 100.0);
+    if (!_memberIsSet(match.alignStats.numPositiveScores) &&
+        _memberIsSet(match.alignStats.alignmentLength) &&
+        _memberIsSet(match.alignStats.alignmentSimilarity))
+        match.alignStats.numPositiveScores = std::lround(double(match.alignStats.alignmentLength) *
+                                            match.alignStats.alignmentSimilarity / 100.0);
+
+    //TODO also transform numbers to percentages; possibly do other calculations
+
+    // and compute gaps from other values
+    // since gaps are included in the mismatch count in BLAST_LEGACY they cannot be computed here
+    if (!context.legacyFormat &&
+        !_memberIsSet(match.alignStats.numGaps) &&
+        _memberIsSet(match.alignStats.alignmentLength) &&
+        _memberIsSet(match.alignStats.numMatches) &&
+        _memberIsSet(match.alignStats.numMismatches))
+        match.alignStats.numGaps = match.alignStats.alignmentLength -
+                                   match.alignStats.numMatches -
+                                   match.alignStats.numMismatches;
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord()
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator,
+          typename TMatch,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_readRecordWithCommentLines(BlastRecord<TMatch> & blastRecord,
+                            TFwdIterator & iter,
+                            BlastIOContext<TScore, p, h> & context,
+                            BlastTabular const &)
+{
+    _readCommentLines(blastRecord, iter, context, BlastTabular());
+
+    if (!context.legacyFormat) // this is detected from the comments
+    {
+        // .matches already resized for us
+        for (auto & m : blastRecord.matches)
+        {
+            if (!_onMatch(context, BlastTabular()))
+            {
+                appendValue(context.conformancyErrors,
+                            "Less matches than promised by the comments");
+                break;
+            }
+
+            _readMatch(m, iter, context, BlastTabular());
+        }
+
+        if ((!atEnd(context, iter, BlastTabular())) && _onMatch(context, BlastTabular()))
+            appendValue(context.conformancyErrors,
+                        "More matches than promised by the comments");
+
+        while ((!atEnd(context, iter, BlastTabular())) && _onMatch(context, BlastTabular()))
+        {
+            blastRecord.matches.emplace_back();
+            _readMatch(back(blastRecord.matches), iter, context, BlastTabular());
+        }
+    } else
+    {
+        while ((!atEnd(context, iter, BlastTabular())) && _onMatch(context, BlastTabular()))
+        {
+            blastRecord.matches.emplace_back();
+            _readMatch(back(blastRecord.matches), iter, context, BlastTabular());
+        }
+    }
+}
+
+template <typename TMatch,
+          typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_readRecordWithoutCommentLines(BlastRecord<TMatch> & blastRecord,
+                               TFwdIterator & iter,
+                               BlastIOContext<TScore, p, h> & context,
+                               BlastTabular const &)
+{
+    ++context._numberOfRecords;
+
+    clear(blastRecord);
+
+    auto it = begin(context._lineBuffer, Rooted()); // move into line below when seqan supports && properly
+    readUntil(blastRecord.qId, it, IsTab());
+
+    auto curIdPlusTab = blastRecord.qId;
+    appendValue(curIdPlusTab, '\t');
+
+    if ((context.fields[0] != BlastMatchField<>::Enum::STD) &&
+        (context.fields[0] != BlastMatchField<>::Enum::Q_SEQ_ID))
+    {
+        SEQAN_FAIL("ERROR: readRecord interface on comment-less format with custom "
+                   "fields not supported, unless first custom field is "
+                   "Q_SEQ_ID. Use the lowlevel readMatch interface instead.");
+    }
+
+    while ((!atEnd(context, iter, BlastTabular())) && _onMatch(context, BlastTabular()))
+    {
+        blastRecord.matches.emplace_back();
+        // read remainder of line
+        _readMatch(back(blastRecord.matches), iter, context, BlastTabular());
+
+        if (!startsWith(context._lineBuffer, curIdPlusTab)) // next record reached
+            break;
+    }
+
+    if (empty(blastRecord.matches))
+        SEQAN_THROW(ParseError("No Matches could be read."));
+}
+
+/*!
+ * @fn BlastTabularFileIn#readRecord
+ * @brief Read a record from a file in BlastTabular format.
+ * @headerfile seqan/blast.h
+ * @signature void readRecord(blastRecord, blastTabularIn);
+ *
+ * @param[out]    blastRecord  A @link BlastRecord @endlink to hold all information related to one query sequence.
+ * @param[in,out] blastTabularIn A @link BlastTabularFileIn @endlink formattedFile.
+ *
+ * @section Remarks
+ *
+ * This function will read an entire record from a blast tabular file, i.e. it will read the comment lines
+ * (if the format is @link BlastTabularSpec::COMMENTS @endlink) and 0-n @link BlastMatch @endlinkes belonging
+ * to one query.
+ *
+ * Please note that if there are no comment lines in the file the boundary
+ * between records is inferred from the indentity of the first field, i.e.
+ * non-standard field configurations must also have Q_SEQ_ID as their first @link BlastMatchField @endlink.
+ *
+ * @subsection Comment lines
+ *
+ * The @link BlastRecord::qId @endlink member of the record is read from the comment lines and the
+ * @link BlastRecord::matches @endlink are resized to the expected number of matches succeeding the comments.
+ *
+ * This function also sets many properties of blastTabularIn's @link BlastIOContext @endlink, including these members:
+ * <li> @link BlastIOContext::versionString @endlink: version string of the program.</li>
+ * <li> @link BlastIOContext::dbName @endlink: name of the database.</li>
+ * <li> @link BlastIOContext::fields @endlink: descriptors for the columns.</li>
+ * <li> @link BlastIOContext::fieldsAsStrings @endlink: labels of the columns
+ * as they appear in the file.</li>
+ * <li> @link BlastIOContext::conformancyErrors @endlink: if this StringSet is not empty, then there are issues in the
+ * comments.</li>
+ * <li> @link BlastIOContext::otherLines @endlink: any lines that cannot be interpreted; these always also imply
+ * conformancyErrors.</li>
+ * <li>@link BlastIOContext::legacyFormat @endlink: whether the record (and likely the entire file) is in
+ * legacyFormat.</li>
+ *
+ * It also sets the blast program run-time parameter of the context depending on the information found in the comments. If
+ * the compile time parameter was set on the context and they are different this will result in a critical error.
+ *
+ * Please note that for @link BlastIOContext::legacyFormat @endlink the @link BlastIOContext::fields @endlink member
+ * is always ignored, however @link BlastIOContext::fieldsAsStrings @endlink is still read from the comments, in case
+ * you want to process it.
+ *
+ * In case you do not wish the @link BlastIOContext::fields @endlink to be read from the comments, you can set
+ * context.@link BlastIOContext::ignoreFieldsInComments @endlink to true. This will be prevent it from being read and will
+ * allow you to specify it manually which might be relevant for reading the match lines.
+ *
+ * If the format is @link BlastTabularSpec::NO_COMMENTS @endlink none of the above happens and
+ * @link BlastRecord::qId @endlink is derived from the first match.
+ *
+ * @subsection Matches
+ *
+ * A match line contains 1 - n columns or fields, 12 by default.
+ * The @link BlastIOContext::fields @endlink member of the context is considered when reading these fields. It is
+ * usually extracted from the comment lines but can also be set by yourself if there are no comments or if you want
+ * to overwrite the comments' information (see above).
+ * You may specify less
+ * fields than are actually present, in this case the additional fields will be
+ * discarded. The parameter is ignored if @link BlastIOContext::legacyFormat @endlink is set.
+ *
+ * To differentiate between members of a @link BlastMatch @endlink that were read from the file and those that have
+ * not been set (e.g. both could be 0), the latter are initialized to their respective max-values.
+ *
+ * Please note that the only transformations made to the data are the following:
+ *
+ *  <li> computation of the number of identities (from the percentage) [default]</li>
+ *  <li> computation of the number of positives (from the percentage) [if given]</li>
+ *  <li> number of gaps computed from other values [default]</li>
+ *
+ * In contrast to @link BlastTabularFileOut#writeRecord @endlink no other transformations
+ * are made, e.g. the positions are still one-indexed and
+ * flipped for reverse strand matches. This is due to the required fields for
+ * retransformation (sequence lengths, frames) not being available in the
+ * default columns.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+template <typename TMatch,
+          typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+readRecord(BlastRecord<TMatch> & blastRecord,
+           TFwdIterator & iter,
+           BlastIOContext<TScore, p, h> & context,
+           BlastTabular const &)
+{
+    if (context.tabularSpec == BlastTabularSpec::NO_COMMENTS)
+        _readRecordWithoutCommentLines(blastRecord, iter, context, BlastTabular());
+    else
+        _readRecordWithCommentLines(blastRecord, iter, context, BlastTabular());
+}
+
+template <typename TMatch,
+          typename TContext>
+inline void
+readRecord(BlastRecord<TMatch> & blastRecord,
+           BlastTabularFileIn<TContext> & formattedFile)
+{
+    readRecord(blastRecord, formattedFile.iter, context(formattedFile), BlastTabular());
+}
+
+// ----------------------------------------------------------------------------
+// Function readHeader()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularFileIn#readHeader
+ * @headerfile seqan/blast.h
+ * @brief Read the header (top-most section) of a BlastTabular file.
+ * @signature void readHeader(blastTabularIn);
+ *
+ * @param[in,out] blastTabularIn A @link BlastTabularFileIn @endlink formattedFile.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+template <typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+readHeader(BlastIOContext<TScore, p, h> & context,
+           TFwdIterator & iter,
+           BlastTabular const & /*tag*/)
+{
+    readLine(context._lineBuffer, iter); // fill the line-buffer the first time
+
+    if (context.tabularSpec == BlastTabularSpec::UNKNOWN)
+    {
+        if (_onMatch(context, BlastTabular()))
+            context.tabularSpec = BlastTabularSpec::NO_COMMENTS;
+        else
+            context.tabularSpec = BlastTabularSpec::COMMENTS;
+    }
+}
+
+template <typename TContext>
+inline void
+readHeader(BlastTabularFileIn<TContext> & formattedFile)
+{
+    readHeader(context(formattedFile), formattedFile.iter, BlastTabular());
+}
+
+// ----------------------------------------------------------------------------
+// Function readFooter()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularFileIn#readFooter
+ * @headerfile seqan/blast.h
+ * @brief Read the footer (bottom-most section) of a BlastTabular file.
+ * @signature void readFooter(blastTabularIn);
+ *
+ * @param[in,out] blastTabularIn A @link BlastTabularFileIn @endlink formattedFile.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+template <typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+readFooter(BlastIOContext<TScore, p, h> & context,
+           TFwdIterator & iter,
+           BlastTabular const & /*tag*/)
+{
+    clear(context.otherLines);
+    clear(context.conformancyErrors);
+    clear(context.fieldsAsStrings);
+    clear(context.fields);
+
+    if ((context.tabularSpec == BlastTabularSpec::COMMENTS) && !context.legacyFormat)
+    {
+        if (SEQAN_UNLIKELY(!startsWith(context._lineBuffer, "# BLAST processed")))
+        {
+            std::cout << "\"" << context._lineBuffer << "\"" << std::endl;
+            SEQAN_FAIL("ERROR: Tried to read footer, but was not on footer.");
+        }
+        clear(context._stringBuffer);
+        auto it = seqan::begin(context._lineBuffer);
+        it += 18; // skip "BLAST processed "
+        readUntil(context._stringBuffer, it,  IsBlank());
+
+        __uint64 numRecords = lexicalCast<__uint64>(context._stringBuffer);
+
+        clear(context.conformancyErrors);
+        if (context._numberOfRecords < numRecords)
+            appendValue(context.conformancyErrors, "The file claims to contain more records than you read.");
+        else if (context._numberOfRecords > numRecords)
+            appendValue(context.conformancyErrors, "The file claims to contain less records than you read.");
+    }
+
+    if (!atEnd(iter))
+        appendValue(context.conformancyErrors, "Expected to be at end of file.");
+
+    _goNextLine(context, iter, BlastTabular());
+}
+
+template <typename TContext>
+inline void
+readFooter(BlastTabularFileIn<TContext> & formattedFile)
+{
+    readFooter(context(formattedFile), formattedFile.iter, BlastTabular());
+}
+
+} // namespace seqan
+
+#endif // SEQAN_BLAST_READ_BLAST_TABULAR_H_
diff --git a/seqan/blast/blast_tabular_lowlevel.h b/seqan/blast/blast_tabular_lowlevel.h
new file mode 100644
index 0000000..d658210
--- /dev/null
+++ b/seqan/blast/blast_tabular_lowlevel.h
@@ -0,0 +1,325 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// This file contains routines to read BLAST tab-seperated output
+// ==========================================================================
+
+#ifndef SEQAN_BLAST_BLAST_TABULAR_LOWLEVEL_H_
+#define SEQAN_BLAST_BLAST_TABULAR_LOWLEVEL_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class BlastTabularLL
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastTabularLL
+ * @signature typedef Tag<BlastTabularLL_> BlastTabularLL;
+ * @headerfile <seqan/blast.h>
+ * @brief Low-Level support for Blast Tabular file formats
+ *
+ * There are three blast format related tags in SeqAn:
+ *
+ * <li> @link BlastReport @endlink with the FormattedFile output specialization @link BlastReportFileOut @endlink</li>
+ * <li> @link BlastTabular @endlink with the FormattedFile output and input specializations
+ * @link BlastTabularFileOut @endlink and @link BlastTabularFileIn @endlink</li>
+ * <li> @link BlastTabularLL @endlink which provides light-weight, but very basic tabular IO </li>
+ *
+ * This is the third tag, it offers <b>low-level</b> support for reading and writing NCBI Blast compatible
+ * <b>tabular</b> files, <b>without comment lines</b> -- although files with comment lines can be read if the comment
+ * lines are skipped. These are the formats that are available in legacy Blast
+ * (<tt>blastall</tt> executable) with the parameters <tt>-m 8</tt> and <tt>-m 9</tt> (with comment lines)
+ * and in BLAST+ (<tt>blastx</tt>, <tt>blastn</tt>...) with
+ * the parameters <tt>-outfmt 6</tt> and <tt>-outfmt 7</tt> respectively.
+ *
+ * For most situations @link BlastTabular @endlink is more adequate. Use this tag's interface only for quick parsing
+ * of matches in a file, e.g counting and filtering purposes. This interface does not offer a FormattedFile
+ * abstraction and no convenience data structures, it does no transformations on the data.
+ *
+ * The reference Blast implementation used for developing the SeqAn support is NCBI Blast+ 2.2.26 and
+ * NCBI Blast 2.2.26 for the legacy support.
+ *
+ * @section Input example
+ *
+ * The following example program extracts the list of matching query-subject-pairs from a blast tabular file and prints
+ * it to std::out:
+ *
+ * @include demos/blast/blast_in_lowlevel.cpp
+ *
+ * The output looks like this:
+ *
+ * @include demos/blast/blast_in_lowlevel.cpp.stdout_
+ *
+ */
+
+struct BlastTabularLL_;
+typedef Tag<BlastTabularLL_> BlastTabularLL;
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function onMatch()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularLL#onMatch
+ * @brief Returns whether the iterator is on the beginning of a match line.
+ * @signature bool onMatch(stream, blastTabularLL)
+ * @headerfile seqan/blast.h
+ *
+ * @param[in] iter              An input iterator over a stream or any fwd-iterator over a string.
+ * @param[in] blastTabularLL    The @link BlastTabularLL @endlink tag.
+ *
+ * @throw IOError On low-level I/O errors.
+ *
+ * @return bool true or false
+ */
+
+template <typename TFwdIterator>
+inline bool
+onMatch(TFwdIterator & iter,
+        BlastTabularLL const &)
+{
+    return (value(iter) != '#');
+}
+
+// ----------------------------------------------------------------------------
+// Function skipUntilMatch()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularLL#skipUntilMatch
+ * @brief Skip arbitrary number of comment lines until the beginning of a match is reached.
+ * @signature void skipUntilMatch(stream, blastTabularLL);
+ * @headerfile seqan/blast.h
+ *
+ * @param[in,out] stream         An input iterator over a stream or any fwd-iterator over a string.
+ * @param[in]     blastTabularLL The @link BlastTabularLL @endlink tag.
+ *
+ * @section Remarks
+ *
+ * This is also part of the low-level IO and not required if you use readRecord.
+ * Call this function whenever you are not @link BlastTabularLL#onMatch @endlink, but want to be, e.g. to
+ * @link BlastTabularLL#readMatch @endlink.
+ *
+ * Since it is legal for files to end with comment lines, this function does not throw if end-of-file is reached.
+ * You need to check that after calling.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+template <typename TFwdIterator>
+inline void
+skipUntilMatch(TFwdIterator & iter,
+               BlastTabularLL const & /*tag*/)
+{
+    while ((!atEnd(iter)) && value(iter) == '#') // skip comments
+        skipLine(iter);
+}
+
+// ----------------------------------------------------------------------------
+// Function readMatch()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularLL#readMatch
+ * @brief Low-level BlastTabular file reading.
+ * @signature void readMatch(stream, blastTabularLL, args ...);
+ * @headerfile seqan/blast.h
+ *
+ * @param[in,out] stream         An input iterator over a stream or any fwd-iterator over a string.
+ * @param[in]     blastTabularLL The @link BlastTabularLL @endlink tag.
+ * @param[out]    args           Arbitrary typed variables able to hold the fields.
+ *
+ * @section Remarks
+ *
+ * Use this signature only if you do not or cannot use @link BlastMatch
+ * @endlinkes. You can specify any number of arguments that are expected
+ * to be able to hold the values in the columns read, i.e. if you pass a
+ * double as argument and the value in the column cannot be successfully cast
+ * to double, an exception will be thrown. If you want to be on the safe side,
+ * you can pass CharStrings and evaluate them in another way.
+ *
+ * You may specify less columns than are available in the file, all but the first
+ * n will be discarded.
+ *
+ * No transformations are made on the data, e.g. the positions are still
+ * one-indexed and flipped for reverse strand matches.
+ *
+ * See @link BlastTabularLL @endlink for an example of low-level IO.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+// arbitrary columns
+template <typename TTarget>
+inline SEQAN_FUNC_ENABLE_IF(IsSequence<TTarget>)
+_assignOrCast(TTarget & target, std::string const & source)
+{
+    assign(target, source);
+}
+
+template <typename TTarget>
+inline SEQAN_FUNC_ENABLE_IF(Is<NumberConcept<TTarget>>)
+_assignOrCast(TTarget & target, std::string const & source)
+{
+    target = lexicalCast<TTarget>(source);
+}
+
+template <typename TFwdIterator,
+          typename TArg>
+inline void
+_readMatchImplBlastTab(TFwdIterator & iter,
+                       TArg & arg)
+{
+    static std::string buffer;
+    clear(buffer);
+
+    readUntil(buffer, iter, OrFunctor<IsTab,IsNewline>());
+    _assignOrCast(arg, buffer);
+
+    // as this is the last requested field, go to beginning of next line
+    skipLine(iter);
+}
+
+template <typename TFwdIterator,
+          typename TArg,
+          typename... TArgs>
+inline void
+_readMatchImplBlastTab(TFwdIterator & iter,
+                       TArg & arg,
+                       TArgs & ... args)
+{
+    static std::string buffer;
+    clear(buffer);
+
+    readUntil(buffer, iter, IsTab());
+    skipOne(iter, IsTab());
+    _assignOrCast(arg, buffer);
+
+    // recurse to next argument
+    _readMatchImplBlastTab(iter, args...);
+}
+
+// custom arguments
+template <typename TFwdIterator,
+          typename... TArgs>
+inline void
+readMatch(TFwdIterator & iter,
+           BlastTabularLL const &,
+           TArgs & ... args)
+{
+    // comment lines should have been read or skipped
+    if (SEQAN_UNLIKELY(!onMatch(iter, BlastTabularLL())))
+        SEQAN_THROW(ParseError("ERROR: Not on beginning of Match (you should have skipped comments)."));
+
+    _readMatchImplBlastTab(iter, args...);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeMatch()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularLL#writeMatch
+ * @headerfile seqan/blast.h
+ * @brief Low-level file-writing for blast tabular formats
+ * @signature void writeMatch(stream, blastTabularLL, columns...)
+ *
+ * @section Remarks
+ *
+ * This is a very leight-weight alternative to @link BlastTabularFileOut#writeRecord @endlink. It doesn't require
+ * @link BlastMatch @endlinkes, @link BlastRecord @endlinks or the use of @link FormattedFile @endlink.
+ * It supports an arbitrary amount of and arbitrary typed columns to be printed.
+ *
+ * Use this only if you do not require comment lines and you are prepared to do all transformations on the data
+ * yourself, i.e. this function does none of the match adjustments mentioned in
+ * @link BlastTabularFileOut#writeRecord @endlink.
+ *
+ * @param[in,out] stream         The file to write to (FILE, fstream, @link OutputStreamConcept @endlink ...).
+ * @param[in]     blastTabularLL The @link BlastTabularLL @endlink tag.
+ * @param[in]     columns...     Any number of printable parameters.
+ *
+ * @throw IOError On low-level I/O errors.
+ */
+
+template <typename TFwdIterator>
+inline void
+_writeFields(TFwdIterator & /**/,
+             BlastTabularLL const & /*tag*/)
+{
+}
+
+template <typename TFwdIterator, typename TField, typename... TFields>
+inline void
+_writeFields(TFwdIterator & stream,
+             BlastTabularLL const & /*tag*/,
+             TField const & field1,
+             TFields const & ... fields)
+{
+    write(stream, '\t');
+    write(stream, field1);
+    _writeFields(stream, BlastTabularLL(), fields... );
+}
+
+// Function for arbitrary number and typed fields
+template <typename TFwdIterator, typename TField, typename... TFields>
+inline void
+writeMatch(TFwdIterator & stream,
+           BlastTabularLL const & /*tag*/,
+           TField const & field1,
+           TFields const & ... fields)
+{
+    write(stream, field1);
+
+    _writeFields(stream, BlastTabularLL(), fields...);
+    write(stream, '\n');
+}
+
+}
+
+#endif // SEQAN_BLAST_BLAST_TABULAR_LOWLEVEL_H_
\ No newline at end of file
diff --git a/seqan/blast/blast_tabular_out.h b/seqan/blast/blast_tabular_out.h
new file mode 100644
index 0000000..d726df4
--- /dev/null
+++ b/seqan/blast/blast_tabular_out.h
@@ -0,0 +1,649 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// This file contains routines to generate BLAST tab-seperated output
+// ==========================================================================
+
+#ifndef SEQAN_BLAST_BLAST_TABULAR_WRITE_H_
+#define SEQAN_BLAST_BLAST_TABULAR_WRITE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Type BlastTabularFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BlastTabularFileOut
+ * @signature template <typename TBlastIOContext>
+ * using BlastTabularFileOut = FormattedFile<BlastTabular, Output, TBlastIOContext>;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/blast.h>
+ * @brief FormattedFileOut abstraction for @link BlastTabular @endlink
+ *
+ * This is a @link FormattedFile @endlink specialization for writing @link BlastTabular @endlink formats. For details
+ * on how to influence the writing of files and how to differentiate between the tabular format with and without
+ * comment lines, see @link BlastIOContext @endlink.
+ * Please note that you have to specify the type of the context as a template parameter to BlastTabularFileOut, see the example
+ * below.
+ *
+ * @section Overview
+ *
+ * <ul>
+ * <li> open @link BlastTabularFileOut @endlink,</li>
+ * <li> configure the @link BlastIOContext @endlink </li>
+ * <li> @link BlastTabularFileOut#writeHeader @endlink </li>
+ * <li> @link BlastTabularFileOut#writeRecord @endlink repeated up to n times</li>
+ * <li> @link BlastTabularFileOut#writeFooter @endlink </li>
+ * </ul>
+ *
+ * The following members of the context have to be defined before writing:
+ * <ul>
+ * <li> @link BlastIOContext::blastProgram @endlink (unless fixed at compile-time)</li>
+ * <li> @link BlastIOContext::scoringScheme @endlink</li>
+ * <li> @link BlastIOContext::dbName @endlink</li>
+ * <li> @link BlastIOContext::dbTotalLength @endlink</li>
+ * <li> @link BlastIOContext::dbNumberOfSeqs @endlink</li>
+ * </ul>
+ *
+ * For a detailed example have a look at the
+ * <a href="http://seqan.readthedocs.org/en/develop/Tutorial/BlastIO.html">Blast IO tutorial</a>.
+ *
+ * Strictly speaking the <tt>writeHeader()</tt> call is not required for BlastTabular, but for consistency with
+ * other (blast) formats and the read interface it is recommended.
+ *
+ * @see BlastRecord
+ */
+
+template <typename TBlastIOContext = BlastIOContext<>>
+using BlastTabularFileOut = FormattedFile<BlastTabular, Output, TBlastIOContext>;
+
+// ============================================================================
+// Metafunctions and global const-expressions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function guessFormat()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+inline bool guessFormat(FormattedFile<BlastTabular, Output, TSpec> &)
+{
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeFieldLabels()
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeFieldLabels(TFwdIterator & stream,
+                  BlastIOContext<TScore, p, h> & context,
+                  BlastTabular const &)
+{
+    if (!empty(context.fieldsAsStrings)) // give preference to string labels
+    {
+         write(stream, context.fieldsAsStrings, ", ");
+    }
+    else
+    {
+        for (auto it = seqan::begin(context.fields),
+                  itB = it,
+                  itEnd = seqan::end(context.fields);
+            it != itEnd;
+            ++it)
+        {
+            if (it != itB)
+                write(stream, ", ");
+
+            write(stream, BlastMatchField<>::columnLabels[static_cast<uint8_t>(*it)]);
+        }
+    }
+
+    writeValue(stream, '\n');
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeCommentLines()
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator,
+          typename TScore,
+          typename TMatch,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeCommentLinesWithoutColumnLabels(TFwdIterator & stream,
+                                      BlastIOContext<TScore, p, h> & context,
+                                      BlastRecord<TMatch> const & r,
+                                      BlastTabular const & /*tag*/)
+{
+    write(stream, "# ");
+    if (empty(context.versionString))
+        context._setDefaultVersionString();
+    write(stream, context.versionString);
+
+    write(stream, "\n# Query: ");
+    write(stream, r.qId);
+    write(stream, "\n# Database: ");
+    write(stream, context.dbName);
+    write(stream, '\n');
+}
+
+template <typename TFwdIterator,
+          typename TScore,
+          typename TMatch,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeCommentLines(TFwdIterator & stream,
+                  BlastIOContext<TScore, p, h> & context,
+                  BlastRecord<TMatch> const & r,
+                  BlastTabular const & /*tag*/)
+{
+    ++context._numberOfRecords;
+
+    if (context.tabularSpec == BlastTabularSpec::NO_COMMENTS)
+        return;
+
+    _writeCommentLinesWithoutColumnLabels(stream, context, r, BlastTabular());
+
+    if (SEQAN_LIKELY(!context.legacyFormat))
+    {
+        // only write fields line if matches will follow
+        if (length(r.matches) > 0)
+        {
+            write(stream, "# Fields: ");
+            _writeFieldLabels(stream, context, BlastTabular());
+        }
+        // write # hits line
+        write(stream, "# ");
+        write(stream, length(r.matches));
+        write(stream, " hits found\n");
+    }
+    else
+    {
+        write(stream, "# Fields: ");
+        write(stream, BlastMatchField<>::legacyColumnLabels);
+        write(stream, '\n');
+
+        #if SEQAN_ENABLE_DEBUG
+        if ((length(context.fields) != 1) || (context.fields[0] != BlastMatchField<>::Enum::STD))
+            std::cerr << "Warning: custom fields set, but will be ignored, because legacyFormat is also set.\n";
+        #endif
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeField() [match object given]
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator,
+          typename TScore,
+          typename TQId,
+          typename TSId,
+          typename TPos,
+          typename TAlignRow0,
+          typename TAlignRow1,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeField(TFwdIterator & s,
+            BlastIOContext<TScore, p, h> & context,
+            BlastMatch<TAlignRow0, TAlignRow1, TPos, TQId, TSId> const & match,
+            typename BlastMatchField<>::Enum const fieldId,
+            BlastTabular const &)
+{
+    switch (fieldId)
+    {
+        case BlastMatchField<>::Enum::STD:
+             // STD is handled from the calling function
+            break;
+        case BlastMatchField<>::Enum::Q_SEQ_ID:
+            write(s, prefix(match.qId,
+                            std::find(begin(match.qId, Standard()), end(match.qId, Standard()), ' ')
+                            - begin(match.qId, Standard()))); // truncate at first ' '
+            break;
+//         case ENUM::Q_GI: write(s,  * ); break;
+//         case ENUM::Q_ACC: write(s,  * ); break;
+//         case ENUM::Q_ACCVER: write(s,  * ); break;
+        case BlastMatchField<>::Enum::Q_LEN:
+            write(s, match.qLength);
+            break;
+        case BlastMatchField<>::Enum::S_SEQ_ID:
+            write(s, prefix(match.sId,
+                            std::find(begin(match.sId, Standard()), end(match.sId, Standard()), ' ')
+                            - begin(match.sId, Standard()))); // truncate at first ' '
+            break;
+//         case ENUM::S_ALL_SEQ_ID: write(s,  * ); break;
+//         case ENUM::S_GI: write(s,  * ); break;
+//         case ENUM::S_ALL_GI: write(s,  * ); break;
+//         case ENUM::S_ACC: write(s,  * ); break;
+//         case ENUM::S_ACCVER: write(s,  * ); break;
+//         case ENUM::S_ALLACC: write(s,  * ); break;
+        case BlastMatchField<>::Enum::S_LEN:
+            write(s, match.sLength);
+            break;
+        case BlastMatchField<>::Enum::Q_START:
+        {
+            TPos effectiveQStart    = match.qStart;
+            TPos effectiveQEnd      = match.qEnd;
+            _untranslateQPositions(effectiveQStart, effectiveQEnd, match.qFrameShift, match.qLength,
+                                   context.blastProgram);
+            write(s, effectiveQStart);
+        } break;
+        case BlastMatchField<>::Enum::Q_END:
+        {
+            TPos effectiveQStart    = match.qStart;
+            TPos effectiveQEnd      = match.qEnd;
+            _untranslateQPositions(effectiveQStart, effectiveQEnd, match.qFrameShift, match.qLength,
+                                   context.blastProgram);
+            write(s, effectiveQEnd);
+        } break;
+        case BlastMatchField<>::Enum::S_START:
+        {
+            TPos effectiveSStart    = match.sStart;
+            TPos effectiveSEnd      = match.sEnd;
+            _untranslateSPositions(effectiveSStart, effectiveSEnd, match.sFrameShift, match.sLength,
+                                   context.blastProgram);
+            write(s, effectiveSStart);
+        } break;
+        case BlastMatchField<>::Enum::S_END:
+        {
+            TPos effectiveSStart    = match.sStart;
+            TPos effectiveSEnd      = match.sEnd;
+            _untranslateSPositions(effectiveSStart, effectiveSEnd, match.sFrameShift, match.sLength,
+                                   context.blastProgram);
+            write(s, effectiveSEnd);
+        } break;
+//         case ENUM::Q_SEQ: write(s,  * ); break;
+//         case ENUM::S_SEQ: write(s,  * ); break;
+        case BlastMatchField<>::Enum::E_VALUE:
+        {
+            std::string formatString;
+            // imported from NCBI code
+            if (match.eValue < 1.0e-180)
+                formatString = "%3.1lf";
+            else if (match.eValue < 1.0e-99)
+                formatString = "%2.0le";
+            else if (match.eValue < 0.0009)
+                formatString = "%3.0le";
+            else if (match.eValue < 0.1)
+                formatString = "%4.3lf";
+            else if (match.eValue < 1.0)
+                formatString = "%3.2lf";
+            else if (match.eValue < 10.0)
+                formatString = "%2.1lf";
+            else
+                formatString = "%5.0lf";
+
+            write(s, FormattedNumber<double>(formatString.c_str(), match.eValue));
+        } break;
+        case BlastMatchField<>::Enum::BIT_SCORE:
+        {
+            std::string formatString;
+            // imported from NCBI code
+            if (match.bitScore > 9999)
+                formatString = "%4.3le";
+            else if (match.bitScore > 99.9)
+                formatString = "%4.0lf";
+            else
+                formatString = "%4.1lf";
+
+            write(s, FormattedNumber<double>(formatString.c_str(), match.bitScore));
+        } break;
+        case BlastMatchField<>::Enum::SCORE:
+            write(s, match.alignStats.alignmentScore);
+            break;
+        case BlastMatchField<>::Enum::LENGTH:
+            write(s, match.alignStats.alignmentLength);
+            break;
+        case BlastMatchField<>::Enum::P_IDENT:
+            write(s, FormattedNumber<float>("%.2f", match.alignStats.alignmentIdentity));
+            break;
+        case BlastMatchField<>::Enum::N_IDENT:
+            write(s, match.alignStats.numMatches);
+            break;
+        case BlastMatchField<>::Enum::MISMATCH:
+            if (context.legacyFormat) // legacy format includes gaps in mismatches
+                write(s, match.alignStats.numMismatches +
+                         match.alignStats.numGaps);
+            else
+                write(s, match.alignStats.numMismatches);
+            break;
+        case BlastMatchField<>::Enum::POSITIVE:
+            write(s, match.alignStats.numPositiveScores);
+            break;
+        case BlastMatchField<>::Enum::GAP_OPEN:
+            write(s, match.alignStats.numGapOpens);
+            break;
+        case BlastMatchField<>::Enum::GAPS:
+            write(s, match.alignStats.numGaps);
+            break;
+        case BlastMatchField<>::Enum::P_POS:
+            write(s, FormattedNumber<double>("%.2f", match.alignStats.alignmentSimilarity));
+            break;
+        case BlastMatchField<>::Enum::FRAMES:
+            // for formats that don't have frames, blast says 0 instead of +1
+            if (qNumFrames(context.blastProgram) > 1)
+                write(s, FormattedNumber<int8_t>("%i", match.qFrameShift));
+            else
+                write(s, FormattedNumber<int8_t>("%i", 0));
+            write(s, '/');
+            if (sNumFrames(context.blastProgram) > 1)
+                write(s, FormattedNumber<int8_t>("%i", match.sFrameShift));
+            else
+                write(s, FormattedNumber<int8_t>("%i", 0));
+            break;
+        case BlastMatchField<>::Enum::Q_FRAME:
+            if (qNumFrames(context.blastProgram) > 1)
+                write(s, FormattedNumber<int8_t>("%i", match.qFrameShift));
+            else
+                write(s, FormattedNumber<int8_t>("%i", 0));
+            break;
+        case BlastMatchField<>::Enum::S_FRAME:
+            if (sNumFrames(context.blastProgram) > 1)
+                write(s, FormattedNumber<int8_t>("%i", match.sFrameShift));
+            else
+                write(s, FormattedNumber<int8_t>("%i", 0));
+            break;
+//         case ENUM::BTOP: write( * ); break;
+//         case ENUM::S_TAX_IDS: write( * ); break;
+//         case ENUM::S_SCI_NAMES: write( * ); break;
+//         case ENUM::S_COM_NAMES: write( * ); break;
+//         case ENUM::S_BLAST_NAMES: write( * ); break;
+//         case ENUM::S_S_KINGDOMS: write( * ); break;
+//         case ENUM::S_TITLE: write( * ); break;
+//         case ENUM::S_ALL_TITLES: write( * ); break;
+//         case ENUM::S_STRAND: write( * ); break;
+//         case ENUM::Q_COV_S: write( * ); break;
+//         case ENUM::Q_COV_HSP:
+        default:
+            write(s, "n/i"); // not implemented
+    };
+}
+
+// ----------------------------------------------------------------------------
+// Function _writeMatch()
+// ----------------------------------------------------------------------------
+
+template <typename TQId,
+          typename TSId,
+          typename TFwdIterator,
+          typename TScore,
+          typename TPos,
+          typename TAlignRow0,
+          typename TAlignRow1,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+_writeMatch(TFwdIterator & stream,
+           BlastIOContext<TScore, p, h> & context,
+           BlastMatch<TAlignRow0, TAlignRow1, TPos, TQId, TSId> const & match,
+           BlastTabular const & /*tag*/)
+{
+    if (SEQAN_LIKELY(!context.legacyFormat))
+    {
+        for (auto it = std::begin(context.fields), itB = it, itEnd = std::end(context.fields); it != itEnd; ++it)
+        {
+            if (it != itB)
+                write(stream, '\t');
+
+            if (*it != BlastMatchField<>::Enum::STD)
+            {
+                _writeField(stream, context, match, *it, BlastTabular());
+            }
+            else // STD is placeholder for multiple fields
+            {
+                for (auto it2 = std::begin(BlastMatchField<>::defaults), it2B = it2,
+                     it2End = std::end(BlastMatchField<>::defaults); it2 != it2End; ++it2)
+                {
+                    if (it2 != it2B)
+                        write(stream, '\t');
+
+                    _writeField(stream, context, match, *it2, BlastTabular());
+                }
+            }
+        }
+    }
+    else
+    {
+        for (auto it = std::begin(BlastMatchField<>::defaults), itB = it,
+             itEnd = std::end(BlastMatchField<>::defaults); it != itEnd; ++it)
+        {
+            if (it != itB)
+                write(stream, '\t');
+
+            _writeField(stream, context, match, *it, BlastTabular());
+        }
+
+        #if SEQAN_ENABLE_DEBUG
+        if ((length(context.fields) != 1) || (context.fields[0] != BlastMatchField<>::Enum::STD))
+            std::cerr << "Warning: custom fields set, but will be ignored, because legacyFormat is also set.\n";
+        #endif
+    }
+
+    write(stream, '\n');
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularFileOut#writeRecord
+ * @headerfile seqan/blast.h
+ * @brief Write a @link BlastRecord @endlink including it's @link BlastMatch @endlinkes and possible comment lines to a file.
+ * @signature void writeRecord(blastTabularOut, blastRecord);
+ *
+ * @param[in,out] blastTabularOut A @link BlastTabularFileOut @endlink formattedFile.
+ * @param[in]     blastRecord     The @link BlastRecord @endlink you wish to print.
+ *
+ * @section Remarks
+ *
+ * This function first writes the comment lines of the record and then writes match lines for every match in it. If the
+ * context's @link BlastIOContext::tabularSpec @endlink is set to BlastTabularSpec::NO_COMMENTS, no
+ * comment lines will be written and this function immediately prints the match lines.
+ *
+ * @subsection Comment lines
+ *
+ * The contents of the comment lines is largely defined by the members of the context.
+ *
+ * If the context's @link BlastIOContext::versionString @endlink is set, this will be written,
+ * otherwise a stanadard version string is generated.
+ *
+ * The context's @link BlastIOContext::dbName @endlink is printed as the database name / path.
+ *
+ * If either the context's @link BlastIOContext::fields @endlink or
+ * @link BlastIOContext::fieldsAsStrings @endlink member are specified these will be printed
+ * as column labels. If both are specified than @link BlastIOContext::fieldsAsStrings @endlink
+ * is given preference. Please note that it is recommended to use
+ * @link BlastIOContext::fields @endlink and not @link BlastIOContext::fieldsAsStrings @endlink to stay
+ * "standards"-compliant. Also only @link BlastIOContext::fields @endlink has an influence on
+ * the values printed in the match lines.
+ *
+ * @subsection Matches
+ *
+ * Please note that BLAST is 1-indexed and considers the last position
+ * to be the back, not the end, i.e. last one included in a match/sequence/...,
+ * not the one behind it (as SeqAn does); this functions corrects for both of
+ * these bahaviours, so you don't have to. Additionally, based on the context's
+ * @link BlastIOContext::blastProgram @endlink, positions are transformed back to DNA space, if
+ * translation has taken place.
+ * Please note also that query and subject IDs are truncated at the first space
+ * character in NCBI BLAST, this is also done by default here.
+ *
+ * By setting the context's @link BlastIOContext::fields @endlink meber you can specify which columns you
+ * wish to print (if you don't want defaults); the same conversions mentioned above will me made. See
+ * @link BlastMatchField::Enum @endlink for a list of fields available. If the context's legacy-flag is set
+ * (@link BlastIOContext::legacyFormat @endlink) the @link BlastIOContext::fields @endlink
+ * variable is ignored.
+ *
+ * Many guides recommend always printing the default 12 columns and using only
+ * additional columns with additional (custom) data.
+ *
+ * @throw IOError On low-level I/O errors.
+ *
+ * @see BlastRecord
+ * @see BlastIOContext
+ */
+
+template <typename TFwdIterator,
+          typename TScore,
+          typename TMatch,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+writeRecord(TFwdIterator & stream,
+            BlastIOContext<TScore, p, h> & context,
+            BlastRecord<TMatch> const & r,
+            BlastTabular const & /*tag*/)
+{
+    //TODO if debug, do lots of sanity checks on record
+
+    //NOOP for TABULAR
+    _writeCommentLines(stream, context, r, BlastTabular());
+    for (auto it = r.matches.begin(); it != r.matches.end(); ++it)
+    {
+        //SOME SANITY CHECKS
+        SEQAN_ASSERT(startsWith(r.qId, it->qId));
+
+        _writeMatch(stream, context, *it, BlastTabular());
+    }
+}
+
+template <typename TContext,
+          typename TMatch>
+inline void
+writeRecord(BlastTabularFileOut<TContext> & formattedFile,
+            BlastRecord<TMatch> const & r)
+{
+    writeRecord(formattedFile.iter, context(formattedFile), r, BlastTabular());
+}
+
+// ----------------------------------------------------------------------------
+// Function writeHeader()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularFileOut#writeHeader
+ * @headerfile seqan/blast.h
+ * @brief Write the header (top-most section) of a BlastTabular file (this is a NOOP).
+ * @signature void writeHeader(blastTabularOut);
+ *
+ * @param[in,out] blastTabularOut A @link BlastTabularFileOut @endlink formattedFile.
+ *
+ * @throw IOError On low-level I/O errors.
+ *
+ * @see BlastRecord
+ * @see BlastIOContext
+ */
+
+template <typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+writeHeader(TFwdIterator & ,
+            BlastIOContext<TScore, p, h> &,
+            BlastTabular const & /*tag*/)
+{
+}
+
+template <typename TContext>
+inline void
+writeHeader(BlastTabularFileOut<TContext> & formattedFile)
+{
+    writeHeader(formattedFile.iter, context(formattedFile), BlastTabular());
+}
+
+// ----------------------------------------------------------------------------
+// Function writeFooter()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn BlastTabularFileOut#writeFooter
+ * @headerfile seqan/blast.h
+ * @brief Write the footer of a BlastTabular file.
+ * @signature void writeFooter(blastTabularOut);
+ *
+ * @param[in,out] blastTabularOut A @link BlastTabularFileOut @endlink formattedFile.
+ *
+ * @throw IOError On low-level I/O errors.
+ *
+ * @see BlastRecord
+ * @see BlastIOContext
+ */
+
+template <typename TFwdIterator,
+          typename TScore,
+          BlastProgram p,
+          BlastTabularSpec h>
+inline void
+writeFooter(TFwdIterator & stream,
+            BlastIOContext<TScore, p, h> & context,
+            BlastTabular const & /*tag*/)
+{
+    if ((!context.legacyFormat) && (context.tabularSpec != BlastTabularSpec::NO_COMMENTS))
+    {
+        write(stream, "# BLAST processed ");
+        write(stream, context._numberOfRecords); // number of records equals number of queries
+        write(stream, " queries\n");
+    }
+}
+
+template <typename TContext>
+inline void
+writeFooter(BlastTabularFileOut<TContext> & formattedFile)
+{
+    writeFooter(formattedFile.iter, context(formattedFile), BlastTabular());
+}
+
+} // namespace seqan
+#endif // header guard
diff --git a/seqan/consensus.h b/seqan/consensus.h
index a0046f2..0b22b65 100644
--- a/seqan/consensus.h
+++ b/seqan/consensus.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,11 +29,16 @@
 // DAMAGE.
 //
 // ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_CONSENSUS_H_
+#define INCLUDE_SEQAN_CONSENSUS_H_
 
-#ifndef SEQAN_HEADER_CONSENSUS_H
-#define SEQAN_HEADER_CONSENSUS_H
+// ==========================================================================
+// Dependencies
+// ==========================================================================
 
-// Seqan
 #include <seqan/score.h>
 #include <seqan/modifier.h>
 #include <seqan/graph_types.h>
@@ -44,10 +49,22 @@
 #include <seqan/store.h>
 #include <seqan/seq_io.h>
 
-// Consensus tool
+// ==========================================================================
+// Old Consensus Module
+// ==========================================================================
+
 #include <seqan/consensus/consensus_base.h>
 #include <seqan/consensus/consensus_score.h>
 #include <seqan/consensus/consensus_realign.h>
 #include <seqan/consensus/consensus_library.h>
 
-#endif //#ifndef SEQAN_HEADER_...
+// ==========================================================================
+// New, Store-Based Module
+// ==========================================================================
+
+#include <seqan/consensus/overlap_info_computation.h>
+#include <seqan/consensus/consensus_builder.h>
+#include <seqan/consensus/consensus_aligner.h>
+#include <seqan/consensus/consensus_aligner_interface.h>
+
+#endif  // #ifndef INCLUDE_SEQAN_CONSENSUS_H_
diff --git a/seqan/consensus/INFO b/seqan/consensus/INFO
deleted file mode 100644
index 8d43d6e..0000000
--- a/seqan/consensus/INFO
+++ /dev/null
@@ -1,11 +0,0 @@
-Name: seqan-consensus
-Author: Tobias Rausch <rausch@embl.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Consensus computation and re-alignment.
- This module contains code for consensus computation and re-alignment of
- sequences.
- .
- It contains most functionality of the seqcons program.
diff --git a/seqan/consensus/consensus_aligner.h b/seqan/consensus/consensus_aligner.h
new file mode 100644
index 0000000..5efbfd4
--- /dev/null
+++ b/seqan/consensus/consensus_aligner.h
@@ -0,0 +1,186 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_H_
+#define INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_H_
+
+#include <map>
+#include <vector>
+#include <stdexcept>
+
+#include <seqan/store.h>
+
+#include "consensus_alignment_options.h"
+#include "consensus_builder.h"
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class ConsensusAlignerIllegalArgumentException
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class ConsensusAlignerIllegalArgumentException
+ * @headerfile <seqan/consensus.h>
+ * @brief Thrown in ConsensusAlignerInputException on invalid arguments.
+ *
+ * @signature class ConsensusAlignerException;
+ */
+
+class ConsensusAlignerException : public std::runtime_error
+{
+public:
+    explicit ConsensusAlignerException(std::string const & whatArg) : std::runtime_error(whatArg)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class ConsensusAligner_
+// ----------------------------------------------------------------------------
+
+// Implementation helper of the consensusAlignment() function.
+
+template <typename TFragmentStore>
+class ConsensusAligner_
+{
+public:
+    ConsensusAligner_(TFragmentStore & store, ConsensusAlignmentOptions const & options) :
+            store(store), options(options)
+    {}
+
+    void run();
+
+private:
+
+    // Checks that there is at most one alignment per read in the store.
+    void checkAlignmentMultiplicity() const;
+    // Normalize reverse-complemented alignments and store the read IDs in rcIDs.
+    void normalizeRCReads();
+    // Restore read orientation of RC reads again.
+    void restoreRCReads();
+
+    // The ids of the reads that had a reverse-complemented alignment.
+    std::set<unsigned> rcIDs;
+    // The FragmentStore to use for consensus computation.
+    TFragmentStore & store;
+    // The configuration of the consensus alignment.
+    ConsensusAlignmentOptions const & options;
+};
+
+template <typename TFragmentStore>
+inline void ConsensusAligner_<TFragmentStore>::normalizeRCReads()
+{
+    for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
+        if (store.alignedReadStore[i].beginPos > store.alignedReadStore[i].endPos)
+        {
+            unsigned readID = store.alignedReadStore[i].readId;
+            rcIDs.insert(readID);
+            reverseComplement(store.readSeqStore[readID]);
+            std::swap(store.alignedReadStore[i].beginPos, store.alignedReadStore[i].endPos);
+        }
+}
+
+template <typename TFragmentStore>
+inline void ConsensusAligner_<TFragmentStore>::restoreRCReads()
+{
+    for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
+    {
+        unsigned readID = store.alignedReadStore[i].readId;
+        if (rcIDs.count(readID))
+        {
+            std::swap(store.alignedReadStore[i].beginPos, store.alignedReadStore[i].endPos);
+            reverseComplement(store.readSeqStore[readID]);
+        }
+    }
+}
+
+template <typename TFragmentStore>
+inline void ConsensusAligner_<TFragmentStore>::checkAlignmentMultiplicity() const
+{
+    std::set<unsigned> seen;
+    for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
+        if (seen.count(store.alignedReadStore[i].readId))
+            throw ConsensusAlignerException("Read with id has more than one alignment.");
+        else
+            seen.insert(store.alignedReadStore[i].readId);
+}
+
+template <typename TFragmentStore>
+inline void ConsensusAligner_<TFragmentStore>::run()
+{
+    // Check that there only is one alignment per read and escape via exception otherwise.
+    checkAlignmentMultiplicity();
+    // Normalize reads with RC alignment.
+    normalizeRCReads();
+
+    if (options.verbosity >= 1)
+        std::cerr << "computing overlap infos...\n";
+    // Build overlap infos, based on position and contig ID if configured to do so.
+    std::vector<OverlapInfo_> overlapInfos;
+    OverlapInfoComputation_<TFragmentStore> ovlInfoHelper(store, options);
+    ovlInfoHelper.run(overlapInfos);
+    if (options.verbosity >= 1)
+        std::cerr << "=> " << overlapInfos.size() << " overlap infos\n";
+
+    // TODO(holtgrew): Pick pairwise best alignments.
+
+    if (options.verbosity >= 1)
+        std::cerr << "building consensus...\n";
+    // Consensus builder.
+    ConsensusBuilder_<TFragmentStore> consBuilder(options);
+    consBuilder.run(store, overlapInfos);
+
+    // Restore RC'ed reads.
+    restoreRCReads();
+}
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_H_
diff --git a/seqan/consensus/consensus_aligner_interface.h b/seqan/consensus/consensus_aligner_interface.h
new file mode 100644
index 0000000..98c1e50
--- /dev/null
+++ b/seqan/consensus/consensus_aligner_interface.h
@@ -0,0 +1,150 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_INTERFACE_H_
+#define INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_INTERFACE_H_
+
+#include <seqan/realign.h>
+#include <seqan/store.h>
+
+#include "consensus_alignment_options.h"
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function consensusAlignment()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn consensusAlignment
+ * @headerfile <seqan/consensus.h>
+ * @brief Compute consensus alignment.
+ *
+ * @signature void consensusAlignment(store, options);
+ *
+ * @param[in,out] store   @link FragmentStore @endlink to use for consensus alignment computation.
+ * @param[in]     options @link ConsensusAlignmentOptions @endlink with configuration.
+ *
+ * @throws ConsensusAlignerIllegalArgumentException in case of invalid arguments (e.g. two alignments for the same
+ *                                                  read).
+ *
+ * This function computes a consensus alignment for a set of nucleic sequences that are stored in a @link FragmentStore
+ * @endlink.  Often, consensus sequences are reads, but they could also be other sequences, such as RNA transcripts.
+ * However, in the following description we call them reads.
+ *
+ * This function uses the @link FragmentStore::contigStore @endlink, @link FragmentStore::alignedReadStore @endlink,
+ * and @link FragmentStore::readSeqStore @endlink members of <tt>store</tt>.
+ *
+ * Each read must have at most one entry in <tt>store.alignedReadStore</tt>.
+ *
+ * @section General Algorithm
+ *
+ * In the most common case, both contig ID information and position information is available.  The algorithm considers
+ * all aligned reads on each contig.  For each read, all overlapping reads (with begin/end position extended
+ * <tt>options.posDelta</tt> to the left/to the right) are considered and overlap alignments are computed.  This
+ * pairwise alignment information is then used to compute a multiple sequence alignment (MSA).
+ *
+ * The resulting MSA is then refined by @link reAlignment @endlink (see @link ConsensusAlignmentOptions::runRealignment
+ * @endlink).
+ *
+ * @section Using position information
+ *
+ * When position information is to be used then this will be used to generate fewer overlap alignments by only
+ * considering possible overlaps in windows around each read alignment as described above.  Note that there can only be
+ * at most one alignment for each read in the <tt>store.alignedReadStore</tt> and the end position must be greater than
+ * or equal to the begin position, i.e., the alignment must be on the forward strand.
+ *
+ * Using position information also requires contig ID information.
+ *
+ * @section Using contigID information
+ *
+ * When contig ID information is to be used and position information is not to be used then the
+ * <tt>consensusAlignment()</tt> will compute pairwise alignments between all pairs of reads on the same contig.
+ *
+ * When contigID information is to be used then only the reads with an entry in <tt>store.alignedReadStore</tt> are
+ * considered.
+ *
+ * When contigID information is not used then an all-to-all pairwise alignment of all reads will be performed.
+ *
+ * <strong>Note</strong> that if reads having the same contig ID cannot be properly aligned and the MSA falls apart then
+ * the reads for one "connected alignment component" are kept on the original contig while the rest are added to new
+ * contigs that are appended to <tt>store.contigStore</tt>.
+ *
+ * @section Example
+ *
+ * The following example program takes a reference sequence and creates overlapping reads from it.  These are then added
+ * to <tt>store</tt> with approximate positions (adding and subtracting a few positions).  The function
+ * <tt>consensusAlignment()</tt> is then used to compute a MSA and the consensus sequence is stored in
+ * <tt>store.contigStore[0].seq</tt>.
+ *
+ * @include demos/dox/consensus/consensus_alignment.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/consensus/consensus_alignment.cpp.stdout
+ */
+
+template <typename TSpec, typename TConfig>
+void consensusAlignment(FragmentStore<TSpec, TConfig> & store,
+                        ConsensusAlignmentOptions const & options)
+{
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+
+    ConsensusAligner_<TFragmentStore> aligner(store, options);
+    aligner.run();
+
+    if (options.runRealignment)
+        for (unsigned contigID = 0; contigID < length(store.contigStore); ++contigID)
+            reAlignment(store, contigID, /*method=*/1, /*bandwidth=*/10, /*includeReference=*/false);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNER_INTERFACE_H_
diff --git a/seqan/consensus/consensus_alignment_options.h b/seqan/consensus/consensus_alignment_options.h
new file mode 100644
index 0000000..d1289eb
--- /dev/null
+++ b/seqan/consensus/consensus_alignment_options.h
@@ -0,0 +1,145 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNMENT_OPTIONS_H_
+#define INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNMENT_OPTIONS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class ConsensusAlignmentOptions
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class ConsensusAlignmentOptions
+ * @headerfile <seqan/consensus.h>
+ * @brief Configuration for @link consensusAlignment @endlink
+ *
+ * @signature struct ConsensusAlignmentOptions;
+ */
+
+struct ConsensusAlignmentOptions
+{
+    /*!
+     * @var unsigned ConsensusAlignmentOptions::INVALID;
+     * @brief Static member variable with a marker for invalid contig ids.
+     */
+    static const unsigned INVALID = (unsigned)-1;
+
+    ConsensusAlignmentOptions() :
+            contigID(INVALID), useContigID(true), usePositions(true), useGlobalAlignment(false),
+            posDelta(30), runRealignment(true), verbosity(0), overlapMaxErrorRate(5), overlapMinLength(20),
+            overlapMinCount(3), kMerSize(20), kMerMaxOcc(200),
+            scoreMatch(5), scoreMismatch(-5), scoreGapOpen(-5), scoreGapExtend(-1)
+    {}
+
+    /*!
+     * @var unsigned ConsensusAlignmentOptions::contigID;
+     * @brief The id of the contig to compute the consensus for, defaults to <tt>INVALID</tt>.
+     *
+     * Set to <tt>INVALID</tt> for all.
+     */
+    unsigned contigID;
+
+    /*!
+     * @var bool ConsensusAlignmentOptions::useContigID;
+     * @brief Whether or not to use the value of <tt>contigID</tt> (default is <tt>true</tt>).
+     *
+     * When this variable is set to <tt>false</tt> then the value of <tt>contigID</tt> is ignored and treated
+     * as if it was <tt>INVALID</tt>.
+     */
+    bool useContigID;
+
+    /*!
+     * @var bool ConsensusAlignmentOptions::usePositions;
+     * @brief Whether or not to use positions of the in the @link FragmentStore::alignedReadStore @endlink (default is <tt>true</tt>).
+     *
+     * When set to <tt>false</tt>, then the @link FragmentStore::alignedReadStore @endlink will be cleared and filled
+     * with new entries, one for each read.
+     */
+    bool usePositions;
+
+    bool useGlobalAlignment;
+
+    /*!
+     * @var unsigned ConsensusAlignmentOptions::posDelta;
+     * @brief Positions are considered with an environment of <tt>posDelta</tt> (default is <tt>30</tt>).
+     *
+     * When positions are not used then this value is ignored.
+     *
+     * See @link consensusAlignment @endlink for more details.
+    */
+    unsigned posDelta;  // TODO(holtgrew): Rename to overlapWindowSize
+
+    /*!
+     * @var bool ConsensusAlignmentOptions::runRealignment;
+     * @brief Perform a realignment using standard parameters, depending on the sequence length (default is <tt>true</tt>).
+     *
+     * Defaults to <tt>true</tt>.
+     */
+    bool runRealignment;
+
+    int verbosity;
+
+    int overlapMaxErrorRate;
+    int overlapMinLength;
+    int overlapMinCount;
+    int kMerSize;
+    int kMerMaxOcc;
+
+    int scoreMatch;
+    int scoreMismatch;
+    int scoreGapOpen;
+    int scoreGapExtend;
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_ALIGNMENT_OPTIONS_H_
diff --git a/seqan/consensus/consensus_base.h b/seqan/consensus/consensus_base.h
index 101e9ad..09e7aff 100644
--- a/seqan/consensus/consensus_base.h
+++ b/seqan/consensus/consensus_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,12 +45,6 @@ namespace SEQAN_NAMESPACE_MAIN
 
 // TODO(holtgrew): This apparently belongs into graph_msa?
 
-/**
-.Tag.Segment Match Generation.value.OverlapLibrary:
-	Segment matches from overlap alignments.
-..include:seqan/consensus.h
-*/
-
 struct OverlapLibrary_;
 typedef Tag<OverlapLibrary_> const OverlapLibrary;
 
@@ -60,8 +54,9 @@ typedef Tag<OverlapLibrary_> const OverlapLibrary;
 // Consensus tag
 //////////////////////////////////////////////////////////////////////////////
 
-/*!
+/*
  * @defgroup ConsensusCallingTags Consensus Calling Tags
+ * @brief Tags for consensus calling.
  *
  * @tag ConsensusCallingTags#MajorityVote
  * @headerfile <seqan/consensus.h>
@@ -72,29 +67,10 @@ typedef Tag<OverlapLibrary_> const OverlapLibrary;
  * @brief Consensus based on a bayesian probability.
  */
 
-/**
-.Tag.Consensus Calling:
-..cat:Consensus
-..summary:A tag that specifies how to call the consensus.
-..include:seqan/consensus.h
-*/
-
-
-/**
-.Tag.Consensus Calling.value.MajorityVote:
-	A consensus based on the most common character.
-..include:seqan/consensus.h
-*/
 
 struct MajorityVote_;
 typedef Tag<MajorityVote_> const MajorityVote;
 
-/**
-.Tag.Consensus Calling.value.Bayesian:
-	A consensus based on bayesian probability.
-..include:seqan/consensus.h
-*/
-
 struct Bayesian_;
 typedef Tag<Bayesian_> const Bayesian;
 
@@ -109,64 +85,64 @@ typedef Tag<Bayesian_> const Bayesian;
 
 struct ConsensusOptions {
 public:
-	// Method
-	// 0: graph-based multiple sequence alignment
-	// 1: realign
-	int method;
-
-	// ReAlign Method
-	// 0: Needleman-Wunsch
-	// 1: Gotoh
-	int rmethod;
-
-	// Bandwidth of overlap alignment
-	int bandwidth;
-
-	// Number of computed overlaps per read (at the beginning and end of a read)
-	int overlaps;
-
-	// Minimum match length of a computed overlap
-	int matchlength;
-
-	// Minimum quality (in percent identity) of a computed overlap
-	int quality;
-
-	// Window size, only relevant for insert sequencing
-	// If window == 0, no insert sequencing is assumed
-	int window;
-	
-	// Output
-	// 0: seqan style
-	// 1: afg output format
-	// 2: frg output format
-	// 3: cgb output format
+    // Method
+    // 0: graph-based multiple sequence alignment
+    // 1: realign
+    int method;
+
+    // ReAlign Method
+    // 0: Needleman-Wunsch
+    // 1: Gotoh
+    int rmethod;
+
+    // Bandwidth of overlap alignment
+    int bandwidth;
+
+    // Number of computed overlaps per read (at the beginning and end of a read)
+    int overlaps;
+
+    // Minimum match length of a computed overlap
+    int matchlength;
+
+    // Minimum quality (in percent identity) of a computed overlap
+    int quality;
+
+    // Window size, only relevant for insert sequencing
+    // If window == 0, no insert sequencing is assumed
+    int window;
+
+    // Output
+    // 0: seqan style
+    // 1: afg output format
+    // 2: frg output format
+    // 3: cgb output format
     // 4: Sam output format
-	int output;
-
-	// Multi-read alignment
-	bool noalign;
-
-	// Offset all reads, so the first read starts at position 0
-	bool moveToFront;
-
-	// Include reference genome
-	bool include;
-
-	// Scoring object for overlap alignments
-	Score<int> sc;
-
-	// Various input and output files
-	std::string readsfile;				// File of reads in FASTA format
-	std::string afgfile;				// AMOS afg file input
-	std::string samfile;				// Sam file input
-	std::string contigsfile;			// FASTA reference file for Sam input
-	std::string outfile;				// Output file name
-	
-	// Initialization
-	ConsensusOptions() 
-	{
-		sc = Score<int>(2,-6,-4,-9);
-	}
+    int output;
+
+    // Multi-read alignment
+    bool noalign;
+
+    // Offset all reads, so the first read starts at position 0
+    bool moveToFront;
+
+    // Include reference genome
+    bool include;
+
+    // Scoring object for overlap alignments
+    Score<int> sc;
+
+    // Various input and output files
+    std::string readsfile;                // File of reads in FASTA format
+    std::string afgfile;                // AMOS afg file input
+    std::string samfile;                // Sam file input
+    std::string contigsfile;            // FASTA reference file for Sam input
+    std::string outfile;                // Output file name
+
+    // Initialization
+    ConsensusOptions() :
+        method(0), rmethod(0), bandwidth(0), overlaps(0), matchlength(0), quality(0),
+        window(0), output(0), noalign(false), moveToFront(0), include(0), sc(2, -6, -4, -9)
+    {}
 };
 
 
@@ -176,43 +152,43 @@ struct ConsensusOptions {
 // positions of the alignments go into startEndPos.
 
 template<typename TValue, typename TStrSpec, typename TPosPair, typename TStringSpec, typename TSpec, typename TConfig, typename TId>
-inline void 
+inline void
 _loadContigReads(StringSet<TValue, Owner<TStrSpec> > & strSet,
-				 String<TPosPair, TStringSpec> & startEndPos,
-				 FragmentStore<TSpec, TConfig> const & fragStore,
-				 TId const contigId)
+                 String<TPosPair, TStringSpec> & startEndPos,
+                 FragmentStore<TSpec, TConfig> const & fragStore,
+                 TId const contigId)
 {
-	typedef FragmentStore<TSpec, TConfig> const TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename TFragmentStore::TReadPos TReadPos;
-
-
-	// Sort aligned reads according to contig id
-	sortAlignedReads(fragStore.alignedReadStore, SortContigId());
-	resize(strSet, length(fragStore.alignedReadStore));
-
-	// Retrieve all reads, limit them to the clear range and if required reverse complement them
-	typedef typename Iterator<typename TFragmentStore::TAlignedReadStore const>::Type TAlignIter;
-	TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	TSize numRead = 0;
-	TReadPos begClr = 0;
-	TReadPos endClr = 0;
-	TSize lenRead = 0;
-	TSize offset = 0;
-	for(;alignIt != alignItEnd; ++alignIt) {
-		offset = _min(alignIt->beginPos, alignIt->endPos);
-		getClrRange(fragStore, *alignIt, begClr, endClr);
-		strSet[numRead] = infix(fragStore.readSeqStore[alignIt->readId], begClr, endClr);
-		lenRead = endClr - begClr;
-		if (alignIt->beginPos < alignIt->endPos) appendValue(startEndPos, TPosPair(offset, offset + lenRead), Generous());
-		else {
-			reverseComplement(strSet[numRead]);
-			appendValue(startEndPos, TPosPair(offset + lenRead, offset), Generous());
-		}
-		++numRead;
-	}
-	resize(strSet, numRead, Exact());
+    typedef FragmentStore<TSpec, TConfig> const TFragmentStore;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename TFragmentStore::TReadPos TReadPos;
+
+
+    // Sort aligned reads according to contig id
+    sortAlignedReads(fragStore.alignedReadStore, SortContigId());
+    resize(strSet, length(fragStore.alignedReadStore));
+
+    // Retrieve all reads, limit them to the clear range and if required reverse complement them
+    typedef typename Iterator<typename TFragmentStore::TAlignedReadStore const>::Type TAlignIter;
+    TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    TSize numRead = 0;
+    TReadPos begClr = 0;
+    TReadPos endClr = 0;
+    TSize lenRead = 0;
+    TSize offset = 0;
+    for(;alignIt != alignItEnd; ++alignIt) {
+        offset = _min(alignIt->beginPos, alignIt->endPos);
+        getClrRange(fragStore, *alignIt, begClr, endClr);
+        strSet[numRead] = infix(fragStore.readSeqStore[alignIt->readId], begClr, endClr);
+        lenRead = endClr - begClr;
+        if (alignIt->beginPos < alignIt->endPos) appendValue(startEndPos, TPosPair(offset, offset + lenRead), Generous());
+        else {
+            reverseComplement(strSet[numRead]);
+            appendValue(startEndPos, TPosPair(offset + lenRead, offset), Generous());
+        }
+        ++numRead;
+    }
+    resize(strSet, numRead, Exact());
 }
 
 
@@ -220,363 +196,324 @@ _loadContigReads(StringSet<TValue, Owner<TStrSpec> > & strSet,
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TSpec, typename TConfig, typename TMatrix, typename TSize2, typename TSize, typename TReadSlot> 
+template<typename TSpec, typename TConfig, typename TMatrix, typename TSize2, typename TSize, typename TReadSlot>
 inline bool
 convertAlignment(FragmentStore<TSpec, TConfig>& fragStore,
-				 TMatrix& mat,
-				 TSize2 contigId,
-				 TSize& coverage,
-				 TReadSlot& slot)
+                 TMatrix& mat,
+                 TSize2 contigId,
+                 TSize& coverage,
+                 TReadSlot& slot)
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Value<TMatrix>::Type TValue;
-	typedef typename TFragmentStore::TContigPos TContigPos;
-
-	// Gap char
-	TValue gapChar = gapValue<TValue>();
-
-	// Sort according to contigId
-	sortAlignedReads(fragStore.alignedReadStore, SortContigId());
-	
-	// Find range of the given contig
-	typedef typename Iterator<typename TFragmentStore::TAlignedReadStore, Standard>::Type TAlignIter;
-	TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-
-	// Sort the reads according to the begin position
-	sortAlignedReads(infix(fragStore.alignedReadStore, alignIt - begin(fragStore.alignedReadStore, Standard()), alignItEnd - begin(fragStore.alignedReadStore, Standard())), SortBeginPos());
-	TAlignIter alignItBegin = alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-
-	// Get the maximum coverage and the slot for each read
-	typedef String<TSize> TFirstFreePos;
-	typedef typename Iterator<TFirstFreePos, Standard>::Type TPosIter;
-	TFirstFreePos freePos;
-	TSize pos = 0;
-	TSize maxTmp = 0;
-	TSize numCol = 0;
-	reserve(slot, alignItEnd - alignIt);
-	for(;alignIt != alignItEnd; ++alignIt) {
-		TPosIter itPos = begin(freePos, Standard());
-		TPosIter itPosEnd = end(freePos, Standard());
-		pos = 0;
-		for(;itPos != itPosEnd; ++itPos, ++pos) 
-			if ((TContigPos)*itPos < _min(alignIt->beginPos, alignIt->endPos)) break;
-		if (pos + 1 > length(freePos)) resize(freePos, pos+1, Generous());
-		maxTmp = _max(alignIt->beginPos, alignIt->endPos);
-		freePos[pos] = maxTmp;
-		if (maxTmp > numCol) numCol = maxTmp;
-		appendValue(slot, pos);
-	}
-	coverage = length(freePos);
-	clear(freePos);
-
-	// Fill the matrix
-	typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
-	resize(mat, coverage * numCol, '.');
-	alignIt = alignItBegin;
-	TSize readPos = 0;
-	TMatIter matIt = begin(mat, Standard());
-	typename TFragmentStore::TReadSeq myRead;
-	for(;alignIt != alignItEnd; ++alignIt, ++readPos) {
-		typedef typename Iterator<String<typename TFragmentStore::TReadGapAnchor>, Standard>::Type TReadGapsIter;
-		TReadGapsIter itGaps = begin(alignIt->gaps, Standard());
-		TReadGapsIter itGapsEnd = end(alignIt->gaps, Standard());
-		
-		// Place each read inside the matrix
-		myRead = fragStore.readSeqStore[alignIt->readId];
-		TSize lenRead = length(myRead);
-		TSize offset = alignIt->beginPos;
-		if (alignIt->beginPos > alignIt->endPos) {
-			reverseComplement(myRead);
-			offset = alignIt->endPos;
-		}
-		matIt = begin(mat, Standard());
-		matIt += (slot[readPos] * numCol + offset);
-
-		typedef typename Iterator<typename TFragmentStore::TReadSeq, Standard>::Type TReadIter;
-		TReadIter seqReadIt = begin(myRead, Standard());
-
-		// First clear range
-		TSize mySeqPos = 0;
-		int diff = 0;
-		if ((itGaps != itGapsEnd) && (itGaps->gapPos == 0)) {
-			mySeqPos = itGaps->seqPos;
-			diff = -1 * mySeqPos;
-			seqReadIt += mySeqPos;
-		}
-		TSize clr2 = lenRead;
-		TSize stop = 0;
-		for(;itGaps != itGapsEnd; ++itGaps) {
-			// Any clipped sequence at the end
-			stop =  itGaps->seqPos;
-			if (diff - ((int) itGaps->gapPos - (int) itGaps->seqPos) > 0) 
-				clr2 = stop = lenRead - (diff - ((int) itGaps->gapPos - (int) itGaps->seqPos));
-			
-			for(;mySeqPos < stop; ++matIt, ++seqReadIt, ++mySeqPos) 
-				*matIt = *seqReadIt;
-
-			for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i, ++matIt) 
-				*matIt = gapChar;
-	
-			diff = (itGaps->gapPos - itGaps->seqPos);
-		}
-		for(;mySeqPos < clr2; ++mySeqPos, ++seqReadIt, ++matIt) 
-			*matIt = *seqReadIt;
-	}
-	//for(TSize row = 0; row < coverage; ++row) {
-	//	for(TSize col = 0; col<numCol; ++col) {
-	//		std::cout << mat[row * numCol + col];
-	//	}
-	//	std::cout << std::endl;
-	//}
-	return true;
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Value<TMatrix>::Type TValue;
+    typedef typename TFragmentStore::TContigPos TContigPos;
+
+    // Gap char
+    TValue gapChar = gapValue<TValue>();
+
+    // Sort according to contigId
+    sortAlignedReads(fragStore.alignedReadStore, SortContigId());
+
+    // Find range of the given contig
+    typedef typename Iterator<typename TFragmentStore::TAlignedReadStore, Standard>::Type TAlignIter;
+    TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+
+    // Sort the reads according to the begin position
+    sortAlignedReads(infix(fragStore.alignedReadStore, alignIt - begin(fragStore.alignedReadStore, Standard()), alignItEnd - begin(fragStore.alignedReadStore, Standard())), SortBeginPos());
+    TAlignIter alignItBegin = alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+
+    // Get the maximum coverage and the slot for each read
+    typedef String<TSize> TFirstFreePos;
+    typedef typename Iterator<TFirstFreePos, Standard>::Type TPosIter;
+    TFirstFreePos freePos;
+    TSize pos = 0;
+    TSize maxTmp = 0;
+    TSize numCol = 0;
+    reserve(slot, alignItEnd - alignIt);
+    for(;alignIt != alignItEnd; ++alignIt) {
+        TPosIter itPos = begin(freePos, Standard());
+        TPosIter itPosEnd = end(freePos, Standard());
+        pos = 0;
+        for(;itPos != itPosEnd; ++itPos, ++pos)
+            if ((TContigPos)*itPos < _min(alignIt->beginPos, alignIt->endPos)) break;
+        if (pos + 1 > length(freePos)) resize(freePos, pos+1, Generous());
+        maxTmp = _max(alignIt->beginPos, alignIt->endPos);
+        freePos[pos] = maxTmp;
+        if (maxTmp > numCol) numCol = maxTmp;
+        appendValue(slot, pos);
+    }
+    coverage = length(freePos);
+    clear(freePos);
+
+    // Fill the matrix
+    typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
+    resize(mat, coverage * numCol, '.');
+    alignIt = alignItBegin;
+    TSize readPos = 0;
+    TMatIter matIt = begin(mat, Standard());
+    typename TFragmentStore::TReadSeq myRead;
+    for(;alignIt != alignItEnd; ++alignIt, ++readPos) {
+        typedef typename Iterator<String<typename TFragmentStore::TReadGapAnchor>, Standard>::Type TReadGapsIter;
+        TReadGapsIter itGaps = begin(alignIt->gaps, Standard());
+        TReadGapsIter itGapsEnd = end(alignIt->gaps, Standard());
+
+        // Place each read inside the matrix
+        myRead = fragStore.readSeqStore[alignIt->readId];
+        TSize lenRead = length(myRead);
+        TSize offset = alignIt->beginPos;
+        if (alignIt->beginPos > alignIt->endPos) {
+            reverseComplement(myRead);
+            offset = alignIt->endPos;
+        }
+        matIt = begin(mat, Standard());
+        matIt += (slot[readPos] * numCol + offset);
+
+        typedef typename Iterator<typename TFragmentStore::TReadSeq, Standard>::Type TReadIter;
+        TReadIter seqReadIt = begin(myRead, Standard());
+
+        // First clear range
+        TSize mySeqPos = 0;
+        int diff = 0;
+        if ((itGaps != itGapsEnd) && (itGaps->gapPos == 0)) {
+            mySeqPos = itGaps->seqPos;
+            diff = -1 * mySeqPos;
+            seqReadIt += mySeqPos;
+        }
+        TSize clr2 = lenRead;
+        TSize stop = 0;
+        for(;itGaps != itGapsEnd; ++itGaps) {
+            // Any clipped sequence at the end
+            stop =  itGaps->seqPos;
+            if (diff - ((int) itGaps->gapPos - (int) itGaps->seqPos) > 0)
+                clr2 = stop = lenRead - (diff - ((int) itGaps->gapPos - (int) itGaps->seqPos));
+
+            for(;mySeqPos < stop; ++matIt, ++seqReadIt, ++mySeqPos)
+                *matIt = *seqReadIt;
+
+            for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i, ++matIt)
+                *matIt = gapChar;
+
+            diff = (itGaps->gapPos - itGaps->seqPos);
+        }
+        for(;mySeqPos < clr2; ++mySeqPos, ++seqReadIt, ++matIt)
+            *matIt = *seqReadIt;
+    }
+    //for(TSize row = 0; row < coverage; ++row) {
+    //    for(TSize col = 0; col<numCol; ++col) {
+    //        std::cout << mat[row * numCol + col];
+    //    }
+    //    std::cout << std::endl;
+    //}
+    return true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TSpec, typename TConfig, typename TMatrix, typename TSize2, typename TSize> 
+template<typename TSpec, typename TConfig, typename TMatrix, typename TSize2, typename TSize>
 inline bool
 convertAlignment(FragmentStore<TSpec, TConfig>& fragStore,
-				 TMatrix& mat,
-				 TSize2 contigId,
-				 TSize& coverage)
+                 TMatrix& mat,
+                 TSize2 contigId,
+                 TSize& coverage)
 {
-	String<TSize> slot;
-	return convertAlignment(fragStore, mat, contigId, coverage, slot);
+    String<TSize> slot;
+    return convertAlignment(fragStore, mat, contigId, coverage, slot);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TSpec, typename TConfig, typename TMatrix> 
+template<typename TSpec, typename TConfig, typename TMatrix>
 inline bool
 convertAlignment(FragmentStore<TSpec, TConfig>& fragStore,
-				 TMatrix& mat)
+                 TMatrix& mat)
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	TSize coverage;
-	return convertAlignment(fragStore, mat, 0, coverage);
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    TSize coverage;
+    return convertAlignment(fragStore, mat, 0, coverage);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TSpec, typename TConfig, typename TGappedConsensus, typename TSize> 
+template<typename TSpec, typename TConfig, typename TGappedConsensus, typename TSize>
 inline void
 getGappedConsensus(FragmentStore<TSpec, TConfig>& fragStore,
-				   TGappedConsensus& gappedConsensus,
-				   TSize contigId)
+                   TGappedConsensus& gappedConsensus,
+                   TSize contigId)
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Value<TGappedConsensus>::Type TValue;
-	typedef typename TFragmentStore::TContigPos TContigPos;
-	
-	TValue gapChar = gapValue<TValue>();
-	typedef typename Iterator<typename TFragmentStore::TContigSeq, Standard>::Type TContigIter;
-	TContigIter seqContigIt = begin(fragStore.contigStore[contigId].seq, Standard());
-	TContigIter seqContigItEnd = end(fragStore.contigStore[contigId].seq, Standard());
-	typedef typename Iterator<String<typename TFragmentStore::TContigGapAnchor>, Standard>::Type TGapsIter;
-	TGapsIter itGaps = begin(fragStore.contigStore[contigId].gaps, Standard());
-	TGapsIter itGapsEnd = end(fragStore.contigStore[contigId].gaps, Standard());
-	int diff = 0;
-	TContigPos mySeqPos = 0;
-	for(;itGaps != itGapsEnd; goNext(itGaps)) {
-		for(;mySeqPos < itGaps->seqPos; ++seqContigIt, ++mySeqPos) 
-			appendValue(gappedConsensus, *seqContigIt, Generous());
-			
-		for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i) 
-			appendValue(gappedConsensus, gapChar, Generous());
-			diff = (itGaps->gapPos - itGaps->seqPos);
-	}
-	for(;seqContigIt != seqContigItEnd; ++seqContigIt) 
-		appendValue(gappedConsensus, *seqContigIt, Generous());
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Value<TGappedConsensus>::Type TValue;
+    typedef typename TFragmentStore::TContigPos TContigPos;
+
+    TValue gapChar = gapValue<TValue>();
+    typedef typename Iterator<typename TFragmentStore::TContigSeq, Standard>::Type TContigIter;
+    TContigIter seqContigIt = begin(fragStore.contigStore[contigId].seq, Standard());
+    TContigIter seqContigItEnd = end(fragStore.contigStore[contigId].seq, Standard());
+    typedef typename Iterator<String<typename TFragmentStore::TContigGapAnchor>, Standard>::Type TGapsIter;
+    TGapsIter itGaps = begin(fragStore.contigStore[contigId].gaps, Standard());
+    TGapsIter itGapsEnd = end(fragStore.contigStore[contigId].gaps, Standard());
+    int diff = 0;
+    TContigPos mySeqPos = 0;
+    for(;itGaps != itGapsEnd; goNext(itGaps)) {
+        for(;mySeqPos < itGaps->seqPos; ++seqContigIt, ++mySeqPos)
+            appendValue(gappedConsensus, *seqContigIt, Generous());
+
+        for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i)
+            appendValue(gappedConsensus, gapChar, Generous());
+            diff = (itGaps->gapPos - itGaps->seqPos);
+    }
+    for(;seqContigIt != seqContigItEnd; ++seqContigIt)
+        appendValue(gappedConsensus, *seqContigIt, Generous());
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TSpec, typename TConfig, typename TGappedConsensus, typename TSize> 
+template<typename TSpec, typename TConfig, typename TGappedConsensus, typename TSize>
 inline void
 assignGappedConsensus(FragmentStore<TSpec, TConfig>& fragStore,
-					  TGappedConsensus& gappedCons,
-					  TSize contigId)
+                      TGappedConsensus& gappedCons,
+                      TSize contigId)
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Value<TGappedConsensus>::Type TValue;
-	TValue gapChar = gapValue<TValue>();
-
-	// Update the contig
-	typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigStoreElement;
-	TContigStoreElement& contigEl = fragStore.contigStore[contigId];
-	clear(contigEl.gaps);
-	clear(contigEl.seq);
-
-	// Create the sequence and the gap anchors
-	typedef typename Iterator<TGappedConsensus, Standard>::Type TStringIter;
-	TStringIter seqIt = begin(gappedCons, Standard());
-	TStringIter seqItEnd = end(gappedCons, Standard());
-	typedef typename TFragmentStore::TReadPos TReadPos;
-	typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
-	TReadPos ungappedPos = 0;
-	TReadPos gappedPos = 0;
-	bool gapOpen = false;
-	for(;seqIt != seqItEnd; ++seqIt, ++gappedPos) {
-		if (*seqIt == gapChar) gapOpen = true;				
-		else {
-			if (gapOpen) {
-				appendValue(contigEl.gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
-				gapOpen = false;
-			}
-			Dna5Q letter = *seqIt;
-			assignQualityValue(letter, 'D');
-			appendValue(contigEl.seq, letter);
-			++ungappedPos;
-		}
-	}
-	if (gapOpen) 
-		appendValue(contigEl.gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Value<TGappedConsensus>::Type TValue;
+    TValue gapChar = gapValue<TValue>();
+
+    // Update the contig
+    typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigStoreElement;
+    TContigStoreElement& contigEl = fragStore.contigStore[contigId];
+    clear(contigEl.gaps);
+    clear(contigEl.seq);
+
+    // Create the sequence and the gap anchors
+    typedef typename Iterator<TGappedConsensus, Standard>::Type TStringIter;
+    TStringIter seqIt = begin(gappedCons, Standard());
+    TStringIter seqItEnd = end(gappedCons, Standard());
+    typedef typename TFragmentStore::TReadPos TReadPos;
+    typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
+    TReadPos ungappedPos = 0;
+    TReadPos gappedPos = 0;
+    bool gapOpen = false;
+    for(;seqIt != seqItEnd; ++seqIt, ++gappedPos) {
+        if (*seqIt == gapChar) gapOpen = true;
+        else {
+            if (gapOpen) {
+                appendValue(contigEl.gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
+                gapOpen = false;
+            }
+            Dna5Q letter = *seqIt;
+            assignQualityValue(letter, 'D');
+            appendValue(contigEl.seq, letter);
+            ++ungappedPos;
+        }
+    }
+    if (gapOpen)
+        appendValue(contigEl.gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
 }
 
 
 
 //////////////////////////////////////////////////////////////////////////////////
 
-/*!
- * @fn consensusAligment
+/*
+ * @fn consensusAlignment
  * @headerfile <seqan/consensus.h>
  * @brief Compute consensus alignment.
- * 
+ *
  * @signature void consensusAlignment(alignmentGraph, beginEndPos[, options])
- * 
+ *
  * @param[out] alignmentGraph  Alignment graph to build.
  * @param[in]  options         Optional settings for the consenus alignment, type: <tt>ConsensusOptions</tt>.
  * @param[in]  beginEndPos     Interval start and end position for the read's alignment; <tt>String&lt;Pair&lt;TPos, TPos&gt; &gt;</tt>.
- * 
+ *
  * @section Example
- * 
+ *
  * @code{.cpp}
  * #include <seqan/sequence.h>
  * #include <seqan/graph_align.h>
  * #include <seqan/consensus.h>
- *  
+ *
  * int main()
  * {
  *     using namespace seqan;
- *  
+ *
  *     typedef StringSet<Dna5String> TStringSet;
  *     typedef Graph<Alignment<TStringSet, void, WithoutEdgeId> > TAlignGraph;
- *  
+ *
  *     TStringSet readSet;
  *     String<Pair<TSize> > begEndPos;
- *  
+ *
  *     appendValue(readSet, "CCCAGTGA");
  *     appendValue(begEndPos, Pair<TSize>(0, 5));
  *     appendValue(readSet, "AGGGACTGT");
  *     appendValue(begEndPos, Pair<TSize>(3, 9));
- *  
+ *
  *     TAlignGraph alignmentGraph(readSet);
  *     consensusAlignment(alignmentGraph, begEndPos);
- *  
+ *
  *     return 0;
  * }
  * @endcode
  */
 
-/**
-.Function.consensusAligment
-..cat:Consensus
-..summary:Compute consensus alignment.
-..signature:consensusAlignment(alignmentGraph, beginEndPos, [options])
-..param.alignmentGraph:
-...type:Spec.Alignment Graph
-..param.beginEndPos:Interval start and end position for the read's alignment.
-...type:nolink:$StringSet<Pair<TPos, TPos> >$
-..param.options:Optional settings for the consenus alignment
-...type:nolink:$ConsensusOptions$
-..include:seqan/consensus.h
-..example.code:
-#include <seqan/sequence.h>
-#include <seqan/graph_align.h>
-#include <seqan/consensus.h>
-
-int main()
-{
-    using namespace seqan;
-
-    typedef StringSet<Dna5String> TStringSet;
-    typedef Graph<Alignment<TStringSet, void, WithoutEdgeId> > TAlignGraph;
-
-    TStringSet readSet;
-    String<Pair<TSize> > begEndPos;
-
-    appendValue(readSet, "CCCAGTGA");
-    appendValue(begEndPos, Pair<TSize>(0, 5));
-    appendValue(readSet, "AGGGACTGT");
-    appendValue(begEndPos, Pair<TSize>(3, 9));
-
-    TAlignGraph alignmentGraph(readSet);
-    consensusAlignment(alignmentGraph, begEndPos);
-
-    return 0;
-}
-*/
-
 template<typename TStringSet, typename TCargo, typename TSpec, typename TSize, typename TConfigOptions>
 inline void
 consensusAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gOut,
-				   String<Pair<TSize, TSize> >& begEndPos,
-				   TConfigOptions const& consOpt) 
+                   String<Pair<TSize, TSize> >& begEndPos,
+                   TConfigOptions const& consOpt)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TOutGraph;
-	typedef typename Id<TOutGraph>::Type TId;
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TOutGraph;
+    typedef typename Id<TOutGraph>::Type TId;
 
-	// Initialization
-	TStringSet& seqSet = stringSet(gOut);
+    // Initialization
+    TStringSet& seqSet = stringSet(gOut);
 
-	// Select all overlapping reads and record the diagonals of the band
-	String<Pair<TId, TId> > pList;
-	String<Pair<int, int> > diagList;
-	if (consOpt.window == 0)
+    // Select all overlapping reads and record the diagonals of the band
+    String<Pair<TId, TId> > pList;
+    String<Pair<int, int> > diagList;
+    if (consOpt.window == 0)
         selectPairsAssembly(seqSet, begEndPos, consOpt.bandwidth, pList, diagList);
-	else
+    else
         selectPairsAllAgainstAll(seqSet, begEndPos, consOpt.window, pList, diagList);
 
-	// Set-up a sparse distance matrix
-	Graph<Undirected<double> > pairGraph;
-	
-	// Containers for segment matches and corresponding scores 
-	typedef String<Fragment<> > TFragmentString;
-	TFragmentString matches;
-	typedef String<int> TScoreValues;
-	TScoreValues scores;
-
-	// Compute segment matches from global pairwise alignments
-	appendSegmentMatches(seqSet, pList, diagList, begEndPos, consOpt.sc, consOpt.matchlength, consOpt.quality, consOpt.overlaps, matches, scores, pairGraph, OverlapLibrary() );
-	clear(pList);
-	clear(diagList);
-
-	// If there are no alignment matches, return
-	if (!length(matches)) return;
-
-	// Use these segment matches for the initial alignment graph
-	typedef Graph<Alignment<TStringSet, TSize> > TGraph;
-	TGraph g(seqSet);
-	buildAlignmentGraph(matches, scores, g, consOpt.sc, ReScore() );
-	clear(matches);
-	clear(scores);
-
-	// Guide Tree
-	Graph<Tree<double> > guideTree;
-	upgmaTree(pairGraph, guideTree);
-	clear(pairGraph);
-
-	// Triplet library extension
-	graphBasedTripletLibraryExtension(g);
-
-	// Perform a progressive alignment
-	progressiveAlignment(g, guideTree, gOut);
-	clear(g);
-	clear(guideTree);
+    // Set-up a sparse distance matrix
+    Graph<Undirected<double> > pairGraph;
+
+    // Containers for segment matches and corresponding scores
+    typedef String<Fragment<> > TFragmentString;
+    TFragmentString matches;
+    typedef String<int> TScoreValues;
+    TScoreValues scores;
+
+    // Compute segment matches from global pairwise alignments
+    appendSegmentMatches(seqSet, pList, diagList, begEndPos, consOpt.sc, consOpt.matchlength, consOpt.quality, consOpt.overlaps, matches, scores, pairGraph, OverlapLibrary() );
+    clear(pList);
+    clear(diagList);
+
+    // If there are no alignment matches, return
+    if (!length(matches)) return;
+
+    // Use these segment matches for the initial alignment graph
+    typedef Graph<Alignment<TStringSet, TSize> > TGraph;
+    TGraph g(seqSet);
+    buildAlignmentGraph(matches, scores, g, consOpt.sc, ReScore() );
+    clear(matches);
+    clear(scores);
+
+    // Guide Tree
+    Graph<Tree<double> > guideTree;
+    upgmaTree(pairGraph, guideTree);
+    clear(pairGraph);
+
+    // Triplet library extension
+    graphBasedTripletLibraryExtension(g);
+
+    // Perform a progressive alignment
+    progressiveAlignment(g, guideTree, gOut);
+    clear(g);
+    clear(guideTree);
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -585,10 +522,10 @@ consensusAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gOut,
 template<typename TStringSet, typename TCargo, typename TSpec, typename TSize>
 inline void
 consensusAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gOut,
-				   String<Pair<TSize, TSize> >& begEndPos) 
+                   String<Pair<TSize, TSize> >& begEndPos)
 {
-	ConsensusOptions consOpt;
-	consensusAlignment(gOut, begEndPos, consOpt);
+    ConsensusOptions consOpt;
+    consensusAlignment(gOut, begEndPos, consOpt);
 }
 
 
@@ -597,232 +534,232 @@ consensusAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gOut,
 template <typename TFragSpec, typename TConfig, typename TStringSet, typename TCargo, typename TSpec, typename TContigId>
 inline void
 updateContig(FragmentStore<TFragSpec, TConfig>& fragStore,
-			 Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-			 TContigId contigId)
+             Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+             TContigId contigId)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Value<TStringSet>::Type TString;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef std::map<TSize, TSize> TComponentLength;
-	typedef char TValue;
-
-	// Initialization
-	TStringSet& strSet = stringSet(g);
-	TSize nseq = length(strSet);
-	TValue gapChar = gapValue<TValue>();
-	TValue specialGap = '.';
-	TSize maxCoverage = 0;
-	TSize len = 0;
-	String<TValue> mat;
-
-	// Store for each read the begin position, the end position and the row in the alignment matrix
-	String<TSize> readBegEndRowPos;
-	resize(readBegEndRowPos, 3*nseq);
-
-	// Strongly Connected Components, topological sort, and length of each component
-	String<TSize> component;
-	String<TSize> order;
-	TComponentLength compLength;
-	if (convertAlignment(g, component, order, compLength)) {
-		TSize numOfComponents = length(order);
-		
-		// Assign to each sequence the start and end (in terms of component ranks)
-		typedef String<std::pair<TSize, TSize> > TComponentToRank;
-		TComponentToRank compToRank;
-		for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex) 
-			appendValue(compToRank, std::make_pair(order[compIndex], compIndex), Generous());
-		::std::sort(begin(compToRank, Standard()), end(compToRank, Standard()));
-
-		typedef Pair<TSize, TSize> TRankPair;
-		typedef String<TRankPair> TSequenceToRanks;
-		TSequenceToRanks seqToRank;
-		resize(seqToRank, nseq);
-		typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-		TVertexIterator itVertex(g);
-		for(;!atEnd(itVertex);++itVertex) {
-			TVertexDescriptor vert = value(itVertex);
-			TSize seq = idToPosition(strSet, sequenceId(g, vert));
-			if (fragmentBegin(g, vert) == 0) 
-				seqToRank[seq].i1 = ::std::lower_bound(begin(compToRank, Standard()), end(compToRank, Standard()), ::std::make_pair((TSize) component[vert], (TSize) 0))->second;
-			if (fragmentBegin(g, vert) + fragmentLength(g, vert) == length(strSet[seq]))
-				seqToRank[seq].i2 = ::std::lower_bound(begin(compToRank, Standard()), end(compToRank, Standard()), ::std::make_pair((TSize) component[vert], (TSize) 0))->second;
-		}
-		clear(compToRank);
-
-		// Assign the sequences to rows
-		String<TSize> seqToRow;
-		resize(seqToRow, nseq);
-		maxCoverage = 0;
-		typedef String<bool> TLeftOver;
-		typedef typename Iterator<TLeftOver, Standard>::Type TLeftOverIter;
-		TLeftOver leftOver;
-		resize(leftOver, nseq, true);
-		typedef String<std::pair<TSize, TSize> > TSeqToBegin;
-		typedef typename Iterator<TSeqToBegin, Standard>::Type TSeqToBeginIter;
-		TSeqToBegin seqToBegin;
-		TSize finishedSeq = 0;
-		while(finishedSeq < nseq) {
-			TLeftOverIter itL = begin(leftOver, Standard());
-			TLeftOverIter itLEnd = end(leftOver, Standard());
-			for(TSize pos = 0; itL != itLEnd; ++itL, ++pos) 
-				if (*itL) appendValue(seqToBegin, std::make_pair((seqToRank[pos]).i1, pos), Generous());
-			::std::sort(begin(seqToBegin, Standard()), end(seqToBegin, Standard()));
-			
-			TSize endPos = 0;
-			TSeqToBeginIter itSB = begin(seqToBegin, Standard());
-			TSeqToBeginIter itSBEnd = end(seqToBegin, Standard());
-			for(;itSB != itSBEnd;++itSB) {
-				if (endPos <= (*itSB).first) {
-					TSize currentSeq = (*itSB).second;
-					seqToRow[currentSeq] = maxCoverage;
-					endPos = (seqToRank[currentSeq]).i2 + 2;
-					leftOver[currentSeq] = false;
-					++finishedSeq;
-				}	
-			}
-			clear(seqToBegin);
-			++maxCoverage;
-		}
-		clear(leftOver);
-
-		// Create the matrix
-		len = 0;
-		String<TSize> compOffset;
-		resize(compOffset, numOfComponents);
-		for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex) {
-			compOffset[order[compIndex]] = len;
-			len+=compLength[order[compIndex]];
-		}
-		resize(mat, len * maxCoverage, gapChar);
-
-		// Fill in the segments
-		typedef typename Infix<TString>::Type TInfix;
-		typedef typename Iterator<TInfix, Standard>::Type TInfixIter;
-		typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
-		for(typename TPosToVertexMap::const_iterator it = g.data_pvMap.begin();it != g.data_pvMap.end(); ++it) {
-			TInfix str = label(g,it->second);
-			TSize c = property(component, it->second);
-			TSize row = seqToRow[idToPosition(strSet, it->first.first)];
-			//if (row == 0) {
-			//	std::cout << sequenceId(g, it->second) << ':' << str << ',' << strSet[sequenceId(g, it->second)] << std::endl;
-			//	std::cout << getProperty(component, it->second) << ',' << order[compIndex] << std::endl;
-			//	std::cout << (seqToRank[sequenceId(g, it->second)]).i1 << ',' << (seqToRank[sequenceId(g, it->second)]).i2 << std::endl;
-			//}
-			TInfixIter sIt = begin(str, Standard());
-			TInfixIter sItEnd = end(str, Standard());
-			TSize i = compOffset[c];
-			for(TSize pCol = i;sIt!=sItEnd;++sIt, ++pCol, ++i) 
-				mat[row * len + pCol] = *sIt;
-		}
-		String<bool> active;
-		for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex) {
-			TSize offset = compOffset[order[compIndex]];
-			TSize currentCompLength = compLength[order[compIndex]];
-
-			clear(active);
-			resize(active, maxCoverage, false);
-
-			// Find the empty rows
-			for(TSize i=0;i<nseq; ++i) {
-				if (((seqToRank[i]).i1 <= compIndex) && ((seqToRank[i]).i2 >= compIndex)) 
-					active[(seqToRow[i])] = true;
-			}
-			
-			// Substitute false gaps with special gap character
-			for(TSize i = 0; i < maxCoverage; ++i) {
-				if (!(active[i])) {
-					for(TSize pCol = offset;pCol < offset + currentCompLength;++pCol) 
-						mat[i * len + pCol] = specialGap;
-				}
-			}
-		}
-
-		// Get the new begin and end positions
-		for(TSize i=0;i<nseq; ++i) {
-			TVertexDescriptor lastVertex = findVertex(const_cast<TGraph&>(g), positionToId(strSet, i), length(strSet[i]) - 1);
-			TSize readBegin = compOffset[getProperty(component, findVertex(const_cast<TGraph&>(g), positionToId(strSet, i), 0))];
-			TSize readEnd = compOffset[getProperty(component, lastVertex)] + fragmentLength(const_cast<TGraph&>(g), lastVertex);
-			readBegEndRowPos[3*i] = readBegin;
-			readBegEndRowPos[3*i+1] = readEnd;
-			readBegEndRowPos[3*i+2] = seqToRow[i];
-		}
-
-	}
-	clear(component);
-	clear(order);
-	compLength.clear();
-
-	
-	//// Debug code
-	//for(TSize row = 0; row<maxCoverage; ++row) {
-	//	for(TSize col = 0; col<len; ++col) {
-	//		std::cout << mat[row * len + col];			
-	//	}
-	//	std::cout << std::endl;
-	//}
-
-	// Create the new consensus
-	typedef typename Value<TString>::Type TAlphabet;
-	String<TValue> gappedCons;
-	consensusCalling(mat, gappedCons, maxCoverage, TAlphabet(), MajorityVote());
-
-	// Assign new consensus
-	assignGappedConsensus(fragStore, gappedCons, contigId);
-
-	// Update all aligned reads
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename TFragmentStore::TReadPos TReadPos;
-	typedef typename TFragmentStore::TContigPos TContigPos;
-	typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
-	//typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
-	typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
-	sortAlignedReads(fragStore.alignedReadStore, SortContigId());
-	TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	TReadPos ungappedPos = 0;
-	TReadPos gappedPos = 0;
-	bool gapOpen;
-	for(TSize i = 0;alignIt != alignItEnd; ++alignIt, ++i) {
-		TSize lenRead = length(fragStore.readSeqStore[alignIt->readId]);
-		TReadPos begClr = 0;
-		TReadPos endClr = 0;
-		getClrRange(fragStore, *alignIt, begClr, endClr);
-		clear(alignIt->gaps);
-		ungappedPos = begClr;
-		if (alignIt->beginPos > alignIt->endPos) ungappedPos = lenRead - endClr;
-		if (ungappedPos != 0) appendValue(alignIt->gaps, TContigGapAnchor(ungappedPos, 0));
-		gappedPos = 0;
-		gapOpen = false;
-		for(TSize column = readBegEndRowPos[3*i]; column<readBegEndRowPos[3*i + 1]; ++column, ++gappedPos) {
-			if (mat[readBegEndRowPos[3*i + 2] * len + column] == gapChar) gapOpen = true;				
-			else {
-				if (gapOpen) {
-					appendValue(alignIt->gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
-					gapOpen = false;
-				}
-				++ungappedPos;
-			}
-		}
-		if (gapOpen) appendValue(alignIt->gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
-		if (alignIt->beginPos < alignIt->endPos) {
-			if (endClr != (TContigPos)lenRead) 
-				appendValue(alignIt->gaps, TContigGapAnchor(lenRead, lenRead + (gappedPos - ungappedPos) - (lenRead - endClr)), Generous());
-		} else {
-			if (begClr != 0) 
-				appendValue(alignIt->gaps, TContigGapAnchor(lenRead, lenRead + (gappedPos - ungappedPos) - begClr), Generous());
-		}
-
-		// Set new begin and end position
-		if (alignIt->beginPos < alignIt->endPos) {
-			alignIt->beginPos = readBegEndRowPos[3*i];
-			alignIt->endPos = readBegEndRowPos[3*i+1];
-		} else {
-			alignIt->beginPos = readBegEndRowPos[3*i+1];
-			alignIt->endPos = readBegEndRowPos[3*i];
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Value<TStringSet>::Type TString;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef std::map<TSize, TSize> TComponentLength;
+    typedef char TValue;
+
+    // Initialization
+    TStringSet& strSet = stringSet(g);
+    TSize nseq = length(strSet);
+    TValue gapChar = gapValue<TValue>();
+    TValue specialGap = '.';
+    TSize maxCoverage = 0;
+    TSize len = 0;
+    String<TValue> mat;
+
+    // Store for each read the begin position, the end position and the row in the alignment matrix
+    String<TSize> readBegEndRowPos;
+    resize(readBegEndRowPos, 3*nseq);
+
+    // Strongly Connected Components, topological sort, and length of each component
+    String<TSize> component;
+    String<TSize> order;
+    TComponentLength compLength;
+    if (convertAlignment(g, component, order, compLength)) {
+        TSize numOfComponents = length(order);
+
+        // Assign to each sequence the start and end (in terms of component ranks)
+        typedef String<std::pair<TSize, TSize> > TComponentToRank;
+        TComponentToRank compToRank;
+        for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex)
+            appendValue(compToRank, std::make_pair(order[compIndex], compIndex), Generous());
+        std::sort(begin(compToRank, Standard()), end(compToRank, Standard()));
+
+        typedef Pair<TSize, TSize> TRankPair;
+        typedef String<TRankPair> TSequenceToRanks;
+        TSequenceToRanks seqToRank;
+        resize(seqToRank, nseq);
+        typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+        TVertexIterator itVertex(g);
+        for(;!atEnd(itVertex);++itVertex) {
+            TVertexDescriptor vert = value(itVertex);
+            TSize seq = idToPosition(strSet, sequenceId(g, vert));
+            if (fragmentBegin(g, vert) == 0)
+                seqToRank[seq].i1 = std::lower_bound(begin(compToRank, Standard()), end(compToRank, Standard()), std::make_pair((TSize) component[vert], (TSize) 0))->second;
+            if (fragmentBegin(g, vert) + fragmentLength(g, vert) == length(strSet[seq]))
+                seqToRank[seq].i2 = std::lower_bound(begin(compToRank, Standard()), end(compToRank, Standard()), std::make_pair((TSize) component[vert], (TSize) 0))->second;
+        }
+        clear(compToRank);
+
+        // Assign the sequences to rows
+        String<TSize> seqToRow;
+        resize(seqToRow, nseq);
+        maxCoverage = 0;
+        typedef String<bool> TLeftOver;
+        typedef typename Iterator<TLeftOver, Standard>::Type TLeftOverIter;
+        TLeftOver leftOver;
+        resize(leftOver, nseq, true);
+        typedef String<std::pair<TSize, TSize> > TSeqToBegin;
+        typedef typename Iterator<TSeqToBegin, Standard>::Type TSeqToBeginIter;
+        TSeqToBegin seqToBegin;
+        TSize finishedSeq = 0;
+        while(finishedSeq < nseq) {
+            TLeftOverIter itL = begin(leftOver, Standard());
+            TLeftOverIter itLEnd = end(leftOver, Standard());
+            for(TSize pos = 0; itL != itLEnd; ++itL, ++pos)
+                if (*itL) appendValue(seqToBegin, std::make_pair((seqToRank[pos]).i1, pos), Generous());
+            std::sort(begin(seqToBegin, Standard()), end(seqToBegin, Standard()));
+
+            TSize endPos = 0;
+            TSeqToBeginIter itSB = begin(seqToBegin, Standard());
+            TSeqToBeginIter itSBEnd = end(seqToBegin, Standard());
+            for(;itSB != itSBEnd;++itSB) {
+                if (endPos <= (*itSB).first) {
+                    TSize currentSeq = (*itSB).second;
+                    seqToRow[currentSeq] = maxCoverage;
+                    endPos = (seqToRank[currentSeq]).i2 + 2;
+                    leftOver[currentSeq] = false;
+                    ++finishedSeq;
+                }
+            }
+            clear(seqToBegin);
+            ++maxCoverage;
+        }
+        clear(leftOver);
+
+        // Create the matrix
+        len = 0;
+        String<TSize> compOffset;
+        resize(compOffset, numOfComponents);
+        for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex) {
+            compOffset[order[compIndex]] = len;
+            len+=compLength[order[compIndex]];
+        }
+        resize(mat, len * maxCoverage, gapChar);
+
+        // Fill in the segments
+        typedef typename Infix<TString>::Type TInfix;
+        typedef typename Iterator<TInfix, Standard>::Type TInfixIter;
+        typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
+        for(typename TPosToVertexMap::const_iterator it = g.data_pvMap.begin();it != g.data_pvMap.end(); ++it) {
+            TInfix str = label(g,it->second);
+            TSize c = property(component, it->second);
+            TSize row = seqToRow[idToPosition(strSet, it->first.first)];
+            //if (row == 0) {
+            //    std::cout << sequenceId(g, it->second) << ':' << str << ',' << strSet[sequenceId(g, it->second)] << std::endl;
+            //    std::cout << getProperty(component, it->second) << ',' << order[compIndex] << std::endl;
+            //    std::cout << (seqToRank[sequenceId(g, it->second)]).i1 << ',' << (seqToRank[sequenceId(g, it->second)]).i2 << std::endl;
+            //}
+            TInfixIter sIt = begin(str, Standard());
+            TInfixIter sItEnd = end(str, Standard());
+            TSize i = compOffset[c];
+            for(TSize pCol = i;sIt!=sItEnd;++sIt, ++pCol, ++i)
+                mat[row * len + pCol] = *sIt;
+        }
+        String<bool> active;
+        for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex) {
+            TSize offset = compOffset[order[compIndex]];
+            TSize currentCompLength = compLength[order[compIndex]];
+
+            clear(active);
+            resize(active, maxCoverage, false);
+
+            // Find the empty rows
+            for(TSize i=0;i<nseq; ++i) {
+                if (((seqToRank[i]).i1 <= compIndex) && ((seqToRank[i]).i2 >= compIndex))
+                    active[(seqToRow[i])] = true;
+            }
+
+            // Substitute false gaps with special gap character
+            for(TSize i = 0; i < maxCoverage; ++i) {
+                if (!(active[i])) {
+                    for(TSize pCol = offset;pCol < offset + currentCompLength;++pCol)
+                        mat[i * len + pCol] = specialGap;
+                }
+            }
+        }
+
+        // Get the new begin and end positions
+        for(TSize i=0;i<nseq; ++i) {
+            TVertexDescriptor lastVertex = findVertex(const_cast<TGraph&>(g), positionToId(strSet, i), length(strSet[i]) - 1);
+            TSize readBegin = compOffset[getProperty(component, findVertex(const_cast<TGraph&>(g), positionToId(strSet, i), 0))];
+            TSize readEnd = compOffset[getProperty(component, lastVertex)] + fragmentLength(const_cast<TGraph&>(g), lastVertex);
+            readBegEndRowPos[3*i] = readBegin;
+            readBegEndRowPos[3*i+1] = readEnd;
+            readBegEndRowPos[3*i+2] = seqToRow[i];
+        }
+
+    }
+    clear(component);
+    clear(order);
+    compLength.clear();
+
+
+    //// Debug code
+    //for(TSize row = 0; row<maxCoverage; ++row) {
+    //    for(TSize col = 0; col<len; ++col) {
+    //        std::cout << mat[row * len + col];
+    //    }
+    //    std::cout << std::endl;
+    //}
+
+    // Create the new consensus
+    typedef typename Value<TString>::Type TAlphabet;
+    String<TValue> gappedCons;
+    consensusCalling(mat, gappedCons, maxCoverage, TAlphabet(), MajorityVote());
+
+    // Assign new consensus
+    assignGappedConsensus(fragStore, gappedCons, contigId);
+
+    // Update all aligned reads
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename TFragmentStore::TReadPos TReadPos;
+    typedef typename TFragmentStore::TContigPos TContigPos;
+    typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
+    //typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
+    typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
+    sortAlignedReads(fragStore.alignedReadStore, SortContigId());
+    TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    TReadPos ungappedPos = 0;
+    TReadPos gappedPos = 0;
+    bool gapOpen;
+    for(TSize i = 0;alignIt != alignItEnd; ++alignIt, ++i) {
+        TSize lenRead = length(fragStore.readSeqStore[alignIt->readId]);
+        TReadPos begClr = 0;
+        TReadPos endClr = 0;
+        getClrRange(fragStore, *alignIt, begClr, endClr);
+        clear(alignIt->gaps);
+        ungappedPos = begClr;
+        if (alignIt->beginPos > alignIt->endPos) ungappedPos = lenRead - endClr;
+        if (ungappedPos != 0) appendValue(alignIt->gaps, TContigGapAnchor(ungappedPos, 0));
+        gappedPos = 0;
+        gapOpen = false;
+        for(TSize column = readBegEndRowPos[3*i]; column<readBegEndRowPos[3*i + 1]; ++column, ++gappedPos) {
+            if (mat[readBegEndRowPos[3*i + 2] * len + column] == gapChar) gapOpen = true;
+            else {
+                if (gapOpen) {
+                    appendValue(alignIt->gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
+                    gapOpen = false;
+                }
+                ++ungappedPos;
+            }
+        }
+        if (gapOpen) appendValue(alignIt->gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
+        if (alignIt->beginPos < alignIt->endPos) {
+            if (endClr != (TContigPos)lenRead)
+                appendValue(alignIt->gaps, TContigGapAnchor(lenRead, lenRead + (gappedPos - ungappedPos) - (lenRead - endClr)), Generous());
+        } else {
+            if (begClr != 0)
+                appendValue(alignIt->gaps, TContigGapAnchor(lenRead, lenRead + (gappedPos - ungappedPos) - begClr), Generous());
+        }
+
+        // Set new begin and end position
+        if (alignIt->beginPos < alignIt->endPos) {
+            alignIt->beginPos = readBegEndRowPos[3*i];
+            alignIt->endPos = readBegEndRowPos[3*i+1];
+        } else {
+            alignIt->beginPos = readBegEndRowPos[3*i+1];
+            alignIt->endPos = readBegEndRowPos[3*i];
+        }
+    }
 }
 
 
@@ -835,37 +772,37 @@ _countLetters(String<TValue, TSpec> const & mat,
               TSize alignDepth,
               TAlphabet)
 {
-	typedef String<TValue, TSpec> const TMatrix;
-	typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
-
-	// Initialization
-	TSize len = length(mat) / alignDepth;
-	TValue gapChar = gapValue<TValue>();
-	TValue specialGap = '.';
-	TSize alphabetSize = ValueSize<TAlphabet>::VALUE;
-
-	// Set-up counter values
-	typedef typename Value<TCounters>::Type TCounter;
-	typedef typename Iterator<TCounters, Standard>::Type TCounterIt;
-	resize(counterValues, len);
-	for(TSize i=0;i<len; ++i) {
-		TCounter counter;
-		resize(counter, alphabetSize + 1, 0);
-		counterValues[i] = counter;
-	}
-
-	// Count all 
-	TMatIter matIt = begin(mat, Standard());
-	TMatIter matItEnd = end(mat, Standard());
-	TCounterIt countIt = begin(counterValues, Standard());
-	TSize pos = 0;
-	for(; matIt != matItEnd; ++matIt, ++countIt, ++pos) {
-		if (pos % len == 0) countIt = begin(counterValues, Standard());
-		if (*matIt != specialGap) {
-			if (*matIt == gapChar) ++value(*countIt, alphabetSize);
-			else ++value(*countIt, ordValue((TAlphabet) *matIt));
-		}
-	}
+    typedef String<TValue, TSpec> const TMatrix;
+    typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
+
+    // Initialization
+    TSize len = length(mat) / alignDepth;
+    TValue gapChar = gapValue<TValue>();
+    TValue specialGap = '.';
+    TSize alphabetSize = ValueSize<TAlphabet>::VALUE;
+
+    // Set-up counter values
+    typedef typename Value<TCounters>::Type TCounter;
+    typedef typename Iterator<TCounters, Standard>::Type TCounterIt;
+    resize(counterValues, len);
+    for(TSize i=0;i<len; ++i) {
+        TCounter counter;
+        resize(counter, alphabetSize + 1, 0);
+        counterValues[i] = counter;
+    }
+
+    // Count all
+    TMatIter matIt = begin(mat, Standard());
+    TMatIter matItEnd = end(mat, Standard());
+    TCounterIt countIt = begin(counterValues, Standard());
+    TSize pos = 0;
+    for(; matIt != matItEnd; ++matIt, ++countIt, ++pos) {
+        if (pos % len == 0) countIt = begin(counterValues, Standard());
+        if (*matIt != specialGap) {
+            if (*matIt == gapChar) ++value(*countIt, alphabetSize);
+            else ++value(*countIt, ordValue((TAlphabet) *matIt));
+        }
+    }
 }
 
 
@@ -874,201 +811,201 @@ _countLetters(String<TValue, TSpec> const & mat,
 template <typename TValue, typename TSpec, typename TGappedCons, typename TAlignDepth, typename TAlphabet>
 inline void
 consensusCalling(String<TValue, TSpec> const& mat,
-				 TGappedCons& gappedConsensus,
-				 TAlignDepth maxCoverage,
-				 TAlphabet,
-				 Bayesian)
+                 TGappedCons& gappedConsensus,
+                 TAlignDepth maxCoverage,
+                 TAlphabet,
+                 Bayesian)
 {
-	typedef double TProbability;
-	typedef String<TProbability> TProbabilityDistribution;
-	typedef String<TProbabilityDistribution> TPositionalPrDist;
-	typedef typename Iterator<TPositionalPrDist, Standard>::Type TPosPrDistIter;
-
-	typedef typename Size<String<TValue, TSpec> >::Type TSize;
-	TSize alphabetSize = ValueSize<TAlphabet>::VALUE;
-	TValue gapChar = gapValue<TValue>();
-	TValue specialGap = '.';
-
-	// Set-up the counters
-	typedef String<TSize> TCounter;
-	typedef String<TCounter> TCounters;
-	TCounters counterValues;
-	_countLetters(mat, counterValues, maxCoverage, TAlphabet() );
-
-
-	// Initialization
-	TSize len = length(mat) / maxCoverage;
-	TProbabilityDistribution backroundDist;
-	resize(backroundDist, alphabetSize + 1, ((TProbability) 1 / (TProbability) (alphabetSize + 1)));
-	
-	// Get an initial consensus
-	typedef typename Iterator<TCounters, Standard>::Type TCounterIt;
-	TCounterIt countIt = begin(counterValues, Standard());
-	TCounterIt countItEnd = end(counterValues, Standard());
-	TPositionalPrDist posPrDist;
-	TValue c = TAlphabet();
-	for(;countIt != countItEnd; ++countIt) {
-		TSize max = 0;
-		typedef typename Iterator<TCounter, Standard>::Type TCIt;
-		TCIt cIt = begin(*countIt, Standard());
-		TCIt cItEnd = end(*countIt, Standard());
-		TSize pos = 0;
-		for(;cIt != cItEnd; ++cIt, ++pos) {
-			if (*cIt > max) {
-				max = *cIt;
-				c = (pos == alphabetSize) ? gapChar : (TValue) TAlphabet(pos);
-			}
-		}
-		TProbabilityDistribution prDist;
-		resize(prDist, alphabetSize + 1, 0);
-		if (c == gapChar) prDist[alphabetSize] = 1;
-		else prDist[ordValue((TAlphabet) c)] = 1;
-		appendValue(posPrDist, prDist, Generous());
-	}
-
-	TSize run = 1;
-	TProbabilityDistribution pI;
-	TProbabilityDistribution pIJ;
-	TProbabilityDistribution pIOld;
-	TProbabilityDistribution pIJOld;
-	while (run) {
-		// Store the values from the last iteration
-		pIOld = pI;
-		pIJOld = pIJ;
-
-		// Count all letters in the consensus
-		TProbabilityDistribution nI;
-		resize(nI, alphabetSize + 1, 0);
-		TPosPrDistIter itPosPrDist = begin(posPrDist, Standard());
-		TPosPrDistIter itPosPrDistEnd = end(posPrDist, Standard());
-		for(;itPosPrDist!=itPosPrDistEnd; ++itPosPrDist) 
-			for(TSize i = 0; i<(alphabetSize + 1); ++i) 
-				nI[i] += (*itPosPrDist)[i];
-	
-		// Composition probabilities
-		clear(pI);
-		resize(pI, alphabetSize + 1);
-		TProbability lenPosPrDist = (TProbability) length(posPrDist);
-		for(TSize i = 0; i<length(pI); ++i) 
-			pI[i] = nI[i] / lenPosPrDist;
-		
-
-		// Count all letters that agree / disagree with the consensus
-		TProbabilityDistribution nIJ;
-		resize(nIJ, (alphabetSize + 1) * (alphabetSize + 1), 0);
-		typedef String<TValue, TSpec> TMatrix;
-		typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
-		TMatIter matIt = begin(mat, Standard());
-		TMatIter matItEnd = end(mat, Standard());
-		itPosPrDist = begin(posPrDist, Standard());
-		TSize pos = 0;
-		for(; matIt != matItEnd; ++matIt, ++itPosPrDist, ++pos) {
-			if (pos % len == 0) itPosPrDist = begin(posPrDist, Standard());
-			TValue c = *matIt;
-			if (c != specialGap) {
-				TSize fragJ = (c != gapChar) ? ordValue(TAlphabet(c)) : alphabetSize;
-				for(TSize consI = 0; consI<(alphabetSize + 1); ++consI) 
-					nIJ[consI * (alphabetSize + 1) + fragJ] += (*itPosPrDist)[consI];	
-			}
-		}
-
-		// Sequencing error probabilities
-		clear(pIJ);
-		resize(pIJ, (alphabetSize + 1) * (alphabetSize + 1));
-		TProbability sumIJ = 0;
-		for(TSize diag = 0; diag<(alphabetSize + 1); ++diag) sumIJ += nIJ[diag * (alphabetSize + 1) + diag];
-		for(TSize consI = 0; consI<(alphabetSize + 1); ++consI) 
-			for(TSize fragJ = 0; fragJ<(alphabetSize + 1); ++fragJ)
-				pIJ[consI * (alphabetSize + 1) + fragJ] = nIJ[consI * (alphabetSize + 1) + fragJ] / sumIJ;
-	
-		// Recompute positional probability distribution
-		itPosPrDist = begin(posPrDist, Standard());
-		TSize col = 0;
-		for(;itPosPrDist!=itPosPrDistEnd; ++itPosPrDist, ++col) {
-			TProbabilityDistribution prDist;
-			resize(prDist, alphabetSize + 1);
-			for(TSize consI = 0; consI<(alphabetSize + 1); ++consI) {
-				TProbability numerator = pI[consI];
-				TProbability denominator = 0;
-				for(TSize allI = 0; allI<(alphabetSize + 1); ++allI) {
-					TProbability denominatorSub = value(pI, allI);
-					for(TSize row = 0; row < maxCoverage; ++row) {
-						TValue c = mat[row * len + col];
-						if (c != specialGap) {
-							TSize fragJ = (c != gapChar) ? ordValue(TAlphabet(c)) : alphabetSize;
-							if (allI == consI) 
-								numerator *= pIJ[allI * (alphabetSize + 1) + fragJ]; 
-							denominatorSub *= pIJ[allI * (alphabetSize + 1) + fragJ]; 
-						}
-					}
-					denominator += denominatorSub;
-				}
-				prDist[consI] = numerator / denominator;
-			}
-			*itPosPrDist = prDist;
-		}	
-
-		// Check termination criterion
-		TProbability eps = 0.00001;
-		typedef typename Iterator<TProbabilityDistribution, Standard>::Type TProbIter;
-		TProbIter pIter = begin(pIOld, Standard());
-		TProbIter pIterCompare = begin(pI, Standard());
-		TProbIter pIterEnd = end(pIOld, Standard());
-		TSize runOld = run;
-		for(;pIter != pIterEnd; ++pIter, ++pIterCompare) {
-			if (*pIter > *pIterCompare) {
-				if (*pIter - *pIterCompare > eps) {
-					++run;
-					break;
-				}
-			} else {
-				if (*pIterCompare - *pIter > eps) {
-					++run;
-					break;
-				}
-			}
-		}
-		if (runOld == run) {
-			pIter = begin(pIJOld, Standard());
-			pIterCompare = begin(pIJ, Standard());
-			pIterEnd = end(pIJOld, Standard());
-			for(;pIter != pIterEnd; ++pIter, ++pIterCompare) {
-				if (*pIter > *pIterCompare) {
-					if (*pIter - *pIterCompare > eps) {
-						++run;
-						break;
-					}
-				} else {
-					if (*pIterCompare - *pIter > eps) {
-						++run;
-						break;
-					}
-				}
-			}
-		}
-
-		if (runOld == run) {
-			std::cout << "Iterations: " << run << std::endl;
-			run = 0;
-		}
-	}
-	
-	// Compute the most likely consensus
-	TPosPrDistIter itPosPrDist = begin(posPrDist, Standard());
-	TPosPrDistIter itPosPrDistEnd = end(posPrDist, Standard());
-	clear(gappedConsensus);
-	for(;itPosPrDist!=itPosPrDistEnd; ++itPosPrDist) {
-		TProbability max = 0;
-		TSize ind = 0;
-		for(TSize consI = 0; consI<(alphabetSize + 1); ++consI) {
-			if ((*itPosPrDist)[consI] > max) {
-				max = (*itPosPrDist)[consI];
-				ind = consI;
-			}
-		}
-		if (ind == alphabetSize) appendValue(gappedConsensus, gapChar);
-		else appendValue(gappedConsensus, TAlphabet(ind));
-	}
+    typedef double TProbability;
+    typedef String<TProbability> TProbabilityDistribution;
+    typedef String<TProbabilityDistribution> TPositionalPrDist;
+    typedef typename Iterator<TPositionalPrDist, Standard>::Type TPosPrDistIter;
+
+    typedef typename Size<String<TValue, TSpec> >::Type TSize;
+    TSize alphabetSize = ValueSize<TAlphabet>::VALUE;
+    TValue gapChar = gapValue<TValue>();
+    TValue specialGap = '.';
+
+    // Set-up the counters
+    typedef String<TSize> TCounter;
+    typedef String<TCounter> TCounters;
+    TCounters counterValues;
+    _countLetters(mat, counterValues, maxCoverage, TAlphabet() );
+
+
+    // Initialization
+    TSize len = length(mat) / maxCoverage;
+    TProbabilityDistribution backroundDist;
+    resize(backroundDist, alphabetSize + 1, ((TProbability) 1 / (TProbability) (alphabetSize + 1)));
+
+    // Get an initial consensus
+    typedef typename Iterator<TCounters, Standard>::Type TCounterIt;
+    TCounterIt countIt = begin(counterValues, Standard());
+    TCounterIt countItEnd = end(counterValues, Standard());
+    TPositionalPrDist posPrDist;
+    TValue c = TAlphabet();
+    for(;countIt != countItEnd; ++countIt) {
+        TSize max = 0;
+        typedef typename Iterator<TCounter, Standard>::Type TCIt;
+        TCIt cIt = begin(*countIt, Standard());
+        TCIt cItEnd = end(*countIt, Standard());
+        TSize pos = 0;
+        for(;cIt != cItEnd; ++cIt, ++pos) {
+            if (*cIt > max) {
+                max = *cIt;
+                c = (pos == alphabetSize) ? gapChar : (TValue) TAlphabet(pos);
+            }
+        }
+        TProbabilityDistribution prDist;
+        resize(prDist, alphabetSize + 1, 0);
+        if (c == gapChar) prDist[alphabetSize] = 1;
+        else prDist[ordValue((TAlphabet) c)] = 1;
+        appendValue(posPrDist, prDist, Generous());
+    }
+
+    TSize run = 1;
+    TProbabilityDistribution pI;
+    TProbabilityDistribution pIJ;
+    TProbabilityDistribution pIOld;
+    TProbabilityDistribution pIJOld;
+    while (run) {
+        // Store the values from the last iteration
+        pIOld = pI;
+        pIJOld = pIJ;
+
+        // Count all letters in the consensus
+        TProbabilityDistribution nI;
+        resize(nI, alphabetSize + 1, 0);
+        TPosPrDistIter itPosPrDist = begin(posPrDist, Standard());
+        TPosPrDistIter itPosPrDistEnd = end(posPrDist, Standard());
+        for(;itPosPrDist!=itPosPrDistEnd; ++itPosPrDist)
+            for(TSize i = 0; i<(alphabetSize + 1); ++i)
+                nI[i] += (*itPosPrDist)[i];
+
+        // Composition probabilities
+        clear(pI);
+        resize(pI, alphabetSize + 1);
+        TProbability lenPosPrDist = (TProbability) length(posPrDist);
+        for(TSize i = 0; i<length(pI); ++i)
+            pI[i] = nI[i] / lenPosPrDist;
+
+
+        // Count all letters that agree / disagree with the consensus
+        TProbabilityDistribution nIJ;
+        resize(nIJ, (alphabetSize + 1) * (alphabetSize + 1), 0);
+        typedef String<TValue, TSpec> TMatrix;
+        typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
+        TMatIter matIt = begin(mat, Standard());
+        TMatIter matItEnd = end(mat, Standard());
+        itPosPrDist = begin(posPrDist, Standard());
+        TSize pos = 0;
+        for(; matIt != matItEnd; ++matIt, ++itPosPrDist, ++pos) {
+            if (pos % len == 0) itPosPrDist = begin(posPrDist, Standard());
+            TValue c = *matIt;
+            if (c != specialGap) {
+                TSize fragJ = (c != gapChar) ? ordValue(TAlphabet(c)) : alphabetSize;
+                for(TSize consI = 0; consI<(alphabetSize + 1); ++consI)
+                    nIJ[consI * (alphabetSize + 1) + fragJ] += (*itPosPrDist)[consI];
+            }
+        }
+
+        // Sequencing error probabilities
+        clear(pIJ);
+        resize(pIJ, (alphabetSize + 1) * (alphabetSize + 1));
+        TProbability sumIJ = 0;
+        for(TSize diag = 0; diag<(alphabetSize + 1); ++diag) sumIJ += nIJ[diag * (alphabetSize + 1) + diag];
+        for(TSize consI = 0; consI<(alphabetSize + 1); ++consI)
+            for(TSize fragJ = 0; fragJ<(alphabetSize + 1); ++fragJ)
+                pIJ[consI * (alphabetSize + 1) + fragJ] = nIJ[consI * (alphabetSize + 1) + fragJ] / sumIJ;
+
+        // Recompute positional probability distribution
+        itPosPrDist = begin(posPrDist, Standard());
+        TSize col = 0;
+        for(;itPosPrDist!=itPosPrDistEnd; ++itPosPrDist, ++col) {
+            TProbabilityDistribution prDist;
+            resize(prDist, alphabetSize + 1);
+            for(TSize consI = 0; consI<(alphabetSize + 1); ++consI) {
+                TProbability numerator = pI[consI];
+                TProbability denominator = 0;
+                for(TSize allI = 0; allI<(alphabetSize + 1); ++allI) {
+                    TProbability denominatorSub = value(pI, allI);
+                    for(TSize row = 0; row < maxCoverage; ++row) {
+                        TValue c = mat[row * len + col];
+                        if (c != specialGap) {
+                            TSize fragJ = (c != gapChar) ? ordValue(TAlphabet(c)) : alphabetSize;
+                            if (allI == consI)
+                                numerator *= pIJ[allI * (alphabetSize + 1) + fragJ];
+                            denominatorSub *= pIJ[allI * (alphabetSize + 1) + fragJ];
+                        }
+                    }
+                    denominator += denominatorSub;
+                }
+                prDist[consI] = numerator / denominator;
+            }
+            *itPosPrDist = prDist;
+        }
+
+        // Check termination criterion
+        TProbability eps = 0.00001;
+        typedef typename Iterator<TProbabilityDistribution, Standard>::Type TProbIter;
+        TProbIter pIter = begin(pIOld, Standard());
+        TProbIter pIterCompare = begin(pI, Standard());
+        TProbIter pIterEnd = end(pIOld, Standard());
+        TSize runOld = run;
+        for(;pIter != pIterEnd; ++pIter, ++pIterCompare) {
+            if (*pIter > *pIterCompare) {
+                if (*pIter - *pIterCompare > eps) {
+                    ++run;
+                    break;
+                }
+            } else {
+                if (*pIterCompare - *pIter > eps) {
+                    ++run;
+                    break;
+                }
+            }
+        }
+        if (runOld == run) {
+            pIter = begin(pIJOld, Standard());
+            pIterCompare = begin(pIJ, Standard());
+            pIterEnd = end(pIJOld, Standard());
+            for(;pIter != pIterEnd; ++pIter, ++pIterCompare) {
+                if (*pIter > *pIterCompare) {
+                    if (*pIter - *pIterCompare > eps) {
+                        ++run;
+                        break;
+                    }
+                } else {
+                    if (*pIterCompare - *pIter > eps) {
+                        ++run;
+                        break;
+                    }
+                }
+            }
+        }
+
+        if (runOld == run) {
+            std::cout << "Iterations: " << run << std::endl;
+            run = 0;
+        }
+    }
+
+    // Compute the most likely consensus
+    TPosPrDistIter itPosPrDist = begin(posPrDist, Standard());
+    TPosPrDistIter itPosPrDistEnd = end(posPrDist, Standard());
+    clear(gappedConsensus);
+    for(;itPosPrDist!=itPosPrDistEnd; ++itPosPrDist) {
+        TProbability max = 0;
+        TSize ind = 0;
+        for(TSize consI = 0; consI<(alphabetSize + 1); ++consI) {
+            if ((*itPosPrDist)[consI] > max) {
+                max = (*itPosPrDist)[consI];
+                ind = consI;
+            }
+        }
+        if (ind == alphabetSize) appendValue(gappedConsensus, gapChar);
+        else appendValue(gappedConsensus, TAlphabet(ind));
+    }
 
 }
 
@@ -1078,29 +1015,29 @@ consensusCalling(String<TValue, TSpec> const& mat,
 template <typename TFragSpec, typename TConfig, typename TContigId>
 inline void
 consensusCalling(FragmentStore<TFragSpec, TConfig>& fragStore,
-				 TContigId contigId,
-				 Bayesian)
+                 TContigId contigId,
+                 Bayesian)
 {
-	SEQAN_CHECKPOINT
-
-	typedef FragmentStore<TFragSpec, TConfig> TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename TFragmentStore::TReadSeq TReadSeq;
-	typedef typename Value<TReadSeq>::Type TAlphabet;
-	typedef char TValue;
-
-	// Convert the contig to an alignment matrix
-	typedef String<TValue> TAlignMat;
-	TAlignMat mat;
-	TSize maxCoverage;
-	convertAlignment(fragStore, mat, contigId, maxCoverage);
-
-	// Call the consensus
-	String<TValue> gappedConsensus;
-	consensusCalling(mat, gappedConsensus, maxCoverage, TAlphabet(), Bayesian());
-
-	// Assign the new consensus
-	assignGappedConsensus(fragStore, gappedConsensus, contigId);
+    SEQAN_CHECKPOINT
+
+    typedef FragmentStore<TFragSpec, TConfig> TFragmentStore;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename TFragmentStore::TReadSeq TReadSeq;
+    typedef typename Value<TReadSeq>::Type TAlphabet;
+    typedef char TValue;
+
+    // Convert the contig to an alignment matrix
+    typedef String<TValue> TAlignMat;
+    TAlignMat mat;
+    TSize maxCoverage;
+    convertAlignment(fragStore, mat, contigId, maxCoverage);
+
+    // Call the consensus
+    String<TValue> gappedConsensus;
+    consensusCalling(mat, gappedConsensus, maxCoverage, TAlphabet(), Bayesian());
+
+    // Assign the new consensus
+    assignGappedConsensus(fragStore, gappedConsensus, contigId);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1108,43 +1045,43 @@ consensusCalling(FragmentStore<TFragSpec, TConfig>& fragStore,
 template <typename TValue, typename TSpec, typename TGappedCons, typename TAlignDepth, typename TAlphabet>
 inline void
 consensusCalling(String<TValue, TSpec> const& mat,
-				 TGappedCons& gappedConsensus,
-				 TAlignDepth maxCoverage,
-				 TAlphabet,
-				 MajorityVote)
+                 TGappedCons& gappedConsensus,
+                 TAlignDepth maxCoverage,
+                 TAlphabet,
+                 MajorityVote)
 {
-	typedef typename Size<String<TValue, TSpec> >::Type TSize;
-	TSize alphabetSize = ValueSize<TAlphabet>::VALUE;
-	TValue gapChar = gapValue<TValue>();
-	
-	// Set-up the counters
-	typedef String<TSize> TCounter;
-	typedef String<TCounter> TCounters;
-	TCounters counterValues;
-	_countLetters(mat, counterValues, maxCoverage, TAlphabet() );
-	
-	// Get the consensus
-	typedef typename Iterator<TCounters, Standard>::Type TCounterIt;
-	TCounterIt countIt = begin(counterValues, Standard());
-	TCounterIt countItEnd = end(counterValues, Standard());
-	clear(gappedConsensus);
-	TSize max = 0;
-	TValue c = TValue();
-	TSize pos = 0;
-	for(;countIt != countItEnd; ++countIt) {
-		max = 0;	
-		typedef typename Iterator<TCounter, Standard>::Type TCIt;
-		TCIt cIt = begin(*countIt, Standard());
-		TCIt cItEnd = end(*countIt, Standard());
-		pos = 0;
-		for(;cIt != cItEnd; ++cIt, ++pos) {
-			if (*cIt > max) {
-				max = *cIt;
-				c = (pos == alphabetSize) ? gapChar : (TValue) TAlphabet(pos);
-			}
-		}
-		appendValue(gappedConsensus, c);
-	}
+    typedef typename Size<String<TValue, TSpec> >::Type TSize;
+    TSize alphabetSize = ValueSize<TAlphabet>::VALUE;
+    TValue gapChar = gapValue<TValue>();
+
+    // Set-up the counters
+    typedef String<TSize> TCounter;
+    typedef String<TCounter> TCounters;
+    TCounters counterValues;
+    _countLetters(mat, counterValues, maxCoverage, TAlphabet() );
+
+    // Get the consensus
+    typedef typename Iterator<TCounters, Standard>::Type TCounterIt;
+    TCounterIt countIt = begin(counterValues, Standard());
+    TCounterIt countItEnd = end(counterValues, Standard());
+    clear(gappedConsensus);
+    TSize max = 0;
+    TValue c = TValue();
+    TSize pos = 0;
+    for(;countIt != countItEnd; ++countIt) {
+        max = 0;
+        typedef typename Iterator<TCounter, Standard>::Type TCIt;
+        TCIt cIt = begin(*countIt, Standard());
+        TCIt cItEnd = end(*countIt, Standard());
+        pos = 0;
+        for(;cIt != cItEnd; ++cIt, ++pos) {
+            if (*cIt > max) {
+                max = *cIt;
+                c = (pos == alphabetSize) ? gapChar : (TValue) TAlphabet(pos);
+            }
+        }
+        appendValue(gappedConsensus, c);
+    }
 }
 
 
@@ -1154,27 +1091,27 @@ consensusCalling(String<TValue, TSpec> const& mat,
 template <typename TFragSpec, typename TConfig, typename TContigId>
 inline void
 consensusCalling(FragmentStore<TFragSpec, TConfig>& fragStore,
-				 TContigId contigId,
-				 MajorityVote)
+                 TContigId contigId,
+                 MajorityVote)
 {
-	typedef FragmentStore<TFragSpec, TConfig> TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename TFragmentStore::TReadSeq TReadSeq;
-	typedef typename Value<TReadSeq>::Type TAlphabet;
-	typedef char TValue;
-
-	// Convert the contig to an alignment matrix
-	typedef String<TValue> TAlignMat;
-	TAlignMat mat;
-	TSize maxCoverage;
-	convertAlignment(fragStore, mat, contigId, maxCoverage);
-
-	// Call the consensus
-	String<TValue> gappedConsensus;
-	consensusCalling(mat, gappedConsensus, maxCoverage, TAlphabet(), MajorityVote());
-
-	// Assign the new consensus
-	assignGappedConsensus(fragStore, gappedConsensus, contigId);
+    typedef FragmentStore<TFragSpec, TConfig> TFragmentStore;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename TFragmentStore::TReadSeq TReadSeq;
+    typedef typename Value<TReadSeq>::Type TAlphabet;
+    typedef char TValue;
+
+    // Convert the contig to an alignment matrix
+    typedef String<TValue> TAlignMat;
+    TAlignMat mat;
+    TSize maxCoverage;
+    convertAlignment(fragStore, mat, contigId, maxCoverage);
+
+    // Call the consensus
+    String<TValue> gappedConsensus;
+    consensusCalling(mat, gappedConsensus, maxCoverage, TAlphabet(), MajorityVote());
+
+    // Assign the new consensus
+    assignGappedConsensus(fragStore, gappedConsensus, contigId);
 }
 
 
@@ -1187,197 +1124,190 @@ consensusCalling(FragmentStore<TFragSpec, TConfig>& fragStore,
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Alignment Graph Format.value.FastaReadFormat:
-	Fasta read format to write a multi-read alignment.
-..include:seqan/consensus.h
-*/
-
 struct FastaReadFormat_;
 typedef Tag<FastaReadFormat_> const FastaReadFormat;
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TSpec, typename TConfig>
-inline int
-write(TFile & file,
-	  FragmentStore<TSpec, TConfig>& fragStore,
-	  FastaReadFormat) 
+inline void
+write(
+    TFile & file,
+    FragmentStore<TSpec, TConfig>& fragStore,
+    FastaReadFormat)
 {
 //IOREV _nodoc_ what has this got to do with consensus? why is it here?
-	// Basic types
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename TFragmentStore::TContigPos TContigPos;
-	//typedef typename Value<TFile>::Type TValue;
-	typedef char TMultiReadChar;
-	TMultiReadChar gapChar = gapValue<TMultiReadChar>();
-
-	typedef typename Iterator<typename TFragmentStore::TContigStore, Standard>::Type TContigIter;
-	TContigIter contigIt = begin(fragStore.contigStore, Standard() );
-	TContigIter contigItEnd = end(fragStore.contigStore, Standard() );
-	for(TSize idCount = 0;contigIt != contigItEnd; ++contigIt, ++idCount) {
-		// Alignment matrix
-		typedef String<TMultiReadChar> TAlignMat;
-		TAlignMat mat;
-		TSize maxCoverage;
-		String<TSize> readSlot;
-		convertAlignment(fragStore, mat, idCount, maxCoverage, readSlot);
-		TSize len = length(mat) / maxCoverage;
-		
-		// Gapped consensus sequence
-		typedef String<TMultiReadChar> TGappedConsensus;
-		TGappedConsensus gappedConsensus;
-		getGappedConsensus(fragStore, gappedConsensus, idCount);
-
-		// Print the alignment matrix
-		String<TSize> coverage;
-		resize(coverage, len, 0);
-		typedef typename Iterator<TGappedConsensus, Standard>::Type TConsIter;
-		TConsIter itCons = begin(gappedConsensus, Standard());
-		TSize winSize = 60;
-		int offset = 2;
-		TSize column = 0;
-		while (column<len) {
-			TSize window_end = column + winSize;
-			if (window_end >= len) window_end = len;
-			// Position
-			for(int i = 0; i<offset - 2; ++i) streamWriteChar(file, ' ');
-			streamWriteBlock(file, "Pos: ", 5);
-			streamPut(file, column);
-			streamWriteChar(file, '\n');
-			// Ruler
-			for(int i = 0; i<offset + 3; ++i) streamWriteChar(file, ' ');
-			for(TSize local_col = 1; local_col<window_end - column + 1; ++local_col) {
-				if ((local_col % 10)==0)
-                    streamWriteChar(file, ':');
-				else if ((local_col % 5)==0)
-                    streamWriteChar(file, '.');
-				else
-                    streamWriteChar(file, ' ');
-			}
-			streamWriteChar(file, '\n');
-			// Matrix
-			for(TSize row = 0; row<maxCoverage; ++row) {
-				TSize tmp = row;
-				int off = 0;
-				while (tmp / 10 != 0) {
-					tmp /= 10;
-					++off;
-				}
-				for(int i = 0; i<offset - off; ++i) streamWriteChar(file, ' ');
-				streamPut(file, row);
-				streamWriteChar(file, ':');
-				streamWriteChar(file, ' ');
-				for(TSize local_col = column; local_col<window_end; ++local_col) {
-					streamWriteChar(file, mat[row * len + local_col]);
-					if (mat[row * len + local_col] != '.') ++coverage[local_col];
-				}
-				streamWriteChar(file, '\n');
-			}
-			streamWriteChar(file, '\n');
-	
-			// Consensus
-			for(int i = 0; i<offset; ++i)
-                streamWriteChar(file, ' ');
-			streamWriteBlock(file, "C: ", 3);
-			for(unsigned int local_col = column; local_col<window_end; ++local_col, ++itCons) 
-				streamWriteChar(file, *itCons);
-			streamWriteChar(file, '\n');
-			for(int i = 0; i<offset-1; ++i)
-                streamWriteChar(file, ' ');
-			streamWriteBlock(file, ">2: ", 4);
-			for(unsigned int local_col = column; local_col<window_end; ++local_col) {
-				if (coverage[local_col] > 2)
-                    streamWriteChar(file, gappedConsensus[local_col]);
-				else
-                    streamWriteChar(file, gapChar);
-			}
-			streamWriteChar(file, '\n');
-			streamWriteChar(file, '\n');
-			column+=winSize;
-		}
-		streamWriteChar(file, '\n');
-		streamWriteChar(file, '\n');
-
-		// Print all aligned reads belonging to this contig
-
-		// Sort according to contigId
-		sortAlignedReads(fragStore.alignedReadStore, SortContigId());
-	
-		// Find range of the given contig
-		typedef typename Iterator<typename TFragmentStore::TAlignedReadStore, Standard>::Type TAlignIter;
-		TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
-		TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
-
-		// Sort the reads according to the begin position
-		sortAlignedReads(infix(fragStore.alignedReadStore, alignIt - begin(fragStore.alignedReadStore, Standard()), alignItEnd - begin(fragStore.alignedReadStore, Standard())), SortBeginPos());
-		TAlignIter alignItTmp = lowerBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
-		TAlignIter alignItTmpEnd = upperBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
-		String<std::pair<TSize, TSize> > idToPos;
-		reserve(idToPos, alignItTmpEnd - alignItTmp);
-		for(TSize iCount = 0; alignItTmp!=alignItTmpEnd; ++iCount, ++alignItTmp) 
-			appendValue(idToPos, std::make_pair(alignItTmp->id, readSlot[iCount]));
-		::std::sort(begin(idToPos, Standard()), end(idToPos, Standard()));
-
-		// Sort the reads according to the id
-		sortAlignedReads(infix(fragStore.alignedReadStore, alignIt - begin(fragStore.alignedReadStore, Standard()), alignItEnd - begin(fragStore.alignedReadStore, Standard())), SortId());
-		alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
-		alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
-
-		bool noNamesPresent = (length(fragStore.readNameStore) == 0);
-		for(TSize iCount = 0;alignIt != alignItEnd; ++alignIt, ++iCount) {
-
-			// Print all reads
-			streamWriteBlock(file, "typ:", 4);
-			if (!noNamesPresent)
+    // Basic types
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename TFragmentStore::TContigPos TContigPos;
+    //typedef typename Value<TFile>::Type TValue;
+    typedef char TMultiReadChar;
+    TMultiReadChar gapChar = gapValue<TMultiReadChar>();
+
+    typename DirectionIterator<TFile, Output>::Type target = directionIterator(file, Output());
+
+    typedef typename Iterator<typename TFragmentStore::TContigStore, Standard>::Type TContigIter;
+    TContigIter contigIt = begin(fragStore.contigStore, Standard() );
+    TContigIter contigItEnd = end(fragStore.contigStore, Standard() );
+    for(TSize idCount = 0;contigIt != contigItEnd; ++contigIt, ++idCount) {
+        // Alignment matrix
+        typedef String<TMultiReadChar> TAlignMat;
+        TAlignMat mat;
+        TSize maxCoverage;
+        String<TSize> readSlot;
+        convertAlignment(fragStore, mat, idCount, maxCoverage, readSlot);
+        TSize len = length(mat) / maxCoverage;
+
+        // Gapped consensus sequence
+        typedef String<TMultiReadChar> TGappedConsensus;
+        TGappedConsensus gappedConsensus;
+        getGappedConsensus(fragStore, gappedConsensus, idCount);
+
+        // Print the alignment matrix
+        String<TSize> coverage;
+        resize(coverage, len, 0);
+        typedef typename Iterator<TGappedConsensus, Standard>::Type TConsIter;
+        TConsIter itCons = begin(gappedConsensus, Standard());
+        TSize winSize = 60;
+        int offset = 2;
+        TSize column = 0;
+        while (column<len) {
+            TSize window_end = column + winSize;
+            if (window_end >= len) window_end = len;
+            // Position
+            for(int i = 0; i<offset - 2; ++i) writeValue(target, ' ');
+            write(target, "Pos: ");
+            appendNumber(target, column);
+            writeValue(target, '\n');
+            // Ruler
+            for(int i = 0; i<offset + 3; ++i) writeValue(target, ' ');
+            for(TSize local_col = 1; local_col<window_end - column + 1; ++local_col) {
+                if ((local_col % 10)==0)
+                    writeValue(target, ':');
+                else if ((local_col % 5)==0)
+                    writeValue(target, '.');
+                else
+                    writeValue(target, ' ');
+            }
+            writeValue(target, '\n');
+            // Matrix
+            for(TSize row = 0; row<maxCoverage; ++row) {
+                TSize tmp = row;
+                int off = 0;
+                while (tmp / 10 != 0) {
+                    tmp /= 10;
+                    ++off;
+                }
+                for(int i = 0; i<offset - off; ++i) writeValue(target, ' ');
+                appendNumber(target, row);
+                writeValue(target, ':');
+                writeValue(target, ' ');
+                for(TSize local_col = column; local_col<window_end; ++local_col) {
+                    writeValue(target, mat[row * len + local_col]);
+                    if (mat[row * len + local_col] != '.') ++coverage[local_col];
+                }
+                writeValue(target, '\n');
+            }
+            writeValue(target, '\n');
+
+            // Consensus
+            for(int i = 0; i<offset; ++i)
+                writeValue(target, ' ');
+            write(target, "C: ");
+            for(unsigned int local_col = column; local_col<window_end; ++local_col, ++itCons)
+                writeValue(target, *itCons);
+            writeValue(target, '\n');
+            for(int i = 0; i<offset-1; ++i)
+                writeValue(target, ' ');
+            write(target, ">2: ");
+            for(unsigned int local_col = column; local_col<window_end; ++local_col) {
+                if (coverage[local_col] > 2)
+                    writeValue(target, gappedConsensus[local_col]);
+                else
+                    writeValue(target, gapChar);
+            }
+            writeValue(target, '\n');
+            writeValue(target, '\n');
+            column+=winSize;
+        }
+        writeValue(target, '\n');
+        writeValue(target, '\n');
+
+        // Print all aligned reads belonging to this contig
+
+        // Sort according to contigId
+        sortAlignedReads(fragStore.alignedReadStore, SortContigId());
+
+        // Find range of the given contig
+        typedef typename Iterator<typename TFragmentStore::TAlignedReadStore, Standard>::Type TAlignIter;
+        TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
+        TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
+
+        // Sort the reads according to the begin position
+        sortAlignedReads(infix(fragStore.alignedReadStore, alignIt - begin(fragStore.alignedReadStore, Standard()), alignItEnd - begin(fragStore.alignedReadStore, Standard())), SortBeginPos());
+        TAlignIter alignItTmp = lowerBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
+        TAlignIter alignItTmpEnd = upperBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
+        String<std::pair<TSize, TSize> > idToPos;
+        reserve(idToPos, alignItTmpEnd - alignItTmp);
+        for(TSize iCount = 0; alignItTmp!=alignItTmpEnd; ++iCount, ++alignItTmp)
+            appendValue(idToPos, std::make_pair(alignItTmp->id, readSlot[iCount]));
+        std::sort(begin(idToPos, Standard()), end(idToPos, Standard()));
+
+        // Sort the reads according to the id
+        sortAlignedReads(infix(fragStore.alignedReadStore, alignIt - begin(fragStore.alignedReadStore, Standard()), alignItEnd - begin(fragStore.alignedReadStore, Standard())), SortId());
+        alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
+        alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, idCount, SortContigId());
+
+        bool noNamesPresent = (length(fragStore.readNameStore) == 0);
+        for(TSize iCount = 0;alignIt != alignItEnd; ++alignIt, ++iCount) {
+
+            // Print all reads
+            write(target, "typ:");
+            if (!noNamesPresent)
             {
-				streamWriteChar(file, 'R');
-				streamPut(file, iCount);
-			}
+                writeValue(target, 'R');
+                appendNumber(target, iCount);
+            }
             else
             {
-                streamPut(file, fragStore.readNameStore[alignIt->readId]);
+                write(target, fragStore.readNameStore[alignIt->readId]);
             }
-			streamWriteChar(file, '\n');
-			streamWriteBlock(file, "seq:", 4);
-			streamPut(file, fragStore.readSeqStore[alignIt->readId]);
-			streamWriteChar(file, '\n');
-			streamWriteBlock(file, "Pos:", 4);
-			streamPut(file, alignIt->beginPos);
-			streamWriteChar(file, ',');
-			streamPut(file, alignIt->endPos);
-			streamWriteChar(file, '\n');
+            write(target, "\nseq:");
+            write(target, fragStore.readSeqStore[alignIt->readId]);
+            write(target, "\nPos:");
+            appendNumber(target, alignIt->beginPos);
+            writeValue(target, ',');
+            appendNumber(target, alignIt->endPos);
+            writeValue(target, '\n');
 #ifndef CELERA_OFFSET
-			TSize begClr = 0;
-			TSize endClr = 0;
-			getClrRange(fragStore, *alignIt, begClr, endClr);
-			streamWriteBlock(file, "clr:", 4);
-			streamPut(file, begClr);
-			streamWriteChar(file, ',');
-			streamPut(file, endClr);
-			streamWriteChar(file, '\n');
+            TSize begClr = 0;
+            TSize endClr = 0;
+            getClrRange(fragStore, *alignIt, begClr, endClr);
+            write(target, "clr:");
+            appendNumber(target, begClr);
+            writeValue(target, ',');
+            appendNumber(target, endClr);
+            writeValue(target, '\n');
 #endif
-			std::stringstream gapCoords;
-			TSize letterCount = 0;
-			TSize gapCount = 0;
-			for(TContigPos column = _min(alignIt->beginPos, alignIt->endPos); column < _max(alignIt->beginPos, alignIt->endPos); ++column) {
-				if (mat[idToPos[iCount].second * len + column] == gapChar) {
-					++gapCount;
-					gapCoords << letterCount << ' ';
-				} else ++letterCount;
-			}
-			streamWriteBlock(file, "dln:", 4);
-			streamPut(file, gapCount);
-			streamWriteChar(file, '\n');
-			streamWriteBlock(file, "del:", 4);
-			streamWriteBlock(file, gapCoords.str().c_str(), gapCoords.str().size());
-			streamWriteChar(file, '\n');
-			streamWriteChar(file, '\n');
-		}
-	}
-
-    return 0;
+            std::stringstream gapCoords;
+            TSize letterCount = 0;
+            TSize gapCount = 0;
+            for(TContigPos column = _min(alignIt->beginPos, alignIt->endPos); column < _max(alignIt->beginPos, alignIt->endPos); ++column) {
+                if (mat[idToPos[iCount].second * len + column] == gapChar) {
+                    ++gapCount;
+                    gapCoords << letterCount << ' ';
+                } else ++letterCount;
+            }
+            write(target, "dln:");
+            appendNumber(target, gapCount);
+            writeValue(target, '\n');
+            write(target, "del:");
+            write(target, gapCoords.str());
+            writeValue(target, '\n');
+            writeValue(target, '\n');
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1389,436 +1319,436 @@ write(TFile & file,
 
 
 template<typename TFile, typename TSpec, typename TConfig, typename TFilePath>
-inline int
-_convertSimpleReadFile(TFile& file,
-					   FragmentStore<TSpec, TConfig>& fragStore,
-					   TFilePath& filePath, 
-					   bool moveToFront)
+inline void
+_convertSimpleReadFile(TFile& /*file*/,
+                       FragmentStore<TSpec, TConfig>& /*fragStore*/,
+                       TFilePath& /*filePath*/,
+                       bool /*moveToFront*/)
 {
-//IOREV _nodoc_ huge undocumented function, uses custom IO based on iostream and FILE* :S
-	// Basic types
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Id<TFragmentStore>::Type TId;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	//typedef typename Value<TFile>::Type TValue;
-	typedef typename TFragmentStore::TContigPos TPos;
-	typedef typename TFragmentStore::TReadSeq TReadSeq;
-
-	// All fragment store element types
-	typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigElement;
-	typedef typename Value<typename TFragmentStore::TLibraryStore>::Type TLibraryStoreElement;
-	typedef typename Value<typename TFragmentStore::TMatePairStore>::Type TMatePairElement;
-	typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement;
-	typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
-	
-
-	// All maps to mirror file ids to our internal ids
-	typedef std::map<TId, TId> TIdMap;
-	TIdMap libIdMap;
-	TIdMap frgIdMap;
-	TIdMap readIdMap;
-
-    // Create RecordReader object.
-    RecordReader<TFile, SinglePass<> > reader(file);
-
-	// Parse the file and convert the internal ids
-	TPos maxPos = 0;
-	TPos minPos = MaxValue<TPos>::VALUE;
-	TId count = 0;
-    if (atEnd(reader))
-        return false;
-    CharString buffer;
-	while (!atEnd(reader))
-    {
-		// New read?
-		if (value(reader) == '>')
-        {
-			TAlignedElement alignEl;
-			TId id = count;
-			TId fragId = TReadStoreElement::INVALID_ID;
-			TId repeatId = 0;
-
-            goNext(reader);
-            if (skipWhitespaces(reader) != 0)
-                return 1;
-
-			// Get the layout positions
-            clear(buffer);
-            if (readDigits(buffer, reader) != 0)
-                return 1;
-            if (!lexicalCast2(alignEl.beginPos, buffer))
-                return 1;
-            goNext(reader);
-            if (skipWhitespaces(reader) != 0)
-                return 1;
-            clear(buffer);
-            if (readDigits(buffer, reader) != 0)
-                return 1;
-            if (!lexicalCast2(alignEl.endPos, buffer))
-                return 1;
-			
-			// Any attributes?
-			String<char> eid;
-			String<char> qlt;
-			TReadSeq seq;
-			if (value(reader) == '[')
-            {
-				String<char> fdIdentifier;
-				while (value(reader) != ']')
-                {
-                    goNext(reader);
-                    if (skipWhitespaces(reader) != 0)
-                        return 1;
-					clear(fdIdentifier);
-                    if (readAlphaNums(fdIdentifier, reader) != 0)
-                        return 1;
-                    goNext(reader);  // Skip "="
-					if (fdIdentifier == "id")
-                    {
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(id, buffer))
-                            return 1;
-					} else if (fdIdentifier == "fragId") {
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(fragId, buffer))
-                            return 1;
-					} else if (fdIdentifier == "repeatId") {
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(repeatId, buffer))
-                            return 1;
-					} else if (fdIdentifier == "eid") {
-                        if (readUntilOneOf(eid, reader, ',', ']') != 0)
-                            return 1;
-					} else if (fdIdentifier == "qlt") {
-                        if (readUntilOneOf(qlt, reader, ',', ']') != 0)
-                            return 1;
-					} else {
-						// Jump to next attribute
-                        // TODO(holtgrew): Add skipUntilOneOf()?
-                        if (readUntilOneOf(buffer, reader, ',', ']') != 0)
-                            return 1;
-					}
-				}
-			}
-            if (skipLine(reader) != 0)
-                return 1;
-            if (skipWhitespaces(reader) != 0)
-                return 1;
-            while (!atEnd(reader) && value(reader) != '>')
-            {
-                if (readLetters(seq, reader) != 0)
-                    return 1;
-                int res = skipWhitespaces(reader);
-                if (res != 0 && res != EOF_BEFORE_SUCCESS)
-                    return 1;
-            }
-			
-			// Set quality
-			typedef typename Iterator<TReadSeq, Standard>::Type TReadIter;
-			typedef typename Iterator<String<char> >::Type TQualIter;
-			TReadIter begIt = begin(seq, Standard() );
-			TReadIter begItEnd = begin(seq, Standard() );
-			if (length(qlt)) {
-				TQualIter qualIt = begin(qlt);
-				TQualIter qualItEnd = end(qlt);
-				for(;qualIt != qualItEnd; goNext(qualIt), goNext(begIt)) assignQualityValue(value(begIt), value(qualIt));
-			} else {
-				for(;begIt != begItEnd; goNext(begIt)) assignQualityValue(value(begIt), 'D');
-			}
-
-			// Set eid if not given
-			if (empty(eid)) {
-				std::stringstream input;
-				input << "R" << id;
-				input << "-" << repeatId;
-				eid = input.str().c_str();
-			}
-
-			// Insert the read
-			readIdMap.insert(std::make_pair(id, static_cast<TId>(length(fragStore.readStore))));
-			appendRead(fragStore, seq, fragId);
-			appendValue(fragStore.readNameStore, eid, Generous());
-
-			// Insert an aligned read
-			TSize readLen = length(seq);
-			if (alignEl.beginPos < alignEl.endPos) {
-				if ((TPos)readLen != alignEl.endPos - alignEl.beginPos) {
-					alignEl.endPos = alignEl.beginPos + readLen;
-				}
-				if (alignEl.beginPos < minPos) minPos = alignEl.beginPos;
-				if (alignEl.endPos > maxPos) maxPos = alignEl.endPos;
-			} else {
-				if ((TPos)readLen != alignEl.beginPos - alignEl.endPos) {
-					alignEl.beginPos = alignEl.endPos + readLen;
-				}
-				if (alignEl.endPos < minPos) minPos = alignEl.endPos;
-				if (alignEl.beginPos > maxPos) maxPos = alignEl.beginPos;
-			}
-			alignEl.readId = id;
-			alignEl.pairMatchId =  fragId;
-			alignEl.contigId = 0;
-			alignEl.id = length(fragStore.alignedReadStore);
-			appendValue(fragStore.alignedReadStore, alignEl, Generous());
-			++count;
-		} else {
-            if (skipLine(reader) != 0)
-                return 1;
-		}
-	}
-
-	// Read contig or reference sequence
-	TContigElement contigEl;
-	std::string fileName = filePath + 'S';
-	FILE* strmRef = fopen(fileName.c_str(), "rb");
-	String<char> contigEid = "C0";
-    if (strmRef)
-    {
-        seqan::RecordReader<FILE *, SinglePass<> > readerRef(strmRef);
-        clear(contigEid);
-        if (readRecord(contigEid, contigEl.seq, readerRef, Fasta()) != 0)
-            return 1;
-		fclose(strmRef);
-	}
-	if (empty(contigEl.seq)) {
-		typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
-		if (moveToFront) appendValue(contigEl.gaps, TContigGapAnchor(0, maxPos - minPos), Generous());
-		else appendValue(contigEl.gaps, TContigGapAnchor(0, maxPos), Generous());
-	}
-	appendValue(fragStore.contigStore, contigEl, Generous());
-	appendValue(fragStore.contigNameStore, contigEid, Generous());
-
-
-	// Read fragments
-	fileName = filePath + 'F';
-	FILE* strmFrag = fopen(fileName.c_str(), "rb");
-    if (!strmFrag)
-        return 1;
-    RecordReader<FILE *, SinglePass<> > readerFrag(strmFrag);
-    while (!atEnd(readerFrag))
-    {
-        if (value(readerFrag) == '>')
-        {
-            TMatePairElement matePairEl;
-            goNext(readerFrag);
-            if (skipWhitespaces(readerFrag) != 0)
-                return 1;
-
-            // Get the fragment id
-            clear(buffer);
-            if (readDigits(buffer, readerFrag) != 0)
-                return 1;
-            TId id = 0;
-            if (!lexicalCast2(id, buffer))
-                return 1;
-			
-            // Any attributes?
-            std::stringstream input;
-            input << "F" << id;
-            String<char> eid(input.str().c_str());
-            if (value(readerFrag) == '[')
-            {
-                String<char> fdIdentifier;
-                while (value(readerFrag) != ']')
-                {
-                    goNext(readerFrag);
-                    if (skipWhitespaces(readerFrag) != 0)
-                        return 1;
-                    clear(fdIdentifier);
-                    if (readAlphaNums(fdIdentifier, readerFrag) != 0)
-                        return 1;
-                    goNext(readerFrag);
-                    if (fdIdentifier == "libId")
-                    {
-                        clear(buffer);
-                        if (readDigits(buffer, readerFrag) != 0)
-                            return 1;
-                        if (!lexicalCast2(matePairEl.libId, buffer))
-                            return 1;
-                    } else if (fdIdentifier == "eid") {
-                        clear(eid);
-                        if (readUntilOneOf(eid, readerFrag, ',', ']') != 0)
-                            return 1;
-                    } else {
-                        // Jump to next attribute
-                        if (readUntilOneOf(buffer, readerFrag, ',', ']') != 0)
-                            return 1;
-                    }
-                }
-            }
-            if (skipLine(readerFrag) != 0)
-                return 1;
-
-            // Read the two reads belonging to this mate pair
-            clear(buffer);
-            for (int i = 0; i < 2; ++i)
-            {
-                if (skipWhitespaces(readerFrag) != 0)
-                    return 1;
-                clear(buffer);
-                if (readDigits(buffer, readerFrag) != 0)
-                    return 1;
-                if (!lexicalCast2(matePairEl.readId[i], buffer))
-                    return 1;
-                if (!i)  // Skip ','.
-                    goNext(readerFrag);
-            }
-            int res = skipLine(readerFrag);
-            if (res != 0 && res != EOF_BEFORE_SUCCESS)
-                return 1;
-
-            // Insert mate pair
-            if (matePairEl.readId[0] != matePairEl.readId[1]) {
-                frgIdMap.insert(std::make_pair(id, static_cast<TId>(length(fragStore.matePairStore))));
-                appendValue(fragStore.matePairStore, matePairEl, Generous());
-                appendValue(fragStore.matePairNameStore, eid, Generous());
-            }
-        } else {
-            int res = skipLine(readerFrag);
-            if (res != 0 && res != EOF_BEFORE_SUCCESS)
-                return 1;
-        }
-    }
-    fclose(strmFrag);
-
-	// Read libraries
-	fileName = filePath + 'L';
-	FILE* strmLib = fopen(fileName.c_str(), "rb");
-    if (!strmLib)
-        return 1;
-    RecordReader<FILE *, SinglePass<> > readerLib(strmLib);
-    while (!atEnd(readerLib))
-    {
-        if (value(readerLib) == '>')
-        {
-            TLibraryStoreElement libEl;
-            goNext(readerLib);
-            if (skipWhitespaces(readerLib) != 0)
-                return 1;
-
-            // Get the fragment id
-            clear(buffer);
-            if (readDigits(buffer, readerLib) != 0)
-                return 1;
-            TId id = 0;
-            if (!lexicalCast2(id, buffer))
-                return 1;
-			
-            // Any attributes?
-            std::stringstream input;
-            input << "L" << id;
-            String<char> eid(input.str().c_str());
-            if (value(readerLib) == '[')
-            {
-                String<char> fdIdentifier;
-                while (value(readerLib) != ']')
-                {
-                    goNext(readerLib);
-                    if (skipWhitespaces(readerLib) != 0)
-                        return 1;
-                    clear(fdIdentifier);
-                    if (readAlphaNums(fdIdentifier, readerLib) != 0)
-                        return 1;
-                    if (fdIdentifier == "eid")
-                    {
-                        clear(eid);
-                        if (readUntilOneOf(eid, readerLib, ',', ']') != 0)
-                            return 1;
-                    } else {
-                        // Jump to next attribute
-                        // TODO(holtgrew): skipUntilOneOf()?
-                        if (readUntilOneOf(buffer, readerLib, ',', ']') != 0)
-                            return 1;
-                    }
-                }
-            }
-            if (skipLine(readerLib) != 0)
-                return 1;
-            if (skipWhitespaces(readerLib) != 0)
-                return 1;
-
-            // Read the mean and standard deviation
-            clear(buffer);
-            if (readDigits(buffer, readerLib) != 0)
-                return 1;
-            if (!lexicalCast2(libEl.mean, buffer))
-                return 1;
-            if (skipWhitespaces(readerLib) != 0)
-                return 1;
-            goNext(readerLib);
-            clear(buffer);
-            if (readDigits(buffer, readerLib) != 0)
-                return 1;
-            if (!lexicalCast2(libEl.std, buffer))
-                return 1;
-            int res = skipLine(readerLib);
-            if (res != 0 && res != EOF_BEFORE_SUCCESS)
-                return 1;
-
-            // Insert mate pair
-            libIdMap.insert(std::make_pair(id, static_cast<TId>(length(fragStore.libraryStore))));
-            appendValue(fragStore.libraryStore, libEl, Generous());
-            appendValue(fragStore.libraryNameStore, eid, Generous());
-        } else {
-            int res = skipLine(readerLib);
-            if (res != 0 && res != EOF_BEFORE_SUCCESS)
-                return 1;
-        }
-    }
-    fclose(strmLib);
-	
-	// Renumber all ids
-	typedef typename TIdMap::const_iterator TIdMapIter;
-	typedef typename Iterator<typename TFragmentStore::TMatePairStore>::Type TMateIter;
-	TMateIter mateIt = begin(fragStore.matePairStore);
-	TMateIter mateItEnd = end(fragStore.matePairStore);
-	for(;mateIt != mateItEnd; goNext(mateIt)) {
-		if (mateIt->libId != TMatePairElement::INVALID_ID) {
-			TIdMapIter libIdPos = libIdMap.find(mateIt->libId);
-			if (libIdPos != libIdMap.end()) mateIt->libId = libIdPos->second;
-			else mateIt->libId = TMatePairElement::INVALID_ID;
-		}
-		if (mateIt->readId[0] != TMatePairElement::INVALID_ID) {
-			TIdMapIter readIdPos = readIdMap.find(mateIt->readId[0]);
-			if (readIdPos != readIdMap.end()) mateIt->readId[0] = readIdPos->second;
-			else mateIt->readId[0] = TMatePairElement::INVALID_ID;
-		}
-		if (mateIt->readId[1]!= TMatePairElement::INVALID_ID) {
-			TIdMapIter readIdPos = readIdMap.find(mateIt->readId[1]);
-			if (readIdPos != readIdMap.end()) mateIt->readId[1] = readIdPos->second;
-			else mateIt->readId[0] = TMatePairElement::INVALID_ID;
-		}
-	}
-	typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter;
-	TReadIter readIt = begin(fragStore.readStore);
-	TReadIter readItEnd = end(fragStore.readStore);
-	for(;readIt != readItEnd; goNext(readIt)) {
-		if (readIt->matePairId != TReadStoreElement::INVALID_ID) {
-			TIdMapIter mateIdPos = frgIdMap.find(readIt->matePairId);
-			if (mateIdPos != frgIdMap.end()) readIt->matePairId = mateIdPos->second;
-			else readIt->matePairId = TReadStoreElement::INVALID_ID;
-		}
-	}
-	typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
-	TAlignIter alignIt = begin(fragStore.alignedReadStore);
-	TAlignIter alignItEnd = end(fragStore.alignedReadStore);
-	for(;alignIt != alignItEnd; goNext(alignIt)) {
-		if (alignIt->readId != TAlignedElement::INVALID_ID) {
-			TIdMapIter readIdPos = readIdMap.find(alignIt->readId);
-			if (readIdPos != readIdMap.end()) alignIt->readId = readIdPos->second;
-			else alignIt->readId = TAlignedElement::INVALID_ID;
-		}
-		if (moveToFront) {
-			alignIt->beginPos -= minPos;
-			alignIt->endPos -= minPos;
-		}
-	}
-	return 0;
+return;
+////IOREV _nodoc_ huge undocumented function, uses custom IO based on iostream and FILE* :S
+//    // Basic types
+//    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+//    typedef typename Id<TFragmentStore>::Type TId;
+//    typedef typename Size<TFragmentStore>::Type TSize;
+//    //typedef typename Value<TFile>::Type TValue;
+//    typedef typename TFragmentStore::TContigPos TPos;
+//    typedef typename TFragmentStore::TReadSeq TReadSeq;
+//
+//    // All fragment store element types
+//    typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigElement;
+//    typedef typename Value<typename TFragmentStore::TLibraryStore>::Type TLibraryStoreElement;
+//    typedef typename Value<typename TFragmentStore::TMatePairStore>::Type TMatePairElement;
+//    typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement;
+//    typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
+//
+//
+//    // All maps to mirror file ids to our internal ids
+//    typedef std::map<TId, TId> TIdMap;
+//    TIdMap libIdMap;
+//    TIdMap frgIdMap;
+//    TIdMap readIdMap;
+//
+//    // Create RecordReader object.
+//    typename DirectionIterator<TFile, Input>::Type reader = directionIterator(file, Input());
+//
+//    // Parse the file and convert the internal ids
+//    TPos maxPos = 0;
+//    TPos minPos = MaxValue<TPos>::VALUE;
+//    TId count = 0;
+//    if (atEnd(reader))
+//        return false;
+//    CharString buffer;
+//    while (!atEnd(reader))
+//    {
+//        // New read?
+//        if (value(reader) == '>')
+//        {
+//            TAlignedElement alignEl;
+//            TId id = count;
+//            TId fragId = TReadStoreElement::INVALID_ID;
+//            TId repeatId = 0;
+//
+//            goNext(reader);
+//            if (skipWhitespaces(reader) != 0)
+//                return 1;
+//
+//            // Get the layout positions
+//            clear(buffer);
+//            if (readDigits(buffer, reader) != 0)
+//                return 1;
+//            if (!lexicalCast2(alignEl.beginPos, buffer))
+//                return 1;
+//            goNext(reader);
+//            if (skipWhitespaces(reader) != 0)
+//                return 1;
+//            clear(buffer);
+//            if (readDigits(buffer, reader) != 0)
+//                return 1;
+//            if (!lexicalCast2(alignEl.endPos, buffer))
+//                return 1;
+//
+//            // Any attributes?
+//            String<char> eid;
+//            String<char> qlt;
+//            TReadSeq seq;
+//            if (value(reader) == '[')
+//            {
+//                String<char> fdIdentifier;
+//                while (value(reader) != ']')
+//                {
+//                    goNext(reader);
+//                    if (skipWhitespaces(reader) != 0)
+//                        return 1;
+//                    clear(fdIdentifier);
+//                    if (readAlphaNums(fdIdentifier, reader) != 0)
+//                        return 1;
+//                    goNext(reader);  // Skip "="
+//                    if (fdIdentifier == "id")
+//                    {
+//                        clear(buffer);
+//                        if (readDigits(buffer, reader) != 0)
+//                            return 1;
+//                        if (!lexicalCast2(id, buffer))
+//                            return 1;
+//                    } else if (fdIdentifier == "fragId") {
+//                        clear(buffer);
+//                        if (readDigits(buffer, reader) != 0)
+//                            return 1;
+//                        if (!lexicalCast2(fragId, buffer))
+//                            return 1;
+//                    } else if (fdIdentifier == "repeatId") {
+//                        clear(buffer);
+//                        if (readDigits(buffer, reader) != 0)
+//                            return 1;
+//                        if (!lexicalCast2(repeatId, buffer))
+//                            return 1;
+//                    } else if (fdIdentifier == "eid") {
+//                        if (readUntilOneOf(eid, reader, ',', ']') != 0)
+//                            return 1;
+//                    } else if (fdIdentifier == "qlt") {
+//                        if (readUntilOneOf(qlt, reader, ',', ']') != 0)
+//                            return 1;
+//                    } else {
+//                        // Jump to next attribute
+//                        // TODO(holtgrew): Add skipUntilOneOf()?
+//                        if (readUntilOneOf(buffer, reader, ',', ']') != 0)
+//                            return 1;
+//                    }
+//                }
+//            }
+//            if (skipLine(reader) != 0)
+//                return 1;
+//            if (skipWhitespaces(reader) != 0)
+//                return 1;
+//            while (!atEnd(reader) && value(reader) != '>')
+//            {
+//                if (readLetters(seq, reader) != 0)
+//                    return 1;
+//                int res = skipWhitespaces(reader);
+//                if (res != 0 && res != EOF_BEFORE_SUCCESS)
+//                    return 1;
+//            }
+//
+//            // Set quality
+//            typedef typename Iterator<TReadSeq, Standard>::Type TReadIter;
+//            typedef typename Iterator<String<char> >::Type TQualIter;
+//            TReadIter begIt = begin(seq, Standard() );
+//            TReadIter begItEnd = begin(seq, Standard() );
+//            if (length(qlt)) {
+//                TQualIter qualIt = begin(qlt);
+//                TQualIter qualItEnd = end(qlt);
+//                for(;qualIt != qualItEnd; goNext(qualIt), goNext(begIt)) assignQualityValue(value(begIt), value(qualIt));
+//            } else {
+//                for(;begIt != begItEnd; goNext(begIt)) assignQualityValue(value(begIt), 'D');
+//            }
+//
+//            // Set eid if not given
+//            if (empty(eid)) {
+//                std::stringstream input;
+//                input << "R" << id;
+//                input << "-" << repeatId;
+//                eid = input.str().c_str();
+//            }
+//
+//            // Insert the read
+//            readIdMap.insert(std::make_pair(id, static_cast<TId>(length(fragStore.readStore))));
+//            appendRead(fragStore, seq, fragId);
+//            appendValue(fragStore.readNameStore, eid, Generous());
+//
+//            // Insert an aligned read
+//            TSize readLen = length(seq);
+//            if (alignEl.beginPos < alignEl.endPos) {
+//                if ((TPos)readLen != alignEl.endPos - alignEl.beginPos) {
+//                    alignEl.endPos = alignEl.beginPos + readLen;
+//                }
+//                if (alignEl.beginPos < minPos) minPos = alignEl.beginPos;
+//                if (alignEl.endPos > maxPos) maxPos = alignEl.endPos;
+//            } else {
+//                if ((TPos)readLen != alignEl.beginPos - alignEl.endPos) {
+//                    alignEl.beginPos = alignEl.endPos + readLen;
+//                }
+//                if (alignEl.endPos < minPos) minPos = alignEl.endPos;
+//                if (alignEl.beginPos > maxPos) maxPos = alignEl.beginPos;
+//            }
+//            alignEl.readId = id;
+//            alignEl.pairMatchId =  fragId;
+//            alignEl.contigId = 0;
+//            alignEl.id = length(fragStore.alignedReadStore);
+//            appendValue(fragStore.alignedReadStore, alignEl, Generous());
+//            ++count;
+//        } else {
+//            if (skipLine(reader) != 0)
+//                return 1;
+//        }
+//    }
+//
+//    // Read contig or reference sequence
+//    TContigElement contigEl;
+//    std::string fileName = filePath + 'S';
+//    SeqFileIn strmRef;
+//    String<char> contigEid = "C0";
+//    if (open(strmRef, fileName.c_str()))
+//    {
+//        typename DirectionIterator<TFile, Input>::Type readerRef = directionIterator(strmRef, Input());
+//        clear(contigEid);
+//        readRecord(contigEid, contigEl.seq, strmRef);
+//        close(strmRef);
+//    }
+//    if (empty(contigEl.seq)) {
+//        typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
+//        if (moveToFront) appendValue(contigEl.gaps, TContigGapAnchor(0, maxPos - minPos), Generous());
+//        else appendValue(contigEl.gaps, TContigGapAnchor(0, maxPos), Generous());
+//    }
+//    appendValue(fragStore.contigStore, contigEl, Generous());
+//    appendValue(fragStore.contigNameStore, contigEid, Generous());
+//
+//
+//    // Read fragments
+//    fileName = filePath + 'F';
+//    FILE* strmFrag = fopen(fileName.c_str(), "rb");
+//    if (!strmFrag)
+//        return 1;
+//    RecordReader<FILE *, SinglePass<> > readerFrag(strmFrag);
+//    while (!atEnd(readerFrag))
+//    {
+//        if (value(readerFrag) == '>')
+//        {
+//            TMatePairElement matePairEl;
+//            goNext(readerFrag);
+//            if (skipWhitespaces(readerFrag) != 0)
+//                return 1;
+//
+//            // Get the fragment id
+//            clear(buffer);
+//            if (readDigits(buffer, readerFrag) != 0)
+//                return 1;
+//            TId id = 0;
+//            if (!lexicalCast2(id, buffer))
+//                return 1;
+//
+//            // Any attributes?
+//            std::stringstream input;
+//            input << "F" << id;
+//            String<char> eid(input.str().c_str());
+//            if (value(readerFrag) == '[')
+//            {
+//                String<char> fdIdentifier;
+//                while (value(readerFrag) != ']')
+//                {
+//                    goNext(readerFrag);
+//                    if (skipWhitespaces(readerFrag) != 0)
+//                        return 1;
+//                    clear(fdIdentifier);
+//                    if (readAlphaNums(fdIdentifier, readerFrag) != 0)
+//                        return 1;
+//                    goNext(readerFrag);
+//                    if (fdIdentifier == "libId")
+//                    {
+//                        clear(buffer);
+//                        if (readDigits(buffer, readerFrag) != 0)
+//                            return 1;
+//                        if (!lexicalCast2(matePairEl.libId, buffer))
+//                            return 1;
+//                    } else if (fdIdentifier == "eid") {
+//                        clear(eid);
+//                        if (readUntilOneOf(eid, readerFrag, ',', ']') != 0)
+//                            return 1;
+//                    } else {
+//                        // Jump to next attribute
+//                        if (readUntilOneOf(buffer, readerFrag, ',', ']') != 0)
+//                            return 1;
+//                    }
+//                }
+//            }
+//            if (skipLine(readerFrag) != 0)
+//                return 1;
+//
+//            // Read the two reads belonging to this mate pair
+//            clear(buffer);
+//            for (int i = 0; i < 2; ++i)
+//            {
+//                if (skipWhitespaces(readerFrag) != 0)
+//                    return 1;
+//                clear(buffer);
+//                if (readDigits(buffer, readerFrag) != 0)
+//                    return 1;
+//                if (!lexicalCast2(matePairEl.readId[i], buffer))
+//                    return 1;
+//                if (!i)  // Skip ','.
+//                    goNext(readerFrag);
+//            }
+//            int res = skipLine(readerFrag);
+//            if (res != 0 && res != EOF_BEFORE_SUCCESS)
+//                return 1;
+//
+//            // Insert mate pair
+//            if (matePairEl.readId[0] != matePairEl.readId[1]) {
+//                frgIdMap.insert(std::make_pair(id, static_cast<TId>(length(fragStore.matePairStore))));
+//                appendValue(fragStore.matePairStore, matePairEl, Generous());
+//                appendValue(fragStore.matePairNameStore, eid, Generous());
+//            }
+//        } else {
+//            int res = skipLine(readerFrag);
+//            if (res != 0 && res != EOF_BEFORE_SUCCESS)
+//                return 1;
+//        }
+//    }
+//    fclose(strmFrag);
+//
+//    // Read libraries
+//    fileName = filePath + 'L';
+//    FILE* strmLib = fopen(fileName.c_str(), "rb");
+//    if (!strmLib)
+//        return 1;
+//    RecordReader<FILE *, SinglePass<> > readerLib(strmLib);
+//    while (!atEnd(readerLib))
+//    {
+//        if (value(readerLib) == '>')
+//        {
+//            TLibraryStoreElement libEl;
+//            goNext(readerLib);
+//            if (skipWhitespaces(readerLib) != 0)
+//                return 1;
+//
+//            // Get the fragment id
+//            clear(buffer);
+//            if (readDigits(buffer, readerLib) != 0)
+//                return 1;
+//            TId id = 0;
+//            if (!lexicalCast2(id, buffer))
+//                return 1;
+//
+//            // Any attributes?
+//            std::stringstream input;
+//            input << "L" << id;
+//            String<char> eid(input.str().c_str());
+//            if (value(readerLib) == '[')
+//            {
+//                String<char> fdIdentifier;
+//                while (value(readerLib) != ']')
+//                {
+//                    goNext(readerLib);
+//                    if (skipWhitespaces(readerLib) != 0)
+//                        return 1;
+//                    clear(fdIdentifier);
+//                    if (readAlphaNums(fdIdentifier, readerLib) != 0)
+//                        return 1;
+//                    if (fdIdentifier == "eid")
+//                    {
+//                        clear(eid);
+//                        if (readUntilOneOf(eid, readerLib, ',', ']') != 0)
+//                            return 1;
+//                    } else {
+//                        // Jump to next attribute
+//                        // TODO(holtgrew): skipUntilOneOf()?
+//                        if (readUntilOneOf(buffer, readerLib, ',', ']') != 0)
+//                            return 1;
+//                    }
+//                }
+//            }
+//            if (skipLine(readerLib) != 0)
+//                return 1;
+//            if (skipWhitespaces(readerLib) != 0)
+//                return 1;
+//
+//            // Read the mean and standard deviation
+//            clear(buffer);
+//            if (readDigits(buffer, readerLib) != 0)
+//                return 1;
+//            if (!lexicalCast2(libEl.mean, buffer))
+//                return 1;
+//            if (skipWhitespaces(readerLib) != 0)
+//                return 1;
+//            goNext(readerLib);
+//            clear(buffer);
+//            if (readDigits(buffer, readerLib) != 0)
+//                return 1;
+//            if (!lexicalCast2(libEl.std, buffer))
+//                return 1;
+//            int res = skipLine(readerLib);
+//            if (res != 0 && res != EOF_BEFORE_SUCCESS)
+//                return 1;
+//
+//            // Insert mate pair
+//            libIdMap.insert(std::make_pair(id, static_cast<TId>(length(fragStore.libraryStore))));
+//            appendValue(fragStore.libraryStore, libEl, Generous());
+//            appendValue(fragStore.libraryNameStore, eid, Generous());
+//        } else {
+//            int res = skipLine(readerLib);
+//            if (res != 0 && res != EOF_BEFORE_SUCCESS)
+//                return 1;
+//        }
+//    }
+//    fclose(strmLib);
+//
+//    // Renumber all ids
+//    typedef typename TIdMap::const_iterator TIdMapIter;
+//    typedef typename Iterator<typename TFragmentStore::TMatePairStore>::Type TMateIter;
+//    TMateIter mateIt = begin(fragStore.matePairStore);
+//    TMateIter mateItEnd = end(fragStore.matePairStore);
+//    for(;mateIt != mateItEnd; goNext(mateIt)) {
+//        if (mateIt->libId != TMatePairElement::INVALID_ID) {
+//            TIdMapIter libIdPos = libIdMap.find(mateIt->libId);
+//            if (libIdPos != libIdMap.end()) mateIt->libId = libIdPos->second;
+//            else mateIt->libId = TMatePairElement::INVALID_ID;
+//        }
+//        if (mateIt->readId[0] != TMatePairElement::INVALID_ID) {
+//            TIdMapIter readIdPos = readIdMap.find(mateIt->readId[0]);
+//            if (readIdPos != readIdMap.end()) mateIt->readId[0] = readIdPos->second;
+//            else mateIt->readId[0] = TMatePairElement::INVALID_ID;
+//        }
+//        if (mateIt->readId[1]!= TMatePairElement::INVALID_ID) {
+//            TIdMapIter readIdPos = readIdMap.find(mateIt->readId[1]);
+//            if (readIdPos != readIdMap.end()) mateIt->readId[1] = readIdPos->second;
+//            else mateIt->readId[0] = TMatePairElement::INVALID_ID;
+//        }
+//    }
+//    typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter;
+//    TReadIter readIt = begin(fragStore.readStore);
+//    TReadIter readItEnd = end(fragStore.readStore);
+//    for(;readIt != readItEnd; goNext(readIt)) {
+//        if (readIt->matePairId != TReadStoreElement::INVALID_ID) {
+//            TIdMapIter mateIdPos = frgIdMap.find(readIt->matePairId);
+//            if (mateIdPos != frgIdMap.end()) readIt->matePairId = mateIdPos->second;
+//            else readIt->matePairId = TReadStoreElement::INVALID_ID;
+//        }
+//    }
+//    typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
+//    TAlignIter alignIt = begin(fragStore.alignedReadStore);
+//    TAlignIter alignItEnd = end(fragStore.alignedReadStore);
+//    for(;alignIt != alignItEnd; goNext(alignIt)) {
+//        if (alignIt->readId != TAlignedElement::INVALID_ID) {
+//            TIdMapIter readIdPos = readIdMap.find(alignIt->readId);
+//            if (readIdPos != readIdMap.end()) alignIt->readId = readIdPos->second;
+//            else alignIt->readId = TAlignedElement::INVALID_ID;
+//        }
+//        if (moveToFront) {
+//            alignIt->beginPos -= minPos;
+//            alignIt->endPos -= minPos;
+//        }
+//    }
+//    return 0;
 }
 
 
@@ -1827,80 +1757,62 @@ _convertSimpleReadFile(TFile& file,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TSpec, typename TConfig>
-inline void 
-_writeCeleraFrg(TFile& target,
-				FragmentStore<TSpec, TConfig>& fragStore) 
+inline void
+_writeCeleraFrg(TFile& file,
+                FragmentStore<TSpec, TConfig>& fragStore)
 {
-//IOREV _nodoc_ 
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename TFragmentStore::TReadPos TReadPos;
-
-	// Iterate over all aligned reads to get the clear ranges
-	typedef Pair<TReadPos, TReadPos> TClrRange;
-	String<TClrRange> clearStr;
-	resize(clearStr, length(fragStore.readStore));
-	typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
-	TAlignIter alignIt = begin(fragStore.alignedReadStore);
-	TAlignIter alignItEnd = end(fragStore.alignedReadStore);
-	for(;alignIt != alignItEnd; goNext(alignIt)) {
-		TReadPos begClr = 0;
-		TReadPos endClr = 0;
-		getClrRange(fragStore, value(alignIt), begClr, endClr);
-		value(clearStr, alignIt->readId) = TClrRange(begClr, endClr);
-	}
-
-	// Write Reads
-	typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter;
-	TReadIter readIt = begin(fragStore.readStore);
-	TReadIter readItEnd = end(fragStore.readStore);
-	bool noNamesPresent = (length(fragStore.readNameStore) == 0);
-	for(TSize idCount = 0;readIt != readItEnd; goNext(readIt), ++idCount) {
-		streamPut(target, "{FRG\n");
-		streamPut(target, "act:");
-		streamPut(target, 'A');
-		streamPut(target, '\n');
-		streamPut(target, "acc:");
-		streamPut(target, idCount + 1);
-		streamPut(target, '\n');
-		streamPut(target, "typ:");
-		streamPut(target, 'R');
-		streamPut(target, '\n');
-		if (!noNamesPresent) {
-			streamPut(target, "src:\n");
-			streamPut(target, value(fragStore.readNameStore, idCount));
-			streamPut(target, "\n.\n");
-		}
-		streamPut(target, "etm:");
-		streamPut(target, '0');
-		streamPut(target, '\n');
-		streamPut(target, "seq:\n");
-		typedef typename Iterator<typename TFragmentStore::TReadSeq>::Type TSeqIter;
-		//typedef typename Value<typename TFragmentStore::TReadSeq>::Type TAlphabet;
-		TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount));
-		TSeqIter seqItEnd = end(value(fragStore.readSeqStore, idCount));
-		for(TSize k = 0;seqIt!=seqItEnd;goNext(seqIt), ++k) {
-			if ((k % 70 == 0) && (k != 0)) streamPut(target, '\n');
-			streamPut(target, getValue(seqIt));
-		}
-		streamPut(target, "\n.\n");
-		streamPut(target, "qlt:\n");
-		seqIt = begin(value(fragStore.readSeqStore, idCount));
-		for(TSize k = 0;seqIt!=seqItEnd;goNext(seqIt), ++k) {
-			if ((k % 70 == 0) && (k != 0)) streamPut(target, '\n');
-			Ascii c = ' ';
-			convertQuality(c, getQualityValue(value(seqIt)));
-			streamPut(target, c);
-		}
-		streamPut(target, "\n.\n");
-		// Note: Clear range does not have to be ordered, e.g. no indication for reverse complemented reads, this is happening in cgb records
-		streamPut(target, "clr:");
-		streamPut(target, (value(clearStr, idCount)).i1);
-		streamPut(target, ',');
-		streamPut(target, (value(clearStr, idCount)).i2);
-		streamPut(target, '\n');
-		streamPut(target, "}\n");
-	}
+//IOREV _nodoc_
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename TFragmentStore::TReadPos TReadPos;
+
+    typename DirectionIterator<TFile, Output>::Type target = directionIterator(file, Output());
+
+    // Iterate over all aligned reads to get the clear ranges
+    typedef Pair<TReadPos, TReadPos> TClrRange;
+    String<TClrRange> clearStr;
+    resize(clearStr, length(fragStore.readStore));
+    typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
+    TAlignIter alignIt = begin(fragStore.alignedReadStore);
+    TAlignIter alignItEnd = end(fragStore.alignedReadStore);
+    for(;alignIt != alignItEnd; goNext(alignIt))
+    {
+        TReadPos begClr = 0;
+        TReadPos endClr = 0;
+        getClrRange(fragStore, value(alignIt), begClr, endClr);
+        value(clearStr, alignIt->readId) = TClrRange(begClr, endClr);
+    }
+
+    // Write Reads
+    typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter;
+    TReadIter readIt = begin(fragStore.readStore);
+    TReadIter readItEnd = end(fragStore.readStore);
+    bool noNamesPresent = (length(fragStore.readNameStore) == 0);
+    for (TSize idCount = 0; readIt != readItEnd; goNext(readIt), ++idCount)
+    {
+        write(target, "{FRG\nact:A\nacc:");
+        appendNumber(target, idCount + 1);
+        write(target, "\ntyp:R\n");
+        if (!noNamesPresent)
+        {
+            write(target, "src:\n");
+            write(target, fragStore.readNameStore[idCount]);
+            write(target, "\n.\n");
+        }
+        write(target, "etm:0\nseq:\n");
+        writeWrappedString(target, fragStore.readSeqStore[idCount], 70);
+        write(target, ".\nqlt:\n");
+        typedef typename Value<typename TFragmentStore::TReadSeqStore>::Type TReadSeq;
+        typedef QualityExtractor<typename Value<TReadSeq>::Type> TQualityExtractor;
+        ModifiedString<TReadSeq const, ModView<TQualityExtractor> > quals(fragStore.readSeqStore[idCount]);
+        writeWrappedString(target, quals, 70);
+        // Note: Clear range does not have to be ordered, e.g. no indication for reverse complemented reads, this is happening in cgb records
+        write(target, ".\nclr:");
+        appendNumber(target, clearStr[idCount].i1);
+        writeValue(target, ',');
+        appendNumber(target, clearStr[idCount].i2);
+        write(target, "\n}\n");
+    }
 }
 
 
@@ -1910,62 +1822,48 @@ _writeCeleraFrg(TFile& target,
 
 // TODO(holtgrew): This is only used in seqcons, should it go into app?
 template<typename TFile, typename TSpec, typename TConfig>
-inline int
-_writeCeleraCgb(TFile& target,
-				FragmentStore<TSpec, TConfig>& fragStore)
+inline void
+_writeCeleraCgb(TFile& file,
+                FragmentStore<TSpec, TConfig>& fragStore)
 {
     typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename Id<TFragmentStore>::Type TId;
-	//typedef typename TFragmentStore::TReadPos TReadPos;
-
-	// Write the first contig
-	TId contigId = 0;
-
-	// Sort the reads according to position
-	sortAlignedReads(fragStore.alignedReadStore, SortBeginPos());
-
-	// Write Header
-	streamPut(target, "{IUM\nacc:0\nsrc:\ngen> @@ [0,0]\n.\ncov:0.000\nsta:X\nfur:X\nabp:0\nbbp:0\n");
-	streamPut(target, "len:");
-	streamPut(target, length((value(fragStore.contigStore, contigId)).seq));
-	streamWriteChar(target, '\n');
-	streamPut(target, "cns:\n.\nqlt:\n.\nfor:0\n");
-	streamPut(target, "nfr:");
-	streamPut(target, length(fragStore.readStore));
-	streamPut(target, '\n');
-
-	// Write reads
-	typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
-	TAlignIter alignIt = begin(fragStore.alignedReadStore);
-	TAlignIter alignItEnd = end(fragStore.alignedReadStore);
-	TSize offsetLeft = _min(alignIt->beginPos, alignIt->endPos);
-	for (;alignIt != alignItEnd; goNext(alignIt))
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename Id<TFragmentStore>::Type TId;
+    //typedef typename TFragmentStore::TReadPos TReadPos;
+
+    typename DirectionIterator<TFile, Output>::Type target = directionIterator(file, Output());
+
+    // Write the first contig
+    TId contigId = 0;
+
+    // Sort the reads according to position
+    sortAlignedReads(fragStore.alignedReadStore, SortBeginPos());
+
+    // Write Header
+    write(target, "{IUM\nacc:0\nsrc:\ngen> @@ [0,0]\n.\ncov:0.000\nsta:X\nfur:X\nabp:0\nbbp:0\nlen:");
+    appendNumber(target, length((value(fragStore.contigStore, contigId)).seq));
+    write(target, "\ncns:\n.\nqlt:\n.\nfor:0\nnfr:");
+    appendNumber(target, length(fragStore.readStore));
+    writeValue(target, '\n');
+
+    // Write reads
+    typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
+    TAlignIter alignIt = begin(fragStore.alignedReadStore);
+    TAlignIter alignItEnd = end(fragStore.alignedReadStore);
+    TSize offsetLeft = _min(alignIt->beginPos, alignIt->endPos);
+    for (;alignIt != alignItEnd; goNext(alignIt))
     {
-		if (contigId != alignIt->contigId)
+        if (contigId != alignIt->contigId)
             continue;
-		streamPut(target, "{IMP\n");
-		streamPut(target, "typ:");
-		streamPut(target, 'R');
-		streamPut(target, '\n');
-		streamPut(target, "mid:");
-		streamPut(target, alignIt->readId + 1);
-		streamPut(target, '\n');
-		streamPut(target, "con:");
-		streamPut(target, '0');
-		streamPut(target, '\n');
-		streamPut(target, "pos:");
-		streamPut(target, alignIt->beginPos - offsetLeft);
-		streamPut(target, ',');
-		streamPut(target, alignIt->endPos - offsetLeft);
-		streamPut(target, '\n');
-		streamPut(target, "dln:0\n");
-		streamPut(target, "del:\n");
-		streamPut(target, "}\n");
-	}
-	streamPut(target, "}\n");
-
-    return streamError(target);
+        write(target, "{IMP\ntyp:R\nmid:");
+        appendNumber(target, alignIt->readId + 1);
+        write(target, "\ncon:0\npos:");
+        appendNumber(target, alignIt->beginPos - offsetLeft);
+        writeValue(target, ',');
+        appendNumber(target, alignIt->endPos - offsetLeft);
+        write(target, "\ndln:0\ndel:\n}\n");
+    }
+    write(target, "}\n");
 }
 
 }  // namespace seqan
diff --git a/seqan/consensus/consensus_builder.h b/seqan/consensus/consensus_builder.h
new file mode 100644
index 0000000..38463b3
--- /dev/null
+++ b/seqan/consensus/consensus_builder.h
@@ -0,0 +1,494 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_BUILDER_H_
+#define INCLUDE_SEQAN_CONSENSUS_CONSENSUS_BUILDER_H_
+
+#include <map>
+
+#include <seqan/graph_types.h>
+#include <seqan/store.h>
+
+#include "consensus_alignment_options.h"
+#include "overlapper.h"
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Class ConsensusBuilder_
+// --------------------------------------------------------------------------
+
+template <typename TFragmentStore>
+class ConsensusBuilder_
+{
+public:
+    ConsensusBuilder_(ConsensusAlignmentOptions const & options) : options(options)
+    {}
+
+    void run(TFragmentStore & store, std::vector<OverlapInfo_> const & overlapInfos) const;
+
+private:
+
+    // Glorified pair<unsigned, int> with more verbose name for readID and offset.
+    struct AlignmentTarget
+    {
+        AlignmentTarget() : readID((unsigned)-1), offset(0) {}
+        AlignmentTarget(unsigned readID, int offset) : readID(readID), offset(offset) {}
+
+        unsigned readID;
+        int offset;
+    };
+
+    // Glorified triple for overlap computation.
+    struct PositionedRead
+    {
+        PositionedRead() : beginPos(0), endPos(0), readID((unsigned)-1) {}
+        PositionedRead(int beginPos, int endPos, unsigned readID) :
+            beginPos(beginPos), endPos(endPos), readID(readID)
+        {}
+
+        int beginPos;
+        int endPos;
+        unsigned readID;
+
+        bool operator<(PositionedRead const & other) const
+        {
+            return (std::make_pair(std::make_pair(beginPos, endPos), readID) <
+                    std::make_pair(std::make_pair(other.beginPos, other.endPos), other.readID));
+        }
+    };
+
+    // Shortcut for fragments.
+    typedef String<Fragment<> > TFragments;
+
+    // Compute pairwise overlaps for the reads of each contig in cg.
+    //
+    // In case that there are regions higher than options.startConsensusCompression, we add subsample these reads and
+    // write out an entry (other read id, offset) to use as a position marker in the resulting MSA.
+    void computeOverlaps(
+            TFragments & fragments,
+            String<int> & scores,
+            Graph<Undirected<double> > & distances,
+            TFragmentStore const & store,
+            std::vector<OverlapInfo_> const & overlapInfos) const;
+
+    // Configuration to use for consensus building.
+    ConsensusAlignmentOptions options;
+};
+
+template <typename TFragmentStore>
+void ConsensusBuilder_<TFragmentStore>::computeOverlaps(
+            typename ConsensusBuilder_<TFragmentStore>::TFragments & fragments,
+            String<int> & scores,
+            Graph<Undirected<double> > & distances,
+            TFragmentStore const & store,
+            std::vector<OverlapInfo_> const & overlapInfos) const
+{
+    // Configure overlapper, no limit in error rate or minimum length.
+    OverlapperOptions_ ovlOptions;
+    ovlOptions.logging = (options.verbosity >= 3);
+    ovlOptions.overlapErrorRate = options.overlapMaxErrorRate;
+    ovlOptions.overlapMinLength = options.overlapMinLength;  // accept all overlaps
+    typedef typename Value<typename TFragmentStore::TReadSeqStore const>::Type TReadSeq;
+    Overlapper_<String<Fragment<> >, TReadSeq> overlapper(ovlOptions);
+
+    for (std::vector<OverlapInfo_>::const_iterator it = overlapInfos.begin(); it != overlapInfos.end(); ++it)
+    {
+        Overlap_ ovl;
+        TFragments frags;
+        if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1],
+                                      OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors,
+                                                        it->pos1 + it->numErrors)))
+        {
+            append(fragments, frags);
+            int ovlScore = ovl.length() - ovl.errors;  // pseudo-score
+            resize(scores, length(fragments), ovlScore);
+            int quality = (ovl.length() > 0) ? (ovl.length() - ovl.errors) * 100 / ovl.length() : 0;
+            addEdge(distances, ovl.seq0, ovl.seq1, quality);
+        }
+    }
+}
+
+// ---------------------------------------------------------------------------
+// Function alignmentGraphToSmoothFragmentStore()
+// ---------------------------------------------------------------------------
+
+// Note that this function relies on the "all mated, adjacent reads" assumption.
+
+template <typename TFragmentStore, typename TSequence, typename TCargo, typename TSetSpec, typename TSpec>
+bool alignmentGraphToFragmentStore(TFragmentStore & store,
+                                   Graph<Alignment<StringSet<TSequence, TSetSpec>, TCargo, TSpec> > const & g,
+                                   Graph<Undirected<double> > const & distances,
+                                   String<unsigned> const & component,
+                                   String<unsigned> const & order,
+                                   unsigned numComponents,
+                                   bool logging)
+{
+    bool const DEBUG_INCONSISTENT_LEN = false;
+
+    // std::cerr << ">>>>>>>>>>>>\n<<<<<<<<<<<<<<<<\n";
+    // NOTE: seqToCluster is indexed by POSITION in the read set of g and not by the ID.
+
+    // TODO(holtgrew): This function is very similar to the updateStoreFromAlignmentGraph computeProfiles functions. Maybe we can share the commonality?
+    typedef Graph<Alignment<StringSet<TSequence, TSetSpec>, TCargo, TSpec> > TAlignmentGraph;
+
+    // -----------------------------------------------------------------------
+    // Get connected components of distances / read alignment clusters.
+    // -----------------------------------------------------------------------
+
+    // Each cluster corresponds to a contig.
+
+    // A cluster is a CC in the graph where each sequences is a vertex and two vertices are connected if they have an
+    // overlap alignment.
+    String<unsigned> seqToCluster;
+    if (logging)
+        std::cerr << "# vertices: " << numVertices(distances) << "\n"
+                  << "# edges: " << numEdges(distances) << "\n";
+    unsigned numClusters = connectedComponents(seqToCluster, distances);
+    if (logging)
+        std::cerr << "# clusters: " << numClusters << std::endl
+                  << "# components: " << numComponents << std::endl;
+    clear(store.contigStore);
+    resize(store.contigStore, numClusters);
+    String<unsigned> contigLengths;
+    resize(contigLengths, numClusters, 0);
+
+    for (unsigned i = 0; i < numClusters; ++i)
+    {
+        std::stringstream ss;
+        ss << "contig_" << i;
+        appendValue(store.contigNameStore, ss.str());
+    }
+
+    // -----------------------------------------------------------------------
+    // Visit components in topological order and generate profile sequences.
+    // -----------------------------------------------------------------------
+
+    // Get mapping from component to vertices.
+    String<String<unsigned> > componentVertices;
+    resize(componentVertices, numComponents);
+    typedef typename Iterator<TAlignmentGraph, VertexIterator>::Type TVertexIterator;
+    for (TVertexIterator itV(g); !atEnd(itV); goNext(itV))
+        appendValue(componentVertices[getProperty(component, *itV)], *itV);
+
+    // For each cluster, the currently overlapping reads.
+    std::vector<std::set<unsigned> > activeReads(numClusters);
+
+    std::vector<unsigned> gapCount(length(stringSet(g)), 0);
+
+    // Recreate alignedReadStore.
+    clear(store.alignedReadStore);
+    resize(store.alignedReadStore, length(store.readSeqStore));
+
+    // Iterate vertices in topological order.
+    for (typename Iterator<String<unsigned> const, Rooted>::Type it = begin(order, Rooted()); !atEnd(it); goNext(it))
+    {
+        unsigned c = *it;     // Current component.
+        unsigned fLen = fragmentLength(g, front(componentVertices[c]));
+        for (unsigned i = 1; i < length(componentVertices[c]); ++i)
+            SEQAN_ASSERT_EQ(fragmentLength(g, front(componentVertices[c][0])),
+                            fragmentLength(g, front(componentVertices[c][i])));
+        unsigned cl = seqToCluster[idToPosition(stringSet(g), sequenceId(g, front(componentVertices[c])))];  // Current cluster/contig.
+
+        // Update contig lengths.
+        unsigned from = contigLengths[cl];
+        contigLengths[cl] += fLen;
+        if (DEBUG_INCONSISTENT_LEN)
+            std::cerr << "==== c == " << c << "\n" << "     from == " << from << "\n";
+
+        // The currently active reads that we see in this round.  Required for inserting gaps below.
+        std::set<unsigned> seen;
+        std::set<unsigned> done;
+
+        // Insert gaps.
+        typedef typename Iterator<String<unsigned>, Rooted>::Type TDescIt;
+        for (TDescIt itV = begin(componentVertices[c], Rooted()); !atEnd(itV); goNext(itV))
+        {
+            unsigned idx = idToPosition(stringSet(g), sequenceId(g, *itV));
+            seen.insert(idx);
+            unsigned fBeg = fragmentBegin(g, *itV);
+            if (DEBUG_INCONSISTENT_LEN)
+                std::cerr << "           fBeg of " << *itV << " is " << fBeg << " (idx == " << idx << ")\n";
+
+            // Register sequence as supporting in profile cl starting at position from in profile.
+            if (fBeg == 0u)
+            {
+                activeReads[cl].insert(idx);
+                store.alignedReadStore[idx].id = idx;
+                store.alignedReadStore[idx].readId = idx;
+                store.alignedReadStore[idx].contigId = cl;
+                store.alignedReadStore[idx].beginPos = from;
+                store.alignedReadStore[idx].endPos = from;
+                // store.alignedReadStore[idx].pairMatchId = idx / 2;  // TODO(holtgrew): Set from read pair info.
+                if (DEBUG_INCONSISTENT_LEN)
+                {
+                    std::cerr << "store.alignedReadStore[" << idx << "].beginPos == " << from << " | *itV == " << *itV << "\n";
+                    std::cerr << "store.alignedReadStore[" << idx << "].endPos (= endPos) == " << from << "| *itV == " << *itV << "\n";
+                }
+            }
+            store.alignedReadStore[idx].endPos = from + fLen;
+            if (DEBUG_INCONSISTENT_LEN)
+                std::cerr << "store.alignedReadStore[" << idx << "].endPos = " << from << " + " << fLen << " == " << (from + fLen) << "| *itV == " << *itV << "\n";
+
+            unsigned fEnd = fBeg + fLen;
+
+            if (fEnd == length(stringSet(g)[idx]))
+                done.insert(idx);
+        }
+
+        // Get not seen reads.
+        typedef std::set<unsigned>::iterator TSetIt;
+        std::set<unsigned> notSeen;
+        for (TSetIt it = activeReads[cl].begin(); it != activeReads[cl].end(); ++it)
+            notSeen.insert(*it);
+        for (TSetIt it = seen.begin(); it != seen.end(); ++it)
+            notSeen.erase(*it);
+        // Insert gaps into these reads.
+        for (TSetIt itS = notSeen.begin(); itS != notSeen.end(); ++itS)
+        {
+            typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore;
+            typedef typename Value<TAlignedReadStore>::Type TAlignedRead;
+            typedef typename TAlignedRead::TGapAnchors TGapAnchors;
+            typedef typename TFragmentStore::TReadSeq TReadSeq;
+            SEQAN_ASSERT_NOT(empty(store.readSeqStore[*itS]));
+            Gaps<TReadSeq, AnchorGaps<TGapAnchors> > gaps(static_cast<TReadSeq>(store.readSeqStore[*itS]),
+                                                          store.alignedReadStore[*itS].gaps);
+            insertGaps(gaps, from - store.alignedReadStore[*itS].beginPos, fLen);
+            store.alignedReadStore[*itS].endPos += fLen;
+            if (DEBUG_INCONSISTENT_LEN)
+                std::cerr << "store.alignedReadStore[" << *itS << "].endPos += " << fLen << " == " << store.alignedReadStore[*itS].endPos << "\n";
+            gapCount[*itS] += fLen;
+            if (DEBUG_INCONSISTENT_LEN)
+                std::cerr << "gapCount[" << *itS << "] == " << gapCount[*itS] << "\n";
+        }
+
+        // Deactive done reads.
+        for (TSetIt it = done.begin(); it != done.end(); ++it)
+            activeReads[cl].erase(*it);
+    }
+
+// #if SEQAN_ENABLE_DEBUG
+    {
+        // Check for consistency.
+        typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore;
+        typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignedReadIter;
+        typedef typename TFragmentStore::TReadSeq           TReadSeq;
+
+        TAlignedReadIter itEnd = end(store.alignedReadStore, Standard());
+        for (TAlignedReadIter it2 = begin(store.alignedReadStore, Standard()); it2 != itEnd; ++it2)
+        {
+            typedef Gaps<TReadSeq, AnchorGaps<String<typename TFragmentStore::TReadGapAnchor> > > TReadGaps;
+            TReadGaps readGaps(static_cast<TReadSeq>(store.readSeqStore[it2->readId]), it2->gaps);
+            SEQAN_ASSERT_EQ(length(readGaps) - length(store.readSeqStore[it2->readId]), gapCount[it2->readId]);
+            if (DEBUG_INCONSISTENT_LEN)
+                std::cerr << "READ GAPS\t" << (it2 - begin(store.alignedReadStore, Standard())) << "\t>>>" << readGaps << "<<< (" << length(readGaps) << ")\n"
+                          << "  beginPos == " << it2->beginPos << ", endPos == " << it2->endPos << ", gapCount == " << gapCount[it2->readId] << "\n";
+            if ((unsigned)std::abs(it2->endPos - it2->beginPos) != length(readGaps))
+            {
+                SEQAN_FAIL("Inconsistent begin/endPos");
+            }
+        }
+    }
+// #endif  // #if SEQAN_ENABLE_DEBUG
+
+    return true;
+}
+
+template <typename TFragmentStore, typename TSequence, typename TCargo, typename TSetSpec, typename TSpec>
+bool alignmentGraphToFragmentStore(TFragmentStore & store,
+                                   Graph<Alignment<StringSet<TSequence, TSetSpec>, TCargo, TSpec> > const & g,
+                                   Graph<Undirected<double> > const & distances,
+                                   bool logging)
+{
+    typedef std::map<unsigned, unsigned> TComponentLength;
+
+    // -----------------------------------------------------------------------
+    // Compute connected components and get topological sorting of them.
+    // -----------------------------------------------------------------------
+      String<unsigned> component;
+      String<unsigned> order;
+      TComponentLength componentLength;
+    if (empty(g))
+        return true;  // Nothing to do for empty graphs.
+      if (!convertAlignment(g, component, order, componentLength))
+        return false;
+    unsigned numComponents = length(order);
+
+    return alignmentGraphToFragmentStore(store, g, distances, component, order, numComponents, logging);
+}
+
+template <typename TFragmentStore>
+void ConsensusBuilder_<TFragmentStore>::run(TFragmentStore & store,
+                                            std::vector<OverlapInfo_> const & overlapInfos) const
+{
+    // The alignments as required by consensus MSA module.
+    TFragments fragments;
+    String<int> scores;
+    Graph<Undirected<double> > distances;
+    _resizeWithRespectToDistance(distances, length(store.readSeqStore));
+
+    // Obtain alignments according to contig graph.
+    computeOverlaps(fragments, scores, distances, store, overlapInfos);
+
+    // Build copy of dependent reads.
+    typedef typename Value<typename TFragmentStore::TReadSeqStore>::Type TReadSeq;
+    StringSet<TReadSeq> seqs;
+    for (unsigned i = 0; i < length(store.readSeqStore); ++i)
+        appendValue(seqs, store.readSeqStore[i]);
+
+    // Build the alignment graph.
+    Score<int, Simple> msaScoringScheme(2, -6, -4, -9);  // TODO(holtgrew): Get from options!
+    typedef StringSet<TReadSeq, Dependent<> > TDepReadSet;
+    typedef Graph<Alignment<TDepReadSet, unsigned> > TInGraph;
+    TDepReadSet depSeqs(seqs);
+    TInGraph inGraph(depSeqs);
+    buildAlignmentGraph(fragments, scores, inGraph, msaScoringScheme, ReScore());
+
+    if (options.verbosity >= 2)
+        std::cerr << "Building alignment graph\n"
+                  << "  # fragments: " << length(fragments) << "\n"
+                  << "  # seqs: " << length(seqs) << "\n";
+
+    // Perform triplet library extension.
+    if (length(seqs) < 1000/*(unsigned)options.texStopCount*/)  // TODO(holtgrew): Clean up.
+        tripletLibraryExtension(inGraph);
+
+    Graph<Tree<double> > guideTree;
+    Graph<Undirected<double> > dCopy(distances);
+    upgmaTree(dCopy, guideTree);
+
+    // Perform progressive alignment.
+    if (options.verbosity >= 2)
+        std::cerr << "progressive alignment...\n";
+    TInGraph graph(depSeqs);
+    assignStringSet(graph, stringSet(inGraph));
+    progressiveAlignment(inGraph, guideTree, graph);
+
+    // Build alignment graph.
+    if (options.verbosity >= 2)
+        std::cerr << "build AG..\n";
+
+    String<unsigned> component;
+    String<unsigned> order;
+    std::map<unsigned, unsigned> componentLength;
+    SEQAN_ASSERT_NOT(empty(graph));
+    bool b = convertAlignment(graph, component, order, componentLength);
+    (void) b;
+    SEQAN_ASSERT(b);
+    unsigned numComponents = length(order);
+    if (options.verbosity >= 2)
+        std::cerr << "AG\n"
+                  << "  numVertices = " << numVertices(graph) << "\n"
+                  << "  numEdges = " << numEdges(graph) << "\n"
+                  << "  componentLength.size() = " << componentLength.size() << "\n"
+                  << "  numComponents = " << numComponents << "\n";
+
+    if (options.verbosity >= 2)
+        std::cerr << "build store..\n";
+    alignmentGraphToFragmentStore(store, graph, distances, component, order, numComponents,
+                                  /*logging=*/(options.verbosity >= 3));
+
+    if (options.verbosity >= 2)
+    {
+        std::cerr << "CONSENSUS RESULT\n";
+        typedef typename Iterator<typename TFragmentStore::TAlignedReadStore, Standard>::Type TAlignedReadIter;
+        for (TAlignedReadIter it = begin(store.alignedReadStore, Standard()); it != end(store.alignedReadStore, Standard()); ++it)
+            std::cerr << "contigID=" << it->contigId
+                      << ", beginPos=" << std::min(it->beginPos, it->endPos)
+                      << ", readID=" << it->readId
+                      << ", seq=" << store.readSeqStore[it->readId]
+                      << "\n";
+        std::cerr << "\n";
+
+
+    }
+
+    if (options.verbosity >= 2)
+    {
+        std::cerr << "before realignment\n";
+        seqan::AlignedReadLayout layout;
+        layoutAlignment(layout, store);
+        for (unsigned contigID = 0; contigID < length(store.contigStore); ++contigID)
+        {
+            int endPos = 0;
+            for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
+                if (store.alignedReadStore[i].contigId == contigID)
+                    endPos = std::max(endPos, (int)store.alignedReadStore[i].endPos);
+            std::cerr << ">contig_" << contigID << "\n";
+            printAlignment(std::cerr, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 30);
+        }
+    }
+
+    if (options.verbosity >= 2)
+        std::cerr << "realigning...\n";
+    for (unsigned i = 0; i < length(store.contigStore); ++i)
+        reAlignment(store, i, 1, 10, false);
+
+
+    if (options.verbosity >= 2)
+    {
+        std::cerr << "after realignment\n";
+        seqan::AlignedReadLayout layout;
+        layoutAlignment(layout, store);
+        for (unsigned contigID = 0; contigID < length(store.contigStore); ++contigID)
+        {
+            int endPos = 0;
+            for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
+                if (store.alignedReadStore[i].contigId == contigID)
+                    endPos = std::max(endPos, (int)store.alignedReadStore[i].endPos);
+            std::cerr << ">contig_" << contigID << "\n";
+            printAlignment(std::cerr, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 30);
+        }
+    }
+}
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_CONSENSUS_CONSENSUS_BUILDER_H_
diff --git a/seqan/consensus/consensus_library.h b/seqan/consensus/consensus_library.h
index 2356aeb..15f04ab 100644
--- a/seqan/consensus/consensus_library.h
+++ b/seqan/consensus/consensus_library.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,45 +41,45 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSize, typename TCargo1, typename TCargo2>
-inline void 
+inline void
 _getAlignmentStatistics(Nothing&,
-						 TSize,
-						 TSize,
-						 TSize,
-						 TCargo1,
-						 TCargo2)
+                         TSize,
+                         TSize,
+                         TSize,
+                         TCargo1,
+                         TCargo2)
 {
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TSpec, typename TSize, typename TCargo1, typename TCargo2>
-inline void 
+inline void
 _getAlignmentStatistics(String<TValue, TSpec>& dist,
-						 TSize i,
-						 TSize j,
-						 TSize nseq,
-						 TCargo1,
-						 TCargo2 quality)
+                         TSize i,
+                         TSize j,
+                         TSize nseq,
+                         TCargo1,
+                         TCargo2 quality)
 {
-	SEQAN_CHECKPOINT
-	dist[i*nseq + j] = (TValue) (100 - quality);
+    SEQAN_CHECKPOINT
+    dist[i*nseq + j] = (TValue) (100 - quality);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TSize, typename TCargo1, typename TCargo2>
-inline void 
+inline void
 _getAlignmentStatistics(Graph<Undirected<TCargo, TSpec> >& dist,
-						 TSize i,
-						 TSize j,
-						 TSize,
-						 TCargo1,
-						 TCargo2 quality)
+                         TSize i,
+                         TSize j,
+                         TSize,
+                         TCargo1,
+                         TCargo2 quality)
 {
-	SEQAN_CHECKPOINT
-	addEdge(dist, i, j, (TCargo) (100 - quality));
+    SEQAN_CHECKPOINT
+    addEdge(dist, i, j, (TCargo) (100 - quality));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -88,23 +88,23 @@ _getAlignmentStatistics(Graph<Undirected<TCargo, TSpec> >& dist,
 
 template<typename TSize>
 struct LessPair_ :
-	public ::std::unary_function<Pair<TSize, TSize>, bool>
+    public std::unary_function<Pair<TSize, TSize>, bool>
 {
-	inline bool 
-	operator() (Pair<TSize, TSize> const& a1, Pair<TSize, TSize> const& a2) const {
-		if (a1.i1 == a2.i1) return (a1.i2 < a2.i2);
-		else return (a1.i1 < a2.i1);
-	}
+    inline bool
+    operator() (Pair<TSize, TSize> const& a1, Pair<TSize, TSize> const& a2) const {
+        if (a1.i1 == a2.i1) return (a1.i2 < a2.i2);
+        else return (a1.i1 < a2.i1);
+    }
 };
 
 template<typename TSize>
 struct _LessTripel :
-	public ::std::unary_function<Pair<TSize, Triple<TSize, TSize, TSize> >, bool>
+    public std::unary_function<Pair<TSize, Triple<TSize, TSize, TSize> >, bool>
 {
-	inline bool 
-	operator() (Pair<TSize, Triple<TSize, TSize, TSize> > const& a1, Pair<TSize, Triple<TSize, TSize, TSize> > const& a2) {
-		return (a1.i1 < a2.i1);
-	}
+    inline bool
+    operator() (Pair<TSize, Triple<TSize, TSize, TSize> > const& a1, Pair<TSize, Triple<TSize, TSize, TSize> > const& a2) {
+        return (a1.i1 < a2.i1);
+    }
 };
 
 
@@ -113,216 +113,216 @@ struct _LessTripel :
 template<typename TString, typename TSpec, typename TBegEndPos, typename TSize, typename TPairList, typename TPos, typename TSpec2>
 inline void
 selectPairsAssembly(StringSet<TString, TSpec> const & str,
-			       TBegEndPos const & begEndPos,
-			       TSize bandwidth,
-			       TPairList & pList,
-			       String<Pair<TPos, TPos>, TSpec2> & dList)
+                   TBegEndPos const & begEndPos,
+                   TSize bandwidth,
+                   TPairList & pList,
+                   String<Pair<TPos, TPos>, TSpec2> & dList)
 {
-	typedef String<Pair<TPos, TPos>, TSpec2>  TDistanceList;
-	//typedef StringSet<TString, TSpec> TStringSet;
-	typedef Pair<TPos, TPos> TDiagPair;
-	typedef typename Value<TPairList>::Type TPair;
-	//typedef typename Iterator<TPairList, Standard>::Type TPairIter;
-	typedef typename Iterator<TBegEndPos const, Standard>::Type TBegEndIter;
+    typedef String<Pair<TPos, TPos>, TSpec2>  TDistanceList;
+    //typedef StringSet<TString, TSpec> TStringSet;
+    typedef Pair<TPos, TPos> TDiagPair;
+    typedef typename Value<TPairList>::Type TPair;
+    //typedef typename Iterator<TPairList, Standard>::Type TPairIter;
+    typedef typename Iterator<TBegEndPos const, Standard>::Type TBegEndIter;
 
-	// Initialization
-	TSize nseq = length(str);
+    // Initialization
+    TSize nseq = length(str);
 
-	// Workaround for strange celera behaviour (just for contained reads)
+    // Workaround for strange celera behaviour (just for contained reads)
 #ifdef CELERA_OFFSET
-	TSize contained_offset=200;
+    TSize contained_offset=200;
 #else
-	TSize contained_offset=0;
+    TSize contained_offset=0;
 #endif
-	
-	// Sort the reads by their first index position
-	TBegEndIter begEndIt = begin(begEndPos, Standard());
-	TBegEndIter begEndItEnd = end(begEndPos, Standard());
-	typedef Triple<TSize, TSize, TSize> TInfo;
-	typedef String<Pair<TSize, TInfo> > TPosIndexList;
-	typedef typename Iterator<TPosIndexList, Standard>::Type TPosIter;
-	TPosIndexList posIndex;
-	resize(posIndex, length(begEndPos));
-	TPosIter posIndexIt = begin(posIndex, Standard());
-	TPosIter posIndexItEnd = end(posIndex, Standard());
-	for(TSize index = 0;begEndIt != begEndItEnd; ++begEndIt, ++posIndexIt, ++index) 
-		*posIndexIt = ((*begEndIt).i1 < (*begEndIt).i2) ? Pair<TSize, TInfo>((*begEndIt).i1,TInfo(index, (*begEndIt).i1, (*begEndIt).i2)) : Pair<TSize, TInfo>((*begEndIt).i2,TInfo(index, (*begEndIt).i1, (*begEndIt).i2));
-	std::sort(begin(posIndex, Standard() ), end(posIndex, Standard() ), _LessTripel<TSize>() );
-
-	// The expected overlap by a pair of reads (represented by its index)
-	typedef String<Pair<TSize, TSize> > TOverlapIndexList;
-	TOverlapIndexList ovlIndex;
-	TSize pairLen = 0;  // Pair Counter
-	TPos const initialRadius = (bandwidth + 1) / 2;
-	TPos const lengthDivider = 5;	// Overlap / 2^lengthDivider is added to the radius
-
-	// Find all overlapping reads
-	TDistanceList preDList;
-	TPairList prePList;
-	reserve(preDList, nseq * 40);
-	reserve(prePList, nseq * 40);
-	reserve(ovlIndex, nseq * 40);
-	posIndexIt = begin(posIndex, Standard());
-	posIndexItEnd = end(posIndex, Standard());
-	for(;posIndexIt != posIndexItEnd; ++posIndexIt) {
-		TSize index1 = ((*posIndexIt).i2).i1;
-		TPos posIi1 = ((*posIndexIt).i2).i2;
-		TPos posIi2 = ((*posIndexIt).i2).i3;
-		bool forwardI = (posIi1 < posIi2) ? true : false;
-		TSize lenI = (posIi1 < posIi2) ? posIi2 - posIi1 : posIi1 - posIi2;
-		TPosIter posIndexIt2 = posIndexIt;
-		++posIndexIt2;
-		for(;posIndexIt2 != posIndexItEnd; ++posIndexIt2) {
-			if ((*posIndexIt).i1 + lenI <= (*posIndexIt2).i1) break;
-			TSize index2 = ((*posIndexIt2).i2).i1;
-			TPos posJi1 = ((*posIndexIt2).i2).i2;
-			TPos posJi2 = ((*posIndexIt2).i2).i3;
-
-			// Diagonal boundaries of the band
-			// Initialization values are used if one read is contained in the other 
-			TSize lenJ = (posJi1 < posJi2) ? posJi2 - posJi1 : posJi1 - posJi2;
-			bool forwardJ = (posJi1 < posJi2) ? true : false;
-			TPos diagLow = -1 * (TPos) lenJ;
-			TPos diagHigh = (TPos) lenI;
-			TPos radius = initialRadius;		// Increased by overlap length
-
-			// Read orientations
-			if (forwardI) {
-				// 1) Forward - Forward
-				if (forwardJ) {
-					if ((posJi2 < posIi2) && (posJi1 < posIi1)) {
-						TPos offset = (posIi1 - posJi1);
-						radius += (posJi2 - posJi1 - offset) >> lengthDivider;
-						if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
-						if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
-					} else if ((posJi1 > posIi1) && (posJi2 > posIi2)) {
-						TPos offset = (posJi1 - posIi1);
-						radius += (posIi2 - posIi1 - offset) >> lengthDivider;
-						if (offset + radius < diagHigh) diagHigh = offset + radius;
-						if (offset - radius > diagLow) diagLow = offset - radius;
-					} else {
-						radius += contained_offset;
-						if (posIi1 < posJi1) {
-							TPos offset = (posJi1 - posIi1);
-							radius += (posJi2 - posJi1) >> lengthDivider;
-							if (offset + radius < diagHigh) diagHigh = offset + radius;
-							if (offset - radius > diagLow) diagLow = offset - radius;
-						} else {
-							TPos offset = (posIi1 - posJi1);
-							radius += (posIi2 - posIi1) >> lengthDivider;
-							if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
-							if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
-						}
-					}
-				} else { // 2) Forward - Reverse
-					if ((posJi1 < posIi2) && (posJi2 < posIi1)) {
-						TPos offset = (posIi1 - posJi2);
-						radius += (posJi1 - posJi2 - offset) >> lengthDivider;
-						if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
-						if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
-					} else if ((posJi2 > posIi1) && (posJi1 > posIi2)) {
-						TPos offset = (posJi2 - posIi1);
-						radius += (posIi2 - posIi1 - offset) >> lengthDivider;
-						if (offset + radius < diagHigh) diagHigh = offset + radius;
-						if (offset - radius > diagLow) diagLow = offset - radius;
-					} else {
-						radius += contained_offset;  
-						if (posIi1 < posJi2) {
-							TPos offset = (posJi2 - posIi1);
-							radius += (posJi1 - posJi2) >> lengthDivider;
-							if (offset + radius < diagHigh) diagHigh = offset + radius;
-							if (offset - radius > diagLow) diagLow = offset - radius;
-						} else {
-							TPos offset = (posIi1 - posJi2);
-							radius += (posIi2 - posIi1) >> lengthDivider;
-							if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
-							if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
-						}	
-					}
-				}
-			} else { 
-				// 3) Reverse - Forward
-				if (forwardJ) {
-					if ((posIi1 > posJi2) && (posIi2 > posJi1)) {
-						TPos offset = (posIi2 - posJi1);
-						radius += (posJi2 - posJi1 - offset) >> lengthDivider;
-						if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
-						if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
-					} else if ((posJi1 > posIi2) && (posJi2 > posIi1)) {
-						TPos offset = (posJi1 - posIi2);
-						radius += (posIi1 - posIi2 - offset) >> lengthDivider;
-						if (offset + radius < diagHigh) diagHigh = offset + radius;
-						if (offset - radius > diagLow) diagLow = offset - radius;
-					} else {
-						radius += contained_offset;  
-						if (posIi2 < posJi1) {
-							TPos offset = (posJi1 - posIi2);
-							radius += (posJi2 - posJi1) >> lengthDivider;
-							if (offset + radius < diagHigh) diagHigh = offset + radius;
-							if (offset - radius > diagLow) diagLow = offset - radius;
-						} else {
-							TPos offset = (posIi2 - posJi1);
-							radius += (posIi1 - posIi2) >> lengthDivider;
-							if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
-							if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
-						}
-					}
-				} else { // 4) Reverse - Reverse
-					if ((posJi1 < posIi1) && (posJi2 < posIi2)) {
-						TPos offset = (posIi2 - posJi2);
-						radius += (posJi1 - posJi2 - offset) >> lengthDivider;
-						if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
-						if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
-					} else if ((posJi2 > posIi2) && (posJi1 > posIi1)) {
-						TPos offset = (posJi2 - posIi2);
-						radius += (posIi1 - posIi2 - offset) >> lengthDivider;
-						if (offset + radius < diagHigh) diagHigh = offset + radius;
-						if (offset - radius > diagLow) diagLow = offset - radius;
-					} else {
-						radius += contained_offset;  
-						if (posIi2 < posJi2) {
-							TPos offset = (posJi2 - posIi2);
-							radius += (posJi1 - posJi2) >> lengthDivider;
-							if (offset + radius < diagHigh) diagHigh = offset + radius;
-							if (offset - radius > diagLow) diagLow = offset - radius;
-						} else {
-							TPos offset = (posIi2 - posJi2);
-							radius += (posIi1 - posIi2) >> lengthDivider;
-							if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
-							if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
-						}
-					}
-				}
-			}
-
-			// Append this pair of reads
-			if (index1 < index2) {
-				appendValue(prePList, TPair(positionToId(str, index1), positionToId(str, index2)), Generous());
-				appendValue(preDList, TDiagPair(diagLow, diagHigh), Generous());
-			} else {
-				appendValue(prePList, TPair(positionToId(str, index2), positionToId(str, index1)), Generous());
-				appendValue(preDList, TDiagPair(-1 * diagHigh, -1 * diagLow), Generous());
-			}
-			// Estimate the overlap quality
-			TPos avgDiag = (diagLow + diagHigh) / 2;
-			if (avgDiag < 0) avgDiag *= -1;
-			appendValue(ovlIndex, Pair<TSize, TSize>((TSize) (avgDiag), pairLen), Generous()); 
-			++pairLen;
-		}
-	}
-
-	// Sort the pairs, better expected overlaps come first
-	std::sort(begin(ovlIndex, Standard() ), end(ovlIndex, Standard() ), LessPair_<TSize>() );
-	typedef typename Iterator<TOverlapIndexList, Standard>::Type TOVLIter;
-	TOVLIter itOvl = begin(ovlIndex, Standard());
-	TOVLIter itOvlEnd = end(ovlIndex, Standard());
-	reserve(dList, pairLen);
-	reserve(pList, pairLen);
-	for(;itOvl != itOvlEnd; ++itOvl) {
-		TSize count = (*itOvl).i2;
-		appendValue(dList, preDList[count], Generous());
-		appendValue(pList, prePList[count], Generous());
-	}
+
+    // Sort the reads by their first index position
+    TBegEndIter begEndIt = begin(begEndPos, Standard());
+    TBegEndIter begEndItEnd = end(begEndPos, Standard());
+    typedef Triple<TSize, TSize, TSize> TInfo;
+    typedef String<Pair<TSize, TInfo> > TPosIndexList;
+    typedef typename Iterator<TPosIndexList, Standard>::Type TPosIter;
+    TPosIndexList posIndex;
+    resize(posIndex, length(begEndPos));
+    TPosIter posIndexIt = begin(posIndex, Standard());
+    TPosIter posIndexItEnd = end(posIndex, Standard());
+    for(TSize index = 0;begEndIt != begEndItEnd; ++begEndIt, ++posIndexIt, ++index)
+        *posIndexIt = ((*begEndIt).i1 < (*begEndIt).i2) ? Pair<TSize, TInfo>((*begEndIt).i1,TInfo(index, (*begEndIt).i1, (*begEndIt).i2)) : Pair<TSize, TInfo>((*begEndIt).i2,TInfo(index, (*begEndIt).i1, (*begEndIt).i2));
+    std::sort(begin(posIndex, Standard() ), end(posIndex, Standard() ), _LessTripel<TSize>() );
+
+    // The expected overlap by a pair of reads (represented by its index)
+    typedef String<Pair<TSize, TSize> > TOverlapIndexList;
+    TOverlapIndexList ovlIndex;
+    TSize pairLen = 0;  // Pair Counter
+    TPos const initialRadius = (bandwidth + 1) / 2;
+    TPos const lengthDivider = 5;    // Overlap / 2^lengthDivider is added to the radius
+
+    // Find all overlapping reads
+    TDistanceList preDList;
+    TPairList prePList;
+    reserve(preDList, nseq * 40);
+    reserve(prePList, nseq * 40);
+    reserve(ovlIndex, nseq * 40);
+    posIndexIt = begin(posIndex, Standard());
+    posIndexItEnd = end(posIndex, Standard());
+    for(;posIndexIt != posIndexItEnd; ++posIndexIt) {
+        TSize index1 = ((*posIndexIt).i2).i1;
+        TPos posIi1 = ((*posIndexIt).i2).i2;
+        TPos posIi2 = ((*posIndexIt).i2).i3;
+        bool forwardI = (posIi1 < posIi2) ? true : false;
+        TSize lenI = (posIi1 < posIi2) ? posIi2 - posIi1 : posIi1 - posIi2;
+        TPosIter posIndexIt2 = posIndexIt;
+        ++posIndexIt2;
+        for(;posIndexIt2 != posIndexItEnd; ++posIndexIt2) {
+            if ((*posIndexIt).i1 + lenI <= (*posIndexIt2).i1) break;
+            TSize index2 = ((*posIndexIt2).i2).i1;
+            TPos posJi1 = ((*posIndexIt2).i2).i2;
+            TPos posJi2 = ((*posIndexIt2).i2).i3;
+
+            // Diagonal boundaries of the band
+            // Initialization values are used if one read is contained in the other
+            TSize lenJ = (posJi1 < posJi2) ? posJi2 - posJi1 : posJi1 - posJi2;
+            bool forwardJ = (posJi1 < posJi2) ? true : false;
+            TPos diagLow = -1 * (TPos) lenJ;
+            TPos diagHigh = (TPos) lenI;
+            TPos radius = initialRadius;        // Increased by overlap length
+
+            // Read orientations
+            if (forwardI) {
+                // 1) Forward - Forward
+                if (forwardJ) {
+                    if ((posJi2 < posIi2) && (posJi1 < posIi1)) {
+                        TPos offset = (posIi1 - posJi1);
+                        radius += (posJi2 - posJi1 - offset) >> lengthDivider;
+                        if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
+                        if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
+                    } else if ((posJi1 > posIi1) && (posJi2 > posIi2)) {
+                        TPos offset = (posJi1 - posIi1);
+                        radius += (posIi2 - posIi1 - offset) >> lengthDivider;
+                        if (offset + radius < diagHigh) diagHigh = offset + radius;
+                        if (offset - radius > diagLow) diagLow = offset - radius;
+                    } else {
+                        radius += contained_offset;
+                        if (posIi1 < posJi1) {
+                            TPos offset = (posJi1 - posIi1);
+                            radius += (posJi2 - posJi1) >> lengthDivider;
+                            if (offset + radius < diagHigh) diagHigh = offset + radius;
+                            if (offset - radius > diagLow) diagLow = offset - radius;
+                        } else {
+                            TPos offset = (posIi1 - posJi1);
+                            radius += (posIi2 - posIi1) >> lengthDivider;
+                            if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
+                            if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
+                        }
+                    }
+                } else { // 2) Forward - Reverse
+                    if ((posJi1 < posIi2) && (posJi2 < posIi1)) {
+                        TPos offset = (posIi1 - posJi2);
+                        radius += (posJi1 - posJi2 - offset) >> lengthDivider;
+                        if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
+                        if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
+                    } else if ((posJi2 > posIi1) && (posJi1 > posIi2)) {
+                        TPos offset = (posJi2 - posIi1);
+                        radius += (posIi2 - posIi1 - offset) >> lengthDivider;
+                        if (offset + radius < diagHigh) diagHigh = offset + radius;
+                        if (offset - radius > diagLow) diagLow = offset - radius;
+                    } else {
+                        radius += contained_offset;
+                        if (posIi1 < posJi2) {
+                            TPos offset = (posJi2 - posIi1);
+                            radius += (posJi1 - posJi2) >> lengthDivider;
+                            if (offset + radius < diagHigh) diagHigh = offset + radius;
+                            if (offset - radius > diagLow) diagLow = offset - radius;
+                        } else {
+                            TPos offset = (posIi1 - posJi2);
+                            radius += (posIi2 - posIi1) >> lengthDivider;
+                            if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
+                            if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
+                        }
+                    }
+                }
+            } else {
+                // 3) Reverse - Forward
+                if (forwardJ) {
+                    if ((posIi1 > posJi2) && (posIi2 > posJi1)) {
+                        TPos offset = (posIi2 - posJi1);
+                        radius += (posJi2 - posJi1 - offset) >> lengthDivider;
+                        if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
+                        if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
+                    } else if ((posJi1 > posIi2) && (posJi2 > posIi1)) {
+                        TPos offset = (posJi1 - posIi2);
+                        radius += (posIi1 - posIi2 - offset) >> lengthDivider;
+                        if (offset + radius < diagHigh) diagHigh = offset + radius;
+                        if (offset - radius > diagLow) diagLow = offset - radius;
+                    } else {
+                        radius += contained_offset;
+                        if (posIi2 < posJi1) {
+                            TPos offset = (posJi1 - posIi2);
+                            radius += (posJi2 - posJi1) >> lengthDivider;
+                            if (offset + radius < diagHigh) diagHigh = offset + radius;
+                            if (offset - radius > diagLow) diagLow = offset - radius;
+                        } else {
+                            TPos offset = (posIi2 - posJi1);
+                            radius += (posIi1 - posIi2) >> lengthDivider;
+                            if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
+                            if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
+                        }
+                    }
+                } else { // 4) Reverse - Reverse
+                    if ((posJi1 < posIi1) && (posJi2 < posIi2)) {
+                        TPos offset = (posIi2 - posJi2);
+                        radius += (posJi1 - posJi2 - offset) >> lengthDivider;
+                        if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
+                        if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
+                    } else if ((posJi2 > posIi2) && (posJi1 > posIi1)) {
+                        TPos offset = (posJi2 - posIi2);
+                        radius += (posIi1 - posIi2 - offset) >> lengthDivider;
+                        if (offset + radius < diagHigh) diagHigh = offset + radius;
+                        if (offset - radius > diagLow) diagLow = offset - radius;
+                    } else {
+                        radius += contained_offset;
+                        if (posIi2 < posJi2) {
+                            TPos offset = (posJi2 - posIi2);
+                            radius += (posJi1 - posJi2) >> lengthDivider;
+                            if (offset + radius < diagHigh) diagHigh = offset + radius;
+                            if (offset - radius > diagLow) diagLow = offset - radius;
+                        } else {
+                            TPos offset = (posIi2 - posJi2);
+                            radius += (posIi1 - posIi2) >> lengthDivider;
+                            if (-1 * offset + radius < diagHigh) diagHigh = -1 * offset + radius;
+                            if (-1 * offset - radius > diagLow) diagLow = -1 * offset - radius;
+                        }
+                    }
+                }
+            }
+
+            // Append this pair of reads
+            if (index1 < index2) {
+                appendValue(prePList, TPair(positionToId(str, index1), positionToId(str, index2)), Generous());
+                appendValue(preDList, TDiagPair(diagLow, diagHigh), Generous());
+            } else {
+                appendValue(prePList, TPair(positionToId(str, index2), positionToId(str, index1)), Generous());
+                appendValue(preDList, TDiagPair(-1 * diagHigh, -1 * diagLow), Generous());
+            }
+            // Estimate the overlap quality
+            TPos avgDiag = (diagLow + diagHigh) / 2;
+            if (avgDiag < 0) avgDiag *= -1;
+            appendValue(ovlIndex, Pair<TSize, TSize>((TSize) (avgDiag), pairLen), Generous());
+            ++pairLen;
+        }
+    }
+
+    // Sort the pairs, better expected overlaps come first
+    std::sort(begin(ovlIndex, Standard() ), end(ovlIndex, Standard() ), LessPair_<TSize>() );
+    typedef typename Iterator<TOverlapIndexList, Standard>::Type TOVLIter;
+    TOVLIter itOvl = begin(ovlIndex, Standard());
+    TOVLIter itOvlEnd = end(ovlIndex, Standard());
+    reserve(dList, pairLen);
+    reserve(pList, pairLen);
+    for(;itOvl != itOvlEnd; ++itOvl) {
+        TSize count = (*itOvl).i2;
+        appendValue(dList, preDList[count], Generous());
+        appendValue(pList, prePList[count], Generous());
+    }
 }
 
 
@@ -330,246 +330,246 @@ selectPairsAssembly(StringSet<TString, TSpec> const & str,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename TBegEndPos, typename TSize, typename TPairList, typename TPos, typename TSpec2>
-inline void 
+inline void
 selectPairsAllAgainstAll(StringSet<TString, TSpec> const & str,
-				         TBegEndPos const & begEndPos,
-				         TSize lookAround,
-				         TPairList& pList,
-				         String<Pair<TPos, TPos>, TSpec2> & dList)
+                         TBegEndPos const & begEndPos,
+                         TSize lookAround,
+                         TPairList& pList,
+                         String<Pair<TPos, TPos>, TSpec2> & dList)
 {
-	//typedef String<Pair<TPos, TPos>, TSpec2>  TDistanceList;
-	//typedef StringSet<TString, TSpec> TStringSet;
-	typedef Pair<TPos, TPos> TDiagPair;
-	typedef typename Value<TPairList>::Type TPair;
-	typedef typename Iterator<TBegEndPos const, Standard>::Type TBegEndIter;
-	
-	TBegEndIter beIt = begin(begEndPos, Standard());
-	TBegEndIter beItEnd = end(begEndPos, Standard());
-	TSize index1 = 0;
-	for(;beIt != beItEnd; ++beIt, ++index1) {
-		TPos beg2 = (beIt->i2 < beIt->i1) ? beIt->i2 : beIt->i1;
-		TPos diagHigh = (beIt->i2 < beIt->i1) ? beIt->i1 - beIt->i2 : beIt->i2 - beIt->i1;
-		TBegEndIter beIt2 = beIt;
-		TSize index2 = index1 + 1;
-		for(;++beIt2 != beItEnd; ++index2) {
-			TPos beg1 = (beIt2->i2 < beIt2->i1) ? beIt2->i2 : beIt2->i1;
-			TPos diagLow = (beIt2->i2 < beIt2->i1) ? beIt2->i2 - beIt2->i1 : beIt2->i1 - beIt2->i2;
-			TPos diff = (beg1 > beg2) ? beg1 - beg2 : beg2 - beg1;
-			if (diff < (TPos) lookAround) {
-				appendValue(pList, TPair(positionToId(str, index1), positionToId(str, index2)), Generous());
-				appendValue(dList, TDiagPair(diagLow, diagHigh), Generous());
-			}
-		}
-	}
+    //typedef String<Pair<TPos, TPos>, TSpec2>  TDistanceList;
+    //typedef StringSet<TString, TSpec> TStringSet;
+    typedef Pair<TPos, TPos> TDiagPair;
+    typedef typename Value<TPairList>::Type TPair;
+    typedef typename Iterator<TBegEndPos const, Standard>::Type TBegEndIter;
+
+    TBegEndIter beIt = begin(begEndPos, Standard());
+    TBegEndIter beItEnd = end(begEndPos, Standard());
+    TSize index1 = 0;
+    for(;beIt != beItEnd; ++beIt, ++index1) {
+        TPos beg2 = (beIt->i2 < beIt->i1) ? beIt->i2 : beIt->i1;
+        TPos diagHigh = (beIt->i2 < beIt->i1) ? beIt->i1 - beIt->i2 : beIt->i2 - beIt->i1;
+        TBegEndIter beIt2 = beIt;
+        TSize index2 = index1 + 1;
+        for(;++beIt2 != beItEnd; ++index2) {
+            TPos beg1 = (beIt2->i2 < beIt2->i1) ? beIt2->i2 : beIt2->i1;
+            TPos diagLow = (beIt2->i2 < beIt2->i1) ? beIt2->i2 - beIt2->i1 : beIt2->i1 - beIt2->i2;
+            TPos diff = (beg1 > beg2) ? beg1 - beg2 : beg2 - beg1;
+            if (diff < (TPos) lookAround) {
+                appendValue(pList, TPair(positionToId(str, index1), positionToId(str, index2)), Generous());
+                appendValue(dList, TDiagPair(diagLow, diagHigh), Generous());
+            }
+        }
+    }
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename TId, typename TDiagList, typename TBegEndPos, typename TScore, typename TSize, typename TSegmentMatches, typename TScoreValues, typename TDistance>
-inline void 
+inline void
 appendSegmentMatches(StringSet<TString, TSpec> const & str,
-					 String<Pair<TId, TId> > const & pList,
-					 TDiagList const & dList,
-					 TBegEndPos const & begEndPos,
-					 TScore const & score_type,
-					 TSize thresholdMatchlength,
-					 TSize thresholdQuality,
-					 TSize maxOvl,
-					 TSegmentMatches & matches,
-					 TScoreValues & scores,
-					 TDistance & dist,
-					 OverlapLibrary)
+                     String<Pair<TId, TId> > const & pList,
+                     TDiagList const & dList,
+                     TBegEndPos const & begEndPos,
+                     TScore const & score_type,
+                     TSize thresholdMatchlength,
+                     TSize thresholdQuality,
+                     TSize maxOvl,
+                     TSegmentMatches & matches,
+                     TScoreValues & scores,
+                     TDistance & dist,
+                     OverlapLibrary)
 {
-	typedef StringSet<TString, Dependent<> > TStringSet;
-	typedef String<Pair<TId, TId> > const TPairList;
-	typedef typename Value<TScoreValues>::Type TScoreValue;
-	typedef typename Iterator<TPairList, Standard>::Type TPairIter;
-	typedef typename Iterator<TDiagList const, Standard>::Type TDiagIter;
-
-	// Initialization
-	TSize nseq = length(str);
-	_resizeWithRespectToDistance(dist, nseq);
-
-	// "Front" and "Back"-overlap counter for each read
-	String<TSize> frontOvl;
-	String<TSize> backOvl;
-	resize(frontOvl, nseq, 0);
-	resize(backOvl, nseq, 0);
-	
-	// Pairwise alignments
-	String<bool> aligned;
-	resize(aligned, length(pList), true);
-	typedef Iterator<String<bool>, Standard>::Type TBoolIter;
-	TBoolIter itAligned = begin(aligned, Standard());
-	TPairIter itPair = begin(pList, Standard());
-	TDiagIter itDiag = begin(dList, Standard());
-	TPairIter itPairEnd = end(pList, Standard());
-	TSize dropCount = 0;
-	for(;itPair != itPairEnd; ++itPair, ++itDiag, ++itAligned) {
-		TId id1 = itPair->i1;
-		TId id2 = itPair->i2;
-		TSize seq1 = idToPosition(str, id1);
-		TSize seq2 = idToPosition(str, id2);
-		if ((frontOvl[seq1] > maxOvl) && (backOvl[seq1] > maxOvl) &&
-			(frontOvl[seq2] > maxOvl) && (backOvl[seq2] > maxOvl)) {
-				++dropCount;
-				continue;
-		}
-
-
-		// Make a pairwise string-set
-		TStringSet pairSet;
-		assignValueById(pairSet, const_cast<StringSet<TString, TSpec>&>(str), id1);
-		assignValueById(pairSet, const_cast<StringSet<TString, TSpec>&>(str), id2);
-		
-
-		// Overlap alignment
-		TSize from = length(matches);
-		TScoreValue myScore = globalAlignment(matches, pairSet, score_type, AlignConfig<true,true,true,true>(), itDiag->i1, itDiag->i2, Gotoh() );
-		TSize to = length(matches);
-
-		// Determine a sequence weight
-		TSize matchLen = 0;
-		TSize overlapLen = 0;
-		TSize alignLen = 0;
-		if (from != to) getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen);
-
-
-		// Get only the good overlap alignments
-		if ((overlapLen) && ((matchLen * 100) / overlapLen >= thresholdQuality) && (matchLen >= thresholdMatchlength)) {
-
-			//// Debug Code
-			//Graph<Alignment<TStringSet, TSize> > tmp(pairSet);
-			//globalAlignment(tmp, pairSet, score_type, AlignConfig<true,true,true,true>(), (value(itDiag)).i1, (value(itDiag)).i2, Gotoh() );
-			////globalAlignment(tmp, pairSet, score_type, Gotoh() );
-			//std::cout << "Match length: " << matchLen << std::endl;
-			//std::cout << "Overlap length: " << overlapLen << std::endl;
-			//std::cout << "Align length: " << alignLen << std::endl;
-			//std::cout << "Quality: " << quality << std::endl;
-			//std::cout << tmp << std::endl;
-
-			// Create a corresponding edge
-			if (seq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen);
-			else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen);
-			
-			// Record the scores
-			resize(scores, to);
-			typedef typename Iterator<TScoreValues, Standard>::Type TScoreIter;
-			TScoreIter itScore = begin(scores, Standard());
-			TScoreIter itScoreEnd = end(scores, Standard());
-			itScore += from;
-			for(;itScore != itScoreEnd; ++itScore) 
-				*itScore = myScore;
-
-			// Update the overlap counter
-			TSize lenLast = matches[from].len; 
-			if (matches[to - 1].begin1 == 0) ++frontOvl[seq1];
-			if (matches[to - 1].begin2 == 0) ++frontOvl[seq2];
-			if (matches[from].begin1 + lenLast == length(pairSet[0])) ++backOvl[seq1];
-			if (matches[from].begin2 + lenLast == length(pairSet[1])) ++backOvl[seq2];
-		} else {
-			resize(matches, from);
-			*itAligned = false;
-		}
-	}
-	//std::cout << "Filtration ration: " << (double) dropCount / (double) length(pList) << std::endl;
-
-	// Find sequences that have no overlap in the front or back
-	String<TSize> noFront;
-	String<TSize> noBack;
-	for(TSize seqI = 0; seqI < nseq; ++seqI) {
-		if (frontOvl[seqI] == 0) appendValue(noFront, seqI, Generous());
-		else if (backOvl[seqI] == 0) appendValue(noBack, seqI, Generous());
-	}
-	// Drop the first and the last sequence
-	typedef typename Iterator<TBegEndPos const, Standard>::Type TBegEndIter;
-	TBegEndIter begEndIt = begin(begEndPos, Standard());
-	TBegEndIter begEndItEnd = end(begEndPos, Standard());
-	TSize minVal = maxValue<TSize>();
-	TSize maxVal = 0;
-	for(;begEndIt != begEndItEnd; ++begEndIt) {
-		TSize pos1 = begEndIt->i1;
-		TSize pos2 = begEndIt->i2;
-		if (pos1 > pos2) { TSize tmp = pos1; pos1 = pos2; pos2 = tmp;}
-		if (pos1 < minVal) minVal = pos1;
-		if (pos2 > maxVal) maxVal = pos2;
-	}
-	// Insert all remaining sequences into a string
-	String<TSize> unalignedReads;
-	for(TSize i = 0; i < (TSize) length(noFront); ++i) {
-		TSize p1 = begEndPos[noFront[i]].i1;
-		TSize p2 = begEndPos[noFront[i]].i2;
-		if (p1 > p2) {TSize tmp = p1; p1 = p2; p2 = tmp; }
-		if (p1 != minVal) appendValue(unalignedReads, noFront[i], Generous());
-	}
-	for(TSize i = 0; i < (TSize) length(noBack); ++i) {
-		TSize p1 = begEndPos[noBack[i]].i1;
-		TSize p2 = begEndPos[noBack[i]].i2;
-		if (p1 > p2) {TSize tmp = p1; p1 = p2; p2 = tmp; }
-		if (p2 != maxVal) appendValue(unalignedReads, noBack[i], Generous());
-	}
-	TSize countUnalignedReads = length(unalignedReads);
-	//std::cout << "Unaligned reads: " << countUnalignedReads << std::endl;
-	if (countUnalignedReads > 0) {
-		// Sort unaligned reads
-		::std::sort(begin(unalignedReads, Standard()), end(unalignedReads, Standard()));
-		
-		// Realign all unaligned sequences
-		itPair = begin(pList, Standard());
-		itDiag = begin(dList, Standard());
-		itAligned = begin(aligned, Standard());
-		for(;itPair != itPairEnd; ++itPair, ++itDiag, ++itAligned) {
-			if (*itAligned == true) continue;
-			TId id1 = itPair->i1;
-			TId id2 = itPair->i2;
-			TSize seq1 = idToPosition(str, id1);
-			TSize seq2 = idToPosition(str, id2);
-			if ((!::std::binary_search(begin(unalignedReads, Standard()), end(unalignedReads, Standard()), seq1)) &&
-				(!::std::binary_search(begin(unalignedReads, Standard()), end(unalignedReads, Standard()), seq2))) 
-				continue;
-			if ((frontOvl[seq1] > maxOvl) && (backOvl[seq1] > maxOvl) &&
-				(frontOvl[seq2] > maxOvl) && (backOvl[seq2] > maxOvl)) 
-				continue;
-
-			// Make a pairwise string-set
-			TStringSet pairSet;
-			assignValueById(pairSet, const_cast<StringSet<TString, TSpec>&>(str), id1);
-			assignValueById(pairSet, const_cast<StringSet<TString, TSpec>&>(str), id2);
-		
-			// Overlap alignment
-			TSize from = length(matches);
-			TScoreValue myScore = globalAlignment(matches, pairSet, score_type, AlignConfig<true,true,true,true>(), Gotoh() );
-			TSize to = length(matches);
-
-			// Determine a sequence weight
-			TSize matchLen = 0;
-			TSize overlapLen = 0;
-			TSize alignLen = 0;
-			getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen);
-
-			if (((matchLen * 100) / overlapLen >= 80) && (matchLen >= 5)) {
-				// Create a corresponding edge
-				if (seq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen);
-				else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen);
-
-				// Record the scores
-				resize(scores, to);
-				typedef typename Iterator<TScoreValues, Standard>::Type TScoreIter;
-				TScoreIter itScore = begin(scores, Standard());
-				TScoreIter itScoreEnd = end(scores, Standard());
-				itScore+=from;
-				for(;itScore != itScoreEnd; ++itScore) *itScore = myScore;
-
-				// Update the overlap counter
-				TSize lenLast = matches[from].len; 
-				if (matches[to - 1].begin1 == 0) ++frontOvl[seq1];
-				if (matches[to - 1].begin2 == 0) ++frontOvl[seq2];
-				if (matches[from].begin1 + lenLast == length(pairSet[0])) ++backOvl[seq1];
-				if (matches[from].begin2 + lenLast == length(pairSet[1])) ++backOvl[seq2];
-			} else resize(matches, from);
-		}
-	}
+    typedef StringSet<TString, Dependent<> > TStringSet;
+    typedef String<Pair<TId, TId> > const TPairList;
+    typedef typename Value<TScoreValues>::Type TScoreValue;
+    typedef typename Iterator<TPairList, Standard>::Type TPairIter;
+    typedef typename Iterator<TDiagList const, Standard>::Type TDiagIter;
+
+    // Initialization
+    TSize nseq = length(str);
+    _resizeWithRespectToDistance(dist, nseq);
+
+    // "Front" and "Back"-overlap counter for each read
+    String<TSize> frontOvl;
+    String<TSize> backOvl;
+    resize(frontOvl, nseq, 0);
+    resize(backOvl, nseq, 0);
+
+    // Pairwise alignments
+    String<bool> aligned;
+    resize(aligned, length(pList), true);
+    typedef Iterator<String<bool>, Standard>::Type TBoolIter;
+    TBoolIter itAligned = begin(aligned, Standard());
+    TPairIter itPair = begin(pList, Standard());
+    TDiagIter itDiag = begin(dList, Standard());
+    TPairIter itPairEnd = end(pList, Standard());
+    TSize dropCount = 0;
+    for(;itPair != itPairEnd; ++itPair, ++itDiag, ++itAligned) {
+        TId id1 = itPair->i1;
+        TId id2 = itPair->i2;
+        TSize seq1 = idToPosition(str, id1);
+        TSize seq2 = idToPosition(str, id2);
+        if ((frontOvl[seq1] > maxOvl) && (backOvl[seq1] > maxOvl) &&
+            (frontOvl[seq2] > maxOvl) && (backOvl[seq2] > maxOvl)) {
+                ++dropCount;
+                continue;
+        }
+
+
+        // Make a pairwise string-set
+        TStringSet pairSet;
+        assignValueById(pairSet, const_cast<StringSet<TString, TSpec>&>(str), id1);
+        assignValueById(pairSet, const_cast<StringSet<TString, TSpec>&>(str), id2);
+
+
+        // Overlap alignment
+        TSize from = length(matches);
+        TScoreValue myScore = globalAlignment(matches, pairSet, score_type, AlignConfig<true,true,true,true>(), itDiag->i1, itDiag->i2, Gotoh() );
+        TSize to = length(matches);
+
+        // Determine a sequence weight
+        TSize matchLen = 0;
+        TSize overlapLen = 0;
+        TSize alignLen = 0;
+        if (from != to) getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen);
+
+
+        // Get only the good overlap alignments
+        if ((overlapLen) && ((matchLen * 100) / overlapLen >= thresholdQuality) && (matchLen >= thresholdMatchlength)) {
+
+            //// Debug Code
+            //Graph<Alignment<TStringSet, TSize> > tmp(pairSet);
+            //globalAlignment(tmp, pairSet, score_type, AlignConfig<true,true,true,true>(), (value(itDiag)).i1, (value(itDiag)).i2, Gotoh() );
+            ////globalAlignment(tmp, pairSet, score_type, Gotoh() );
+            //std::cout << "Match length: " << matchLen << std::endl;
+            //std::cout << "Overlap length: " << overlapLen << std::endl;
+            //std::cout << "Align length: " << alignLen << std::endl;
+            //std::cout << "Quality: " << quality << std::endl;
+            //std::cout << tmp << std::endl;
+
+            // Create a corresponding edge
+            if (seq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen);
+            else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen);
+
+            // Record the scores
+            resize(scores, to);
+            typedef typename Iterator<TScoreValues, Standard>::Type TScoreIter;
+            TScoreIter itScore = begin(scores, Standard());
+            TScoreIter itScoreEnd = end(scores, Standard());
+            itScore += from;
+            for(;itScore != itScoreEnd; ++itScore)
+                *itScore = myScore;
+
+            // Update the overlap counter
+            TSize lenLast = matches[from].len;
+            if (matches[to - 1].begin1 == 0) ++frontOvl[seq1];
+            if (matches[to - 1].begin2 == 0) ++frontOvl[seq2];
+            if (matches[from].begin1 + lenLast == length(pairSet[0])) ++backOvl[seq1];
+            if (matches[from].begin2 + lenLast == length(pairSet[1])) ++backOvl[seq2];
+        } else {
+            resize(matches, from);
+            *itAligned = false;
+        }
+    }
+    //std::cout << "Filtration ration: " << (double) dropCount / (double) length(pList) << std::endl;
+
+    // Find sequences that have no overlap in the front or back
+    String<TSize> noFront;
+    String<TSize> noBack;
+    for(TSize seqI = 0; seqI < nseq; ++seqI) {
+        if (frontOvl[seqI] == 0) appendValue(noFront, seqI, Generous());
+        else if (backOvl[seqI] == 0) appendValue(noBack, seqI, Generous());
+    }
+    // Drop the first and the last sequence
+    typedef typename Iterator<TBegEndPos const, Standard>::Type TBegEndIter;
+    TBegEndIter begEndIt = begin(begEndPos, Standard());
+    TBegEndIter begEndItEnd = end(begEndPos, Standard());
+    TSize minVal = maxValue<TSize>();
+    TSize maxVal = 0;
+    for(;begEndIt != begEndItEnd; ++begEndIt) {
+        TSize pos1 = begEndIt->i1;
+        TSize pos2 = begEndIt->i2;
+        if (pos1 > pos2) { TSize tmp = pos1; pos1 = pos2; pos2 = tmp;}
+        if (pos1 < minVal) minVal = pos1;
+        if (pos2 > maxVal) maxVal = pos2;
+    }
+    // Insert all remaining sequences into a string
+    String<TSize> unalignedReads;
+    for(TSize i = 0; i < (TSize) length(noFront); ++i) {
+        TSize p1 = begEndPos[noFront[i]].i1;
+        TSize p2 = begEndPos[noFront[i]].i2;
+        if (p1 > p2) {TSize tmp = p1; p1 = p2; p2 = tmp; }
+        if (p1 != minVal) appendValue(unalignedReads, noFront[i], Generous());
+    }
+    for(TSize i = 0; i < (TSize) length(noBack); ++i) {
+        TSize p1 = begEndPos[noBack[i]].i1;
+        TSize p2 = begEndPos[noBack[i]].i2;
+        if (p1 > p2) {TSize tmp = p1; p1 = p2; p2 = tmp; }
+        if (p2 != maxVal) appendValue(unalignedReads, noBack[i], Generous());
+    }
+    TSize countUnalignedReads = length(unalignedReads);
+    //std::cout << "Unaligned reads: " << countUnalignedReads << std::endl;
+    if (countUnalignedReads > 0) {
+        // Sort unaligned reads
+        std::sort(begin(unalignedReads, Standard()), end(unalignedReads, Standard()));
+
+        // Realign all unaligned sequences
+        itPair = begin(pList, Standard());
+        itDiag = begin(dList, Standard());
+        itAligned = begin(aligned, Standard());
+        for(;itPair != itPairEnd; ++itPair, ++itDiag, ++itAligned) {
+            if (*itAligned == true) continue;
+            TId id1 = itPair->i1;
+            TId id2 = itPair->i2;
+            TSize seq1 = idToPosition(str, id1);
+            TSize seq2 = idToPosition(str, id2);
+            if ((!std::binary_search(begin(unalignedReads, Standard()), end(unalignedReads, Standard()), seq1)) &&
+                (!std::binary_search(begin(unalignedReads, Standard()), end(unalignedReads, Standard()), seq2)))
+                continue;
+            if ((frontOvl[seq1] > maxOvl) && (backOvl[seq1] > maxOvl) &&
+                (frontOvl[seq2] > maxOvl) && (backOvl[seq2] > maxOvl))
+                continue;
+
+            // Make a pairwise string-set
+            TStringSet pairSet;
+            assignValueById(pairSet, const_cast<StringSet<TString, TSpec>&>(str), id1);
+            assignValueById(pairSet, const_cast<StringSet<TString, TSpec>&>(str), id2);
+
+            // Overlap alignment
+            TSize from = length(matches);
+            TScoreValue myScore = globalAlignment(matches, pairSet, score_type, AlignConfig<true,true,true,true>(), Gotoh() );
+            TSize to = length(matches);
+
+            // Determine a sequence weight
+            TSize matchLen = 0;
+            TSize overlapLen = 0;
+            TSize alignLen = 0;
+            getAlignmentStatistics(matches, pairSet, from, to, matchLen, overlapLen, alignLen);
+
+            if (((matchLen * 100) / overlapLen >= 80) && (matchLen >= 5)) {
+                // Create a corresponding edge
+                if (seq1<seq2) _getAlignmentStatistics(dist, seq1, seq2, nseq, matchLen, (matchLen * 100) / overlapLen);
+                else _getAlignmentStatistics(dist, seq2, seq1, nseq, matchLen, (matchLen * 100) / overlapLen);
+
+                // Record the scores
+                resize(scores, to);
+                typedef typename Iterator<TScoreValues, Standard>::Type TScoreIter;
+                TScoreIter itScore = begin(scores, Standard());
+                TScoreIter itScoreEnd = end(scores, Standard());
+                itScore+=from;
+                for(;itScore != itScoreEnd; ++itScore) *itScore = myScore;
+
+                // Update the overlap counter
+                TSize lenLast = matches[from].len;
+                if (matches[to - 1].begin1 == 0) ++frontOvl[seq1];
+                if (matches[to - 1].begin2 == 0) ++frontOvl[seq2];
+                if (matches[from].begin1 + lenLast == length(pairSet[0])) ++backOvl[seq1];
+                if (matches[from].begin2 + lenLast == length(pairSet[1])) ++backOvl[seq2];
+            } else resize(matches, from);
+        }
+    }
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/consensus/consensus_realign.h b/seqan/consensus/consensus_realign.h
index 6a698b9..76d7d7b 100644
--- a/seqan/consensus/consensus_realign.h
+++ b/seqan/consensus/consensus_realign.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,20 +43,20 @@ namespace SEQAN_NAMESPACE_MAIN
 template <typename TPos, typename TGapAnchor, typename TSpec, typename TGapPos>
 inline void
 removeGap(AlignedReadStoreElement<TPos, TGapAnchor, TSpec>& alignedRead,
-		  TGapPos const gapPos) 
+          TGapPos const gapPos)
 {
-	typedef String<TGapAnchor> TGaps;
-	typedef typename Iterator<TGaps, Standard>::Type TGapIter;
-	if (gapPos < (TGapPos) alignedRead.beginPos) {
-		--alignedRead.beginPos; --alignedRead.endPos;
-	} else if (gapPos < (TGapPos) alignedRead.endPos) {
-		--alignedRead.endPos;
-		TGapIter gapIt = upperBoundGapAnchor(alignedRead.gaps, gapPos - alignedRead.beginPos, SortGapPos() );
-		TGapIter gapItEnd = end(alignedRead.gaps, Standard());
-		// Note: We might create empty gaps here
-		for(;gapIt != gapItEnd; ++gapIt) 
-			--(gapIt->gapPos);
-	}
+    typedef String<TGapAnchor> TGaps;
+    typedef typename Iterator<TGaps, Standard>::Type TGapIter;
+    if (gapPos < (TGapPos) alignedRead.beginPos) {
+        --alignedRead.beginPos; --alignedRead.endPos;
+    } else if (gapPos < (TGapPos) alignedRead.endPos) {
+        --alignedRead.endPos;
+        TGapIter gapIt = upperBoundGapAnchor(alignedRead.gaps, gapPos - alignedRead.beginPos, SortGapPos() );
+        TGapIter gapItEnd = end(alignedRead.gaps, Standard());
+        // Note: We might create empty gaps here
+        for(;gapIt != gapItEnd; ++gapIt)
+            --(gapIt->gapPos);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -64,15 +64,15 @@ removeGap(AlignedReadStoreElement<TPos, TGapAnchor, TSpec>& alignedRead,
 template <typename TAlignedReads, typename TSpec, typename TGapPos>
 inline void
 removeGap(String<TAlignedReads, TSpec>& alignedReadStore,
-		  TGapPos const gapPos) 
+          TGapPos const gapPos)
 {
-	typedef String<TAlignedReads, TSpec> TAlignedReadStore;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
+    typedef String<TAlignedReads, TSpec> TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
 
-	TAlignIter alignIt = begin(alignedReadStore, Standard());
-	TAlignIter alignItEnd = end(alignedReadStore, Standard());
-	for(;alignIt != alignItEnd; ++alignIt) 
-		removeGap(*alignIt, gapPos);
+    TAlignIter alignIt = begin(alignedReadStore, Standard());
+    TAlignIter alignItEnd = end(alignedReadStore, Standard());
+    for(;alignIt != alignItEnd; ++alignIt)
+        removeGap(*alignIt, gapPos);
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -80,59 +80,60 @@ removeGap(String<TAlignedReads, TSpec>& alignedReadStore,
 template <typename TPos, typename TGapAnchor, typename TSpec, typename TGapPos>
 inline int
 insertGap(AlignedReadStoreElement<TPos, TGapAnchor, TSpec>& alignedRead,
-		  TGapPos const gapPos) 
+          TGapPos const gapPos)
 {
-	typedef String<TGapAnchor> TGaps;
-	typedef typename Iterator<TGaps, Standard>::Type TGapIter;
-	
-	if (gapPos <= alignedRead.beginPos) {
-		++alignedRead.beginPos; ++alignedRead.endPos;
-		return 0;
-	} else if (gapPos < alignedRead.endPos) {
-		++alignedRead.endPos;
-		TGapIter gapIt = lowerBoundGapAnchor(alignedRead.gaps, gapPos - alignedRead.beginPos, SortGapPos() );
-		TGapIter gapItEnd = end(alignedRead.gaps, Standard());
-		TGapPos insertPos = (gapPos - alignedRead.beginPos);
-		if (gapIt == gapItEnd) {
-			int gapLen = 0;
-			if (gapItEnd != begin(alignedRead.gaps)) {
-				--gapItEnd;
-				gapLen = (int) gapItEnd->gapPos - (int) gapItEnd->seqPos;
-			}
-			appendValue(alignedRead.gaps, TGapAnchor(insertPos - gapLen, insertPos + 1), Generous());
-		}
-		else {		
-			int gapPrev = 0;
-			if (gapIt != begin(alignedRead.gaps)) {
-				TGapIter gapPrevious = gapIt;
-				--gapPrevious;
-				gapPrev = (int) gapPrevious->gapPos - (int) gapPrevious->seqPos;
-			}
-			// If gap is within an existing gap, extend this gap
-			if ((gapIt->gapPos - (((int) gapIt->gapPos - (int) gapIt->seqPos) - gapPrev) <= insertPos) && (gapIt->gapPos >= insertPos)) {
-				for(;gapIt != gapItEnd; ++gapIt) 
-					++(gapIt->gapPos);
-			} else {
-				// Otherwise, create a new gap
-				TGapAnchor tmp = value(gapIt);
-				++tmp.gapPos;
-				gapIt->gapPos = insertPos + 1;
-				gapIt->seqPos = insertPos - gapPrev;
-				do {
-					++gapIt;
-					TGapAnchor newTmp;
-					if (gapIt != gapItEnd) {
-						newTmp = *gapIt;
-						++newTmp.gapPos;
-						*gapIt = tmp;
-					} else appendValue(alignedRead.gaps, tmp, Generous() );
-					tmp = newTmp;
-				} while (gapIt != gapItEnd);
-			}
-		}
-		return 1;
-	}
-	return 0;
+    typedef String<TGapAnchor> TGaps;
+    typedef typename Iterator<TGaps, Standard>::Type TGapIter;
+
+    if (gapPos <= (TGapPos)alignedRead.beginPos) {
+        ++alignedRead.beginPos; ++alignedRead.endPos;
+        return 0;
+    } else if (gapPos < (TGapPos)alignedRead.endPos) {
+        ++alignedRead.endPos;
+        TGapIter gapIt = lowerBoundGapAnchor(alignedRead.gaps, gapPos - alignedRead.beginPos, SortGapPos() );
+        TGapIter gapItEnd = end(alignedRead.gaps, Standard());
+        TGapPos insertPos = (gapPos - alignedRead.beginPos);
+        if (gapIt == gapItEnd) {
+            int gapLen = 0;
+            if (gapItEnd != begin(alignedRead.gaps)) {
+                --gapItEnd;
+                gapLen = (int) gapItEnd->gapPos - (int) gapItEnd->seqPos;
+            }
+            appendValue(alignedRead.gaps, TGapAnchor(insertPos - gapLen, insertPos + 1), Generous());
+        }
+        else {
+            int gapPrev = 0;
+            if (gapIt != begin(alignedRead.gaps)) {
+                TGapIter gapPrevious = gapIt;
+                --gapPrevious;
+                gapPrev = (int) gapPrevious->gapPos - (int) gapPrevious->seqPos;
+            }
+            // If gap is within an existing gap, extend this gap
+            if (((TGapPos)(gapIt->gapPos - (((int) gapIt->gapPos - (int) gapIt->seqPos) - gapPrev)) <= insertPos) &&
+                ((TGapPos)gapIt->gapPos >= insertPos)) {
+                for(;gapIt != gapItEnd; ++gapIt)
+                    ++(gapIt->gapPos);
+            } else {
+                // Otherwise, create a new gap
+                TGapAnchor tmp = value(gapIt);
+                ++tmp.gapPos;
+                gapIt->gapPos = insertPos + 1;
+                gapIt->seqPos = insertPos - gapPrev;
+                do {
+                    ++gapIt;
+                    TGapAnchor newTmp;
+                    if (gapIt != gapItEnd) {
+                        newTmp = *gapIt;
+                        ++newTmp.gapPos;
+                        *gapIt = tmp;
+                    } else appendValue(alignedRead.gaps, tmp, Generous() );
+                    tmp = newTmp;
+                } while (gapIt != gapItEnd);
+            }
+        }
+        return 1;
+    }
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -140,17 +141,17 @@ insertGap(AlignedReadStoreElement<TPos, TGapAnchor, TSpec>& alignedRead,
 template <typename TAlignedReads, typename TSpec, typename TGapPos>
 inline int
 insertGap(String<TAlignedReads, TSpec>& alignedReadStore,
-		  TGapPos const gapPos) 
+          TGapPos const gapPos)
 {
-	typedef String<TAlignedReads, TSpec> TAlignedReadStore;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
-
-	int numGaps = 0;
-	TAlignIter alignIt = begin(alignedReadStore, Standard());
-	TAlignIter alignItEnd = end(alignedReadStore, Standard());
-	for(;alignIt != alignItEnd; ++alignIt) 
-		numGaps += insertGap(*alignIt, gapPos);
-	return numGaps;
+    typedef String<TAlignedReads, TSpec> TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
+
+    int numGaps = 0;
+    TAlignIter alignIt = begin(alignedReadStore, Standard());
+    TAlignIter alignItEnd = end(alignedReadStore, Standard());
+    for(;alignIt != alignItEnd; ++alignIt)
+        numGaps += insertGap(*alignIt, gapPos);
+    return numGaps;
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -159,25 +160,25 @@ template<typename TConsensus>
 inline int
 scoreConsensus(TConsensus& consensus)
 {
-	typedef typename Size<TConsensus>::Type TSize;
-	typedef typename Iterator<TConsensus, Standard>::Type TConsIter;
-
-	// Compute the score
-	int score = 0;
-	TConsIter itCons = begin(consensus, Standard() );
-	TConsIter itConsEnd = end(consensus, Standard() );
-	TSize maxCount = 0;
-	TSize sumCount = 0;
-	TSize tmp;
-	for(;itCons != itConsEnd; ++itCons) {
-		maxCount = 0; sumCount = 0;
-		for(TSize i = 0; i < ValueSize<typename Value<TConsensus>::Type>::VALUE; ++i) {
-			if ((tmp = (*itCons).count[i]) > maxCount) maxCount = tmp;
-			sumCount += tmp;
-		}
-		score += (sumCount - maxCount);
-	}
-	return score;
+    typedef typename Size<TConsensus>::Type TSize;
+    typedef typename Iterator<TConsensus, Standard>::Type TConsIter;
+
+    // Compute the score
+    int score = 0;
+    TConsIter itCons = begin(consensus, Standard() );
+    TConsIter itConsEnd = end(consensus, Standard() );
+    TSize maxCount = 0;
+    TSize sumCount = 0;
+    TSize tmp;
+    for(;itCons != itConsEnd; ++itCons) {
+        maxCount = 0; sumCount = 0;
+        for(TSize i = 0; i < ValueSize<typename Value<TConsensus>::Type>::VALUE; ++i) {
+            if ((tmp = (*itCons).count[i]) > maxCount) maxCount = tmp;
+            sumCount += tmp;
+        }
+        score += (sumCount - maxCount);
+    }
+    return score;
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -186,44 +187,44 @@ scoreConsensus(TConsensus& consensus)
 // TODO(holtgrew): Rename to reflect this more clearly.
 // TODO(holtgrew): TConsensus/consensus are profiles, really.
 template<typename TFragSpec, typename TConfig, typename TAlignedRead, typename TSpec, typename TConsensus, typename TScore, typename TMethod, typename TBandwidth>
-void 
+void
 reAlign(FragmentStore<TFragSpec, TConfig>& fragStore,
-		String<TAlignedRead, TSpec>& contigReads,
-		TConsensus& consensus,
-		TScore& consScore,
-		TMethod const rmethod,
-		TBandwidth const bandwidth,
-		bool includeReference,
+        String<TAlignedRead, TSpec>& contigReads,
+        TConsensus& consensus,
+        TScore& consScore,
+        TMethod const rmethod,
+        TBandwidth const bandwidth,
+        bool includeReference,
         double & timeBeforeAlign,
         double & timeAlign,
         double & timeAfterAlign
         )
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef String<TAlignedRead, TSpec> TAlignedReadStore;
-	typedef typename TFragmentStore::TReadPos TReadPos;
-	typedef typename TFragmentStore::TReadSeq TReadSeq;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename TFragmentStore::TReadGapAnchor TGapAnchor;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignedReadIter;
-	typedef typename Iterator<TConsensus, Standard>::Type TConsIter;
-
-	// Initialization
-	typedef typename Value<TConsensus>::Type TProfileChar;
-	TSize gapPos = ValueSize<TProfileChar>::VALUE - 1;
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef String<TAlignedRead, TSpec> TAlignedReadStore;
+    typedef typename TFragmentStore::TReadPos TReadPos;
+    typedef typename TFragmentStore::TReadSeq TReadSeq;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename TFragmentStore::TReadGapAnchor TGapAnchor;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignedReadIter;
+    typedef typename Iterator<TConsensus, Standard>::Type TConsIter;
+
+    // Initialization
+    typedef typename Value<TConsensus>::Type TProfileChar;
+    TSize gapPos = ValueSize<TProfileChar>::VALUE - 1;
 //    int refId = length(fragStore.readSeqStore) - 1;
 
-	// Remove each fragment and realign it to the profile.
-//	TAlignedReadIter beg = begin(contigReads, Standard());
-	TAlignedReadIter alignIt = begin(contigReads, Standard());
-	TAlignedReadIter alignItEnd = end(contigReads, Standard());
-	if (includeReference)
+    // Remove each fragment and realign it to the profile.
+//    TAlignedReadIter beg = begin(contigReads, Standard());
+    TAlignedReadIter alignIt = begin(contigReads, Standard());
+    TAlignedReadIter alignItEnd = end(contigReads, Standard());
+    if (includeReference)
         --alignItEnd;
-	TConsensus bandConsensus;
-	TConsensus myRead;
-	TConsensus newConsensus;
+    TConsensus bandConsensus;
+    TConsensus myRead;
+    TConsensus newConsensus;
     int i = 0;
-	for (; alignIt != alignItEnd; ++alignIt) {
+    for (; alignIt != alignItEnd; ++alignIt) {
         double tBegin = sysTime();
         if (i++ > 1000 || i == 1) {
             //printf("realigning %u/%u\r", unsigned(alignIt-beg), unsigned(alignItEnd-beg));
@@ -231,169 +232,169 @@ reAlign(FragmentStore<TFragSpec, TConfig>& fragStore,
                 i = 0;
             fflush(stdout);
         }
-		//// Debug code
-		//for(TSize i = 0; i<length(consensus); ++i) {
-		//	std::cout << consensus[i] << std::endl;
-		//}
-		//TAlignedReadIter debugIt = begin(contigReads, Standard() );
-		//TAlignedReadIter debugItEnd = end(contigReads, Standard() );
-		//for(;debugIt != debugItEnd; goNext(debugIt)) {
-		//	std::cout << debugIt->beginPos << ',' << debugIt->endPos << ':';
-		//	typedef typename Iterator<String<TGapAnchor> , Standard>::Type TGapIter;
-		//	TGapIter gapIt = begin(debugIt->gaps, Standard());
-		//	TGapIter gapItEnd = end(debugIt->gaps, Standard());
-		//	for(;gapIt != gapItEnd; goNext(gapIt)) {
-		//		std::cout << '(' << gapIt->seqPos << ',' << gapIt->gapPos << ')' << ',';
-		//	}
-		//	std::cout << std::endl;
-		//}
-
-		TSize itConsPos = 0;
-		TConsIter itCons = begin(consensus, Standard());
-		TConsIter itConsEnd = end(consensus, Standard());
-
-		// Initialize the consensus of the band.
-		clear(myRead);
-		resize(myRead, length(fragStore.readSeqStore[alignIt->readId]), TProfileChar());
-		resize(bandConsensus, 2 * bandwidth + (alignIt->endPos - alignIt->beginPos), Generous());
-		TConsIter bandConsIt = begin(bandConsensus);
-		TConsIter bandConsItEnd = end(bandConsensus);
-		TConsIter myReadIt = begin(myRead);
-		TReadPos bandOffset = 0;
-		if (bandwidth < (TBandwidth) alignIt->beginPos) {
-			bandOffset = alignIt->beginPos - bandwidth;
-			itCons += bandOffset; itConsPos += bandOffset;
-			SEQAN_ASSERT_LEQ(itCons, itConsEnd);
-		}
-		int leftDiag = (alignIt->beginPos - bandOffset) - bandwidth;
-		int rightDiag = leftDiag + 2 * bandwidth;
-		//int increaseBand = 0;
-		int increaseBandLeft = 0;
-		int increaseBandRight = 0;
-		int removedBeginPos = 0;
-		int removedEndPos = 0;
-		for (TReadPos iPos = bandOffset; iPos < alignIt->beginPos && itCons != itConsEnd && bandConsIt != bandConsItEnd; ++itCons, ++bandConsIt, ++itConsPos, ++iPos)
-			*bandConsIt = *itCons; // fill in positions left of readbegin
-		TSize itConsPosBegin = itConsPos;  // start position of read basically, right? if(itConsPosBegin != alignIt->beginPos) std::cout <<"nicht unbedingt gleich\n";
-		alignIt->beginPos = alignIt->endPos = 0; // So this read is discarded in all gap operations
-
-		// Remove sequence from profile (and add to the consensus??)  // TODO(holtgrew): Add to consensus part right?
-		typedef typename Iterator<TReadSeq, Standard>::Type TReadIter;
-		TReadIter itRead = begin(fragStore.readSeqStore[alignIt->readId], Standard());
-		TReadIter itReadEnd = end(fragStore.readSeqStore[alignIt->readId], Standard());
-		typedef typename Iterator<String<TGapAnchor>, Standard>::Type TReadGapsIter;
-		TReadGapsIter itGaps = begin(alignIt->gaps, Standard());
-		TReadGapsIter itGapsEnd = end(alignIt->gaps, Standard());
-		TReadPos old = 0;
-		int diff = 0;
-		TReadPos clippedBeginPos = 0;
-		TReadPos clippedEndPos = 0;
-		SEQAN_ASSERT_LT(itRead, itReadEnd);
-		if ((itGaps != itGapsEnd) && (itGaps->gapPos == 0)) {
-			old = itGaps->seqPos;
-			clippedBeginPos = old; // gaps at beginning? or really clipped?
-			//std::cout << "clippedBeginPos = " << clippedBeginPos << std::endl;
-			itRead += old;
-			diff -= old;
-			++itGaps;
-			SEQAN_ASSERT_LT(itRead, itReadEnd);
-		}
-		for (; itGaps != itGapsEnd && itCons != itConsEnd; ++itGaps) {
-			// limit should never be larger than read length 
-			TReadPos limit = itGaps->seqPos;
-			SEQAN_ASSERT_LT(itGaps->seqPos, (TReadPos)length(fragStore.readSeqStore[alignIt->readId]));
-			int newDiff = (itGaps->gapPos - limit);
-			SEQAN_ASSERT_LT(itGaps->gapPos, (TReadPos)length(consensus));
-			if (diff > newDiff) {
-				clippedEndPos = diff - newDiff;
-				limit -= clippedEndPos;
-			}
-			for (; old < limit && itCons != itConsEnd && itRead != itReadEnd && bandConsIt != bandConsItEnd; ++old, ++itRead) {
+        //// Debug code
+        //for(TSize i = 0; i<length(consensus); ++i) {
+        //    std::cout << consensus[i] << std::endl;
+        //}
+        //TAlignedReadIter debugIt = begin(contigReads, Standard() );
+        //TAlignedReadIter debugItEnd = end(contigReads, Standard() );
+        //for(;debugIt != debugItEnd; goNext(debugIt)) {
+        //    std::cout << debugIt->beginPos << ',' << debugIt->endPos << ':';
+        //    typedef typename Iterator<String<TGapAnchor> , Standard>::Type TGapIter;
+        //    TGapIter gapIt = begin(debugIt->gaps, Standard());
+        //    TGapIter gapItEnd = end(debugIt->gaps, Standard());
+        //    for(;gapIt != gapItEnd; goNext(gapIt)) {
+        //        std::cout << '(' << gapIt->seqPos << ',' << gapIt->gapPos << ')' << ',';
+        //    }
+        //    std::cout << std::endl;
+        //}
+
+        TSize itConsPos = 0;
+        TConsIter itCons = begin(consensus, Standard());
+        TConsIter itConsEnd = end(consensus, Standard());
+
+        // Initialize the consensus of the band.
+        clear(myRead);
+        resize(myRead, length(fragStore.readSeqStore[alignIt->readId]), TProfileChar());
+        resize(bandConsensus, 2 * bandwidth + (alignIt->endPos - alignIt->beginPos), Generous());
+        TConsIter bandConsIt = begin(bandConsensus);
+        TConsIter bandConsItEnd = end(bandConsensus);
+        TConsIter myReadIt = begin(myRead);
+        TReadPos bandOffset = 0;
+        if (bandwidth < (TBandwidth) alignIt->beginPos) {
+            bandOffset = alignIt->beginPos - bandwidth;
+            itCons += bandOffset; itConsPos += bandOffset;
+            SEQAN_ASSERT_LEQ(itCons, itConsEnd);
+        }
+        int leftDiag = (alignIt->beginPos - bandOffset) - bandwidth;
+        int rightDiag = leftDiag + 2 * bandwidth;
+        //int increaseBand = 0;
+        int increaseBandLeft = 0;
+        int increaseBandRight = 0;
+        int removedBeginPos = 0;
+        int removedEndPos = 0;
+        for (TReadPos iPos = bandOffset; iPos < alignIt->beginPos && itCons != itConsEnd && bandConsIt != bandConsItEnd; ++itCons, ++bandConsIt, ++itConsPos, ++iPos)
+            *bandConsIt = *itCons; // fill in positions left of readbegin
+        TSize itConsPosBegin = itConsPos;  // start position of read basically, right? if(itConsPosBegin != alignIt->beginPos) std::cout <<"nicht unbedingt gleich\n";
+        alignIt->beginPos = alignIt->endPos = 0; // So this read is discarded in all gap operations
+
+        // Remove sequence from profile (and add to the consensus??)  // TODO(holtgrew): Add to consensus part right?
+        typedef typename Iterator<TReadSeq, Standard>::Type TReadIter;
+        TReadIter itRead = begin(fragStore.readSeqStore[alignIt->readId], Standard());
+        TReadIter itReadEnd = end(fragStore.readSeqStore[alignIt->readId], Standard());
+        typedef typename Iterator<String<TGapAnchor>, Standard>::Type TReadGapsIter;
+        TReadGapsIter itGaps = begin(alignIt->gaps, Standard());
+        TReadGapsIter itGapsEnd = end(alignIt->gaps, Standard());
+        TReadPos old = 0;
+        int diff = 0;
+        TReadPos clippedBeginPos = 0;
+        TReadPos clippedEndPos = 0;
+        SEQAN_ASSERT_LT(itRead, itReadEnd);
+        if ((itGaps != itGapsEnd) && (itGaps->gapPos == 0)) {
+            old = itGaps->seqPos;
+            clippedBeginPos = old; // gaps at beginning? or really clipped?
+            //std::cout << "clippedBeginPos = " << clippedBeginPos << std::endl;
+            itRead += old;
+            diff -= old;
+            ++itGaps;
+            SEQAN_ASSERT_LT(itRead, itReadEnd);
+        }
+        for (; itGaps != itGapsEnd && itCons != itConsEnd; ++itGaps) {
+            // limit should never be larger than read length
+            TReadPos limit = itGaps->seqPos;
+            SEQAN_ASSERT_LT(itGaps->seqPos, (TReadPos)length(fragStore.readSeqStore[alignIt->readId]));
+            int newDiff = (itGaps->gapPos - limit);
+            SEQAN_ASSERT_LT(itGaps->gapPos, (TReadPos)length(consensus));
+            if (diff > newDiff) {
+                clippedEndPos = diff - newDiff;
+                limit -= clippedEndPos;
+            }
+            for (; old < limit && itCons != itConsEnd && itRead != itReadEnd && bandConsIt != bandConsItEnd; ++old, ++itRead) {
                 //SEQAN_ASSERT_LT(itCons, itConsEnd);
-				--(*itCons).count[ordValue(*itRead)];
-				if (!empty(*itCons)) {
-					*bandConsIt = *itCons; 
-					++bandConsIt;
-					++itConsPos;
-					removedEndPos = 0;
-				} else {
-					if (itConsPosBegin != itConsPos) {
+                --(*itCons).count[ordValue(*itRead)];
+                if (!empty(*itCons)) {
+                    *bandConsIt = *itCons;
+                    ++bandConsIt;
+                    ++itConsPos;
+                    removedEndPos = 0;
+                } else {
+                    if (itConsPosBegin != itConsPos) {
                         ++increaseBandLeft; // insertion --> increaseBandLeft, read has character here, consensus doesnt
-						++removedEndPos;
-					} else ++removedBeginPos; // begin gaps
-					removeGap(contigReads, itConsPos);
-				}
-				(*myReadIt).count[0] = ordValue(*itRead); 
-				++myReadIt;
-				++itCons;
+                        ++removedEndPos;
+                    } else ++removedBeginPos; // begin gaps
+                    removeGap(contigReads, itConsPos);
+                }
+                (*myReadIt).count[0] = ordValue(*itRead);
+                ++myReadIt;
+                ++itCons;
                 //SEQAN_ASSERT_LT(itRead, itReadEnd);
-			}
-			for (; diff < newDiff && itCons != itConsEnd && bandConsIt != bandConsItEnd; ++diff) {
+            }
+            for (; diff < newDiff && itCons != itConsEnd && bandConsIt != bandConsItEnd; ++diff) {
                 ++increaseBandRight; // deletion --> increaseBandRight, read has gaps here, consensus doesnt
-				//SEQAN_ASSERT_LT(itCons, itConsEnd);
-				--(*itCons).count[gapPos];
-				if (!empty(*itCons)) {
-					*bandConsIt = *itCons; 
-					++bandConsIt;
-					++itConsPos;
-				} else removeGap(contigReads, itConsPos);  //++increaseBandRight;}
-				++itCons;
-			}
-		}
-		if (!clippedEndPos) {
-			for (; itRead!=itReadEnd && itCons != itConsEnd && bandConsIt != bandConsItEnd; ++itRead) {
-				//SEQAN_ASSERT_LT(itCons, itConsEnd);
+                //SEQAN_ASSERT_LT(itCons, itConsEnd);
+                --(*itCons).count[gapPos];
+                if (!empty(*itCons)) {
+                    *bandConsIt = *itCons;
+                    ++bandConsIt;
+                    ++itConsPos;
+                } else removeGap(contigReads, itConsPos);  //++increaseBandRight;}
+                ++itCons;
+            }
+        }
+        if (!clippedEndPos) {
+            for (; itRead!=itReadEnd && itCons != itConsEnd && bandConsIt != bandConsItEnd; ++itRead) {
+                //SEQAN_ASSERT_LT(itCons, itConsEnd);
                 //SEQAN_ASSERT_LT(itRead, itReadEnd);
-				--(*itCons).count[ordValue(*itRead)];  //subtract the read base to get bandConsensus wo myRead
-				if (!empty(*itCons)) {
-					*bandConsIt = *itCons; 
-					++bandConsIt;
-					++itConsPos;
-					removedEndPos = 0;
-				} else {  // only gaps left in this column after removing myRead
-					if (itConsPosBegin != itConsPos) {
+                --(*itCons).count[ordValue(*itRead)];  //subtract the read base to get bandConsensus wo myRead
+                if (!empty(*itCons)) {
+                    *bandConsIt = *itCons;
+                    ++bandConsIt;
+                    ++itConsPos;
+                    removedEndPos = 0;
+                } else {  // only gaps left in this column after removing myRead
+                    if (itConsPosBegin != itConsPos) {
                         ++increaseBandLeft; // insertion --> increaseBandLeft, read is longer than consensus here
-                        ++removedEndPos; 
-					} else ++removedBeginPos;
-					removeGap(contigReads, itConsPos);
-				}
-				(*myReadIt).count[0] = ordValue(*itRead);   
-				++myReadIt;
-				++itCons;
-			}
-		}
-		bool singleton = (itConsPosBegin == itConsPos);
-		increaseBandLeft -= removedEndPos; 
+                        ++removedEndPos;
+                    } else ++removedBeginPos;
+                    removeGap(contigReads, itConsPos);
+                }
+                (*myReadIt).count[0] = ordValue(*itRead);
+                ++myReadIt;
+                ++itCons;
+            }
+        }
+        bool singleton = (itConsPosBegin == itConsPos);
+        increaseBandLeft -= removedEndPos;
         //increaseBand = increaseBandLeft + increaseBandRight;
-        
-		// Go further up to the bandwidth
-		for (TReadPos iPos = 0; ((itCons != itConsEnd) && (iPos < (TReadPos) bandwidth)) && bandConsIt != bandConsItEnd; ++itCons, ++iPos, ++bandConsIt)
+
+        // Go further up to the bandwidth
+        for (TReadPos iPos = 0; ((itCons != itConsEnd) && (iPos < (TReadPos) bandwidth)) && bandConsIt != bandConsItEnd; ++itCons, ++iPos, ++bandConsIt)
             *bandConsIt = *itCons;
-		resize(bandConsensus, bandConsIt - begin(bandConsensus, Standard()), Generous());
-		resize(myRead, myReadIt - begin(myRead, Standard()), Generous());
-
-		// Realign the consensus with the sequence.
-		typedef StringSet<TConsensus, Dependent<> > TStringSet;
-		TStringSet pairSet;
-		appendValue(pairSet, bandConsensus);
-		appendValue(pairSet, myRead);
-
-		//for(TSize i = 0; i<length( pairSet[0]); ++i) {
-		//	std::cout <<  pairSet[0][i] << std::endl;
-		//}
-		//std::cout << "_______________" << std::endl;
-		//for(TSize i = 0; i<length( pairSet[1]); ++i) {
-		//	std::cout <<   pairSet[1][i] << std::endl;
-		//}
-		//std::cout << "..............." << std::endl;
-
-		typedef String<Fragment<> > TFragmentString;
-		TFragmentString matches;
-		assignProfile(consScore, bandConsensus);
+        resize(bandConsensus, bandConsIt - begin(bandConsensus, Standard()), Generous());
+        resize(myRead, myReadIt - begin(myRead, Standard()), Generous());
+
+        // Realign the consensus with the sequence.
+        typedef StringSet<TConsensus, Dependent<> > TStringSet;
+        TStringSet pairSet;
+        appendValue(pairSet, bandConsensus);
+        appendValue(pairSet, myRead);
+
+        //for(TSize i = 0; i<length( pairSet[0]); ++i) {
+        //    std::cout <<  pairSet[0][i] << std::endl;
+        //}
+        //std::cout << "_______________" << std::endl;
+        //for(TSize i = 0; i<length( pairSet[1]); ++i) {
+        //    std::cout <<   pairSet[1][i] << std::endl;
+        //}
+        //std::cout << "..............." << std::endl;
+
+        typedef String<Fragment<> > TFragmentString;
+        TFragmentString matches;
+        assignProfile(consScore, bandConsensus);
 
         double tBegAlign = sysTime();
-		leftDiag -= removedBeginPos;
-		rightDiag -= removedBeginPos;
+        leftDiag -= removedBeginPos;
+        rightDiag -= removedBeginPos;
         //if(alignIt->readId == refId)
         //{
         //    std::cout << "length(Cons)=" <<  (int) length(pairSet[0]) << std::endl;
@@ -401,119 +402,119 @@ reAlign(FragmentStore<TFragSpec, TConfig>& fragStore,
         //    std::cout << "-->leftDiag" << _max(leftDiag - increaseBandLeft, -1 * (int) length(pairSet[1])) << std::endl;
         //    std::cout << "-->rightDiag" << _min(rightDiag + increaseBandRight, (int) length(pairSet[0])) << std::endl;
         //}
-		if (!singleton) {
-			if (rmethod == 0)
+        if (!singleton) {
+            if (rmethod == 0)
                 globalAlignment(matches, pairSet, consScore, AlignConfig<true,false,false,true>(), _max(leftDiag - increaseBandLeft, -1 * (int) length(pairSet[1])), _min(rightDiag + increaseBandRight, (int) length(pairSet[0])), NeedlemanWunsch());
-			else if (rmethod == 1)
+            else if (rmethod == 1)
                 globalAlignment(matches, pairSet, consScore, AlignConfig<true,false,false,true>(), _max(leftDiag - increaseBandLeft, -1 * (int) length(pairSet[1])), _min(rightDiag + increaseBandRight, (int) length(pairSet[0])), Gotoh());
-		}
+        }
         double tEndAlign = sysTime();
 
-		//// Debug code
-		//Graph<Alignment<TStringSet, void, WithoutEdgeId> > g1(pairSet);
-		//int sc1 = globalAlignment(g1, consScore, AlignConfig<true,false,false,true>(), _max(leftDiag - increaseBand, -1 * (int) length(pairSet[1])), _min(rightDiag + increaseBand, (int) length(pairSet[0])), Gotoh());
-		//std::cout << sc1 << std::endl;
-		//std::cout << g1 << std::endl;
-		
-		// Add the read back to the consensus and build the new consensus.
-		resize(newConsensus, length(bandConsensus) + length(myRead), Generous());
-		TConsIter newConsIt = begin(newConsensus, Standard());
-		TConsIter bandIt = begin(bandConsensus, Standard());
-		TConsIter bandItEnd = end(bandConsensus, Standard());
-		typedef typename Iterator<TFragmentString, Standard>::Type TFragIter;
-		TFragIter fragIt = end(matches, Standard());
-		TFragIter fragItEnd = begin(matches, Standard());
-		TReadPos consPos = 0;
-		TReadPos readPos = 0;
-		TReadPos alignPos = 0;
-		clear(alignIt->gaps);
-		diff = 0;
-		if (clippedBeginPos) {
-			appendValue(alignIt->gaps, TGapAnchor(clippedBeginPos, 0), Generous() );
-			diff -= clippedBeginPos;
-		}
-		bool firstMatch = true;
-		if (fragIt != fragItEnd) { // walk through segment matches that represent read-msa alignment
-			do {
-				--fragIt;
-				int gapLen = fragIt->begin1 - consPos;
-				if (firstMatch) gapLen = 0; // gap between two adjacent segment matches
+        //// Debug code
+        //Graph<Alignment<TStringSet, void, WithoutEdgeId> > g1(pairSet);
+        //int sc1 = globalAlignment(g1, consScore, AlignConfig<true,false,false,true>(), _max(leftDiag - increaseBand, -1 * (int) length(pairSet[1])), _min(rightDiag + increaseBand, (int) length(pairSet[0])), Gotoh());
+        //std::cout << sc1 << std::endl;
+        //std::cout << g1 << std::endl;
+
+        // Add the read back to the consensus and build the new consensus.
+        resize(newConsensus, length(bandConsensus) + length(myRead), Generous());
+        TConsIter newConsIt = begin(newConsensus, Standard());
+        TConsIter bandIt = begin(bandConsensus, Standard());
+        TConsIter bandItEnd = end(bandConsensus, Standard());
+        typedef typename Iterator<TFragmentString, Standard>::Type TFragIter;
+        TFragIter fragIt = end(matches, Standard());
+        TFragIter fragItEnd = begin(matches, Standard());
+        TReadPos consPos = 0;
+        TReadPos readPos = 0;
+        TReadPos alignPos = 0;
+        clear(alignIt->gaps);
+        diff = 0;
+        if (clippedBeginPos) {
+            appendValue(alignIt->gaps, TGapAnchor(clippedBeginPos, 0), Generous() );
+            diff -= clippedBeginPos;
+        }
+        bool firstMatch = true;
+        if (fragIt != fragItEnd) { // walk through segment matches that represent read-msa alignment
+            do {
+                --fragIt;
+                int gapLen = fragIt->begin1 - consPos;
+                if (firstMatch) gapLen = 0; // gap between two adjacent segment matches
                 // equivalent to profilePos + fraglen < nextProfilePos
-				while (consPos < (TReadPos)fragIt->begin1) { // cons stretch before newCons start
-					SEQAN_ASSERT_LT(bandIt, bandItEnd);
-					SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
-					if (!firstMatch) ++(*bandIt).count[gapPos]; // fill with gaps if we are between two segment matches
-					*newConsIt = *bandIt;
-					++newConsIt;
-					++bandIt; 
-					++consPos; 
-					++alignPos;
-				}
+                while (consPos < (TReadPos)fragIt->begin1) { // cons stretch before newCons start
+                    SEQAN_ASSERT_LT(bandIt, bandItEnd);
+                    SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
+                    if (!firstMatch) ++(*bandIt).count[gapPos]; // fill with gaps if we are between two segment matches
+                    *newConsIt = *bandIt;
+                    ++newConsIt;
+                    ++bandIt;
+                    ++consPos;
+                    ++alignPos;
+                }
                 // equivalent to refPos + fraglen < nextRefPos
-				while (readPos < (TReadPos)fragIt->begin2) { // read stretch before matching fragment starts
-					SEQAN_ASSERT_LT(readPos, (TReadPos)length(fragStore.readSeqStore[alignIt->readId]));
-					SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
+                while (readPos < (TReadPos)fragIt->begin2) { // read stretch before matching fragment starts
+                    SEQAN_ASSERT_LT(readPos, (TReadPos)length(fragStore.readSeqStore[alignIt->readId]));
+                    SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
                     // equivalent to profileDel
                     if (gapLen) {
-						diff += gapLen; // add gap of length gaplen to readGaps
-						appendValue(alignIt->gaps, TGapAnchor(clippedBeginPos + readPos, clippedBeginPos + readPos + diff), Generous() );
-						gapLen = 0; // do this only once
-					}
-					int numGaps = insertGap(contigReads, bandOffset + alignPos);
-					TProfileChar tmpChar;
-					++tmpChar.count[myRead[readPos].count[0]]; // insert new column in profile
-					tmpChar.count[gapPos] += numGaps;
-					*newConsIt = tmpChar; ++newConsIt;
-					++readPos; ++alignPos;
-				}
-				for (TSize i = 0; i<fragIt->len; ++i, ++bandIt, ++consPos, ++readPos, ++alignPos, ++newConsIt) {
-					SEQAN_ASSERT_LT(bandIt, bandItEnd);
-					SEQAN_ASSERT_LT(readPos, (TReadPos)length(fragStore.readSeqStore[alignIt->readId]));
-					SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
-					if (firstMatch) {
-						firstMatch = false;
-						alignIt->beginPos = bandOffset + consPos;
-					} else if (gapLen) {
-						diff += gapLen;
-						appendValue(alignIt->gaps, TGapAnchor(clippedBeginPos + readPos, clippedBeginPos + readPos + diff), Generous() );
-						gapLen = 0;
-					}
-					SEQAN_ASSERT_LT(bandIt, bandItEnd);
-					++(*bandIt).count[myRead[readPos].count[0]];
-					*newConsIt = *bandIt; 
-				}
-			} while (fragIt != fragItEnd);
-		}
-		
-		for (; readPos < (TReadPos)length(myRead); ++readPos) {
-			int numGaps = insertGap(contigReads, bandOffset + alignPos);
-			TProfileChar tmpChar;
-			++tmpChar.count[myRead[readPos].count[0]];
-			tmpChar.count[gapPos] += numGaps;
-			SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
-			*newConsIt = tmpChar; ++newConsIt;
-			++alignPos;
-		}
-		if (singleton) alignIt->beginPos = bandOffset;
-		alignIt->endPos = alignIt->beginPos + clippedBeginPos + readPos + diff;
-		if (clippedEndPos) {
-			diff -= clippedEndPos;
-			appendValue(alignIt->gaps, TGapAnchor(clippedBeginPos + readPos + clippedEndPos, clippedBeginPos + readPos + clippedEndPos + diff), Generous() );
-		}
-		for (; bandIt != bandItEnd; ++bandIt, ++newConsIt) 
-		{
-			SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
-			*newConsIt = *bandIt;
-		}
-		resize(newConsensus, newConsIt - begin(newConsensus, Standard()), Generous());
-
-		replace(consensus, bandOffset, itCons - begin(consensus), newConsensus);
+                        diff += gapLen; // add gap of length gaplen to readGaps
+                        appendValue(alignIt->gaps, TGapAnchor(clippedBeginPos + readPos, clippedBeginPos + readPos + diff), Generous() );
+                        gapLen = 0; // do this only once
+                    }
+                    int numGaps = insertGap(contigReads, bandOffset + alignPos);
+                    TProfileChar tmpChar;
+                    ++tmpChar.count[myRead[readPos].count[0]]; // insert new column in profile
+                    tmpChar.count[gapPos] += numGaps;
+                    *newConsIt = tmpChar; ++newConsIt;
+                    ++readPos; ++alignPos;
+                }
+                for (TSize i = 0; i<fragIt->len; ++i, ++bandIt, ++consPos, ++readPos, ++alignPos, ++newConsIt) {
+                    SEQAN_ASSERT_LT(bandIt, bandItEnd);
+                    SEQAN_ASSERT_LT(readPos, (TReadPos)length(fragStore.readSeqStore[alignIt->readId]));
+                    SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
+                    if (firstMatch) {
+                        firstMatch = false;
+                        alignIt->beginPos = bandOffset + consPos;
+                    } else if (gapLen) {
+                        diff += gapLen;
+                        appendValue(alignIt->gaps, TGapAnchor(clippedBeginPos + readPos, clippedBeginPos + readPos + diff), Generous() );
+                        gapLen = 0;
+                    }
+                    SEQAN_ASSERT_LT(bandIt, bandItEnd);
+                    ++(*bandIt).count[myRead[readPos].count[0]];
+                    *newConsIt = *bandIt;
+                }
+            } while (fragIt != fragItEnd);
+        }
+
+        for (; readPos < (TReadPos)length(myRead); ++readPos) {
+            int numGaps = insertGap(contigReads, bandOffset + alignPos);
+            TProfileChar tmpChar;
+            ++tmpChar.count[myRead[readPos].count[0]];
+            tmpChar.count[gapPos] += numGaps;
+            SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
+            *newConsIt = tmpChar; ++newConsIt;
+            ++alignPos;
+        }
+        if (singleton) alignIt->beginPos = bandOffset;
+        alignIt->endPos = alignIt->beginPos + clippedBeginPos + readPos + diff;
+        if (clippedEndPos) {
+            diff -= clippedEndPos;
+            appendValue(alignIt->gaps, TGapAnchor(clippedBeginPos + readPos + clippedEndPos, clippedBeginPos + readPos + clippedEndPos + diff), Generous() );
+        }
+        for (; bandIt != bandItEnd; ++bandIt, ++newConsIt)
+        {
+            SEQAN_ASSERT_LT(newConsIt, end(newConsensus,Standard()));
+            *newConsIt = *bandIt;
+        }
+        resize(newConsensus, newConsIt - begin(newConsensus, Standard()), Generous());
+
+        replace(consensus, bandOffset, itCons - begin(consensus), newConsensus);
         double tEnd = sysTime();
 
         timeBeforeAlign += tBegAlign - tBegin;
         timeAlign += tEndAlign - tBegAlign;
         timeAfterAlign += tEnd -tEndAlign;
-	}
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -523,16 +524,16 @@ reAlign(FragmentStore<TFragSpec, TConfig>& fragStore,
  * @headerfile <seqan/consensus.h>
  * @brief Perform realignment using the Anson-Myers realignment.
  *
+ * @deprecated Do not use this function but use the new function @link reAlignment @endlink instead.
+ *
  * @signature void reAlign(fragStore, consensusScore, contigID, [realignmentMethod,] bandwidth, includeReference);
  *
  * @param[in,out] fragStore        The @link FragmentStore @endlink with the alignment to realign.
  * @param[in]     consensusScore   The @link Score @endlink to use for scoring alignments.
  * @param[in]     contigID         The integer id of the contig to realign.
- * @param[in]     bandwidth        The bandwidth to use for realignment.
+ * @param[in]     bandwidth        The integer bandwidth to use for realignment.
  * @param[in]     includeReference A <tt>bool</tt> flag that indicates whether to include the reference as a pseudo-read.
  *
- * @section Remarks
- *
  * If <tt>includeReference</tt> then the reference of the given contig will be used as a pseudo-read.  In this case, the
  * reference will be replaced by the consensus.  When included as a pseudo-read, the alignment of the consensus relative
  * to the original refernence can be used to call variants.
@@ -540,245 +541,236 @@ reAlign(FragmentStore<TFragSpec, TConfig>& fragStore,
 
 // TODO(holtgrew): realignmentMethod should not be optional or moved to the end of the list.
 // TODO(holtgrew): The method should be selected with an enum instead of an int.
-/**
-.Function.reAlign:
-..cat:Consensus
-..summary:Perform realignment similar to Anson-Myers algorithm.
-..signature:reAlignment(fragmentStore, consensusScore, contigId, [realignmentMethod,] bandwidth, includeReference)
-..category:Alignments
-..remark:The consensus sequence will be appended to the readSeqStore of fragmentStore if includeReference is true.
-..include:seqan/consensus.h
-*/
 template<typename TSpec, typename TConfig, typename TScore, typename TId, typename TMethod, typename TBandwidth>
-void 
+void
 reAlign(FragmentStore<TSpec, TConfig> & fragStore,
-		TScore & consScore,
-		TId const contigId,
-		TMethod const rmethod,
-		TBandwidth const bandwidth,
-		bool includeReference)
+        TScore & consScore,
+        TId const contigId,
+        TMethod const rmethod,
+        TBandwidth const bandwidth,
+        bool includeReference)
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore;
-	typedef typename TFragmentStore::TReadPos TReadPos;
-	
-	typedef typename TFragmentStore::TContigStore		TContigStore;
-	typedef typename Value<TContigStore>::Type		TContig;
-	typedef typename TFragmentStore::TContigPos 		TContigPos;
-	typedef typename TFragmentStore::TContigSeq 		TContigSeq;
-	typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> >	TContigGaps;
-	
-	typedef typename TFragmentStore::TReadSeq TReadSeq;
-	typedef typename TFragmentStore::TReadGapAnchor TGapAnchor;
-	typedef typename Value<typename TFragmentStore::TReadSeq>::Type TStoreAlphabet;
-	typedef typename BaseAlphabet<TStoreAlphabet>::Type TAlphabet;
-	typedef typename Value<TAlignedReadStore>::Type TAlignedElement;
-	//typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadElement;
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore;
+    typedef typename TFragmentStore::TReadPos TReadPos;
+
+    typedef typename TFragmentStore::TContigStore        TContigStore;
+    typedef typename Value<TContigStore>::Type        TContig;
+    typedef typename TFragmentStore::TContigPos         TContigPos;
+    typedef typename TFragmentStore::TContigSeq         TContigSeq;
+    typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> >    TContigGaps;
+
+    typedef typename TFragmentStore::TReadSeq TReadSeq;
+    typedef typename TFragmentStore::TReadGapAnchor TGapAnchor;
+    typedef typename Value<typename TFragmentStore::TReadSeq>::Type TStoreAlphabet;
+    typedef typename BaseAlphabet<TStoreAlphabet>::Type TAlphabet;
+    typedef typename Value<TAlignedReadStore>::Type TAlignedElement;
+    //typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadElement;
 
     // double beginTime, endTime;
-    
+
     // beginTime = sysTime();
     // TODO(holtgrew): Unnecessary, only required once.
-	// Sort according to contigId
-	sortAlignedReads(fragStore.alignedReadStore, SortContigId());
-	
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
-	TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-
-	// Sort the reads according to their begin position.
-	sortAlignedReads(infix(fragStore.alignedReadStore, alignIt - begin(fragStore.alignedReadStore, Standard()), alignItEnd - begin(fragStore.alignedReadStore, Standard())), SortBeginPos());
-	alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    // Sort according to contigId
+    sortAlignedReads(fragStore.alignedReadStore, SortContigId());
+
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
+    TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+
+    // Sort the reads according to their begin position.
+    sortAlignedReads(infix(fragStore.alignedReadStore, alignIt - begin(fragStore.alignedReadStore, Standard()), alignItEnd - begin(fragStore.alignedReadStore, Standard())), SortBeginPos());
+    alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
     // endTime = sysTime();
 //    std::cerr << "TIME sorting " << endTime - beginTime << std::endl;
 
     // beginTime = sysTime();
-	// Copy all reads belonging to this contig and reverse complement them if necessary.
-	TAlignedReadStore contigReads;  // TODO(holtgrew): Rather contigAlignedReads?
-	TReadPos maxPos = 0;
-	TReadPos minPos = MaxValue<TReadPos>::VALUE;
-	for (; alignIt != alignItEnd; ++alignIt) {
-		if (alignIt->beginPos > alignIt->endPos) {
-			reverseComplement(fragStore.readSeqStore[alignIt->readId]);
-			TAlignedElement alignedEl = *alignIt;
-			TReadPos tmp = alignedEl.beginPos;
-			alignedEl.beginPos = alignedEl.endPos;
-			alignedEl.endPos = tmp;
-			if (alignedEl.beginPos < minPos)
+    // Copy all reads belonging to this contig and reverse complement them if necessary.
+    TAlignedReadStore contigReads;  // TODO(holtgrew): Rather contigAlignedReads?
+    TReadPos maxPos = 0;
+    TReadPos minPos = MaxValue<TReadPos>::VALUE;
+    for (; alignIt != alignItEnd; ++alignIt) {
+        if (alignIt->beginPos > alignIt->endPos) {
+            reverseComplement(fragStore.readSeqStore[alignIt->readId]);
+            TAlignedElement alignedEl = *alignIt;
+            TReadPos tmp = alignedEl.beginPos;
+            alignedEl.beginPos = alignedEl.endPos;
+            alignedEl.endPos = tmp;
+            if (alignedEl.beginPos < minPos)
                 minPos = alignedEl.beginPos;
-			if (alignedEl.endPos > maxPos)
+            if (alignedEl.endPos > maxPos)
                 maxPos = alignedEl.endPos;
-			appendValue(contigReads, alignedEl, Generous() );
-		} else {
-			if (alignIt->beginPos < minPos)
+            appendValue(contigReads, alignedEl, Generous() );
+        } else {
+            if (alignIt->beginPos < minPos)
                 minPos = alignIt->beginPos;
-			if (alignIt->endPos > maxPos)
+            if (alignIt->endPos > maxPos)
                 maxPos = alignIt->endPos;
-			appendValue(contigReads, value(alignIt), Generous() );
-		}
-	}
+            appendValue(contigReads, value(alignIt), Generous() );
+        }
+    }
 
     // Append reference sequence to aligned reads for contigs if requested to do so.
-	if (includeReference) {
-		TId dummyReadId = length(fragStore.readSeqStore);
-		TId dummyMatchId = length(fragStore.alignedReadStore);
-		appendRead(fragStore, fragStore.contigStore[contigId].seq);
-		appendValue(fragStore.readNameStore, fragStore.contigNameStore[contigId], Generous());
-		fragStore.contigNameStore[contigId] += "Consensus_";
-        
-		TAlignedElement el;
-		el.id = dummyMatchId;
-		el.readId = dummyReadId;
-		el.contigId = contigId;
-		minPos = el.beginPos = 0;
-		TContigGaps contigGaps(fragStore.contigStore[contigId].seq, fragStore.contigStore[contigId].gaps);
-		maxPos = el.endPos = _max(maxPos,(TReadPos)positionSeqToGap(contigGaps,length(fragStore.contigStore[contigId].seq)-1)+1);
-		maxPos = el.endPos = _max(maxPos,(TReadPos)length(fragStore.contigStore[contigId].seq));
-		el.gaps = fragStore.contigStore[contigId].gaps;
-		appendValue(contigReads, el, Generous());
-	}
+    if (includeReference) {
+        TId dummyReadId = length(fragStore.readSeqStore);
+        TId dummyMatchId = length(fragStore.alignedReadStore);
+        appendRead(fragStore, fragStore.contigStore[contigId].seq);
+        appendValue(fragStore.readNameStore, fragStore.contigNameStore[contigId], Generous());
+        fragStore.contigNameStore[contigId] += "Consensus_";
+
+        TAlignedElement el;
+        el.id = dummyMatchId;
+        el.readId = dummyReadId;
+        el.contigId = contigId;
+        minPos = el.beginPos = 0;
+        TContigGaps contigGaps(fragStore.contigStore[contigId].seq, fragStore.contigStore[contigId].gaps);
+        maxPos = el.endPos = _max(maxPos,(TReadPos)positionSeqToGap(contigGaps,length(fragStore.contigStore[contigId].seq)-1)+1);
+        maxPos = el.endPos = _max(maxPos,(TReadPos)length(fragStore.contigStore[contigId].seq));
+        el.gaps = fragStore.contigStore[contigId].gaps;
+        appendValue(contigReads, el, Generous());
+    }
     // endTime = sysTime();
 //    std::cerr << "TIME copying " << endTime - beginTime << std::endl;
 
     // beginTime = sysTime();
-	// Create the consensus sequence
-	TSize gapPos = ValueSize<TAlphabet>::VALUE;
-	typedef ProfileChar<TAlphabet> TProfile;
-	typedef String<TProfile> TProfileString;
-	typedef typename Iterator<TProfileString, Standard>::Type TConsIter;
-	TProfileString consensus;
-	resize(consensus, maxPos - minPos, TProfile());
-
-	TConsIter itCons = begin(consensus, Standard() );
-	TConsIter itConsEnd = end(consensus, Standard());
-	TAlignIter contigReadsIt = begin(contigReads, Standard() );
-	TAlignIter contigReadsItEnd = end(contigReads, Standard() );
-	for(;contigReadsIt != contigReadsItEnd; ++contigReadsIt) {
-		contigReadsIt->beginPos -= minPos;
-		contigReadsIt->endPos -= minPos;
-		itCons = begin(consensus, Standard() );
-		itCons += contigReadsIt->beginPos;
-
-		typedef typename Iterator<TReadSeq, Standard>::Type TReadIter;
-		TReadIter itRead = begin(fragStore.readSeqStore[contigReadsIt->readId], Standard() );
-		TReadIter itReadEnd = end(fragStore.readSeqStore[contigReadsIt->readId], Standard() );
-		typedef typename Iterator<String<typename TFragmentStore::TReadGapAnchor>, Standard>::Type TReadGapsIter;
-		TReadGapsIter itGaps = begin(contigReadsIt->gaps, Standard() );
-		TReadGapsIter itGapsEnd = end(contigReadsIt->gaps, Standard() );
-
-		TReadPos old = 0;
-		int diff = 0;
-		bool clippedEnd = false;
-		if ((itGaps != itGapsEnd) && (itGaps->gapPos == 0)) {
-			old = itGaps->seqPos;
-			itRead += old;
-			diff -= old;
-			++itGaps;
-		}
-		for(;itGaps != itGapsEnd; ++itGaps) {
-			TReadPos limit = itGaps->seqPos;
-			int newDiff = (itGaps->gapPos - limit);
-			SEQAN_ASSERT_LT(itGaps->gapPos, (int)length(consensus));
-			if (diff > newDiff) {
-				limit -= (diff - newDiff);
-				clippedEnd = true;
-			}
-			for(;old < limit && itRead != itReadEnd && itCons != itConsEnd; ++old, ++itRead) 
-			{
-				SEQAN_ASSERT_LT(itRead, itReadEnd);
-				++(value(itCons++)).count[ordValue(*itRead)];
-			}
-			for(;diff < newDiff; ++diff) 
-				++(value(itCons++)).count[gapPos];
-		}
-		if (!clippedEnd) {
-			for( ; itRead!=itReadEnd && itCons != itConsEnd;++itRead) 
-				++(value(itCons++)).count[ordValue(*itRead)];
-		}
-	}
+    // Create the consensus sequence
+    TSize gapPos = ValueSize<TAlphabet>::VALUE;
+    typedef ProfileChar<TAlphabet> TProfile;
+    typedef String<TProfile> TProfileString;
+    typedef typename Iterator<TProfileString, Standard>::Type TConsIter;
+    TProfileString consensus;
+    resize(consensus, maxPos - minPos, TProfile());
+
+    TConsIter itCons = begin(consensus, Standard() );
+    TConsIter itConsEnd = end(consensus, Standard());
+    TAlignIter contigReadsIt = begin(contigReads, Standard() );
+    TAlignIter contigReadsItEnd = end(contigReads, Standard() );
+    for(;contigReadsIt != contigReadsItEnd; ++contigReadsIt) {
+        contigReadsIt->beginPos -= minPos;
+        contigReadsIt->endPos -= minPos;
+        itCons = begin(consensus, Standard() );
+        itCons += contigReadsIt->beginPos;
+
+        typedef typename Iterator<TReadSeq, Standard>::Type TReadIter;
+        TReadIter itRead = begin(fragStore.readSeqStore[contigReadsIt->readId], Standard() );
+        TReadIter itReadEnd = end(fragStore.readSeqStore[contigReadsIt->readId], Standard() );
+        typedef typename Iterator<String<typename TFragmentStore::TReadGapAnchor>, Standard>::Type TReadGapsIter;
+        TReadGapsIter itGaps = begin(contigReadsIt->gaps, Standard() );
+        TReadGapsIter itGapsEnd = end(contigReadsIt->gaps, Standard() );
+
+        TReadPos old = 0;
+        int diff = 0;
+        bool clippedEnd = false;
+        if ((itGaps != itGapsEnd) && (itGaps->gapPos == 0)) {
+            old = itGaps->seqPos;
+            itRead += old;
+            diff -= old;
+            ++itGaps;
+        }
+        for(;itGaps != itGapsEnd; ++itGaps) {
+            TReadPos limit = itGaps->seqPos;
+            int newDiff = (itGaps->gapPos - limit);
+            SEQAN_ASSERT_LT(itGaps->gapPos, (int)length(consensus));
+            if (diff > newDiff) {
+                limit -= (diff - newDiff);
+                clippedEnd = true;
+            }
+            for(;old < limit && itRead != itReadEnd && itCons != itConsEnd; ++old, ++itRead)
+            {
+                SEQAN_ASSERT_LT(itRead, itReadEnd);
+                ++(value(itCons++)).count[ordValue(*itRead)];
+            }
+            for(;diff < newDiff; ++diff)
+                ++(value(itCons++)).count[gapPos];
+        }
+        if (!clippedEnd) {
+            for( ; itRead!=itReadEnd && itCons != itConsEnd;++itRead)
+                ++(value(itCons++)).count[ordValue(*itRead)];
+        }
+    }
     // endTime = sysTime();
 //    std::cerr << "TIME consensus " << endTime - beginTime << std::endl;
-	
+
     // beginTime = sysTime();
     double tBefore = 0, tAlign = 0, tAfter = 0;
-	reAlign(fragStore, contigReads, consensus, consScore, rmethod, bandwidth, includeReference, tBefore, tAlign, tAfter);
+    reAlign(fragStore, contigReads, consensus, consScore, rmethod, bandwidth, includeReference, tBefore, tAlign, tAfter);
 //    fprintf(stderr, "TIME before align: %f s\nTIME align: %f s\nTIME after align: %f s\n", tBefore, tAlign, tAfter);
     // endTime = sysTime();
 //    std::cerr << "TIME realign " << endTime - beginTime << std::endl;
-	int score = scoreConsensus(consensus);
-	int oldScore = score + 1;
-	while(score < oldScore) {
-		//std::cout << "Score: " << score << std::endl;
-		oldScore = score;
+    int score = scoreConsensus(consensus);
+    int oldScore = score + 1;
+    while(score < oldScore) {
+        //std::cout << "Score: " << score << std::endl;
+        oldScore = score;
 //        double beginTime = sysTime();
         double tBefore = 0, tAlign = 0, tAfter = 0;
-		reAlign(fragStore, contigReads, consensus, consScore, rmethod, bandwidth, includeReference, tBefore, tAlign, tAfter);
+        reAlign(fragStore, contigReads, consensus, consScore, rmethod, bandwidth, includeReference, tBefore, tAlign, tAfter);
 //        fprintf(stderr, "TIME before align: %f s\nTIME align: %f s\nTIME after align: %f s\n", tBefore, tAlign, tAfter);
 //        double endTime = sysTime();
 //        std::cerr << "TIME realign " << endTime - beginTime << std::endl;
-		score = scoreConsensus(consensus);
-	}
-	//std::cout << "FinalScore: " << score << std::endl;
+        score = scoreConsensus(consensus);
+    }
+    //std::cout << "FinalScore: " << score << std::endl;
 
     // beginTime = sysTime();
-	// Update all the aligned reads and the new consensus
-	alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
-	TAlignIter contigReadIt = begin(contigReads, Standard());
-	for (; alignIt != alignItEnd; ++alignIt) {
-		if (alignIt->beginPos > alignIt->endPos) {
-			reverseComplement(fragStore.readSeqStore[alignIt->readId]);
-			alignIt->beginPos = contigReadIt->endPos;
-			alignIt->endPos = contigReadIt->beginPos;
-		} else {
-			alignIt->beginPos = contigReadIt->beginPos;
-			alignIt->endPos = contigReadIt->endPos;
-		}
-		// Remove empty gap anchors
-		clear(alignIt->gaps);
-		typedef typename Iterator<TGapAnchor, Standard>::Type TGapIter;
-		TGapIter gapIt = begin(contigReadIt->gaps, Standard());
-		TGapIter gapItEnd = end(contigReadIt->gaps, Standard());
-		int diff = 0;
-		for(;gapIt != gapItEnd; ++gapIt) {
-			if ((int) gapIt->gapPos - (int) gapIt->seqPos != diff) {
-				diff = (int) gapIt->gapPos - (int) gapIt->seqPos;
-				appendValue(alignIt->gaps, *gapIt, Generous() );
-			}
-		}
-		++contigReadIt;
-	}
-	typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigElement;
-	TContigElement& contigEl = fragStore.contigStore[contigId];
-	typedef typename Iterator<TProfileString, Standard>::Type TConsIter;
-	TConsIter itConsensus = begin(consensus, Standard());
-	TConsIter itConsensusEnd = end(consensus, Standard());
-	char gapChar = gapValue<char>();
-	TSize gapLen = 0;
-	TContigPos contigPos = 0;
-	int diff = 0;
-	clear(contigEl.seq);
-	clear(contigEl.gaps);
-	for (; itConsensus != itConsensusEnd; ++itConsensus, ++contigPos) {
-		if ((char) *itConsensus == gapChar) ++gapLen;
-		else {
-			if (gapLen) {
-				diff += (int) gapLen;
-				appendValue(contigEl.gaps, TGapAnchor(contigPos - diff, contigPos), Generous() );
-				gapLen = 0;
-			}
-			// TODO(weese): Here we convert from ProfileChar<Dna5>->Dna5->Dna5Q
-			// instead diverting through Dna5 we could think of directly converting
-			// a profile to a quality value, e.g. like the base caller Phred does.
-			// Therefore the conversion ProfileChar<Dna5> <-> Dna5Q needs to be
-			// defined.
-			appendValue(contigEl.seq, (TAlphabet)value(itConsensus), Generous() );
-		}
-
-	}
-	if (includeReference) 
-		appendValue(fragStore.alignedReadStore, contigReads[length(contigReads) - 1], Generous() );
+    // Update all the aligned reads and the new consensus
+    alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
+    TAlignIter contigReadIt = begin(contigReads, Standard());
+    for (; alignIt != alignItEnd; ++alignIt) {
+        if (alignIt->beginPos > alignIt->endPos) {
+            reverseComplement(fragStore.readSeqStore[alignIt->readId]);
+            alignIt->beginPos = contigReadIt->endPos;
+            alignIt->endPos = contigReadIt->beginPos;
+        } else {
+            alignIt->beginPos = contigReadIt->beginPos;
+            alignIt->endPos = contigReadIt->endPos;
+        }
+        // Remove empty gap anchors
+        clear(alignIt->gaps);
+        typedef typename Iterator<TGapAnchor, Standard>::Type TGapIter;
+        TGapIter gapIt = begin(contigReadIt->gaps, Standard());
+        TGapIter gapItEnd = end(contigReadIt->gaps, Standard());
+        int diff = 0;
+        for(;gapIt != gapItEnd; ++gapIt) {
+            if ((int) gapIt->gapPos - (int) gapIt->seqPos != diff) {
+                diff = (int) gapIt->gapPos - (int) gapIt->seqPos;
+                appendValue(alignIt->gaps, *gapIt, Generous() );
+            }
+        }
+        ++contigReadIt;
+    }
+    typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigElement;
+    TContigElement& contigEl = fragStore.contigStore[contigId];
+    typedef typename Iterator<TProfileString, Standard>::Type TConsIter;
+    TConsIter itConsensus = begin(consensus, Standard());
+    TConsIter itConsensusEnd = end(consensus, Standard());
+    char gapChar = gapValue<char>();
+    TSize gapLen = 0;
+    TContigPos contigPos = 0;
+    int diff = 0;
+    clear(contigEl.seq);
+    clear(contigEl.gaps);
+    for (; itConsensus != itConsensusEnd; ++itConsensus, ++contigPos) {
+        if ((char) *itConsensus == gapChar) ++gapLen;
+        else {
+            if (gapLen) {
+                diff += (int) gapLen;
+                appendValue(contigEl.gaps, TGapAnchor(contigPos - diff, contigPos), Generous() );
+                gapLen = 0;
+            }
+            // TODO(weese): Here we convert from ProfileChar<Dna5>->Dna5->Dna5Q
+            // instead diverting through Dna5 we could think of directly converting
+            // a profile to a quality value, e.g. like the base caller Phred does.
+            // Therefore the conversion ProfileChar<Dna5> <-> Dna5Q needs to be
+            // defined.
+            appendValue(contigEl.seq, (TAlphabet)value(itConsensus), Generous() );
+        }
+
+    }
+    if (includeReference)
+        appendValue(fragStore.alignedReadStore, contigReads[length(contigReads) - 1], Generous() );
     // endTime = sysTime();
 //    std::cerr << "TIME finalizing " << endTime - beginTime << std::endl;
 }
@@ -787,14 +779,14 @@ reAlign(FragmentStore<TSpec, TConfig> & fragStore,
 
 // Forwards to the overload that accepts the alignment method.
 template<typename TSpec, typename TConfig, typename TScore, typename TId, typename TBandwidth>
-inline void 
+inline void
 reAlign(FragmentStore<TSpec, TConfig>& fragStore,
-		TScore& consScore,
-		TId const contigId,
-		TBandwidth const bandwidth,
-		bool includeReference)
+        TScore& consScore,
+        TId const contigId,
+        TBandwidth const bandwidth,
+        bool includeReference)
 {
-	reAlign(fragStore, consScore, contigId, 0, bandwidth, includeReference);
+    reAlign(fragStore, consScore, contigId, 0, bandwidth, includeReference);
 }
 
 }  // namespace seqan
diff --git a/seqan/consensus/consensus_score.h b/seqan/consensus/consensus_score.h
index fb383fd..7ec1f6a 100644
--- a/seqan/consensus/consensus_score.h
+++ b/seqan/consensus/consensus_score.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Tobias Rausch <rausch@embl.de>
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_SEQAN_CONSENSUS_SCORE_H
-#define SEQAN_HEADER_SEQAN_CONSENSUS_SCORE_H
+#ifndef SEQAN_HEADER_SEQAN_CONSENSUS_SH
+#define SEQAN_HEADER_SEQAN_CONSENSUS_SH
 
 
 namespace SEQAN_NAMESPACE_MAIN
@@ -85,10 +85,10 @@ template <typename TValue>
 class Score<TValue, ConsensusScore>
 {
 public:
-	String<TValue> consensus_set;		// Is the alphabet character part of the consensus set for each column
+    String<TValue> consensus_set;        // Is the alphabet character part of the consensus set for each column
 
 public:
-	Score() {}
+    Score() {}
 
 };
 
@@ -109,19 +109,6 @@ class Score<TValue, ConsensusScore>
  * This is used for unified interfaces for position dependent and independetn scores.
  */
 
-/**
-.Class.ConsensusScoreSequenceEntry
-..cat:Alignments
-..signature:ConsensusScoreSequenceEntry<TSequence>
-..summary:Wrapper for a pointer to a sequence and a position in this sequence.
-..description:This is used for unified interfaces for position dependent and independent scores.
-..param.TSequence:The underlying sequence of the alignments or gaps.
-...type:Concept.SequenceConcept
-..see:Metafunction.Score#SequenceEntryForScore
-..see:Function.Score#sequenceEntryForScore
-..include:seqan/consensus.h
-*/
-
 template <typename TSequence>
 class ConsensusScoreSequenceEntry
 {
@@ -142,26 +129,14 @@ class ConsensusScoreSequenceEntry
 /*!
  * @fn ConsensusScoreSequenceEntry#host
  * @brief Returns reference to sequence from entry.
- * 
+ *
  * @signature TSequence host(entry);
- * 
- * @param[in] entry The entry to query for its host.
- * 
+ *
+ * @param[in] entry The ConsensusScoreSequenceEntry to query for its host.
+ *
  * @return TSequence A reference to the underlying sequence.
  */
 
-/**
-.Function.ConsensusScoreSequenceEntry#host
-..cat:Alignments
-..class:Class.ConsensusScoreSequenceEntry
-..signature:TSequence host(entry)
-..summary:Returns reference to sequence from entry.
-..param.entry:The entry to query.
-...type:Class.ConsensusScoreSequenceEntry
-..return:Reference to the underying sequence, is of type $TSequence const &$.
-..include:seqan/consensus.h
-*/
-
 template <typename TSequence>
 inline TSequence const &
 host(ConsensusScoreSequenceEntry<TSequence> & entry)
@@ -179,26 +154,15 @@ host(ConsensusScoreSequenceEntry<TSequence> const & entry)
 /*!
  * @fn ConsensusScoreSequenceEntry#position
  * @brief Returns position stored in <tt>entry</tt>.
- * 
+ *
  * @signature TPosition position(entry);
- * 
- * @param[in] entry The entry to query.
- * 
+ *
+ * @param[in] entry The ConsensusScoreSequenceEntry to query.
+ *
  * @return TPosition The position of the entry.  The type is
  *                   <tt>ConsensusScoreSequenceEntry&lt;TSequence&gt;::TPosition</tt>.
  */
 
-/**
-.Function.ConsensusScoreSequenceEntry#position
-..cat:Alignments
-..class:Class.ConsensusScoreSequenceEntry
-..signature:TPosition position(entry)
-..summary:Returns position stored in $entry$.
-..param.entry:The entry to query.
-...type:Class.ConsensusScoreSequenceEntry
-..return:The position of the score, has type $Position<TSequence>::Type$ where $TSequence$ is the parameter from type type of $entry$.
-..include:seqan/consensus.h
-*/
 template <typename TSequence>
 inline typename ConsensusScoreSequenceEntry<TSequence>::TPosition
 position(ConsensusScoreSequenceEntry<TSequence> const & entry)
@@ -209,25 +173,14 @@ position(ConsensusScoreSequenceEntry<TSequence> const & entry)
 /*!
  * @fn ConsensusScoreSequenceEntry#value
  * @brief Returns value of character referenced by <tt>entry</tt>.
- * 
+ *
  * @signature TValue value(entry);
  *
- * @param entry The entry to query.
+ * @param[in] entry The ConsensusScoreSequenceEntry to query.
  *
  * @return TValue The value of the sequence at the current position.
  */
 
-/**
-.Function.ConsensusScoreSequenceEntry#value
-..cat:Alignments
-..class:Class.ConsensusScoreSequenceEntry
-..signature:TPosition value(entry)
-..summary:Returns value of character referenced by $entry$.
-..param.entry:The entry to query.
-...type:Class.ConsensusScoreSequenceEntry
-..return:The value, of type $Value<TSequence>::Type$.
-..include:seqan/consensus.h
-*/
 template <typename TSequence>
 inline typename Value<TSequence>::Type
 value(ConsensusScoreSequenceEntry<TSequence> & entry)
@@ -299,67 +252,67 @@ sequenceEntryForScore(Score<TScoreValue, ConsensusScore> const &, TSequence cons
 template <typename TValue, typename TString>
 inline void
 assignProfile(Score<TValue, ConsensusScore>& me,
-			  TString const & profile)
+              TString const & profile)
 {
 //IOREV _notio_
-	typedef typename Size<TString>::Type TSize;
-	TSize alphSize = ValueSize<typename Value<TString>::Type>::VALUE;
-	resize(me.consensus_set, alphSize * length(profile));
-
-	typedef typename Iterator<TString const, Standard>::Type TIter;
-	typedef typename Iterator<String<TValue>, Standard>::Type TConsSetIter;
-	TConsSetIter itConsSet = begin(me.consensus_set, Standard());
-	TIter it = begin(profile, Standard());
-	TIter itEnd = end(profile, Standard());
-	TSize maxCount = 0;
-	for(;it!=itEnd;++it) {
-		maxCount = 0;
-		for(TSize i = 0; i<alphSize; ++i)
-			if ((*it).count[i] > maxCount) maxCount = (*it).count[i];
-		for(TSize i = 0; i<alphSize; ++i, ++itConsSet)
-			*itConsSet = ((*it).count[i] == maxCount)? 0 : (-SEQAN_CONSENSUS_UNITY);
-	}
+    typedef typename Size<TString>::Type TSize;
+    TSize alphSize = ValueSize<typename Value<TString>::Type>::VALUE;
+    resize(me.consensus_set, alphSize * length(profile));
+
+    typedef typename Iterator<TString const, Standard>::Type TIter;
+    typedef typename Iterator<String<TValue>, Standard>::Type TConsSetIter;
+    TConsSetIter itConsSet = begin(me.consensus_set, Standard());
+    TIter it = begin(profile, Standard());
+    TIter itEnd = end(profile, Standard());
+    TSize maxCount = 0;
+    for(;it!=itEnd;++it) {
+        maxCount = 0;
+        for(TSize i = 0; i<alphSize; ++i)
+            if ((*it).count[i] > maxCount) maxCount = (*it).count[i];
+        for(TSize i = 0; i<alphSize; ++i, ++itConsSet)
+            *itConsSet = ((*it).count[i] == maxCount)? 0 : (-SEQAN_CONSENSUS_UNITY);
+    }
 }
 
 
 template <typename TValue, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapExtendHorizontal(
-	Score<TValue, ConsensusScore> const & me,
+    Score<TValue, ConsensusScore> const & me,
     ConsensusScoreSequenceEntry<TSeq1> const & entry1,
     ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return ((int)position(entry2) < 0) ? -SEQAN_CONSENSUS_UNITY : me.consensus_set[position(entry1) * (ValueSize<typename Value<TSeq1>::Type>::VALUE) + (ValueSize<typename Value<TSeq1>::Type>::VALUE - 1)];
+    return ((int)position(entry2) < 0) ? -SEQAN_CONSENSUS_UNITY : me.consensus_set[position(entry1) * (ValueSize<typename Value<TSeq1>::Type>::VALUE) + (ValueSize<typename Value<TSeq1>::Type>::VALUE - 1)];
 }
 
 template <typename TValue, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapOpenHorizontal(
-	Score<TValue, ConsensusScore> const & me,
+    Score<TValue, ConsensusScore> const & me,
     ConsensusScoreSequenceEntry<TSeq1> const & entry1,
     ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return ((int)position(entry2) < 0) ? -2 * SEQAN_CONSENSUS_UNITY : 2 * me.consensus_set[position(entry1) * (ValueSize<typename Value<TSeq1>::Type>::VALUE) + (ValueSize<typename Value<TSeq1>::Type>::VALUE - 1)];
+    return ((int)position(entry2) < 0) ? -2 * SEQAN_CONSENSUS_UNITY : 2 * me.consensus_set[position(entry1) * (ValueSize<typename Value<TSeq1>::Type>::VALUE) + (ValueSize<typename Value<TSeq1>::Type>::VALUE - 1)];
 }
 
 template <typename TValue, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapExtendVertical(
-	Score<TValue, ConsensusScore> const &,
+    Score<TValue, ConsensusScore> const &,
     ConsensusScoreSequenceEntry<TSeq1> const & /*entry1*/,
     ConsensusScoreSequenceEntry<TSeq2> const & /*entry2*/)
 {
-	return -SEQAN_CONSENSUS_UNITY;
+    return -SEQAN_CONSENSUS_UNITY;
 }
 
 template <typename TValue, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapOpenVertical(
-	Score<TValue, ConsensusScore> const &,
+    Score<TValue, ConsensusScore> const &,
     ConsensusScoreSequenceEntry<TSeq1> const & /*entry1*/,
     ConsensusScoreSequenceEntry<TSeq2> const & /*entry2*/)
 {
-	return -2 * SEQAN_CONSENSUS_UNITY;
+    return -2 * SEQAN_CONSENSUS_UNITY;
 }
 
 
@@ -369,7 +322,7 @@ score(Score<TValue, ConsensusScore> const & me,
       ConsensusScoreSequenceEntry<TSeq1> const & entry1,
       ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return me.consensus_set[position(entry1) * (ValueSize<typename Value<TSeq1>::Type>::VALUE) + value(entry2).count[0]];
+    return me.consensus_set[position(entry1) * (ValueSize<typename Value<TSeq1>::Type>::VALUE) + value(entry2).count[0]];
 }
 
 
@@ -391,10 +344,10 @@ template <typename TValue>
 class Score<TValue, FractionalScore>
 {
 public:
-	String<int> sum;		// Total number of profile characters in each column
+    String<int> sum;        // Total number of profile characters in each column
 
 public:
-	Score() {}
+    Score() {}
 };
 
 
@@ -412,63 +365,63 @@ sequenceEntryForScore(Score<TScoreValue, FractionalScore> const &, TSequence con
 template <typename TValue, typename TString>
 inline void
 assignProfile(Score<TValue, FractionalScore> & me,
-			  TString const & profile)
+              TString const & profile)
 {
 //IOREV _notio_
-	typedef typename Size<TString>::Type TSize;
-	resize(me.sum, length(profile));
-	typedef typename Iterator<TString const, Standard>::Type TIter;
-	typedef typename Iterator<String<int>, Standard>::Type TSumIter;
-	TSumIter itSum = begin(me.sum, Standard());
-	TIter it = begin(profile, Standard());
-	TIter itEnd = end(profile, Standard());
-	for (; it!=itEnd; ++it, ++itSum)
+    typedef typename Size<TString>::Type TSize;
+    resize(me.sum, length(profile));
+    typedef typename Iterator<TString const, Standard>::Type TIter;
+    typedef typename Iterator<String<int>, Standard>::Type TSumIter;
+    TSumIter itSum = begin(me.sum, Standard());
+    TIter it = begin(profile, Standard());
+    TIter itEnd = end(profile, Standard());
+    for (; it!=itEnd; ++it, ++itSum)
     {
-		*itSum = 0;
-		for (TSize i = 0; i < (TSize) ValueSize<typename Value<TString>::Type>::VALUE; ++i) 
-			*itSum += (*it).count[i];
-	}
+        *itSum = 0;
+        for (TSize i = 0; i < (TSize) ValueSize<typename Value<TString>::Type>::VALUE; ++i)
+            *itSum += (*it).count[i];
+    }
 }
 
 
 template <typename TValue, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapExtendHorizontal(
-	Score<TValue, FractionalScore> const & me,
+    Score<TValue, FractionalScore> const & me,
     ConsensusScoreSequenceEntry<TSeq1> const & entry1,
     ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return (( (int)position(entry2) < 0) || (!me.sum[position(entry1)])) ? -SEQAN_CONSENSUS_UNITY : ((TValue) (( (int)value(entry1).count[ValueSize<typename Value<TSeq1>::Type>::VALUE - 1] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
+    return (( (int)position(entry2) < 0) || (!me.sum[position(entry1)])) ? -SEQAN_CONSENSUS_UNITY : ((TValue) (( (int)value(entry1).count[ValueSize<typename Value<TSeq1>::Type>::VALUE - 1] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
 }
 
 template <typename TValue, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapOpenHorizontal(
-	Score<TValue, FractionalScore> const & me,
+    Score<TValue, FractionalScore> const & me,
     ConsensusScoreSequenceEntry<TSeq1> const & entry1,
     ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return (( (int)position(entry2) < 0) || (!me.sum[position(entry1)])) ? -SEQAN_CONSENSUS_UNITY : ((TValue) (( (int) value(entry1).count[ValueSize<typename Value<TSeq1>::Type>::VALUE - 1] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
+    return (( (int)position(entry2) < 0) || (!me.sum[position(entry1)])) ? -SEQAN_CONSENSUS_UNITY : ((TValue) (( (int) value(entry1).count[ValueSize<typename Value<TSeq1>::Type>::VALUE - 1] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
 }
 
 template <typename TValue, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapExtendVertical(
-	Score<TValue, FractionalScore> const &,
+    Score<TValue, FractionalScore> const &,
     ConsensusScoreSequenceEntry<TSeq1> const & /*entry1*/,
     ConsensusScoreSequenceEntry<TSeq2> const & /*entry2*/)
 {
-	return -SEQAN_CONSENSUS_UNITY;
+    return -SEQAN_CONSENSUS_UNITY;
 }
 
 template <typename TValue, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapOpenVertical(
-	Score<TValue, FractionalScore> const &,
+    Score<TValue, FractionalScore> const &,
     ConsensusScoreSequenceEntry<TSeq1> const & /*entry1*/,
     ConsensusScoreSequenceEntry<TSeq2> const & /*entry2*/)
 {
-	return -SEQAN_CONSENSUS_UNITY;
+    return -SEQAN_CONSENSUS_UNITY;
 }
 
 template <typename TValue, typename TSeq1, typename TSeq2>
@@ -477,7 +430,7 @@ score(Score<TValue, FractionalScore> const & me,
       ConsensusScoreSequenceEntry<TSeq1> const & entry1,
       ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return (!me.sum[position(entry1)]) ? -SEQAN_CONSENSUS_UNITY : ((TValue) (((int)value(entry1).count[value(entry2).count[0]] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
+    return (!me.sum[position(entry1)]) ? -SEQAN_CONSENSUS_UNITY : ((TValue) (((int)value(entry1).count[value(entry2).count[0]] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]);
 }
 
 
@@ -498,11 +451,11 @@ template <typename TValue, typename TScore1, typename TScore2>
 class Score<TValue, WeightedConsensusScore<TScore1, TScore2> >
 {
 public:
-	TScore1 sc1;
-	TScore2 sc2;
+    TScore1 sc1;
+    TScore2 sc2;
 
 public:
-	Score() : sc1(), sc2() {}
+    Score() : sc1(), sc2() {}
 
 };
 
@@ -522,11 +475,11 @@ sequenceEntryForScore(Score<TScoreValue, WeightedConsensusScore<TScore1, TScore2
 template <typename TValue, typename TScore1, typename TScore2, typename TString>
 inline void
 assignProfile(Score<TValue, WeightedConsensusScore<TScore1, TScore2> >& me,
-			  TString const& profile)
+              TString const& profile)
 {
 //IOREV _notio_
-	assignProfile(me.sc1, profile);
-	assignProfile(me.sc2, profile);
+    assignProfile(me.sc1, profile);
+    assignProfile(me.sc2, profile);
 }
 
 
@@ -534,42 +487,42 @@ assignProfile(Score<TValue, WeightedConsensusScore<TScore1, TScore2> >& me,
 template <typename TValue, typename TScore1, typename TScore2, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapExtendHorizontal(
-	Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
+    Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
     ConsensusScoreSequenceEntry<TSeq1> const & entry1,
     ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return (scoreGapExtendHorizontal(me.sc1, entry1, entry2) + scoreGapExtendHorizontal(me.sc2, entry1, entry2)) / (TValue) 2;
+    return (scoreGapExtendHorizontal(me.sc1, entry1, entry2) + scoreGapExtendHorizontal(me.sc2, entry1, entry2)) / (TValue) 2;
 }
 
 template <typename TValue, typename TScore1, typename TScore2, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapOpenHorizontal(
-	Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
+    Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
     ConsensusScoreSequenceEntry<TSeq1> const & entry1,
     ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return (scoreGapOpenHorizontal(me.sc1, entry1, entry2) + scoreGapOpenHorizontal(me.sc2, entry1, entry2)) / (TValue) 2;
+    return (scoreGapOpenHorizontal(me.sc1, entry1, entry2) + scoreGapOpenHorizontal(me.sc2, entry1, entry2)) / (TValue) 2;
 }
 
 
 template <typename TValue, typename TScore1, typename TScore2, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapExtendVertical(
-	Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
+    Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
     ConsensusScoreSequenceEntry<TSeq1> const & entry1,
     ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return (scoreGapExtendVertical(me.sc1, entry1, entry2) + scoreGapExtendVertical(me.sc2, entry1, entry2)) / (TValue) 2;
+    return (scoreGapExtendVertical(me.sc1, entry1, entry2) + scoreGapExtendVertical(me.sc2, entry1, entry2)) / (TValue) 2;
 }
 
 template <typename TValue, typename TScore1, typename TScore2, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapOpenVertical(
-	Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
+    Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
     ConsensusScoreSequenceEntry<TSeq1> const & entry1,
     ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return (scoreGapOpenVertical(me.sc1, entry1, entry2) + scoreGapOpenVertical(me.sc2, entry1, entry2)) / (TValue) 2;
+    return (scoreGapOpenVertical(me.sc1, entry1, entry2) + scoreGapOpenVertical(me.sc2, entry1, entry2)) / (TValue) 2;
 }
 
 
@@ -579,7 +532,7 @@ score(Score<TValue, WeightedConsensusScore<TScore1, TScore2> > const & me,
       ConsensusScoreSequenceEntry<TSeq1> const & entry1,
       ConsensusScoreSequenceEntry<TSeq2> const & entry2)
 {
-	return (score(me.sc1, entry1, entry2) + score(me.sc2, entry1, entry2)) / (TValue) 2;
+    return (score(me.sc1, entry1, entry2) + score(me.sc2, entry1, entry2)) / (TValue) 2;
 }
 
 }
diff --git a/seqan/consensus/overlap_info_computation.h b/seqan/consensus/overlap_info_computation.h
new file mode 100644
index 0000000..fc57c6c
--- /dev/null
+++ b/seqan/consensus/overlap_info_computation.h
@@ -0,0 +1,425 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_CONSENSUS_OVERLAP_INFO_COMPUTATION_H_
+#define INCLUDE_SEQAN_CONSENSUS_OVERLAP_INFO_COMPUTATION_H_
+
+#include <seqan/index.h>
+#include <seqan/index/find_pigeonhole.h>
+
+#include "consensus_alignment_options.h"
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class OverlapInfo_
+// ----------------------------------------------------------------------------
+
+// Store an overlap candidate between sequences seq0 and seq1 (seq0 left of seq1), starting at pos1 in seq0:
+//
+// Examples (independent of relative read lengths):
+//
+// (1)   XXXXXXXXXXXXXXXXXX      seq0
+//         XXXXXXXXXXXXXXXXXXXX  seq1, pos1 = 2
+//
+// (2)   XXXXXXXXXXXXXXXXXX      seq0
+//       XXXXXXXXXXXXXXXXXXXX  seq1, pos1 = 0
+//
+// (3)   XXXXXXXXXXXXXXXXXX      seq0
+//           XXXXXXXXXXXXXXXXXXXX  seq1, pos1 = 4
+
+struct OverlapInfo_
+{
+    unsigned seq0;
+    unsigned seq1;
+    int len0, pos1;
+    int numErrors;  // number of alignment errors
+
+    OverlapInfo_() : seq0(-1), seq1(-1), len0(0), pos1(0), numErrors(0) {}
+    OverlapInfo_(unsigned seq0, unsigned seq1, int len0, int pos1, int numErrors = -1) :
+            seq0(seq0), seq1(seq1), len0(len0), pos1(pos1), numErrors(numErrors) {}
+
+    bool operator<(OverlapInfo_ const & other) const
+    {
+        return (std::make_pair(std::make_pair(seq0, seq1), pos1) <
+                std::make_pair(std::make_pair(other.seq0, other.seq1), other.pos1));
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class OverlapInfoComputation_
+// ----------------------------------------------------------------------------
+
+// Helper class for the overlap info computation.
+
+template <typename TFragmentStore>
+class OverlapInfoComputation_
+{
+public:
+    OverlapInfoComputation_(TFragmentStore const & store, ConsensusAlignmentOptions const & options) :
+            store(store), options(options)
+    {}
+
+    void run(std::vector<OverlapInfo_> & infos) const;
+
+private:
+
+    // Compute overlap info using banded alignment.
+    OverlapInfo_ computeOverlapInfo(unsigned lhs, unsigned rhs, int lDiag, int uDiag) const;
+
+    // Build overlap infos through global alignment.
+    void buildGlobalAlignmentOverlapInfos(std::vector<OverlapInfo_> & infos) const;
+    // Build position-based all-to-all overlap infos.
+    void buildPositionBasedOverlapInfos(std::vector<OverlapInfo_> & infos) const;
+    // Build contig-wise all-to-all overlap infos.
+    void buildContigAllToAllOverlapInfos(std::vector<OverlapInfo_> & infos) const;
+    // Build all-to-all overlap infos for all reads.
+    void buildAllToAllOverlapInfos(std::vector<OverlapInfo_> & infos) const;
+    // Build all-to-all overlap infos for the given read ids.
+    void buildAllToAllOverlapInfos(std::vector<OverlapInfo_> & infos,
+                                   std::vector<unsigned> const & readIDs) const;
+
+    template <typename TSequenceH, typename TSequenceV, typename TAlignConfig, typename TAlgoTag>
+    void _fixBandSize(int & lDiag,
+                      int & uDiag,
+                      TSequenceH const & seqH,
+                      TSequenceV const & seqV,
+                      TAlignConfig const & /*alignConfig*/,
+                      TAlgoTag const & /*algoTag*/) const
+    {
+        // typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+        typedef typename If<typename IsSameType<TAlgoTag, Gotoh>::Type, AffineGaps, LinearGaps>::Type TGapsType;
+        typedef typename SetupAlignmentProfile_<DPGlobal, TAlignConfig, TGapsType, TracebackConfig_<SingleTrace, GapsLeft> >::Type TDPProfile;
+
+        if (uDiag < -(int)length(seqV))
+            uDiag = -(int)length(seqV);
+        if (lDiag > (int)length(seqH))
+            lDiag = length(seqV);
+
+        if (uDiag < 0 && !IsFreeEndGap_<TDPProfile, DPFirstColumn>::VALUE)
+            uDiag = 0;
+
+        if (lDiag > 0 && !IsFreeEndGap_<TDPProfile, DPFirstRow>::VALUE)
+            lDiag = 0;
+
+        if (uDiag + (int)length(seqV) < (int)length(seqH) && !IsFreeEndGap_<TDPProfile, DPLastRow>::VALUE)
+            uDiag = (int)length(seqH) - (int)length(seqV);
+
+        if (lDiag + (int)length(seqV) > (int)length(seqH) && !IsFreeEndGap_<TDPProfile, DPLastColumn>::VALUE)
+            lDiag = (int)length(seqH) - (int)length(seqV);
+    }
+
+    // The FragmentStore to use for consensus computation.
+    TFragmentStore const & store;
+    // The configuration of the consensus alignment.
+    ConsensusAlignmentOptions const & options;
+};
+
+template <typename TFragmentStore>
+inline void OverlapInfoComputation_<TFragmentStore>::run(std::vector<OverlapInfo_> & overlapInfos) const
+{
+    if (options.useGlobalAlignment)
+        buildGlobalAlignmentOverlapInfos(overlapInfos);
+    else if (!options.useContigID)
+        buildAllToAllOverlapInfos(overlapInfos);
+    else if (!options.usePositions)
+        buildContigAllToAllOverlapInfos(overlapInfos);
+    else
+        buildPositionBasedOverlapInfos(overlapInfos);
+}
+
+template <typename TFragmentStore>
+inline OverlapInfo_ OverlapInfoComputation_<TFragmentStore>::computeOverlapInfo(
+        unsigned lhs, unsigned rhs, int lDiag, int uDiag) const
+{
+    typedef typename TFragmentStore::TReadSeqStore const TReadSeqStore;
+    typedef typename Value<TReadSeqStore>::Type TReadSeq;
+
+    Align<TReadSeq> align;
+    resize(rows(align), 2);
+    assignSource(row(align, 0), store.readSeqStore[lhs]);  // TODO(holtgrew): setSource cannot use infix!
+    assignSource(row(align, 1), store.readSeqStore[rhs]);
+
+    Score<int, Simple> scoringScheme(options.scoreMatch, options.scoreMismatch,
+                                     options.scoreGapExtend, options.scoreGapOpen);
+
+    AlignConfig<true, true, true, true> alignConfig;
+
+    if (lDiag != seqan::minValue<int>() && uDiag != seqan::minValue<int>())
+    {
+        if (options.verbosity >= 2)
+            std::cerr << "global alignment with bands " << lDiag << ", " << uDiag << "\n";
+        _fixBandSize(lDiag, uDiag, store.readSeqStore[lhs], store.readSeqStore[rhs], alignConfig, NeedlemanWunsch());
+        globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag);
+    }
+    else
+    {
+        globalAlignment(align, scoringScheme, alignConfig);
+    }
+
+    if (options.verbosity >= 2)
+        std::cerr << "before swapping\n" << align << "\n";
+
+    // Create overlap candidate.
+    if (isGap(row(align, 0), 0))  // lhs is right and rhs is left, swap roles
+    {
+        using std::swap;
+        swap(lhs, rhs);
+        swap(row(align, 0), row(align, 1));
+    }
+
+    if (options.verbosity >= 2)
+        std::cerr << "after swapping\n" << align << "\n";
+
+    // Count errors in overlap of alignment.
+    int beginPos = countGaps(begin(row(align, 1), Standard()));
+    int endPosH = length(row(align, 0));
+    for (; endPosH > beginPos && isGap(row(align, 0), endPosH - 1); --endPosH)
+        continue;
+    int endPosV = length(row(align, 1));
+    for (; endPosV > beginPos && isGap(row(align, 1), endPosV - 1); --endPosV)
+        continue;
+    int endPos = std::min(endPosH, endPosV);
+
+    typedef typename Row<Align<TReadSeq> >::Type TRow;
+    typedef typename Iterator<TRow, Standard>::Type TIterator;
+    TIterator itH = iter(row(align, 0), beginPos, Standard());
+    TIterator itHEnd = iter(row(align, 0), endPos, Standard());
+    TIterator itV = iter(row(align, 1), beginPos, Standard());
+    TIterator itVEnd = iter(row(align, 1), endPos, Standard());
+    int numErrors = 0;
+    for (; itH != itHEnd; ++itH, ++itV)
+        numErrors += (isGap(itH) || isGap(itV) || (*itH != *itV));
+    SEQAN_ASSERT(itV == itVEnd);
+    (void)itVEnd;  // only used when assertions are enabled
+
+    // Build result.
+    return OverlapInfo_(lhs, rhs, length(store.readSeqStore[lhs]), beginPos, numErrors);
+}
+
+template <typename TFragmentStore>
+inline void OverlapInfoComputation_<TFragmentStore>::buildGlobalAlignmentOverlapInfos(
+        std::vector<OverlapInfo_> & infos) const
+{
+    for (unsigned i = 0; i < length(store.readStore); ++i)
+        for (unsigned j = i + 1; j < length(store.readStore); ++j)
+        {
+            OverlapInfo_ info = computeOverlapInfo(i, j,
+                                                   seqan::minValue<int>(), seqan::minValue<int>());
+            int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1;
+            // if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxErrorRate)
+            // {
+            //     if (options.verbosity >= 2)
+            //         std::cerr << "DISCARDING OVL\t" << store.readSeqStore[info.seq0] << "\tseq0=" << info.seq0
+            //                   << "\t" << store.readSeqStore[info.seq1] << "\tseq1=" << info.seq1
+            //                   << "\tlen0=" << info.len0 << "\tpos1=" << info.pos1
+            //                   << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n";
+            //     continue;  // skip, does not pass quality control
+            // }
+
+            infos.push_back(info);
+            if (options.verbosity >= 2)
+                std::cerr << "OVERLAP\t" << store.readSeqStore[info.seq0] << "\tseq0=" << info.seq0
+                          << "\t" << store.readSeqStore[info.seq1] << "\tseq1=" << info.seq1
+                          << "\tlen0=" << info.len0 << "\tpos1=" << info.pos1
+                          << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n";
+        }
+}
+
+template <typename TFragmentStore>
+inline void OverlapInfoComputation_<TFragmentStore>::buildPositionBasedOverlapInfos(
+        std::vector<OverlapInfo_> & infos) const
+{
+    typedef typename TFragmentStore::TAlignedReadStore const TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignedReadStoreIter;
+
+    // Obtain sorted copy of store's aligned read store.
+    TAlignedReadStore sortedAlignedReads = store.alignedReadStore;
+    sortAlignedReads(sortedAlignedReads, SortBeginPos());
+    sortAlignedReads(sortedAlignedReads, SortContigId());
+
+    // Iterate over aligned read store, compute overlaps indicated in this multi-read alignment, and collect them.
+    std::vector<OverlapInfo_> overlaps;  // will be expanded to alignments later
+    TAlignedReadStoreIter it = begin(sortedAlignedReads, Standard());
+    TAlignedReadStoreIter itEnd = end(sortedAlignedReads, Standard());
+    for (; it != itEnd; ++it)
+        // Consider all overlaps with it->readId right of it but overlapping.
+        for (TAlignedReadStoreIter it2 = it; it2 != itEnd; ++it2)
+        {
+            if (it == it2)
+                continue;  // no overlap with self
+            if (it2->contigId != it->contigId || static_cast<unsigned>(it2->beginPos) > static_cast<unsigned>(it->endPos + options.posDelta))
+                break;  // traversed contig or went too far to the right on same contig
+            int pos = it2->beginPos - it->beginPos;
+            OverlapInfo_ info = computeOverlapInfo(it->readId, it2->readId,
+                                                   pos - options.posDelta, pos + options.posDelta);
+            int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1;
+            if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxErrorRate)
+            {
+                if (options.verbosity >= 2)
+                    std::cerr << "DISCARDING OVL\t" << store.readSeqStore[info.seq0] << "\tseq0=" << info.seq0
+                              << "\t" << store.readSeqStore[info.seq1] << "\tseq1=" << info.seq1
+                              << "\tlen0=" << info.len0 << "\tpos1=" << info.pos1
+                              << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n";
+                continue;  // skip, does not pass quality control
+            }
+
+            infos.push_back(info);
+            if (options.verbosity >= 2)
+                std::cerr << "OVERLAP\t" << store.readSeqStore[info.seq0] << "\tseq0=" << info.seq0
+                          << "\t" << store.readSeqStore[info.seq1] << "\tseq1=" << info.seq1
+                          << "\tlen0=" << info.len0 << "\tpos1=" << info.pos1
+                          << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n";
+        }
+}
+
+template <typename TFragmentStore>
+inline void OverlapInfoComputation_<TFragmentStore>::buildContigAllToAllOverlapInfos(
+        std::vector<OverlapInfo_> & infos) const
+{
+    std::map<unsigned, std::vector<unsigned> > readIDs;  // factorized by contig ID
+    for (unsigned i = 0; i < length(store.alignedReadStore); ++i)
+        readIDs[store.alignedReadStore[i].contigId].push_back(store.alignedReadStore[i].readId);
+
+    for (std::map<unsigned, std::vector<unsigned> >::const_iterator it = readIDs.begin(); it != readIDs.end(); ++it)
+        buildAllToAllOverlapInfos(infos, it->second);
+}
+
+template <typename TFragmentStore>
+inline void OverlapInfoComputation_<TFragmentStore>::buildAllToAllOverlapInfos(
+        std::vector<OverlapInfo_> & infos) const
+{
+    std::vector<unsigned> readIDs;
+    for (unsigned readID = 0; readID < length(store.readSeqStore); ++readID)
+        readIDs.push_back(readID);
+    buildAllToAllOverlapInfos(infos, readIDs);
+}
+
+template <typename TFragmentStore>
+inline void OverlapInfoComputation_<TFragmentStore>::buildAllToAllOverlapInfos(
+        std::vector<OverlapInfo_> & infos,
+        std::vector<unsigned> const & readIDs) const
+{
+    typedef typename TFragmentStore::TReadSeqStore const TReadSeqStore;
+    typedef typename Value<TReadSeqStore>::Type TReadSeq;
+    typedef typename Value<TReadSeq>::Type TAlphabet;
+    typedef StringSet<TReadSeq, Dependent<> > TStringSet;
+    typedef StringSet<TReadSeq> TSuperStringSet;  // owner
+    typedef typename Iterator<TStringSet, Standard>::Type TStringSetIter;
+
+    // Get copy of fragment store's read seq store.
+    TSuperStringSet superSet;
+    for (unsigned i = 0; i < length(store.readSeqStore); ++i)
+        appendValue(superSet, store.readSeqStore[i]);
+
+    // Obtain subset of fragment store's read sequences.
+    TStringSet subSet;
+    for (std::vector<unsigned>::const_iterator it = readIDs.begin(); it != readIDs.end(); ++it)
+        assignValueById(subSet, superSet, *it);
+
+    // Build q-gram index over the read subset.
+    typedef Shape<TAlphabet, OneGappedShape>        TShape;
+    typedef IndexQGram<TShape, OpenAddressing>      TIndexSpec;
+    typedef Index<TStringSet const, TIndexSpec>     TIndex;
+    typedef Pattern<TIndex, Pigeonhole<> >          TFilterPattern;
+    typedef Finder<TReadSeq const, Pigeonhole<> > TFilterFinder;
+
+    double maxErrorRate = 1.0 / options.kMerSize;
+
+    TIndex index(subSet);
+    TFilterPattern filterPattern(index);
+    _patternInit(filterPattern, maxErrorRate);
+
+    // Perform the pigeonhole-based search.
+    for (TStringSetIter it = begin(subSet, seqan::Rooted()); !atEnd(it); ++it)
+    {
+        unsigned seq0 = position(it);
+        TFilterFinder filterFinder(*it);
+        while (find(filterFinder, filterPattern, maxErrorRate))
+        {
+            if (length(countOccurrencesMultiple(index, filterPattern.shape)) > (unsigned)options.kMerMaxOcc)
+                continue;  // Ignore, too many matching sequences.
+
+            unsigned seq1 = filterFinder.curHit->ndlSeqNo;
+            // TODO(holtgrew): Care about dupes, i.e. use >=.
+            if (seq1 == seq0)
+                continue;  // Skip hits with self.
+            // TODO(holtgrew): bands not tight...
+            __int64 lDiag = beginPosition(filterFinder);//.curHit->hstkPos;
+            __int64 uDiag = endPosition(filterFinder);//filterFinder.curHit->hstkPos + filterFinder.curHit->bucketWidth - length(subSet[seq1]);
+            SEQAN_ASSERT_GEQ(uDiag, lDiag);
+
+            OverlapInfo_ info(computeOverlapInfo(positionToId(subSet, seq0), positionToId(subSet, seq1),
+                                                 lDiag, uDiag));
+
+            int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1;
+            if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxErrorRate)
+            {
+                if (options.verbosity >= 2)
+                    std::cerr << "DISCARDING OVL\t" << store.readSeqStore[info.seq0] << "\tseq0=" << info.seq0
+                              << "\t" << store.readSeqStore[info.seq1] << "\tseq1=" << info.seq1
+                              << "\tlen0=" << info.len0 << "\tpos1=" << info.pos1
+                              << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n";
+                continue;  // skip, does not pass quality control
+            }
+
+            infos.push_back(info);
+            if (options.verbosity >= 2)
+                std::cerr << "OVERLAP\t" << store.readSeqStore[info.seq0] << "\tseq0=" << info.seq0
+                          << "\t" << store.readSeqStore[info.seq1] << "\tseq1=" << info.seq1
+                          << "\tlen0=" << info.len0 << "\tpos1=" << info.pos1
+                          << "\tnumErrors=" << info.numErrors << "\n";
+        }
+    }
+}
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_CONSENSUS_OVERLAP_INFO_COMPUTATION_H_
diff --git a/seqan/consensus/overlapper.h b/seqan/consensus/overlapper.h
new file mode 100644
index 0000000..c5207b0
--- /dev/null
+++ b/seqan/consensus/overlapper.h
@@ -0,0 +1,395 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_CONSENSUS_OVERLAPPER_H_
+#define INCLUDE_SEQAN_CONSENSUS_OVERLAPPER_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class OverlapperOptions_
+// ----------------------------------------------------------------------------
+
+// Overlapper configuration.
+struct OverlapperOptions_
+{
+    OverlapperOptions_() : overlapErrorRate(0.05), overlapMinLength(40), logging(false)
+    {}
+
+    double overlapErrorRate;
+    int overlapMinLength;
+    bool logging;
+};
+
+// ----------------------------------------------------------------------------
+// Class OverlapCandidate_
+// ----------------------------------------------------------------------------
+
+class OverlapCandidate_
+{
+public:
+    unsigned seq0;
+    unsigned seq1;
+    int lDiag;
+    int uDiag;
+
+    // Constructors.
+    OverlapCandidate_() : seq0(0), seq1(0), lDiag(0), uDiag(0) {}
+    OverlapCandidate_(unsigned seq0, unsigned seq1, int lDiag, int uDiag) :
+            seq0(seq0), seq1(seq1), lDiag(lDiag), uDiag(uDiag)
+    {}
+
+    // Compares two OverlapCanidate objects lexicographically.
+    bool operator<(OverlapCandidate_ const & other) const
+    { return std::make_pair(seq0, seq1) < std::make_pair(other.seq0, other.seq1); }
+};
+
+inline std::ostream & operator<<(std::ostream & out, OverlapCandidate_ const & cand)
+{
+    return out << "OverlapCandidate_(seq0=" << cand.seq0 << ", seq1=" << cand.seq1
+               << ", lDiag=" << cand.lDiag << ", uDiag=" << cand.uDiag << ")";
+}
+
+// ----------------------------------------------------------------------------
+// Class Overlap_
+// ----------------------------------------------------------------------------
+
+// Stores an overlap, usually such that seq0 is left of seq1 or if both start at the same position then seq0 is the id
+// of the longer sequence (container).  In case of stacking, seq0 < seq1.
+
+class Overlap_
+{
+public:
+    // Value for invalid entry below.
+    static const unsigned INVALID = (unsigned)-1;
+
+    // Identifiers of the sequence.
+    unsigned seq0;
+    unsigned seq1;
+    // Lengths of the sequences.
+    unsigned len0;
+    unsigned len1;
+    // Begin positions of the sequences.
+    unsigned begin0;
+    unsigned begin1;
+    // Edit distance errors of the alignment.
+    unsigned errors;
+
+    // Default constructor and construct with all values.
+    Overlap_() : seq0(INVALID), seq1(INVALID), len0(INVALID), len1(INVALID), begin0(INVALID), begin1(INVALID),
+                 errors(INVALID)
+    {}
+
+    Overlap_(unsigned seq0, unsigned seq1, unsigned len0, unsigned len1, unsigned begin0, unsigned begin1,
+             unsigned errors = INVALID) :
+            seq0(seq0), seq1(seq1), len0(len0), len1(len1), begin0(begin0), begin1(begin1), errors(errors)
+    {}
+
+    // Returns a "flipped" alignment, i.e. seq0 and seq1 change roles.
+    Overlap_ flip() const { return Overlap_(seq1, seq0, len1, len0, begin1, begin0, errors); }
+
+    // Returns a normalized overlap, i.e. if begin0 != begin1 then seq0 < seq1.  If begin0 == begin1 then ties are
+    // broken by length (such that the container comes first), in case of stacks, ties are broken by id.
+    Overlap_ normalize() const
+    {
+        if (begin0 != begin1)
+        {
+            return (begin0 < begin1) ? *this : flip();
+        }
+        else  // begin0 == begin1
+        {
+            if (len0 != len1)
+                return (len0 > len1) ? *this : flip();
+            else  // begin0 == begin1 && len0 == len1
+                return (seq0 < seq1) ? *this : flip();
+        }
+    }
+
+    // Returns the length of the overlap.
+    int length() const
+    {
+        Overlap_ o = normalize();
+        return (o.len0 - o.begin1);
+    }
+
+    // Returns "key", i.e. (seq0, seq1).
+    std::pair<unsigned, unsigned> key() const { return std::make_pair(seq0, seq1); }
+
+    // Compares two Overlap_ objects lexicographically.
+    bool operator<(Overlap_ const & other) const { return (key() < other.key()); }
+};
+
+inline std::ostream & operator<<(std::ostream & out, Overlap_ const & ovl)
+{
+    return out << "Overlap_(seq0=" << ovl.seq0 << ", seq1=" << ovl.seq1 << ", len0=" << ovl.len0
+               << ", len1=" << ovl.len1 << ", begin0=" << ovl.begin0 << ", begin1=" << ovl.begin1
+               << ", errors=" << ovl.errors << ")";
+}
+
+// ----------------------------------------------------------------------------
+// Class Overlapper_
+// ----------------------------------------------------------------------------
+
+template <typename TFragments, typename TSequence>
+class Overlapper_
+{
+public:
+    explicit Overlapper_(OverlapperOptions_ options = OverlapperOptions_()) : options(options)
+    {}
+
+    // Compute overlap from candidate and store it in overlap and alignment on success.  Return false if the overlap did
+    // not exist.
+    bool computeOverlap(Overlap_ & overlap,
+                        TFragments & alignment,
+                        TSequence const & seqH,
+                        TSequence const & seqV,
+                        OverlapCandidate_ const & candidate) const;
+
+private:
+    // Generate Overlap_ record from the alignment stored in fragments.  Length information is taken from seqs.
+    Overlap_ overlapFromAlignment(
+            String<Fragment<> > const & fragments,
+            StringSet<TSequence, Dependent<> > const & strings) const;
+
+    template <typename TSequenceH, typename TSequenceV, typename TAlignConfig, typename TAlgoTag>
+    void _fixBandSize(int & lDiag,
+                      int & uDiag,
+                      TSequenceH const & seqH,
+                      TSequenceV const & seqV,
+                      TAlignConfig const & /*alignConfig*/,
+                      TAlgoTag const & /*algoTag*/) const
+    {
+        // typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+        typedef typename If<typename IsSameType<TAlgoTag, Gotoh>::Type, AffineGaps, LinearGaps>::Type TGapsType;
+        typedef typename SetupAlignmentProfile_<DPGlobal, TAlignConfig, TGapsType, TracebackConfig_<SingleTrace, GapsLeft> >::Type TDPProfile;
+
+        if (uDiag < -(int)length(seqV))
+            uDiag = -(int)length(seqV);
+        if (lDiag > (int)length(seqH))
+            lDiag = length(seqV);
+
+        if (uDiag < 0 && !IsFreeEndGap_<TDPProfile, DPFirstColumn>::VALUE)
+            uDiag = 0;
+
+        if (lDiag > 0 && !IsFreeEndGap_<TDPProfile, DPFirstRow>::VALUE)
+            lDiag = 0;
+
+        if (uDiag + (int)length(seqV) < (int)length(seqH) && !IsFreeEndGap_<TDPProfile, DPLastRow>::VALUE)
+            uDiag = (int)length(seqH) - (int)length(seqV);
+
+        if (lDiag + (int)length(seqV) > (int)length(seqH) && !IsFreeEndGap_<TDPProfile, DPLastColumn>::VALUE)
+            lDiag = (int)length(seqH) - (int)length(seqV);
+    }
+
+    OverlapperOptions_ options;
+};
+
+template <typename TFragments, typename TSequence>
+Overlap_ Overlapper_<TFragments, TSequence>::overlapFromAlignment(
+        String<Fragment<> > const & fragments,
+        StringSet<TSequence, Dependent<> > const & strings) const
+{
+    typedef StringSet<TSequence, Dependent<> > TStringSet;
+    typedef typename Value<TStringSet>::Type TString;
+    TStringSet & stringsNC = const_cast<StringSet<TSequence, Dependent<> > &>(strings);
+
+    if (options.logging)
+    {
+        std::cerr << "FRAGMENTS\n";
+        for (unsigned i = 0; i < length(fragments); ++i)
+            std::cerr << "  Fragment(" << fragments[i].seqId1 << ", " << fragments[i].begin1
+                      << ", " << fragments[i].seqId2 << ", " << fragments[i].begin2 << ", "
+                      << fragments[i].len << ")\n";
+    }
+
+    // TODO(holtgrew): overlap length should actually be the length of the alignment
+
+    TFragments frags = fragments;
+    std::sort(begin(frags, seqan::Standard()), end(frags, seqan::Standard()));
+
+    typename Value<TFragments>::Type frag0 = front(frags);  // first
+    unsigned id0 = sequenceId(frag0, 0);
+    unsigned id1 = sequenceId(frag0, 1);
+    unsigned len0 = length(strings[0]);
+    unsigned len1 = length(strings[1]);
+
+    typedef int TPos;
+    std::pair<TPos, TPos> range0(seqan::maxValue<TPos>(), seqan::minValue<TPos>());
+    std::pair<TPos, TPos> range1 = range0;
+    int errors = 0;
+    typedef typename Iterator<TFragments, Standard>::Type TFragmentsIter;
+    for (TFragmentsIter itF = begin(frags, seqan::Standard()); itF != end(frags, seqan::Standard()); ++itF)
+    {
+        // Get some shortcuts.
+        TPos fLen = fragmentLength(*itF);
+        TPos begin0 = fragmentBegin(*itF, id0);
+        TPos begin1 = fragmentBegin(*itF, id1);
+
+        // Count indels.
+        if (itF != begin(frags, seqan::Standard()))
+        {
+            SEQAN_ASSERT_LEQ(range0.second, begin0);
+            SEQAN_ASSERT_LEQ(range1.second, begin1);
+            SEQAN_ASSERT_NEQ((begin0 != range0.second), (begin1 != range1.second));
+            errors += (begin0 - range0.second);
+            errors += (begin1 - range1.second);
+        }
+
+        // Update begin/end position in either read.
+        range0.first = std::min(range0.first, begin0);
+        range0.second = std::max(range0.second, begin0 + fLen);
+        range1.first = std::min(range1.first, begin1);
+        range1.second = std::max(range1.second, begin1 + fLen);
+
+        // Count matches/mismatches.
+        typedef typename Infix<TString>::Type TInfix;
+        typedef typename Iterator<TInfix, Standard>::Type TInfixIter;
+        TInfix label0 = label(*itF, stringsNC, id0);
+        TInfix label1 = label(*itF, stringsNC, id1);
+        for (TInfixIter it0 = begin(label0, seqan::Standard()), it1 = begin(label1, seqan::Standard());
+             it0 != end(label0, seqan::Standard()); ++it0, ++it1)
+            errors += ((seqan::Dna5)*it0 == 'N' ||
+                       (seqan::Dna5)*it1 == 'N' ||
+                       (seqan::Dna5)*it0 != (seqan::Dna5)*it1);
+    }
+
+    // In case that the alignment to the right aligns to a gap, flush left.
+    int delta = std::min(range0.first, range1.first);
+    range0.first -= delta;
+    range1.first -= delta;
+
+    SEQAN_ASSERT_MSG(range0.first == 0 || range1.first == 0, "One must start at beginning");
+    // NB: Do not activate the following, does not have to be true, can end in alignment to gap.
+    // SEQAN_ASSERT_MSG(range0.second == len0 || range1.second == len1, "One must end at last");
+
+    TPos begin1 = range0.first, begin0 = range1.first;
+    // int overlapLen = std::max(range0.second - range0.first, range1.second - range1.first);
+
+    if (options.logging)
+    {
+        std::cerr << "range0 = (" << range0.first << ", " << range0.second << ")\n"
+                  << "range1 = (" << range1.first << ", " << range1.second << ")\n";
+    }
+
+    return Overlap_(id0, id1, len0, len1, begin0, begin1, errors);
+}
+
+template <typename TFragments, typename TSequence>
+inline bool Overlapper_<TFragments, TSequence>::computeOverlap(Overlap_ & overlap,
+                                                               TFragments & frags,
+                                                               TSequence const & seqH,
+                                                               TSequence const & seqV,
+                                                               OverlapCandidate_ const & candidate) const
+{
+    clear(frags);
+
+    if (options.logging)
+        std::cerr << "Computing overlap\n"
+                  << "  seqH: " << seqH << "\n"
+                  << "  seqV: " << seqV << "\n"
+                  << "  cand: " << candidate << "\n";
+
+    StringSet<TSequence, Dependent<> > pairSet;
+    appendValue(pairSet, const_cast<TSequence &>(seqH));  // id 0
+    appendValue(pairSet, const_cast<TSequence &>(seqV));  // id 1
+
+    Score<int, Simple> scoringScheme(1000, -1000, -1001);
+
+    AlignConfig<true, true, true, true> alignConfig;
+    int uDiag = candidate.uDiag;
+    int lDiag = candidate.lDiag;
+
+    _fixBandSize(lDiag, uDiag, pairSet[0], pairSet[1], alignConfig, Gotoh());
+
+    // DEBUG
+    if (options.logging)
+    {
+        std::cerr << "\n\n(alignment of " << candidate << ")\n"
+                  << "0:\t" << pairSet[0] << "\n"
+                  << "1:\t" << pairSet[1] << "\n";
+        typedef typename Value<StringSet<TSequence> >::Type TStringSeq;
+        Align<TStringSeq> align;
+        resize(rows(align), 2);
+        setSource(row(align, 0), pairSet[0]);
+        setSource(row(align, 1), pairSet[1]);
+        globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh());
+        std::cerr << "\n" << align << "\n";
+    }
+    // /DEBUG
+
+    int overlapScore = globalAlignment(frags, pairSet, scoringScheme, alignConfig, lDiag, uDiag,
+                                       NeedlemanWunsch());
+    (void)overlapScore;
+    if (empty(frags))
+        return false;
+
+    overlap = overlapFromAlignment(frags, pairSet);
+
+    // Replace ids in fragments and overlap.
+    overlap.seq0 = candidate.seq0;
+    overlap.seq1 = candidate.seq1;
+    for (unsigned i = 0; i < length(frags); ++i)
+    {
+        sequenceId(frags[i], 0) = candidate.seq0;
+        sequenceId(frags[i], 1) = candidate.seq1;
+    }
+
+    int ovlLen = overlap.length();
+    bool ok = ((options.overlapMinLength < 0 || ovlLen >= options.overlapMinLength) &&
+               ((options.overlapErrorRate < 0 || ovlLen == 0)
+                || (1.0 * overlap.errors / ovlLen) <= options.overlapErrorRate + 0.00001));
+    if (options.logging)
+        std::cerr << "Resulting overlap:\t" << overlap << " (passes quality? " << ok << ")\n";
+    return ok;
+}
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_CONSENSUS_OVERLAPPER_H_
diff --git a/seqan/file.h b/seqan/file.h
index 0886dde..a1b592d 100644
--- a/seqan/file.h
+++ b/seqan/file.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,13 @@
 #ifndef SEQAN_HEADER_FILE_H
 #define SEQAN_HEADER_FILE_H
 
-//____________________________________________________________________________
-// prerequisites
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+// ----------------------------------------------------------------------------
+// STL prerequisites
+// ----------------------------------------------------------------------------
 
 #include <iostream>
 #include <climits>
@@ -43,81 +48,47 @@
 #include <vector>
 #include <map>
 #include <cmath>
+#include <sstream>
+#include <cctype>
+
+// ----------------------------------------------------------------------------
+// SeqAn prerequisites
+// ----------------------------------------------------------------------------
 
 #include <seqan/sequence.h>
 #include <seqan/modifier.h>
 
-#ifdef SEQAN_NEW_IO
-#include <cctype>
-#endif
-
-
-//____________________________________________________________________________
+// ===========================================================================
+// Forwards.
+// ===========================================================================
 
 #include <seqan/file/file_forwards.h>
 
-#ifndef SEQAN_NEW_IO
-#include <seqan/file/cstream.h>
-#include <seqan/file/stream.h>
-#endif
-
-#include <seqan/file/chunk_collector.h>
-// #include <seqan/file/meta.h>
-
-//____________________________________________________________________________
-// files
+// ===========================================================================
+// File.
+// ===========================================================================
 
 #include <seqan/file/file_interface.h>
-#ifndef SEQAN_NEW_IO
-#include <seqan/file/file_cstyle.h>
-#endif
 #include <seqan/file/file_base.h>
+#include <seqan/system.h>    // async file (default file type of File<>)
 
-#include <seqan/system.h>	// async file (default file type of File<>)
-
-/*#include <seqan/system/file_sync.h>
-#include <seqan/system/system_event.h>
-#include <seqan/system/file_async.h>
-*/
-
-//____________________________________________________________________________
-// file formats
-#ifndef SEQAN_NEW_IO
-#include <seqan/file/file_filereaderiterator.h>
-#include <seqan/file/file_filereader.h>
-
-#include <seqan/file/file_format.h>
+// ===========================================================================
+// External Strings.
+// ===========================================================================
 
-#include <seqan/file/stream_algorithms.h>
-
-//file formats for sequences
-#include <seqan/file/file_format_raw.h>
-#include <seqan/file/file_format_fasta.h>
-#include <seqan/file/file_format_embl.h>
-#include <seqan/file/file_format_genbank.h>
-
-//file formats for alignments
-#include <seqan/file/file_format_fasta_align.h>
-
-//others
-#include <seqan/file/file_format_cgviz.h>
-#endif
-
-//____________________________________________________________________________
-
-//#include <seqan/file/file_format_guess.h>
-
-//____________________________________________________________________________
-// external strings
+// ----------------------------------------------------------------------------
+// Paging and mapping
+// ----------------------------------------------------------------------------
 
 #include <seqan/file/file_page.h>
 #include <seqan/file/file_mapping.h>
-#include <seqan/file/string_mmap.h>
 //#include <seqan/file/file_pager.h>
-#include <seqan/file/string_external.h>
 
-#ifndef SEQAN_NEW_IO
-#include <seqan/file/file_format_mmap.h>
-#endif
+// ----------------------------------------------------------------------------
+// String specializations
+// ----------------------------------------------------------------------------
+
+#include <seqan/file/string_mmap.h>
+#include <seqan/file/string_external.h>
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/INFO b/seqan/file/INFO
deleted file mode 100644
index 8bca5e0..0000000
--- a/seqan/file/INFO
+++ /dev/null
@@ -1,13 +0,0 @@
-Name: seqan-file
-Author: David Weese <david.weese@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature, known issues
-Description: Implementation file I/O and parsing.
- This module contains code for reading and parsing files in different formats.
- Also, it contains the external and memory mapped string specializations.
- .
- Eventually, it will be replaced by the module stream from extras.
diff --git a/seqan/file/chunk_collector.h b/seqan/file/chunk_collector.h
deleted file mode 100644
index 2089b0b..0000000
--- a/seqan/file/chunk_collector.h
+++ /dev/null
@@ -1,598 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_CHUNK_COLLECTOR_H
-#define SEQAN_HEADER_CHUNK_COLLECTOR_H
-
-/* IOREV
- * _tested_
- * _nodoc_
- * 
- * this class is only used file_format_raw
- * it is tested by test_file which tests file_format_raw
- * it is sparsely documented, but marked as Internal anyway (does it need doku
- * then?)
- * TODO not fully understood implications of assign and replace
- */
-
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal.ChunkCollector_:
-..cat:Classes
-..summary:Reads piecewise from stream, collects pieces (chunks) in a vector.
-..signature:ChunkCollector_<Host>
-..param.Host:Type of host object that is used as allocator.
-*/
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename T>
-struct ChunkLength
-{
-//IOREV
-	enum { VALUE = 1024 };
-};
-
-//////////////////////////////////////////////////////////////////////////////
-// StreamChunkCollector_ class: collects content of a stream in chunks
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename THost>
-class ChunkCollector_
-{
-//IOREV
-public:
-	THost * data_host;
-	typename Size<THost>::Type data_length;
-
-	typedef ::std::vector<typename Value<THost>::Type *, ToStdAllocator<THost, typename Value<THost>::Type *> > Chunk_Holder;
-	Chunk_Holder data_chunks; 
-
-public:
-	static int const CHUNK_LENGTH = ChunkLength<ChunkCollector_>::VALUE;
-
-public:
-	ChunkCollector_(THost & _host):
-		data_host(& _host),
-		data_length(0),
-		data_chunks(typename Chunk_Holder::allocator_type(_host))
-	{
-	}
-
-	~ChunkCollector_()
-	{
-		clear(*this);
-	}
-
-};
-
-template <typename THost>
-inline void
-clear(ChunkCollector_<THost> & me)
-{
-//IOREV
-   typedef ChunkCollector_<THost> TChunkCollector;
-   typedef typename TChunkCollector::Chunk_Holder Chunk_Holder;
-      
-	typename Chunk_Holder::iterator it = me.data_chunks.begin();
-	typename Chunk_Holder::iterator it_end = me.data_chunks.end();
-
-	for (; it != it_end; ++it)
-	{
-		deallocate(me.data_host, *it, TChunkCollector::CHUNK_LENGTH);
-	}
-
-	me.data_chunks.clear();
-	me.data_length = 0;
-}
-
-template <typename THost>
-inline typename Size<THost>::Type
-length(ChunkCollector_<THost> const & me)
-{
-//IOREV 
-	return me.data_length;
-}
-
-template <typename THost>
-inline void
-_setLength(ChunkCollector_<THost> & me, typename Size<THost>::Type new_length)
-{
-//IOREV
-	me.data_length = new_length;
-}
-
-template <typename THost>
-inline int
-chunkCount(ChunkCollector_<THost> const & me)
-{
-//IOREV
-	return me.data_chunks.size();
-}
-
-template <typename THost>
-inline typename Value<THost>::Type *
-getChunk(ChunkCollector_<THost> const & me, int chunk_number)
-{
-//IOREV
-	return me.data_chunks[chunk_number];
-}
-
-template <typename THost>
-inline typename Value<THost>::Type *
-createChunk(ChunkCollector_<THost> & me)
-{
-//IOREV
-   typedef ChunkCollector_<THost> TChunkCollector;
-	typename Value<THost>::Type * new_chunk;
-	allocate(me.data_host, new_chunk, TChunkCollector::CHUNK_LENGTH);
-	me.data_chunks.push_back(new_chunk);
-	return new_chunk;
-}
-	
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename THost>
-struct Host<ChunkCollector_<THost> >
-{
-//IOREV
-	typedef THost Type;
-};
-
-template <typename THost>
-struct Host<ChunkCollector_<THost> const >
-{
-//IOREV
-	typedef THost Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename THost>
-struct Value<ChunkCollector_<THost> >
-{
-//IOREV
-	typedef typename Value<THost>::Type Type;
-};
-
-template <typename THost>
-struct Value<ChunkCollector_<THost> const >
-{
-//IOREV
-	typedef typename Value<THost>::Type Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename THost>
-struct GetValue<ChunkCollector_<THost> >
-{
-//IOREV
-	typedef typename GetValue<THost>::Type Type;
-};
-
-template <typename THost>
-struct GetValue<ChunkCollector_<THost> const >
-{
-//IOREV
-	typedef typename GetValue<THost>::Type Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename THost>
-struct Size<ChunkCollector_<THost> >
-{
-//IOREV
-	typedef typename Size<THost>::Type Type;
-};
-
-template <typename THost>
-struct Size<ChunkCollector_<THost> const >
-{
-//IOREV
-	typedef typename Size<THost>::Type Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-struct AssignStreamToChunkCollector_
-{
-//IOREV
-	template <typename THost, typename TSource>
-	static inline void 
-	assign_(ChunkCollector_<THost> & target,
-		TSource & source)
-	{
-		clear(target);
-
-		while (!_streamEOF(source))
-		{
-			typename Value<THost>::Type * chunk = createChunk(target);
-			typename Size<THost>::Type count = _streamRead(chunk, source, ChunkLength< ChunkCollector_<THost> >::VALUE);
-			_setLength(target, length(target) + count);
-		}
-	}
-
-	template <typename THost, typename TSource>
-	static inline void 
-	assign_(ChunkCollector_<THost> & target,
-		TSource & source,
-		typename Size< ChunkCollector_<THost> >::Type limit)
-	{
-		clear(target);
-
-		while (!_streamEOF(source))
-		{
-			typename Value<THost>::Type * chunk = createChunk(target);
-			typename Size<THost>::Type count = _streamRead(chunk, source, ChunkLength< ChunkCollector_<THost> >::VALUE);
-			_setLength(target, length(target) + count);
-
-			if (length(target) >= limit)
-			{
-				_setLength(target, limit);
-				break;
-			}
-		}
-	}
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename THost, typename TSource>
-inline void 
-assign(ChunkCollector_<THost> & target,
-	   TSource & source)
-{
-//IOREV
-	AssignStreamToChunkCollector_::assign_(target, source);
-}
-template <typename THost, typename TSource>
-inline void 
-assign(ChunkCollector_<THost> & target,
-	   TSource const & source)
-{
-//IOREV
-	AssignStreamToChunkCollector_::assign_(target, source);
-}
-
-template <typename THost, typename TSource, typename TSize>
-inline void 
-assign(ChunkCollector_<THost> & target,
-	   TSource & source,
-	   TSize limit)
-{
-//IOREV
-	AssignStreamToChunkCollector_::assign_(target, source, limit);
-}
-template <typename THost, typename TSource, typename TSize>
-inline void 
-assign(ChunkCollector_<THost> & target,
-	   TSource const & source,
-	   TSize limit)
-{
-//IOREV
-	AssignStreamToChunkCollector_::assign_(target, source, limit);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TExpand>
-struct AssignChunkCollectorToString_
-{
-//IOREV
-	template <typename TTarget, typename TSource>
-	static void assign_(
-		TTarget & target, 
-		TSource & source)
-	{
-		typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), TExpand());
-
-		int i_end = chunkCount(source);
-		typename Value<TTarget>::Type * pos = begin(target);
-		for (int i = 0; i < i_end; ++i)
-		{
-			bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
-			typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
-			typename Value<TSource>::Type * chunk = getChunk(source, i);
-			
-			arrayConstructCopy(chunk, chunk + chunk_length, pos);
-			if (is_last_chunk) break;
-			pos += chunk_length;
-		}
-	}
-
-	template <typename TTarget, typename TSource>
-	static void assign_(
-		TTarget & target, 
-		TSource & source,
-		typename Size<TTarget>::Type limit)
-	{
-		typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), limit, TExpand());
-
-		int i_end = chunkCount(source);
-		typename Value<TTarget>::Type * pos = begin(target);
-		for (int i = 0; i < i_end; ++i)
-		{
-			bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
-			typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
-			typename Value<TSource>::Type * chunk = getChunk(source, i);
-			
-			arrayConstructCopy(chunk, chunk + chunk_length, pos);
-			if (is_last_chunk) break;
-			pos += chunk_length;
-		}
-	}
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
-inline void 
-assign(String<TTargetValue, TTargetSpec> & target,
-	   ChunkCollector_<TSourceHost> const & source,
-	   Tag<TExpand> /*tag*/)
-{
-//IOREV
-	AssignChunkCollectorToString_<Tag<TExpand> >::assign_(target, source);
-}
-template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
-inline void 
-assign(String<TTargetValue, TTargetSpec> & target,
-	   ChunkCollector_<TSourceHost> const & source,
-	   typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
-	   Tag<TExpand> /*tag*/)
-{
-//IOREV
-	AssignChunkCollectorToString_<Tag<TExpand> >::assign_(target, source, limit);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TExpand>
-struct AppendChunkCollectorToString_
-{
-//IOREV
-	template <typename TTarget, typename TSource>
-	static void append_(
-		TTarget & target, 
-		TSource & source)
-	{
-		typedef typename Size<TTarget>::Type TSize;
-		TSize target_length_old = length(target);
-		TSize part_length = _clearSpace(target, length(source), target_length_old, target_length_old, TExpand());
-
-		int i_end = chunkCount(source);
-		typename Value<TTarget>::Type * pos = begin(target) + target_length_old; //begin(target) was possibly changed by _clearSpace
-		for (int i = 0; i < i_end; ++i)
-		{
-			bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
-			typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : (TSize) ChunkLength<TSource>::VALUE;
-			typename Value<TSource>::Type * chunk = getChunk(source, i);
-			
-			arrayConstructCopy(chunk, chunk + chunk_length, pos);
-			if (is_last_chunk) break;
-			pos += chunk_length;
-		}
-	}
-
-	template <typename TTarget, typename TSource>
-	static void append_(
-		TTarget & target, 
-		TSource & source,
-		typename Size<TTarget>::Type limit)
-	{
-		typedef typename Size<TTarget>::Type TSize;
-		TSize target_length_old = length(target);
-		TSize part_length = _clearSpace(target, length(source), target_length_old, target_length_old, limit, TExpand());
-
-		int i_end = chunkCount(source);
-		typename Value<TTarget>::Type * pos = begin(target) + target_length_old; //begin(target) was possibly changed by _clearSpace
-		for (int i = 0; i < i_end; ++i)
-		{
-			bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
-			typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : (TSize) ChunkLength<TSource>::VALUE;
-			typename Value<TSource>::Type * chunk = getChunk(source, i);
-			
-			arrayConstructCopy(chunk, chunk + chunk_length, pos);
-			if (is_last_chunk) break;
-			pos += chunk_length;
-		}
-	}
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
-inline void 
-append(String<TTargetValue, TTargetSpec> & target,
-	   ChunkCollector_<TSourceHost> const & source,
-	   Tag<TExpand> )
-{
-//IOREV
-	AppendChunkCollectorToString_<Tag<TExpand> >::append_(target, source);
-}
-template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
-inline void 
-append(String<TTargetValue, TTargetSpec> & target,
-	   ChunkCollector_<TSourceHost> const & source,
-	   typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
-	   Tag<TExpand> )
-{
-//IOREV
-	AppendChunkCollectorToString_<Tag<TExpand> >::append_(target, source, limit);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TExpand>
-struct ReplaceChunkCollectorToString_
-{
-//IOREV
-	template <typename TTarget, typename TSource>
-	static void replace_(
-		TTarget & target,
-		typename Size<TTarget>::Type pos_begin,
-		typename Size<TTarget>::Type pos_end,
-		TSource & source)
-	{
-		typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, TExpand());
-
-		int i_end = chunkCount(source);
-		typename Value<TTarget>::Type * pos = begin(target) + pos_begin;
-		for (int i = 0; i < i_end; ++i)
-		{
-			bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
-			typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
-			typename Value<TSource>::Type * chunk = getChunk(source, i);
-			
-			arrayConstructCopy(chunk, chunk + chunk_length, pos);
-			if (is_last_chunk) break;
-			pos += chunk_length;
-		}
-	}
-
-	template <typename TTarget, typename TSource>
-	static void replace_(
-		TTarget & target, 
-		typename Size<TTarget>::Type pos_begin,
-		typename Size<TTarget>::Type pos_end,
-		TSource & source,
-		typename Size<TTarget>::Type limit)
-	{
-		typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, limit, TExpand());
-
-		int i_end = chunkCount(source);
-		typename Value<TTarget>::Type * pos = begin(target) + pos_begin;
-		for (int i = 0; i < i_end; ++i)
-		{
-			bool is_last_chunk = ( part_length <= ChunkLength<TSource>::VALUE);
-			typename Size<TTarget>::Type chunk_length = (is_last_chunk) ? part_length : ChunkLength<TSource>::VALUE;
-			typename Value<TSource>::Type * chunk = getChunk(source, i);
-			
-			arrayConstructCopy(chunk, chunk + chunk_length, pos);
-			if (is_last_chunk) break;
-			pos += chunk_length;
-		}
-	}
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
-inline void 
-replace(String<TTargetValue, TTargetSpec> & target,
-		typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
-		typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
-	   ChunkCollector_<TSourceHost> const & source,
-	   Tag<TExpand> /*tag*/)
-{
-//IOREV
-	ReplaceChunkCollectorToString_<Tag<TExpand> >::replace_(target, pos_begin, pos_end, source);
-}
-
-template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
-inline void 
-replace(String<TTargetValue, TTargetSpec> & target,
-		typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
-		typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
-	   ChunkCollector_<TSourceHost> const & source,
-	   typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
-	   Tag<TExpand> /*tag*/)
-{
-//IOREV
-	ReplaceChunkCollectorToString_<Tag<TExpand> >::replace_(target, pos_begin, pos_end, source, limit);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TTargetValue, typename TSourceHost, typename TExpand>
-inline void 
-replace(TTargetValue * target,
-		size_t pos_begin,
-		size_t pos_end,
-		ChunkCollector_<TSourceHost> const & source,
-		Tag<TExpand> /*tag*/)
-{
-//IOREV
-	ReplaceChunkCollectorToString_<Tag<TExpand> >::replace_(target, pos_begin, pos_end, source);
-}
-
-template <typename TTargetValue, typename TSourceHost, typename TExpand>
-inline void 
-replace(TTargetValue * target,
-		size_t pos_begin,
-		size_t pos_end,
-		ChunkCollector_<TSourceHost> const & source,
-		size_t limit,
-		Tag<TExpand> /*tag*/)
-{
-//IOREV
-	ReplaceChunkCollectorToString_<Tag<TExpand> >::replace_(target, pos_begin, pos_end, source, limit);
-}
-//____________________________________________________________________________
-/*
-template <typename TTargetValue, typename TSourceHost, typename TExpand>
-inline void 
-replace(TTargetValue * target,
-		size_t pos_begin,
-		size_t pos_end,
-	   ChunkCollector_<TSourceHost> const & source,
-	   Tag<TExpand> tag)
-{
-	ReplaceChunkCollectorToString_<Tag<TExpand> >::replace_(target, pos_begin, pos_end, source);
-}
-
-template <typename TTargetValue, typename TTargetSpec, typename TSourceHost, typename TExpand>
-inline void 
-replace(String<TTargetValue, TTargetSpec> & target,
-		typename Size< String<TTargetValue, TTargetSpec> >::Type pos_begin,
-		typename Size< String<TTargetValue, TTargetSpec> >::Type pos_end,
-	   ChunkCollector_<TSourceHost> const & source,
-	   typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
-	   Tag<TExpand> tag)
-{
-	ReplaceChunkCollectorToString_<Tag<TExpand> >::replace_(target, pos_begin, pos_end, source, limit);
-}
-*/
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/cstream.h b/seqan/file/cstream.h
deleted file mode 100644
index 96d03ec..0000000
--- a/seqan/file/cstream.h
+++ /dev/null
@@ -1,337 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_CSTREAM_H
-#define SEQAN_HEADER_CSTREAM_H
- 
-#include <cstdio>
-
-/* IOREV
- * _tested_
- * _nodoc_
- * 
- * 
- * Tested by tests/file
- * documentation non-existent
- * relation to file_cstyle.h not clear
- * Metafunctions supposedly moved to file_cstyle.h are commented there too
- */
-
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Adaption."std::FILE *":
-..summary:Standard library C style streams.
-*/
-
-//////////////////////////////////////////////////////////////////////////////
-// Position is now defined in file/file_cstyle.h
-/*
-template <>
-struct Position<FILE *>
-{
-	typedef long Type;
-};
-*/
-//////////////////////////////////////////////////////////////////////////////
-
-template <>
-struct Value<FILE *>
-{
-//IOREV
-	typedef char Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-/*
-template <>
-struct Position<FILE *>
-{
-	typedef ::std::fpos_t Type;
-};
-*/
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename T>
-struct IsTellAndSeekStream_;
-//IOREV
-
-template <>
-struct IsTellAndSeekStream_<FILE *>
-{
-//IOREV
-	typedef True Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-inline bool 
-_streamOpen(::std::FILE * & me, String<char> path, bool for_read = true)
-{
-//IOREV _duplicate_ of file_cstyle's  "open"
-SEQAN_CHECKPOINT
-	if (for_read)
-	{
-		me = fopen(toCString(path), "rb");
-	}
-	else
-	{
-		me = fopen(toCString(path), "wb");
-	}
-	return (me != 0);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-inline void 
-_streamClose(::std::FILE * & me)
-{
-//IOREV _duplicate_ of file_cstyle's  "close"
-SEQAN_CHECKPOINT
-	if (me)
-	{
-		fclose(me);
-		me = 0;
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamEOF.param.stream.type:Adaption."std::FILE *"
-
-inline bool 
-_streamEOF(::std::FILE * me)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	int c = fgetc(me);
-    ungetc(c, me);
-	return (c == EOF) || ferror(me);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamRead.param.stream.type:Adaption."std::FILE *"
-
-template <typename TValue>
-inline size_t 
-_streamRead(TValue * target,
-			::std::FILE * source,
-			size_t limit)
-{
-//IOREV _duplicate_ of file_cstyle.h's  "read"
-SEQAN_CHECKPOINT
-	return ::std::fread(target, sizeof(TValue), limit, source);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamGet.param.stream.type:Adaption."std::FILE *"
-
-inline char 
-_streamGet(::std::FILE * source)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return getc(source);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamPut.param.stream.type:Adaption."std::FILE *"
-
-inline void
-_streamPut(::std::FILE * target,
-		   char character)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	putc(character, target);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamPut.param.stream.type:Adaption."std::FILE *"
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamTellG.param.stream.type:Adaption."std::FILE *"
-
-inline Position<FILE *>::Type
-_streamTellG(FILE * me)
-{
-//IOREV _duplicate_ overlaps in function with file_cstyle.h's  "tell"
-SEQAN_CHECKPOINT
-	return ::std::ftell(me);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamTellP.param.stream.type:Adaption."std::FILE *"
-
-inline Position<FILE *>::Type
-_streamTellP(FILE * me)
-{
-//IOREV _duplicate_ overlaps in function with file_cstyle.h's  "tell"
-SEQAN_CHECKPOINT
-	return ::std::ftell(me);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamSeekG.param.stream.type:Adaption."std::FILE *"
-
-inline void
-_streamSeekG(FILE * me,
-			 Position<FILE *>::Type pos)
-{
-//IOREV _duplicate_ overlaps in function with file_cstyle.h's  "seek"
-SEQAN_CHECKPOINT
-	::std::fseek(me, pos, SEEK_SET);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamSeekP.param.stream.type:Adaption."std::FILE *"
-
-inline void
-_streamSeekP(FILE * me,
-			 Position<FILE *>::Type pos)
-{
-//IOREV _duplicate_ overlaps in function with file_cstyle.h's  "seek"
-SEQAN_CHECKPOINT
-	::std::fseek(me, pos, SEEK_SET);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamSeek2G.param.stream.type:Adaption."std::FILE *"
-
-inline void
-_streamSeek2G(FILE * me,
-	 int off)
-{
-//IOREV _duplicate_ overlaps in function with file_cstyle.h's  "seek"
-SEQAN_CHECKPOINT
-	::std::fseek(me, off, SEEK_CUR);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Internal._streamUnget.param.stream.type:Adaption."std::FILE *"
-
-inline void
-_streamUnget(::std::FILE * stream)
-{
-//IOREV _duplicate_ overlaps in function with file_cstyle.h's  "seek"
-SEQAN_CHECKPOINT
-	_streamSeek2G(stream, -1);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// holder<FILE *>
-
-template <typename THolder>
-inline void
-_holderDeallocate(THolder &, FILE *)
-{
-//IOREV whats this good for?
-}
-template <typename THolder>
-inline FILE *
-_holderAllocatePointer(THolder &, FILE * data)
-{
-//IOREV whats this good for?
-	return data;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// Stream operators for FILE *
-//////////////////////////////////////////////////////////////////////////////
-
-
-// ISO C++ operators are only allowed for classes, not for pointers
-
-/*
-template <typename TSource>
-inline FILE *
-operator << (FILE * target, 
-			 TSource & source)
-{
-SEQAN_CHECKPOINT
-	write(target, source);
-	return target;
-}
-template <typename TSource>
-inline FILE *
-operator << (FILE * target, 
-			 TSource const & source)
-{
-SEQAN_CHECKPOINT
-	write(target, source);
-	return target;
-}
-
-//____________________________________________________________________________
-
-template <typename TTarget>
-inline FILE *
-operator >> (FILE * source, 
-			 TTarget & target)
-{
-SEQAN_CHECKPOINT
-	read(source, target);
-	return source;
-}
-template <typename TTarget>
-inline FILE *
-operator >> (FILE * source, 
-			 TTarget const & target)
-{
-SEQAN_CHECKPOINT
-	read(source, target);
-	return source;
-}
-*/
-
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_base.h b/seqan/file/file_base.h
index 6464edd..126c01c 100644
--- a/seqan/file/file_base.h
+++ b/seqan/file/file_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,18 +34,18 @@
 // Defines basic file access functions.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_FILE_BASE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_FILE_BASE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_FILE_BASE_H_
+#define SEQAN_INCLUDE_SEQAN_FILE_BASE_H_
 
 /* IOREV
  * _doc_
- * 
+ *
  * base class with SPecs and Tags
  * also contains standard calls for IO as wrappers around members
  * in system/file_sync.h and system/file_ssync.h
  * (hese files are built around c++ fstream IO)
  * well documented (in comparison to other files)
- * 
+ *
  * SEQAN_DIRECTIO Macro mentioned here but not documented or tested
  */
 
@@ -76,35 +76,18 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.open:
-..class:Class.File
-..summary:Opens a file, stream, or persistent string.
-..cat:Input/Output
-..signature:open(file, fileName[, openMode])
-..param.file:A File object.
-...type:Class.File
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened. See @Enum.FileOpenMode@ for more details.
-...remarks:If you omit the $OPEN_APPEND$ flag in write mode, the file will be cleared when opened.
-...type:Enum.FileOpenMode
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
     template < typename TSpec >
-    inline bool open(File<TSpec> &me, const char *fileName, int openMode) 
-	{
+    inline bool open(File<TSpec> &me, const char *fileName, int openMode)
+    {
 //IOREV resolves to member in file_(a)sync.h which resolves to fstream
         return me.open(fileName, openMode);
     }
 
     template < typename TSpec >
-    inline bool open(File<TSpec> &me, const char *fileName) 
-	{
+    inline bool open(File<TSpec> &me, const char *fileName)
+    {
 //IOREV
-		return open(me, fileName, DefaultOpenMode<File<TSpec> >::VALUE);
+        return open(me, fileName, DefaultOpenMode<File<TSpec> >::VALUE);
     }
 
 /*!
@@ -125,39 +108,25 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on success <tt>false</tt> on failure.
  */
 
-/**
-.Function.openTemp:
-..class:Class.File
-..summary:Opens a temporary file.
-..cat:Input/Output
-..signature:openTemp(file)
-..param.file:A File object.
-...type:Class.File
-..remarks:After closing this file will automatically be deleted.
-..remarks:The openmode (see @Function.open@) is $OPEN_RDWR | OPEN_CREATE$.
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
     template < typename TSpec >
-    inline bool openTemp(File<TSpec> &me) 
-	{
+    inline bool openTemp(File<TSpec> &me)
+    {
 //IOREV
         return me.openTemp();
     }
 
     template < typename TSpec >
-    inline bool openTemp(File<TSpec> &me, int openMode) 
-	{
+    inline bool openTemp(File<TSpec> &me, int openMode)
+    {
 //IOREV
         return me.openTemp(openMode);
     }
 
     template < typename File >
-    inline void reopen(File &, int) 
-	{
+    inline void reopen(File &, int)
+    {
 //IOREV _stub_ _nodoc_ This is currently a no-op. Is that intended?
-	}
+    }
 
 /*!
  * @fn File#close
@@ -170,28 +139,16 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.close:
-..class:Class.File
-..cat:Input/Output
-..summary:Closes a file.
-..signature:close(file)
-..param.file:A File object.
-...type:Class.File
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
     template < typename TSpec >
-    inline bool close(File<TSpec> & me) 
-	{
+    inline bool close(File<TSpec> & me)
+    {
 //IOREV
         return me.close();
     }
 
     template < typename TSpec >
-    inline unsigned sectorSize(File<TSpec> const & /*me*/) 
-	{
+    inline unsigned sectorSize(File<TSpec> const & /*me*/)
+    {
 //IOREV _duplicate_ _nodoc_ duplicate or identical spec. in file_cstyle.h should'nt this be variable
         return 4096;
     }
@@ -217,28 +174,13 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * The records are read from the position pointed to by the current file pointer (see @link File#seek @endlink).
  */
 
-/**
-.Function.read:
-..class:Class.File
-..cat:Input/Output
-..summary:Loads records from a file.
-..signature:read(file, memPtr, count)
-..param.file:A File object.
-...type:Class.File
-..param.memPtr:A pointer to the first destination record in memory.
-..param.count:The amount of records to be read.
-..returns:A $bool$ which is $true$ on success.
-..remarks:The records are read from the position pointed by the current file pointer (see @Function.seek@).
-..include:seqan/file.h
-*/
-
-	template < typename TSpec, typename TValue, typename TSize >
-    inline bool read(File<TSpec> & me, TValue *memPtr, TSize const count) 
-	{
+    template < typename TSpec, typename TValue, typename TSize >
+    inline bool read(File<TSpec> & me, TValue *memPtr, TSize const count)
+    {
 //IOREV
         typedef typename Size<File<TSpec> >::Type TFileSize;
         TFileSize nbytes = (TFileSize)count * (TFileSize)sizeof(TValue);
-		return me.read(memPtr, nbytes) == nbytes;
+        return me.read(memPtr, nbytes) == nbytes;
     }
 
 /*!
@@ -258,28 +200,13 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * The records are written at the position pointed to by th ecurrent file pointer (see @link File#seek @endlink).
  */
 
-/**
-.Function.write:
-..class:Class.File
-..cat:Input/Output
-..summary:Saves records to a file.
-..signature:write(file, memPtr, count)
-..param.file:A File object.
-...type:Class.File
-..param.memPtr:A pointer to the first source record in memory.
-..param.count:The amount of records to be written.
-..returns:A $bool$ which is $true$ on success.
-..remarks:The records are written at the position pointed by the current file pointer (see @Function.seek@).
-..include:seqan/file.h
-*/
-
-	template < typename TSpec, typename TValue, typename TSize >
-    inline bool write(File<TSpec> & me, TValue const *memPtr, TSize const count) 
-	{
+    template < typename TSpec, typename TValue, typename TSize >
+    inline bool write(File<TSpec> & me, TValue const *memPtr, TSize const count)
+    {
 //IOREV
         typedef typename Size<File<TSpec> >::Type TFileSize;
         TFileSize nbytes = (TFileSize)count * (TFileSize)sizeof(TValue);
-		return me.write(memPtr, nbytes) == nbytes;
+        return me.write(memPtr, nbytes) == nbytes;
     }
 
 /*!
@@ -296,28 +223,13 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on success and <tt>false</tt> on failure.
  */
 
-/**
-.Function.readAt:
-..class:Class.File
-..summary:Loads records from a specific position in a file.
-..cat:Input/Output
-..signature:readAt(file, memPtr, count, fileOfs)
-..param.file:A File object.
-...type:Class.File
-..param.memPtr:A pointer to the first destination record in memory.
-..param.count:The amount of records to be read.
-..param.fileOfs:The absolute file position in bytes measured from the beginning.
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
     template < typename TFile, typename TValue, typename TSize, typename TPos >
-    inline bool readAt(TFile & me, TValue *memPtr, TSize const count, TPos const fileOfs) 
-	{
+    inline bool readAt(TFile & me, TValue *memPtr, TSize const count, TPos const fileOfs)
+    {
 //IOREV
-		typedef typename Position<TFile>::Type pos_t;
-		seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
-		return read(me, memPtr, count);
+        typedef typename Position<TFile>::Type pos_t;
+        seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
+        return read(me, memPtr, count);
     }
 
 /*!
@@ -334,28 +246,13 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.writeAt:
-..class:Class.File
-..summary:Saves records to a specific position in a file.
-..cat:Input/Output
-..signature:writeAt(file, memPtr, count, fileOfs)
-..param.file:A File object.
-...type:Class.File
-..param.memPtr:A pointer to the first source record in memory.
-..param.count:The amount of records to be written.
-..param.fileOfs:The absolute file position in bytes measured from the beginning.
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
     template < typename TFile, typename TValue, typename TSize, typename TPos >
-    inline bool writeAt(TFile & me, TValue const *memPtr, TSize const count, TPos const fileOfs) 
-	{
+    inline bool writeAt(TFile & me, TValue const *memPtr, TSize const count, TPos const fileOfs)
+    {
 //IOREV
-		typedef typename Position<TFile>::Type pos_t;
-		seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
-		return write(me, memPtr, count);
+        typedef typename Position<TFile>::Type pos_t;
+        seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
+        return write(me, memPtr, count);
     }
 
 
@@ -378,42 +275,26 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return TPosition The new file position measured in bytes from the beginning.
  */
 
-/**
-.Function.seek:
-..class:Class.File
-..summary:Changes the current file pointer.
-..cat:Input/Output
-..signature:seek(file, fileOfs[, origin])
-..param.file:A File object.
-...type:Class.File
-..param.fileOfs:A file offset measured in bytes relative to $origin$.
-..param.origin:Selects the origin from where to calculate the new position.
-...default:$SEEK_BEGIN$
-...remarks:For $SEEK_BEGIN$, $SEEK_CURRENT$, or $SEEK_END$ the origin is the beginning, the current pointer, or the end of the file.
-..returns:The new file position measured in bytes from the beginning.
-..include:seqan/file.h
-*/
-
-	template < typename TSpec, typename TPos >
-    inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs, int origin) 
-	{
+    template < typename TSpec, typename TPos >
+    inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs, int origin)
+    {
 //IOREV
-		typedef typename Position< File<TSpec> >::Type TFilePos;
-		TFilePos newOfs = me.seek(fileOfs, origin);
+        typedef typename Position< File<TSpec> >::Type TFilePos;
+        TFilePos newOfs = me.seek(fileOfs, origin);
         #if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
-			if (origin == SEEK_BEGIN && newOfs != (TFilePos)fileOfs) {
-				::std::cerr << "seek returned " << ::std::hex << newOfs << " instead of " << fileOfs << ::std::dec << ::std::endl;
-			}
+            if (origin == SEEK_BEGIN && newOfs != (TFilePos)fileOfs) {
+                std::cerr << "seek returned " << std::hex << newOfs << " instead of " << fileOfs << std::dec << std::endl;
+            }
         #endif
         return newOfs;
     }
-    
-	template < typename TSpec, typename TPos >
-    inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs) 
-	{
+
+    template < typename TSpec, typename TPos >
+    inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const fileOfs)
+    {
 //IOREV
-		return seek(me, fileOfs, SEEK_BEGIN);
-	}
+        return seek(me, fileOfs, SEEK_BEGIN);
+    }
 
 /*!
  * @fn File#tell
@@ -426,21 +307,9 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return TPosition The current position in the file.
  */
 
-/**
-.Function.tell:
-..class:Class.File
-..summary:Gets the current file pointer.
-..cat:Input/Output
-..signature:tell(file)
-..param.file:A File object.
-...type:Class.File
-..returns:The current file position measured in bytes from the beginning.
-..include:seqan/file.h
-*/
-
     template < typename TSpec >
-    inline typename Position< File<TSpec> >::Type tell(File<TSpec> &me) 
-	{
+    inline typename Position< File<TSpec> >::Type tell(File<TSpec> &me)
+    {
 //IOREV
         return me.tell();
     }
@@ -454,51 +323,27 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @param[in,out] file The file to reset the file pointer of.
  */
 
-/**
-.Function.rewind:
-..class:Class.File
-..summary:Sets the current file pointer to the beginning.
-..cat:Input/Output
-..signature:rewind(file)
-..param.file:A File object.
-...type:Class.File
-..remarks:Calls @Function.seek@$(file, 0)$ by default.
-..include:seqan/file.h
-*/
-
     template < typename File >
-    inline void rewind(File &me) 
-	{
+    inline void rewind(File &me)
+    {
 //IOREV
-		seek(me, 0);
+        seek(me, 0);
     }
 
 /*!
- * @fn File#size
+ * @fn File#length
  * @brief Return the file size.
  *
- * @signature TSize size(file);
+ * @signature TSize length(file);
  *
  * @param[in] file The File object to query for its size.
  *
  * @return TSize The file size measured in bytes.
  */
 
-/**
-.Function.size:
-..class:Class.File
-..summary:Gets the file size.
-..cat:Input/Output
-..signature:size(file)
-..param.file:A File object.
-...type:Class.File
-..returns:The file size measured in bytes.
-..include:seqan/file.h
-*/
-
     template < typename TSpec >
-    inline typename Size<File<TSpec> >::Type size(File<TSpec> &me) 
-	{
+    inline typename Size<File<TSpec> >::Type length(File<TSpec> &me)
+    {
 //IOREV
         typename Size<File<TSpec> >::Type old_pos = tell(me);
         typename Size<File<TSpec> >::Type result = seek(me, 0, SEEK_END);
@@ -516,20 +361,9 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @param[in]     newLength The file size in bytes to resize to in bytes.
  */
 
-/**
-.Function.resize:
-..class:Class.File
-..cat:Input/Output
-..signature:resize(file, new_length)
-..param.file:A File object.
-...type:Class.File
-..param.new_length:The new file size measured in bytes.
-..include:seqan/file.h
-*/
-
     template < typename TSpec, typename TSize >
-    inline void resize(File<TSpec> &me, TSize new_length) 
-	{
+    inline void resize(File<TSpec> &me, TSize new_length)
+    {
 //IOREV possibly not standard-conformant, see resize() in file_cstyle.h
         typename Size<File<TSpec> >::Type old_pos = tell(me);
         seek(me, new_length, SEEK_BEGIN);
@@ -548,23 +382,12 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.setEof:
-..class:Class.File
-..summary:Sets the file end to the current pointer.
-..cat:Input/Output
-..signature:setEof(file)
-..param.file:A File object.
-...type:Class.File
-..include:seqan/file.h
-*/
-
     template < typename TSpec >
-    inline bool setEof(File<TSpec> &/*me*/) 
-	{ 
+    inline bool setEof(File<TSpec> &/*me*/)
+    {
 //IOREV _noop_ specialized for async file access but not for sync
-		return true; 
-	}
+        return true;
+    }
 
 
     //////////////////////////////////////////////////////////////////////
@@ -584,7 +407,7 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
         cb(hint);
         return NULL;
     }
-    
+
     template < typename File, typename TValue, typename TSize,
                typename aCallback, typename aHint >
     inline typename AsyncRequest<File>::Type
@@ -606,7 +429,7 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
         cb(hint);
         return NULL;
     }
-    
+
     template < typename File, typename TValue, typename TSize, typename TPos,
                typename aCallback, typename aHint >
     inline typename AsyncRequest<File>::Type
@@ -632,7 +455,7 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
         event.signal();
         return NULL;
     }
-    
+
     template < typename File, typename TValue, typename TSize,
                typename aEvent >
     inline typename AsyncRequest<File>::Type
@@ -654,7 +477,7 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
         event.signal();
         return NULL;
     }
-    
+
     template < typename File, typename TValue, typename TSize, typename TPos,
                typename aEvent >
     inline typename AsyncRequest<File>::Type
@@ -686,27 +509,10 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.asyncReadAt:
-..class:Class.File
-..summary:Asynchronously loads records from a specific position in a file.
-..cat:Input/Output
-..signature:asyncReadAt(file, memPtr, count, fileOfs, request)
-..param.file:A File object.
-...type:Class.File
-..param.memPtr:A pointer to the first destination record in memory.
-..param.count:The amount of records to be read.
-..param.fileOfs:The absolute file position in bytes measured from the beginning.
-..param.request:Reference to a structure that will be associated with this asynchronous request.
-...type:Class.AsyncRequest
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
     template < typename File, typename TValue, typename TSize, typename TPos,
                typename AsyncRequest >
-    inline bool 
-	asyncReadAt(File & me, TValue *memPtr, TSize const count, TPos const fileOfs,
+    inline bool
+    asyncReadAt(File & me, TValue *memPtr, TSize const count, TPos const fileOfs,
         AsyncRequest &)
     {
 //IOREV _stub_ see general discussion about AsynRequest
@@ -728,35 +534,18 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on succcess, <tt>false</tt> on failure.
  */
 
-/**
-.Function.asyncWriteAt:
-..class:Class.File
-..summary:Asynchronously saves records to a specific position in a file.
-..cat:Input/Output
-..signature:asyncWriteAt(file, memPtr, count, fileOfs, request)
-..param.file:A File object.
-...type:Class.File
-..param.memPtr:A pointer to the first source record in memory.
-..param.count:The amount of records to be written.
-..param.fileOfs:The absolute file position in bytes measured from the beginning.
-..param.request:Reference to a structure that will be associated with this asynchronous request.
-...type:Class.AsyncRequest
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
     template < typename File, typename TValue, typename TSize, typename TPos,
-               typename AsyncRequest >
+               typename TAsyncRequest >
     inline bool
-	asyncWriteAt(File & me, TValue const *memPtr, TSize const count, TPos const fileOfs,
-        AsyncRequest &)
+    asyncWriteAt(File & me, TValue const *memPtr, TSize const count, TPos const fileOfs,
+        TAsyncRequest &)
     {
 //IOREV _stub_ see general discussion about AsynRequest
         return writeAt(me, memPtr, count, fileOfs);
     }
 
-	
-	//////////////////////////////////////////////////////////////////////
+
+    //////////////////////////////////////////////////////////////////////
     // pseudo queue specific functions
 
 /*!
@@ -768,23 +557,11 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @param[in,out] file The File object to flush.
  */
 
-/**
-.Function.flush:
-..class:Class.File
-..summary:Waits for all open requests to complete.
-..cat:Input/Output
-..signature:flush(file)
-..param.file:A File object.
-...type:Class.File
-..remarks:$flush$ returns after all pending requests are completed.
-..include:seqan/file.h
-*/
-
     template < typename TSpec >
-    inline void flush(File<TSpec> &) 
-	{
+    inline void flush(File<TSpec> &)
+    {
 //IOREV _noop_ specialized for async file access but not for sync
-	}
+    }
 
 /*!
  * @fn File#waitFor
@@ -804,42 +581,26 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * <tt>timeout</tt> milliseconds.
  */
 
-/**
-.Function.waitFor:
-..class:Class.AsyncRequest
-..summary:Waits for an asynchronous request to complete.
-..cat:Input/Output
-..signature:waitFor(request[, timeoutMilliSec])
-..param.request:Reference to an AsyncRequest object.
-...type:Class.AsyncRequest
-..param.timeoutMilliSec:Timout value in milliseconds.
-...remarks:A value of 0 can be used to test for completion without waiting.
-...default:Infinity.
-..returns:A $bool$ which is $true$ on completion and $false$ on timeout.
-..remarks:$waitFor$ suspends the calling process until $request$ is completed or after $timeoutMilliSec$ milliseconds.
-..include:seqan/file.h
-*/
-
-    inline bool waitFor(AsyncDummyRequest &) 
-	{ 
+    inline bool waitFor(AsyncDummyRequest &)
+    {
 //IOREV _noop_ see general discussion about AsynRequest
-		return true; 
-	}
+        return true;
+    }
 
-	template < typename TTime >
+    template < typename TTime >
     inline bool waitFor(AsyncDummyRequest &, TTime, bool &inProgress)
-	{ 
+    {
 //IOREV _noop_ see general discussion about AsynRequest
         inProgress = false;
-		return true; 
-	}
+        return true;
+    }
 
-	// deprecated
-	template < typename TSpec, typename AsyncRequest >
-    inline void release(File<TSpec> &, AsyncRequest &) 
-	{
+    // deprecated
+    template < typename TSpec, typename AsyncRequest >
+    inline void release(File<TSpec> &, AsyncRequest &)
+    {
 //IOREV _noop_ see general discussion about AsynRequest
-	}
+    }
 
 /*!
  * @fn File#cancel
@@ -853,46 +614,32 @@ inline typename Position< File<TSpec> >::Type seek(File<TSpec> &me, TPos const f
  * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.cancel:
-..class:Class.File
-..summary:Cancels an asynchronous request.
-..cat:Input/Output
-..signature:cancel(file, request)
-..param.file:A File object.
-...type:Class.File
-..param.request:Reference to an AsyncRequest object.
-...type:Class.AsyncRequest
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
     template < typename TSpec, typename AsyncRequest >
-    inline bool cancel(File<TSpec> &, AsyncRequest &) 
-	{
+    inline bool cancel(File<TSpec> &, AsyncRequest &)
+    {
 //IOREV _noop_ see general discussion about AsynRequest
-		return true; 
-	}
+        return true;
+    }
 
 
-	// little helpers
+    // little helpers
 
-	template <typename T1, typename T2> inline
-	T1 enclosingBlocks(T1 _size, T2 _blockSize) 
-	{
+    template <typename T1, typename T2> inline
+    T1 enclosingBlocks(T1 _size, T2 _blockSize)
+    {
 //IOREV not sure what this does, but is used in several places
-		return (_size + (T1)_blockSize - (T1)1) / (T1)_blockSize;
-	}
+        return (_size + (T1)_blockSize - (T1)1) / (T1)_blockSize;
+    }
 
-	template <typename T1, typename T2> inline
-	T1 alignSize(T1 _size, T2 _aligning) 
-	{
+    template <typename T1, typename T2> inline
+    T1 alignSize(T1 _size, T2 _aligning)
+    {
 //IOREV not sure what this does, but is used in several places
         if (_size < (T1)_aligning)
             return _aligning;
         else
-		    return (_size / (T1)_aligning) * (T1)_aligning;
-	}
+            return (_size / (T1)_aligning) * (T1)_aligning;
+    }
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_FILE_BASE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_FILE_BASE_H_
diff --git a/seqan/file/file_cstyle.h b/seqan/file/file_cstyle.h
index ddf6d5b..de3f004 100644
--- a/seqan/file/file_cstyle.h
+++ b/seqan/file/file_cstyle.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,8 +40,8 @@
 /* IOREV
  * _tested_
  * _nodoc_
- * 
- * 
+ *
+ *
  * Tested by tests/file
  * documentation non-existent
  * relation to cstream.h not clear
@@ -56,7 +56,7 @@ namespace SEQAN_NAMESPACE_MAIN
 /*    template <>
     struct Value< FILE* >
     {
-	    typedef unsigned char Type;
+        typedef unsigned char Type;
     };
 */
 /*  already defined in "seqan/cstream.h" ...
@@ -64,14 +64,14 @@ namespace SEQAN_NAMESPACE_MAIN
     template <>
     struct Position< FILE* >
     {
-	    typedef long Type;
+        typedef long Type;
     };
 */
 /*
     template <>
     struct Size< FILE* >
     {
-	    typedef size_t Type;
+        typedef size_t Type;
     };
 */
 /*
@@ -79,22 +79,22 @@ namespace SEQAN_NAMESPACE_MAIN
     template <>
     struct Position< FILE* >
     {
-	    typedef long Type;
+        typedef long Type;
     };
 */
     template <>
     struct Difference< FILE* >
     {
 //IOREV shouldnt this be ulong, as the file can be ulong bytes big?
-	    typedef long Type;
+        typedef long Type;
     };
 
 
-	inline const char * 
-	_getCStyleOpenMode(int openMode) 
-	{
+    inline const char *
+    _getCStyleOpenMode(int openMode)
+    {
 //IOREV double check whether this translates FileOpenMode correctly (doesnt look like it)
-		switch (openMode & OPEN_MASK) {
+        switch (openMode & OPEN_MASK) {
             case OPEN_WRONLY:
                 if (!(openMode & OPEN_APPEND))
                     if (openMode & OPEN_CREATE)
@@ -111,76 +111,76 @@ namespace SEQAN_NAMESPACE_MAIN
                         return "r+";
                 else
                     return "a+";
-			default:
-		        return "r";
-		}
+            default:
+                return "r";
+        }
     }
 
-    inline bool 
-	open(FILE* &me, const char *fileName, int openMode) 
-	{
+    inline bool
+    open(FILE* &me, const char *fileName, int openMode)
+    {
 //IOREV _duplicate_ of cstream.h's  "open"
-		SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
+        SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
         return (me = fopen(fileName, _getCStyleOpenMode(openMode))) != NULL;
     }
 
-    inline bool 
-	open(FILE* &me, const char *fileName) 
-	{
+    inline bool
+    open(FILE* &me, const char *fileName)
+    {
 //IOREV _duplicate_ of cstream.h's  "open"
-		return open(me, fileName, DefaultOpenMode<FILE*>::VALUE);
-	}
+        return open(me, fileName, DefaultOpenMode<FILE*>::VALUE);
+    }
 
-    inline bool 
-	openTemp(FILE* &me) 
-	{
+    inline bool
+    openTemp(FILE* &me)
+    {
 //IOREV
-		SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
+        SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
         return (me = tmpfile()) != NULL;
     }
 
-    inline bool 
-	close(FILE* me) 
-	{
+    inline bool
+    close(FILE* me)
+    {
 //IOREV _duplicate_ of cstream.h's  "close"
-		SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
+        SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
         return fclose(me) == 0;
     }
 
-    inline unsigned 
-	sectorSize(FILE* const &) 
-	{
+    inline unsigned
+    sectorSize(FILE* const &)
+    {
 //IOREV _duplicate_ _nodoc_ duplicate or identical spec. in file_base.h should'nt this be variable
         return 4096;
     }
 
     template < typename TPos >
-    inline Size<FILE*>::Type 
-	seek(FILE* me, TPos const fileOfs, int origin) 
-	{
+    inline Size<FILE*>::Type
+    seek(FILE* me, TPos const fileOfs, int origin)
+    {
 //IOREV _duplicate_ overlaps in function with multiple function in cstream.h
         fseek(me, fileOfs, origin);
-		return ftell(me);
+        return ftell(me);
     }
     template < typename TPos >
-    inline Size<FILE*>::Type 
-	seek(FILE* me, TPos const fileOfs) 
-	{
+    inline Size<FILE*>::Type
+    seek(FILE* me, TPos const fileOfs)
+    {
 //IOREV shouldnt it be SEEK_SET instead of SEEK_BEGIN?
-		return seek(me, fileOfs, SEEK_BEGIN);
+        return seek(me, fileOfs, SEEK_BEGIN);
     }
 
-    inline Size<FILE*>::Type 
-	tell(FILE* me) 
-	{
+    inline Size<FILE*>::Type
+    tell(FILE* me)
+    {
 //IOREV _duplicate_ overlaps in function with multiple functions in cstream.h
-		return ftell(me);
+        return ftell(me);
     }
 
     template < typename TValue, typename TSize >
-    inline bool 
-	read(FILE* me, TValue *memPtr, TSize const count) 
-	{
+    inline bool
+    read(FILE* me, TValue *memPtr, TSize const count)
+    {
 //IOREV _duplicate_ of cstream.h's  "read"
         SEQAN_PROADD(SEQAN_PROIO, (sizeof(TValue) * count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
         SEQAN_PROTIMESTART(tw);
@@ -190,9 +190,9 @@ namespace SEQAN_NAMESPACE_MAIN
     }
 
     template < typename TValue, typename TSize >
-    inline bool 
-	write(FILE* me, TValue const *memPtr, TSize const count) 
-	{
+    inline bool
+    write(FILE* me, TValue const *memPtr, TSize const count)
+    {
 //IOREV
         SEQAN_PROADD(SEQAN_PROIO, (sizeof(TValue) * count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
         SEQAN_PROTIMESTART(tw);
@@ -202,26 +202,26 @@ namespace SEQAN_NAMESPACE_MAIN
     }
 
     template < typename TValue, typename TSize, typename TPos >
-    inline bool 
-	readAt(FILE* me, TValue *memPtr, TSize const count, TPos const fileOfs) 
-	{
+    inline bool
+    readAt(FILE* me, TValue *memPtr, TSize const count, TPos const fileOfs)
+    {
 //IOREV
-		typedef typename Position<FILE*>::Type pos_t;
-		seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
+        typedef typename Position<FILE*>::Type pos_t;
+        seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
         SEQAN_PROADD(SEQAN_PROIO, (sizeof(TValue) * count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
         SEQAN_PROTIMESTART(tw);
         bool result = fread(memPtr, sizeof(TValue), count, me) == (size_t)count;
         SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
         return result;
     }
-    
+
     template < typename TValue, typename TSize, typename TPos >
-    inline bool 
-	writeAt(FILE* me, TValue const *memPtr, TSize const count, TPos const fileOfs) 
-	{
+    inline bool
+    writeAt(FILE* me, TValue const *memPtr, TSize const count, TPos const fileOfs)
+    {
 //IOREV
-		typedef typename Position<FILE*>::Type pos_t;
-		seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
+        typedef typename Position<FILE*>::Type pos_t;
+        seek(me, (pos_t)fileOfs * (pos_t)sizeof(TValue));
         SEQAN_PROADD(SEQAN_PROIO, (sizeof(TValue) * count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
         SEQAN_PROTIMESTART(tw);
         bool result = fwrite(memPtr, sizeof(TValue), count, me) == (size_t)count;
@@ -229,9 +229,9 @@ namespace SEQAN_NAMESPACE_MAIN
         return result;
     }
 
-    inline Size<FILE*>::Type 
-	size(FILE* me) 
-	{
+    inline Size<FILE*>::Type
+    size(FILE* me)
+    {
 //IOREV
         Size<FILE*>::Type old_pos = tell(me);
         Size<FILE*>::Type result = 0;
@@ -242,36 +242,36 @@ namespace SEQAN_NAMESPACE_MAIN
     }
 
     template < typename TSize >
-    inline void 
-	resize(FILE* me, TSize new_length) 
-	{
+    inline void
+    resize(FILE* me, TSize new_length)
+    {
 //IOREV I think this is not c-standard and only works on POSIX-compliant systems
         Size<FILE*>::Type old_pos = tell(me);
         seek(me, new_length, SEEK_BEGIN);
         seek(me, old_pos, SEEK_BEGIN);
     }
 
-	inline bool 
-	flush(FILE*) 
-	{
+    inline bool
+    flush(FILE*)
+    {
 //IOREV _notimplemented_
-		return true; 
-	}
+        return true;
+    }
 
     template < typename AsyncRequest >
-	inline void 
-	release(FILE*, AsyncRequest &) 
-	{
+    inline void
+    release(FILE*, AsyncRequest &)
+    {
 //IOREV _notimplemented_
-	}
+    }
 
     template < typename AsyncRequest >
-    inline bool 
-	cancel(FILE*, AsyncRequest &) 
-	{
+    inline bool
+    cancel(FILE*, AsyncRequest &)
+    {
 //IOREV _notimplemented_
-		return true; 
-	}
+        return true;
+    }
 
 }
 
diff --git a/seqan/file/file_filereader.h b/seqan/file/file_filereader.h
deleted file mode 100644
index 24e5c9d..0000000
--- a/seqan/file/file_filereader.h
+++ /dev/null
@@ -1,1034 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_FILEREADER_H
-#define SEQAN_HEADER_FILE_FILEREADER_H
-
-/* IOREV
- * _tested_
- * _doc_
- * 
- * 
- * Tested by tests/file and various demos, but only the fasta-specialization
- * basic documentation
- * uses cstream.h's functions
- * Metafunctions supposedly moved hereto from file_cstyle.h are commented here awell
- * 
- * not fully understood how this works and what relation of the iterators is
- *
- * possibly broken according to holtgrew
- * 
- */
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-template <typename TFormat, typename TFile, typename TSpec>
-struct FileReader;
-//IOREV
-
-//////////////////////////////////////////////////////////////////////////////
-// FileReader String
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Spec.File Reader String:
-..cat:Strings
-..cat:Files
-..general:Class.String
-..summary:Read sequence data from file.
-..signature:String<TValue, FileReader<TFormat, TFile, TSpec> >
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...metafunction:Metafunction.Value
-..param.TFormat:A file format.
-...type:Tag.File Format
-..param.TFile:A file.
-..param.TSpec:A further specializing type.
-...default:@Tag.Default@
-..include:seqan/file.h
-*/
-
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-class String<TValue, FileReader<TFormat, TFile, TSpec> >
-{
-//IOREV
-public:
-	enum 
-	{
-		BLOCK_SIZE = 0x1000
-	}; //IOREV is this supposed to be constant?
-
-	typedef typename Position<TFile>::Type TFilePosition;
-
-	typedef typename Size<TFile>::Type TFileSize;
-	typedef String<TFileSize> TABL;
-
-	typedef typename Position<TABL>::Type TABLPosition;
-
-	typedef String<TValue> TBuf;
-
-	TFile *data_file;
-	bool data_file_owner;
-	TFilePosition data_file_begin;		//file pointer to begin of data in file
-	TABL data_abl;						//accumulated block lengths
-	TABLPosition data_active_block;		//number of active block
-	TFileSize data_active_block_begin;	//begin position of active block
-	TFileSize data_active_block_end;	//end position of active block
-	TBuf data_buf;						//data of active block
-	bool data_scanned;					//true if the complete string was scanned
-
-
-	//TODO
-	//String()...
-
-	String(TFile & fl_)
-		: data_scanned(false)
-	{
-		reserve(data_buf, (size_t) BLOCK_SIZE, Exact());
-
-		data_file = &fl_;
-		data_file_owner = false;
-		_constructFileReaderString(*this);
-	}
-	template <typename TString>
-	String(TString const & str_)
-		: data_scanned(false)
-	{
-		reserve(data_buf, (size_t) BLOCK_SIZE, Exact());
-
-		data_file = new TFile();
-		data_file_owner = true;
-		if (!_streamOpen(value(data_file), str_))
-		{
-			clear(data_file);
-		}
-		else
-		{
-			_constructFileReaderString(*this);
-		}
-	}
-	~String()
-	{
-		if (data_file_owner && data_file != NULL)
-		{
-			_streamClose(value(data_file));
-			delete data_file;
-			data_file = NULL;
-		}
-	}
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-//template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec>
-//struct Iterator<String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec>;
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-struct Value<String<TValue, FileReader<TFormat, TFile, TSpec> > >
-{
-//IOREV
-	typedef TValue Type;
-};
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-struct GetValue<String<TValue, FileReader<TFormat, TFile, TSpec> > >
-{
-//IOREV
-	typedef TValue Type;
-};
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-struct Reference<String<TValue, FileReader<TFormat, TFile, TSpec> > >
-{
-//IOREV
-	typedef TValue Type;
-};
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-struct Size<String<TValue, FileReader<TFormat, TFile, TSpec> > >:
-	Size<TFile>
-{
-//IOREV
-};
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-struct Difference<String<TValue, FileReader<TFormat, TFile, TSpec> > >:
-	Difference<TFile>
-{
-//IOREV
-};
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-struct Position<String<TValue, FileReader<TFormat, TFile, TSpec> > >:
-	Position<TFile>
-{
-//IOREV
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-inline TFile &
-_dataFile(String<TValue, FileReader<TFormat, TFile, TSpec> > & me)
-{
-//IOREV
-	return value(me.data_file);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition>
-inline void
-_loadBlockFileReaderString(String<TValue, FileReader<TFormat, TFile, TSpec> > & me,
-							TPosition blocknum)
-{
-//IOREV
-	typedef String<TValue, FileReader<TFormat, TFile, TSpec> > TString;
-
-	typedef typename Size<TFile>::Type TFileSize;
-	typedef String<TFileSize> TABL;
-	typedef typename Position<TABL>::Type TABLPosition;
-	TABLPosition blocknum2 = blocknum;
-
-	if (blocknum2 > length(me.data_abl))
-	{
-		if (me.data_scanned)
-		{
-			_loadBlockFileReaderString(me, length(me.data_abl) - 1);
-		}
-		else
-		{
-			for (TABLPosition bp = length(me.data_abl); !me.data_scanned && (bp <= blocknum2); ++bp)
-			{
-				_loadBlockFileReaderString(me, bp);
-			}
-		}
-	}
-	else
-	{
-		typedef Iter<TFile, FileReader<TFormat> > TFileReaderIt;
-		_streamSeekG(_dataFile(me), me.data_file_begin + blocknum2 * TString::BLOCK_SIZE);
-		TABLPosition end_filepos = me.data_file_begin + (blocknum2 + 1) * TString::BLOCK_SIZE;
-		TFileReaderIt fit(_dataFile(me), false);
-
-		unsigned int len;
-		resize(me.data_buf, static_cast<TFileSize>(TString::BLOCK_SIZE));  // Maybe too large, but will shrink below.
-		for (len = 0; !atEnd(fit) && (fit.data_file_pos < end_filepos); goNext(fit))
-		{
-			me.data_buf[len] = value(fit);
-			++len;
-		}
-		resize(me.data_buf, len);
-
-		if (blocknum2 == length(me.data_abl))
-		{
-			if (blocknum2 > 0)
-			{
-				appendValue(me.data_abl, me.data_abl[blocknum2-1] + length(me.data_buf));
-			}
-			else
-			{
-				appendValue(me.data_abl, length(me.data_buf));
-			}
-
-			if (atEnd(fit))
-			{
-				me.data_scanned = true;
-			}
-		}
-
-		me.data_active_block = blocknum2;
-		me.data_active_block_begin = (blocknum2) ? me.data_abl[blocknum2 - 1] : 0;
-		me.data_active_block_end = me.data_abl[blocknum2];
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition>
-inline unsigned int
-_findBlockFileReaderString(String<TValue, FileReader<TFormat, TFile, TSpec> > & me,
-							TPosition pos)
-{
-//IOREV
-	typedef typename Size<TFile>::Type TFileSize;
-
-	while (!me.data_scanned && (me.data_abl[length(me.data_abl) - 1] <= static_cast<TFileSize>(pos)))
-	{
-		_loadBlockFileReaderString(me, length(me.data_abl));
-	}
-
-	if (static_cast<TFileSize>(pos) >= me.data_abl[length(me.data_abl) - 1])
-	{//pos greater than file length
-		return length(me.data_abl);
-	}
-
-	return ::std::lower_bound(begin(me.data_abl, Standard()), end(me.data_abl, Standard()), (TFileSize) pos) - begin(me.data_abl, Standard());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-inline void
-_constructFileReaderString(String<TValue, FileReader<TFormat, TFile, TSpec> > & me)
-{
-//IOREV
-	//find begin of data in file
-	typedef Iter<TFile, FileReader<TFormat> > TFileReaderIt;
-	TFileReaderIt fit(_dataFile(me));
-	me.data_file_begin = fit.data_file_pos;
-
-	_loadBlockFileReaderString(me, 0);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-//tests whether block_number will exist when the file was scanned completely
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TUint>
-inline bool
-_isValidBlockFileReaderString(String<TValue, FileReader<TFormat, TFile, TSpec> > & me,
-							   TUint block_number)
-{
-//IOREV
-	typedef typename Size<TFile>::Type TFileSize;
-	TFileSize block_number2 = block_number;
-
-	while (!me.data_scanned && (length(me.data_abl) <= block_number2))
-	{
-		_loadBlockFileReaderString(me, length(me.data_abl));
-	}
-	return (length(me.data_abl) > block_number2);
-
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-inline void
-_loadCompleteFileReaderString(String<TValue, FileReader<TFormat, TFile, TSpec> > & me)
-{
-//IOREV
-	if (!me.data_scanned)
-	{//scan the whole sequence
-		typedef typename Position<TFile>::Type TPosition;
-		_loadBlockFileReaderString(me, maxValue<TPosition>());
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
- 
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-inline void const * 
-getObjectId(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return &me;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPos>
-inline TValue
-value(String<TValue, FileReader<TFormat, TFile, TSpec> > & me,
-	  TPos pos)
-{
-//IOREV
-	typedef typename Size<TFile>::Type TFileSize;
-	TFileSize pos2 = pos;
-
-	if ((me.data_active_block_begin > pos2) || (me.data_active_block_end <= pos2))
-	{//change block
-		_loadBlockFileReaderString(me, _findBlockFileReaderString(me, pos2));
-	}
-	return me.data_buf[pos2 - me.data_active_block_begin];
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-inline typename Size< String<TValue, FileReader<TFormat, TFile, TSpec> > >::Type
-length(String<TValue, FileReader<TFormat, TFile, TSpec> > & me)
-{
-//IOREV
-	_loadCompleteFileReaderString(me);
-
-	return me.data_abl[length(me.data_abl) - 1];
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec>
-inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type
-begin(String<TValue, FileReader<TFormat, TFile, TSpec> > & me,
-	  Tag<TIteratorSpec> const)
-{
-//IOREV
-	typedef typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type TIterator;
-	return TIterator(me);
-}
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec>
-inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type
-begin(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me,
-	  Tag<TIteratorSpec> const)
-{
-//IOREV
-	typedef String<TValue, FileReader<TFormat, TFile, TSpec> > TString;
-	typedef typename Iterator< TString const, TIteratorSpec >::Type TIterator;
-	return TIterator(const_cast<TString &>(me));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec>
-inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type
-end(String<TValue, FileReader<TFormat, TFile, TSpec> > & me,
-	Tag<TIteratorSpec> const)
-{
-//IOREV
-	typedef typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type TIterator;
-	return TIterator(me, GoEnd());
-}
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec>
-inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type
-end(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me,
-	Tag<TIteratorSpec> const)
-{
-//IOREV
-	typedef String<TValue, FileReader<TFormat, TFile, TSpec> > TString;
-	typedef typename Iterator< TString const, TIteratorSpec >::Type TIterator;
-	return TIterator(const_cast<TString &>(me), GoEnd());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition, typename TIteratorSpec>
-inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type
-iter(String<TValue, FileReader<TFormat, TFile, TSpec> > & me,
-	 TPosition pos,
-	 Tag<TIteratorSpec> const)
-{
-//IOREV
-	typedef typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec >::Type TIterator;
-	return TIterator(me, pos);
-}
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TPosition, typename TIteratorSpec>
-inline typename Iterator< String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec >::Type
-iter(String<TValue, FileReader<TFormat, TFile, TSpec> > const & me,
-	 TPosition pos,
-	 Tag<TIteratorSpec> const)
-{
-//IOREV
-	typedef String<TValue, FileReader<TFormat, TFile, TSpec> > TString;
-	typedef typename Iterator< TString const, TIteratorSpec >::Type TIterator;
-	return TIterator(const_cast<TString &>(me), pos);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-// Iterator for FileReader String
-// (note: do not confuse with FileReader Iterator, see file_filereaderiterator.h)
-//////////////////////////////////////////////////////////////////////////////
-
-struct FileReaderIterator;
-//IOREV this is supposedly not the same as FileReaderIterator from file_filereaderiterator. Make this less confusing
-
-//helper meta function for storing types associated with file reader string.
-//Due to a bug in VC++, FileReaderTypes_ is instantiated for arbitrary TContainer types
-//when instantiating Iter<TContainer, FileReaderIterator>
-//"ABL" = "active buffer lengths" table
-template <typename T>
-struct FileReaderTypes_
-{// dummy implementation to make VC++ happy
-//IOREV
-	typedef int TABLPosition;
-	typedef int TBuf;
-};
-template <typename TValue, typename TFormat, typename TFile, typename TSpec>
-struct FileReaderTypes_<String<TValue, FileReader<TFormat, TFile, TSpec> > >
-{
-//IOREV
-	typedef typename Size<TFile>::Type TFileSize;
-	typedef String<TFileSize> TABL;
-	typedef typename Position<TABL>::Type TABLPosition;
-	typedef String<TValue> TBuf;
-};
-
-
-template <typename TContainer>
-class Iter<TContainer, FileReaderIterator>
-{
-//IOREV
-public:
-	typedef typename FileReaderTypes_<TContainer>::TABLPosition TABLPosition;
-	typedef typename FileReaderTypes_<TContainer>::TBuf TBuf;
-
-	typedef typename Position<TBuf>::Type TBufPosition;
-	typedef typename Size<TBuf>::Type TBufSize;
-
-	TContainer * data_container;
-	TABLPosition data_abl_pos;		//number of block
-	TBufPosition data_buf_pos;		//number of char in block
-	TBufSize data_buf_len;			//length of block
-	bool data_atEnd;				//true if iterator is atEnd
-
-	Iter(TContainer & cont_)
-		: data_container(& cont_)
-	{
-		goBegin(*this);
-	}
-
-	Iter(TContainer & cont_, GoEnd)
-		: data_container(& cont_)
-	{
-		goEnd(*this);
-	}
-
-	template <typename TPos>
-	Iter(TContainer & cont_, TPos pos_)
-		: data_container(& cont_)
-	{
-		setPosition(*this, pos_);
-	}
-
-	Iter(Iter const & other_)
-		: data_container(other_.data_container)
-		, data_abl_pos(other_.data_abl_pos)
-		, data_buf_pos(other_.data_buf_pos)
-		, data_buf_len(other_.data_buf_len)
-		, data_atEnd(other_.data_atEnd)
-	{
-	}
-
-	Iter &
-	operator = (Iter const & other_)
-	{
-		data_container = other_.data_container;
-		data_abl_pos = other_.data_abl_pos;
-		data_buf_pos = other_.data_buf_pos;
-		data_buf_len = other_.data_buf_len;
-		data_atEnd = other_.data_atEnd;
-
-		return *this;
-	}
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec>
-struct Iterator<String<TValue, FileReader<TFormat, TFile, TSpec> >, TIteratorSpec>
-{
-//IOREV
-	typedef Iter<String<TValue, FileReader<TFormat, TFile, TSpec> >, FileReaderIterator> Type;
-};
-template <typename TValue, typename TFormat, typename TFile, typename TSpec, typename TIteratorSpec>
-struct Iterator<String<TValue, FileReader<TFormat, TFile, TSpec> > const, TIteratorSpec>
-{
-//IOREV
-	typedef Iter<String<TValue, FileReader<TFormat, TFile, TSpec> >, FileReaderIterator> Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-struct Value<Iter<TContainer, FileReaderIterator> >:
-	Value<TContainer>
-{
-//IOREV
-};
-template <typename TContainer>
-struct GetValue<Iter<TContainer, FileReaderIterator> >:
-	Value<TContainer>
-{
-//IOREV
-};
-template <typename TContainer>
-struct Reference<Iter<TContainer, FileReaderIterator> >:
-	Value<TContainer>
-{
-//IOREV
-};
-
-template <typename TContainer>
-struct Size<Iter<TContainer, FileReaderIterator> >:
-	Size<TContainer>
-{
-//IOREV
-};
-template <typename TContainer>
-struct Difference<Iter<TContainer, FileReaderIterator> >:
-	Difference<TContainer>
-{
-//IOREV
-};
-template <typename TContainer>
-struct Position<Iter<TContainer, FileReaderIterator> >:
-	Position<TContainer>
-{
-//IOREV
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline typename GetValue<Iter<TContainer, FileReaderIterator> >::Type
-getValue(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	TContainer & cont = *(it.data_container);
-	if (cont.data_active_block != it.data_abl_pos)
-	{
-		_loadBlockFileReaderString(cont, it.data_abl_pos);
-	}
-	return cont.data_buf[it.data_buf_pos];
-}
-template <typename TContainer>
-inline typename GetValue<Iter<TContainer, FileReaderIterator> >::Type
-getValue(Iter<TContainer, FileReaderIterator> const & it)
-{
-//IOREV
-	TContainer & cont = *(it.data_container);
-	if (cont.data_active_block != it.data_abl_pos)
-	{
-		_loadBlockFileReaderString(cont, it.data_abl_pos);
-	}
-	return cont.data_buf[it.data_buf_pos];
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline typename Reference<Iter<TContainer, FileReaderIterator> >::Type
-value(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	return getValue(it);
-}
-template <typename TContainer>
-inline typename Reference<Iter<TContainer, FileReaderIterator> >::Type
-value(Iter<TContainer, FileReaderIterator> const & it)
-{
-//IOREV
-	return getValue(it);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline TContainer &
-container(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	return *(it.data_container);
-}
-template <typename TContainer>
-inline TContainer &
-container(Iter<TContainer, FileReaderIterator> const & it)
-{
-//IOREV
-	return *(it.data_container);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline typename Position<Iter<TContainer, FileReaderIterator> >::Type
-position(Iter<TContainer, FileReaderIterator> const & it)
-{
-//IOREV
-	TContainer & cont = *(it.data_container);
-	if (it.data_atEnd)
-	{
-		return length(cont);
-	}
-	else
-	{
-		if (it.data_abl_pos)
-		{
-			return cont.data_abl[it.data_abl_pos-1] + it.data_buf_pos;
-		}
-		else
-		{
-			return it.data_buf_pos;
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer, typename TPos>
-inline void
-setPosition(Iter<TContainer, FileReaderIterator> & it,
-			TPos pos)
-{
-//IOREV
-    typedef typename Size<TContainer>::Type TSize;
-	TContainer & cont = *(it.data_container);
-	it.data_abl_pos = _findBlockFileReaderString(cont, pos);
-	it.data_atEnd = (cont.data_scanned && (static_cast<TSize>(pos) >= length(cont)));
-	if (it.data_atEnd)
-	{
-		it.data_buf_pos = 0;
-		it.data_buf_len = 0;
-	}
-	else
-	{
-		if (it.data_abl_pos == 0)
-		{
-			it.data_buf_pos = pos;
-		}
-		else
-		{
-			it.data_buf_pos = pos - cont.data_abl[it.data_abl_pos - 1];
-		}
-		if (cont.data_active_block != it.data_abl_pos)
-		{
-			_loadBlockFileReaderString(cont, it.data_abl_pos);
-		}
-		it.data_buf_len = length(cont.data_buf);
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline void
-goNext(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	++it.data_buf_pos;
-	if (it.data_buf_pos >= it.data_buf_len)
-	{
-		if (!it.data_atEnd)
-		{
-			it.data_buf_pos = 0;
-			++it.data_abl_pos;
-
-			TContainer & cont = *(it.data_container);
-			it.data_atEnd = !_isValidBlockFileReaderString(cont, it.data_abl_pos);
-			if (it.data_atEnd)
-			{//at end
-				it.data_buf_len = 0;
-			}
-			else
-			{//not at end
-				if (cont.data_active_block != it.data_abl_pos)
-				{
-					_loadBlockFileReaderString(cont, it.data_abl_pos);
-				}
-				it.data_buf_len = length(cont.data_buf);
-			}
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline void
-goPrevious(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	if (it.data_buf_pos > 0)
-	{
-		--it.data_buf_pos;
-	}
-	else
-	{
-		TContainer & cont = *(it.data_container);
-		if (it.data_atEnd)
-		{
-			//_loadCompleteFileReaderString(cont);// length(cont) will do it
-			it.data_atEnd = (length(cont) == 0);
-			it.data_abl_pos = length(cont.data_abl) - 1;
-		}
-		else if (it.data_abl_pos)
-		{
-			--it.data_abl_pos;
-		}
-		else return; //already in begin pos
-
-		if (cont.data_active_block != it.data_abl_pos)
-		{
-			_loadBlockFileReaderString(cont, it.data_abl_pos);
-		}
-		it.data_buf_len = length(cont.data_buf);
-		it.data_buf_pos = it.data_buf_len - 1;
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline void
-goBegin(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	it.data_abl_pos = 0;
-	it.data_buf_pos = 0;
-
-	TContainer & cont = *(it.data_container);
-	if (_isValidBlockFileReaderString(cont, 0))
-	{
-		it.data_buf_len = cont.data_abl[0];
-		it.data_atEnd = false;
-	}
-	else
-	{
-		it.data_buf_len = 0;
-		it.data_atEnd = true;
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline void
-goEnd(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	it.data_abl_pos = 0;
-	it.data_buf_pos = 0;
-	it.data_buf_len = 0;
-	it.data_atEnd = true;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline bool
-atEnd(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	return it.data_atEnd;
-}
-template <typename TContainer>
-inline bool
-atEnd(Iter<TContainer, FileReaderIterator> const & it)
-{
-//IOREV
-	return it.data_atEnd;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline bool
-atBegin(Iter<TContainer, FileReaderIterator> & it)
-{
-//IOREV
-	return (it.data_abl_pos == 0) && (it.data_buf_pos == 0);
-}
-template <typename TContainer>
-inline bool
-atBegin(Iter<TContainer, FileReaderIterator> const & it)
-{
-//IOREV
-	return (it.data_abl_pos == 0) && (it.data_buf_pos == 0);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// operator ==
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline bool 
-operator == (Iter<TContainer, FileReaderIterator> const & left,
-			 Iter<TContainer, FileReaderIterator> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return (atEnd(left) == atEnd(right)) && ((atEnd(left) && atEnd(right)) || position(left) == position(right));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// operator !=
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline bool 
-operator != (Iter<TContainer, FileReaderIterator> const & left,
-			 Iter<TContainer, FileReaderIterator> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return (atEnd(left) != atEnd(right)) || (position(left) != position(right));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// operator < / >
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline bool 
-operator < (Iter<TContainer, FileReaderIterator> const & left,
-			Iter<TContainer, FileReaderIterator> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return (atEnd(right) && !atEnd(left)) || (position(left) < position(right));
-}
-
-template <typename TContainer>
-inline bool 
-operator > (Iter<TContainer, FileReaderIterator> const & left,
-			Iter<TContainer, FileReaderIterator> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return (atEnd(left) && !atEnd(right)) || (position(left) > position(right));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// operator <= / >=
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer>
-inline bool 
-operator <= (Iter<TContainer, FileReaderIterator> const & left,
-			 Iter<TContainer, FileReaderIterator> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return atEnd(right) || (position(left) <= position(right));
-}
-
-template <typename TContainer>
-inline bool 
-operator >= (Iter<TContainer, FileReaderIterator> const & left,
-			 Iter<TContainer, FileReaderIterator> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return atEnd(left) || (position(left) >= position(right));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// operator +
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, FileReaderIterator>  
-operator + (Iter<TContainer, FileReaderIterator> const & left,
-			TIntegral right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return Iter<TContainer, FileReaderIterator>(container(left), position(left) + right);
-}
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, FileReaderIterator>  
-operator + (TIntegral left,
-			Iter<TContainer, FileReaderIterator> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return Iter<TContainer, FileReaderIterator>(container(right), position(right) + left);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// operator +=
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, FileReaderIterator> &
-operator += (Iter<TContainer, FileReaderIterator> & left,
-			 TIntegral right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	left.data_buf_pos += right;
-	if (left.data_buf_pos >= left.data_buf_len)
-	{
-		setPosition(left, position(left) + right);
-	}
-	return left;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// operator -
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, FileReaderIterator>  
-operator - (Iter<TContainer, FileReaderIterator> const & left,
-			TIntegral right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return Iter<TContainer, FileReaderIterator>(container(left), position(left) - right);
-}
-
-//____________________________________________________________________________
-
-template <typename TContainer>
-inline typename Difference<Iter<TContainer, FileReaderIterator> >::Type  
-operator - (Iter<TContainer, FileReaderIterator> const & left,
-			Iter<TContainer, FileReaderIterator> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return position(left) - position(right);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// operator -=
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TContainer, typename TIntegral>
-inline Iter<TContainer, FileReaderIterator> &
-operator -= (Iter<TContainer, FileReaderIterator> & left,
-			TIntegral right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	if (left.data_buf_pos < right)
-	{
-		setPosition(left, position(left) - right);
-	}
-	else
-	{
-		left.data_buf_pos -= right;
-	}
-	return left;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-//////////////////////////////////////////////////////////////////////////////
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_filereaderiterator.h b/seqan/file/file_filereaderiterator.h
deleted file mode 100644
index 6b3a568..0000000
--- a/seqan/file/file_filereaderiterator.h
+++ /dev/null
@@ -1,182 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
-
-#ifndef SEQAN_HEADER_FILE_FILEREADEITERATOR_H
-#define SEQAN_HEADER_FILE_FILEREADEITERATOR_H
-
-/* IOREV
- * _nodoc_
- * 
- * 
- * relation to file_filereader.h not totally clear
- *
- * broken according to holtgrew, but used by many file_format implementations
- * that supposedly work
- *
- * not yet fully understood how this works or is supposed to
- *
- * 
- */
-
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFormat, typename TFile = FILE*, typename TSpec = Default>
-struct FileReader;
-//IOREV
-
-// Manual forward for the skipMeta goBegin() overload.
-//template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-//void
-//goBegin(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it, bool skip_meta);
-
-//////////////////////////////////////////////////////////////////////////////
-// FileReader: an iterator that scans through the data of a file
-// note: this is not the iterator of the FileReader string (see file_filereader.h)
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-class Iter<TFile, FileReader<TFormat, TFile2, TSpec> >
-{
-//IOREV
-public:
-	typedef typename Value<TFile>::Type TValue;
-	typedef typename Position<TFile>::Type TPosition;
-
-	TPosition data_file_pos;	//position of the last read char relative to data begin (only valid if data_eof == false)
-	TFile * data_host;		//the host file
-	TValue data_char;		//the last read char
-	bool data_eof;			//true if reached end of record
-//	TFilePosition data_begin_pos;
-
-	Iter(TFile & file_, bool skip_meta = true):
-		data_file_pos(0),
-		data_host(& file_),
-		data_eof(false)
-	{
-		data_char = _streamGet(file_);
-		goBegin(*this, skip_meta);
-	}
-	Iter(Iter const & other_):
-		data_file_pos(other_.data_file_pos),
-		data_host(other_.data_host),
-		data_char(other_.data_char),
-		data_eof(other_.data_eof)
-	{
-	}
-	~Iter() 
-	{
-	}
-
-	Iter const &
-	operator = (Iter const & other_)
-	{
-		data_file_pos = other_.data_file_pos;
-		data_host = other_.data_host;
-		data_char = other_.data_char;
-		data_eof = other_.data_eof;
-		return *this;
-	}
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-struct Value< Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >:
-	Value<TFile>
-{
-//IOREV
-};
-
-template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-struct GetValue< Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >
-{
-//IOREV
-	typedef typename Value< Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >::Type Type;
-};
-
-template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-struct Reference< Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >
-{
-//IOREV
-	typedef typename Value< Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >::Type & Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-inline TFile &
-host(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it)
-{
-//IOREV
-	return *(it.data_host);
-}
-
-
-template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-inline typename Reference<Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >::Type
-value(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it)
-{
-//IOREV
-	return it.data_char;
-}
-
-template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-inline typename GetValue<Iter<TFile, FileReader<TFormat, TFile2, TSpec> > >::Type
-getValue(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it)
-{
-//IOREV
-	return it.data_char;
-}
-
-template <typename TFile, typename TFormat, typename TFile2, typename TSpec>
-inline bool
-atEnd(Iter<TFile, FileReader<TFormat, TFile2, TSpec> > & it)
-{
-//IOREV
-	return it.data_eof;
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-//////////////////////////////////////////////////////////////////////////////
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_format.h b/seqan/file/file_format.h
deleted file mode 100644
index e6378b3..0000000
--- a/seqan/file/file_format.h
+++ /dev/null
@@ -1,785 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_FORMAT_H
-#define SEQAN_HEADER_FILE_FORMAT_H
-
-/* IOREV
- * _tested_
- * _doc_
- *
- *
- * well documented
- * apperently tested by tests/file/test_file.h
- *
- * 
- * AFAICT this not really used widely, as the FileFormat specialization
- * tags are used diretly e.g.
- *      read(TFile, TData, TMeta, Fasta)
- * and not
- *      read(TFile, TData, TMeta, FileFormat<TFile, TData, TMeta, Fasta>)
- *
- * the global wrappers in this file also break down to this behaviours
- *
- * however it is not evident what the purpose of the FileFormat class is
- * altogether and especially the virtual members
- * (except being return value for guessFileFormat, which could aswell return
- * the tag)
- *
- *------------------
- *
- * contains all sorts of stream-IO helper functions that should go someplace
- * else.
- *
- * For all of these: Should we really look at c passed as argument, how do
- * we know, c is actually current character?
- *
- * For the iterators the current mechanism is error-prone:
- *
- * foobar (TInput & input, TIterator it)
- * {
- *     Iterator<TInput, Standard()> it_end = end(input);
- *     while (it != it_end)
- *          ...
- *
- * }
- *
- * this does not guarantee, that it and it_end are the same type, since
- * it maybe non-standard
- *
- * also some functions set it_end = end(input) - 1; which seems to be related
- * to change of atEnd behaviour http://trac.mi.fu-berlin.de/seqan/wiki/IoRevision
- *
- * IMO all these functions should be changed to not construct a 2nd iterator
- * but use atEnd() directly
- *      
- */
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Tag.File Format:
-..cat:Input/Output
-..summary:A file format.
-..include:seqan/file.h
-*/
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-//Base Class for all FileFormat classes
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Class.FileFormat:
-..cat:Input/Output
-..summary:Object that stores a file format.
-..signature:FileFormat<File, Data [, Format [, Meta] ]>
-..see:Tag.File Format
-..include:seqan/file.h
-*/
-
-template <
-	typename TFile, 
-	typename TData,
-	typename TMeta,
-	typename TFormat = void >
-struct FileFormat:
-	public FileFormat<TFile, TData, TMeta, void>
-{
-//IOREV
-public:
-	typedef typename Size<TData>::Type TSize;
-
-	FileFormat() {}
-	FileFormat(FileFormat const &) {}
-	~FileFormat() {}
-	FileFormat const & operator =(FileFormat const &) { return *this; }
-
-	inline void * 
-	formatID_() const
-	{
-SEQAN_CHECKPOINT
-		return ClassIdentifier_<TFormat>::getID();
-	}
-
-	virtual void
-	read_(TFile & file, TData & data) const
-	{
-SEQAN_CHECKPOINT
-		read(file, data, TFormat());
-	}
-	virtual void
-	read_(TFile & file, TData & data, TSize limit) const
-	{
-SEQAN_CHECKPOINT
-		read(file, data, limit, TFormat());
-	}
-
-	virtual void
-	readMeta_(TFile & file, TMeta & meta) const
-	{
-SEQAN_CHECKPOINT
-		readMeta(file, meta, TFormat());
-	}
-
-	virtual void
-	goNext_(TFile & file) const
-	{
-SEQAN_CHECKPOINT
-		goNext(file, TFormat());
-	}
-
-	virtual TSize
-	length_(TFile & file) const
-	{
-SEQAN_CHECKPOINT
-		length(file, TFormat());
-	}
-
-	virtual void
-	write_(TFile & file, TData & data) const
-	{
-SEQAN_CHECKPOINT
-		write(file, data, TFormat());
-	}
-	virtual void
-	write_(TFile & file, TData & data, TMeta & meta) const
-	{
-SEQAN_CHECKPOINT
-		write(file, data, meta, TFormat());
-	}
-};
-
-//____________________________________________________________________________
-
-//base class for all file format classes 
-
-template <typename TFile, typename TData, typename TMeta>
-struct FileFormat<TFile, TData, TMeta, void>
-{
-//IOREV
-public:
-	typedef typename Size<TData>::Type TSize;
-
-	FileFormat() {}
-	FileFormat(FileFormat const &) {}
-	~FileFormat() {}
-	FileFormat const & operator =(FileFormat const &) { return *this; }
-
-	virtual void *
-	formatID_() const = 0;
-
-	virtual void
-	read_(TFile & file, TData & data) const = 0;
-	virtual void
-	read_(TFile & file, TData & data, TSize limit) const = 0;
-
-	virtual void
-	readMeta_(TFile & file, TMeta & meta) const = 0;
-
-	virtual void
-	goNext_(TFile & file) const = 0;
-
-	virtual TSize
-	length_(TFile & file) const = 0;
-
-	virtual void
-	write_(TFile & file, TData & data) const = 0;
-	virtual void
-	write_(TFile & file, TData & data, TMeta & meta) const = 0;
-
-};
-
-//////////////////////////////////////////////////////////////////////////////
-// Wrapper for functions to virtuals
-//////////////////////////////////////////////////////////////////////////////
-
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat>
-inline void *
-formatID(FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return file_format.formatID_();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.FileFormat#read:
-..cat:Input/Output
-..summary:Loads a record from file.
-..signature:read(file, data [, meta], format)
-..signature:read(file, data [, meta], tag)
-..param.file:An input file.
-..param.data:A container that gets the data read from $file$.
-..param.meta:A container that gets meta data from $file$. (optional)
-..param.format:A file format object.
-...type:Class.FileFormat.File Format object
-..param.tag:A file format tag.
-...type:Tag.File Format.File Format tag
-..remarks:The result of this operation is stored in $data$.
-..remarks:The function leaves $file$ at the position for reading the next record.
-..see:Function.assign
-..include:seqan/file.h
-*/
-template <typename TFile, typename TData, typename TMeta, typename TFormat>
-inline void
-read(TFile & file,
-	 TData & data,
-	 FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	file_format.read_(file, data);
-}
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TSize>
-inline void
-read(TFile & file,
-	 TData & data,
-	 TSize limit,
-	 FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	file_format.read_(file, data, limit);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.readMeta:
-..cat:Input/Output
-..summary:Read meta information from file.
-..signature:readMeta(file, meta, file_format)
-..param.file:A file that contains data in the format specified by $file_format$.
-..param.meta:A data structure that is able to store meta informations stored in $file$.
-..param.file_format:A file format.
-..returns.param.meta:The meta data read from $file$.
-...type:Tag.File Format
-..include:seqan/file.h
-*/
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat>
-inline void
-readMeta(TFile & file,
-		 TMeta & meta,
-		 FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	file_format.readMeta_(file, meta);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.goNext:
-..cat:Input/Output
-..include:seqan/file.h
-*/
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat>
-inline void
-goNext(TFile & file,
-	   FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	file_format.goNext_(file);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.length:
-..cat:Input/Output
-..include:seqan/file.h
-*/
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat>
-inline void
-length(TFile & file,
-	   FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	file_format.length_(file);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.FileFormat#write:
-..class:Adaption."std::iostream"
-..cat:Input/Output
-..summary:Writes to stream.
-..signature:write(stream, source)
-..signature:write(stream, begin, end)
-..param.stream: A stream object.
-...type:Adaption."std::iostream"
-..param.source: Container that is written to $stream$.
-..param.begin: Iterator to the first character of the range.
-..param.end: Iterator behind the last character of the range.
-..remarks:The content of $source$ is written 'as-is' to $stream$.
-..include:seqan/file.h
-*/
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat>
-inline void
-write(TFile & file,
-	  TData & data,
-	  FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	file_format.write_(file, data);
-}
-template <typename TFile, typename TData, typename TMeta, typename TFormat>
-inline void
-write(TFile & file,
-	  TData & data,
-	  TMeta & meta,
-	  FileFormat<TFile, TData, TMeta, TFormat> const & file_format)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	file_format.write_(file, data, meta);
-}
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Comparison of two FileFormat objects
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFileLeft, typename TDataLeft, typename TMetaLeft, typename TFormatLeft, typename TFileRight, typename TDataRight, typename TMetaRight, typename TFormatRight>
-inline bool
-operator == (FileFormat<TFileLeft, TDataLeft, TMetaLeft, TFormatLeft> const & left, 
-			 FileFormat<TFileRight, TDataRight, TMetaRight, TFormatRight> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return formatID(left) == formatID(right);
-}
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2>
-inline bool
-operator == (FileFormat<TFile, TData, TMeta, TFormat> const & left, 
-			 Tag<TFormat2> const)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return formatID(left) == ClassIdentifier_<Tag<TFormat2> const>::getID();
-}
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2>
-inline bool
-operator == (Tag<TFormat2> const,
-			 FileFormat<TFile, TData, TMeta, TFormat> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return ClassIdentifier_<Tag<TFormat2> const>::getID() == formatID(right);
-}
-
-//____________________________________________________________________________
-
-template <typename TFileLeft, typename TDataLeft, typename TMetaLeft, typename TFormatLeft, typename TFileRight, typename TDataRight, typename TMetaRight, typename TFormatRight>
-inline bool
-operator != (FileFormat<TFileLeft, TDataLeft, TMetaLeft, TFormatLeft> const & left, 
-			 FileFormat<TFileRight, TDataRight, TMetaRight, TFormatRight> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return formatID(left) != formatID(right);
-}
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2>
-inline bool
-operator != (FileFormat<TFile, TData, TMeta, TFormat> const & left, 
-			 Tag<TFormat2> const)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return formatID(left) != ClassIdentifier_<Tag<TFormat2> const>::getID();
-}
-
-template <typename TFile, typename TData, typename TMeta, typename TFormat, typename TFormat2>
-inline bool
-operator != (Tag<TFormat2> const,
-			 FileFormat<TFile, TData, TMeta, TFormat> const & right)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return ClassIdentifier_<Tag<TFormat2> const>::getID() != formatID(right);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// allgemeine Funktionen fuer Streams
-//////////////////////////////////////////////////////////////////////////////
-//TODO??? Das muss in eine extra Datei
-
-
-/*
-template <typename TStream, typename TIterator>
-inline void
-write(TStream & target,
-	  TIterator begin_,
-	  TIterator end_)
-{
-	while (begin_ != end_)
-	{
-		_streamPut(target, convert<char>(*begin_));
-		++begin_;
-	}
-}
-
-//____________________________________________________________________________
-
-template <typename TStream, typename TSource>
-inline void
-write(TStream & target,
-	  TSource const & source)
-{
-	write(target, begin(source), end(source));
-}
-//TODO???: Spezialisierungen zum blockweise schreiben bei contiguous strings von char
-//Anmerkungen: write wird nach dem zweiten Argument (source) spezialisiert!
-
-//____________________________________________________________________________
-
-template <typename TStream, typename TSource>
-inline void
-write(TStream & target,
-	  TSource const & source,
-	  typename Size<TSource>::Type limit_)
-{
-	if (length(source) > limit_)
-	{
-		write(target, begin(source), begin(source) + limit_);
-	}
-	else
-	{
-		write(target, begin(source), end(source));
-	}
-}
-
-*/
-//////////////////////////////////////////////////////////////////////////////
-
-// Helper function for scanning a stream
-// c = next character, pass it to the next call of the function
-
-template <typename TFile, typename TString, typename TChar>
-inline void
-_streamAppendLine(TFile & file,
-				   TString & str,
-				   TChar & c)
-{
-//IOREV _nodoc_ _hasCRef_ wrong place
-	while (true)
-	{
-		if (_streamEOF(file)) break;
-
-		if (c == '\r')
-		{
-			c = _streamGet(file);
-			if (c == '\n') 
-			{
-				c = _streamGet(file);
-			}
-			break;
-		}
-		if (c == '\n')
-		{
-			c = _streamGet(file);
-			break;
-		}
-
-		appendValue(str, c);
-
-		c = _streamGet(file);
-	}
-}
-//____________________________________________________________________________
-
-template <typename TFile, typename TChar>
-inline void
-_streamCountLine(TFile & file,
-				  TChar & c)
-
-{
-//IOREV _nodoc_ _notused_ _hasCRef_ wrong place
-	while (true)
-	{
-		if (_streamEOF(file)) break;
-
-		if (c == '\r')
-		{
-			c = _streamGet(file);
-			if (c == '\n') 
-			{
-				c = _streamGet(file);
-			}
-			break;
-		}
-		if (c == '\n')
-		{
-			c = _streamGet(file);
-			break;
-		}
-
-		c = _streamGet(file);
-	}
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TChar>
-inline typename Size<TFile>::Type
-_streamSkipLine(TFile & file,
-				 TChar & c)
-
-{
-//IOREV _nodoc_ _hasCRef_ wrong place
-	typename Size<TFile>::Type count = 0;
-	while (true)
-	{
-		if (_streamEOF(file)) break;
-
-		if (c == '\r')
-		{
-			c = _streamGet(file);
-			if (c == '\n') 
-			{
-				c = _streamGet(file);
-			}
-			break;
-		}
-		if (c == '\n')
-		{
-			c = _streamGet(file);
-			break;
-		}
-
-		++count;
-
-		c = _streamGet(file);
-	}
-
-	return count;
-}
-
-
-
-
-////////////////////////////////////////////////////////////////////////////
-//new ones
-
-//new ones for streams
-template<typename TFile, typename TChar>
-inline void 
-_streamSkipWhitespace(TFile& file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ wrong place; according to POSIX \v\f\r\n are also whitespace
-	if ((c!=' ') && (c != '\t')) return;
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if ((c!=' ') && (c != '\t')) break;
-	}
-}
-
-////////////////////////////////////////////////////////////////////////////
-
-template<typename TChar>
-inline bool
-_streamIsLetter(TChar const c)
-{
-//IOREV _nodoc_ wrong place; what about return ( ((c >= 'a') && (c <= 'z')) || ((c >= 'A') && (c <= 'Z')) [better performance] replace with _parseIsLetter()
-	return ((c == 'a') || (c == 'b') || (c == 'c') || (c == 'd') || (c == 'e') || 
-			(c == 'f') || (c == 'g') || (c == 'h') || (c == 'i') || (c == 'j') ||
-			(c == 'k') || (c == 'l') || (c == 'm') || (c == 'n') || (c == 'o') || 
-			(c == 'p') || (c == 'q') || (c == 'r') || (c == 's') || (c == 't') ||
-			(c == 'u') || (c == 'v') || (c == 'w') || (c == 'x') || (c == 'y') || 
-			(c == 'z') || (c == 'A') || (c == 'B') || (c == 'C') || (c == 'D') ||
-			(c == 'E') || (c == 'F') || (c == 'G') || (c == 'H') || (c == 'I') || 
-			(c == 'J') || (c == 'K') || (c == 'L') || (c == 'M') || (c == 'N') ||
-			(c == 'O') || (c == 'P') || (c == 'Q') || (c == 'R') || (c == 'S') || 
-			(c == 'T') || (c == 'U') || (c == 'V') || (c == 'W') || (c == 'X') ||
-			(c == 'Y') || (c == 'Z'));
-}
-
-
-////////////////////////////////////////////////////////////////////////////
-
-
-template<typename TFile, typename TChar>
-inline String<char>
-_streamReadWord(TFile & file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ wrong place
-	// Read word
-	String<char> str(c);
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (!_streamIsLetter(c)) break;
-		append(str, c);
-	}
-	return str;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-//new ones for strings
-
-template <typename TString, typename TIter>
-inline typename Size<TString>::Type
-_stringSkipLine(TString & str,
-				 TIter & it)
-
-{
-//IOREV _nodoc_ _bug_ wrong place; possible request for *it but it could be it_end in l 672; iterator akwardness, see head of file
-	typename Size<TString>::Type count = 0;
-	typename Iterator<TString,Standard>::Type end_it = end(str,Standard());
-	while (true)
-	{
-		if (it == end_it) break;
-
-		if (*it == '\r')
-		{
-			++it;
-			if (*it == '\n') 
-			{
-				++it;
-			}
-			break;
-		}
-		if (*it == '\n')
-		{
-			++it;
-			break;
-		}
-
-		++count;
-		++it;
-	}
-
-	return count;
-}
-
-/////////////////////////////////////////////////////////////////////////
-
-template <typename TString1, typename TString2, typename TIter>
-inline void
-_stringAppendLine(TString1 & str,
-				   TString2 & a_str,
-				   TIter & it)
-{
-//IOREV _nodoc_ _bug_ wrong place; possible request for *it but it could be it_end in l 708; iterator akwardness, see head of file
-	typename Iterator<TString1,Standard>::Type end_it = end(str,Standard());
-	while (true)
-	{
-		if (it == end_it) break;
-
-		if (*it == '\r')
-		{
-			++it; 
-			if (*it == '\n') 
-			{
-				++it;
-			}
-			break;
-		}
-		if (*it == '\n')
-		{
-			++it;
-			break;
-		}
-
-		appendValue(a_str, getValue(it));
-		++it;
-	}
-}
-
-////////////////////////////////////////////////////////////////////////////
-
-template<typename TString, typename TIter>
-inline void 
-_stringSkipWhitespace(TString& str, TIter& it)
-{
-//IOREV _nodoc_ _bug_ wrong place; according to POSIX \v\f\r\n are also whitespace; iterator akwardness, see head of file
-	typename Iterator<TString,Standard>::Type end_it = end(str,Standard())-1;
-	while (it != end_it) {
-		if ((*it!=' ') && (*it != '\t')) break;
-		++it;
-	}
-}
-
-////////////////////////////////////////////////////////////////////////////
-
-template<typename TString, typename TIter>
-inline int
-_stringReadNumber(TString & str, TIter& it)
-{
-//IOREV _nodoc_ wrong place; iterator akwardness, see head of file
-	// Read number
-	typename Iterator<TString,Standard>::Type end_it = end(str,Standard())-1;
-	String<char> numstr(getValue(it));
-	while (it != end_it) {
-		++it;
-		if (!_parseIsDigit(*it)) break;
-		append(numstr, getValue(it));
-	}
- 	return atoi(toCString(numstr));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-//////////////////////////////////////////////////////////////////////////////
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_format_cgviz.h b/seqan/file/file_format_cgviz.h
deleted file mode 100644
index 9b3ddf0..0000000
--- a/seqan/file/file_format_cgviz.h
+++ /dev/null
@@ -1,259 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_CGVIZ_H
-#define SEQAN_HEADER_FILE_CGVIZ_H
-
-/* IOREV
- * _tested_
- * _nodoc_
- *
- * tested in tests/file/test_file.h
- * tag mentionen in doc, but no further documentation, no link to spec
- * 
- */
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - CGViz
-//////////////////////////////////////////////////////////////////////////////
-
-
-/**
-.Tag.File Format.tag.CGViz:
-	CGViz file format for sequences. Only output.
-..include:seqan/file.h
-*/
-struct TagCGViz_;
-//IOREV
-typedef Tag<TagCGViz_> const CGViz; //IOREV
-
-/////////////////////////////////////////////////////////////////////////
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// goNext
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile>
-void goNext(TFile & file, CGViz) {
-//IOREV _notinlined_ purpose not clear to me
-	SEQAN_CHECKPOINT;
-    (void) file; // When compiled without assertions.
-	SEQAN_ASSERT_NOT(streamEof(file));
-	
-	return;
-}
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// write
-//////////////////////////////////////////////////////////////////////////////
-
-// Returns status code.
-
-template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
-int _writeImpl(TFile& target, Align<TSource, TSpec>& align, TStringContainer& ids, CGViz)
-{
-    typedef Align<TSource, TSpec> const TAlign;
-    typedef typename Position<typename Rows<TAlign>::Type>::Type TRowsPosition;
-    typedef typename Position<TAlign>::Type TPosition;
-    TRowsPosition row_count = length(rows(align));
-    if (row_count < 2)
-        return 1;
-
-    unsigned int pair=1;
-    unsigned int count=0;
-    for (TRowsPosition i=0;i<row_count-1;++i)
-    {
-        for (TRowsPosition j=i+1;j<row_count;++j)
-        {
-            // Print header
-            streamPut(target, "{DATA dat");
-            streamPut(target, pair);
-            streamPut(target, '\n');
-            streamPut(target, "[__GLOBAL__] dimension=2:\n");
-
-            TPosition begin_ = beginPosition(cols(align));
-            TPosition end_ = endPosition(cols(align));
-
-            bool match = false;
-            while(begin_ < end_)
-            {
-                if ((row(align, i)[begin_]==row(align, j)[begin_]) && (row(align, i)[begin_]!='-'))
-                {
-                    if (!match)
-                    {
-                        match = true;
-                        streamPut(target, toSourcePosition(row(align,i),begin_+1));
-                        streamPut(target, ' ');
-                        streamPut(target, toSourcePosition(row(align,j),begin_+1));
-                        streamPut(target, ' ');
-                    }
-                }
-                if ((row(align, i)[begin_]!=row(align, j)[begin_]) || (row(align, i)[begin_]=='-') ||
-                    (row(align, j)[begin_]=='-'))
-                {
-                    if (match)
-                    {
-                        streamPut(target, toSourcePosition(row(align,i),begin_));
-                        streamPut(target, ' ');
-                        streamPut(target, toSourcePosition(row(align,j),begin_));
-                        streamPut(target, '\n');
-                        match = false;
-                    }
-                }
-                begin_++;
-            }
-            if (match)
-            {
-                streamPut(target, toSourcePosition(row(align,i),begin_));
-                streamPut(target, ' ');
-                streamPut(target, toSourcePosition(row(align,j),begin_));
-                streamPut(target, '\n');
-                match = false;
-            }
-            streamPut(target, '}');
-            streamPut(target, '\n');
-
-            // Write footer
-            streamPut(target, "{GLYPH Glyph");
-            streamPut(target, pair);
-            streamPut(target, '\n');
-            streamPut(target, "drawerName=Lines\n");
-            streamPut(target, "lineWidth=3\n");
-            streamPut(target, '}');
-            streamPut(target, '\n');
-            streamPut(target, "{PANE Pane");
-            streamPut(target, pair);
-            streamPut(target, '\n');
-            streamPut(target, "uLabel=");
-            streamPut(target, getValue(ids,i));
-            streamPut(target, '\n');
-            streamPut(target, "uStop=");
-            streamPut(target, length(source(row(align,i))));
-            streamPut(target, '\n');
-            streamPut(target, "vLabel=");
-            streamPut(target, getValue(ids,j));
-            streamPut(target, '\n');
-            streamPut(target, "vStop=");
-            streamPut(target, length(source(row(align,j))));
-            streamPut(target, '\n');
-            streamPut(target, '}');
-            streamPut(target, '\n');
-            streamPut(target, "{WINDOW Window");
-            streamPut(target, pair);
-            streamPut(target, '\n');
-            streamPut(target, '}');
-            streamPut(target, '\n');
-            streamPut(target, "{FEEDER Feeder<");
-            streamPut(target, pair);
-            streamPut(target, '>');
-            streamPut(target, ' ');
-            streamPut(target, count);
-            streamPut(target, ' ');
-            streamPut(target, count+1);
-            streamPut(target, '\n');
-            streamPut(target, '}');
-            streamPut(target, '\n');
-            ++count;
-            streamPut(target, "{THREADER Threader<");
-            streamPut(target, pair);
-            streamPut(target, '>');
-            streamPut(target, ' ');
-            streamPut(target, count);
-            streamPut(target, ' ');
-            streamPut(target, count+1);
-            streamPut(target, '\n');
-            streamPut(target, '}');
-            streamPut(target, '\n');
-            ++count;
-            streamPut(target, "{ANCHOR Anchor<");
-            streamPut(target, pair);
-            streamPut(target, '>');
-            streamPut(target, ' ');
-            streamPut(target, count);
-            streamPut(target, ' ');
-            streamPut(target, count+1);
-            streamPut(target, '\n');
-            streamPut(target, '}');
-            streamPut(target, '\n');
-            count+=2;
-            ++pair;
-        }
-    }
-
-    return streamError(target);
-}
-
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TSource, typename TSpec>
-int write(TFile & file, Align<TSource, TSpec>& align, CGViz)
-{
-	return _writeImpl(file, align, String<String<char> >(), CGViz());
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
-int write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, CGViz)
-{
-    return _writeImpl(file, align, ids, CGViz());
-}
-
-
-// TODO(holtgrew): Is this still necessary? I believe this is a VS2005 issue.
-//VisualC++ const array bug workaround
-template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
-int write(TFile & file, Align<TSource, TSpec>* align, TStringContainer & ids, CGViz)
-{
-	return _writeImpl(file, align, ids, CGViz());
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta>
-int write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, TMeta &, CGViz)
-{
-	return _writeImpl(file, align, ids, CGViz());
-}
-
-}  // namespace seqan
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_format_embl.h b/seqan/file/file_format_embl.h
deleted file mode 100644
index 88a825f..0000000
--- a/seqan/file/file_format_embl.h
+++ /dev/null
@@ -1,664 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_EMBL_H
-#define SEQAN_HEADER_FILE_EMBL_H
-
-/* IOREV
- * _tested_
- * _nodoc_
- *
- * tested in tests/file/test_file.h
- * tag mentioned in doc, but no further documentation, no link to spec
- *
- * should be broken, because based on filereaderiterator which is broken
- * according to holtgrew.
- *
- * IMPORTANT: from what I understand: fileReaderIterator does not iterate
- * through records, but through lines of the sequence of one record.
- * goNext() on the iterator goes to beginning of next line and sets
- * data boundaries for next iteration
- *
- * goNext() on the file itself goes to the beginning of the next record.
- *
- */
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - Embl
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Tag.File Format.tag.Embl:EMBL format for sequences.
-..include:seqan/file.h
-*/
-struct TagEmbl_;
-//IOREV
-typedef Tag<TagEmbl_> const Embl; //IOREV
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// FileReader Iterator
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goBegin(Iter<TFile, FileReader<Embl, TFile2, TSpec> > & it, bool skip_meta)
-{
-//IOREV _bug_ i am not convinced this works. current position is never reset
-SEQAN_CHECKPOINT
-	if (skip_meta)
-	{
-		while (true)
-		{
-			if (_streamEOF(host(it)))
-			{
-				it.data_eof = true;
-				return;
-			}
-			if (it.data_char == '/')
-			{//end of record
-				_streamSkipLine(host(it), it.data_char);
-				it.data_eof = true;
-				return;
-			}
-			if (it.data_char == ' ')
-			{
-				break;
-			}
-			//skip meta line
-			_streamSkipLine(host(it), it.data_char);
-		}
-	}
-
-	//find first character
-	while (true)
-	{
-		if (_streamEOF(host(it)))
-		{
-			it.data_eof = true;
-			return;
-		}
-		if ((it.data_char != ' ') && ((it.data_char < '0') || (it.data_char > '9')))
-		{
-			if ((it.data_char != '\n') && (it.data_char != '\r')) break;
-
-			it.data_char = _streamGet(host(it));
-			if (it.data_char == '/')
-			{//end of record
-				_streamSkipLine(host(it), it.data_char);
-				it.data_eof = true;
-				return;
-			}
-		}
-		else
-		{
-			it.data_char = _streamGet(host(it));
-		}
-	}
-
-//	it.data_file_pos = _streamTellG(host(it));
-	it.data_file_pos -= 1;
-	it.data_eof = _streamEOF(host(it));
-}
-
-
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goBegin(Iter<TFile, FileReader<Embl, TFile2, TSpec> > & it)
-{
-//IOREV
-    SEQAN_CHECKPOINT;
-    goBegin(it, true);
-}
-
-
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goNext(Iter<TFile, FileReader<Embl, TFile2, TSpec> > & it)
-{
-//IOREV this iterates through the characters of a line in one record
-SEQAN_CHECKPOINT
-	do
-	{
-		it.data_char = _streamGet(host(it));
-		if (_streamEOF(host(it)))
-		{
-			it.data_eof = true;
-			return;
-		}
-		it.data_file_pos += 1;
-
-		if ((it.data_char == '\n') || (it.data_char == '\r'))
-		{//linebreak detected: find begin of next line
-			do
-			{
-				it.data_char = _streamGet(host(it));
-				if (_streamEOF(host(it)))
-				{
-					it.data_eof = true;
-					return;
-				}
-				it.data_file_pos += 1;
-			} while ((it.data_char == '\n') || (it.data_char == '\r'));
-
-			if (it.data_char == '/')
-			{//end of record
-				_streamSkipLine(host(it), it.data_char);
-				_streamUnget(host(it));
-				it.data_eof = true;
-				return;
-			}
-		}
-	} while ((it.data_char == ' ') || ((it.data_char >= '0') && (it.data_char <= '9')));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// File Format Access Function
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TData>
-inline void
-read(TFile & file,
-	 TData & data,
-	 Embl)
-{
-//IOREV _recordreading_
-SEQAN_CHECKPOINT
-	Iter<TFile, FileReader<Embl> > it(file);
-
-	clear(data);
-	while (!atEnd(it))
-	{
-		appendValue(data, getValue(it));
-		goNext(it);
-	}
-}
-
-template <typename TFile, typename TData, typename TSize>
-inline void
-read(TFile & file,
-	 TData & data,
-	 TSize limit,
-	 Embl)
-{
-//IOREV _recordreading_
-SEQAN_CHECKPOINT
-	typename Size<TData>::Type siz = length(data);
-	Iter<TFile, FileReader<Embl> > it(file);
-
-	clear(data);
-	while (!atEnd(it) && (siz < limit))
-	{
-		appendValue(data, getValue(it));
-		goNext(it);
-	}
-	while (!atEnd(it))
-	{
-		goNext(it);
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-template <typename TFile, typename TMeta>
-inline void
-readMeta(TFile & file,
-		 TMeta & meta,
-		 Embl)
-{
-//IOREV _recordreading_ weird! 
-SEQAN_CHECKPOINT
-	typedef typename Value<TMeta>::Type TValue;
-
-	clear(meta);
-	if (_streamEOF(file))
-	{
-		return;
-	}
-
-	TValue c = _streamGet(file);
-
-	while (!_streamEOF(file))
-	{
-		if (c == ' ')
-		{//end of meta data
-			_streamUnget(file);
-			return;
-		}
-		if (c == '/')
-		{//end of record
-			_streamSkipLine(file, c);
-			_streamUnget(file);
-			return;
-		}
-
-		_streamAppendLine(file, meta, c);
-		appendValue(meta, '\n');
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-
-/**
-.Function.readLineType:
-..cat:Input/Output
-..summary:Reads the information belonging to the two-character line code specified.
-..signature:readLineType(file,data,key,Embl);
-..param.file:The input file or string.
-...remarks:This function works on an open file stream or on the string data obtained from calling Function.readMeta
-..param.data:The target container that will be filled.
-..param.key:The two-character code specifying the file entry to be read, e.g. "AC" for the acession number line or "DE" for the description line. 
-..see:Function.readMeta
-..see:Function.readFeature
-..include:seqan/file.h
-*/
-template<typename TFile, typename TData, typename TKey>
-inline void
-readLineType(TFile & file,
-			 TData & data,
-			 TKey key,
-			 Embl)
-
-{
-//IOREV _recordreading_ weird! 
-SEQAN_CHECKPOINT
-
-	//this function is meant to be used for two letter codes only 
-	SEQAN_ASSERT(length(key)==2); ;
-
-	typedef typename Value<TFile>::Type TValue;
-	typedef typename Position<TFile>::Type TPosition;
-
-	clear(data);
-	if(_streamEOF(file))
-		return;
-	
-	TPosition pos = _streamTellG(file);
-	TValue c = _streamGet(file);
-	while (!_streamEOF(file))
-	{
-		if(c == '/')
-		{
-			_streamSeekG(file,pos);
-			return;
-		}
-		if(c == key[0])
-		{
-			c = _streamGet(file);
-			if(c == key[1])
-			{
-				for(unsigned int i = 0; i < 4; ++i)
-					c = _streamGet(file);
-				_streamAppendLine(file, data, c);
-				while(!_streamEOF(file) && _streamReadWord(file,c) == key)
-				{
-					appendValue(data, '\n');
-					for(unsigned int i = 0; i < 3; ++i)
-						c = _streamGet(file);
-					_streamAppendLine(file, data, c);
-				}
-				_streamSeekG(file,pos);
-				return;
-			}
-		}
-		_streamSkipLine(file, c);
-	}
-
-	_streamSeekG(file,pos);
-	
-}
-
-
-
-template<typename TData, typename TValue, typename TSpec, typename TKey>
-inline void
-readLineType(String<TValue,TSpec> & meta,
-			 TData & data,
-			 TKey key,
-			 Embl)
-
-{
-//IOREV
-	//this function is meant to be used for two letter codes only
-	SEQAN_ASSERT(length(key)==2); ;
-
-	typedef typename Iterator<String<TValue,TSpec>,Standard>::Type TIterator;
-
-	clear(data);
-	if(empty(meta))
-		return;
-
-	TIterator it = begin(meta,Standard());
-	TIterator end_it = end(meta,Standard());
-
-	while (it != end_it)
-	{
-		if(*it == '/')
-			return;
-
-		if(*it == key[0])
-		{
-			++it;
-			if(*it == key[1])
-			{
-				it+=4;
-				_stringAppendLine(meta, data, it);
-				while(it!=end_it && *it==key[0] && *(++it)==key[1])
-				{
-					appendValue(data, '\n');
-					it+=4;
-					_stringAppendLine(meta, data, it);
-				}
-				return;
-			}
-		}
-		_stringSkipLine(meta, it);
-	}
-
-	
-}
-
-
-/**
-.Function.readFeature:
-..cat:Input/Output
-..summary:Finds the first feature specified by 'key' starting from position 'start' in the feature table (the feature table can be
-obtained by calling readLineType with the two-character code "FT").
-..signature:readFeature(ft_string,start,data,key,Embl);
-..param.ft_string:The feature table.
-..param.start:Position in feature table where search begins.
-..param.data:The target container that will be filled.
-..param.key:The key word specifying the feature to be read, e.g. "mRNA" or "CDS".
-..return:The position behind the feature if found, 0 otherwise.
-..see:Function.readMeta
-..see:Function.readFeature
-..include:seqan/file.h
-*/
-//read parts of feature table (those that belong to key)
-template<typename TData, typename TKey, typename TString>
-inline typename Position<TString>::Type
-readFeature(TString & str,
-			typename Position<TString>::Type start_pos,
-			TData & data,
-			TKey key,
-			Embl)
-
-{
-//IOREV
-	typedef typename Iterator<TString,Standard>::Type TIterator;
-
-	clear(data);
-	if(empty(str) || start_pos >= length(str))
-		return 0;
-	TIterator it = iter(str,start_pos,Standard());
-	TIterator end_it = end(str,Standard());
-
-	while (it != end_it)
-	{
-		if(*it == key[0])
-		{
-			++it;
-			bool found = true;
-			for(unsigned int i = 1; i < length(key); ++i)
-			{
-				if(key[i] != *it)
-				{
-					found = false;
-					break;
-				}
-				++it;
-			}
-			if(found)
-			{
-				_stringSkipWhitespace(str,it);
-				_stringAppendLine(str, data, it);
-				while(it!=end_it && *it == ' ')
-				{
-					appendValue(data, '\n');
-					_stringSkipWhitespace(str,it);
-					_stringAppendLine(str, data, it);
-				}
-				return position(it,str);
-			}
-		}
-		_stringSkipLine(str, it);
-	}
-
-	return 0;
-	
-}
-	
-
-
-//////////////////////////////////////////////////////////////////////////////
-template <typename TFile>
-inline void
-goNext(TFile & file,
-	   Embl)
-{
-//IOREV this iterates to the next record
-SEQAN_CHECKPOINT
-	typedef typename Value<TFile>::Type TValue;
-
-	if (_streamEOF(file))
-	{
-		return;
-	}
-
-	while (!_streamEOF(file))
-	{
-		TValue c = _streamGet(file);
-		if (c == '/')
-		{//end of record
-			_streamSkipLine(file, c);
-			_streamUnget(file);
-			return;
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-/*
-template <typename TFile>
-inline void
-length(TFile & file,
-	   Embl)
-{
-SEQAN_CHECKPOINT
-}
-*/
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TData>
-inline void
-write(TFile & file,
-	  TData & data,
-	  Embl)
-{
-//IOREV _recordreading_ weird. see above; for-loops would make code more readable
-SEQAN_CHECKPOINT
-	enum
-	{
-		BLOCK_SIZE = 10,
-		BLOCKS_PER_LINE = 6,
-		FIRST_INDENT = 5
-	};
-	char const * NUM_BLOCK_FORMAT = "%9d";
-
-	typedef typename Size<TData>::Type TSize;
-	typedef typename Iterator<TData, Standard>::Type TIterator;
-
-	TSize count = 0;
-	int block_count = 0;
-	int char_in_block_count = 0;
-	TIterator it = begin(data, Standard());
-	TIterator it_end = end(data, Standard());
-
-	while (it != it_end)
-	{
-		//write indent
-		for (int j = 0; j < FIRST_INDENT; ++j) _streamPut(file, ' ');
-
-		//write rest of line
-		while (true)
-		{
-			//write next character
-			if (it != it_end)
-			{
-				_streamPut(file, *it);
-				++it;
-				++count;
-			}
-			else
-			{//no more chars left: fill up with ' '
-				_streamPut(file, ' ');
-			}
-			++char_in_block_count;
-
-			if (char_in_block_count >= BLOCK_SIZE)
-			{//end of block
-				char_in_block_count = 0;
-				_streamPut(file, ' ');
-				++block_count;
-
-				if (block_count >= BLOCKS_PER_LINE)
-				{//enough blocks: write end of line
-					block_count = 0;
-					_streamPutInt(file, count, NUM_BLOCK_FORMAT);
-					_streamPut(file, '\n');
-					break; //end of line
-				}
-			}
-		}
-	}
-
-	write(file, "//\n");
-}
-
-template <typename TFile, typename TData, typename TMeta>
-inline void
-write(TFile & file,
-	  TData & data,
-	  TMeta & meta,
-	  Embl)
-{
-//IOREV _recordreading_
-SEQAN_CHECKPOINT
-	write(file, meta);
-	write(file, data, Embl());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*leere Vorlage
-template <typename TFile, typename TData>
-inline void
-read(TFile & file,
-	 TData & data,
-	 Embl)
-{
-SEQAN_CHECKPOINT
-}
-
-template <typename TFile, typename TData, typename TSize>
-inline void
-read(TFile & file,
-	 TData & data,
-	 TSize limit,
-	 Embl)
-{
-SEQAN_CHECKPOINT
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TMeta>
-inline void
-readMeta(TFile & file,
-		 TMeta & meta,
-		 Embl)
-{
-SEQAN_CHECKPOINT
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile>
-inline void
-goNext(TFile & file,
-	   Embl)
-{
-SEQAN_CHECKPOINT
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile>
-inline void
-length(TFile & file,
-	   Embl)
-{
-SEQAN_CHECKPOINT
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TData>
-inline void
-write(TFile & file,
-	  TData & data,
-	  Embl)
-{
-SEQAN_CHECKPOINT
-}
-template <typename TFile, typename TData, typename TMeta>
-inline void
-write(TFile & file,
-	  TData & data,
-	  TMeta & meta,
-	  Embl)
-{
-SEQAN_CHECKPOINT
-}
-*/
-
-//////////////////////////////////////////////////////////////////////////////
-} //namespace SEQAN_NAMESPACE_MAIN
-
-//////////////////////////////////////////////////////////////////////////////
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_format_fasta.h b/seqan/file/file_format_fasta.h
deleted file mode 100644
index 4b37b90..0000000
--- a/seqan/file/file_format_fasta.h
+++ /dev/null
@@ -1,621 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_FASTA_H
-#define SEQAN_HEADER_FILE_FASTA_H
-
-/* IOREV
- * _tested_
- * _nodoc_
- *
- * tested in tests/file/test_file.h
- * tag mentionen in doc, but no further documentation, no link to spec
- * 
- * IMPORTANT: from what I understand: fileReaderIterator does not iterate
- * through records, but through lines of the sequence of one record.
- * goNext() on the iterator goes to beginning of next line and sets
- * data boundaries for next iteration
- *
- * goNext() on the file itself goes to the beginning of the next record.
- */
-
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - Fasta
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Tag.File Format.tag.Fasta:
-	FASTA file format for sequences.
-..include:seqan/file.h
-*/
-struct TagFasta_;
-//IOREV
-typedef Tag<TagFasta_> Fasta; //IOREV
-
-//////////////////////////////////////////////////////////////////////////////
-// Filereader
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goBegin(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it, bool skip_meta)
-{
-//IOREV _postponed_ due to unclear state of filereaderiterator
-	if (_streamEOF(host(it)))
-	{
-		it.data_eof = true;
-		return;
-	}
-
-	if (skip_meta && (it.data_char == '>'))
-	{
-		//skip meta line
-		_streamSkipLine(host(it), it.data_char);
-	}
-
-	//eliminate linebreaks
-	while ((it.data_char == '\n') || (it.data_char == '\r'))
-	{
-		if (_streamEOF(host(it)))
-		{
-			it.data_eof = true;
-			return;
-		}
-		it.data_char = _streamGet(host(it));
-	}
-
-	if (it.data_char == '>')
-	{//end of record
-		it.data_eof = true;
-		_streamUnget(host(it));
-		return;
-	}
-
-	it.data_file_pos = _streamTellG(host(it)) - 1;
-	it.data_eof = _streamEOF(host(it));
-}
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goBegin(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it)
-{
-//IOREV
-	goBegin(it, true);
-}
-
-
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goNext(Iter<TFile, FileReader<Fasta, TFile2, TSpec> > & it)
-{
-//IOREV goto next line of sequence in current record, set boundaries for
-/*
-	if (_streamEOF(host(it)))
-	{
-		it.data_eof = true;
-		return;
-	}
-*/
-	it.data_char = _streamGet(host(it));
-	++it.data_file_pos;
-
-	if (_streamEOF(host(it)))
-	{
-		it.data_eof = true;
-		return;
-	}
-
-	if ((it.data_char == '\n') || (it.data_char == '\r'))
-	{//linebreak detected: find begin of next line
-		do
-		{
-			it.data_char = _streamGet(host(it));
-			if (_streamEOF(host(it)))
-			{
-				it.data_eof = true;
-				return;
-			}
-			++it.data_file_pos;
-		} while ((it.data_char == '\n') || (it.data_char == '\r'));
-
-		if (it.data_char == '>')
-		{//end of record
-			_streamUnget(host(it));
-			it.data_eof = true;
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// FileFormat Interface
-//////////////////////////////////////////////////////////////////////////////
-
-
-
-/////////////////////////////////////////////////////////////////////////
-//count_valid: zaehlt die nicht-Zeilenumbrueche (input/output)
-//count_all: zaehlt alle Zeichen incl. Zeilenumbrueche (input/output)
-//returns: zuletzt gelesenes Zeichen = das erste hinter dem Zeilenumbruch bzw. eof
-//the last read char is not counted!
-//count_valid and count_all are not resetted but counted up
-template <typename TFile, typename TSize>
-inline typename Value<TFile>::Type
-_fastaScanLine(TFile & file,
-				 TSize & count_valid,
-				 TSize & count_all)
-{
-//IOREV _nodoc_ has doc but in wrong format
-SEQAN_CHECKPOINT
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-
-	TSize count = 0;
-	typename Value<TFile>::Type c;
-
-	do
-	{
-		c = _streamGet(file);
-		if (c == '\n' || c == '\r')
-		{
-			while (!_streamEOF(file))
-			{
-				++count_all;
-				c = _streamGet(file);
-				if (c != '\n' && c != '\r')
-					break;
-			}
-			break;
-		}
-
-		++count;
-	} while (!_streamEOF(file));
-	
-	count_valid += count;
-	count_all += count;
-	return c;
-}
-
-
-/////////////////////////////////////////////////////////////////////////
-template <typename TFile, typename TSize>
-inline void
-_readNCharsFromFile(TFile & file, TSize count)
-{
-//IOREV shouldn't this check for EOF? Shouldn't it be renamed to sth like skipNChars, since it doesn't save them anywhere?
-SEQAN_CHECKPOINT
-	for (TSize i = 0; i < count; ++i)
-	{
-		_streamGet(file);
-	}
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// read
-//////////////////////////////////////////////////////////////////////////////
-
-// TODO(holtgrew): The interface of this function does not correlate with documentation where the third parameter is metadata!
-template <typename TFile, typename TData, typename TSize>
-void
-read(TFile & file,
-	 TData & data,
-	 TSize limit,
-	 Fasta)
-{
-//IOREV _recordreading_ _notinlined_ see comment by holtgrew, signature is wrong for most file formats specializations
-SEQAN_CHECKPOINT
-
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-	clear(data);
-
-	//determine begin position
-	typename Value<TFile>::Type c_first = _streamGet(file);
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-
-	typename Position<TFile>::Type begin_pos = _streamTellG(file);
-	typename Size<TData>::Type count_valid = 1; //"valid" characters read (without line breaks)
-	typename Size<TData>::Type count_all = 1;	//all characters read (with line breaks)
-
-	if (_streamEOF(file))
-	{
-		return;
-	}	
-
-	if (c_first == '>')
-	{//there is an id line: skip it
-		c_first = _fastaScanLine(file, count_valid, count_all);
-	}
-
-	if ((c_first == '>') || _streamEOF(file)) 
-	{//another id line = empty entry
-		_streamSeekG(file, begin_pos);
-		_readNCharsFromFile(file, count_all-1);
-		return;
-	}
-
-	begin_pos = _streamTellG(file);
-
-	count_valid = 1;
-	count_all = 1;
-	typename Value<TFile>::Type c;
-	bool eof_reached = false;
-	//determine length
-	while (true)
-	{
-		c = _fastaScanLine(file, count_valid, count_all);
-		if (_streamEOF(file)) 
-		{//end of file: stop searching
-			eof_reached = true;
-			break;
-		}
-		if (c == '>')
-		{//next entry found: stop seaching
-			break;
-		}
-		if ((c != '\n') && (c != '\r'))
-		{
-			++count_valid; //count c
-		}
-		++count_all;
-	}
-
-	//reserve space
-	typename Size<TData>::Type count = count_valid;
-	if (count > limit)
-		count = limit;
-	
-	resize(data, count);
-	if (count > length(data))
-		count = length(data);
-
-	//read sequence
-	_streamSeekG(file, begin_pos);
-
-	typename Position<TData>::Type pos = 0;
-	c = c_first;
-	while (true)
-	{
-		if ((c != '\n') && (c != '\r'))
-		{
-			data[pos] = c;
-			++pos;
-		}
-		if (pos >= count) break;
-
-		c = _streamGet(file);
-		--count_all;
-	}
-
-	//move file ptr to next entry
-	_readNCharsFromFile(file, count_all - 1);
-	if(eof_reached)
-		_streamGet(file);
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TData>
-void
-read(TFile & file,
-	 TData & data,
-	 Fasta tag)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	typedef typename Size<TData>::Type TSize;
-	read(file, data, maxValue<TSize>(), tag);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// readID
-//////////////////////////////////////////////////////////////////////////////
- 
-//the ID is the complete first line (without the leading '>'-sign)
-
-template <typename TFile, typename TString>
-void
-readID(TFile & file,
-	   TString & seqId,
-	   Fasta)
-{
-//IOREV _nodoc_ _notinlined_ name ambiguous with readId-memfunc
-SEQAN_CHECKPOINT
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-
-	typename Position<TFile>::Type start_pos = _streamTellG(file);
-
-	typename Value<TFile>::Type c = _streamGet(file);
-	if (c != '>')
-	{
-		clear(seqId);
-	}
-	else
-	{
-		typename Size<TString>::Type count_valid = 0;
-		typename Size<TString>::Type count_all = 0;
-		_fastaScanLine(file, count_valid, count_all);
-
-		if (! count_valid)
-		{
-			clear(seqId);
-		}
-		else
-		{
-			resize(seqId, count_valid);
-			if (length(seqId) < count_valid)
-			{
-				count_valid = length(seqId);
-			}
-
-			_streamSeekG(file, start_pos);
-			c = _streamGet(file); //pop the '>' character
-			for (typename Position<TString>::Type pos = 0; count_valid; --count_valid)
-			{
-				seqId[pos] = _streamGet(file);
-				++pos;
-			}
-		}
-	}
-	_streamSeekG(file, start_pos);
-}
-
-//short ID, read fasta header up to first whitespace
-template <typename TFile, typename TString>
-void
-readShortID(TFile & file,
-	   TString & seqId,
-	   Fasta)
-{
-//IOREV _nodoc_ _notinlined_ better to use _stream* or _parse* calls to get first word
-SEQAN_CHECKPOINT
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-
-	typename Position<TFile>::Type start_pos = _streamTellG(file);
-
-	typename Value<TFile>::Type c = _streamGet(file);
-	if (c != '>')
-	{
-		clear(seqId);
-	}
-	else
-	{
-		typename Size<TString>::Type count_valid = 0;
-		typename Size<TString>::Type count_all = 0;
-		_fastaScanLine(file, count_valid, count_all);
-
-		if (! count_valid)
-		{
-			clear(seqId);
-		}
-		else
-		{
-			resize(seqId, count_valid);
-			if (length(seqId) < count_valid)
-			{
-				count_valid = length(seqId);
-			}
-
-			_streamSeekG(file, start_pos);
-			c = _streamGet(file); //pop the '>' character
-			for (typename Position<TString>::Type pos = 0; count_valid; --count_valid)
-			{
-				seqId[pos] = _streamGet(file);
-				if(seqId[pos]=='\t' || seqId[pos]=='\b' || seqId[pos]==' ')
-				{
-					resize(seqId,pos);
-					break;
-				}
-				++pos;
-			}
-		}
-	}
-	_streamSeekG(file, start_pos);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// readMeta
-//////////////////////////////////////////////////////////////////////////////
-
-//Fasta file records have no meta data
-
-template <typename TFile, typename TMeta>
-void
-readMeta(TFile & file,
-		 TMeta & meta,
-		 Fasta)
-{
-//IOREV _nodoc_ _notinlined_ code documentation wrong
-SEQAN_CHECKPOINT
-	readID(file, meta, Fasta());
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// goNext
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile>
-void
-goNext(TFile & file,
-	   Fasta)
-{
-//IOREV _notinlined_ goto next record
-SEQAN_CHECKPOINT
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-
-//	bool found_data = false;
-	while (true)
-	{
-		typename Value<TFile>::Type c = _streamGet(file);
-
-		if (_streamEOF(file)) return;
-
-		if (c == '\n' || c == '\r')
-		{
-			do {
-				c = _streamGet(file);
-				if (_streamEOF(file)) return;
-			} while (c == '\n' || c == '\r');
-/*
-// weese: I changed the following lines, as otherwises empty
-//        sequences (seq1) will be overread. See:
-// >seq1
-// >seq2
-// ACTGGT
-			if (c != '>')
-			{
-				found_data = true;
-			}
-			else if (found_data)
-			{
-				_streamUnget(file);
-				return;
-			}
-*/			if (c == '>')
-			{
-				_streamUnget(file);
-				return;
-			}
-		}
-	}
-}
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// write
-//////////////////////////////////////////////////////////////////////////////
-
-
-template <typename TFile, typename TString, typename TData>
-void
-_writeImpl(TFile & file,
-			TData & data,
-			TString & seqId,
-			Fasta)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	_streamPut(file, '>');
-	_streamWrite(file, seqId);
-	_streamPut(file, '\n');
-
-	//typename Iterator<TData, Standard>::Type it = begin(data, Standard());
-	//typename Iterator<TData, Standard>::Type it_end = end(data, Standard());
-	typename Iterator<TData>::Type it = begin(data);
-	typename Iterator<TData>::Type it_end = end(data);
-
-	int i = 0;
-
-	for (; it < it_end; ++it)
-	{
-		if (i == 60)
-		{
-			_streamPut(file, '\n');
-			i = 0;
-		}
-		++i;
-
-		_streamPut(file, *it);
-	}
-	_streamPut(file, '\n');
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TString, typename TData, typename TMeta>
-void
-write(TFile & file,
-	  TData & data,
-	  Fasta)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	_writeImpl(file, data, "", Fasta());
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TString, typename TData>
-void
-write(TFile & file,
-	  TData & data,
-	  TString & seqId,
-	  Fasta)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	_writeImpl(file, data, seqId, Fasta());
-}
-
-
-//VisualC++ const array bug workaround
-template <typename TFile, typename TString, typename TDataValue>
-void
-write(TFile & file,
-	  TDataValue * data,
-	  TString & seqId,
-	  Fasta)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	_writeImpl(file, data, seqId, Fasta());
-
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TString, typename TData, typename TMeta>
-void
-write(TFile & file,
-	  TData & data,
-	  TString & seqId,
-	  TMeta &,
-	  Fasta)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	_writeImpl(file, data, seqId, Fasta());
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-} //namespace SEQAN_NAMESPACE_MAIN
-
-//////////////////////////////////////////////////////////////////////////////
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_format_fasta_align.h b/seqan/file/file_format_fasta_align.h
deleted file mode 100644
index 9db51ac..0000000
--- a/seqan/file/file_format_fasta_align.h
+++ /dev/null
@@ -1,368 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-// ==========================================================================
-// Support for writing and reading FASTA alignment files.
-// ==========================================================================
-
-#ifndef SEQAN_FILE_FILE_FORMAT_FASTA_ALIGN_H_
-#define SEQAN_FILE_FILE_FORMAT_FASTA_ALIGN_H_
-
-/* IOREV
- * _tested_
- * _nodoc_
- *
- * tested in tests/file/test_file.h
- * tag mentionen in doc, but no further documentation, no link to spec
- *
- *
- * bacthreading and -writing
- *
- * does not treat IDs as Meta-Data, while format_fasta does
- * 
- */
-
-
-namespace seqan {
-
-// ===========================================================================
-// Forward Declarations
-// ===========================================================================
-
-//forward declarations
-template <typename T>
-struct Row;
-//IOREV
-
-template <typename T>
-struct Rows;
-//IOREV
-
-// ===========================================================================
-// Tags, Enums, Classes, Specializations
-// ===========================================================================
-
-/**
-.Tag.File Format.tag.Fasta alignment:
-	FASTA alignment file format for sequences.
-..include:seqan/file.h
-*/
-struct FastaAlign_;
-//IOREV
-typedef Tag<FastaAlign_> FastaAlign; //IOREV
-
-// ===========================================================================
-// Metafunctions
-// ===========================================================================
-
-// ===========================================================================
-// Functions
-// ===========================================================================
-
-template <typename TFile, typename TSize>
-void _fastaAlignScanLine(TFile & file, TSize & count) {
-//IOREV _notinlined_ no EOF check in beginning; non-default EOL-handling
-
-	SEQAN_CHECKPOINT;
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-
-	while (true) {
-		typename Value<TFile>::Type c = _streamGet(file);
-
-		if (_streamEOF(file)) return;
-		if (c == '\n') return;
-
-		if ((c != '\r') && (c!='-'))
-			++count;
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// read
-//////////////////////////////////////////////////////////////////////////////
-template <typename TFile, typename TSource, typename TSpec>
-void read(TFile & file, Align<TSource, TSpec> & align, FastaAlign const &) {
-//IOREV _notinlined_ _batchreading_ not sure whether begin_pos is absolute
-    SEQAN_CHECKPOINT;
-
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-	
-	typedef typename Value<TSource>::Type TSourceValue;
-	typedef typename Size<TSourceValue>::Type TSize;
-	typedef typename Position<TFile>::Type TFilePos;
-	typedef Triple<TFilePos, TFilePos, TSize> TTriple;
-	TSize limit = maxValue<TSize>();
-
-	//Determine begin position, end position and length of each sequence
-	String<TTriple> beg_end_length;
-	
-	TFilePos begin_pos;
-	TFilePos end_pos;
-	typename Value<TFile>::Type c;
-	TSize count;
-
-	while (!_streamEOF(file)) {
-		begin_pos = _streamTellG(file);
-		count = 0;
-		SEQAN_ASSERT_NOT(_streamEOF(file));
-
-	
-		c = _streamGet(file);
-		
-		// Skip id
-		if (c == '>') {
-			_fastaAlignScanLine(file, count);
-			begin_pos = _streamTellG(file);
-			count = 0;
-		} else {  //If no id first letter belongs to sequence
-			count = 1;
-		}
-
-		// Count letters
-		while (true) {
-			_fastaAlignScanLine(file, count);
-
-			typename Value<TFile>::Type c = _streamGet(file);
-			if (c == '>') {
-				_streamSeek2G(file, -1);
-				end_pos = _streamTellG(file);
-				break;
-			}
-			if (_streamEOF(file)) {
-				end_pos = _streamTellG(file);
-				break;
-			}
-			if ((c != '\n') && (c != '\r') && (c!='-'))	{
-				++count;
-			}
-		}
-		if (count > limit) {
-			count = limit;
-		}
-
-		appendValue(beg_end_length, TTriple(begin_pos, end_pos, count));
-	}
-
-	// Resize alignment data structure
-	TSize numRows=length(beg_end_length);
-	resize(rows(align), numRows);	//rows
-
-	//typedef Align<TSource, TSpec> TAlign;
-
-	for(TSize i=0;i<numRows;++i) {
-		TSize begin = beg_end_length[i].i1;
-//		TSize end = beg_end_length[i].i2;
-		count = beg_end_length[i].i3;
-
-		//Reserve space
-        TSource buffer;
-        resize(buffer, count);
-        assignSource(row(align, i), buffer);
-		// clear(row(align,i));
-		// createSource(row(align,i));
-		// resize(source(row(align,i)),count);
-		// if (length(source(row(align,i))) < count) {
-		//	count = length(source(row(align,i)));
-		// }
-		// setClippedEndPosition(row(align,i),count);
-
-		//Read sequence
-		_streamSeekG(file, begin);
-
-		typename Position<TSource>::Type pos, viewPos;
-		for (pos = 0, viewPos = 0; pos < count; ++viewPos) {
-			c = _streamGet(file);
-			if ((c != '\n') && (c != '\r') && (c != '-'))	{
-				source(row(align,i))[pos] = c;
-				++pos;
-			}
-			if (c=='-') {
-				insertGap(row(align,i), viewPos);
-			}
-		}
-	}
-
-	_streamSeekG(file, 0);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// readIDs
-//////////////////////////////////////////////////////////////////////////////
- 
-template <typename TFile, typename TStringContainer>
-void readIDs(TFile& file, TStringContainer& ids, FastaAlign) {
-//IOREV _notinlined_ _batchreading_ _nodoc_
-	
-	SEQAN_CHECKPOINT;
-	
-    SEQAN_ASSERT_NOT(_streamEOF(file));
-
-	typedef typename Value<TStringContainer>::Type TString;
-	typename Position<TFile>::Type start_pos;
-	typename Value<TFile>::Type c;
-
-
-	TString seqId;
-	while(true) {
-		c = _streamGet(file);
-		while ((!_streamEOF(file)) && (c != '>')) c = _streamGet(file);
-		if (!_streamEOF(file)) {
-			start_pos = _streamTellG(file);
-			typename Size<TString>::Type count = 0;
-			_fastaAlignScanLine(file, count);
-			if (! count) clear(seqId);
-			else {
-				resize(seqId, count);
-				if (length(seqId) < count)	{
-					count = length(seqId);
-				}
-				_streamSeekG(file, start_pos);
-				for (typename Position<TString>::Type pos = 0; pos<count; ++pos) {
-					seqId[pos] = _streamGet(file);
-				}
-			}
-			appendValue(ids, seqId);
-		} else {
-			break;
-		}
-	}
-	_streamSeekG(file, 0);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// readMeta
-//////////////////////////////////////////////////////////////////////////////
-
-//Fasta file records have no meta data
-
-template <typename TFile, typename TMeta>
-void readMeta(TFile & /*file*/, TMeta & meta, FastaAlign) {
-//IOREV _notinlined_ _bug_ ids is meta-data, at least it is handled this way in format_fasta
-	SEQAN_CHECKPOINT
-	clear(meta);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// goNext
-//////////////////////////////////////////////////////////////////////////////
-template <typename TFile>
-void goNext(TFile & file, FastaAlign) {
-//IOREV
-	SEQAN_CHECKPOINT;
-	(void) file; // When compiled without assertions.
-	SEQAN_ASSERT_NOT(_streamEOF(file));
-	
-	return;
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// write
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
-void _writeImpl(TFile & file, Align<TSource, TSpec> const & align, TStringContainer const & ids, FastaAlign const &) {
-//IOREV _notinlined_ _batchreading_
-	SEQAN_CHECKPOINT
-
-	typedef Align<TSource, TSpec> const TAlign;
-	typedef typename Row<TAlign>::Type TRow;
-	typedef typename Position<typename Rows<TAlign>::Type>::Type TRowsPosition;
-	TRowsPosition row_count = length(rows(align));
-
-	for(TRowsPosition i=0;i<row_count;++i) {
-		TRow & row_ = row(align, i);
-
-		typedef typename Iterator<typename Row<TAlign>::Type const, Standard>::Type TIter;
-		TIter begin_ = iter(row_, beginPosition(cols(align)));
-		TIter end_ = iter(row_, endPosition(cols(align)));
-
-		_streamPut(file, '>');
-		_streamWrite(file, getValue(ids,i));
-		_streamPut(file, '\n');
-
-		int chars=0;
-		while(begin_ != end_) {
-			if (chars == 60) {
-				_streamPut(file, '\n');
-				chars = 0;
-			}
-			if (isGap(begin_)) _streamPut(file, gapValue<char>());
-			else _streamPut(file, getValue(begin_));
-			chars++;
-			++begin_;
-		}
-		_streamPut(file, '\n');
-	}
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TSource, typename TSpec>
-void write(TFile & file, Align<TSource, TSpec> const & align, FastaAlign const & ) {
-//IOREV _notinlined_ _batchreading_
-	SEQAN_CHECKPOINT
-	_writeImpl(file, align, String<String<char> >(), FastaAlign());
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
-void write(TFile & file, Align<TSource, TSpec> const & align, TStringContainer const & ids, FastaAlign const & ) {
-//IOREV _notinlined_ _batchreading_
-	SEQAN_CHECKPOINT
-	_writeImpl(file, align, ids, FastaAlign());
-}
-
-
-//VisualC++ const array bug workaround
-// TODO(holtgrew): Superflous?!
-template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
-void write(TFile & file, Align<TSource, TSpec> const * align, TStringContainer const & ids, FastaAlign const & ) {
-//IOREV  _notinlined_ _batchreading_ _windows_
-	SEQAN_CHECKPOINT
-	_writeImpl(file, align, ids, FastaAlign());
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta>
-void write(TFile & file, Align<TSource, TSpec> const & align, TStringContainer const & ids, TMeta &, FastaAlign const & ) {
-//IOREV _notinlined_ _batchreading_
-	SEQAN_CHECKPOINT;
-	_writeImpl(file, align, ids, FastaAlign());
-}
-
-}  // namespace seqan
-
-#endif   // #ifndef SEQAN_FILE_FILE_FORMAT_FASTA_ALIGN_H_
diff --git a/seqan/file/file_format_genbank.h b/seqan/file/file_format_genbank.h
deleted file mode 100644
index c6e31fd..0000000
--- a/seqan/file/file_format_genbank.h
+++ /dev/null
@@ -1,412 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_GENBANK_H
-#define SEQAN_HEADER_FILE_GENBANK_H
-
-/* IOREV
- * _tested_
- * _nodoc_
- *
- * tested in tests/file/test_file.h
- * tag mentionen in doc, but no further documentation, no link to spec
- *
- * current spec:
- * ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
- *
- * IMPORTANT: from what I understand: fileReaderIterator does not iterate
- * through records, but through lines of the sequence of one record.
- * goNext() on the iterator goes to beginning of next line and sets
- * data boundaries for next iteration
- *
- * goNext() on the file itself goes to the beginning of the next record.
- *
- * THIS is not intuitive AT ALL.
- */
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - Genbank
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Tag.File Format.tag.Genbank:
-	Genbank format for sequences from the Genbank database.
-..include:seqan/file.h
-*/
-struct TagGenbank_;
-//IOREV
-typedef Tag<TagGenbank_> const Genbank; //IOREV
-
-
-//////////////////////////////////////////////////////////////////////////////
-// FileReader Iterator
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goBegin(Iter<TFile, FileReader<Genbank, TFile2, TSpec> > & it, bool skip_meta)
-{
-//IOREV not sure whether begin_pos is absolute; parsing could be done simpler; no error handling
-SEQAN_CHECKPOINT
-	String<char> line;
-
-	if (_streamEOF(host(it)))
-	{//end of file
-		it.data_eof = true;
-		return;
-	}
-
-	if (skip_meta && (it.data_char != ' '))
-	{//skip metadata block
-		while (true)
-		{
-			if (it.data_char == '/')
-			{//end of record
-				_streamSkipLine(host(it), it.data_char);
-				it.data_eof = true;
-				return;
-			}
-			if ((it.data_char == 'O') || (it.data_char == 'o'))
-			{
-				clear(line);
-				_streamAppendLine(host(it), line, it.data_char);
-				if ((prefix(line, 6) == "ORIGIN") || (prefix(line, 6) == "origin"))
-				{//end of metadata
-					break;
-				}
-			}
-			//skip meta line
-			_streamSkipLine(host(it), it.data_char);
-
-			if (_streamEOF(host(it)))
-			{//end of file
-				it.data_eof = true;
-				return;
-			}
-		}
-	}
-
-	//find first character
-	while (true)
-	{
-		if (_streamEOF(host(it)))
-		{//end of file
-			it.data_eof = true;
-			return;
-		}
-		if ((it.data_char != ' ') && ((it.data_char < '0') || (it.data_char > '9')))
-		{
-			if ((it.data_char != '\n') && (it.data_char != '\r'))
-			{//fist char found
-				break;
-			}
-
-			it.data_char = _streamGet(host(it));
-			if (it.data_char == '/')
-			{//end of record
-				_streamSkipLine(host(it), it.data_char);
-				it.data_eof = true;
-				return;
-			}
-		}
-		else
-		{
-			it.data_char = _streamGet(host(it));
-		}
-	}
-
-	it.data_file_pos = _streamTellG(host(it));
-	it.data_file_pos -=1;
-	it.data_eof = _streamEOF(host(it));
-}
-
-
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goBegin(Iter<TFile, FileReader<Genbank, TFile2, TSpec> > & it)
-{
-//IOREV
-    SEQAN_CHECKPOINT;
-    goBegin(it, true);
-}
-
-
-template <typename TFile, typename TFile2, typename TSpec>
-inline void
-goNext(Iter<TFile, FileReader<Genbank, TFile2, TSpec> > & it)
-{
-//IOREV this iterates through the characters of a line in one record
-SEQAN_CHECKPOINT
-	do
-	{
-		it.data_char = _streamGet(host(it));
-		if (_streamEOF(host(it)))
-		{
-			it.data_eof = true;
-			return;
-		}
-		it.data_file_pos += 1;
-
-		if ((it.data_char == '\n') || (it.data_char == '\r'))
-		{//linebreak detected: find begin of next line
-			do
-			{
-				it.data_char = _streamGet(host(it));
-				if (_streamEOF(host(it)))
-				{
-					it.data_eof = true;
-					return;
-				}
-				it.data_file_pos += 1;
-			} while ((it.data_char == '\n') || (it.data_char == '\r'));
-
-			if (it.data_char == '/')
-			{//end of record
-				_streamSkipLine(host(it), it.data_char);
-				_streamUnget(host(it));
-				//it.data_file_pos is invalid now
-				it.data_eof = true;
-				return;
-			}
-		}
-	} while ((it.data_char == ' ') || ((it.data_char >= '0') && (it.data_char <= '9')));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// File Format Access Function
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TData>
-inline void
-read(TFile & file,
-	 TData & data,
-	 Genbank)
-{
-//IOREV _recordreading_ see above
-SEQAN_CHECKPOINT
-	Iter<TFile, FileReader<Genbank> > it(file);
-
-	clear(data);
-	while (!atEnd(it))
-	{
-		appendValue(data, getValue(it));
-		goNext(it);
-	}
-}
-
-template <typename TFile, typename TData, typename TSize>
-inline void
-read(TFile & file,
-	 TData & data,
-	 TSize limit,
-	 Genbank)
-{
-//IOREV _nodoc_ _recordreading_ see above
-SEQAN_CHECKPOINT
-	typename Size<TData>::Type siz = length(data);
-	Iter<TFile, FileReader<Genbank> > it(file);
-
-	clear(data);
-	while (!atEnd(it) && (siz < limit))
-	{
-		appendValue(data, getValue(it));
-		goNext(it);
-	}
-	while (!atEnd(it))
-	{
-		goNext(it);
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TMeta>
-inline void
-readMeta(TFile & file,
-		 TMeta & meta,
-		 Genbank)
-{
-//IOREV _ndoc_ _recordreading_ see above
-SEQAN_CHECKPOINT
-	typedef typename Value<TMeta>::Type TValue;
-	String<char> line;
-
-	clear(meta);
-
-	if (_streamEOF(file))
-	{
-		return;
-	}
-
-	TValue c = _streamGet(file);
-
-	while (!_streamEOF(file))
-	{
-		clear(line);
-		_streamAppendLine(file, line, c);
-
-		if (c == '/')
-		{//end of record
-			_streamUnget(file);
-			break;
-		}
-
-		append(meta, line);
-		appendValue(meta, '\n');
-
-		if ((prefix(line, 6) == "ORIGIN") || (prefix(line, 6) == "origin"))
-		{//end of metadata
-			_streamUnget(file);
-			break;
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile>
-inline void
-goNext(TFile & file,
-	   Genbank)
-{
-//IOREV this seems to iterate to the enxt record
-SEQAN_CHECKPOINT
-	typedef typename Value<TFile>::Type TValue;
-
-	if (_streamEOF(file))
-	{
-		return;
-	}
-
-	while (!_streamEOF(file))
-	{
-		TValue c = _streamGet(file);
-		if (c == '/')
-		{//end of record
-			_streamSkipLine(file, c);
-			_streamUnget(file);
-			return;
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-/*
-template <typename TFile>
-inline void
-length(TFile & file,
-	   Genbank)
-{
-SEQAN_CHECKPOINT
-}
-*/
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TData>
-inline void
-write(TFile & file,
-	  TData & data,
-	  Genbank)
-{
-//IOREV _recordreading_
-SEQAN_CHECKPOINT
-	enum
-	{
-		BLOCK_SIZE = 10,
-		BLOCKS_PER_LINE = 6
-	};
-	char const * NUM_BLOCK_FORMAT = "%9d";
-
-	typedef typename Size<TData>::Type TSize;
-	typedef typename Iterator<TData, Standard>::Type TIterator;
-
-	TSize count = 0;
-	TIterator it = begin(data, Standard());
-	TIterator it_end = end(data, Standard());
-
-	while (it != it_end)
-	{
-		//write count 
-		_streamPutInt(file, count+1, NUM_BLOCK_FORMAT);
-
-		int block_count = 0;
-		int char_in_block_count = BLOCK_SIZE;
-
-		//write rest of line
-		while (it != it_end)
-		{
-			if (char_in_block_count == BLOCK_SIZE)
-			{//begin new block
-				if (block_count >= BLOCKS_PER_LINE)
-				{//end of line
-					_streamPut(file, '\n');
-					break;
-				}
-				_streamPut(file, ' ');
-				char_in_block_count = 0;
-				++block_count;
-			}
-
-			//write next character
-			_streamPut(file, *it);
-			++it;
-			++count;
-			++char_in_block_count;
-		}
-	}
-
-	write(file, "\n//\n");
-}
-
-template <typename TFile, typename TData, typename TMeta>
-inline void
-write(TFile & file,
-	  TData & data,
-	  TMeta & meta,
-	  Genbank)
-{
-//IOREV _recordreading_
-SEQAN_CHECKPOINT
-	write(file, meta);
-	write(file, data, Genbank());
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-} //namespace SEQAN_NAMESPACE_MAIN
-//////////////////////////////////////////////////////////////////////////////
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_format_guess.h b/seqan/file/file_format_guess.h
deleted file mode 100644
index a3a7ab6..0000000
--- a/seqan/file/file_format_guess.h
+++ /dev/null
@@ -1,129 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_GUESS_H
-#define SEQAN_HEADER_FILE_GUESS_H
-
-/* IOREV
- * _tested_
- * _doc_
- *
- * only works if seeking is possible
- * 
- * the whole FileFormat class seems useless, see file_format.h
- * this could aswell return the specific tag
- *
- * description in code comments not plausible
- */
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// guessFileFormat
-//////////////////////////////////////////////////////////////////////////////
-
-//guessFileFormat braucht auch data, weil die FileFormat-Klasse von TData
-//abhaengig, und das ist so, weil sonst die Kombination von Templates mit
-//virtuellen Funktionen nicht funktionieren wuerde.
-/**
-.Function.guessFileFormat
-..cat:Input/Output
-..summary:Tries to determine the format of a file.
-..signature:guessFileFormat(file, data)
-..param.file: An input file.
-..param.data: The target container.
-...remarks:This container is not modified by this function.
-..returns:A file format object instance that represents the determined file format.
-...type:Class.FileFormat
-..remarks:The $data$-argument is used here as a tag to determine the type of the target.
-..see:Function.FileFormat#read
-..see:Tag.File Format
-..include:seqan/file.h
-*/
-template <typename TFile, typename TData, typename TMeta>
-inline FileFormat<TFile, TData, TMeta, void> 
-guessFileFormat(TFile & file,
-				TData & data)
-{
-//IOREV _doc_ see head of file_format_guess.h
-SEQAN_CHECKPOINT
-	typename Position<TFile>::Type old_pos = _streamTellG(file);
-	typename Value<TFile>::Type c;
-
-	_streamSeekG(file, 0); /// move to beginning of file
-	c = _streamGet(file);
-		
-	if (c=='>') 
-	{
-		_streamSeekG(file, old_pos);
-		return getFileFormatInstance<TFile, TData, Fasta, TMeta>();
-	}
-	
-	if (c=='L')
-	{
-		_streamSeekG(file, old_pos);
-		return getFileFormatInstance<TFile, TData, Genbank, TMeta>();
-	}
-
-	if (c=='I')
-	{
-		_streamSeekG(file, old_pos);
-		return getFileFormatInstance<TFile, TData, Embl, TMeta>();
-	}
-
-	else
-	{
-		_streamSeekG(file, old_pos);
-		return getFileFormatInstance<TFile, TData, Raw, TMeta>();
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/* DOCH NICHT:
-template <typename TTarget, typename TSource>
-inline void
-read(TTarget & target,
-	 TSource & source)
-{
-SEQAN_CHECKPOINT
-	read(target, source, guessFileFormat(target, source));
-}
-*/
-
-//////////////////////////////////////////////////////////////////////////////
-} //namespace SEQAN_NAMESPACE_MAIN
-
-//////////////////////////////////////////////////////////////////////////////
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_format_mmap.h b/seqan/file/file_format_mmap.h
deleted file mode 100644
index 091b882..0000000
--- a/seqan/file/file_format_mmap.h
+++ /dev/null
@@ -1,1656 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: David Weese <david.weese@fu-berlin.de>
-// ==========================================================================
-// Provides functionality to map a sequence file into memory and split into
-// segments (one for each sequence). Implements different sequence file
-// formats, e.g. Fastq, Fasta, QSeq, Raw, and auto detection (via the
-// TagSelector AutoSeqFormat) based on content or file extension.
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_FORMAT_MMAP_H
-#define SEQAN_HEADER_FILE_FORMAT_MMAP_H
-
-
-
-/* IOREV
- * _tested_
- *
- *
- * mostly documented
- * contents seems to be used widely in apps
- * 
- * contains all sorts of private _is* and _stream* functions
- *
- * contains many file format specific functions and even two new file format
- * definitions (fastq and qsec) that should definitely go someplace else,
- *
- * contains almost nothing specific to MemoryMapped strings, other than
- * the split()-calls
- */
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - Fastq (Fasta extension for quality values)
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Tag.File Format.tag.Fastq:
-    FASTQ file format for sequences.
-..include:seqan/file.h
-*/
-
-    struct TagFastq_;
-    //IOREV _doc_ this should ge somewhere else!
-    typedef Tag<TagFastq_> Fastq; //IOREV
-
-/**
-.Tag.File Format.tag.QSeq:
-	QSeq format, used for most of the Illumina read files.
-..include:seqan/file.h
-*/
-	struct QSeq_;
-	//IOREV _doc_ this whole part should go someplace different
-	typedef Tag<QSeq_> QSeq; //IOREV
-
-
-    template <typename TFormat, typename T = void>
-    struct FileFormatExtensions;
-    
-
-    template <typename T>
-    struct FileFormatExtensions<Fasta, T>
-    {
-        static char const * VALUE[6];
-    };
-
-    template <typename T>
-    char const * FileFormatExtensions<Fasta, T>::VALUE[6] = {
-        ".fa",      // default output extension
-        ".fasta",
-        ".faa",     // FASTA Amino Acid file
-        ".ffn",     // FASTA nucleotide coding regions file
-        ".fna",     // FASTA Nucleic Acid file
-        ".frn" };
-
-
-    template <typename T>
-    struct FileFormatExtensions<Fastq, T>
-    {
-        static char const * VALUE[2];
-    };
-
-    template <typename T>
-    char const * FileFormatExtensions<Fastq, T>::VALUE[2] = {
-        ".fq",      // default output extension
-        ".fastq" };
-
-
-    template <typename T>
-    struct FileFormatExtensions<QSeq, T>
-    {
-        static char const * VALUE[2];
-    };
-
-    template <typename T>
-    char const * FileFormatExtensions<QSeq, T>::VALUE[2] = {
-        ".txt",     // default output extension
-        ".seq" };
-
-
-    template <typename T>
-    struct FileFormatExtensions<Raw, T>
-    {
-        static char const * VALUE[1];	// default is one extension
-    };
-
-    template <typename T>
-    char const * FileFormatExtensions<Raw, T>::VALUE[1] = {
-        ".qseq" };  // default output extension
-
-/**
-.Shortcut.MultiFasta
-..summary:A sequence file mapped in memory as a StringSet of concatenated sequence file fragments.
-..cat:Input/Output
-..signature:MultiSeqFile
-..shortcutfor:Spec.ConcatDirect
-..shortcutfor:Spec.MMap String
-...signature:StringSet<String<char, MMap<> >, Owner<ConcatDirect<> > >
-..status:deprecated, will be removed in favour of @Shortcut.MultiSeqFile@
-*/
-
-/*!
- * @typedef MultiSeqFile
- * @headerfile <seqan/file.h>
- * @brief A sequence file mapped in memory as a StringSet of concatenated sequence file fragments.
- *
- * @signature typedef StringSet<String<char, MMap<> >, Owner<ConcatDirect<> > > MultiSeqFile;
- */
-
-/**
-.Shortcut.MultiSeqFile
-..summary:A sequence file mapped in memory as a StringSet of concatenated sequence file fragments.
-..cat:Input/Output
-..signature:MultiSeqFile
-..shortcutfor:Spec.ConcatDirect
-..shortcutfor:Spec.MMap String
-...signature:StringSet<String<char, MMap<> >, Owner<ConcatDirect<> > >
-*/
-
-	// define memory mapped stringset
-	typedef StringSet<String<char, MMap<> >, Owner<ConcatDirect<> > >	MultiFasta;	//deprecated (use MultiSeqFile instead) //IOREV _doc_ _delcandidate_
-	typedef StringSet<String<char, MMap<> >, Owner<ConcatDirect<> > >	MultiSeqFile; //IOREV _doc_
-
-
-	template <typename TValue>
-	inline bool
-	_isLineBreak(TValue value)
-	{
-//IOREV _nodoc_ will return true twice on Windows (ANSI EOL = "\r\n"); unclear whether \r on its own should be considered EOL
-		return (value == '\n' || value == '\r');
-	}
-
-	template <typename TIterator>
-	inline bool
-	_seekLineBreak(TIterator &it, TIterator itEnd)
-	{
-//IOREV _nodoc_
-		while (!_isLineBreak(*it))
-			if (++it == itEnd) return false;
-		return true;
-	}
-
-	template <typename TIterator>
-	inline bool
-	_seekNonLineBreak(TIterator &it, TIterator itEnd)
-	{
-//IOREV _bug_ _nodoc_ this returns true on [2] of "\n\n\n" (there is no loop)
-		if (*it == '\n')
-		{
-			if (++it == itEnd) return false;
-			if (*it == '\r')
-				if (++it == itEnd) return false;
-		} else
-			if (*it == '\r')
-			{
-				if (++it == itEnd) return false;
-				if (*it == '\n')
-					if (++it == itEnd) return false;
-			}
-		return true;
-	}
-
-        // Returns true iff value is a whitespace.
-	template <typename TValue>
-	inline bool
-	_isWhiteSpace(TValue value)
-	{
-//IOREV according to POSIX \v and \f are also whitespace, see also file_format.h:_streamSkipWhiteSpace(), misc_parsing.h: _parseSkipWhitespace() and misc_parsing.h:_parseReadWordUntilWhitespace()
-		return (value == ' ' || value == '\t' || value == '\r' || value == '\n');
-	}
-
-        // Increment iterator until end of sequence or *it is a whitespace.
-	template <typename TIterator>
-	inline bool
-	_seekWhiteSpace(TIterator &it, TIterator itEnd)
-	{
-//IOREV _nodoc_
-		while (!_isWhiteSpace(*it))
-			if (++it == itEnd) return false;
-		return true;
-	}
-
-	template <typename TIterator>
-	inline bool
-	_seekTab(TIterator& it, TIterator itEnd)
-	{
-//IOREV _nodoc_
-		for (; it != itEnd; ++it)
-			if (*it == '\t') return true;
-		return false;
-	}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - Fasta
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn guessFormat
- * @headerfile <seqan/file.h>
- * @brief Guesses a file format from the contents of a sequence file.
- *
- * @signature bool guessFormat(text, formatTag);
- *
- * @param[in] text      A string storing the contents of a sequence file.
- * @param[in] formatTag A file format tag.
- *
- * @return bool <tt>true</tt> if the format represented by <tt>formatTag</tt> was recognized in <tt>text</tt>.
- *
- * @see guessFormatFromFilename
- */
-
-/**
-.Function.guessFormat:
-..summary:Guesses a file format from the contents of a sequence file.
-..cat:Input/Output
-..signature:guessFormat(text, formatTag)
-..param.text:A string storing the contents of a sequence file.
-...see:Class.String
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..returns:$true$ if the format represented by $formatTag$ was recognized in $text$.
-..see:Function.guessFormatFromFilename
-..include:seqan/file.h
-*/
-
-	// test for Fasta format
-	template < typename TSeq >
-	inline bool
-	guessFormat(
-		TSeq const & seq,
-		Fasta)
-	{
-//IOREV _doc_ in competition with file_format_guess.h:guessFileFormat()
-		return seq[0] == '>';
-	}
-
-/*!
- * @fn guessFormatFromFilename
- * @headerfile <seqan/file.h>
- * @brief Guesses a file format from a sequence file name.
- *
- * @signature bool guessFormatFromFilename(fileName, formatTag);
- *
- * @param[in] fileName  A filename of a sequence file.
- * @param[in] formatTag A file format tag.
- *
- * @return bool <tt>true</tt> if the format represented by <tt>formatTag</tt> was recognized in <tt>fileName</tt>.
- */
-
-/**
-.Function.guessFormatFromFilename:
-..summary:Guesses a file format from a sequence file name.
-..cat:Input/Output
-..signature:guessFormatFromFilename(fileName, formatTag)
-..param.fileName:A filename of a sequence file.
-...see:Class.String
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..returns:$true$ if the format represented by $formatTag$ was recognized in $fileName$.
-..see:Function.guessFormatFromFilename
-..include:seqan/file.h
-*/
-
-	template <typename TFilename, typename TFormat_>
-	inline bool
-	guessFormatFromFilename(
-		TFilename const & fileName,
-		Tag<TFormat_> /*formatTag*/)
-	{
-		typedef typename Value<TFilename>::Type                                 TValue;
-		typedef ModifiedString<TFilename const, ModView<FunctorLowcase<TValue> > >	TLowcase;
-		typedef Tag<TFormat_>                                                   TFormat;
-		
-		TLowcase lowcaseFileName(fileName);
-		for (unsigned i = 0; i < sizeof(FileFormatExtensions<TFormat>::VALUE) / sizeof(char*); ++i)
-			if (endsWith(lowcaseFileName, FileFormatExtensions<TFormat>::VALUE[i]))
-				return true;
-
-		return false;
-	}
-
-    template <typename TStringSet, typename TFormat_>
-    inline void
-    _getFileFormatExtensions(TStringSet &stringSet, Tag<TFormat_> /*formatTag*/)
-    {
-		typedef Tag<TFormat_> TFormat;
-		for (unsigned i = 0; i < sizeof(FileFormatExtensions<TFormat>::VALUE) / sizeof(char*); ++i)
-			appendValue(stringSet, FileFormatExtensions<TFormat>::VALUE[i]);
-    }
-
-    template <typename TStringSet, typename TTag>
-    inline void
-    _getFileFormatExtensions(TStringSet &stringSet, TagList<TTag, void> const /*formatTag*/)
-    {
-        _getFileFormatExtensions(stringSet, TTag());
-    }
-
-    template <typename TStringSet, typename TTag, typename TSubList>
-    inline void
-    _getFileFormatExtensions(TStringSet &stringSet, TagList<TTag, TSubList> const /*formatTag*/)
-    {
-        _getFileFormatExtensions(stringSet, TTag());
-        _getFileFormatExtensions(stringSet, TSubList());
-    }
-
-    template <typename TStringSet, typename TTagList>
-    inline void
-    _getFileFormatExtensions(TStringSet &stringSet, TagSelector<TTagList> const /*formatTag*/)
-    {
-        _getFileFormatExtensions(stringSet, TTagList());
-    }
-
-/*!
- * @fn split
- * @headerfile <seqan/file.h>
- * @brief Divides the contents of a sequence file into sequence file fragments separated by a file format specific
- *        delimiter.
- *
- * @signature void split(stringSet, formatTag);
- *
- * @param[in,out] stringSet A @link ConcatDirectStringSet @endlink.  The <tt>concat</tt> member (concatenation string)
- *                          contains the contents of a sequence file.
- * @param[in]     formatTag A file format tag.
- *
- * @section Remarks
- *
- * The @link ConcatDirectStringSet::concat @endlink member should contain the contents of the sequence file by a prior
- * call of <tt>open</tt>.
- *
- * This function expects a @link ConcatDirectStringSet @endlink and divides the underlying concatenation string into
- * sequence fragments separated by a file format specific delimiter.
- *
- * After calling this function, the StringSet length is the number of sequence fragments and each fragment can be
- * retrieve by <tt>value</tt> or <tt>getValue</tt>.
- */
-
-/**
-.Function.split:
-..summary:Divides the contents of a sequence file into sequence file fragments separated by a file format specific delimiter.
-..cat:Input/Output
-..signature:split(stringSet, formatTag)
-..param.stringSet:A @Spec.ConcatDirect@ StringSet. The concat member (concatenation string) contains the contents of a sequence file.
-...type:Spec.ConcatDirect
-...type:Shortcut.MultiSeqFile
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..remarks:The @Memvar.ConcatDirect#concat@ member should contain the contents of the sequence file by a prior call of @Function.open@.
-..remarks:This function expects a @Spec.ConcatDirect@ StringSet and divides the underlying concatenation string into
-sequence fragments separated by a file format specific delimiter.
-After calling this function, the StringSet length is the number of sequence fragments and each fragment can be retrieved by @Function.value@ or @Function.getValue@.
-..see:Function.guessFormat
-..include:seqan/file.h
-*/
-
-    // split stringset into single Fasta sequences
-    template <typename TValue, typename TSpec, typename TStringSetSpec>
-    inline void split(StringSet<String<TValue, TSpec>, TStringSetSpec> &me, Fasta /* tag */)
-    {
-//IOREV _doc_
-        typedef String<TValue, TSpec>                               TString;
-        typedef typename Iterator<TString const, Standard>::Type	TIterator;
-
-        clear(me.limits);
-
-        TIterator itBeg = begin(me.concat, Standard());
-        TIterator itEnd = end(me.concat, Standard());
-        bool newLine = true;
-        for (TIterator it = itBeg; it != itEnd; ++it)
-        {
-            TValue c = *it;
-            if (newLine && c == '>')
-                appendValue(me.limits, it - itBeg, Generous());
-            newLine = _isLineBreak(c);
-        }
-        if (empty(me.limits))
-            appendValue(me.limits, 0);
-        appendValue(me.limits, itEnd - itBeg);
-    }
-
-/*!
- * @fn assignSeq
- * @headerfile <seqan/file.h>
- * @brief Extracts the sequence part of a sequence file fragment.
- *
- * @signature void assignSeq(sequence, seqFragment, formatTag);
- *
- * @param[out] sequence    The resulting sequence of the fragment.  Type: @link String @endlink.
- * @param[in]  seqFragment A sequence file fragment.  Type: @link String @endlink.
- * @param[in]  formatTag   A file format tag.  Type: @link AutoSeqFormat @endlink.
- *
- * @section Remarks
- *
- * After calling <tt>split</tt> on a @link ConcatDirectStringSet @endlink to dvide a file into fragments, this function
- * can be used to extract the sequence of every fragment in the @link StringSet @endlink.
- */
-
-/**
-.Function.assignSeq:
-..summary:Extracts the sequence part of a sequence file fragment.
-..cat:Input/Output
-..signature:assignSeq(sequence, seqFragment, formatTag)
-..param.sequence:The resulting sequence of the fragment.
-...type:Class.String
-..param.seqFragment:A sequence file fragment.
-...type:Class.String
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..remarks:After calling @Function.split@ on a @Spec.ConcatDirect@ StringSet to divide a file into fragments, 
-this function can be used to extract the sequence of every fragment in the StringSet.
-..see:Function.split
-..include:seqan/file.h
-*/
-
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignSeq(
-		TSeq & dst,
-		TFastaSeq const & fasta,
-		Fasta)
-	{
-//IOREV _doc_
-		typedef typename Iterator<TFastaSeq const, Standard>::Type	TIterator;
-		typedef typename Iterator<TSeq, Standard>::Type				TDstIterator;
-
-		TIterator it = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-
-		clear(dst);
-		
-		// skip Fasta id
-		if (it == itEnd) return;
-		if (*it == '>')
-		{
-			if (!_seekLineBreak(it, itEnd)) return;
-			if (!_seekNonLineBreak(it, itEnd)) return;
-		}
-
-		// copy sequence
-		resize(dst, itEnd - it);		
-		TDstIterator dit = begin(dst, Standard());
-		for (; it != itEnd; ++it)
-			if (!_isLineBreak(*it))
-			{
-				*dit = *it;
-				++dit;
-			}
-		resize(dst, dit - begin(dst, Standard()));
-	}
-
-/*!
- * @fn assignSeqId
- * @headerfile <seqan/file.h>
- * @brief Extracts the sequence id of a sequence file fragment.
- *
- * @signature void assignSeqId(id, seqFragment, fragmentTag);
- *
- * @param[out] id          The resulting sequence id of the fragment.  Type: @link CharString @endlink.
- * @param[in]  seqFragment A sequence file fragment.  Type: @link CharString @endlink.
- * @param[in]  fragmentTag A flie format.
- *
- * @section Remarks
- *
- * After calling <tt>split</tt> on a @link ConcatDirectStringSet @endlink to divide a file into fragments, this function
- * can be used to extrac the sequence id of every fragment in the @link StringSet @endlink.
- */
-
-/**
-.Function.assignSeqId:
-..summary:Extracts the sequence id of a sequence file fragment.
-..cat:Input/Output
-..signature:assignSeqId(id, seqFragment, formatTag)
-..param.id:The resulting sequence id of the fragment (e.g. Fasta Id).
-...type:Shortcut.CharString
-..param.seqFragment:A sequence file fragment.
-...type:Class.String
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..remarks:After calling @Function.split@ on a @Spec.ConcatDirect@ StringSet to divide a file into fragments, 
-this function can be used to extract the sequence id of every fragment in the StringSet.
-..see:Function.split
-..include:seqan/file.h
-*/
-
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignSeqId(
-		TSeq & dst,
-		TFastaSeq const & fasta,
-		Fasta)
-	{
-//IOREV _doc_
-		typedef typename Iterator<TFastaSeq const, Standard>::Type	TIterator;
-
-		TIterator itBeg = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-		TIterator it = itBeg;
-		
-		clear(dst);
-		if (it == itEnd) return;
-		if (*it == '>')
-		{
-			_seekLineBreak(it, itEnd);
-			assign(dst, infix(fasta, 1, it - itBeg));
-		}
-	}
-
-/*!
- * @fn assignCroppedSeqId
- * @headerfile <seqan/file>
- * @brief Extracts the sequence id up to the first whitespace of a sequence file fragment.
- *
- * @signature void assignCroppedSeqId(id, seqFragment, formatTag);
- *
- * @param[out] id          The resulting cropped sequence id of the fragment (e.g. Fasta ID).  The resulting id
- *                         contains no whitespaces.  Type: @link CharString @endlink.
- * @param[out] seqFragment A sequence file fragment.  Type: @link CharString @endlink.
- * @param[in]  formatTag   A file format tag.
- *
- * @section Remarks
- *
- * After calling <tt>split</tt> on a @link ConcatDirectStringSet @endlink to divide a file into fragments, this function
- * can e used to extract the sequence id up to the first whitespace of every fragment in the @link StringSet @endlink.
- */
-
-/**
-.Function.assignCroppedSeqId:
-..summary:Extracts the sequence id up to the first whitespace of a sequence file fragment.
-..cat:Input/Output
-..signature:assignCroppedSeqId(id, seqFragment, formatTag)
-..param.id:The resulting cropped sequence id of the fragment (e.g. Fasta Id).
-...note:The resulting id contains no whitespaces.
-...type:Shortcut.CharString
-..param.seqFragment:A sequence file fragment.
-...type:Class.String
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..remarks:After calling @Function.split@ on a @Spec.ConcatDirect@ StringSet to divide a file into fragments, 
-this function can be used to extract the sequence id up to the first whitespace of every fragment in the StringSet.
-..see:Function.split
-..include:seqan/file.h
-*/
-
-	// Assign sequence id up to first whitespace.
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignCroppedSeqId(
-		TSeq & dst,
-		TFastaSeq const & fasta,
-		Fasta)
-	{
-//IOREV _doc_
-		typedef typename Iterator<TFastaSeq const, Standard>::Type	TIterator;
-
-		TIterator itBeg = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-		TIterator it = itBeg;
-		
-		clear(dst);
-		if (it == itEnd) return;
-		if (*it == '>')
-		{
-			_seekWhiteSpace(it, itEnd);
-			assign(dst, infix(fasta, 1, it - itBeg));
-		}
-	}
-
-/*!
- * @fn assignQual
- * @headerfile <seqan/file.h>
- *
- * @brief Extracts the quality values o a sequence file fragment.
- *
- * @signature void assignQual(qualities, seqFragment, formatTag);
- *
- * @param[out] qualities   The result quality values encoded in ASCII.  The quality values are in encoded in ASCII
- *                         and must be manuall converted into zero-based values.  Type: @link CharString @endlink.
- * @param[in]  seqFragment A sequence file fragment.
- * @param[in]  formatTag   A file format tag.
- *
- * @section Remarks
- *
- * After calling <tt>split</tt> on a @link ConcatDirectStringSet @endlink to divide a file into fragments, this function
- * can be used to extrac the sequence quality values of every fragment in the StringSet.
- */
-
-/**
-.Function.assignQual:
-..summary:Extracts the quality values of a sequence file fragment.
-..cat:Input/Output
-..signature:assignQual(qualities, seqFragment, formatTag)
-..param.qualities:The resulting quality values encoded in ASCII.
-...remarks:The quality values are encoded in ASCII and must be manually converted into zero-based values.
-...type:Shortcut.CharString
-..param.seqFragment:A sequence file fragment.
-...type:Class.String
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..remarks:After calling @Function.split@ on a @Spec.ConcatDirect@ StringSet to divide a file into fragments, 
-this function can be used to extract the sequence quality values of every fragment in the StringSet.
-..see:Function.split
-..include:seqan/file.h
-*/
-
-  	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignQual(
-		TSeq & dst,
-		TFastaSeq const &,
-		Fasta)
-	{
-//IOREV _doc_
-		clear(dst);
-	}
-
-/*!
- * @fn assignQualId
- * @headerfile <seqan/file.h>
- * @brief Extracts the quality value id of a sequence file fragment.
- *
- * @signature void assignQualId(id, seqFragment, formatTag);
- *
- * @param[out] id          The resulting quality value id of a sequence (e.g. Fastq Quality ID).  Type: @link CharString
- *                         @endlink.
- * @param[in]  seqFragment A sequence file framant.  Type: @link String @endlink.
- * @param[in]  formatTag   A file format tag.
- *
- * @section Remarks
- *
- * After calling <tt>split</tt> on a @link ConcatDirectStringSet @endlink to divide a file into fragments, this function
- * can be used to extrac the sequence quality value id of every fragment in the StringSet.
- */
-
-/**
-.Function.assignQualId:
-..summary:Extracts the quality value id of a sequence file fragment.
-..cat:Input/Output
-..signature:assignQualId(id, seqFragment, formatTag)
-..param.id:The resulting quality value id of a sequence (e.g. Fastq Quality Id).
-...type:Shortcut.CharString
-..param.seqFragment:A sequence file fragment.
-...type:Class.String
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..remarks:After calling @Function.split@ on a @Spec.ConcatDirect@ StringSet to divide a file into fragments, 
-this function can be used to extract the quality value id of every fragment in the StringSet.
-..see:Function.split
-..include:seqan/file.h
-*/
-
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignQualId(
-		TSeq & dst,
-		TFastaSeq const &,
-		Fasta)
-	{
-//IOREV _doc_
-		clear(dst);
-	}
-
-
-	// test for Fastq format
-	template < typename TSeq >
-	inline bool
-	guessFormat(
-		TSeq const & seq,
-		Fastq)
-	{
-//IOREV _doc_
-		return seq[0] == '@';
-	}
-
-    // split stringset into single Fasta sequences
-    template <typename TValue, typename TSpec, typename TStringSetSpec>
-    inline void
-    split(StringSet<String<TValue, TSpec>, TStringSetSpec> & me, Fastq /* tag */)
-    {
-        //IOREV
-        typedef String<TValue, TSpec>                               TString;
-        typedef typename Iterator<TString const, Standard>::Type	TIterator;
-
-        clear(me.limits);
-
-        TIterator itBeg = begin(me.concat, Standard());
-        TIterator itEnd = end(me.concat, Standard());
-        bool newLine = true;
-        for (TIterator it = itBeg; it != itEnd; ++it)
-        {
-            if (newLine && *it == '@')
-                appendValue(me.limits, it - itBeg, Generous());
-            if (newLine && *it == '+')
-            {
-                // skip qualitity fasta id
-                if (!_seekLineBreak(it, itEnd)) break;
-                if (!_seekNonLineBreak(it, itEnd)) break;
-                // skip qualitity values
-                if (!_seekLineBreak(it, itEnd)) break;
-            }
-            newLine = _isLineBreak(*it);
-        }
-        if (empty(me.limits))
-            appendValue(me.limits, 0);
-        appendValue(me.limits, itEnd - itBeg);
-    }
-    
-
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignSeq(
-		TSeq & dst,
-		TFastaSeq const & fasta,
-		Fastq)
-	{
-//IOREV _doc_
-		typedef typename Iterator<TFastaSeq const, Standard>::Type	TIterator;
-		typedef typename Iterator<TSeq, Standard>::Type				TDstIterator;
-
-		TIterator it = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-
-		clear(dst);
-		
-		// skip Fasta id
-		if (it == itEnd) return;
-		if (*it == '@')
-		{
-			if (!_seekLineBreak(it, itEnd)) return;
-			if (!_seekNonLineBreak(it, itEnd)) return;
-		}
-
-		// copy sequence
-		resize(dst, itEnd - it);		
-		TDstIterator dit = begin(dst, Standard());
-		for (; it != itEnd; ++it) 
-		{
-			if (_isLineBreak(*it))
-			{
-				if (!_seekNonLineBreak(it, itEnd)) break;
-				if (*it == '+') break;
-			}
-			*dit = *it;
-			++dit;
-		}
-		resize(dst, dit - begin(dst, Standard()));
-	}
-
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignSeqId(
-		TSeq & dst,
-		TFastaSeq const & fasta,
-		Fastq)
-	{
-//IOREV _doc_
-		typedef typename Iterator<TFastaSeq const, Standard>::Type	TIterator;
-
-		TIterator itBeg = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-		TIterator it = itBeg;
-		
-		clear(dst);
-		if (it == itEnd) return;
-		if (*it == '@')
-		{
-			_seekLineBreak(it, itEnd);
-			assign(dst, infix(fasta, 1, it - itBeg));
-		}
-	}
-
-        // Assign sequence id up to first whitespace.
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignCroppedSeqId(
-		TSeq & dst,
-		TFastaSeq const & fasta,
-		Fastq)
-	{
-//IOREV _doc_ probably some more code sharing between these functions possible
-		typedef typename Iterator<TFastaSeq const, Standard>::Type	TIterator;
-
-		TIterator itBeg = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-		TIterator it = itBeg;
-		
-		clear(dst);
-		if (it == itEnd) return;
-		if (*it == '@')
-		{
-			_seekWhiteSpace(it, itEnd);
-			assign(dst, infix(fasta, 1, it - itBeg));
-		}
-	}
-
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignQual(
-		TSeq & dst,
-		TFastaSeq const & fasta,
-		Fastq)
-	{
-//IOREV _doc_
-		typedef typename Iterator<TFastaSeq const, Standard>::Type	TIterator;
-		typedef typename Iterator<TSeq, Standard>::Type				TDstIterator;
-
-		TIterator it = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-
-		clear(dst);
-		
-		if (it == itEnd) return;
-		if (*it == '@')
-		{
-			// seek quality id
-			do {
-				if (!_seekLineBreak(it, itEnd)) return;
-				if (!_seekNonLineBreak(it, itEnd)) return;
-			} while (*it != '+');
-
-			// skip quality id
-			if (!_seekLineBreak(it, itEnd)) return;
-			if (!_seekNonLineBreak(it, itEnd)) return;
-
-			// copy sequence
-			resize(dst, itEnd - it);		
-			TDstIterator dit = begin(dst, Standard());
-			for (; it != itEnd; ++it)
-				if (!_isLineBreak(*it))
-				{
-					*dit = *it;
-					++dit;
-				}
-			resize(dst, dit - begin(dst, Standard()));
-		}
-	}
-
-	template <typename TSeq, typename TFastaSeq>
-	inline void
-	assignQualId(
-		TSeq & dst,
-		TFastaSeq const & fasta,
-		Fastq)
-	{
-//IOREV _doc_
-		typedef typename Iterator<TFastaSeq const, Standard>::Type	TIterator;
-
-		TIterator itBeg = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-		TIterator it1 = itBeg;
-		
-		clear(dst);
-		if (it1 == itEnd) return;
-		if (*it1 == '@')
-		{
-			do {
-				if (!_seekLineBreak(it1, itEnd)) return;
-				if (!_seekNonLineBreak(it1, itEnd)) return;
-			} while (*it1 != '+');
-			TIterator it2 = it1;
-			_seekLineBreak(it2, itEnd);
-			assign(dst, infix(fasta, (it1 - itBeg) + 1, it2 - itBeg));
-		}
-	}
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - QSeq (used by Illumina for most of their read files)
-//////////////////////////////////////////////////////////////////////////////
-
-	// FIXME The following enum is more or less arbitrary since the information
-	// in a QSeq file may differ depending on where they come from. Not sure if
-	// this is something that needs to be fixed here, rather than in the Illu-
-	// mina pipeline itself.
-	//
-	// Also, this enum is quite convoluted but I don't feel like spilling a lot
-	// of common symbols (e.g. 'X', 'Y') into the SeqAn namespace.
-	struct QSeqEntry {
-//IOREV _bug_ has FIXME in code comments
-		enum {
-			MachineName,
-			Run,
-			Lane,
-			Tile,
-			X,
-			Y,
-			Index,
-			Read,
-			Sequence,
-			Quality,
-			Filter
-		};
-	};
-
-	template < typename TString >
-	inline bool _isQSeqFile(TString const& filename)
-	{
-//IOREV _doc_ has some comments in code
-        unsigned int const namelen = 19;
-        unsigned int const pathlen = length(filename);
-        if (pathlen < namelen) return false;
-		::std::string str;
-		assign(str, suffix(filename, pathlen - namelen));
-		::std::istringstream is(str);
-		unsigned int num;
-		// Format (as regex): /^s_\d_\d_\d{4}_qseq.txt$/
-		return is.get() == 's' && is.get() == '_' &&
-			isdigit(is.get()) && is.get() == '_' &&
-			isdigit(is.get()) && is.get() == '_' &&
-			is >> num &&
-			getline(is, str) && str == "_qseq.txt" && is.eof();
-	}
-
-//	// Needed?
-//	template < typename TString >
-//	inline TString _getFirstFile(
-//		char const* dirname,
-//		QSeq)
-//	{
-//		Directory dir(dirname);
-//		
-//		for ( ; dir; ++dir)
-//			if (_isQSeqFile(*dir))
-//				return *dir;
-//	}
-//
-//	template < typename TString >
-//	inline String< TString >
-//	_getAllFiles(
-//		char const* dirname,
-//		QSeq)
-//	{
-//		String< TString > ret;
-//		Directory dir(dirname);
-//
-//		for (; dir; ++dir)
-//			if (_isQSeqFile(*dir))
-//				appendValue(ret, *dir);
-//
-//		return ret;
-//	}
-
-	// test for QSeq format
-	template < typename TSeq >
-	inline bool
-	guessFormat(
-		TSeq const & seq,
-		QSeq)
-	{
-//IOREV _nodoc_ code comments suggest that it is guessing
-		typedef typename Iterator<TSeq const>::Type TIter;
-		TIter front = begin(seq);
-		TIter const back = end(seq);
-		if (!_seekTab(front, back)) return false;
-		::std::string token_base;
-		assign(token_base, seq);
-		::std::istringstream is(token_base);
-		::std::string mname;
-		unsigned int numval;
-		// Actual information encoded in qseq file may vary. Take a few guesses:
-		//     machine name, run number, lane number, tile number
-		is >> mname >> numval >> numval >> numval;
-		return is.good();
-	}
-	
-	template < typename TFilename >
-	inline bool
-	guessFormatFromFilename(
-		TFilename const & fname,
-		QSeq)
-	{
-//IOREV _nodoc_ need proper QSeq documentation
-		// QSeq files come in a variety of ways throughout the Gerald pipeline.
-		// In this simplest case, "sorted.txt" is a file in a fragment genome
-		// directory, each corresponding to 10MB worth of DNA.
-		static CharString const standalone_name = "sorted.txt";
-		typename Size<TFilename>::Type len = length(fname);
-        bool const bLen = len >= length(standalone_name);
-        bool const bSuff = suffix(fname, len - length(standalone_name)) == standalone_name;
-		return (bLen && bSuff) || _isQSeqFile(fname);
-	}
-
-	// split stringset into single QSeq sequences
-	template <typename TValue, typename TSpec, typename TStringSetSpec>
-	inline void
-	split(StringSet<String<TValue, TSpec>, TStringSetSpec> & me, QSeq const & /* tag */)
-	{
-//IOREV
-		typedef String<TValue, TSpec>                               TString;
-		typedef typename Iterator<TString const, Standard>::Type	TIterator;
-
-		clear(me.limits);
-
-		TIterator const front = begin(me.concat, Standard());
-		TIterator const back = end(me.concat, Standard());
-
-		appendValue(me.limits, 0, Generous());
-		for (TIterator i = front; i != back; ++i)
-			if (_isLineBreak(*i))
-				appendValue(me.limits, i - front, Generous());
-
-		if (!_isLineBreak(*(back - 1))) // Ignore final line break.
-			appendValue(me.limits, back - front);
-	}
-
-	template <typename TSequence, typename TSource>
-	void assignQSeqEntry(
-		TSequence& destination,
-		TSource const& source,
-		unsigned int entry
-	) {
-//IOREV _nodoc_
-		typedef typename Iterator<TSource const>::Type TIterator;
-
-		TIterator const front = begin(source, Standard());
-		TIterator const back = end(source, Standard());
-
-		TIterator infixStart = front;
-
-		for (unsigned int i = QSeqEntry::MachineName; i < entry; ++i) {
-			_seekTab(infixStart, back);
-			++infixStart;
-		}
-
-		SEQAN_ASSERT(infixStart != back);
-
-		TIterator infixEnd = infixStart + 1;
-		_seekTab(infixEnd, back);
-
-		assign(destination, infix(source, infixStart - front, infixEnd - front));
-	}
-
-	template <typename TSeq, typename TQSeqSeq>
-	inline void
-	assignSeq(
-		TSeq & dst,
-		TQSeqSeq const & fasta,
-		QSeq)
-	{
-//IOREV _nodoc_ why fasta input?
-		assignQSeqEntry(dst, fasta, QSeqEntry::Sequence);
-	}
-
-	template <typename TSeq, typename TQSeqSeq>
-	inline void
-	assignSeqId(
-		TSeq & dst,
-		TQSeqSeq const & fasta,
-		QSeq)
-	{
-//IOREV _nodoc_ why fasta input?
-		// For now: just return the whole line.
-		typename Position<TQSeqSeq const>::Type front = 0;
-		while (_isLineBreak(fasta[front]))
-			++front;
-		assign(dst, infix(fasta, front, length(fasta)));
-	}
-
-        // Assign sequence id up to first whitespace.
-	template <typename TSeq, typename TQSeqSeq>
-	inline void
-	assignCroppedSeqId(
-		TSeq & dst,
-		TQSeqSeq const & fasta,
-		QSeq)
-	{
-//IOREV _nodoc_ why fasta input?
-		// For now: just return the whole line.
-		typename Position<TQSeqSeq const>::Type front = 0;
-		while (_isWhiteSpace(fasta[front]))
-			++front;
-		assign(dst, infix(fasta, front, length(fasta)));
-	}
-
-	template <typename TSeq, typename TQSeqSeq>
-	inline void
-	assignQual(
-		TSeq & dst,
-		TQSeqSeq const & fasta,
-		QSeq)
-	{
-//IOREV _nodoc_ why fasta input
-		assignQSeqEntry(dst, fasta, QSeqEntry::Quality);
-	}
-
-	template <typename TSeq, typename TQSeqSeq>
-	inline void
-	assignQualId(
-		TSeq & dst,
-		TQSeqSeq const & fasta,
-		QSeq)
-	{
-//IOREV _nodoc_ why fasta input
-		assignSeqId(dst, fasta, QSeq());
-	}
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - Raw (multiple sequences, separated by line breaks)
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Tag.File Format.tag.Raw:
-	Raw file format for sequences.
-..include:seqan/file.h
-*/
-struct TagRaw_;
-//IOREV _doc_ whats this doing here?
-typedef Tag<TagRaw_> Raw; //IOREV
-
-	// test for Fastq format
-	template < typename TSeq >
-	inline bool
-	guessFormat(
-		TSeq const &,
-		Raw)
-	{
-//IOREV _doc_
-		return true;
-	}
-	
-    // split stringset into single Fasta sequences
-    template <typename TValue, typename TSpec, typename TStringSetSpec>
-    inline void split(StringSet<String<TValue, TSpec>, TStringSetSpec> & me, Raw /* tag */)
-    {
-//IOREV _doc_
-        typedef String<TValue, TSpec>                               TString;
-        typedef typename Iterator<TString const, Standard>::Type	TIterator;
-
-        clear(me.limits);
-
-        TIterator itBeg = begin(me.concat, Standard());
-        TIterator itEnd = end(me.concat, Standard());
-        bool newLine = true;
-        for (TIterator it = itBeg; it != itEnd; ++it)
-        {
-            if (newLine)
-                appendValue(me.limits, it - itBeg, Generous());
-            newLine = _isLineBreak(*it);
-        }
-        appendValue(me.limits, itEnd - itBeg);
-    }
-
-	template <typename TSeq, typename TRawSeq>
-	inline void
-	assignSeq(
-		TSeq & dst,
-		TRawSeq const & fasta,
-		Raw)
-	{
-//IOREV _doc_
-		typedef typename Iterator<TRawSeq const, Standard>::Type	TIterator;
-		typedef typename Iterator<TSeq, Standard>::Type				TDstIterator;
-
-		TIterator it = begin(fasta, Standard());
-		TIterator itEnd = end(fasta, Standard());
-
-		clear(dst);
-		if (it == itEnd) return;
-
-		// copy sequence
-		resize(dst, itEnd - it);		
-		TDstIterator dit = begin(dst, Standard());
-		for (; it != itEnd; ++it) 
-		{
-			if (_isLineBreak(*it)) continue;
-			*dit = *it;
-			++dit;
-		}
-		resize(dst, dit - begin(dst, Standard()));
-	}
-	
-  	template <typename TSeq, typename TRawSeq>
-	inline void
-	assignSeqId(
-		TSeq & dst,
-		TRawSeq const &,
-		Raw)
-	{
-//IOREV _doc_
-		clear(dst);
-	}
-	
-  	template <typename TSeq, typename TRawSeq>
-	inline void
-	assignCroppedSeqId(
-		TSeq & dst,
-		TRawSeq const &,
-		Raw)
-	{
-//IOREV _doc_
-		clear(dst);
-	}
-	
-  	template <typename TSeq, typename TRawSeq>
-	inline void
-	assignQual(
-		TSeq & dst,
-		TRawSeq const &,
-		Raw)
-	{
-//IOREV _doc_
-		clear(dst);
-	}
-	
-  	template <typename TSeq, typename TRawSeq>
-	inline void
-	assignQualId(
-		TSeq & dst,
-		TRawSeq const &,
-		Raw)
-	{
-//IOREV _doc_
-		clear(dst);
-	}
-	
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - Auto-Format
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @class AutoSeqFormat
- * @extends TagSelector
- * @headerfile <seqan/file.h>
- * @brief Auto-detects and stores a file format.
- *
- * @signature typedef TagList<Fastq, TagList<Fasta, TagList<Raw> > > SeqFormats;
- * @signature typedef TagSelector<SeqFormat> AutoSeqFormat;
- */
-
-/**
-.Class.AutoSeqFormat
-..summary:Auto-detects and stores a file format.
-..cat:Input/Output
-..general:Class.TagSelector
-..signature:AutoSeqFormat
-..remarks:Currently, it is defined as $TagSelector<SeqFormats>$, with:
-...code:
-	typedef
-		TagList<Fastq,
-		TagList<Fasta,
-		TagList<QSeq,
-		TagList<Raw> > > > 						SeqFormats;
-..include:seqan/file.h
-*/
-
-	typedef
-		TagList<Fastq,
-		TagList<Fasta,
-//		TagList<QSeq,   // doesn't work as it uses STL strings and parsers
-		TagList<Raw> /* > */ > > SeqFormats;  // if TagSelector is set to -1, the file format is auto-detected
-
-	typedef TagSelector<SeqFormats> AutoSeqFormat;
-
-//____________________________________________________________________________
-// guess file format
-
-	template <typename TFileSeq>
-	inline bool
-	guessFormat(TFileSeq const &, TagSelector<> &)
-	{
-        // we get here if the file format could not be determined
-		return false;
-	}
-	
-	template <typename TFileSeq, typename TTagList>
-	inline bool
-	guessFormat(TFileSeq const &seq, TagSelector<TTagList> &format)
-	{
-//IOREV _doc_ as mentionened this recursive method is not intuitive, also inlining doesn't really make sense for recursive functions, does it?
-//(weese:) ANSWER: This is not a recursive function as TTagList is different for each called instance.
-//                 It will be expanded (inlined) completely.
-
-        typedef typename TTagList::Type TFormatTag;
-
-        if (value(format) == -1 || value(format) == LENGTH<TTagList>::VALUE - 1)
-        {
-            // if tagId is set to -1 (auto-detect) or the current format (TFormatTag) then test for TFormatTag format
-            if (guessFormat(seq, TFormatTag()))
-            {
-                value(format) = LENGTH<TTagList>::VALUE - 1;
-                return true;
-            }
-        }
-		return guessFormat(seq, static_cast<typename TagSelector<TTagList>::Base &>(format));
-	}
-	
-//____________________________________________________________________________
-// guess file format from filename
-
-	template <typename TFilename>
-	inline bool
-	guessFormatFromFilename(TFilename const &, TagSelector<>)
-	{
-        // we get here if the file format could not be determined
-		return false;
-	}
-	
-	template <typename TFilename, typename TTagList>
-	inline bool
-	guessFormatFromFilename(TFilename const &fname, TagSelector<TTagList> &format)
-	{
-        typedef typename TTagList::Type TFormatTag;
-
-        if (value(format) == -1 || value(format) == LENGTH<TTagList>::VALUE - 1)
-        {
-            // if tagId is set to -1 (auto-detect) or the current format (TFormatTag) then test for TFormatTag format
-            if (guessFormatFromFilename(fname, TFormatTag()))
-            {
-                value(format) = LENGTH<TTagList>::VALUE - 1;
-                return true;
-            }
-        }
-		return guessFormatFromFilename(fname, static_cast<typename TagSelector<TTagList>::Base &>(format));
-	}
-
-//____________________________________________________________________________
-// split stringset into single sequences
-
-    template <typename TValue, typename TSpec, typename TStringSetSpec>
-    inline void split(StringSet<String<TValue, TSpec>, TStringSetSpec> &,
-                      TagSelector<void> const & /* tag */)
-    {
-//IOREV _doc_
-    }
-
-    template <typename TValue, typename TSpec, typename TStringSetSpec, typename TTagList>
-    inline void split(StringSet<String<TValue, TSpec>, TStringSetSpec> & me,
-                      TagSelector<TTagList> const & format)
-    {
-//IOREV _doc_
-        typedef typename TTagList::Type TFormatTag;
-
-		if (value(format) == LENGTH<TTagList>::VALUE - 1)
-            split(me, TFormatTag());
-        else
-            split(me, static_cast<typename TagSelector<TTagList>::Base const &>(format));
-    }
-    
-
-//____________________________________________________________________________
-// assignSeq
-
-	template <typename TSeq, typename TFileSeq>
-	inline void
-	assignSeq(
-		TSeq &,
-		TFileSeq const &,
-		TagSelector<> const &)
-	{
-//IOREV _doc_
-	}
-
-	template <typename TSeq, typename TFileSeq, typename TTagList>
-	inline void
-	assignSeq(
-		TSeq & dst,
-		TFileSeq const & seq,
-		TagSelector<TTagList> const &format)
-	{
-//IOREV _doc_
-        typedef typename TTagList::Type TFormatTag;
-
-		if (value(format) == LENGTH<TTagList>::VALUE - 1)
-			assignSeq(dst, seq, TFormatTag());
-		else
-			assignSeq(dst, seq, static_cast<typename TagSelector<TTagList>::Base const &>(format));
-	}
-
-//____________________________________________________________________________
-// assignSeqId
-
-	template <typename TSeqId, typename TFileSeq>
-	inline void
-	assignSeqId(
-		TSeqId &,
-		TFileSeq const &,
-		TagSelector<> const &)
-	{
-//IOREV _doc_
-	}
-
-	template <typename TSeqId, typename TFileSeq, typename TTagList>
-	inline void
-	assignSeqId(
-		TSeqId & dst,
-		TFileSeq const & seq,
-		TagSelector<TTagList> const &format)
-	{
-//IOREV _doc_
-        typedef typename TTagList::Type TFormatTag;
-
-		if (value(format) == LENGTH<TTagList>::VALUE - 1)
-			assignSeqId(dst, seq, TFormatTag());
-		else
-			assignSeqId(dst, seq, static_cast<typename TagSelector<TTagList>::Base const &>(format));
-	}
-
-//____________________________________________________________________________
-// assignCroppedSeqId
-
-	template <typename TSeqId, typename TFileSeq>
-	inline void
-	assignCroppedSeqId(
-		TSeqId &,
-		TFileSeq const &,
-		TagSelector<> const &)
-	{
-//IOREV _doc_
-	}
-
-	template <typename TSeqId, typename TFileSeq, typename TTagList>
-	inline void
-	assignCroppedSeqId(
-		TSeqId & dst,
-		TFileSeq const & seq,
-		TagSelector<TTagList> const &format)
-	{
-//IOREV _doc_
-        typedef typename TTagList::Type TFormatTag;
-
-		if (value(format) == LENGTH<TTagList>::VALUE - 1)
-			assignCroppedSeqId(dst, seq, TFormatTag());
-		else
-			assignCroppedSeqId(dst, seq, static_cast<typename TagSelector<TTagList>::Base const &>(format));
-	}
-
-//____________________________________________________________________________
-// assignQual
-
-	template <typename TSeq, typename TFileSeq>
-	inline void
-	assignQual(
-		TSeq &,
-		TFileSeq const &,
-		TagSelector<> const &)
-	{
-//IOREV _doc_
-	}
-	
-	template <typename TSeq, typename TFileSeq, typename TTagList>
-	inline void
-	assignQual(
-		TSeq & dst,
-		TFileSeq const & seq,
-		TagSelector<TTagList> const &format)
-	{
-//IOREV _doc_
-        typedef typename TTagList::Type TFormatTag;
-
-		if (value(format) == LENGTH<TTagList>::VALUE - 1)
-			assignQual(dst, seq, TFormatTag());
-		else
-			assignQual(dst, seq, static_cast<typename TagSelector<TTagList>::Base const &>(format));
-	}
-
-//____________________________________________________________________________
-// assignQualId
-
-	template <typename TSeq, typename TFileSeq>
-	inline void
-	assignQualId(
-		TSeq &,
-		TFileSeq const &,
-		TagSelector<> const &)
-	{
-//IOREV _doc_
-	}
-	
-	template <typename TSeq, typename TFileSeq, typename TTagList>
-	inline void
-	assignQualId(
-		TSeq & dst,
-		TFileSeq const & seq,
-		TagSelector<TTagList> const &format)
-	{
-//IOREV _doc_
-        typedef typename TTagList::Type TFormatTag;
-
-		if (value(format) == LENGTH<TTagList>::VALUE - 1)
-			assignQualId(dst, seq, TFormatTag());
-		else
-			assignQualId(dst, seq, static_cast<typename TagSelector<TTagList>::Base const &>(format));
-	}
-
-//////////////////////////////////////////////////////////////////////////////
-// Directory import
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn appendSeqs
- * @headerfile <seqan/file.h>
- * @brief Appends all sequences stored in files of a dirctory to a StringSet.
- *
- * @signature void appendSeqs(seqSet, dirName, formatTag);
- *
- * @param[out] seqSet    A @link StringSet @endlink of sequences to append to.
- * @param[in]  dirName   A path to a dirctory or single file.
- * @param[in]  formatTag A file format tag.
- *
- * @section Remarks
- *
- * This function scans a directory and searches for filenames corresponding to the sequence format stored in
- * <tt>formatTag</tt>, opens them and appends their contained sequences to the <tt>seqSet</tt>.  If <tt>formatTag</tt>
- * is a @link AutoSeqFormat @endlink object, the file form is set to the first known sequence format guessed from a file
- * name.
- *
- * @see assignSeq
- */
-
-/**
-.Function.appendSeqs:
-..summary:Appends all sequences stored in files of directory to a StringSet.
-..cat:Input/Output
-..signature:appendSeqs(seqSet, dirName, formatTag)
-..param.seqSet:A @Class.StringSet@ of sequences to append to.
-...type:Class.StringSet
-..param.dirName:A path to a directory or single file.
-...type:Class.String
-..param.formatTag:A file format tag.
-...type:Tag.File Format
-...type:Class.AutoSeqFormat
-..remarks:This function scans a directory and searches for filenames corresponding to the sequence format store in $formatTag$, 
-opens them and append their contained sequences to the $seqSet$.
-If $formatTag$ is a @Class.AutoSeqFormat@ object, the file format is set to the first known sequence format guessed from a file name.
-..see:Function.assignSeq
-..include:seqan/file.h
-*/
-
-	template <typename TSeqSet, typename TFilename, typename TSeqFormat>
-	inline void
-	appendSeqs(
-		TSeqSet &seqSet,
-		TFilename &dirname,
-		TSeqFormat format)
-	{
-//IOREV _doc_
-		typedef typename Value<TSeqSet>::Type TSeq;
-		
-		Directory		dir(dirname);
-		TSeq			seq;
-		MultiSeqFile	multiSeqFile;
-		
-		if (!atEnd(dir))
-		{
-			// dirname is path of a directory
-			CharString fname = dirname;
-#ifdef PLATFORM_WINDOWS
-			appendValue(fname, '\\');
-#else
-			appendValue(fname, '/');
-#endif
-			size_t len = length(fname);
-
-			for (; !atEnd(dir); goNext(dir))
-			{
-                replace(fname, length(fname) - len, length(fname), value(dir));
-				if (guessFormatFromFilename(fname, format))
-				{
-					if (!open(multiSeqFile.concat, toCString(fname), OPEN_RDONLY)) continue;
-
-					split(multiSeqFile, format);
-					unsigned seqCount = length(multiSeqFile);
-					
-					reserve(seqSet, length(seqSet) + seqCount, Generous());					
-					for(unsigned i = 0; i < seqCount; ++i)
-					{
-						assignSeq(seq, multiSeqFile[i], format);
-						appendValue(seqSet, seq, Generous());
-					}
-					close(multiSeqFile.concat);
-				}
-			}
-		} 
-		else
-		{
-			// dirname is path of a file
-			if (guessFormatFromFilename(dirname, format))
-			{
-				if (!open(multiSeqFile.concat, toCString(dirname), OPEN_RDONLY)) return;
-
-				split(multiSeqFile, format);
-				unsigned seqCount = length(multiSeqFile);
-				
-				reserve(seqSet, length(seqSet) + seqCount, Generous());					
-				for(unsigned i = 0; i < seqCount; ++i)
-				{
-					assignSeq(seq, multiSeqFile[i], format);
-					appendValue(seqSet, seq, Generous());
-				}
-				close(multiSeqFile.concat);
-			}
-		}
-	}
-	
-}
-
-#endif
diff --git a/seqan/file/file_format_raw.h b/seqan/file/file_format_raw.h
deleted file mode 100644
index 3710ce1..0000000
--- a/seqan/file/file_format_raw.h
+++ /dev/null
@@ -1,351 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_FILE_RAW_H
-#define SEQAN_HEADER_FILE_RAW_H
-
-
-/* IOREV
- * _tested_
- * _doc_
- *
- *
- * has some documentation, but could be better
- * apperently tested by tests/file/test_file.h, used in some other places
- *
- * unclear why static members are used and functions not overloaded directly
- *
- * raw is defined as default behaviour for read and write, is this desired
- * or should read and write maybe auto-detect fileformat?
- * 
- */
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// File Formats - Raw
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Tag.File Format.tag.Raw:
-	The file contains data in a raw format.
-..remark:It is supposed that the file contains one single piece of data, 
-that is the file cannot store multiple records.
-..include:seqan/file.h
-*/
-
-struct TagRaw_;
-//IOREV
-typedef Tag<TagRaw_> Raw; //IOREV
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// read
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TData, typename TTag>
-struct ReadRaw_;
-//IOREV
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TData>
-struct ReadRaw_<TFile, TData, True>
-{
-//IOREV
-	template <typename TSize>
-	inline static void
-	read_(TFile & file,
-		TData & data,
-		TSize _limit)
-	{
-SEQAN_CHECKPOINT
-		SEQAN_ASSERT_NOT(_streamEOF(file));
-
-		typename Size<TData>::Type limit = _limit;
-
-		//determine length
-		typename Position<TFile>::Type begin_pos = _streamTellG(file);
-		typename Size<TData>::Type count;
-		typename Position<TData>::Type pos;
-
-		for (count = 0; !_streamEOF(file) && count != limit; ++count)
-			_streamGet(file);
-
-		//reserve space
-		resize(data, count);
-
-		if (!count) return;
-
-		if (length(data) < count)
-			count = length(data);
-
-		//read sequence
-		_streamSeekG(file, begin_pos);
-
-		for (pos = 0; pos < count; ++pos)
-			assignValue(data, pos, _streamGet(file));
-	}
-
-//____________________________________________________________________________
-
-	inline static void
-	read_(TFile & file,	
-		TData & data)
-	{
-SEQAN_CHECKPOINT
-		typedef typename Size<TData>::Type TSize;
-		read(file, data, maxValue<TSize>());
-	}
-
-};
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TData>
-struct ReadRaw_<TFile, TData, False>
-{
-//IOREV _notinlined_
-	static void
-	read_(TFile & file,
-		TData & data)
-	{
-SEQAN_CHECKPOINT
-
-		clear(data);
-		if (!_streamEOF(file))
-		{
-SEQAN_CHECKPOINT
-			ChunkCollector_<TData> chunk_collector(data);
-			assign(chunk_collector, file);
-			append(data, chunk_collector);
-		}
-	}
-
-//____________________________________________________________________________
-
-	template <typename TSize>
-	static void
-	read_(TFile & file,
-		TData & data,
-		TSize limit)
-	{
-SEQAN_CHECKPOINT
-
-		clear(data);
-		if (!_streamEOF(file))
-		{
-SEQAN_CHECKPOINT
-			ChunkCollector_<TData> chunk_collector(data);
-			assign(chunk_collector, file, limit);
-			append(data, chunk_collector, limit);
-		}
-	}
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-template <typename TFile, typename TData>
-void
-read(TFile & file,
-	 TData & data,
-	 Raw)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	ReadRaw_<TFile, TData, typename IsTellAndSeekStream_<TFile>::Type>::read_(file, data);
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TData, typename TSize>
-void
-read(TFile & file,
-	 TData & data,
-	 TSize limit,
-	 Raw)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	ReadRaw_<TFile, TData, typename IsTellAndSeekStream_<TFile>::Type>::read_(file, data, limit);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// readID
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TString>
-void
-readID(TFile & /*file*/,
-	   TString & id,
-	   Raw)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	clear(id);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// readMeta
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TMeta>
-void
-readMeta(TFile & /*file*/,
-		 TMeta & meta,
-		 Raw)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	clear(meta);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// goNext
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile>
-void
-goNext(TFile & file,
-	   Raw)
-{
-//IOREV  _notinlined_ _nodoc_ needs some documented defined behaviour
-SEQAN_CHECKPOINT
-  (void) file;  // When compiled without assertions.
-	SEQAN_ASSERT(!_streamEOF(file));
-
-//??? TODO: set file to eof
-}
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// write
-//////////////////////////////////////////////////////////////////////////////
-
-
-template <typename TFile, typename TData>
-void
-write(TFile & file,
-	  TData const & data,
-	  Raw)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	_streamWrite(file, data);
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TData, typename TString>
-void
-write(TFile & file,
-	  TData const & data,
-	  TString const &,
-	  Raw)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	_streamWrite(file, data);
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TString, typename TData, typename TMeta>
-void
-write(TFile & file,
-	  TData const & data,
-	  TString const &,
-	  TMeta const &,
-	  Raw)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	_streamWrite(file, data);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// default functions
-//////////////////////////////////////////////////////////////////////////////
-
-
-template <typename TFile, typename TData>
-void
-read(TFile & file,
-	 TData & data)
-{
-//IOREV _notinlined_
-	read(file, data, Raw());
-}
-
-template <typename TFile, typename TData, typename TSize>
-void
-read(TFile & file,
-	 TData & data,
-	 TSize limit)
-{
-//IOREV  _notinlined_
-SEQAN_CHECKPOINT
-	read(file, data, limit, Raw());
-}
-
-//____________________________________________________________________________
-
-template <typename TFile, typename TData>
-void
-write(TFile & file,
-	  TData & data)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	write(file, data, "", Raw());
-}
-template <typename TFile, typename TData>
-void
-write(TFile & file,
-	  TData const & data)
-{
-//IOREV _notinlined_
-SEQAN_CHECKPOINT
-	write(file, data, "", Raw());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-} //namespace SEQAN_NAMESPACE_MAIN
-
-//////////////////////////////////////////////////////////////////////////////
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/file_forwards.h b/seqan/file/file_forwards.h
index 488fc05..5f6fb6f 100644
--- a/seqan/file/file_forwards.h
+++ b/seqan/file/file_forwards.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,14 +32,14 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_FILE_FORWARDS_H 
-#define SEQAN_HEADER_FILE_FORWARDS_H 
+#ifndef SEQAN_HEADER_FILE_FORWARDS_H
+#define SEQAN_HEADER_FILE_FORWARDS_H
 
 //////////////////////////////////////////////////////////////////////////////
 
-namespace SEQAN_NAMESPACE_MAIN 
+namespace SEQAN_NAMESPACE_MAIN
 {
-    
+
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSource, typename TSpec>
diff --git a/seqan/file/file_interface.h b/seqan/file/file_interface.h
index 2192bc6..e5e1ae9 100644
--- a/seqan/file/file_interface.h
+++ b/seqan/file/file_interface.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,13 +34,14 @@
 // Defines basic tags and flags for file access.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_FILE_INTERFACE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_FILE_INTERFACE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_FILE_INTERFACE_H_
+#define SEQAN_INCLUDE_SEQAN_FILE_INTERFACE_H_
 
 namespace seqan {
 
 /*!
  * @class SyncFile
+ * @extends File
  * @headerfile <seqan/file.h>
  * @brief File structure supporting synchronous input/output access.
  *
@@ -49,28 +50,16 @@ namespace seqan {
  *
  * @tparam TSpec Further specializing type.  Default: <tt>void</tt>.
  *
- * @section Remarks
- *
  * This class supports pseudo-asynchronous access methods, i.e. the method to initiate an I/O request blocks until the
  * request completion.
  */
 
-/**
-.Spec.Sync:
-..cat:Files
-..general:Class.File
-..summary:File structure supporting synchronous input/output access.
-..signature:File<Sync<> >
-..remarks:This class suports pseudo-asynchronous access methods, i.e. the methods to initiate a I/O request return after request completion.
-..include:seqan/file.h
-*/
-
-	template <typename TSpec = void>
-    struct Sync;
-//IOREV
+template <typename TSpec = void>
+struct Sync;
 
 /*!
  * @class AsyncFile
+ * @extends File
  * @headerfile <seqan/file.h>
  * @brief File structure supporting asynchronous input/output access.
  *
@@ -80,18 +69,8 @@ namespace seqan {
  * @tparam TSpec Further specializing type.  Default: <tt>void</tt>.
  */
 
-/**
-.Spec.Async:
-..cat:Files
-..general:Class.File
-..summary:File structure supporting synchronous and asynchronous input/output access.
-..signature:File<Async<> >
-..include:seqan/file.h
-*/
-
-	template <typename TSpec = void>
-    struct Async;
-//IOREV
+template <typename TSpec = void>
+struct Async;
 
 /*!
  * @class File
@@ -99,134 +78,162 @@ namespace seqan {
  * @brief Represents a file.
  *
  * @signature template <[typename TSpec]>
- *            class File;
+ *            class File<TSpec>;
  *
  * @tparam TSpec Specializing type.  Default: <tt>Async&lt;&gt;</tt>.
  */
 
-/**
-.Class.File:
-..cat:Input/Output
-..summary:Represents a file.
-..signature:File<TSpec>
-..param.TSpec:The specializing type.
-...default:$Async<>$, see @Spec.Async@.
-..include:seqan/file.h
-*/
-
-	template <typename TSpec = Async<> >
-    class File;
-//IOREV
+template <typename TSpec = Async<> >
+class File;
 
 /*!
  * @enum FileOpenMode
  * @headerfile <seqan/file.h>
  * @brief Flags to select th eopen mode of a @link File @endlink or external string.
  *
- * @section Remarks
- *
- * These flags can be comined via the <tt>|</tt> operator (bitwise OR).  The defualt open mode is <tt>OPEN_RDWR |
+ * These flags can be combined via the <tt>|</tt> operator (bitwise OR).  The defualt open mode is <tt>OPEN_RDWR |
  * OPEN_CREATE | OPEN_APPEND</tt>.
  *
  * If you omit the <tt>OPEN_APPEND</tt> flag in write mode, the file will be truncated to size 0 when opened.
  *
- * @var FileOpenMode OPEN_RDONLY
+ * @section Examples
+ *
+ * Code example to test for read-only mode:
+ *
+ * @code{.cpp}
+ * if (openMode & OPEN_MASK == OPEN_READ)
+ *     // do something if opened in read-only mode
+ * @endcode
+ *
+ * @val FileOpenMode OPEN_RDONLY
  * @brief Open in read-only mode.
  *
- * @var FileOpenMode OPEN_WRONLY
+ * @val FileOpenMode OPEN_WRONLY
  * @brief Open in write-only mode.
  *
- * @var FileOpenMode OPEN_RDWR
+ * @val FileOpenMode OPEN_RDWR
  * @brief Open for reading and writing.
  *
- * @var FileOpenMode OPEN_CREATE
+ * @val FileOpenMode OPEN_CREATE
  * @brief Create the file if it does not yet exists.
  *
- * @var FileOpenMode OPEN_APPEND
+ * @val FileOpenMode OPEN_APPEND
  * @brief Keep the existing data.  If this flag is not given then the file is cleared in write mode.
  *
- * @var FileOpenMode OPEN_QUIET
+ * @val FileOpenMode OPEN_QUIET
  * @brief Don't print any warning message if the file could not be opened.
  *
- * @var FileOpenMode OPEN_MASK
+ * @val FileOpenMode OPEN_MASK
  * @brief (Internal) Bitmask to extract the read/write open mode.
  *
- * @section Examples
- *
- * Code example to test for read-only mode:
- *
- * @code{.cpp}
- * if (openMode & OPEN_MASK == OPEN_READ)
- *     // do something if opened in read-only mode
- * @endlink
- *
- * @var FileOpenMode OPEN_ASYNC
+ * @val FileOpenMode OPEN_ASYNC
  * @brief (Internal) Open the file for asynchronous file access.  For asynchronous file access, use the @link AsyncFile
  *                   @endlink.
  *
- * @var FileOpenMode OPEN_TEMPORARY
+ * @val FileOpenMode OPEN_TEMPORARY
  * @brief (Internal) Open automatically delete the file after close.  Use the <tt>openTemp</tt> methods to open
  *        temporary files.
  */
 
-/**
-.Enum.FileOpenMode
-..cat:Input/Output
-..summary:Flags to select the open mode of a @Class.File@ or external string.
-..value.OPEN_RDONLY:Open for only reading.
-..value.OPEN_WRONLY:Open for only writing.
-..value.OPEN_RDWR:Open for reading and writing.
-..value.OPEN_CREATE:Create a file if it not yet exists.
-..value.OPEN_APPEND:Keep the existing data. If this flag is not given, the file is cleared in write mode.
-..value.OPEN_QUIET:Don't print any warning message if the file could not be opened.
-..value.OPEN_MASK:(Internal) Bitmask to extract the read/write open mode.
-..example.text:Code example to test for read-only mode.
-..example.code:
-if (openMode & OPEN_MASK == OPEN_READ)
-    // do something if opened in read-only mode
-..value.OPEN_ASYNC:(Internal) Open the file for asynchronous file access. For asynchronous file access, use @Spec.Async@.
-..value.OPEN_TEMPORARY:(Internal) Automatically delete the file after close. Use @Function.openTemp@ to open temporary files.
-..remarks:These flags can be combined via the $|$ operator. The default open mode is $OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$.
-..remarks:If you omit the $OPEN_APPEND$ flag in write mode, the file will be cleared when opened.
-..include:seqan/seq_io.h
-*/
-    enum FileOpenMode {
-        OPEN_RDONLY     = 1,
-        OPEN_WRONLY     = 2,
-        OPEN_RDWR       = 3,
-        OPEN_MASK       = 3,
-        OPEN_CREATE     = 4,
-        OPEN_APPEND     = 8,
-        OPEN_ASYNC      = 16,
-		OPEN_TEMPORARY	= 32,
-		OPEN_QUIET		= 128
-    }; //IOREV is it intended that two labels share the same value? What is OPEN_MASK anyway?
-
-	template <typename T>
-	struct DefaultOpenMode {
-//IOREV
-		enum { VALUE = OPEN_RDWR | OPEN_CREATE | OPEN_APPEND };
-	};
-
-	template <typename T>
-	struct DefaultOpenTempMode {
-//IOREV
-		enum { VALUE = OPEN_RDWR | OPEN_CREATE };
-	};
-
-    enum FileSeekMode {
-        SEEK_BEGIN   = 0,
-        SEEK_CURRENT = 1
+// --------------------------------------------------------------------------
+// Enum FileOpenMode
+// --------------------------------------------------------------------------
+
+enum FileOpenMode {
+    OPEN_RDONLY     = 1,
+    OPEN_WRONLY     = 2,
+    OPEN_RDWR       = 3,
+    OPEN_MASK       = 3,
+    OPEN_CREATE     = 4,
+    OPEN_APPEND     = 8,
+    OPEN_ASYNC      = 16,
+    OPEN_TEMPORARY    = 32,
+    OPEN_QUIET        = 128
+}; //IOREV is it intended that two labels share the same value? What is OPEN_MASK anyway?
+
+// --------------------------------------------------------------------------
+// Direction Tags
+// --------------------------------------------------------------------------
+
+struct Input_;
+typedef Tag<Input_> Input;
+
+struct Output_;
+typedef Tag<Output_> Output;
+
+struct Bidirectional_;
+typedef Tag<Bidirectional_> Bidirectional;
+
+// --------------------------------------------------------------------------
+// Metafunction DefaultOpenMode
+// --------------------------------------------------------------------------
+
+// helper metafunction to avoid ambigous partial specializations of the 1st/2nd argument
+template <typename TDirection>
+struct DefaultFileOpenMode_
+{
+    enum { VALUE = OPEN_RDWR | OPEN_CREATE | OPEN_APPEND };
+};
+
+template <>
+struct DefaultFileOpenMode_<Input>
+{
+    enum { VALUE = OPEN_RDONLY };
+};
+
+template <>
+struct DefaultFileOpenMode_<Output>
+{
+    enum { VALUE = OPEN_WRONLY | OPEN_CREATE };
+};
+
+template <typename T, typename TDirection = Bidirectional>
+struct DefaultOpenMode:
+    DefaultFileOpenMode_<TDirection> {};
+
+// --------------------------------------------------------------------------
+// Metafunction DefaultOpenTempMode
+// --------------------------------------------------------------------------
+
+template <typename T>
+struct DefaultOpenTempMode
+{
+    enum { VALUE = OPEN_RDWR | OPEN_CREATE };
+};
+
+enum FileSeekMode {
+    SEEK_BEGIN   = 0,
+    SEEK_CURRENT = 1
 #ifndef SEEK_END
-      , SEEK_END     = 2
+  , SEEK_END     = 2
+#endif
+}; //IOREV why not use constants SEEK_SET, SEEK_CUR, SEEK_END from cstdio?
+
+//////////////////////////////////////////////////////////////////////////////
+// result type of asynch. functions
+// you have to call release(AsyncRequest<T>) after a finished *event based* transfer
+struct AsyncDummyRequest
+{
+    AsyncDummyRequest()
+    {}
+
+    AsyncDummyRequest(AsyncDummyRequest &, Move)
+    {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    AsyncDummyRequest(AsyncDummyRequest &&)
+    {}
 #endif
-    }; //IOREV why not use constants SEEK_SET, SEEK_CUR, SEEK_END from cstdio?
 
-    //////////////////////////////////////////////////////////////////////////////
-    // result type of asynch. functions
-    // you have to call release(AsyncRequest<T>) after a finished *event based* transfer
-	struct AsyncDummyRequest {};
-//IOREV
+private:
+    AsyncDummyRequest(AsyncDummyRequest const &)
+    {}
+};
+
+template <>
+struct HasMoveConstructor<AsyncDummyRequest> : True {};
+
+
 
 /*!
  * @class AsyncRequest
@@ -238,27 +245,87 @@ if (openMode & OPEN_MASK == OPEN_READ)
  *
  * @tparam TFile The file type.
  *
- * @section Remarks
- *
  * This structure is used to identify asynchronous requests after their initiation.
  */
 
-/**
-.Class.AsyncRequest:
-..cat:Input/Output
-..summary:Associated with an asynchronous I/O request.
-..signature:AsyncRequest<TFile>
-..param.TFile:A File type.
-..remarks:This structure is used to identify asynchronous requests after their initiation.
-..include:seqan/file.h
-*/
-
     template < typename T >
     struct AsyncRequest
     {
 //IOREV _stub_ this seems not to be implemented at all, most functions are commented
         typedef AsyncDummyRequest Type;
     };
+
+
+// ============================================================================
+// Exceptions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Exception IOError
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class IOError
+ * @headerfile <seqan/basic.h>
+ * @brief Input/Output error exception.
+ *
+ * @signature typedef std::ios_base::failure IOError;
+ *
+ *
+ * @fn IOError::IOError
+ * @brief Constructor
+ *
+ * @signature IOError::IOError(msg, errorCode);
+ *
+ * @param[in] msg       Message as <tt>std::string</tt>.
+ * @param[in] errorCode The error code as an <tt>int</tt>.
+ */
+
+typedef std::ios_base::failure  IOError;
+
+// ----------------------------------------------------------------------------
+// Exception FileOpenError
+// ----------------------------------------------------------------------------
+
+struct FileOpenError : IOError
+{
+public:
+    FileOpenError(const char *fileName):
+        IOError((std::string)"Could not open file " + fileName)
+    {}
+
+protected:
+    FileOpenError(std::string const &msg):
+        IOError(msg)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Exception UnknownFileFormat
+// ----------------------------------------------------------------------------
+
+struct UnknownFileFormat : FileOpenError
+{
+    UnknownFileFormat():
+        FileOpenError(std::string("Could not detect file format"))
+    {}
+
+    UnknownFileFormat(const char *fileName):
+        FileOpenError(std::string("Could not detect file format of ") + fileName)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Exception UnknownExtensionError
+// ----------------------------------------------------------------------------
+
+struct UnknownExtensionError : FileOpenError
+{
+    UnknownExtensionError(const char *fileName):
+        FileOpenError(std::string("Unknown file extension of ") + fileName)
+    {}
+};
+
 }  // namespace seqan;
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_FILE_INTERFACE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_FILE_INTERFACE_H_
diff --git a/seqan/file/file_mapping.h b/seqan/file/file_mapping.h
index 98a335d..1da975f 100644
--- a/seqan/file/file_mapping.h
+++ b/seqan/file/file_mapping.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -35,8 +35,8 @@
 // Provides a platform independent access to memory mapping of files.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_FILE_MAPPING_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_FILE_MAPPING_H_
+#ifndef SEQAN_INCLUDE_SEQAN_FILE_MAPPING_H_
+#define SEQAN_INCLUDE_SEQAN_FILE_MAPPING_H_
 
 namespace seqan {
 
@@ -53,38 +53,24 @@ namespace seqan {
  * @headerfile <seqan/file.h>
  * @brief Flags to determine the mapping mode of mapFileSegment.
  *
- * @var FileMappingMode MAP_RDONLY = 1;
+ * @signature enum FileMappingMode;
+ *
+ * The mapping mode must be compatible to the open mode of a @link FileMapping @endlink, e.g. <tt>MAP_RDWR</tt> is not
+ * allowed if the file mapping was opened with <tt>OPEN_RDONLY</tt>.
+ *
+ * @val FileMappingMode MAP_RDONLY = 1;
  * @brief Map the segment in read-only mode.
  *
- * @var FileMappingMode MAP_WRONLY = 2;
+ * @val FileMappingMode MAP_WRONLY = 2;
  * @brief Map the segment in write-only mode.
  *
- * @var FileMappingMode MAP_RDWR = 3;
+ * @val FileMappingMode MAP_RDWR = 3;
  * @brief Map the segment for reading and writing.
  *
- * @var FileMappingMode MAP_COPYONWRITE = 4;
+ * @val FileMappingMode MAP_COPYONWRITE = 4;
  * @brief Write accesses are not written back to file and not shared among different mappings.
- *
- * @section Remarks
- *
- * The mapping mode must be compatible to the open mode of a @link FileMapping @endlink, e.g. <tt>MAP_RDWR</tt> is not
- * allowed if the file mapping was opened with <tt>OPEN_RDONLY</tt>.
  */
 
-/**
-.Enum.FileMappingMode
-..cat:Sequences
-..cat:Input/Output
-..summary:Flags to define the mapping mode of @Function.mapFileSegment@.
-..value.MAP_COPYONWRITE:Write accesses are not written back to file and not shared among different mappings.
-..value.MAP_RDONLY:Map the segment in read-only mode.
-..value.MAP_RDWR:Map the segment for reading and writing.
-..value.MAP_WRONLY:Map the segment in write-only mode.
-..remarks:The mapping mode must be compatible to the open mode of a @Class.FileMapping@,
-e.g. $MAP_RDWR$ is not allowed if the file mapping was opened with $OPEN_RDONLY$.
-..include:seqan/file.h
-*/
-
 enum FileMappingMode {
     MAP_RDONLY = 1,
     MAP_WRONLY = 2,
@@ -97,35 +83,24 @@ enum FileMappingMode {
  * @headerfile <seqan/file.h>
  * @brief Enum with MMAP advise values.
  *
- * @var FileMappingAdvise MAP_NORMAL;
+ * @signature enum FileMappingAdvise;
+ *
+ * @val FileMappingAdvise MAP_NORMAL;
  * @brief There is no advise on the given address range.
  *
- * @var FileMappingAdvise MAP_RANDOM;
+ * @val FileMappingAdvise MAP_RANDOM;
  * @brief The address range will be accessed with random access memory pattern.
  *
- * @var FileMappingAdvise MAP_SEQUENTIAL;
+ * @val FileMappingAdvise MAP_SEQUENTIAL;
  * @brief The address range will be accessed sequentially.
  *
- * @var FileMappingAdvise MAP_WILLNEED;
+ * @val FileMappingAdvise MAP_WILLNEED;
  * @brief The address range in the advise will be needed in the future.
  *
- * @var FileMappingAdvise MAP_DONTNEED;
+ * @val FileMappingAdvise MAP_DONTNEED;
  * @brief The address range in the advise will not be needed any more.
  */
 
-/**
-.Enum.FileMappingAdvise
-..cat:Sequences
-..cat:Input/Output
-..summary:Enum with mmap advise values.
-..value.MAP_NORMAL:There is no advise on the given address range.
-..value.MAP_RANDOM:The address range will be accessed with a random access memory pattern.
-..value.MAP_SEQUENTIAL:The address range will be accessed sequentially.
-..value.MAP_WILLNEED:The address range in the advise will be needed in the future.
-..value.MAP_DONTNEED:The address range in the advise will not be needed any more.
-..include:seqan/file.h
-*/
-
 #ifdef PLATFORM_WINDOWS
 
 enum FileMappingAdvise {
@@ -153,27 +128,14 @@ enum FileMappingAdvise {
  * @headerfile <seqan/file.h>
  * @brief A structure to memory-map a file.
  *
- * @signature template <typename TSpec>
- *            stuct FileMapping;
+ * @signature template <[typename TSpec]>
+ *            struct FileMapping;
  *
  * @tparam TSpec The specializing type.  Default: <tt>void</tt>.
  *
- * @section Remarks
- *
  * This structure represents both a file and its memory mapping.
  */
 
-/**
-.Class.FileMapping:
-..cat:File
-..summary:A structure to memory-map a file.
-..signature:FileMapping<TSpec>
-..param.TSpec:The specializing type.
-...default:$void$
-..remarks:This structure represents both a file and its memory mapping.
-..include:seqan/file.h
-*/
-
 #ifdef PLATFORM_WINDOWS
 static SECURITY_ATTRIBUTES FileMappingDefaultAttributes =
 {
@@ -222,10 +184,58 @@ struct FileMapping
 //____________________________________________________________________________
 };
 
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn FileMapping#Size
+ * @brief Return the size type of the FileMapping.
+ *
+ * @signature Size<TFileMapping>::Type;
+ *
+ * @tparam TFileMapping FileMapping to query.
+ *
+ * @return Type The size type of the FileMapping.
+ */
+
 template <typename TSpec>
 struct Size<FileMapping<TSpec> >:
     public Size<typename FileMapping<TSpec>::TFile> {};
 
+// ----------------------------------------------------------------------------
+// Metafunction DefaultOpenMode
+// ----------------------------------------------------------------------------
+
+template <typename TDirection>
+struct DefaultMMapOpenMode_
+{
+    enum { VALUE = OPEN_RDWR | OPEN_CREATE | OPEN_APPEND };
+};
+
+template <>
+struct DefaultMMapOpenMode_<Input>
+{
+    enum { VALUE = OPEN_RDWR | OPEN_APPEND };
+};
+
+template <>
+struct DefaultMMapOpenMode_<Output>
+{
+    enum { VALUE = OPEN_RDWR | OPEN_CREATE };
+};
+
+template <typename TSpec, typename TDirection>
+struct DefaultOpenMode<FileMapping<TSpec>, TDirection>:
+    DefaultMMapOpenMode_<TDirection> {};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _initialize()
+// ----------------------------------------------------------------------------
 
 template <typename TSpec>
 inline void
@@ -240,6 +250,9 @@ _initialize(FileMapping<TSpec> &mapping)
     mapping.temporary = true;
 }
 
+// ----------------------------------------------------------------------------
+// Function _mapFile()
+// ----------------------------------------------------------------------------
 
 template <typename TSpec, typename TSize>
 inline bool
@@ -281,7 +294,7 @@ _mapFile(FileMapping<TSpec> &mapping, TSize mappingSize)
             (LPTSTR) &lpMsgBuf,
             0,
             NULL);
-    
+
         SEQAN_FAIL("CreateFileMapping failed in resize: \"%s\"", lpMsgBuf /*strerror(GetLastError())*/);
         LocalFree(lpMsgBuf);
     }
@@ -289,6 +302,10 @@ _mapFile(FileMapping<TSpec> &mapping, TSize mappingSize)
     return result;
 }
 
+// ----------------------------------------------------------------------------
+// Function _unmapFile()
+// ----------------------------------------------------------------------------
+
 template <typename TSpec>
 inline bool
 _unmapFile(FileMapping<TSpec> &mapping)
@@ -319,28 +336,14 @@ _unmapFile(FileMapping<TSpec> &mapping)
  * @param[in]     openMode    The mode to open the file in, flags from @link FileOpenMode @endlink to combine
  *                            using OR.  Write-only mode is not supported, use <tt>OPEN_RDWR</tt> if you need
  *                            write access.  If you omit the <tt>OPEN_APPEND</tt> flag in write mode, the file
- *                            will be cleared when opened.  Default: <tt>OPEN_RDWR | OPEN_CREATe | OPEN_APPEND</tt>.
+ *                            will be cleared when opened.  Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>.
  *
  * @return bool <tt>true</tt> if the opening was successful, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.FileMapping#open:
-..class:Class.FileMapping
-..summary:Open a file to be mapped into memory.
-..cat:Input/Output
-..signature:open(mapping, fileName[, openMode])
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened. See @Enum.FileOpenMode@ for more details.
-...remarks:Write-only mode is not supported, use OPEN_RDWR if you need write access.
-If you omit the $OPEN_APPEND$ flag in write mode, the file will be cleared when opened.
-...type:Enum.FileOpenMode
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
 
 template <typename TSpec>
 inline bool
@@ -351,7 +354,7 @@ open(FileMapping<TSpec> &mapping, const char *filename, int openMode)
     mapping.openMode = openMode;
     mapping.ownFile = true;
     mapping.temporary = false;
-    mapping.fileSize = (result)? size(mapping.file) : 0ul;
+    mapping.fileSize = (result)? length(mapping.file) : 0ul;
     result &= _mapFile(mapping, mapping.fileSize);
     return result;
 }
@@ -367,7 +370,7 @@ open(FileMapping<TSpec> &mapping, TFile const &file)
     mapping.temporary = false;
     if (mapping.file)
     {
-        mapping.fileSize = size(mapping.file);
+        mapping.fileSize = length(mapping.file);
         return _mapFile(mapping, mapping.fileSize);
     }
     return false;
@@ -384,17 +387,9 @@ open(FileMapping<TSpec> &mapping, TFile const &file)
  * @return bool <tt>true</tt> on success, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.FileMapping#openTemp:
-..class:Class.FileMapping
-..summary:Open a temporary file to be mapped into memory.
-..cat:Input/Output
-..signature:openTemp(mapping)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
+// ----------------------------------------------------------------------------
+// Function openTemp()
+// ----------------------------------------------------------------------------
 
 template <typename TSpec>
 inline bool
@@ -411,25 +406,17 @@ openTemp(FileMapping<TSpec> &mapping)
 /*!
  * @fn FileMapping#close
  * @brief Close a file and its memory mapping.
- * 
- * @signature bool close(mapping);
  *
- * @param[in,out] mapping The FileMapping to close
+ * @signature bool close(fileMapping);
+ *
+ * @param[in,out] fileMapping The FileMapping to close
  *
  * @return bool <tt>true</tt> on success, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.FileMapping#close:
-..class:Class.FileMapping
-..summary:Close a file and its memory mapping.
-..cat:Input/Output
-..signature:close(mapping)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
+// ----------------------------------------------------------------------------
+// Function close()
+// ----------------------------------------------------------------------------
 
 template <typename TSpec>
 inline bool
@@ -446,26 +433,17 @@ close(FileMapping<TSpec> &mapping)
  * @fn FileMapping#closeAndResize
  * @brief Close a memory mapping and resize and close the underlying file.
  *
- * @signature bool closeAndResize(mapping, newFileSize);
+ * @signature bool closeAndResize(fileMapping, newFileSize);
  *
- * @param[in,out] mapping     The FileMapping to close.
+ * @param[in,out] fileMapping The FileMapping to close.
  * @param[in]     newFileSize The size the file should have after closing.
  *
  * @return bool <tt>true</tt> indicating success, <tt>false</tt> failure.
  */
 
-/**
-.Function.FileMapping#closeAndResize:
-..class:Class.FileMapping
-..summary:Close a memory mapping and resize and close the underlying file.
-..cat:Input/Output
-..signature:closeAndResize(mapping, newFileSize)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.newFileSize:The new file size.
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
+// ----------------------------------------------------------------------------
+// Function closeAndResize()
+// ----------------------------------------------------------------------------
 
 template <typename TSpec, typename TSize>
 inline bool
@@ -483,25 +461,17 @@ closeAndResize(FileMapping<TSpec> &mapping, TSize newFileSize)
 /*!
  * @fn FileMapping#length
  * @brief Return the file size of a memory mapping.
- * 
- * @signature TSize length(mapping);
  *
- * @param[in] mapping The FileMapping to return the length for.
+ * @signature TSize length(fileMapping);
  *
- * @return TSize The file size.  TSize is the size type of the file, as returned by the Size metafunction.
+ * @param[in] fileMapping The FileMapping to return the length for.
+ *
+ * @return TSize The file size  (Metafunction: @link FileMapping#Size @endlink).
  */
 
-/**
-.Function.FileMapping#length:
-..class:Class.FileMapping
-..summary:Return the file size of a memory mapping.
-..cat:Input/Output
-..signature:length(mapping)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..returns:The size of the underlying file.
-..include:seqan/file.h
-*/
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
 
 template <typename TSpec>
 inline typename Size<FileMapping<TSpec> >::Type
@@ -521,9 +491,9 @@ length(FileMapping<TSpec> const &mapping)
  * @fn FileMapping#resize
  * @brief Resize the underlying file.
  *
- * @signature bool resize(mapping, newFileSize);
+ * @signature bool resize(fileMapping, newFileSize);
  *
- * @param[in,out] mapping     The FileMapping to resize.
+ * @param[in,out] fileMapping The FileMapping to resize.
  * @param[in]     newFileSize The new file size to set.
  *
  * @return bool <tt>true</tt> on success, <tt>false</tt> otherwise.
@@ -534,20 +504,6 @@ length(FileMapping<TSpec> const &mapping)
  * claling this function.
  */
 
-/**
-.Function.FileMapping#resize:
-..class:Class.FileMapping
-..summary:Resize the underlying file.
-..cat:Input/Output
-..signature:resize(mapping, newFileSize)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.newFileSize:The new file size.
-..returns:A $bool$ which is $true$ on success.
-..remarks:Under Windows, all existing file mappings must be unmapped via @Function.unmapFileSegment@ prior calling this function.
-..include:seqan/file.h
-*/
-
 template <typename TSpec, typename TSize>
 inline bool
 resize(FileMapping<TSpec> &mapping, TSize newFileSize)
@@ -583,23 +539,6 @@ resize(FileMapping<TSpec> &mapping, TSize newFileSize)
  * needed to synchronize file accesses in non-shared-memory environments.
  */
 
-/**
-.Function.flushFileSegment:
-..class:Class.FileMapping
-..summary:Wait for all outstanding transactions of a memory-mapped file segment.
-..cat:Input/Output
-..signature:flushFileSegment(mapping, addr, fileOfs, size)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.addr:A pointer to the beginning of the memory-mapped segment in memory (returned by a prior call of @Function.mapFileSegment@).
-..param.fileOfs:The absolute start address of the segment in bytes.
-..param.size:The segment length in bytes.
-..returns:A $bool$ which is $true$ on success.
-..remarks:This function has no effect under Windows. On all other platforms it calls $msync$.
-This function is only needed to synchronize file accesses in non-shared-memory environments.
-..include:seqan/file.h
-*/
-
 template <typename TSpec, typename TPos, typename TSize>
 inline bool
 flushFileSegment(FileMapping<TSpec> &, void *addr, TPos beginPos, TSize size)
@@ -626,25 +565,9 @@ flushFileSegment(FileMapping<TSpec> &, void *addr, TPos beginPos, TSize size)
  * @param[in]     beginPos    the absolute start address of the segment in bytes.
  * @param[in]     size        The segment length in bytes.
  *
- * @returns bool <tt>true</tt> on success, <tt>false</tt> on failure.
+ * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.cancelFileSegment:
-..class:Class.FileMapping
-..summary:Cancel all outstanding transactions of a memory-mapped file segment.
-..cat:Input/Output
-..signature:cancelFileSegment(mapping, addr, fileOfs, size)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.addr:A pointer to the beginning of the memory-mapped segment in memory (returned by a prior call of @Function.mapFileSegment@).
-..param.fileOfs:The absolute start address of the segment in bytes.
-..param.size:The segment length in bytes.
-..returns:A $bool$ which is $true$ on success.
-..remarks:This function has no effect under Windows. On all other platforms it calls $msync$.
-..include:seqan/file.h
-*/
-
 template <typename TSpec, typename TPos, typename TSize>
 inline bool
 cancelFileSegment(FileMapping<TSpec> &, void *addr, TPos fileOfs, TSize size)
@@ -679,23 +602,6 @@ cancelFileSegment(FileMapping<TSpec> &, void *addr, TPos fileOfs, TSize size)
  * This function has no effect on Windows.  On all other platforms it calls <tt>posix_madvise</tt>.
  */
 
-/**
-.Function.adviseFileSegment:
-..class:Class.FileMapping
-..summary:Give advice about use of a memory-mapped file segment.
-..cat:Input/Output
-..signature:adviseFileSegment(mapping, advise, addr, fileOfs, size)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.advise:Advise flags
-...type:Enum.FileMappingAdvise
-..param.addr:A pointer to the beginning of the memory-mapped segment in memory (returned by a prior call of @Function.mapFileSegment@).
-..param.fileOfs:The absolute start address of the segment in bytes.
-..param.size:The segment length in bytes.
-..returns:A $bool$ which is $true$ on success.
-..remarks:This function has no effect under Windows. On all other platforms it calls $posix_madvise$.
-..include:seqan/file.h
-*/
 template <typename TSpec, typename TPos, typename TSize>
 inline bool
 adviseFileSegment(FileMapping<TSpec> &, FileMappingAdvise advise, void *addr, TPos fileOfs, TSize size)
@@ -707,7 +613,7 @@ adviseFileSegment(FileMapping<TSpec> &, FileMappingAdvise advise, void *addr, TP
     ignoreUnusedVariableWarning(size);
     return true;
 #else
-//		posix_fadvise(mapping.file.handle, beginPos, size, advise);
+//        posix_fadvise(mapping.file.handle, beginPos, size, advise);
     return (posix_madvise(static_cast<char*>(addr) + fileOfs, size, advise) == 0);
 #endif
 }
@@ -728,25 +634,6 @@ adviseFileSegment(FileMapping<TSpec> &, FileMappingAdvise advise, void *addr, TP
  *              <tt>void *</tt>.
  */
 
-/**
-.Function.mapFileSegment:
-..class:Class.FileMapping
-..summary:Map a segment of a file into memory.
-..cat:Input/Output
-..signature:mapFileSegment(mapping, fileOfs[, size[, mode]])
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.fileOfs:The absolute start address of the segment in bytes.
-..param.size:The segment length in bytes.
-...default:The rest of the file.
-..param.mode:The mapping access mode.
-...type:Enum.FileMappingMode
-...default:The read/write open mode of the underlying file.
-..returns:A pointer to the beginning of the memory-mapped segment in memory or NULL on error. 
-...type:nolink:$void *$
-..include:seqan/file.h
-*/
-
 template <typename TSpec, typename TPos, typename TSize, typename TFileMappingMode>
 inline void *
 mapFileSegment(FileMapping<TSpec> &mapping, TPos fileOfs, TSize size, TFileMappingMode mode)
@@ -797,7 +684,7 @@ mapFileSegment(FileMapping<TSpec> &mapping, TPos fileOfs, TSize size, TFileMappi
 #endif
     if (addr == NULL)
     {
-        SEQAN_FAIL("mapFileSegment(%i,%i,%i) failed (filesize=%i): \"%s\"", fileOfs, size, mode, seqan::size(mapping.file), strerror(errno));
+        SEQAN_FAIL("mapFileSegment(%i,%i,%i) failed (filesize=%i): \"%s\"", fileOfs, size, mode, length(mapping.file), strerror(errno));
     }
     return addr;
 }
@@ -829,20 +716,6 @@ mapFileSegment(FileMapping<TSpec> &mapping, TPos fileOfs = 0)
  * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
  */
 
-/**
-.Function.unmapFileSegment:
-..class:Class.FileMapping
-..summary:Unmap a memory-mapped file segment.
-..cat:Input/Output
-..signature:unmapFileSegment(mapping, addr, size)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.addr:A pointer to the beginning of the memory-mapped segment in memory.
-..param.size:The segment length in bytes.
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/file.h
-*/
-
 template <typename TSpec, typename TSize>
 inline bool
 unmapFileSegment(FileMapping<TSpec> &, void *addr, TSize size)
@@ -877,23 +750,6 @@ unmapFileSegment(FileMapping<TSpec> &, void *addr, TSize size)
  *              <tt>void*</tt>.
  */
 
-/**
-.Function.remapFileSegment:
-..class:Class.FileMapping
-..summary:Change the size of a memory-mapped file segment.
-..cat:Input/Output
-..signature:remapFileSegment(mapping, oldAddr, oldFileOfs, oldSize, newSize)
-..param.mapping:A file mapping object.
-...type:Class.FileMapping
-..param.oldAddr:The address returned by @Function.mapFileSegment@.
-..param.oldFileOfs:The fileOfs parameter used in @Function.mapFileSegment@.
-..param.oldSize:The size parameter used in @Function.mapFileSegment@.
-..param.newSize:The new segment length in bytes.
-..returns:A pointer to the beginning of the memory-mapped segment in memory or NULL on error. 
-...type:nolink:$void *$
-..include:seqan/file.h
-*/
-
 template <typename TSpec, typename TPos, typename TSize>
 inline void *
 remapFileSegment(FileMapping<TSpec> &mapping, void *oldAddr, TPos oldFileOfs, TSize oldSize, TSize newSize)
@@ -918,4 +774,4 @@ remapFileSegment(FileMapping<TSpec> &mapping, void *oldAddr, TPos oldFileOfs, TS
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_FILE_MAPPING_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_FILE_MAPPING_H_
diff --git a/seqan/file/file_page.h b/seqan/file/file_page.h
index 1b63f1c..ff48ae5 100644
--- a/seqan/file/file_page.h
+++ b/seqan/file/file_page.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -68,28 +68,28 @@ template <typename TConfig>
 struct MMap;
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// base class for memory buffers
+    //////////////////////////////////////////////////////////////////////////////
+    // base class for memory buffers
 
     struct Dynamic;
 
     template <size_t PAGESIZE>
     struct Fixed;
 
-	template <typename TFile, typename TSpec = Dynamic>
+    template <typename TFile, typename TSpec = Dynamic>
     struct PageFrame;
 
 
-	template <typename TValue, typename TSpec = Simple>
-	struct Buffer
-	{
+    template <typename TValue, typename TSpec = Simple>
+    struct Buffer
+    {
 //IOREV _nodoc_
-		typedef	typename Size<Buffer>::Type                 TSize;
-		typedef	typename Iterator<Buffer, Standard>::Type   TIterator;
+        typedef    typename Size<Buffer>::Type                 TSize;
+        typedef    typename Iterator<Buffer, Standard>::Type   TIterator;
 
-		TIterator	begin;      // the beginning of the buffer
-        TIterator	end;        // end of valid data
-        TSize		pageSize;   // size of allocated memory
+        TIterator    begin;      // the beginning of the buffer
+        TIterator    end;        // end of valid data
+        TSize        pageSize;   // size of allocated memory
 
         Buffer():
             begin(NULL),
@@ -119,76 +119,76 @@ struct MMap;
 
         inline TValue       & operator[](TSize i)       { return begin[i]; }
         inline TValue const & operator[](TSize i) const { return begin[i]; }
-	};
+    };
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// meta-function interface
+    //////////////////////////////////////////////////////////////////////////////
+    // meta-function interface
 
-	template <typename TValue, typename TSpec>
+    template <typename TValue, typename TSpec>
     struct Value<Buffer<TValue, TSpec> >
     {
         typedef TValue Type;
     };
 
-	template <typename TValue, typename TSpec>
-	struct Size<Buffer<TValue, TSpec> >
+    template <typename TValue, typename TSpec>
+    struct Size<Buffer<TValue, TSpec> >
     {
         typedef size_t Type;
     };
 
-	template <typename TValue, typename TSpec>
+    template <typename TValue, typename TSpec>
     struct Iterator<Buffer<TValue, TSpec>, Standard>
     {
         typedef TValue *Type;
     };
 
-	template <typename TValue, typename TSpec>
+    template <typename TValue, typename TSpec>
     struct Iterator<Buffer<TValue, TSpec> const, Standard>
     {
         typedef TValue const *Type;
     };
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// global interface
+    //////////////////////////////////////////////////////////////////////////////
+    // global interface
 
-	template <typename TValue, typename TSpec>
+    template <typename TValue, typename TSpec>
     inline typename Size<Buffer<TValue, TSpec> >::Type
     capacity(Buffer<TValue, TSpec> const &me)
     {
         return me.pageSize;
     }
 
-	template <typename TValue, typename TFile, size_t PAGESIZE>
+    template <typename TValue, typename TFile, size_t PAGESIZE>
     inline typename Size<Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE> > > >::Type
     capacity(Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE> > > const &)
     {
         return PAGESIZE;
     }
 
-	template <typename TValue, typename TSpec, typename TSize>
+    template <typename TValue, typename TSpec, typename TSize>
     inline void
     _setCapacity(Buffer<TValue, TSpec> &me, TSize size)
     {
         me.pageSize = size;
     }
 
-	template <typename TValue, typename TSpec>
+    template <typename TValue, typename TSpec>
     inline typename Size<Buffer<TValue, TSpec> >::Type
     length(Buffer<TValue, TSpec> const &me)
     {
         return me.end - me.begin;
     }
 
-	template <typename TValue, typename TFile, size_t PAGESIZE>
+    template <typename TValue, typename TFile, size_t PAGESIZE>
     inline typename Size<Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE> > > >::Type
     length(Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE> > > const &)
     {
         return PAGESIZE;
     }
 
-	template <typename TValue, typename TSpec, typename TSize>
+    template <typename TValue, typename TSpec, typename TSize>
     inline void
     resize(Buffer<TValue, TSpec> &me, TSize size)
     {
@@ -196,86 +196,86 @@ struct MMap;
     }
 
     template <typename TValue, typename TSpec, typename TSize, typename T>
-	inline bool
+    inline bool
     allocPage(Buffer<TValue, TSpec> &buffer, TSize size, T const & me)
     {
 //IOREV _nodoc_
         allocate(me, buffer.begin, size);
         _setCapacity(buffer, size);
         resize(buffer, size);
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "allocPage: " << ::std::hex << (void*)buffer.begin << ::std::dec << ::std::endl;
-		#endif
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "allocPage: " << std::hex << (void*)buffer.begin << std::dec << std::endl;
+        #endif
         return buffer.begin != NULL;
-	}
+    }
 
-	template <typename TValue, typename TSpec, typename T>
-	inline void
+    template <typename TValue, typename TSpec, typename T>
+    inline void
     freePage(Buffer<TValue, TSpec> &buffer, T const & me)
     {
 //IOREV _nodoc_
-		#ifdef SEQAN_VVERBOSE
-			if ((void*)buffer.begin)
-				::std::cerr << "freePage:  " << ::std::hex << (void*)buffer.begin << ::std::dec << ::std::endl;
-		#endif
-		deallocate(me, buffer.begin, capacity(buffer));
-		buffer.begin = NULL;
+        #ifdef SEQAN_VVERBOSE
+            if ((void*)buffer.begin)
+                std::cerr << "freePage:  " << std::hex << (void*)buffer.begin << std::dec << std::endl;
+        #endif
+        deallocate(me, buffer.begin, capacity(buffer));
+        buffer.begin = NULL;
         resize(buffer, 0);
         _setCapacity(buffer, 0);
-	}
+    }
 
-	template <typename TValue, typename TSpec>
-	inline typename Iterator<Buffer<TValue, TSpec>, Standard>::Type
+    template <typename TValue, typename TSpec>
+    inline typename Iterator<Buffer<TValue, TSpec>, Standard>::Type
     begin(Buffer<TValue, TSpec> &pf, Standard)
     {
-		return pf.begin;
-	}
+        return pf.begin;
+    }
 
-	template <typename TValue, typename TSpec>
-	inline typename Iterator<Buffer<TValue, TSpec> const, Standard>::Type
+    template <typename TValue, typename TSpec>
+    inline typename Iterator<Buffer<TValue, TSpec> const, Standard>::Type
     begin(Buffer<TValue, TSpec> const &pf, Standard)
     {
-		return pf.begin;
-	}
+        return pf.begin;
+    }
 
-	template <typename TValue, typename TSpec>
-	inline typename Iterator<Buffer<TValue, TSpec>, Standard>::Type
+    template <typename TValue, typename TSpec>
+    inline typename Iterator<Buffer<TValue, TSpec>, Standard>::Type
     end(Buffer<TValue, TSpec> &pf, Standard)
     {
-		return pf.end;
-	}
+        return pf.end;
+    }
 
-	template <typename TValue, typename TSpec>
-	inline typename Iterator<Buffer<TValue, TSpec> const, Standard>::Type
+    template <typename TValue, typename TSpec>
+    inline typename Iterator<Buffer<TValue, TSpec> const, Standard>::Type
     end(Buffer<TValue, TSpec> const &pf, Standard)
     {
-		return pf.end;
-	}
+        return pf.end;
+    }
 
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// a bucket is a structure to represent a small window of a page
+    // a bucket is a structure to represent a small window of a page
     // used by algorithms which need a global view of all pages (merge sort, mapper)
 
-	template <typename TValue>
+    template <typename TValue>
     struct PageBucket
-	{
+    {
 //IOREV _nodoc_ has some unformatted comments in code, but not enough doc
-		typedef	typename Iterator<PageBucket, Standard>::Type TIterator;
+        typedef    typename Iterator<PageBucket, Standard>::Type TIterator;
 
         unsigned    pageOfs;                // begin of bucket window with relation to page begin
-        TIterator	begin, cur, end;        // begin/end of buckets memory buffer and a pointer
+        TIterator    begin, cur, end;        // begin/end of buckets memory buffer and a pointer
     };
 
     template <typename TValue>
     struct PageBucketExtended : public PageBucket< TValue > {
 //IOREV _nodoc_
-		int     	pageNo;		            // related page (needed by merger sort)
+        int         pageNo;                    // related page (needed by merger sort)
     };
-    
-	template <typename TValue>
-    ::std::ostream& operator<<(::std::ostream &out, const PageBucketExtended<TValue> &pb) {
+
+    template <typename TValue>
+    std::ostream& operator<<(std::ostream &out, const PageBucketExtended<TValue> &pb) {
 //IOREV _ _nodoc_
         for(TValue *cur = pb.begin; cur != pb.end; cur++)
             out << *cur << " ";
@@ -283,26 +283,22 @@ struct MMap;
     }
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// meta-function interface
+    //////////////////////////////////////////////////////////////////////////////
+    // meta-function interface
 
-	template <typename TValue>
-    struct Value< PageBucket<TValue> >		{ typedef TValue Type; };
-//IOREV
+    template <typename TValue>
+    struct Value< PageBucket<TValue> >        { typedef TValue Type; };
 
     template <typename TValue>
-    struct Size< PageBucket<TValue> >		{ typedef size_t Type; };
-//IOREV
+    struct Size< PageBucket<TValue> >        { typedef size_t Type; };
 
     template <typename TValue>
-    struct Iterator< PageBucket<TValue>, Standard >			{ typedef TValue *Type; };
-//IOREV
+    struct Iterator< PageBucket<TValue>, Standard >            { typedef TValue *Type; };
 
     template <typename TValue>
-    struct Iterator< PageBucket<TValue> const, Standard >	{ typedef TValue const *Type; };
-//IOREV
+    struct Iterator< PageBucket<TValue> const, Standard >    { typedef TValue const *Type; };
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
 
     template <typename TFilePos, typename TSize>
     struct FilePageRequest
@@ -316,94 +312,147 @@ struct MMap;
         TFilePos            filePos;
         TSize               size;
         FilePageRequestMode mode;
+
+        FilePageRequest() : filePos(0), size(0), mode(MODE_RDONLY)
+        {}
     };
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
 
-    enum PageFrameStatus
+    enum PageFrameState
     {
         UNUSED,
         READING,
+        READING_DONE,
         PREPROCESSING,
+        PREPROCESSING_DONE,
         READY,
         POSTPROCESSING,
-        POSTPROCESSED,
-        WRITING
+        POSTPROCESSING_DONE,
+        WRITING,
+        WRITING_DONE
     };
 
-	//////////////////////////////////////////////////////////////////////////////
-	// page frame of dynamic size
+    //////////////////////////////////////////////////////////////////////////////
+    // page frame of dynamic size
 
     template <typename TValue, typename TFile>
-	struct Buffer<TValue, PageFrame<TFile, Dynamic> > :
+    struct Buffer<TValue, PageFrame<TFile, Dynamic> > :
         public Buffer<TValue>
-	{
+    {
 //IOREV _nodoc_
-		typedef Buffer<TValue>                      TBase;
-		typedef TFile                               File;
-		typedef typename Size<TFile>::Type          TFileSize;
+        typedef Buffer<TValue>                      TBase;
+        typedef TFile                               File;
+        typedef typename Size<TFile>::Type          TFileSize;
         typedef typename AsyncRequest<TFile>::Type  AsyncRequest;
         typedef FilePageRequest<TFileSize, size_t>  TFilePageRequest;
 
         TFilePageRequest pageRequest;
 
-		bool			dirty;		// data needs to be written to disk before freeing
-		unsigned		pageNo;		// maps frames to pages (reverse vector mapper)
+        bool            dirty;        // data needs to be written to disk before freeing
+        unsigned        pageNo;        // maps frames to pages (reverse vector mapper)
         AsyncRequest    request;    // request structure of the async io process
-		PageFrameStatus status;
+        PageFrameState  status;
         Buffer          *next;      // next buffer in a chained list
 
         Buffer():
-			TBase(),
+            TBase(),
             dirty(false),
             pageNo(MaxValue<unsigned>::VALUE),
-			status(READY),
-			next(NULL) {}
+            status(READY),
+            next(NULL) {}
+
+        Buffer(Buffer & other, Move) :
+            TBase(other),
+            dirty(other.dirty),
+            pageNo(other.pageNo),
+            request(other.request, Move()),
+            status(other.status),
+            next(other.next)
+        {}
+
+#ifdef SEQAN_CXX11_STANDARD
+        Buffer(Buffer && other) :
+            TBase(other),
+            dirty(other.dirty),
+            pageNo(other.pageNo),
+            request(other.request, Move()),
+            status(other.status),
+            next(other.next)
+        {}
+#endif
+    private:
+        Buffer(Buffer const &)
+        {}
     };
 
+    template <typename TValue, typename TFile>
+    struct HasMoveConstructor<Buffer<TValue, PageFrame<TFile, Dynamic> > > : True {};
 
-	//////////////////////////////////////////////////////////////////////////////
-	// page frame of static size
+    //////////////////////////////////////////////////////////////////////////////
+    // page frame of static size
 
-//IOREV
 
-    typedef ::std::list<Position<String<void*> >::Type> PageLRUList;    // least recently usage list
-	typedef PageLRUList::iterator PageLRUEntry;
+    typedef std::list<Position<String<void*> >::Type> PageLRUList;    // least recently usage list
+    typedef PageLRUList::iterator PageLRUEntry;
 
     template < typename TValue,
                typename TFile,
                size_t PAGESIZE_ >
-	struct Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE_> > >
+    struct Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE_> > >
     {
-		typedef TFile                                       File;
+        typedef TFile                                       File;
         typedef typename AsyncRequest<TFile>::Type          AsyncRequest;
-		typedef	typename Iterator<Buffer, Standard>::Type   TIterator;
+        typedef    typename Iterator<Buffer, Standard>::Type   TIterator;
 
-		enum            { PAGESIZE = PAGESIZE_ };
-		enum DataStatus	{ ON_DISK = -1, UNINITIALIZED = -2 };
-		enum Priority	{ NORMAL_LEVEL = 0, PREFETCH_LEVEL = 1, ITERATOR_LEVEL = 2, PERMANENT_LEVEL = 3 };
+        enum            { PAGESIZE = PAGESIZE_ };
+        enum DataStatus    { ON_DISK = -1, UNINITIALIZED = -2 };
+        enum Priority    { NORMAL_LEVEL = 0, PREFETCH_LEVEL = 1, ITERATOR_LEVEL = 2, PERMANENT_LEVEL = 3 };
 
         TIterator       begin;
         TIterator       end;
         AsyncRequest    request;    // request structure of the async io process
-		PageFrameStatus status;
-		DataStatus		dataStatus;
-		PageLRUEntry	lruEntry;   // priority based lru
+        PageFrameState  status;
+        DataStatus        dataStatus;
+        PageLRUEntry    lruEntry;   // priority based lru
         Priority        priority;
-		int     		pageNo;		// maps frames to pages (reverse vector mapper)
-		bool			dirty;		// data needs to be written to disk before freeing
+        int             pageNo;        // maps frames to pages (reverse vector mapper)
+        bool            dirty;        // data needs to be written to disk before freeing
 
-		Buffer():
+        Buffer():
             begin(NULL),
-            end(NULL),
-			status(READY),
-			dataStatus(UNINITIALIZED),
-            priority(NORMAL_LEVEL),
-            pageNo(-1),
-            dirty(false) {}
+            end(NULL)
+        {
+            clear(*this);
+        }
 
+        Buffer(Buffer & other, Move):
+            begin(other.begin),
+            end(other.end),
+            request(other.request, Move()),
+            status(other.status),
+            dataStatus(other.dataStatus),
+            lruEntry(other.lruEntry),
+            priority(other.priority),
+            pageNo(other.pageNo),
+            dirty(other.dirty)
+        {}
+
+#ifdef SEQAN_CXX11_STANDARD
+        Buffer(Buffer && other) :
+            begin(other.begin),
+            end(other.end),
+            request(other.request, Move()),
+            status(other.status),
+            dataStatus(other.dataStatus),
+            lruEntry(other.lruEntry),
+            priority(other.priority),
+            pageNo(other.pageNo),
+            dirty(other.dirty)
+        {}
+#endif
         template <typename TPos>
-		inline TValue &
+        inline TValue &
         operator[] (TPos i)
         {
             return begin[i];
@@ -415,40 +464,64 @@ struct MMap;
         {
             return begin[i];
         }
-	};
 
+    private:
+        Buffer(Buffer const &)
+        {}
+    };
+
+    template < typename TValue,
+               typename TFile,
+               size_t PAGESIZE_ >
+    struct HasMoveConstructor<Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE_> > > > : True {};
 
-	//////////////////////////////////////////////////////////////////////////////
-	// a memory-mapped page frame
+
+    template < typename TValue,
+               typename TFile,
+               size_t PAGESIZE_ >
+    inline void
+    clear(Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE_> > > &me)
+    {
+        typedef Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE_> > > TPageFrame;
+        me.status = READY;
+        me.dataStatus = TPageFrame::UNINITIALIZED;
+        me.priority = TPageFrame::NORMAL_LEVEL;
+        me.pageNo = -1;
+        me.dirty = false;
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // a memory-mapped page frame
 /*
     template <typename TValue, typename TFile, typename TConfig>
-	struct PageFrame< TValue, TFile, MMap<TConfig> >: public Buffer<TValue>
+    struct PageFrame< TValue, TFile, MMap<TConfig> >: public Buffer<TValue>
     {
-		typedef Buffer<TValue> TBase;
+        typedef Buffer<TValue> TBase;
 
-        enum Status		{ READY, READING, WRITING };
+        enum Status        { READY, READING, WRITING };
 
-		unsigned   		pageNo;		// maps frames to pages (reverse vector mapper)
-		Status			status;
+        unsigned           pageNo;        // maps frames to pages (reverse vector mapper)
+        Status            status;
         PageFrame       *next;      // next buffer in a chained list
 
         PageFrame():
-			TBase(),
+            TBase(),
             pageNo(MaxValue<unsigned>::VALUE),
-			next(NULL) {}
+            next(NULL) {}
     };
 */
 
-	//////////////////////////////////////////////////////////////////////////////
-	// meta-function interface
+    //////////////////////////////////////////////////////////////////////////////
+    // meta-function interface
 
-	template <typename TValue, typename TFile, size_t PAGESIZE>
+    template <typename TValue, typename TFile, size_t PAGESIZE>
     struct Iterator<Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE> > >, Standard >
     {
         typedef VolatilePtr<TValue> Type;
     };
 
-	template <typename TValue, typename TFile, size_t PAGESIZE>
+    template <typename TValue, typename TFile, size_t PAGESIZE>
     struct Iterator<Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE> > > const, Standard >
     {
         typedef VolatilePtr<TValue> const Type;
@@ -457,37 +530,42 @@ struct MMap;
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// various page frame methods
+    //////////////////////////////////////////////////////////////////////////////
+    // various page frame methods
 
-	template <typename TValue, typename TFile, typename TSpec>
     inline const char *
-    _pageFrameStatusString(Buffer<TValue, PageFrame<TFile, TSpec> > const &pf)
+    _pageFrameStatusString(PageFrameState state)
     {
-        switch (pf.status)
+        switch (state)
         {
-			case READY:
-                return "READY";
-			case READING:
-                return "READING";
-			case WRITING:
-                return "WRITING";
             case UNUSED:
                 return "UNUSED";
+            case READING:
+                return "READING";
+            case READING_DONE:
+                return "READING_DONE";
             case PREPROCESSING:
                 return "PREPROCESSING";
+            case PREPROCESSING_DONE:
+                return "PREPROCESSING_DONE";
+            case READY:
+                return "READY";
             case POSTPROCESSING:
                 return "POSTPROCESSING";
-            case POSTPROCESSED:
-                return "POSTPROCESSED";
+            case POSTPROCESSING_DONE:
+                return "POSTPROCESSING_DONE";
+            case WRITING:
+                return "WRITING";
+            case WRITING_DONE:
+                return "WRITING_DONE";
             default:
                 return "UNKNOWN";
         }
     }
 
-	template <typename TValue, typename TFile, typename TSpec>
-    ::std::ostream& operator<<(::std::ostream &out, const Buffer<TValue, PageFrame<TFile, TSpec> > &pf)
-	{
+    template <typename TValue, typename TFile, typename TSpec>
+    std::ostream& operator<<(std::ostream &out, const Buffer<TValue, PageFrame<TFile, TSpec> > &pf)
+    {
 //IOREV _nodoc_
         out << "PageFrame @ " << pf.pageNo;
         if (pf.dirty)
@@ -495,7 +573,7 @@ struct MMap;
         else
             out << " CLEAN ";
 
-        out << _pageFrameStatusString(pf);
+        out << _pageFrameStatusString(pf.status);
 
 //        if (pf.dataStatus == pf.ON_DISK)
 //            out << " ON_DISK";
@@ -506,117 +584,117 @@ struct MMap;
         out << " Buffer:" << (void*)pf.begin;
 
         return out;
-	}
+    }
 
-	template <typename TValue, typename TFile, typename TSpec, typename T> inline
-	void allocPage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, T const & me) 
-	{
+    template <typename TValue, typename TFile, typename TSpec, typename T> inline
+    void allocPage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, T const & me)
+    {
 //IOREV _nodoc_
-		TValue* tmp = NULL;
-		allocate(me, tmp, capacity(pf));
-		//bzero(tmp, sizeof(TValue) * capacity(pf));
-		pf.begin = tmp;
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "allocPage: " << ::std::hex << &pf << '\t' << tmp << ::std::dec << ::std::endl;
-		#endif
-	}
-
-	template <typename TValue, typename TFile, typename TSpec, typename T> inline
-	void freePage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, T const & me) 
-	{
+        TValue* tmp = NULL;
+        allocate(me, tmp, capacity(pf));
+        //bzero(tmp, sizeof(TValue) * capacity(pf));
+        pf.begin = tmp;
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "allocPage: " << std::hex << &pf << '\t' << tmp << std::dec << std::endl;
+        #endif
+    }
+
+    template <typename TValue, typename TFile, typename TSpec, typename T> inline
+    void freePage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, T const & me)
+    {
 //IOREV _nodoc_
-		#ifdef SEQAN_VVERBOSE
-			if ((void*)pf.begin)
-				::std::cerr << "freePage:  " << ::std::hex << &pf << '\t' << (void*)pf.begin << ::std::dec << ::std::endl;
-		#endif
+        #ifdef SEQAN_VVERBOSE
+            if ((void*)pf.begin)
+                std::cerr << "freePage:  " << std::hex << &pf << '\t' << (void*)pf.begin << std::dec << std::endl;
+        #endif
         nukeCopies(pf.begin);
-		deallocate(me, (TValue*)pf.begin, capacity(pf));
-		pf.begin = NULL;
+        deallocate(me, (TValue*)pf.begin, capacity(pf));
+        pf.begin = NULL;
         resize(pf, 0);
-	}
+    }
 
-	template <typename TValue, typename TFile, typename TSpec> inline
-	bool readPage(int pageNo, Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file)
-	{
+    template <typename TValue, typename TFile, typename TSpec> inline
+    bool readPage(int pageNo, Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file)
+    {
 //IOREV _nodoc_
-		typedef typename Position<TFile>::Type TPos;
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "readPage:  " << ::std::hex << &pf << '\t' << (void*)pf.begin;
-			::std::cerr << " from page " << ::std::dec << pageNo << ::std::endl;
-		#endif
-		pf.dirty = false;
-		pf.status = READING;
+        typedef typename Position<TFile>::Type TPos;
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "readPage:  " << std::hex << &pf << '\t' << (void*)pf.begin;
+            std::cerr << " from page " << std::dec << pageNo << std::endl;
+        #endif
+        pf.dirty = false;
+        pf.status = READING;
 //        resize(pf, capacity(pf));
 
-		bool readResult = asyncReadAt(file, (TValue*)pf.begin, length(pf), (TPos)pageNo * (TPos)capacity(pf), pf.request);
+        bool readResult = asyncReadAt(file, (TValue*)pf.begin, length(pf), (TPos)pageNo * (TPos)capacity(pf), pf.request);
 
         // TODO(weese): Throw an I/O exception
         if (!readResult)
-            SEQAN_FAIL("%s operation could not be initiated: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+            SEQAN_FAIL("%s operation could not be initiated: \"%s\"", _pageFrameStatusString(pf.status), strerror(errno));
 
         return readResult;
-	}
+    }
 
-	template <typename TValue, typename TFile, typename TSpec> inline
-	bool unmapPage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &)
-	{
+    template <typename TValue, typename TFile, typename TSpec> inline
+    bool unmapPage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &)
+    {
         if (pf.begin)
         {
 #ifdef PLATFORM_WINDOWS
 #else
             munmap(pf.begin, length(pf) * sizeof(TValue));
 #endif
-			pf.begin = NULL;
+            pf.begin = NULL;
         }
         return true;
     }
 
-	template <typename TValue, typename TFile, typename TSpec, typename TSize> inline
-	bool mapReadPage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file, TSize size)
-	{
-		typedef typename Position<TFile>::Type TPos;
+    template <typename TValue, typename TFile, typename TSpec, typename TSize> inline
+    bool mapReadPage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file, TSize size)
+    {
+        typedef typename Position<TFile>::Type TPos;
         unmapPage(pf, file);
-		pf.status = READY;
+        pf.status = READY;
         SEQAN_ASSERT_GT(size, 0);
 
 #ifdef PLATFORM_WINDOWS
 #if 0
-		DWORD prot = 0;
-		DWORD access = 0;
-		if ((me._openMode & OPEN_MASK) == OPEN_RDONLY) 
-		{
-			prot = PAGE_READONLY;
-			access = FILE_MAP_READ;
-		} else {
-			prot = PAGE_READWRITE;
-			access = FILE_MAP_ALL_ACCESS;
-		}
+        DWORD prot = 0;
+        DWORD access = 0;
+        if ((me._openMode & OPEN_MASK) == OPEN_RDONLY)
+        {
+            prot = PAGE_READONLY;
+            access = FILE_MAP_READ;
+        } else {
+            prot = PAGE_READWRITE;
+            access = FILE_MAP_ALL_ACCESS;
+        }
         LARGE_INTEGER largeSize;
-		largeSize.QuadPart = new_capacity;
-		largeSize.QuadPart *= sizeof(TValue);
+        largeSize.QuadPart = new_capacity;
+        largeSize.QuadPart *= sizeof(TValue);
 
-		me.handle = CreateFileMapping(file.handle, &MMapStringDefaultAttributes, prot, largeSize.HighPart, largeSize.LowPart, NULL);
-		if (me.handle == NULL)
-		{
+        me.handle = CreateFileMapping(file.handle, &MMapStringDefaultAttributes, prot, largeSize.HighPart, largeSize.LowPart, NULL);
+        if (me.handle == NULL)
+        {
             SEQAN_FAIL(
                 "CreateFileMapping(%d, %d, 0, 0, 0) failed in mapReadPage: \"%s\"",
                 file.handle, access, strerror(errno));
-		#if SEQAN_ENABLE_DEBUG
-			::std::cerr << "CreateFileMapping failed. (ErrNo=" << GetLastError() << ")" << ::std::endl;
-		#endif
-			return false;
-		}
-
-		pf.begin = (TValue *) MapViewOfFile(pf.handle, access, 0, 0, 0);	
-		if (pf.begin == NULL)
-		{
+        #if SEQAN_ENABLE_DEBUG
+            std::cerr << "CreateFileMapping failed. (ErrNo=" << GetLastError() << ")" << std::endl;
+        #endif
+            return false;
+        }
+
+        pf.begin = (TValue *) MapViewOfFile(pf.handle, access, 0, 0, 0);
+        if (pf.begin == NULL)
+        {
             SEQAN_FAIL(
                 "MapViewOfFile(%d, %d, 0, 0, 0) failed in mapReadPage: \"%s\"",
                 pf.handle, access, strerror(errno));
-			return false;
-		}
-				
-		me.data_begin = (TValue *) addr;
+            return false;
+        }
+
+        me.data_begin = (TValue *) addr;
 #endif
 #else
         pf.begin = (TValue*)mmap(NULL, size * sizeof(TValue), PROT_READ | PROT_WRITE, MAP_PRIVATE, file.handle, (TPos)pf.pageNo * (TPos)capacity(pf) * (TPos)sizeof(TValue));
@@ -634,14 +712,14 @@ struct MMap;
         return true;
     }
 
-	template <typename TValue, typename TFile, typename TSpec, typename TSize> inline
-	bool mapWritePage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file, TSize size) 
-	{
-		typedef typename Position<TFile>::Type TPos;
+    template <typename TValue, typename TFile, typename TSpec, typename TSize> inline
+    bool mapWritePage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file, TSize size)
+    {
+        typedef typename Position<TFile>::Type TPos;
         unmapPage(pf, file);
         pf.status = READY;
         SEQAN_ASSERT_GT(size, 0u);
-        
+
 #ifdef PLATFORM_WINDOWS
 #else
         pf.begin = (TValue*)mmap(NULL, size * sizeof(TValue), PROT_READ | PROT_WRITE, MAP_SHARED, file.handle, (TPos)pf.pageNo * (TPos)capacity(pf) * (TPos)sizeof(TValue));
@@ -659,76 +737,76 @@ struct MMap;
         return true;
     }
 
-	template <typename TValue, typename TFile, typename TSpec> inline
-	bool writePage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, int pageNo, TFile &file) 
-	{
+    template <typename TValue, typename TFile, typename TSpec> inline
+    bool writePage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, int pageNo, TFile &file)
+    {
 //IOREV _nodoc_
-		typedef typename Position<TFile>::Type TPos;
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "writePage: " << ::std::hex << &pf << '\t' << (void*)pf.begin;
-			::std::cerr << " from page " << ::std::dec << pageNo << ::std::endl;
-		#endif
-		pf.status = WRITING;
+        typedef typename Position<TFile>::Type TPos;
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "writePage: " << std::hex << &pf << '\t' << (void*)pf.begin;
+            std::cerr << " from page " << std::dec << pageNo << std::endl;
+        #endif
+        pf.status = WRITING;
 //        resize(pf, capacity(pf));
 
-		bool writeResult = asyncWriteAt(file, (TValue*)pf.begin, length(pf), (TPos)pageNo * (TPos)capacity(pf), pf.request);
+        bool writeResult = asyncWriteAt(file, (TValue*)pf.begin, length(pf), (TPos)pageNo * (TPos)capacity(pf), pf.request);
 
         // TODO(weese): Throw an I/O exception
         if (!writeResult)
-            SEQAN_FAIL("%s operation could not be initiated: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+            SEQAN_FAIL("%s operation could not be initiated: \"%s\"", _pageFrameStatusString(pf.status), strerror(errno));
 
         return writeResult;
-	}
+    }
 
-	template < typename TValue, typename TFile, typename TSpec, typename TSize> inline
-    bool readLastPage(int pageNo, Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file, TSize size) 
-	{
+    template < typename TValue, typename TFile, typename TSpec, typename TSize> inline
+    bool readLastPage(int pageNo, Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file, TSize size)
+    {
 //IOREV _nodoc_
-		typedef typename Position<TFile>::Type TPos;
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "readPage:  " << ::std::hex << &pf << '\t' << (void*)pf.begin;
-			::std::cerr << " from page " << ::std::dec << pageNo << " size " << size << ::std::endl;
-		#endif
-		pf.dirty = false;
-		pf.status = READY;
+        typedef typename Position<TFile>::Type TPos;
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "readPage:  " << std::hex << &pf << '\t' << (void*)pf.begin;
+            std::cerr << " from page " << std::dec << pageNo << " size " << size << std::endl;
+        #endif
+        pf.dirty = false;
+        pf.status = READY;
 //        resize(pf, size);
 
-		bool readResult = readAt(file, (TValue*)pf.begin, size, (TPos)pageNo * (TPos)capacity(pf));
+        bool readResult = readAt(file, (TValue*)pf.begin, size, (TPos)pageNo * (TPos)capacity(pf));
 
         // TODO(weese): Throw an I/O exception
         if (!readResult)
-            SEQAN_FAIL("%s operation could not be initiated: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+            SEQAN_FAIL("%s operation could not be initiated: \"%s\"", _pageFrameStatusString(pf.status), strerror(errno));
 
         return readResult;
-	}
+    }
 
-	template <typename TValue, typename TFile, typename TSpec, typename TSize> inline
-	bool writeLastPage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, int pageNo, TFile &file, TSize size) 
-	{
+    template <typename TValue, typename TFile, typename TSpec, typename TSize> inline
+    bool writeLastPage(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, int pageNo, TFile &file, TSize size)
+    {
 //IOREV _nodoc_
-		typedef typename Position<TFile>::Type TPos;
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "writePage: " << ::std::hex << &pf << '\t' << (void*)pf.begin;
-			::std::cerr << " from page " << ::std::dec << pageNo << " size " << size << ::std::endl;
-		#endif
-		pf.dirty = false;
-		pf.status = READY;
+        typedef typename Position<TFile>::Type TPos;
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "writePage: " << std::hex << &pf << '\t' << (void*)pf.begin;
+            std::cerr << " from page " << std::dec << pageNo << " size " << size << std::endl;
+        #endif
+        pf.dirty = false;
+        pf.status = READY;
 //        resize(pf, size);
 
-		bool writeResult = writeAt(file, (TValue*)pf.begin, size, (TPos)pageNo * (TPos)capacity(pf));
+        bool writeResult = writeAt(file, (TValue*)pf.begin, size, (TPos)pageNo * (TPos)capacity(pf));
 
         // TODO(weese): Throw an I/O exception
         if (!writeResult)
-            SEQAN_FAIL("%s operation could not be initiated: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+            SEQAN_FAIL("%s operation could not be initiated: \"%s\"", _pageFrameStatusString(pf.status), strerror(errno));
 
         return writeResult;
-	}
+    }
 
-	template <typename TValue, typename TFile, typename TSpec> inline
-	bool waitFor(Buffer<TValue, PageFrame<TFile, TSpec> > &pf) 
-	{
+    template <typename TValue, typename TFile, typename TSpec> inline
+    bool waitFor(Buffer<TValue, PageFrame<TFile, TSpec> > &pf)
+    {
 //IOREV _nodoc_ equally named functions with different purposes in system_thread.h, system_event.h and file_async.h
-		if (pf.status == READY)
+        if (pf.status == READY)
             return true;
 
         bool waitResult = waitFor(pf.request);
@@ -737,19 +815,19 @@ struct MMap;
         if (!waitResult)
         {
             //printRequest(pf.request);
-            SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+            SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf.status), strerror(errno));
         }
 
         pf.status = READY;
         pf.dirty = false;
         return waitResult;
-	}
+    }
 
-	template <typename TValue, typename TFile, typename TSpec, typename TTime> inline
-	bool waitFor(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TTime timeOut, bool &inProgress)
-	{
+    template <typename TValue, typename TFile, typename TSpec, typename TTime> inline
+    bool waitFor(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TTime timeOut, bool &inProgress)
+    {
 //IOREV _nodoc_ equally named functions with different purposes in system_thread.h, system_event.h and file_async.h (none documented)
-		if (pf.status == READY)
+        if (pf.status == READY)
         {
             inProgress = false;
             return true;
@@ -761,7 +839,7 @@ struct MMap;
         if (!waitResult)
         {
             //printRequest(pf.request);
-            SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+            SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf.status), strerror(errno));
         }
 
         if (!inProgress)
@@ -770,56 +848,56 @@ struct MMap;
             pf.dirty = false;
         }
         return waitResult;
-	}
+    }
 
-	template <typename TValue, typename TFile, typename TSpec> inline
-	bool cancel(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file) 
-	{
+    template <typename TValue, typename TFile, typename TSpec> inline
+    bool cancel(Buffer<TValue, PageFrame<TFile, TSpec> > &pf, TFile &file)
+    {
 //IOREV _nodoc_ equally named functions with different purposes in pipe/pool_*.h, system_thread.h, and file_async.h (only the latter documented)
         bool dummy;
         waitFor(pf, 0, dummy);
-		if (pf.status != READY) 
-		{
+        if (pf.status != READY)
+        {
             if (!cancel(file, pf.request)) return false;
             pf.status = READY;
         }
         return true;
-	}
+    }
 
-	//////////////////////////////////////////////////////////////////////////////
-	// page based read/write methods used by Pool classes
+    //////////////////////////////////////////////////////////////////////////////
+    // page based read/write methods used by Pool classes
 
     template <typename TValue, typename TFile> inline
-	bool readPage(Buffer<TValue, PageFrame<TFile, Dynamic> > &pf, TFile &file) 
-	{
+    bool readPage(Buffer<TValue, PageFrame<TFile, Dynamic> > &pf, TFile &file)
+    {
 //IOREV _nodoc_
         if (length(pf) == capacity(pf))
             return readPage(pf.pageNo, pf, file);
         else
             return readLastPage(pf.pageNo, pf, file, length(pf));
-	}
+    }
 
-	template <typename TValue, typename TFile> inline
-	bool writePage(Buffer<TValue, PageFrame<TFile, Dynamic> > &pf, TFile &file) 
-	{
+    template <typename TValue, typename TFile> inline
+    bool writePage(Buffer<TValue, PageFrame<TFile, Dynamic> > &pf, TFile &file)
+    {
 //IOREV _nodoc_
         if (length(pf) == capacity(pf))
             return writePage(pf, pf.pageNo, file);
         else
             return writeLastPage(pf, pf.pageNo, file, length(pf));
-	}
+    }
 
-	template <typename TValue, typename TFile> inline
-	unsigned readBucket(PageBucket<TValue> &b, int pageNo, size_t pageSize, size_t dataSize, TFile &file) 
-	{
+    template <typename TValue, typename TFile> inline
+    unsigned readBucket(PageBucket<TValue> &b, int pageNo, size_t pageSize, size_t dataSize, TFile &file)
+    {
 //IOREV _nodoc_
-		typedef typename Position<TFile>::Type TPos;
+        typedef typename Position<TFile>::Type TPos;
         size_t readSize = _min(dataSize - b.pageOfs, (size_t)(b.end - b.begin));
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "readBucket:  " << ::std::hex << b.begin;
-			::std::cerr << " from page " << ::std::dec << pageNo << " at " << (TPos)pageNo * (TPos)pageSize + b.pageOfs;
-			::std::cerr << " size " << readSize << ::std::endl;
-		#endif
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "readBucket:  " << std::hex << b.begin;
+            std::cerr << " from page " << std::dec << pageNo << " at " << (TPos)pageNo * (TPos)pageSize + b.pageOfs;
+            std::cerr << " size " << readSize << std::endl;
+        #endif
         if (readSize && readAt(file, b.begin, readSize, (TPos)pageNo * (TPos)pageSize + b.pageOfs)) {
             b.pageOfs += readSize;
             b.cur = b.begin;
@@ -827,36 +905,36 @@ struct MMap;
             return readSize;
         } else
             return 0;
-	}
+    }
 
-	template <typename TValue, typename TFile> inline
-	bool writeBucket(PageBucket<TValue> &b, int pageNo, size_t pageSize, TFile &file) 
-	{
+    template <typename TValue, typename TFile> inline
+    bool writeBucket(PageBucket<TValue> &b, int pageNo, size_t pageSize, TFile &file)
+    {
 //IOREV _nodoc_
-		typedef typename Position<TFile>::Type TPos;
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "writeBucket: " << ::std::hex << b.begin;
-			::std::cerr << " from page " << ::std::dec << pageNo << " at " << (TPos)pageNo * (TPos)pageSize + b.pageOfs;
-			::std::cerr << " size " << b.cur - b.begin << ::std::endl;
-		#endif
+        typedef typename Position<TFile>::Type TPos;
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "writeBucket: " << std::hex << b.begin;
+            std::cerr << " from page " << std::dec << pageNo << " at " << (TPos)pageNo * (TPos)pageSize + b.pageOfs;
+            std::cerr << " size " << b.cur - b.begin << std::endl;
+        #endif
         if ((b.cur == b.begin) || writeAt(file, b.begin, b.cur - b.begin, (TPos)pageNo * (TPos)pageSize + b.pageOfs)) {
             b.pageOfs += b.cur - b.begin;
             b.cur = b.begin;
             return true;
         } else
             return false;
-	}
+    }
 
-	template <typename TValue, typename TPageOfs, typename TFile> inline
-	bool writeBucket(Buffer<TValue, PageFrame<TFile, Dynamic> > &pf, TPageOfs &pageOfs, TFile &file)
-	{
+    template <typename TValue, typename TPageOfs, typename TFile> inline
+    bool writeBucket(Buffer<TValue, PageFrame<TFile, Dynamic> > &pf, TPageOfs &pageOfs, TFile &file)
+    {
 //IOREV _nodoc_
-		typedef typename Position<TFile>::Type TPos;
-		#ifdef SEQAN_VVERBOSE
-			::std::cerr << "writeBucket: " << ::std::hex << pf.begin;
-			::std::cerr << " from page " << ::std::dec << pf.pageNo << " at " << (TPos)pf.pageNo * (TPos)capacity(pf) + pageOfs;
-			::std::cerr << " size " << length(pf) << ::std::endl;
-		#endif
+        typedef typename Position<TFile>::Type TPos;
+        #ifdef SEQAN_VVERBOSE
+            std::cerr << "writeBucket: " << std::hex << pf.begin;
+            std::cerr << " from page " << std::dec << pf.pageNo << " at " << (TPos)pf.pageNo * (TPos)capacity(pf) + pageOfs;
+            std::cerr << " size " << length(pf) << std::endl;
+        #endif
         if (pf.end == pf.begin) return true;
         if (asyncWriteAt(file, pf.begin, length(pf), (TPos)pf.pageNo * (TPos)capacity(pf) + pageOfs, pf.request)) {
             pf.status = WRITING;
@@ -864,547 +942,512 @@ struct MMap;
             return true;
         } else
             return false;
-	}
+    }
 
 
-	//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
 
-    template <typename TPageFrame>
-    struct PageChain 
-	{
+template <typename TPageFrame>
+struct PageChain
+{
 //IOREV _nodoc_
-        TPageFrame          *first, *last;
-        unsigned            frames, maxFrames;
-        
-        PageChain(unsigned _maxFrames = 0):
-            first(NULL),
-            last(NULL),
-            frames(0),
-            maxFrames(_maxFrames)
-        {
-            for(unsigned i = 0; i < _maxFrames; ++i)
-                pushBack();
-        }
-        
-        ~PageChain()
-        {
-            while (!empty())
-                delete &popFront();
-        }
-        
-        inline TPageFrame & operator[](int k) 
-		{
-            TPageFrame *p = first;
-            for (; k > 0; --k)
-                p = p->next;
-            return *p;
-        }
-        
-        inline TPageFrame const & operator[](int k) const 
-		{
-            TPageFrame *p = first;
-            for (; k > 0; --k)
-                p = p->next;
-            return *p;
-        }
+    TPageFrame          *first, *last;
+    unsigned            frames, maxFrames;
+
+    PageChain(unsigned _maxFrames = 0):
+        first(NULL),
+        last(NULL),
+        frames(0),
+        maxFrames(_maxFrames)
+    {
+        for(unsigned i = 0; i < _maxFrames; ++i)
+            pushBack(*this, *(new TPageFrame()));
+    }
 
-        inline TPageFrame * getReadyPage() 
-		{
-            if (empty())
-                return &pushBack();
-
-            if (frames < maxFrames)
-            {
-                bool inProgress;
-                bool waitResult = waitFor(*first, 0, inProgress);
-                
-                // TODO(weese): Throw an I/O exception
-                if (!waitResult)
-                    SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(*first), strerror(errno));
-
-                if (!inProgress)
-                    return &pushBack();
-            }
+    ~PageChain()
+    {
+        while (!empty(*this))
+            delete &popFront(*this);
+    }
 
-            bool waitResult = waitFor(*first);
+    inline TPageFrame & operator[](int k)
+    {
+        TPageFrame *p = first;
+        for (; k > 0; --k)
+            p = p->next;
+        return *p;
+    }
+
+    inline TPageFrame const & operator[](int k) const
+    {
+        TPageFrame *p = first;
+        for (; k > 0; --k)
+            p = p->next;
+        return *p;
+    }
+
+    inline TPageFrame * getReadyPage()
+    {
+        if (empty(*this))
+            return &pushBack(*this, *(new TPageFrame()));
+
+        if (frames < maxFrames)
+        {
+            bool inProgress;
+            bool waitResult = waitFor(*first, 0, inProgress);
 
             // TODO(weese): Throw an I/O exception
             if (!waitResult)
-                SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(*first), strerror(errno));
+                SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(first->status), strerror(errno));
 
-            return &firstToEnd();
+            if (!inProgress)
+                return &pushBack(*this, *(new TPageFrame()));
         }
 
-        template <typename TFile>
-        inline void cancelAll(TFile &file) 
-		{
-            TPageFrame *p = first;
-            for (; p != NULL; p = p->next)
-                cancel(*p, file);
-        }
+        bool waitResult = waitFor(*first);
 
-        inline void waitForAll() 
-		{
-            for (TPageFrame *p = first; p != NULL; p = p->next)
-            {
-                bool waitResult = waitFor(*p);
+        // TODO(weese): Throw an I/O exception
+        if (!waitResult)
+            SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(first->status), strerror(errno));
 
-                // TODO(weese): Throw an I/O exception
-                if (!waitResult)
-                    SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(*p), strerror(errno));
-            }
-        }
+        return &firstToEnd(*this);
+    }
 
-    public:
+    template <typename TFile>
+    inline void cancelAll(TFile &file)
+    {
+        TPageFrame *p = first;
+        for (; p != NULL; p = p->next)
+            cancel(*p, file);
+    }
 
-        inline bool
-        empty()
+    inline void waitForAll()
+    {
+        for (TPageFrame *p = first; p != NULL; p = p->next)
         {
-            return first == NULL;
-        }
+            bool waitResult = waitFor(*p);
 
-        inline unsigned
-        size()
-        {
-            return frames;
+            // TODO(weese): Throw an I/O exception
+            if (!waitResult)
+                SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(p->status), strerror(errno));
         }
+    }
+};
 
-        inline TPageFrame &
-        front()
-        {
-            return *first;
-        }
+//////////////////////////////////////////////////////////////////////////////
+// meta-function interface
+
+template <typename TPageFrame>
+struct Value< PageChain<TPageFrame> >
+{
+    typedef TPageFrame Type;
+};
+
+template <typename TPageFrame>
+struct Size< PageChain<TPageFrame> >
+{
+    typedef unsigned Type;
+};
+
+template <typename TPageFrame>
+struct Iterator< PageChain<TPageFrame> >
+{
+    typedef TPageFrame *Type;
+};
+
+template <typename TPageFrame>
+struct Iterator< PageChain<TPageFrame> const >
+{
+    typedef TPageFrame const *Type;
+};
+
+
+template <typename TPageFrame>
+inline bool
+empty(PageChain<TPageFrame> &pageChain)
+{
+    return pageChain.first == NULL;
+}
 
-        inline TPageFrame &
-        back()
-        {
-            return *last;
-        }
+template <typename TPageFrame>
+inline unsigned
+length(PageChain<TPageFrame> &pageChain)
+{
+    return pageChain.frames;
+}
 
-        //
-        // append a PageFrame at the end of this chain
-        //
-        inline TPageFrame &
-        pushBack(TPageFrame &pageFrame)
-		{
-            if (last != NULL)
-                last->next = &pageFrame;
-            else
-                first = &pageFrame;
-            
-            last = &pageFrame;
-            pageFrame.next = NULL;
-            ++frames;
+template <typename TPageFrame>
+inline TPageFrame &
+front(PageChain<TPageFrame> &pageChain)
+{
+    return *pageChain.first;
+}
 
-            return pageFrame;
-        }
+template <typename TPageFrame>
+inline TPageFrame &
+back(PageChain<TPageFrame> &pageChain)
+{
+    return *pageChain.last;
+}
 
-        //
-        // append a *new* PageFrame at the end of this chain
-        //
-        inline TPageFrame &
-        pushBack()
-		{
-            TPageFrame *pageFrame = new TPageFrame();
-            return pushBack(*pageFrame);
-        }
+//
+// append a PageFrame at the end of this chain
+//
+template <typename TPageFrame>
+inline TPageFrame &
+pushBack(PageChain<TPageFrame> &pageChain, TPageFrame &pageFrame)
+{
+    if (pageChain.last != NULL)
+        pageChain.last->next = &pageFrame;
+    else
+        pageChain.first = &pageFrame;
+
+    pageChain.last = &pageFrame;
+    pageFrame.next = NULL;
+    ++pageChain.frames;
+
+    return pageFrame;
+}
 
-        //
-        // remove a PageFrame from this chain
-        //
-        inline TPageFrame &
-        erase(TPageFrame & pageFrame)
+//
+// remove a PageFrame from this chain
+//
+template <typename TPageFrame>
+inline TPageFrame &
+erase(PageChain<TPageFrame> &pageChain, TPageFrame & pageFrame)
+{
+    TPageFrame *prev = NULL;
+    TPageFrame *p;
+
+    for (p = pageChain.first; p != NULL; p = p->next)
+    {
+        if (p == &pageFrame)
         {
-            TPageFrame *prev = NULL;
-            TPageFrame *p;
-
-            for (p = first; p != NULL; p = p->next)
-            {
-                if (p == &pageFrame)
-                {
-                    // found it, now detach from neighbors
-                    if (prev == NULL)
-                        first = p->next;
-                    else
-                        prev->next = p->next;
+            // found it, now detach from neighbors
+            if (prev == NULL)
+                pageChain.first = p->next;
+            else
+                prev->next = p->next;
 
-                    p->next = NULL;
+            p->next = NULL;
 
-                    // were we the last?
-                    if (last == p)
-                        last = prev;
+            // were we the last?
+            if (pageChain.last == p)
+                pageChain.last = prev;
 
-                    --frames;
-                    break;
-                }
-                prev = p;
-            }
-            // we assert that the page has been found
-            SEQAN_ASSERT(p != NULL);
-            return pageFrame;
+            --pageChain.frames;
+            break;
         }
+        prev = p;
+    }
+    // we assert that the page has been found
+    SEQAN_ASSERT(p != NULL);
+    return pageFrame;
+}
 
-        inline TPageFrame &
-        popFront()
-        {
-            // equivalent to erase(front())
-            TPageFrame *p = first;
-            if (p != NULL)
-            {
-                first = p->next;
-                p->next = NULL;
-                if (first == NULL)
-                    last = NULL;
-                --frames;
-            }
-            else
-                SEQAN_FAIL("pop() was called on an empty PageChain.");
-            return *p;
-        }
+template <typename TPageFrame>
+inline TPageFrame &
+popFront(PageChain<TPageFrame> &pageChain)
+{
+    // equivalent to erase(front())
+    TPageFrame *p = pageChain.first;
+    if (p != NULL)
+    {
+        pageChain.first = p->next;
+        p->next = NULL;
+        if (pageChain.first == NULL)
+            pageChain.last = NULL;
+        --pageChain.frames;
+    }
+    else
+        SEQAN_FAIL("pop() was called on an empty PageChain.");
+    return *p;
+}
 
-        //
-        // move first page to the end of this chain
-        // return the moved page
-        //
-        inline TPageFrame &
-        firstToEnd()
-		{
-            // equivalent to pushBack(popFront())
-            last->next = first;
-            last = first;
-            first = first->next;
-            last->next = NULL;
-            return *last;
-        }
+//
+// move first page to the end of this chain
+// return the moved page
+//
+template <typename TPageFrame>
+inline TPageFrame &
+firstToEnd(PageChain<TPageFrame> &pageChain)
+{
+    // equivalent to pushBack(popFront())
+    pageChain.last->next = pageChain.first;
+    pageChain.last = pageChain.first;
+    pageChain.first = pageChain.first->next;
+    pageChain.last->next = NULL;
+    return *pageChain.last;
+}
 
 
-// call pop(chain.front())
 
-//        inline TPageFrame &
-//        popFront()
-//		{
-//            TPageFrame *p = first;
-//            if (p) {
-//                first = first->next;
-//                if (!first) last = NULL;
-//                --frames;
-//                delete p;
-//            }
-//            return p;
-//        }
-    };
 
-	//////////////////////////////////////////////////////////////////////////////
-	// meta-function interface
-
-    template <typename TPageFrame>    
-	struct Value< PageChain<TPageFrame> > 
-	{
-//IOREV
-		typedef TPageFrame Type;
-	};
-
-    template <typename TPageFrame>    
-	struct Size< PageChain<TPageFrame> > 
-	{
-//IOREV
-		typedef unsigned Type;
-	};
-
-    template <typename TPageFrame>    
-	struct Iterator< PageChain<TPageFrame> > 
-	{
-//IOREV
-		typedef TPageFrame *Type;
-	};
-
-    template <typename TPageFrame>    
-	struct Iterator< PageChain<TPageFrame> const > 
-	{
-//IOREV
-		typedef TPageFrame const *Type;
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// page container with lru mechanism
-	// the lru strategy uses different priorities
-	// the page with the least priority is used first
-	// 0..random access pages
-	// 1..forward iterator pages
-	// 2..quasi permanent pages
+    //////////////////////////////////////////////////////////////////////////////
+    // page container with lru mechanism
+    // the lru strategy uses different priorities
+    // the page with the least priority is used first
+    // 0..random access pages
+    // 1..forward iterator pages
+    // 2..quasi permanent pages
 
     template < typename TPageFrame,
                unsigned FRAMES,
                unsigned PRIORITY_LEVELS = TPageFrame::PERMANENT_LEVEL + 1 >
-	struct PageContainer
-	{
+    struct PageContainer
+    {
 //IOREV _nodoc_ has some in-code comments
-		typedef String<TPageFrame>					TPages;
-		typedef typename Position<TPages>::Type		TPos;
+        typedef String<TPageFrame>                    TPages;
+        typedef typename Position<TPages>::Type        TPos;
 
-		enum { PriorityLevels = PRIORITY_LEVELS };
+        enum { PriorityLevels = PRIORITY_LEVELS };
 
-		TPages			pages;
-        PageLRUList		*lruList;
+        TPages            pages;
+        PageLRUList        *lruList;
 
-		PageContainer()
-		{
-			lruList = new PageLRUList[PRIORITY_LEVELS];
-			resize(pages, FRAMES, Exact());
+        PageContainer()
+        {
+            lruList = new PageLRUList[PRIORITY_LEVELS];
+            resize(pages, FRAMES, Exact());
             for(TPos i = 0; i < FRAMES; ++i)
-			    pages[i].lruEntry = lruList[0].insert(lruList[0].end(), i);
+                pages[i].lruEntry = lruList[0].insert(lruList[0].end(), i);
         }
 
-		~PageContainer()
-		{
-			delete[] lruList;
-		}
+        ~PageContainer()
+        {
+            delete[] lruList;
+        }
 
         inline TPageFrame       & operator[](TPos i)       { return pages[i]; }
         inline TPageFrame const & operator[](TPos i) const { return pages[i]; }
 
-		inline void push_back() 
-		{
-			TPos last = length(pages);
-			resize(pages, last + 1);
-			pages[last].lruEntry = lruList[0].insert(lruList[0].end(), last);
-		}
+        inline void push_back()
+        {
+            TPos last = length(pages);
+            resize(pages, last + 1);
+            pages[last].lruEntry = lruList[0].insert(lruList[0].end(), last);
+        }
 
-		inline void erase(int frameNo) 
-		{
-			lruList[pages[frameNo].priority].erase(pages[frameNo].lruEntry);
+        inline void erase(int frameNo)
+        {
+            lruList[pages[frameNo].priority].erase(pages[frameNo].lruEntry);
             seqan::erase(pages, frameNo);
-		}
+        }
 
-        inline void rename(int frameNo) 
-		{
+        inline void rename(int frameNo)
+        {
             *(pages[frameNo].lruEntry) = frameNo;
         }
 
-		inline void pop_back() 
-		{
-			lruList[back(pages).priority].erase(back(pages).lruEntry);
-			seqan::erase(pages, endPosition(pages) - 1);
-		}
+        inline void pop_back()
+        {
+            lruList[back(pages).priority].erase(back(pages).lruEntry);
+            seqan::erase(pages, endPosition(pages) - 1);
+        }
 
         inline void _print()
         {
             std::cout << std::endl;
             for(TPos i = 0; i < FRAMES; ++i)
-			    std::cout << pages[i] << std::endl;
+                std::cout << pages[i] << std::endl;
         }
 
-		//////////////////////////////////////////////////////////////////////////////
-		// lru strategy interface
-
-		inline void upgrade(const TPageFrame &pf) 
-		{
-			lruList[pf.priority].splice(lruList[pf.priority].begin(), lruList[pf.priority], pf.lruEntry);
-			pf.lruEntry = lruList[pf.priority].begin();
-		}
-
-		inline void downgrade(const TPageFrame &pf) 
-		{
-			lruList[pf.priority].splice(lruList[pf.priority].end(), lruList[pf.priority], pf.lruEntry);
-			pf.lruEntry = lruList[pf.priority].end();
-			--pf.lruEntry;
-		}
-
-		inline void upgrade(TPageFrame &pf, int newPriority) 
-		{
-			lruList[newPriority].splice(lruList[newPriority].begin(), lruList[pf.priority], pf.lruEntry);
-			pf.lruEntry = lruList[newPriority].begin();
-			pf.priority = static_cast<typename TPageFrame::Priority> (newPriority);
-		}
-
-		inline void downgrade(TPageFrame &pf, int newPriority) 
-		{
-			lruList[newPriority].splice(lruList[newPriority].end(), lruList[pf.priority], pf.lruEntry);
-			pf.lruEntry = lruList[newPriority].end();
-			--pf.lruEntry;
-			pf.priority = static_cast<typename TPageFrame::Priority> (newPriority);
-		}
-
-		inline void _dump() 
-		{
-			for(unsigned i = 0; i < PRIORITY_LEVELS; ++i) {
-                ::std::cerr << "|";
+        //////////////////////////////////////////////////////////////////////////////
+        // lru strategy interface
+
+        inline void upgrade(const TPageFrame &pf)
+        {
+            lruList[pf.priority].splice(lruList[pf.priority].begin(), lruList[pf.priority], pf.lruEntry);
+            pf.lruEntry = lruList[pf.priority].begin();
+        }
+
+        inline void downgrade(const TPageFrame &pf)
+        {
+            lruList[pf.priority].splice(lruList[pf.priority].end(), lruList[pf.priority], pf.lruEntry);
+            pf.lruEntry = lruList[pf.priority].end();
+            --pf.lruEntry;
+        }
+
+        inline void upgrade(TPageFrame &pf, int newPriority)
+        {
+            lruList[newPriority].splice(lruList[newPriority].begin(), lruList[pf.priority], pf.lruEntry);
+            pf.lruEntry = lruList[newPriority].begin();
+            pf.priority = static_cast<typename TPageFrame::Priority> (newPriority);
+        }
+
+        inline void downgrade(TPageFrame &pf, int newPriority)
+        {
+            lruList[newPriority].splice(lruList[newPriority].end(), lruList[pf.priority], pf.lruEntry);
+            pf.lruEntry = lruList[newPriority].end();
+            --pf.lruEntry;
+            pf.priority = static_cast<typename TPageFrame::Priority> (newPriority);
+        }
+
+        inline void _dump()
+        {
+            for(unsigned i = 0; i < PRIORITY_LEVELS; ++i) {
+                std::cerr << "|";
                 PageLRUList::const_iterator I = lruList[i].end();
                 PageLRUList::const_iterator first = lruList[i].begin();
-				while (I != first) {
-					--I;
+                while (I != first) {
+                    --I;
                     TPageFrame &pf = pages[*I];
-                    ::std::cerr << pf.pageNo;
-                    if (pf.dirty) ::std::cerr << "*";
-                    else          ::std::cerr << " ";
-                    if (pf.status == READY) ::std::cerr << "  ";
-                    else                    ::std::cerr << ". ";
-				};
+                    std::cerr << pf.pageNo;
+                    if (pf.dirty) std::cerr << "*";
+                    else          std::cerr << " ";
+                    if (pf.status == READY) std::cerr << "  ";
+                    else                    std::cerr << ". ";
+                };
             }
-            ::std::cerr << ::std::endl;
-		}
+            std::cerr << std::endl;
+        }
 
         // Function is a functor which is called with a PageFrame object,
         // that is dirty or not READY (in an IO transfer)
-		template <class Function>
-		inline int mru(Function Func_, unsigned maxLevel = PRIORITY_LEVELS - 1) 
-		{
-			for(unsigned i = 0; i <= maxLevel; ++i) {
+        template <class Function>
+        inline int mru(Function Func_, unsigned maxLevel = PRIORITY_LEVELS - 1)
+        {
+            for(unsigned i = 0; i <= maxLevel; ++i) {
                 PageLRUList::const_iterator I = lruList[i].end();
                 PageLRUList::const_iterator first = lruList[i].begin();
-				while (I != first) {
-					--I;
-					TPageFrame& pf = pages[*I];
-					if (pf.status == READY && !pf.dirty)
-						return *I;
-					else
-						if (Func_(pf)) return *I;
-				};
+                while (I != first) {
+                    --I;
+                    TPageFrame& pf = pages[*I];
+                    if (pf.status == READY && !pf.dirty)
+                        return *I;
+                    else
+                        if (Func_(pf)) return *I;
+                };
             }
-			#ifdef SEQAN_VVERBOSE
-				::std::cerr << "ALL PAGES DIRTY Or IN USE (try to use const iterators) :-(" << ::std::endl;
-			#endif
-			return -1;
-		}
-
-		inline int mruDirty() 
-		{
+            #ifdef SEQAN_VVERBOSE
+                std::cerr << "ALL PAGES DIRTY OR IN USE (try to use const iterators) :-(" << std::endl;
+            #endif
+            return -1;
+        }
+
+        inline int mruDirty()
+        {
             for(unsigned i = 0; i < PRIORITY_LEVELS; ++i)
                 if (!lruList[i].empty())
                     return lruList[i].back();
-			return -1;
-		}
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// meta-function interface
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	struct Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> > 
-	{
-//IOREV
-		typedef String<TPageFrame> Type;
-	};
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	struct Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const > 
-	{
-//IOREV
-		typedef String<TPageFrame> const Type;
-	};
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	struct Value< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> > 
-	{
-//IOREV
-		typedef TPageFrame Type;
-	};
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	struct Size< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >:
-		public Size< typename Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >::Type> {};
-//IOREV
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	struct Position< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >:
-		public Position< typename Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >::Type> {};
-//IOREV
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	struct Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >:
-		public Iterator< typename Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >::Type> {};
-//IOREV
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	struct Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const >:
-		public Iterator< typename Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const>::Type> {};
-//IOREV
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// global interface
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS, typename TExpand>
-	inline void reserve(
-		PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> &pageCont,
-		unsigned Count_,
-		Tag<TExpand> expand)
-	{
-//IOREV
-		reserve(pageCont.pages, Count_, expand);
-	}
+            return -1;
+        }
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // meta-function interface
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    struct Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >
+    {
+        typedef String<TPageFrame> Type;
+    };
 
     template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	inline void resize(
-		PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> &pageCont, 
-		unsigned Count_) 
-	{
-//IOREV
-		unsigned Size_ = length(pageCont.pages);
-		if (Size_ < Count_) {
-			reserve(pageCont.pages, Count_);
+    struct Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const >
+    {
+        typedef String<TPageFrame> const Type;
+    };
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    struct Value< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >
+    {
+        typedef TPageFrame Type;
+    };
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    struct Size< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >:
+        public Size< typename Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >::Type> {};
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    struct Position< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >:
+        public Position< typename Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >::Type> {};
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    struct Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >:
+        public Iterator< typename Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >::Type> {};
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    struct Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const >:
+        public Iterator< typename Host< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const>::Type> {};
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // global interface
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS, typename TExpand>
+    inline void reserve(
+        PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> &pageCont,
+        unsigned Count_,
+        Tag<TExpand> expand)
+    {
+        reserve(pageCont.pages, Count_, expand);
+    }
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    inline void resize(
+        PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> &pageCont,
+        unsigned Count_)
+    {
+        unsigned Size_ = length(pageCont.pages);
+        if (Size_ < Count_) {
+            reserve(pageCont.pages, Count_);
             for(unsigned i = Size_; i < Count_; ++i)
                 pageCont.push_back();
-		} else 
-			if (Size_ > Count_)
-				for(unsigned i = Count_; i < Size_; ++i)
-					pageCont.pop_back();
-	}
+        } else
+            if (Size_ > Count_)
+                for(unsigned i = Count_; i < Size_; ++i)
+                    pageCont.pop_back();
+    }
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    inline typename Size< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >::Type
+    length(PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const &pageCont)
+    {
+        return length(pageCont.pages);
+    }
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    inline typename Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS>, Standard >::Type
+    begin(
+        PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> &pageCont,
+        Standard const)
+    {
+        return begin(pageCont.pages, Standard());
+    }
 
     template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	inline typename Size< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> >::Type
-	length(PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const &pageCont) 
-	{
-//IOREV
-		return length(pageCont.pages);
-	}
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	inline typename Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS>, Standard >::Type
-	begin(
-		PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> &pageCont,
-		Standard const) 
-	{
-//IOREV
-		return begin(pageCont.pages, Standard());
-	}
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	inline typename Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const, Standard >::Type
-	begin(
-		PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const &pageCont,
-		Standard const) 
-	{
-//IOREV
-		return begin(pageCont.pages, Standard());
-	}
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	inline typename Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS>, Standard >::Type
-	end(
-		PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> &pageCont,
-		Standard const) 
-	{
-//IOREV
-		return end(pageCont.pages, Standard());
-	}
-
-	template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
-	inline typename Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const, Standard >::Type
-	end(
-		PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const &pageCont,
-		Standard const) 
-	{
-//IOREV
-		return end(pageCont.pages, Standard());
-	}
-
-
-
-
-	//////////////////////////////////////////////////////////////////////////////
+    inline typename Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const, Standard >::Type
+    begin(
+        PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const &pageCont,
+        Standard const)
+    {
+        return begin(pageCont.pages, Standard());
+    }
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    inline typename Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS>, Standard >::Type
+    end(
+        PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> &pageCont,
+        Standard const)
+    {
+        return end(pageCont.pages, Standard());
+    }
+
+    template <typename TPageFrame, unsigned FRAMES, unsigned PRIORITY_LEVELS>
+    inline typename Iterator< PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const, Standard >::Type
+    end(
+        PageContainer<TPageFrame, FRAMES, PRIORITY_LEVELS> const &pageCont,
+        Standard const)
+    {
+        return end(pageCont.pages, Standard());
+    }
+
+
+
+
+    //////////////////////////////////////////////////////////////////////////////
 
     template <typename TValue, typename TSize, typename T, class Function>
     inline bool equiDistantDistribution(
@@ -1413,15 +1456,15 @@ struct MMap;
         Function const &Func_)
     {
 //IOREV _nodoc_
-//        ::std::cerr << "equiDistantDistribution: size=" << _size << "\tpageSize=" << _pageSize << ::std::endl;
+//        std::cerr << "equiDistantDistribution: size=" << _size << "\tpageSize=" << _pageSize << std::endl;
         unsigned _pages         = enclosingBlocks(_size, _pageSize);
         if (!_pages) {
-			::std::cerr << "equiDistantDistribution: _pages is null!" << ::std::endl;
+            std::cerr << "equiDistantDistribution: _pages is null!" << std::endl;
             return false;
         }
 
         if (_bufferSize < _pages) {
-			::std::cerr << "equiDistantDistribution: clusterBufferSize is too small -> raised to " << _pages << ::std::endl;
+            std::cerr << "equiDistantDistribution: clusterBufferSize is too small -> raised to " << _pages << std::endl;
             _bufferSize = _pages;
         }
 
@@ -1436,7 +1479,7 @@ struct MMap;
         pb.begin = _clusterBuffer.begin;
 
         size_t clusterSize = _bufferSize / pages;
-//        ::std::cerr << "equiDistantDistribution: pages=" << _pages << "\tclusterSize=" << clusterSize << ::std::endl;
+//        std::cerr << "equiDistantDistribution: pages=" << _pages << "\tclusterSize=" << clusterSize << std::endl;
         if (lastPageSize > 0 && clusterSize >= lastPageSize) {
             // last page bucket would get more memory than page would need
             // --> exclude from equi-size distribution
@@ -1456,7 +1499,7 @@ struct MMap;
                 }
                 pb.cur = pb.begin;
                 pb.pageOfs = 0;
-			    Func_(pb);
+                Func_(pb);
                 pb.begin = pb.end;
             }
         }
@@ -1465,7 +1508,7 @@ struct MMap;
             pb.end = pb.begin + lastPageSize;
             pb.cur = pb.begin;
             pb.pageOfs = 0;
-			Func_(pb);
+            Func_(pb);
         }
 
         return true;
@@ -1479,14 +1522,14 @@ struct MMap;
     {
 //IOREV _nodoc_
         unsigned _pages         = enclosingBlocks(_size, _pageSize);
-//        ::std::cerr << "equiDistantAlignedDistribution: size=" << _size << "\tpageSize=" << _pageSize << ::std::endl;
+//        std::cerr << "equiDistantAlignedDistribution: size=" << _size << "\tpageSize=" << _pageSize << std::endl;
         if (!_pages) {
-			::std::cerr << "equiDistantAlignedDistribution: _pages is null!" << ::std::endl;
+            std::cerr << "equiDistantAlignedDistribution: _pages is null!" << std::endl;
             return 0;
         }
 
         if (_bufferSize < _pages) {
-			::std::cerr << "equiDistantAlignedDistribution: clusterBufferSize is too small -> raised to " << _pages << ::std::endl;
+            std::cerr << "equiDistantAlignedDistribution: clusterBufferSize is too small -> raised to " << _pages << std::endl;
             _bufferSize = _pages;
         }
 
@@ -1501,38 +1544,38 @@ struct MMap;
         if (clusterSize - aclusterSize > aligning / 2)
             aclusterSize += aligning;
 
-//        ::std::cerr << "equiDistantAlignedDistribution: pages=" << _pages << "\tclusterSize=" << aclusterSize << ::std::endl;
-
-		if (aclusterSize != 0) {
-
-			if (lastPageSize > 0 && aclusterSize > lastPageSize) {
-				// last page bucket would get more memory than page would need
-				// --> exclude from equi-size distribution
-				--pages;
-				allocPage(_clusterBuffer, aclusterSize * pages + lastPageSize, me);
-			} else
-				allocPage(_clusterBuffer, aclusterSize * pages, me);
-
-			PageBucketExtended<TValue> pb;
-			pb.begin = _clusterBuffer.begin;
-
-			if (pages) {
-				for(unsigned i = 0; i < pages; ++i) {
-					pb.end = pb.begin + aclusterSize;
-					pb.cur = pb.begin;
-					pb.pageOfs = 0;
-					Func_(pb);
-					pb.begin = pb.end;
-				}
-			}
-
-			if (pages < _pages) {
-				pb.end = pb.begin + lastPageSize;
-				pb.cur = pb.begin;
-				pb.pageOfs = 0;
-				Func_(pb);
-			}
-		}
+//        std::cerr << "equiDistantAlignedDistribution: pages=" << _pages << "\tclusterSize=" << aclusterSize << std::endl;
+
+        if (aclusterSize != 0) {
+
+            if (lastPageSize > 0 && aclusterSize > lastPageSize) {
+                // last page bucket would get more memory than page would need
+                // --> exclude from equi-size distribution
+                --pages;
+                allocPage(_clusterBuffer, aclusterSize * pages + lastPageSize, me);
+            } else
+                allocPage(_clusterBuffer, aclusterSize * pages, me);
+
+            PageBucketExtended<TValue> pb;
+            pb.begin = _clusterBuffer.begin;
+
+            if (pages) {
+                for(unsigned i = 0; i < pages; ++i) {
+                    pb.end = pb.begin + aclusterSize;
+                    pb.cur = pb.begin;
+                    pb.pageOfs = 0;
+                    Func_(pb);
+                    pb.begin = pb.end;
+                }
+            }
+
+            if (pages < _pages) {
+                pb.end = pb.begin + lastPageSize;
+                pb.cur = pb.begin;
+                pb.pageOfs = 0;
+                Func_(pb);
+            }
+        }
 
         return aclusterSize;
     }
diff --git a/seqan/file/stream.h b/seqan/file/stream.h
deleted file mode 100644
index a5fc0b1..0000000
--- a/seqan/file/stream.h
+++ /dev/null
@@ -1,496 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_STREAM_H
-#define SEQAN_HEADER_STREAM_H
-
-#include <iosfwd>
-
-/* IOREV
- * _doc_
- * _tested_
- * 
- * well documented
- * tested by tests/file and probably used by a lot of stuff
- * c++ equivalent to  cstream.h
- */
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Adaption."std::iostream":
-..summary:Standard library stream classes.
-*/
-
-//////////////////////////////////////////////////////////////////////////////
-	
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_ios<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ios<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_streambuf<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_streambuf<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_istream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_istream<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_ostream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ostream<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_iostream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_iostream<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_stringbuf<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_stringbuf<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_istringstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_istringstream<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_ostringstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ostringstream<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_stringstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_stringstream<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_filebuf<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_filebuf<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_ifstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ifstream<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_ofstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ofstream<TValue, TTraits>::pos_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Position< ::std::basic_fstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_fstream<TValue, TTraits>::pos_type Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-	
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_ios<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ios<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_streambuf<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_streambuf<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_istream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_istream<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_ostream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ostream<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_iostream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_iostream<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_stringbuf<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_stringbuf<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_istringstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_istringstream<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_ostringstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ostringstream<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_stringstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_stringstream<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_filebuf<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_filebuf<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_ifstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ifstream<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_ofstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_ofstream<TValue, TTraits>::char_type Type;
-};
-template <typename TValue, typename TTraits>
-struct Value< ::std::basic_fstream<TValue, TTraits> >
-{
-//IOREV
-	typedef typename ::std::basic_fstream<TValue, TTraits>::char_type Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**.interal.IsTellAndSeekStream_:
-..summary:Determines whether stream supports tell and seek functions.
-..cat:Metafunction
-*/
-
-template <typename T>
-struct IsTellAndSeekStream_
-{
-//IOREV can't I tell and seek e.g. in an ofstream?
-	typedef False Type;
-};
-
-
-template <typename TValue, typename TTraits>
-struct IsTellAndSeekStream_< ::std::basic_ifstream<TValue, TTraits> >
-{
-//IOREV
-	typedef True Type;
-};
-template <typename TValue, typename TTraits>
-struct IsTellAndSeekStream_< ::std::basic_fstream<TValue, TTraits> >
-{
-//IOREV
-	typedef True Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamEOF:
-..summary:Test stream for being in eof or error state.
-..cat:Streams
-..signature:_streamEOF(stream)
-..param.stream:A stream object.
-...type:Adaption."std::iostream"
-..returns:$true$, if stream is at end of file or was set to error state, $false$ otherwise.
-*/
-template <typename TValue, typename TTraits>
-inline bool 
-_streamEOF(::std::basic_istream<TValue, TTraits> const & me)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	// Andreas missed the fact that eof() of a stream is true after reading the eof character
-	// So reading the last character eof() is false, reading beyond eof() is true
-	// To fix that we use peek() to get the next character and compare it with the eof character
-	typedef ::std::basic_istream<TValue, TTraits> TStream;
-	return me.fail() || const_cast<TStream &>(me).peek() == TTraits::eof();
-}
-
-//////////////////////////////////////////////////////////////////////////////
- 
-/**
-.Internal._streamRead:
-..summary:Read some characters from stream into a buffer.
-..cat:Streams
-..signature:_streamRead(target, stream, limit)
-..param.target:A buffer that is filled.
-..param.stream:An input stream.
-...type:Adaption."std::iostream"
-..param.limit:The maximal number of characters that is read from $stream$.
-..returns:The number of characters read from $stream$.
-*/
-template <typename TValue, typename TTraits>
-inline ::std::streamsize 
-_streamRead(TValue * target,
-			::std::basic_istream<TValue, TTraits> & source,
-			::std::streamsize limit)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	source.read(target, limit);
-	return source.gcount();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamGet:
-..summary:Read one character from stream.
-..cat:Streams
-..signature:_streamGet(stream)
-..param.stream:An input stream.
-...type:Adaption."std::iostream"
-..returns:The character read.
-*/
-
-template <typename TValue, typename TTraits>
-inline TValue 
-_streamGet(::std::basic_istream<TValue, TTraits> & source)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return source.get();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamPeek:
-..summary:Return the next character to be read from stream.
-..cat:Streams
-..signature:_streamPeek(stream)
-..param.stream:An input stream.
-...type:Adaption."std::iostream"
-..returns:The character to be read.
-*/
-
-template <typename TValue, typename TTraits>
-inline TValue 
-_streamPeek(::std::basic_istream<TValue, TTraits> & source)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return source.peek();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamUnget:
-..summary:Put the last read character back into stream.
-..cat:Streams
-..signature:_streamUnget(stream)
-..param.stream:An input stream.
-...type:Adaption."std::iostream"
-*/
-
-template <typename TValue, typename TTraits>
-inline void
-_streamUnget(::std::basic_istream<TValue, TTraits> & source)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	source.unget();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamPut:
-..summary:Writes one character to stream.
-..cat:Streams
-..signature:_streamPut(stream, character)
-..param.stream:An input stream.
-...type:Adaption."std::iostream"
-..param.character:A character that is written to $stream$.
-*/
-
-template <typename TValue, typename TTraits, typename TChar>
-inline void
-_streamPut(::std::basic_ostream<TValue, TTraits> & target,
-		   TChar character)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	target.put(convert<TValue>(character));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamTellG:
-..cat:Streams
-..summary:Gets current position of input stream.
-..signature:_streamTellG(stream)
-..param.stream:An input stream.
-...type:Adaption."std::iostream"
-..returns:The current position in $stream$.
-*/
-template <typename TValue, typename TTraits>
-inline typename Position< ::std::basic_istream<TValue, TTraits> >::Type
-_streamTellG(::std::basic_istream<TValue, TTraits> & me)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return me.tellg();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Internal._streamTellP:
-..cat:Streams
-..summary:Gets current position of output stream.
-..signature:_streamTellP(stream)
-..param.stream:An ouput stream.
-...type:Adaption."std::iostream"
-..returns:The current position in $stream$.
-..see:Internal._streamTellG
-*/
-template <typename TValue, typename TTraits>
-inline typename Position< ::std::basic_ostream<TValue, TTraits> >::Type
-_streamTellP(::std::basic_ostream<TValue, TTraits> & me)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	return me.tellp();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamSeekG:
-..summary:Moves input stream to a position.
-..cat:Streams
-..signature:_streamSeekG(stream, position)
-..param.stream:An input stream.
-...type:Adaption."std::iostream"
-..param.position:A position within the stream.
-...remarks:Use @Function._streamTellG@ to get valid stream positions.
-..see:Internal._streamTellG
-*/
-template <typename TValue, typename TTraits>
-inline void
-_streamSeekG(::std::basic_istream<TValue, TTraits> & me,
-	 typename Position< ::std::basic_istream<TValue, TTraits> >::Type pos)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	me.clear();
-	me.seekg(pos);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamSeekP:
-..summary:Moves output stream to a position.
-..cat:Streams
-..signature:_streamSeekP(stream, position)
-..param.stream:An output stream.
-...type:Adaption."std::iostream"
-..param.position:A position within the stream.
-...remarks:Use @Function._streamTellP@ to get valid stream positions.
-..see:Internal._streamTellP
-..see:Internal._streamSeekG
-*/
-template <typename TValue, typename TTraits>
-inline void
-_streamSeekP(::std::basic_ostream<TValue, TTraits> & me,
-	 typename Position< ::std::basic_ostream<TValue, TTraits> >::Type pos)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	me.clear();
-	me.seekp(pos);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamSeek2G:
-..summary:Moves input stream position relative to current position.
-..cat:Streams
-..signature:_streamSeek2G(stream, offset)
-..param.stream:An input stream.
-...type:Adaption."std::iostream"
-..param.offset:The amout the position is changed.
-...remarks:If this value is negative.
-..see:Internal._streamSeekG
-*/
-template <typename TValue, typename TTraits>
-inline void
-_streamSeek2G(::std::basic_istream<TValue, TTraits> & me,
-	 int off)
-{
-//IOREV
-SEQAN_CHECKPOINT
-	me.seekg(off, ::std::ios_base::cur);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/stream_algorithms.h b/seqan/file/stream_algorithms.h
deleted file mode 100644
index bdaa3b2..0000000
--- a/seqan/file/stream_algorithms.h
+++ /dev/null
@@ -1,254 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_STREAM_ALGORITHMS_H
-#define SEQAN_HEADER_STREAM_ALGORITHMS_H
-
-// These includes will go away when remainders of file module and the new stream module are merged
-#include <seqan/stream/concept_stream.h>
-#include <seqan/stream/adapt_fstream.h>
-#include <seqan/stream/adapt_iostream.h>
-#include <seqan/stream/adapt_cstdio.h>
-#include <seqan/stream/adapt_sstream.h>
-
-/* IOREV
- * _tested_
- * _doc_
- *
- *
- * mostly documented (doc for some functions missing)
- * used ubiquitously, but possibly not all specializations
- * 
- * functions seem to be agnostic of FileType (stream.h or cstream.)
- * it is not clear if both are actually tested (but shouldn't matter
- * if underlying routines work correctly)
- */
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
-
-// Manual Forward
-template <typename TTarget, typename TSource>
-inline void _streamWrite(TTarget & target, TSource const & source);
-
-/**
-.Internal._streamPutInt:
-..summary:Converts an integer to a character and writes it to stream.
-..cat:Streams
-..signature:_streamPutInt(stream, number [, format_string])
-..param.target:An output stream.
-...type:Adaption."std::iostream"
-..param.number:A number that is written to $stream$.
-*/
-template <typename TStream>
-inline void
-_streamPutInt(TStream & target,
-			  int number, 
-			  char const * format_string)
-{
-//IOREV _doc_
-SEQAN_CHECKPOINT
-	char str[BitsPerValue<int>::VALUE];
-	sprintf(str, format_string, number);
-	_streamWrite(target, str);
-}
-template <typename TStream>
-inline void
-_streamPutInt(TStream & target,
-			  int number)
-{
-//IOREV _doc_
-SEQAN_CHECKPOINT
-	_streamPutInt(target, number, "%d");
-}
-
-/**
-.Internal._streamPutFloat:
-..summary:Converts a float to a character and writes it to stream.
-..cat:Streams
-..signature:_streamPutFloat(stream, number [, format_string])
-..param.target:An output stream.
-...type:Adaption."std::iostream"
-..param.number:A number that is written to $stream$.
-*/
-template <typename TStream>
-inline void
-_streamPutFloat(TStream & target,
-			  double number, 
-			  char const * format_string)
-{
-//IOREV _doc_
-    SEQAN_CHECKPOINT;
-	char str[BitsPerValue<float>::VALUE];
-	sprintf(str, format_string, number);
-	_streamWrite(target, str);
-}
-template <typename TStream>
-inline void
-_streamPutFloat(TStream & target,
-				double number)
-{
-//IOREV _doc_
-    SEQAN_CHECKPOINT;
-	_streamPutFloat(target, number, "%f");
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TTarget, typename T1, typename T2, typename TPack>
-inline void
-_streamWrite(TTarget & target,
-			 Pair<T1, T2, TPack> const & source)
-{
-//IOREV _nodoc_
-SEQAN_CHECKPOINT
-	_streamWrite(target, getValueI1(source));
-	_streamWrite(target, getValueI2(source));
-}
-
-template <typename TTarget, typename T1, typename T2, typename T3, typename TPack>
-inline void
-_streamWrite(TTarget & target,
-			 Triple<T1, T2, T3, TPack> const & source)
-{
-//IOREV _nodoc_
-SEQAN_CHECKPOINT
-	_streamWrite(target, getValueI1(source));
-	_streamWrite(target, getValueI2(source));
-	_streamWrite(target, getValueI3(source));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-
-/**
-.Internal._streamWrite:
-..summary:Writes a sequence to stream.
-..cat:Streams
-..signature:_streamWrite(stream, sequence)
-..param.stream:An input stream.
-..param.sequence:A sequence that is written to $stream$.
-*/
-
-template <typename TTarget, typename TSource>
-inline void
-_streamWriteSeq(TTarget & target,
-				TSource const & source,
-				False const)
-{
-//IOREV  _nodoc_
-	streamPut(target, source);
-}
-
-//____________________________________________________________________________
-
-template <typename TTarget, typename TSource>
-inline void
-_streamWriteSeq(TTarget & target,
-				TSource const & source,
-				True const)
-{
-//IOREV _nodoc_
-SEQAN_CHECKPOINT
-	typename Iterator<TSource const, Standard>::Type it = begin(source, Standard());
-	typename Iterator<TSource const, Standard>::Type it_end = end(source, Standard());
-
-	for (; it != it_end; ++it)
-	{
-		typename GetValue<TSource const>::Type val_ = getValue(it);
-		_streamWrite(target, val_);
-	}
-}
-
-template <typename TTarget, typename TSourceValue>
-inline void
-_streamWriteSeq(TTarget & target,
-			    TSourceValue const * source,
-				True const)
-{
-//IOREV _nodoc_
-SEQAN_CHECKPOINT
-
-	for (; !atEnd(source); ++source)
-	{
-		_streamWrite(target, *source);
-	}
-}
-
-//____________________________________________________________________________
-
-template <typename TTarget, typename TSource>
-inline void
-_streamWrite(TTarget & target,
-			 TSource const & source)
-{
-//IOREV _doc_
-SEQAN_CHECKPOINT
-	_streamWriteSeq(target, source, typename IsSequence<TSource const>::Type());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Internal._streamWriteRange:
-..summary:Writes a range to stream.
-..cat:Streams
-..signature:_streamWriteRange(stream, begin_iterator, end_iterator)
-..param.stream:An input stream.
-..param.sequence:A sequence that is written to $stream$.
-*/
-
-template <typename TTarget, typename TIterator>
-inline void
-_streamWriteRange(TTarget & target,
-				  TIterator begin_,
-				  TIterator end_)
-{
-//IOREV _doc_
-SEQAN_CHECKPOINT
-	for (; begin_ != end_; ++begin_)
-	{
-		streamPut(target, *begin_);
-	}
-}
-
-
-	
-
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/file/string_external.h b/seqan/file/string_external.h
index 7d973e3..375c3a9 100644
--- a/seqan/file/string_external.h
+++ b/seqan/file/string_external.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -59,20 +59,21 @@ namespace SEQAN_NAMESPACE_MAIN
  * @headerfile <seqan/file.h>
  * @brief Standard configuration for the @link ExternalString @endlink.
  *
- * @signature template <[typename TFile[, unsigned PAGE_SIZE[, unsigned FRAMES]]>
+ * @signature template <[typename TFile[, unsigned PAGESIZE[, unsigned FRAMES]]>
  *            struct ExternalConfig;
  *
  * @tparam TFile     The @link File @endlink type to use.  Default: <tt>File&lt;&gt;</tt>.
- * @tparam PAGE_SIZE The number of values in one page.  This should be a power of 2 to speed up transfer and
+ * @tparam PAGESIZE The number of values in one page.  This should be a power of 2 to speed up transfer and
  *                   calculations.  Default: 2<sup>20</sup>.
  * @tparam FRAMES    The number of pages that should reside in internal memory.  To enable prefetching and automatic
  *                   swap-out, <tt>frames</tt> should be greater than 1.  Default: 2.
  *
- * @section Remarks
+ * When using this configuration, the Size type of the ExternalString is <tt>unsigned</tt>.  Thus, with this configuration at
+ * most 4.294.967.296 values can be stored in an ExternalString on a 32 bit system.
  *
- * When using this configuration, the Size type of the ExternalString is <tt>unsigned</tt>.  Thus, with this configuration at most 4.294.967.296 values can be stored in an ExternalString on a 32 bit system.
+ * For a larger size type use @link ExternalConfigLarge @endlink.
  *
- * For a larger size type use ExternalConfigLarge.
+ * @see ExternalConfigLarge
  */
 
 /*!
@@ -80,15 +81,17 @@ namespace SEQAN_NAMESPACE_MAIN
  * @headerfile <seqan/file.h>
  * @brief Large size type configuration for the @link ExternalString @endlink.
  *
- * @signature template <[typename TFile[, unsigned PAGE_SIZE[, unsigned FRAMES]]>
+ * @signature template <[typename TFile[, unsigned PAGESIZE[, unsigned FRAMES]]>
  *            struct ExternalConfigLarge;
  *
  * @tparam TFile     The @link File @endlink type to use.  Default: <tt>File&lt;&gt;</tt>.
- * @tparam PAGE_SIZE The number of values in one page.  This should be a power of 2 to speed up transfer and
+ * @tparam PAGESIZE The number of values in one page.  This should be a power of 2 to speed up transfer and
  *                   calculations.  Default: 2<sup>20</sup>.
  * @tparam FRAMES    The number of pages that should reside in internal memory.  To enable prefetching and automatic
  *                   swap-out, <tt>frames</tt> should be greater than 1.  Default: 2.
  *
+ * @see ExternalConfig
+ *
  * @section Remarks
  *
  * When using this configuration ,th eSize type o fthe ExternalString is Size type of <tt>TFile</tt>.  Normally, this is
@@ -103,12 +106,12 @@ namespace SEQAN_NAMESPACE_MAIN
  * @headerfile <seqan/file.h>
  * @brief Arbitrary size type configuration for @link ExternalString @endlink.
  *
- * @signature template <typename TSize[, typename TFile[, unsigned PAGE_SIZE[, unsigned FRAMEs]]]>
+ * @signature template <typename TSize[, typename TFile[, unsigned PAGESIZE[, unsigned FRAMEs]]]>
  *            class ExternalConfigSize;
  *
  * @tparam TSize The size type of the ExternalString.
  * @tparam TFile Type of file the ExternalString will be based on.  Defaults to <tt>File&lt;&gt;</tt>.
- * @tparam PAGE_SIZE The number of values in one page.  This should be a power of 2 to speed up transfer and
+ * @tparam PAGESIZE The number of values in one page.  This should be a power of 2 to speed up transfer and
  *                   calculations.  Default: 2<sup>20</sup>.
  * @tparam FRAMES    The number of pages that should reside in internal memory.  To enable prefetching and automatic
  *                   swap-out, <tt>frames</tt> should be greater than 1.  Default: 2.
@@ -116,6 +119,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
 /*!
  * @class ExternalString External String
+ * @extends String
  * @headerfile <seqan/file.h>
  * @brief String that is stored in external memory.
  *
@@ -126,8 +130,6 @@ namespace SEQAN_NAMESPACE_MAIN
  * @tparam TConfig A structure to confgure the external string.  Defaults to <tt>ExternalConfigLarge&lt;&gt;.  See
  *                 ExternalConfig, ExternalConfigLarge, and ExternalConfigSize.
  *
- * @section Remarks
- *
  * The External String enables to access sequences larger than the available internal memory (RAM) by using external
  * memory (e.g. Hard disk, Network storage, ...) via a File object.  Sequences of nearly arbitrary size can be accessed
  * even larger than the logically addressable memory, i.e. they can in particular contain more than 2^32 elements on a
@@ -140,70 +142,22 @@ namespace SEQAN_NAMESPACE_MAIN
  * pages that certainly won't be accessed any more in the iteration process.
  *
  * The String is implemented like a virtual memory manager.  It divides its character sequence into pages of a fixed
- * length (e.g. 1MB) and maintains a page table with information for each page (e.g. resides in memory or was swapped
+ * length (e.g. 4MB) and maintains a page table with information for each page (e.g. resides in memory or was swapped
  * out, is dirty and needs to be saved, ...).  Besides the page table the String also contains a size-limited list of
  * page frames.  A page frame is reserved internal memory for a page.  When accessing values of a page that is stored in
  * external memory, the page is loaded to a page frame first.  In case that there is no page frame free, another page is
  * swapped out before to free a page frame.
  */
 
-/**
-.Spec.External String:
-..cat:Strings
-..general:Class.String
-..summary:String that is stored in external memory.
-..signature:String<TValue, External<> >
-..signature:String<TValue, External<TConfig> >
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..param.TConfig:A structure to configure the external string.
-...type:Tag.ExternalConfig
-...type:Tag.ExternalConfigLarge
-...type:Tag.ExternalConfigSize
-...default:@Tag.ExternalConfigLarge@
-..remarks:The External String enables to access sequences larger than the available internal memory (RAM)
-by using external memory (e.g. Hard disk, Network storage, ...) via a @Class.File@ object.
-Sequences of nearly arbitrary size can be accessed even larger than the logically addressable memory,
-i.e. they can in particular contain more than 2^32 elements on a 32bit system (see Tag.ExternalConfigLarge).
-See the @Memfunc.External String#String@ constructor for more details.
-..remarks:This String also supports fast appending and removing of values at the end (see @Spec.Block String@, @Function.appendValue@)
-..remarks:The External String implements a LRU mechanism to swap out pages.
-The External String's @Metafunction.Iterator@ detects a forward or backward iteration and asynchronously prefetches pages that
-certainly will be accessed and automatically swaps out pages that certainly won't be accessed any more in the iteration
-process.
-..remarks:The String is implemented like a virtual memory manager.
-It divides its character sequence into pages of a fixed length (e.g. 1MB) and maintains a
-page table with information for each page (e.g. resides in memory or was swapped out, is dirty and needs to be saved, ...).
-Besides the page table the String also contains a size-limited list of page frames. A page frame is reserved internal
-memory for a page. When accessing values of a page that is stored in external memory, the page is loaded to a page frame
-first. In case that there is no page frame free, another page is swapped out before to free a page frame.
-..include:seqan/file.h
-*/
+#ifndef _EXTERNAL_STRING_DEFAULT_PAGE_SIZE
+#define _EXTERNAL_STRING_DEFAULT_PAGE_SIZE 4 * 1024 * 1024 // 4MTypes per default
+#endif
 
-/**
-.Tag.ExternalConfig:
-..cat:Strings
-..summary:Standard configuration for the @Spec.External String@.
-..signature:String<TValue, External< ExternalConfig<> > >
-..signature:String<TValue, External< ExternalConfig<TFile[, pageSize[, frames]]> > >
-..param.TFile:Type of file the External String will be based on.
-...type:Class.File
-..param.pageSize:A positive integer that specifies the number of values in one page.
-...remarks:This should be a power of 2, to speed up transfer and calculations.
-...default:2^20
-..param.frames:A positive integer that specifies the maximum number of pages that should reside in internal memory.
-...remarks:To enable prefetching and automatic swap-out, $frames$ should be greater than 1.
-...default:2
-..remarks:When using this configuration, the @Metafunction.Size@ type of the @Spec.External String@ is $unsigned int$.
-Thus, with this configuration at most 4.294.967.296 values can be stored in an @Spec.External String@ on a 32bit system.
-For a larger size type, use @Tag.ExternalConfigLarge@.
-..include:seqan/file.h
-*/
     // standard external string
     // size is uint32
-    template < typename TFile_ = File<>,				// default file type
-               unsigned PAGESIZE_ = 4 * 1024 * 1024,	// 1MTypes per default
-			   unsigned FRAMES_ = 2 >					// simultanous frames
+    template < typename TFile_ = File<>,                                // default file type
+               unsigned PAGESIZE_ = _EXTERNAL_STRING_DEFAULT_PAGE_SIZE,
+               unsigned FRAMES_ = 2 >                                   // simultanous frames
     struct ExternalConfig {
 //IOREV _bug_ doc says default page size is 2^20, but it is 2^22
         typedef TFile_ TFile;
@@ -212,35 +166,15 @@ For a larger size type, use @Tag.ExternalConfigLarge@.
         enum { FRAMES = FRAMES_ };
     };
 
-/**
-.Tag.ExternalConfigLarge:
-..cat:Strings
-..summary:Large size type configuration for the @Spec.External String@.
-..signature:String<TValue, External< ExternalConfigLarge<> > >
-..signature:String<TValue, External< ExternalConfigLarge<TFile[, pageSize[, frames]]> > >
-..param.TFile:Type of file the External String will be based on.
-...type:Class.File
-..param.pageSize:A positive integer that specifies the number of values in one page.
-...remarks:This should be a power of 2, to speed up transfer and calculations.
-...default:2^20
-..param.frames:A positive integer that specifies the maximum number of pages that should reside in internal memory.
-...remarks:To enable prefetching and automatic swap-out, $frames$ should be greater than 1.
-...default:2
-..remarks:When using this configuration, the @Metafunction.Size@ type of the @Spec.External String@ is the @Metafunction.Size@
-type of $TFile$. Normally this is a 64bit integer. For a smaller size type, use @Tag.ExternalConfig@.
-..remarks:Some data structures store size type values (e.g. suffix arrays in @Class.Index@). To save memory,
-you should think of using @Tag.ExternalConfig@.
-..include:seqan/file.h
-*/
     // the same as ExternalConfig
     // but size type is size type of TFile_ (i.e. uint64)
     //
     // ATTENTION:
-    // pipes use the size type 
+    // pipes use the size type
     // uint64 blows up your suffix arrays, lcp-tables, ...
-    template < typename TFile_ = File<>,				// default file type
-               unsigned PAGESIZE_ = 4 * 1024 * 1024,	// 1MTypes per default
-			   unsigned FRAMES_ = 2 >					// simultanous frames
+    template < typename TFile_ = File<>,                                // default file type
+               unsigned PAGESIZE_ = _EXTERNAL_STRING_DEFAULT_PAGE_SIZE,
+               unsigned FRAMES_ = 2 >                                   // simultanous frames
     struct ExternalConfigLarge {
 //IOREV contains warning in code comments, need to investigate
         typedef TFile_ TFile;
@@ -249,35 +183,14 @@ you should think of using @Tag.ExternalConfig@.
         enum { FRAMES = FRAMES_ };
     };
 
-/**
-.Tag.ExternalConfigSize:
-..cat:Strings
-..summary:Arbitrary size type configuration for the @Spec.External String@.
-..signature:String<TValue, External< ExternalConfigSize< TSize > > >
-..signature:String<TValue, External< ExternalConfigSize< TSize, TFile[, pageSize[, frames]]> > >
-..param.TSize:Size type the External String will return via @Metafunction.Size@.
-..param.TFile:Type of file the External String will be based on.
-...type:Class.File
-..param.pageSize:A positive integer that specifies the number of values in one page.
-...remarks:This should be a power of 2, to speed up transfer and calculations.
-...default:2^20
-..param.frames:A positive integer that specifies the maximum number of pages that should reside in internal memory.
-...remarks:To enable prefetching and automatic swap-out, $frames$ should be greater than 1.
-...default:2
-..remarks:When using this configuration, the @Metafunction.Size@ type of the @Spec.External String@ is the @Metafunction.Size@
-type of $TFile$. Normally this is a 64bit integer. For a smaller size type, use @Tag.ExternalConfig@.
-..remarks:Some data structures store size type values (e.g. suffix arrays in @Class.Index@). To save memory,
-you should think of using @Tag.ExternalConfig@.
-..include:seqan/file.h
-*/
     // custom size type
     template < typename TSize_,
-		       typename TFile_ = File<>,				// default file type
-               unsigned PAGESIZE_ = 1 * 1024 * 1024,	// 1MTypes per default
-			   unsigned FRAMES_ = 2 >					// simultanous frames
+               typename TFile_ = File<>,                                // default file type
+               unsigned PAGESIZE_ = _EXTERNAL_STRING_DEFAULT_PAGE_SIZE,
+               unsigned FRAMES_ = 2 >                                   // simultanous frames
     struct ExternalConfigSize {
 //IOREV
-		typedef TSize_ TSize;
+        typedef TSize_ TSize;
         typedef TFile_ TFile;
         enum { PAGESIZE = PAGESIZE_ };
         enum { FRAMES = FRAMES_ };
@@ -289,287 +202,292 @@ you should think of using @Tag.ExternalConfig@.
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// random External String iterator
-	template < typename TExtString >
-	struct ExtStringIterator
-	{
+    // random External String iterator
+    template < typename TExtString >
+    struct ExtStringIterator
+    {
 //IOREV
-		typedef ExtStringIterator						TIterator;
-        typedef ExtStringIterator						TStdIterator;
+        typedef ExtStringIterator                        TIterator;
+        typedef ExtStringIterator                        TStdIterator;
 
-        typedef typename Value<TExtString>::Type		TValue;
-		typedef typename Size<TExtString>::Type			TSize;
-		typedef typename Difference<TExtString>::Type	TDifference;
-		typedef typename TExtString::TVolatilePtr		TVolatilePtr;
+        typedef typename Value<TExtString>::Type        TValue;
+        typedef typename Size<TExtString>::Type            TSize;
+        typedef typename Difference<TExtString>::Type    TDifference;
+        typedef typename TExtString::TVolatilePtr        TVolatilePtr;
 
         enum { PAGESIZE = TExtString::PAGESIZE };
 
-		TSize		offset;
-		TExtString	*extString;
+        TSize        offset;
+        TExtString    *extString;
 
 
-	    ExtStringIterator():
-			offset(0),
-			extString(NULL) {}
+        ExtStringIterator():
+            offset(0),
+            extString(NULL) {}
 
-	    explicit ExtStringIterator(TExtString *_extString, TSize _offset):
-			extString(_extString),
-			offset(_offset) {}
+        explicit ExtStringIterator(TExtString *_extString, TSize _offset):
+            extString(_extString),
+            offset(_offset) {}
 
-		//////////////////////////////////////////////////////////////////////////////
-		// iterator conversion interface
+        //////////////////////////////////////////////////////////////////////////////
+        // iterator conversion interface
 
         ExtStringIterator(const TStdIterator &I):
-			offset(I.offset),
-			extString(I.extString) {}
+            offset(I.offset),
+            extString(I.extString) {}
 
-		//////////////////////////////////////////////////////////////////////////////
-		// iterator arithmetic
+        //////////////////////////////////////////////////////////////////////////////
+        // iterator arithmetic
 
         inline TDifference operator- (const TIterator &I) const {
-			return offset - I.offset;
-		}
-		
-		inline TIterator operator- (TDifference delta) const {
-			return TIterator(extString, offset - delta);
-		}
-		
-		inline TIterator& operator-= (TDifference delta) const {
-			offset -= delta;
-			return *this;
-		}
-		
-		inline TIterator operator+ (TDifference delta) const {
-			return TIterator(extString, offset + delta);
-		}
-		
-		inline TIterator& operator+= (TDifference delta) const {
-			offset += delta;
-			return *this;
-		}
-		
-		inline TValue & operator* () const {
-			return (*extString)[offset];
-		}
-    
-/*		inline TValue const & operator* () const {
-			return (*extString)[offset];
-		}
-*/  
-		inline TIterator& operator++ () {
-			++offset; return *this;
-		}
-
-		inline TIterator operator++ (int) {
-			TIterator before = *this;
-			++offset; return before;
-		}
-
-		inline TIterator& operator-- () {
-			--offset; return *this;
-		}
-
-		inline TIterator operator-- (int) {
-			TIterator before = *this;
-			--offset; return before;
-		}
-
-		inline bool operator== (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return offset == I.offset;
-		}
-
-		inline bool operator!= (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return offset != I.offset;
-		}
-
-		inline bool operator< (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return offset < I.offset;
-		}
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// const random External String iterator
-	template < typename TExtString >
-	struct ExtStringConstIterator
-	{
-//IOREV
-		typedef ExtStringConstIterator					TIterator;
-        typedef ExtStringIterator<TExtString>			TStdIterator;
-        typedef ExtStringConstIterator					TStdConstIterator;
-
-        typedef typename Value<TExtString>::Type		TValue;
-		typedef typename Size<TExtString>::Type			TSize;
-		typedef typename Difference<TExtString>::Type	TDifference;
-		typedef typename TExtString::TVolatilePtr	    TVolatilePtr;
+            return offset - I.offset;
+        }
+
+        inline TIterator operator- (TDifference delta) const {
+            return TIterator(extString, offset - delta);
+        }
+
+        inline TIterator& operator-= (TDifference delta) const {
+            offset -= delta;
+            return *this;
+        }
+
+        inline TIterator operator+ (TDifference delta) const {
+            return TIterator(extString, offset + delta);
+        }
+
+        inline TIterator& operator+= (TDifference delta) const {
+            offset += delta;
+            return *this;
+        }
+
+        inline TValue & operator* () const {
+            return (*extString)[offset];
+        }
+
+/*        inline TValue const & operator* () const {
+            return (*extString)[offset];
+        }
+*/
+        inline TIterator& operator++ () {
+            ++offset; return *this;
+        }
+
+        inline TIterator operator++ (int) {
+            TIterator before = *this;
+            ++offset; return before;
+        }
+
+        inline TIterator& operator-- () {
+            --offset; return *this;
+        }
+
+        inline TIterator operator-- (int) {
+            TIterator before = *this;
+            --offset; return before;
+        }
+
+        inline bool operator== (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return offset == I.offset;
+        }
+
+        inline bool operator!= (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return offset != I.offset;
+        }
+
+        inline bool operator< (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return offset < I.offset;
+        }
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // const random External String iterator
+    template < typename TExtString >
+    struct ExtStringConstIterator
+    {
+//IOREV
+        typedef ExtStringConstIterator                    TIterator;
+        typedef ExtStringIterator<TExtString>            TStdIterator;
+        typedef ExtStringConstIterator                    TStdConstIterator;
+
+        typedef typename Value<TExtString>::Type        TValue;
+        typedef typename Size<TExtString>::Type            TSize;
+        typedef typename Difference<TExtString>::Type    TDifference;
+        typedef typename TExtString::TVolatilePtr        TVolatilePtr;
 
         enum { PAGESIZE = TExtString::PAGESIZE };
 
-		TSize		offset;
-		TExtString	*extString;
-		
-		
-	    ExtStringConstIterator():
-			offset(0),
-			extString(NULL) {}
-
-	    explicit ExtStringConstIterator(TExtString *_extString, TSize _offset):
-			extString(_extString),
-			offset(_offset) {}
-
-		//////////////////////////////////////////////////////////////////////////////
-		// iterator conversion interface
-
-		ExtStringConstIterator(const TStdIterator &I):
-			offset(I.offset),
-			extString(I.extString) {}
-
-		ExtStringConstIterator(const TStdConstIterator &I):
-			offset(I.offset),
-			extString(I.extString) {}
-
-		//////////////////////////////////////////////////////////////////////////////
-		// iterator arithmetic
-
-		inline TDifference operator- (const TIterator &I) const {
-			return offset - I.offset;
-		}
-		
-		inline TIterator operator- (TDifference delta) const {
-			return TIterator(extString, offset - delta);
-		}
-		
-		inline TIterator& operator-= (TDifference delta) const {
-			offset -= delta;
-			return *this;
-		}
-		
-		inline TIterator operator+ (TDifference delta) const {
-			return TIterator(extString, offset + delta);
-		}
-		
-		inline TIterator& operator+= (TDifference delta) const {
-			offset += delta;
-			return *this;
-		}
-		
-		inline TValue const & operator* () const {
-			return (*extString)[offset];
-		}
-    
-		inline TIterator& operator++ () {
-			++offset; return *this;
-		}
-
-		inline TIterator operator++ (int) {
-			TIterator before = *this;
-			++offset; return before;
-		}
-
-		inline TIterator& operator-- () {
-			--offset; return *this;
-		}
-
-		inline TIterator operator-- (int) {
-			TIterator before = *this;
-			--offset; return before;
-		}
-
-		inline bool operator== (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return offset == I.offset;
-		}
-
-		inline bool operator!= (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return offset != I.offset;
-		}
-
-		inline bool operator< (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return offset < I.offset;
-		}		
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// forward External String iterator
-	template < typename TExtString >
+        TSize        offset;
+        TExtString    *extString;
+
+
+        ExtStringConstIterator():
+            offset(0),
+            extString(NULL) {}
+
+        explicit ExtStringConstIterator(TExtString *_extString, TSize _offset):
+            extString(_extString),
+            offset(_offset) {}
+
+        //////////////////////////////////////////////////////////////////////////////
+        // iterator conversion interface
+
+        ExtStringConstIterator(const TStdIterator &I):
+            offset(I.offset),
+            extString(I.extString) {}
+
+        ExtStringConstIterator(const TStdConstIterator &I):
+            offset(I.offset),
+            extString(I.extString) {}
+
+        //////////////////////////////////////////////////////////////////////////////
+        // iterator arithmetic
+
+        inline TDifference operator- (const TIterator &I) const {
+            return offset - I.offset;
+        }
+
+        inline TIterator operator- (TDifference delta) const {
+            return TIterator(extString, offset - delta);
+        }
+
+        inline TIterator& operator-= (TDifference delta) const {
+            offset -= delta;
+            return *this;
+        }
+
+        inline TIterator operator+ (TDifference delta) const {
+            return TIterator(extString, offset + delta);
+        }
+
+        inline TIterator& operator+= (TDifference delta) const {
+            offset += delta;
+            return *this;
+        }
+
+        inline TValue const & operator* () const {
+            return (*extString)[offset];
+        }
+
+        inline TIterator& operator++ () {
+            ++offset; return *this;
+        }
+
+        inline TIterator operator++ (int) {
+            TIterator before = *this;
+            ++offset; return before;
+        }
+
+        inline TIterator& operator-- () {
+            --offset; return *this;
+        }
+
+        inline TIterator operator-- (int) {
+            TIterator before = *this;
+            --offset; return before;
+        }
+
+        inline bool operator== (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return offset == I.offset;
+        }
+
+        inline bool operator!= (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return offset != I.offset;
+        }
+
+        inline bool operator< (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return offset < I.offset;
+        }
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // forward External String iterator
+    template < typename TExtString >
     struct ExtStringFwdIterator
-	{
+    {
 //IOREV
-		typedef ExtStringFwdIterator					TIterator;
-        typedef ExtStringIterator<TExtString>			TStdIterator;
-        typedef ExtStringConstIterator<TExtString>		TStdConstIterator;
+        typedef ExtStringFwdIterator                    TIterator;
+        typedef ExtStringIterator<TExtString>            TStdIterator;
+        typedef ExtStringConstIterator<TExtString>        TStdConstIterator;
 
-		typedef typename Value<TExtString>::Type		TValue;
-		typedef typename Size<TExtString>::Type			TSize;
-		typedef typename Difference<TExtString>::Type	TDifference;
-		typedef typename TExtString::TVolatilePtr	    TVolatilePtr;
+        typedef typename Value<TExtString>::Type        TValue;
+        typedef typename Size<TExtString>::Type            TSize;
+        typedef typename Difference<TExtString>::Type    TDifference;
+        typedef typename TExtString::TVolatilePtr        TVolatilePtr;
 
         enum { PAGESIZE = TExtString::PAGESIZE };
 
 
-		TExtString		*extString;
+        TExtString        *extString;
 
         bool            dirty;
-		int     		pageNo;
-		unsigned		pageOfs;
+        int             pageNo;
+        unsigned        pageOfs;
         int             prefetch;   // -n .. prefetch n pages downwards, n .. prefetch n pages upwards, 0 .. disabled
-		TVolatilePtr	begin;
-		
-	    ExtStringFwdIterator():
-			extString(NULL),
-			pageNo(0),
-			pageOfs(0),
+        TVolatilePtr    begin;
+
+        ExtStringFwdIterator():
+            extString(NULL),
+            dirty(true),
+            pageNo(0),
+            pageOfs(0),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		ExtStringFwdIterator(const TIterator &I):
-			extString(I.extString),
-			pageNo(I.pageNo),
-			pageOfs(I.pageOfs),
+        ExtStringFwdIterator(const TIterator &I):
+            extString(I.extString),
+            dirty(true),
+            pageNo(I.pageNo),
+            pageOfs(I.pageOfs),
             prefetch(I.prefetch),
-			begin(NULL) {}
+            begin(NULL) {}
 
-	    explicit ExtStringFwdIterator(TExtString *_extString, TSize _offset):
-			extString(_extString),
-			pageNo(_offset / PAGESIZE),
-			pageOfs(_offset % PAGESIZE),
+        explicit ExtStringFwdIterator(TExtString *_extString, TSize _offset):
+            extString(_extString),
+            dirty(true),
+            pageNo(_offset / PAGESIZE),
+            pageOfs(_offset % PAGESIZE),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		explicit ExtStringFwdIterator(TExtString *_extString, TSize _pageNo, TSize _pageOfs):
-			extString(_extString),
-			pageNo(_pageNo),
-			pageOfs(_pageOfs),
+        explicit ExtStringFwdIterator(TExtString *_extString, TSize _pageNo, TSize _pageOfs):
+            extString(_extString),
+            dirty(true),
+            pageNo(_pageNo),
+            pageOfs(_pageOfs),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		~ExtStringFwdIterator() {
-			invalidate();
-		}
+        ~ExtStringFwdIterator()
+        {
+            invalidate();
+        }
 
-		//////////////////////////////////////////////////////////////////////////////
-		// iterator conversion interface
+        //////////////////////////////////////////////////////////////////////////////
+        // iterator conversion interface
 
-		ExtStringFwdIterator(const TStdIterator &I):
-			extString(I.extString),
-			pageNo(I.offset / PAGESIZE),
+        ExtStringFwdIterator(const TStdIterator &I):
+            extString(I.extString),
+            pageNo(I.offset / PAGESIZE),
             pageOfs(I.offset % PAGESIZE),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		inline TIterator& operator=(TStdIterator const & Right_) {
-			invalidate();
-			pageNo = Right_.offset / PAGESIZE;
-			pageOfs = Right_.offset % PAGESIZE;
+        inline TIterator& operator=(TStdIterator const & Right_) {
+            invalidate();
+            pageNo = Right_.offset / PAGESIZE;
+            pageOfs = Right_.offset % PAGESIZE;
             extString = Right_.extString;
-			return *this;
-		}
+            return *this;
+        }
 
         inline TSize position() const
         {
@@ -584,257 +502,257 @@ you should think of using @Tag.ExternalConfig@.
             return TStdConstIterator(extString, position());
         }
 
-		inline TIterator& operator=(TIterator const & Right_) {
-			invalidate();
-			extString = Right_.extString;
-			pageNo = Right_.pageNo;
-			pageOfs = Right_.pageOfs;
+        inline TIterator& operator=(TIterator const & Right_) {
+            invalidate();
+            extString = Right_.extString;
+            pageNo = Right_.pageNo;
+            pageOfs = Right_.pageOfs;
             prefetch = Right_.prefetch;
-			return *this;
-		}
+            return *this;
+        }
 
-		//////////////////////////////////////////////////////////////////////////////
-		// iterator arithmetic
+        //////////////////////////////////////////////////////////////////////////////
+        // iterator arithmetic
 
-		inline TDifference operator- (const TIterator &I) const
+        inline TDifference operator- (const TIterator &I) const
         {
             return position() - I.position();
-		}
-		
-		inline TIterator operator- (TDifference delta) const {
-			TDifference dPNo  = delta / PAGESIZE;
-			TDifference dPOfs = delta % PAGESIZE;
-			if (pageOfs >= dPOfs)
-				return TIterator(extString, pageNo - dPNo, pageOfs - dPOfs);
-			else
-				return TIterator(extString, pageNo - dPNo - 1, PAGESIZE + pageOfs - dPOfs);
-		}
-		
-		inline TIterator& operator-= (TDifference delta) {
-			TDifference dPNo  = delta / PAGESIZE;
-			TDifference dPOfs = delta % PAGESIZE;
-			if (pageOfs < dPOfs) {
-				++dPNo;
-				pageOfs = PAGESIZE + pageOfs - dPOfs;
-			} else
-				pageOfs -= dPOfs;
-			if (dPNo) invalidate(0);
-			pageNo -= dPNo;
-			return *this;
-		}
-		
-		inline TIterator operator+ (TDifference delta) const {
-			TDifference dPNo  = delta / PAGESIZE;
-			TDifference nPOfs = pageOfs + delta % PAGESIZE;
-			if (nPOfs < PAGESIZE)
-				return TIterator(extString, pageNo + dPNo, nPOfs);
-			else
-				return TIterator(extString, pageNo + dPNo + 1, nPOfs - PAGESIZE);
-		}
-		
-		inline TIterator& operator+= (TDifference delta) {
-			TDifference dPNo  = delta / PAGESIZE;
-			TDifference nPOfs = pageOfs + delta % PAGESIZE;
-			if (nPOfs >= PAGESIZE) {
-				++dPNo;
-				nPOfs -= PAGESIZE;
-			}
-			if (dPNo) invalidate(0);
-			pageNo += dPNo;
-			pageOfs = nPOfs;
-			return *this;
-		}
-		
-		inline void validate() const 
+        }
+
+        inline TIterator operator- (TDifference delta) const {
+            TDifference dPNo  = delta / PAGESIZE;
+            TDifference dPOfs = delta % PAGESIZE;
+            if (static_cast<TDifference>(pageOfs) >= dPOfs)
+                return TIterator(extString, pageNo - dPNo, pageOfs - dPOfs);
+            else
+                return TIterator(extString, pageNo - dPNo - 1, PAGESIZE + pageOfs - dPOfs);
+        }
+
+        inline TIterator& operator-= (TDifference delta) {
+            TDifference dPNo  = delta / PAGESIZE;
+            TDifference dPOfs = delta % PAGESIZE;
+            if (pageOfs < dPOfs) {
+                ++dPNo;
+                pageOfs = PAGESIZE + pageOfs - dPOfs;
+            } else
+                pageOfs -= dPOfs;
+            if (dPNo) invalidate(0);
+            pageNo -= dPNo;
+            return *this;
+        }
+
+        inline TIterator operator+ (TDifference delta) const {
+            TDifference dPNo  = delta / PAGESIZE;
+            TDifference nPOfs = pageOfs + delta % PAGESIZE;
+            if (nPOfs < PAGESIZE)
+                return TIterator(extString, pageNo + dPNo, nPOfs);
+            else
+                return TIterator(extString, pageNo + dPNo + 1, nPOfs - PAGESIZE);
+        }
+
+        inline TIterator& operator+= (TDifference delta) {
+            TDifference dPNo  = delta / PAGESIZE;
+            TDifference nPOfs = pageOfs + delta % PAGESIZE;
+            if (nPOfs >= PAGESIZE) {
+                ++dPNo;
+                nPOfs -= PAGESIZE;
+            }
+            if (dPNo) invalidate(0);
+            pageNo += dPNo;
+            pageOfs = nPOfs;
+            return *this;
+        }
+
+        inline void validate() const
         {
-			typename TExtString::TPageFrame &pf = extString->getSharedPage(pageNo, prefetch);
+            typename TExtString::TPageFrame &pf = extString->getSharedPage(pageNo, prefetch);
             const_cast<TIterator*>(this)->dirty = pf.dirty;
-			const_cast<TIterator*>(this)->begin = pf.begin;
-		}
+            const_cast<TIterator*>(this)->begin = pf.begin;
+        }
 
-        inline void invalidate(int _prefetch = 0) const 
+        inline void invalidate(int _prefetch = 0) const
         {
-            if (begin) 
+            if (begin)
             {
                 const_cast<TIterator*>(this)->begin = NULL;
-				extString->releasePage(pageNo, (prefetch != 0) || (_prefetch != 0));
+                extString->releasePage(pageNo, (prefetch != 0) || (_prefetch != 0));
                 const_cast<TIterator*>(this)->prefetch = _prefetch;
             }
-		}
+        }
 
-		inline TValue & operator* () const 
+        inline TValue & operator* () const
         {
-			if (!begin) validate();
+            if (!begin) validate();
             // synchronize PageFrame dirty flag on dirty false->true change
             if (!dirty) {
                 const_cast<TIterator*>(this)->dirty = true;
-    			extString->getPage(pageNo).dirty = true;
+                extString->getPage(pageNo).dirty = true;
             }
-			return const_cast<TIterator*>(this)->begin[pageOfs];
-		}
-/*    
-		inline TValue const & operator* () const {
-			if (!begin) validate();
-			return begin[pageOfs];
-		}
-*/    
-		inline TIterator& operator++ () {
-			if (++pageOfs == PAGESIZE) {
-				invalidate(1);
-				pageOfs = 0;
-				++pageNo;
-			}
-			return *this;
-		}
-
-		inline TIterator operator++ (int) {
-			TIterator before = *this;
-			if (++pageOfs == PAGESIZE) {
-				invalidate(1);
-				pageOfs = 0;
-				++pageNo;
-			}
-			return before;
-		}
-
-		inline TIterator& operator-- () {
-			if (pageOfs)
-				--pageOfs;
-			else {
-				invalidate(-1);
-				pageOfs = PAGESIZE - 1;
-				--pageNo;
-			}
-			return *this;
-		}
-
-		inline TIterator operator-- (int) {
-			TIterator before = *this;
-			if (pageOfs)
-				--pageOfs;
-			else {
-				invalidate(-1);
-				pageOfs = PAGESIZE - 1;
-				--pageNo;
-			}
-			return before;
-		}
-
-		inline bool operator== (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return pageNo == I.pageNo && pageOfs == I.pageOfs;
-		}
-
-		inline bool operator!= (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return pageNo != I.pageNo || pageOfs != I.pageOfs;
-		}
-
-		inline bool operator< (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return pageNo < I.pageNo || (pageNo == I.pageNo && pageOfs < I.pageOfs);
-		}
+            return const_cast<TIterator*>(this)->begin[pageOfs];
+        }
+/*
+        inline TValue const & operator* () const {
+            if (!begin) validate();
+            return begin[pageOfs];
+        }
+*/
+        inline TIterator& operator++ () {
+            if (++pageOfs == PAGESIZE) {
+                invalidate(1);
+                pageOfs = 0;
+                ++pageNo;
+            }
+            return *this;
+        }
+
+        inline TIterator operator++ (int) {
+            TIterator before = *this;
+            if (++pageOfs == PAGESIZE) {
+                invalidate(1);
+                pageOfs = 0;
+                ++pageNo;
+            }
+            return before;
+        }
+
+        inline TIterator& operator-- () {
+            if (pageOfs)
+                --pageOfs;
+            else {
+                invalidate(-1);
+                pageOfs = PAGESIZE - 1;
+                --pageNo;
+            }
+            return *this;
+        }
+
+        inline TIterator operator-- (int) {
+            TIterator before = *this;
+            if (pageOfs)
+                --pageOfs;
+            else {
+                invalidate(-1);
+                pageOfs = PAGESIZE - 1;
+                --pageNo;
+            }
+            return before;
+        }
+
+        inline bool operator== (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return pageNo == I.pageNo && pageOfs == I.pageOfs;
+        }
+
+        inline bool operator!= (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return pageNo != I.pageNo || pageOfs != I.pageOfs;
+        }
+
+        inline bool operator< (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return pageNo < I.pageNo || (pageNo == I.pageNo && pageOfs < I.pageOfs);
+        }
     };
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// const forward External String iterator
-	template < typename TExtString >
+    //////////////////////////////////////////////////////////////////////////////
+    // const forward External String iterator
+    template < typename TExtString >
     struct ExtStringFwdConstIterator
-	{
-//IOREV _nottested_ 
-		typedef ExtStringFwdConstIterator				TIterator;
-        typedef ExtStringIterator<TExtString>			TStdIterator;
-        typedef ExtStringConstIterator<TExtString>		TStdConstIterator;
-        typedef ExtStringFwdIterator<TExtString>		TFwdIterator;
+    {
+//IOREV _nottested_
+        typedef ExtStringFwdConstIterator                TIterator;
+        typedef ExtStringIterator<TExtString>            TStdIterator;
+        typedef ExtStringConstIterator<TExtString>        TStdConstIterator;
+        typedef ExtStringFwdIterator<TExtString>        TFwdIterator;
+
+        typedef typename Value<TExtString>::Type        TValue;
+        typedef typename Size<TExtString>::Type            TSize;
+        typedef typename Difference<TExtString>::Type    TDifference;
+        typedef typename TExtString::TVolatilePtr        TVolatilePtr;
 
-		typedef typename Value<TExtString>::Type		TValue;
-		typedef typename Size<TExtString>::Type			TSize;
-		typedef typename Difference<TExtString>::Type	TDifference;
-		typedef typename TExtString::TVolatilePtr	    TVolatilePtr;
+        enum { PAGESIZE = TExtString::PAGESIZE };
 
-		enum { PAGESIZE = TExtString::PAGESIZE };
 
-		
-		TExtString		*extString;
+        TExtString        *extString;
 
-		int     		pageNo;
-		unsigned		pageOfs;
+        int             pageNo;
+        unsigned        pageOfs;
         int             prefetch;   // -n .. prefetch n pages downwards, n .. prefetch n pages upwards, 0 .. disabled
-		TVolatilePtr	begin;
-		
+        TVolatilePtr    begin;
+
 
         ExtStringFwdConstIterator():
-			extString(NULL),
-			pageNo(0),
-			pageOfs(0),
+            extString(NULL),
+            pageNo(0),
+            pageOfs(0),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		ExtStringFwdConstIterator(const TIterator &I):
-			extString(I.extString),
-			pageNo(I.pageNo),
-			pageOfs(I.pageOfs),
+        ExtStringFwdConstIterator(const TIterator &I):
+            extString(I.extString),
+            pageNo(I.pageNo),
+            pageOfs(I.pageOfs),
             prefetch(I.prefetch),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		ExtStringFwdConstIterator(const TFwdIterator &I):
-			extString(I.extString),
-			pageNo(I.pageNo),
-			pageOfs(I.pageOfs),
+        ExtStringFwdConstIterator(const TFwdIterator &I):
+            extString(I.extString),
+            pageNo(I.pageNo),
+            pageOfs(I.pageOfs),
             prefetch(I.prefetch),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		~ExtStringFwdConstIterator() {
-			invalidate();
-		}
+        ~ExtStringFwdConstIterator() {
+            invalidate();
+        }
 
-	    ExtStringFwdConstIterator(TExtString *_extString, TSize _offset):
-			extString(_extString),
-			pageNo(_offset / PAGESIZE),
-			pageOfs(_offset % PAGESIZE),
+        ExtStringFwdConstIterator(TExtString *_extString, TSize _offset):
+            extString(_extString),
+            pageNo(_offset / PAGESIZE),
+            pageOfs(_offset % PAGESIZE),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		ExtStringFwdConstIterator(TExtString *_extString, TSize _pageNo, TSize _pageOfs):
-			extString(_extString),
-			pageNo(_pageNo),
-			pageOfs(_pageOfs),
+        ExtStringFwdConstIterator(TExtString *_extString, TSize _pageNo, TSize _pageOfs):
+            extString(_extString),
+            pageNo(_pageNo),
+            pageOfs(_pageOfs),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		//////////////////////////////////////////////////////////////////////////////
-		// iterator conversion interface
+        //////////////////////////////////////////////////////////////////////////////
+        // iterator conversion interface
 
-		ExtStringFwdConstIterator(TStdIterator &I):
-			extString(I.extString),
-			pageNo(I.offset / PAGESIZE),
+        ExtStringFwdConstIterator(TStdIterator &I):
+            extString(I.extString),
+            pageNo(I.offset / PAGESIZE),
             pageOfs(I.offset % PAGESIZE),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
         ExtStringFwdConstIterator(TStdConstIterator const &I):
-			extString(I.extString),
-			pageNo(I.offset / PAGESIZE),
+            extString(I.extString),
+            pageNo(I.offset / PAGESIZE),
             pageOfs(I.offset % PAGESIZE),
             prefetch(0),
-			begin(NULL) {}
+            begin(NULL) {}
 
-		inline TIterator& operator=(TStdIterator const & Right_) {
-			invalidate();
-			pageNo = Right_.offset / PAGESIZE;
-			pageOfs = Right_.offset % PAGESIZE;
+        inline TIterator& operator=(TStdIterator const & Right_) {
+            invalidate();
+            pageNo = Right_.offset / PAGESIZE;
+            pageOfs = Right_.offset % PAGESIZE;
             extString = Right_.extString;
-			return *this;
-		}
+            return *this;
+        }
 
-		inline TIterator& operator=(TStdConstIterator const & Right_) {
-			invalidate();
-			pageNo = Right_.offset / PAGESIZE;
-			pageOfs = Right_.offset % PAGESIZE;
+        inline TIterator& operator=(TStdConstIterator const & Right_) {
+            invalidate();
+            pageNo = Right_.offset / PAGESIZE;
+            pageOfs = Right_.offset % PAGESIZE;
             extString = Right_.extString;
-			return *this;
-		}
+            return *this;
+        }
 
         inline TSize position() const
         {
@@ -845,395 +763,381 @@ you should think of using @Tag.ExternalConfig@.
             return TStdConstIterator(extString, position());
         }
 
-		inline TIterator& operator=(TIterator const & Right_) {
-			invalidate();
-			extString = Right_.extString;
-			pageNo = Right_.pageNo;
-			pageOfs = Right_.pageOfs;
+        inline TIterator& operator=(TIterator const & Right_) {
+            invalidate();
+            extString = Right_.extString;
+            pageNo = Right_.pageNo;
+            pageOfs = Right_.pageOfs;
             prefetch = Right_.prefetch;
-			return *this;
-		}
-
-		inline TIterator& operator=(TFwdIterator const & Right_) {
-			invalidate();
-			extString = Right_.extString;
-			pageNo = Right_.pageNo;
-			pageOfs = Right_.pageOfs;
+            return *this;
+        }
+
+        inline TIterator& operator=(TFwdIterator const & Right_) {
+            invalidate();
+            extString = Right_.extString;
+            pageNo = Right_.pageNo;
+            pageOfs = Right_.pageOfs;
             prefetch = Right_.prefetch;
-			return *this;
-		}
+            return *this;
+        }
 
-		//////////////////////////////////////////////////////////////////////////////
-		// iterator arithmetic
+        //////////////////////////////////////////////////////////////////////////////
+        // iterator arithmetic
 
-		inline TDifference operator- (const TIterator &I) const
+        inline TDifference operator- (const TIterator &I) const
         {
             return position() - I.position();
-		}
-		
-		inline TIterator operator- (TDifference delta) const {
-			TDifference dPNo  = delta / PAGESIZE;
-			TDifference dPOfs = delta % PAGESIZE;
-			if (pageOfs >= dPOfs)
-				return TIterator(extString, pageNo - dPNo, pageOfs - dPOfs);
-			else
-				return TIterator(extString, pageNo - dPNo - 1, PAGESIZE + pageOfs - dPOfs);
-		}
-		
-		inline TIterator& operator-= (TDifference delta) {
-			TDifference dPNo  = delta / PAGESIZE;
-			TDifference dPOfs = delta % PAGESIZE;
-			if (pageOfs < dPOfs) {
-				++dPNo;
-				pageOfs = PAGESIZE + pageOfs - dPOfs;
-			} else
-				pageOfs -= dPOfs;
-			if (dPNo) invalidate(0);
-			pageNo -= dPNo;
-			return *this;
-		}
-
-		inline TIterator operator+ (TDifference delta) const {
-			TDifference dPNo  = delta / PAGESIZE;
-			TDifference nPOfs = pageOfs + delta % PAGESIZE;
-			if (nPOfs < PAGESIZE)
-				return TIterator(extString, pageNo + dPNo, nPOfs);
-			else
-				return TIterator(extString, pageNo + dPNo + 1, nPOfs - PAGESIZE);
-		}
-		
-		inline TIterator& operator+= (TDifference delta) {
-			TDifference dPNo  = delta / PAGESIZE;
-			TDifference nPOfs = pageOfs + delta % PAGESIZE;
-			if (nPOfs >= PAGESIZE) {
-				++dPNo;
-				nPOfs -= PAGESIZE;
-			}
-			if (dPNo) invalidate(0);
-			pageNo += dPNo;
-			pageOfs = nPOfs;
-			return *this;
-		}
-		
-		inline void validate() const {
-			typename TExtString::TPageFrame &pf = extString->getSharedPage(pageNo, prefetch);
-			const_cast<TIterator*>(this)->begin = pf.begin;
-		}
+        }
+
+        inline TIterator operator- (TDifference delta) const {
+            TDifference dPNo  = delta / PAGESIZE;
+            TDifference dPOfs = delta % PAGESIZE;
+            if (pageOfs >= dPOfs)
+                return TIterator(extString, pageNo - dPNo, pageOfs - dPOfs);
+            else
+                return TIterator(extString, pageNo - dPNo - 1, PAGESIZE + pageOfs - dPOfs);
+        }
+
+        inline TIterator& operator-= (TDifference delta) {
+            TDifference dPNo  = delta / PAGESIZE;
+            TDifference dPOfs = delta % PAGESIZE;
+            if (pageOfs < dPOfs) {
+                ++dPNo;
+                pageOfs = PAGESIZE + pageOfs - dPOfs;
+            } else
+                pageOfs -= dPOfs;
+            if (dPNo) invalidate(0);
+            pageNo -= dPNo;
+            return *this;
+        }
+
+        inline TIterator operator+ (TDifference delta) const {
+            TDifference dPNo  = delta / PAGESIZE;
+            TDifference nPOfs = pageOfs + delta % PAGESIZE;
+            if (nPOfs < PAGESIZE)
+                return TIterator(extString, pageNo + dPNo, nPOfs);
+            else
+                return TIterator(extString, pageNo + dPNo + 1, nPOfs - PAGESIZE);
+        }
+
+        inline TIterator& operator+= (TDifference delta) {
+            TDifference dPNo  = delta / PAGESIZE;
+            TDifference nPOfs = pageOfs + delta % PAGESIZE;
+            if (nPOfs >= PAGESIZE) {
+                ++dPNo;
+                nPOfs -= PAGESIZE;
+            }
+            if (dPNo) invalidate(0);
+            pageNo += dPNo;
+            pageOfs = nPOfs;
+            return *this;
+        }
+
+        inline void validate() const {
+            typename TExtString::TPageFrame &pf = extString->getSharedPage(pageNo, prefetch);
+            const_cast<TIterator*>(this)->begin = pf.begin;
+        }
 
         inline void invalidate(int _prefetch = 0) const {
             if (begin) {
                 const_cast<TIterator*>(this)->begin = NULL;
-				extString->releasePage(pageNo, (prefetch != 0) || (_prefetch != 0));
+                extString->releasePage(pageNo, (prefetch != 0) || (_prefetch != 0));
                 const_cast<TIterator*>(this)->prefetch = _prefetch;
             }
-		}
-
-		inline TValue const & operator* () const {
-			if (!begin) validate();
-			return begin[pageOfs];
-		}
-    
-		inline TIterator& operator++ () {
-			if (++pageOfs == PAGESIZE) {
-				invalidate(1);
-				pageOfs = 0;
-				++pageNo;
-			}
-			return *this;
-		}
+        }
 
-		inline TIterator operator++ (int) {
-			TIterator before = *this;
-			if (++pageOfs == PAGESIZE) {
-				invalidate(1);
-				pageOfs = 0;
-				++pageNo;
-			}
-			return before;
-		}
+        inline TValue const & operator* () const {
+            if (!begin) validate();
+            return begin[pageOfs];
+        }
 
-		inline TIterator& operator-- () {
-			if (pageOfs)
-				--pageOfs;
-			else {
-				invalidate(-1);
-				pageOfs = PAGESIZE - 1;
-				--pageNo;
-			}
-			return *this;
-		}
+        inline TIterator& operator++ () {
+            if (++pageOfs == PAGESIZE) {
+                invalidate(1);
+                pageOfs = 0;
+                ++pageNo;
+            }
+            return *this;
+        }
 
-		inline TIterator operator-- (int) {
-			TIterator before = *this;
-			if (pageOfs)
-				--pageOfs;
-			else {
-				invalidate(-1);
-				pageOfs = PAGESIZE - 1;
-				--pageNo;
-			}
-			return before;
-		}
+        inline TIterator operator++ (int) {
+            TIterator before = *this;
+            if (++pageOfs == PAGESIZE) {
+                invalidate(1);
+                pageOfs = 0;
+                ++pageNo;
+            }
+            return before;
+        }
 
-		inline bool operator== (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return pageNo == I.pageNo && pageOfs == I.pageOfs;
-		}
+        inline TIterator& operator-- () {
+            if (pageOfs)
+                --pageOfs;
+            else {
+                invalidate(-1);
+                pageOfs = PAGESIZE - 1;
+                --pageNo;
+            }
+            return *this;
+        }
 
-		inline bool operator!= (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return pageNo != I.pageNo || pageOfs != I.pageOfs;
-		}
+        inline TIterator operator-- (int) {
+            TIterator before = *this;
+            if (pageOfs)
+                --pageOfs;
+            else {
+                invalidate(-1);
+                pageOfs = PAGESIZE - 1;
+                --pageNo;
+            }
+            return before;
+        }
 
-		inline bool operator< (const TIterator &I) const {
-			SEQAN_ASSERT_EQ(extString, I.extString);
-			return pageNo < I.pageNo || (pageNo == I.pageNo && pageOfs < I.pageOfs);
-		}
+        inline bool operator== (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return pageNo == I.pageNo && pageOfs == I.pageOfs;
+        }
 
-	};
+        inline bool operator!= (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return pageNo != I.pageNo || pageOfs != I.pageOfs;
+        }
+
+        inline bool operator< (const TIterator &I) const {
+            SEQAN_ASSERT_EQ(extString, I.extString);
+            return pageNo < I.pageNo || (pageNo == I.pageNo && pageOfs < I.pageOfs);
+        }
+
+    };
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// iterator metafunctions
+    //////////////////////////////////////////////////////////////////////////////
+    // iterator metafunctions
 
-	template < typename TString >
-    struct Container< ExtStringIterator<TString> >			{ typedef TString Type; };
+    template < typename TString >
+    struct Container< ExtStringIterator<TString> >            { typedef TString Type; };
 //IOREV
-	template < typename TString >
-    struct Container< ExtStringConstIterator<TString> >		{ typedef TString Type; };
+    template < typename TString >
+    struct Container< ExtStringConstIterator<TString> >        { typedef TString Type; };
 //IOREV
-	template < typename TString >
-    struct Container< ExtStringFwdIterator<TString> >		{ typedef TString Type; };
+    template < typename TString >
+    struct Container< ExtStringFwdIterator<TString> >        { typedef TString Type; };
 //IOREV
-	template < typename TString >
-    struct Container< ExtStringFwdConstIterator<TString> >	{ typedef TString Type; };
+    template < typename TString >
+    struct Container< ExtStringFwdConstIterator<TString> >    { typedef TString Type; };
 //IOREV
 
-	template < typename TString >
-    struct Value< ExtStringIterator<TString> >				{ typedef typename Value<TString>::Type Type; };
+    template < typename TString >
+    struct Value< ExtStringIterator<TString> >                { typedef typename Value<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Value< ExtStringConstIterator<TString> >			{ typedef typename Value<TString>::Type Type; };
+    template < typename TString >
+    struct Value< ExtStringConstIterator<TString> >            { typedef typename Value<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Value< ExtStringFwdIterator<TString> >			{ typedef typename Value<TString>::Type Type; };
+    template < typename TString >
+    struct Value< ExtStringFwdIterator<TString> >            { typedef typename Value<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Value< ExtStringFwdConstIterator<TString> >		{ typedef typename Value<TString>::Type Type; };
+    template < typename TString >
+    struct Value< ExtStringFwdConstIterator<TString> >        { typedef typename Value<TString>::Type Type; };
 //IOREV
 
-	template < typename TString >
-	struct Reference< ExtStringConstIterator<TString> >:
-		public Reference<TString const> {};
+    template < typename TString >
+    struct Reference< ExtStringConstIterator<TString> >:
+        public Reference<TString const> {};
 //IOREV
 
-	template < typename TString >
-	struct Reference< ExtStringFwdConstIterator<TString> >:
-		public Reference<TString const> {};
+    template < typename TString >
+    struct Reference< ExtStringFwdConstIterator<TString> >:
+        public Reference<TString const> {};
 //IOREV
 
-	template < typename TString >
-    struct Size< ExtStringIterator<TString> >				{ typedef typename Size<TString>::Type Type; };
+    template < typename TString >
+    struct Size< ExtStringIterator<TString> >                { typedef typename Size<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Size< ExtStringConstIterator<TString> >			{ typedef typename Size<TString>::Type Type; };
+    template < typename TString >
+    struct Size< ExtStringConstIterator<TString> >            { typedef typename Size<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Size< ExtStringFwdIterator<TString> >			{ typedef typename Size<TString>::Type Type; };
+    template < typename TString >
+    struct Size< ExtStringFwdIterator<TString> >            { typedef typename Size<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Size< ExtStringFwdConstIterator<TString> >		{ typedef typename Size<TString>::Type Type; };
+    template < typename TString >
+    struct Size< ExtStringFwdConstIterator<TString> >        { typedef typename Size<TString>::Type Type; };
 //IOREV
 
-	template < typename TString >
-    struct Position< ExtStringIterator<TString> >			{ typedef typename Position<TString>::Type Type; };
+    template < typename TString >
+    struct Position< ExtStringIterator<TString> >            { typedef typename Position<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Position< ExtStringConstIterator<TString> >		{ typedef typename Position<TString>::Type Type; };
+    template < typename TString >
+    struct Position< ExtStringConstIterator<TString> >        { typedef typename Position<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Position< ExtStringFwdIterator<TString> >		{ typedef typename Position<TString>::Type Type; };
+    template < typename TString >
+    struct Position< ExtStringFwdIterator<TString> >        { typedef typename Position<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Position< ExtStringFwdConstIterator<TString> >	{ typedef typename Position<TString>::Type Type; };
+    template < typename TString >
+    struct Position< ExtStringFwdConstIterator<TString> >    { typedef typename Position<TString>::Type Type; };
 //IOREV
 
-	template < typename TString >
-    struct Difference< ExtStringIterator<TString> >			{ typedef typename Difference<TString>::Type Type; };
+    template < typename TString >
+    struct Difference< ExtStringIterator<TString> >            { typedef typename Difference<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Difference< ExtStringConstIterator<TString> >	{ typedef typename Difference<TString>::Type Type; };
+    template < typename TString >
+    struct Difference< ExtStringConstIterator<TString> >    { typedef typename Difference<TString>::Type Type; };
 //IOREV
-	template < typename TString >
-    struct Difference< ExtStringFwdIterator<TString> >		{ typedef typename Difference<TString>::Type Type; };
+    template < typename TString >
+    struct Difference< ExtStringFwdIterator<TString> >        { typedef typename Difference<TString>::Type Type; };
 //IOREV
-	template < typename TString >
+    template < typename TString >
     struct Difference< ExtStringFwdConstIterator<TString> > { typedef typename Difference<TString>::Type Type; };
 //IOREV
 
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // global interface
 
-	template <typename TExtString>
-	inline TExtString &	container(ExtStringIterator<TExtString> &it) { return *(it.extString); }
+    template <typename TExtString>
+    inline TExtString &    container(ExtStringIterator<TExtString> &it) { return *(it.extString); }
 //IOREV
-	template <typename TExtString>
-	inline TExtString &	container(ExtStringIterator<TExtString> const &it) { return *(it.extString); }
+    template <typename TExtString>
+    inline TExtString &    container(ExtStringIterator<TExtString> const &it) { return *(it.extString); }
 //IOREV
 
-	template <typename TExtString>
-	inline TExtString &	container(ExtStringConstIterator<TExtString> &it) { return *(it.extString); }
+    template <typename TExtString>
+    inline TExtString &    container(ExtStringConstIterator<TExtString> &it) { return *(it.extString); }
 //IOREV
-	template <typename TExtString>
-	inline TExtString &	container(ExtStringConstIterator<TExtString> const &it) { return *(it.extString); }
+    template <typename TExtString>
+    inline TExtString &    container(ExtStringConstIterator<TExtString> const &it) { return *(it.extString); }
 //IOREV
 
-	template <typename TExtString>
-	inline TExtString &	container(ExtStringFwdIterator<TExtString> &it) { return *(it.extString); }
+    template <typename TExtString>
+    inline TExtString &    container(ExtStringFwdIterator<TExtString> &it) { return *(it.extString); }
 //IOREV
-	template <typename TExtString>
-	inline TExtString &	container(ExtStringFwdIterator<TExtString> const &it) { return *(it.extString); }
+    template <typename TExtString>
+    inline TExtString &    container(ExtStringFwdIterator<TExtString> const &it) { return *(it.extString); }
 //IOREV
 
-	template <typename TExtString>
-	inline TExtString &	container(ExtStringFwdConstIterator<TExtString> &it) { return *(it.extString); }
+    template <typename TExtString>
+    inline TExtString &    container(ExtStringFwdConstIterator<TExtString> &it) { return *(it.extString); }
 //IOREV
-	template <typename TExtString>
-	inline TExtString &	container(ExtStringFwdConstIterator<TExtString> const &it) { return *(it.extString); }
+    template <typename TExtString>
+    inline TExtString &    container(ExtStringFwdConstIterator<TExtString> const &it) { return *(it.extString); }
 //IOREV
 //____________________________________________________________________________
 
-	template <typename TExtString>
-	inline bool	atBegin(ExtStringIterator<TExtString> &it) { return it.offset == 0; }
+    template <typename TExtString>
+    inline bool    atBegin(ExtStringIterator<TExtString> &it) { return it.offset == 0; }
 //IOREV
-	template <typename TExtString>
-	inline bool	atBegin(ExtStringIterator<TExtString> const &it) { return it.offset == 0; }
+    template <typename TExtString>
+    inline bool    atBegin(ExtStringIterator<TExtString> const &it) { return it.offset == 0; }
 //IOREV
 
-	template <typename TExtString>
-	inline bool	atBegin(ExtStringConstIterator<TExtString> &it) { return it.offset == 0; }
+    template <typename TExtString>
+    inline bool    atBegin(ExtStringConstIterator<TExtString> &it) { return it.offset == 0; }
 //IOREV
-	template <typename TExtString>
-	inline bool	atBegin(ExtStringConstIterator<TExtString> const &it) { return it.offset == 0; }
+    template <typename TExtString>
+    inline bool    atBegin(ExtStringConstIterator<TExtString> const &it) { return it.offset == 0; }
 //IOREV
 
-	template <typename TExtString>
-	inline bool	atBegin(ExtStringFwdIterator<TExtString> &it) { 
+    template <typename TExtString>
+    inline bool    atBegin(ExtStringFwdIterator<TExtString> &it) {
 //IOREV
-		return it.pageNo == 0 && it.pageOfs == 0;
-	}
-	template <typename TExtString>
-	inline bool	atBegin(ExtStringFwdIterator<TExtString> const &it) {
+        return it.pageNo == 0 && it.pageOfs == 0;
+    }
+    template <typename TExtString>
+    inline bool    atBegin(ExtStringFwdIterator<TExtString> const &it) {
 //IOREV
-		return it.pageNo == 0 && it.pageOfs == 0;
-	}
+        return it.pageNo == 0 && it.pageOfs == 0;
+    }
 
-	template <typename TExtString>
-	inline bool	atBegin(ExtStringFwdConstIterator<TExtString> &it) { 
+    template <typename TExtString>
+    inline bool    atBegin(ExtStringFwdConstIterator<TExtString> &it) {
 //IOREV
-		return it.pageNo == 0 && it.pageOfs == 0;
-	}
-	template <typename TExtString>
-	inline bool	atBegin(ExtStringFwdConstIterator<TExtString> const &it) {
+        return it.pageNo == 0 && it.pageOfs == 0;
+    }
+    template <typename TExtString>
+    inline bool    atBegin(ExtStringFwdConstIterator<TExtString> const &it) {
 //IOREV
-		return it.pageNo == 0 && it.pageOfs == 0;
-	}
+        return it.pageNo == 0 && it.pageOfs == 0;
+    }
 //____________________________________________________________________________
 
-	template <typename TExtString>
-	inline bool	atEnd(ExtStringIterator<TExtString> &it) { return it.offset == it.extString->data_size; }
+    template <typename TExtString>
+    inline bool    atEnd(ExtStringIterator<TExtString> &it) { return it.offset == it.extString->data_size; }
 //IOREV
-	template <typename TExtString>
-	inline bool	atEnd(ExtStringIterator<TExtString> const &it) { return it.offset == it.extString->data_size; }
+    template <typename TExtString>
+    inline bool    atEnd(ExtStringIterator<TExtString> const &it) { return it.offset == it.extString->data_size; }
 //IOREV
 
-	template <typename TExtString>
-	inline bool	atEnd(ExtStringConstIterator<TExtString> &it) { return it.offset == it.extString->data_size; }
+    template <typename TExtString>
+    inline bool    atEnd(ExtStringConstIterator<TExtString> &it) { return it.offset == it.extString->data_size; }
 //IOREV
-	template <typename TExtString>
-	inline bool	atEnd(ExtStringConstIterator<TExtString> const &it) { return it.offset == it.extString->data_size; }
+    template <typename TExtString>
+    inline bool    atEnd(ExtStringConstIterator<TExtString> const &it) { return it.offset == it.extString->data_size; }
 //IOREV
 
-	template <typename TExtString>
-	inline bool	atEnd(ExtStringFwdIterator<TExtString> &it) { 
+    template <typename TExtString>
+    inline bool    atEnd(ExtStringFwdIterator<TExtString> &it) {
 //IOREV
-		return TExtString::PAGESIZE * it.pageNo + it.pageOfs == it.extString->data_size;
-	}
-	template <typename TExtString>
-	inline bool	atEnd(ExtStringFwdIterator<TExtString> const &it) {
+        return TExtString::PAGESIZE * it.pageNo + it.pageOfs == it.extString->data_size;
+    }
+    template <typename TExtString>
+    inline bool    atEnd(ExtStringFwdIterator<TExtString> const &it) {
 //IOREV
-		return TExtString::PAGESIZE * it.pageNo + it.pageOfs == it.extString->data_size;
-	}
+        return TExtString::PAGESIZE * it.pageNo + it.pageOfs == it.extString->data_size;
+    }
 
-	template <typename TExtString>
-	inline bool	atEnd(ExtStringFwdConstIterator<TExtString> &it) { 
+    template <typename TExtString>
+    inline bool    atEnd(ExtStringFwdConstIterator<TExtString> &it) {
 //IOREV
-		return TExtString::PAGESIZE * it.pageNo + it.pageOfs == it.extString->data_size;
-	}
-	template <typename TExtString>
-	inline bool	atEnd(ExtStringFwdConstIterator<TExtString> const &it) {
+        return TExtString::PAGESIZE * it.pageNo + it.pageOfs == it.extString->data_size;
+    }
+    template <typename TExtString>
+    inline bool    atEnd(ExtStringFwdConstIterator<TExtString> const &it) {
 //IOREV
-		return TExtString::PAGESIZE * it.pageNo + it.pageOfs == it.extString->data_size;
-	}
+        return TExtString::PAGESIZE * it.pageNo + it.pageOfs == it.extString->data_size;
+    }
+
+
 
 
-	
-	
-	
-	
-	//////////////////////////////////////////////////////////////////////////////
+
+
+    //////////////////////////////////////////////////////////////////////////////
     // External String
     //////////////////////////////////////////////////////////////////////////////
 
     template < typename TValue,
                typename TConfig >
-	class String<TValue, External<TConfig> >
-	{
+    class String<TValue, External<TConfig> >
+    {
 //IOREV _doc_ contains TODOs by holtgrew
-	public:
+    public:
         enum { FRAMES    = TConfig::FRAMES,
                PAGESIZE = TConfig::PAGESIZE };
 
         typedef typename TConfig::TFile                                 TFile;
         typedef typename TConfig::TSize                                 TSize;
 
-		typedef String<int>                                             TPageTable;
-		typedef Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE> > >    TPageFrame;
-		typedef PageContainer<TPageFrame, FRAMES>                       TCache;
-		typedef VolatilePtr<TValue>                                     TVolatilePtr;
+        typedef String<int>                                             TPageTable;
+        typedef Buffer<TValue, PageFrame<TFile, Fixed<PAGESIZE> > >     TPageFrame;
+        typedef PageContainer<TPageFrame, FRAMES>                       TCache;
+        typedef VolatilePtr<TValue>                                     TVolatilePtr;
 
-		TPageTable			pager;
-		TCache				cache;
-		TFile				file;
+        TPageTable            pager;
+        TCache                cache;
+        TFile                file;
         bool                _temporary, _ownFile;
-		TSize				data_size;
-        int                 lastDiskPage;       // the last page on disk and in mem 
+        TSize                data_size;
+        int                 lastDiskPage;       // the last page on disk and in mem
         unsigned            lastDiskPageSize;   // can be smaller than PAGESIZE
 
-		String(TSize size = 0):
-            file(NULL),
-			data_size(0)
+        String(TSize size = 0) :
+            file(NULL), _temporary(true), _ownFile(false), data_size(0),
+            lastDiskPage(0),     // the last two values need not to be initialized here
+            lastDiskPageSize(0)  // because of "write before read"
         {
-            _temporary = true;
-            _ownFile = false;
-            lastDiskPage = 0;       // actually, these values need not to be initialized
-            lastDiskPageSize = 0;   // here, because of "write before read"
-
-			resize(*this, size);
+            resize(*this, size);
         }
 
-/*
-	private:	// making these C'tors private clashes with Holder<external String>
-		String(String &) {}
-		String(String const &) {}
-
-	public:
-*/
-		String(String &) { SEQAN_ASSERT_FAIL("Aborted attempt to copy a String<..,External<..> >"); }  // TODO(holtgrew): Actually, this should be an ABORT
-		String(String const &) { SEQAN_ASSERT_FAIL("Aborted attempt to copy a String<..,External<..> >"); }  // TODO(holtgrew): Actually, this should be an ABORT
-
 /*!
  * @fn ExternalString::String
  * @brief Constructor
@@ -1261,192 +1165,192 @@ you should think of using @Tag.ExternalConfig@.
  * openTemp afterwards to reach the same behaviour.
  */
 
-/**
-.Memfunc.External String#String:
-..class:Spec.External String
-..summary:Constructor
-..signature:String<TValue, External<TConfig> > ()
-..signature:String<TValue, External<TConfig> > (file)
-..signature:String<TValue, External<TConfig> > (fileName[, openMode])
-..param.file:The @Spec.External String@ will use the file associated with $file$.
-...remarks:You must ensure that $file$ is open, as the string won't call @Function.open@ and @Function.close@ on it.
-...type:Class.File
-..param.fileName:The @Spec.External String@ will @Function.open@ the file with the path $fileName$.
-..param.openMode:File mode for @Function.open@.
-..remarks:When a file or file name is given, this file will be used for the @Spec.External String@.
-If the file exists, this file will be used and determines the strings length and content.
-If the file doesn't exist, a new and empty file will be created and used for the string.
-In both cases, the string won't delete the file in the destructor.
-..remarks:
-When no file is given (default c'tor) the string will be empty and no file is used until the string 
-needs to swap out page frames. Then a temporary file will be used which will be deleted when the string is destroyed.
-..remarks:
-Instead of giving $file$ or $fileName$ to the constructor, you could also use the default constructor and call @Function.open@
-or @Function.openTemp@ afterwards to reach the same behaviour.
-*/
-		String(TFile &_file)
+        explicit
+        String(TFile &_file) :
+            file(NULL), _temporary(true), _ownFile(false), data_size(0), lastDiskPage(0), lastDiskPageSize(0)
+        {
+            open(*this, _file);
+        }
+
+        explicit
+        String(const char *fileName, int openMode = DefaultOpenMode<TFile>::VALUE) :
+            file(NULL), _temporary(true), _ownFile(false), data_size(0), lastDiskPage(0), lastDiskPageSize(0)
+        {
+            open(*this, fileName, openMode);
+        }
+
+        // copy the contents from another string
+        String(String const & source):
+            file(NULL), _temporary(true), _ownFile(false), data_size(0), lastDiskPage(0), lastDiskPageSize(0)
+        {
+            assign(*this, source);
+        }
+
+        template <typename TSource>
+        String(TSource const & source) :
+            file(NULL), _temporary(true), _ownFile(false), data_size(0), lastDiskPage(0), lastDiskPageSize(0)
+        {
+            assign(*this, source);
+        }
+
+        ~String()
         {
-			open(*this, _file);
+            close(*this);
+        }
+
+        inline TValue & operator[] (TSize offset) {
+            TPageFrame &pf = getPage(offset / PAGESIZE);
+            pf.dirty = true;
+            return pf[offset % PAGESIZE];
         }
 
-		String(const char *fileName, int openMode = DefaultOpenMode<TFile>::VALUE):
-			file(NULL)
+        inline TValue const & operator[] (TSize offset) const {
+            return const_cast<String*>(this)->getPage(offset / PAGESIZE)[offset % PAGESIZE];
+        }
+
+        template <typename TSource>
+        inline String & operator= (TSource const & source)
+        {
+            assign(*this, source);
+            return *this;
+        }
+
+        inline String & operator= (String const & source)
+        {
+            assign(*this, source);
+            return *this;
+        }
+
+        inline operator bool()
         {
-			open(*this, fileName, openMode);
-        }
-
-		~String() 
-		{
-			close(*this);
-		}
-
-		inline TValue & operator[] (TSize offset) {
-			TPageFrame &pf = getPage(offset / PAGESIZE);
-			pf.dirty = true;
-			return pf[offset % PAGESIZE];
-		}
-
-		inline TValue const & operator[] (TSize offset) const {
-			return const_cast<String*>(this)->getPage(offset / PAGESIZE)[offset % PAGESIZE];
-		}
-
-	    template <typename TSource>
-	    inline String & operator= (TSource const & source)
-	    {
-		    assign(*this, source);
-		    return *this;
-	    }
-
-	    inline String & operator= (String const & source)
-	    {
-		    assign(*this, source);
-		    return *this;
-	    }
-
-        inline operator bool() 
-		{
             return file;
         }
 
-		//////////////////////////////////////////////////////////////////////////////
-		// swapping interface
-
-		// when a page has to be swapped out and file is not open, open a temporary file
-		inline void _ensureFileIsOpen() 
-		{
-			if (!file) 
-			{
-				_temporary = true;
-				if (!(_ownFile = openTemp(file)))
-					::std::cerr << "External String couldn't open temporary file" << ::std::endl;
-			}
-		}
-
-		// for debugging
-        void _dumpCache() 
-		{
-            for(int i = 0; i < length(cache); ++i) 
-			{
+        //////////////////////////////////////////////////////////////////////////////
+        // swapping interface
+
+        // when a page has to be swapped out and file is not open, open a temporary file
+        inline void _ensureFileIsOpen()
+        {
+            if (!file)
+            {
+                _temporary = true;
+                if (!(_ownFile = openTemp(file)))
+                    std::cerr << "External String couldn't open temporary file" << std::endl;
+            }
+        }
+
+        // for debugging
+        void _dumpCache()
+        {
+            for(int i = 0; i < length(cache); ++i)
+            {
                 TPageFrame &pf = cache[i];
-                ::std::cerr << "[" << pf.pageNo << "]";
+                std::cerr << "[" << pf.pageNo << "]";
                 if (pf.dirty)
-                    ::std::cerr << "*";
+                    std::cerr << "*";
                 else
-                    ::std::cerr << " ";
+                    std::cerr << " ";
 
                 if (pf.status == READY)
-                    ::std::cerr << "   ";
+                    std::cerr << "   ";
                 else
-                    ::std::cerr << ".  ";
+                    std::cerr << ".  ";
             }
-            ::std::cerr << ::std::endl;
+            std::cerr << std::endl;
         }
 
         // return a priority for a page frame (the higher is more persistent)
-        inline typename TPageFrame::Priority getPriority(int /*pageNo*/) const 
-		{
+        inline typename TPageFrame::Priority getPriority(int /*pageNo*/) const
+        {
 /*            if (keepFirst && pageNo < (int)(length(cache)) - 10) // save 1 for random access
                 return TPageFrame::PERMANENT_LEVEL;
             else*/
                 return TPageFrame::NORMAL_LEVEL;
         }
 
-		// write page to disk if dirty and remove from page table now or after finishing IO
-		inline void flush(TPageFrame &pf) 
-		{
+        // write page to disk if dirty and remove from page table now or after finishing IO
+        inline void flush(TPageFrame &pf)
+        {
             if (pf.status == READY && pf.dirty) {    // write if dirty and not i/o transferring
-				nukeCopies(pf.begin);				            // proceeding writes should wait and set dirty bit
+                nukeCopies(pf.begin);                            // proceeding writes should wait and set dirty bit
 
                 if (pf.priority > TPageFrame::NORMAL_LEVEL && pf.priority <= TPageFrame::ITERATOR_LEVEL)
-					cache.upgrade(pf, TPageFrame::PREFETCH_LEVEL);
+                    cache.upgrade(pf, TPageFrame::PREFETCH_LEVEL);
 
-				_ensureFileIsOpen();
-				if (pf.pageNo != (int)(data_size / (TSize)PAGESIZE))
-    				writePage(pf, pf.pageNo, file);
+                _ensureFileIsOpen();
+                if (pf.pageNo != (int)(data_size / (TSize)PAGESIZE))
+                    writePage(pf, pf.pageNo, file);
                 else {
                     lastDiskPage = data_size / PAGESIZE;
                     lastDiskPageSize = data_size % PAGESIZE;
-				    writeLastPage(pf, pf.pageNo, file, lastDiskPageSize);
+                    writeLastPage(pf, pf.pageNo, file, lastDiskPageSize);
                 }
                 pf.dataStatus = TPageFrame::ON_DISK;
-			}
-		}
+            }
+        }
 
-		// write page synchronously to disk if dirty and remove from page table
-		inline void swapOutAndWait(TPageFrame &pf) 
-		{
-			nukeCopies(pf.begin);      				// proceeding writes should wait and set dirty bit
+        // write page synchronously to disk if dirty and remove from page table
+        inline void swapOutAndWait(TPageFrame &pf)
+        {
+            nukeCopies(pf.begin);                      // proceeding writes should wait and set dirty bit
 
             if (pf.status != READY)
             {
-				pager[pf.pageNo] = TPageFrame::ON_DISK;		// page is not dirty and on disk
-				bool waitResult = waitFor(pf);              // after finishing I/O transfer
+                pager[pf.pageNo] = TPageFrame::ON_DISK;        // page is not dirty and on disk
+                bool waitResult = waitFor(pf);              // after finishing I/O transfer
 
                 // TODO(weese): Throw an I/O exception
                 if (!waitResult)
-                    SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+                    SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                               _pageFrameStatusString(pf.status),
+                               strerror(errno));
 
                 pf.pageNo = -1;                             // cut back link
                 return;
             }
 
-			if (pf.dirty) {                                 // write if dirty
-				_ensureFileIsOpen();
+            if (pf.dirty) {                                 // write if dirty
+                _ensureFileIsOpen();
                 if (pf.pageNo != (int)(data_size / (TSize)PAGESIZE)) {
-    				writePage(pf, pf.pageNo, file);
+                    writePage(pf, pf.pageNo, file);
                     if (pf.pageNo >= lastDiskPage)
-                        lastDiskPage = -1;       			// make lastDiskPage(Size) invalid because file size is aligned
+                        lastDiskPage = -1;                   // make lastDiskPage(Size) invalid because file size is aligned
                 } else {
-				    writeLastPage(pf, pf.pageNo, file, data_size % PAGESIZE);
+                    writeLastPage(pf, pf.pageNo, file, data_size % PAGESIZE);
                     lastDiskPage = data_size / PAGESIZE;
                     lastDiskPageSize = data_size % PAGESIZE;
                 }
-				pager[pf.pageNo] = TPageFrame::ON_DISK;		// page is marked to be on disk
-				bool waitResult = waitFor(pf);              // after finishing I/O transfer
+                pager[pf.pageNo] = TPageFrame::ON_DISK;        // page is marked to be on disk
+                bool waitResult = waitFor(pf);              // after finishing I/O transfer
 
                 // TODO(weese): Throw an I/O exception
                 if (!waitResult)
-                    SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
-			} else
-				pager[pf.pageNo] = pf.dataStatus;			// restore original data status
+                    SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                               _pageFrameStatusString(pf.status),
+                               strerror(errno));
+            } else
+                pager[pf.pageNo] = pf.dataStatus;            // restore original data status
 
             pf.pageNo = -1;                                 // cut back link
-		}
+        }
 
-		struct testIODone : public ::std::unary_function<TPageFrame&,bool> 
-		{
-			String &me;
-			testIODone(String &_me): me(_me) {}
+        struct testIODone : public std::unary_function<TPageFrame&,bool>
+        {
+            String &me;
+            testIODone(String &_me): me(_me) {}
 
-			inline bool operator() (TPageFrame &pf)
+            inline bool operator() (TPageFrame &pf)
             {
-                PageFrameStatus oldStatus = pf.status;
+                PageFrameState oldStatus = pf.status;
                 bool inProgress;
                 bool waitResult = waitFor(pf, 0, inProgress);
 
                 // TODO(weese): Throw an I/O exception
                 if (!waitResult)
-                    SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+                    SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                               _pageFrameStatusString(pf.status),
+                               strerror(errno));
 
                 if (!inProgress && (oldStatus != READY))
                 {
@@ -1454,8 +1358,8 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
                         me.lastDiskPage = -1;    // make lastDiskPage(Size) invalid because file size is aligned
                 }
                 return !inProgress;
-			}
-		};
+            }
+        };
 
         inline TPageFrame &getPage(
             int pageNo,
@@ -1463,187 +1367,191 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
             typename TPageFrame::Priority newLevel,
             int prefetchPages)
         {
-			int frameNo = pager[pageNo];
-			if (frameNo >= 0)					// cache hit
+            int frameNo = pager[pageNo];
+            if (frameNo >= 0)                    // cache hit
             {
-				TPageFrame &pf = cache[frameNo];
-				cache.upgrade(
-                    pf, 
-                    _max(pf.priority, newLevel));    		// update lru order
+                TPageFrame &pf = cache[frameNo];
+                cache.upgrade(
+                    pf,
+                    _max(pf.priority, newLevel));            // update lru order
 
-                PageFrameStatus oldStatus = pf.status;
-				bool waitResult = waitFor(pf);              // wait for I/O transfer to complete
+                PageFrameState oldStatus = pf.status;
+                bool waitResult = waitFor(pf);              // wait for I/O transfer to complete
 
                 // TODO(weese): Throw an I/O exception
                 if (!waitResult)
-                    SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+                    SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                               _pageFrameStatusString(pf.status),
+                               strerror(errno));
 
-				if (oldStatus != READY)
+                if (oldStatus != READY)
                     if (pf.pageNo >= lastDiskPage)
-                        lastDiskPage = -1;       			// make lastDiskPage(Size) invalid because file size is aligned
+                        lastDiskPage = -1;                   // make lastDiskPage(Size) invalid because file size is aligned
 
                 if (prefetchPages > 0) prefetch(pageNo + 1, pageNo + 1 + prefetchPages, frameNo);
                 else if (prefetchPages < 0) prefetch(pageNo + prefetchPages, pageNo, frameNo);
 
-				return pf;
+                return pf;
 
-			} else {							// cache miss
+            } else {                            // cache miss
 
-				typename TPageFrame::DataStatus dataStatus = static_cast<typename TPageFrame::DataStatus>(frameNo);
-				frameNo = cache.mru(testIODone(*this), maxLevel);   // try to get an undirty and READY pageframe
-				if (frameNo < 0)							// if there is none,
-					frameNo = cache.mruDirty();				// get the most recently used dirty frame
-				TPageFrame &pf = cache[frameNo];
+                typename TPageFrame::DataStatus dataStatus = static_cast<typename TPageFrame::DataStatus>(frameNo);
+                frameNo = cache.mru(testIODone(*this), maxLevel);   // try to get an undirty and READY pageframe
+                if (frameNo < 0)                            // if there is none,
+                    frameNo = cache.mruDirty();                // get the most recently used dirty frame
+                TPageFrame &pf = cache[frameNo];
 
-				// *** frame is choosen ***
+                // *** frame is choosen ***
 
-				if (pf.begin)
-					swapOutAndWait(pf);						// write synchronously to disk, if page is dirty
-				else
-					allocPage(pf, file);                    // allocate memory if page is virgin
+                if (pf.begin)
+                    swapOutAndWait(pf);                        // write synchronously to disk, if page is dirty
+                else
+                    allocPage(pf, file);                    // allocate memory if page is virgin
 
-				// *** frame is free now ***
+                // *** frame is free now ***
 
-				pf.dataStatus = dataStatus;
-				if (dataStatus == TPageFrame::ON_DISK)
-				{
+                pf.dataStatus = dataStatus;
+                if (dataStatus == TPageFrame::ON_DISK)
+                {
                     if (pageNo != lastDiskPage)
-					    readPage(pageNo, pf, file);
+                        readPage(pageNo, pf, file);
                     else
                         readLastPage(pageNo, pf, file, lastDiskPageSize);
-				}
-				pager[pageNo] = frameNo;					// assign new page to page table
-				pf.pageNo = pageNo;							// set back link
-				cache.upgrade(
+                }
+                pager[pageNo] = frameNo;                    // assign new page to page table
+                pf.pageNo = pageNo;                            // set back link
+                cache.upgrade(
                     pf,
                     _max(getPriority(pageNo), newLevel));    // update lru order
 
                 if (prefetchPages > 0) prefetch(pageNo + 1, pageNo + 1 + prefetchPages, frameNo);
                 else if (prefetchPages < 0) prefetch(pageNo + prefetchPages, pageNo, frameNo);
-                
-				bool waitResult = waitFor(pf);              // wait for I/O transfer to complete
+
+                bool waitResult = waitFor(pf);              // wait for I/O transfer to complete
 
                 // TODO(weese): Throw an I/O exception
                 if (!waitResult)
-                    SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(pf), strerror(errno));
+                    SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                               _pageFrameStatusString(pf.status),
+                               strerror(errno));
 
-				return pf;
-			}
-		}
-        
-		inline TPageFrame &getPage(int pageNo)
+                return pf;
+            }
+        }
+
+        inline TPageFrame &getPage(int pageNo)
         {
-			return getPage(pageNo, TPageFrame::NORMAL_LEVEL, TPageFrame::NORMAL_LEVEL, 0);
-		}
+            return getPage(pageNo, TPageFrame::NORMAL_LEVEL, TPageFrame::NORMAL_LEVEL, 0);
+        }
 
         // prefetch is non-blocking and should speed up swapping
-		inline void prefetch(int pageBegin, int pageEnd, int except = -1) 
-		{
+        inline void prefetch(int pageBegin, int pageEnd, int except = -1)
+        {
             if (!file) return;
-            if (pageBegin < 0)					pageBegin = 0;
-            if (pageEnd >= (int)length(pager))	pageEnd = (int)length(pager) - 1;
+            if (pageBegin < 0)                    pageBegin = 0;
+            if (pageEnd >= (int)length(pager))    pageEnd = (int)length(pager) - 1;
             for(int pageNo = pageBegin; pageNo < pageEnd; ++pageNo) {
-			    int frameNo = pager[pageNo];
-				typename TPageFrame::DataStatus dataStatus = static_cast<typename TPageFrame::DataStatus>(frameNo);
+                int frameNo = pager[pageNo];
+                typename TPageFrame::DataStatus dataStatus = static_cast<typename TPageFrame::DataStatus>(frameNo);
                 if (dataStatus == TPageFrame::ON_DISK &&             // prefetch only if page is on disk
                     pageNo != lastDiskPage)                         // reading the last page is blocking
-                {   
-				    frameNo = cache.mru(
+                {
+                    frameNo = cache.mru(
                         testIODone(*this),
                         TPageFrame::NORMAL_LEVEL);                   // choose undirty and ready page
 
                     if (frameNo < 0 || frameNo == except) return;   // no lowlevel-page left for prefetching
-				    TPageFrame &pf = cache[frameNo];
+                    TPageFrame &pf = cache[frameNo];
                     #ifdef SEQAN_VERBOSE
-						::std::cerr << "prefetch: page " << pageNo << ::std::endl;
+                        std::cerr << "prefetch: page " << pageNo << std::endl;
                     #endif
 
                     // *** frame is choosen ***
 
-				    if (pf.begin)
-					    swapOutAndWait(pf);						    // write synchronously to disk, if page is dirty
-				    else
-					    allocPage(pf, file);                        // allocate memory if page is virgin
+                    if (pf.begin)
+                        swapOutAndWait(pf);                            // write synchronously to disk, if page is dirty
+                    else
+                        allocPage(pf, file);                        // allocate memory if page is virgin
 
-    				// *** frame is free now ***
+                    // *** frame is free now ***
 
-    				pf.dataStatus = dataStatus;
+                    pf.dataStatus = dataStatus;
                     readPage(pageNo, pf, file);
-				    pager[pageNo] = frameNo;					    // assign new page to page table
-    				pf.pageNo = pageNo;							    // set back link
+                    pager[pageNo] = frameNo;                        // assign new page to page table
+                    pf.pageNo = pageNo;                                // set back link
                     cache.upgrade(pf, TPageFrame::PREFETCH_LEVEL);  // update lru order
                 }
             }
-		}
-		
-	    template < typename T >
-		inline static int _prefetchIffAsync(int /*prefetchPages*/, T const &) {
-			return 0;
-		}
-		
-		template < typename TSpec >
-		inline static int _prefetchIffAsync(int prefetchPages, File<Async<TSpec> > const &) {
-			return prefetchPages;
-		}
-
-		inline TPageFrame &getSharedPage(int pageNo, int prefetchPages = 0) 
-		{
-			return getPage(
-                pageNo, 
-                TPageFrame::PREFETCH_LEVEL, 
+        }
+
+        template < typename T >
+        inline static int _prefetchIffAsync(int /*prefetchPages*/, T const &) {
+            return 0;
+        }
+
+        template < typename TSpec >
+        inline static int _prefetchIffAsync(int prefetchPages, File<Async<TSpec> > const &) {
+            return prefetchPages;
+        }
+
+        inline TPageFrame &getSharedPage(int pageNo, int prefetchPages = 0)
+        {
+            return getPage(
+                pageNo,
+                TPageFrame::PREFETCH_LEVEL,
                 TPageFrame::ITERATOR_LEVEL,
                 _prefetchIffAsync(prefetchPages, file));
-		}
-
-		inline void releasePage(int pageNo, bool writeThrough = false) 
-		{
-			int frameNo = pager[pageNo];
-			if (frameNo >= 0)							// release only cached pages
-			{								        
-				TPageFrame &pf = cache[frameNo];
-				if (pf.begin.isLonely() && pf.priority <= TPageFrame::ITERATOR_LEVEL) 
-				{
-					cache.upgrade(pf, _max(getPriority(pageNo), TPageFrame::NORMAL_LEVEL));
-                    if (writeThrough) 
-					{
+        }
+
+        inline void releasePage(int pageNo, bool writeThrough = false)
+        {
+            int frameNo = pager[pageNo];
+            if (frameNo >= 0)                            // release only cached pages
+            {
+                TPageFrame &pf = cache[frameNo];
+                if (pf.begin.isLonely() && pf.priority <= TPageFrame::ITERATOR_LEVEL)
+                {
+                    cache.upgrade(pf, _max(getPriority(pageNo), TPageFrame::NORMAL_LEVEL));
+                    if (writeThrough)
+                    {
                         #ifdef SEQAN_VERBOSE
                             if (pf.dirty)
-								::std::cerr << "writeThrough: page " << pageNo << ::std::endl;
+                                std::cerr << "writeThrough: page " << pageNo << std::endl;
                         #endif
-					    flush(pf);							        // write if dirty
+                        flush(pf);                                    // write if dirty
                     }
-				}
-			}
-		}
-        
-        inline void rename(unsigned frameNo) 
-		{
-			TPageFrame &pf = cache[frameNo];
+                }
+            }
+        }
+
+        inline void rename(unsigned frameNo)
+        {
+            TPageFrame &pf = cache[frameNo];
             cache.rename(frameNo);                                  // update lru entry
             if (pf.pageNo >= 0)
-                pager[pf.pageNo] = frameNo;					        // update back link
+                pager[pf.pageNo] = frameNo;                            // update back link
         }
 
         // change the number of in-mem pageframes
-        // more pages mean less swapping, 
+        // more pages mean less swapping,
         // less pages mean more free mem
-        inline void resizeCache(unsigned newFrames) 
-		{
+        inline void resizeCache(unsigned newFrames)
+        {
             unsigned oldFrames = length(cache);
             if (data_size)
                 newFrames = _min(newFrames, (unsigned) enclosingBlocks(data_size, (unsigned)PAGESIZE));
             if (newFrames < oldFrames) {
                 flush(*this);
                 for(unsigned i = newFrames; i < oldFrames; ++i) {
-    			    int frameNo = cache.mruDirty();             // get the most recently used frame (can be dirty)
+                    int frameNo = cache.mruDirty();             // get the most recently used frame (can be dirty)
                     if (frameNo < 0) break;
-				    TPageFrame &pf = cache[frameNo];
+                    TPageFrame &pf = cache[frameNo];
 
-				    // *** frame is choosen ***
+                    // *** frame is choosen ***
 
                     if (pf.begin) {
-					    swapOutAndWait(pf);						// write synchronously to disk, if page is dirty
-        				freePage(pf, file);                     // free memory
+                        swapOutAndWait(pf);                        // write synchronously to disk, if page is dirty
+                        freePage(pf, file);                     // free memory
                     }
 
                     cache.erase(frameNo);                       // erase page frame from cache
@@ -1673,7 +1581,7 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
     struct Difference< String<TValue, External<TConfig> > >
     {
 //IOREV
-		typedef typename MakeSigned_<typename String<TValue, External<TConfig> >::TSize>::Type Type;
+        typedef typename MakeSigned_<typename String<TValue, External<TConfig> >::TSize>::Type Type;
     };
 
     template < typename TValue, typename TConfig, typename TSpec >
@@ -1684,7 +1592,7 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
     };
 
     template < typename TValue, typename TConfig, typename TSpec >
-    struct Iterator< String<TValue, External<TConfig> >, Tag<TSpec> const > 
+    struct Iterator< String<TValue, External<TConfig> >, Tag<TSpec> const >
     {
 //IOREV
         typedef ExtStringFwdIterator< String<TValue, External<TConfig> > > Type;
@@ -1692,76 +1600,78 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig >
-	struct DefaultOverflowExplicit<String<TValue, External<TConfig> > >
-	{
+    struct DefaultOverflowExplicit<String<TValue, External<TConfig> > >
+    {
 //IOREV
-		typedef Generous Type;
-	};
+        typedef Generous Type;
+    };
 
     template < typename TValue, typename TConfig >
-	struct DefaultOverflowImplicit<String<TValue, External<TConfig> > >
-	{
+    struct DefaultOverflowImplicit<String<TValue, External<TConfig> > >
+    {
 //IOREV
-		typedef Generous Type;
-	};
+        typedef Generous Type;
+    };
 //____________________________________________________________________________
 
 /*
     template < typename TValue, typename TConfig >
-	struct DefaultIteratorSpec< String<TValue, External<TConfig> > > {
-		typedef Standard Type;
-	};
-	
+    struct DefaultIteratorSpec< String<TValue, External<TConfig> > > {
+        typedef Standard Type;
+    };
+
     template < typename TValue, typename TConfig >
-	struct DefaultIteratorSpec< String<TValue, External<TConfig> > const > {
-		typedef Standard Type;
-	};
+    struct DefaultIteratorSpec< String<TValue, External<TConfig> > const > {
+        typedef Standard Type;
+    };
 */
 
     template < typename TValue, typename TConfig >
-	struct AllowsFastRandomAccess< String<TValue, External<TConfig> > >
-	{
+    struct AllowsFastRandomAccess< String<TValue, External<TConfig> > >
+    {
 //IOREV
-		typedef False Type;
-		enum { VALUE = false };
-	};
+        typedef False Type;
+        enum { VALUE = false };
+    };
 
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // global interface
 
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig >
-    inline void 
-    clear(String<TValue, External<TConfig> > &me) 
-	{
+    inline void
+    clear(String<TValue, External<TConfig> > &me)
+    {
 //IOREV
-		clear(me.pager);
+//        clear(me.pager);
         resize(me, 0);
     }
 //____________________________________________________________________________
 
-	// wait until IO of every page is finished
+    // wait until IO of every page is finished
     template < typename TValue, typename TConfig >
-	inline void 
-	waitForAll(String<TValue, External<TConfig> > &me)
-	{
+    inline void
+    waitForAll(String<TValue, External<TConfig> > &me)
+    {
 //IOREV _nodoc_
-		typedef typename String<TValue, External<TConfig> >::TCache	TCache;
-		typedef typename Iterator<TCache, Standard>::Type			TIter;
+        typedef typename String<TValue, External<TConfig> >::TCache    TCache;
+        typedef typename Iterator<TCache, Standard>::Type            TIter;
 
-		TIter f = begin(me.cache, Standard());
-		TIter fEnd = end(me.cache, Standard());
+        TIter f = begin(me.cache, Standard());
+        TIter fEnd = end(me.cache, Standard());
 
-		for(; f != fEnd ; ++f)
+        for(; f != fEnd ; ++f)
         {
             bool waitResult = waitFor(*f);              // wait for I/O transfer to complete
 
             if (!waitResult)
-                SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(*f), strerror(errno));
+                SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                           _pageFrameStatusString(f->status),
+                           strerror(errno));
         }
-	}
+    }
 
 /*!
  * @fn ExternalString#flush
@@ -1772,107 +1682,100 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
  * @param[in,out] str The ExternalString to flush.
  */
 
-/**
-.Function.flush:
-..signature:flush(string)
-..param.string:An external string. All dirty pages are flushed to disk.
-...type:Spec.External String
-..include:seqan/file.h
-*/
     template < typename TValue, typename TConfig >
-    inline void 
-	flush(String<TValue, External<TConfig> > &me) 
-	{
+    inline void
+    flush(String<TValue, External<TConfig> > &me)
+    {
 //IOREV _doc_
-		typedef typename String<TValue, External<TConfig> >::TCache	TCache;
-		typedef typename Iterator<TCache, Standard>::Type			TIter;
-
-		// write all dirty pages to disk
-		if (me.file)
-		{
-			TIter f = begin(me.cache, Standard());
-			TIter fEnd = end(me.cache, Standard());
-
-			for(; f != fEnd ; ++f)
-				if ((*f).begin) me.flush(*f);
-			waitForAll(me);
-		}
+        typedef typename String<TValue, External<TConfig> >::TCache    TCache;
+        typedef typename Iterator<TCache, Standard>::Type            TIter;
+
+        // write all dirty pages to disk
+        if (me.file)
+        {
+            TIter f = begin(me.cache, Standard());
+            TIter fEnd = end(me.cache, Standard());
+
+            for(; f != fEnd ; ++f)
+                if ((*f).begin) me.flush(*f);
+            waitForAll(me);
+        }
     }
 
-	// cancel all transactions
+    // cancel all transactions
     template < typename TValue, typename TConfig >
-	inline void 
-	cancel(String<TValue, External<TConfig> > &me)
-	{
+    inline void
+    cancel(String<TValue, External<TConfig> > &me)
+    {
 //IOREV _nodoc_
-		typedef typename String<TValue, External<TConfig> >::TCache	TCache;
-		typedef typename Iterator<TCache, Standard>::Type			TIter;
+        typedef typename String<TValue, External<TConfig> >::TCache    TCache;
+        typedef typename Iterator<TCache, Standard>::Type            TIter;
 
-		if (me.file) 
-		{
-			TIter f = begin(me.cache, Standard());
-			TIter fEnd = end(me.cache, Standard());
+        if (me.file)
+        {
+            TIter f = begin(me.cache, Standard());
+            TIter fEnd = end(me.cache, Standard());
 
-			for(; f != fEnd ; ++f)
-				if ((*f).begin) cancel(*f, me.file);
-		}
-	}
+            for(; f != fEnd ; ++f)
+                if ((*f).begin) cancel(*f, me.file);
+        }
+    }
 
-	// cancel all transactions and free allocated pages
+    // cancel all transactions and free allocated pages
     template < typename TValue, typename TConfig >
-	inline void 
-	cancelAndFree(String<TValue, External<TConfig> > &me)
-	{
+    inline void
+    cancelAndFree(String<TValue, External<TConfig> > &me)
+    {
 //IOREV _nodoc_
-		typedef String<TValue, External<TConfig> >					TExtString;
-		typedef typename TExtString::TPageFrame						TPageFrame;
-		typedef typename String<TValue, External<TConfig> >::TCache	TCache;
-		typedef typename Iterator<TCache, Standard>::Type			TIter;
+        typedef String<TValue, External<TConfig> >                    TExtString;
+        typedef typename TExtString::TPageFrame                        TPageFrame;
+        typedef typename String<TValue, External<TConfig> >::TCache    TCache;
+        typedef typename Iterator<TCache, Standard>::Type            TIter;
 
         TIter f = begin(me.cache, Standard());
         TIter fEnd = end(me.cache, Standard());
 
-        for(; f != fEnd ; ++f) 
+        for(; f != fEnd ; ++f)
         {
             if ((me.file) && (*f).begin) cancel(*f, me.file);
-            if ((*f).pageNo >= 0) 
+            if ((*f).pageNo >= 0)
             {
                 me.pager[(*f).pageNo] = (*f).dataStatus;
                 (*f).pageNo = TPageFrame::UNINITIALIZED;
             }
-//			::std::cerr << *f << ::std::endl;
+//            std::cerr << *f << std::endl;
             if ((*f).begin)
                 freePage(*f, me.file);
-  		}
-	}
+          }
+    }
 
-	// flush and free all allocated pages
+    // flush and free all allocated pages
     template < typename TValue, typename TConfig >
-	inline void 
-	flushAndFree(String<TValue, External<TConfig> > &me)
-	{
+    inline void
+    flushAndFree(String<TValue, External<TConfig> > &me)
+    {
 //IOREV _nodoc_
-		typedef String<TValue, External<TConfig> >			TExtString;
-		typedef typename TExtString::TPageFrame				TPageFrame;
-		typedef typename TExtString::TCache					TCache;
-		typedef typename Iterator<TCache, Standard>::Type	TIter;
+        typedef String<TValue, External<TConfig> >            TExtString;
+        typedef typename TExtString::TPageFrame                TPageFrame;
+        typedef typename TExtString::TCache                    TCache;
+        typedef typename Iterator<TCache, Standard>::Type    TIter;
 
         flush(me);
 
         TIter f = begin(me.cache, Standard());
         TIter fEnd = end(me.cache, Standard());
 
-        for(; f != fEnd ; ++f) 
+        for(; f != fEnd ; ++f)
         {
-            if ((*f).pageNo >= 0) 
+            if (f->pageNo >= 0)
             {
-                me.pager[(*f).pageNo] = (*f).dataStatus;
-                (*f).pageNo = TPageFrame::UNINITIALIZED;
+                me.pager[f->pageNo] = f->dataStatus;
+                f->pageNo = TPageFrame::UNINITIALIZED;
             }
-//			::std::cerr << *f << ::std::endl;
-            if ((*f).begin) freePage(*f, me.file);
+//            std::cerr << *f << std::endl;
+            if (f->begin) freePage(*f, me.file);
         }
-	}
+    }
 //____________________________________________________________________________
 
 /*!
@@ -1888,78 +1791,70 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
  * @return bool <tt>true</tt> if the operation succeeded and <tt>false</tt> otherwise.
  */
 
-/**
-.Function.open:
-..signature:open(string, fileName[, openMode]))
-..param.string:A persistent string, e.g. a @Spec.External String@ or @Spec.MMap String@.
-...type:Spec.External String
-..include:seqan/file.h
-*/
-
-	template < typename TValue, typename TConfig >
-    inline bool 
-    open(String<TValue, External<TConfig> > &me, const char *fileName, int openMode) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    open(String<TValue, External<TConfig> > &me, const char *fileName, int openMode)
+    {
 //IOREV _doc_
-		typedef String<TValue, External<TConfig> >			TExtString;
-		typedef typename TExtString::TPageFrame				TPageFrame;
+        typedef String<TValue, External<TConfig> >            TExtString;
+        typedef typename TExtString::TPageFrame                TPageFrame;
 
-		me._temporary = false;
-		if ((me._ownFile = open(me.file, fileName, openMode)))
-            me.data_size = size(me.file) / sizeof(TValue);
+        me._temporary = false;
+        if ((me._ownFile = open(me.file, fileName, openMode)))
+            me.data_size = length(me.file) / sizeof(TValue);
         else
             me.data_size = 0;
 
-		resize(me.pager, enclosingBlocks(me.data_size, 
-			(unsigned)me.PAGESIZE), (me.data_size)? 
-				TPageFrame::ON_DISK: 
-				TPageFrame::UNINITIALIZED);
+        resize(me.pager, enclosingBlocks(me.data_size,
+            (unsigned)me.PAGESIZE), (me.data_size)?
+                TPageFrame::ON_DISK:
+                TPageFrame::UNINITIALIZED);
 
         me.lastDiskPage = me.data_size / me.PAGESIZE;
         me.lastDiskPageSize = me.data_size % me.PAGESIZE;
-		return me._ownFile;
+        return me._ownFile;
     }
 
-	template < typename TValue, typename TConfig >
-    inline bool 
-    open(String<TValue, External<TConfig> > &me, const char *fileName) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    open(String<TValue, External<TConfig> > &me, const char *fileName)
+    {
 //IOREV _doc_
-		typedef String<TValue, External<TConfig> >	TExtString;
-		typedef typename TExtString::TFile			TFile;
+        typedef String<TValue, External<TConfig> >    TExtString;
+        typedef typename TExtString::TFile            TFile;
 
-		return open(me, fileName, DefaultOpenMode<TFile>::VALUE);
+        return open(me, fileName, DefaultOpenMode<TFile>::VALUE);
     }
 
-	template < typename TValue, typename TConfig >
-    inline bool 
-    open(String<TValue, External<TConfig> > &me, typename TConfig::TFile file) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    open(String<TValue, External<TConfig> > &me, typename TConfig::TFile file)
+    {
 //IOREV _doc_
-		typedef String<TValue, External<TConfig> >	TExtString;
-		typedef typename TExtString::TPageFrame		TPageFrame;
+        typedef String<TValue, External<TConfig> >    TExtString;
+        typedef typename TExtString::TPageFrame        TPageFrame;
 
-		me.file = file;
+        me.file = file;
         me._temporary = false;
         me._ownFile = false;
         if (me.file)
-            me.data_size = size(me.file) / sizeof(TValue);
+            me.data_size = length(me.file) / sizeof(TValue);
         else
             me.data_size = 0;
 
-		resize(me.pager, enclosingBlocks(me.data_size, 
-			(unsigned)me.PAGESIZE), (me.data_size)? 
-				TPageFrame::ON_DISK: 
-				TPageFrame::UNINITIALIZED);
+        resize(me.pager, enclosingBlocks(me.data_size,
+            (unsigned)me.PAGESIZE), (me.data_size)?
+                TPageFrame::ON_DISK:
+                TPageFrame::UNINITIALIZED);
 
         me.lastDiskPage = me.data_size / me.PAGESIZE;
         me.lastDiskPageSize = me.data_size % me.PAGESIZE;
-		return me._file;
+        return me._file;
     }
 
 /*!
  * @fn ExternalString#openTemp
- * @signature Open an ExternalString using an temporary file.
+ * @brief Open an ExternalString using an temporary file.
  *
  * @signature bool openTemp(str);
  *
@@ -1968,52 +1863,45 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
  * @return bool <tt>true</tt> if opening succeeded, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.openTemp:
-..signature:openTemp(string)
-..param.string:An external string.
-...type:Spec.External String
-..include:seqan/file.h
-*/
-	template < typename TValue, typename TConfig >
-    inline bool 
-    openTemp(String<TValue, External<TConfig> > &me) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    openTemp(String<TValue, External<TConfig> > &me)
+    {
 //IOREV _doc_
         me._temporary = true;
         me.lastDiskPage = 0;
         me.lastDiskPageSize = 0;
-		clear(me.pager);
-		return me._ownFile = openTemp(me.file);
+        clear(me.pager);
+        return me._ownFile = openTemp(me.file);
     }
 //____________________________________________________________________________
 
-	template < typename TValue, typename TConfig >
-    inline bool 
+    template < typename TValue, typename TConfig >
+    inline bool
     save(String<TValue, External<TConfig> > const &/*me*/, const char * /*fileName*/, int /*openMode*/) {
 //IOREV _nodoc_ shouldn't we flush here? in case of abnormal termination...
-		// External Strings are persistent, thus there is no need to save them
-		//ExtStringsDontNeedToBeSaved error;
-		return true;
-	}
+        // External Strings are persistent, thus there is no need to save them
+        //ExtStringsDontNeedToBeSaved error;
+        return true;
+    }
 
-	template < typename TValue, typename TConfig >
-    inline bool 
+    template < typename TValue, typename TConfig >
+    inline bool
     save(String<TValue, External<TConfig> > const &/*me*/, const char * /*fileName*/) {
 //IOREV _nodoc_ shouldn't we flush here? in case of abnormal termination...
-		// External Strings are persistent, thus there is no need to save them
-		//ExtStringsDontNeedToBeSaved error;
-		return true;
-	}
+        // External Strings are persistent, thus there is no need to save them
+        //ExtStringsDontNeedToBeSaved error;
+        return true;
+    }
 
-	template < typename TValue, typename TConfig >
-    inline bool 
+    template < typename TValue, typename TConfig >
+    inline bool
     save(String<TValue, External<TConfig> > const &/*me*/, typename TConfig::TFile /*file*/) {
 //IOREV _nodoc_ shouldn't we flush here? in case of abnormal termination...
-		// External Strings are persistent, thus there is no need to save them
-		//ExtStringsDontNeedToBeSaved error;
-		return true;
-	}
+        // External Strings are persistent, thus there is no need to save them
+        //ExtStringsDontNeedToBeSaved error;
+        return true;
+    }
 //____________________________________________________________________________
 
 /*!
@@ -2026,38 +1914,29 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
  *
  * @return bool <tt>true</tt> if the closing succeeded, <tt>false</tt> otherwise.
  */
-    
-/**
-.Function.close:
-..signature:close(string)
-..param.string:An external string.
-...type:Spec.External String
-..include:seqan/file.h
-*/
-	template < typename TValue, typename TConfig >
-    inline bool 
-    close(String<TValue, External<TConfig> > &me) 
-	{
+
+    template < typename TValue, typename TConfig >
+    inline bool
+    close(String<TValue, External<TConfig> > &me)
+    {
 //IOREV _doc_
-		// close associated file
-		if (me._temporary)
-			cancelAndFree(me);
-		else
-			flushAndFree(me);
-		clear(me.pager);
-
-		if (me._ownFile) 
-		{
-			me._ownFile = false;
-			return close(me.file);
-		} 
-		else
-			return true;
+        // close associated file
+        if (me._temporary)
+            cancelAndFree(me);
+        else
+            flushAndFree(me);
+        clear(me.pager);
+
+        if (me._ownFile)
+        {
+            me._ownFile = false;
+            return close(me.file);
+        }
+        else
+            return true;
     }
 //____________________________________________________________________________
-///.Function.length.param.object.type:Class.Shape
-
-	template < typename TValue, typename TConfig >
+    template < typename TValue, typename TConfig >
     inline typename Size< String<TValue, External<TConfig> > >::Type
     length(String<TValue, External<TConfig> > const &me)
     {
@@ -2065,12 +1944,12 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
         return me.data_size;
     }
 
-	template < typename TValue, typename TConfig >
+    template < typename TValue, typename TConfig >
     inline typename Size< String<TValue, External<TConfig> > >::Type
     capacity(String<TValue, External<TConfig> > const &me)
     {
 //IOREV
-		typedef typename Size< String<TValue, External<TConfig> > >::Type TSize;
+        typedef typename Size< String<TValue, External<TConfig> > >::Type TSize;
         return (TSize)capacity(me.pager) * (TSize)me.PAGESIZE;
     }
 //____________________________________________________________________________
@@ -2078,235 +1957,192 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
     template < typename TValue, typename TConfig, typename TNewSize, typename TExpand >
     inline typename Size< String<TValue, External<TConfig> > >::Type
     resize(
-	    String<TValue, External<TConfig> > &me,
-		TNewSize new_length,
-		Tag<TExpand> expand)
-	{
-//IOREV
-		typedef String<TValue, External<TConfig> >	TString;
-		typedef typename TString::TPageFrame		TPageFrame;
-		typedef typename Size<TString>::Type		TSize;
-
-		resize(me.pager, enclosingBlocks(new_length, (unsigned)me.PAGESIZE), TPageFrame::UNINITIALIZED, expand);
-        if ((TSize)new_length < me.data_size && me.file) 
-		{
-			// wait for all pending transfers
-            waitForAll(me);
+        String<TValue, External<TConfig> > &me,
+        TNewSize new_length,
+        Tag<TExpand> expand)
+    {
+//IOREV
+        typedef String<TValue, External<TConfig> >          TString;
+        typedef typename TString::TPageFrame                TPageFrame;
+        typedef typename Size<TString>::Type                TSize;
+        typedef typename TString::TCache                    TCache;
+        typedef typename Iterator<TCache, Standard>::Type    TIter;
+
+        resize(me.pager, enclosingBlocks(new_length, (unsigned)me.PAGESIZE), TPageFrame::UNINITIALIZED, expand);
+        if ((TSize)new_length < me.data_size)
+        {
+
+            TIter f = begin(me.cache, Standard());
+            TIter fEnd = end(me.cache, Standard());
+
+            // remove pages from cache that are behind our new file end
+            int new_pages = (new_length + me.PAGESIZE - 1) / me.PAGESIZE;
+            for(; f != fEnd ; ++f)
+                if (f->begin && f->pageNo >= new_pages)
+                {
+                    if (f->status != READY)
+                        cancel(*f, me.file);
+                    clear(*f);
+                }
 
-			// before shrinking the file size
-            resize(me.file, (TSize)new_length * (TSize)sizeof(TValue));
+            // before shrinking the file size
             me.lastDiskPage = new_length / me.PAGESIZE;
             me.lastDiskPageSize = new_length % me.PAGESIZE;
+
+            if (me.file)
+                resize(me.file, (TSize)new_length * (TSize)sizeof(TValue));
         }
-		me.data_size = new_length;
-		return length(me);
-	}
+        me.data_size = new_length;
+        return length(me);
+    }
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig, typename TSize, typename TExpand >
     inline typename Size< String<TValue, External<TConfig> > >::Type
     reserve(
-	    String<TValue, External<TConfig> > &me,
-		TSize new_capacity,
-		Tag<TExpand> expand)
-	{
-//IOREV
-		reserve(me.pager, enclosingBlocks(new_capacity, (unsigned)me.PAGESIZE), expand);
-		return capacity(me);
-	}
+        String<TValue, External<TConfig> > &me,
+        TSize new_capacity,
+        Tag<TExpand> expand)
+    {
+//IOREV
+        reserve(me.pager, enclosingBlocks(new_capacity, (unsigned)me.PAGESIZE), expand);
+        return capacity(me);
+    }
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig, typename TSpec >
     inline typename Iterator<String<TValue, External<TConfig> >, Tag<TSpec> const>::Type
-    begin(String<TValue, External<TConfig> > &me, Tag<TSpec> const) 
-	{
+    begin(String<TValue, External<TConfig> > &me, Tag<TSpec> const)
+    {
 //IOREV
-		typedef String<TValue, External<TConfig> > TString;
-		return typename Iterator<TString, Tag<TSpec> const>::Type (&me, 0);
+        typedef String<TValue, External<TConfig> > TString;
+        return typename Iterator<TString, Tag<TSpec> const>::Type (&me, 0);
     }
 
     template < typename TValue, typename TConfig, typename TSpec >
     inline typename Iterator<String<TValue, External<TConfig> > const, Tag<TSpec> const>::Type
-    begin(String<TValue, External<TConfig> > const &me, Tag<TSpec> const) 
-	{
+    begin(String<TValue, External<TConfig> > const &me, Tag<TSpec> const)
+    {
 //IOREV
-		typedef String<TValue, External<TConfig> > TString;
-		return typename Iterator<TString const, Tag<TSpec> const>::Type (const_cast<TString*>(&me), 0);
+        typedef String<TValue, External<TConfig> > TString;
+        return typename Iterator<TString const, Tag<TSpec> const>::Type (const_cast<TString*>(&me), 0);
     }
 
     template < typename TValue, typename TConfig, typename TSpec >
     inline typename Iterator<String<TValue, External<TConfig> >, Tag<TSpec> const>::Type
-    end(String<TValue, External<TConfig> > &me, Tag<TSpec> const) 
-	{
+    end(String<TValue, External<TConfig> > &me, Tag<TSpec> const)
+    {
 //IOREV
-		typedef String<TValue, External<TConfig> > TString;
-		return typename Iterator<TString, Tag<TSpec> const>::Type (&me, length(me));
+        typedef String<TValue, External<TConfig> > TString;
+        return typename Iterator<TString, Tag<TSpec> const>::Type (&me, length(me));
     }
 
     template < typename TValue, typename TConfig, typename TSpec >
     inline typename Iterator<String<TValue, External<TConfig> > const, Tag<TSpec> const>::Type
-    end(String<TValue, External<TConfig> > const &me, Tag<TSpec> const) 
-	{
+    end(String<TValue, External<TConfig> > const &me, Tag<TSpec> const)
+    {
 //IOREV
-		typedef String<TValue, External<TConfig> > TString;
-		return typename Iterator<TString const, Tag<TSpec> const>::Type (const_cast<TString*>(&me), length(me));
+        typedef String<TValue, External<TConfig> > TString;
+        return typename Iterator<TString const, Tag<TSpec> const>::Type (const_cast<TString*>(&me), length(me));
     }
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig, typename TPos >
-    inline typename Reference<String<TValue, External<TConfig> > >::Type 
+    inline typename Reference<String<TValue, External<TConfig> > >::Type
     value(String<TValue, External<TConfig> > &me, TPos pos)
     {
 //IOREV
-	    return me[pos];
+        return me[pos];
     }
 
     template < typename TValue, typename TConfig, typename TPos >
-    inline typename Reference<String<TValue, External<TConfig> > const>::Type 
+    inline typename Reference<String<TValue, External<TConfig> > const>::Type
     value(String<TValue, External<TConfig> > const &me, TPos pos)
     {
 //IOREV
-	    return me[pos];
+        return me[pos];
     }
 //____________________________________________________________________________
 
-	template < typename TValue, typename TConfig, typename TExpand >
-	inline void
-	appendValue(String<TValue, External<TConfig> > &me, 
-				TValue const &Val_,
-				Tag<TExpand> expand)
-	{
-//IOREV
-		resize(me, me.data_size + 1, expand);
-		back(me) = Val_;
-	}
-
-//____________________________________________________________________________
-// stack interface
-
-    template < typename TValue, typename TConfig >
+    template < typename TTargetValue, typename TConfig, typename TValue, typename TExpand >
     inline void
-    push(String<TValue, External<TConfig> > &me, TValue const &Val_)
+    appendValue(String<TTargetValue, External<TConfig> > &me,
+                TValue SEQAN_FORWARD_CARG value,
+                Tag<TExpand> expand)
     {
-//IOREV
-		appendValue(me, Val_);
+        resize(me, me.data_size + 1, expand);
+        back(me) = SEQAN_FORWARD(TValue, value);
     }
 
-    template < typename TValue, typename TConfig >
+//____________________________________________________________________________
+
+    template < typename TValue, typename TConfig, typename TSource, typename TExpand >
     inline void
-    push_back(String<TValue, External<TConfig> > &me, TValue const &Val_)
+    append(String<TValue, External<TConfig> > &target,
+                TSource const &source,
+                Tag<TExpand> expand)
     {
-//IOREV _nodoc_
-		appendValue(me, Val_);
-    }
+//IOREV doc says, resize() my invalidate iterators, therefore it_target might be bogus
+        typedef String<TValue, External<TConfig> >                    TTarget;
+        typedef typename Iterator<TSource const, Standard>::Type    ISource;
+        typedef typename Iterator<TTarget, Standard>::Type            ITarget;
 
-    template < typename TValue, typename TConfig >
-	inline void pop_back(String<TValue, External<TConfig> > &me)
-    {
-//IOREV _nodoc_
-		resize(me, me.data_size - 1);
-	}
+        ITarget it_target       = end(target, Standard());
 
-    template < typename TValue, typename TConfig >
-	inline TValue &
-	front(String<TValue, External<TConfig> > &me)
-    {
-//IOREV
-		return me[0];
-	}
+        resize(target, length(target) + length(source), expand);
 
-    template < typename TValue, typename TConfig >
-	inline TValue const &
-	front(String<TValue, External<TConfig> > const &me)
-    {
-//IOREV
-		return me[0];
-	}
+        ISource it_source       = begin(source, Standard());
+        ISource it_source_end   = end(source, Standard());
 
-    template < typename TValue, typename TConfig >
-	inline TValue &
-	back(String<TValue, External<TConfig> > &me)
-    {
-//IOREV
-		return me[me.data_size - 1];
-	}
+        for (; it_source != it_source_end; ++it_source, ++it_target)
+            *it_target = *it_source;
+    }
 
-    template < typename TValue, typename TConfig >
-	inline TValue const &
-	back(String<TValue, External<TConfig> > const &me)
+    template < typename TValue, typename TConfig, typename TSourceValue, typename TExpand >
+    inline void
+    append(String<TValue, External<TConfig> > &target,
+                TSourceValue * source,
+                Tag<TExpand> expand)
     {
-//IOREV
-		return me[me.data_size - 1];
-	}
-//____________________________________________________________________________
-
-	template < typename TValue, typename TConfig, typename TSource, typename TExpand >
-	inline void
-	append(String<TValue, External<TConfig> > &target, 
-				TSource const &source,
-				Tag<TExpand> expand)
-	{
 //IOREV doc says, resize() my invalidate iterators, therefore it_target might be bogus
-		typedef String<TValue, External<TConfig> >					TTarget;
-        typedef typename Iterator<TSource const, Standard>::Type	ISource;
-        typedef typename Iterator<TTarget, Standard>::Type			ITarget;
+        typedef String<TValue, External<TConfig> >                    TTarget;
+        typedef typename Iterator<TSourceValue *, Standard>::Type    ISource;
+        typedef typename Iterator<TTarget, Standard>::Type            ITarget;
 
         ITarget it_target       = end(target, Standard());
-		
-		resize(target, length(target) + length(source), expand);
-		
-        ISource it_source       = begin(source, Standard());
-        ISource it_source_end   = end(source, Standard());
-		
-		for (; it_source != it_source_end; ++it_source, ++it_target)
-			*it_target = *it_source;
-	}
-
-	template < typename TValue, typename TConfig, typename TSourceValue, typename TExpand >
-	inline void
-	append(String<TValue, External<TConfig> > &target, 
-				TSourceValue * source,
-				Tag<TExpand> expand)
-	{
-//IOREV doc says, resize() my invalidate iterators, therefore it_target might be bogus
-		typedef String<TValue, External<TConfig> >					TTarget;
-        typedef typename Iterator<TSourceValue *, Standard>::Type	ISource;
-        typedef typename Iterator<TTarget, Standard>::Type			ITarget;
 
-        ITarget it_target       = end(target, Standard());
-		
-		resize(target, length(target) + length(source), expand);
-		
+        resize(target, length(target) + length(source), expand);
+
         ISource it_source       = begin(source, Standard());
         ISource it_source_end   = end(source, Standard());
-		
-		for (; it_source != it_source_end; ++it_source, ++it_target)
-			*it_target = *it_source;
-	}
+
+        for (; it_source != it_source_end; ++it_source, ++it_target)
+            *it_target = *it_source;
+    }
 
 
 /*
     template < typename TSpec >
-	std::ostream& operator<<(std::ostream &out, String<char, TSpec > &p) {
+    std::ostream& operator<<(std::ostream &out, String<char, TSpec > &p) {
 
         typename Iterator< String<char, TSpec > >::Type _cur = begin(p), _end = end(p);
         while (_cur != _end) {
-		    out << *_cur;
+            out << *_cur;
             ++_cur;
         }
-		return out;
-	}
+        return out;
+    }
 
     template < typename TValue, typename TSpec >
-	std::ostream& operator<<(std::ostream &out, String<TValue, TSpec > &p) {
+    std::ostream& operator<<(std::ostream &out, String<TValue, TSpec > &p) {
 
         typename Iterator< String<TValue, TSpec > >::Type _cur = begin(p), _end = end(p);
         while (_cur != _end) {
-		    out << *_cur << " ";
+            out << *_cur << " ";
             ++_cur;
         }
-		return out;
-	}
+        return out;
+    }
 */
 //____________________________________________________________________________
 // sequence -> external string
@@ -2314,55 +2150,55 @@ or @Function.openTemp@ afterwards to reach the same behaviour.
     template < typename TValue,
                typename TConfig,
                typename TSource,
-			   typename TExpand >
+               typename TExpand >
     inline void assign(
-		String<TValue, External<TConfig> > &target, 
-		TSource const &source, 
-		Tag<TExpand>) 
-	{
+        String<TValue, External<TConfig> > &target,
+        TSource const &source,
+        Tag<TExpand>)
+    {
 //IOREV
-		typedef String<TValue, External<TConfig> >					TTarget;
-        typedef typename Iterator<TSource const, Standard>::Type	ISource;
-        typedef typename Iterator<TTarget, Standard>::Type			ITarget;
+        typedef String<TValue, External<TConfig> >                    TTarget;
+        typedef typename Iterator<TSource const, Standard>::Type    ISource;
+        typedef typename Iterator<TTarget, Standard>::Type            ITarget;
 
         resize(target, length(source));
 
         ISource it_source       = begin(source, Standard());
         ISource it_source_end   = end(source, Standard());
         ITarget it_target       = begin(target, Standard());
-		
-		for (; it_source != it_source_end; ++it_source, ++it_target)
-			*it_target = *it_source;
-    }
 
+        for (; it_source != it_source_end; ++it_source, ++it_target)
+            *it_target = *it_source;
+    }
+/*
     template < typename TValue,
                typename TConfig,
                typename TSourceValue,
-			   typename TExpand >
+               typename TExpand >
     inline void assign(
-		String<TValue, External<TConfig> > &target, 
-		TSourceValue * source,
-		Tag<TExpand>) 
-	{
+        String<TValue, External<TConfig> > &target,
+        TSourceValue const * source,
+        Tag<TExpand>)
+    {
 //IOREV
-		typedef String<TValue, External<TConfig> >					TTarget;
-        typedef typename Iterator<TSourceValue *, Standard>::Type	ISource;
-        typedef typename Iterator<TTarget, Standard>::Type			ITarget;
+        typedef String<TValue, External<TConfig> >                    TTarget;
+        typedef typename Iterator<TSourceValue *, Standard>::Type    ISource;
+        typedef typename Iterator<TTarget, Standard>::Type            ITarget;
 
         resize(target, length(source));
 
         ISource it_source       = begin(source, Standard());
         ISource it_source_end   = end(source, Standard());
         ITarget it_target       = begin(target, Standard());
-		
-		for (; it_source != it_source_end; ++it_source, ++it_target)
-			*it_target = *it_source;
-    }
 
+        for (; it_source != it_source_end; ++it_source, ++it_target)
+            *it_target = *it_source;
+    }
+*/
 //____________________________________________________________________________
 
-	template < typename TValue, typename TConfig >
-    inline void const * 
+    template < typename TValue, typename TConfig >
+    inline void const *
     getObjectId(String<TValue, External<TConfig> > const &me)
     {
 //IOREV
diff --git a/seqan/file/string_mmap.h b/seqan/file/string_mmap.h
index 5cab62f..fe91fa3 100644
--- a/seqan/file/string_mmap.h
+++ b/seqan/file/string_mmap.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,6 +33,7 @@
 // ==========================================================================
 // Memory map a whole file and use it as a string.
 // ==========================================================================
+// NOTE(esiragusa): this file is deprecated.
 
 #ifndef SEQAN_HEADER_STRING_MMAP_H
 #define SEQAN_HEADER_STRING_MMAP_H
@@ -59,18 +60,27 @@ namespace SEQAN_NAMESPACE_MAIN
 
 /*!
  * @class MMapConfig
- * @headerfile <seqan/file>
- * @brief Configuration for MMapStrings.
+ * @headerfile <seqan/file.h>
+ * @brief Configuration for @link MMapString MMapStrings @endlink.
  *
  * @signature template <[typename TFile, [typename TSize]]>
  *            class MMapConfig;
  *
  * @tparam TFile The file type to use for the memory mapped string.  Defaults to <tt>File&lt;&gt;</tt>
  * @tparam TSize The size type to use.  Defaults to <tt>size_t</tt>.
+ *
+ *
+ * @typedef MMapConfig::TFile;
+ * @signature typedef (..) MMapConfig::TFile;
+ * @brief The type to use for files.
+ *
+ * @typedef MMapConfig::TSize;
+ * @signature typedef (..) MMapConfig::TSize;
+ * @brief The type to use for sizes.
  */
 
-    template < typename TFile_ = File<>,				// default file type
-               typename TSize_ = size_t >				// size type
+    template < typename TFile_ = File<>,                // default file type
+               typename TSize_ = size_t >                // size type
     struct MMapConfig {
 //IOREV _nodoc_ doc says using MMap<MMapConfig> is correct, whats this for?
         typedef TFile_ TFile;
@@ -80,24 +90,23 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TConfig = MMapConfig<> >
     struct MMap {};
 //IOREV
-	
-	
-	//////////////////////////////////////////////////////////////////////////////
+
+
+    //////////////////////////////////////////////////////////////////////////////
     // Memory Mapped String
     //////////////////////////////////////////////////////////////////////////////
 
 /*!
- * @class MMapString
+ * @class MMapString MMap String
  * @headerfile <seqan/file.h>
+ * @extends String
  * @brief String that is stored in external memory using direct memory mapping.
  *
  * @signature template <typename TValue[, typename TConfig]>
  *            class String<TValue, MMap<TConfig> >;
  *
  * @tparam TValue  The value type to use for the items/characters.
- * @tparam TConfig The configuration to use for the underlying file.  Default: MMapConfig.
- *
- * @section Remarks
+ * @tparam TConfig The configuration to use for the underlying file.  Default: @link MMapConfig @endlink.
  *
  * The MMap String enables to access sequences larger than the available physical memory (RAM) by using external memory
  * (e.g. Hard disk, Network storage, ...) mapped into memory.  The size of the string is limited by external memory and
@@ -114,118 +123,111 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature String::String(file);
  * @signature String::String(fileName[, openMode]);
  *
- * @param[in]     file     The @link File @endlink to use for reading and writing.  You must ensture that
+ * @param[in,out] file     The @link File @endlink to use for reading and writing.  You must ensture that
  *                         <tt>file</tt> is open as the string will not call <tt>open</tt> and <tt>close</tt>
  *                         on the file.
- * @param[in]     fileName The path to open. Type: <tt>char const *</tt>
- * @param[in,out] openMode The open mode.
+ * @param[in]     fileName The path to open.  Type: <tt>char const *</tt>
+ * @param[in]     openMode The open mode.
  */
 
-/**
-.Spec.MMap String:
-..cat:Strings
-..general:Class.String
-..summary:String that is stored in external memory. Uses memory mapping.
-..signature:String<TValue, MMap<> >
-..signature:String<TValue, MMap<TConfig> >
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..param.TConfig:A structure to configure the memory mapped string.
-...type:Tag.ExternalConfig
-...type:Tag.ExternalConfigLarge
-...type:Tag.ExternalConfigSize
-...default:@Tag.ExternalConfig@
-..remarks:The MMap String enables to access sequences larger than the available physical memory (RAM) by using
-external memory (e.g. Hard disk, Network storage, ...) mapped into memory.
-The size of the string is limited by external memory and the logical address space (4GB on a 32bit OS).
-See the @Memfunc.External String#String@ constructor for more details.
-..remarks:This String also supports fast appending and removing of values at the end (see @Spec.Block String@, @Function.appendValue@)
-..include:seqan/file.h
-*/
-
     template < typename TValue,
                typename TConfig >
-	class String<TValue, MMap<TConfig> >
-	{
+    class String<TValue, MMap<TConfig> >
+    {
 //IOREV
-	public:
+    public:
 
-        typedef typename TConfig::TFile		TFile;
-        typedef typename TConfig::TSize		TSize;
+        typedef typename TConfig::TFile        TFile;
+        typedef typename TConfig::TSize        TSize;
 
-		TValue                  *data_begin;
-		TValue                  *data_end;
+        TValue                  *data_begin;
+        TValue                  *data_end;
 
-		FileMapping<>           mapping;
-		FileMappingAdvise       advise;
+        FileMapping<>           mapping;
+        FileMappingAdvise       advise;
 
-		explicit
+        explicit
         String(TSize size = 0):
-			data_begin(NULL),
-			data_end(NULL),
-			advise(MAP_NORMAL)
+            data_begin(NULL),
+            data_end(NULL),
+            advise(MAP_NORMAL)
         {
-			resize(*this, size);
+            resize(*this, size);
         }
 
-		explicit
+        // associate a file
+        explicit
         String(TFile &_file):
-			data_begin(NULL),
-			data_end(NULL),
-			advise(MAP_NORMAL)
+            data_begin(NULL),
+            data_end(NULL),
+            advise(MAP_NORMAL)
         {
-			open(*this, _file);
+            open(*this, _file);
         }
 
-		explicit
+        // associate a file given filename [and open mode]
+        explicit
         String(const char *fileName, int openMode = DefaultOpenMode<TFile>::VALUE):
-			data_begin(NULL),
-			data_end(NULL),
-			advise(MAP_NORMAL)
+            data_begin(NULL),
+            data_end(NULL),
+            advise(MAP_NORMAL)
+        {
+            open(*this, fileName, openMode);
+        }
+
+        // copy the contents from another string
+        String(String const & source):
+            data_begin(NULL),
+            data_end(NULL),
+            advise(MAP_NORMAL)
+        {
+            assign(*this, source);
+        }
+        template <typename TSource>
+        String(TSource const & source):
+            data_begin(NULL),
+            data_end(NULL),
+            advise(MAP_NORMAL)
+        {
+            assign(*this, source);
+        }
+
+        template <typename TSource>
+        String & operator =(TSource const & source)
+        {
+            assign(*this, source);
+            return *this;
+        }
+        String & operator =(String const & source)
         {
-			open(*this, fileName, openMode);
+            assign(*this, source);
+            return *this;
         }
 
-		template <typename TSource>
-		String & operator =(TSource const & source)
-		{
-	SEQAN_CHECKPOINT
-			assign(*this, source);
-			return *this;
-		}
-		String & operator =(String const & source)
-		{
-	SEQAN_CHECKPOINT
-			assign(*this, source);
-			return *this;
-		}
-
-		~String() 
-		{
-			close(*this);
-		}
+        ~String()
+        {
+            close(*this);
+        }
 
 //____________________________________________________________________________
 
-		template <typename TPos>
-		inline typename Reference<String>::Type
-		operator [] (TPos pos)
-		{
-	SEQAN_CHECKPOINT
-			return value(*this, pos);
-		}
-
-		template <typename TPos>
-		inline typename Reference<String const>::Type 
-		operator [] (TPos pos) const
-		{
-	SEQAN_CHECKPOINT
-			return value(*this, pos);
-		}
+        template <typename TPos>
+        inline typename Reference<String>::Type
+        operator [] (TPos pos)
+        {
+            return value(*this, pos);
+        }
+
+        template <typename TPos>
+        inline typename Reference<String const>::Type
+        operator [] (TPos pos) const
+        {
+            return value(*this, pos);
+        }
 
 //____________________________________________________________________________
 
-        inline operator bool() 
+        inline operator bool()
         {
             return mapping;
         }
@@ -235,68 +237,68 @@ See the @Memfunc.External String#String@ constructor for more details.
 };
 
     template < typename TValue, typename TConfig >
-	inline typename Iterator<String<TValue, MMap<TConfig> > , Standard>::Type
-	begin(String<TValue, MMap<TConfig> > & me,
-		Standard)
-	{
+    inline typename Iterator<String<TValue, MMap<TConfig> > , Standard>::Type
+    begin(String<TValue, MMap<TConfig> > & me,
+        Standard)
+    {
 //IOREV
 SEQAN_CHECKPOINT
-		return me.data_begin;
-	}
+        return me.data_begin;
+    }
     template < typename TValue, typename TConfig >
-	inline typename Iterator<String<TValue, MMap<TConfig> >  const, Standard>::Type
-	begin(String<TValue, MMap<TConfig> > const & me,
-		Standard)
-	{
+    inline typename Iterator<String<TValue, MMap<TConfig> >  const, Standard>::Type
+    begin(String<TValue, MMap<TConfig> > const & me,
+        Standard)
+    {
 //IOREV
 SEQAN_CHECKPOINT
-		return me.data_begin;
-	}
+        return me.data_begin;
+    }
 
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig >
     inline typename Iterator<String<TValue, MMap<TConfig> > , Standard>::Type
-	end(String<TValue, MMap<TConfig> > & me,
-		Standard)
-	{
+    end(String<TValue, MMap<TConfig> > & me,
+        Standard)
+    {
 //IOREV
 SEQAN_CHECKPOINT
-		return me.data_end;
-	}
+        return me.data_end;
+    }
     template < typename TValue, typename TConfig >
-	inline typename Iterator<String<TValue, MMap<TConfig> >  const, Standard>::Type
-	end(String<TValue, MMap<TConfig> > const & me,
-		Standard)
-	{
+    inline typename Iterator<String<TValue, MMap<TConfig> >  const, Standard>::Type
+    end(String<TValue, MMap<TConfig> > const & me,
+        Standard)
+    {
 //IOREV
 SEQAN_CHECKPOINT
-		return me.data_end;
-	}
+        return me.data_end;
+    }
 
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig >
-	inline typename Size<String<TValue, MMap<TConfig> > >::Type
-	capacity(String<TValue, MMap<TConfig> > const & me) 
-	{
+    inline typename Size<String<TValue, MMap<TConfig> > >::Type
+    capacity(String<TValue, MMap<TConfig> > const & me)
+    {
 //IOREV
 SEQAN_CHECKPOINT
-		return length(me.mapping) / sizeof(TValue);
-	}
+        return length(me.mapping) / sizeof(TValue);
+    }
 
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig >
-	inline void 
-	_setLength(
-		String<TValue, MMap<TConfig> > & me, 
-		size_t new_length)
-	{
+    inline void
+    _setLength(
+        String<TValue, MMap<TConfig> > & me,
+        size_t new_length)
+    {
 //IOREV
 SEQAN_CHECKPOINT
-		me.data_end = me.data_begin + new_length;
-	}
+        me.data_end = me.data_begin + new_length;
+    }
 
     //////////////////////////////////////////////////////////////////////////////
     // meta-function interface
@@ -312,43 +314,43 @@ SEQAN_CHECKPOINT
     struct Difference< String<TValue, MMap<TConfig> > >
     {
 //IOREV
-		typedef typename MakeSigned_<typename TConfig::TSize>::Type Type;
+        typedef typename MakeSigned_<typename TConfig::TSize>::Type Type;
     };
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig >
-	struct DefaultOverflowExplicit<String<TValue, MMap<TConfig> > >
-	{
+    struct DefaultOverflowExplicit<String<TValue, MMap<TConfig> > >
+    {
 //IOREV
-		typedef Generous Type;
-	};
+        typedef Generous Type;
+    };
 
     template < typename TValue, typename TConfig >
-	struct DefaultOverflowImplicit<String<TValue, MMap<TConfig> > >
-	{
+    struct DefaultOverflowImplicit<String<TValue, MMap<TConfig> > >
+    {
 //IOREV
-		typedef Generous Type;
-	};
+        typedef Generous Type;
+    };
 //____________________________________________________________________________
 
     template < typename TValue, typename TConfig >
-	struct IsContiguous< String<TValue, MMap<TConfig> > >
-	{
+    struct IsContiguous< String<TValue, MMap<TConfig> > >
+    {
 //IOREV
-		typedef True Type;
-		enum { VALUE = true };
-	};
+        typedef True Type;
+        enum { VALUE = true };
+    };
 
     template < typename TValue, typename TConfig >
-	struct AllowsFastRandomAccess< String<TValue, MMap<TConfig> > >
-	{
+    struct AllowsFastRandomAccess< String<TValue, MMap<TConfig> > >
+    {
 //IOREV
-		typedef False Type;
-		enum { VALUE = false };
-	};
+        typedef False Type;
+        enum { VALUE = false };
+    };
 
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // global interface
 
 //____________________________________________________________________________
@@ -363,51 +365,35 @@ SEQAN_CHECKPOINT
  */
 
     template < typename TValue, typename TConfig >
-	inline bool
-	flush(String<TValue, MMap<TConfig> > &me)
-	{
+    inline bool
+    flush(String<TValue, MMap<TConfig> > &me)
+    {
         typedef typename Size<typename TConfig::TFile>::Type TFileSize;
         return flushFileSegment(
             me.mapping,
             me.data_begin,
             0,
             (TFileSize)capacity(me) * (TFileSize)sizeof(TValue));
-	}
+    }
 
 /*!
  * @fn MMapString#mmapAdvise
  * @brief Call advise function for memory mapped files.
  *
- * @signature bool mmapAdvise(mmapString, scheme[, beginPos, size]);
+ * @signature bool mmapAdvise(str, scheme[, beginPos, size]);
  *
- * @param mmapString The MMapString to call advise in.
- * @param scheme     The memory access scheme to use.  Type: FileMappingAdvise.
- * @param beginPos   Begin position in the string for the advise call.
- * @param size       Size of the range used for the advise call.
+ * @param[in,out] str        The MMapString to call advise in.
+ * @param[in]     scheme     The memory access scheme to use.  Type: FileMappingAdvise.
+ * @param[in]     beginPos   Begin position in the string for the advise call.
+ * @param[in]     size       Size of the range used for the advise call.
  *
  * @return bool <tt>true</tt> if the advise was successful, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.mmapAdvise
-..class:Spec.MMap String
-..cat:Sequences
-..summary:Call advise function for memory mapped files.
-..signature:mmapAdvise(mmapString, scheme[, beginPos, size])
-..param.mmapString:The @Spec.MMap String@ that contains the location in the advise call.
-...type:Spec.MMap String
-..param.scheme:The memory access scheme to use.
-...type:Enum.FileMappingAdvise
-..param.beginPos:Begin position in the string for the advise call.
-..param.size:Size of the range used for the advise call.
-..returns:$int$, return code 0 on success.
-..see:Enum.FileMappingAdvise
-..include:seqan/file.h
- */
     template <typename TValue, typename TConfig, typename TPos, typename TSize>
-	inline bool
-	mmapAdvise(String<TValue, MMap<TConfig> > &me, FileMappingAdvise advise, TPos beginPos, TSize size)
-	{
+    inline bool
+    mmapAdvise(String<TValue, MMap<TConfig> > &me, FileMappingAdvise advise, TPos beginPos, TSize size)
+    {
         typedef typename Size<typename TConfig::TFile>::Type TFileSize;
         me.advise = advise;
         return adviseFileSegment(
@@ -416,57 +402,57 @@ SEQAN_CHECKPOINT
             me.data_begin,
             (TFileSize)beginPos * (TFileSize)sizeof(TValue),
             (TFileSize)size * (TFileSize)sizeof(TValue));
-	}
+    }
 
     template <typename TValue, typename TConfig, typename TPos>
-	inline int
-	mmapAdvise(String<TValue, MMap<TConfig> > &me, FileMappingAdvise advise, TPos beginPos)
-	{
-		return mmapAdvise(me, advise, beginPos, capacity(me) - beginPos);
-	}
-		
+    inline int
+    mmapAdvise(String<TValue, MMap<TConfig> > &me, FileMappingAdvise advise, TPos beginPos)
+    {
+        return mmapAdvise(me, advise, beginPos, capacity(me) - beginPos);
+    }
+
     template <typename TValue, typename TConfig>
-	inline int
-	mmapAdvise(String<TValue, MMap<TConfig> > &me, FileMappingAdvise advise)
-	{
-		return mmapAdvise(me, advise, 0, capacity(me));
-	}
-		
+    inline int
+    mmapAdvise(String<TValue, MMap<TConfig> > &me, FileMappingAdvise advise)
+    {
+        return mmapAdvise(me, advise, 0, capacity(me));
+    }
+
 //____________________________________________________________________________
 
-	// cancel all transactions
+    // cancel all transactions
     template < typename TValue, typename TConfig >
-	inline void 
-	cancel(String<TValue, MMap<TConfig> > &me)
-	{
+    inline void
+    cancel(String<TValue, MMap<TConfig> > &me)
+    {
         typedef typename Size<typename TConfig::TFile>::Type TFileSize;
         cancelFileSegment(
             me.mapping,
             me.data_begin,
             0,
             (TFileSize)capacity(me) * (TFileSize)sizeof(TValue));
-	}
+    }
 
 //____________________________________________________________________________
 
-	// flush and free all allocated pages
+    // flush and free all allocated pages
     template < typename TValue, typename TConfig >
-	inline bool
-	flushAndFree(String<TValue, MMap<TConfig> > &me)
-	{
+    inline bool
+    flushAndFree(String<TValue, MMap<TConfig> > &me)
+    {
         return flush(me) && mmapAdvise(me, MAP_DONTNEED);
-	}
-    
+    }
+
 //____________________________________________________________________________
 
-	template < typename TValue, typename TConfig >
-    inline bool 
+    template < typename TValue, typename TConfig >
+    inline bool
     _map(String<TValue, MMap<TConfig> > &me, size_t new_capacity)
-	{
+    {
         typedef typename Size<typename TConfig::TFile>::Type TFileSize;
-		if (new_capacity > 0)
-		{
-			_ensureFileIsOpen(me);
+        if (new_capacity > 0)
+        {
+            _ensureFileIsOpen(me);
             if (capacity(me) < new_capacity)
                 resize(me.mapping, (TFileSize)new_capacity * (TFileSize)sizeof(TValue));
             me.data_begin = static_cast<TValue*>(mapFileSegment(me.mapping, 0, length(me.mapping)));
@@ -476,33 +462,33 @@ SEQAN_CHECKPOINT
                 return false;
             }
             adviseFileSegment(me.mapping, me.advise, me.data_begin, 0, length(me.mapping));
-		}
+        }
         else
-			resize(me.mapping, 0);
+            resize(me.mapping, 0);
         _setLength(me, new_capacity);
-		return true;
-	}
-
-	template < typename TValue, typename TConfig >
-    inline bool 
-    _unmap(String<TValue, MMap<TConfig> > &me) 
-	{
-		bool result = true;
-		if (me.data_begin != NULL)
-		{
+        return true;
+    }
+
+    template < typename TValue, typename TConfig >
+    inline bool
+    _unmap(String<TValue, MMap<TConfig> > &me)
+    {
+        bool result = true;
+        if (me.data_begin != NULL)
+        {
             result = unmapFileSegment(me.mapping, me.data_begin, length(me.mapping));
-			me.data_begin = NULL;
-		}
+            me.data_begin = NULL;
+        }
         me.data_end = NULL;
-		return result;
-	}
+        return result;
+    }
 
-	template < typename TValue, typename TConfig, typename TCapSize >
-    inline bool 
-    _remap(String<TValue, MMap<TConfig> > &me, TCapSize new_capacity) 
-	{
-		typedef typename Size<String<TValue, MMap<TConfig> > >::Type	TSize;
-        typedef typename Size<typename TConfig::TFile>::Type			TFileSize;
+    template < typename TValue, typename TConfig, typename TCapSize >
+    inline bool
+    _remap(String<TValue, MMap<TConfig> > &me, TCapSize new_capacity)
+    {
+        typedef typename Size<String<TValue, MMap<TConfig> > >::Type    TSize;
+        typedef typename Size<typename TConfig::TFile>::Type            TFileSize;
 
         bool result = true;
 
@@ -538,50 +524,47 @@ SEQAN_CHECKPOINT
         result &= _unmap(me);
         result &= _map(me, new_capacity);
         return result;
-	}
+    }
 
-	template < typename TValue, typename TConfig >
-    inline void 
-    clear(String<TValue, MMap<TConfig> > &me) 
-	{
+    template < typename TValue, typename TConfig >
+    inline void
+    clear(String<TValue, MMap<TConfig> > &me)
+    {
 //IOREV
-		cancel(me);
-		_unmap(me);
-		resize(me.mapping, 0);
-	}
+        cancel(me);
+        _unmap(me);
+        resize(me.mapping, 0);
+    }
 //____________________________________________________________________________
 
-	template < typename TValue, typename TConfig, typename TSize >
-    inline typename Value<String<TValue, MMap<TConfig> > >::Type * 
-    _allocateStorage(String<TValue, MMap<TConfig> > &me, TSize new_capacity) 
-	{
+    template < typename TValue, typename TConfig, typename TSize >
+    inline typename Value<String<TValue, MMap<TConfig> > >::Type *
+    _allocateStorage(String<TValue, MMap<TConfig> > &me, TSize new_capacity)
+    {
 //IOREV
-		_map(me, _computeSizeForCapacity(me, new_capacity));
-		return NULL;
-	}
+        _map(me, _computeSizeForCapacity(me, new_capacity));
+        return NULL;
+    }
 
-	template < typename TValue, typename TConfig, typename TSize >
-    inline typename Value<String<TValue, MMap<TConfig> > >::Type * 
+    template < typename TValue, typename TConfig, typename TSize >
+    inline typename Value<String<TValue, MMap<TConfig> > >::Type *
     _reallocateStorage(
-		String<TValue, MMap<TConfig> > &me,
-		TSize new_capacity) 
-	{
+        String<TValue, MMap<TConfig> > &me,
+        TSize new_capacity)
+    {
 //IOREV
-		TSize size = _computeSizeForCapacity(me, new_capacity);
-		_remap(me, size);
-		return NULL;
-	}
+        TSize size = _computeSizeForCapacity(me, new_capacity);
+        _remap(me, size);
+        return NULL;
+    }
 
-	template < typename TValue, typename TConfig, typename TSize >
+    template < typename TValue, typename TConfig, typename TSize >
     inline void
     _deallocateStorage(String<TValue, MMap<TConfig> > &/*me*/, TValue * /*ptr*/, TSize /*capacity*/)
-	{
+    {
 //IOREV
-	}
+    }
 //____________________________________________________________________________
-///.Function.open.param.string.type:Spec.MMap String
-///.Function.open.class:Spec.MMap String
-
 /*!
  * @fn MMapString#open
  * @brief Open the MMapString's underlying file from a path.
@@ -595,43 +578,40 @@ SEQAN_CHECKPOINT
  * @return bool <tt>true</tt> if the operation succeeded and <tt>false</tt> otherwise.
  */
 
-	template < typename TValue, typename TConfig >
-    inline bool 
-    open(String<TValue, MMap<TConfig> > &me, const char *fileName, int openMode) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    open(String<TValue, MMap<TConfig> > &me, const char *fileName, int openMode)
+    {
 //IOREV
-		close(me);
-		if (open(me.mapping, fileName, openMode))
-			return _map(me, capacity(me));
-		return false;
+        close(me);
+        if (open(me.mapping, fileName, openMode))
+            return _map(me, capacity(me));
+        return false;
     }
 
-	template < typename TValue, typename TConfig >
-    inline bool 
-    open(String<TValue, MMap<TConfig> > &me, const char *fileName) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    open(String<TValue, MMap<TConfig> > &me, const char *fileName)
+    {
 //IOREV
-		typedef typename String<TValue, MMap<TConfig> >::TFile	TFile;
-		return open(me, fileName, DefaultOpenMode<TFile>::VALUE);
+        typedef typename String<TValue, MMap<TConfig> >::TFile    TFile;
+        return open(me, fileName, DefaultOpenMode<TFile>::VALUE);
     }
 
-	template < typename TValue, typename TConfig >
-    inline bool 
-    open(String<TValue, MMap<TConfig> > &me, typename TConfig::TFile file) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    open(String<TValue, MMap<TConfig> > &me, typename TConfig::TFile file)
+    {
 //IOREV
-		close(me);
-		if (open(me.mapping, file))
-			return _map(me, capacity(me));
-		return false;
+        close(me);
+        if (open(me.mapping, file))
+            return _map(me, capacity(me));
+        return false;
     }
 
-///.Function.openTemp.param.string.type:Spec.MMap String
-///.Function.openTemp.class:Spec.MMap String
-
 /*!
  * @fn MMapString#openTemp
- * @signature Open an MMapString using an temporary file.
+ * @brief Open an MMapString using an temporary file.
  *
  * @signature bool openTemp(str);
  *
@@ -640,59 +620,56 @@ SEQAN_CHECKPOINT
  * @return bool <tt>true</tt> if opening succeeded, <tt>false</tt> otherwise.
  */
 
-	template < typename TValue, typename TConfig >
-    inline bool 
-    openTemp(String<TValue, MMap<TConfig> > &me) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    openTemp(String<TValue, MMap<TConfig> > &me)
+    {
 //IOREV
-		close(me);
-		return openTemp(me.mapping);
+        close(me);
+        return openTemp(me.mapping);
     }
 //____________________________________________________________________________
 
-	template < typename TValue, typename TConfig >
-	inline void
+    template < typename TValue, typename TConfig >
+    inline void
     _ensureFileIsOpen(String<TValue, MMap<TConfig> > &me)
-	{
+    {
 //IOREV
-		if (!me)
-		{
-			if (!openTemp(me.mapping))
-				SEQAN_FAIL("Memory Mapped String couldn't open temporary file");
-		}
-	}
+        if (!me)
+        {
+            if (!openTemp(me.mapping))
+                SEQAN_FAIL("Memory Mapped String couldn't open temporary file");
+        }
+    }
 //____________________________________________________________________________
 
-	template < typename TValue, typename TConfig >
-    inline bool 
+    template < typename TValue, typename TConfig >
+    inline bool
     save(String<TValue, MMap<TConfig> > const &/*me*/, const char * /*fileName*/, int /*openMode*/) {
 //IOREV _nodoc_ shouldn't we flush here? in case of abnormal termination...
-		// Memory Mapped Strings are persistent, thus there is no need to save them
-		//MMapStringsDontNeedToBeSaved error;
-		return true;
-	}
+        // Memory Mapped Strings are persistent, thus there is no need to save them
+        //MMapStringsDontNeedToBeSaved error;
+        return true;
+    }
 
-	template < typename TValue, typename TConfig >
-    inline bool 
+    template < typename TValue, typename TConfig >
+    inline bool
     save(String<TValue, MMap<TConfig> > const &/*me*/, const char * /*fileName*/) {
 //IOREV _nodoc_ shouldn't we flush here? in case of abnormal termination...
-		// Memory Mapped Strings are persistent, thus there is no need to save them
-		//MMapStringsDontNeedToBeSaved error;
-		return true;
-	}
+        // Memory Mapped Strings are persistent, thus there is no need to save them
+        //MMapStringsDontNeedToBeSaved error;
+        return true;
+    }
 
-	template < typename TValue, typename TConfig >
-    inline bool 
+    template < typename TValue, typename TConfig >
+    inline bool
     save(String<TValue, MMap<TConfig> > const &/*me*/, typename TConfig::TFile /*file*/) {
 //IOREV _nodoc_ shouldn't we flush here? in case of abnormal termination...
-		// Memory Mapped Strings are persistent, thus there is no need to save them
-		//MMapStringsDontNeedToBeSaved error;
-		return true;
-	}
+        // Memory Mapped Strings are persistent, thus there is no need to save them
+        //MMapStringsDontNeedToBeSaved error;
+        return true;
+    }
 //____________________________________________________________________________
-///.Function.close.param.string.type:Spec.MMap String
-///.Function.close.class:Spec.MMap String
-
 /*!
  * @fn MMapString#close
  * @brief Close the MMapString.
@@ -704,24 +681,32 @@ SEQAN_CHECKPOINT
  * @return bool <tt>true</tt> if the closing succeeded, <tt>false</tt> otherwise.
  */
 
-	template < typename TValue, typename TConfig >
-    inline bool 
-    close(String<TValue, MMap<TConfig> > &me) 
-	{
+    template < typename TValue, typename TConfig >
+    inline bool
+    close(String<TValue, MMap<TConfig> > &me)
+    {
         typedef typename Size<typename TConfig::TFile>::Type TFileSize;
 
-		if (me)
-		{
+        if (me)
+        {
             TFileSize finalLen = (TFileSize)length(me) * (TFileSize)sizeof(TValue);
 
-			// close associated file
-			if (me.mapping.temporary)
-				cancel(me);
+            // close associated file
+            if (me.mapping.temporary)
+                cancel(me);
 
             _unmap(me);
-			closeAndResize(me.mapping, finalLen);
-		}
-		return true;
+            closeAndResize(me.mapping, finalLen);
+        }
+        return true;
+    }
+
+
+    template < typename TValue, typename TConfig >
+    inline void
+    shrinkToFit(String<TValue, MMap<TConfig> > &me)
+    {
+        _remap(me, length(me));
     }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/find.h b/seqan/find.h
index 20309e0..3f3130d 100644
--- a/seqan/find.h
+++ b/seqan/find.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,11 +33,11 @@
 #ifndef SEQAN_HEADER_FIND_H
 #define SEQAN_HEADER_FIND_H
 
-//____________________________________________________________________________
-// prerequisites
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
 
 #include <cmath>
-
 #include <deque>
 
 #include <seqan/sequence.h>
@@ -46,14 +46,19 @@
 #include <seqan/graph_types.h>
 #include <seqan/graph_algorithms.h>
 #include <seqan/map.h>
+#include <seqan/parallel.h>
 
-//____________________________________________________________________________
+// ===========================================================================
+// Base headers.
+// ===========================================================================
 
 #include <seqan/find/find_base.h>
 #include <seqan/find/find_pattern_base.h>
 
-//____________________________________________________________________________
-// exact pattern matching
+// ===========================================================================
+// Exact pattern matching.
+// ===========================================================================
+
 #include <seqan/find/find_simple.h>
 #include <seqan/find/find_horspool.h>
 #include <seqan/find/find_shiftand.h>
@@ -61,22 +66,28 @@
 #include <seqan/find/find_bndm.h>
 #include <seqan/find/find_bom.h>
 
-//____________________________________________________________________________
-//complex pattern matching
+// ===========================================================================
+// Pattern matching with wildcards.
+// ===========================================================================
+
 #include <seqan/find/find_wild_shiftand.h>
 
-//____________________________________________________________________________
-//multiple pattern search
+// ===========================================================================
+// Multiple exact pattern matching.
+// ===========================================================================
+
 #include <seqan/find/find_ahocorasick.h>
 #include <seqan/find/find_multiple_shiftand.h>
 #include <seqan/find/find_set_horspool.h>
 
 //#include <seqan/find/find_multi.h> //wegwerfen
-#include <seqan/find/find_wumanber.h> 
+#include <seqan/find/find_wumanber.h>
 #include <seqan/find/find_multiple_bfam.h>
 
-//____________________________________________________________________________
-// approximate pattern matching
+// ===========================================================================
+// Approximate pattern matching.
+// ===========================================================================
+
 #include <seqan/find/find_begin.h>
 
 #include <seqan/find/find_score.h>
@@ -86,6 +97,12 @@
 
 #include <seqan/find/find_hamming_simple.h>
 
-//____________________________________________________________________________
+// ===========================================================================
+// Lambda interface.
+// ===========================================================================
+
+#ifdef SEQAN_CXX11_STANDARD
+#include <seqan/find/find_lambda.h>
+#endif
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/find/INFO b/seqan/find/INFO
deleted file mode 100644
index 40c592a..0000000
--- a/seqan/find/INFO
+++ /dev/null
@@ -1,13 +0,0 @@
-Name: seqan-find
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: SeqAn core module with online string search algorithms.
- The find module contains the basic types and interface functions for online
- string search algorithm, together with implementations of approximate (with
- Hamming distance, Levenshtein distance and score-based error models) and
- implementations of string search algorithms for one or multiple patterns.
diff --git a/seqan/find/find_abndm.h b/seqan/find/find_abndm.h
index 42efb43..d7958ae 100644
--- a/seqan/find/find_abndm.h
+++ b/seqan/find/find_abndm.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -53,7 +53,7 @@ inline void _printMask(String <unsigned> const &  mask,String <char> name)
         }
         std::cout << " ";
     }
-    std::cout << ::std::endl;
+    std::cout << std::endl;
 }
 
 inline void _printMask(String <unsigned> const &  mask,unsigned start, unsigned len,String <char> name)
@@ -65,7 +65,7 @@ inline void _printMask(String <unsigned> const &  mask,unsigned start, unsigned
         }
         std::cout << " ";
     }
-    std::cout << ::std::endl;
+    std::cout << std::endl;
 }
 
 #endif
@@ -80,40 +80,24 @@ inline void _printMask(String <unsigned> const &  mask,unsigned start, unsigned
  * @headerfile <seqan/find.h>
  * @brief Approximate Backward Nondeterministic Dawg Matching algorithm.
  *
- * Approximate string matchin gusing bit parallelism.
+ * Approximate string matching using bit parallelism.
  *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, AbndmAlgo>;
  *
- * @tparam TNeedle The needle type.  Type @link SequenceConcept @endlink.
+ * @tparam TNeedle The needle type.  Type @link ContainerConcept @endlink.
  *
- * @section Remarks
- *
- * The types of the needle and the haystack have to match.
+ * @note The types of the needle and the haystack have to match.
  */
 
-/**
-.Spec.AbndmAlgo:
-..summary: Approximate Backward Nondeterministic Dawg Matching algorithm. Approximate string matching using bit parallelism.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, AbndmAlgo>
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks.text:The types of the needle and the haystack have to match.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.AbndmAlgo
-
 
-struct AbndmAlgo; 
+struct AbndmAlgo;
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle>
 struct FindBeginPatternSpec< Pattern<TNeedle, AbndmAlgo> >:
-	DefaultFindBeginPatternSpec<>
+    DefaultFindBeginPatternSpec<>
 {
 };
 
@@ -121,7 +105,7 @@ struct FindBeginPatternSpec< Pattern<TNeedle, AbndmAlgo> >:
 
 template <typename TNeedle>
 class Pattern<TNeedle, AbndmAlgo>:
-	public FindBegin_<Pattern<TNeedle, AbndmAlgo> >
+    public FindBegin_<Pattern<TNeedle, AbndmAlgo> >
 {
 //////////////////////////////////////////////////////////////////////////////
 public:
@@ -133,7 +117,7 @@ class Pattern<TNeedle, AbndmAlgo>:
 
     TWord blockCount;
     TWord last;
-    TWord needleLength;				// e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
+    TWord needleLength;                // e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
     TWord haystackLength;
     TWord limit;                    // the maximal accepted error
     TWord cP;  // save current position of the nfa
@@ -143,73 +127,102 @@ class Pattern<TNeedle, AbndmAlgo>:
     Pattern<TNeedle,MyersUkkonen> verifier;
 //////////////////////////////////////////////////////////////////////////////
 
-    Pattern() {}
+    Pattern() :
+        blockCount(0), last(0), needleLength(0), haystackLength(0), limit(1), cP(0), findNext(false)
+    {}
 
+#ifdef SEQAN_CXX11_STANDARD
     template <typename TNeedle2>
-    Pattern(TNeedle2 const & ndl)
-        : limit(1),cP(0),verifier(ndl,-1)
-	{
-            setHost(*this, ndl);
-	}
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>)) :
+        blockCount(0),
+        last(0),
+        needleLength(0),
+        haystackLength(0),
+        limit(1),
+        cP(0),
+        findNext(false),
+        verifier(std::forward<TNeedle2>(ndl), -1)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
 
     template <typename TNeedle2>
-    Pattern(TNeedle2 const & ndl, int _limit = -1)
-		: limit(- _limit)
-		, cP(0)
-		, verifier(ndl,_limit)
-	{
-		SEQAN_CHECKPOINT
-		setHost(*this, ndl);
-	}
-
-
+    Pattern(TNeedle2 && ndl, int _limit = -1) :
+        blockCount(0),
+        last(0),
+        needleLength(0),
+        haystackLength(0),
+        limit(- _limit),
+        cP(0),
+        findNext(false),
+        verifier(std::forward<TNeedle2>(ndl), _limit)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl) :
+        blockCount(0), last(0), needleLength(0), haystackLength(0), limit(1), cP(0), findNext(false),
+        verifier(ndl,-1)
+    {
+        setHost(*this, ndl);
+    }
 
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl, int _limit = -1) :
+        limit(- _limit), cP(0), verifier(ndl,_limit)
+    {
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle>
-void _printR(Pattern<TNeedle, AbndmAlgo> & me) 
+void _printR(Pattern<TNeedle, AbndmAlgo> & me)
 {
-    ::std::cout << "R ----------------------------- " << ::std::endl;
+    std::cout << "R ----------------------------- " << std::endl;
     for(unsigned i = 0;i <= me.limit;++i)
     {
         _printMask(me.r_table,me.blockCount * i, me.blockCount ," ");
     }
-    ::std::cout << " ------------------------------ " << ::std::endl;
+    std::cout << " ------------------------------ " << std::endl;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, AbndmAlgo> & me, TNeedle2 const& needle) 
+template <typename TNeedle>
+void _reinitPattern(Pattern<TNeedle, AbndmAlgo> & me)
 {
 SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
+    typedef unsigned int TWord;
     typedef typename Value<TNeedle>::Type TValue;
 
     me.cP = 0;
     me.findNext = false;
 
-    me.needleLength = length(needle);
-    if (me.needleLength<1) 
+    me.needleLength = length(needle(me));
+    if (me.needleLength<1)
         me.blockCount = 1;
-    else 
+    else
         me.blockCount = ((me.needleLength-1) / BitsPerValue<TWord>::VALUE)+1;
-			
+
     clear(me.b_table);
     resize(me.b_table, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
 
     for (TWord j = 0; j < me.needleLength; ++j) {
         // Determine character position in array table
-        TWord pos = convert<TWord>(getValue(needle,j));
+        TWord pos = convert<TWord>(getValue(needle(me),j));
         me.b_table[me.blockCount*pos + j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
     }
 
 #ifdef SEQAN_DEBUG_ABNDM
-    std::cout << "Needle:   " << needle << ::std::endl;    
-    std::cout << "|Needle|: " << length(needle) << ::std::endl;
-    std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << ::std::endl;
+    std::cout << "Needle:   " << needle(me) << std::endl;
+    std::cout << "|Needle|: " << length(needle(me)) << std::endl;
+    std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << std::endl;
 
     for(unsigned i=0;i<ValueSize<TValue>::VALUE;++i) {
         if (((i<97) && (4 < i) ) || (i>122)) continue;
@@ -220,70 +233,56 @@ SEQAN_CHECKPOINT
             }
             std::cout << " ";
         }
-        std::cout << ::std::endl;
+        std::cout << std::endl;
     }
 #endif
     clear(me.r_table); // init is only possible if we know the the error count
 
-    me.data_host = needle;
-    setHost(me.verifier,needle);
-}
-
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, AbndmAlgo> & me, TNeedle2 & needle)
-{
-    setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
+    setHost(me.verifier, needle(me));  // Set the same host to the verifier.
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle>
-inline void _patternInit (Pattern<TNeedle, AbndmAlgo> & me) 
+inline void _patternInit (Pattern<TNeedle, AbndmAlgo> & me)
 {
     SEQAN_CHECKPOINT
-	clear(me.r_table);
+    clear(me.r_table);
     resize(me.r_table, me.blockCount * (me.limit + 1), 0, Exact());
     me.findNext = false;
     me.last = 0;
-	_findBeginInit(me, needle(me));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, AbndmAlgo> >::Type & 
-host(Pattern<TNeedle, AbndmAlgo> & me)
-{
-    SEQAN_CHECKPOINT
-	return value(me.data_host);
-}
-
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, AbndmAlgo> const>::Type & 
-host(Pattern<TNeedle, AbndmAlgo> const & me)
-{
-    SEQAN_CHECKPOINT
-	return value(me.data_host);
+    _findBeginInit(me, needle(me));
 }
 
 //////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn AbndmAlgoPattern#getScore
+ * @headerfile <seqan/find.h>
+ * @brief Score of the last found match in approximate searching.
+ *
+ * @signature TScoreValue getScore(pattern);
+ *
+ * @param[in] pattern A abndmAlgo pattern that can be used for approximate searching.
+ *
+ * @return TScoreValue The score of the last match found using <tt>pattern</tt>.  If no match was found then the value
+ *                     is undefined.
+ */
 
-///.Function.getScore.param.pattern.type:Spec.AbndmAlgo
 
 template <typename TNeedle>
-int getScore(Pattern<TNeedle, AbndmAlgo > & me) 
+int getScore(Pattern<TNeedle, AbndmAlgo > & me)
 {
     SEQAN_CHECKPOINT
-	return getScore(me.verifier);
+    return getScore(me.verifier);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TFinder, typename TNeedle>
-inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me) 
+inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me)
 {
     SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
+    typedef unsigned int TWord;
 
     typedef typename Host<TFinder>::Type    THost;
     typedef Segment<THost>                  THostSegment;
@@ -292,7 +291,7 @@ inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
     TWord j,nR,oR,i,cB;
     TWord startPos = position(finder);
 
-    // if returned from previous search we need to check the current position for additional matches    
+    // if returned from previous search we need to check the current position for additional matches
     if(me.findNext)
     {
         // reset the finder
@@ -305,16 +304,16 @@ inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
         THostSegment s(infix(host(finder),me.cP, end));
         THSFinder f(s);
 #ifdef SEQAN_DEBUG_ABNDM
-        ::std::cout << "additional verification of current position" << ::std::endl;
-        ::std::cout << "initialized on: " << s << ::std::endl;
-        ::std::cout << "parameters are: " << me.cP << " " << (me.cP + me.needleLength + me.limit) << ::std::endl;
-        ::std::cout << "original start pos: " << startPos << ::std::endl;
+        std::cout << "additional verification of current position" << std::endl;
+        std::cout << "initialized on: " << s << std::endl;
+        std::cout << "parameters are: " << me.cP << " " << (me.cP + me.needleLength + me.limit) << std::endl;
+        std::cout << "original start pos: " << startPos << std::endl;
 #endif
 
         while(find(f,me.verifier,- (int) me.limit)){
             TWord newP = position(finder) + position(f);
 #ifdef SEQAN_DEBUG_ABNDM
-            ::std::cout << "found on new position: " << newP << ::std::endl; 
+            std::cout << "found on new position: " << newP << std::endl;
 #endif
             if(newP > startPos){
                 finder += position(f);
@@ -322,29 +321,29 @@ inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
             }
         }
 #ifdef SEQAN_DEBUG_ABNDM
-        ::std::cout << "additional verification done .. shifted by last=" << me.last << ::std::endl << ::std::endl;
-#endif 
+        std::cout << "additional verification done .. shifted by last=" << me.last << std::endl << std::endl;
+#endif
         finder += me.last;
         me.cP += me.last;
     }
-    
+
     me.cP = position(finder);
-    // walk on  
-    while (position(finder) <= me.haystackLength - me.needleLength) 
+    // walk on
+    while (position(finder) <= me.haystackLength - me.needleLength)
     {
         SEQAN_CHECKPOINT
             j = me.needleLength - me.limit - 1;
         me.last = j;
-    
+
         // init R_0
         TWord pos = convert<TWord>(*(finder + j));
 
-        me.r_table[0] = me.b_table[pos];				    
+        me.r_table[0] = me.b_table[pos];
         nR = (TWord)-1;
-	for(i = 1;i <= me.limit;++i) me.r_table[i] = nR;
+    for(i = 1;i <= me.limit;++i) me.r_table[i] = nR;
 
 #ifdef SEQAN_DEBUG_ABNDM
-        ::std::cout << "reading " << *(finder + j) << ::std::endl;
+        std::cout << "reading " << *(finder + j) << std::endl;
         _printMask(me.b_table[pos],"");
         _printR(me);
 #endif
@@ -363,7 +362,7 @@ inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
                 me.r_table[i] = nR;
             }
 #ifdef SEQAN_DEBUG_ABNDM
-            ::std::cout << "reading " << *(finder + j - 1) << ::std::endl;
+            std::cout << "reading " << *(finder + j - 1) << std::endl;
             _printMask(me.b_table[pos],"");
             _printR(me);
 #endif
@@ -371,26 +370,26 @@ inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
             if((nR & 1) != 0){
                 if(j > 0){
 #ifdef SEQAN_DEBUG_ABNDM
-                    ::std::cout << "last bit is set so last is set to " << j << ::std::endl;
-#endif 
+                    std::cout << "last bit is set so last is set to " << j << std::endl;
+#endif
                     me.last = j;
                 }
                 else // verify
                 {
-                    // call find 
+                    // call find
                     int end = me.cP + me.needleLength + me.limit;
                     // adjust end if it points over the edges of host(finder)
                     end = (end > static_cast<int>(length(host(finder))) ? static_cast<int>(length(host(finder))) : end);
 
                     THostSegment s(infix(host(finder),me.cP, end));
                     THSFinder f(s);
-                    
+
 #ifdef SEQAN_DEBUG_ABNDM
-                    ::std::cout << "found verifiable prefix" << ::std::endl;
-                    // init finder on infix 
-                    ::std::cout << "parameters are " << me.cP << " " << (me.cP + me.needleLength + me.limit) << ::std::endl;
-		    ::std::cout << "init finder on: " << s << ::std::endl;
-#endif                  
+                    std::cout << "found verifiable prefix" << std::endl;
+                    // init finder on infix
+                    std::cout << "parameters are " << me.cP << " " << (me.cP + me.needleLength + me.limit) << std::endl;
+            std::cout << "init finder on: " << s << std::endl;
+#endif
                     // try to find the sequence
                     while(find(f,me.verifier,- (int) me.limit)){
                         TWord nP = position(finder) + position(f);
@@ -400,12 +399,12 @@ inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
                             return true;
                         }
                     }
-                }  
+                }
             }
         }
 #ifdef SEQAN_DEBUG_ABNDM
-        ::std::cout << "automaton runs out of active stats so window is shifted by last=" << me.last << ::std::endl << ::std::endl;
-#endif 
+        std::cout << "automaton runs out of active stats so window is shifted by last=" << me.last << std::endl << std::endl;
+#endif
 
         finder += me.last;
         me.cP += me.last;
@@ -414,7 +413,7 @@ inline bool _findAbndmSmallNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
 }
 
 template <typename TFinder, typename TNeedle>
-inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me) 
+inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo> & me)
 {
     SEQAN_CHECKPOINT
         typedef unsigned int TWord;
@@ -427,7 +426,7 @@ inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
     String<TWord> nR,oR;
     TWord startPos = position(finder);
 
-    // if returned from previous search we need to check the current position for additional matches    
+    // if returned from previous search we need to check the current position for additional matches
     if(me.findNext)
     {
         // reset the finder
@@ -441,16 +440,16 @@ inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
         THostSegment s(infix(host(finder),me.cP, end));
         THSFinder f(s);
 #ifdef SEQAN_DEBUG_ABNDM
-        ::std::cout << "additional verification of current position" << ::std::endl;
-        ::std::cout << "initialized on: " << s << ::std::endl;
-        ::std::cout << "parameters are: " << me.cP << " " << (me.cP + me.needleLength + me.limit) << ::std::endl;
-        ::std::cout << "original start pos: " << startPos << ::std::endl;
+        std::cout << "additional verification of current position" << std::endl;
+        std::cout << "initialized on: " << s << std::endl;
+        std::cout << "parameters are: " << me.cP << " " << (me.cP + me.needleLength + me.limit) << std::endl;
+        std::cout << "original start pos: " << startPos << std::endl;
 #endif
 
         while(find(f,me.verifier,- (int) me.limit)){
             TWord newP = position(finder) + position(f);
 #ifdef SEQAN_DEBUG_ABNDM
-            ::std::cout << "found on new position: " << newP << ::std::endl; 
+            std::cout << "found on new position: " << newP << std::endl;
 #endif
             if(newP > startPos){
                 finder += position(f);
@@ -458,43 +457,43 @@ inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
             }
         }
 #ifdef SEQAN_DEBUG_ABNDM
-        ::std::cout << "additional verification done .. shifted by last=" << me.last << ::std::endl << ::std::endl;
-#endif 
+        std::cout << "additional verification done .. shifted by last=" << me.last << std::endl << std::endl;
+#endif
         finder += me.last;
         me.cP += me.last;
     }else me.cP = position(finder);
-    // walk on  
-    while (position(finder) <= me.haystackLength - me.needleLength) 
+    // walk on
+    while (position(finder) <= me.haystackLength - me.needleLength)
     {
         SEQAN_CHECKPOINT
             j = me.needleLength - me.limit - 1;
         me.last = j;
 
-#ifdef SEQAN_DEBUG_ABNDM    
-	::std::cout << "starting new frame ending at position " << me.cP + j << ::std::endl;
+#ifdef SEQAN_DEBUG_ABNDM
+    std::cout << "starting new frame ending at position " << me.cP + j << std::endl;
 #endif
         // init R_0
         TWord pos = convert<TWord>(*(finder + j));
-	for(int block = me.blockCount - 1;block >= 0;--block){
+    for(int block = me.blockCount - 1;block >= 0;--block){
             me.r_table[block] = me.b_table[pos * me.blockCount + block];
-	}
-        //me.r_table[0] = me.b_table[pos];				    
-        
-	resize(nR,me.blockCount,0 - 1);
-	resize(oR,me.blockCount,0);
-	// nR = 0 - 1;
-	//for(i = me.blockCount;i <= me.limit * me.blockCount;++i) me.r_table[i] = 0 - 1;//set all states in r_table to 1
-	for(i = 1;i <= me.limit;++i){
+    }
+        //me.r_table[0] = me.b_table[pos];
+
+    resize(nR,me.blockCount,0 - 1);
+    resize(oR,me.blockCount,0);
+    // nR = 0 - 1;
+    //for(i = me.blockCount;i <= me.limit * me.blockCount;++i) me.r_table[i] = 0 - 1;//set all states in r_table to 1
+    for(i = 1;i <= me.limit;++i){
             for(int block = me.blockCount - 1;block >= 0;--block){
                 me.r_table[me.blockCount * i + block] = 0 -1 ;
             }
-	}
+    }
 
-	// track active states in nR
-	TWord nRTrack = 1;
+    // track active states in nR
+    TWord nRTrack = 1;
 
 #ifdef SEQAN_DEBUG_ABNDM
-        ::std::cout << "reading " << *(finder + j) << ::std::endl;
+        std::cout << "reading " << *(finder + j) << std::endl;
         _printMask(me.b_table,pos * me.blockCount, me.blockCount," ");
         _printR(me);
 #endif
@@ -505,16 +504,16 @@ inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
 
             bool carry = 0;
             for(int block = me.blockCount -1;block >= 0;--block){
-                oR[block] = me.r_table[block];	    
-                bool nCarry=((oR[block] & 1) != 0);	    
+                oR[block] = me.r_table[block];
+                bool nCarry=((oR[block] & 1) != 0);
                 TWord toR = oR[block] >> 1;
                 if(carry) toR |= carryPattern;
                 carry = nCarry;
                 nR[block] = toR & me.b_table[pos*me.blockCount + block];
                 me.r_table[block] = nR[block];
             }
-	    
-	    
+
+
             for(i = 1;i <= me.limit;++i){
                 bool rCarry = 0;
                 bool nCarry = 0;
@@ -532,8 +531,8 @@ inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
                 }
             }
 #ifdef SEQAN_DEBUG_ABNDM
-            ::std::cout << "reading " << *(finder + j - 1) << ::std::endl;
- 	    _printMask(me.b_table,pos*me.blockCount, me.blockCount," ");
+            std::cout << "reading " << *(finder + j - 1) << std::endl;
+         _printMask(me.b_table,pos*me.blockCount, me.blockCount," ");
             _printR(me);
 #endif
             --j;
@@ -544,44 +543,44 @@ inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
             if((nR[0] & 1) != 0){
                 if(j > 0){
 #ifdef SEQAN_DEBUG_ABNDM
-                    ::std::cout << "last bit is set so last is set to " << j << ::std::endl;
-#endif 
+                    std::cout << "last bit is set so last is set to " << j << std::endl;
+#endif
                     me.last = j;
                 }
                 else // verify
                 {
-                    // call find 
+                    // call find
                     int end = me.cP + me.needleLength + me.limit;
                     // adjust end if it points over the edges of host(finder)
                     end = (end > static_cast<int>(length(host(finder))) ? static_cast<int>(length(host(finder))) : end);
 
                     THostSegment s(infix(host(finder),me.cP, end));
                     THSFinder f(s);
-                    
+
 #ifdef SEQAN_DEBUG_ABNDM
-                    ::std::cout << "found verifiable prefix" << ::std::endl;
-                    // init finder on infix 
-                    ::std::cout << "parameters are " << me.cP << " " << (me.cP + me.needleLength + me.limit) << ::std::endl;
-                    ::std::cout << "init finder on: " << s << ::std::endl;
-#endif                  
+                    std::cout << "found verifiable prefix" << std::endl;
+                    // init finder on infix
+                    std::cout << "parameters are " << me.cP << " " << (me.cP + me.needleLength + me.limit) << std::endl;
+                    std::cout << "init finder on: " << s << std::endl;
+#endif
                     // try to find the sequence
                     while(find(f,me.verifier,- (int) me.limit)){
                         TWord nP = position(finder) + position(f);
                         if(nP > startPos){
                             finder += position(f);
 #ifdef SEQAN_DEBUG_ABNDM
-                            ::std::cout << "found pattern at position " << position(finder) << ::std::endl;
+                            std::cout << "found pattern at position " << position(finder) << std::endl;
 #endif
                             me.findNext = true;
                             return true;
                         }
                     }
-                }  
+                }
             }
         }
 #ifdef SEQAN_DEBUG_ABNDM
-        ::std::cout << "automaton runs out of active stats so window is shifted by last=" << me.last << ::std::endl << ::std::endl;
-#endif 
+        std::cout << "automaton runs out of active stats so window is shifted by last=" << me.last << std::endl << std::endl;
+#endif
 
         finder += me.last;
         me.cP += me.last;
@@ -590,25 +589,43 @@ inline bool _findAbndmLargeNeedle(TFinder & finder, Pattern<TNeedle, AbndmAlgo>
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.scoreLimit.param.pattern.type:Spec.AbndmAlgo
-///.Function.scoreLimit.class:Spec.AbndmAlgo
-
+/*!
+ * @fn AbndmAlgoPattern#scoreLimit
+ * @headerfile <seqan/find.h>
+ * @brief The minimal score a match must reach in approximate searching.
+ *
+ * @signature TScoreValue scoreLimit(pattern);
+ *
+ * @param[in] pattern The AbndmAlgoPattern to query.
+ *
+ * @return TScoreValue The score limit value.
+ */
 template <typename TNeedle>
-inline int 
+inline int
 scoreLimit(Pattern<TNeedle, AbndmAlgo > const & me)
 {
     SEQAN_CHECKPOINT
-	return - (int) me.limit;
+    return - (int) me.limit;
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.setScoreLimit.param.pattern.type:Spec.AbndmAlgo
-///.Function.setScoreLimit.class:Spec.AbndmAlgo
+/*!
+ * @fn AbndmAlgoPattern#setSoreLimit
+ * @headerfile <seqan/find.h>
+ * @brief Set the minimal score a match must reach in approximate serach.
+ *
+ * @signature void setScoreLimit(pattern, limit);
+ *
+ * @param[in,out] pattern The AbndmAlgoPattern to set the limit for.
+ * @param[in]     limit   The limit score value to set.
+ *
+ * @return TScoreValue The score limit value.
+ */
 
 template <typename TNeedle, typename TScoreValue>
-inline void 
-setScoreLimit(Pattern<TNeedle, AbndmAlgo > & me, 
+inline void
+setScoreLimit(Pattern<TNeedle, AbndmAlgo > & me,
               TScoreValue _limit)
 {
     SEQAN_CHECKPOINT
@@ -619,37 +636,37 @@ setScoreLimit(Pattern<TNeedle, AbndmAlgo > & me,
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TFinder, typename TNeedle>
-inline bool find (TFinder & finder, 
+inline bool find (TFinder & finder,
                   Pattern<TNeedle, AbndmAlgo > & me)
 {
     SEQAN_CHECKPOINT
-	if (empty(finder)) {
+    if (empty(finder)) {
             _patternInit(me);
             _finderSetNonEmpty(finder);
             me.haystackLength = length(container(finder));
-	} 
+    }
 
-	bool ret;
+    bool ret;
     if (me.blockCount == 1) {
         ret = _findAbndmSmallNeedle(finder, me);
     } else {
         ret = _findAbndmLargeNeedle(finder, me);
     }
-	if (ret) 
-	{
-		_setFinderEnd(finder);
-	}
-	return ret;
+    if (ret)
+    {
+        _setFinderEnd(finder);
+    }
+    return ret;
 
 }
 
 template <typename TFinder, typename TNeedle>
-inline bool find (TFinder & finder, 
-                  Pattern<TNeedle, AbndmAlgo > & me, 
+inline bool find (TFinder & finder,
+                  Pattern<TNeedle, AbndmAlgo > & me,
                   int const k)
 {
     SEQAN_CHECKPOINT
-	setScoreLimit(me, k);
+    setScoreLimit(me, k);
     return find(finder, me);
 }
 
diff --git a/seqan/find/find_ahocorasick.h b/seqan/find/find_ahocorasick.h
index 7ddaad2..c299a5f 100644
--- a/seqan/find/find_ahocorasick.h
+++ b/seqan/find/find_ahocorasick.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -55,23 +55,21 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * @tparam TNeedle The needle type, a string of keywords.
  *
- * @section Remarks
- *
  * The types of the keywords in the needle container and the haystack have to match.
- * 
+ *
  * Matching positions do not come in order because we report beginning positions of matches.
- * 
+ *
  * Likewise, if multiple keywords match at a given position no pre-specified order is guaranteed.
- * 
+ *
  * @section Examples
- * 
+ *
  * The following example program searches for three needles (<tt>queries</tt>) in two haystack sequences (<tt>db</tt>)
  * using the Aho-Corasick algorithm.
- * 
- * @include demos/find/finder_aho_corasick.cpp
- * 
+ *
+ * @include demos/dox/find/finder_aho_corasick.cpp
+ *
  * When executed, this program will create the following output.
- * 
+ *
  * @code{.console}
  * DB      POS     ENDPOS  TEXT
  * 0       0       4       MARD
@@ -81,31 +79,6 @@ namespace SEQAN_NAMESPACE_MAIN
  * @endcode
  */
 
-/**
-.Spec.AhoCorasick:
-..summary: Multiple exact string matching using Aho-Corasick.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, AhoCorasick>
-..param.TNeedle:The needle type, a string of keywords.
-...type:Class.String
-..remarks.text:The types of the keywords in the needle container and the haystack have to match.
-..remarks.text:Matching positions do not come in order because we report beginning positions of matches.
-..remarks.text:Likewise, if multiple keywords match at a given position no pre-specified order is guaranteed.
-..example.text:The following example program searches for three needles ($queries$) in two haystack sequences ($db$) using the Aho-Corasick algorithm.
-..example.file:demos/find/finder_aho_corasick.cpp
-..example.remark:Note that you have to provide a String of Strings for the queries at the moment. This will be changed to a StringSet in the future.
-..example.text:When executed, this program will create the following output.
-..example.output:DB      POS     ENDPOS  TEXT
-0       0       4       MARD
-0       3       7       DPLY
-1       1       6       VGGGG
-1       6       9       AAA
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.AhoCorasick
-
 struct AhoCorasick_;
 typedef Tag<AhoCorasick_> AhoCorasick;
 
@@ -115,64 +88,54 @@ template <typename TNeedle>
 class Pattern<TNeedle, AhoCorasick> {
 //____________________________________________________________________________
 private:
-	Pattern(Pattern const& other);
-	Pattern const& operator=(Pattern const & other);
+    Pattern(Pattern const& other);
+    Pattern const& operator=(Pattern const & other);
 
 //____________________________________________________________________________
 public:
-	typedef typename Size<TNeedle>::Type TSize;
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Value<TKeyword>::Type TAlphabet;
-	typedef Graph<Automaton<TAlphabet> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	
-	Holder<TNeedle> data_host;
-	String<TVertexDescriptor> data_supplyMap;
-	String<String<TSize> > data_terminalStateMap;
-	TGraph data_graph;
-
-	// To restore the automaton after a hit
-	String<TSize> data_endPositions;	// All remaining keyword indices
-	TSize data_keywordIndex;			// Current keyword that produced a hit
-	TSize data_needleLength;			// Last length of needle to reposition finder
-	TVertexDescriptor data_lastState;   // Last state in the trie
+    typedef typename Size<TNeedle>::Type TSize;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Value<TKeyword>::Type TAlphabet;
+    typedef Graph<Automaton<TAlphabet> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    Holder<TNeedle> data_host;
+    String<TVertexDescriptor> data_supplyMap;
+    String<String<TSize> > data_terminalStateMap;
+    TGraph data_graph;
+
+    // To restore the automaton after a hit
+    String<TSize> data_endPositions;    // All remaining keyword indices
+    TSize data_keywordIndex;            // Current keyword that produced a hit
+    TSize data_needleLength;            // Last length of needle to reposition finder
+    TVertexDescriptor data_lastState;   // Last state in the trie
 
 //____________________________________________________________________________
 
-	Pattern() {
-	}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		SEQAN_CHECKPOINT
-		setHost(*this, ndl);
-	}
-
-	~Pattern() {
-		SEQAN_CHECKPOINT
-	}
+    Pattern() : data_keywordIndex(0), data_needleLength(0)
+    {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+        : data_keywordIndex(0), data_needleLength(0)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl) : data_keywordIndex(0), data_needleLength(0)
+    {
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
 
-//////////////////////////////////////////////////////////////////////////////
-// Host Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, AhoCorasick> >
-{
-	typedef TNeedle Type;
-};
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, AhoCorasick> const>
-{
-	typedef TNeedle const Type;
-};
-
-
 //////////////////////////////////////////////////////////////////////////////
 // Functions
 //////////////////////////////////////////////////////////////////////////////
@@ -181,113 +144,105 @@ template <typename TNeedle>
 inline void
 _createAcTrie(Pattern<TNeedle, AhoCorasick> & me)
 {
-	typedef typename Position<TNeedle>::Type TPosition;
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Value<TKeyword>::Type TAlphabet;
-	typedef Graph<Automaton<TAlphabet> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-
-	// Create regular trie
-	createTrie(me.data_graph,me.data_terminalStateMap, host(me));
-
-	// Create parent map
-	String<TVertexDescriptor> parentMap;
-	String<TAlphabet> parentCharMap;
-	resizeVertexMap(me.data_graph,parentMap);
-	resizeVertexMap(me.data_graph,parentCharMap);
-	for(TPosition i = 0;i<length(parentMap);++i) {
-		assignProperty(parentMap, i, nilVal);
-	}
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	TEdgeIterator itEd(me.data_graph);
-	for(;!atEnd(itEd);goNext(itEd)) {
-		assignProperty(parentMap, targetVertex(itEd), sourceVertex(itEd));
-		assignProperty(parentCharMap, targetVertex(itEd), label(itEd));
-	}
-
-	// Build AC
-	TVertexDescriptor root = getRoot(me.data_graph);
-	resizeVertexMap(me.data_graph,me.data_supplyMap);
-	assignProperty(me.data_supplyMap, root, nilVal);
-
-	// Bfs Traversal
-	typedef typename Iterator<TGraph, BfsIterator>::Type TBfsIterator;
-	TBfsIterator it(me.data_graph,root);
-	for(;!atEnd(it);goNext(it)) {
-		if (atBegin(it)) continue;
-		TVertexDescriptor parent = getProperty(parentMap, *it);
-		TAlphabet sigma = getProperty(parentCharMap, *it);
-		TVertexDescriptor down = getProperty(me.data_supplyMap, parent);
-		while ((down != nilVal) &&
-			(getSuccessor(me.data_graph, down, sigma) == nilVal)) 
-		{
-			down = getProperty(me.data_supplyMap, down);
-		}
-		if (down != nilVal) {
-			assignProperty(me.data_supplyMap, *it, getSuccessor(me.data_graph, down, sigma));
-			String<TPosition> endPositions = getProperty(me.data_terminalStateMap, getProperty(me.data_supplyMap, *it));
-			if (!empty(endPositions)) {
-				String<TPosition> endPositionsCurrent = getProperty(me.data_terminalStateMap, *it);
-				typedef typename Iterator<String<TPosition>, Rooted >::Type TStringIterator;
-				TStringIterator sit = begin(endPositions);
-				for(;!atEnd(sit);goNext(sit)) {
-					appendValue(endPositionsCurrent, *sit);
-				}
-				assignProperty(me.data_terminalStateMap, *it, endPositionsCurrent);
-			}
-		} else {
-			assignProperty(me.data_supplyMap, *it, root);
-		}
-
-	}
+    typedef typename Position<TNeedle>::Type TPosition;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Value<TKeyword>::Type TAlphabet;
+    typedef Graph<Automaton<TAlphabet> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+
+    // Create regular trie
+    createTrie(me.data_graph,me.data_terminalStateMap, host(me));
+
+    // Create parent map
+    String<TVertexDescriptor> parentMap;
+    String<TAlphabet> parentCharMap;
+    resizeVertexMap(parentMap, me.data_graph);
+    resizeVertexMap(parentCharMap, me.data_graph);
+    for(TPosition i = 0;i<length(parentMap);++i) {
+        assignProperty(parentMap, i, nilVal);
+    }
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    TEdgeIterator itEd(me.data_graph);
+    for(;!atEnd(itEd);goNext(itEd)) {
+        assignProperty(parentMap, targetVertex(itEd), sourceVertex(itEd));
+        assignProperty(parentCharMap, targetVertex(itEd), label(itEd));
+    }
+
+    // Build AC
+    TVertexDescriptor root = getRoot(me.data_graph);
+    resizeVertexMap(me.data_supplyMap, me.data_graph);
+    assignProperty(me.data_supplyMap, root, nilVal);
+
+    // Bfs Traversal
+    typedef typename Iterator<TGraph, BfsIterator>::Type TBfsIterator;
+    TBfsIterator it(me.data_graph,root);
+    for(;!atEnd(it);goNext(it)) {
+        if (atBegin(it)) continue;
+        TVertexDescriptor parent = getProperty(parentMap, *it);
+        TAlphabet sigma = getProperty(parentCharMap, *it);
+        TVertexDescriptor down = getProperty(me.data_supplyMap, parent);
+        while ((down != nilVal) &&
+            (getSuccessor(me.data_graph, down, sigma) == nilVal))
+        {
+            down = getProperty(me.data_supplyMap, down);
+        }
+        if (down != nilVal) {
+            assignProperty(me.data_supplyMap, *it, getSuccessor(me.data_graph, down, sigma));
+            String<TPosition> endPositions = getProperty(me.data_terminalStateMap, getProperty(me.data_supplyMap, *it));
+            if (!empty(endPositions)) {
+                String<TPosition> endPositionsCurrent = getProperty(me.data_terminalStateMap, *it);
+                typedef typename Iterator<String<TPosition>, Rooted >::Type TStringIterator;
+                TStringIterator sit = begin(endPositions);
+                for(;!atEnd(sit);goNext(sit)) {
+                    appendValue(endPositionsCurrent, *sit);
+                }
+                assignProperty(me.data_terminalStateMap, *it, endPositionsCurrent);
+            }
+        } else {
+            assignProperty(me.data_supplyMap, *it, root);
+        }
+
+    }
 }
 
 
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, AhoCorasick> & me, TNeedle2 const & needle) {
-	SEQAN_CHECKPOINT;
-	SEQAN_ASSERT_NOT(empty(needle));
-	setValue(me.data_host, needle);
-	clear(me.data_graph);
-	clear(me.data_supplyMap);
-	clear(me.data_endPositions);
-	clear(me.data_terminalStateMap);
-	_createAcTrie(me);
-	me.data_needleLength = 0;
-
-
-	//fstream strm;
-	//strm.open(TEST_PATH "my_trie.dot", ios_base::out | ios_base::trunc);
-	//String<String<char> > nodeMap;
-	//_createTrieNodeAttributes(me.data_graph, me.data_terminalStateMap, nodeMap);
-	//String<String<char> > edgeMap;
-	//_createEdgeAttributes(me.data_graph,edgeMap);
-	//write(strm,me.data_graph,nodeMap,edgeMap,DotDrawing());
-	//strm.close();
-	// Supply links
-	//for(unsigned int i=0;i<length(me.data_supplyMap);++i) {
-	//	std::cout << i << "->" << getProperty(me.data_supplyMap,i) << ::std::endl;
-	//}
-}
-
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost (Pattern<TNeedle, AhoCorasick> & me, TNeedle2 & needle)
-{
-	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
+template <typename TNeedle>
+void _reinitPattern(Pattern<TNeedle, AhoCorasick> & me) {
+    SEQAN_CHECKPOINT;
+    SEQAN_ASSERT_NOT(empty(needle(me)));
+    clear(me.data_graph);
+    clear(me.data_supplyMap);
+    clear(me.data_endPositions);
+    clear(me.data_terminalStateMap);
+    _createAcTrie(me);
+    me.data_needleLength = 0;
+
+
+    //fstream strm;
+    //strm.open(TEST_PATH "my_trie.dot", ios_base::out | ios_base::trunc);
+    //String<String<char> > nodeMap;
+    //_createTrieNodeAttributes(me.data_graph, me.data_terminalStateMap, nodeMap);
+    //String<String<char> > edgeMap;
+    //_createEdgeAttributes(me.data_graph,edgeMap);
+    //writeRecords(strm,me.data_graph,nodeMap,edgeMap,DotDrawing());
+    //strm.close();
+    // Supply links
+    //for(unsigned int i=0;i<length(me.data_supplyMap);++i) {
+    //    std::cout << i << "->" << getProperty(me.data_supplyMap,i) << std::endl;
+    //}
 }
 
 //____________________________________________________________________________
 
 
 template <typename TNeedle>
-inline void _patternInit (Pattern<TNeedle, AhoCorasick> & me) 
+inline void _patternInit (Pattern<TNeedle, AhoCorasick> & me)
 {
 SEQAN_CHECKPOINT
-	clear(me.data_endPositions);
-	me.data_keywordIndex = 0;
-	me.data_lastState = getRoot(me.data_graph);
+    clear(me.data_endPositions);
+    me.data_keywordIndex = 0;
+    me.data_lastState = getRoot(me.data_graph);
 }
 
 
@@ -298,67 +253,67 @@ template <typename TNeedle>
 inline typename Size<TNeedle>::Type
 position(Pattern<TNeedle, AhoCorasick> & me)
 {
-	return me.data_keywordIndex;
+    return me.data_keywordIndex;
 }
 
 
 template <typename TFinder, typename TNeedle>
 inline bool find(TFinder & finder, Pattern<TNeedle, AhoCorasick> & me) {
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Value<TKeyword>::Type TAlphabet;
-	typedef Graph<Automaton<TAlphabet> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	if (empty(finder)) {
-		_patternInit(me);
-		_finderSetNonEmpty(finder);
-	} else {
-		finder += me.data_needleLength;
-		++finder; // Set forward the finder
-	}
-
-	// Process left-over hits
-	if (!empty(me.data_endPositions)) {
-		--finder; // Set back the finder
-		me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
-		me.data_needleLength = length(value(host(me), me.data_keywordIndex))-1;
-		if (length(me.data_endPositions) > 1) resize(me.data_endPositions, (length(me.data_endPositions)-1));
-		else clear(me.data_endPositions);
-		finder -= me.data_needleLength;
-		_setFinderLength(finder, me.data_needleLength+1);
-		_setFinderEnd(finder, position(finder)+length(finder));
-		return true;
-	}
-
-	TVertexDescriptor current = me.data_lastState;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	while (!atEnd(finder)) {
-		while ((getSuccessor(me.data_graph, current, *finder) == nilVal) &&
-			(getProperty(me.data_supplyMap, current) != nilVal))
-		{
-			current = getProperty(me.data_supplyMap,current);
-		}
-		if (getSuccessor(me.data_graph, current, *finder) != nilVal) {
-			current = getSuccessor(me.data_graph, current, *finder);
-		}
-		else {
-			current = getRoot(me.data_graph);
-		}
-		me.data_endPositions = getProperty(me.data_terminalStateMap,current);
-		if (!empty(me.data_endPositions)) {
-			me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
-			me.data_needleLength = length(value(host(me), me.data_keywordIndex))-1;
-			if (length(me.data_endPositions) > 1) resize(me.data_endPositions, length(me.data_endPositions)-1);
-			else clear(me.data_endPositions);
-			me.data_lastState = current;
-			finder -= me.data_needleLength;
-			_setFinderLength(finder, me.data_needleLength+1);
-			_setFinderEnd(finder, position(finder)+length(finder));
-			return true;
-		}
-		++finder;
-	}
-	return false;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Value<TKeyword>::Type TAlphabet;
+    typedef Graph<Automaton<TAlphabet> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    if (empty(finder)) {
+        _patternInit(me);
+        _finderSetNonEmpty(finder);
+    } else {
+        finder += me.data_needleLength;
+        ++finder; // Set forward the finder
+    }
+
+    // Process left-over hits
+    if (!empty(me.data_endPositions)) {
+        --finder; // Set back the finder
+        me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
+        me.data_needleLength = length(value(host(me), me.data_keywordIndex))-1;
+        if (length(me.data_endPositions) > 1) resize(me.data_endPositions, (length(me.data_endPositions)-1));
+        else clear(me.data_endPositions);
+        finder -= me.data_needleLength;
+        _setFinderLength(finder, me.data_needleLength+1);
+        _setFinderEnd(finder, position(finder)+length(finder));
+        return true;
+    }
+
+    TVertexDescriptor current = me.data_lastState;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    while (!atEnd(finder)) {
+        while ((getSuccessor(me.data_graph, current, *finder) == nilVal) &&
+            (getProperty(me.data_supplyMap, current) != nilVal))
+        {
+            current = getProperty(me.data_supplyMap,current);
+        }
+        if (getSuccessor(me.data_graph, current, *finder) != nilVal) {
+            current = getSuccessor(me.data_graph, current, *finder);
+        }
+        else {
+            current = getRoot(me.data_graph);
+        }
+        me.data_endPositions = getProperty(me.data_terminalStateMap,current);
+        if (!empty(me.data_endPositions)) {
+            me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
+            me.data_needleLength = length(value(host(me), me.data_keywordIndex))-1;
+            if (length(me.data_endPositions) > 1) resize(me.data_endPositions, length(me.data_endPositions)-1);
+            else clear(me.data_endPositions);
+            me.data_lastState = current;
+            finder -= me.data_needleLength;
+            _setFinderLength(finder, me.data_needleLength+1);
+            _setFinderEnd(finder, position(finder)+length(finder));
+            return true;
+        }
+        ++finder;
+    }
+    return false;
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_base.h b/seqan/find/find_base.h
index c941ead..ecc2651 100644
--- a/seqan/find/find_base.h
+++ b/seqan/find/find_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -49,47 +49,38 @@ namespace seqan {
 // TODO(holtgrew): Define as Tag<FindInfix_>?
 
 /*!
- * @tag FindInfix
+ * @defgroup ApproximateFinderSearchTypeTags Approximate Finder Search Type Tags
+ * @brief Tags for specifying the @link Finder @endlink search type (prefix or infix).
+ *
+ * There are two interesting kinds of search for approximate string search algorithms: (1) search for a matching
+ * substring anywhere in the text, infix search, and (2) search for a matching prefix, prefix search.  The tags
+ * in this group can be used to select this search for approximate string search algorithms.
+ */
+
+/*!
+ * @tag ApproximateFinderSearchTypeTags#FindInfix
  * @headerfile <seqan/find.h>
  *
- * @brief Find needle as a substring of the hasystack (infix search).
+ * @brief Find needle as a substring of the haystack (infix search).
  *
  * @signature struct FindInfix;
  *
- * @see FindPrefix
+ * @see ApproximateFinderSearchTypeTags#FindPrefix
  */
 
-/**
-.Tag.FindInfix:
-..cat:Searching
-..summary:Find needle as a substring of haystack (infix search).
-..see:Tag.FindPrefix
-..see:Spec.Myers
-..see:Spec.DPSearch
-..include:seqan/find.h
- */
 struct FindInfix;
 
 /*!
- * @tag FindPrefix
+ * @tag ApproximateFinderSearchTypeTags#FindPrefix
  * @headerfile <seqan/find.h>
  *
- * @brief Find needle as a substring of the hasystack (prefix search).
+ * @brief Find needle as a substring of the haystack (prefix search).
  *
  * @signature struct FindPrefix;
  *
- * @see FindInfix
+ * @see ApproximateFinderSearchTypeTags#FindInfix
  */
 
-/**
-.Tag.FindPrefix:
-..cat:Searching
-..summary:Find needle as a prefix of the haystack (prefix serach)
-..see:Tag.FindInfix
-..see:Spec.Myers
-..see:Spec.DPSearch
-..include:seqan/find.h
-*/
 struct FindPrefix;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -103,23 +94,14 @@ struct FindPrefix;
  *
  * @tparam THaystack The given haystack type.
  *
- * @return Type The Finder specialization.  By default, this is <tt>void</tt> and <tt>EsaFindMlr</tt> is an @link Index
+ * @return Type The Finder specialization.  By default, this is <tt>void</tt> and <tt>FinderMlr</tt> is an @link Index
  *              @endlink.
  */
 
-/**
-.Metafunction.DefaultFinder:
-..cat:Searching
-..summary:Default @Class.Finder@ specialization type.
-..signature:DefaultFinder<THaystack>::Type
-..param.THaystack:The given haystack type.
-..returns:Is $void$ by default and @Tag.Index Find Algorithm.EsaFindMlr@ if $THaystack$ is an @Class.Index@.
-..include:seqan/find.h
-*/
 template < typename TObject >
-struct DefaultFinder 
+struct DefaultFinder
 {
-	typedef void Type;
+    typedef void Type;
 };
 
 /*!
@@ -134,19 +116,10 @@ struct DefaultFinder
  * @return Type Is <tt>void</tt> by default
  */
 
-/**
-.Metafunction.DefaultPattern:
-..cat:Searching
-..summary:Default @Class.Pattern@ specialization type.
-..signature:DefaultPattern<TNeedle>::Type
-..param.TNeedle:The given needle type.
-..returns:Is $void$ by default.
-..include:seqan/find.h
-*/
 template < typename TObject >
-struct DefaultPattern 
+struct DefaultPattern
 {
-	typedef void Type;
+    typedef void Type;
 };
 
 /*!
@@ -154,7 +127,7 @@ struct DefaultPattern
  * @headerfile <seqan/file.h>
  * @brief Returns the haystack type of a @link Finder @endlink type.
  *
- * @signature Hasytack<TFinder>::Type;
+ * @signature Haystack<TFinder>::Type;
  *
  * @tparam TFinder The finder to query.
  *
@@ -162,28 +135,14 @@ struct DefaultPattern
  *              TSpec&gt;</tt>.  This is an alias to function <tt>host()</tt> of the pattern function.
  */
 
-/**
-.Metafunction.Haystack:
-..summary:Returns the haystack type of a @Class.Finder@ type.
-..cat:Searching
-..signature:Haystack<TFinder>::Type
-..class:Class.Finder
-..param.TFinder:A @Class.Finder@ type.
-...type:Class.Finder
-..returns:The haystack type of $TFinder$, i.e. $THaystack$ for $Finder<THaystack, TSpec>$.
-This is an alias to function @Function.host@ of the pattern function.
-..see:Function.host
-..include:seqan/find.h
-*/
-
 template <typename TFinder>
-struct Haystack 
+struct Haystack
 {
-	typedef typename Container<TFinder>::Type Type;
+    typedef typename Container<TFinder>::Type Type;
 };
 
 /*!
- * @mfn Needle
+ * @mfn Pattern#Needle
  * @headerfile <seqan/find.h>
  * @brief Returns the needle type of a @link Pattern @endlink type.
  *
@@ -194,34 +153,22 @@ struct Haystack
  * @return Type The needle type of <tt>TPattern</tt., i.e. <tt>TNeedle</tt> for <tt>Pattern&lt;TNeedle, TSpec&gt;</tt>.
  */
 
-/**
-.Metafunction.Needle:
-..summary:Returns the needle type of a @Class.Pattern@ type.
-..cat:Searching
-..signature:Needle<TPattern>::Type
-..class:Class.Pattern
-..param.TPattern:A @Class.Pattern@ type.
-...type:Class.Pattern
-..returns:The needle type of $TPattern$, i.e. $TNeedle$ for $Pattern<TNeedle, TSpec>$.
-..include:seqan/find.h
-*/
-
 template <typename TPattern>
-struct Needle 
+struct Needle
 {
-	typedef typename Host<TPattern>::Type Type;
+    typedef typename Host<TPattern>::Type Type;
 };
 
 template <typename THost, typename TSpec>
-struct Needle<Segment<THost, TSpec> > 
+struct Needle<Segment<THost, TSpec> >
 {
-	typedef Segment<THost, TSpec> Type;
+    typedef Segment<THost, TSpec> Type;
 };
 
 template <typename THost, typename TSpec>
-struct Needle<Segment<THost, TSpec> const> 
+struct Needle<Segment<THost, TSpec> const>
 {
-	typedef Segment<THost, TSpec> const Type;
+    typedef Segment<THost, TSpec> const Type;
 };
 
 
@@ -234,7 +181,7 @@ struct Needle<Segment<THost, TSpec> const>
  *
  * @signature bool find(finder, pattern[, k]);
  *
- * @param[in,out] finder  The @link Finder @endlink object to search through. 
+ * @param[in,out] finder  The @link Finder @endlink object to search through.
  * @param[in]     pattern The @link Pattern @endlink to search for.  For index finders, pattern can also be a text.
  *                        Types: @link Pattern @endlink, @link TextConcept @endlink.
  * @param[in]     k       Desired minimal score (for approximate matching).  <tt>k</tt> is a number <tt>&lt;= 0</tt>.
@@ -242,8 +189,6 @@ struct Needle<Segment<THost, TSpec> const>
  *
  * @return bool <tt>true</tt> if an occurence was found and <tt>false</tt> if not.
  *
- * @section Remarks
- *
  * Repeated calls of this function iterate through all occurences of <tt>pattern</tt>.
  *
  * @section Examples
@@ -251,99 +196,33 @@ struct Needle<Segment<THost, TSpec> const>
  * The following example shows how one can search online for a pattern in a haystack.  Note that it is neccessary to
  * reset the finder befor searching for another pattern.
  *
- * @include demos/find/finder_online.cpp
+ * @include demos/dox/find/finder_online.cpp
  *
  * The output is as follows.
  *
- * @include demos/find/finder_online.cpp.stdout
+ * @include demos/dox/find/finder_online.cpp.stdout
  *
  * In contrast to the example above the code below shows how one can use a Finder with an index as base.  Again, note
  * that it is neccessary to reset the finder befor searching for another pattern.
  *
- * @include demos/find/finder_index.cpp
+ * @include demos/dox/find/finder_index.cpp
  *
  * The output is as follows.
  *
- * @include demos/find/finder_index.cpp.stdout
+ * @include demos/dox/find/finder_index.cpp.stdout
  */
 
-/**
-.Function.find:
-..summary:Search for a @Class.Pattern@ in a @Class.Finder@ object.
-..cat:Searching
-..signature:find(finder, pattern)
-..signature:find(finder, pattern, k)
-..class:Class.Finder
-..param.finder:The @Class.Finder@ object to search through.
-...remarks:For online-algorithm $patterns$, finder can also be an arbitrary @Concept.RootedIteratorConcept|Rooted Iterator@.
-...type:Class.Finder
-...type:Concept.RootedIteratorConcept
-..param.pattern:The @Class.Pattern@ object to search for.
-...remarks:For index $finders$, pattern can also be a Sequence.
-...type:Class.Pattern
-..param.k:Desired minimal score (for approximate matching).
-...remarks:$k$ has to be a number <= 0.
-...remarks:Differences are deletions, insertions and substitutions.
-..returns:$boolean$ that indicates whether an occurrence of $pattern$ was found or not.
-..remarks:Repeated calls of this function iterate through all occurrences of $pattern$.
-..include:seqan/find.h
-*/
-
-/**
-.Class.Finder:
-..summary:Holds the haystack and a current search context.
-..cat:Searching
-..signature:Finder<THaystack[, TSpec]>
-..param.THaystack:The haystack type.
-...type:Class.String
-...type:Class.Index
-..param.TSpec:The index-algorithm to search with (Optional).
-...default:The result of @Metafunction.DefaultFinder@
-...remarks:Leave empty for online pattern matching (see @Class.Pattern@).
-...remarks:If $THaystack$ is an @Class.Index@, then $TSpec$ specifies the index search algorithm.
-..remarks:$position(finder)$ returns the position of the current hit in the haystack.
-If $THaystack$ is a set of strings or an index of a set of strings, then $position(finder)$ returns a @Class.Pair@$(hayNo, pos)$,
-in which $hayNo$ is the haystack index and $pos$ the local position of the hit.
-..remarks:To reset the finder object and use it on another text or different text position, use $clear(finder)$
-Note that $clear(finder)$ doesn't move the text iterator. To start the search from the beginning or somewhere else in the text, use
-@Function.goBegin@ or @Function.setPosition@.
-..example
-...text:The following example shows how one can search online for a pattern in a haystack. Note that it is neccessary to reset the finder befor searching for another pattern.
-...file:demos/find/finder_online.cpp
-...output:Hit at position: 4
-Hit at position: 12
-Hit at position: 22
-Hit at position: 43
-Hit at position: 8
-Hit at position: 16
-Hit at position: 17
-Hit at position: 29
-Hit at position: 35
-Hit at position: 38
-...text:In contrast to the example above the code below shows how one can use a Finder with an index as base. Again, note that it is neccessary to reset the finder befor searching for another pattern.
-...file:demos/find/finder_index.cpp
-...output:Hit at position: 12
-Hit at position: 4
-Hit at position: 22
-Hit at position: 43
-Hit at position: 38
-Hit at position: 8
-Hit at position: 35
-Hit at position: 29
-Hit at position: 17
-Hit at position: 16
-..include:seqan/find.h
-*/
 
 /*!
  * @class Finder
- * 
- * @headerfile seqan/find.h
- * 
+ *
+ * @headerfile <seqan/find.h>
+ *
  * @brief Holds the haystack and a current search context.
- * 
- * @signature Finder<THaystack[, TSpec]>
- * 
+ *
+ * @signature template <typename THaystack[, typename TSpec]>
+ *            class Finder;
+ *
  * @tparam TSpec The index-algorithm to search with (Optional).Leave empty for
  *               online pattern matching (see @link Pattern @endlink).If
  *               <tt>THaystack</tt> is an @link Index @endlink, then
@@ -351,58 +230,51 @@ Hit at position: 16
  *               Pigeonhole, Swift, Backtracking Default: The result of @link
  *               DefaultFinder @endlink
  * @tparam THaystack The haystack type. Types: String, Index
- * 
- * @section Remarks
- * 
+ *
  * <tt>position(finder)</tt> returns the position of the current hit in the haystack.  If <tt>THaystack</tt> is a set of
  * strings or an index of a set of strings, then <tt>position(finder)</tt> returns a @link Pair @endlink <tt>(hayNo,
  * pos)</tt>, in which <tt>hayNo</tt> is the haystack index and <tt>pos</tt> the local position of the hit.
- * 
+ *
  * To reset the finder object and use it on another text or different text position, use <tt>clear(finder)</tt> Note
  * that <tt>clear(finder)</tt> doesn't move the text iterator. To start the search from the beginning or somewhere else
  * in the text, use @link Finder#goBegin @endlink or @link Finder#setPosition @endlink.
- * 
+ *
  * @section Examples
- * 
+ *
  * The following example shows how to restart a search from the beginning of a
  * text.
- * 
+ *
  * @code{.cpp}
  * CharString hstck = "I spy with my little eye something that is yellow";
  * Finder<CharString> finder(hstck);
- *  
+ *
  * Pattern<CharString, Horspool> p1("y");
  * findAll(finder, p1);
- *  
+ *
  * goBegin(finder);    // move Finder to the beginning of the text
  * clear(finder);      // reset Finder
- *  
+ *
  * Pattern<CharString, Horspool> p2("t");
  * findAll(finder, p2);
  * @endcode
  * Demo: Demo.Index Finder StringSet
- * 
+ *
  * Demo: Demo.Index Finder
  */
 
-///.Function.clear.param.object.type:Class.Finder
-///.Function.clear.class:Class.Finder
-///.Function.position.param.iterator.type:Class.Finder
-///.Function.position.class:Class.Finder
-
 template < typename THaystack, typename TSpec = typename DefaultFinder<THaystack>::Type >
 class Finder
 {
 public:
-	typedef typename Iterator<THaystack, Rooted>::Type TIterator;
-	typedef typename Position<THaystack>::Type TPosition;
-	typedef typename Size<THaystack>::Type TSize;
+    typedef typename Iterator<THaystack, Rooted>::Type TIterator;
+    typedef typename Position<THaystack>::Type TPosition;
+    typedef typename Size<THaystack>::Type TSize;
 
-	TIterator data_iterator;
-	TPosition data_endPos; //note: we need this since iterator could point to begin or end (depending on pattern type)
-	TSize data_length;
-	bool _needReinit;					// if true, the Pattern needs to be reinitialized
-	bool _beginFind_called;					// if false, then findBegin was not yet called for this match position (see findBegin default implementation)
+    TIterator data_iterator;
+    TPosition data_endPos; //note: we need this since iterator could point to begin or end (depending on pattern type)
+    TSize data_length;
+    bool _needReinit;                    // if true, the Pattern needs to be reinitialized
+    bool _beginFind_called;                    // if false, then findBegin was not yet called for this match position (see findBegin default implementation)
 
 /*!
  * @fn Finder::Finder
@@ -418,105 +290,83 @@ class Finder
  * @param[in] iter     The iter to work on on, either const or non-const.
  */
 
-/**
-.Memfunc.Finder#Finder:
-..class:Class.Finder
-..summary:Constructor
-..signature:Finder()
- */
-	Finder()
-		: data_endPos(0)
-		, data_length(0)
-		, _needReinit(true)
-		, _beginFind_called(false)
-	{}
-
-	/**
-.Memfunc.Finder#Finder:
-..signature:Finder(haystack)
-..param.haystack:The haystack to work on, $THaystack$.
-	 */
-	Finder(THaystack & haystack)
-		: data_iterator(begin(haystack, Rooted()))
-		, data_endPos(0)
-		, data_length(0)
-		, _needReinit(true) 
-		, _beginFind_called(false)
-	{}
-
-	/**
-.Memfunc.Finder#Finder:
-..signature:Finder(iter)
-..param.iter:The iterator to work on, either const or non-const.
-	 */
-	Finder(TIterator &iter)
-		: data_iterator(iter)
-		, data_endPos(0)
-		, data_length(0)
-		, _needReinit(true) 
-		, _beginFind_called(false)
-	{}
-
-	Finder(TIterator const &iter)
-		: data_iterator(iter)
-		, data_endPos(0)
-		, data_length(0)
-		, _needReinit(true) 
-		, _beginFind_called(false)
-	{}
-	
-	/**
-.Memfunc.Finder#Finder:
-..signature:Finder(orig)
-..param.orig:Finder object to copy from (copy constructor).
-...type:Class.Finder
-	 */
-	Finder(Finder const &orig)
-		: data_iterator(orig.data_iterator)
-		, data_endPos(orig.data_endPos)
-		, data_length(orig.data_length)
-		, _needReinit(orig._needReinit) 
-		, _beginFind_called(orig._beginFind_called)
-	{}
-
-	~Finder() {}
+    Finder()
+        : data_endPos(0)
+        , data_length(0)
+        , _needReinit(true)
+        , _beginFind_called(false)
+    {}
+
+    Finder(THaystack & haystack)
+        : data_iterator(begin(haystack, Rooted()))
+        , data_endPos(0)
+        , data_length(0)
+        , _needReinit(true)
+        , _beginFind_called(false)
+    {}
+
+    Finder(TIterator &iter)
+        : data_iterator(iter)
+        , data_endPos(0)
+        , data_length(0)
+        , _needReinit(true)
+        , _beginFind_called(false)
+    {}
+
+    Finder(TIterator const &iter)
+        : data_iterator(iter)
+        , data_endPos(0)
+        , data_length(0)
+        , _needReinit(true)
+        , _beginFind_called(false)
+    {}
+
+    Finder(Finder const &orig)
+        : data_iterator(orig.data_iterator)
+        , data_endPos(orig.data_endPos)
+        , data_length(orig.data_length)
+        , _needReinit(orig._needReinit)
+        , _beginFind_called(orig._beginFind_called)
+    {}
+
+    ~Finder() {}
 
 //____________________________________________________________________________
 
-	Finder const &
-	operator = (Finder const & other)
-	{
-		data_iterator = other.data_iterator;
-		data_endPos = other.data_endPos;
-		data_length = other.data_length;
-		_needReinit = other._needReinit;
-		_beginFind_called = other._beginFind_called;
-		return *this;
-	}
+    Finder const &
+    operator = (Finder const & other)
+    {
+        data_iterator = other.data_iterator;
+        data_endPos = other.data_endPos;
+        data_length = other.data_length;
+        _needReinit = other._needReinit;
+        _beginFind_called = other._beginFind_called;
+        return *this;
+    }
 
 //____________________________________________________________________________
 
-	inline typename Reference<TIterator>::Type 
-	operator* () 
-	{
+    inline typename Reference<TIterator>::Type
+    operator* ()
+    {
 SEQAN_CHECKPOINT
-		return value(hostIterator(*this));
-	}
+        return value(hostIterator(*this));
+    }
 
-	inline typename Reference<TIterator const>::Type 
-	operator* () const
-	{
+    inline typename Reference<TIterator const>::Type
+    operator* () const
+    {
 SEQAN_CHECKPOINT
-		return value(hostIterator(*this));
-	}
+        return value(hostIterator(*this));
+    }
 
 //____________________________________________________________________________
 
-	operator TIterator () const
-	{
+    operator TIterator () const
+    {
 SEQAN_CHECKPOINT
-		return data_iterator;
-	}
+        return data_iterator;
+    }
 
 //____________________________________________________________________________
 
@@ -537,16 +387,16 @@ template <typename THaystack, typename TSpec>
 inline void
 _setFinderEnd(Finder<THaystack, TSpec> & me)
 {//shortcut: move end position to iterator position +1
-	me._beginFind_called = false;
-	me.data_endPos = position(me)+1;
+    me._beginFind_called = false;
+    me.data_endPos = position(me)+1;
 }
 template <typename THaystack, typename TSpec, typename TPosition>
 inline void
 _setFinderEnd(Finder<THaystack, TSpec> & me,
-			  TPosition end_pos)
+              TPosition end_pos)
 {
-	me._beginFind_called = false;
-	me.data_endPos = end_pos;
+    me._beginFind_called = false;
+    me.data_endPos = end_pos;
 }
 
 //____________________________________________________________________________
@@ -558,15 +408,12 @@ _setFinderLength(T &, TSize) {}
 template <typename THaystack, typename TSpec, typename TSize>
 inline void
 _setFinderLength(Finder<THaystack, TSpec> & me,
-				 TSize _length)
+                 TSize _length)
 {
-	me.data_length = _length;
+    me.data_length = _length;
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.beginPosition.param.object.type:Class.Finder
-///.Function.beginPosition.class:Class.Finder
-
 /*!
  * @fn Finder#beginPosition
  * @brief Return begin position of match.
@@ -579,11 +426,11 @@ _setFinderLength(Finder<THaystack, TSpec> & me,
  */
 
 template <typename THaystack, typename TSpec>
-inline typename Position<THaystack>::Type 
+inline typename Position<THaystack>::Type
 beginPosition(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_endPos - me.data_length;
+    return me.data_endPos - me.data_length;
 }
 
 template <typename THaystack, typename TSpec>
@@ -591,13 +438,10 @@ inline typename Position<THaystack const>::Type
 beginPosition(Finder<THaystack, TSpec> const & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_endPos - me.data_length;
+    return me.data_endPos - me.data_length;
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.begin.param.object.type:Class.Finder
-///.Function.begin.class:Class.Finder
-
 /*!
  * @fn Finder#begin
  * @brief Return begin iterator of the match in the haystack.
@@ -614,25 +458,22 @@ SEQAN_CHECKPOINT
 template <typename THaystack, typename TSpec, typename TTag>
 inline typename Iterator<THaystack, Tag<TTag> const>::Type
 begin(Finder<THaystack, TSpec> & me,
-	  Tag<TTag> const tag)
+      Tag<TTag> const tag)
 {
 SEQAN_CHECKPOINT
-	return iter(haystack(me), beginPosition(me), tag);
+    return iter(haystack(me), beginPosition(me), tag);
 }
 
 template <typename THaystack, typename TSpec, typename TTag>
 inline typename Iterator<THaystack const, Tag<TTag> const>::Type
 begin(Finder<THaystack, TSpec> const & me,
-	  Tag<TTag> const tag)
+      Tag<TTag> const tag)
 {
 SEQAN_CHECKPOINT
-	return iter(haystack(me), beginPosition(me), tag);
+    return iter(haystack(me), beginPosition(me), tag);
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.endPosition.param.object.type:Class.Finder
-///.Function.endPosition.class:Class.Finder
-
 /*!
  * @fn Finder#endPosition
  * @brief Return end position of match.
@@ -645,11 +486,11 @@ SEQAN_CHECKPOINT
  */
 
 template <typename THaystack, typename TSpec>
-inline typename Position<THaystack>::Type 
+inline typename Position<THaystack>::Type
 endPosition(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_endPos;
+    return me.data_endPos;
 }
 
 template <typename THaystack, typename TSpec>
@@ -657,13 +498,10 @@ inline typename Position<THaystack const>::Type
 endPosition(Finder<THaystack, TSpec> const & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_endPos;
+    return me.data_endPos;
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.end.param.object.type:Class.Finder
-///.Function.end.class:Class.Finder
-
 /*!
  * @fn Finder#end
  * @brief Return end iterator of the match in the haystack.
@@ -680,25 +518,22 @@ SEQAN_CHECKPOINT
 template <typename THaystack, typename TSpec, typename TTag>
 inline typename Iterator<THaystack, Tag<TTag> const>::Type
 end(Finder<THaystack, TSpec> & me,
-	Tag<TTag> const tag)
+    Tag<TTag> const tag)
 {
 SEQAN_CHECKPOINT
-	return iter(haystack(me), endPosition(me), tag);
+    return iter(haystack(me), endPosition(me), tag);
 }
 
 template <typename THaystack, typename TSpec, typename TTag>
 inline typename Iterator<THaystack const, Tag<TTag> const>::Type
 end(Finder<THaystack, TSpec> const & me,
-	Tag<TTag> const tag)
+    Tag<TTag> const tag)
 {
 SEQAN_CHECKPOINT
-	return iter(haystack(me), endPosition(me), tag);
+    return iter(haystack(me), endPosition(me), tag);
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.length.param.object.type:Class.Finder
-///.Function.length.class:Class.Finder
-
 /*!
  * @fn Finder#length
  * @brief Return the length of the match.
@@ -709,18 +544,18 @@ SEQAN_CHECKPOINT
  */
 
 template <typename THaystack, typename TSpec>
-inline typename Size<THaystack>::Type 
+inline typename Size<THaystack>::Type
 length(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_length;
+    return me.data_length;
 }
 template <typename THaystack, typename TSpec>
-inline typename Size<THaystack const>::Type 
+inline typename Size<THaystack const>::Type
 length(Finder<THaystack, TSpec> const & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_length;
+    return me.data_length;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -735,92 +570,78 @@ SEQAN_CHECKPOINT
  *
  * @return TInfix The @link SegmentableConcept#Infix @endlink of the match in the haystack.
  *
- * @section Remarks
- *
  * This function works only correct if the begin position of the match was already found, see @link Finder#findBegin @endlink
  *
  * For finders or patterns of filtering algorithms (e.g. @Spec.Swift@) the returned infix is a potential match.
  */
 
-/**
-.Function.Finder#infix:
-..summary:Returns the segment of the last found match in haystack.
-..signature:Infix infix(finder)
-..param.finder:An online finder.
-...type:Class.Finder
-..returns:An @Metafunction.Infix.infix@ of the @Metafunction.Haystack.haystack@.
-...metafunction:Metafunction.Infix
-..remarks:This function works only correct if the begin position of the match was already found,
-see @Function.findBegin@.
-..include:seqan/find.h
-*/
 template <typename THaystack, typename TSpec>
 inline typename Infix<THaystack>::Type
 infix(Finder<THaystack, TSpec> & me)
 {
-	return infix(haystack(me), beginPosition(me), endPosition(me));
+    return infix(haystack(me), beginPosition(me), endPosition(me));
 }
 
 template <typename THaystack, typename TSpec>
 inline typename Infix<THaystack const>::Type
 infix(Finder<THaystack, TSpec> const & me)
 {
-	return infix(haystack(me), beginPosition(me), endPosition(me));
+    return infix(haystack(me), beginPosition(me), endPosition(me));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename THaystack, typename TSpec>
-inline typename Parameter_<THaystack>::Type 
+inline typename Parameter_<THaystack>::Type
 host(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return container(hostIterator(me));
+    return container(hostIterator(me));
 }
 
 template <typename THaystack, typename TSpec>
-inline typename Parameter_<THaystack>::Type 
+inline typename Parameter_<THaystack>::Type
 host(Finder<THaystack, TSpec> const & me)
 {
 SEQAN_CHECKPOINT
-	return container(hostIterator(me));
+    return container(hostIterator(me));
 }
 
 template <typename THaystack, typename TSpec>
-inline typename Parameter_<THaystack>::Type 
+inline typename Parameter_<THaystack>::Type
 container(Finder<THaystack, TSpec> & me)
 {
-	return container(hostIterator(me));
+    return container(hostIterator(me));
 }
 
 template <typename THaystack, typename TSpec>
-inline typename Parameter_<THaystack>::Type 
+inline typename Parameter_<THaystack>::Type
 container(Finder<THaystack, TSpec> const & me)
 {
 SEQAN_CHECKPOINT
-	return container(hostIterator(me));
+    return container(hostIterator(me));
 }
 
 //____________________________________________________________________________
 
 template <typename THaystack, typename TSpec>
 inline void
-setHost(Finder<THaystack, TSpec> & me, 
-		typename Parameter_<THaystack>::Type container_)
+setHost(Finder<THaystack, TSpec> & me,
+        typename Parameter_<THaystack>::Type container_)
 {
 SEQAN_CHECKPOINT
-	setContainer(hostIterator(me), container_);
-	goBegin(me);
+    setContainer(hostIterator(me), container_);
+    goBegin(me);
 }
 
 template <typename THaystack, typename TSpec>
 inline void
-setContainer(Finder<THaystack, TSpec> & me, 
-			 typename Parameter_<THaystack>::Type container_)
+setContainer(Finder<THaystack, TSpec> & me,
+             typename Parameter_<THaystack>::Type container_)
 {
 SEQAN_CHECKPOINT
-	setContainer(hostIterator(me), container_);
-	goBegin(me);
+    setContainer(hostIterator(me), container_);
+    goBegin(me);
 }
 
 //____________________________________________________________________________
@@ -830,7 +651,7 @@ inline typename Iterator<THaystack, Rooted>::Type &
 hostIterator(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_iterator;
+    return me.data_iterator;
 }
 
 template <typename THaystack, typename TSpec>
@@ -838,7 +659,7 @@ inline typename Iterator<THaystack, Rooted>::Type const &
 hostIterator(Finder<THaystack, TSpec> const & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_iterator;
+    return me.data_iterator;
 }
 
 //____________________________________________________________________________
@@ -848,15 +669,25 @@ inline bool
 empty(Finder<THaystack, TSpec> const & me)
 {
 SEQAN_CHECKPOINT
-	return me._needReinit;
+    return me._needReinit;
 }
 
+/*!
+ * @fn Finder#clear
+ * @headerfile <seqan/find.h>
+ * @brief Clear the Finder.
+ *
+ * @signature void clear(finder);
+ *
+ * @param[in,out] finder The Finder to clear.
+ */
+
 template <typename THaystack, typename TSpec>
 inline void
 clear(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	me._needReinit = true;
+    me._needReinit = true;
 }
 
 //____________________________________________________________________________
@@ -866,7 +697,7 @@ inline void
 _finderSetNonEmpty(T & me)
 {
 SEQAN_CHECKPOINT
-	goBegin(me);
+    goBegin(me);
 }
 
 
@@ -875,7 +706,7 @@ inline void
 _finderSetNonEmpty(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	me._needReinit = false;
+    me._needReinit = false;
 }
 
 //____________________________________________________________________________
@@ -885,7 +716,7 @@ inline bool
 atBegin(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return (!empty(me) && atBegin(hostIterator(me)));
+    return (!empty(me) && atBegin(hostIterator(me)));
 }
 
 template <typename THaystack, typename TSpec>
@@ -893,7 +724,7 @@ inline bool
 atEnd(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return (!empty(me) && atEnd(hostIterator(me)));
+    return (!empty(me) && atEnd(hostIterator(me)));
 }
 
 //____________________________________________________________________________
@@ -907,20 +738,13 @@ SEQAN_CHECKPOINT
  * @param[in] finder The finder to reset to the beginning of the text.
  */
 
-/**
-.Function.goBegin
-..signature:goBegin(finder)
-..class:Class.Finder
-...param.finder:Finder object to go to beginning in.
-..include:seqan/find.h
- */
 template <typename THaystack, typename TSpec>
 inline void
 goBegin(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	//_finderSetNonEmpty(me);
-	goBegin(hostIterator(me));
+    //_finderSetNonEmpty(me);
+    goBegin(hostIterator(me));
 }
 
 /*!
@@ -932,20 +756,13 @@ SEQAN_CHECKPOINT
  * @param[in] finder The finder to reset to the end of the text.
  */
 
-/**
-.Function.goEnd
-..signature:goEnd(finder)
-..class:Class.Finder
-...param.finder:Finder object to go to end in.
-..include:seqan/find.h
- */
 template <typename THaystack, typename TSpec>
 inline void
 goEnd(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	//_finderSetNonEmpty(me);
-	goEnd(hostIterator(me));
+    //_finderSetNonEmpty(me);
+    goEnd(hostIterator(me));
 }
 
 //____________________________________________________________________________
@@ -955,7 +772,7 @@ SEQAN_CHECKPOINT
  * @brief Return current position of the finder in the haystack.
  *
  * @signature TPosition position(finder);
- * 
+ *
  * @param[in] finder The Finder to query.
  *
  * @return TPosition The current position.  TPosition is the position type of the haystack.
@@ -966,8 +783,8 @@ inline typename Position<Finder<THaystack, TSpec> >::Type
 position(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	if (empty(me)) return 0;
-	return position(hostIterator(me));
+    if (empty(me)) return 0;
+    return position(hostIterator(me));
 }
 
 template <typename THaystack, typename TSpec>
@@ -975,8 +792,8 @@ inline typename Position<Finder<THaystack, TSpec> >::Type
 position(Finder<THaystack, TSpec> const & me)
 {
 SEQAN_CHECKPOINT
-	if (empty(me)) return 0;
-	return position(hostIterator(me));
+    if (empty(me)) return 0;
+    return position(hostIterator(me));
 }
 
 //____________________________________________________________________________
@@ -991,26 +808,12 @@ SEQAN_CHECKPOINT
  * @param[in]     pos    The position to set the finder to.
  */
 
-/**
-.Function.setPosition:
-..cat:Searching
-..summary:Sets the position of a finder.
-..signature:setPosition(finder, pos)
-..class:Class.Finder
-..param.finder:A finder.
-...type:Class.Finder
-..param.pos:A position.
-...metafunction:Metafunction.Position
-..see:Function.position
-..include:seqan/find.h
-*/
-
 template <typename THaystack, typename TSpec, typename TPosition>
-inline void 
+inline void
 setPosition(Finder<THaystack, TSpec> & me, TPosition pos_)
 {
 SEQAN_CHECKPOINT
-	setPosition(hostIterator(me), pos_);
+    setPosition(hostIterator(me), pos_);
 }
 
 //____________________________________________________________________________
@@ -1020,8 +823,8 @@ inline Finder<THaystack, TSpec> &
 operator--(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	--hostIterator(me);
-	return me;
+    --hostIterator(me);
+    return me;
 }
 
 template <typename THaystack, typename TSpec>
@@ -1029,11 +832,11 @@ inline Finder<THaystack, TSpec> &
 operator++(Finder<THaystack, TSpec> & me)
 {
 SEQAN_CHECKPOINT
-/*			if (beforeBegin()) {
-		goBegin(hostIterator(me));
-	} else*/
-		++hostIterator(me);
-	return me;
+/*            if (beforeBegin()) {
+        goBegin(hostIterator(me));
+    } else*/
+        ++hostIterator(me);
+    return me;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1045,7 +848,7 @@ inline Finder<THaystack, TSpec> const
 operator + (Finder<THaystack, TSpec> const & left, TIntegral right)
 {
 SEQAN_CHECKPOINT
-	return Finder<THaystack, TSpec>(hostIterator(left) + right);
+    return Finder<THaystack, TSpec>(hostIterator(left) + right);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1055,11 +858,11 @@ SEQAN_CHECKPOINT
 template <typename THaystack, typename TSpec, typename TIntegral>
 inline Finder<THaystack, TSpec> &
 operator += (Finder<THaystack, TSpec> & left,
-				TIntegral right)
+                TIntegral right)
 {
 SEQAN_CHECKPOINT
-	hostIterator(left) += right;
-	return left;
+    hostIterator(left) += right;
+    return left;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1071,7 +874,7 @@ inline Finder<THaystack, TSpec> const
 operator - (Finder<THaystack, TSpec> const & left, TIntegral right)
 {
 SEQAN_CHECKPOINT
-	return Finder<THaystack, TSpec>(hostIterator(left) - right);
+    return Finder<THaystack, TSpec>(hostIterator(left) - right);
 }
 
 template <typename THaystack, typename TSpec, typename TIntegral>
@@ -1079,7 +882,7 @@ inline typename Difference<Finder<THaystack, TSpec> const>::Type
 operator - (Finder<THaystack, TSpec> const & left, Finder<THaystack, TSpec> const & right)
 {
 SEQAN_CHECKPOINT
-	return hostIterator(left) - hostIterator(right);
+    return hostIterator(left) - hostIterator(right);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1089,11 +892,11 @@ SEQAN_CHECKPOINT
 template <typename THaystack, typename TSpec, typename TIntegral>
 inline Finder<THaystack, TSpec> &
 operator -= (Finder<THaystack, TSpec> & left,
-				TIntegral right)
+                TIntegral right)
 {
 SEQAN_CHECKPOINT
-	hostIterator(left) -= right;
-	return left;
+    hostIterator(left) -= right;
+    return left;
 }
 
 //____________________________________________________________________________
@@ -1108,23 +911,10 @@ SEQAN_CHECKPOINT
  * @param[in]     haystack The haystack to set.
  */
 
-/**
-.Function.setHaystack:
-..summary:Sets the haystack of a @Class.Finder@ object.
-..cat:Searching
-..signature:setHaystack(finder, haystack)
-..class:Class.Finder
-..param.finder:The @Class.Finder@ object to search with.
-...type:Class.Finder
-..param.haystack:The haystack object the finder searches through.
-...type:Class.String
-..include:seqan/find.h
-*/
-
 template < typename THaystack, typename TSpec >
 inline void
 setHaystack(Finder<THaystack, TSpec> &obj, THaystack const &hstk) {
-	setHost(obj, hstk);
+    setHost(obj, hstk);
 }
 
 template < typename THaystack, typename TSpec >
@@ -1146,70 +936,49 @@ setHaystack(Finder<THaystack, TSpec> &obj, THaystack &hstk)
  * @return THaystack The result type can be retrieved using @link Finder#Haystack @endlink.
  */
 
-/**
-.Function.haystack:
-..summary:Returns the haystack of a @Class.Finder@ object.
-..cat:Searching
-..signature:haystack(finder)
-..class:Class.Finder
-..param.finder:The @Class.Finder@ object to search through.
-...type:Class.Finder
-..returns:The haystack object.
-..remarks:The result type is @Metafunction.Haystack@$<TFinder>::Type$ for finder of type $TFinder$.
-..include:seqan/find.h
-*/
-
 template < typename TObject >
 inline typename Parameter_<typename Haystack<TObject>::Type>::Type
 haystack(TObject &obj) {
-	return container(obj);
+    return container(obj);
 }
 
 template < typename TObject >
 inline typename Parameter_<typename Haystack<TObject const>::Type>::Type
 haystack(TObject const &obj) {
-	return container(obj);
+    return container(obj);
 }
 
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Container.param.T.type:Class.Finder
-///.Metafunction.Container.class:Class.Finder
 template <typename THaystack, typename TSpec>
 struct Container< Finder<THaystack, TSpec> > {
-	typedef THaystack Type;
+    typedef THaystack Type;
 };
 
 template <typename THaystack, typename TSpec>
 struct Container< Finder<THaystack, TSpec> const> {
-	typedef THaystack const Type;
+    typedef THaystack const Type;
 };
 
 
-///.Metafunction.Host.param.T.type:Class.Finder
-///.Metafunction.Host.class:Class.Finder
 template <typename THaystack, typename TSpec>
 struct Host< Finder<THaystack, TSpec> > {
-	typedef THaystack Type;
+    typedef THaystack Type;
 };
 
 template <typename THaystack, typename TSpec>
 struct Host< Finder<THaystack, TSpec> const> {
-	typedef THaystack const Type;
+    typedef THaystack const Type;
 };
 
 
-///.Metafunction.Value.param.T.type:Class.Finder
-///.Metafunction.Value.class:Class.Finder
 template <typename THaystack, typename TSpec>
 struct Value< Finder<THaystack, TSpec> > {
-	typedef typename Value<THaystack>::Type Type;
+    typedef typename Value<THaystack>::Type Type;
 };
 
-///.Metafunction.Reference.param.T.type:Class.Finder
-///.Metafunction.Reference.class:Class.Finder
 template <typename THaystack, typename TSpec>
 struct Reference< Finder<THaystack, TSpec> >
 {
@@ -1223,38 +992,32 @@ struct Reference< Finder<THaystack, TSpec> const>
 };
 
 
-///.Metafunction.Position.param.T.type:Class.Finder
-///.Metafunction.Position.class:Class.Finder
 template <typename THaystack, typename TSpec>
 struct Position< Finder<THaystack, TSpec> >:
-	Position<THaystack> {};
+    Position<THaystack> {};
 
 
-///.Metafunction.Difference.param.T.type:Class.Finder
-///.Metafunction.Difference.class:Class.Finder
 template <typename THaystack, typename TSpec>
 struct Difference< Finder<THaystack, TSpec> > {
-	typedef typename Difference<THaystack>::Type Type;
+    typedef typename Difference<THaystack>::Type Type;
 };
 
 template <typename THaystack, typename TSpec>
 struct Size< Finder<THaystack, TSpec> > {
-	typedef typename Size<THaystack>::Type Type;
+    typedef typename Size<THaystack>::Type Type;
 };
 
 
-///.Metafunction.Iterator.param.T.type:Class.Finder
-///.Metafunction.Iterator.class:Class.Finder
 template <typename THaystack, typename TSpec, typename TIteratorSpec>
 struct Iterator< Finder<THaystack, TSpec>, TIteratorSpec >
 {
-	typedef typename Iterator<THaystack>::Type Type;
+    typedef typename Iterator<THaystack>::Type Type;
 };
 
 template <typename THaystack, typename TSpec, typename TIteratorSpec>
 struct Iterator< Finder<THaystack, TSpec> const, TIteratorSpec >
 {
-	typedef typename Iterator<THaystack>::Type Type;
+    typedef typename Iterator<THaystack>::Type Type;
 };
 
 
@@ -1262,13 +1025,13 @@ struct Iterator< Finder<THaystack, TSpec> const, TIteratorSpec >
 // .Metafunction.DefaultGetIterator.param.T.type:Class.Finder
 template <typename THaystack, typename TSpec>
 struct DefaultGetIteratorSpec< Finder<THaystack, TSpec> >:
-	DefaultGetIteratorSpec< THaystack >
+    DefaultGetIteratorSpec< THaystack >
 {
 };
 
 template <typename THaystack, typename TSpec>
 struct DefaultGetIteratorSpec< Finder<THaystack, TSpec> const>:
-	DefaultGetIteratorSpec< THaystack const>
+    DefaultGetIteratorSpec< THaystack const>
 {
 };
 
diff --git a/seqan/find/find_begin.h b/seqan/find/find_begin.h
index c954de3..47588e2 100644
--- a/seqan/find/find_begin.h
+++ b/seqan/find/find_begin.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -67,36 +67,26 @@ struct Myers;
  * @return Type The pattern specialization to use as a default.
  */
 
-/**
-.Metafunction.DefaultFindBeginPatternSpec:
-..cat:Searching
-..summary:Type of the default findBegin pattern specialization, given a score.
-..signature:DefaultBeginPatternSpec<TScore>
-..param.TScore:A score type.
-...type:Class.Score
-..returns.param.Type:The pattern specialization to use as a default.
-..include:seqan/find.h
- */
 template <typename TScore = EditDistanceScore, typename THasState = True>
 struct DefaultFindBeginPatternSpec
 {
-	typedef DPSearch<TScore, FindPrefix, void> Type;
+    typedef DPSearch<TScore, FindPrefix, void> Type;
 };
 
 template <typename THasState>
 struct DefaultFindBeginPatternSpec<EditDistanceScore, THasState>
 {
-	// typedef Myers<FindPrefix, void, True> Type;
-	typedef Myers<FindPrefix, THasState, void> Type;
+    // typedef Myers<FindPrefix, void, True> Type;
+    typedef Myers<FindPrefix, THasState, void> Type;
 };
 
 //____________________________________________________________________________
 //must be implemented for all patterns that do approximate infix finding
 
 template <typename TPattern>
-struct FindBeginPatternSpec 
+struct FindBeginPatternSpec
 {
-	typedef void Type; //void means: no find begin (see FindBegin_)
+    typedef void Type; //void means: no find begin (see FindBegin_)
 };
 
 //____________________________________________________________________________
@@ -105,10 +95,10 @@ struct FindBeginPatternSpec
 template <typename TPattern>
 struct FindBeginPattern
 {
-	typedef typename Needle<TPattern>::Type TNeedle_;
-	typedef ModifiedString<TNeedle_, ModReverse> TReverseNeedle_;
-	typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec_;
-	typedef Pattern<TReverseNeedle_, TFindBeginPatternSpec_> Type;
+    typedef typename Needle<TPattern>::Type TNeedle_;
+    typedef ModifiedString<TNeedle_, ModReverse> TReverseNeedle_;
+    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec_;
+    typedef Pattern<TReverseNeedle_, TFindBeginPatternSpec_> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -117,9 +107,9 @@ struct FindBeginPattern
 template <typename TPattern, typename TFindBeginPatternSpec = typename FindBeginPatternSpec<TPattern>::Type >
 struct FindBegin_
 {
-	typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern_;
+    typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern_;
 
-	TFindBeginPattern_ data_findBeginPattern;
+    TFindBeginPattern_ data_findBeginPattern;
 };
 
 template <typename TPattern>
@@ -134,75 +124,79 @@ struct FindBegin_ <TPattern, void>
 template <typename TFindBeginPatternSpec>
 struct FindBeginImpl_
 {
-	template <typename TPattern, typename TNeedle>
-	static inline void
-	_findBeginInit(TPattern & pattern, TNeedle & needle_)
-	{
-//		setNeedle(pattern.data_findBeginPattern, reverseString(needle(pattern)));
-		setHost(needle(pattern.data_findBeginPattern), needle_);
-		setScoringScheme(pattern.data_findBeginPattern, scoringScheme(pattern));
-	}
+    template <typename TPattern, typename TNeedle>
+    static inline void
+    _findBeginInit(TPattern & pattern, TNeedle & needle_)
+    {
+//        setNeedle(pattern.data_findBeginPattern, reverseString(needle(pattern)));
+        // TODO(rrahn): Mhmm, is this really intended here, or is it due to a wrong design of setHost of patterns which always copies instread of strong the reference where it can?
+        // It could happen, that we are really overwriting the original needle, if it was passed as non-const lvalue reference.
+        // The version above would be safer, as reverseString always returns a copy.
+        // But maybe the set function of ModifiedStrings is overloaded such that we will do a copy anyway in the holder class.
+        setHost(needle(pattern.data_findBeginPattern), needle_);
+        setScoringScheme(pattern.data_findBeginPattern, scoringScheme(pattern));
+    }
 //____________________________________________________________________________
 
-	template <typename TFinder, typename TPattern, typename TLimit>
-	static inline bool
-	findBegin(TFinder & finder, TPattern & pattern, TLimit limit)
-	{
-		typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern;
-		typedef typename Haystack<TFinder>::Type THaystack;
-		typedef ModifiedString<THaystack, ModReverse> TReverseHaystack;
-		typedef Finder<TReverseHaystack> TBeginFinder;
-		typedef typename Position<THaystack>::Type TPosition;
-
-		TFindBeginPattern & find_begin_pattern = pattern.data_findBeginPattern;
-		setScoreLimit(find_begin_pattern, limit);
-
-		//build begin_finder
-		TBeginFinder begin_finder;
-		THaystack & hayst = haystack(finder);
-		setContainer(host(hostIterator(begin_finder)), hayst);
-		TPosition begin_finder_beginPosition = position(finder);
-		TPosition begin_finder_position;
-
-		if (!finder._beginFind_called)
-		{//start finding
-			finder._beginFind_called = true;
-			_setFinderLength(finder, 0);
-			clear(begin_finder);
-			begin_finder_position = begin_finder_beginPosition;
-		}
-		else
-		{//resume finding
-			_finderSetNonEmpty(begin_finder);
-			SEQAN_ASSERT_GT(length(finder), 0u);
-			begin_finder_position = endPosition(finder) - length(finder);
-		}
-		setPosition(host(hostIterator(begin_finder)), begin_finder_position);
-		_setFinderEnd(begin_finder);
-		_setFinderLength(begin_finder, length(finder));
-
-		bool begin_found = find(begin_finder, find_begin_pattern);
-		if (begin_found)
-		{//new begin found: report in finder
-			_setFinderLength(finder, begin_finder_beginPosition - position(host(hostIterator(begin_finder)))+1);
-		}
-		return begin_found;
-	}
-	template <typename TFinder, typename TPattern>
-	static inline bool
-	findBegin(TFinder & finder, TPattern & pattern)
-	{
-		return findBegin(finder, pattern, scoreLimit(pattern));
-	}
+    template <typename TFinder, typename TPattern, typename TLimit>
+    static inline bool
+    findBegin(TFinder & finder, TPattern & pattern, TLimit limit)
+    {
+        typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern;
+        typedef typename Haystack<TFinder>::Type THaystack;
+        typedef ModifiedString<THaystack, ModReverse> TReverseHaystack;
+        typedef Finder<TReverseHaystack> TBeginFinder;
+        typedef typename Position<THaystack>::Type TPosition;
+
+        TFindBeginPattern & find_begin_pattern = pattern.data_findBeginPattern;
+        setScoreLimit(find_begin_pattern, limit);
+
+        //build begin_finder
+        TBeginFinder begin_finder;
+        THaystack & hayst = haystack(finder);
+        setContainer(host(hostIterator(begin_finder)), hayst);
+        TPosition begin_finder_beginPosition = position(finder);
+        TPosition begin_finder_position;
+
+        if (!finder._beginFind_called)
+        {//start finding
+            finder._beginFind_called = true;
+            _setFinderLength(finder, 0);
+            clear(begin_finder);
+            begin_finder_position = begin_finder_beginPosition;
+        }
+        else
+        {//resume finding
+            _finderSetNonEmpty(begin_finder);
+            SEQAN_ASSERT_GT(length(finder), 0u);
+            begin_finder_position = endPosition(finder) - length(finder);
+        }
+        setPosition(host(hostIterator(begin_finder)), begin_finder_position);
+        _setFinderEnd(begin_finder);
+        _setFinderLength(begin_finder, length(finder));
+
+        bool begin_found = find(begin_finder, find_begin_pattern);
+        if (begin_found)
+        {//new begin found: report in finder
+            _setFinderLength(finder, begin_finder_beginPosition - position(host(hostIterator(begin_finder)))+1);
+        }
+        return begin_found;
+    }
+    template <typename TFinder, typename TPattern>
+    static inline bool
+    findBegin(TFinder & finder, TPattern & pattern)
+    {
+        return findBegin(finder, pattern, scoreLimit(pattern));
+    }
 
 //____________________________________________________________________________
 
-	template <typename TPattern>
-	static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
-	getBeginScore(TPattern & pattern)
-	{
-		return getScore(pattern.data_findBeginPattern);
-	}
+    template <typename TPattern>
+    static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
+    getBeginScore(TPattern & pattern)
+    {
+        return getScore(pattern.data_findBeginPattern);
+    }
 };
 
 
@@ -210,118 +204,118 @@ struct FindBeginImpl_
 template <typename THasState>
 struct FindBeginImpl_<Myers<FindPrefix, THasState, void> >
 {
-	template <typename TPattern, typename TNeedle>
-	static inline void
-	_findBeginInit(TPattern & pattern, TNeedle & needle_)
-	{
-//		setNeedle(pattern.data_findBeginPattern, reverseString(needle(pattern)));
-		setHost(pattern.data_findBeginPattern, reverseString(needle_));
+    template <typename TPattern, typename TNeedle>
+    static inline void
+    _findBeginInit(TPattern & pattern, TNeedle & needle_)
+    {
+//        setNeedle(pattern.data_findBeginPattern, reverseString(needle(pattern)));
+        setHost(pattern.data_findBeginPattern, reverseString(needle_));
 //         _patternFirstInit(pattern.data_findBeginPattern, host(pattern));
-	}
+    }
 //____________________________________________________________________________
 
-	template <typename TFinder, typename TPattern, typename TLimit>
-	static inline bool
-	findBegin(TFinder & finder, TPattern & pattern, TLimit limit)
-	{
-		typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern;
-		typedef typename Haystack<TFinder>::Type THaystack;
-		typedef ModifiedString<THaystack, ModReverse> TReverseHaystack;
-		typedef Finder<TReverseHaystack> TBeginFinder;
-		typedef typename Position<THaystack>::Type TPosition;
-
-		TFindBeginPattern & find_begin_pattern = pattern.data_findBeginPattern;
-		setScoreLimit(find_begin_pattern, limit);
-
-		//build begin_finder
-		TBeginFinder begin_finder;
-		typename Parameter_<THaystack>::Type hayst = haystack(finder);
-		setContainer(host(hostIterator(begin_finder)), hayst);
-		TPosition begin_finder_beginPosition = position(finder);
-		TPosition begin_finder_position;
-
-		if (!finder._beginFind_called)
-		{//start finding
-			finder._beginFind_called = true;
-			_setFinderLength(finder, 0);
-			clear(begin_finder);
-			begin_finder_position = begin_finder_beginPosition;
-		}
-		else
-		{//resume finding
-			_finderSetNonEmpty(begin_finder);
-			SEQAN_ASSERT_GT(length(finder), 0u);
-			begin_finder_position = endPosition(finder) - length(finder);
-		}
-		setPosition(host(hostIterator(begin_finder)), begin_finder_position);
-		_setFinderEnd(begin_finder);
-		_setFinderLength(begin_finder, length(finder));
-
-		bool begin_found = find(begin_finder, find_begin_pattern);
-		if (begin_found)
-		{//new begin found: report in finder
-			_setFinderLength(finder, begin_finder_beginPosition - position(host(hostIterator(begin_finder)))+1);
-		}
-		return begin_found;
-	}
-	template <typename TFinder, typename TPattern>
-	static inline bool
-	findBegin(TFinder & finder, TPattern & pattern)
-	{
-		return findBegin(finder, pattern, scoreLimit(pattern));
-	}
+    template <typename TFinder, typename TPattern, typename TLimit>
+    static inline bool
+    findBegin(TFinder & finder, TPattern & pattern, TLimit limit)
+    {
+        typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern;
+        typedef typename Haystack<TFinder>::Type THaystack;
+        typedef ModifiedString<THaystack, ModReverse> TReverseHaystack;
+        typedef Finder<TReverseHaystack> TBeginFinder;
+        typedef typename Position<THaystack>::Type TPosition;
+
+        TFindBeginPattern & find_begin_pattern = pattern.data_findBeginPattern;
+        setScoreLimit(find_begin_pattern, limit);
+
+        //build begin_finder
+        TBeginFinder begin_finder;
+        typename Parameter_<THaystack>::Type hayst = haystack(finder);
+        setContainer(host(hostIterator(begin_finder)), hayst);
+        TPosition begin_finder_beginPosition = position(finder);
+        TPosition begin_finder_position;
+
+        if (!finder._beginFind_called)
+        {//start finding
+            finder._beginFind_called = true;
+            _setFinderLength(finder, 0);
+            clear(begin_finder);
+            begin_finder_position = begin_finder_beginPosition;
+        }
+        else
+        {//resume finding
+            _finderSetNonEmpty(begin_finder);
+            SEQAN_ASSERT_GT(length(finder), 0u);
+            begin_finder_position = endPosition(finder) - length(finder);
+        }
+        setPosition(host(hostIterator(begin_finder)), begin_finder_position);
+        _setFinderEnd(begin_finder);
+        _setFinderLength(begin_finder, length(finder));
+
+        bool begin_found = find(begin_finder, find_begin_pattern);
+        if (begin_found)
+        {//new begin found: report in finder
+            _setFinderLength(finder, begin_finder_beginPosition - position(host(hostIterator(begin_finder)))+1);
+        }
+        return begin_found;
+    }
+    template <typename TFinder, typename TPattern>
+    static inline bool
+    findBegin(TFinder & finder, TPattern & pattern)
+    {
+        return findBegin(finder, pattern, scoreLimit(pattern));
+    }
 
 //____________________________________________________________________________
 
-	template <typename TPattern>
-	static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
-	getBeginScore(TPattern & pattern)
-	{
-		return getScore(pattern.data_findBeginPattern);
-	}
+    template <typename TPattern>
+    static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
+    getBeginScore(TPattern & pattern)
+    {
+        return getScore(pattern.data_findBeginPattern);
+    }
 };
 
-//default implementation of findBegin emulates the behaviour 
+//default implementation of findBegin emulates the behaviour
 //of findBegin for approximate string matching algorithms
 //for exact algorithms:
 //the first call returns true ("begin position found")
 //the next calls return false ("no further begin position found")
-//no searching needed, since the exact algorithms set the 
+//no searching needed, since the exact algorithms set the
 //match length manually via "_setFinderLength" (it's the needle length)
 
 template <>
 struct FindBeginImpl_<void>
 {
-	template <typename TPattern, typename TNeedle>
-	static inline void
-	_findBeginInit(TPattern &, TNeedle &)
-	{
-	}
-
-	template <typename TFinder, typename TPattern, typename TLimit>
-	static inline bool
-	findBegin(TFinder & finder, TPattern &, TLimit)
-	{
-		if (!finder._beginFind_called)
-		{
-			finder._beginFind_called = true;
-			return true;
-		}
-		return false;
-	}
-	template <typename TFinder, typename TPattern>
-	static inline bool
-	findBegin(TFinder & finder, TPattern & pattern)
-	{
-		return findBegin(finder, pattern, 0);
-	}
-
-	template <typename TPattern>
-	static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
-	getBeginScore(TPattern & pattern)
-	{
-		return getScore(pattern);
-	}
+    template <typename TPattern, typename TNeedle>
+    static inline void
+    _findBeginInit(TPattern &, TNeedle &)
+    {
+    }
+
+    template <typename TFinder, typename TPattern, typename TLimit>
+    static inline bool
+    findBegin(TFinder & finder, TPattern &, TLimit)
+    {
+        if (!finder._beginFind_called)
+        {
+            finder._beginFind_called = true;
+            return true;
+        }
+        return false;
+    }
+    template <typename TFinder, typename TPattern>
+    static inline bool
+    findBegin(TFinder & finder, TPattern & pattern)
+    {
+        return findBegin(finder, pattern, 0);
+    }
+
+    template <typename TPattern>
+    static inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
+    getBeginScore(TPattern & pattern)
+    {
+        return getScore(pattern);
+    }
 };
 
 
@@ -332,13 +326,13 @@ template <typename TPattern, typename TNeedle>
 inline void
 _findBeginInit(TPattern & pattern, TNeedle & needle_)
 {
-	typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
-	return FindBeginImpl_<TFindBeginPatternSpec>::_findBeginInit(pattern, needle_);
+    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
+    return FindBeginImpl_<TFindBeginPatternSpec>::_findBeginInit(pattern, needle_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-//find begin main interface 
+//find begin main interface
 
 /*!
  * @fn Finder#findBegin
@@ -347,61 +341,39 @@ _findBeginInit(TPattern & pattern, TNeedle & needle_)
  *
  * @signature bool findBegin(finder, pattern[, limit]);
  *
- * @param finder[in,out]  The Finder object to search through.
- * @param pattern[in,out] The Pattern object to search for.  This must be a pattern for approximate string matching.
- * @param limit[in]       The score limit.  The default is the limit used during the last <tt>find</tt> call, see
+ * @param[in,out] finder  The Finder object to search through.
+ * @param[in,out] pattern The Pattern object to search for.  This must be a pattern for approximate string matching.
+ * @param[in]     limit   The score limit.  The default is the limit used during the last <tt>find</tt> call, see
  *                        <tt>getScore</tt>.  All occurences that score at least <tt>limit</tt> are reported.
  *
  * @return bool <tt>true</tt> indicates a match, <tt>false</tt> indicates no match.
  *
- * @section Remarks
- *
  * The function <tt>find</tT> successfully called be called - that is an end position was found - before calling
  * findBegin to find a begin position.
  */
 
-/**
-.Function.findBegin:
-..summary:Search the begin of an approximate match.
-..cat:Searching
-..signature:findBegin(finder, pattern [, limit])
-..class:Class.Finder
-..param.finder:The @Class.Finder@ object to search through.
-...type:Class.Finder
-..param.pattern:The @Class.Pattern@ object to search for.
-...remarks:This must be a pattern for approximate string matching.
-...type:Class.Pattern
-..param.limit:The score limit.
-...default:The limit used during the last @Function.find@ call, see @Function.getScore@.
-...remarks:All occurrences that score at least $limit$ are reported.
-..returns:$boolean$ that indicates whether an begin position was found.
-..remarks:The function @Function.find@ successfully called be called - that is an end position was found - before calling $findBegin$ to find a begin position.
-..see:Function.getBeginScore
-..see:Function.find
-..include:seqan/find.h
-*/
 template <typename TFinder, typename TPattern>
 inline bool
 findBegin(TFinder & finder,
-		  TPattern & pattern)
+          TPattern & pattern)
 {
-	typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
-	return FindBeginImpl_<TFindBeginPatternSpec>::findBegin(finder, pattern);
+    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
+    return FindBeginImpl_<TFindBeginPatternSpec>::findBegin(finder, pattern);
 }
 template <typename TFinder, typename TPattern, typename TLimit>
 inline bool
 findBegin(TFinder & finder,
-		  TPattern & pattern,
-		  TLimit limit)
+          TPattern & pattern,
+          TLimit limit)
 {
-	typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
-	return FindBeginImpl_<TFindBeginPatternSpec>::findBegin(finder, pattern, limit);
+    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
+    return FindBeginImpl_<TFindBeginPatternSpec>::findBegin(finder, pattern, limit);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
- * @fn getBeginScore
+ * @fn Pattern#getBeginScore
  * @headerfile <seqan/find.h>
  * @brief Score of the last match found by @link Finder#findBegin @endlink during approximate searching.
  *
@@ -413,26 +385,12 @@ findBegin(TFinder & finder,
  *                     call of @link Finder#findBegin @endlink.  If no match was found, the value is undefined.
  */
 
-/**.Function.getBeginScore
-..cat:Searching
-..summary:Score of the last match found by @Function.findBegin@ during approximate searching.
-..signature:getBeginScore(pattern)
-..class:Class.Finder
-..param.pattern:A @Class.Pattern@ that can be used for approximate searching.
-...type:Spec.DPSearch
-..returns:The score of the last match found using $pattern$.
-...remarks:The value is set after a successfully call of @Function.findBegin@.
-If no match was found, the value is undefined.
-..see:Function.findBegin
-..see:Function.getScore
-*/
-
 template <typename TPattern>
 inline typename Value<typename ScoringScheme<TPattern>::Type>::Type
 getBeginScore(TPattern & pattern)
 {
-	typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
-	return FindBeginImpl_<TFindBeginPatternSpec>::getBeginScore(pattern);
+    typedef typename FindBeginPatternSpec<TPattern>::Type TFindBeginPatternSpec;
+    return FindBeginImpl_<TFindBeginPatternSpec>::getBeginScore(pattern);
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/find/find_bndm.h b/seqan/find/find_bndm.h
index ba43c19..3bc86fe 100644
--- a/seqan/find/find_bndm.h
+++ b/seqan/find/find_bndm.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,32 +47,15 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pattern
  * @headerfile <seqan/find.h>
  * @brief Backward Nondeterministic Dawg Matching algorithm.  Exact string matching using bit parallelism.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, BndmAlgo>;
- * 
+ *
  * @tparam TNeedle The needle type.  Types: String
- * 
- * @section Remarks
- * 
+ *
  * The types of the needle and the haystack have to match.
  */
 
-/**
-.Spec.BndmAlgo:
-..summary: Backward Nondeterministic Dawg Matching algorithm. Exact string matching using bit parallelism.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, BndmAlgo>
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks.text:The types of the needle and the haystack have to match.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.BndmAlgo
-///.Class.Pattern.class:Spec.BndmAlgo
-
 struct BndmAlgo_;
 typedef Tag<BndmAlgo_> BndmAlgo;
 
@@ -82,26 +65,37 @@ template <typename TNeedle>
 class Pattern<TNeedle, BndmAlgo> {
 //____________________________________________________________________________
 public:
-	typedef unsigned int TWord;
+    typedef unsigned int TWord;
 
-	Holder<TNeedle> data_host;
-	String<TWord> table;			// Look up table for each character in the alphabet (called B in "Navarro")
-	String<TWord> activeFactors;	// The active factors in the pattern (called D in "Navarro")
-	TWord needleLength;				// e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
-	TWord haystackLength;			// Length of haystack
-	TWord blockCount;				// #unsigned ints required to store needle
-	TWord last;
+    Holder<TNeedle> data_host;
+    String<TWord> table;            // Look up table for each character in the alphabet (called B in "Navarro")
+    String<TWord> activeFactors;    // The active factors in the pattern (called D in "Navarro")
+    TWord needleLength;                // e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
+    TWord haystackLength;            // Length of haystack
+    TWord blockCount;                // #unsigned ints required to store needle
+    TWord last;
 
 //____________________________________________________________________________
 
-	Pattern() {}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		setHost(*this, ndl);
-	}
-
+    Pattern() {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+#else
+
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
@@ -110,61 +104,53 @@ class Pattern<TNeedle, BndmAlgo> {
 // Functions
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, BndmAlgo> & me, TNeedle2 const& needle) {
-	SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
-	typedef typename Value<TNeedle>::Type TValue;
-
-	me.needleLength = length(needle);
-	if (me.needleLength<1) me.blockCount=1;
-	else me.blockCount=((me.needleLength-1) / BitsPerValue<TWord>::VALUE)+1;
-			
-	clear(me.table);
-	resize(me.table, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
-
-	for (TWord j = 0; j < me.needleLength; ++j) {
-		// Determine character position in array table
-		TWord pos = convert<TWord>(getValue(needle,j));
-		me.table[me.blockCount*pos + j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
-	}
-
-	setValue(me.data_host, needle);
-	/*
-	// Debug code
-	std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << ::std::endl;
-	std::cout << "Needle length: " << me.needleLength << ::std::endl;
-	std::cout << "Block count: " << me.blockCount << ::std::endl;
-
-	for(unsigned int i=0;i<ValueSize<TValue>::VALUE;++i) {
-		if ((i<97) || (i>122)) continue;
-		std::cout << static_cast<char>(i) << ": ";
-		for(int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-				std::cout << ((me.table[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-	}
-	*/
-}
-
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, BndmAlgo> & me, TNeedle2 & needle)
-{
-	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
+template <typename TNeedle>
+void _reinitPattern(Pattern<TNeedle, BndmAlgo> & me) {
+    SEQAN_CHECKPOINT
+    typedef unsigned int TWord;
+    typedef typename Value<TNeedle>::Type TValue;
+
+    me.needleLength = length(needle(me));
+    if (me.needleLength<1) me.blockCount=1;
+    else me.blockCount=((me.needleLength-1) / BitsPerValue<TWord>::VALUE)+1;
+
+    clear(me.table);
+    resize(me.table, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
+
+    for (TWord j = 0; j < me.needleLength; ++j) {
+        // Determine character position in array table
+        TWord pos = convert<TWord>(getValue(needle(me),j));
+        me.table[me.blockCount*pos + j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
+    }
+    /*
+    // Debug code
+    std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << std::endl;
+    std::cout << "Needle length: " << me.needleLength << std::endl;
+    std::cout << "Block count: " << me.blockCount << std::endl;
+
+    for(unsigned int i=0;i<ValueSize<TValue>::VALUE;++i) {
+        if ((i<97) || (i>122)) continue;
+        std::cout << static_cast<char>(i) << ": ";
+        for(int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                std::cout << ((me.table[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+    }
+    */
 }
 
 //____________________________________________________________________________
 
 
 template <typename TNeedle>
-inline void _patternInit (Pattern<TNeedle, BndmAlgo> & me) 
+inline void _patternInit (Pattern<TNeedle, BndmAlgo> & me)
 {
 SEQAN_CHECKPOINT
-	clear(me.activeFactors);
-	resize(me.activeFactors, me.blockCount, 0, Exact());
-	me.last = 0;
+    clear(me.activeFactors);
+    resize(me.activeFactors, me.blockCount, 0, Exact());
+    me.last = 0;
 }
 
 
@@ -172,105 +158,109 @@ SEQAN_CHECKPOINT
 
 
 template <typename TFinder, typename TNeedle>
-inline bool _findBndmSmallNeedle(TFinder & finder, 
-								  Pattern<TNeedle, BndmAlgo> & me) {
-	SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
-	if (me.haystackLength < me.needleLength) return false;
-	while (position(finder) <= me.haystackLength - me.needleLength) 
-	{
-		me.last=me.needleLength;
-		TWord j=me.needleLength;
-		me.activeFactors[0]=~0;
-		while (me.activeFactors[0]!=0) 
-		{
-			TWord pos = convert<TWord>(*(finder+j-1));
-			me.activeFactors[0] = (me.activeFactors[0] & me.table[me.blockCount*pos]);
-			j--;
-			if ((me.activeFactors[0] & 1) != 0) 
-			{
-				if (j>0) me.last=j;
-				else
-				{
-					_setFinderEnd(finder, position(finder) + me.needleLength);
-					return true;
-				}
-			}
-			me.activeFactors[0] = me.activeFactors[0] >> 1;
-		}
-		finder+=me.last;
-	}
-	return false;
+inline bool _findBndmSmallNeedle(TFinder & finder,
+                                  Pattern<TNeedle, BndmAlgo> & me) {
+    SEQAN_CHECKPOINT
+    typedef unsigned int TWord;
+    typedef typename Value<TNeedle>::Type TNeedleAlphabet;
+
+    if (me.haystackLength < me.needleLength) return false;
+    while (position(finder) <= me.haystackLength - me.needleLength)
+    {
+        me.last=me.needleLength;
+        TWord j=me.needleLength;
+        me.activeFactors[0]=~0;
+        while (me.activeFactors[0]!=0)
+        {
+            TWord pos = convert<TWord>(convert<TNeedleAlphabet>(*(finder+j-1)));
+            me.activeFactors[0] = (me.activeFactors[0] & me.table[me.blockCount*pos]);
+            j--;
+            if ((me.activeFactors[0] & 1) != 0)
+            {
+                if (j>0) me.last=j;
+                else
+                {
+                    _setFinderEnd(finder, position(finder) + me.needleLength);
+                    return true;
+                }
+            }
+            me.activeFactors[0] = me.activeFactors[0] >> 1;
+        }
+        finder+=me.last;
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
 inline bool _findBndmLargeNeedle(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me) {
-	SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
-	TWord carryPattern = ((TWord)1 << (BitsPerValue<TWord>::VALUE - 1));
-	while (position(finder) <= me.haystackLength - me.needleLength) {
-		me.last=me.needleLength;
-		TWord j=me.needleLength;
-		for(TWord block=0;block<me.blockCount;++block) me.activeFactors[block]=~0;
-		bool zeroPrefSufMatch = false;
-		while (!zeroPrefSufMatch) {
-			TWord pos = convert<TWord>(*(finder+j-1));
-
-			/*	
-			// Debug code
-			std::cout << "   ";
-			for(int j=0;j<me.blockCount;++j) {
-				for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-					std::cout << ((me.activeFactors[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-				}
-			}
-			std::cout << ::std::endl;
-			*/
-
-			for(TWord block=0;block<me.blockCount;++block) me.activeFactors[block] &= me.table[me.blockCount*pos+block];
-			j--;
-			if ((me.activeFactors[0] & 1) != 0) 
-			{
-				if (j>0) me.last=j;
-				else 
-				{
-					_setFinderEnd(finder, position(finder) + me.needleLength);
-					return true;
-				}
-			}
-			bool carry=0;
-			zeroPrefSufMatch=true;
-			for(int block=me.blockCount-1;block>=0;--block) {
-				bool newCarry=((me.activeFactors[block] & 1)!=0); 
-				me.activeFactors[block]>>=1;
-				if (carry) me.activeFactors[block]|=carryPattern;
-				carry=newCarry;
-				if (me.activeFactors[block]!=0) zeroPrefSufMatch=false;
-			}
-		}
-		finder+=me.last;
-	}
-	return false;
+    SEQAN_CHECKPOINT
+    typedef unsigned int TWord;
+    typedef typename Value<TNeedle>::Type TNeedleAlphabet;
+
+    TWord carryPattern = ((TWord)1 << (BitsPerValue<TWord>::VALUE - 1));
+    while (position(finder) <= me.haystackLength - me.needleLength) {
+        me.last=me.needleLength;
+        TWord j=me.needleLength;
+        for(TWord block=0;block<me.blockCount;++block) me.activeFactors[block]=~0;
+        bool zeroPrefSufMatch = false;
+        while (!zeroPrefSufMatch) {
+            TWord pos = convert<TWord>(convert<TNeedleAlphabet>(*(finder+j-1)));
+
+            /*
+            // Debug code
+            std::cout << "   ";
+            for(int j=0;j<me.blockCount;++j) {
+                for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                    std::cout << ((me.activeFactors[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+                }
+            }
+            std::cout << std::endl;
+            */
+
+            for(TWord block=0;block<me.blockCount;++block) me.activeFactors[block] &= me.table[me.blockCount*pos+block];
+            j--;
+            if ((me.activeFactors[0] & 1) != 0)
+            {
+                if (j>0) me.last=j;
+                else
+                {
+                    _setFinderEnd(finder, position(finder) + me.needleLength);
+                    return true;
+                }
+            }
+            bool carry=0;
+            zeroPrefSufMatch=true;
+            for(int block=me.blockCount-1;block>=0;--block) {
+                bool newCarry=((me.activeFactors[block] & 1)!=0);
+                me.activeFactors[block]>>=1;
+                if (carry) me.activeFactors[block]|=carryPattern;
+                carry=newCarry;
+                if (me.activeFactors[block]!=0) zeroPrefSufMatch=false;
+            }
+        }
+        finder+=me.last;
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
 inline bool find(TFinder & finder, Pattern<TNeedle, BndmAlgo> & me) {
-	SEQAN_CHECKPOINT
-
-	if (empty(finder)) {
-		_patternInit(me);
-		_setFinderLength(finder, length(needle(me)));
-		_finderSetNonEmpty(finder);
-		me.haystackLength = length(container(finder));
-	} else
-		finder+=me.last;
-
-	// Fast algorithm for needles < machine word?
-	if (me.blockCount == 1) {
-		return _findBndmSmallNeedle(finder, me);
-	} else {
-		return _findBndmLargeNeedle(finder, me);
-	}
+    SEQAN_CHECKPOINT
+
+    if (empty(finder)) {
+        _patternInit(me);
+        _setFinderLength(finder, length(needle(me)));
+        _finderSetNonEmpty(finder);
+        me.haystackLength = length(container(finder));
+    } else
+        finder+=me.last;
+
+    // Fast algorithm for needles < machine word?
+    if (me.blockCount == 1) {
+        return _findBndmSmallNeedle(finder, me);
+    } else {
+        return _findBndmLargeNeedle(finder, me);
+    }
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_bom.h b/seqan/find/find_bom.h
index 4de321f..039d5e0 100644
--- a/seqan/find/find_bom.h
+++ b/seqan/find/find_bom.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,17 +47,15 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pattern
  * @headerfile <seqan/find.h>
  * @brief Backward Factor Automaton Matching algorithm.
- * 
+ *
  * @signature template <typename TNeedle, typename TAutomaton>
  *            class Pattern<TNeedle, Bfam<TAutomaton> >;
- * 
+ *
  * @tparam TAutomaton A tag that specifies the used automaton. Default: <tt>Bfam&lt;Oracle&gt;.
  * @tparam TNeedle    The needle type. Types: String
- * 
- * @section Remarks
- * 
+ *
  * To be used in combination with the default specialization of @link Finder @endlink.
- * 
+ *
  * @see MultiBfamPattern
  */
 
@@ -66,16 +64,14 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends BfamPattern
  * @headerfile <seqan/find.h>
  * @brief Backward Oracle Matching algorithm.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, Bfam<Oracle> >;
- * 
+ *
  * @tparam TNeedle The needle type. Types: String
- * 
- * @section Remarks
- * 
+ *
  * To be used in combination with the default specialization of @link Finder @endlink.
- * 
+ *
  * @see TrieBfamPattern
  * @see OracleMultiBfamPattern
  */
@@ -85,62 +81,19 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends BfamPattern
  * @headerfile <seqan/find.h>
  * @brief Backward Suffix Trie Matching algorithm.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, Bfam<Trie> >;
- * 
+ *
  * @tparam TNeedle The needle type. Types: String
- * 
- * @section Remarks
- * 
+ *
  * To be used in combination with the default specialization of @link Finder @endlink.
- * 
+ *
  * @see OracleBfamPattern
  */
 
-/**
-.Spec.Bfam:
-..summary:Backward Factor Automaton Matching algorithm.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, Bfam<TAutomaton> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..param.TAutomaton:A tag that specifies the used automaton.
-...default:@Spec.Bfam<Oracle>@
-..remarks.text:To be used in combination with the default specialization of @Class.Finder@.
-..include:seqan/find.h
-*/
-
-/**
-.Spec.Bfam<Oracle>:
-..summary:Backward Oracle Matching algorithm.
-..general:Spec.Bfam
-..cat:Searching
-..signature:Pattern<TNeedle, Bfam<Oracle> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks.text:To be used in combination with the default specialization of @Class.Finder@.
-..see:Spec.Bfam<Trie>
-..include:seqan/find.h
-*/
-/**
-.Spec.Bfam<Trie>:
-..summary:Backward Suffix Trie Matching algorithm.
-..general:Spec.Bfam
-..cat:Searching
-..signature:Pattern<TNeedle, Bfam<Trie> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks.text:To be used in combination with the default specialization of @Class.Finder@.
-..see:Spec.Bfam<Oracle>
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.Bfam
-
 struct Oracle; //Oracle Tag => "BOM"
-struct Trie; //Trie Tag => "BTM"
+struct Trie {}; //Trie Tag => "BTM"
 
 template <typename TSpec = Oracle>
 struct Bfam; //backward factor automaton searching
@@ -153,100 +106,79 @@ template <typename TNeedle, typename TSpec>
 class Pattern<TNeedle, Bfam<TSpec> > {
 //____________________________________________________________________________
 public:
-	typedef typename Value<TNeedle>::Type TAlphabet;
-	typedef typename Size<TNeedle>::Type TSize;
-	Holder<TNeedle> data_host;
-	TSize needleLength;
-	TSize haystackLength;
-	TSize step;
-	Graph<Automaton<TAlphabet, void, WithoutEdgeId> > automaton;
+    typedef typename Value<TNeedle>::Type TAlphabet;
+    typedef typename Size<TNeedle>::Type TSize;
+    Holder<TNeedle> data_host;
+    TSize needleLength;
+    TSize haystackLength;
+    TSize step;
+    Graph<Automaton<TAlphabet, void, WithoutEdgeId> > automaton;
 
 //____________________________________________________________________________
 
-	Pattern() {
-	}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
+    Pattern() {
+    }
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        ignoreUnusedVariableWarning(dummy);
+        setHost(*this, std::forward<TNeedle2>(ndl));
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
 SEQAN_CHECKPOINT
-		setHost(*this, ndl);
-	}
-
-	~Pattern() {
-		SEQAN_CHECKPOINT
-	}
+        setHost(*this, ndl);
+    }
+#endif
 //____________________________________________________________________________
 };
 
-//////////////////////////////////////////////////////////////////////////////
-// Host Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, BomAlgo> >
-{
-	typedef TNeedle Type;
-};
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, BomAlgo> const>
-{
-	typedef TNeedle const Type;
-};
-
-
 //////////////////////////////////////////////////////////////////////////////
 // Functions
 //////////////////////////////////////////////////////////////////////////////
 
 //Bfam<Oracle>: BOM Algorithm
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost (Pattern<TNeedle, Bfam<Oracle> > & me, TNeedle2 const& needle) 
+template <typename TNeedle>
+inline void
+_reinitPattern(Pattern<TNeedle, Bfam<Oracle> > & me)
 {
-	SEQAN_CHECKPOINT
-	me.needleLength = length(needle);
-	clear(me.automaton);
-	createOracleOnReverse(me.automaton,needle);
-	setValue(me.data_host, needle);
+    SEQAN_CHECKPOINT
+    me.needleLength = length(needle(me));
+    clear(me.automaton);
+    createOracleOnReverse(me.automaton,needle(me));
 }
 
 //Bfam<Trie>: BTM Algorithm (the same as BOM, but with an trie)
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost (Pattern<TNeedle, Bfam<Trie> > & me, TNeedle2 const& needle) 
+template <typename TNeedle>
+inline void
+_reinitPattern(Pattern<TNeedle, Bfam<Trie> > & me)
 {
-	SEQAN_CHECKPOINT;
-	typedef typename Position<TNeedle>::Type TPosition;
-	me.needleLength = length(needle);
-	clear(me.automaton);
-
-	String<String<TPosition> > terminal_state_map; //dummy
-	typedef typename Value<TNeedle2 const>::Type TValue;
-	String<TValue> reverse_string = needle;
-	reverse(reverse_string);
-
-	createSuffixTrie(me.automaton, terminal_state_map, reverse_string);
+    SEQAN_CHECKPOINT;
+    typedef typename Position<TNeedle>::Type TPosition;
+    me.needleLength = length(needle(me));
+    clear(me.automaton);
 
-	setValue(me.data_host, needle);
-}
+    String<String<TPosition> > terminal_state_map; //dummy
+    typedef typename Value<TNeedle const>::Type TValue;
+    String<TValue> reverse_string = needle(me);
+    reverse(reverse_string);
 
-template <typename TNeedle, typename TNeedle2, typename TSpec>
-inline void 
-setHost (Pattern<TNeedle, Bfam<TSpec> > & me, TNeedle2 & needle)
-{
-	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
+    createSuffixTrie(me.automaton, terminal_state_map, reverse_string);
 }
 
 //____________________________________________________________________________
 
 
 template <typename TNeedle, typename TSpec>
-inline void _patternInit (Pattern<TNeedle, Bfam<TSpec> > & me) 
+inline void _patternInit (Pattern<TNeedle, Bfam<TSpec> > & me)
 {
 SEQAN_CHECKPOINT
-	me.step = 0;
+    me.step = 0;
 }
 
 
@@ -257,37 +189,37 @@ template <typename TFinder, typename TNeedle, typename TSpec>
 inline bool
 find(TFinder & finder, Pattern<TNeedle, Bfam<TSpec> > & me)
 {
-	if (empty(finder)) {
-		_patternInit(me);
-		_setFinderLength(finder, length(needle(me)));
-		_finderSetNonEmpty(finder);
-		me.haystackLength = length(container(finder));
-	} else
-		finder+=me.step;
-
-	if (me.haystackLength < me.needleLength) return false;
-	typedef typename Value<TNeedle>::Type TAlphabet;
-	typedef Graph<Automaton<TAlphabet> > TOracle;
-	typedef typename Size<TNeedle>::Type TSize;
-	typedef typename VertexDescriptor<TOracle>::Type TVertexDescriptor;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	while (position(finder) <= me.haystackLength - me.needleLength) {
-		TVertexDescriptor current = getRoot(me.automaton);
-		TSize j = me.needleLength;
-		while ((j>0) &&	(current != nilVal))
-		{
-			TAlphabet c = *(finder+(j-1));
-			current = targetVertex(me.automaton, findEdge(me.automaton, current, c));
-			--j;
-		}
-		if (current != nilVal) {
-			me.step = j + 1;
-			_setFinderEnd(finder, position(finder) + me.needleLength);
-			return true;
-		}
-		finder += j + 1;
-	}
-	return false;
+    if (empty(finder)) {
+        _patternInit(me);
+        _setFinderLength(finder, length(needle(me)));
+        _finderSetNonEmpty(finder);
+        me.haystackLength = length(container(finder));
+    } else
+        finder+=me.step;
+
+    if (me.haystackLength < me.needleLength) return false;
+    typedef typename Value<TNeedle>::Type TAlphabet;
+    typedef Graph<Automaton<TAlphabet> > TOracle;
+    typedef typename Size<TNeedle>::Type TSize;
+    typedef typename VertexDescriptor<TOracle>::Type TVertexDescriptor;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    while (position(finder) <= me.haystackLength - me.needleLength) {
+        TVertexDescriptor current = getRoot(me.automaton);
+        TSize j = me.needleLength;
+        while ((j>0) &&    (current != nilVal))
+        {
+            TAlphabet c = *(finder+(j-1));
+            current = targetVertex(me.automaton, findEdge(me.automaton, current, c));
+            --j;
+        }
+        if (current != nilVal) {
+            me.step = j + 1;
+            _setFinderEnd(finder, position(finder) + me.needleLength);
+            return true;
+        }
+        finder += j + 1;
+    }
+    return false;
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_hamming_simple.h b/seqan/find/find_hamming_simple.h
index 621c68c..8de5ff0 100644
--- a/seqan/find/find_hamming_simple.h
+++ b/seqan/find/find_hamming_simple.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,32 +47,15 @@ namespace SEQAN_NAMESPACE_MAIN {
  * @extends Pattern
  * @headerfile <seqan/find.h>
  * @brief A brute force online searching algorithm for approximate string matching with hamming distance.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, HammingSimple>;
- * 
+ *
  * @tparam TNeedle The needle type. Types: String
- * 
- * @section Remarks
- * 
+ *
  * This specialization should only be used if no other is applicable or for verification purposes.
  */
 
-/**
-.Spec.HammingSimpleFinder:
-..summary:A brute force online searching algorithm for approximate string matching with hamming distance.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, HammingSimple>
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks:This specialization should only be used if no other is applicable or for verification purposes.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.HammingSimpleFinder
-///.Class.Pattern.class:Spec.HammingSimpleFinder
-
 struct HammingSimple_;
 typedef Tag<HammingSimple_> HammingSimple;
 
@@ -95,11 +78,26 @@ class Pattern<TNeedle, HammingSimple> {
 
     Pattern() : maxDistance(-1), distance(0), matchNFlags(0) {}
 
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            int k = -1,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+                :   maxDistance(-k),
+                    distance(0),
+                    matchNFlags(0)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+#else
     template <typename TNeedle2>
-    Pattern(const TNeedle2 &ndl, int k = -1) : maxDistance(-1), distance(0), matchNFlags(0) {
+    Pattern(const TNeedle2 &ndl, int k = -1) : maxDistance(-k), distance(0), matchNFlags(0) {
         SEQAN_CHECKPOINT;
-        setHost(*this, ndl, k);
+        setHost(*this, ndl);
     }
+#endif  // SEQAN_CXX11_STANDARD
 };
 
 
@@ -124,28 +122,6 @@ inline void _patternMatchNOfFinder(Pattern<TNeedle, HammingSimple> & pattern, bo
     pattern.matchNFlags |= 4;
 }
 
-
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, HammingSimple> & me, 
-              const TNeedle2 & needle, int k) {
-    SEQAN_CHECKPOINT;
-
-    SEQAN_ASSERT_NOT(empty(needle));
-    SEQAN_ASSERT_LEQ_MSG(k, 0, "Are you confusing distances and scores?");
-
-    setValue(me.data_host, needle);
-    me.maxDistance = -k;
-}
-
-
-template <typename TNeedle, typename TNeedle2>
-void
-setHost(Pattern<TNeedle, HammingSimple> &horsp, TNeedle2 &ndl, int k) {
-    SEQAN_CHECKPOINT;
-    setHost(horsp, reinterpret_cast<const TNeedle2&>(ndl), k);
-}
-
-
 template <typename TNeedle>
 inline void _finderInit(Pattern<TNeedle, HammingSimple> & me) {
     SEQAN_CHECKPOINT;
@@ -212,7 +188,7 @@ inline bool _findHammingSimpleCharsEqual(Dna5Q const & a, Dna5Q const & b, Patte
 
 
 template <typename TFinder, typename TNeedle>
-inline bool find(TFinder &finder, 
+inline bool find(TFinder &finder,
                  Pattern<TNeedle, HammingSimple> &me,
                  int minScore) {
     SEQAN_CHECKPOINT;
@@ -282,11 +258,11 @@ inline bool find(TFinder &finder,
 
     _setFinderEnd(finder, i + length(ndl));
     setPosition(finder, beginPosition(finder));
-    return true; 
+    return true;
 }
 
 template <typename TFinder, typename TNeedle>
-inline bool find(TFinder &finder, 
+inline bool find(TFinder &finder,
                  Pattern<TNeedle, HammingSimple> &me)
 {
     return find(finder, me, -me.maxDistance);
diff --git a/seqan/find/find_horspool.h b/seqan/find/find_horspool.h
index 24e3de4..4e87897 100644
--- a/seqan/find/find_horspool.h
+++ b/seqan/find/find_horspool.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,28 +46,15 @@ namespace SEQAN_NAMESPACE_MAIN
  * @class HorspoolPattern
  * @extends Pattern
  * @headerfile <seqan/find.h>
- * 
+ *
  * @brief Exact string matching using Horspool's algorithm (1980).
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, Horspool>;
- * 
+ *
  * @tparam TNeedle The needle type. Types: String
  */
 
-/**
-.Spec.Horspool:
-..summary: Exact string matching using Horspool's algorithm (1980).
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, Horspool>
-..param.TNeedle:The needle type.
-...type:Class.String
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.Horspool
-
 struct Horspool_;
 typedef Tag<Horspool_> Horspool;
 
@@ -79,61 +66,61 @@ class Pattern<TNeedle, Horspool>
 //____________________________________________________________________________
 
 public:
-	typedef typename Size<TNeedle>::Type TSize;
+    typedef typename Size<TNeedle>::Type TSize;
 
-	Holder<TNeedle>		data_host;
-	String<TSize>		data_map;
+    Holder<TNeedle>      data_host;
+    String<TSize>        data_map;
 
 //____________________________________________________________________________
 
 public:
-	Pattern() {}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		setHost(*this, ndl);
-	}
+    Pattern() {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl, SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
 
-template <typename TNeedle, typename TNeedle2>
-void
-setHost(Pattern<TNeedle, Horspool> & me, TNeedle2 const & ndl)
-{
-	typedef typename Value<TNeedle>::Type TValue;
-	typedef typename Size<TNeedle>::Type TSize;
-
-	SEQAN_ASSERT_NOT(empty(ndl));
-
-	TSize value_size = ValueSize<TValue>::VALUE;
-
-	//make room for map
-	resize(me.data_map, value_size);
-
-	//fill map
-	typename Value<String<TSize> >::Type jump_width = length(ndl); //das ist so umstaendlich wegen VC++ 2003
-	arrayFill(begin(me.data_map, Standard()), begin(me.data_map, Standard()) + value_size, jump_width);
-
-	typename Iterator<TNeedle2 const, Standard>::Type it;
-	it = begin(ndl, Standard());
-	while (jump_width > 1)
-	{
-		--jump_width;
-		unsigned int pos_ = *it; //conversion value type to unsigned int
-		me.data_map[pos_] = jump_width;
-		++it;
-	}
-
-	me.data_host = ndl;
-}
-
-template <typename TNeedle, typename TNeedle2>
+template <typename TNeedle>
 void
-setHost(Pattern<TNeedle, Horspool> & horsp, TNeedle2 & ndl)
+_reinitPattern(Pattern<TNeedle, Horspool> & me)
 {
-	setHost(horsp, reinterpret_cast<TNeedle2 const &>(ndl));
+    typedef typename Value<TNeedle>::Type TValue;
+    typedef typename Size<TNeedle>::Type TSize;
+
+    TNeedle& ndl = needle(me);
+    SEQAN_ASSERT_NOT(empty(ndl));
+
+    TSize value_size = ValueSize<TValue>::VALUE;
+    //make room for map
+    resize(me.data_map, value_size);
+
+    //fill map
+    typename Value<String<TSize> >::Type jump_width = length(ndl); //das ist so umstaendlich wegen VC++ 2003
+    arrayFill(begin(me.data_map, Standard()), begin(me.data_map, Standard()) + value_size, jump_width);
+
+    typename Iterator<TNeedle, Standard>::Type it;
+    it = begin(ndl, Standard());
+    while (jump_width > 1)
+    {
+        --jump_width;
+        unsigned int pos_ = *it; //conversion value type to unsigned int
+        me.data_map[pos_] = jump_width;
+        ++it;
+    }
 }
 
 //____________________________________________________________________________
@@ -147,67 +134,68 @@ inline void _patternInit (Pattern<TNeedle, Horspool> &) {}
 
 template <typename TFinder, typename TNeedle2>
 bool
-_findHorspool(TFinder & finder, 
-			  Pattern<TNeedle2, Horspool> & me,
-			  bool find_first)
+_findHorspool(TFinder & finder,
+              Pattern<TNeedle2, Horspool> & me,
+              bool find_first)
 {
 SEQAN_CHECKPOINT
-	typedef typename Haystack<TFinder>::Type THaystack;
+    typedef typename Haystack<TFinder>::Type THaystack;
     typedef typename Parameter_<THaystack>::Type TParamHaystack;
 
     TParamHaystack hayst = haystack(finder);
 
-	typedef Pattern<TNeedle2, Horspool> TPattern;
-	typedef typename Needle<TPattern>::Type TNeedle;
-	TNeedle & ndl = needle(me);
+    typedef Pattern<TNeedle2, Horspool> TPattern;
+    typedef typename Needle<TPattern>::Type TNeedle;
+    typedef typename Value<TNeedle>::Type   TNeedleAlphabet;
+    TNeedle & ndl = needle(me);
 
-	typedef typename Size<TNeedle>::Type TNeedleSize;
-	TNeedleSize ndl_size = length(ndl);
+    typedef typename Size<TNeedle>::Type TNeedleSize;
+    TNeedleSize ndl_size = length(ndl);
 
-	typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
-	THaystackIterator haystack_end = end(hayst, Standard());
-	THaystackIterator it = begin(hayst, Standard());
-	it += position(finder) + ndl_size - 1; //it points to the last character
-	THaystackIterator it_next = it;
+    typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+    THaystackIterator haystack_end = end(hayst, Standard());
+    THaystackIterator it = begin(hayst, Standard());
+    it += position(finder) + ndl_size - 1; //it points to the last character
+    THaystackIterator it_next = it;
 
-	typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
-	TNeedleIterator nit; //needle iterator
-	TNeedleIterator nit_begin = begin(ndl, Standard());
-	TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
+    typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+    TNeedleIterator nit; //needle iterator
+    TNeedleIterator nit_begin = begin(ndl, Standard());
+    TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
 
-	unsigned int char_i;
+    unsigned int char_i;
 
-	if (find_first)
-	{
-		goto VALIDATE;
-	}
+    if (find_first)
+    {
+        goto VALIDATE;
+    }
 
 MOVE_FURTHER:
-	//move to next position
-	char_i = *it; //conversion to unsigned integer
-	it_next = it + me.data_map[char_i];
-	if (it_next >= haystack_end)
-	{//found nothing
-		return false;
-	}
+    //move to next position
+    char_i = convert<TNeedleAlphabet>(*it); //conversion to unsigned integer -> into needle space.
+    it_next = it + me.data_map[char_i];
+    if (it_next >= haystack_end)
+    {//found nothing
+        return false;
+    }
 
-	it = it_next;
+    it = it_next;
 
 VALIDATE:
-	//validate current position
-	for (nit = nit_end; nit >= nit_begin; --nit)
-	{
-		if (*nit != *it_next)
-		{//invalid!
-			goto MOVE_FURTHER;
-		}
-		--it_next;
-	}
-
-	//valid! return hit
-	_setFinderEnd(finder, it - begin(hayst, Standard()) + 1);
-	setPosition(finder, beginPosition(finder));
-	return true;
+    //validate current position
+    for (nit = nit_end; nit >= nit_begin; --nit)
+    {
+        if (*nit != *it_next)
+        {//invalid!
+            goto MOVE_FURTHER;
+        }
+        --it_next;
+    }
+
+    //valid! return hit
+    _setFinderEnd(finder, it - begin(hayst, Standard()) + 1);
+    setPosition(finder, beginPosition(finder));
+    return true;
 }
 
 //____________________________________________________________________________
@@ -216,93 +204,93 @@ SEQAN_CHECKPOINT
 /*
 template <typename TFinder, typename TNeedle2>
 bool
-find_horspool_sentinel(TFinder & finder, 
-					   Pattern<TNeedle2, Horspool> & me,
-					   bool find_first)
+find_horspool_sentinel(TFinder & finder,
+                       Pattern<TNeedle2, Horspool> & me,
+                       bool find_first)
 {
 SEQAN_CHECKPOINT
-	typedef typename Haystack<TFinder>::Type THaystack;
-	THaystack & hayst = haystack(finder);
-	
-
-	typedef Pattern<TNeedle2, Horspool> TPattern;
-	typedef typename Needle<TPattern>::Type TNeedle;
-	TNeedle & ndl = needle(me);
-
-	//implant sentinel
-	typename Size<THaystack>::Type old_haystack_size = length(hayst);
-	if (find_first)
-	{
-		typedef typename Position<TFinder>::Type TFinderPosition;
-		TFinderPosition finder_pos = position(finder);
-
-		append(hayst, ndl, Exact());
-		if (length(hayst) != old_haystack_size + length(ndl))
-		{//not enough place in haystack
+    typedef typename Haystack<TFinder>::Type THaystack;
+    THaystack & hayst = haystack(finder);
+
+
+    typedef Pattern<TNeedle2, Horspool> TPattern;
+    typedef typename Needle<TPattern>::Type TNeedle;
+    TNeedle & ndl = needle(me);
+
+    //implant sentinel
+    typename Size<THaystack>::Type old_haystack_size = length(hayst);
+    if (find_first)
+    {
+        typedef typename Position<TFinder>::Type TFinderPosition;
+        TFinderPosition finder_pos = position(finder);
+
+        append(hayst, ndl, Exact());
+        if (length(hayst) != old_haystack_size + length(ndl))
+        {//not enough place in haystack
 //TODO!!!
 printf("error!");
 return false;
-		}
-		setPosition(finder, finder_pos);
-	}
-	else
-	{
-		_setLength(hayst, old_haystack_size + length(ndl));
-	}
-
-	typedef typename Size<TNeedle>::Type TNeedleSize;
-	TNeedleSize ndl_size = length(ndl);
-
-	typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
-	THaystackIterator it = begin(hayst, Standard());
-	THaystackIterator haystack_end = it + old_haystack_size;
-	it += position(finder) + ndl_size - 1; //it points to the last character
-
-	typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
-	TNeedleIterator nit; //needle iterator
-	TNeedleIterator nit_begin = begin(ndl, Standard());
-	TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
-
-	typedef typename Value<TNeedle>::Type TNeedleValue;
-	TNeedleValue char_needle_last = *nit_end;
-	TNeedleValue char_haystack_last;
-
-	char_haystack_last = *it;
-
-	if (find_first)
-	{
-		goto VALIDATE;
-	}
-
-	//main loop
+        }
+        setPosition(finder, finder_pos);
+    }
+    else
+    {
+        _setLength(hayst, old_haystack_size + length(ndl));
+    }
+
+    typedef typename Size<TNeedle>::Type TNeedleSize;
+    TNeedleSize ndl_size = length(ndl);
+
+    typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+    THaystackIterator it = begin(hayst, Standard());
+    THaystackIterator haystack_end = it + old_haystack_size;
+    it += position(finder) + ndl_size - 1; //it points to the last character
+
+    typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+    TNeedleIterator nit; //needle iterator
+    TNeedleIterator nit_begin = begin(ndl, Standard());
+    TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
+
+    typedef typename Value<TNeedle>::Type TNeedleValue;
+    TNeedleValue char_needle_last = *nit_end;
+    TNeedleValue char_haystack_last;
+
+    char_haystack_last = *it;
+
+    if (find_first)
+    {
+        goto VALIDATE;
+    }
+
+    //main loop
 MOVE_FURTHER:
-	it += me.data_map[_ord(char_haystack_last)];
-	char_haystack_last = *it;
-	if (char_haystack_last != char_needle_last) goto MOVE_FURTHER;
+    it += me.data_map[_ord(char_haystack_last)];
+    char_haystack_last = *it;
+    if (char_haystack_last != char_needle_last) goto MOVE_FURTHER;
 
 
-	if (it >= haystack_end)
-	{//found nothing
-		resize(hayst, old_haystack_size);
-		return false;
-	}
+    if (it >= haystack_end)
+    {//found nothing
+        resize(hayst, old_haystack_size);
+        return false;
+    }
 
 VALIDATE:
-	//validate current position
-	THaystackIterator it_back = it;
-	for (nit = nit_end; nit >= nit_begin; --nit)
-	{
-		if (*nit != *it_back)
-		{//invalid!
-			goto MOVE_FURTHER;
-		}
-		--it_back;
-	}
-
-	//valid! return hit
-	setPosition(finder, it - begin(hayst, Standard()) - ndl_size + 1);
-	resize(hayst, old_haystack_size);
-	return true;
+    //validate current position
+    THaystackIterator it_back = it;
+    for (nit = nit_end; nit >= nit_begin; --nit)
+    {
+        if (*nit != *it_back)
+        {//invalid!
+            goto MOVE_FURTHER;
+        }
+        --it_back;
+    }
+
+    //valid! return hit
+    setPosition(finder, it - begin(hayst, Standard()) - ndl_size + 1);
+    resize(hayst, old_haystack_size);
+    return true;
 }
 */
 //____________________________________________________________________________
@@ -314,139 +302,141 @@ struct FileReader;
 
 template <typename TValue, typename TFormat, typename TFile, typename FileReaderTSpec, typename TFinderSpec, typename TNeedle2>
 bool
-_findHorspool(Finder<String<TValue, FileReader<TFormat, TFile, FileReaderTSpec> >, TFinderSpec > & finder, 
-			  Pattern<TNeedle2, Horspool> & me,
-			  bool find_first)
+_findHorspool(Finder<String<TValue, FileReader<TFormat, TFile, FileReaderTSpec> >, TFinderSpec > & finder,
+              Pattern<TNeedle2, Horspool> & me,
+              bool find_first)
 {
 SEQAN_CHECKPOINT
-	typedef Finder<String<TValue, FileReader<TFormat, TFile, FileReaderTSpec> >, TFinderSpec > TFinder;
-	typedef typename Haystack<TFinder>::Type THaystack;
-	THaystack & hayst = haystack(finder);
+    typedef Finder<String<TValue, FileReader<TFormat, TFile, FileReaderTSpec> >, TFinderSpec > TFinder;
+    typedef typename Haystack<TFinder>::Type THaystack;
+    THaystack & hayst = haystack(finder);
+
+    typedef Pattern<TNeedle2, Horspool> TPattern;
+    typedef typename Needle<TPattern>::Type TNeedle;
+    typedef typename Value<TNeedle>::Type   TNeedleAlphabet;
 
-	typedef Pattern<TNeedle2, Horspool> TPattern;
-	typedef typename Needle<TPattern>::Type TNeedle;
-	TNeedle & ndl = needle(me);
+    TNeedle & ndl = needle(me);
 
-	typedef typename Size<TNeedle>::Type TNeedleSize;
-	TNeedleSize ndl_size = length(ndl);
+    typedef typename Size<TNeedle>::Type TNeedleSize;
+    TNeedleSize ndl_size = length(ndl);
 
-	typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
-	THaystackIterator it(hayst, position(finder) + ndl_size - 1); //it points to the last character
+    typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+    THaystackIterator it(hayst, position(finder) + ndl_size - 1); //it points to the last character
 
-	typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
-	TNeedleIterator nit; //needle iterator
-	TNeedleIterator nit_begin = begin(ndl, Standard());
-	TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
+    typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+    TNeedleIterator nit; //needle iterator
+    TNeedleIterator nit_begin = begin(ndl, Standard());
+    TNeedleIterator nit_end = end(ndl, Standard()) - 1; //here the verification begins
 
-	unsigned int char_i;
+    unsigned int char_i;
 
-	if (find_first)
-	{
-		goto VALIDATE;
-	}
+    if (find_first)
+    {
+        goto VALIDATE;
+    }
 
 MOVE_FURTHER:
-	//move to next position
-	char_i = *it; //conversion to unsigned integer
-	it += me.data_map[char_i];
-	if (atEnd(it))
-	{//found nothing
-		return false;
-	}
+    //move to next position
+    char_i = convert<TNeedleAlphabet>(*it); //conversion to unsigned integer
+    it += me.data_map[char_i];
+    if (atEnd(it))
+    {//found nothing
+        return false;
+    }
 
 VALIDATE:
-	//validate current position
-	for (nit = nit_end; nit >= nit_begin; --nit)
-	{
-		if (*nit != *it)
-		{//invalid!
-			it += (nit_end - nit);
-			goto MOVE_FURTHER;
-		}
-		--it;
-	}
-
-	//valid! return hit
-	setPosition(finder, it - begin(hayst, Standard()) + 1);
-	return true;
+    //validate current position
+    for (nit = nit_end; nit >= nit_begin; --nit)
+    {
+        if (*nit != *it)
+        {//invalid!
+            it += (nit_end - nit);
+            goto MOVE_FURTHER;
+        }
+        --it;
+    }
+
+    //valid! return hit
+    setPosition(finder, it - begin(hayst, Standard()) + 1);
+    return true;
 
 }
 
 //____________________________________________________________________________
-/* groepl variante 
+/* groepl variante
 (Beruht vermutlich auf einem Missverstehen von Navarro/Raffinot Seite 26:
-Mit "the main loop can be 'unrolled'" ist dort naemlich 
+Mit "the main loop can be 'unrolled'" ist dort naemlich
 "the INNER loop can be 'unrolled'" gemeint.)
 
 template <typename TFinder, typename TNeedle2>
 bool
-_findHorspool(TFinder & finder, 
-	Pattern<TNeedle2, Horspool> & me,
-	bool find_first)
+_findHorspool(TFinder & finder,
+    Pattern<TNeedle2, Horspool> & me,
+    bool find_first)
 {
 SEQAN_CHECKPOINT
-	typedef typename Haystack<TFinder>::Type THaystack;
-	THaystack & hayst = haystack(finder);
+    typedef typename Haystack<TFinder>::Type THaystack;
+    THaystack & hayst = haystack(finder);
 
-	typedef Pattern<TNeedle2, Horspool> TPattern;
-	typedef typename Needle<TPattern>::Type TNeedle;
-	TNeedle & ndl = needle(me);
+    typedef Pattern<TNeedle2, Horspool> TPattern;
+    typedef typename Needle<TPattern>::Type TNeedle;
+    TNeedle & ndl = needle(me);
 
-	typename Size<TNeedle>::Type ndl_size = length(ndl);
+    typename Size<TNeedle>::Type ndl_size = length(ndl);
 
-	typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
-	THaystackIterator haystack_end = end(hayst, Standard());
-	THaystackIterator it = begin(hayst, Standard());
-	it += position(finder) + ndl_size - 1; //it points to the last character
-	THaystackIterator it2;
+    typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+    THaystackIterator haystack_end = end(hayst, Standard());
+    THaystackIterator it = begin(hayst, Standard());
+    it += position(finder) + ndl_size - 1; //it points to the last character
+    THaystackIterator it2;
 
-	typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
-	TNeedleIterator nit; //needle iterator
-	TNeedleIterator nit_begin = begin(ndl, Standard());
-	TNeedleIterator nit_end = end(ndl, Standard()) - 2; //here the verification begins
+    typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+    TNeedleIterator nit; //needle iterator
+    TNeedleIterator nit_begin = begin(ndl, Standard());
+    TNeedleIterator nit_end = end(ndl, Standard()) - 2; //here the verification begins
 
-	typedef typename Value<TNeedle>::Type TNeedleValue;
-	TNeedleValue last_needle_char = value(ndl, ndl_size - 1);
+    typedef typename Value<TNeedle>::Type TNeedleValue;
+    TNeedleValue last_needle_char = value(ndl, ndl_size - 1);
 
-	unsigned int char_i;
+    unsigned int char_i;
 
-	if (!find_first)
-	{
-		++it;
-	}
+    if (!find_first)
+    {
+        ++it;
+    }
 
 MOVE_FURTHER:
-	//scan for the last character
-	while (true)
-	{
-		if (it >= haystack_end)
-		{//found nothing
-			return false;
-		}
-		if (*it == last_needle_char) 
-		{
-			break;
-		}
-		++it;
-	}
+    //scan for the last character
+    while (true)
+    {
+        if (it >= haystack_end)
+        {//found nothing
+            return false;
+        }
+        if (*it == last_needle_char)
+        {
+            break;
+        }
+        ++it;
+    }
 
 VALIDATE:
-	it2 = it;
-	//validate current position
-	for (nit = nit_end; nit >= nit_begin; --nit)
-	{
-		--it2;
-		if (*nit != *it2)
-		{//invalid! skip!
-			char_i = *it; //conversion to unsigned integer
-			it += me.data_map[char_i];
-			goto MOVE_FURTHER;
-		}
-	}
-
-	//valid! return hit
-	setPosition(finder, it - begin(hayst, Standard()) - ndl_size + 1);
-	return true;
+    it2 = it;
+    //validate current position
+    for (nit = nit_end; nit >= nit_begin; --nit)
+    {
+        --it2;
+        if (*nit != *it2)
+        {//invalid! skip!
+            char_i = *it; //conversion to unsigned integer
+            it += me.data_map[char_i];
+            goto MOVE_FURTHER;
+        }
+    }
+
+    //valid! return hit
+    setPosition(finder, it - begin(hayst, Standard()) - ndl_size + 1);
+    return true;
 }
 */
 
@@ -455,35 +445,19 @@ bool
 find(TFinder & finder, Pattern<TNeedle2, Horspool> & me)
 {
 SEQAN_CHECKPOINT
-	bool find_first = empty(finder);
-	if (find_first)
-	{
-		_patternInit(me);
-		_setFinderLength(finder, length(needle(me)));
-		_finderSetNonEmpty(finder);
-	}
+    bool find_first = empty(finder);
+    if (find_first)
+    {
+        _patternInit(me);
+        _setFinderLength(finder, length(needle(me)));
+        _finderSetNonEmpty(finder);
+    }
 
-	SEQAN_ASSERT_GT(length(needle(me)), 0u);
+    SEQAN_ASSERT_GT(length(needle(me)), 0u);
 
-	return _findHorspool(finder, me, find_first);
+    return _findHorspool(finder, me, find_first);
 }
 
-//////////////////////////////////////////////////////////////////////////////
-// Host
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, Horspool> >
-{
-	typedef TNeedle Type;
-};
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, Horspool> const>
-{
-	typedef TNeedle const Type;
-};
-
 
 //////////////////////////////////////////////////////////////////////////////
 
diff --git a/seqan/find/find_lambda.h b/seqan/find/find_lambda.h
new file mode 100644
index 0000000..42a1531
--- /dev/null
+++ b/seqan/find/find_lambda.h
@@ -0,0 +1,239 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_FIND_LAMBDA_H
+#define SEQAN_FIND_LAMBDA_H
+
+namespace seqan {
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultFind<>
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern>
+struct DefaultFind
+{
+    typedef void Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FindState_<>
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TAlgorithm>
+struct FindState_
+{
+    typedef Nothing Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction HasStatesPool_<>
+// ----------------------------------------------------------------------------
+
+template <typename TState, typename TThreading>
+struct HasStatesPool_
+{
+    typedef typename IsSameType<TThreading, Parallel>::Type         IsParallel;
+    typedef typename Not<IsSameType<TState, Nothing> >::Type        IsStateful;
+    typedef typename And<IsParallel, IsStateful>::Type              Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction StatesPool_<>
+// ----------------------------------------------------------------------------
+
+template <typename TState, typename TThreading>
+struct StatesPool_
+{
+    typedef typename HasStatesPool_<TState, TThreading>::Type           HasStatesPool;
+    typedef typename If<HasStatesPool, String<TState>, TState>::Type    Type;
+};
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class FindDelegator_
+// ----------------------------------------------------------------------------
+
+template <typename TDelegate, typename TNeedlesIt>
+struct FindDelegator_
+{
+    TDelegate & delegate;
+    TNeedlesIt & needlesIt;
+
+    FindDelegator_(TDelegate & delegate, TNeedlesIt & needlesIt) :
+        delegate(delegate),
+        needlesIt(needlesIt)
+    {}
+
+    template <typename TTextIt, typename TScore>
+    void operator()(TTextIt & textIt, TScore score)
+    {
+        delegate(textIt, needlesIt, score);
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function find(text, pattern, errors, [](...){}, Algorithm());
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TThreshold, typename TDelegate, typename TAlgorithm>
+inline void find(TText & text, TPattern const & pattern, TThreshold threshold, TDelegate && delegate, TAlgorithm)
+{
+    typedef typename FindState_<TText, TPattern const, TAlgorithm>::Type    TState;
+
+    TState state;
+    _findStateInit(state, text, pattern, threshold, TAlgorithm());
+    _findImpl(state, text, pattern, threshold, delegate, TAlgorithm());
+}
+
+// ----------------------------------------------------------------------------
+// Function find(text, pattern, [](...){});
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TDelegate>
+inline void find(TText & text, TPattern const & pattern, TDelegate && delegate)
+{
+    typedef typename DefaultFind<TText, TPattern const>::Type   TAlgorithm;
+
+    find(text, pattern, unsigned(), delegate, TAlgorithm());
+}
+
+// ----------------------------------------------------------------------------
+// Function _findStateInit()
+// ----------------------------------------------------------------------------
+// Stateless algorithm.
+
+template <typename TState, typename TText, typename TPattern, typename TThreshold, typename TAlgorithm>
+inline void
+_findStateInit(TState & /* s */, TText const & /* t */, TPattern const & /* p */, TThreshold /* t */, TAlgorithm) {}
+
+// ----------------------------------------------------------------------------
+// Function _findStatesPoolInit()
+// ----------------------------------------------------------------------------
+
+template <typename TState>
+inline void _findStatesPoolInit(TState & /* pool */, False) {}
+
+template <typename TStates>
+inline void _findStatesPoolInit(TStates & pool, True)
+{
+    resize(pool, omp_get_num_threads(), Exact());
+}
+
+// ----------------------------------------------------------------------------
+// Function _findPickState()
+// ----------------------------------------------------------------------------
+
+template <typename TState>
+inline TState &
+_findPickState(TState & state, False)
+{
+    return state;
+}
+
+template <typename TStates>
+inline typename Value<TStates>::Type &
+_findPickState(TStates & pool, True)
+{
+    return pool[omp_get_thread_num()];
+}
+
+// ----------------------------------------------------------------------------
+// Function find(text, needles, errors, [](...){}, Algorithm(), Parallel());
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TNeedle_, typename TSSetSpec,
+          typename TThreshold, typename TDelegate, typename TAlgorithm, typename TThreading>
+inline void find(TText & text,
+                 StringSet<TNeedle_, TSSetSpec> const & needles,
+                 TThreshold threshold,
+                 TDelegate && delegate,
+                 TAlgorithm,
+                 TThreading)
+{
+    typedef StringSet<TNeedle_, TSSetSpec> const                    TNeedles;
+    typedef typename Value<TNeedles>::Type                          TNeedle;
+    typedef typename Iterator<TNeedles, Rooted>::Type               TNeedlesIt;
+    typedef typename Reference<TNeedlesIt>::Type                    TNeedleRef;
+
+    typedef typename FindState_<TText, TNeedle, TAlgorithm>::Type   TState;
+    typedef typename StatesPool_<TState, TThreading>::Type          TStatesPool;
+    typedef typename HasStatesPool_<TState, TThreading>::Type       HasStatesPool;
+
+    typedef FindDelegator_<TDelegate, TNeedlesIt const>             TDelegator;
+
+    TStatesPool pool;
+    _findStatesPoolInit(pool, HasStatesPool());
+
+    iterate(needles, [&](TNeedlesIt const & needlesIt)
+    {
+        TState & state = _findPickState(pool, HasStatesPool());
+        TNeedleRef needle = value(needlesIt);
+        TDelegator delegator(delegate, needlesIt);
+
+        _findStateInit(state, text, needle, threshold, TAlgorithm());
+        _findImpl(state, text, needle, threshold, delegator, TAlgorithm());
+    },
+    Rooted(), TThreading());
+}
+
+// ----------------------------------------------------------------------------
+// Function find(text, needles, errors, [](...){}, Algorithm());
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TNeedle, typename TSSetSpec,
+          typename TThreshold, typename TDelegate, typename TAlgorithm>
+inline void find(TText & text,
+                 StringSet<TNeedle, TSSetSpec> const & needles,
+                 TThreshold threshold,
+                 TDelegate && delegate,
+                 TAlgorithm)
+{
+    find(text, needles, threshold, delegate, TAlgorithm(), Serial());
+}
+
+}
+
+#endif  // #ifndef SEQAN_FIND_LAMBDA_H
diff --git a/seqan/find/find_multi.h b/seqan/find/find_multi.h
index abb731f..4ff1ee2 100644
--- a/seqan/find/find_multi.h
+++ b/seqan/find/find_multi.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,7 +42,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
 struct MultiPatternFinder_;
 typedef Tag<MultiPatternFinder_> MultipatternFinder;
-	
+
 //____________________________________________________________________________
 
 template <typename THaystack>
@@ -50,34 +50,34 @@ class Finder<THaystack, MultipatternFinder>
 {
 //____________________________________________________________________________
 private:
-	unsigned int data_pattern;
+    unsigned int data_pattern;
 
 public:
-	Finder():
-		data_pattern(0)
-	{
+    Finder():
+        data_pattern(0)
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	Finder(Finder const & other_):
-		data_pattern(other_.data_pattern)
-	{
+    Finder(Finder const & other_):
+        data_pattern(other_.data_pattern)
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	~Finder()
-	{
+    ~Finder()
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 //____________________________________________________________________________
 
-	Finder & 
-	operator = (Finder const & other_)
-	{
+    Finder &
+    operator = (Finder const & other_)
+    {
 SEQAN_CHECKPOINT
-		data_pattern = other_.data_pattern;
-		return *this;
-	}
+        data_pattern = other_.data_pattern;
+        return *this;
+    }
 //____________________________________________________________________________
 
 
@@ -87,12 +87,12 @@ SEQAN_CHECKPOINT
 template <typename THaystack, typename TNeedle>
 bool
 findNext(Finder & me,
-		 THaystack & hstk,
-		 TNeedle const & ndl)
+         THaystack & hstk,
+         TNeedle const & ndl)
 {
 SEQAN_CHECKPOINT
-	++hstk;
-	return find(me, hstk, ndl);
+    ++hstk;
+    return find(me, hstk, ndl);
 }*/
 
 //////////////////////////////////////////////////////////////////////////////
@@ -104,14 +104,14 @@ inline unsigned int &
 needle(Finder<THaystack, MultipatternFinder> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_pattern;
+    return me.data_pattern;
 }
 template <typename THaystack>
 inline unsigned int const &
 needle(Finder<THaystack, MultipatternFinder> const & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_pattern;
+    return me.data_pattern;
 }
 //____________________________________________________________________________
 
@@ -120,7 +120,7 @@ inline void
 setNeedle(Finder<THaystack, MultipatternFinder> & me, unsigned int const needleIndex_)
 {
 SEQAN_CHECKPOINT
-	me.data_pattern = needleIndex_;
+    me.data_pattern = needleIndex_;
 }
 
 //____________________________________________________________________________
@@ -130,7 +130,7 @@ inline void
 init(Finder<THaystack, MultipatternFinder> & me)
 {
 SEQAN_CHECKPOINT
-	me.data_pattern = 0;
+    me.data_pattern = 0;
 }
 //____________________________________________________________________________
 
@@ -138,22 +138,22 @@ SEQAN_CHECKPOINT
 template <typename THaystack, typename THaystack2, typename TNeedle>
 inline bool
 find(Finder<THaystack, MultipatternFinder> & me,
-	 THaystack2 & hstk,
-	 TNeedle const & ndl)
+     THaystack2 & hstk,
+     TNeedle const & ndl)
 {
 SEQAN_CHECKPOINT
-	while ( needle(me) < length(ndl) )
-	{
-		Finder<THaystack2, Horspool> horspool(ndl[needle(me)]);
-		bool found = find(horspool, hstk, ndl[needle(me)]);
-		if (found)
-		{
-			return true;
-		}
-		setPosition(hstk, 0);
-		++needle(me);
-	}
-	return false;
+    while ( needle(me) < length(ndl) )
+    {
+        Finder<THaystack2, Horspool> horspool(ndl[needle(me)]);
+        bool found = find(horspool, hstk, ndl[needle(me)]);
+        if (found)
+        {
+            return true;
+        }
+        setPosition(hstk, 0);
+        ++needle(me);
+    }
+    return false;
 }
 }// namespace SEQAN_NAMESPACE_MAIN
 
diff --git a/seqan/find/find_multiple_bfam.h b/seqan/find/find_multiple_bfam.h
index 656c252..0a2daeb 100644
--- a/seqan/find/find_multiple_bfam.h
+++ b/seqan/find/find_multiple_bfam.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,13 +47,13 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pattern
  * @headerfile <seqan/find.h>
  * @brief Multi-Pattern Backward Factor Automaton Matching.
- * 
+ *
  * @signature template <typename TNeedle, typename TAutomaton>
  *            class Pattern<TNeedle, MultiBfam<TAutomaton> >;
- * 
- * @tparam TAutomaton A tag that specifies the used automaton. Default: @link OracleMultiBfam @endlink.
+ *
+ * @tparam TAutomaton A tag that specifies the used automaton. Default: @link OracleMultiBfamPattern @endlink.
  * @tparam TNeedle    The needle type. Types: String
- * 
+ *
  * @see BfamPattern
  */
 
@@ -62,42 +62,15 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends MultiBfamPattern
  * @headerfile <seqan/find.h>
  * @brief Multi-Pattern Backward Factor Automaton Matching using an oracle automaton.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, MultiBfam<Oracle> >;
- * 
+ *
  * @tparam TNeedle The needle type. Types: String
- * 
+ *
  * @see OracleBfamPattern
  */
 
-/**
-.Spec.MultiBfam:
-..general:Class.Pattern
-..cat:Searching
-..summary:Multi-Pattern Backward Factor Automaton Matching.
-..signature:Pattern<TNeedle, MultiBfam<TAutomaton> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..param.TAutomaton:A tag that specifies the used automaton.
-...default:@Spec.MultiBfam<Oracle>@
-..see:Spec.Bfam
-..include:seqan/find.h
-*/
-/**
-.Spec.MultiBfam<Oracle>:
-..general:Spec.MultiBfam
-..cat:Searching
-..summary:Multi-Pattern Backward Factor Automaton Matching using an oracle automaton.
-..signature:Pattern<TNeedle, MultiBfam<Oracle> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..see:Spec.Bfam<Oracle>
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.MultiBfam
-
 //struct Oracle //defined in find_bom.h
 
 template <typename TSpec = Oracle>
@@ -108,51 +81,63 @@ typedef MultiBfam<Oracle> SBomAlgo; //deprecated
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle, typename TSpec>
-class Pattern<TNeedle, MultiBfam<TSpec> > 
+class Pattern<TNeedle, MultiBfam<TSpec> >
 {
 //____________________________________________________________________________
 public:
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Position<TNeedle>::Type TNeedlePosition;
-	typedef typename Size<TKeyword>::Type TSize;
-	typedef typename Value<TKeyword>::Type TValue;
-	typedef Graph<Automaton<TValue, void, WithoutEdgeId> > TGraph;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Position<TNeedle>::Type TNeedlePosition;
+    typedef typename Size<TKeyword>::Type TSize;
+    typedef typename Value<TKeyword>::Type TValue;
+    typedef Graph<Automaton<TValue, void, WithoutEdgeId> > TGraph;
 
-	//searching data: these members are initialized in _patternInit or during search
-	TNeedlePosition * position;		//pointer to last found position
-	TNeedlePosition * position_end; //end of list in verify
-			//note: if to_verify_begin == to_verify_end then searching in Haystack must go on
+    //searching data: these members are initialized in _patternInit or during search
+    TNeedlePosition * position;        //pointer to last found position
+    TNeedlePosition * position_end; //end of list in verify
+            //note: if to_verify_begin == to_verify_end then searching in Haystack must go on
 
-	//preprocessed data: these members are initialized in setHost
-	Holder<TNeedle> needle;
-	TGraph automaton; //automaton of the reverse lmin-prefixes of the keywords
-	String<String<TNeedlePosition> > terminals; //map of terminal states in automaton
+    //preprocessed data: these members are initialized in setHost
+    Holder<TNeedle> data_host;
+    TGraph automaton; //automaton of the reverse lmin-prefixes of the keywords
+    String<String<TNeedlePosition> > terminals; //map of terminal states in automaton
 
-	TSize lmin;	//min length of keyword
+    TSize lmin;    //min length of keyword
 
 //____________________________________________________________________________
 
-	Pattern():
-		lmin(0)
-	{
-	}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		SEQAN_CHECKPOINT
-		setHost(*this, ndl);
-	}
-
-	~Pattern() 
-	{
-	}
+    Pattern():
+        lmin(0)
+    {
+    }
+
+#if defined(SEQAN_CXX11_STANDARD)
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        SEQAN_CHECKPOINT
+        setHost(*this, ndl);
+    }
+# endif  // SEQAN_CXX11_STANDARD
+
+    ~Pattern()
+    {}
 //____________________________________________________________________________
 
 private:
-	Pattern(Pattern const& other);
-	Pattern const & operator=(Pattern const & other);
-
+    Pattern(Pattern const& other);
+    Pattern const & operator=(Pattern const & other);
+#if defined(SEQAN_CXX11_STANDARD)
+    Pattern(Pattern && other);
+    Pattern & operator=(Pattern && other);
+#endif  // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
@@ -161,98 +146,63 @@ class Pattern<TNeedle, MultiBfam<TSpec> >
 
 template <typename TNeedle, typename TStrs>
 inline void
-_buildAutomatonMultiBfam(Pattern<TNeedle, MultiBfam<Oracle> > & me, 
-						  TStrs const & strs)
+_buildAutomatonMultiBfam(Pattern<TNeedle, MultiBfam<Oracle> > & me,
+                          TStrs const & strs)
 {
-	createSetOracle(me.automaton, me.terminals, strs);
+    createSetOracle(me.automaton, me.terminals, strs);
 }
 
 template <typename TNeedle, typename TStrs>
 inline void
-_buildAutomatonMultiBfam(Pattern<TNeedle, MultiBfam<Trie> > & me, 
-						  TStrs const & strs)
+_buildAutomatonMultiBfam(Pattern<TNeedle, MultiBfam<Trie> > & me,
+                          TStrs const & strs)
 {
-	createSetSuffixTrie(me.automaton, me.terminals, strs);
+    createSetSuffixTrie(me.automaton, me.terminals, strs);
 }
 
 //____________________________________________________________________________
 
-template <typename TNeedle, typename TAutomaton, typename TNeedle2>
-void _setHostMultiBfam(Pattern<TNeedle, MultiBfam<TAutomaton> > & me, 
-						TNeedle2 const & needle_)
-{
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Value<TKeyword>::Type TValue;
-	typedef typename Size<TKeyword>::Type TSize;
-
-	//me.needle
-	setValue(me.needle, needle_);
-	TNeedle & ndl = needle(me);
-
-	//determine lmin
-	TSize len = length(ndl);
-	if (len == 0)
-	{
-		me.lmin = 0;
-		return;
-	}
-
-	me.lmin = length(ndl[0]);
-	for (TSize i = 1; i < len; ++i)
-	{
-		TSize len = length(ndl[i]);
-		if (len < me.lmin)
-		{
-			me.lmin = len;
-		}
-	}
-
-	if (me.lmin == 0) return;
-
-	//collect reverse prefixes for automaton
-	String<String<TValue> > strs;
-	resize(strs, len);
-	for (unsigned int i = 0; i < len; ++i)
-	{
-		strs[i] = prefix(ndl[i], me.lmin);
-		reverse(strs[i]);
-	}
-
-	//build automaton
-	_buildAutomatonMultiBfam(me, strs);
-}
-
-template <typename TNeedle, typename TAutomaton, typename TNeedle2>
-void setHost (Pattern<TNeedle, MultiBfam<TAutomaton> > & me, 
-			  TNeedle2 const & needle) 
-{
-	_setHostMultiBfam(me, needle);
-}
-
-template <typename TNeedle, typename TAutomaton, typename TNeedle2>
-inline void 
-setHost(Pattern<TNeedle, MultiBfam<TAutomaton> > & me, 
-		TNeedle2 & needle)
-{
-	_setHostMultiBfam(me, needle);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
 template <typename TNeedle, typename TAutomaton>
-inline typename Host<Pattern<TNeedle, MultiBfam<TAutomaton> > >::Type & 
-host(Pattern<TNeedle, MultiBfam<TAutomaton> > & me)
+void _reinitPattern(Pattern<TNeedle, MultiBfam<TAutomaton> > & me)
 {
-SEQAN_CHECKPOINT
-	return value(me.needle);
-}
-
-template <typename TNeedle, typename TAutomaton>
-inline typename Host<Pattern<TNeedle, MultiBfam<TAutomaton> > const>::Type & 
-host(Pattern<TNeedle, MultiBfam<TAutomaton> > const & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.needle);
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Value<TKeyword>::Type TValue;
+    typedef typename Size<TKeyword>::Type TSize;
+
+    //me.needle
+    TNeedle & ndl = needle(me);
+
+    //determine lmin
+    TSize len = length(ndl);
+    if (len == 0)
+    {
+        me.lmin = 0;
+        return;
+    }
+
+    me.lmin = length(ndl[0]);
+    for (TSize i = 1; i < len; ++i)
+    {
+        TSize len = length(ndl[i]);
+        if (len < me.lmin)
+        {
+            me.lmin = len;
+        }
+    }
+
+    if (me.lmin == 0) return;
+
+    //collect reverse prefixes for automaton
+    String<String<TValue> > strs;
+    resize(strs, len);
+    for (unsigned int i = 0; i < len; ++i)
+    {
+        strs[i] = prefix(ndl[i], me.lmin);
+        reverse(strs[i]);
+    }
+
+    //build automaton
+    _buildAutomatonMultiBfam(me, strs);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -261,18 +211,18 @@ template <typename TNeedle, typename TAutomaton>
 inline typename Size<TNeedle>::Type
 position(Pattern<TNeedle, MultiBfam<TAutomaton> > & me)
 {
-	return *(me.position);
+    return *(me.position);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 //called when search begins
 template <typename TNeedle, typename TAutomaton>
-inline void _patternInit (Pattern<TNeedle, MultiBfam<TAutomaton> > & me) 
+inline void _patternInit (Pattern<TNeedle, MultiBfam<TAutomaton> > & me)
 {
 SEQAN_CHECKPOINT
-	me.position = 0;
-	me.position_end = 0;
+    me.position = 0;
+    me.position_end = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -281,144 +231,144 @@ SEQAN_CHECKPOINT
 //the Haystack is long enough that *(it+me.lmin) is a valid value.
 //default implementation: it is assumed that if me.automaton parses a me.lmin-length string S, then S is a pattern
 template <typename TNeedle, typename TAutomaton, typename THaystackIterator>
-inline bool 
-_startVerifyMultiBfam(Pattern<TNeedle, MultiBfam<TAutomaton> > &, 
-					   THaystackIterator) 
+inline bool
+_startVerifyMultiBfam(Pattern<TNeedle, MultiBfam<TAutomaton> > &,
+                       THaystackIterator)
 {
-	return true;
+    return true;
 }
 
 //specialization for oracles: must test explicitely, since set-oracles may also parse me.lmin-length strings that are no patterns
 template <typename TNeedle, typename THaystackIterator>
-inline bool 
-_startVerifyMultiBfam(Pattern<TNeedle, MultiBfam<Oracle> > & me, 
-					   THaystackIterator tit) 
+inline bool
+_startVerifyMultiBfam(Pattern<TNeedle, MultiBfam<Oracle> > & me,
+                       THaystackIterator tit)
 {
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Iterator<TKeyword, Standard>::Type TKeywordIterator;
-	TKeyword & keyword = needle(me)[*(me.position)];
-	TKeywordIterator kit = begin(keyword);
-	TKeywordIterator kit_end = kit + me.lmin;
-	while (kit != kit_end)
-	{
-		if (*kit != *tit)
-		{
-			return false;
-		}
-		++kit;
-		++tit;
-	}
-
-	return true;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Iterator<TKeyword, Standard>::Type TKeywordIterator;
+    TKeyword & keyword = needle(me)[*(me.position)];
+    TKeywordIterator kit = begin(keyword);
+    TKeywordIterator kit_end = kit + me.lmin;
+    while (kit != kit_end)
+    {
+        if (*kit != *tit)
+        {
+            return false;
+        }
+        ++kit;
+        ++tit;
+    }
+
+    return true;
 }
 
 //____________________________________________________________________________
 
 template <typename TFinder, typename TAutomaton, typename TNeedle>
-inline bool find(TFinder & finder, 
-				 Pattern<TNeedle, MultiBfam<TAutomaton> > & me) 
+inline bool find(TFinder & finder,
+                 Pattern<TNeedle, MultiBfam<TAutomaton> > & me)
 {
 SEQAN_CHECKPOINT
-	typedef typename Haystack<TFinder>::Type THaystack;
-	typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Value<TKeyword>::Type TValue;
-	typedef typename Size<TKeyword>::Type TSize;
-	typedef typename Iterator<TKeyword, Standard>::Type TKeywordIterator;
-	typedef Graph<Automaton<TValue, void, WithoutEdgeId> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	if (me.lmin == 0) return false;
-
-	//some variables
-	THaystackIterator haystack_end = end(haystack(finder));
-	THaystackIterator it1;
-	THaystackIterator it1_end = haystack_end - me.lmin + 1;
-	THaystackIterator it2;
-	TGraph & automaton = me.automaton;
-	TVertexDescriptor root = getRoot(automaton);
-	TVertexDescriptor nil_ = getNil<TVertexDescriptor>();
-	TVertexDescriptor current;
-	TKeywordIterator kit;
-	TKeywordIterator kit_end;
-	THaystackIterator tit;
-	TKeyword * p_keyword;
-	TSize len;
-
-	if (empty(finder)) 
-	{
+    typedef typename Haystack<TFinder>::Type THaystack;
+    typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Value<TKeyword>::Type TValue;
+    typedef typename Size<TKeyword>::Type TSize;
+    typedef typename Iterator<TKeyword, Standard>::Type TKeywordIterator;
+    typedef Graph<Automaton<TValue, void, WithoutEdgeId> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    if (me.lmin == 0) return false;
+
+    //some variables
+    THaystackIterator haystack_end = end(haystack(finder));
+    THaystackIterator it1;
+    THaystackIterator it1_end = haystack_end - me.lmin + 1;
+    THaystackIterator it2;
+    TGraph & automaton = me.automaton;
+    TVertexDescriptor root = getRoot(automaton);
+    TVertexDescriptor nil_ = getNil<TVertexDescriptor>();
+    TVertexDescriptor current;
+    TKeywordIterator kit;
+    TKeywordIterator kit_end;
+    THaystackIterator tit;
+    TKeyword * p_keyword;
+    TSize len;
+
+    if (empty(finder))
+    {
 //START
-		_patternInit(me);
-		_finderSetNonEmpty(finder);
-		it1 = hostIterator(finder);
-	} 
-	else 
-	{
+        _patternInit(me);
+        _finderSetNonEmpty(finder);
+        it1 = hostIterator(finder);
+    }
+    else
+    {
 //RESUME
-		it1 = hostIterator(finder);
-		goto VERIFY_NEXT;
-	}
+        it1 = hostIterator(finder);
+        goto VERIFY_NEXT;
+    }
 
 //SEARCH
-	while (it1 < it1_end)
-	{
-		it2 = it1 + me.lmin; //me.lmin > 0 => it1 != it2
-		current = root;
-		while (true)
-		{
-			--it2;
-			current = getSuccessor(automaton, current, *it2);
-			if (current == nil_)
-			{
+    while (it1 < it1_end)
+    {
+        it2 = it1 + me.lmin; //me.lmin > 0 => it1 != it2
+        current = root;
+        while (true)
+        {
+            --it2;
+            current = getSuccessor(automaton, current, *it2);
+            if (current == nil_)
+            {
 //SKIP
-				it1 = it2 + 1;
-				break;
-			}
-			if (it1 == it2)
-			{
+                it1 = it2 + 1;
+                break;
+            }
+            if (it1 == it2)
+            {
 //VERIFY
-				me.position = begin(property(me.terminals, current), Standard());
-				me.position_end = end(property(me.terminals, current), Standard());
-				SEQAN_ASSERT_NEQ(me.position, me.position_end);
-
-				if (_startVerifyMultiBfam(me, it1)) //this returns true if the lmin-length prefixe matches
-				{
-					while (me.position != me.position_end)
-					{
-						p_keyword = & needle(me)[*me.position];
-						len = length(*p_keyword);
-						if ((it1 + len) <= haystack_end)
-						{
-							//compare rest
-							kit = begin(*p_keyword) + me.lmin;
-							kit_end = end(*p_keyword);
-							tit = it1 + me.lmin;
-							while (true)
-							{
-								if (kit == kit_end)
-								{
+                me.position = begin(property(me.terminals, current), Standard());
+                me.position_end = end(property(me.terminals, current), Standard());
+                SEQAN_ASSERT_NEQ(me.position, me.position_end);
+
+                if (_startVerifyMultiBfam(me, it1)) //this returns true if the lmin-length prefixe matches
+                {
+                    while (me.position != me.position_end)
+                    {
+                        p_keyword = & needle(me)[*me.position];
+                        len = length(*p_keyword);
+                        if ((it1 + len) <= haystack_end)
+                        {
+                            //compare rest
+                            kit = begin(*p_keyword) + me.lmin;
+                            kit_end = end(*p_keyword);
+                            tit = it1 + me.lmin;
+                            while (true)
+                            {
+                                if (kit == kit_end)
+                                {
 //MATCH FOUND
-									setPosition(finder, it1 - begin(haystack(finder), Standard()));
-									_setFinderLength(finder, length(needle(*p_keyword)));
-									_setFinderEnd(finder, position(finder) + length(finder));
-									return true;
-								}
-								if (*kit != *tit) break;
-								++kit;
-								++tit;
-							}
-						}
+                                    setPosition(finder, it1 - begin(haystack(finder), Standard()));
+                                    _setFinderLength(finder, length(needle(*p_keyword)));
+                                    _setFinderEnd(finder, position(finder) + length(finder));
+                                    return true;
+                                }
+                                if (*kit != *tit) break;
+                                ++kit;
+                                ++tit;
+                            }
+                        }
 VERIFY_NEXT:
-						++me.position;
-					}
-				}
-				++it1;
-				break;
-			}
-
-		}
-	}
-	return false;
+                        ++me.position;
+                    }
+                }
+                ++it1;
+                break;
+            }
+
+        }
+    }
+    return false;
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/find/find_multiple_shiftand.h b/seqan/find/find_multiple_shiftand.h
index d459aec..157ae84 100644
--- a/seqan/find/find_multiple_shiftand.h
+++ b/seqan/find/find_multiple_shiftand.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -49,31 +49,15 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Multiple exact string matching using bit parallelism.
  *
  * The total size of the patterns should fit into a computer word.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, MultipleShiftAnd>;
- * 
+ *
  * @tparam TNeedle The needle type, a string of keywords. Types: String
- * 
- * @section Remarks
- * 
+ *
  * The types of all keywords in the needle and the haystack have to match.
  */
 
-/**
-.Spec.MultipleShiftAnd:
-..summary: Multiple exact string matching using bit parallelism. The total size of the patterns should fit into a computer word.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, MultipleShiftAnd>
-..param.TNeedle:The needle type, a string of keywords.
-...type:Class.String
-..remarks.text:The types of all keywords in the needle and the haystack have to match.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.MultipleShiftAnd
-
 struct MultipleShiftAnd_;
 typedef Tag<MultipleShiftAnd_> MultipleShiftAnd;
 
@@ -83,53 +67,53 @@ template <typename TNeedle>
 class Pattern<TNeedle, MultipleShiftAnd> {
 //____________________________________________________________________________
 private:
-	Pattern(Pattern const& other);
-	Pattern const& operator=(Pattern const & other);
+    Pattern(Pattern const& other);
+    Pattern const& operator=(Pattern const & other);
 
 //____________________________________________________________________________
 public:
-	typedef unsigned int TWord;
-	typedef typename Size<TNeedle>::Type TSize;
-	Holder<TNeedle> data_host;
-	TWord* table;			// Look up table for each character in the alphabet (called B in "Navarro")
-	TWord* prefSufMatch;	// Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
-	TWord* di;				// Initialization word
-	TWord* df;				// Final test word
-	TWord alphabetSize;		// e.g., char --> 256
-	TWord totalLength;		// Lenght of concatenated keywords
-	TWord blockCount;		// #unsigned ints required to store needle	
-	std::deque<Pair<TSize, TSize> > data_keyword;  // All keywords that produced a hit here
-	TSize data_keywordIndex;  // Last keyword index
-	TSize data_needleLength;  // Last needle length
+    typedef unsigned int TWord;
+    typedef typename Size<TNeedle>::Type TSize;
+    Holder<TNeedle> data_host;
+    TWord* table;            // Look up table for each character in the alphabet (called B in "Navarro")
+    TWord* prefSufMatch;    // Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
+    TWord* di;                // Initialization word
+    TWord* df;                // Final test word
+    TWord alphabetSize;        // e.g., char --> 256
+    TWord totalLength;        // Lenght of concatenated keywords
+    TWord blockCount;        // #unsigned ints required to store needle
+    std::deque<Pair<TSize, TSize> > data_keyword;  // All keywords that produced a hit here
+    TSize data_keywordIndex;  // Last keyword index
+    TSize data_needleLength;  // Last needle length
 
 //____________________________________________________________________________
 
-	Pattern() {
-		table = 0;
-		prefSufMatch=0;
-		di = 0;
-		df = 0;
-	}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		table = 0;
-		prefSufMatch=0;
-		di = 0;
-		df = 0;
-		setHost(*this, ndl);
-	}
-
-	~Pattern() {
-		SEQAN_CHECKPOINT
-		if (table != 0) {
-			deallocate(this, table, alphabetSize * blockCount);
-			deallocate(this, prefSufMatch, blockCount);
-			deallocate(this, di, blockCount);
-			deallocate(this, df, blockCount);
-		}
-	}		
+    Pattern() {
+        table = 0;
+        prefSufMatch=0;
+        di = 0;
+        df = 0;
+    }
+
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        table = 0;
+        prefSufMatch=0;
+        di = 0;
+        df = 0;
+        setHost(*this, ndl);
+    }
+
+    ~Pattern() {
+        SEQAN_CHECKPOINT
+        if (table != 0) {
+            deallocate(this, table, alphabetSize * blockCount);
+            deallocate(this, prefSufMatch, blockCount);
+            deallocate(this, di, blockCount);
+            deallocate(this, df, blockCount);
+        }
+    }
 //____________________________________________________________________________
 };
 
@@ -140,13 +124,13 @@ class Pattern<TNeedle, MultipleShiftAnd> {
 template <typename TNeedle>
 struct Host< Pattern<TNeedle, MultipleShiftAnd> >
 {
-	typedef TNeedle Type;
+    typedef TNeedle Type;
 };
 
 template <typename TNeedle>
 struct Host< Pattern<TNeedle, MultipleShiftAnd> const>
 {
-	typedef TNeedle const Type;
+    typedef TNeedle const Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -155,92 +139,92 @@ struct Host< Pattern<TNeedle, MultipleShiftAnd> const>
 
 template <typename TNeedle, typename TNeedle2>
 void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 const & needle) {
-	SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Value<TKeyword>::Type TAlphabet;
-	if (me.table != 0) {
-		deallocate(me, me.table, me.alphabetSize * me.blockCount);
-		deallocate(me, me.di, me.blockCount);
-		deallocate(me, me.df, me.blockCount);
-	}
-
-	typename Iterator<TNeedle2 const, Rooted>::Type it = begin(needle);
-	me.totalLength = 0;
-	for(;!atEnd(it);goNext(it)) {
-		me.totalLength += length(*it);
-	}
-	me.alphabetSize = ValueSize<TAlphabet>::VALUE;
-	if (me.totalLength<1) me.blockCount=1;
-	else me.blockCount=((me.totalLength-1) / BitsPerValue<TWord>::VALUE)+1;
-			
-	allocate (me, me.table, me.blockCount * me.alphabetSize);
-	arrayFill (me.table, me.table + me.blockCount * me.alphabetSize, 0);
-
-	allocate (me, me.di, me.blockCount);
-	arrayFill (me.di, me.di + me.blockCount, 0);
-
-	allocate (me, me.df, me.blockCount);
-	arrayFill (me.df, me.df + me.blockCount, 0);
-
-	goBegin(it);
-	TWord j = 0;
-	for(;!atEnd(it);goNext(it)) {
-		me.di[j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
-		for (TWord posInKeyword = 0; posInKeyword < length(*it); ++posInKeyword) {
-			// Determine character position in array table
-			TWord index = convert<TWord>(getValue(*it,posInKeyword));
-			me.table[me.blockCount*index + j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
-			++j;
-		}
-		me.df[(j - 1) / BitsPerValue<TWord>::VALUE] |= (1<<((j-1)%BitsPerValue<TWord>::VALUE));
-	}
-	setValue(me.data_host, needle);
-
-	/*
-	// Debug code
-	std::cout << "Alphabet size: " << me.alphabetSize << ::std::endl;
-	std::cout << "Needle length: " << me.totalLength << ::std::endl;
-	std::cout << "Block count: " << me.blockCount << ::std::endl;
-	std::cout << "K: ";
-	goBegin(it);
-	for(;!atEnd(it);goNext(it)) {
-		std::cout << *it;
-	}
-	std::cout << ::std::endl;
-	std::cout << "Table: " << ::std::endl;
-	for(unsigned int i=0;i<me.alphabetSize;++i) {
-		//if ((i<97) || (i>122)) continue;
-		std::cout << TAlphabet(i) << ": ";
-		for(int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-				std::cout << ((me.table[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-	}
-	std::cout << "DI and DF: " << ::std::endl;
-	std::cout << "I: ";
-	for(int j=0;j<me.blockCount;++j) {
-		for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-			std::cout << ((me.di[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-		}
-	}
-	std::cout << ::std::endl;
-	std::cout << "F: ";
-	for(int j=0;j<me.blockCount;++j) {
-		for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-			std::cout << ((me.df[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-		}
-	}
-	std::cout << ::std::endl;
-	*/
+    SEQAN_CHECKPOINT
+    typedef unsigned int TWord;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Value<TKeyword>::Type TAlphabet;
+    if (me.table != 0) {
+        deallocate(me, me.table, me.alphabetSize * me.blockCount);
+        deallocate(me, me.di, me.blockCount);
+        deallocate(me, me.df, me.blockCount);
+    }
+
+    typename Iterator<TNeedle2 const, Rooted>::Type it = begin(needle);
+    me.totalLength = 0;
+    for(;!atEnd(it);goNext(it)) {
+        me.totalLength += length(*it);
+    }
+    me.alphabetSize = ValueSize<TAlphabet>::VALUE;
+    if (me.totalLength<1) me.blockCount=1;
+    else me.blockCount=((me.totalLength-1) / BitsPerValue<TWord>::VALUE)+1;
+
+    allocate (me, me.table, me.blockCount * me.alphabetSize);
+    arrayFill (me.table, me.table + me.blockCount * me.alphabetSize, 0);
+
+    allocate (me, me.di, me.blockCount);
+    arrayFill (me.di, me.di + me.blockCount, 0);
+
+    allocate (me, me.df, me.blockCount);
+    arrayFill (me.df, me.df + me.blockCount, 0);
+
+    goBegin(it);
+    TWord j = 0;
+    for(;!atEnd(it);goNext(it)) {
+        me.di[j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
+        for (TWord posInKeyword = 0; posInKeyword < length(*it); ++posInKeyword) {
+            // Determine character position in array table
+            TWord index = convert<TWord>(getValue(*it,posInKeyword));
+            me.table[me.blockCount*index + j / BitsPerValue<TWord>::VALUE] |= (1<<(j%BitsPerValue<TWord>::VALUE));
+            ++j;
+        }
+        me.df[(j - 1) / BitsPerValue<TWord>::VALUE] |= (1<<((j-1)%BitsPerValue<TWord>::VALUE));
+    }
+    setValue(me.data_host, needle);
+
+    /*
+    // Debug code
+    std::cout << "Alphabet size: " << me.alphabetSize << std::endl;
+    std::cout << "Needle length: " << me.totalLength << std::endl;
+    std::cout << "Block count: " << me.blockCount << std::endl;
+    std::cout << "K: ";
+    goBegin(it);
+    for(;!atEnd(it);goNext(it)) {
+        std::cout << *it;
+    }
+    std::cout << std::endl;
+    std::cout << "Table: " << std::endl;
+    for(unsigned int i=0;i<me.alphabetSize;++i) {
+        //if ((i<97) || (i>122)) continue;
+        std::cout << TAlphabet(i) << ": ";
+        for(int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                std::cout << ((me.table[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+    }
+    std::cout << "DI and DF: " << std::endl;
+    std::cout << "I: ";
+    for(int j=0;j<me.blockCount;++j) {
+        for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+            std::cout << ((me.di[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+        }
+    }
+    std::cout << std::endl;
+    std::cout << "F: ";
+    for(int j=0;j<me.blockCount;++j) {
+        for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+            std::cout << ((me.df[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+        }
+    }
+    std::cout << std::endl;
+    */
 }
 
 template <typename TNeedle, typename TNeedle2>
 void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 & needle)
 {
-	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
+    setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
 }
 
 //____________________________________________________________________________
@@ -249,30 +233,30 @@ void setHost (Pattern<TNeedle, MultipleShiftAnd> & me, TNeedle2 & needle)
 template <typename TNeedle>
 inline void _patternInit (Pattern<TNeedle, MultipleShiftAnd> & me)
 {
-	if (me.prefSufMatch != 0)
-		deallocate(me, me.prefSufMatch, me.blockCount);
-	allocate (me, me.prefSufMatch, me.blockCount);
-	arrayFill (me.prefSufMatch, me.prefSufMatch + me.blockCount, 0);
-	me.data_keyword.clear();
-	me.data_keywordIndex = 0;
+    if (me.prefSufMatch != 0)
+        deallocate(me, me.prefSufMatch, me.blockCount);
+    allocate (me, me.prefSufMatch, me.blockCount);
+    arrayFill (me.prefSufMatch, me.prefSufMatch + me.blockCount, 0);
+    me.data_keyword.clear();
+    me.data_keywordIndex = 0;
 }
 
 //____________________________________________________________________________
 
 template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type & 
+inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type &
 host(Pattern<TNeedle, MultipleShiftAnd> & me)
 {
 SEQAN_CHECKPOINT
-	return value(me.data_host);
+    return value(me.data_host);
 }
 
 template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type & 
+inline typename Host<Pattern<TNeedle, MultipleShiftAnd>const>::Type &
 host(Pattern<TNeedle, MultipleShiftAnd> const & me)
 {
 SEQAN_CHECKPOINT
-	return value(me.data_host);
+    return value(me.data_host);
 }
 
 //____________________________________________________________________________
@@ -282,167 +266,167 @@ template <typename TNeedle>
 inline typename Size<TNeedle>::Type
 position(Pattern<TNeedle, MultipleShiftAnd> & me)
 {
-	return me.data_keywordIndex;
+    return me.data_keywordIndex;
 }
 
 
 template <typename TFinder, typename TNeedle>
 bool _findShiftAndSmallNeedle(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me) {
-	SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
-	typedef typename Size<TNeedle>::Type TSize;
-	while (!atEnd(finder)) {
-		TWord pos = convert<TWord>(*finder);
-		me.prefSufMatch[0] = ((me.prefSufMatch[0] << 1) | me.di[0]) & me.table[me.blockCount*pos];
-
-		/*
-		// Debug code
-		std::cout << "   ";
-		for(int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-				std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-		*/
-
-		if ((me.prefSufMatch[0] & me.df[0]) != 0) {
-			// Check which pattern has matched
-			typename Iterator<TNeedle, Rooted>::Type it = begin(value(me.data_host));
-			TWord j = 0;
-			for(;!atEnd(it);goNext(it)) {
-				j += length(*it);
-				TWord test = (1<<((j-1)%BitsPerValue<TWord>::VALUE));
-				/*
-				// Debug code
-				std::cout << "Tes";
-				for(int j=0;j<me.blockCount;++j) {
-					for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-						std::cout << ((test & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-					}
-				}
-				std::cout << ::std::endl;
-				*/
-				if ((me.prefSufMatch[0] & test) != 0) {
-					me.data_keyword.push_back(Pair<TSize,TSize>(position(it),length(*it)));
-				}
-			}
-			me.data_keywordIndex = (me.data_keyword.front()).i1;
-			me.data_needleLength = (me.data_keyword.front()).i2;
-			me.data_keyword.pop_front();
-			_setFinderEnd(finder);
-			_setFinderLength(finder, me.data_needleLength);
-			finder -= (me.data_needleLength - 1);
-			return true;
-		}
-		goNext(finder);
-	}
-	return false;
+    SEQAN_CHECKPOINT
+    typedef unsigned int TWord;
+    typedef typename Size<TNeedle>::Type TSize;
+    while (!atEnd(finder)) {
+        TWord pos = convert<TWord>(*finder);
+        me.prefSufMatch[0] = ((me.prefSufMatch[0] << 1) | me.di[0]) & me.table[me.blockCount*pos];
+
+        /*
+        // Debug code
+        std::cout << "   ";
+        for(int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+        */
+
+        if ((me.prefSufMatch[0] & me.df[0]) != 0) {
+            // Check which pattern has matched
+            typename Iterator<TNeedle, Rooted>::Type it = begin(value(me.data_host));
+            TWord j = 0;
+            for(;!atEnd(it);goNext(it)) {
+                j += length(*it);
+                TWord test = (1<<((j-1)%BitsPerValue<TWord>::VALUE));
+                /*
+                // Debug code
+                std::cout << "Tes";
+                for(int j=0;j<me.blockCount;++j) {
+                    for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                        std::cout << ((test & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+                    }
+                }
+                std::cout << std::endl;
+                */
+                if ((me.prefSufMatch[0] & test) != 0) {
+                    me.data_keyword.push_back(Pair<TSize,TSize>(position(it),length(*it)));
+                }
+            }
+            me.data_keywordIndex = (me.data_keyword.front()).i1;
+            me.data_needleLength = (me.data_keyword.front()).i2;
+            me.data_keyword.pop_front();
+            _setFinderEnd(finder);
+            _setFinderLength(finder, me.data_needleLength);
+            finder -= (me.data_needleLength - 1);
+            return true;
+        }
+        goNext(finder);
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
 bool _findShiftAndLargeNeedle(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me) {
-	SEQAN_CHECKPOINT
-	typedef typename Size<TNeedle>::Type TSize;
-	typedef unsigned int TWord;
-	while (!atEnd(finder)) {
-		TWord pos = convert<TWord>(*finder);
-		TWord carry = 1;
-		for(TWord block=0;block<me.blockCount;++block) {
-			bool newCarry = ((me.prefSufMatch[block] & (1<< (BitsPerValue<TWord>::VALUE - 1)))!=0); 
-			me.prefSufMatch[block]<<=1;
-			me.prefSufMatch[block]|=carry;
-			carry = newCarry;
-		}
-		for(TWord block=0;block<me.blockCount;++block) me.prefSufMatch[block] |= me.di[block];
-		for(TWord block=0;block<me.blockCount;++block) me.prefSufMatch[block] &= me.table[me.blockCount*pos+block];
-
-		/*
-		// Debug code
-		std::cout << "   ";
-		for(int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-				std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-		*/
-
-		bool match = false;
-		for(TWord block=0;block<me.blockCount;++block) {
-			if ((me.prefSufMatch[block] & me.df[block]) != 0) {
-				match = true;
-				break;
-			}
-		}
-		if (match) {
-			// Check which pattern has matched
-			typename Iterator<TNeedle, Rooted>::Type it = begin(value(me.data_host));
-			TWord j = 0;
-			for(;!atEnd(it);goNext(it)) {
-				j += length(*it);
-				TWord* test;
-				allocate (me, test, me.blockCount);
-				arrayFill (test, test + me.blockCount, 0);
-				test[(j - 1) / BitsPerValue<TWord>::VALUE] |= (1<<((j-1)%BitsPerValue<TWord>::VALUE));
-
-				/*
-				// Debug code
-				std::cout << "Tes";
-				for(int i=0;i<me.blockCount;++i) {
-					for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-						std::cout << ((test[i] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-					}
-				}
-				std::cout << ::std::endl;
-				*/
-
-				if ((me.prefSufMatch[(j - 1) / BitsPerValue<TWord>::VALUE] & test[(j - 1) / BitsPerValue<TWord>::VALUE]) != 0) {
-					me.data_keyword.push_back(Pair<TSize,TSize>(position(it),length(*it)));			
-				}
-				deallocate(me, test, me.blockCount);
-			}
-			me.data_keywordIndex = (me.data_keyword.front()).i1;
-			me.data_needleLength = (me.data_keyword.front()).i2;
-			me.data_keyword.pop_front();
-			_setFinderEnd(finder);
-			_setFinderLength(finder, me.data_needleLength);
-			finder -= (me.data_needleLength - 1);
-			return true;
-		}
-		goNext(finder);
-	}
-	return false;
+    SEQAN_CHECKPOINT
+    typedef typename Size<TNeedle>::Type TSize;
+    typedef unsigned int TWord;
+    while (!atEnd(finder)) {
+        TWord pos = convert<TWord>(*finder);
+        TWord carry = 1;
+        for(TWord block=0;block<me.blockCount;++block) {
+            bool newCarry = ((me.prefSufMatch[block] & (1<< (BitsPerValue<TWord>::VALUE - 1)))!=0);
+            me.prefSufMatch[block]<<=1;
+            me.prefSufMatch[block]|=carry;
+            carry = newCarry;
+        }
+        for(TWord block=0;block<me.blockCount;++block) me.prefSufMatch[block] |= me.di[block];
+        for(TWord block=0;block<me.blockCount;++block) me.prefSufMatch[block] &= me.table[me.blockCount*pos+block];
+
+        /*
+        // Debug code
+        std::cout << "   ";
+        for(int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+        */
+
+        bool match = false;
+        for(TWord block=0;block<me.blockCount;++block) {
+            if ((me.prefSufMatch[block] & me.df[block]) != 0) {
+                match = true;
+                break;
+            }
+        }
+        if (match) {
+            // Check which pattern has matched
+            typename Iterator<TNeedle, Rooted>::Type it = begin(value(me.data_host));
+            TWord j = 0;
+            for(;!atEnd(it);goNext(it)) {
+                j += length(*it);
+                TWord* test;
+                allocate (me, test, me.blockCount);
+                arrayFill (test, test + me.blockCount, 0);
+                test[(j - 1) / BitsPerValue<TWord>::VALUE] |= (1<<((j-1)%BitsPerValue<TWord>::VALUE));
+
+                /*
+                // Debug code
+                std::cout << "Tes";
+                for(int i=0;i<me.blockCount;++i) {
+                    for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                        std::cout << ((test[i] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+                    }
+                }
+                std::cout << std::endl;
+                */
+
+                if ((me.prefSufMatch[(j - 1) / BitsPerValue<TWord>::VALUE] & test[(j - 1) / BitsPerValue<TWord>::VALUE]) != 0) {
+                    me.data_keyword.push_back(Pair<TSize,TSize>(position(it),length(*it)));
+                }
+                deallocate(me, test, me.blockCount);
+            }
+            me.data_keywordIndex = (me.data_keyword.front()).i1;
+            me.data_needleLength = (me.data_keyword.front()).i2;
+            me.data_keyword.pop_front();
+            _setFinderEnd(finder);
+            _setFinderLength(finder, me.data_needleLength);
+            finder -= (me.data_needleLength - 1);
+            return true;
+        }
+        goNext(finder);
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
 inline bool find(TFinder & finder, Pattern<TNeedle, MultipleShiftAnd> & me) {
-	SEQAN_CHECKPOINT
-
-	// Check for left-over keywords
-	if ((!empty(finder)) &&
-		(!me.data_keyword.empty())) {
-		finder += me.data_needleLength - 1;
-		me.data_keywordIndex = (me.data_keyword.front()).i1;
-		me.data_needleLength = (me.data_keyword.front()).i2;
-		me.data_keyword.pop_front();
-		finder -= (me.data_needleLength - 1);
-		return true;
-	}
-
-
-	if (empty(finder)) {
-		_patternInit(me);
-		_finderSetNonEmpty(finder);
-	} else
-		finder += me.data_needleLength;
-
-	// Fast algorithm for needles < machine word?
-	if (me.blockCount == 1) {
-		return _findShiftAndSmallNeedle(finder, me);
-	} else {
-		return _findShiftAndLargeNeedle(finder, me);
-	}
+    SEQAN_CHECKPOINT
+
+    // Check for left-over keywords
+    if ((!empty(finder)) &&
+        (!me.data_keyword.empty())) {
+        finder += me.data_needleLength - 1;
+        me.data_keywordIndex = (me.data_keyword.front()).i1;
+        me.data_needleLength = (me.data_keyword.front()).i2;
+        me.data_keyword.pop_front();
+        finder -= (me.data_needleLength - 1);
+        return true;
+    }
+
+
+    if (empty(finder)) {
+        _patternInit(me);
+        _finderSetNonEmpty(finder);
+    } else
+        finder += me.data_needleLength;
+
+    // Fast algorithm for needles < machine word?
+    if (me.blockCount == 1) {
+        return _findShiftAndSmallNeedle(finder, me);
+    } else {
+        return _findShiftAndLargeNeedle(finder, me);
+    }
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_myers_ukkonen.h b/seqan/find/find_myers_ukkonen.h
index f76cb58..94dc224 100644
--- a/seqan/find/find_myers_ukkonen.h
+++ b/seqan/find/find_myers_ukkonen.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,9 +35,7 @@
 #ifndef SEQAN_HEADER_FIND_MYERS_UKKONEN_H
 #define SEQAN_HEADER_FIND_MYERS_UKKONEN_H
 
-#include <seqan/misc/misc_sse2.h>
-
-namespace SEQAN_NAMESPACE_MAIN 
+namespace seqan
 {
 
 //////////////////////////////////////////////////////////////////////////////
@@ -50,49 +48,26 @@ namespace SEQAN_NAMESPACE_MAIN
  * @headerfile <seqan/find.h>
  * @brief Provides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with
  *        application of the Ukkonen- trick.
- * 
+ *
  * @signature template <typename TNeedle[, typename TSpec[, typename TFindBeginPatternSpec]]>
  *            class Pattern<TNeedle, Myers<TSpec, TFindBeginPatternSpec> >;
- * 
- * @tparam TSpec   Specialization tag.  This could be @link FindInfix @endlink for infix search or <tt>FindPrefix</tt>
- *                 for prefix search. Default: Tag.FindInfix
- * @tparam TFindBeginPatternSpec 
+ *
+ * @tparam TSpec   Specialization tag.  This is @link ApproximateFinderSearchTypeTags#FindInfix @endlink for
+ *                 infix search or @link ApproximateFinderSearchTypeTags#FindPrefix @endlink for prefix search.
+ *                 Defaults to @linkApproximateFinderSearchTypeTags#FindInfix @endlink.
+ * @tparam TFindBeginPatternSpec
  *               Specialization of @link Pattern @endlink used to find the begin of matches.This must be a finder for
- *               prefix search, e.g. @link DPSearch <tt>DPSearch&lt;TScore, FindPrefix&gt;</tt> @endlink or @link
+ *               prefix search, e.g. @link DPSearchPattern <tt>DPSearch&lt;TScore, FindPrefix&gt;</tt> @endlink or @link
  *               MyersPattern <tt>Myers&lt;FindPrefix&gt;</tt> @endlink. Specify <tt>void</tt> to suppress prefix
  *               searching. Default: @link DefaultFindBeginPatternSpec @endlink
  * @tparam TNeedle The needle type. Types: String
- * 
- * @section Remarks
- * 
+ *
  * The needle-length must be smaller than the highest number that can be stored in an unsigned int.
  */
 
-/**
-.Spec.Myers:
-..cat:Searching
-..general:Class.Pattern
-..summary:Provides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with application of the Ukkonen-trick.
-..signature:Pattern<TNeedle, Myers< [TSpec [, TFindBeginPatternSpec] ]> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..param.TSpec:Specialization tag.
-...default:Tag.FindInfix
-...remarks:This could be @Tag.FindInfix@ for infix search or $FindPrefix$ for prefix search.
-..param.TFindBeginPatternSpec:Specialization of @Class.Pattern@ used to find the begin of matches.
-...default:@Metafunction.DefaultFindBeginPatternSpec@
-...metafunction:Metafunction.DefaultFindBeginPatternSpec
-...remarks:This must be a finder for prefix search, e.g. @Spec.DPSearch|$DPSearch<TScore, FindPrefix>$@ or @Spec.Myers|$Myers<FindPrefix>$@.
-Specify $void$ to suppress prefix searching.
-..remarks.text:The needle-length must be smaller than the highest number that can be stored in an unsigned int.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.Myers
-
-template <typename TSpec = FindInfix, 
-		  typename THasState = True,
-		  typename TFindBeginPatternSpec = typename DefaultFindBeginPatternSpec<EditDistanceScore, THasState>::Type>
+template <typename TSpec = FindInfix,
+          typename THasState = True,
+          typename TFindBeginPatternSpec = typename DefaultFindBeginPatternSpec<EditDistanceScore, THasState>::Type>
 struct Myers {};
 
 struct NMatchesNone_;
@@ -108,96 +83,43 @@ struct AlignTextBanded; // search query in a parallelogram
 
 /*!
  * @typedef MyersUkkonen
- * 
+ * @headerfile <seqan/find.h>
  * @brief Semi-global (query-global, text-local) pattern matching without
  *        findBegin() support.
- * 
+ *
  * @signature typedef Myers<FindInfix, True, void> MyersUkkonen;
- * 
+ *
  * @deprecated Use <tt>Myers&lt;FindInfix&gt;</tt> instead.
  */
 
-/**
-.Shortcut.MyersUkkonen:
-..status:deprecated, use $Myers<FindInfix>$
-..cat:Searching
-..summary:Semi-global (query-global, text-local) pattern matching without findBegin() support.
-..signature:MyersUkkonen
-..shortcutfor:Spec.Myers
-...signature:Myers<FindInfix, void>
-..see:Spec.Myers
-..see:Shortcut.MyersUkkonenBanded
-..see:Shortcut.MyersUkkonenGlobal
-..see:Shortcut.MyersUkkonenGlobalBanded
-*/
 typedef Myers<FindInfix, True, void> MyersUkkonen;
 
 /*!
  * @typedef MyersUkkonenGlobal
- * 
+ * @headerfile <seqan/find.h>
  * @brief Global (query-global, text-global) pattern matching without findBegin() support.
- * 
+ *
  * @signature typedef Myers<FindInfix, True, void> MyersUkkonenGlobal;
  */
 
-/**
-.Shortcut.MyersUkkonenGlobal:
-..status:deprecated, use $Myers<FindPrefix>$
-..cat:Searching
-..summary:Global (query-global, text-global) pattern matching without findBegin() support.
-..signature:MyersUkkonen
-..shortcutfor:Spec.Myers
-...signature:Myers<FindPrefix, void>
-..see:Spec.Myers
-..see:Shortcut.MyersUkkonenGlobalBanded
-..see:Shortcut.MyersUkkonen
-..see:Shortcut.MyersUkkonenBanded
-*/
 typedef Myers<FindPrefix, True, void> MyersUkkonenGlobal;
 
 /*!
  * @typedef MyersUkkonenBanded
- * 
+ * @headerfile <seqan/find.h>
  * @brief Global (query-global, text-local) pattern matching without findBegin() support.
- * 
+ *
  * @signature Myers<AlignTextBanded<FindInfix, NMatchesN_, NMatchesN_>, True, void> MyersUkkonenBanded;
  */
 
-/**
-.Shortcut.MyersUkkonenBanded:
-..status:deprecated, use $Myers<AlignTextBanded<FindInfix, NMatchesN_, NMatchesN_> >$
-..cat:Searching
-..summary:Semin-global (query-global, text-local) pattern matching without findBegin() support.
-..signature:MyersUkkonen
-..shortcutfor:Spec.Myers
-...signature:Myers<AlignTextBanded, void>
-..see:Spec.Myers
-..see:Shortcut.MyersUkkonen
-..see:Shortcut.MyersUkkonenGlobal
-..see:Shortcut.MyersUkkonenGlobalBanded
-*/
-
 /*!
  * @typedef MyersUkkonenGlobalBanded
- * 
+ * @headerfile <seqan/find.h>
  * @brief Global (query-global, text-global) pattern matching without findBegin() support.
- * 
+ *
  * @signature Myers<AlignTextBanded<FindPrefix, NMatchesN_, NMatchesN_>, True, void> MyersUkkonenGlobalBanded;
  */
 
-/**
-.Shortcut.MyersUkkonenGlobalBanded:
-..status:deprecated, use $Myers<AlignTextBanded<FindPrefix, NMatchesN_, NMatchesN_> >$
-..cat:Searching
-..summary:global (query-global, text-global) pattern matching without findBegin() support.
-..signature:MyersUkkonen
-..shortcutfor:Spec.Myers
-...signature:Myers<MyersUkkonenGlobalBanded, void>
-..see:Spec.Myers
-..see:Shortcut.MyersUkkonen
-..see:Shortcut.MyersUkkonenGlobal
-..see:Shortcut.MyersUkkonenBanded
-*/
 typedef Myers<AlignTextBanded<FindInfix, NMatchesN_, NMatchesN_>, True, void> MyersUkkonenBanded;
 typedef Myers<AlignTextBanded<FindPrefix, NMatchesN_, NMatchesN_>, True, void> MyersUkkonenGlobalBanded;
 
@@ -209,17 +131,17 @@ typedef Myers<AlignTextBanded<FindPrefix, NMatchesN_, NMatchesN_>, True, void> M
 
 template <typename T>
 struct MyersUkkonenHP0_ {
-	enum { VALUE = 0 };
+    enum { VALUE = 0 };
 };
 
 template <>
 struct MyersUkkonenHP0_<FindPrefix> {
-	enum { VALUE = 1 };
+    enum { VALUE = 1 };
 };
 
 template <typename TValue>
 struct MyersSmallAlphabet_:
-	public Eval<ValueSize<TValue>::VALUE <= 8> {};
+    public Eval<ValueSize<TValue>::VALUE <= 8> {};
 
 
 //////////////////////////////////////////////////////////////////////////////
@@ -229,19 +151,19 @@ template <typename TNeedle, typename TSpec, typename THasState, typename TFindBe
 struct FindBegin_< Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >, TFindBeginPatternSpec2>
 {
 private:
-	typedef Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > TPattern;
-	typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern;
+    typedef Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > TPattern;
+    typedef typename FindBeginPattern<TPattern>::Type TFindBeginPattern;
 
 public:
-	TFindBeginPattern data_findBeginPattern;
-// 	Holder<TNeedle>	data_host;	//defines the 
-	typedef False HasHost;
+    TFindBeginPattern data_findBeginPattern;
+//     Holder<TNeedle>    data_host;    //defines the
+    typedef False HasHost;
 };
 
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
 struct FindBegin_< Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >, void>
 {
-	typedef False HasHost;
+    typedef False HasHost;
 //need no findBegin if FindBeginPatternSpec is void
 };
 
@@ -255,15 +177,15 @@ template <typename TNeedle, typename TSpec>
 struct MyersSmallState_
 {
 #ifdef SEQAN_SSE2_INT128
-	typedef Sse2Int128 TWord;
+    typedef Sse2Int128 TWord;
 #else
-	typedef unsigned long TWord;
+    typedef unsigned long TWord;
 #endif
 
-	TWord VP0;					// VP[0] (saves one dereferentiation)
-	TWord VN0;					// VN[0]
-    unsigned int errors;		// the current number of errors
-    unsigned int maxErrors;		// the maximal number of errors allowed
+    TWord VP0;                    // VP[0] (saves one dereferentiation)
+    TWord VN0;                    // VN[0]
+    unsigned int errors;        // the current number of errors
+    unsigned int maxErrors;        // the maximal number of errors allowed
 
     MyersSmallState_() : VP0(0), VN0(0), errors(0), maxErrors(0)
     {}
@@ -281,24 +203,24 @@ struct MyersSmallState_<TNeedle, AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>
     public MyersSmallStateBandedShift_<TNeedle, typename MyersSmallAlphabet_<typename Value<TNeedle>::Type>::Type>
 {
 #ifdef SEQAN_SSE2_INT128
-	typedef Sse2Int128 TWord;
+    typedef Sse2Int128 TWord;
 #else
 #ifdef SEQAN_DEBUG_MYERSBITVECTOR
-	typedef unsigned char TWord;
+    typedef unsigned char TWord;
 #else
-	typedef unsigned long TWord;
+    typedef unsigned long TWord;
 #endif
 #endif
     typedef typename Value<TNeedle>::Type TValue;
 
     TWord bitMasks[ValueSize<TValue>::VALUE];
-	TWord VP0;					// VP[0] (saves one dereferentiation)
-	TWord VN0;					// VN[0]
+    TWord VP0;                    // VP[0] (saves one dereferentiation)
+    TWord VN0;                    // VN[0]
     unsigned short errors;      // the current number of errors
     unsigned short maxErrors;   // the maximal number of errors allowed
     unsigned short leftClip;    // clip that many characters from the text begin
 //    unsigned short rightClip;   // stop alignment that many characters before the end   <<<< currently unused (autom. determined)
-    
+
 #ifdef SEQAN_DEBUG_MYERSBITVECTOR
     String<int> DPMat;
 #endif
@@ -310,14 +232,14 @@ template <typename TNeedle, typename TSpec>
 struct MyersLargeState_
 {
 #ifdef SEQAN_SSE2_INT128
-	typedef Sse2Int128 TWord;
+    typedef Sse2Int128 TWord;
 #else
-	typedef unsigned long TWord;
+    typedef unsigned long TWord;
 #endif
-	unsigned lastBlock;			// the block containing the last active cell
-	String<TWord> VP;
-	String<TWord> VN;
-	TWord scoreMask;			// the mask with a bit set at the position of the last active cell
+    unsigned lastBlock;            // the block containing the last active cell
+    String<TWord> VP;
+    String<TWord> VN;
+    TWord scoreMask;            // the mask with a bit set at the position of the last active cell
 
     MyersLargeState_() : lastBlock(0), scoreMask(0) {}
 };
@@ -325,18 +247,18 @@ template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatte
 struct MyersLargeState_<TNeedle, AlignTextBanded<TSpec, TFinderCSP, TPatternCSP> >
 {
 #ifdef SEQAN_SSE2_INT128
-	typedef Sse2Int128 TWord;
+    typedef Sse2Int128 TWord;
 #else
 #ifdef SEQAN_DEBUG_MYERSBITVECTOR
-	typedef unsigned char TWord;
+    typedef unsigned char TWord;
 #else
-	typedef unsigned long TWord;
+    typedef unsigned long TWord;
 #endif
 #endif
-	unsigned lastBlock;			// the block containing the last active cell
-	unsigned blockCount;		// the number of blocks
-	String<TWord> VP;
-	String<TWord> VN;
+    unsigned lastBlock;            // the block containing the last active cell
+    unsigned blockCount;        // the number of blocks
+    String<TWord> VP;
+    String<TWord> VN;
 };
 
 // TODO: should go elsewhere
@@ -353,67 +275,93 @@ class PatternState_<TNeedle, Myers<TSpec, False, TFindBeginPatternSpec> > {};
 template <typename TNeedle, typename TSpec, typename TFindBeginPatternSpec>
 class PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> >:
     public MyersSmallState_<TNeedle, TSpec>
-{	
+{
 public:
     typedef MyersSmallState_<TNeedle, TSpec>    TSmallState;
     typedef MyersLargeState_<TNeedle, TSpec>    TLargeState;
     typedef typename TSmallState::TWord         TWord;
 
-	enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
+    enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
 
-	TLargeState *largeState;
+    TLargeState *largeState;
 
 //____________________________________________________________________________
 
-	PatternState_():
-		largeState(NULL) {}
+    PatternState_():
+        largeState(NULL) {}
 
-	PatternState_(PatternState_ const & other):
+    PatternState_(PatternState_ const & other):
         TSmallState(other),
-		largeState(NULL)
-	{
-		if (other.largeState)
-			largeState = new TLargeState(*other.largeState);
-	}
-
-	~PatternState_()
-	{
-		delete largeState;
-	}
-	
-	PatternState_ &
-	operator = (PatternState_ const & other)
-	{
+        largeState(NULL)
+    {
+        if (other.largeState)
+            largeState = new TLargeState(*other.largeState);
+    }
+
+#ifdef SEQAN_CXX11_STANDARD
+    // Add move constructor.
+    PatternState_(PatternState_ && other):
+        TSmallState(std::forward<PatternState_>(other)),
+        largeState(NULL)
+    {
+        largeState = other.largeState;
+        other.largeState = NULL;
+    }
+#endif  // SEQAN_CXX11_STANDARD
+
+    ~PatternState_()
+    {
+        delete largeState;
+    }
+
+    PatternState_ &
+    operator = (PatternState_ const & other)
+    {
         TSmallState::operator=(other);
-		if (other.largeState)
-		{
-			if (largeState == NULL)
-				largeState = new TLargeState;
-			(*largeState) = *(other.largeState);
-		} else {
-			delete largeState;
+        if (other.largeState)
+        {
+            if (largeState == NULL)
+                largeState = new TLargeState;
+            (*largeState) = *(other.largeState);
+        } else {
+            delete largeState;
             largeState = NULL;
         }
-		return *this;
-	}
+        return *this;
+    }
+
+#ifdef SEQAN_CXX11_STANDARD
+    // Add move assignment.
+    PatternState_&
+    operator=(PatternState_ && other)
+    {
+        TSmallState::operator=(std::forward<PatternState_>(other));
+        delete largeState;
+        largeState = NULL; // *this is now in a valid state in case of self assignment.
+        largeState = other.largeState;
+        other.largeState = NULL;  // We moved the data.
+        return *this;
+    }
+#endif  // SEQAN_CXX11_STANDARD
 };
 
 
 //////////////////////////////////////////////////////////////////////////////
 // Pattern Data
 //////////////////////////////////////////////////////////////////////////////
- 
+
 template <typename TNeedle, typename TSpec>
 struct MyersSmallPattern_
 {
 #ifdef SEQAN_SSE2_INT128
-	typedef Sse2Int128 TWord;
+    typedef Sse2Int128 TWord;
 #else
-	typedef unsigned long TWord;
+    typedef unsigned long TWord;
 #endif
 
-	String<TWord> bitMasks;		// encode the needle with bitmasks for each alphabet character
-	unsigned needleSize;        // needle size
+    Holder<TNeedle> data_host;   // Hold a reference to the needle
+    String<TWord> bitMasks;        // encode the needle with bitmasks for each alphabet character
+    unsigned needleSize;        // needle size
 
     MyersSmallPattern_():
         needleSize(0) {}
@@ -422,16 +370,16 @@ template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatte
 struct MyersSmallPattern_<TNeedle, AlignTextBanded<TSpec, TFinderCSP, TPatternCSP> >
 {
 #ifdef SEQAN_SSE2_INT128
-	typedef Sse2Int128 TWord;
+    typedef Sse2Int128 TWord;
 #else
 #ifdef SEQAN_DEBUG_MYERSBITVECTOR
-	typedef unsigned char TWord;
+    typedef unsigned char TWord;
 #else
-	typedef unsigned long TWord;
+    typedef unsigned long TWord;
 #endif
 #endif
 
-	Holder<TNeedle> data_host;  // needle holder (the banded version needs no preprocessed bitmasks)
+    Holder<TNeedle> data_host;  // needle holder (the banded version needs no preprocessed bitmasks)
 };
 
 // large basic pattern
@@ -439,13 +387,13 @@ template <typename TNeedle, typename TSpec>
 struct MyersLargePattern_
 {
 #ifdef SEQAN_SSE2_INT128
-	typedef Sse2Int128 TWord;
+    typedef Sse2Int128 TWord;
 #else
-	typedef unsigned long TWord;
+    typedef unsigned long TWord;
 #endif
 
-	unsigned blockCount;		// the number of blocks
-	TWord finalScoreMask;		// a mask with a bit set on the position of the last row
+    unsigned blockCount;        // the number of blocks
+    TWord finalScoreMask;        // a mask with a bit set on the position of the last row
 };
 template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP>
 struct MyersLargePattern_<TNeedle, AlignTextBanded<TSpec, TFinderCSP, TPatternCSP> > {};
@@ -455,59 +403,79 @@ template <typename TNeedle, typename TSpec, typename THasState, typename TFindBe
 class Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >:
     public MyersSmallPattern_<TNeedle, TSpec>,
     public FindBegin_<Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > >,
-	public PatternState_<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >
+    public PatternState_<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >
 {
-	
+
 public:
     typedef MyersSmallPattern_<TNeedle, TSpec>      TSmallPattern;
     typedef MyersLargePattern_<TNeedle, TSpec>      TLargePattern;
     typedef typename TSmallPattern::TWord           TWord;
-	
-	enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
 
-	typedef PatternState_<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > TPatternState;
+    enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
+
+    typedef PatternState_<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > TPatternState;
 
-	TLargePattern *largePattern;	// extra preprocessing info for large patterns
+    TLargePattern *largePattern;    // extra preprocessing info for large patterns
 
 //____________________________________________________________________________
 
-	Pattern():
-		largePattern(NULL) {}
+    Pattern():
+        largePattern(NULL) {}
 
-	Pattern(int _limit):
-		largePattern(NULL) 
-	{
-		setScoreLimit(*this, _limit);
-	}
+    Pattern(int _limit):
+        largePattern(NULL)
+    {
+        setScoreLimit(*this, _limit);
+    }
 
-	Pattern(Pattern const & other) :
+    Pattern(Pattern const & other) :
         TSmallPattern(other),
         TPatternState(other),
         largePattern(NULL)
-	{
-		if (other.largePattern)
-			largePattern = new TLargePattern(*other.largePattern);
-	}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl, int _limit = -1):
-		largePattern(NULL)
-	{
-		setScoreLimit(*this, _limit);
-		setHost(*this, ndl);
-	}
-
-	~Pattern()
-	{
-		delete largePattern;
-	}
-
-	Pattern &
-	operator = (Pattern const & other)
-	{
+    {
+        if (other.largePattern)
+            largePattern = new TLargePattern(*other.largePattern);
+    }
+
+#ifdef SEQAN_CXX11_STANDARD
+    // Add move constructor.
+    Pattern(Pattern && other) :
+        TSmallPattern(std::forward<Pattern>(other)),
+        TPatternState(std::forward<Pattern>(other)),
+        largePattern(NULL)
+    {
+		largePattern = other.largePattern;
+		other.largePattern = NULL;
+    }
+
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl, int _limit = -1) :
+        largePattern(NULL)
+    {
+        setScoreLimit(*this, _limit);
+        setHost(*this, std::forward<TNeedle2>(ndl));
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl, int _limit = -1):
+        largePattern(NULL)
+    {
+        setScoreLimit(*this, _limit);
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
+
+    ~Pattern()
+    {
+        delete largePattern;
+    }
+
+    Pattern &
+    operator = (Pattern const & other)
+    {
         TSmallPattern::operator=(other);
         TPatternState::operator=(other);
-		if (other.largePattern)
+        if (other.largePattern)
         {
             if (largePattern == NULL)
                 largePattern = new TLargePattern;
@@ -516,8 +484,23 @@ class Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >:
             delete largePattern;
             largePattern = NULL;
         }
-		return *this;
-	}
+        return *this;
+    }
+
+#ifdef SEQAN_CXX11_STANDARD
+    // Add move assignment.
+    Pattern &
+    operator= (Pattern && other)
+    {
+        TSmallPattern::operator=(std::forward<Pattern>(other));
+        TPatternState::operator=(std::forward<Pattern>(other));
+        delete largePattern;  // delete old data.
+        largePattern = NULL;  // *this is now in a valid state in case of self-assignment.
+        largePattern = other.largePattern;  // Move data.
+        other.largePattern = NULL;  // Reset other to default.
+        return *this;
+    }
+#endif  // SEQAN_CXX11_STANDARD
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -525,14 +508,14 @@ class Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >:
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
-struct FindBeginPatternSpec <Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > > 
+struct FindBeginPatternSpec <Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > >
 {
-	typedef TFindBeginPatternSpec Type;
+    typedef TFindBeginPatternSpec Type;
 };
 template <typename TNeedle, typename THasState, typename TFindBeginPatternSpec>
 struct FindBeginPatternSpec <Pattern<TNeedle, Myers<FindPrefix, THasState, TFindBeginPatternSpec> > >
 {// no find begin for FindPrefix
-	typedef void Type;
+    typedef void Type;
 };
 
 
@@ -542,7 +525,7 @@ struct PatternState {};
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
 struct PatternState<Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > >
 {
-	typedef PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > Type;
+    typedef PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > Type;
 };
 
 
@@ -552,89 +535,89 @@ struct PatternState<Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSp
 
 
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec, typename TNeedle2>
-inline void _patternFirstInit(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern, 
-							  TNeedle2 & needle)
+inline void _patternFirstInit(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern,
+                              TNeedle2 & needle)
 {
 SEQAN_CHECKPOINT
 
-	typedef typename Pattern<TNeedle, Myers<TSpec, TFindBeginPatternSpec> >::TWord TWord;
-	typedef typename Value<TNeedle>::Type TValue;
+    typedef typename Pattern<TNeedle, Myers<TSpec, TFindBeginPatternSpec> >::TWord TWord;
+    typedef typename Value<TNeedle>::Type TValue;
 
-	pattern.needleSize = length(needle);
-	unsigned blockCount = (pattern.needleSize + pattern.MACHINE_WORD_SIZE - 1) / pattern.MACHINE_WORD_SIZE;
+    pattern.needleSize = length(needle);
+    unsigned blockCount = (pattern.needleSize + pattern.MACHINE_WORD_SIZE - 1) / pattern.MACHINE_WORD_SIZE;
 
-	if (blockCount > 1) 
-	{
-		if (pattern.largePattern == NULL)
-			pattern.largePattern = new MyersLargePattern_<TNeedle, TSpec>();
+    if (blockCount > 1)
+    {
+        if (pattern.largePattern == NULL)
+            pattern.largePattern = new MyersLargePattern_<TNeedle, TSpec>();
 
-		pattern.largePattern->blockCount = blockCount;
-		pattern.largePattern->finalScoreMask = (TWord)1 << ((pattern.needleSize + pattern.MACHINE_WORD_SIZE - 1) % pattern.MACHINE_WORD_SIZE);
-	} 
-	else 
-	{
-		delete pattern.largePattern;
-		pattern.largePattern = NULL;
-	}
+        pattern.largePattern->blockCount = blockCount;
+        pattern.largePattern->finalScoreMask = (TWord)1 << ((pattern.needleSize + pattern.MACHINE_WORD_SIZE - 1) % pattern.MACHINE_WORD_SIZE);
+    }
+    else
+    {
+        delete pattern.largePattern;
+        pattern.largePattern = NULL;
+    }
 
-	clear(pattern.bitMasks);
-	resize(pattern.bitMasks, (ValueSize<TValue>::VALUE + 1) * blockCount, 0, Exact());
+    clear(pattern.bitMasks);
+    resize(pattern.bitMasks, (ValueSize<TValue>::VALUE + 1) * blockCount, 0, Exact());
 
-	// encoding the letters as bit-vectors
+    // encoding the letters as bit-vectors
     for (unsigned j = 0; j < pattern.needleSize; j++)
-		pattern.bitMasks[
-			blockCount * ordValue(convert<typename Value<TNeedle>::Type>(getValue(needle, j)))
-			+ j / pattern.MACHINE_WORD_SIZE
-		] |= (TWord)1 << (j % pattern.MACHINE_WORD_SIZE);
-		//pattern.bitMasks[pattern.blockCount * ordValue((CompareType< Value< TNeedle >::Type, Value< Container< THaystack >::Type >::Type >::Type) needle[j]) + j/pattern.MACHINE_WORD_SIZE] = pattern.bitMasks[pattern.blockCount * ordValue((CompareType< Value< TNeedle >::Type, Value< Container< THaystack >::Type >::Type >::Type) needle[j]) + j/MACHINE_WORD_SIZE] | ((TWord)1 << (j%MACHINE_WORD_SIZE));
-		
-	_findBeginInit(pattern, needle);
+        pattern.bitMasks[
+            blockCount * ordValue(convert<typename Value<TNeedle>::Type>(getValue(needle, j)))
+            + j / pattern.MACHINE_WORD_SIZE
+        ] |= (TWord)1 << (j % pattern.MACHINE_WORD_SIZE);
+        //pattern.bitMasks[pattern.blockCount * ordValue((CompareType< Value< TNeedle >::Type, Value< Container< THaystack >::Type >::Type >::Type) needle[j]) + j/pattern.MACHINE_WORD_SIZE] = pattern.bitMasks[pattern.blockCount * ordValue((CompareType< Value< TNeedle >::Type, Value< Container< THaystack >::Type >::Type >::Type) needle[j]) + j/MACHINE_WORD_SIZE] | ((TWord)1 << (j%MACHINE_WORD_SIZE));
+
+    _findBeginInit(pattern, needle);
 }
 
 
 template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename THasState, typename TFindBeginPatternSpec, typename TNeedle2>
 inline void _patternFirstInit(Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, THasState, TFindBeginPatternSpec> > & pattern,
-							  TNeedle2 & ndl)
+                              TNeedle2 & ndl)
 {
-	_findBeginInit(pattern, ndl);
+    _findBeginInit(pattern, ndl);
 }
 
 
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
 inline void _patternMatchNOfPatternImpl(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern,
-										bool match)
+                                        bool match)
 {
-	typedef typename Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >::TWord TWord;
-	unsigned blockCount = (pattern.largePattern == NULL)? 1: pattern.largePattern->blockCount;
-
-	// letters are encoded as bit-vectors
-	for (unsigned j = 0; j < pattern.needleSize; j++)
-	{
-		TWord bit = (TWord)1 << (j % pattern.MACHINE_WORD_SIZE);
-		bool allNull = true;
-		int idx = j / pattern.MACHINE_WORD_SIZE;
-
-		for (int i = 0; i < 4; ++i, idx += blockCount)
-			allNull &= (pattern.bitMasks[idx] & bit) == (TWord)0;
-
-		if (allNull)
-		{	// all bits are 0 => this letter must be 'N'
-			if (match)
-			{
-				for (; idx >= 0; idx -= blockCount)
-					pattern.bitMasks[idx] |= bit;
-			} else
-			{
-				for (; idx >= 0; idx -= blockCount)
-					pattern.bitMasks[idx] &= ~bit;
-			}
-		}
-	}
+    typedef typename Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >::TWord TWord;
+    unsigned blockCount = (pattern.largePattern == NULL)? 1: pattern.largePattern->blockCount;
+
+    // letters are encoded as bit-vectors
+    for (unsigned j = 0; j < pattern.needleSize; j++)
+    {
+        TWord bit = (TWord)1 << (j % pattern.MACHINE_WORD_SIZE);
+        bool allNull = true;
+        int idx = j / pattern.MACHINE_WORD_SIZE;
+
+        for (int i = 0; i < 4; ++i, idx += blockCount)
+            allNull &= (pattern.bitMasks[idx] & bit) == (TWord)0;
+
+        if (allNull)
+        {    // all bits are 0 => this letter must be 'N'
+            if (match)
+            {
+                for (; idx >= 0; idx -= blockCount)
+                    pattern.bitMasks[idx] |= bit;
+            } else
+            {
+                for (; idx >= 0; idx -= blockCount)
+                    pattern.bitMasks[idx] &= ~bit;
+            }
+        }
+    }
 }
 
 
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
-inline void 
+inline void
 _patternMatchNOfPattern(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern, bool match)
 {
     SEQAN_CHECKPOINT;
@@ -644,7 +627,7 @@ _patternMatchNOfPattern(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatte
 
 
 template <typename TNeedle, typename TSpec, typename THasState>
-inline void 
+inline void
 _patternMatchNOfPattern(Pattern<TNeedle, Myers<TSpec, THasState, void> > & pattern, bool match)
 {
     SEQAN_CHECKPOINT;
@@ -653,28 +636,28 @@ _patternMatchNOfPattern(Pattern<TNeedle, Myers<TSpec, THasState, void> > & patte
 
 
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
-inline void 
+inline void
 _patternMatchNOfFinderImpl(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern, bool match)
 {
-	SEQAN_CHECKPOINT;
-
-	typedef typename Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >::TWord TWord;
-	unsigned blockCount = (pattern.largePattern == NULL)? 1: pattern.largePattern->blockCount;
-
-	// letters are encoded as bit-vectors
-	if (match)
-	{
-		for (unsigned j = 0; j < pattern.needleSize; j++)
-			pattern.bitMasks[blockCount * 4 + j / pattern.MACHINE_WORD_SIZE] |= (TWord)1 << (j % pattern.MACHINE_WORD_SIZE);
-	} else {
-		for (unsigned j = 0; j < pattern.needleSize; j++)
-			pattern.bitMasks[blockCount * 4 + j / pattern.MACHINE_WORD_SIZE] &= ~((TWord)1 << (j % pattern.MACHINE_WORD_SIZE));
-	}
+    SEQAN_CHECKPOINT;
+
+    typedef typename Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >::TWord TWord;
+    unsigned blockCount = (pattern.largePattern == NULL)? 1: pattern.largePattern->blockCount;
+
+    // letters are encoded as bit-vectors
+    if (match)
+    {
+        for (unsigned j = 0; j < pattern.needleSize; j++)
+            pattern.bitMasks[blockCount * 4 + j / pattern.MACHINE_WORD_SIZE] |= (TWord)1 << (j % pattern.MACHINE_WORD_SIZE);
+    } else {
+        for (unsigned j = 0; j < pattern.needleSize; j++)
+            pattern.bitMasks[blockCount * 4 + j / pattern.MACHINE_WORD_SIZE] &= ~((TWord)1 << (j % pattern.MACHINE_WORD_SIZE));
+    }
 }
 
 
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
-inline void 
+inline void
 _patternMatchNOfFinder(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern, bool match)
 {
     SEQAN_CHECKPOINT;
@@ -684,130 +667,39 @@ _patternMatchNOfFinder(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatter
 
 
 template <typename TNeedle, typename TSpec, typename THasState>
-inline void 
+inline void
 _patternMatchNOfFinder(Pattern<TNeedle, Myers<TSpec, THasState, void> > & pattern, bool match)
 {
     SEQAN_CHECKPOINT;
     _patternMatchNOfFinderImpl(pattern, match);
 }
 
-
-// data_host is not used anymore, the needle can be reconstructed from the bitmasks
-template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec, typename TNeedle2>
-inline void
-_myersSetHost(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > &, TNeedle2 const &)
-{
-}
-
-template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename THasState, typename TFindBeginPatternSpec, typename TNeedle2>
-inline void
-_myersSetHost(Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, THasState, TFindBeginPatternSpec> > & pattern, TNeedle2 const & ndl)
-{
-	setValue(pattern.data_host, ndl);
-}
-
-template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec, typename TNeedle2>
-inline void
-setHost(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern, TNeedle2 & ndl)
-{
-	_myersSetHost(pattern, ndl);
-	_patternFirstInit(pattern, ndl);
-}
-
-
-template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec, typename TNeedle2>
-inline void
-setHost(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern, TNeedle2 const & ndl)
-{
-	_myersSetHost(pattern, ndl);
-	_patternFirstInit(pattern, ndl);
-}
-
-
-//____________________________________________________________________________
-
-
-template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename THasState, typename TFindBeginPatternSpec>
-inline typename Host<Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, THasState, TFindBeginPatternSpec> > >::Type & 
-host(Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, THasState, TFindBeginPatternSpec> > & pattern)
-{
-SEQAN_CHECKPOINT
-	return value(pattern.data_host);
-}
-
-
-template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename THasState, typename TFindBeginPatternSpec>
-inline typename Host<Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, THasState, TFindBeginPatternSpec> > const>::Type & 
-host(Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, THasState, TFindBeginPatternSpec> > const & pattern)
-{
-SEQAN_CHECKPOINT
-	return value(pattern.data_host);
-}
-
-
-template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
-inline TNeedle
-host(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern)
-{
-SEQAN_CHECKPOINT
-
-	typedef typename Pattern<TNeedle, Myers<TSpec, TFindBeginPatternSpec> >::TWord TWord;
-	typedef typename Value<TNeedle>::Type TValue;
-
-	TNeedle temp;
-	resize(temp, pattern.needleSize, Exact());
-
-	unsigned blockCount = (pattern.needleSize + pattern.MACHINE_WORD_SIZE - 1) / pattern.MACHINE_WORD_SIZE;
-	TValue v = TValue();
-	for (unsigned i = 0; i < length(pattern.bitMasks); i += blockCount)
-	{
-		for (unsigned j = 0; j < pattern.needleSize; j++)
-			if ((pattern.bitMasks[i + j / pattern.MACHINE_WORD_SIZE] & (TWord)1 << (j % pattern.MACHINE_WORD_SIZE)) != (TWord)0)
-				temp[j] = v;
-		++v;
-	}
-	return temp;
-}
-
-template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
-inline TNeedle
-host(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern)
-{
-SEQAN_CHECKPOINT
-	typedef Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > TPattern;
-	return host(const_cast<TPattern const &>(pattern));
-}
-
-//____________________________________________________________________________
-
-template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
-inline TNeedle
-needle(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern)
-{
-SEQAN_CHECKPOINT
-	return host(pattern);
-}
-
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
-inline TNeedle
-needle(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern)
+inline void
+_reinitPattern(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > & pattern)
 {
-SEQAN_CHECKPOINT
-	typedef Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > TPattern;
-	return host(const_cast<TPattern const &>(pattern));
+    _patternFirstInit(pattern, needle(pattern));
 }
 
 //____________________________________________________________________________
-
-///.Function.scoreLimit.param.pattern.type:Spec.Myers
-///.Function.scoreLimit.class:Spec.Myers
+/*!
+ * @fn MyersPattern#scoreLimit
+ * @headerfile <seqan/find.h>
+ * @brief The minimal score a match must reach in approximate searching.
+ *
+ * @signature TScoreValue scoreLimit(pattern);
+ *
+ * @param[in] pattern The pattern to query.
+ *
+ * @return TScoreValue The score limit value.
+ */
 
 template <typename TNeedle, typename TSpec, typename TFindBeginPatternSpec>
-inline int 
+inline int
 scoreLimit(PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > const & state)
 {
 SEQAN_CHECKPOINT
-	return - (int) state.maxErrors;
+    return - (int) state.maxErrors;
 }
 
 template <typename TNeedle, typename TSpec, typename TFindBeginPatternSpec>
@@ -815,17 +707,26 @@ inline int
 scoreLimit(Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > const & pattern)
 {
 SEQAN_CHECKPOINT
-	return - (int) pattern.maxErrors;
+    return - (int) pattern.maxErrors;
 }
 
 
 //____________________________________________________________________________
-
-///.Function.setScoreLimit.param.pattern.type:Spec.Myers
-///.Function.setScoreLimit.class.type:Spec.Myers
+/*!
+ * @fn MyersPattern#setSoreLimit
+ * @headerfile <seqan/find.h>
+ * @brief Set the minimal score a match must reach in approximate serach.
+ *
+ * @signature void setScoreLimit(pattern, limit);
+ *
+ * @param[in,out] pattern The pattern to set the limit for.
+ * @param[in]     limit   The limit score value to set.
+ *
+ * @return TScoreValue The score limit value.
+ */
 
 template <typename TNeedle, typename TSpec, typename TFindBeginPatternSpec, typename TScoreValue>
-inline void 
+inline void
 setScoreLimit(PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & state,
            TScoreValue minScore)
 {
@@ -835,8 +736,8 @@ SEQAN_CHECKPOINT
     state.maxErrors = -minScore;
 }
 template <typename TNeedle, typename TSpec, typename TFindBeginPatternSpec, typename TScoreValue>
-inline void 
-setScoreLimit(Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & pattern, 
+inline void
+setScoreLimit(Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & pattern,
            TScoreValue minScore)
 {
 SEQAN_CHECKPOINT
@@ -848,63 +749,72 @@ SEQAN_CHECKPOINT
 
 
 //____________________________________________________________________________
-
-///.Function.getScore.param.pattern.type:Spec.Myers
-///.Function.getScore.class:Spec.Myers
+/*!
+ * @fn MyersPattern#getScore
+ * @headerfile <seqan/find.h>
+ * @brief Score of the last found match in approximate searching.
+ *
+ * @signature TScoreValue getScore(pattern);
+ *
+ * @param[in] pattern A myers pattern that can be used for approximate searching.
+ *
+ * @return TScoreValue The score of the last match found using <tt>pattern</tt>.  If no match was found then the value
+ *                     is undefined.
+ */
 
 template <typename TNeedle, typename TSpec, typename TFindBeginPatternSpec>
-inline int 
+inline int
 getScore(PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > const & state)
 {
-	return -(int)state.errors;
+    return -(int)state.errors;
 }
 template<typename TNeedle, typename TSpec, typename TFindBeginPatternSpec>
-inline int 
+inline int
 getScore(Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > const & state)
 {
-	return -(int)state.errors;
+    return -(int)state.errors;
 }
 
 
 template <typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec, typename TFinder>
-inline bool 
-_patternInit(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern, 
-		     PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & state,
-		     TFinder &)
+inline bool
+_patternInit(Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
+             PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & state,
+             TFinder &)
 {
 SEQAN_CHECKPOINT
     typedef MyersLargeState_<TNeedle, TSpec> TLargeState;
     typedef typename TLargeState::TWord TWord;
 
-	if (pattern.largePattern == NULL)
-	{
-		state.errors = pattern.needleSize;
-		state.VP0 = ~(TWord)0;
-		state.VN0 = 0;
+    if (pattern.largePattern == NULL)
+    {
+        state.errors = pattern.needleSize;
+        state.VP0 = ~(TWord)0;
+        state.VN0 = 0;
         delete state.largeState;
         state.largeState = NULL;
-	} 
-	else 
-	{
-		if (state.largeState == NULL)
-			state.largeState = new TLargeState;
-		
-		TLargeState &largeState = *state.largeState;
-		// localMaxErrors either stores the maximal number of errors (me.maxErrors) or the needle size minus one.
-		// It is used for the mask computation and setting the initial score (the minus one is there because of the Ukkonen trick).
-		int localMaxErrors = _min(state.maxErrors, pattern.needleSize - 1);
-		state.errors = localMaxErrors + 1;
-		largeState.scoreMask = (TWord)1 << (localMaxErrors % pattern.MACHINE_WORD_SIZE);
-		largeState.lastBlock = localMaxErrors / pattern.MACHINE_WORD_SIZE; 
-		if (largeState.lastBlock >= pattern.largePattern->blockCount)
-			largeState.lastBlock = pattern.largePattern->blockCount - 1;
-
-		clear(largeState.VP);
-		resize(largeState.VP, pattern.largePattern->blockCount, ~(TWord)0, Exact());
-
-		clear(largeState.VN);
-		resize(largeState.VN, pattern.largePattern->blockCount, 0, Exact());
-	}
+    }
+    else
+    {
+        if (state.largeState == NULL)
+            state.largeState = new TLargeState;
+
+        TLargeState &largeState = *state.largeState;
+        // localMaxErrors either stores the maximal number of errors (me.maxErrors) or the needle size minus one.
+        // It is used for the mask computation and setting the initial score (the minus one is there because of the Ukkonen trick).
+        int localMaxErrors = _min(state.maxErrors, pattern.needleSize - 1);
+        state.errors = localMaxErrors + 1;
+        largeState.scoreMask = (TWord)1 << (localMaxErrors % pattern.MACHINE_WORD_SIZE);
+        largeState.lastBlock = localMaxErrors / pattern.MACHINE_WORD_SIZE;
+        if (largeState.lastBlock >= pattern.largePattern->blockCount)
+            largeState.lastBlock = pattern.largePattern->blockCount - 1;
+
+        clear(largeState.VP);
+        resize(largeState.VP, pattern.largePattern->blockCount, ~(TWord)0, Exact());
+
+        clear(largeState.VN);
+        resize(largeState.VN, pattern.largePattern->blockCount, 0, Exact());
+    }
     return true;
 }
 
@@ -912,35 +822,35 @@ SEQAN_CHECKPOINT
 // bitmask operations - small alphabet
 
 template <typename TNeedle, typename TSpec>
-finline void 
-_myersPreInit(PatternState_<TNeedle, TSpec> &state, True) 
+finline void
+_myersPreInit(PatternState_<TNeedle, TSpec> &state, True)
 {
-	typedef typename Value<TNeedle>::Type TValue;
+    typedef typename Value<TNeedle>::Type TValue;
     for (unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
         state.bitMasks[i] = 0;
 }
 
 template <typename TNeedle, typename TSpec>
-finline void 
-_myersPostInit(PatternState_<TNeedle, TSpec> &state, True) 
+finline void
+_myersPostInit(PatternState_<TNeedle, TSpec> &state, True)
 {
-	typedef typename Value<TNeedle>::Type TValue;
-	for (unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
-		state.bitMasks[i] >>= 1;
+    typedef typename Value<TNeedle>::Type TValue;
+    for (unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
+        state.bitMasks[i] >>= 1;
 }
 
 template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename TFindBeginPatternSpec, typename TValue, typename TShift>
-finline void 
-_myersAdjustBitmask(PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > &state, TValue const value, TShift, True) 
+finline void
+_myersAdjustBitmask(PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > &state, TValue const value, TShift, True)
 {
-	typedef typename PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> >::TWord TWord;
-    
+    typedef typename PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> >::TWord TWord;
+
     // compiler will optimize that
     if (IsSameType<TPatternCSP, NMatchesAll_>::VALUE && value == unknownValue<TValue>())
     {
         for (unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
             state.bitMasks[i] = (state.bitMasks[i] >> 1) | ((TWord)1 << (BitsPerValue<TWord>::VALUE - 1));
-    } 
+    }
     else
     {
         for (unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
@@ -957,9 +867,9 @@ _myersAdjustBitmask(PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderC
 
 template <typename TNeedle, typename TSpec, typename TValue, typename TShift>
 finline typename PatternState_<TNeedle, TSpec>::TWord
-_myersGetBitmask(PatternState_<TNeedle, TSpec> &state, TValue const value, TShift, True) 
+_myersGetBitmask(PatternState_<TNeedle, TSpec> &state, TValue const value, TShift, True)
 {
-	return state.bitMasks[ordValue(value)];
+    return state.bitMasks[ordValue(value)];
 }
 
 
@@ -968,63 +878,63 @@ _myersGetBitmask(PatternState_<TNeedle, TSpec> &state, TValue const value, TShif
 // bitmask operations - large alphabet
 
 template <typename TNeedle, typename TSpec>
-finline void 
-_myersPreInit(PatternState_<TNeedle, TSpec> &state, False) 
+finline void
+_myersPreInit(PatternState_<TNeedle, TSpec> &state, False)
 {
-	typedef typename Value<TNeedle>::Type TValue;
+    typedef typename Value<TNeedle>::Type TValue;
     memset(state.bitMasks, 0, (ValueSize<TValue>::VALUE + 1) * sizeof(state.bitMasks[0]));
     memset(state.shift, 0, ValueSize<TValue>::VALUE * sizeof(state.shift[0]));
 }
 
 template <typename TNeedle, typename TSpec>
-finline void 
-_myersPostInit(PatternState_<TNeedle, TSpec> &, False) 
+finline void
+_myersPostInit(PatternState_<TNeedle, TSpec> &, False)
 {
 }
 
 template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename TFindBeginPatternSpec, typename TValue, typename TShift>
-finline void 
-_myersAdjustBitmask(PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > &state, TValue const value, TShift const shift, False) 
+finline void
+_myersAdjustBitmask(PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > &state, TValue const value, TShift const shift, False)
 {
-	typedef typename PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> >::TWord TWord;
-    
+    typedef typename PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> >::TWord TWord;
+
     if (IsSameType<TPatternCSP, NMatchesNone_>::VALUE && value == unknownValue<TValue>())
         return;
-    
-    register unsigned ord = ordValue(value);
-	register unsigned short x = shift - state.shift[ord];
-	if (x < BitsPerValue<TWord>::VALUE)
-		state.bitMasks[ord] = (state.bitMasks[ord] >> x) | ((TWord)1 << (BitsPerValue<TWord>::VALUE - 1));
-	else
-		state.bitMasks[ord] = (TWord)1 << (BitsPerValue<TWord>::VALUE - 1);
-	state.shift[ord] = shift;
+
+    unsigned ord = ordValue(value);
+    unsigned short x = shift - state.shift[ord];
+    if (x < BitsPerValue<TWord>::VALUE)
+        state.bitMasks[ord] = (state.bitMasks[ord] >> x) | ((TWord)1 << (BitsPerValue<TWord>::VALUE - 1));
+    else
+        state.bitMasks[ord] = (TWord)1 << (BitsPerValue<TWord>::VALUE - 1);
+    state.shift[ord] = shift;
 }
 
 template <typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename TFindBeginPatternSpec, typename TValue, typename TShift>
 finline typename PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> >::TWord
-_myersGetBitmask(PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > &state, TValue const value, TShift const shift, False) 
+_myersGetBitmask(PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > &state, TValue const value, TShift const shift, False)
 {
-	typedef typename PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> >::TWord TWord;
+    typedef typename PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> >::TWord TWord;
 
     if (IsSameType<TFinderCSP, NMatchesNone_>::VALUE && value == unknownValue<TValue>())
         return 0;
 
     if (IsSameType<TFinderCSP, NMatchesAll_>::VALUE && value == unknownValue<TValue>())
         return (shift < BitsPerValue<TWord>::VALUE)? -1 << shift: -1;
-    
-    register unsigned ord = ordValue(value);
-    register TWord res;
-    register TShift x = shift - state.shift[ord];
-	if (x < BitsPerValue<TWord>::VALUE) 
-		res = state.bitMasks[ord] >> x;
-	else
-		res = 0;
-    
+
+    unsigned ord = ordValue(value);
+    TWord res;
+    TShift x = shift - state.shift[ord];
+    if (x < BitsPerValue<TWord>::VALUE)
+        res = state.bitMasks[ord] >> x;
+    else
+        res = 0;
+
     if (IsSameType<TPatternCSP, NMatchesAll_>::VALUE)
     {
         ord = ordValue(unknownValue<TValue>());
         x = shift - state.shift[ord];
-        if (x < BitsPerValue<TWord>::VALUE) 
+        if (x < BitsPerValue<TWord>::VALUE)
             res |= state.bitMasks[ord] >> x;
     }
     return res;
@@ -1032,16 +942,16 @@ _myersGetBitmask(PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP,
 
 
 template <typename TFinder, typename TNeedle, typename TNeedle2, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename TFindBeginPatternSpec>
-inline bool 
+inline bool
 _patternInitSmallStateBanded(
     TFinder &finder,
-	TNeedle2 const & needle, 
+    TNeedle2 const & needle,
     PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > & state)
 {
-	typedef Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > TPattern;
-	typedef typename TPattern::TWord TWord;
-	typedef typename Iterator<TNeedle2 const, Standard>::Type TIter;
-	typedef typename Value<TNeedle>::Type TValue;
+    typedef Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > TPattern;
+    typedef typename TPattern::TWord TWord;
+    typedef typename Iterator<TNeedle2 const, Standard>::Type TIter;
+    typedef typename Value<TNeedle>::Type TValue;
 
 #ifdef SEQAN_DEBUG_MYERSBITVECTOR
     int col = state.leftClip + 1;
@@ -1059,167 +969,167 @@ _patternInitSmallStateBanded(
 
     _myersPreInit(state, typename MyersSmallAlphabet_<TValue>::Type());
 
-	typename Size<TNeedle>::Type const ndlLength = length(needle);
-	
-	// Initialize row 0 either with zeros or increasing numbers
-	// This can be realized using the following DP pattern and
-	// assuming character mismatches at rows -1, -2,...
-	// Thus we initialize the bitmasks and VN with 0.
-	// VP depends on global/local alignment
-	//
-	//  0  1  2  3  4   -2 -2 -2 -2 -2   (row -2)
-	//  0  1  2  3  4   -1 -1 -1 -1 -1   (row -1)
-	//  0  1  2  3  4    0  0  0  0  0   (row  0)
-	//  1                1
-	//	    global           local
-	//
-	//  VP = 100...      VP = 111...
-	//
-
-    register TWord VP = (MyersUkkonenHP0_<TSpec>::VALUE == 1)? (TWord)1 << ((int)BitsPerValue<TWord>::VALUE-1): maxValue<TWord>(); // HP[0]==1 <-> global, HP[0]==0 <-> local
-    register TWord VN = 0;
-	
-	// Errors are counted along the lowest diagonal and the
-	// lowest row of the band.
-	// The errors in the top-left corner are 0.
-	//
-	// 0 * * * *
-	//   x * * * *
-	//     x * * * *
-	//       x x x x x
-	//
-	//       |-------|
-	//     diagWidth + 1 = 5
-	//
-	// diagWidth = length(container(finder)) + state.leftClip + state.rightClip - length(needle)
-	
-    register unsigned errors = 0;
-	TIter ndlIter = begin(needle, Standard());
-	TIter ndlEnd;
-	
-	// The errors along the diagonal can only increase or stay the same.
-	// There is only the last row of length diagWidth where errors can decrease.
-	// If errors exceeds cutOff it cannot reach maxErrors again.
-	
-	
-	typename Size<TFinder>::Type const columns = length(container(finder)) + state.leftClip;
-    register unsigned cutOff = state.maxErrors;
-	if (columns > ndlLength)
-	{
-		cutOff += columns - ndlLength;		// clipping case *0
-		ndlEnd = end(needle, Standard());
-	} else {
+    typename Size<TNeedle>::Type const ndlLength = length(needle);
+
+    // Initialize row 0 either with zeros or increasing numbers
+    // This can be realized using the following DP pattern and
+    // assuming character mismatches at rows -1, -2,...
+    // Thus we initialize the bitmasks and VN with 0.
+    // VP depends on global/local alignment
+    //
+    //  0  1  2  3  4   -2 -2 -2 -2 -2   (row -2)
+    //  0  1  2  3  4   -1 -1 -1 -1 -1   (row -1)
+    //  0  1  2  3  4    0  0  0  0  0   (row  0)
+    //  1                1
+    //        global           local
+    //
+    //  VP = 100...      VP = 111...
+    //
+
+    TWord VP = (MyersUkkonenHP0_<TSpec>::VALUE == 1)? (TWord)1 << ((int)BitsPerValue<TWord>::VALUE-1): maxValue<TWord>(); // HP[0]==1 <-> global, HP[0]==0 <-> local
+    TWord VN = 0;
+
+    // Errors are counted along the lowest diagonal and the
+    // lowest row of the band.
+    // The errors in the top-left corner are 0.
+    //
+    // 0 * * * *
+    //   x * * * *
+    //     x * * * *
+    //       x x x x x
+    //
+    //       |-------|
+    //     diagWidth + 1 = 5
+    //
+    // diagWidth = length(container(finder)) + state.leftClip + state.rightClip - length(needle)
+
+    unsigned errors = 0;
+    TIter ndlIter = begin(needle, Standard());
+    TIter ndlEnd;
+
+    // The errors along the diagonal can only increase or stay the same.
+    // There is only the last row of length diagWidth where errors can decrease.
+    // If errors exceeds cutOff it cannot reach maxErrors again.
+
+
+    typename Size<TFinder>::Type const columns = length(container(finder)) + state.leftClip;
+    unsigned cutOff = state.maxErrors;
+    if (columns > ndlLength)
+    {
+        cutOff += columns - ndlLength;        // clipping case *0
+        ndlEnd = end(needle, Standard());
+    } else {
         errors += ndlLength - columns;
-		ndlEnd = ndlIter + columns;			// clipping case *1
-	}
+        ndlEnd = ndlIter + columns;            // clipping case *1
+    }
 
 //    std::cerr<<std::hex<<"\t  "<<std::setw(17)<<' '<<"\tVN"<<std::setw(17)<<VN<<"\tVP"<<std::setw(17)<<VP<<std::dec<<std::endl;
 
-	register unsigned short shift = 0;
-	
-	if (state.leftClip != 0)
-	{
-		//////////////////////////////////////////////////////////////////
-		// PART 0: go down the parallelogram in a empty (clipped) area
-		//////////////////////////////////////////////////////////////////
-
-		errors += state.leftClip;
-		if (errors > ndlLength) errors = ndlLength;
-		if (errors > cutOff) return false;
-
-	// leftClip = 2
-	//   |-|
-	//
-	//   . . * * *
-	//     . * * * *
-	//       * * * * *
-	//         * * * * .
-	//           * * * . .
-	//             * * . . .
-	//
-	//                 |---|
-	//               rightClip = 3
+    unsigned short shift = 0;
+
+    if (state.leftClip != 0)
+    {
+        //////////////////////////////////////////////////////////////////
+        // PART 0: go down the parallelogram in a empty (clipped) area
+        //////////////////////////////////////////////////////////////////
+
+        errors += state.leftClip;
+        if (errors > ndlLength) errors = ndlLength;
+        if (errors > cutOff) return false;
+
+    // leftClip = 2
+    //   |-|
+    //
+    //   . . * * *
+    //     . * * * *
+    //       * * * * *
+    //         * * * * .
+    //           * * * . .
+    //             * * . . .
+    //
+    //                 |---|
+    //               rightClip = 3
+    //
+    // We divide the parallelogam into 3 sections:
+    //
+    //   A A A A
+    //     A A A B
+    //       A A B B
+    //         A B B C
+    //           B B C C
+    //             B C C C
+    //               C C C C
+    //
+    // Depending on where the clipping ends we identify 4 different clipping cases:
+    //
+    //     case 00            case 10            case 01            case 11
+    //   . . * *            . . . .            . . * *            . . . .
+    //     . * * *            . . . *            . * * *            . . . *
+    //       * * * *            . . * *            * * * .            . . * .
+    //         * * * *            . * * *            * * . .            . * . .
+    //           * * * .            * * * .            * . . .            * . . .
+    //             * * . .            * * . .            . . . .            . . . .
     //
-	// We divide the parallelogam into 3 sections:
-	//
-	//   A A A A
-	//     A A A B
-	//       A A B B
-	//         A B B C
-	//           B B C C
-	//             B C C C
-	//               C C C C
-	//
-	// Depending on where the clipping ends we identify 4 different clipping cases:
-	//
-	//	 case 00            case 10            case 01            case 11
-	//   . . * *            . . . .            . . * *            . . . .
-	//     . * * *            . . . *            . * * *            . . . *
-	//       * * * *            . . * *            * * * .            . . * .
-	//         * * * *            . * * *            * * . .            . * . .
-	//           * * * .            * * * .            * . . .            * . . .
-	//             * * . .            * * . .            . . . .            . . . .
-	//
-
-		// adjust bitmasks (errors = number of needle chars to preprocess)
-		for (; shift < errors; ++ndlIter, ++shift)
-			_myersAdjustBitmask(state, getValue(ndlIter), shift, typename MyersSmallAlphabet_<TValue>::Type());
-
-		// initialise left column with
-		//
-		//  0  1  2  3  4   -2 -2 -2 -2 -2
-		//  0  1  2  3  4   -1 -1 -1 -1 -1
-		//  0  1  2  3  4    0  0  0  0  0
-		//  1                1
-		//  2   global       2   local
-		//  3                3
-		//  4                4
-		//
-		//  VP = 111100...   VP = 111111...
-		if (errors < (unsigned)BitsPerValue<TWord>::VALUE-1)
-			VP |= ((TWord) -1) << ((unsigned)BitsPerValue<TWord>::VALUE-1 - errors);
-		else
-			VP = (TWord)-1;
-	}
+
+        // adjust bitmasks (errors = number of needle chars to preprocess)
+        for (; shift < errors; ++ndlIter, ++shift)
+            _myersAdjustBitmask(state, getValue(ndlIter), shift, typename MyersSmallAlphabet_<TValue>::Type());
+
+        // initialise left column with
+        //
+        //  0  1  2  3  4   -2 -2 -2 -2 -2
+        //  0  1  2  3  4   -1 -1 -1 -1 -1
+        //  0  1  2  3  4    0  0  0  0  0
+        //  1                1
+        //  2   global       2   local
+        //  3                3
+        //  4                4
+        //
+        //  VP = 111100...   VP = 111111...
+        if (errors < (unsigned)BitsPerValue<TWord>::VALUE-1)
+            VP |= ((TWord) -1) << ((unsigned)BitsPerValue<TWord>::VALUE-1 - errors);
+        else
+            VP = (TWord)-1;
+    }
 
     for (; ndlIter != ndlEnd; ++ndlIter, goNext(finder), ++shift)
     {
-		//////////////////////////////////////////////////////////////////
+        //////////////////////////////////////////////////////////////////
         // PART 1: go down the parallelogram
-		//////////////////////////////////////////////////////////////////
-        
+        //////////////////////////////////////////////////////////////////
+
         // adjust bitmask
         _myersAdjustBitmask(state, getValue(ndlIter), shift, typename MyersSmallAlphabet_<TValue>::Type());
-        
-		/////////////////////////
+
+        /////////////////////////
         // DIAGONAL MYERS CORE
-		
-		// VP/VN --> D0  (original Myers)
-        register TWord X = _myersGetBitmask(state, ordValue(*finder), shift, typename MyersSmallAlphabet_<TValue>::Type()) | VN;
-        register TWord D0 = ((VP + (X & VP)) ^ VP) | X;
-		
-		// adjust errors corresponding to rightmost bit of D0
+
+        // VP/VN --> D0  (original Myers)
+        TWord X = _myersGetBitmask(state, ordValue(*finder), shift, typename MyersSmallAlphabet_<TValue>::Type()) | VN;
+        TWord D0 = ((VP + (X & VP)) ^ VP) | X;
+
+        // adjust errors corresponding to rightmost bit of D0
         errors += (~D0 >> (BitsPerValue<TWord>::VALUE - 1)) & 1;
         if (errors > cutOff) return false;
 
-		// D0 --> HP/HN  (original Myers)
-        register TWord HN = VP & D0;
-        register TWord HP = VN | ~(VP | D0);
+        // D0 --> HP/HN  (original Myers)
+        TWord HN = VP & D0;
+        TWord HP = VN | ~(VP | D0);
     //    const int PADDING = sizeof(TWord)*2 + 1;
     //    std::cerr << std::hex;
     //    std::cerr << "\tD0"<<std::setw(PADDING)<<(__uint64)D0<<"\tHN"<<std::setw(PADDING)<<(__uint64)HN<<"\tHP"<<std::setw(PADDING)<<(__uint64)HP << std::endl;
 
-		// moving register down corresponds to shifting HP/HN up (right shift)
-		// HP/HN --> shift --> VP/VN (modified Myers)
+        // moving register down corresponds to shifting HP/HN up (right shift)
+        // HP/HN --> shift --> VP/VN (modified Myers)
         X = D0 >> 1;
         VN = X & HP;
         VP = HN | ~(X | HP);
     //    std::cerr << "\t  "<<std::setw(PADDING)<<' '<<"\tVN"<<std::setw(PADDING)<<(__uint64)VN<<"\tVP"<<std::setw(PADDING)<<(__uint64)VP << std::endl;
     //    std::cerr << std::dec;
-    
+
 #ifdef SEQAN_DEBUG_MYERSBITVECTOR
 #ifdef SEQAN_DEBUG_MYERSBITVECTOR_DUMP
-        std::cerr << "diag ";        
+        std::cerr << "diag ";
 #endif
         int val = errors;
         state.DPMat[(col-state.leftClip)*(length(needle)+1)+col] = val;
@@ -1268,16 +1178,16 @@ _patternInitSmallStateBanded(
 
 template <typename TFinder, typename TNeedle, typename TNeedle2, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename TFindBeginPatternSpec>
 bool _stateInit(
-	TFinder &finder,
-	TNeedle const & needle,
-	PatternState_<TNeedle2, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > & state)
+    TFinder &finder,
+    TNeedle const & needle,
+    PatternState_<TNeedle2, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > & state)
 {
-	typedef PatternState_<TNeedle2, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > TState;
+    typedef PatternState_<TNeedle2, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > TState;
     typedef typename TState::TLargeState TLargeState;
 
-//	unsigned diagWidth = length(container(finder)) + state.leftClip - length(needle);
-//	unsigned blockCount = diagWidth / state.MACHINE_WORD_SIZE + 1;
-	unsigned blockCount = 1;
+//    unsigned diagWidth = length(container(finder)) + state.leftClip - length(needle);
+//    unsigned blockCount = diagWidth / state.MACHINE_WORD_SIZE + 1;
+    unsigned blockCount = 1;
 
 //    SEQAN_ASSERT_GEQ(length(container(finder)), length(needle));
 
@@ -1290,35 +1200,35 @@ bool _stateInit(
         state.DPMat[i * (length(needle) + 1)] = 0;
 #endif
 
-	if (blockCount <= 1)
+    if (blockCount <= 1)
     {
         delete state.largeState;
         state.largeState = NULL;
         return _patternInitSmallStateBanded(finder, needle, state);
-	}
-	else
-	{
-		// TODO: is that good here?
-		if (state.largeState == NULL)
-			state.largeState = new TLargeState;
-		
-		TLargeState &largeState = *state.largeState;
+    }
+    else
+    {
+        // TODO: is that good here?
+        if (state.largeState == NULL)
+            state.largeState = new TLargeState;
+
+        TLargeState &largeState = *state.largeState;
         largeState.blockCount = blockCount;
 
-		clear(largeState.VP);
-		resize(largeState.VP, blockCount, ~0, Exact());
+        clear(largeState.VP);
+        resize(largeState.VP, blockCount, ~0, Exact());
+
+        clear(largeState.VN);
+        resize(largeState.VN, blockCount, 0, Exact());
 
-		clear(largeState.VN);
-		resize(largeState.VN, blockCount, 0, Exact());
-        
         state.errors = 0;
-        
+
         return true;
-	}
+    }
 }
 
 template <typename TNeedle, typename TSpec, typename TFindBeginPatternSpec, typename TFinder>
-inline bool 
+inline bool
 _patternInit(Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & pattern, TFinder & finder)
 {
     SEQAN_CHECKPOINT;
@@ -1334,170 +1244,170 @@ _patternInit(Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & patt
 
 
 template <typename TFinder, typename TNeedle, typename TSpec, typename THasState, typename THasState2, typename TFindBeginPatternSpec, typename TSize>
-inline bool _findMyersLargePatterns (TFinder & finder, 
-									 Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
-									 PatternState_<TNeedle, Myers<TSpec, THasState2, TFindBeginPatternSpec> > & state,
-									 TSize haystack_length) 
+inline bool _findMyersLargePatterns (TFinder & finder,
+                                     Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
+                                     PatternState_<TNeedle, Myers<TSpec, THasState2, TFindBeginPatternSpec> > & state,
+                                     TSize haystack_length)
 {
 SEQAN_CHECKPOINT
-	typedef MyersLargePattern_<TNeedle, TSpec> TLargePattern;
-	typedef MyersLargeState_<TNeedle, TSpec> TLargeState;
+    typedef MyersLargePattern_<TNeedle, TSpec> TLargePattern;
+    typedef MyersLargeState_<TNeedle, TSpec> TLargeState;
     typedef typename TLargeState::TWord TWord;
-    
-	TWord X, D0, HN, HP, temp;
-	TWord carryD0, carryHP, carryHN;
-	unsigned shift, limit, currentBlock;
-    
-	TLargePattern &largePattern = *pattern.largePattern;
-	TLargeState &largeState = *state.largeState;
-
-	while (position(finder) < haystack_length) 
-	{
-		carryD0 = carryHN = 0;
-		carryHP = (int)MyersUkkonenHP0_<TSpec>::VALUE; // FIXME: replace Noting with TSpec
-
-		// if the active cell is the last of it's block, one additional block has to be calculated
-		limit = largeState.lastBlock + (unsigned)(largeState.scoreMask >> (pattern.MACHINE_WORD_SIZE - 1));
-
-		if (limit == largePattern.blockCount)
-			limit--;
-
-		shift = largePattern.blockCount * ordValue((typename Value< TNeedle >::Type) *finder);
-
-		// computing the necessary blocks, carries between blocks following one another are stored
-		for (currentBlock = 0; currentBlock <= limit; currentBlock++) 
-		{
-			X = pattern.bitMasks[shift + currentBlock] | largeState.VN[currentBlock];
-	
-			temp = largeState.VP[currentBlock] + (X & largeState.VP[currentBlock]) + carryD0;
-			if (carryD0 != (TWord)0)
-				carryD0 = temp <= largeState.VP[currentBlock];
-			else
-				carryD0 = temp < largeState.VP[currentBlock];
-			
-			D0 = (temp ^ largeState.VP[currentBlock]) | X;
-			HN = largeState.VP[currentBlock] & D0;
-			HP = largeState.VN[currentBlock] | ~(largeState.VP[currentBlock] | D0);
-			
-			X = (HP << 1) | carryHP;
-			carryHP = HP >> (pattern.MACHINE_WORD_SIZE - 1);
-			
-			largeState.VN[currentBlock] = X & D0;
-
-			temp = (HN << 1) | carryHN;
-			carryHN = HN >> (pattern.MACHINE_WORD_SIZE - 1);
-								
-		 	largeState.VP[currentBlock] = temp | ~(X | D0);
-
-			// if the current block is the one containing the last active cell
-			// the new number of errors is computed
-			if (currentBlock == largeState.lastBlock) {
-				if ((HP & largeState.scoreMask) != (TWord)0)
-					state.errors++;
-				else if ((HN & largeState.scoreMask) != (TWord)0)
-					state.errors--;
-			}
-		}
-
-		// updating the last active cell
-		while (state.errors > state.maxErrors) {
-			if ((largeState.VP[largeState.lastBlock] & largeState.scoreMask) != (TWord)0)
-				state.errors--;
-			else if ((largeState.VN[largeState.lastBlock] & largeState.scoreMask) != (TWord)0)
-				state.errors++;
-
-			largeState.scoreMask >>= 1;
-			if (largeState.scoreMask == (TWord)0) 
-			{
-				largeState.lastBlock--;
-				if (IsSameType<TSpec, FindPrefix>::VALUE && largeState.lastBlock == (unsigned)-1)
-					break;
-				largeState.scoreMask = (TWord)1 << (pattern.MACHINE_WORD_SIZE - 1);
-			}
-		}
-
-		if ((largeState.scoreMask == largePattern.finalScoreMask) && (largeState.lastBlock == largePattern.blockCount - 1))
-		{
-			_setFinderEnd(finder);
-			if (IsSameType<TSpec, FindPrefix>::VALUE)
-			{
-				_setFinderLength(finder, endPosition(finder));
-			}
-			return true;
-		}
-		else {
-			largeState.scoreMask <<= 1;
-			if (!largeState.scoreMask) {
-				largeState.scoreMask = 1;
-				largeState.lastBlock++;
-			}
-			
-			if ((largeState.VP[largeState.lastBlock] & largeState.scoreMask) != (TWord)0)
-				state.errors++;
-			else if ((largeState.VN[largeState.lastBlock] & largeState.scoreMask) != (TWord)0)
-				state.errors--;
-		}
-
-//		SEQAN_ASSERT (state.errors >= 0);
-
-		goNext(finder);
-	}
-
-	return false;
+
+    TWord X, D0, HN, HP, temp;
+    TWord carryD0, carryHP, carryHN;
+    unsigned shift, limit, currentBlock;
+
+    TLargePattern &largePattern = *pattern.largePattern;
+    TLargeState &largeState = *state.largeState;
+
+    while (position(finder) < haystack_length)
+    {
+        carryD0 = carryHN = 0;
+        carryHP = (int)MyersUkkonenHP0_<TSpec>::VALUE; // FIXME: replace Noting with TSpec
+
+        // if the active cell is the last of it's block, one additional block has to be calculated
+        limit = largeState.lastBlock + (unsigned)(largeState.scoreMask >> (pattern.MACHINE_WORD_SIZE - 1));
+
+        if (limit == largePattern.blockCount)
+            limit--;
+
+        shift = largePattern.blockCount * ordValue((typename Value< TNeedle >::Type) *finder);
+
+        // computing the necessary blocks, carries between blocks following one another are stored
+        for (currentBlock = 0; currentBlock <= limit; currentBlock++)
+        {
+            X = pattern.bitMasks[shift + currentBlock] | largeState.VN[currentBlock];
+
+            temp = largeState.VP[currentBlock] + (X & largeState.VP[currentBlock]) + carryD0;
+            if (carryD0 != (TWord)0)
+                carryD0 = temp <= largeState.VP[currentBlock];
+            else
+                carryD0 = temp < largeState.VP[currentBlock];
+
+            D0 = (temp ^ largeState.VP[currentBlock]) | X;
+            HN = largeState.VP[currentBlock] & D0;
+            HP = largeState.VN[currentBlock] | ~(largeState.VP[currentBlock] | D0);
+
+            X = (HP << 1) | carryHP;
+            carryHP = HP >> (pattern.MACHINE_WORD_SIZE - 1);
+
+            largeState.VN[currentBlock] = X & D0;
+
+            temp = (HN << 1) | carryHN;
+            carryHN = HN >> (pattern.MACHINE_WORD_SIZE - 1);
+
+             largeState.VP[currentBlock] = temp | ~(X | D0);
+
+            // if the current block is the one containing the last active cell
+            // the new number of errors is computed
+            if (currentBlock == largeState.lastBlock) {
+                if ((HP & largeState.scoreMask) != (TWord)0)
+                    state.errors++;
+                else if ((HN & largeState.scoreMask) != (TWord)0)
+                    state.errors--;
+            }
+        }
+
+        // updating the last active cell
+        while (state.errors > state.maxErrors) {
+            if ((largeState.VP[largeState.lastBlock] & largeState.scoreMask) != (TWord)0)
+                state.errors--;
+            else if ((largeState.VN[largeState.lastBlock] & largeState.scoreMask) != (TWord)0)
+                state.errors++;
+
+            largeState.scoreMask >>= 1;
+            if (largeState.scoreMask == (TWord)0)
+            {
+                largeState.lastBlock--;
+                if (IsSameType<TSpec, FindPrefix>::VALUE && largeState.lastBlock == (unsigned)-1)
+                    break;
+                largeState.scoreMask = (TWord)1 << (pattern.MACHINE_WORD_SIZE - 1);
+            }
+        }
+
+        if ((largeState.scoreMask == largePattern.finalScoreMask) && (largeState.lastBlock == largePattern.blockCount - 1))
+        {
+            _setFinderEnd(finder);
+            if (IsSameType<TSpec, FindPrefix>::VALUE)
+            {
+                _setFinderLength(finder, endPosition(finder));
+            }
+            return true;
+        }
+        else {
+            largeState.scoreMask <<= 1;
+            if (!largeState.scoreMask) {
+                largeState.scoreMask = 1;
+                largeState.lastBlock++;
+            }
+
+            if ((largeState.VP[largeState.lastBlock] & largeState.scoreMask) != (TWord)0)
+                state.errors++;
+            else if ((largeState.VN[largeState.lastBlock] & largeState.scoreMask) != (TWord)0)
+                state.errors--;
+        }
+
+//        SEQAN_ASSERT (state.errors >= 0);
+
+        goNext(finder);
+    }
+
+    return false;
 }
 
 
 template <typename TFinder, typename TNeedle, typename TSpec, typename THasState, typename THasState2, typename TFindBeginPatternSpec, typename TSize>
-inline bool 
+inline bool
 _findMyersSmallPatterns(
-	TFinder & finder, 
-	Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
-	PatternState_<TNeedle, Myers<TSpec, THasState2, TFindBeginPatternSpec> > & state,
-	TSize haystack_length) 
+    TFinder & finder,
+    Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
+    PatternState_<TNeedle, Myers<TSpec, THasState2, TFindBeginPatternSpec> > & state,
+    TSize haystack_length)
 {
 SEQAN_CHECKPOINT
 
-	typedef typename Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >::TWord TWord;
-
-	TWord X, D0, HN, HP;
-	TWord lastBit = (TWord)1 << (pattern.needleSize - 1);
-
-	// computing the blocks
-	while (position(finder) < haystack_length) 
-	{
-		X = pattern.bitMasks[ordValue((typename Value<TNeedle>::Type) *finder)] | state.VN0;
-		
-		D0 = ((state.VP0 + (X & state.VP0)) ^ state.VP0) | X;
-		HN = state.VP0 & D0;
-		HP = state.VN0 | ~(state.VP0 | D0);
-		X = (HP << 1) | (TWord)(int)MyersUkkonenHP0_<TSpec>::VALUE; // FIXME: replace Nothing by TSpec
-		state.VN0 = X & D0;
-		state.VP0 = (HN << 1) | ~(X | D0);
-
-		if ((HP & lastBit) != (TWord)0)
-			state.errors++;
-		else if ((HN & lastBit) != (TWord)0)
-			state.errors--;
-
-		if (state.errors <= state.maxErrors)
-		{
-			_setFinderEnd(finder);
-			if (IsSameType<TSpec, FindPrefix>::VALUE)
-			{
-				_setFinderLength(finder, endPosition(finder));
-			}
-			return true;
-		}
-		// 
-		// if (IsSameType<TSpec, FindPrefix>::VALUE)
-		// {//limit haystack length during prefix search
-		// 
-		// }
-		
-		goNext(finder);
-	}
-
-	return false;
+    typedef typename Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> >::TWord TWord;
+
+    TWord X, D0, HN, HP;
+    TWord lastBit = (TWord)1 << (pattern.needleSize - 1);
+
+    // computing the blocks
+    while (position(finder) < haystack_length)
+    {
+        X = pattern.bitMasks[ordValue((typename Value<TNeedle>::Type) *finder)] | state.VN0;
+
+        D0 = ((state.VP0 + (X & state.VP0)) ^ state.VP0) | X;
+        HN = state.VP0 & D0;
+        HP = state.VN0 | ~(state.VP0 | D0);
+        X = (HP << 1) | (TWord)(int)MyersUkkonenHP0_<TSpec>::VALUE; // FIXME: replace Nothing by TSpec
+        state.VN0 = X & D0;
+        state.VP0 = (HN << 1) | ~(X | D0);
+
+        if ((HP & lastBit) != (TWord)0)
+            state.errors++;
+        else if ((HN & lastBit) != (TWord)0)
+            state.errors--;
+
+        if (state.errors <= state.maxErrors)
+        {
+            _setFinderEnd(finder);
+            if (IsSameType<TSpec, FindPrefix>::VALUE)
+            {
+                _setFinderLength(finder, endPosition(finder));
+            }
+            return true;
+        }
+        //
+        // if (IsSameType<TSpec, FindPrefix>::VALUE)
+        // {//limit haystack length during prefix search
+        //
+        // }
+
+        goNext(finder);
+    }
+
+    return false;
 }
 
 
@@ -1508,54 +1418,54 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////
 
 template <
-    typename TFinder, 
-    typename TNeedle, 
-    typename TNeedle2, 
-    typename TSpec, 
-    typename TFinderCSP, 
+    typename TFinder,
+    typename TNeedle,
+    typename TNeedle2,
+    typename TSpec,
+    typename TFinderCSP,
     typename TPatternCSP,
     typename TFindBeginPatternSpec,
-	typename TDoPatternSearch
+    typename TDoPatternSearch
 >
-inline bool 
+inline bool
 _findMyersSmallPatternsBanded(
-	TFinder & finder, 
-	TNeedle const & needle,
+    TFinder & finder,
+    TNeedle const & needle,
     PatternState_<TNeedle2, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > & state,
-	TDoPatternSearch const)
+    TDoPatternSearch const)
 {
-	typedef PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > TState;
-	typedef typename TState::TWord TWord;
-	typedef typename Value<TNeedle>::Type TValue;
+    typedef PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > TState;
+    typedef typename TState::TWord TWord;
+    typedef typename Value<TNeedle>::Type TValue;
 
-    register TWord VP = state.VP0;
-    register TWord VN = state.VN0;
-    register TWord errors = state.errors;
-    register TWord const maxErrors = state.maxErrors;
-	register unsigned short const shift = length(needle);
+    TWord VP = state.VP0;
+    TWord VN = state.VN0;
+    TWord errors = state.errors;
+    TWord const maxErrors = state.maxErrors;
+    unsigned short const shift = length(needle);
 
 #ifdef SEQAN_DEBUG_MYERSBITVECTOR
     unsigned col = position(finder) + 1;
 #endif
 
-	for (; !atEnd(finder); goNext(finder))
+    for (; !atEnd(finder); goNext(finder))
     {
-		// PART 2: go right
-
-		// normal Myers
-		register TWord X = _myersGetBitmask(state, ordValue(*finder), shift, typename MyersSmallAlphabet_<TValue>::Type()) | VN;
-		register TWord D0 = ((VP + (X & VP)) ^ VP) | X;
-		register TWord HN = VP & D0;
-		register TWord HP = VN | ~(VP | D0);
-	//    const int PADDING = sizeof(TWord)*2 + 1;
-	//    std::cerr << std::hex;
-	//    std::cerr << "\tD0"<<std::setw(PADDING)<<(__uint64)D0<<"\tHN"<<std::setw(PADDING)<<(__uint64)HN<<"\tHP"<<std::setw(PADDING)<<(__uint64)HP<<std::endl;
-		X = (HP << 1) | 1;
-		VN = X & D0;
-		VP = (HN << 1) | ~(X | D0);
-	//    std::cerr << "\t  "<<std::setw(PADDING)<<' '<<"\tVN"<<std::setw(PADDING)<<(__uint64)VN<<"\tVP"<<std::setw(PADDING)<<(__uint64)VP<<std::endl;
-	//    std::cerr << std::dec;
-		errors += (HP >> (BitsPerValue<TWord>::VALUE - 2)) & 1;
+        // PART 2: go right
+
+        // normal Myers
+        TWord X = _myersGetBitmask(state, ordValue(*finder), shift, typename MyersSmallAlphabet_<TValue>::Type()) | VN;
+        TWord D0 = ((VP + (X & VP)) ^ VP) | X;
+        TWord HN = VP & D0;
+        TWord HP = VN | ~(VP | D0);
+    //    const int PADDING = sizeof(TWord)*2 + 1;
+    //    std::cerr << std::hex;
+    //    std::cerr << "\tD0"<<std::setw(PADDING)<<(__uint64)D0<<"\tHN"<<std::setw(PADDING)<<(__uint64)HN<<"\tHP"<<std::setw(PADDING)<<(__uint64)HP<<std::endl;
+        X = (HP << 1) | 1;
+        VN = X & D0;
+        VP = (HN << 1) | ~(X | D0);
+    //    std::cerr << "\t  "<<std::setw(PADDING)<<' '<<"\tVN"<<std::setw(PADDING)<<(__uint64)VN<<"\tVP"<<std::setw(PADDING)<<(__uint64)VP<<std::endl;
+    //    std::cerr << std::dec;
+        errors += (HP >> (BitsPerValue<TWord>::VALUE - 2)) & 1;
         errors -= (HN >> (BitsPerValue<TWord>::VALUE - 2)) & 1;
 
         // shift bitmasks and states
@@ -1591,52 +1501,52 @@ _findMyersSmallPatternsBanded(
         ++col;
 #endif
 
-		if (TDoPatternSearch::VALUE)
-		{
-			// pattern search
-	        if (errors <= maxErrors)
-	        {
-	            state.VP0 = VP;
-	            state.VN0 = VN;
-	            state.errors = errors;
-				_setFinderEnd(finder);
-				if (IsSameType<TSpec, FindPrefix>::VALUE)
-				{
-					_setFinderLength(finder, endPosition(finder));
-				}
-	            return true;
-	        }
-		}
-		else
-		{
-			// edit distance
-		}
+        if (TDoPatternSearch::VALUE)
+        {
+            // pattern search
+            if (errors <= maxErrors)
+            {
+                state.VP0 = VP;
+                state.VN0 = VN;
+                state.errors = errors;
+                _setFinderEnd(finder);
+                if (IsSameType<TSpec, FindPrefix>::VALUE)
+                {
+                    _setFinderLength(finder, endPosition(finder));
+                }
+                return true;
+            }
+        }
+        else
+        {
+            // edit distance
+        }
     }
 
-	if (!TDoPatternSearch::VALUE)
-	{
-		// edit distance
-	    state.errors = errors;
-	}
+    if (!TDoPatternSearch::VALUE)
+    {
+        // edit distance
+        state.errors = errors;
+    }
     return false;
 }
 
 template <typename TSeq1, typename TSeq2>
-inline unsigned 
+inline unsigned
 _computeEditDistanceBanded(
-	TSeq1 const &seq1,
-	TSeq2 const &seq2,
-	unsigned maxErrors)
+    TSeq1 const &seq1,
+    TSeq2 const &seq2,
+    unsigned maxErrors)
 {
-	PatternState_<TSeq2, MyersUkkonenGlobalBanded> state;
-	state.maxErrors = maxErrors;
-	state.leftClip = (length(seq2) - length(seq1) + maxErrors) / 2;
-	typename Iterator<TSeq1 const, Rooted>::Type seq1Iter = begin(seq1, Rooted());
-	
-	if (!_patternInitSmallStateBanded(seq1Iter, seq2, state))
-		return maxErrors + 1;
-	_findMyersSmallPatternsBanded(seq1Iter, seq2, state, False());
-	return state.errors;
+    PatternState_<TSeq2, MyersUkkonenGlobalBanded> state;
+    state.maxErrors = maxErrors;
+    state.leftClip = (length(seq2) - length(seq1) + maxErrors) / 2;
+    typename Iterator<TSeq1 const, Rooted>::Type seq1Iter = begin(seq1, Rooted());
+
+    if (!_patternInitSmallStateBanded(seq1Iter, seq2, state))
+        return maxErrors + 1;
+    _findMyersSmallPatternsBanded(seq1Iter, seq2, state, False());
+    return state.errors;
 }
 
 
@@ -1645,13 +1555,13 @@ _computeEditDistanceBanded(
 
 template <typename TFinder, typename TNeedle, typename TNeedle2, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename TFindBeginPatternSpec>
 inline bool find (TFinder & finder,
-				  TNeedle const & needle,
+                  TNeedle const & needle,
                   PatternState_<TNeedle2, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > & state)
 {
-	if (empty(finder))
-	{
-		_finderSetNonEmpty(finder);
-		if (!_stateInit(finder, needle, state))
+    if (empty(finder))
+    {
+        _finderSetNonEmpty(finder);
+        if (!_stateInit(finder, needle, state))
         {
             goEnd(finder);
             return false;
@@ -1660,118 +1570,119 @@ inline bool find (TFinder & finder,
         if (state.errors <= state.maxErrors)
         {
             goPrevious(finder);
-			_setFinderEnd(finder);
-			if (IsSameType<TSpec, FindPrefix>::VALUE)
-			{
-				_setFinderLength(finder, endPosition(finder));
-			}
+            _setFinderEnd(finder);
+            if (IsSameType<TSpec, FindPrefix>::VALUE)
+            {
+                _setFinderLength(finder, endPosition(finder));
+            }
             return true;
         }
-		//TODO: adapt myers-ukkonnen to dynamically change maxErrors
-	}
-	else
-	{
-		if (atEnd(finder)) return false;
-		goNext(finder);
-	}
-
-	// distinguish between the version for needles not longer than one machineword and the version for longer needles
-	if (state.largeState == NULL) 
-		return _findMyersSmallPatternsBanded(finder, needle, state, True());
-//	else
-//		return _findMyersLargePatterns(finder, needle, state);
-	return false;
+        //TODO: adapt myers-ukkonnen to dynamically change maxErrors
+    }
+    else
+    {
+        if (atEnd(finder)) return false;
+        goNext(finder);
+    }
+
+    // distinguish between the version for needles not longer than one machineword and the version for longer needles
+    if (state.largeState == NULL)
+        return _findMyersSmallPatternsBanded(finder, needle, state, True());
+//    else
+//        return _findMyersLargePatterns(finder, needle, state);
+    return false;
 }
 
 // First two for AlignTextBanded
 template <typename TFinder, typename TNeedle, typename TSpec, typename TFinderCSP, typename TPatternCSP, typename THasState, typename TFindBeginPatternSpec>
-inline bool find (TFinder & finder, 
-				  Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, THasState, TFindBeginPatternSpec> > const & pattern,
+inline bool find (TFinder & finder,
+                  Pattern<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, THasState, TFindBeginPatternSpec> > const & pattern,
                   PatternState_<TNeedle, Myers<AlignTextBanded<TSpec, TFinderCSP, TPatternCSP>, True, TFindBeginPatternSpec> > & state)
 {
 SEQAN_CHECKPOINT
-	return find(finder, host(pattern), state);
+    return find(finder, host(pattern), state);
 }
 
 template <typename TFinder, typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
 inline bool find (TFinder & finder,
-				  Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
-				  PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & state)
+                  Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
+                  PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & state)
 {
 SEQAN_CHECKPOINT
-	typedef typename Haystack<TFinder>::Type THaystack;
-	typedef typename Size<THaystack>::Type TSize;
-
-	TSize prefix_begin_position; //for prefix search: the position where the prefix begins
-
-	if (empty(finder))
-	{
-		_patternInit(pattern, state, finder);
-		_finderSetNonEmpty(finder);
-
-		prefix_begin_position = position(finder);
-
-		//TODO: adapt myers-ukkonnen to dynamically change maxErrors
-	}
-	else
-	{
-		if (atEnd(finder)) return false;
-		goNext(finder);
-
-		prefix_begin_position = beginPosition(finder);
-	}
-
-	TSize haystack_length = length(container(finder));
-	// limit search width for prefix search
-	if (IsSameType<TSpec, FindPrefix>::VALUE)
-	{
-		TSize maxlen = prefix_begin_position + pattern.needleSize - scoreLimit(state) + 1;
-		if (haystack_length > maxlen)
-			haystack_length = maxlen;
-	}
-
-	// distinguish between the version for needles not longer than one machineword and the version for longer needles
-	if (pattern.largePattern == NULL) 
-		return _findMyersSmallPatterns(finder, pattern, state, haystack_length);
-	else
-		return _findMyersLargePatterns(finder, pattern, state, haystack_length);
+    typedef typename Haystack<TFinder>::Type THaystack;
+    typedef typename Size<THaystack>::Type TSize;
+
+    TSize prefix_begin_position; //for prefix search: the position where the prefix begins
+
+    if (empty(finder))
+    {
+        _patternInit(pattern, state, finder);
+        _finderSetNonEmpty(finder);
+
+        prefix_begin_position = position(finder);
+
+        //TODO: adapt myers-ukkonnen to dynamically change maxErrors
+    }
+    else
+    {
+        if (atEnd(finder)) return false;
+        goNext(finder);
+
+        prefix_begin_position = beginPosition(finder);
+    }
+
+    TSize haystack_length = length(container(finder));
+    // limit search width for prefix search
+    if (IsSameType<TSpec, FindPrefix>::VALUE)
+    {
+        TSize maxlen = prefix_begin_position + pattern.needleSize - scoreLimit(state) + 1;
+        if (haystack_length > maxlen)
+            haystack_length = maxlen;
+    }
+
+    // distinguish between the version for needles not longer than one machineword and the version for longer needles
+    if (pattern.largePattern == NULL)
+        return _findMyersSmallPatterns(finder, pattern, state, haystack_length);
+    else
+        return _findMyersLargePatterns(finder, pattern, state, haystack_length);
 }
 
 
 template <typename TFinder, typename TNeedle, typename TSpec, typename TFindBeginPatternSpec>
 inline bool find (TFinder & finder,
-				  Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & pattern)
+                  Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & pattern)
 {
-	return find(finder, pattern, pattern);
+    typedef typename Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> >::TPatternState TPatternState;
+    return find(finder, pattern, static_cast<TPatternState&>(pattern));
 }
 
 
 template <typename TFinder, typename TNeedle, typename TSpec, typename THasState, typename TFindBeginPatternSpec>
 inline bool find (TFinder & finder,
-				  Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
-				  PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & state,
-				  int const minScore)
+                  Pattern<TNeedle, Myers<TSpec, THasState, TFindBeginPatternSpec> > const & pattern,
+                  PatternState_<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & state,
+                  int const minScore)
 {
-	setScoreLimit(state, minScore);
-	return find(finder, pattern, state);
+    setScoreLimit(state, minScore);
+    return find(finder, pattern, state);
 }
 
 template <typename TFinder, typename TNeedle, typename TNeedle2, typename TSpec, typename TFindBeginPatternSpec>
 inline bool find (TFinder & finder,
-				  TNeedle const & needle,
-				  PatternState_<TNeedle2, Myers<TSpec, True, TFindBeginPatternSpec> > & state,
-				  int const minScore)
+                  TNeedle const & needle,
+                  PatternState_<TNeedle2, Myers<TSpec, True, TFindBeginPatternSpec> > & state,
+                  int const minScore)
 {
-	setScoreLimit(state, minScore);
-	return find(finder, needle, state);
+    setScoreLimit(state, minScore);
+    return find(finder, needle, state);
 }
 
 template <typename TFinder, typename TNeedle, typename TSpec, typename TFindBeginPatternSpec>
 inline bool find (TFinder & finder,
-				  Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & pattern,
-				  int const minScore)
+                  Pattern<TNeedle, Myers<TSpec, True, TFindBeginPatternSpec> > & pattern,
+                  int const minScore)
 {
-	return find(finder, pattern, pattern, minScore); //static cast
+    return find(finder, pattern, pattern, minScore); //static cast
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_pattern_base.h b/seqan/find/find_pattern_base.h
index dde6bf0..799ed17 100644
--- a/seqan/find/find_pattern_base.h
+++ b/seqan/find/find_pattern_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,29 +54,13 @@ namespace seqan {
  *            class Pattern;
  *
  * @tparam TNeedle The needle type.  Types: @link TextConcept @endlink.
- * @tparam TSpec   The specializing type; gives the online algorithm to use for the search.  Defaults to the result of
+ * @tparam TSpec   A tag that specifies the online algorithm to use for the search.  Defaults to the result of
  *                 @link DefaultPattern @endlink.
  *
- * @section Remarks
- *
- * If <tt>Needle</tt> is a StringSet then <tt>position(pattern)</tt> returns a pair with the index of the currently
+ * If <tt>Needle</tt> is a StringSet then <tt>position(pattern)</tt> returns a @link Pair @endlink with the index of the currently
  * matching needle and the position in the needle.
  */
 
-/**
-.Class.Pattern:
-..summary:Holds the needle and preprocessing data (depends on algorithm).
-..cat:Searching
-..signature:Pattern<TNeedle[, TSpec]>
-..param.TNeedle:The needle type.
-...type:Class.String
-..param.TSpec:The online-algorithm to search with.
-...remarks:Leave empty for index-based pattern matching (see @Class.Index@).
-...default:The result of @Metafunction.DefaultPattern@
-..remarks:If $TNeedle$ is a set of strings, then $position(pattern)$ returns the index of the currently matching needle.
-..include:seqan/find.h
-*/
-
 template < typename TNeedle, typename TSpec = typename DefaultPattern<TNeedle>::Type >
 class Pattern;
 
@@ -85,22 +69,23 @@ template < typename TNeedle >
 class Pattern<TNeedle, void>
 {
 public:
-	typedef typename Position<TNeedle>::Type TNeedlePosition;
+    typedef typename Position<TNeedle>::Type TNeedlePosition;
 
-	Holder<TNeedle> data_host;
-	TNeedlePosition data_begin_position;
-	TNeedlePosition data_end_position;
 
-	Pattern() {}
+    Holder<TNeedle> data_host;
+    TNeedlePosition data_begin_position;
+    TNeedlePosition data_end_position;
 
-	template <typename TNeedle_>
-	Pattern(TNeedle_ & ndl):
-		data_host(ndl) {}
+    Pattern() : data_host(), data_begin_position(), data_end_position()
+    {}
 
-	template <typename TNeedle_>
-	Pattern(TNeedle_ const & ndl):
-		data_host(ndl) {}
+    template <typename TNeedle_>
+    Pattern(TNeedle_ & ndl) : data_host(ndl), data_begin_position(), data_end_position()
+    {}
 
+    template <typename TNeedle_>
+    Pattern(TNeedle_ const & ndl) : data_host(ndl), data_begin_position(), data_end_position()
+    {}
 };
 //////////////////////////////////////////////////////////////////////////////
 
@@ -108,7 +93,7 @@ class Pattern<TNeedle, void>
  * @mfn Pattern#Container
  * @brief Returns the needle type of the pattern.
  *
- * @signature Container<TPattern>::Type
+ * @signature Container<TPattern>::Type;
  *
  * @tparam TPattern The pattern to query for its needle type.
  *
@@ -117,42 +102,40 @@ class Pattern<TNeedle, void>
 
 template <typename TNeedle, typename TSpec>
 struct Container< Pattern<TNeedle, TSpec> > {
-	typedef TNeedle Type;
+    typedef TNeedle Type;
 };
 
 template <typename TNeedle, typename TSpec>
 struct Container< Pattern<TNeedle, TSpec> const > {
-	typedef TNeedle const Type;
+    typedef TNeedle const Type;
 };
 
 /*!
  * @mfn Pattern#Host
  * @brief Returns the host type of the pattern.
  *
- * @signature Host<TPattern>::Type
+ * @signature Host<TPattern>::Type;
  *
  * @tparam TPattern The pattern to query for its host type.
  *
  * @return Type The host type.
  */
 
-///.Metafunction.Host.param.T.type:Class.Pattern
-///.Metafunction.Host.class:Class.Pattern
 template <typename TNeedle, typename TSpec>
 struct Host< Pattern<TNeedle, TSpec> > {
-	typedef TNeedle Type;
+    typedef TNeedle Type;
 };
 
 template <typename TNeedle, typename TSpec>
 struct Host< Pattern<TNeedle, TSpec> const > {
-	typedef TNeedle const Type;
+    typedef TNeedle const Type;
 };
 
 /*!
- * @fn Pattern#Value
+ * @mfn Pattern#Value
  * @brief Returns the value type of the underlying pattern.
  *
- * @signature Value<TPattern>::Type
+ * @signature Value<TPattern>::Type;
  *
  * @tparam TPattern The Pattern to query.
  *
@@ -161,14 +144,14 @@ struct Host< Pattern<TNeedle, TSpec> const > {
 
 template <typename TPattern, typename TSpec>
 struct Value< Pattern<TPattern, TSpec> > {
-	typedef typename Value<TPattern>::Type Type;
+    typedef typename Value<TPattern>::Type Type;
 };
 
 /*!
- * @fn Pattern#Position
+ * @mfn Pattern#Position
  * @brief Returns the position type of the underlying pattern.
  *
- * @signature Position<TPattern>::Type
+ * @signature Position<TPattern>::Type;
  *
  * @tparam TPattern The Pattern to query.
  *
@@ -177,14 +160,14 @@ struct Value< Pattern<TPattern, TSpec> > {
 
 template <typename TPattern, typename TSpec>
 struct Position< Pattern<TPattern, TSpec> > {
-	typedef typename Position<TPattern>::Type Type;
+    typedef typename Position<TPattern>::Type Type;
 };
 
 /*!
- * @fn Pattern#Difference
+ * @mfn Pattern#Difference
  * @brief Returns the difference type of the underlying pattern.
  *
- * @signature Difference<TPattern>::Type
+ * @signature Difference<TPattern>::Type;
  *
  * @tparam TPattern The Pattern to query.
  *
@@ -193,14 +176,14 @@ struct Position< Pattern<TPattern, TSpec> > {
 
 template <typename TPattern, typename TSpec>
 struct Difference< Pattern<TPattern, TSpec> > {
-	typedef typename Difference<TPattern>::Type Type;
+    typedef typename Difference<TPattern>::Type Type;
 };
 
 /*!
- * @fn Pattern#Size
+ * @mfn Pattern#Size
  * @brief Returns the size type of the underlying pattern.
  *
- * @signature Size<TPattern>::Type
+ * @signature Size<TPattern>::Type;
  *
  * @tparam TPattern The Pattern to query.
  *
@@ -209,14 +192,14 @@ struct Difference< Pattern<TPattern, TSpec> > {
 
 template <typename TPattern, typename TSpec>
 struct Size< Pattern<TPattern, TSpec> > {
-	typedef typename Size<TPattern>::Type Type;
+    typedef typename Size<TPattern>::Type Type;
 };
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
- * @fn Pattern#ScoringScheme
+ * @mfn Pattern#ScoringScheme
  * @brief Returns the scoring scheme type of an approximate search algorithm.
  *
  * @signature ScoringScheme<TPattern>::Type;
@@ -224,124 +207,142 @@ struct Size< Pattern<TPattern, TSpec> > {
  * @tparam TPattern The Pattern to query for its scoring scheme type.  Default: EditDistanceScore.
  */
 
-/**
-.Metafunction.ScoringScheme:
-..summary:Returns the scoring scheme of an approximate searching algorithm.
-..cat:Searching
-..signature:ScoringScheme<TPattern>::Type
-..param.TPattern:A @Class.Pattern@ type.
-...type:Class.Pattern
-..returns:The scoring scheme.
-...default:@Shortcut.EditDistanceScore@
-..include:seqan/find.h
-*/
-
 template <typename TNeedle>
 struct ScoringScheme
 {
-	typedef EditDistanceScore Type;
+    typedef EditDistanceScore Type;
 };
 template <typename TNeedle>
 struct ScoringScheme<TNeedle const>:
-	ScoringScheme<TNeedle>
+    ScoringScheme<TNeedle>
 {
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle, typename TSpec>
-inline Holder<TNeedle> & 
-_dataHost(Pattern<TNeedle, TSpec> & me) 
-{ 
-	return me.data_host;
+inline void
+_reinitPattern(Pattern<TNeedle, TSpec> &)
+{
+    // no-op.
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TNeedle, typename TSpec>
+inline Holder<TNeedle> &
+_dataHost(Pattern<TNeedle, TSpec> & me)
+{
+    return me.data_host;
 }
+
 template <typename TNeedle, typename TSpec>
-inline Holder<TNeedle> & 
-_dataHost(Pattern<TNeedle, TSpec> const & me) 
+inline Holder<TNeedle> const &
+_dataHost(Pattern<TNeedle, TSpec> const & me)
 {
-	return const_cast<Holder<TNeedle> &>(me.data_host);
+    return me.data_host;
 }
 
 //host access: see basic_host.h
 
+#ifdef SEQAN_CXX11_STANDARD
 
-//???TODO: Diese Funktion entfernen! (sobald setHost bei anderen pattern nicht mehr eine Art "assignHost" ist)
 template <typename TNeedle, typename TSpec, typename TNeedle2>
-inline void 
+inline void
 setHost(Pattern<TNeedle, TSpec> & me,
-		TNeedle2 const & ndl) 
+        TNeedle2 && ndl)
 {
-	 me.data_host = ndl; //assign => Pattern haelt eine Kopie => doof!
+    SEQAN_ASSERT(!empty(ndl));
+    setValue(_dataHost(me), std::forward<TNeedle2>(ndl));
+    _reinitPattern(me);
 }
+
+#else  // SEQAN_CXX11_STANDARD
+
 template <typename TNeedle, typename TSpec, typename TNeedle2>
-inline void 
+inline void
 setHost(Pattern<TNeedle, TSpec> & me,
-		TNeedle2 & ndl) 
-{ 
-	 me.data_host = ndl; //assign => Pattern haelt eine Kopie => doof!
+        TNeedle2 const & ndl)
+{
+    SEQAN_ASSERT(!empty(ndl));
+    setValue(_dataHost(me), ndl);
+    _reinitPattern(me);
 }
+
+template <typename TNeedle, typename TSpec, typename TNeedle2>
+inline void
+setHost(Pattern<TNeedle, TSpec> & me,
+        TNeedle2 & ndl)
+{
+    SEQAN_ASSERT(!empty(ndl));
+    setValue(_dataHost(me), ndl);
+    _reinitPattern(me);
+}
+
+#endif  // SEQAN_CXX11_STANDARD
+
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle, typename TSpec>
-inline typename Position<Pattern<TNeedle, TSpec> >::Type & 
-beginPosition(Pattern<TNeedle, TSpec> & me) 
+inline typename Position<Pattern<TNeedle, TSpec> >::Type &
+beginPosition(Pattern<TNeedle, TSpec> & me)
 {
-	return me.data_begin_position;
+    return me.data_begin_position;
 }
 template <typename TNeedle, typename TSpec>
-inline typename Position<Pattern<TNeedle, TSpec> const >::Type & 
-beginPosition(Pattern<TNeedle, TSpec> const & me) 
+inline typename Position<Pattern<TNeedle, TSpec> const >::Type &
+beginPosition(Pattern<TNeedle, TSpec> const & me)
 {
-	return me.data_begin_position;
+    return me.data_begin_position;
 }
 
 
 template <typename TNeedle, typename TSpec, typename TPosition>
 inline void
-setBeginPosition(Pattern<TNeedle, TSpec> & me, 
-				 TPosition _pos) 
+setBeginPosition(Pattern<TNeedle, TSpec> & me,
+                 TPosition _pos)
 {
-	me.data_begin_position = _pos;
+    me.data_begin_position = _pos;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle, typename TSpec>
-inline typename Position<Pattern<TNeedle, TSpec> >::Type & 
-endPosition(Pattern<TNeedle, TSpec> & me) 
+inline typename Position<Pattern<TNeedle, TSpec> >::Type &
+endPosition(Pattern<TNeedle, TSpec> & me)
 {
-	return me.data_end_position;
+    return me.data_end_position;
 }
 template <typename TNeedle, typename TSpec>
-inline typename Position<Pattern<TNeedle, TSpec> const >::Type & 
-endPosition(Pattern<TNeedle, TSpec> const & me) 
+inline typename Position<Pattern<TNeedle, TSpec> const >::Type &
+endPosition(Pattern<TNeedle, TSpec> const & me)
 {
-	return me.data_end_position;
+    return me.data_end_position;
 }
 
 template <typename TNeedle, typename TSpec, typename TPosition>
 inline void
-setEndPosition(Pattern<TNeedle, TSpec> & me, 
-			   TPosition _pos) 
+setEndPosition(Pattern<TNeedle, TSpec> & me,
+               TPosition _pos)
 {
-	me.data_end_position = _pos;
+    me.data_end_position = _pos;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle, typename TSpec>
-inline typename Infix<TNeedle>::Type 
-segment(Pattern<TNeedle, TSpec> & me) 
+inline typename Infix<TNeedle>::Type
+segment(Pattern<TNeedle, TSpec> & me)
 {
-	typedef typename Infix<TNeedle>::Type TInfix;
-	return TInfix(host(me), me.data_begin_position, me.data_end_position);
+    typedef typename Infix<TNeedle>::Type TInfix;
+    return TInfix(host(me), me.data_begin_position, me.data_end_position);
 }
 template <typename TNeedle, typename TSpec>
-inline typename Infix<TNeedle>::Type 
-segment(Pattern<TNeedle, TSpec> const & me) 
+inline typename Infix<TNeedle>::Type
+segment(Pattern<TNeedle, TSpec> const & me)
 {
-	typedef typename Infix<TNeedle>::Type TInfix;
-	return TInfix(host(me), me.data_begin_position, me.data_end_position);
+    typedef typename Infix<TNeedle>::Type TInfix;
+    return TInfix(host(me), me.data_begin_position, me.data_end_position);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -357,72 +358,50 @@ segment(Pattern<TNeedle, TSpec> const & me)
  * @return THost Reference to the host.
  */
 
-///.Function.host.param.object.type:Class.Pattern
-///.Function.host.class:Class.Pattern
-
 template <typename TNeedle, typename TSpec>
-inline typename Host<Pattern<TNeedle, TSpec> >::Type & 
+inline typename Host<Pattern<TNeedle, TSpec> >::Type &
 host(Pattern<TNeedle, TSpec> & me)
 {
-SEQAN_CHECKPOINT
-	return value(me.data_host);
+    SEQAN_CHECKPOINT
+    return value(me.data_host);
 }
 
 template <typename TNeedle, typename TSpec>
-inline typename Host<Pattern<TNeedle, TSpec> const>::Type & 
+inline typename Host<Pattern<TNeedle, TSpec> const>::Type &
 host(Pattern<TNeedle, TSpec> const & me)
 {
-SEQAN_CHECKPOINT
-	return value(me.data_host);
+    SEQAN_CHECKPOINT
+    return value(me.data_host);
 }
 
-
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn Pattern#needle
- * @brief Returns the needle of a Pattern object (not implemented for some online-algorithms).
+ * @brief Returns the needle of a @link Pattern @endlink object (not implemented for some online-algorithms).
  *
  * @signature TNeedle needle(pattern);
  *
  * @param[in] pattern The Pattern to query for its needle.
  *
- * @return TNeedle Reference ot the needle object.
+ * @return TNeedle Reference of the needle object.
  *
- * @section Remarks
- *
- * TNeedle is the result of the Needle metafunction of TPattern.  This is an alias to the function Pattern#host.
+ * TNeedle is the result of the Needle metafunction of TPattern.  This is an alias to the function @link Pattern#host @endlink.
  */
 
-/**
-.Function.needle:
-..summary:Returns the needle of a @Class.Pattern@ object (not implemented for some online-algorithms).
-..cat:Searching
-..signature:needle(pattern)
-..class:Class.Pattern
-..param.pattern:The @Class.Pattern@ object to search with.
-...type:Class.Pattern
-..returns:The needle object to search for.
-..remarks:The result type is @Metafunction.Needle@$<TPattern>::Type$ for pattern of type $TPattern$.
-This is an alias to function @Function.host@ of the pattern function.
-..see:Function.host
-..include:seqan/find.h
-*/
-///.Function.host.remarks:Aliased to @Function.needle@ and @Function.haystack@ for classes @Class.Pattern@ and @Class.Finder@.
-
 
 template < typename TObject >
 inline typename Needle<TObject>::Type &
-needle(TObject &obj) 
+needle(TObject &obj)
 {
-	return obj;
+    return obj;
 }
 
 template < typename TObject >
 inline typename Needle<TObject const>::Type &
-needle(TObject const &obj) 
+needle(TObject const &obj)
 {
-	return obj;
+    return obj;
 }
 
 
@@ -437,21 +416,18 @@ needle(TObject const &obj)
  * @return TPosition The position of the last match in the pattern.
  */
 
-///.Function.position.param.iterator.type:Class.Pattern
-///.Function.position.class:Class.Pattern
-
 template < typename TNeedle, typename TSpec >
 inline typename Needle< Pattern<TNeedle, TSpec> >::Type &
-needle(Pattern<TNeedle, TSpec> & obj) 
+needle(Pattern<TNeedle, TSpec> & obj)
 {
-	return host(obj);
+    return host(obj);
 }
 
 template < typename TNeedle, typename TSpec >
 inline typename Needle< Pattern<TNeedle, TSpec> const>::Type &
-needle(Pattern<TNeedle, TSpec> const & obj) 
+needle(Pattern<TNeedle, TSpec> const & obj)
 {
-	return host(obj);
+    return host(obj);
 }
 
 /*!
@@ -464,23 +440,10 @@ needle(Pattern<TNeedle, TSpec> const & obj)
  * @param[in]     needle  The needle to set.
  */
 
-/**
-.Function.setNeedle:
-..summary:Sets the needle of a @Class.Pattern@ object and optionally induces preprocessing.
-..cat:Searching
-..signature:setNeedle(pattern, needle)
-..class:Class.Pattern
-..param.pattern:The @Class.Pattern@ object to search with.
-...type:Class.Pattern
-..param.needle:The needle object to search for.
-...type:Class.String
-..include:seqan/find.h
-*/
-
 template < typename TNeedle, typename TSpec >
 inline void
 setNeedle(Pattern<TNeedle, TSpec> &obj, TNeedle const &ndl) {
-	setHost(obj, ndl);
+    setHost(obj, ndl);
 }
 
 
@@ -497,32 +460,19 @@ setNeedle(Pattern<TNeedle, TSpec> &obj, TNeedle const &ndl) {
  * @return TScoringScheme The scoring scheme of the pattern.
  */
 
-/**.Function.scoringScheme
-..cat:Searching
-..summary:The @glos:Scoring Scheme|scoring scheme@ used for finding or aligning.
-..signature:scoringScheme(obj)
-..class:Class.Pattern
-..param.obj:Object that holds a @glos:Scoring Scheme|scoring scheme@
-...type:Class.Pattern
-..returns:The @glos:Scoring Scheme|scoring scheme@ used in $obj$
-...default:@Shortcut.EditDistanceScore@
-..see:glos:Scoring Scheme|scoring scheme
-..see:Metafunction.ScoringScheme
-*/
-
 template <typename TNeedle, typename TSpec>
-inline typename ScoringScheme<Pattern<TNeedle, TSpec> >::Type 
+inline typename ScoringScheme<Pattern<TNeedle, TSpec> >::Type
 scoringScheme(Pattern<TNeedle, TSpec> &)
 {
 SEQAN_CHECKPOINT
-	return typename ScoringScheme<Pattern<TNeedle, TSpec> >::Type();
+    return typename ScoringScheme<Pattern<TNeedle, TSpec> >::Type();
 }
 template <typename TNeedle, typename TSpec>
-inline typename ScoringScheme<Pattern<TNeedle, TSpec> const>::Type 
+inline typename ScoringScheme<Pattern<TNeedle, TSpec> const>::Type
 scoringScheme(Pattern<TNeedle, TSpec> const &)
 {
 SEQAN_CHECKPOINT
-	return typename ScoringScheme<Pattern<TNeedle, TSpec> const>::Type();
+    return typename ScoringScheme<Pattern<TNeedle, TSpec> const>::Type();
 }
 
 //____________________________________________________________________________
@@ -537,22 +487,10 @@ SEQAN_CHECKPOINT
  * @param[in]     score   The scoring scheme to set.
  */
 
-/**.Function.setScoringScheme
-..cat:Searching
-..summary:Sets the @glos:Scoring Scheme|scoring scheme@ used for finding or aligning.
-..signature:setScoringScheme(obj, score)
-..class:Class.Pattern
-..param.obj:Object that holds a @glos:Scoring Scheme|scoring scheme@.
-...type:Class.Pattern
-..param.score:The new @glos:Scoring Scheme|scoring scheme@ used by $obj$.
-..see:glos:Scoring Scheme|scoring scheme
-..see:Function.scoringScheme
-*/
-
 template <typename TNeedle, typename TSpec, typename TScore2>
 inline void
-setScoringScheme(Pattern<TNeedle, TSpec> & /*me*/, 
-				 TScore2 & /*score*/)
+setScoringScheme(Pattern<TNeedle, TSpec> & /*me*/,
+                 TScore2 & /*score*/)
 {
 //dummy implementation for compatibility reasons
 }
diff --git a/seqan/find/find_pex.h b/seqan/find/find_pex.h
index 58f0d8e..11684d6 100644
--- a/seqan/find/find_pex.h
+++ b/seqan/find/find_pex.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,10 +38,10 @@
 // uncomment this for verbose debug output
 //#define SEQAN_DEBUG_PEX
 
-namespace SEQAN_NAMESPACE_MAIN 
+namespace SEQAN_NAMESPACE_MAIN
 {
 
-struct Hierarchical;			
+struct Hierarchical;
 struct NonHierarchical;
 
 
@@ -55,7 +55,7 @@ typedef Pex<NonHierarchical,AhoCorasick>   PexNonHierarchical;
 
 template <typename TNeedle, typename TVerification, typename TMultiFinder>
 struct FindBeginPatternSpec< Pattern<TNeedle, Pex<TVerification , TMultiFinder > > >:
-	DefaultFindBeginPatternSpec<>
+    DefaultFindBeginPatternSpec<>
 {
 };
 
@@ -69,32 +69,16 @@ struct FindBeginPatternSpec< Pattern<TNeedle, Pex<TVerification , TMultiFinder >
  * @signature PexMultiFinder<Pattern<TNeedle,Pex<TVerification, TMultiFinder> > >::Type;
  *
  * @tparam TMultiFinder The specification for the multiple exact string matching algorithm that should be used
- *                      with the Pex algorithm. 
+ *                      with the Pex algorithm.
  *
- * @returns Type Pattern type of the multiple exact string matching algorithm for the specified Pattern.
- *
- * @section Remarks
+ * @return Type Pattern type of the multiple exact string matching algorithm for the specified Pattern.
  *
  * For a description of Pattern usage, see @link Pattern @endlink.
- * 
+ *
  * Overload this metafunction if you want to use something else for verification then
  * <tt>Pattern&lt;String&lt;Segment&l;tNeedle&gt; &gt;, TMultiFinder&gt;</tt>.
  */
 
-/**
-.Metafunction.PexMultiFinder:
-..cat:Searching
-..summary:Determines the multiple exact string matching algorithm used by the Pex algorithm.
-..signature:PexMultiFinder< Pattern<TNeedle,Pex<TVerification,TMultiFinder> > >::Type
-..class:Class.Pattern
-..param.TMultiFinder:The specification for the multiple exact string matching algorithm that should be used with the Pex algorithm.
-..returns.param.Type:Pattern type of the multiple exact string matching algorithm for the specified Pattern.
-..see:Spec.Pex
-..remarks: For a description of Pattern usage see @Class.Pattern@.
-..remarks: Overload this Metafunction if you want to use something else for verification then $Pattern<String<Segment<TNeedle> > , TMultiFinder>$.
-..include:seqan/find.h
-*/
-
 template<typename T>
 struct PexMultiFinder;
 
@@ -103,7 +87,7 @@ struct PexMultiFinder< Pattern<TNeedle, Pex<TVerification , TMultiFinder > > >
 {
   typedef Pattern<String<Segment<TNeedle> > , TMultiFinder> Type;
 };
- 
+
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TPosition,typename TScore,typename TVerifier,typename TNeedle>
@@ -117,6 +101,7 @@ struct PexRange_{
 
 /*!
  * @class PexPattern
+ * @extends Pattern
  * @headerfile <seqan/find.h>
  * @brief Provides a fast approximate string matching filter that splits the needle into several pieces that are
  *        searched with a multiple exact string matching algorithm and later verified.
@@ -124,34 +109,16 @@ struct PexRange_{
  * @signature template <typename TNeedle, typename TVerification, typename TMultiFinder>
  *            class Pattern<TNeedle, Pex<TVerification, TMultiFinder> >;
  *
- * @tparam TNeedle       The needle type.
+ * @tparam TNeedle       The needle type. Type: @link ContainerConcept @endlink
  * @tparam TVerification Determines if the hierarchical verification proposed by Navarro and Beaza-Yates is used or
  *                       not.
- * @tparam TMultiFinder  Specifies the algorithm for th emultiple exact string matching algorithm.  Type: AhoCorasick.
- *
- * @section Remarks
+ * @tparam TMultiFinder  Specifies the algorithm for the multiple exact string matching algorithm.  Type: AhoCorasick.
  *
  * There are two defaults available: <tt>PexHierarchical</tt> and <tt>PexNonHiearchical</tt> (e.g.
  * <tt>Pattern&lt;CharString&gt;, PexHierarchical&gt;</tt> that both use the @link AhoCorasickPattern Aho-Corasick
  * @endlink algorithm for the multiple exact string matching.
  */
 
-/**
-.Spec.Pex:
-..summary: Provides a fast approximate string matching filter that splits the needle into several pieces that are searched with a multiple exact string matching algorithm and later verified.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, Pex<TVerification,TMultiFinder> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..param.TVerification: Determines if the hierarchical verification proposed by Navarro and Baeza-Yates is used or not.
-..param.TMultiFinder: Specifies the algorithm for the multiple exact string matching algorithm
-...type:Spec.AhoCorasick
-..remarks: There are two defaults available $PexHierarchical$ and $PexNonHierarchical$ (e.g. $Pattern<String<char> ,PexHierarchical> $) that both use the @Spec.AhoCorasick@ algorithm for the multiple exact string matching.
-..include:seqan/find.h
-*/
-///.Class.Pattern.param.TSpec.type:Spec.Pex
-
 /*!
  * @class HierarchicalPexPattern
  * @extends PexPattern
@@ -161,23 +128,10 @@ struct PexRange_{
  * @signature template <typename TNeedle, typename TMultiFinder>
  *            class Pattern<TNeedle, Pex<Hierarchical, TMultiFinder> >;
  *
- * @tparam TNeedle      The needle type.
+ * @tparam TNeedle      The needle type. Type: @link ContainerConcept @endlink
  * @tparam TMultiFinder Specifies the algorithm for th emultiple exact string matching algorithm.
  */
 
-/**
-.Spec.Hierarchical:
-..summary: By using this Specialization the hierarchical verification is enabled.
-..general:Spec.Pex
-..cat:Searching
-..signature:Pattern<TNeedle, Pex<Hierarchical,TMultiFinder> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..param.TMultiFinder: Specifies the algorithm for the multiple exact string matching algorithm
-..include:seqan/find.h
-*/
-///.Spec.Pex.param.TVerification.type:Spec.Hierarchical
-
 /*!
  * @class NonHierarchicalPexPattern
  * @extends PexPattern
@@ -187,35 +141,22 @@ struct PexRange_{
  * @signature template <typename TNeedle, typename TMultiFinder>
  *            class Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder> >;
  *
- * @tparam TNeedle      The needle type.
+ * @tparam TNeedle      The needle type. Type: @link ContainerConcept @endlink
  * @tparam TMultiFinder Specifies the algorithm for th emultiple exact string matching algorithm.
  */
 
-/**
-.Spec.NonHierarchical:
-..summary: By using this Specialization the hierarchical verification is disabled.
-..general:Spec.Pex
-..cat:Searching
-..signature:Pattern<TNeedle, Pex<NonHierarchical,TMultiFinder> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..param.TMultiFinder: Specifies the algorithm for the multiple exact string matching algorithm
-..include:seqan/find.h
-*/
-///.Spec.Pex.param.TVerification.type:Spec.NonHierarchical
-
 template <typename TNeedle, typename TVerification, typename TMultiFinder>
 class Pattern<TNeedle, Pex<TVerification, TMultiFinder > >:
-	public FindBegin_<Pattern<TNeedle, Pex<TVerification, TMultiFinder > > >
+    public FindBegin_<Pattern<TNeedle, Pex<TVerification, TMultiFinder > > >
 {
  public:
    typedef typename Position<TNeedle>::Type TPosition;
    typedef unsigned TScore;
    typedef Pattern<TNeedle, MyersUkkonen > TVerifier;
-   typedef typename PexMultiFinder< 
-                       Pattern<TNeedle, Pex<TVerification,TMultiFinder > > 
-                                  >::Type TMFinder; 
-  
+   typedef typename PexMultiFinder<
+                       Pattern<TNeedle, Pex<TVerification,TMultiFinder > >
+                                  >::Type TMFinder;
+
    // the maximal accepted error
    TScore limit;
    // reference to the needle
@@ -224,116 +165,132 @@ class Pattern<TNeedle, Pex<TVerification, TMultiFinder > >:
    TMFinder multiPattern;
    // needles for the multi pattern search
    String<Segment<TNeedle> >  splitted_needles;
-   
+
    // data store for the verification tree respectively the splitted needle
-   ::std::map<unsigned, PexRange_<TPosition,TScore,TVerifier,TNeedle> > range_table;
+   std::map<unsigned, PexRange_<TPosition,TScore,TVerifier,TNeedle> > range_table;
    // map leafs of the tree to parts of the needle
-   ::std::map<unsigned, unsigned> leaf_map;
+   std::map<unsigned, unsigned> leaf_map;
 
    // store the infixes for the verifiers
    String<Segment<TNeedle> > segment_store;
-  
+
    // track position where the last occurrence was found
    unsigned lastFPos;
    unsigned lastFNdl;
-   
+
    // indicator to track if we already found an occurrence
-   bool findNext,patternNeedsInit; 
+   bool findNext,patternNeedsInit;
 
    unsigned needleLength;
 
-   Pattern() {}
+   Pattern() :
+       limit(1), lastFPos(0), lastFNdl(0), findNext(false), patternNeedsInit(true)
+   {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>)) :
+        limit(1),
+        lastFPos(0),
+        lastFNdl(0),
+        findNext(false),
+        patternNeedsInit(true)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl, int _limit = -1) :
+        limit(-_limit),
+        lastFPos(0),
+        lastFNdl(0),
+        findNext(false),
+        patternNeedsInit(true)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+    }
 
+#else
    template <typename TNeedle2>
-   Pattern(TNeedle2 const & ndl)
-     : limit(1)
+   Pattern(TNeedle2 const & ndl) :
+       limit(1), lastFPos(0), lastFNdl(0), findNext(false), patternNeedsInit(true)
    {
      setHost(*this, ndl);
    }
 
    template <typename TNeedle2>
-   Pattern(TNeedle2 const & ndl, int _limit = -1)
-     : limit(- _limit)
+   Pattern(TNeedle2 const & ndl, int _limit = -1) :
+       limit(-_limit), lastFPos(0), lastFNdl(0), findNext(false), patternNeedsInit(true)
    {
-SEQAN_CHECKPOINT
      setHost(*this, ndl);
    }
-
-   ~Pattern() {
-     SEQAN_CHECKPOINT
-    }
+#endif  // SEQAN_CXX11_STANDARD
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2, typename TVerification, typename TMultiFinder>
-void setHost (Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, TNeedle2 const & needle) 
+template <typename TNeedle, typename TVerification, typename TMultiFinder>
+void _reinitPattern(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me)
 {
   // initialisation of the find-tree etc. will be done when patternInit
   // is called to assure that we already know the scoreLimit
-  me.data_host = needle;
-  me.needleLength = length(needle);
+  me.needleLength = length(needle(me));
   me.findNext = false;
   me.patternNeedsInit = true;
 }
 
-template <typename TNeedle, typename TNeedle2, typename TVerification, typename TMultiFinder>
-void setHost (Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, TNeedle2 & needle)
-{
-  setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TNeedle, typename TVerification, typename TMultiFinder>
-inline typename Host<Pattern<TNeedle, Pex<TVerification,TMultiFinder > > >::Type & 
-host(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me)
-{
-SEQAN_CHECKPOINT
-  return value(me.data_host);
-}
-
-template <typename TNeedle, typename TVerification, typename TMultiFinder>
-inline typename Host<Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const>::Type & 
-host(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const & me)
-{
-SEQAN_CHECKPOINT
-  return value(me.data_host);
-}
-
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle, typename TMultiFinder>
-int _getRoot(Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder > > & me) 
+int _getRoot(Pattern<TNeedle, Pex<NonHierarchical, TMultiFinder > > & me)
 {
 SEQAN_CHECKPOINT
   return length(me.splitted_needles);
 }
 
 template <typename TNeedle, typename TMultiFinder>
-int _getRoot(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &) 
+int _getRoot(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &)
 {
 SEQAN_CHECKPOINT
   return 1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.getScore.param.pattern.type:Spec.Pex
-///.Function.getScore.class:Spec.Pex
-
+/*!
+ * @fn PexPattern#getScore
+ * @headerfile <seqan/find.h>
+ * @brief Score of the last found match in approximate searching.
+ *
+ * @signature TScoreValue getScore(pattern);
+ *
+ * @param[in] pattern A pex pattern that can be used for approximate searching.
+ *
+ * @return TScoreValue The score of the last match found using <tt>pattern</tt>.  If no match was found then the value
+ *                     is undefined.
+ */
 template <typename TNeedle, typename TVerification, typename TMultiFinder>
-int getScore(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me) 
+int getScore(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me)
 {
 SEQAN_CHECKPOINT
   return getScore(me.range_table[_getRoot(me)].verifier);
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.scoreLimit.param.pattern.type:Spec.Pex
-///.Function.scoreLimit.class:Spec.Pex
-
+/*!
+ * @fn PexPattern#scoreLimit
+ * @headerfile <seqan/find.h>
+ * @brief The minimal score a match must reach in approximate searching.
+ *
+ * @signature TScoreValue scoreLimit(pattern);
+ *
+ * @param[in] pattern The pattern to query.
+ *
+ * @return TScoreValue The score limit value.
+ */
 template <typename TNeedle, typename TVerification, typename TMultiFinder>
-inline int 
+inline int
 scoreLimit(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > const & me)
 {
 SEQAN_CHECKPOINT
@@ -342,13 +299,24 @@ SEQAN_CHECKPOINT
 
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.setScoreLimit.param.pattern.type:Spec.Pex
-///.Function.setScoreLimit.class:Spec.Pex
+/*!
+ * @fn PexPattern#setSoreLimit
+ * @headerfile <seqan/find.h>
+ * @brief Set the minimal score a match must reach in approximate serach.
+ *
+ * @signature void setScoreLimit(pattern, limit);
+ *
+ * @param[in,out] pattern The pattern to set the limit for.
+ * @param[in]     limit   The limit score value to set.
+ *
+ * @return TScoreValue The score limit value.
+ */
+
 
 template <typename TNeedle, typename TScoreValue,typename TVerification, typename TMultiFinder>
-inline void 
-setScoreLimit(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me, 
-			  TScoreValue _limit)
+inline void
+setScoreLimit(Pattern<TNeedle, Pex<TVerification,TMultiFinder > > & me,
+              TScoreValue _limit)
 {
 SEQAN_CHECKPOINT
   me.patternNeedsInit = true;
@@ -370,8 +338,8 @@ SEQAN_CHECKPOINT
 /*
   // split pattern
   unsigned k = me.limit + 1;
-  unsigned seg_len = me.needleLength / k; //::std::floor(me.needleLength/k); 
-  
+  unsigned seg_len = me.needleLength / k; //std::floor(me.needleLength/k);
+
   clear(me.splitted_needles);
   clear(me.range_table);
   clear(me.segment_store);
@@ -379,13 +347,13 @@ SEQAN_CHECKPOINT
   unsigned c = 0;
   unsigned i = 0;
   while(s < me.needleLength)
-  { 
+  {
     PexRange_<TPosition,TScore,TVerifier,TNeedle> pr;
     pr.start = s;
     pr.end = (c == me.limit ? me.needleLength : s + seg_len);
     pr.error = 0;
 
-	insert(me.range_table,i,pr);
+    insert(me.range_table,i,pr);
     appendValue(me.splitted_needles,infix(value(me.data_host),pr.start,pr.end));
     s += (c == me.limit ? me.needleLength : seg_len);
     ++c;
@@ -406,7 +374,7 @@ SEQAN_CHECKPOINT
     pr.end = (pos = me.needleLength * (i + 1) / k);
     pr.error = 0;
 
-	insert(me.range_table, i, pr);
+    insert(me.range_table, i, pr);
     appendValue(me.splitted_needles, infix(value(me.data_host), pr.start, pr.end));
   }
 //*/
@@ -421,28 +389,28 @@ SEQAN_CHECKPOINT
   pr.end = me.needleLength;
   pr.error = me.limit;
   setHost(pr.verifier,me.segment_store[0]);
-  setScoreLimit(pr.verifier, - static_cast<int>(me.limit));  
+  setScoreLimit(pr.verifier, - static_cast<int>(me.limit));
   insert(me.range_table,length(me.splitted_needles),pr);
-  
+
   // init multipattern finder
   setHost(me.multiPattern,me.splitted_needles);
-  
+
   me.patternNeedsInit = false;
   me.findNext = false;
   _findBeginInit(me, needle(me));
 
 #ifdef SEQAN_DEBUG_PEX
-  ::std::cout << " -------------------------------------------------  " << ::std::endl;
-  ::std::cout << "                   PATTERN INIT                     " << ::std::endl;
-  ::std::cout << "Needle:   " << value(me.data_host) << ::std::endl;
-  ::std::cout << "|Needle|: " << me.needleLength << ::std::endl;
-  ::std::cout << "seg_len:  " << me.needleLength / k << ::std::endl;
-  ::std::cout << "limit:    " << me.limit << ::std::endl;
-  ::std::cout << "k:        " << k << ::std::endl;
-  ::std::cout << "computed following needles for multipattern search: " << ::std::endl;
-  for(unsigned i = 0;i < length(me.splitted_needles);++i)  ::std::cout << me.splitted_needles[i] << ::std::endl;
-  ::std::cout << " -------------------------------------------------  " << ::std::endl;
-#endif  
+  std::cout << " -------------------------------------------------  " << std::endl;
+  std::cout << "                   PATTERN INIT                     " << std::endl;
+  std::cout << "Needle:   " << value(me.data_host) << std::endl;
+  std::cout << "|Needle|: " << me.needleLength << std::endl;
+  std::cout << "seg_len:  " << me.needleLength / k << std::endl;
+  std::cout << "limit:    " << me.limit << std::endl;
+  std::cout << "k:        " << k << std::endl;
+  std::cout << "computed following needles for multipattern search: " << std::endl;
+  for(unsigned i = 0;i < length(me.splitted_needles);++i)  std::cout << me.splitted_needles[i] << std::endl;
+  std::cout << " -------------------------------------------------  " << std::endl;
+#endif
 
 }
 
@@ -472,7 +440,7 @@ SEQAN_CHECKPOINT
     startPos = position(finder);
     int start = me.lastFPos - me.range_table[me.lastFNdl].start - me.limit;
     int end   = me.lastFPos + (me.needleLength - me.range_table[me.lastFNdl].start) + me.limit;
-    
+
     // adjust start and end if they point over the edges of host(finder)
     start = (start < 0 ? 0 : start);
     end = (end > static_cast<int>(length(host(finder))) ? static_cast<int>(length(host(finder))) : end);
@@ -484,12 +452,12 @@ SEQAN_CHECKPOINT
     {
       unsigned nP = start + position(f);
       if(nP > startPos){
-	// compute new position
-	unsigned offset = nP - position(finder);
-	finder += offset;
-	me.findNext = true;
-	_setFinderEnd(finder);
-	return true;
+    // compute new position
+    unsigned offset = nP - position(finder);
+    finder += offset;
+    me.findNext = true;
+    _setFinderEnd(finder);
+    return true;
       }
     }
     // reset mf finder to old position
@@ -514,14 +482,14 @@ SEQAN_CHECKPOINT
     {
       unsigned nP = s + position(f);
       if(nP > startPos){
-	// compute new position
-	unsigned offset = nP - position(finder);
-	finder += offset;
-	me.lastFPos = position(mf);
-	me.lastFNdl = position(me.multiPattern);
-	me.findNext = true;	  
-	_setFinderEnd(finder);
-	return true;
+    // compute new position
+    unsigned offset = nP - position(finder);
+    finder += offset;
+    me.lastFPos = position(mf);
+    me.lastFNdl = position(me.multiPattern);
+    me.findNext = true;
+    _setFinderEnd(finder);
+    return true;
       }
     }
   }
@@ -540,27 +508,27 @@ SEQAN_CHECKPOINT
 /*
 template <typename TNeedle, typename TMultiFinder>
 void _createTree(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, unsigned start, unsigned end,
-		 unsigned k, unsigned parent, unsigned direction ,unsigned idx, unsigned plen)
+         unsigned k, unsigned parent, unsigned direction ,unsigned idx, unsigned plen)
 {
   //create tree like proposed in Navarro & Raffinot
   // direction == 0 .. choose left child in the tree
   // direction == 1 .. choose right child in the tree
 
 #ifdef SEQAN_DEBUG_PEX
-  ::std::cout << "called _createTree:" << ::std::endl;
-  ::std::cout << "  start: " << start << ::std::endl;
-  ::std::cout << "  end  : " << end << ::std::endl;
-  ::std::cout << "  seq  : " << infix(value(me.data_host),start,end + 1) << ::std::endl;
-  ::std::cout << "  k    : " << k << ::std::endl;
-  ::std::cout << "  paren: " << parent << ::std::endl;
-  ::std::cout << "  direc: " << direction << ::std::endl;
-  ::std::cout << "  idx  : " << idx << ::std::endl;
-  ::std::cout << "  plen : " << plen << ::std::endl;
-  ::std::cout << " ----------------------------- " << ::std::endl;
+  std::cout << "called _createTree:" << std::endl;
+  std::cout << "  start: " << start << std::endl;
+  std::cout << "  end  : " << end << std::endl;
+  std::cout << "  seq  : " << infix(value(me.data_host),start,end + 1) << std::endl;
+  std::cout << "  k    : " << k << std::endl;
+  std::cout << "  paren: " << parent << std::endl;
+  std::cout << "  direc: " << direction << std::endl;
+  std::cout << "  idx  : " << idx << std::endl;
+  std::cout << "  plen : " << plen << std::endl;
+  std::cout << " ----------------------------- " << std::endl;
 #endif
   typedef typename Position<TNeedle>::Type TPosition;
   typedef unsigned TScore;
-  typedef Pattern<TNeedle,MyersUkkonen> TVerifier; 
+  typedef Pattern<TNeedle,MyersUkkonen> TVerifier;
 
   PexRange_<TPosition,TScore,TVerifier,TNeedle> pr;
   pr.start = start;
@@ -570,42 +538,42 @@ void _createTree(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, unsign
   appendValue(me.segment_store,infix(value(me.data_host),pr.start,pr.end + 1));
   setScoreLimit(pr.verifier, - static_cast<int>(pr.error));
   setHost(pr.verifier, me.segment_store[length(me.segment_store) - 1]);
-  
-  unsigned left = k/2 + 1; //::std::ceil(static_cast<double>(k + 1)/2);
+
+  unsigned left = k/2 + 1; //std::ceil(static_cast<double>(k + 1)/2);
   unsigned cur_idx = (parent << 1) + direction;
 
   // insert pr into the tree
   insert(me.range_table,cur_idx,pr);
-  
+
   if(k == 0){
     appendValue(me.splitted_needles,infix(value(me.data_host),pr.start,pr.end + 1));
 #ifdef SEQAN_DEBUG_PEX
-    ::std::cout << "inserted : " << me.splitted_needles[length(me.splitted_needles) - 1] << " into splitted needles" << ::std::endl;
-    ::std::cout << "assign to leaf_map " << length(me.splitted_needles) - 1 << " value " << cur_idx << ::std::endl;
-    ::std::cout << " ----------------------------- " << ::std::endl;
+    std::cout << "inserted : " << me.splitted_needles[length(me.splitted_needles) - 1] << " into splitted needles" << std::endl;
+    std::cout << "assign to leaf_map " << length(me.splitted_needles) - 1 << " value " << cur_idx << std::endl;
+    std::cout << " ----------------------------- " << std::endl;
 #endif
     me.leaf_map[length(me.splitted_needles) - 1] = cur_idx;
   }else{
     // recusivly create the rest of the tree
-//    _createTree(me, start, start + left * plen - 1, ::std::floor(static_cast<double>(left * k)/ static_cast<double>(k + 1)),cur_idx,0,idx,plen);
+//    _createTree(me, start, start + left * plen - 1, std::floor(static_cast<double>(left * k)/ static_cast<double>(k + 1)),cur_idx,0,idx,plen);
     _createTree(me, start, start + left * plen - 1, left * k / (k+1),cur_idx,0,idx,plen);
-//    _createTree(me,  start + left * plen, end, ::std::floor(static_cast<double>((k + 1 - left)*k)/ static_cast<double>(k + 1)),cur_idx,1,idx + left,plen);
+//    _createTree(me,  start + left * plen, end, std::floor(static_cast<double>((k + 1 - left)*k)/ static_cast<double>(k + 1)),cur_idx,1,idx + left,plen);
     _createTree(me,  start + left * plen, end, (k + 1 - left)*k / (k+1),cur_idx,1,idx + left,plen);
   }
 }
 */
 template <typename TNeedle, typename TMultiFinder>
-void _createTree(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, 
-				 unsigned start, unsigned end,
-				 unsigned k, 
-				 unsigned parent, 
-				 unsigned direction,
-				 unsigned idx, 
-				 unsigned plen)
+void _createTree(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me,
+                 unsigned start, unsigned end,
+                 unsigned k,
+                 unsigned parent,
+                 unsigned direction,
+                 unsigned idx,
+                 unsigned plen)
 {
   typedef typename Position<TNeedle>::Type TPosition;
   typedef unsigned TScore;
-  typedef Pattern<TNeedle,MyersUkkonen> TVerifier; 
+  typedef Pattern<TNeedle,MyersUkkonen> TVerifier;
 
   PexRange_<TPosition,TScore,TVerifier,TNeedle> pr;
   pr.start = start;
@@ -615,12 +583,12 @@ void _createTree(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me,
   appendValue(me.segment_store,infix(value(me.data_host),pr.start,pr.end + 1));
   setScoreLimit(pr.verifier, - static_cast<int>(pr.error));
   setHost(pr.verifier, me.segment_store[length(me.segment_store) - 1]);
-  
+
   unsigned cur_idx = (parent << 1) + direction;
 
   // insert pr into the tree
   insert(me.range_table,cur_idx,pr);
-  
+
   if(k == 0)
   {
     appendValue(me.splitted_needles,infix(value(me.data_host),pr.start,pr.end + 1));
@@ -628,13 +596,13 @@ void _createTree(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me,
   }
   else
   {
-	  unsigned int lower_2power = 1 << log2(k+1);
-	  unsigned int len = end - start+1;
-	  unsigned int right_k = lower_2power/2-1;
-	  unsigned int left_k = k - right_k-1;
-	  unsigned int left_len = len * (left_k+1) / (k+1);
-	  _createTree(me, start, start + left_len-1, left_k, cur_idx, 0, idx,plen);
-	  _createTree(me, start + left_len, end, right_k, cur_idx, 1, idx + (left_k+1),plen);
+      unsigned int lower_2power = 1 << log2(k+1);
+      unsigned int len = end - start+1;
+      unsigned int right_k = lower_2power/2-1;
+      unsigned int left_k = k - right_k-1;
+      unsigned int left_len = len * (left_k+1) / (k+1);
+      _createTree(me, start, start + left_len-1, left_k, cur_idx, 0, idx,plen);
+      _createTree(me, start + left_len, end, right_k, cur_idx, 1, idx + (left_k+1),plen);
   }
 }
 
@@ -642,7 +610,7 @@ template <typename TNeedle, typename TFinder, typename TMultiFinder>
 void _patternInit(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, TFinder &)
 {
   unsigned k = me.limit + 1;
-  unsigned plen = me.needleLength / k; //::std::floor(static_cast<double>(me.needleLength)/static_cast<double>(k));
+  unsigned plen = me.needleLength / k; //std::floor(static_cast<double>(me.needleLength)/static_cast<double>(k));
 
   // reset
   clear(me.splitted_needles);
@@ -662,16 +630,16 @@ void _patternInit(Pattern<TNeedle, Pex<Hierarchical, TMultiFinder > > &me, TFind
   _findBeginInit(me, needle(me));
 
 #ifdef SEQAN_DEBUG_PEX
-  ::std::cout << " -------------------------------------------------  " << ::std::endl;
-  ::std::cout << "                   PATTERN INIT                     " << ::std::endl;
-  ::std::cout << "Needle:   " << value(me.data_host) << ::std::endl;
-  ::std::cout << "|Needle|: " << me.needleLength << ::std::endl;
-  ::std::cout << "limit:    " << me.limit << ::std::endl;
-  ::std::cout << "k:        " << k << ::std::endl;
-  ::std::cout << "computed following needles for multipattern search: " << ::std::endl;
-  for(unsigned i = 0;i < length(me.splitted_needles);++i)  ::std::cout << me.splitted_needles[i] << ::std::endl;
-  ::std::cout << " -------------------------------------------------  " << ::std::endl;
-#endif  
+  std::cout << " -------------------------------------------------  " << std::endl;
+  std::cout << "                   PATTERN INIT                     " << std::endl;
+  std::cout << "Needle:   " << value(me.data_host) << std::endl;
+  std::cout << "|Needle|: " << me.needleLength << std::endl;
+  std::cout << "limit:    " << me.limit << std::endl;
+  std::cout << "k:        " << k << std::endl;
+  std::cout << "computed following needles for multipattern search: " << std::endl;
+  for(unsigned i = 0;i < length(me.splitted_needles);++i)  std::cout << me.splitted_needles[i] << std::endl;
+  std::cout << " -------------------------------------------------  " << std::endl;
+#endif
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -698,9 +666,9 @@ SEQAN_CHECKPOINT
   if(me.findNext){
     // we found an occurrence
     startPos = position(finder);
-    unsigned pnode = _getRoot(me); // use root 
+    unsigned pnode = _getRoot(me); // use root
     unsigned in = me.range_table[me.leaf_map[me.lastFNdl]].start;
-    
+
     int p1 = me.lastFPos - (in - me.range_table[pnode].start) - me.range_table[pnode].error;
     int p2 = me.lastFPos + (me.range_table[pnode].end - in + 1) + me.range_table[pnode].error;
 
@@ -714,14 +682,14 @@ SEQAN_CHECKPOINT
     {
       unsigned nP = p1 + position(f);
       if(nP > startPos)
-	{
-	  // compute new position
-	  unsigned offset = nP - position(finder);
-	  finder += offset;
-	  me.findNext = true;
-	  _setFinderEnd(finder);
-	  return true;
-	}      
+    {
+      // compute new position
+      unsigned offset = nP - position(finder);
+      finder += offset;
+      me.findNext = true;
+      _setFinderEnd(finder);
+      return true;
+    }
     }
     // reset mf finder to old position
     unsigned mf_offset = position(finder) - me.lastFPos;
@@ -754,7 +722,7 @@ SEQAN_CHECKPOINT
     // if we verfied till here .. verify the complete pattern
     if(cand){
       // we found an occurrence
-      node = _getRoot(me); // use root 
+      node = _getRoot(me); // use root
       int p1 = position(mf) - (in - me.range_table[node].start) - me.range_table[node].error;
       int p2 = position(mf) + (me.range_table[node].end - in + 1) + me.range_table[node].error;
 
@@ -765,18 +733,18 @@ SEQAN_CHECKPOINT
       THSFinder f(i);
       while(find(f,me.range_table[node].verifier))
       {
-	unsigned nP = p1 + position(f);
-	if(nP > startPos)
-	{
-	  // compute new position
-	  unsigned offset = nP - position(finder);
-	  finder += offset;
-	  me.lastFPos = position(mf);
-	  me.lastFNdl = position(me.multiPattern);
-	  me.findNext = true;
-	  _setFinderEnd(finder);
-	  return true;
-	}      
+    unsigned nP = p1 + position(f);
+    if(nP > startPos)
+    {
+      // compute new position
+      unsigned offset = nP - position(finder);
+      finder += offset;
+      me.lastFPos = position(mf);
+      me.lastFNdl = position(me.multiPattern);
+      me.findNext = true;
+      _setFinderEnd(finder);
+      return true;
+    }
       }
     }
   }
diff --git a/seqan/find/find_score.h b/seqan/find/find_score.h
index 9d12733..5b44d9d 100644
--- a/seqan/find/find_score.h
+++ b/seqan/find/find_score.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_FIND_SCORE_H
-#define SEQAN_HEADER_FIND_SCORE_H
+#ifndef SEQAN_HEADER_FIND_SH
+#define SEQAN_HEADER_FIND_SH
 
 namespace SEQAN_NAMESPACE_MAIN
 {
@@ -51,107 +51,101 @@ struct DPSearch {};
  * @extends Pattern
  * @headerfile <seqan/find.h>
  * @brief A dynamic programming algorithm for approximate string-matching with a user-definable scoring function.
- * 
+ *
  * @signature template <typename TNeedle, typename TScore[, typename TSpec[, typename TFindBeginPatternSpec]]>
  *            class Pattern<TNeedle, DPSearch<TScore[, TSpec[, TFindBeginPatternSpec]]> >;
- * 
+ *
  * @tparam TScore  The scoring function. Types: Score
  * @tparam TNeedle The needle type. Types: String
- * 
- * @section Remarks
- * 
+ *
  * The algorithm is based on the Sellers/Needleman-Wunsch dynamic progamming algorithm. The <tt>Pattern</tt> object only
  * contains the right-most column of the dynamic programming matrix.
  */
 
-/**
-.Spec.DPSearch:
-..cat:Searching
-..general:Class.Pattern
-..summary:A dynamic programming algorithm for approximate string-matching with a user-definable scoring function.
-..signature:Pattern<TNeedle, DPSearch<TScore [, TSpec [, TFindBeginPatternSpec] ]> >
-..param.TNeedle:The needle type.
-...type:Class.String
-..param.TScore:The scoring function.
-...type:Class.Score
-..remarks.text:The algorithm is based on the Sellers/Needleman-Wunsch dynamic progamming algorithm. 
-The $Pattern$ object only contains the right-most column of the dynamic programming matrix.
-...note:At the moment, the algorithm only works on linear gap costs.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Class.Score
-
 
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
 class Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> >:
-	public FindBegin_<Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > >
+    public FindBegin_<Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > >
 {
 public:
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef FindBegin_<Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > > TBase;
-
-	Holder<TNeedle>		data_host;
-	TScore				data_score;
-	TScoreValue			data_limit;
-	String<TScoreValue>	data_tab;
-	TScoreValue			data_maxscore;  //score of the needle matching itself (needed for banding FindPrefix)
-
-public: 
-	Pattern(): 
-		data_limit(0)
-	{ 
-SEQAN_CHECKPOINT
-	}
-
-	Pattern(TNeedle & _needle, 
-			TScore const & _score_func, 
-			TScoreValue _limit = 0): 
-		data_score(_score_func),
-		data_limit(_limit)
-	{ 
-SEQAN_CHECKPOINT
-		setHost(*this, _needle);
-	}
-
-	Pattern(TNeedle & _needle,
-			TScoreValue _limit = 0): 
-		data_limit(_limit)
-	{ 
-SEQAN_CHECKPOINT
-		setHost(*this, _needle);
-	}
-
-	Pattern(TScoreValue _limit): 
-		data_limit(_limit)
-	{ 
-SEQAN_CHECKPOINT
-		create(data_score);
-	}
-
-	Pattern(Pattern const & other):
-		TBase(other),	
-		data_host( other.data_host ),
-		data_score( other.data_score ), 
-		data_limit( other.data_limit ),
-		data_tab( other.data_tab ),
-		data_maxscore( other.data_maxscore)
-	{
-SEQAN_CHECKPOINT
-	}
-
-	inline Pattern & 
-	operator = (Pattern const & other) 
-	{ 
-SEQAN_CHECKPOINT
-		this->data_host = other.data_host;
-		this->data_score = other.data_score;
-		this->data_limit = other.data_limit;
-		this->data_tab = other.data_tab;
-		this->data_maxscore = other.data_maxscore;
-
-		return *this;
-	}
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef FindBegin_<Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > > TBase;
+
+    Holder<TNeedle>        data_host;
+    TScore                data_score;
+    TScoreValue            data_limit;
+    String<TScoreValue>    data_tab;
+    TScoreValue            data_maxscore;  //score of the needle matching itself (needed for banding FindPrefix)
+
+public:
+    Pattern() : data_limit(0), data_maxscore(0)
+    {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl, TScore const & _score_func, TScoreValue _limit = 0) :
+        data_score(_score_func),
+        data_limit(_limit),
+        data_maxscore(0)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+    }
+
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl, TScoreValue _limit = 0) :
+        data_limit(_limit),
+        data_maxscore(0)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+    }
+#else  // TODO(rrahn): Replace when c11 is standard.
+    Pattern(TNeedle & _needle, TScore const & _score_func, TScoreValue _limit = 0) :
+        data_score(_score_func), data_limit(_limit), data_maxscore(0)
+    {
+        setHost(*this, _needle);
+    }
+
+    Pattern(TNeedle & _needle, TScoreValue _limit = 0):
+        data_limit(_limit), data_maxscore(0)
+    {
+        setHost(*this, _needle);
+    }
+#endif  // SEQAN_CXX11_STANDARD
+
+    Pattern(TScoreValue _limit) : data_limit(_limit), data_maxscore(0)
+    {
+        create(data_score);
+    }
+
+    Pattern(Pattern const & other):
+        TBase(other),
+        data_host( other.data_host ),
+        data_score( other.data_score ),
+        data_limit( other.data_limit ),
+        data_tab( other.data_tab ),
+        data_maxscore( other.data_maxscore)
+    {}
+
+#ifdef SEQAN_CXX11_STANDARD
+#if (!defined(_MSC_VER) || _MSC_VER >= 1900) && (!defined(PLATFORM_WINDOWS_MINGW))
+    Pattern(Pattern && other) = default;
+    Pattern& operator = (Pattern && other) = default;
+#endif  // (!defined(_MSC_VER) || _MSC_VER >= 1900) && (!defined(PLATFORM_WINDOWS_MINGW))
+#endif  // SEQAN_CXX11_STANDARD
+    inline Pattern &
+    operator = (Pattern const & other)
+    {
+        this->data_host = other.data_host;
+        this->data_score = other.data_score;
+        this->data_limit = other.data_limit;
+        this->data_tab = other.data_tab;
+        this->data_maxscore = other.data_maxscore;
+
+        return *this;
+    }
+
+    ~Pattern()
+    {}
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -159,7 +153,7 @@ SEQAN_CHECKPOINT
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
 struct ScoringScheme <Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > >
 {
-	typedef TScore Type;
+    typedef TScore Type;
 };
 
 
@@ -167,7 +161,7 @@ struct ScoringScheme <Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPattern
 //.Metafunction.ScoreValue.param.T.type:Spec.DPSearch
 //template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
 //class ScoreValue <Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > >:
-//	Value<TScore>
+//    Value<TScore>
 //{
 //};
 
@@ -175,65 +169,34 @@ struct ScoringScheme <Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPattern
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-struct FindBeginPatternSpec <Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > > 
+struct FindBeginPatternSpec <Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > >
 {
-	typedef TFindBeginPatternSpec Type;
+    typedef TFindBeginPatternSpec Type;
 };
 template <typename TNeedle, typename TScore, typename TFindBeginPatternSpec>
 struct FindBeginPatternSpec <Pattern<TNeedle, DPSearch<TScore, FindPrefix, TFindBeginPatternSpec> > >
 {// no find begin for FindPrefix
-	typedef void Type;
+    typedef void Type;
 };
 
-//////////////////////////////////////////////////////////////////////////////
-
-
-template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-inline typename Host<Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > >::Type & 
-host(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.data_host);
-}
-
-template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-inline typename Host<Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > const>::Type & 
-host(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> >  const & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.data_host);
-}
-
 
 //____________________________________________________________________________
 
-template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec, typename TNeedle2>
-void 
-setHost(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me, 
-		TNeedle2 & ndl)
-{
-	me.data_host = ndl;
-	clear(me.data_tab);
-}
-template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec, typename TNeedle2>
-void 
-setHost(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me, 
-		TNeedle2 const & ndl)
+template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
+inline void
+_reinitPattern(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
 {
-	me.data_host = ndl;
-	clear(me.data_tab);
+    clear(me.data_tab);
 }
 
-
 //____________________________________________________________________________
 
 
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-inline TScore const & 
+inline TScore const &
 scoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
 {
-SEQAN_CHECKPOINT
-	return me.data_score;
+    return me.data_score;
 }
 
 //____________________________________________________________________________
@@ -241,21 +204,19 @@ SEQAN_CHECKPOINT
 
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec, typename TScore2>
 inline void
-setScoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me, 
-				 TScore2 & score)
+setScoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me,
+                 TScore2 & score)
 {
-SEQAN_CHECKPOINT
-	me.data_score = score;
-	clear(me.data_tab);
+    me.data_score = score;
+    clear(me.data_tab);
 }
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec, typename TScore2>
 inline void
-setScoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me, 
-				 TScore2 const & score)
+setScoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me,
+                 TScore2 const & score)
 {
-SEQAN_CHECKPOINT
-	me.data_score = score;
-	clear(me.data_tab);
+    me.data_score = score;
+    clear(me.data_tab);
 }
 
 //____________________________________________________________________________
@@ -272,22 +233,11 @@ SEQAN_CHECKPOINT
  * @return TScoreValue The score limit value.
  */
 
-/**.Function.scoreLimit
-..cat:Searching
-..summary:The minimal score a match must reach in approximate searching.
-..signature:scoreLimit(pattern)
-..class:Spec.DPSearch
-..param.pattern:A @Class.Pattern@ that can be used for approximate searching.
-...type:Spec.DPSearch
-..returns:The current score limit of $pattern$.
-*/
-
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-inline typename Value<TScore>::Type 
+inline typename Value<TScore>::Type
 scoreLimit(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > const & me)
 {
-SEQAN_CHECKPOINT
-	return me.data_limit;
+    return me.data_limit;
 }
 
 //____________________________________________________________________________
@@ -295,7 +245,7 @@ SEQAN_CHECKPOINT
 /*!
  * @fn DPSearchPattern#setSoreLimit
  * @headerfile <seqan/find.h>
- * @brief Set the minimal score a match must reach in approximate serach..
+ * @brief Set the minimal score a match must reach in approximate serach.
  *
  * @signature void setScoreLimit(pattern, limit);
  *
@@ -305,24 +255,12 @@ SEQAN_CHECKPOINT
  * @return TScoreValue The score limit value.
  */
 
-/**.Function.setScoreLimit
-..cat:Searching
-..summary:Sets the minimal score a match must reach in approximate searching.
-..signature:setScoreLimit(pattern, limit)
-..class:Spec.DPSearch
-..param.pattern:A @Class.Pattern@ that can be used for approximate searching.
-...type:Spec.DPSearch
-..param.limit:The new score limit.
-..see:Function.scoreLimit
-*/
-
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec, typename TScoreValue>
-inline void 
-setScoreLimit(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me, 
-			  TScoreValue _limit)
+inline void
+setScoreLimit(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me,
+              TScoreValue _limit)
 {
-SEQAN_CHECKPOINT
-	me.data_limit = _limit;
+    me.data_limit = _limit;
 }
 
 //____________________________________________________________________________
@@ -341,82 +279,68 @@ SEQAN_CHECKPOINT
  *                     is undefined.
  */
 
-/**.Function.getScore
-..cat:Searching
-..summary:Score of the last found match in approximate searching.
-..signature:getScore(pattern)
-..class:Spec.DPSearch
-..param.pattern:A @Class.Pattern@ that can be used for approximate searching.
-...type:Spec.DPSearch
-..returns:The score of the last match found using $pattern$.
-...remarks:If no match was found, the value is undefined.
-..see:Function.scoreLimit
-..see:Function.setScoreLimit
-..see:Function.find
-*/
-
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
 inline typename Value<TScore>::Type
 getScore(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
 {
-	return front(me.data_tab);
+    return front(me.data_tab);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 
 template <typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-inline void _patternInit (Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me) 
+inline void _patternInit (Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
 {
-	typedef Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > TPattern;
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef typename Size<TPattern>::Type TSize;
-	typedef String<TScoreValue> TTab;
-	typedef typename Iterator<TTab, Standard>::Type TIterator;
-	typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
-
-	TScore const & scoring = scoringScheme(me);
-	TScoreValue score_gap = scoreGapExtend(scoring);
-
-	TTab & string_tab = me.data_tab;
-
-	//allocate enough memory for one column of DP matrix
-
-	TSize need_length = length(needle(me));
-	SEQAN_ASSERT_GT(need_length, 0u);
-
-	resize(string_tab, need_length);
-	SEQAN_ASSERT_GEQ(length(string_tab), need_length);
-
-//	if (length(_dataNeedle(me)) < got_length) throw(0); //???TODO: Throw "not enough memory" exception
-
-	//init matrix
-	//note: The column is stored in reverse order
-	TIterator tab_end = begin(string_tab, Standard());
-	TIterator tab = end(string_tab, Standard());
-	
-	TScoreValue x = score_gap;
-
-	while (tab > tab_end)
-	{
-		--tab;
-		*tab = x;
-		x += score_gap;
-	}
-
-	if (IsSameType<TSpec, FindPrefix>::VALUE)
-	{//compute data_maxscore
-		me.data_maxscore = 0;
-		TNeedleIterator it = begin(needle(me), Standard());
-		TNeedleIterator it_end = end(needle(me), Standard());
-		for (; it != it_end; ++it)
-		{
-			me.data_maxscore += score(scoring, *it, *it);
-		}
-
-	}
-
-	_findBeginInit(me, needle(me));
+    typedef Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > TPattern;
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef typename Size<TPattern>::Type TSize;
+    typedef String<TScoreValue> TTab;
+    typedef typename Iterator<TTab, Standard>::Type TIterator;
+    typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+
+    TScore const & scoring = scoringScheme(me);
+    TScoreValue score_gap = scoreGapExtend(scoring);
+
+    TTab & string_tab = me.data_tab;
+
+    //allocate enough memory for one column of DP matrix
+
+    TSize need_length = length(needle(me));
+    SEQAN_ASSERT_GT(need_length, 0u);
+
+    resize(string_tab, need_length);
+    SEQAN_ASSERT_GEQ(length(string_tab), need_length);
+
+//    if (length(_dataNeedle(me)) < got_length) throw(0); //???TODO: Throw "not enough memory" exception
+
+    //init matrix
+    //note: The column is stored in reverse order
+    TIterator tab_end = begin(string_tab, Standard());
+    TIterator tab = end(string_tab, Standard());
+
+    TScoreValue x = score_gap;
+
+    while (tab > tab_end)
+    {
+        --tab;
+        *tab = x;
+        x += score_gap;
+    }
+
+    if (IsSameType<TSpec, FindPrefix>::VALUE)
+    {//compute data_maxscore
+        me.data_maxscore = 0;
+        TNeedleIterator it = begin(needle(me), Standard());
+        TNeedleIterator it_end = end(needle(me), Standard());
+        for (; it != it_end; ++it)
+        {
+            me.data_maxscore += score(scoring, *it, *it);
+        }
+
+    }
+
+    _findBeginInit(me, needle(me));
 }
 
 
@@ -425,131 +349,131 @@ inline void _patternInit (Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPat
 // find, findNext
 //////////////////////////////////////////////////////////////////////////////
 
-//proportional gap cost: Needleman-Wunsch 
+//proportional gap cost: Needleman-Wunsch
 
 //???TODO: Ukkonen trick?
 //???TODO: Finder for affine gap costs?
 
 template <typename TFinder, typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-bool 
+bool
 _findScoreSimpleProportional(TFinder & finder, Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
 {
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef String<TScoreValue> TTab;
-	typedef typename Iterator<TTab, Standard>::Type TTabIterator;
-	typedef typename Iterator<TNeedle const, Standard>::Type TNeedleIterator;
-	typedef typename Value<typename Haystack<TFinder>::Type>::Type THaystackValue;
-	typedef typename Haystack<TFinder>::Type THaystack;
-	typedef typename Size<THaystack>::Type TSize;
-
-	String<TScoreValue> & string_tab = me.data_tab;
-	TScore const & scoring = scoringScheme(me);
-
-	TScoreValue score_gap = scoreGapExtend(scoring);
-//	TScoreValue score_match = scoreMatch(scoringScheme(me));
-//	TScoreValue score_mismatch = scoreMismatch(scoringScheme(me));
-
-	TSize prefix_begin_position;	
-
-	if (empty(finder))
-	{
-		clear(me.data_tab);
-		_patternInit(me);
-		_finderSetNonEmpty(finder);
-		prefix_begin_position = position(finder);
-	}
-	else
-	{
-		goNext(finder);
-		prefix_begin_position = beginPosition(finder);
-	}
-
-	
-	TSize haystack_length = length(container(hostIterator(finder)));
-
-	//limit search width for prefix search
-	if (IsSameType<TSpec, FindPrefix>::VALUE && (score_gap < 0))
-	{
-		TSize maxlen = prefix_begin_position + length(needle(me)) + ((scoreLimit(me) - me.data_maxscore) / score_gap) + 1;
-		if (haystack_length > maxlen)
-		{
-			haystack_length = maxlen;
-		}
-	}
-
-	//start searching
-
-	TTabIterator tab_begin = end(string_tab, Standard());
-
-	TNeedle const & ndl = needle(me);
-	TNeedleIterator it_begin = begin(ndl, Standard());
-	TNeedleIterator it_end = end(ndl, Standard());
-
-	//for each character in haystack, do...
-	for (; position(finder) < haystack_length; ++finder)
-	{
-		//get character
-		THaystackValue c = *finder;
-
-		//init some variables
-		TNeedleIterator it = it_begin;
-		TScoreValue * tab = tab_begin;
-		TScoreValue h = (IsSameType<TSpec, FindPrefix>::VALUE) ? score_gap * (position(finder)-prefix_begin_position) : 0;
-		TScoreValue v = (IsSameType<TSpec, FindPrefix>::VALUE) ? h + score_gap : 0;
-
-		//fill the column
-		while (it < it_end)
-		{
-			--tab; //note: the column is stored in "reverse order"
-
-//			TScoreValue m2 = (c == *it) ? h + score_match : h + score_mismatch;
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef String<TScoreValue> TTab;
+    typedef typename Iterator<TTab, Standard>::Type TTabIterator;
+    typedef typename Iterator<TNeedle const, Standard>::Type TNeedleIterator;
+    typedef typename Value<typename Haystack<TFinder>::Type>::Type THaystackValue;
+    typedef typename Haystack<TFinder>::Type THaystack;
+    typedef typename Size<THaystack>::Type TSize;
+
+    String<TScoreValue> & string_tab = me.data_tab;
+    TScore const & scoring = scoringScheme(me);
+
+    TScoreValue score_gap = scoreGapExtend(scoring);
+//    TScoreValue score_match = scoreMatch(scoringScheme(me));
+//    TScoreValue score_mismatch = scoreMismatch(scoringScheme(me));
+
+    TSize prefix_begin_position;
+
+    if (empty(finder))
+    {
+        clear(me.data_tab);
+        _patternInit(me);
+        _finderSetNonEmpty(finder);
+        prefix_begin_position = position(finder);
+    }
+    else
+    {
+        goNext(finder);
+        prefix_begin_position = beginPosition(finder);
+    }
+
+
+    TSize haystack_length = length(container(hostIterator(finder)));
+
+    //limit search width for prefix search
+    if (IsSameType<TSpec, FindPrefix>::VALUE && (score_gap < 0))
+    {
+        TSize maxlen = prefix_begin_position + length(needle(me)) + ((scoreLimit(me) - me.data_maxscore) / score_gap) + 1;
+        if (haystack_length > maxlen)
+        {
+            haystack_length = maxlen;
+        }
+    }
+
+    //start searching
+
+    TTabIterator tab_begin = end(string_tab, Standard());
+
+    TNeedle const & ndl = needle(me);
+    TNeedleIterator it_begin = begin(ndl, Standard());
+    TNeedleIterator it_end = end(ndl, Standard());
+
+    //for each character in haystack, do...
+    for (; position(finder) < haystack_length; ++finder)
+    {
+        //get character
+        THaystackValue c = *finder;
+
+        //init some variables
+        TNeedleIterator it = it_begin;
+        TScoreValue * tab = tab_begin;
+        TScoreValue h = (IsSameType<TSpec, FindPrefix>::VALUE) ? score_gap * (position(finder)-prefix_begin_position) : 0;
+        TScoreValue v = (IsSameType<TSpec, FindPrefix>::VALUE) ? h + score_gap : 0;
+
+        //fill the column
+        while (it < it_end)
+        {
+            --tab; //note: the column is stored in "reverse order"
+
+//            TScoreValue m2 = (c == *it) ? h + score_match : h + score_mismatch;
 //char d = *it;
-			TScoreValue m2 = h + score(scoring, c, *it);
-			h = *tab;
-			TScoreValue m1 = (h > v) ? h + score_gap : v + score_gap;
-
-			v = (m1 > m2) ? m1 : m2;
-			*tab = v;
-
-			++it;
-		}
-
-		if (*tab >= scoreLimit(me) )
-		{//found a hit
-			_setFinderEnd(finder);
-			if (IsSameType<TSpec, FindPrefix>::VALUE)
-			{
-				_setFinderLength(finder, endPosition(finder));
-			}
-			return true;
-		}
-
-	}
-
-	//found nothing
-	return false;
+            TScoreValue m2 = h + score(scoring, c, *it);
+            h = *tab;
+            TScoreValue m1 = (h > v) ? h + score_gap : v + score_gap;
+
+            v = (m1 > m2) ? m1 : m2;
+            *tab = v;
+
+            ++it;
+        }
+
+        if (*tab >= scoreLimit(me) )
+        {//found a hit
+            _setFinderEnd(finder);
+            if (IsSameType<TSpec, FindPrefix>::VALUE)
+            {
+                _setFinderLength(finder, endPosition(finder));
+            }
+            return true;
+        }
+
+    }
+
+    //found nothing
+    return false;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TFinder, typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-inline bool 
-find(TFinder & finder, 
-	 Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
+inline bool
+find(TFinder & finder,
+     Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
 {
-	SEQAN_ASSERT_EQ(scoreGapOpen(scoringScheme(me)), scoreGapExtend(scoringScheme(me))); //this finder is only defined for linear gap costs
-	return _findScoreSimpleProportional(finder, me);
+    SEQAN_ASSERT_EQ(scoreGapOpen(scoringScheme(me)), scoreGapExtend(scoringScheme(me))); //this finder is only defined for linear gap costs
+    return _findScoreSimpleProportional(finder, me);
 }
 
 template <typename TFinder, typename TNeedle, typename TScore, typename TSpec, typename TFindBeginPatternSpec>
-inline bool 
-find(TFinder & finder, 
-	 Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me,
-	 int const limit_)
+inline bool
+find(TFinder & finder,
+     Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me,
+     int const limit_)
 {
-	SEQAN_ASSERT_EQ(scoreGapOpen(scoringScheme(me)), scoreGapExtend(scoringScheme(me))); //this finder is only defined for linear gap costs
-	setScoreLimit(me, limit_);
-	return _findScoreSimpleProportional(finder, me);
+    SEQAN_ASSERT_EQ(scoreGapOpen(scoringScheme(me)), scoreGapExtend(scoringScheme(me))); //this finder is only defined for linear gap costs
+    setScoreLimit(me, limit_);
+    return _findScoreSimpleProportional(finder, me);
 }
 
 
diff --git a/seqan/find/find_set_horspool.h b/seqan/find/find_set_horspool.h
index b7f39c7..24e7a4d 100644
--- a/seqan/find/find_set_horspool.h
+++ b/seqan/find/find_set_horspool.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,33 +46,17 @@ namespace SEQAN_NAMESPACE_MAIN
  * @class SetHorspoolPattern
  * @extends Pattern
  * @headerfile <seqan/find.h>
- * 
+ *
  * @brief Multiple exact string matching using set horspool algorithm.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, SetHorspool>;
- * 
- * @tparam TNeedle The needle type, a string of keywords.  Types: @link SequenceConcept @endlink.
- * 
- * @section Remarks
- * 
+ *
+ * @tparam TNeedle The needle type, a string of keywords.  Types: @link ContainerConcept @endlink.
+ *
  * The types of all keywords in the needle and the haystack have to match.
  */
 
-/**
-.Spec.SetHorspool:
-..summary: Multiple exact string matching using set horspool algorithm.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, SetHorspool>
-..param.TNeedle:The needle type, a string of keywords.
-...type:Class.String
-..remarks.text:The types of all keywords in the needle and the haystack have to match.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.SetHorspool
-
 struct SetHorspool_;
 typedef Tag<SetHorspool_> SetHorspool;
 
@@ -82,152 +66,118 @@ template <typename TNeedle>
 class Pattern<TNeedle, SetHorspool> {
 //____________________________________________________________________________
 private:
-	Pattern(Pattern const& other);
-	Pattern const& operator=(Pattern const & other);
+    Pattern(Pattern const& other);
+    Pattern const& operator=(Pattern const & other);
 
 //____________________________________________________________________________
 public:
-	typedef typename Size<TNeedle>::Type TSize;
-	typedef typename Value<TNeedle>::Type TValue;
-	typedef typename Value<TValue>::Type TAlphabet;
-	typedef Graph<Automaton<TAlphabet> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	
-	Holder<TNeedle> data_host;
-	Graph<Automaton<TAlphabet> > data_reverseTrie;  // Search trie
-	String<String<TSize> > data_terminalStateMap;
-	String<TSize> data_dMap;	// Jump table
-	TSize data_lmin;
-	String<TSize> data_endPositions;	// All remaining keyword indices
-	TSize data_keywordIndex;			// Current keyword that produced a hit
-	TSize data_needleLength;			// Last length of needle to reposition finder
-	TVertexDescriptor data_lastState;   // Last state in the trie
+    typedef typename Size<TNeedle>::Type TSize;
+    typedef typename Value<TNeedle>::Type TValue;
+    typedef typename Value<TValue>::Type TAlphabet;
+    typedef Graph<Automaton<TAlphabet> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    Holder<TNeedle> data_host;
+    Graph<Automaton<TAlphabet> > data_reverseTrie;  // Search trie
+    String<String<TSize> > data_terminalStateMap;
+    String<TSize> data_dMap;    // Jump table
+    TSize data_lmin;
+    String<TSize> data_endPositions;    // All remaining keyword indices
+    TSize data_keywordIndex;            // Current keyword that produced a hit
+    TSize data_needleLength;            // Last length of needle to reposition finder
+    TVertexDescriptor data_lastState;   // Last state in the trie
 
 //____________________________________________________________________________
 
-	Pattern() {
-	}
+    Pattern() {
+    }
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		setHost(*this, ndl);
-	}
-
-	~Pattern() {
-		SEQAN_CHECKPOINT
-	}		
 //____________________________________________________________________________
 };
 
-//////////////////////////////////////////////////////////////////////////////
-// Host Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, SetHorspool> >
-{
-	typedef TNeedle Type;
-};
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, SetHorspool> const>
-{
-	typedef TNeedle const Type;
-};
-
 //////////////////////////////////////////////////////////////////////////////
 // Functions
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, SetHorspool> & me, TNeedle2 const & needle) {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Size<TKeyword>::Type TSize;
-	typedef typename Value<TKeyword>::Type TAlphabet;
-
-	// clean-up
-	clear(me.data_reverseTrie);
-	clear(me.data_terminalStateMap);
-	clear(me.data_endPositions);
-	clear(me.data_dMap);
-	me.data_lmin=0;
-
-	// Create Trie
-	createTrieOnReverse(me.data_reverseTrie,me.data_terminalStateMap,needle);
-	assignRoot(me.data_reverseTrie,0);
-	setValue(me.data_host, needle);
-
-	// Create jump map
-	TSize alphabet_size = ValueSize<TAlphabet>::VALUE;
-	resize(me.data_dMap, alphabet_size);
-	me.data_lmin = _getInfinity<TSize>();
-	typename Iterator<TNeedle2 const, Rooted>::Type it = begin(needle);
-	for(;!atEnd(it);goNext(it)) {
-		TSize tmp = length(*it);
-		if (tmp<me.data_lmin) me.data_lmin = tmp;
-	}
-	for(TSize i=0;i<alphabet_size;++i) {
-		me.data_dMap[i]=me.data_lmin;
-	}
-	goBegin(it);
-	for(;!atEnd(it);goNext(it)) {
-		for(TSize pos = 0;pos < length(*it) - 1; ++pos) {
-			TSize ind = ordValue((TAlphabet)(*it)[pos]);	
-			if ((length(*it)- 1 - pos) < me.data_dMap[ind]) {
-				me.data_dMap[ind] = (length(*it) - 1 - pos);
-			}
-		}
-	}
-
-	/*
-	fstream strm;
-	strm.open(TEST_PATH "my_trie.dot", ios_base::out | ios_base::trunc);
-	String<String<char> > nodeMap;
-	_createTrieNodeNames(me.data_reverseTrie, me.data_terminalStateMap, nodeMap);
-	String<String<char> > edgeMap;
-	_createEdgeNames(me.data_reverseTrie,edgeMap);
-	write(strm,me.data_reverseTrie,nodeMap,edgeMap,DotDrawing());
-	strm.close();
-	*/
-}
-
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, SetHorspool> & me, TNeedle2 & needle)
-{
-	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
-}
-
-//____________________________________________________________________________
-
-
 template <typename TNeedle>
-inline void _patternInit (Pattern<TNeedle, SetHorspool> & me) 
+void _reinitPattern(Pattern<TNeedle, SetHorspool> & me)
 {
-SEQAN_CHECKPOINT
-	clear(me.data_endPositions);
-	me.data_keywordIndex = 0;
-	me.data_lastState = getRoot(me.data_reverseTrie);
+    SEQAN_CHECKPOINT
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Size<TKeyword>::Type TSize;
+    typedef typename Value<TKeyword>::Type TAlphabet;
+
+    // clean-up
+    clear(me.data_reverseTrie);
+    clear(me.data_terminalStateMap);
+    clear(me.data_endPositions);
+    clear(me.data_dMap);
+    me.data_lmin=0;
+
+    // Create Trie
+    createTrieOnReverse(me.data_reverseTrie,me.data_terminalStateMap, needle(me));
+    assignRoot(me.data_reverseTrie,0);
+
+    // Create jump map
+    TSize alphabet_size = ValueSize<TAlphabet>::VALUE;
+    resize(me.data_dMap, alphabet_size);
+    me.data_lmin = _getInfinity<TSize>();
+    typename Iterator<TNeedle, Rooted>::Type it = begin(needle(me));
+    for(;!atEnd(it);goNext(it)) {
+        TSize tmp = length(*it);
+        if (tmp<me.data_lmin) me.data_lmin = tmp;
+    }
+    for(TSize i=0;i<alphabet_size;++i) {
+        me.data_dMap[i]=me.data_lmin;
+    }
+    goBegin(it);
+    for(;!atEnd(it);goNext(it)) {
+        for(TSize pos = 0;pos < length(*it) - 1; ++pos) {
+            TSize ind = ordValue((TAlphabet)(*it)[pos]);
+            if ((length(*it)- 1 - pos) < me.data_dMap[ind]) {
+                me.data_dMap[ind] = (length(*it) - 1 - pos);
+            }
+        }
+    }
+
+    /*
+    fstream strm;
+    strm.open(TEST_PATH "my_trie.dot", ios_base::out | ios_base::trunc);
+    String<String<char> > nodeMap;
+    _createTrieNodeNames(me.data_reverseTrie, me.data_terminalStateMap, nodeMap);
+    String<String<char> > edgeMap;
+    _createEdgeNames(me.data_reverseTrie,edgeMap);
+    writeRecords(strm,me.data_reverseTrie,nodeMap,edgeMap,DotDrawing());
+    strm.close();
+    */
 }
 
-
 //____________________________________________________________________________
 
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, SetHorspool>const>::Type & 
-host(Pattern<TNeedle, SetHorspool> & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.data_host);
-}
 
 template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, SetHorspool>const>::Type & 
-host(Pattern<TNeedle, SetHorspool> const & me)
+inline void _patternInit (Pattern<TNeedle, SetHorspool> & me)
 {
 SEQAN_CHECKPOINT
-	return value(me.data_host);
+    clear(me.data_endPositions);
+    me.data_keywordIndex = 0;
+    me.data_lastState = getRoot(me.data_reverseTrie);
 }
 
 //____________________________________________________________________________
@@ -237,80 +187,82 @@ template <typename TNeedle>
 inline typename Size<TNeedle>::Type
 position(Pattern<TNeedle, SetHorspool> & me)
 {
-	return me.data_keywordIndex;
+    return me.data_keywordIndex;
 }
 
 
 template <typename TFinder, typename TNeedle>
 inline bool find(TFinder & finder, Pattern<TNeedle, SetHorspool> & me) {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Size<TKeyword>::Type TSize;
-	typedef typename Value<TKeyword>::Type TAlphabet;
-	typedef Graph<Automaton<TAlphabet> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	TVertexDescriptor current = getRoot(me.data_reverseTrie); 
-
-	// Process left-over hits
-	if ((!empty(finder)) &&
-		(!empty(me.data_endPositions))) {
-		finder += me.data_needleLength;
-		current = me.data_lastState;
-		me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
-		me.data_needleLength = length(getValue(host(me), me.data_keywordIndex))-1;
-		if (length(me.data_endPositions) > 1) resize(me.data_endPositions, (length(me.data_endPositions)-1));
-		else clear(me.data_endPositions);
-		me.data_lastState = current;
-		finder -= me.data_needleLength;
-		return true;
-	}
-
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	TSize j = 0;
-	if (empty(finder)) {
-		_patternInit(me);
-		_finderSetNonEmpty(finder);
-		finder += me.data_lmin - 1;
-	} else {
-		finder += me.data_needleLength;
-		j = me.data_needleLength + 1;
-		current = me.data_lastState;
-	}
-
-	TSize haystackLength = length(container(finder));
-	bool oldMatch = true;
-	// Do not change to !atEnd(finder) because of jump map!
-	while(position(finder) < haystackLength) {
-		while ((position(finder)>=j) && 
-				(getSuccessor(me.data_reverseTrie, current, *(finder-j))!= nilVal))
-		{
-			me.data_endPositions = getProperty(me.data_terminalStateMap,current);
-			if ((!oldMatch) && (!empty(me.data_endPositions))) break;
-			current = getSuccessor(me.data_reverseTrie, current, *(finder-j));
-			if (current == nilVal) break;
-			++j;
-			oldMatch = false;
-		}
-		me.data_endPositions = getProperty(me.data_terminalStateMap,current);
-		if ((!oldMatch) &&
-			(!empty(me.data_endPositions)))
-		{
-			me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
-			me.data_needleLength = length(getValue(host(me), me.data_keywordIndex))-1;
-			if (length(me.data_endPositions) > 1) resize(me.data_endPositions, length(me.data_endPositions)-1);
-			else clear(me.data_endPositions);
-			me.data_lastState = current;
-			finder -= me.data_needleLength;
-			return true;
-		}
-		oldMatch = false;
-		TSize ind = ordValue(*finder);
-		setPosition(finder, position(finder) + getValue(me.data_dMap, ind));
-		j = 0;
-		current = getRoot(me.data_reverseTrie);
-	}
-	return false;
+    SEQAN_CHECKPOINT
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Size<TKeyword>::Type TSize;
+    typedef typename Value<TKeyword>::Type TAlphabet;
+    typedef Graph<Automaton<TAlphabet> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    TVertexDescriptor current = getRoot(me.data_reverseTrie);
+
+    // Process left-over hits
+    if ((!empty(finder)) &&
+        (!empty(me.data_endPositions))) {
+        finder += me.data_needleLength;
+        current = me.data_lastState;
+        me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
+        me.data_needleLength = length(getValue(host(me), me.data_keywordIndex))-1;
+        if (length(me.data_endPositions) > 1) resize(me.data_endPositions, (length(me.data_endPositions)-1));
+        else clear(me.data_endPositions);
+        me.data_lastState = current;
+        finder -= me.data_needleLength;
+        return true;
+    }
+
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    TSize j = 0;
+    if (empty(finder)) {
+        _patternInit(me);
+        _finderSetNonEmpty(finder);
+        finder += me.data_lmin - 1;
+    } else {
+        finder += me.data_needleLength;
+        j = me.data_needleLength + 1;
+        current = me.data_lastState;
+    }
+
+    TSize haystackLength = length(container(finder));
+    bool oldMatch = true;
+    // Do not change to !atEnd(finder) because of jump map!
+    while(position(finder) < haystackLength) {
+        while ((position(finder)>=j) &&
+                (getSuccessor(me.data_reverseTrie, current, *(finder-j))!= nilVal))
+        {
+            me.data_endPositions = getProperty(me.data_terminalStateMap,current);
+            if ((!oldMatch) && (!empty(me.data_endPositions))) break;
+            current = getSuccessor(me.data_reverseTrie, current, *(finder-j));
+            if (current == nilVal) break;
+            ++j;
+            oldMatch = false;
+        }
+        me.data_endPositions = getProperty(me.data_terminalStateMap,current);
+        if ((!oldMatch) &&
+            (!empty(me.data_endPositions)))
+        {
+            me.data_keywordIndex = me.data_endPositions[length(me.data_endPositions)-1];
+            me.data_needleLength = length(getValue(host(me), me.data_keywordIndex))-1;
+            if (length(me.data_endPositions) > 1) resize(me.data_endPositions, length(me.data_endPositions)-1);
+            else clear(me.data_endPositions);
+            me.data_lastState = current;
+            finder -= me.data_needleLength;
+            _setFinderLength(finder, me.data_needleLength+1);
+            _setFinderEnd(finder, position(finder)+length(finder));            
+            return true;
+        }
+        oldMatch = false;
+        TSize ind = ordValue(*finder);
+        setPosition(finder, position(finder) + getValue(me.data_dMap, ind));
+        j = 0;
+        current = getRoot(me.data_reverseTrie);
+    }
+    return false;
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_shiftand.h b/seqan/find/find_shiftand.h
index 77e6acd..210b2ab 100644
--- a/seqan/find/find_shiftand.h
+++ b/seqan/find/find_shiftand.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -49,60 +49,54 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Exact string matching using bit parallelism.
  *
  * The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, ShiftAnd>;
- * 
+ *
  * @tparam TNeedle The needle type. Types: String
- * 
- * @section Remarks
- * 
+ *
  * The types of the needle and the haystack have to match.
  */
 
-/**
-.Spec.ShiftAnd:
-..summary: Exact string matching using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, ShiftAnd>
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks.text:The types of the needle and the haystack have to match.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.ShiftAnd
-
 struct ShiftAnd_;
 typedef Tag<ShiftAnd_> ShiftAnd;
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle>
-class Pattern<TNeedle, ShiftAnd> {
+class Pattern<TNeedle, ShiftAnd>
+{
 //____________________________________________________________________________
 public:
-	typedef unsigned int TWord;
-	enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
-
-//	Holder<TNeedle> data_host;
-	String<TWord> bitMasks;			// Look up table for each character in the alphabet (called B in "Navarro")
-	String<TWord> prefSufMatch;		// Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
-	TWord needleLength;				// e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
-	TWord blockCount;				// #unsigned ints required to store needle	
-
-//____________________________________________________________________________
-
-	Pattern() {}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		setHost(*this, ndl);
-	}
+    typedef unsigned int TWord;
+    enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
+
+    Holder<TNeedle>  data_host;
+    String<TWord> bitMasks;            // Look up table for each character in the alphabet (called B in "Navarro")
+    String<TWord> prefSufMatch;        // Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
+    TWord needleLength;                // e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
+    TWord blockCount;                // #unsigned ints required to store needle
+
+    Pattern()
+    {}
+
+#ifdef SEQAN_CXX11_STANDARD
+
+    // Custom c'tor setting a needle.
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl, SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 
-//____________________________________________________________________________
 };
 
 
@@ -110,204 +104,148 @@ class Pattern<TNeedle, ShiftAnd> {
 // Functions
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2>
-inline void
-setHost(Pattern<TNeedle, ShiftAnd> & me, TNeedle2 const & needle) 
-{
-	SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
-	typedef typename Value<TNeedle>::Type TValue;
-	
-	me.needleLength = length(needle);
-	if (me.needleLength < 1)
-		me.blockCount = 1;
-	else
-		me.blockCount = (me.needleLength - 1) / BitsPerValue<TWord>::VALUE + 1;
-	
-	clear(me.bitMasks);
-	resize(me.bitMasks, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
-
-	for (TWord j = 0; j < me.needleLength; ++j)
-		me.bitMasks[
-			me.blockCount * ordValue(convert<TValue>(getValue(needle, j)))
-			+ j / me.MACHINE_WORD_SIZE
-		] |= (TWord)1 << (j % me.MACHINE_WORD_SIZE);
-
-//	setValue(me.data_host, needle);
-
-	/*
-	// Debug code
-	std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << ::std::endl;
-	std::cout << "Needle length: " << me.needleLength << ::std::endl;
-	std::cout << "Block count: " << me.blockCount << ::std::endl;
-
-	for(unsigned int i=0;i<ValueSize<TValue>::VALUE;++i) {
-		if ((i<97) || (i>122)) continue;
-		std::cout << static_cast<char>(i) << ": ";
-		for(int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-				std::cout << ((me.bitMasks[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-	}
-	*/
-}
-
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost(Pattern<TNeedle, ShiftAnd> & me, TNeedle2 & needle)
-{
-	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
-}
-
-//____________________________________________________________________________
-
 template <typename TNeedle>
-inline TNeedle
-host(Pattern<TNeedle, ShiftAnd> const & pattern)
-{
-SEQAN_CHECKPOINT
-
-	typedef typename Pattern<TNeedle, ShiftAnd>::TWord TWord;
-	typedef typename Value<TNeedle>::Type TValue;
-
-	TNeedle temp;
-	resize(temp, pattern.needleLength, Exact());
-
-	TValue v = TValue();
-	for (unsigned i = 0; i < length(pattern.bitMasks); i += pattern.blockCount)
-	{
-		for (unsigned j = 0; j < pattern.needleLength; j++)
-			if ((pattern.bitMasks[i + j / pattern.MACHINE_WORD_SIZE] & (TWord)1 << (j % pattern.MACHINE_WORD_SIZE)) != (TWord)0)
-				temp[j] = v;
-		++v;
-	}
-	return temp;
-}
-
-template <typename TNeedle>
-inline TNeedle
-host(Pattern<TNeedle, ShiftAnd> & pattern)
-{
-SEQAN_CHECKPOINT
-	return host(const_cast<Pattern<TNeedle, ShiftAnd> const &>(pattern));
-}
-
-//____________________________________________________________________________
-
-template <typename TNeedle>
-inline TNeedle
-needle(Pattern<TNeedle, ShiftAnd> const & pattern)
-{
-SEQAN_CHECKPOINT
-	return host(pattern);
-}
-
-template <typename TNeedle>
-inline TNeedle
-needle(Pattern<TNeedle, ShiftAnd> & pattern)
+inline void
+_reinitPattern(Pattern<TNeedle, ShiftAnd> & me)
 {
-SEQAN_CHECKPOINT
-	return host(const_cast<Pattern<TNeedle, ShiftAnd> const &>(pattern));
+    SEQAN_CHECKPOINT
+    typedef unsigned int TWord;
+    typedef typename Value<TNeedle>::Type TValue;
+
+    TNeedle& ndl = needle(me);
+
+    me.needleLength = length(ndl);
+    if (me.needleLength < 1)
+        me.blockCount = 1;
+    else
+        me.blockCount = (me.needleLength - 1) / BitsPerValue<TWord>::VALUE + 1;
+
+    clear(me.bitMasks);
+    resize(me.bitMasks, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
+
+    for (TWord j = 0; j < me.needleLength; ++j)
+        me.bitMasks[
+            me.blockCount * ordValue(convert<TValue>(getValue(ndl, j)))
+            + j / me.MACHINE_WORD_SIZE
+        ] |= (TWord)1 << (j % me.MACHINE_WORD_SIZE);
+
+//    setValue(me.data_host, needle);
+
+    /*
+    // Debug code
+    std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << std::endl;
+    std::cout << "Needle length: " << me.needleLength << std::endl;
+    std::cout << "Block count: " << me.blockCount << std::endl;
+
+    for(unsigned int i=0;i<ValueSize<TValue>::VALUE;++i) {
+        if ((i<97) || (i>122)) continue;
+        std::cout << static_cast<char>(i) << ": ";
+        for(int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                std::cout << ((me.bitMasks[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+    }
+    */
 }
 
 //____________________________________________________________________________
 
 template <typename TNeedle>
-inline void 
-_patternInit (Pattern<TNeedle, ShiftAnd> & me) 
+inline void
+_patternInit (Pattern<TNeedle, ShiftAnd> & me)
 {
 SEQAN_CHECKPOINT
-	clear(me.prefSufMatch);
-	resize(me.prefSufMatch, me.blockCount, 0, Exact());
+    clear(me.prefSufMatch);
+    resize(me.prefSufMatch, me.blockCount, 0, Exact());
 }
 
 //____________________________________________________________________________
 
 template <typename TFinder, typename TNeedle>
-inline bool 
-_findShiftAndSmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me) 
+inline bool
+_findShiftAndSmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me)
 {
 SEQAN_CHECKPOINT
-	typedef typename Value<TNeedle>::Type TValue;
-	typedef unsigned int TWord;
-	TWord compare = (TWord)1 << (me.needleLength - 1);
-	while (!atEnd(finder)) 
-	{
-		TWord pos = ordValue(convert<TValue>(getValue(finder)));
-		me.prefSufMatch[0] = ((me.prefSufMatch[0] << 1) | (TWord)1) & me.bitMasks[pos];
-		if ((me.prefSufMatch[0] & compare) != 0) 
-		{
-			_setFinderEnd(finder);
-			finder -= me.needleLength - 1;
-			return true; 
-		}
-		goNext(finder);
-	}
-	return false;
+    typedef typename Value<TNeedle>::Type TValue;
+    typedef unsigned int TWord;
+    TWord compare = (TWord)1 << (me.needleLength - 1);
+    while (!atEnd(finder))
+    {
+        TWord pos = ordValue(convert<TValue>(getValue(finder)));
+        me.prefSufMatch[0] = ((me.prefSufMatch[0] << 1) | (TWord)1) & me.bitMasks[pos];
+        if ((me.prefSufMatch[0] & compare) != 0)
+        {
+            _setFinderEnd(finder);
+            finder -= me.needleLength - 1;
+            return true;
+        }
+        goNext(finder);
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
-inline bool 
-_findShiftAndLargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me) 
+inline bool
+_findShiftAndLargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me)
 {
 SEQAN_CHECKPOINT
-	typedef typename Value<TNeedle>::Type TValue;
-	typedef unsigned int TWord;
-	
-	TWord compare = (TWord)1 << ((me.needleLength - 1) % BitsPerValue<TWord>::VALUE);
-	while (!atEnd(finder)) 
-	{
-		TWord pos = ordValue(convert<TValue>(getValue(finder)));
-		TWord carry = 1;
-		for(TWord block = 0; block < me.blockCount; ++block)
-		{
-			bool newCarry = (me.prefSufMatch[block] & ((TWord)1<< (BitsPerValue<TWord>::VALUE - 1))) != 0; 
-			me.prefSufMatch[block] <<= 1;
-			me.prefSufMatch[block] |= carry;
-			carry = newCarry;
-		}
-		for(TWord block = 0; block < me.blockCount; ++block)
-			me.prefSufMatch[block] &= me.bitMasks[me.blockCount * pos + block];
-		if ((me.prefSufMatch[me.blockCount-1] & compare) != 0) 
-		{
-			_setFinderEnd(finder);
-			finder -= me.needleLength - 1;
-			return true; 
-		}
-
-		/*
-		// Debug code
-		std::cout << "   ";
-		for(int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-				std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-		*/
-		goNext(finder);
-	}
-	return false;
+    typedef typename Value<TNeedle>::Type TValue;
+    typedef unsigned int TWord;
+
+    TWord compare = (TWord)1 << ((me.needleLength - 1) % BitsPerValue<TWord>::VALUE);
+    while (!atEnd(finder))
+    {
+        TWord pos = ordValue(convert<TValue>(getValue(finder)));
+        TWord carry = 1;
+        for(TWord block = 0; block < me.blockCount; ++block)
+        {
+            bool newCarry = (me.prefSufMatch[block] & ((TWord)1<< (BitsPerValue<TWord>::VALUE - 1))) != 0;
+            me.prefSufMatch[block] <<= 1;
+            me.prefSufMatch[block] |= carry;
+            carry = newCarry;
+        }
+        for(TWord block = 0; block < me.blockCount; ++block)
+            me.prefSufMatch[block] &= me.bitMasks[me.blockCount * pos + block];
+        if ((me.prefSufMatch[me.blockCount-1] & compare) != 0)
+        {
+            _setFinderEnd(finder);
+            finder -= me.needleLength - 1;
+            return true;
+        }
+
+        /*
+        // Debug code
+        std::cout << "   ";
+        for(int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+        */
+        goNext(finder);
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
 inline bool find(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me) {
-	SEQAN_CHECKPOINT
-
-	if (empty(finder)) {
-		_patternInit(me);
-		_setFinderLength(finder, me.needleLength);
-		_finderSetNonEmpty(finder);
-	} else
-		finder += me.needleLength;
-
-	// Fast algorithm for needles < machine word?
-	if (me.blockCount == 1)
-		return _findShiftAndSmallNeedle(finder, me);
-	else
-		return _findShiftAndLargeNeedle(finder, me);
+    SEQAN_CHECKPOINT
+
+    if (empty(finder)) {
+        _patternInit(me);
+        _setFinderLength(finder, me.needleLength);
+        _finderSetNonEmpty(finder);
+    } else
+        finder += me.needleLength;
+
+    // Fast algorithm for needles < machine word?
+    if (me.blockCount == 1)
+        return _findShiftAndSmallNeedle(finder, me);
+    else
+        return _findShiftAndLargeNeedle(finder, me);
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_shiftor.h b/seqan/find/find_shiftor.h
index 247ae17..58f06f6 100644
--- a/seqan/find/find_shiftor.h
+++ b/seqan/find/find_shiftor.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -49,59 +49,54 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Exact string matching using bit parallelism.
  *
  * The Shift-Or algorithm is applicable to search small patterns in texts using a small alphabet.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, ShiftOr>;
- * 
+ *
  * @tparam TNeedle The needle type. Types: @link String @endlink.
- * 
- * @section Remarks
- * 
+ *
  * The types of the needle and the haystack have to match.
  */
 
-/**
-.Spec.ShiftOr:
-..summary: Exact string matching using bit parallelism. The Shift-Or algorithm is applicable to search small patterns in texts using a small alphabet.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, ShiftOr>
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks.text:The types of the needle and the haystack have to match.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.ShiftOr
-
 struct ShiftOr_;
 typedef Tag<ShiftOr_> ShiftOr;
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle>
-class Pattern<TNeedle, ShiftOr> {
+class Pattern<TNeedle, ShiftOr>
+{
 //____________________________________________________________________________
 public:
-	typedef unsigned int TWord;
-	enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
+    typedef unsigned int TWord;
+    enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
 
-//	Holder<TNeedle> data_host;
-	String<TWord> bitMasks;			// Look up table for each character in the alphabet (called B in "Navarro")
-	String<TWord> prefSufMatch;		// Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
-	TWord needleLength;				// e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
-	TWord blockCount;				// #unsigned ints required to store needle	
+    Holder<TNeedle> data_host;
+    String<TWord> bitMasks;            // Look up table for each character in the alphabet (called B in "Navarro")
+    String<TWord> prefSufMatch;        // Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
+    TWord needleLength;                // e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
+    TWord blockCount;                // #unsigned ints required to store needle
 
 //____________________________________________________________________________
 
-	Pattern() {}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		setHost(*this, ndl);
-	}
-
+    Pattern()
+    {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    // Custom c'tor setting a needle.
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl, SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
@@ -110,119 +105,63 @@ class Pattern<TNeedle, ShiftOr> {
 // Functions
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost(Pattern<TNeedle, ShiftOr> & me, TNeedle2 const & needle) 
-{
-	SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
-	typedef typename Value<TNeedle>::Type TValue;
-	
-	me.needleLength = length(needle);
-	if (me.needleLength < 1)
-		me.blockCount = 1;
-	else
-		me.blockCount = (me.needleLength - 1) / BitsPerValue<TWord>::VALUE + 1;
-	
-	clear(me.bitMasks);
-	resize(me.bitMasks, me.blockCount * ValueSize<TValue>::VALUE, (TWord)~0, Exact());
-
-	for (TWord j = 0; j < me.needleLength; ++j)
-		me.bitMasks[
-			me.blockCount * ordValue(convert<TValue>(getValue(needle, j)))
-			+ j / me.MACHINE_WORD_SIZE
-		] ^= (TWord)1 << (j % me.MACHINE_WORD_SIZE);
-
-//	setValue(me.data_host, needle);
-
-	/*
-	// Debug code
-	std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << ::std::endl;
-	std::cout << "Needle length: " << me.needleLength << ::std::endl;
-	std::cout << "Block count: " << me.blockCount << ::std::endl;
-
-	for(unsigned int i=0;i<ValueSize<TValue>::VALUE;++i) {
-		if ((i<97) || (i>122)) continue;
-		std::cout << static_cast<char>(i) << ": ";
-		for(int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-				std::cout << ((me.bitMasks[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-	}
-	*/
-}
-
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost(Pattern<TNeedle, ShiftOr> & me, TNeedle2 & needle)
-{
-	setHost(me, const_cast<TNeedle2 const &>(needle));
-}
-
-//____________________________________________________________________________
-
-template <typename TNeedle>
-inline TNeedle
-host(Pattern<TNeedle, ShiftOr> const & pattern)
-{
-SEQAN_CHECKPOINT
-
-	typedef typename Pattern<TNeedle, ShiftOr>::TWord TWord;
-	typedef typename Value<TNeedle>::Type TValue;
-
-	TNeedle temp;
-	resize(temp, pattern.needleLength, Exact());
-
-	TValue v = TValue();
-	for (unsigned i = 0; i < length(pattern.bitMasks); i += pattern.blockCount)
-	{
-		for (unsigned j = 0; j < pattern.needleLength; j++)
-			if ((pattern.bitMasks[i + j / pattern.MACHINE_WORD_SIZE] & (TWord)1 << (j % pattern.MACHINE_WORD_SIZE)) == (TWord)0)
-				temp[j] = v;
-		++v;
-	}
-	return temp;
-}
-
-template <typename TNeedle>
-inline TNeedle
-host(Pattern<TNeedle, ShiftOr> & pattern)
-{
-SEQAN_CHECKPOINT
-	return host(const_cast<Pattern<TNeedle, ShiftOr> const &>(pattern));
-}
-
-//____________________________________________________________________________
-
+// TODO(rrahn): Change to rvalue reference for TNeedle2 as soon as all pattern store pointer to the needle.
 template <typename TNeedle>
-inline TNeedle
-needle(Pattern<TNeedle, ShiftOr> const & pattern)
+inline void
+_reinitPattern(Pattern<TNeedle, ShiftOr> & me)
 {
-SEQAN_CHECKPOINT
-	return host(pattern);
-}
-
-template <typename TNeedle>
-inline TNeedle
-needle(Pattern<TNeedle, ShiftOr> & pattern)
-{
-SEQAN_CHECKPOINT
-	return host(const_cast<Pattern<TNeedle, ShiftOr> const &>(pattern));
+    SEQAN_CHECKPOINT
+    typedef unsigned int TWord;
+    typedef typename Value<TNeedle>::Type TValue;
+
+    TNeedle& ndl = needle(me);
+    me.needleLength = length(ndl);
+    if (me.needleLength < 1)
+        me.blockCount = 1;
+    else
+        me.blockCount = (me.needleLength - 1) / BitsPerValue<TWord>::VALUE + 1;
+
+    clear(me.bitMasks);
+    resize(me.bitMasks, me.blockCount * ValueSize<TValue>::VALUE, (TWord)~0, Exact());
+
+    for (TWord j = 0; j < me.needleLength; ++j)
+        me.bitMasks[
+            me.blockCount * ordValue(convert<TValue>(getValue(ndl, j)))
+            + j / me.MACHINE_WORD_SIZE
+        ] ^= (TWord)1 << (j % me.MACHINE_WORD_SIZE);
+
+//    setValue(me.data_host, needle);
+
+    /*
+    // Debug code
+    std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << std::endl;
+    std::cout << "Needle length: " << me.needleLength << std::endl;
+    std::cout << "Block count: " << me.blockCount << std::endl;
+
+    for(unsigned int i=0;i<ValueSize<TValue>::VALUE;++i) {
+        if ((i<97) || (i>122)) continue;
+        std::cout << static_cast<char>(i) << ": ";
+        for(int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                std::cout << ((me.bitMasks[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+    }
+    */
 }
 
 //____________________________________________________________________________
 
 template <typename TNeedle>
-inline void 
-_patternInit (Pattern<TNeedle, ShiftOr> & me) 
+inline void
+_patternInit (Pattern<TNeedle, ShiftOr> & me)
 {
 SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
+    typedef unsigned int TWord;
 
-	clear(me.prefSufMatch);
-	resize(me.prefSufMatch, me.blockCount, (TWord) ~0, Exact());
+    clear(me.prefSufMatch);
+    resize(me.prefSufMatch, me.blockCount, (TWord) ~0, Exact());
 }
 
 //____________________________________________________________________________
@@ -230,121 +169,121 @@ SEQAN_CHECKPOINT
 /*
 template <typename TFinder, typename TNeedle>
 bool _findShiftOrSmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me) {
-	SEQAN_CHECKPOINT
-	typedef unsigned int TWord;
-	TWord compare= (~(1 << (me.needleLength-1)));
-	while (!atEnd(finder)) {
-		TWord pos = convert<TWord>(*finder);
-		me.prefSufMatch[0] = (me.prefSufMatch[0] << 1) | me.bitMasks[me.blockCount*pos];
-		if ((me.prefSufMatch[0] | compare) != (TWord) ~0) {
-			finder-=(me.needleLength-1);
-			return true; 
-		}
-		goNext(finder);
-	}
-	return false;
+    SEQAN_CHECKPOINT
+    typedef unsigned int TWord;
+    TWord compare= (~(1 << (me.needleLength-1)));
+    while (!atEnd(finder)) {
+        TWord pos = convert<TWord>(*finder);
+        me.prefSufMatch[0] = (me.prefSufMatch[0] << 1) | me.bitMasks[me.blockCount*pos];
+        if ((me.prefSufMatch[0] | compare) != (TWord) ~0) {
+            finder-=(me.needleLength-1);
+            return true;
+        }
+        goNext(finder);
+    }
+    return false;
 }
 */
 template <typename TFinder, typename TNeedle>
-inline bool 
-_findShiftOrSmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me) 
+inline bool
+_findShiftOrSmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me)
 {
 SEQAN_CHECKPOINT
-	typedef typename Haystack<TFinder>::Type THaystack;
+    typedef typename Haystack<TFinder>::Type THaystack;
     typedef typename Parameter_<THaystack>::Type TParamHaystack;
-	typedef typename Value<TNeedle>::Type TValue;
-
-	TParamHaystack hstk = haystack(finder);
-
-	typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
-	THaystackIterator hayit = iter(hstk, position(finder));
-	THaystackIterator hayit_end = end(hstk, Standard());
-
-	typedef unsigned int TWord;
-	TWord mask = (TWord)1 << (me.needleLength - 1);
-	TWord pref_suf_match = me.prefSufMatch[0];
-
-	for (; hayit < hayit_end; ++hayit)
-	{
-		pref_suf_match <<= 1;				//shift...
-		pref_suf_match |= me.bitMasks[ordValue(convert<TValue>(getValue(hayit)))];	//...or
-
-		if (pref_suf_match & mask) 
-			continue;
-
-		//found a hit!
-		//set finder to start position
-		_setFinderEnd(finder, (hayit - begin(hstk, Standard())) + 1);
-		setPosition(finder,  beginPosition(finder)); 
-		//save machine state
-		me.prefSufMatch[0] = pref_suf_match; 
-		return true;
-	}
-	return false;
+    typedef typename Value<TNeedle>::Type TValue;
+
+    TParamHaystack hstk = haystack(finder);
+
+    typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+    THaystackIterator hayit = iter(hstk, position(finder));
+    THaystackIterator hayit_end = end(hstk, Standard());
+
+    typedef unsigned int TWord;
+    TWord mask = (TWord)1 << (me.needleLength - 1);
+    TWord pref_suf_match = me.prefSufMatch[0];
+
+    for (; hayit < hayit_end; ++hayit)
+    {
+        pref_suf_match <<= 1;                //shift...
+        pref_suf_match |= me.bitMasks[ordValue(convert<TValue>(getValue(hayit)))];    //...or
+
+        if (pref_suf_match & mask)
+            continue;
+
+        //found a hit!
+        //set finder to start position
+        _setFinderEnd(finder, (hayit - begin(hstk, Standard())) + 1);
+        setPosition(finder,  beginPosition(finder));
+        //save machine state
+        me.prefSufMatch[0] = pref_suf_match;
+        return true;
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
-inline bool 
-_findShiftOrLargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me) 
+inline bool
+_findShiftOrLargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftOr> & me)
 {
 SEQAN_CHECKPOINT
-	typedef typename Value<TNeedle>::Type TValue;
-	typedef unsigned int TWord;
-
-	TWord compare = ~((TWord)1 << ((me.needleLength - 1) % BitsPerValue<TWord>::VALUE));
-	while (!atEnd(finder))
-	{
-		TWord pos = ordValue(convert<TValue>(getValue(finder)));
-		TWord carry = 0;
-		for(TWord block = 0; block < me.blockCount; ++block)
-		{
-			bool newCarry = (me.prefSufMatch[block] & ((TWord)1 << (BitsPerValue<TWord>::VALUE - 1))) != 0;
-			me.prefSufMatch[block] <<= 1;
-			me.prefSufMatch[block] |= carry;
-			carry = newCarry;
-		}
-		for(TWord block = 0; block < me.blockCount; ++block)
-			me.prefSufMatch[block] |= me.bitMasks[me.blockCount * pos + block];
-		if ((me.prefSufMatch[me.blockCount - 1] | compare) != (TWord) ~0) 
-		{
-			_setFinderEnd(finder);
-			finder -= me.needleLength - 1;
-			return true;  
-		}
-
-		/*
-		// Debug code
-		std::cout << "   ";
-		for(int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-				std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-		*/
-		goNext(finder);
-	}
-	return false;
+    typedef typename Value<TNeedle>::Type TValue;
+    typedef unsigned int TWord;
+
+    TWord compare = ~((TWord)1 << ((me.needleLength - 1) % BitsPerValue<TWord>::VALUE));
+    while (!atEnd(finder))
+    {
+        TWord pos = ordValue(convert<TValue>(getValue(finder)));
+        TWord carry = 0;
+        for(TWord block = 0; block < me.blockCount; ++block)
+        {
+            bool newCarry = (me.prefSufMatch[block] & ((TWord)1 << (BitsPerValue<TWord>::VALUE - 1))) != 0;
+            me.prefSufMatch[block] <<= 1;
+            me.prefSufMatch[block] |= carry;
+            carry = newCarry;
+        }
+        for(TWord block = 0; block < me.blockCount; ++block)
+            me.prefSufMatch[block] |= me.bitMasks[me.blockCount * pos + block];
+        if ((me.prefSufMatch[me.blockCount - 1] | compare) != (TWord) ~0)
+        {
+            _setFinderEnd(finder);
+            finder -= me.needleLength - 1;
+            return true;
+        }
+
+        /*
+        // Debug code
+        std::cout << "   ";
+        for(int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+                std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+        */
+        goNext(finder);
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
-inline bool 
-find(TFinder & finder, Pattern<TNeedle, ShiftOr> & me) 
+inline bool
+find(TFinder & finder, Pattern<TNeedle, ShiftOr> & me)
 {
 SEQAN_CHECKPOINT
-	if (empty(finder)) {
-		_patternInit(me);
-		_setFinderLength(finder, me.needleLength);
-		_finderSetNonEmpty(finder);
-	} else
-		finder += me.needleLength;
-
-	// Fast algorithm for needles < machine word?
-	if (me.blockCount == 1) {
-		return _findShiftOrSmallNeedle(finder, me);
-	} else {
-		return _findShiftOrLargeNeedle(finder, me);
-	}
+    if (empty(finder)) {
+        _patternInit(me);
+        _setFinderLength(finder, me.needleLength);
+        _finderSetNonEmpty(finder);
+    } else
+        finder += me.needleLength;
+
+    // Fast algorithm for needles < machine word?
+    if (me.blockCount == 1) {
+        return _findShiftOrSmallNeedle(finder, me);
+    } else {
+        return _findShiftOrLargeNeedle(finder, me);
+    }
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_simple.h b/seqan/find/find_simple.h
index 8911b4b..0997652 100644
--- a/seqan/find/find_simple.h
+++ b/seqan/find/find_simple.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,63 +47,41 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pattern
  * @headerfile <seqan/find.h>
  * @brief A brute force online searching algorithm.
- * 
+ *
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, Simple>;
- * 
- * @tparam TNeedle The needle type.  Types: @link SequenceConcept @endlink.
- * 
- * @section Remarks
- * 
+ *
+ * @tparam TNeedle The needle type.  Types: @link ContainerConcept @endlink.
+ *
  * This specialization should only be used if no other is applicable.
  */
 
-/**
-.Spec.Simple Finder:
-..summary:A brute force online searching algorithm.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, Simple>
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks:This specialization should only be used if no other is applicable.
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.Simple Finder
-
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle>
 class Pattern<TNeedle, Simple> {
 //____________________________________________________________________________
 public:
-	Holder<TNeedle> data_host;
+    Holder<TNeedle> data_host;
 
 //____________________________________________________________________________
 
-	Pattern() {}
-
-	Pattern(Pattern const & other):
-		data_host(other.data_host)
-	{
-	}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		setHost(*this, ndl);
-	}
-
-	~Pattern(){}
-
-	Pattern const & 
-	operator = (Pattern const & other)
-	{
-		data_host = other.data_host;
-		return *this;
-	}
-
+    Pattern() {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl, SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        setHost(*this, ndl);
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
@@ -112,61 +90,48 @@ class Pattern<TNeedle, Simple> {
 // Functions
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, Simple> & me, 
-			  TNeedle2 & needle) 
-{
-	setValue(me.data_host, needle);
-}
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, Simple> & me, 
-			  TNeedle2 const & needle) 
-{
-	setValue(me.data_host, needle);
-}
-
 //____________________________________________________________________________
 
 
 template <typename TFinder, typename TNeedle>
 inline bool find(TFinder & finder,
-				 Pattern<TNeedle, Simple> & me)
+                 Pattern<TNeedle, Simple> & me)
 {
-	typedef typename Haystack<TFinder>::Type THaystack;
-	typedef typename Parameter_<THaystack const>::Type TParamHaystack;
-	typedef typename Iterator<THaystack const, Standard>::Type THaystackIterator;
+    typedef typename Haystack<TFinder>::Type THaystack;
+    typedef typename Parameter_<THaystack const>::Type TParamHaystack;
+    typedef typename Iterator<THaystack const, Standard>::Type THaystackIterator;
 
-	if (empty(finder))
-	{
-		_setFinderLength(finder, length(needle(me)));
-		_finderSetNonEmpty(finder);
-	}
-	else ++finder;
+    if (empty(finder))
+    {
+        _setFinderLength(finder, length(needle(me)));
+        _finderSetNonEmpty(finder);
+    }
+    else ++finder;
 
-	TParamHaystack hstk = haystack(finder);
-	TNeedle const & ndl = needle(me);
+    TParamHaystack hstk = haystack(finder);
+    TNeedle const & ndl = needle(me);
 
-	THaystackIterator res = ::std::search(begin(hstk, Standard())+position(finder), end(hstk, Standard()), begin(ndl, Standard()), end(ndl, Standard()));
+    THaystackIterator res = std::search(begin(hstk, Standard())+position(finder), end(hstk, Standard()), begin(ndl, Standard()), end(ndl, Standard()));
 
-	if (res == end(hstk, Standard())) return false;
+    if (res == end(hstk, Standard())) return false;
 
-	_setFinderEnd(finder, (res - begin(hstk, Standard())) + length(ndl));
-	setPosition(finder, beginPosition(finder));
-	return true; 
+    _setFinderEnd(finder, (res - begin(hstk, Standard())) + length(ndl));
+    setPosition(finder, beginPosition(finder));
+    return true;
 
 /*
-	TSize n = length(hstk);
-	TSize m = length(ndl);
-	while (position(finder)+m <= n)
-	{
-		if (ndl == infix(hstk, position(finder), position(finder)+m))
-		{
-			_setFinderEnd(finder, position(finder)+m);
-			return true; 
-		}
-		++finder;
-	}
-	return false;
+    TSize n = length(hstk);
+    TSize m = length(ndl);
+    while (position(finder)+m <= n)
+    {
+        if (ndl == infix(hstk, position(finder), position(finder)+m))
+        {
+            _setFinderEnd(finder, position(finder)+m);
+            return true;
+        }
+        ++finder;
+    }
+    return false;
 */
 }
 
diff --git a/seqan/find/find_wild_shiftand.h b/seqan/find/find_wild_shiftand.h
index 9bdb090..01582ce 100644
--- a/seqan/find/find_wild_shiftand.h
+++ b/seqan/find/find_wild_shiftand.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,6 +47,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
 /*!
  * @class WildShiftAndPattern
+ * @extends Pattern
  * @headerfile <seqan/find.h>
  * @brief Exact string matching with wildcards using bit parallelism.
  *
@@ -55,39 +56,19 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, WildShiftAnd>;
  *
- * @tparam TNeedle The needle type.  Type: @link SequenceConcept @endlink.
- *
- * @section Remarks
+ * @tparam TNeedle The needle type.  Type: @link ContainerConcept @endlink.
  *
  * The supported wildcards are <tt>*</tt> (zero or more occurrence), <tt>+</tt> (one or more occurrences), <tt>?</tt>
  * (optional character), <tt>.</tt> (every character), character classes (e.g. <tt>[a-z]</tt>) and bounded repeats (e.g.
  * <tt>{n,m}</tt>).
- * 
+ *
  * After the find-Method returned the Finder will point to the last position of the occurrence
- * 
+ *
  * We encourage the user to intialize the Pattern with a <tt>String&lt;char&gt;</tt> (@link HostedConcept#setHost
  * @endlink or the C'tor). If you use for instance <tt>String&lt;Dna&gt;</tt> instead you won't be able to specify
  * wildcards.
  */
 
-/**
-.Spec.WildShiftAnd:
-..summary: Exact string matching with wildcards using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet.
-..general:Class.Pattern
-..cat:Searching
-..signature:Pattern<TNeedle, WildShiftAnd>
-..param.TNeedle:The needle type.
-...type:Class.String
-..remarks.text:The supported wildcards are $*$ (zero or more occurrence), $+$ (one or more occurrences), $?$ (optional character), $.$ 
-(every character), character classes (e.g. $[a-z]$) and bounded repeats (e.g. ${n,m}$).
-..remarks.text:After the find-Method returned the Finder will point to the last position of the occurrence
-..remarks.text:We encourage the user to intialize the Pattern with a $String<char>$ (@Function.setHost@ or the C'tor).
-If you use for instance $String <Dna>$ instead you won't be able to specify wildcards
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.WildShiftAnd
-
 struct WildShiftAnd_;
 typedef Tag<WildShiftAnd_> WildShiftAnd;
 
@@ -97,37 +78,48 @@ template <typename TNeedle>
 class Pattern<TNeedle, WildShiftAnd> {
 //____________________________________________________________________________
 public:
-	typedef unsigned TWord;
-
-	Holder<TNeedle> data_host;
-	String<TWord> table;			// Look up table for each character in the alphabet (called B in "Navarro")
-	
-	String<TWord> s_table;			// marks all positions, that can remain active, after reading a specific character (called S in "Navarro")
-	String<TWord> a_table;			// marks all positions of optional characters in the pattern (called A in "Navarro")
-	String<TWord> i_table;			// marks all positions in the pattern, that preceed a block of optional characters (called I in "Navarro")
-	String<TWord> f_table;			// marks all end-positions of blocks of optional characters (called F in "Navarro")
-	
-	String<TWord> prefSufMatch;		// Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
-	String<TWord> df;				// additional bit mask to enable flooding of bits
-	
-	TWord needleLength;				// e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
-	TWord character_count;			// number of normal characters in the needle
-	TWord blockCount;				// #unsigned ints required to store needle	
-
-	bool _valid;					// is the pattern valid or not
+    typedef unsigned TWord;
 
-//____________________________________________________________________________
+    Holder<TNeedle> data_host;
+    String<TWord> table;            // Look up table for each character in the alphabet (called B in "Navarro")
+
+    String<TWord> s_table;            // marks all positions, that can remain active, after reading a specific character (called S in "Navarro")
+    String<TWord> a_table;            // marks all positions of optional characters in the pattern (called A in "Navarro")
+    String<TWord> i_table;            // marks all positions in the pattern, that preceed a block of optional characters (called I in "Navarro")
+    String<TWord> f_table;            // marks all end-positions of blocks of optional characters (called F in "Navarro")
+
+    String<TWord> prefSufMatch;        // Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
+    String<TWord> df;                // additional bit mask to enable flooding of bits
 
-	Pattern()
-		: _valid(false)
-		{}
+    TWord needleLength;                // e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
+    TWord character_count;            // number of normal characters in the needle
+    TWord blockCount;                // #unsigned ints required to store needle
 
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-		: _valid(false) {
-		setHost(*this, ndl);
-	}
+    bool _valid;                    // is the pattern valid or not
 
+//____________________________________________________________________________
+
+    Pattern()
+        : _valid(false)
+        {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+        : _valid(false)
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+        : _valid(false) {
+        setHost(*this, ndl);
+    }
+#endif // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
@@ -140,449 +132,475 @@ class Pattern<TNeedle, WildShiftAnd> {
 // debug method to visualize bitmasks
 inline void _printMask(String <unsigned> const &  mask,unsigned line,String <char> name)
 {
-	unsigned len = length(mask);
-	std::cout << name << " " << line << "   ";
-	for(unsigned int j=0;j<len;++j) {
-		for(unsigned int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
-			std::cout << ((mask[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
-		}
-		std::cout << " ";
-	}
-	std::cout << ::std::endl;
+    unsigned len = length(mask);
+    std::cout << name << " " << line << "   ";
+    for(unsigned int j=0;j<len;++j) {
+        for(unsigned int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
+            std::cout << ((mask[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
+        }
+        std::cout << " ";
+    }
+    std::cout << std::endl;
 }
 */
 
 //____________________________________________________________________________
-//								VALIDATION
+//                                VALIDATION
 
 inline bool _isUnsigned(String<char> const & number)
 {
 //IOREV move to future is-module, maybe just use: return (strtol(number) >= 0) [if I understand this correctly)
-	unsigned int len = length(number);
-	for(unsigned int i = 0;i < len;++i){
-		if(!(convert<unsigned int>(getValue(number,i)) <= 57 && convert<unsigned int>(getValue(number,i)) >= 47))
-			return false;
-	}
-	return true;
+    unsigned int len = length(number);
+    for(unsigned int i = 0;i < len;++i){
+        if(!(convert<unsigned int>(getValue(number,i)) <= 57 && convert<unsigned int>(getValue(number,i)) >= 47))
+            return false;
+    }
+    return true;
 }
 
 // check if the pattern is valid
 template <typename TNeedle2>
 bool _validate(TNeedle2 const & needle)
 {
-	typedef unsigned TWord;
-	
-	TWord nl = length(needle);
-	TWord len = nl;
-	TWord i = 0;
-	
-	while (i < nl){
-		if (convert<char>(getValue(needle,i)) == '['){
-			// check if class ends
-		  while(i < nl && convert<char>(getValue(needle,i)) != ']')++i;
-			if(i == nl)	return false;
-		}
-		else if(convert<char>(getValue(needle,i)) == '*' || convert<char>(getValue(needle,i)) == '+' || convert<char>(getValue(needle,i)) == '?'){
-			// check for consecutive runs of +,*,?
-			++i;
-			if(convert<char>(getValue(needle,i)) == '*' || convert<char>(getValue(needle,i)) == '+' || convert<char>(getValue(needle,i)) == '?')
-				return false;
-			++i;
-		}
-		else if(convert<char>(getValue(needle,i)) == '{'){
-SEQAN_CHECKPOINT
-			String <char> number;
-			TWord n,m;
-			n = m = 0;
-			--len;++i; // get to the first number
-			while(i < nl && convert<char>(getValue(needle,i)) != '}' && convert<char>(getValue(needle,i)) != ',') {			
-SEQAN_CHECKPOINT
-				append(number,convert<char>(getValue(needle,i)));
-				--len;++i;
-			}
-			// class didn't ended
-			if(i == nl)	return false;
-			
-			// isNumber
-			if(!_isUnsigned(number)) return false;
-			n = atoi(toCString(number));
-			
-			// check the second number
-			if (convert<char>(getValue(needle,i)) == ','){
-SEQAN_CHECKPOINT
-				--len;++i;
-				clear(number);
-				while(i < nl && convert<char>(getValue(needle,i)) != '}') {			
-SEQAN_CHECKPOINT
-					append(number,convert<char>(getValue(needle,i)));
-					--len;++i;
-				}
-			
-				// class didn't ended
-				if(i == nl) return false;
-				
-				// isNumber
-				if(!_isUnsigned(number)) return false;
-				m = atoi(toCString(number));
-				--len;
-			}
-			else --len;
-			
-			// check if optional part is greater or equal then fixed
-			if(m < n && m != 0)	return false;
-		}
-		else if(convert<char>(getValue(needle,i)) == '\\'){
-SEQAN_CHECKPOINT
-			// check if there exists a next character
-			if(i == nl - 1)	return false;
-			else ++i;
-		}
-		++i;
-	}
-	return true;
+    typedef unsigned TWord;
+
+    TWord nl = length(needle);
+    TWord len = nl;
+    TWord i = 0;
+
+    while (i < nl){
+        if (convert<char>(getValue(needle,i)) == '['){
+            // check if class ends
+          while(i < nl && convert<char>(getValue(needle,i)) != ']')++i;
+            if(i == nl)    return false;
+        }
+        else if(convert<char>(getValue(needle,i)) == '*' || convert<char>(getValue(needle,i)) == '+' || convert<char>(getValue(needle,i)) == '?'){
+            // check for consecutive runs of +,*,?
+            ++i;
+            if(convert<char>(getValue(needle,i)) == '*' || convert<char>(getValue(needle,i)) == '+' || convert<char>(getValue(needle,i)) == '?')
+                return false;
+            ++i;
+        }
+        else if(convert<char>(getValue(needle,i)) == '{'){
+SEQAN_CHECKPOINT
+            String <char> number;
+            TWord n,m;
+            n = m = 0;
+            --len;++i; // get to the first number
+            while(i < nl && convert<char>(getValue(needle,i)) != '}' && convert<char>(getValue(needle,i)) != ',') {
+SEQAN_CHECKPOINT
+                append(number,convert<char>(getValue(needle,i)));
+                --len;++i;
+            }
+            // class didn't ended
+            if(i == nl)    return false;
+
+            // isNumber
+            if(!_isUnsigned(number)) return false;
+            n = atoi(toCString(number));
+
+            // check the second number
+            if (convert<char>(getValue(needle,i)) == ','){
+SEQAN_CHECKPOINT
+                --len;++i;
+                clear(number);
+                while(i < nl && convert<char>(getValue(needle,i)) != '}') {
+SEQAN_CHECKPOINT
+                    append(number,convert<char>(getValue(needle,i)));
+                    --len;++i;
+                }
+
+                // class didn't ended
+                if(i == nl) return false;
+
+                // isNumber
+                if(!_isUnsigned(number)) return false;
+                m = atoi(toCString(number));
+                --len;
+            }
+            else --len;
+
+            // check if optional part is greater or equal then fixed
+            if(m < n && m != 0)    return false;
+        }
+        else if(convert<char>(getValue(needle,i)) == '\\'){
+SEQAN_CHECKPOINT
+            // check if there exists a next character
+            if(i == nl - 1)    return false;
+            else ++i;
+        }
+        ++i;
+    }
+    return true;
 }
 
-/* 
+/*
   determine the original pattern length -- wo wildcard-chars
   currently supported +,*,[..],?,.,{n,m}
 */
 template <typename TNeedle>
 unsigned _lengthWithoutWildcards(TNeedle const & needle) {
 
-	typedef unsigned TWord;
-
-	TWord nl = length(needle);
-	TWord len = nl;
-	TWord i = 0;
-	while(i < nl) {
-		if(convert<char>(getValue(needle,i)) == '+'){
-SEQAN_CHECKPOINT
-			--len;
-		}
-		else if(convert<char>(getValue(needle,i)) == '*'){
-SEQAN_CHECKPOINT
-			--len;
-		}
-		else if(convert<char>(getValue(needle,i)) == '?'){
-SEQAN_CHECKPOINT
-			--len;
-		}
-		else if(convert<char>(getValue(needle,i)) == '['){
-SEQAN_CHECKPOINT
-			while(convert<char>(getValue(needle,i)) != ']') {			
-SEQAN_CHECKPOINT
-				--len;++i;
-			}
-		}
-		else if(convert<char>(getValue(needle,i)) == '{'){
-SEQAN_CHECKPOINT
-			String <char> number;
-			TWord n,m;
-			n = m = 0;
-			--len;++i; // get to the first number
-			while(convert<char>(getValue(needle,i)) != '}' && convert<char>(getValue(needle,i)) != ',') {			
-SEQAN_CHECKPOINT
-				append(number,convert<char>(getValue(needle,i)));
-				--len;++i;
-			}
-			// we also have to read the second number
-			n = atoi(toCString(number));
-			if (convert<char>(getValue(needle,i)) == ','){
-SEQAN_CHECKPOINT
-				--len;++i;
-				//lets get m
-				clear(number);
-				while(convert<char>(getValue(needle,i)) != '}') {			
-SEQAN_CHECKPOINT
-					append(number,convert<char>(getValue(needle,i)));
-					--len;++i;
-				}
-				m = atoi(toCString(number));
-				--len;
-			}
-			else
-				--len;
-			
-			len += (m != 0 ? m : n) - 1;
-		}
-		else if(convert<char>(getValue(needle,i)) == '\\'){
-SEQAN_CHECKPOINT
-			--len;++i; // next character could be a \ too
-		}
-		++i;
-	}
-
-	return len;
+    typedef unsigned TWord;
+
+    TWord nl = length(needle);
+    TWord len = nl;
+    TWord i = 0;
+    while(i < nl) {
+        if(convert<char>(getValue(needle,i)) == '+'){
+SEQAN_CHECKPOINT
+            --len;
+        }
+        else if(convert<char>(getValue(needle,i)) == '*'){
+SEQAN_CHECKPOINT
+            --len;
+        }
+        else if(convert<char>(getValue(needle,i)) == '?'){
+SEQAN_CHECKPOINT
+            --len;
+        }
+        else if(convert<char>(getValue(needle,i)) == '['){
+SEQAN_CHECKPOINT
+            while(convert<char>(getValue(needle,i)) != ']') {
+SEQAN_CHECKPOINT
+                --len;++i;
+            }
+        }
+        else if(convert<char>(getValue(needle,i)) == '{'){
+SEQAN_CHECKPOINT
+            String <char> number;
+            TWord n,m;
+            n = m = 0;
+            --len;++i; // get to the first number
+            while(convert<char>(getValue(needle,i)) != '}' && convert<char>(getValue(needle,i)) != ',') {
+SEQAN_CHECKPOINT
+                append(number,convert<char>(getValue(needle,i)));
+                --len;++i;
+            }
+            // we also have to read the second number
+            n = atoi(toCString(number));
+            if (convert<char>(getValue(needle,i)) == ','){
+SEQAN_CHECKPOINT
+                --len;++i;
+                //lets get m
+                clear(number);
+                while(convert<char>(getValue(needle,i)) != '}') {
+SEQAN_CHECKPOINT
+                    append(number,convert<char>(getValue(needle,i)));
+                    --len;++i;
+                }
+                m = atoi(toCString(number));
+                --len;
+            }
+            else
+                --len;
+
+            len += (m != 0 ? m : n) - 1;
+        }
+        else if(convert<char>(getValue(needle,i)) == '\\'){
+SEQAN_CHECKPOINT
+            --len;++i; // next character could be a \ too
+        }
+        ++i;
+    }
+
+    return len;
 }
 
 /*
-	returns all character codes contained in the class
+    returns all character codes contained in the class
 */
 template <typename TValue,typename TNeedle2>
 String <unsigned> _getCharacterClass(TNeedle2 const & host,unsigned start,unsigned end){
-	typedef unsigned TWord;
-	String <unsigned> ret;
-	unsigned pos = start;
-	while (pos < end){
-SEQAN_CHECKPOINT
-		if(convert<char>(getValue(host,pos)) != '-')
-			append(ret,convert<TWord>(convert<TValue>(getValue(host,pos))));
-		else{
-SEQAN_CHECKPOINT
-			// could be a range
-			if (pos > start && pos < end && (convert<TWord>(convert<TValue>(getValue(host,pos-1))) < convert<TWord>(convert<TValue>(getValue(host,pos+1)))) ){
-				unsigned r_s = convert<TWord>(convert<TValue>(getValue(host,pos-1))) + 1;
-				while(r_s < convert<TWord>(convert<TValue>(getValue(host,pos+1)))){
-					append(ret,r_s);
-					++r_s;
-				}
-			}
-			else // or simply a '-'
-				append(ret,convert<TWord>(convert<TValue>(getValue(host,pos))));
-		}
-		++pos;
-	}
-	return ret;
+    typedef unsigned TWord;
+    String <unsigned> ret;
+    unsigned pos = start;
+    while (pos < end){
+SEQAN_CHECKPOINT
+        if(convert<char>(getValue(host,pos)) != '-')
+            append(ret,convert<TWord>(convert<TValue>(getValue(host,pos))));
+        else{
+SEQAN_CHECKPOINT
+            // could be a range
+            if (pos > start && pos < end && (convert<TWord>(convert<TValue>(getValue(host,pos-1))) < convert<TWord>(convert<TValue>(getValue(host,pos+1)))) ){
+                unsigned r_s = convert<TWord>(convert<TValue>(getValue(host,pos-1))) + 1;
+                while(r_s < convert<TWord>(convert<TValue>(getValue(host,pos+1)))){
+                    append(ret,r_s);
+                    ++r_s;
+                }
+            }
+            else // or simply a '-'
+                append(ret,convert<TWord>(convert<TValue>(getValue(host,pos))));
+        }
+        ++pos;
+    }
+    return ret;
 }
 
 
 template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, WildShiftAnd> & me, TNeedle2 const & needle) {
-SEQAN_CHECKPOINT
-	me._valid = _validate(needle);
-
-	if(!valid(me)) return;
-
-	typedef unsigned TWord;
-	typedef typename Value<TNeedle>::Type TValue;
-	
-	me.needleLength = length(needle);
-	me.character_count = _lengthWithoutWildcards(needle);
-
-	if (me.character_count<1) me.blockCount=1;
-	else me.blockCount=((me.character_count-1) / BitsPerValue<TWord>::VALUE)+1;
-	
-	clear(me.table);
-	resize(me.table, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
-
-	clear(me.s_table);
-	resize(me.s_table, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
-
-	clear(me.a_table);
-	resize(me.a_table,me.blockCount,0,Exact());
-
-	int i = -1;
-	String <TWord> last_char; // stores the character (or characters) that were read in the last step
-	TWord j=0;
-	while(j < me.needleLength){
-SEQAN_CHECKPOINT
-		if (convert<char>(getValue(needle,j)) == '+'){
-SEQAN_CHECKPOINT
-			TWord len = length(last_char);
-			for (unsigned int k = 0; k < len; ++k)
-				me.s_table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-		} 
-		else if (convert<char>(getValue(needle,j)) == '?'){
-SEQAN_CHECKPOINT
-			me.a_table[i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-		}
-		else if (convert<char>(getValue(needle,j)) == '*'){
-SEQAN_CHECKPOINT
-			TWord len = length(last_char);
-			for (unsigned int k = 0; k < len; ++k)
-				me.s_table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-			me.a_table[i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-		}
-		else if(convert<char>(getValue(needle,j)) == '['){
-SEQAN_CHECKPOINT
-			/* find characters in class */
-			TWord e = j;
-			while(convert<char>(getValue(needle,e)) != ']') ++e;
-			/* get character codes of class */
-			last_char = _getCharacterClass<TValue>(needle,j+1,e);
-			TWord len = length(last_char);			
-			
-			/* add class to the mask */
-			++i;
-			for (unsigned int k = 0; k < len; ++k){
-SEQAN_CHECKPOINT
-				me.table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-			}
-			j = e;
-		}
-		else if(convert<char>(getValue(needle,j)) == '.'){ // matches all characters in the current alphabet
-SEQAN_CHECKPOINT
-			clear(last_char);
-			++i;
-			for(unsigned int l = 0;l < ValueSize<TValue>::VALUE;++l){
-				append(last_char,l);
-				me.table[me.blockCount*l + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-			}
-			
-		}
-		else if(convert<char>(getValue(needle,j)) == '\\'){ // handle escape characters
-SEQAN_CHECKPOINT
-			/* goto next character use this for the bit mask */
-			++i;++j;
-			clear(last_char);
-			append(last_char, convert<TWord>(convert<TValue>(getValue(needle,j))));
-			me.table[me.blockCount*last_char[0] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));			
-		}
-		else if(convert<char>(getValue(needle,j)) == '{'){ // handle bounded character repeats
-SEQAN_CHECKPOINT
-			String <char> number;
-			TWord n,m,r;
-			TWord len = length(last_char);			
-			n = m = 0;
-			++j;
-			while(convert<char>(getValue(needle,j)) != '}' && convert<char>(getValue(needle,j)) != ',') {			
-SEQAN_CHECKPOINT
-				append(number,convert<char>(getValue(needle,j)));
-				++j;
-			}
-			n = atoi(toCString(number));
-			if (convert<char>(getValue(needle,j)) == ','){
-SEQAN_CHECKPOINT
-				++j;
-				clear(number);
-				while(convert<char>(getValue(needle,j)) != '}') {			
-SEQAN_CHECKPOINT
-					append(number,convert<char>(getValue(needle,j)));
-					++j;
-				}
-				m = atoi(toCString(number));
-			}
-			// we already have seen one required occurrence of the character (last_char)
-			n -= 1;
-			r = 0;
-			while(r < n){ // add n normal characters
-SEQAN_CHECKPOINT
-				++i;
-				for (unsigned int k = 0; k < len; ++k){
-					me.table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-				}
-				++r;
-			}
-			++r; // correct the -1 of n to get in the correct relation to m
-			while (r < m){ // if there was no m specified this won't be used
-SEQAN_CHECKPOINT
-				// add m - n charaters and make them optional
-				++i;
-				for (unsigned int k = 0; k < len; ++k){
-SEQAN_CHECKPOINT
-					me.table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-				}
-				me.a_table[i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-				++r;
-			}			
-		}
-
-		else // we have a character here
-		{
-SEQAN_CHECKPOINT
-			// determine character position in array table
-			clear(last_char);
-			append(last_char, convert<TWord>(convert<TValue>(getValue(needle,j))));
-			++i;
-			me.table[me.blockCount*last_char[0] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
-		}
-		++j;
-	}
-
-	clear(me.i_table);
-	resize(me.i_table,me.blockCount,0,Exact());
-
-	clear(me.f_table);
-	resize(me.f_table,me.blockCount,0,Exact());
-
-	for (unsigned int i = 0; i < me.character_count; ++i){
-SEQAN_CHECKPOINT
-		if ((me.a_table[i / BitsPerValue<TWord>::VALUE] & (1 << (i % BitsPerValue<TWord>::VALUE))) != 0){
-SEQAN_CHECKPOINT
-			if ((me.f_table[i / BitsPerValue<TWord>::VALUE] & (1 << ((i-1) % BitsPerValue<TWord>::VALUE))) == 0){
-SEQAN_CHECKPOINT
-
-				if(i > 0)
-					me.i_table[(i-1) / BitsPerValue<TWord>::VALUE] |= 1 << ((i-1) % BitsPerValue<TWord>::VALUE);
-				me.f_table[i / BitsPerValue<TWord>::VALUE] |= 1 << (i % BitsPerValue<TWord>::VALUE);
+void _reinitPattern(Pattern<TNeedle, WildShiftAnd> & me,
+                    TNeedle2 const & ndl)
+{
+SEQAN_CHECKPOINT
+
+    me._valid = _validate(ndl);
+
+    if(!valid(me)) return;
+
+    typedef unsigned TWord;
+    typedef typename Value<TNeedle>::Type TValue;
+
+    me.needleLength = length(ndl);
+    me.character_count = _lengthWithoutWildcards(ndl);
+
+    if (me.character_count<1) me.blockCount=1;
+    else me.blockCount=((me.character_count-1) / BitsPerValue<TWord>::VALUE)+1;
+
+    clear(me.table);
+    resize(me.table, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
+
+    clear(me.s_table);
+    resize(me.s_table, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
+
+    clear(me.a_table);
+    resize(me.a_table,me.blockCount,0,Exact());
+
+    int i = -1;
+    String <TWord> last_char; // stores the character (or characters) that were read in the last step
+    TWord j=0;
+    while(j < me.needleLength){
+SEQAN_CHECKPOINT
+        if (convert<char>(getValue(ndl,j)) == '+'){
+SEQAN_CHECKPOINT
+            TWord len = length(last_char);
+            for (unsigned int k = 0; k < len; ++k)
+                me.s_table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+        }
+        else if (convert<char>(getValue(ndl,j)) == '?'){
+SEQAN_CHECKPOINT
+            me.a_table[i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+        }
+        else if (convert<char>(getValue(ndl,j)) == '*'){
+SEQAN_CHECKPOINT
+            TWord len = length(last_char);
+            for (unsigned int k = 0; k < len; ++k)
+                me.s_table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+            me.a_table[i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+        }
+        else if(convert<char>(getValue(ndl,j)) == '['){
+SEQAN_CHECKPOINT
+            /* find characters in class */
+            TWord e = j;
+            while(convert<char>(getValue(ndl,e)) != ']') ++e;
+            /* get character codes of class */
+            last_char = _getCharacterClass<TValue>(ndl,j+1,e);
+            TWord len = length(last_char);
+
+            /* add class to the mask */
+            ++i;
+            for (unsigned int k = 0; k < len; ++k){
+SEQAN_CHECKPOINT
+                me.table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+            }
+            j = e;
+        }
+        else if(convert<char>(getValue(ndl,j)) == '.'){ // matches all characters in the current alphabet
+SEQAN_CHECKPOINT
+            clear(last_char);
+            ++i;
+            for(unsigned int l = 0;l < ValueSize<TValue>::VALUE;++l){
+                append(last_char,l);
+                me.table[me.blockCount*l + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+            }
+
+        }
+        else if(convert<char>(getValue(ndl,j)) == '\\'){ // handle escape characters
+SEQAN_CHECKPOINT
+            /* goto next character use this for the bit mask */
+            ++i;++j;
+            clear(last_char);
+            append(last_char, convert<TWord>(convert<TValue>(getValue(ndl,j))));
+            me.table[me.blockCount*last_char[0] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+        }
+        else if(convert<char>(getValue(ndl,j)) == '{'){ // handle bounded character repeats
+SEQAN_CHECKPOINT
+            String <char> number;
+            TWord n,m,r;
+            TWord len = length(last_char);
+            n = m = 0;
+            ++j;
+            while(convert<char>(getValue(ndl,j)) != '}' && convert<char>(getValue(ndl,j)) != ',') {
+SEQAN_CHECKPOINT
+                append(number,convert<char>(getValue(ndl,j)));
+                ++j;
+            }
+            n = atoi(toCString(number));
+            if (convert<char>(getValue(ndl,j)) == ','){
+SEQAN_CHECKPOINT
+                ++j;
+                clear(number);
+                while(convert<char>(getValue(ndl,j)) != '}') {
+SEQAN_CHECKPOINT
+                    append(number,convert<char>(getValue(ndl,j)));
+                    ++j;
+                }
+                m = atoi(toCString(number));
+            }
+            // we already have seen one required occurrence of the character (last_char)
+            n -= 1;
+            r = 0;
+            while(r < n){ // add n normal characters
+SEQAN_CHECKPOINT
+                ++i;
+                for (unsigned int k = 0; k < len; ++k){
+                    me.table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+                }
+                ++r;
+            }
+            ++r; // correct the -1 of n to get in the correct relation to m
+            while (r < m){ // if there was no m specified this won't be used
+SEQAN_CHECKPOINT
+                // add m - n charaters and make them optional
+                ++i;
+                for (unsigned int k = 0; k < len; ++k){
+SEQAN_CHECKPOINT
+                    me.table[me.blockCount*last_char[k] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+                }
+                me.a_table[i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+                ++r;
+            }
+        }
+
+        else // we have a character here
+        {
+SEQAN_CHECKPOINT
+            // determine character position in array table
+            clear(last_char);
+            append(last_char, convert<TWord>(convert<TValue>(getValue(ndl,j))));
+            ++i;
+            me.table[me.blockCount*last_char[0] + i / BitsPerValue<TWord>::VALUE] |= (1<<(i%BitsPerValue<TWord>::VALUE));
+        }
+        ++j;
+    }
+
+    clear(me.i_table);
+    resize(me.i_table,me.blockCount,0,Exact());
+
+    clear(me.f_table);
+    resize(me.f_table,me.blockCount,0,Exact());
+
+    for (unsigned int i = 0; i < me.character_count; ++i){
+SEQAN_CHECKPOINT
+        if ((me.a_table[i / BitsPerValue<TWord>::VALUE] & (1 << (i % BitsPerValue<TWord>::VALUE))) != 0){
+SEQAN_CHECKPOINT
+            if ((me.f_table[i / BitsPerValue<TWord>::VALUE] & (1 << ((i-1) % BitsPerValue<TWord>::VALUE))) == 0){
+SEQAN_CHECKPOINT
+
+                if(i > 0)
+                    me.i_table[(i-1) / BitsPerValue<TWord>::VALUE] |= 1 << ((i-1) % BitsPerValue<TWord>::VALUE);
+                me.f_table[i / BitsPerValue<TWord>::VALUE] |= 1 << (i % BitsPerValue<TWord>::VALUE);
 #ifdef SEQAN_WILD_SHIFTAND_DEBUG
-				std::cout << "Update F and I" << std::endl;
-				_printMask(me.f_table,0,"F ");
-				_printMask(me.i_table,0,"I ");
-				_printMask(me.a_table,0,"A ");
-				std::cout << std::endl;
+                std::cout << "Update F and I" << std::endl;
+                _printMask(me.f_table,0,"F ");
+                _printMask(me.i_table,0,"I ");
+                _printMask(me.a_table,0,"A ");
+                std::cout << std::endl;
 #endif
-			}
-			else{
+            }
+            else{
 SEQAN_CHECKPOINT
-				TWord curBlock = i / BitsPerValue<TWord>::VALUE;
-				for (unsigned int k = 0; k < me.blockCount; ++k){
+                TWord curBlock = i / BitsPerValue<TWord>::VALUE;
+                for (unsigned int k = 0; k < me.blockCount; ++k){
 SEQAN_CHECKPOINT
-					if(k != curBlock)
-						me.f_table[i / BitsPerValue<TWord>::VALUE] &= ~0;
-					else
-						me.f_table[i / BitsPerValue<TWord>::VALUE] &= ~(1 << ((i-1) % BitsPerValue<TWord>::VALUE));
+                    if(k != curBlock)
+                        me.f_table[i / BitsPerValue<TWord>::VALUE] &= ~0;
+                    else
+                        me.f_table[i / BitsPerValue<TWord>::VALUE] &= ~(1 << ((i-1) % BitsPerValue<TWord>::VALUE));
 
-				}
-				//me.f_table[i / BitsPerValue<TWord>::VALUE] &= ~(1 << ((i-1) % BitsPerValue<TWord>::VALUE));
-				me.f_table[i / BitsPerValue<TWord>::VALUE] |= 1 << (i % BitsPerValue<TWord>::VALUE);
+                }
+                //me.f_table[i / BitsPerValue<TWord>::VALUE] &= ~(1 << ((i-1) % BitsPerValue<TWord>::VALUE));
+                me.f_table[i / BitsPerValue<TWord>::VALUE] |= 1 << (i % BitsPerValue<TWord>::VALUE);
 #ifdef SEQAN_WILD_SHIFTAND_DEBUG
-				std::cout << "Update F" << std::endl;
-				_printMask(me.f_table,0,"F ");
-				std::cout << std::endl;
+                std::cout << "Update F" << std::endl;
+                _printMask(me.f_table,0,"F ");
+                std::cout << std::endl;
 #endif
-			}
-		}
-	}
-
-	setValue(me.data_host, needle);
-
-#ifdef SEQAN_WILD_SHIFTAND_DEBUG	
-	// Debug code
-	std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << ::std::endl;
-	std::cout << "Needle length (with wildcards): " << me.needleLength << ::std::endl;
-	std::cout << "Needle length (wo wildcards): " << me.character_count << ::std::endl;
-	std::cout << "Block count: " << me.blockCount << ::std::endl;
-
-	std::cout << "Needle:" << needle << ::std::endl;
-
-	_printMask(me.f_table,0,"F ");
-	_printMask(me.i_table,0,"I ");
-	_printMask(me.a_table,0,"A ");
-	std::cout << std::endl << std::endl;
-
-	for(unsigned i=0;i<ValueSize<TValue>::VALUE;++i) {
-		if (((i<97) && (4 < i) ) || (i>122)) continue;
-		std::cout << static_cast<TValue>(i) << ": ";
-		for(unsigned int j=0;j<me.blockCount;++j) {
-			for(int bit_pos=0;bit_pos<BitsPerValue<unsigned>::VALUE;++bit_pos) {
-				std::cout << ((me.table[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned>::VALUE))) !=0);
-			}
-		}
-		std::cout << ::std::endl;
-	}
+            }
+        }
+    }
+
+#ifdef SEQAN_WILD_SHIFTAND_DEBUG
+    // Debug code
+    std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << std::endl;
+    std::cout << "Needle length (with wildcards): " << me.needleLength << std::endl;
+    std::cout << "Needle length (wo wildcards): " << me.character_count << std::endl;
+    std::cout << "Block count: " << me.blockCount << std::endl;
+
+    std::cout << "Needle:" << ndl << std::endl;
+
+    _printMask(me.f_table,0,"F ");
+    _printMask(me.i_table,0,"I ");
+    _printMask(me.a_table,0,"A ");
+    std::cout << std::endl << std::endl;
+
+    for(unsigned i=0;i<ValueSize<TValue>::VALUE;++i) {
+        if (((i<97) && (4 < i) ) || (i>122)) continue;
+        std::cout << static_cast<TValue>(i) << ": ";
+        for(unsigned int j=0;j<me.blockCount;++j) {
+            for(int bit_pos=0;bit_pos<BitsPerValue<unsigned>::VALUE;++bit_pos) {
+                std::cout << ((me.table[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned>::VALUE))) !=0);
+            }
+        }
+        std::cout << std::endl;
+    }
 #endif
 
 }
 
+//____________________________________________________________________________
+
+// Need to overload setHost, since we cannot convert the needle if TNeedle of pattern is a different alphabet,
+// which does not handle wildcard characters.
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TNeedle, typename TNeedle2>
+inline void setHost(Pattern<TNeedle, WildShiftAnd> & me,
+                    TNeedle2 && ndl)
+{
+    _reinitPattern(me, ndl);
+    setValue(_dataHost(me), std::forward<TNeedle2>(ndl));
+}
+#else
 template <typename TNeedle, typename TNeedle2>
-inline void setHost (Pattern<TNeedle, WildShiftAnd> & me, TNeedle2 & needle)
+inline void setHost(Pattern<TNeedle, WildShiftAnd> & me,
+                    TNeedle2 & ndl)
 {
-	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
+    _reinitPattern(me, ndl);
+    setValue(_dataHost(me), ndl);
 }
 
+template <typename TNeedle, typename TNeedle2>
+inline void setHost(Pattern<TNeedle, WildShiftAnd> & me,
+                    TNeedle2 const & ndl)
+{
+    _reinitPattern(me, ndl);
+    setValue(_dataHost(me), ndl);
+}
+
+#endif
 //____________________________________________________________________________
 
 
 template <typename TNeedle>
-inline void _patternInit (Pattern<TNeedle, WildShiftAnd> & me) 
+inline void _patternInit (Pattern<TNeedle, WildShiftAnd> & me)
 {
 SEQAN_CHECKPOINT
-	clear(me.prefSufMatch);
-	resize(me.prefSufMatch, me.blockCount, 0, Exact());
+    clear(me.prefSufMatch);
+    resize(me.prefSufMatch, me.blockCount, 0, Exact());
 
-	clear(me.df);
-	resize(me.df, me.blockCount, 0, Exact());
+    clear(me.df);
+    resize(me.df, me.blockCount, 0, Exact());
 
 }
 
@@ -591,7 +609,7 @@ template <typename TNeedle>
 inline bool valid(Pattern <TNeedle,WildShiftAnd> & me)
 {
 SEQAN_CHECKPOINT
-	return me._valid;
+    return me._valid;
 }
 
 //____________________________________________________________________________
@@ -599,26 +617,7 @@ template <typename TNeedle>
 inline bool valid(Pattern <TNeedle,WildShiftAnd> const & me)
 {
 SEQAN_CHECKPOINT
-	return me._valid;
-}
-
-//____________________________________________________________________________
-
-
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, WildShiftAnd>const>::Type & 
-host(Pattern<TNeedle, WildShiftAnd> & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.data_host);
-}
-
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, WildShiftAnd>const>::Type & 
-host(Pattern<TNeedle, WildShiftAnd> const & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.data_host);
+    return me._valid;
 }
 
 //____________________________________________________________________________
@@ -627,87 +626,90 @@ SEQAN_CHECKPOINT
 template <typename TFinder, typename TNeedle>
 inline bool _findShiftAndSmallNeedle(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me) {
 SEQAN_CHECKPOINT
-	typedef unsigned TWord;
-	TWord compare = (1 << (me.character_count-1));
-	while (!atEnd(finder)) {
+    typedef typename Value<TNeedle>::Type TNdlAlphabet;
+    typedef unsigned TWord;
+
+    TWord compare = (1 << (me.character_count-1));
+    while (!atEnd(finder)) {
 SEQAN_CHECKPOINT
-		TWord pos = convert<TWord>(*finder);
-		/* added  | (me.prefSufMatch[0] & me.s_table[me.blockCount*pos]) at the end of the line */
-		me.prefSufMatch[0] = (((me.prefSufMatch[0] << 1) | 1) & me.table[me.blockCount*pos]) | (me.prefSufMatch[0] & me.s_table[me.blockCount*pos]) ;
+        TWord pos = convert<TWord>(convert<TNdlAlphabet>(*finder));
+        /* added  | (me.prefSufMatch[0] & me.s_table[me.blockCount*pos]) at the end of the line */
+        me.prefSufMatch[0] = (((me.prefSufMatch[0] << 1) | 1) & me.table[me.blockCount*pos]) | (me.prefSufMatch[0] & me.s_table[me.blockCount*pos]) ;
 
-		/* additional bit operations */
-		me.df[0] = me.prefSufMatch[0] | me.f_table[0];
-		me.prefSufMatch[0] |= ((me.a_table[0] & (~(me.df[0] - me.i_table[0]))) ^ me.df[0]);
-		if ((me.prefSufMatch[0] & compare) != 0) {
+        /* additional bit operations */
+        me.df[0] = me.prefSufMatch[0] | me.f_table[0];
+        me.prefSufMatch[0] |= ((me.a_table[0] & (~(me.df[0] - me.i_table[0]))) ^ me.df[0]);
+        if ((me.prefSufMatch[0] & compare) != 0) {
 SEQAN_CHECKPOINT
-			return true; 
-		}
-		goNext(finder);
-	}
-	return false;
+            return true;
+        }
+        goNext(finder);
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
 inline bool _findShiftAndLargeNeedle(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me) {
 SEQAN_CHECKPOINT
-	typedef unsigned TWord;
-	const TWord all1 = ~0;	
-	TWord compare = (1 << ((me.character_count-1) % BitsPerValue<TWord>::VALUE));
+    typedef typename Value<TNeedle>::Type TNdlAlphabet;
+    typedef unsigned TWord;
+    const TWord all1 = ~0;
+    TWord compare = (1 << ((me.character_count-1) % BitsPerValue<TWord>::VALUE));
 
-	while (!atEnd(finder)) {
+    while (!atEnd(finder)) {
 SEQAN_CHECKPOINT
-		TWord pos = convert<TWord>(*finder);
-		TWord carry = 1;
-		TWord wc_carry = 0;
-		// shift of blocks with carry
-		for(TWord block=0;block<me.blockCount;++block) {
+        TWord pos = convert<TWord>(convert<TNdlAlphabet>(*finder));
+        TWord carry = 1;
+        TWord wc_carry = 0;
+        // shift of blocks with carry
+        for(TWord block=0;block<me.blockCount;++block) {
 SEQAN_CHECKPOINT
-			bool newCarry = ((me.prefSufMatch[block] & (1<< (BitsPerValue<TWord>::VALUE - 1)))!=0); 
-			me.prefSufMatch[block] = (((me.prefSufMatch[block] << 1) | carry) & me.table[me.blockCount*pos+block]) | (me.prefSufMatch[block] & me.s_table[me.blockCount*pos+block]) ;
-			carry = newCarry;
-			
-			me.df[block] = me.prefSufMatch[block] | me.f_table[block];
-			TWord Z = me.df[block] - me.i_table[block] - wc_carry;
-			wc_carry = ((me.df[block] < Z) || (me.i_table[block]==all1 && wc_carry)) ? 1 : 0;
-			me.prefSufMatch[block] |= (me.a_table[block] & (~Z ^ me.df[block]));
-		}
+            bool newCarry = ((me.prefSufMatch[block] & (1<< (BitsPerValue<TWord>::VALUE - 1)))!=0);
+            me.prefSufMatch[block] = (((me.prefSufMatch[block] << 1) | carry) & me.table[me.blockCount*pos+block]) | (me.prefSufMatch[block] & me.s_table[me.blockCount*pos+block]) ;
+            carry = newCarry;
+
+            me.df[block] = me.prefSufMatch[block] | me.f_table[block];
+            TWord Z = me.df[block] - me.i_table[block] - wc_carry;
+            wc_carry = ((me.df[block] < Z) || (me.i_table[block]==all1 && wc_carry)) ? 1 : 0;
+            me.prefSufMatch[block] |= (me.a_table[block] & (~Z ^ me.df[block]));
+        }
 
 #ifdef SEQAN_WILD_SHIFTAND_DEBUG
-		std::cout << "reading " << *finder << std::endl;
-		_printMask(me.prefSufMatch,position(finder),"D ");
-		_printMask(me.df,position(finder),"Df");
-		std::cout << std::endl;
+        std::cout << "reading " << *finder << std::endl;
+        _printMask(me.prefSufMatch,position(finder),"D ");
+        _printMask(me.df,position(finder),"Df");
+        std::cout << std::endl;
 #endif
-		
-		// check for match
-		if ((me.prefSufMatch[me.blockCount-1] & compare) != 0)
-			return true; 
-
-		goNext(finder);
-	}
-	return false;
+
+        // check for match
+        if ((me.prefSufMatch[me.blockCount-1] & compare) != 0)
+            return true;
+
+        goNext(finder);
+    }
+    return false;
 }
 
 template <typename TFinder, typename TNeedle>
 inline bool find(TFinder & finder, Pattern<TNeedle, WildShiftAnd> & me) {
 SEQAN_CHECKPOINT
 
-	if (empty(finder)) {
-		_patternInit(me);
-		_finderSetNonEmpty(finder);
+    if (empty(finder)) {
+        _patternInit(me);
+        _finderSetNonEmpty(finder);
 
-		if(!valid(me))
-			return false;
-	} 
-	else
-		goNext(finder);	
+        if(!valid(me))
+            return false;
+    }
+    else
+        goNext(finder);
 
-	// Fast algorithm for needles < machine word?
-	if (me.blockCount == 1) {
-		return _findShiftAndSmallNeedle(finder, me);
-	} else {
-		return _findShiftAndLargeNeedle(finder, me);
-	}
+    // Fast algorithm for needles < machine word?
+    if (me.blockCount == 1) {
+        return _findShiftAndSmallNeedle(finder, me);
+    } else {
+        return _findShiftAndLargeNeedle(finder, me);
+    }
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/find/find_wumanber.h b/seqan/find/find_wumanber.h
index 86affdf..9a2bcf5 100644
--- a/seqan/find/find_wumanber.h
+++ b/seqan/find/find_wumanber.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -51,74 +51,74 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature template <typename TNeedle>
  *            class Pattern<TNeedle, WuManber>;
  *
- * @tparam TNeedle The type of the needle to search for.  Type: @link SequenceConcept @endlink.
+ * @tparam TNeedle The type of the needle to search for.  Type: @link ContainerConcept @endlink.
  */
 
-/**
-.Spec.WuManber:
-..general:Class.Pattern
-..cat:Searching
-..summary:Online-algorithm for multi-pattern search.
-..signature:Pattern<TNeedle, WuManber>
-..param.TNeedle:The needle type.
-...type:Class.String
-..include:seqan/find.h
-*/
-
-///.Class.Pattern.param.TSpec.type:Spec.WuManber
-
 struct WuManber_;
 typedef Tag<WuManber_> WuManber;
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TNeedle>
-class Pattern<TNeedle, WuManber> 
+class Pattern<TNeedle, WuManber>
 {
 //____________________________________________________________________________
 public:
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Position<TNeedle>::Type TNeedlePosition;
-	typedef typename Size<TKeyword>::Type TSize;
-	typedef typename Value<TKeyword>::Type TValue;
-
-	//searching data: these members are initialized in _patternInit
-	TNeedlePosition position; //last found keyword
-	TNeedlePosition * to_verify_begin; //next entry in verify
-	TNeedlePosition * to_verify_end; //end of list in verify
-			//note: if to_verify_begin == to_verify_end then searching in Haystack must go on
-
-	//preprocessed data: these members are initialized in setHost
-	Holder<TNeedle> needle;
-	String<TNeedlePosition> verify_tab; //table of keywords to verify depending on the last value (HASH)
-	String<TNeedlePosition *> verify; //directory into verify_tab
-	String<TSize> shift; //table of skip widths (SHIFT)
-
-	TSize lmin;	//min length of keyword
-	unsigned char q; //length of hashed q-grams
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Position<TNeedle>::Type TNeedlePosition;
+    typedef typename Size<TKeyword>::Type TSize;
+    typedef typename Value<TKeyword>::Type TValue;
+
+    //searching data: these members are initialized in _patternInit
+    TNeedlePosition position; //last found keyword
+    TNeedlePosition * to_verify_begin; //next entry in verify
+    TNeedlePosition * to_verify_end; //end of list in verify
+            //note: if to_verify_begin == to_verify_end then searching in Haystack must go on
+
+    //preprocessed data: these members are initialized in setHost
+    Holder<TNeedle> data_host;
+    String<TNeedlePosition> verify_tab; //table of keywords to verify depending on the last value (HASH)
+    String<TNeedlePosition *> verify; //directory into verify_tab
+    String<TSize> shift; //table of skip widths (SHIFT)
+
+    TSize lmin;    //min length of keyword
+    unsigned char q; //length of hashed q-grams
 //____________________________________________________________________________
 
-	Pattern():
-		lmin(0)
-	{
-	}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
-		SEQAN_CHECKPOINT
-		setHost(*this, ndl);
-	}
-
-	~Pattern() 
-	{
-	}
+    Pattern():
+        lmin(0)
+    {
+    }
+
+#if defined(SEQAN_CXX11_STANDARD)
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        setHost(*this, std::forward<TNeedle2>(ndl));
+        ignoreUnusedVariableWarning(dummy);
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
+        SEQAN_CHECKPOINT
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
+
+    ~Pattern()
+    {
+    }
 //____________________________________________________________________________
 
 private:
-	Pattern(Pattern const& other);
-	Pattern const & operator=(Pattern const & other);
-
+    Pattern(Pattern const& other);
+    Pattern const & operator=(Pattern const & other);
+#if defined(SEQAN_CXX11_STANDARD)
+    Pattern(Pattern && other);
+    Pattern & operator=(Pattern && other);
+#endif  // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
@@ -130,194 +130,194 @@ struct WuManberHash_;
 
 
 //////////////////////////////////////////////////////////////////////////////
-//implementation kernel of WuManber 
+//implementation kernel of WuManber
 
 template <typename TNeedle, int Q>
 struct WuManberImpl_
 {
 //____________________________________________________________________________
 
-	typedef Pattern<TNeedle, WuManber> TPattern;
+    typedef Pattern<TNeedle, WuManber> TPattern;
 
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Position<TNeedle>::Type TNeedlePosition;
-	typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Position<TNeedle>::Type TNeedlePosition;
+    typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
 
-	typedef typename Size<TKeyword>::Type TSize;
-	typedef typename Value<TKeyword>::Type TValue;
-	typedef typename Iterator<TKeyword, Standard>::Type TIterator;
+    typedef typename Size<TKeyword>::Type TSize;
+    typedef typename Value<TKeyword>::Type TValue;
+    typedef typename Iterator<TKeyword, Standard>::Type TIterator;
 
 //____________________________________________________________________________
 
-	enum 
-	{
-		C = BitsPerValue<TValue>::VALUE, //bits per value
-		W = (C*Q <= 16) ? C*Q : 16,	//bits per hash values
+    enum
+    {
+        C = BitsPerValue<TValue>::VALUE, //bits per value
+        W = (C*Q <= 16) ? C*Q : 16,    //bits per hash values
 
-		DIR_SIZE = 1 << W,			//size of verify_dir and shift_dir
+        DIR_SIZE = 1 << W,            //size of verify_dir and shift_dir
 
-		//shift width for Q = 2:
-		SHIFT = (W > 2*C) ? C : W-C,			
+        //shift width for Q = 2:
+        SHIFT = (W > 2*C) ? C : W-C,
 
-		//shift widths for Q = 3:
-		SHIFT_LEFT = (W > 3*C) ? 2*C : W-C,
-		SHIFT_MIDDLE = SHIFT_LEFT / 2
-	};
+        //shift widths for Q = 3:
+        SHIFT_LEFT = (W > 3*C) ? 2*C : W-C,
+        SHIFT_MIDDLE = SHIFT_LEFT / 2
+    };
 //____________________________________________________________________________
 
-	inline static unsigned short
-	hash(TValue * vals)
-	{
-		return WuManberHash_<TNeedle, Q>::hash(vals);
-	}
+    inline static unsigned short
+    hash(TValue * vals)
+    {
+        return WuManberHash_<TNeedle, Q>::hash(vals);
+    }
 //____________________________________________________________________________
 
-	inline static void
-	initialize(TPattern & me)
-	{
-		//note: me.needle, me.q, and me.lmin were already set in setHost before initialize was called
+    inline static void
+    initialize(TPattern & me)
+    {
+        //note: me.needle, me.q, and me.lmin were already set in setHost before initialize was called
 
-		//some variables
-		TNeedleIterator pit;
-		TNeedleIterator pit_end = end(needle(me));
+        //some variables
+        TNeedleIterator pit;
+        TNeedleIterator pit_end = end(needle(me));
 
-		TSize k = length(needle(me));
+        TSize k = length(needle(me));
 
-		//resize and init tables
-		resize(me.verify_tab, (unsigned) k);
-		resize(me.verify, (unsigned) DIR_SIZE+1);
-		resize(me.shift, (unsigned) DIR_SIZE);
+        //resize and init tables
+        resize(me.verify_tab, (unsigned) k);
+        resize(me.verify, (unsigned) DIR_SIZE+1);
+        resize(me.shift, (unsigned) DIR_SIZE);
 
-		arrayFill(begin(me.shift), begin(me.shift) + (unsigned) DIR_SIZE, me.lmin-Q+1); //maximal shift width is me.lmin-B+1
+        arrayFill(begin(me.shift), begin(me.shift) + (unsigned) DIR_SIZE, me.lmin-Q+1); //maximal shift width is me.lmin-B+1
 
-		//init counters
-		unsigned int verify_count[DIR_SIZE];
-		arrayFill(verify_count, verify_count + DIR_SIZE, 0);
+        //init counters
+        unsigned int verify_count[DIR_SIZE];
+        arrayFill(verify_count, verify_count + DIR_SIZE, 0);
 
-		//1: first scan: fill me.shift and count verify
-		for (pit = begin(needle(me)); pit != pit_end; ++pit)
-		{
+        //1: first scan: fill me.shift and count verify
+        for (pit = begin(needle(me)); pit != pit_end; ++pit)
+        {
             if (empty(*pit))
                 continue;  // Skip empty needles.
-			unsigned short hash;
-			TIterator kit = begin(*pit);
-			for (unsigned int i = 0; i <= me.lmin-Q; ++i)
-			{
-				hash = WuManberHash_<TNeedle, Q>::hash(kit + i);
-				if (me.shift[hash] > me.lmin-Q - i)
-				{
-					me.shift[hash] = me.lmin-Q - i;
-				}
-			}
-			++(verify_count[hash]);
-		}
-
-		//2: add up and convert to pointers
-		TNeedlePosition * verify_ptr = begin(me.verify_tab);
-		
-		me.verify[0] = verify_ptr;
-		unsigned int sum = 0;
-		for (unsigned int i = 0; i < DIR_SIZE; ++i)
-		{
-			me.verify[i+1] = verify_ptr + sum;
-			sum += verify_count[i];
-		}
-
-		//3: second scan: fill verify and shift
-		pit = begin(needle(me));
-		for (unsigned int i = 0; pit != pit_end; ++i, ++pit)
-		{
+            unsigned short hash;
+            TIterator kit = begin(*pit);
+            for (unsigned int i = 0; i <= me.lmin-Q; ++i)
+            {
+                hash = WuManberHash_<TNeedle, Q>::hash(kit + i);
+                if (me.shift[hash] > me.lmin-Q - i)
+                {
+                    me.shift[hash] = me.lmin-Q - i;
+                }
+            }
+            ++(verify_count[hash]);
+        }
+
+        //2: add up and convert to pointers
+        TNeedlePosition * verify_ptr = begin(me.verify_tab);
+
+        me.verify[0] = verify_ptr;
+        unsigned int sum = 0;
+        for (unsigned int i = 0; i < DIR_SIZE; ++i)
+        {
+            me.verify[i+1] = verify_ptr + sum;
+            sum += verify_count[i];
+        }
+
+        //3: second scan: fill verify and shift
+        pit = begin(needle(me));
+        for (unsigned int i = 0; pit != pit_end; ++i, ++pit)
+        {
             if (empty(*pit))
                 continue;  // Skip empty needles.
-			unsigned short hash_plus_1;
-			hash_plus_1 = WuManberHash_<TNeedle, Q>::hash(begin(*pit) + me.lmin-Q) + 1;
+            unsigned short hash_plus_1;
+            hash_plus_1 = WuManberHash_<TNeedle, Q>::hash(begin(*pit) + me.lmin-Q) + 1;
 
-			//write into verify_tab
-			*(me.verify[hash_plus_1]) = i;
+            //write into verify_tab
+            *(me.verify[hash_plus_1]) = i;
 
-			//update verify
-			++me.verify[hash_plus_1];
-		}
-	}
+            //update verify
+            ++me.verify[hash_plus_1];
+        }
+    }
 //____________________________________________________________________________
 
-	template <typename TFinder>
-	static inline bool
-	find(TFinder & finder, TPattern & me) 
-	{
-		typedef typename Haystack<TFinder>::Type THaystack;
-		typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
+    template <typename TFinder>
+    static inline bool
+    find(TFinder & finder, TPattern & me)
+    {
+        typedef typename Haystack<TFinder>::Type THaystack;
+        typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
 
-		THaystackIterator tit;
-		THaystackIterator haystack_end = end(haystack(finder));
-		THaystackIterator tit_end = haystack_end - Q + 1;
-		unsigned short hash;
+        THaystackIterator tit;
+        THaystackIterator haystack_end = end(haystack(finder));
+        THaystackIterator tit_end = haystack_end - Q + 1;
+        unsigned short hash;
 
-		if (empty(finder)) 
-		{
+        if (empty(finder))
+        {
 //START
-			_patternInit(me);
-			_finderSetNonEmpty(finder);
-			tit = hostIterator(finder) + me.lmin-Q;
-		} 
-		else 
-		{
+            _patternInit(me);
+            _finderSetNonEmpty(finder);
+            tit = hostIterator(finder) + me.lmin-Q;
+        }
+        else
+        {
 //RESUME
-			tit = hostIterator(finder) + me.lmin-Q;
-			goto VERIFY;
-		}
+            tit = hostIterator(finder) + me.lmin-Q;
+            goto VERIFY;
+        }
 
 //SEARCH
-		while (tit < tit_end)
-		{
-			hash = WuManberHash_<TNeedle, Q>::hash(tit);
+        while (tit < tit_end)
+        {
+            hash = WuManberHash_<TNeedle, Q>::hash(tit);
 
-			if (me.shift[hash])
-			{
+            if (me.shift[hash])
+            {
 //SHIFT
-				tit += me.shift[hash];
-			}
-			else
-			{
-				me.to_verify_begin = me.verify[hash];
-				me.to_verify_end = me.verify[hash+1];
+                tit += me.shift[hash];
+            }
+            else
+            {
+                me.to_verify_begin = me.verify[hash];
+                me.to_verify_end = me.verify[hash+1];
 //VERIFY
 VERIFY:
-				while (me.to_verify_begin != me.to_verify_end)
-				{
-					me.position = *me.to_verify_begin;
-					++me.to_verify_begin;
+                while (me.to_verify_begin != me.to_verify_end)
+                {
+                    me.position = *me.to_verify_begin;
+                    ++me.to_verify_begin;
 
-					TKeyword & kw = needle(me)[me.position];
+                    TKeyword & kw = needle(me)[me.position];
 
-					TIterator pit = begin(kw, Standard());
-					TIterator pit_end = end(kw, Standard());
-					THaystackIterator tit2 = tit - (me.lmin-Q);
+                    TIterator pit = begin(kw, Standard());
+                    TIterator pit_end = end(kw, Standard());
+                    THaystackIterator tit2 = tit - (me.lmin-Q);
 
-					if ((pit_end - pit) > (haystack_end - tit2)) continue; //rest of haystack too short
+                    if ((pit_end - pit) > (haystack_end - tit2)) continue; //rest of haystack too short
 
-					while (true)
-					{
-						if (pit == pit_end)
-						{
+                    while (true)
+                    {
+                        if (pit == pit_end)
+                        {
 //FOUND
-							setPosition(finder, tit - (me.lmin-Q) - begin(haystack(finder), Standard()));
-							_setFinderLength(finder, length(kw));
-							_setFinderEnd(finder, position(finder) + length(finder));
-							return true;
-						}
-						if (*pit != *tit2) break;
-						++pit;
-						++tit2;
-					}
-				}
-
-				++tit;
-			}
-		}
+                            setPosition(finder, tit - (me.lmin-Q) - begin(haystack(finder), Standard()));
+                            _setFinderLength(finder, length(kw));
+                            _setFinderEnd(finder, position(finder) + length(finder));
+                            return true;
+                        }
+                        if (*pit != *tit2) break;
+                        ++pit;
+                        ++tit2;
+                    }
+                }
+
+                ++tit;
+            }
+        }
 //END
-		return false;
-	}
+        return false;
+    }
 //____________________________________________________________________________
 };
 
@@ -328,127 +328,89 @@ struct WuManberImpl_
 template <typename TNeedle>
 struct WuManberHash_<TNeedle, 1>
 {
-	template <typename TIterator>
-	inline static unsigned short
-	hash(TIterator vals)
-	{
-		return ordValue(*vals);
-	}
+    template <typename TIterator>
+    inline static unsigned short
+    hash(TIterator vals)
+    {
+        return ordValue(*vals);
+    }
 };
 template <typename TNeedle>
 struct WuManberHash_<TNeedle, 2>
 {
-	template <typename TIterator>
-	inline static unsigned short
-	hash(TIterator vals)
-	{
-		return ordValue(*vals)
-			+ (ordValue(*(vals+1)) << WuManberImpl_<TNeedle, 2>::SHIFT);
-	}
+    template <typename TIterator>
+    inline static unsigned short
+    hash(TIterator vals)
+    {
+        return ordValue(*vals)
+            + (ordValue(*(vals+1)) << WuManberImpl_<TNeedle, 2>::SHIFT);
+    }
 };
 template <typename TNeedle>
 struct WuManberHash_<TNeedle, 3>
 {
-	template <typename TIterator>
-	inline static unsigned short
-	hash(TIterator vals)
-	{
-		return ordValue(*vals) 
-			+ (ordValue(*(vals+1)) << WuManberImpl_<TNeedle, 3>::SHIFT_MIDDLE)
-			+ (ordValue(*(vals+2)) << WuManberImpl_<TNeedle, 3>::SHIFT_LEFT);
-	}
+    template <typename TIterator>
+    inline static unsigned short
+    hash(TIterator vals)
+    {
+        return ordValue(*vals)
+            + (ordValue(*(vals+1)) << WuManberImpl_<TNeedle, 3>::SHIFT_MIDDLE)
+            + (ordValue(*(vals+2)) << WuManberImpl_<TNeedle, 3>::SHIFT_LEFT);
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2>
-void _setHostWuManber(Pattern<TNeedle, WuManber> & me, 
-					   TNeedle2 const & needle_)
+template <typename TNeedle>
+void _reinitPattern(Pattern<TNeedle, WuManber> & me)
 {
     SEQAN_CHECKPOINT;
-    SEQAN_ASSERT_NOT(empty(needle_));
-
-	typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
-	typedef typename Value<TNeedle>::Type TKeyword;
-	typedef typename Value<TKeyword>::Type TValue;
-	typedef typename Size<TKeyword>::Type TSize;
-
-	//me.needle
-	setValue(me.needle, needle_);
-
-	//determine lmin
-	me.lmin = maxValue<TSize>();
-	for (TNeedleIterator it = begin(needle(me)); it != end(needle(me)); ++it)
-		if (!empty(*it) && length(*it) < me.lmin)  // skipping empty needles
-			me.lmin = length(*it);
-	if (me.lmin == maxValue<TSize>())
-        return;  // only empty needles
-
-	//compute q:
-	unsigned int C = BitsPerValue<TValue>::VALUE;
-	if (C > 12)
-	{
-		me.q = 1;
-	}
-	else 
-	{
-		//according to Wu & Manber: B = log_c(2mk) "is a good value"
-		//i.e. C^B = 2mk
-		//m = lmin
-		//k = length(needle)
-		//our heuristic: take B = 2 if C^2 >= mk, else B = 3
-
-		if (C * C >= me.lmin * length(needle(me)))
-		{
-			me.q = 2;
-		}
-		else
-		{
-			me.q = 3;
-		}
-	}
-	if (me.q > me.lmin) 
-	{
-		me.q = me.lmin;
-	}
-
-	//rest of preprocessing is done in WuManberImpl_
-	if (me.q == 2) WuManberImpl_<TNeedle, 2>::initialize(me);
-	else if (me.q == 3) WuManberImpl_<TNeedle, 3>::initialize(me);
-	else WuManberImpl_<TNeedle, 1>::initialize(me);
-}
-
-template <typename TNeedle, typename TNeedle2>
-void setHost (Pattern<TNeedle, WuManber> & me, 
-			  TNeedle2 const & needle) 
-{
-	_setHostWuManber(me, needle);
-}
 
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost(Pattern<TNeedle, WuManber> & me, 
-		TNeedle2 & needle)
-{
-	_setHostWuManber(me, needle);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, WuManber> >::Type & 
-host(Pattern<TNeedle, WuManber> & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.needle);
-}
+    typedef typename Iterator<TNeedle, Standard>::Type TNeedleIterator;
+    typedef typename Value<TNeedle>::Type TKeyword;
+    typedef typename Value<TKeyword>::Type TValue;
+    typedef typename Size<TKeyword>::Type TSize;
+
+    //determine lmin
+    me.lmin = maxValue<TSize>();
+    for (TNeedleIterator it = begin(needle(me)); it != end(needle(me)); ++it)
+        if (!empty(*it) && length(*it) < me.lmin)  // skipping empty needles
+            me.lmin = length(*it);
+    if (me.lmin == maxValue<TSize>())
+        return;  // only empty needles
 
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, WuManber> const>::Type & 
-host(Pattern<TNeedle, WuManber> const & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.needle);
+    //compute q:
+    unsigned int C = BitsPerValue<TValue>::VALUE;
+    if (C > 12)
+    {
+        me.q = 1;
+    }
+    else
+    {
+        //according to Wu & Manber: B = log_c(2mk) "is a good value"
+        //i.e. C^B = 2mk
+        //m = lmin
+        //k = length(needle)
+        //our heuristic: take B = 2 if C^2 >= mk, else B = 3
+
+        if (C * C >= me.lmin * length(needle(me)))
+        {
+            me.q = 2;
+        }
+        else
+        {
+            me.q = 3;
+        }
+    }
+    if (me.q > me.lmin)
+    {
+        me.q = me.lmin;
+    }
+
+    //rest of preprocessing is done in WuManberImpl_
+    if (me.q == 2) WuManberImpl_<TNeedle, 2>::initialize(me);
+    else if (me.q == 3) WuManberImpl_<TNeedle, 3>::initialize(me);
+    else WuManberImpl_<TNeedle, 1>::initialize(me);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -457,33 +419,33 @@ template <typename TNeedle>
 inline typename Size<TNeedle>::Type
 position(Pattern<TNeedle, WuManber> & me)
 {
-	return me.position;
+    return me.position;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 //called when search begins
 template <typename TNeedle>
-inline void _patternInit (Pattern<TNeedle, WuManber> & me) 
+inline void _patternInit (Pattern<TNeedle, WuManber> & me)
 {
 SEQAN_CHECKPOINT
-	me.to_verify_begin = 0;
-	me.to_verify_end = 0;
+    me.to_verify_begin = 0;
+    me.to_verify_end = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TFinder, typename TNeedle>
-inline bool find(TFinder & finder, 
-				 Pattern<TNeedle, WuManber> & me) 
+inline bool find(TFinder & finder,
+                 Pattern<TNeedle, WuManber> & me)
 {
 SEQAN_CHECKPOINT
 
-	if (me.lmin == 0) return false;
+    if (me.lmin == 0) return false;
 
-	if (me.q == 2) return WuManberImpl_<TNeedle, 2>::find(finder, me);
-	else if (me.q == 3) return WuManberImpl_<TNeedle, 3>::find(finder, me);
-	else return WuManberImpl_<TNeedle, 1>::find(finder, me);
+    if (me.q == 2) return WuManberImpl_<TNeedle, 2>::find(finder, me);
+    else if (me.q == 3) return WuManberImpl_<TNeedle, 3>::find(finder, me);
+    else return WuManberImpl_<TNeedle, 1>::find(finder, me);
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/gff_io.h b/seqan/gff_io.h
index 320e254..741385a 100644
--- a/seqan/gff_io.h
+++ b/seqan/gff_io.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                   gff_io
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for module gff_io.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_GFF_IO_H_
-#define CORE_INCLUDE_SEQAN_GFF_IO_H_
+#ifndef INCLUDE_SEQAN_GFF_IO_H_
+#define INCLUDE_SEQAN_GFF_IO_H_
 
 // ===========================================================================
 // Prerequisites.
@@ -45,14 +45,12 @@
 #include <seqan/file.h>
 #include <seqan/sequence.h>
 #include <seqan/stream.h>
-#include <seqan/misc/misc_name_store_cache.h>
 
 // ===========================================================================
 // First Header Group.
 // ===========================================================================
 
-#include <seqan/gff_io/gff_io_context.h>
 #include <seqan/gff_io/gff_io_base.h>
-#include <seqan/gff_io/gff_stream.h>
+#include <seqan/gff_io/gff_file.h>
 
-#endif  // CORE_INCLUDE_SEQAN_GFF_IO_H_
+#endif  // INCLUDE_SEQAN_GFF_IO_H_
diff --git a/seqan/gff_io/INFO b/seqan/gff_io/INFO
deleted file mode 100644
index 918fae0..0000000
--- a/seqan/gff_io/INFO
+++ /dev/null
@@ -1,10 +0,0 @@
-Name: seqan-gff_io
-Author: Jochen Singer <jochen.singer@fu-berlin.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Jochen Singer <jochen.singer@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: under development
-Description: Gff and Gtf record I/O code.
-  This module contains code for streaming through Gff and Gtf files.
diff --git a/seqan/gff_io/gff_file.h b/seqan/gff_io/gff_file.h
new file mode 100644
index 0000000..9216433
--- /dev/null
+++ b/seqan/gff_io/gff_file.h
@@ -0,0 +1,165 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Class for reading/writing files in GFF or GTF format.
+// ==========================================================================
+
+#ifndef SEQAN_GFF_IO_GFF_FILE_H_
+#define SEQAN_GFF_IO_GFF_FILE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Typedefs
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Typedef GffFileIn
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class GffFileIn
+ * @signature typedef FormattedFile<Gff, Input> GffFileIn;
+ * @extends FormattedFileIn
+ * @headerfile <seqan/gff_io.h>
+ * @brief Class for reading GFF and GTF files.
+ *
+ * @see GffRecord
+ */
+
+typedef FormattedFile<Gff, Input>   GffFileIn;
+
+// ----------------------------------------------------------------------------
+// Typedef GffFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class GffFileOut
+ * @signature typedef FormattedFile<Gff, Output> GffFileOut;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/gff_io.h>
+ * @brief Class for writing GFF and GTF files.
+ *
+ * @see GffRecord
+ */
+
+typedef FormattedFile<Gff, Output>  GffFileOut;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<Gff, Input, TSpec>, TStorageSpec>
+{
+    typedef CharString Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec>
+struct FileFormat<FormattedFile<Gff, TDirection, TSpec> >
+{
+    typedef TagSelector<
+                TagList<Gff,
+                TagList<Gtf
+                > >
+            > Type;
+};
+
+// ----------------------------------------------------------------------------
+// Function readRecord()
+// ----------------------------------------------------------------------------
+
+template <typename TForwardIter, typename TFormats>
+inline void
+readRecord(GffRecord & record,
+           CharString & buffer,
+           TForwardIter & iter,
+           TagSelector<TFormats> const & /* format */)  // format is ignored as it will be autodetected per record
+{
+    readRecord(record, buffer, iter);
+}
+
+// convient GffFile variant
+template <typename TSpec>
+inline void
+readRecord(GffRecord & record, FormattedFile<Gff, Input, TSpec> & file)
+{
+    readRecord(record, context(file), file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()
+// ----------------------------------------------------------------------------
+
+// support for dynamically chosen file formats
+template <typename TTarget>
+inline void
+writeRecord(TTarget & /* target */,
+            GffRecord & /* record */,
+            TagSelector<> const & /* format */)
+{
+    SEQAN_FAIL("GffFileOut: File format not specified.");
+}
+
+template <typename TTarget, typename TTagList>
+inline void
+writeRecord(TTarget & target,
+            GffRecord & record,
+            TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        writeRecord(target, record, TFormat());
+    else
+        writeRecord(target, record, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+template <typename TSpec>
+inline void
+writeRecord(FormattedFile<Gff, Output, TSpec> & file, GffRecord & record)
+{
+    writeRecord(file.iter, record, file.format);
+}
+
+}  // namespace seqan
+
+#endif // SEQAN_GFF_IO_GFF_FILE_H_
diff --git a/seqan/gff_io/gff_io_base.h b/seqan/gff_io/gff_io_base.h
index 11b2ac5..d1ec0a8 100644
--- a/seqan/gff_io/gff_io_base.h
+++ b/seqan/gff_io/gff_io_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,15 +32,11 @@
 // Author: Jochen Singer <jochen.singer@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_GFF_IO_GFF_IO_BASE_H_
-#define CORE_INCLUDE_SEQAN_GFF_IO_GFF_IO_BASE_H_
+#ifndef INCLUDE_SEQAN_GFF_IO_GFF_IO_BASE_H_
+#define INCLUDE_SEQAN_GFF_IO_GFF_IO_BASE_H_
 
 namespace seqan {
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
 // ============================================================================
 // Tags, Classes, Enums
 // ============================================================================
@@ -50,24 +46,14 @@ namespace seqan {
 // ----------------------------------------------------------------------------
 
 /*!
- * @defgroup GffIO GFF I/O
- * @brief I/O functionality for the GFF and GTF file formats.
- */
-
-/*!
- * @tag GffIO#Gff
+ * @tag FileFormats#Gff
  * @brief Tag for selecting the GFF format.
  *
+ * Both the GFF and the GTF file format are represented by @link GffRecord @endlink in SeqAn.
+ * Tags and functions in this group can be used for I/O of both formats to and from @link GffRecord @endlink objects.
+ *
  * @signature typedef Tag<TagGff_> Gff;
  */
-
-/**
-.Tag.File Format.tag.Gff:
-    Gff annotation file.
-..include:seqan/gff_io.h
-*/
-
-// TODO(singer): const should be non const, but is const elsewhere
 struct TagGff_;
 typedef Tag<TagGff_> Gff;
 
@@ -76,198 +62,164 @@ typedef Tag<TagGff_> Gff;
 // ----------------------------------------------------------------------------
 
 /*!
- * @tag GffIO#Gtf
+ * @tag FileFormats#Gtf
  * @brief Tag for selecting the GTF format.
  *
  * @signature typedef Tag<TagGtf_> Gtf;
  */
-
-/**
-.Tag.File Format.tag.Gtf:
-    Gtf annotation file.
-..include:seqan/gff_io.h
-*/
-
-// TODO(singer): const should be non const, but is const elsewhere
 struct TagGtf_;
 typedef Tag<TagGtf_> Gtf;
 
+// ----------------------------------------------------------------------------
+// Class MagicHeader
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<Gtf, T> :
+    public MagicHeader<Nothing, T> {};
+
+template <typename T>
+struct MagicHeader<Gff, T> :
+    public MagicHeader<Nothing, T> {};
+
+// ----------------------------------------------------------------------------
+// Class FileExtensions
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<Gff, T>
+{
+    static char const * VALUE[2];    // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<Gff, T>::VALUE[2] =
+{
+    ".gff",     // default output extension
+    ".gff3"
+};
+
+template <typename T>
+struct FileExtensions<Gtf, T>
+{
+    static char const * VALUE[1];    // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<Gtf, T>::VALUE[1] =
+{
+    ".gtf"     // default output extension
+};
+
 // ----------------------------------------------------------------------------
 // Class GffRecord
 // ----------------------------------------------------------------------------
 
 /*!
  * @class GffRecord
+ * @implements FormattedFileRecordConcept
  * @headerfile <seqan/gff_io.h>
- * @brief Represent a record from a Gff file.
+ * @brief Represent a record from a GFF or GTF file.
  *
  * @signature class GffRecord;
- *
- * @var __int32 GffRecord::INVALID_POS
- * @brief Static member with invalid/sentinel position value.
- *
- * @var __int32 GffRecord::INVALID_IDX
- * @brief Static member with invalid/sentinel rID value.
- *
- * @fn GffRecord::INVALID_SCORE
- * @brief Returns invalid score (NaN float value).
- *
- * @signature float GffRecord::INVALID_SCORE();
- * 
- * @var CharString GffRecord::ref
- * @brief The sequence name of the record.
- *
- * @var __int32 GffRecord::rID
- * @brief Integer representing ref, defaults to INVALID_IDX.
- * 
- * @var CharString GffRecord::source
- * @brief The source of the record.
- * 
- * @var CharString GffRecord::type
- * @brief The type of the record.
- * 
- * @var __int32 GffRecord::beginPos
- * @brief The begin position of the record.
- * 
- * @var __int32 GffRecord::endPos
- * @brief The end position of the record.
- * 
- * @var float GffRecord::score
- * @brief The score of the record.
- * 
- * @var char GffRecord::strand
- * @brief The strand the record belongs to.
- * 
- * @var char GffRecord::phase
- * @brief The phase of the record.
- * 
- * @section Remarks
- * 
- * For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame.  The
- * phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of
- * this feature to reach the first base of the next codon
- * 
- * @var TCharStringSet GffRecord::tagName
- * @brief The names of the attributes of the record, StringSet of CharString.
- * 
- * @var TCharStringSet GffRecord::tagValue
- * @brief The values of the attributes of the record, StringSet of CharString.
- * 
- * @section Remarks
- * 
- * For each value there is a name associated in GffRecord::tagName.
- *
- * @section Remarks
- * 
- * For each name there is a value associated in GffRecord::tagValue.
  */
-
-/**
-.Class.GffRecord
-..cat:BAM I/O
-..summary:Represent a record from a Gff file.
-..include:seqan/gff_io.h
-
-.Memvar.GffRecord#INVALID_POS
-..class:Class.GffRecord
-..summary:Static member with invalid/sentinel position value.
-..type:nolink:$__uint32$
-
-.Memvar.GffRecord#INVALID_SCORE
-..class:Class.GffRecord
-..summary:Static member with invalid score value.
-..type:nolink:$float$
-
-.Memvar.GffRecord#ref
-..class:Class.GffRecord
-..summary:The sequence id of the record.
-..type:Shortcut.CharString
-
-.Memvar.GffRecord#source
-..class:Class.GffRecord
-..summary:The source of the record.
-..type:Shortcut.CharString
-
-.Memvar.GffRecord#type
-..class:Class.GffRecord
-..summary:The type of the record.
-..type:Shortcut.CharString
-
-.Memvar.GffRecord#beginPos
-..class:Class.GffRecord
-..summary:The begin position of the record.
-..type:nolink:$__uint32$
-
-.Memvar.GffRecord#endPos
-..class:Class.GffRecord
-..summary:The end position of the record.
-..type:nolink:$__uint32$
-
-.Memvar.GffRecord#score
-..class:Class.GffRecord
-..summary:The score of the record.
-..type:nolink:$float$
-
-.Memvar.GffRecord#strand
-..class:Class.GffRecord
-..summary:The strand the record belongs to.
-..type:nolink:$char$
-
-.Memvar.GffRecord#phase
-..class:Class.GffRecord
-..summary:The phase of the record.
-..remarks:For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon
-..type:nolink:$char$
-
-.Memvar.GffRecord#tagName
-..class:Class.GffRecord
-..summary:The names of the attributes of the record.
-..type:Class.StringSet
-..remarks:For each name there is a value associated in $Memvar.GffRecord#tagValue$
-
-.Memvar.GffRecord#tagValue
-..class:Class.GffRecord
-..summary:The values of the attributes of the record.
-..type:Class.StringSet
-..remarks:For each value there is a name associated in $Memvar.GffRecord#tagName$
-*/
-
 struct GffRecord
 {
+    /*!
+     * @var __int32 GffRecord::INVALID_IDX;
+     * @brief Static member with invalid/sentinel rID value.
+     */
     static __int32 const INVALID_POS = 2147483647;  // TODO(singer): Should be MaxValue<__int32>::VALUE, but that is not a constant expression :(
-    static __int32 const INVALID_IDX = -1;
-
-    // The member descriptions are taken from: http://gmod.org/wiki/GFF
-
-    // TODO(singer): Maybe use a I/O context object and store ids as integers
-    // The ID of the landmark used to establish the coordinate system for the current feature.
-    String<char> ref;
-    int rID;
-
-    // The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature.
-    String<char> source;
-
-    // The type of the feature
-    String<char> type;
-
-    // A list of feature attributes in the format tag=value.
-    StringSet<String<char> > tagName;
-    StringSet<String<char> > tagValue;
 
-    // The start and end of the feature, in 1-based integer coordinates, relative to the landmark given in column 1
+    /*!
+     * @var CharString GffRecord::ref;
+     * @brief The sequence name of the record.
+     *
+     * The ID of the landmark used to establish the coordinate system for the current feature, most often the
+     * contig/chromosome name.
+     */
+    CharString ref;
+
+    /*!
+     * @var CharString GffRecord::source;
+     * @brief The source of the record.
+     *
+     * The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this
+     * feature.
+     */
+    CharString source;
+
+    /*!
+     * @var CharString GffRecord::type;
+     * @brief The type of the record.
+     */
+    CharString type;
+
+    /*!
+     * @var TCharStringSet GffRecord::tagNames;
+     * @brief The names of the attributes of the record, StringSet of CharString.
+     *
+     * For each value there is a name associated in @link GffRecord::tagNames tagNames @endlink.
+     */
+    StringSet<CharString> tagNames;
+
+    /*!
+     * @var TCharStringSet GffRecord::tagValues;
+     * @brief The values of the attributes of the record, StringSet of CharString.
+     *
+     * @section Remarks
+     *
+     * For each name there is a value associated in GffRecord::tagValues.
+     */
+    StringSet<CharString> tagValues;
+
+    /*!
+     * @var __int32 GffRecord::beginPos;
+     * @brief The begin position of the record.
+     */
     __uint32 beginPos;
+
+    /*!
+     * @var __int32 GffRecord::endPos;
+     * @brief The end position of the record.
+     *
+     * GFF and GTF use 1-based positions in text, but they are stored as 0-based coordinates.
+     */
     __uint32 endPos;
 
-    // The score of the feature
+    /*!
+     * @var float GffRecord::score;
+     * @brief The score of the record.
+     */
     float score;
 
-    // The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for features that are not stranded.
+    /*!
+     * @var char GffRecord::strand;
+     * @brief The strand the record belongs to.
+     *
+     * The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for
+     * features that are not stranded.
+     */
     char strand;
 
-    // For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame.
-    // The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon.
+    /*!
+     * @var char GffRecord::phase;
+     * @brief The phase of the record.
+     *
+     * For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame.
+     * The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the
+     * beginning of this feature to reach the first base of the next codon.
+     */
     char phase;
 
+    // TODO(holtgrew): C++11 will have a nan() function, use this instead then.
+    /*!
+     * @fn GffRecord::INVALID_SCORE
+     * @signature static float INVALID_SCORE()
+     * @brief Returns invalid score (NaN float value).
+     *
+     * The term <tt>x != x</tt> (for <tt>float x</tt> is only true if <tt>x</tt> is a NaN.
+     */
     static float INVALID_SCORE()
     {
         union
@@ -280,15 +232,11 @@ struct GffRecord
     }
 
     GffRecord() :
-        rID(INVALID_IDX), beginPos(-1), endPos(-1), score(INVALID_SCORE()),
+        beginPos(-1), endPos(-1), score(INVALID_SCORE()),
         strand('.'), phase('.')
     {}
 };
 
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
 // ============================================================================
 // Functions
 // ============================================================================
@@ -297,81 +245,59 @@ struct GffRecord
 // Function _parseReadGffKeyValue
 // ----------------------------------------------------------------------------
 
-template <typename TReader, typename TKeyString, typename TValueString>
-inline int
-_parseReadGffKeyValue(TValueString & outValue, TKeyString & key, TReader & reader)
+template <typename TForwardIter, typename TKeyString, typename TValueString>
+inline void
+_parseReadGffKeyValue(TValueString & outValue, TKeyString & key, TForwardIter & iter)
 {
-    char c = value(reader);
-    if (c == ' ' || c == '\t' || c == '\n' || c == '=')
-        return 1;  // Key cannot be empty.
+    //TODO(singer): AssertList functor would be need
+    char c = value(iter);
+    if (IsWhitespace()(c) || c == '=')
+        SEQAN_THROW(ParseError("The key field of an attribute is empty!"));
 
-    for (; !atEnd(reader); goNext(reader))
+    for (; !atEnd(iter); goNext(iter))
     {
-        c = value(reader);
-        if (c == ' ' || c == '\t' || c == '\n' || c == '=' || c == ';')
+        c = value(iter);
+        if (IsNewline()(c) || c == ' ' || c == '=' || c == ';')
             break;
         appendValue(key, c);
     }
-    if (!atEnd(reader) && value(reader) == ';')
+    if (!atEnd(iter) && value(iter) == ';')
     {
-        goNext(reader);
-        return 0;
+        skipOne(iter);
+        return;
     }
-    if (!atEnd(reader) && (value(reader) == '\r' || value(reader) == '\n'))
-        return 0;
 
-    if (skipWhitespaces(reader) != 0)
-        return 1;
+    if (IsNewline()(value(iter)))
+        return;
 
-    if (value(reader) == '=')
-    {
-        goNext(reader);
-        if (skipBlanks(reader) != 0)
-            return 1;
+    skipUntil(iter, NotFunctor<IsWhitespace>());
 
-        if (atEnd(reader))
-            return 1;
+    if (value(iter) == '=')
+    {
+        skipOne(iter);
+        skipUntil(iter, NotFunctor<IsWhitespace>());
     }
 
-    if (value(reader) == '"')
+    if (value(iter) == '"')
     {
         // Handle the case of a string literal.
+        skipOne(iter);
+        skipUntil(iter, NotFunctor<IsWhitespace>());
+        readUntil(outValue, iter, OrFunctor<EqualsChar<'"'>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Gff> >());
+        skipOne(iter);
 
-        goNext(reader);
-        // Append all characters in the literal to outValue until the first i
-        // line break or the closing '"'.
-        for (; !atEnd(reader); goNext(reader))
-        {
-            if (value(reader) == '\n')
-                return 1;
-
-            if (value(reader) == '"')
-            {
-                goNext(reader);
-                break;
-            }
-            appendValue(outValue, value(reader));
-        }
         // Go over the trailing semicolon and any trailing space.
-        while (!atEnd(reader) && (value(reader) == ';' || value(reader) == ' '))
-            goNext(reader);
+        skipUntil(iter, NotFunctor<OrFunctor<EqualsChar<';'>, EqualsChar<' '> > >());
     }
     else
     {
-        // Handle the non literal case.
-
         // Read until the first semicolon, return at whitespace.
-        for (; !atEnd(reader); goNext(reader))
-        {
-            if (value(reader) == ';' || value(reader) == '\n' || value(reader) == '\r')
-                break;
-            appendValue(outValue, value(reader));
-        }
+        readUntil(outValue, iter, OrFunctor<EqualsChar<';'>, IsNewline>());
+
         // Skip semicolon and spaces if any.
-        while (!atEnd(reader) && (value(reader) == ';' || value(reader) == ' '))
-            goNext(reader);
+        skipUntil(iter, NotFunctor<OrFunctor<EqualsChar<';'>, EqualsChar<' '> > >());
     }
-    return 0;
+    return;
 }
 
 // ----------------------------------------------------------------------------
@@ -381,288 +307,133 @@ _parseReadGffKeyValue(TValueString & outValue, TKeyString & key, TReader & reade
 /*!
  * @fn GffRecord#clear
  * @brief Reset a @link GffRecord @endlink object.
- * 
+ *
  * @signature void clear(record);
- * 
+ *
  * @param[in,out] record The GffRecord to reset.
  */
-
-/**
-.Function.GffRecord#clear
-..class:Class.GffRecord
-..cat:Input/Output
-..signature:clear(record)
-..param.record:The @Class.GffRecord@ to reset.
-...type:Class.GffRecord
-..summary:Reset a @Class.GffRecord@ object.
-..include:seqan/gff_io.h
-*/
-
 inline void clear(GffRecord & record)
 {
+    record.beginPos = -1;
+    record.endPos = -1;
+    record.score = record.INVALID_SCORE();
+    record.strand = '.';
+    record.phase = '.';
+
     clear(record.ref);
     clear(record.source);
     clear(record.type);
-    clear(record.tagName);
-    clear(record.tagValue);
+    clear(record.tagNames);
+    clear(record.tagValues);
 }
 
 // ----------------------------------------------------------------------------
 // Function readRecord
 // ----------------------------------------------------------------------------
 
-/*!
- * @fn GffIO#readRecord
+// NOTE(esiragusa): dox disabled.
+/*
+ * @fn GffFileIO#readRecord
  * @brief Read one GFF/GTF record from a SinglePassRecordReader.
  *
- * @signature int readRecord(record, reader[, context, [, tag]]);
+ * @signature void readRecord(record, context, iter);
  *
  * @param[out]    record  The GffRecord to write the results to.
- * @param[in,out] reader  The SinglePassRecordReader to use for reading.
- * @param[in,out] context The GffIOContext to use for reading.  If present then ref will be translated to rID using the
- *                        reference name store from context.
- * @param[in]     tag     The format to read from, one of Gtf and Gff.  Note that the parser transparently parses both
- *                        GFF and GTF.
+ * @param[in,out] context A CharString to use for buffers.
+ * @param[in,out] iter    A @link ForwardIteratorConcept forward iterator @endlink to use for reading.
  *
- * @return int A status code, 0 on success, a different value on failures.
+ * @throws IOError if something went wrong.
  */
-
-/**
-.Function.GffRecord#readRecord
-..class:Class.GffRecord
-..cat:Input/Output
-..summary:Read one gff record.
-..signature:readRecord(record, reader)
-..param.record:The gff record.
-...type:Class.GffRecord
-..param.reader: The record reader object.
-...type:Class.RecordReader
-..include:seqan/gff_io.h
-*/
-
-template <typename TStream, typename TRecordReaderSpec>
-inline int
-_readGffRecord(GffRecord & record, RecordReader<TStream, TRecordReaderSpec> & reader)
+template <typename TFwdIterator>
+void readRecord(GffRecord & record, CharString & buffer, TFwdIterator & iter)
 {
-    clear(record);
+    IsNewline isNewline;
 
-    // read column 1: seqid
-    // The letters until the first whitespace will be read.
-    // Then, we skip until we hit the first tab character.
-    if (readUntilTabOrLineBreak(record.ref, reader))
-        return 1;
-    record.rID = GffRecord::INVALID_IDX;
+    // skip commented lines
+    while (!atEnd(iter) && value(iter) == '#')
+        skipLine(iter);
 
-    if (!empty(record.ref) && record.ref[0] == '#')
-    {
-        if (skipLine(reader))
-            return 1;
+    clear(record);
+    skipUntil(iter, NotFunctor<IsWhitespace>());  //skip empty lines
 
-        return 1;
-    }
-    if (skipWhitespaces(reader))
-        return 1;
+    // read column 1: seqid
+    readUntil(record.ref, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Gff> >());
+    skipOne(iter);
 
     // read column 2: source
-    if (readUntilTabOrLineBreak(record.source, reader))
-        return 1;
+    readUntil(record.source, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Gff> >());
 
     if (record.source == ".")
         clear(record.source);
 
-    if (skipWhitespaces(reader))
-        return 1;
+    skipOne(iter);
 
     // read column 3: type
-    if (readUntilTabOrLineBreak(record.type, reader))
-        return 1;
-
-    if (skipWhitespaces(reader))
-        return 1;
+    readUntil(record.type, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Gff> >());
+    skipOne(iter);
 
     // read column 4: begin position
-    String<char> temp;
-    if (readDigits(temp, reader))
-        return 1;
-
-    if (length(temp) > 0u)
-    {
-        if (!lexicalCast2(record.beginPos, temp))
-            return 1;
-
-        --record.beginPos;  // Translate from 1-based to 0-based.
-    }
-    else
-    {
-        record.beginPos = GffRecord::INVALID_POS;
-        if (skipUntilWhitespace(reader))
-            return 1;
-    }
-    if (skipBlanks(reader))
-        return 1;
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Gff> >());
+    record.beginPos = lexicalCast<__uint32>(buffer);
+    --record.beginPos;  // Translate from 1-based to 0-based.
+    skipOne(iter);
 
     // read column 5: end position
-    clear(temp);
-    if (readDigits(temp, reader))
-        return 1;
-
-    if (length(temp) > 0u)
-    {
-        if (!lexicalCast2(record.endPos, temp))
-            return 1;
-    }
-    else
-    {
-        record.endPos = GffRecord::INVALID_POS;
-        if (skipUntilWhitespace(reader))
-            return 1;
-    }
-    if (skipBlanks(reader))
-        return 1;
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Gff> >());
+    record.endPos = lexicalCast<__uint32>(buffer);
+    skipOne(iter);
 
+    //check if end < begin
+    if (record.endPos < record.beginPos)
+        SEQAN_THROW(ParseError("Begin position of GFF/GTF record is larger than end position!"));
 
     // read column 6: score
-    clear(temp);
-    readFloat(temp, reader);
-
-    if (length(temp) > 0u)
-    {
-        if (temp != ".")
-        {
-            if (!lexicalCast2(record.score, temp))
-                return 1;
-        }
-        else
-        {
-            record.score = GffRecord::INVALID_SCORE();
-            if (skipUntilWhitespace(reader))
-                return 1;
-        }
-    }
-    else
-    {
-        return 1;
-    }
-
-    if (skipBlanks(reader))
-        return 1;
+    clear(buffer);
+    readUntil(buffer, iter, OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Gff> >());
+    if (buffer != ".")
+        record.score = lexicalCast<float>(buffer);
+    skipOne(iter, IsTab());
 
     // read column 7: strand
-    clear(temp);
-    if (readUntilTabOrLineBreak(temp, reader))
-        return 1;
-
-    if (temp[0] != '-' && temp[0] != '+')
-    {
-        record.strand = '.';
-    }
-    else
-    {
-        record.strand = temp[0];
-    }
-
-    if (skipBlanks(reader))
-        return 1;
+    readOne(record.strand, iter, OrFunctor<OrFunctor<EqualsChar<'-'>, EqualsChar<'+'> >, EqualsChar<'.'> >());
+    skipOne(iter, IsTab());
 
     // read column 8: phase
-    clear(temp);
-    if (readUntilTabOrLineBreak(temp, reader))
-        return 1;
+    readOne(record.phase, iter, OrFunctor<EqualsChar<'.'>, IsInRange<'0', '2'> >());
 
-    if (temp != "0" && temp != "1" && temp != "2")
-    {
-        record.phase = '.';
-    }
-    else
+    // It's fine if there are no attributes and the line ends here.
+    if (atEnd(iter) || isNewline(value(iter)))
     {
-        record.phase = temp[0];
+        skipLine(iter);
+        return;
     }
-
-    if (skipBlanks(reader))
-        return 1;
-
-    // It's fine if there are no attributes and the line ends here.
-    if (atEnd(reader))
-        return 0;
-    if (value(reader) == '\n' || value(reader) == '\r')
-        return skipLine(reader);
+    skipOne(iter, IsTab());
 
     // read column 9: attributes
-    while (!atEnd(reader))
+    while (!atEnd(iter))
     {
 
-        String<char> _key;
-        String<char> _value;
+        CharString _key;
+        CharString _value;
         // Read next key/value pair.
-        if (_parseReadGffKeyValue(_value, _key, reader) != 0)
-            return 1;
+        _parseReadGffKeyValue(_value, _key, iter);
 
-        appendValue(record.tagName, _key);
-        appendValue(record.tagValue, _value);
+        appendValue(record.tagNames, _key);
+        appendValue(record.tagValues, _value);
 
         clear(_key);
         clear(_value);
 
         // At end of line:  Skip EOL and break.
-        if (!atEnd(reader) && (value(reader) == '\r' || value(reader) == '\n'))
+        if (!atEnd(iter) && isNewline(value(iter)))
         {
-            if (skipLine(reader) != 0)
-                return 1;
-
+            skipOne(iter);
             break;
         }
     }
-    return 0;
-}
-
-template <typename TRecordReader>
-inline int
-readRecord(GffRecord & record, TRecordReader & reader, Gff /*tag*/)
-{
-    return _readGffRecord(record, reader);
-}
-
-template <typename TRecordReader>
-inline int
-readRecord(GffRecord & record, TRecordReader & reader, Gtf /*tag*/)
-{
-    return _readGffRecord(record, reader);
-}
-
-// TODO(singer): Needs proper documentation!!! Check the length of the stores!!!
-template <typename TRecordReader, typename TContextSpec, typename TContextSpec2>
-inline int
-_readGffRecord(GffRecord & record, TRecordReader & reader, GffIOContext<TContextSpec, TContextSpec2> & context)
-{
-    // Read record with string ref from GFF file.
-    int res = _readGffRecord(record, reader);
-    if (res != 0)
-        return res;
-
-    // Translate ref to rID using the context.  If there is no such sequence name in the context yet then we add it.
-    unsigned idx = 0;
-    if (!getIdByName(nameStore(context), record.ref, idx, nameStoreCache(context)))
-    {
-        idx = length(nameStore(context));
-        appendName(nameStore(context), record.ref, nameStoreCache(context));
-    }
-    record.rID = idx;
-
-    return 0;
-}
-
-template <typename TRecordReader, typename TContextSpec, typename TContextSpec2>
-inline int
-readRecord(GffRecord & record, TRecordReader & reader, GffIOContext<TContextSpec, TContextSpec2> & context, Gff /*tag*/)
-{
-    return _readGffRecord(record, reader, context);
-}
-
-template <typename TRecordReader, typename TContextSpec, typename TContextSpec2>
-inline int
-readRecord(GffRecord & record, TRecordReader & reader, GffIOContext<TContextSpec, TContextSpec2> & context, Gtf /*tag*/)
-{
-    return _readGffRecord(record, reader, context);
+    return;
 }
 
 // ----------------------------------------------------------------------------
@@ -674,66 +445,56 @@ readRecord(GffRecord & record, TRecordReader & reader, GffIOContext<TContextSpec
 // Returns false on success.
 
 template <typename TTargetStream, typename TString>
-inline bool
+inline void
 _writeInQuotes(TTargetStream & target, TString & temp)
 {
     // TODO(jsinger): What about escaping quote chars '"'?
-    if (streamWriteChar(target, '"') || streamWriteBlock(target, begin(temp, Standard()), length(temp)) < length(temp) ||
-        streamWriteChar(target, '"'))
-        return true;
-
-    return false;
+    writeValue(target, '"');
+    write(target, temp);
+    writeValue(target, '"');
 }
 
-template <typename TTargetStream, typename TString, typename TMustBeQuotedFunctor>
-inline bool
-_writePossiblyInQuotes(TTargetStream & target, TString & source, TMustBeQuotedFunctor const &func)
+template <typename TTarget, typename TString, typename TMustBeQuotedFunctor>
+inline void
+_writePossiblyInQuotes(TTarget& target, TString & source, TMustBeQuotedFunctor const &func)
 {
     // TODO(jsinger): What about escaping quote chars '"'?
-    typedef typename Iterator<TString, Standard>::Type TIter;
-
+    typedef typename Iterator<TString>::Type TIter;
     TIter itEnd = end(source, Standard());
     for (TIter it = begin(source, Standard()); it != itEnd; ++it)
     {
         // we have a problem if the string contains a '"' or a line break
-        if (*it == '\n' || *it == '"')
-            return 1;
+        if (value(it) =='\n' || value(it) == '"')
+            SEQAN_THROW(ParseError("Attribute contains illegal character!"));
 
         if (func(*it))
-            return _writeInQuotes(target, source);
+        {
+            _writeInQuotes(target, source);
+            return;
+        }
     }
-    return (streamWriteBlock(target, begin(source, Standard()), length(source)) < length(source));
+    write(target, source);
 }
 
 // ----------------------------------------------------------------------------
-// Function writeRecord
+// Function writeRecord()
 // ----------------------------------------------------------------------------
 
-/*!
- * @fn GffIO#writeRecord
- * @brief Writes on GFF/GTF record to a stream.
+// NOTE(esiragusa): dox disabled.
+/*
+ * @fn GffFileIO#writeRecord
+ * @brief Writes a @link GffRecord @endlink to a stream as GFF or GTF.
  *
- * @signature int writeRecord(stream, record);
+ * @signature void writeRecord(stream, record, tag);
  *
- * @param[in,out] stream The StreamConcept to write to.
- * @param[in]     record The GffRecord to write.
+ * @param[in,out] stream  The @link OutputIteratorConcept output iterator @endlink to write to.
+ * @param[in]     record  The @link GffRecord @endlink to write out.
+ * @param[in]     tag     A tag to select the file format, either @link GffFileIO#Gff @endlink or @link GffFileIO#Gtf
+ *                        @endlink.
  *
- * @return int A status code, 0 on success, a different value on errors.
+ * @throws IOError if something went wrong.
  */
 
-/**
-.Function.GffRecord#writeRecord
-..class:Class.GffRecord
-..cat:Input/Output
-..summary:Writes one gff record to a stream.
-..signature:writeRecord(TSreamm stream, GffRecord record)
-..param.stream:The output stream.
-...type:Concept.StreamConcept
-..param.record:The gff record.
-...type:Class.GffRecord
-..include:seqan/gff_io.h
-*/
-
 template <typename TFormatTag>
 struct GffRecordKeyMustBeQuoted_;
 
@@ -776,172 +537,116 @@ struct GffRecordValueMustBeQuoted_<Gtf>
     }
 };
 
+template <typename TTarget>
+inline void
+_writeAdditionalSeperator(TTarget const & /*target*/, Gff)
+{
+    return;
+}
+
+template <typename TTarget>
+inline void
+_writeAdditionalSeperator(TTarget & target, Gtf)
+{
+    writeValue(target, ' ');
+    return;
+}
 
 
-template <typename TStream, typename TTag>
-inline int
-_writeAttributes(TStream & stream, GffRecord const & record, TTag)
+template <typename TTarget, typename TTag>
+inline void
+_writeAttributes(TTarget & target, GffRecord const & record, TTag const & tag)
 {
     const char separatorBetweenTagAndValue = (IsSameType<TTag, Gff>::VALUE)? '=' : ' ';
-    for (unsigned i = 0; i < length(record.tagName); ++i)
+    for (unsigned i = 0; i < length(record.tagNames); ++i)
     {
         if (i != 0)
         {
-            if (streamWriteChar(stream, ';'))
-                return 1;
+            writeValue(target, ';');
 
             // In GTF files a space follows the semicolon
-            if (IsSameType<TTag, Gtf>::VALUE && streamWriteChar(stream, ' '))
-                return 1;
-        }
+            _writeAdditionalSeperator(target, tag);
+       }
 
-        if (_writePossiblyInQuotes(stream, record.tagName[i], GffRecordKeyMustBeQuoted_<TTag>()))
-            return 1;
+        _writePossiblyInQuotes(target, record.tagNames[i], GffRecordKeyMustBeQuoted_<TTag>());
 
-        if (!empty(record.tagValue[i]))
+        if (!empty(record.tagValues[i]))
         {
-            if (streamWriteChar(stream, separatorBetweenTagAndValue))
-                return 1;
-
-            if (_writePossiblyInQuotes(stream, record.tagValue[i], GffRecordValueMustBeQuoted_<TTag>()))
-                return 1;
+            writeValue(target, separatorBetweenTagAndValue);
+            _writePossiblyInQuotes(target, record.tagValues[i], GffRecordValueMustBeQuoted_<TTag>());
         }
     }
-    
+
     // In GTF files each (especially the last) attribute must end with a semi-colon
-    if (IsSameType<TTag, Gtf>::VALUE && !empty(record.tagName) && streamWriteChar(stream, ';'))
-        return 1;
+    if (IsSameType<TTag, Gtf>::VALUE && !empty(record.tagNames))
+        writeValue(target, ';');
 
-    return 0;
+    return;
 }
 
-template <typename TStream, typename TSeqId, typename TTag>
-inline int
-_writeRecordImpl(TStream & stream, GffRecord const & record, TSeqId const & ref, TTag tag)
+template <typename TTarget, typename TFormat>
+inline void
+writeRecord(TTarget & target, GffRecord const & record, Tag<TFormat> const & tag)
 {
     // ignore empty annotations, i.e. annotations that are 'guessed' by implicit information from their children (in GFF)
-    if (empty(ref))
-        return 0;
+    if (empty(record.ref))
+        return;
 
     // write column 1: seqid
-    if (streamWriteBlock(stream, begin(ref, Standard()), length(ref)) != length(ref))
-        return 1;
-
-    if (streamWriteChar(stream, '\t'))
-        return 1;
+    //typename Iterator<TSeqId const, Rooted>::Type itRef = begin(record.ref);
+    write(target, record.ref);
+    writeValue(target, '\t');
 
     // write column 2: source
     if (empty(record.source))
-    {
-        if (streamWriteChar(stream, '.'))
-            return 1;
-    }
+        writeValue(target, '.');
     else
-    {
-        if (streamWriteBlock(stream, begin(record.source, Standard()), length(record.source)) != length(record.source))
-            return 1;
-    }
-
-    if (streamWriteChar(stream, '\t'))
-        return 1;
+        write(target, record.source);
+    writeValue(target, '\t');
 
     // write column 3: type
-    if (streamWriteBlock(stream, begin(record.type, Standard()), length(record.type)) != length(record.type))
-        return 1;
-
-    if (streamWriteChar(stream, '\t'))
-        return 1;
+    write(target, record.type);
+    writeValue(target, '\t');
 
     // write column 4: begin position
     if (record.beginPos != (unsigned)-1)
-    {
-        if (streamPut(stream, record.beginPos + 1))
-            return 1;
-    }
+        appendNumber(target, record.beginPos + 1);
     else
-    {
-        if (streamWriteChar(stream, '.'))
-            return 1;
-    }
-
-    if (streamWriteChar(stream, '\t'))
-        return 1;
-
+        SEQAN_THROW(ParseError("No start position!"));
+    writeValue(target, '\t');
 
     // write column 5: end position
-    if (record.endPos != (unsigned)-1)
-    {
-        if (streamPut(stream, record.endPos))
-            return 1;
-    }
+    if (record.endPos != (unsigned)-1 && record.beginPos <= record.endPos)
+        appendNumber(target, record.endPos);
     else
-    {
-        if (streamWriteChar(stream, '.'))
-            return 1;
-    }
-
-    if (streamWriteChar(stream, '\t'))
-        return 1;
+        SEQAN_THROW(ParseError("No end position!"));
+    writeValue(target, '\t');
 
     // write column 6: score
     if (record.score != record.score)
-    {
-        if (streamWriteChar(stream, '.'))
-            return 1;
-    }
+        writeValue(target, '.');
     else
-    {
-        if (streamPut(stream, record.score))
-            return 1;
-    }
-
-    if (streamWriteChar(stream, '\t'))
-        return 1;
+        appendNumber(target, record.score);
+    writeValue(target, '\t');
 
     // write column 7: strand
-    if (streamWriteChar(stream, record.strand))
-        return 1;
-
-    if (streamWriteChar(stream, '\t'))
-        return 1;
+    writeValue(target, record.strand);
+    writeValue(target, '\t');
 
     // write column 8: phase
-    if (streamWriteChar(stream, record.phase))
-        return 1;
-
-    if (streamWriteChar(stream, '\t'))
-        return 1;
+    writeValue(target, record.phase);
+    writeValue(target, '\t');
 
     // write column 9: attributes
     // only until length - 1, because there is no semicolon at the end of the line
 
-    _writeAttributes(stream, record, tag);
-
-    if (streamWriteChar(stream, '\n'))
-        return 1;
-
-    return 0;
-}
+    _writeAttributes(target, record, tag);
 
-template <typename TStream, typename TTag>
-inline int
-writeRecord(TStream & stream, GffRecord const & record, TTag const tag)
-{
-    return _writeRecordImpl(stream, record, record.ref, tag);
-}
-
-template <typename TStream, typename TContextSpec, typename TContextSpec2, typename TTag>
-inline int
-writeRecord(TStream & stream, GffRecord const & record, GffIOContext<TContextSpec, TContextSpec2> & context, TTag const tag)
-{
-    if (record.rID != GffRecord::INVALID_IDX)
-    {
-        String<char> tempSeqId = nameStore(context)[record.rID];
-        return _writeRecordImpl(stream, record, tempSeqId, tag);
-    }
-    return _writeRecordImpl(stream, record, record.ref, tag);
+    writeValue(target, '\n');
+    return;
 }
 
 }  // namespace seqan
 
-#endif  // CORE_INCLUDE_SEQAN_GFF_IO_GFF_IO_BASE_H_
+#endif  // INCLUDE_SEQAN_GFF_IO_GFF_IO_BASE_H_
+
diff --git a/seqan/gff_io/gff_io_context.h b/seqan/gff_io/gff_io_context.h
deleted file mode 100644
index 14d69fa..0000000
--- a/seqan/gff_io/gff_io_context.h
+++ /dev/null
@@ -1,274 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Class GffIOContext, accessor functions.
-// ==========================================================================
-
-#ifndef CORE_INCLUDE_SEQAN_GFF_IO_GFF_IO_CONTEXT_H_
-#define CORE_INCLUDE_SEQAN_GFF_IO_GFF_IO_CONTEXT_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class GffIOContext
- * @headerfile <seqan/bam_io.h>
- * @brief The I/O context to use for GFF I/O.
- * 
- * @signature template <typename TNameStore, typename TNameStoreCache = NameStoreCache<TNameStore> >
- *            class GffIOContext;
- * 
- * @tparam TNameStore      The name store class.
- * @tparam TNameStoreCache The name store cache class, default: NameStoreCache&lt;TNameStore&gt;.
- * 
- * @section Examples
- * 
- * Creating a GffIOContext for a raw StringSet of CharString.
- * 
- * @code{.cpp}
- * StringSet<CharString> nameStore;
- * NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
- * GffIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
- * // ...
- * @endcode
- *
- * Using a GffIOContext with a FragmentStore.
- * 
- * @code{.cpp}
- * typedef FragmentStore<>::TContigNameStore         TNameStore;
- * typedef NameStoreCache<TNameStore>                TNameStoreCache;
- * FragmentStore<> store;
- * // Optionally, do something with store.
- * typedef GffIOContext<TNameStore, TNameStoreCache> TGffIOContext;
- * TGffIOContext bamIOContext(store.contigNameStore, store.contigNameStoreCache);
- * // ...
- * @endcode
- *
- *
- * @fn GffIOContext::GffIOContext
- * @brief Constructor.
- * @signature GffIOContext::GffIOContext();
- * 
- * @section Remarks
- * 
- * Only the default constructor is provided.
- * 
- *
- * @typedef GffIOContext::TNameStore
- * @brief The name store class.
- *
- * @signature typedef (...) TNameStore;
- * 
- * @see GffIOContext#nameStore
- * 
- *
- * @typedef GffIOContext::TNameStoreCache
- * @brief The name store cache class.
- *
- * @signature typedef (...) TNameStoreCache;
- * 
- * @see GffIOContext#nameStoreCache
- */
-
-/**
-.Class.GffIOContext
-..cat:GFF I/O
-..signature:GffIOContext<TNameStore[, TNameStoreCache]>
-..summary:The I/O context to use for GFF I/O.
-..param.TNameStore:The name store class.
-..param.TNameStoreCache:The name store cache class.
-...default:@Class.NameStoreCache@<TNameStore>
-..include:bam_io.h
-..example.text:Creating a @Class.GffIOContext@ for a raw @Class.StringSet@ of @Shortcut.CharString@.
-..example.code:
-StringSet<CharString> nameStore;
-NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
-GffIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
-// ...
-..example.text:Using a @Class.GffIOContext@ with a @Class.FragmentStore@.
-..example.code:
-typedef FragmentStore<>::TContigNameStore         TNameStore;
-typedef NameStoreCache<TNameStore>                TNameStoreCache;
-FragmentStore<> store;
-// Optionally, do something with store.
-typedef GffIOContext<TNameStore, TNameStoreCache> TGffIOContext;
-TGffIOContext bamIOContext(store.contigNameStore, store.contigNameStoreCache);
-// ...
-
-.Memfunc.GffIOContext#GffIOContext
-..class:Class.GffIOContext
-..signature:GffIOContext()
-..summary:Constructor.
-..remarks:Only the default constructor is provided.
-
-.Typedef.GffIOContext#TNameStore
-..class:Class.GffIOContext
-..summary:The name store class.
-
-.Typedef.GffIOContext#TNameStoreCache
-..class:Class.GffIOContext
-..summary:The name store cache class.
-*/
-
-template <typename TNameStore_, typename TNameStoreCache_ = NameStoreCache<TNameStore_> >
-class GffIOContext
-{
-public:
-    typedef TNameStore_ TNameStore;
-    typedef TNameStoreCache_ TNameStoreCache;
-
-    TNameStore * _nameStore;
-    TNameStoreCache * _nameStoreCache;
-
-    GffIOContext() : _nameStore(0), _nameStoreCache(0)
-    {}
-
-    GffIOContext(TNameStore & nameStore, TNameStoreCache & nameStoreCache) :
-            _nameStore(&nameStore), _nameStoreCache(&nameStoreCache)
-    {}
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function nameStore()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffIOContext#nameStore
- * @brief Return reference to name store from @link GffIOContext @endlink.
- * 
- * @signature TNameStore nameStore(context);
- * 
- * @param[in] context The GffIOContext to query.
- * 
- * @return Reference to the name store of the context (TNameStore).
- *
- * @see GffIOContext::TNameStore
- * @see GffIOContext#nameStoreCache
- */
-
-/**
-.Function.GffIOContext#nameStore
-..class:Class.GffIOContext
-..cat:GFF I/O
-..summary:Return reference to name store from @Class.GffIOContext@.
-..signature:nameStore(context)
-..param.context:The @Class.GffIOContext@ to query.
-...type:Class.GffIOContext
-..see:Typedef.GffIOContext#TNameStore
-..include:seqan/bam_io.h
-*/
-
-// TODO(holtgrew): Rename to referenceNameStore
-template <typename TNameStore, typename TNameStoreCache>
-TNameStore &
-nameStore(GffIOContext<TNameStore, TNameStoreCache> & context)
-{
-    SEQAN_ASSERT(context._nameStore != 0);
-    return *context._nameStore;
-}
-
-template <typename TNameStore, typename TNameStoreCache>
-TNameStore const &
-nameStore(GffIOContext<TNameStore, TNameStoreCache> const & context)
-{
-    SEQAN_ASSERT(context._nameStore != 0);
-    return *context._nameStore;
-}
-
-// ----------------------------------------------------------------------------
-// Function nameStoreCache()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffIOContext#nameStoreCache
- * @brief Return reference to name store cache from @link GffIOContext @endlink.
- * 
- * @signature TNameStoreCache nameStoreCache(context);
- * 
- * @param[in] context The GffIOContext to query.
- *
- * @return TNameStoreCache A reference to the NameStoreCache of the context.
- * 
- * @see GffIOContext::TNameStoreCache
- * @see GffIOContext#nameStore
- */
-
-/**
-.Function.GffIOContext#nameStoreCache
-..class:Class.GffIOContext
-..cat:GFF I/O
-..summary:Return reference to name store cache from @Class.GffIOContext@.
-..signature:nameStoreCache(context)
-..param.context:The @Class.GffIOContext@ to query.
-...type:Class.GffIOContext
-..see:Typedef.GffIOContext#TNameStoreCache
-..include:seqan/bam_io.h
-..see:Function.GffIOContext#nameStore
-*/
-
-// TODO(holtgrew): Rename to referenceNameStoreCache
-template <typename TNameStore, typename TNameStoreCache>
-TNameStoreCache &
-nameStoreCache(GffIOContext<TNameStore, TNameStoreCache> & context)
-{
-    SEQAN_ASSERT(context._nameStoreCache != 0);
-    return *context._nameStoreCache;
-}
-
-template <typename TNameStore, typename TNameStoreCache>
-TNameStoreCache const &
-nameStoreCache(GffIOContext<TNameStore, TNameStoreCache> const & context)
-{
-    SEQAN_ASSERT(context._nameStoreCache != 0);
-    return *context._nameStoreCache;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef CORE_INCLUDE_SEQAN_GFF_IO_GFF_IO_CONTEXT_H_
-
diff --git a/seqan/gff_io/gff_stream.h b/seqan/gff_io/gff_stream.h
deleted file mode 100644
index 0e94963..0000000
--- a/seqan/gff_io/gff_stream.h
+++ /dev/null
@@ -1,597 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-
-// TODO(holtgrew): Currently the parsers for GFF and GTF are the same. Thus, we need no file format tag for reading.  We always write GFF.
-
-#ifndef SEQAN_EXTRAS_INCLUDE_SEQAN_GFF_IO_GFF_STREAM_H_
-#define SEQAN_EXTRAS_INCLUDE_SEQAN_GFF_IO_GFF_STREAM_H_
-
-#include <memory>
-#include <fstream>
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class GffStream
- * @headerfile <seqan/gff_io.h>
- * @brief High-level GFF/GTF I/O class.
- * 
- * @signature class GffStream;
- * 
- * The GffStream class allows to read and write GTF and GFF files.
- * 
- * @section Remarks
- * 
- * Note that the class <tt>GffStream</tt> allows to read both GFF 2, 3, and GTF.  For writing, only GFF 3 and GTF are
- * supported.
- * 
- * @section Examples
- * 
- * The following example demonstrates reading a GFF file and printing the annotation locations.
- * 
- * @include demos/gff_io/gff_stream_read.cpp
- * 
- * @see GffStream::FileFormat
- * 
- *
- * @var TCharStringSet GffStream::sequenceNames
- * @brief The names of the sequences (StringSet of CharString), updated when new sequences are seen in GFF file.
- * 
- * @var GffStream::FileFormat GffStream::fileFormat
- * @brief File format to use for writing.
- * 
- *
- * @fn GffStream::GffStream
- * @brief Constructor.
- * 
- * @signature GffStream::GffStream();
- * @signature GffStream::GffStream(fileName[, mode=READ[, fileFormat=GFF]]);
- * 
- * @param[in] fileName   The path to the file to open, <tt>char const *</tt>.
- * @param[in] mode       The open mode, GffStream::Mode, default is READ.
- * @param[in] fileFormat The open mode, GffStream::FileFormat, default is auto-detect.
- * 
- * @see GffStream::Mode
- *
- * @see GffStream#open
- */
-
-/**
-.Class.GffStream
-..cat:GFF I/O
-..summary:High-level GFF/GTF I/O class.
-..description:The GffStream class allows to read and write GTF and GFF files.
-..signature:class GffStream
-..remarks:
-Note that the class $GffStream$ allows to read both GFF 2, 3, and GTF.
-For writing, only GFF 3 and GTF are supported.
-..example:The following example demonstrates reading a GFF file and printing the annotation locations.
-..example.file:demos/gff_io/gff_stream_read.cpp
-..include:seqan/gff_io.h
-..see:Enum.GffStream\colon\colonFileFormat
-
-.Memfunc.GffStream#GffStream
-..class:Class.GffStream
-..summary:Constructor.
-..signature:GffStream::GffStream()
-..signature:GffStream::GffStream(fileName[, mode=READ[, fileFormat=GFF]])
-..param.fileName:The path to the file to open.
-...type:nolink:$char const *$
-..param.mode:The open mode.
-...type:Enum.GffStream\colon\colonMode
-...default:$GffStream\colon\colonMode::READ$
-..see:Enum.GffStream\colon\colonMode
-
-.Memvar.GffStream#fileFormat
-..class:Class.GffStream
-..summary:File format to use for writing.
-
-.Memvar.GffStream#sequenceNames
-..class:Class.GffStream
-..summary:The names of the sequences (@Class.StringSet@ of @Shortcut.CharString@), updated when new sequences are seen in GFF file.
-
-.Enum.GffStream\colon\colonMode
-..cat:GFF I/O
-..summary:Open mode for the @Class.GffStream@ class.
-..value.INVALID:Invalid open mode.
-..value.READ:Open in read mode.
-..value.WRITE:Open in write mode.
-..include:seqan/gff_io.h
-
-.Enum.GffStream\colon\colonFileFormat
-..cat:GFF I/O
-..summary:File format for writing in the @Class.GffStream@ class.
-..value.GFF:GFF file format.
-..value.GTF:GTF file format.
-..include:seqan/gff_io.h
-*/
-
-/*!
- * @enum GffStream::FileFormat
- * @headerfile <seqan/gff_io.h>
- *
- * @signature enum GffStream::FileFormat;
- * 
- * @brief File format for writing in the @link GffStream @endlink class.
- * 
- * @see GffStream
- * 
- * @var GffStream::FileFormat GffStream::GFF
- * @brief GFF file format.
- * 
- * @var GffStream::FileFormat GffStream::GTF
- * @brief GTF file format.
- */
-
-/*!
- * @enum GffStream::Mode
- * @headerfile <seqan/gff_io.h>
- * @brief Open mode for the GffStream class.
- * 
- * @signature enum GffStream::Mode;
- *
- * @see GffStream#open
- * @see GffStream::GffStream
- * 
- * @var GffStream::Mode GffStream::READ
- * @brief Open in read mode.
- * 
- * @var GffStream::Mode GffStream::WRITE
- * @brief Open in write mode.
- * 
- * @var GffStream::Mode GffStream::INVALID
- * @brief Invalid open mode.
- */
-
-class GffStream
-{
-public:
-    typedef RecordReader<std::istream, SinglePass<> > TReader_;
-    typedef seqan::StringSet<seqan::CharString> TNameStore;
-    typedef seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > TNameStoreCache;
-    typedef GffIOContext<TNameStore, TNameStoreCache> TGffIOContext;
-
-    // The open mode.
-    enum Mode
-    {
-        INVALID,
-        READ,
-        WRITE
-    };
-
-    // The file format.
-    enum FileFormat
-    {
-        GFF,
-        GTF
-    };
-
-    std::SEQAN_AUTO_PTR_NAME<std::fstream> _stream;
-    std::ostream * _outStream;
-    std::istream * _inStream;
-    CharString _filename;
-    std::SEQAN_AUTO_PTR_NAME<TReader_> _reader;
-    Mode _mode;
-    FileFormat fileFormat;
-    int _error;
-    bool _isGood;
-
-    TNameStore sequenceNames;
-    TNameStoreCache _sequenceNamesCache;
-    TGffIOContext _context;
-
-    GffStream() : _outStream(), _inStream(), _mode(INVALID), fileFormat(GFF), _error(0), _isGood(true),
-                  _sequenceNamesCache(sequenceNames), _context(sequenceNames, _sequenceNamesCache)
-    {}
-
-    GffStream(char const * filename, Mode mode = READ, FileFormat fileFormat = GFF) :
-            _outStream(), _inStream(), _filename(filename), _mode(mode), fileFormat(fileFormat), _error(0),
-            _isGood(true), _sequenceNamesCache(sequenceNames), _context(sequenceNames, _sequenceNamesCache)
-    {
-        _open(filename, mode);
-    }
-
-    bool _open(char const * filename, Mode mode)
-    {
-        // Reset.
-        _filename = filename;
-        _mode = mode;
-        _error = 0;
-        _isGood = true;
-
-        if (mode == READ)
-        {
-            if (_filename == "-")
-            {
-                _stream.reset();
-                _inStream = &std::cin;
-            }
-            else
-            {
-                _stream.reset(new std::fstream);
-                _stream->open(toCString(_filename), std::ios::binary | std::ios::in);
-                if (!_stream->good())
-                {
-                    _isGood = false;
-                    return false;
-                }
-                _inStream = _stream.get();
-            }
-            _reader.reset(new TReader_(*_inStream));
-            _outStream = 0;
-        }
-        else if (mode == WRITE)
-        {
-            if (_filename == "-")
-            {
-                _stream.reset();
-                _outStream = &std::cout;
-            }
-            else
-            {
-                _stream.reset(new std::fstream);
-                _stream->open(toCString(_filename), std::ios::binary | std::ios::out);
-                if (!_stream->good())
-                {
-                    _isGood = false;
-                    return false;
-                }
-                _reader.reset();
-                _outStream = _stream.get();
-            }
-            _inStream = 0;
-        }
-        return true;
-    }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function open()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffStream#open
- * @brief Open a GffStream .
- * 
- * @signature bool open(gffStream, fileName[, mode[, fileFormat]]);
- * 
- * @param[in,out] gffStream  The GffStream to open.
- * @param[in]     fileName   The path to the file to open, <tt>char const *</tt>.
- * @param[in]     mode       The open mode, GffStream::Mode, defaults to <tt>GffStream::Mode::READ</tt>.
- * @param[in]     fileFormat File format to use for writing, GffStream::FileFormat.
- * 
- * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
- * 
- * @see GffStream#isGood
- * @see GffStream::Mode
- */
-
-/**
-.Function.GffStream#open
-..class:Class.GffStream
-..cat:GFF I/O
-..summary:Open a @Class.GffStream@.
-..signature:bool open(gffStream, fileName[, mode[, fileFormat]])
-..param.gffStream:The @Class.GffStream@ to open.
-...type:Class.GffStream
-..param.fileName:The path to the file to open.
-...type:nolink:$char const *$
-..param.mode:The open mode.
-...type:Enum.GffStream\colon\colonMode
-...default:$GffStream\colon\colonMode::READ$
-..param.fileFormat:File format to use for writing.
-...type:Enum.GffStream\colon\colonFileFormat
-..returns:$true$ on success, $false$ on failure.
-..see:Function.GffStream#isGood
-..see:Enum.GffStream\colon\colonMode
-..include:seqan/gff_io.h
-*/
-
-inline bool open(GffStream & stream, char const * filename, GffStream::Mode mode = GffStream::READ,
-                 GffStream::FileFormat fileFormat = GffStream::GFF)
-{
-    stream.fileFormat = fileFormat;
-    return stream._open(filename, mode);
-}
-
-// ----------------------------------------------------------------------------
-// Function addSequenceName()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffStream#addSequenceName
- * @brief Add the name of a sequence to a GffStream .
- * 
- * @signature void addSequenceName(gffStream, seqName);
- * 
- * @param[in,out] gffStream The GffStream to add the name to
- * @param[in]     seqName   The name of the sequence to append, CharString.
- */
-
-/**
-.Function.GffStream#addSequenceName
-..class:Class.GffStream
-..cat:GFF I/O
-..summary:Add the name of a sequence to a @Class.GffStream@.
-..signature:void addSequenceName(gffStream, seqName);
-..param.gffStream:The @Class.GffStream@ to add the name to.
-...type:Class.GffStream
-..param.seqName:The name of the sequence to append.
-...type:Shortcut.CharString
-..include:seqan/gff_io.h
-*/
-
-inline void addSequenceName(GffStream & stream, CharString const & name)
-{
-    appendName(stream.sequenceNames, name, stream._sequenceNamesCache);
-}
-
-// ----------------------------------------------------------------------------
-// Function readRecord()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffStream#readRecord
- * @brief Read a record from a GffStream
- * 
- * @signature int readRecord(record, gffStream);
- * 
- * @param[out]    record    The GffRecord to read into, GffRecord.
- * @param[in,out] gffStream The GffStream to read from, GffStream.
- * 
- * @return int <tt>0</tt> on success, non-<tt>0</tt> on failure.
- */
-
-/**
-.Function.GffStream#readRecord
-..class:Class.GffStream
-..cat:GFF I/O
-..summary:Read a record from a @Class.GffStream@
-..signature:int readRecord(record, gffStream)
-..param.record:The @Class.GffRecord@ to read into.
-...type:Class.GffRecord
-..param.gffStream:The @Class.GffStream@ to read from.
-...type:Class.GffStream
-..returns:$0$ on success, non-$0$ on failure.
-..include:seqan/gff_io.h
-*/
-
-inline int readRecord(GffRecord & record,
-                      GffStream & stream)
-{
-    int res = readRecord(record, *stream._reader, stream._context, Gff());
-    if (res != 0)
-        stream._isGood = false;
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function writeRecord()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffStream#writeRecord
- * @brief Write a record to a GffStream.
- *
- * @signature int writeRecord(gffStream, record);
- * 
- * @param[in,out] gffStream The GffStream to write to.
- * @param[in]     record    The GffRecord to write.
- * 
- * @return int <tt>0</tt> on success, non-<tt>0</tt> on failure.
- */
-
-/**
-.Function.GffStream#writeRecord
-..class:Class.GffStream
-..cat:GFF I/O
-..summary:Write a record to a @Class.GffStream@
-..signature:int writeRecord(gffStream, record)
-..param.gffStream:The @Class.GffStream@ to write to.
-...type:Class.GffStream
-..param.record:The @Class.GffRecord@ to write.
-...type:Class.GffRecord
-..returns:$0$ on success, non-$0$ on failure.
-..include:seqan/gff_io.h
-*/
-
-inline int writeRecord(GffStream & stream,
-                       GffRecord const & record)
-{
-    int res = 0;
-    if (stream.fileFormat == GffStream::GFF)
-        res = writeRecord(*stream._outStream, record, stream._context, Gff());
-    else
-        res = writeRecord(*stream._outStream, record, stream._context, Gtf());
-    if (res != 0)
-        stream._isGood = false;
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function flush()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffStream#flush
- * @brief Flush to a GffStream.
- * 
- * @signature int flush(gffStream);
- * 
- * @param[in,out] gffStream The GffStream to flush. Types: GffStream
- * 
- * @return int <tt>0</tt> on success, non-<tt>0</tt> on failure.
- */
-
-/**
-.Function.GffStream#flush
-..class:Class.GffStream
-..cat:GFF I/O
-..summary:Flush to a @Class.GffStream@
-..signature:int flush(gffStream)
-..param.gffStream:The @Class.GffStream@ to flush.
-...type:Class.GffStream
-..returns:$0$ on success, non-$0$ on failure.
-..include:seqan/gff_io.h
-*/
-
-inline int flush(GffStream & stream)
-{
-    if (stream._stream.get())
-        stream._stream->flush();
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function close()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffStream#close
- * @brief Closes a GffStream
- * 
- * @signature int close(gffStream);
- * 
- * @param[in,out] gffStream The GffStream to close. Types: GffStream
- * 
- * @return int <tt>0</tt> on success, non-<tt>0</tt> on failure.
- */
-
-/**
-.Function.GffStream#close
-..class:Class.GffStream
-..cat:GFF I/O
-..summary:Closes a @Class.GffStream@
-..signature:int close(gffStream)
-..param.gffStream:The @Class.GffStream@ to close.
-...type:Class.GffStream
-..returns:$0$ on success, non-$0$ on failure.
-..include:seqan/gff_io.h
-*/
-
-inline int close(GffStream & stream)
-{
-    if (stream._stream.get())
-        stream._stream->close();
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isGood()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffStream#isGood
- * @brief Query a GffStream for errors.
- * 
- * @signature bool isGood(gffStream);
- * 
- * @param[in] gffStream The GffStream to query.
- * 
- * @return bool <tt>true</tt> if stream is good, <tt>false</tt> otherwise.
- */
-
-/**
-.Function.GffStream#isGood
-..class:Class.GffStream
-..cat:GFF I/O
-..summary:Query a @Class.GffStream@ for errors.
-..signature:bool isGood(gffStream)
-..param.gffStream:The @Class.GffStream@ to query.
-...type:Class.GffStream
-..returns:$true$ if stream is good, $false$ otherwise.
-..include:seqan/gff_io.h
-*/
-
-inline bool isGood(GffStream const & stream)
-{
-    return stream._isGood;
-}
-
-// ----------------------------------------------------------------------------
-// Function atEnd()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GffStream#atEnd
- * @brief Query a GffStream for being at the end of the file.
- * 
- * @signature bool atEnd(gffStream);
- * 
- * @param[in] gffStream The GffStream to query. Types: GffStream
- * 
- * @return bool <tt>true</tt> if stream is at the end, <tt>false</tt> otherwise.
- */
-
-/**
-.Function.GffStream#atEnd
-..class:Class.GffStream
-..cat:GFF I/O
-..summary:Query a @Class.GffStream@ for being at the end of the file.
-..signature:bool atEnd(gffStream)
-..param.gffStream:The @Class.GffStream@ to query.
-...type:Class.GffStream
-..returns:$true$ if stream is at the end, $false$ otherwise.
-..include:seqan/gff_io.h
-*/
-
-inline bool atEnd(GffStream const & stream)
-{
-    return atEnd(*stream._reader);
-}
-
-inline bool atEnd(GffStream & stream)
-{
-    return atEnd(*stream._reader);
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_EXTRAS_INCLUDE_SEQAN_GFF_IO_GFF_STREAM_H_
diff --git a/seqan/graph_algorithms.h b/seqan/graph_algorithms.h
index 8e4b470..3d6820e 100644
--- a/seqan/graph_algorithms.h
+++ b/seqan/graph_algorithms.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,13 +40,31 @@
 // Seqan
 #include <seqan/graph_types.h>
 #include <seqan/random.h>
-#include <seqan/misc/misc_union_find.h>
+#include <seqan/misc/union_find.h>
 
 // Graph algorithms
 #include <seqan/graph_algorithms/graph_algorithm_heap_tree.h>
-#include <seqan/graph_algorithms/graph_algorithm.h>
 #include <seqan/graph_algorithms/graph_algorithm_hmm.h>
 #include <seqan/graph_algorithms/graph_algorithm_lis_his.h>
 
+// Individual graph algorithms.
+#include <seqan/graph_algorithms/all_pairs_shortest_path.h>
+#include <seqan/graph_algorithms/bellman_ford.h>
+#include <seqan/graph_algorithms/bipartite_matching.h>
+#include <seqan/graph_algorithms/breadth_first_search.h>
+#include <seqan/graph_algorithms/connected_components.h>
+#include <seqan/graph_algorithms/depth_first_search.h>
+#include <seqan/graph_algorithms/dijkstra.h>
+#include <seqan/graph_algorithms/floyd_warshall.h>
+#include <seqan/graph_algorithms/ford_fulkerson.h>
+#include <seqan/graph_algorithms/kruskal.h>
+#include <seqan/graph_algorithms/path_growing.h>
+#include <seqan/graph_algorithms/prim.h>
+#include <seqan/graph_algorithms/single_source_shortest_path.h>
+#include <seqan/graph_algorithms/strongly_connected_compnents.h>
+#include <seqan/graph_algorithms/topological_sort.h>
+#include <seqan/graph_algorithms/transitive_closure.h>
+#include <seqan/graph_algorithms/weakly_connected_components.h>
+#include <seqan/graph_algorithms/weighted_bipartite_matching.h>
 
-#endif //#ifndef SEQAN_HEADER_...
+#endif  // #ifndef SEQAN_HEADER_GRAPH_ALGORITHMS_H
diff --git a/seqan/graph_algorithms/INFO b/seqan/graph_algorithms/INFO
deleted file mode 100644
index 28ac8e5..0000000
--- a/seqan/graph_algorithms/INFO
+++ /dev/null
@@ -1,11 +0,0 @@
-Name: seqan-graph_algorithms
-Author: Tobias Rausch <rausch@embl.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Common graph algorithms.
- This module contains implementation for classic and common graph algorithms
- such as maximum flow, spanning tree, (strongly) connected components algorithms
- and others.
diff --git a/seqan/graph_algorithms/all_pairs_shortest_path.h b/seqan/graph_algorithms/all_pairs_shortest_path.h
new file mode 100644
index 0000000..e0df2f2
--- /dev/null
+++ b/seqan/graph_algorithms/all_pairs_shortest_path.h
@@ -0,0 +1,202 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of All-Pairs-Shortest-Path algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_ALL_PAIRS_SHORTEST_PATH_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_ALL_PAIRS_SHORTEST_PATH_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function allPairsShortestPath()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TPredecessor, typename TVertexDescriptor>
+inline void
+_printAllPairsShortestPath(Graph<TSpec> const& g,
+                           TPredecessor& predecessor,
+                           TVertexDescriptor const i,
+                           TVertexDescriptor const j)
+{
+    typedef typename Size<TPredecessor>::Type TSize;
+    TSize len = getIdUpperBound(g.data_id_managerV);
+    if (i==j) {
+        std::cout << i;
+    } else if (getValue(predecessor, i*len+j) == getNil<typename VertexDescriptor<Graph<TSpec> >::Type>()) {
+        std::cout << "No path from " << i << " to " << j << " exists.";
+    } else {
+        _printAllPairsShortestPath(g,predecessor, i, (TVertexDescriptor) getValue(predecessor, i*len+j));
+        std::cout << "," << j;
+    }
+}
+
+template <typename TSpec, typename TWeightMap, typename TMatrix, typename TPredecessor>
+void
+_initializeAllPairs(Graph<TSpec> const& g,
+                        TWeightMap const& weight,
+                        TMatrix& matrix,
+                        TPredecessor& predecessor)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Size<TMatrix>::Type TSize;
+    typedef typename Value<TWeightMap>::Type TWeightVal;
+    typedef typename Value<TPredecessor>::Type TPredVal;
+
+    // Create adjacency-like matrix
+    TSize len = getIdUpperBound(g.data_id_managerV);
+    resize(matrix, len * len);
+    resize(predecessor, len * len);
+    TWeightVal infWeight = _getInfinityDistance(weight);
+    TPredVal nilPred = getNil<TVertexDescriptor>();
+    for (TSize row=0;row < len;++row) {
+        for (TSize col=0;col < len;++col) {
+            if (row != col) assignValue(matrix, row*len + col, infWeight);
+            else assignValue(matrix, row*len + col, 0);
+            assignValue(predecessor, row*len + col, nilPred);
+        }
+    }
+
+    // Include edge weights and initial predecessors
+    TVertexIterator it(g);
+    for(;!atEnd(it);goNext(it)) {
+        TVertexDescriptor u = getValue(it);
+        TOutEdgeIterator itout(g, u);
+        for(;!atEnd(itout);++itout) {
+            TVertexDescriptor v = targetVertex(g,getValue(itout));
+            assignValue(matrix, u*len + v, getProperty(weight, getValue(itout)));
+            assignValue(predecessor, u*len + v, u);
+        }
+    }
+}
+
+template <typename TMatrix, typename TPredecessor, typename TInfDist>
+void
+_extendShortestPaths(TMatrix& local,
+                       TMatrix& w,
+                       TPredecessor& predecessor,
+                       TInfDist const infDist)
+{
+    typedef typename Value<TMatrix>::Type TMatrixVal;
+    typedef typename Value<TPredecessor>::Type TPredVal;
+    typedef typename Size<TMatrix>::Type TSize;
+    TMatrix oldLocal = local;
+    TPredecessor oldPredecessor = predecessor;
+    TSize len = (TSize) std::sqrt((double) length(oldLocal));
+    for(TSize i = 0; i<len;++i) {
+        for(TSize j = 0; j<len;++j) {
+            if (i==j) continue;
+            assignValue(local, i*len+j,infDist);
+            TPredVal ind = 0;
+            for(TSize k = 0; k<len;++k) {
+                TMatrixVal min1 = getValue(local, i*len+j);
+                TMatrixVal min2 = getValue(oldLocal, i*len+k) + getValue(w, k*len + j);
+                if (min2 < min1) {
+                    assignValue(local, i*len+j,min2);
+                    ind = k;
+                }
+            }
+            if (getValue(oldLocal, i*len+j) > getValue(local, i*len+j)) {
+                assignValue(predecessor, i*len+j,ind);
+            }
+        }
+    }
+}
+
+/*!
+ * @fn allPairsShortestPath
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Finds shortest paths between all pairs of vertices in a graph.
+ * @signature void allPairsShortestPath(graph, weight, distance, predecessor);
+ *
+ * @param[out] distance    A @link Matrix @endlink with distances. Entry <tt>(i,j)</tt> in this matrix indicates the
+ *                         distance from vertex <tt>i</tt> to vertex <tt>j</tt>.
+ * @param[out] predecessor A @link Matrix @endlink with predecessors. Entry <tt>(i,j)</tt> in this matrix indicates the
+ *                         predecessor of <tt>j</tt> on a shortest path from vertex <tt>i</tt> to vertex <tt>j</tt>.
+ *                         You can use <tt>_printAllPairsShortestPath(graph, predecessor, i, j)</tt> to print the
+ *                         shortest path from <tt>i</tt> to <tt>j</tt>.
+ * @param[in]  graph       A @link DirectedGraph Directed Graph @endlink.
+ * @param[in]  weight      A property map with edge weights. Edge weights may be negative.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/all_pairs_shortest_path.cpp
+ *
+ * @include demos/dox/graph_algorithms/all_pairs_shortest_path.cpp.stdout
+ *
+ * @see floydWarshallAlgorithm
+ */
+template <typename TSpec, typename TWeightMap, typename TMatrix, typename TPredecessor>
+void allPairsShortestPath(TMatrix & distMatrix,
+                          TPredecessor & predecessor,
+                          Graph<TSpec> const & g,
+                          TWeightMap const & weight)
+{
+    typedef typename Size<TMatrix>::Type TSize;
+    typedef typename Value<TWeightMap>::Type TWeightVal;
+    TWeightVal infWeight = _getInfinityDistance(weight);
+
+    // Initialize first distance matrix
+    _initializeAllPairs(g,weight,distMatrix,predecessor);
+
+    TSize len = (TSize) sqrt((double) length(distMatrix));
+    TMatrix local = distMatrix;
+    for(TSize m=2;m<len;++m) {
+        _extendShortestPaths(local,distMatrix,predecessor, infWeight);
+    }
+    distMatrix = local;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_ALL_PAIRS_SHORTEST_PATH_H_
diff --git a/seqan/graph_algorithms/bellman_ford.h b/seqan/graph_algorithms/bellman_ford.h
new file mode 100644
index 0000000..dee3e62
--- /dev/null
+++ b/seqan/graph_algorithms/bellman_ford.h
@@ -0,0 +1,136 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Bellman-Ford algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_BELLMAN_FORD_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_BELLMAN_FORD_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function bellmanFordAlgorithm()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn bellmanFordAlgorithm
+ *
+ * @headerfile <seqan/graph_algorithms.h>
+ *
+ * @brief Computes shortest paths from a single source in a directed graph.
+ *
+ * @signature bool bellmanFordAlgorithm(g, source, weight, predecessor, distance)
+ *
+ * @param[out] predecessor A property map.  A property map that represents predecessor relationships among vertices.
+ *                         It determines a shortest-paths tree.
+ * @param[out] distance    A property map.Indicates for each vertex the distance from the source.
+ * @param[in]  g           A directed graph. Types: Directed Graph
+ * @param[in]  source      A source vertex. Types: VertexDescriptor
+ * @param[in]  weight      A weight map.A property map with edge weights.  Edge weights may be negative.
+ *
+ * @return bool true if the graph has no negative weight cycles, false otherwise.
+ *
+ * Edge weights may be negative in the Bellman-Ford algorithm.  The out parameters are only valid if the algorithm
+ * returns true.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/bellman_ford_algorithm.cpp
+ *
+ * @include demos/dox/graph_algorithms/bellman_ford_algorithm.cpp.stdout
+ *
+ * @see dagShortestPath
+ * @see dijkstra
+ */
+template <typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap>
+bool bellmanFordAlgorithm(TPredecessorMap & predecessor,
+                          TDistanceMap & distance,
+                          Graph<TSpec> const & g,
+                          TVertexDescriptor const source,
+                          TWeightMap const & weight)
+{
+    typedef typename Size<Graph<TSpec> >::Type TSize;
+
+    // Initialization
+    typedef typename Iterator<Graph<TSpec>, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
+    resizeVertexMap(predecessor, g);
+    resizeVertexMap(distance, g);
+    _initializeSingleSource(predecessor, distance, g, source, weight);
+
+    // Run Bellman-Ford
+    for(TSize i=0; i<numVertices(g) - 1; ++i) {
+        TVertexIterator it(g);
+        for(;!atEnd(it);goNext(it)) {
+            TVertexDescriptor u = getValue(it);
+            TOutEdgeIterator itout(g, u);
+            for(;!atEnd(itout);++itout) {
+                _relax(g,weight,predecessor, distance, u, getValue(itout));
+            }
+        }
+    }
+
+    TVertexIterator it(g);
+    for(;!atEnd(it);goNext(it)) {
+        TVertexDescriptor u = getValue(it);
+        TOutEdgeIterator itout(g, u);
+        for(;!atEnd(itout);++itout) {
+            TVertexDescriptor v = targetVertex(g, getValue(itout));
+            if (getProperty(distance, v) > getProperty(distance,u) + getProperty(weight,getValue(itout))) {
+                return false;
+            }
+        }
+    }
+    return true;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_BELLMAN_FORD_H_
diff --git a/seqan/graph_algorithms/bipartite_matching.h b/seqan/graph_algorithms/bipartite_matching.h
new file mode 100644
index 0000000..99af28b
--- /dev/null
+++ b/seqan/graph_algorithms/bipartite_matching.h
@@ -0,0 +1,116 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of the Bipartite Matching algorithm.
+//
+// WARNING: Functionality not carefully tested!
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_BIPARTITE_MATCHING_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_BIPARTITE_MATCHING_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function bipartiteMatching()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TVertexMap, typename TEdges>
+typename Size<Graph<TSpec> >::Type
+bipartiteMatching(String<TEdges> & edges,
+                  Graph<TSpec> const & g,
+                  TVertexMap const & vertMap)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIter;
+
+    clear(edges);
+    TVertexDescriptor source = addVertex(g);
+    TVertexDescriptor target = addVertex(g);
+    TVertexIter itV(g);
+    for(;!atEnd(itV); goNext(itV)) {
+        if ((value(itV) != source) && (value(itV) != target)) {
+            if (getProperty(vertMap, value(itV)) == false) {
+                addEdge(g, source, value(itV));
+            } else {
+                addEdge(g, value(itV), target);
+            }
+        }
+    }
+
+    // Use Ford-Fulkerson to determine a matching
+    String<TSize> capMap;
+    resizeEdgeMap(capMap, g);
+    typedef typename Iterator<String<TSize> >::Type TCapIter;
+    TCapIter capIt = begin(capMap);
+    TCapIter capItEnd = end(capMap);
+    for(;capIt != capItEnd; ++capIt) value(capIt) = 1;
+    String<TSize> flow;
+    TSize valF = fordFulkersonAlgorithm(g, source, target, capMap, flow);
+
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    TEdgeIterator itEdge(g);
+    for(;!atEnd(itEdge);goNext(itEdge)) {
+        if (getProperty(flow, getValue(itEdge)) == 1) {
+            TVertexDescriptor sV = sourceVertex(itEdge);
+            TVertexDescriptor tV = targetVertex(itEdge);
+            if ((sV != source) && (tV != target)) appendValue(edges, TEdges(sV, tV));
+        }
+    }
+    removeVertex(g, source);
+    removeVertex(g, target);
+
+    return valF;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_BIPARTITE_MATCHING_H_
diff --git a/seqan/graph_algorithms/breadth_first_search.h b/seqan/graph_algorithms/breadth_first_search.h
new file mode 100644
index 0000000..8c8730f
--- /dev/null
+++ b/seqan/graph_algorithms/breadth_first_search.h
@@ -0,0 +1,138 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Breadth-First-Search.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_BREADTH_FIRST_SEARCH_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_BREADTH_FIRST_SEARCH_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function breadthFirstSearch()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn breadthFirstSearch
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Implements a breadth-first search on a graph.
+ *
+ * @signature void breadthFirstSearch(predecessor, distance, g, source);
+ *
+ * @param[out] predecessor A property map.  The predecessor map stores implicitly the breadth-first tree.
+ * @param[out] distance    A property map.  The distance map indicates at what depth a vertex was discovered.
+ * @param[in]  g           Undirected Graph, Directed Graph
+ * @param[in]  source      A vertex descriptor.  The breadth-first search is started from this vertex.
+ *                         Types: VertexDescriptor
+ *
+ * Breadth-first search computes the distance from source to all reachable vertices.  It also produces a breath-first
+ * tree where each node has a predecessor/parent.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/breadth_first_search.cpp
+ *
+ * @include demos/dox/graph_algorithms/breadth_first_search.cpp.stdout
+ *
+ * @see depthFirstSearch
+ */
+
+template <typename TSpec, typename TVertexDescriptor, typename TPredecessorMap, typename TDistanceMap>
+void breadthFirstSearch(TPredecessorMap & predecessor,
+                        TDistanceMap & distance,
+                        Graph<TSpec> const & g,
+                        TVertexDescriptor const source)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Value<TPredecessorMap>::Type TPredVal;
+    typedef typename Value<TDistanceMap>::Type TDistVal;
+
+    // Initialization
+    resizeVertexMap(predecessor, g);
+    resizeVertexMap(distance, g);
+    TPredVal nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
+    TDistVal infDist = _getInfinityDistance(distance);
+
+    String<bool> tokenMap;
+    resizeVertexMap(tokenMap, g);
+    TVertexIterator it(g);
+    for(;!atEnd(it);goNext(it)) {
+        assignProperty(tokenMap, getValue(it), false);
+        assignProperty(distance, getValue(it), infDist);
+        assignProperty(predecessor, getValue(it), nilPred);
+    }
+    assignProperty(tokenMap, source, true);
+    assignProperty(distance, source, 0);
+    assignProperty(predecessor, source, nilPred);
+    std::deque<TVertexDescriptor> queue;
+    queue.push_back(source);
+
+    // Bfs
+    while (!queue.empty()) {
+        TVertexDescriptor u = queue.front();
+        queue.pop_front();
+        typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
+        TOutEdgeIterator itout(g,u);
+        for(;!atEnd(itout);goNext(itout)) {
+            TVertexDescriptor v = targetVertex(itout);
+            if (getProperty(tokenMap, v) == false) {
+                assignProperty(tokenMap, v, true);
+                assignProperty(distance, v, getProperty(distance,u) + 1);
+                assignProperty(predecessor, v, u);
+                queue.push_back(v);
+            }
+        }
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_BREADTH_FIRST_SEARCH_H_
diff --git a/seqan/graph_algorithms/connected_components.h b/seqan/graph_algorithms/connected_components.h
new file mode 100644
index 0000000..13839c4
--- /dev/null
+++ b/seqan/graph_algorithms/connected_components.h
@@ -0,0 +1,150 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Implementation of the Connected-Components algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_CONNECTED_COMPONENTS_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_CONNECTED_COMPONENTS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function connectedComponents()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn connectedComponents
+ *
+ * @headerfile <seqan/graph_algorithms.h>
+ *
+ * @brief Decomposes an undirected graph into its connected components.
+ *
+ * @signature TSize connectedComponents(components, g);
+ *
+ * @param[out] components
+ *               A property map.  Each vertex is mapped to a component id.  If two vertices share the same id
+ *               they are in the same component.
+ * @param[in]  g An undirected graph. Types: Undirected Graph
+ *
+ * @return TSize The number of components.
+ *
+ * @section Examples
+ *
+ * A simple example on how to use this function.
+ *
+ * @code{.cpp}
+ * // Build Input.
+ * Graph<Undirected<> > graph;
+ * for (unsigned i = 0; i < 5; ++i)
+ *     addVertex(graph);
+ * addEdge(graph, 0, 1);
+ * addEdge(graph, 0, 3);
+ * addEdge(graph, 2, 4);
+ * String<unsigned> components;
+ * unsigned numComponents = 0;
+ *
+ * // Call Algorithm.
+ * numComponents = connectedComponents(g, components);
+ *
+ * // Print Result.
+ * std::cout << "Number of components: " << numComponents << std::endl;
+ * std::cout << std::endl << "Vertex -> Component" << std::endl;
+ * for (unsigned i = 0; i < length(components); ++i)
+ *     std::cout << i << " -> " << components[i] << std::endl;
+ * @endcode
+ * The output now is:
+ *
+ * @code{.console}
+ * Number of components: 2
+ *
+ * Vertex -> Component
+ * 0 -> 0
+ * 1 -> 0
+ * 2 -> 1
+ * 3 -> 0
+ * 4 -> 1
+ * @endcode
+ */
+template <typename TSpec, typename TComponents>
+typename Size<Graph<TSpec> >::Type
+connectedComponents(TComponents & components,
+                    Graph<TSpec> const & g)
+{
+    typedef typename VertexDescriptor<Graph<TSpec> >::Type TVertexDescriptor;
+
+    // Initialize Union-Find data structure.
+    UnionFind<TVertexDescriptor> uf;
+    resizeVertexMap(uf, g);
+
+    // Use Union-Find data structure to compute connected components.
+    for (typename Iterator<Graph<TSpec>, EdgeIterator>::Type it(g); !atEnd(it); goNext(it))
+        joinSets(uf, findSet(uf, sourceVertex(it)), findSet(uf, targetVertex(it)));
+
+    // Build final component map.
+    resizeVertexMap(components, g);
+    unsigned c = 0;
+    std::map<TVertexDescriptor, unsigned> reprToComponent;
+    for (typename Iterator<Graph<TSpec>, VertexIterator>::Type it(g); !atEnd(it); goNext(it))
+    {
+        TVertexDescriptor v = findSet(uf, *it);
+
+        // Build mapping from representant to component id on the fly.
+        if (!reprToComponent.count(v))
+            reprToComponent[v] = c++;
+
+        assignProperty(components, *it, reprToComponent[v]);
+    }
+
+    return c;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_CONNECTED_COMPONENTS_H_
diff --git a/seqan/graph_algorithms/depth_first_search.h b/seqan/graph_algorithms/depth_first_search.h
new file mode 100644
index 0000000..7966b42
--- /dev/null
+++ b/seqan/graph_algorithms/depth_first_search.h
@@ -0,0 +1,152 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Depth-First-Search algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_DEPTH_FIRST_SEARCH_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_DEPTH_FIRST_SEARCH_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function depthFirstSearch()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TVertexDescriptor, typename TTokenMap, typename TPredecessorMap, typename TDiscoveryTimeMap, typename TFinishingTimeMap, typename TVal>
+void
+_dfsVisit(Graph<TSpec> const& g,
+           TVertexDescriptor const u,
+           TTokenMap& tokenMap,
+           TPredecessorMap& predecessor,
+           TDiscoveryTimeMap& disc,
+           TFinishingTimeMap& finish,
+           TVal& time)
+{
+    typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type TAdjacencyIterator;
+
+    assignProperty(tokenMap, u, true);
+    ++time;
+    assignProperty(disc, u, time);
+    TAdjacencyIterator itad(g,u);
+    for(;!atEnd(itad);goNext(itad)) {
+        TVertexDescriptor v = getValue(itad);
+        if (getProperty(tokenMap, v) == false) {
+            assignProperty(predecessor, v, u);
+            _dfsVisit(g, v, tokenMap, predecessor, disc, finish, time);
+        }
+    }
+    ++time;
+    assignProperty(finish, u, time);
+}
+
+/*!
+ * @fn depthFirstSearch
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Implements a depth-first search on a graph.
+ *
+ * @signature void depthFirstSearch(predecessor, discovery, finish, g);
+ *
+ * @param[out] predecessor A property map.Predecessor subgraph produced by the depth-first search.
+ * @param[out] discovery   A property map.The discovery time of a vertex v.
+ * @param[out] finish      A property map.The time when v's adjacency list has been fully explored.
+ * @param[in]  g           A graph. Types: Undirected Graph, Directed Graph
+ *
+ * In contrast to a breadth-first search the depth-first search is repeated from multiple sources if the graph is not
+ * connected.  Hence, depth-first search produces a depth-first forest.  To ensure each vertex ends up in exactly one
+ * tree we need not just a distance but a discovery and finishing time.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/depth_first_search.cpp
+ *
+ * @include demos/dox/graph_algorithms/depth_first_search.cpp.stdout
+ *
+ * @see breadthFirstSearch
+ */
+template <typename TSpec, typename TPredecessorMap, typename TDiscoveryTimeMap, typename TFinishingTimeMap>
+void depthFirstSearch(TPredecessorMap & predecessor,
+                      TDiscoveryTimeMap & disc,
+                      TFinishingTimeMap & finish,
+                      Graph<TSpec> const & g)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Value<TPredecessorMap>::Type TPredVal;
+
+    // Initialization
+    resizeVertexMap(predecessor, g);
+    resizeVertexMap(disc, g);
+    resizeVertexMap(finish, g);
+    TPredVal nilPred = getNil<TVertexDescriptor>();
+
+    String<bool> tokenMap;
+    resizeVertexMap(tokenMap, g);
+    TVertexIterator it(g);
+    for(;!atEnd(it);goNext(it)) {
+        assignProperty(tokenMap, getValue(it), false);
+        assignProperty(predecessor, getValue(it), nilPred);
+    }
+
+    TSize time = 0;
+
+    goBegin(it);
+    for(;!atEnd(it);goNext(it)) {
+        TVertexDescriptor u = getValue(it);
+        if (getProperty(tokenMap, u) == false) {
+            _dfsVisit(g, u, tokenMap, predecessor, disc, finish, time);
+        }
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_DEPTH_FIRST_SEARCH_H_
diff --git a/seqan/graph_algorithms/dijkstra.h b/seqan/graph_algorithms/dijkstra.h
new file mode 100644
index 0000000..683a04d
--- /dev/null
+++ b/seqan/graph_algorithms/dijkstra.h
@@ -0,0 +1,144 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Dijkstra's algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_DIJKSTRA_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_DIJKSTRA_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function dijkstra()
+// ----------------------------------------------------------------------------
+
+  /*!
+ * @fn dijkstra
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Computes shortest paths from a single source in a graph.
+ * @signature void dijkstra(predecessor, distance, g, source, weight);
+ *
+ * @param[out] predecessor A property map.  A property map that represents predecessor relationships among vertices.
+ *                         It determines a shortest-paths tree.
+ * @param[out] distance    A property map.Indicates for each vertex the distance from the source.
+ * @param[in]  g           A graph. Types: Directed Graph
+ * @param[in]  source      A source vertex.  Types: VertexDescriptor
+ * @param[in]  weight      A weight map.  A property map with edge weights. Edge weights have to be nonnegative.
+ *
+ * @section Remarks
+ *
+ * Edge weights have to be nonnegative.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/dijkstra.cpp
+ *
+ * @include demos/dox/graph_algorithms/dijkstra.cpp.stdout
+ *
+ * @see dagShortestPath
+ * @see bellmanFordAlgorithm
+ */
+template <typename TSpec, typename TVertexDescriptor, typename TWeightMap,
+          typename TPredecessorMap, typename TDistanceMap>
+void dijkstra(TPredecessorMap & predecessor,
+              TDistanceMap & distance,
+              Graph<TSpec> const & g,
+              TVertexDescriptor const source,
+              TWeightMap const & weight)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Value<TDistanceMap>::Type TDistVal;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    // Initialization
+    resizeVertexMap(predecessor, g);
+    resizeVertexMap(distance, g);
+
+    // S is initially empty
+    String<bool> setS;
+    resize(setS, getIdUpperBound(_getVertexIdManager(g)), false);
+
+    // Set-up the priority queue
+    typedef Pair<TVertexDescriptor, TDistVal> TKeyValue;
+    typedef HeapTree<TKeyValue, std::less<TDistVal>, KeyedHeap<> > TKeyedHeap;
+    TKeyedHeap priorityQueue;
+    TDistVal infDist = _getInfinityDistance(weight);
+    TVertexDescriptor nilVertex = getNil<typename VertexDescriptor<TGraph>::Type>();
+    TVertexIterator it(g);
+    for(;!atEnd(it);goNext(it)) {
+        assignProperty(predecessor, value(it), nilVertex);
+        assignProperty(distance, value(it), infDist);
+        heapInsert(priorityQueue, TKeyValue(value(it), infDist));
+    }
+    assignProperty(distance, source, 0);
+    heapChangeValue(priorityQueue, source, 0);
+
+    // Run Dijkstra
+    while (!empty(priorityQueue)) {
+        // Extract min
+        TVertexDescriptor u = heapExtractRoot(priorityQueue).i1;
+        assignProperty(setS, u, true);
+        TOutEdgeIterator itout(g, u);
+        for(;!atEnd(itout);++itout) {
+            TVertexDescriptor v = targetVertex(itout);
+            if (property(setS, v) == true) continue;
+            if (getProperty(distance, v) > getProperty(distance,u) + getProperty(weight,value(itout))) {
+                assignProperty(distance, v, getProperty(distance,u) + getProperty(weight,value(itout)));
+                assignProperty(predecessor, v, u);
+                heapChangeValue(priorityQueue, v, getProperty(distance,u) + getProperty(weight,value(itout)));
+            }
+        }
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_DIJKSTRA_H_
diff --git a/seqan/graph_algorithms/floyd_warshall.h b/seqan/graph_algorithms/floyd_warshall.h
new file mode 100644
index 0000000..8d399f9
--- /dev/null
+++ b/seqan/graph_algorithms/floyd_warshall.h
@@ -0,0 +1,122 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of the Floyd-Warshall algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_FLOYD_WARSHALL_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_FLOYD_WARSHALL_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function floydWarshallAlgorithm()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn floydWarshallAlgorithm
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Finds shortest paths between all pairs of vertices in a graph.
+ *
+ * @signature void floydWarshallAlgorithm(g, weight, distance, predecessor);
+ *
+ * @param[out] predecessor A matrix with predecessors.  Entry (i,j) in this matrix indicates the predecessor of j on
+ *                         a shortest path from vertex i to vertex j.  You can use <tt>_printAllPairsShortestPath(g,
+ *                         predecessor, i, j)</tt> to print the shortest path from i to j.  Types: Matrix
+ * @param[out] distance    A matrix with distances.Entry (i,j) in this matrix indicates the distance from vertex i
+ *                         to vertex j.  Types: Matrix
+ * @param[in]  weight      A weight map.  A property map with edge weights.  Edge weights may be negative.
+ * @param[in]  g           A directed graph.  Types: Directed Graph
+ *
+ * The graph must be free of negative-weight cycles.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp
+ *
+ * @include demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp.stdout
+ *
+ * @see allPairsShortestPath
+ */
+template <typename TSpec, typename TWeightMap, typename TMatrix, typename TPredecessor>
+void floydWarshallAlgorithm(TMatrix & distMatrix,
+                            TPredecessor & predecessor,
+                            Graph<TSpec> const & g,
+                            TWeightMap const & weight)
+{
+    typedef typename Size<TMatrix>::Type TSize;
+    typedef typename Value<TMatrix>::Type TMatrixVal;
+
+    // Initialize first distance matrix
+    _initializeAllPairs(g,weight,distMatrix,predecessor);
+
+    // Floyd-Warshall
+    TSize len = (TSize) std::sqrt((double) length(distMatrix));
+    TMatrix local = distMatrix;
+    for(TSize k=0;k<len;++k) {
+        for(TSize i=0;i<len;++i) {
+            for(TSize j=0;j<len;++j) {
+                TMatrixVal min1 = getValue(distMatrix, i*len+j);
+                TMatrixVal min2 = getValue(distMatrix, i*len+k) + getValue(distMatrix, k*len + j);
+                if (min2 < min1) {
+                    assignValue(local, i*len+j,min2);
+                    assignValue(predecessor, i*len+j,getValue(predecessor, k*len+j));
+                } else {
+                    assignValue(local, i*len+j,min1);
+                    assignValue(predecessor, i*len+j, getValue(predecessor, i*len+j));
+                }
+            }
+        }
+        distMatrix=local;
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_FLOYD_WARSHALL_H_
diff --git a/seqan/graph_algorithms/ford_fulkerson.h b/seqan/graph_algorithms/ford_fulkerson.h
new file mode 100644
index 0000000..08d8e90
--- /dev/null
+++ b/seqan/graph_algorithms/ford_fulkerson.h
@@ -0,0 +1,220 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of the Ford-Fulkerson algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_FORD_FULKERSON_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_FORD_FULKERSON_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function fordFulkersonAlgorithm()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TCapMap, typename TFlowMap, typename TResidualGraph>
+void
+_buildResidualGraph(Graph<TSpec> const& g,
+                      TCapMap const& capacity,
+                      TFlowMap const& flow,
+                      TResidualGraph& rG)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Value<TFlowMap>::Type TFlow;
+    typedef typename Value<TCapMap>::Type TCap;
+
+    clear(rG);
+    TVertexIterator itV(g);
+    for(;!atEnd(itV);goNext(itV)) {
+        _createVertices(rG, getValue(itV));
+    }
+
+    TEdgeIterator itE(g);
+    for(;!atEnd(itE);goNext(itE)) {
+        typedef typename EdgeDescriptor<TResidualGraph>::Type TEdgeDescriptor;
+        TFlow f = getProperty(flow, getValue(itE));
+        TCap cap = getProperty(capacity, getValue(itE));
+        if (f > 0) {
+            TEdgeDescriptor e_rG = findEdge(rG, targetVertex(itE), sourceVertex(itE));
+            if (e_rG == 0) addEdge(rG, targetVertex(itE), sourceVertex(itE), f);
+            else cargo(e_rG) += f;
+        }
+        if (f < cap) {
+            TEdgeDescriptor e_rG = findEdge(rG, sourceVertex(itE), targetVertex(itE));
+            if (e_rG == 0) addEdge(rG, sourceVertex(itE), targetVertex(itE), cap - f);
+            else cargo(e_rG) += cap - f;
+        }
+    }
+}
+
+template <typename TSpec, typename TPredecessorMap, typename TVertexDescriptor>
+inline typename Size<Graph<TSpec> >::Type
+_getMinimumAug(Graph<TSpec> const & rG,
+                 TPredecessorMap & predecessor,
+                 TVertexDescriptor const source,
+                 TVertexDescriptor sink)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef TSize TFlow;
+    typedef typename Iterator<String<TVertexDescriptor>, Rooted>::Type TIterator;
+
+    // Build secondary predecessor map just containing the path
+    TVertexDescriptor nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
+    String<TVertexDescriptor> predMap;
+    resizeVertexMap(predMap, rG);
+    TIterator it = begin(predMap);
+    for(;!atEnd(it);goNext(it)) {
+        *it = nilPred;
+    }
+
+    // Find minimum flow
+    TVertexDescriptor pred = getProperty(predecessor, sink);
+    TFlow f = getCargo(findEdge(rG, pred,sink));
+    assignProperty(predMap, sink, pred);
+    while(pred != source) {
+        sink = pred;
+        pred = getProperty(predecessor, sink);
+        TFlow f2 = getCargo(findEdge(rG, pred,sink));
+        assignProperty(predMap, sink, pred);
+        if (f2 < f) f = f2;
+    }
+
+    // Just return the augmenting path
+    predecessor = predMap;
+    return f;
+}
+
+/*!
+ * @fn fordFulkersonAlgorithm
+ *
+ * @headerfile <seqan/graph_algorithms.h>
+ *
+ * @brief Computes a maximum flow in a directed graph.
+ *
+ * @signature TValue fordFulkeronAlgorithm(flow, g, source, sink, capacity);
+ *
+ * @param[out] flow     A property map with the flow of each edge.
+ * @param[in]  g        A directed graph.  Types: Directed Graph
+ * @param[in]  source   A source vertex.  Types: VertexDescriptor
+ * @param[in]  sink     A sink vertex.  Types: VertexDescriptor
+ * @param[in]  capacity A property map of edge capacities.
+ *
+ * @return TValue The value of the flow.  TValue is the Value tpye of the type of flow.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp
+ *
+ * @include demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp.stdout
+ */
+template <typename TSpec, typename TVertexDescriptor, typename TCapMap, typename TFlowMap>
+typename Value<TFlowMap>::Type
+fordFulkersonAlgorithm(TFlowMap & flow,
+                       Graph<TSpec> const & g,
+                       TVertexDescriptor const source,
+                       TVertexDescriptor const sink,
+                       TCapMap const & capacity)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Value<TFlowMap>::Type TFlow;
+
+    // Initialization
+    TVertexDescriptor nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
+    resizeEdgeMap(flow, g);
+    TEdgeIterator itE(g);
+    for(;!atEnd(itE);goNext(itE)) {
+        assignProperty(flow, getValue(itE), 0);
+    }
+
+    // Build the residual graph
+    Graph<Directed<TFlow> > rG;
+    _buildResidualGraph(g,capacity, flow, rG);
+
+
+    // Determine whether the sink is reachable
+    String<TVertexDescriptor> predMap;
+    String<TVertexDescriptor> distMap;
+    breadthFirstSearch(predMap, distMap, rG, source);
+
+    while (getProperty(predMap, sink) != nilPred) {
+        TFlow inc = _getMinimumAug(rG, predMap, source, sink);
+        TEdgeIterator itEdge(g);
+        for(;!atEnd(itEdge);goNext(itEdge)) {
+            TVertexDescriptor u = sourceVertex(itEdge);
+            TVertexDescriptor v = targetVertex(itEdge);
+            TEdgeDescriptor e = getValue(itEdge);
+            if (getProperty(predMap, v) == u) assignProperty(flow, e, getProperty(flow, e) + inc);
+            if (getProperty(predMap, u) == v) assignProperty(flow, e, getProperty(flow, e) - inc);
+        }
+        // Build the residual graph
+        _buildResidualGraph(g, capacity, flow, rG);
+        // Determine whether the sink is reachable
+        clear(predMap);
+        clear(distMap);
+        breadthFirstSearch(predMap, distMap, rG, source);
+    }
+
+    TFlow valF = 0;
+    TOutEdgeIterator itOutEdge(g, source);
+    for(;!atEnd(itOutEdge);goNext(itOutEdge)) {
+        valF += getProperty(flow, getValue(itOutEdge));
+    }
+    return valF;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_FORD_FULKERSON_H_
diff --git a/seqan/graph_algorithms/graph_algorithm.h b/seqan/graph_algorithms/graph_algorithm.h
deleted file mode 100644
index a82c8ed..0000000
--- a/seqan/graph_algorithms/graph_algorithm.h
+++ /dev/null
@@ -1,2415 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_GRAPH_ALGORITHM_H
-#define SEQAN_HEADER_GRAPH_ALGORITHM_H
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Graph - Algorithms
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-// Elementary graph algorithms
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Breadth-first search
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn breadthFirstSearch
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Implements a breadth-first search on a graph.
- * 
- * @signature void breadthFirstSearch(g, source, predecessor, distance);
- * 
- * @param[in]  g           Undirected Graph, Directed Graph
- * @param[in]  source      A vertex descriptor.  The breadth-first search is started from this vertex.
- *                         Types: VertexDescriptor
- * @param[out] predecessor A property map.  The predecessor map stores implicitly the breadth-first tree.
- * @param[out] distance    A property map.  The distance map indicates at what depth a vertex was discovered.
- * 
- * @section Remarks
- * 
- * Breadth-first search computes the distance from source to all reachable vertices.  It also produces a breath-first
- * tree where each node has a predecessor/parent.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/breadth_first_search.cpp
- *
- * @include demos/graph_algorithms/breadth_first_search.cpp.stdout
- *
- * @see depthFirstSearch
- */
-
-/**
-.Function.breadthFirstSearch:
-..cat:Graph
-..summary:Implements a breadth-first search on a graph.
-..remarks:Breadth-first search computes the distance from source to all reachable
-vertices. It also produces a breath-first tree where each node has a predecessor / parent.
-..signature:breadthFirstSearch(g, source, predecessor, distance)
-..param.g:In-parameter:A graph.
-...type:Spec.Undirected Graph
-...type:Spec.Directed Graph
-..param.source:In-parameter:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-...remarks:The breadth-first search is started from this vertex.
-..param.predecessor:Out-parameter:A property map.
-...remarks:The predecessor map stores implicitly the breadth-first tree.
-..param.distance:Out-parameter:A property map.
-...remarks:The distance map indicates at what depth a vertex was discovered.
-..returns:void.
-..see:Function.depthFirstSearch
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TVertexDescriptor, typename TPredecessorMap, typename TDistanceMap>
-void
-breadthFirstSearch(Graph<TSpec> const& g,
-					 TVertexDescriptor const source,
-					 TPredecessorMap& predecessor, 
-					 TDistanceMap& distance)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Value<TPredecessorMap>::Type TPredVal;
-	typedef typename Value<TDistanceMap>::Type TDistVal;
-
-	// Initialization
-	resizeVertexMap(g,predecessor);
-	resizeVertexMap(g,distance);
-	TPredVal nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
-	TDistVal infDist = _getInfinityDistance(distance);
-	
-	String<bool> tokenMap;
-	resizeVertexMap(g, tokenMap);
-	TVertexIterator it(g);
-	for(;!atEnd(it);goNext(it)) {
-		assignProperty(tokenMap, getValue(it), false);
-		assignProperty(distance, getValue(it), infDist);
-		assignProperty(predecessor, getValue(it), nilPred);
-	}
-	assignProperty(tokenMap, source, true);
-	assignProperty(distance, source, 0);
-	assignProperty(predecessor, source, nilPred);
-	std::deque<TVertexDescriptor> queue;
-	queue.push_back(source);
-	
-	// Bfs
-	while (!queue.empty()) {
-		TVertexDescriptor u = queue.front();
-		queue.pop_front();
-		typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
-		TOutEdgeIterator itout(g,u);
-		for(;!atEnd(itout);goNext(itout)) {
-			TVertexDescriptor v = targetVertex(itout);
-			if (getProperty(tokenMap, v) == false) {
-				assignProperty(tokenMap, v, true);
-				assignProperty(distance, v, getProperty(distance,u) + 1);
-				assignProperty(predecessor, v, u);
-				queue.push_back(v);
-			}
-		}
-	}
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Depth-first search
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TVertexDescriptor, typename TTokenMap, typename TPredecessorMap, typename TDiscoveryTimeMap, typename TFinishingTimeMap, typename TVal>
-void
-_dfsVisit(Graph<TSpec> const& g,
-		   TVertexDescriptor const u,
-		   TTokenMap& tokenMap,
-		   TPredecessorMap& predecessor,
-		   TDiscoveryTimeMap& disc,
-		   TFinishingTimeMap& finish,
-		   TVal& time)
-{
-	SEQAN_CHECKPOINT
-
-	typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type TAdjacencyIterator;
-
-	assignProperty(tokenMap, u, true);
-	++time;
-	assignProperty(disc, u, time);
-	TAdjacencyIterator itad(g,u);
-	for(;!atEnd(itad);goNext(itad)) {
-		TVertexDescriptor v = getValue(itad);
-		if (getProperty(tokenMap, v) == false) {
-			assignProperty(predecessor, v, u);
-			_dfsVisit(g, v, tokenMap, predecessor, disc, finish, time);
-		}
-	}
-	++time;
-	assignProperty(finish, u, time);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn depthFirstSearch
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Implements a depth-first search on a graph.
- * 
- * @signature void depthFirstSearch(g, predecessor, discovery, finish);
- * 
- * @param[in]  g           A graph. Types: Undirected Graph, Directed Graph
- * @param[out] predecessor A property map.Predecessor subgraph produced by the depth-first search.
- * @param[out] discovery   A property map.The discovery time of a vertex v.
- * @param[out] finish      A property map.The time when v's adjacency list has been fully explored.
- * 
- * @section Remarks
- * 
- * In contrast to a breadth-first search the depth-first search is repeated from multiple sources if the graph is not
- * connected.  Hence, depth-first search produces a depth-first forest.  To ensure each vertex ends up in exactly one
- * tree we need not just a distance but a discovery and finishing time.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/depth_first_search.cpp
- *
- * @include demos/graph_algorithms/depth_first_search.cpp.stdout
- * 
- * @see breadthFirstSearch
- */
-
-/**
-.Function.depthFirstSearch:
-..cat:Graph
-..summary:Implements a depth-first search on a graph.
-..remarks:In contrast to a breadth-first search the depth-first search is repeated from multiple sources if the graph is not connected.
-Hence, depth-first search produces a depth-first forest. To ensure each vertex ends up in exactly one tree we need not just a distance but a
-discovery and finishing time.
-..signature:depthFirstSearch(g, predecessor, discovery, finish)
-..param.g:In-parameter:A graph.
-...type:Spec.Undirected Graph
-...type:Spec.Directed Graph
-..param.predecessor:Out-parameter:A property map.
-...remarks:Predecessor subgraph produced by the depth-first search.
-..param.discovery:Out-parameter:A property map.
-...remarks:The discovery time of a vertex v.
-..param.finish:Out-parameter:A property map.
-...remarks:The time when v's adjacency list has been fully explored.
-..returns:void.
-..see:Function.breadthFirstSearch
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TPredecessorMap, typename TDiscoveryTimeMap, typename TFinishingTimeMap>
-void
-depthFirstSearch(Graph<TSpec> const& g,
-				   TPredecessorMap& predecessor,
-				   TDiscoveryTimeMap& disc,
-				   TFinishingTimeMap& finish)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Value<TPredecessorMap>::Type TPredVal;
-
-	// Initialization
-	resizeVertexMap(g,predecessor);
-	resizeVertexMap(g,disc);
-	resizeVertexMap(g,finish);
-	TPredVal nilPred = getNil<TVertexDescriptor>();
-
-	String<bool> tokenMap;
-	resizeVertexMap(g, tokenMap);
-	TVertexIterator it(g);
-	for(;!atEnd(it);goNext(it)) {
-		assignProperty(tokenMap, getValue(it), false);
-		assignProperty(predecessor, getValue(it), nilPred);
-	}
-
-	TSize time = 0;
-
-	goBegin(it);
-	for(;!atEnd(it);goNext(it)) {
-		TVertexDescriptor u = getValue(it);
-		if (getProperty(tokenMap, u) == false) {
-			_dfsVisit(g, u, tokenMap, predecessor, disc, finish, time);
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// Topological sort
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn topologicalSort
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Performs a topological sort on a directed acyclic graph (DAG).
- * 
- * @signature void topologicalSort(g, topSort);
- * 
- * @param[in]  g       A directed acyclic graph. Types: Directed Graph
- * @param[out] topSort A topological ordering of the vertices. Types: String.
- * 
- * @section Remarks
- * 
- * A topological sort is a linear ordering of all its vertices such that if the graph contains an edge (u,v) then u
- * appears before v in the ordering.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/topological_sort.cpp
- *
- * @include demos/graph_algorithms/topological_sort.cpp.stdout
- */
-
-/**
-.Function.topologicalSort:
-..cat:Graph
-..summary:Performs a topological sort on a directed acyclic graph (DAG).
-..remarks:A topological sort is a linear ordering of all its vertices such that if the graph contains an edge (u,v) then u appears before v in the ordering.
-..signature:topologicalSort(g, topSort)
-..param.g:In-parameter:A directed acyclic graph.
-...type:Spec.Directed Graph
-..param.topSort:Out-parameter:A topological ordering of the vertices.
-...type:Class.String
-..returns:void.
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TVertexDescriptor>
-void
-topologicalSort(Graph<TSpec> const & g,
-				 String<TVertexDescriptor> & topSort)
-{
-	typedef typename Size<Graph<TSpec> >::Type TSize;
-
-	// Variable definition.
-	String<TSize> predMap;
-	String<TSize> discoveryTimeMap;
-	String<TSize> finishingTimeMap;
-	
-	// Perform DFS.
-	depthFirstSearch(g, predMap, discoveryTimeMap, finishingTimeMap);
-    SEQAN_ASSERT_EQ(numVertices(g), length(predMap));
-    SEQAN_ASSERT_EQ(numVertices(g), length(discoveryTimeMap));
-    SEQAN_ASSERT_EQ(numVertices(g), length(finishingTimeMap));
-
-	// Order vertices.
-	typedef ::std::pair<TSize, TVertexDescriptor> TTimeVertexPair;
-	std::priority_queue<TTimeVertexPair> q;
-	typedef typename Iterator<Graph<TSpec>, VertexIterator>::Type TVertexIterator;
-	TVertexIterator it(g);
-	for (; !atEnd(it); goNext(it))
-		q.push(std::make_pair(getProperty(finishingTimeMap, getValue(it)), getValue(it)));
-
-	// Create topological order.
-	resize(topSort, numVertices(g));
-	TSize count = 0;
-	while (!q.empty())
-    {
-		assignValue(topSort, count, q.top().second);
-		q.pop();
-		++count;
-	}
-    SEQAN_ASSERT_EQ(length(topSort), numVertices(g));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// Strongly connected components
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn stronglyConnectedComponents
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Decomposes a directed graph into its strongly connected components.
- * @signature TSize stronglyConnectedComponents(g, components);
- *
- * @param[in]  g A directed graph. Types: Directed Graph
- * @param[out] components
- *               A property map.Each vertex is mapped to a component id.  If two vertices share the same id they are
- *               in the same component.
- *
- * @return TSize Number of strongly connected components, Size type of g.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/strongly_connected_components.cpp
- *
- * @include demos/graph_algorithms/strongly_connected_components.cpp.stdout
- */
-
-/**
-.Function.stronglyConnectedComponents:
-..cat:Graph
-..summary:Decomposes a directed graph into its strongly connected components.
-..signature:stronglyConnectedComponents(g, components)
-..param.g:In-parameter:A directed graph.
-...type:Spec.Directed Graph
-..param.components:Out-parameter:A property map.
-...remarks:Each vertex is mapped to a component id. If two vertices share the same id they are in the same component.
-..returns:$Size<TGraph>::Type$, number of strongly connected components.
-..include:seqan/graph_algorithms.h
-*/
-
-template<typename TSpec, typename TComponents>
-typename Size<Graph<TSpec> >::Type
-stronglyConnectedComponents(Graph<TSpec> const& g_source,
-							  TComponents& components)
-{
-	// Initialization
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Value<TComponents>::Type TCompVal;
-	resizeVertexMap(g_source,components);
-	String<TSize> predMap;
-	String<TSize> discoveryTimeMap;
-	String<TSize> finishingTimeMap;
-
-	// Dfs
-	depthFirstSearch(g_source, predMap, discoveryTimeMap, finishingTimeMap);
-
-	Graph<TSpec> g;
-	transpose(g_source, g);
-
-	// Second Dfs
-	String<TSize> predecessor;
-	String<TSize> disc;
-	String<TSize> finish;
-	resizeVertexMap(g,predecessor);
-	resizeVertexMap(g,disc);
-	resizeVertexMap(g,finish);
-	TCompVal nilPred = getNil<TVertexDescriptor>();
-	String<bool> tokenMap;
-	resizeVertexMap(g, tokenMap);
-	TVertexIterator it(g);
-	for(;!atEnd(it);goNext(it)) {
-		assignProperty(components, getValue(it), nilPred);
-		assignProperty(tokenMap, getValue(it), false);
-		assignProperty(predecessor, getValue(it), nilPred);
-	}
-
-	// Order vertices
-	typedef ::std::pair<TSize, TVertexDescriptor> TTimeVertexPair;
-	std::priority_queue<TTimeVertexPair> q;
-	goBegin(it);
-	for(;!atEnd(it);++it) {
-		q.push(std::make_pair(getProperty(finishingTimeMap, getValue(it)), getValue(it)));
-	}
-
-	TSize time = 0;
-	TSize label = 0;
-	while(!q.empty()) {
-		TVertexDescriptor u = q.top().second;
-		q.pop();
-		if (getProperty(tokenMap, u) == false) {
-			_dfsVisit(g, u, tokenMap, predecessor, disc, finish, time);
-			TVertexIterator it_label(g);
-			for(;!atEnd(it_label);goNext(it_label)) {
-				if ((getProperty(tokenMap, getValue(it_label)) == true) &&
-					(getProperty(components, getValue(it_label)) == nilPred)) {
-					assignProperty(components, getValue(it_label), label);
-				}
-			}
-			++label;
-		}
-	}
-
-    return label;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// Connected components
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-/*!
- * @fn connectedComponents
- * 
- * @headerfile seqan/graph_algorithms.h
- * 
- * @brief Decomposes an undirected graph into its connected components.
- * 
- * @signature TSize connectedComponents(g, components);
- * 
- * @param[in]  g An undirected graph. Types: Undirected Graph
- * @param[out] components
- *               A property map.  Each vertex is mapped to a component id.  If two vertices share the same id
- *               they are in the same component.
- * 
- * @return TSize The number of components.
- * 
- * @section Examples
- * 
- * A simple example on how to use this function.
- * 
- * @code{.cpp}
- * // Build Input.
- * Graph<Undirected<> > graph;
- * for (unsigned i = 0; i < 5; ++i)
- *     addVertex(graph);
- * addEdge(graph, 0, 1);
- * addEdge(graph, 0, 3);
- * addEdge(graph, 2, 4);
- * String<unsigned> components;
- * unsigned numComponents = 0;
- *  
- * // Call Algorithm.
- * numComponents = connectedComponents(g, components);
- *  
- * // Print Result.
- * std::cout << "Number of components: " << numComponents << std::endl;
- * std::cout << std::endl << "Vertex -> Component" << std::endl;
- * for (unsigned i = 0; i < length(components); ++i)
- *     std::cout << i << " -> " << components[i] << std::endl;
- * @endcode
- * The output now is:
- * 
- * @code{.console}
- * Number of components: 2
- *  
- * Vertex -> Component
- * 0 -> 0
- * 1 -> 0
- * 2 -> 1
- * 3 -> 0
- * 4 -> 1
- * @endcode
- */
-
-/**
-.Function.connectedComponents:
-..cat:Graph
-..summary:Decomposes an undirected graph into its connected components.
-..signature:connectedComponents(g, components)
-..param.g:In-parameter:An undirected graph.
-...type:Spec.Undirected Graph
-..param.components:Out-parameter:A property map.
-...remarks:Each vertex is mapped to a component id. If two vertices share the same id they are in the same component.
-..returns: The number of components.
-..example:A simple example on how to use this function.
-..example.code:
-// Build Input.
-Graph<Undirected<> > graph;
-for (unsigned i = 0; i < 5; ++i)
-    addVertex(graph);
-addEdge(graph, 0, 1);
-addEdge(graph, 0, 3);
-addEdge(graph, 2, 4);
-String<unsigned> components;
-unsigned numComponents = 0;
-
-// Call Algorithm.
-numComponents = connectedComponents(g, components);
-
-// Print Result.
-std::cout << "Number of components: " << numComponents << std::endl;
-std::cout << std::endl << "Vertex -> Component" << std::endl;
-for (unsigned i = 0; i < length(components); ++i)
-    std::cout << i << " -> " << components[i] << std::endl;
-..example:The output now is:
-..example.code:
-Number of components: 2
-
-Vertex -> Component
-0 -> 0
-1 -> 0
-2 -> 1
-3 -> 0
-4 -> 1
-..include:seqan/graph_algorithms.h
-*/
-
-template<typename TSpec, typename TComponents>
-typename Size<Graph<TSpec> >::Type
-connectedComponents(Graph<TSpec> const & g,
-                    TComponents & components)
-{
-    typedef typename VertexDescriptor<Graph<TSpec> >::Type TVertexDescriptor;
-
-    // Initialize Union-Find data structure.
-    UnionFind<TVertexDescriptor> uf;
-    resizeVertexMap(g, uf);
-
-    // Use Union-Find data structure to compute connected components.
-    for (typename Iterator<Graph<TSpec>, EdgeIterator>::Type it(g); !atEnd(it); goNext(it))
-        joinSets(uf, findSet(uf, sourceVertex(it)), findSet(uf, targetVertex(it)));
-
-    // Build final component map.
-    resizeVertexMap(g, components);
-    unsigned c = 0;
-    std::map<TVertexDescriptor, unsigned> reprToComponent;
-    for (typename Iterator<Graph<TSpec>, VertexIterator>::Type it(g); !atEnd(it); goNext(it))
-    {
-        TVertexDescriptor v = findSet(uf, *it);
-
-        // Build mapping from representant to component id on the fly.
-        if (!reprToComponent.count(v))
-            reprToComponent[v] = c++;
-
-        assignProperty(components, *it, reprToComponent[v]);
-    }
-
-    return c;
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-// Minimum Spanning Trees
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Prim's algorithm
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn primsAlgorithm
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Computes a minimum spanning tree on a graph.
- *
- * @signature void primsAlgorithm(g, source, weight, predecessor);
- *
- * @param[in] g      An undirected graph. Types: Undirected Graph
- * @param[in] source A source vertex. Types: VertexDescriptor
- * @param[in] weight Edge weights.
- * @param[out] predecessor
- *                   A property map.  A property map that represents predecessor relationships among vertices.  It
- *                   determines a minimum spanning tree.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/prims_algorithm.cpp
- *
- * @include demos/graph_algorithms/prims_algorithm.cpp.stdout
- *
- * @see kruskalsAlgorithm
- */
-
-/**
-.Function.primsAlgorithm:
-..cat:Graph
-..summary:Computes a minimum spanning tree on a graph.
-..signature:primsAlgorithm(g, source, weight, predecessor)
-..param.g:In-parameter:An undirected graph.
-...type:Spec.Undirected Graph
-..param.source:In-parameter:A source vertex.
-...type:Metafunction.VertexDescriptor
-..param.weight:In-parameter:Edge weights.
-..param.predecessor:Out-parameter:A property map.
-...remarks:A property map that represents predecessor relationships among vertices. It determines a minimum spanning tree.
-..returns:void.
-..see:Function.kruskalsAlgorithm
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap>
-void
-primsAlgorithm(Graph<TSpec> const& g,
-				TVertexDescriptor const source,
-				TWeightMap const& weight,
-				TPredecessorMap& predecessor)
-{
-	SEQAN_CHECKPOINT
-	typedef Graph<TSpec> TGraph;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Value<TPredecessorMap>::Type TPred;
-	typedef typename Value<TWeightMap>::Type TWeight;
-
-	typedef ::std::pair<TWeight, TVertexDescriptor> TWeightVertexPair;
-	std::priority_queue<TWeightVertexPair, std::vector<TWeightVertexPair>, std::greater<TWeightVertexPair> > q;
-	
-	// Initialization
-	String<bool> tokenMap;
-	String<TWeight> key;
-	TPred nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
-	TWeight infWeight = _getInfinityDistance(weight);
-	resizeVertexMap(g,predecessor);
-	resizeVertexMap(g,tokenMap);
-	resizeVertexMap(g,key);
-
-	TVertexIterator it(g);
-	while(!atEnd(it)) {
-		TVertexDescriptor u = getValue(it);
-		if (u == source) q.push(std::make_pair(0, u));
-		assignProperty(predecessor, u, nilPred);
-		assignProperty(key, u, infWeight);
-		assignProperty(tokenMap, u, false);
-		goNext(it);
-	}
-
-	assignProperty(key, source, 0);
-	while(!q.empty()) {
-		TVertexDescriptor u = q.top().second;
-		q.pop();
-		if (getProperty(tokenMap, u)) continue;
-		assignProperty(tokenMap, u, true);
-		TOutEdgeIterator itOut(g,u);
-		while(!atEnd(itOut)) {
-			TVertexDescriptor v = targetVertex(itOut);
-			TWeight w = getProperty(weight, getValue(itOut));
-			if ((!getProperty(tokenMap, v)) &&
-				(w < getProperty(key, v))) {
-					assignProperty(predecessor, v, u);
-					assignProperty(key, v, w);
-					q.push(std::make_pair(w, v));
-			}
-			goNext(itOut);
-		}
-	}
-}
-
-template<typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap>
-void
-primsAlgorithmSpaceEfficient(Graph<TSpec> const& g,
-							   TVertexDescriptor const source,
-							   TWeightMap const& weight,
-							   TPredecessorMap& predecessor)
-{
-	SEQAN_CHECKPOINT
-	typedef Graph<TSpec> TGraph;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Value<TPredecessorMap>::Type TPred;
-	typedef typename Value<TWeightMap>::Type TWeight;
-
-	// Set-up the priority queue
-	typedef Pair<TVertexDescriptor, TWeight> TKeyValue;
-	typedef HeapTree<TKeyValue, std::less<TWeight>, KeyedHeap<> > TKeyedHeap;
-	TKeyedHeap priorityQueue;
-	
-	// Initialization
-	String<bool> tokenMap;
-	TPred nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
-	TWeight infWeight = _getInfinityDistance(weight);
-	resizeVertexMap(g,predecessor);
-	resizeVertexMap(g,tokenMap);
-
-	TVertexIterator it(g);
-	for(;!atEnd(it);goNext(it)) {
-		TVertexDescriptor u = value(it);
-		heapInsert(priorityQueue, TKeyValue(u, infWeight));
-		assignProperty(predecessor, u, nilPred);
-		assignProperty(tokenMap, u, false);
-	}
-	heapChangeValue(priorityQueue, source, 0);
-
-	// Iterate until queue is empty
-	while(!empty(priorityQueue)) {
-		TKeyValue kv = heapExtractRoot(priorityQueue);
-		TVertexDescriptor u = kv.i1;
-		assignProperty(tokenMap, u, true);
-		if (kv.i2 == infWeight) continue;
-		TOutEdgeIterator itOut(g,u);
-		for(;!atEnd(itOut);goNext(itOut)) {
-			TVertexDescriptor v = targetVertex(itOut);
-			if (getProperty(tokenMap, v)) continue;
-			TWeight w = getProperty(weight, getValue(itOut));
-			if (w < heapGetValue(priorityQueue, v)) {
-				assignProperty(predecessor, v, u);
-				heapChangeValue(priorityQueue, v, w);
-			}
-		}
-	}
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Kruskal's algorithm
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TWeight, typename TPair>
-struct LessPairI1_ :
-	public ::std::unary_function<Pair<TWeight, TPair>, bool>
-{
-	inline bool
-	operator() (Pair<TWeight, TPair> const& a1, Pair<TWeight, TPair> const& a2) const {
-		return (a1.i1 < a2.i1);
-	}
-};
-
-/*!
- * @fn kruskalsAlgorithm
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Computes a minimum spanning tree on a graph.
- *
- * @signature void kruskalsAlgorithm(g, source, weight, edges);
- *
- * @param[in] g      An undirected graph. Types: Undirected Graph
- * @param[in] source A source vertex. Types: VertexDescriptor
- * @param[in] weight Edge weights.
- * @param[out] edges A String of vertex descriptors that represent edges.  Each consecutive pair is an edge with the
- *                   two end points.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/kruskals_algorithm.cpp
- *
- * @include demos/graph_algorithms/kruskals_algorithm.cpp.stdout
- *
- * @see primsAlgorithm
- */
-
-/**
-.Function.kruskalsAlgorithm:
-..cat:Graph
-..summary:Computes a minimum spanning tree on a graph.
-..signature:kruskalsAlgorithm(g, source, weight, edges)
-..param.g:In-parameter:An undirected graph.
-...type:Spec.Undirected Graph
-..param.source:In-parameter:A source vertex.
-...type:Metafunction.VertexDescriptor
-..param.weight:In-parameter:Edge weights.
-..param.edges:Out-parameter:Array of vertex descriptors.
-...remarks:Array or string where two consecutive entries are an edge.
-..returns:void.
-..see:Function.primsAlgorithm
-..include:seqan/graph_algorithms.h
-*/
-
-template<typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TEdges>
-void
-kruskalsAlgorithm(Graph<TSpec> const & g,
-				   TVertexDescriptor const,
-				   TWeightMap const & weight,
-				   TEdges & edges)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Value<TWeightMap>::Type TWeight;
-
-	typedef Pair<TVertexDescriptor, TVertexDescriptor> TVertexPair;
-	typedef Pair<TWeight, TVertexPair> TWeightEdgePair;
-	typedef String<TWeightEdgePair>  TEdgeList;
-	typedef typename Iterator<TEdgeList>::Type TEdgeListIter;
-	TEdgeList edgeList;
-
-	// Initialization
-	reserve(edges, 2 * (numVertices(g) - 1));
-    UnionFind<TVertexDescriptor> unionFind;
-    resizeVertexMap(g, unionFind);
-	
-	// Sort the edges
-	TEdgeIterator itE(g);
-	for(;!atEnd(itE);goNext(itE)) appendValue(edgeList, TWeightEdgePair(getProperty(weight, getValue(itE)), TVertexPair(sourceVertex(itE),targetVertex(itE))));
-	std::sort(begin(edgeList, Standard() ), end(edgeList, Standard() ), LessPairI1_<TWeight, TVertexPair>() );
-
-	// Process each edge
-	TEdgeListIter itEdgeList = begin(edgeList, Standard());
-	TEdgeListIter itEdgeListEnd = end(edgeList, Standard());
-	for (; itEdgeList != itEdgeListEnd; goNext(itEdgeList)) {
-		TVertexDescriptor x = value(itEdgeList).i2.i1;
-		TVertexDescriptor y = value(itEdgeList).i2.i2;
-
-        if (findSet(unionFind, x) == findSet(unionFind, y))
-            continue;
-
-        appendValue(edges, x);
-        appendValue(edges, y);
-        joinSets(unionFind, findSet(unionFind, x), findSet(unionFind, y));
-	}
-}
-
-// ----------------------------------------------------------------------------
-// Weakly Connected Components
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn weaklyConnectedComponents
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Compute weakly connected components of a directed graph.
- * 
- * @signature TSize weaklyConnectedComponents(g, components)
- * 
- * @param[in]  g A directed graph. Types: Directed Graph
- * @param[out] components
- *               A property map.  Each vertex is mapped to a component id.  If two vertices share the same id they
- *               are in the same component.
- * 
- * @return TSize The number of weakly connected components.  TSize is <tt>Size&lt;TGraph&gt;::Type</tt>.
- * 
- * @section Remarks
- * 
- * The running time is <tt>O(n a(n, n))</tt> where <tt>a</tt> is the inverse Ackermann function and thus almost linear.
- * The union find data structure is used since the graph implementations do not allow the efficient iteration of
- * in-edges.
- */
-
-/**
-.Function.weaklyConnectedComponents:
-..cat:Graph
-..summary:Compute weakly connected components of a directed graph.
-..signature:weaklyConnectedComponents(g, components)
-..param.g:In-parameter:A directed graph.
-...type:Spec.Directed Graph
-..param.components:Out-parameter:A property map.
-...remarks:Each vertex is mapped to a component id. If two vertices share the same id they are in the same component.
-..returns:$Size<TGraph>::Type$, number of weakly connected components.
-..remarks:The running time is $O(n a(n, n))$ where $a$ is the inverse Ackermann function and thus almost linear. The union find data structure is used since the graph implementations do not allow the efficient iteration of in-edges.
-..include:seqan/graph_algorithms.h
- */
-
-template<typename TSpec, typename TComponents>
-typename Size<Graph<TSpec> >::Type
-weaklyConnectedComponents(Graph<TSpec> const & g,
-                          TComponents & components)
-{
-	SEQAN_CHECKPOINT;
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	// Initialization.
-    UnionFind<TVertexDescriptor> unionFind;
-    resizeVertexMap(g, unionFind);
-
-    // Iterate over all edges, joining weakly connected components.
-    for (TEdgeIterator itE(g); !atEnd(itE); goNext(itE))
-        joinSets(unionFind, findSet(unionFind, sourceVertex(itE)), findSet(unionFind, targetVertex(itE)));
-
-    // Count number of sets.
-    TSize setCount = 0;
-    for (TVertexIterator itV(g); !atEnd(itV); goNext(itV))
-        setCount += (findSet(unionFind, *itV) == *itV);
-
-    // Build a map from graph vertex descriptor to component id.
-    TSize nextId = 0;
-    clear(components);
-    resizeVertexMap(g, components, setCount);  // setCount is sentinel value
-    for (TVertexIterator itV(g); !atEnd(itV); goNext(itV)) {
-        if (getProperty(components, findSet(unionFind, *itV)) == setCount)
-            assignProperty(components, findSet(unionFind, *itV), nextId++);
-        assignProperty(components, *itV, getProperty(components, findSet(unionFind, *itV)));
-    }
-
-    return setCount;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-// Single-Source Shortest Paths
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-// INTERNAL FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TPredecessorMap, typename TVertexDescriptor, typename TNameMap>
-inline void
-_printPath(Graph<TSpec> const& g,
-			TPredecessorMap const& predecessor,
-			TVertexDescriptor const source,
-			TVertexDescriptor const v,
-			TNameMap const& nameMap)
-{
-	if (source == v) {
-		std::cout << getProperty(nameMap, source);
-	} else if (getProperty(predecessor, v) == getNil<typename VertexDescriptor<Graph<TSpec> >::Type>()) {
-		std::cout << "No path from " << getProperty(nameMap, source) << " to " << getProperty(nameMap, v) << " exists.";
-	} else {
-		_printPath(g,predecessor, source, getProperty(predecessor, v), nameMap);
-		std::cout << "," << getProperty(nameMap, v);
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TPredecessorMap, typename TVertexDescriptor1, typename TVertexDescriptor2>
-inline void
-_printPath(Graph<TSpec> const& g,
-			TPredecessorMap const& predecessor,
-			TVertexDescriptor1 const source,
-			TVertexDescriptor2 const v)
-{
-	if (source == v) {
-		std::cout << source;
-	} else if (getProperty(predecessor, v) == getNil<typename VertexDescriptor<Graph<TSpec> >::Type>()) {
-		std::cout << "No path from " << source << " to " << v << " exists.";
-	} else {
-		_printPath(g,predecessor, source, getProperty(predecessor, v));
-		std::cout << "," << v;
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TPredecessorMap, typename TVertexDescriptor1, typename TVertexDescriptor2, typename TEdgeSet>
-inline bool
-_collectEdges(Graph<TSpec> const& g,
-			   TPredecessorMap const& predecessor,
-			   TVertexDescriptor1 const source,
-			   TVertexDescriptor2 const v,
-			   TEdgeSet& edgeSet)
-{
-	if ((TVertexDescriptor1) source == (TVertexDescriptor1) v) {
-		return true;
-	} else if (getProperty(predecessor, v) == getNil<typename VertexDescriptor<Graph<TSpec> >::Type>()) {
-		return false;
-	} else {
-		edgeSet.insert(findEdge(g, getProperty(predecessor, v), v));
-		return _collectEdges(g,predecessor, source, getProperty(predecessor, v), edgeSet);
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TPredecessorMap, typename TVertexDescriptor, typename TEdgeSet>
-inline bool
-_collectEdges(Graph<TSpec> const& g,
-			   TPredecessorMap const& predecessor,
-			   TVertexDescriptor const source,
-			   TEdgeSet& edgeSet)
-{
-	typedef Iterator<Graph<Undirected<> >, VertexIterator>::Type TVertexIterator;
-	TVertexIterator it(g);
-	for(;!atEnd(it); goNext(it)) {
-		if (!_collectEdges(g, predecessor, source, value(it), edgeSet)) {
-			edgeSet.clear();
-			return false;
-		}
-	}
-	return true;
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap>
-inline void 
-_initializeSingleSource(Graph<TSpec> const& g,
-						  TVertexDescriptor const source,
-						  TWeightMap const& weight,
-						  TPredecessorMap& predecessor, 
-						  TDistanceMap& distance)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Value<TPredecessorMap>::Type TPredVal;
-	typedef typename Value<TWeightMap>::Type TDistVal;
-	TPredVal nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
-	TDistVal infDist = _getInfinityDistance(weight);
-	
-	TVertexIterator it(g);
-	for(;!atEnd(it);goNext(it)) {
-		assignProperty(distance, getValue(it), infDist);
-		assignProperty(predecessor, getValue(it), nilPred);
-	}
-	assignProperty(distance, source, 0);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap, typename TVertexDescriptor, typename TEdgeDescriptor>
-inline void 
-_relax(Graph<TSpec> const& g,
-	    TWeightMap const& weight,
-		TPredecessorMap& predecessor, 
-		TDistanceMap& distance,
-		TVertexDescriptor const u,
-		TEdgeDescriptor const e)
-{
-	TVertexDescriptor v = targetVertex(g,e);
-	if (getProperty(distance, v) > getProperty(distance,u) + getProperty(weight,e)) {
-		assignProperty(distance, v, getProperty(distance,u) + getProperty(weight,e));
-		assignProperty(predecessor, v, u);
-	}
-}
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// DAG Shortest Path
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-// TODO(holtgrew): This looks broken (distance too high below).
-
-/*!
- * @fn dagShortestPath
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Computes shortest paths from a single source in a directed acyclic graph (DAG).
- *
- * @signature void dagShortestPath(g, source, weight, predecessor, distance);
- *
- * @param[out] predecessor A property map.  A property map that represents predecessor relationships among vertices.
- *                         It determines a shortest-paths tree.
- * @param[out] distance    A property map.  Indicates for each vertex th distance from the source.
- * @param[out] weight      A weight map.  In a directed acyclic graph edge weights can be negative because no cycles
- *                         do exist.
- * @param[in] g            A directed acyclic graph. Types: Directed Graph
- * @param[in] source       A source vertex. Types: VertexDescriptor
- *
- * @section Example
- *
- * @include demos/graph_algorithms/dag_shortest_path.cpp
- *
- * @include demos/graph_algorithms/dag_shortest_path.cpp.stdout
- *
- * @see bellmanFordAlgorithm
- * @see dijkstra
- */
-
-/**
-.Function.dagShortestPath:
-..cat:Graph
-..summary:Computes shortest paths from a single source in a directed acyclic graph (DAG).
-..signature:dagShortestPath(g, source, weight, predecessor, distance)
-..param.g:In-parameter:A directed acyclic graph.
-...type:Spec.Directed Graph
-..param.source:In-parameter:A source vertex.
-...type:Metafunction.VertexDescriptor
-..param.weight:In-parameter:A weight map.
-...remarks:In a directed acyclic graph edge weights can be negative because no cycles do exist.
-..param.predecessor:Out-parameter:A property map.
-...remarks:A property map that represents predecessor relationships among vertices. It determines a shortest-paths tree.
-..param.distance:Out-parameter:A property map.
-...remarks:Indicates for each vertex the distance from the source.
-..returns:void.
-..see:Function.bellmanFordAlgorithm
-..see:Function.dijkstra
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap>
-void
-dagShortestPath(Graph<TSpec> const& g,
-				  TVertexDescriptor const source,
-				  TWeightMap const& weight,
-				  TPredecessorMap& predecessor,
-				  TDistanceMap& distance)
-{
-	typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Iterator<String<TVertexDescriptor>, Rooted>::Type TStringIterator;
-
-	// Initialization
-	resizeVertexMap(g,predecessor);
-	resizeVertexMap(g,distance);
-
-	// Topological sort
-	String<TVertexDescriptor> order;
-	topologicalSort(g, order);
-
-	_initializeSingleSource(g, source, weight, predecessor, distance);
-
-	//DAG Shortest Paths
-	TStringIterator it = begin(order);
-	while(!atEnd(it)) {
-		TOutEdgeIterator itout(g, getValue(it));
-		for(;!atEnd(itout);++itout) {
-			_relax(g,weight,predecessor, distance, getValue(it), getValue(itout));
-		}
-		goNext(it);
-	}
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Bellman-Ford
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-/*!
- * @fn bellmanFordAlgorithm
- *
- * @headerfile seqan/graph_algorithms.h
- *
- * @brief Computes shortest paths from a single source in a directed graph.
- *
- * @signature bool bellmanFordAlgorithm(g, source, weight, predecessor, distance)
- *
- * @param[in]  g           A directed graph. Types: Directed Graph
- * @param[in]  source      A source vertex. Types: VertexDescriptor
- * @param[in]  weight      A weight map.A property map with edge weights.  Edge weights may be negative.
- * @param[out] predecessor A property map.  A property map that represents predecessor relationships among vertices.
- *                         It determines a shortest-paths tree.
- * @param[out] distance    A property map.Indicates for each vertex the distance from the source.
- *
- * @return bool true if the graph has no negative weight cycles, false otherwise.
- *
- * @section Remarks
- *
- * Edge weights may be negative in the Bellman-Ford algorithm.  The out parameters are only valid if the algorithm
- * returns true.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/bellman_ford_algorithm.cpp
- *
- * @include demos/graph_algorithms/bellman_ford_algorithm.cpp.stdout
- *
- * @see dagShortestPath
- * @see dijkstra
- */
-
-/**
-.Function.bellmanFordAlgorithm:
-..cat:Graph
-..summary:Computes shortest paths from a single source in a directed graph.
-..remarks:Edge weights may be negative in the Bellman-Ford algorithm.
-The out parameters are only valid if the algorithm returns true.
-..signature:bellmanFordAlgorithm(g, source, weight, predecessor, distance)
-..param.g:In-parameter:A directed graph.
-...type:Spec.Directed Graph
-..param.source:In-parameter:A source vertex.
-...type:Metafunction.VertexDescriptor
-..param.weight:In-parameter:A weight map.
-...remarks:A property map with edge weights. Edge weights may be negative.
-..param.predecessor:Out-parameter:A property map.
-...remarks:A property map that represents predecessor relationships among vertices. It determines a shortest-paths tree.
-..param.distance:Out-parameter:A property map.
-...remarks:Indicates for each vertex the distance from the source.
-..returns:True if the graph has no negative weight cycles, false otherwise.
-..see:Function.dagShortestPath
-..see:Function.dijkstra
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap>
-bool
-bellmanFordAlgorithm(Graph<TSpec> const& g,
-					   TVertexDescriptor const source,
-					   TWeightMap const& weight,
-					   TPredecessorMap& predecessor,
-					   TDistanceMap& distance)
-{
-	SEQAN_CHECKPOINT
-	typedef typename Size<Graph<TSpec> >::Type TSize;
-
-	// Initialization
-	typedef typename Iterator<Graph<TSpec>, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
-	resizeVertexMap(g,predecessor);
-	resizeVertexMap(g,distance);
-	_initializeSingleSource(g, source, weight, predecessor, distance);
-
-	// Run Bellman-Ford
-	for(TSize i=0; i<numVertices(g) - 1; ++i) {
-		TVertexIterator it(g);
-		for(;!atEnd(it);goNext(it)) {
-			TVertexDescriptor u = getValue(it);
-			TOutEdgeIterator itout(g, u);
-			for(;!atEnd(itout);++itout) {
-				_relax(g,weight,predecessor, distance, u, getValue(itout));
-			}
-		}
-	}
-
-	TVertexIterator it(g);
-	for(;!atEnd(it);goNext(it)) {
-		TVertexDescriptor u = getValue(it);
-		TOutEdgeIterator itout(g, u);
-		for(;!atEnd(itout);++itout) {
-			TVertexDescriptor v = targetVertex(g, getValue(itout));
-			if (getProperty(distance, v) > getProperty(distance,u) + getProperty(weight,getValue(itout))) {
-				return false;
-			}
-		}
-	}
-	return true;
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Dijkstra
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn dijkstra
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Computes shortest paths from a single source in a graph.
- * @signature void dijkstra(g, source, weight, predecessor, distance);
- *
- * @param[out] predecessor A property map.  A property map that represents predecessor relationships among vertices.
- *                         It determines a shortest-paths tree.
- * @param[out] distance    A property map.Indicates for each vertex the distance from the source.
- * @param[in]  g           A graph. Types: Directed Graph
- * @param[in]  source      A source vertex.  Types: VertexDescriptor
- * @param[in]  weight      A weight map.  A property map with edge weights. Edge weights have to be nonnegative.
- *
- * @section Remarks
- *
- * Edge weights have to be nonnegative.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/dijkstra.cpp
- *
- * @include demos/graph_algorithms/dijkstra.cpp.stdout
- *
- * @see dagShortestPath
- * @see bellmanFordAlgorithm
- */
-
-/**
-.Function.dijkstra:
-..cat:Graph
-..summary:Computes shortest paths from a single source in a graph.
-..remarks:Edge weights have to be nonnegative.
-..signature:dijkstra(g, source, weight, predecessor, distance)
-..param.g:In-parameter:A graph.
-...type:Spec.Directed Graph
-..param.source:In-parameter:A source vertex.
-...type:Metafunction.VertexDescriptor
-..param.weight:In-parameter:A weight map.
-...remarks:A property map with edge weights. Edge weights have to be nonnegative.
-..param.predecessor:Out-parameter:A property map.
-...remarks:A property map that represents predecessor relationships among vertices. It determines a shortest-paths tree.
-..param.distance:Out-parameter:A property map.
-...remarks:Indicates for each vertex the distance from the source.
-..returns:void
-..see:Function.dagShortestPath
-..see:Function.bellmanFordAlgorithm
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap>
-void
-dijkstra(Graph<TSpec> const& g,
-		 TVertexDescriptor const source,
-		 TWeightMap const& weight,
-		 TPredecessorMap& predecessor,
-		 TDistanceMap& distance)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Value<TDistanceMap>::Type TDistVal;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-
-	// Initialization
-	resizeVertexMap(g,predecessor);
-	resizeVertexMap(g,distance);
-
-	// S is initially empty
-	String<bool> setS;
-	resize(setS, getIdUpperBound(_getVertexIdManager(g)), false);
-
-	// Set-up the priority queue
-	typedef Pair<TVertexDescriptor, TDistVal> TKeyValue;
-	typedef HeapTree<TKeyValue, std::less<TDistVal>, KeyedHeap<> > TKeyedHeap;
-	TKeyedHeap priorityQueue;
-	TDistVal infDist = _getInfinityDistance(weight);
-	TVertexDescriptor nilVertex = getNil<typename VertexDescriptor<TGraph>::Type>();
-	TVertexIterator it(g);
-	for(;!atEnd(it);goNext(it)) {
-		assignProperty(predecessor, value(it), nilVertex);
-		assignProperty(distance, value(it), infDist);
-		heapInsert(priorityQueue, TKeyValue(value(it), infDist));
-	}
-	assignProperty(distance, source, 0);
-	heapChangeValue(priorityQueue, source, 0);
-
-	// Run Dijkstra
-	while (!empty(priorityQueue)) {
-		// Extract min
-		TVertexDescriptor u = heapExtractRoot(priorityQueue).i1;
-		assignProperty(setS, u, true);
-		TOutEdgeIterator itout(g, u);
-		for(;!atEnd(itout);++itout) {
-			TVertexDescriptor v = targetVertex(itout);
-			if (property(setS, v) == true) continue;
-			if (getProperty(distance, v) > getProperty(distance,u) + getProperty(weight,value(itout))) {
-				assignProperty(distance, v, getProperty(distance,u) + getProperty(weight,value(itout)));
-				assignProperty(predecessor, v, u);
-				heapChangeValue(priorityQueue, v, getProperty(distance,u) + getProperty(weight,value(itout)));
-			}
-		}
-	}
-}
-
-//template<typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap>
-//void 
-//dijkstra(Graph<TSpec> const& g,
-//		 TVertexDescriptor const source,
-//		 TWeightMap const& weight,
-//		 TPredecessorMap& predecessor, 
-//		 TDistanceMap& distance)
-//{
-//	SEQAN_CHECKPOINT
-//	typedef Graph<TSpec> TGraph;
-//	typedef typename Size<TGraph>::Type TSize;
-//	typedef typename Value<TDistanceMap>::Type TDistVal;
-//	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-//	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-//	
-//	// Initialization
-//	resizeVertexMap(g,predecessor);
-//	resizeVertexMap(g,distance);
-//
-//	_initializeSingleSource(g, source, weight, predecessor, distance);
-//	
-//	String<bool> setS;
-//	resizeVertexMap(g, setS);
-//	TVertexIterator it(g);
-//	for(;!atEnd(it);++it) {
-//		assignProperty(setS, getValue(it), false);
-//	}
-//	TDistVal infDist = _getInfinityDistance(weight);
-//	TVertexDescriptor nilVertex = getNil<typename VertexDescriptor<TGraph>::Type>();
-//
-//	// Run Dijkstra
-//	TSize count = numVertices(g);
-//	while (count > 0) {
-//		// Extract min
-//		TDistVal min = infDist;
-//		TVertexDescriptor u = nilVertex;
-//		TVertexIterator it_find(g);
-//		for(;!atEnd(it_find);++it_find) {
-//			if(getProperty(setS,getValue(it_find))==true) continue;
-//			if ((u == nilVertex) ||
-//				(getProperty(distance,getValue(it_find))<getProperty(distance,u))) {
-//					u = getValue(it_find);
-//					min = getProperty(distance,getValue(it_find));
-//			}
-//		}
-//		assignProperty(setS, u, true);
-//		TOutEdgeIterator itout(g, u);
-//		for(;!atEnd(itout);++itout) {
-//			_relax(g,weight,predecessor, distance, u, getValue(itout));
-//		}
-//		--count;
-//	}
-//}
-
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-// All-Pairs shortest paths
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-// INTERNAL FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TPredecessor, typename TVertexDescriptor>
-inline void
-_printAllPairsShortestPath(Graph<TSpec> const& g,
-                           TPredecessor& predecessor, 
-                           TVertexDescriptor const i,
-                           TVertexDescriptor const j)
-{
-	typedef typename Size<TPredecessor>::Type TSize;
-	TSize len = getIdUpperBound(g.data_id_managerV);
-	if (i==j) {
-		std::cout << i;
-	} else if (getValue(predecessor, i*len+j) == getNil<typename VertexDescriptor<Graph<TSpec> >::Type>()) {
-		std::cout << "No path from " << i << " to " << j << " exists.";
-	} else {
-		_printAllPairsShortestPath(g,predecessor, i, (TVertexDescriptor) getValue(predecessor, i*len+j));
-		std::cout << "," << j;
-	}
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TWeightMap, typename TMatrix, typename TPredecessor>
-void 
-_initializeAllPairs(Graph<TSpec> const& g,
-						TWeightMap const& weight,
-						TMatrix& matrix,
-						TPredecessor& predecessor)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Size<TMatrix>::Type TSize;
-	typedef typename Value<TWeightMap>::Type TWeightVal;
-	typedef typename Value<TPredecessor>::Type TPredVal;
-	
-	// Create adjacency-like matrix
-	TSize len = getIdUpperBound(g.data_id_managerV);
-	resize(matrix, len * len);
-	resize(predecessor, len * len);
-	TWeightVal infWeight = _getInfinityDistance(weight);
-	TPredVal nilPred = getNil<TVertexDescriptor>();
-	for (TSize row=0;row < len;++row) {
-		for (TSize col=0;col < len;++col) {
-			if (row != col) assignValue(matrix, row*len + col, infWeight);
-			else assignValue(matrix, row*len + col, 0);
-			assignValue(predecessor, row*len + col, nilPred);
-		}
-	}
-
-	// Include edge weights and initial predecessors
-	TVertexIterator it(g);
-	for(;!atEnd(it);goNext(it)) {
-		TVertexDescriptor u = getValue(it);
-		TOutEdgeIterator itout(g, u);
-		for(;!atEnd(itout);++itout) {
-			TVertexDescriptor v = targetVertex(g,getValue(itout));
-			assignValue(matrix, u*len + v, getProperty(weight, getValue(itout)));
-			assignValue(predecessor, u*len + v, u);
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TMatrix, typename TPredecessor, typename TInfDist>
-void 
-_extendShortestPaths(TMatrix& local,
-					   TMatrix& w,
-					   TPredecessor& predecessor,
-					   TInfDist const infDist)
-{
-	typedef typename Value<TMatrix>::Type TMatrixVal;
-	typedef typename Value<TPredecessor>::Type TPredVal;
-	typedef typename Size<TMatrix>::Type TSize;
-	TMatrix oldLocal = local;
-	TPredecessor oldPredecessor = predecessor;
-	TSize len = (TSize) std::sqrt((double) length(oldLocal));
-	for(TSize i = 0; i<len;++i) {
-		for(TSize j = 0; j<len;++j) {
-			if (i==j) continue;
-			assignValue(local, i*len+j,infDist);
-			TPredVal ind = 0;
-			for(TSize k = 0; k<len;++k) {
-				TMatrixVal min1 = getValue(local, i*len+j);
-				TMatrixVal min2 = getValue(oldLocal, i*len+k) + getValue(w, k*len + j);
-				if (min2 < min1) {
-					assignValue(local, i*len+j,min2);
-					ind = k;
-				}
-			}
-			if (getValue(oldLocal, i*len+j) > getValue(local, i*len+j)) {
-				assignValue(predecessor, i*len+j,ind);
-			}
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// All-Pairs shortest path
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn allPairsShortestPath
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Finds shortest paths between all pairs of vertices in a graph.
- * @signature void allPairsShortestPath(g, weight, distance, predecessor);
- *
- * @param[out] predecessor A matrix with predecessors.  Entry (i,j) in this matrix indicates the predecessor of j on
- *                         a shortest path from vertex i to vertex j.  You can use <tt>_printAllPairsShortestPath(g,
- *                         predecessor, i, j)</tt> to print the shortest path from i to j. Types: Matrix
- * @param[out] distance    A matrix with distances.Entry (i,j) in this matrix indicates the distance from vertex i to
- *                         vertex j. Types: Matrix
- * @param[in]  weight      A weight map.A property map with edge weights.  Edge weights may be negative.
- * @param[in]  g           A directed graph. Types: Directed Graph
- *
- * @section Example
- *
- * @include demos/graph_algorithms/all_pairs_shortest_path.cpp
- *
- * @include demos/graph_algorithms/all_pairs_shortest_path.cpp.stdout
- *
- * @see floydWarshallAlgorithm
- */
-
-/**
-.Function.allPairsShortestPath:
-..cat:Graph
-..summary:Finds shortest paths between all pairs of vertices in a graph.
-..signature:allPairsShortestPath(g, weight, distance, predecessor)
-..param.g:In-parameter:A directed graph.
-...type:Spec.Directed Graph
-..param.weight:In-parameter:A weight map.
-...remarks:A property map with edge weights. Edge weights may be negative.
-..param.distance:Out-parameter:A matrix with distances.
-...type:Class.Matrix
-...remarks:Entry (i,j) in this matrix indicates the distance from vertex i to vertex j.
-..param.predecessor:Out-parameter:A matrix with predecessors.
-...type:Class.Matrix
-...remarks:Entry (i,j) in this matrix indicates the predecessor of j on a shortest path from vertex i to vertex j.
-You can use _printAllPairsShortestPath(g, predecessor, i, j) to print the shortest path from i to j.
-..returns:void
-..see:Function.floydWarshallAlgorithm
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TWeightMap, typename TMatrix, typename TPredecessor>
-void 
-allPairsShortestPath(Graph<TSpec> const& g,
-						TWeightMap const& weight,
-						TMatrix& distMatrix,
-						TPredecessor& predecessor)
-{
-	SEQAN_CHECKPOINT
-	typedef typename Size<TMatrix>::Type TSize;
-	typedef typename Value<TWeightMap>::Type TWeightVal;
-	TWeightVal infWeight = _getInfinityDistance(weight);
-
-	// Initialize first distance matrix
-	_initializeAllPairs(g,weight,distMatrix,predecessor);
-
-	TSize len = (TSize) sqrt((double) length(distMatrix));
-	TMatrix local = distMatrix;
-	for(TSize m=2;m<len;++m) {
-		_extendShortestPaths(local,distMatrix,predecessor, infWeight);
-	}
-	distMatrix = local;
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Floyd-Warshall
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn floydWarshallAlgorithm
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Finds shortest paths between all pairs of vertices in a graph.
- *
- * @signature void floydWarshallAlgorithm(g, weight, distance, predecessor);
- *
- * @param[out] predecessor A matrix with predecessors.  Entry (i,j) in this matrix indicates the predecessor of j on
- *                         a shortest path from vertex i to vertex j.  You can use <tt>_printAllPairsShortestPath(g,
- *                         predecessor, i, j)</tt> to print the shortest path from i to j.  Types: Matrix
- * @param[out] distance    A matrix with distances.Entry (i,j) in this matrix indicates the distance from vertex i
- *                         to vertex j.  Types: Matrix
- * @param[in]  weight      A weight map.  A property map with edge weights.  Edge weights may be negative.
- * @param[in]  g           A directed graph.  Types: Directed Graph
- *
- * @section Remarks
- *
- * The graph must be free of negative-weight cycles.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/floyd_warshall_algorithm.cpp
- *
- * @include demos/graph_algorithms/floyd_warshall_algorithm.cpp.stdout
- *
- * @see allPairsShortestPath
- */
-
-/**
-.Function.floydWarshallAlgorithm:
-..cat:Graph
-..summary:Finds shortest paths between all pairs of vertices in a graph.
-..signature:floydWarshallAlgorithm(g, weight, distance, predecessor)
-..remarks:The graph must be free of negative-weight cycles.
-..param.g:In-parameter:A directed graph.
-...type:Spec.Directed Graph
-..param.weight:In-parameter:A weight map.
-...remarks:A property map with edge weights. Edge weights may be negative.
-..param.distance:Out-parameter:A matrix with distances.
-...type:Class.Matrix
-...remarks:Entry (i,j) in this matrix indicates the distance from vertex i to vertex j.
-..param.predecessor:Out-parameter:A matrix with predecessors.
-...type:Class.Matrix
-...remarks:Entry (i,j) in this matrix indicates the predecessor of j on a shortest path from vertex i to vertex j.
-You can use _printAllPairsShortestPath(g, predecessor, i, j) to print the shortest path from i to j.
-..returns:void
-..see:Function.allPairsShortestPath
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TWeightMap, typename TMatrix, typename TPredecessor>
-void
-floydWarshallAlgorithm(Graph<TSpec> const& g,
-			   TWeightMap const& weight,
-			   TMatrix& distMatrix,
-			   TPredecessor& predecessor)
-{
-	SEQAN_CHECKPOINT
-	typedef typename Size<TMatrix>::Type TSize;
-	typedef typename Value<TMatrix>::Type TMatrixVal;
-
-	// Initialize first distance matrix
-	_initializeAllPairs(g,weight,distMatrix,predecessor);
-
-	// Floyd-Warshall
-	TSize len = (TSize) std::sqrt((double) length(distMatrix));
-	TMatrix local = distMatrix;
-	for(TSize k=0;k<len;++k) {
-		for(TSize i=0;i<len;++i) {
-			for(TSize j=0;j<len;++j) {
-				TMatrixVal min1 = getValue(distMatrix, i*len+j);
-				TMatrixVal min2 = getValue(distMatrix, i*len+k) + getValue(distMatrix, k*len + j);
-				if (min2 < min1) {
-					assignValue(local, i*len+j,min2);
-					assignValue(predecessor, i*len+j,getValue(predecessor, k*len+j));
-				} else {
-					assignValue(local, i*len+j,min1);
-					assignValue(predecessor, i*len+j, getValue(predecessor, i*len+j));
-				}
-			}
-		}
-		distMatrix=local;
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// Transitive Closure
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn transitiveClosure
- * @headerfile <seqan/graph_algorithms.h>
- * @brief Determines whether there is a path between any two given vertices or not.
- *
- * @signature void transitiveClosure(g, closure);
- *
- * @param[out] closure A matrix which indicates the closure.  Entry (i,j) in this matrix indicates whether there is a
- *                     path from i to j in the graph or not.  Types: Matrix
- * @param[in]   g      A directed graph.  Types: Directed Graph
- *
- * @section Example
- *
- * @include demos/graph_algorithms/transitive_closure.cpp
- *
- * @include demos/graph_algorithms/transitive_closure.cpp.stdout
- */
-
-/**
-.Function.transitiveClosure:
-..cat:Graph
-..summary:Determines whether there is a path between any two given vertices or not.
-..signature:transitiveClosure(g, closure)
-..param.g:In-parameter:A directed graph.
-...type:Spec.Directed Graph
-..param.closure:Out-parameter:A matrix which indicates the closure.
-...type:Class.Matrix
-...remarks:Entry (i,j) in this matrix indicates whether there is a path from i to j in the graph or not.
-..returns:void
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TMatrix>
-void
-transitiveClosure(Graph<TSpec> const& g,
-				   TMatrix& closure)
-{
-	SEQAN_CHECKPOINT
-	typedef typename Size<TMatrix>::Type TSize;
-
-	// Initialize first closure matrix
-	getAdjacencyMatrix(g,closure);
-	TSize len = (TSize) std::sqrt((double) length(closure));
-	for (TSize diag=0;diag < len;++diag) assignValue(closure, diag*len+diag,1);
-
-	// Transitive Closure
-	TMatrix local = closure;
-	for (TSize k=0;k<len;++k) {
-		for(TSize i=0;i<len;++i) {
-			for(TSize j=0;j<len;++j) {
-				bool t_ij = static_cast<int>(getValue(closure, i*len+j)) > 0;
-                bool t_ik = static_cast<int>(getValue(closure, i*len+k)) > 0;
-                bool t_kj = static_cast<int>(getValue(closure, k*len+j)) > 0;
-				assignValue(local, i*len+j, t_ij || (t_ik && t_kj));
-			}
-		}
-		closure = local;
-	}
-}
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-// Maximum Flow
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-// INTERNAL FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-template<typename TSpec, typename TCapMap, typename TFlowMap, typename TResidualGraph>
-void
-_buildResidualGraph(Graph<TSpec> const& g,
-					  TCapMap const& capacity,
-					  TFlowMap const& flow,
-					  TResidualGraph& rG)
-{
-	SEQAN_CHECKPOINT
-	typedef Graph<TSpec> TGraph;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Value<TFlowMap>::Type TFlow;
-	typedef typename Value<TCapMap>::Type TCap;
-
-	clear(rG);
-	TVertexIterator itV(g);
-	for(;!atEnd(itV);goNext(itV)) {
-		_createVertices(rG, getValue(itV));
-	}
-
-	TEdgeIterator itE(g);
-	for(;!atEnd(itE);goNext(itE)) {
-		typedef typename EdgeDescriptor<TResidualGraph>::Type TEdgeDescriptor;
-		TFlow f = getProperty(flow, getValue(itE));
-		TCap cap = getProperty(capacity, getValue(itE));
-		if (f > 0) {
-			TEdgeDescriptor e_rG = findEdge(rG, targetVertex(itE), sourceVertex(itE));
-			if (e_rG == 0) addEdge(rG, targetVertex(itE), sourceVertex(itE), f);
-			else cargo(e_rG) += f;
-		}
-		if (f < cap) {
-			TEdgeDescriptor e_rG = findEdge(rG, sourceVertex(itE), targetVertex(itE));
-			if (e_rG == 0) addEdge(rG, sourceVertex(itE), targetVertex(itE), cap - f);
-			else cargo(e_rG) += cap - f;			
-		}
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TPredecessorMap, typename TVertexDescriptor>
-inline typename Size<Graph<TSpec> >::Type
-_getMinimumAug(Graph<TSpec> const& rG,
-				 TPredecessorMap& predecessor,
-				 TVertexDescriptor const source,
-				 TVertexDescriptor sink)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef TSize TFlow;
-	typedef typename Iterator<String<TVertexDescriptor>, Rooted>::Type TIterator;
-	
-	// Build secondary predecessor map just containing the path
-	TVertexDescriptor nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
-	String<TVertexDescriptor> predMap;
-	resizeVertexMap(rG, predMap);
-	TIterator it = begin(predMap);
-	for(;!atEnd(it);goNext(it)) {
-		*it = nilPred;
-	}
-
-	// Find minimum flow
-	TVertexDescriptor pred = getProperty(predecessor, sink);
-	TFlow f = getCargo(findEdge(rG, pred,sink));
-	assignProperty(predMap, sink, pred);
-	while(pred != source) {
-		sink = pred;
-		pred = getProperty(predecessor, sink);
-		TFlow f2 = getCargo(findEdge(rG, pred,sink));
-		assignProperty(predMap, sink, pred);
-		if (f2 < f) f = f2;
-	}
-
-	// Just return the augmenting path
-	predecessor = predMap;
-	return f;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// Ford Fulkerson
-//////////////////////////////////////////////////////////////////////////////
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn fordFulkersonAlgorithm
- * 
- * @headerfile seqan/graph_algorithms.h
- * 
- * @brief Computes a maximum flow in a directed graph.
- * 
- * @signature TValue fordFulkeronAlgorithm(g, source, sink, capacity, flow);
- * 
- * @param[out] flow     A property map with the flow of each edge.
- * @param[in]  capacity A property map of edge capacities.
- * @param[in]  sink     A sink vertex.  Types: VertexDescriptor
- * @param[in]  g        A directed graph.  Types: Directed Graph
- * @param[in]  source   A source vertex.  Types: VertexDescriptor
- * 
- * @return TValue The value of the flow.  TValue is the Value tpye of the type of flow.
- *
- * @section Example
- *
- * @include demos/graph_algorithms/ford_fulkerson_algorithm.cpp
- *
- * @include demos/graph_algorithms/ford_fulkerson_algorithm.cpp.stdout
- */
-
-/**
-.Function.fordFulkersonAlgorithm:
-..cat:Graph
-..summary:Computes a maximum flow in a directed graph.
-..signature:fordFulkersonAlgorithm(g, source, sink, capacity, flow)
-..param.g:In-parameter:A directed graph.
-...type:Spec.Directed Graph
-..param.source:In-parameter:A source vertex.
-...type:Metafunction.VertexDescriptor
-..param.sink:In-parameter:A sink vertex.
-...type:Metafunction.VertexDescriptor
-..param.capacity:In-parameter:A property map of edge capacities.
-..param.flow:Out-parameter:A property map with the flow of each edge.
-..returns:The value of the flow.
-..include:seqan/graph_algorithms.h
-*/
-template<typename TSpec, typename TVertexDescriptor, typename TCapMap, typename TFlowMap>
-typename Value<TFlowMap>::Type
-fordFulkersonAlgorithm(Graph<TSpec> const& g,
-			   TVertexDescriptor const source,
-			   TVertexDescriptor const sink,
-			   TCapMap const& capacity,
-			   TFlowMap& flow)
-{
-	SEQAN_CHECKPOINT
-	typedef Graph<TSpec> TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Value<TFlowMap>::Type TFlow;
-
-	// Initialization
-	TVertexDescriptor nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
-	resizeEdgeMap(g,flow);
-	TEdgeIterator itE(g);
-	for(;!atEnd(itE);goNext(itE)) {
-		assignProperty(flow, getValue(itE), 0);
-	}
-
-	// Build the residual graph
-	Graph<Directed<TFlow> > rG;
-	_buildResidualGraph(g,capacity, flow, rG);
-
-		
-	// Determine whether the sink is reachable
-	String<TVertexDescriptor> predMap;
-	String<TVertexDescriptor> distMap;
-	breadthFirstSearch(rG, source, predMap, distMap);
-	
-	while (getProperty(predMap, sink) != nilPred) {
-		TFlow inc = _getMinimumAug(rG, predMap, source, sink);
-		TEdgeIterator itEdge(g);
-		for(;!atEnd(itEdge);goNext(itEdge)) {
-			TVertexDescriptor u = sourceVertex(itEdge);
-			TVertexDescriptor v = targetVertex(itEdge);
-			TEdgeDescriptor e = getValue(itEdge);
-			if (getProperty(predMap, v) == u) assignProperty(flow, e, getProperty(flow, e) + inc);
-			if (getProperty(predMap, u) == v) assignProperty(flow, e, getProperty(flow, e) - inc);
-		}
-		// Build the residual graph
-		_buildResidualGraph(g,capacity, flow, rG);
-		// Determine whether the sink is reachable
-		clear(predMap);
-		clear(distMap);
-		breadthFirstSearch(rG, source, predMap, distMap);
-	}
-
-	TFlow valF = 0;
-	TOutEdgeIterator itOutEdge(g, source);
-	for(;!atEnd(itOutEdge);goNext(itOutEdge)) {
-		valF += getProperty(flow, getValue(itOutEdge));
-	}
-	return valF;
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// ToDo: Not yet tested, use with care
-//////////////////////////////////////////////////////////////////////////////
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Matching
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Path Growing Algorithm
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TWeightMap, typename TEdgeMap>
-typename Value<TWeightMap>::Type
-pathGrowingAlgorithm(Graph<TSpec>& g,
-					   TWeightMap const& weightMap,
-					   TEdgeMap& edgeMap1)
-{
-	SEQAN_CHECKPOINT
-	typedef Graph<TSpec> TGraph;
-	typedef typename Value<TWeightMap>::Type TValue;
-	typedef typename Size<Graph<TSpec> >::Type TSize;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-
-	// Make a copy of the graph
-	TGraph mutant(g);
-
-	// Initialy not a single edge is selected
-	resize(edgeMap1, getIdUpperBound(_getEdgeIdManager(g)), false);
-	TEdgeMap edgeMap2 = edgeMap1;
-	TValue edgeMap1Sum = 0;
-	TValue edgeMap2Sum = 0;
-	
-	// Run the algorithm
-	TSize i = 1;
-	while (numEdges(mutant) > 0) {
-		TVertexIterator itVert(mutant);
-		while (outDegree(mutant, *itVert) < 1) goNext(itVert);
-		TVertexDescriptor x = *itVert;
-		TVertexDescriptor y;
-		while (outDegree(mutant, x) >= 1) {
-			TOutEdgeIterator itOut(mutant, x);
-			TEdgeDescriptor e = *itOut;
-			TValue max = getProperty(weightMap, e);
-			y = targetVertex(itOut);
-			goNext(itOut);
-			for(;!atEnd(itOut);++itOut) {
-				if (getProperty(weightMap, *itOut) > max) {
-					e = *itOut;
-					max = getProperty(weightMap, e);
-					y = targetVertex(itOut);
-				}
-			}
-			if (i == 1) {
-				// Mark the edge for m1
-				assignProperty(edgeMap1, e, true);
-				edgeMap1Sum += max;
-			} else {
-				// Mark the edge for m2
-				assignProperty(edgeMap2, e, true);
-				edgeMap2Sum += max;
-			}
-			i = 3 - i;
-			removeVertex(mutant, x);
-			x = y;
-		}
-	}
-	
-
-	// Check whether we have to swap bool arrays
-	if (edgeMap2Sum > edgeMap1Sum) {
-		edgeMap1Sum = edgeMap2Sum;
-		edgeMap1 = edgeMap2;
-	}
-
-	return edgeMap1Sum;
-}
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Weighted bipartite Matching
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TVertexMap, typename TEdges>
-inline typename Size<Graph<TSpec> >::Type
-bipartiteMatching(Graph<TSpec>& g,			  
-					TVertexMap& vertMap,
-					String<TEdges>& edges)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIter;
-
-	clear(edges);
-	TVertexDescriptor source = addVertex(g);
-	TVertexDescriptor target = addVertex(g);
-	TVertexIter itV(g);
-	for(;!atEnd(itV); goNext(itV)) {
-		if ((value(itV) != source) && (value(itV) != target)) {
-			if (getProperty(vertMap, value(itV)) == false) {
-				addEdge(g, source, value(itV));
-			} else {
-				addEdge(g, value(itV), target);
-			}
-		}
-	}
-
-	// Use Ford-Fulkerson to determine a matching
-	String<TSize> capMap;	
-	resizeEdgeMap(g,capMap);
-	typedef typename Iterator<String<TSize> >::Type TCapIter;
-	TCapIter capIt = begin(capMap);
-	TCapIter capItEnd = end(capMap);
-	for(;capIt != capItEnd; ++capIt) value(capIt) = 1;
-	String<TSize> flow;	
-	TSize valF = fordFulkersonAlgorithm(g, source, target, capMap, flow);
-
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	TEdgeIterator itEdge(g);
-	for(;!atEnd(itEdge);goNext(itEdge)) {
-		if (getProperty(flow, getValue(itEdge)) == 1) {
-			TVertexDescriptor sV = sourceVertex(itEdge);
-			TVertexDescriptor tV = targetVertex(itEdge);
-			if ((sV != source) && (tV != target)) appendValue(edges, TEdges(sV, tV));
-		}
-	}
-	removeVertex(g, source);
-	removeVertex(g, target);
-
-	return valF;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TVertexMap, typename TWeightMap, typename TEdges>
-inline typename Value<TWeightMap>::Type
-_weightedBipartiteMatching(Graph<TSpec>& g,
-							  TVertexMap& vertMap,
-							  TWeightMap& weightMap,
-							  String<TEdges>& edges)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIter;
-	typedef typename Value<TWeightMap>::Type TCargo;
-
-	TSize numVert = numVertices(g);
-	TCargo maxEdgeVal = 0;
-
-	// Find an initial labeling
-	String<TCargo> label;
-	resizeVertexMap(g, label);
-	TVertexIterator itV(g);
-	for(;!atEnd(itV); goNext(itV)) {
-		if (getProperty(vertMap, value(itV)) == true) value(label, value(itV)) = 0;
-		else {
-			TCargo maxCargo = 0;
-			for(TOutEdgeIter itOutE(g, value(itV));!atEnd(itOutE); goNext(itOutE)) {
-				if (property(weightMap, (value(itOutE))) > maxCargo) maxCargo = property(weightMap, (value(itOutE)));
-			}
-			value(label, value(itV)) = maxCargo;
-			if (maxCargo > maxEdgeVal) maxEdgeVal = maxCargo;
-		}
-	}
-
-	// Generate Equality Graph
-	typedef Graph<Directed<void> > TEqualityGraph;
-	typedef typename EdgeType<TEqualityGraph>::Type TEdgeStump;
-	TEqualityGraph equalGraph;
-	resize(equalGraph.data_vertex, length(_getVertexString(g)), (TEdgeStump*) 0);
-	equalGraph.data_id_managerV = g.data_id_managerV;
-	TEdgeIterator itE(g);
-	for(;!atEnd(itE); goNext(itE)) {
-		if (property(weightMap, (value(itE))) == property(label, sourceVertex(itE)) + property(label, targetVertex(itE))) {
-			// For the Ford-Fulkerson all edges must go from true to false
-			if (getProperty(vertMap, sourceVertex(itE)) == true) addEdge(equalGraph, targetVertex(itE), sourceVertex(itE));
-			else addEdge(equalGraph, sourceVertex(itE), targetVertex(itE));
-		}
-	}
-
-	// Find an initial bipartite matching
-	clear(edges);
-	TSize matchSize = bipartiteMatching(equalGraph, vertMap, edges);
-	
-
-	String<bool> free;
-	String<TVertexDescriptor> reverseMatchMap;
-	typedef std::set<TVertexDescriptor> TVertexSet;
-	TVertexSet setS;
-	TVertexSet setNeighborS;
-	TVertexSet setT;
-	while (matchSize != numVert / 2) {
-
-		// Initialization
-		setS.clear();
-		setT.clear();
-		setNeighborS.clear();
-		clear(free);
-		resize(free, getIdUpperBound(_getVertexIdManager(g)), true);
-		clear(reverseMatchMap);
-		resizeVertexMap(g, reverseMatchMap);
-		
-		// Find free vertex
-		typedef typename Iterator<String<TEdges> >::Type TStringEdgeIter;
-		TStringEdgeIter itSE = begin(edges);
-		TStringEdgeIter itSEEnd = end(edges);
-		for(;itSE != itSEEnd; goNext(itSE)) {
-			value(free, (value(itSE)).i1) = false;
-			value(free, (value(itSE)).i2) = false;
-			value(reverseMatchMap, (value(itSE)).i2) = (value(itSE)).i1;
-		}
-		TVertexIterator itVert(g);
-		for(;!atEnd(itVert); goNext(itVert)) {
-			if ((getProperty(vertMap, value(itVert)) == false) &&
-				(value(free, value(itVert)) == true)) {
-					setS.insert(value(itVert));
-					typedef typename Iterator<TEqualityGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-					TOutEdgeIterator itOE(equalGraph, value(itVert));
-					for(;!atEnd(itOE); ++itOE) {
-						setNeighborS.insert(targetVertex(itOE));
-						if (value(free, targetVertex(itOE)) == true) setT.insert(targetVertex(itOE));
-					}
-					break;
-			}
-		}
-
-		// Find matched vertices
-		typedef typename TVertexSet::iterator TVertexSetIter;
-		while (setNeighborS != setT) {
-			TVertexSet diffSet;
-			TVertexSetIter itT = setT.begin();
-			TVertexSetIter itTEnd = setT.end();
-			TVertexSetIter itN = setNeighborS.begin();
-			TVertexSetIter itNEnd = setNeighborS.end();
-			while (itN != itNEnd) {
-				if ((itT == itTEnd) || (*itN < *itT)) { diffSet.insert(*itN); ++itN; }
-				else { ++itN; ++itT; }
-			}
-			TVertexDescriptor y = *(diffSet.begin());
-			setT.insert(y);
-			setS.insert(value(reverseMatchMap, y));
-			typedef typename Iterator<TEqualityGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-			TOutEdgeIterator itOE(equalGraph, value(reverseMatchMap, y));
-			for(;!atEnd(itOE); ++itOE) {
-				setNeighborS.insert(targetVertex(itOE));
-				if (value(free, targetVertex(itOE)) == true) setT.insert(targetVertex(itOE));
-			}
-		}
-		clear(reverseMatchMap);
-	
-		// Update Labels
-		TCargo minVal = maxEdgeVal;
-		TEdgeIterator itEdge(g);
-		for(;!atEnd(itEdge); goNext(itEdge)) {
-			TVertexDescriptor sV = sourceVertex(itEdge);
-			TVertexDescriptor tV = targetVertex(itEdge);
-			if (property(vertMap, sV) == true) {	TVertexDescriptor tmp = sV;	sV = tV; tV = tmp;	}
-			if ((setS.find(sV) != setS.end()) &&
-				(setT.find(tV) == setT.end())) {
-				TCargo thisVal = getProperty(label, sV) + getProperty(label, tV) - getProperty(weightMap, (value(itEdge)));
-				if (thisVal < minVal) minVal = thisVal;
-			}
-		}
-		TVertexIterator myVertexIt(g);
-		for(;!atEnd(myVertexIt); goNext(myVertexIt)) {
-			if (setS.find(value(myVertexIt)) != setS.end()) value(label, value(myVertexIt)) -= minVal;
-			else if (setT.find(value(myVertexIt)) != setT.end()) value(label, value(myVertexIt)) += minVal;
-		}
-
-		// Build new equal graph
-		clear(equalGraph);
-		resize(equalGraph.data_vertex, length(_getVertexString(g)), (TEdgeStump*) 0);
-		equalGraph.data_id_managerV = g.data_id_managerV;
-		TEdgeIterator itE(g);
-		for(;!atEnd(itE); goNext(itE)) {
-			if (property(weightMap, (value(itE))) == property(label, sourceVertex(itE)) + property(label, targetVertex(itE))) {
-				if (property(vertMap, sourceVertex(itE)) == true) addEdge(equalGraph, targetVertex(itE), sourceVertex(itE));
-				else addEdge(equalGraph, sourceVertex(itE), targetVertex(itE));
-			}
-		}
-
-		// Create a new matching
-		clear(edges);
-		matchSize = bipartiteMatching(equalGraph, vertMap, edges);
-	}
-
-	typedef typename Iterator<String<TEdges> >::Type TStringEdgeIter;
-	TStringEdgeIter itSE = begin(edges);
-	TStringEdgeIter itSEEnd = end(edges);
-	TCargo sumWeight = 0;
-	for(;itSE != itSEEnd; goNext(itSE)) sumWeight += property(weightMap, findEdge(g, (value(itSE)).i1, (value(itSE)).i2));
-
-	return sumWeight;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TVertexMap, typename TWeightMap, typename TEdges>
-inline typename Value<TWeightMap>::Type
-weightedBipartiteMatching(Graph<TSpec>& g,
-							TVertexMap& vertMap,
-							TWeightMap& weightMap,
-							String<TEdges>& edges)
-{
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Value<TWeightMap>::Type TCargo;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-
-	// Collect the two vertex sets, set1 is marked with false, set2 with true
-	typedef String<TVertexDescriptor> TVertexSet;
-	typedef typename Iterator<TVertexSet>::Type TVertexSetIter;
-	TVertexSet set1;
-	TVertexSet set2;
-	TVertexIterator itV(g);
-	for(;!atEnd(itV); goNext(itV)) {
-		if (property(vertMap, value(itV)) == false) appendValue(set1, value(itV));
-		else appendValue(set2, value(itV));
-	}
-	bool setIdentifier = true;		// Indicates what set needs more vertices
-	TSize maxN = length(set1);
-	if (maxN < length(set2)) {	maxN = length(set2); setIdentifier = false; }
-
-
-	// Copy the original graph
-	TGraph fullGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	resize(fullGraph.data_vertex, length(_getVertexString(g)), (TEdgeStump*) 0);
-	fullGraph.data_id_managerV = g.data_id_managerV;
-	TVertexMap myVertexMap = vertMap;
-	resize(myVertexMap, maxN + maxN, setIdentifier);
-	String<TCargo> myWeightMap;
-	resize(myWeightMap, maxN * maxN, 0);
-	TEdgeIterator itE(g);
-	typedef std::pair<TVertexDescriptor, TVertexDescriptor> TEdge;
-	typedef std::set<TEdge> TEdgeSet;
-	TEdgeSet edgeSet;
-	for(;!atEnd(itE); goNext(itE)) {
-		TVertexDescriptor sV = sourceVertex(itE);
-		TVertexDescriptor tV = targetVertex(itE);
-		TEdgeDescriptor e = addEdge(fullGraph, sV, tV);
-		if (sV < tV) edgeSet.insert(std::make_pair(sV, tV));
-		else edgeSet.insert(std::make_pair(tV, sV));
-		property(myWeightMap, e) = getProperty(weightMap, (value(itE)));
-	}
-
-	// Build a full graph
-	if (setIdentifier == false) {
-		TSize inc = maxN - length(set1);
-		for(TSize i = 0; i< inc; ++i) appendValue(set1, addVertex(fullGraph));
-	} else {
-		TSize inc = maxN - length(set2);
-		for(TSize i = 0; i<inc ; ++i) appendValue(set2, addVertex(fullGraph));
-	}
-	TVertexSetIter set1It = begin(set1);
-	TVertexSetIter set1ItEnd = end(set1);
-	for(;set1It != set1ItEnd; ++set1It) {
-		TVertexSetIter set2It = begin(set2);
-		TVertexSetIter set2ItEnd = end(set2);
-		for(;set2It != set2ItEnd; ++set2It) {
-			TVertexDescriptor sV = value(set1It);
-			TVertexDescriptor tV = value(set2It);
-			if (sV > tV) { TVertexDescriptor tmp = sV; sV = tV; tV = tmp; }
-			if (edgeSet.find(std::make_pair(sV, tV)) == edgeSet.end()) addEdge(fullGraph, sV, tV);
-		}
-	}
-
-	// Find a maximum weight matching
-	String<TEdges> pseudo_edges;
-	TCargo weight = _weightedBipartiteMatching(fullGraph, myVertexMap, myWeightMap, pseudo_edges);
-
-	// Copy the relevant edges
-	clear(edges);
-	typedef typename Iterator<String<TEdges> >::Type TEdgeIter;
-	TEdgeIter eIt = begin(pseudo_edges);
-	TEdgeIter eItEnd = end(pseudo_edges);
-	for(;eIt != eItEnd; ++eIt) {
-		TVertexDescriptor sV = (value(eIt)).i1;
-		TVertexDescriptor tV = (value(eIt)).i2;
-		if (sV > tV) { TVertexDescriptor tmp = sV; sV = tV; tV = tmp; }
-		if (edgeSet.find(std::make_pair(sV, tV)) != edgeSet.end()) appendValue(edges, value(eIt));
-	}
-	return weight;
-}
-
-
-}// namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/graph_algorithms/graph_algorithm_heap_tree.h b/seqan/graph_algorithms/graph_algorithm_heap_tree.h
index 6a3ba38..f32ac27 100644
--- a/seqan/graph_algorithms/graph_algorithm_heap_tree.h
+++ b/seqan/graph_algorithms/graph_algorithm_heap_tree.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,11 +43,11 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec = Default>
-struct KeylessHeap;	
+struct KeylessHeap;
 
 
 template<typename TSpec = Default>
-struct KeyedHeap;	
+struct KeyedHeap;
 
 
 //////////////////////////////////////////////////////////////////////////////
@@ -62,48 +62,48 @@ class HeapTree;
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec>
-class HeapTree<TValue, TPredicate, KeylessHeap<TSpec> > 
+class HeapTree<TValue, TPredicate, KeylessHeap<TSpec> >
 {
-public:	
-	typedef typename Size<HeapTree>::Type TSize;
-	String<TValue> data_value;
-	TSize data_heap_size;
-	TPredicate data_predicate;
+public:
+    typedef typename Size<HeapTree>::Type TSize;
+    String<TValue> data_value;
+    TSize data_heap_size;
+    TPredicate data_predicate;
 
-	
 
-	//////////////////////////////////////////////////////////////////////////////
 
-	HeapTree() : data_heap_size(0) {
-		SEQAN_CHECKPOINT
-	}
+    //////////////////////////////////////////////////////////////////////////////
 
-	//////////////////////////////////////////////////////////////////////////////
+    HeapTree() : data_heap_size(0) {
+        SEQAN_CHECKPOINT
+    }
 
-	HeapTree(HeapTree const& _other) {
-		SEQAN_CHECKPOINT
-		data_value = _other.data_value;
-		data_heap_size = _other.data_heap_size;
-		data_predicate = _other.data_predicate;
-	}
+    //////////////////////////////////////////////////////////////////////////////
 
-	//////////////////////////////////////////////////////////////////////////////
+    HeapTree(HeapTree const& _other) {
+        SEQAN_CHECKPOINT
+        data_value = _other.data_value;
+        data_heap_size = _other.data_heap_size;
+        data_predicate = _other.data_predicate;
+    }
 
-	~HeapTree() {
-		SEQAN_CHECKPOINT
-	}
+    //////////////////////////////////////////////////////////////////////////////
 
+    ~HeapTree() {
+        SEQAN_CHECKPOINT
+    }
 
-	//////////////////////////////////////////////////////////////////////////////
 
-	HeapTree& operator=(HeapTree const& _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_value = _other.data_value;
-		data_heap_size = _other.data_heap_size;
-		data_predicate = _other.data_predicate;
-		return *this;
-	}
+    //////////////////////////////////////////////////////////////////////////////
+
+    HeapTree& operator=(HeapTree const& _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_value = _other.data_value;
+        data_heap_size = _other.data_heap_size;
+        data_predicate = _other.data_predicate;
+        return *this;
+    }
 };
 
 
@@ -112,7 +112,7 @@ class HeapTree<TValue, TPredicate, KeylessHeap<TSpec> >
 template<typename TValue, typename TPredicate, typename TSpec>
 struct Value<HeapTree<TValue, TPredicate, TSpec> >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -120,7 +120,7 @@ struct Value<HeapTree<TValue, TPredicate, TSpec> >
 template<typename TValue, typename TPredicate, typename TSpec>
 struct Value<HeapTree<TValue, TPredicate, TSpec> const>
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 
 
@@ -128,34 +128,34 @@ struct Value<HeapTree<TValue, TPredicate, TSpec> const>
 
 template<typename TSize>
 inline TSize _left(TSize i) {
-	SEQAN_CHECKPOINT
-	return i << 1;
+    SEQAN_CHECKPOINT
+    return i << 1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSize>
 inline TSize _right(TSize i) {
-	SEQAN_CHECKPOINT
-	return ((i << 1) + 1);
+    SEQAN_CHECKPOINT
+    return ((i << 1) + 1);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSize>
 inline TSize _parent(TSize i) {
-	SEQAN_CHECKPOINT
-	return (i >> 1);
+    SEQAN_CHECKPOINT
+    return (i >> 1);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec>
-inline bool 
-empty(HeapTree<TValue, TPredicate, TSpec> const& mHeap) 
+inline bool
+empty(HeapTree<TValue, TPredicate, TSpec> const& mHeap)
 {
-	SEQAN_CHECKPOINT
-	return (mHeap.data_heap_size == 0); 
+    SEQAN_CHECKPOINT
+    return (mHeap.data_heap_size == 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -163,89 +163,89 @@ empty(HeapTree<TValue, TPredicate, TSpec> const& mHeap)
 template<typename TValue, typename TPredicate, typename TSpec>
 inline typename Size<HeapTree<TValue, TPredicate, TSpec> >::Type
 length(HeapTree<TValue, TPredicate, TSpec> const& mHeap)
-{ 
-	SEQAN_CHECKPOINT
-	return mHeap.data_heap_size;
+{
+    SEQAN_CHECKPOINT
+    return mHeap.data_heap_size;
 }
 
 /////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec>
-inline TValue 
-heapRoot(HeapTree<TValue, TPredicate, TSpec>& mHeap) 
+inline TValue
+heapRoot(HeapTree<TValue, TPredicate, TSpec>& mHeap)
 {
-	return value(mHeap.data_value, 1);
+    return value(mHeap.data_value, 1);
 }
 
 /////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec>
-inline TValue 
-heapRoot(HeapTree<TValue, TPredicate, TSpec> const& mHeap) 
+inline TValue
+heapRoot(HeapTree<TValue, TPredicate, TSpec> const& mHeap)
 {
-	return value(mHeap.data_value, 1);
+    return value(mHeap.data_value, 1);
 }
 
 /////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec, typename TObject>
-inline void 
+inline void
 heapInsert(HeapTree<TValue, TPredicate, TSpec>& mHeap,
-		   TObject object) 
+           TObject object)
 {
-	SEQAN_CHECKPOINT
-	typedef HeapTree<TValue, TPredicate, TSpec> THeapTree;
-	typedef typename Size<THeapTree>::Type TSize;
-	
-	++mHeap.data_heap_size;
-	resize(mHeap.data_value, mHeap.data_heap_size + 1, Generous() );
-	TSize i = mHeap.data_heap_size;
-	_insertObject(mHeap, i, object);
-	while ((i>1) && (!(mHeap.data_predicate(value(mHeap.data_value, _parent(i)), value(mHeap.data_value, i))))) {
-		_swapObjects(mHeap, i, _parent(i));
-		i = _parent(i);
-	}
+    SEQAN_CHECKPOINT
+    typedef HeapTree<TValue, TPredicate, TSpec> THeapTree;
+    typedef typename Size<THeapTree>::Type TSize;
+
+    ++mHeap.data_heap_size;
+    resize(mHeap.data_value, mHeap.data_heap_size + 1, Generous() );
+    TSize i = mHeap.data_heap_size;
+    _insertObject(mHeap, i, object);
+    while ((i>1) && (!(mHeap.data_predicate(value(mHeap.data_value, _parent(i)), value(mHeap.data_value, i))))) {
+        _swapObjects(mHeap, i, _parent(i));
+        i = _parent(i);
+    }
 }
 
 /////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec, typename TSize>
-inline void 
+inline void
 heapify(HeapTree<TValue, TPredicate, TSpec>& mHeap,
-		TSize i) 
+        TSize i)
 {
-	SEQAN_CHECKPOINT
-	TSize l = _left(i);
-	TSize r = _right(i);
-	TSize largest = i;
-	if ((l <= (TSize) mHeap.data_heap_size) && (mHeap.data_predicate(value(mHeap.data_value, l), value(mHeap.data_value, i)))) largest = l;
-	if ((r <= (TSize) mHeap.data_heap_size) && (mHeap.data_predicate(value(mHeap.data_value, r), value(mHeap.data_value, largest)))) largest = r;
-	if (largest != i) {
-		_swapObjects(mHeap, i, largest);
-		heapify(mHeap, largest);
-	}
+    SEQAN_CHECKPOINT
+    TSize l = _left(i);
+    TSize r = _right(i);
+    TSize largest = i;
+    if ((l <= (TSize) mHeap.data_heap_size) && (mHeap.data_predicate(value(mHeap.data_value, l), value(mHeap.data_value, i)))) largest = l;
+    if ((r <= (TSize) mHeap.data_heap_size) && (mHeap.data_predicate(value(mHeap.data_value, r), value(mHeap.data_value, largest)))) largest = r;
+    if (largest != i) {
+        _swapObjects(mHeap, i, largest);
+        heapify(mHeap, largest);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec, typename TITBegin, typename TITEnd>
-inline void 
+inline void
 buildHeap(HeapTree<TValue, TPredicate, TSpec>& mHeap,
-		  TITBegin itBeg,
-		  TITEnd itEnd) 
+          TITBegin itBeg,
+          TITEnd itEnd)
 {
-	SEQAN_CHECKPOINT
-	typedef HeapTree<TValue, TPredicate, TSpec> THeapTree;
-	typedef typename Size<THeapTree>::Type TSize;
-
-	// Leave out the first element
-	resize(mHeap.data_value, (itEnd - itBeg) + 1);
-	value(mHeap.data_value, 0) = TValue();
-	mHeap.data_heap_size = 0;
-	for(;itBeg != itEnd; goNext(itBeg), ++mHeap.data_heap_size) {
-		_insertObject(mHeap, mHeap.data_heap_size + 1, value(itBeg));
-	}
-	for(TSize i = (mHeap.data_heap_size / 2); i>0; --i) heapify(mHeap, i);
+    SEQAN_CHECKPOINT
+    typedef HeapTree<TValue, TPredicate, TSpec> THeapTree;
+    typedef typename Size<THeapTree>::Type TSize;
+
+    // Leave out the first element
+    resize(mHeap.data_value, (itEnd - itBeg) + 1);
+    value(mHeap.data_value, 0) = TValue();
+    mHeap.data_heap_size = 0;
+    for(;itBeg != itEnd; goNext(itBeg), ++mHeap.data_heap_size) {
+        _insertObject(mHeap, mHeap.data_heap_size + 1, value(itBeg));
+    }
+    for(TSize i = (mHeap.data_heap_size / 2); i>0; --i) heapify(mHeap, i);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -253,13 +253,13 @@ buildHeap(HeapTree<TValue, TPredicate, TSpec>& mHeap,
 template<typename TValue, typename TPredicate, typename TSpec, typename TIndex1, typename TIndex2>
 inline void
 _swapObjects(HeapTree<TValue, TPredicate, KeylessHeap<TSpec> >& mHeap,
-			 TIndex1 i,
-			 TIndex2 j) 
+             TIndex1 i,
+             TIndex2 j)
 {
-	SEQAN_CHECKPOINT
-	TValue tmp = value(mHeap.data_value, i);
-	value(mHeap.data_value, i) = value(mHeap.data_value, j);
-	value(mHeap.data_value, j) = tmp;
+    SEQAN_CHECKPOINT
+    TValue tmp = value(mHeap.data_value, i);
+    value(mHeap.data_value, i) = value(mHeap.data_value, j);
+    value(mHeap.data_value, j) = tmp;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -267,71 +267,71 @@ _swapObjects(HeapTree<TValue, TPredicate, KeylessHeap<TSpec> >& mHeap,
 template<typename TValue, typename TPredicate, typename TSpec, typename TIndex, typename TObject>
 inline void
 _insertObject(HeapTree<TValue, TPredicate, KeylessHeap<TSpec> >& mHeap,
-			  TIndex i,
-			  TObject obj)
+              TIndex i,
+              TObject obj)
 {
-	SEQAN_CHECKPOINT
-	value(mHeap.data_value, i) = obj;
+    SEQAN_CHECKPOINT
+    value(mHeap.data_value, i) = obj;
 }
-		
+
 /////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec>
-inline TValue 
-heapExtractRoot(HeapTree<TValue, TPredicate, KeylessHeap<TSpec> >& mHeap) 
+inline TValue
+heapExtractRoot(HeapTree<TValue, TPredicate, KeylessHeap<TSpec> >& mHeap)
 {
-	SEQAN_CHECKPOINT
-	TValue rootVal = value(mHeap.data_value, 1);
-	value(mHeap.data_value, 1) = value(mHeap.data_value, mHeap.data_heap_size);
-	--mHeap.data_heap_size;
-	heapify(mHeap, 1);
-	return rootVal;
+    SEQAN_CHECKPOINT
+    TValue rootVal = value(mHeap.data_value, 1);
+    value(mHeap.data_value, 1) = value(mHeap.data_value, mHeap.data_heap_size);
+    --mHeap.data_heap_size;
+    heapify(mHeap, 1);
+    return rootVal;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TPredicate, typename TSpec>
-inline void 
+inline void
 clear(HeapTree<TValue, TPredicate, TSpec>& mHeap)
 {
-	clear(mHeap.data_value); 
-	mHeap.data_heap_size = 0;
+    clear(mHeap.data_value);
+    mHeap.data_heap_size = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TITBegin, typename TITEnd, typename TPredicate>
-inline void 
+inline void
 heapSort(TITBegin itBeg,
-		 TITEnd itEnd,
-		 TPredicate)
+         TITEnd itEnd,
+         TPredicate)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TITBegin>::Type TValue;
-	typedef typename Size<TITBegin>::Type TSize;
-	HeapTree<TValue, TPredicate> mHeap;
-	TITBegin itFill = itBeg;
-	buildHeap(mHeap, itBeg, itEnd);
-	for(TSize i = mHeap.data_heap_size; i>1; --i) {
-		value(itFill) = value(mHeap.data_value, 1);
-		goNext(itFill);
-		value(mHeap.data_value, 1) = value(mHeap.data_value, i);
-		--mHeap.data_heap_size;
-		heapify(mHeap, 1);
-	}
-	value(itFill) = value(mHeap.data_value, 2);
+    SEQAN_CHECKPOINT
+    typedef typename Value<TITBegin>::Type TValue;
+    typedef typename Size<TITBegin>::Type TSize;
+    HeapTree<TValue, TPredicate> mHeap;
+    TITBegin itFill = itBeg;
+    buildHeap(mHeap, itBeg, itEnd);
+    for(TSize i = mHeap.data_heap_size; i>1; --i) {
+        value(itFill) = value(mHeap.data_value, 1);
+        goNext(itFill);
+        value(mHeap.data_value, 1) = value(mHeap.data_value, i);
+        --mHeap.data_heap_size;
+        heapify(mHeap, 1);
+    }
+    value(itFill) = value(mHeap.data_value, 2);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TITBegin, typename TITEnd>
-inline void 
+inline void
 heapSort(TITBegin itBeg,
-		 TITEnd itEnd)
+         TITEnd itEnd)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TITBegin>::Type TValue;
-	heapSort(itBeg, itEnd, std::less<TValue>());
+    SEQAN_CHECKPOINT
+    typedef typename Value<TITBegin>::Type TValue;
+    heapSort(itBeg, itEnd, std::less<TValue>());
 }
 
 
@@ -339,13 +339,13 @@ heapSort(TITBegin itBeg,
 
 template<typename TKey, typename TValue, typename TPredicate>
 struct LessPairI2WithFunctor :
-	public ::std::unary_function<Pair<TKey, TValue>, bool>
+    public std::unary_function<Pair<TKey, TValue>, bool>
 {
-	inline bool 
-	operator() (Pair<TKey, TValue> const& a1, Pair<TKey, TValue> const& a2) {
-		TPredicate private_Predicate;
-		return private_Predicate(a1.i2, a2.i2);
-	}
+    inline bool
+    operator() (Pair<TKey, TValue> const& a1, Pair<TKey, TValue> const& a2) {
+        TPredicate private_Predicate;
+        return private_Predicate(a1.i2, a2.i2);
+    }
 };
 
 
@@ -354,47 +354,47 @@ struct LessPairI2WithFunctor :
 template<typename TKey, typename TValue, typename TPredicate, typename TSpec>
 class HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >
 {
-public:	
-	typedef typename Size<HeapTree>::Type TSize;
-	String<Pair<TKey, TValue> > data_value;
-	std::map<TKey, TSize> data_map;
-	TSize data_heap_size;
-	LessPairI2WithFunctor<TKey, TValue, TPredicate> data_predicate;
-	
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	HeapTree() : data_heap_size(0) {
-		SEQAN_CHECKPOINT
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	HeapTree(HeapTree const& _other) {
-		SEQAN_CHECKPOINT
-		data_value = _other.data_value;
-		data_map = _other.data_map;
-		data_heap_size = _other.data_heap_size;
-		data_predicate = _other.data_predicate;
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	~HeapTree() {
-		SEQAN_CHECKPOINT
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	HeapTree& operator=(HeapTree const& _other) {
-		SEQAN_CHECKPOINT
-		data_value = _other.data_value;
-		data_map = _other.data_map;
-		data_heap_size = _other.data_heap_size;
-		data_predicate = _other.data_predicate;
-		return *this;
-	}
+public:
+    typedef typename Size<HeapTree>::Type TSize;
+    String<Pair<TKey, TValue> > data_value;
+    std::map<TKey, TSize> data_map;
+    TSize data_heap_size;
+    LessPairI2WithFunctor<TKey, TValue, TPredicate> data_predicate;
+
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    HeapTree() : data_heap_size(0) {
+        SEQAN_CHECKPOINT
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    HeapTree(HeapTree const& _other) {
+        SEQAN_CHECKPOINT
+        data_value = _other.data_value;
+        data_map = _other.data_map;
+        data_heap_size = _other.data_heap_size;
+        data_predicate = _other.data_predicate;
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    ~HeapTree() {
+        SEQAN_CHECKPOINT
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    HeapTree& operator=(HeapTree const& _other) {
+        SEQAN_CHECKPOINT
+        data_value = _other.data_value;
+        data_map = _other.data_map;
+        data_heap_size = _other.data_heap_size;
+        data_predicate = _other.data_predicate;
+        return *this;
+    }
 };
 
 
@@ -403,25 +403,25 @@ class HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >
 template<typename TKey, typename TValue, typename TPredicate, typename TSpec, typename TIndex1, typename TIndex2>
 inline void
 _swapObjects(HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >& mHeap,
-			 TIndex1 i,
-			 TIndex2 j) 
+             TIndex1 i,
+             TIndex2 j)
 {
-	SEQAN_CHECKPOINT
-	typedef HeapTree<Pair<TKey, TValue>, TPredicate, TSpec> THeapTree;
-	typedef typename Size<THeapTree>::Type TSize;
-	typedef std::map<TKey, TSize> TMap;
-	typedef typename TMap::iterator TMapIter;
-	// Swap keys
-	TMapIter pos1 = mHeap.data_map.find(value(mHeap.data_value, i).i1);
-	TMapIter pos2 = mHeap.data_map.find(value(mHeap.data_value, j).i1);
-	TSize tmpVal = pos1->second;
-	pos1->second = pos2->second;
-	pos2->second = tmpVal;
-
-	// Swap object in heap tree
-	Pair<TKey, TValue> tmp = value(mHeap.data_value, i);
-	value(mHeap.data_value, i) = value(mHeap.data_value, j);
-	value(mHeap.data_value, j) = tmp;
+    SEQAN_CHECKPOINT
+    typedef HeapTree<Pair<TKey, TValue>, TPredicate, TSpec> THeapTree;
+    typedef typename Size<THeapTree>::Type TSize;
+    typedef std::map<TKey, TSize> TMap;
+    typedef typename TMap::iterator TMapIter;
+    // Swap keys
+    TMapIter pos1 = mHeap.data_map.find(value(mHeap.data_value, i).i1);
+    TMapIter pos2 = mHeap.data_map.find(value(mHeap.data_value, j).i1);
+    TSize tmpVal = pos1->second;
+    pos1->second = pos2->second;
+    pos2->second = tmpVal;
+
+    // Swap object in heap tree
+    Pair<TKey, TValue> tmp = value(mHeap.data_value, i);
+    value(mHeap.data_value, i) = value(mHeap.data_value, j);
+    value(mHeap.data_value, j) = tmp;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -429,84 +429,84 @@ _swapObjects(HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >& mHeap,
 template<typename TKey, typename TValue, typename TPredicate, typename TSpec, typename TIndex, typename TObject>
 inline void
 _insertObject(HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >& mHeap,
-			  TIndex i,
-			  TObject obj)
+              TIndex i,
+              TObject obj)
 {
-	SEQAN_CHECKPOINT
-	typedef HeapTree<Pair<TKey, TValue>, TPredicate, TSpec> THeapTree;
-	typedef typename Size<THeapTree>::Type TSize;
-	value(mHeap.data_value, i) = obj;
-	if (!mHeap.data_map.insert(std::pair<TKey, TSize>(obj.i1, i)).second) {
-		mHeap.data_map.find(obj.i1)->second = i;
-	};
+    SEQAN_CHECKPOINT
+    typedef HeapTree<Pair<TKey, TValue>, TPredicate, TSpec> THeapTree;
+    typedef typename Size<THeapTree>::Type TSize;
+    value(mHeap.data_value, i) = obj;
+    if (!mHeap.data_map.insert(std::pair<TKey, TSize>(obj.i1, i)).second) {
+        mHeap.data_map.find(obj.i1)->second = i;
+    };
 }
 
 /////////////////////////////////////////////////////////////////////////////
 
 template<typename TKey, typename TValue, typename TPredicate, typename TSpec>
-inline Pair<TKey, TValue> 
-heapExtractRoot(HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >& mHeap) 
+inline Pair<TKey, TValue>
+heapExtractRoot(HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >& mHeap)
 {
-	SEQAN_CHECKPOINT
-	Pair<TKey, TValue> rootVal = value(mHeap.data_value, 1);
-	mHeap.data_map.erase(mHeap.data_map.find(rootVal.i1));
-	if (mHeap.data_heap_size != 1) {
-		value(mHeap.data_value, 1) = value(mHeap.data_value, mHeap.data_heap_size);
-		mHeap.data_map.find(value(mHeap.data_value, 1).i1)->second = 1;
-	}
-	--mHeap.data_heap_size;
-	heapify(mHeap, 1);
-	return rootVal;
+    SEQAN_CHECKPOINT
+    Pair<TKey, TValue> rootVal = value(mHeap.data_value, 1);
+    mHeap.data_map.erase(mHeap.data_map.find(rootVal.i1));
+    if (mHeap.data_heap_size != 1) {
+        value(mHeap.data_value, 1) = value(mHeap.data_value, mHeap.data_heap_size);
+        mHeap.data_map.find(value(mHeap.data_value, 1).i1)->second = 1;
+    }
+    --mHeap.data_heap_size;
+    heapify(mHeap, 1);
+    return rootVal;
 }
 
 /////////////////////////////////////////////////////////////////////////////
 
 template<typename TKey, typename TValue, typename TPredicate, typename TSpec, typename TKey1, typename TValue2>
-inline void 
+inline void
 heapChangeValue(HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >& mHeap,
-				TKey1 key,
-				TValue2 val) 
+                TKey1 key,
+                TValue2 val)
 {
-	SEQAN_CHECKPOINT
-	typedef HeapTree<Pair<TKey, TValue>, TPredicate, TSpec> THeapTree;
-	typedef typename Size<THeapTree>::Type TSize;
-	TSize i = mHeap.data_map.find(key)->second;
-	Pair<TKey, TValue> obj = Pair<TKey, TValue>(key,val);
-	if (!(mHeap.data_predicate(obj, value(mHeap.data_value, i)))) {
-		_insertObject(mHeap, i, obj);
-		heapify(mHeap, i);
-	} else {
-		_insertObject(mHeap, i, obj);
-		while ((i>1) && (!mHeap.data_predicate(value(mHeap.data_value, _parent(i)), value(mHeap.data_value, i)))) {
-			_swapObjects(mHeap, i, _parent(i));
-			i = _parent(i);
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef HeapTree<Pair<TKey, TValue>, TPredicate, TSpec> THeapTree;
+    typedef typename Size<THeapTree>::Type TSize;
+    TSize i = mHeap.data_map.find(key)->second;
+    Pair<TKey, TValue> obj = Pair<TKey, TValue>(key,val);
+    if (!(mHeap.data_predicate(obj, value(mHeap.data_value, i)))) {
+        _insertObject(mHeap, i, obj);
+        heapify(mHeap, i);
+    } else {
+        _insertObject(mHeap, i, obj);
+        while ((i>1) && (!mHeap.data_predicate(value(mHeap.data_value, _parent(i)), value(mHeap.data_value, i)))) {
+            _swapObjects(mHeap, i, _parent(i));
+            i = _parent(i);
+        }
+    }
 }
 
 /////////////////////////////////////////////////////////////////////////////
 
 template<typename TKey, typename TValue, typename TPredicate, typename TSpec, typename TKey1>
-inline TValue 
+inline TValue
 heapGetValue(HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >& mHeap,
-			 TKey1 key) 
+             TKey1 key)
 {
-	SEQAN_CHECKPOINT
-	typedef HeapTree<Pair<TKey, TValue>, TPredicate, TSpec> THeapTree;
-	typedef typename Size<THeapTree>::Type TSize;
-	TSize i = mHeap.data_map.find(key)->second;
-	return value(mHeap.data_value, i).i2;
+    SEQAN_CHECKPOINT
+    typedef HeapTree<Pair<TKey, TValue>, TPredicate, TSpec> THeapTree;
+    typedef typename Size<THeapTree>::Type TSize;
+    TSize i = mHeap.data_map.find(key)->second;
+    return value(mHeap.data_value, i).i2;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TKey, typename TValue, typename TPredicate, typename TSpec>
-inline void 
+inline void
 clear(HeapTree<Pair<TKey, TValue>, TPredicate, KeyedHeap<TSpec> >& mHeap)
 {
-	clear(mHeap.data_value); 
-	mHeap.data_map.clear();
-	mHeap.data_heap_size = 0;
+    clear(mHeap.data_value);
+    mHeap.data_map.clear();
+    mHeap.data_heap_size = 0;
 }
 
 
diff --git a/seqan/graph_algorithms/graph_algorithm_hmm.h b/seqan/graph_algorithms/graph_algorithm_hmm.h
index 61adde3..412292c 100644
--- a/seqan/graph_algorithms/graph_algorithm_hmm.h
+++ b/seqan/graph_algorithms/graph_algorithm_hmm.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,15 +33,28 @@
 #ifndef SEQAN_HEADER_GRAPH_ALGORITHM_HMM_H
 #define SEQAN_HEADER_GRAPH_ALGORITHM_HMM_H
 
-namespace SEQAN_NAMESPACE_MAIN
+namespace seqan
 {
 
-//////////////////////////////////////////////////////////////////////////////
-// Basic HMM algorithms
-//////////////////////////////////////////////////////////////////////////////
+// ============================================================================
+// Forwards
+// ============================================================================
 
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
 
-//////////////////////////////////////////////////////////////////////////////
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function viterbiAlgorithm()
+// --------------------------------------------------------------------------
 
 /*!
  * @defgroup HmmAlgorithms HMM Algorithms
@@ -52,311 +65,289 @@ namespace SEQAN_NAMESPACE_MAIN
  * @fn HmmAlgorithms#viterbiAlgorithm
  * @headerfile <seqan/graph_algorithms.h>
  * @brief Implements the Viterbi algorithm for Hidden Markov Models.
- * 
- * @signature TProbability viterbiAlgorithm(hmm, seq, path);
- * 
+ *
+ * @signature TCargo viterbiAlgorithm(path, hmm, seq);
+ *
+ * @param[out] path The state path;  String of vertex descriptors.
  * @param[in]  hmm  The @link HmmGraph @endlink to use.
  * @param[in]  seq  Input sequence.
- * @param[out] path The state path;  String of vertex descriptors.
- * 
+ *
  * @return TCargo Probability of the path, the type parameter <tt>TCargo</tt> from type of <tt>hmm</tt>.
- * 
+ *
  * The Viterbi algorithm computes the most likely sequence of hidden states of the Hidden Markov Model <tt>hmm</tt>
  * given the sequence <tt>seq</tt> using dynamic programming.  The result is the most likely sequence of hidden states
  * and returned in <tt>path</tt>.
- * 
+ *
  * @section Remarks
- * 
+ *
  * See the <a href="http://wikipedia.org/wiki/Viterbi_algorithm"> Wikipedia article on the Viterbi algorithm</a> for an
  * introduction to the algorithm itself.
- * 
+ *
  * @see HmmAlgorithms#forwardAlgorithm
  * @see HmmAlgorithms#backwardAlgorithm
  */
-
-/**
-.Function.viterbiAlgorithm:
-..cat:Graph
-..summary:Implements the Viterbi algorithm
-..description:
-The Viterbi algorithm computes the most likely sequence of hidden states of the Hidden Markov Model $hmm$ given the sequence $seq$ using dynamic programming.
-The result is the most likely sequence of hidden states and returned in $path$.
-..signature:TProbability viterbiAlgorithm(hmm, seq, path);
-..param.hmm:In-parameter:Input HMM.
-...type:Spec.Hmm
-..param.seq:In-parameter:Input sequence.
-..param.path:Out-parameter:State path.
-..returns:Probability of the path, the type parameter $TCargo$ from type of $hmm$.
-..see:Function.forwardAlgorithm
-..see:Function.backwardAlgorithm
-..remarks:
-See the @http://en.wikipedia.org/wiki/Viterbi_algorithm|Wikipedia article on the Viterbi algorithm@ for an introduction to the algorithm itself.
-..include:seqan/graph_algorithms.h
-*/
 template<typename TAlphabet, typename TProbability, typename TSpec, typename TSequence, typename TPath>
 inline TProbability
-viterbiAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
-				 TSequence const& seq,
-				 TPath& path)
+viterbiAlgorithm(TPath & path,
+                 Graph<Hmm<TAlphabet, TProbability, TSpec> > const & hmm,
+                 TSequence const & seq)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-
-	// Initialization
-	String<TProbability> vMat;
-	String<TSize> traceback;
-	TSize numCols = length(seq) + 2;
-	TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
-	resize(vMat, numCols * numRows, 0.0);
-	resize(traceback, numCols * numRows);
-	value(vMat, getBeginState(hmm)) = 1.0;
-	TVertexDescriptor bState = getBeginState(hmm);
-	TVertexDescriptor eState = getEndState(hmm);
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-
-	// Distinct between silent states and real states
-	typedef String<TVertexDescriptor> TStateSet;
-	typedef typename Iterator<TStateSet>::Type TStateIter;
-	TStateSet silentStates;
-	TStateSet realStates;
-	TVertexIterator itVertex(hmm);
-	for(;!atEnd(itVertex);goNext(itVertex)) {
-		if (isSilent(hmm, value(itVertex))) { 
-			appendValue(silentStates, value(itVertex));
-		} else {
-			appendValue(realStates, value(itVertex));
-		}
-	}
-
-	// Initialization for silent states connected to the begin state
-	TStateIter itSilentStateEnd = end(silentStates);
-	for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-		if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
-		TProbability maxValue = 0.0;
-		TVertexDescriptor maxVertex = nilVertex;
-
-		for(TStateIter itBelow = begin(silentStates); itBelow != itSilentState; goNext(itBelow)) {
-			TProbability local = value(vMat, value(itBelow)) * getTransitionProbability(hmm, value(itBelow), value(itSilentState));
-			if (local > maxValue) {
-				maxValue = local;
-				maxVertex = value(itBelow);
-			}
-		}
-
-		// Set traceback vertex
-		if (maxVertex != nilVertex) {
-			value(vMat, value(itSilentState)) = maxValue;		
-			value(traceback, value(itSilentState)) = maxVertex;
-		}
-	}
-
-	// Recurrence
-	TSize len = length(seq);
-	for(TSize i=1; i<=len; ++i) {
-		// Iterate over real states
-		TStateIter itRealStateEnd = end(realStates);
-		for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-			// Find maximum
-			TProbability maxValue = 0.0;
-			TVertexDescriptor maxVertex = nilVertex;
-			TVertexIterator itMax(hmm);
-			for(;!atEnd(itMax);++itMax) {
-				TProbability local = value(vMat, (i-1) * numRows + value(itMax)) * getTransitionProbability(hmm, value(itMax), value(itRealState));
-				if (local > maxValue) {
-					maxValue = local;
-					maxVertex = *itMax;
-				}
-			}
-			// Set traceback vertex
-			if (maxVertex != nilVertex) {
-				value(vMat, i * numRows + value(itRealState)) = maxValue * getEmissionProbability(hmm, value(itRealState), value(seq, i-1));
-				value(traceback, i * numRows + value(itRealState)) = maxVertex;
-			}
-		}
-
-		// Iterate over silent states
-		for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-			if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
-			// Find maximum
-			TProbability maxValue = 0.0;
-			TVertexDescriptor maxVertex = nilVertex;
-	
-			// Iterate over real states
-			for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-				TProbability local = value(vMat, i * numRows + value(itRealState)) * getTransitionProbability(hmm, value(itRealState), value(itSilentState));
-				if (local > maxValue) {
-					maxValue = local;
-					maxVertex = value(itRealState);
-				}
-			}
-			// Iterate over silent states in increasing order
-			for(TStateIter itBelow = begin(silentStates); itBelow != itSilentState; goNext(itBelow)) {
-				TProbability local = value(vMat, i * numRows + value(itBelow)) * getTransitionProbability(hmm, value(itBelow), value(itSilentState));
-				if (local > maxValue) {
-					maxValue = local;
-					maxVertex = value(itBelow);
-				}
-			}
-			// Set traceback vertex
-			if (maxVertex != nilVertex) {
-				value(traceback, i * numRows + value(itSilentState)) = maxVertex;
-				value(vMat, i * numRows + value(itSilentState)) = maxValue;		
-			}
-		}
-	}
-
-	// Termination
-	TProbability maxValue = 0.0;
-	TVertexDescriptor maxVertex = 0;
-	TVertexIterator itMax(hmm);
-	for(;!atEnd(itMax);++itMax) {
-		TProbability local = value(vMat, len * numRows + *itMax) * getTransitionProbability(hmm, value(itMax), eState);
-		if (local > maxValue) {
-			maxValue = local;
-			maxVertex = value(itMax);
-		}
-	}
-	value(traceback, (len + 1) * numRows + eState) = maxVertex;
-	if (maxVertex != nilVertex) value(vMat, (len+1) * numRows + eState) = maxValue;
-
-	// Traceback
-	if (maxValue > 0.0) {
-		clear(path);
-		TVertexDescriptor oldState = eState;
-		appendValue(path, oldState);
-		for(TSize i = len + 1; i>=1; --i) {
-			do {
-				if ((!isSilent(hmm, oldState)) || (oldState == eState)) oldState = value(traceback, i * numRows + oldState);
-				else oldState = value(traceback, (i - 1) * numRows + oldState);
-				appendValue(path, oldState);
-			} while ((isSilent(hmm, oldState)) && (oldState != bState));
-		}
-		std::reverse(begin(path), end(path));
-	}
-	
-	//// Debug code
-	//for(TSize i = 0; i<numRows; ++i) {
-	//	for(TSize j=0; j<numCols; ++j) {
-	//		std::cout << value(vMat, j*numRows + i) << ',';
-	//		//std::cout << value(traceback, j*numRows + i) << ',';
-	//	}
-	//	std::cout << std::endl;
-	//}
-	//for(TSize i = 0; i<length(path); ++i) {
-	//	std::cout << path[i] << ',';
-	//}
-	//std::cout << std::endl;
-
-	return value(vMat, (len+1) * numRows + eState);
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+
+    // Initialization
+    String<TProbability> vMat;
+    String<TSize> traceback;
+    TSize numCols = length(seq) + 2;
+    TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
+    resize(vMat, numCols * numRows, 0.0);
+    resize(traceback, numCols * numRows);
+    value(vMat, getBeginState(hmm)) = 1.0;
+    TVertexDescriptor bState = getBeginState(hmm);
+    TVertexDescriptor eState = getEndState(hmm);
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+
+    // Distinct between silent states and real states
+    typedef String<TVertexDescriptor> TStateSet;
+    typedef typename Iterator<TStateSet>::Type TStateIter;
+    TStateSet silentStates;
+    TStateSet realStates;
+    TVertexIterator itVertex(hmm);
+    for(;!atEnd(itVertex);goNext(itVertex)) {
+        if (isSilent(hmm, value(itVertex))) {
+            appendValue(silentStates, value(itVertex));
+        } else {
+            appendValue(realStates, value(itVertex));
+        }
+    }
+
+    // Initialization for silent states connected to the begin state
+    TStateIter itSilentStateEnd = end(silentStates);
+    for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+        if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
+        TProbability maxValue = 0.0;
+        TVertexDescriptor maxVertex = nilVertex;
+
+        for(TStateIter itBelow = begin(silentStates); itBelow != itSilentState; goNext(itBelow)) {
+            TProbability local = value(vMat, value(itBelow)) * getTransitionProbability(hmm, value(itBelow), value(itSilentState));
+            if (local > maxValue) {
+                maxValue = local;
+                maxVertex = value(itBelow);
+            }
+        }
+
+        // Set traceback vertex
+        if (maxVertex != nilVertex) {
+            value(vMat, value(itSilentState)) = maxValue;
+            value(traceback, value(itSilentState)) = maxVertex;
+        }
+    }
+
+    // Recurrence
+    TSize len = length(seq);
+    for(TSize i=1; i<=len; ++i) {
+        // Iterate over real states
+        TStateIter itRealStateEnd = end(realStates);
+        for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+            // Find maximum
+            TProbability maxValue = 0.0;
+            TVertexDescriptor maxVertex = nilVertex;
+            TVertexIterator itMax(hmm);
+            for(;!atEnd(itMax);++itMax) {
+                TProbability local = value(vMat, (i-1) * numRows + value(itMax)) * getTransitionProbability(hmm, value(itMax), value(itRealState));
+                if (local > maxValue) {
+                    maxValue = local;
+                    maxVertex = *itMax;
+                }
+            }
+            // Set traceback vertex
+            if (maxVertex != nilVertex) {
+                value(vMat, i * numRows + value(itRealState)) = maxValue * getEmissionProbability(hmm, value(itRealState), value(seq, i-1));
+                value(traceback, i * numRows + value(itRealState)) = maxVertex;
+            }
+        }
+
+        // Iterate over silent states
+        for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+            if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
+            // Find maximum
+            TProbability maxValue = 0.0;
+            TVertexDescriptor maxVertex = nilVertex;
+
+            // Iterate over real states
+            for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+                TProbability local = value(vMat, i * numRows + value(itRealState)) * getTransitionProbability(hmm, value(itRealState), value(itSilentState));
+                if (local > maxValue) {
+                    maxValue = local;
+                    maxVertex = value(itRealState);
+                }
+            }
+            // Iterate over silent states in increasing order
+            for(TStateIter itBelow = begin(silentStates); itBelow != itSilentState; goNext(itBelow)) {
+                TProbability local = value(vMat, i * numRows + value(itBelow)) * getTransitionProbability(hmm, value(itBelow), value(itSilentState));
+                if (local > maxValue) {
+                    maxValue = local;
+                    maxVertex = value(itBelow);
+                }
+            }
+            // Set traceback vertex
+            if (maxVertex != nilVertex) {
+                value(traceback, i * numRows + value(itSilentState)) = maxVertex;
+                value(vMat, i * numRows + value(itSilentState)) = maxValue;
+            }
+        }
+    }
+
+    // Termination
+    TProbability maxValue = 0.0;
+    TVertexDescriptor maxVertex = 0;
+    TVertexIterator itMax(hmm);
+    for(;!atEnd(itMax);++itMax) {
+        TProbability local = value(vMat, len * numRows + *itMax) * getTransitionProbability(hmm, value(itMax), eState);
+        if (local > maxValue) {
+            maxValue = local;
+            maxVertex = value(itMax);
+        }
+    }
+    value(traceback, (len + 1) * numRows + eState) = maxVertex;
+    if (maxVertex != nilVertex) value(vMat, (len+1) * numRows + eState) = maxValue;
+
+    // Traceback
+    if (maxValue > 0.0) {
+        clear(path);
+        TVertexDescriptor oldState = eState;
+        appendValue(path, oldState);
+        for(TSize i = len + 1; i>=1; --i) {
+            do {
+                if ((!isSilent(hmm, oldState)) || (oldState == eState)) oldState = value(traceback, i * numRows + oldState);
+                else oldState = value(traceback, (i - 1) * numRows + oldState);
+                appendValue(path, oldState);
+            } while ((isSilent(hmm, oldState)) && (oldState != bState));
+        }
+        std::reverse(begin(path), end(path));
+    }
+
+    //// Debug code
+    //for(TSize i = 0; i<numRows; ++i) {
+    //  for(TSize j=0; j<numCols; ++j) {
+    //      std::cout << value(vMat, j*numRows + i) << ',';
+    //      //std::cout << value(traceback, j*numRows + i) << ',';
+    //  }
+    //  std::cout << std::endl;
+    //}
+    //for(TSize i = 0; i<length(path); ++i) {
+    //  std::cout << path[i] << ',';
+    //}
+    //std::cout << std::endl;
+
+    return value(vMat, (len+1) * numRows + eState);
 }
 
-
-//////////////////////////////////////////////////////////////////////////////
+// --------------------------------------------------------------------------
+// Function forwardAlgorithm()
+// --------------------------------------------------------------------------
 
 template<typename TAlphabet, typename TProbability, typename TSpec, typename TSequence, typename TForwardMatrix>
 inline TProbability
 _forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
-				   TSequence const& seq,
-				   TForwardMatrix& fMat)
+                   TSequence const& seq,
+                   TForwardMatrix& fMat)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-
-	// Initialization
-	TSize numCols = length(seq) + 2;
-	TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
-	resize(fMat, numCols * numRows, 0.0);
-	value(fMat, getBeginState(hmm)) = 1.0;
-	TVertexDescriptor bState = getBeginState(hmm);
-	TVertexDescriptor eState = getEndState(hmm);
-
-	// Distinct between silent states and real states
-	typedef String<TVertexDescriptor> TStateSet;
-	typedef typename Iterator<TStateSet>::Type TStateIter;
-	TStateSet silentStates;
-	TStateSet realStates;
-	TVertexIterator itVertex(hmm);
-	for(;!atEnd(itVertex);goNext(itVertex)) {
-		if (isSilent(hmm, value(itVertex))) { 
-			appendValue(silentStates, value(itVertex));
-		} else {
-			appendValue(realStates, value(itVertex));
-		}
-	}
-
-	// Initialization for silent states connected to the begin state
-	TStateIter itSilentStateEnd = end(silentStates);
-	for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-		if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
-		TProbability sumValue = 0.0;
-		for(TStateIter itBelow = begin(silentStates); itBelow != itSilentState; goNext(itBelow)) {
-			sumValue += value(fMat, value(itBelow)) * getTransitionProbability(hmm, value(itBelow), value(itSilentState));
-		}
-		value(fMat, value(itSilentState)) = sumValue;		
-	}
-
-	// Recurrence
-	TSize len = length(seq);
-	for(TSize i=1; i<=len; ++i) {
-		// Iterate over real states
-		TStateIter itRealStateEnd = end(realStates);
-		for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-			TProbability sum = 0.0;
-			TVertexIterator itAll(hmm);
-			for(;!atEnd(itAll);++itAll) sum += value(fMat, (i-1) * numRows + value(itAll)) * getTransitionProbability(hmm, value(itAll), value(itRealState));
-			value(fMat, i * numRows + value(itRealState)) = getEmissionProbability(hmm, value(itRealState), seq[i-1]) * sum;
-		}
-
-		// Iterate over silent states
-		for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-			if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
-			TProbability sumValue = 0.0;
-			// Iterate over real states
-			for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-				sumValue += value(fMat, i * numRows + value(itRealState)) * getTransitionProbability(hmm, value(itRealState), value(itSilentState));
-			}
-			// Iterate over silent states in increasing order
-			for(TStateIter itBelow = begin(silentStates); itBelow != itSilentState; goNext(itBelow)) {
-				sumValue += value(fMat, i * numRows + value(itBelow)) * getTransitionProbability(hmm, value(itBelow), value(itSilentState));
-			}
-			value(fMat, i * numRows + value(itSilentState)) = sumValue;
-		}
-	}
-
-	// Termination
-	TProbability sum = 0.0;
-	TVertexIterator itAll(hmm);
-	for(;!atEnd(itAll);++itAll) {
-		sum += value(fMat, len * numRows + value(itAll)) * getTransitionProbability(hmm, value(itAll), eState);
-	}
-	value(fMat, (len+1) * numRows + eState) = sum;
-
-	//// Debug code
-	//for(TSize i = 0; i<numRows; ++i) {
-	//	for(TSize j=0; j<numCols; ++j) {
-	//		std::cout << value(fMat, j*numRows + i) << ',';
-	//	}
-	//	std::cout << std::endl;
-	//}
-
-	return value(fMat, (len+1) * numRows + eState);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+
+    // Initialization
+    TSize numCols = length(seq) + 2;
+    TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
+    resize(fMat, numCols * numRows, 0.0);
+    value(fMat, getBeginState(hmm)) = 1.0;
+    TVertexDescriptor bState = getBeginState(hmm);
+    TVertexDescriptor eState = getEndState(hmm);
+
+    // Distinct between silent states and real states
+    typedef String<TVertexDescriptor> TStateSet;
+    typedef typename Iterator<TStateSet>::Type TStateIter;
+    TStateSet silentStates;
+    TStateSet realStates;
+    TVertexIterator itVertex(hmm);
+    for(;!atEnd(itVertex);goNext(itVertex)) {
+        if (isSilent(hmm, value(itVertex))) {
+            appendValue(silentStates, value(itVertex));
+        } else {
+            appendValue(realStates, value(itVertex));
+        }
+    }
+
+    // Initialization for silent states connected to the begin state
+    TStateIter itSilentStateEnd = end(silentStates);
+    for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+        if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
+        TProbability sumValue = 0.0;
+        for(TStateIter itBelow = begin(silentStates); itBelow != itSilentState; goNext(itBelow)) {
+            sumValue += value(fMat, value(itBelow)) * getTransitionProbability(hmm, value(itBelow), value(itSilentState));
+        }
+        value(fMat, value(itSilentState)) = sumValue;
+    }
+
+    // Recurrence
+    TSize len = length(seq);
+    for(TSize i=1; i<=len; ++i) {
+        // Iterate over real states
+        TStateIter itRealStateEnd = end(realStates);
+        for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+            TProbability sum = 0.0;
+            TVertexIterator itAll(hmm);
+            for(;!atEnd(itAll);++itAll) sum += value(fMat, (i-1) * numRows + value(itAll)) * getTransitionProbability(hmm, value(itAll), value(itRealState));
+            value(fMat, i * numRows + value(itRealState)) = getEmissionProbability(hmm, value(itRealState), seq[i-1]) * sum;
+        }
+
+        // Iterate over silent states
+        for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+            if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
+            TProbability sumValue = 0.0;
+            // Iterate over real states
+            for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+                sumValue += value(fMat, i * numRows + value(itRealState)) * getTransitionProbability(hmm, value(itRealState), value(itSilentState));
+            }
+            // Iterate over silent states in increasing order
+            for(TStateIter itBelow = begin(silentStates); itBelow != itSilentState; goNext(itBelow)) {
+                sumValue += value(fMat, i * numRows + value(itBelow)) * getTransitionProbability(hmm, value(itBelow), value(itSilentState));
+            }
+            value(fMat, i * numRows + value(itSilentState)) = sumValue;
+        }
+    }
+
+    // Termination
+    TProbability sum = 0.0;
+    TVertexIterator itAll(hmm);
+    for(;!atEnd(itAll);++itAll) {
+        sum += value(fMat, len * numRows + value(itAll)) * getTransitionProbability(hmm, value(itAll), eState);
+    }
+    value(fMat, (len+1) * numRows + eState) = sum;
+
+    //// Debug code
+    //for(TSize i = 0; i<numRows; ++i) {
+    //  for(TSize j=0; j<numCols; ++j) {
+    //      std::cout << value(fMat, j*numRows + i) << ',';
+    //  }
+    //  std::cout << std::endl;
+    //}
+
+    return value(fMat, (len+1) * numRows + eState);
 }
 
-//////////////////////////////////////////////////////////////////////////////
-
 /*!
  * @fn HmmAlgorithms#forwardAlgorithm
  * @headerfile <seqan/graph_algorithms.h>
  * @brief Given a Hidden Markov Model <tt>hmm</tt>, the forward algorithm computes the probability of the sequence
  *        <tt>seq</tt>.
  *
- * @signature TProbability forwardAlgorithm(hmm, seq);
+ * @signature TCargo forwardAlgorithm(hmm, seq);
  *
  * @param[in] hmm The @link HmmGraph @endlink with the HMM to use.
  * @param[in] seq Input sequence to use in the forward algorithm.
@@ -372,170 +363,152 @@ _forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
  * @see HmmAlgorithms#viterbiAlgorithm
  * @see HmmAlgorithms#backwardAlgorithm
  */
-
-/**
-.Function.forwardAlgorithm
-..cat:Graph
-..summary:Implements the forward algorithm.
-..description:Given a Hidden Markov Model $hmm$, the forward algorithm computes the probability of the sequence $seq$.
-..signature:TProbability forwardAlgorithm(hmm, seq);
-..param.hmm:In-parameter:Input HMM.
-...type:Spec.Hmm
-..param.seq:In-parameter:Input sequence.
-..returns:Probability of the sequence $seq$, $TProbability$ is the type parameter $TCargo$ of the type of $hmm$.
-..see:Function.viterbiAlgorithm
-..see:Function.backwardAlgorithm
-..remarks:See the @http://en.wikipedia.org/wiki/Forward_algorithm|Wikipedia article on the Foward algorithm@ for an introduction to the algorithm itself.
-..include:seqan/graph_algorithms.h
-*/
 template<typename TAlphabet, typename TProbability, typename TSpec, typename TSequence>
-inline TProbability
-forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
-				 TSequence const& seq)
+TProbability
+forwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const & hmm,
+                 TSequence const & seq)
 {
-	SEQAN_CHECKPOINT
-	String<TProbability> fMat;
-	return _forwardAlgorithm(hmm, seq, fMat);
+    SEQAN_CHECKPOINT
+    String<TProbability> fMat;
+    return _forwardAlgorithm(hmm, seq, fMat);
 }
 
-//////////////////////////////////////////////////////////////////////////////
+// --------------------------------------------------------------------------
+// Function backwardAlgorithm()
+// --------------------------------------------------------------------------
 
 template<typename TAlphabet, typename TProbability, typename TSpec, typename TSequence, typename TBackwardMatrix>
 inline TProbability
 _backwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
-					TSequence const& seq,
-					TBackwardMatrix& bMat)
+                    TSequence const& seq,
+                    TBackwardMatrix& bMat)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-
-	// Initialization
-	TSize numCols = length(seq) + 2;
-	TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
-	resize(bMat, numCols * numRows, 0.0);
-	TVertexDescriptor bState = getBeginState(hmm);
-	TVertexDescriptor eState = getEndState(hmm);
-	TSize len = length(seq);
-	value(bMat, (len + 1) * numRows + eState) = 1.0;
-	
-	// Distinct between silent states and real states
-	typedef String<TVertexDescriptor> TStateSet;
-	typedef typename Iterator<TStateSet>::Type TStateIter;
-	TStateSet silentStates;
-	TStateSet realStates;
-	TVertexIterator itVertex(hmm);
-	for(;!atEnd(itVertex);goNext(itVertex)) {
-		if (isSilent(hmm, value(itVertex))) { 
-			appendValue(silentStates, value(itVertex));
-		} else {
-			appendValue(realStates, value(itVertex));
-		}
-	}
-	// Reverse the silent states order
-	std::reverse(begin(silentStates), end(silentStates));
-
-	// Initialization for silent states connected to the end state
-	TStateIter itSilentStateEnd = end(silentStates);
-	for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-		if (value(itSilentState) == eState) continue;
-		TProbability sumValue = getTransitionProbability(hmm, value(itSilentState), eState);
-		for(TStateIter itAbove = begin(silentStates); itAbove != itSilentState; goNext(itAbove)) {
-			sumValue += value(bMat, len * numRows + value(itAbove)) * getTransitionProbability(hmm, value(itSilentState), value(itAbove));
-		}
-		value(bMat, len * numRows + value(itSilentState)) = sumValue;
-	}
-
-	// Initialization for real states
-	TStateIter itRealStateEnd = end(realStates);
-	for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-		TProbability sumValue = getTransitionProbability(hmm, value(itRealState), eState);
-		for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-			sumValue += value(bMat, len * numRows + value(itSilentState)) * getTransitionProbability(hmm, value(itRealState), value(itSilentState));
-		}
-		value(bMat, len * numRows + value(itRealState)) = sumValue;
-	}
-
-	
-	// Recurrence
-	if (len > 0) {
-		for(TSize i=len - 1; i>0; --i) {
-			// Iterate over silent states
-			for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-				if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
-				TProbability sumValue = 0.0;
-				// Iterate over real states
-				for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-					sumValue += value(bMat, (i+1) * numRows + value(itRealState)) * getTransitionProbability(hmm, value(itSilentState), value(itRealState))* getEmissionProbability(hmm, value(itRealState), value(seq, i));
-				}
-				// Iterate over silent states in decreasing order
-				for(TStateIter itAbove = begin(silentStates); itAbove != itSilentState; goNext(itAbove)) {
-					if ((value(itAbove) == bState) || (value(itAbove) == eState)) continue;
-					sumValue += value(bMat, i * numRows + value(itAbove)) * getTransitionProbability(hmm, value(itSilentState), value(itAbove));
-				}
-				value(bMat, i * numRows + value(itSilentState)) = sumValue;
-			}
-
-			// Iteration over real states
-			for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-				TProbability sumValue = 0.0;
-				// Iterate over silent states
-				for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-					if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
-					sumValue += value(bMat, i * numRows + value(itSilentState)) * getTransitionProbability(hmm, value(itRealState), value(itSilentState));
-				}
-				// Iterate over real states
-				for(TStateIter itR = begin(realStates); itR != itRealStateEnd; goNext(itR)) {
-					sumValue += value(bMat, (i+1) * numRows + value(itR)) * getTransitionProbability(hmm, value(itRealState), value(itR)) * getEmissionProbability(hmm, value(itR), value(seq, i));
-				}
-				value(bMat, i * numRows + value(itRealState)) =  sumValue;
-			}
-		}
-	
-		// Termination
-		// Iterate over silent states
-		for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-			if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
-			TProbability sumValue = 0.0;
-			// Iterate over real states
-			for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-				sumValue += value(bMat, 1 * numRows + value(itRealState)) * getTransitionProbability(hmm, value(itSilentState), value(itRealState))* getEmissionProbability(hmm, value(itRealState), value(seq, 0));
-			}
-			// Iterate over silent states in decreasing order
-			for(TStateIter itAbove = begin(silentStates); itAbove != itSilentState; goNext(itAbove)) {
-				if ((value(itAbove) == bState) || (value(itAbove) == eState)) continue;
-				sumValue += value(bMat, value(itAbove)) * getTransitionProbability(hmm, value(itSilentState), value(itAbove));
-			}
-			value(bMat, value(itSilentState)) = sumValue;
-		}
-		// Sum up all values
-		TProbability sumValue = 0.0;
-		for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
-			if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
-			sumValue += value(bMat, value(itSilentState)) * getTransitionProbability(hmm, bState, value(itSilentState));
-		}
-		for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
-			sumValue += value(bMat, 1 * numRows + value(itRealState)) * getTransitionProbability(hmm, bState, value(itRealState)) * getEmissionProbability(hmm, value(itRealState), value(seq, 0));
-		}
-		value(bMat, bState) = sumValue;
-	}
-
-	//// Debug code
-	//for(TSize i = 0; i<numRows; ++i) {
-	//	for(TSize j=0; j<numCols; ++j) {
-	//		std::cout << value(bMat, j*numRows + i) << ',';
-	//	}
-	//	std::cout << std::endl;
-	//}
-
-	return value(bMat, bState);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+
+    // Initialization
+    TSize numCols = length(seq) + 2;
+    TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
+    resize(bMat, numCols * numRows, 0.0);
+    TVertexDescriptor bState = getBeginState(hmm);
+    TVertexDescriptor eState = getEndState(hmm);
+    TSize len = length(seq);
+    value(bMat, (len + 1) * numRows + eState) = 1.0;
+
+    // Distinct between silent states and real states
+    typedef String<TVertexDescriptor> TStateSet;
+    typedef typename Iterator<TStateSet>::Type TStateIter;
+    TStateSet silentStates;
+    TStateSet realStates;
+    TVertexIterator itVertex(hmm);
+    for(;!atEnd(itVertex);goNext(itVertex)) {
+        if (isSilent(hmm, value(itVertex))) {
+            appendValue(silentStates, value(itVertex));
+        } else {
+            appendValue(realStates, value(itVertex));
+        }
+    }
+    // Reverse the silent states order
+    std::reverse(begin(silentStates), end(silentStates));
+
+    // Initialization for silent states connected to the end state
+    TStateIter itSilentStateEnd = end(silentStates);
+    for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+        if (value(itSilentState) == eState) continue;
+        TProbability sumValue = getTransitionProbability(hmm, value(itSilentState), eState);
+        for(TStateIter itAbove = begin(silentStates); itAbove != itSilentState; goNext(itAbove)) {
+            sumValue += value(bMat, len * numRows + value(itAbove)) * getTransitionProbability(hmm, value(itSilentState), value(itAbove));
+        }
+        value(bMat, len * numRows + value(itSilentState)) = sumValue;
+    }
+
+    // Initialization for real states
+    TStateIter itRealStateEnd = end(realStates);
+    for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+        TProbability sumValue = getTransitionProbability(hmm, value(itRealState), eState);
+        for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+            sumValue += value(bMat, len * numRows + value(itSilentState)) * getTransitionProbability(hmm, value(itRealState), value(itSilentState));
+        }
+        value(bMat, len * numRows + value(itRealState)) = sumValue;
+    }
+
+
+    // Recurrence
+    if (len > 0) {
+        for(TSize i=len - 1; i>0; --i) {
+            // Iterate over silent states
+            for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+                if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
+                TProbability sumValue = 0.0;
+                // Iterate over real states
+                for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+                    sumValue += value(bMat, (i+1) * numRows + value(itRealState)) * getTransitionProbability(hmm, value(itSilentState), value(itRealState))* getEmissionProbability(hmm, value(itRealState), value(seq, i));
+                }
+                // Iterate over silent states in decreasing order
+                for(TStateIter itAbove = begin(silentStates); itAbove != itSilentState; goNext(itAbove)) {
+                    if ((value(itAbove) == bState) || (value(itAbove) == eState)) continue;
+                    sumValue += value(bMat, i * numRows + value(itAbove)) * getTransitionProbability(hmm, value(itSilentState), value(itAbove));
+                }
+                value(bMat, i * numRows + value(itSilentState)) = sumValue;
+            }
+
+            // Iteration over real states
+            for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+                TProbability sumValue = 0.0;
+                // Iterate over silent states
+                for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+                    if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
+                    sumValue += value(bMat, i * numRows + value(itSilentState)) * getTransitionProbability(hmm, value(itRealState), value(itSilentState));
+                }
+                // Iterate over real states
+                for(TStateIter itR = begin(realStates); itR != itRealStateEnd; goNext(itR)) {
+                    sumValue += value(bMat, (i+1) * numRows + value(itR)) * getTransitionProbability(hmm, value(itRealState), value(itR)) * getEmissionProbability(hmm, value(itR), value(seq, i));
+                }
+                value(bMat, i * numRows + value(itRealState)) =  sumValue;
+            }
+        }
+
+        // Termination
+        // Iterate over silent states
+        for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+            if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
+            TProbability sumValue = 0.0;
+            // Iterate over real states
+            for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+                sumValue += value(bMat, 1 * numRows + value(itRealState)) * getTransitionProbability(hmm, value(itSilentState), value(itRealState))* getEmissionProbability(hmm, value(itRealState), value(seq, 0));
+            }
+            // Iterate over silent states in decreasing order
+            for(TStateIter itAbove = begin(silentStates); itAbove != itSilentState; goNext(itAbove)) {
+                if ((value(itAbove) == bState) || (value(itAbove) == eState)) continue;
+                sumValue += value(bMat, value(itAbove)) * getTransitionProbability(hmm, value(itSilentState), value(itAbove));
+            }
+            value(bMat, value(itSilentState)) = sumValue;
+        }
+        // Sum up all values
+        TProbability sumValue = 0.0;
+        for(TStateIter itSilentState = begin(silentStates); itSilentState != itSilentStateEnd; goNext(itSilentState)) {
+            if ((value(itSilentState) == bState) || (value(itSilentState) == eState)) continue;
+            sumValue += value(bMat, value(itSilentState)) * getTransitionProbability(hmm, bState, value(itSilentState));
+        }
+        for(TStateIter itRealState = begin(realStates); itRealState != itRealStateEnd; goNext(itRealState)) {
+            sumValue += value(bMat, 1 * numRows + value(itRealState)) * getTransitionProbability(hmm, bState, value(itRealState)) * getEmissionProbability(hmm, value(itRealState), value(seq, 0));
+        }
+        value(bMat, bState) = sumValue;
+    }
+
+    //// Debug code
+    //for(TSize i = 0; i<numRows; ++i) {
+    //  for(TSize j=0; j<numCols; ++j) {
+    //      std::cout << value(bMat, j*numRows + i) << ',';
+    //  }
+    //  std::cout << std::endl;
+    //}
+
+    return value(bMat, bState);
 }
-	
-
-
-//////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn HmmAlgorithms#backwardAlgorithm
@@ -543,15 +516,13 @@ _backwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
  * @brief Given a Hidden Markov Model <tt>hmm</tt>, the backward algorithm computes the probability of the sequence
  *        <tt>seq</tt>.
  *
- * @signature TProbability backwardAlgorithm(hmm, seq);
+ * @signature TCargo backwardAlgorithm(hmm, seq);
  *
  * @param[in] hmm The @link HmmGraph @endlink with the HMM to use.
  * @param[in] seq Input sequence to use in the backward algorithm.
  *
- * @return TProbability The probability of the sequence <tt>seq</tt>.  <tt>TProbability</tt> is the type parameter
- *                      <tt>TCargo</tt> of the type of <tt>hmm</tt>.
- *
- * @section Remarks
+ * @return TCargo The probability of the sequence <tt>seq</tt>.  <tt>TProbability</tt> is the type parameter
+ *                <tt>TCargo</tt> of the type of <tt>hmm</tt>.
  *
  * See the <a href="http://en.wikipedia.org/wiki/Forward-backward_algorithm">Wikipedia article on the Forward-backward
  * algorithm</a> for an introduction to the algorithm itself.
@@ -559,33 +530,19 @@ _backwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
  * @see HmmAlgorithms#viterbiAlgorithm
  * @see HmmAlgorithms#forwardAlgorithm
  */
-
-/**
-.Function.backwardAlgorithm
-..cat:Graph
-..summary:Implements the backward algorithm.
-..description:Execute the backward algorithm on the Hidden Markov Model $hmm$ to get the probability of $seq$.
-..signature:TProbability backwardAlgorithm(hmm, seq);
-..param.hmm:In-parameter:Input HMM.
-...type:Spec.Hmm
-..param.seq:In-parameter:Input sequence.
-..returns:Probability of the sequence $seq$.  $TProbability$ is the type parameter $TCargo$ of the type of $hmm$.
-..see:Function.viterbiAlgorithm
-..see:Function.forwardAlgorithm
-..remarks:See the @http://en.wikipedia.org/wiki/Forward-backward_algorithm|Wikipedia article on the Forward-backward algorithm@ for an introduction to the algorithm.
-..include:seqan/graph_algorithms.h
-*/
 template<typename TAlphabet, typename TProbability, typename TSpec, typename TSequence>
-inline TProbability
-backwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
-				  TSequence const& seq)
+TProbability
+backwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const & hmm,
+                  TSequence const & seq)
 {
-	SEQAN_CHECKPOINT
-	String<TProbability> bMat;
-	return _backwardAlgorithm(hmm, seq, bMat);
+    SEQAN_CHECKPOINT
+    String<TProbability> bMat;
+    return _backwardAlgorithm(hmm, seq, bMat);
 }
 
-///////////////////////////////////////////////////////////////////////////////////////
+// --------------------------------------------------------------------------
+// Function generateSequence()
+// --------------------------------------------------------------------------
 
 /*!
  * @fn HmmAlgorithms#generateSequence
@@ -594,9 +551,9 @@ backwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
  *
  * @signature void generateSequence(hmm, seq, states, numSeq, maxLen);
  *
- * @param[in] hmm     The @link HmmGraph @endlink to use.
  * @param[out] seq    A @link StringSet @endlink of alphabet sequences.
- * @param[out] states A @link SequenceConcept @endlink object of state sequences.
+ * @param[out] states A @link ContainerConcept @endlink object of state sequences.
+ * @param[in]  hmm    The @link HmmGraph @endlink to use.
  * @param[in]  numSeq The number of sequences to generate.
  * @param[in]  maxLen The maximum length of the sequences.  The sequences might be shorter if the ends tate is reached
  *                    before maxLen.
@@ -605,428 +562,395 @@ backwardAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
  *
  * Because of silent states, generated alphabet and state sequences might have different lengths.
  */
-
-/**
-.Function.generateSequence:
-..cat:Graph
-..summary:Generates random state and alphabet sequences of a given HMM.
-..signature:generateSequence(hmm, sequences, states, numSeq, maxLength)
-..param.hmm:In-parameter:Input HMM.
-...type:Spec.Hmm
-..param.sequences:The StringSet of alphabet sequences.
-...type:Class.StringSet
-..param.sequences:The StringSet of state sequences.
-...type:Class.StringSet
-..param.numSeq:The number of sequences to generate.
-..param.maxLength:The maximum length of the sequences.
-...remarks:Sequences might be shorter if the end state is reached prior to maxLength. 
-..remarks: Because of silent states, generated alphabet and state sequences might have different length.
-..returns:void
-..include:seqan/graph_algorithms.h
-*/
 template<typename TAlphabet, typename TProbability, typename TSpec,typename TSequenceSet, typename TStateSeqSet, typename TSize>
-inline void
-generateSequence(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
-				 TSequenceSet& sequences,
-				 TStateSeqSet& states,
-				 TSize numSeq,
-				 TSize maxLength) 
+void generateSequence(TSequenceSet & sequences,
+                      TStateSeqSet & states,
+                      Graph<Hmm<TAlphabet, TProbability, TSpec> > const & hmm,
+                      TSize numSeq,
+                      TSize maxLength)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Value<TSequenceSet>::Type TSequence;
-	typedef typename Value<TStateSeqSet>::Type TStateSeq;
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Value<TSequenceSet>::Type TSequence;
+    typedef typename Value<TStateSeqSet>::Type TStateSeq;
 
     // TODO(holtgrew): It should be possible to use a per-call RNG.
-	typedef typename GetDefaultRng<TGraph>::Type TRng;
-	typedef Pdf<Uniform<double> > TPdf;
-	TPdf pdf(0.0, 1.0);
-	TRng & rng = defaultRng(TGraph());
-	
-	// Initialization
-	clear(sequences);
-	clear(states);
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	
-	// Simulate sequences
-	TVertexDescriptor currentState;
-	TVertexDescriptor endState = getEndState(hmm);
-	for(TSize i=0;i<numSeq;++i){
-		currentState = getBeginState(hmm);
-		TSequence seq;
-		TStateSeq stat;
-		appendValue(stat, getBeginState(hmm));
-		bool stop = false;
-		TSize pos = 0; 
-		while (pos < maxLength) {
-			TProbability prob = pickRandomNumber(rng, pdf);
-			TProbability compareProb = 0.0;
-			TOutEdgeIterator itState(hmm, currentState);
-			// Determine the next state
-			for(;!atEnd(itState);++itState) {
-				// Probability of the next transition
-				compareProb += getTransitionProbability(hmm, value(itState));
-				// Compare with random probability
-				if (prob <= compareProb){
-					TVertexDescriptor nextState = targetVertex(hmm, value(itState));
-					if (nextState == endState) {
-						stop = true;
-						break;
-					}
-					appendValue(stat, nextState);
-					if (!isSilent(hmm, nextState)) {
-						compareProb =0.0;
-						prob = pickRandomNumber(rng, pdf);
-						for (TSize c=0;c<alphSize;++c){
-							compareProb += getEmissionProbability(hmm,targetVertex(hmm, value(itState)), TAlphabet(c));
-							if (prob <= compareProb) {
-								appendValue(seq, TAlphabet(c));
-								++pos;
-								break;
-							}
-						}
-					}
-					currentState = nextState;
-					break;
-				}
-			}
-			if (stop==true) break;
-		}
-		appendValue(stat, getEndState(hmm));
-		appendValue(sequences, seq);
-		appendValue(states, stat);
-	}
+    typedef typename GetDefaultRng<TGraph>::Type TRng;
+    typedef Pdf<Uniform<double> > TPdf;
+    TPdf pdf(0.0, 1.0);
+    TRng & rng = defaultRng(TGraph());
+
+    // Initialization
+    clear(sequences);
+    clear(states);
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+
+    // Simulate sequences
+    TVertexDescriptor currentState;
+    TVertexDescriptor endState = getEndState(hmm);
+    for(TSize i=0;i<numSeq;++i){
+        currentState = getBeginState(hmm);
+        TSequence seq;
+        TStateSeq stat;
+        appendValue(stat, getBeginState(hmm));
+        bool stop = false;
+        TSize pos = 0;
+        while (pos < maxLength) {
+            TProbability prob = pickRandomNumber(rng, pdf);
+            TProbability compareProb = 0.0;
+            TOutEdgeIterator itState(hmm, currentState);
+            // Determine the next state
+            for(;!atEnd(itState);++itState) {
+                // Probability of the next transition
+                compareProb += getTransitionProbability(hmm, value(itState));
+                // Compare with random probability
+                if (prob <= compareProb){
+                    TVertexDescriptor nextState = targetVertex(hmm, value(itState));
+                    if (nextState == endState) {
+                        stop = true;
+                        break;
+                    }
+                    appendValue(stat, nextState);
+                    if (!isSilent(hmm, nextState)) {
+                        compareProb =0.0;
+                        prob = pickRandomNumber(rng, pdf);
+                        for (TSize c=0;c<alphSize;++c){
+                            compareProb += getEmissionProbability(hmm,targetVertex(hmm, value(itState)), TAlphabet(c));
+                            if (prob <= compareProb) {
+                                appendValue(seq, TAlphabet(c));
+                                ++pos;
+                                break;
+                            }
+                        }
+                    }
+                    currentState = nextState;
+                    break;
+                }
+            }
+            if (stop==true) break;
+        }
+        appendValue(stat, getEndState(hmm));
+        appendValue(sequences, seq);
+        appendValue(states, stat);
+    }
 }
 
-///////////////////////////////////////////////////////////////////////////////////////
-
 template<typename TAlphabet, typename TProbability, typename TSpec,typename TSequenceSet, typename TSize>
 inline void
 generateSequence(Graph<Hmm<TAlphabet, TProbability, TSpec> > const& hmm,
-				 TSequenceSet& sequences,
-				 TSize numSeq,
-				 TSize maxLength) 
+                 TSequenceSet& sequences,
+                 TSize numSeq,
+                 TSize maxLength)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	StringSet<String<TVertexDescriptor> > states;
-	generateSequence(hmm, sequences, states, numSeq, maxLength);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    StringSet<String<TVertexDescriptor> > states;
+    generateSequence(hmm, sequences, states, numSeq, maxLength);
 }
 
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Training algorithms
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
+// --------------------------------------------------------------------------
+// Function estimationWithStates()
+// --------------------------------------------------------------------------
 
 template<typename TAlphabet, typename TProbability, typename TSpec,typename TEmissionCounter, typename TTransitionCounter>
 inline void
 _parameterEstimator(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm,
-					 TEmissionCounter const& emission,
-					 TTransitionCounter const& transition)
+                     TEmissionCounter const& emission,
+                     TTransitionCounter const& transition)
 {
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Value<TTransitionCounter>::Type TCounterValue;
-
-	// Initialization
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	TCounterValue pseudoCount = (TCounterValue) 1.0;
-
-	// Estimate the parameters from the counter values
-	TVertexIterator itAll(hmm);
-	for(;!atEnd(itAll);++itAll){
-		if (!isSilent(hmm, value(itAll))) {
-			TCounterValue summedCount = (TCounterValue) (0.0);
-			for(TSize i=0; i<alphSize;++i) summedCount += (pseudoCount + value(value(emission, value(itAll)),i));
-			for(TSize i=0; i<alphSize;++i) emissionProbability(hmm,value(itAll),TAlphabet(i)) = (pseudoCount + value(value(emission, value(itAll)),i)) / summedCount;
-		}
-		TCounterValue summedCount = (TCounterValue) (0.0);
-		TOutEdgeIterator itOutSum(hmm,value(itAll));
-		for(;!atEnd(itOutSum);++itOutSum) summedCount += (pseudoCount + getProperty(transition, value(itOutSum)));
-		TOutEdgeIterator itOut(hmm, value(itAll));
-		for(;!atEnd(itOut);++itOut) transitionProbability(hmm, value(itOut)) = (pseudoCount + getProperty(transition, value(itOut))) / summedCount;
-	}
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Value<TTransitionCounter>::Type TCounterValue;
+
+    // Initialization
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+    TCounterValue pseudoCount = (TCounterValue) 1.0;
+
+    // Estimate the parameters from the counter values
+    TVertexIterator itAll(hmm);
+    for(;!atEnd(itAll);++itAll){
+        if (!isSilent(hmm, value(itAll))) {
+            TCounterValue summedCount = (TCounterValue) (0.0);
+            for(TSize i=0; i<alphSize;++i) summedCount += (pseudoCount + value(value(emission, value(itAll)),i));
+            for(TSize i=0; i<alphSize;++i) emissionProbability(hmm,value(itAll),TAlphabet(i)) = (pseudoCount + value(value(emission, value(itAll)),i)) / summedCount;
+        }
+        TCounterValue summedCount = (TCounterValue) (0.0);
+        TOutEdgeIterator itOutSum(hmm,value(itAll));
+        for(;!atEnd(itOutSum);++itOutSum) summedCount += (pseudoCount + getProperty(transition, value(itOutSum)));
+        TOutEdgeIterator itOut(hmm, value(itAll));
+        for(;!atEnd(itOut);++itOut) transitionProbability(hmm, value(itOut)) = (pseudoCount + getProperty(transition, value(itOut))) / summedCount;
+    }
 }
 
 ///////////////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TProbability, typename TSpec, typename TSequenceSet, typename TStateSeqSet>
-inline void 
+inline void
 estimationWithStates(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm,
-					 TSequenceSet& sequences,
-					 TStateSeqSet& states)
+                     TSequenceSet& sequences,
+                     TStateSeqSet& states)
 {
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Value<TStateSeqSet>::Type TStateSeq;
-	typedef typename Value<TStateSeq>::Type TState;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-
-	// Initialization
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	typedef String<TSize> TCountString;
-	TCountString transitionCounter;
-	resize(transitionCounter, getIdUpperBound(_getEdgeIdManager(hmm)), 0);
-	StringSet<TCountString> emissionCounter;
-	TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
-	for(TSize i =0; i<numRows;++i) {
-		TCountString emisCount;
-		resize(emisCount,alphSize,0);
-		appendValue(emissionCounter,emisCount);
-	}
-	
-	// Iterate over all sequences
-	for (TSize j=0;j<length(states);++j) {
-		TSize posSeq = 0;
-		for (TSize i = 0;i<length(value(states,j));++i) {
-			TState s = value(value(states,j),i);
-			if (!isSilent(hmm, s)) {
-				TAlphabet c = value(value(sequences,j),posSeq);
-				value(value(emissionCounter, s), ordValue(c)) += 1;
-				++posSeq;
-			}
-			if (i<(length(value(states,j))-1)) {
-				TEdgeDescriptor currEdge = findEdge(hmm, s, value(value(states,j), (i+1)));
-				property(transitionCounter, currEdge) += 1;
-			}
-		}
-	}
-
-	//// Debug Code
-	//typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	//TEdgeIterator itE(hmm);
-	//for(;!atEnd(itE);goNext(itE)) std::cout << sourceVertex(itE) << ',' << targetVertex(itE) << ':' << property(transitionCounter, value(itE)) << std::endl;
-	//for(TSize j=0; j<length(emissionCounter); ++j) {
-	//	for(TSize i=0;i<length(value(emissionCounter, j));++i) {
-	//		std::cout << j << ":" << TAlphabet(i) << '=' << value(value(emissionCounter, j), i) << std::endl;
-	//	}
-	//}
-
-	// Estimate Parameters
-	_parameterEstimator(hmm,emissionCounter, transitionCounter);
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Value<TStateSeqSet>::Type TStateSeq;
+    typedef typename Value<TStateSeq>::Type TState;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+
+    // Initialization
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+    typedef String<TSize> TCountString;
+    TCountString transitionCounter;
+    resize(transitionCounter, getIdUpperBound(_getEdgeIdManager(hmm)), 0);
+    StringSet<TCountString> emissionCounter;
+    TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
+    for(TSize i =0; i<numRows;++i) {
+        TCountString emisCount;
+        resize(emisCount,alphSize,0);
+        appendValue(emissionCounter,emisCount);
+    }
+
+    // Iterate over all sequences
+    for (TSize j=0;j<length(states);++j) {
+        TSize posSeq = 0;
+        for (TSize i = 0;i<length(value(states,j));++i) {
+            TState s = value(value(states,j),i);
+            if (!isSilent(hmm, s)) {
+                TAlphabet c = value(value(sequences,j),posSeq);
+                value(value(emissionCounter, s), ordValue(c)) += 1;
+                ++posSeq;
+            }
+            if (i<(length(value(states,j))-1)) {
+                TEdgeDescriptor currEdge = findEdge(hmm, s, value(value(states,j), (i+1)));
+                property(transitionCounter, currEdge) += 1;
+            }
+        }
+    }
+
+    //// Debug Code
+    //typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    //TEdgeIterator itE(hmm);
+    //for(;!atEnd(itE);goNext(itE)) std::cout << sourceVertex(itE) << ',' << targetVertex(itE) << ':' << property(transitionCounter, value(itE)) << std::endl;
+    //for(TSize j=0; j<length(emissionCounter); ++j) {
+    //  for(TSize i=0;i<length(value(emissionCounter, j));++i) {
+    //      std::cout << j << ":" << TAlphabet(i) << '=' << value(value(emissionCounter, j), i) << std::endl;
+    //  }
+    //}
+
+    // Estimate Parameters
+    _parameterEstimator(hmm,emissionCounter, transitionCounter);
 }
 
-///////////////////////////////////////////////////////////////////////////////////////
+// --------------------------------------------------------------------------
+// Function baumWelchAlgorithm()
+// --------------------------------------------------------------------------
 
 template<typename TAlphabet, typename TProbability, typename TSpec>
 inline void
 _fillHmmUniform(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	
-	// Initialization
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	
-	// Iterate over all states
-	TVertexIterator itState(hmm);
-	for(;!atEnd(itState);goNext(itState)) {		//pass through the states of the hmm	
-		TSize oD = outDegree(hmm, value(itState));
-		TOutEdgeIterator itOut(hmm, value(itState));
-		for (;!atEnd(itOut);goNext(itOut)) transitionProbability(hmm, value(itOut)) = (TProbability) (1.0 / (double) (oD));
-		if (!isSilent(hmm, value(itState))) {
-			for(TSize i=0;i<alphSize;++i){
-				emissionProbability(hmm,value(itState),TAlphabet(i)) = (TProbability) (1.0 / (double) (alphSize));
-			}
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    // Initialization
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+
+    // Iterate over all states
+    TVertexIterator itState(hmm);
+    for(;!atEnd(itState);goNext(itState)) {     //pass through the states of the hmm
+        TSize oD = outDegree(hmm, value(itState));
+        TOutEdgeIterator itOut(hmm, value(itState));
+        for (;!atEnd(itOut);goNext(itOut)) transitionProbability(hmm, value(itOut)) = (TProbability) (1.0 / (double) (oD));
+        if (!isSilent(hmm, value(itState))) {
+            for(TSize i=0;i<alphSize;++i){
+                emissionProbability(hmm,value(itState),TAlphabet(i)) = (TProbability) (1.0 / (double) (alphSize));
+            }
+        }
+    }
 }
 
-///////////////////////////////////////////////////////////////////////////////////////
-
 template<typename TAlphabet, typename TProbability, typename TSpec, typename TRNG>
 inline void
 _fillHmmRandom(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm,
                 TRNG & rng)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	
-	// Initialization
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    // Initialization
     Pdf<Uniform<TSize> > pdf(20, 99);
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	
-	// Iterate over all states
-	TVertexIterator itState(hmm);
-	for(;!atEnd(itState);goNext(itState)) {		//pass through the states of the hmm	
-		TSize oD = outDegree(hmm, value(itState));
-		if (oD > 0) {
-			String<TSize> counts;
-			TSize sum = 0;
-			for(TSize i = 0;i<oD;++i) {
-				TSize rd = pickRandomNumber(rng, pdf);
-				sum += rd;
-				appendValue(counts, rd);
-			}
-			TSize pos = 0;
-			TOutEdgeIterator itOut(hmm, value(itState));
-			for (;!atEnd(itOut);goNext(itOut), ++pos) transitionProbability(hmm, value(itOut)) = (TProbability) ((double) (value(counts, pos)) / (double) (sum));
-		}	
-		if (!isSilent(hmm, value(itState))) {
-			String<TSize> counts;
-			TSize sum = 0;
-			for(TSize i = 0;i<alphSize;++i) {
-				TSize rd = pickRandomNumber(rng, pdf);
-				sum += rd;
-				appendValue(counts, rd);
-			}
-			for(TSize i=0;i<alphSize;++i) emissionProbability(hmm,value(itState),TAlphabet(i)) = (TProbability) ((double) (value(counts, i)) / (double) (sum));
-		}
-	}
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+
+    // Iterate over all states
+    TVertexIterator itState(hmm);
+    for(;!atEnd(itState);goNext(itState)) {     //pass through the states of the hmm
+        TSize oD = outDegree(hmm, value(itState));
+        if (oD > 0) {
+            String<TSize> counts;
+            TSize sum = 0;
+            for(TSize i = 0;i<oD;++i) {
+                TSize rd = pickRandomNumber(rng, pdf);
+                sum += rd;
+                appendValue(counts, rd);
+            }
+            TSize pos = 0;
+            TOutEdgeIterator itOut(hmm, value(itState));
+            for (;!atEnd(itOut);goNext(itOut), ++pos) transitionProbability(hmm, value(itOut)) = (TProbability) ((double) (value(counts, pos)) / (double) (sum));
+        }
+        if (!isSilent(hmm, value(itState))) {
+            String<TSize> counts;
+            TSize sum = 0;
+            for(TSize i = 0;i<alphSize;++i) {
+                TSize rd = pickRandomNumber(rng, pdf);
+                sum += rd;
+                appendValue(counts, rd);
+            }
+            for(TSize i=0;i<alphSize;++i) emissionProbability(hmm,value(itState),TAlphabet(i)) = (TProbability) ((double) (value(counts, i)) / (double) (sum));
+        }
+    }
 }
 
-///////////////////////////////////////////////////////////////////////////////////////
-
 template<typename TAlphabet, typename TProbability, typename TSpec, typename TRNG>
 inline void
 randomizeHmm(Graph<Hmm<TAlphabet, TProbability, TSpec> >& hmm,
              TRNG & /*rng*/)
 {
-	// TODO(holtgrew): Why uniform and not random?
-	//_fillHmmRandom(hmm, rng);
-	_fillHmmUniform(hmm);
+    // TODO(holtgrew): Why uniform and not random?
+    //_fillHmmRandom(hmm, rng);
+    _fillHmmUniform(hmm);
 }
 
-///////////////////////////////////////////////////////////////////////////////////////
-
 template <typename TAlphabet, typename TProbability, typename TSpec, typename TSequence, typename TSize>
 inline TProbability
 _baumWelchAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec > >& hmm,
-					 StringSet<TSequence> const& seqSet,
-					 TSize maxIter,
-					 TProbability epsilon)
+                     StringSet<TSequence> const& seqSet,
+                     TSize maxIter,
+                     TProbability epsilon)
 {
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef String<TProbability> TCountString;
-
-	// Initialization
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	TProbability lastTotalModelProb = 0.0;
-
-	// Randomize current HMM so only topology is preserved
-	randomizeHmm(hmm);
-
-	// Iterative Optimization
-	for(TSize iter=0; iter<maxIter; ++iter){
-		std::cout << "Iteration: "<< iter << std::endl;
-		std::cout << hmm << std::endl;
-		TCountString transitionCounter;
-		resize(transitionCounter, getIdUpperBound(_getEdgeIdManager(hmm)), 0.0);
-		StringSet<TCountString> emissionCounter;
-		TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
-		for(TSize i =0; i<numRows;++i) {
-			TCountString emisCount;
-			resize(emisCount,alphSize, 0.0);
-			appendValue(emissionCounter,emisCount);
-		}
-						
-		// MaximationStep
-		// Determine new contributions
-		TProbability totalModelLogProb = 0.0;
-		for (TSize i=0; i <length(seqSet);++i){		//sequences
-			TSize len = length(value(seqSet,i));
-
-			// Forward algorithm
-			String<TProbability> fMat;
-			TProbability modelLogProb = _forwardAlgorithm(hmm, value(seqSet,i), fMat);
-			totalModelLogProb += modelLogProb;
-			
-			// Backward algorithm
-			String<TProbability> bMat;
-			_backwardAlgorithm(hmm, value(seqSet,i), bMat);
-			
-			// Use the posterior probabilities to estimate counter values
-			for (TSize j=0;j<len;++j){  
-				TAlphabet c = value(value(seqSet,i),j);
-				TAlphabet nextC = c;
-				if (j < (len - 1))  nextC = value(value(seqSet,i),(j+1));
-				
-				// Iterate over all states
-				TVertexIterator itAll(hmm);		
-				for(;!atEnd(itAll);++itAll) {
-					// Handle begin state
-					if (value(itAll) == beginState(hmm)) {
-						if (j == 0) {
-							TOutEdgeIterator itOut(hmm, value(itAll));
-							for(;!atEnd(itOut); goNext(itOut)) {
-								if (!isSilent(hmm, targetVertex(itOut))) {
-									property(transitionCounter, value(itOut)) += (value(fMat, beginState(hmm)) * getTransitionProbability(hmm, value(itOut)) * getEmissionProbability(hmm, targetVertex(itOut), c) * value(bMat, numRows + targetVertex(itOut)) / modelLogProb);
-								} else {
-									property(transitionCounter, value(itOut)) += (value(fMat, beginState(hmm)) * getTransitionProbability(hmm, value(itOut)) * value(bMat, targetVertex(itOut)) / modelLogProb);
-								}
-							}
-						
-						}
-						continue;
-					}
-					// Ignore the end state
-					if (value(itAll) == endState(hmm)) continue;
-
-					// Determine emission expectation values
-					if (!isSilent(hmm, value(itAll))) value(value(emissionCounter, value(itAll)),ordValue(c)) += ((value(fMat, (j+1) * numRows + value(itAll)) * value(bMat, (j+1) * numRows + value(itAll))) / modelLogProb);
-					
-					// Determine transition expectation values
-					TOutEdgeIterator itOut(hmm, value(itAll));
-					for(;!atEnd(itOut); goNext(itOut)) {
-						// Handle the end state
-						if ((j == (len - 1)) && (targetVertex(itOut)==endState(hmm))) {
-							property(transitionCounter, value(itOut)) += (value(fMat, (j+1) * numRows + value(itAll)) * getTransitionProbability(hmm, value(itAll),endState(hmm)) / modelLogProb);
-						} else {
-							if (!isSilent(hmm, targetVertex(itOut))) {
-								if (j < (len - 1)) property(transitionCounter, value(itOut)) += (value(fMat, (j+1) * numRows + value(itAll)) * getTransitionProbability(hmm, value(itOut)) * getEmissionProbability(hmm, targetVertex(itOut), nextC) * value(bMat, (j+2) * numRows + targetVertex(itOut)) / modelLogProb);
-							} else {
-								property(transitionCounter, value(itOut)) += (value(fMat, (j+1) * numRows + value(itAll)) * getTransitionProbability(hmm, value(itOut)) * value(bMat, (j+1) * numRows + targetVertex(itOut)) / modelLogProb);
-							}
-						}
-					}
-				}
-			}
-		}
-		// Expectation step
-		_parameterEstimator(hmm,emissionCounter, transitionCounter);
-		
-
-		// Termination?
-		if ((iter > 5) && ((totalModelLogProb - lastTotalModelProb) < epsilon)) {
-			lastTotalModelProb = totalModelLogProb;
-			break;
-		} else {
-			lastTotalModelProb = totalModelLogProb;
-		}
-	}
-	return lastTotalModelProb;
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef String<TProbability> TCountString;
+
+    // Initialization
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+    TProbability lastTotalModelProb = 0.0;
+
+    // Randomize current HMM so only topology is preserved
+    randomizeHmm(hmm);
+
+    // Iterative Optimization
+    for(TSize iter=0; iter<maxIter; ++iter){
+        std::cout << "Iteration: "<< iter << std::endl;
+        std::cout << hmm << std::endl;
+        TCountString transitionCounter;
+        resize(transitionCounter, getIdUpperBound(_getEdgeIdManager(hmm)), 0.0);
+        StringSet<TCountString> emissionCounter;
+        TSize numRows = getIdUpperBound(_getVertexIdManager(hmm));
+        for(TSize i =0; i<numRows;++i) {
+            TCountString emisCount;
+            resize(emisCount,alphSize, 0.0);
+            appendValue(emissionCounter,emisCount);
+        }
+
+        // MaximationStep
+        // Determine new contributions
+        TProbability totalModelLogProb = 0.0;
+        for (TSize i=0; i <length(seqSet);++i){     //sequences
+            TSize len = length(value(seqSet,i));
+
+            // Forward algorithm
+            String<TProbability> fMat;
+            TProbability modelLogProb = _forwardAlgorithm(hmm, value(seqSet,i), fMat);
+            totalModelLogProb += modelLogProb;
+
+            // Backward algorithm
+            String<TProbability> bMat;
+            _backwardAlgorithm(hmm, value(seqSet,i), bMat);
+
+            // Use the posterior probabilities to estimate counter values
+            for (TSize j=0;j<len;++j){
+                TAlphabet c = value(value(seqSet,i),j);
+                TAlphabet nextC = c;
+                if (j < (len - 1))  nextC = value(value(seqSet,i),(j+1));
+
+                // Iterate over all states
+                TVertexIterator itAll(hmm);
+                for(;!atEnd(itAll);++itAll) {
+                    // Handle begin state
+                    if (value(itAll) == beginState(hmm)) {
+                        if (j == 0) {
+                            TOutEdgeIterator itOut(hmm, value(itAll));
+                            for(;!atEnd(itOut); goNext(itOut)) {
+                                if (!isSilent(hmm, targetVertex(itOut))) {
+                                    property(transitionCounter, value(itOut)) += (value(fMat, beginState(hmm)) * getTransitionProbability(hmm, value(itOut)) * getEmissionProbability(hmm, targetVertex(itOut), c) * value(bMat, numRows + targetVertex(itOut)) / modelLogProb);
+                                } else {
+                                    property(transitionCounter, value(itOut)) += (value(fMat, beginState(hmm)) * getTransitionProbability(hmm, value(itOut)) * value(bMat, targetVertex(itOut)) / modelLogProb);
+                                }
+                            }
+
+                        }
+                        continue;
+                    }
+                    // Ignore the end state
+                    if (value(itAll) == endState(hmm)) continue;
+
+                    // Determine emission expectation values
+                    if (!isSilent(hmm, value(itAll))) value(value(emissionCounter, value(itAll)),ordValue(c)) += ((value(fMat, (j+1) * numRows + value(itAll)) * value(bMat, (j+1) * numRows + value(itAll))) / modelLogProb);
+
+                    // Determine transition expectation values
+                    TOutEdgeIterator itOut(hmm, value(itAll));
+                    for(;!atEnd(itOut); goNext(itOut)) {
+                        // Handle the end state
+                        if ((j == (len - 1)) && (targetVertex(itOut)==endState(hmm))) {
+                            property(transitionCounter, value(itOut)) += (value(fMat, (j+1) * numRows + value(itAll)) * getTransitionProbability(hmm, value(itAll),endState(hmm)) / modelLogProb);
+                        } else {
+                            if (!isSilent(hmm, targetVertex(itOut))) {
+                                if (j < (len - 1)) property(transitionCounter, value(itOut)) += (value(fMat, (j+1) * numRows + value(itAll)) * getTransitionProbability(hmm, value(itOut)) * getEmissionProbability(hmm, targetVertex(itOut), nextC) * value(bMat, (j+2) * numRows + targetVertex(itOut)) / modelLogProb);
+                            } else {
+                                property(transitionCounter, value(itOut)) += (value(fMat, (j+1) * numRows + value(itAll)) * getTransitionProbability(hmm, value(itOut)) * value(bMat, (j+1) * numRows + targetVertex(itOut)) / modelLogProb);
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        // Expectation step
+        _parameterEstimator(hmm,emissionCounter, transitionCounter);
+
+
+        // Termination?
+        if ((iter > 5) && ((totalModelLogProb - lastTotalModelProb) < epsilon)) {
+            lastTotalModelProb = totalModelLogProb;
+            break;
+        } else {
+            lastTotalModelProb = totalModelLogProb;
+        }
+    }
+    return lastTotalModelProb;
 }
 
-///////////////////////////////////////////////////////////////////////////////////////
-
 template <typename TAlphabet, typename TProbability, typename TSpec, typename TSequence>
-inline TProbability 
+inline TProbability
 baumWelchAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec > >& hmm,
-				   StringSet<TSequence> const& seqSet)
+                   StringSet<TSequence> const& seqSet)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	TSize maxIter = 100;
-	TProbability epsilon = 0.00001;
-	return _baumWelchAlgorithm(hmm, seqSet, maxIter, epsilon);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    TSize maxIter = 100;
+    TProbability epsilon = 0.00001;
+    return _baumWelchAlgorithm(hmm, seqSet, maxIter, epsilon);
 }
 
 /*
@@ -1040,99 +964,99 @@ baumWelchAlgorithm(Graph<Hmm<TAlphabet, TProbability, TSpec > >& hmm,
 template < typename TAlphabet, typename TProbability, typename TSpec, typename TMat, typename TConsensus, typename TSize>
 inline void
 _profileHmmCounter(Graph<Hmm<TAlphabet, TProbability, TSpec> >& pHmm,
-					TMat const& matr,
-					TConsensus const& consensus,
-					TSize const& numRows,
-					TSize const& numCols)
+                    TMat const& matr,
+                    TConsensus const& consensus,
+                    TSize const& numRows,
+                    TSize const& numCols)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Value<TConsensus>::Type TValue;
-
-	// Initialization
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	TValue gapChar = gapValue<TValue>();
-	TVertexDescriptor begState = beginState(pHmm);
-	TVertexDescriptor eState = endState(pHmm);
-	TVertexDescriptor matchState = 1;
-	TVertexDescriptor insertState = 2;
-	TVertexDescriptor deleteState = 3;
-
-	typedef String<TProbability> TCountString;
-	TCountString transitionCounter;
-	resize(transitionCounter, getIdUpperBound(_getEdgeIdManager(pHmm)), 0.0);
-	StringSet<TCountString> emissionCounter;
-	TSize nR = getIdUpperBound(_getVertexIdManager(pHmm));
-	for(TSize i =0; i<nR;++i) {
-		TCountString emisCount;
-		resize(emisCount,alphSize, 0.0);
-		appendValue(emissionCounter,emisCount);
-	}
-
-
-	String<TVertexDescriptor> oldCol;
-	String<TVertexDescriptor> currCol;
-	resize(oldCol, numRows, begState);
-	resize(currCol, numRows, 0);
-	TEdgeDescriptor currEdge;
-	
-	for(TSize i = 0; i<length(consensus); ++i) {
-		//transitionvalues
-		
-		//being in insertState
-		if (value(consensus, i)==gapChar){
-			for(TSize j = 0; j<numRows; ++j){
-				if ((value(matr, j * numCols + i)!=gapChar)){
-					value(currCol,j) = insertState; 
-					currEdge = findEdge(pHmm, value(oldCol,j), value(currCol,j));
-					property(transitionCounter, currEdge) += 1;
-					value(oldCol,j) = value(currCol,j);
-				}
-				else if ((value(matr, j * numCols + i)==gapChar) ){
-					value(currCol,j) = value(oldCol,j);
-				}
-			}
-		}
-		//being in normal State
-		else{
-			for(TSize j = 0; j<numRows; ++j){
-				if(value(matr, j * numCols + i)!=gapChar) value(currCol,j) = matchState; 
-				else value(currCol,j) = deleteState;
-				currEdge = findEdge(pHmm, value(oldCol,j), value(currCol,j));
-				property(transitionCounter, currEdge) += 1;
-				value(oldCol,j)=value(currCol,j);
-			}
-		}
-		//emissionvalues
-		if (value(consensus, i)==gapChar) {
-			for(TSize j = 0; j<numRows; ++j) 
-				if(value(matr, j * numCols + i)!=gapChar) 
-					value(value(emissionCounter, insertState), ordValue( (TAlphabet)  value(matr, j * numCols + i) ) ) += 1;
-			
-			continue;
-		}
-		else 
-			for(TSize j = 0; j<numRows; ++j) 
-				if(value(matr, j * numCols + i)!=gapChar) 
-					value(value(emissionCounter, matchState), ordValue( (TAlphabet)  value(matr, j * numCols + i) ) ) += 1;
-		
-		matchState+=3;
-		if ((insertState+3)==eState) insertState+=2;
-		else insertState+=3;
-		deleteState+=3;
-	}
-	
-	//transition in endState
-	for(TSize j = 0; j<numRows; ++j){
-		currEdge = findEdge(pHmm,value(currCol,j),eState);
-		property(transitionCounter, currEdge) += 1;
-	}
-	
-	_parameterEstimator(pHmm, emissionCounter, transitionCounter);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Value<TConsensus>::Type TValue;
+
+    // Initialization
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+    TValue gapChar = gapValue<TValue>();
+    TVertexDescriptor begState = beginState(pHmm);
+    TVertexDescriptor eState = endState(pHmm);
+    TVertexDescriptor matchState = 1;
+    TVertexDescriptor insertState = 2;
+    TVertexDescriptor deleteState = 3;
+
+    typedef String<TProbability> TCountString;
+    TCountString transitionCounter;
+    resize(transitionCounter, getIdUpperBound(_getEdgeIdManager(pHmm)), 0.0);
+    StringSet<TCountString> emissionCounter;
+    TSize nR = getIdUpperBound(_getVertexIdManager(pHmm));
+    for(TSize i =0; i<nR;++i) {
+        TCountString emisCount;
+        resize(emisCount,alphSize, 0.0);
+        appendValue(emissionCounter,emisCount);
+    }
+
+
+    String<TVertexDescriptor> oldCol;
+    String<TVertexDescriptor> currCol;
+    resize(oldCol, numRows, begState);
+    resize(currCol, numRows, 0);
+    TEdgeDescriptor currEdge;
+
+    for(TSize i = 0; i<length(consensus); ++i) {
+        //transitionvalues
+
+        //being in insertState
+        if (value(consensus, i)==gapChar){
+            for(TSize j = 0; j<numRows; ++j){
+                if ((value(matr, j * numCols + i)!=gapChar)){
+                    value(currCol,j) = insertState;
+                    currEdge = findEdge(pHmm, value(oldCol,j), value(currCol,j));
+                    property(transitionCounter, currEdge) += 1;
+                    value(oldCol,j) = value(currCol,j);
+                }
+                else if ((value(matr, j * numCols + i)==gapChar) ){
+                    value(currCol,j) = value(oldCol,j);
+                }
+            }
+        }
+        //being in normal State
+        else{
+            for(TSize j = 0; j<numRows; ++j){
+                if(value(matr, j * numCols + i)!=gapChar) value(currCol,j) = matchState;
+                else value(currCol,j) = deleteState;
+                currEdge = findEdge(pHmm, value(oldCol,j), value(currCol,j));
+                property(transitionCounter, currEdge) += 1;
+                value(oldCol,j)=value(currCol,j);
+            }
+        }
+        //emissionvalues
+        if (value(consensus, i)==gapChar) {
+            for(TSize j = 0; j<numRows; ++j)
+                if(value(matr, j * numCols + i)!=gapChar)
+                    value(value(emissionCounter, insertState), ordValue( (TAlphabet)  value(matr, j * numCols + i) ) ) += 1;
+
+            continue;
+        }
+        else
+            for(TSize j = 0; j<numRows; ++j)
+                if(value(matr, j * numCols + i)!=gapChar)
+                    value(value(emissionCounter, matchState), ordValue( (TAlphabet)  value(matr, j * numCols + i) ) ) += 1;
+
+        matchState+=3;
+        if ((insertState+3)==eState) insertState+=2;
+        else insertState+=3;
+        deleteState+=3;
+    }
+
+    //transition in endState
+    for(TSize j = 0; j<numRows; ++j){
+        currEdge = findEdge(pHmm,value(currCol,j),eState);
+        property(transitionCounter, currEdge) += 1;
+    }
+
+    _parameterEstimator(pHmm, emissionCounter, transitionCounter);
 }
 
 
@@ -1141,85 +1065,85 @@ _profileHmmCounter(Graph<Hmm<TAlphabet, TProbability, TSpec> >& pHmm,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TConsensus>
 inline void
 _createProfileHmm(Graph<Hmm<TAlphabet, TCargo, TSpec> >& pHmm,
-				   TConsensus const& consensus)
+                   TConsensus const& consensus)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Value<TConsensus>::Type TValue;
-	
-	// Initialization
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	TValue gapChar = gapValue<TValue>();
-	clear(pHmm);
-	
-	// Add begin state
-	TVertexDescriptor begState = addVertex(pHmm);
-	assignBeginState(pHmm, begState);
-	
-	// Add for each consensus letter 3 states
-	for (TSize i=0;i<length(consensus);++i){
-		if (value(consensus,i) == gapChar) continue;
-		addVertex(pHmm); addVertex(pHmm); addVertex(pHmm, true);
-	}
-	
-	// Add last insertion state
-	TVertexDescriptor lastIState = addVertex(pHmm);
-	
-	// Add end state
-	TVertexDescriptor endState = addVertex(pHmm);
-	assignEndState(pHmm, endState);
-	
-	// Is there no consensus letter?
-	if (lastIState == 1) {
-		clear(pHmm);
-		return;
-	}
-
-	// Remember the kind of state
-	TVertexDescriptor mState = 1;
-	TVertexDescriptor iState = 2;
-	TVertexDescriptor dState = 3;
-
-	// Add tranistions from begin state
-	addEdge(pHmm, begState, mState);
-	addEdge(pHmm, begState, iState);
-	addEdge(pHmm, begState, dState);
-
-	// Add all remaining transitions
-	for (TSize i=0;i<length(consensus);++i){	
-		if (value(consensus,i) == gapChar) continue;
-		else if ((mState + 3) == lastIState) {
-			addEdge(pHmm, iState, mState);	
-			addEdge(pHmm, iState, iState);
-			addEdge(pHmm, iState, dState);
-			break;
-		}
-		else{
-			addEdge(pHmm, mState, (mState+3));
-			addEdge(pHmm, iState, mState);
-			addEdge(pHmm, dState, (mState+3));
-			addEdge(pHmm, mState, (iState+3));
-			addEdge(pHmm, iState, iState);
-			addEdge(pHmm, dState, (iState+3));
-			addEdge(pHmm, mState, (dState+3));
-			addEdge(pHmm, iState, dState);
-			addEdge(pHmm, dState, (dState+3));
-			mState+=3;
-			iState+=3;
-			dState+=3;
-		}
-	}
-
-	// Transitions to the endState and the last I-state
-	addEdge(pHmm, mState, endState);
-	addEdge(pHmm, mState, lastIState);
-	addEdge(pHmm, lastIState, endState);
-	addEdge(pHmm, lastIState, lastIState);
-	addEdge(pHmm, dState, endState);
-	addEdge(pHmm, dState, lastIState);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Value<TConsensus>::Type TValue;
+
+    // Initialization
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+    TValue gapChar = gapValue<TValue>();
+    clear(pHmm);
+
+    // Add begin state
+    TVertexDescriptor begState = addVertex(pHmm);
+    assignBeginState(pHmm, begState);
+
+    // Add for each consensus letter 3 states
+    for (TSize i=0;i<length(consensus);++i){
+        if (value(consensus,i) == gapChar) continue;
+        addVertex(pHmm); addVertex(pHmm); addVertex(pHmm, true);
+    }
+
+    // Add last insertion state
+    TVertexDescriptor lastIState = addVertex(pHmm);
+
+    // Add end state
+    TVertexDescriptor endState = addVertex(pHmm);
+    assignEndState(pHmm, endState);
+
+    // Is there no consensus letter?
+    if (lastIState == 1) {
+        clear(pHmm);
+        return;
+    }
+
+    // Remember the kind of state
+    TVertexDescriptor mState = 1;
+    TVertexDescriptor iState = 2;
+    TVertexDescriptor dState = 3;
+
+    // Add tranistions from begin state
+    addEdge(pHmm, begState, mState);
+    addEdge(pHmm, begState, iState);
+    addEdge(pHmm, begState, dState);
+
+    // Add all remaining transitions
+    for (TSize i=0;i<length(consensus);++i){
+        if (value(consensus,i) == gapChar) continue;
+        else if ((mState + 3) == lastIState) {
+            addEdge(pHmm, iState, mState);
+            addEdge(pHmm, iState, iState);
+            addEdge(pHmm, iState, dState);
+            break;
+        }
+        else{
+            addEdge(pHmm, mState, (mState+3));
+            addEdge(pHmm, iState, mState);
+            addEdge(pHmm, dState, (mState+3));
+            addEdge(pHmm, mState, (iState+3));
+            addEdge(pHmm, iState, iState);
+            addEdge(pHmm, dState, (iState+3));
+            addEdge(pHmm, mState, (dState+3));
+            addEdge(pHmm, iState, dState);
+            addEdge(pHmm, dState, (dState+3));
+            mState+=3;
+            iState+=3;
+            dState+=3;
+        }
+    }
+
+    // Transitions to the endState and the last I-state
+    addEdge(pHmm, mState, endState);
+    addEdge(pHmm, mState, lastIState);
+    addEdge(pHmm, lastIState, endState);
+    addEdge(pHmm, lastIState, lastIState);
+    addEdge(pHmm, dState, endState);
+    addEdge(pHmm, dState, lastIState);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1229,31 +1153,31 @@ _createProfileHmm(Graph<Hmm<TAlphabet, TCargo, TSpec> >& pHmm,
 //msaToProfileHmm(matr, hmm, 5);
 
 template<typename TAlignmentChar, typename TAlphabet, typename TProbability, typename TSpec, typename TSize>
-inline void 
+inline void
 msaToProfileHmm(String<TAlignmentChar> const& matr,
-				Graph<Hmm<TAlphabet, TProbability, TSpec> >& pHmm,
-				TSize nSeq)
+                Graph<Hmm<TAlphabet, TProbability, TSpec> >& pHmm,
+                TSize nSeq)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > THmm;
-	
-	// Consensus 
-	String<unsigned int> coverage;
-	String<char> gappedConsensus;
-	String<Dna> consensusSequence;
-	consensusCalling(matr, consensusSequence, gappedConsensus, coverage, nSeq, MajorityVote() );
-
-	// Build the HMM topology
-	_createProfileHmm(pHmm,gappedConsensus);
-
-	// Parameterize the pHmm
-	TSize numCols = length(matr) / nSeq;
-	_profileHmmCounter(pHmm, matr, gappedConsensus, nSeq, numCols);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > THmm;
+
+    // Consensus
+    String<unsigned int> coverage;
+    String<char> gappedConsensus;
+    String<Dna> consensusSequence;
+    consensusCalling(matr, consensusSequence, gappedConsensus, coverage, nSeq, MajorityVote() );
+
+    // Build the HMM topology
+    _createProfileHmm(pHmm,gappedConsensus);
+
+    // Parameterize the pHmm
+    TSize numCols = length(matr) / nSeq;
+    _profileHmmCounter(pHmm, matr, gappedConsensus, nSeq, numCols);
 }
 
 */
 
 
-}// namespace SEQAN_NAMESPACE_MAIN
+}  // namespace seqan
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/graph_algorithms/graph_algorithm_lis_his.h b/seqan/graph_algorithms/graph_algorithm_lis_his.h
index 6aef58e..e1cfa6c 100644
--- a/seqan/graph_algorithms/graph_algorithm_lis_his.h
+++ b/seqan/graph_algorithms/graph_algorithm_lis_his.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -50,26 +50,26 @@ typedef Tag<Lcs_> Lcs;
 template<typename TSortedSequence, typename TKey>
 inline typename TSortedSequence::const_iterator
 _previousInSortedSequence(TSortedSequence const& list, TKey const key) {
-	SEQAN_CHECKPOINT
-	typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
-
-	TSortedSequenceIter a_k_it = list.lower_bound(key);
-	// Now we need to move one to the front
-
-	if (a_k_it != list.end()) {
-		// If we are at the beginning, no predecessor
-		if (a_k_it == list.begin()) a_k_it = list.end();
-		else --a_k_it;
-	} else {
-		// If we are at the end, the predecessor is the last element of the list
-		TSortedSequenceIter tmp = list.begin();
-		if (tmp != list.end()) {
-			do {
-				a_k_it = tmp;
-			} while(++tmp != list.end());
-		}
-	}
-	return a_k_it;
+    SEQAN_CHECKPOINT
+    typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
+
+    TSortedSequenceIter a_k_it = list.lower_bound(key);
+    // Now we need to move one to the front
+
+    if (a_k_it != list.end()) {
+        // If we are at the beginning, no predecessor
+        if (a_k_it == list.begin()) a_k_it = list.end();
+        else --a_k_it;
+    } else {
+        // If we are at the end, the predecessor is the last element of the list
+        TSortedSequenceIter tmp = list.begin();
+        if (tmp != list.end()) {
+            do {
+                a_k_it = tmp;
+            } while(++tmp != list.end());
+        }
+    }
+    return a_k_it;
 }
 
 
@@ -79,14 +79,14 @@ _previousInSortedSequence(TSortedSequence const& list, TKey const key) {
 template<typename TSortedSequence, typename TIterator>
 inline typename TSortedSequence::const_iterator
 _nextInSortedSequence(TSortedSequence const& list, TIterator const& prev) {
-	SEQAN_CHECKPOINT
-	typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
-		
-	TSortedSequenceIter b_l_it;
-	if (prev == list.end()) b_l_it = list.begin();
-	else b_l_it = list.upper_bound(*prev);
-
-	return b_l_it;
+    SEQAN_CHECKPOINT
+    typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
+
+    TSortedSequenceIter b_l_it;
+    if (prev == list.end()) b_l_it = list.begin();
+    else b_l_it = list.upper_bound(*prev);
+
+    return b_l_it;
 }
 
 
@@ -99,7 +99,7 @@ _nextInSortedSequence(TSortedSequence const& list, TIterator const& prev) {
  *
  * @signature void longestIncreasingSubsequence(str, pos);
  *
- * @param[in]  str An arbitrary @link SequenceConcept @endlink object.
+ * @param[in]  str An arbitrary @link ContainerConcept @endlink object.
  * @param[out] pos A String with the positions that belong to the longest increasing subsequence.
  *
  * @section Remarks
@@ -108,11 +108,11 @@ _nextInSortedSequence(TSortedSequence const& list, TIterator const& prev) {
  *
  * @section Example
  *
- * @include demos/graph_algorithms/longest_increasing_subsequence.cpp
+ * @include demos/dox/graph_algorithms/longest_increasing_subsequence.cpp
  *
  * @code{.console}
  * 5,3,4,9,6,2,1,8,7,10,
- * Lis: 
+ * Lis:
  * 3,4,6,7,10,
  * @endcode
  *
@@ -120,72 +120,59 @@ _nextInSortedSequence(TSortedSequence const& list, TIterator const& prev) {
  * @see longestCommonSubsequence
  */
 
-/**
-.Function.longestIncreasingSubsequence:
-..summary:Computes the longest increasing subsequence.
-..cat:Alignments
-..signature:longestIncreasingSubsequence(str, pos)
-..param.str:In-parameter: An arbitrary string.
-...type:Class.String
-..param.pos:Out-parameter: A String with the positions that belong to the longest increasing subsequence.
-...remarks:
-The last position in pos indicates the first element in the longest increasing subsequence.
-That's why pos should be a Block-String (Stack).
-..include:seqan/graph_algorithms.h
-*/
 template<typename TString, typename TPositions>
 inline void
 longestIncreasingSubsequence(TString const& str, TPositions& pos) {
-	SEQAN_CHECKPOINT
-
-	// The list of decreasing covers, only the smallest number must be remembered
-	// See Gusfield
-	typedef std::pair<typename Value<TString>::Type, typename Position<TPositions>::Type> TKey;
-	typedef std::set<TKey, std::less<TKey> > TSortedSequence;
-	typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
-	TSortedSequence list;
-
-	// The trace-back graph
-	typedef Graph<Directed<void, WithoutEdgeId> > TGraph;
-	typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TGraph g;
-
-	// Walk through the sequence and build the decreasing covers
-	typedef typename Iterator<TString const, Rooted>::Type TStringIter;
-	TStringIter endIt = end(str);
-	for(TStringIter it = begin(str); it != endIt; ++it) {
-		// Get previous element
-		TSortedSequenceIter a_k_it = _previousInSortedSequence(list, std::make_pair(*it, 0)); 
-		
-		// Get next element
-		TSortedSequenceIter b_l_it = _nextInSortedSequence(list, a_k_it);
-		
-		// Delete from list
-		if (b_l_it != list.end()) list.erase(*b_l_it);
-
-		// Insert new list element
-		list.insert(std::make_pair(*it, position(it)));
-
-		// Create the corresponding node
-		// Note: The VertexDescriptor == position(it)
-		addVertex(g);
-
-
-		// Connect to predecessor
-		if (a_k_it != list.end()) addEdge(g, (TVertexDescriptor) position(it), (TVertexDescriptor) a_k_it->second);
-	}
-
-	// Trace-back
-	if (list.rbegin() == list.rend()) return;
-	else {
-		// Start with the maximal position in the list == Vertex Descriptor
-		TVertexDescriptor v = list.rbegin()->second;
-		while (true) {
-			appendValue(pos, v, Generous());
-			if (g.data_vertex[v]) v = (*g.data_vertex[v]).data_target;
-			else break;
-		}
-	}
+    SEQAN_CHECKPOINT
+
+    // The list of decreasing covers, only the smallest number must be remembered
+    // See Gusfield
+    typedef std::pair<typename Value<TString>::Type, typename Position<TPositions>::Type> TKey;
+    typedef std::set<TKey, std::less<TKey> > TSortedSequence;
+    typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
+    TSortedSequence list;
+
+    // The trace-back graph
+    typedef Graph<Directed<void, WithoutEdgeId> > TGraph;
+    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TGraph g;
+
+    // Walk through the sequence and build the decreasing covers
+    typedef typename Iterator<TString const, Rooted>::Type TStringIter;
+    TStringIter endIt = end(str);
+    for(TStringIter it = begin(str); it != endIt; ++it) {
+        // Get previous element
+        TSortedSequenceIter a_k_it = _previousInSortedSequence(list, std::make_pair(*it, 0));
+
+        // Get next element
+        TSortedSequenceIter b_l_it = _nextInSortedSequence(list, a_k_it);
+
+        // Delete from list
+        if (b_l_it != list.end()) list.erase(*b_l_it);
+
+        // Insert new list element
+        list.insert(std::make_pair(*it, position(it)));
+
+        // Create the corresponding node
+        // Note: The VertexDescriptor == position(it)
+        addVertex(g);
+
+
+        // Connect to predecessor
+        if (a_k_it != list.end()) addEdge(g, (TVertexDescriptor) position(it), (TVertexDescriptor) a_k_it->second);
+    }
+
+    // Trace-back
+    if (list.rbegin() == list.rend()) return;
+    else {
+        // Start with the maximal position in the list == Vertex Descriptor
+        TVertexDescriptor v = list.rbegin()->second;
+        while (true) {
+            appendValue(pos, v, Generous());
+            if (g.data_vertex[v]) v = (*g.data_vertex[v]).data_target;
+            else break;
+        }
+    }
 }
 
 
@@ -202,21 +189,21 @@ longestIncreasingSubsequence(TString const& str, TPositions& pos) {
  *
  * @signature void longestCommonSubsequence(str1, str2, nSize, pos);
  *
- * @param[in]  str1  An arbitrary @link SequenceConcept @endlink object.
- * @param[in]  str2  A second arbitrary @link SequenceConcept @endlink object.
+ * @param[in]  str1  An arbitrary @link ContainerConcept @endlink object.
+ * @param[in]  str2  A second arbitrary @link ContainerConcept @endlink object.
  * @param[in]  nSize The neighbourhood size to use.
  * @param[out] pos   A String with pairs of positions that indicate the longest common subsequence.
  *
  * @section Example
  *
- * @include demos/graph_algorithms/longest_common_subsequence.cpp
+ * @include demos/dox/graph_algorithms/longest_common_subsequence.cpp
  *
  * @code{.console}
  * Score = 3
  * Alignment matrix:
- *       0     .    
+ *       0     .
  *         aba--cx-
- *          ||  |  
+ *          ||  |
  *         -baabc-a
  * @endcode
  *
@@ -224,71 +211,58 @@ longestIncreasingSubsequence(TString const& str, TPositions& pos) {
  * @see longestIncreasingSubsequence
  */
 
-/**
-.Function.longestCommonSubsequence:
-..summary:Computes the longest common subsequence.
-..cat:Alignments
-..signature:longestCommonSubsequence(str1, str2, nSize, pos)
-..param.str1:In-parameter: An arbitrary string.
-...type:Class.String
-..param.str2:In-parameter: An arbitrary string.
-...type:Class.String
-..param.pos:Out-parameter: A String with pairs of positions that indicate the longest common subsequence.
-...remarks:
-..include:seqan/graph_algorithms.h
-*/
 template<typename TString1, typename TString2, typename TNeighborhoodSize, typename TFinalPos>
 inline void
 longestCommonSubsequence(TString1 const& str1,
-						 TString2 const& str2,
-						 TNeighborhoodSize nSize,
-						 TFinalPos& pos) 
+                         TString2 const& str2,
+                         TNeighborhoodSize nSize,
+                         TFinalPos& pos)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TString1>::Type TValue;
-	typedef typename Size<TString1>::Type TSize;
-	typedef typename Position<TString1>::Type TPos;
-	TSize alphabet_size = ValueSize<TValue>::VALUE;
-
-	// The occurrences of each letter in the second string
-	typedef String<TPos> TPositions;
-	String<TPositions> occ;
-	resize(occ, alphabet_size, TPositions());
-	typedef typename Iterator<TString2 const, Standard>::Type TStringIter;
-	TStringIter itStr2 = begin(str2, Standard());
-	TStringIter endItStr2 = end(str2, Standard());
-	TPos current_pos = 0;
-	for(; itStr2 != endItStr2; ++itStr2, ++current_pos) appendValue(occ[ordValue(*itStr2)], current_pos, Generous());
-
-	// Build the combined string
-	String<TPos> finalSeq;
-	String<TPos> mapping;
-	TStringIter itStr1 = begin(str1, Standard());
-	TStringIter endItStr1 = end(str1, Standard());
-	current_pos = 0;
-	TPos diff = 0;
-	for(; itStr1 != endItStr1; ++itStr1, ++current_pos) {
-		TPositions& current_occ = occ[ordValue(*itStr1)];
-		for(int i = length(current_occ)-1; i>=0; --i) {
-			// Do we have a neighborhood
-			diff = (current_pos < current_occ[i]) ? current_occ[i] - current_pos : current_pos - current_occ[i];
-			if (diff > (TPos) nSize) continue;
-			appendValue(finalSeq, current_occ[i], Generous());
-			appendValue(mapping, current_pos, Generous());
-		}
-	}
-
-	// Call longest increasing subsequence
-	typedef String<TSize> TResult;
-	TResult result;
-	longestIncreasingSubsequence(finalSeq, result);
-	
-	// Insert the common pairs
-	typedef typename Iterator<TResult, Standard>::Type TResultIter;
-	TResultIter itResult = begin(result, Standard());
-	TResultIter endResult = end(result, Standard());
-	for(; itResult != endResult; ++itResult) 
-		appendValue(pos, std::make_pair(mapping[*itResult], finalSeq[*itResult]), Generous());
+    SEQAN_CHECKPOINT
+    typedef typename Value<TString1>::Type TValue;
+    typedef typename Size<TString1>::Type TSize;
+    typedef typename Position<TString1>::Type TPos;
+    TSize alphabet_size = ValueSize<TValue>::VALUE;
+
+    // The occurrences of each letter in the second string
+    typedef String<TPos> TPositions;
+    String<TPositions> occ;
+    resize(occ, alphabet_size, TPositions());
+    typedef typename Iterator<TString2 const, Standard>::Type TStringIter;
+    TStringIter itStr2 = begin(str2, Standard());
+    TStringIter endItStr2 = end(str2, Standard());
+    TPos current_pos = 0;
+    for(; itStr2 != endItStr2; ++itStr2, ++current_pos) appendValue(occ[ordValue(*itStr2)], current_pos, Generous());
+
+    // Build the combined string
+    String<TPos> finalSeq;
+    String<TPos> mapping;
+    TStringIter itStr1 = begin(str1, Standard());
+    TStringIter endItStr1 = end(str1, Standard());
+    current_pos = 0;
+    TPos diff = 0;
+    for(; itStr1 != endItStr1; ++itStr1, ++current_pos) {
+        TPositions& current_occ = occ[ordValue(*itStr1)];
+        for(int i = length(current_occ)-1; i>=0; --i) {
+            // Do we have a neighborhood
+            diff = (current_pos < current_occ[i]) ? current_occ[i] - current_pos : current_pos - current_occ[i];
+            if (diff > (TPos) nSize) continue;
+            appendValue(finalSeq, current_occ[i], Generous());
+            appendValue(mapping, current_pos, Generous());
+        }
+    }
+
+    // Call longest increasing subsequence
+    typedef String<TSize> TResult;
+    TResult result;
+    longestIncreasingSubsequence(finalSeq, result);
+
+    // Insert the common pairs
+    typedef typename Iterator<TResult, Standard>::Type TResultIter;
+    TResultIter itResult = begin(result, Standard());
+    TResultIter endResult = end(result, Standard());
+    for(; itResult != endResult; ++itResult)
+        appendValue(pos, std::make_pair(mapping[*itResult], finalSeq[*itResult]), Generous());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -296,60 +270,60 @@ longestCommonSubsequence(TString1 const& str1,
 template<typename TAlign, typename TStringSet>
 inline int
 globalAlignment(TAlign& align,
-				TStringSet const& str,
-				Lcs)
+                TStringSet const& str,
+                Lcs)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Id<TStringSet>::Type TId;
-	typedef typename Size<TStringSet>::Type TSize;
-	TId id1 = positionToId(str, 0);
-	TId id2 = positionToId(str, 1);
-		
-	// Lcs between first and second string
-	String<std::pair<TSize, TSize> > pos1;
-	longestCommonSubsequence(str[0], str[1], 100, pos1);
-	//longestCommonSubsequence(str[0], str[1], 800, pos1);
-
-	// Extend the matches as long as possible
-	TSize oldI = 0;
-	TSize oldJ = 0;
-	TSize totalLen = 0;
-	if (length(pos1)) {
-		TSize lenMatch = 1;				
-		int last = length(pos1)-1;		
-		TSize iBegin = pos1[last].first;
-		TSize jBegin = pos1[last].second;
-		for(int z = last - 1; z>=0; --z) {
-			if ((pos1[z].first == pos1[z+1].first + 1) &&
-				(pos1[z].second == pos1[z+1].second + 1)) 
-			{
-				++lenMatch;
-			} else {
-				if (oldI < iBegin) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) iBegin - oldI, 1);
-				if (oldJ < jBegin) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) jBegin - oldJ, 2);
-				oldI = iBegin + lenMatch;
-				oldJ = jBegin + lenMatch;
-			
-				_alignTracePrint(align, str[0], str[1], id1, iBegin, id2, jBegin, lenMatch, 0);
-				totalLen += lenMatch;
-				lenMatch = 1;
-				iBegin = pos1[z].first;
-				jBegin = pos1[z].second;
-			}
-		}
-		// Process last match
-		if (oldI < iBegin) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) iBegin - oldI, 1);
-		if (oldJ < jBegin) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) jBegin - oldJ, 2);
-		oldI = iBegin + lenMatch;
-		oldJ = jBegin + lenMatch;
-		_alignTracePrint(align, str[0], str[1], id1, iBegin, id2, jBegin, lenMatch, 0);
-		totalLen += lenMatch;
-	}
-	// Process left overs
-	if (oldI < length(str[0])) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) length(str[0]) - oldI,  1);
-	if (oldJ < length(str[1])) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) length(str[1]) - oldJ, 2);
-	
-	return (int) totalLen;
+    SEQAN_CHECKPOINT
+    typedef typename Id<TStringSet>::Type TId;
+    typedef typename Size<TStringSet>::Type TSize;
+    TId id1 = positionToId(str, 0);
+    TId id2 = positionToId(str, 1);
+
+    // Lcs between first and second string
+    String<std::pair<TSize, TSize> > pos1;
+    longestCommonSubsequence(str[0], str[1], 100, pos1);
+    //longestCommonSubsequence(str[0], str[1], 800, pos1);
+
+    // Extend the matches as long as possible
+    TSize oldI = 0;
+    TSize oldJ = 0;
+    TSize totalLen = 0;
+    if (length(pos1)) {
+        TSize lenMatch = 1;
+        int last = length(pos1)-1;
+        TSize iBegin = pos1[last].first;
+        TSize jBegin = pos1[last].second;
+        for(int z = last - 1; z>=0; --z) {
+            if ((pos1[z].first == pos1[z+1].first + 1) &&
+                (pos1[z].second == pos1[z+1].second + 1))
+            {
+                ++lenMatch;
+            } else {
+                if (oldI < iBegin) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) iBegin - oldI, 1);
+                if (oldJ < jBegin) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) jBegin - oldJ, 2);
+                oldI = iBegin + lenMatch;
+                oldJ = jBegin + lenMatch;
+
+                _alignTracePrint(align, str[0], str[1], id1, iBegin, id2, jBegin, lenMatch, 0);
+                totalLen += lenMatch;
+                lenMatch = 1;
+                iBegin = pos1[z].first;
+                jBegin = pos1[z].second;
+            }
+        }
+        // Process last match
+        if (oldI < iBegin) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) iBegin - oldI, 1);
+        if (oldJ < jBegin) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) jBegin - oldJ, 2);
+        oldI = iBegin + lenMatch;
+        oldJ = jBegin + lenMatch;
+        _alignTracePrint(align, str[0], str[1], id1, iBegin, id2, jBegin, lenMatch, 0);
+        totalLen += lenMatch;
+    }
+    // Process left overs
+    if (oldI < length(str[0])) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) length(str[0]) - oldI,  1);
+    if (oldJ < length(str[1])) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) length(str[1]) - oldJ, 2);
+
+    return (int) totalLen;
 }
 
 
@@ -366,7 +340,7 @@ globalAlignment(TAlign& align,
  *
  * @signature void heaviestIncreasingSubsequence(str, weights, pos);
  *
- * @param[in]  str     An arbitrary @link SequenceConcept @endlink object.
+ * @param[in]  str     An arbitrary @link ContainerConcept @endlink object.
  * @param[in]  weights A String with a weight for each position in the string.
  * @param[out] pos     A String with positions that indicate the members of the heaviest increasing subsequence.
  *
@@ -377,11 +351,11 @@ globalAlignment(TAlign& align,
  *
  * @section Example
  *
- * @include demos/graph_algorithms/heaviest_increasing_subsequence.cpp
+ * @include demos/dox/graph_algorithms/heaviest_increasing_subsequence.cpp
  *
  * @code{.console}
  * z(Weight=1),e(Weight=1),i(Weight=10),t(Weight=1),g(Weight=1),e(Weight=1),i(Weight=1),s(Weight=1),t(Weight=1),
- * His: 
+ * His:
  * e,i,s,t,(Weight=13)
  * @endcode
  *
@@ -389,104 +363,89 @@ globalAlignment(TAlign& align,
  * @see longestIncreasingSubsequence
  */
 
-/**
-.Function.heaviestIncreasingSubsequence:
-..summary:Computes the heaviest increasing subsequence.
-..cat:Alignments
-..signature:heaviestIncreasingSubsequence(str, weights, pos)
-..param.str:In-parameter: An arbitrary string.
-...type:Class.String
-..param.weights:In-parameter: A weight for each position in the string.
-..param.pos:Out-parameter: A String of positions that indicate the members of the heaviest increasing subsequence.
-...remarks:
-The last position in pos indicates the first member of the heaviest increasing subsequence.
-That's why pos should be a Block-String (Stack).
-Note that only members that contribute a weight are selected, that is, positions with associated weight=0 are ignored.
-..include:seqan/graph_algorithms.h
-*/
 template<typename TString, typename TWeightMap, typename TPositions>
 inline typename Value<TWeightMap>::Type
-heaviestIncreasingSubsequence(TString const& str, 
-							  TWeightMap const& weights, 
-							  TPositions& pos) 
+heaviestIncreasingSubsequence(TString const& str,
+                              TWeightMap const& weights,
+                              TPositions& pos)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Size<TString>::Type TSize;
-	typedef typename Value<TString>::Type TValue;
-	typedef typename Value<TPositions>::Type TPos;
-	typedef typename Value<TWeightMap>::Type TWeight;
-
-	// The list of decreasing covers, only the smallest element of each member must be remembered
-	typedef std::pair<TValue, std::pair<TWeight, TPos> > TKey;
-	typedef std::set<TKey, std::less<TKey> > TSortedSequence;
-	typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
-	TSortedSequence list;
-	
-	// The trace-back graph
-	typedef Graph<Directed<void, WithoutEdgeId> > TGraph;
-	typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TGraph g;
-
-	// Walk through the sequence and build the decreasing covers
-	typedef typename Iterator<TString const, Standard>::Type TStringIter;
-	TStringIter it = begin(str, Standard());
-	TStringIter endIt = end(str, Standard());
-	TSize pos_of_iterator = 0;
-	TWeight w = 0;
-	for(; it != endIt; ++it, ++pos_of_iterator) {
-		w = weights[pos_of_iterator];
-		// Letters that do not contribute a weight (e.g., w = 0) are excluded!
-		// Weights must increase!
-		if (w == 0) {
-			addVertex(g);  // Note: The vertex id corresponds to the position
-			continue;
-		}
-
-
-		// Get previous element
-		TSortedSequenceIter a_k_it = _previousInSortedSequence(list, std::make_pair(*it, std::make_pair(0, 0))); 
-		
-		// Get next element
-		TSortedSequenceIter b_l_it = _nextInSortedSequence(list, a_k_it);
-
-		// Determine new weight
-		if (a_k_it != list.end()) w += a_k_it->second.first;
-
-		// Delete from list
-		while ((b_l_it != list.end()) && 
-				(w >= b_l_it->second.first)) {
-					TSortedSequenceIter tmp = b_l_it;
-					b_l_it = _nextInSortedSequence(list, b_l_it);
-					list.erase(*tmp);
-		}
-
-		// Insert new list element
-		if ((b_l_it == list.end()) ||
-			(*it < b_l_it->first)) {
-				list.insert(std::make_pair(*it, std::make_pair(w, pos_of_iterator)));
-		}
-
-		// Create the corresponding node, pos_of_iterator == Vertex Descriptor
-		addVertex(g);
-
-		// Connect to predecessor
-		if (a_k_it != list.end()) addEdge(g, (TVertexDescriptor) pos_of_iterator, (TVertexDescriptor) a_k_it->second.second);
-	}
-
-	// Trace-back
-	w = 0;
-	if (list.rbegin() == list.rend()) return 0;
-	else {
-		// Last vertex is end of heaviest increasing subsequence
-		TVertexDescriptor v = list.rbegin()->second.second;
-		while (true) {
-			appendValue(pos, v, Generous());
-			w+=weights[v];
-			if (g.data_vertex[v]) v = (*g.data_vertex[v]).data_target;
-			else break;
-		}
-	}
-	return w;
+    SEQAN_CHECKPOINT
+    typedef typename Size<TString>::Type TSize;
+    typedef typename Value<TString>::Type TValue;
+    typedef typename Value<TPositions>::Type TPos;
+    typedef typename Value<TWeightMap>::Type TWeight;
+
+    // The list of decreasing covers, only the smallest element of each member must be remembered
+    typedef std::pair<TValue, std::pair<TWeight, TPos> > TKey;
+    typedef std::set<TKey, std::less<TKey> > TSortedSequence;
+    typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
+    TSortedSequence list;
+
+    // The trace-back graph
+    typedef Graph<Directed<void, WithoutEdgeId> > TGraph;
+    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TGraph g;
+
+    // Walk through the sequence and build the decreasing covers
+    typedef typename Iterator<TString const, Standard>::Type TStringIter;
+    TStringIter it = begin(str, Standard());
+    TStringIter endIt = end(str, Standard());
+    TSize pos_of_iterator = 0;
+    TWeight w = 0;
+    for(; it != endIt; ++it, ++pos_of_iterator) {
+        w = weights[pos_of_iterator];
+        // Letters that do not contribute a weight (e.g., w = 0) are excluded!
+        // Weights must increase!
+        if (w == 0) {
+            addVertex(g);  // Note: The vertex id corresponds to the position
+            continue;
+        }
+
+
+        // Get previous element
+        TSortedSequenceIter a_k_it = _previousInSortedSequence(list, std::make_pair(*it, std::make_pair(0, 0)));
+
+        // Get next element
+        TSortedSequenceIter b_l_it = _nextInSortedSequence(list, a_k_it);
+
+        // Determine new weight
+        if (a_k_it != list.end()) w += a_k_it->second.first;
+
+        // Delete from list
+        while ((b_l_it != list.end()) &&
+                (w >= b_l_it->second.first)) {
+                    TSortedSequenceIter tmp = b_l_it;
+                    b_l_it = _nextInSortedSequence(list, b_l_it);
+                    list.erase(*tmp);
+        }
+
+        // Insert new list element
+        if ((b_l_it == list.end()) ||
+            (*it < b_l_it->first)) {
+                list.insert(std::make_pair(*it, std::make_pair(w, pos_of_iterator)));
+        }
+
+        // Create the corresponding node, pos_of_iterator == Vertex Descriptor
+        addVertex(g);
+
+        // Connect to predecessor
+        if (a_k_it != list.end()) addEdge(g, (TVertexDescriptor) pos_of_iterator, (TVertexDescriptor) a_k_it->second.second);
+    }
+
+    // Trace-back
+    w = 0;
+    if (list.rbegin() == list.rend()) return 0;
+    else {
+        // Last vertex is end of heaviest increasing subsequence
+        TVertexDescriptor v = list.rbegin()->second.second;
+        while (true) {
+            appendValue(pos, v, Generous());
+            w+=weights[v];
+            if (g.data_vertex[v]) v = (*g.data_vertex[v]).data_target;
+            else break;
+        }
+    }
+    return w;
 }
 
 
diff --git a/seqan/graph_algorithms/kruskal.h b/seqan/graph_algorithms/kruskal.h
new file mode 100644
index 0000000..ab5316b
--- /dev/null
+++ b/seqan/graph_algorithms/kruskal.h
@@ -0,0 +1,137 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Kruskal's algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_KRUSKAL_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_KRUSKAL_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function kruskalsAlgorithm()
+// ----------------------------------------------------------------------------
+
+template <typename TWeight, typename TPair>
+struct LessPairI1_ : public std::unary_function<Pair<TWeight, TPair>, bool>
+{
+    bool operator() (Pair<TWeight, TPair> const & a1,
+                     Pair<TWeight, TPair> const & a2) const
+    {
+        return (a1.i1 < a2.i1);
+    }
+};
+
+/*!
+ * @fn kruskalsAlgorithm
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Computes a minimum spanning tree on a graph.
+ *
+ * @signature void kruskalsAlgorithm(edges, g, source, weight);
+ *
+ * @param[out] edges A String of vertex descriptors that represent edges.  Each consecutive pair is an edge with the
+ *                   two end points.
+ * @param[in] g      An undirected graph. Types: Undirected Graph
+ * @param[in] source A source vertex. Types: VertexDescriptor
+ * @param[in] weight Edge weights.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/kruskals_algorithm.cpp
+ *
+ * @include demos/dox/graph_algorithms/kruskals_algorithm.cpp.stdout
+ *
+ * @see primsAlgorithm
+ */
+template <typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TEdges>
+void kruskalsAlgorithm(TEdges & edges,
+                       Graph<TSpec> const & g,
+                       TVertexDescriptor const,
+                       TWeightMap const & weight)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Value<TWeightMap>::Type TWeight;
+
+    typedef Pair<TVertexDescriptor, TVertexDescriptor> TVertexPair;
+    typedef Pair<TWeight, TVertexPair> TWeightEdgePair;
+    typedef String<TWeightEdgePair>  TEdgeList;
+    typedef typename Iterator<TEdgeList>::Type TEdgeListIter;
+    TEdgeList edgeList;
+
+    // Initialization
+    reserve(edges, 2 * (numVertices(g) - 1));
+    UnionFind<TVertexDescriptor> unionFind;
+    resizeVertexMap(unionFind, g);
+
+    // Sort the edges
+    TEdgeIterator itE(g);
+    for(;!atEnd(itE);goNext(itE)) appendValue(edgeList, TWeightEdgePair(getProperty(weight, getValue(itE)), TVertexPair(sourceVertex(itE),targetVertex(itE))));
+    std::sort(begin(edgeList, Standard() ), end(edgeList, Standard() ), LessPairI1_<TWeight, TVertexPair>() );
+
+    // Process each edge
+    TEdgeListIter itEdgeList = begin(edgeList, Standard());
+    TEdgeListIter itEdgeListEnd = end(edgeList, Standard());
+    for (; itEdgeList != itEdgeListEnd; goNext(itEdgeList)) {
+        TVertexDescriptor x = value(itEdgeList).i2.i1;
+        TVertexDescriptor y = value(itEdgeList).i2.i2;
+
+        if (findSet(unionFind, x) == findSet(unionFind, y))
+            continue;
+
+        appendValue(edges, x);
+        appendValue(edges, y);
+        joinSets(unionFind, findSet(unionFind, x), findSet(unionFind, y));
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_KRUSKAL_H_
diff --git a/seqan/graph_algorithms/path_growing.h b/seqan/graph_algorithms/path_growing.h
new file mode 100644
index 0000000..31cf8ab
--- /dev/null
+++ b/seqan/graph_algorithms/path_growing.h
@@ -0,0 +1,134 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Path-Growing algorithm.
+//
+// WARNING: Functionality not carefully tested!
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_PATH_GROWING_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_PATH_GROWING_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Functions
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TWeightMap, typename TEdgeMap>
+typename Value<TWeightMap>::Type
+pathGrowingAlgorithm(TEdgeMap & edgeMap1,
+                     Graph<TSpec> const & g,
+                     TWeightMap const & weightMap)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Value<TWeightMap>::Type TValue;
+    typedef typename Size<Graph<TSpec> >::Type TSize;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    // Make a copy of the graph
+    TGraph mutant(g);
+
+    // Initialy not a single edge is selected
+    resize(edgeMap1, getIdUpperBound(_getEdgeIdManager(g)), false);
+    TEdgeMap edgeMap2 = edgeMap1;
+    TValue edgeMap1Sum = 0;
+    TValue edgeMap2Sum = 0;
+
+    // Run the algorithm
+    TSize i = 1;
+    while (numEdges(mutant) > 0) {
+        TVertexIterator itVert(mutant);
+        while (outDegree(mutant, *itVert) < 1) goNext(itVert);
+        TVertexDescriptor x = *itVert;
+        TVertexDescriptor y;
+        while (outDegree(mutant, x) >= 1) {
+            TOutEdgeIterator itOut(mutant, x);
+            TEdgeDescriptor e = *itOut;
+            TValue max = getProperty(weightMap, e);
+            y = targetVertex(itOut);
+            goNext(itOut);
+            for(;!atEnd(itOut);++itOut) {
+                if (getProperty(weightMap, *itOut) > max) {
+                    e = *itOut;
+                    max = getProperty(weightMap, e);
+                    y = targetVertex(itOut);
+                }
+            }
+            if (i == 1) {
+                // Mark the edge for m1
+                assignProperty(edgeMap1, e, true);
+                edgeMap1Sum += max;
+            } else {
+                // Mark the edge for m2
+                assignProperty(edgeMap2, e, true);
+                edgeMap2Sum += max;
+            }
+            i = 3 - i;
+            removeVertex(mutant, x);
+            x = y;
+        }
+    }
+
+
+    // Check whether we have to swap bool arrays
+    if (edgeMap2Sum > edgeMap1Sum) {
+        edgeMap1Sum = edgeMap2Sum;
+        edgeMap1 = edgeMap2;
+    }
+
+    return edgeMap1Sum;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_PATH_GROWING_H_
diff --git a/seqan/graph_algorithms/prim.h b/seqan/graph_algorithms/prim.h
new file mode 100644
index 0000000..0aa30dc
--- /dev/null
+++ b/seqan/graph_algorithms/prim.h
@@ -0,0 +1,194 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Prim's algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_PRIM_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_PRIM_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function primsAlgorithm()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn primsAlgorithm
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Computes a minimum spanning tree on a graph.
+ *
+ * @signature void primsAlgorithm(predecessor, g, source, weight);
+ *
+ * @param[out] predecessor
+ *                   A property map.  A property map that represents predecessor relationships among vertices.  It
+ *                   determines a minimum spanning tree.
+ * @param[in] g      An undirected graph. Types: Undirected Graph
+ * @param[in] source A source vertex. Types: VertexDescriptor
+ * @param[in] weight Edge weights.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/prims_algorithm.cpp
+ *
+ * @include demos/dox/graph_algorithms/prims_algorithm.cpp.stdout
+ *
+ * @see kruskalsAlgorithm
+ */
+template <typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap>
+void primsAlgorithm(TPredecessorMap & predecessor,
+                    Graph<TSpec> const & g,
+                    TVertexDescriptor const source,
+                    TWeightMap const & weight)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Value<TPredecessorMap>::Type TPred;
+    typedef typename Value<TWeightMap>::Type TWeight;
+
+    typedef std::pair<TWeight, TVertexDescriptor> TWeightVertexPair;
+    std::priority_queue<TWeightVertexPair, std::vector<TWeightVertexPair>, std::greater<TWeightVertexPair> > q;
+
+    // Initialization
+    String<bool> tokenMap;
+    String<TWeight> key;
+    TPred nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
+    TWeight infWeight = _getInfinityDistance(weight);
+    resizeVertexMap(predecessor, g);
+    resizeVertexMap(tokenMap, g);
+    resizeVertexMap(key, g);
+
+    TVertexIterator it(g);
+    while(!atEnd(it)) {
+        TVertexDescriptor u = getValue(it);
+        if (u == source) q.push(std::make_pair(0, u));
+        assignProperty(predecessor, u, nilPred);
+        assignProperty(key, u, infWeight);
+        assignProperty(tokenMap, u, false);
+        goNext(it);
+    }
+
+    assignProperty(key, source, 0);
+    while(!q.empty()) {
+        TVertexDescriptor u = q.top().second;
+        q.pop();
+        if (getProperty(tokenMap, u)) continue;
+        assignProperty(tokenMap, u, true);
+        TOutEdgeIterator itOut(g,u);
+        while(!atEnd(itOut)) {
+            TVertexDescriptor v = targetVertex(itOut);
+            TWeight w = getProperty(weight, getValue(itOut));
+            if ((!getProperty(tokenMap, v)) &&
+                (w < getProperty(key, v))) {
+                    assignProperty(predecessor, v, u);
+                    assignProperty(key, v, w);
+                    q.push(std::make_pair(w, v));
+            }
+            goNext(itOut);
+        }
+    }
+}
+
+// TODO(holtgrew): Document.
+template <typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap>
+void primsAlgorithmSpaceEfficient(TPredecessorMap & predecessor,
+                                  Graph<TSpec> const & g,
+                                  TVertexDescriptor const source,
+                                  TWeightMap const & weight)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Value<TPredecessorMap>::Type TPred;
+    typedef typename Value<TWeightMap>::Type TWeight;
+
+    // Set-up the priority queue
+    typedef Pair<TVertexDescriptor, TWeight> TKeyValue;
+    typedef HeapTree<TKeyValue, std::less<TWeight>, KeyedHeap<> > TKeyedHeap;
+    TKeyedHeap priorityQueue;
+
+    // Initialization
+    String<bool> tokenMap;
+    TPred nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
+    TWeight infWeight = _getInfinityDistance(weight);
+    resizeVertexMap(predecessor, g);
+    resizeVertexMap(tokenMap, g);
+
+    TVertexIterator it(g);
+    for(;!atEnd(it);goNext(it)) {
+        TVertexDescriptor u = value(it);
+        heapInsert(priorityQueue, TKeyValue(u, infWeight));
+        assignProperty(predecessor, u, nilPred);
+        assignProperty(tokenMap, u, false);
+    }
+    heapChangeValue(priorityQueue, source, 0);
+
+    // Iterate until queue is empty
+    while(!empty(priorityQueue)) {
+        TKeyValue kv = heapExtractRoot(priorityQueue);
+        TVertexDescriptor u = kv.i1;
+        assignProperty(tokenMap, u, true);
+        if (kv.i2 == infWeight) continue;
+        TOutEdgeIterator itOut(g,u);
+        for(;!atEnd(itOut);goNext(itOut)) {
+            TVertexDescriptor v = targetVertex(itOut);
+            if (getProperty(tokenMap, v)) continue;
+            TWeight w = getProperty(weight, getValue(itOut));
+            if (w < heapGetValue(priorityQueue, v)) {
+                assignProperty(predecessor, v, u);
+                heapChangeValue(priorityQueue, v, w);
+            }
+        }
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_PRIM_H_
diff --git a/seqan/graph_algorithms/single_source_shortest_path.h b/seqan/graph_algorithms/single_source_shortest_path.h
new file mode 100644
index 0000000..74e6219
--- /dev/null
+++ b/seqan/graph_algorithms/single_source_shortest_path.h
@@ -0,0 +1,233 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Single-Source-Shortest-Path algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_SINGLE_SOURCE_SHORTEST_PATH_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_SINGLE_SOURCE_SHORTEST_PATH_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function singleSourceShortestPath()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TPredecessorMap, typename TVertexDescriptor, typename TNameMap>
+inline void
+_printPath(Graph<TSpec> const& g,
+            TPredecessorMap const& predecessor,
+            TVertexDescriptor const source,
+            TVertexDescriptor const v,
+            TNameMap const& nameMap)
+{
+    if (source == v) {
+        std::cout << getProperty(nameMap, source);
+    } else if (getProperty(predecessor, v) == getNil<typename VertexDescriptor<Graph<TSpec> >::Type>()) {
+        std::cout << "No path from " << getProperty(nameMap, source) << " to " << getProperty(nameMap, v) << " exists.";
+    } else {
+        _printPath(g,predecessor, source, getProperty(predecessor, v), nameMap);
+        std::cout << "," << getProperty(nameMap, v);
+    }
+}
+
+template <typename TSpec, typename TPredecessorMap, typename TVertexDescriptor1, typename TVertexDescriptor2>
+inline void
+_printPath(Graph<TSpec> const& g,
+            TPredecessorMap const& predecessor,
+            TVertexDescriptor1 const source,
+            TVertexDescriptor2 const v)
+{
+    if (source == v) {
+        std::cout << source;
+    } else if (getProperty(predecessor, v) == getNil<typename VertexDescriptor<Graph<TSpec> >::Type>()) {
+        std::cout << "No path from " << source << " to " << v << " exists.";
+    } else {
+        _printPath(g,predecessor, source, getProperty(predecessor, v));
+        std::cout << "," << v;
+    }
+}
+
+template <typename TSpec, typename TPredecessorMap, typename TVertexDescriptor1, typename TVertexDescriptor2, typename TEdgeSet>
+inline bool
+_collectEdges(Graph<TSpec> const& g,
+               TPredecessorMap const& predecessor,
+               TVertexDescriptor1 const source,
+               TVertexDescriptor2 const v,
+               TEdgeSet& edgeSet)
+{
+    if ((TVertexDescriptor1) source == (TVertexDescriptor1) v) {
+        return true;
+    } else if (getProperty(predecessor, v) == getNil<typename VertexDescriptor<Graph<TSpec> >::Type>()) {
+        return false;
+    } else {
+        edgeSet.insert(findEdge(g, getProperty(predecessor, v), v));
+        return _collectEdges(g,predecessor, source, getProperty(predecessor, v), edgeSet);
+    }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSpec, typename TPredecessorMap, typename TVertexDescriptor, typename TEdgeSet>
+inline bool
+_collectEdges(Graph<TSpec> const& g,
+               TPredecessorMap const& predecessor,
+               TVertexDescriptor const source,
+               TEdgeSet& edgeSet)
+{
+    typedef Iterator<Graph<Undirected<> >, VertexIterator>::Type TVertexIterator;
+    TVertexIterator it(g);
+    for(;!atEnd(it); goNext(it)) {
+        if (!_collectEdges(g, predecessor, source, value(it), edgeSet)) {
+            edgeSet.clear();
+            return false;
+        }
+    }
+    return true;
+}
+
+template <typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap>
+inline void
+_initializeSingleSource(TPredecessorMap & predecessor,
+                        TDistanceMap & distance,
+                        Graph<TSpec> const & g,
+                        TVertexDescriptor const source,
+                        TWeightMap const & weight)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Value<TPredecessorMap>::Type TPredVal;
+    typedef typename Value<TWeightMap>::Type TDistVal;
+    TPredVal nilPred = getNil<typename VertexDescriptor<TGraph>::Type>();
+    TDistVal infDist = _getInfinityDistance(weight);
+
+    TVertexIterator it(g);
+    for(;!atEnd(it);goNext(it)) {
+        assignProperty(distance, getValue(it), infDist);
+        assignProperty(predecessor, getValue(it), nilPred);
+    }
+    assignProperty(distance, source, 0);
+}
+
+template <typename TSpec, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap, typename TVertexDescriptor, typename TEdgeDescriptor>
+inline void
+_relax(Graph<TSpec> const& g,
+        TWeightMap const& weight,
+        TPredecessorMap& predecessor,
+        TDistanceMap& distance,
+        TVertexDescriptor const u,
+        TEdgeDescriptor const e)
+{
+    TVertexDescriptor v = targetVertex(g,e);
+    if (getProperty(distance, v) > getProperty(distance,u) + getProperty(weight,e)) {
+        assignProperty(distance, v, getProperty(distance,u) + getProperty(weight,e));
+        assignProperty(predecessor, v, u);
+    }
+}
+
+// TODO(holtgrew): This looks broken (distance too high below).
+
+/*!
+ * @fn dagShortestPath
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Computes shortest paths from a single source in a directed acyclic graph (DAG).
+ *
+ * @signature void dagShortestPath(predecessor, distance, g, source, weight);
+ *
+ * @param[out] predecessor A property map.  A property map that represents predecessor relationships among vertices.
+ *                         It determines a shortest-paths tree.
+ * @param[out] distance    A property map.  Indicates for each vertex th distance from the source.
+ *                         do exist.
+ * @param[in]  g           A directed acyclic graph. Types: Directed Graph
+ * @param[in]  source      A source vertex. Types: VertexDescriptor
+ * @param[in]  weight      A weight map.  In a directed acyclic graph edge weights can be negative because no cycles
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/dag_shortest_path.cpp
+ *
+ * @include demos/dox/graph_algorithms/dag_shortest_path.cpp.stdout
+ *
+ * @see bellmanFordAlgorithm
+ * @see dijkstra
+ */
+template <typename TSpec, typename TVertexDescriptor, typename TWeightMap, typename TPredecessorMap, typename TDistanceMap>
+void dagShortestPath(TPredecessorMap & predecessor,
+                     TDistanceMap & distance,
+                     Graph<TSpec> const & g,
+                     TVertexDescriptor const source,
+                     TWeightMap const & weight)
+{
+    typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Iterator<String<TVertexDescriptor>, Rooted>::Type TStringIterator;
+
+    // Initialization
+    resizeVertexMap(predecessor, g);
+    resizeVertexMap(distance, g);
+
+    // Topological sort
+    String<TVertexDescriptor> order;
+    topologicalSort(order, g);
+
+    _initializeSingleSource(predecessor, distance, g, source, weight);
+
+    //DAG Shortest Paths
+    TStringIterator it = begin(order);
+    while(!atEnd(it)) {
+        TOutEdgeIterator itout(g, getValue(it));
+        for(;!atEnd(itout);++itout) {
+            _relax(g,weight,predecessor, distance, getValue(it), getValue(itout));
+        }
+        goNext(it);
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_SINGLE_SOURCE_SHORTEST_PATH_H_
diff --git a/seqan/graph_algorithms/strongly_connected_compnents.h b/seqan/graph_algorithms/strongly_connected_compnents.h
new file mode 100644
index 0000000..deccda6
--- /dev/null
+++ b/seqan/graph_algorithms/strongly_connected_compnents.h
@@ -0,0 +1,151 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Strongly-Connected-Compnonents algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_STRONGLY_CONNECTED_COMPNENTS_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_STRONGLY_CONNECTED_COMPNENTS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function stronglyConnectedComponents()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn stronglyConnectedComponents
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Decomposes a directed graph into its strongly connected components.
+ * @signature TSize stronglyConnectedComponents(components, g);
+ *
+ * @param[out] components
+ *               A property map.Each vertex is mapped to a component id.  If two vertices share the same id they are
+ *               in the same component.
+ * @param[in]  g A directed graph. Types: Directed Graph
+ *
+ * @return TSize Number of strongly connected components, Size type of g.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/strongly_connected_components.cpp
+ *
+ * @include demos/dox/graph_algorithms/strongly_connected_components.cpp.stdout
+ */
+template <typename TSpec, typename TComponents>
+typename Size<Graph<TSpec> >::Type
+stronglyConnectedComponents(TComponents & components,
+                            Graph<TSpec> const & g_source)
+{
+    // Initialization
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Value<TComponents>::Type TCompVal;
+    resizeVertexMap(components, g_source);
+    String<TSize> predMap;
+    String<TSize> discoveryTimeMap;
+    String<TSize> finishingTimeMap;
+
+    // Dfs
+    depthFirstSearch(predMap, discoveryTimeMap, finishingTimeMap, g_source);
+
+    Graph<TSpec> g;
+    transpose(g_source, g);
+
+    // Second Dfs
+    String<TSize> predecessor;
+    String<TSize> disc;
+    String<TSize> finish;
+    resizeVertexMap(predecessor, g);
+    resizeVertexMap(disc, g);
+    resizeVertexMap(finish, g);
+    TCompVal nilPred = getNil<TVertexDescriptor>();
+    String<bool> tokenMap;
+    resizeVertexMap(tokenMap, g);
+    TVertexIterator it(g);
+    for(;!atEnd(it);goNext(it)) {
+        assignProperty(components, getValue(it), nilPred);
+        assignProperty(tokenMap, getValue(it), false);
+        assignProperty(predecessor, getValue(it), nilPred);
+    }
+
+    // Order vertices
+    typedef std::pair<TSize, TVertexDescriptor> TTimeVertexPair;
+    std::priority_queue<TTimeVertexPair> q;
+    goBegin(it);
+    for(;!atEnd(it);++it) {
+        q.push(std::make_pair(getProperty(finishingTimeMap, getValue(it)), getValue(it)));
+    }
+
+    TSize time = 0;
+    TSize label = 0;
+    while(!q.empty()) {
+        TVertexDescriptor u = q.top().second;
+        q.pop();
+        if (getProperty(tokenMap, u) == false) {
+            _dfsVisit(g, u, tokenMap, predecessor, disc, finish, time);
+            TVertexIterator it_label(g);
+            for(;!atEnd(it_label);goNext(it_label)) {
+                if ((getProperty(tokenMap, getValue(it_label)) == true) &&
+                    (getProperty(components, getValue(it_label)) == nilPred)) {
+                    assignProperty(components, getValue(it_label), label);
+                }
+            }
+            ++label;
+        }
+    }
+
+    return label;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_STRONGLY_CONNECTED_COMPNENTS_H_
diff --git a/seqan/seq_io/simple_read_fasta.h b/seqan/graph_algorithms/topological_sort.h
similarity index 54%
rename from seqan/seq_io/simple_read_fasta.h
rename to seqan/graph_algorithms/topological_sort.h
index f42b1a9..35a7048 100644
--- a/seqan/seq_io/simple_read_fasta.h
+++ b/seqan/graph_algorithms/topological_sort.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,13 +29,13 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Tobias Raussch <rausch@embl.de>
 // ==========================================================================
-// This header provides the readFasta() function to be used in demos.
+// Implementation of Topological-Sort algorithm.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEQ_IO_SIMPLE_READ_FASTA_H_
-#define CORE_INCLUDE_SEQAN_SEQ_IO_SIMPLE_READ_FASTA_H_
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_TOPOLOGICAL_SORT_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_TOPOLOGICAL_SORT_H_
 
 namespace seqan {
 
@@ -56,90 +56,65 @@ namespace seqan {
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function readFasta()
+// Function topologicalSort()
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn readFasta
- * @headerfile <seqan/seq_io.h>
- * @brief Read first sequence from a FASTA file.
- * 
- * @signature int readFasta(seq, filename);
- * 
- * @param[out] seq      @link String @endlink to store the result.  Type: String
- * @param[in]  filename Path to the file to read from.  Type: <tt>char const *</tt>.
- * 
- * @return int 0 on success, non-0 value on error.
- * 
- * This function is meant for demo programs and allows to read the first sequence from a FASTA file very easily.
- * 
- * @section Examples
- * 
- * Read the file given by the first parameter to the program and print it to the screen.
- * 
- * @code{.cpp}
- * #include <iostream>
- * #include <seqan/sequence.h>
- * #include <seqan/seq_io.h>
- *  
- * int main(int argc, char const ** argv)
- * {
- *     if (argc != 2)
- *         return 1;
- *  
- *     seqan::Dna5String seq;
- *     if (readFasta(seq, argv[1]) != 0)
- *         return 1;
- *  
- *     std::cout << seq << '\n';
- *     return 0;
- * }
- * @endcode
+ * @fn topologicalSort
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Performs a topological sort on a directed acyclic graph (DAG).
+ *
+ * @signature void topologicalSort(topSort, g);
+ *
+ * @param[out] topSort A topological ordering of the vertices. Types: String.
+ * @param[in]  g       A directed acyclic graph. Types: Directed Graph
+ *
+ * A topological sort is a linear ordering of all its vertices such that if the graph contains an edge (u,v) then u
+ * appears before v in the ordering.
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/topological_sort.cpp
+ *
+ * @include demos/dox/graph_algorithms/topological_sort.cpp.stdout
  */
-
-/**
-.Function.readFasta
-..cat:Input/Output
-..signature:int readFasta(seq, filename)
-..summary:Read first sequence from a FASTA file.
-..description:
-This function is meant for demo programs and allows to read the first sequence from a FASTA file very easily.
-..param.seq:@Class.String@ to store the result.
-...type:Class.String
-..param.filename:Path to the file to read from.
-...type:nolink:$char const *$
-..returns:$int$ with status code, $0$ for success, $1$ for error.
-..example.text:Read the file given by the first parameter to the program and print it to the screen.
-..example.code:
-#include <iostream>
-#include <seqan/sequence.h>
-#include <seqan/seq_io.h>
-
-int main(int argc, char const ** argv)
+template <typename TSpec, typename TVertexDescriptor>
+void topologicalSort(String<TVertexDescriptor> & topSort,
+                     Graph<TSpec> const & g)
 {
-    if (argc != 2)
-        return 1;
+    typedef typename Size<Graph<TSpec> >::Type TSize;
 
-    seqan::Dna5String seq;
-    if (readFasta(seq, argv[1]) != 0)
-        return 1;
+    // Variable definition.
+    String<TSize> predMap;
+    String<TSize> discoveryTimeMap;
+    String<TSize> finishingTimeMap;
 
-    std::cout << seq << '\n';
-    return 0;
-}
-..include:seqan/seq_io.h
-*/
+    // Perform DFS.
+    depthFirstSearch(predMap, discoveryTimeMap, finishingTimeMap, g);
+    SEQAN_ASSERT_EQ(numVertices(g), length(predMap));
+    SEQAN_ASSERT_EQ(numVertices(g), length(discoveryTimeMap));
+    SEQAN_ASSERT_EQ(numVertices(g), length(finishingTimeMap));
 
-template <typename TValue, typename TSpec>
-int readFasta(String<TValue, TSpec> & seq, char const * filename)
-{
-    SequenceStream seqStream(filename);
-    if (!isGood(seqStream))
-        return 1;
-    CharString id;
-    return readRecord(id, seq, seqStream);
+    // Order vertices.
+    typedef std::pair<TSize, TVertexDescriptor> TTimeVertexPair;
+    std::priority_queue<TTimeVertexPair> q;
+    typedef typename Iterator<Graph<TSpec>, VertexIterator>::Type TVertexIterator;
+    TVertexIterator it(g);
+    for (; !atEnd(it); goNext(it))
+        q.push(std::make_pair(getProperty(finishingTimeMap, getValue(it)), getValue(it)));
+
+    // Create topological order.
+    resize(topSort, numVertices(g));
+    TSize count = 0;
+    while (!q.empty())
+    {
+        assignValue(topSort, count, q.top().second);
+        q.pop();
+        ++count;
+    }
+    SEQAN_ASSERT_EQ(length(topSort), numVertices(g));
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEQ_IO_SIMPLE_READ_FASTA_H_
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_TOPOLOGICAL_SORT_H_
diff --git a/seqan/stream/write.h b/seqan/graph_algorithms/transitive_closure.h
similarity index 53%
rename from seqan/stream/write.h
rename to seqan/graph_algorithms/transitive_closure.h
index 8a079c9..b553c86 100644
--- a/seqan/stream/write.h
+++ b/seqan/graph_algorithms/transitive_closure.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,14 +29,13 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// Author: Tobias Raussch <rausch@embl.de>
 // ==========================================================================
-// Main File for record- and Document-writing. Contains only doc right now.
+// Implementation of Transitive-Closure algorithm.
 // ==========================================================================
 
-
-#ifndef SEQAN_STREAM_WRITE_H_
-#define SEQAN_STREAM_WRITE_H_
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_TRANSITIVE_CLOSURE_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_TRANSITIVE_CLOSURE_H_
 
 namespace seqan {
 
@@ -56,69 +55,53 @@ namespace seqan {
 // Functions
 // ============================================================================
 
-// TODO(holtgrew): These functions do not really belong to the Stream concept.
+// ----------------------------------------------------------------------------
+// Function transitiveClosure()
+// ----------------------------------------------------------------------------
 
 /*!
- * @fn StreamConcept#writeRecord
- * @headerfile <seqan/stream.h>
- * @brief Write one record (e.g. a single DNA-sequence and its meta data) to a @link StreamConcept @endlink
- * 
- * @signature int writeRecord(stream, RECORD, tag);
- * 
- * @param[in]     RECORD possibly multiple fields (e.g. meta and sequence)
- * @param[in]     tag    The file format tag
- * @param[in,out] stream The Stream object to write to. Type: StreamConcept
+ * @fn transitiveClosure
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Determines whether there is a path between any two given vertices or not.
  *
- * @return int An integer with the status code (0 on success).
- * 
- * @see StreamConcept#write2
- */
-
-/**
-.Function.writeRecord
-..cat:Input/Output
-..summary:write one record (e.g. a single DNA-sequence and its meta data) to a @Concept.StreamConcept@
-..signature:writeRecord(TStream & stream, <format specific>, TTag const &)
-..param.stream:The Stream object to write to
-...type:Concept.StreamConcept
-..param.format specific: possibly multiple fields (e.g. meta and sequence)
-..param.TTag:The file format tag
-..see:Function.write2
-..include:seqan/stream.h
-*/
-
-/*!
- * @fn StreamConcept#write2
- * @headerfile <seqan/stream.h>
- * @brief Writes an entire document to a @link StreamConcept @endlink.
- * 
- * @signature write2(stream, DOCUMENT, tag);
- * 
- * @param[in,out] stream   The Stream object to write to. Types: StreamConcept
- * @param[in]     DOCUMENT Format specific possibly multiple StringSets (e.g. of meta and sequences).
- * @param[in]     tag      The file format tag
- * 
- * @section Status
+ * @signature void transitiveClosure(closure, g);
  *
- * Should be renamed to "write" once the old IO-Code is removed
- * 
- * @see StreamConcept#writeRecord
+ * @param[out] closure A matrix which indicates the closure.  Entry (i,j) in this matrix indicates whether there is a
+ *                     path from i to j in the graph or not.  Types: Matrix
+ * @param[in]  g       A directed graph.  Types: Directed Graph
+ *
+ * @section Example
+ *
+ * @include demos/dox/graph_algorithms/transitive_closure.cpp
+ *
+ * @include demos/dox/graph_algorithms/transitive_closure.cpp.stdout
  */
+template <typename TSpec, typename TMatrix>
+void transitiveClosure(TMatrix & closure,
+                       Graph<TSpec> const & g)
+{
+    typedef typename Size<TMatrix>::Type TSize;
+
+    // Initialize first closure matrix
+    getAdjacencyMatrix(g,closure);
+    TSize len = (TSize) std::sqrt((double) length(closure));
+    for (TSize diag=0;diag < len;++diag) assignValue(closure, diag*len+diag,1);
 
-/**
-.Function.write2
-..cat:Input/Output
-..summary:writes an entire document to a @Concept.StreamConcept@
-..signature:write2(TStream & stream, <format specific>, TTag const &)
-..param.stream:The Stream object to write to
-...type:Concept.StreamConcept
-..param.format specific: possibly multiple StringSets (e.g. of meta and sequences)
-..param.TTag:The file format tag
-..status:Should be renamed to "write" once the old IO-Code is removed
-..include:seqan/stream.h
-..see:Function.writeRecord
-*/
+    // Transitive Closure
+    TMatrix local = closure;
+    for (TSize k=0;k<len;++k) {
+        for(TSize i=0;i<len;++i) {
+            for(TSize j=0;j<len;++j) {
+                bool t_ij = static_cast<int>(getValue(closure, i*len+j)) > 0;
+                bool t_ik = static_cast<int>(getValue(closure, i*len+k)) > 0;
+                bool t_kj = static_cast<int>(getValue(closure, k*len+j)) > 0;
+                assignValue(local, i*len+j, t_ij || (t_ik && t_kj));
+            }
+        }
+        closure = local;
+    }
+}
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_STREAM_WRITE_H_
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_TRANSITIVE_CLOSURE_H_
diff --git a/seqan/graph_algorithms/weakly_connected_components.h b/seqan/graph_algorithms/weakly_connected_components.h
new file mode 100644
index 0000000..bef8d09
--- /dev/null
+++ b/seqan/graph_algorithms/weakly_connected_components.h
@@ -0,0 +1,121 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Implementation of Weakly-Connected-Components algorithm.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_WEAKLY_CONNECTED_COMPONENTS_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_WEAKLY_CONNECTED_COMPONENTS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function weaklyConnectedComponents()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn weaklyConnectedComponents
+ * @headerfile <seqan/graph_algorithms.h>
+ * @brief Compute weakly connected components of a directed graph.
+ *
+ * @signature TSize weaklyConnectedComponents(components, g);
+ *
+ * @param[out] components
+ *               A property map.  Each vertex is mapped to a component id.  If two vertices share the same id they
+ *               are in the same component.
+ * @param[in]  g A @link DirectedGraph @endlink to use for the input.
+ *
+ * @return TSize The number of weakly connected components  (Metafunction: @link Graph#Size @endlink of the type
+ *               of <tt>g</tt>).
+ *
+ * The running time is <tt>O(n a(n, n))</tt> where <tt>a</tt> is the inverse Ackermann function and thus almost linear.
+ * The union find data structure is used since the graph implementations do not allow the efficient iteration of
+ * in-edges.
+ */
+template <typename TSpec, typename TComponents>
+typename Size<Graph<TSpec> >::Type
+weaklyConnectedComponents(TComponents & components,
+                          Graph<TSpec> const & g)
+
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    // Initialization.
+    UnionFind<TVertexDescriptor> unionFind;
+    resizeVertexMap(unionFind, g);
+
+    // Iterate over all edges, joining weakly connected components.
+    for (TEdgeIterator itE(g); !atEnd(itE); goNext(itE))
+        joinSets(unionFind, findSet(unionFind, sourceVertex(itE)), findSet(unionFind, targetVertex(itE)));
+
+    // Count number of sets.
+    TSize setCount = 0;
+    for (TVertexIterator itV(g); !atEnd(itV); goNext(itV))
+        setCount += (findSet(unionFind, *itV) == *itV);
+
+    // Build a map from graph vertex descriptor to component id.
+    TSize nextId = 0;
+    clear(components);
+    resizeVertexMap(components, g, setCount);  // setCount is sentinel value
+    for (TVertexIterator itV(g); !atEnd(itV); goNext(itV)) {
+        if (getProperty(components, findSet(unionFind, *itV)) == setCount)
+            assignProperty(components, findSet(unionFind, *itV), nextId++);
+        assignProperty(components, *itV, getProperty(components, findSet(unionFind, *itV)));
+    }
+
+    return setCount;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_WEAKLY_CONNECTED_COMPONENTS_H_
diff --git a/seqan/graph_algorithms/weighted_bipartite_matching.h b/seqan/graph_algorithms/weighted_bipartite_matching.h
new file mode 100644
index 0000000..0350785
--- /dev/null
+++ b/seqan/graph_algorithms/weighted_bipartite_matching.h
@@ -0,0 +1,323 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Raussch <rausch@embl.de>
+// ==========================================================================
+// Implementation of Weighted-Bipartite-Matching algorithm.
+//
+// WARNING: Functionality not carefully tested!
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_WEIGHTED_BIPARTITE_MATCHING_H_
+#define INCLUDE_SEQAN_GRAPH_ALGORITHMS_WEIGHTED_BIPARTITE_MATCHING_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function weightedBipartiteMatching()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TVertexMap, typename TWeightMap, typename TEdges>
+inline typename Value<TWeightMap>::Type
+_weightedBipartiteMatching(Graph<TSpec>& g,
+                              TVertexMap& vertMap,
+                              TWeightMap& weightMap,
+                              String<TEdges>& edges)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIter;
+    typedef typename Value<TWeightMap>::Type TCargo;
+
+    TSize numVert = numVertices(g);
+    TCargo maxEdgeVal = 0;
+
+    // Find an initial labeling
+    String<TCargo> label;
+    resizeVertexMap(label, g);
+    TVertexIterator itV(g);
+    for(;!atEnd(itV); goNext(itV)) {
+        if (getProperty(vertMap, value(itV)) == true) value(label, value(itV)) = 0;
+        else {
+            TCargo maxCargo = 0;
+            for(TOutEdgeIter itOutE(g, value(itV));!atEnd(itOutE); goNext(itOutE)) {
+                if (property(weightMap, (value(itOutE))) > maxCargo) maxCargo = property(weightMap, (value(itOutE)));
+            }
+            value(label, value(itV)) = maxCargo;
+            if (maxCargo > maxEdgeVal) maxEdgeVal = maxCargo;
+        }
+    }
+
+    // Generate Equality Graph
+    typedef Graph<Directed<void> > TEqualityGraph;
+    typedef typename EdgeType<TEqualityGraph>::Type TEdgeStump;
+    TEqualityGraph equalGraph;
+    resize(equalGraph.data_vertex, length(_getVertexString(g)), (TEdgeStump*) 0);
+    equalGraph.data_id_managerV = g.data_id_managerV;
+    TEdgeIterator itE(g);
+    for(;!atEnd(itE); goNext(itE)) {
+        if (property(weightMap, (value(itE))) == property(label, sourceVertex(itE)) + property(label, targetVertex(itE))) {
+            // For the Ford-Fulkerson all edges must go from true to false
+            if (getProperty(vertMap, sourceVertex(itE)) == true) addEdge(equalGraph, targetVertex(itE), sourceVertex(itE));
+            else addEdge(equalGraph, sourceVertex(itE), targetVertex(itE));
+        }
+    }
+
+    // Find an initial bipartite matching
+    clear(edges);
+    TSize matchSize = bipartiteMatching(equalGraph, vertMap, edges);
+
+
+    String<bool> free;
+    String<TVertexDescriptor> reverseMatchMap;
+    typedef std::set<TVertexDescriptor> TVertexSet;
+    TVertexSet setS;
+    TVertexSet setNeighborS;
+    TVertexSet setT;
+    while (matchSize != numVert / 2) {
+
+        // Initialization
+        setS.clear();
+        setT.clear();
+        setNeighborS.clear();
+        clear(free);
+        resize(free, getIdUpperBound(_getVertexIdManager(g)), true);
+        clear(reverseMatchMap);
+        resizeVertexMap(reverseMatchMap, g);
+
+        // Find free vertex
+        typedef typename Iterator<String<TEdges> >::Type TStringEdgeIter;
+        TStringEdgeIter itSE = begin(edges);
+        TStringEdgeIter itSEEnd = end(edges);
+        for(;itSE != itSEEnd; goNext(itSE)) {
+            value(free, (value(itSE)).i1) = false;
+            value(free, (value(itSE)).i2) = false;
+            value(reverseMatchMap, (value(itSE)).i2) = (value(itSE)).i1;
+        }
+        TVertexIterator itVert(g);
+        for(;!atEnd(itVert); goNext(itVert)) {
+            if ((getProperty(vertMap, value(itVert)) == false) &&
+                (value(free, value(itVert)) == true)) {
+                    setS.insert(value(itVert));
+                    typedef typename Iterator<TEqualityGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+                    TOutEdgeIterator itOE(equalGraph, value(itVert));
+                    for(;!atEnd(itOE); ++itOE) {
+                        setNeighborS.insert(targetVertex(itOE));
+                        if (value(free, targetVertex(itOE)) == true) setT.insert(targetVertex(itOE));
+                    }
+                    break;
+            }
+        }
+
+        // Find matched vertices
+        typedef typename TVertexSet::iterator TVertexSetIter;
+        while (setNeighborS != setT) {
+            TVertexSet diffSet;
+            TVertexSetIter itT = setT.begin();
+            TVertexSetIter itTEnd = setT.end();
+            TVertexSetIter itN = setNeighborS.begin();
+            TVertexSetIter itNEnd = setNeighborS.end();
+            while (itN != itNEnd) {
+                if ((itT == itTEnd) || (*itN < *itT)) { diffSet.insert(*itN); ++itN; }
+                else { ++itN; ++itT; }
+            }
+            TVertexDescriptor y = *(diffSet.begin());
+            setT.insert(y);
+            setS.insert(value(reverseMatchMap, y));
+            typedef typename Iterator<TEqualityGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+            TOutEdgeIterator itOE(equalGraph, value(reverseMatchMap, y));
+            for(;!atEnd(itOE); ++itOE) {
+                setNeighborS.insert(targetVertex(itOE));
+                if (value(free, targetVertex(itOE)) == true) setT.insert(targetVertex(itOE));
+            }
+        }
+        clear(reverseMatchMap);
+
+        // Update Labels
+        TCargo minVal = maxEdgeVal;
+        TEdgeIterator itEdge(g);
+        for(;!atEnd(itEdge); goNext(itEdge)) {
+            TVertexDescriptor sV = sourceVertex(itEdge);
+            TVertexDescriptor tV = targetVertex(itEdge);
+            if (property(vertMap, sV) == true) {    TVertexDescriptor tmp = sV; sV = tV; tV = tmp;  }
+            if ((setS.find(sV) != setS.end()) &&
+                (setT.find(tV) == setT.end())) {
+                TCargo thisVal = getProperty(label, sV) + getProperty(label, tV) - getProperty(weightMap, (value(itEdge)));
+                if (thisVal < minVal) minVal = thisVal;
+            }
+        }
+        TVertexIterator myVertexIt(g);
+        for(;!atEnd(myVertexIt); goNext(myVertexIt)) {
+            if (setS.find(value(myVertexIt)) != setS.end()) value(label, value(myVertexIt)) -= minVal;
+            else if (setT.find(value(myVertexIt)) != setT.end()) value(label, value(myVertexIt)) += minVal;
+        }
+
+        // Build new equal graph
+        clear(equalGraph);
+        resize(equalGraph.data_vertex, length(_getVertexString(g)), (TEdgeStump*) 0);
+        equalGraph.data_id_managerV = g.data_id_managerV;
+        TEdgeIterator itE(g);
+        for(;!atEnd(itE); goNext(itE)) {
+            if (property(weightMap, (value(itE))) == property(label, sourceVertex(itE)) + property(label, targetVertex(itE))) {
+                if (property(vertMap, sourceVertex(itE)) == true) addEdge(equalGraph, targetVertex(itE), sourceVertex(itE));
+                else addEdge(equalGraph, sourceVertex(itE), targetVertex(itE));
+            }
+        }
+
+        // Create a new matching
+        clear(edges);
+        matchSize = bipartiteMatching(equalGraph, vertMap, edges);
+    }
+
+    typedef typename Iterator<String<TEdges> >::Type TStringEdgeIter;
+    TStringEdgeIter itSE = begin(edges);
+    TStringEdgeIter itSEEnd = end(edges);
+    TCargo sumWeight = 0;
+    for(;itSE != itSEEnd; goNext(itSE)) sumWeight += property(weightMap, findEdge(g, (value(itSE)).i1, (value(itSE)).i2));
+
+    return sumWeight;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSpec, typename TVertexMap, typename TWeightMap, typename TEdges>
+typename Value<TWeightMap>::Type
+weightedBipartiteMatching(String<TEdges> & edges,
+                          Graph<TSpec> const & g,
+                          TVertexMap const & vertMap,
+                          TWeightMap const & weightMap)
+{
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Value<TWeightMap>::Type TCargo;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+
+    // Collect the two vertex sets, set1 is marked with false, set2 with true
+    typedef String<TVertexDescriptor> TVertexSet;
+    typedef typename Iterator<TVertexSet>::Type TVertexSetIter;
+    TVertexSet set1;
+    TVertexSet set2;
+    TVertexIterator itV(g);
+    for(;!atEnd(itV); goNext(itV)) {
+        if (property(vertMap, value(itV)) == false) appendValue(set1, value(itV));
+        else appendValue(set2, value(itV));
+    }
+    bool setIdentifier = true;      // Indicates what set needs more vertices
+    TSize maxN = length(set1);
+    if (maxN < length(set2)) {  maxN = length(set2); setIdentifier = false; }
+
+
+    // Copy the original graph
+    TGraph fullGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    resize(fullGraph.data_vertex, length(_getVertexString(g)), (TEdgeStump*) 0);
+    fullGraph.data_id_managerV = g.data_id_managerV;
+    TVertexMap myVertexMap = vertMap;
+    resize(myVertexMap, maxN + maxN, setIdentifier);
+    String<TCargo> myWeightMap;
+    resize(myWeightMap, maxN * maxN, 0);
+    TEdgeIterator itE(g);
+    typedef std::pair<TVertexDescriptor, TVertexDescriptor> TEdge;
+    typedef std::set<TEdge> TEdgeSet;
+    TEdgeSet edgeSet;
+    for(;!atEnd(itE); goNext(itE)) {
+        TVertexDescriptor sV = sourceVertex(itE);
+        TVertexDescriptor tV = targetVertex(itE);
+        TEdgeDescriptor e = addEdge(fullGraph, sV, tV);
+        if (sV < tV) edgeSet.insert(std::make_pair(sV, tV));
+        else edgeSet.insert(std::make_pair(tV, sV));
+        property(myWeightMap, e) = getProperty(weightMap, (value(itE)));
+    }
+
+    // Build a full graph
+    if (setIdentifier == false) {
+        TSize inc = maxN - length(set1);
+        for(TSize i = 0; i< inc; ++i) appendValue(set1, addVertex(fullGraph));
+    } else {
+        TSize inc = maxN - length(set2);
+        for(TSize i = 0; i<inc ; ++i) appendValue(set2, addVertex(fullGraph));
+    }
+    TVertexSetIter set1It = begin(set1);
+    TVertexSetIter set1ItEnd = end(set1);
+    for(;set1It != set1ItEnd; ++set1It) {
+        TVertexSetIter set2It = begin(set2);
+        TVertexSetIter set2ItEnd = end(set2);
+        for(;set2It != set2ItEnd; ++set2It) {
+            TVertexDescriptor sV = value(set1It);
+            TVertexDescriptor tV = value(set2It);
+            if (sV > tV) { TVertexDescriptor tmp = sV; sV = tV; tV = tmp; }
+            if (edgeSet.find(std::make_pair(sV, tV)) == edgeSet.end()) addEdge(fullGraph, sV, tV);
+        }
+    }
+
+    // Find a maximum weight matching
+    String<TEdges> pseudo_edges;
+    TCargo weight = _weightedBipartiteMatching(fullGraph, myVertexMap, myWeightMap, pseudo_edges);
+
+    // Copy the relevant edges
+    clear(edges);
+    typedef typename Iterator<String<TEdges> >::Type TEdgeIter;
+    TEdgeIter eIt = begin(pseudo_edges);
+    TEdgeIter eItEnd = end(pseudo_edges);
+    for(;eIt != eItEnd; ++eIt) {
+        TVertexDescriptor sV = (value(eIt)).i1;
+        TVertexDescriptor tV = (value(eIt)).i2;
+        if (sV > tV) { TVertexDescriptor tmp = sV; sV = tV; tV = tmp; }
+        if (edgeSet.find(std::make_pair(sV, tV)) != edgeSet.end()) appendValue(edges, value(eIt));
+    }
+    return weight;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_ALGORITHMS_WEIGHTED_BIPARTITE_MATCHING_H_
diff --git a/seqan/graph_align.h b/seqan/graph_align.h
index 619c931..5d8ffa3 100644
--- a/seqan/graph_align.h
+++ b/seqan/graph_align.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,14 +35,15 @@
 // Umbrella header for the moduel graph_align.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_H_
 
 // External STL
 #include <map>
 
 // Seqan
 #include <seqan/score.h>
+#include <seqan/align/fragment.h>
 #include <seqan/graph_types.h>
 #include <seqan/graph_algorithms.h>
 
@@ -52,7 +53,7 @@
 #include <seqan/graph_align/graph_impl_align_adapt.h>
 
 // Interval trees
-#include <seqan/misc/misc_interval_tree.h>
+#include <seqan/misc/interval_tree.h>
 
 // Refinement
 //#include <seqan/graph_align/graph_algorithm_refine.h>
@@ -65,4 +66,4 @@
 #include <seqan/graph_align/graph_algorithm_refine_inexact.h>
 #include <seqan/graph_align/graph_algorithm_refine_annotation.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_H_
diff --git a/seqan/graph_align/INFO b/seqan/graph_align/INFO
deleted file mode 100644
index a6e1de4..0000000
--- a/seqan/graph_align/INFO
+++ /dev/null
@@ -1,9 +0,0 @@
-Name: seqan-graph_align
-Author: Tobias Rausch <rausch@embl.de>
-Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Rene Rahn <rene.rahn@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Alignment graph data structure and supporting algorithms.
diff --git a/seqan/graph_align/graph_algorithm_refine_align.h b/seqan/graph_align/graph_algorithm_refine_align.h
index b1557c1..4ddef4a 100644
--- a/seqan/graph_align/graph_algorithm_refine_align.h
+++ b/seqan/graph_align/graph_algorithm_refine_align.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,57 +33,57 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
 
 namespace seqan {
 
 
-///////////////////////////////////////////////////////////////////////////////////////////////////////	
+///////////////////////////////////////////////////////////////////////////////////////////////////////
 //Functions for Align<TSource,TSpec>
-//project onto other sequence 
+//project onto other sequence
 template<typename TSource,typename TSpec,typename TValue, typename TId1, typename TPos1, typename TId2, typename TPos2,typename TMap>
 void
-_getOtherSequenceAndProject(Align<TSource,TSpec> & segment, 
-				TValue seg_num,
-							TMap & seq_map, 
-						   TId1 , 
-						   TPos1 node_i, 
-						   TId2 & seq_j_id, 
-						   TPos2 & node_j)
+_getOtherSequenceAndProject(Align<TSource,TSpec> & segment,
+                TValue seg_num,
+                            TMap & seq_map,
+                           TId1 ,
+                           TPos1 node_i,
+                           TId2 & seq_j_id,
+                           TPos2 & node_j)
 {
 SEQAN_CHECKPOINT
 
-	if(seg_num == 0)
-	{
-		seq_j_id = seq_map[getObjectId(source(row(segment, 1)))];
+    if(seg_num == 0)
+    {
+        seq_j_id = seq_map[getObjectId(source(row(segment, 1)))];
         TPos1 view_clipped_end_pos = clippedEndPosition(row(segment,0)) - clippedBeginPosition(row(segment, 0));
-		if(node_i >= (TPos1)toSourcePosition(row(segment, 0), view_clipped_end_pos))
+        if(node_i >= (TPos1)toSourcePosition(row(segment, 0), view_clipped_end_pos))
             node_j = static_cast<TPos2>(-1);
-		else
+        else
             node_j = toSourcePosition(row(segment, 1), toViewPosition(row(segment, 0), node_i));
-	}
-	else
-	{
-		seq_j_id  = seq_map[getObjectId(source(row(segment, 0)))];
+    }
+    else
+    {
+        seq_j_id  = seq_map[getObjectId(source(row(segment, 0)))];
         TPos1 view_clipped_end_pos = clippedEndPosition(row(segment, 1)) - clippedBeginPosition(row(segment, 1));
-		if(node_i >= (TPos1)toSourcePosition(row(segment, 1), view_clipped_end_pos))
+        if(node_i >= (TPos1)toSourcePosition(row(segment, 1), view_clipped_end_pos))
             node_j = static_cast<TPos2>(-1);
-		else
+        else
             node_j = toSourcePosition(row(segment, 0), toViewPosition(row(segment, 1), node_i));
-	}
+    }
 }
 
 
 //unspektakul�re funktion, die die int ID zur�ckgibt (braucht man damit es f�r alle alignment typen geht)
-//template<typename TSource,typename TSpec, typename TValue, typename TSeqMap>					
-//int 
+//template<typename TSource,typename TSpec, typename TValue, typename TSeqMap>
+//int
 //_getSeqMapId(TSeqMap & seq_map,
-//			Align<TSource,TSpec> & segment,
-//			TValue seq_i)
+//            Align<TSource,TSpec> & segment,
+//            TValue seq_i)
 //{
 //SEQAN_CHECKPOINT
-//	return seq_map[getObjectId(source(row(segment,seq_i)))];
+//    return seq_map[getObjectId(source(row(segment,seq_i)))];
 //}
 //
 //given seq and segment, get the sequenceId (seq_i) and its begin and end
@@ -92,15 +92,15 @@ SEQAN_CHECKPOINT
 template<typename TAliSource,typename TAliSpec, typename TId, typename TPosition, typename TId2>
 void
 _getSeqBeginAndEnd(Align<TAliSource,TAliSpec> & segment,
-				  std::map<const void * ,int> & seq_map, 
-				  TId & seq_i_id, 
-				  TPosition & begin_i, 
-				  TPosition & end_i,
-				  TId2 seq)
+                  std::map<const void * ,int> & seq_map,
+                  TId & seq_i_id,
+                  TPosition & begin_i,
+                  TPosition & end_i,
+                  TId2 seq)
 {
-	seq_i_id = seq_map[getObjectId(source(row(segment,seq)))];
-	begin_i = clippedBeginPosition(row(segment, seq));
-	end_i = toSourcePosition(row(segment, seq), clippedEndPosition(row(segment, seq)) - begin_i);
+    seq_i_id = seq_map[getObjectId(source(row(segment,seq)))];
+    begin_i = clippedBeginPosition(row(segment, seq));
+    end_i = toSourcePosition(row(segment, seq), clippedEndPosition(row(segment, seq)) - begin_i);
 }
 
 
@@ -109,86 +109,91 @@ _getSeqBeginAndEnd(Align<TAliSource,TAliSpec> & segment,
 // 50000 _getRefinedMatchScore Functions
 ////////////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////
+
+//TODO(singer): Remove this forward
+template <typename T>
+struct Row;
+
 //for Align<TAliSource,TAliSpec>
 //get score for alignment of length len starting at pos_i on first sequence
-//and pos_j on second sequence 
+//and pos_j on second sequence
 template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TAliSource,typename TAliSpec,typename TValue>
 TScoreValue
 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
-		 TStringSet &,
-		 Align<TAliSource,TAliSpec> & segment,
-		 TValue pos_i,
-		 TValue pos_j,
-		 TValue len,
-		 TValue)
+         TStringSet &,
+         Align<TAliSource,TAliSpec> & segment,
+         TValue pos_i,
+         TValue pos_j,
+         TValue len,
+         TValue)
 {
-SEQAN_CHECKPOINT     
-	typedef Align<TAliSource,TAliSpec> TAlign;
-	typedef typename Row<TAlign>::Type TRow;
-//	typedef typename Iterator<TRow,GapsIterator<ArrayGaps> >::Type TIterator;	
-	typedef typename Iterator<TRow, Rooted>::Type TIterator;
-	TIterator row0_it, row1_it;
-	row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
-	row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
-	len = toViewPosition(row(segment,0),pos_i + len) - toViewPosition(row(segment,0),pos_i);
-	TValue i = 0;
-	TScoreValue ret_score = 0;
-	while(i < len)
-	{
-		if(isGap(row1_it)||isGap(row0_it))
-			ret_score += scoreGapExtend(score_type);
-		else
-			ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
-		++i;
-		++row0_it; 
-		++row1_it; 
-	}
-	return ret_score;
-}				
-					
-
-//get score for alignment starting at pos_i on first sequence 
+SEQAN_CHECKPOINT
+    typedef Align<TAliSource,TAliSpec> TAlign;
+    typedef typename Row<TAlign>::Type TRow;
+//    typedef typename Iterator<TRow,GapsIterator<ArrayGaps> >::Type TIterator;
+    typedef typename Iterator<TRow, Rooted>::Type TIterator;
+    TIterator row0_it, row1_it;
+    row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
+    row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
+    len = toViewPosition(row(segment,0),pos_i + len) - toViewPosition(row(segment,0),pos_i);
+    TValue i = 0;
+    TScoreValue ret_score = 0;
+    while(i < len)
+    {
+        if(isGap(row1_it)||isGap(row0_it))
+            ret_score += scoreGapExtend(score_type);
+        else
+            ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
+        ++i;
+        ++row0_it;
+        ++row1_it;
+    }
+    return ret_score;
+}
+
+
+//get score for alignment starting at pos_i on first sequence
 //and pos_j on second sequence, if len1!=len2 then the refinement
 //process was stopped (the cut is not exact)
 //template<typename TScore,typename TStringSet, typename TAliSource,typename TAliSpec,typename TValue>
 //typename Value<TScore>::Type
 //_getRefinedMatchScore(TScore & score_type,
-//		 TStringSet &, 
-//		 Align<TAliSource,TAliSpec> & segment,
-//		 TValue pos_i,
-//		 TValue pos_j,
-//		 TValue len1,
-//		 TValue len2)
+//         TStringSet &,
+//         Align<TAliSource,TAliSpec> & segment,
+//         TValue pos_i,
+//         TValue pos_j,
+//         TValue len1,
+//         TValue len2)
 //{
 //SEQAN_CHECKPOINT
-//	typedef Align<TAliSource,TAliSpec> TAlign;
-//	typedef typename Row<TAlign>::Type TRow;
-//	typedef typename Iterator<TRow>::Type TIterator;	
-//	TIterator row0_it, row1_it;
-//	TValue len;
-//	row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
-//	row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
-//	len1 = toViewPosition(row(segment,0),pos_i + len1) - toViewPosition(row(segment,0),pos_i);
-//	len2 = toViewPosition(row(segment,1),pos_j + len2) - toViewPosition(row(segment,1),pos_j);
-//	len = (len1 < len2) ? len1 : len2;
-//	int i = 0;
-//	typename Value<TScore>::Type ret_score = 0;
-//	
-//	//calculate score for aligned region
-//	while(i < len)
-//	{
-//		ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
-//		++i;
-//		++row0_it;
-//		++row1_it;
-//	}
-//	//fill up with gaps if one sequence is longer than the other
-//	len = (len1 > len2) ? len1 : len2;
-//	ret_score += (len - i) * scoreGapExtend(score_type);
-//	
-//	return ret_score;
-//}				
+//    typedef Align<TAliSource,TAliSpec> TAlign;
+//    typedef typename Row<TAlign>::Type TRow;
+//    typedef typename Iterator<TRow>::Type TIterator;
+//    TIterator row0_it, row1_it;
+//    TValue len;
+//    row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
+//    row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
+//    len1 = toViewPosition(row(segment,0),pos_i + len1) - toViewPosition(row(segment,0),pos_i);
+//    len2 = toViewPosition(row(segment,1),pos_j + len2) - toViewPosition(row(segment,1),pos_j);
+//    len = (len1 < len2) ? len1 : len2;
+//    int i = 0;
+//    typename Value<TScore>::Type ret_score = 0;
+//
+//    //calculate score for aligned region
+//    while(i < len)
+//    {
+//        ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
+//        ++i;
+//        ++row0_it;
+//        ++row1_it;
+//    }
+//    //fill up with gaps if one sequence is longer than the other
+//    len = (len1 > len2) ? len1 : len2;
+//    ret_score += (len - i) * scoreGapExtend(score_type);
+//
+//    return ret_score;
+//}
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
diff --git a/seqan/graph_align/graph_algorithm_refine_aligngraph.h b/seqan/graph_align/graph_algorithm_refine_aligngraph.h
index 106d2a0..9bb4e73 100644
--- a/seqan/graph_align/graph_algorithm_refine_aligngraph.h
+++ b/seqan/graph_align/graph_algorithm_refine_aligngraph.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,28 +33,28 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_
 
 //SEQAN_NO_DDDOC: do not generate documentation for this file
 
 namespace seqan {
 
-	
-///////////////////////////////////////////////////////////////////////////////////////////////////////	
+
+///////////////////////////////////////////////////////////////////////////////////////////////////////
 //Functios for Align Graphs
 //project onto other sequence for Graph<Alignment>
 template<typename TAlignment,typename TId1, typename TPos1, typename TId2, typename TPos2, typename TValue,typename TMap>
 void
-_getOtherSequenceAndProject(Graph<TAlignment> & segment, 
-			    TValue seg_num,
-                            TMap &, 
- 							TId1 seq_i_id, 
-							TPos1 pos_i, 
-							TId2 & seq_j_id, 
-							TPos2 & pos_j)
+_getOtherSequenceAndProject(Graph<TAlignment> & segment,
+                TValue seg_num,
+                            TMap &,
+                             TId1 seq_i_id,
+                            TPos1 pos_i,
+                            TId2 & seq_j_id,
+                            TPos2 & pos_j)
 {
-	getProjectedPosition(segment,seg_num,seq_i_id, pos_i,seq_j_id,pos_j);
+    getProjectedPosition(segment,seg_num,seq_i_id, pos_i,seq_j_id,pos_j);
 
 }
 
@@ -67,34 +67,34 @@ _getOtherSequenceAndProject(Graph<TAlignment> & segment,
 template<typename TAlign, typename TId, typename TPosition, typename TId2>
 void
 _getSeqBeginAndEnd(Graph<TAlign> & segment,
-				  std::map<const void * ,int> &, 
-				  TId & seq_i_id, 
-				  TPosition & begin_i, 
-				  TPosition & end_i,
-				  TId2 seq)
+                  std::map<const void * ,int> &,
+                  TId & seq_i_id,
+                  TPosition & begin_i,
+                  TPosition & end_i,
+                  TId2 seq)
 {
 SEQAN_CHECKPOINT
-	//walk through edges, take first edge, target, source,
-	//define: seq == 0   ==> seq_i_id = id of source of first edge
-	//        seq == 1   ==> seq_i_id = id of target of first edge
-	typedef Graph<TAlign> TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	
-	TEdgeIterator ed_it(segment);
-	//goBegin(ed_it);
-	if(seq==0)
-	{
-		TVertexDescriptor src = sourceVertex(ed_it);
-		seq_i_id = sequenceId(segment,src);
-	}
-	else
-	{
-		TVertexDescriptor trg = targetVertex(ed_it);
-		seq_i_id = sequenceId(segment,trg);
-	}
-	begin_i = getFirstCoveredPosition(segment,seq_i_id);
-	end_i = getLastCoveredPosition(segment,seq_i_id);
+    //walk through edges, take first edge, target, source,
+    //define: seq == 0   ==> seq_i_id = id of source of first edge
+    //        seq == 1   ==> seq_i_id = id of target of first edge
+    typedef Graph<TAlign> TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+
+    TEdgeIterator ed_it(segment);
+    //goBegin(ed_it);
+    if(seq==0)
+    {
+        TVertexDescriptor src = sourceVertex(ed_it);
+        seq_i_id = sequenceId(segment,src);
+    }
+    else
+    {
+        TVertexDescriptor trg = targetVertex(ed_it);
+        seq_i_id = sequenceId(segment,trg);
+    }
+    begin_i = getFirstCoveredPosition(segment,seq_i_id);
+    end_i = getLastCoveredPosition(segment,seq_i_id);
 
 
 }
@@ -108,46 +108,45 @@ SEQAN_CHECKPOINT
 //template<typename TScore,typename TStringSet,typename TAlignment,typename TValue>
 //typename Value<TScore>::Type
 //_getRefinedMatchScore(TScore & score_type,
-//		 TStringSet & seqs,
-//		 Graph<TAlignment> & segment,
-//		 TValue pos_i,
-//		 TValue pos_j,
-//		 TValue len)
+//         TStringSet & seqs,
+//         Graph<TAlignment> & segment,
+//         TValue pos_i,
+//         TValue pos_j,
+//         TValue len)
 //{
 //SEQAN_CHECKPOINT
-//	int pseudo_map = 0;
-//	TValue pos_j_check,seq_j_id;
-//	_getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,pos_i,seq_j_id,pos_j_check);
-//	SEQAN_ASSERT(pos_j_check==pos_j);
-//	TValue last_pos_i = pos_i + len;
-//	TValue last_pos_j;
-//	_getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,last_pos_i,seq_j_id,last_pos_j);
+//    int pseudo_map = 0;
+//    TValue pos_j_check,seq_j_id;
+//    _getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,pos_i,seq_j_id,pos_j_check);
+//    SEQAN_ASSERT(pos_j_check==pos_j);
+//    TValue last_pos_i = pos_i + len;
+//    TValue last_pos_j;
+//    _getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,last_pos_i,seq_j_id,last_pos_j);
 //
-////	typename Infix<typename Value<TStringSet>::Type>::Type label0 = infix(getValueById(seqs,seq_i_id),pos_i,last_pos_i);
-////	typename Infix<typename Value<TStringSet>::Type>::Type label1 = infix(getValueById(seqs,seq_j_id),pos_j,last_pos_j);
-//	
-//	typename Value<TScore>::Type score = 0;
-//	TValue i = 0;
-//	while (i < len)
-//	{
-//		next_pos_j = getProjectedPosition(segment,seq_i_id,pos_i);
-//		//gaps
-//		if(pos_j+1 != next_pos_j)
-//		{
-//			if(pos_j == next_pos_j)
-//			{
-//				score += scoreGapExtend(score_type);
-//				++pos_i;
-//				++i;
-//				continue;
-//			}
-//		}		
-//		pos_j = next_pos_j;
-//		score += score(score_type,getValueById(seqs,seq_i_id)[pos_i],getValueById(seqs,seq_j_id)[pos_j]);
-//		++i;
-//		++pos_i;
-//	}
+////    typename Infix<typename Value<TStringSet>::Type>::Type label0 = infix(getValueById(seqs,seq_i_id),pos_i,last_pos_i);
+////    typename Infix<typename Value<TStringSet>::Type>::Type label1 = infix(getValueById(seqs,seq_j_id),pos_j,last_pos_j);
 //
+//    typename Value<TScore>::Type score = 0;
+//    TValue i = 0;
+//    while (i < len)
+//    {
+//        next_pos_j = getProjectedPosition(segment,seq_i_id,pos_i);
+//        //gaps
+//        if(pos_j+1 != next_pos_j)
+//        {
+//            if(pos_j == next_pos_j)
+//            {
+//                score += scoreGapExtend(score_type);
+//                ++pos_i;
+//                ++i;
+//                continue;
+//            }
+//        }
+//        pos_j = next_pos_j;
+//        score += score(score_type,getValueById(seqs,seq_i_id)[pos_i],getValueById(seqs,seq_j_id)[pos_j]);
+//        ++i;
+//        ++pos_i;
+//    }
 //
 //
 //
@@ -155,138 +154,139 @@ SEQAN_CHECKPOINT
 //
 //
 //
-//	typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,stringSet(segment)[0]);
-//	typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,stringSet(segment)[1]);
 //
+//    typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,stringSet(segment)[0]);
+//    typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,stringSet(segment)[1]);
 //
-//	//typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,0);
-//	//typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,1);
-//	int i = 0;
-//	typename Value<TScore>::Type ret_score = 0;
-//	while(i < len)
-//	{
-//		ret_score += score(score_type,label0[i],label1[i]);
-//		++i;
-//	}
-//	//ret_score = scoreMatch(score_type);
-//	//ret_score *= len;
-//	return ret_score;
-//}				
+//
+//    //typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,0);
+//    //typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,1);
+//    int i = 0;
+//    typename Value<TScore>::Type ret_score = 0;
+//    while(i < len)
+//    {
+//        ret_score += score(score_type,label0[i],label1[i]);
+//        ++i;
+//    }
+//    //ret_score = scoreMatch(score_type);
+//    //ret_score *= len;
+//    return ret_score;
+//}
 
 
 //////////////////////////
 // get score for part of pairwise alignment graph starting in pos_i in first sequence and in
 // pos_j in second sequence, and with length len and len_j respectively
-// only for exact refinement 
+// only for exact refinement
 template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TAlignment,typename TValue>
 TScoreValue
 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
-		 TStringSet & seqs,
-		 Graph<TAlignment> & segment,
-		 TValue pos_i,
-		 TValue pos_j,
-		 TValue len,
-		 TValue len_j)
+         TStringSet & seqs,
+         Graph<TAlignment> & segment,
+         TValue pos_i,
+         TValue pos_j,
+         TValue len,
+         TValue len_j)
 {
 SEQAN_CHECKPOINT
 
-	typedef Graph<TAlignment> TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename TGraph::TPosToVertexMap TPosToVertexMap;
-	typedef typename TPosToVertexMap::const_iterator TVertexMapIter;
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	
-	TValue seq_i_id;
-	TEdgeIterator ed(segment);
-	//goBegin(ed);
-	seq_i_id = sequenceId(segment,sourceVertex(ed));
-		
-	int pseudo_map = 0;
-	TValue pos_j_check,seq_j_id;
-	_getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,pos_i,seq_j_id,pos_j_check);
-	SEQAN_ASSERT(pos_j_check==pos_j);
-	TValue last_pos_j = pos_j + len_j;
-		
-	TScoreValue ret_score = 0;
-	bool last_one_was_aligned = false;
+    typedef Graph<TAlignment> TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename TGraph::TPosToVertexMap TPosToVertexMap;
+    typedef typename TPosToVertexMap::const_iterator TVertexMapIter;
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+
+    TValue seq_i_id;
+    TEdgeIterator ed(segment);
+    //goBegin(ed);
+    seq_i_id = sequenceId(segment,sourceVertex(ed));
 
-	while(len != 0)
-	{
-		TValue rest = 0;
-		TVertexMapIter it = segment.data_pvMap.upper_bound(std::make_pair(seq_i_id, pos_i));
-		// it->second is nilVertex if pos_i lies within gap	
-		if(it->second == nilVertex)
-		{	
-			++it;
-			if(it != segment.data_pvMap.end() && it->first.first == seq_i_id)
-			{
-				rest = fragmentBegin(segment,it->second)-pos_i;
-				last_one_was_aligned = false;
-				if(rest < len)//add rest many gaps
-						ret_score += rest * scoreGapExtend(score_type);
-				else
-				{//add len many gaps
-					ret_score += len * scoreGapExtend(score_type);
-					return ret_score;	//and done!
-				}
-			}
-			else
-			{//add len many gaps
-				ret_score += len * scoreGapExtend(score_type);
-				return ret_score;	//and done!
-			}
-		}
-		else{
-			TVertexDescriptor vd = it->second;
-			rest = fragmentBegin(segment,vd)+fragmentLength(segment,vd)-pos_i;
-			TOutEdgeIterator ed_it(segment,vd);
-			if(!atEnd(ed_it)) //aligned stretch
-			{
-				if(last_one_was_aligned)
-				{
-					TValue next_pos_j,temp;
-					getProjectedPosition(segment,seq_i_id,pos_i,temp,next_pos_j);
-					ret_score += (next_pos_j-pos_j) * scoreGapExtend(score_type);
-					pos_j = next_pos_j; 
-				}
-				last_one_was_aligned = true;
-				TValue i = 0;
-				while(i < rest && i < len)
-				{
-					ret_score += score(score_type,getValueById(seqs,seq_i_id)[pos_i++],getValueById(seqs,seq_j_id)[pos_j++]);
-					++i;
-				}
-				if(rest>len) return ret_score; //done (last_pos_i is somewhere inside the current node)
-				else 
-				{//last_pos_i is the first position of the next node
-					if(rest == len) //check if there is an unalgined stretch on seq_j_id that needs to be included
-					{
-						if(pos_j != last_pos_j)
-							ret_score += (last_pos_j-pos_j) * scoreGapExtend(score_type);
-					}
-				}
-			}
-			else //gap
-			{
-				last_one_was_aligned = false;
-				if(rest < len)//add rest many gaps
-						ret_score += rest * scoreGapExtend(score_type);
-				else
-				{//add len many gaps
-					ret_score += len * scoreGapExtend(score_type);
-					return ret_score;	//and done!
-				}
-			}
-		}
-		len -= rest;	
-	}
+    int pseudo_map = 0;
+    TValue pos_j_check,seq_j_id;
+    _getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,pos_i,seq_j_id,pos_j_check);
+    SEQAN_ASSERT(pos_j_check==pos_j);
+    TValue last_pos_j = pos_j + len_j;
 
+    TScoreValue ret_score = 0;
+    bool last_one_was_aligned = false;
 
-	return ret_score;
-}				
+    while(len != 0)
+    {
+        TValue rest = 0;
+        TVertexMapIter it = segment.data_pvMap.upper_bound(std::make_pair(seq_i_id, pos_i));
+        // it->second is nilVertex if pos_i lies within gap
+        if(it->second == nilVertex)
+        {
+            ++it;
+            if(it != segment.data_pvMap.end() && it->first.first == seq_i_id)
+            {
+                rest = fragmentBegin(segment,it->second)-pos_i;
+                last_one_was_aligned = false;
+                if(rest < len)//add rest many gaps
+                        ret_score += rest * scoreGapExtend(score_type);
+                else
+                {//add len many gaps
+                    ret_score += len * scoreGapExtend(score_type);
+                    return ret_score;    //and done!
+                }
+            }
+            else
+            {//add len many gaps
+                ret_score += len * scoreGapExtend(score_type);
+                return ret_score;    //and done!
+            }
+        }
+        else{
+            TVertexDescriptor vd = it->second;
+            rest = fragmentBegin(segment,vd)+fragmentLength(segment,vd)-pos_i;
+            TOutEdgeIterator ed_it(segment,vd);
+            if(!atEnd(ed_it)) //aligned stretch
+            {
+                if(last_one_was_aligned)
+                {
+                    TValue next_pos_j,temp;
+                    getProjectedPosition(segment,seq_i_id,pos_i,temp,next_pos_j);
+                    ret_score += (next_pos_j-pos_j) * scoreGapExtend(score_type);
+                    pos_j = next_pos_j;
+                }
+                last_one_was_aligned = true;
+                TValue i = 0;
+                while(i < rest && i < len)
+                {
+                    ret_score += score(score_type,getValueById(seqs,seq_i_id)[pos_i++],getValueById(seqs,seq_j_id)[pos_j++]);
+                    ++i;
+                }
+                if(rest>len) return ret_score; //done (last_pos_i is somewhere inside the current node)
+                else
+                {//last_pos_i is the first position of the next node
+                    if(rest == len) //check if there is an unalgined stretch on seq_j_id that needs to be included
+                    {
+                        if(pos_j != last_pos_j)
+                            ret_score += (last_pos_j-pos_j) * scoreGapExtend(score_type);
+                    }
+                }
+            }
+            else //gap
+            {
+                last_one_was_aligned = false;
+                if(rest < len)//add rest many gaps
+                        ret_score += rest * scoreGapExtend(score_type);
+                else
+                {//add len many gaps
+                    ret_score += len * scoreGapExtend(score_type);
+                    return ret_score;    //and done!
+                }
+            }
+        }
+        len -= rest;
+    }
+
+
+    return ret_score;
+}
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_
diff --git a/seqan/graph_align/graph_algorithm_refine_annotation.h b/seqan/graph_align/graph_algorithm_refine_annotation.h
index 955557c..b6d7464 100644
--- a/seqan/graph_align/graph_algorithm_refine_annotation.h
+++ b/seqan/graph_align/graph_algorithm_refine_annotation.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,8 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ANNOTATION_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ANNOTATION_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ANNOTATION_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ANNOTATION_H_
 
 //SEQAN_NO_DDDOC: do not generate documentation for this file
 
@@ -46,99 +46,78 @@ class Annotation;
 
 
 
-/**
-.Class.Annotation:
-..cat:Sequences
-..summary:Class for annotating sequences. 
-..signature:Annotation<TSequence, TLabel, TSpec>  
-..param.TSequence:The sequence that annotation is available for.
-..param.TLabel:The label type (e.g. int or String<char>)
-..param.TSpec:The specializing type.
-...default:Simple
-..include:graph_align.h
-*/
 template<typename TSequence,typename TValue>
 class Annotation<TSequence,TValue,Simple>{
 
 public:
-	typedef typename Id<TSequence>::Type TId_;
-	typedef typename Position<TSequence>::Type TPos_;
-	typedef typename Size<TSequence>::Type TSize_;
-
-	TId_ data_seq_id;
-	TPos_ data_begin;
-	TSize_ data_length;
-	//String<char> data_label;
-	TValue data_label;
-
-	Annotation()
-	{
-	}
-
-    /**
-.Memfunc.Annotation#Annotation:
-..class:Class.Annotation
-..summary:Constructor.
-..signature:Annotation(seqId, begin, len, label)
-..param.seqId:The sequence ID of the annotated sequence of type Id<TSequence>::Type.
-..param.begin:The begin position of the annotated interval of type Position<TSequence>::Type.
-..param.len:The length of the annotated interval of type Size<TSequence>::Type.
-..param.cargo:The annotation label/identifier of type TValue.
-     */
-	
-	Annotation(TId_ seqId, TPos_ begin, TSize_ len, TValue label) :
-			data_seq_id(seqId),
-			data_begin(begin), 
-			data_length(len),
-			data_label(label)
-	{
-	}
-
-	~Annotation()
-	{
-	}
+    typedef typename Id<TSequence>::Type TId_;
+    typedef typename Position<TSequence>::Type TPos_;
+    typedef typename Size<TSequence>::Type TSize_;
+
+    TId_ data_seq_id;
+    TPos_ data_begin;
+    TSize_ data_length;
+    //String<char> data_label;
+    TValue data_label;
+
+    Annotation()
+    {
+    }
+
+
+    Annotation(TId_ seqId, TPos_ begin, TSize_ len, TValue label) :
+            data_seq_id(seqId),
+            data_begin(begin),
+            data_length(len),
+            data_label(label)
+    {
+    }
+
+    ~Annotation()
+    {
+    }
 
 };
 
 
 
-template<typename TSequence,typename TValue,typename TSpec>	
+template<typename TSequence,typename TValue,typename TSpec>
 typename Id<TSequence>::Type&
 sequenceId(Annotation<TSequence,TValue,TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_seq_id;
+    return me.data_seq_id;
 }
 
-template<typename TSequence,typename TValue,typename TSpec>	
+template<typename TSequence,typename TValue,typename TSpec>
 typename Position<TSequence>::Type&
 fragmentBegin(Annotation<TSequence,TValue,TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_begin;
+    return me.data_begin;
 }
 
-template<typename TSequence,typename TValue,typename TSpec>	
+template<typename TSequence,typename TValue,typename TSpec>
 typename Size<TSequence>::Type&
 fragmentLength(Annotation<TSequence,TValue,TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_length;
+    return me.data_length;
 }
 
-template<typename TSequence,typename TValue,typename TSpec>	
+template<typename TSequence,typename TValue,typename TSpec>
 TValue
 label(Annotation<TSequence,TValue,TSpec> & me)
 {
 SEQAN_CHECKPOINT
-	return me.data_label;
+    return me.data_label;
 }
 
 
-template<typename TSequence,typename TValue,typename TSpec>	
+template<typename TSequence,typename TValue,typename TSpec>
 struct Value<Annotation<TSequence,TValue,TSpec> >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 
 
@@ -146,17 +125,17 @@ struct Value<Annotation<TSequence,TValue,TSpec> >
 template<typename TValue, typename TAliString, typename TGraph, typename TPropertyMap, typename TStringSet, typename TMap, typename TTagSpec>
 inline void
 _addAnnotationCuts(String<std::set<TValue> > &,
-				   TAliString &, 
-				   String<TGraph> &, 
-				   String<TPropertyMap> &, 
-				   TStringSet &,
-				   TMap &,
-				   bool,
-				   TValue,
-				   Tag<TTagSpec>)
+                   TAliString &,
+                   String<TGraph> &,
+                   String<TPropertyMap> &,
+                   TStringSet &,
+                   TMap &,
+                   bool,
+                   TValue,
+                   Tag<TTagSpec>)
 {
 SEQAN_CHECKPOINT
-	return;
+    return;
 }
 
 
@@ -166,101 +145,101 @@ SEQAN_CHECKPOINT
 template<typename TValue, typename TAliString, typename TGraph, typename TPropertyMap, typename TStringSet, typename TMap, typename TAnnoString, typename TTagSpec>
 inline void
 _addAnnotationCuts(String<std::set<TValue> > & all_nodes,
-				   TAliString & alis, 
-				   String<TGraph> & gs, 
-				   String<TPropertyMap> & pms, 
-				   TStringSet & seq,
-				   TMap & seq_map,
-				   TAnnoString & annotation,
-				   TValue min_fragment_len,
-				   Tag<TTagSpec> tag)
+                   TAliString & alis,
+                   String<TGraph> & gs,
+                   String<TPropertyMap> & pms,
+                   TStringSet & seq,
+                   TMap & seq_map,
+                   TAnnoString & annotation,
+                   TValue min_fragment_len,
+                   Tag<TTagSpec> tag)
 {
 SEQAN_CHECKPOINT
 
-	//typedef typename Value<TAnnoString>::Type TAnnotation;
-	typedef typename Iterator<TAnnoString,Standard>::Type TAnnoIter;
-	typedef typename std::set<TValue>::iterator TSetIterator;
-	//call function _refine for each position that annotation is given for (the borders of annotated stretches)
-	TAnnoIter anno_it = begin(annotation,Standard());
-	TAnnoIter anno_end = end(annotation,Standard());
-	//for each annotated stretch
-	while(anno_it != anno_end)
-	{
-		
-		TValue seq_i_id = sequenceId(*anno_it);
-		TValue begin_i = fragmentBegin(*anno_it);
-		TValue end_i = begin_i + fragmentLength(*anno_it);
-		TValue seq_i_pos = idToPosition(seq,seq_i_id);
-		
-		//refine begin
-		TSetIterator iter = all_nodes[seq_i_pos].find(begin_i);		
-		if(_cutIsValid(all_nodes,seq_i_pos,begin_i,iter,min_fragment_len,tag))
-		{
-			all_nodes[seq_i_pos].insert(begin_i);
-			_refine(begin_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes,min_fragment_len,tag);//TStop());
-		}
-		//and end position
-		iter = all_nodes[seq_i_pos].find(end_i);		
-		if(_cutIsValid(all_nodes,seq_i_pos,end_i,iter,min_fragment_len,tag))
-		{
-			all_nodes[seq_i_pos].insert(end_i);
-			_refine(end_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes,min_fragment_len,tag);//TStop());
-		}
-		++anno_it;
-	}
-	      	
+    //typedef typename Value<TAnnoString>::Type TAnnotation;
+    typedef typename Iterator<TAnnoString,Standard>::Type TAnnoIter;
+    typedef typename std::set<TValue>::iterator TSetIterator;
+    //call function _refine for each position that annotation is given for (the borders of annotated stretches)
+    TAnnoIter anno_it = begin(annotation,Standard());
+    TAnnoIter anno_end = end(annotation,Standard());
+    //for each annotated stretch
+    while(anno_it != anno_end)
+    {
+
+        TValue seq_i_id = sequenceId(*anno_it);
+        TValue begin_i = fragmentBegin(*anno_it);
+        TValue end_i = begin_i + fragmentLength(*anno_it);
+        TValue seq_i_pos = idToPosition(seq,seq_i_id);
+
+        //refine begin
+        TSetIterator iter = all_nodes[seq_i_pos].find(begin_i);
+        if(_cutIsValid(all_nodes,seq_i_pos,begin_i,iter,min_fragment_len,tag))
+        {
+            all_nodes[seq_i_pos].insert(begin_i);
+            _refine(begin_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes,min_fragment_len,tag);//TStop());
+        }
+        //and end position
+        iter = all_nodes[seq_i_pos].find(end_i);
+        if(_cutIsValid(all_nodes,seq_i_pos,end_i,iter,min_fragment_len,tag))
+        {
+            all_nodes[seq_i_pos].insert(end_i);
+            _refine(end_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes,min_fragment_len,tag);//TStop());
+        }
+        ++anno_it;
+    }
+
 }
-	      
+
 
 // add annotation labels to nodes, as given in annotation, store as node properties in pm
 template<typename TPropertyMap, typename TStringSet, typename TMap, typename TAnnoString, typename TAliGraph,typename TTagSpec>
 inline void
 _addNodeAnnotation(TStringSet &,
-				   TMap &,
-				   TAnnoString & annotation,
-				   TPropertyMap & pm,
-				   TAliGraph & ali_g,
-				   Tag<TTagSpec>)
+                   TMap &,
+                   TAnnoString & annotation,
+                   TPropertyMap & pm,
+                   TAliGraph & ali_g,
+                   Tag<TTagSpec>)
 {
 SEQAN_CHECKPOINT
 
-	resizeVertexMap(ali_g, pm);
+    resizeVertexMap(pm, ali_g);
 
-	typedef typename Value<TAnnoString>::Type TAnnotation;
-	typedef typename Id<TAnnotation>::Type TId;
-	typedef typename Position<TAnnotation>::Type TPos;
-	typedef typename Value<TAnnotation>::Type TLabel;
-	typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
-	
-	typedef typename Iterator<TAnnoString,Standard>::Type TAnnoIter;
-	TAnnoIter anno_it = begin(annotation,Standard());
-	TAnnoIter anno_end = end(annotation,Standard());
+    typedef typename Value<TAnnoString>::Type TAnnotation;
+    typedef typename Id<TAnnotation>::Type TId;
+    typedef typename Position<TAnnotation>::Type TPos;
+    typedef typename Value<TAnnotation>::Type TLabel;
+    typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
 
-	//for each annotated stretch
-	while(anno_it != anno_end)
-	{
-		TLabel label_ = label(*anno_it);
-		TId seq_id = sequenceId(*anno_it);
-		TPos act_pos = fragmentBegin(*anno_it);
-		TPos end_pos = act_pos + fragmentLength(*anno_it);
+    typedef typename Iterator<TAnnoString,Standard>::Type TAnnoIter;
+    TAnnoIter anno_it = begin(annotation,Standard());
+    TAnnoIter anno_end = end(annotation,Standard());
 
-		//for each interval that lies within the current segment/fragement/alignment
-		while(act_pos < end_pos)
-		{
-			//get the node represents the current interval (begin_pos until next_cut_pos or end_pos)
-			TVertexDescriptor act_knot = findVertex(ali_g,seq_id,act_pos);
+    //for each annotated stretch
+    while(anno_it != anno_end)
+    {
+        TLabel label_ = label(*anno_it);
+        TId seq_id = sequenceId(*anno_it);
+        TPos act_pos = fragmentBegin(*anno_it);
+        TPos end_pos = act_pos + fragmentLength(*anno_it);
 
-			String<TLabel> property = getProperty(pm, act_knot);
-			appendValue(property,label_);
-			assignProperty(pm, act_knot, property);
-			SEQAN_ASSERT(fragmentBegin(ali_g,act_knot)==act_pos);
+        //for each interval that lies within the current segment/fragement/alignment
+        while(act_pos < end_pos)
+        {
+            //get the node represents the current interval (begin_pos until next_cut_pos or end_pos)
+            TVertexDescriptor act_knot = findVertex(ali_g,seq_id,act_pos);
 
-			//prepare for next interval
-			act_pos += fragmentLength(ali_g,act_knot);
-		}
-		++anno_it;
+            String<TLabel> property = getProperty(pm, act_knot);
+            appendValue(property,label_);
+            assignProperty(pm, act_knot, property);
+            SEQAN_ASSERT(fragmentBegin(ali_g,act_knot)==act_pos);
 
-	}
+            //prepare for next interval
+            act_pos += fragmentLength(ali_g,act_knot);
+        }
+        ++anno_it;
+
+    }
 
 
 
@@ -270,144 +249,120 @@ SEQAN_CHECKPOINT
 // compute annotation score: 2 if vd1 and vd2 share same annotation
 // 1 if they are not the same (--> edgescore = alignmentscore)
 template<typename TAliGraph,typename TScore, typename TPropertyMap>
-typename Value<TScore>::Type 
+typename Value<TScore>::Type
 _getRefinedAnnoScore(TAliGraph &,
-			 TPropertyMap & pm,
-			 typename VertexDescriptor<TAliGraph>::Type vd1,
-			 typename VertexDescriptor<TAliGraph>::Type vd2,
-			 TScore &)
+             TPropertyMap & pm,
+             typename VertexDescriptor<TAliGraph>::Type vd1,
+             typename VertexDescriptor<TAliGraph>::Type vd2,
+             TScore &)
 {
 SEQAN_CHECKPOINT
-	typedef typename Value<TPropertyMap>::Type TProperty;
-	//typedef typename Value<TProperty>::Type TChar;
-	typedef typename Iterator<TProperty,Standard>::Type TIterator;
-
-	TIterator prop1_it = begin(property(pm,vd1),Standard());
-	TIterator prop1_end = end(property(pm,vd1),Standard());
-	while(prop1_it != prop1_end)
-	{
-		TIterator prop2_it = begin(property(pm,vd2),Standard());
-		TIterator prop2_end = end(property(pm,vd2),Standard());
-		while(prop2_it != prop2_end)
-		{
-			if(*prop2_it==*prop1_it)
-				return 2;/*scoreMatch(score_type);*/
-			++prop2_it;
-		}
-		++prop1_it;
-	}
-	return 1;
+    typedef typename Value<TPropertyMap>::Type TProperty;
+    //typedef typename Value<TProperty>::Type TChar;
+    typedef typename Iterator<TProperty,Standard>::Type TIterator;
+
+    TIterator prop1_it = begin(property(pm,vd1),Standard());
+    TIterator prop1_end = end(property(pm,vd1),Standard());
+    while(prop1_it != prop1_end)
+    {
+        TIterator prop2_it = begin(property(pm,vd2),Standard());
+        TIterator prop2_end = end(property(pm,vd2),Standard());
+        while(prop2_it != prop2_end)
+        {
+            if(*prop2_it==*prop1_it)
+                return 2;/*scoreMatch(score_type);*/
+            ++prop2_it;
+        }
+        ++prop1_it;
+    }
+    return 1;
 
 }
 
 // default score 1 --> edgescore = alignmentscore
 template<typename TAliGraph,typename TScore>
-typename Value<TScore>::Type 
+typename Value<TScore>::Type
 _getRefinedAnnoScore(TAliGraph &,
-			 bool,
-			 typename VertexDescriptor<TAliGraph>::Type,
-			 typename VertexDescriptor<TAliGraph>::Type,
-			 TScore &)
+             bool,
+             typename VertexDescriptor<TAliGraph>::Type,
+             typename VertexDescriptor<TAliGraph>::Type,
+             TScore &)
 {
 SEQAN_CHECKPOINT
-	return (typename Value<TScore>::Type) 1;
+    return (typename Value<TScore>::Type) 1;
 }
 
 
 
 
-/**
-.Function.matchRefinement:
-..class:Spec.Alignment Graph
-..signature:matchRefinement(matches,annotation,stringSet,scoringScheme,refinedGraph)
-..param.annotation:Sequence annotation data. 
-...remarks: Additional semgent match subdivisions will be made at sequence positions at which the annotation label changes.
-...type:Class.Annotation
-..include:seqan/graph_align.h
-*/
 //annotation given,exact refinement, score type given
 template<typename TAlignmentString, typename TScoreValue,typename TScoreSpec,typename TAnnoString,typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				TAnnoString & anno,
-				StringSet<TSequence, TSetSpec> & seq, 
-				Score<TScoreValue,TScoreSpec> & score_type,
-				TOutGraph & ali_graph)
+                TAnnoString & anno,
+                StringSet<TSequence, TSetSpec> & seq,
+                Score<TScoreValue,TScoreSpec> & score_type,
+                TOutGraph & ali_graph)
 {
 SEQAN_CHECKPOINT
-	//min_fragment_len = 1   ==> Exact cutting
-	matchRefinement(alis,seq,score_type,ali_graph,1,anno,ExactRefinement());
+    //min_fragment_len = 1   ==> Exact cutting
+    matchRefinement(alis,seq,score_type,ali_graph,1,anno,ExactRefinement());
 }
 
 
-/**
-.Function.matchRefinement:
-..signature:matchRefinement(matches,annotation,stringSet,scoringScheme,refinedGraph,minFragmentLen)
-..include:seqan/graph_align.h
-*/
 //annotation given,score type given, min fragment length given, if > 1 ==> inexact refinement
 template<typename TAlignmentString, typename TScoreValue,typename TScoreSpec,typename TAnnoString, typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				TAnnoString & anno,
-				StringSet<TSequence, TSetSpec> & seq, 
-				Score<TScoreValue,TScoreSpec> & score_type,
-				TOutGraph & ali_graph,
-				unsigned int min_frag_len)
+                TAnnoString & anno,
+                StringSet<TSequence, TSetSpec> & seq,
+                Score<TScoreValue,TScoreSpec> & score_type,
+                TOutGraph & ali_graph,
+                unsigned int min_frag_len)
 {
 SEQAN_CHECKPOINT
-	if(min_frag_len > 1)
+    if(min_frag_len > 1)
         matchRefinement(alis,seq,score_type,ali_graph,min_frag_len,anno,InexactRefinement());
-	else
+    else
         matchRefinement(alis,seq,score_type,ali_graph,min_frag_len,anno,ExactRefinement());
 }
 
 
 
-/**
-.Function.matchRefinement:
-..signature:matchRefinement(matches,annotation,stringSet,refinedGraph,minFragmentLen)
-..include:seqan/graph_align.h
-*/
 //annotation given,score type not given, min fragment length given, if > 1 ==> inexact refinement
 template<typename TAlignmentString, typename TOutGraph, typename TAnnoString, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				TAnnoString & anno,
-				StringSet<TSequence, TSetSpec> & seq, 
-				TOutGraph & ali_graph,
-				unsigned int min_frag_len)
+                TAnnoString & anno,
+                StringSet<TSequence, TSetSpec> & seq,
+                TOutGraph & ali_graph,
+                unsigned int min_frag_len)
 {
 SEQAN_CHECKPOINT
-//	Score<int,FakeScore > fake_score;
-	typename Cargo<TOutGraph>::Type fake_score = 1;
-	if(min_frag_len > 1)
+//    Score<int,FakeScore > fake_score;
+    typename Cargo<TOutGraph>::Type fake_score = 1;
+    if(min_frag_len > 1)
         matchRefinement(alis,seq,fake_score,ali_graph,min_frag_len,anno,InexactRefinement());
-	else
+    else
         matchRefinement(alis,seq,fake_score,ali_graph,min_frag_len,anno,ExactRefinement());
 }
-	
 
 
-/**
-.Function.matchRefinement:
-..signature:matchRefinement(matches,annotation,stringSet,refinedGraph)
-..include:seqan/graph_align.h
-*/
+
 //annotation given,exact refinement, score type not given
 template<typename TAlignmentString,typename TAnnoString, typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				TAnnoString & anno,
-				StringSet<TSequence, TSetSpec> & seq, 
-				TOutGraph & ali_graph)
+                TAnnoString & anno,
+                StringSet<TSequence, TSetSpec> & seq,
+                TOutGraph & ali_graph)
 {
 SEQAN_CHECKPOINT
-//	Score<int,FakeScore > fake_score;
-	typename Cargo<TOutGraph>::Type fake_score = 1;
-	matchRefinement(alis,seq,fake_score,ali_graph,1,anno,ExactRefinement());
+//    Score<int,FakeScore > fake_score;
+    typename Cargo<TOutGraph>::Type fake_score = 1;
+    matchRefinement(alis,seq,fake_score,ali_graph,1,anno,ExactRefinement());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ANNOTATION_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ANNOTATION_H_
diff --git a/seqan/graph_align/graph_algorithm_refine_exact.h b/seqan/graph_align/graph_algorithm_refine_exact.h
index c3f116e..0ecb8b2 100644
--- a/seqan/graph_align/graph_algorithm_refine_exact.h
+++ b/seqan/graph_align/graph_algorithm_refine_exact.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,11 +33,11 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_H_
 
 namespace seqan {
-	
+
 struct TagExactRefinement_;
 typedef Tag<TagExactRefinement_> const ExactRefinement;
 
@@ -45,17 +45,17 @@ typedef Tag<TagExactRefinement_> const ExactRefinement;
 template<typename TValue, typename TValue2, typename TSize>
 inline bool
 _cutIsValid(String<std::set<TValue> > & all_nodes,
-		TValue2 seq_i_pos,
-		TSize,
-		typename std::set<TValue>::iterator iter,
-		TSize,
-		Tag<TagExactRefinement_> const)
+        TValue2 seq_i_pos,
+        TSize,
+        typename std::set<TValue>::iterator iter,
+        TSize,
+        Tag<TagExactRefinement_> const)
 {
 SEQAN_CHECKPOINT
-	//cut already exists
-	if(iter != all_nodes[seq_i_pos].end())
-		return false;
-	return true;
+    //cut already exists
+    if(iter != all_nodes[seq_i_pos].end())
+        return false;
+    return true;
 }
 
 
@@ -63,15 +63,15 @@ template<typename TSize, typename TSpec,typename TPos>
 inline void
 _updateCutPosition(Fragment<TSize, ExactReversableFragment<TSpec> > & f, TPos & pos_j)
 {
-	if(f.reversed)
-		++pos_j;
+    if(f.reversed)
+        ++pos_j;
 }
 //template<typename TSize, typename TSpec,typename TPos>
 //inline void
 //_updateCutPosition(Fragment<TSize, ExactReversableFragment<TSpec> > const& f, TPos & pos_j)
 //{
-//	if(f.reversed)
-//		++pos_j;
+//    if(f.reversed)
+//        ++pos_j;
 //}
 
 
@@ -79,157 +79,157 @@ template<typename TFrag,typename TPos>
 inline void
 _updateCutPosition(TFrag &, TPos &)
 {
-	return;
+    return;
 }
 
-///////////////////////////////////////////////////////////////////////////////////////////////////////	
+///////////////////////////////////////////////////////////////////////////////////////////////////////
 //Recursive Refinement
 //refine position node_i on sequence seq_i
 template<typename TValue, typename TAlignmentString, typename TStringSet,typename TGraph, typename TPropertyMap,typename TSeqMap, typename TTagSpec>
 inline void
-_refine(TValue node_i, 
-	 TValue seq_i_id, 
-	 TStringSet & seqs,
-	 TSeqMap & seq_map,
-	 TAlignmentString & alis, 
-	 String<TGraph> & gs, 
-	 String<TPropertyMap> & pms, 
-     String<std::set<TValue> > & all_nodes, 
-	 TValue min_len,
-	 Tag<TTagSpec> tag)
+_refine(TValue node_i,
+     TValue seq_i_id,
+     TStringSet & seqs,
+     TSeqMap & seq_map,
+     TAlignmentString & alis,
+     String<TGraph> & gs,
+     String<TPropertyMap> & pms,
+     String<std::set<TValue> > & all_nodes,
+     TValue min_len,
+     Tag<TTagSpec> tag)
 {
 SEQAN_CHECKPOINT
-	typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type TAlignmentPointer;
-	typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type TSegmentIterator;
-	//find all segment matches that contain the current position (node_i)
-	String<TAlignmentPointer> relevant_segments;
-	TValue seq_i_pos = idToPosition(seqs,seq_i_id);
-	findIntervalsExcludeTouching(gs[seq_i_pos],pms[seq_i_pos],node_i,relevant_segments);
-
-	
-	TSegmentIterator segment_it = begin(relevant_segments);
-	TSegmentIterator segment_end = end(relevant_segments);
-	//foreach of those segments
-	while(segment_it != segment_end)
-	{
-		TValue match_id = (*segment_it).i1;
-		TValue seg_num = (*segment_it).i2; // first or second segment in seg match
-
-		//get the sequence that node_i needs to be projected onto (seq_j)
-		//and get the projected position (pos_j)
-		TValue seq_j_id, node_j;
-		_getOtherSequenceAndProject(alis[match_id],seg_num,seq_map,seq_i_id,node_i,seq_j_id,node_j);
-		TValue seq_j_pos = idToPosition(seqs,seq_j_id);
-		_updateCutPosition(alis[match_id],node_j);
-
-		typename std::set<TValue>::iterator iter;
-		iter = all_nodes[seq_j_pos].find(node_j);
-		
-		//if node does not exist yet ---> insert and continue cutting
-		if(_cutIsValid(all_nodes,seq_j_pos,node_j,iter,min_len,tag))
-		{
-			all_nodes[seq_j_pos].insert(node_j);
-			_refine(node_j,seq_j_id,seqs,seq_map,alis,gs,pms,all_nodes,min_len,tag);
-			//TODO: else //verschmelzen, abschneiden und �bergehen, erst sp�ter... 	
-			//do nothing or resolve problems  
-		}
-	
-		++segment_it;
-	}
+    typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type TAlignmentPointer;
+    typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type TSegmentIterator;
+    //find all segment matches that contain the current position (node_i)
+    String<TAlignmentPointer> relevant_segments;
+    TValue seq_i_pos = idToPosition(seqs,seq_i_id);
+    findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i);
+
+
+    TSegmentIterator segment_it = begin(relevant_segments);
+    TSegmentIterator segment_end = end(relevant_segments);
+    //foreach of those segments
+    while(segment_it != segment_end)
+    {
+        TValue match_id = (*segment_it).i1;
+        TValue seg_num = (*segment_it).i2; // first or second segment in seg match
+
+        //get the sequence that node_i needs to be projected onto (seq_j)
+        //and get the projected position (pos_j)
+        TValue seq_j_id, node_j;
+        _getOtherSequenceAndProject(alis[match_id],seg_num,seq_map,seq_i_id,node_i,seq_j_id,node_j);
+        TValue seq_j_pos = idToPosition(seqs,seq_j_id);
+        _updateCutPosition(alis[match_id],node_j);
+
+        typename std::set<TValue>::iterator iter;
+        iter = all_nodes[seq_j_pos].find(node_j);
+
+        //if node does not exist yet ---> insert and continue cutting
+        if(_cutIsValid(all_nodes,seq_j_pos,node_j,iter,min_len,tag))
+        {
+            all_nodes[seq_j_pos].insert(node_j);
+            _refine(node_j,seq_j_id,seqs,seq_map,alis,gs,pms,all_nodes,min_len,tag);
+            //TODO: else //verschmelzen, abschneiden und �bergehen, erst sp�ter...
+            //do nothing or resolve problems
+        }
+
+        ++segment_it;
+    }
 }
 
 
-///////////////////////////////////////////////////////////////////////////////////////////////////////	
-//Construct interval trees 
+///////////////////////////////////////////////////////////////////////////////////////////////////////
+//Construct interval trees
 ////////////////////////////////////////////////////////////////////////////////////////////////////
 //construct intervals from allignments for each sequence (other Alignment types)
 template<typename TInterval, typename TStringSet, typename TAlignmentString, typename TSeqMap>
 void
-_buildIntervalsForAllSequences(TAlignmentString & alis, 
-							   String<String<TInterval> > & intervals, 
-	   						   TStringSet & seqs,
-							   TSeqMap & seq_map)
+_buildIntervalsForAllSequences(TAlignmentString & alis,
+                               String<String<TInterval> > & intervals,
+                                  TStringSet & seqs,
+                               TSeqMap & seq_map)
 {
 SEQAN_CHECKPOINT
-	
-	typedef typename Value<TInterval>::Type TValue;
-	typedef typename Cargo<TInterval>::Type TCargo;
-	typedef typename Iterator<TAlignmentString,Standard>::Type TAliIterator;
-	TAliIterator ali_it = begin(alis,Standard());
-	TAliIterator ali_end = end(alis,Standard());
-	TValue ali_counter = 0;
-	//foreach alignment
-	while(ali_it != ali_end)
-	{
-		TValue seq_i_id,begin_,end_;
-	
-		//get the first sequence (and its begin and end) that takes part in the alignment (seq_i)
-		_getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,0);
-		TValue seq_i_pos = idToPosition(seqs, seq_i_id);
-		//and append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
-		appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,0))); 
-	
-		//get the second sequence (and its begin and end) that takes part in the alignment (seq_i)
-		_getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,1);
-		seq_i_pos = idToPosition(seqs, seq_i_id);
-		//and again append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
-		appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,1))); 
-	
-		++ali_counter;
-		++ali_it;
-	}
+
+    typedef typename Value<TInterval>::Type TValue;
+    typedef typename Cargo<TInterval>::Type TCargo;
+    typedef typename Iterator<TAlignmentString,Standard>::Type TAliIterator;
+    TAliIterator ali_it = begin(alis,Standard());
+    TAliIterator ali_end = end(alis,Standard());
+    TValue ali_counter = 0;
+    //foreach alignment
+    while(ali_it != ali_end)
+    {
+        TValue seq_i_id,begin_,end_;
+
+        //get the first sequence (and its begin and end) that takes part in the alignment (seq_i)
+        _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,0);
+        TValue seq_i_pos = idToPosition(seqs, seq_i_id);
+        //and append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
+        appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,0)));
+
+        //get the second sequence (and its begin and end) that takes part in the alignment (seq_i)
+        _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,1);
+        seq_i_pos = idToPosition(seqs, seq_i_id);
+        //and again append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
+        appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,1)));
+
+        ++ali_counter;
+        ++ali_it;
+    }
 }
 
 
 //get all intervals from the alignments and construct an interval tree for each sequence
 template<typename TGraph, typename TPropertyMap, typename TAlignmentString, typename TSequence, typename TSetSpec, typename TValue, typename TSeqMap>
 void
-_createTreesForAllSequences(String<TGraph> & gs, 
-						   String<TPropertyMap> & pms, 
-						   TAlignmentString & alis, 
-						   StringSet<TSequence,TSetSpec> & seqs,
+_createTreesForAllSequences(String<TGraph> & gs,
+                           String<TPropertyMap> & pms,
+                           TAlignmentString & alis,
+                           StringSet<TSequence,TSetSpec> & seqs,
                            TSeqMap & seq_map,
-						   TValue numSequences)
+                           TValue numSequences)
 {
 SEQAN_CHECKPOINT
-	typedef typename Value<TAlignmentString>::Type TAlignment;
-//	typedef TValue TCargo;
-	typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
-	typedef IntervalAndCargo<int,TCargo> TInterval;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	
-	//std::cout <<"create interval trees...";
-	clock_t start, finish1;
-	double duration;
-	start = clock();
-	//one tree for each sequence
-	resize(gs,numSequences);
-	resize(pms,numSequences);
-	
-	//and one string of intervals for each sequence
-	String<String<TInterval> > intervals;
-	resize(intervals,numSequences);
-	//fill intervals
-	_buildIntervalsForAllSequences(alis,intervals,seqs,seq_map);
-	
-	TValue i = 0;
-	
-	while(i < numSequences)
-	{
-		//std::cout << (numSequences-i) <<" more ("<<length(intervals[i])<<" intervals)... "<<std::flush;
-		//vllt zum speicher sparen: numSequences mal alle alis durchgehen
-		//und jedes mal nur buildIntervalsForJustOneSequence(); 
-		TValue center = length(seqs[i])/2; // center raus, hat hier nix zu suchen
-		//create interval tree!
-		createIntervalTree(gs[i],pms[i],intervals[i],center);
-		
-		//intervals for sequence i are not needed anymore
-		clear(intervals[i]);
-		++i;
-	}
-	finish1 = clock();
-	duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
-	//std::cout << "\ntook " << duration << " seconds.\n";
+    typedef typename Value<TAlignmentString>::Type TAlignment;
+//    typedef TValue TCargo;
+    typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
+    typedef IntervalAndCargo<int,TCargo> TInterval;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    //std::cout <<"create interval trees...";
+    clock_t start, finish1;
+    double duration;
+    start = clock();
+    //one tree for each sequence
+    resize(gs,numSequences);
+    resize(pms,numSequences);
+
+    //and one string of intervals for each sequence
+    String<String<TInterval> > intervals;
+    resize(intervals,numSequences);
+    //fill intervals
+    _buildIntervalsForAllSequences(alis,intervals,seqs,seq_map);
+
+    TValue i = 0;
+
+    while(i < numSequences)
+    {
+        //std::cout << (numSequences-i) <<" more ("<<length(intervals[i])<<" intervals)... "<<std::flush;
+        //vllt zum speicher sparen: numSequences mal alle alis durchgehen
+        //und jedes mal nur buildIntervalsForJustOneSequence();
+        TValue center = length(seqs[i])/2; // center raus, hat hier nix zu suchen
+        //create interval tree!
+        createIntervalTree(gs[i],pms[i],intervals[i],center);
+
+        //intervals for sequence i are not needed anymore
+        clear(intervals[i]);
+        ++i;
+    }
+    finish1 = clock();
+    duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+    //std::cout << "\ntook " << duration << " seconds.\n";
 }
 
 
@@ -237,107 +237,107 @@ SEQAN_CHECKPOINT
 template<typename TStringSet,typename TValue,typename TAliGraph>
 void
 _makeRefinedGraphNodes(String<std::set<TValue> > & all_nodes,
-					  TStringSet & seqs,
-					  TAliGraph & ali_g)
+                      TStringSet & seqs,
+                      TAliGraph & ali_g)
 {
 SEQAN_CHECKPOINT
-	typedef typename std::set<TValue>::iterator TSetIterator;
-	//for each sequence look at all cut positions and create nodes between them
-	for(unsigned int seq_i_pos = 0; seq_i_pos < length(seqs); ++seq_i_pos)
-	{
-		TValue seq_i_id = positionToId(stringSet(ali_g), seq_i_pos);
-		TSetIterator it = all_nodes[seq_i_pos].begin();
-		TSetIterator end_it = all_nodes[seq_i_pos].end();
-		TSetIterator next_it = it;
-		if(next_it != end_it)
-			++next_it;
-		else
-			addVertex(ali_g, seq_i_id, 0, length(seqs[seq_i_pos]));
-		
-		//first unaligned node
-		if(it != end_it && *it != 0)
-			addVertex(ali_g, seq_i_id, 0, *it);
-		//a new node for each interval
-		while(next_it != end_it)
-		{
-			TValue pos_i = *it;
-			addVertex(ali_g, seq_i_id, pos_i, *next_it - pos_i); 
-			++it;
-			++next_it;
-		}
-		//last unaligned node
-		if(it !=end_it && *it<length(seqs[seq_i_pos]))
-			addVertex(ali_g, seq_i_id, *it, (length(seqs[seq_i_pos])) - *it);
-		all_nodes[seq_i_pos].clear();
-	}
+    typedef typename std::set<TValue>::iterator TSetIterator;
+    //for each sequence look at all cut positions and create nodes between them
+    for(unsigned int seq_i_pos = 0; seq_i_pos < length(seqs); ++seq_i_pos)
+    {
+        TValue seq_i_id = positionToId(stringSet(ali_g), seq_i_pos);
+        TSetIterator it = all_nodes[seq_i_pos].begin();
+        TSetIterator end_it = all_nodes[seq_i_pos].end();
+        TSetIterator next_it = it;
+        if(next_it != end_it)
+            ++next_it;
+        else
+            addVertex(ali_g, seq_i_id, 0, length(seqs[seq_i_pos]));
+
+        //first unaligned node
+        if(it != end_it && *it != 0)
+            addVertex(ali_g, seq_i_id, 0, *it);
+        //a new node for each interval
+        while(next_it != end_it)
+        {
+            TValue pos_i = *it;
+            addVertex(ali_g, seq_i_id, pos_i, *next_it - pos_i);
+            ++it;
+            ++next_it;
+        }
+        //last unaligned node
+        if(it !=end_it && *it<length(seqs[seq_i_pos]))
+            addVertex(ali_g, seq_i_id, *it, (length(seqs[seq_i_pos])) - *it);
+        all_nodes[seq_i_pos].clear();
+    }
 }
 
 
-//step 2 of constructing the refined alignment graph: add all edges    
+//step 2 of constructing the refined alignment graph: add all edges
 //version for exact refinement
 template<typename TAlignmentString,typename TStringSet,typename TSeqMap, typename TPropertyMap,typename TScore,typename TAliGraph>
 void
 _makeRefinedGraphEdges(TAlignmentString & alis,
-					   TPropertyMap & pm,
-					  TStringSet & seqs,
-				      TSeqMap & seq_map,
-				      TScore & score_type,
-					  TAliGraph & ali_g,
-					  Tag<TagExactRefinement_> const)
+                       TPropertyMap & pm,
+                      TStringSet & seqs,
+                      TSeqMap & seq_map,
+                      TScore & score_type,
+                      TAliGraph & ali_g,
+                      Tag<TagExactRefinement_> const)
 {
 SEQAN_CHECKPOINT
-	typedef typename Value<TAlignmentString>::Type TAlign;
-	typedef typename Size<TAlign>::Type TValue;
-	typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
-	typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
-	typedef typename Cargo<TAliGraph>::Type TCargo;
-	//make edges
-	TAliIterator ali_it = begin(alis);
-	TAliIterator ali_end = end(alis);
-	//for each segment/fragment/alignment
-	while(ali_it != ali_end)
-	{
-		//get sequence, begin position and end position
-		TValue seq_id,begin_pos,end_pos;
-		_getSeqBeginAndEnd(*ali_it,seq_map,seq_id,begin_pos,end_pos,(TValue)0);
-		
-		//get the node represents the current interval (begin_pos until next_cut_pos or end_pos)
-		TVertexDescriptor act_knot = findVertex(ali_g,seq_id,begin_pos);
-		TValue act_pos = begin_pos;
-	
-		//for each interval that lies within the current segment/fragement/alignment
-		while(act_pos < end_pos)
-		{
-			//get other sequence and projected position
-			TValue seq_j_id,pos_j;
-			_getOtherSequenceAndProject(*ali_it,(TValue)0,seq_map,seq_id,act_pos,seq_j_id,pos_j);
-			//find node that contains the projected position (pos_j)
-			TVertexDescriptor vd = findVertex(ali_g, seq_j_id, pos_j);
-		
-			SEQAN_ASSERT(fragmentBegin(ali_g,vd)==pos_j);
-			typename Value<TScore>::Type score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos,pos_j,fragmentLength(ali_g,act_knot),fragmentLength(ali_g,vd));//,fragmentLength(ali_g,vd));
-	//		typename Value<TScore>::Type score = fragmentLength(ali_g,vd);
-			score *= _getRefinedAnnoScore(ali_g,pm,vd,act_knot,score_type);
-		//this needs to be generalized (makes sense for positive scores only)
-			if(score <= 0) score = 1;
-			if(score > 0)
-			{
-				if (findEdge(ali_g, act_knot, vd) == 0) addEdge(ali_g,act_knot,vd,(TCargo)score);
-				else {
-					TEdgeDescriptor ed = findEdge(ali_g, act_knot, vd);
-					//if((TCargo)score > getCargo(ed))
-						//assignCargo(ed, score);
-					assignCargo(ed, getCargo(ed)+score);
-				}
-			}
-			//prepare for next interval
-			act_pos += fragmentLength(ali_g,act_knot);
-			act_knot = findVertex(ali_g,seq_id,act_pos);
-		
-		}
-		++ali_it;
-	}
+    typedef typename Value<TAlignmentString>::Type TAlign;
+    typedef typename Size<TAlign>::Type TValue;
+    typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
+    typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
+    typedef typename Cargo<TAliGraph>::Type TCargo;
+    //make edges
+    TAliIterator ali_it = begin(alis);
+    TAliIterator ali_end = end(alis);
+    //for each segment/fragment/alignment
+    while(ali_it != ali_end)
+    {
+        //get sequence, begin position and end position
+        TValue seq_id,begin_pos,end_pos;
+        _getSeqBeginAndEnd(*ali_it,seq_map,seq_id,begin_pos,end_pos,(TValue)0);
+
+        //get the node represents the current interval (begin_pos until next_cut_pos or end_pos)
+        TVertexDescriptor act_knot = findVertex(ali_g,seq_id,begin_pos);
+        TValue act_pos = begin_pos;
+
+        //for each interval that lies within the current segment/fragement/alignment
+        while(act_pos < end_pos)
+        {
+            //get other sequence and projected position
+            TValue seq_j_id,pos_j;
+            _getOtherSequenceAndProject(*ali_it,(TValue)0,seq_map,seq_id,act_pos,seq_j_id,pos_j);
+            //find node that contains the projected position (pos_j)
+            TVertexDescriptor vd = findVertex(ali_g, seq_j_id, pos_j);
+
+            SEQAN_ASSERT(fragmentBegin(ali_g,vd)==pos_j);
+            typename Value<TScore>::Type score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos,pos_j,fragmentLength(ali_g,act_knot),fragmentLength(ali_g,vd));//,fragmentLength(ali_g,vd));
+    //        typename Value<TScore>::Type score = fragmentLength(ali_g,vd);
+            score *= _getRefinedAnnoScore(ali_g,pm,vd,act_knot,score_type);
+        //this needs to be generalized (makes sense for positive scores only)
+            if(score <= 0) score = 1;
+            if(score > 0)
+            {
+                if (findEdge(ali_g, act_knot, vd) == 0) addEdge(ali_g,act_knot,vd,(TCargo)score);
+                else {
+                    TEdgeDescriptor ed = findEdge(ali_g, act_knot, vd);
+                    //if((TCargo)score > getCargo(ed))
+                        //assignCargo(ed, score);
+                    assignCargo(ed, getCargo(ed)+score);
+                }
+            }
+            //prepare for next interval
+            act_pos += fragmentLength(ali_g,act_knot);
+            act_knot = findVertex(ali_g,seq_id,act_pos);
+
+        }
+        ++ali_it;
+    }
 }
 
 
@@ -345,78 +345,78 @@ SEQAN_CHECKPOINT
 
 
 ////////////////////////////////////////////////////////////////////////////////////////
-//build refined alignment graph 
+//build refined alignment graph
 ////////////////////////////////////////////////////////////////////////////////////////
 //nodes are numbered ascendingly:
-//seq1   0  1  2  3  4 
+//seq1   0  1  2  3  4
 //seq2   5  6  7  8  9 10
-//seq3  11 12 13 14 15 
+//seq3  11 12 13 14 15
 template<typename TValue,typename TAlignmentString,typename TScore,typename TSequence, typename TSetSpec,typename TAliGraph,typename TSeqMap,typename TTagSpec>
 void
 _makeAlignmentGraphFromRefinedSegments(String<std::set<TValue> > & all_nodes,
-				   TAlignmentString & alis,
-				   TScore & score_type,
-				   StringSet<TSequence, TSetSpec> & seqs,
-				   TSeqMap & seq_map,
-				   TAliGraph & ali_g,
-			   	   Tag<TTagSpec> const tag, 
-				   bool)
+                   TAlignmentString & alis,
+                   TScore & score_type,
+                   StringSet<TSequence, TSetSpec> & seqs,
+                   TSeqMap & seq_map,
+                   TAliGraph & ali_g,
+                      Tag<TTagSpec> const tag,
+                   bool)
 {
 SEQAN_CHECKPOINT
-	//std::cout << "making refined alignment graph...";
-	//clock_t start, finish1;
-	//double duration;
-	//start = clock();
-	
-	//make nodes (same function for inexact and exact refinement)
-	_makeRefinedGraphNodes(all_nodes,seqs,ali_g);
-
-	bool pm = false;
-	//add edges (different functions depending on exact/inexact refinement)
-	_makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);
-	
-	//std::cout << "check\n";
-	//finish1 = clock();
-	//duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
-	//std::cout << "\ntook " << duration << " seconds.\n";
+    //std::cout << "making refined alignment graph...";
+    //clock_t start, finish1;
+    //double duration;
+    //start = clock();
+
+    //make nodes (same function for inexact and exact refinement)
+    _makeRefinedGraphNodes(all_nodes,seqs,ali_g);
+
+    bool pm = false;
+    //add edges (different functions depending on exact/inexact refinement)
+    _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);
+
+    //std::cout << "check\n";
+    //finish1 = clock();
+    //duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+    //std::cout << "\ntook " << duration << " seconds.\n";
 }
 
 
-      
+
 template<typename TValue,typename TAlignmentString,typename TScore,typename TSequence, typename TSetSpec,typename TAliGraph,typename TSeqMap,typename TAnnoString,typename TTagSpec>
 void
 _makeAlignmentGraphFromRefinedSegments(String<std::set<TValue> > & all_nodes,
-				   TAlignmentString & alis,
-				   TScore & score_type,
-				   StringSet<TSequence, TSetSpec> & seqs,
-				   TSeqMap & seq_map,
-				   TAliGraph & ali_g,
-			   	   Tag<TTagSpec> const tag,
-				   TAnnoString & annotation)
+                   TAlignmentString & alis,
+                   TScore & score_type,
+                   StringSet<TSequence, TSetSpec> & seqs,
+                   TSeqMap & seq_map,
+                   TAliGraph & ali_g,
+                      Tag<TTagSpec> const tag,
+                   TAnnoString & annotation)
 {
 SEQAN_CHECKPOINT
-	//std::cout << "making refined alignment graph...";
-	//clock_t start, finish1;
-	//double duration;
-	//start = clock();
-	
-	//make nodes (same function for inexact and exact refinement)
-	_makeRefinedGraphNodes(all_nodes,seqs,ali_g);
-
-	//add annotation to nodes
-	typedef typename Value<TAnnoString>::Type TAnnotation;
-	//typedef typename Value<TAnnotation>::Type TLabel;
-	typedef char TLabel;
-	String<String<TLabel> > pm;
-	_addNodeAnnotation(seqs,seq_map,annotation,pm,ali_g,tag);
-
-	//add edges (different functions depending on exact/inexact refinement)
-	_makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);
-	
-	//std::cout << "check\n";
-	//finish1 = clock();
-	//duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
-	//std::cout << "\ntook " << duration << " seconds.\n";
+    //std::cout << "making refined alignment graph...";
+    //clock_t start, finish1;
+    //double duration;
+    //start = clock();
+
+    //make nodes (same function for inexact and exact refinement)
+    _makeRefinedGraphNodes(all_nodes,seqs,ali_g);
+
+    //add annotation to nodes
+    typedef typename Value<TAnnoString>::Type TAnnotation;
+    //typedef typename Value<TAnnotation>::Type TLabel;
+    typedef char TLabel;
+    String<String<TLabel> > pm;
+    _addNodeAnnotation(seqs,seq_map,annotation,pm,ali_g,tag);
+
+    //add edges (different functions depending on exact/inexact refinement)
+    _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);
+
+    //std::cout << "check\n";
+    //finish1 = clock();
+    //duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+    //std::cout << "\ntook " << duration << " seconds.\n";
 }
 
 
@@ -424,110 +424,110 @@ SEQAN_CHECKPOINT
 
 
 ////////////////////////////////////////////////////////////////////////////////////////
-//The big matchRefinement function that does everything: build interval trees, do the 
+//The big matchRefinement function that does everything: build interval trees, do the
 //refinement and construct a refined alignment graph
 ////////////////////////////////////////////////////////////////////////////////////////
 template<typename TAlignmentString, typename TAnnotation, typename TOutGraph, typename TSequence, typename TSetSpec, typename TScore,typename TTagSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				StringSet<TSequence, TSetSpec> & seq, 
-				TScore & score_type,
-				TOutGraph & ali_graph,
-				typename Size<typename Value<TAlignmentString>::Type>::Type min_fragment_len,
-				TAnnotation & annotation,
-				Tag<TTagSpec> const tag)
+                StringSet<TSequence, TSetSpec> & seq,
+                TScore & score_type,
+                TOutGraph & ali_graph,
+                typename Size<typename Value<TAlignmentString>::Type>::Type min_fragment_len,
+                TAnnotation & annotation,
+                Tag<TTagSpec> const tag)
 {
 SEQAN_CHECKPOINT
-	////////////////////////////////////////////////////////////////
-	//typedefs
-	typedef typename Value<TAlignmentString>::Type TAlign;
-	typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
-	typedef typename Size<TAlign>::Type TValue;
-//	typedef TValue TCargo;
-	typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
-	typedef IntervalAndCargo<int,TCargo> TInterval;
-	typedef Graph<Directed<void,WithoutEdgeId> > TGraph;
-	typedef IntervalTreeNode<TInterval> TNode;
-	typedef String<TNode> TPropertyMap;
-	typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef String<TCargo> TList;
-	typedef typename std::set<TValue>::iterator TSetIterator;
-	
-	////////////////////////////////////////////////////////////////
-	TValue numSequences = length(seq);
-	//weird ID --> good ID map
-	std::map<const void * ,int> seq_map;
-	for(int i = 0; i < (int) numSequences; ++i)
-		seq_map[getObjectId(seq[i])] = i;
-	////////////////////////////////////////////////////////////////
-	//build interval trees
-	String<TGraph> gs;
-	String<TPropertyMap> pms;
-	_createTreesForAllSequences(gs, pms, alis, seq, seq_map, numSequences);
-	
-	////////////////////////////////////////////////////////////////
-	//do refinement
-	//std::cout <<"refining..."<<std::flush;
-	clock_t start, finish1;
-	double duration;
-	start = clock();
-	
-	//all_nodes = set of all cut positions
-	String<std::set<TValue> > all_nodes;
-	resize(all_nodes,numSequences);
-	//call function _refine for each startknoten
-	TAliIterator ali_it = begin(alis);
-	TAliIterator ali_end = end(alis);
-	//for each segment/fragement/alignment
-	while(ali_it != ali_end)
-	{
-		//for each of the two sequences
-		for(TValue i = 0; i < 2; ++i)
-		{
-			TValue seq_i_id,begin_i,end_i;
-			_getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_i,end_i,i);
-			TValue seq_i_pos = idToPosition(seq,seq_i_id);
-			
-			//refine begin
-			TSetIterator iter = all_nodes[seq_i_pos].find(begin_i);		
-			if(_cutIsValid(all_nodes,seq_i_pos,begin_i,iter,min_fragment_len,tag))
-			{
-				all_nodes[seq_i_pos].insert(begin_i);
-				_refine(begin_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes,min_fragment_len,tag);//TStop());
-			}
-			//and end position
-			iter = all_nodes[seq_i_pos].find(end_i);		
-			if(_cutIsValid(all_nodes,seq_i_pos,end_i,iter,(TValue) min_fragment_len,tag))
-			{
-				all_nodes[seq_i_pos].insert(end_i);
-				_refine(end_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes, min_fragment_len,tag);//TStop());
-			}
-		}	
-		++ali_it;
-	}
-
-	_addAnnotationCuts(all_nodes,alis,gs,pms,seq,seq_map,annotation,min_fragment_len,tag);
-
-	finish1 = clock();
-	duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
-	//std::cout << "\ntook " << duration << " seconds.\n";
-	//for(int seq_i = 0; seq_i < length(seq); ++seq_i)
-	//{
-	//	typename std::set<TValue>::iterator it = all_nodes[seq_i].begin();
-	//	typename std::set<TValue>::iterator end_it = all_nodes[seq_i].end();
-	//
-	//	while(it != end_it)
-	//	{
-	//		std::cout << *it << ",";
-	//		++it;
-	//	}
-	//	std::cout << "\n";
-	//}
-	//std::cout <<"building tree..."<<std::flush;
-	
-	////////////////////////////////////////////////////////////////
-	//build refined alignment graph
-	_makeAlignmentGraphFromRefinedSegments(all_nodes,alis,score_type,seq,seq_map,ali_graph,tag,annotation);
+    ////////////////////////////////////////////////////////////////
+    //typedefs
+    typedef typename Value<TAlignmentString>::Type TAlign;
+    typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
+    typedef typename Size<TAlign>::Type TValue;
+//    typedef TValue TCargo;
+    typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
+    typedef IntervalAndCargo<int,TCargo> TInterval;
+    typedef Graph<Directed<void,WithoutEdgeId> > TGraph;
+    typedef IntervalTreeNode<TInterval> TNode;
+    typedef String<TNode> TPropertyMap;
+    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef String<TCargo> TList;
+    typedef typename std::set<TValue>::iterator TSetIterator;
+
+    ////////////////////////////////////////////////////////////////
+    TValue numSequences = length(seq);
+    //weird ID --> good ID map
+    std::map<const void * ,int> seq_map;
+    for(int i = 0; i < (int) numSequences; ++i)
+        seq_map[getObjectId(seq[i])] = i;
+    ////////////////////////////////////////////////////////////////
+    //build interval trees
+    String<TGraph> gs;
+    String<TPropertyMap> pms;
+    _createTreesForAllSequences(gs, pms, alis, seq, seq_map, numSequences);
+
+    ////////////////////////////////////////////////////////////////
+    //do refinement
+    //std::cout <<"refining..."<<std::flush;
+    clock_t start, finish1;
+    double duration;
+    start = clock();
+
+    //all_nodes = set of all cut positions
+    String<std::set<TValue> > all_nodes;
+    resize(all_nodes,numSequences);
+    //call function _refine for each startknoten
+    TAliIterator ali_it = begin(alis);
+    TAliIterator ali_end = end(alis);
+    //for each segment/fragement/alignment
+    while(ali_it != ali_end)
+    {
+        //for each of the two sequences
+        for(TValue i = 0; i < 2; ++i)
+        {
+            TValue seq_i_id,begin_i,end_i;
+            _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_i,end_i,i);
+            TValue seq_i_pos = idToPosition(seq,seq_i_id);
+
+            //refine begin
+            TSetIterator iter = all_nodes[seq_i_pos].find(begin_i);
+            if(_cutIsValid(all_nodes,seq_i_pos,begin_i,iter,min_fragment_len,tag))
+            {
+                all_nodes[seq_i_pos].insert(begin_i);
+                _refine(begin_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes,min_fragment_len,tag);//TStop());
+            }
+            //and end position
+            iter = all_nodes[seq_i_pos].find(end_i);
+            if(_cutIsValid(all_nodes,seq_i_pos,end_i,iter,(TValue) min_fragment_len,tag))
+            {
+                all_nodes[seq_i_pos].insert(end_i);
+                _refine(end_i, seq_i_id, seq, seq_map, alis, gs,pms,all_nodes, min_fragment_len,tag);//TStop());
+            }
+        }
+        ++ali_it;
+    }
+
+    _addAnnotationCuts(all_nodes,alis,gs,pms,seq,seq_map,annotation,min_fragment_len,tag);
+
+    finish1 = clock();
+    duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+    //std::cout << "\ntook " << duration << " seconds.\n";
+    //for(int seq_i = 0; seq_i < length(seq); ++seq_i)
+    //{
+    //    typename std::set<TValue>::iterator it = all_nodes[seq_i].begin();
+    //    typename std::set<TValue>::iterator end_it = all_nodes[seq_i].end();
+    //
+    //    while(it != end_it)
+    //    {
+    //        std::cout << *it << ",";
+    //        ++it;
+    //    }
+    //    std::cout << "\n";
+    //}
+    //std::cout <<"building tree..."<<std::flush;
+
+    ////////////////////////////////////////////////////////////////
+    //build refined alignment graph
+    _makeAlignmentGraphFromRefinedSegments(all_nodes,alis,score_type,seq,seq_map,ali_graph,tag,annotation);
 }
 
 
@@ -537,14 +537,14 @@ SEQAN_CHECKPOINT
 template<typename TAlignmentString, typename TScoreValue,typename TScoreSpec,typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				StringSet<TSequence, TSetSpec> & seq, 
-				Score<TScoreValue,TScoreSpec> & score_type,
-				TOutGraph & ali_graph)
+                StringSet<TSequence, TSetSpec> & seq,
+                Score<TScoreValue,TScoreSpec> & score_type,
+                TOutGraph & ali_graph)
 {
 SEQAN_CHECKPOINT
-	//min_fragment_len = 1   ==> Exact cutting
-	bool anno = false;
-	matchRefinement(alis,seq,score_type,ali_graph,1,anno,ExactRefinement());
+    //min_fragment_len = 1   ==> Exact cutting
+    bool anno = false;
+    matchRefinement(alis,seq,score_type,ali_graph,1,anno,ExactRefinement());
 }
 
 
@@ -552,15 +552,15 @@ SEQAN_CHECKPOINT
 template<typename TFragmentString, typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TFragmentString & matches,
-				StringSet<TSequence, TSetSpec> & strSet, 
-				TOutGraph & ali_graph)
+                StringSet<TSequence, TSetSpec> & strSet,
+                TOutGraph & ali_graph)
 {
-	SEQAN_CHECKPOINT
-	typename Cargo<TOutGraph>::Type fake_score = 1;
-	bool anno = false;
-	matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement());
+    SEQAN_CHECKPOINT
+    typename Cargo<TOutGraph>::Type fake_score = 1;
+    bool anno = false;
+    matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_H_
diff --git a/seqan/graph_align/graph_algorithm_refine_exact_iterative.h b/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
index 66cc26d..1616ff9 100644
--- a/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
+++ b/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,11 +36,11 @@
 // This is required for some large inputs to circumvent stack overflows.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_
 
 namespace seqan {
-	
+
 struct TagExactRefinement_;
 typedef Tag<TagExactRefinement_> const ExactRefinement;
 
@@ -48,17 +48,17 @@ typedef Tag<TagExactRefinement_> const ExactRefinement;
 template<typename TValue, typename TValue2, typename TSize>
 inline bool
 _cutIsValid(String<std::set<TValue> > & all_nodes,
-		TValue2 seq_i_pos,
-		TSize,
-		typename std::set<TValue>::iterator iter,
-		TSize,
-		Tag<TagExactRefinement_> const)
+        TValue2 seq_i_pos,
+        TSize,
+        typename std::set<TValue>::iterator iter,
+        TSize,
+        Tag<TagExactRefinement_> const)
 {
 SEQAN_CHECKPOINT
-	//cut already exists
-	if(iter != all_nodes[seq_i_pos].end())
-		return false;
-	return true;
+    //cut already exists
+    if(iter != all_nodes[seq_i_pos].end())
+        return false;
+    return true;
 }
 
 
@@ -67,138 +67,138 @@ template<typename TSize, typename TSpec,typename TPos>
 inline void
 _updateCutPosition(Fragment<TSize, ExactReversableFragment<TSpec> > & f, TPos & pos_j)
 {
-	if(f.reversed)
-		++pos_j;
+    if(f.reversed)
+        ++pos_j;
 }
 //template<typename TSize, typename TSpec,typename TPos>
 //inline void
 //_updateCutPosition(Fragment<TSize, ExactReversableFragment<TSpec> > const& f, TPos & pos_j)
 //{
-//	if(f.reversed)
-//		++pos_j;
+//    if(f.reversed)
+//        ++pos_j;
 //}
 
-// for all other fragment types --> no shifting necessary 
+// for all other fragment types --> no shifting necessary
 template<typename TFrag,typename TPos>
 inline void
 _updateCutPosition(TFrag &, TPos &)
 {
-	return;
+    return;
 }
 
-///////////////////////////////////////////////////////////////////////////////////////////////////////	
+///////////////////////////////////////////////////////////////////////////////////////////////////////
 //Recursive Refinement
 //refine position node_i on sequence seq_i
 template<typename TValue, typename TAlignmentString, typename TStringSet,typename TGraph, typename TPropertyMap,typename TSeqMap, typename TTagSpec>
 inline void
-_refine(TValue node_i, 
-	 TValue seq_i_id, 
-	 TStringSet & seqs,
-	 TSeqMap & seq_map,
-	 TAlignmentString & alis, 
-	 String<TGraph> & gs, 
-	 String<TPropertyMap> & pms, 
-     String<std::set<TValue> > & all_nodes, 
-	 TValue min_len,
-	 Tag<TTagSpec> tag)
+_refine(TValue node_i,
+     TValue seq_i_id,
+     TStringSet & seqs,
+     TSeqMap & seq_map,
+     TAlignmentString & alis,
+     String<TGraph> & gs,
+     String<TPropertyMap> & pms,
+     String<std::set<TValue> > & all_nodes,
+     TValue min_len,
+     Tag<TTagSpec> tag)
 {
 SEQAN_CHECKPOINT
-	typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type TAlignmentPointer;
-	typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type TSegmentIterator;
-	//find all segment matches that contain the current position (node_i)
-	String<TAlignmentPointer> relevant_segments;
-	TValue seq_i_pos = idToPosition(seqs,seq_i_id);
-	findIntervalsExcludeTouching(gs[seq_i_pos],pms[seq_i_pos],node_i,relevant_segments);
-
-	
-	TSegmentIterator segment_it = begin(relevant_segments);
-	TSegmentIterator segment_end = end(relevant_segments);
-	//foreach of those segments
-	while(segment_it != segment_end)
-	{
-		TValue match_id = (*segment_it).i1; // segment match
-		TValue seg_num = (*segment_it).i2; // first or second segment in segment match?
-
-		//get the sequence that node_i needs to be projected onto (seq_j)
-		//and get the projected position (pos_j)
-		TValue seq_j_id, node_j;
-		_getOtherSequenceAndProject(alis[match_id],seg_num,seq_map,seq_i_id,node_i,seq_j_id,node_j);
-		TValue seq_j_pos = idToPosition(seqs,seq_j_id);
-		_updateCutPosition(alis[match_id],node_j);
-
-		typename std::set<TValue>::iterator iter;
-		iter = all_nodes[seq_j_pos].find(node_j);
-		
-		//if node does not exist yet ---> insert and continue cutting
-		if(_cutIsValid(all_nodes,seq_j_pos,node_j,iter,min_len,tag))
-		{
-			all_nodes[seq_j_pos].insert(node_j);
-			_refine(node_j,seq_j_id,seqs,seq_map,alis,gs,pms,all_nodes,min_len,tag);
-		}
-		// TODO: else //verschmelzen, abschneiden und ergehen, erst sp�ter... 	
-		// do nothing or resolve problems  
-	
-		++segment_it;
-	}
+    typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type TAlignmentPointer;
+    typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type TSegmentIterator;
+    //find all segment matches that contain the current position (node_i)
+    String<TAlignmentPointer> relevant_segments;
+    TValue seq_i_pos = idToPosition(seqs,seq_i_id);
+    findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i);
+
+
+    TSegmentIterator segment_it = begin(relevant_segments);
+    TSegmentIterator segment_end = end(relevant_segments);
+    //foreach of those segments
+    while(segment_it != segment_end)
+    {
+        TValue match_id = (*segment_it).i1; // segment match
+        TValue seg_num = (*segment_it).i2; // first or second segment in segment match?
+
+        //get the sequence that node_i needs to be projected onto (seq_j)
+        //and get the projected position (pos_j)
+        TValue seq_j_id, node_j;
+        _getOtherSequenceAndProject(alis[match_id],seg_num,seq_map,seq_i_id,node_i,seq_j_id,node_j);
+        TValue seq_j_pos = idToPosition(seqs,seq_j_id);
+        _updateCutPosition(alis[match_id],node_j);
+
+        typename std::set<TValue>::iterator iter;
+        iter = all_nodes[seq_j_pos].find(node_j);
+
+        //if node does not exist yet ---> insert and continue cutting
+        if(_cutIsValid(all_nodes,seq_j_pos,node_j,iter,min_len,tag))
+        {
+            all_nodes[seq_j_pos].insert(node_j);
+            _refine(node_j,seq_j_id,seqs,seq_map,alis,gs,pms,all_nodes,min_len,tag);
+        }
+        // TODO: else //verschmelzen, abschneiden und ergehen, erst sp�ter...
+        // do nothing or resolve problems
+
+        ++segment_it;
+    }
 }
 
 //template<typename TFragSize, typename TFragSpec>
 //void
 //printMatch(Fragment<TFragSize,TFragSpec> & f)
 //{
-//	::std::cout << "FRAGMENT:" << " f.len = "<< f.len <<std::endl;
-//	::std::cout << "f.seqId1 = "<< f.seqId1 << " f.begin1 = " << f.begin1 << std::endl;
-//	::std::cout << "f.seqId2 = "<< f.seqId2 << " f.begin2 = " << f.begin2 << std::endl;
+//    std::cout << "FRAGMENT:" << " f.len = "<< f.len <<std::endl;
+//    std::cout << "f.seqId1 = "<< f.seqId1 << " f.begin1 = " << f.begin1 << std::endl;
+//    std::cout << "f.seqId2 = "<< f.seqId2 << " f.begin2 = " << f.begin2 << std::endl;
 //}
 
 //template<typename TAlign>
 //void
 //printMatch(TAlign & f)
 //{
-//	::std::cout << f;
+//    std::cout << f;
 //}
 
-///////////////////////////////////////////////////////////////////////////////////////////////////////	
-// Construct interval trees 
+///////////////////////////////////////////////////////////////////////////////////////////////////////
+// Construct interval trees
 ////////////////////////////////////////////////////////////////////////////////////////////////////
 
 
 //construct intervals from allignments for each sequence (other Alignment types)
 template<typename TInterval, typename TStringSet, typename TAlignmentString, typename TSeqMap>
 void
-_buildIntervalsForAllSequences(TAlignmentString & alis, 
-							   String<String<TInterval> > & intervals, 
-	   						   TStringSet & seqs,
-							   TSeqMap & seq_map)
+_buildIntervalsForAllSequences(TAlignmentString & alis,
+                               String<String<TInterval> > & intervals,
+                                  TStringSet & seqs,
+                               TSeqMap & seq_map)
 {
 SEQAN_CHECKPOINT
-	
-	typedef typename Value<TInterval>::Type TValue;
-	typedef typename Cargo<TInterval>::Type TCargo;
-	typedef typename Iterator<TAlignmentString,Standard>::Type TAliIterator;
-	TAliIterator ali_it = begin(alis,Standard());
-	TAliIterator ali_end = end(alis,Standard());
-	TValue ali_counter = 0;
-	//foreach alignment
-	while(ali_it != ali_end)
-	{
-		TValue seq_i_id,begin_,end_;
-		//printMatch(*ali_it);
-		//get the first sequence (and its begin and end) that takes part in the alignment (seq_i)
-		_getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,0);
-		TValue seq_i_pos = idToPosition(seqs, seq_i_id);
-		//and append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
-		appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,0))); 
-	
-		//get the second sequence (and its begin and end) that takes part in the alignment (seq_i)
-		_getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,1);
-		seq_i_pos = idToPosition(seqs, seq_i_id);
-		//and again append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
-		appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,1))); 
-	
-		++ali_counter;
-		++ali_it;
-	}
+
+    typedef typename Value<TInterval>::Type TValue;
+    typedef typename Cargo<TInterval>::Type TCargo;
+    typedef typename Iterator<TAlignmentString,Standard>::Type TAliIterator;
+    TAliIterator ali_it = begin(alis,Standard());
+    TAliIterator ali_end = end(alis,Standard());
+    TValue ali_counter = 0;
+    //foreach alignment
+    while(ali_it != ali_end)
+    {
+        TValue seq_i_id,begin_,end_;
+        //printMatch(*ali_it);
+        //get the first sequence (and its begin and end) that takes part in the alignment (seq_i)
+        _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,0);
+        TValue seq_i_pos = idToPosition(seqs, seq_i_id);
+        //and append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
+        appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,0)));
+
+        //get the second sequence (and its begin and end) that takes part in the alignment (seq_i)
+        _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,1);
+        seq_i_pos = idToPosition(seqs, seq_i_id);
+        //and again append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
+        appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,1)));
+
+        ++ali_counter;
+        ++ali_it;
+    }
 
 }
 
@@ -206,193 +206,193 @@ SEQAN_CHECKPOINT
 //get all intervals from the alignments and construct an interval tree for each sequence
 template<typename TGraph, typename TPropertyMap, typename TAlignmentString, typename TSequence, typename TSetSpec, typename TValue, typename TSeqMap>
 void
-_createTreesForAllSequences(String<TGraph> & gs, 
-						   String<TPropertyMap> & pms, 
-						   TAlignmentString & alis, 
-						   StringSet<TSequence,TSetSpec> & seqs,
+_createTreesForAllSequences(String<TGraph> & gs,
+                           String<TPropertyMap> & pms,
+                           TAlignmentString & alis,
+                           StringSet<TSequence,TSetSpec> & seqs,
                            TSeqMap & seq_map,
-						   TValue numSequences)
+                           TValue numSequences)
 {
-	//typedef typename Value<TAlignmentString>::Type TAlignment;
-//	typedef TAlignment* TCargo;
-	typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
-	typedef IntervalAndCargo<int,TCargo> TInterval;
-	//typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	//std::cout <<"create interval trees...";
-	// clock_t start, finish1;
-	// double duration;
-	// start = clock();
-	//one tree for each sequence
-	resize(gs,numSequences);
-	resize(pms,numSequences);
-	
-	// and one string of intervals for each sequence
-	String<String<TInterval> > intervals;
-	resize(intervals,numSequences);
-	// fill intervals
-	_buildIntervalsForAllSequences(alis,intervals,seqs,seq_map);
-	
-	TValue i = 0;
-	
-	while(i < numSequences)
-	{
-		//std::cout << (numSequences-i) <<" more ("<<length(intervals[i])<<" intervals)... "<<std::flush;
-		TValue center = length(seqs[i])/2; // center raus, hat hier nix zu suchen
-		//create interval tree!
-		createIntervalTree(gs[i], pms[i], intervals[i], center);
-		
-		//intervals for sequence i are not needed anymore
-		clear(intervals[i]);
-		++i;
-	}
-	// finish1 = clock();
-	// duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
-	// std::cout << "\ntook " << duration << " seconds.\n";
+    //typedef typename Value<TAlignmentString>::Type TAlignment;
+//    typedef TAlignment* TCargo;
+    typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
+    typedef IntervalAndCargo<int,TCargo> TInterval;
+    //typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    //std::cout <<"create interval trees...";
+    // clock_t start, finish1;
+    // double duration;
+    // start = clock();
+    //one tree for each sequence
+    resize(gs,numSequences);
+    resize(pms,numSequences);
+
+    // and one string of intervals for each sequence
+    String<String<TInterval> > intervals;
+    resize(intervals,numSequences);
+    // fill intervals
+    _buildIntervalsForAllSequences(alis,intervals,seqs,seq_map);
+
+    TValue i = 0;
+
+    while(i < numSequences)
+    {
+        //std::cout << (numSequences-i) <<" more ("<<length(intervals[i])<<" intervals)... "<<std::flush;
+        TValue center = length(seqs[i])/2; // center raus, hat hier nix zu suchen
+        //create interval tree!
+        createIntervalTree(gs[i], pms[i], intervals[i], center);
+
+        //intervals for sequence i are not needed anymore
+        clear(intervals[i]);
+        ++i;
+    }
+    // finish1 = clock();
+    // duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+    // std::cout << "\ntook " << duration << " seconds.\n";
 }
 
 
-///////////////////////////////////////////////////////////////////////////////////////////////////////	
-// Construct refined alignment graph 
+///////////////////////////////////////////////////////////////////////////////////////////////////////
+// Construct refined alignment graph
 ////////////////////////////////////////////////////////////////////////////////////////////////////
 
 // step 1 of constructing the refined alignment graph: create all nodes
 template<typename TStringSet,typename TValue,typename TAliGraph>
 void
 _makeRefinedGraphNodes(String<std::set<TValue> > & all_nodes,
-					  TStringSet & seqs,
-					  TAliGraph & ali_g)
+                      TStringSet & seqs,
+                      TAliGraph & ali_g)
 {
 SEQAN_CHECKPOINT
-	typedef typename std::set<TValue>::iterator TSetIterator;
-	//for each sequence look at all cut positions and create nodes between them
-	for(unsigned int seq_i_pos = 0; seq_i_pos < length(seqs); ++seq_i_pos)
-	{
-		TValue seq_i_id = positionToId(stringSet(ali_g), seq_i_pos);
-		TSetIterator it = all_nodes[seq_i_pos].begin();
-		TSetIterator end_it = all_nodes[seq_i_pos].end();
-		TSetIterator next_it = it;
-		if(next_it != end_it)
-			++next_it;
-		else
-			addVertex(ali_g, seq_i_id, 0, length(seqs[seq_i_pos]));
-		
-		//first unaligned node
-		if(it != end_it && *it != 0)
-			addVertex(ali_g, seq_i_id, 0, *it);
-		//a new node for each interval
-		while(next_it != end_it)
-		{
-			TValue pos_i = *it;
-			addVertex(ali_g, seq_i_id, pos_i, *next_it - pos_i); 
-			++it;
-			++next_it;
-		}
-		//last unaligned node
-		if(it !=end_it && *it<length(seqs[seq_i_pos]))
-			addVertex(ali_g, seq_i_id, *it, (length(seqs[seq_i_pos])) - *it);
-		all_nodes[seq_i_pos].clear();
-	}
+    typedef typename std::set<TValue>::iterator TSetIterator;
+    //for each sequence look at all cut positions and create nodes between them
+    for(unsigned int seq_i_pos = 0; seq_i_pos < length(seqs); ++seq_i_pos)
+    {
+        TValue seq_i_id = positionToId(stringSet(ali_g), seq_i_pos);
+        TSetIterator it = all_nodes[seq_i_pos].begin();
+        TSetIterator end_it = all_nodes[seq_i_pos].end();
+        TSetIterator next_it = it;
+        if(next_it != end_it)
+            ++next_it;
+        else
+            addVertex(ali_g, seq_i_id, 0, length(seqs[seq_i_pos]));
+
+        //first unaligned node
+        if(it != end_it && *it != 0)
+            addVertex(ali_g, seq_i_id, 0, *it);
+        //a new node for each interval
+        while(next_it != end_it)
+        {
+            TValue pos_i = *it;
+            addVertex(ali_g, seq_i_id, pos_i, *next_it - pos_i);
+            ++it;
+            ++next_it;
+        }
+        //last unaligned node
+        if(it !=end_it && *it<length(seqs[seq_i_pos]))
+            addVertex(ali_g, seq_i_id, *it, (length(seqs[seq_i_pos])) - *it);
+        all_nodes[seq_i_pos].clear();
+    }
 }
 
 
-// step 2 of constructing the refined alignment graph: add all edges    
+// step 2 of constructing the refined alignment graph: add all edges
 // version for exact refinement
-template<typename TAlignmentString,typename TStringSet,typename TSeqMap, typename TPropertyMap,typename TScore,typename TAliGraph > 
+template<typename TAlignmentString,typename TStringSet,typename TSeqMap, typename TPropertyMap,typename TScore,typename TAliGraph >
 void
 _makeRefinedGraphEdges(TAlignmentString & alis,
-					   TPropertyMap & pm,
-					  TStringSet & seqs,
-				      TSeqMap & seq_map,
-				      TScore & score_type,
-					  TAliGraph & ali_g,
-					  Tag<TagExactRefinement_> const)
+                       TPropertyMap & pm,
+                      TStringSet & seqs,
+                      TSeqMap & seq_map,
+                      TScore & score_type,
+                      TAliGraph & ali_g,
+                      Tag<TagExactRefinement_> const)
 {
 SEQAN_CHECKPOINT
-	typedef typename Value<TAlignmentString>::Type TAlign;
-	typedef typename Size<TAlign>::Type TValue;
-	typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
-	typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
-	typedef typename Cargo<TAliGraph>::Type TCargo;
-	//make edges
-	TAliIterator ali_it = begin(alis);
-	TAliIterator ali_end = end(alis);
-	//for each segment/fragment/alignment
-	while(ali_it != ali_end)
-	{
-		//get sequence, begin position and end position
-		TValue seq_id,begin_pos,end_pos;
-		_getSeqBeginAndEnd(*ali_it,seq_map,seq_id,begin_pos,end_pos,(TValue)0);
+    typedef typename Value<TAlignmentString>::Type TAlign;
+    typedef typename Size<TAlign>::Type TValue;
+    typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
+    typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
+    typedef typename Cargo<TAliGraph>::Type TCargo;
+    //make edges
+    TAliIterator ali_it = begin(alis);
+    TAliIterator ali_end = end(alis);
+    //for each segment/fragment/alignment
+    while(ali_it != ali_end)
+    {
+        //get sequence, begin position and end position
+        TValue seq_id,begin_pos,end_pos;
+        _getSeqBeginAndEnd(*ali_it,seq_map,seq_id,begin_pos,end_pos,(TValue)0);
         SEQAN_ASSERT_LEQ(end_pos, length(seqs[idToPosition(seqs, seq_id)]));
         SEQAN_ASSERT(ali_it.data_container == ali_end.data_container);
         SEQAN_ASSERT(ali_it.data_iterator != ali_end.data_iterator);
-		
-		//get the node represents the current interval (begin_pos until next_cut_pos or end_pos)
-		TVertexDescriptor act_knot = findVertex(ali_g,seq_id,begin_pos);
-		TValue act_pos = begin_pos;
-		TValue seq_j_id_temp,pos_j_begin;
-		_getOtherSequenceAndProject(*ali_it,(TValue)0,seq_map,seq_id,act_pos,seq_j_id_temp,pos_j_begin);
-	
-		//for each interval that lies within the current segment/fragement/alignment
-		while(act_pos < end_pos)
-		{
-			//get other sequence and projected position
-			TValue seq_j_id,pos_j;
-			_getOtherSequenceAndProject(*ali_it,(TValue)0,seq_map,seq_id,act_pos,seq_j_id,pos_j);
-			SEQAN_ASSERT_NEQ(pos_j, static_cast<TValue>(-1));
-			//find node that contains the projected position (pos_j)
-			TVertexDescriptor vd = findVertex(ali_g, seq_j_id, pos_j);
-			bool doAddEdge = true;
-
-//			if(doAddEdge && fragmentBegin(ali_g,vd)!=pos_j) // check if edge makes sense
-			if (vd == getNil<TVertexDescriptor>())
-				doAddEdge = false;
-			else
-			{ 
-				TValue temp_seq_i_id,temp_act_pos;
-				_getOtherSequenceAndProject(*ali_it,(TValue)1,seq_map,seq_j_id,static_cast<TValue>(fragmentBegin(ali_g,vd)),temp_seq_i_id,temp_act_pos);
-				if(temp_act_pos == static_cast<TValue>(-1))
-					doAddEdge = false;
-				else 
-				{
-					TVertexDescriptor temp_act_knot = findVertex(ali_g, temp_seq_i_id, temp_act_pos);
-					if(act_knot!=temp_act_knot)
-						doAddEdge = false;
-				}
-			}
-			if(doAddEdge)
-			{
-				typename Value<TScore>::Type score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos,pos_j,fragmentLength(ali_g,act_knot),fragmentLength(ali_g,vd));//,fragmentLength(ali_g,vd));
-		//		typename Value<TScore>::Type score = fragmentLength(ali_g,vd);
-				score *= _getRefinedAnnoScore(ali_g,pm,vd,act_knot,score_type);
-			//this needs to be generalized (makes sense for positive scores only)
-				if(score <= 0) score = 1;
-				if(score > 0)
-				{
-					if (findEdge(ali_g, act_knot, vd) == 0) {
-						//if(abs((double)fragmentLength(ali_g, act_knot) - (double)fragmentLength(ali_g, vd)) > 20) {
-						//	std::cerr << "added edge: " << fragmentLength(ali_g, act_knot) << "  " <<  fragmentLength(ali_g, vd) << std::endl;
-						//	std::cerr << *ali_it;
-						//	std::cerr << "act_pos=" << act_pos-begin_pos << " pos_j=" << pos_j-pos_j_begin << std::endl; 
-						//} else {
-							addEdge(ali_g,act_knot,vd,(TCargo)score);
-						//}
-					}
-					else {
-						TEdgeDescriptor ed = findEdge(ali_g, act_knot, vd);
-						//if((TCargo)score > getCargo(ed))
-							//assignCargo(ed, score);
-						assignCargo(ed, getCargo(ed)+score);
-					}
-				}
-			}
-			//prepare for next interval
-			act_pos += fragmentLength(ali_g,act_knot);
-			act_knot = findVertex(ali_g,seq_id,act_pos);
-		}
-		++ali_it;
-	}
+
+        //get the node represents the current interval (begin_pos until next_cut_pos or end_pos)
+        TVertexDescriptor act_knot = findVertex(ali_g,seq_id,begin_pos);
+        TValue act_pos = begin_pos;
+        TValue seq_j_id_temp,pos_j_begin;
+        _getOtherSequenceAndProject(*ali_it,(TValue)0,seq_map,seq_id,act_pos,seq_j_id_temp,pos_j_begin);
+
+        //for each interval that lies within the current segment/fragement/alignment
+        while(act_pos < end_pos)
+        {
+            //get other sequence and projected position
+            TValue seq_j_id,pos_j;
+            _getOtherSequenceAndProject(*ali_it,(TValue)0,seq_map,seq_id,act_pos,seq_j_id,pos_j);
+            SEQAN_ASSERT_NEQ(pos_j, static_cast<TValue>(-1));
+            //find node that contains the projected position (pos_j)
+            TVertexDescriptor vd = findVertex(ali_g, seq_j_id, pos_j);
+            bool doAddEdge = true;
+
+//            if(doAddEdge && fragmentBegin(ali_g,vd)!=pos_j) // check if edge makes sense
+            if (vd == getNil<TVertexDescriptor>())
+                doAddEdge = false;
+            else
+            {
+                TValue temp_seq_i_id,temp_act_pos;
+                _getOtherSequenceAndProject(*ali_it,(TValue)1,seq_map,seq_j_id,static_cast<TValue>(fragmentBegin(ali_g,vd)),temp_seq_i_id,temp_act_pos);
+                if(temp_act_pos == static_cast<TValue>(-1))
+                    doAddEdge = false;
+                else
+                {
+                    TVertexDescriptor temp_act_knot = findVertex(ali_g, temp_seq_i_id, temp_act_pos);
+                    if(act_knot!=temp_act_knot)
+                        doAddEdge = false;
+                }
+            }
+            if(doAddEdge)
+            {
+                typename Value<TScore>::Type score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos,pos_j,fragmentLength(ali_g,act_knot),fragmentLength(ali_g,vd));//,fragmentLength(ali_g,vd));
+        //        typename Value<TScore>::Type score = fragmentLength(ali_g,vd);
+                score *= _getRefinedAnnoScore(ali_g,pm,vd,act_knot,score_type);
+            //this needs to be generalized (makes sense for positive scores only)
+                if(score <= 0) score = 1;
+                if(score > 0)
+                {
+                    if (findEdge(ali_g, act_knot, vd) == 0) {
+                        //if(abs((double)fragmentLength(ali_g, act_knot) - (double)fragmentLength(ali_g, vd)) > 20) {
+                        //    std::cerr << "added edge: " << fragmentLength(ali_g, act_knot) << "  " <<  fragmentLength(ali_g, vd) << std::endl;
+                        //    std::cerr << *ali_it;
+                        //    std::cerr << "act_pos=" << act_pos-begin_pos << " pos_j=" << pos_j-pos_j_begin << std::endl;
+                        //} else {
+                            addEdge(ali_g,act_knot,vd,(TCargo)score);
+                        //}
+                    }
+                    else {
+                        TEdgeDescriptor ed = findEdge(ali_g, act_knot, vd);
+                        //if((TCargo)score > getCargo(ed))
+                            //assignCargo(ed, score);
+                        assignCargo(ed, getCargo(ed)+score);
+                    }
+                }
+            }
+            //prepare for next interval
+            act_pos += fragmentLength(ali_g,act_knot);
+            act_knot = findVertex(ali_g,seq_id,act_pos);
+        }
+        ++ali_it;
+    }
 }
 
 
@@ -400,37 +400,37 @@ SEQAN_CHECKPOINT
 
 
 //build refined alignment graph, nodes are numbered ascendingly:
-//seq1   0  1  2  3  4 
+//seq1   0  1  2  3  4
 //seq2   5  6  7  8  9 10
-//seq3  11 12 13 14 15 
+//seq3  11 12 13 14 15
 template<typename TValue,typename TAlignmentString,typename TScore,typename TSequence, typename TSetSpec,typename TAliGraph,typename TSeqMap,typename TTagSpec>
 void
 _makeAlignmentGraphFromRefinedSegments(String<std::set<TValue> > & all_nodes,
-				   TAlignmentString & alis,
-				   TScore & score_type,
-				   StringSet<TSequence, TSetSpec> & seqs,
-				   TSeqMap & seq_map,
-				   TAliGraph & ali_g,
-			   	   Tag<TTagSpec> const tag, 
-				   bool)
+                   TAlignmentString & alis,
+                   TScore & score_type,
+                   StringSet<TSequence, TSetSpec> & seqs,
+                   TSeqMap & seq_map,
+                   TAliGraph & ali_g,
+                      Tag<TTagSpec> const tag,
+                   bool)
 {
 SEQAN_CHECKPOINT
-	//std::cout << "making refined alignment graph...";
-	//clock_t start, finish1;
-	//double duration;
-	//start = clock();
-	
-	//make nodes (same function for inexact and exact refinement)
-	_makeRefinedGraphNodes(all_nodes,seqs,ali_g);
-
-	bool pm = false;
-	//add edges (different functions depending on exact/inexact refinement)
-	_makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);
-	
-	//std::cout << "check\n";
-	//finish1 = clock();
-	//duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
-	//std::cout << "\ntook " << duration << " seconds.\n";
+    //std::cout << "making refined alignment graph...";
+    //clock_t start, finish1;
+    //double duration;
+    //start = clock();
+
+    //make nodes (same function for inexact and exact refinement)
+    _makeRefinedGraphNodes(all_nodes,seqs,ali_g);
+
+    bool pm = false;
+    //add edges (different functions depending on exact/inexact refinement)
+    _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);
+
+    //std::cout << "check\n";
+    //finish1 = clock();
+    //duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+    //std::cout << "\ntook " << duration << " seconds.\n";
 }
 
 
@@ -438,37 +438,37 @@ SEQAN_CHECKPOINT
 template<typename TValue,typename TAlignmentString,typename TScore,typename TSequence, typename TSetSpec,typename TAliGraph,typename TSeqMap,typename TAnnoString,typename TTagSpec>
 void
 _makeAlignmentGraphFromRefinedSegments(String<std::set<TValue> > & all_nodes,
-				   TAlignmentString & alis,
-				   TScore & score_type,
-				   StringSet<TSequence, TSetSpec> & seqs,
-				   TSeqMap & seq_map,
-				   TAliGraph & ali_g,
-			   	   Tag<TTagSpec> const tag,
-				   TAnnoString & annotation)
+                   TAlignmentString & alis,
+                   TScore & score_type,
+                   StringSet<TSequence, TSetSpec> & seqs,
+                   TSeqMap & seq_map,
+                   TAliGraph & ali_g,
+                      Tag<TTagSpec> const tag,
+                   TAnnoString & annotation)
 {
 SEQAN_CHECKPOINT
-	//std::cout << "making refined alignment graph...";
-	//clock_t start, finish1;
-	//double duration;
-	//start = clock();
-	
-	//make nodes (same function for inexact and exact refinement)
-	_makeRefinedGraphNodes(all_nodes,seqs,ali_g);
-
-	//add annotation to nodes
-	//typedef typename Value<TAnnoString>::Type TAnnotation;
-	//typedef typename Value<TAnnotation>::Type TLabel;
-	typedef char TLabel;
-	String<String<TLabel> > pm;
-	_addNodeAnnotation(seqs,seq_map,annotation,pm,ali_g,tag);
-
-	//add edges (different functions depending on exact/inexact refinement)
-	_makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);
-	
-	//std::cout << "check\n";
-	//finish1 = clock();
-	//duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
-	//std::cout << "\ntook " << duration << " seconds.\n";
+    //std::cout << "making refined alignment graph...";
+    //clock_t start, finish1;
+    //double duration;
+    //start = clock();
+
+    //make nodes (same function for inexact and exact refinement)
+    _makeRefinedGraphNodes(all_nodes,seqs,ali_g);
+
+    //add annotation to nodes
+    //typedef typename Value<TAnnoString>::Type TAnnotation;
+    //typedef typename Value<TAnnotation>::Type TLabel;
+    typedef char TLabel;
+    String<String<TLabel> > pm;
+    _addNodeAnnotation(seqs,seq_map,annotation,pm,ali_g,tag);
+
+    //add edges (different functions depending on exact/inexact refinement)
+    _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);
+
+    //std::cout << "check\n";
+    //finish1 = clock();
+    //duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+    //std::cout << "\ntook " << duration << " seconds.\n";
 }
 
 
@@ -476,230 +476,204 @@ SEQAN_CHECKPOINT
 
 
 ////////////////////////////////////////////////////////////////////////////////////////
-//The big matchRefinement function that does everything: build interval trees, do the 
+//The big matchRefinement function that does everything: build interval trees, do the
 //refinement and construct a refined alignment graph
 ////////////////////////////////////////////////////////////////////////////////////////
 template<typename TAlignmentString, typename TAnnotation, typename TOutGraph, typename TSequence, typename TSetSpec, typename TScore,typename TTagSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				StringSet<TSequence, TSetSpec> & seq, 
-				TScore & score_type,
-				TOutGraph & ali_graph,
-				typename Size<typename Value<TAlignmentString>::Type>::Type min_fragment_len,
-				TAnnotation & annotation,
-				Tag<TTagSpec> const tag)
+                StringSet<TSequence, TSetSpec> & seq,
+                TScore & score_type,
+                TOutGraph & ali_graph,
+                typename Size<typename Value<TAlignmentString>::Type>::Type min_fragment_len,
+                TAnnotation & annotation,
+                Tag<TTagSpec> const tag)
 {
 SEQAN_CHECKPOINT
-	////////////////////////////////////////////////////////////////
-	//typedefs
-	typedef typename Value<TAlignmentString>::Type TAlign;
-	typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
-	typedef typename Size<TAlign>::Type TValue;
-//	typedef TValue TCargo;
-//	typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
-	typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
-	typedef IntervalAndCargo<int,TCargo> TInterval;
-	typedef Graph<Directed<void,WithoutEdgeId> > TGraph;
-	typedef IntervalTreeNode<TInterval> TNode;
-	typedef String<TNode> TPropertyMap;
-	typedef typename std::set<TValue>::iterator TSetIterator;
-	typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type TAlignmentPointer;
-	typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type TSegmentIterator;
-
-
-	////////////////////////////////////////////////////////////////
-	TValue numSequences = length(seq);
-	//weird ID --> good ID map
-	std::map<const void * ,int> seq_map;
-	for(int i = 0; i < (int) numSequences; ++i)
-		seq_map[getObjectId(seq[i])] = i;
-	////////////////////////////////////////////////////////////////
-	//build interval trees
-	String<TGraph> gs;
-	String<TPropertyMap> pms;
-	_createTreesForAllSequences(gs, pms, alis, seq, seq_map, numSequences);
-
-	////////////////////////////////////////////////////////////////
-	//do refinement
-	//std::cout <<"refining..."<<std::flush;
-	// clock_t start, finish1;
-	// double duration;
-	// start = clock();
-	
-	//all_nodes = set of all cut positions
-	String<std::set<TValue> > all_nodes;
-	resize(all_nodes,numSequences);
-
-	//all_nodes that need to be processed set of all cut positions
-	String<std::set<TValue> > all_node_queues;
-	resize(all_node_queues,numSequences);
-
-	//call function _refine for each startknoten
-	TAliIterator ali_it = begin(alis);
-	TAliIterator ali_end = end(alis);
-	//for each segment/fragement/alignment
-	while(ali_it != ali_end)
-	{
-		//for each of the two sequences
-		for(TValue i = 0; i < 2; ++i)
-		{
-			TValue seq_i_id,begin_i,end_i;
-			_getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_i,end_i,i);
-			TValue seq_i_pos = idToPosition(seq,seq_i_id);
-			
-			all_node_queues[seq_i_pos].insert(begin_i);
-			all_node_queues[seq_i_pos].insert(end_i);
-		}	
-		++ali_it;
-	}
-
-
-	TSetIterator queueIt;
-	bool done = false;
-	while(!done)
-	{
-		for(unsigned seq_i_pos = 0; seq_i_pos < numSequences; ++seq_i_pos)
-		{
-			queueIt = all_node_queues[seq_i_pos].begin();
-			while (queueIt != all_node_queues[seq_i_pos].end())
-			{
-				TValue node_i = *queueIt;
-				TSetIterator iter = all_nodes[seq_i_pos].find(node_i);		
-		//		TSetIterator qiter = all_node_queues[seq_i_pos].find(node_i);		
+    ////////////////////////////////////////////////////////////////
+    //typedefs
+    typedef typename Value<TAlignmentString>::Type TAlign;
+    typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
+    typedef typename Size<TAlign>::Type TValue;
+//    typedef TValue TCargo;
+//    typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
+    typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
+    typedef IntervalAndCargo<int,TCargo> TInterval;
+    typedef Graph<Directed<void,WithoutEdgeId> > TGraph;
+    typedef IntervalTreeNode<TInterval> TNode;
+    typedef String<TNode> TPropertyMap;
+    typedef typename std::set<TValue>::iterator TSetIterator;
+    typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type TAlignmentPointer;
+    typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type TSegmentIterator;
+
+
+    ////////////////////////////////////////////////////////////////
+    TValue numSequences = length(seq);
+    //weird ID --> good ID map
+    std::map<const void * ,int> seq_map;
+    for(int i = 0; i < (int) numSequences; ++i)
+        seq_map[getObjectId(seq[i])] = i;
+    ////////////////////////////////////////////////////////////////
+    //build interval trees
+    String<TGraph> gs;
+    String<TPropertyMap> pms;
+    _createTreesForAllSequences(gs, pms, alis, seq, seq_map, numSequences);
+
+    ////////////////////////////////////////////////////////////////
+    //do refinement
+    //std::cout <<"refining..."<<std::flush;
+    // clock_t start, finish1;
+    // double duration;
+    // start = clock();
+
+    //all_nodes = set of all cut positions
+    String<std::set<TValue> > all_nodes;
+    resize(all_nodes,numSequences);
+
+    //all_nodes that need to be processed set of all cut positions
+    String<std::set<TValue> > all_node_queues;
+    resize(all_node_queues,numSequences);
+
+    //call function _refine for each startknoten
+    TAliIterator ali_it = begin(alis);
+    TAliIterator ali_end = end(alis);
+    //for each segment/fragement/alignment
+    while(ali_it != ali_end)
+    {
+        //for each of the two sequences
+        for(TValue i = 0; i < 2; ++i)
+        {
+            TValue seq_i_id,begin_i,end_i;
+            _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_i,end_i,i);
+            TValue seq_i_pos = idToPosition(seq,seq_i_id);
+
+            all_node_queues[seq_i_pos].insert(begin_i);
+            all_node_queues[seq_i_pos].insert(end_i);
+        }
+        ++ali_it;
+    }
+
+
+    TSetIterator queueIt;
+    bool done = false;
+    while(!done)
+    {
+        for(unsigned seq_i_pos = 0; seq_i_pos < numSequences; ++seq_i_pos)
+        {
+            queueIt = all_node_queues[seq_i_pos].begin();
+            while (queueIt != all_node_queues[seq_i_pos].end())
+            {
+                TValue node_i = *queueIt;
+                TSetIterator iter = all_nodes[seq_i_pos].find(node_i);
+        //        TSetIterator qiter = all_node_queues[seq_i_pos].find(node_i);
                 if(_cutIsValid(all_nodes,seq_i_pos,node_i,iter,min_fragment_len,tag))
                    //&& _cutIsValid(all_node_queues,seq_i_pos,node_i,qiter,min_fragment_len,tag))
-//				if(iter == all_nodes[seq_i_pos].end())
-				{
-					TValue seq_i_id = positionToId(seq, seq_i_pos);
-					all_nodes[seq_i_pos].insert(node_i);
-					String<TAlignmentPointer> relevant_segments;
-					findIntervalsExcludeTouching(gs[seq_i_pos],pms[seq_i_pos],node_i,relevant_segments);
-					
-					TSegmentIterator segment_it = begin(relevant_segments);
-					TSegmentIterator segment_end = end(relevant_segments);
-					//foreach of those segments
-					while(segment_it != segment_end)
-					{
-						TValue match_id = (*segment_it).i1;
-						TValue seg_num = (*segment_it).i2;						//get the sequence that node_i needs to be projected onto (seq_j)
-						//and get the projected position (pos_j)
-						TValue seq_j_id, node_j;
-						_getOtherSequenceAndProject(alis[match_id],seg_num,seq_map,seq_i_id,node_i,seq_j_id,node_j);
-						TValue seq_j_pos = idToPosition(seq,seq_j_id);
-						_updateCutPosition(alis[match_id],node_j);
-
-						typename std::set<TValue>::iterator iter_j, qiter_j;
-						iter_j = all_nodes[seq_j_pos].find(node_j);
-						qiter_j = all_node_queues[seq_j_pos].find(node_j);
-						
-						//if node does not exist yet ---> insert and continue cutting
+//                if(iter == all_nodes[seq_i_pos].end())
+                {
+                    TValue seq_i_id = positionToId(seq, seq_i_pos);
+                    all_nodes[seq_i_pos].insert(node_i);
+                    String<TAlignmentPointer> relevant_segments;
+                    findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i);
+
+                    TSegmentIterator segment_it = begin(relevant_segments);
+                    TSegmentIterator segment_end = end(relevant_segments);
+                    //foreach of those segments
+                    while(segment_it != segment_end)
+                    {
+                        TValue match_id = (*segment_it).i1;
+                        TValue seg_num = (*segment_it).i2;                        //get the sequence that node_i needs to be projected onto (seq_j)
+                        //and get the projected position (pos_j)
+                        TValue seq_j_id, node_j;
+                        _getOtherSequenceAndProject(alis[match_id],seg_num,seq_map,seq_i_id,node_i,seq_j_id,node_j);
+                        TValue seq_j_pos = idToPosition(seq,seq_j_id);
+                        _updateCutPosition(alis[match_id],node_j);
+
+                        typename std::set<TValue>::iterator iter_j, qiter_j;
+                        iter_j = all_nodes[seq_j_pos].find(node_j);
+                        qiter_j = all_node_queues[seq_j_pos].find(node_j);
+
+                        //if node does not exist yet ---> insert and continue cutting
                         if(_cutIsValid(all_nodes,seq_j_pos,node_j,iter_j,min_fragment_len,tag)
                             && _cutIsValid(all_node_queues,seq_j_pos,node_j,qiter_j,min_fragment_len,tag))
-                        //if(iter_j == all_nodes[seq_j_pos].end())   
-						{
-							all_node_queues[seq_j_pos].insert(node_j);
-						}
-					
-						++segment_it;
-					}
-						
-				}
-				++queueIt;
-			}
-			all_node_queues[seq_i_pos].clear();
-		}
-		unsigned i;
-		for(i = 0; i < numSequences; ++i)
-		{
-			queueIt = all_node_queues[i].begin();
-			if (queueIt != all_node_queues[i].end())
-				break;
-		}
-		if(i==numSequences)
-			done=true;
-	}
-	_addAnnotationCuts(all_nodes,alis,gs,pms,seq,seq_map,annotation,min_fragment_len,tag);
-
-	// finish1 = clock();
-	// duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
-	//std::cout << "\ntook " << duration << " seconds.\n";
-	//for(int seq_i = 0; seq_i < length(seq); ++seq_i)
-	//{
-	//	typename std::set<TValue>::iterator it = all_nodes[seq_i].begin();
-	//	typename std::set<TValue>::iterator end_it = all_nodes[seq_i].end();
-	//
-	//	while(it != end_it)
-	//	{
-	//		std::cout << *it << ",";
-	//		++it;
-	//	}
-	//	std::cout << "\n";
-	//}
-	//std::cout <<"building tree..."<<std::flush;
-	
-	////////////////////////////////////////////////////////////////
-	//build refined alignment graph
-	_makeAlignmentGraphFromRefinedSegments(all_nodes,alis,score_type,seq,seq_map,ali_graph,tag,annotation);
+                        //if(iter_j == all_nodes[seq_j_pos].end())
+                        {
+                            all_node_queues[seq_j_pos].insert(node_j);
+                        }
+
+                        ++segment_it;
+                    }
+
+                }
+                ++queueIt;
+            }
+            all_node_queues[seq_i_pos].clear();
+        }
+        unsigned i;
+        for(i = 0; i < numSequences; ++i)
+        {
+            queueIt = all_node_queues[i].begin();
+            if (queueIt != all_node_queues[i].end())
+                break;
+        }
+        if(i==numSequences)
+            done=true;
+    }
+    _addAnnotationCuts(all_nodes,alis,gs,pms,seq,seq_map,annotation,min_fragment_len,tag);
+
+    // finish1 = clock();
+    // duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+    //std::cout << "\ntook " << duration << " seconds.\n";
+    //for(int seq_i = 0; seq_i < length(seq); ++seq_i)
+    //{
+    //    typename std::set<TValue>::iterator it = all_nodes[seq_i].begin();
+    //    typename std::set<TValue>::iterator end_it = all_nodes[seq_i].end();
+    //
+    //    while(it != end_it)
+    //    {
+    //        std::cout << *it << ",";
+    //        ++it;
+    //    }
+    //    std::cout << "\n";
+    //}
+    //std::cout <<"building tree..."<<std::flush;
+
+    ////////////////////////////////////////////////////////////////
+    //build refined alignment graph
+    _makeAlignmentGraphFromRefinedSegments(all_nodes,alis,score_type,seq,seq_map,ali_graph,tag,annotation);
 }
 
 
 ///////WRAPPERS
 
-/**
-.Function.matchRefinement:
-..signature:matchRefinement(matches,stringSet,scoringScheme,refinedGraph)
-..param.matches:The set of matches.
-...type:Class.Fragment
-...type:Class.Align
-...type:Spec.Alignment Graph
-..param.scoringScheme:The scoring scheme used to score the refined matches (scores are attached to 
-edges in the refined Alignment Graph).
-...remarks:If no scoring scheme is given, all edges get weight 1.
-...type:Class.Score
-..include:seqan/graph_align.h
-*/
 //exact refinement, score type given
 template<typename TAlignmentString, typename TScoreValue,typename TScoreSpec,typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				StringSet<TSequence, TSetSpec> & seq, 
-				Score<TScoreValue,TScoreSpec> & score_type,
-				TOutGraph & ali_graph)
+                StringSet<TSequence, TSetSpec> & seq,
+                Score<TScoreValue,TScoreSpec> & score_type,
+                TOutGraph & ali_graph)
 {
 SEQAN_CHECKPOINT
-	//min_fragment_len = 1   ==> Exact cutting
-	bool anno = false;
-	matchRefinement(alis,seq,score_type,ali_graph,1,anno,ExactRefinement());
+    //min_fragment_len = 1   ==> Exact cutting
+    bool anno = false;
+    matchRefinement(alis,seq,score_type,ali_graph,1,anno,ExactRefinement());
 }
 
 
 
-/**
-.Function.matchRefinement:
-..cat:Alignments
-..summary:Refines (i.e. cuts into smaller parts) a set of pairwise segment 
-matches in such a way that none of the segments partly overlap. They are either 
-identical (fully overlapping) or non-overlapping.
-..signature:matchRefinement(matches,stringSet,refinedGraph)
-..param.stringSet:The StringSet containing the sequences which the matches lie on.
-...type:Class.StringSet
-..param.refinedGraph:The resulting refined set of matches stored in a graph.
-...type:Spec.Alignment Graph
-..include:seqan/graph_align.h
-*/
 //exact refinement, score type not given
 template<typename TFragmentString, typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TFragmentString & matches,
-				StringSet<TSequence, TSetSpec> & strSet, 
-				TOutGraph & ali_graph)
+                StringSet<TSequence, TSetSpec> & strSet,
+                TOutGraph & ali_graph)
 {
-	SEQAN_CHECKPOINT
-	typename Cargo<TOutGraph>::Type fake_score = 1;
-	bool anno = false;
-	matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement());
+    SEQAN_CHECKPOINT
+    typename Cargo<TOutGraph>::Type fake_score = 1;
+    bool anno = false;
+    matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_
diff --git a/seqan/graph_align/graph_algorithm_refine_fragment.h b/seqan/graph_align/graph_algorithm_refine_fragment.h
index c609796..669d82b 100644
--- a/seqan/graph_align/graph_algorithm_refine_fragment.h
+++ b/seqan/graph_align/graph_algorithm_refine_fragment.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,32 +33,32 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
 
 namespace seqan {
 
-	
-///////////////////////////////////////////////////////////////////////////////////////////////////////	
+
+///////////////////////////////////////////////////////////////////////////////////////////////////////
 //Functions for Fragments
 //project onto other sequence for Graph<Alignment>
 template<typename TFragSize, typename TFragSpec,typename TValue,typename TId1, typename TPos1, typename TId2, typename TPos2, typename TMap>
 void
 _getOtherSequenceAndProject(Fragment<TFragSize,TFragSpec> & segment,
-						TValue seg_num,
-						   TMap &,
-						   TId1 seq_i_id,
-						   TPos1 pos_i,
-						   TId2 & seq_j_id,
-						   TPos2 & pos_j)
+                        TValue seg_num,
+                           TMap &,
+                           TId1 seq_i_id,
+                           TPos1 pos_i,
+                           TId2 & seq_j_id,
+                           TPos2 & pos_j)
 {
 SEQAN_CHECKPOINT
-	getProjectedPosition(segment,seg_num, seq_i_id, pos_i,seq_j_id,pos_j);
-	
-	//if(seq_i_id == sequenceId(segment,0))
-	//	seq_j_id = sequenceId(segment,1);
-	//else
-	//	seq_j_id = sequenceId(segment,0);
+    getProjectedPosition(segment,seg_num, seq_i_id, pos_i,seq_j_id,pos_j);
+
+    //if(seq_i_id == sequenceId(segment,0))
+    //    seq_j_id = sequenceId(segment,1);
+    //else
+    //    seq_j_id = sequenceId(segment,0);
 }
 
 
@@ -68,19 +68,19 @@ SEQAN_CHECKPOINT
 template<typename TFragSize, typename TFragSpec, typename TId, typename TPosition, typename TId2>
 void
 _getSeqBeginAndEnd(Fragment<TFragSize,TFragSpec> & segment,
-				  std::map<const void * ,int> &, 
-				  TId & seq_i_id, 
-				  TPosition & begin_i, 
-				  TPosition & end_i,
-				  TId2 seq)
+                  std::map<const void * ,int> &,
+                  TId & seq_i_id,
+                  TPosition & begin_i,
+                  TPosition & end_i,
+                  TId2 seq)
 {
 SEQAN_CHECKPOINT
-	seq_i_id = sequenceId(segment,seq);
-	if(seq==0)
-		begin_i = segment.begin1; // fragmentBegin(segment,seq_i_id);
-	else
-		begin_i = segment.begin2; // fragmentBegin(segment,seq_i_id);
-	end_i = begin_i + segment.len; //fragmentLength(segment,seq_i_id);
+    seq_i_id = sequenceId(segment,seq);
+    if(seq==0)
+        begin_i = segment.begin1; // fragmentBegin(segment,seq_i_id);
+    else
+        begin_i = segment.begin2; // fragmentBegin(segment,seq_i_id);
+    end_i = begin_i + segment.len; //fragmentLength(segment,seq_i_id);
 }
 
 
@@ -92,29 +92,29 @@ SEQAN_CHECKPOINT
 //process was stopped (the cut is not exact)
 //template<typename TScore,typename TStringSet,typename TFragId,typename TFragPos,typename TFragSize, typename TFragSpec,typename TValue>
 //typename Value<TScore>::Type
-//_getRefinedMatchScore(TScore & score_type, 
-//		 TStringSet & seqs,
-//		 Fragment<TFragId,TFragPos,TFragSize,TFragSpec> & segment, 
-//		 TValue pos_i, 
-//		 TValue pos_j,
-//		 TValue len1, 
-//		 TValue len2)
+//_getRefinedMatchScore(TScore & score_type,
+//         TStringSet & seqs,
+//         Fragment<TFragId,TFragPos,TFragSize,TFragSpec> & segment,
+//         TValue pos_i,
+//         TValue pos_j,
+//         TValue len1,
+//         TValue len2)
 //{
 //SEQAN_CHECKPOINT
-//	typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,seqs,sequenceId(segment,0));
-//	typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,seqs,sequenceId(segment,1));
-//	int i = 0;
-//	typename Value<TScore>::Type ret_score = 0;
-//	TValue len = (len1 < len2) ? len1 : len2;
-//	while(i < len)
-//	{
-//		ret_score += score(score_type,label0[i],label1[i]);
-//		++i;
-//	}
-//	len = (len1 > len2) ? len1 : len2;
-//	ret_score += (len - i) * scoreGapExtend(score_type);
-//	return ret_score;
-//}				
+//    typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,seqs,sequenceId(segment,0));
+//    typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,seqs,sequenceId(segment,1));
+//    int i = 0;
+//    typename Value<TScore>::Type ret_score = 0;
+//    TValue len = (len1 < len2) ? len1 : len2;
+//    while(i < len)
+//    {
+//        ret_score += score(score_type,label0[i],label1[i]);
+//        ++i;
+//    }
+//    len = (len1 > len2) ? len1 : len2;
+//    ret_score += (len - i) * scoreGapExtend(score_type);
+//    return ret_score;
+//}
 //
 //
 ///////////////////////////////////////////////////////////////////////////////////////////////
@@ -127,31 +127,31 @@ SEQAN_CHECKPOINT
 //template<typename TScoreValue,typename TStringSet,typename TFragId,typename TFragPos,typename TFragSize, typename TFragSpec>
 //TScoreValue
 //_getRefinedMatchScore(Score<TScoreValue, Simple> & score_type,
-//		 TStringSet & seqs, 
-//		 Fragment<TFragId,TFragPos,TFragSize,TFragSpec> & segment, 
-//		 TFragPos pos_i, 
-//		 TFragPos pos_j, 
-//		 TFragSize len1, 
-//		 TFragSize len2)
+//         TStringSet & seqs,
+//         Fragment<TFragId,TFragPos,TFragSize,TFragSpec> & segment,
+//         TFragPos pos_i,
+//         TFragPos pos_j,
+//         TFragSize len1,
+//         TFragSize len2)
 //{
 //SEQAN_CHECKPOINT
-//	typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,seqs,sequenceId(segment,0));
-//	typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,seqs,sequenceId(segment,1));
-//	TScoreValue ret_score = 0;
-//	TFragSize len;
-//	if (len1 < len2) len = len1;
-//	else len = len2;
-//	if(len1 <= len2)
-//	{
-//		ret_score += len1 * scoreMatch(score_type);
-//		ret_score += (len2 - len1) * scoreGapExtend(score_type);
-//	}
-//	else{
-//		ret_score += len2 * scoreMatch(score_type);
-//		ret_score += (len1 - len2) * scoreGapExtend(score_type);
-//	}
-//	return ret_score;
-//}				
+//    typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,seqs,sequenceId(segment,0));
+//    typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,seqs,sequenceId(segment,1));
+//    TScoreValue ret_score = 0;
+//    TFragSize len;
+//    if (len1 < len2) len = len1;
+//    else len = len2;
+//    if(len1 <= len2)
+//    {
+//        ret_score += len1 * scoreMatch(score_type);
+//        ret_score += (len2 - len1) * scoreGapExtend(score_type);
+//    }
+//    else{
+//        ret_score += len2 * scoreMatch(score_type);
+//        ret_score += (len1 - len2) * scoreGapExtend(score_type);
+//    }
+//    return ret_score;
+//}
 
 
 //get score for alignment of length len starting at pos_i on one sequence (first sequence if i_am_first==true)
@@ -159,30 +159,30 @@ SEQAN_CHECKPOINT
 template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TFragment,typename TFragPos,typename TFragSize>
 TScoreValue
 _getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
-		 TStringSet & seqs,
-		 TFragment& segment,
-		 TFragPos pos_i,
-		 TFragPos pos_j,
-		 TFragSize len,
-		 TFragSize)
+         TStringSet & seqs,
+         TFragment& segment,
+         TFragPos pos_i,
+         TFragPos pos_j,
+         TFragSize len,
+         TFragSize)
 {
 SEQAN_CHECKPOINT
-	typedef typename Infix<typename Value<TStringSet>::Type>::Type TSegmentLabel;
-	TSegmentLabel label0 = label(segment,seqs, sequenceId(segment, 0));
-	TSegmentLabel label1 = label(segment,seqs, sequenceId(segment, 1));
-	typename Iterator<TSegmentLabel, Rooted>::Type label_it0 = begin(label0) + (pos_i - fragmentBegin(segment,sequenceId(segment,0)));
-	typename Iterator<TSegmentLabel, Rooted>::Type label_it1 = begin(label1) + (pos_j - fragmentBegin(segment,sequenceId(segment,1)));
-	int i = 0;
-	TScoreValue ret_score = 0;
-	while(i < (int) len)
-	{
-		ret_score += score(score_type,*label_it0,*label_it1);
-		++label_it0;
-		++label_it1;
-		++i;
-	}
-	return ret_score;
-}				
+    typedef typename Infix<typename Value<TStringSet>::Type>::Type TSegmentLabel;
+    TSegmentLabel label0 = label(segment,seqs, sequenceId(segment, 0));
+    TSegmentLabel label1 = label(segment,seqs, sequenceId(segment, 1));
+    typename Iterator<TSegmentLabel, Rooted>::Type label_it0 = begin(label0) + (pos_i - fragmentBegin(segment,sequenceId(segment,0)));
+    typename Iterator<TSegmentLabel, Rooted>::Type label_it1 = begin(label1) + (pos_j - fragmentBegin(segment,sequenceId(segment,1)));
+    int i = 0;
+    TScoreValue ret_score = 0;
+    while(i < (int) len)
+    {
+        ret_score += score(score_type,*label_it0,*label_it1);
+        ++label_it0;
+        ++label_it1;
+        ++i;
+    }
+    return ret_score;
+}
 
 
 //get score for alignment of length len starting at pos_i on one sequence (first sequence if i_am_first==true)
@@ -190,18 +190,18 @@ SEQAN_CHECKPOINT
 template<typename TScoreValue,typename TStringSet,typename TFragPos,typename TFragSize, typename TSpec>
 TScoreValue
 _getRefinedMatchScore(Score<TScoreValue, Simple> & score_type,
-		 TStringSet &,
-		 Fragment<TFragSize,ExactFragment<TSpec> > &,
-		 TFragPos,
-		 TFragPos,
-		 TFragSize len,
-		 TFragSize)
+         TStringSet &,
+         Fragment<TFragSize,ExactFragment<TSpec> > &,
+         TFragPos,
+         TFragPos,
+         TFragSize len,
+         TFragSize)
 {
 SEQAN_CHECKPOINT
-	return len*scoreMatch(score_type);
-}				
+    return len*scoreMatch(score_type);
+}
 
 
 }  // namespace
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
diff --git a/seqan/graph_align/graph_algorithm_refine_inexact.h b/seqan/graph_align/graph_algorithm_refine_inexact.h
index b9c66d4..2c3a94a 100644
--- a/seqan/graph_align/graph_algorithm_refine_inexact.h
+++ b/seqan/graph_align/graph_algorithm_refine_inexact.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,8 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_INEXACT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_INEXACT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_INEXACT_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_INEXACT_H_
 
 //SEQAN_NO_DDDOC: do not generate documentation for this file
 
@@ -49,45 +49,45 @@ typedef Tag<TagInexactRefinement_> const InexactRefinement;
 template<typename TValue, typename TValue2, typename TSize>
 inline bool
 _cutIsValid(String<std::set<TValue> > & all_nodes,
-		TValue2 seq_i_pos,
-		TSize pos_i,
-		typename std::set<TValue>::iterator iter,
-		TSize min_len,
-		Tag<TagInexactRefinement_> const)
+        TValue2 seq_i_pos,
+        TSize pos_i,
+        typename std::set<TValue>::iterator iter,
+        TSize min_len,
+        Tag<TagInexactRefinement_> const)
 {
 SEQAN_CHECKPOINT
-	
-	//cut already exists
-	if(iter != all_nodes[seq_i_pos].end())
-		return false;
-	typename std::set<TValue>::iterator tmp_iter = all_nodes[seq_i_pos].upper_bound(pos_i);
-	if(tmp_iter != all_nodes[seq_i_pos].end())
-		if((*tmp_iter - pos_i) < min_len)
-			return false;
-	if(tmp_iter != all_nodes[seq_i_pos].begin())
-	{
-		--tmp_iter;
-		if((pos_i - *tmp_iter) < min_len)
-			return false;
-	}
-	return true;
+
+    //cut already exists
+    if(iter != all_nodes[seq_i_pos].end())
+        return false;
+    typename std::set<TValue>::iterator tmp_iter = all_nodes[seq_i_pos].upper_bound(pos_i);
+    if(tmp_iter != all_nodes[seq_i_pos].end())
+        if((*tmp_iter - pos_i) < min_len)
+            return false;
+    if(tmp_iter != all_nodes[seq_i_pos].begin())
+    {
+        --tmp_iter;
+        if((pos_i - *tmp_iter) < min_len)
+            return false;
+    }
+    return true;
 }
 
 
 // returns node begin or end position closest to pos
-// i.e. closest refined position 
+// i.e. closest refined position
 template<typename TAliGraph, typename TVertexDescriptor, typename TId, typename TPosition>
 TPosition
 _getClosestRefinedNeighbor(TAliGraph & ali_g,
-						   TVertexDescriptor & vd,
-						   TId /*seq*/,
-						   TPosition pos)
+                           TVertexDescriptor & vd,
+                           TId /*seq*/,
+                           TPosition pos)
 {
 SEQAN_CHECKPOINT
-	if(pos-fragmentBegin(ali_g,vd) < fragmentBegin(ali_g,vd)+fragmentLength(ali_g,vd)-pos)
-		return fragmentBegin(ali_g,vd);
-	else
-		return fragmentBegin(ali_g,vd) + fragmentLength(ali_g,vd);
+    if(pos-fragmentBegin(ali_g,vd) < fragmentBegin(ali_g,vd)+fragmentLength(ali_g,vd)-pos)
+        return fragmentBegin(ali_g,vd);
+    else
+        return fragmentBegin(ali_g,vd) + fragmentLength(ali_g,vd);
 }
 
 
@@ -95,27 +95,27 @@ SEQAN_CHECKPOINT
 // and corresponding node (end_knot)
 template<typename TAliGraph, typename TId, typename TPosition>
 void
-_getCutEndPos(TAliGraph & ali_g, 
-			  typename VertexDescriptor<TAliGraph>::Type & end_knot,
-			  TId seq,
-			  TPosition act_begin_pos,
-			  TPosition end_pos,
-			  TPosition & cut_end_pos)
+_getCutEndPos(TAliGraph & ali_g,
+              typename VertexDescriptor<TAliGraph>::Type & end_knot,
+              TId seq,
+              TPosition act_begin_pos,
+              TPosition end_pos,
+              TPosition & cut_end_pos)
 {
 SEQAN_CHECKPOINT
-	end_knot = findVertex(ali_g,seq,end_pos-1);//end_pos1 is the first position of the next node
-	if(end_pos == fragmentBegin(ali_g,end_knot) + fragmentBegin(ali_g,end_knot))
-		cut_end_pos = end_pos;
-	else
-	{
-		cut_end_pos = _getClosestRefinedNeighbor(ali_g,end_knot,seq,end_pos);
+    end_knot = findVertex(ali_g,seq,end_pos-1);//end_pos1 is the first position of the next node
+    if(end_pos == fragmentBegin(ali_g,end_knot) + fragmentBegin(ali_g,end_knot))
+        cut_end_pos = end_pos;
+    else
+    {
+        cut_end_pos = _getClosestRefinedNeighbor(ali_g,end_knot,seq,end_pos);
         if(cut_end_pos <= act_begin_pos) end_knot = getNil<typename VertexDescriptor<TAliGraph>::Type>();
-		else 
+        else
         {
             end_knot =  findVertex(ali_g,seq,cut_end_pos-1);
-		    SEQAN_ASSERT(cut_end_pos == fragmentBegin(ali_g,end_knot)+fragmentLength(ali_g,end_knot));
+            SEQAN_ASSERT(cut_end_pos == fragmentBegin(ali_g,end_knot)+fragmentLength(ali_g,end_knot));
         }
-	}
+    }
 }
 
 
@@ -123,172 +123,172 @@ SEQAN_CHECKPOINT
 // and corresponding node (act_knot)
 template<typename TAliGraph, typename TId, typename TPosition>
 void
-_getCutBeginPos(TAliGraph & ali_g, 
-			  typename VertexDescriptor<TAliGraph>::Type & act_knot,
-			  TId seq,
-			  TPosition act_end_pos,
-			  TPosition act_pos,
-			  TPosition & cut_act_pos)
+_getCutBeginPos(TAliGraph & ali_g,
+              typename VertexDescriptor<TAliGraph>::Type & act_knot,
+              TId seq,
+              TPosition act_end_pos,
+              TPosition act_pos,
+              TPosition & cut_act_pos)
 {
 SEQAN_CHECKPOINT
-	
-	act_knot = findVertex(ali_g,seq,act_pos);
-	//if completely refined
-	if(act_pos == fragmentBegin(ali_g,act_knot))
-		cut_act_pos = act_pos;
-	else //if incompletely refined
-	{
-		cut_act_pos = _getClosestRefinedNeighbor(ali_g,act_knot,seq,act_pos);
+
+    act_knot = findVertex(ali_g,seq,act_pos);
+    //if completely refined
+    if(act_pos == fragmentBegin(ali_g,act_knot))
+        cut_act_pos = act_pos;
+    else //if incompletely refined
+    {
+        cut_act_pos = _getClosestRefinedNeighbor(ali_g,act_knot,seq,act_pos);
         if(cut_act_pos > act_end_pos) act_knot = getNil<typename VertexDescriptor<TAliGraph>::Type>();
-		else 
+        else
         {
-    		act_knot =  findVertex(ali_g,seq,cut_act_pos); // have to watch out with cut_act_pos==seqLength!
-	        SEQAN_ASSERT(act_knot == getNil<typename VertexDescriptor<TAliGraph>::Type>() ||
-	                     cut_act_pos == fragmentBegin(ali_g, act_knot));
+            act_knot =  findVertex(ali_g,seq,cut_act_pos); // have to watch out with cut_act_pos==seqLength!
+            SEQAN_ASSERT(act_knot == getNil<typename VertexDescriptor<TAliGraph>::Type>() ||
+                         cut_act_pos == fragmentBegin(ali_g, act_knot));
         }
-	}
+    }
 }
 
 
 
-//step 2 of constructing the refined alignment graph: add all edges    
+//step 2 of constructing the refined alignment graph: add all edges
 //version for inexact refinement
 template<typename TAlignmentString,typename TPropertyMap,typename TStringSet,typename TSeqMap, typename TScore,typename TAliGraph>
 void
 _makeRefinedGraphEdges(TAlignmentString & alis,
-					   TPropertyMap & , //pm,
-					  TStringSet & seqs,
-				      TSeqMap & seq_map,
-				      TScore & score_type,
-					  TAliGraph & ali_g,
-					  Tag<TagInexactRefinement_> const)
+                       TPropertyMap & , //pm,
+                      TStringSet & seqs,
+                      TSeqMap & seq_map,
+                      TScore & score_type,
+                      TAliGraph & ali_g,
+                      Tag<TagInexactRefinement_> const)
 {
 SEQAN_CHECKPOINT
-	typedef typename Value<TAlignmentString>::Type TAlign;
-	typedef typename Position<TAlign>::Type TPosition;
-	typedef typename Id<TAlign>::Type TId;
-	typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
-	typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
-	//typedef typename Cargo<TAliGraph>::Type TCargo;
+    typedef typename Value<TAlignmentString>::Type TAlign;
+    typedef typename Position<TAlign>::Type TPosition;
+    typedef typename Id<TAlign>::Type TId;
+    typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
+    typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
+    //typedef typename Cargo<TAliGraph>::Type TCargo;
 
         TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	//make edges
-	TAliIterator ali_it = begin(alis);
-	TAliIterator ali_end = end(alis);
-	//for each segment/fragment/alignment
-	while(ali_it != ali_end)
-	{
-		//get first sequence that takes part in the alignment + boundaries of the ali
-		TId seq1;
+    //make edges
+    TAliIterator ali_it = begin(alis);
+    TAliIterator ali_end = end(alis);
+    //for each segment/fragment/alignment
+    while(ali_it != ali_end)
+    {
+        //get first sequence that takes part in the alignment + boundaries of the ali
+        TId seq1;
         TPosition begin_pos1,end_pos1;
-		_getSeqBeginAndEnd(*ali_it,seq_map,seq1,begin_pos1,end_pos1,(TId)0);
+        _getSeqBeginAndEnd(*ali_it,seq_map,seq1,begin_pos1,end_pos1,(TId)0);
 
-		//get second sequence that takes part in the alignment + boundaries of the ali
-		TId seq2;
+        //get second sequence that takes part in the alignment + boundaries of the ali
+        TId seq2;
         TPosition begin_pos2,end_pos2;
-		_getSeqBeginAndEnd(*ali_it,seq_map,seq2,begin_pos2,end_pos2,(TId)1);
+        _getSeqBeginAndEnd(*ali_it,seq_map,seq2,begin_pos2,end_pos2,(TId)1);
 
-		//get the last node that is within the current ali
-		TVertexDescriptor end_knot1;
-		TPosition cut_end_pos1;
+        //get the last node that is within the current ali
+        TVertexDescriptor end_knot1;
+        TPosition cut_end_pos1;
         _getCutEndPos(ali_g,end_knot1,seq1,begin_pos1,end_pos1,cut_end_pos1);
         if(end_knot1 == nilVertex) // there is no node --> fragment disappeared in min_frag_len heuristic
-            continue; 
-	
-		//get the node that represents the current interval (begin_pos until next_cut_pos or end_pos)
-		TVertexDescriptor act_knot1;
-		TPosition cut_act_pos1,act_pos1;
-		act_pos1 = begin_pos1;
-		_getCutBeginPos(ali_g,act_knot1,seq1,end_pos1,act_pos1,cut_act_pos1);
+            continue;
+
+        //get the node that represents the current interval (begin_pos until next_cut_pos or end_pos)
+        TVertexDescriptor act_knot1;
+        TPosition cut_act_pos1,act_pos1;
+        act_pos1 = begin_pos1;
+        _getCutBeginPos(ali_g,act_knot1,seq1,end_pos1,act_pos1,cut_act_pos1);
         if(act_knot1 == nilVertex) // there is no node, can this happen here?
-            continue; 
-		TPosition act_end_pos1 = cut_act_pos1 + fragmentLength(ali_g,act_knot1);
-		//walk through cuts on the first sequence
-//		while (act_end_pos1 <= cut_end_pos1)
-		while (true)
-		{
-			//get other sequence and projected position
-			//TId seq2;
+            continue;
+        TPosition act_end_pos1 = cut_act_pos1 + fragmentLength(ali_g,act_knot1);
+        //walk through cuts on the first sequence
+//        while (act_end_pos1 <= cut_end_pos1)
+        while (true)
+        {
+            //get other sequence and projected position
+            //TId seq2;
             TPosition act_pos2;
-			_getOtherSequenceAndProject(*ali_it,0,seq_map,seq1,act_pos1,seq2,act_pos2);
-		
-			//get node that corresponds to that position
-			TVertexDescriptor act_knot2;
-			TPosition cut_act_pos2;
-			_getCutBeginPos(ali_g,act_knot2,seq2,end_pos2,act_pos2,cut_act_pos2);
+            _getOtherSequenceAndProject(*ali_it,0,seq_map,seq1,act_pos1,seq2,act_pos2);
+
+            //get node that corresponds to that position
+            TVertexDescriptor act_knot2;
+            TPosition cut_act_pos2;
+            _getCutBeginPos(ali_g,act_knot2,seq2,end_pos2,act_pos2,cut_act_pos2);
             if(act_knot2 == nilVertex) // there is no corresponding node in second sequence
-                break; 
-			//corresponding end on seq2 (there might be more than one node on seq2 that corresponds
-			//to the same interval (=node) on seq1)
-			TPosition act_end_pos2;
- 			_getOtherSequenceAndProject(*ali_it,0,seq_map,seq1,_min(act_end_pos1,end_pos1)-1,seq2,act_end_pos2);
-			++act_end_pos2;
-			TVertexDescriptor act_end_knot2;
-			TPosition cut_act_end_pos2;
-			_getCutEndPos(ali_g,act_end_knot2,seq2,begin_pos2,act_end_pos2,cut_act_end_pos2);
+                break;
+            //corresponding end on seq2 (there might be more than one node on seq2 that corresponds
+            //to the same interval (=node) on seq1)
+            TPosition act_end_pos2;
+             _getOtherSequenceAndProject(*ali_it,0,seq_map,seq1,_min(act_end_pos1,end_pos1)-1,seq2,act_end_pos2);
+            ++act_end_pos2;
+            TVertexDescriptor act_end_knot2;
+            TPosition cut_act_end_pos2;
+            _getCutEndPos(ali_g,act_end_knot2,seq2,begin_pos2,act_end_pos2,cut_act_end_pos2);
             if(act_end_knot2 == nilVertex) // there is no node at all in second sequence
-                break; 
-			
-			if(cut_act_pos2 == cut_act_end_pos2)
-				break;
-			while(true)
-			{
-				//should at the moment return score for:
-				//
-				//seq1 = ....cr...rc....
-				//            ||||||
-				//seq2 = ...c.r...rc....
-				//bzw
-				//seq1 = ..cr.....x....   man will aber nur    ..cr......x....
-				//          |||||||-							 ---||||||  
-				//seq2 = ...r.c...rc... 					   ...r.c...rc....
-				typename Value<TScore>::Type score = 0;
-				score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos1,act_pos2,act_end_pos1-act_pos1,cut_act_end_pos2);
-				//score *= _getRefinedAnnoScore(ali_g,pm,act_knot1,act_knot2,score_type);
-				//add score for
-				//
-				//seq1 = ...-cr....x....
-				//          ||
-				//seq2 = ...c.r...rc....
-//					score += getLeftRestScore(score_type,seqs,seq1,seq2,act_pos1,cut_act_pos1,act_pos2,cut_act_pos2);
-				if(score > 0)
-				{	if(findEdge(ali_g,act_knot1,act_knot2)==0)
-						addEdge(ali_g,act_knot1,act_knot2,score);
-					else
-					{
-						TEdgeDescriptor ed = findEdge(ali_g, act_knot1, act_knot2);
-						//if((TCargo)score > getCargo(ed))
-							//assignCargo(ed, score);
-						assignCargo(ed, getCargo(ed)+score);
-					}
-				}
-				if(act_knot2==act_end_knot2)
-					break;
-				act_pos2 = cut_act_pos2 + fragmentLength(ali_g,act_knot2);
-				_getCutBeginPos(ali_g,act_knot2,seq2,end_pos2,act_pos2,cut_act_pos2);
-			}
-			if(act_knot1 == end_knot1)
-				break;
-			act_pos1 = act_end_pos1;
-			act_knot1 = findVertex(ali_g,seq1,act_pos1);
-			cut_act_pos1 = act_pos1;
-			act_end_pos1 = cut_act_pos1 + fragmentLength(ali_g,act_knot1);
-		}
-		++ali_it;
-	}
+                break;
+
+            if(cut_act_pos2 == cut_act_end_pos2)
+                break;
+            while(true)
+            {
+                //should at the moment return score for:
+                //
+                //seq1 = ....cr...rc....
+                //            ||||||
+                //seq2 = ...c.r...rc....
+                //bzw
+                //seq1 = ..cr.....x....   man will aber nur    ..cr......x....
+                //          |||||||-                             ---||||||
+                //seq2 = ...r.c...rc...                        ...r.c...rc....
+                typename Value<TScore>::Type score = 0;
+                score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos1,act_pos2,act_end_pos1-act_pos1,cut_act_end_pos2);
+                //score *= _getRefinedAnnoScore(ali_g,pm,act_knot1,act_knot2,score_type);
+                //add score for
+                //
+                //seq1 = ...-cr....x....
+                //          ||
+                //seq2 = ...c.r...rc....
+//                    score += getLeftRestScore(score_type,seqs,seq1,seq2,act_pos1,cut_act_pos1,act_pos2,cut_act_pos2);
+                if(score > 0)
+                {    if(findEdge(ali_g,act_knot1,act_knot2)==0)
+                        addEdge(ali_g,act_knot1,act_knot2,score);
+                    else
+                    {
+                        TEdgeDescriptor ed = findEdge(ali_g, act_knot1, act_knot2);
+                        //if((TCargo)score > getCargo(ed))
+                            //assignCargo(ed, score);
+                        assignCargo(ed, getCargo(ed)+score);
+                    }
+                }
+                if(act_knot2==act_end_knot2)
+                    break;
+                act_pos2 = cut_act_pos2 + fragmentLength(ali_g,act_knot2);
+                _getCutBeginPos(ali_g,act_knot2,seq2,end_pos2,act_pos2,cut_act_pos2);
+            }
+            if(act_knot1 == end_knot1)
+                break;
+            act_pos1 = act_end_pos1;
+            act_knot1 = findVertex(ali_g,seq1,act_pos1);
+            cut_act_pos1 = act_pos1;
+            act_end_pos1 = cut_act_pos1 + fragmentLength(ali_g,act_knot1);
+        }
+        ++ali_it;
+    }
 }
 
 // TODO(holtgrew): Documentation is incomplete.
 
 /*!
  * @fn matchRefinement
- * @headerfile seqan/graph_align.h
+ * @headerfile <seqan/graph_align.h>
  * @brief Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the
  *        segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
- * 
+ *
  * @signature void matchRefinement(matches, stringSet[, scoringScheme], refinedGraph);
- * 
+ *
  * @param[out] matches       The set of matches. Types: Fragment, Align, Alignment Graph
  * @param[out] refinedGraph  The resulting refined set of matches stored in a graph.  Types: Alignment Graph
  * @param[out] stringSet     The StringSet containing the sequences which the matches lie on. Types: StringSet
@@ -297,56 +297,42 @@ SEQAN_CHECKPOINT
  *                           Types: Score
  */
 
-/**
-.Function.matchRefinement:
-..signature:matchRefinement(matches,stringSet,scoringScheme,refinedGraph,minFragmentLen)
-..param.minFragmentLen:The minimal segment length allowed (unsigned int).
-...remarks:If in the refinement process a cut would result in
-a segment shorter than minFragmentLen, then the cut is not made and a heuristic is applied to refine this short overlap.
-...remarks:If no minFragmentLen is given, then all cuts are made. This corresponds to a minFragmentLen of 1.
-..include:seqan/graph_align.h
-*/
 //score type given, min fragment length given, if > 1 ==> inexact refinement
 template<typename TAlignmentString, typename TScoreValue,typename TScoreSpec, typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				StringSet<TSequence, TSetSpec> & seq, 
-				Score<TScoreValue,TScoreSpec> & score_type,
-				TOutGraph & ali_graph,
-				unsigned int min_frag_len)
+                StringSet<TSequence, TSetSpec> & seq,
+                Score<TScoreValue,TScoreSpec> & score_type,
+                TOutGraph & ali_graph,
+                unsigned int min_frag_len)
 {
 SEQAN_CHECKPOINT
-	bool anno = false;
-	if(min_frag_len > 1)
+    bool anno = false;
+    if(min_frag_len > 1)
         matchRefinement(alis,seq,score_type,ali_graph,min_frag_len,anno,InexactRefinement());
-	else
+    else
         matchRefinement(alis,seq,score_type,ali_graph,min_frag_len,anno,ExactRefinement());
 }
 
 
-/**
-.Function.matchRefinement:
-..signature:matchRefinement(matches,stringSet,refinedGraph,minFragmentLen)
-..include:seqan/graph_align.h
-*/
 //score type not given, min fragment length given, if > 1 ==> inexact refinement
 template<typename TAlignmentString, typename TOutGraph, typename TSequence, typename TSetSpec>
 void
 matchRefinement(TAlignmentString & alis,
-				StringSet<TSequence, TSetSpec> & seq, 
-				TOutGraph & ali_graph,
-				unsigned int min_frag_len)
+                StringSet<TSequence, TSetSpec> & seq,
+                TOutGraph & ali_graph,
+                unsigned int min_frag_len)
 {
 SEQAN_CHECKPOINT
-//	Score<int,FakeScore > fake_score;
-	typename Cargo<TOutGraph>::Type fake_score = 1;
-	bool anno = false;
-	if(min_frag_len > 1)
+//    Score<int,FakeScore > fake_score;
+    typename Cargo<TOutGraph>::Type fake_score = 1;
+    bool anno = false;
+    if(min_frag_len > 1)
         matchRefinement(alis,seq,fake_score,ali_graph,min_frag_len,anno,InexactRefinement());
-	else
+    else
         matchRefinement(alis,seq,fake_score,ali_graph,min_frag_len,anno,ExactRefinement());
 }
-	
+
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_INEXACT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_INEXACT_H_
diff --git a/seqan/graph_align/graph_algorithm_refine_scoring.h b/seqan/graph_align/graph_algorithm_refine_scoring.h
index 516ec3c..a99b2b3 100644
--- a/seqan/graph_align/graph_algorithm_refine_scoring.h
+++ b/seqan/graph_align/graph_algorithm_refine_scoring.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,8 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_REFINE_SCORING_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_REFINE_SCORING_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_REFINE_SCORING_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_REFINE_SCORING_H_
 
 namespace seqan {
 
@@ -44,9 +44,9 @@ template<typename TScoreValue,typename TStringSet,typename TAlign,typename TValu
 TScoreValue
 _getRefinedMatchScore(TScoreValue const &, TStringSet const &, TAlign const &, TValue, TValue, TSize, TSize)
 {
-	return 1;
+    return 1;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_REFINE_SCORING_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_REFINE_SCORING_H_
diff --git a/seqan/graph_align/graph_impl_align.h b/seqan/graph_align/graph_impl_align.h
index 17d7571..4313fbd 100644
--- a/seqan/graph_align/graph_impl_align.h
+++ b/seqan/graph_align/graph_impl_align.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,8 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_H_
 
 namespace seqan {
 
@@ -55,66 +55,41 @@ namespace seqan {
 
 /*!
  * @defgroup AlignmentGraphFormatTags Alignment Graph Formats
- * @brief File formats to write an alignment graph.
+ * @brief File formats to write an @link AlignmentGraph @endlink.
  *
  * @tag AlignmentGraphFormatTags#MsfFormat
  * @headerfile <seqan/graph_align.h>
- * @brief MSF Format to write an alignment graph.
+ * @brief MSF Format to write an @link AlignmentGraph @endlink.
  *
  * @signature typedef Tag<MsfFormat_> const MsfFormat;
  *
  * @tag AlignmentGraphFormatTags#FastaFormat
  * @headerfile <seqan/graph_align.h>
- * @brief Fasta Format to write an alignment graph.
+ * @brief Fasta Format to write an @link AlignmentGraph @endlink.
  *
  * @signature typedef Tag<FastaFormat_> const FastaFormat;
  *
  * @tag AlignmentGraphFormatTags#CgVizFormat
  * @headerfile <seqan/graph_align.h>
- * @brief CgViz Format to write an alignment graph.
+ * @brief CgViz Format to write an @link AlignmentGraph @endlink.
  *
  * @signature typedef Tag<CgVizFormat_> const CgVizFormat;
  */
 
-/**
-.Tag.Alignment Graph Format:
-..cat:Input/Output
-..summary:A file format to write an alignment graph.
-..include:seqan/graph_align.h
-*/
-
 //////////////////////////////////////////////////////////////////////////////
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Alignment Graph Format.value.MsfFormat:
-	Msf format to write an alignment graph.
-..include:seqan/graph_align.h
-*/
-
 struct MsfFormat_;
 typedef Tag<MsfFormat_> const MsfFormat;
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Alignment Graph Format.value.FastaFormat:
-	Fasta format to write an alignment graph.
-..include:seqan/graph_align.h
-*/
-
 struct FastaFormat_;
 typedef Tag<FastaFormat_> const FastaFormat;
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Alignment Graph Format.value.CgVizFormat:
-	Cgviz format to write an alignment graph.
-..include:seqan/graph_align.h
-*/
-
 struct CgVizFormat_;
 typedef Tag<CgVizFormat_> const CgVizFormat;
 
@@ -139,14 +114,14 @@ struct Alignment;
 
 template<typename TStringSet, typename TCargo, typename TSpec>
 struct EdgeType<Graph<Alignment<TStringSet, TCargo, TSpec> > const> {
-	typedef typename EdgeType<Graph<Undirected<TCargo, TSpec> > const>::Type Type;
+    typedef typename EdgeType<Graph<Undirected<TCargo, TSpec> > const>::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
 struct EdgeType<Graph<Alignment<TStringSet, TCargo, TSpec> > > {
-	typedef typename EdgeType<Graph<Undirected<TCargo, TSpec> > >::Type Type;
+    typedef typename EdgeType<Graph<Undirected<TCargo, TSpec> > >::Type Type;
 };
 
 
@@ -154,14 +129,14 @@ struct EdgeType<Graph<Alignment<TStringSet, TCargo, TSpec> > > {
 
 template<typename TStringSet, typename TCargo, typename TSpec>
 struct Host<Graph<Alignment<TStringSet, TCargo, TSpec> > > {
-	typedef TStringSet Type;
+    typedef TStringSet Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
 struct Host<Graph<Alignment<TStringSet, TCargo, TSpec> > const> {
-	typedef TStringSet const Type;
+    typedef TStringSet const Type;
 };
 
 
@@ -179,23 +154,23 @@ struct Host<Graph<Alignment<TStringSet, TCargo, TSpec> > const> {
 template<typename TId = unsigned int, typename TSize = unsigned int>
 class FragmentInfo {
 public:
-	TId data_seq_id;
-	TSize data_begin;
-	TSize data_length;
-
-	FragmentInfo() :
-		data_seq_id(0),
-		data_begin(0),
-		data_length(0)
-	{
-	}
-
-	FragmentInfo(TId id, TSize beg, TSize len) :
-		data_seq_id(id),
-		data_begin(beg),
-		data_length(len)
-	{
-	}
+    TId data_seq_id;
+    TSize data_begin;
+    TSize data_length;
+
+    FragmentInfo() :
+        data_seq_id(0),
+        data_begin(0),
+        data_length(0)
+    {
+    }
+
+    FragmentInfo(TId id, TSize beg, TSize len) :
+        data_seq_id(id),
+        data_begin(beg),
+        data_length(len)
+    {
+    }
 
 };
 
@@ -203,13 +178,14 @@ class FragmentInfo {
 
 /*!
  * @class AlignmentGraph
+ * @extends Graph
  * @headerfile <seqan/graph_align.h>
  * @brief Alignment graph type.
  *
  * <img src="alignmentGraph.png" tite="An alignment graph with 3 sequences." />
  *
  * @signature template <typename TStringSet[, typename TCargo[, typename TSpec]]>
- *            class Alignment;
+ *            class Graph<Alignment<TStringSet, TCargo, TSpec> >;
  *
  * @tparam TStringSet The type of the @link StringSet @endlink containing the sequence information.  <b>Must be a
  *                    @link DependentStringSet @endlink.</b>
@@ -219,111 +195,90 @@ class FragmentInfo {
  *
  * @section Example
  *
- * @include demos/graph_align/graph_align.cpp
+ * @include demos/dox/graph_align/graph_align.cpp
  *
  * @code{.console}
  * Score = -8
  * Alignment matrix:
- *       0     .    :   
+ *       0     .    :
  *         ATCGAATGCGGA
  *         |     |||  |
  *         ACTCGTTGC--A
  * @endcode
  */
 
-/**
-.Spec.Alignment Graph:
-..cat:Graph
-..general:Class.Graph
-..summary:An alignment graph.
-..description:
-...image:alignmentGraph|An alignment graph with 3 sequences.
-..signature:Graph<Alignment<TStringSet, TCargo, TSpec> > 
-..param.TStringSet:The type of the string set containing the sequence information, must be a @Spec.Dependent|Dependent StringSet@
-...default:@Spec.Dependent|Dependent StringSet@
-..param.TCargo:The cargo type that can be attached to the edges.
-...metafunction:Metafunction.Cargo
-...remarks:Use @Metafunction.Cargo@ to get the cargo type of an undirected graph.
-...default:$void$
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-...remarks:Use WithoutEdgeId here to omit edge ids.
-Note: If edges do not store ids external property maps do not work.
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_align.h
-*/
 template<typename TString, typename TSpecial, typename TCargo, typename TSpec>
-class Graph<Alignment<StringSet<TString, Dependent<TSpecial> >, TCargo, TSpec> > 
+class Graph<Alignment<StringSet<TString, Dependent<TSpecial> >, TCargo, TSpec> >
 {
-	public:
-		typedef typename Id<Graph>::Type TIdType_;
-		typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
-		typedef typename Size<Graph>::Type TSize_;
-		typedef std::pair<TIdType_, TSize_> TKey_;
-		typedef std::map<TKey_, TVertexDescriptor_> TPosToVertexMap_;
-		typedef FragmentInfo<TIdType_, TSize_> TFragmentInfo_;
-
-		// Alignment graph
-		Graph<Undirected<TCargo, TSpec> > data_align;
-
-		// Sequences
-		Holder<StringSet<TString, Dependent<TSpecial> > > data_sequence;
-		
-		// Alignment specific members
-		String<TFragmentInfo_> data_fragment;
-
-		// STL Map to retrieve a vertex given SeqId, Position
-		TPosToVertexMap_ data_pvMap;
-
-
-		Graph() {
-		}
-
-
-		template <typename TDefault>
-		Graph(StringSet<TString, Dependent<TDefault> > const& sSet) {
-			SEQAN_CHECKPOINT
-			data_sequence = sSet;
-
-			// Cover all sequences with nil vertices
-			TVertexDescriptor_ nilVertex = getNil<TVertexDescriptor_>();
-			TSize_ lenSet = length(sSet);
-			for(TSize_ k=0; k<lenSet;++k) 
-				data_pvMap.insert(std::make_pair(TKey_(positionToId(sSet,k), length(sSet[k])), nilVertex));
-		}
-
-		template <typename TDefault>
-		Graph(StringSet<TString, Owner<TDefault> > const& sSet) {
-			SEQAN_CHECKPOINT
-			StringSet<TString, Dependent<> > depStr(sSet);
-			data_sequence = depStr;
-
-			// Cover all sequences with nil vertices
-			TVertexDescriptor_ nilVertex = getNil<TVertexDescriptor_>();
-			TSize_ lenSet = length(sSet);
-			for(TSize_ k=0; k<lenSet;++k) 
-				data_pvMap.insert(std::make_pair(TKey_(positionToId(const_cast<StringSet<TString, Owner<TDefault> >&>(sSet),k), length(sSet[k])), nilVertex));
-		}
-
-
-		~Graph() {
-			SEQAN_CHECKPOINT
-			clear(*this);
-		}
-
-		Graph(Graph const & _other) 
-		{
-			SEQAN_CHECKPOINT
-			_copyGraph(_other, *this);	
-		}
-	
-		Graph const& operator = (Graph const & _other) {
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			clear(*this);
-			_copyGraph(_other, *this);
-			return *this;
-		}
+    public:
+        typedef typename Id<Graph>::Type TIdType_;
+        typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
+        typedef typename Size<Graph>::Type TSize_;
+        typedef std::pair<TIdType_, TSize_> TKey_;
+        typedef std::map<TKey_, TVertexDescriptor_> TPosToVertexMap_;
+        typedef FragmentInfo<TIdType_, TSize_> TFragmentInfo_;
+
+        // Alignment graph
+        Graph<Undirected<TCargo, TSpec> > data_align;
+
+        // Sequences
+        Holder<StringSet<TString, Dependent<TSpecial> > > data_sequence;
+
+        // Alignment specific members
+        String<TFragmentInfo_> data_fragment;
+
+        // STL Map to retrieve a vertex given SeqId, Position
+        TPosToVertexMap_ data_pvMap;
+
+
+        Graph() {
+        }
+
+
+        template <typename TDefault>
+        Graph(StringSet<TString, Dependent<TDefault> > const& sSet) {
+            SEQAN_CHECKPOINT
+            data_sequence = sSet;
+
+            // Cover all sequences with nil vertices
+            TVertexDescriptor_ nilVertex = getNil<TVertexDescriptor_>();
+            TSize_ lenSet = length(sSet);
+            for(TSize_ k=0; k<lenSet;++k)
+                data_pvMap.insert(std::make_pair(TKey_(positionToId(sSet,k), length(sSet[k])), nilVertex));
+        }
+
+        template <typename TDefault>
+        Graph(StringSet<TString, Owner<TDefault> > const& sSet) {
+            SEQAN_CHECKPOINT
+            StringSet<TString, Dependent<> > depStr(sSet);
+            data_sequence = depStr;
+
+            // Cover all sequences with nil vertices
+            TVertexDescriptor_ nilVertex = getNil<TVertexDescriptor_>();
+            TSize_ lenSet = length(sSet);
+            for(TSize_ k=0; k<lenSet;++k)
+                data_pvMap.insert(std::make_pair(TKey_(positionToId(const_cast<StringSet<TString, Owner<TDefault> >&>(sSet),k), length(sSet[k])), nilVertex));
+        }
+
+
+        ~Graph() {
+            SEQAN_CHECKPOINT
+            clear(*this);
+        }
+
+        Graph(Graph const & _other)
+        {
+            SEQAN_CHECKPOINT
+            _copyGraph(_other, *this);
+        }
+
+        Graph const& operator = (Graph const & _other) {
+            SEQAN_CHECKPOINT
+            if (this == &_other) return *this;
+            clear(*this);
+            _copyGraph(_other, *this);
+            return *this;
+        }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -335,10 +290,10 @@ class Graph<Alignment<StringSet<TString, Dependent<TSpecial> >, TCargo, TSpec> >
 template<typename TStringSet, typename TCargo, typename TSpec>
 inline String<typename EdgeType<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type*>&
 _getVertexString(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	return const_cast<String<TEdgeStump*>&>(g.data_align.data_vertex);
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    return const_cast<String<TEdgeStump*>&>(g.data_align.data_vertex);
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -346,10 +301,10 @@ _getVertexString(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) {
 template<typename TStringSet, typename TCargo, typename TSpec>
 inline typename VertexIdHandler<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&
 _getVertexIdManager(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
-	return const_cast<TVertexIdManager&>(g.data_align.data_id_managerV);
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
+    return const_cast<TVertexIdManager&>(g.data_align.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -357,10 +312,10 @@ _getVertexIdManager(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) {
 template<typename TStringSet, typename TCargo, typename TSpec>
 inline typename EdgeIdHandler<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&
 _getEdgeIdManager(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
-	return const_cast<TEdgeIdManager&>(g.data_align.data_id_managerE);
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
+    return const_cast<TEdgeIdManager&>(g.data_align.data_id_managerE);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -368,15 +323,15 @@ _getEdgeIdManager(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) {
 template<typename TStringSet, typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& source,
-		   Graph<Alignment<TStringSet, TCargo, TSpec> >& dest,
-		   bool) 
+           Graph<Alignment<TStringSet, TCargo, TSpec> >& dest,
+           bool)
 {
-	SEQAN_CHECKPOINT
-	clear(dest);
-	dest.data_align = source.data_align;
-	dest.data_sequence = source.data_sequence;
-	dest.data_fragment = source.data_fragment;
-	dest.data_pvMap = source.data_pvMap;
+    SEQAN_CHECKPOINT
+    clear(dest);
+    dest.data_align = source.data_align;
+    dest.data_sequence = source.data_sequence;
+    dest.data_fragment = source.data_fragment;
+    dest.data_pvMap = source.data_pvMap;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -384,9 +339,9 @@ _copyGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& source,
 template<typename TStringSet, typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& source,
-		   Graph<Alignment<TStringSet, TCargo, TSpec> >& dest) 
+           Graph<Alignment<TStringSet, TCargo, TSpec> >& dest)
 {
-	_copyGraph(source, dest, false); // Never transpose, underlying graph is undirected
+    _copyGraph(source, dest, false); // Never transpose, underlying graph is undirected
 }
 
 
@@ -398,206 +353,206 @@ _copyGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& source,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
-inline void 
+inline void
 transpose(Graph<Alignment<TStringSet, TCargo, TSpec> > const& source,
-		  Graph<Alignment<TStringSet, TCargo, TSpec> >& dest)
+          Graph<Alignment<TStringSet, TCargo, TSpec> >& dest)
 {
-	SEQAN_CHECKPOINT
-	// Alignment graph, no transpose just copy
-	_copyGraph(source, dest, false);
+    SEQAN_CHECKPOINT
+    // Alignment graph, no transpose just copy
+    _copyGraph(source, dest, false);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
-inline void 
+inline void
 transpose(Graph<Alignment<TStringSet, TCargo, TSpec> >&)
 {
-	SEQAN_CHECKPOINT
-	// Nothing to do in an alignment graph
+    SEQAN_CHECKPOINT
+    // Nothing to do in an alignment graph
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
-inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
-numEdges(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
+numEdges(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return numEdges(g.data_align);
+    SEQAN_CHECKPOINT
+    return numEdges(g.data_align);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
-inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
-numVertices(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
+numVertices(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return numVertices(g.data_align);
+    SEQAN_CHECKPOINT
+    return numVertices(g.data_align);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
-inline bool 
-empty(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g) 
+inline bool
+empty(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return empty(g.data_align);
+    SEQAN_CHECKPOINT
+    return empty(g.data_align);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
 inline void
-clearEdges(Graph<Alignment<TStringSet, TCargo, TSpec> >& g) 
+clearEdges(Graph<Alignment<TStringSet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearEdges(g.data_align);
+    SEQAN_CHECKPOINT
+    clearEdges(g.data_align);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
 inline void
-clearVertices(Graph<Alignment<TStringSet, TCargo, TSpec> >& g) 
+clearVertices(Graph<Alignment<TStringSet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TStringSet>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename TGraph::TKey_ TKey;
-
-	clear(g.data_fragment);
-	g.data_pvMap.clear();
-	clearVertices(g.data_align);
-
-
-	// Don't forget to cover the sequences with nil vertices again
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	if(!empty(value(g.data_sequence))) {
-		TSize lenSet = length(stringSet(g));
-		for(TSize k=0; k<lenSet;++k) 
-			g.data_pvMap.insert(std::make_pair(TKey(positionToId(stringSet(g),k), length(stringSet(g)[k])), nilVertex));
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TStringSet>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename TGraph::TKey_ TKey;
+
+    clear(g.data_fragment);
+    g.data_pvMap.clear();
+    clearVertices(g.data_align);
+
+
+    // Don't forget to cover the sequences with nil vertices again
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+    if(!empty(value(g.data_sequence))) {
+        TSize lenSet = length(stringSet(g));
+        for(TSize k=0; k<lenSet;++k)
+            g.data_pvMap.insert(std::make_pair(TKey(positionToId(stringSet(g),k), length(stringSet(g)[k])), nilVertex));
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
-inline void 
-clear(Graph<Alignment<TStringSet, TCargo, TSpec> >& g) 
+inline void
+clear(Graph<Alignment<TStringSet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	// Only clear also removes the sequences
-	clear(value(g.data_sequence));
-	clearVertices(g);
+    SEQAN_CHECKPOINT
+    // Only clear also removes the sequences
+    clear(value(g.data_sequence));
+    clearVertices(g);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
-outDegree(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, 
-		  TVertexDescriptor const vertex) 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
+outDegree(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+          TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return outDegree(g.data_align, vertex);
+    SEQAN_CHECKPOINT
+    return outDegree(g.data_align, vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
-inDegree(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, 
-		 TVertexDescriptor const vertex) 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
+inDegree(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+         TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return inDegree(g.data_align, vertex);
+    SEQAN_CHECKPOINT
+    return inDegree(g.data_align, vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 degree(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-	   TVertexDescriptor const vertex) 
+       TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return degree(g.data_align, vertex);
+    SEQAN_CHECKPOINT
+    return degree(g.data_align, vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TId, typename TPos, typename TLength> 
-inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TId, typename TPos, typename TLength>
+inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 addVertex(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-		  TId id,
-		  TPos begin,
-		  TLength len)
+          TId id,
+          TPos begin,
+          TLength len)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Id<TGraph>::Type TIdType;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename TGraph::TFragmentInfo_ TFragmentInfo;
-	typedef typename TGraph::TKey_ TKey;
-	typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
-	//typedef typename TPosToVertexMap::key_type TKey;
-
-	//for(TPosToVertexMap::const_iterator p = g.data_pvMap.begin(); p != g.data_pvMap.end(); ++p) {
-	//	std::cout << p->first.first << ',' << p->first.second << ':' << p->second << std::endl;
-	//}
-
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-
-	// Store the new fragment
-	typename TPosToVertexMap::iterator interval = g.data_pvMap.lower_bound(TKey((TIdType)id, (TSize)begin + (TSize)len));
-	// Segment does not belong to Sequence anymore
-	SEQAN_ASSERT(interval != g.data_pvMap.end());
-	// Segment end must be assigned to nil so far
-	SEQAN_ASSERT(interval->second == nilVertex);
-	// Segment must belong to the whole old interval
-	SEQAN_ASSERT(*interval == *g.data_pvMap.upper_bound(TKey((TIdType)id, (TSize)begin)));
-
-	// Insert new vertex
-	TVertexDescriptor vd = addVertex(g.data_align);
-	if (length(g.data_fragment) <= vd) resize(g.data_fragment, vd + 1, Generous());
-	assignProperty(g.data_fragment, vd, TFragmentInfo(id, begin, len));
-
-	// Update position to vertex map
-	// Does the end of the new fragment coincides with the end of the interval?
-	if ( (TSize) begin + len == (TSize) interval->first.second) {
-		// Does the beginning of the new fragment coincides with the beginning of the interval?
-		if ((begin == 0) ||
-			(g.data_pvMap.find(TKey((TIdType)id, (TSize)begin)) != g.data_pvMap.end())) {
-			// Replace interval
-			interval->second = vd;
-		} else {
-			// Split interval once
-			g.data_pvMap.insert(std::make_pair(TKey(interval->first.first,(TSize)begin), interval->second));
-			g.data_pvMap.erase(interval);
-			g.data_pvMap.insert(std::make_pair(TKey((TIdType)id,(TSize)begin+len), vd));
-		}
-	} else {
-		// Does the beginning of the new fragment coincides with the beginning of the interval?
-		if ((begin == 0) ||
-			(g.data_pvMap.find(TKey((TIdType)id, (TSize)begin)) != g.data_pvMap.end())) {
-			// Split interval once
-			// Just insert here because we store interval ends
-			g.data_pvMap.insert(std::make_pair(TKey((TIdType)id,(TSize)begin+len), vd));
-		} else {
-			// Split interval twice
-			TSize tmp = interval->first.second;
-			g.data_pvMap.insert(std::make_pair(TKey(interval->first.first,begin), interval->second));
-			g.data_pvMap.erase(interval);
-			g.data_pvMap.insert(std::make_pair(TKey((TIdType)id,(TSize)begin+len), vd));
-			g.data_pvMap.insert(std::make_pair(TKey((TIdType)id,tmp), nilVertex));
-		}
-	}
-	return vd;
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Id<TGraph>::Type TIdType;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename TGraph::TFragmentInfo_ TFragmentInfo;
+    typedef typename TGraph::TKey_ TKey;
+    typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
+    //typedef typename TPosToVertexMap::key_type TKey;
+
+    //for(TPosToVertexMap::const_iterator p = g.data_pvMap.begin(); p != g.data_pvMap.end(); ++p) {
+    //    std::cout << p->first.first << ',' << p->first.second << ':' << p->second << std::endl;
+    //}
+
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+
+    // Store the new fragment
+    typename TPosToVertexMap::iterator interval = g.data_pvMap.lower_bound(TKey((TIdType)id, (TSize)begin + (TSize)len));
+    // Segment does not belong to Sequence anymore
+    SEQAN_ASSERT(interval != g.data_pvMap.end());
+    // Segment end must be assigned to nil so far
+    SEQAN_ASSERT(interval->second == nilVertex);
+    // Segment must belong to the whole old interval
+    SEQAN_ASSERT(*interval == *g.data_pvMap.upper_bound(TKey((TIdType)id, (TSize)begin)));
+
+    // Insert new vertex
+    TVertexDescriptor vd = addVertex(g.data_align);
+    if (length(g.data_fragment) <= vd) resize(g.data_fragment, vd + 1, Generous());
+    assignProperty(g.data_fragment, vd, TFragmentInfo(id, begin, len));
+
+    // Update position to vertex map
+    // Does the end of the new fragment coincides with the end of the interval?
+    if ( (TSize) begin + len == (TSize) interval->first.second) {
+        // Does the beginning of the new fragment coincides with the beginning of the interval?
+        if ((begin == 0) ||
+            (g.data_pvMap.find(TKey((TIdType)id, (TSize)begin)) != g.data_pvMap.end())) {
+            // Replace interval
+            interval->second = vd;
+        } else {
+            // Split interval once
+            g.data_pvMap.insert(std::make_pair(TKey(interval->first.first,(TSize)begin), interval->second));
+            g.data_pvMap.erase(interval);
+            g.data_pvMap.insert(std::make_pair(TKey((TIdType)id,(TSize)begin+len), vd));
+        }
+    } else {
+        // Does the beginning of the new fragment coincides with the beginning of the interval?
+        if ((begin == 0) ||
+            (g.data_pvMap.find(TKey((TIdType)id, (TSize)begin)) != g.data_pvMap.end())) {
+            // Split interval once
+            // Just insert here because we store interval ends
+            g.data_pvMap.insert(std::make_pair(TKey((TIdType)id,(TSize)begin+len), vd));
+        } else {
+            // Split interval twice
+            TSize tmp = interval->first.second;
+            g.data_pvMap.insert(std::make_pair(TKey(interval->first.first,begin), interval->second));
+            g.data_pvMap.erase(interval);
+            g.data_pvMap.insert(std::make_pair(TKey((TIdType)id,(TSize)begin+len), vd));
+            g.data_pvMap.insert(std::make_pair(TKey((TIdType)id,tmp), nilVertex));
+        }
+    }
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -605,278 +560,274 @@ addVertex(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
 template<typename TStringSet, typename TCargo, typename TSpec, typename TVD>
 inline void
 removeVertex(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-			 TVD const v)
+             TVD const v)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename TGraph::TKey_ TKey;
-	typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
-	typename TPosToVertexMap::iterator interval = (g.data_pvMap.lower_bound(TKey(sequenceId(g,v), fragmentBegin(g,v) + fragmentLength(g,v))));
-
-	// Clear the interval
-	interval->second = getNil<TVertexDescriptor>();
-	typename TPosToVertexMap::iterator interval_iter = interval;
-	if (interval_iter != g.data_pvMap.begin()) {
-		--interval_iter;
-		if ((interval_iter->second == getNil<TVertexDescriptor>()) &&
-			(interval_iter->first.first == interval->first.first)) {
-			g.data_pvMap.erase(interval_iter);
-		}
-	}
-	interval_iter = interval;
-	++interval_iter;
-	if (interval_iter != g.data_pvMap.end()) {
-		if ((interval_iter->second == getNil<TVertexDescriptor>()) &&
-			(interval_iter->first.first == interval->first.first)) {
-			g.data_pvMap.erase(interval);
-		}
-	}
-
-	// Remove the vertex
-	removeVertex(g.data_align,v);
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename TGraph::TKey_ TKey;
+    typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
+    typename TPosToVertexMap::iterator interval = (g.data_pvMap.lower_bound(TKey(sequenceId(g,v), fragmentBegin(g,v) + fragmentLength(g,v))));
+
+    // Clear the interval
+    interval->second = getNil<TVertexDescriptor>();
+    typename TPosToVertexMap::iterator interval_iter = interval;
+    if (interval_iter != g.data_pvMap.begin()) {
+        --interval_iter;
+        if ((interval_iter->second == getNil<TVertexDescriptor>()) &&
+            (interval_iter->first.first == interval->first.first)) {
+            g.data_pvMap.erase(interval_iter);
+        }
+    }
+    interval_iter = interval;
+    ++interval_iter;
+    if (interval_iter != g.data_pvMap.end()) {
+        if ((interval_iter->second == getNil<TVertexDescriptor>()) &&
+            (interval_iter->first.first == interval->first.first)) {
+            g.data_pvMap.erase(interval);
+        }
+    }
+
+    // Remove the vertex
+    removeVertex(g.data_align,v);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename EdgeDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
-addEdge(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target) 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename EdgeDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
+addEdge(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target)
 {
-	SEQAN_CHECKPOINT
-	return addEdge(g.data_align, source, target);
+    SEQAN_CHECKPOINT
+    return addEdge(g.data_align, source, target);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TCargo2> 
-inline typename EdgeDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
-addEdge(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target,
-		TCargo2 const cargo) 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TCargo2>
+inline typename EdgeDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
+addEdge(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target,
+        TCargo2 const cargo)
 {
-	SEQAN_CHECKPOINT
-	return addEdge(g.data_align, source, target, cargo);
+    SEQAN_CHECKPOINT
+    return addEdge(g.data_align, source, target, cargo);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeEdge(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, 
-		   TVertexDescriptor const source, 
-		   TVertexDescriptor const target) 
+inline void
+removeEdge(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
+           TVertexDescriptor const source,
+           TVertexDescriptor const target)
 {
-	SEQAN_CHECKPOINT
-	removeEdge(g.data_align, source, target);
+    SEQAN_CHECKPOINT
+    removeEdge(g.data_align, source, target);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline void 
+inline void
 removeEdge(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-		   TEdgeDescriptor const edge)
+           TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	removeEdge(g.data_align, sourceVertex(g.data_align,edge), targetVertex(g.data_align,edge));
+    SEQAN_CHECKPOINT
+    removeEdge(g.data_align, sourceVertex(g.data_align,edge), targetVertex(g.data_align,edge));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
-removeOutEdges(Graph<Alignment<TStringSet, TCargo, TSpec> >& g, 
-			   TVertexDescriptor const v) 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeOutEdges(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
+               TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	removeOutEdges(g.data_align, v);
+    SEQAN_CHECKPOINT
+    removeOutEdges(g.data_align, v);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
 removeInEdges(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-			  TVertexDescriptor const v) 
+              TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	removeInEdges(g.data_align,v);
+    SEQAN_CHECKPOINT
+    removeInEdges(g.data_align,v);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TEdgeDescriptor> 
-inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
+inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 targetVertex(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return targetVertex(g.data_align, edge);
+    SEQAN_CHECKPOINT
+    return targetVertex(g.data_align, edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 sourceVertex(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return sourceVertex(g.data_align, edge);
+    SEQAN_CHECKPOINT
+    return sourceVertex(g.data_align, edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TMatrix>
 inline void
-getAdjacencyMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g, 
-				   TMatrix& mat) 
+getAdjacencyMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+                   TMatrix& mat)
 {
-	SEQAN_CHECKPOINT
-	getAdjacencyMatrix(g.data_align, mat);
+    SEQAN_CHECKPOINT
+    getAdjacencyMatrix(g.data_align, mat);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename EdgeDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
+inline typename EdgeDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 findEdge(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-		 TVertexDescriptor const v,
-		 TVertexDescriptor const w)
+         TVertexDescriptor const v,
+         TVertexDescriptor const w)
 {
-	SEQAN_CHECKPOINT
-	return findEdge(g.data_align, v, w);
+    SEQAN_CHECKPOINT
+    return findEdge(g.data_align, v, w);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TIDString>
+template <typename TFile, typename TStringSet, typename TCargo, typename TSpec>
 inline void
 write(TFile & target,
-	  Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-	  TIDString const &,
-	  Raw)
+      Graph<Alignment<TStringSet, TCargo, TSpec> > const& g)
 {
 //IOREV _nodoc_ specialization not documented (at least not obviously)
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename TGraph::TFragmentInfo_ TSegment;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-
-	String<char> align;
-	if (!convertAlignment(g, align)) {
-		streamPut(target,"Adjacency list:\n");
-		TIterConst it = begin(g.data_align.data_vertex, Standard());
-		TIterConst itEnd = end(g.data_align.data_vertex, Standard());
-		TVertexDescriptor pos = 0;
-		for(;it!=itEnd; ++it, ++pos) {
-			if (!idInUse(g.data_align.data_id_managerV, pos)) continue;
-			TVertexDescriptor sourceV = pos;
-			streamPut(target, (int)sourceV);
-			TSegment seg = getProperty(g.data_fragment, sourceV);
-			streamPut(target," (SeqId:");
-			streamPut(target, (int)seg.data_seq_id);
-			streamPut(target," ,Begin:");
-			streamPut(target, (int)seg.data_begin);
-			streamPut(target," ,Length:");
-			streamPut(target, (int)seg.data_length);
-			streamPut(target,") -> ");
-			TEdgeStump* current = *it;
-			while(current!=0) {
-				TVertexDescriptor adjV = getTarget(current);
-				if (adjV != sourceV) {
-					streamPut(target, (int)adjV);
-					streamPut(target, ',');
-					current=getNextS(current);
-				} else {
-					adjV = getSource(current);
-					streamPut(target, (int)adjV);
-					streamPut(target, ',');
-					current=getNextT(current);
-				}
-			}
-			streamPut(target, '\n');
-		}
-		streamPut(target,"Edge list:\n");
-		it = begin(g.data_align.data_vertex, Standard());
-		pos = 0;
-		for(;it!=itEnd; ++it, ++pos) {
-			TVertexDescriptor sourceV = pos;
-			TEdgeStump* current = *it;
-			while(current!=0) {
-				TVertexDescriptor targetV = getTarget(current);
-				if (sourceV != targetV) {
-					streamPut(target,"Source: ");
-					streamPut(target, (int)sourceV);
-					streamPut(target, ',');
-					streamPut(target,"Target: ");
-					streamPut(target, (int)targetV);
-					streamPut(target, ' ');
-					streamPut(target,"(Id: ");
-					streamPut(target, (int)_getId(current));
-					streamPut(target, ')');
-					streamPut(target, '\n');
-					current=getNextS(current);
-				} else {
-					current=getNextT(current);
-				}
-			}
-		}
-	} else {
-		TSize nseq = length(stringSet(g));
-		TSize colLen = length(align) / nseq;
-		
-		TSize baseCount=0;
-		TSize leftSpace=6;
-		TSize xPos = 0;
-		streamPut(target,"Alignment matrix:\n");
-		while (xPos < colLen) {
-			TSize windowSize = 50;
-			if ((xPos + windowSize)>colLen) windowSize = colLen - xPos;
-			
-			// Print header line
-			TSize offset=0;
-			// Larger numbers need to be further left
-			if (baseCount != 0) offset = (unsigned int) floor(log((double)baseCount) / log((double)10));
-			for(TSize j = 0;j<leftSpace-offset;++j) streamPut(target, ' ');
-			streamPut(target, (int)baseCount);
-			baseCount+=windowSize;
-			streamPut(target, ' ');
-			for(TSize col = 1;col<=windowSize;++col) {
-				if ((col % 10)==0) streamPut(target, ':');
-				else if ((col % 5)==0) streamPut(target, '.');
-				else streamPut(target, ' ');
-			}
-			streamPut(target, ' ');
-			streamPut(target, '\n');
-
-			// Print sequences
-			for(TSize row=0;row<2*nseq-1;++row) {
-				for(TSize col = 0;col<leftSpace+2;++col) streamPut(target, ' ');
-				if ((row % 2)==0) {
-					for(TSize col = xPos;col<xPos+windowSize;++col) 
-						streamPut(target, align[(row/2)*colLen+col]);
-				} else {
-					for(TSize col = xPos;col<xPos+windowSize;++col) {
-						if ((align[((row-1)/2)*colLen + col] != gapValue<char>()) &&
-							(align[((row+1)/2)*colLen + col] != gapValue<char>()) &&
-							(align[((row-1)/2)*colLen + col] == align[((row+1)/2)*colLen + col])) 
-							streamPut(target, '|');
-						else streamPut(target, ' ');
-					}
-				}
-				streamPut(target, '\n');
-			}
-			streamPut(target, '\n');
-			xPos+=windowSize;
-		}
-		streamPut(target, '\n');
-	}
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename TGraph::TFragmentInfo_ TSegment;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+
+    String<char> align;
+    if (!convertAlignment(g, align)) {
+        write(target,"Adjacency list:\n");
+        TIterConst it = begin(g.data_align.data_vertex, Standard());
+        TIterConst itEnd = end(g.data_align.data_vertex, Standard());
+        TVertexDescriptor pos = 0;
+        for(;it!=itEnd; ++it, ++pos) {
+            if (!idInUse(g.data_align.data_id_managerV, pos)) continue;
+            TVertexDescriptor sourceV = pos;
+            appendNumber(target, (int)sourceV);
+            TSegment seg = getProperty(g.data_fragment, sourceV);
+            write(target," (SeqId:");
+            appendNumber(target, (int)seg.data_seq_id);
+            write(target," ,Begin:");
+            appendNumber(target, (int)seg.data_begin);
+            write(target," ,Length:");
+            appendNumber(target, (int)seg.data_length);
+            write(target,") -> ");
+            TEdgeStump* current = *it;
+            while(current!=0) {
+                TVertexDescriptor adjV = getTarget(current);
+                if (adjV != sourceV) {
+                    appendNumber(target, (int)adjV);
+                    writeValue(target, ',');
+                    current=getNextS(current);
+                } else {
+                    adjV = getSource(current);
+                    appendNumber(target, (int)adjV);
+                    writeValue(target, ',');
+                    current=getNextT(current);
+                }
+            }
+            writeValue(target, '\n');
+        }
+        write(target,"Edge list:\n");
+        it = begin(g.data_align.data_vertex, Standard());
+        pos = 0;
+        for(;it!=itEnd; ++it, ++pos) {
+            TVertexDescriptor sourceV = pos;
+            TEdgeStump* current = *it;
+            while(current!=0) {
+                TVertexDescriptor targetV = getTarget(current);
+                if (sourceV != targetV) {
+                    write(target,"Source: ");
+                    appendNumber(target, (int)sourceV);
+                    write(target, ",Target: ");
+                    appendNumber(target, (int)targetV);
+                    write(target, " (Id: ");
+                    appendNumber(target, (int)_getId(current));
+                    write(target, ")\n");
+                    current=getNextS(current);
+                } else {
+                    current=getNextT(current);
+                }
+            }
+        }
+    } else {
+        TSize nseq = length(stringSet(g));
+        TSize colLen = length(align) / nseq;
+
+        TSize baseCount=0;
+        TSize leftSpace=6;
+        TSize xPos = 0;
+        write(target,"Alignment matrix:\n");
+        while (xPos < colLen) {
+            TSize windowSize = 50;
+            if ((xPos + windowSize)>colLen) windowSize = colLen - xPos;
+
+            // Print header line
+            TSize offset=0;
+            // Larger numbers need to be further left
+            if (baseCount != 0) offset = (unsigned int) floor(log((double)baseCount) / log((double)10));
+            for(TSize j = 0;j<leftSpace-offset;++j) writeValue(target, ' ');
+            appendNumber(target, (int)baseCount);
+            baseCount+=windowSize;
+            writeValue(target, ' ');
+            for(TSize col = 1;col<=windowSize;++col) {
+                if ((col % 10)==0) writeValue(target, ':');
+                else if ((col % 5)==0) writeValue(target, '.');
+                else writeValue(target, ' ');
+            }
+            write(target, " \n");
+
+            // Print sequences
+            for(TSize row=0;row<2*nseq-1;++row) {
+                for(TSize col = 0;col<leftSpace+2;++col)
+                    writeValue(target, ' ');
+                if ((row % 2)==0) {
+                    for(TSize col = xPos;col<xPos+windowSize;++col)
+                        writeValue(target, align[(row/2)*colLen+col]);
+                } else {
+                    for(TSize col = xPos;col<xPos+windowSize;++col) {
+                        if ((align[((row-1)/2)*colLen + col] != gapValue<char>()) &&
+                            (align[((row+1)/2)*colLen + col] != gapValue<char>()) &&
+                            (align[((row-1)/2)*colLen + col] == align[((row+1)/2)*colLen + col]))
+                            writeValue(target, '|');
+                        else
+                            writeValue(target, ' ');
+                    }
+                }
+                writeValue(target, '\n');
+            }
+            writeValue(target, '\n');
+            xPos+=windowSize;
+        }
+        writeValue(target, '\n');
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -884,34 +835,36 @@ write(TFile & target,
 template <typename TFile, typename TSpec, typename TNames>
 inline void
 write(TFile & file,
-	  Graph<TSpec> const& g,
-	  TNames const& names,
-	  FastaFormat) 
+      Graph<TSpec> const& g,
+      TNames const& names,
+      FastaFormat)
 {
 //IOREV _nodoc_ specialization not documented
-	SEQAN_CHECKPOINT
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-
-	String<char> align;
-	if (convertAlignment(g, align)) {	
-		TSize nseq = length(stringSet(g));
-		TSize colLen = length(align) / nseq;
-		typedef typename Iterator<String<char>, Standard>::Type TIter;
-		TIter it = begin(align, Standard());
-		for(TSize i = 0; i<nseq; ++i) {
-			streamPut(file, '>');
-			streamPut(file,names[i]);
-			streamPut(file, '\n');
-			TSize col = 0;
-			while(col < colLen) {
-				TSize max = ((colLen - col) < 60) ? colLen - col : 60;
-				for(TSize finger = 0; finger<max; ++finger, ++col, ++it) 
-					streamPut(file, *it);
-				streamPut(file, '\n');
-			}
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+
+    typename DirectionIterator<TFile, Output>::Type target = directionIterator(file, Output());
+
+    String<char> align;
+    if (convertAlignment(g, align)) {
+        TSize nseq = length(stringSet(g));
+        TSize colLen = length(align) / nseq;
+        typedef typename Iterator<String<char>, Standard>::Type TIter;
+        TIter it = begin(align, Standard());
+        for(TSize i = 0; i<nseq; ++i) {
+            writeValue(target, '>');
+            write(target,names[i]);
+            writeValue(target, '\n');
+            TSize col = 0;
+            while(col < colLen) {
+                TSize max = ((colLen - col) < 60) ? colLen - col : 60;
+                for(TSize finger = 0; finger<max; ++finger, ++col, ++it)
+                    writeValue(target, *it);
+                writeValue(target, '\n');
+            }
+        }
+    }
 }
 
 
@@ -921,65 +874,64 @@ write(TFile & file,
 template <typename TFile, typename TSpec, typename TNames>
 inline void
 write(TFile & file,
-	  Graph<TSpec> const& g,
-	  TNames const& names,
-	  MsfFormat) 
+      Graph<TSpec> const& g,
+      TNames const& names,
+      MsfFormat)
 {
 //IOREV _nodoc_ specialization not documented
-	SEQAN_CHECKPOINT
-	typedef Graph<TSpec> TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-
-	String<char> align;
-	if (convertAlignment(g, align)) {	
-		TSize nseq = length(stringSet(g));
-		TSize colLen = length(align) / nseq;
-	
-		streamPut(file,"PileUp\n");
-		streamPut(file, '\n');
-		streamPut(file," MSF: ");
-		streamPut(file, (unsigned)colLen);
-		streamPut(file," Type: P");
-		streamPut(file," Check: 0 ..");
-		streamPut(file, '\n');
-		streamPut(file, '\n');
-		TSize offset = 0;
-		for(TSize i = 0; i<nseq; ++i) {
-			streamPut(file," Name: ");
-			streamPut(file,names[i]);
-			streamPut(file," oo  Len:  ");
-			TSize len = length(names[i]);
-			if (len > offset) offset = len;
-			streamPut(file, (unsigned)colLen);
-			streamPut(file," Check: 0");
-			streamPut(file," Weight: 1.00");
-			streamPut(file, '\n');
-		}
-		offset += 5;
-		streamPut(file, '\n');
-		streamPut(file,"//\n");
-		streamPut(file, '\n');
-		streamPut(file, '\n');
-		TSize col = 0;
-		while(col < colLen) {
-			TSize max = 0;
-			for(TSize i = 0; i<nseq; ++i) {
-				max = ((colLen - col) < 50) ? colLen - col : 50;
-				streamPut(file,names[i]);
-				for(TSize j = 0; j<offset - length(names[i]); ++j) 
-					streamPut(file, ' ');
-				for(TSize finger = col; finger<col+max; ++finger) {
-					if ((finger - col) % 10 == 0) streamPut(file, ' ');
-					if (align[i*colLen + finger] == '-') streamPut(file, '.');
-					else streamPut(file, align[i*colLen + finger]);
-				}
-				streamPut(file, '\n');
-			}
-			col += max;
-			streamPut(file, '\n');
-			streamPut(file, '\n');
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<TSpec> TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+
+    typename DirectionIterator<TFile, Output>::Type target = directionIterator(file, Output());
+
+    String<char> align;
+    if (convertAlignment(g, align)) {
+        TSize nseq = length(stringSet(g));
+        TSize colLen = length(align) / nseq;
+
+        write(target,"PileUp\n");
+        writeValue(target, '\n');
+        write(target," MSF: ");
+        appendNumber(target, (unsigned)colLen);
+        write(target," Type: P Check: 0 ..\n\n");
+        TSize offset = 0;
+        for(TSize i = 0; i<nseq; ++i) {
+            write(target," Name: ");
+            write(target,names[i]);
+            write(target," oo  Len:  ");
+            TSize len = length(names[i]);
+            if (len > offset) offset = len;
+            appendNumber(target, (unsigned)colLen);
+            write(target," Check: 0");
+            write(target," Weight: 1.00");
+            writeValue(target, '\n');
+        }
+        offset += 5;
+        writeValue(target, '\n');
+        write(target, "//\n");
+        writeValue(target, '\n');
+        writeValue(target, '\n');
+        TSize col = 0;
+        while(col < colLen) {
+            TSize max = 0;
+            for(TSize i = 0; i<nseq; ++i) {
+                max = ((colLen - col) < 50) ? colLen - col : 50;
+                write(target,names[i]);
+                for(TSize j = 0; j<offset - length(names[i]); ++j)
+                    writeValue(target, ' ');
+                for(TSize finger = col; finger<col+max; ++finger) {
+                    if ((finger - col) % 10 == 0) writeValue(target, ' ');
+                    if (align[i*colLen + finger] == '-') writeValue(target, '.');
+                    else writeValue(target, align[i*colLen + finger]);
+                }
+                writeValue(target, '\n');
+            }
+            col += max;
+            writeValue(target, '\n');
+            writeValue(target, '\n');
+        }
+    }
 }
 
 
@@ -987,20 +939,20 @@ write(TFile & file,
 template <typename TFile, typename TStringSet, typename TSpec, typename TEdge>
 inline void
 _writeCargo(TFile & file,
-			 Graph<Alignment<TStringSet, void, TSpec> > const&,
-			 TEdge const&)
+             Graph<Alignment<TStringSet, void, TSpec> > const&,
+             TEdge const&)
 {
-	streamPut(file, 0);
+    appendNumber(file, 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 template <typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TEdge>
 inline void
 _writeCargo(TFile & file,
-			 Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
-			 TEdge const& edge)
+             Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
+             TEdge const& edge)
 {
-	streamPut(file, (int)getCargo(edge));
+    appendNumber(file, (int)getCargo(edge));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1009,118 +961,111 @@ _writeCargo(TFile & file,
 template <typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TNames>
 inline void
 write(TFile & file,
-	  Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-	  TNames const& names,
-	  CgVizFormat)
+      Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+      TNames const& names,
+      CgVizFormat)
 {
 //IOREV _nodoc_ specialization not documented
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Id<TGraph>::Type TId;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*> const, Rooted>::Type TIterConst;
-
-	TStringSet& str = stringSet(g);
-	TSize nseq = length(str);
-
-	streamPut(file,"{DATA Data\n");
-	streamPut(file,"\t[__GLOBAL__] tracks=");
-	streamPut(file, nseq);
-	streamPut(file, '\n');
-	for(TSize i = 0; i<nseq; ++i) {
-		streamPut(file,"\tfasta_id=\"");
-		streamPut(file,names[i]);
-		streamPut(file,"\" sequence=\"");
-		streamPut(file,str[i]);
-		streamPut(file,"\" track=");
-		streamPut(file, i);
-		streamPut(file," type=\"");
-		streamPut(file,"DNA");
-		streamPut(file,"\": ");
-		streamPut(file, 0);
-		streamPut(file, ' ');
-		streamPut(file, length(str[i])- 1);
-		streamPut(file, '\n');
-	}
-	streamPut(file,"}\n");
-	for(TSize i = 0; i<nseq; ++i) {
-		streamPut(file,"{DATA ");
-		streamPut(file, i);
-		//streamPut(file,names[i]);
-		streamPut(file,"-seqlen\n");
-		streamPut(file,"\t[__GLOBAL__]\n");
-		streamPut(file,"\tlength=");
-		streamPut(file, length(str[i]));
-		streamPut(file,":\t");
-		streamPut(file, 0);
-		streamPut(file, ' ');
-		streamPut(file, length(str[i])- 1);
-		streamPut(file, '\n');
-		streamPut(file,"}\n");
-	}
-	for(TSize i=0; i<nseq; ++i) {
-		for(TSize j=i+1; j<nseq; ++j) {
-			streamPut(file,"{DATA ");
-			streamPut(file, i);
-			//streamPut(file,names[i]);
-			streamPut(file,"-vs-");
-			streamPut(file, j);
-			//streamPut(file,names[j]);
-			streamPut(file, '\n');
-			streamPut(file,"\t[__GLOBAL__]\n");
-			for(TIterConst it = begin(g.data_align.data_vertex);!atEnd(it);goNext(it)) {
-				TVertexDescriptor sourceV = position(it);
-				TId id1 = sequenceId(g, sourceV);
-				if ((positionToId(str, id1) != i) &&
-					(positionToId(str, id1) != j)) continue;
-				TEdgeStump* current = getValue(it);
-				while(current!=0) {
-					TVertexDescriptor targetV = getTarget(current);
-					TId id2 = sequenceId(g, targetV);
-					if (sourceV != targetV) {
-						if ((positionToId(str, id2) != i) &&
-							(positionToId(str, id2) != j)) {
-								current=getNextS(current);
-								continue;
-						}
-						streamPut(file,"\t");
-						streamPut(file,"source=");
-						streamPut(file, (int)sourceV);		
-						streamPut(file, ' ');
-						streamPut(file,"target=");
-						streamPut(file, (int)targetV);
-						streamPut(file, ' ');
-						streamPut(file,"edgeId=");
-						streamPut(file, (int)_getId(current));
-						streamPut(file, ' ');
-						streamPut(file,"cargo=");
-						_writeCargo(file,g,current);
-						streamPut(file, ' ');
-						streamPut(file,"label=");
-						streamPut(file,label(g,sourceV));
-						streamPut(file, ' ');
-						streamPut(file,"labelOpp=");
-						streamPut(file,label(g,targetV));
-						streamPut(file, ':');
-						streamPut(file, '\t');
-						streamPut(file, (int)fragmentBegin(g, sourceV));
-						streamPut(file, ' ');
-						streamPut(file, (int)fragmentBegin(g, targetV));
-						streamPut(file, ' ');
-                        streamPut(file, (int)(fragmentBegin(g, sourceV) + fragmentLength(g, sourceV)));
-						streamPut(file, ' ');
-                        streamPut(file, (int)(fragmentBegin(g, targetV) + fragmentLength(g, targetV)));
-						streamPut(file, '\n');
-						current=getNextS(current);
-					} else {
-						current=getNextT(current);
-					}
-				}
-			}
-			streamPut(file,"}\n");	
-		}
-	}
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Id<TGraph>::Type TId;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*> const, Rooted>::Type TIterConst;
+
+    typename DirectionIterator<TFile, Output>::Type target = directionIterator(file, Output());
+
+    TStringSet& str = stringSet(g);
+    TSize nseq = length(str);
+
+    write(target, "{DATA Data\n");
+    write(target, "\t[__GLOBAL__] tracks=");
+    appendNumber(target, nseq);
+    writeValue(target, '\n');
+    for(TSize i = 0; i<nseq; ++i) {
+        write(target, "\tfasta_id=\"");
+        write(target,names[i]);
+        write(target, "\" sequence=\"");
+        write(target,str[i]);
+        write(target, "\" track=");
+        appendNumber(target, i);
+        write(target, " type=\"DNA\": 0 ");
+        appendNumber(target, length(str[i])- 1);
+        writeValue(target, '\n');
+    }
+    write(target, "}\n");
+    for(TSize i = 0; i<nseq; ++i) {
+        write(target, "{DATA ");
+        appendNumber(target, i);
+        //write(target,names[i]);
+        write(target, "-seqlen\n\t[__GLOBAL__]\n\tlength=");
+        appendNumber(target, length(str[i]));
+        write(target, ":\t0 ");
+        appendNumber(target, length(str[i])- 1);
+        write(target, "\n}\n");
+    }
+    for(TSize i=0; i<nseq; ++i) {
+        for(TSize j=i+1; j<nseq; ++j) {
+            write(target, "{DATA ");
+            appendNumber(target, i);
+            //write(target,names[i]);
+            write(target, "-vs-");
+            appendNumber(target, j);
+            //write(target,names[j]);
+            writeValue(target, '\n');
+            write(target, "\t[__GLOBAL__]\n");
+            for(TIterConst it = begin(g.data_align.data_vertex);!atEnd(it);goNext(it)) {
+                TVertexDescriptor sourceV = position(it);
+                TId id1 = sequenceId(g, sourceV);
+                if ((positionToId(str, id1) != i) &&
+                    (positionToId(str, id1) != j)) continue;
+                TEdgeStump* current = getValue(it);
+                while(current!=0) {
+                    TVertexDescriptor targetV = getTarget(current);
+                    TId id2 = sequenceId(g, targetV);
+                    if (sourceV != targetV) {
+                        if ((positionToId(str, id2) != i) &&
+                            (positionToId(str, id2) != j)) {
+                                current=getNextS(current);
+                                continue;
+                        }
+                        write(target, "\t");
+                        write(target, "source=");
+                        appendNumber(target, (int)sourceV);
+                        writeValue(target, ' ');
+                        write(target, "target=");
+                        appendNumber(target, (int)targetV);
+                        writeValue(target, ' ');
+                        write(target, "edgeId=");
+                        appendNumber(target, (int)_getId(current));
+                        writeValue(target, ' ');
+                        write(target, "cargo=");
+                        _writeCargo(target,g,current);
+                        writeValue(target, ' ');
+                        write(target, "label=");
+                        write(target,label(g,sourceV));
+                        writeValue(target, ' ');
+                        write(target, "labelOpp=");
+                        write(target,label(g,targetV));
+                        writeValue(target, ':');
+                        writeValue(target, '\t');
+                        appendNumber(target, (int)fragmentBegin(g, sourceV));
+                        writeValue(target, ' ');
+                        appendNumber(target, (int)fragmentBegin(g, targetV));
+                        writeValue(target, ' ');
+                        appendNumber(target, (int)(fragmentBegin(g, sourceV) + fragmentLength(g, sourceV)));
+                        writeValue(target, ' ');
+                        appendNumber(target, (int)(fragmentBegin(g, targetV) + fragmentLength(g, targetV)));
+                        writeValue(target, '\n');
+                        current=getNextS(current);
+                    } else {
+                        current=getNextT(current);
+                    }
+                }
+            }
+            write(target, "}\n");
+        }
+    }
 }
 
 
@@ -1139,36 +1084,23 @@ write(TFile & file,
  * @see AlignmentGraph#stringSet
  */
 
-/**
-.Function.assignStringSet
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Assigns a new string set to an alignment graph.
-..signature:assignStringSet(g, str)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.str:A string set.
-..see:Function.getStringSet
-..see:Function.stringSet
-..include:seqan/graph_align.h
-*/
 template<typename TString, typename TDefault, typename TCargo, typename TSpec, typename TDefault2>
 inline void
 assignStringSet(Graph<Alignment<StringSet<TString, Dependent<TDefault> >, TCargo, TSpec> >& g,
-				StringSet<TString, Dependent<TDefault2> > const& sStr)
+                StringSet<TString, Dependent<TDefault2> > const& sStr)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<StringSet<TString, Dependent<TDefault> >, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename TGraph::TKey_ TKey;
-	typedef typename Size<TGraph>::Type TSize;
-
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	clear(g);
-	g.data_sequence = (StringSet<TString, Dependent<TDefault> >) sStr;
-	TSize lenSet = length(sStr);
-	for(TSize k=0; k<lenSet;++k) 
-		g.data_pvMap.insert(std::make_pair(TKey(positionToId(sStr,k), length(sStr[k])), nilVertex));
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<StringSet<TString, Dependent<TDefault> >, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename TGraph::TKey_ TKey;
+    typedef typename Size<TGraph>::Type TSize;
+
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+    clear(g);
+    g.data_sequence = (StringSet<TString, Dependent<TDefault> >) sStr;
+    TSize lenSet = length(sStr);
+    for(TSize k=0; k<lenSet;++k)
+        g.data_pvMap.insert(std::make_pair(TKey(positionToId(sStr,k), length(sStr[k])), nilVertex));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1176,11 +1108,11 @@ assignStringSet(Graph<Alignment<StringSet<TString, Dependent<TDefault> >, TCargo
 template<typename TString, typename TDefault, typename TCargo, typename TSpec, typename TDefault2>
 inline void
 assignStringSet(Graph<Alignment<StringSet<TString, Dependent<TDefault> >, TCargo, TSpec> >& g,
-				StringSet<TString, Owner<TDefault2> > const& sStr)
+                StringSet<TString, Owner<TDefault2> > const& sStr)
 {
-	SEQAN_CHECKPOINT
-	StringSet<TString, Dependent<> > depStr(sStr);
-	assignStringSet(g, depStr);
+    SEQAN_CHECKPOINT
+    StringSet<TString, Dependent<> > depStr(sStr);
+    assignStringSet(g, depStr);
 }
 
 
@@ -1200,25 +1132,12 @@ assignStringSet(Graph<Alignment<StringSet<TString, Dependent<TDefault> >, TCargo
  * @see AlignmentGraph#stringSet
  */
 
-/**
-.Function.getStringSet
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Gets the string set of an alignment graph.
-..signature:getStringSet(g)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..returns:A string set.
-..see:Function.assignStringSet
-..see:Function.stringSet
-..include:seqan/graph_align.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec>
 inline typename Host<Graph<Alignment<TStringSet, TCargo, TSpec> > const>::Type&
 getStringSet(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return value(g.data_sequence);
+    SEQAN_CHECKPOINT
+    return value(g.data_sequence);
 }
 
 
@@ -1238,27 +1157,13 @@ getStringSet(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g)
  * @see AlignmentGraph#getStringSet
  */
 
-/**
-.Function.stringSet
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Gets the string set of an alignment graph.
-..signature:stringSet(g)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..returns:A reference or temporary of @Class.StringSet.string set@ type.
-..see:Function.assignStringSet
-..see:Function.getStringSet
-..include:seqan/graph_align.h
-*/
-
 template <typename T>
 struct StringSetType;
 
 template <typename TStringSet, typename TCargo, typename TSpec>
 struct StringSetType<Graph<Alignment<TStringSet, TCargo, TSpec> > >
 {
-	typedef typename Host<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type & Type;
+    typedef typename Host<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type & Type;
 };
 
 
@@ -1266,8 +1171,8 @@ template<typename TStringSet, typename TCargo, typename TSpec>
 inline typename StringSetType<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 stringSet(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return const_cast<TStringSet&>(value(g.data_sequence));
+    SEQAN_CHECKPOINT
+    return const_cast<TStringSet&>(value(g.data_sequence));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1284,34 +1189,21 @@ stringSet(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g)
  * @return TInfix An infix representing the sequence label.
  */
 
-/**
-.Function.label
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Gets the label that is associated with this vertex descriptor.
-..signature:label(g, v)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:An infix representing the sequence label.
-..include:seqan/graph_align.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline typename Infix<typename Value<TStringSet>::Type>::Type
 label(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-	  TVertexDescriptor const v)
+      TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename TGraph::TFragmentInfo_ TSegment;
-	TSegment seg = getProperty(g.data_fragment, v);
-	//std::cout << seg.data_seq_id << ",";
-	//std::cout << seg.data_begin << ",";
-	//std::cout << seg.data_length << ",";
-	//std::cout << getValueById(value(g.data_sequence), seg.data_seq_id) << std::endl;
-	//std::cout << infix(getValueById(value(g.data_sequence), seg.data_seq_id), seg.data_begin, seg.data_begin + seg.data_length) << std::endl;
-	return infix(getValueById(value(g.data_sequence), seg.data_seq_id), seg.data_begin, seg.data_begin + seg.data_length);
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename TGraph::TFragmentInfo_ TSegment;
+    TSegment seg = getProperty(g.data_fragment, v);
+    //std::cout << seg.data_seq_id << ",";
+    //std::cout << seg.data_begin << ",";
+    //std::cout << seg.data_length << ",";
+    //std::cout << getValueById(value(g.data_sequence), seg.data_seq_id) << std::endl;
+    //std::cout << infix(getValueById(value(g.data_sequence), seg.data_seq_id), seg.data_begin, seg.data_begin + seg.data_length) << std::endl;
+    return infix(getValueById(value(g.data_sequence), seg.data_seq_id), seg.data_begin, seg.data_begin + seg.data_length);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1328,26 +1220,13 @@ label(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
  * @return TId The sequence id.
  */
 
-/**
-.Function.sequenceId
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Gets the sequence id that is associated with this vertex descriptor or with a sequence of a fragment.
-..signature:sequenceId(g, v)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:The sequence id.
-..include:seqan/graph_align.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline typename Id<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&
 sequenceId(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-		   TVertexDescriptor const v)
+           TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	return const_cast<typename Id<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&>(g.data_fragment[v].data_seq_id);
+    SEQAN_CHECKPOINT
+    return const_cast<typename Id<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&>(g.data_fragment[v].data_seq_id);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1364,26 +1243,13 @@ sequenceId(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
  * @return TPos The begin position.
  */
 
-/**
-.Function.fragmentBegin
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Gets the begin position for this fragment or this vertex descriptor in the sequence.
-..signature:fragmentBegin(g, v)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:The begin position.
-..include:seqan/graph_align.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline typename Position<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&
 fragmentBegin(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-			  TVertexDescriptor const v)
+              TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	return const_cast<typename Position<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&>(g.data_fragment[v].data_begin);
+    SEQAN_CHECKPOINT
+    return const_cast<typename Position<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&>(g.data_fragment[v].data_begin);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1400,26 +1266,13 @@ fragmentBegin(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
  * @return TPos The fragment size.
  */
 
-/**
-.Function.fragmentLength
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Gets the length of the label of a given vertex descriptor in the sequence.
-..signature:fragmentLength(g, v)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:The length of the fragment represented by this vertex descriptor.
-..include:seqan/graph_align.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&
 fragmentLength(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-			   TVertexDescriptor const v)
+               TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	return const_cast<typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&>(g.data_fragment[v].data_length);
+    SEQAN_CHECKPOINT
+    return const_cast<typename Size<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type&>(g.data_fragment[v].data_length);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1438,33 +1291,20 @@ fragmentLength(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
  * <tt>getNil&lt;TVertexDescriptor&gt;()</tt> if none could be found.
  */
 
-/**
-.Function.findVertex
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Finds a vertex given a sequence id and a position.
-..signature:findVertex(g, id, pos)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.id:A sequence id.
-..param.pos:A position.
-..returns:The vertex covering the given position on the specified sequence, $getNil<TVertexDescriptor>()$ if none could be found.
-..include:seqan/graph_align.h
-*/
-template<typename TStringSet, typename TCargo, typename TSpec, typename TSeqId, typename TPos> 
-inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TSeqId, typename TPos>
+inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 findVertex(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-		   TSeqId id,
-		   TPos pos)
+           TSeqId id,
+           TPos pos)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename TGraph::TKey_ TKey;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Id<TGraph>::Type TIdType;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	
-	return (pos >= (TPos) length(getValueById(stringSet(g),id))) ? getNil<TVertexDescriptor>() : g.data_pvMap.upper_bound(TKey((TIdType)id, (TSize)pos))->second;
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename TGraph::TKey_ TKey;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Id<TGraph>::Type TIdType;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    return (pos >= (TPos) length(getValueById(stringSet(g),id))) ? getNil<TVertexDescriptor>() : g.data_pvMap.upper_bound(TKey((TIdType)id, (TSize)pos))->second;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1482,102 +1322,95 @@ findVertex(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
  * @param[out] pos2   The reuslting position of the sequence was was projected onto.
  */
 
-/**
-.Function.getProjectedPosition
-..class:Spec.Alignment Graph
-..signature:getProjectedPosition(g,seqId,pos,seqId2,pos2)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-*/
-template<typename TStringSet, typename TCargo, typename TSpec, typename TSeqId, typename TPosition, typename TSeqId2, typename TPosition2> 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TSeqId, typename TPosition, typename TSeqId2, typename TPosition2>
 inline void
 getProjectedPosition(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-					 TSeqId const id1,
-					 TPosition const pos1,
-					 TSeqId2& id2,
-					 TPosition2& pos2)
+                     TSeqId const id1,
+                     TPosition const pos1,
+                     TSeqId2& id2,
+                     TPosition2& pos2)
 {
-	SEQAN_ASSERT(length(stringSet(g)) == 2);
-
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	TStringSet& str = stringSet(g);
-	TVertexDescriptor sV = findVertex(g, id1, pos1);
-
-	// Case 1: No projection possible
-	if (sV == getNil<TVertexDescriptor>()) {
-		if ( (TSeqId) positionToId(str, 0) == id1) id2 = (TSeqId2) positionToId(str,1);
-		else id2 = (TSeqId2) positionToId(str,0);
-		pos2 = 0;
-		return;
-	}
-
-	// Case 2: Projection is possible
-	TEdgeStump* current = getValue(g.data_align.data_vertex, sV);
-	if(current != (TEdgeStump*) 0) {
-		TVertexDescriptor tV = target(current);
-		if (tV == sV) tV = source(current);
-		pos2 = (TPosition2) (fragmentBegin(g,tV) + (pos1 - fragmentBegin(g, sV)));
-		id2 = (TSeqId2) sequenceId(g, tV);
-		return;
-	} else {
-		// If no out-going edge, get the preceding or following vertex
-		if (fragmentBegin(g, sV) == 0) {
-			getProjectedPosition(g, id1, fragmentBegin(g,sV) + fragmentLength(g, sV), id2, pos2);
-			return;
-		} else {
-			getProjectedPosition(g, id1, fragmentBegin(g,sV) - 1, id2, pos2);
-			return;
-		}
-	}
+    SEQAN_ASSERT(length(stringSet(g)) == 2);
+
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    TStringSet& str = stringSet(g);
+    TVertexDescriptor sV = findVertex(g, id1, pos1);
+
+    // Case 1: No projection possible
+    if (sV == getNil<TVertexDescriptor>()) {
+        if ( (TSeqId) positionToId(str, 0) == id1) id2 = (TSeqId2) positionToId(str,1);
+        else id2 = (TSeqId2) positionToId(str,0);
+        pos2 = 0;
+        return;
+    }
+
+    // Case 2: Projection is possible
+    TEdgeStump* current = getValue(g.data_align.data_vertex, sV);
+    if(current != (TEdgeStump*) 0) {
+        TVertexDescriptor tV = target(current);
+        if (tV == sV) tV = source(current);
+        pos2 = (TPosition2) (fragmentBegin(g,tV) + (pos1 - fragmentBegin(g, sV)));
+        id2 = (TSeqId2) sequenceId(g, tV);
+        return;
+    } else {
+        // If no out-going edge, get the preceding or following vertex
+        if (fragmentBegin(g, sV) == 0) {
+            getProjectedPosition(g, id1, fragmentBegin(g,sV) + fragmentLength(g, sV), id2, pos2);
+            return;
+        } else {
+            getProjectedPosition(g, id1, fragmentBegin(g,sV) - 1, id2, pos2);
+            return;
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TValue, typename TCargo, typename TSpec, typename TSeqId, typename TPosition, typename TSeqId2, typename TPosition2> 
+template<typename TStringSet, typename TValue, typename TCargo, typename TSpec, typename TSeqId, typename TPosition, typename TSeqId2, typename TPosition2>
 inline void
 getProjectedPosition(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-					 TValue seg_num,
-					 TSeqId const id1,
-					 TPosition const pos1,
-					 TSeqId2& id2,
-					 TPosition2& pos2)
+                     TValue seg_num,
+                     TSeqId const id1,
+                     TPosition const pos1,
+                     TSeqId2& id2,
+                     TPosition2& pos2)
 {
-	SEQAN_ASSERT(length(stringSet(g)) == 2);
-
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	TStringSet& str = stringSet(g);
-	TVertexDescriptor sV = findVertex(g, id1, pos1);
-
-	// Case 1: No projection possible
-	if (sV == getNil<TVertexDescriptor>()) {
-		if ( (TSeqId) positionToId(str, 0) == id1) id2 = (TSeqId2) positionToId(str,1);
-		else id2 = (TSeqId2) positionToId(str,0);
-		pos2 = 0;
-		return;
-	}
-
-	// Case 2: Projection is possible
-	TEdgeStump* current = getValue(g.data_align.data_vertex, sV);
-	if(current != (TEdgeStump*) 0) {
-		TVertexDescriptor tV = target(current);
-		if (seg_num == 0) tV = source(current); // segnum 0 is defined as the sourceVertex, segnum 1 is targetVertex
-		pos2 = (TPosition2) (fragmentBegin(g,tV) + (pos1 - fragmentBegin(g, sV)));
-		id2 = (TSeqId2) sequenceId(g, tV);
-		return;
-	} else {
-		// If no out-going edge, get the preceding or following vertex
-		if (fragmentBegin(g, sV) == 0) {
-			getProjectedPosition(g, seg_num, id1, fragmentBegin(g,sV) + fragmentLength(g, sV), id2, pos2);
-			return;
-		} else {
-			getProjectedPosition(g, seg_num, id1, fragmentBegin(g,sV) - 1, id2, pos2);
-			return;
-		}
-	}
+    SEQAN_ASSERT(length(stringSet(g)) == 2);
+
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    TStringSet& str = stringSet(g);
+    TVertexDescriptor sV = findVertex(g, id1, pos1);
+
+    // Case 1: No projection possible
+    if (sV == getNil<TVertexDescriptor>()) {
+        if ( (TSeqId) positionToId(str, 0) == id1) id2 = (TSeqId2) positionToId(str,1);
+        else id2 = (TSeqId2) positionToId(str,0);
+        pos2 = 0;
+        return;
+    }
+
+    // Case 2: Projection is possible
+    TEdgeStump* current = getValue(g.data_align.data_vertex, sV);
+    if(current != (TEdgeStump*) 0) {
+        TVertexDescriptor tV = target(current);
+        if (seg_num == 0) tV = source(current); // segnum 0 is defined as the sourceVertex, segnum 1 is targetVertex
+        pos2 = (TPosition2) (fragmentBegin(g,tV) + (pos1 - fragmentBegin(g, sV)));
+        id2 = (TSeqId2) sequenceId(g, tV);
+        return;
+    } else {
+        // If no out-going edge, get the preceding or following vertex
+        if (fragmentBegin(g, sV) == 0) {
+            getProjectedPosition(g, seg_num, id1, fragmentBegin(g,sV) + fragmentLength(g, sV), id2, pos2);
+            return;
+        } else {
+            getProjectedPosition(g, seg_num, id1, fragmentBegin(g,sV) - 1, id2, pos2);
+            return;
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1585,54 +1418,41 @@ getProjectedPosition(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
 /*!
  * @fn AlignmentGraph#getFirstCoveredPosition
  * @brief Finds the first position in a sequence that is not assigned to a nil vertex.
- * 
+ *
  * @signature TPos getFirstCoveredPosition(ag, id);
- * 
+ *
  * @param[in] ag An @link AlignmentGraph @endlink.
  * @param[in] id A sequence id.
- * 
+ *
  * @return TPos A sequence position.
  *
  * @see AlignmentGraph#getLastCoveredPosition
  */
 
-/**
-.Function.getFirstCoveredPosition
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Finds the first position in a sequence that is not assigned to a nil vertex.
-..signature:getFirstCoveredPosition(g, id)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.id:A sequence id.
-..returns:A sequence position
-..see:Function.getLastCoveredPosition
-..include:seqan/graph_align.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec, typename TSeqId>
 inline typename Position<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 getFirstCoveredPosition(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-						TSeqId const id)
+                        TSeqId const id)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
 
 
-	typename TPosToVertexMap::const_iterator it = g.data_pvMap.upper_bound(std::make_pair(id, 0));
+    typename TPosToVertexMap::const_iterator it = g.data_pvMap.upper_bound(std::make_pair(id, 0));
 
-	// Case 1: id is not covered
-	if (it == g.data_pvMap.end()) return length(getValueById(stringSet(g), id));
+    // Case 1: id is not covered
+    if (it == g.data_pvMap.end()) return length(getValueById(stringSet(g), id));
 
-	// Case 2: We found a nil vertex, go one forward
-	if (it->second == getNil<TVertexDescriptor>()) {
-		++it;
-		if (it == g.data_pvMap.end()) return length(getValueById(stringSet(g), id));
-	}
+    // Case 2: We found a nil vertex, go one forward
+    if (it->second == getNil<TVertexDescriptor>()) {
+        ++it;
+        if (it == g.data_pvMap.end()) return length(getValueById(stringSet(g), id));
+    }
 
-	// Now we have the right vertex, return the beginning if the sequence id still fits
-	if (it->first.first != id) return length(getValueById(stringSet(g), id));
-	else return fragmentBegin(g, it->second);
+    // Now we have the right vertex, return the beginning if the sequence id still fits
+    if (it->first.first != id) return length(getValueById(stringSet(g), id));
+    else return fragmentBegin(g, it->second);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1640,269 +1460,233 @@ getFirstCoveredPosition(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
 /*!
  * @fn AlignmentGraph#getLastCoveredPosition
  * @brief Finds the last position in a sequence that is not assigned to a nil vertex.
- * 
+ *
  * @signature TPos getLastCoveredPosition(ag, id);
- * 
+ *
  * @param[in] ag An @link AlignmentGraph @endlink.
  * @param[in] id A sequence id.
- * 
+ *
  * @return TPos A sequence position.
  *
  * @see AlignmentGraph#getFirstCoveredPosition
  */
 
-/**
-.Function.getLastCoveredPosition
-..class:Spec.Alignment Graph
-..cat:Graph
-..summary:Finds the last position in a sequence that is not assigned to a nil vertex.
-..signature:getLastCoveredPosition(g, id)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.id:A sequence id.
-..returns:A sequence position
-..see:Function.getFirstCoveredPosition
-..include:seqan/graph_align.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec, typename TSeqId>
 inline typename Position<Graph<Alignment<TStringSet, TCargo, TSpec> > >::Type
 getLastCoveredPosition(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-					   TSeqId id)
+                       TSeqId id)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
 
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	typename TPosToVertexMap::const_iterator it = g.data_pvMap.lower_bound(std::make_pair(id, length(getValueById(stringSet(g), id))));
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+    typename TPosToVertexMap::const_iterator it = g.data_pvMap.lower_bound(std::make_pair(id, length(getValueById(stringSet(g), id))));
 
-	// Case 1: No last position (all nil)
-	if ((it == g.data_pvMap.begin()) && (it->second == nilVertex)) return 0;
+    // Case 1: No last position (all nil)
+    if ((it == g.data_pvMap.begin()) && (it->second == nilVertex)) return 0;
 
-	// Case 2: Found a nil position but there is a vertex before
-	if (it->second == nilVertex) {
-		--it;
-	}
+    // Case 2: Found a nil position but there is a vertex before
+    if (it->second == nilVertex) {
+        --it;
+    }
 
-	// If the sequence id still matches return the position behind the last position belonging to this vertex
-	if (it->first.first != id) return 0;
-	return fragmentBegin(g, it->second) + fragmentLength(g, it->second);
+    // If the sequence id still matches return the position behind the last position belonging to this vertex
+    if (it->first.first != id) return 0;
+    return fragmentBegin(g, it->second) + fragmentLength(g, it->second);
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-/*
+/*!
  * @fn AlignmentGraph#convertAlignment
  * @brief Converts an alignment graph into an alignment matrix.
- * 
+ *
  * @signature bool convertAlignment(g, component, order, compLength);
  * @signature bool convertAlignment(g, matrix);
- * 
+ *
  * @param[in]  g          AlignmentGraph to convert.  An alignment graph.
  * @param[out] component  Vertex to component mapping.
  * @param[out] order      The order of the component graph when sorting topologically.
  * @param[out] compLength Component sizes.
  * @param[out] matrix     A string that represents an alignment matrix.
- * 
+ *
  * @return bool true iff the alignment graph is a valid alignment and false otherwise.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The variant with <tt>component</tt> and <tt>order</tt> computes a topological sorting of connected components.
  */
 
-/**
-.Function.convertAlignment
-..class:Spec.Alignment Graph
-..signature:convertAlignment(g, component, order, compLength)
-..remarks:The variant with $component$ and $order$ computes a topological sorting of connected components.
-..param.g:Alignment graph to convert.
-..param.component:Vertex to component mapping.
-..param.order:The order of the component graph when sorting topologically.
-..param.compLength:Component sizes.
-..include:seqan/graph_align.h
-*/
-
-template<typename TStringSet, typename TCargo, typename TSpec, typename TComponentMap, typename TOrderMap, typename TComponentLength> 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TComponentMap, typename TOrderMap, typename TComponentLength>
 inline bool
 convertAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-				 TComponentMap& component,
-				 TOrderMap& order,
-				 TComponentLength& compLength)
+                 TComponentMap& component,
+                 TOrderMap& order,
+                 TComponentLength& compLength)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Id<TGraph>::Type TIdType;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Value<TComponentMap>::Type TComponent;
-	typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
-	typedef typename TComponentLength::mapped_type TMappedType;
-	typedef typename TComponentLength::key_type TKeyType;
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-
-	// Check for empty graph
-	if (empty(g)) return false;
-
-	// Connected Components
-	TSize numComponents = connectedComponents(g, component);
-
-	// Make a directed graph to represent the ordering of the components
-	// Note: Multiple vertices might have the same component
-	Graph<Directed<void, WithoutEdgeId> > componentGraph;
-	reserve(_getVertexString(componentGraph), numComponents);
-	for(TSize i = 0; i<numComponents;++i) addVertex(componentGraph);
-	
-	TSize nseq = length(value(g.data_sequence));
-	String<std::set<TComponent> > componentsPerSeq;
-	typedef String<String<TComponent> > TOrderedComponents;
-	TOrderedComponents orderedComponentsPerSeq;
-	resize(componentsPerSeq, nseq);
-	resize(orderedComponentsPerSeq, nseq);
-	typename TPosToVertexMap::const_iterator it1 = g.data_pvMap.begin();
-	typename TPosToVertexMap::const_iterator it1End = g.data_pvMap.end();
-	for(;it1!=it1End;++it1) {
-		// If sections are not assigned to a vertex -> no alignment
-		if (it1->second == nilVertex) return false;
-		
-		// Remember the sequence that component belongs to 
-		TSize currentSeq = idToPosition(value(g.data_sequence), it1->first.first);
-
-		// Append component
-		TComponent c = getProperty(component, it1->second);
-		if ((value(componentsPerSeq,currentSeq)).empty()) {
-			String<TComponent> tmp;
-			value(orderedComponentsPerSeq, currentSeq) = tmp;
-		}
-		appendValue(value(orderedComponentsPerSeq, currentSeq), c, Generous());
-		// If two components appear twice in the same sequence -> no alignment
-		if (!((value(componentsPerSeq,currentSeq)).insert(c)).second) return false;	
-	}
-	clear(componentsPerSeq);
-
-	// Draw edges for the components within a sequence
-	typedef typename Iterator<TOrderedComponents>::Type TIterTOrderedComponents;
-	TIterTOrderedComponents itBegin = begin(orderedComponentsPerSeq);
-	TIterTOrderedComponents itEnd = end(orderedComponentsPerSeq);
-	for(;itBegin != itEnd; ++itBegin) {
-		TSize n = length(*itBegin);
-		for(TSize i = 0; i<n-1; ++i) {
-			addEdge(componentGraph, value((*itBegin), i), value((*itBegin), i+1));
-		}
-	}
-	
-	// Make a topological sort of the component graph
-	topologicalSort(componentGraph, order);
-
-	//// Debug code
-	//std::cout << "Topological sort: " << std::endl;
-	//for(TSize i = 0; i<length(order);++i) {
-	//	std::cout << order[i] << ',';
-	//}
-	//std::cout << std::endl;
-
-	// Walk through all sequences and check the component order
-	unsigned int compIndex = 0;
-	unsigned int compIndexLen = length(order);
-	typename TPosToVertexMap::const_iterator it = g.data_pvMap.begin();
-	TIdType currentSeq = it->first.first;
-	for(; it != g.data_pvMap.end(); ++it) {
-		if (it->first.first != currentSeq) {
-			compIndex = 0;
-			currentSeq = it->first.first;
-		}
-		TKeyType c = (TKeyType) getProperty(component, it->second);
-		if(!compLength.insert(std::make_pair(c, (TMappedType) fragmentLength(g, it->second))).second) {
-			compLength[c] = _max(compLength[c], (TMappedType) fragmentLength(g, it->second));
-		}
-		while ((compIndex < compIndexLen) && (order[compIndex] != c)) ++compIndex;
-		// Crossing components -> no alignment
-		if (compIndex >= compIndexLen) return false;
-		// Next component
-		++compIndex;
-	}
-
-	return true;
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Id<TGraph>::Type TIdType;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Value<TComponentMap>::Type TComponent;
+    typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
+    typedef typename TComponentLength::mapped_type TMappedType;
+    typedef typename TComponentLength::key_type TKeyType;
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+
+    // Check for empty graph
+    if (empty(g)) return false;
+
+    // Connected Components
+    TSize numComponents = connectedComponents(component, g);
+
+    // Make a directed graph to represent the ordering of the components
+    // Note: Multiple vertices might have the same component
+    Graph<Directed<void, WithoutEdgeId> > componentGraph;
+    reserve(_getVertexString(componentGraph), numComponents);
+    for(TSize i = 0; i<numComponents;++i) addVertex(componentGraph);
+
+    TSize nseq = length(value(g.data_sequence));
+    String<std::set<TComponent> > componentsPerSeq;
+    typedef String<String<TComponent> > TOrderedComponents;
+    TOrderedComponents orderedComponentsPerSeq;
+    resize(componentsPerSeq, nseq);
+    resize(orderedComponentsPerSeq, nseq);
+    typename TPosToVertexMap::const_iterator it1 = g.data_pvMap.begin();
+    typename TPosToVertexMap::const_iterator it1End = g.data_pvMap.end();
+    for(;it1!=it1End;++it1) {
+        // If sections are not assigned to a vertex -> no alignment
+        if (it1->second == nilVertex) return false;
+
+        // Remember the sequence that component belongs to
+        TSize currentSeq = idToPosition(value(g.data_sequence), it1->first.first);
+
+        // Append component
+        TComponent c = getProperty(component, it1->second);
+        if ((value(componentsPerSeq,currentSeq)).empty()) {
+            String<TComponent> tmp;
+            value(orderedComponentsPerSeq, currentSeq) = tmp;
+        }
+        appendValue(value(orderedComponentsPerSeq, currentSeq), c, Generous());
+        // If two components appear twice in the same sequence -> no alignment
+        if (!((value(componentsPerSeq,currentSeq)).insert(c)).second) return false;
+    }
+    clear(componentsPerSeq);
+
+    // Draw edges for the components within a sequence
+    typedef typename Iterator<TOrderedComponents>::Type TIterTOrderedComponents;
+    TIterTOrderedComponents itBegin = begin(orderedComponentsPerSeq);
+    TIterTOrderedComponents itEnd = end(orderedComponentsPerSeq);
+    for(;itBegin != itEnd; ++itBegin) {
+        TSize n = length(*itBegin);
+        for(TSize i = 0; i<n-1; ++i) {
+            addEdge(componentGraph, value((*itBegin), i), value((*itBegin), i+1));
+        }
+    }
+
+    // Make a topological sort of the component graph
+    topologicalSort(order, componentGraph);
+
+    //// Debug code
+    //std::cout << "Topological sort: " << std::endl;
+    //for(TSize i = 0; i<length(order);++i) {
+    //    std::cout << order[i] << ',';
+    //}
+    //std::cout << std::endl;
+
+    // Walk through all sequences and check the component order
+    unsigned int compIndex = 0;
+    unsigned int compIndexLen = length(order);
+    typename TPosToVertexMap::const_iterator it = g.data_pvMap.begin();
+    TIdType currentSeq = it->first.first;
+    for(; it != g.data_pvMap.end(); ++it) {
+        if (it->first.first != currentSeq) {
+            compIndex = 0;
+            currentSeq = it->first.first;
+        }
+        TKeyType c = (TKeyType) getProperty(component, it->second);
+        if(!compLength.insert(std::make_pair(c, (TMappedType) fragmentLength(g, it->second))).second) {
+            compLength[c] = _max(compLength[c], (TMappedType) fragmentLength(g, it->second));
+        }
+        while ((compIndex < compIndexLen) && (order[compIndex] != c)) ++compIndex;
+        // Crossing components -> no alignment
+        if (compIndex >= compIndexLen) return false;
+        // Next component
+        ++compIndex;
+    }
+
+    return true;
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.convertAlignment
-..cat:Graph
-..summary:Converts an alignment graph into an alignment matrix.
-..signature:convertAlignment(g, matrix)
-..param.g:In-parameter: An alignment graph.
-...type:Spec.Alignment Graph
-..param.matrix:Out-parameter: A string that represents an alignment matrix.
-..returns: A bool that is true iff the alignment graph is a valid alignment
-..include:seqan/graph_align.h
-*/
-template<typename TStringSet, typename TCargo, typename TSpec, typename TMatrix> 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TMatrix>
 inline bool
 convertAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-				 TMatrix& mat)
+                 TMatrix& mat)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Value<TMatrix>::Type TValue;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Id<TGraph>::Type TIdType;
-	typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
-	typedef std::map<unsigned int, unsigned int> TComponentLength;
-
-	// Strongly Connected Components, topological sort, and length of each component
-	String<unsigned int> component;
-	String<unsigned int> order;
-	TComponentLength compLength;
-
-	if (!convertAlignment(g, component, order, compLength)) return false;
-
-	// Create the matrix
-	TSize len = 0;
-	TSize nseq = length(stringSet(g));
-	for(TComponentLength::iterator cIt=compLength.begin(); cIt != compLength.end(); ++cIt) len+=cIt->second;
-	char gapChar = gapValue<char>();
-	resize(mat, len * nseq, gapChar);
-
-	// Fill the matrix
-	TSize row = 0;
-	TSize col = 0;
-	typename TPosToVertexMap::const_iterator it = g.data_pvMap.begin();
-	unsigned int compIndex = 0;
-	unsigned int compIndexLen = length(order);
-	TIdType currentSeq = it->first.first;
-	for(; it != g.data_pvMap.end(); ++it) {
-		if (it->first.first != currentSeq) {
-			SEQAN_ASSERT(col <= len);
-			//std::cout << std::endl;
-			++row;col=0;
-			compIndex = 0;
-			currentSeq = it->first.first;
-		}
-		unsigned int c = getProperty(component, it->second);
-		while ((compIndex < compIndexLen) && (order[compIndex] != c)) {
-			for(TSize i=0;i<compLength[order[compIndex]];++i, ++col) 
-				mat[row*len + col] = gapValue<char>();
-			++compIndex;
-		}
-		typedef typename Value<TStringSet>::Type TStringSetStr;
-		TStringSetStr str = label(g,it->second);
-		typedef typename Iterator<TStringSetStr, Standard>::Type TStringSetStrIter;
-		TStringSetStrIter itStr = begin(str, Standard());
-		TStringSetStrIter itStrEnd = end(str, Standard());
-		for(;itStr != itStrEnd; goNext(itStr), ++col) 
-			mat[row*len + col] = (TValue) (*itStr);
-		for(TSize i = length(str); i < compLength[order[compIndex]]; ++i, ++col)
-			mat[row*len + col] = gapValue<char>();
-		++compIndex;
-	}
-	SEQAN_ASSERT(row + 1 == nseq);
-	//std::cout << std::endl;
-
-	return true;
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Value<TMatrix>::Type TValue;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Id<TGraph>::Type TIdType;
+    typedef typename TGraph::TPosToVertexMap_ TPosToVertexMap;
+    typedef std::map<unsigned int, unsigned int> TComponentLength;
+
+    // Strongly Connected Components, topological sort, and length of each component
+    String<unsigned int> component;
+    String<unsigned int> order;
+    TComponentLength compLength;
+
+    if (!convertAlignment(g, component, order, compLength)) return false;
+
+    // Create the matrix
+    TSize len = 0;
+    TSize nseq = length(stringSet(g));
+    for(TComponentLength::iterator cIt=compLength.begin(); cIt != compLength.end(); ++cIt) len+=cIt->second;
+    char gapChar = gapValue<char>();
+    resize(mat, len * nseq, gapChar);
+
+    // Fill the matrix
+    TSize row = 0;
+    TSize col = 0;
+    typename TPosToVertexMap::const_iterator it = g.data_pvMap.begin();
+    unsigned int compIndex = 0;
+    unsigned int compIndexLen = length(order);
+    TIdType currentSeq = it->first.first;
+    for(; it != g.data_pvMap.end(); ++it) {
+        if (it->first.first != currentSeq) {
+            SEQAN_ASSERT(col <= len);
+            //std::cout << std::endl;
+            ++row;col=0;
+            compIndex = 0;
+            currentSeq = it->first.first;
+        }
+        unsigned int c = getProperty(component, it->second);
+        while ((compIndex < compIndexLen) && (order[compIndex] != c)) {
+            for(TSize i=0;i<compLength[order[compIndex]];++i, ++col)
+                mat[row*len + col] = gapValue<char>();
+            ++compIndex;
+        }
+        typedef typename Value<TStringSet>::Type TStringSetStr;
+        TStringSetStr str = label(g,it->second);
+        typedef typename Iterator<TStringSetStr, Standard>::Type TStringSetStrIter;
+        TStringSetStrIter itStr = begin(str, Standard());
+        TStringSetStrIter itStrEnd = end(str, Standard());
+        for(;itStr != itStrEnd; goNext(itStr), ++col)
+            mat[row*len + col] = (TValue) (*itStr);
+        for(TSize i = length(str); i < compLength[order[compIndex]]; ++i, ++col)
+            mat[row*len + col] = gapValue<char>();
+        ++compIndex;
+    }
+    SEQAN_ASSERT(row + 1 == nseq);
+    //std::cout << std::endl;
+
+    return true;
 }
 
 
@@ -1912,43 +1696,43 @@ convertAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
 template<typename TValue, typename TSpec1, typename TStringSet, typename TCargo, typename TSpec2>
 inline bool
 convertAlignment(String<TValue, TSpec1> const& mat,
-				 Graph<Alignment<TStringSet, TCargo, TSpec2> >& g)
+                 Graph<Alignment<TStringSet, TCargo, TSpec2> >& g)
 {
-	typedef String<TValue, TSpec1> TMatrix;
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec2> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
-	clearVertices(g);
-	TValue gapChar = gapValue<TValue>();
-	TSize nseq = length(stringSet(g));
-	TSize alignLen = length(mat) / nseq;
-	String<Fragment<> > matches;
-	for(TSize seq1 = 0; seq1<nseq; ++seq1) {
-		for(TSize seq2 = seq1 + 1; seq2<nseq; ++seq2) {
-			TMatIter seq1It = begin(mat);
-			seq1It += seq1 * alignLen;
-			TMatIter seq2It = begin(mat);
-			seq2It += seq2 * alignLen;
-			TSize alignPos = 0;
-			TSize length = 0;
-			TSize offset1 = 0;
-			TSize offset2 = 0;
-			for(TSize col = 0; col<alignLen; ++col, ++seq1It, ++seq2It, ++alignPos) {
-				if ((*seq1It == gapChar) || (*seq2It == gapChar)) {
-					if (length) {
-						appendValue(matches, Fragment<>(seq1, alignPos - offset1 - length, seq2, alignPos - offset2 - length, length));
-						length = 0;
-					}
-					if (*seq1It == gapChar) ++offset1;
-					if (*seq2It == gapChar) ++offset2;
-				} else ++length;
-			}
-			if (length) appendValue(matches, Fragment<>(seq1, alignPos - offset1 - length, seq2, alignPos - offset2 - length, length));
-		}
-	}
-	//_debugMatches(stringSet(g), matches);
-	matchRefinement(matches,stringSet(g),g);
-	return true;
+    typedef String<TValue, TSpec1> TMatrix;
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec2> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
+    clearVertices(g);
+    TValue gapChar = gapValue<TValue>();
+    TSize nseq = length(stringSet(g));
+    TSize alignLen = length(mat) / nseq;
+    String<Fragment<> > matches;
+    for(TSize seq1 = 0; seq1<nseq; ++seq1) {
+        for(TSize seq2 = seq1 + 1; seq2<nseq; ++seq2) {
+            TMatIter seq1It = begin(mat);
+            seq1It += seq1 * alignLen;
+            TMatIter seq2It = begin(mat);
+            seq2It += seq2 * alignLen;
+            TSize alignPos = 0;
+            TSize length = 0;
+            TSize offset1 = 0;
+            TSize offset2 = 0;
+            for(TSize col = 0; col<alignLen; ++col, ++seq1It, ++seq2It, ++alignPos) {
+                if ((*seq1It == gapChar) || (*seq2It == gapChar)) {
+                    if (length) {
+                        appendValue(matches, Fragment<>(seq1, alignPos - offset1 - length, seq2, alignPos - offset2 - length, length));
+                        length = 0;
+                    }
+                    if (*seq1It == gapChar) ++offset1;
+                    if (*seq2It == gapChar) ++offset2;
+                } else ++length;
+            }
+            if (length) appendValue(matches, Fragment<>(seq1, alignPos - offset1 - length, seq2, alignPos - offset2 - length, length));
+        }
+    }
+    //_debugMatches(stringSet(g), matches);
+    matchRefinement(matches,stringSet(g),g);
+    return true;
 }
 
 
@@ -1960,70 +1744,70 @@ template<typename TStringSet, typename TCargo, typename TSpec>
 inline void
 rebuildGraph(Graph<Alignment<TStringSet, TCargo, TSpec> >& g)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Size<TGraph>::Type TSize;
-
-	// Initialization
-	typedef Fragment<> TFragment;
-	typedef String<TFragment> TFragmentString;
-	TFragmentString matches;
-	TSize nseq = length(stringSet(g));
-
-	// Collect all character pairs
-	typedef std::pair<TSize, TSize> TResiduePair;
-	typedef std::set<TResiduePair> TResiduePairSet;
-	String<TResiduePairSet> resPair;
-	resize(resPair, nseq * nseq);
-	TEdgeIterator itE(g);
-	for(;!atEnd(itE);++itE) {
-		TVertexDescriptor sV = sourceVertex(itE);
-		TVertexDescriptor tV = targetVertex(itE);
-		TSize seq1 = idToPosition(stringSet(g), sequenceId(g, sV));
-		TSize seq2 = idToPosition(stringSet(g), sequenceId(g, tV));
-		TSize index = 0;
-		TSize pos1 = 0;
-		TSize pos2 = 0;
-		if (seq1 < seq2) {
-			index = seq1 * nseq + seq2;
-			pos1 = fragmentBegin(g, sV);
-			pos2 = fragmentBegin(g, tV);
-		} else {
-			index = seq2 * nseq + seq1;
-			pos1 = fragmentBegin(g, tV);
-			pos2 = fragmentBegin(g, sV);
-		}
-		for(TSize i = 0; i<fragmentLength(g, sV); ++i) {
-			resPair[index].insert(std::make_pair(pos1 + i, pos2 + i));
-		}
-	}
-
-	// Rebuild the graph with maximal segments
-	for(TSize i = 0; i<length(resPair); ++i) {
-		if (resPair[i].empty()) continue;
-		TSize seq1 = i / nseq;
-		TSize seq2 = i % nseq;
-		typename TResiduePairSet::const_iterator pos = resPair[i].begin();
-		typename TResiduePairSet::const_iterator posEnd = resPair[i].end();
-		TSize startMatch1 = pos->first;
-		TSize startMatch2 = pos->second;
-		TSize len = 1;
-		++pos;
-		while(pos != posEnd) {
-			if ((startMatch1 + len == pos->first) && (startMatch2 + len == pos->second)) ++len;
-			else {
-				appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len), Generous());
-				startMatch1 = pos->first;
-				startMatch2 = pos->second;
-				len = 1;
-			}
-			++pos;
-		}
-		appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len), Generous());
-	}
-	clearVertices(g);
-	matchRefinement(matches,stringSet(g),g);
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Size<TGraph>::Type TSize;
+
+    // Initialization
+    typedef Fragment<> TFragment;
+    typedef String<TFragment> TFragmentString;
+    TFragmentString matches;
+    TSize nseq = length(stringSet(g));
+
+    // Collect all character pairs
+    typedef std::pair<TSize, TSize> TResiduePair;
+    typedef std::set<TResiduePair> TResiduePairSet;
+    String<TResiduePairSet> resPair;
+    resize(resPair, nseq * nseq);
+    TEdgeIterator itE(g);
+    for(;!atEnd(itE);++itE) {
+        TVertexDescriptor sV = sourceVertex(itE);
+        TVertexDescriptor tV = targetVertex(itE);
+        TSize seq1 = idToPosition(stringSet(g), sequenceId(g, sV));
+        TSize seq2 = idToPosition(stringSet(g), sequenceId(g, tV));
+        TSize index = 0;
+        TSize pos1 = 0;
+        TSize pos2 = 0;
+        if (seq1 < seq2) {
+            index = seq1 * nseq + seq2;
+            pos1 = fragmentBegin(g, sV);
+            pos2 = fragmentBegin(g, tV);
+        } else {
+            index = seq2 * nseq + seq1;
+            pos1 = fragmentBegin(g, tV);
+            pos2 = fragmentBegin(g, sV);
+        }
+        for(TSize i = 0; i<fragmentLength(g, sV); ++i) {
+            resPair[index].insert(std::make_pair(pos1 + i, pos2 + i));
+        }
+    }
+
+    // Rebuild the graph with maximal segments
+    for(TSize i = 0; i<length(resPair); ++i) {
+        if (resPair[i].empty()) continue;
+        TSize seq1 = i / nseq;
+        TSize seq2 = i % nseq;
+        typename TResiduePairSet::const_iterator pos = resPair[i].begin();
+        typename TResiduePairSet::const_iterator posEnd = resPair[i].end();
+        TSize startMatch1 = pos->first;
+        TSize startMatch2 = pos->second;
+        TSize len = 1;
+        ++pos;
+        while(pos != posEnd) {
+            if ((startMatch1 + len == pos->first) && (startMatch2 + len == pos->second)) ++len;
+            else {
+                appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len), Generous());
+                startMatch1 = pos->first;
+                startMatch2 = pos->second;
+                len = 1;
+            }
+            ++pos;
+        }
+        appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len), Generous());
+    }
+    clearVertices(g);
+    matchRefinement(matches,stringSet(g),g);
 }
 
 
@@ -2039,16 +1823,16 @@ rebuildGraph(Graph<Alignment<TStringSet, TCargo, TSpec> >& g)
 template<typename TStringSet, typename TCargo, typename TSpec, typename TSize2, typename TSpec2, typename TPositions, typename TSize, typename TVertexDescriptor, typename TString>
 inline void
 _heaviestCommonSubsequence(Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
-							String<TSize2, TSpec2> const& /*slotToPos*/,
-							TPositions const&,
-							TSize const,
-							TSize const,
-							TVertexDescriptor const,
-							TString const&, 
-							TString const&,
-							Nothing&) 
+                            String<TSize2, TSpec2> const& /*slotToPos*/,
+                            TPositions const&,
+                            TSize const,
+                            TSize const,
+                            TVertexDescriptor const,
+                            TString const&,
+                            TString const&,
+                            Nothing&)
 {
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -2056,116 +1840,116 @@ _heaviestCommonSubsequence(Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
 template<typename TStringSet, typename TCargo, typename TSpec, typename TSize2, typename TSpec2, typename TPositions, typename TSize, typename TString, typename TOutString>
 inline void
 _heaviestCommonSubsequence(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-							String<TSize2, TSpec2> const& slotToPos,
-							TPositions const& positions,
-							TSize const m,
-							TSize const n,
-							TString const& str1, 
-							TString const& str2,
-							TOutString& align) 
+                            String<TSize2, TSpec2> const& slotToPos,
+                            TPositions const& positions,
+                            TSize const m,
+                            TSize const n,
+                            TString const& str1,
+                            TString const& str2,
+                            TOutString& align)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TString>::Type TVertexSet;
-	typedef typename Iterator<TString const, Standard>::Type TStringIter;
-	typedef typename Iterator<TString, Standard>::Type TSIter;
-	typedef typename Iterator<TVertexSet const, Standard>::Type TVertexSetIter;
-
-	// Create the alignment sequence
-	TSize numMatches = length(positions);
-	TSize alignLength = numMatches + (n - numMatches) + (m - numMatches);
-	clear(align);
-	resize(align, alignLength, TVertexSet(), Exact() );
-	TSIter pointerAlign = begin(align, Standard());
-	TSIter pointerAlignEnd = end(align, Standard());
-	TStringIter pointerStr1 = begin(str1, Standard());
-	TSize posStr1 = 0;
-	TSize posStr2 = 0;
-	TStringIter pointerStr2 = begin(str2, Standard());
-	int p = length(positions) - 1;
-	while(pointerAlign != pointerAlignEnd) {
-		TSize i = m;
-		TSize j = n;
-		if (p>=0) {
-			i = (TSize) (slotToPos[positions[p]] / (TSize) n);   // Get the index in str1
-			j = n - 1 - (TSize) (slotToPos[positions[p]] % (TSize) n); // Get the index in str2
-		};
-
-		// In what order do we insert gaps? -> Only important at the beginning and at the end, not between matches
-		bool firstI = true;
-		if ((i != posStr1) && (j != posStr2)) 
-		{
-			if ((posStr1 == 0) && (posStr2 == 0)) {
-				TStringIter tmpPointerStr1 = pointerStr1;
-				TStringIter tmpPointerStr2 = pointerStr2;
-				TSize tmpPosStr1 = posStr1;
-				TSize tmpPosStr2 = posStr2;
-				TSize len1 = 0;
-				TSize len2 = 0;
-				for(;i != tmpPosStr1; ++tmpPosStr1, ++tmpPointerStr1) len1 += fragmentLength(g, value(*tmpPointerStr1, 0));
-				for(;j != tmpPosStr2; ++tmpPosStr2, ++tmpPointerStr2) len2 += fragmentLength(g, value(*tmpPointerStr2, 0));
-				if (len1 > len2) firstI = false;
-			} else if ((i == m) && (i == n)) {
-				TStringIter tmpPointerStr1 = pointerStr1;
-				TStringIter tmpPointerStr2 = pointerStr2;
-				TSize tmpPosStr1 = posStr1;
-				TSize tmpPosStr2 = posStr2;
-				TSize len1 = 0;
-				TSize len2 = 0;
-				for(;i != tmpPosStr1; ++tmpPosStr1, ++tmpPointerStr1) len1 += fragmentLength(g, value(*tmpPointerStr1, 0));
-				for(;j != tmpPosStr2; ++tmpPosStr2, ++tmpPointerStr2) len2 += fragmentLength(g, value(*tmpPointerStr2, 0));
-				if (len1 < len2) firstI = false;
-			}
-		}
-		if (firstI) {
-			// Gaps in seq 2
-			while (i != posStr1) {
-				TVertexSetIter itV = begin(*pointerStr1, Standard());
-				TVertexSetIter itVEnd = end(*pointerStr1, Standard());
-				for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
-				++pointerAlign;
-				++pointerStr1; ++posStr1;
-			}
-			// Gaps in seq 1
-			while (j != posStr2) {
-				TVertexSetIter itV = begin(*pointerStr2, Standard());
-				TVertexSetIter itVEnd = end(*pointerStr2, Standard());
-				for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
-				++pointerAlign;
-				++pointerStr2; ++posStr2;
-			}
-		} else {
-			// Gaps in seq 1
-			while (j != posStr2) {
-				TVertexSetIter itV = begin(*pointerStr2, Standard());
-				TVertexSetIter itVEnd = end(*pointerStr2, Standard());
-				for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
-				++pointerAlign;
-				++pointerStr2; ++posStr2;
-			}
-			// Gaps in seq 2
-			while (i != posStr1) {
-				TVertexSetIter itV = begin(*pointerStr1, Standard());
-				TVertexSetIter itVEnd = end(*pointerStr1, Standard());
-				for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
-				++pointerAlign;
-				++pointerStr1; ++posStr1;
-			}
-		}
-
-		// Matches
-		if (p>=0) {
-			TVertexSetIter itV = begin(*pointerStr1, Standard());
-			TVertexSetIter itVEnd = end(*pointerStr1, Standard());
-			for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
-			TVertexSetIter itV2 = begin(*pointerStr2, Standard());
-			TVertexSetIter itVEnd2 = end(*pointerStr2, Standard());
-			for(;itV2 != itVEnd2;++itV2) appendValue(*pointerAlign, *itV2, Generous());
-			++pointerAlign;
-			++pointerStr1; ++posStr1;
-			++pointerStr2; ++posStr2;
-			--p;
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Value<TString>::Type TVertexSet;
+    typedef typename Iterator<TString const, Standard>::Type TStringIter;
+    typedef typename Iterator<TString, Standard>::Type TSIter;
+    typedef typename Iterator<TVertexSet const, Standard>::Type TVertexSetIter;
+
+    // Create the alignment sequence
+    TSize numMatches = length(positions);
+    TSize alignLength = numMatches + (n - numMatches) + (m - numMatches);
+    clear(align);
+    resize(align, alignLength, TVertexSet(), Exact() );
+    TSIter pointerAlign = begin(align, Standard());
+    TSIter pointerAlignEnd = end(align, Standard());
+    TStringIter pointerStr1 = begin(str1, Standard());
+    TSize posStr1 = 0;
+    TSize posStr2 = 0;
+    TStringIter pointerStr2 = begin(str2, Standard());
+    int p = length(positions) - 1;
+    while(pointerAlign != pointerAlignEnd) {
+        TSize i = m;
+        TSize j = n;
+        if (p>=0) {
+            i = (TSize) (slotToPos[positions[p]] / (TSize) n);   // Get the index in str1
+            j = n - 1 - (TSize) (slotToPos[positions[p]] % (TSize) n); // Get the index in str2
+        };
+
+        // In what order do we insert gaps? -> Only important at the beginning and at the end, not between matches
+        bool firstI = true;
+        if ((i != posStr1) && (j != posStr2))
+        {
+            if ((posStr1 == 0) && (posStr2 == 0)) {
+                TStringIter tmpPointerStr1 = pointerStr1;
+                TStringIter tmpPointerStr2 = pointerStr2;
+                TSize tmpPosStr1 = posStr1;
+                TSize tmpPosStr2 = posStr2;
+                TSize len1 = 0;
+                TSize len2 = 0;
+                for(;i != tmpPosStr1; ++tmpPosStr1, ++tmpPointerStr1) len1 += fragmentLength(g, value(*tmpPointerStr1, 0));
+                for(;j != tmpPosStr2; ++tmpPosStr2, ++tmpPointerStr2) len2 += fragmentLength(g, value(*tmpPointerStr2, 0));
+                if (len1 > len2) firstI = false;
+            } else if ((i == m) && (i == n)) {
+                TStringIter tmpPointerStr1 = pointerStr1;
+                TStringIter tmpPointerStr2 = pointerStr2;
+                TSize tmpPosStr1 = posStr1;
+                TSize tmpPosStr2 = posStr2;
+                TSize len1 = 0;
+                TSize len2 = 0;
+                for(;i != tmpPosStr1; ++tmpPosStr1, ++tmpPointerStr1) len1 += fragmentLength(g, value(*tmpPointerStr1, 0));
+                for(;j != tmpPosStr2; ++tmpPosStr2, ++tmpPointerStr2) len2 += fragmentLength(g, value(*tmpPointerStr2, 0));
+                if (len1 < len2) firstI = false;
+            }
+        }
+        if (firstI) {
+            // Gaps in seq 2
+            while (i != posStr1) {
+                TVertexSetIter itV = begin(*pointerStr1, Standard());
+                TVertexSetIter itVEnd = end(*pointerStr1, Standard());
+                for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
+                ++pointerAlign;
+                ++pointerStr1; ++posStr1;
+            }
+            // Gaps in seq 1
+            while (j != posStr2) {
+                TVertexSetIter itV = begin(*pointerStr2, Standard());
+                TVertexSetIter itVEnd = end(*pointerStr2, Standard());
+                for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
+                ++pointerAlign;
+                ++pointerStr2; ++posStr2;
+            }
+        } else {
+            // Gaps in seq 1
+            while (j != posStr2) {
+                TVertexSetIter itV = begin(*pointerStr2, Standard());
+                TVertexSetIter itVEnd = end(*pointerStr2, Standard());
+                for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
+                ++pointerAlign;
+                ++pointerStr2; ++posStr2;
+            }
+            // Gaps in seq 2
+            while (i != posStr1) {
+                TVertexSetIter itV = begin(*pointerStr1, Standard());
+                TVertexSetIter itVEnd = end(*pointerStr1, Standard());
+                for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
+                ++pointerAlign;
+                ++pointerStr1; ++posStr1;
+            }
+        }
+
+        // Matches
+        if (p>=0) {
+            TVertexSetIter itV = begin(*pointerStr1, Standard());
+            TVertexSetIter itVEnd = end(*pointerStr1, Standard());
+            for(;itV != itVEnd;++itV) appendValue(*pointerAlign, *itV, Generous());
+            TVertexSetIter itV2 = begin(*pointerStr2, Standard());
+            TVertexSetIter itVEnd2 = end(*pointerStr2, Standard());
+            for(;itV2 != itVEnd2;++itV2) appendValue(*pointerAlign, *itV2, Generous());
+            ++pointerAlign;
+            ++pointerStr1; ++posStr1;
+            ++pointerStr2; ++posStr2;
+            --p;
+        }
+    }
 }
 
 
@@ -2175,137 +1959,123 @@ _heaviestCommonSubsequence(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g
 
 // TODO(holtgrew): Where does this belong? This is also there in graph_algorithms.h...
 
-/**
-.Function.heaviestCommonSubsequence:
-..summary:Computes the heaviest common subsequence between two strings using the match information given in an alignment graph.
-..cat:Alignments
-..signature:heaviestCommonSubsequence(g, str1, str2, align)
-..signature:heaviestCommonSubsequence(g, str1, str2)
-..param.g:An alignment graph.
-...type:Spec.Alignment Graph
-..param.str1:A string.
-..param.str2:Another string.
-..param.align:Out-parameter: A String of vertex strings that indicate the members of the heaviest common subsequence.
-..returns:Score of the heaviest common subsequence.
-..include:seqan/graph_algorithms.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec, typename TString, typename TOutString>
 inline TCargo
 heaviestCommonSubsequence(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-						  TString const& str1, 
-						  TString const& str2,
-						  TOutString& align) 
+                          TString const& str1,
+                          TString const& str2,
+                          TOutString& align)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Value<TString>::Type TVertexSet;
-
-	TSize m = length(str1);  // How many sets of vertex descriptors in seq1
-	TSize n = length(str2);  // How many sets of vertex descriptors in seq2
-
-	// Size of the sequences
-	// Note for profile alignments every member of the sequence is a String!!! of vertex descriptors
-	
-	// Fill the vertex to position map for str1
-	// Remember for each vertex descriptor the position in the sequence
-	typedef String<TSize> TMapVertexPos;
-	TMapVertexPos map;
-	resize(map, getIdUpperBound(_getVertexIdManager(g)), MaxValue<TSize>::VALUE);
-	typedef typename Iterator<TString const, Standard>::Type TStringIterConst;
-	typedef typename Iterator<TVertexSet const, Standard>::Type TVertexSetIterConst;
-	TStringIterConst itStr1 = begin(str1, Standard());
-	TStringIterConst itStrEnd1 = end(str1, Standard());
-	TSize pos = 0;
-	TVertexSetIterConst itV;
-	TVertexSetIterConst itVEnd;
-	for(;itStr1 != itStrEnd1;++itStr1, ++pos) {
-		itV = begin(*itStr1, Standard());
-		itVEnd = end(*itStr1, Standard());	
-		for(;itV != itVEnd;++itV) map[*itV] = pos;
-	}
-
-	// We could create the full graph -> too expensive
-	// Remember which edges are actually present
-	typedef String<TSize> TOccupiedPositions;
-	typedef typename Iterator<TOccupiedPositions, Standard>::Type TOccIter;
-	TOccupiedPositions occupiedPositions;
-	TStringIterConst itStr2 = begin(str2, Standard());
-	TStringIterConst itStrEnd2 = end(str2, Standard());
-	TSize posItStr2 = 0;
-	TSize pPos = 0;
-	for(;itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
-		itV = begin(*itStr2, Standard());
-		itVEnd = end(*itStr2, Standard());
-		for(;itV != itVEnd;++itV) {
-			TOutEdgeIterator itOut(g, *itV);
-			for(;!atEnd(itOut); ++itOut) {
-				// Target vertex must be in the map
-				pPos = map[targetVertex(itOut)];
-				if (pPos != MaxValue<TSize>::VALUE) 
-					appendValue(occupiedPositions, pPos * n + (TSize) (n - posItStr2 - 1), Generous());
-			}
-		}
-	}
-	::std::sort(begin(occupiedPositions, Standard()), end(occupiedPositions, Standard()));
-	// Get all occupied positions
-	typedef String<TSize> TSlotToPos;
-	typedef typename Iterator<TSlotToPos, Standard>::Type TSlotToPosIter;
-	TSlotToPos slotToPos;
-	TSize counter = 0;
-	TSize oldVal = MaxValue<TSize>::VALUE;
-	TOccIter occIt = begin(occupiedPositions, Standard());
-	TOccIter occItEnd = end(occupiedPositions, Standard());
-	for(;occIt != occItEnd; ++occIt) {
-		if (oldVal != *occIt) {
-			appendValue(slotToPos, *occIt, Generous());
-			oldVal = *occIt;
-			++counter;
-		}
-	}
-	clear(occupiedPositions);
-
-	// Walk through str2 and fill in the weights of the actual edges
-	typedef String<TCargo> TWeights;
-	TWeights weights;
-	resize(weights, length(slotToPos), 0);
-	itStr2 = begin(str2, Standard());
-	posItStr2 = 0;
-	for(;itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
-		itV = begin(*itStr2, Standard());
-		itVEnd = end(*itStr2, Standard());
-		for(;itV != itVEnd;++itV) {
-			TOutEdgeIterator itOut(g, *itV);
-			for(;!atEnd(itOut); ++itOut) {
-				// Target vertex must be in the map
-				pPos = map[targetVertex(itOut)];
-				if ( pPos != MaxValue<TSize>::VALUE) 
-					weights[::std::distance(begin(slotToPos, Standard()), ::std::lower_bound(begin(slotToPos, Standard()), end(slotToPos, Standard()), pPos * n + (TSize) (n - posItStr2 - 1)))] += (TCargo) cargo(*itOut);
-			}
-		}
-	}
-	clear(map);
-
-	// Now the tough part: Find the right number for a given position
-	typedef String<TSize> TSequenceString;
-	typedef typename Iterator<TSequenceString, Standard>::Type TSeqIter;
-	TSequenceString seq;
-	resize(seq, length(slotToPos));
-	TSeqIter itSeq = begin(seq, Standard());
-	TSlotToPosIter itSlotPos = begin(slotToPos, Standard());
-	TSlotToPosIter itSlotPosEnd = end(slotToPos, Standard());
-	for(;itSlotPos != itSlotPosEnd; ++itSlotPos, ++itSeq) 
-		*itSeq = n - 1 - (*itSlotPos % n); 
-
-	// Calculate the heaviest increasing subsequence
-	String<TSize> positions;
-	TCargo score = (TCargo) heaviestIncreasingSubsequence(seq, weights, positions);
-
-	// Retrieve the alignment sequence
-	_heaviestCommonSubsequence(g, slotToPos, positions, m, n, str1, str2, align);
-
-	return score;
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Value<TString>::Type TVertexSet;
+
+    TSize m = length(str1);  // How many sets of vertex descriptors in seq1
+    TSize n = length(str2);  // How many sets of vertex descriptors in seq2
+
+    // Size of the sequences
+    // Note for profile alignments every member of the sequence is a String!!! of vertex descriptors
+
+    // Fill the vertex to position map for str1
+    // Remember for each vertex descriptor the position in the sequence
+    typedef String<TSize> TMapVertexPos;
+    TMapVertexPos map;
+    resize(map, getIdUpperBound(_getVertexIdManager(g)), MaxValue<TSize>::VALUE);
+    typedef typename Iterator<TString const, Standard>::Type TStringIterConst;
+    typedef typename Iterator<TVertexSet const, Standard>::Type TVertexSetIterConst;
+    TStringIterConst itStr1 = begin(str1, Standard());
+    TStringIterConst itStrEnd1 = end(str1, Standard());
+    TSize pos = 0;
+    TVertexSetIterConst itV;
+    TVertexSetIterConst itVEnd;
+    for(;itStr1 != itStrEnd1;++itStr1, ++pos) {
+        itV = begin(*itStr1, Standard());
+        itVEnd = end(*itStr1, Standard());
+        for(;itV != itVEnd;++itV) map[*itV] = pos;
+    }
+
+    // We could create the full graph -> too expensive
+    // Remember which edges are actually present
+    typedef String<TSize> TOccupiedPositions;
+    typedef typename Iterator<TOccupiedPositions, Standard>::Type TOccIter;
+    TOccupiedPositions occupiedPositions;
+    TStringIterConst itStr2 = begin(str2, Standard());
+    TStringIterConst itStrEnd2 = end(str2, Standard());
+    TSize posItStr2 = 0;
+    TSize pPos = 0;
+    for(;itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
+        itV = begin(*itStr2, Standard());
+        itVEnd = end(*itStr2, Standard());
+        for(;itV != itVEnd;++itV) {
+            TOutEdgeIterator itOut(g, *itV);
+            for(;!atEnd(itOut); ++itOut) {
+                // Target vertex must be in the map
+                pPos = map[targetVertex(itOut)];
+                if (pPos != MaxValue<TSize>::VALUE)
+                    appendValue(occupiedPositions, pPos * n + (TSize) (n - posItStr2 - 1), Generous());
+            }
+        }
+    }
+    std::sort(begin(occupiedPositions, Standard()), end(occupiedPositions, Standard()));
+    // Get all occupied positions
+    typedef String<TSize> TSlotToPos;
+    typedef typename Iterator<TSlotToPos, Standard>::Type TSlotToPosIter;
+    TSlotToPos slotToPos;
+    TSize counter = 0;
+    TSize oldVal = MaxValue<TSize>::VALUE;
+    TOccIter occIt = begin(occupiedPositions, Standard());
+    TOccIter occItEnd = end(occupiedPositions, Standard());
+    for(;occIt != occItEnd; ++occIt) {
+        if (oldVal != *occIt) {
+            appendValue(slotToPos, *occIt, Generous());
+            oldVal = *occIt;
+            ++counter;
+        }
+    }
+    clear(occupiedPositions);
+
+    // Walk through str2 and fill in the weights of the actual edges
+    typedef String<TCargo> TWeights;
+    TWeights weights;
+    resize(weights, length(slotToPos), 0);
+    itStr2 = begin(str2, Standard());
+    posItStr2 = 0;
+    for(;itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
+        itV = begin(*itStr2, Standard());
+        itVEnd = end(*itStr2, Standard());
+        for(;itV != itVEnd;++itV) {
+            TOutEdgeIterator itOut(g, *itV);
+            for(;!atEnd(itOut); ++itOut) {
+                // Target vertex must be in the map
+                pPos = map[targetVertex(itOut)];
+                if ( pPos != MaxValue<TSize>::VALUE)
+                    weights[std::distance(begin(slotToPos, Standard()), std::lower_bound(begin(slotToPos, Standard()), end(slotToPos, Standard()), pPos * n + (TSize) (n - posItStr2 - 1)))] += (TCargo) cargo(*itOut);
+            }
+        }
+    }
+    clear(map);
+
+    // Now the tough part: Find the right number for a given position
+    typedef String<TSize> TSequenceString;
+    typedef typename Iterator<TSequenceString, Standard>::Type TSeqIter;
+    TSequenceString seq;
+    resize(seq, length(slotToPos));
+    TSeqIter itSeq = begin(seq, Standard());
+    TSlotToPosIter itSlotPos = begin(slotToPos, Standard());
+    TSlotToPosIter itSlotPosEnd = end(slotToPos, Standard());
+    for(;itSlotPos != itSlotPosEnd; ++itSlotPos, ++itSeq)
+        *itSeq = n - 1 - (*itSlotPos % n);
+
+    // Calculate the heaviest increasing subsequence
+    String<TSize> positions;
+    TCargo score = (TCargo) heaviestIncreasingSubsequence(seq, weights, positions);
+
+    // Retrieve the alignment sequence
+    _heaviestCommonSubsequence(g, slotToPos, positions, m, n, str1, str2, align);
+
+    return score;
 
 }
 
@@ -2314,12 +2084,12 @@ heaviestCommonSubsequence(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
 template<typename TStringSet, typename TCargo, typename TSpec, typename TString>
 inline TCargo
 heaviestCommonSubsequence(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-						  TString const& str1, 
-						  TString const& str2) 
+                          TString const& str1,
+                          TString const& str2)
 {
-	SEQAN_CHECKPOINT
-	Nothing noth;
-	return heaviestCommonSubsequence(g, str1, str2, noth);
+    SEQAN_CHECKPOINT
+    Nothing noth;
+    return heaviestCommonSubsequence(g, str1, str2, noth);
 }
 
 template <typename TStringSet, typename TCargo, typename TSpec, typename TSequenceH, typename TSequenceV, typename TId, typename TPos, typename TTraceValue>
@@ -2372,4 +2142,4 @@ _alignTracePrint(String<TFragment>& matches,
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_H_
diff --git a/seqan/graph_align/graph_impl_align_adapt.h b/seqan/graph_align/graph_impl_align_adapt.h
index 3d2a217..4961495 100644
--- a/seqan/graph_align/graph_impl_align_adapt.h
+++ b/seqan/graph_align/graph_impl_align_adapt.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +33,8 @@
 // Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_
+#define SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_
 
 namespace seqan {
 
@@ -55,49 +55,49 @@ namespace seqan {
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TIteratorSpec>
-class Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > 
+class Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > >
 {
 public:
-	typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph_;
-	typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
-	typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;
-	
-	TGraph_ const* data_host;
-	TVertexDescriptor_ data_source;
-	TEdgeDescriptor_ data_edge;
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) : 
-		data_host(&_graph),
-		data_source(v)
-	{
-		SEQAN_CHECKPOINT
-		if (empty(_graph)) data_edge = 0;
-		else data_edge = getValue(_graph.data_align.data_vertex,v);
-	}
-	
-	Iter(Iter const& _iter) : 
-		data_host(_iter.data_host),
-		data_source(_iter.data_source),
-		data_edge(_iter.data_edge)
-	{
-	}
-
-	~Iter() {
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host = _other.data_host;
-		data_source = _other.data_source;
-		data_edge = _other.data_edge;
-		return *this;
-	}
+    typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph_;
+    typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
+    typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;
+
+    TGraph_ const* data_host;
+    TVertexDescriptor_ data_source;
+    TEdgeDescriptor_ data_edge;
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) :
+        data_host(&_graph),
+        data_source(v)
+    {
+        SEQAN_CHECKPOINT
+        if (empty(_graph)) data_edge = 0;
+        else data_edge = getValue(_graph.data_align.data_vertex,v);
+    }
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_source(_iter.data_source),
+        data_edge(_iter.data_edge)
+    {
+    }
+
+    ~Iter() {
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host = _other.data_host;
+        data_source = _other.data_source;
+        data_edge = _other.data_edge;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -110,14 +110,14 @@ class Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<Inte
 
 template<typename TStringSet, typename TCargo, typename TGraphSpec>
 struct Iterator<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, OutEdgeIterator>
-{	
-	typedef Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
+{
+    typedef Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
 };
 
 template<typename TStringSet, typename TCargo, typename TGraphSpec>
 struct Iterator<Graph<Alignment<TStringSet, TCargo, TGraphSpec> > const, OutEdgeIterator>
-{	
-	typedef Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> > const, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
+{
+    typedef Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> > const, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
 };
 
 
@@ -131,8 +131,8 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline typename GetValue<Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 getValue(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -141,8 +141,8 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline typename Reference<Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 value(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -151,8 +151,8 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline bool
 atBegin(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == getValue(_getVertexString(*it.data_host), it.data_source));
+    SEQAN_CHECKPOINT
+    return (it.data_edge == getValue(_getVertexString(*it.data_host), it.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -161,8 +161,8 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline void
 goBegin(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = getValue(_getVertexString(*it.data_host),it.data_source);
+    SEQAN_CHECKPOINT
+    it.data_edge = getValue(_getVertexString(*it.data_host),it.data_source);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -171,8 +171,8 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline bool
 atEnd(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == 0);
+    SEQAN_CHECKPOINT
+    return (it.data_edge == 0);
 }
 
 
@@ -182,8 +182,8 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline void
 goEnd(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = 0;
+    SEQAN_CHECKPOINT
+    it.data_edge = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -192,11 +192,11 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline void
 goNext(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atEnd(it)) {
-		if (it.data_source == getSource(it.data_edge)) it.data_edge = getNextS(it.data_edge);
-		else it.data_edge = getNextT(it.data_edge);
-	}
+    SEQAN_CHECKPOINT
+    if (!atEnd(it)) {
+        if (it.data_source == getSource(it.data_edge)) it.data_edge = getNextS(it.data_edge);
+        else it.data_edge = getNextT(it.data_edge);
+    }
 }
 
 
@@ -206,21 +206,21 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline void
 goPrevious(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	TEdge* current = getValue(_getVertexString(*it.data_host), it.data_source);
-	if (current == it.data_edge) return;
-	while (current != 0) {
-		if (it.data_source == getSource(current)) {
-			if (it.data_edge == getNextS(current)) break;
-			else current = getNextS(current);
-		} else {
-			if (it.data_edge == getNextT(current)) break;
-			else current = getNextT(current);
-		}
-	}
-	it.data_edge = current;
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    TEdge* current = getValue(_getVertexString(*it.data_host), it.data_source);
+    if (current == it.data_edge) return;
+    while (current != 0) {
+        if (it.data_source == getSource(current)) {
+            if (it.data_edge == getNextS(current)) break;
+            else current = getNextS(current);
+        } else {
+            if (it.data_edge == getNextT(current)) break;
+            else current = getNextT(current);
+        }
+    }
+    it.data_edge = current;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -228,11 +228,11 @@ goPrevious(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator
 template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator ==(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge==it2.data_edge) && 
-			(it1.data_source==it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge==it2.data_edge) &&
+            (it1.data_source==it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -240,11 +240,11 @@ operator ==(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterato
 template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator !=(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge!=it2.data_edge) || 
-			(it1.data_source!=it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge!=it2.data_edge) ||
+            (it1.data_source!=it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -253,12 +253,12 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline typename VertexDescriptor<Graph<Alignment<TStringSet, TCargo, TGraphSpec> > >::Type
 targetVertex(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor target = targetVertex(*it.data_host, it.data_edge);
-	if (target != it.data_source) return target;
-	else return sourceVertex(*it.data_host, it.data_edge);
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor target = targetVertex(*it.data_host, it.data_edge);
+    if (target != it.data_source) return target;
+    else return sourceVertex(*it.data_host, it.data_edge);
 }
 
 
@@ -273,15 +273,15 @@ template<typename TStringSet, typename TCargo, typename TGraphSpec, typename TSp
 inline void
 goNext(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	_goNextInternal(it);
-	TVertexDescriptor sourceV = sourceVertex(it.data_edge_it);
-	while((!atEnd(it)) && (targetVertex(hostGraph(it), getValue(it.data_edge_it)) == sourceV)) {
-		_goNextInternal(it);
-		sourceV = sourceVertex(it.data_edge_it);
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    _goNextInternal(it);
+    TVertexDescriptor sourceV = sourceVertex(it.data_edge_it);
+    while((!atEnd(it)) && (targetVertex(hostGraph(it), getValue(it.data_edge_it)) == sourceV)) {
+        _goNextInternal(it);
+        sourceV = sourceVertex(it.data_edge_it);
+    }
 }
 
 
@@ -298,30 +298,30 @@ goNext(Iter<Graph<Alignment<TStringSet, TCargo, TGraphSpec> >, GraphIterator<Int
 template <typename TStringSet, typename TCargo, typename TSpec, typename TNodeAttributes>
 inline void
 _createNodeAttributes(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-					  TNodeAttributes& nodeMap)
+                      TNodeAttributes& nodeMap)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Id<TGraph>::Type TIdType;
-	resizeVertexMap(g, nodeMap);
-
-	unsigned int scaling = 20 / length(value(g.data_sequence));
-	if (scaling == 0) scaling = 1;
-
-	typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
-	TConstIter it(g);
-	for(;!atEnd(it);++it) {
-		TIdType id = sequenceId(g, *it);
-		std::ostringstream outs; 
-		outs << "label = \"";
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Id<TGraph>::Type TIdType;
+    resizeVertexMap(nodeMap, g);
+
+    unsigned int scaling = 20 / length(value(g.data_sequence));
+    if (scaling == 0) scaling = 1;
+
+    typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
+    TConstIter it(g);
+    for(;!atEnd(it);++it) {
+        TIdType id = sequenceId(g, *it);
+        std::ostringstream outs;
+        outs << "label = \"";
         outs << "[" << fragmentBegin(g, *it) << "," << fragmentBegin(g, *it)+fragmentLength(g, *it) << ")";
         // the lower command outputs the fragemtn of the string it is replaced by the interval
-		//outs << label(g, *it);
-		outs << "\", group = ";
-		outs << id;
-		append(property(nodeMap, *it), outs.str().c_str());		
-		//std::cout << property(nodeMap, *it) << std::endl;
-	}
+        //outs << label(g, *it);
+        outs << "\", group = ";
+        outs << id;
+        append(property(nodeMap, *it), outs.str().c_str());
+        //std::cout << property(nodeMap, *it) << std::endl;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -329,10 +329,10 @@ _createNodeAttributes(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
 template <typename TStringSet, typename TSpec, typename TEdgeAttributes>
 inline void
 _createEdgeAttributes(Graph<Alignment<TStringSet, void, TSpec> > const& g,
-					  TEdgeAttributes& edgeMap)
+                      TEdgeAttributes& edgeMap)
 {
-	SEQAN_CHECKPOINT
-	_createEmptyEdgeAttributes(g.data_align,edgeMap);
+    SEQAN_CHECKPOINT
+    _createEmptyEdgeAttributes(g.data_align,edgeMap);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -340,87 +340,87 @@ _createEdgeAttributes(Graph<Alignment<TStringSet, void, TSpec> > const& g,
 template <typename TStringSet, typename TCargo, typename TSpec, typename TEdgeAttributes>
 inline void
 _createEdgeAttributes(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-					  TEdgeAttributes& edgeMap)
+                      TEdgeAttributes& edgeMap)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	resizeEdgeMap(g, edgeMap);
-
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
-	TConstEdIter itEd(g);
-	for(;!atEnd(itEd);++itEd) {
-		TCargo c = getCargo(*itEd);
-		std::ostringstream outs; 
-		outs << "label = \"";
-		outs << (TCargo) c;
-		outs << "\",";
-		outs << "len = 10.0";
-		append(property(edgeMap, *itEd), outs.str().c_str());
-	}
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    resizeEdgeMap(edgeMap, g);
+
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
+    TConstEdIter itEd(g);
+    for(;!atEnd(itEd);++itEd) {
+        TCargo c = getCargo(*itEd);
+        std::ostringstream outs;
+        outs << "label = \"";
+        outs << (TCargo) c;
+        outs << "\",";
+        outs << "len = 10.0";
+        append(property(edgeMap, *itEd), outs.str().c_str());
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TFile, typename TStringSet, typename TCargo, typename TSpec>
+template <typename TTarget, typename TStringSet, typename TCargo, typename TSpec>
 inline void
-_writeGraphFooter(TFile & file,
-				  Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-				  DotDrawing)
+_writeGraphFooter(TTarget & iter,
+                  Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+                  DotDrawing)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Id<TGraph>::Type TId;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	TStringSet& str = stringSet(g);
-	TSize len = length(str);
-	for(TSize i = 0; i<len; ++i) {
-		TId seqId = positionToId(str, i);
-		TSize j = 0;
-		TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();	
-		TVertexDescriptor previousVertex = nilVertex;
-		while(j<length(str[i])) {
-			TVertexDescriptor nextVertex = findVertex(const_cast<TGraph&>(g), seqId, j);
-			if (nextVertex == nilVertex) {
-				++j;
-				continue;
-			}
-			if (previousVertex != nilVertex) {
-				streamPut(file, previousVertex);
-				streamPut(file, " -- ");
-				streamPut(file, nextVertex);
-				streamPut(file, " [");
-				streamPut(file, "len=3.0, arrowhead=vee");
-				streamPut(file, "];\n");
-			}
-			previousVertex = nextVertex;
-			j += fragmentLength(g, nextVertex);
-		}
-	}
-	streamPut(file, '\n');
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Id<TGraph>::Type TId;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    TStringSet& str = stringSet(g);
+    TSize len = length(str);
+    for(TSize i = 0; i<len; ++i) {
+        TId seqId = positionToId(str, i);
+        TSize j = 0;
+        TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+        TVertexDescriptor previousVertex = nilVertex;
+        while(j<length(str[i]))
+        {
+            TVertexDescriptor nextVertex = findVertex(const_cast<TGraph&>(g), seqId, j);
+            if (nextVertex == nilVertex) {
+                ++j;
+                continue;
+            }
+            if (previousVertex != nilVertex)
+            {
+                appendNumber(iter, previousVertex);
+                write(iter, " -- ");
+                appendNumber(iter, nextVertex);
+                write(iter, " [len=3.0, arrowhead=vee];\n");
+            }
+            previousVertex = nextVertex;
+            j += fragmentLength(g, nextVertex);
+        }
+    }
+    writeValue(iter, '\n');
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TFile, typename TStringSet, typename TCargo, typename TSpec>
+template <typename TTarget, typename TStringSet, typename TCargo, typename TSpec>
 inline void
-_writeGraphType(TFile & file,
-				Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
-				DotDrawing)
+_writeGraphType(TTarget & iter,
+                Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
+                DotDrawing)
 {
-    streamPut(file, "graph");
+    write(iter, "graph");
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TFile, typename TStringSet, typename TCargo, typename TSpec>
+template <typename TTarget, typename TStringSet, typename TCargo, typename TSpec>
 inline void
-_writeEdgeType(TFile & file,
-			   Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
-			   DotDrawing)
+_writeEdgeType(TTarget & iter,
+               Graph<Alignment<TStringSet, TCargo, TSpec> > const&,
+               DotDrawing)
 {
-    streamPut(file, " -- ");
+    write(iter, " -- ");
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_IMPL_ALIGN_ADAPT_H_
diff --git a/seqan/graph_msa.h b/seqan/graph_msa.h
index 4f7e8f9..325f592 100644
--- a/seqan/graph_msa.h
+++ b/seqan/graph_msa.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/graph_msa/INFO b/seqan/graph_msa/INFO
deleted file mode 100644
index e686c32..0000000
--- a/seqan/graph_msa/INFO
+++ /dev/null
@@ -1,9 +0,0 @@
-Name: seqan-graph_msa
-Author: Tobias Rausch <rausch@embl.de>
-Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
-Maintainer: Rene Rahn <rene.rahn@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Multiple sequence alignment and guide tree computation.
- This module contains most of the functionality for the program SeqAn::T-Coffee.
diff --git a/seqan/graph_msa/graph_align_tcoffee_base.h b/seqan/graph_msa/graph_align_tcoffee_base.h
index 295ad16..8199d52 100644
--- a/seqan/graph_msa/graph_align_tcoffee_base.h
+++ b/seqan/graph_msa/graph_align_tcoffee_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -76,35 +76,13 @@ static const int SEQAN_DISTANCE_UNITY = 1;
  * @signature typedef Tag<FractionalScore_> const ReScore;
  */
 
-/**
-.Tag.Alignment Graph Combination:
-..cat:Alignments
-..summary:A tag to specify how to combine alignment graphs.
-..include:seqan/graph_msa.h
-*/
-
-/**
-.Tag.Alignment Graph Combination.value.FractionalScore:
-	Rescores matches with the appropriate fractional score.
-..include:seqan/graph_msa.h
-*/
 struct FractionalScore_;
 typedef Tag<FractionalScore_> const FractionalScore;
 
 
-/**
-.Tag.Alignment Graph Combination.value.FrequencyCount:
-	Rescores matches with the frequency count for this edge.
-..include:seqan/graph_msa.h
-*/
 struct FrequencyCounting_;
 typedef Tag<FrequencyCounting_> const FrequencyCounting;
 
-/**
-.Tag.Alignment Graph Combination.value.ReScore:
-	Rescores the matches after segment-match refinement.
-..include:seqan/graph_msa.h
-*/
 struct ReScore_;
 typedef Tag<ReScore_> const ReScore;
 
@@ -117,7 +95,7 @@ typedef Tag<ReScore_> const ReScore;
  * @fn buildAlignmentGraph
  * @headerfile <seqan/graph_msa.h>
  * @brief Builds an @link AlignmentGraph @endlink from a seqt of input alignments.
- 
+
  * @signature void buildAlignmentGraph(matches[, score], outGraph, tag);
  * @signature void buildAlignmentGraph(matches, score, outGraph, scoreType, ReScore);
  *
@@ -129,186 +107,163 @@ typedef Tag<ReScore_> const ReScore;
  *
  * Calls the function @link matchRefinement @endlink and adapts the scores according to <tt>tag</tt>.
  */
- 
-
-/**
-.Function.buildAlignmentGraph
-..class:Spec.Alignment Graph
-..summary:Builds an @Spec.Alignment Graph@ from a set of input alignments.
-..cat:Graph
-..signature:
-buildAlignmentGraph(matches, [scores,] outGraph, tag)
-buildAlignmentGraph(matches, scores, outGraph, scoreType, ReScore)
-..param.matches:A string of alignments, e.g. @Class.Fragment@ or @Class.Align@.
-...type:Class.String
-..param.scores:A string of scores.
-...type:Class.String
-..param.outGraph:An alignment graph with a set string set.
-...type:Spec.Alignment Graph
-..param.scoreType:A score type.
-...type:Class.Score
-..param.tag:A tag indicating the scoring of matches.
-...type:Tag.Alignment Graph Combination
-..returns:void
-..include:seqan/graph_msa.h
-..remarks:Calls the function @Function.matchRefinement@ and adapts scores according to tag.
-*/
+
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec> 
+template<typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec>
 inline void
 buildAlignmentGraph(String<TFragment, TSpec1>& matches,
-					String<TScoreValue, TSpec2>& scores,
-					Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph,
-					FractionalScore)
+                    String<TScoreValue, TSpec2>& scores,
+                    Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph,
+                    FractionalScore)
 {
-	SEQAN_CHECKPOINT
-	typedef String<TFragment, TSpec1> TFragmentString;
-	typedef typename Iterator<TFragmentString, Standard>::Type TFragmentStringIter;
-	typedef String<TScoreValue, TSpec2> TScoreValues;
-	typedef typename Iterator<TScoreValues, Standard>::Type TScoreValuesIter;
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TOutGraph;
-	typedef typename Size<TFragmentString>::Type TSize;
-	typedef typename Id<TOutGraph>::Type TId;
-	//typedef typename EdgeDescriptor<TOutGraph>::Type TEdgeDescriptor;
-	typedef typename VertexDescriptor<TOutGraph>::Type TVertexDescriptor;
-
-	// Initialization
-	clearVertices(outGraph);
-	TStringSet& strSet = stringSet(outGraph);
-
-	// Segment-match refinement
-	matchRefinement(matches,strSet,outGraph);
-
-	// Clear edge-weights
-	typedef typename Iterator<TOutGraph, EdgeIterator>::Type TEdgeIterator;
-	TEdgeIterator itE(outGraph);
-	for(;!atEnd(itE);goNext(itE)) cargo(value(itE)) = 1;
-
-	// Adapt the scores
-	TFragmentStringIter it = begin(matches, Standard() );
-	TFragmentStringIter endIt = end(matches, Standard() );
-	TScoreValuesIter scoreIt = begin(scores, Standard() );
-	for(; it != endIt; ++it, ++scoreIt) {
-		TId id1 = sequenceId(*it,0);
-		TId id2 = sequenceId(*it,1);
-		TSize pos1 = fragmentBegin(*it, id1);
-		TSize pos2 = fragmentBegin(*it, id2);
-		TSize fragLen = fragmentLength(*it, id1);
-		TSize end1 = pos1 + fragLen;
-		while(pos1 < end1) {
-			TVertexDescriptor p1 = findVertex(outGraph, id1, pos1);
-			TVertexDescriptor p2 = findVertex(outGraph, id2, pos2);
-			TSize vertexLen = fragmentLength(outGraph, p1);
-			cargo(findEdge(outGraph, p1, p2)) += (TCargo) ((vertexLen * (*scoreIt)) / fragLen);
-			pos1 += vertexLen;
-			pos2 += vertexLen;
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef String<TFragment, TSpec1> TFragmentString;
+    typedef typename Iterator<TFragmentString, Standard>::Type TFragmentStringIter;
+    typedef String<TScoreValue, TSpec2> TScoreValues;
+    typedef typename Iterator<TScoreValues, Standard>::Type TScoreValuesIter;
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TOutGraph;
+    typedef typename Size<TFragmentString>::Type TSize;
+    typedef typename Id<TOutGraph>::Type TId;
+    //typedef typename EdgeDescriptor<TOutGraph>::Type TEdgeDescriptor;
+    typedef typename VertexDescriptor<TOutGraph>::Type TVertexDescriptor;
+
+    // Initialization
+    clearVertices(outGraph);
+    TStringSet& strSet = stringSet(outGraph);
+
+    // Segment-match refinement
+    matchRefinement(matches,strSet,outGraph);
+
+    // Clear edge-weights
+    typedef typename Iterator<TOutGraph, EdgeIterator>::Type TEdgeIterator;
+    TEdgeIterator itE(outGraph);
+    for(;!atEnd(itE);goNext(itE)) cargo(value(itE)) = 1;
+
+    // Adapt the scores
+    TFragmentStringIter it = begin(matches, Standard() );
+    TFragmentStringIter endIt = end(matches, Standard() );
+    TScoreValuesIter scoreIt = begin(scores, Standard() );
+    for(; it != endIt; ++it, ++scoreIt) {
+        TId id1 = sequenceId(*it,0);
+        TId id2 = sequenceId(*it,1);
+        TSize pos1 = fragmentBegin(*it, id1);
+        TSize pos2 = fragmentBegin(*it, id2);
+        TSize fragLen = fragmentLength(*it, id1);
+        TSize end1 = pos1 + fragLen;
+        while(pos1 < end1) {
+            TVertexDescriptor p1 = findVertex(outGraph, id1, pos1);
+            TVertexDescriptor p2 = findVertex(outGraph, id2, pos2);
+            TSize vertexLen = fragmentLength(outGraph, p1);
+            cargo(findEdge(outGraph, p1, p2)) += (TCargo) ((vertexLen * (*scoreIt)) / fragLen);
+            pos1 += vertexLen;
+            pos2 += vertexLen;
+        }
+    }
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TFragment, typename TSpec1, typename TStringSet, typename TCargo, typename TSpec> 
+template<typename TFragment, typename TSpec1, typename TStringSet, typename TCargo, typename TSpec>
 inline void
 buildAlignmentGraph(String<TFragment, TSpec1>& matches,
-					Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph,
-					FrequencyCounting)
+                    Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph,
+                    FrequencyCounting)
 {
-	//typedef String<TFragment, TSpec1> TFragmentString;
-	//typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TOutGraph;
-	//typedef typename Size<TFragmentString>::Type TSize;
+    //typedef String<TFragment, TSpec1> TFragmentString;
+    //typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TOutGraph;
+    //typedef typename Size<TFragmentString>::Type TSize;
 
-	// Initialization
-	clearVertices(outGraph);
-	TStringSet& strSet = stringSet(outGraph);
+    // Initialization
+    clearVertices(outGraph);
+    TStringSet& strSet = stringSet(outGraph);
 
-	// Segment-match refinement
-	matchRefinement(matches,strSet,outGraph);
+    // Segment-match refinement
+    matchRefinement(matches,strSet,outGraph);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec> 
+template<typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec>
 inline void
 buildAlignmentGraph(String<TFragment, TSpec1>& matches,
-					String<TScoreValue, TSpec2>&,
-					Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph,
-					FrequencyCounting)
+                    String<TScoreValue, TSpec2>&,
+                    Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph,
+                    FrequencyCounting)
 {
-	buildAlignmentGraph(matches, outGraph, FrequencyCounting() );
+    buildAlignmentGraph(matches, outGraph, FrequencyCounting() );
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TString, typename TSpec, typename TScoreType, typename TSize, typename TSpec2, typename TScoreString, typename TScoreValue> 
+template<typename TString, typename TSpec, typename TScoreType, typename TSize, typename TSpec2, typename TScoreString, typename TScoreValue>
 inline void
 _scoreMatches(StringSet<TString, TSpec> const & seqSet,
-			  TScoreType const & scType,
-			  String<Fragment<TSize, ExactFragment<> >, TSpec2> const & matches,
-			  TScoreString & scores,
-			  TScoreValue offset)
+              TScoreType const & scType,
+              String<Fragment<TSize, ExactFragment<> >, TSpec2> const & matches,
+              TScoreString & scores,
+              TScoreValue offset)
 {
-	typedef String<Fragment<TSize, ExactFragment<> >, TSpec2> const TFragmentString;
-	typedef typename Id<typename Value<TFragmentString>::Type>::Type TId;
-	typedef typename Iterator<TFragmentString, Standard>::Type TFragmentStringIter;
-	typedef typename Iterator<TString const, Standard>::Type TStringIter;
-	typedef typename Iterator<TScoreString, Standard>::Type TScoreStringIter;
-	resize(scores, length(matches));
-
-	// Get the scores
-	TFragmentStringIter itF = begin(matches, Standard() );
-	TFragmentStringIter itFEnd = end(matches, Standard() );
-	TScoreStringIter itSc = begin(scores, Standard() );
-	TId id1 = 0; TId id2 = 0;
-	TSize pos1 = 0; TSize pos2 = 0;	TSize fragLen = 0;
-	for(; itF != itFEnd; ++itF, ++itSc) {
-		id1 = sequenceId(*itF,0);
-		id2 = sequenceId(*itF,1);
-		pos1 = fragmentBegin(*itF, id1);
-		pos2 = fragmentBegin(*itF, id2);
-		fragLen = fragmentLength(*itF, id1);
-		TStringIter itS1 = begin(seqSet[idToPosition(seqSet, id1)], Standard() );
-		itS1 += pos1;
-		TStringIter itS2 = begin(seqSet[idToPosition(seqSet, id2)], Standard() );
-		itS2 += pos2;
-		*itSc = 0;
-		for(TSize i = 0; i<fragLen; ++i, ++itS1, ++itS2) 
-			*itSc += offset + score(scType, *itS1, *itS2);
-	}
+    typedef String<Fragment<TSize, ExactFragment<> >, TSpec2> const TFragmentString;
+    typedef typename Id<typename Value<TFragmentString>::Type>::Type TId;
+    typedef typename Iterator<TFragmentString, Standard>::Type TFragmentStringIter;
+    typedef typename Iterator<TString const, Standard>::Type TStringIter;
+    typedef typename Iterator<TScoreString, Standard>::Type TScoreStringIter;
+    resize(scores, length(matches));
+
+    // Get the scores
+    TFragmentStringIter itF = begin(matches, Standard() );
+    TFragmentStringIter itFEnd = end(matches, Standard() );
+    TScoreStringIter itSc = begin(scores, Standard() );
+    TId id1 = 0; TId id2 = 0;
+    TSize pos1 = 0; TSize pos2 = 0;    TSize fragLen = 0;
+    for(; itF != itFEnd; ++itF, ++itSc) {
+        id1 = sequenceId(*itF,0);
+        id2 = sequenceId(*itF,1);
+        pos1 = fragmentBegin(*itF, id1);
+        pos2 = fragmentBegin(*itF, id2);
+        fragLen = fragmentLength(*itF, id1);
+        TStringIter itS1 = begin(seqSet[idToPosition(seqSet, id1)], Standard() );
+        itS1 += pos1;
+        TStringIter itS2 = begin(seqSet[idToPosition(seqSet, id2)], Standard() );
+        itS2 += pos2;
+        *itSc = 0;
+        for(TSize i = 0; i<fragLen; ++i, ++itS1, ++itS2)
+            *itSc += offset + score(scType, *itS1, *itS2);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TString, typename TSpec, typename TScoreType, typename TFragment, typename TSpec2, typename TScoreString> 
+template<typename TString, typename TSpec, typename TScoreType, typename TFragment, typename TSpec2, typename TScoreString>
 inline void
 _scoreMatches(StringSet<TString, TSpec> const& seqSet,
-			  TScoreType const& scType,
-			  String<TFragment, TSpec2> const& matches,
-			  TScoreString& scores)
+              TScoreType const& scType,
+              String<TFragment, TSpec2> const& matches,
+              TScoreString& scores)
 {
-	SEQAN_CHECKPOINT
-	_scoreMatches(seqSet, scType, matches, scores, (typename Value<TScoreString>::Type) 10);
+    SEQAN_CHECKPOINT
+    _scoreMatches(seqSet, scType, matches, scores, (typename Value<TScoreString>::Type) 10);
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec, typename TScore> 
+template<typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec, typename TScore>
 inline void
 buildAlignmentGraph(String<TFragment, TSpec1>& matches,
-					String<TScoreValue, TSpec2>& scores,
-					Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph,
-					TScore const& scType,
-					ReScore)
+                    String<TScoreValue, TSpec2>& scores,
+                    Graph<Alignment<TStringSet, TCargo, TSpec> >& outGraph,
+                    TScore const& scType,
+                    ReScore)
 {
-	// ReScore
-	_scoreMatches(stringSet(outGraph), scType, matches, scores);
-	
-	// Use fractinal score
-	buildAlignmentGraph(matches, scores, outGraph, FractionalScore() );
+    // ReScore
+    _scoreMatches(stringSet(outGraph), scType, matches, scores);
+
+    // Use fractinal score
+    buildAlignmentGraph(matches, scores, outGraph, FractionalScore() );
 }
 
 
@@ -325,29 +280,29 @@ buildAlignmentGraph(String<TFragment, TSpec1>& matches,
 template<typename TVertexDescriptor, typename TCargo>
 struct MsaEdgeCargo_ {
  public:
-	 TVertexDescriptor v1;
-	 TVertexDescriptor v2;
-	 TCargo c;
+     TVertexDescriptor v1;
+     TVertexDescriptor v2;
+     TCargo c;
+
+     MsaEdgeCargo_() {}
 
-	 MsaEdgeCargo_() {}
 
-	
-	 MsaEdgeCargo_(TVertexDescriptor vert1, TVertexDescriptor vert2, TCargo carg) :
-	 v1(vert1), v2(vert2), c(carg) {}
+     MsaEdgeCargo_(TVertexDescriptor vert1, TVertexDescriptor vert2, TCargo carg) :
+     v1(vert1), v2(vert2), c(carg) {}
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TVertexDescriptor, typename TCargo>
 struct LessMsaEdgeCargo_ :
-	public ::std::binary_function<TVertexDescriptor, TCargo, bool>
+    public std::binary_function<TVertexDescriptor, TCargo, bool>
 {
-	inline bool 
-	operator() (MsaEdgeCargo_<TVertexDescriptor, TCargo> const& a1, 
-				MsaEdgeCargo_<TVertexDescriptor, TCargo> const& a2) const 
-	{
-		return (a1.v1 == a2.v1) ? (a1.v2 < a2.v2) : (a1.v1 < a2.v1);
-	}
+    inline bool
+    operator() (MsaEdgeCargo_<TVertexDescriptor, TCargo> const& a1,
+                MsaEdgeCargo_<TVertexDescriptor, TCargo> const& a2) const
+    {
+        return (a1.v1 == a2.v1) ? (a1.v2 < a2.v2) : (a1.v1 < a2.v1);
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -364,454 +319,436 @@ struct LessMsaEdgeCargo_ :
  * @param[in]     minMembers Minimum number of sequences per group.  If a guide tree and a minimum number of members
  *                           if given then the triplet extension is limited to groups of sequences.
  *
- * @section Remarks
- *
- * The running time is quadratic in the number of pairwise edes.
+ * The running time is quadratic in the number of pairwise edges.
  */
 
-/**
-.Function.tripletLibraryExtension
-..class:Spec.Alignment Graph
-..summary:Performs a full or group-based consistency extension.
-..cat:Graph
-..signature:
-void tripletLibraryExtension(graph, [,guideTree, minMembers])
-..param.graph:An alignment graph.
-...type:Spec.Alignment Graph
-..param.guideTree:A guide tree.
-..param.minMembers:Minimum number of sequences per group.
-...remarks:If a guide tree and a minimum number of memebers is given, the triplet extension is limited to groups of sequences.
-..remarks:The running time is quadratic in the number of pairwise edges.
-..returns:void
-..include:seqan/graph_msa.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec>
-inline void 
+inline void
 tripletLibraryExtension(Graph<Alignment<TStringSet, TCargo, TSpec> >& g)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	//typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-
-	// Store all edges
-	typedef std::pair<TVertexDescriptor, TVertexDescriptor> TNewEdge;
-	typedef std::map<TNewEdge, TCargo> TEdgeMap;
-	typedef typename TEdgeMap::iterator TEdgeMapIter;
-	TEdgeMap newEMap;
-	typedef MsaEdgeCargo_<TVertexDescriptor, TCargo> TEdge;
-	typedef String<TEdge> TEdgeString;
-	TEdgeString fullEdges;
-	TEdgeIterator itE(g);
-	for(;!atEnd(itE);goNext(itE)) {
-		TVertexDescriptor sV = sourceVertex(itE);
-		TVertexDescriptor tV = targetVertex(itE);
-		TCargo c = cargo(*itE);
-		appendValue(fullEdges, TEdge(sV, tV, c), Generous());
-		appendValue(fullEdges, TEdge(tV, sV, c), Generous());
-		newEMap.insert(std::make_pair(TNewEdge(sV, tV), c));
-	}
-	clearEdges(g);
-	::std::sort(begin(fullEdges, Standard()), end(fullEdges, Standard()), LessMsaEdgeCargo_<TVertexDescriptor, TCargo>() );
-	
-	// Perform triplet extension
-	typedef typename Iterator<TEdgeString, Standard>::Type TEdgeIter;
-	TEdgeIter itEdges1 = begin(fullEdges, Standard());
-	TEdgeIter itEdgesEnd = end(fullEdges, Standard());
-	for(; itEdges1 != itEdgesEnd; ++itEdges1) {
-		for(TEdgeIter itEdges2 = itEdges1; ++itEdges2 != itEdgesEnd;) {
-			if ((*itEdges1).v1 != (*itEdges2).v1) break;
-			if (sequenceId(g, (*itEdges1).v2) != sequenceId(g, (*itEdges2).v2)) {
-				TCargo weight = ((*itEdges1).c < (*itEdges2).c) ? (*itEdges1).c : (*itEdges2).c;
-				if ((*itEdges1).v2 < (*itEdges2).v2) {
-					TEdgeMapIter pos = newEMap.find(TNewEdge((*itEdges1).v2, (*itEdges2).v2));
-					if (pos != newEMap.end()) (*pos).second += weight;
-					else newEMap.insert(std::make_pair(TNewEdge((*itEdges1).v2, (*itEdges2).v2), weight));
-				} else {
-					TEdgeMapIter pos = newEMap.find(TNewEdge((*itEdges2).v2, (*itEdges1).v2));
-					if (pos != newEMap.end()) (*pos).second += weight;
-					else newEMap.insert(std::make_pair(TNewEdge((*itEdges2).v2, (*itEdges1).v2), weight));
-				}	
-			}
-		}
-	}
-	clear(fullEdges);
-
-	// Insert edges
-	for(TEdgeMapIter itE = newEMap.begin(); itE != newEMap.end(); ++itE) 
-		addEdge(g, (*itE).first.first, (*itE).first.second, (*itE).second);
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    //typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+
+    // Store all edges
+    typedef std::pair<TVertexDescriptor, TVertexDescriptor> TNewEdge;
+    typedef std::map<TNewEdge, TCargo> TEdgeMap;
+    typedef typename TEdgeMap::iterator TEdgeMapIter;
+    TEdgeMap newEMap;
+    typedef MsaEdgeCargo_<TVertexDescriptor, TCargo> TEdge;
+    typedef String<TEdge> TEdgeString;
+    TEdgeString fullEdges;
+    TEdgeIterator itE(g);
+    for(;!atEnd(itE);goNext(itE)) {
+        TVertexDescriptor sV = sourceVertex(itE);
+        TVertexDescriptor tV = targetVertex(itE);
+        TCargo c = cargo(*itE);
+        appendValue(fullEdges, TEdge(sV, tV, c), Generous());
+        appendValue(fullEdges, TEdge(tV, sV, c), Generous());
+        newEMap.insert(std::make_pair(TNewEdge(sV, tV), c));
+    }
+    clearEdges(g);
+    std::sort(begin(fullEdges, Standard()), end(fullEdges, Standard()), LessMsaEdgeCargo_<TVertexDescriptor, TCargo>() );
+
+    // Perform triplet extension
+    typedef typename Iterator<TEdgeString, Standard>::Type TEdgeIter;
+    TEdgeIter itEdges1 = begin(fullEdges, Standard());
+    TEdgeIter itEdgesEnd = end(fullEdges, Standard());
+    for(; itEdges1 != itEdgesEnd; ++itEdges1) {
+        for(TEdgeIter itEdges2 = itEdges1; ++itEdges2 != itEdgesEnd;) {
+            if ((*itEdges1).v1 != (*itEdges2).v1) break;
+            if (sequenceId(g, (*itEdges1).v2) != sequenceId(g, (*itEdges2).v2)) {
+                TCargo weight = ((*itEdges1).c < (*itEdges2).c) ? (*itEdges1).c : (*itEdges2).c;
+                if ((*itEdges1).v2 < (*itEdges2).v2) {
+                    TEdgeMapIter pos = newEMap.find(TNewEdge((*itEdges1).v2, (*itEdges2).v2));
+                    if (pos != newEMap.end()) (*pos).second += weight;
+                    else newEMap.insert(std::make_pair(TNewEdge((*itEdges1).v2, (*itEdges2).v2), weight));
+                } else {
+                    TEdgeMapIter pos = newEMap.find(TNewEdge((*itEdges2).v2, (*itEdges1).v2));
+                    if (pos != newEMap.end()) (*pos).second += weight;
+                    else newEMap.insert(std::make_pair(TNewEdge((*itEdges2).v2, (*itEdges1).v2), weight));
+                }
+            }
+        }
+    }
+    clear(fullEdges);
+
+    // Insert edges
+    for(TEdgeMapIter itE = newEMap.begin(); itE != newEMap.end(); ++itE)
+        addEdge(g, (*itE).first.first, (*itE).first.second, (*itE).second);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TGuideTree, typename TSeqGroups, typename TGroupRoot, typename TSize>
-inline void 
-_subTreeSearch(TGuideTree& guideTree, 
-			   TSeqGroups& seqGroups,
-			   TGroupRoot& groupRoot,
-			   TSize minMembers) 
+inline void
+_subTreeSearch(TGuideTree& guideTree,
+               TSeqGroups& seqGroups,
+               TGroupRoot& groupRoot,
+               TSize minMembers)
 {
-	typedef typename Value<TSeqGroups>::Type TSeqGroup;
-	typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
-	
-	// Initialization
-	TVertexDescriptor rootVertex = getRoot(guideTree);
-	TSize nVertices = numVertices(guideTree);
-	TSize nSeq = (nVertices / 2) + 1;
-
-	// Number of subsequent leaves for each node
-	typedef typename Iterator<TGuideTree, BfsIterator>::Type TBfsIterator;
-	String<TSize> numLeaves;
-	resizeVertexMap(guideTree, numLeaves);
-
-	// All vertices in reversed bfs order
-	typedef String<TVertexDescriptor> TVertexString;
-	TVertexString vertices;
-	resize(vertices, nVertices);
-	
-	// Walk through the tree in bfs order	
-	TBfsIterator bfsIt(guideTree, rootVertex);
-	TSize pos = length(vertices) - 1;
-	for(;!atEnd(bfsIt);goNext(bfsIt), --pos) {
-		if (isLeaf(guideTree, *bfsIt)) property(numLeaves, *bfsIt) = 1;
-		else property(numLeaves, *bfsIt) = 0;
-		value(vertices, pos) = *bfsIt;
-	}
-
-	// Count the number of leaves for each internal node
-	typedef typename Iterator<TVertexString, Standard>::Type TVertexIter;
-	TVertexIter itVert = begin(vertices, Standard());
-	TVertexIter itVertEnd = end(vertices, Standard());
-	for(;itVert != itVertEnd; ++itVert) {
-		if (!isLeaf(guideTree, *itVert)) {
-			typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjacencyIterator;
-			TAdjacencyIterator adjIt(guideTree, *itVert);
-			for(;!atEnd(adjIt);goNext(adjIt)) property(numLeaves, *itVert) += property(numLeaves, *adjIt);
-		}	
-	}
-
-	// Delineate the groups
-	itVert = begin(vertices, Standard());
-	for(;itVert != itVertEnd; ++itVert) {
-		if (property(numLeaves, *itVert) >= minMembers) {
-			appendValue(seqGroups, TSeqGroup(), Generous());
-			appendValue(groupRoot, *itVert, Generous());
-			TSize elem = length(seqGroups) - 1;
-			collectLeaves(guideTree, *itVert, seqGroups[elem]);
-			property(numLeaves, *itVert) = 0;
-			// Do not take any parent of the group root
-			if (*itVert != rootVertex) {
-				TVertexDescriptor pVert = parentVertex(guideTree, *itVert);
-				while(pVert != rootVertex) {
-					property(numLeaves, pVert) = 0;
-					pVert = parentVertex(guideTree, pVert);
-				}
-				property(numLeaves, pVert) = 0;
-			}
-		}
-	}
-	if (!length(seqGroups)) {
-		appendValue(seqGroups, TSeqGroup());
-		appendValue(groupRoot, rootVertex);
-		collectLeaves(guideTree, rootVertex, seqGroups[0]);
-	}
-
-	// Label all internal vertices with the closest root node
-	typedef Pair<TSize, TSize> TDistGroup; // Distance, group index
-	String<TDistGroup> closestRoot;  
-	resize(closestRoot, getIdUpperBound(_getVertexIdManager(guideTree)), TDistGroup(0,0), Exact());
-	for(TSize i=0; i< (TSize) length(groupRoot); ++i) {
-		TVertexDescriptor v = groupRoot[i];
-		TSize dist = 0;
-		while(v != rootVertex) {
-			++dist;
-			v = parentVertex(guideTree, v);
-			if ((property(closestRoot,v).i1 == 0) || 
-				(property(closestRoot,v).i1 > dist)) {
-				property(closestRoot, v) = TDistGroup(dist,i);
-			}
-		}
-	}
-
-	// Find ungrouped vertices
-	typedef typename Iterator<TSeqGroup, Standard>::Type TSeqGroupIter;
-	TSeqGroup allGroupedLeaves;
-	for(TSize i=0; i< (TSize) length(seqGroups); ++i) {
-		TSeqGroupIter itSeqGroup = begin(seqGroups[i], Standard());
-		TSeqGroupIter itSeqGroupEnd = end(seqGroups[i], Standard());
-		for(;itSeqGroup != itSeqGroupEnd; ++itSeqGroup) 
-			appendValue(allGroupedLeaves, *itSeqGroup, Generous());
-	}
-	appendValue(allGroupedLeaves, nSeq);
-	::std::sort(begin(allGroupedLeaves, Standard()), end(allGroupedLeaves, Standard()));
-	TSeqGroupIter itSeqGroup = begin(allGroupedLeaves, Standard());
-	TSeqGroupIter itSeqGroupEnd = end(allGroupedLeaves, Standard());
-	TSize leftover = 0;
-	TSeqGroup ungroupedLeaves;
-	for(;itSeqGroup != itSeqGroupEnd; ++itSeqGroup, ++leftover) {
-		while (leftover<*itSeqGroup) {
-			appendValue(ungroupedLeaves, leftover, Generous());
-			++leftover;
-		}
-	}
-	
-
-	//std::cout << guideTree << std::endl;
-	//std::cout << nSeq << std::endl;
-	//std::cout << length(groupRoot) << std::endl;
-	//std::cout << length(allGroupedLeaves) << std::endl;
-	//std::cout << length(ungroupedLeaves) << std::endl;
-
-	// Group the ungrouped vertices to the closest group
-	clear(allGroupedLeaves);
-	itSeqGroup = begin(ungroupedLeaves, Standard());
-	itSeqGroupEnd = end(ungroupedLeaves, Standard());
-	for(; itSeqGroup != itSeqGroupEnd; ++itSeqGroup) {
-		TVertexDescriptor v = *itSeqGroup;
-		while(v != rootVertex) {
-			v = parentVertex(guideTree, v);
-			if (property(closestRoot,v).i1 != 0) {
-				appendValue(seqGroups[property(closestRoot,v).i2], *itSeqGroup, Generous());
-				break;
-			}
-		}
-	}
+    typedef typename Value<TSeqGroups>::Type TSeqGroup;
+    typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
+
+    // Initialization
+    TVertexDescriptor rootVertex = getRoot(guideTree);
+    TSize nVertices = numVertices(guideTree);
+    TSize nSeq = (nVertices / 2) + 1;
+
+    // Number of subsequent leaves for each node
+    typedef typename Iterator<TGuideTree, BfsIterator>::Type TBfsIterator;
+    String<TSize> numLeaves;
+    resizeVertexMap(numLeaves, guideTree);
+
+    // All vertices in reversed bfs order
+    typedef String<TVertexDescriptor> TVertexString;
+    TVertexString vertices;
+    resize(vertices, nVertices);
+
+    // Walk through the tree in bfs order
+    TBfsIterator bfsIt(guideTree, rootVertex);
+    TSize pos = length(vertices) - 1;
+    for(;!atEnd(bfsIt);goNext(bfsIt), --pos) {
+        if (isLeaf(guideTree, *bfsIt)) property(numLeaves, *bfsIt) = 1;
+        else property(numLeaves, *bfsIt) = 0;
+        value(vertices, pos) = *bfsIt;
+    }
+
+    // Count the number of leaves for each internal node
+    typedef typename Iterator<TVertexString, Standard>::Type TVertexIter;
+    TVertexIter itVert = begin(vertices, Standard());
+    TVertexIter itVertEnd = end(vertices, Standard());
+    for(;itVert != itVertEnd; ++itVert) {
+        if (!isLeaf(guideTree, *itVert)) {
+            typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjacencyIterator;
+            TAdjacencyIterator adjIt(guideTree, *itVert);
+            for(;!atEnd(adjIt);goNext(adjIt)) property(numLeaves, *itVert) += property(numLeaves, *adjIt);
+        }
+    }
+
+    // Delineate the groups
+    itVert = begin(vertices, Standard());
+    for(;itVert != itVertEnd; ++itVert) {
+        if (property(numLeaves, *itVert) >= minMembers) {
+            appendValue(seqGroups, TSeqGroup(), Generous());
+            appendValue(groupRoot, *itVert, Generous());
+            TSize elem = length(seqGroups) - 1;
+            collectLeaves(guideTree, *itVert, seqGroups[elem]);
+            property(numLeaves, *itVert) = 0;
+            // Do not take any parent of the group root
+            if (*itVert != rootVertex) {
+                TVertexDescriptor pVert = parentVertex(guideTree, *itVert);
+                while(pVert != rootVertex) {
+                    property(numLeaves, pVert) = 0;
+                    pVert = parentVertex(guideTree, pVert);
+                }
+                property(numLeaves, pVert) = 0;
+            }
+        }
+    }
+    if (!length(seqGroups)) {
+        appendValue(seqGroups, TSeqGroup());
+        appendValue(groupRoot, rootVertex);
+        collectLeaves(guideTree, rootVertex, seqGroups[0]);
+    }
+
+    // Label all internal vertices with the closest root node
+    typedef Pair<TSize, TSize> TDistGroup; // Distance, group index
+    String<TDistGroup> closestRoot;
+    resize(closestRoot, getIdUpperBound(_getVertexIdManager(guideTree)), TDistGroup(0,0), Exact());
+    for(TSize i=0; i< (TSize) length(groupRoot); ++i) {
+        TVertexDescriptor v = groupRoot[i];
+        TSize dist = 0;
+        while(v != rootVertex) {
+            ++dist;
+            v = parentVertex(guideTree, v);
+            if ((property(closestRoot,v).i1 == 0) ||
+                (property(closestRoot,v).i1 > dist)) {
+                property(closestRoot, v) = TDistGroup(dist,i);
+            }
+        }
+    }
+
+    // Find ungrouped vertices
+    typedef typename Iterator<TSeqGroup, Standard>::Type TSeqGroupIter;
+    TSeqGroup allGroupedLeaves;
+    for(TSize i=0; i< (TSize) length(seqGroups); ++i) {
+        TSeqGroupIter itSeqGroup = begin(seqGroups[i], Standard());
+        TSeqGroupIter itSeqGroupEnd = end(seqGroups[i], Standard());
+        for(;itSeqGroup != itSeqGroupEnd; ++itSeqGroup)
+            appendValue(allGroupedLeaves, *itSeqGroup, Generous());
+    }
+    appendValue(allGroupedLeaves, nSeq);
+    std::sort(begin(allGroupedLeaves, Standard()), end(allGroupedLeaves, Standard()));
+    TSeqGroupIter itSeqGroup = begin(allGroupedLeaves, Standard());
+    TSeqGroupIter itSeqGroupEnd = end(allGroupedLeaves, Standard());
+    TSize leftover = 0;
+    TSeqGroup ungroupedLeaves;
+    for(;itSeqGroup != itSeqGroupEnd; ++itSeqGroup, ++leftover) {
+        while (leftover<*itSeqGroup) {
+            appendValue(ungroupedLeaves, leftover, Generous());
+            ++leftover;
+        }
+    }
+
+
+    //std::cout << guideTree << std::endl;
+    //std::cout << nSeq << std::endl;
+    //std::cout << length(groupRoot) << std::endl;
+    //std::cout << length(allGroupedLeaves) << std::endl;
+    //std::cout << length(ungroupedLeaves) << std::endl;
+
+    // Group the ungrouped vertices to the closest group
+    clear(allGroupedLeaves);
+    itSeqGroup = begin(ungroupedLeaves, Standard());
+    itSeqGroupEnd = end(ungroupedLeaves, Standard());
+    for(; itSeqGroup != itSeqGroupEnd; ++itSeqGroup) {
+        TVertexDescriptor v = *itSeqGroup;
+        while(v != rootVertex) {
+            v = parentVertex(guideTree, v);
+            if (property(closestRoot,v).i1 != 0) {
+                appendValue(seqGroups[property(closestRoot,v).i2], *itSeqGroup, Generous());
+                break;
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TSize>
-inline void 
+inline void
 tripletLibraryExtension(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-						TGuideTree& guideTree,
-						TSize minMembers)
+                        TGuideTree& guideTree,
+                        TSize minMembers)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename VertexDescriptor<TGuideTree>::Type TTreeVertex;
-	TStringSet& strSet = stringSet(g);
-	TSize nSeq = length(strSet);
-
-	// Identify large subtrees
-	typedef String<TSize> TSequenceGroups;
-	String<TSequenceGroups> seqGroup;
-	typedef String<TTreeVertex> TGroupRoot;
-	TGroupRoot groupRoot;
-	_subTreeSearch(guideTree, seqGroup, groupRoot, minMembers);
-	
-	// Label the subtree sequences
-	String<TSize> seqLabels;
-	resize(seqLabels, nSeq);
-	typedef typename Iterator<TSequenceGroups, Standard>::Type TSeqSetIter;
-	for(TSize i=0; i< (TSize) length(seqGroup); ++i) {
-		TSeqSetIter itSeqGroup = begin(seqGroup[i], Standard());
-		TSeqSetIter itSeqGroupEnd = end(seqGroup[i], Standard());
-		for(;itSeqGroup != itSeqGroupEnd; ++itSeqGroup) 
-			seqLabels[*itSeqGroup] = i;
-	}
-
-	// Store all edges
-	typedef std::pair<TVertexDescriptor, TVertexDescriptor> TNewEdge;
-	typedef std::map<TNewEdge, TCargo> TEdgeMap;
-	typedef typename TEdgeMap::iterator TEdgeMapIter;
-	TEdgeMap newEMap;
-	typedef MsaEdgeCargo_<TVertexDescriptor, TCargo> TEdge;
-	typedef String<TEdge> TEdgeString;
-	TEdgeString initialEdges;
-	TEdgeIterator itE(g);
-	for(;!atEnd(itE);goNext(itE)) {
-		TVertexDescriptor sV = sourceVertex(itE);
-		TVertexDescriptor tV = targetVertex(itE);
-		TCargo c = cargo(*itE);
-		appendValue(initialEdges, TEdge(sV, tV, c), Generous());
-		newEMap.insert(std::make_pair(TNewEdge(sV, tV), c));
-	}
-	clearEdges(g);
-
-	
-	// Perform triplet extension
-	typedef typename Iterator<TEdgeString, Standard>::Type TEdgeIter;
-	TEdgeString fullEdges;
-	for(TSize i=0; i< (TSize) length(seqGroup); ++i) {
-		TEdgeIter itInitial = begin(initialEdges, Standard());
-		TEdgeIter itInitialEnd = end(initialEdges, Standard());
-		for(; itInitial != itInitialEnd; ++itInitial) {
-			TSize seq1 = idToPosition(strSet, sequenceId(g, (*itInitial).v1));
-			TSize seq2 = idToPosition(strSet, sequenceId(g, (*itInitial).v2));
-			if ((seqLabels[seq1] == i) && (seqLabels[seq2] == i)) {
-				appendValue(fullEdges, *itInitial, Generous());
-				appendValue(fullEdges, TEdge((*itInitial).v2, (*itInitial).v1, (*itInitial).c), Generous());
-			}
-		}
-		::std::sort(begin(fullEdges, Standard()), end(fullEdges, Standard()), LessMsaEdgeCargo_<TVertexDescriptor, TCargo>() );
-		typedef typename Iterator<TEdgeString, Standard>::Type TEdgeIter;
-		TEdgeIter itEdges1 = begin(fullEdges, Standard());
-		TEdgeIter itEdgesEnd = end(fullEdges, Standard());
-		for(; itEdges1 != itEdgesEnd; ++itEdges1) {
-			for(TEdgeIter itEdges2 = itEdges1; ++itEdges2 != itEdgesEnd;) {
-				if ((*itEdges1).v1 != (*itEdges2).v1) break;
-				if (sequenceId(g, (*itEdges1).v2) != sequenceId(g, (*itEdges2).v2)) {
-					TCargo weight = ((*itEdges1).c < (*itEdges2).c) ? (*itEdges1).c : (*itEdges2).c;
-					if ((*itEdges1).v2 < (*itEdges2).v2) {
-						TEdgeMapIter pos = newEMap.find(TNewEdge((*itEdges1).v2, (*itEdges2).v2));
-						if (pos != newEMap.end()) (*pos).second += weight;
-						else newEMap.insert(std::make_pair(TNewEdge((*itEdges1).v2, (*itEdges2).v2), weight));
-					} else {
-						TEdgeMapIter pos = newEMap.find(TNewEdge((*itEdges2).v2, (*itEdges1).v2));
-						if (pos != newEMap.end()) (*pos).second += weight;
-						else newEMap.insert(std::make_pair(TNewEdge((*itEdges2).v2, (*itEdges1).v2), weight));
-					}
-				}
-			}
-		}
-		clear(fullEdges);
-	}
-
-	// Insert edges
-	for(TEdgeMapIter itE = newEMap.begin(); itE != newEMap.end(); ++itE) 
-		addEdge(g, (*itE).first.first, (*itE).first.second, (*itE).second);
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename VertexDescriptor<TGuideTree>::Type TTreeVertex;
+    TStringSet& strSet = stringSet(g);
+    TSize nSeq = length(strSet);
+
+    // Identify large subtrees
+    typedef String<TSize> TSequenceGroups;
+    String<TSequenceGroups> seqGroup;
+    typedef String<TTreeVertex> TGroupRoot;
+    TGroupRoot groupRoot;
+    _subTreeSearch(guideTree, seqGroup, groupRoot, minMembers);
+
+    // Label the subtree sequences
+    String<TSize> seqLabels;
+    resize(seqLabels, nSeq);
+    typedef typename Iterator<TSequenceGroups, Standard>::Type TSeqSetIter;
+    for(TSize i=0; i< (TSize) length(seqGroup); ++i) {
+        TSeqSetIter itSeqGroup = begin(seqGroup[i], Standard());
+        TSeqSetIter itSeqGroupEnd = end(seqGroup[i], Standard());
+        for(;itSeqGroup != itSeqGroupEnd; ++itSeqGroup)
+            seqLabels[*itSeqGroup] = i;
+    }
+
+    // Store all edges
+    typedef std::pair<TVertexDescriptor, TVertexDescriptor> TNewEdge;
+    typedef std::map<TNewEdge, TCargo> TEdgeMap;
+    typedef typename TEdgeMap::iterator TEdgeMapIter;
+    TEdgeMap newEMap;
+    typedef MsaEdgeCargo_<TVertexDescriptor, TCargo> TEdge;
+    typedef String<TEdge> TEdgeString;
+    TEdgeString initialEdges;
+    TEdgeIterator itE(g);
+    for(;!atEnd(itE);goNext(itE)) {
+        TVertexDescriptor sV = sourceVertex(itE);
+        TVertexDescriptor tV = targetVertex(itE);
+        TCargo c = cargo(*itE);
+        appendValue(initialEdges, TEdge(sV, tV, c), Generous());
+        newEMap.insert(std::make_pair(TNewEdge(sV, tV), c));
+    }
+    clearEdges(g);
+
+
+    // Perform triplet extension
+    typedef typename Iterator<TEdgeString, Standard>::Type TEdgeIter;
+    TEdgeString fullEdges;
+    for(TSize i=0; i< (TSize) length(seqGroup); ++i) {
+        TEdgeIter itInitial = begin(initialEdges, Standard());
+        TEdgeIter itInitialEnd = end(initialEdges, Standard());
+        for(; itInitial != itInitialEnd; ++itInitial) {
+            TSize seq1 = idToPosition(strSet, sequenceId(g, (*itInitial).v1));
+            TSize seq2 = idToPosition(strSet, sequenceId(g, (*itInitial).v2));
+            if ((seqLabels[seq1] == i) && (seqLabels[seq2] == i)) {
+                appendValue(fullEdges, *itInitial, Generous());
+                appendValue(fullEdges, TEdge((*itInitial).v2, (*itInitial).v1, (*itInitial).c), Generous());
+            }
+        }
+        std::sort(begin(fullEdges, Standard()), end(fullEdges, Standard()), LessMsaEdgeCargo_<TVertexDescriptor, TCargo>() );
+        typedef typename Iterator<TEdgeString, Standard>::Type TEdgeIter;
+        TEdgeIter itEdges1 = begin(fullEdges, Standard());
+        TEdgeIter itEdgesEnd = end(fullEdges, Standard());
+        for(; itEdges1 != itEdgesEnd; ++itEdges1) {
+            for(TEdgeIter itEdges2 = itEdges1; ++itEdges2 != itEdgesEnd;) {
+                if ((*itEdges1).v1 != (*itEdges2).v1) break;
+                if (sequenceId(g, (*itEdges1).v2) != sequenceId(g, (*itEdges2).v2)) {
+                    TCargo weight = ((*itEdges1).c < (*itEdges2).c) ? (*itEdges1).c : (*itEdges2).c;
+                    if ((*itEdges1).v2 < (*itEdges2).v2) {
+                        TEdgeMapIter pos = newEMap.find(TNewEdge((*itEdges1).v2, (*itEdges2).v2));
+                        if (pos != newEMap.end()) (*pos).second += weight;
+                        else newEMap.insert(std::make_pair(TNewEdge((*itEdges1).v2, (*itEdges2).v2), weight));
+                    } else {
+                        TEdgeMapIter pos = newEMap.find(TNewEdge((*itEdges2).v2, (*itEdges1).v2));
+                        if (pos != newEMap.end()) (*pos).second += weight;
+                        else newEMap.insert(std::make_pair(TNewEdge((*itEdges2).v2, (*itEdges1).v2), weight));
+                    }
+                }
+            }
+        }
+        clear(fullEdges);
+    }
+
+    // Insert edges
+    for(TEdgeMapIter itE = newEMap.begin(); itE != newEMap.end(); ++itE)
+        addEdge(g, (*itE).first.first, (*itE).first.second, (*itE).second);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec>
-inline void 
+inline void
 graphBasedTripletLibraryExtension(Graph<Alignment<TStringSet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	// Two tasks:
-	// 1) Add edges for the case that a and c is aligned, b and c is aligned, but a and b are not, give these edges the appropriate weight
-	// 2) Augment all existing edges
-	String<TCargo> newCargoMap;
-	typedef String<TVertexDescriptor> TVertexString;
-	typedef String<TCargo> TCargoString;
-	TVertexString edges_vertices;
-	TCargoString edges_cargo;
-	
-	// Triplet Extension
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-
-	// Remember the old cargo
-	resize(newCargoMap, getIdUpperBound(_getEdgeIdManager(g)), Exact());
-	TEdgeIterator it(g);
-	for(;!atEnd(it);++it) 
-		property(newCargoMap, *it) = cargo(*it);
-
-	// Iterate over all vertices
-	for(TVertexIterator itVertex(g);!atEnd(itVertex);++itVertex) {
-		TOutEdgeIterator outIt1(g, *itVertex);
-		while (!atEnd(outIt1)) {
-			TOutEdgeIterator outIt2 = outIt1;
-			goNext(outIt2);
-			// Consider always 2 neighbors
-			while (!atEnd(outIt2)) {
-				TVertexDescriptor tV1 = targetVertex(outIt1);
-				TVertexDescriptor tV2 = targetVertex(outIt2);
-				if (sequenceId(g, tV1) != sequenceId(g,tV2)) {
-					TEdgeDescriptor e = findEdge(g, tV1, tV2);
-					if (e == 0) {
-						// New edge
-						TCargo val = (cargo(*outIt1) < cargo(*outIt2)) ? cargo(*outIt1) : cargo(*outIt2);
-						
-						// Remember the edge with cargo
-						appendValue(edges_vertices, tV1, Generous());
-						appendValue(edges_vertices, tV2, Generous());
-						appendValue(edges_cargo, val, Generous());
-					} else {
-						// Increase weight of existing edge
-						if (cargo(*outIt2) > cargo(*outIt1)) property(newCargoMap, e) += cargo(*outIt1);
-						else property(newCargoMap, e) += cargo(*outIt2);	
-					}
-				}
-				goNext(outIt2);
-			}
-			goNext(outIt1);
-		}
-	}
-
-
-	// Assign the new weights and clean-up the cargo map
-	TEdgeIterator itE(g);
-	for(;!atEnd(itE);++itE) cargo(*itE) = property(newCargoMap, *itE);
-	clear(newCargoMap);
-
-	// Add edges
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Iterator<TVertexString, Standard>::Type TVertexStringIter;
-	typedef typename Iterator<TCargoString, Standard>::Type TCargoStringIter;
-
-	// Finally add the new edges created by the triplet approach
-	TVertexStringIter itV = begin(edges_vertices, Standard());
-	TVertexStringIter itVNext = begin(edges_vertices, Standard());
-	++itVNext;
-	TVertexStringIter endIt = end(edges_vertices, Standard());
-	TCargoStringIter itC = begin(edges_cargo, Standard());
-	for(;itV != endIt; itV += 2, itVNext +=2, ++itC) {
-		// The same edge could have been created multiple times, so check if it exists
-		TEdgeDescriptor e = findEdge(g, *itV, *itVNext);
-		if (e == 0) addEdge(g, *itV, *itVNext, *itC);
-		else cargo(e) += *itC;
-	}
-	SEQAN_ASSERT(itC == end(edges_cargo));
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    // Two tasks:
+    // 1) Add edges for the case that a and c is aligned, b and c is aligned, but a and b are not, give these edges the appropriate weight
+    // 2) Augment all existing edges
+    String<TCargo> newCargoMap;
+    typedef String<TVertexDescriptor> TVertexString;
+    typedef String<TCargo> TCargoString;
+    TVertexString edges_vertices;
+    TCargoString edges_cargo;
+
+    // Triplet Extension
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    // Remember the old cargo
+    resize(newCargoMap, getIdUpperBound(_getEdgeIdManager(g)), Exact());
+    TEdgeIterator it(g);
+    for(;!atEnd(it);++it)
+        property(newCargoMap, *it) = cargo(*it);
+
+    // Iterate over all vertices
+    for(TVertexIterator itVertex(g);!atEnd(itVertex);++itVertex) {
+        TOutEdgeIterator outIt1(g, *itVertex);
+        while (!atEnd(outIt1)) {
+            TOutEdgeIterator outIt2 = outIt1;
+            goNext(outIt2);
+            // Consider always 2 neighbors
+            while (!atEnd(outIt2)) {
+                TVertexDescriptor tV1 = targetVertex(outIt1);
+                TVertexDescriptor tV2 = targetVertex(outIt2);
+                if (sequenceId(g, tV1) != sequenceId(g,tV2)) {
+                    TEdgeDescriptor e = findEdge(g, tV1, tV2);
+                    if (e == 0) {
+                        // New edge
+                        TCargo val = (cargo(*outIt1) < cargo(*outIt2)) ? cargo(*outIt1) : cargo(*outIt2);
+
+                        // Remember the edge with cargo
+                        appendValue(edges_vertices, tV1, Generous());
+                        appendValue(edges_vertices, tV2, Generous());
+                        appendValue(edges_cargo, val, Generous());
+                    } else {
+                        // Increase weight of existing edge
+                        if (cargo(*outIt2) > cargo(*outIt1)) property(newCargoMap, e) += cargo(*outIt1);
+                        else property(newCargoMap, e) += cargo(*outIt2);
+                    }
+                }
+                goNext(outIt2);
+            }
+            goNext(outIt1);
+        }
+    }
+
+
+    // Assign the new weights and clean-up the cargo map
+    TEdgeIterator itE(g);
+    for(;!atEnd(itE);++itE) cargo(*itE) = property(newCargoMap, *itE);
+    clear(newCargoMap);
+
+    // Add edges
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Iterator<TVertexString, Standard>::Type TVertexStringIter;
+    typedef typename Iterator<TCargoString, Standard>::Type TCargoStringIter;
+
+    // Finally add the new edges created by the triplet approach
+    TVertexStringIter itV = begin(edges_vertices, Standard());
+    TVertexStringIter itVNext = begin(edges_vertices, Standard());
+    ++itVNext;
+    TVertexStringIter endIt = end(edges_vertices, Standard());
+    TCargoStringIter itC = begin(edges_cargo, Standard());
+    for(;itV != endIt; itV += 2, itVNext +=2, ++itC) {
+        // The same edge could have been created multiple times, so check if it exists
+        TEdgeDescriptor e = findEdge(g, *itV, *itVNext);
+        if (e == 0) addEdge(g, *itV, *itVNext, *itC);
+        else cargo(e) += *itC;
+    }
+    SEQAN_ASSERT(itC == end(edges_cargo));
 }
 
 ////////////////////////////////////////////////////////////////////////////////
 //
 //template<typename TStringSet, typename TCargo, typename TSpec>
-//inline void 
+//inline void
 //reducedTripletLibraryExtension(Graph<Alignment<TStringSet, TCargo, TSpec> >& g)
 //{
-//	SEQAN_CHECKPOINT
-//	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-//	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-//	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-//	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-//	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-//	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+//    SEQAN_CHECKPOINT
+//    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+//    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+//    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+//    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+//    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+//    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
 //
 //
-//	// Just augment existing edges
-//	String<TCargo> newCargoMap;
-//	resize(newCargoMap, getIdUpperBound(_getEdgeIdManager(g)), Exact());
-//	TEdgeIterator it(g);
-//	for(;!atEnd(it);++it) assignProperty(newCargoMap, *it, cargo(*it));
+//    // Just augment existing edges
+//    String<TCargo> newCargoMap;
+//    resize(newCargoMap, getIdUpperBound(_getEdgeIdManager(g)), Exact());
+//    TEdgeIterator it(g);
+//    for(;!atEnd(it);++it) assignProperty(newCargoMap, *it, cargo(*it));
 //
-//	// Iterate over all vertices
-//	for(TVertexIterator itVertex(g);!atEnd(itVertex);++itVertex) {
-//		TOutEdgeIterator outIt1(g, *itVertex);
-//		while (!atEnd(outIt1)) {
-//			TOutEdgeIterator outIt2 = outIt1;
-//			goNext(outIt2);
-//			// Consider always 2 neighbors
-//			while (!atEnd(outIt2)) {
-//				TVertexDescriptor tV1 = targetVertex(outIt1);
-//				TVertexDescriptor tV2 = targetVertex(outIt2);
-//				if (sequenceId(g, tV1) != sequenceId(g,tV2)) {
-//					TEdgeDescriptor e = findEdge(g, tV1, tV2);
-//					if (e != 0) {
-//						// Increase weight of existing edge
-//						if (getCargo(*outIt2) > getCargo(*outIt1)) property(newCargoMap, e) += getCargo(*outIt1);
-//						else property(newCargoMap, e) += getCargo(*outIt2);	
-//					}
-//				}
-//				goNext(outIt2);
-//			}
-//			goNext(outIt1);
-//		}
-//	}
+//    // Iterate over all vertices
+//    for(TVertexIterator itVertex(g);!atEnd(itVertex);++itVertex) {
+//        TOutEdgeIterator outIt1(g, *itVertex);
+//        while (!atEnd(outIt1)) {
+//            TOutEdgeIterator outIt2 = outIt1;
+//            goNext(outIt2);
+//            // Consider always 2 neighbors
+//            while (!atEnd(outIt2)) {
+//                TVertexDescriptor tV1 = targetVertex(outIt1);
+//                TVertexDescriptor tV2 = targetVertex(outIt2);
+//                if (sequenceId(g, tV1) != sequenceId(g,tV2)) {
+//                    TEdgeDescriptor e = findEdge(g, tV1, tV2);
+//                    if (e != 0) {
+//                        // Increase weight of existing edge
+//                        if (getCargo(*outIt2) > getCargo(*outIt1)) property(newCargoMap, e) += getCargo(*outIt1);
+//                        else property(newCargoMap, e) += getCargo(*outIt2);
+//                    }
+//                }
+//                goNext(outIt2);
+//            }
+//            goNext(outIt1);
+//        }
+//    }
 //
-//	// Assign the new weights and clean-up the cargo map
-//	TEdgeIterator itE(g);
-//	for(;!atEnd(itE);goNext(itE)) cargo(value(itE)) = property(newCargoMap, value(itE));
-//	clear(newCargoMap);
+//    // Assign the new weights and clean-up the cargo map
+//    TEdgeIterator itE(g);
+//    for(;!atEnd(itE);goNext(itE)) cargo(value(itE)) = property(newCargoMap, value(itE));
+//    clear(newCargoMap);
 //}
 
 //////////////////////////////////////////////////////////////////////////////
@@ -826,128 +763,112 @@ graphBasedTripletLibraryExtension(Graph<Alignment<TStringSet, TCargo, TSpec> >&
  * @fn sumOfPairsScore
  * @headerfile <seqan/graph_msa.h>
  * @brief Given a multiple alignment, this function calculates the sum-of-pairs score.
- * 
+ *
  * @signature TScoreValue sumOfPairsScore(graph, scoringScheme);
- * 
+ *
  * @param[in] graph         An @link AlignmentGraph @endlink to use for the evaluation.
  * @param[in] ScoringScheme The @link Score @endlink to use.
- * 
- * @return TReturn void
- * 
- * @section Remarks
- * 
+ *
+ * @return TScoreValue The SOP score of the MSA  (Metafunction: @link Score#Value @endlink of the type of
+ *                     <tt>scoringScheme</tt>).
+ *
  * This function does NOT assume independent columns.  That is, gap openings are properly scored.  If you want the fast
  * version assuming independ columns use sumOfPairsScoreInd.
  */
 
-/**
-.Function.sumOfPairsScore
-..class:Spec.Alignment Graph
-..summary:Given a multiple alignment, this function calculates the sum-of-pairs score.
-..cat:Graph
-..signature:
-sumOfPairsScore(graph, score_type)
-..param.graph:An alignment graph.
-...type:Spec.Alignment Graph
-..param.score_type:A score object.
-...type:Class.Score
-..remarks:This function does NOT assume independent columns. 
-That is, gap openings are properly scored. 
-If you want the fast version assuming independ columns use sumOfPairsScoreInd.
-..returns:void
-..include:seqan/graph_msa.h
-*/
-template<typename TStringSet, typename TCargo, typename TSpec, typename TScore> 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TScore>
 inline typename Value<TScore>::Type
 sumOfPairsScore(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-				TScore const& score_type)
+                TScore const& score_type)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef typename Value<typename Value<TStringSet>::Type>::Type TAlphabet;
-
-	// Convert the graph
-	String<char> mat;
-	convertAlignment(g, mat);
-	char gapChar = gapValue<char>();
-
-	TScoreValue gap = scoreGapExtend(score_type);
-	TScoreValue gapOpen = scoreGapOpen(score_type);
-	TSize nseq = length(stringSet(g));
-	TSize len = length(mat) / nseq;
-	
-	bool gapOpeni = false;
-	bool gapOpenj = false;
-	TScoreValue totalScore = 0;
-	for(TSize i = 0; i<nseq-1; ++i) {
-		for(TSize j=i+1; j<nseq; ++j) {
-			for(TSize k=0;k<len; ++k) {
-				if (value(mat, i*len+k) != gapChar) {
-					if (value(mat, j*len + k) != gapChar) {
-						gapOpeni = false;
-						gapOpenj = false;
-						totalScore += score(const_cast<TScore&>(score_type), TAlphabet(value(mat, i*len+k)), TAlphabet(value(mat, j*len + k)));
-					} else {
-						if (gapOpenj) {
-							totalScore += gap;
-						} else {
-							gapOpenj = true;
-							totalScore += gapOpen;
-						}
-					}
-				} else if (value(mat, j*len + k) != gapChar) {
-						if (gapOpeni) {
-							totalScore += gap;
-						} else {
-							gapOpeni = true;
-							totalScore += gapOpen;
-						}
-				}
-			}
-		}
-	}
-	return totalScore;
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef typename Value<typename Value<TStringSet>::Type>::Type TAlphabet;
+
+    // Convert the graph
+    String<char> mat;
+    convertAlignment(g, mat);
+    char gapChar = gapValue<char>();
+
+    TScoreValue gap = scoreGapExtend(score_type);
+    TScoreValue gapOpen = scoreGapOpen(score_type);
+    TSize nseq = length(stringSet(g));
+    TSize len = length(mat) / nseq;
+
+    bool gapOpeni = false;
+    bool gapOpenj = false;
+    TScoreValue totalScore = 0;
+    for(TSize i = 0; i<nseq-1; ++i) {
+        for(TSize j=i+1; j<nseq; ++j) {
+            for(TSize k=0;k<len; ++k) {
+                if (value(mat, i*len+k) != gapChar) {
+                    if (value(mat, j*len + k) != gapChar) {
+                        gapOpeni = false;
+                        gapOpenj = false;
+                        totalScore += score(const_cast<TScore&>(score_type), TAlphabet(value(mat, i*len+k)), TAlphabet(value(mat, j*len + k)));
+                    } else {
+                        if (gapOpenj) {
+                            totalScore += gap;
+                        } else {
+                            gapOpenj = true;
+                            totalScore += gapOpen;
+                        }
+                    }
+                } else if (value(mat, j*len + k) != gapChar) {
+                        if (gapOpeni) {
+                            totalScore += gap;
+                        } else {
+                            gapOpeni = true;
+                            totalScore += gapOpen;
+                        }
+                }
+            }
+        }
+    }
+    return totalScore;
 }
 
+// TODO(holtgrew): Document sumOfPairsScoreInd.
+
 //////////////////////////////////////////////////////////////////////////////
 // This version is insensitive to gap openings, assumes independent columns
-template<typename TStringSet, typename TCargo, typename TSpec, typename TScore> 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TScore>
 inline typename Value<TScore>::Type
 sumOfPairsScoreInd(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-				   TScore const& score_type)
+                   TScore const& score_type)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef typename Value<typename Value<TStringSet>::Type>::Type TAlphabet;
-
-	// Convert the graph
-	String<char> mat;
-	convertAlignment(g, mat);
-	char gapChar = gapValue<char>();
-
-	TScoreValue gap = scoreGapExtend(score_type);
-	TSize nseq = length(stringSet(g));
-	TSize len = length(mat) / nseq;
-	
-	TScoreValue totalScore = 0;
-	for(TSize k=0;k<len; ++k) {
-		for(TSize i = 0; i<nseq-1; ++i) {
-			for(TSize j=i+1; j<nseq; ++j) {
-				if (value(mat, i*len+k) != gapChar) {
-					if (value(mat, j*len + k) != gapChar) {
-						totalScore += score(const_cast<TScore&>(score_type), TAlphabet(value(mat, i*len+k)), TAlphabet(value(mat, j*len + k)));
-					} else totalScore += gap;
-				} else if (value(mat, j*len + k) != gapChar) {
-						totalScore += gap;
-				}
-			}
-		}
-	}
-	return totalScore;
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef typename Value<typename Value<TStringSet>::Type>::Type TAlphabet;
+
+    // Convert the graph
+    String<char> mat;
+    convertAlignment(g, mat);
+    char gapChar = gapValue<char>();
+
+    TScoreValue gap = scoreGapExtend(score_type);
+    TSize nseq = length(stringSet(g));
+    TSize len = length(mat) / nseq;
+
+    TScoreValue totalScore = 0;
+    for(TSize k=0;k<len; ++k) {
+        for(TSize i = 0; i<nseq-1; ++i) {
+            for(TSize j=i+1; j<nseq; ++j) {
+                if (value(mat, i*len+k) != gapChar) {
+                    if (value(mat, j*len + k) != gapChar) {
+                        totalScore += score(const_cast<TScore&>(score_type), TAlphabet(value(mat, i*len+k)), TAlphabet(value(mat, j*len + k)));
+                    } else totalScore += gap;
+                } else if (value(mat, j*len + k) != gapChar) {
+                        totalScore += gap;
+                }
+            }
+        }
+    }
+    return totalScore;
 }
 
 
@@ -955,214 +876,197 @@ sumOfPairsScoreInd(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
 
 /*!
  * @fn alignmentEvaluation
- * @headerfile <seqan/graph_align.h>
- * @brief Given a multiple sequence alignment, this function calcualtes all kinds of alignment statistics.
+ * @headerfile <seqan/graph_msa.h>
+ * @brief Given a multiple sequence alignment, this function calculates different kinds of alignment statistics.
  *
  * @signature TScoreVal alignmentEvaluation(graph, scoringScheme, gapExCount, gapCount, pairCount, numPairs, len);
  *
- * @param[in] graph         The AlignmentGraph to compute statistics for.
- * @param[in] scoringScheme The @link Score @endlink to use.
- * @param[in] gapExCount    The number of gap extensions.
- * @param[in] gapCount      The number of gaps.
- * @param[in] paircount     The number of aligned pairs.
- * @param[in] numPairs      Counter for each pair.
- * @param[in] len           Alignment length.
+ * @param[in]  graph         The @link AlignmentGraph @endlink object to compute statistics for.
+ * @param[in]  scoringScheme The @link Score @endlink object to use.
+ * @param[out] gapExCount    The number of gap extensions.
+ * @param[out] gapCount      The number of gaps.
+ * @param[out] pairCount     The number of aligned pairs.
+ * @param[out] numPairs      Counter for each pair. A @link String @endlink resized to size <tt>n*n</tt>, where
+                             <tt>n</tt> is the @link FiniteOrderedAlphabetConcept#ValueSize @endlink of the alphabet
+                             of the aligned sequences.
+ * @param[out] len           Alignment length.
  *
- * @return TScoreVal The score of the alignment.  TScoreVal is the value type of scoringScheme.
+ * @return TScoreVal The score of the alignment  (Metafunction: @link Score#Value @endlink).
  */
 
-/**
-.Function.alignmentEvaluation
-..class:Spec.Alignment Graph
-..summary:Given a multiple alignment, this function calculates all kinds of alignment statistics.
-..cat:Graph
-..signature:
-alignmentEvaluation(graph, score_type, gapExCount, gapCount, pairCount, numPairs, len)
-..param.graph:An alignment graph.
-...type:Spec.Alignment Graph
-..param.score_type:A score object.
-...type:Class.Score
-..param.gapExCount:Number of gap extensions.
-..param.gapCount:Number of gaps.
-..param.pairCount:Number of aligned pairs.
-..param.numPairs:Counter for each pair.
-..param.len:Alignment length.
-..returns:Score of the alignment.
-..include:seqan/graph_msa.h
-*/
-template<typename TStringSet, typename TCargo, typename TSpec, typename TScore, typename TSize> 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TScore, typename TSize>
 inline typename Value<TScore>::Type
-alignmentEvaluation(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-					TScore const& score_type,
-					TSize& gapExCount,
-					TSize& gapCount,
-					TSize& pairCount,
-					String<TSize>& numPairs,
-					TSize& len)
+alignmentEvaluation(Graph<Alignment<TStringSet, TCargo, TSpec> > const & g,
+                    TScore const& score_type,
+                    TSize& gapExCount,
+                    TSize& gapCount,
+                    TSize& pairCount,
+                    String<TSize> & numPairs,
+                    TSize& len)
 {
-	//typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef typename Value<typename Value<TStringSet>::Type>::Type TAlphabet;
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-
-	// Initialization;
-	gapExCount = 0;
-	gapCount = 0;
-	pairCount = 0;
-	clear(numPairs);
-
-	// Convert the graph
-	String<char> mat;
-	convertAlignment(g, mat);
-	char gapChar = gapValue<char>();
-
-	TScoreValue gap = scoreGapExtend(score_type);
-	TScoreValue gapOpen = scoreGapOpen(score_type);
-	TSize nseq = length(stringSet(g));
-	len = length(mat) / nseq;
-	
-	bool gapOpeni = false;
-	bool gapOpenj = false;
-	TScoreValue totalScore = 0;
-	resize(numPairs, alphSize * alphSize, 0);
-	for(TSize i = 0; i<nseq-1; ++i) {
-		for(TSize j=i+1; j<nseq; ++j) {
-			for(TSize k=0;k<len; ++k) {
-				if (value(mat, i*len+k) != gapChar) {
-					if (value(mat, j*len + k) != gapChar) {
-						gapOpeni = false;
-						gapOpenj = false;
-						++pairCount;
-						TSize index1 = ordValue(TAlphabet(value(mat, i*len+k)));
-						TSize index2 = ordValue(TAlphabet(value(mat, j*len + k)));
-						value(numPairs, index1 * alphSize + index2) += 1;
-						totalScore += score(const_cast<TScore&>(score_type), TAlphabet(value(mat, i*len+k)), TAlphabet(value(mat, j*len + k)));
-					} else {
-						if (gapOpenj) {
-							++gapExCount;
-							totalScore += gap;
-						} else {
-							gapOpenj = true;
-							++gapCount;
-							totalScore += gapOpen;
-						}
-					}
-				} else if (value(mat, j*len + k) != gapChar) {
-						if (gapOpeni) {
-							++gapExCount;
-							totalScore += gap;
-						} else {
-							++gapCount;
-							gapOpeni = true;
-							totalScore += gapOpen;
-						}
-				}
-			}
-		}
-	}
-	return totalScore;
+    //typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef typename Value<typename Value<TStringSet>::Type>::Type TAlphabet;
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+
+    // Initialization;
+    gapExCount = 0;
+    gapCount = 0;
+    pairCount = 0;
+    clear(numPairs);
+
+    // Convert the graph
+    String<char> mat;
+    convertAlignment(g, mat);
+    char gapChar = gapValue<char>();
+
+    TScoreValue gap = scoreGapExtend(score_type);
+    TScoreValue gapOpen = scoreGapOpen(score_type);
+    TSize nseq = length(stringSet(g));
+    len = length(mat) / nseq;
+
+    bool gapOpeni = false;
+    bool gapOpenj = false;
+    TScoreValue totalScore = 0;
+    resize(numPairs, alphSize * alphSize, 0);
+    for(TSize i = 0; i<nseq-1; ++i) {
+        for(TSize j=i+1; j<nseq; ++j) {
+            for(TSize k=0;k<len; ++k) {
+                if (value(mat, i*len+k) != gapChar) {
+                    if (value(mat, j*len + k) != gapChar) {
+                        gapOpeni = false;
+                        gapOpenj = false;
+                        ++pairCount;
+                        TSize index1 = ordValue(TAlphabet(value(mat, i*len+k)));
+                        TSize index2 = ordValue(TAlphabet(value(mat, j*len + k)));
+                        value(numPairs, index1 * alphSize + index2) += 1;
+                        totalScore += score(const_cast<TScore&>(score_type), TAlphabet(value(mat, i*len+k)), TAlphabet(value(mat, j*len + k)));
+                    } else {
+                        if (gapOpenj) {
+                            ++gapExCount;
+                            totalScore += gap;
+                        } else {
+                            gapOpenj = true;
+                            ++gapCount;
+                            totalScore += gapOpen;
+                        }
+                    }
+                } else if (value(mat, j*len + k) != gapChar) {
+                        if (gapOpeni) {
+                            ++gapExCount;
+                            totalScore += gap;
+                        } else {
+                            ++gapCount;
+                            gapOpeni = true;
+                            totalScore += gapOpen;
+                        }
+                }
+            }
+        }
+    }
+    return totalScore;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TSource, typename TSpec2> 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TSource, typename TSpec2>
 inline bool
 convertAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> > const& gAlign,
-				 Align<TSource, TSpec2>& align)
+                 Align<TSource, TSpec2>& align)
 {
-	// Pipe into Align data structure
-	String<char> mat;
-	if (convertAlignment(gAlign, mat)) {
-		typedef Align<TSource, TSpec2> TAlign;
-		typedef typename Size<TAlign>::Type TSize;
-		typedef typename Row<TAlign>::Type TRow;
-		typedef typename Iterator<TRow>::Type TRowIterator;
-		TStringSet& sourceSet = stringSet(gAlign);
-		TSize nseq = length(sourceSet);
-		clearGaps(align);
-		if (empty(rows(align))) {
-			resize(rows(align), nseq);
-			for(TSize i = 0; i<nseq; ++i) assignSource(row(align, i), sourceSet[i]);
-		}
-		String<TRowIterator> rowIter;
-		resize(rowIter, nseq);
-		for(TSize i = 0; i<nseq; ++i) value(rowIter, i) = begin(row(align, i));
-		TSize lenMat = length(mat);
-		TSize colLen = lenMat / nseq;
-		TSize gapCount = 0;
-		char gapChar = gapValue<char>();
-		for(TSize alignRow = 0; alignRow < nseq; ++alignRow) {
-			for(TSize pos = alignRow * colLen; pos < (alignRow + 1) * colLen; ++pos) {
-				if (value(mat, pos) != gapChar) {
-					if (gapCount) {
-						insertGaps(value(rowIter, alignRow), gapCount);
-						goFurther(value(rowIter, alignRow), gapCount);
-						gapCount = 0;
-					}
-					goNext(value(rowIter,alignRow));
-				} else ++gapCount;
-			}
-			if (gapCount) {
-				insertGaps(value(rowIter, alignRow), gapCount);
-				goFurther(value(rowIter, alignRow), gapCount);
-				gapCount = 0;
-			}
-		}
-	} else return false;
-	return true;
+    // Pipe into Align data structure
+    String<char> mat;
+    if (convertAlignment(gAlign, mat)) {
+        typedef Align<TSource, TSpec2> TAlign;
+        typedef typename Size<TAlign>::Type TSize;
+        typedef typename Row<TAlign>::Type TRow;
+        typedef typename Iterator<TRow>::Type TRowIterator;
+        TStringSet& sourceSet = stringSet(gAlign);
+        TSize nseq = length(sourceSet);
+        clearGaps(align);
+        if (empty(rows(align))) {
+            resize(rows(align), nseq);
+            for(TSize i = 0; i<nseq; ++i) assignSource(row(align, i), sourceSet[i]);
+        }
+        String<TRowIterator> rowIter;
+        resize(rowIter, nseq);
+        for(TSize i = 0; i<nseq; ++i) value(rowIter, i) = begin(row(align, i));
+        TSize lenMat = length(mat);
+        TSize colLen = lenMat / nseq;
+        TSize gapCount = 0;
+        char gapChar = gapValue<char>();
+        for(TSize alignRow = 0; alignRow < nseq; ++alignRow) {
+            for(TSize pos = alignRow * colLen; pos < (alignRow + 1) * colLen; ++pos) {
+                if (value(mat, pos) != gapChar) {
+                    if (gapCount) {
+                        insertGaps(value(rowIter, alignRow), gapCount);
+                        goFurther(value(rowIter, alignRow), gapCount);
+                        gapCount = 0;
+                    }
+                    goNext(value(rowIter,alignRow));
+                } else ++gapCount;
+            }
+            if (gapCount) {
+                insertGaps(value(rowIter, alignRow), gapCount);
+                goFurther(value(rowIter, alignRow), gapCount);
+                gapCount = 0;
+            }
+        }
+    } else return false;
+    return true;
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TSource, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec> 
+template<typename TSource, typename TSpec2, typename TStringSet, typename TCargo, typename TSpec>
 inline bool
 convertAlignment(Align<TSource, TSpec2> const& align,
-				 Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign)
+                 Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign)
 {
-	typedef Align<TSource, TSpec2> const TAlign;
-	//typedef typename Value<TSource>::Type TAlphabet;
-	typedef typename Size<TAlign>::Type TSize;
-	typedef typename Row<TAlign>::Type TRow;
-	typedef typename Iterator<TRow, Standard>::Type TRowIterator;
-	clearVertices(gAlign);
-	if (!length(stringSet(gAlign))) {
-		TStringSet sourceSet = stringSet(const_cast<Align<TSource, TSpec2>&>(align));
-		assignStringSet(gAlign, sourceSet);
-	}
-	TSize nseq = length(rows(align));
-	String<TRowIterator> rowIter;
-	String<TRowIterator> rowIterEnd;
-	resize(rowIter, nseq);
-	resize(rowIterEnd, nseq);
-	for(TSize i = 0; i<nseq; ++i) {
-		value(rowIter, i) = begin(row(align, i), Standard());
-		value(rowIterEnd, i) = end(row(align, i), Standard());
-	}
-	String<Fragment<> > matches;
-	for(TSize alignRow1 = 0; alignRow1 < nseq; ++alignRow1) {
-		for(TSize alignRow2 = alignRow1 + 1; alignRow2 < nseq; ++alignRow2) {
-			TRowIterator pos1 = value(rowIter,alignRow1);
-			TRowIterator pos2 = value(rowIter,alignRow2);
-			TSize alignPos = 0;
-			TSize length = 0;
-			TSize offset1 = 0;
-			TSize offset2 = 0;
-			for(;pos1 != value(rowIterEnd, alignRow1); ++pos1, ++pos2, ++alignPos) {
-				if ((isGap(pos1)) || (isGap(pos2))) {
-					if (length) {
-						appendValue(matches, Fragment<>(alignRow1, alignPos - offset1 - length, alignRow2, alignPos - offset2 - length, length));
-						length = 0;
-					}
-					if (isGap(pos1)) ++offset1;
-					if (isGap(pos2)) ++offset2;
-				} else ++length;
-			}
-			if (length) appendValue(matches, Fragment<>(alignRow1, alignPos - offset1 - length, alignRow2, alignPos - offset2 - length, length));
-		}
-	}
-	matchRefinement(matches,stringSet(gAlign),gAlign);
-	return true;
+    typedef Align<TSource, TSpec2> const TAlign;
+    //typedef typename Value<TSource>::Type TAlphabet;
+    typedef typename Size<TAlign>::Type TSize;
+    typedef typename Row<TAlign>::Type TRow;
+    typedef typename Iterator<TRow, Standard>::Type TRowIterator;
+    clearVertices(gAlign);
+    if (!length(stringSet(gAlign))) {
+        TStringSet sourceSet = stringSet(const_cast<Align<TSource, TSpec2>&>(align));
+        assignStringSet(gAlign, sourceSet);
+    }
+    TSize nseq = length(rows(align));
+    String<TRowIterator> rowIter;
+    String<TRowIterator> rowIterEnd;
+    resize(rowIter, nseq);
+    resize(rowIterEnd, nseq);
+    for(TSize i = 0; i<nseq; ++i) {
+        value(rowIter, i) = begin(row(align, i), Standard());
+        value(rowIterEnd, i) = end(row(align, i), Standard());
+    }
+    String<Fragment<> > matches;
+    for(TSize alignRow1 = 0; alignRow1 < nseq; ++alignRow1) {
+        for(TSize alignRow2 = alignRow1 + 1; alignRow2 < nseq; ++alignRow2) {
+            TRowIterator pos1 = value(rowIter,alignRow1);
+            TRowIterator pos2 = value(rowIter,alignRow2);
+            TSize alignPos = 0;
+            TSize length = 0;
+            TSize offset1 = 0;
+            TSize offset2 = 0;
+            for(;pos1 != value(rowIterEnd, alignRow1); ++pos1, ++pos2, ++alignPos) {
+                if ((isGap(pos1)) || (isGap(pos2))) {
+                    if (length) {
+                        appendValue(matches, Fragment<>(alignRow1, alignPos - offset1 - length, alignRow2, alignPos - offset2 - length, length));
+                        length = 0;
+                    }
+                    if (isGap(pos1)) ++offset1;
+                    if (isGap(pos2)) ++offset2;
+                } else ++length;
+            }
+            if (length) appendValue(matches, Fragment<>(alignRow1, alignPos - offset1 - length, alignRow2, alignPos - offset2 - length, length));
+        }
+    }
+    matchRefinement(matches,stringSet(gAlign),gAlign);
+    return true;
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_msa/graph_align_tcoffee_distance.h b/seqan/graph_msa/graph_align_tcoffee_distance.h
index eca306a..d205632 100644
--- a/seqan/graph_msa/graph_align_tcoffee_distance.h
+++ b/seqan/graph_msa/graph_align_tcoffee_distance.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -59,27 +59,10 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature typedef Tag<LibraryDistance_> const KmerDistance;
  */
 
-/**
-.Tag.Distance Calculation:
-..cat:Alignments
-..summary:A tag to specify how to calculate distance matrices.
-..include:seqan/graph_msa.h
-*/
-
-/**
-.Tag.Distance Calculation.value.LibraryDistance:
-	Using the library itself and heaviest common subsequence to determine a distance matrix
-..include:seqan/graph_msa.h
-*/
 struct LibraryDistance_;
 typedef Tag<LibraryDistance_> const LibraryDistance;
 
 
-/**
-.Tag.Distance Calculation.value.KmerDistance:
-	Using a simple kmer count to determine a distance matrix
-..include:seqan/graph_msa.h
-*/
 struct KmerDistance_;
 typedef Tag<KmerDistance_> const KmerDistance;
 
@@ -97,52 +80,52 @@ typedef Tag<KmerDistance_> const KmerDistance;
 template<typename TStringSet, typename TCargo, typename TSpec, typename TMatrix>
 inline void
 getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-				  TMatrix& distanceMatrix,
-				  LibraryDistance)
+                  TMatrix& distanceMatrix,
+                  LibraryDistance)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	//typedef typename Id<TGraph>::Type TId;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	//typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	//typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	typedef typename Value<TMatrix>::Type TValue;
-
-	// Initialization
-	clear(distanceMatrix);
-	TStringSet& str = stringSet(g);
-	TSize nseq = length(str);
-	resize(distanceMatrix, nseq * nseq, 0);
-
-	// All pairwise alignments
-	typedef String<String<TVertexDescriptor> > TSegmentString;
-	TValue maxScore = 0;
-	for(TSize i=0; i<nseq; ++i) {
-		TSegmentString seq1;
-		TSize len1 = length(str[i]);
-		_buildLeafString(g, i, seq1);
-		for(TSize j=i+1; j<nseq; ++j) {
-			// Align the 2 strings
-			TSegmentString seq2;
-			TSize len2 = length(str[j]);
-			_buildLeafString(g, j, seq2);
-			TSegmentString alignSeq;
-			TValue score = heaviestCommonSubsequence(g,seq1,seq2,alignSeq);
-			
-			// Normalize by distance
-			if (len1 > len2) score /= len1;
-			else score /= len2;
-			if (score > maxScore) maxScore = score;
-			
-			// Remember the value
-			distanceMatrix[i*nseq+j] = score;
-		}
-	}
-
-	// Normalize values
-	for(TSize i=0; i<nseq; ++i) 
-		for(TSize j=i+1; j<nseq; ++j) 
-			distanceMatrix[i*nseq+j] = SEQAN_DISTANCE_UNITY - ((distanceMatrix[i*nseq+j] * SEQAN_DISTANCE_UNITY) / maxScore );
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    //typedef typename Id<TGraph>::Type TId;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    //typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    //typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    typedef typename Value<TMatrix>::Type TValue;
+
+    // Initialization
+    clear(distanceMatrix);
+    TStringSet& str = stringSet(g);
+    TSize nseq = length(str);
+    resize(distanceMatrix, nseq * nseq, 0);
+
+    // All pairwise alignments
+    typedef String<String<TVertexDescriptor> > TSegmentString;
+    TValue maxScore = 0;
+    for(TSize i=0; i<nseq; ++i) {
+        TSegmentString seq1;
+        TSize len1 = length(str[i]);
+        _buildLeafString(g, i, seq1);
+        for(TSize j=i+1; j<nseq; ++j) {
+            // Align the 2 strings
+            TSegmentString seq2;
+            TSize len2 = length(str[j]);
+            _buildLeafString(g, j, seq2);
+            TSegmentString alignSeq;
+            TValue score = heaviestCommonSubsequence(g,seq1,seq2,alignSeq);
+
+            // Normalize by distance
+            if (len1 > len2) score /= len1;
+            else score /= len2;
+            if (score > maxScore) maxScore = score;
+
+            // Remember the value
+            distanceMatrix[i*nseq+j] = score;
+        }
+    }
+
+    // Normalize values
+    for(TSize i=0; i<nseq; ++i)
+        for(TSize j=i+1; j<nseq; ++j)
+            distanceMatrix[i*nseq+j] = SEQAN_DISTANCE_UNITY - ((distanceMatrix[i*nseq+j] * SEQAN_DISTANCE_UNITY) / maxScore );
 }
 
 
@@ -156,53 +139,53 @@ getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
 template<typename TStringSet, typename TCargo, typename TSpec, typename TMatrix, typename TSize, typename TAlphabet>
 inline void
 getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-				  TMatrix& distanceMatrix,
-				  TSize ktup,
-				  TAlphabet,
-				  KmerDistance)
+                  TMatrix& distanceMatrix,
+                  TSize ktup,
+                  TAlphabet,
+                  KmerDistance)
 {
-	//typedef typename Value<TMatrix>::Type TValue;
-	typedef typename Iterator<TMatrix, Standard>::Type TMatrixIterator;
+    //typedef typename Value<TMatrix>::Type TValue;
+    typedef typename Iterator<TMatrix, Standard>::Type TMatrixIterator;
 
-	getKmerSimilarityMatrix(stringSet(g), distanceMatrix, ktup, TAlphabet());
+    getKmerSimilarityMatrix(stringSet(g), distanceMatrix, ktup, TAlphabet());
 
-	// Similarity to distance conversion
-	TMatrixIterator matIt = begin(distanceMatrix, Standard());
-	TMatrixIterator endMatIt = end(distanceMatrix, Standard());
-	for(;matIt != endMatIt;++matIt)
-		*matIt = SEQAN_DISTANCE_UNITY - (*matIt);
+    // Similarity to distance conversion
+    TMatrixIterator matIt = begin(distanceMatrix, Standard());
+    TMatrixIterator endMatIt = end(distanceMatrix, Standard());
+    for(;matIt != endMatIt;++matIt)
+        *matIt = SEQAN_DISTANCE_UNITY - (*matIt);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TMatrix, typename TSize>
-inline void 
+inline void
 getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-				  TMatrix& distanceMatrix,
-				  TSize ktup,
-				  KmerDistance)
+                  TMatrix& distanceMatrix,
+                  TSize ktup,
+                  KmerDistance)
 {
-	SEQAN_CHECKPOINT
-	getDistanceMatrix(g, distanceMatrix, ktup, typename Value<typename Value<TStringSet>::Type>::Type(), KmerDistance() );
+    SEQAN_CHECKPOINT
+    getDistanceMatrix(g, distanceMatrix, ktup, typename Value<typename Value<TStringSet>::Type>::Type(), KmerDistance() );
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TMatrix>
-inline void 
+inline void
 getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-				  TMatrix& distanceMatrix,
-				  KmerDistance)
+                  TMatrix& distanceMatrix,
+                  KmerDistance)
 {
-	SEQAN_CHECKPOINT
-	getDistanceMatrix(g, distanceMatrix, 3, KmerDistance() );
+    SEQAN_CHECKPOINT
+    getDistanceMatrix(g, distanceMatrix, 3, KmerDistance() );
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
- * @fn getDistanceMatrix
+ * @fn AlignmentGraph#getDistanceMatrix
  * @headerfile <seqan/graph_msa.h>
  * @brief Computes a pairwise distance matrix from an @link AlignmentGraph @endlink.
  *
@@ -215,38 +198,15 @@ getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
  * @param[in]  alphabet For KMerDistance, the alphabet to use for k-mer counting (e.g. compressed alphabets).
  * @param[in]  tag      See @link DistanceCalculationTags @endlink.  Default: <tt>KMerDistance</tt>.
  */
- 
-
-/**
-.Function.getDistanceMatrix
-..class:Spec.Alignment Graph
-..summary:Computes a pairwise distance matrix from an alignment graph.
-..cat:Graph
-..signature:
-getDistanceMatrix(graph, mat [, tag])
-getDistanceMatrix(graph, mat [, ktup] [, alphabet], KmerDistance)
-..param.graph:An alignment graph containing the sequences and possible alignment edges.
-...type:Spec.Alignment Graph
-..param.mat:Out-parameter:Pairwise distance matrix.
-...type:Class.String
-..param.ktup:Length of k-mers.
-...remarks:For KmerDistance the length of the k-mers.
-..param.alphabet:Alphabet
-...remarks:For KmerDistance the alphabet to use for k-mer counting (e.g., compressed alphabets).
-..param.tag:Distance tag
-...type:Tag.Distance Calculation
-...remarks:Possible values are LibraryDistance or KmerDistance.
-...default:KmerDistance
-..returns:void
-..include:seqan/graph_msa.h
-*/
+
+
 template<typename TStringSet, typename TCargo, typename TSpec, typename TMatrix>
-inline void 
+inline void
 getDistanceMatrix(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-				  TMatrix& distanceMatrix)
+                  TMatrix& distanceMatrix)
 {
-	SEQAN_CHECKPOINT
-	getDistanceMatrix(g, distanceMatrix, KmerDistance() );
+    SEQAN_CHECKPOINT
+    getDistanceMatrix(g, distanceMatrix, KmerDistance() );
 }
 
 
diff --git a/seqan/graph_msa/graph_align_tcoffee_guidetree.h b/seqan/graph_msa/graph_align_tcoffee_guidetree.h
index 7fdf801..7734958 100644
--- a/seqan/graph_msa/graph_align_tcoffee_guidetree.h
+++ b/seqan/graph_msa/graph_align_tcoffee_guidetree.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -77,32 +77,18 @@ _roundToSignificantFigures(double num, int n)
  * @param[out] tree The guide tree.
  */
 
-/**
-.Function.njTree
-..summary:Computes a guide tree from a distance matrix.
-..cat:Graph
-..signature:
-njTree(mat, graph)
-..param.mat:A string of pairwise distance values, representing a square matrix.
-...type:Class.String
-...remarks: String must use double values because the algorithm recycles this string to store intermediate possibly fractional results.
-..param.graph:Out-parameter:The guide tree.
-...type:Spec.Tree
-..returns:void
-..include:seqan/graph_msa.h
-*/
 template<typename TValue, typename TStringSpec, typename TCargo, typename TSpec>
 inline void
 njTree(String<TValue, TStringSpec> const & matIn,
-	   Graph<Tree<TCargo, TSpec> >& g) 
+       Graph<Tree<TCargo, TSpec> >& g)
 {
-	typedef String<TValue, TStringSpec> TMatrix;
-	typedef typename Size<TMatrix>::Type TSize;
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	TSize nseq = (TSize) std::sqrt((double)length(matIn));
+    typedef String<TValue, TStringSpec> TMatrix;
+    typedef typename Size<TMatrix>::Type TSize;
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+    TSize nseq = (TSize) std::sqrt((double)length(matIn));
 
     // Assert that the input matrix has no negative values.
 // #if SEQAN_ENABLE_DEBUG
@@ -110,30 +96,30 @@ njTree(String<TValue, TStringSpec> const & matIn,
 //         SEQAN_ASSERT_GEQ_MSG(matIn[i], 0, "i = %u", i);
 // #endif  // #if SEQAN_ENABLE_DEBUG
 
-	//for(TSize i=0;i<nseq;++i) {
-	//	for(TSize j=0;j<nseq;++j) {
-	//		std::cout << getValue(matIn, i*nseq+j) << ",";
-	//	}
-	//	std::cout << std::endl;
-	//}
+    //for(TSize i=0;i<nseq;++i) {
+    //    for(TSize j=0;j<nseq;++j) {
+    //        std::cout << getValue(matIn, i*nseq+j) << ",";
+    //    }
+    //    std::cout << std::endl;
+    //}
 
     // Handle base cases for one and two sequences.
-	clearVertices(g);
-	if (nseq == 1)
+    clearVertices(g);
+    if (nseq == 1)
     {
-		g.data_root = addVertex(g);
-		return;
-	}
+        g.data_root = addVertex(g);
+        return;
+    }
     else if (nseq == 2)
     {
-		TVertexDescriptor v1 = addVertex(g);
-		TVertexDescriptor v2 = addVertex(g);
-		TVertexDescriptor internalVertex = addVertex(g);
-		addEdge(g, internalVertex, v1, (TCargo) _roundToSignificantFigures(matIn[1] / 2.0, 5));
+        TVertexDescriptor v1 = addVertex(g);
+        TVertexDescriptor v2 = addVertex(g);
+        TVertexDescriptor internalVertex = addVertex(g);
+        addEdge(g, internalVertex, v1, (TCargo) _roundToSignificantFigures(matIn[1] / 2.0, 5));
         addEdge(g, internalVertex, v2, (TCargo) _roundToSignificantFigures(matIn[1] / 2.0, 5));
-		g.data_root = internalVertex;
-		return;
-	}
+        g.data_root = internalVertex;
+        return;
+    }
 
     // Create a normalized copy of matIn with fixed point numbers, precision of 10 digits.
     TValue normFactor = 0;
@@ -148,171 +134,171 @@ njTree(String<TValue, TStringSpec> const & matIn,
     for (unsigned i = 0; i < length(mat); ++i)
         mat[i] = static_cast<__int64>(10000000.0 * ((double)(matIn[i]) / (double)(normFactor)));
 
-	// First initialization
-	String<__int64> av;    // Average branch length to a combined node
-	resize(av,nseq,0);
+    // First initialization
+    String<__int64> av;    // Average branch length to a combined node
+    resize(av,nseq,0);
 
-	String<TVertexDescriptor> connector;   // Nodes that need to be connected
-	resize(connector, nseq);
+    String<TVertexDescriptor> connector;   // Nodes that need to be connected
+    resize(connector, nseq);
 
-	for(TSize i=0;i<nseq;++i)
+    for(TSize i=0;i<nseq;++i)
     {
-		addVertex(g);  // Add all the nodes that correspond to sequences
-		connector[i] = i;
-		mat[i*nseq+i] = 0;
-	}
-
-	// Main cycle
-	__int64 fnseqs = static_cast<__int64>(nseq);
-	for(TSize nc=0; nc<(nseq-3); ++nc) {
-		__int64 sumOfBranches = 0;
-
-		// Determine the sum of all branches and
-		// copy upper triangle matrix to lower triangle
-		for(TSize col=1; col<nseq; ++col) 
-			for(TSize row=0; row<col; ++row) 
-				sumOfBranches += mat[col*nseq+row] = mat[row*nseq+col];
-
-		// Compute the sum of branch lengths for all possible pairs
-		bool notFound = true;
-		__int64 tmin = 0;	
-		TSize mini = 0;  // Next pair of seq i and j to join
-		TSize minj = 0;
-		__int64 diToAllOthers = 0;
-		__int64 djToAllOthers = 0;
-		__int64 total = 0;
-		for(TSize col=1; col<nseq; ++col)  {
-			if (connector[col] != nilVertex) {
-				for(TSize row=0; row<col; ++row) {
-					if (connector[row] != nilVertex) {
-						diToAllOthers = 0;
-						djToAllOthers = 0;
-						
-						for(TSize i=0; i<nseq; ++i) {
-							diToAllOthers += mat[i*nseq+row];
-							djToAllOthers += mat[i*nseq+col];
-						}
-
-						total = diToAllOthers + djToAllOthers + (fnseqs - 2) * mat[row*nseq+col] + 2 * (sumOfBranches - diToAllOthers - djToAllOthers);
-						total /= (2*(fnseqs - 2));
-
-						if ((notFound) || (total < tmin)) {
-							notFound = false;
-							tmin = total;
-							mini = row;
-							minj = col;
-						}
-					}
-				}
-			}
-		}
-
-		// Print nodes that are about to be joined
-		//std::cout << mini << std::endl;
-		//std::cout << minj << std::endl;
-		//std::cout << tmin << std::endl;
-		//std::cout << std::endl;
-		
-		// Compute branch lengths
-		__int64 dMinIToOthers = 0;
-		__int64 dMinJToOthers = 0;
-		for(TSize i=0; i<nseq; ++i) {
-			dMinIToOthers += mat[i*nseq + mini];
-			dMinJToOthers += mat[i*nseq + minj];
-		}
-		__int64 dmin = mat[mini*nseq + minj];
-		dMinIToOthers = dMinIToOthers / (fnseqs - 2);
-		dMinJToOthers = dMinJToOthers / (fnseqs - 2);
-		__int64 iBranch = (dmin + dMinIToOthers - dMinJToOthers) / 2;
-		__int64 jBranch = dmin - iBranch;
-		iBranch -= av[mini];
-		jBranch -= av[minj];
-		
-		// Set negative branch length to zero
-		if( iBranch < 0) iBranch = 0;
-		if( jBranch < 0) jBranch = 0;
-	
-		// Print branch lengths
-		//std::cout << iBranch << std::endl;
-		//std::cout << jBranch << std::endl;
-		//std::cout << std::endl;
-		
-		// Build tree
-		TVertexDescriptor internalVertex = addVertex(g);
-		addEdge(g, internalVertex, connector[mini], (TCargo) _roundToSignificantFigures((iBranch / 10000000.0) * normFactor, 5));
+        addVertex(g);  // Add all the nodes that correspond to sequences
+        connector[i] = i;
+        mat[i*nseq+i] = 0;
+    }
+
+    // Main cycle
+    __int64 fnseqs = static_cast<__int64>(nseq);
+    for(TSize nc=0; nc<(nseq-3); ++nc) {
+        __int64 sumOfBranches = 0;
+
+        // Determine the sum of all branches and
+        // copy upper triangle matrix to lower triangle
+        for(TSize col=1; col<nseq; ++col)
+            for(TSize row=0; row<col; ++row)
+                sumOfBranches += mat[col*nseq+row] = mat[row*nseq+col];
+
+        // Compute the sum of branch lengths for all possible pairs
+        bool notFound = true;
+        __int64 tmin = 0;
+        TSize mini = 0;  // Next pair of seq i and j to join
+        TSize minj = 0;
+        __int64 diToAllOthers = 0;
+        __int64 djToAllOthers = 0;
+        __int64 total = 0;
+        for(TSize col=1; col<nseq; ++col)  {
+            if (connector[col] != nilVertex) {
+                for(TSize row=0; row<col; ++row) {
+                    if (connector[row] != nilVertex) {
+                        diToAllOthers = 0;
+                        djToAllOthers = 0;
+
+                        for(TSize i=0; i<nseq; ++i) {
+                            diToAllOthers += mat[i*nseq+row];
+                            djToAllOthers += mat[i*nseq+col];
+                        }
+
+                        total = diToAllOthers + djToAllOthers + (fnseqs - 2) * mat[row*nseq+col] + 2 * (sumOfBranches - diToAllOthers - djToAllOthers);
+                        total /= (2*(fnseqs - 2));
+
+                        if ((notFound) || (total < tmin)) {
+                            notFound = false;
+                            tmin = total;
+                            mini = row;
+                            minj = col;
+                        }
+                    }
+                }
+            }
+        }
+
+        // Print nodes that are about to be joined
+        //std::cout << mini << std::endl;
+        //std::cout << minj << std::endl;
+        //std::cout << tmin << std::endl;
+        //std::cout << std::endl;
+
+        // Compute branch lengths
+        __int64 dMinIToOthers = 0;
+        __int64 dMinJToOthers = 0;
+        for(TSize i=0; i<nseq; ++i) {
+            dMinIToOthers += mat[i*nseq + mini];
+            dMinJToOthers += mat[i*nseq + minj];
+        }
+        __int64 dmin = mat[mini*nseq + minj];
+        dMinIToOthers = dMinIToOthers / (fnseqs - 2);
+        dMinJToOthers = dMinJToOthers / (fnseqs - 2);
+        __int64 iBranch = (dmin + dMinIToOthers - dMinJToOthers) / 2;
+        __int64 jBranch = dmin - iBranch;
+        iBranch -= av[mini];
+        jBranch -= av[minj];
+
+        // Set negative branch length to zero
+        if( iBranch < 0) iBranch = 0;
+        if( jBranch < 0) jBranch = 0;
+
+        // Print branch lengths
+        //std::cout << iBranch << std::endl;
+        //std::cout << jBranch << std::endl;
+        //std::cout << std::endl;
+
+        // Build tree
+        TVertexDescriptor internalVertex = addVertex(g);
+        addEdge(g, internalVertex, connector[mini], (TCargo) _roundToSignificantFigures((iBranch / 10000000.0) * normFactor, 5));
         addEdge(g, internalVertex, connector[minj], (TCargo) _roundToSignificantFigures((jBranch / 10000000.0) * normFactor, 5));
 
-		// Remember the average branch length for the new combined node
-		// Must be subtracted from all branches that include this node
-		if(dmin < 0) dmin = 0;
-		av[mini] = dmin / 2;
-
-
-		// Re-initialisation
-		// mini becomes the new combined node, minj is killed
-		--fnseqs;
-		connector[minj] = nilVertex;
-		connector[mini] = internalVertex;
-
-		for(TSize j=0; j<nseq; ++j) {
-			if( connector[j] != nilVertex ) {
-				// Use upper triangle
-				if((TSize) mini < j) mat[mini*nseq+j] = (mat[mini*nseq+j] + mat[minj*nseq+j]) / 2;
-				if((TSize) mini > j) mat[j*nseq+mini] = (mat[mini*nseq+j] + mat[minj*nseq+j]) / 2;
-			}
-		}
-		for(TSize j=0; j<nseq; ++j)
-			mat[j*nseq+minj] = mat[minj*nseq+j] = 0;
-	}
-
-	// Only three nodes left
-
-	// Find the remaining nodes
-	String<TSize> l;
-	resize(l,3);
-	TSize count = 0;
-	for(TSize i=0; i<nseq; ++i) {
-		if(connector[i] != nilVertex) {
-			l[count] = i;
-			++count;
-		}
-	}
-
-	// Remaining nodes
-	//std::cout << l[0] << std::endl;
-	//std::cout << l[1] << std::endl;
-	//std::cout << l[2] << std::endl;
-	//std::cout << std::endl;
-
-	String<__int64> branch;
-	resize(branch, 3);
-	branch[0] = (mat[l[0]*nseq+l[1]] + mat[l[0]*nseq+l[2]] - mat[l[1]*nseq+l[2]]) / 2;
-	branch[1] = (mat[l[1]*nseq+l[2]] + mat[l[0]*nseq+l[1]] - mat[l[0]*nseq+l[2]]) / 2;
-	branch[2] = (mat[l[1]*nseq+l[2]] + mat[l[0]*nseq+l[2]] - mat[l[0]*nseq+l[1]]) / 2;
-    
-	branch[0] -= av[l[0]];
-	branch[1] -= av[l[1]];
-	branch[2] -= av[l[2]];
-
-	// Print branch lengths
-	//std::cout << branch[0] << std::endl;
-	//std::cout << branch[1] << std::endl;
-	//std::cout << branch[2] << std::endl;
-	//std::cout << std::endl;
-    
-	// Reset negative branch lengths to zero
-	if( branch[0] < 0) branch[0] = 0;
-	if( branch[1] < 0) branch[1] = 0;
-	if( branch[2] < 0) branch[2] = 0;
-    
-	// Build tree
-	TVertexDescriptor internalVertex = addVertex(g);
-	addEdge(g, internalVertex, getValue(connector, l[0]), (TCargo) _roundToSignificantFigures((branch[0] / 10000000.0)* normFactor, 5));
+        // Remember the average branch length for the new combined node
+        // Must be subtracted from all branches that include this node
+        if(dmin < 0) dmin = 0;
+        av[mini] = dmin / 2;
+
+
+        // Re-initialisation
+        // mini becomes the new combined node, minj is killed
+        --fnseqs;
+        connector[minj] = nilVertex;
+        connector[mini] = internalVertex;
+
+        for(TSize j=0; j<nseq; ++j) {
+            if( connector[j] != nilVertex ) {
+                // Use upper triangle
+                if((TSize) mini < j) mat[mini*nseq+j] = (mat[mini*nseq+j] + mat[minj*nseq+j]) / 2;
+                if((TSize) mini > j) mat[j*nseq+mini] = (mat[mini*nseq+j] + mat[minj*nseq+j]) / 2;
+            }
+        }
+        for(TSize j=0; j<nseq; ++j)
+            mat[j*nseq+minj] = mat[minj*nseq+j] = 0;
+    }
+
+    // Only three nodes left
+
+    // Find the remaining nodes
+    String<TSize> l;
+    resize(l,3);
+    TSize count = 0;
+    for(TSize i=0; i<nseq; ++i) {
+        if(connector[i] != nilVertex) {
+            l[count] = i;
+            ++count;
+        }
+    }
+
+    // Remaining nodes
+    //std::cout << l[0] << std::endl;
+    //std::cout << l[1] << std::endl;
+    //std::cout << l[2] << std::endl;
+    //std::cout << std::endl;
+
+    String<__int64> branch;
+    resize(branch, 3);
+    branch[0] = (mat[l[0]*nseq+l[1]] + mat[l[0]*nseq+l[2]] - mat[l[1]*nseq+l[2]]) / 2;
+    branch[1] = (mat[l[1]*nseq+l[2]] + mat[l[0]*nseq+l[1]] - mat[l[0]*nseq+l[2]]) / 2;
+    branch[2] = (mat[l[1]*nseq+l[2]] + mat[l[0]*nseq+l[2]] - mat[l[0]*nseq+l[1]]) / 2;
+
+    branch[0] -= av[l[0]];
+    branch[1] -= av[l[1]];
+    branch[2] -= av[l[2]];
+
+    // Print branch lengths
+    //std::cout << branch[0] << std::endl;
+    //std::cout << branch[1] << std::endl;
+    //std::cout << branch[2] << std::endl;
+    //std::cout << std::endl;
+
+    // Reset negative branch lengths to zero
+    if( branch[0] < 0) branch[0] = 0;
+    if( branch[1] < 0) branch[1] = 0;
+    if( branch[2] < 0) branch[2] = 0;
+
+    // Build tree
+    TVertexDescriptor internalVertex = addVertex(g);
+    addEdge(g, internalVertex, getValue(connector, l[0]), (TCargo) _roundToSignificantFigures((branch[0] / 10000000.0)* normFactor, 5));
     addEdge(g, internalVertex, getValue(connector, l[1]), (TCargo) _roundToSignificantFigures((branch[1] / 10000000.0) * normFactor, 5));
-	TVertexDescriptor the_root = addVertex(g);
-	addEdge(g, the_root, getValue(connector, l[2]), (TCargo) _roundToSignificantFigures((branch[2] / 20000000.0) * normFactor, 5));
-	addEdge(g, the_root, internalVertex, (TCargo) _roundToSignificantFigures((branch[2] / 20000000.0) * normFactor, 5));
-	g.data_root = the_root;
+    TVertexDescriptor the_root = addVertex(g);
+    addEdge(g, the_root, getValue(connector, l[2]), (TCargo) _roundToSignificantFigures((branch[2] / 20000000.0) * normFactor, 5));
+    addEdge(g, the_root, internalVertex, (TCargo) _roundToSignificantFigures((branch[2] / 20000000.0) * normFactor, 5));
+    g.data_root = the_root;
 }
 
 
@@ -353,54 +339,23 @@ njTree(String<TValue, TStringSpec> const & matIn,
  * @signature typedef Tag<UpgmaAvg_> const UpgmaWeightAvg;
  */
 
-/**
-.Tag.Upgma Configurator:
-..cat:Alignments
-..summary:A tag to configure the guide tree construction.
-..include:seqan/graph_msa.h
-*/
-
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Upgma Configurator.value.UpgmaMin:
-	Uses the min operation in the upgma algorithm
-..include:seqan/graph_msa.h
-*/
-
 struct UpgmaMin_;
 typedef Tag<UpgmaMin_> const UpgmaMin;
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Upgma Configurator.value.UpgmaMax:
-	Uses the max operation in the upgma algorithm
-..include:seqan/graph_msa.h
-*/
-
 struct UpgmaMax_;
 typedef Tag<UpgmaMax_> const UpgmaMax;
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Upgma Configurator.value.UpgmaAvg:
-	Uses the average operation in the upgma algorithm
-..include:seqan/graph_msa.h
-*/
-
 struct UpgmaAvg_;
 typedef Tag<UpgmaAvg_> const UpgmaAvg;
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Upgma Configurator.value.UpgmaWeightAvg:
-	Uses the weighted average operation in the upgma algorithm
-..include:seqan/graph_msa.h
-*/
-
 struct UpgmaWeightAvg_;
 typedef Tag<UpgmaWeightAvg_> const UpgmaWeightAvg;
 
@@ -410,29 +365,29 @@ typedef Tag<UpgmaWeightAvg_> const UpgmaWeightAvg;
 
 template<typename TMatrix, typename TActive, typename TSize>
 inline void
-_upgmaTreeMerge(TMatrix& mat, 
-				TActive& active,
-				TSize index_i,
-				TSize index_j,
-				TSize nseq,
-				UpgmaWeightAvg) 
+_upgmaTreeMerge(TMatrix& mat,
+                TActive& active,
+                TSize index_i,
+                TSize index_j,
+                TSize nseq,
+                UpgmaWeightAvg)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TMatrix>::Type TValue;
-	// Average
-	for(TSize i=0;i<nseq;++i) {
-		if ((i != index_i) && (i != index_j) && (active[i] != 0)) {
-			if (index_i < i) {
-				mat[index_i*nseq + i] = ((TValue) active[index_i] / (TValue) (active[index_i] + active[index_j])) * mat[index_i * nseq + i];
-				if (index_j < i) mat[index_i*nseq + i] += ((TValue) active[index_j] / (TValue) (active[index_i] + active[index_j])) * mat[index_j * nseq + i];
-				else mat[index_i*nseq + i] += ((TValue) active[index_j] / (TValue) (active[index_i] + active[index_j])) * mat[i * nseq + index_j];
-			} else {
-				mat[i*nseq + index_i] = ((TValue) active[index_i] / (TValue) (active[index_i] + active[index_j])) * mat[i * nseq + index_i];
-				if (index_j < i) value(mat, i*nseq + index_i) += ((TValue) active[index_j] / (TValue) (active[index_i] + active[index_j])) * mat[index_j * nseq + i];
-				else mat[i*nseq + index_i] += ((TValue) active[index_j] / (TValue) (active[index_i] + active[index_j])) * mat[i * nseq + index_j];
-			}
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Value<TMatrix>::Type TValue;
+    // Average
+    for(TSize i=0;i<nseq;++i) {
+        if ((i != index_i) && (i != index_j) && (active[i] != 0)) {
+            if (index_i < i) {
+                mat[index_i*nseq + i] = ((TValue) active[index_i] / (TValue) (active[index_i] + active[index_j])) * mat[index_i * nseq + i];
+                if (index_j < i) mat[index_i*nseq + i] += ((TValue) active[index_j] / (TValue) (active[index_i] + active[index_j])) * mat[index_j * nseq + i];
+                else mat[index_i*nseq + i] += ((TValue) active[index_j] / (TValue) (active[index_i] + active[index_j])) * mat[i * nseq + index_j];
+            } else {
+                mat[i*nseq + index_i] = ((TValue) active[index_i] / (TValue) (active[index_i] + active[index_j])) * mat[i * nseq + index_i];
+                if (index_j < i) value(mat, i*nseq + index_i) += ((TValue) active[index_j] / (TValue) (active[index_i] + active[index_j])) * mat[index_j * nseq + i];
+                else mat[i*nseq + index_i] += ((TValue) active[index_j] / (TValue) (active[index_i] + active[index_j])) * mat[i * nseq + index_j];
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -440,25 +395,25 @@ _upgmaTreeMerge(TMatrix& mat,
 
 template<typename TMatrix, typename TActive, typename TSize>
 inline void
-_upgmaTreeMerge(TMatrix& mat, 
-				TActive& active,
-				TSize index_i,
-				TSize index_j,
-				TSize nseq,
-				UpgmaAvg) 
+_upgmaTreeMerge(TMatrix& mat,
+                TActive& active,
+                TSize index_i,
+                TSize index_j,
+                TSize nseq,
+                UpgmaAvg)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TMatrix>::Type TValue;
-
-	// Minimum
-	for(TSize i=0;i<nseq;++i) {
-		if ((i != index_i) && (i != index_j) && (active[i] != 0)) {
-			TValue val1 = (index_i < i) ? mat[index_i * nseq + i] : mat[i * nseq + index_i];
-			TValue val2 = (index_j < i) ? mat[index_j * nseq + i] : mat[i * nseq + index_j];
-			if (index_i < i) mat[index_i * nseq + i] = (val1 + val2) / 2;
-			else mat[i * nseq + index_i] = (val1 + val2) / 2;
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Value<TMatrix>::Type TValue;
+
+    // Minimum
+    for(TSize i=0;i<nseq;++i) {
+        if ((i != index_i) && (i != index_j) && (active[i] != 0)) {
+            TValue val1 = (index_i < i) ? mat[index_i * nseq + i] : mat[i * nseq + index_i];
+            TValue val2 = (index_j < i) ? mat[index_j * nseq + i] : mat[i * nseq + index_j];
+            if (index_i < i) mat[index_i * nseq + i] = (val1 + val2) / 2;
+            else mat[i * nseq + index_i] = (val1 + val2) / 2;
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -466,50 +421,50 @@ _upgmaTreeMerge(TMatrix& mat,
 
 template<typename TMatrix, typename TActive, typename TSize>
 inline void
-_upgmaTreeMerge(TMatrix& mat, 
-				TActive& active,
-				TSize index_i,
-				TSize index_j,
-				TSize nseq,
-				UpgmaMin) 
+_upgmaTreeMerge(TMatrix& mat,
+                TActive& active,
+                TSize index_i,
+                TSize index_j,
+                TSize nseq,
+                UpgmaMin)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TMatrix>::Type TValue;
-
-	// Minimum
-	for(TSize i=0;i<nseq;++i) {
-		if ((i != index_i) && (i != index_j) && (active[i] != 0)) {
-			TValue newDist = (index_i < i) ? mat[index_i * nseq + i] : mat[i * nseq + index_i];
-			TValue newDist2 = (index_j < i) ? mat[index_j * nseq + i] : mat[i * nseq + index_j];
-			if (index_i < i) mat[index_i * nseq + i] = _min(newDist, newDist2);
-			else mat[i * nseq + index_i] = _min(newDist, newDist2);
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Value<TMatrix>::Type TValue;
+
+    // Minimum
+    for(TSize i=0;i<nseq;++i) {
+        if ((i != index_i) && (i != index_j) && (active[i] != 0)) {
+            TValue newDist = (index_i < i) ? mat[index_i * nseq + i] : mat[i * nseq + index_i];
+            TValue newDist2 = (index_j < i) ? mat[index_j * nseq + i] : mat[i * nseq + index_j];
+            if (index_i < i) mat[index_i * nseq + i] = _min(newDist, newDist2);
+            else mat[i * nseq + index_i] = _min(newDist, newDist2);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TMatrix, typename TActive, typename TSize>
 inline void
-_upgmaTreeMerge(TMatrix& mat, 
-				TActive& active,
-				TSize index_i,
-				TSize index_j,
-				TSize nseq,
-				UpgmaMax) 
+_upgmaTreeMerge(TMatrix& mat,
+                TActive& active,
+                TSize index_i,
+                TSize index_j,
+                TSize nseq,
+                UpgmaMax)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TMatrix>::Type TValue;
-
-	// Maximum
-	for(TSize i=0;i<nseq;++i) {
-		if ((i != index_i) && (i != index_j) && (active[i] != 0)) {
-			TValue newDist = (index_i < i) ? mat[index_i * nseq + i] : mat[i * nseq + index_i];
-			TValue newDist2 = (index_j < i) ? mat[index_j * nseq + i] : mat[i * nseq + index_j];
-			if (index_i < i) mat[index_i * nseq + i] = _max(newDist, newDist2);
-			else mat[i * nseq + index_i] = _max(newDist, newDist2);
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Value<TMatrix>::Type TValue;
+
+    // Maximum
+    for(TSize i=0;i<nseq;++i) {
+        if ((i != index_i) && (i != index_j) && (active[i] != 0)) {
+            TValue newDist = (index_i < i) ? mat[index_i * nseq + i] : mat[i * nseq + index_i];
+            TValue newDist2 = (index_j < i) ? mat[index_j * nseq + i] : mat[i * nseq + index_j];
+            if (index_i < i) mat[index_i * nseq + i] = _max(newDist, newDist2);
+            else mat[i * nseq + index_i] = _max(newDist, newDist2);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -517,63 +472,63 @@ _upgmaTreeMerge(TMatrix& mat,
 template<typename TCargo, typename TSpec, typename TActive, typename TEdgeDescriptor>
 inline void
 _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph,
-				TActive const&,
-				TEdgeDescriptor best,
-				UpgmaMax)
+                TActive const&,
+                TEdgeDescriptor best,
+                UpgmaMax)
 {
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	//typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-
-	TVertexDescriptor s = sourceVertex(pairGraph,best);
-	TVertexDescriptor t = targetVertex(pairGraph,best);
-	typedef String<TEdgeDescriptor> TEdgeString;
-	typedef typename Iterator<TEdgeString>::Type TEdgeIter;
-	TEdgeString removeEdges;
-	for(TOutEdgeIterator outIt(pairGraph, s);!atEnd(outIt);goNext(outIt)) {
-		if (targetVertex(outIt) == t) continue;
-		TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), t);
-		if (e == 0) appendValue(removeEdges, value(outIt));
-		else {
-			if (cargo(e) > cargo(value(outIt))) cargo(value(outIt)) = cargo(e);
-		}
-	}
-	TEdgeIter eIt = begin(removeEdges);
-	TEdgeIter eItEnd = end(removeEdges);
-	for(;eIt != eItEnd; goNext(eIt)) removeEdge(pairGraph, value(eIt));
-	removeVertex(pairGraph, t);
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    //typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    TVertexDescriptor s = sourceVertex(pairGraph,best);
+    TVertexDescriptor t = targetVertex(pairGraph,best);
+    typedef String<TEdgeDescriptor> TEdgeString;
+    typedef typename Iterator<TEdgeString>::Type TEdgeIter;
+    TEdgeString removeEdges;
+    for(TOutEdgeIterator outIt(pairGraph, s);!atEnd(outIt);goNext(outIt)) {
+        if (targetVertex(outIt) == t) continue;
+        TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), t);
+        if (e == 0) appendValue(removeEdges, value(outIt));
+        else {
+            if (cargo(e) > cargo(value(outIt))) cargo(value(outIt)) = cargo(e);
+        }
+    }
+    TEdgeIter eIt = begin(removeEdges);
+    TEdgeIter eItEnd = end(removeEdges);
+    for(;eIt != eItEnd; goNext(eIt)) removeEdge(pairGraph, value(eIt));
+    removeVertex(pairGraph, t);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TActive, typename TEdgeDescriptor>
 inline void
-_upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph, 
-				TActive const&,
-				TEdgeDescriptor best,
-				UpgmaMin)
+_upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph,
+                TActive const&,
+                TEdgeDescriptor best,
+                UpgmaMin)
 {
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	//typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-
-	TVertexDescriptor s = sourceVertex(pairGraph,best);
-	TVertexDescriptor t = targetVertex(pairGraph,best);
-	for(TOutEdgeIterator outIt(pairGraph, s);!atEnd(outIt);goNext(outIt)) {
-		if (targetVertex(outIt) == t) continue;
-		TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), t);
-		if (e != 0) {
-			if (cargo(e) < cargo(value(outIt))) cargo(value(outIt)) = cargo(e);
-		}
-	}
-	for(TOutEdgeIterator outIt(pairGraph, t);!atEnd(outIt);goNext(outIt)) {
-		if (targetVertex(outIt) == s) continue;
-		TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), s);
-		if (e == 0) addEdge(pairGraph, s, targetVertex(outIt), cargo(value(outIt)));
-	}
-	removeVertex(pairGraph, t);
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    //typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    TVertexDescriptor s = sourceVertex(pairGraph,best);
+    TVertexDescriptor t = targetVertex(pairGraph,best);
+    for(TOutEdgeIterator outIt(pairGraph, s);!atEnd(outIt);goNext(outIt)) {
+        if (targetVertex(outIt) == t) continue;
+        TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), t);
+        if (e != 0) {
+            if (cargo(e) < cargo(value(outIt))) cargo(value(outIt)) = cargo(e);
+        }
+    }
+    for(TOutEdgeIterator outIt(pairGraph, t);!atEnd(outIt);goNext(outIt)) {
+        if (targetVertex(outIt) == s) continue;
+        TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), s);
+        if (e == 0) addEdge(pairGraph, s, targetVertex(outIt), cargo(value(outIt)));
+    }
+    removeVertex(pairGraph, t);
 }
 
 
@@ -581,34 +536,34 @@ _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph,
 
 template<typename TCargo, typename TSpec, typename TActive, typename TEdgeDescriptor>
 inline void
-_upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph, 
-				TActive const& active,
-				TEdgeDescriptor best,
-				UpgmaWeightAvg) 
+_upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph,
+                TActive const& active,
+                TEdgeDescriptor best,
+                UpgmaWeightAvg)
 {
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	//typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-
-	TCargo infCargo = _getInfinity<TCargo>();
-	TVertexDescriptor s = sourceVertex(pairGraph,best);
-	TVertexDescriptor t = targetVertex(pairGraph,best);
-
-	for(TOutEdgeIterator outIt(pairGraph, s);!atEnd(outIt);goNext(outIt)) {
-		if (targetVertex(outIt) == t) continue;
-		TEdgeDescriptor e1 = value(outIt);
-		TEdgeDescriptor e2 = findEdge(pairGraph, targetVertex(outIt), t);
-		if (e2 != 0) cargo(e1) = ((TCargo) value(active,s) / (TCargo) (value(active,s) + value(active,t))) * cargo(e1) + ((TCargo) value(active,t) / (TCargo) (value(active,s) + value(active,t))) * cargo(e2);
-		else cargo(e1) = ((TCargo) value(active,s) / (TCargo) (value(active,s) + value(active,t))) * cargo(e1) + ((TCargo) value(active,t) / (TCargo) (value(active,s) + value(active,t))) * infCargo;
-	}
-	for(TOutEdgeIterator outIt(pairGraph, t);!atEnd(outIt);goNext(outIt)) {
-		if (targetVertex(outIt) == s) continue;
-		TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), s);
-		TCargo c = ((TCargo) value(active,s) / (TCargo) (value(active,s) + value(active,t))) * infCargo + ((TCargo) value(active,t) / (TCargo) (value(active,s) + value(active,t))) * cargo(value(outIt));
-		if (e == 0)  addEdge(pairGraph, s, targetVertex(outIt), c);
-	}
-	removeVertex(pairGraph, t);
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    //typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    TCargo infCargo = _getInfinity<TCargo>();
+    TVertexDescriptor s = sourceVertex(pairGraph,best);
+    TVertexDescriptor t = targetVertex(pairGraph,best);
+
+    for(TOutEdgeIterator outIt(pairGraph, s);!atEnd(outIt);goNext(outIt)) {
+        if (targetVertex(outIt) == t) continue;
+        TEdgeDescriptor e1 = value(outIt);
+        TEdgeDescriptor e2 = findEdge(pairGraph, targetVertex(outIt), t);
+        if (e2 != 0) cargo(e1) = ((TCargo) value(active,s) / (TCargo) (value(active,s) + value(active,t))) * cargo(e1) + ((TCargo) value(active,t) / (TCargo) (value(active,s) + value(active,t))) * cargo(e2);
+        else cargo(e1) = ((TCargo) value(active,s) / (TCargo) (value(active,s) + value(active,t))) * cargo(e1) + ((TCargo) value(active,t) / (TCargo) (value(active,s) + value(active,t))) * infCargo;
+    }
+    for(TOutEdgeIterator outIt(pairGraph, t);!atEnd(outIt);goNext(outIt)) {
+        if (targetVertex(outIt) == s) continue;
+        TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), s);
+        TCargo c = ((TCargo) value(active,s) / (TCargo) (value(active,s) + value(active,t))) * infCargo + ((TCargo) value(active,t) / (TCargo) (value(active,s) + value(active,t))) * cargo(value(outIt));
+        if (e == 0)  addEdge(pairGraph, s, targetVertex(outIt), c);
+    }
+    removeVertex(pairGraph, t);
 }
 
 
@@ -616,306 +571,306 @@ _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph,
 
 template<typename TCargo, typename TSpec, typename TActive, typename TEdgeDescriptor>
 inline void
-_upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph, 
-				TActive const&,
-				TEdgeDescriptor best,
-				UpgmaAvg) 
+_upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >& pairGraph,
+                TActive const&,
+                TEdgeDescriptor best,
+                UpgmaAvg)
 {
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	//typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-
-	TCargo infCargo = _getInfinity<TCargo>();
-	TVertexDescriptor s = sourceVertex(pairGraph,best);
-	TVertexDescriptor t = targetVertex(pairGraph,best);
-
-	for(TOutEdgeIterator outIt(pairGraph, s);!atEnd(outIt);goNext(outIt)) {
-		if (targetVertex(outIt) == t) continue;
-		TEdgeDescriptor e1 = value(outIt);
-		TEdgeDescriptor e2 = findEdge(pairGraph, targetVertex(outIt), t);
-		cargo(e1) = (e2 != 0) ? (cargo(e1) + cargo(e2)) / 2 : (cargo(e1) + infCargo) / 2;
-	}
-	for(TOutEdgeIterator outIt(pairGraph, t);!atEnd(outIt);goNext(outIt)) {
-		if (targetVertex(outIt) == s) continue;
-		TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), s);
-		if (e == 0) {
-			TCargo c = (infCargo + cargo(value(outIt))) / 2;
-			addEdge(pairGraph, s, targetVertex(outIt), c);
-		}
-	}
-	removeVertex(pairGraph, t);
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    //typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    TCargo infCargo = _getInfinity<TCargo>();
+    TVertexDescriptor s = sourceVertex(pairGraph,best);
+    TVertexDescriptor t = targetVertex(pairGraph,best);
+
+    for(TOutEdgeIterator outIt(pairGraph, s);!atEnd(outIt);goNext(outIt)) {
+        if (targetVertex(outIt) == t) continue;
+        TEdgeDescriptor e1 = value(outIt);
+        TEdgeDescriptor e2 = findEdge(pairGraph, targetVertex(outIt), t);
+        cargo(e1) = (e2 != 0) ? (cargo(e1) + cargo(e2)) / 2 : (cargo(e1) + infCargo) / 2;
+    }
+    for(TOutEdgeIterator outIt(pairGraph, t);!atEnd(outIt);goNext(outIt)) {
+        if (targetVertex(outIt) == s) continue;
+        TEdgeDescriptor e = findEdge(pairGraph, targetVertex(outIt), s);
+        if (e == 0) {
+            TCargo c = (infCargo + cargo(value(outIt))) / 2;
+            addEdge(pairGraph, s, targetVertex(outIt), c);
+        }
+    }
+    removeVertex(pairGraph, t);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringValue, typename TStringSpec, typename TCargo, typename TSpec, typename TTag>
 inline void
-upgmaTree(String<TStringValue, TStringSpec>& mat, 
-		  Graph<Tree<TCargo, TSpec> >& g,
-		  TTag) 
+upgmaTree(String<TStringValue, TStringSpec>& mat,
+          Graph<Tree<TCargo, TSpec> >& g,
+          TTag)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef String<TStringValue, TStringSpec> TMatrix;
-	typedef typename Value<TMatrix>::Type TValue;
-	//typedef typename Iterator<TMatrix>::Type TMatrixIter;
-
-	// First initialization
-	TSize nseq = (TSize) std::sqrt((double)length(mat));
-	clearVertices(g);
-
-	// Is it possible to make a guide tree?
-	if (nseq == 1) {
-		g.data_root = addVertex(g);
-		return;
-	} else if (nseq == 2) {
-		TVertexDescriptor v1 = addVertex(g);
-		TVertexDescriptor v2 = addVertex(g);
-		TVertexDescriptor internalVertex = addVertex(g);
-		addEdge(g, internalVertex, v1, (TCargo) 1);
-		addEdge(g, internalVertex, v2, (TCargo) 1);
-		g.data_root = internalVertex;
-		return;
-	}
-
-	// Which entries in the matrix are still active and how many members belong to this group
-	String<TSize> active;
-	resize(active, nseq, 1);
-	// Vertex descriptor that represents that entry
-	String<TVertexDescriptor> nodes;
-	reserve(nodes, nseq);
-
-
-	// Find the minimal value
-	bool notFound = true;
-	TValue minVal = 0;
-	TSize index_i = 0;
-	TSize index_j = 1;
-	for(TSize row=0;row<nseq;++row) {
-		for(TSize col=row+1;col<nseq;++col) {
-			if ((notFound) || (minVal > mat[row*nseq + col])) {
-				notFound = false;
-				minVal = mat[row*nseq + col];
-				index_i = row;
-				index_j = col;
-			}
-		}
-		appendValue(nodes, addVertex(g));	// For each sequence one vertex
-	}
-
-	// Property map for sum of weights for each node
-	String<TCargo> weights;
-	resize(weights, nseq, (TCargo) 0);
-	reserve(weights, 2*nseq - 1);
-
-	// Merge groups
-	TSize m = nseq;
-	while (m>1) {
-		// Merge nodes
-		TVertexDescriptor internalNode = addVertex(g);
-
-		//// Debug code
-		//for(TSize i=0;i<nseq;++i) {
-		//	if (value(active,i)==0) continue;
-		//	for(TSize j=i+1;j<nseq;++j) {
-		//		if (value(active,j)==0) continue;
-		//		std::cout << value(mat, i*nseq+j) << ",";
-		//	}
-		//	std::cout << std::endl;
-		//}
-		//std::cout << minVal << ',' << index_i << ',' << index_j << ',' << std::endl;
-		//std::cout << nodes[index_i] << ',' << nodes[index_j] << std::endl;
-		//std::cout << std::endl;
-
-		TCargo w = (TCargo) (minVal / 2);
-		addEdge(g, internalNode, nodes[index_i], w - property(weights, nodes[index_i]));
-		addEdge(g, internalNode, nodes[index_j], w - property(weights, nodes[index_j]));
-		appendValue(weights, w);		
-
-		// Get the new distance values
-		_upgmaTreeMerge(mat, active, index_i, index_j, nseq, TTag());
-
-		// Inactivate one group, adjust the member count for the other one
-		active[index_i] += active[index_j];
-		active[index_j] = 0;
-		nodes[index_i] = internalNode;
-		
-		// Find new minimum
-		notFound = true;
-		for(TSize i=0;i<nseq;++i) {
-			if (active[i] == 0) continue;
-			for(TSize j=i+1;j<nseq;++j) {
-				if (active[j] == 0) continue;
-				if ((notFound) || (minVal > mat[i*nseq + j])) {
-					notFound = false;
-					minVal = mat[i*nseq + j];
-					index_i = i;
-					index_j = j;
-				}
-			}
-		}
-		--m;
-	}
-	g.data_root = numVertices(g) - 1;
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef String<TStringValue, TStringSpec> TMatrix;
+    typedef typename Value<TMatrix>::Type TValue;
+    //typedef typename Iterator<TMatrix>::Type TMatrixIter;
+
+    // First initialization
+    TSize nseq = (TSize) std::sqrt((double)length(mat));
+    clearVertices(g);
+
+    // Is it possible to make a guide tree?
+    if (nseq == 1) {
+        g.data_root = addVertex(g);
+        return;
+    } else if (nseq == 2) {
+        TVertexDescriptor v1 = addVertex(g);
+        TVertexDescriptor v2 = addVertex(g);
+        TVertexDescriptor internalVertex = addVertex(g);
+        addEdge(g, internalVertex, v1, (TCargo) 1);
+        addEdge(g, internalVertex, v2, (TCargo) 1);
+        g.data_root = internalVertex;
+        return;
+    }
+
+    // Which entries in the matrix are still active and how many members belong to this group
+    String<TSize> active;
+    resize(active, nseq, 1);
+    // Vertex descriptor that represents that entry
+    String<TVertexDescriptor> nodes;
+    reserve(nodes, nseq);
+
+
+    // Find the minimal value
+    bool notFound = true;
+    TValue minVal = 0;
+    TSize index_i = 0;
+    TSize index_j = 1;
+    for(TSize row=0;row<nseq;++row) {
+        for(TSize col=row+1;col<nseq;++col) {
+            if ((notFound) || (minVal > mat[row*nseq + col])) {
+                notFound = false;
+                minVal = mat[row*nseq + col];
+                index_i = row;
+                index_j = col;
+            }
+        }
+        appendValue(nodes, addVertex(g));    // For each sequence one vertex
+    }
+
+    // Property map for sum of weights for each node
+    String<TCargo> weights;
+    resize(weights, nseq, (TCargo) 0);
+    reserve(weights, 2*nseq - 1);
+
+    // Merge groups
+    TSize m = nseq;
+    while (m>1) {
+        // Merge nodes
+        TVertexDescriptor internalNode = addVertex(g);
+
+        //// Debug code
+        //for(TSize i=0;i<nseq;++i) {
+        //    if (value(active,i)==0) continue;
+        //    for(TSize j=i+1;j<nseq;++j) {
+        //        if (value(active,j)==0) continue;
+        //        std::cout << value(mat, i*nseq+j) << ",";
+        //    }
+        //    std::cout << std::endl;
+        //}
+        //std::cout << minVal << ',' << index_i << ',' << index_j << ',' << std::endl;
+        //std::cout << nodes[index_i] << ',' << nodes[index_j] << std::endl;
+        //std::cout << std::endl;
+
+        TCargo w = (TCargo) (minVal / 2);
+        addEdge(g, internalNode, nodes[index_i], w - property(weights, nodes[index_i]));
+        addEdge(g, internalNode, nodes[index_j], w - property(weights, nodes[index_j]));
+        appendValue(weights, w);
+
+        // Get the new distance values
+        _upgmaTreeMerge(mat, active, index_i, index_j, nseq, TTag());
+
+        // Inactivate one group, adjust the member count for the other one
+        active[index_i] += active[index_j];
+        active[index_j] = 0;
+        nodes[index_i] = internalNode;
+
+        // Find new minimum
+        notFound = true;
+        for(TSize i=0;i<nseq;++i) {
+            if (active[i] == 0) continue;
+            for(TSize j=i+1;j<nseq;++j) {
+                if (active[j] == 0) continue;
+                if ((notFound) || (minVal > mat[i*nseq + j])) {
+                    notFound = false;
+                    minVal = mat[i*nseq + j];
+                    index_i = i;
+                    index_j = j;
+                }
+            }
+        }
+        --m;
+    }
+    g.data_root = numVertices(g) - 1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TSpec1, typename TCargo, typename TSpec2, typename TTag>
 inline void
-upgmaTree(Graph<Undirected<TValue, TSpec1> >& pairGraph, 
-		  Graph<Tree<TCargo, TSpec2> >& g,
-		  TTag) 
+upgmaTree(Graph<Undirected<TValue, TSpec1> >& pairGraph,
+          Graph<Tree<TCargo, TSpec2> >& g,
+          TTag)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TValue, TSpec1> > TPairGraph;
-	typedef Graph<Tree<TCargo, TSpec2> > TGuideTree;
-	typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
-	typedef typename VertexDescriptor<TPairGraph>::Type TVD;
-	typedef typename EdgeDescriptor<TPairGraph>::Type TED;
-	typedef typename Iterator<TPairGraph, EdgeIterator>::Type TEdgeI;
-	typedef typename Iterator<TPairGraph, OutEdgeIterator>::Type TEdgeOutI;
-	typedef typename Iterator<TPairGraph, VertexIterator>::Type TVertexI;
-	typedef typename Size<TPairGraph>::Type TSize;
-
-	// First initialization
-	TCargo const maxVal = maxValue<TCargo>();
-	TSize nseq = numVertices(pairGraph);
-	TCargo infCargo = _getInfinity<TCargo>();
-	clearVertices(g);
-
-	// Is it possible to make a guide tree?
-	if (nseq == 1) {
-		g.data_root = addVertex(g);
-		return;
-	} else if (nseq == 2) {
-		TVertexDescriptor v1 = addVertex(g);
-		TVertexDescriptor v2 = addVertex(g);
-		TVertexDescriptor internalVertex = addVertex(g);
-		addEdge(g, internalVertex, v1, (TCargo) 1);
-		addEdge(g, internalVertex, v2, (TCargo) 1);
-		g.data_root = internalVertex;
-		return;
-	}
-
-	// Which entries in the matrix are still active and how many members belong to this group
-	String<TSize> active;
-	resize(active, nseq, 1);
-	// Vertex descriptor that represents that entry
-	typedef String<TVertexDescriptor> TNodeString;
-	typedef typename Iterator<TNodeString, Standard>::Type TNodeIter;
-	TNodeString nodes;
-	resize(nodes, nseq);
-	TNodeIter nodeIt = begin(nodes, Standard() );
-	TNodeIter nodeItEnd = end(nodes, Standard() );
-	for(;nodeIt<nodeItEnd;goNext(nodeIt)) 
-		*nodeIt = addVertex(g);	// For each sequence one vertex
-
-	// Find the minimal value for all vertices (with respect to all greater vertices)
-	typedef Pair<TValue, TVD> TWeightEdgePair;
-	typedef String<TWeightEdgePair> TMinValues;
-	TMinValues minValues;
-	resize(minValues, nseq, TWeightEdgePair(maxVal, 0));
-	TEdgeI itE(pairGraph);
-	for(;!atEnd(itE);goNext(itE)) {
-		TVD s = sourceVertex(itE);
-		TVD t = targetVertex(itE);
-		if (cargo(*itE) < (minValues[s].i1)) 
-			minValues[s] = TWeightEdgePair(cargo(*itE), t);		
-	}
-	// Find the overall minimum
-	typedef typename Iterator<TMinValues, Standard>::Type TMinIter;
-	TMinIter itMin = begin(minValues, Standard() );
-	TMinIter itMinEnd = end(minValues, Standard() );
-	TValue minVal = maxVal;
-	TVD sourceBest = 0;
-	TVD targetBest = 0;
-	for(TVD index=0;itMin != itMinEnd; goNext(itMin), ++index) {
-		if ((*itMin).i1 < minVal) {
-			minVal = (*itMin).i1;
-			sourceBest = index;
-			targetBest = (*itMin).i2;
-		}
-	}
-	TED best = 0;
-	if (sourceBest == targetBest) { // If none is found we have to insert a new edge
-		TVertexI itV(pairGraph);
-		sourceBest = value(itV); goNext(itV);
-		targetBest = value(itV);
-		best = addEdge(pairGraph, sourceBest, targetBest, infCargo);
-	} else best = findEdge(pairGraph, sourceBest, targetBest);
-	
-	// Property map for sum of weights for each node
-	String<TCargo> weights;
-	resize(weights, nseq, (TCargo) 0);
-	reserve(weights, 2*nseq - 1);
-
-	// Merge groups
-	TSize m = nseq;
-	while (m>1) {
-		// Merge nodes
-		TVertexDescriptor internalNode = addVertex(g);
-		
-		// Set the weights
-		TCargo w = (TCargo) (minVal / 2);
-		addEdge(g, internalNode, nodes[sourceBest], w - property(weights, nodes[sourceBest]));
-		addEdge(g, internalNode, nodes[targetBest], w - property(weights, nodes[targetBest]));
-		appendValue(weights, w);		
-
-		// Get the new distance values
-		_upgmaTreeMerge(pairGraph, active, best, TTag());
-		
-		// Inactivate one group, adjust the member count for the other one
-		active[sourceBest] += active[targetBest];
-		active[targetBest] = 0;
-		nodes[sourceBest] = internalNode;
-	
-		// Update the minimum values
-		minValues[sourceBest] = TWeightEdgePair(maxVal, 0);
-		for(TEdgeOutI itOutE(pairGraph, sourceBest);!atEnd(itOutE);goNext(itOutE)) {
-			TVD localTVD = targetVertex(itOutE);
-			if (sourceBest < localTVD) {
-				if (cargo(value(itOutE)) < (minValues[sourceBest].i1)) minValues[sourceBest] = TWeightEdgePair(cargo(value(itOutE)), localTVD);
-			}
-		}
-		// Find the new minimum value
-		itMin = begin(minValues, Standard() );
-		itMinEnd = end(minValues, Standard() );
-		minVal = maxVal;
-		TVD oldSourceBest = sourceBest;
-		sourceBest = 0;
-		targetBest = 0;
-		for(TVD index= 0;itMin != itMinEnd; goNext(itMin), ++index) {
-			if (active[index] == 0) continue;
-			if (((*itMin).i2 == oldSourceBest) || (active[(*itMin).i2] == 0)) {
-				// Update the values
-				(*itMin).i1 = maxVal;
-				TEdgeOutI itOutLocal(pairGraph, index);
-				for(;!atEnd(itOutLocal);goNext(itOutLocal)) {
-					TVD targ = targetVertex(itOutLocal);
-					if (targ < index) continue;
-					if (cargo(value(itOutLocal)) < (*itMin).i1) *itMin = TWeightEdgePair(cargo(value(itOutLocal)), targ);
-				}
-			}
-			if ((*itMin).i1 < minVal) {
-				minVal = (*itMin).i1;
-				sourceBest = index;
-				targetBest = (*itMin).i2;
-			}
-		}
-		// If none is found we have to insert a new edge
-		if ((sourceBest == targetBest) && (m>2)) {
-			TVertexI itV(pairGraph);
-			sourceBest = value(itV); goNext(itV);
-			targetBest = value(itV);
-			best = addEdge(pairGraph, sourceBest, targetBest, infCargo);
-		} else best = findEdge(pairGraph, sourceBest, targetBest);
-		--m;
-	}
-	g.data_root = numVertices(g) - 1;
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TValue, TSpec1> > TPairGraph;
+    typedef Graph<Tree<TCargo, TSpec2> > TGuideTree;
+    typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
+    typedef typename VertexDescriptor<TPairGraph>::Type TVD;
+    typedef typename EdgeDescriptor<TPairGraph>::Type TED;
+    typedef typename Iterator<TPairGraph, EdgeIterator>::Type TEdgeI;
+    typedef typename Iterator<TPairGraph, OutEdgeIterator>::Type TEdgeOutI;
+    typedef typename Iterator<TPairGraph, VertexIterator>::Type TVertexI;
+    typedef typename Size<TPairGraph>::Type TSize;
+
+    // First initialization
+    TCargo const maxVal = maxValue<TCargo>();
+    TSize nseq = numVertices(pairGraph);
+    TCargo infCargo = _getInfinity<TCargo>();
+    clearVertices(g);
+
+    // Is it possible to make a guide tree?
+    if (nseq == 1) {
+        g.data_root = addVertex(g);
+        return;
+    } else if (nseq == 2) {
+        TVertexDescriptor v1 = addVertex(g);
+        TVertexDescriptor v2 = addVertex(g);
+        TVertexDescriptor internalVertex = addVertex(g);
+        addEdge(g, internalVertex, v1, (TCargo) 1);
+        addEdge(g, internalVertex, v2, (TCargo) 1);
+        g.data_root = internalVertex;
+        return;
+    }
+
+    // Which entries in the matrix are still active and how many members belong to this group
+    String<TSize> active;
+    resize(active, nseq, 1);
+    // Vertex descriptor that represents that entry
+    typedef String<TVertexDescriptor> TNodeString;
+    typedef typename Iterator<TNodeString, Standard>::Type TNodeIter;
+    TNodeString nodes;
+    resize(nodes, nseq);
+    TNodeIter nodeIt = begin(nodes, Standard() );
+    TNodeIter nodeItEnd = end(nodes, Standard() );
+    for(;nodeIt<nodeItEnd;goNext(nodeIt))
+        *nodeIt = addVertex(g);    // For each sequence one vertex
+
+    // Find the minimal value for all vertices (with respect to all greater vertices)
+    typedef Pair<TValue, TVD> TWeightEdgePair;
+    typedef String<TWeightEdgePair> TMinValues;
+    TMinValues minValues;
+    resize(minValues, nseq, TWeightEdgePair(maxVal, 0));
+    TEdgeI itE(pairGraph);
+    for(;!atEnd(itE);goNext(itE)) {
+        TVD s = sourceVertex(itE);
+        TVD t = targetVertex(itE);
+        if (cargo(*itE) < (minValues[s].i1))
+            minValues[s] = TWeightEdgePair(cargo(*itE), t);
+    }
+    // Find the overall minimum
+    typedef typename Iterator<TMinValues, Standard>::Type TMinIter;
+    TMinIter itMin = begin(minValues, Standard() );
+    TMinIter itMinEnd = end(minValues, Standard() );
+    TValue minVal = maxVal;
+    TVD sourceBest = 0;
+    TVD targetBest = 0;
+    for(TVD index=0;itMin != itMinEnd; goNext(itMin), ++index) {
+        if ((*itMin).i1 < minVal) {
+            minVal = (*itMin).i1;
+            sourceBest = index;
+            targetBest = (*itMin).i2;
+        }
+    }
+    TED best = 0;
+    if (sourceBest == targetBest) { // If none is found we have to insert a new edge
+        TVertexI itV(pairGraph);
+        sourceBest = value(itV); goNext(itV);
+        targetBest = value(itV);
+        best = addEdge(pairGraph, sourceBest, targetBest, infCargo);
+    } else best = findEdge(pairGraph, sourceBest, targetBest);
+
+    // Property map for sum of weights for each node
+    String<TCargo> weights;
+    resize(weights, nseq, (TCargo) 0);
+    reserve(weights, 2*nseq - 1);
+
+    // Merge groups
+    TSize m = nseq;
+    while (m>1) {
+        // Merge nodes
+        TVertexDescriptor internalNode = addVertex(g);
+
+        // Set the weights
+        TCargo w = (TCargo) (minVal / 2);
+        addEdge(g, internalNode, nodes[sourceBest], w - property(weights, nodes[sourceBest]));
+        addEdge(g, internalNode, nodes[targetBest], w - property(weights, nodes[targetBest]));
+        appendValue(weights, w);
+
+        // Get the new distance values
+        _upgmaTreeMerge(pairGraph, active, best, TTag());
+
+        // Inactivate one group, adjust the member count for the other one
+        active[sourceBest] += active[targetBest];
+        active[targetBest] = 0;
+        nodes[sourceBest] = internalNode;
+
+        // Update the minimum values
+        minValues[sourceBest] = TWeightEdgePair(maxVal, 0);
+        for(TEdgeOutI itOutE(pairGraph, sourceBest);!atEnd(itOutE);goNext(itOutE)) {
+            TVD localTVD = targetVertex(itOutE);
+            if (sourceBest < localTVD) {
+                if (cargo(value(itOutE)) < (minValues[sourceBest].i1)) minValues[sourceBest] = TWeightEdgePair(cargo(value(itOutE)), localTVD);
+            }
+        }
+        // Find the new minimum value
+        itMin = begin(minValues, Standard() );
+        itMinEnd = end(minValues, Standard() );
+        minVal = maxVal;
+        TVD oldSourceBest = sourceBest;
+        sourceBest = 0;
+        targetBest = 0;
+        for(TVD index= 0;itMin != itMinEnd; goNext(itMin), ++index) {
+            if (active[index] == 0) continue;
+            if (((*itMin).i2 == oldSourceBest) || (active[(*itMin).i2] == 0)) {
+                // Update the values
+                (*itMin).i1 = maxVal;
+                TEdgeOutI itOutLocal(pairGraph, index);
+                for(;!atEnd(itOutLocal);goNext(itOutLocal)) {
+                    TVD targ = targetVertex(itOutLocal);
+                    if (targ < index) continue;
+                    if (cargo(value(itOutLocal)) < (*itMin).i1) *itMin = TWeightEdgePair(cargo(value(itOutLocal)), targ);
+                }
+            }
+            if ((*itMin).i1 < minVal) {
+                minVal = (*itMin).i1;
+                sourceBest = index;
+                targetBest = (*itMin).i2;
+            }
+        }
+        // If none is found we have to insert a new edge
+        if ((sourceBest == targetBest) && (m>2)) {
+            TVertexI itV(pairGraph);
+            sourceBest = value(itV); goNext(itV);
+            targetBest = value(itV);
+            best = addEdge(pairGraph, sourceBest, targetBest, infCargo);
+        } else best = findEdge(pairGraph, sourceBest, targetBest);
+        --m;
+    }
+    g.data_root = numVertices(g) - 1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -935,34 +890,13 @@ upgmaTree(Graph<Undirected<TValue, TSpec1> >& pairGraph,
  *                  Default: <tt>UpgmaWeightAvg</tt>.
  */
 
-/**
-.Function.upgmaTree
-..summary:Computes a guide tree from a distance matrix.
-..cat:Graph
-..signature:
-upgmaTree(mat, graph [,tag])
-upgmaTree(sparse_mat, graph [,tag])
-..param.mat:A string of pairwise distance values, representing a square matrix.
-...type:Class.String
-...remarks: String must use double values because the algorithm recycles this string to store intermediate possibly fractional results.
-..param.sparse_mat:An undirected graph where each edge corresponds to the distance between sequence i and sequence j.
-...type:Spec.Undirected Graph
-..param.graph:Out-parameter:The guide tree.
-...type:Spec.Tree
-..param.tag:Tag that indicates how to calculate cluster distances.
-...remarks:Possible values are UpgmaWeightAvg, UpgmaAvg, UpgmaMax, and UpgmaMin.
-...type:Tag.Upgma Configurator
-...default:UpgmaWeightAvg
-..returns:void
-..include:seqan/graph_msa.h
-*/
 template<typename TDistance, typename TCargo, typename TSpec>
 inline void
-upgmaTree(TDistance& dist, 
-		  Graph<Tree<TCargo, TSpec> >& g) 
+upgmaTree(TDistance& dist,
+          Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	upgmaTree(dist, g, UpgmaWeightAvg());
+    SEQAN_CHECKPOINT
+    upgmaTree(dist, g, UpgmaWeightAvg());
 }
 
 
diff --git a/seqan/graph_msa/graph_align_tcoffee_io.h b/seqan/graph_msa/graph_align_tcoffee_io.h
index 5e79c8c..d8cb971 100644
--- a/seqan/graph_msa/graph_align_tcoffee_io.h
+++ b/seqan/graph_msa/graph_align_tcoffee_io.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,6 +29,10 @@
 // DAMAGE.
 //
 // ==========================================================================
+// Author: Tobias Rausch <rausch@embl.de>
+// ==========================================================================
+// Input and Output of an alignment graph, Tree Reading im Newick Format
+// ==========================================================================
 
 #ifndef SEQAN_HEADER_GRAPH_ALIGN_TCOFFEE_IO_H
 #define SEQAN_HEADER_GRAPH_ALIGN_TCOFFEE_IO_H
@@ -38,15 +42,16 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-/////////////////////////////////////////////////////////////////////////////
-// Input and Output of an alignment graph, Tree Reading im Newick Format
-//////////////////////////////////////////////////////////////////////////////
+// ============================================================================
+// Forwards
+// ============================================================================
 
+struct FastaAlign_;
+typedef Tag<FastaAlign_> FastaAlign;
 
-
-/////////////////////////////////////////////////////////////////////////////
+// ============================================================================
 // Tags
-//////////////////////////////////////////////////////////////////////////////
+// ============================================================================
 
 //////////////////////////////////////////////////////////////////////////////
 
@@ -72,50 +77,32 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature typedef Tag<NewickFormat_> const NewickFormat;
  */
 
-/**
-.Tag.Alignment Graph Format.value.TCoffeeLib:
-	T-Coffee library format to read and write an alignment graph.
-..include:seqan/graph_msa.h
-*/
-
 struct TCoffeeLib_;
 typedef Tag<TCoffeeLib_> const TCoffeeLib;
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Alignment Graph Format.value.BlastLib:
-	A blast library for matches for an alignment graph.
-..include:seqan/graph_msa.h
-*/
-
 struct BlastLib_;
 typedef Tag<BlastLib_> const BlastLib;
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Alignment Graph Format.value.MummerLib:
-	A mummer library for matches for an alignment graph.
-..include:seqan/graph_msa.h
-*/
-
 struct MummerLib_;
 typedef Tag<MummerLib_> const MummerLib;
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.Alignment Graph Format.value.NewickFormat:
-	NewickFormat format to write a guide tree.
-..include:seqan/graph_msa.h
-*/
-
 struct NewickFormat_;
 typedef Tag<NewickFormat_> const NewickFormat;
 
+typedef OrFunctor<EqualsChar<';'>,
+                  OrFunctor<EqualsChar<')'>,
+                  OrFunctor<EqualsChar<','>, EqualsChar<':'> > > > IsNewickNodeStop_;
 
+typedef OrFunctor<EqualsChar<'['>,
+                  OrFunctor<EqualsChar<']'>,
+                  OrFunctor<EqualsChar<'('>, IsWhitespace> > > IsForbiddenNewickIdentifierChar_;
 
 /////////////////////////////////////////////////////////////////////////////
 // T-Coffee Library Reading / Writing
@@ -130,265 +117,264 @@ typedef Tag<NewickFormat_> const NewickFormat;
 template<typename TFile, typename TFragment, typename TSpec, typename TScoreValue, typename TSpec2, typename TNames>
 void
 read(TFile & file,
-	 String<TFragment, TSpec>& matches,
-	 String<TScoreValue, TSpec2>& scores,
-	 TNames const& names,
-	 TCoffeeLib)
+     String<TFragment, TSpec>& matches,
+     String<TScoreValue, TSpec2>& scores,
+     TNames const& names,
+     TCoffeeLib)
 {
 //IOREV _nodoc_ _notinlined_ specialization not documented
-	typedef typename Size<TFragment>::Type TSize;
-	//typedef typename Value<TFile>::Type TValue;
-	typedef typename Value<TNames>::Type TName;
-
-	// We will use this RecordReader object for reading the file.
-	RecordReader<TFile, SinglePass<> > reader(file);
-	CharString buffer;
-	
-	// Map the names to slots
-	typedef std::map<TName, TSize> TNameToPosition;
-	TNameToPosition namePosMap;
-	for(TSize i = 0;i<length(names);++i) namePosMap.insert(std::make_pair(names[i], i));
-	
-	// Remember the correct spots
-	if (atEnd(reader))
-	    return;
-	skipLine(reader);
-	clear(buffer);
-    readDigits(buffer, reader);
-    TSize nseq = 0;
-    lexicalCast2(nseq, buffer);
+    typedef typename Size<TFragment>::Type TSize;
+    //typedef typename Value<TFile>::Type TValue;
+    typedef typename Value<TNames>::Type TName;
+
+    typename DirectionIterator<TFile, Input>::Type reader = directionIterator(file, Input());
+    CharString buffer;
+
+    // Map the names to slots
+    typedef std::map<TName, TSize> TNameToPosition;
+    TNameToPosition namePosMap;
+    for(TSize i = 0;i<length(names);++i) namePosMap.insert(std::make_pair(names[i], i));
+
+    // Remember the correct spots
+    if (atEnd(reader))
+        return;
+    skipLine(reader);
+    clear(buffer);
+    readUntil(buffer, reader, NotFunctor<IsDigit>());
+    TSize nseq = lexicalCast<TSize>(buffer);
     skipLine(reader);
 
-	// Read sequences
-	typedef String<TSize> TMapping;
-	TMapping posMap;
-	resize(posMap, nseq);
-	for(TSize i=0; i<nseq; ++i) {
-		TName myName;
-        readIdentifier(myName, reader);
-		value(posMap, i) = namePosMap.find(myName)->second;
+    // Read sequences
+    typedef String<TSize> TMapping;
+    TName myName;
+    TMapping posMap;
+    resize(posMap, nseq);
+    for (TSize i=0; i<nseq; ++i)
+    {
+        clear(myName);
+        readUntil(myName, reader, IsWhitespace());
+        value(posMap, i) = namePosMap.find(myName)->second;
         skipLine(reader);
-	}
-
-	bool seq1ToN = false;
-	if (atEnd(reader)) return;
-	
-	typedef std::pair<std::pair<TSize, TSize>, TScoreValue> TResiduePair;
-	typedef std::set<TResiduePair> TResiduePairSet;
-	String<TResiduePairSet> resPair;
-	resize(resPair, nseq * nseq);	
-	TSize seq1 = 0;
-	TSize seq2 = 0;
-	bool firstPass = true;
-	while (!atEnd(reader)) {
-        skipWhitespaces(reader);
-		if (atEnd(reader)) break;
-		if (value(reader) == '#') {
+    }
+
+    bool seq1ToN = false;
+    if (atEnd(reader))
+        return;
+
+    typedef std::pair<std::pair<TSize, TSize>, TScoreValue> TResiduePair;
+    typedef std::set<TResiduePair> TResiduePairSet;
+    String<TResiduePairSet> resPair;
+    resize(resPair, nseq * nseq);
+    TSize seq1 = 0;
+    TSize seq2 = 0;
+    bool firstPass = true;
+    while (!atEnd(reader))
+    {
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+        if (atEnd(reader))
+            break;
+        if (value(reader) == '#') {
             goNext(reader);
-            skipWhitespaces(reader);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             clear(buffer);
-            readDigits(buffer, reader);
-            lexicalCast2(seq1, buffer);
-            skipWhitespaces(reader);
+            readUntil(buffer, reader, IsWhitespace());
+            seq1 = lexicalCast<TSize>(buffer);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             clear(buffer);
-            readDigits(buffer, reader);
-            lexicalCast2(seq2, buffer);
-			if (firstPass) {
-				firstPass = false;
-				if ((seq1 != 0) && (seq2 != 0)) seq1ToN = true;
-			}
-			if (seq1ToN) {
-				--seq1;
-				--seq2;
-			}
-			seq1 = value(posMap, seq1);
-			seq2 = value(posMap, seq2);
-		} else if (value(reader) == '!') {
-            skipWhitespaces(reader);
-		} else {
-            TSize res1 = 0, res2 = 0;
+            readUntil(buffer, reader, IsWhitespace());
+            seq2 = lexicalCast<TSize>(buffer);
+            if (firstPass) {
+                firstPass = false;
+                if ((seq1 != 0) && (seq2 != 0)) seq1ToN = true;
+            }
+            if (seq1ToN) {
+                --seq1;
+                --seq2;
+            }
+            seq1 = value(posMap, seq1);
+            seq2 = value(posMap, seq2);
+        } else if (value(reader) == '!') {
+            skipUntil(reader, NotFunctor<IsWhitespace>());
+        } else {
             clear(buffer);
-            readDigits(buffer, reader);
-            lexicalCast2(res1, buffer);
-            skipWhitespaces(reader);
+            readUntil(buffer, reader, IsWhitespace());
+            TSize res1 = lexicalCast<TSize>(buffer);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             clear(buffer);
-            readDigits(buffer, reader);
-            lexicalCast2(res2, buffer);
-            skipWhitespaces(reader);
-            TScoreValue weight = 0;
+            readUntil(buffer, reader, IsWhitespace());
+            TSize res2 = lexicalCast<TSize>(buffer);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             clear(buffer);
-            readDigits(buffer, reader);
-            lexicalCast2(weight, buffer);
+            readUntil(buffer, reader, IsWhitespace());
+            TScoreValue weight = lexicalCast<TScoreValue>(buffer);
             skipLine(reader);
 
-			if (seq1 < seq2) {
-				TSize index = seq1 * nseq + seq2;
-				resPair[index].insert(std::make_pair(std::make_pair(--res1,--res2), weight));
-			} else {
-				TSize index = seq2 * nseq + seq1;
-				resPair[index].insert(std::make_pair(std::make_pair(--res2,--res1), weight));
-			}		
-		}
-	}
-	for(TSize i = 0; i<length(resPair); ++i) {
-		if (resPair[i].empty()) continue;
-		TSize seq1 = i / nseq;
-		TSize seq2 = i % nseq;
-		//std::cout << "#" << seq1 << ',' << seq2 << std::endl;
-		typename TResiduePairSet::const_iterator pos = resPair[i].begin();
-		typename TResiduePairSet::const_iterator posEnd = resPair[i].end();
-		TSize startMatch1 = pos->first.first;
-		TSize startMatch2 = pos->first.second;
-		TScoreValue carg = pos->second;
-		TSize len = 1;
-		//std::cout << pos->first.first << ',' << pos->first.second << ',' << pos->second << std::endl;
-		++pos;
-		while(pos != posEnd) {
-			if ((startMatch1 + len == pos->first.first) &&
-				(startMatch2 + len == pos->first.second) &&
-				(carg / (TScoreValue) len == pos->second)) {
-					carg += pos->second;
-					++len;
-			} else {
-				appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len));
-				appendValue(scores, carg);
-				startMatch1 = pos->first.first;
-				startMatch2 = pos->first.second;
-				carg = pos->second;
-				len = 1;
-			}
-			//std::cout << pos->first.first << ',' << pos->first.second << ',' << pos->second << std::endl;
-			++pos;
-		}
-		appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len));
-		appendValue(scores, carg);
-	}
+            if (seq1 < seq2) {
+                TSize index = seq1 * nseq + seq2;
+                resPair[index].insert(std::make_pair(std::make_pair(--res1,--res2), weight));
+            } else {
+                TSize index = seq2 * nseq + seq1;
+                resPair[index].insert(std::make_pair(std::make_pair(--res2,--res1), weight));
+            }
+        }
+    }
+    for(TSize i = 0; i<length(resPair); ++i) {
+        if (resPair[i].empty()) continue;
+        TSize seq1 = i / nseq;
+        TSize seq2 = i % nseq;
+        //std::cout << "#" << seq1 << ',' << seq2 << std::endl;
+        typename TResiduePairSet::const_iterator pos = resPair[i].begin();
+        typename TResiduePairSet::const_iterator posEnd = resPair[i].end();
+        TSize startMatch1 = pos->first.first;
+        TSize startMatch2 = pos->first.second;
+        TScoreValue carg = pos->second;
+        TSize len = 1;
+        //std::cout << pos->first.first << ',' << pos->first.second << ',' << pos->second << std::endl;
+        ++pos;
+        while(pos != posEnd) {
+            if ((startMatch1 + len == pos->first.first) &&
+                (startMatch2 + len == pos->first.second) &&
+                (carg / (TScoreValue) len == pos->second)) {
+                    carg += pos->second;
+                    ++len;
+            } else {
+                appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len));
+                appendValue(scores, carg);
+                startMatch1 = pos->first.first;
+                startMatch2 = pos->first.second;
+                carg = pos->second;
+                len = 1;
+            }
+            //std::cout << pos->first.first << ',' << pos->first.second << ',' << pos->second << std::endl;
+            ++pos;
+        }
+        appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len));
+        appendValue(scores, carg);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TString, typename TSpec, typename TNames>
-void 
+void
 read(TFile & file,
-	 StringSet<TString, TSpec>& oriStr,
-	 TNames& names,
-	 TCoffeeLib) 
+     StringSet<TString, TSpec>& oriStr,
+     TNames& names,
+     TCoffeeLib)
 {
 //IOREV _nodoc_ _notinlined_ specialization not documented
-	typedef typename Size<TNames>::Type TSize;
-	//typedef typename Position<TFile>::Type TPosition;
-	//typedef typename Value<TFile>::Type TValue;
+    typedef typename Size<TNames>::Type TSize;
+    //typedef typename Position<TFile>::Type TPosition;
+    //typedef typename Value<TFile>::Type TValue;
 
     CharString buffer;
-    RecordReader<TFile, SinglePass<> > reader(file);
-	
-	if (atEnd(reader))
+    typename DirectionIterator<TFile, Input>::Type reader = directionIterator(file, Input());
+
+    if (atEnd(reader))
         return;
 
-	// Ignore first line
+    // Ignore first line
     skipLine(reader);
-	
-	// Read number of sequences
-    TSize nSeq = 0;
+
+    // Read number of sequences
     clear(buffer);
-    readDigits(buffer, reader);
-    lexicalCast2(nSeq, buffer);
-	resize(oriStr, nSeq);
+    readUntil(buffer, reader, IsWhitespace());
+    TSize nSeq = lexicalCast<TSize>(buffer);
+    resize(oriStr, nSeq);
     skipLine(reader);
 
-	// Read sequences
-	for(TSize i = 0; i < nSeq; ++i)
+    // Read sequences
+    for(TSize i = 0; i < nSeq; ++i)
     {
         clear(buffer);
-        readIdentifier(buffer, reader);
-		appendValue(names, buffer);
-        skipWhitespaces(reader);
-        clear(buffer);
-        readDigits(buffer, reader);
+        readUntil(buffer, reader, IsWhitespace());
+        appendValue(names, buffer);
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+        skipUntil(reader, IsWhitespace());
         // Note, not used.
-        skipWhitespaces(reader);
-        readLetters(oriStr[i], reader);
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+        readUntil(oriStr[i], reader, IsWhitespace());
         skipLine(reader);
-	}
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TNames>
-void write(TFile & file, 
-		   Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-		   TNames& names,
-		   TCoffeeLib) 
+void write(TFile & file,
+           Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+           TNames& names,
+           TCoffeeLib)
 {
 //IOREV _nodoc_ _notinlined_ specialization not documented
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	//typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Value<TStringSet>::Type TString;
-	typedef typename Size<TStringSet>::Type TSize;
-	
-	typedef std::pair<std::pair<TSize, TSize>, TCargo> TResiduePair;
-	typedef std::set<TResiduePair> TResiduePairSet;
-	TSize nseq = length(stringSet(g));
-	String<TResiduePairSet> resPair;
-	resize(resPair, nseq * nseq);
-	
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TIter;
-	TIter it(g);
-	for(;!atEnd(it);++it) {
-		TVertexDescriptor sV = sourceVertex(it);
-		TVertexDescriptor tV = targetVertex(it);
-		TSize fragLen = fragmentLength(g,sV);
-		TSize fragPos1 = fragmentBegin(g,sV);
-		TSize fragPos2 = fragmentBegin(g,tV);
-		TSize seq1 = sequenceId(g,sV);
-		TSize seq2 = sequenceId(g,tV);
-		TCargo my_carg =  getCargo(*it);
-		if (my_carg <= 0) my_carg = 1;
-		else my_carg = (TCargo) ((double) my_carg / (double) fragLen);
-		for(TSize i = 0; i<fragLen; ++i) {
-			resPair[seq1 * nseq + seq2].insert(std::make_pair(std::make_pair(fragPos1 + i, fragPos2 + i), my_carg));
-		}
-	}
-
-	streamPut(file, "! TC_LIB_FORMAT_01\n");
-	TSize len = length(getStringSet(g));
-	streamPut(file, (int)len);
-	streamPut(file, '\n');
-	for(TSize i=0;i<len;++i) {
-		streamPut(file, names[i]);
-		streamPut(file, ' ');
-		TString str = value(getStringSet(g), i);
-		streamPut(file, length(str));
-		streamPut(file, ' ');
-		streamPut(file, str);
-		streamPut(file, '\n');
-	}
-
-	for(TSize i = 0; i<length(resPair); ++i) {
-		if (resPair[i].empty()) continue;
-		TSize seq1 = i / nseq;
-		TSize seq2 = i % nseq;
-		streamPut(file, '#');
-		streamPut(file, seq1 + 1);
-		streamPut(file, ' ');
-		streamPut(file, seq2 + 1);
-		streamPut(file, '\n');	
-		typename TResiduePairSet::const_iterator pos = resPair[i].begin();
-		typename TResiduePairSet::const_iterator posEnd = resPair[i].end();
-		while(pos != posEnd) {
-			streamPut(file, pos->first.first + 1);
-			streamPut(file, ' ');
-			streamPut(file, pos->first.second + 1);
-			streamPut(file, ' ');
-			streamPut(file, pos->second);
-			streamPut(file, '\n');	
-			++pos;
-		}
-	}
-	streamPut(file, "! SEQ_1_TO_N");
-	streamPut(file, '\n');
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    //typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Value<TStringSet>::Type TString;
+    typedef typename Size<TStringSet>::Type TSize;
+
+    typedef std::pair<std::pair<TSize, TSize>, TCargo> TResiduePair;
+    typedef std::set<TResiduePair> TResiduePairSet;
+    TSize nseq = length(stringSet(g));
+    String<TResiduePairSet> resPair;
+    resize(resPair, nseq * nseq);
+
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TIter;
+    TIter it(g);
+    for(;!atEnd(it);++it) {
+        TVertexDescriptor sV = sourceVertex(it);
+        TVertexDescriptor tV = targetVertex(it);
+        TSize fragLen = fragmentLength(g,sV);
+        TSize fragPos1 = fragmentBegin(g,sV);
+        TSize fragPos2 = fragmentBegin(g,tV);
+        TSize seq1 = sequenceId(g,sV);
+        TSize seq2 = sequenceId(g,tV);
+        TCargo my_carg =  getCargo(*it);
+        if (my_carg <= 0) my_carg = 1;
+        else my_carg = (TCargo) ((double) my_carg / (double) fragLen);
+        for(TSize i = 0; i<fragLen; ++i) {
+            resPair[seq1 * nseq + seq2].insert(std::make_pair(std::make_pair(fragPos1 + i, fragPos2 + i), my_carg));
+        }
+    }
+
+    write(file, "! TC_LIB_FORMAT_01\n");
+    TSize len = length(getStringSet(g));
+    appendNumber(file, (int)len);
+    writeValue(file, '\n');
+    for(TSize i=0;i<len;++i) {
+        write(file, names[i]);
+        writeValue(file, ' ');
+        TString str = value(getStringSet(g), i);
+        appendNumber(file, length(str));
+        writeValue(file, ' ');
+        write(file, str);
+        writeValue(file, '\n');
+    }
+
+    for(TSize i = 0; i<length(resPair); ++i) {
+        if (resPair[i].empty()) continue;
+        TSize seq1 = i / nseq;
+        TSize seq2 = i % nseq;
+        writeValue(file, '#');
+        appendNumber(file, seq1 + 1);
+        writeValue(file, ' ');
+        appendNumber(file, seq2 + 1);
+        writeValue(file, '\n');
+        typename TResiduePairSet::const_iterator pos = resPair[i].begin();
+        typename TResiduePairSet::const_iterator posEnd = resPair[i].end();
+        while(pos != posEnd) {
+            appendNumber(file, pos->first.first + 1);
+            writeValue(file, ' ');
+            appendNumber(file, pos->first.second + 1);
+            writeValue(file, ' ');
+            appendNumber(file, pos->second);
+            writeValue(file, '\n');
+            ++pos;
+        }
+    }
+    write(file, "! SEQ_1_TO_N");
+    writeValue(file, '\n');
 }
 
 
@@ -399,187 +385,187 @@ void write(TFile & file,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TString, typename TSpec, typename TNames>
-void 
+void
 read(TFile & file,
-	 StringSet<TString, TSpec>& oriStr,
-	 TNames& names,
-	 FastaAlign) 
+     StringSet<TString, TSpec>& oriStr,
+     TNames& names,
+     FastaAlign)
 {
 //IOREV _nodoc_ _notinlined_ specialization not documented
-	SEQAN_CHECKPOINT
-	//typedef typename Size<TNames>::Type TSize;
-	//typedef TSize TWord;
-	//typedef typename Value<TFile>::Type TValue;
+    SEQAN_CHECKPOINT
+    //typedef typename Size<TNames>::Type TSize;
+    //typedef TSize TWord;
+    //typedef typename Value<TFile>::Type TValue;
 
     CharString buffer;
-    RecordReader<TFile, SinglePass<> > reader(file);
+    typename DirectionIterator<TFile, Input>::Type reader = directionIterator(file, Input());
     if (atEnd(reader))
         return;
 
-	// Read sequences
-	TString seq;
-	while(!atEnd(reader))
+    // Read sequences
+    TString seq;
+    while(!atEnd(reader))
     {
-        skipWhitespaces(reader);
-		if (atEnd(reader))
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+        if (atEnd(reader))
             break;
-		if (value(reader) == '>')
+        if (value(reader) == '>')
         {
-			if (!empty(seq))
+            if (!empty(seq))
             {
-				appendValue(oriStr, seq);
-				clear(seq);
-			}
+                appendValue(oriStr, seq);
+                clear(seq);
+            }
             goNext(reader);
             clear(buffer);
-            readIdentifier(buffer, reader);
-			appendValue(names, buffer);
+            readUntil(buffer, reader, IsWhitespace());
+            appendValue(names, buffer);
             skipLine(reader);
-		}
+        }
         else if ((value(reader) == '-') || (value(reader) == '.') || (value(reader) == '\n') ||
                  (value(reader) == '\r'))
         {
             goNext(reader);
-		}
+        }
         else
         {
-			appendValue(seq, value(reader));
+            appendValue(seq, value(reader));
             goNext(reader);
-		}
-	}
-	if (!empty(seq))
+        }
+    }
+    if (!empty(seq))
         appendValue(oriStr, seq);
 }
 
 
 template<typename TValue, typename TSpec2, typename TFragment, typename TSpec, typename TScores, typename TSize>
-void 
+void
 _collectSegmentMatches(String<TValue, TSpec2> const& mat,
-					   String<TFragment, TSpec>& matches,
-					   TScores& scores,
-					   TSize nseq) 
+                       String<TFragment, TSpec>& matches,
+                       TScores& scores,
+                       TSize nseq)
 {
-	SEQAN_CHECKPOINT
-	TSize len = length(mat) / nseq;
-	TValue gapChar = gapValue<TValue>();
-
-	// Create the anchor graph
-	//typedef String<TFragment, TSpec> TFragmentString;
-	//typedef typename Iterator<TFragmentString>::Type TFragmentStringIter;
-	typedef std::pair<TSize, TSize> TResiduePair;
-	typedef std::set<TResiduePair> TResiduePairSet;
-	String<TResiduePairSet> resPair;
-	resize(resPair, nseq * nseq);	
-	for(TSize seq1 = 0; seq1 < nseq - 1; ++seq1) {
-		for(TSize seq2 = seq1 + 1; seq2 < nseq; ++seq2) {
-			TSize index = seq1 * nseq + seq2;
-			TSize offset1 = 0;
-			TSize offset2 = 0;
-			for(TSize col = 0; col<len; ++col) {
-				if (value(mat, seq1 * len + col) != gapChar) {
-					if (value(mat, seq2 * len + col) != gapChar) {
-						resPair[index].insert(std::make_pair(offset1, offset2));
-						++offset1;
-						++offset2;
-					} else ++offset1;
-				} else if (value(mat, seq2 * len + col) != gapChar) ++offset2;
-			}
-		}
-	}
-	for(TSize i = 0; i<length(resPair); ++i) {
-		if (resPair[i].empty()) continue;
-		TSize seq1 = i / nseq;
-		TSize seq2 = i % nseq;
-		typename TResiduePairSet::const_iterator pos = resPair[i].begin();
-		typename TResiduePairSet::const_iterator posEnd = resPair[i].end();
-		TSize startMatch1 = pos->first;
-		TSize startMatch2 = pos->second;
-		TSize len = 1;
-		++pos;
-		while(pos != posEnd) {
-			if ((startMatch1 + len == pos->first) && (startMatch2 + len == pos->second)) ++len;
-			else {
-				appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len));
-				appendValue(scores, len);
-				startMatch1 = pos->first;
-				startMatch2 = pos->second;
-				len = 1;
-			}
-			++pos;
-		}
-		appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len));
-		appendValue(scores, len);
-	}
+    SEQAN_CHECKPOINT
+    TSize len = length(mat) / nseq;
+    TValue gapChar = gapValue<TValue>();
+
+    // Create the anchor graph
+    //typedef String<TFragment, TSpec> TFragmentString;
+    //typedef typename Iterator<TFragmentString>::Type TFragmentStringIter;
+    typedef std::pair<TSize, TSize> TResiduePair;
+    typedef std::set<TResiduePair> TResiduePairSet;
+    String<TResiduePairSet> resPair;
+    resize(resPair, nseq * nseq);
+    for(TSize seq1 = 0; seq1 < nseq - 1; ++seq1) {
+        for(TSize seq2 = seq1 + 1; seq2 < nseq; ++seq2) {
+            TSize index = seq1 * nseq + seq2;
+            TSize offset1 = 0;
+            TSize offset2 = 0;
+            for(TSize col = 0; col<len; ++col) {
+                if (value(mat, seq1 * len + col) != gapChar) {
+                    if (value(mat, seq2 * len + col) != gapChar) {
+                        resPair[index].insert(std::make_pair(offset1, offset2));
+                        ++offset1;
+                        ++offset2;
+                    } else ++offset1;
+                } else if (value(mat, seq2 * len + col) != gapChar) ++offset2;
+            }
+        }
+    }
+    for(TSize i = 0; i<length(resPair); ++i) {
+        if (resPair[i].empty()) continue;
+        TSize seq1 = i / nseq;
+        TSize seq2 = i % nseq;
+        typename TResiduePairSet::const_iterator pos = resPair[i].begin();
+        typename TResiduePairSet::const_iterator posEnd = resPair[i].end();
+        TSize startMatch1 = pos->first;
+        TSize startMatch2 = pos->second;
+        TSize len = 1;
+        ++pos;
+        while(pos != posEnd) {
+            if ((startMatch1 + len == pos->first) && (startMatch2 + len == pos->second)) ++len;
+            else {
+                appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len));
+                appendValue(scores, len);
+                startMatch1 = pos->first;
+                startMatch2 = pos->second;
+                len = 1;
+            }
+            ++pos;
+        }
+        appendValue(matches, TFragment(seq1, startMatch1, seq2, startMatch2, len));
+        appendValue(scores, len);
+    }
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TFragment, typename TSpec, typename TScoreValue, typename TSpec2, typename TNames>
-void 
+void
 read(TFile & file,
-	 String<TFragment, TSpec>& matches,
-	 String<TScoreValue, TSpec2>& scores,
-	 TNames const& origNames,
-	 FastaAlign) 
+     String<TFragment, TSpec>& matches,
+     String<TScoreValue, TSpec2>& scores,
+     TNames const& origNames,
+     FastaAlign)
 {
 //IOREV _nodoc_ _notinlined_ specialization not documented
-	SEQAN_CHECKPOINT
-	typedef typename Size<TNames>::Type TSize;
-	typedef typename Value<TFile>::Type TValue;
-	typedef typename Value<TNames>::Type TName;
-	
+    SEQAN_CHECKPOINT
+    typedef typename Size<TNames>::Type TSize;
+    typedef typename Value<TFile>::Type TValue;
+    typedef typename Value<TNames>::Type TName;
+
     CharString buffer;
-    RecordReader<TFile, SinglePass<> > reader(file);
+    typename DirectionIterator<TFile, Input>::Type reader = directionIterator(file, Input());
     if (atEnd(reader))
         return;
 
-	// Read sequences
-	String<TValue> mat;
-	TNames names;
-	TName nextSeq;
-	while (!atEnd(reader))
+    // Read sequences
+    String<TValue> mat;
+    TNames names;
+    TName nextSeq;
+    while (!atEnd(reader))
     {
-        skipWhitespaces(reader);
-		if (atEnd(reader))
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+        if (atEnd(reader))
             break;
-		if (value(reader) == '>')
+        if (value(reader) == '>')
         {
             goNext(reader);
-			clear(nextSeq);
-            readIdentifier(nextSeq, reader);
-			appendValue(names, nextSeq);
+            clear(nextSeq);
+            readUntil(nextSeq, reader, IsWhitespace());
+            appendValue(names, nextSeq);
             skipLine(reader);
-		}
+        }
         else if ((value(reader) == '\n') || (value(reader) == '\r'))
         {
             goNext(reader);
-		}
+        }
         else
         {
             appendValue(mat, value(reader));
             goNext(reader);
-		}
-	}
-	// Reorder rows according to names order
-	String<TValue> finalMat = mat;
-	TSize nseq = length(names);
-	TSize len = length(mat) / nseq;
-	for(TSize i = 0; i<nseq; ++i) {
-		if (value(names, i) == value(origNames, i)) continue;
-		else {
-			for(TSize j = 0; j<length(origNames); ++j) {
-				if (value(names, i) != value(origNames, j)) continue;
-				// Copy the whole row
-				replace(finalMat, j * len, j * len + len, infix(mat, i * len, i*len + len));
-				break;
-			}
-		}
-	}
-	clear(mat);
-
-	// Collect the segment matches
-	_collectSegmentMatches(finalMat, matches, scores, nseq); 
+        }
+    }
+    // Reorder rows according to names order
+    String<TValue> finalMat = mat;
+    TSize nseq = length(names);
+    TSize len = length(mat) / nseq;
+    for(TSize i = 0; i<nseq; ++i) {
+        if (value(names, i) == value(origNames, i)) continue;
+        else {
+            for(TSize j = 0; j<length(origNames); ++j) {
+                if (value(names, i) != value(origNames, j)) continue;
+                // Copy the whole row
+                replace(finalMat, j * len, j * len + len, infix(mat, i * len, i*len + len));
+                break;
+            }
+        }
+    }
+    clear(mat);
+
+    // Collect the segment matches
+    _collectSegmentMatches(finalMat, matches, scores, nseq);
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -589,219 +575,206 @@ read(TFile & file,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSizeSpec, typename TSpec1, typename TSpec2, typename TSize>
-inline void 
-_appendFragment(String<Fragment<TSizeSpec, ExactReversableFragment<TSpec1> >, TSpec2>& matches, 
-				  TSize seq1Id, 
-				  TSize beg1, 
-				  TSize seq2Id, 
-				  TSize beg2, 
-				  TSize len, 
-				  bool reversed)
+inline void
+_appendFragment(String<Fragment<TSizeSpec, ExactReversableFragment<TSpec1> >, TSpec2>& matches,
+                  TSize seq1Id,
+                  TSize beg1,
+                  TSize seq2Id,
+                  TSize beg2,
+                  TSize len,
+                  bool reversed)
 {
-	SEQAN_CHECKPOINT
-	typedef Fragment<TSizeSpec, ExactReversableFragment<TSpec1> > TFragment;
-	appendValue(matches, TFragment(seq1Id, beg1, seq2Id, beg2, len, reversed));
+    SEQAN_CHECKPOINT
+    typedef Fragment<TSizeSpec, ExactReversableFragment<TSpec1> > TFragment;
+    appendValue(matches, TFragment(seq1Id, beg1, seq2Id, beg2, len, reversed));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSizeSpec, typename TSpec1, typename TSpec2, typename TSize>
-inline void 
-_appendFragment(String<Fragment<TSizeSpec, ExactFragment<TSpec1> >, TSpec2>& matches, 
-				  TSize seq1Id, 
-				  TSize beg1, 
-				  TSize seq2Id, 
-				  TSize beg2, 
-				  TSize len, 
-				  bool reversed)
+inline void
+_appendFragment(String<Fragment<TSizeSpec, ExactFragment<TSpec1> >, TSpec2>& matches,
+                  TSize seq1Id,
+                  TSize beg1,
+                  TSize seq2Id,
+                  TSize beg2,
+                  TSize len,
+                  bool reversed)
 {
-	SEQAN_CHECKPOINT
-	typedef Fragment<TSizeSpec, ExactFragment<TSpec1> > TFragment;
-	if (!reversed) appendValue(matches, TFragment(seq1Id, beg1, seq2Id, beg2, len));
+    SEQAN_CHECKPOINT
+    typedef Fragment<TSizeSpec, ExactFragment<TSpec1> > TFragment;
+    if (!reversed) appendValue(matches, TFragment(seq1Id, beg1, seq2Id, beg2, len));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TNames>
-inline void 
+inline void
 read(TFile & file,
-	 String<TFragment, TSpec1>& matches,
-	 String<TScoreValue, TSpec2>& scores,
-	 TNames& names,
-	 BlastLib) 
+     String<TFragment, TSpec1>& matches,
+     String<TScoreValue, TSpec2>& scores,
+     TNames& names,
+     BlastLib)
 {
 //IOREV _nodoc_ specialization not documented
-	SEQAN_CHECKPOINT
-	typedef typename Size<TNames>::Type TSize;
-	//typedef typename Value<TFile>::Type TValue;
-	typedef typename Value<TNames>::Type TName;
-	
-	// Map the names to slots
-	typedef std::map<TName, TSize> TNameToPosition;
-	TNameToPosition namePosMap;
-	for(TSize i = 0;i<length(names);++i) namePosMap.insert(std::make_pair(names[i], i));
-	
+    SEQAN_CHECKPOINT
+    typedef typename Size<TNames>::Type TSize;
+    //typedef typename Value<TFile>::Type TValue;
+    typedef typename Value<TNames>::Type TName;
+
+    // Map the names to slots
+    typedef std::map<TName, TSize> TNameToPosition;
+    TNameToPosition namePosMap;
+    for(TSize i = 0;i<length(names);++i) namePosMap.insert(std::make_pair(names[i], i));
+
     CharString buffer;
-    RecordReader<TFile, SinglePass<> > reader(file);
+    typename DirectionIterator<TFile, Input>::Type reader = directionIterator(file, Input());
 
-	TName seq1;
-	TName seq2;
-	while (!atEnd(reader))
+    TName seq1;
+    TName seq2;
+    while (!atEnd(reader))
     {
-		clear(seq1);
-		clear(seq2);
-        skipWhitespaces(reader);
-        readIdentifier(seq1, reader);
-        skipWhitespaces(reader);
-        readIdentifier(seq2, reader);
-        skipWhitespaces(reader);
-		if (seq1 == seq2)
+        clear(seq1);
+        clear(seq2);
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+        readUntil(seq1, reader, IsWhitespace());
+
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+        readUntil(seq2, reader, IsWhitespace());
+
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+        if (seq1 == seq2)
         {
             skipLine(reader);
-			continue;
-		}
-		TSize seq1Id = namePosMap[seq1];
-		TSize seq2Id = namePosMap[seq2];
-        skipWhitespaces(reader);
+            continue;
+        }
+        TSize seq1Id = namePosMap[seq1];
+        TSize seq2Id = namePosMap[seq2];
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+
         // We skip the data from the file, buffer is only rarely used.
+        for (unsigned i = 0; i < 4; ++i)
+        {
+            skipUntil(reader, IsWhitespace());
+            skipUntil(reader, NotFunctor<IsWhitespace>());
+        }
+
         clear(buffer);
-        readFloat(buffer, reader);
-        skipWhitespaces(reader);
-        clear(buffer);
-        readDigits(buffer, reader);
-        skipWhitespaces(reader);
-        clear(buffer);
-        readDigits(buffer, reader);
-        skipWhitespaces(reader);
-        clear(buffer);
-        readDigits(buffer, reader);
-        skipWhitespaces(reader);
-        TSize beg1 = 0;
-        clear(buffer);
-        readDigits(buffer, reader);
-        lexicalCast2(beg1, buffer);
-        skipWhitespaces(reader);
-		TSize end1 = 0;
-        clear(buffer);
-        readDigits(buffer, reader);
-        lexicalCast2(end1, buffer);
-        skipWhitespaces(reader);
-		TSize len = end1 - beg1 + 1;
-		TSize beg2 = 0;
+        readUntil(buffer, reader, IsWhitespace());
+        TSize beg1 = lexicalCast<TSize>(buffer);
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+
         clear(buffer);
-        readDigits(buffer, reader);
-        lexicalCast2(beg2, buffer);
-        skipWhitespaces(reader);
-		TSize end2 = 0;
+        readUntil(buffer, reader, IsWhitespace());
+        TSize end1 = lexicalCast<TSize>(buffer);
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+
+        TSize len = end1 - beg1 + 1;
         clear(buffer);
-        readDigits(buffer, reader);
-        lexicalCast2(end2, buffer);
-        skipWhitespaces(reader);
+        readUntil(buffer, reader, IsWhitespace());
+        TSize beg2 = lexicalCast<TSize>(buffer);
+
+        skipUntil(reader, NotFunctor<IsWhitespace>());
         clear(buffer);
-        readIdentifier(buffer, reader);
-        skipWhitespaces(reader);
+        readUntil(buffer, reader, IsWhitespace());
+        TSize end2 = lexicalCast<TSize>(buffer);
+
+        skipUntil(reader, IsWhitespace());
+        skipUntil(reader, NotFunctor<IsWhitespace>());
+
         clear(buffer);
-        readFloat(buffer, reader);
-        double tmpDouble = 0;
-        lexicalCast2(tmpDouble, buffer);
-        TScoreValue rawScore = static_cast<TScoreValue>(tmpDouble);
-
-		bool reversed = false;
-		if (beg1 > end1) { TSize tmp = beg1; beg1 = end1; end1 = tmp; reversed = !reversed; }
-		if (beg2 > end2) { TSize tmp = beg2; beg2 = end2; end2 = tmp; reversed = !reversed; }
-		//// Debug code
-		//std::cout << seq1Id << ',' << beg1 << ',' << seq2Id << ',' << beg2 << ',' << len << std::endl;
-		//std::cout << infix(strSet[seq1Id], beg1, beg1+len) << std::endl;
-		//std::cout << infix(strSet[seq2Id], beg2, beg2+len) << std::endl;
-
-		_appendFragment(matches, seq1Id, --beg1, seq2Id, --beg2, len, reversed);
-		appendValue(scores, rawScore);
-		skipLine(reader);
-	}
+        readUntil(buffer, reader, IsWhitespace());
+        TScoreValue rawScore = static_cast<TScoreValue>(lexicalCast<double>(buffer));
+
+        bool reversed = false;
+        if (beg1 > end1) { TSize tmp = beg1; beg1 = end1; end1 = tmp; reversed = !reversed; }
+        if (beg2 > end2) { TSize tmp = beg2; beg2 = end2; end2 = tmp; reversed = !reversed; }
+        //// Debug code
+        //std::cout << seq1Id << ',' << beg1 << ',' << seq2Id << ',' << beg2 << ',' << len << std::endl;
+        //std::cout << infix(strSet[seq1Id], beg1, beg1+len) << std::endl;
+        //std::cout << infix(strSet[seq2Id], beg2, beg2+len) << std::endl;
+
+        _appendFragment(matches, seq1Id, --beg1, seq2Id, --beg2, len, reversed);
+        appendValue(scores, rawScore);
+        skipLine(reader);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TNames, typename TEdgeMap>
-void write(TFile & file, 
-		   Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-		   TNames& names,
-		   TEdgeMap& edgeMap,
-		   BlastLib) 
+void write(TFile & file,
+           Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+           TNames& names,
+           TEdgeMap& edgeMap,
+           BlastLib)
 {
 //IOREV _nodoc_ _notinlined_ specialization not documented
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	//typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	//typedef typename Value<TStringSet>::Type TString;
-	typedef typename Size<TStringSet>::Type TSize;
-	
-	TStringSet& str = stringSet(g);
-	
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TIter;
-	TIter it(g);
-	for(;!atEnd(it);++it) {
-		TVertexDescriptor sV = sourceVertex(it);
-		TVertexDescriptor tV = targetVertex(it);
-		if (sequenceId(g,sV) < sequenceId(g,tV)) {
-			TVertexDescriptor tmp = sV;
-			sV = tV;
-			tV = tmp;
-		}
-		TSize fragLen = fragmentLength(g,sV);
-		TSize fragPos1 = fragmentBegin(g,sV);
-		TSize fragPos2 = fragmentBegin(g,tV);
-		TSize seq1 = idToPosition(str, sequenceId(g,sV));
-		TSize seq2 = idToPosition(str, sequenceId(g,tV));
-		TCargo my_carg =  getCargo(*it);
-		streamPut(file, names[seq1]);
-		streamPut(file, '\t');	
-		streamPut(file, names[seq2]);
-		streamPut(file, '\t');	
-		streamPut(file, 0);
-		streamPut(file, '\t');	
-		streamPut(file, fragLen);
-		streamPut(file, '\t');	
-		streamPut(file, 0);
-		streamPut(file, '\t');	
-		streamPut(file, 0);
-		streamPut(file, '\t');	
-		streamPut(file, fragPos1+1);
-		streamPut(file, '\t');	
-		streamPut(file, fragPos1 + fragLen);
-		streamPut(file, '\t');	
-		if (!property(edgeMap, *it)) {
-			streamPut(file, fragPos2+1);
-			streamPut(file, '\t');	
-			streamPut(file, fragPos2 + fragLen);
-			streamPut(file, '\t');	
-		} else {
-			streamPut(file, fragPos2 + fragLen);
-			streamPut(file, '\t');		
-			streamPut(file, fragPos2+1);
-			streamPut(file, '\t');	
-		}
-		streamPut(file, 0);
-		streamPut(file, '\t');	
-		streamPut(file, my_carg);
-		streamPut(file, '\n');
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    //typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    //typedef typename Value<TStringSet>::Type TString;
+    typedef typename Size<TStringSet>::Type TSize;
+
+    TStringSet& str = stringSet(g);
+
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TIter;
+    TIter it(g);
+    for(;!atEnd(it);++it) {
+        TVertexDescriptor sV = sourceVertex(it);
+        TVertexDescriptor tV = targetVertex(it);
+        if (sequenceId(g,sV) < sequenceId(g,tV)) {
+            TVertexDescriptor tmp = sV;
+            sV = tV;
+            tV = tmp;
+        }
+        TSize fragLen = fragmentLength(g,sV);
+        TSize fragPos1 = fragmentBegin(g,sV);
+        TSize fragPos2 = fragmentBegin(g,tV);
+        TSize seq1 = idToPosition(str, sequenceId(g,sV));
+        TSize seq2 = idToPosition(str, sequenceId(g,tV));
+        TCargo my_carg =  getCargo(*it);
+        write(file, names[seq1]);
+        writeValue(file, '\t');
+        write(file, names[seq2]);
+        write(file, "\t0\t");
+        appendNumber(file, fragLen);
+        write(file, "\t0\t0\t");
+        appendNumber(file, fragPos1+1);
+        writeValue(file, '\t');
+        appendNumber(file, fragPos1 + fragLen);
+        writeValue(file, '\t');
+        if (!property(edgeMap, *it)) {
+            appendNumber(file, fragPos2+1);
+            writeValue(file, '\t');
+            appendNumber(file, fragPos2 + fragLen);
+            writeValue(file, '\t');
+        } else {
+            appendNumber(file, fragPos2 + fragLen);
+            writeValue(file, '\t');
+            appendNumber(file, fragPos2+1);
+            writeValue(file, '\t');
+        }
+        write(file, "0\t");
+        write(file, my_carg);
+        writeValue(file, '\n');
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TStringSet, typename TCargo, typename TSpec, typename TNames>
-void write(TFile & file, 
-		   Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-		   TNames& names,
-		   BlastLib) 
+void write(TFile & file,
+           Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
+           TNames& names,
+           BlastLib)
 {
 //IOREV _nodoc_ _notinlined_ specialization not documented
-	SEQAN_CHECKPOINT
-	String<bool> edgeMap;
-	resize(edgeMap, getIdUpperBound(_getEdgeIdManager(g)), false);
-	write(file, g, names, edgeMap, BlastLib());
+    SEQAN_CHECKPOINT
+    String<bool> edgeMap;
+    resize(edgeMap, getIdUpperBound(_getEdgeIdManager(g)), false);
+    write(file, g, names, edgeMap, BlastLib());
 }
 
 
@@ -814,127 +787,124 @@ void write(TFile & file,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TPos, typename TSpec2, typename TSpec1, typename TScores, typename TId, typename TSize>
-inline void 
+inline void
 _appendNewMatch(String<Fragment<TPos, ExactReversableFragment<TSpec2> >, TSpec1>& matches,
-				 TScores& scores,
-				 TId seq1Id,
-				 TId seq2Id,
-				 TSize beg1,
-				 TSize beg2,
-				 TSize len,
-				 bool) 
+                 TScores& scores,
+                 TId seq1Id,
+                 TId seq2Id,
+                 TSize beg1,
+                 TSize beg2,
+                 TSize len,
+                 bool)
 {
-	typedef Fragment<TPos, ExactReversableFragment<TSpec2> > TFragment;
-	appendValue(matches, TFragment(seq1Id, beg1, seq2Id, beg2, len));
-	appendValue(scores, len * len);
+    typedef Fragment<TPos, ExactReversableFragment<TSpec2> > TFragment;
+    appendValue(matches, TFragment(seq1Id, beg1, seq2Id, beg2, len));
+    appendValue(scores, len * len);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TPos, typename TSpec2, typename TSpec1, typename TScores, typename TId, typename TSize>
-inline void 
+inline void
 _appendNewMatch(String<Fragment<TPos, ExactFragment<TSpec2> >, TSpec1>& matches,
-				 TScores& scores,
-				 TId seq1Id,
-				 TId seq2Id,
-				 TSize beg1,
-				 TSize beg2,
-				 TSize len,
-				 bool reversed) 
+                 TScores& scores,
+                 TId seq1Id,
+                 TId seq2Id,
+                 TSize beg1,
+                 TSize beg2,
+                 TSize len,
+                 bool reversed)
 {
-	typedef Fragment<TPos, ExactFragment<TSpec2> > TFragment;
-	if (!reversed) {
-		appendValue(matches, TFragment(seq1Id, beg1, seq2Id, beg2, len));
-		appendValue(scores, len * len);
-	}
+    typedef Fragment<TPos, ExactFragment<TSpec2> > TFragment;
+    if (!reversed) {
+        appendValue(matches, TFragment(seq1Id, beg1, seq2Id, beg2, len));
+        appendValue(scores, len * len);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TFragment, typename TSpec1, typename TScoreValue, typename TSpec2, typename TStringSet, typename TNames>
-inline void 
+inline void
 read(TFile & file,
-	 String<TFragment, TSpec1>& matches,
-	 String<TScoreValue, TSpec2>& scores,
-	 TStringSet const& strSet,
-	 TNames const& names,
-	 MummerLib) 
+     String<TFragment, TSpec1>& matches,
+     String<TScoreValue, TSpec2>& scores,
+     TStringSet const& strSet,
+     TNames const& names,
+     MummerLib)
 {
 //IOREV _nodoc_ specialization not documented
-	SEQAN_CHECKPOINT
-	typedef typename Size<TNames>::Type TSize;
-	//typedef typename Value<TFile>::Type TValue;
-	typedef typename Value<TNames>::Type TName;
+    SEQAN_CHECKPOINT
+    typedef typename Size<TNames>::Type TSize;
+    //typedef typename Value<TFile>::Type TValue;
+    typedef typename Value<TNames>::Type TName;
 
     CharString buffer;
-    RecordReader<TFile, SinglePass<> > reader(file);
-	
-	// Map the names to slots
-	typedef std::map<TName, TSize> TNameToPosition;
-	TNameToPosition namePosMap;
-	for(TSize i = 0;i<length(names);++i) namePosMap.insert(std::make_pair(value(names, i), i));
-	
-	// Read the Mummer file
+    typename DirectionIterator<TFile, Input>::Type reader = directionIterator(file, Input());
+
+    // Map the names to slots
+    typedef std::map<TName, TSize> TNameToPosition;
+    TNameToPosition namePosMap;
+    for(TSize i = 0;i<length(names);++i) namePosMap.insert(std::make_pair(value(names, i), i));
+
+    // Read the Mummer file
     if (atEnd(reader))
         return ;
-	TName seq1;
-	TName seq2;
-	TSize seq1Id = 0;
-	TSize seq2Id = 0;
-	bool reversed = false;
-	while (!atEnd(reader))
+    TName seq1;
+    TName seq2;
+    TSize seq1Id = 0;
+    TSize seq2Id = 0;
+    bool reversed = false;
+    while (!atEnd(reader))
     {
-		if (value(reader) == '>')
+        if (value(reader) == '>')
         {
             goNext(reader);
-            skipWhitespaces(reader);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             clear(seq1);
-            readIdentifier(seq1, reader);
+            readUntil(seq1, reader, IsWhitespace());
             seq1Id = namePosMap[seq1];
-            skipWhitespaces(reader);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             if (value(reader) == 'R')
             {
-				 reversed = true;
+                 reversed = true;
                  skipLine(reader);
             }
             else
             {
                 reversed = false;
             }
-		}
+        }
         else
         {
-            skipWhitespaces(reader);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             if (atEnd(reader))
                 break;
             clear(seq2);
-            readIdentifier(seq2, reader);
-			seq2Id = namePosMap[seq2];
-            skipWhitespaces(reader);
-            TSize beg2 = 0;
+            readUntil(seq2, reader, IsWhitespace());
+            seq2Id = namePosMap[seq2];
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             clear(buffer);
-            readDigits(buffer, reader);
-            lexicalCast2(beg2, buffer);
-            skipWhitespaces(reader);
-            TSize beg1 = 0;
+            readUntil(buffer, reader, IsWhitespace());
+            TSize beg2 = lexicalCast<TSize>(buffer);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             clear(buffer);
-            readDigits(buffer, reader);
-            lexicalCast2(beg1, buffer);
-            skipWhitespaces(reader);
-            TSize len = 0;
+            readUntil(buffer, reader, IsWhitespace());
+            TSize beg1 = lexicalCast<TSize>(buffer);
+            skipUntil(reader, NotFunctor<IsWhitespace>());
             clear(buffer);
-            readDigits(buffer, reader);
-            lexicalCast2(len, buffer);
+            readUntil(buffer, reader, IsWhitespace());
+            TSize len = lexicalCast<TSize>(buffer);
             skipLine(reader);
-			if (seq1Id == seq2Id)
+            if (seq1Id == seq2Id)
                 continue;
-			
-			if (!reversed)
+
+            if (!reversed)
                 _appendNewMatch(matches, scores, seq1Id, seq2Id, --beg1, --beg2, len, reversed);
-			else
+            else
                 _appendNewMatch(matches, scores, seq1Id, seq2Id, (length(value(strSet, seq1Id)) - (--beg1 + len)), --beg2, len, reversed);
-		}
-	}
+        }
+    }
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -944,234 +914,235 @@ read(TFile & file,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFile, typename TCargo, typename TSpec, typename TNames>
-void 
+void
 read(TFile & file,
-	 Graph<Tree<TCargo, TSpec> >& guideTree,
-	 TNames& names,
-	 NewickFormat) 
+     Graph<Tree<TCargo, TSpec> >& guideTree,
+     TNames& names,
+     NewickFormat)
 {
 //IOREV _nodoc_ _notinlined_ specialization not documented
-	typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
-	typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
-	//typedef typename EdgeDescriptor<TGuideTree>::Type TEdgeDescriptor;
-	//typedef typename Size<TGuideTree>::Type TSize;
-	typedef typename Id<TGuideTree>::Type TId;
-	//typedef typename Position<TFile>::Type TPosition;
-	//typedef typename Value<TFile>::Type TValue;
-	typedef typename Value<TNames>::Type TName;
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-
-
-	if (length(names) < 3)
+    typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
+    typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
+    //typedef typename EdgeDescriptor<TGuideTree>::Type TEdgeDescriptor;
+    //typedef typename Size<TGuideTree>::Type TSize;
+    typedef typename Id<TGuideTree>::Type TId;
+    //typedef typename Position<TFile>::Type TPosition;
+    //typedef typename Value<TFile>::Type TValue;
+    typedef typename Value<TNames>::Type TName;
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+
+
+    if (length(names) < 3)
     {
-		TVertexDescriptor v1 = addVertex(guideTree);
-		TVertexDescriptor v2 = addVertex(guideTree);
-		TVertexDescriptor internalVertex = addVertex(guideTree);
-		addEdge(guideTree, internalVertex, v1, (TCargo) 1 * SEQAN_DISTANCE_UNITY);
-		addEdge(guideTree, internalVertex, v2, (TCargo) 1 * SEQAN_DISTANCE_UNITY);
-		assignRoot(guideTree, internalVertex);
-		return;
-	}
-
-	typedef std::map<TName, TId> TNameToId;
-	TNameToId nameToId;
-	for(TId i=0; i<length(names);++i) {
-		addVertex(guideTree);	// Create the sequence vertices
-		nameToId.insert(std::make_pair(names[i], i));
-	}
+        TVertexDescriptor v1 = addVertex(guideTree);
+        TVertexDescriptor v2 = addVertex(guideTree);
+        TVertexDescriptor internalVertex = addVertex(guideTree);
+        addEdge(guideTree, internalVertex, v1, (TCargo) 1 * SEQAN_DISTANCE_UNITY);
+        addEdge(guideTree, internalVertex, v2, (TCargo) 1 * SEQAN_DISTANCE_UNITY);
+        assignRoot(guideTree, internalVertex);
+        return;
+    }
+
+    typedef std::map<TName, TId> TNameToId;
+    TNameToId nameToId;
+    for(TId i=0; i<length(names);++i) {
+        addVertex(guideTree);    // Create the sequence vertices
+        nameToId.insert(std::make_pair(names[i], i));
+    }
 
     CharString buffer;
-    RecordReader<TFile, SinglePass<> > reader(file);
+    typename DirectionIterator<TFile, Input>::Type reader = directionIterator(file, Input());
     if (atEnd(reader))
         return;
 
-	TVertexDescriptor lastVertex = nilVertex;
-	TVertexDescriptor lastChild = nilVertex;
-	while (!atEnd(reader))
+    TVertexDescriptor lastVertex = nilVertex;
+    TVertexDescriptor lastChild = nilVertex;
+    while (!atEnd(reader))
     {
-		if (value(reader) == '(')
+        if (value(reader) == '(')
         {
-			if (lastVertex == nilVertex) {
-				lastVertex = addVertex(guideTree);
-				assignRoot(guideTree, lastVertex);
-			} else {
-				TVertexDescriptor ch = addChild(guideTree, lastVertex);
-				lastVertex = ch;
-			}
+            if (lastVertex == nilVertex) {
+                lastVertex = addVertex(guideTree);
+                assignRoot(guideTree, lastVertex);
+            } else {
+                TVertexDescriptor ch = addChild(guideTree, lastVertex);
+                lastVertex = ch;
+            }
             goNext(reader);
-            skipWhitespaces(reader);
-		}
+            skipUntil(reader, NotFunctor<IsWhitespace>());
+        }
         else if (value(reader) == ')')
         {
-			if (!isRoot(guideTree, lastVertex)) {
-				lastChild = lastVertex;
-				lastVertex = parentVertex(guideTree, lastVertex);
-			} else {
-				lastChild = lastVertex;
-				lastVertex = nilVertex;
-			}
+            if (!isRoot(guideTree, lastVertex)) {
+                lastChild = lastVertex;
+                lastVertex = parentVertex(guideTree, lastVertex);
+            } else {
+                lastChild = lastVertex;
+                lastVertex = nilVertex;
+            }
             goNext(reader);
-            skipWhitespaces(reader);
-		} else if (value(reader) == ',') {
+            skipUntil(reader, NotFunctor<IsWhitespace>());
+        } else if (value(reader) == ',') {
             goNext(reader);
-            skipWhitespaces(reader);
-		} else if (value(reader) == ':') {
+            skipUntil(reader, NotFunctor<IsWhitespace>());
+        } else if (value(reader) == ':') {
             goNext(reader);
             clear(buffer);
-            readFloat(buffer, reader);
-            double tmpDouble = 0;
-            lexicalCast2(tmpDouble, buffer);
-			cargo(findEdge(guideTree, lastVertex, lastChild)) = (TCargo) (tmpDouble * SEQAN_DISTANCE_UNITY);
-		} else if (value(reader) == ';') {
+            readUntil(buffer, reader, IsNewickNodeStop_());
+            double tmpDouble = lexicalCast<double>(buffer);
+            cargo(findEdge(guideTree, lastVertex, lastChild)) = (TCargo) (tmpDouble * SEQAN_DISTANCE_UNITY);
+        } else if (value(reader) == ';') {
             goNext(reader);
-            skipWhitespaces(reader);
-		} else {
+            skipUntil(reader, NotFunctor<IsWhitespace>());
+        } else {
             TName tmp;
-            readIdentifier(tmp, reader);
-			//std::cout << tmp << std::endl;
-			if (lastVertex == nilVertex) {
-				// Tree is rooted at a leaf
-				// Create artificial root node
-				lastVertex = length(names);
-				assignRoot(guideTree, addVertex(guideTree));
-				addEdge(guideTree, getRoot(guideTree), lastVertex);
-				addEdge(guideTree, getRoot(guideTree), nameToId[tmp]);
-			} else {
-				addEdge(guideTree, lastVertex, nameToId[tmp]);
-			}
-			lastChild = nameToId[tmp];
-		}
-	}
-	
-	// Root the tree if necessary 
-	if (outDegree(guideTree, lastChild) > 2) {
-		TVertexDescriptor myRoot = addVertex(guideTree);
-		assignRoot(guideTree, myRoot);
-		typedef typename Iterator<TGuideTree, OutEdgeIterator>::Type TOutEdgeIterator;
-		TOutEdgeIterator it(guideTree, lastChild);
-		goNext(it); goNext(it);
-		TVertexDescriptor tV = targetVertex(it);
-		TCargo c = cargo(*it);
-		removeEdge(guideTree, lastChild, tV);
-		addEdge(guideTree, myRoot, tV, (TCargo) (c / 2));
-		addEdge(guideTree, myRoot, lastChild, (TCargo) (c / 2));
-	}
-
-	//std::fstream strm1; // Alignment graph as dot
-	//strm1.open("tree23.dot", std::ios_base::out | std::ios_base::trunc);
-	//write(strm1,guideTree,DotDrawing());
-	//strm1.close();
-
-	//std::cout << guideTree << std::endl;
+            readUntil(tmp, reader, IsNewickNodeStop_(),
+                                   AssertFunctor<NotFunctor<IsForbiddenNewickIdentifierChar_>, ParseError>());
+            //std::cout << tmp << std::endl;
+            if (lastVertex == nilVertex) {
+                // Tree is rooted at a leaf
+                // Create artificial root node
+                lastVertex = length(names);
+                assignRoot(guideTree, addVertex(guideTree));
+                addEdge(guideTree, getRoot(guideTree), lastVertex);
+                addEdge(guideTree, getRoot(guideTree), nameToId[tmp]);
+            } else {
+                addEdge(guideTree, lastVertex, nameToId[tmp]);
+            }
+            lastChild = nameToId[tmp];
+        }
+    }
+
+    // Root the tree if necessary
+    if (outDegree(guideTree, lastChild) > 2) {
+        TVertexDescriptor myRoot = addVertex(guideTree);
+        assignRoot(guideTree, myRoot);
+        typedef typename Iterator<TGuideTree, OutEdgeIterator>::Type TOutEdgeIterator;
+        TOutEdgeIterator it(guideTree, lastChild);
+        goNext(it); goNext(it);
+        TVertexDescriptor tV = targetVertex(it);
+        TCargo c = cargo(*it);
+        removeEdge(guideTree, lastChild, tV);
+        addEdge(guideTree, myRoot, tV, (TCargo) (c / 2));
+        addEdge(guideTree, myRoot, lastChild, (TCargo) (c / 2));
+    }
+
+    //std::fstream strm1; // Alignment graph as dot
+    //strm1.open("tree23.dot", std::ios_base::out | std::ios_base::trunc);
+    //writeRecords(strm1,guideTree,DotDrawing());
+    //strm1.close();
+
+    //std::cout << guideTree << std::endl;
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TNames, typename TNewickString, typename TVertexDescriptor>
-void 
+void
 _buildNewickString(Graph<Tree<TCargo, TSpec> >& guideTree,
-				   TNames& names,
-				   TNewickString& str,
-				   TVertexDescriptor v,
-				   bool collapseRoot) 
+                   TNames& names,
+                   TNewickString& str,
+                   TVertexDescriptor v,
+                   bool collapseRoot)
 {
-	typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
-	typedef typename EdgeDescriptor<TGuideTree>::Type TEdgeDescriptor;
-	typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjIter;
-	if (isLeaf(guideTree, v)) {
-		append(str, names[v], Generous());
-	} else {
-		if ((collapseRoot) && (isRoot(guideTree, v))) {
-			TAdjIter adjIterRoot(guideTree, v);
-			TVertexDescriptor v1 = *adjIterRoot;
-			goNext(adjIterRoot);
-			TVertexDescriptor v2 = *adjIterRoot;
-			if (isLeaf(guideTree, v2)) {
-				TVertexDescriptor tmp = v1;
-				v1 = v2;
-				v2 = tmp;
-			}
-			String<char> subStr;
-			appendValue(subStr, '(', Generous());
-			_buildNewickString(guideTree, names, subStr, v1, collapseRoot);
-			TEdgeDescriptor e1 = findEdge(guideTree, v, v1);
-			TEdgeDescriptor e2 = findEdge(guideTree, v, v2);
-			appendValue(subStr, ':', Generous());
-			::std::ostringstream weight;
-			weight << (cargo(e1) + cargo(e2));
-			append(subStr, weight.str().c_str(), Generous());
-			TAdjIter adjIter(guideTree, v2);
-			for(;!atEnd(adjIter); goNext(adjIter)) {
-				appendValue(subStr, ',', Generous());
-				_buildNewickString(guideTree, names, subStr, *adjIter, collapseRoot);
-				TEdgeDescriptor e = findEdge(guideTree, v2, *adjIter);
-				appendValue(subStr, ':', Generous());
-				::std::ostringstream weight;
-				weight << cargo(e);
-				append(subStr, weight.str().c_str(), Generous());
-			}
-			appendValue(subStr, ')', Generous());
-			append(str, subStr, Generous());
-		} else {
-			TAdjIter adjIter(guideTree, v);
-			String<char> subStr;
-			appendValue(subStr, '(', Generous());
-			_buildNewickString(guideTree, names, subStr, *adjIter, collapseRoot);
-			TEdgeDescriptor e = findEdge(guideTree, v, *adjIter);
-			appendValue(subStr, ':', Generous());
-			::std::ostringstream weight;
-			weight << cargo(e);
-			append(subStr, weight.str().c_str(), Generous());
-			goNext(adjIter);
-			for(;!atEnd(adjIter); goNext(adjIter)) {
-				appendValue(subStr, ',', Generous());
-				_buildNewickString(guideTree, names, subStr, *adjIter, collapseRoot);
-				TEdgeDescriptor e = findEdge(guideTree, v, *adjIter);
-				appendValue(subStr, ':', Generous());
-				::std::ostringstream weight;
-				weight << cargo(e);
-				append(subStr, weight.str().c_str(), Generous());
-			}
-			appendValue(subStr, ')', Generous());
-			append(str, subStr, Generous());
-		}
-	}
+    typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
+    typedef typename EdgeDescriptor<TGuideTree>::Type TEdgeDescriptor;
+    typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjIter;
+    if (isLeaf(guideTree, v)) {
+        append(str, names[v], Generous());
+    } else {
+        if ((collapseRoot) && (isRoot(guideTree, v))) {
+            TAdjIter adjIterRoot(guideTree, v);
+            TVertexDescriptor v1 = *adjIterRoot;
+            goNext(adjIterRoot);
+            TVertexDescriptor v2 = *adjIterRoot;
+            if (isLeaf(guideTree, v2)) {
+                TVertexDescriptor tmp = v1;
+                v1 = v2;
+                v2 = tmp;
+            }
+            String<char> subStr;
+            appendValue(subStr, '(', Generous());
+            _buildNewickString(guideTree, names, subStr, v1, collapseRoot);
+            TEdgeDescriptor e1 = findEdge(guideTree, v, v1);
+            TEdgeDescriptor e2 = findEdge(guideTree, v, v2);
+            appendValue(subStr, ':', Generous());
+            std::ostringstream weight;
+            weight << (cargo(e1) + cargo(e2));
+            append(subStr, weight.str().c_str(), Generous());
+            TAdjIter adjIter(guideTree, v2);
+            for(;!atEnd(adjIter); goNext(adjIter)) {
+                appendValue(subStr, ',', Generous());
+                _buildNewickString(guideTree, names, subStr, *adjIter, collapseRoot);
+                TEdgeDescriptor e = findEdge(guideTree, v2, *adjIter);
+                appendValue(subStr, ':', Generous());
+                std::ostringstream weight;
+                weight << cargo(e);
+                append(subStr, weight.str().c_str(), Generous());
+            }
+            appendValue(subStr, ')', Generous());
+            append(str, subStr, Generous());
+        } else {
+            TAdjIter adjIter(guideTree, v);
+            String<char> subStr;
+            appendValue(subStr, '(', Generous());
+            _buildNewickString(guideTree, names, subStr, *adjIter, collapseRoot);
+            TEdgeDescriptor e = findEdge(guideTree, v, *adjIter);
+            appendValue(subStr, ':', Generous());
+            std::ostringstream weight;
+            weight << cargo(e);
+            append(subStr, weight.str().c_str(), Generous());
+            goNext(adjIter);
+            for(;!atEnd(adjIter); goNext(adjIter)) {
+                appendValue(subStr, ',', Generous());
+                _buildNewickString(guideTree, names, subStr, *adjIter, collapseRoot);
+                TEdgeDescriptor e = findEdge(guideTree, v, *adjIter);
+                appendValue(subStr, ':', Generous());
+                std::ostringstream weight;
+                weight << cargo(e);
+                append(subStr, weight.str().c_str(), Generous());
+            }
+            appendValue(subStr, ')', Generous());
+            append(str, subStr, Generous());
+        }
+    }
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TFile, typename TCargo, typename TSpec, typename TNames>
-void 
-write(TFile & file,
-	  Graph<Tree<TCargo, TSpec> >& guideTree,
-	  TNames& names,
-	  bool collapseRoot,
-	  NewickFormat) 
+template<typename TTarget, typename TCargo, typename TSpec, typename TNames>
+inline void
+writeRecords(TTarget & target,
+             Graph<Tree<TCargo, TSpec> >& guideTree,
+             TNames& names,
+             bool collapseRoot,
+             NewickFormat)
 {
-//IOREV _nodoc_ _notinlined_ specialization not documented
-	//typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
-	//typedef typename Size<TGuideTree>::Type TSize;
-	//typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
-
-	String<char> myNewickString;
-	_buildNewickString(guideTree, names, myNewickString, getRoot(guideTree), collapseRoot);
-	streamPut(file, myNewickString);
-	streamPut(file, ";\n");	
+//IOREV _nodoc_ specialization not documented
+    //typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
+    //typedef typename Size<TGuideTree>::Type TSize;
+    //typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
+    typename DirectionIterator<TTarget, Output>::Type iter = directionIterator(target, Output());
+
+    String<char> myNewickString;
+    _buildNewickString(guideTree, names, myNewickString, getRoot(guideTree), collapseRoot);
+    write(iter, myNewickString);
+    write(iter, ";\n");
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TFile, typename TCargo, typename TSpec, typename TNames>
-void 
-write(TFile & file,
-	  Graph<Tree<TCargo, TSpec> >& guideTree,
-	  TNames& names,
-	  NewickFormat) 
+template<typename TTarget, typename TCargo, typename TSpec, typename TNames>
+inline void
+writeRecords(TTarget & target,
+             Graph<Tree<TCargo, TSpec> >& guideTree,
+             TNames& names,
+             NewickFormat)
 {
-//IOREV _nodoc_ _notinlined_ specialization not documented
-	write(file,guideTree, names, false, NewickFormat());
+//IOREV _nodoc_ specialization not documented
+    write(target, guideTree, names, false, NewickFormat());
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_msa/graph_align_tcoffee_kmer.h b/seqan/graph_msa/graph_align_tcoffee_kmer.h
index 8e61584..679c702 100644
--- a/seqan/graph_msa/graph_align_tcoffee_kmer.h
+++ b/seqan/graph_msa/graph_align_tcoffee_kmer.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,107 +44,107 @@ namespace SEQAN_NAMESPACE_MAIN
 
 template<typename TString, typename TTupelString, typename TKTup, typename TAlphabet>
 inline void
-_getTupelString(TString const& str, 
-				TTupelString& tupelString,
-				TKTup const ktup, 
-				TAlphabet) 
+_getTupelString(TString const& str,
+                TTupelString& tupelString,
+                TKTup const ktup,
+                TAlphabet)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<typename Value<TTupelString>::Type>::Type TWord;
-	
-	// Alphabet size
-	TWord alphabet_size = ValueSize<TAlphabet>::VALUE;
-
-	// Assign a unique number to each k-tupel
-	String<TWord> prod;  // Scaling according to position in k-tupel
-	resize(prod,ktup);
-	for (TWord i=0; i< (TWord) ktup;++i) {
-		prod[ktup-i-1] = 1;
-		for(TWord j=0;j<i;++j) prod[ktup-i-1] *= alphabet_size;
-	}
-
-	TWord len = length(str);
-	clear(tupelString);
-	if(len < ktup) return;
-	resize(tupelString, len-(ktup - 1)); 
-	TWord tupelIndex = 0;
-	TWord endTupel = 0;
-	tupelString[tupelIndex] = 0;
-	for(;endTupel< (TWord) ktup;++endTupel) {
-		tupelString[tupelIndex] += (TWord) (ordValue((TAlphabet) str[endTupel])) * prod[endTupel];
-	}
-	++tupelIndex;
-	for(;endTupel<len;++endTupel) {
-		tupelString[tupelIndex] = tupelString[tupelIndex - 1];
-		tupelString[tupelIndex] -= (TWord) (ordValue((TAlphabet) str[endTupel - ktup])) * prod[0];
-		tupelString[tupelIndex] *= alphabet_size;
-		tupelString[tupelIndex] += (TWord) (ordValue((TAlphabet) str[endTupel]));
-		++tupelIndex;
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Value<typename Value<TTupelString>::Type>::Type TWord;
+
+    // Alphabet size
+    TWord alphabet_size = ValueSize<TAlphabet>::VALUE;
+
+    // Assign a unique number to each k-tupel
+    String<TWord> prod;  // Scaling according to position in k-tupel
+    resize(prod,ktup);
+    for (TWord i=0; i< (TWord) ktup;++i) {
+        prod[ktup-i-1] = 1;
+        for(TWord j=0;j<i;++j) prod[ktup-i-1] *= alphabet_size;
+    }
+
+    TWord len = length(str);
+    clear(tupelString);
+    if(len < ktup) return;
+    resize(tupelString, len-(ktup - 1));
+    TWord tupelIndex = 0;
+    TWord endTupel = 0;
+    tupelString[tupelIndex] = 0;
+    for(;endTupel< (TWord) ktup;++endTupel) {
+        tupelString[tupelIndex] += (TWord) (ordValue((TAlphabet) str[endTupel])) * prod[endTupel];
+    }
+    ++tupelIndex;
+    for(;endTupel<len;++endTupel) {
+        tupelString[tupelIndex] = tupelString[tupelIndex - 1];
+        tupelString[tupelIndex] -= (TWord) (ordValue((TAlphabet) str[endTupel - ktup])) * prod[0];
+        tupelString[tupelIndex] *= alphabet_size;
+        tupelString[tupelIndex] += (TWord) (ordValue((TAlphabet) str[endTupel]));
+        ++tupelIndex;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename THitMatrix, typename TSize, typename TAlphabet>
 inline void
-getKmerSimilarityMatrix(StringSet<TString, TSpec> const& strSet, 
-						THitMatrix& mat, 
-						TSize ktup, 
-						TAlphabet) 
+getKmerSimilarityMatrix(StringSet<TString, TSpec> const& strSet,
+                        THitMatrix& mat,
+                        TSize ktup,
+                        TAlphabet)
 {
-	SEQAN_CHECKPOINT
-	typedef TSize TWord;
-	typedef String<TWord> TTupelString;
-	typedef String<TTupelString> TTupelStringSet;
-	typedef typename Value<THitMatrix>::Type TValue;
-
-	// Number of sequences
-	TSize nseq = length(strSet);
-	TSize alphabet_size = ValueSize<TAlphabet>::VALUE;
-	TWord qIndexSize = (TWord) std::pow((double)alphabet_size, (double)ktup);
-
-	// Initialization
-	// Matrix for common k-tupels between sequence i and j
-	resize(mat, nseq*nseq);
-
-	// Transform the set of strings into a set of strings of k-tupels
-	TTupelStringSet tupSet;
-	resize(tupSet, length(strSet));
-	for(TSize k=0;k<(TSize) length(strSet);++k) _getTupelString(strSet[k], tupSet[k], ktup, TAlphabet());
-
-	// Build for each sequence the q-gram Index and count common hits
-	String<TWord> qIndex;
-	String<TWord> compareIndex;
-	for(TSize k=0;k<nseq;++k) {
-		clear(qIndex);
-		resize(qIndex, qIndexSize, (TWord) 0, Exact());
-		for(TSize i = 0;i < (TSize) length(tupSet[k]);++i) ++qIndex[ tupSet[k][i] ];
-		TWord value;
-	    for (TSize k2=k; k2<nseq; ++k2) {
-			clear(compareIndex);
-			resize(compareIndex, qIndexSize, (TWord) 0, Exact());
-			value = 0;
-			for(TSize i = 0;i < (TSize) length(tupSet[k2]);++i) {
-				//std::cout << tupSet[k2][i] << "," << compareIndex[ tupSet[k2][i] ] << "," << qIndex[ tupSet[k2][i] ]<< std::endl;
-				if (compareIndex[ tupSet[k2][i] ] < qIndex[ tupSet[k2][i] ]) ++value;
-				++compareIndex[ tupSet[k2][i] ];
-			}
-			mat[k*nseq+k2] = value;
-		}
-	}
-
-	// Scale counts
-	for(TWord row = 0; row < (TWord) nseq; ++row) {
-		for(TWord col = row+1; col < (TWord) nseq; ++col) {
-			// Fractional common kmer count
-			// = Number of common q-grams / Number of possible common q-grams
-			TValue minVal = (mat[col*nseq+col] < mat[row*nseq+row]) ? mat[col*nseq+col] : mat[row*nseq+row];
-			if (minVal == 0) mat[row*nseq+col] = 0;
-			else mat[row*nseq+col] = (mat[row*nseq+col] * SEQAN_DISTANCE_UNITY) / minVal;
-			//std::cout << mat[row*nseq+col] << ",";
-		}
-		//std::cout << std::endl;
-	}
+    SEQAN_CHECKPOINT
+    typedef TSize TWord;
+    typedef String<TWord> TTupelString;
+    typedef String<TTupelString> TTupelStringSet;
+    typedef typename Value<THitMatrix>::Type TValue;
+
+    // Number of sequences
+    TSize nseq = length(strSet);
+    TSize alphabet_size = ValueSize<TAlphabet>::VALUE;
+    TWord qIndexSize = (TWord) std::pow((double)alphabet_size, (double)ktup);
+
+    // Initialization
+    // Matrix for common k-tupels between sequence i and j
+    resize(mat, nseq*nseq);
+
+    // Transform the set of strings into a set of strings of k-tupels
+    TTupelStringSet tupSet;
+    resize(tupSet, length(strSet));
+    for(TSize k=0;k<(TSize) length(strSet);++k) _getTupelString(strSet[k], tupSet[k], ktup, TAlphabet());
+
+    // Build for each sequence the q-gram Index and count common hits
+    String<TWord> qIndex;
+    String<TWord> compareIndex;
+    for(TSize k=0;k<nseq;++k) {
+        clear(qIndex);
+        resize(qIndex, qIndexSize, (TWord) 0, Exact());
+        for(TSize i = 0;i < (TSize) length(tupSet[k]);++i) ++qIndex[ tupSet[k][i] ];
+        TWord value;
+        for (TSize k2=k; k2<nseq; ++k2) {
+            clear(compareIndex);
+            resize(compareIndex, qIndexSize, (TWord) 0, Exact());
+            value = 0;
+            for(TSize i = 0;i < (TSize) length(tupSet[k2]);++i) {
+                //std::cout << tupSet[k2][i] << "," << compareIndex[ tupSet[k2][i] ] << "," << qIndex[ tupSet[k2][i] ]<< std::endl;
+                if (compareIndex[ tupSet[k2][i] ] < qIndex[ tupSet[k2][i] ]) ++value;
+                ++compareIndex[ tupSet[k2][i] ];
+            }
+            mat[k*nseq+k2] = value;
+        }
+    }
+
+    // Scale counts
+    for(TWord row = 0; row < (TWord) nseq; ++row) {
+        for(TWord col = row+1; col < (TWord) nseq; ++col) {
+            // Fractional common kmer count
+            // = Number of common q-grams / Number of possible common q-grams
+            TValue minVal = (mat[col*nseq+col] < mat[row*nseq+row]) ? mat[col*nseq+col] : mat[row*nseq+row];
+            if (minVal == 0) mat[row*nseq+col] = 0;
+            else mat[row*nseq+col] = (mat[row*nseq+col] * SEQAN_DISTANCE_UNITY) / minVal;
+            //std::cout << mat[row*nseq+col] << ",";
+        }
+        //std::cout << std::endl;
+    }
 }
 
 
diff --git a/seqan/graph_msa/graph_align_tcoffee_library.h b/seqan/graph_msa/graph_align_tcoffee_library.h
index 1da9454..4e5e4f8 100644
--- a/seqan/graph_msa/graph_align_tcoffee_library.h
+++ b/seqan/graph_msa/graph_align_tcoffee_library.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -57,7 +57,7 @@ namespace SEQAN_NAMESPACE_MAIN
  * @headerfile <seqan/graph_msa.h>
  * @brief Segment matches from pairwise global alignment.
  *
- * @typedef Tag<GlobalPairwiseLibrary_> const GlobalPairwiseLibrary;
+ * @signature typedef Tag<GlobalPairwiseLibrary_> const GlobalPairwiseLibrary;
  *
  *
  * @tag SegmentMatchGenerationTags#LocalPairwiseLibrary
@@ -69,59 +69,28 @@ namespace SEQAN_NAMESPACE_MAIN
  * @headerfile <seqan/graph_msa.h>
  * @brief Segment matches from pairwise k-mer library.
  *
- * @typedef Tag<KmerLibrary_> const KmerLibrary;
+ * @signature typedef Tag<KmerLibrary_> const KmerLibrary;
  *
  *
  * @tag SegmentMatchGenerationTags#LcsLibrary
  * @headerfile <seqan/graph_msa.h>
  * @brief Segment matches from pairwise longest common subsequence comparison.
  *
- * @typedef Tag<LcsLibrary_> const LcsLibrary;
+ * @signature typedef Tag<LcsLibrary_> const LcsLibrary;
  */
 
-/**
-.Tag.Segment Match Generation:
-..cat:Alignments
-..summary:A tag that specifies how to generate segment matches.
-..include:seqan/graph_msa.h
-*/
-
-
-/**
-.Tag.Segment Match Generation.value.GlobalPairwiseLibrary:
-	Segment matches from pairwise global alignments.
-..include:seqan/graph_msa.h
-*/
 
 struct GlobalPairwiseLibrary_;
 typedef Tag<GlobalPairwiseLibrary_> const GlobalPairwiseLibrary;
 
 
-/**
-.Tag.Segment Match Generation.value.LocalPairwiseLibrary:
-	Segment matches from pairwise local alignments.
-..include:seqan/graph_msa.h
-*/
-
 struct LocalPairwiseLibrary_;
 typedef Tag<LocalPairwiseLibrary_> const LocalPairwiseLibrary;
 
-/**
-.Tag.Segment Match Generation.value.KmerLibrary:
-	Segment matches from pairwise kmer alignments.
-..include:seqan/graph_msa.h
-*/
-
 struct KmerLibrary_;
 typedef Tag<KmerLibrary_> const KmerLibrary;
 
 
-/**
-.Tag.Segment Match Generation.value.LcsLibrary:
-	Segment matches from pairwise longest common subsequence comparisons.
-..include:seqan/graph_msa.h
-*/
-
 struct LcsLibrary_;
 typedef Tag<LcsLibrary_> const LcsLibrary;
 
@@ -134,21 +103,21 @@ typedef Tag<LcsLibrary_> const LcsLibrary;
 template<typename TSpec, typename TSize>
 inline bool
 _isClumping(String<bool, TSpec> const& forbidden,
-			TSize row,
-			TSize col,
-			TSize len2)
+            TSize row,
+            TSize col,
+            TSize len2)
 {
-	return forbidden[(col-1) * len2 + (row-1)];
+    return forbidden[(col-1) * len2 + (row-1)];
 }
 
 template<typename TSize>
 inline bool
 _isClumping(Nothing&,
-			TSize,
-			TSize,
-			TSize)
+            TSize,
+            TSize,
+            TSize)
 {
-	return false;
+    return false;
 }
 
 struct SmithWatermanClump_;
@@ -157,322 +126,322 @@ typedef Tag<SmithWatermanClump_> SmithWatermanClump;
 template <typename TAlign, typename TStringSet, typename TTrace, typename TVal, typename TIndexPair, typename TForbidden>
 inline void
 _alignSmithWatermanTrace(TAlign& align,
-							TStringSet const& str,
-							TTrace const& trace,
-							TVal const initialDir,
-							TIndexPair const& indexPair,
-							TForbidden& forbidden)
+                            TStringSet const& str,
+                            TTrace const& trace,
+                            TVal const initialDir,
+                            TIndexPair const& indexPair,
+                            TForbidden& forbidden)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Size<TTrace>::Type TSize;
-	typedef typename Value<TTrace>::Type TTraceValue;
-	typedef typename Id<TStringSet>::Type TId;
-
-	// TraceBack values for Gotoh
-	TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; TTraceValue Stop = 3;
-
-	TId id1 = positionToId(const_cast<TStringSet&>(str), 0);
-	TId id2 = positionToId(const_cast<TStringSet&>(str), 1);	 
-	TSize len1 = indexPair[1];
-	TSize len2 = indexPair[0];
-	if ((indexPair[0] == 0) || (indexPair[1] == 0)) return;
-	TSize numCols = length(str[0]);
-	TSize numRowsOrig = length(str[1]);
-	if (len1 < numCols) _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, numCols - len1, Horizontal);
-	if (len2 < numRowsOrig) _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, numRowsOrig - len2, Vertical);
-	TSize numRows = (numRowsOrig >> 1) + (numRowsOrig & 1);
-	
-	
-
-	// Initialize everything	
-	TTraceValue nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)];
-	TTraceValue tv = Diagonal;
-	if (initialDir == Diagonal) tv = (nextTraceValue & 3);
-	else if (initialDir == Horizontal) {
-		if ((nextTraceValue >> 2) & 1) _alignTracePrint(align, str[0], str[1], id1, --len1, id2, len2, (TSize) 1, Horizontal);
-		else tv = Horizontal;
-	} else if (initialDir == Vertical) {
-		if ((nextTraceValue >> 3) & 1) _alignTracePrint(align, str[0], str[1], id1, len1, id2, --len2, (TSize) 1, Vertical);
-		else tv = Vertical;
-	}
-	TSize segLen = 0;
-	TTraceValue tvOld = tv;
-
-	// Now follow the trace
-	do {
-		nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)];
-		if ((nextTraceValue & 3) == Stop) break;
-		_setForbiddenCell(forbidden, len1, len2, numRowsOrig);	
-		if (tv == Diagonal) tv = (nextTraceValue & 3);
-		else if (tv == Horizontal) {
-			if ((nextTraceValue >> 2) & 1) tv = Diagonal; 
-			else tv =  Horizontal;
-		} else if (tv == Vertical) {
-			if ((nextTraceValue >> 3) & 1) tv =  Diagonal; 
-			else tv =  Vertical;
-		}
-		if (tv == Diagonal) {
-			if (tv != tvOld) {
-				if (tvOld == Vertical) --len2;
-				else --len1;
-				_alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, ++segLen, tvOld);
-				tvOld = tv; segLen = 0;
-			} else {
-				++segLen;
-				--len1; --len2;
-			}
-		} else if (tv == Horizontal) {
-			if (tv != tvOld) {
-				_alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, segLen, tvOld);
-				if ((nextTraceValue >> 2) & 1) {
-					_alignTracePrint(align, str[0], str[1], id1, --len1, id2, len2, (TSize) 1, Horizontal);
-					tv = Diagonal; segLen = 0;
-				} else {
-					tvOld = tv; segLen = 1;
-					--len1;
-				}
-			} else {
-				++segLen;
-				--len1;
-			}
-		} else if (tv == Vertical) {
-			if (tv != tvOld) {
-				_alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, segLen, tvOld);
-				if ((nextTraceValue >> 3) & 1) {
-					_alignTracePrint(align, str[0], str[1], id1, len1, id2, --len2, (TSize) 1, Vertical);
-					tv = Diagonal; segLen = 0;
-				} else {
-					tvOld = tv; segLen = 1;
-					--len2;
-				}
-			} else {
-				++segLen;
-				--len2;
-			}
-		}
-	} while ((len1 != 0) && (len2 !=0));
-	// Process left-overs
-	if (segLen) _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, segLen, tvOld);
-
-	// Handle the remaining sequence
-	if (len1 != 0) _alignTracePrint(align, str[0], str[1], (TId) id1, (TSize) 0, (TId) 0, (TSize) 0, (TSize) len1, Horizontal);
-	if (len2 != 0) _alignTracePrint(align, str[0], str[1], (TId) 0, (TSize) 0, (TId) id2, (TSize) 0, (TSize) len2, Vertical);
+    SEQAN_CHECKPOINT
+    typedef typename Size<TTrace>::Type TSize;
+    typedef typename Value<TTrace>::Type TTraceValue;
+    typedef typename Id<TStringSet>::Type TId;
+
+    // TraceBack values for Gotoh
+    TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; TTraceValue Stop = 3;
+
+    TId id1 = positionToId(const_cast<TStringSet&>(str), 0);
+    TId id2 = positionToId(const_cast<TStringSet&>(str), 1);
+    TSize len1 = indexPair[1];
+    TSize len2 = indexPair[0];
+    if ((indexPair[0] == 0) || (indexPair[1] == 0)) return;
+    TSize numCols = length(str[0]);
+    TSize numRowsOrig = length(str[1]);
+    if (len1 < numCols) _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, numCols - len1, Horizontal);
+    if (len2 < numRowsOrig) _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, numRowsOrig - len2, Vertical);
+    TSize numRows = (numRowsOrig >> 1) + (numRowsOrig & 1);
+
+
+
+    // Initialize everything
+    TTraceValue nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)];
+    TTraceValue tv = Diagonal;
+    if (initialDir == Diagonal) tv = (nextTraceValue & 3);
+    else if (initialDir == Horizontal) {
+        if ((nextTraceValue >> 2) & 1) _alignTracePrint(align, str[0], str[1], id1, --len1, id2, len2, (TSize) 1, Horizontal);
+        else tv = Horizontal;
+    } else if (initialDir == Vertical) {
+        if ((nextTraceValue >> 3) & 1) _alignTracePrint(align, str[0], str[1], id1, len1, id2, --len2, (TSize) 1, Vertical);
+        else tv = Vertical;
+    }
+    TSize segLen = 0;
+    TTraceValue tvOld = tv;
+
+    // Now follow the trace
+    do {
+        nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)];
+        if ((nextTraceValue & 3) == Stop) break;
+        _setForbiddenCell(forbidden, len1, len2, numRowsOrig);
+        if (tv == Diagonal) tv = (nextTraceValue & 3);
+        else if (tv == Horizontal) {
+            if ((nextTraceValue >> 2) & 1) tv = Diagonal;
+            else tv =  Horizontal;
+        } else if (tv == Vertical) {
+            if ((nextTraceValue >> 3) & 1) tv =  Diagonal;
+            else tv =  Vertical;
+        }
+        if (tv == Diagonal) {
+            if (tv != tvOld) {
+                if (tvOld == Vertical) --len2;
+                else --len1;
+                _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, ++segLen, tvOld);
+                tvOld = tv; segLen = 0;
+            } else {
+                ++segLen;
+                --len1; --len2;
+            }
+        } else if (tv == Horizontal) {
+            if (tv != tvOld) {
+                _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, segLen, tvOld);
+                if ((nextTraceValue >> 2) & 1) {
+                    _alignTracePrint(align, str[0], str[1], id1, --len1, id2, len2, (TSize) 1, Horizontal);
+                    tv = Diagonal; segLen = 0;
+                } else {
+                    tvOld = tv; segLen = 1;
+                    --len1;
+                }
+            } else {
+                ++segLen;
+                --len1;
+            }
+        } else if (tv == Vertical) {
+            if (tv != tvOld) {
+                _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, segLen, tvOld);
+                if ((nextTraceValue >> 3) & 1) {
+                    _alignTracePrint(align, str[0], str[1], id1, len1, id2, --len2, (TSize) 1, Vertical);
+                    tv = Diagonal; segLen = 0;
+                } else {
+                    tvOld = tv; segLen = 1;
+                    --len2;
+                }
+            } else {
+                ++segLen;
+                --len2;
+            }
+        }
+    } while ((len1 != 0) && (len2 !=0));
+    // Process left-overs
+    if (segLen) _alignTracePrint(align, str[0], str[1], id1, len1, id2, len2, segLen, tvOld);
+
+    // Handle the remaining sequence
+    if (len1 != 0) _alignTracePrint(align, str[0], str[1], (TId) id1, (TSize) 0, (TId) 0, (TSize) 0, (TSize) len1, Horizontal);
+    if (len2 != 0) _alignTracePrint(align, str[0], str[1], (TId) 0, (TSize) 0, (TId) id2, (TSize) 0, (TSize) len2, Vertical);
 }
 
 template <typename TTrace, typename TStringSet, typename TScore, typename TIndexPair, typename TForbidden>
 inline typename Value<TScore>::Type
 _alignSmithWaterman(TTrace& trace,
-					  TStringSet const& str,
-					  TScore const & sc,
-					  typename Value<TTrace>::Type& initialDir,
-					  TIndexPair& indexPair,
-					  TForbidden& forbidden)
+                      TStringSet const& str,
+                      TScore const & sc,
+                      typename Value<TTrace>::Type& initialDir,
+                      TIndexPair& indexPair,
+                      TForbidden& forbidden)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Size<TTrace>::Type TSize;
-	typedef typename Value<TTrace>::Type TTraceValue;
-	
-	// TraceBack values for Smith Waterman
-	TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; TTraceValue Stop = 3;
-
-	// The DP Matrix for diagonal walks
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef String<TScoreValue> TColumn;
-	TColumn mat;
-	// The DP Matrix for gaps from the left
-	TColumn horizontal;
-	// The DP Matrix for gaps from the top
-	TScoreValue vert = 0;
-
-	typedef typename Iterator<TColumn, Standard>::Type TMatIter;
-
-	// Initialization
-	typedef typename Value<TStringSet>::Type TString;
-	TString const& str1 = str[0];
-	TString const& str2 = str[1];		
-	TSize len1 = length(str1);
-	TSize len2 = length(str2);
-	resize(mat, (len2+1));   // One column for the diagonal matrix
-	resize(horizontal, (len2+1));   // One column for the horizontal matrix
-	resize(trace, len1 * ((len2 >> 1) + (len2 & 1)), 0);
-	TTraceValue tvMat= 0;
-
-	// Record the max score
-	TScoreValue score_max = 0;
-	indexPair[0] = 0; indexPair[1] = 0;
-	initialDir = Stop;
-	
-	// Classical DP
-	TScoreValue max_val = 0;
-	TScoreValue a = 0;
-	TScoreValue b = 0;
-	typedef typename Iterator<TTrace, Standard>::Type TTraceIter;
-	TTraceIter it = begin(trace, Standard() );
-	TMatIter matIt = begin(mat, Standard() );
-	TMatIter horiIt = begin(horizontal, Standard() );
-	*matIt = 0;
-	for(TSize row = 1; row <= len2; ++row) {
-		*(++matIt) = 0;
+    SEQAN_CHECKPOINT
+    typedef typename Size<TTrace>::Type TSize;
+    typedef typename Value<TTrace>::Type TTraceValue;
+
+    // TraceBack values for Smith Waterman
+    TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; TTraceValue Stop = 3;
+
+    // The DP Matrix for diagonal walks
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef String<TScoreValue> TColumn;
+    TColumn mat;
+    // The DP Matrix for gaps from the left
+    TColumn horizontal;
+    // The DP Matrix for gaps from the top
+    TScoreValue vert = 0;
+
+    typedef typename Iterator<TColumn, Standard>::Type TMatIter;
+
+    // Initialization
+    typedef typename Value<TStringSet>::Type TString;
+    TString const& str1 = str[0];
+    TString const& str2 = str[1];
+    TSize len1 = length(str1);
+    TSize len2 = length(str2);
+    resize(mat, (len2+1));   // One column for the diagonal matrix
+    resize(horizontal, (len2+1));   // One column for the horizontal matrix
+    resize(trace, len1 * ((len2 >> 1) + (len2 & 1)), 0);
+    TTraceValue tvMat= 0;
+
+    // Record the max score
+    TScoreValue score_max = 0;
+    indexPair[0] = 0; indexPair[1] = 0;
+    initialDir = Stop;
+
+    // Classical DP
+    TScoreValue max_val = 0;
+    TScoreValue a = 0;
+    TScoreValue b = 0;
+    typedef typename Iterator<TTrace, Standard>::Type TTraceIter;
+    TTraceIter it = begin(trace, Standard() );
+    TMatIter matIt = begin(mat, Standard() );
+    TMatIter horiIt = begin(horizontal, Standard() );
+    *matIt = 0;
+    for(TSize row = 1; row <= len2; ++row) {
+        *(++matIt) = 0;
         *(++horiIt) = scoreGapOpenHorizontal(sc, sequenceEntryForScore(sc, str1, 0),
                                              sequenceEntryForScore(sc, str2, row - 1)) -
                      scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, 0),
                                               sequenceEntryForScore(sc, str2, row - 1));
-	}
-	for(TSize col = 1; col <= len1; ++col) {
-		matIt = begin(mat, Standard() );
-		horiIt = begin(horizontal, Standard() );
-		TScoreValue diagValMat = *matIt;
-		*matIt = 0;
-		vert = scoreGapOpenVertical(sc, sequenceEntryForScore(sc, str1, col-1), sequenceEntryForScore(sc, str2, 0)) -
-		       scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, col-1), sequenceEntryForScore(sc, str2, 0));
-		TSize row = 1;
-		while(row <= len2) {
-			if (_isClumping(forbidden, row, col, len2)) {
-				*it <<= 3;
-				*it |= Stop;
-				max_val = 0;
-				vert = 0;
-				*(++horiIt) = 0;
-				++matIt;
-			} else {
-				// Get the new maximum for vertical
-				a = *matIt + scoreGapOpenVertical(sc, sequenceEntryForScore(sc, str1, col-1),
-				                                  sequenceEntryForScore(sc, str2, row-1));
-				b = vert + scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, col-1),
+    }
+    for(TSize col = 1; col <= len1; ++col) {
+        matIt = begin(mat, Standard() );
+        horiIt = begin(horizontal, Standard() );
+        TScoreValue diagValMat = *matIt;
+        *matIt = 0;
+        vert = scoreGapOpenVertical(sc, sequenceEntryForScore(sc, str1, col-1), sequenceEntryForScore(sc, str2, 0)) -
+               scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, col-1), sequenceEntryForScore(sc, str2, 0));
+        TSize row = 1;
+        while(row <= len2) {
+            if (_isClumping(forbidden, row, col, len2)) {
+                *it <<= 3;
+                *it |= Stop;
+                max_val = 0;
+                vert = 0;
+                *(++horiIt) = 0;
+                ++matIt;
+            } else {
+                // Get the new maximum for vertical
+                a = *matIt + scoreGapOpenVertical(sc, sequenceEntryForScore(sc, str1, col-1),
+                                                  sequenceEntryForScore(sc, str2, row-1));
+                b = vert + scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, col-1),
                                                   sequenceEntryForScore(sc, str2, row-1));
-				if (a > b) { vert = a; *it |= 1;} 
-				else vert = b;
-	
-				// Get the new maximum for horizontal
-				*it <<= 1;
-				a = *(++matIt) + scoreGapOpenHorizontal(sc, sequenceEntryForScore(sc, str1, col-1),
-				                                        sequenceEntryForScore(sc, str2, row-1));
-				b = *(++horiIt) + scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, col-1),
-				                                           sequenceEntryForScore(sc, str2, row-1));
-				if (a > b) {*horiIt = a; *it |= 1; } 
-				else *horiIt =  b;
-	
-				// Get the new maximum for mat
-				*it <<= 2;
-				max_val = diagValMat + score(const_cast<TScore&>(sc), sequenceEntryForScore(sc, str1, col-1),
-				                             sequenceEntryForScore(sc, str2, row-1));
-				tvMat =  Diagonal;
-				if (vert > max_val) {
-					max_val = vert;
-					tvMat =  Vertical;
-				}
-				if (*horiIt > max_val) {
-					max_val = *horiIt;
-					tvMat =  Horizontal;
-				}
-				if (0 >= max_val) {
-					max_val = 0;
-					tvMat =  Stop;
-				}
-				*it |= tvMat;
-			}
-
-			// Assign the new diagonal values
-			diagValMat = *matIt;
-			*matIt = max_val;
-
-			// Record the new best score
-			if (max_val > score_max) {
-				indexPair[0] = row; indexPair[1] = col;
-				score_max = max_val;
-				initialDir = tvMat;
-			}
-
-			if (row & 1) *it <<= 1; else ++it;
-			++row;
-		}
-		if (!(row & 1)) {*it <<= 3; ++it; }
-	}
-
-	//// Debug code
-	//for(TSize i= 0; i<len2;++i) {
-	//	for(TSize j= 0; j<len1;++j) {
-	//		std::cout << (TSize) getValue(trace, j*len2 + i) << ',';
-	//	}
-	//	std::cout << std::endl;
-	//}
-	//std::cout << "Max score: " << best_row << ',' << best_col << ':' << score_max << " (" << (TSize) initialDir << ")" << std::endl;
-
-	return score_max;
+                if (a > b) { vert = a; *it |= 1;}
+                else vert = b;
+
+                // Get the new maximum for horizontal
+                *it <<= 1;
+                a = *(++matIt) + scoreGapOpenHorizontal(sc, sequenceEntryForScore(sc, str1, col-1),
+                                                        sequenceEntryForScore(sc, str2, row-1));
+                b = *(++horiIt) + scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, col-1),
+                                                           sequenceEntryForScore(sc, str2, row-1));
+                if (a > b) {*horiIt = a; *it |= 1; }
+                else *horiIt =  b;
+
+                // Get the new maximum for mat
+                *it <<= 2;
+                max_val = diagValMat + score(const_cast<TScore&>(sc), sequenceEntryForScore(sc, str1, col-1),
+                                             sequenceEntryForScore(sc, str2, row-1));
+                tvMat =  Diagonal;
+                if (vert > max_val) {
+                    max_val = vert;
+                    tvMat =  Vertical;
+                }
+                if (*horiIt > max_val) {
+                    max_val = *horiIt;
+                    tvMat =  Horizontal;
+                }
+                if (0 >= max_val) {
+                    max_val = 0;
+                    tvMat =  Stop;
+                }
+                *it |= tvMat;
+            }
+
+            // Assign the new diagonal values
+            diagValMat = *matIt;
+            *matIt = max_val;
+
+            // Record the new best score
+            if (max_val > score_max) {
+                indexPair[0] = row; indexPair[1] = col;
+                score_max = max_val;
+                initialDir = tvMat;
+            }
+
+            if (row & 1) *it <<= 1; else ++it;
+            ++row;
+        }
+        if (!(row & 1)) {*it <<= 3; ++it; }
+    }
+
+    //// Debug code
+    //for(TSize i= 0; i<len2;++i) {
+    //    for(TSize j= 0; j<len1;++j) {
+    //        std::cout << (TSize) getValue(trace, j*len2 + i) << ',';
+    //    }
+    //    std::cout << std::endl;
+    //}
+    //std::cout << "Max score: " << best_row << ',' << best_col << ':' << score_max << " (" << (TSize) initialDir << ")" << std::endl;
+
+    return score_max;
 }
 
 template<typename TAlign, typename TStringSet, typename TForbidden, typename TScore>
 inline typename Value<TScore>::Type
 _localAlignment(TAlign& align,
-				TStringSet& str,
-				TForbidden& forbidden,
-				TScore const& sc,
-				SmithWatermanClump)
+                TStringSet& str,
+                TForbidden& forbidden,
+                TScore const& sc,
+                SmithWatermanClump)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef typename Size<TStringSet>::Type TSize;
-	  
-	TScoreValue maxScore;
-	TSize indexPair[2];
-	
-	// Trace
-	String<unsigned char> trace;
-	unsigned char initialDir;
-
-	// Create the trace
-	maxScore = _alignSmithWaterman(trace, str, sc, initialDir, indexPair, forbidden);	
-
-	//// Debug code
-	//for(TSize i= 0; i<length(str[1]);++i) {
-	//	for(TSize j= 0; j<length(str[0]);++j) {
-	//		std::cout << (TSize) getValue(forbidden, j*length(str[1]) + i) << ',';
-	//	}
-	//	std::cout << std::endl;
-	//}
-	//std::cout << std::endl;
-	
-	// Follow the trace and create the alignment
-	_alignSmithWatermanTrace(align, str, trace, initialDir, indexPair, forbidden);
-	
-	return maxScore;
+    SEQAN_CHECKPOINT
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef typename Size<TStringSet>::Type TSize;
+
+    TScoreValue maxScore;
+    TSize indexPair[2];
+
+    // Trace
+    String<unsigned char> trace;
+    unsigned char initialDir;
+
+    // Create the trace
+    maxScore = _alignSmithWaterman(trace, str, sc, initialDir, indexPair, forbidden);
+
+    //// Debug code
+    //for(TSize i= 0; i<length(str[1]);++i) {
+    //    for(TSize j= 0; j<length(str[0]);++j) {
+    //        std::cout << (TSize) getValue(forbidden, j*length(str[1]) + i) << ',';
+    //    }
+    //    std::cout << std::endl;
+    //}
+    //std::cout << std::endl;
+
+    // Follow the trace and create the alignment
+    _alignSmithWatermanTrace(align, str, trace, initialDir, indexPair, forbidden);
+
+    return maxScore;
 }
 
 template<typename TString, typename TMatches, typename TScores, typename TScore, typename TSize1>
 inline void
 _localAlignment(StringSet<TString, Dependent<> > const& str,
-				TMatches& matches,
-				TScores& scores,
-				TScore const& sc,
-				TSize1 numAlignments,
-				SmithWatermanClump)
+                TMatches& matches,
+                TScores& scores,
+                TScore const& sc,
+                TSize1 numAlignments,
+                SmithWatermanClump)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef typename Size<TMatches>::Type TSize;
-  
-	// For clumpping remember the used positions
-	TSize len0 = length(str[0]);
-	TSize len1 = length(str[1]);
-	String<bool> forbidden;
-	resize(forbidden, len0 * len1, false);
-
-	// Stop looking for local alignments, if there score is too low
-	TScoreValue local_score = 0;
-	TScoreValue last_score = 0;
-	for(TSize count = 0; count < (TSize) numAlignments; ++count) {
-		// Create the local alignment
-		TSize from = length(matches);
-		local_score = _localAlignment(matches, str, forbidden, sc, SmithWatermanClump());
-		TSize to = length(matches);
-		if (2 * local_score < last_score) {
-			resize(matches, from, Generous());
-			break;
-		} 
-		last_score = local_score;
-		resize(scores, to);
-		for(TSize k = from; k<to; ++k) scores[k] = local_score;
-	}
+    SEQAN_CHECKPOINT
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef typename Size<TMatches>::Type TSize;
+
+    // For clumpping remember the used positions
+    TSize len0 = length(str[0]);
+    TSize len1 = length(str[1]);
+    String<bool> forbidden;
+    resize(forbidden, len0 * len1, false);
+
+    // Stop looking for local alignments, if there score is too low
+    TScoreValue local_score = 0;
+    TScoreValue last_score = 0;
+    for(TSize count = 0; count < (TSize) numAlignments; ++count) {
+        // Create the local alignment
+        TSize from = length(matches);
+        local_score = _localAlignment(matches, str, forbidden, sc, SmithWatermanClump());
+        TSize to = length(matches);
+        if (2 * local_score < last_score) {
+            resize(matches, from, Generous());
+            break;
+        }
+        last_score = local_score;
+        resize(scores, to);
+        for(TSize k = from; k<to; ++k) scores[k] = local_score;
+    }
 }
 
 template<typename TString, typename TMatches, typename TScores, typename TScoreValue, typename TSpec2, typename TSize, typename TTag>
@@ -484,8 +453,8 @@ _multiLocalAlignment(StringSet<TString, Dependent<> > const& str,
                      TSize numAlignments,
                      TTag)
 {
-	// Make a multiple local alignment and get all matches
-	_localAlignment(str,matches,scores,sc,numAlignments,TTag());
+    // Make a multiple local alignment and get all matches
+    _localAlignment(str,matches,scores,sc,numAlignments,TTag());
 }
 
 // ---------------------------------------------------------------------------
@@ -500,24 +469,24 @@ _multiLocalAlignment(StringSet<TString, Dependent<> > const& str,
 
 // Dummy function selecting all pairs
 template<typename TString, typename TSpec, typename TSize2, typename TSpec2>
-inline void 
+inline void
 selectPairs(StringSet<TString, TSpec> const& str,
-			String<TSize2, TSpec2>& pList)
+            String<TSize2, TSpec2>& pList)
 {
-	SEQAN_CHECKPOINT
-	typedef StringSet<TString, TSpec> TStringSet;
-	typedef typename Size<TStringSet>::Type TSize;
-	typedef typename Iterator<String<TSize2, TSpec2>, Standard>::Type TPairIter;
-
-	TSize nseq = length(str);
-	resize(pList, nseq * (nseq - 1));
-	TPairIter itPair = begin(pList, Standard());
-	for(TSize i=0; i<nseq-1; ++i) {
-		for(TSize j=i+1; j<nseq; ++j) {
-			*itPair = i; ++itPair;
-			*itPair = j; ++itPair;
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef StringSet<TString, TSpec> TStringSet;
+    typedef typename Size<TStringSet>::Type TSize;
+    typedef typename Iterator<String<TSize2, TSpec2>, Standard>::Type TPairIter;
+
+    TSize nseq = length(str);
+    resize(pList, nseq * (nseq - 1));
+    TPairIter itPair = begin(pList, Standard());
+    for(TSize i=0; i<nseq-1; ++i) {
+        for(TSize j=i+1; j<nseq; ++j) {
+            *itPair = i; ++itPair;
+            *itPair = j; ++itPair;
+        }
+    }
 }
 
 
@@ -530,62 +499,62 @@ selectPairs(StringSet<TString, TSpec> const& str,
 // TODO(holtgrew): Hard-code TSize1 as __int64, size_t?
 
 template<typename TFragment, typename TSpec1, typename TStringSet, typename TPos, typename TSize1>
-inline void 
+inline void
 getAlignmentStatistics(String<TFragment, TSpec1> const& matches,
-					   TStringSet& str,
-					   TPos const from,
-					   TPos const to,
-					   TSize1& matchLength,	// Number of identical characters
-					   TSize1& overlapLength,	// Number of character in overlapping segments (with mismatches and gaps)
-					   TSize1& alignLength)	// Length of the alignment
+                       TStringSet& str,
+                       TPos const from,
+                       TPos const to,
+                       TSize1& matchLength,    // Number of identical characters
+                       TSize1& overlapLength,    // Number of character in overlapping segments (with mismatches and gaps)
+                       TSize1& alignLength)    // Length of the alignment
 {
-	typedef String<TFragment, TSpec1> const TFragmentMatches;
-	typedef typename Size<TFragmentMatches>::Type TSize;
-	typedef typename Id<TFragmentMatches>::Type TId;
-	typedef typename Iterator<TFragmentMatches, Standard>::Type TFragIter;
-	typedef typename Value<TStringSet>::Type TString;
-	typedef typename Value<TString>::Type TAlphabet; 
-	matchLength = 0;
-	TSize len1 = length(str[0]);
-	TSize len2 = length(str[1]);
-
-	
-	TSize minId1 = len1 + len2;
-	TSize minId2 = len1 + len2;
-	TSize maxId1 = 0;
-	TSize maxId2 = 0;
-	TSize matchMismatch_length = 0;
-
-	TFragIter itFrag = begin(matches, Standard());
-	TFragIter itFragEnd = itFrag;
-	itFrag += from;
-	itFragEnd += to;
-	TId id1 = sequenceId(*itFrag, 0);
-	TId id2 = sequenceId(*itFrag, 1);
-	TSize fragLen = 0;
-	TSize beginI = 0;
-	TSize beginJ = 0;
-	for(;itFrag != itFragEnd; ++itFrag) {
-		fragLen = fragmentLength(*itFrag, id1);
-		beginI = fragmentBegin(*itFrag, id1);
-		beginJ = fragmentBegin(*itFrag, id2);
-		if (beginI < minId1) minId1 = beginI;
-		if (beginJ < minId2) minId2 = beginJ;
-		if (beginI + fragLen > maxId1) maxId1 = beginI + fragLen;
-		if (beginJ + fragLen > maxId2) maxId2 = beginJ + fragLen;
-		typedef typename Infix<TString>::Type TInfix;
-		typedef typename Iterator<TInfix, Standard>::Type TInfixIter;
-		TInfix inf1 = label(*itFrag, str, id1);
-		TInfix inf2 = label(*itFrag, str, id2);
-		TInfixIter sIt1 = begin(inf1, Standard());
-		TInfixIter sIt2 = begin(inf2, Standard());
-		TInfixIter sIt1End = end(inf1, Standard());
-		matchMismatch_length += fragLen;
-		for(;sIt1 != sIt1End; ++sIt1, ++sIt2) 
-			if ( (TAlphabet) *sIt1  == (TAlphabet) *sIt2) ++matchLength;
-	}
-	alignLength = static_cast<TSize1>(matchMismatch_length + (len1 - matchMismatch_length) + (len2 - matchMismatch_length));
-	overlapLength = alignLength -  minId1 - minId2 - (len1 + len2 - maxId1 - maxId2);
+    typedef String<TFragment, TSpec1> const TFragmentMatches;
+    typedef typename Size<TFragmentMatches>::Type TSize;
+    typedef typename Id<TFragmentMatches>::Type TId;
+    typedef typename Iterator<TFragmentMatches, Standard>::Type TFragIter;
+    typedef typename Value<TStringSet>::Type TString;
+    typedef typename Value<TString>::Type TAlphabet;
+    matchLength = 0;
+    TSize len1 = length(str[0]);
+    TSize len2 = length(str[1]);
+
+
+    TSize minId1 = len1 + len2;
+    TSize minId2 = len1 + len2;
+    TSize maxId1 = 0;
+    TSize maxId2 = 0;
+    TSize matchMismatch_length = 0;
+
+    TFragIter itFrag = begin(matches, Standard());
+    TFragIter itFragEnd = itFrag;
+    itFrag += from;
+    itFragEnd += to;
+    TId id1 = sequenceId(*itFrag, 0);
+    TId id2 = sequenceId(*itFrag, 1);
+    TSize fragLen = 0;
+    TSize beginI = 0;
+    TSize beginJ = 0;
+    for(;itFrag != itFragEnd; ++itFrag) {
+        fragLen = fragmentLength(*itFrag, id1);
+        beginI = fragmentBegin(*itFrag, id1);
+        beginJ = fragmentBegin(*itFrag, id2);
+        if (beginI < minId1) minId1 = beginI;
+        if (beginJ < minId2) minId2 = beginJ;
+        if (beginI + fragLen > maxId1) maxId1 = beginI + fragLen;
+        if (beginJ + fragLen > maxId2) maxId2 = beginJ + fragLen;
+        typedef typename Infix<TString>::Type TInfix;
+        typedef typename Iterator<TInfix, Standard>::Type TInfixIter;
+        TInfix inf1 = label(*itFrag, str, id1);
+        TInfix inf2 = label(*itFrag, str, id2);
+        TInfixIter sIt1 = begin(inf1, Standard());
+        TInfixIter sIt2 = begin(inf2, Standard());
+        TInfixIter sIt1End = end(inf1, Standard());
+        matchMismatch_length += fragLen;
+        for(;sIt1 != sIt1End; ++sIt1, ++sIt2)
+            if ( (TAlphabet) *sIt1  == (TAlphabet) *sIt2) ++matchLength;
+    }
+    alignLength = static_cast<TSize1>(matchMismatch_length + (len1 - matchMismatch_length) + (len2 - matchMismatch_length));
+    overlapLength = alignLength -  minId1 - minId2 - (len1 + len2 - maxId1 - maxId2);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -596,47 +565,47 @@ getAlignmentStatistics(String<TFragment, TSpec1> const& matches,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename TSize2, typename TSpec2, typename TSegmentMatches, typename TScores>
-inline void 
+inline void
 appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str,
-					 String<TSize2, TSpec2> const& pList,
-					 TSegmentMatches& matches,
-					 TScores& scores,
-					 LcsLibrary)
+                     String<TSize2, TSpec2> const& pList,
+                     TSegmentMatches& matches,
+                     TScores& scores,
+                     LcsLibrary)
 {
-	typedef StringSet<TString, Dependent<TSpec> > TStringSet;
-	typedef String<TSize2, TSpec2> TPairList;
-	typedef typename Size<TStringSet>::Type TSize;
-	typedef typename Id<TStringSet>::Type TId;
-	//typedef typename Value<TSegmentMatches>::Type TFragment;
-	//typedef typename Value<TScores>::Type TScoreValue;
-	typedef typename Iterator<TPairList const, Standard>::Type TPairIter;
-
-	// Pairwise longest common subsequence
-	TPairIter itPair = begin(pList, Standard());
-	TPairIter itPairEnd = end(pList, Standard());
-	for(;itPair != itPairEnd; ++itPair) {
-		TStringSet pairSet;
-		TId id1 = positionToId(str, *itPair); ++itPair;
-		TId id2 = positionToId(str, *itPair);
-		assignValueById(pairSet, const_cast<TStringSet&>(str), id1);
-		assignValueById(pairSet, const_cast<TStringSet&>(str), id2);
-
-		// Lcs between first and second string
-		TSize from = length(matches);
-		globalAlignment(matches, pairSet, Lcs());
-		TSize to = length(matches);
-
-		// Record the scores
-		resize(scores, to);
-		typedef typename Iterator<TSegmentMatches, Standard>::Type TMatchIter;
-		typedef typename Iterator<TScores, Standard>::Type TScoreIter;
-		TScoreIter itScore = begin(scores, Standard());
-		TScoreIter itScoreEnd = end(scores, Standard());
-		TMatchIter itMatch = begin(matches, Standard());
-		itScore+=from;
-		itMatch+=from;
-		for(;itScore != itScoreEnd; ++itScore, ++itMatch) *itScore = (*itMatch).len;
-	}
+    typedef StringSet<TString, Dependent<TSpec> > TStringSet;
+    typedef String<TSize2, TSpec2> TPairList;
+    typedef typename Size<TStringSet>::Type TSize;
+    typedef typename Id<TStringSet>::Type TId;
+    //typedef typename Value<TSegmentMatches>::Type TFragment;
+    //typedef typename Value<TScores>::Type TScoreValue;
+    typedef typename Iterator<TPairList const, Standard>::Type TPairIter;
+
+    // Pairwise longest common subsequence
+    TPairIter itPair = begin(pList, Standard());
+    TPairIter itPairEnd = end(pList, Standard());
+    for(;itPair != itPairEnd; ++itPair) {
+        TStringSet pairSet;
+        TId id1 = positionToId(str, *itPair); ++itPair;
+        TId id2 = positionToId(str, *itPair);
+        assignValueById(pairSet, const_cast<TStringSet&>(str), id1);
+        assignValueById(pairSet, const_cast<TStringSet&>(str), id2);
+
+        // Lcs between first and second string
+        TSize from = length(matches);
+        globalAlignment(matches, pairSet, Lcs());
+        TSize to = length(matches);
+
+        // Record the scores
+        resize(scores, to);
+        typedef typename Iterator<TSegmentMatches, Standard>::Type TMatchIter;
+        typedef typename Iterator<TScores, Standard>::Type TScoreIter;
+        TScoreIter itScore = begin(scores, Standard());
+        TScoreIter itScoreEnd = end(scores, Standard());
+        TMatchIter itMatch = begin(matches, Standard());
+        itScore+=from;
+        itMatch+=from;
+        for(;itScore != itScoreEnd; ++itScore, ++itMatch) *itScore = (*itMatch).len;
+    }
 }
 
 
@@ -645,129 +614,129 @@ appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str,
 template<typename TString, typename TSpec, typename TSegmentMatches, typename TScores, typename TAlphabet, typename TSize>
 inline void
 appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str,
-					 TSegmentMatches& matches,
-					 TScores& scores,
-					 TSize ktup,
-					 TAlphabet,
-					 KmerLibrary)
+                     TSegmentMatches& matches,
+                     TScores& scores,
+                     TSize ktup,
+                     TAlphabet,
+                     KmerLibrary)
 {
-	//typedef StringSet<TString, Dependent<TSpec> > TStringSet;
-	typedef typename Value<TScores>::Type TScoreValue;
-	typedef typename Value<TSegmentMatches>::Type TFragment;
-	//typedef typename Id<TStringSet>::Type TId;
-	typedef String<TSize> TTupelString;
-	typedef String<TTupelString> TTupelStringSet;
-
-	// Initialization
-	TSize nseq = length(str);
-	TSize alphabet_size = ValueSize<TAlphabet>::VALUE;
-
-	// Transform the set of strings into a set of strings of k-tupels
-	TTupelStringSet tupSet;
-	resize(tupSet, nseq);
-	for(TSize k=0;k<nseq;++k) {
-		_getTupelString(str[k], tupSet[k], ktup, TAlphabet());
-	}
-
-	// Build one q-gram Index for all sequences
-	typedef std::pair<TSize, TSize> TPosSeqPair;
-	typedef std::set<TPosSeqPair> TQGramOcc;
-	String<TQGramOcc> qIndex;
-	TSize qIndexSize = 1;
-	for(TSize i=0; i<(TSize) ktup;++i) qIndexSize *= alphabet_size;
-	resize(qIndex, qIndexSize);
-	for(TSize k=0;k<nseq;++k) {
-		for(TSize i = 0;i < (TSize) length(tupSet[k]);++i) {
-			qIndex[ tupSet[k][i] ].insert(std::make_pair(i, k));
-		}
-	}
-	for(TSize q=0;q< (TSize) qIndexSize;++q) {
-		typename TQGramOcc::const_iterator pos = qIndex[q].begin();
-		typename TQGramOcc::const_iterator posEnd = qIndex[q].end();
-		while (pos != posEnd) {
-			typename TQGramOcc::const_iterator pos2 = pos;
-			++pos2;
-			while (pos2 != posEnd) {
-				if (pos->second != pos2->second) {
-					appendValue(matches, TFragment(positionToId(str, pos->second), pos->first, positionToId(str, pos2->second), pos2->first, ktup));
-					appendValue(scores, (TScoreValue) ktup);
-				}
-				++pos2;
-			}
-			++pos;
-		}
-	}
+    //typedef StringSet<TString, Dependent<TSpec> > TStringSet;
+    typedef typename Value<TScores>::Type TScoreValue;
+    typedef typename Value<TSegmentMatches>::Type TFragment;
+    //typedef typename Id<TStringSet>::Type TId;
+    typedef String<TSize> TTupelString;
+    typedef String<TTupelString> TTupelStringSet;
+
+    // Initialization
+    TSize nseq = length(str);
+    TSize alphabet_size = ValueSize<TAlphabet>::VALUE;
+
+    // Transform the set of strings into a set of strings of k-tupels
+    TTupelStringSet tupSet;
+    resize(tupSet, nseq);
+    for(TSize k=0;k<nseq;++k) {
+        _getTupelString(str[k], tupSet[k], ktup, TAlphabet());
+    }
+
+    // Build one q-gram Index for all sequences
+    typedef std::pair<TSize, TSize> TPosSeqPair;
+    typedef std::set<TPosSeqPair> TQGramOcc;
+    String<TQGramOcc> qIndex;
+    TSize qIndexSize = 1;
+    for(TSize i=0; i<(TSize) ktup;++i) qIndexSize *= alphabet_size;
+    resize(qIndex, qIndexSize);
+    for(TSize k=0;k<nseq;++k) {
+        for(TSize i = 0;i < (TSize) length(tupSet[k]);++i) {
+            qIndex[ tupSet[k][i] ].insert(std::make_pair(i, k));
+        }
+    }
+    for(TSize q=0;q< (TSize) qIndexSize;++q) {
+        typename TQGramOcc::const_iterator pos = qIndex[q].begin();
+        typename TQGramOcc::const_iterator posEnd = qIndex[q].end();
+        while (pos != posEnd) {
+            typename TQGramOcc::const_iterator pos2 = pos;
+            ++pos2;
+            while (pos2 != posEnd) {
+                if (pos->second != pos2->second) {
+                    appendValue(matches, TFragment(positionToId(str, pos->second), pos->first, positionToId(str, pos2->second), pos2->first, ktup));
+                    appendValue(scores, (TScoreValue) ktup);
+                }
+                ++pos2;
+            }
+            ++pos;
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename TSegmentMatches, typename TScores, typename TSize>
-inline void 
+inline void
 appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str,
-					 TSegmentMatches& matches,
-					 TScores& scores,
-					 TSize ktup,
-					 KmerLibrary)
+                     TSegmentMatches& matches,
+                     TScores& scores,
+                     TSize ktup,
+                     KmerLibrary)
 {
-	SEQAN_CHECKPOINT
-	appendSegmentMatches(str, matches, scores, ktup,  typename Value<TString>::Type(), KmerLibrary());
+    SEQAN_CHECKPOINT
+    appendSegmentMatches(str, matches, scores, ktup,  typename Value<TString>::Type(), KmerLibrary());
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename TSegmentMatches, typename TScores>
-inline void 
+inline void
 appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str,
-					 TSegmentMatches& matches,
-					 TScores& scores,
-					 KmerLibrary)
+                     TSegmentMatches& matches,
+                     TScores& scores,
+                     KmerLibrary)
 {
-	SEQAN_CHECKPOINT
-	appendSegmentMatches(str, matches, scores, 3, KmerLibrary());
+    SEQAN_CHECKPOINT
+    appendSegmentMatches(str, matches, scores, 3, KmerLibrary());
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename TSize2, typename TSpec2, typename TScore, typename TSegmentMatches, typename TScores>
-inline void 
+inline void
 appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str,
-					 String<TSize2, TSpec2> const& pList,
-					 TScore const& score_type,
-					 TSegmentMatches& matches,
-					 TScores& scores,
-					 LocalPairwiseLibrary)
+                     String<TSize2, TSpec2> const& pList,
+                     TScore const& score_type,
+                     TSegmentMatches& matches,
+                     TScores& scores,
+                     LocalPairwiseLibrary)
 {
-	typedef StringSet<TString, Dependent<TSpec> > TStringSet;
-	typedef String<TSize2, TSpec2> TPairList;
-	//typedef typename Size<TStringSet>::Type TSize;
-	typedef typename Id<TStringSet>::Type TId;
-	typedef typename Iterator<TPairList const, Standard>::Type TPairIter;
-
-	// Pairwise alignments
-	TPairIter itPair = begin(pList, Standard());
-	TPairIter itPairEnd = end(pList, Standard());
-	for(;itPair != itPairEnd; ++itPair) {
-		// Make a pairwise string-set
-		TStringSet pairSet;
-		TId id1 = positionToId(str, *itPair); ++itPair;
-		TId id2 = positionToId(str, *itPair);
-		assignValueById(pairSet, const_cast<TStringSet&>(str), id1);
-		assignValueById(pairSet, const_cast<TStringSet&>(str), id2);
-
-		_multiLocalAlignment(pairSet, matches, scores, score_type, 4, SmithWatermanClump());
-	}
+    typedef StringSet<TString, Dependent<TSpec> > TStringSet;
+    typedef String<TSize2, TSpec2> TPairList;
+    //typedef typename Size<TStringSet>::Type TSize;
+    typedef typename Id<TStringSet>::Type TId;
+    typedef typename Iterator<TPairList const, Standard>::Type TPairIter;
+
+    // Pairwise alignments
+    TPairIter itPair = begin(pList, Standard());
+    TPairIter itPairEnd = end(pList, Standard());
+    for(;itPair != itPairEnd; ++itPair) {
+        // Make a pairwise string-set
+        TStringSet pairSet;
+        TId id1 = positionToId(str, *itPair); ++itPair;
+        TId id2 = positionToId(str, *itPair);
+        assignValueById(pairSet, const_cast<TStringSet&>(str), id1);
+        assignValueById(pairSet, const_cast<TStringSet&>(str), id2);
+
+        _multiLocalAlignment(pairSet, matches, scores, score_type, 4, SmithWatermanClump());
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TSpec, typename TSize>
 inline void
-_resizeWithRespectToDistance(String<TValue, TSpec>& dist, 
-							  TSize nseq)
+_resizeWithRespectToDistance(String<TValue, TSpec>& dist,
+                              TSize nseq)
 {
-	SEQAN_CHECKPOINT;
-	resize(dist, nseq * nseq, 0);
+    SEQAN_CHECKPOINT;
+    resize(dist, nseq * nseq, 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -776,10 +745,10 @@ template<typename TCargo, typename TSpec, typename TSize>
 inline void
 _resizeWithRespectToDistance(Graph<Undirected<TCargo, TSpec> >& dist, TSize nseq)
 {
-	SEQAN_CHECKPOINT
-	clear(dist);
-	reserve(_getVertexString(dist), nseq);
-	for(TSize i=0;i<nseq; ++i) addVertex(dist);
+    SEQAN_CHECKPOINT
+    clear(dist);
+    reserve(_getVertexString(dist), nseq);
+    for(TSize i=0;i<nseq; ++i) addVertex(dist);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -788,148 +757,148 @@ template<typename TSize>
 inline void
 _resizeWithRespectToDistance(Nothing&, TSize)
 {
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFragment, typename TSpec1, typename TString, typename TSpec2, typename TValue,  typename TSpec, typename TSize>
-inline void 
+inline void
 _setDistanceValue(String<TFragment, TSpec1>& matches,
-				   StringSet<TString, TSpec2>& pairSet,			
-				   String<TValue, TSpec>& dist,
-				   TSize i,
-				   TSize j,
-				   TSize nseq,
-				   TSize from)
+                   StringSet<TString, TSpec2>& pairSet,
+                   String<TValue, TSpec>& dist,
+                   TSize i,
+                   TSize j,
+                   TSize nseq,
+                   TSize from)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Position<String<TFragment, TSpec1> >::Type TPos;
-	
-	// Determine a sequence weight
-	TValue matchLen = 0;
-	TValue overlapLen = 0;
-	TValue alignLen = 0;
-	getAlignmentStatistics(matches, pairSet, (TPos) from, (TPos) length(matches),  matchLen, overlapLen, alignLen);
-			
-	// Calculate sequence similarity
-	TValue x = SEQAN_DISTANCE_UNITY - static_cast<TValue>(static_cast<double>(matchLen) / static_cast<double>(alignLen) * static_cast<double>(SEQAN_DISTANCE_UNITY));
-	if (i < j)
-	  dist[i * nseq + j] = x;
-	else
-	  dist[j * nseq + i] = x;
+    SEQAN_CHECKPOINT
+    typedef typename Position<String<TFragment, TSpec1> >::Type TPos;
+
+    // Determine a sequence weight
+    TValue matchLen = 0;
+    TValue overlapLen = 0;
+    TValue alignLen = 0;
+    getAlignmentStatistics(matches, pairSet, (TPos) from, (TPos) length(matches),  matchLen, overlapLen, alignLen);
+
+    // Calculate sequence similarity
+    TValue x = SEQAN_DISTANCE_UNITY - static_cast<TValue>(static_cast<double>(matchLen) / static_cast<double>(alignLen) * static_cast<double>(SEQAN_DISTANCE_UNITY));
+    if (i < j)
+      dist[i * nseq + j] = x;
+    else
+      dist[j * nseq + i] = x;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFragment, typename TSpec1, typename TString, typename TSpec2, typename TCargo,  typename TSpec, typename TSize>
-inline void 
+inline void
 _setDistanceValue(String<TFragment, TSpec1>& matches,
-				   StringSet<TString, TSpec2>& pairSet,
-				   Graph<Undirected<TCargo, TSpec> >& dist,
-				   TSize i,
-				   TSize j,
-				   TSize,
-				   TSize from)
+                   StringSet<TString, TSpec2>& pairSet,
+                   Graph<Undirected<TCargo, TSpec> >& dist,
+                   TSize i,
+                   TSize j,
+                   TSize,
+                   TSize from)
 {
-	SEQAN_CHECKPOINT
-		
-	// Determine a sequence weight
-	TCargo matchLen = 0;
-	TCargo overlapLen = 0;
-	TCargo alignLen = 0;
-	getAlignmentStatistics(matches, pairSet, (TSize) from, (TSize) length(matches),  matchLen, overlapLen, alignLen);
-			
-	// Calculate sequence similarity
-	TCargo normalizedSimilarity = SEQAN_DISTANCE_UNITY - (TCargo) (((double) matchLen / (double) overlapLen) * ((double) overlapLen / (double) alignLen) * (double) SEQAN_DISTANCE_UNITY);
-
-	addEdge(dist, i, j, normalizedSimilarity);
+    SEQAN_CHECKPOINT
+
+    // Determine a sequence weight
+    TCargo matchLen = 0;
+    TCargo overlapLen = 0;
+    TCargo alignLen = 0;
+    getAlignmentStatistics(matches, pairSet, (TSize) from, (TSize) length(matches),  matchLen, overlapLen, alignLen);
+
+    // Calculate sequence similarity
+    TCargo normalizedSimilarity = SEQAN_DISTANCE_UNITY - (TCargo) (((double) matchLen / (double) overlapLen) * ((double) overlapLen / (double) alignLen) * (double) SEQAN_DISTANCE_UNITY);
+
+    addEdge(dist, i, j, normalizedSimilarity);
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TFragment, typename TSpec, typename TString, typename TSpec2, typename TSize>
-inline void 
+inline void
 _setDistanceValue(String<TFragment, TSpec>&,
-				   StringSet<TString, TSpec2>&,
-				   Nothing&,
-				   TSize,
-				   TSize,
-				   TSize,
-				   TSize)
+                   StringSet<TString, TSpec2>&,
+                   Nothing&,
+                   TSize,
+                   TSize,
+                   TSize,
+                   TSize)
 {
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename TSize2, typename TSpec2, typename TScore, typename TSegmentMatches, typename TScoreValues, typename TDistance, typename TAlignConfig>
-inline void 
+inline void
 appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str,
-					 String<TSize2, TSpec2> const& pList,
-					 TScore const& score_type,
-					 TSegmentMatches& matches,
-					 TScoreValues& scores,
-					 TDistance& dist,
-					 TAlignConfig const& ac,
-					 GlobalPairwiseLibrary)
+                     String<TSize2, TSpec2> const& pList,
+                     TScore const& score_type,
+                     TSegmentMatches& matches,
+                     TScoreValues& scores,
+                     TDistance& dist,
+                     TAlignConfig const& ac,
+                     GlobalPairwiseLibrary)
 {
-	SEQAN_CHECKPOINT
-	typedef StringSet<TString, Dependent<TSpec> > TStringSet;
-	typedef typename Id<TStringSet>::Type TId;
-	typedef typename Size<TStringSet>::Type TSize;
-	typedef typename Value<TScoreValues>::Type TScoreValue;
-	typedef typename Iterator<String<TSize2, TSpec2> const, Standard>::Type TPairIter;
-
-	// Initialization
-	TSize nseq = length(str);
-	_resizeWithRespectToDistance(dist, nseq);
-	
-	// Pairwise alignments
-	TPairIter itPair = begin(pList, Standard());
-	TPairIter itPairEnd = end(pList, Standard());
-	for(;itPair != itPairEnd; ++itPair) {
-		// Make a pairwise string-set
-		TStringSet pairSet;
-		TId id1 = positionToId(str, *itPair); ++itPair;
-		TId id2 = positionToId(str, *itPair);
-		assignValueById(pairSet, const_cast<TStringSet&>(str), id1);
-		assignValueById(pairSet, const_cast<TStringSet&>(str), id2);
-				
-		// Alignment
-		TSize from = length(matches);
-		TScoreValue myScore = globalAlignment(matches, pairSet, score_type, ac, Gotoh() );
-		TSize to = length(matches);
-
-		// Record the scores
-		resize(scores, to);
-		typedef typename Iterator<TScoreValues, Standard>::Type TScoreIter;
-		TScoreIter itScore = begin(scores, Standard());
-		TScoreIter itScoreEnd = end(scores, Standard());
-		itScore+=from;
-		for(;itScore != itScoreEnd; ++itScore) *itScore = myScore;
-			
-		// Get the alignment statistics
-		_setDistanceValue(matches, pairSet, dist, (TSize) *(itPair-1), (TSize) *itPair, (TSize) nseq, (TSize)from);
-	}
+    SEQAN_CHECKPOINT
+    typedef StringSet<TString, Dependent<TSpec> > TStringSet;
+    typedef typename Id<TStringSet>::Type TId;
+    typedef typename Size<TStringSet>::Type TSize;
+    typedef typename Value<TScoreValues>::Type TScoreValue;
+    typedef typename Iterator<String<TSize2, TSpec2> const, Standard>::Type TPairIter;
+
+    // Initialization
+    TSize nseq = length(str);
+    _resizeWithRespectToDistance(dist, nseq);
+
+    // Pairwise alignments
+    TPairIter itPair = begin(pList, Standard());
+    TPairIter itPairEnd = end(pList, Standard());
+    for(;itPair != itPairEnd; ++itPair) {
+        // Make a pairwise string-set
+        TStringSet pairSet;
+        TId id1 = positionToId(str, *itPair); ++itPair;
+        TId id2 = positionToId(str, *itPair);
+        assignValueById(pairSet, const_cast<TStringSet&>(str), id1);
+        assignValueById(pairSet, const_cast<TStringSet&>(str), id2);
+
+        // Alignment
+        TSize from = length(matches);
+        TScoreValue myScore = globalAlignment(matches, pairSet, score_type, ac, Gotoh() );
+        TSize to = length(matches);
+
+        // Record the scores
+        resize(scores, to);
+        typedef typename Iterator<TScoreValues, Standard>::Type TScoreIter;
+        TScoreIter itScore = begin(scores, Standard());
+        TScoreIter itScoreEnd = end(scores, Standard());
+        itScore+=from;
+        for(;itScore != itScoreEnd; ++itScore) *itScore = myScore;
+
+        // Get the alignment statistics
+        _setDistanceValue(matches, pairSet, dist, (TSize) *(itPair-1), (TSize) *itPair, (TSize) nseq, (TSize)from);
+    }
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TString, typename TSpec, typename TSize2, typename TSpec2, typename TScore, typename TSegmentMatches, typename TScoreValues, typename TDistance>
-inline void 
+inline void
 appendSegmentMatches(StringSet<TString, Dependent<TSpec> > const& str,
-					 String<TSize2, TSpec2> const& pList,
-					 TScore const& score_type,
-					 TSegmentMatches& matches,
-					 TScoreValues& scores,
-					 TDistance& dist,					 
-					 GlobalPairwiseLibrary)
+                     String<TSize2, TSpec2> const& pList,
+                     TScore const& score_type,
+                     TSegmentMatches& matches,
+                     TScoreValues& scores,
+                     TDistance& dist,
+                     GlobalPairwiseLibrary)
 {
-	SEQAN_CHECKPOINT
-	appendSegmentMatches(str, pList, score_type, matches, scores, dist, AlignConfig<>(), GlobalPairwiseLibrary() );
+    SEQAN_CHECKPOINT
+    appendSegmentMatches(str, pList, score_type, matches, scores, dist, AlignConfig<>(), GlobalPairwiseLibrary() );
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_msa/graph_align_tcoffee_msa.h b/seqan/graph_msa/graph_align_tcoffee_msa.h
index 4e7cbfc..628933b 100644
--- a/seqan/graph_msa/graph_align_tcoffee_msa.h
+++ b/seqan/graph_msa/graph_align_tcoffee_msa.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,469 +29,525 @@
 // DAMAGE.
 //
 // ==========================================================================
+// Author: Tobias Rausch <rausch@embl.de>
+// ==========================================================================
 
 #ifndef SEQAN_HEADER_GRAPH_ALIGN_TCOFFEE_MSA_H
 #define SEQAN_HEADER_GRAPH_ALIGN_TCOFFEE_MSA_H
 
-namespace SEQAN_NAMESPACE_MAIN
+namespace seqan
 {
 
-template<typename TAlphabet, typename TScore>
-struct MsaOptions {
+// ==========================================================================
+// Classes
+// ==========================================================================
+
+// --------------------------------------------------------------------------
+// Class MsaOptions
+// --------------------------------------------------------------------------
+
+/*!
+ * @class MsaOptions
+ * @headerfile <seqan/graph_msa.h>
+ * @brief Configuration for @link globalMsaAlignment @endlink
+ *
+ * @signature template <typename TAlphabet, typename TScore>
+ *            struct MsaOptions;
+ *
+ * @tparam TAlphabet The alphabet type to use.
+ * @tparam TScore    The @link Score @endlink type to use.
+ */
+
+template <typename TAlphabet, typename TScore>
+struct MsaOptions
+{
 public:
-	// Rescore segment matches after refinement
-	bool rescore;
-
-	// Output format
-	// 0: Fasta
-	// 1: Msf
-	unsigned int outputFormat;
-
-	// Scoring object
-	TScore sc;
-
-	// All methods to compute a guide tree
-	// 0: Neighbor-joining
-	// 1: UPGMA single linkage
-	// 2: UPGMA complete linkage
-	// 3: UPGMA average linkage
-	// 4: UPGMA weighted average linkage
-	unsigned int build;
-
-	// All methods to compute segment matches
-	// 0: global alignment
-	// 1: local alignments
-	// 2: overlap alignments
-	// 3: longest common subsequence
-	String<unsigned int> method;
-
-	// Various input and output file names
-	String<std::string> alnfiles;		// External alignment files
-	String<std::string> libfiles;		// T-Coffee library files
-	String<std::string> blastfiles;		// Blast match files
-	String<std::string> mummerfiles;	// MUMmer files
-	std::string outfile;				// Output file name
-	std::string seqfile;				// Sequence file name
-	std::string infile;					// Alignment file for alignment evaluation
-	std::string treefile;				// Guide tree file
-	
-	// Initialization
-	MsaOptions() : rescore(true), outputFormat(0), build(0) {}
+    /*!
+     * @var bool MsaOptions::rescore
+     * @brief Whether or not to rescore segment matches after refinment (default: <tt>true</tt>).
+     */
+    bool rescore;
+
+    /*!
+     * @var unsigned MsaOptions::outputFormat;
+     * @brief Output Format (<tt>0</tt> - FASTA, <tt>1</tt> MSF, default: <tt>0</tt>).
+     */
+    unsigned outputFormat;
+
+    /*!
+     * @var TScore MsaOptions::sc;
+     * @brief The @link Score @endlink object to use.
+     */
+    TScore sc;
+
+    /*!
+     * @var unsigned MsaOptions::build;
+     * @brief Methods for computing guide tre.
+     *
+     * 0 Neighbor-joining, 1 UPGMA single linkage, 2 UPGMA complete linkage,
+     * 3 UPGMA average linkage, 4 UPGMA weighted average linkage.
+     */
+    unsigned build;
+
+    /*!
+     * @var TUnsignedString MsaOptions::method;
+     * @brief All methods to compute segment matches, of Type <tt>String&lt;unsigned&gt;</tt>.
+     *
+     * 0 global alignment, 1 local alignments, 2 overlap alignments, 3 longest common subsequence
+     */
+    String<unsigned> method;
+
+    // TODO(holtgrew): Document me!
+    // Various input and output file names
+    String<std::string> alnfiles;       // External alignment files
+    String<std::string> libfiles;       // T-Coffee library files
+    String<std::string> blastfiles;     // Blast match files
+    String<std::string> mummerfiles;    // MUMmer files
+    std::string outfile;                // Output file name
+    std::string seqfile;                // Sequence file name
+    std::string infile;                 // Alignment file for alignment evaluation
+    std::string treefile;               // Guide tree file
+
+    /*!
+     * @fn MsaOptions::MsaOptions
+     * @brief Default constructor.
+     * @signature MsaOptions::MsaOptions();
+     */
+    MsaOptions() : rescore(true), outputFormat(0), build(0)
+    {}
 };
 
-//////////////////////////////////////////////////////////////////////////////////
-
-template<typename TAlphabet, typename TScore>
-inline void
-evaluateAlignment(MsaOptions<TAlphabet, TScore> const& msaOpt) {
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef String<TAlphabet> TSequence;
-	typedef typename Size<TSequence>::Type TSize;
-	StringSet<TSequence, Owner<> > origStrSet;
-	StringSet<String<char> > names;
-
-	// Read the sequences
-	std::fstream strm;
-	strm.open(msaOpt.infile.c_str(), ::std::ios_base::in | ::std::ios_base::binary);
-	read(strm,origStrSet,names,FastaAlign());	
-	strm.close();
-
-	// Make a dependent StringSet
-	typedef StringSet<TSequence, Dependent<> > TDepSequenceSet;
-	TDepSequenceSet strSet(origStrSet);
-	
-	// Read the alignment
-	typedef String<Fragment<> > TFragmentString;
-	String<TScoreValue> scores;
-	TFragmentString matches;
-	std::fstream strm_lib;
-	strm_lib.open(msaOpt.infile.c_str(), ::std::ios_base::in | ::std::ios_base::binary);
-	read(strm_lib,matches, scores, names, FastaAlign());	
-	strm_lib.close();
-
-	// Build the alignment graph
-	typedef Graph<Alignment<TDepSequenceSet, TSize> > TGraph;
-	TGraph g(strSet);
-	buildAlignmentGraph(matches, g, FrequencyCounting() );
-
-	// Print the scoring information
-	TScoreValue gop = msaOpt.sc.data_gap_open;
-	TScoreValue gex = msaOpt.sc.data_gap_extend;
-	std::cout << "Scoring parameters:" << std::endl;
-	std::cout << "*Gap opening: " << gop << std::endl;
-	std::cout << "*Gap extension: " << gex << std::endl;
-	std::cout << "*Scoring matrix: " << std::endl;
-	TSize alphSize = ValueSize<TAlphabet>::VALUE;
-	std::cout << "   ";
-	for(TSize col = 0; col<alphSize; ++col) std::cout << TAlphabet(col) << ',';
-	std::cout << std::endl;
-	for(TSize row = 0; row<alphSize; ++row) {
-		for(TSize col = 0; col<alphSize; ++col) {
-			if (col == 0) std::cout << TAlphabet(row) << ": ";
-			std::cout << score(msaOpt.sc, TAlphabet(row), TAlphabet(col));
-			if (col < alphSize - 1) std::cout << ',';
-		}
-		std::cout << std::endl;
-	}
-	std::cout << std::endl;
-
-	// Print the alignment information
-	TSize numGapEx = 0;
-	TSize numGap = 0;
-	TSize numPairs = 0;
-	TSize alignLen = 0;
-	String<TSize> pairCount;
-	String<char> mat;
-	if (convertAlignment(g, mat)) {
-		TScoreValue alignScore = alignmentEvaluation(g, msaOpt.sc, numGapEx, numGap, numPairs, pairCount, alignLen);
-		std::cout << "Alignment Score: " << alignScore << std::endl;
-		std::cout << "Alignment Length: " << alignLen << std::endl;
-		std::cout << "#Match-Mismatch pairs: " << numPairs << std::endl;
-		std::cout << "Score contribution by match-mismatch pairs: " << (alignScore - (((TScoreValue) numGap * gop) + ((TScoreValue) numGapEx * gex))) << std::endl;
-		std::cout << "#Gap extensions: " << numGapEx << std::endl;
-		std::cout << "Score contribution by gap extensions: " << ((TScoreValue) numGapEx * gex) << std::endl;
-		std::cout << "#Gap openings: " << numGap << std::endl;
-		std::cout << "Score contribution by gap openings: " << ((TScoreValue) numGap * gop) << std::endl;
-		std::cout << std::endl;
-		std::cout << "#Pairs: " << std::endl;
-		std::cout << "   ";
-		for(TSize col = 0; col<alphSize; ++col) std::cout << TAlphabet(col) << ',';
-		std::cout << std::endl;
-		for(TSize row = 0; row<alphSize; ++row) {
-			for(TSize col = 0; col<alphSize; ++col) {
-				if (col == 0) std::cout << TAlphabet(row) << ": ";
-				std::cout << value(pairCount, row * alphSize + col);
-				if (col < alphSize - 1) std::cout << ',';
-			}
-			std::cout << std::endl;
-		}
-	} else {
-		std::cout << "No valid alignment!" << std::endl;
-	}
-}
-
+// --------------------------------------------------------------------------
+// Function evaluateAlignment()
+// --------------------------------------------------------------------------
 
-//////////////////////////////////////////////////////////////////////////////
+// TODO(holtgrew): Document me!
 
-template<typename TStrSpec, typename TSpec, typename TList, typename TScore, typename TSegmentMatches, typename TScores>
-inline void 
-_appendSegmentMatches(StringSet<String<AminoAcid, TStrSpec>, Dependent<TSpec> > const& str,
-					   TList const& pList,
-					   TScore const&,
-					   TSegmentMatches& matches,
-					   TScores& scores)
+template <typename TAlphabet, typename TScore>
+void evaluateAlignment(MsaOptions<TAlphabet, TScore> const & msaOpt)
 {
-	Blosum62 local_score(-1,-8);
-	appendSegmentMatches(str, pList, local_score, matches, scores, LocalPairwiseLibrary() );
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef String<TAlphabet> TSequence;
+    typedef typename Size<TSequence>::Type TSize;
+    StringSet<TSequence, Owner<> > origStrSet;
+    StringSet<String<char> > names;
+
+    // Read the sequences
+    std::fstream strm;
+    strm.open(msaOpt.infile.c_str(), std::ios_base::in | std::ios_base::binary);
+    read(strm, origStrSet, names, FastaAlign());
+    strm.close();
+
+    // Make a dependent StringSet
+    typedef StringSet<TSequence, Dependent<> > TDepSequenceSet;
+    TDepSequenceSet strSet(origStrSet);
+
+    // Read the alignment
+    typedef String<Fragment<> > TFragmentString;
+    String<TScoreValue> scores;
+    TFragmentString matches;
+    std::fstream strm_lib;
+    strm_lib.open(msaOpt.infile.c_str(), std::ios_base::in | std::ios_base::binary);
+    read(strm_lib, matches, scores, names, FastaAlign());
+    strm_lib.close();
+
+    // Build the alignment graph
+    typedef Graph<Alignment<TDepSequenceSet, TSize> > TGraph;
+    TGraph g(strSet);
+    buildAlignmentGraph(matches, g, FrequencyCounting());
+
+    // Print the scoring information
+    TScoreValue gop = msaOpt.sc.data_gap_open;
+    TScoreValue gex = msaOpt.sc.data_gap_extend;
+    std::cout << "Scoring parameters:" << std::endl;
+    std::cout << "*Gap opening: " << gop << std::endl;
+    std::cout << "*Gap extension: " << gex << std::endl;
+    std::cout << "*Scoring matrix: " << std::endl;
+    TSize alphSize = ValueSize<TAlphabet>::VALUE;
+    std::cout << "   ";
+    for (TSize col = 0; col < alphSize; ++col)
+        std::cout << TAlphabet(col) << ',';
+    std::cout << std::endl;
+    for (TSize row = 0; row < alphSize; ++row)
+    {
+        for (TSize col = 0; col < alphSize; ++col)
+        {
+            if (col == 0)
+                std::cout << TAlphabet(row) << ": ";
+            std::cout << score(msaOpt.sc, TAlphabet(row), TAlphabet(col));
+            if (col < alphSize - 1)
+                std::cout << ',';
+        }
+        std::cout << std::endl;
+    }
+    std::cout << std::endl;
+
+    // Print the alignment information
+    TSize numGapEx = 0;
+    TSize numGap = 0;
+    TSize numPairs = 0;
+    TSize alignLen = 0;
+    String<TSize> pairCount;
+    String<char> mat;
+    if (convertAlignment(g, mat))
+    {
+        TScoreValue alignScore = alignmentEvaluation(g, msaOpt.sc, numGapEx, numGap, numPairs, pairCount, alignLen);
+        std::cout << "Alignment Score: " << alignScore << std::endl;
+        std::cout << "Alignment Length: " << alignLen << std::endl;
+        std::cout << "#Match-Mismatch pairs: " << numPairs << std::endl;
+        std::cout << "Score contribution by match-mismatch pairs: " << (alignScore - (((TScoreValue) numGap * gop) + ((TScoreValue) numGapEx * gex))) << std::endl;
+        std::cout << "#Gap extensions: " << numGapEx << std::endl;
+        std::cout << "Score contribution by gap extensions: " << ((TScoreValue) numGapEx * gex) << std::endl;
+        std::cout << "#Gap openings: " << numGap << std::endl;
+        std::cout << "Score contribution by gap openings: " << ((TScoreValue) numGap * gop) << std::endl;
+        std::cout << std::endl;
+        std::cout << "#Pairs: " << std::endl;
+        std::cout << "   ";
+        for (TSize col = 0; col < alphSize; ++col)
+            std::cout << TAlphabet(col) << ',';
+        std::cout << std::endl;
+        for (TSize row = 0; row < alphSize; ++row)
+        {
+            for (TSize col = 0; col < alphSize; ++col)
+            {
+                if (col == 0)
+                    std::cout << TAlphabet(row) << ": ";
+                std::cout << value(pairCount, row * alphSize + col);
+                if (col < alphSize - 1)
+                    std::cout << ',';
+            }
+            std::cout << std::endl;
+        }
+    }
+    else
+    {
+        std::cout << "No valid alignment!" << std::endl;
+    }
 }
 
-//////////////////////////////////////////////////////////////////////////////
+// --------------------------------------------------------------------------
+// Function globalMsaAlignment()
+// --------------------------------------------------------------------------
 
-template<typename TValue, typename TStrSpec, typename TSpec, typename TList, typename TScore, typename TSegmentMatches, typename TScores>
-inline void 
-_appendSegmentMatches(StringSet<String<TValue, TStrSpec>, Dependent<TSpec> > const& str,
-					   TList const& pList,
-					   TScore const& score_type,
-					   TSegmentMatches& matches,
-					   TScores& scores)
+template <typename TStrSpec, typename TSpec, typename TList, typename TScore, typename TSegmentMatches, typename TScores>
+void _appendSegmentMatches(StringSet<String<AminoAcid, TStrSpec>, Dependent<TSpec> > const & str,
+                             TList const & pList,
+                             TScore const &,
+                             TSegmentMatches & matches,
+                             TScores & scores)
 {
-	appendSegmentMatches(str, pList, score_type, matches, scores, LocalPairwiseLibrary() );
+    Blosum62 local_score(-1, -8);
+    appendSegmentMatches(str, pList, local_score, matches, scores, LocalPairwiseLibrary());
 }
 
-
 //////////////////////////////////////////////////////////////////////////////
 
+template <typename TValue, typename TStrSpec, typename TSpec, typename TList, typename TScore, typename TSegmentMatches, typename TScores>
+void _appendSegmentMatches(StringSet<String<TValue, TStrSpec>, Dependent<TSpec> > const & str,
+                             TList const & pList,
+                             TScore const & score_type,
+                             TSegmentMatches & matches,
+                             TScores & scores)
+{
+    appendSegmentMatches(str, pList, score_type, matches, scores, LocalPairwiseLibrary());
+}
+
 /*!
  * @fn globalMsaAlignment
  * @headerfile <seqan/graph_msa.h>
  * @brief Compute a global multiple sequence alignment.
  *
  * @signature void globalMsaAlignment(align, score);
+ * @signature void globalMsaAlignment(gAlign, score[, options]);
  *
- * @param[in,out] align An @link AlignmentGraph @endlink containing two or more sequences.
- * @param[in]     score The @link Score @endlink to use for computing the alignment.
+ * @param[in,out] gAlign  An @link AlignmentGraph @endlink containing two or more sequences.
+ * @param[in,out] align   A @link Align @endlink object with two or more sequences to align.
+ * @param[in]     score   The @link Score @endlink to use for computing the alignment.
+ * @param[in]     options The @link MsaOptions @endlink to use for the configuration.
  *
- * The resulting alignment is stored in <tt>align</tt>.
+ * The resulting alignment is stored in <tt>align</tt>/<tt>gAlign</tt>.
  */
 
-/**
-.Function.globalMsaAlignment:
-..class:Spec.Alignment Graph
-..summary:Computes a global multiple alignment.
-..cat:Alignments
-..signature:globalMsaAlignment(align, score)
-..param.align:An alignment data structure containing two or more sequences.
-...type:Spec.Alignment Graph
-..param.score:The score values to be used for computing the alignment.
-...type:Class.Score
-..returns:void
-...remarks:The resulting alignment is stored in $align$.
-..include:seqan/graph_msa.h
-*/
-template<typename TStringSet, typename TCargo, typename TSpec, typename TStringSet1, typename TNames, typename TAlphabet, typename TScore>
-inline void
-globalMsaAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign, 
-				   TStringSet1& sequenceSet,
-				   TNames& sequenceNames,
-				   MsaOptions<TAlphabet, TScore> const& msaOpt)
+template <typename TStringSet, typename TCargo, typename TSpec, typename TStringSet1, typename TNames, typename TAlphabet, typename TScore>
+void globalMsaAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> > & gAlign,
+                        TStringSet1 & sequenceSet,
+                        TNames & sequenceNames,
+                        MsaOptions<TAlphabet, TScore> const & msaOpt)
 {
-	typedef typename Value<TScore>::Type TScoreValue;
-	typedef typename Size<TStringSet>::Type TSize;
-	typedef Graph<Alignment<TStringSet, TSize> > TGraph;
-	//typedef typename Id<TGraph>::Type TId;
-	typedef double TDistanceValue;
-
-	// Initialize alignment object
-	clear(gAlign);
-	assignStringSet(gAlign, sequenceSet);
-
-	// Some alignment constants
-	TStringSet& seqSet = stringSet(gAlign);
-	TSize nSeq = length(seqSet);
-	TSize threshold = 30;
-
-	// Select all possible pairs for global and local alignments
-	String<TSize> pList;
-	selectPairs(seqSet, pList);
-
-	// Set-up a distance matrix
-	typedef String<TDistanceValue> TDistanceMatrix;
-	TDistanceMatrix distanceMatrix;
-
-	// Containers for segment matches and corresponding scores 
-	typedef String<Fragment<> > TFragmentString;
-	TFragmentString matches;
-	typedef String<TScoreValue> TScoreValues;
-	TScoreValues scores;
-
-	// Include segment matches from subalignments
-	if (!empty(msaOpt.alnfiles)) {
-		typedef typename Iterator<String<std::string> const, Standard>::Type TIter;
-		TIter begIt = begin(msaOpt.alnfiles, Standard() );
-		TIter begItEnd = end(msaOpt.alnfiles, Standard() );
-		for(;begIt != begItEnd; goNext(begIt)) {
-			std::ifstream strm_lib;
-			strm_lib.open((*begIt).c_str(), ::std::ios_base::in | ::std::ios_base::binary);
-			read(strm_lib, matches, scores, sequenceNames, FastaAlign());
-			strm_lib.close();
-		}
-	}
-
-	// Include computed segment matches
-	if (!empty(msaOpt.method)) {
-		typedef typename Iterator<String<unsigned int> const, Standard>::Type TIter;
-		TIter begIt = begin(msaOpt.method, Standard() );
-		TIter begItEnd = end(msaOpt.method, Standard() );
-		for(;begIt != begItEnd; goNext(begIt)) {
-			if (*begIt == 0) appendSegmentMatches(seqSet, pList, msaOpt.sc, matches, scores, distanceMatrix, GlobalPairwiseLibrary() );
-			else if (*begIt == 1) _appendSegmentMatches(seqSet, pList, msaOpt.sc, matches, scores);
-			else if (*begIt == 2) {
-				Nothing noth;
-				appendSegmentMatches(seqSet, pList, msaOpt.sc, matches, scores, noth, AlignConfig<true,true,true, true>(), GlobalPairwiseLibrary() );
-			}
-			else if (*begIt == 3) appendSegmentMatches(seqSet, pList, matches, scores, LcsLibrary() );
-		}	
-	}
-
-	// Include a T-Coffee library
-	if (!empty(msaOpt.libfiles)) {
-		typedef typename Iterator<String<std::string> const, Standard>::Type TIter;
-		TIter begIt = begin(msaOpt.libfiles, Standard() );
-		TIter begItEnd = end(msaOpt.libfiles, Standard() );
-		for(;begIt != begItEnd; goNext(begIt)) {
-			std::ifstream strm_lib;
-			strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary);
-			read(strm_lib, matches, scores, sequenceNames, TCoffeeLib());
-			strm_lib.close();
-		}
-	}
-
-	// Include MUMmer segment matches
-	if (!empty(msaOpt.mummerfiles)) {
-		typedef typename Iterator<String<std::string> const, Standard>::Type TIter;
-		TIter begIt = begin(msaOpt.mummerfiles, Standard() );
-		TIter begItEnd = end(msaOpt.mummerfiles, Standard() );
-		for(;begIt != begItEnd; goNext(begIt)) {
-			std::ifstream strm_lib;
-			strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary);
-			read(strm_lib, matches, scores, seqSet, sequenceNames, MummerLib());		
-			strm_lib.close();
-		}
-	}
-
-	// Include BLAST segment matches
-	if (!empty(msaOpt.blastfiles)) {
-		typedef typename Iterator<String<std::string> const, Standard>::Type TIter;
-		TIter begIt = begin(msaOpt.blastfiles, Standard() );
-		TIter begItEnd = end(msaOpt.blastfiles, Standard() );
-		for(;begIt != begItEnd; goNext(begIt)) {
-			std::ifstream strm_lib;
-			strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary);
-			read(strm_lib, matches, scores, sequenceNames, BlastLib());
-			strm_lib.close();
-		}
-	}
-
-	// Use these segment matches for the initial alignment graph
-	TGraph g(seqSet);
-	if (!msaOpt.rescore) buildAlignmentGraph(matches, scores, g, FractionalScore() );
-	else buildAlignmentGraph(matches, scores, g, msaOpt.sc, ReScore() );
-	clear(matches);
-	clear(scores);
-
-	// Guide tree
-	Graph<Tree<TDistanceValue> > guideTree;
-	if (!empty(msaOpt.treefile)) {
-		std::fstream strm_tree;
-		strm_tree.open(msaOpt.treefile.c_str(), ::std::ios_base::in | ::std::ios_base::binary);
-		read(strm_tree, guideTree, sequenceNames, NewickFormat());	// Read newick tree
-		strm_tree.close();
-	} else {
-		// Check if we have a valid distance matrix
-		if (empty(distanceMatrix))
-		  getDistanceMatrix(g, distanceMatrix, KmerDistance());
-		// Get distance matrix values for a precision of 10 decimal digits.
-		for (unsigned i = 0; i < length(distanceMatrix); ++i)
-		  distanceMatrix[i] = static_cast<__int64>(distanceMatrix[i] * 1e10) / 1e10;
-		if (msaOpt.build == 0) njTree(distanceMatrix, guideTree);
-		else if (msaOpt.build == 1) upgmaTree(distanceMatrix, guideTree, UpgmaMin());
-		else if (msaOpt.build == 2) upgmaTree(distanceMatrix, guideTree, UpgmaMax());
-		else if (msaOpt.build == 3) upgmaTree(distanceMatrix, guideTree, UpgmaAvg());
-		else if (msaOpt.build == 4) upgmaTree(distanceMatrix, guideTree, UpgmaWeightAvg());
-	}
-	clear(distanceMatrix);
-		
-	// Triplet extension
-	if (nSeq < threshold) tripletLibraryExtension(g);
-	else tripletLibraryExtension(g, guideTree, threshold / 2);
-
-	// Progressive Alignment
-	progressiveAlignment(g, guideTree, gAlign);
-
-	clear(guideTree);
-	clear(g);
-
-	//TStringSet& str = stringSet(gAlign);
-	//for(TSize i = 0; i<length(str);++i) {
-	//	for(TSize j=0;j<length(str[i]);++j) {
-	//		std::cout << ordValue(str[i][j]) << ',';
-	//	}
-	//	std::cout << std::endl;
-	//}
+    typedef typename Value<TScore>::Type TScoreValue;
+    typedef typename Size<TStringSet>::Type TSize;
+    typedef Graph<Alignment<TStringSet, TSize> > TGraph;
+    //typedef typename Id<TGraph>::Type TId;
+    typedef double TDistanceValue;
+
+    // Initialize alignment object
+    clear(gAlign);
+    assignStringSet(gAlign, sequenceSet);
+
+    // Some alignment constants
+    TStringSet & seqSet = stringSet(gAlign);
+    TSize nSeq = length(seqSet);
+    TSize threshold = 30;
+
+    // Select all possible pairs for global and local alignments
+    String<TSize> pList;
+    selectPairs(seqSet, pList);
+
+    // Set-up a distance matrix
+    typedef String<TDistanceValue> TDistanceMatrix;
+    TDistanceMatrix distanceMatrix;
+
+    // Containers for segment matches and corresponding scores
+    typedef String<Fragment<> > TFragmentString;
+    TFragmentString matches;
+    typedef String<TScoreValue> TScoreValues;
+    TScoreValues scores;
+
+    // Include segment matches from subalignments
+    if (!empty(msaOpt.alnfiles))
+    {
+        typedef typename Iterator<String<std::string> const, Standard>::Type TIter;
+        TIter begIt = begin(msaOpt.alnfiles, Standard());
+        TIter begItEnd = end(msaOpt.alnfiles, Standard());
+        for (; begIt != begItEnd; goNext(begIt))
+        {
+            std::ifstream strm_lib;
+            strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary);
+            read(strm_lib, matches, scores, sequenceNames, FastaAlign());
+            strm_lib.close();
+        }
+    }
+
+    // Include computed segment matches
+    if (!empty(msaOpt.method))
+    {
+        typedef typename Iterator<String<unsigned int> const, Standard>::Type TIter;
+        TIter begIt = begin(msaOpt.method, Standard());
+        TIter begItEnd = end(msaOpt.method, Standard());
+        for (; begIt != begItEnd; goNext(begIt))
+        {
+            if (*begIt == 0)
+                appendSegmentMatches(seqSet, pList, msaOpt.sc, matches, scores, distanceMatrix, GlobalPairwiseLibrary());
+            else if (*begIt == 1)
+                _appendSegmentMatches(seqSet, pList, msaOpt.sc, matches, scores);
+            else if (*begIt == 2)
+            {
+                Nothing noth;
+                appendSegmentMatches(seqSet, pList, msaOpt.sc, matches, scores, noth, AlignConfig<true, true, true, true>(), GlobalPairwiseLibrary());
+            }
+            else if (*begIt == 3)
+                appendSegmentMatches(seqSet, pList, matches, scores, LcsLibrary());
+        }
+    }
+
+    // Include a T-Coffee library
+    if (!empty(msaOpt.libfiles))
+    {
+        typedef typename Iterator<String<std::string> const, Standard>::Type TIter;
+        TIter begIt = begin(msaOpt.libfiles, Standard());
+        TIter begItEnd = end(msaOpt.libfiles, Standard());
+        for (; begIt != begItEnd; goNext(begIt))
+        {
+            std::ifstream strm_lib;
+            strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary);
+            read(strm_lib, matches, scores, sequenceNames, TCoffeeLib());
+            strm_lib.close();
+        }
+    }
+
+    // Include MUMmer segment matches
+    if (!empty(msaOpt.mummerfiles))
+    {
+        typedef typename Iterator<String<std::string> const, Standard>::Type TIter;
+        TIter begIt = begin(msaOpt.mummerfiles, Standard());
+        TIter begItEnd = end(msaOpt.mummerfiles, Standard());
+        for (; begIt != begItEnd; goNext(begIt))
+        {
+            std::ifstream strm_lib;
+            strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary);
+            read(strm_lib, matches, scores, seqSet, sequenceNames, MummerLib());
+            strm_lib.close();
+        }
+    }
+
+    // Include BLAST segment matches
+    if (!empty(msaOpt.blastfiles))
+    {
+        typedef typename Iterator<String<std::string> const, Standard>::Type TIter;
+        TIter begIt = begin(msaOpt.blastfiles, Standard());
+        TIter begItEnd = end(msaOpt.blastfiles, Standard());
+        for (; begIt != begItEnd; goNext(begIt))
+        {
+            std::ifstream strm_lib;
+            strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary);
+            read(strm_lib, matches, scores, sequenceNames, BlastLib());
+            strm_lib.close();
+        }
+    }
+
+    // Use these segment matches for the initial alignment graph
+    TGraph g(seqSet);
+    if (!msaOpt.rescore)
+        buildAlignmentGraph(matches, scores, g, FractionalScore());
+    else
+        buildAlignmentGraph(matches, scores, g, msaOpt.sc, ReScore());
+    clear(matches);
+    clear(scores);
+
+    // Guide tree
+    Graph<Tree<TDistanceValue> > guideTree;
+    if (!empty(msaOpt.treefile))
+    {
+        std::fstream strm_tree;
+        strm_tree.open(msaOpt.treefile.c_str(), std::ios_base::in | std::ios_base::binary);
+        read(strm_tree, guideTree, sequenceNames, NewickFormat());  // Read newick tree
+        strm_tree.close();
+    }
+    else
+    {
+        // Check if we have a valid distance matrix
+        if (empty(distanceMatrix))
+            getDistanceMatrix(g, distanceMatrix, KmerDistance());
+        // Get distance matrix values for a precision of 10 decimal digits.
+        for (unsigned i = 0; i < length(distanceMatrix); ++i)
+            distanceMatrix[i] = static_cast<__int64>(distanceMatrix[i] * 1e10) / 1e10;
+        if (msaOpt.build == 0)
+            njTree(distanceMatrix, guideTree);
+        else if (msaOpt.build == 1)
+            upgmaTree(distanceMatrix, guideTree, UpgmaMin());
+        else if (msaOpt.build == 2)
+            upgmaTree(distanceMatrix, guideTree, UpgmaMax());
+        else if (msaOpt.build == 3)
+            upgmaTree(distanceMatrix, guideTree, UpgmaAvg());
+        else if (msaOpt.build == 4)
+            upgmaTree(distanceMatrix, guideTree, UpgmaWeightAvg());
+    }
+    clear(distanceMatrix);
+
+    // Triplet extension
+    if (nSeq < threshold)
+        tripletLibraryExtension(g);
+    else
+        tripletLibraryExtension(g, guideTree, threshold / 2);
+
+    // Progressive Alignment
+    progressiveAlignment(g, guideTree, gAlign);
+
+    clear(guideTree);
+    clear(g);
+
+    //TStringSet& str = stringSet(gAlign);
+    //for(TSize i = 0; i<length(str);++i) {
+    //    for(TSize j=0;j<length(str[i]);++j) {
+    //        std::cout << ordValue(str[i][j]) << ',';
+    //    }
+    //    std::cout << std::endl;
+    //}
 }
 
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-template<typename TStringSet, typename TCargo, typename TSpec, typename TScore>
-inline void
-globalMsaAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign,
-				   TScore const& scoreObject)
+template <typename TStringSet, typename TCargo, typename TSpec, typename TScore>
+void globalMsaAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> > & gAlign,
+                        TScore const & scoreObject)
 {
-	//typedef typename Value<TStringSet>::Type TString;
-	//typedef typename Value<TString>::Type TAlphabet;
-	TStringSet sequenceSet = stringSet(gAlign);
-	String<String<char> > sequenceNames;
-	resize(sequenceNames, length(sequenceSet), String<char>("tmpName"));
-	MsaOptions<AminoAcid, TScore> msaOpt;
-	msaOpt.sc = scoreObject;
-	appendValue(msaOpt.method, 0);  // Global pairwise
-	appendValue(msaOpt.method, 1);	// Local pairwise
-	globalMsaAlignment(gAlign, sequenceSet, sequenceNames, msaOpt);
+    //typedef typename Value<TStringSet>::Type TString;
+    //typedef typename Value<TString>::Type TAlphabet;
+    TStringSet sequenceSet = stringSet(gAlign);
+    String<String<char> > sequenceNames;
+    resize(sequenceNames, length(sequenceSet), String<char>("tmpName"));
+    MsaOptions<AminoAcid, TScore> msaOpt;
+    msaOpt.sc = scoreObject;
+    appendValue(msaOpt.method, 0);  // Global pairwise
+    appendValue(msaOpt.method, 1);  // Local pairwise
+    globalMsaAlignment(gAlign, sequenceSet, sequenceNames, msaOpt);
 }
 
-//////////////////////////////////////////////////////////////////////////////
-
-
-template<typename TSource, typename TSpec, typename TScore>
-inline void
-globalMsaAlignment(Align<TSource, TSpec>& align,
-				   TScore const& scoreObject)
+template <typename TSource, typename TSpec, typename TScore>
+void globalMsaAlignment(Align<TSource, TSpec> & align,
+                        TScore const & scoreObject)
 {
-	typedef StringSet<TSource, Dependent<> > TStringSet;
-	TStringSet sequenceSet = stringSet(align);
-	Graph<Alignment<TStringSet, void, WithoutEdgeId> > gAlign(sequenceSet);
-	globalMsaAlignment(gAlign, scoreObject);
-	convertAlignment(gAlign, align);
+    typedef StringSet<TSource, Dependent<> > TStringSet;
+    TStringSet sequenceSet = stringSet(align);
+    Graph<Alignment<TStringSet, void, WithoutEdgeId> > gAlign(sequenceSet);
+    globalMsaAlignment(gAlign, scoreObject);
+    convertAlignment(gAlign, align);
 }
 
+// TODO(holtgrew): Remove the following?
 
 //////////////////////////////////////////////////////////////////////////////
 // Just two testing functions
 //////////////////////////////////////////////////////////////////////////////
 
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TStringSet, typename TMatches>
+template <typename TStringSet, typename TMatches>
 void
-_debugMatches(TStringSet& str, 
-			  TMatches& matches)
+_debugMatches(TStringSet & str,
+              TMatches & matches)
 {
-	typedef typename Id<TStringSet>::Type TId;
-	typedef typename Size<TStringSet>::Type TSize;
-
-	// Print all the matches
-	std::cout << "The sequences:" << std::endl;
-	for(TSize i = 0;i<length(str);++i) {
-		std::cout << positionToId(str,i) << ':' << str[i] << std::endl;
-	}
-	std::cout << "The matches:" << std::endl;
-	for(TSize i = 0;i<length(matches);++i) {
-		TId tmp_id1 = sequenceId(matches[i],0);
-		std::cout << tmp_id1 << ',' << fragmentBegin(matches[i],tmp_id1) << ',';
-		for(TSize j = fragmentBegin(matches[i],tmp_id1); j < fragmentBegin(matches[i],tmp_id1) + fragmentLength(matches[i],tmp_id1); ++j) {
-			std::cout << str[idToPosition(str, tmp_id1)][j];
-		}
-		TId tmp_id2 = sequenceId(matches[i],1);
-		std::cout << ',' <<	tmp_id2 << ',' << fragmentBegin(matches[i],tmp_id2) << ',';
-		for(TSize j = fragmentBegin(matches[i],tmp_id2); j < fragmentBegin(matches[i],tmp_id2) + fragmentLength(matches[i],tmp_id2); ++j) {
-			std::cout << str[idToPosition(str, tmp_id2)][j];
-		}
-		std::cout << std::endl;
-
-		SEQAN_ASSERT(sequenceId(matches[i],0) != sequenceId(matches[i],1));
-		SEQAN_ASSERT(fragmentBegin(matches[i],tmp_id1) < length(str[idToPosition(str, tmp_id1)]));
-		SEQAN_ASSERT(fragmentBegin(matches[i],tmp_id1) + fragmentLength(matches[i],tmp_id1) <= length(str[idToPosition(str, tmp_id1)]));
-		SEQAN_ASSERT(fragmentBegin(matches[i],tmp_id2) < length(str[idToPosition(str, tmp_id2)]));
-		SEQAN_ASSERT(fragmentBegin(matches[i],tmp_id2) + fragmentLength(matches[i],tmp_id2) <= length(str[idToPosition(str, tmp_id2)]));
-		SEQAN_ASSERT(fragmentLength(matches[i],tmp_id2) == fragmentLength(matches[i],tmp_id1));
-	}
+    typedef typename Id<TStringSet>::Type TId;
+    typedef typename Size<TStringSet>::Type TSize;
+
+    // Print all the matches
+    std::cout << "The sequences:" << std::endl;
+    for (TSize i = 0; i < length(str); ++i)
+    {
+        std::cout << positionToId(str, i) << ':' << str[i] << std::endl;
+    }
+    std::cout << "The matches:" << std::endl;
+    for (TSize i = 0; i < length(matches); ++i)
+    {
+        TId tmp_id1 = sequenceId(matches[i], 0);
+        std::cout << tmp_id1 << ',' << fragmentBegin(matches[i], tmp_id1) << ',';
+        for (TSize j = fragmentBegin(matches[i], tmp_id1); j < fragmentBegin(matches[i], tmp_id1) + fragmentLength(matches[i], tmp_id1); ++j)
+        {
+            std::cout << str[idToPosition(str, tmp_id1)][j];
+        }
+        TId tmp_id2 = sequenceId(matches[i], 1);
+        std::cout << ',' << tmp_id2 << ',' << fragmentBegin(matches[i], tmp_id2) << ',';
+        for (TSize j = fragmentBegin(matches[i], tmp_id2); j < fragmentBegin(matches[i], tmp_id2) + fragmentLength(matches[i], tmp_id2); ++j)
+        {
+            std::cout << str[idToPosition(str, tmp_id2)][j];
+        }
+        std::cout << std::endl;
+
+        SEQAN_ASSERT(sequenceId(matches[i], 0) != sequenceId(matches[i], 1));
+        SEQAN_ASSERT(fragmentBegin(matches[i], tmp_id1) < length(str[idToPosition(str, tmp_id1)]));
+        SEQAN_ASSERT(fragmentBegin(matches[i], tmp_id1) + fragmentLength(matches[i], tmp_id1) <= length(str[idToPosition(str, tmp_id1)]));
+        SEQAN_ASSERT(fragmentBegin(matches[i], tmp_id2) < length(str[idToPosition(str, tmp_id2)]));
+        SEQAN_ASSERT(fragmentBegin(matches[i], tmp_id2) + fragmentLength(matches[i], tmp_id2) <= length(str[idToPosition(str, tmp_id2)]));
+        SEQAN_ASSERT(fragmentLength(matches[i], tmp_id2) == fragmentLength(matches[i], tmp_id1));
+    }
 }
 
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TGraph>
-void
-_debugRefinedMatches(TGraph& g)
+template <typename TGraph>
+void _debugRefinedMatches(TGraph & g)
 {
-	typedef typename Id<TGraph>::Type TId;
-	//typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-
-	std::cout << "Refined matches" << std::endl;
-	TEdgeIterator it_tmp(g);
-	for(;!atEnd(it_tmp);++it_tmp) {
-		TId id1 = sequenceId(g,sourceVertex(it_tmp));
-		TId id2 = sequenceId(g,targetVertex(it_tmp));
-		std::cout << id1 << ',' << fragmentBegin(g,sourceVertex(it_tmp)) << ',';
-		std::cout << label(g,sourceVertex(it_tmp));
-		std::cout << ',' <<	id2 << ',' << fragmentBegin(g,targetVertex(it_tmp)) << ',';
-		std::cout << label(g,targetVertex(it_tmp));
-		std::cout << " (" << cargo(*it_tmp) << ")";
-		std::cout << std::endl;	
-
-		SEQAN_ASSERT(sequenceId(g,sourceVertex(it_tmp)) != sequenceId(g,targetVertex(it_tmp)));
-		SEQAN_ASSERT(fragmentBegin(g,sourceVertex(it_tmp)) < length((stringSet(g))[idToPosition((stringSet(g)), id1)]));
-		SEQAN_ASSERT(fragmentBegin(g,sourceVertex(it_tmp)) + fragmentLength(g,sourceVertex(it_tmp)) <= length((stringSet(g))[idToPosition((stringSet(g)), id1)]));
-		SEQAN_ASSERT(fragmentBegin(g,targetVertex(it_tmp)) < length((stringSet(g))[idToPosition((stringSet(g)), id2)]));
-		SEQAN_ASSERT(fragmentBegin(g,targetVertex(it_tmp)) + fragmentLength(g,targetVertex(it_tmp)) <= length((stringSet(g))[idToPosition((stringSet(g)), id2)]));
-		SEQAN_ASSERT(fragmentLength(g,sourceVertex(it_tmp)) == fragmentLength(g,targetVertex(it_tmp)));
-
-	}
+    typedef typename Id<TGraph>::Type TId;
+    //typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+
+    std::cout << "Refined matches" << std::endl;
+    TEdgeIterator it_tmp(g);
+    for (; !atEnd(it_tmp); ++it_tmp)
+    {
+        TId id1 = sequenceId(g, sourceVertex(it_tmp));
+        TId id2 = sequenceId(g, targetVertex(it_tmp));
+        std::cout << id1 << ',' << fragmentBegin(g, sourceVertex(it_tmp)) << ',';
+        std::cout << label(g, sourceVertex(it_tmp));
+        std::cout << ',' << id2 << ',' << fragmentBegin(g, targetVertex(it_tmp)) << ',';
+        std::cout << label(g, targetVertex(it_tmp));
+        std::cout << " (" << cargo(*it_tmp) << ")";
+        std::cout << std::endl;
+
+        SEQAN_ASSERT(sequenceId(g, sourceVertex(it_tmp)) != sequenceId(g, targetVertex(it_tmp)));
+        SEQAN_ASSERT(fragmentBegin(g, sourceVertex(it_tmp)) < length((stringSet(g))[idToPosition((stringSet(g)), id1)]));
+        SEQAN_ASSERT(fragmentBegin(g, sourceVertex(it_tmp)) + fragmentLength(g, sourceVertex(it_tmp)) <= length((stringSet(g))[idToPosition((stringSet(g)), id1)]));
+        SEQAN_ASSERT(fragmentBegin(g, targetVertex(it_tmp)) < length((stringSet(g))[idToPosition((stringSet(g)), id2)]));
+        SEQAN_ASSERT(fragmentBegin(g, targetVertex(it_tmp)) + fragmentLength(g, targetVertex(it_tmp)) <= length((stringSet(g))[idToPosition((stringSet(g)), id2)]));
+        SEQAN_ASSERT(fragmentLength(g, sourceVertex(it_tmp)) == fragmentLength(g, targetVertex(it_tmp)));
+
+    }
 }
 
-}// namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
+}  // namespace seqan
 
+#endif  // #ifndef SEQAN_HEADER_GRAPH_ALIGN_TCOFFEE_MSA_H
diff --git a/seqan/graph_msa/graph_align_tcoffee_progressive.h b/seqan/graph_msa/graph_align_tcoffee_progressive.h
index 4545581..18cdb5d 100644
--- a/seqan/graph_msa/graph_align_tcoffee_progressive.h
+++ b/seqan/graph_msa/graph_align_tcoffee_progressive.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,72 +43,74 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TPosition, typename TSequence>
-inline void 
+inline void
 _buildLeafString(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-				 TPosition const pos,
-				 TSequence& alignSeq)
+                 TPosition const pos,
+                 TSequence& alignSeq)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Id<TGraph>::Type TId;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Value<TSequence>::Type TVertexString;
-
-	//TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	TStringSet& str = stringSet(g);
-	TId seqId = positionToId(str, pos);
-	TSize lenRoot = length(str[pos]);
-	TSize i = 0;
-	while(i<lenRoot) {
-		TVertexDescriptor nextVertex = findVertex(const_cast<TGraph&>(g), seqId, i);
-		//SEQAN_ASSERT(nextVertex != nilVertex);
-		//if (nextVertex == nilVertex) {
-		//	std::cout << "Warning: Nil Vertex" << std::endl;
-		//	TSize j = i + 1;
-		//	while ((j < lenRoot) && (findVertex(const_cast<TGraph&>(g), seqId, j) == nilVertex)) ++j;
-		//	nextVertex = addVertex(const_cast<TGraph&>(g), seqId, i, j-i);
-		//}
-		appendValue(alignSeq, TVertexString(nextVertex), Generous());
-		i += fragmentLength(g, nextVertex);
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Id<TGraph>::Type TId;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Value<TSequence>::Type TVertexString;
+
+    //TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+    TStringSet& str = stringSet(g);
+    TId seqId = positionToId(str, pos);
+    TSize lenRoot = length(str[pos]);
+    TSize i = 0;
+    while(i<lenRoot) {
+        TVertexDescriptor nextVertex = findVertex(const_cast<TGraph&>(g), seqId, i);
+        //SEQAN_ASSERT(nextVertex != nilVertex);
+        //if (nextVertex == nilVertex) {
+        //    std::cout << "Warning: Nil Vertex" << std::endl;
+        //    TSize j = i + 1;
+        //    while ((j < lenRoot) && (findVertex(const_cast<TGraph&>(g), seqId, j) == nilVertex)) ++j;
+        //    nextVertex = addVertex(const_cast<TGraph&>(g), seqId, i, j-i);
+        //}
+        TVertexString vs;
+        appendValue(vs, nextVertex);
+        appendValue(alignSeq, vs, Generous());
+        i += fragmentLength(g, nextVertex);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TSegmentString, typename TOutGraph>
-inline void 
+inline void
 _createAlignmentGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-					  TSegmentString& alignSeq,
-					  TOutGraph& gOut)			 
+                      TSegmentString& alignSeq,
+                      TOutGraph& gOut)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef String<TVertexDescriptor> TVertexString;
-
-	// Create the alignment graph
-	TSize alignSeqLen = length(alignSeq);
-	for(TSize i = 0; i<alignSeqLen;++i) {
-		TVertexString& alignSeq_i = alignSeq[i];
-		TSize len_i = length(alignSeq_i);
-		for(TSize j=0; j<len_i; ++j) {
-			TVertexDescriptor v = alignSeq_i[j];
-			SEQAN_ASSERT(fragmentBegin(g,v) < length(getValueById(stringSet(g), sequenceId(g,v))));
-			SEQAN_ASSERT(fragmentLength(g,v) > 0);
-			SEQAN_ASSERT(fragmentBegin(g,v) + fragmentLength(g,v) <= length(getValueById(stringSet(g), sequenceId(g,v))));
-			TVertexDescriptor l = addVertex(gOut, sequenceId(g, v), fragmentBegin(g,v), fragmentLength(g,v));
-			//std::cout << l << label(gOut, l) << ',';
-			TSize count = 1;
-			for(TSize k = j; k>0; --k) {
-				//SEQAN_ASSERT(fragmentLength(gOut,l) == fragmentLength(gOut,l - count));
-				addEdge(gOut, (TVertexDescriptor) (l - count), (TVertexDescriptor) l);
-				++count;
-			}
-		}
-		//std::cout << std::endl;
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef String<TVertexDescriptor> TVertexString;
+
+    // Create the alignment graph
+    TSize alignSeqLen = length(alignSeq);
+    for(TSize i = 0; i<alignSeqLen;++i) {
+        TVertexString& alignSeq_i = alignSeq[i];
+        TSize len_i = length(alignSeq_i);
+        for(TSize j=0; j<len_i; ++j) {
+            TVertexDescriptor v = alignSeq_i[j];
+            SEQAN_ASSERT(fragmentBegin(g,v) < length(getValueById(stringSet(g), sequenceId(g,v))));
+            SEQAN_ASSERT(fragmentLength(g,v) > 0);
+            SEQAN_ASSERT(fragmentBegin(g,v) + fragmentLength(g,v) <= length(getValueById(stringSet(g), sequenceId(g,v))));
+            TVertexDescriptor l = addVertex(gOut, sequenceId(g, v), fragmentBegin(g,v), fragmentLength(g,v));
+            //std::cout << l << label(gOut, l) << ',';
+            TSize count = 1;
+            for(TSize k = j; k>0; --k) {
+                //SEQAN_ASSERT(fragmentLength(gOut,l) == fragmentLength(gOut,l - count));
+                addEdge(gOut, (TVertexDescriptor) (l - count), (TVertexDescriptor) l);
+                ++count;
+            }
+        }
+        //std::cout << std::endl;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -125,75 +127,59 @@ _createAlignmentGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
  * @param[out] outputGraph An @link AlignmentGraph @endlink for the final MSA.
  */
 
-/**
-.Function.progressiveAlignment
-..class:Spec.Alignment Graph
-..summary:Performs a progressive alignment.
-..cat:Graph
-..signature:
-progressiveAlignment(inputGraph, guideTree, outputGraph)
-..param.inputGraph:The alignment graph with multiple sequence information.
-...type:Spec.Alignment Graph
-..param.guideTree:A guide tree.
-...type:Spec.Tree
-..param.outputGraph:An alignment graph for the final MSA.
-...type:Spec.Alignment Graph
-..returns:void
-..include:seqan/graph_msa.h
-*/
 template<typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TOutGraph>
-inline void 
+inline void
 progressiveAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-					 TGuideTree& tree,
-					 TOutGraph& gOut)			 
+                     TGuideTree& tree,
+                     TOutGraph& gOut)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
-	typedef typename Iterator<TGuideTree, BfsIterator>::Type TBfsIterator;
-	typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjacencyIterator;
-	typedef String<TVertexDescriptor> TVertexString;
-	typedef String<TVertexString> TSegmentString;
-	
-	// Initialization
-	TVertexDescriptor rootVertex = getRoot(tree);
-	TSize nVertices = numVertices(tree);
-
-	// Vertices in reversed bfs order
-	TVertexString vertices;
-	resize(vertices, nVertices);
-
-	// All Strings of Strings of vertices for each node of the guide tree
-	String<TSegmentString> segString;
-	resize(segString, nVertices);
-	
-	// Walk through the tree in bfs order	
-	typedef typename Iterator<TVertexString, Standard>::Type TVertexIter;
-	TVertexIter itVert = begin(vertices, Standard());
-	TVertexIter itVertEnd = end(vertices, Standard());
-	--itVertEnd;
-	TBfsIterator bfsIt(tree, rootVertex);
-	for(;!atEnd(bfsIt);goNext(bfsIt), --itVertEnd) 
-		*itVertEnd = *bfsIt;
-
-	// Progressive alignment
-	itVert = begin(vertices, Standard());
-	itVertEnd = end(vertices, Standard());
-	for(;itVert != itVertEnd; ++itVert) {
-		if(isLeaf(tree, *itVert)) _buildLeafString(g, *itVert, segString[*itVert]);
-		else {
-			// Align the two children (Binary tree)
-			TAdjacencyIterator adjIt(tree, *itVert);
-			TVertexDescriptor child1 = *adjIt; goNext(adjIt);
-			heaviestCommonSubsequence(g, segString[child1], segString[*adjIt], segString[*itVert]);
-			clear(segString[child1]);
-			clear(segString[*adjIt]);
-		}
-	}
-
-	// Create the alignment graph
-	_createAlignmentGraph(g, segString[rootVertex], gOut);
+    SEQAN_CHECKPOINT
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
+    typedef typename Iterator<TGuideTree, BfsIterator>::Type TBfsIterator;
+    typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjacencyIterator;
+    typedef String<TVertexDescriptor> TVertexString;
+    typedef String<TVertexString> TSegmentString;
+
+    // Initialization
+    TVertexDescriptor rootVertex = getRoot(tree);
+    TSize nVertices = numVertices(tree);
+
+    // Vertices in reversed bfs order
+    TVertexString vertices;
+    resize(vertices, nVertices);
+
+    // All Strings of Strings of vertices for each node of the guide tree
+    String<TSegmentString> segString;
+    resize(segString, nVertices);
+
+    // Walk through the tree in bfs order
+    typedef typename Iterator<TVertexString, Standard>::Type TVertexIter;
+    TVertexIter itVert = begin(vertices, Standard());
+    TVertexIter itVertEnd = end(vertices, Standard());
+    --itVertEnd;
+    TBfsIterator bfsIt(tree, rootVertex);
+    for(;!atEnd(bfsIt);goNext(bfsIt), --itVertEnd)
+        *itVertEnd = *bfsIt;
+
+    // Progressive alignment
+    itVert = begin(vertices, Standard());
+    itVertEnd = end(vertices, Standard());
+    for(;itVert != itVertEnd; ++itVert) {
+        if(isLeaf(tree, *itVert)) _buildLeafString(g, *itVert, segString[*itVert]);
+        else {
+            // Align the two children (Binary tree)
+            TAdjacencyIterator adjIt(tree, *itVert);
+            TVertexDescriptor child1 = *adjIt; goNext(adjIt);
+            heaviestCommonSubsequence(g, segString[child1], segString[*adjIt], segString[*itVert]);
+            clear(segString[child1]);
+            clear(segString[*adjIt]);
+        }
+    }
+
+    // Create the alignment graph
+    _createAlignmentGraph(g, segString[rootVertex], gOut);
 }
 
 
@@ -206,45 +192,45 @@ progressiveAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TStringSet, typename TCargo, typename TSpec, typename TSegmentString, typename TEdgeMap, typename TOutGraph>
-inline void 
+inline void
 _createMatchingGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-					 TSegmentString& alignSeq,
-					 TEdgeMap& edgeMap,
-					 TOutGraph& gOut,
-					 TEdgeMap& edgeMapOut)			 
+                     TSegmentString& alignSeq,
+                     TEdgeMap& edgeMap,
+                     TOutGraph& gOut,
+                     TEdgeMap& edgeMapOut)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef String<TVertexDescriptor> TVertexString;
-
-	// Initialization
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-
-	// Create the matching graph
-	clear(edgeMapOut);
-	TSize alignSeqLen = length(alignSeq);
-	for(TSize i = 0; i<alignSeqLen;++i) {
-		TVertexString& alignSeq_i = alignSeq[i];
-		TSize len_i = length(alignSeq_i);
-		for(TSize j=0; j<len_i - 1; ++j) {
-			for(TSize k=j+1; k<len_i; ++k) {
-				TVertexDescriptor v1 = getValue(alignSeq_i, j);
-				TVertexDescriptor v2 = getValue(alignSeq_i, k);
-				if ((v1 == nilVertex) || (v2 == nilVertex)) continue;
-				
-				TVertexDescriptor v1New = findVertex(gOut, sequenceId(g, v1), fragmentBegin(g,v1));
-				if (v1New == nilVertex) v1New = addVertex(gOut, sequenceId(g, v1), fragmentBegin(g,v1), fragmentLength(g,v1));
-				TVertexDescriptor v2New = findVertex(gOut, sequenceId(g, v2), fragmentBegin(g,v2));
-				if (v2New == nilVertex) v2New = addVertex(gOut, sequenceId(g, v2), fragmentBegin(g,v2), fragmentLength(g,v2));
-			
-				TEdgeDescriptor e = findEdge(g, v1, v2);
-				addEdge(gOut, v1New, v2New, cargo(e));
-				appendValue(edgeMapOut, property(edgeMap, e));
-			}
-		}
-	}
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef String<TVertexDescriptor> TVertexString;
+
+    // Initialization
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+
+    // Create the matching graph
+    clear(edgeMapOut);
+    TSize alignSeqLen = length(alignSeq);
+    for(TSize i = 0; i<alignSeqLen;++i) {
+        TVertexString& alignSeq_i = alignSeq[i];
+        TSize len_i = length(alignSeq_i);
+        for(TSize j=0; j<len_i - 1; ++j) {
+            for(TSize k=j+1; k<len_i; ++k) {
+                TVertexDescriptor v1 = getValue(alignSeq_i, j);
+                TVertexDescriptor v2 = getValue(alignSeq_i, k);
+                if ((v1 == nilVertex) || (v2 == nilVertex)) continue;
+
+                TVertexDescriptor v1New = findVertex(gOut, sequenceId(g, v1), fragmentBegin(g,v1));
+                if (v1New == nilVertex) v1New = addVertex(gOut, sequenceId(g, v1), fragmentBegin(g,v1), fragmentLength(g,v1));
+                TVertexDescriptor v2New = findVertex(gOut, sequenceId(g, v2), fragmentBegin(g,v2));
+                if (v2New == nilVertex) v2New = addVertex(gOut, sequenceId(g, v2), fragmentBegin(g,v2), fragmentLength(g,v2));
+
+                TEdgeDescriptor e = findEdge(g, v1, v2);
+                addEdge(gOut, v1New, v2New, cargo(e));
+                appendValue(edgeMapOut, property(edgeMap, e));
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -252,183 +238,183 @@ _createMatchingGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
 template<typename TStringSet, typename TCargo, typename TSpec, typename TString, typename TOutString>
 inline TCargo
 heaviestMatching(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
-				 TString const& str1, 
-				 TString const& str2,
-				 TOutString& align) 
+                 TString const& str1,
+                 TString const& str2,
+                 TOutString& align)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef __int64 TLargeSize;
-	typedef typename Size<TStringSet>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename Value<TString>::Type TVertexSet;
-
-	TSize m = length(str1);  // How many sets of vertex descriptors in seq1
-	TSize n = length(str2);  // How many sets of vertex descriptors in seq1
-
-	// Size of the sequences
-	// Note for profile alignments every member of the sequence is a String!!! of vertex descriptors
-	TCargo divider = (TCargo) length(str1[0]) * (TCargo) length(str2[0]);
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	
-	// Fill the vertex to position map for str1
-	// Remember for each vertex descriptor the position in the sequence
-	typedef std::map<TVertexDescriptor, TSize> TVertexToPosMap;
-	typedef typename TVertexToPosMap::const_iterator TVertexToPosMapIter;
-	TVertexToPosMap map;
-	typedef typename Iterator<TString const>::Type TStringIterConst;
-	typedef typename Iterator<TVertexSet const>::Type TVertexSetIterConst;
-	TStringIterConst itStrEnd1 = end(str1);
-	TSize pos = 0;
-	for(TStringIterConst itStr1 = begin(str1);itStr1 != itStrEnd1;++itStr1, ++pos) {
-		TVertexSetIterConst itVEnd = end(getValue(itStr1));	
-		for(TVertexSetIterConst itV = begin(getValue(itStr1));itV != itVEnd;++itV) {
-			if (*itV != nilVertex) map.insert(std::make_pair(*itV, pos));
-		}
-	}
-
-	// Given a full graph, what positions are occupied?
-	typedef std::set<TLargeSize> TOccupiedPositions;
-	TOccupiedPositions occupiedPositions;
-	TStringIterConst itStrEnd2 = end(str2);
-	TSize posItStr2 = 0;
-	for(TStringIterConst itStr2 = begin(str2);itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
-		TVertexSetIterConst itVEnd = end(getValue(itStr2));
-		for(TVertexSetIterConst itV = begin(getValue(itStr2));itV != itVEnd;++itV) {
-			if (*itV != nilVertex) {
-				TOutEdgeIterator itOut(g, *itV);
-				for(;!atEnd(itOut); ++itOut) {
-					// Target vertex must be in the map
-					TVertexToPosMapIter pPos = map.find(targetVertex(itOut));
-					if (pPos != map.end()) occupiedPositions.insert( (TLargeSize) (pPos->second) * (TLargeSize) n + (TLargeSize) (n - posItStr2 - 1) );
-				}
-			}
-		}
-	}
-	// Map the occupied positions to slots
-	typedef std::map<TLargeSize, TSize> TPositionToSlotMap;
-	TPositionToSlotMap posToSlotMap;
-	TSize counter = 0;
-	for(typename TOccupiedPositions::const_iterator setIt = occupiedPositions.begin();setIt != occupiedPositions.end(); ++setIt, ++counter) {
-		posToSlotMap.insert(std::make_pair(*setIt, counter));
-	}
-	occupiedPositions.clear();
-
-	// Walk through str2 and fill in the weights of the actual edges
-	typedef String<TCargo> TWeights;
-	typedef typename Iterator<TWeights>::Type TWeightsIter;
-	TWeights weights;
-	resize(weights, posToSlotMap.size(),0);
-	posItStr2 = 0;
-	for(TStringIterConst itStr2 = begin(str2);itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
-		TVertexSetIterConst itVEnd = end(getValue(itStr2));
-		for(TVertexSetIterConst itV = begin(getValue(itStr2));itV != itVEnd;++itV) {
-			if (*itV != nilVertex) {
-				TOutEdgeIterator itOut(g, *itV);
-				for(;!atEnd(itOut); ++itOut) {
-					// Target vertex must be in the map
-					TVertexToPosMapIter pPos = map.find(targetVertex(itOut));
-					if (pPos != map.end()) weights[posToSlotMap[ (TLargeSize) (pPos->second) * (TLargeSize) n + (TLargeSize) (n - posItStr2 - 1) ]] += (TCargo) cargo(*itOut);
-				}
-			}
-		}
-	}
-	map.clear();
-	// Average weights
-	TWeightsIter itWeights = begin(weights);
-	TWeightsIter itWeightsEnd = begin(weights);
-	for(;itWeights != itWeightsEnd; ++itWeights) *itWeights /= divider;
-
-	// Create the match graph
-	Graph<Undirected<void> > matchGraph;
-	typedef typename VertexDescriptor<Graph<Undirected<void> > >::Type TVD;
-	String<bool> vertexMap;
-	resize(vertexMap, m + n, false);
-	for(TSize i = 0; i < m; ++i) addVertex(matchGraph);
-	for(TSize i = 0; i < n; ++i) value(vertexMap, addVertex(matchGraph)) = true;
-	for(typename TPositionToSlotMap::const_iterator mapIt = posToSlotMap.begin();mapIt != posToSlotMap.end(); ++mapIt) {
-		TLargeSize pos = mapIt->first;
-		TSize i = (TSize) (pos / (TLargeSize) n);   // Get the index in str1
-		TSize j = n - 1 - (TSize) (pos % (TLargeSize) n); // Get the index in str2
-		addEdge(matchGraph, i, m+j);
-	}
-
-	// Compute the best matching
-	typedef String<Pair<TVD, TVD> > TEdges;
-	TEdges edges;
-
-	//std::fstream strm;
-	//strm.open("Z:\\my_graph.dot", std::ios_base::out | std::ios_base::trunc);
-	//write(strm,matchGraph,DotDrawing());
-	//strm.close();
-
-	TCargo val = weightedBipartiteMatching(matchGraph, vertexMap, weights, edges);
-
-	// Retrieve the aligned segments
-	TSize seqsInStr1 = length(str1[0]);
-	TSize seqsInStr2 = length(str2[0]);
-	typedef typename Value<TString>::Type TVertexSet;
-	//typedef typename Iterator<TString const, Rooted>::Type TStringIter;
-	//typedef typename Iterator<TString, Rooted>::Type TSIter;
-	typedef typename Iterator<TVertexSet const, Rooted>::Type TVertexSetIter;
-	//typedef typename Iterator<TVertexSet, Rooted>::Type TIter;
-	clear(align);
-	// Retrieve all matches
-	String<bool> matchedVertices;
-	resize(matchedVertices, n + m, false);
-	typedef typename Iterator<TEdges>::Type TEdgesIter;
-	TEdgesIter itEdges = begin(edges);
-	TEdgesIter itEdgesEnd = end(edges);
-	for(;itEdges != itEdgesEnd; ++itEdges) {
-		TSize i = (value(itEdges)).i1;
-		TSize j = (value(itEdges)).i2 - m;
-		value(matchedVertices, i) = true;
-		value(matchedVertices, m+j) = true;
-		TVertexSet tmp;
-		resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
-		TVertexSetIter itVEnd = end(value(str1,i));
-		TSize count = 0;
-		for(TVertexSetIter itV = begin(value(str1,i));itV != itVEnd;++itV) {
-			tmp[count] = *itV;
-			++count;
-		}
-		TVertexSetIter itVEnd2 = end(value(str2,j));
-		for(TVertexSetIter itV2 = begin(value(str2,j));itV2 != itVEnd2;++itV2) {
-			tmp[count] = *itV2;
-			++count;
-		}
-		appendValue(align, tmp);
-	}
-	typedef typename Iterator<Graph<Undirected<void> >, VertexIterator>::Type TVertexIterator;
-	TVertexIterator itVertex(matchGraph);
-	for(;!atEnd(itVertex);++itVertex) {
-		if (getProperty(matchedVertices, *itVertex) == true) continue;
-		if (*itVertex < m) {
-			TSize i = *itVertex;
-			TVertexSet tmp;
-			resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
-			TVertexSetIter itVEnd = end(value(str1, i));
-			TSize count = 0;
-			for(TVertexSetIter itV = begin(value(str1, i));itV != itVEnd;++itV) {
-				tmp[count] = *itV;
-				++count;
-			}
-			appendValue(align, tmp);
-		} else {
-			TSize j = *itVertex - m;
-			TVertexSet tmp;
-			resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
-			TVertexSetIter itVEnd = end(value(str2, j));
-			TSize count = 0;
-			for(TVertexSetIter itV = begin(value(str2, j));itV != itVEnd;++itV) {
-				tmp[count] = *itV;
-				++count;
-			}
-			appendValue(align, tmp);
-		}
-	}
-
-	return val;
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef __int64 TLargeSize;
+    typedef typename Size<TStringSet>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename Value<TString>::Type TVertexSet;
+
+    TSize m = length(str1);  // How many sets of vertex descriptors in seq1
+    TSize n = length(str2);  // How many sets of vertex descriptors in seq1
+
+    // Size of the sequences
+    // Note for profile alignments every member of the sequence is a String!!! of vertex descriptors
+    TCargo divider = (TCargo) length(str1[0]) * (TCargo) length(str2[0]);
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+
+    // Fill the vertex to position map for str1
+    // Remember for each vertex descriptor the position in the sequence
+    typedef std::map<TVertexDescriptor, TSize> TVertexToPosMap;
+    typedef typename TVertexToPosMap::const_iterator TVertexToPosMapIter;
+    TVertexToPosMap map;
+    typedef typename Iterator<TString const>::Type TStringIterConst;
+    typedef typename Iterator<TVertexSet const>::Type TVertexSetIterConst;
+    TStringIterConst itStrEnd1 = end(str1);
+    TSize pos = 0;
+    for(TStringIterConst itStr1 = begin(str1);itStr1 != itStrEnd1;++itStr1, ++pos) {
+        TVertexSetIterConst itVEnd = end(getValue(itStr1));
+        for(TVertexSetIterConst itV = begin(getValue(itStr1));itV != itVEnd;++itV) {
+            if (*itV != nilVertex) map.insert(std::make_pair(*itV, pos));
+        }
+    }
+
+    // Given a full graph, what positions are occupied?
+    typedef std::set<TLargeSize> TOccupiedPositions;
+    TOccupiedPositions occupiedPositions;
+    TStringIterConst itStrEnd2 = end(str2);
+    TSize posItStr2 = 0;
+    for(TStringIterConst itStr2 = begin(str2);itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
+        TVertexSetIterConst itVEnd = end(getValue(itStr2));
+        for(TVertexSetIterConst itV = begin(getValue(itStr2));itV != itVEnd;++itV) {
+            if (*itV != nilVertex) {
+                TOutEdgeIterator itOut(g, *itV);
+                for(;!atEnd(itOut); ++itOut) {
+                    // Target vertex must be in the map
+                    TVertexToPosMapIter pPos = map.find(targetVertex(itOut));
+                    if (pPos != map.end()) occupiedPositions.insert( (TLargeSize) (pPos->second) * (TLargeSize) n + (TLargeSize) (n - posItStr2 - 1) );
+                }
+            }
+        }
+    }
+    // Map the occupied positions to slots
+    typedef std::map<TLargeSize, TSize> TPositionToSlotMap;
+    TPositionToSlotMap posToSlotMap;
+    TSize counter = 0;
+    for(typename TOccupiedPositions::const_iterator setIt = occupiedPositions.begin();setIt != occupiedPositions.end(); ++setIt, ++counter) {
+        posToSlotMap.insert(std::make_pair(*setIt, counter));
+    }
+    occupiedPositions.clear();
+
+    // Walk through str2 and fill in the weights of the actual edges
+    typedef String<TCargo> TWeights;
+    typedef typename Iterator<TWeights>::Type TWeightsIter;
+    TWeights weights;
+    resize(weights, posToSlotMap.size(),0);
+    posItStr2 = 0;
+    for(TStringIterConst itStr2 = begin(str2);itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
+        TVertexSetIterConst itVEnd = end(getValue(itStr2));
+        for(TVertexSetIterConst itV = begin(getValue(itStr2));itV != itVEnd;++itV) {
+            if (*itV != nilVertex) {
+                TOutEdgeIterator itOut(g, *itV);
+                for(;!atEnd(itOut); ++itOut) {
+                    // Target vertex must be in the map
+                    TVertexToPosMapIter pPos = map.find(targetVertex(itOut));
+                    if (pPos != map.end()) weights[posToSlotMap[ (TLargeSize) (pPos->second) * (TLargeSize) n + (TLargeSize) (n - posItStr2 - 1) ]] += (TCargo) cargo(*itOut);
+                }
+            }
+        }
+    }
+    map.clear();
+    // Average weights
+    TWeightsIter itWeights = begin(weights);
+    TWeightsIter itWeightsEnd = begin(weights);
+    for(;itWeights != itWeightsEnd; ++itWeights) *itWeights /= divider;
+
+    // Create the match graph
+    Graph<Undirected<void> > matchGraph;
+    typedef typename VertexDescriptor<Graph<Undirected<void> > >::Type TVD;
+    String<bool> vertexMap;
+    resize(vertexMap, m + n, false);
+    for(TSize i = 0; i < m; ++i) addVertex(matchGraph);
+    for(TSize i = 0; i < n; ++i) value(vertexMap, addVertex(matchGraph)) = true;
+    for(typename TPositionToSlotMap::const_iterator mapIt = posToSlotMap.begin();mapIt != posToSlotMap.end(); ++mapIt) {
+        TLargeSize pos = mapIt->first;
+        TSize i = (TSize) (pos / (TLargeSize) n);   // Get the index in str1
+        TSize j = n - 1 - (TSize) (pos % (TLargeSize) n); // Get the index in str2
+        addEdge(matchGraph, i, m+j);
+    }
+
+    // Compute the best matching
+    typedef String<Pair<TVD, TVD> > TEdges;
+    TEdges edges;
+
+    //std::fstream strm;
+    //strm.open("Z:\\my_graph.dot", std::ios_base::out | std::ios_base::trunc);
+    //writeRecords(strm,matchGraph,DotDrawing());
+    //strm.close();
+
+    TCargo val = weightedBipartiteMatching(matchGraph, vertexMap, weights, edges);
+
+    // Retrieve the aligned segments
+    TSize seqsInStr1 = length(str1[0]);
+    TSize seqsInStr2 = length(str2[0]);
+    typedef typename Value<TString>::Type TVertexSet;
+    //typedef typename Iterator<TString const, Rooted>::Type TStringIter;
+    //typedef typename Iterator<TString, Rooted>::Type TSIter;
+    typedef typename Iterator<TVertexSet const, Rooted>::Type TVertexSetIter;
+    //typedef typename Iterator<TVertexSet, Rooted>::Type TIter;
+    clear(align);
+    // Retrieve all matches
+    String<bool> matchedVertices;
+    resize(matchedVertices, n + m, false);
+    typedef typename Iterator<TEdges>::Type TEdgesIter;
+    TEdgesIter itEdges = begin(edges);
+    TEdgesIter itEdgesEnd = end(edges);
+    for(;itEdges != itEdgesEnd; ++itEdges) {
+        TSize i = (value(itEdges)).i1;
+        TSize j = (value(itEdges)).i2 - m;
+        value(matchedVertices, i) = true;
+        value(matchedVertices, m+j) = true;
+        TVertexSet tmp;
+        resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
+        TVertexSetIter itVEnd = end(value(str1,i));
+        TSize count = 0;
+        for(TVertexSetIter itV = begin(value(str1,i));itV != itVEnd;++itV) {
+            tmp[count] = *itV;
+            ++count;
+        }
+        TVertexSetIter itVEnd2 = end(value(str2,j));
+        for(TVertexSetIter itV2 = begin(value(str2,j));itV2 != itVEnd2;++itV2) {
+            tmp[count] = *itV2;
+            ++count;
+        }
+        appendValue(align, tmp);
+    }
+    typedef typename Iterator<Graph<Undirected<void> >, VertexIterator>::Type TVertexIterator;
+    TVertexIterator itVertex(matchGraph);
+    for(;!atEnd(itVertex);++itVertex) {
+        if (getProperty(matchedVertices, *itVertex) == true) continue;
+        if (*itVertex < m) {
+            TSize i = *itVertex;
+            TVertexSet tmp;
+            resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
+            TVertexSetIter itVEnd = end(value(str1, i));
+            TSize count = 0;
+            for(TVertexSetIter itV = begin(value(str1, i));itV != itVEnd;++itV) {
+                tmp[count] = *itV;
+                ++count;
+            }
+            appendValue(align, tmp);
+        } else {
+            TSize j = *itVertex - m;
+            TVertexSet tmp;
+            resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
+            TVertexSetIter itVEnd = end(value(str2, j));
+            TSize count = 0;
+            for(TVertexSetIter itV = begin(value(str2, j));itV != itVEnd;++itV) {
+                tmp[count] = *itV;
+                ++count;
+            }
+            appendValue(align, tmp);
+        }
+    }
+
+    return val;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -436,40 +422,40 @@ heaviestMatching(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
 template<typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TVertexDescriptor, typename TSequence>
 inline void
 _recursiveProgressiveMatching(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-							  TGuideTree& tree,
-							  TVertexDescriptor const root,
-							  TSequence& alignSeq)
+                              TGuideTree& tree,
+                              TVertexDescriptor const root,
+                              TSequence& alignSeq)
 {
-	//typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	//typedef typename Size<TGraph>::Type TSize;
-	//typedef typename Id<TGraph>::Type TId;
-	typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjacencyIterator;
-	//typedef typename Iterator<TGuideTree, DfsPreorder>::Type TDfsPreorderIterator;
-
-	if(isLeaf(tree, root)) {
-		_buildLeafString(g, root, alignSeq);
-	} else {
-		// Align the two children (Binary tree)
-		typedef String<String<TVertexDescriptor> > TSegmentString;
-		TSegmentString seq1;
-		TSegmentString seq2;
-		TAdjacencyIterator adjIt(tree, root);
-		_recursiveProgressiveMatching(g,tree, *adjIt, seq1);
-		goNext(adjIt);
-		_recursiveProgressiveMatching(g,tree, *adjIt, seq2);
-
-		heaviestMatching(g, seq1, seq2, alignSeq);
-
-		//// Debug Code
-		//for(TSize i = 0; i<length(alignSeq);++i) {
-		//	std::cout << '(';
-		//	for(TSize j=0; j<length(alignSeq[i]);++j) {
-		//		std::cout << getValue(alignSeq[i], j) << ',';
-		//	}
-		//	std::cout << ')' << ',';
-		//}
-		//std::cout << std::endl;
-	}
+    //typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    //typedef typename Size<TGraph>::Type TSize;
+    //typedef typename Id<TGraph>::Type TId;
+    typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjacencyIterator;
+    //typedef typename Iterator<TGuideTree, DfsPreorder>::Type TDfsPreorderIterator;
+
+    if(isLeaf(tree, root)) {
+        _buildLeafString(g, root, alignSeq);
+    } else {
+        // Align the two children (Binary tree)
+        typedef String<String<TVertexDescriptor> > TSegmentString;
+        TSegmentString seq1;
+        TSegmentString seq2;
+        TAdjacencyIterator adjIt(tree, root);
+        _recursiveProgressiveMatching(g,tree, *adjIt, seq1);
+        goNext(adjIt);
+        _recursiveProgressiveMatching(g,tree, *adjIt, seq2);
+
+        heaviestMatching(g, seq1, seq2, alignSeq);
+
+        //// Debug Code
+        //for(TSize i = 0; i<length(alignSeq);++i) {
+        //    std::cout << '(';
+        //    for(TSize j=0; j<length(alignSeq[i]);++j) {
+        //        std::cout << getValue(alignSeq[i], j) << ',';
+        //    }
+        //    std::cout << ')' << ',';
+        //}
+        //std::cout << std::endl;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -477,23 +463,23 @@ _recursiveProgressiveMatching(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
 template<typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TEdgeMap, typename TOutGraph>
 inline void
 progressiveMatching(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
-					TGuideTree& tree,
-					TEdgeMap& edgeMap,
-					TOutGraph& gOut,
-					TEdgeMap& edgeMapOut)
+                    TGuideTree& tree,
+                    TEdgeMap& edgeMap,
+                    TOutGraph& gOut,
+                    TEdgeMap& edgeMapOut)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	//typedef typename Size<TGraph>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef String<TVertexDescriptor> TVertexString;
-	typedef String<TVertexString> TSegmentString;
-
-	// Perform progressive alignment
-	TSegmentString alignSeq;
-	_recursiveProgressiveMatching(g,tree,getRoot(tree),alignSeq);
-
-	// Create the alignment graph
-	_createMatchingGraph(g, alignSeq, edgeMap, gOut, edgeMapOut);
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    //typedef typename Size<TGraph>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef String<TVertexDescriptor> TVertexString;
+    typedef String<TVertexString> TSegmentString;
+
+    // Perform progressive alignment
+    TSegmentString alignSeq;
+    _recursiveProgressiveMatching(g,tree,getRoot(tree),alignSeq);
+
+    // Create the alignment graph
+    _createMatchingGraph(g, alignSeq, edgeMap, gOut, edgeMapOut);
 }
 
 
diff --git a/seqan/graph_msa/graph_align_tcoffee_refinement.h b/seqan/graph_msa/graph_align_tcoffee_refinement.h
index 6fd0fcb..18f8f33 100644
--- a/seqan/graph_msa/graph_align_tcoffee_refinement.h
+++ b/seqan/graph_msa/graph_align_tcoffee_refinement.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,40 +40,40 @@ namespace SEQAN_NAMESPACE_MAIN
 
 template<typename TScore, typename TSc>
 inline void
-_matchScore(TScore&, 
-			 TSc) 
+_matchScore(TScore&,
+             TSc)
 {
-	// No operation
+    // No operation
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template<typename TScore, typename TSc>
 inline void
-_mismatchScore(TScore&, 
-				TSc) 
+_mismatchScore(TScore&,
+                TSc)
 {
-	// No operation
+    // No operation
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TSc>
 inline void
-_matchScore(Score<TValue, Simple>& sc, 
-			 TSc msc) 
+_matchScore(Score<TValue, Simple>& sc,
+             TSc msc)
 {
-	sc.data_match = msc;
+    sc.data_match = msc;
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template<typename TValue, typename TSc>
 inline void
-_mismatchScore(Score<TValue, Simple>& sc, 
-				TSc mmsc) 
+_mismatchScore(Score<TValue, Simple>& sc,
+                TSc mmsc)
 {
-	sc.data_mismatch = mmsc;
+    sc.data_mismatch = mmsc;
 }
 
 
@@ -90,425 +90,425 @@ template <typename TValue, typename TScoreMember>
 class Score<TValue, ProfileProfileScore<TScoreMember> >
 {
 public:
-	TScoreMember sc;
-
-	Score() {}
-
-	template<typename TSpec>
-	Score(Score<TValue, TSpec>& old_sc) 
-	{
-		sc.data_gap_extend = scoreGapExtend(old_sc);
-		sc.data_gap_open = scoreGapOpen(old_sc);
-	}
-
-	Score(Score<TValue, Simple>& old_sc) 
-	{
-		sc.data_gap_extend = scoreGapExtend(old_sc);
-		sc.data_gap_open = scoreGapOpen(old_sc);
-		_matchScore(sc, scoreMatch(old_sc));
-		_mismatchScore(sc, scoreMismatch(old_sc));
-	}
-
-	Score(TValue gap_extend, TValue gap_open) 
-	{
-		sc.data_gap_extend = gap_extend;
-		sc.data_gap_open = gap_open;
-	}
-
-	Score(TValue match, TValue mismatch, TValue gap_extend, TValue gap_open)
-	{
-		sc.data_gap_extend = gap_extend;
-		sc.data_gap_open = gap_open;
-		_matchScore(sc, match);
-		_mismatchScore(sc, mismatch);
-	}
+    TScoreMember sc;
+
+    Score() {}
+
+    template<typename TSpec>
+    Score(Score<TValue, TSpec>& old_sc)
+    {
+        sc.data_gap_extend = scoreGapExtend(old_sc);
+        sc.data_gap_open = scoreGapOpen(old_sc);
+    }
+
+    Score(Score<TValue, Simple>& old_sc)
+    {
+        sc.data_gap_extend = scoreGapExtend(old_sc);
+        sc.data_gap_open = scoreGapOpen(old_sc);
+        _matchScore(sc, scoreMatch(old_sc));
+        _mismatchScore(sc, scoreMismatch(old_sc));
+    }
+
+    Score(TValue gap_extend, TValue gap_open)
+    {
+        sc.data_gap_extend = gap_extend;
+        sc.data_gap_open = gap_open;
+    }
+
+    Score(TValue match, TValue mismatch, TValue gap_extend, TValue gap_open)
+    {
+        sc.data_gap_extend = gap_extend;
+        sc.data_gap_open = gap_open;
+        _matchScore(sc, match);
+        _mismatchScore(sc, mismatch);
+    }
 };
 
 
 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapExtendHorizontal(
-	Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
-	TPos1 pos1,
-	TPos2,
-	TSeq1 const& seq1,
-	TSeq2 const&)
+    Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
+    TPos1 pos1,
+    TPos2,
+    TSeq1 const& seq1,
+    TSeq2 const&)
 {
-	typedef typename Size<TSeq1>::Type TSize;
-	typedef typename Value<TSeq1>::Type TAlphabet1;
-	//typedef typename Value<TSeq2>::Type TAlphabet2;
-	typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
-
-	// Last character is a gap
-	// std::cout << seq1[pos1] << std::endl;
-
-	TSize alph_size = ValueSize<TSourceValue>::VALUE;
-	TValue n1 = 0;
-	for(TSize i = 0; i < alph_size; ++i) n1 += seq1[pos1].count[i];
-	TValue totalSc = n1 * scoreGapExtend(me.sc);
-	n1 += seq1[pos1].count[alph_size];
-	//std::cout <<  totalSc / n1 << ',';
-	return totalSc / n1;
+    typedef typename Size<TSeq1>::Type TSize;
+    typedef typename Value<TSeq1>::Type TAlphabet1;
+    //typedef typename Value<TSeq2>::Type TAlphabet2;
+    typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
+
+    // Last character is a gap
+    // std::cout << seq1[pos1] << std::endl;
+
+    TSize alph_size = ValueSize<TSourceValue>::VALUE;
+    TValue n1 = 0;
+    for(TSize i = 0; i < alph_size; ++i) n1 += seq1[pos1].count[i];
+    TValue totalSc = n1 * scoreGapExtend(me.sc);
+    n1 += seq1[pos1].count[alph_size];
+    //std::cout <<  totalSc / n1 << ',';
+    return totalSc / n1;
 }
 
 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapOpenHorizontal(
-	Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
-	TPos1 pos1,
-	TPos2,
-	TSeq1 const & seq1,
-	TSeq2 const &)
+    Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
+    TPos1 pos1,
+    TPos2,
+    TSeq1 const & seq1,
+    TSeq2 const &)
 {
-	typedef typename Size<TSeq1>::Type TSize;
-	typedef typename Value<TSeq1>::Type TAlphabet1;
-	//typedef typename Value<TSeq2>::Type TAlphabet2;
-	typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
-
-	TSize alph_size = ValueSize<TSourceValue>::VALUE;
-	TValue n1 = 0;
-	for(TSize i = 0; i < alph_size+1; ++i) n1 += seq1[pos1].count[i];
-	TSize newGapOpen = n1;
-	if ((pos1) && (seq1[pos1 - 1].count[alph_size] < seq1[pos1].count[alph_size])) {
-		newGapOpen -= (seq1[pos1].count[alph_size] - seq1[pos1 - 1].count[alph_size]);
-	} else if (!pos1) {
-		newGapOpen -= seq1[pos1].count[alph_size];
-	}
-	TValue totalSc = newGapOpen * scoreGapOpen(me.sc);
-	return totalSc / n1;
+    typedef typename Size<TSeq1>::Type TSize;
+    typedef typename Value<TSeq1>::Type TAlphabet1;
+    //typedef typename Value<TSeq2>::Type TAlphabet2;
+    typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
+
+    TSize alph_size = ValueSize<TSourceValue>::VALUE;
+    TValue n1 = 0;
+    for(TSize i = 0; i < alph_size+1; ++i) n1 += seq1[pos1].count[i];
+    TSize newGapOpen = n1;
+    if ((pos1) && (seq1[pos1 - 1].count[alph_size] < seq1[pos1].count[alph_size])) {
+        newGapOpen -= (seq1[pos1].count[alph_size] - seq1[pos1 - 1].count[alph_size]);
+    } else if (!pos1) {
+        newGapOpen -= seq1[pos1].count[alph_size];
+    }
+    TValue totalSc = newGapOpen * scoreGapOpen(me.sc);
+    return totalSc / n1;
 }
 
 
 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapExtendVertical(
-	Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
-	TPos1,
-	TPos2 pos2,
-	TSeq1 const &,
-	TSeq2 const & seq2)
+    Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
+    TPos1,
+    TPos2 pos2,
+    TSeq1 const &,
+    TSeq2 const & seq2)
 {
-	typedef typename Size<TSeq1>::Type TSize;
-	typedef typename Value<TSeq1>::Type TAlphabet1;
-	//typedef typename Value<TSeq2>::Type TAlphabet2;
-	typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
-
-	// Last character is a gap
-	// std::cout << seq2[pos2] << std::endl;
-
-	TSize alph_size = ValueSize<TSourceValue>::VALUE;
-	TValue n2 = 0;
-	for(TSize j = 0; j < alph_size; ++j) n2 += seq2[pos2].count[j];
-	TValue totalSc = n2 * scoreGapExtend(me.sc);
-	n2 += seq2[pos2].count[alph_size];
-	//std::cout <<  totalSc / n2 << ',';
-	return totalSc / n2;
+    typedef typename Size<TSeq1>::Type TSize;
+    typedef typename Value<TSeq1>::Type TAlphabet1;
+    //typedef typename Value<TSeq2>::Type TAlphabet2;
+    typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
+
+    // Last character is a gap
+    // std::cout << seq2[pos2] << std::endl;
+
+    TSize alph_size = ValueSize<TSourceValue>::VALUE;
+    TValue n2 = 0;
+    for(TSize j = 0; j < alph_size; ++j) n2 += seq2[pos2].count[j];
+    TValue totalSc = n2 * scoreGapExtend(me.sc);
+    n2 += seq2[pos2].count[alph_size];
+    //std::cout <<  totalSc / n2 << ',';
+    return totalSc / n2;
 }
 
 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2>
 inline TValue
 scoreGapOpenVertical(
-	Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
-	TPos1,
-	TPos2 pos2,
-	TSeq1 const &,
-	TSeq2 const & seq2)
+    Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
+    TPos1,
+    TPos2 pos2,
+    TSeq1 const &,
+    TSeq2 const & seq2)
 {
-	typedef typename Size<TSeq1>::Type TSize;
-	typedef typename Value<TSeq1>::Type TAlphabet1;
-	//typedef typename Value<TSeq2>::Type TAlphabet2;
-	typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
-
-	TSize alph_size = ValueSize<TSourceValue>::VALUE;
-	TValue n2 = 0;
-	for(TSize j = 0; j < alph_size+1; ++j) n2 += seq2[pos2].count[j];
-	TSize newGapOpen = n2;
-	if ((pos2) && (seq2[pos2 - 1].count[alph_size] < seq2[pos2].count[alph_size])) {
-		newGapOpen -= (seq2[pos2].count[alph_size] - seq2[pos2 - 1].count[alph_size]);
-	} else if (!pos2) {
-		newGapOpen -= seq2[pos2].count[alph_size];
-	}
-	TValue totalSc = newGapOpen * scoreGapOpen(me.sc);
-	return totalSc / n2;
+    typedef typename Size<TSeq1>::Type TSize;
+    typedef typename Value<TSeq1>::Type TAlphabet1;
+    //typedef typename Value<TSeq2>::Type TAlphabet2;
+    typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
+
+    TSize alph_size = ValueSize<TSourceValue>::VALUE;
+    TValue n2 = 0;
+    for(TSize j = 0; j < alph_size+1; ++j) n2 += seq2[pos2].count[j];
+    TSize newGapOpen = n2;
+    if ((pos2) && (seq2[pos2 - 1].count[alph_size] < seq2[pos2].count[alph_size])) {
+        newGapOpen -= (seq2[pos2].count[alph_size] - seq2[pos2 - 1].count[alph_size]);
+    } else if (!pos2) {
+        newGapOpen -= seq2[pos2].count[alph_size];
+    }
+    TValue totalSc = newGapOpen * scoreGapOpen(me.sc);
+    return totalSc / n2;
 }
 
 
 template <typename TValue, typename TScoreMember, typename TPos1, typename TPos2, typename TSeq1, typename TSeq2>
 inline TValue
 score(Score<TValue, ProfileProfileScore<TScoreMember> > const & me,
-	  TPos1 pos1,
-	  TPos2 pos2,
-	  TSeq1 const &seq1,
-	  TSeq2 const &seq2)
+      TPos1 pos1,
+      TPos2 pos2,
+      TSeq1 const &seq1,
+      TSeq2 const &seq2)
 {
-	typedef typename Size<TSeq1>::Type TSize;
-	typedef typename Value<TSeq1>::Type TAlphabet1;
-	//typedef typename Value<TSeq2>::Type TAlphabet2;
-	typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
-
-	// Last character is a gap
-	//std::cout << seq1[pos1] << std::endl;
-	//std::cout << seq2[pos2] << std::endl;
-
-	TValue totalSc = 0;
-	TSize alph_size = ValueSize<TSourceValue>::VALUE;
-	TValue n1 = 0;
-	TValue n2 = 0;
-	for(TSize j = 0; j < alph_size; ++j) n2 += seq2[pos2].count[j];
-	for(TSize i = 0; i < alph_size; ++i) {
-		if (seq1[pos1].count[i]) {
-			n1 += seq1[pos1].count[i];
-			for(TSize j = 0; j < alph_size; ++j) {
-				if (seq2[pos2].count[j]) {
-					//std::cout << TSourceValue(i) << ',' << TSourceValue(j) << ',' << score(me.sc, TSourceValue(i), TSourceValue(j)) << std::endl;
-					totalSc += seq1[pos1].count[i] * seq2[pos2].count[j] * score(me.sc, TSourceValue(i), TSourceValue(j));
-				}
-			}
-		}
-	}
-	totalSc += n2 * seq1[pos1].count[alph_size] * scoreGapExtend(me.sc);
-	totalSc += n1 * seq2[pos2].count[alph_size] * scoreGapExtend(me.sc);
-	n1 += seq1[pos1].count[alph_size];
-	n2 += seq2[pos2].count[alph_size];
-	//std::cout <<  totalSc / (n1 * n2) << ',';
-	return totalSc / (n1 * n2);
+    typedef typename Size<TSeq1>::Type TSize;
+    typedef typename Value<TSeq1>::Type TAlphabet1;
+    //typedef typename Value<TSeq2>::Type TAlphabet2;
+    typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
+
+    // Last character is a gap
+    //std::cout << seq1[pos1] << std::endl;
+    //std::cout << seq2[pos2] << std::endl;
+
+    TValue totalSc = 0;
+    TSize alph_size = ValueSize<TSourceValue>::VALUE;
+    TValue n1 = 0;
+    TValue n2 = 0;
+    for(TSize j = 0; j < alph_size; ++j) n2 += seq2[pos2].count[j];
+    for(TSize i = 0; i < alph_size; ++i) {
+        if (seq1[pos1].count[i]) {
+            n1 += seq1[pos1].count[i];
+            for(TSize j = 0; j < alph_size; ++j) {
+                if (seq2[pos2].count[j]) {
+                    //std::cout << TSourceValue(i) << ',' << TSourceValue(j) << ',' << score(me.sc, TSourceValue(i), TSourceValue(j)) << std::endl;
+                    totalSc += seq1[pos1].count[i] * seq2[pos2].count[j] * score(me.sc, TSourceValue(i), TSourceValue(j));
+                }
+            }
+        }
+    }
+    totalSc += n2 * seq1[pos1].count[alph_size] * scoreGapExtend(me.sc);
+    totalSc += n1 * seq2[pos2].count[alph_size] * scoreGapExtend(me.sc);
+    n1 += seq1[pos1].count[alph_size];
+    n2 += seq2[pos2].count[alph_size];
+    //std::cout <<  totalSc / (n1 * n2) << ',';
+    return totalSc / (n1 * n2);
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TValue, typename TSpec, typename TSize, typename TAlphabet, typename TScore> 
+template<typename TValue, typename TSpec, typename TSize, typename TAlphabet, typename TScore>
 inline void
 _msaRefinement(String<TValue, TSpec>& mat,
-			   TSize nseq,
-			   TSize splitPos,
-			   TScore& sc,
-			   TAlphabet)
+               TSize nseq,
+               TSize splitPos,
+               TScore& sc,
+               TAlphabet)
 {
-	// Is it a valid split?
-	if ((splitPos == 0) || (splitPos > nseq - 1)) return;
-
-	// Initialization
-	typedef String<TValue, TSpec> TAlignMat;
-	typedef typename Iterator<TAlignMat, Standard>::Type TMatIter;
-	TSize alignLen = length(mat) / nseq;
-
-	//// Debug code
-	//for(TSize row = 0; row < nseq; ++row) {
-	//	for(TSize col = 0; col < alignLen; ++col) {
-	//		std::cout << mat[row * alignLen + col];
-	//	}
-	//	std::cout << std::endl;
-	//}
-
-	char gapChar = gapValue<char>();
-	TSize nseq1 = splitPos;
-	TSize nseq2 = nseq - nseq1;
-	TSize gapPos = ValueSize<TAlphabet>::VALUE;
-	typedef ProfileChar<TAlphabet> TProfile;
-	typedef String<TProfile> TProfileString;
-	typedef typename Iterator<TProfileString, Standard>::Type TProfIter;
-	TProfileString prof1;
-	TProfileString prof2;
-	resize(prof1, alignLen, TProfile());
-	resize(prof2, alignLen, TProfile());
-	TMatIter itMat = begin(mat, Standard());
-	TMatIter itMatEnd = begin(mat, Standard());
-	itMatEnd += nseq1 * alignLen;
-	TProfIter itProf = begin(prof1, Standard());
-	for(TSize i = 0;itMat != itMatEnd;++itMat, ++itProf, ++i) {
-		if (i % alignLen == 0) itProf = begin(prof1, Standard());
-		if (*itMat == gapChar) ++(itProf->count[gapPos]);
-		else ++(itProf->count[ordValue((TAlphabet) *itMat)]);
-	}
-	itProf = begin(prof2, Standard());
-	itMatEnd = end(mat, Standard());
-	for(TSize i = 0;itMat != itMatEnd;++itMat, ++itProf, ++i) {
-		if (i % alignLen == 0) itProf = begin(prof2, Standard());
-		if (*itMat == gapChar) ++(itProf->count[gapPos]);
-		else ++(itProf->count[ordValue((TAlphabet) *itMat)]);
-	}
-
-
-	TProfileString alignProf1;
-	reserve(alignProf1, alignLen);
-	itProf = begin(prof1, Standard());
-	TProfIter itProfEnd = end(prof1, Standard());
-	typedef String<TSize> TDelGap;
-	typedef typename Iterator<TDelGap, Standard>::Type TDelGapIter;
-	TDelGap delGapCol;
-	for(TSize i = 0;itProf != itProfEnd;++itProf, ++i) {
-		if (itProf->count[gapPos] != nseq1) appendValue(alignProf1, *itProf);
-		else appendValue(delGapCol, i, Generous());
-	}
-	TDelGapIter itDelGap = begin(delGapCol, Standard());
-	TDelGapIter itDelGapEnd = end(delGapCol, Standard());
-	TAlignMat mat1;
-	TSize alignLen1 = alignLen - length(delGapCol);
-	resize(mat1, nseq1 * alignLen1);
-	itMat = begin(mat, Standard());
-	itMatEnd = begin(mat, Standard());
-	itMatEnd += nseq1 * alignLen;
-	TMatIter itMat1 = begin(mat1, Standard());
-	for(TSize col = 0;itMat != itMatEnd;++itMat, ++col) {
-		if (col % alignLen == 0) itDelGap = begin(delGapCol, Standard());
-		if ((itDelGap != itDelGapEnd) && (col % alignLen == *itDelGap)) {
-			++itDelGap;
-			continue;
-		}
-		*itMat1 = *itMat;
-		++itMat1;
-	}
-
-	//// Debug code
-	//for(TSize row = 0; row < nseq1; ++row) {
-	//	for(TSize col = 0; col < alignLen1; ++col) {
-	//		std::cout << mat1[row * alignLen1 + col];
-	//	}
-	//	std::cout << std::endl;
-	//}
-
-
-	TProfileString alignProf2;
-	reserve(alignProf2, alignLen);
-	itProf = begin(prof2, Standard());
-	itProfEnd = end(prof2, Standard());
-	clear(delGapCol);
-	for(TSize i = 0;itProf != itProfEnd;++itProf, ++i) {
-		if (itProf->count[gapPos] != nseq2) appendValue(alignProf2, *itProf);
-		else appendValue(delGapCol, i, Generous());
-	}
-	itDelGap = begin(delGapCol, Standard());
-	itDelGapEnd = end(delGapCol, Standard());
-	TAlignMat mat2;
-	TSize alignLen2 = alignLen - length(delGapCol);
-	resize(mat2, nseq2 * alignLen2);
-	itMatEnd = end(mat, Standard());
-	TMatIter itMat2 = begin(mat2, Standard());
-	for(TSize col = 0;itMat != itMatEnd;++itMat, ++col) {
-		if (col % alignLen == 0) itDelGap = begin(delGapCol, Standard());
-		if ((itDelGap != itDelGapEnd) && (col % alignLen == *itDelGap)) {
-			++itDelGap;
-			continue;
-		}
-		*itMat2 = *itMat;
-		++itMat2;
-	}
-
-	//// Debug code
-	//for(TSize row = 0; row < nseq2; ++row) {
-	//	for(TSize col = 0; col < alignLen2; ++col) {
-	//		std::cout << mat2[row * alignLen2 + col];
-	//	}
-	//	std::cout << std::endl;
-	//}
-
-
-	// ReAlign the consensus with the sequence
-	typedef StringSet<TProfileString, Dependent<> > TStringSet;
-	TStringSet pairSet;
-	appendValue(pairSet, alignProf1);
-	appendValue(pairSet, alignProf2);
-
-	typedef String<Fragment<> > TFragmentString;
-	TFragmentString matches;
-	globalAlignment(matches, pairSet, sc, Gotoh());
-	
-	typedef typename Iterator<TFragmentString, Standard>::Type TFragIter;
-	TFragIter fragIt = end(matches, Standard() );
-	TFragIter fragItEnd = begin(matches, Standard() );
-	typedef String<TSize> TInsertPattern;
-	typedef typename Iterator<TInsertPattern, Standard>::Type TInsertIter;
-	TInsertPattern insertPattern1;
-	TInsertPattern insertPattern2;
-	TSize begin1Pos = 0;
-	TSize begin2Pos = 0;
-	if (fragIt != fragItEnd) {
-		do {
-			--fragIt;
-			appendValue(insertPattern1, fragIt->begin2 - begin2Pos, Generous());
-			appendValue(insertPattern1, fragIt->begin1 - begin1Pos, Generous());
-			appendValue(insertPattern1, fragIt->len, Generous());
-			appendValue(insertPattern2, fragIt->begin2 - begin2Pos, Generous());
-			appendValue(insertPattern2, fragIt->begin1 - begin1Pos, Generous());
-			appendValue(insertPattern2, fragIt->len, Generous());
-			begin1Pos = fragIt->begin1 + fragIt->len;
-			begin2Pos = fragIt->begin2 + fragIt->len;
-		} while (fragIt != fragItEnd);
-	}
-	appendValue(insertPattern1, alignLen2 - begin2Pos, Generous());
-	appendValue(insertPattern1, alignLen1 - begin1Pos, Generous());
-	appendValue(insertPattern2, alignLen2 - begin2Pos, Generous());
-	appendValue(insertPattern2, alignLen1 - begin1Pos, Generous());
-	clear(matches);
-	
-	TInsertIter itInsert = begin(insertPattern1, Standard());
-	TInsertIter itInsertEnd = end(insertPattern1, Standard());
-	TSize totalAlignLen = 0;
-	for(;itInsert != itInsertEnd; ++itInsert) totalAlignLen += *itInsert;
-	itMat1 = begin(mat1, Standard());
-	TMatIter itMat1End = end(mat1, Standard());
-	clear(mat);
-	while(itMat1 != itMat1End) {
-		itInsert = begin(insertPattern1, Standard());
-		for(TSize i = 0; i < *itInsert; ++i) appendValue(mat, gapChar, Generous());
-		++itInsert;
-		for(TSize i = 0; i < *itInsert; ++i, ++itMat1) appendValue(mat, *itMat1, Generous());
-		++itInsert;
-		while(itInsert!=itInsertEnd) {
-			for(TSize i = 0; i < *itInsert; ++i, ++itMat1) appendValue(mat, *itMat1, Generous());
-			++itInsert;
-			for(TSize i = 0; i < *itInsert; ++i) appendValue(mat, gapChar, Generous());
-			++itInsert;
-			for(TSize i = 0; i < *itInsert; ++i, ++itMat1) appendValue(mat, *itMat1, Generous());
-			++itInsert;
-		}
-	}
-	
-	itInsertEnd = end(insertPattern2, Standard());
-	itMat2 = begin(mat2, Standard());
-	TMatIter itMat2End = end(mat2, Standard());
-	while(itMat2 != itMat2End) {
-		itInsert = begin(insertPattern2, Standard());
-		for(TSize i = 0; i < *itInsert; ++i, ++itMat2) appendValue(mat, *itMat2, Generous());
-		++itInsert;
-		for(TSize i = 0; i < *itInsert; ++i) appendValue(mat, gapChar, Generous());
-		++itInsert;
-		while(itInsert!=itInsertEnd) {
-			for(TSize i = 0; i < *itInsert; ++i, ++itMat2) appendValue(mat, *itMat2, Generous());
-			++itInsert;
-			for(TSize i = 0; i < *itInsert; ++i, ++itMat2) appendValue(mat, *itMat2, Generous());
-			++itInsert;
-			for(TSize i = 0; i < *itInsert; ++i) appendValue(mat, gapChar, Generous());
-			++itInsert;
-		}
-	}
-	
-	//// Debug code
-	//for(TSize row = 0; row < nseq; ++row) {
-	//	for(TSize col = 0; col < totalAlignLen; ++col) {
-	//		std::cout << mat[row * totalAlignLen + col];
-	//	}
-	//	std::cout << std::endl;
-	//}
+    // Is it a valid split?
+    if ((splitPos == 0) || (splitPos > nseq - 1)) return;
+
+    // Initialization
+    typedef String<TValue, TSpec> TAlignMat;
+    typedef typename Iterator<TAlignMat, Standard>::Type TMatIter;
+    TSize alignLen = length(mat) / nseq;
+
+    //// Debug code
+    //for(TSize row = 0; row < nseq; ++row) {
+    //    for(TSize col = 0; col < alignLen; ++col) {
+    //        std::cout << mat[row * alignLen + col];
+    //    }
+    //    std::cout << std::endl;
+    //}
+
+    char gapChar = gapValue<char>();
+    TSize nseq1 = splitPos;
+    TSize nseq2 = nseq - nseq1;
+    TSize gapPos = ValueSize<TAlphabet>::VALUE;
+    typedef ProfileChar<TAlphabet> TProfile;
+    typedef String<TProfile> TProfileString;
+    typedef typename Iterator<TProfileString, Standard>::Type TProfIter;
+    TProfileString prof1;
+    TProfileString prof2;
+    resize(prof1, alignLen, TProfile());
+    resize(prof2, alignLen, TProfile());
+    TMatIter itMat = begin(mat, Standard());
+    TMatIter itMatEnd = begin(mat, Standard());
+    itMatEnd += nseq1 * alignLen;
+    TProfIter itProf = begin(prof1, Standard());
+    for(TSize i = 0;itMat != itMatEnd;++itMat, ++itProf, ++i) {
+        if (i % alignLen == 0) itProf = begin(prof1, Standard());
+        if (*itMat == gapChar) ++(itProf->count[gapPos]);
+        else ++(itProf->count[ordValue((TAlphabet) *itMat)]);
+    }
+    itProf = begin(prof2, Standard());
+    itMatEnd = end(mat, Standard());
+    for(TSize i = 0;itMat != itMatEnd;++itMat, ++itProf, ++i) {
+        if (i % alignLen == 0) itProf = begin(prof2, Standard());
+        if (*itMat == gapChar) ++(itProf->count[gapPos]);
+        else ++(itProf->count[ordValue((TAlphabet) *itMat)]);
+    }
+
+
+    TProfileString alignProf1;
+    reserve(alignProf1, alignLen);
+    itProf = begin(prof1, Standard());
+    TProfIter itProfEnd = end(prof1, Standard());
+    typedef String<TSize> TDelGap;
+    typedef typename Iterator<TDelGap, Standard>::Type TDelGapIter;
+    TDelGap delGapCol;
+    for(TSize i = 0;itProf != itProfEnd;++itProf, ++i) {
+        if (itProf->count[gapPos] != nseq1) appendValue(alignProf1, *itProf);
+        else appendValue(delGapCol, i, Generous());
+    }
+    TDelGapIter itDelGap = begin(delGapCol, Standard());
+    TDelGapIter itDelGapEnd = end(delGapCol, Standard());
+    TAlignMat mat1;
+    TSize alignLen1 = alignLen - length(delGapCol);
+    resize(mat1, nseq1 * alignLen1);
+    itMat = begin(mat, Standard());
+    itMatEnd = begin(mat, Standard());
+    itMatEnd += nseq1 * alignLen;
+    TMatIter itMat1 = begin(mat1, Standard());
+    for(TSize col = 0;itMat != itMatEnd;++itMat, ++col) {
+        if (col % alignLen == 0) itDelGap = begin(delGapCol, Standard());
+        if ((itDelGap != itDelGapEnd) && (col % alignLen == *itDelGap)) {
+            ++itDelGap;
+            continue;
+        }
+        *itMat1 = *itMat;
+        ++itMat1;
+    }
+
+    //// Debug code
+    //for(TSize row = 0; row < nseq1; ++row) {
+    //    for(TSize col = 0; col < alignLen1; ++col) {
+    //        std::cout << mat1[row * alignLen1 + col];
+    //    }
+    //    std::cout << std::endl;
+    //}
+
+
+    TProfileString alignProf2;
+    reserve(alignProf2, alignLen);
+    itProf = begin(prof2, Standard());
+    itProfEnd = end(prof2, Standard());
+    clear(delGapCol);
+    for(TSize i = 0;itProf != itProfEnd;++itProf, ++i) {
+        if (itProf->count[gapPos] != nseq2) appendValue(alignProf2, *itProf);
+        else appendValue(delGapCol, i, Generous());
+    }
+    itDelGap = begin(delGapCol, Standard());
+    itDelGapEnd = end(delGapCol, Standard());
+    TAlignMat mat2;
+    TSize alignLen2 = alignLen - length(delGapCol);
+    resize(mat2, nseq2 * alignLen2);
+    itMatEnd = end(mat, Standard());
+    TMatIter itMat2 = begin(mat2, Standard());
+    for(TSize col = 0;itMat != itMatEnd;++itMat, ++col) {
+        if (col % alignLen == 0) itDelGap = begin(delGapCol, Standard());
+        if ((itDelGap != itDelGapEnd) && (col % alignLen == *itDelGap)) {
+            ++itDelGap;
+            continue;
+        }
+        *itMat2 = *itMat;
+        ++itMat2;
+    }
+
+    //// Debug code
+    //for(TSize row = 0; row < nseq2; ++row) {
+    //    for(TSize col = 0; col < alignLen2; ++col) {
+    //        std::cout << mat2[row * alignLen2 + col];
+    //    }
+    //    std::cout << std::endl;
+    //}
+
+
+    // ReAlign the consensus with the sequence
+    typedef StringSet<TProfileString, Dependent<> > TStringSet;
+    TStringSet pairSet;
+    appendValue(pairSet, alignProf1);
+    appendValue(pairSet, alignProf2);
+
+    typedef String<Fragment<> > TFragmentString;
+    TFragmentString matches;
+    globalAlignment(matches, pairSet, sc, Gotoh());
+
+    typedef typename Iterator<TFragmentString, Standard>::Type TFragIter;
+    TFragIter fragIt = end(matches, Standard() );
+    TFragIter fragItEnd = begin(matches, Standard() );
+    typedef String<TSize> TInsertPattern;
+    typedef typename Iterator<TInsertPattern, Standard>::Type TInsertIter;
+    TInsertPattern insertPattern1;
+    TInsertPattern insertPattern2;
+    TSize begin1Pos = 0;
+    TSize begin2Pos = 0;
+    if (fragIt != fragItEnd) {
+        do {
+            --fragIt;
+            appendValue(insertPattern1, fragIt->begin2 - begin2Pos, Generous());
+            appendValue(insertPattern1, fragIt->begin1 - begin1Pos, Generous());
+            appendValue(insertPattern1, fragIt->len, Generous());
+            appendValue(insertPattern2, fragIt->begin2 - begin2Pos, Generous());
+            appendValue(insertPattern2, fragIt->begin1 - begin1Pos, Generous());
+            appendValue(insertPattern2, fragIt->len, Generous());
+            begin1Pos = fragIt->begin1 + fragIt->len;
+            begin2Pos = fragIt->begin2 + fragIt->len;
+        } while (fragIt != fragItEnd);
+    }
+    appendValue(insertPattern1, alignLen2 - begin2Pos, Generous());
+    appendValue(insertPattern1, alignLen1 - begin1Pos, Generous());
+    appendValue(insertPattern2, alignLen2 - begin2Pos, Generous());
+    appendValue(insertPattern2, alignLen1 - begin1Pos, Generous());
+    clear(matches);
+
+    TInsertIter itInsert = begin(insertPattern1, Standard());
+    TInsertIter itInsertEnd = end(insertPattern1, Standard());
+    TSize totalAlignLen = 0;
+    for(;itInsert != itInsertEnd; ++itInsert) totalAlignLen += *itInsert;
+    itMat1 = begin(mat1, Standard());
+    TMatIter itMat1End = end(mat1, Standard());
+    clear(mat);
+    while(itMat1 != itMat1End) {
+        itInsert = begin(insertPattern1, Standard());
+        for(TSize i = 0; i < *itInsert; ++i) appendValue(mat, gapChar, Generous());
+        ++itInsert;
+        for(TSize i = 0; i < *itInsert; ++i, ++itMat1) appendValue(mat, *itMat1, Generous());
+        ++itInsert;
+        while(itInsert!=itInsertEnd) {
+            for(TSize i = 0; i < *itInsert; ++i, ++itMat1) appendValue(mat, *itMat1, Generous());
+            ++itInsert;
+            for(TSize i = 0; i < *itInsert; ++i) appendValue(mat, gapChar, Generous());
+            ++itInsert;
+            for(TSize i = 0; i < *itInsert; ++i, ++itMat1) appendValue(mat, *itMat1, Generous());
+            ++itInsert;
+        }
+    }
+
+    itInsertEnd = end(insertPattern2, Standard());
+    itMat2 = begin(mat2, Standard());
+    TMatIter itMat2End = end(mat2, Standard());
+    while(itMat2 != itMat2End) {
+        itInsert = begin(insertPattern2, Standard());
+        for(TSize i = 0; i < *itInsert; ++i, ++itMat2) appendValue(mat, *itMat2, Generous());
+        ++itInsert;
+        for(TSize i = 0; i < *itInsert; ++i) appendValue(mat, gapChar, Generous());
+        ++itInsert;
+        while(itInsert!=itInsertEnd) {
+            for(TSize i = 0; i < *itInsert; ++i, ++itMat2) appendValue(mat, *itMat2, Generous());
+            ++itInsert;
+            for(TSize i = 0; i < *itInsert; ++i, ++itMat2) appendValue(mat, *itMat2, Generous());
+            ++itInsert;
+            for(TSize i = 0; i < *itInsert; ++i) appendValue(mat, gapChar, Generous());
+            ++itInsert;
+        }
+    }
+
+    //// Debug code
+    //for(TSize row = 0; row < nseq; ++row) {
+    //    for(TSize col = 0; col < totalAlignLen; ++col) {
+    //        std::cout << mat[row * totalAlignLen + col];
+    //    }
+    //    std::cout << std::endl;
+    //}
 }
 
 
 
-template<typename TStringSet, typename TCargo, typename TSpec, typename TScore> 
+template<typename TStringSet, typename TCargo, typename TSpec, typename TScore>
 inline void
 msaRefinement(Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign,
-			  TScore& sc)
+              TScore& sc)
 {
-	typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Value<TStringSet>::Type TSequence;
-	typedef typename Value<TSequence>::Type TAlphabet;
-	TSize nseq = length(stringSet(gAlign));
-	String<char> mat;
-	convertAlignment(gAlign, mat);
-	for(TSize i = 1; i<nseq; ++i) _msaRefinement(mat, nseq, i, sc, TAlphabet());
-	convertAlignment(mat, gAlign);
+    typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Value<TStringSet>::Type TSequence;
+    typedef typename Value<TSequence>::Type TAlphabet;
+    TSize nseq = length(stringSet(gAlign));
+    String<char> mat;
+    convertAlignment(gAlign, mat);
+    for(TSize i = 1; i<nseq; ++i) _msaRefinement(mat, nseq, i, sc, TAlphabet());
+    convertAlignment(mat, gAlign);
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types.h b/seqan/graph_types.h
index 67ccdc0..8d9579d 100644
--- a/seqan/graph_types.h
+++ b/seqan/graph_types.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,18 +44,17 @@
 
 // Basic graph stuff
 #include <seqan/graph_types/graph_base.h>
-#include <seqan/graph_types/graph_idmanager.h>	// Id manager
-#include <seqan/graph_types/graph_edgestump.h>	// EdgeStumps
-#include <seqan/graph_types/graph_interface.h>	// Graph metafunctions
+#include <seqan/graph_types/graph_idmanager.h>    // Id manager
+#include <seqan/graph_types/graph_edgestump.h>    // EdgeStumps
+#include <seqan/graph_types/graph_interface.h>    // Graph metafunctions
 
 // Graph types
-#include <seqan/graph_types/graph_impl_directed.h>		// Directed Graph
-#include <seqan/graph_types/graph_impl_undirected.h>	// Undirected graph
-#include <seqan/graph_types/graph_impl_automaton.h>		// Automaton
-#include <seqan/graph_types/graph_impl_wordgraph.h>		// Specialized automaton: Word graph
-#include <seqan/graph_types/graph_impl_tree.h>			// Tree
-#include <seqan/graph_types/graph_impl_fragment.h>		// Fragment
-#include <seqan/graph_types/graph_impl_hmm.h>			// HMM
+#include <seqan/graph_types/graph_impl_directed.h>        // Directed Graph
+#include <seqan/graph_types/graph_impl_undirected.h>    // Undirected graph
+#include <seqan/graph_types/graph_impl_automaton.h>        // Automaton
+#include <seqan/graph_types/graph_impl_wordgraph.h>        // Specialized automaton: Word graph
+#include <seqan/graph_types/graph_impl_tree.h>            // Tree
+#include <seqan/graph_types/graph_impl_hmm.h>            // HMM
 
 // Graph iterators
 #include <seqan/graph_types/graph_iterator.h>
@@ -65,11 +64,13 @@
 #include <seqan/graph_types/graph_iterator_edge.h>
 
 // Graph property maps
-#include <seqan/graph_types/graph_property.h>
+#include <seqan/graph_types/property_map_generic.h>
+#include <seqan/graph_types/property_map_internal.h>
+#include <seqan/graph_types/property_map_internal_pointer.h>
 
 // Specializations
-#include <seqan/graph_types/graph_impl_oracle.h>	// Oracle
-#include <seqan/graph_types/graph_impl_trie.h>		// Trie
+#include <seqan/graph_types/graph_impl_oracle.h>    // Oracle
+#include <seqan/graph_types/graph_impl_trie.h>        // Trie
 
 // Specialized iterators
 #include <seqan/graph_types/graph_iterator_bfs.h>
@@ -77,7 +78,5 @@
 
 // Graph drawing and some file parsing
 #include <seqan/graph_types/graph_drawing.h>
-#include <seqan/misc/misc_parsing.h>
-#include <seqan/graph_types/graph_utility_parsing.h>
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/graph_types/INFO b/seqan/graph_types/INFO
deleted file mode 100644
index 09b4a89..0000000
--- a/seqan/graph_types/INFO
+++ /dev/null
@@ -1,9 +0,0 @@
-Name: seqan-graph_types
-Author: Tobias Rausch <rausch@embl.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Graph implementations.
- This module contains the definition of various graph types as well as the
- various iterators.
diff --git a/seqan/graph_types/graph_base.h b/seqan/graph_types/graph_base.h
index cc4428c..76d38b9 100644
--- a/seqan/graph_types/graph_base.h
+++ b/seqan/graph_types/graph_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -48,7 +48,7 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * @signature EdgeDescriptor<T>::Type;
  *
- * @tparam The @link Graph @endlink type to query.
+ * @tparam T The @link Graph @endlink type to query.
  *
  * @return Type The resulting edge descriptor type.
  *
@@ -56,27 +56,13 @@ namespace SEQAN_NAMESPACE_MAIN
  * remove edges, to assign cargo to an edge or to get the end points of an edge.  It is also used to attache properties
  * to edges via property maps.
  *
- * @examples
+ * @section Examples
  *
  * @code{.cpp}
  * EdgeDescriptor<Graph<> >::Type ed;  // eD is an edge descriptor
  * @endcode
  */
 
-/**
-.Metafunction.EdgeDescriptor
-..class:Class.Graph
-..cat:Graph
-..summary:Type of an object that represents an edge descriptor.
-..signature:EdgeDescriptor<T>::Type
-..param.T:Type T must be a graph. All graphs use a pointer to an edge stump as an edge descriptor.
-..returns.param.Type:EdgeDescriptor type.
-..remarks.text:The edge descriptor is a unique handle to a given edge in a graph.
-It is used in various graph functions, e.g., to remove edges, to assign a cargo to an edge or to get the endpoints of an edge.
-It is also used to attach properties to edges.
-..example.code:EdgeDescriptor<Graph<> >::Type eD; //eD is an edge descriptor
-..include:seqan/graph_types.h
-*/
 template<typename T>
 struct EdgeDescriptor;
 
@@ -93,13 +79,6 @@ struct EdgeDescriptor;
  * @return Type The resulting cargo type.
  */
 
-/**
-.Metafunction.Cargo
-..class:Class.Graph
-..cat:Graph
-..example.code:Cargo<Graph<Directed<int> > >::Type c; //c has type int
-..include:seqan/graph_types.h
-*/
 template<typename T>
 struct Cargo;
 
@@ -123,18 +102,6 @@ struct Cargo;
  * @endcode
  */
 
-/**
-.Metafunction.EdgeType:
-..class:Class.Graph
-..cat:Graph
-..summary:Edge type of a graph object.
-..signature:EdgeType<T>::Type
-..param.T:Type T must be a graph.
-..returns.param.Type:Edge type.
-..remarks.text:The specific edge stump type that is used in a graph.
-..example.code:EdgeType<TGraph>::Type e; //e is an edge in TGraph
-..include:seqan/graph_types.h
-*/
 template<typename T>
 struct EdgeType;
 
@@ -160,19 +127,6 @@ struct EdgeType;
  * @endcode
  */
 
-/**
-.Metafunction.Alphabet:
-..class:Spec.Word Graph
-..class:Spec.Automaton
-..cat:Graph
-..summary:Access to the Alphabet type.
-..signature:Alphabet<T>::Type
-..param.T:Type T must be a type that uses some kind of alphabet internally.
-..returns.param.Type:Alphabet type.
-..remarks.text:Type T can be for example an automaton where the alphabet type describes the domain of the transition labels.
-..example.code:Alphabet<Graph<Automaton<Dna> > >::Type alph; //alph is of type Dna
-..include:seqan/graph_types.h
-*/
 template<typename T>
 struct Alphabet;
 
@@ -193,20 +147,6 @@ struct Alphabet;
  * counts edge ids and otherwise it manages a list of free and used ids.
  */
 
-/**
-.Metafunction.EdgeIdHandler:
-..class:Class.Graph
-..cat:Graph
-..summary:Type of an object that represents an Id Manager.
-..signature:EdgeIdHandler<T>::Type
-..param.T:A graph.
-...type:Class.Graph
-..returns.param.Type:IdManager type.
-..remarks.text:The exact IdManager type depends on the edge stump.
-If the edge stump is id-free the IdManager simply counts edge ids, 
-otherwise it manages a list of free and used ids.
-..include:seqan/graph_types.h
-*/
 template<typename T>
 struct EdgeIdHandler;
 
@@ -224,16 +164,6 @@ struct EdgeIdHandler;
  * @return Type The IdManager type.
  */
 
-/**
-.Metafunction.VertexIdHandler:
-..class:Class.Graph
-..cat:Graph
-..summary:Type of an object that represents an Id Manager.
-..signature:VertexIdHandler<T>::Type
-..param.T:A graph.
-..returns.param.Type:IdManager type.
-..include:seqan/graph_types.h
-*/
 template<typename T>
 struct VertexIdHandler;
 
@@ -252,6 +182,10 @@ typedef Tag<WithoutEdgeId_> const WithoutEdgeId;
 struct TreeTag_;
 typedef Tag<TreeTag_> const TreeTag;
 
+//////////////////////////////////////////////////////////////////////////////
+
+struct WithSourceId_;
+typedef Tag<WithSourceId_> const WithSourceId;
 
 //////////////////////////////////////////////////////////////////////////////
 // Graph Iterator Tags
@@ -294,66 +228,29 @@ typedef Tag<TreeTag_> const TreeTag;
  * @signature typedef Tag<DfsPreorder_> const DfsPreorder;
  */
 
-/**
-.Tag.Graph Iterator:
-..cat:Graph
-..summary:A specification of the iterator to traverse a graph.
-..include:seqan/graph_types.h
-*/
-
 //////////////////////////////////////////////////////////////////////////////
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Tag.Graph Iterator.value.VertexIterator:
-	Traverses all vertices of a graph.
-..include:seqan/graph_types.h
-*/
 struct VertexIterator_;
 typedef Tag<VertexIterator_> const VertexIterator;
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Tag.Graph Iterator.value.EdgeIterator:
-	Traverses all edges of a graph.
-..include:seqan/graph_types.h
-*/
 struct EdgeIterator_;
 typedef Tag<EdgeIterator_> const EdgeIterator;
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Tag.Graph Iterator.value.OutEdgeIterator:
-	Traverses all edges of a graph given a vertex.
-..include:seqan/graph_types.h
-*/
 struct OutEdgeIterator_;
 typedef Tag<OutEdgeIterator_> const OutEdgeIterator;
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Tag.Graph Iterator.value.AdjacencyIterator:
-	Traverses all neighbors of a graph given a vertex.
-..include:seqan/graph_types.h
-*/
 struct AdjacencyIterator_;
 typedef Tag<AdjacencyIterator_> const AdjacencyIterator;
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Tag.Graph Iterator.value.BfsIterator:
-	Traverses all vertices of a graph in Bfs order.
-..include:seqan/graph_types.h
-*/
 struct BfsIterator_;
 typedef Tag<BfsIterator_> const BfsIterator;
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Tag.Graph Iterator.value.DfsPreorder:
-	Traverses all vertices of a graph in Dfs order.
-..include:seqan/graph_types.h
-*/
 struct DfsPreorder_;
 typedef Tag<DfsPreorder_> const DfsPreorder;
 
@@ -372,21 +269,18 @@ class EdgeStump;
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.VertexDescriptor.param.T.type:Class.EdgeStump
-///.Metafunction.VertexDescriptor.class:Class.EdgeStump
-
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
-struct VertexDescriptor<EdgeStump<TCargo, TList, TSource, TId, TSpec> > 
+struct VertexDescriptor<EdgeStump<TCargo, TList, TSource, TId, TSpec> >
 {
-	typedef typename Id<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type Type;
+    typedef typename Id<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
-struct VertexDescriptor<EdgeStump<TCargo, TList, TSource, TId, TSpec> const> 
+struct VertexDescriptor<EdgeStump<TCargo, TList, TSource, TId, TSpec> const>
 {
-	typedef typename Id<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type Type;
+    typedef typename Id<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type Type;
 };
 
 
@@ -403,26 +297,23 @@ class IdManager;
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.EdgeIdHandler.param.T.type:Class.EdgeStump
-///.Metafunction.EdgeIdHandler.class:Class.EdgeStump
-
 template<typename TCargo, bool TList, bool TSource, typename TSpec>
 struct EdgeIdHandler<EdgeStump<TCargo, TList, TSource, false, TSpec> > {
-	typedef IdManager<void> Type;
+    typedef IdManager<void> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, typename TSpec>
 struct EdgeIdHandler<EdgeStump<TCargo, TList, TSource, true, TSpec> > {
-	typedef IdManager<typename Id<EdgeStump<TCargo, TList, TSource, true, TSpec> >::Type> Type;
+    typedef IdManager<typename Id<EdgeStump<TCargo, TList, TSource, true, TSpec> >::Type> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename T>
 struct VertexIdHandler {
-	typedef IdManager<> Type;
+    typedef IdManager<> Type;
 };
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_drawing.h b/seqan/graph_types/graph_drawing.h
index 35fb3a2..cdfbaa1 100644
--- a/seqan/graph_types/graph_drawing.h
+++ b/seqan/graph_types/graph_drawing.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -60,52 +60,52 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TAttributes>
-inline void 
+inline void
 _markRootVertex(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-				TVertexDescriptor const& v,
-				TAttributes& str)
+                TVertexDescriptor const& v,
+                TAttributes& str)
 {
-	SEQAN_CHECKPOINT
-	if (isRoot(g,v)) {
-		append(str, ", shape = doublecircle");
-	}
+    SEQAN_CHECKPOINT
+    if (isRoot(g,v)) {
+        append(str, ", shape = doublecircle");
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TCargo, typename TSpec, typename TVertexDescriptor, typename TAttributes>
-inline void 
+inline void
 _markRootVertex(Graph<Directed<TCargo, TSpec> > const&,
-				TVertexDescriptor const&,
-				TAttributes&)
+                TVertexDescriptor const&,
+                TAttributes&)
 {
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TCargo, typename TSpec, typename TVertexDescriptor, typename TAttributes>
-inline void 
+inline void
 _markRootVertex(Graph<Undirected<TCargo, TSpec> > const&,
-				TVertexDescriptor const&,
-				TAttributes&)
+                TVertexDescriptor const&,
+                TAttributes&)
 {
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TCargo, typename TSpec, typename TVertexDescriptor, typename TAttributes>
-inline void 
+inline void
 _markRootVertex(Graph<Tree<TCargo, TSpec> > const& g,
-				TVertexDescriptor const& v,
-				TAttributes& str)
+                TVertexDescriptor const& v,
+                TAttributes& str)
 {
-	SEQAN_CHECKPOINT
-	if (isRoot(g,v)) {
-		append(str, ", shape = doublecircle");
-	}
+    SEQAN_CHECKPOINT
+    if (isRoot(g,v)) {
+        append(str, ", shape = doublecircle");
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -113,37 +113,37 @@ _markRootVertex(Graph<Tree<TCargo, TSpec> > const& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TPosition, typename TNodeMap>
 inline void
 _createTrieNodeAttributes(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-						  String<String<TPosition> > pos,
-						  TNodeMap& nodeMap)
-{
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	resizeVertexMap(g, nodeMap);
-	typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
-	TConstIter it(g);
-	for(;!atEnd(it);++it) {
-		String<char> tmp;
-		std::stringstream s;
-		s << *it;
-		String<TPosition> endPositions = getProperty(pos,*it);
-		if (!empty(endPositions)) {
-			s <<  " {";
-			append(tmp, "shape = box, ");
-			typename Iterator<String<TPosition>, Rooted>::Type itP = begin(endPositions);
-			typename Iterator<String<TPosition>, Rooted>::Type beginP = itP;
-			for(;!atEnd(itP);goNext(itP)) {
-				if (beginP != itP) s << ", ";
-				s << *itP;
-			}
-			s << "}";
-		}
-		
-		append(tmp, "label = \"");
-		append(tmp, s.str().c_str());
-		append(tmp, "\"");
-		_markRootVertex(g, *it, tmp);
-		assignProperty(nodeMap, *it, tmp);
-	}
+                          String<String<TPosition> > pos,
+                          TNodeMap& nodeMap)
+{
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    resizeVertexMap(nodeMap, g);
+    typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
+    TConstIter it(g);
+    for(;!atEnd(it);++it) {
+        String<char> tmp;
+        std::stringstream s;
+        s << *it;
+        String<TPosition> endPositions = getProperty(pos,*it);
+        if (!empty(endPositions)) {
+            s <<  " {";
+            append(tmp, "shape = box, ");
+            typename Iterator<String<TPosition>, Rooted>::Type itP = begin(endPositions);
+            typename Iterator<String<TPosition>, Rooted>::Type beginP = itP;
+            for(;!atEnd(itP);goNext(itP)) {
+                if (beginP != itP) s << ", ";
+                s << *itP;
+            }
+            s << "}";
+        }
+
+        append(tmp, "label = \"");
+        append(tmp, s.str().c_str());
+        append(tmp, "\"");
+        _markRootVertex(g, *it, tmp);
+        assignProperty(nodeMap, *it, tmp);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -151,23 +151,23 @@ _createTrieNodeAttributes(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
 template<typename TSpec, typename TNodeAttributes>
 inline void
 _createNodeAttributes(Graph<TSpec> const& g,
-					  TNodeAttributes& nodeMap)
+                      TNodeAttributes& nodeMap)
 {
     typedef Graph<TSpec> TGraph;
-	resizeVertexMap(g, nodeMap);
+    resizeVertexMap(nodeMap, g);
 
-	typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
-	TConstIter it(g);
-	for(;!atEnd(it);++it) {
-		std::ostringstream outs;
-		outs << "label = \"";
-		outs << *it;
-		outs << "\"";
-		String<char> tmp;
-		append(tmp, outs.str().c_str());
-		_markRootVertex(g, *it, tmp);
-		assignProperty(nodeMap, *it, tmp);
-	}
+    typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
+    TConstIter it(g);
+    for(;!atEnd(it);++it) {
+        std::ostringstream outs;
+        outs << "label = \"";
+        outs << *it;
+        outs << "\"";
+        String<char> tmp;
+        append(tmp, outs.str().c_str());
+        _markRootVertex(g, *it, tmp);
+        assignProperty(nodeMap, *it, tmp);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -175,40 +175,40 @@ _createNodeAttributes(Graph<TSpec> const& g,
 template<typename TSpec, typename TNodeAttributes, typename TNameMap>
 inline void
 _createNodeAttributes(Graph<TSpec> const& g,
-					  TNodeAttributes& nodeMap,
-					  TNameMap const& nameMap)
+                      TNodeAttributes& nodeMap,
+                      TNameMap const& nameMap)
 {
     typedef Graph<TSpec> TGraph;
-	resizeVertexMap(g, nodeMap);
+    resizeVertexMap(nodeMap, g);
 
-	typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
-	TConstIter it(g);
-	for(;!atEnd(it);++it) {
-		std::ostringstream outs; 
-		outs << "label = \"";
-		outs << getProperty(nameMap,*it);
-		outs << "\"";
-		String<char> tmp;
-		append(tmp, outs.str().c_str());
-		_markRootVertex(g, *it, tmp);
-		assignProperty(nodeMap, *it, tmp);
-	}
+    typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
+    TConstIter it(g);
+    for(;!atEnd(it);++it) {
+        std::ostringstream outs;
+        outs << "label = \"";
+        outs << getProperty(nameMap,*it);
+        outs << "\"";
+        String<char> tmp;
+        append(tmp, outs.str().c_str());
+        _markRootVertex(g, *it, tmp);
+        assignProperty(nodeMap, *it, tmp);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 template<typename TSpec, typename TEdgeAttributes>
 inline void
 _createEmptyEdgeAttributes(Graph<TSpec> const& g,
-						   TEdgeAttributes& edgeMap)
+                           TEdgeAttributes& edgeMap)
 {
-	typedef Graph<TSpec> TGraph;
-	resizeEdgeMap(g, edgeMap);
+    typedef Graph<TSpec> TGraph;
+    resizeEdgeMap(edgeMap, g);
 
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
-	TConstEdIter itEd(g);
-	for(;!atEnd(itEd);++itEd) {
-		assignProperty(edgeMap, *itEd, String<char>(""));
-	}
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
+    TConstEdIter itEd(g);
+    for(;!atEnd(itEd);++itEd) {
+        assignProperty(edgeMap, *itEd, String<char>(""));
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -216,9 +216,9 @@ _createEmptyEdgeAttributes(Graph<TSpec> const& g,
 template <typename TCargo, typename TSpec, typename TEdgeAttributes>
 inline void
 _createEdgeAttributes(Graph<Directed<TCargo, TSpec> > const& g,
-					  TEdgeAttributes& edgeMap)
+                      TEdgeAttributes& edgeMap)
 {
-	_createEmptyEdgeAttributes(g,edgeMap);
+    _createEmptyEdgeAttributes(g,edgeMap);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -226,10 +226,10 @@ _createEdgeAttributes(Graph<Directed<TCargo, TSpec> > const& g,
 template <typename TCargo, typename TSpec, typename TEdgeAttributes>
 inline void
 _createEdgeAttributes(Graph<Undirected<TCargo, TSpec> > const& g,
-					  TEdgeAttributes& edgeMap)
+                      TEdgeAttributes& edgeMap)
 {
-	SEQAN_CHECKPOINT
-	_createEmptyEdgeAttributes(g,edgeMap);
+    SEQAN_CHECKPOINT
+    _createEmptyEdgeAttributes(g,edgeMap);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -237,10 +237,10 @@ _createEdgeAttributes(Graph<Undirected<TCargo, TSpec> > const& g,
 template <typename TSpec, typename TEdgeAttributes>
 inline void
 _createEdgeAttributes(Graph<Tree<void, TSpec> > const& g,
-					  TEdgeAttributes& edgeMap)
+                      TEdgeAttributes& edgeMap)
 {
-	SEQAN_CHECKPOINT
-	_createEmptyEdgeAttributes(g,edgeMap);
+    SEQAN_CHECKPOINT
+    _createEmptyEdgeAttributes(g,edgeMap);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -248,20 +248,20 @@ _createEdgeAttributes(Graph<Tree<void, TSpec> > const& g,
 template <typename TCargo, typename TSpec, typename TEdgeAttributes>
 inline void
 _createEdgeAttributes(Graph<Tree<TCargo, TSpec> > const& g,
-					  TEdgeAttributes& edgeMap)
+                      TEdgeAttributes& edgeMap)
 {
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	resizeEdgeMap(g, edgeMap);
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    resizeEdgeMap(edgeMap, g);
 
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
-	TConstEdIter itEd(g);
-	for(;!atEnd(itEd);++itEd) {
-		std::ostringstream outs; 
-		outs << "label = \"";
-		outs << (TCargo) getCargo(*itEd);
-		outs << "\"";
-		append(property(edgeMap, *itEd), outs.str().c_str());
-	}
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
+    TConstEdIter itEd(g);
+    for(;!atEnd(itEd);++itEd) {
+        std::ostringstream outs;
+        outs << "label = \"";
+        outs << (TCargo) getCargo(*itEd);
+        outs << "\"";
+        append(property(edgeMap, *itEd), outs.str().c_str());
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -269,20 +269,20 @@ _createEdgeAttributes(Graph<Tree<TCargo, TSpec> > const& g,
 template <typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeAttributes>
 inline void
 _createEdgeAttributes(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-					  TEdgeAttributes& edgeMap)
+                      TEdgeAttributes& edgeMap)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	resizeEdgeMap(g, edgeMap);
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    resizeEdgeMap(edgeMap, g);
 
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
-	TConstEdIter itEd(g);
-	for(;!atEnd(itEd);++itEd) {
-		String<char> tmp("label = \"");
-		append(tmp, label(itEd));
-		append(tmp, "\"");
-		assignProperty(edgeMap, *itEd, tmp);
-	}
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
+    TConstEdIter itEd(g);
+    for(;!atEnd(itEd);++itEd) {
+        String<char> tmp("label = \"");
+        append(tmp, label(itEd));
+        append(tmp, "\"");
+        assignProperty(edgeMap, *itEd, tmp);
+    }
 }
 
 
@@ -291,29 +291,29 @@ _createEdgeAttributes(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
 template <typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeAttributes>
 inline void
 _createEdgeAttributes(Graph<Automaton<TAlphabet, TCargo, WordGraph<TSpec> > > const& g,
-					  TEdgeAttributes& edgeMap)
+                      TEdgeAttributes& edgeMap)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, WordGraph<TSpec> > > TGraph;
-	resizeEdgeMap(g, edgeMap);
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, WordGraph<TSpec> > > TGraph;
+    resizeEdgeMap(edgeMap, g);
 
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
-	TConstEdIter itEd(g);
-	for(;!atEnd(itEd);++itEd) {
-		String<TAlphabet> labelTmp = getCargo(*itEd);
-		String<char> str;
-		resize(str,length(labelTmp)+1);
-		value(str,0) = label(itEd);
-		typename Iterator<String<TAlphabet>, Rooted>::Type it = begin(labelTmp);
-		for(;!atEnd(it);++it) {
-			char c = convert<char>(getValue(it));
-			value(str,position(it) + 1) = c;
-		}
-		String<char> tmp("label = \"");
-		append(tmp, str);
-		append(tmp, "\"");
-		assignProperty(edgeMap, *itEd, tmp);
-	}
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
+    TConstEdIter itEd(g);
+    for(;!atEnd(itEd);++itEd) {
+        String<TAlphabet> labelTmp = getCargo(*itEd);
+        String<char> str;
+        resize(str,length(labelTmp)+1);
+        value(str,0) = label(itEd);
+        typename Iterator<String<TAlphabet>, Rooted>::Type it = begin(labelTmp);
+        for(;!atEnd(it);++it) {
+            char c = convert<char>(getValue(it));
+            value(str,position(it) + 1) = c;
+        }
+        String<char> tmp("label = \"");
+        append(tmp, str);
+        append(tmp, "\"");
+        assignProperty(edgeMap, *itEd, tmp);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -321,11 +321,11 @@ _createEdgeAttributes(Graph<Automaton<TAlphabet, TCargo, WordGraph<TSpec> > > co
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeGraphFooter(TFile &,
-				  Graph<Directed<TCargo, TSpec> > const&,
-				  DotDrawing)
+                  Graph<Directed<TCargo, TSpec> > const&,
+                  DotDrawing)
 {
 //IOREV
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -333,11 +333,11 @@ _writeGraphFooter(TFile &,
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeGraphFooter(TFile &,
-				  Graph<Undirected<TCargo, TSpec> > const&,
-				  DotDrawing)
+                  Graph<Undirected<TCargo, TSpec> > const&,
+                  DotDrawing)
 {
 //IOREV
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -345,11 +345,11 @@ _writeGraphFooter(TFile &,
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeGraphFooter(TFile &,
-				  Graph<Tree<TCargo, TSpec> > const&,
-				  DotDrawing)
+                  Graph<Tree<TCargo, TSpec> > const&,
+                  DotDrawing)
 {
 //IOREV
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 
@@ -358,11 +358,11 @@ _writeGraphFooter(TFile &,
 template <typename TFile, typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 _writeGraphFooter(TFile &,
-				  Graph<Automaton<TAlphabet, TCargo, TSpec> > const&,
-				  DotDrawing)
+                  Graph<Automaton<TAlphabet, TCargo, TSpec> > const&,
+                  DotDrawing)
 {
 //IOREV
-	SEQAN_CHECKPOINT
+    SEQAN_CHECKPOINT
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -370,11 +370,11 @@ _writeGraphFooter(TFile &,
 template <typename TFile, typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 _writeGraphType(TFile & file,
-				Graph<Automaton<TAlphabet, TCargo, TSpec> > const&,
-				DotDrawing)
+                Graph<Automaton<TAlphabet, TCargo, TSpec> > const&,
+                DotDrawing)
 {
 //IOREV
-	streamPut(file, "digraph");
+    write(file, "digraph");
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -382,11 +382,11 @@ _writeGraphType(TFile & file,
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeGraphType(TFile & file,
-				Graph<Directed<TCargo, TSpec> > const&,
-				DotDrawing)
+                Graph<Directed<TCargo, TSpec> > const&,
+                DotDrawing)
 {
 //IOREV
-	streamPut(file, "digraph");
+    write(file, "digraph");
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -394,11 +394,11 @@ _writeGraphType(TFile & file,
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeGraphType(TFile & file,
-				Graph<Undirected<TCargo, TSpec> > const&,
-				DotDrawing)
+                Graph<Undirected<TCargo, TSpec> > const&,
+                DotDrawing)
 {
 //IOREV
-	streamPut(file, "graph");
+    write(file, "graph");
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -406,11 +406,11 @@ _writeGraphType(TFile & file,
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeGraphType(TFile & file,
-				Graph<Tree<TCargo, TSpec> > const&,
-				DotDrawing)
+                Graph<Tree<TCargo, TSpec> > const&,
+                DotDrawing)
 {
 //IOREV
-	streamPut(file, "digraph");
+    write(file, "digraph");
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -418,11 +418,11 @@ _writeGraphType(TFile & file,
 template <typename TFile, typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 _writeEdgeType(TFile & file,
-			   Graph<Automaton<TAlphabet, TCargo, TSpec> > const&,
-			   DotDrawing)
+               Graph<Automaton<TAlphabet, TCargo, TSpec> > const&,
+               DotDrawing)
 {
 //IOREV
-	streamPut(file, " -> ");
+    write(file, " -> ");
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -430,11 +430,11 @@ _writeEdgeType(TFile & file,
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeEdgeType(TFile & file,
-			   Graph<Directed<TCargo, TSpec> > const&,
-			   DotDrawing)
+               Graph<Directed<TCargo, TSpec> > const&,
+               DotDrawing)
 {
 //IOREV
-	streamPut(file, " -> ");
+    write(file, " -> ");
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -442,11 +442,11 @@ _writeEdgeType(TFile & file,
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeEdgeType(TFile & file,
-			   Graph<Undirected<TCargo, TSpec> > const&,
-			   DotDrawing)
+               Graph<Undirected<TCargo, TSpec> > const&,
+               DotDrawing)
 {
 //IOREV
-	streamPut(file, " -- ");
+    write(file, " -- ");
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -454,11 +454,11 @@ _writeEdgeType(TFile & file,
 template <typename TFile, typename TCargo, typename TSpec>
 inline void
 _writeEdgeType(TFile & file,
-			   Graph<Tree<TCargo, TSpec> > const&,
-			   DotDrawing)
+               Graph<Tree<TCargo, TSpec> > const&,
+               DotDrawing)
 {
 //IOREV
-	streamPut(file, " -> ");
+    write(file, " -> ");
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -481,114 +481,95 @@ _writeEdgeType(TFile & file,
  * @param[in]     tag     Format tag to use for writing.  Types: DotDrawing.
  */
 
-/**
-.Function.write
-..class:Class.Graph
-..signature:write(file, graph, nodeMap, edgeMap, tag)
-..param.graph:The graph to write out.
-...type:Class.Graph
-..param.nodeMap:A mapping from vertex descriptor to vertex label.
-..param.edgeMap:A mapping from edge descriptor to edge label.
-..param.tag:A tag to select the output format.
-...type:Tag.DotDrawing
-..include:seqan/graph_types.h
- */
-template <typename TFile, typename TSpec, typename TNodeAttributes, typename TEdgeAttributes>
+template <typename TTarget, typename TSpec, typename TNodeAttributes, typename TEdgeAttributes>
 void
-write(TFile & file,
-	  Graph<TSpec> const& g,
-	  TNodeAttributes const& nodeMap,
-	  TEdgeAttributes const& edgeMap,
-	  DotDrawing)
+writeRecords(
+    TTarget & target,
+    Graph<TSpec> const& g,
+    TNodeAttributes const& nodeMap,
+    TEdgeAttributes const& edgeMap,
+    DotDrawing)
 {
-//IOREV _doc_ _batchreading_
-	typedef Graph<TSpec> TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	_writeGraphType(file,g,DotDrawing());
-	streamPut(file, " G {\n");
-	streamPut(file, '\n');
-	streamPut(file, "/* Graph Attributes */\n");
-	streamPut(file, "graph [rankdir = LR];\n");
-	streamPut(file, '\n');
-	streamPut(file, "/* Node Attributes */\n");
-	streamPut(file, "node [shape = rectangle, fillcolor = white, style = filled, fontname = \"Times-Italic\"];\n");
-	streamPut(file, '\n');
-	streamPut(file, "/* Edge Attributes */\n");
-	streamPut(file, "edge [fontname = \"Times-Italic\", arrowsize = 0.75, fontsize = 16];\n");
-	streamPut(file, '\n');
-
-	streamPut(file, "/* Nodes */\n");
-	typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
-	TConstIter it(g);
-	for(;!atEnd(it);++it) {
-		streamPut(file, (int)*it);
-		streamPut(file, " [");
-		streamPut(file, getProperty(nodeMap, *it));
-		streamPut(file, "];\n");
-	}
-	streamPut(file, '\n');
-
-	streamPut(file, "/* Edges */\n");
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
-	TConstEdIter itEd(g);
-	for(;!atEnd(itEd);++itEd) {
-		TVertexDescriptor sc = sourceVertex(itEd);
-		TVertexDescriptor tr = targetVertex(itEd);
-		streamPut(file, (int)sc);
-		_writeEdgeType(file, g, DotDrawing());
-		streamPut(file, (int)tr);
-		streamPut(file, " [");
-		streamPut(file, getProperty(edgeMap, *itEd));
-		streamPut(file, "];\n");
-	}
-	streamPut(file, '\n');
-
-	_writeGraphFooter(file,g,DotDrawing());
-
-	streamPut(file, "}\n");
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.write
-..signature:write(file, graph, nodeMap, tag)
-..include:seqan/graph_types.h
- */
+    typedef Graph<TSpec> TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typename DirectionIterator<TTarget, Output>::Type iter = directionIterator(target, Output());
+
+    _writeGraphType(iter,g,DotDrawing());
+    write(iter, " G {\n");
+    writeValue(iter, '\n');
+    write(iter, "/* Graph Attributes */\n");
+    write(iter, "graph [rankdir = LR];\n");
+    writeValue(iter, '\n');
+    write(iter, "/* Node Attributes */\n");
+    write(iter, "node [shape = rectangle, fillcolor = white, style = filled, fontname = \"Times-Italic\"];\n");
+    writeValue(iter, '\n');
+    write(iter, "/* Edge Attributes */\n");
+    write(iter, "edge [fontname = \"Times-Italic\", arrowsize = 0.75, fontsize = 16];\n");
+    writeValue(iter, '\n');
+
+    write(iter, "/* Nodes */\n");
+    typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
+    TConstIter it(g);
+    for(;!atEnd(it);++it) {
+        appendNumber(iter, (int)*it);
+        write(iter, " [");
+        write(iter, getProperty(nodeMap, *it));
+        write(iter, "];\n");
+    }
+    writeValue(iter, '\n');
+
+    write(iter, "/* Edges */\n");
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
+    TConstEdIter itEd(g);
+    for(;!atEnd(itEd);++itEd) {
+        TVertexDescriptor sc = sourceVertex(itEd);
+        TVertexDescriptor tr = targetVertex(itEd);
+        appendNumber(iter, sc);
+        _writeEdgeType(iter, g, DotDrawing());
+        appendNumber(iter, tr);
+        write(iter, " [");
+        write(iter, getProperty(edgeMap, *itEd));
+        write(iter, "];\n");
+    }
+    writeValue(iter, '\n');
+
+    _writeGraphFooter(iter,g,DotDrawing());
+
+    write(iter, "}\n");
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
 template <typename TFile, typename TSpec, typename TNodeAttributes>
 inline void
-write(TFile & file,
-	  Graph<TSpec> const& g, 
-	  TNodeAttributes const& nodeMap,
-	  DotDrawing) 
+writeRecords(
+    TFile & file,
+    Graph<TSpec> const& g,
+    TNodeAttributes const& nodeMap,
+    DotDrawing)
 {
 //IOREV _doc_ _batchreading_
-	String<String<char> > edgeMap;
-	_createEdgeAttributes(g,edgeMap);
-	write(file,g,nodeMap,edgeMap,DotDrawing());
+    String<String<char> > edgeMap;
+    _createEdgeAttributes(g,edgeMap);
+    writeRecords(file,g,nodeMap,edgeMap,DotDrawing());
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.write
-..signature:write(file, graph, tag)
-..include:seqan/graph_types.h
- */
 template <typename TFile, typename TSpec>
 inline void
-write(TFile & file,
-	  Graph<TSpec> const& g, 
-	  DotDrawing) 
+writeRecords(
+    TFile & file,
+    Graph<TSpec> const& g,
+    DotDrawing)
 {
 //IOREV _doc_ _batchreading_
-	String<String<char> > nodeMap;
-	_createNodeAttributes(g,nodeMap);
-	String<String<char> > edgeMap;
-	_createEdgeAttributes(g,edgeMap);
-	write(file,g,nodeMap,edgeMap,DotDrawing());
+    String<String<char> > nodeMap;
+    _createNodeAttributes(g,nodeMap);
+    String<String<char> > edgeMap;
+    _createEdgeAttributes(g,edgeMap);
+    writeRecords(file,g,nodeMap,edgeMap,DotDrawing());
 }
 
 
@@ -604,21 +585,21 @@ write(TFile & file,
 template<typename TSpec, typename TStatement, typename TNodeAttributes, typename TEdgeAttributes, typename TNodeIdMap>
 inline void
 _addNode(Graph<TSpec>& g,
-		 TStatement& node_id,
-		 TStatement& attr_list,
-		 TNodeAttributes& nodeMap,
-		 TEdgeAttributes&,			  
-		 TNodeIdMap& nodeIdMap)
+         TStatement& node_id,
+         TStatement& attr_list,
+         TNodeAttributes& nodeMap,
+         TEdgeAttributes&,
+         TNodeIdMap& nodeIdMap)
 {
-	typedef Graph<TSpec> TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef Graph<TSpec> TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
 
-	if (nodeIdMap.find(node_id) == nodeIdMap.end()) {
-		TVertexDescriptor _id = addVertex(g);
-		nodeIdMap.insert(std::make_pair(node_id, _id));
-		resizeVertexMap(g, nodeMap);
-		assignProperty(nodeMap, _id, attr_list);
-	}
+    if (nodeIdMap.find(node_id) == nodeIdMap.end()) {
+        TVertexDescriptor _id = addVertex(g);
+        nodeIdMap.insert(std::make_pair(node_id, _id));
+        resizeVertexMap(nodeMap, g);
+        assignProperty(nodeMap, _id, attr_list);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -626,17 +607,17 @@ _addNode(Graph<TSpec>& g,
 template<typename TCargo, typename TSpec, typename TVertexDescriptor, typename TNodeAttributes, typename TEdgeAttributes, typename TStatement>
 inline void
 _addEdge(Graph<Directed<TCargo, TSpec> >& g,
-		 TVertexDescriptor sourceV,
-		 TVertexDescriptor targetV,
-		 TNodeAttributes&,
-		 TEdgeAttributes& edgeMap,
-		 TStatement& attr_list)
+         TVertexDescriptor sourceV,
+         TVertexDescriptor targetV,
+         TNodeAttributes&,
+         TEdgeAttributes& edgeMap,
+         TStatement& attr_list)
 {
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = addEdge(g, sourceV, targetV);
-	resizeEdgeMap(g, edgeMap);
-	assignProperty(edgeMap, e, attr_list);
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = addEdge(g, sourceV, targetV);
+    resizeEdgeMap(edgeMap, g);
+    assignProperty(edgeMap, e, attr_list);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -644,17 +625,17 @@ _addEdge(Graph<Directed<TCargo, TSpec> >& g,
 template<typename TCargo, typename TSpec, typename TVertexDescriptor, typename TNodeAttributes, typename TEdgeAttributes, typename TStatement>
 inline void
 _addEdge(Graph<Undirected<TCargo, TSpec> >& g,
-		 TVertexDescriptor sourceV,
-		 TVertexDescriptor targetV,
-		 TNodeAttributes&,
-		 TEdgeAttributes& edgeMap,
-		 TStatement& attr_list)
+         TVertexDescriptor sourceV,
+         TVertexDescriptor targetV,
+         TNodeAttributes&,
+         TEdgeAttributes& edgeMap,
+         TStatement& attr_list)
 {
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = addEdge(g, sourceV, targetV);
-	resizeEdgeMap(g, edgeMap);
-	assignProperty(edgeMap, e, attr_list);
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = addEdge(g, sourceV, targetV);
+    resizeEdgeMap(edgeMap, g);
+    assignProperty(edgeMap, e, attr_list);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -662,17 +643,17 @@ _addEdge(Graph<Undirected<TCargo, TSpec> >& g,
 template<typename TCargo, typename TSpec, typename TVertexDescriptor, typename TNodeAttributes, typename TEdgeAttributes, typename TStatement>
 inline void
 _addEdge(Graph<Tree<TCargo, TSpec> >& g,
-		 TVertexDescriptor sourceV,
-		 TVertexDescriptor targetV,
-		 TNodeAttributes&,
-		 TEdgeAttributes& edgeMap,
-		 TStatement& attr_list)
+         TVertexDescriptor sourceV,
+         TVertexDescriptor targetV,
+         TNodeAttributes&,
+         TEdgeAttributes& edgeMap,
+         TStatement& attr_list)
 {
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = addEdge(g, sourceV, targetV);
-	resizeEdgeMap(g, edgeMap);
-	assignProperty(edgeMap, e, attr_list);
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = addEdge(g, sourceV, targetV);
+    resizeEdgeMap(edgeMap, g);
+    assignProperty(edgeMap, e, attr_list);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -680,9 +661,9 @@ _addEdge(Graph<Tree<TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TString>
 inline typename Alphabet<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 _getInternalLabel(Graph<Automaton<TAlphabet, TCargo, TSpec> >&,
-				  TString& str)
+                  TString& str)
 {
-	return str[0];
+    return str[0];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -690,9 +671,9 @@ _getInternalLabel(Graph<Automaton<TAlphabet, TCargo, TSpec> >&,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TString>
 inline String<TAlphabet>
 _getInternalLabel(Graph<Automaton<TAlphabet, TCargo, WordGraph<TSpec> > >&,
-				  TString& str)
+                  TString& str)
 {
-	return str;
+    return str;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -700,39 +681,39 @@ _getInternalLabel(Graph<Automaton<TAlphabet, TCargo, WordGraph<TSpec> > >&,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TNodeAttributes, typename TEdgeAttributes, typename TStatement>
 inline void
 _addEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-		 TVertexDescriptor sourceV,
-		 TVertexDescriptor targetV,
-		 TNodeAttributes&,
-		 TEdgeAttributes& edgeMap,
-		 TStatement& attr_list)
-{
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-
-	// We need the label
-	typedef typename Value<TStatement>::Type TValue;
-	typedef typename Iterator<TStatement>::Type TIter;
-	typedef typename Position<TIter>::Type TPos;
-	
-	String<TValue> label;
-	TIter it = begin(attr_list);
-	bool found = false;
-	for(;!atEnd(it);goNext(it)) {
-		TPos pos = position(it);
-		if (*it == ',') {
-			found = false;
-		} else if (found) {
-			append(label, *it);
-		} else if ((pos + 5 < length(attr_list)) &&
-			(infix(attr_list, it, it + 5) == "label")) 
-		{
-				found = true;
-				it += 5;
-		}
-	}
-	TEdgeDescriptor e = addEdge(g, sourceV, targetV, _getInternalLabel(g, label));
-	resizeEdgeMap(g, edgeMap);
-	assignProperty(edgeMap, e, attr_list);
+         TVertexDescriptor sourceV,
+         TVertexDescriptor targetV,
+         TNodeAttributes&,
+         TEdgeAttributes& edgeMap,
+         TStatement& attr_list)
+{
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+
+    // We need the label
+    typedef typename Value<TStatement>::Type TValue;
+    typedef typename Iterator<TStatement>::Type TIter;
+    typedef typename Position<TIter>::Type TPos;
+
+    String<TValue> label;
+    TIter it = begin(attr_list);
+    bool found = false;
+    for(;!atEnd(it);goNext(it)) {
+        TPos pos = position(it);
+        if (*it == ',') {
+            found = false;
+        } else if (found) {
+            append(label, *it);
+        } else if ((pos + 5 < length(attr_list)) &&
+            (infix(attr_list, it, it + 5) == "label"))
+        {
+                found = true;
+                it += 5;
+        }
+    }
+    TEdgeDescriptor e = addEdge(g, sourceV, targetV, _getInternalLabel(g, label));
+    resizeEdgeMap(edgeMap, g);
+    assignProperty(edgeMap, e, attr_list);
 }
 
 
@@ -741,31 +722,31 @@ _addEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template<typename TSpec, typename TStatement, typename TNodeAttributes, typename TEdgeAttributes, typename TNodeIdMap>
 inline void
 _addEdge(Graph<TSpec>& g,
-		 TStatement& left_node_id,
-		 TStatement& right_node_id,
-		 TStatement& attr_list,
-		 TNodeAttributes& nodeMap,
-		 TEdgeAttributes& edgeMap,
-		 TNodeIdMap& nodeIdMap)
+         TStatement& left_node_id,
+         TStatement& right_node_id,
+         TStatement& attr_list,
+         TNodeAttributes& nodeMap,
+         TEdgeAttributes& edgeMap,
+         TNodeIdMap& nodeIdMap)
 {
-	typedef Graph<TSpec> TGraph;
-	typedef typename Value<TStatement>::Type TValue;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef std::map<String<TValue>, TVertexDescriptor> TMap;
+    typedef Graph<TSpec> TGraph;
+    typedef typename Value<TStatement>::Type TValue;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef std::map<String<TValue>, TVertexDescriptor> TMap;
 
-	TVertexDescriptor sourceV;
-	TVertexDescriptor targetV;
+    TVertexDescriptor sourceV;
+    TVertexDescriptor targetV;
 
-	typename TMap::iterator pos;
-	pos = nodeIdMap.find(left_node_id);
-	if (pos == nodeIdMap.end()) return;
-	else sourceV = pos->second;
+    typename TMap::iterator pos;
+    pos = nodeIdMap.find(left_node_id);
+    if (pos == nodeIdMap.end()) return;
+    else sourceV = pos->second;
 
-	pos = nodeIdMap.find(right_node_id);
-	if (pos == nodeIdMap.end()) return;
-	else targetV = pos->second;
+    pos = nodeIdMap.find(right_node_id);
+    if (pos == nodeIdMap.end()) return;
+    else targetV = pos->second;
 
-	_addEdge(g, sourceV, targetV, nodeMap, edgeMap, attr_list);
+    _addEdge(g, sourceV, targetV, nodeMap, edgeMap, attr_list);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -773,36 +754,36 @@ _addEdge(Graph<TSpec>& g,
 template<typename TSpec, typename TStatement, typename TNodeAttributes, typename TEdgeAttributes, typename TNodeIdMap>
 inline void
 _processNodeStatement(Graph<TSpec>& g,
-					  TStatement& stmt,
-					  TNodeAttributes& nodeMap,
-					  TEdgeAttributes& edgeMap,
-					  TNodeIdMap& nodeIdMap) 
-{
-	typedef typename Value<TStatement>::Type TValue;
-	typedef typename Iterator<TStatement>::Type TIter;
-	
-	String<TValue> node_id;
-	String<TValue> attr_list;  // Multiple attribute lists are ignored
-	bool inAttr = false;
-	TIter it = begin(stmt);
-	for(;!atEnd(it);goNext(it)) {
-		if (*it == '[') {
-			inAttr = true;
-			continue;
-		} else if (*it == ']') {
-			// Finished
-			break;
-		} else if ((*it == ' ') ||
-			(*it == '"')) {
-			continue;
-		}
-		if (inAttr) {
-			append(attr_list, *it);
-		} else {
-			append(node_id, *it);
-		}
-	}
-	_addNode(g, node_id, attr_list, nodeMap, edgeMap, nodeIdMap);
+                      TStatement& stmt,
+                      TNodeAttributes& nodeMap,
+                      TEdgeAttributes& edgeMap,
+                      TNodeIdMap& nodeIdMap)
+{
+    typedef typename Value<TStatement>::Type TValue;
+    typedef typename Iterator<TStatement>::Type TIter;
+
+    String<TValue> node_id;
+    String<TValue> attr_list;  // Multiple attribute lists are ignored
+    bool inAttr = false;
+    TIter it = begin(stmt);
+    for(;!atEnd(it);goNext(it)) {
+        if (*it == '[') {
+            inAttr = true;
+            continue;
+        } else if (*it == ']') {
+            // Finished
+            break;
+        } else if ((*it == ' ') ||
+            (*it == '"')) {
+            continue;
+        }
+        if (inAttr) {
+            append(attr_list, *it);
+        } else {
+            append(node_id, *it);
+        }
+    }
+    _addNode(g, node_id, attr_list, nodeMap, edgeMap, nodeIdMap);
 }
 
 
@@ -811,42 +792,42 @@ _processNodeStatement(Graph<TSpec>& g,
 template<typename TSpec, typename TStatement, typename TNodeAttributes, typename TEdgeAttributes, typename TPosition, typename TNodeIdMap>
 inline void
 _processEdgeStatement(Graph<TSpec>& g,
-					  TStatement& stmt,
-					  TNodeAttributes& nodeMap,
-					  TEdgeAttributes& edgeMap,
-					  TPosition pos,
-					  TNodeIdMap& nodeIdMap) 
-{
-	typedef typename Value<TStatement>::Type TValue;
-	typedef typename Iterator<TStatement>::Type TIter;
-	
-	String<TValue> left_node_id;
-	String<TValue> right_node_id;
-	String<TValue> attr_list;  // Multiple attribute lists are ignored
-	bool inAttr = false;
-	TIter it = begin(stmt);
-	unsigned int localPos = 0;
-	for(;!atEnd(it);goNext(it), ++localPos) {
-		if (*it == '[') {
-			inAttr = true;
-			continue;
-		} else if (*it == ']') {
-			// Finished
-			break;
-		} else if ((*it == ' ') ||
-			(*it == '"')) {
-			continue;
-		}
-		if (inAttr) {
-			append(attr_list, *it);
-		} else if (localPos < pos) {
-			append(left_node_id, *it);
-		} else if (localPos > pos+1) {
-			append(right_node_id, *it);
-		}
-	}
-	//std::cout << left_node_id << "," << right_node_id << "," << std::endl;
-	_addEdge(g, left_node_id, right_node_id, attr_list, nodeMap, edgeMap, nodeIdMap);
+                      TStatement& stmt,
+                      TNodeAttributes& nodeMap,
+                      TEdgeAttributes& edgeMap,
+                      TPosition pos,
+                      TNodeIdMap& nodeIdMap)
+{
+    typedef typename Value<TStatement>::Type TValue;
+    typedef typename Iterator<TStatement>::Type TIter;
+
+    String<TValue> left_node_id;
+    String<TValue> right_node_id;
+    String<TValue> attr_list;  // Multiple attribute lists are ignored
+    bool inAttr = false;
+    TIter it = begin(stmt);
+    unsigned int localPos = 0;
+    for(;!atEnd(it);goNext(it), ++localPos) {
+        if (*it == '[') {
+            inAttr = true;
+            continue;
+        } else if (*it == ']') {
+            // Finished
+            break;
+        } else if ((*it == ' ') ||
+            (*it == '"')) {
+            continue;
+        }
+        if (inAttr) {
+            append(attr_list, *it);
+        } else if (localPos < pos) {
+            append(left_node_id, *it);
+        } else if (localPos > pos+1) {
+            append(right_node_id, *it);
+        }
+    }
+    //std::cout << left_node_id << "," << right_node_id << "," << std::endl;
+    _addEdge(g, left_node_id, right_node_id, attr_list, nodeMap, edgeMap, nodeIdMap);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -854,93 +835,90 @@ _processEdgeStatement(Graph<TSpec>& g,
 template<typename TSpec, typename TStatement, typename TNodeAttributes, typename TEdgeAttributes, typename TNodeIdMap>
 inline void
 _processStatement(Graph<TSpec>& g,
-				  TStatement& stmt,
-				  TNodeAttributes& nodeMap,
-				  TEdgeAttributes& edgeMap,
-				  TNodeIdMap& nodeIdMap) 
-{
-	// Clear everything up to the last line
-	typedef typename Value<TStatement>::Type TValue;
-	typedef typename Iterator<TStatement>::Type TIter;
-
-	// Exclude header and empty lines
-	TIter it = begin(stmt);
-	String<TValue> _id;
-	for(;!atEnd(it);goNext(it)) {
-	  if ((*it != '\t') && (*it != ' ') && (*it != '\n') && (*it != '\r')) {
-	    append(_id, *it);
-	  } else {
-	    // Exclude any graph, subgraph, node and edge processing attributes
-	    if ((_id == "graph") || (_id == "node") || (_id == "edge") || (_id == "subgraph") || (length(_id)<1)) {
-	      clear(stmt);
-	      return;
-	    } else break; 
-	  }
-	}
-
-	// Process Edges
-	it = begin(stmt);
-	clear(_id);
-	_id = "00";
-	unsigned int pos = 0;
-	for(;!atEnd(it);goNext(it), ++pos) {
-	  _id[pos % 2] = *it;
-	  if ((_id == "--") || (_id == "->")) {
-	    //std::cout << stmt << std::endl;
-	    _processEdgeStatement(g, stmt, nodeMap, edgeMap, pos - 1, nodeIdMap);
-	    clear(stmt);
-	    return;
-	  }
-	}
-
-	// Process nodes
-	//std::cout << stmt << std::endl;
-	_processNodeStatement(g, stmt, nodeMap, edgeMap, nodeIdMap);
-	clear(stmt);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TSpec, typename TNodeAttributes, typename TEdgeAttributes>
-void read(TFile & file,
-		  Graph<TSpec>& g,
-		  TNodeAttributes& nodeMap,
-		  TEdgeAttributes& edgeMap,
-		  DotDrawing)
-{
-    // TODO(holtgrew): Could be adapted to use RecordReader for parsing.
-	typedef Graph<TSpec> TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Value<TFile>::Type TValue;
-	typedef std::map<String<TValue>, TVertexDescriptor> TMap;
-	TMap nodeIdMap;
-
-	TValue c;
-	String<TValue> stmt;
-	while (!streamEOF(file)) {
-        streamReadChar(c, file);
-
-		if (c == ';') _processStatement(g,stmt, nodeMap, edgeMap, nodeIdMap);
-		else if ((c == '\n') ||
-				(c == '\r')) {
-					clear(stmt);
-		}
-		else append(stmt,c);
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TSpec>
-void read(TFile & file,
-		  Graph<TSpec>& g,
-		  DotDrawing) 
-{
-//IOREV _batchreading_ 
-	String<String<char> > nodeMap;
-	String<String<char> > edgeMap;
-	read(file,g,nodeMap,edgeMap,DotDrawing());
+                  TStatement& stmt,
+                  TNodeAttributes& nodeMap,
+                  TEdgeAttributes& edgeMap,
+                  TNodeIdMap& nodeIdMap)
+{
+    // Clear everything up to the last line
+    typedef typename Value<TStatement>::Type TValue;
+    typedef typename Iterator<TStatement>::Type TIter;
+
+    // Exclude header and empty lines
+    TIter it = begin(stmt);
+    String<TValue> _id;
+    for(;!atEnd(it);goNext(it)) {
+      if ((*it != '\t') && (*it != ' ') && (*it != '\n') && (*it != '\r')) {
+        append(_id, *it);
+      } else {
+        // Exclude any graph, subgraph, node and edge processing attributes
+        if ((_id == "graph") || (_id == "node") || (_id == "edge") || (_id == "subgraph") || (length(_id)<1)) {
+          clear(stmt);
+          return;
+        } else break;
+      }
+    }
+
+    // Process Edges
+    it = begin(stmt);
+    clear(_id);
+    _id = "00";
+    unsigned int pos = 0;
+    for(;!atEnd(it);goNext(it), ++pos) {
+      _id[pos % 2] = *it;
+      if ((_id == "--") || (_id == "->")) {
+        //std::cout << stmt << std::endl;
+        _processEdgeStatement(g, stmt, nodeMap, edgeMap, pos - 1, nodeIdMap);
+        clear(stmt);
+        return;
+      }
+    }
+
+    // Process nodes
+    //std::cout << stmt << std::endl;
+    _processNodeStatement(g, stmt, nodeMap, edgeMap, nodeIdMap);
+    clear(stmt);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSpec, typename TNodeAttributes, typename TEdgeAttributes, typename TInStream>
+void readRecords(
+    Graph<TSpec>& g,
+    TNodeAttributes& nodeMap,
+    TEdgeAttributes& edgeMap,
+    TInStream & stream,
+    DotDrawing)
+{
+    typename DirectionIterator<TInStream, Input>::Type reader = directionIterator(stream, Input());
+
+    typedef Graph<TSpec> TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef std::map<CharString, TVertexDescriptor> TMap;
+    TMap nodeIdMap;
+
+    CharString stmt;
+    while (!atEnd(reader))
+    {
+        clear(stmt);
+        readUntil(stmt, reader, EqualsChar<';'>());
+        _processStatement(g, stmt, nodeMap, edgeMap, nodeIdMap);
+        skipLine(reader);
+    }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TSpec, typename TInStream>
+void readRecords(
+    Graph<TSpec>& g,
+    TInStream & stream,
+    DotDrawing)
+{
+    String<CharString> nodeMap;
+    String<CharString> edgeMap;
+    readRecords(g, nodeMap, edgeMap, stream, DotDrawing());
 }
 
 
diff --git a/seqan/graph_types/graph_edgestump.h b/seqan/graph_types/graph_edgestump.h
index b0f8cf4..d031af2 100644
--- a/seqan/graph_types/graph_edgestump.h
+++ b/seqan/graph_types/graph_edgestump.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,7 +36,7 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 //////////////////////////////////////////////////////////////////////////////
-//	Graph - EdgeStump
+//    Graph - EdgeStump
 //////////////////////////////////////////////////////////////////////////////
 
 //////////////////////////////////////////////////////////////////////////////
@@ -53,7 +53,7 @@ namespace SEQAN_NAMESPACE_MAIN
  *            class EdgeStump;
  *
  * @tparam TCargo       The cargo type of an edge.  The cargo can be used to store arbitrary information with an
- *                      edge or be <tt>void</tt.>.  Default: <tt>void</tt>.
+ *                      edge or be <tt>void</tt>.  Default: <tt>void</tt>.
  * @tparam IS_LIST      A bool value that indicates whether it is a list or not.  Default: <tt>true</tt>.
  * @tparam STORE_SOURCE A bool value that indicates whether the source is stored in the EdgeStump or not.
  *                      Default: <tt>false</tt>.
@@ -67,35 +67,8 @@ namespace SEQAN_NAMESPACE_MAIN
  * an edge id.  Edge ids are used to append additional properties to edges with the help of external property maps.
  */
 
-/**
-.Class.EdgeStump:
-..cat:Graph
-..summary:The EdgeStump class encapsulates a single edge. 
-It represents either a list node in the adjacency list of a graph or an array field if edges are stored in an array.
-..signature:EdgeStump<TCargo, bool TList, bool TSource, bool TId, TSpec>
-..param.TCargo:The cargo type of an edge.
-...metafunction:Metafunction.Cargo
-...remarks:The cargo can be used to store arbitrary information with an edge.
-...default:$void$
-..param.TList:Boolean value that indicates whether it is a list node or not.
-...remarks:If it is a list node it has one or two next pointers.
-...default:$true$
-..param.TSource:Boolean value that indicates whether the source is stored in the EdgeStump or not.
-...remarks:If this value is true and it is a list node an additional source next pointer is present.
-...default:$false$
-..param.TId:Boolean value that indicates whether an id is stored in the EdgeStump or not.
-Note: Without edge ids external property maps do not work for edges!
-...default:$true$
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:$Default$, see @Tag.Default@.
-..remarks:The default EdgeStump in all graph types does not consider a cargo. 
-However, in default usage every graph does store an edge id. 
-Edge ids are used to append additional properties to edges with the help of external property maps.
-..include:seqan/graph_types.h
-*/
 template<typename TCargo, typename TSpec>
-class EdgeStump<TCargo, true, false, false, TSpec> 
+class EdgeStump<TCargo, true, false, false, TSpec>
 {
 public:
     EdgeStump() : data_target(), data_cargo(), data_nextT()
@@ -110,7 +83,7 @@ class EdgeStump<TCargo, true, false, false, TSpec>
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-class EdgeStump<TCargo, true, false, true, TSpec> 
+class EdgeStump<TCargo, true, false, true, TSpec>
 {
 public:
     EdgeStump() : data_target(), data_id(), data_cargo(), data_nextT()
@@ -127,7 +100,7 @@ class EdgeStump<TCargo, true, false, true, TSpec>
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-class EdgeStump<TCargo, true, true, false, TSpec> 
+class EdgeStump<TCargo, true, true, false, TSpec>
 {
 public:
     EdgeStump() : data_target(), data_source(), data_cargo(), data_nextT(), data_nextS()
@@ -145,7 +118,7 @@ class EdgeStump<TCargo, true, true, false, TSpec>
 
 
 template<typename TCargo, typename TSpec>
-class EdgeStump<TCargo, true, true, true, TSpec> 
+class EdgeStump<TCargo, true, true, true, TSpec>
 {
 public:
     EdgeStump() : data_target(), data_source(), data_id(), data_cargo(), data_nextT(), data_nextS()
@@ -230,7 +203,7 @@ class EdgeStump<TCargo, false, true, true, TSpec>
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec>
-class EdgeStump<void, true, false, false, TSpec> 
+class EdgeStump<void, true, false, false, TSpec>
 {
 public:
     EdgeStump() : data_target(), data_nextT()
@@ -244,7 +217,7 @@ class EdgeStump<void, true, false, false, TSpec>
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec>
-class EdgeStump<void, true, false, true, TSpec> 
+class EdgeStump<void, true, false, true, TSpec>
 {
 public:
     EdgeStump() : data_target(), data_id(), data_nextT()
@@ -260,7 +233,7 @@ class EdgeStump<void, true, false, true, TSpec>
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec>
-class EdgeStump<void, true, true, false, TSpec> 
+class EdgeStump<void, true, true, false, TSpec>
 {
 public:
     EdgeStump() : data_target(), data_source(), data_nextT(), data_nextS()
@@ -277,7 +250,7 @@ class EdgeStump<void, true, true, false, TSpec>
 
 
 template<typename TSpec>
-class EdgeStump<void, true, true, true, TSpec> 
+class EdgeStump<void, true, true, true, TSpec>
 {
 public:
     EdgeStump() : data_target(), data_source(), data_id(), data_nextT(), data_nextS()
@@ -356,46 +329,40 @@ class EdgeStump<void, false, true, true, TSpec>
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Cargo.param.T.type:Class.EdgeStump
-///.Metafunction.Cargo.class:Class.EdgeStump
-
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 struct Cargo<EdgeStump<TCargo, TList, TSource, TId, TSpec> > {
-	typedef TCargo Type;
+    typedef TCargo Type;
 };
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 struct Cargo<EdgeStump<TCargo, TList, TSource, TId, TSpec> const> {
-	typedef TCargo const Type;
+    typedef TCargo const Type;
 };
 
 
 template<bool TList, bool TSource, bool TId, typename TSpec>
 struct Cargo<EdgeStump<void, TList, TSource, TId, TSpec> > {
-	typedef void* Type;
+    typedef void* Type;
 };
 
 template<bool TList, bool TSource, bool TId, typename TSpec>
 struct Cargo<EdgeStump<void, TList, TSource, TId, TSpec> const> {
-	typedef void* Type;
+    typedef void* Type;
 };
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Spec.param.T.type:Class.EdgeStump
-///.Metafunction.Spec.class:Class.EdgeStump
-
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
-struct Spec<EdgeStump<TCargo, TList, TSource, TId, TSpec> > 
+struct Spec<EdgeStump<TCargo, TList, TSource, TId, TSpec> >
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
-struct Spec<EdgeStump<TCargo, TList, TSource, TId, TSpec> const> 
+struct Spec<EdgeStump<TCargo, TList, TSource, TId, TSpec> const>
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -416,60 +383,45 @@ struct Spec<EdgeStump<TCargo, TList, TSource, TId, TSpec> const>
  * @return TCargo Reference to the cargo of the EdgeStump.
  */
 
-/**
-.Function.getCargo
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Get method for the edge cargo.
-..signature:getCargo(es)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Returns the cargo.
-..remarks:If cargo is not present the return value is (void*) 0.
-..see:Function.cargo
-..see:Function.assignCargo
-..include:seqan/graph_types.h
-*/
-
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 inline typename Cargo<EdgeStump<TCargo, TList, TSource, TId, TSpec> const>::Type&
 getCargo(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_cargo;
+    SEQAN_CHECKPOINT
+    return es->data_cargo;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 inline typename Cargo<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type&
-getCargo(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es) 
+getCargo(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_cargo;
+    SEQAN_CHECKPOINT
+    return es->data_cargo;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<bool TList, bool TSource, bool TId, typename TSpec>
 inline typename Cargo<EdgeStump<void, TList, TSource, TId, TSpec> const>::Type
-getCargo(EdgeStump<void, TList, TSource, TId, TSpec> const*) 
+getCargo(EdgeStump<void, TList, TSource, TId, TSpec> const*)
 {
-	SEQAN_CHECKPOINT
-	// No real cargo
-	return 0;
+    SEQAN_CHECKPOINT
+    // No real cargo
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<bool TList, bool TSource, bool TId, typename TSpec>
 inline typename Cargo<EdgeStump<void, TList, TSource, TId, TSpec> >::Type
-getCargo(EdgeStump<void, TList, TSource, TId, TSpec>*) 
+getCargo(EdgeStump<void, TList, TSource, TId, TSpec>*)
 {
-	SEQAN_CHECKPOINT
-	// No real cargo
-	return 0;
+    SEQAN_CHECKPOINT
+    // No real cargo
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -485,38 +437,23 @@ getCargo(EdgeStump<void, TList, TSource, TId, TSpec>*)
  * @return TCargo Reference to the cargo of the EdgeStump.
  */
 
-/**
-.Function.cargo
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Access to the cargo.
-..signature:cargo(es)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Returns a reference to the cargo.
-..remarks:If cargo is not present the return value is (void*) 0.
-..see:Function.getCargo
-..see:Function.assignCargo
-..include:seqan/graph_types.h
-*/
-
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 inline typename Cargo<EdgeStump<TCargo, TList, TSource, TId, TSpec> const>::Type&
-cargo(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es) 
+cargo(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_cargo;
+    SEQAN_CHECKPOINT
+    return es->data_cargo;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
-inline typename Cargo<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type& 
-cargo(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es) 
+inline typename Cargo<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type&
+cargo(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_cargo;
+    SEQAN_CHECKPOINT
+    return es->data_cargo;
 }
 
 
@@ -524,22 +461,22 @@ cargo(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es)
 
 template<bool TList, bool TSource, bool TId, typename TSpec>
 inline typename Cargo<EdgeStump<void, TList, TSource, TId, TSpec> >::Type
-cargo(EdgeStump<void, TList, TSource, TId, TSpec>*) 
+cargo(EdgeStump<void, TList, TSource, TId, TSpec>*)
 {
-	SEQAN_CHECKPOINT
-	// No real cargo
-	return 0;
+    SEQAN_CHECKPOINT
+    // No real cargo
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<bool TList, bool TSource, bool TId, typename TSpec>
 inline typename Cargo<EdgeStump<void, TList, TSource, TId, TSpec> const>::Type
-cargo(EdgeStump<void, TList, TSource, TId, TSpec> const*) 
+cargo(EdgeStump<void, TList, TSource, TId, TSpec> const*)
 {
-	SEQAN_CHECKPOINT
-	// No real cargo
-	return 0;
+    SEQAN_CHECKPOINT
+    // No real cargo
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -557,41 +494,24 @@ cargo(EdgeStump<void, TList, TSource, TId, TSpec> const*)
  * Calling assignCargo on EdgeStump objects without cargo does nothing.
  */
 
-/**
-.Function.assignCargo
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Assigns a new cargo to the edge.
-..signature:assignCargo(es, cargo)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..param.cargo:New cargo object.
-...remarks:Type of the new cargo object must match Cargo<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type.
-..returns:void
-..remarks:In cargoless EdgeStumps this operation is a NOP.
-..see:Function.cargo
-..see:Function.getCargo
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec, typename TCargo2>
-inline void 
+inline void
 assignCargo(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es,
-			TCargo2 const& t) 
+            TCargo2 const& t)
 {
-	SEQAN_CHECKPOINT
-	es->data_cargo =  (TCargo) t;
+    SEQAN_CHECKPOINT
+    es->data_cargo =  (TCargo) t;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<bool TList, bool TSource, bool TId, typename TSpec, typename TCargo2>
-inline void 
-assignCargo(EdgeStump<void, TList, TSource, TId, TSpec>*, 
-			TCargo2 const&) 
+inline void
+assignCargo(EdgeStump<void, TList, TSource, TId, TSpec>*,
+            TCargo2 const&)
 {
-	SEQAN_CHECKPOINT
-	// No real cargo
+    SEQAN_CHECKPOINT
+    // No real cargo
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -606,29 +526,14 @@ assignCargo(EdgeStump<void, TList, TSource, TId, TSpec>*,
  * @param[in]     t     Vertex descriptor to assign as the target.
  */
 
-/**
-.Function.assignTarget
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Assigns a target vertex to an edge.
-..signature:assignTarget(es, t)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..param.t:Target vertex.
-..returns:void
-..see:Function.target
-..see:Function.getTarget
-..include:seqan/graph_types.h
-*/
-
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec, typename TVertexDescriptor>
-inline void 
-assignTarget(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es, 
-			 TVertexDescriptor const t) 
+inline void
+assignTarget(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es,
+             TVertexDescriptor const t)
 {
-	SEQAN_CHECKPOINT
-	es->data_target = t;
+    SEQAN_CHECKPOINT
+    es->data_target = t;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -644,36 +549,22 @@ assignTarget(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es,
  * @return TVertexDescriptor Reference to the target vertex descriptor of stump.
  */
 
-/**
-.Function.target
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Accesses the target of an EdgeStump.
-..signature:target(es)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Reference to the target vertex.
-..see:Function.assignTarget
-..see:Function.getTarget
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type&
-target(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es) 
+target(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_target;
+    SEQAN_CHECKPOINT
+    return es->data_target;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type
-target(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es) 
+target(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_target;
+    SEQAN_CHECKPOINT
+    return es->data_target;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -689,36 +580,22 @@ target(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es)
  * @return TVertexDescriptor The vetex descriptor stored in stump.
  */
 
-/**
-.Function.getTarget
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Get method for the target.
-..signature:getTarget(es)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Target vertex.
-..see:Function.assignTarget
-..see:Function.target
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, TSource, TId, TSpec> const>::Type
-getTarget(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es) 
+getTarget(EdgeStump<TCargo, TList, TSource, TId, TSpec> const* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_target;
+    SEQAN_CHECKPOINT
+    return es->data_target;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, TSource, TId, TSpec> >::Type
-getTarget(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es) 
+getTarget(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_target;
+    SEQAN_CHECKPOINT
+    return es->data_target;
 }
 
 
@@ -739,41 +616,24 @@ getTarget(EdgeStump<TCargo, TList, TSource, TId, TSpec>* es)
  * vertex, as in undirected graphs.
  */
 
-/**
-.Function.Graph#assignSource
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Assigns a source vertex to an edge.
-..remarks:A source vertex is not required in an edge stump.
-However, EdgeStumps can be configured to contain a source vertex, e.g., in undirected graphs.
-..signature:assignSource(es, s)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..param.s:Source vertex.
-..returns:void
-..see:Function.source
-..see:Function.getSource
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TList, bool TId, typename TSpec, typename TVertexDescriptor>
-inline void 
-assignSource(EdgeStump<TCargo, TList, true, TId, TSpec>* es, 
-			 TVertexDescriptor const s) 
+inline void
+assignSource(EdgeStump<TCargo, TList, true, TId, TSpec>* es,
+             TVertexDescriptor const s)
 {
-	SEQAN_CHECKPOINT
-	es->data_source = s;
+    SEQAN_CHECKPOINT
+    es->data_source = s;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TId, typename TSpec, typename TVertexDescriptor>
-inline void 
-assignSource(EdgeStump<TCargo, TList, false, TId, TSpec>*, 
-			 TVertexDescriptor const) 
+inline void
+assignSource(EdgeStump<TCargo, TList, false, TId, TSpec>*,
+             TVertexDescriptor const)
 {
-	SEQAN_CHECKPOINT
-	// NOP
+    SEQAN_CHECKPOINT
+    // NOP
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -796,20 +656,20 @@ assignSource(EdgeStump<TCargo, TList, false, TId, TSpec>*,
 
 template<typename TCargo, bool TList, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, true, TId, TSpec> >::Type&
-source(EdgeStump<TCargo, TList, true, TId, TSpec>* es) 
+source(EdgeStump<TCargo, TList, true, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_source;
+    SEQAN_CHECKPOINT
+    return es->data_source;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, true, TId, TSpec> >::Type
-source(EdgeStump<TCargo, TList, true, TId, TSpec> const* es) 
+source(EdgeStump<TCargo, TList, true, TId, TSpec> const* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_source;
+    SEQAN_CHECKPOINT
+    return es->data_source;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -817,11 +677,11 @@ source(EdgeStump<TCargo, TList, true, TId, TSpec> const* es)
 
 template<typename TCargo, bool TList, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, false, TId, TSpec> >::Type
-source(EdgeStump<TCargo, TList, false, TId, TSpec>*) 
+source(EdgeStump<TCargo, TList, false, TId, TSpec>*)
 {
-	SEQAN_CHECKPOINT
-	// No source available
-	return 0;
+    SEQAN_CHECKPOINT
+    // No source available
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -829,11 +689,11 @@ source(EdgeStump<TCargo, TList, false, TId, TSpec>*)
 
 template<typename TCargo, bool TList, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, false, TId, TSpec> >::Type
-source(EdgeStump<TCargo, TList, false, TId, TSpec> const*) 
+source(EdgeStump<TCargo, TList, false, TId, TSpec> const*)
 {
-	SEQAN_CHECKPOINT
-	// No source available
-	return 0;
+    SEQAN_CHECKPOINT
+    // No source available
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -854,60 +714,44 @@ source(EdgeStump<TCargo, TList, false, TId, TSpec> const*)
  * vertex, as in undirected graphs.
  */
 
-/**
-.Function.getSource
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Get method for the source.
-..remarks:A source vertex is not required in an edge stump.
-However, EdgeStumps can be configured to contain a source vertex, e.g., in undirected graphs.
-..signature:getSource(es)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Source vertex.
-..see:Function.Graph#assignSource
-..see:Function.source
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TList, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, true, TId, TSpec> const>::Type
-getSource(EdgeStump<TCargo, TList, true, TId, TSpec> const* es) 
+getSource(EdgeStump<TCargo, TList, true, TId, TSpec> const* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_source;
+    SEQAN_CHECKPOINT
+    return es->data_source;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, true, TId, TSpec> >::Type
-getSource(EdgeStump<TCargo, TList, true, TId, TSpec>* es) 
+getSource(EdgeStump<TCargo, TList, true, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_source;
+    SEQAN_CHECKPOINT
+    return es->data_source;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, false, TId, TSpec> const>::Type
-getSource(EdgeStump<TCargo, TList, false, TId, TSpec> const*) 
+getSource(EdgeStump<TCargo, TList, false, TId, TSpec> const*)
 {
-	SEQAN_CHECKPOINT
-	// Nop
-	return 0;
+    SEQAN_CHECKPOINT
+    // Nop
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TId, typename TSpec>
 inline typename VertexDescriptor<EdgeStump<TCargo, TList, false, TId, TSpec> >::Type
-getSource(EdgeStump<TCargo, TList, false, TId, TSpec>*) 
+getSource(EdgeStump<TCargo, TList, false, TId, TSpec>*)
 {
-	SEQAN_CHECKPOINT
-	// Nop
-	return 0;
+    SEQAN_CHECKPOINT
+    // Nop
+    return 0;
 }
 
 
@@ -925,29 +769,13 @@ getSource(EdgeStump<TCargo, TList, false, TId, TSpec>*)
  * @param[in]     es2 Pointer to the following EdgeStump.
  */
 
-/**
-.Function.assignNextT
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Assigns another EdgeStump to the next target pointer.
-..signature:assignNextT(es, es2)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..param.es2:Pointer to the following EdgeStump.
-...type:Class.EdgeStump
-..returns:void
-..see:Function.nextT
-..see:Function.getNextT
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TSource, bool TId, typename TSpec>
-inline void 
-assignNextT(EdgeStump<TCargo, true, TSource, TId, TSpec>* es, 
-			EdgeStump<TCargo, true, TSource, TId, TSpec>* es2) 
+inline void
+assignNextT(EdgeStump<TCargo, true, TSource, TId, TSpec>* es,
+            EdgeStump<TCargo, true, TSource, TId, TSpec>* es2)
 {
-	SEQAN_CHECKPOINT
-	es->data_nextT = es2;
+    SEQAN_CHECKPOINT
+    es->data_nextT = es2;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -963,35 +791,21 @@ assignNextT(EdgeStump<TCargo, true, TSource, TId, TSpec>* es,
  * @return TEdgeStump Reference to the next target pointer.
  */
 
-/**
-.Function.nextT
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Accesses the next target pointer.
-..signature:nextT(es)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Reference to the next target pointer.
-..see:Function.assignNextT
-..see:Function.getNextT
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TSource, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, TSource, TId, TSpec>* &
-nextT(EdgeStump<TCargo, true, TSource, TId, TSpec>* es) 
+nextT(EdgeStump<TCargo, true, TSource, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_nextT;
+    SEQAN_CHECKPOINT
+    return es->data_nextT;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TSource, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, TSource, TId, TSpec>* &
-nextT(EdgeStump<TCargo, true, TSource, TId, TSpec> const* es) 
+nextT(EdgeStump<TCargo, true, TSource, TId, TSpec> const* es)
 {
-	return es->data_nextT;
+    return es->data_nextT;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1007,26 +821,12 @@ nextT(EdgeStump<TCargo, true, TSource, TId, TSpec> const* es)
  * @return TEdgeStump Reference to the next target pointer.
  */
 
-/**
-.Function.getNextT
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Get method for the next target pointer.
-..signature:getNextT(es)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Pointer to the next edge stump in target list.
-..see:Function.assignNextT
-..see:Function.nextT
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TSource, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, TSource, TId, TSpec>*
-getNextT(EdgeStump<TCargo, true, TSource, TId, TSpec>* es) 
+getNextT(EdgeStump<TCargo, true, TSource, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_nextT;
+    SEQAN_CHECKPOINT
+    return es->data_nextT;
 }
 
 
@@ -1034,9 +834,9 @@ getNextT(EdgeStump<TCargo, true, TSource, TId, TSpec>* es)
 
 template<typename TCargo, bool TSource, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, TSource, TId, TSpec>*
-getNextT(EdgeStump<TCargo, true, TSource, TId, TSpec> const* es) 
+getNextT(EdgeStump<TCargo, true, TSource, TId, TSpec> const* es)
 {
-	return es->data_nextT;
+    return es->data_nextT;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1053,42 +853,25 @@ getNextT(EdgeStump<TCargo, true, TSource, TId, TSpec> const* es)
  * Edge Stumps can be configured to have no source.  In this case, there is no next source pointer.
  */
 
-/**
-.Function.assignNextS
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Assigns another EdgeStump to the next source pointer.
-..signature:assignNextS(es, es2)
-..remarks:EdgeStumps can be configured to have no source. Then there is no next source pointer.
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..param.es2:Pointer to the following EdgeStump.
-...type:Class.EdgeStump
-..returns:void
-..see:Function.nextS
-..see:Function.getNextS
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TId, typename TSpec>
-inline void 
-assignNextS(EdgeStump<TCargo, true, true, TId, TSpec>* es, 
-			EdgeStump<TCargo, true, true, TId, TSpec>* es2) 
+inline void
+assignNextS(EdgeStump<TCargo, true, true, TId, TSpec>* es,
+            EdgeStump<TCargo, true, true, TId, TSpec>* es2)
 {
-	SEQAN_CHECKPOINT
-	es->data_nextS = es2;
+    SEQAN_CHECKPOINT
+    es->data_nextS = es2;
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TId, typename TSpec>
-inline void 
-assignNextS(EdgeStump<TCargo, true, false, TId, TSpec>*, 
-			EdgeStump<TCargo, true, false, TId, TSpec>*) 
+inline void
+assignNextS(EdgeStump<TCargo, true, false, TId, TSpec>*,
+            EdgeStump<TCargo, true, false, TId, TSpec>*)
 {
-	SEQAN_CHECKPOINT
-	// Nop
+    SEQAN_CHECKPOINT
+    // Nop
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1106,57 +889,42 @@ assignNextS(EdgeStump<TCargo, true, false, TId, TSpec>*,
  * Edge Stumps can be configured to have no source.  In this case, there is no next source pointer.
  */
 
-/**
-.Function.nextS
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Accesses the next source pointer.
-..signature:nextS(es)
-..remarks:EdgeStumps can be configured to have no source. Then there is no next source pointer.
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Reference to the next source pointer.
-..see:Function.assignNextS
-..see:Function.getNextS
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, true, TId, TSpec>* &
-nextS(EdgeStump<TCargo, true, true, TId, TSpec>* es) 
+nextS(EdgeStump<TCargo, true, true, TId, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_nextS;
+    SEQAN_CHECKPOINT
+    return es->data_nextS;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, true, TId, TSpec>* &
-nextS(EdgeStump<TCargo, true, true, TId, TSpec> const* es) 
+nextS(EdgeStump<TCargo, true, true, TId, TSpec> const* es)
 {
-	return es->data_nextS;
+    return es->data_nextS;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, false, TId, TSpec>*
-nextS(EdgeStump<TCargo, true, false, TId, TSpec>*) 
+nextS(EdgeStump<TCargo, true, false, TId, TSpec>*)
 {
-	SEQAN_CHECKPOINT
-	// Nop
-	return 0;
+    SEQAN_CHECKPOINT
+    // Nop
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, false, TId, TSpec>*
-nextS(EdgeStump<TCargo, true, false, TId, TSpec> const*) 
+nextS(EdgeStump<TCargo, true, false, TId, TSpec> const*)
 {
-	// Nop
-	return 0;
+    // Nop
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1174,38 +942,23 @@ nextS(EdgeStump<TCargo, true, false, TId, TSpec> const*)
  * Edge Stumps can be configured to have no source.  In this case, there is no next source pointer.
  */
 
-/**
-.Function.getNextS
-..class:Class.EdgeStump
-..cat:Graph
-..summary:Get method for the next source pointer.
-..remarks:EdgeStumps can be configured to have no source. Then there is no next source pointer.
-..signature:getNextS(es)
-..param.es:Pointer to the EdgeStump.
-...type:Class.EdgeStump
-..returns:Pointer to the next edge stump in source list.
-..see:Function.assignNextS
-..see:Function.nextS
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, true, TId, TSpec>*
-getNextS(EdgeStump<TCargo, true, true, TId, TSpec> const* es) 
+getNextS(EdgeStump<TCargo, true, true, TId, TSpec> const* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_nextS;
+    SEQAN_CHECKPOINT
+    return es->data_nextS;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TId, typename TSpec>
 inline EdgeStump<TCargo, true, false, TId, TSpec>*
-getNextS(EdgeStump<TCargo, true, false, TId, TSpec> const*) 
+getNextS(EdgeStump<TCargo, true, false, TId, TSpec> const*)
 {
-	SEQAN_CHECKPOINT
-	// No source pointer
-	return 0;
+    SEQAN_CHECKPOINT
+    // No source pointer
+    return 0;
 }
 
 
@@ -1220,96 +973,96 @@ getNextS(EdgeStump<TCargo, true, false, TId, TSpec> const*)
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, typename TSpec, typename TId2>
-void 
-_assignId(EdgeStump<TCargo, TList, TSource, true, TSpec>* es, 
-		  TId2 const id) 
+void
+_assignId(EdgeStump<TCargo, TList, TSource, true, TSpec>* es,
+          TId2 const id)
 {
-	SEQAN_CHECKPOINT
-	es->data_id = id;
+    SEQAN_CHECKPOINT
+    es->data_id = id;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, typename TSpec, typename TId2>
-void 
-_assignId(EdgeStump<TCargo, TList, TSource, false, TSpec>*, 
-		  TId2 const) 
+void
+_assignId(EdgeStump<TCargo, TList, TSource, false, TSpec>*,
+          TId2 const)
 {
-	// No id -> does nothing
+    // No id -> does nothing
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, typename TId2>
-void 
-_assignId(EdgeStump<TCargo, TList, TSource, false, TreeTag>*, 
-		  TId2 const) 
+void
+_assignId(EdgeStump<TCargo, TList, TSource, false, TreeTag>*,
+          TId2 const)
 {
-	// For a tree do nothing, child id = tree id
+    // For a tree do nothing, child id = tree id
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, typename TSpec>
 inline typename Id<EdgeStump<TCargo, TList, TSource, true, TSpec> const>::Type
-_getId(EdgeStump<TCargo, TList, TSource, true, TSpec> const* es) 
+_getId(EdgeStump<TCargo, TList, TSource, true, TSpec> const* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_id;
+    SEQAN_CHECKPOINT
+    return es->data_id;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, typename TSpec>
 inline typename Id<EdgeStump<TCargo, TList, TSource, true, TSpec> >::Type
-_getId(EdgeStump<TCargo, TList, TSource, true, TSpec>* es) 
+_getId(EdgeStump<TCargo, TList, TSource, true, TSpec>* es)
 {
-	SEQAN_CHECKPOINT
-	return es->data_id;
+    SEQAN_CHECKPOINT
+    return es->data_id;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource>
 inline typename Id<EdgeStump<TCargo, TList, TSource, false, TreeTag> const>::Type
-_getId(EdgeStump<TCargo, TList, TSource, false, TreeTag> const* es) 
+_getId(EdgeStump<TCargo, TList, TSource, false, TreeTag> const* es)
 {
-	SEQAN_CHECKPOINT
-	// Child id = edge id in a tree
-	return es->data_target;
+    SEQAN_CHECKPOINT
+    // Child id = edge id in a tree
+    return es->data_target;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource>
 inline typename Id<EdgeStump<TCargo, TList, TSource, false, TreeTag> >::Type
-_getId(EdgeStump<TCargo, TList, TSource, false, TreeTag>* es) 
+_getId(EdgeStump<TCargo, TList, TSource, false, TreeTag>* es)
 {
-	SEQAN_CHECKPOINT
-	// Child id = edge id in a tree
-	return es->data_target;
+    SEQAN_CHECKPOINT
+    // Child id = edge id in a tree
+    return es->data_target;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, typename TSpec>
-inline typename Id<EdgeStump<TCargo, TList, TSource, false, TSpec> >::Type 
-_getId(EdgeStump<TCargo, TList, TSource, false, TSpec> const*) 
+inline typename Id<EdgeStump<TCargo, TList, TSource, false, TSpec> >::Type
+_getId(EdgeStump<TCargo, TList, TSource, false, TSpec> const*)
 {
-	SEQAN_CHECKPOINT
-	// No real id
-	return 0;
+    SEQAN_CHECKPOINT
+    // No real id
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, bool TList, bool TSource, typename TSpec>
-inline typename Id<EdgeStump<TCargo, TList, TSource, false, TSpec> >::Type 
-_getId(EdgeStump<TCargo, TList, TSource, false, TSpec>*) 
+inline typename Id<EdgeStump<TCargo, TList, TSource, false, TSpec> >::Type
+_getId(EdgeStump<TCargo, TList, TSource, false, TSpec>*)
 {
-	SEQAN_CHECKPOINT
-	// No real id
-	return 0;
+    SEQAN_CHECKPOINT
+    // No real id
+    return 0;
 }
 
 
diff --git a/seqan/graph_types/graph_idmanager.h b/seqan/graph_types/graph_idmanager.h
index 8c528b6..4d7264d 100644
--- a/seqan/graph_types/graph_idmanager.h
+++ b/seqan/graph_types/graph_idmanager.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,61 +54,47 @@ namespace SEQAN_NAMESPACE_MAIN
  * @tparam TSpec   Specializing type.
  */
 
-/**
-.Class.IdManager:
-..cat:Graph
-..summary:Id manager that provides unique ids for vertices and edges.
-..signature:IdManager<TIdType,TSpec>
-..param.TIdType:The id type of the managed ids.
-...metafunction:Metafunction.Value
-...remarks:Use the Value Metafunction to get the id type managed by a given id manager.
-...default:$unsigned int$
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
-template<typename TIdType, typename TSpec>
-class IdManager 
+template <typename TIdType, typename TSpec>
+class IdManager
 {
-	public:
-		String<TIdType> data_freeIds;  
-		String<bool> data_in_use;   //1 = in use, 0 = not in use
-
-//____________________________________________________________________________	
-	public:
-		IdManager()
-		{
-			SEQAN_CHECKPOINT
-			clear(data_in_use);
-			clear(data_freeIds);
-		}
-
-		~IdManager() 
-		{
-			SEQAN_CHECKPOINT
-		}
-
-		IdManager(IdManager const & _other)
-		{
-			SEQAN_CHECKPOINT
-			data_freeIds = _other.data_freeIds;
-			data_in_use = _other.data_in_use;
-		}
-
-		IdManager const& 
-		operator = (IdManager const& _other) 
-		{
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			data_freeIds = _other.data_freeIds;
-			data_in_use = _other.data_in_use;
-			return *this;
-		}
+    public:
+        String<TIdType> data_freeIds;
+        String<bool> data_in_use;   //1 = in use, 0 = not in use
+
+//____________________________________________________________________________
+    public:
+        IdManager()
+        {
+            SEQAN_CHECKPOINT
+            clear(data_in_use);
+            clear(data_freeIds);
+        }
+
+        ~IdManager()
+        {
+            SEQAN_CHECKPOINT
+        }
+
+        IdManager(IdManager const & _other)
+        {
+            SEQAN_CHECKPOINT
+            data_freeIds = _other.data_freeIds;
+            data_in_use = _other.data_in_use;
+        }
+
+        IdManager const&
+        operator = (IdManager const& _other)
+        {
+            SEQAN_CHECKPOINT
+            if (this == &_other) return *this;
+            data_freeIds = _other.data_freeIds;
+            data_in_use = _other.data_in_use;
+            return *this;
+        }
 
 //____________________________________________________________________________
 };
-	
+
 
 //////////////////////////////////////////////////////////////////////////////
 // IdManager - Metafunctions
@@ -123,19 +109,16 @@ class IdManager
  * @signature Value<TIdManager>::Type;
  */
 
-///.Metafunction.Value.param.T.type:Class.IdManager
-///.Metafunction.Value.class:Class.IdManager
-
-template<typename TIdType, typename TSpec> 
-struct Value<IdManager<TIdType, TSpec> > 
+template<typename TIdType, typename TSpec>
+struct Value<IdManager<TIdType, TSpec> >
 {
-	typedef TIdType Type;
+    typedef TIdType Type;
 };
 
-template<typename TIdType, typename TSpec> 
-struct Value<IdManager<TIdType, TSpec> const> 
+template<typename TIdType, typename TSpec>
+struct Value<IdManager<TIdType, TSpec> const>
 {
-	typedef TIdType Type;
+    typedef TIdType Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -147,19 +130,16 @@ struct Value<IdManager<TIdType, TSpec> const>
  * @signature Spec<TIdManager>::Type;
  */
 
-///.Metafunction.Spec.param.T.type:Class.IdManager
-///.Metafunction.Spec.class:Class.IdManager
-
-template<typename TIdType, typename TSpec> 
-struct Spec<IdManager<TIdType, TSpec> > 
+template<typename TIdType, typename TSpec>
+struct Spec<IdManager<TIdType, TSpec> >
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
-template<typename TIdType, typename TSpec> 
-struct Spec<IdManager<TIdType, TSpec> const> 
+template<typename TIdType, typename TSpec>
+struct Spec<IdManager<TIdType, TSpec> const>
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -179,38 +159,24 @@ struct Spec<IdManager<TIdType, TSpec> const>
  * @return TId A new unique id.
  */
 
-/**
-.Function.obtainId
-..class:Class.IdManager
-..cat:Graph
-..summary:Obtains a new id from the id manager.
-..signature:obtainId(idm)
-..param.idm:The IdManager.
-...type:Class.IdManager
-..returns:Returns a new unique id.
-..remarks:If it is a dummy id manager, i.e., IdManager<void>, the return type is (void*) 0.
-..see:Function.releaseId
-..include:seqan/graph_types.h
-*/
-
 template<typename TIdType, typename TSpec>
-inline typename Value<IdManager<TIdType, TSpec> >::Type 
-obtainId(IdManager<TIdType, TSpec>& idm) 
+inline typename Value<IdManager<TIdType, TSpec> >::Type
+obtainId(IdManager<TIdType, TSpec>& idm)
 {
-	SEQAN_CHECKPOINT
-
-	TIdType _id;
-	if (!empty(idm.data_freeIds)) {
-		_id = getValue(idm.data_freeIds, length(idm.data_freeIds) - 1);
-		resize(idm.data_freeIds, length(idm.data_freeIds) - 1, Generous());
-		assignValue(idm.data_in_use, _id, true);
-	} else {
-		if (empty(idm.data_in_use)) _id = 0;
-		else _id = (TIdType) length(idm.data_in_use);
-		resize(idm.data_in_use, _id + 1, Generous());
-		assignValue(idm.data_in_use, _id, true);
-	}
-	return _id;
+    SEQAN_CHECKPOINT
+
+    TIdType _id;
+    if (!empty(idm.data_freeIds)) {
+        _id = getValue(idm.data_freeIds, length(idm.data_freeIds) - 1);
+        resize(idm.data_freeIds, length(idm.data_freeIds) - 1, Generous());
+        assignValue(idm.data_in_use, _id, true);
+    } else {
+        if (empty(idm.data_in_use)) _id = 0;
+        else _id = (TIdType) length(idm.data_in_use);
+        resize(idm.data_in_use, _id + 1, Generous());
+        assignValue(idm.data_in_use, _id, true);
+    }
+    return _id;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -225,36 +191,22 @@ obtainId(IdManager<TIdType, TSpec>& idm)
  * @param[in]     id      The ID to release.
  */
 
-/**
-.Function.releaseId
-..class:Class.IdManager
-..cat:Graph
-..summary:Releases a given id so it can be redistributed later on.
-..signature:releaseId(idm, id)
-..param.idm:The IdManager.
-...type:Class.IdManager
-..param.id:The id that is to be released.
-..returns:void
-..see:Function.obtainId
-..include:seqan/graph_types.h
-*/
-
 template<typename TIdType, typename TSpec, typename TId>
-inline void 
-releaseId(IdManager<TIdType, TSpec>& idm, 
-		  TId const id) 
+inline void
+releaseId(IdManager<TIdType, TSpec>& idm,
+          TId const id)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(idm,id));
-	if (id == (TId) length(idm.data_in_use) - 1) {
-		resize(idm.data_in_use, length(idm.data_in_use) - 1, Generous());
-	} else {
-		assignValue(idm.data_in_use, id, false);
-		appendValue(idm.data_freeIds, id, Generous());
-	}
-	if (idCount(idm)==0) {
-		releaseAll(idm);
-	}
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(idm,id));
+    if (id == (TId) length(idm.data_in_use) - 1) {
+        resize(idm.data_in_use, length(idm.data_in_use) - 1, Generous());
+    } else {
+        assignValue(idm.data_in_use, id, false);
+        appendValue(idm.data_freeIds, id, Generous());
+    }
+    if (idCount(idm)==0) {
+        releaseAll(idm);
+    }
 }
 
 
@@ -269,27 +221,14 @@ releaseId(IdManager<TIdType, TSpec>& idm,
  * @param[in,out] manager The IdManager to release the ids from.
  */
 
-/**
-.Function.releaseAll
-..class:Class.IdManager
-..cat:Graph
-..summary:Releases all ids handled by this id manager at once.
-..signature:releaseAll(idm)
-..param.idm:The IdManager.
-...type:Class.IdManager
-..returns:void
-..see:Function.releaseId
-..include:seqan/graph_types.h
-*/
-
 
 template<typename TIdType, typename TSpec>
-inline void 
-releaseAll(IdManager<TIdType, TSpec>& idm) 
+inline void
+releaseAll(IdManager<TIdType, TSpec>& idm)
 {
-	SEQAN_CHECKPOINT
-	clear(idm.data_freeIds);
-	clear(idm.data_in_use);
+    SEQAN_CHECKPOINT
+    clear(idm.data_freeIds);
+    clear(idm.data_in_use);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -305,25 +244,12 @@ releaseAll(IdManager<TIdType, TSpec>& idm)
  * @return TId The return value is guaranteed to be an upper bound on all distributed ids.
  */
 
-/**
-.Function.getIdUpperBound
-..class:Class.IdManager
-..cat:Graph
-..summary:Returns the largest distributed id plus 1. That is, the return value is guaranteed to be an upper bound on all distributed ids.
-..signature:getIdUpperBound(idm)
-..param.idm:The IdManager.
-...type:Class.IdManager
-..returns:An upper bound on all distributed ids.
-..see:Function.getIdLowerBound
-..include:seqan/graph_types.h
-*/
-
 template<typename TIdType, typename TSpec>
-inline typename Value<IdManager<TIdType, TSpec> >::Type 
+inline typename Value<IdManager<TIdType, TSpec> >::Type
 getIdUpperBound(IdManager<TIdType, TSpec> const& idm)
 {
-	SEQAN_CHECKPOINT
-	return (empty(idm.data_in_use)) ? 0 : (typename Value<IdManager<TIdType, TSpec> >::Type) length(idm.data_in_use);
+    SEQAN_CHECKPOINT
+    return (empty(idm.data_in_use)) ? 0 : (typename Value<IdManager<TIdType, TSpec> >::Type) length(idm.data_in_use);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -339,28 +265,15 @@ getIdUpperBound(IdManager<TIdType, TSpec> const& idm)
  * @return TId The smallest obtained id so far.
  */
 
-/**
-.Function.getIdLowerBound
-..class:Class.IdManager
-..cat:Graph
-..summary:Returns the smallest distributed id. That is, the return value is guaranteed to be the smallest id obtained so far.
-..signature:getIdLowerBound(idm)
-..param.idm:The IdManager.
-...type:Class.IdManager
-..returns:The smallest obtained id.
-..see:Function.getIdUpperBound
-..include:seqan/graph_types.h
-*/
-
 template<typename TIdType, typename TSpec>
-inline typename Value<IdManager<TIdType, TSpec> >::Type 
+inline typename Value<IdManager<TIdType, TSpec> >::Type
 getIdLowerBound(IdManager<TIdType, TSpec> const& idm)
 {
-	SEQAN_CHECKPOINT
-	for(TIdType it = 0; it < length(idm.data_in_use); ++it) {
-		if (getValue(idm.data_in_use, it)) return it;
-	}
-	return 0;
+    SEQAN_CHECKPOINT
+    for(TIdType it = 0; it < length(idm.data_in_use); ++it) {
+        if (getValue(idm.data_in_use, it)) return it;
+    }
+    return 0;
 }
 
 
@@ -368,6 +281,7 @@ getIdLowerBound(IdManager<TIdType, TSpec> const& idm)
 
 /*!
  * @fn IdManager#idCount
+ * @brief Return the number of obtained ids.
  *
  * @signature TId idCount(manager);
  *
@@ -376,24 +290,12 @@ getIdLowerBound(IdManager<TIdType, TSpec> const& idm)
  * @return TId The number of ids obtained so far.
  */
 
-/**
-.Function.idCount:
-..class:Class.IdManager
-..cat:Graph
-..summary:Determines the number of ids that were obtained.
-..signature:idCount(idm)
-..param.idm:The IdManager.
-...type:Class.IdManager
-..returns:Number of ids in use.
-..include:seqan/graph_types.h
-*/
-
 template<typename TIdType, typename TSpec>
-inline typename Value<IdManager<TIdType, TSpec> >::Type 
+inline typename Value<IdManager<TIdType, TSpec> >::Type
 idCount(IdManager<TIdType, TSpec> const& idm)
 {
-	SEQAN_CHECKPOINT
-	return (length(idm.data_in_use) - length(idm.data_freeIds));
+    SEQAN_CHECKPOINT
+    return (length(idm.data_in_use) - length(idm.data_freeIds));
 }
 
 
@@ -401,6 +303,7 @@ idCount(IdManager<TIdType, TSpec> const& idm)
 
 /*!
  * @fn IdManager#idInUse
+ * @brief Return whether an id is in use.
  *
  * @signature bool idInUse(manager, id);
  *
@@ -410,26 +313,13 @@ idCount(IdManager<TIdType, TSpec> const& idm)
  * @return bool true if the id is already in use and false otherwise.
  */
 
-/**
-.Function.idInUse:
-..class:Class.IdManager
-..cat:Graph
-..summary:Checks whether the given id is in use or not.
-..signature:idInUse(idm, id)
-..param.idm:The IdManager.
-...type:Class.IdManager
-..param.id:The given id.
-..returns:True if the id was distributed, false otherwise.
-..include:seqan/graph_types.h
-*/
-
 template<typename TIdType, typename TSpec, typename TId>
-inline bool 
-idInUse(IdManager<TIdType, TSpec> const& idm, 
-		TId const id)
+inline bool
+idInUse(IdManager<TIdType, TSpec> const& idm,
+        TId const id)
 {
-	SEQAN_CHECKPOINT
-	return (id < static_cast<TId>(length(idm.data_in_use))) ? idm.data_in_use[id] : false;
+    SEQAN_CHECKPOINT
+    return (id < static_cast<TId>(length(idm.data_in_use))) ? idm.data_in_use[id] : false;
 }
 
 
@@ -449,49 +339,38 @@ idInUse(IdManager<TIdType, TSpec> const& idm,
  * @tparam TSpec Specializing type.
  */
 
-/**
-.Spec.Counting IdManager:
-..cat:Graph
-..general:Class.IdManager
-..summary:Id Manager that just counts the number of ids in use.
-..signature:IdManager<void, TSpec>
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
 template<typename TSpec>
-class IdManager<void, TSpec> 
+class IdManager<void, TSpec>
 {
-	public:
-		typedef typename Id<IdManager>::Type TIdType;
-		TIdType data_idCount;
-
-//____________________________________________________________________________	
-	public:
-		IdManager() : data_idCount(0) 
-		{
-			SEQAN_CHECKPOINT
-		}
-
-		~IdManager() 
-		{
-			SEQAN_CHECKPOINT
-		}
-
-		IdManager(IdManager const & _other) : data_idCount(_other.data_idCount) 
-		{
-			SEQAN_CHECKPOINT
-		}
-
-		IdManager const& 
-		operator = (IdManager const& _other) 
-		{
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			data_idCount = _other.data_idCount;
-			return *this;
-		}
+    public:
+        typedef typename Id<IdManager>::Type TIdType;
+        TIdType data_idCount;
+
+//____________________________________________________________________________
+    public:
+        IdManager() : data_idCount(0)
+        {
+            SEQAN_CHECKPOINT
+        }
+
+        ~IdManager()
+        {
+            SEQAN_CHECKPOINT
+        }
+
+        IdManager(IdManager const & _other) : data_idCount(_other.data_idCount)
+        {
+            SEQAN_CHECKPOINT
+        }
+
+        IdManager const&
+        operator = (IdManager const& _other)
+        {
+            SEQAN_CHECKPOINT
+            if (this == &_other) return *this;
+            data_idCount = _other.data_idCount;
+            return *this;
+        }
 
 //____________________________________________________________________________
 };
@@ -503,17 +382,14 @@ class IdManager<void, TSpec>
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Value.param.T.type:Class.IdManager
-///.Metafunction.Value.class:Class.IdManager
-
-template<typename TSpec> 
+template<typename TSpec>
 struct Value<IdManager<void, TSpec> > {
-	typedef typename Size<IdManager<void, TSpec> >::Type Type;
+    typedef typename Size<IdManager<void, TSpec> >::Type Type;
 };
 
-template<typename TSpec> 
+template<typename TSpec>
 struct Value<IdManager<void, TSpec> const> {
-	typedef typename Size<IdManager<void, TSpec> const>::Type Type;
+    typedef typename Size<IdManager<void, TSpec> const>::Type Type;
 };
 
 
@@ -525,78 +401,78 @@ struct Value<IdManager<void, TSpec> const> {
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec>
-inline typename Value<IdManager<void, TSpec> >::Type 
-obtainId(IdManager<void, TSpec>& idm) 
+inline typename Value<IdManager<void, TSpec> >::Type
+obtainId(IdManager<void, TSpec>& idm)
 {
-	SEQAN_CHECKPOINT
-	++idm.data_idCount;
-	return 0;
+    SEQAN_CHECKPOINT
+    ++idm.data_idCount;
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSpec, typename TId>
-inline void 
-releaseId(IdManager<void, TSpec>& idm, 
-		  TId const) 
+inline void
+releaseId(IdManager<void, TSpec>& idm,
+          TId const)
 {
-	SEQAN_CHECKPOINT
-	if (idm.data_idCount > 0) --idm.data_idCount;
+    SEQAN_CHECKPOINT
+    if (idm.data_idCount > 0) --idm.data_idCount;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec>
-inline void 
-releaseAll(IdManager<void, TSpec>& idm) 
+inline void
+releaseAll(IdManager<void, TSpec>& idm)
 {
-	SEQAN_CHECKPOINT
-	idm.data_idCount = 0;
+    SEQAN_CHECKPOINT
+    idm.data_idCount = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec>
-inline typename Value<IdManager<void, TSpec> >::Type 
+inline typename Value<IdManager<void, TSpec> >::Type
 getIdUpperBound(IdManager<void, TSpec> const& idm)
 {
-	SEQAN_CHECKPOINT
-	// Must be data_idCount in order to resize property maps!!!
-	// Don't change to 0
-	return idm.data_idCount;
+    SEQAN_CHECKPOINT
+    // Must be data_idCount in order to resize property maps!!!
+    // Don't change to 0
+    return idm.data_idCount;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec>
-inline typename Value<IdManager<void, TSpec> >::Type 
+inline typename Value<IdManager<void, TSpec> >::Type
 getIdLowerBound(IdManager<void, TSpec> const&)
 {
-	SEQAN_CHECKPOINT
-	return 0;
+    SEQAN_CHECKPOINT
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 
 template <typename TSpec>
-inline typename Value<IdManager<void, TSpec> >::Type 
+inline typename Value<IdManager<void, TSpec> >::Type
 idCount(IdManager<void, TSpec> const& idm)
 {
-	SEQAN_CHECKPOINT
-	return idm.data_idCount;
+    SEQAN_CHECKPOINT
+    return idm.data_idCount;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 
 template <typename TSpec, typename TId>
-inline bool 
-idInUse(IdManager<void, TSpec> const&, 
-		TId const) 
+inline bool
+idInUse(IdManager<void, TSpec> const&,
+        TId const)
 {
-	SEQAN_CHECKPOINT
-	return false;
+    SEQAN_CHECKPOINT
+    return false;
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_impl_automaton.h b/seqan/graph_types/graph_impl_automaton.h
index 019830c..1505a08 100644
--- a/seqan/graph_types/graph_impl_automaton.h
+++ b/seqan/graph_types/graph_impl_automaton.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,16 +44,16 @@ namespace SEQAN_NAMESPACE_MAIN
 template<typename TEdge, typename TAlphabet>
 class AutomatonEdgeArray {
 public:
-	TEdge data_edge[ValueSize<TAlphabet>::VALUE];
-
-	AutomatonEdgeArray() 
-	{
-		typedef typename VertexDescriptor<TEdge>::Type TVertexDescriptor;
-		typedef typename Size<TAlphabet>::Type TSize;
-		TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-		for(TSize i=0;i < (TSize) ValueSize<TAlphabet>::VALUE;++i) 
-			assignTarget(&data_edge[i], nilVal);
-	}
+    TEdge data_edge[ValueSize<TAlphabet>::VALUE];
+
+    AutomatonEdgeArray()
+    {
+        typedef typename VertexDescriptor<TEdge>::Type TVertexDescriptor;
+        typedef typename Size<TAlphabet>::Type TSize;
+        TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+        for(TSize i=0;i < (TSize) ValueSize<TAlphabet>::VALUE;++i)
+            assignTarget(&data_edge[i], nilVal);
+    }
 };
 
 /*!
@@ -76,70 +76,46 @@ class AutomatonEdgeArray {
  *                   NB: if edges to not store ids then external property maps do not work.
  */
 
-/**
-.Spec.Automaton:
-..cat:Graph
-..general:Class.Graph
-..summary:An Automaton has directed edges, labeled with input symbols, and a distinct start state, called root. The
-input symbols require the use of a third parameter: The alphabet of the input symbols.
-..description:
-...image:automatonGraph|An automaton, where $0$ is the start state.
-..signature:Graph<Automaton<TAlphabet, TCargo, TSpec> > 
-..param.TAlphabet:The alphabet type that is used for the transition labels.
-...metafunction:Metafunction.Alphabet
-...remarks:Use @Metafunction.Alphabet@ to get the type of the labels in an automaton.
-...default:$char$
-..param.TCargo:The cargo type that can be attached to the edges.
-...metafunction:Metafunction.Cargo
-...remarks:Use @Metafunction.Cargo@ to get the cargo type of an undirected graph.
-...default:$void$
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-...remarks:Use WithoutEdgeId here to omit edge ids.
-Note: If edges do not store ids external property maps do not work.
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec>
-class Graph<Automaton<TAlphabet, TCargo, TSpec> > 
+class Graph<Automaton<TAlphabet, TCargo, TSpec> >
 {
-	public:
-		typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
-		typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
-		typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
-		typedef typename EdgeType<Graph>::Type TEdge_;
-
-		String<AutomatonEdgeArray<TEdge_, TAlphabet> > data_vertex;		// List of tables
-		TVertexIdManager_ data_id_managerV;
-		TEdgeIdManager_ data_id_managerE;
-		TVertexDescriptor_ data_root;
-	
+    public:
+        typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
+        typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
+        typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
+        typedef typename EdgeType<Graph>::Type TEdge_;
+
+        String<AutomatonEdgeArray<TEdge_, TAlphabet> > data_vertex;        // List of tables
+        TVertexIdManager_ data_id_managerV;
+        TEdgeIdManager_ data_id_managerE;
+        TVertexDescriptor_ data_root;
+
 
 //____________________________________________________________________________
 
 
-		Graph() : data_root(0) {
-			SEQAN_CHECKPOINT
-		}
-
-
-		~Graph() {
-			SEQAN_CHECKPOINT
-			clear(*this);
-		}
-
-		Graph(Graph const & _other)
-		{
-			SEQAN_CHECKPOINT
-			_copyGraph(_other, *this);
-		}
-	
-		Graph const& operator = (Graph const & _other) {
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			_copyGraph(_other, *this);
-			return *this;
-		}
+        Graph() : data_root(0) {
+            SEQAN_CHECKPOINT
+        }
+
+
+        ~Graph() {
+            SEQAN_CHECKPOINT
+            clear(*this);
+        }
+
+        Graph(Graph const & _other)
+        {
+            SEQAN_CHECKPOINT
+            _copyGraph(_other, *this);
+        }
+
+        Graph const& operator = (Graph const & _other) {
+            SEQAN_CHECKPOINT
+            if (this == &_other) return *this;
+            _copyGraph(_other, *this);
+            return *this;
+        }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -151,10 +127,10 @@ class Graph<Automaton<TAlphabet, TCargo, TSpec> >
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline String<AutomatonEdgeArray<typename EdgeType<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type, TAlphabet> >&
 _getVertexString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	return const_cast<String<AutomatonEdgeArray<TEdge, TAlphabet> >&>(g.data_vertex);
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    return const_cast<String<AutomatonEdgeArray<TEdge, TAlphabet> >&>(g.data_vertex);
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -162,10 +138,10 @@ _getVertexString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g) {
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename VertexIdHandler<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type&
 _getVertexIdManager(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
-	return const_cast<TVertexIdManager&>(g.data_id_managerV);
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
+    return const_cast<TVertexIdManager&>(g.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -173,10 +149,10 @@ _getVertexIdManager(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g) {
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename EdgeIdHandler<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type&
 _getEdgeIdManager(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
-	return const_cast<TEdgeIdManager&>(g.data_id_managerE);
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
+    return const_cast<TEdgeIdManager&>(g.data_id_managerE);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -185,44 +161,44 @@ _getEdgeIdManager(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g) {
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& source,
-		   Graph<Automaton<TAlphabet, TCargo, TSpec> >& dest,
-		   bool transpose)
-{
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	typedef typename Size<TAlphabet>::Type TSize;
-	typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Standard>::Type TIterConst;
-
-	clear(dest);
-	resize(dest.data_vertex, length(_getVertexString(source)));
-	dest.data_root = source.data_root;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	TIterConst it = begin(source.data_vertex, Standard());
-	TIterConst itEnd = end(source.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		TSize table_length = ValueSize<TAlphabet>::VALUE;
-		TVertexDescriptor sourceVertex = pos;
-		for(TSize i=0;i<table_length;++i) {
-			TEdgeDescriptor const edSource = (TEdgeDescriptor) &source.data_vertex[sourceVertex].data_edge[i];
-			TVertexDescriptor targetVertex = getTarget(edSource);
-			if (targetVertex == nilVal) continue;
-			TEdgeDescriptor edTarget;
-			if (!transpose) {
-				edTarget = &dest.data_vertex[sourceVertex].data_edge[i];
-				assignTarget(edTarget, targetVertex);
-			} else {
-				edTarget = &dest.data_vertex[targetVertex].data_edge[i];
-				assignTarget(edTarget, sourceVertex);
-			}
-			_assignId(edTarget, _getId(edSource));
-			assignCargo(edTarget, getCargo(edSource));
-		}
-	}
-	dest.data_id_managerV = source.data_id_managerV;
-	dest.data_id_managerE = source.data_id_managerE;
+           Graph<Automaton<TAlphabet, TCargo, TSpec> >& dest,
+           bool transpose)
+{
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    typedef typename Size<TAlphabet>::Type TSize;
+    typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Standard>::Type TIterConst;
+
+    clear(dest);
+    resize(dest.data_vertex, length(_getVertexString(source)));
+    dest.data_root = source.data_root;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    TIterConst it = begin(source.data_vertex, Standard());
+    TIterConst itEnd = end(source.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        TSize table_length = ValueSize<TAlphabet>::VALUE;
+        TVertexDescriptor sourceVertex = pos;
+        for(TSize i=0;i<table_length;++i) {
+            TEdgeDescriptor const edSource = (TEdgeDescriptor) &source.data_vertex[sourceVertex].data_edge[i];
+            TVertexDescriptor targetVertex = getTarget(edSource);
+            if (targetVertex == nilVal) continue;
+            TEdgeDescriptor edTarget;
+            if (!transpose) {
+                edTarget = &dest.data_vertex[sourceVertex].data_edge[i];
+                assignTarget(edTarget, targetVertex);
+            } else {
+                edTarget = &dest.data_vertex[targetVertex].data_edge[i];
+                assignTarget(edTarget, sourceVertex);
+            }
+            _assignId(edTarget, _getId(edSource));
+            assignCargo(edTarget, getCargo(edSource));
+        }
+    }
+    dest.data_id_managerV = source.data_id_managerV;
+    dest.data_id_managerE = source.data_id_managerE;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -230,9 +206,9 @@ _copyGraph(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& source,
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& source,
-		   Graph<Automaton<TAlphabet, TCargo, TSpec> >& dest)
+           Graph<Automaton<TAlphabet, TCargo, TSpec> >& dest)
 {
-	_copyGraph(source,dest,false);
+    _copyGraph(source,dest,false);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -243,54 +219,54 @@ _copyGraph(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& source,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline void 
+inline void
 transpose(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& source,
-		  Graph<Automaton<TAlphabet, TCargo, TSpec> >& dest)
+          Graph<Automaton<TAlphabet, TCargo, TSpec> >& dest)
 {
-	SEQAN_CHECKPOINT
-	_copyGraph(source, dest, true);
+    SEQAN_CHECKPOINT
+    _copyGraph(source, dest, true);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline void 
+inline void
 transpose(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	Graph<Automaton<TAlphabet, TCargo, TSpec> > dest;
-	_copyGraph(g, dest, true);
-	g = dest;
+    SEQAN_CHECKPOINT
+    Graph<Automaton<TAlphabet, TCargo, TSpec> > dest;
+    _copyGraph(g, dest, true);
+    g = dest;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 numEdges(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return idCount(g.data_id_managerE);
+    SEQAN_CHECKPOINT
+    return idCount(g.data_id_managerE);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
-numVertices(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
+numVertices(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return idCount(g.data_id_managerV);
+    SEQAN_CHECKPOINT
+    return idCount(g.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline bool 
-empty(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g) 
+inline bool
+empty(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return (!(idCount(g.data_id_managerV)));
+    SEQAN_CHECKPOINT
+    return (!(idCount(g.data_id_managerV)));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -299,10 +275,10 @@ template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 clearEdges(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clear(g.data_vertex);
-	releaseAll(g.data_id_managerE);
-	resize(g.data_vertex, getIdUpperBound(g.data_id_managerV));
+    SEQAN_CHECKPOINT
+    clear(g.data_vertex);
+    releaseAll(g.data_id_managerE);
+    resize(g.data_vertex, getIdUpperBound(g.data_id_managerV));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -311,131 +287,131 @@ template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 clearVertices(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearEdges(g);
-	releaseAll(g.data_id_managerV);
-	clear(g.data_vertex);
+    SEQAN_CHECKPOINT
+    clearEdges(g);
+    releaseAll(g.data_id_managerV);
+    clear(g.data_vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline void 
-clear(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g) 
+inline void
+clear(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearVertices(g);
+    SEQAN_CHECKPOINT
+    clearVertices(g);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 outDegree(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-		  TVertexDescriptor const vertex)
+          TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	TSize count=0;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE; ++i) 
-		if ( (TVertexDescriptor) getTarget(&g.data_vertex[vertex].data_edge[i])!=nilVal) ++count;
-	return count;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    TSize count=0;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE; ++i)
+        if ( (TVertexDescriptor) getTarget(&g.data_vertex[vertex].data_edge[i])!=nilVal) ++count;
+    return count;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 inDegree(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-		 TVertexDescriptor const vertex)
+         TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	typedef typename Size<TGraph>::Type TSize;
-	TSize count=0;
-	typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd; ++it, ++pos) {
-		if (idInUse(g.data_id_managerV, pos)) {
-			for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) 
-				if ( (TVertexDescriptor) getTarget(&(*it).data_edge[i]) == vertex) ++count;			
-		}
-	}
-	return count;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    typedef typename Size<TGraph>::Type TSize;
+    TSize count=0;
+    typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd; ++it, ++pos) {
+        if (idInUse(g.data_id_managerV, pos)) {
+            for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i)
+                if ( (TVertexDescriptor) getTarget(&(*it).data_edge[i]) == vertex) ++count;
+        }
+    }
+    return count;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
-degree(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g, 
-	   TVertexDescriptor const vertex) 
+inline typename Size<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
+degree(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
+       TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return (inDegree(g,vertex)+outDegree(g,vertex));
+    SEQAN_CHECKPOINT
+    return (inDegree(g,vertex)+outDegree(g,vertex));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 addVertex(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph >::Type TEdge;
-
-	TVertexDescriptor vd = obtainId(g.data_id_managerV);
-	if (vd == length(g.data_vertex)) appendValue(g.data_vertex, AutomatonEdgeArray<TEdge, TAlphabet>()); 
-	else g.data_vertex[vd] =  AutomatonEdgeArray<TEdge, TAlphabet>();
-	return vd;
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph >::Type TEdge;
+
+    TVertexDescriptor vd = obtainId(g.data_id_managerV);
+    if (vd == length(g.data_vertex)) appendValue(g.data_vertex, AutomatonEdgeArray<TEdge, TAlphabet>());
+    else g.data_vertex[vd] =  AutomatonEdgeArray<TEdge, TAlphabet>();
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeVertex(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g, 
-			 TVertexDescriptor const v) 
+inline void
+removeVertex(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
+             TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
 
-	removeOutEdges(g,v); // Remove all outgoing edges
-	removeInEdges(g,v); // Remove all incoming edges
-	releaseId(g.data_id_managerV, v); // Release id
+    removeOutEdges(g,v); // Remove all outgoing edges
+    removeInEdges(g,v); // Remove all incoming edges
+    releaseId(g.data_id_managerV, v); // Release id
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TLabel>
-inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
-addEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target,
-		TLabel const label) 
+inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
+addEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target,
+        TLabel const label)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	
-	TEdgeDescriptor e = findEdge(g, source, (TAlphabet) label);
-	_assignId(e, obtainId(g.data_id_managerE));
-	assignTarget(e, target);
-	return e;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+
+    TEdgeDescriptor e = findEdge(g, source, (TAlphabet) label);
+    _assignId(e, obtainId(g.data_id_managerE));
+    assignTarget(e, target);
+    return e;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -443,19 +419,19 @@ addEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TLabel, typename TEdgeCargo>
 inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 addEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-				  TVertexDescriptor const source,
-				  TVertexDescriptor const target,
-				  TLabel const label,
-				  TEdgeCargo const cargo)
+                  TVertexDescriptor const source,
+                  TVertexDescriptor const target,
+                  TLabel const label,
+                  TEdgeCargo const cargo)
 {
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Id<TGraph>::Type TId;
-	TEdgeDescriptor e = addEdge(g,source,target, (TAlphabet) label);
-	assignCargo(e,cargo);
-	TId id = obtainId(g.data_id_managerE);
-	_assignId(e, id);
-	return e;
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Id<TGraph>::Type TId;
+    TEdgeDescriptor e = addEdge(g,source,target, (TAlphabet) label);
+    assignCargo(e,cargo);
+    TId id = obtainId(g.data_id_managerE);
+    _assignId(e, id);
+    return e;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -463,16 +439,16 @@ addEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TLabel>
 inline void
 removeEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-	       TVertexDescriptor const source,
-	       TVertexDescriptor const target,
-		   TLabel const label)
+           TVertexDescriptor const source,
+           TVertexDescriptor const target,
+           TLabel const label)
 {
-	SEQAN_CHECKPOINT;
+    SEQAN_CHECKPOINT;
     (void) source;  // If compiled without assertions.
     (void) target;  // If compiled without assertions.
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
-	removeEdge(g, &g.data_vertex[source].data_edge[ordValue((TAlphabet) label)]);
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+    removeEdge(g, &g.data_vertex[source].data_edge[ordValue((TAlphabet) label)]);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -480,15 +456,15 @@ removeEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
 inline void
 removeEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-		   TEdgeDescriptor const edge)
+           TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, _getId(edge)));
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, _getId(edge)));
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
 
-	releaseId(g.data_id_managerE, _getId(edge));
-	assignTarget(edge, getNil<TVertexDescriptor>());
+    releaseId(g.data_id_managerE, _getId(edge));
+    assignTarget(edge, getNil<TVertexDescriptor>());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -496,20 +472,20 @@ removeEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline void
 removeOutEdges(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-			   TVertexDescriptor const vertex)
+               TVertexDescriptor const vertex)
 {
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Size<TGraph>::Type TSize;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) {
-		TEdgeDescriptor ed = &g.data_vertex[vertex].data_edge[i];
-		if ( (TVertexDescriptor) getTarget(ed) == nilVal) continue;
-		assignTarget(ed, nilVal);
-		releaseId(g.data_id_managerE, _getId(ed));
-	}
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Size<TGraph>::Type TSize;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) {
+        TEdgeDescriptor ed = &g.data_vertex[vertex].data_edge[i];
+        if ( (TVertexDescriptor) getTarget(ed) == nilVal) continue;
+        assignTarget(ed, nilVal);
+        releaseId(g.data_id_managerE, _getId(ed));
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -517,74 +493,74 @@ removeOutEdges(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline void
 removeInEdges(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-			  TVertexDescriptor const vertex)
+              TVertexDescriptor const vertex)
 {
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Size<TGraph>::Type TSize;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> >, Standard>::Type TIter;
-	TIter it = begin(g.data_vertex, Standard());
-	TIter itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		if (idInUse(g.data_id_managerV, pos)) {
-			for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) {
-				TEdgeDescriptor ed = &(value(it)).data_edge[i];
-				if (( (TVertexDescriptor) getTarget(ed) == nilVal) ||  ( (TVertexDescriptor) getTarget(ed) != vertex)) continue;
-				assignTarget(ed, nilVal);
-				releaseId(g.data_id_managerE, _getId(ed));	
-			}
-		}
-	}
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Size<TGraph>::Type TSize;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> >, Standard>::Type TIter;
+    TIter it = begin(g.data_vertex, Standard());
+    TIter itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        if (idInUse(g.data_id_managerV, pos)) {
+            for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) {
+                TEdgeDescriptor ed = &(value(it)).data_edge[i];
+                if (( (TVertexDescriptor) getTarget(ed) == nilVal) ||  ( (TVertexDescriptor) getTarget(ed) != vertex)) continue;
+                assignTarget(ed, nilVal);
+                releaseId(g.data_id_managerE, _getId(ed));
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 targetVertex(Graph<Automaton<TAlphabet, TCargo, TSpec> > const&,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return (getTarget(edge));
+    SEQAN_CHECKPOINT
+    return (getTarget(edge));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 sourceVertex(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-			 TEdgeDescriptor const edge) 
-{
-	SEQAN_CHECKPOINT
-		
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Size<TGraph>::Type TSize;
-
-	TSize table_length = ValueSize<TAlphabet>::VALUE;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> >, Standard>::Type TIter;
-	TIter it = begin(g.data_vertex, Standard());
-	TIter itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd; ++it, ++pos) {
-		if (idInUse(g.data_id_managerV, pos)) {
-			for(TSize i=0;i<table_length;++i) {
-				TEdgeDescriptor ed = &(*it).data_edge[i];
-				if (getTarget(ed) == nilVal) continue;
-				if (ed==edge) return pos;
-			}
-		}
-	}
+             TEdgeDescriptor const edge)
+{
+    SEQAN_CHECKPOINT
+
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Size<TGraph>::Type TSize;
+
+    TSize table_length = ValueSize<TAlphabet>::VALUE;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> >, Standard>::Type TIter;
+    TIter it = begin(g.data_vertex, Standard());
+    TIter itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd; ++it, ++pos) {
+        if (idInUse(g.data_id_managerV, pos)) {
+            for(TSize i=0;i<table_length;++i) {
+                TEdgeDescriptor ed = &(*it).data_edge[i];
+                if (getTarget(ed) == nilVal) continue;
+                if (ed==edge) return pos;
+            }
+        }
+    }
     SEQAN_ASSERT_FAIL("We should never reach this point.");
-	return 0;
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -593,33 +569,33 @@ sourceVertex(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TMatrix>
 inline void
 getAdjacencyMatrix(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-				   TMatrix& mat) 
-{
-	SEQAN_CHECKPOINT
-
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Size<TMatrix>::Type TMatrixSize;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	TMatrixSize len = getIdUpperBound(g.data_id_managerV);
-	resize(mat, len*len, 0);
-	typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		if (!idInUse(g.data_id_managerV, pos)) continue;
-		for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) {
-			if (((*it).data_edge[i].data_target!=nilVal))
-			{
-				TVertexDescriptor const source = pos;
-				TVertexDescriptor const target = (*it).data_edge[i].data_target;
-				++mat[source*len+target];
-			}
-		}
-	}
+                   TMatrix& mat)
+{
+    SEQAN_CHECKPOINT
+
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Size<TMatrix>::Type TMatrixSize;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    TMatrixSize len = getIdUpperBound(g.data_id_managerV);
+    resize(mat, len*len, 0);
+    typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        if (!idInUse(g.data_id_managerV, pos)) continue;
+        for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) {
+            if (((*it).data_edge[i].data_target!=nilVal))
+            {
+                TVertexDescriptor const source = pos;
+                TVertexDescriptor const target = (*it).data_edge[i].data_target;
+                ++mat[source*len+target];
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -627,69 +603,68 @@ getAdjacencyMatrix(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TLabel>
 inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 findEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-		 TVertexDescriptor const v,
-		 TLabel const c)
+         TVertexDescriptor const v,
+         TLabel const c)
 {
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-	return &g.data_vertex[v].data_edge[ordValue((TAlphabet) c)];
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+    return &g.data_vertex[v].data_edge[ordValue((TAlphabet) c)];
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TLabel>
-inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 findEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-		 TVertexDescriptor const v,
-		 TLabel const c)
+         TVertexDescriptor const v,
+         TLabel const c)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	TGraph* graph = const_cast<TGraph*>(&g);
-	return findEdge(*graph, v, c);
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    TGraph* graph = const_cast<TGraph*>(&g);
+    return findEdge(*graph, v, c);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TFile, typename TAlphabet, typename TCargo, typename TSpec, typename TIDString>
+template<typename TFile, typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 write(TFile & target,
-	  Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-	  TIDString const &,
-	  Raw)
+      Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g)
 {
 //IOREV _nodoc_
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	typedef typename Size<TAlphabet>::Type TSize;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-
-	streamPut(target,"Automaton - State: (Input / NextState)\n");
-	typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		if (!idInUse(g.data_id_managerV, pos)) continue;
-		TVertexDescriptor sourceVertex = pos;
-		streamPut(target, (int)sourceVertex);
-		streamPut(target,": ");
-		for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) {
-			streamPut(target, ' ');
-			streamPut(target, '(');
-			streamPut(target, TAlphabet(i));
-			streamPut(target, ' ');
-			streamPut(target, '/');
-			streamPut(target, ' ');
-			if (g.data_vertex[sourceVertex].data_edge[i].data_target ==  nilVal) streamPut(target,"nil");
-			else streamPut(target, (int)g.data_vertex[sourceVertex].data_edge[i].data_target);
-			streamPut(target, ')');
-			streamPut(target, ' ');
-		}
-		streamPut(target, '\n');
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    typedef typename Size<TAlphabet>::Type TSize;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+
+    write(target, "Automaton - State: (Input / NextState)\n");
+    typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for (; it != itEnd; ++it, ++pos)
+    {
+        if (!idInUse(g.data_id_managerV, pos))
+            continue;
+        TVertexDescriptor sourceVertex = pos;
+        appendNumber(target, (int)sourceVertex);
+        write(target, ": ");
+        for (TSize i = 0; i < (TSize) ValueSize<TAlphabet>::VALUE; ++i)
+        {
+            write(target, " (");
+            writeValue(target, TAlphabet(i));
+            write(target, " / ");
+            if (g.data_vertex[sourceVertex].data_edge[i].data_target ==  nilVal)
+                write(target, "nil");
+            else
+                appendNumber(target, (int)g.data_vertex[sourceVertex].data_edge[i].data_target);
+            write(target, ") ");
+        }
+        writeValue(target, '\n');
+    }
 }
 
 
@@ -704,26 +679,12 @@ write(TFile & target,
  * @param[in,out] g The Automaton to create the root for.
  */
 
-/**
-.Function.createRoot
-..class:Spec.Automaton
-..class:Spec.Tree
-..cat:Graph
-..summary:Creates the root in a tree or an automaton.
-..signature:createRoot(g)
-..param.g:A tree or an automaton.
-...type:Spec.Automaton
-...type:Spec.Tree
-..returns:void
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 createRoot(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	g.data_root = addVertex(g);
+    SEQAN_CHECKPOINT
+    g.data_root = addVertex(g);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -738,39 +699,20 @@ createRoot(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g)
  * @param[in]     v A vertex descriptor.
  */
 
-/**
-.Function.assignRoot
-..class:Spec.Automaton
-..class:Spec.Tree
-..cat:Graph
-..summary:Assigns a new root vertex to the graph.
-..signature:assignRoot(g, vertex)
-..param.g:A tree or automaton.
-...type:Spec.Automaton
-...type:Spec.Tree
-..param.vertex:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:void
-..see:Function.getRoot
-..see:Function.root
-..see:Function.Graph#isRoot
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline void
 assignRoot(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-		   TVertexDescriptor const vertex)
+           TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	g.data_root = vertex;
+    SEQAN_CHECKPOINT
+    g.data_root = vertex;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn Automaton#root
- * @signature Gets reference to the root of the automaton.
+ * @brief Gets reference to the root of the automaton.
  *
  * @signature TVertexDescriptor root(a);
  *
@@ -779,37 +721,19 @@ assignRoot(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
  * @return TVertexDescriptor Reference to the root's vertex descriptor.
  */
 
-/**
-.Function.root
-..class:Spec.Automaton
-..class:Spec.Tree
-..cat:Graph
-..summary:Gets a reference to the root of the tree.
-..signature:root(g)
-..param.g:A tree or an automaton.
-...type:Spec.Automaton
-...type:Spec.Tree
-..returns:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..see:Function.getRoot
-..see:Function.assignRoot
-..see:Function.Graph#isRoot
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type&
 root(Graph<Automaton<TAlphabet, TCargo, TSpec> > & g)
 {
-	SEQAN_CHECKPOINT
-	return g.data_root;
+    SEQAN_CHECKPOINT
+    return g.data_root;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn Automaton#getRoot
- * @signature Gets the root of the automaton.
+ * @brief Gets the root of the automaton.
  *
  * @signature TVertexDescriptor getRoot(a);
  *
@@ -818,37 +742,19 @@ root(Graph<Automaton<TAlphabet, TCargo, TSpec> > & g)
  * @return TVertexDescriptor The root's vertex descriptor.
  */
 
-/**
-.Function.getRoot
-..class:Spec.Automaton
-..class:Spec.Tree
-..cat:Graph
-..summary:Get method for the root of a tree or an automaton.
-..signature:getRoot(g)
-..param.g:An automaton or a tree.
-...type:Spec.Automaton
-...type:Spec.Tree
-..returns:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..see:Function.assignRoot
-..see:Function.root
-..see:Function.Graph#isRoot
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 getRoot(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return g.data_root;
+    SEQAN_CHECKPOINT
+    return g.data_root;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn Automaton#isRoot
- * @signature Tests whether a given vertex is the root or not.
+ * @brief Tests whether a given vertex is the root or not.
  *
  * @signature bool isRoot(a, v);
  *
@@ -858,32 +764,13 @@ getRoot(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g)
  * @return bool true if v is the root and false otherwise.
  */
 
-/**
-.Function.Graph#isRoot
-..class:Spec.Automaton
-..class:Spec.Tree
-..cat:Graph
-..summary:Tests whether a given vertex is the root or not.
-..signature:isRoot(g, v)
-..param.g:An automaton or a tree.
-...type:Spec.Automaton
-...type:Spec.Tree
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:True if vertex is the root.
-..see:Function.getRoot
-..see:Function.assignRoot
-..see:Function.root
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline bool
 isRoot(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-	   TVertexDescriptor v)
+       TVertexDescriptor v)
 {
-	SEQAN_CHECKPOINT
-	return ( (TVertexDescriptor) g.data_root == v);
+    SEQAN_CHECKPOINT
+    return ( (TVertexDescriptor) g.data_root == v);
 }
 
 
@@ -905,40 +792,15 @@ isRoot(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
  * @see Graph#getNil
  */
 
-/**
-.Function.getSuccessor
-..class:Spec.Automaton
-..class:Spec.Word Graph
-..cat:Graph
-..summary:Gets the successor for a given vertex and an edge label.
-For an automaton a single character is required whereas for a word graph getSuccessor takes a string.
-..signature:getSuccessor(g, v, c)
-..signature:getSuccessor(g, v, str)
-..param.g:An automaton or a word graph.
-...type:Spec.Automaton
-...type:Spec.Word Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.c:A label.
-...type:Metafunction.Alphabet
-..param.str:A string.
-...type:Class.String
-..returns:A vertex descriptor or nil if successor is not defined.
-...type:Metafunction.VertexDescriptor
-..see:Function.parseString
-..see:Function.getNil
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TChar>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 getSuccessor(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-			 TVertexDescriptor vertex,
-			 TChar const c) 
+             TVertexDescriptor vertex,
+             TChar const c)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-	return getTarget(findEdge(g, vertex, c));
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+    return getTarget(findEdge(g, vertex, c));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -952,7 +814,7 @@ getSuccessor(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
  *
  * @param[in]     a       An Automaton.
  * @param[in]     v       The descriptor of the vertex to start at.
- * @param[in]     str     The @link SequenceConcept @endlink to parse.
+ * @param[in]     str     The @link ContainerConcept @endlink to parse.
  * @param[in,out] beginIt Begin iterator to sequence to parse.  Set to the first character that could not be parsed
  *                        or to the value of endIt if all of the string was parsed.
  * @param[in]     endIt   End iterator to sequence to parse.
@@ -963,89 +825,60 @@ getSuccessor(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
  * read.
  */
 
-/**
-.Function.parseString
-..class:Spec.Automaton
-..class:Spec.Word Graph
-..cat:Graph
-..summary:Parses a string one character at a time and moves accordingly in the automaton.
-..signature:parseString(g, v, beginIt, endIt)
-..signature:parseString(g, v, str)
-..param.g:An automaton or a word graph.
-...type:Spec.Automaton
-...type:Spec.Word Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.beginIt:An iterator to the beginning of the string. (Input and Output)
-...type:Metafunction.Iterator.
-..param.endIt:An iterator to the end of the string.
-...type:Metafunction.Iterator.
-..param.str:A string.
-...type:Class.String
-..returns:The vertex descriptor of the state that was reached after parsing.
-...type:Metafunction.VertexDescriptor
-..returns.param.beginIt:Iterator to the first character that could not be parsed, 
-	or $endIt$ if the complete string was parsed.
-..remarks:The parsing stops before @Function.getSuccessor@ reaches the $nil$ state, 
-	or if the the complete sequences is read.
-..see:Function.getSuccessor
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TIterator>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 parseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-			TVertexDescriptor const vertex,
-			TIterator & beginIt,
-			TIterator const & endIt)
-{
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	TVertexDescriptor succ = vertex;
-	while (beginIt!=endIt) {
-		TVertexDescriptor tmp = getSuccessor(g,succ,*beginIt);
-		if (tmp == nilVal) break;
-		succ = tmp;
-		++beginIt;
-	}
-	return succ;
+            TVertexDescriptor const vertex,
+            TIterator & beginIt,
+            TIterator const & endIt)
+{
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    TVertexDescriptor succ = vertex;
+    while (beginIt!=endIt) {
+        TVertexDescriptor tmp = getSuccessor(g,succ,*beginIt);
+        if (tmp == nilVal) break;
+        succ = tmp;
+        ++beginIt;
+    }
+    return succ;
 }
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TIterator>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 parseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-			TVertexDescriptor const vertex,
-			TIterator const & beginIt,
-			TIterator const & endIt)
+            TVertexDescriptor const vertex,
+            TIterator const & beginIt,
+            TIterator const & endIt)
 {
-	SEQAN_CHECKPOINT
-	TIterator beginIt2 = beginIt;
-	return parseString(g, vertex, beginIt2, endIt);
+    SEQAN_CHECKPOINT
+    TIterator beginIt2 = beginIt;
+    return parseString(g, vertex, beginIt2, endIt);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo,  typename TSpec, typename TVertexDescriptor, typename TCharacters>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 parseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-			TVertexDescriptor const vertex,
-			TCharacters const& chars)
+            TVertexDescriptor const vertex,
+            TCharacters const& chars)
 {
-	SEQAN_CHECKPOINT
-	return parseString(g,vertex,begin(chars),end(chars));
+    SEQAN_CHECKPOINT
+    return parseString(g,vertex,begin(chars),end(chars));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TCharacters>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TSpec> > >::Type
 parseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
-			TVertexDescriptor const vertex,
-			TCharacters const* chars)
+            TVertexDescriptor const vertex,
+            TCharacters const* chars)
 {
-	SEQAN_CHECKPOINT
-	return parseString(g,vertex,chars,chars+length(chars));
+    SEQAN_CHECKPOINT
+    return parseString(g,vertex,chars,chars+length(chars));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1064,70 +897,49 @@ parseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const& g,
  *              <tt>false</tt> otherwise.
  */
 
-/**
-.Function.canParseString
-..class:Spec.Automaton
-..class:Spec.Word Graph
-..cat:Graph
-..summary:Test whether an automaton can parse a string completely.
-..signature:canParseString(g [, v], str)
-..param.g:An automaton or a word graph.
-...type:Spec.Automaton
-...type:Spec.Word Graph
-..param.v:A vertex descriptor. (optional)
-...type:Metafunction.VertexDescriptor
-...default:The @Function.root@ of $g$.
-..param.str:A string.
-...type:Class.String
-..returns:$true$ if $g$ parses $str$ starting at $v$ completely, $false$ otherwise.
-..see:Function.getSuccessor
-..see:Function.parseString
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo,  typename TSpec, typename TVertexDescriptor, typename TCharacters>
-inline bool 
+inline bool
 canParseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const & g,
-			   TVertexDescriptor const vertex,
-			   TCharacters const & chars)
+               TVertexDescriptor const vertex,
+               TCharacters const & chars)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Iterator<TCharacters const, Standard>::Type TIterator;
-	TIterator it = begin(chars, Standard());
-	TIterator it_end = end(chars, Standard());
-	parseString(g, vertex, it, it_end);
-	return (it == it_end);
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TCharacters const, Standard>::Type TIterator;
+    TIterator it = begin(chars, Standard());
+    TIterator it_end = end(chars, Standard());
+    parseString(g, vertex, it, it_end);
+    return (it == it_end);
 }
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TCharacters>
 inline bool
 canParseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > const & g,
-			   TVertexDescriptor const vertex,
-			   TCharacters const * chars)
+               TVertexDescriptor const vertex,
+               TCharacters const * chars)
 {
-	SEQAN_CHECKPOINT
-	typedef TCharacters const * TIterator;
-	TIterator it = begin(chars, Standard());
-	TIterator it_end = end(chars, Standard());
-	parseString(g, vertex, it, it_end);
-	return (it == it_end);
+    SEQAN_CHECKPOINT
+    typedef TCharacters const * TIterator;
+    TIterator it = begin(chars, Standard());
+    TIterator it_end = end(chars, Standard());
+    parseString(g, vertex, it, it_end);
+    return (it == it_end);
 }
 
 template<typename TAlphabet, typename TCargo,  typename TSpec, typename TCharacters>
-inline bool 
+inline bool
 canParseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > & g,
-			   TCharacters const & chars)
+               TCharacters const & chars)
 {
-	SEQAN_CHECKPOINT
-	return canParseString(g, root(g), chars);
+    SEQAN_CHECKPOINT
+    return canParseString(g, root(g), chars);
 }
 
 template<typename TAlphabet, typename TCargo,  typename TSpec, typename TCharacters>
-inline bool 
+inline bool
 canParseString(Graph<Automaton<TAlphabet, TCargo, TSpec> > & g,
-			   TCharacters const * chars)
+               TCharacters const * chars)
 {
-	SEQAN_CHECKPOINT
-	return canParseString(g, root(g), chars);
+    SEQAN_CHECKPOINT
+    return canParseString(g, root(g), chars);
 }
 
 
diff --git a/seqan/graph_types/graph_impl_directed.h b/seqan/graph_types/graph_impl_directed.h
index 2c68c03..9bf1111 100644
--- a/seqan/graph_types/graph_impl_directed.h
+++ b/seqan/graph_types/graph_impl_directed.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -58,68 +58,88 @@ namespace SEQAN_NAMESPACE_MAIN
  *                ids.  NB: if edges do not store ids then external property maps do not work.
  */
 
-/**
-.Spec.Directed Graph:
-..cat:Graph
-..general:Class.Graph
-..summary:A directed graph that stores the edges in an adjacency list.
-..description:
-...image:directedGraph|A directed graph.
-..signature:Graph<Directed<TCargo, TSpec> >
-..param.TCargo:The cargo type that can be attached to the edges.
-...metafunction:Metafunction.Cargo
-...remarks:Use @Metafunction.Cargo@ to get the cargo type of a directed graph.
-...default:$void$
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-...remarks:Use WithoutEdgeId here to omit edge ids.
-Note: If edges do not store ids external property maps do not work.
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
-template<typename TCargo, typename TSpec>
-class Graph<Directed<TCargo, TSpec> > 
+template <typename TCargo, typename TSpec>
+class Graph<Directed<TCargo, TSpec> >
 {
-	public:
-		typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
-		typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
-		typedef typename EdgeType<Graph>::Type TEdgeStump_;	
-		typedef Allocator<SinglePool<sizeof(TEdgeStump_)> > TAllocator_;
-		
-		String<TEdgeStump_*> data_vertex;			// Pointers to EdgeStump lists
-		TVertexIdManager_ data_id_managerV;
-		TEdgeIdManager_ data_id_managerE;		
-		TAllocator_ data_allocator;
+    public:
+        typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
+        typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
+        typedef typename EdgeType<Graph>::Type TEdgeStump_;
+        typedef Allocator<SinglePool<sizeof(TEdgeStump_)> > TAllocator_;
 
-//____________________________________________________________________________
+        String<TEdgeStump_*> data_vertex;            // Pointers to EdgeStump lists
+        TVertexIdManager_ data_id_managerV;
+        TEdgeIdManager_ data_id_managerE;
+        TAllocator_ data_allocator;
 
+//____________________________________________________________________________
 
-		Graph() {
-			SEQAN_CHECKPOINT
-		}
-
-		~Graph() {
-			SEQAN_CHECKPOINT
-			clear(*this);
-		}
-
-		Graph(Graph const & _other) :
-			data_allocator(_other.data_allocator)
-		{
-			SEQAN_CHECKPOINT
-			_copyGraph(_other, *this);		
-		}
-	
-		Graph const& operator = (Graph const & _other) {
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			clear(*this);
-			data_allocator = _other.data_allocator;
-			_copyGraph(_other, *this);
-			return *this;
-		}
+        Graph() {}
+
+        ~Graph()
+        {
+            clear(*this);
+        }
+
+        Graph(Graph const & _other) :
+            data_allocator(_other.data_allocator)
+        {
+            _copyGraph(*this, _other);
+        }
+
+        Graph const & operator = (Graph const & _other)
+        {
+            if (this == &_other)
+                return *this;
+
+            clear(*this);
+            data_allocator = _other.data_allocator;
+            _copyGraph(*this, _other);
+            return *this;
+        }
 };
 
+template <typename TCargo>
+class Graph<Directed<TCargo, WithSourceId> >
+{
+    public:
+        typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
+        typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
+        typedef typename EdgeType<Graph>::Type TEdgeStump_;
+        typedef Allocator<SinglePool<sizeof(TEdgeStump_)> > TAllocator_;
+
+        String<TEdgeStump_*> data_vertex;            // Pointers to EdgeStump lists
+        String<TEdgeStump_*> data_vertex_in;         
+        TVertexIdManager_ data_id_managerV;
+        TEdgeIdManager_ data_id_managerE;
+        TAllocator_ data_allocator;
+
+//____________________________________________________________________________
+
+        Graph() {}
+
+        ~Graph()
+        {
+            clear(*this);
+        }
+
+        Graph(Graph const & _other) :
+            data_allocator(_other.data_allocator)
+        {
+            _copyGraph(*this, _other);
+        }
+
+        Graph const & operator = (Graph const & _other)
+        {
+            if (this == &_other)
+                return *this;
+
+            clear(*this);
+            data_allocator = _other.data_allocator;
+            _copyGraph(*this, _other);
+            return *this;
+        }
+};
 
 //////////////////////////////////////////////////////////////////////////////
 // INTERNAL FUNCTIONS
@@ -127,920 +147,824 @@ class Graph<Directed<TCargo, TSpec> >
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec>
-inline String<typename EdgeType<Graph<Directed<TCargo, TSpec> > >::Type*>&
-_getVertexString(Graph<Directed<TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	return const_cast<String<TEdgeStump*>&>(g.data_vertex);
+template <typename TCargo, typename TSpec>
+inline String<typename EdgeType<Graph<Directed<TCargo, TSpec> > >::Type*> &
+_getVertexString(Graph<Directed<TCargo, TSpec> > const & g)
+{
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    return const_cast<String<TEdgeStump*>&>(g.data_vertex);
 }
 
 /////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec>
-inline typename VertexIdHandler<Graph<Directed<TCargo, TSpec> > >::Type&
-_getVertexIdManager(Graph<Directed<TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
-	return const_cast<TVertexIdManager&>(g.data_id_managerV);
+template <typename TCargo, typename TSpec>
+inline typename VertexIdHandler<Graph<Directed<TCargo, TSpec> > >::Type &
+_getVertexIdManager(Graph<Directed<TCargo, TSpec> > const & g)
+{
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
+    return const_cast<TVertexIdManager&>(g.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec>
-inline typename EdgeIdHandler<Graph<Directed<TCargo, TSpec> > >::Type&
-_getEdgeIdManager(Graph<Directed<TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
-	return const_cast<TEdgeIdManager&>(g.data_id_managerE);
+template <typename TCargo, typename TSpec>
+inline typename EdgeIdHandler<Graph<Directed<TCargo, TSpec> > >::Type &
+_getEdgeIdManager(Graph<Directed<TCargo, TSpec> > const & g)
+{
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
+    return const_cast<TEdgeIdManager&>(g.data_id_managerE);
 }
 
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TCargo>
+inline void
+_copyGraph(Graph<Directed<TCargo, WithSourceId> > & dest,
+           Graph<Directed<TCargo, WithSourceId> > const & source,
+           bool const & transpose)
+{
+    typedef Graph<Directed<TCargo, WithSourceId> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+    clear(dest);
+    resize(dest.data_vertex, length(source.data_vertex));
+    resize(dest.data_vertex_in, length(source.data_vertex_in));
+    TIter itInit = begin(dest.data_vertex, Standard());
+    TIter itInitEnd = end(dest.data_vertex, Standard());
+    for (;itInit != itInitEnd; ++itInit)
+        *itInit = (TEdgeStump*) 0;
+
+    TIter itInitIn = begin(dest.data_vertex_in, Standard());
+    TIter itInitInEnd = end(dest.data_vertex_in, Standard());
+    for (;itInitIn != itInitInEnd; ++itInitIn)
+        *itInitIn = (TEdgeStump*) 0;
+
+    TIterConst it = begin(source.data_vertex, Standard());
+    TIterConst itEnd = end(source.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for (;it != itEnd; ++it, ++pos)
+    {
+        TEdgeStump* current = *it;
+        TVertexDescriptor sourceVertex = pos;
+        while (current != (TEdgeStump*) 0)
+        {
+            TVertexDescriptor targetVertex = current->data_target;
+            // Create missing vertices
+            if (sourceVertex>targetVertex)
+                _createVertices(dest,sourceVertex);
+            else
+                _createVertices(dest,targetVertex);
+
+            // Add edge
+            TEdgeDescriptor e;
+            if (!transpose)
+                e = addEdge(dest, sourceVertex, targetVertex);
+            else
+                e = addEdge(dest, targetVertex, sourceVertex);
+
+            _assignId(e, _getId(current));
+            assignCargo(e, getCargo(current));
+            current = getNextT(current);
+        }
+    }
+    dest.data_id_managerV = source.data_id_managerV;
+    dest.data_id_managerE = source.data_id_managerE;
+}
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec>
+template <typename TCargo, typename TSpec>
 inline void
-_copyGraph(Graph<Directed<TCargo, TSpec> > const& source,
-		   Graph<Directed<TCargo, TSpec> >& dest,
-		   bool transpose) 
+_copyGraph(Graph<Directed<TCargo, TSpec> > & dest,
+           Graph<Directed<TCargo, TSpec> > const & source,
+           bool const & transpose)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
-	clear(dest);
-	resize(dest.data_vertex, length(_getVertexString(source)));
-	TIter itInit = begin(dest.data_vertex, Standard());
-	TIter itInitEnd = end(dest.data_vertex, Standard());
-	for(;itInit != itInitEnd; ++itInit) *itInit = (TEdgeStump*) 0;
-	TIterConst it = begin(source.data_vertex, Standard());
-	TIterConst itEnd = end(source.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it != itEnd; ++it, ++pos) {
-		TEdgeStump* current = *it;
-		TVertexDescriptor sourceVertex = pos;
-		while(current != (TEdgeStump*) 0) {
-			TVertexDescriptor targetVertex = current->data_target;
-			// Create missing vertices
-			if (sourceVertex>targetVertex) _createVertices(dest,sourceVertex);
-			else _createVertices(dest,targetVertex);
-			// Add edge
-			TEdgeDescriptor e;
-			if (!transpose) e = addEdge(dest, sourceVertex, targetVertex);
-			else e = addEdge(dest, targetVertex, sourceVertex);
-			_assignId(e, _getId(current));
-			assignCargo(e, getCargo(current));
-			current = getNextT(current);
-		}
-	}
-	dest.data_id_managerV = source.data_id_managerV;
-	dest.data_id_managerE = source.data_id_managerE;
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+    clear(dest);
+    resize(dest.data_vertex, length(source.data_vertex));
+    TIter itInit = begin(dest.data_vertex, Standard());
+    TIter itInitEnd = end(dest.data_vertex, Standard());
+    for (;itInit != itInitEnd; ++itInit)
+    {
+        *itInit = (TEdgeStump*) 0;
+    }
+    TIterConst it = begin(source.data_vertex, Standard());
+    TIterConst itEnd = end(source.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for (;it != itEnd; ++it, ++pos)
+    {
+        TEdgeStump* current = *it;
+        TVertexDescriptor sourceVertex = pos;
+        while (current != (TEdgeStump*) 0)
+        {
+            TVertexDescriptor targetVertex = current->data_target;
+            // Create missing vertices
+            if (sourceVertex>targetVertex)
+                _createVertices(dest,sourceVertex);
+            else
+                _createVertices(dest,targetVertex);
+            // Add edge
+            TEdgeDescriptor e;
+            if (!transpose)
+                e = addEdge(dest, sourceVertex, targetVertex);
+            else
+                e = addEdge(dest, targetVertex, sourceVertex);
+
+            _assignId(e, _getId(current));
+            assignCargo(e, getCargo(current));
+            current = getNextT(current);
+        }
+    }
+    dest.data_id_managerV = source.data_id_managerV;
+    dest.data_id_managerE = source.data_id_managerE;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec>
+template <typename TCargo, typename TSpec>
 inline void
-_copyGraph(Graph<Directed<TCargo, TSpec> > const& source,
-		   Graph<Directed<TCargo, TSpec> >& dest) 
+_copyGraph(Graph<Directed<TCargo, TSpec> > & dest,
+           Graph<Directed<TCargo, TSpec> > const & source)
 {
-	_copyGraph(source, dest, false);
+    _copyGraph(dest, source, false);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 // FUNCTIONS
 //////////////////////////////////////////////////////////////////////////////
 
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TCargo, typename TSpec>
+inline void
+transpose(Graph<Directed<TCargo, TSpec> > const & source,
+          Graph<Directed<TCargo, TSpec> > & dest)
+{
+    _copyGraph(dest, source, true);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TCargo, typename TSpec>
+inline void
+transpose(Graph<Directed<TCargo, TSpec> > & g)
+{
+    Graph<Directed<TCargo, TSpec> > dest;
+    _copyGraph(dest, g, true);
+    g = dest;
+}
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.transpose
-..class:Class.Graph
-..cat:Graph
-..summary:Transposes a graph, either in-place or from source to dest.
-..signature:transpose(source [, dest])
-..param.source:Source graph.
-...type:Class.Graph
-..param.dest:Destination graph.
-...type:Class.Graph
-..returns:void
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec>
-inline void 
-transpose(Graph<Directed<TCargo, TSpec> > const& source,
-		  Graph<Directed<TCargo, TSpec> >& dest)
+template <typename TCargo, typename TSpec>
+inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type
+numEdges(Graph<Directed<TCargo, TSpec> > const & g)
 {
-	SEQAN_CHECKPOINT
-	_copyGraph(source, dest, true);
+    return idCount(g.data_id_managerE);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec>
-inline void 
-transpose(Graph<Directed<TCargo, TSpec> >& g)
+template <typename TCargo, typename TSpec>
+inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type
+numVertices(Graph<Directed<TCargo, TSpec> > const & g)
 {
-	SEQAN_CHECKPOINT
-	Graph<Directed<TCargo, TSpec> > dest;
-	_copyGraph(g, dest, true);
-	g = dest;
+    return idCount(g.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.numEdges
-..class:Class.Graph
-..cat:Graph
-..summary:Number of edges in a graph.
-..signature:numEdges(g)
-..param.g:A graph.
-...type:Class.Graph
-..returns:Number of edges.
-..see:Function.numVertices
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec>
-inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type 
-numEdges(Graph<Directed<TCargo, TSpec> > const& g) 
+template <typename TCargo, typename TSpec>
+inline bool
+empty(Graph<Directed<TCargo, TSpec> > const & g)
 {
-	SEQAN_CHECKPOINT
-	return idCount(g.data_id_managerE);
+    return !(idCount(g.data_id_managerV));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.numVertices
-..class:Class.Graph
-..cat:Graph
-..summary:Number of vertices in a graph.
-..signature:numVertices(g)
-..param.g:A graph.
-...type:Class.Graph
-..returns:Number of vertices.
-..see:Function.numEdges
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec>
-inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type 
-numVertices(Graph<Directed<TCargo, TSpec> > const& g) 
+template <typename TCargo, typename TSpec>
+inline void
+clearEdges(Graph<Directed<TCargo, TSpec> > & g)
 {
-	SEQAN_CHECKPOINT
-	return idCount(g.data_id_managerV);
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+    TIter it = begin(g.data_vertex, Standard());
+    TIter itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for (; it != itEnd; ++it, ++pos)
+    {
+        if (*it != (TEdgeStump*) 0)
+            removeOutEdges(g, pos);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.empty
-..class:Class.Graph
-..cat:Graph
-..param.object.type:Class.Graph
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec>
-inline bool 
-empty(Graph<Directed<TCargo, TSpec> > const& g) 
+template <typename TCargo>
+inline void
+clearVertices(Graph<Directed<TCargo, WithSourceId> > & g)
 {
-	SEQAN_CHECKPOINT
-	return (!(idCount(g.data_id_managerV)));
+    clearEdges(g);
+    releaseAll(g.data_id_managerV);
+    clear(g.data_vertex);
+    clear(g.data_vertex_in);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.clearEdges
-..class:Class.Graph
-..cat:Graph
-..summary:Removes all edges in a graph.
-..signature:clearEdges(g)
-..param.g:A graph.
-...type:Class.Graph
-..returns:void
-..see:Function.clearVertices
-..see:Function.clear
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec>
+template <typename TCargo, typename TSpec>
 inline void
-clearEdges(Graph<Directed<TCargo, TSpec> >& g) 
+clearVertices(Graph<Directed<TCargo, TSpec> > & g)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
-	TIter it = begin(g.data_vertex, Standard());
-	TIter itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it != itEnd; ++it, ++pos) 
-		if (*it != (TEdgeStump*) 0) removeOutEdges(g, pos);
+    clearEdges(g);
+    releaseAll(g.data_id_managerV);
+    clear(g.data_vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.clearVertices
-..class:Class.Graph
-..cat:Graph
-..summary:Removes all vertices in a graph.
-..signature:clearVertices(g)
-..param.g:A graph.
-...type:Class.Graph
-..returns:void
-..see:Function.clearEdges
-..see:Function.clear
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec>
+
+template <typename TCargo, typename TSpec>
 inline void
-clearVertices(Graph<Directed<TCargo, TSpec> >& g) 
+clear(Graph<Directed<TCargo, TSpec> > & g)
 {
-	SEQAN_CHECKPOINT
-	clearEdges(g);
-	releaseAll(g.data_id_managerV);
-	clear(g.data_vertex);
+    clearVertices(g);
 }
 
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type
+outDegree(Graph<Directed<TCargo, TSpec> > const & g,
+          TVertexDescriptor const & vertex)
+{
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TGraph>::Type TSize;
+    TSize count = 0;
+    TEdgeStump* current = getValue(g.data_vertex, vertex);
+    while (current != 0)
+    {
+        current = getNextT(current);
+        ++count;
+    }
+    return count;
+}
 
 //////////////////////////////////////////////////////////////////////////////
 
+template <typename TCargo, typename TVertexDescriptor>
+inline typename Size<Graph<Directed<TCargo, WithSourceId> > >::Type
+inDegree(Graph<Directed<TCargo, WithSourceId> > const & g,
+         TVertexDescriptor const & vertex)
+{
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Directed<TCargo, WithSourceId> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TGraph>::Type TSize;
+    TEdgeStump* current = g.data_vertex_in[vertex];
+    TSize count = 0;
+    while (current != 0)
+    {
+        current = getNextS(current);
+        ++count;
+    }
+    return count;
+}
 
-/**
-.Function.clear
-..class:Class.Graph
-..cat:Graph
-..param.object.type:Class.Graph
-..remarks:If $object$ is a @Class.Graph.graph@, then all vertices and all edges are removed.
-..include:seqan/graph_types.h
-*/
+//////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec>
-inline void 
-clear(Graph<Directed<TCargo, TSpec> >& g) 
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type
+inDegree(Graph<Directed<TCargo, TSpec> > const & g,
+         TVertexDescriptor const & vertex)
 {
-	SEQAN_CHECKPOINT
-	clearVertices(g);
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+
+    TSize count=0;
+    for (; it != itEnd; ++it)
+    {
+        TEdgeStump* current = *it;
+        while (current!=0)
+        {
+            if (static_cast<TVertexDescriptor>(getTarget(current)) == vertex)
+                ++count;
+
+            current = getNextT(current);
+        }
+    }
+    return count;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.outDegree
-..class:Class.Graph
-..cat:Graph
-..summary:Number of outgoing edges for a given vertex.
-..signature:outDegree(g, vertex)
-..param.g:A graph.
-...type:Class.Graph
-..param.g:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:Number of out-edges.
-..see:Function.inDegree
-..see:Function.degree
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type 
-outDegree(Graph<Directed<TCargo, TSpec> > const& g, 
-		  TVertexDescriptor const vertex) 
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type
+degree(Graph<Directed<TCargo, TSpec> > const & g,
+       TVertexDescriptor const & vertex)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TGraph>::Type TSize;
-	TSize count=0;
-	TEdgeStump* current = getValue(g.data_vertex, vertex);
-	while(current!=0) {
-		current = getNextT(current);
-		++count;
-	}
-	return count;
+    return inDegree(g,vertex) + outDegree(g,vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.inDegree
-..class:Class.Graph
-..cat:Graph
-..summary:Number of incoming edges for a given vertex.
-..signature:inDegree(g, vertex)
-..param.g:A graph.
-...type:Class.Graph
-..param.g:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:Number of in-edges.
-..see:Function.outDegree
-..see:Function.degree
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type 
-inDegree(Graph<Directed<TCargo, TSpec> > const& g, 
-		 TVertexDescriptor const vertex) 
+template <typename TCargo>
+inline typename VertexDescriptor<Graph<Directed<TCargo, WithSourceId> > >::Type
+addVertex(Graph<Directed<TCargo, WithSourceId> > & g)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-
-	TSize count=0;
-	for(;it!=itEnd;++it) {
-		TEdgeStump* current = *it;
-		while(current!=0) {
-			if ( (TVertexDescriptor) getTarget(current) == vertex) ++count;
-			current = getNextT(current);
-		}
-	}
-	return count;
+    typedef Graph<Directed<TCargo, WithSourceId> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    TVertexDescriptor vd = obtainId(g.data_id_managerV);
+    if (vd == length(g.data_vertex))
+    {
+        appendValue(g.data_vertex, (TEdgeStump*) 0);
+        appendValue(g.data_vertex_in, (TEdgeStump*) 0);
+    }
+    else
+    {
+        g.data_vertex[vd] = (TEdgeStump*) 0;
+        g.data_vertex_in[vd] = (TEdgeStump*) 0;
+    }
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.degree
-..class:Class.Graph
-..cat:Graph
-..summary:Number of incident edges for a given vertex.
-..signature:degree(g, vertex)
-..param.g:A graph.
-...type:Class.Graph
-..param.g:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:Number of incident edges.
-..see:Function.outDegree
-..see:Function.inDegree
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename Size<Graph<Directed<TCargo, TSpec> > >::Type 
-degree(Graph<Directed<TCargo, TSpec> > const& g, 
-	   TVertexDescriptor const vertex) 
+template <typename TCargo, typename TSpec>
+inline typename VertexDescriptor<Graph<Directed<TCargo, TSpec> > >::Type
+addVertex(Graph<Directed<TCargo, TSpec> > & g)
 {
-	SEQAN_CHECKPOINT
-	return (inDegree(g,vertex)+outDegree(g,vertex));
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    TVertexDescriptor vd = obtainId(g.data_id_managerV);
+    if (vd == length(g.data_vertex))
+        appendValue(g.data_vertex, (TEdgeStump*) 0);
+    else
+        g.data_vertex[vd] = (TEdgeStump*) 0;
+
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.addVertex
-..class:Class.Graph
-..cat:Graph
-..summary:Adds a new vertex to the graph.
-..signature:addVertex(g)
-..param.g:A graph.
-...type:Class.Graph
-..returns:A new vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..see:Function.removeVertex
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec> 
-inline typename VertexDescriptor<Graph<Directed<TCargo, TSpec> > >::Type 
-addVertex(Graph<Directed<TCargo, TSpec> >& g) 
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeVertex(Graph<Directed<TCargo, TSpec> > & g,
+             TVertexDescriptor const & v)
 {
-	SEQAN_CHECKPOINT	
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	TVertexDescriptor vd = obtainId(g.data_id_managerV);
-	if (vd == length(g.data_vertex)) appendValue(g.data_vertex, (TEdgeStump*) 0); 
-	else g.data_vertex[vd] = (TEdgeStump*) 0;
-	return vd;
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+
+    removeOutEdges(g, v); // Remove all outgoing edges
+    removeInEdges(g, v); // Remove all incoming edges
+    releaseId(g.data_id_managerV, v); // Release id
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.removeVertex
-..class:Class.Graph
-..cat:Graph
-..summary:Removes a vertex.
-..signature:removeVertex(g, v)
-..param.g:A graph.
-...type:Class.Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:void
-..see:Function.addVertex
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeVertex(Graph<Directed<TCargo, TSpec> >& g, 
-			 TVertexDescriptor const v) 
+template <typename TCargo, typename TVertexDescriptor>
+inline typename EdgeDescriptor<Graph<Directed<TCargo, WithSourceId> > >::Type
+addEdge(Graph<Directed<TCargo, WithSourceId> > & g,
+        TVertexDescriptor const & source,
+        TVertexDescriptor const & target)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+
+    typedef Graph<Directed<TCargo, WithSourceId> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Id<TGraph>::Type TId;
+
+    TEdgeStump* edge_ptr;
+    allocate(g.data_allocator, edge_ptr, 1);
+    valueConstruct(edge_ptr);
+    assignSource(edge_ptr, source);
+    assignTarget(edge_ptr, target);
+    assignNextS(edge_ptr, (TEdgeStump*) 0);
+    assignNextT(edge_ptr, (TEdgeStump*) 0);
+    TId id = obtainId(g.data_id_managerE);
+    _assignId(edge_ptr, id);
+
+    if (g.data_vertex[source] != 0)
+        assignNextT(edge_ptr, getValue(g.data_vertex, source));
+
+    if (g.data_vertex_in[target] != 0)
+        assignNextS(edge_ptr, getValue(g.data_vertex_in, target));
+
+    g.data_vertex[source] = edge_ptr;
+    g.data_vertex_in[target] = edge_ptr;
+    return edge_ptr;
+}
 
-	removeOutEdges(g,v); // Remove all outgoing edges
-	removeInEdges(g,v); // Remove all incoming edges
-	releaseId(g.data_id_managerV, v); // Release id
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename EdgeDescriptor<Graph<Directed<TCargo, TSpec> > >::Type
+addEdge(Graph<Directed<TCargo, TSpec> > & g,
+        TVertexDescriptor const & source,
+        TVertexDescriptor const & target)
+{
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Id<TGraph>::Type TId;
+
+    TEdgeStump* edge_ptr;
+    allocate(g.data_allocator, edge_ptr, 1);
+    valueConstruct(edge_ptr);
+    assignTarget(edge_ptr, target);
+    assignNextT(edge_ptr, (TEdgeStump*) 0);
+    TId id = obtainId(g.data_id_managerE);
+    _assignId(edge_ptr, id);
+
+    if (g.data_vertex[source] != 0)
+        assignNextT(edge_ptr, getValue(g.data_vertex, source));
+
+    value(g.data_vertex, source) = edge_ptr;
+    return edge_ptr;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.addEdge
-..class:Class.Graph
-..cat:Graph
-..summary:Adds a new edge to the graph, either with or without cargo.
-..remarks:For automatons a label is required.
-..signature:addEdge(g, source, target [,cargo | ,label])
-..signature:addEdge(g, source, target [,label ,cargo])
-..param.g:A graph.
-...type:Class.Graph
-..param.source:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.target:A second vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.label:A label for the edge.
-...type:Metafunction.Alphabet
-...remarks:Can only be used with @Spec.Automaton@.
-..param.cargo:A cargo object.
-...type:Metafunction.Cargo
-..returns:A new edge descriptor.
-...type:Metafunction.EdgeDescriptor
-..see:Function.removeEdge
-..see:Function.addEdges
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename EdgeDescriptor<Graph<Directed<TCargo, TSpec> > >::Type 
-addEdge(Graph<Directed<TCargo, TSpec> >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target) 
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename EdgeDescriptor<Graph<Directed<TCargo, TSpec> > >::Type
+addEdge(Graph<Directed<TCargo, TSpec> > & g,
+        TVertexDescriptor const & source,
+        TVertexDescriptor const & target,
+        TCargo const cargo)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
-
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Id<TGraph>::Type TId;
-
-	TEdgeStump* edge_ptr;
-	allocate(g.data_allocator, edge_ptr, 1);
-	valueConstruct(edge_ptr);
-	assignTarget(edge_ptr, target);
-	assignNextT(edge_ptr, (TEdgeStump*) 0);
-	TId id = obtainId(g.data_id_managerE);
-	_assignId(edge_ptr, id);
-	if (g.data_vertex[source]!=0) assignNextT(edge_ptr, getValue(g.data_vertex, source));
-	value(g.data_vertex, source)=edge_ptr;
-	return edge_ptr;
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = addEdge(g, source, target);
+    assignCargo(e, cargo);
+    return e;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename EdgeDescriptor<Graph<Directed<TCargo, TSpec> > >::Type 
-addEdge(Graph<Directed<TCargo, TSpec> >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target,
-		TCargo const cargo) 
+template <typename TCargo, typename TVertexDescriptor>
+inline void
+removeEdge(Graph<Directed<TCargo, WithSourceId> > & g,
+           TVertexDescriptor const & source,
+           TVertexDescriptor const & target)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = addEdge(g,source,target);
-	assignCargo(e,cargo);
-	return e;
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+
+    typedef Graph<Directed<TCargo, WithSourceId> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    // Find edge and predecessor
+    TEdgeStump* pred = 0;
+    TEdgeStump* current = g.data_vertex[source];
+    while (current != (TEdgeStump*) 0)
+    {
+        if (static_cast<TVertexDescriptor>(getTarget(current)) == target)
+            break;
+
+        pred = current;
+        current = getNextT(current);
+    }
+
+    // Not found?
+    if (current == (TEdgeStump*) 0)
+        return;
+
+    // Relink the next pointer of predecessor
+    if (pred != (TEdgeStump*) 0)
+    {
+        assignNextT(pred, getNextT(current));
+    }
+    else
+    {
+        g.data_vertex[source] = getNextT(current);
+        g.data_vertex_in[target] = getNextT(current);
+    } 
+
+    // Deallocate
+    releaseId(g.data_id_managerE, _getId(current));
+    valueDestruct(current);
+    deallocate(g.data_allocator, current, 1);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.removeEdge
-..class:Class.Graph
-..cat:Graph
-..summary:Removes an edge from the graph. For automatons a label is required.
-..signature:removeEdge(g, source, target [, label])
-..signature:removeEdge(g, e)
-..param.g:A graph.
-...type:Class.Graph
-..param.source:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.target:A second vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.label:A label for the edge.
-...type:Metafunction.Alphabet
-...remarks:Required to remove an edge in an @Spec.Automaton@.
-..param.e:An edge descriptor.
-...type:Metafunction.EdgeDescriptor
-..returns:void
-..see:Function.addEdge
-..see:Function.addEdges
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeEdge(Graph<Directed<TCargo, TSpec> >& g, 
-		   TVertexDescriptor const source, 
-		   TVertexDescriptor const target) 
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeEdge(Graph<Directed<TCargo, TSpec> > & g,
+           TVertexDescriptor const & source,
+           TVertexDescriptor const & target)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
-	
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-
-	// Find edge and predecessor
-	TEdgeStump* pred = 0;
-	TEdgeStump* current = g.data_vertex[source];
-	while(current != (TEdgeStump*) 0) {
-		if ( (TVertexDescriptor) getTarget(current) == target) break;
-		pred = current;
-		current = getNextT(current);
-	}
-	
-	// Not found?
-	if (current == (TEdgeStump*) 0) return;
-	
-	// Relink the next pointer of predecessor
-	if (pred != (TEdgeStump*) 0) assignNextT(pred, getNextT(current));
-	else g.data_vertex[source] = getNextT(current);
-	
-	// Deallocate
-	releaseId(g.data_id_managerE, _getId(current));
-	valueDestruct(current);
-	deallocate(g.data_allocator, current, 1);
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    // Find edge and predecessor
+    TEdgeStump* pred = 0;
+    TEdgeStump* current = g.data_vertex[source];
+    while (current != (TEdgeStump*) 0)
+    {
+        if (static_cast<TVertexDescriptor>(getTarget(current)) == target)
+            break;
+
+        pred = current;
+        current = getNextT(current);
+    }
+
+    // Not found?
+    if (current == (TEdgeStump*) 0)
+        return;
+
+    // Relink the next pointer of predecessor
+    if (pred != (TEdgeStump*) 0)
+        assignNextT(pred, getNextT(current));
+    else
+        g.data_vertex[source] = getNextT(current);
+
+    // Deallocate
+    releaseId(g.data_id_managerE, _getId(current));
+    valueDestruct(current);
+    deallocate(g.data_allocator, current, 1);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline void 
-removeEdge(Graph<Directed<TCargo, TSpec> >& g,
-		   TEdgeDescriptor const edge)
+template <typename TCargo, typename TSpec, typename TEdgeDescriptor>
+inline void
+removeEdge(Graph<Directed<TCargo, TSpec> > & g,
+           TEdgeDescriptor const & edge)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, sourceVertex(g,edge)));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, targetVertex(g,edge)));
-	
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-
-	// Find edge and predecessor
-	TEdgeStump* pred = 0;
-	TEdgeStump* current = g.data_vertex[sourceVertex(g,edge)];
-	while(current != (TEdgeStump*) 0) {
-		if (current == edge) break;
-		pred = current;
-		current = getNextT(current);
-	}
-	
-	// Not found?
-	if (current == (TEdgeStump*) 0) return;
-	
-	// Relink the next pointer of predecessor
-	if (pred != (TEdgeStump*) 0) assignNextT(pred, getNextT(current));
-	else g.data_vertex[sourceVertex(g,edge)] = getNextT(current);
-	
-	// Deallocate
-	releaseId(g.data_id_managerE, _getId(current));
-	valueDestruct(current);
-	deallocate(g.data_allocator, current, 1);
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, sourceVertex(g,edge)));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, targetVertex(g,edge)));
+
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    // Find edge and predecessor
+    TEdgeStump* pred = 0;
+    TEdgeStump* current = g.data_vertex[sourceVertex(g,edge)];
+    while (current != (TEdgeStump*) 0)
+    {
+        if (current == edge)
+            break;
+
+        pred = current;
+        current = getNextT(current);
+    }
+
+    // Not found?
+    if (current == (TEdgeStump*) 0)
+        return;
+
+    // Relink the next pointer of predecessor
+    if (pred != (TEdgeStump*) 0)
+        assignNextT(pred, getNextT(current));
+    else
+        g.data_vertex[sourceVertex(g,edge)] = getNextT(current);
+
+    // Deallocate
+    releaseId(g.data_id_managerE, _getId(current));
+    valueDestruct(current);
+    deallocate(g.data_allocator, current, 1);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.removeOutEdges
-..class:Class.Graph
-..cat:Graph
-..summary:Removes the outgoing edges of a given vertex.
-..signature:removeOutEdges(g, v)
-..param.g:A graph.
-...type:Class.Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:void
-..see:Function.removeInEdges
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
-removeOutEdges(Graph<Directed<TCargo, TSpec> >& g, 
-			   TVertexDescriptor const v) 
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeOutEdges(Graph<Directed<TCargo, TSpec> > & g,
+               TVertexDescriptor const & v)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	while(g.data_vertex[v] != (TEdgeStump*) 0) {
-		TVertexDescriptor target = targetVertex(g, g.data_vertex[v]);
-		removeEdge(g,v,target);
-	}
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    while (g.data_vertex[v] != (TEdgeStump*) 0)
+    {
+        TVertexDescriptor target = targetVertex(g, g.data_vertex[v]);
+        removeEdge(g, v, target);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.removeInEdges
-..class:Class.Graph
-..cat:Graph
-..summary:Removes the incoming edges of a given vertex.
-..signature:removeInEdges(g, v)
-..param.g:A graph.
-...type:Class.Graph
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:void
-..see:Function.removeOutEdges
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
-removeInEdges(Graph<Directed<TCargo, TSpec> >& g, 
-			   TVertexDescriptor const v) 
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeInEdges(Graph<Directed<TCargo, TSpec> > & g,
+              TVertexDescriptor const & v)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
-	TIter it = begin(g.data_vertex, Standard());
-	TIter itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		TEdgeStump* current = *it;
-		TVertexDescriptor const sourceVertex = pos;
-		while(current!=0) {
-			if ( (TVertexDescriptor) current->data_target==v) {
-				removeEdge(g, sourceVertex, v);
-				current = g.data_vertex[sourceVertex];
-			} else {
-				current = getNextT(current);
-			}
-		}
-	}
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+    TIter it = begin(g.data_vertex, Standard());
+    TIter itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for (; it != itEnd; ++it, ++pos)
+    {
+        TEdgeStump* current = *it;
+        TVertexDescriptor const sourceVertex = pos;
+        while (current!=0)
+        {
+            if (static_cast<TVertexDescriptor>(current->data_target) == v)
+            {
+                removeEdge(g, sourceVertex, v);
+                current = g.data_vertex[sourceVertex];
+            }
+            else
+            {
+                current = getNextT(current);
+            }
+        }
+    }
 }
 
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TCargo, typename TSpec, typename TEdgeDescriptor>
+inline typename VertexDescriptor<Graph<Directed<TCargo, TSpec> > >::Type
+targetVertex(Graph<Directed<TCargo, TSpec> > const &,
+             TEdgeDescriptor const & edge)
+{
+    return getTarget(edge);
+}
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.targetVertex
-..class:Class.Graph
-..cat:Graph
-..summary:Returns the target vertex of an edge.
-..remarks:In a tree the target vertex is always the child. 
-In an undirected graph the larger vertex descriptor of the two endpoints is the target.
-For an out-edge iterator the target is always the vertex the out-edge iterator has not been initialized with.
-..signature:targetVertex(g, e)
-..signature:targetVertex(it)
-..param.g:A graph.
-...type:Class.Graph
-..param.e:An edge descriptor.
-...type:Metafunction.EdgeDescriptor
-..param.it:An edge iterator.
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-..returns:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..see:Function.sourceVertex
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Directed<TCargo, TSpec> > >::Type 
-targetVertex(Graph<Directed<TCargo, TSpec> > const&,
-			 TEdgeDescriptor const edge) 
+template<typename TCargo, typename TEdgeDescriptor>
+inline typename VertexDescriptor<Graph<Directed<TCargo, WithSourceId> > >::Type
+sourceVertex(Graph<Directed<TCargo, WithSourceId> > const &,
+             TEdgeDescriptor const & edge)
 {
-	SEQAN_CHECKPOINT
-	return getTarget(edge);
+    return getSource(edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.sourceVertex
-..class:Class.Graph
-..cat:Graph
-..summary:Returns the source vertex of an edge.
-..remarks:In a tree the source vertex is always the parent. 
-In an undirected graph the smaller vertex descriptor is the source.
-Note: If source vertices are not stored in the EdgeStump this operation is expensive.
-Consider using sourceVertex directly on an edge iterator where this operation is fast!
-..signature:sourceVertex(g, e)
-..signature:sourceVertex(it)
-..param.g:A graph.
-...type:Class.Graph
-..param.e:An edge descriptor.
-...type:Metafunction.EdgeDescriptor
-..param.it:An edge iterator.
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-..returns:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..see:Function.targetVertex
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Directed<TCargo, TSpec> > >::Type 
-sourceVertex(Graph<Directed<TCargo, TSpec> > const& g,
-			 TEdgeDescriptor const edge) 
+template <typename TCargo, typename TSpec, typename TEdgeDescriptor>
+inline typename VertexDescriptor<Graph<Directed<TCargo, TSpec> > >::Type
+sourceVertex(Graph<Directed<TCargo, TSpec> > const & g,
+             TEdgeDescriptor const & edge)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		TEdgeDescriptor current = *it;
-		while(current!=(TEdgeDescriptor) 0) {
-			if (current == edge) return pos;
-			current=getNextT(current);
-		}
-	}
-	return 0;
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for (; it != itEnd; ++it, ++pos)
+    {
+        TEdgeDescriptor current = *it;
+        while (current != (TEdgeDescriptor) 0)
+        {
+            if (current == edge)
+                return pos;
+
+            current = getNextT(current);
+        }
+    }
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.getAdjacencyMatrix
-..class:Class.Graph
-..cat:Graph
-..summary:Returns an adjacency matrix representation of the graph.
-..signature:getAdjacencyMatrix(g, mat)
-..param.g:In-parameter: A graph.
-...type:Class.Graph
-..param.mat:Out-parameter: A matrix.
-...type:Class.Matrix
-..returns:void
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TMatrix>
+template <typename TCargo, typename TSpec, typename TMatrix>
 inline void
-getAdjacencyMatrix(Graph<Directed<TCargo, TSpec> > const& g, 
-				   TMatrix& mat) 
+getAdjacencyMatrix(Graph<Directed<TCargo, TSpec> > const & g,
+                   TMatrix & mat)
 {
-	SEQAN_CHECKPOINT
-
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
     typedef typename Size<TGraph>::Type TGraphSize;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TMatrix>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	typedef typename Value<TMatrix>::Type TMatValue;
-	TSize len = getIdUpperBound(g.data_id_managerV);
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TMatrix>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    typedef typename Value<TMatrix>::Type TMatValue;
+    TSize len = getIdUpperBound(g.data_id_managerV);
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
     clear(mat);
-	resize(mat, len * len, (TMatValue) 0);
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd; ++it, ++pos) {
-		TEdgeStump* current = *it;
-		TVertexDescriptor const source = pos;
-		while(current != (TEdgeStump*) 0) {
-			TVertexDescriptor target = targetVertex(g,current);
-			mat[source * len + target] = static_cast<TMatValue>(static_cast<TGraphSize>(mat[source * len + target]) + 1);
-			current = getNextT(current);
-		}
-	}
+    resize(mat, len * len, (TMatValue) 0);
+    TVertexDescriptor pos = 0;
+    for (; it != itEnd; ++it, ++pos)
+    {
+        TEdgeStump* current = *it;
+        TVertexDescriptor const source = pos;
+        while (current != (TEdgeStump*) 0)
+        {
+            TVertexDescriptor target = targetVertex(g, current);
+            mat[source * len + target] = static_cast<TMatValue>(static_cast<TGraphSize>(mat[source * len + target]) + 1);
+            current = getNextT(current);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-
-/**
-.Function.findEdge
-..class:Class.Graph
-..cat:Graph
-..summary:Finds an edge. 
-..remarks:In an automaton an edge is uniquely defined by a vertex and a label.
-In all other graphs two adjacent vertices uniquely define an edge.
-If there are multiple edges between two vertices the behaviour is undefined.
-..signature:findEdge(g, v, c)
-..signature:findEdge(g, v, w)
-..param.g:A graph.
-...type:Class.Graph
-..param.v:The source vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.c:An edge label.
-...type:Metafunction.Alphabet
-..param.w:The target vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:An edge descriptor or 0 if edge is not present. 
-Note: In automatons there is always a valid edge descriptor but the target may be nil.
-...type:Metafunction.EdgeDescriptor
-..include:seqan/graph_types.h
-*/
-template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename EdgeDescriptor<Graph<Directed<TCargo, TSpec> > >::Type 
-findEdge(Graph<Directed<TCargo, TSpec> > const& g,
-		 TVertexDescriptor const v,
-		 TVertexDescriptor const w)
+template <typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename EdgeDescriptor<Graph<Directed<TCargo, TSpec> > >::Type
+findEdge(Graph<Directed<TCargo, TSpec> > const & g,
+         TVertexDescriptor const & v,
+         TVertexDescriptor const & w)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, w));
-	
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	
-	TEdgeStump* current = g.data_vertex[v];
-	while(current != (TEdgeStump*) 0) {
-		if ( (TVertexDescriptor) getTarget(current) == w) return current;
-		current = getNextT(current);
-	}
-	return 0;
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, w));
+
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    TEdgeStump* current = g.data_vertex[v];
+    while (current != (TEdgeStump*) 0)
+    {
+        if (static_cast<TVertexDescriptor>(getTarget(current)) == w)
+            return current;
+
+        current = getNextT(current);
+    }
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TFile, typename TCargo, typename TSpec, typename TIDString>
+template <typename TFile, typename TCargo, typename TSpec>
 inline void
 write(TFile & target,
-	  Graph<Directed<TCargo, TSpec> > const& g,
-	  TIDString const &,
-	  Raw)
+      Graph<Directed<TCargo, TSpec> > const & g)
 {
 //IOREV _nodoc_
-	SEQAN_CHECKPOINT
-	typedef Graph<Directed<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	streamPut(target,"Adjacency list:\n");
-	for(;it!=itEnd;++it, ++pos) {
-		if (!idInUse(_getVertexIdManager(g), pos)) continue;
-		TEdgeStump* current = getValue(it);
-		streamPut(target, (int)pos);
-		streamPut(target," -> ");
-		while(current!=0) {
-			streamPut(target, (int)getTarget(current));
-			streamPut(target, ',');
-			current=getNextT(current);
-		}
-		streamPut(target, '\n');
-	}
-	it = begin(g.data_vertex, Standard());
-	pos = 0;
-	streamPut(target,"Edge list:\n");
-	for(;it!=itEnd;++it, ++pos) {
-		TEdgeStump* current = getValue(it);
-		while(current!=0) {
-			streamPut(target,"Source: ");
-			streamPut(target, (int)pos);		
-			streamPut(target, ',');
-			streamPut(target,"Target: ");
-			streamPut(target, (int)getTarget(current));
-			streamPut(target, ' ');
-			streamPut(target,"(Id: ");
-			streamPut(target, (int)_getId(current));
-			streamPut(target, ')');
-			streamPut(target, '\n');
-			current=getNextT(current);
-		}
-	}
+    typedef Graph<Directed<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    write(target, "Adjacency list:\n");
+    for (; it != itEnd; ++it, ++pos)
+    {
+        if (!idInUse(_getVertexIdManager(g), pos))
+            continue;
+
+        TEdgeStump* current = getValue(it);
+        appendNumber(target, static_cast<int>(pos));
+        write(target, " -> ");
+        while (current != 0)
+        {
+            appendNumber(target, static_cast<int>(getTarget(current)));
+            writeValue(target, ',');
+            current = getNextT(current);
+        }
+        writeValue(target, '\n');
+    }
+    it = begin(g.data_vertex, Standard());
+    pos = 0;
+    write(target, "Edge list:\n");
+    for (; it != itEnd; ++it, ++pos)
+    {
+        TEdgeStump* current = getValue(it);
+        while (current != 0)
+        {
+            write(target, "Source: ");
+            appendNumber(target, static_cast<int>(pos));
+            write(target, ",Target: ");
+            appendNumber(target, static_cast<int>(getTarget(current)));
+            write(target, " (Id: ");
+            appendNumber(target, static_cast<int>(_getId(current)));
+            write(target, ")\n");
+            current = getNextT(current);
+        }
+    }
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_impl_hmm.h b/seqan/graph_types/graph_impl_hmm.h
index 42a2a23..fe1c6bd 100644
--- a/seqan/graph_types/graph_impl_hmm.h
+++ b/seqan/graph_types/graph_impl_hmm.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -60,73 +60,46 @@ namespace SEQAN_NAMESPACE_MAIN
  *                   edge ids.  NB: if edges do not store ids then external property maps do not work.
  */
 
-/**
-.Spec.Hmm:
-..cat:Graph
-..general:Class.Graph
-..summary:An Hmm is a directed graph with edges labeled with transition probabilities and emission profiles for each vertex.
-Vertices correspond to states in an HMM.
-..description:
-..signature:Graph<Hmm<TAlphabet, TCargo, TSpec> > 
-..param.TAlphabet:The alphabet type that is used for the emission profile in each vertex.
-...metafunction:Metafunction.Alphabet
-...remarks:Use @Metafunction.Alphabet@ to get the alphabet type.
-...default:$Dna$
-..param.TCargo:The cargo type that can be attached to the edges (the tranisition probabilities).
-...metafunction:Metafunction.Cargo
-...remarks:Use @Metafunction.Cargo@ to get the cargo type.
-...default:$double$
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-...remarks:Use WithoutEdgeId here to omit edge ids.
-Note: If edges do not store ids external property maps do not work.
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec>
-class Graph<Hmm<TAlphabet, TCargo, TSpec> > 
+class Graph<Hmm<TAlphabet, TCargo, TSpec> >
 {
-	public:
-		typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
-		
-		//HMM Model
-		Graph<Directed<TCargo, TSpec> > data_model;
-
-		//Emission probabilities
-		String<TCargo> data_emission;
-
-		//Silent state map
-		String<bool> data_silent;
-
-		//Begin and end state
-		TVertexDescriptor_ data_begin;
-		TVertexDescriptor_ data_end;
-
-	
-//____________________________________________________________________________
-
-		Graph() {
-		}
-
-
-		~Graph() {
-			SEQAN_CHECKPOINT
-			clear(*this);
-		}
-
-		Graph(Graph const & _other) 
-		{
-			SEQAN_CHECKPOINT
-			_copyGraph(_other, *this);	
-		}
-	
-		Graph const& operator = (Graph const & _other) {
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			clear(*this);
-			_copyGraph(_other, *this);
-			return *this;
-		}
+public:
+    typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
+
+    // HMM Model
+    Graph<Directed<TCargo, TSpec> > data_model;
+
+    // Emission probabilities
+    String<TCargo> data_emission;
+
+    // Silent state map
+    String<bool> data_silent;
+
+    // Begin and end state
+    TVertexDescriptor_ data_begin;
+    TVertexDescriptor_ data_end;
+
+    Graph() : data_begin(), data_end()
+    {}
+
+    ~Graph()
+    {
+        clear(*this);
+    }
+
+    Graph(Graph const & _other)
+    {
+        _copyGraph(_other, *this);
+    }
+
+    Graph const& operator = (Graph const & _other)
+    {
+        if (this == &_other)
+            return *this;
+        clear(*this);
+        _copyGraph(_other, *this);
+        return *this;
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -138,10 +111,10 @@ class Graph<Hmm<TAlphabet, TCargo, TSpec> >
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline String<typename EdgeType<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type*>&
 _getVertexString(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	return const_cast<String<TEdgeStump*>&>(g.data_model.data_vertex);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    return const_cast<String<TEdgeStump*>&>(g.data_model.data_vertex);
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -149,10 +122,10 @@ _getVertexString(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) {
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename VertexIdHandler<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type&
 _getVertexIdManager(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
-	return const_cast<TVertexIdManager&>(g.data_model.data_id_managerV);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
+    return const_cast<TVertexIdManager&>(g.data_model.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -160,10 +133,10 @@ _getVertexIdManager(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) {
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename EdgeIdHandler<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type&
 _getEdgeIdManager(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
-	return const_cast<TEdgeIdManager&>(g.data_model.data_id_managerE);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
+    return const_cast<TEdgeIdManager&>(g.data_model.data_id_managerE);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -171,24 +144,24 @@ _getEdgeIdManager(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) {
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& source,
-		   Graph<Hmm<TAlphabet, TCargo, TSpec> >& dest,
-		   bool transp) 
+           Graph<Hmm<TAlphabet, TCargo, TSpec> >& dest,
+           bool transp)
 {
-	SEQAN_CHECKPOINT
-	clear(dest);
-	if (transp) {
-		transpose(source.data_model, dest.data_model);
-		dest.data_emission = source.data_emission;
-		dest.data_silent = source.data_silent;
-		dest.data_begin = source.data_end;
-		dest.data_end = source.data_begin;
-	} else {
-		dest.data_model = source.data_model;
-		dest.data_emission = source.data_emission;
-		dest.data_silent = source.data_silent;
-		dest.data_begin = source.data_begin;
-		dest.data_end = source.data_end;
-	}
+    SEQAN_CHECKPOINT
+    clear(dest);
+    if (transp) {
+        transpose(source.data_model, dest.data_model);
+        dest.data_emission = source.data_emission;
+        dest.data_silent = source.data_silent;
+        dest.data_begin = source.data_end;
+        dest.data_end = source.data_begin;
+    } else {
+        dest.data_model = source.data_model;
+        dest.data_emission = source.data_emission;
+        dest.data_silent = source.data_silent;
+        dest.data_begin = source.data_begin;
+        dest.data_end = source.data_end;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -196,9 +169,9 @@ _copyGraph(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& source,
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& source,
-		   Graph<Hmm<TAlphabet, TCargo, TSpec> >& dest) 
+           Graph<Hmm<TAlphabet, TCargo, TSpec> >& dest)
 {
-	_copyGraph(source, dest, false);
+    _copyGraph(source, dest, false);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -208,64 +181,64 @@ _copyGraph(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& source,
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline void 
+inline void
 transpose(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& source,
-		  Graph<Hmm<TAlphabet, TCargo, TSpec> >& dest)
+          Graph<Hmm<TAlphabet, TCargo, TSpec> >& dest)
 {
-	SEQAN_CHECKPOINT
-	_copyGraph(source, dest, true);
+    SEQAN_CHECKPOINT
+    _copyGraph(source, dest, true);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline void 
+inline void
 transpose(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	Graph<Hmm<TAlphabet, TCargo, TSpec> > dest;
-	_copyGraph(g, dest, true);
-	g = dest;
+    SEQAN_CHECKPOINT
+    Graph<Hmm<TAlphabet, TCargo, TSpec> > dest;
+    _copyGraph(g, dest, true);
+    g = dest;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
-numEdges(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
+numEdges(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return numEdges(g.data_model);
+    SEQAN_CHECKPOINT
+    return numEdges(g.data_model);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
-numVertices(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
+numVertices(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return numVertices(g.data_model);
+    SEQAN_CHECKPOINT
+    return numVertices(g.data_model);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline bool 
-empty(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g) 
+inline bool
+empty(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return empty(g.data_model);
+    SEQAN_CHECKPOINT
+    return empty(g.data_model);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
-clearEdges(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g) 
+clearEdges(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearEdges(g.data_model);
+    SEQAN_CHECKPOINT
+    clearEdges(g.data_model);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -274,358 +247,356 @@ template<typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 clearVertices(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
 {
-	g.data_begin = 0;
-	g.data_end = 0;
-	clear(g.data_emission);
-	clear(g.data_silent);
-	clearVertices(g.data_model);
+    g.data_begin = 0;
+    g.data_end = 0;
+    clear(g.data_emission);
+    clear(g.data_silent);
+    clearVertices(g.data_model);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
-inline void 
-clear(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g) 
+inline void
+clear(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearVertices(g);
+    SEQAN_CHECKPOINT
+    clearVertices(g);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
-outDegree(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g, 
-		  TVertexDescriptor const vertex) 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
+outDegree(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
+          TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return outDegree(g.data_model, vertex);
+    SEQAN_CHECKPOINT
+    return outDegree(g.data_model, vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
-inDegree(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g, 
-		 TVertexDescriptor const vertex) 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
+inDegree(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
+         TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return inDegree(g.data_model, vertex);
+    SEQAN_CHECKPOINT
+    return inDegree(g.data_model, vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 degree(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
-	   TVertexDescriptor const vertex) 
+       TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return degree(g.data_model, vertex);
+    SEQAN_CHECKPOINT
+    return degree(g.data_model, vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec> 
-inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
-addVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g, 
-		  bool silent)
+template<typename TAlphabet, typename TCargo, typename TSpec>
+inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
+addVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
+          bool silent)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TAlphabet>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<String<TCargo>, Standard>::Type TEmisIter;
-	TSize alph_size = ValueSize<TAlphabet>::VALUE;
-
-	TVertexDescriptor vd = addVertex(g.data_model);
-	if (length(g.data_emission) / alph_size <= vd) resize(g.data_emission, (vd + 1) * alph_size, Generous());
-	if (length(g.data_silent) <= vd) resize(g.data_silent, (vd + 1), Generous());
-	g.data_silent[vd] = silent;
-	TEmisIter it = begin(g.data_emission, Standard());
-	it += vd * alph_size;
-	for(TSize counter = 0; counter < alph_size; ++counter, ++it) *it = (TCargo) 0.0;
-	return vd;
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TAlphabet>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<String<TCargo>, Standard>::Type TEmisIter;
+    TSize alph_size = ValueSize<TAlphabet>::VALUE;
+
+    TVertexDescriptor vd = addVertex(g.data_model);
+    if (length(g.data_emission) / alph_size <= vd) resize(g.data_emission, (vd + 1) * alph_size, Generous());
+    if (length(g.data_silent) <= vd) resize(g.data_silent, (vd + 1), Generous());
+    g.data_silent[vd] = silent;
+    TEmisIter it = begin(g.data_emission, Standard());
+    it += vd * alph_size;
+    for(TSize counter = 0; counter < alph_size; ++counter, ++it) *it = (TCargo) 0.0;
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec> 
-inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
+template<typename TAlphabet, typename TCargo, typename TSpec>
+inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 addVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	return addVertex(g, false);
+    SEQAN_CHECKPOINT
+    return addVertex(g, false);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TEmission> 
-inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TEmission>
+inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 addVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> > & g,
-		  String<TEmission> const & emis)
-{
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TAlphabet>::Type TSize;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<String<TCargo>, Standard>::Type TEmisIter;
-	typedef typename Iterator<String<TEmission> const, Standard>::Type TInputIter;
-	TSize alph_size = ValueSize<TAlphabet>::VALUE;
-
-	SEQAN_ASSERT_EQ(alph_size, length(emis));
-
-	TVertexDescriptor vd = addVertex(g);
-	TEmisIter it = begin(g.data_emission, Standard());
-	it += vd * alph_size;
-	TInputIter itIn = begin(emis, Standard());
-	for (TSize counter = 0; counter < alph_size; ++counter, ++itIn, ++it)
+          String<TEmission> const & emis)
+{
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TAlphabet>::Type TSize;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<String<TCargo>, Standard>::Type TEmisIter;
+    typedef typename Iterator<String<TEmission> const, Standard>::Type TInputIter;
+    TSize alph_size = ValueSize<TAlphabet>::VALUE;
+
+    SEQAN_ASSERT_EQ(alph_size, length(emis));
+
+    TVertexDescriptor vd = addVertex(g);
+    TEmisIter it = begin(g.data_emission, Standard());
+    it += vd * alph_size;
+    TInputIter itIn = begin(emis, Standard());
+    for (TSize counter = 0; counter < alph_size; ++counter, ++itIn, ++it)
         *it = *itIn;
-	return vd;
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TEmission> 
-inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TEmission>
+inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 addVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-		  TEmission const& emis,
-		  bool silent)
+          TEmission const& emis,
+          bool silent)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor vd = addVertex(g, emis);
-	g.data_silent[vd] = silent;
-	return vd;
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor vd = addVertex(g, emis);
+    g.data_silent[vd] = silent;
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g, 
-			 TVertexDescriptor const v) 
+inline void
+removeVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
+             TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	// Remove the vertex
-	removeVertex(g.data_model,v);
+    SEQAN_CHECKPOINT
+    // Remove the vertex
+    removeVertex(g.data_model,v);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename EdgeDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
-addEdge(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target) 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename EdgeDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
+addEdge(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target)
 {
-	SEQAN_CHECKPOINT
-	return addEdge(g, source, target, (TCargo) 0.0);
+    SEQAN_CHECKPOINT
+    return addEdge(g, source, target, (TCargo) 0.0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TCargo2> 
-inline typename EdgeDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
-addEdge(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target,
-		TCargo2 const cargo) 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TCargo2>
+inline typename EdgeDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
+addEdge(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target,
+        TCargo2 const cargo)
 {
-	SEQAN_CHECKPOINT
-	return addEdge(g.data_model, source, target, (TCargo) cargo);
+    SEQAN_CHECKPOINT
+    return addEdge(g.data_model, source, target, (TCargo) cargo);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeEdge(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g, 
-		   TVertexDescriptor const source, 
-		   TVertexDescriptor const target) 
+inline void
+removeEdge(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
+           TVertexDescriptor const source,
+           TVertexDescriptor const target)
 {
-	SEQAN_CHECKPOINT
-	removeEdge(g.data_model, source, target);
+    SEQAN_CHECKPOINT
+    removeEdge(g.data_model, source, target);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline void 
+inline void
 removeEdge(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-		   TEdgeDescriptor const edge)
+           TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	removeEdge(g.data_model, sourceVertex(g.data_model,edge), targetVertex(g.data_model,edge));
+    SEQAN_CHECKPOINT
+    removeEdge(g.data_model, sourceVertex(g.data_model,edge), targetVertex(g.data_model,edge));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
-removeOutEdges(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g, 
-			   TVertexDescriptor const v) 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeOutEdges(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
+               TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	removeOutEdges(g.data_model, v);
+    SEQAN_CHECKPOINT
+    removeOutEdges(g.data_model, v);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
 removeInEdges(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-			  TVertexDescriptor const v) 
+              TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	removeInEdges(g.data_model,v);
+    SEQAN_CHECKPOINT
+    removeInEdges(g.data_model,v);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor> 
-inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
+template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
+inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 targetVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return targetVertex(g.data_model, edge);
+    SEQAN_CHECKPOINT
+    return targetVertex(g.data_model, edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 sourceVertex(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return sourceVertex(g.data_model, edge);
+    SEQAN_CHECKPOINT
+    return sourceVertex(g.data_model, edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TMatrix>
 inline void
-getAdjacencyMatrix(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g, 
-				   TMatrix& mat) 
+getAdjacencyMatrix(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
+                   TMatrix& mat)
 {
-	getAdjacencyMatrix(g.data_model, mat);
+    getAdjacencyMatrix(g.data_model, mat);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename EdgeDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type 
+inline typename EdgeDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 findEdge(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
-		 TVertexDescriptor const v,
-		 TVertexDescriptor const w)
+         TVertexDescriptor const v,
+         TVertexDescriptor const w)
 {
-	SEQAN_CHECKPOINT
-	return findEdge(g.data_model, v, w);
+    SEQAN_CHECKPOINT
+    return findEdge(g.data_model, v, w);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TFile, typename TAlphabet, typename TCargo, typename TSpec, typename TIDString>
+template <typename TFile, typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 write(TFile & target,
-	  Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
-	  TIDString const &,
-	  Raw)
+      Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g)
 {
 //IOREV _nodoc_
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename Size<TAlphabet>::Type TSize;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIterConst;
-	TSize alph_size = ValueSize<TAlphabet>::VALUE;
-
-	typedef typename Iterator<String<TCargo> const, Standard>::Type TEmisIter;
-
-	// Alphabet
-	streamPut(target,"Alphabet:\n");
-	streamPut(target,'{');
-	for(TSize counter = 0; counter<alph_size-1;++counter) {
-		streamPut(target,TAlphabet(counter));
-		streamPut(target,',');
-	}
-	streamPut(target,TAlphabet(alph_size-1));
-	streamPut(target,'}');
-	streamPut(target,'\n');
-
-	// States
-	streamPut(target,"States:\n");
-	streamPut(target,'{');
-	TIterConst it = begin(_getVertexString(g), Standard());
-	TIterConst itEnd = end(_getVertexString(g), Standard());
-	bool first = true;
-	for(TSize pos = 0;it!=itEnd;goNext(it), ++pos) {
-		if (!idInUse(_getVertexIdManager(g), pos)) continue;
-		if (!first) streamPut(target,',');
-		else first = false;
-		streamPut(target, (int)pos);	
-		if (isSilent(g, pos)) streamPut(target," (Silent)");
-	}
-	streamPut(target,'}');
-	streamPut(target,'\n');
-
-	// Begin and end state
-	streamPut(target,"Begin state: ");
-	streamPut(target, (int)getBeginState(g));
-	streamPut(target,'\n');
-	streamPut(target,"End state: ");
-	streamPut(target, (int)getEndState(g));
-	streamPut(target,'\n');
-
-	// Transition probabilities
-	streamPut(target,"Transition probabilities:\n");
-	itEnd = end(_getVertexString(g));
-	it = begin(_getVertexString(g));
-	for(TSize pos = 0;it!=itEnd;goNext(it), ++pos) {
-		if (!idInUse(_getVertexIdManager(g), pos)) continue;
-		TEdgeStump* current = getValue(it);
-		streamPut(target, (int)pos);
-		streamPut(target," -> ");
-		first = true;
-		while(current!=0) {
-			if (!first) streamPut(target, ',');
-			else first = false;
-			streamPut(target, (int)getTarget(current));
-			streamPut(target," (");
-			streamPut(target, (double)cargo(current));
-			streamPut(target,") ");
-			current=getNextT(current);
-		}
-		streamPut(target, '\n');
-	}
-
-	// Emission probabilities
-	streamPut(target,"Emission probabilities:\n");
-	TEmisIter itEmis = begin(g.data_emission, Standard());
-	itEnd = end(_getVertexString(g), Standard());
-	it = begin(_getVertexString(g), Standard());	
-	first = true;
-	for(TSize pos = 0;it!=itEnd;++it, ++pos) {
-		if (!idInUse(_getVertexIdManager(g), pos)) continue;
-		if (isSilent(g, pos)) continue;
-		if (!first) streamPut(target,'\n');
-		else first = false;
-		streamPut(target, (int)pos);
-		streamPut(target,": ");
-		bool my_first = true;
-		itEmis = begin(g.data_emission, Standard());
-		itEmis += pos * alph_size;
-		for(TSize counter = 0; counter < alph_size; ++itEmis, ++counter) {
-			if (!my_first) streamPut(target, ',');
-			else my_first = false;
-			streamPut(target, TAlphabet(counter));
-			streamPut(target," (");
-			streamPut(target, (double)*itEmis);
-			streamPut(target,") ");
-			
-		}
-	}
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename Size<TAlphabet>::Type TSize;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIterConst;
+    TSize alph_size = ValueSize<TAlphabet>::VALUE;
+
+    typedef typename Iterator<String<TCargo> const, Standard>::Type TEmisIter;
+
+    // Alphabet
+    write(target, "Alphabet:\n");
+    writeValue(target, '{');
+    for(TSize counter = 0; counter<alph_size-1;++counter) {
+        writeValue(target,TAlphabet(counter));
+        writeValue(target, ',');
+    }
+    writeValue(target,TAlphabet(alph_size-1));
+    writeValue(target, '}');
+    writeValue(target, '\n');
+
+    // States
+    write(target, "States:\n");
+    writeValue(target, '{');
+    TIterConst it = begin(_getVertexString(g), Standard());
+    TIterConst itEnd = end(_getVertexString(g), Standard());
+    bool first = true;
+    for(TSize pos = 0;it!=itEnd;goNext(it), ++pos) {
+        if (!idInUse(_getVertexIdManager(g), pos)) continue;
+        if (!first) writeValue(target, ',');
+        else first = false;
+        appendNumber(target, (int)pos);
+        if (isSilent(g, pos)) write(target, " (Silent)");
+    }
+    writeValue(target, '}');
+    writeValue(target, '\n');
+
+    // Begin and end state
+    write(target, "Begin state: ");
+    appendNumber(target, (int)getBeginState(g));
+    writeValue(target, '\n');
+    write(target, "End state: ");
+    appendNumber(target, (int)getEndState(g));
+    writeValue(target, '\n');
+
+    // Transition probabilities
+    write(target, "Transition probabilities:\n");
+    itEnd = end(_getVertexString(g));
+    it = begin(_getVertexString(g));
+    for(TSize pos = 0;it!=itEnd;goNext(it), ++pos) {
+        if (!idInUse(_getVertexIdManager(g), pos)) continue;
+        TEdgeStump* current = getValue(it);
+        appendNumber(target, (int)pos);
+        write(target, " -> ");
+        first = true;
+        while(current!=0) {
+            if (!first) writeValue(target, ',');
+            else first = false;
+            appendNumber(target, (int)getTarget(current));
+            write(target, " (");
+            write(target, (double)cargo(current));
+            write(target, ") ");
+            current=getNextT(current);
+        }
+        writeValue(target, '\n');
+    }
+
+    // Emission probabilities
+    write(target, "Emission probabilities:\n");
+    TEmisIter itEmis = begin(g.data_emission, Standard());
+    itEnd = end(_getVertexString(g), Standard());
+    it = begin(_getVertexString(g), Standard());
+    first = true;
+    for(TSize pos = 0;it!=itEnd;++it, ++pos) {
+        if (!idInUse(_getVertexIdManager(g), pos)) continue;
+        if (isSilent(g, pos)) continue;
+        if (!first) writeValue(target, '\n');
+        else first = false;
+        appendNumber(target, (int)pos);
+        write(target, ": ");
+        bool my_first = true;
+        itEmis = begin(g.data_emission, Standard());
+        itEmis += pos * alph_size;
+        for(TSize counter = 0; counter < alph_size; ++itEmis, ++counter) {
+            if (!my_first) writeValue(target, ',');
+            else my_first = false;
+            writeValue(target, TAlphabet(counter));
+            write(target, " (");
+            appendNumber(target, (double)*itEmis);
+            write(target, ") ");
+
+        }
+    }
 
 }
 
@@ -643,29 +614,16 @@ write(TFile & target,
  * @param[in]     v   The descriptor of the vertex to assign as begin state.
  */
 
-/**
-.Function.assignBeginState
-..class:Spec.Hmm
-..cat:Graph
-..summary:Assigns a begin state.
-..signature:assignBeginState(g, vertex)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.vertex:The new begin state.
-...type:Metafunction.VertexDescriptor
-..returns:void.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline void
 assignBeginState(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-				 TVertexDescriptor const vertex)
+                 TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT;
-	SEQAN_ASSERT(idInUse(_getVertexIdManager(g), vertex));
+    SEQAN_CHECKPOINT;
+    SEQAN_ASSERT(idInUse(_getVertexIdManager(g), vertex));
 
-	g.data_begin = vertex;
-	g.data_silent[vertex] = true;
+    g.data_begin = vertex;
+    g.data_silent[vertex] = true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -681,29 +639,16 @@ assignBeginState(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
  * @param[in]     v   The descriptor of the vertex to assign as end state.
  */
 
-/**
-.Function.assignEndState:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Assigns an end state.
-..signature:assignEndState(g, vertex)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.vertex:The new end state.
-...type:Metafunction.VertexDescriptor
-..returns:void.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline void
 assignEndState(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-			   TVertexDescriptor const vertex)
+               TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(_getVertexIdManager(g), vertex));
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(_getVertexIdManager(g), vertex));
 
-	g.data_end = vertex;
-	g.data_silent[vertex] = true;
+    g.data_end = vertex;
+    g.data_silent[vertex] = true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -719,23 +664,12 @@ assignEndState(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
  * @return TVertexDescriptor A reference to the begin state vertex descriptor.
  */
 
-/**
-.Function.beginState:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Returns a reference to the begin state.
-..signature:beginState(g)
-..param.g:A HMM.
-...type:Spec.Hmm
-..returns:Reference to begin state.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type&
 beginState(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	return (g.data_begin);
+    SEQAN_CHECKPOINT
+    return (g.data_begin);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -751,23 +685,12 @@ beginState(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
  * @return TVertexDescriptor A reference to the end state vertex descriptor.
  */
 
-/**
-.Function.endState:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Returns a reference to the end state.
-..signature:endState(g)
-..param.g:A HMM.
-...type:Spec.Hmm
-..returns:Reference to end state.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type&
 endState(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	return (g.data_end);
+    SEQAN_CHECKPOINT
+    return (g.data_end);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -783,23 +706,12 @@ endState(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
  * @return TVertexDescriptor The begin state vertex descriptor.
  */
 
-/**
-.Function.getBeginState:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Returns the begin state.
-..signature:getBeginState(g)
-..param.g:A HMM.
-...type:Spec.Hmm
-..returns:Returns the begin state.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 getBeginState(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return (g.data_begin);
+    SEQAN_CHECKPOINT
+    return (g.data_begin);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -815,23 +727,12 @@ getBeginState(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g)
  * @return TVertexDescriptor The end state vertex descriptor.
  */
 
-/**
-.Function.getEndState:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Returns the end state.
-..signature:getEndState(g)
-..param.g:A HMM.
-...type:Spec.Hmm
-..returns:Returns the end state.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec>
 inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TSpec> > >::Type
 getEndState(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return (g.data_end);
+    SEQAN_CHECKPOINT
+    return (g.data_end);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -851,35 +752,18 @@ getEndState(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g)
  * @return TCargo Return the transition probability.
  */
 
-/**
-.Function.getTransitionProbability:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Returns the transition probability.
-..signature:getTransitionProbability(g, [s1, s2 | e])
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.s1:State 1.
-...type:Metafunction.VertexDescriptor
-..param.s2:State 2.
-...type:Metafunction.VertexDescriptor
-..param.e:Edge between two states.
-...type:Metafunction.EdgeDescriptor
-..returns:Returns the transition probability.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline TCargo
 getTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
-						 TVertexDescriptor const state1,
-						 TVertexDescriptor const state2)
+                         TVertexDescriptor const state1,
+                         TVertexDescriptor const state2)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > const TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = findEdge(g, state1, state2);
-	if (e == 0) return 0.0;
-	else return cargo(e);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > const TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = findEdge(g, state1, state2);
+    if (e == 0) return 0.0;
+    else return cargo(e);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -887,10 +771,10 @@ getTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
 inline TCargo
 getTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> > const&,
-						 TEdgeDescriptor const e)
+                         TEdgeDescriptor const e)
 {
-	SEQAN_CHECKPOINT
-	return getCargo(e);
+    SEQAN_CHECKPOINT
+    return getCargo(e);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -910,34 +794,17 @@ getTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> > const&,
  * @return TCargo Returns a reference to the transition probability.
  */
 
-/**
-.Function.transitionProbability:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Returns a reference to the transition probability.
-..signature:transitionProbability(g, [s1, s2 | e])
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.s1:State 1.
-...type:Metafunction.VertexDescriptor
-..param.s2:State 2.
-...type:Metafunction.VertexDescriptor
-..param.e:Edge connecting two states.
-...type:Metafunction.EdgeDescriptor
-..returns:Returns a reference to the transition probability.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline TCargo&
 transitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-					  TVertexDescriptor const state1,
-					  TVertexDescriptor const state2)
+                      TVertexDescriptor const state1,
+                      TVertexDescriptor const state2)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = findEdge(g, state1, state2);
-	return cargo(e);
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = findEdge(g, state1, state2);
+    return cargo(e);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -945,10 +812,10 @@ transitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor>
 inline TCargo&
 transitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >&,
-					  TEdgeDescriptor e)
+                      TEdgeDescriptor e)
 {
-	SEQAN_CHECKPOINT
-	return cargo(e);
+    SEQAN_CHECKPOINT
+    return cargo(e);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -966,34 +833,18 @@ transitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >&,
  * @param[in] e      Assign probability to edge with this edge descriptor.
  */
 
-/**
-.Function.assignTransitionProbability:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Assigns a new transition probability to an existing edge.
-..signature:assignTransitionProbability(g, s1, s2, prob)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.s1:State 1.
-...type:Metafunction.VertexDescriptor
-..param.s2:State 2.
-...type:Metafunction.VertexDescriptor
-..param.prob:New probability.
-..returns:void.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TTransProb>
 inline void
 assignTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-							TVertexDescriptor const state1,
-							TVertexDescriptor const state2,
-							TTransProb const t)
+                            TVertexDescriptor const state1,
+                            TVertexDescriptor const state2,
+                            TTransProb const t)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = findEdge(g, state1, state2);
-	cargo(e) = t;
+    SEQAN_CHECKPOINT
+    typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = findEdge(g, state1, state2);
+    cargo(e) = t;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1001,11 +852,11 @@ assignTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TEdgeDescriptor, typename TTransProb>
 inline void
 assignTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >&,
-							TEdgeDescriptor e,
-							TTransProb const t)
+                            TEdgeDescriptor e,
+                            TTransProb const t)
 {
-	SEQAN_CHECKPOINT
-	cargo(e) = t;
+    SEQAN_CHECKPOINT
+    cargo(e) = t;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1023,35 +874,20 @@ assignTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >&,
  * @return TCargo The emission probability.
  */
 
-/**
-.Function.getEmissionProbability:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Returns the emission probability.
-..signature:getEmissionProbability(g, state, symbol)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.state:A given state.
-...type:Metafunction.VertexDescriptor
-..param.symbol:A given symbol.
-...type:Metafunction.Alphabet
-..returns:Returns the emission probability.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline TCargo
 getEmissionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
-					   TVertexDescriptor const state,
-					   TAlphabet const symbol)
+                       TVertexDescriptor const state,
+                       TAlphabet const symbol)
 {
-	typedef typename Size<TAlphabet>::Type TSize;
-	return g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE + ordValue(symbol)];
+    typedef typename Size<TAlphabet>::Type TSize;
+    return g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE + ordValue(symbol)];
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
- * @fn HmmGraph#emissionsProbability
+ * @fn HmmGraph#emissionProbability
  * @brief Returns a reference to the emissions probability.
  *
  * @signature TCargo emissionProbability(hmm, state, symbol);
@@ -1063,29 +899,14 @@ getEmissionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
  * @return TCargo Reference to the emission probability.
  */
 
-/**
-.Function.emissionProbability:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Returns a reference to the emission probability.
-..signature:emissionProbability(g, state, symbol)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.state:A given state.
-...type:Metafunction.VertexDescriptor
-..param.symbol:A given symbol.
-...type:Metafunction.Alphabet
-..returns:Returns a reference to the emission probability.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline TCargo&
 emissionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-					TVertexDescriptor const state,
-					TAlphabet const symbol)
+                    TVertexDescriptor const state,
+                    TAlphabet const symbol)
 {
-	typedef typename Size<TAlphabet>::Type TSize;
-	return g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE + ordValue(symbol)];
+    typedef typename Size<TAlphabet>::Type TSize;
+    return g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE + ordValue(symbol)];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1102,31 +923,15 @@ emissionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
  * @param[in]     eProb  Emission probability to assign.
  */
 
-/**
-.Function.assignEmissionProbability:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Assigns a new emission probability.
-..signature:assignEmissionProbability(g, state, symbol, prob)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.state:A given state.
-...type:Metafunction.VertexDescriptor
-..param.symbol:A given symbol.
-...type:Metafunction.Alphabet
-..param.prob:The new emission probability.
-..returns:void.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor, typename TEmisProb>
 inline void
 assignEmissionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-						  TVertexDescriptor const state,
-						  TAlphabet const symbol,
-						  TEmisProb const eProb)
+                          TVertexDescriptor const state,
+                          TAlphabet const symbol,
+                          TEmisProb const eProb)
 {
-	typedef typename Size<TAlphabet>::Type TSize;
-	g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE + ordValue(symbol)] = (TCargo) eProb;
+    typedef typename Size<TAlphabet>::Type TSize;
+    g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE + ordValue(symbol)] = (TCargo) eProb;
 }
 
 
@@ -1144,29 +949,15 @@ assignEmissionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
  * @param[in] silent A bool with the silent status.
  */
 
-/**
-.Function.assignSilentStatus:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Assigns a silent status to a state.
-..signature:assignBeginState(g, vertex, silent)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.vertex:A state.
-...type:Metafunction.VertexDescriptor
-..param.silent:A boolean value which is true for silent states.
-..returns:void.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline void
 assignSilentStatus(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-				   TVertexDescriptor const vertex,
-				   bool const silent)
+                   TVertexDescriptor const vertex,
+                   bool const silent)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(_getVertexIdManager(g), vertex));
-	g.data_silent[vertex] = silent;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(_getVertexIdManager(g), vertex));
+    g.data_silent[vertex] = silent;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1183,26 +974,13 @@ assignSilentStatus(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
  * @return TBoolRef Reference to bool silent status flag.
  */
 
-/**
-.Function.silentStatus:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Reference to the silent status of a state.
-..signature:silentStatus(g, vertex)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.vertex:A state.
-...type:Metafunction.VertexDescriptor
-..returns:Reference to silent status of the given state.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline bool&
 silentStatus(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
-			 TVertexDescriptor const vertex)
+             TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return g.data_silent[vertex];
+    SEQAN_CHECKPOINT
+    return g.data_silent[vertex];
 }
 
 
@@ -1220,26 +998,13 @@ silentStatus(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g,
  * @return bool true if the state is silent and false if not.
  */
 
-/**
-.Function.isSilent:
-..class:Spec.Hmm
-..cat:Graph
-..summary:Indicates whether a state is silent or not.
-..signature:isSilent(g, vertex)
-..param.g:A HMM.
-...type:Spec.Hmm
-..param.vertex:A state.
-...type:Metafunction.VertexDescriptor
-..returns:The silent status of that state.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline bool
 isSilent(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
-		 TVertexDescriptor const vertex)
+         TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return g.data_silent[vertex];
+    SEQAN_CHECKPOINT
+    return g.data_silent[vertex];
 }
 
 
diff --git a/seqan/graph_types/graph_impl_oracle.h b/seqan/graph_types/graph_impl_oracle.h
index 9348452..3e5897b 100644
--- a/seqan/graph_types/graph_impl_oracle.h
+++ b/seqan/graph_types/graph_impl_oracle.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,30 +44,6 @@ namespace SEQAN_NAMESPACE_MAIN
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Spec.Oracle:
-..cat:Graph
-..general:Class.Graph
-..summary:A factor oracle.
-..remarks:A factor oracle is a special automaton and thus, it is not implemented in its own class.
-It solely provides create functions where based upon a string an oracle is created.
-..signature:Graph<Automaton<TAlphabet, TCargo, TSpec> > 
-..param.TAlphabet:The alphabet type that is used for the transition labels.
-...metafunction:Metafunction.Alphabet
-...remarks:Use @Metafunction.Alphabet@ to get the type of the labels in an automaton.
-...default:$char$
-..param.TCargo:The cargo type that can be attached to the edges.
-...metafunction:Metafunction.Cargo
-...remarks:Use @Metafunction.Cargo@ to get the cargo type of an undirected graph.
-...default:$void$
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-...remarks:Use WithoutEdgeId here to omit edge ids.
-Note: If edges do not store ids external property maps do not work.
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
-
 //////////////////////////////////////////////////////////////////////////////
 // INTERNAL FUNCTIONS
 //////////////////////////////////////////////////////////////////////////////
@@ -77,26 +53,26 @@ Note: If edges do not store ids external property maps do not work.
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TPropertyMap, typename TChar>
 inline void
 _addLetterToOracle(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-				   TPropertyMap& supplyState,
-				   TChar const c)
+                   TPropertyMap& supplyState,
+                   TChar const c)
 {
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	TVertexDescriptor newState = addVertex(g);
-	TVertexDescriptor pred = newState - 1;
-	addEdge(g, pred, newState, c);
-	TVertexDescriptor k = getProperty(supplyState, pred);
-	while ((k!=nilVal) &&
-			(getTarget(&g.data_vertex[k].data_edge[ordValue(TAlphabet(c))])==nilVal))
-	{
-		addEdge(g,k,newState,c);
-		k = getProperty(supplyState, k);
-	}
-	TVertexDescriptor s;
-	if (k==nilVal) s=0;
-	else s = getTarget(&g.data_vertex[k].data_edge[ordValue(TAlphabet(c))]);
-	assignProperty(supplyState, newState, s);
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    TVertexDescriptor newState = addVertex(g);
+    TVertexDescriptor pred = newState - 1;
+    addEdge(g, pred, newState, c);
+    TVertexDescriptor k = getProperty(supplyState, pred);
+    while ((k!=nilVal) &&
+            (getTarget(&g.data_vertex[k].data_edge[ordValue(TAlphabet(c))])==nilVal))
+    {
+        addEdge(g,k,newState,c);
+        k = getProperty(supplyState, k);
+    }
+    TVertexDescriptor s;
+    if (k==nilVal) s=0;
+    else s = getTarget(&g.data_vertex[k].data_edge[ordValue(TAlphabet(c))]);
+    assignProperty(supplyState, newState, s);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -118,37 +94,23 @@ _addLetterToOracle(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
  * @see Automaton#createOracleOnReverse
  */
 
-/**
-.Function.createOracle
-..class:Spec.Oracle
-..cat:Graph
-..summary:Creates a factor oracle.
-..signature:createOracle(g, text)
-..param.g:Out-parameter: An oracle.
-...type:Spec.Oracle
-..param.text:In-parameter: A string.
-...type:Class.String
-..returns:void
-..see:Function.createOracleOnReverse
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TText>
 inline void
 createOracle(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-			 TText const text)
+             TText const text)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Size<TText>::Type TSize;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	TSize len = length(text);
-	String<TVertexDescriptor> supplyState;
-	resize(supplyState, len+1);
-	TVertexDescriptor v1 = addVertex(g);
-	assignRoot(g,v1);
-	assignProperty(supplyState, v1, nilVal);
-	for(TSize i = 0; i<len; ++i) _addLetterToOracle(g, supplyState, getValue(text,i));
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Size<TText>::Type TSize;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    TSize len = length(text);
+    String<TVertexDescriptor> supplyState;
+    resize(supplyState, len+1);
+    TVertexDescriptor v1 = addVertex(g);
+    assignRoot(g,v1);
+    assignProperty(supplyState, v1, nilVal);
+    for(TSize i = 0; i<len; ++i) _addLetterToOracle(g, supplyState, getValue(text,i));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -165,38 +127,24 @@ createOracle(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
  * @see Automaton#createOracle
  */
 
-/**
-.Function.createOracleOnReverse
-..class:Spec.Oracle
-..cat:Graph
-..summary:Creates a factor oracle for the reversed string.
-..signature:createOracleOnReverse(g, text)
-..param.g:Out-parameter: An oracle.
-...type:Spec.Oracle
-..param.text:In-parameter: A string.
-...type:Class.String
-..returns:void
-..see:Function.createOracle
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TText>
 inline void
 createOracleOnReverse(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-					  TText const text)
+                      TText const text)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Size<TText>::Type TSize;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	TSize len = length(text);
-	String<TVertexDescriptor> supplyState;
-	resize(supplyState, len+1);
-	TVertexDescriptor v1 = addVertex(g);
-	assignRoot(g,v1);
-	assignProperty(supplyState, v1, nilVal);
-	for(TSize i = len-1; i>0; --i) _addLetterToOracle(g, supplyState, getValue(text,i));
-	_addLetterToOracle(g, supplyState, getValue(text,0));
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Size<TText>::Type TSize;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    TSize len = length(text);
+    String<TVertexDescriptor> supplyState;
+    resize(supplyState, len+1);
+    TVertexDescriptor v1 = addVertex(g);
+    assignRoot(g,v1);
+    assignProperty(supplyState, v1, nilVal);
+    for(TSize i = len-1; i>0; --i) _addLetterToOracle(g, supplyState, getValue(text,i));
+    _addLetterToOracle(g, supplyState, getValue(text,0));
 }
 
 
@@ -205,79 +153,79 @@ createOracleOnReverse(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TTerminalStateMap, typename TKeywords>
 inline void
 createSetOracle(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-				TTerminalStateMap& terminalStateMap,
-				TKeywords const& keywords)
+                TTerminalStateMap& terminalStateMap,
+                TKeywords const& keywords)
 {
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Position<TKeywords>::Type TPos;
-	typedef typename Value<TKeywords>::Type TKeyword;
-	typedef typename Iterator<TKeyword const, Standard>::Type TIterator;
-
-	createTrie(g, terminalStateMap, keywords);
-
-	String<TVertexDescriptor> supplyState;
-	resizeVertexMap(g, supplyState);
-	String<bool> visited;
-	resizeVertexMap(g, visited);
-	arrayFill(begin(visited), end(visited), false);
-
-	TVertexDescriptor nil_ = getNil<TVertexDescriptor>();
-	assignProperty(supplyState, root(g), nil_);
-
-	TVertexDescriptor _root = getRoot(g);
-
-	TPos len = length(keywords);
-	String<TVertexDescriptor> _here_v;
-	resize(_here_v, len, _root);
-	String<TIterator> _here_it;
-	resize(_here_it, len);
-	for (TPos i = 0; i < len; ++i)
-	{
-		_here_it[i] = begin(keywords[i], Standard());
-	}
-	TPos _active_count = len;
-	while (_active_count)
-	{
-		for (TPos i = 0; i < len; ++i)
-		{
-			TIterator & it = _here_it[i];
-			TIterator it_end = end(keywords[i], Standard());
-			TVertexDescriptor & _parent = _here_v[i];
-			
-			if (it != it_end)
-			{
-				TVertexDescriptor _current = getSuccessor(g, _parent, *it);
-
-				if (!getProperty(visited, _current))
-				{
-					assignProperty(visited, _current, true);
-
-					TVertexDescriptor _down = getProperty(supplyState, _parent);
-					TVertexDescriptor _supply = _root;
-					while (_down != nil_)
-					{
-						TVertexDescriptor _next = getSuccessor(g, _down, *it);
-						if (_next != nil_)
-						{
-							_supply = _next;
-							break;
-						}
-
-						addEdge(g, _down, _current, *it);
-						_down = getProperty(supplyState, _down);
-					}
-					assignProperty(supplyState, _current, _supply);
-				}
-				_parent = _current;
-				++it;
-				if (it == it_end)
-				{
-					--_active_count;
-				}
-			}
-		}
-	}
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Position<TKeywords>::Type TPos;
+    typedef typename Value<TKeywords>::Type TKeyword;
+    typedef typename Iterator<TKeyword const, Standard>::Type TIterator;
+
+    createTrie(g, terminalStateMap, keywords);
+
+    String<TVertexDescriptor> supplyState;
+    resizeVertexMap(supplyState, g);
+    String<bool> visited;
+    resizeVertexMap(visited, g);
+    arrayFill(begin(visited), end(visited), false);
+
+    TVertexDescriptor nil_ = getNil<TVertexDescriptor>();
+    assignProperty(supplyState, root(g), nil_);
+
+    TVertexDescriptor _root = getRoot(g);
+
+    TPos len = length(keywords);
+    String<TVertexDescriptor> _here_v;
+    resize(_here_v, len, _root);
+    String<TIterator> _here_it;
+    resize(_here_it, len);
+    for (TPos i = 0; i < len; ++i)
+    {
+        _here_it[i] = begin(keywords[i], Standard());
+    }
+    TPos _active_count = len;
+    while (_active_count)
+    {
+        for (TPos i = 0; i < len; ++i)
+        {
+            TIterator & it = _here_it[i];
+            TIterator it_end = end(keywords[i], Standard());
+            TVertexDescriptor & _parent = _here_v[i];
+
+            if (it != it_end)
+            {
+                TVertexDescriptor _current = getSuccessor(g, _parent, *it);
+
+                if (!getProperty(visited, _current))
+                {
+                    assignProperty(visited, _current, true);
+
+                    TVertexDescriptor _down = getProperty(supplyState, _parent);
+                    TVertexDescriptor _supply = _root;
+                    while (_down != nil_)
+                    {
+                        TVertexDescriptor _next = getSuccessor(g, _down, *it);
+                        if (_next != nil_)
+                        {
+                            _supply = _next;
+                            break;
+                        }
+
+                        addEdge(g, _down, _current, *it);
+                        _down = getProperty(supplyState, _down);
+                    }
+                    assignProperty(supplyState, _current, _supply);
+                }
+                _parent = _current;
+                ++it;
+                if (it == it_end)
+                {
+                    --_active_count;
+                }
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/graph_types/graph_impl_tree.h b/seqan/graph_types/graph_impl_tree.h
index e85be0d..1deac4b 100644
--- a/seqan/graph_types/graph_impl_tree.h
+++ b/seqan/graph_types/graph_impl_tree.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -57,69 +57,51 @@ namespace SEQAN_NAMESPACE_MAIN
  * @tparam TSpec  Specializing type.  Default: <tt>Default</tt>.
  */
 
-/**
-.Spec.Tree:
-..cat:Graph
-..general:Class.Graph
-..summary:A Tree has a distinct root and directed edges. The source vertex of each edge is the parent vertex, 
-the target vertex of each edge is the child. Trees provide fast access to child vertices and the parent.
-..description:
-...image:treeGraph|A tree, where $0$ is the root vertex.
-..signature:Graph<Tree<TCargo, TSpec> >
-..param.TCargo:The cargo type that can be attached to the edges.
-...metafunction:Metafunction.Cargo
-...remarks:Use @Metafunction.Cargo@ to get the cargo type of the tree.
-...default:$void$
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
 template<typename TCargo, typename TSpec>
-class Graph<Tree<TCargo, TSpec> > 
+class Graph<Tree<TCargo, TSpec> >
 {
-	public:
-		typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
-		typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
-		typedef typename EdgeType<Graph>::Type TEdgeStump_;	
-		typedef Allocator<SinglePool<sizeof(TEdgeStump_)> > TAllocator_;
-		
-		TVertexDescriptor_ data_root;
-		String<TEdgeStump_*> data_vertex;			// Pointers to EdgeStumpT lists
-		String<TVertexDescriptor_> data_parent;		// Map to the parents of each node
-		TVertexIdManager_ data_id_managerV;
-		TAllocator_ data_allocator;
-		
+    public:
+        typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
+        typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
+        typedef typename EdgeType<Graph>::Type TEdgeStump_;
+        typedef Allocator<SinglePool<sizeof(TEdgeStump_)> > TAllocator_;
+
+        TVertexDescriptor_ data_root;
+        String<TEdgeStump_*> data_vertex;            // Pointers to EdgeStumpT lists
+        String<TVertexDescriptor_> data_parent;        // Map to the parents of each node
+        TVertexIdManager_ data_id_managerV;
+        TAllocator_ data_allocator;
+
 
 //____________________________________________________________________________
 
 
-		Graph() : data_root(getNil<TVertexDescriptor_>()) {
-			SEQAN_CHECKPOINT
-		}
-
-
-		~Graph() {
-			SEQAN_CHECKPOINT
-			clear(*this);
-		}
-
-		Graph(Graph const & _other) :
-			data_root(getNil<TVertexDescriptor_>()),
-			data_allocator(_other.data_allocator)
-		{
-			SEQAN_CHECKPOINT
-			_copyGraph(_other, *this);		
-		}
-	
-		Graph const& operator = (Graph const & _other) {
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			clear(*this);
-			data_allocator = _other.data_allocator;
-			_copyGraph(_other, *this);
-			return *this;
-		}
+        Graph() : data_root(getNil<TVertexDescriptor_>()) {
+            SEQAN_CHECKPOINT
+        }
+
+
+        ~Graph() {
+            SEQAN_CHECKPOINT
+            clear(*this);
+        }
+
+        Graph(Graph const & _other) :
+            data_root(getNil<TVertexDescriptor_>()),
+            data_allocator(_other.data_allocator)
+        {
+            SEQAN_CHECKPOINT
+            _copyGraph(_other, *this);
+        }
+
+        Graph const& operator = (Graph const & _other) {
+            SEQAN_CHECKPOINT
+            if (this == &_other) return *this;
+            clear(*this);
+            data_allocator = _other.data_allocator;
+            _copyGraph(_other, *this);
+            return *this;
+        }
 };
 
 
@@ -133,10 +115,10 @@ class Graph<Tree<TCargo, TSpec> >
 template<typename TCargo, typename TSpec>
 inline String<typename EdgeType<Graph<Tree<TCargo, TSpec> > >::Type*>&
 _getVertexString(Graph<Tree<TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	return const_cast<String<TEdgeStump*>&>(g.data_vertex);
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    return const_cast<String<TEdgeStump*>&>(g.data_vertex);
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -144,7 +126,7 @@ _getVertexString(Graph<Tree<TCargo, TSpec> > const& g) {
 template<typename TCargo, typename TSpec>
 inline IdManager<typename Id<Graph<Tree<TCargo, TSpec> > >::Type, Default> const &
 _getVertexIdManager(Graph<Tree<TCargo, TSpec> > const& g) {
-	return g.data_id_managerV;
+    return g.data_id_managerV;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -152,7 +134,7 @@ _getVertexIdManager(Graph<Tree<TCargo, TSpec> > const& g) {
 template<typename TCargo, typename TSpec>
 inline IdManager<typename Id<Graph<Tree<TCargo, TSpec> > >::Type, Default> &
 _getVertexIdManager(Graph<Tree<TCargo, TSpec> >& g) {
-	return g.data_id_managerV;
+    return g.data_id_managerV;
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -160,7 +142,7 @@ _getVertexIdManager(Graph<Tree<TCargo, TSpec> >& g) {
 template<typename TCargo, typename TSpec>
 inline IdManager<typename Id<Graph<Tree<TCargo, TSpec> > >::Type, Default> const &
 _getEdgeIdManager(Graph<Tree<TCargo, TSpec> > const& g) {
-	return g.data_id_managerV;
+    return g.data_id_managerV;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -168,32 +150,32 @@ _getEdgeIdManager(Graph<Tree<TCargo, TSpec> > const& g) {
 template<typename TCargo, typename TSpec>
 inline IdManager<typename Id<Graph<Tree<TCargo, TSpec> > >::Type, Default> &
 _getEdgeIdManager(Graph<Tree<TCargo, TSpec> >& g) {
-	return g.data_id_managerV;
+    return g.data_id_managerV;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec> 
+template<typename TCargo, typename TSpec>
 inline void
-_rebuildParentMap(Graph<Tree<TCargo, TSpec> >& g) 
+_rebuildParentMap(Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd; ++it, ++pos) {
-		TVertexDescriptor parent = pos;
-		TEdgeStump* current = *it;
-		while(current!=0) {
-			g.data_parent[getTarget(current)] = parent;
-			current = getNextT(current);
-		}
-	}
+    SEQAN_CHECKPOINT
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd; ++it, ++pos) {
+        TVertexDescriptor parent = pos;
+        TEdgeStump* current = *it;
+        while(current!=0) {
+            g.data_parent[getTarget(current)] = parent;
+            current = getNextT(current);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -201,51 +183,51 @@ _rebuildParentMap(Graph<Tree<TCargo, TSpec> >& g)
 template<typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Tree<TCargo, TSpec> > const& source,
-		   Graph<Tree<TCargo, TSpec> >& dest,
-		   bool transpose) 
+           Graph<Tree<TCargo, TSpec> >& dest,
+           bool transpose)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
-	clear(dest);
-	resize(dest.data_vertex, length(source.data_vertex));
-	resize(dest.data_parent, length(source.data_parent));
-	TIter itInit = begin(dest.data_vertex, Standard());
-	TIter itInitEnd = end(dest.data_vertex, Standard());
-	for(;itInit != itInitEnd; ++itInit) *itInit = (TEdgeStump*) 0;
-	TIterConst it = begin(source.data_vertex, Standard());
-	TIterConst itEnd = end(source.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		TEdgeStump* current = *it;
-		TVertexDescriptor parentVertex = pos;
-		while(current != (TEdgeStump*) 0) {
-			TVertexDescriptor childVertex = getTarget(current);
-			// Create missing vertices
-			if (parentVertex > childVertex) _createVertices(dest,parentVertex);
-			else _createVertices(dest,childVertex);
-			// Add edge
-			TEdgeDescriptor e;
-			if (!transpose) e = addEdge(dest, parentVertex, childVertex);
-			else e = addEdge(dest, childVertex, parentVertex);
-			assignCargo(e, getCargo(current));
-			current = getNextT(current);
-		}
-	}
-	dest.data_id_managerV = source.data_id_managerV;
-	dest.data_root = source.data_root;
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+    clear(dest);
+    resize(dest.data_vertex, length(source.data_vertex));
+    resize(dest.data_parent, length(source.data_parent));
+    TIter itInit = begin(dest.data_vertex, Standard());
+    TIter itInitEnd = end(dest.data_vertex, Standard());
+    for(;itInit != itInitEnd; ++itInit) *itInit = (TEdgeStump*) 0;
+    TIterConst it = begin(source.data_vertex, Standard());
+    TIterConst itEnd = end(source.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        TEdgeStump* current = *it;
+        TVertexDescriptor parentVertex = pos;
+        while(current != (TEdgeStump*) 0) {
+            TVertexDescriptor childVertex = getTarget(current);
+            // Create missing vertices
+            if (parentVertex > childVertex) _createVertices(dest,parentVertex);
+            else _createVertices(dest,childVertex);
+            // Add edge
+            TEdgeDescriptor e;
+            if (!transpose) e = addEdge(dest, parentVertex, childVertex);
+            else e = addEdge(dest, childVertex, parentVertex);
+            assignCargo(e, getCargo(current));
+            current = getNextT(current);
+        }
+    }
+    dest.data_id_managerV = source.data_id_managerV;
+    dest.data_root = source.data_root;
 }
 
 template<typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Tree<TCargo, TSpec> > const& source,
-		   Graph<Tree<TCargo, TSpec> >& dest) 
+           Graph<Tree<TCargo, TSpec> >& dest)
 {
-	_copyGraph(source, dest, false); 
+    _copyGraph(source, dest, false);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -258,11 +240,11 @@ _copyGraph(Graph<Tree<TCargo, TSpec> > const& source,
 template<typename TCargo, typename TSpec>
 inline void
 transpose(Graph<Tree<TCargo, TSpec> > const& source,
-		  Graph<Tree<TCargo, TSpec> >& dest)
+          Graph<Tree<TCargo, TSpec> >& dest)
 {
-	SEQAN_CHECKPOINT
-	_copyGraph(source, dest, true);
-	
+    SEQAN_CHECKPOINT
+    _copyGraph(source, dest, true);
+
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -271,210 +253,210 @@ template<typename TCargo, typename TSpec>
 inline void
 transpose(Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	Graph<Tree<TCargo, TSpec> > dest;
-	_copyGraph(g, dest, true);
-	g = dest;
+    SEQAN_CHECKPOINT
+    Graph<Tree<TCargo, TSpec> > dest;
+    _copyGraph(g, dest, true);
+    g = dest;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type 
-numEdges(Graph<Tree<TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type
+numEdges(Graph<Tree<TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TSize count=0;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	for(;it!=itEnd;++it) {
-		TEdgeStump* current = *it;
-		while(current!=0) {
-			++count;
-			current = getNextT(current);
-		}
-	}
-	return count;
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TSize count=0;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    for(;it!=itEnd;++it) {
+        TEdgeStump* current = *it;
+        while(current!=0) {
+            ++count;
+            current = getNextT(current);
+        }
+    }
+    return count;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type 
-numVertices(Graph<Tree<TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type
+numVertices(Graph<Tree<TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return idCount(g.data_id_managerV);
+    SEQAN_CHECKPOINT
+    return idCount(g.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline bool 
-empty(Graph<Tree<TCargo, TSpec> > const& g) 
+inline bool
+empty(Graph<Tree<TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return (!idCount(g.data_id_managerV));
+    SEQAN_CHECKPOINT
+    return (!idCount(g.data_id_managerV));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 inline void
-clearEdges(Graph<Tree<TCargo, TSpec> >& g) 
+clearEdges(Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
-	TIter it = begin(g.data_vertex, Standard());
-	TIter itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		TEdgeStump* current = *it;
-		if(current != (TEdgeStump*) 0) {
-			g.data_parent[pos] = nilVertex;
-			removeOutEdges(g, pos);
-		}
-	}
+    SEQAN_CHECKPOINT
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+    TIter it = begin(g.data_vertex, Standard());
+    TIter itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        TEdgeStump* current = *it;
+        if(current != (TEdgeStump*) 0) {
+            g.data_parent[pos] = nilVertex;
+            removeOutEdges(g, pos);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 inline void
-clearVertices(Graph<Tree<TCargo, TSpec> >& g) 
+clearVertices(Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearEdges(g);
-	releaseAll(g.data_id_managerV);
-	clear(g.data_vertex);
-	clear(g.data_parent);
+    SEQAN_CHECKPOINT
+    clearEdges(g);
+    releaseAll(g.data_id_managerV);
+    clear(g.data_vertex);
+    clear(g.data_parent);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline void 
-clear(Graph<Tree<TCargo, TSpec> >& g) 
+inline void
+clear(Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearVertices(g);
+    SEQAN_CHECKPOINT
+    clearVertices(g);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type 
-outDegree(Graph<Tree<TCargo, TSpec> > const& g, 
-		  TVertexDescriptor const vertex) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type
+outDegree(Graph<Tree<TCargo, TSpec> > const& g,
+          TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TGraph>::Type TSize;
-	TSize count=0;
-	TEdgeStump* current = g.data_vertex[vertex];
-	while(current!=0) {
-		current = getNextT(current);
-		++count;
-	}
-	return count;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TGraph>::Type TSize;
+    TSize count=0;
+    TEdgeStump* current = g.data_vertex[vertex];
+    while(current!=0) {
+        current = getNextT(current);
+        ++count;
+    }
+    return count;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type 
-inDegree(Graph<Tree<TCargo, TSpec> > const& g, 
-		 TVertexDescriptor const vertex) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type
+inDegree(Graph<Tree<TCargo, TSpec> > const& g,
+         TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-	
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TGraph>::Type TSize;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TSize count=0;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	for(;it!=itEnd;++it) {
-		TEdgeStump* current = *it;
-		while(current!=0) {
-			if ( (TVertexDescriptor) getTarget(current)==vertex) ++count;
-			current = getNextT(current);
-		}
-	}
-	return count;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TGraph>::Type TSize;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TSize count=0;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    for(;it!=itEnd;++it) {
+        TEdgeStump* current = *it;
+        while(current!=0) {
+            if ( (TVertexDescriptor) getTarget(current)==vertex) ++count;
+            current = getNextT(current);
+        }
+    }
+    return count;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type
 degree(Graph<Tree<TCargo, TSpec> > const& g,
-	   TVertexDescriptor const vertex) 
+       TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	return (inDegree(g,vertex)+outDegree(g,vertex));
+    SEQAN_CHECKPOINT
+    return (inDegree(g,vertex)+outDegree(g,vertex));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec> 
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
-addVertex(Graph<Tree<TCargo, TSpec> >& g) 
+template<typename TCargo, typename TSpec>
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
+addVertex(Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT	
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	TVertexDescriptor vd;
-	if (empty(g)) g.data_root = vd = obtainId(g.data_id_managerV);
-	else vd = obtainId(g.data_id_managerV);
-	if (vd == length(g.data_vertex)) {
-		appendValue(g.data_vertex, (TEdgeStump*) 0);
-		resize(g.data_parent, vd + 1, nilVertex, Generous());
-	} else {
-		g.data_vertex[vd] = (TEdgeStump*) 0;
-		g.data_parent[vd] = nilVertex;
-	}
-	return vd;
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+    TVertexDescriptor vd;
+    if (empty(g)) g.data_root = vd = obtainId(g.data_id_managerV);
+    else vd = obtainId(g.data_id_managerV);
+    if (vd == length(g.data_vertex)) {
+        appendValue(g.data_vertex, (TEdgeStump*) 0);
+        resize(g.data_parent, vd + 1, nilVertex, Generous());
+    } else {
+        g.data_vertex[vd] = (TEdgeStump*) 0;
+        g.data_parent[vd] = nilVertex;
+    }
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeVertex(Graph<Tree<TCargo, TSpec> >& g, 
-			 TVertexDescriptor const v) 
+inline void
+removeVertex(Graph<Tree<TCargo, TSpec> >& g,
+             TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
-	TEdgeStump* current = getValue(g.data_vertex, v);
-	while(current!=0) {
-		g.data_parent[childVertex(g, current)] = nilVertex;
-		current = getNextT(current);
-	}
-	g.data_parent[v] = nilVertex;
-	removeOutEdges(g,v); // Remove all outgoing edges
-	removeInEdges(g,v); // Remove all incoming edges
-	releaseId(g.data_id_managerV, v); // Release id
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
+    TEdgeStump* current = getValue(g.data_vertex, v);
+    while(current!=0) {
+        g.data_parent[childVertex(g, current)] = nilVertex;
+        current = getNextT(current);
+    }
+    g.data_parent[v] = nilVertex;
+    removeOutEdges(g,v); // Remove all outgoing edges
+    removeInEdges(g,v); // Remove all incoming edges
+    releaseId(g.data_id_managerV, v); // Release id
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -482,288 +464,286 @@ removeVertex(Graph<Tree<TCargo, TSpec> >& g,
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline typename EdgeDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 addEdge(Graph<Tree<TCargo, TSpec> >& g,
-		TVertexDescriptor const parent,
-		TVertexDescriptor const child)
+        TVertexDescriptor const parent,
+        TVertexDescriptor const child)
 {
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, child));
-	SEQAN_ASSERT(findEdge(g, parent, child) == 0); // No multi-graphs as trees!!!
-
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-
-	TEdgeStump* edge_ptr;
-	allocate(g.data_allocator, edge_ptr, 1);
-	valueConstruct(edge_ptr);
-	assignTarget(edge_ptr, child);
-	g.data_parent[child] = parent;
-	assignNextT(edge_ptr, (TEdgeStump*) 0);
-	if (g.data_vertex[parent]!=0) assignNextT(edge_ptr, g.data_vertex[parent]);
-	g.data_vertex[parent]=edge_ptr;
-	return edge_ptr;
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, child));
+    SEQAN_ASSERT(findEdge(g, parent, child) == 0); // No multi-graphs as trees!!!
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    TEdgeStump* edge_ptr;
+    allocate(g.data_allocator, edge_ptr, 1);
+    valueConstruct(edge_ptr);
+    assignTarget(edge_ptr, child);
+    g.data_parent[child] = parent;
+    assignNextT(edge_ptr, (TEdgeStump*) 0);
+    if (g.data_vertex[parent]!=0) assignNextT(edge_ptr, g.data_vertex[parent]);
+    g.data_vertex[parent]=edge_ptr;
+    return edge_ptr;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename EdgeDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
-addEdge(Graph<Tree<TCargo, TSpec> >& g, 
-		TVertexDescriptor const parent, 
-		TVertexDescriptor const child,
-		TCargo const cargo) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename EdgeDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
+addEdge(Graph<Tree<TCargo, TSpec> >& g,
+        TVertexDescriptor const parent,
+        TVertexDescriptor const child,
+        TCargo const cargo)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = addEdge(g,parent,child);
-	assignCargo(e,cargo);
-	return e;
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = addEdge(g,parent,child);
+    assignCargo(e,cargo);
+    return e;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
+inline void
 removeEdge(Graph<Tree<TCargo, TSpec> >& g,
-		   TVertexDescriptor const parent,
-		   TVertexDescriptor const child) 
+           TVertexDescriptor const parent,
+           TVertexDescriptor const child)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, child));
-	
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-
-	// Find edge and predecessor
-	TEdgeStump* pred = 0;
-	TEdgeStump* current = g.data_vertex[parent];
-	while(current != (TEdgeStump*) 0) {
-		if ( (TVertexDescriptor) getTarget(current) == child) break;
-		pred = current;
-		current = getNextT(current);
-	}
-	
-	// Not found?
-	if (current == (TEdgeStump*) 0) return;
-	g.data_parent[child] = getNil<TVertexDescriptor>();
-	
-	// Relink the next pointer of predecessor
-	if (pred != (TEdgeStump*) 0) assignNextT(pred, getNextT(current));
-	else g.data_vertex[parent] = getNextT(current);
-	
-	// Deallocate
-	valueDestruct(current);
-	deallocate(g.data_allocator, current, 1);
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, child));
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    // Find edge and predecessor
+    TEdgeStump* pred = 0;
+    TEdgeStump* current = g.data_vertex[parent];
+    while(current != (TEdgeStump*) 0) {
+        if ( (TVertexDescriptor) getTarget(current) == child) break;
+        pred = current;
+        current = getNextT(current);
+    }
+
+    // Not found?
+    if (current == (TEdgeStump*) 0) return;
+    g.data_parent[child] = getNil<TVertexDescriptor>();
+
+    // Relink the next pointer of predecessor
+    if (pred != (TEdgeStump*) 0) assignNextT(pred, getNextT(current));
+    else g.data_vertex[parent] = getNextT(current);
+
+    // Deallocate
+    valueDestruct(current);
+    deallocate(g.data_allocator, current, 1);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline void 
+inline void
 removeEdge(Graph<Tree<TCargo, TSpec> >& g,
-		   TEdgeDescriptor const edge)
+           TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	removeEdge(g, parentVertex(g,edge), childVertex(g,edge));
+    SEQAN_CHECKPOINT
+    removeEdge(g, parentVertex(g,edge), childVertex(g,edge));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
-removeOutEdges(Graph<Tree<TCargo, TSpec> >& g, 
-			   TVertexDescriptor const v) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeOutEdges(Graph<Tree<TCargo, TSpec> >& g,
+               TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	while(g.data_vertex[v] != (TEdgeStump*) 0) {
-		TVertexDescriptor target = targetVertex(g,g.data_vertex[v]);
-		removeEdge(g,v,target);
-	}
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    while(g.data_vertex[v] != (TEdgeStump*) 0) {
+        TVertexDescriptor target = targetVertex(g,g.data_vertex[v]);
+        removeEdge(g,v,target);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
 removeInEdges(Graph<Tree<TCargo, TSpec> >& g,
-			  TVertexDescriptor const v) 
+              TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
-	TIter it = begin(g.data_vertex, Standard());
-	TIter itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		if (!idInUse(g.data_id_managerV, pos)) continue;
-		TEdgeStump* current = *it;
-		TVertexDescriptor const sourceVertex = pos;
-		while(current!=0) {
-			if ( (TVertexDescriptor) current->data_target==v) {
-				removeEdge(g, sourceVertex, v);
-				current = g.data_vertex[sourceVertex];
-			} else {
-				current = getNextT(current);
-			}
-		}
-	}
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+    TIter it = begin(g.data_vertex, Standard());
+    TIter itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        if (!idInUse(g.data_id_managerV, pos)) continue;
+        TEdgeStump* current = *it;
+        TVertexDescriptor const sourceVertex = pos;
+        while(current!=0) {
+            if ( (TVertexDescriptor) current->data_target==v) {
+                removeEdge(g, sourceVertex, v);
+                current = g.data_vertex[sourceVertex];
+            } else {
+                current = getNextT(current);
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 targetVertex(Graph<Tree<TCargo, TSpec> > const&,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return getTarget(edge);
+    SEQAN_CHECKPOINT
+    return getTarget(edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 sourceVertex(Graph<Tree<TCargo, TSpec> > const& g,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		TEdgeDescriptor current = *it;
-		while(current!=(TEdgeDescriptor) 0) {
-			if (current == edge) return pos;
-			current=getNextT(current);
-		}
-	}
-	return 0;
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        TEdgeDescriptor current = *it;
+        while(current!=(TEdgeDescriptor) 0) {
+            if (current == edge) return pos;
+            current=getNextT(current);
+        }
+    }
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TMatrix>
 inline void
-getAdjacencyMatrix(Graph<Tree<TCargo, TSpec> > const& g, 
-				   TMatrix& mat) 
+getAdjacencyMatrix(Graph<Tree<TCargo, TSpec> > const& g,
+                   TMatrix& mat)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TMatrix>::Type TSize;
-	TSize len = getIdUpperBound(g.data_id_managerV);
-	resize(mat, len*len, 0);
-	
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it,++pos) {
-		TVertexDescriptor parentV = pos;
-		TEdgeStump* current = *it;
-		while(current!=0) {
-			TVertexDescriptor childV = getTarget(current);
-			++mat[parentV*len+childV];
-			current=getNextT(current);
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TMatrix>::Type TSize;
+    TSize len = getIdUpperBound(g.data_id_managerV);
+    resize(mat, len*len, 0);
+
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it,++pos) {
+        TVertexDescriptor parentV = pos;
+        TEdgeStump* current = *it;
+        while(current!=0) {
+            TVertexDescriptor childV = getTarget(current);
+            ++mat[parentV*len+childV];
+            current=getNextT(current);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename EdgeDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+inline typename EdgeDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 findEdge(Graph<Tree<TCargo, TSpec> >& g,
-		 TVertexDescriptor const v,
-		 TVertexDescriptor const w)
+         TVertexDescriptor const v,
+         TVertexDescriptor const w)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, w));
-	
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-
-	if ((TVertexDescriptor)g.data_parent[w] == v) {
-		TEdgeStump* current = g.data_vertex[v];
-		while((TEdgeStump*) current != 0) {
-			if ((TVertexDescriptor) getTarget(current) == w) return current;
-			current = getNextT(current);
-		}
-	} else if ((TVertexDescriptor) g.data_parent[v] == w) {
-		TEdgeStump* current = g.data_vertex[w];
-		while((TEdgeStump*) current != 0) {
-			if ((TVertexDescriptor) getTarget(current) == v) return current;
-			current = getNextT(current);
-		}
-	}
-	return 0;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, w));
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    if ((TVertexDescriptor)g.data_parent[w] == v) {
+        TEdgeStump* current = g.data_vertex[v];
+        while((TEdgeStump*) current != 0) {
+            if ((TVertexDescriptor) getTarget(current) == w) return current;
+            current = getNextT(current);
+        }
+    } else if ((TVertexDescriptor) g.data_parent[v] == w) {
+        TEdgeStump* current = g.data_vertex[w];
+        while((TEdgeStump*) current != 0) {
+            if ((TVertexDescriptor) getTarget(current) == v) return current;
+            current = getNextT(current);
+        }
+    }
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TFile, typename TCargo, typename TSpec, typename TIDString>
+template <typename TFile, typename TCargo, typename TSpec>
 inline void
 write(TFile & target,
-	  Graph<Tree<TCargo, TSpec> > const& g,
-	  TIDString const &,
-	  Raw)
+      Graph<Tree<TCargo, TSpec> > const& g)
 {
 //IOREV _nodoc_
-	SEQAN_CHECKPOINT
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	streamPut(target,"Adjacency list:\n");
-	for(;it!=itEnd;++it, ++pos) {
-		if (!idInUse(_getVertexIdManager(g),pos)) continue;
-		TEdgeStump* current = *it;
-		streamPut(target, (int)pos);
-		streamPut(target," -> ");
-		while(current!=0) {
-			streamPut(target, (int)getTarget(current));
-			streamPut(target, ',');
-			current=getNextT(current);
-		}
-		streamPut(target, '\n');
-	}
-	it = begin(g.data_vertex, Standard());
-	pos = 0;
-	streamPut(target,"Edge list:\n");
-	for(;it!=itEnd;++it, ++pos) {
-		TEdgeStump* current = getValue(it);
-		while(current!=0) {
-			streamPut(target,"Source: ");
-			streamPut(target, (int)pos);		
-			streamPut(target, ',');
-			streamPut(target,"Target: ");
-			streamPut(target, (int)getTarget(current));
-			streamPut(target, ' ');
-			streamPut(target,"(Id: ");
-			streamPut(target, (int)_getId(current));
-			streamPut(target, ')');
-			streamPut(target, '\n');
-			current=getNextT(current);
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    write(target, "Adjacency list:\n");
+    for(;it!=itEnd;++it, ++pos) {
+        if (!idInUse(_getVertexIdManager(g),pos)) continue;
+        TEdgeStump* current = *it;
+        appendNumber(target, (int)pos);
+        write(target, " -> ");
+        while(current!=0) {
+            appendNumber(target, (int)getTarget(current));
+            writeValue(target, ',');
+            current=getNextT(current);
+        }
+        writeValue(target, '\n');
+    }
+    it = begin(g.data_vertex, Standard());
+    pos = 0;
+    write(target, "Edge list:\n");
+    for(;it!=itEnd;++it, ++pos) {
+        TEdgeStump* current = getValue(it);
+        while(current!=0) {
+            write(target, "Source: ");
+            appendNumber(target, (int)pos);
+            writeValue(target, ',');
+            write(target, "Target: ");
+            appendNumber(target, (int)getTarget(current));
+            writeValue(target, ' ');
+            write(target, "(Id: ");
+            appendNumber(target, (int)_getId(current));
+            writeValue(target, ')');
+            writeValue(target, '\n');
+            current=getNextT(current);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -781,12 +761,12 @@ write(TFile & target,
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline void
 assignRoot(Graph<Tree<TCargo, TSpec> >& g,
-		   TVertexDescriptor const vertex)
+           TVertexDescriptor const vertex)
 {
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
 
-	g.data_root = vertex;
-	g.data_parent[vertex] = getNil<TVertexDescriptor>();
+    g.data_root = vertex;
+    g.data_parent[vertex] = getNil<TVertexDescriptor>();
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -804,15 +784,15 @@ template<typename TCargo, typename TSpec>
 inline void
 createRoot(Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	g.data_root = addVertex(g);
+    SEQAN_CHECKPOINT
+    g.data_root = addVertex(g);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn Tree#root
- * @signature Gets reference to the root of the tree.
+ * @brief Gets reference to the root of the tree.
  *
  * @signature TVertexDescriptor root(t);
  *
@@ -825,15 +805,15 @@ template<typename TCargo, typename TSpec>
 inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type&
 root(Graph<Tree<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	return g.data_root;
+    SEQAN_CHECKPOINT
+    return g.data_root;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn Tree#getRoot
- * @signature Gets the root of the tree.
+ * @brief Gets the root of the tree.
  *
  * @signature TVertexDescriptor getRoot(t);
  *
@@ -843,18 +823,18 @@ root(Graph<Tree<TCargo, TSpec> >& g)
  */
 
 template<typename TCargo, typename TSpec>
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 getRoot(Graph<Tree<TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return g.data_root;
+    SEQAN_CHECKPOINT
+    return g.data_root;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @fn Tree#isRoot
- * @signature Tests whether a given vertex is the root or not.
+ * @brief Tests whether a given vertex is the root or not.
  *
  * @signature bool isRoot(t, v);
  *
@@ -867,10 +847,10 @@ getRoot(Graph<Tree<TCargo, TSpec> > const& g)
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline bool
 isRoot(Graph<Tree<TCargo, TSpec> > const& g,
-	   TVertexDescriptor v)
+       TVertexDescriptor v)
 {
-	SEQAN_CHECKPOINT
-	return ( (TVertexDescriptor) g.data_root == v);
+    SEQAN_CHECKPOINT
+    return ( (TVertexDescriptor) g.data_root == v);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -885,37 +865,23 @@ isRoot(Graph<Tree<TCargo, TSpec> > const& g,
  * @param[in] v The descriptor of the vertex to query for.
  */
 
-/**
-.Function.Graph#isLeaf
-..class:Spec.Tree
-..cat:Graph
-..summary:Tests whether a given vertex is a leaf or not.
-..signature:isLeaf(g, v)
-..param.g:A tree.
-...type:Spec.Tree
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:True if vertex is a leaf.
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
 inline bool
 isLeaf(Graph<Tree<TCargo, TSpec> > const& g,
-	   TVertexDescriptor v)
+       TVertexDescriptor v)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-	
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	return (g.data_vertex[v] ==  (TEdgeStump*) 0);
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    return (g.data_vertex[v] ==  (TEdgeStump*) 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
- * @fn Graph#numTreeEdges
+ * @fn Tree#numTreeEdges
  * @brief Number of tree edges.
  *
  * @signature TSize numTreeEdges(g);
@@ -925,25 +891,13 @@ isLeaf(Graph<Tree<TCargo, TSpec> > const& g,
  * @return TSize The number of tree edges.  Faster than @link Graph#numEdges @endlink for trees.
  */
 
-/**
-.Function.numTreeEdges
-..class:Spec.Tree
-..cat:Graph
-..summary:Number of tree edges.
-..signature:numTreeEdges(g)
-..param.g:A tree.
-...type:Spec.Tree
-..returns:Number of tree edges. Faster than numEdges for trees.
-..include:seqan/graph_types.h
-*/
-
 template<typename TCargo, typename TSpec>
-inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type 
-numTreeEdges(Graph<Tree<TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type
+numTreeEdges(Graph<Tree<TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	if (empty(g)) return 0;
-	else return numVertices(g) - 1;
+    SEQAN_CHECKPOINT
+    if (empty(g)) return 0;
+    else return numVertices(g) - 1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -960,28 +914,14 @@ numTreeEdges(Graph<Tree<TCargo, TSpec> > const& g)
  * @return TSize The number of children.
  */
 
-/**
-.Function.numChildren:
-..class:Spec.Tree
-..cat:Graph
-..summary:Number of children of a given tree vertex.
-..signature:numChildren(g, v)
-..param.g:A tree.
-...type:Spec.Tree
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:Number of children
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Tree<TCargo, TSpec> > >::Type
 numChildren(Graph<Tree<TCargo, TSpec> > const& g,
-			TVertexDescriptor const vertex) 
+            TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	
-	return outDegree(g, vertex);
+    SEQAN_CHECKPOINT
+
+    return outDegree(g, vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -999,51 +939,31 @@ numChildren(Graph<Tree<TCargo, TSpec> > const& g,
  * @return TVertexDescriptor Vertex descriptor of the added vertex.
  */
 
-/**
-.Function.addChild
-..class:Spec.Tree
-..cat:Graph
-..summary:Adds a new child vertex to a parent vertex.
-Optionally a cargo can be attached to the parent-child edge.
-..signature:addChild(g, parent [, cargo])
-..param.g:A tree.
-...type:Spec.Tree
-..param.parent:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.cargo:A cargo object.
-...type:Metafunction.Cargo
-..returns:A new vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..see:Function.removeChild
-..see:Function.removeAllChildren
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 addChild(Graph<Tree<TCargo, TSpec> >& g,
-		 TVertexDescriptor parent) 
+         TVertexDescriptor parent)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
-	TVertexDescriptor child = addVertex(g);
-	addEdge(g,parent,child);
-	return child;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
+    TVertexDescriptor child = addVertex(g);
+    addEdge(g,parent,child);
+    return child;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 addChild(Graph<Tree<TCargo, TSpec> >& g,
-		 TVertexDescriptor const parent,
-		 TCargo const cargo) 
+         TVertexDescriptor const parent,
+         TCargo const cargo)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
-	TVertexDescriptor child = addVertex(g);
-	addEdge(g,parent,child,cargo);
-	return child;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
+    TVertexDescriptor child = addVertex(g);
+    addEdge(g,parent,child,cargo);
+    return child;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1059,34 +979,16 @@ addChild(Graph<Tree<TCargo, TSpec> >& g,
  * @param[in]     child  The descriptor of the child vertex.
  */
 
-/**
-.Function.removeChild
-..class:Spec.Tree
-..cat:Graph
-..summary:Removes a child from the tree given a parent.
-..signature:removeChild(g, parent, child)
-..param.g:A tree.
-...type:Spec.Tree
-..param.parent:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.child:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:void
-..see:Function.addChild
-..see:Function.removeAllChildren
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
 removeChild(Graph<Tree<TCargo, TSpec> >& g,
-			TVertexDescriptor const parent,
-			TVertexDescriptor const child)
+            TVertexDescriptor const parent,
+            TVertexDescriptor const child)
 {
-	SEQAN_CHECKPOINT
-	if (!isLeaf(g,child)) removeAllChildren(g,child);
-	removeEdge(g,parent, child);  // Parent map is cleared in removeEdge
-	releaseId(g.data_id_managerV, child); // Release id
+    SEQAN_CHECKPOINT
+    if (!isLeaf(g,child)) removeAllChildren(g,child);
+    removeEdge(g,parent, child);  // Parent map is cleared in removeEdge
+    releaseId(g.data_id_managerV, child); // Release id
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1101,38 +1003,22 @@ removeChild(Graph<Tree<TCargo, TSpec> >& g,
  * @param[in]     parent Descriptor of the vertex to remove children of.
  */
 
-/**
-.Function.removeAllChildren
-..class:Spec.Tree
-..cat:Graph
-..summary:Removes all children from the tree given a parent.
-..signature:removeChild(g, parent)
-..param.g:A tree.
-...type:Spec.Tree
-..param.parent:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:void
-..see:Function.addChild
-..see:Function.removeChild
-..include:seqan/graph_types.h
-*/
-
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
-removeAllChildren(Graph<Tree<TCargo, TSpec> >& g, 
-				  TVertexDescriptor const parent) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeAllChildren(Graph<Tree<TCargo, TSpec> >& g,
+                  TVertexDescriptor const parent)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-
-	while(g.data_vertex[parent] != (TEdgeStump*) 0) {
-		TVertexDescriptor child = childVertex(g,g.data_vertex[parent]);
-		if (!isLeaf(g,child)) removeAllChildren(g,child);
-		removeEdge(g,parent, child);  // Parent map is cleared in removeEdge
-		releaseId(g.data_id_managerV, child); // Release id
-	}
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, parent));
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    while(g.data_vertex[parent] != (TEdgeStump*) 0) {
+        TVertexDescriptor child = childVertex(g,g.data_vertex[parent]);
+        if (!isLeaf(g,child)) removeAllChildren(g,child);
+        removeEdge(g,parent, child);  // Parent map is cleared in removeEdge
+        releaseId(g.data_id_managerV, child); // Release id
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1149,28 +1035,13 @@ removeAllChildren(Graph<Tree<TCargo, TSpec> >& g,
  * @return TVertexDescriptor The descriptor of the child vertex.
  */
 
-/**
-.Function.childVertex
-..class:Spec.Tree
-..cat:Graph
-..summary:Returns the child vertex of an edge.
-..signature:childVertex(g, e)
-..param.g:A tree.
-...type:Spec.Tree
-..param.e:An edge descriptor.
-...type:Metafunction.EdgeDescriptor
-..returns:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..see:Function.parentVertex
-..include:seqan/graph_types.h
-*/
 template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 childVertex(Graph<Tree<TCargo, TSpec> > const&,
-			TEdgeDescriptor const edge) 
+            TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return getTarget(edge);
+    SEQAN_CHECKPOINT
+    return getTarget(edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1189,42 +1060,24 @@ childVertex(Graph<Tree<TCargo, TSpec> > const&,
  * @return TVertexDescriptor The descriptor of the child vertex.
  */
 
-/**
-.Function.parentVertex
-..class:Spec.Tree
-..cat:Graph
-..summary:Returns the parent vertex of an edge or vertex.
-..signature:parentVertex(g, e)
-..signature:parentVertex(g, v)
-..param.g:A tree.
-...type:Spec.Tree
-..param.e:An edge descriptor.
-...type:Metafunction.EdgeDescriptor
-..param.v:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..returns:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..see:Function.parentVertex
-..include:seqan/graph_types.h
-*/
 template<typename TCargo, typename TSpec>
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 parentVertex(Graph<Tree<TCargo, TSpec> > const& g,
-			 typename EdgeDescriptor<Graph<Tree<TCargo, TSpec> > >::Type const edge) 
+             typename EdgeDescriptor<Graph<Tree<TCargo, TSpec> > >::Type const edge)
 {
-	SEQAN_CHECKPOINT
-	return g.data_parent[getTarget(edge)];
+    SEQAN_CHECKPOINT
+    return g.data_parent[getTarget(edge)];
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type
 parentVertex(Graph<Tree<TCargo, TSpec> > const& g,
-			 typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type const v) 
+             typename VertexDescriptor<Graph<Tree<TCargo, TSpec> > >::Type const v)
 {
-	SEQAN_CHECKPOINT
-	return g.data_parent[v];
+    SEQAN_CHECKPOINT
+    return g.data_parent[v];
 }
 
 ///////////////////////////////////////////////////////////////////////////////
@@ -1240,36 +1093,22 @@ parentVertex(Graph<Tree<TCargo, TSpec> > const& g,
  * @param[out] group A @link String @endlink of leaf vertex descriptors.
  */
 
-/**
-.Function.collectLeaves
-..class:Spec.Tree
-..cat:Graph
-..summary:Returns all leaves underneath a given vertex.
-..signature:collectLeaves(g, subtree_root, group)
-..param.g:A tree.
-...type:Spec.Tree
-..param.subtree_root:A vertex descriptor.
-...type:Metafunction.VertexDescriptor
-..param.group:A group of vertex descriptors
-...type:Class.String
-..include:seqan/graph_types.h
-*/
 template<typename TCargo, typename TSpec, typename TVertexDescriptor, typename TGroup>
 inline void
 collectLeaves(Graph<Tree<TCargo, TSpec> > const& g,
-			  TVertexDescriptor const root,
-			  TGroup& group)
+              TVertexDescriptor const root,
+              TGroup& group)
 {
-	typedef Graph<Tree<TCargo, TSpec> > TGraph;
-	typedef typename Iterator<TGraph, AdjacencyIterator>::Type TAdjacencyIterator;
-
-	if (isLeaf(g, root)) appendValue(group, root, Generous());
-	else {
-		TAdjacencyIterator adjIt(g, root);
-		for(;!atEnd(adjIt);goNext(adjIt)) {
-			collectLeaves(g, *adjIt, group);
-		}
-	}
+    typedef Graph<Tree<TCargo, TSpec> > TGraph;
+    typedef typename Iterator<TGraph, AdjacencyIterator>::Type TAdjacencyIterator;
+
+    if (isLeaf(g, root)) appendValue(group, root, Generous());
+    else {
+        TAdjacencyIterator adjIt(g, root);
+        for(;!atEnd(adjIt);goNext(adjIt)) {
+            collectLeaves(g, *adjIt, group);
+        }
+    }
 }
 
 
diff --git a/seqan/graph_types/graph_impl_trie.h b/seqan/graph_types/graph_impl_trie.h
index 17d5788..0f470ac 100644
--- a/seqan/graph_types/graph_impl_trie.h
+++ b/seqan/graph_types/graph_impl_trie.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,32 +44,6 @@ namespace SEQAN_NAMESPACE_MAIN
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Spec.Trie:
-..cat:Graph
-..general:Class.Graph
-..summary:A keyword trie.
-..description:
-...image:trieGraph|A trie for the words announce, annual, and annually.
-..remarks:A keyword trie is a special automaton and thus, it is not implemented in its own class.
-It solely provides create functions where based upon a set of strings a keyword trie is created.
-..signature:Graph<Automaton<TAlphabet, TCargo, TSpec> > 
-..param.TAlphabet:The alphabet type that is used for the transition labels.
-...metafunction:Metafunction.Alphabet
-...remarks:Use @Metafunction.Alphabet@ to get the type of the labels in an automaton.
-...default:$char$
-..param.TCargo:The cargo type that can be attached to the edges.
-...metafunction:Metafunction.Cargo
-...remarks:Use @Metafunction.Cargo@ to get the cargo type of an undirected graph.
-...default:$void$
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-...remarks:Use WithoutEdgeId here to omit edge ids.
-Note: If edges do not store ids external property maps do not work.
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
-
 
 //////////////////////////////////////////////////////////////////////////////
 // INTERNAL FUNCTIONS
@@ -80,30 +54,30 @@ Note: If edges do not store ids external property maps do not work.
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TTerminalStateMap, typename TKeyword, typename TPos>
 inline void
 _addStringToTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-				 TTerminalStateMap& terminalStateMap,
-				 TKeyword const& str,
-				 TPos const& keywordIndex)
+                 TTerminalStateMap& terminalStateMap,
+                 TKeyword const& str,
+                 TPos const& keywordIndex)
 {
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-	TVertexDescriptor current = getRoot(g);
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	typename Iterator<TKeyword const, Rooted>::Type sIt = begin(str);
-	for(;!atEnd(sIt);goNext(sIt)) {
-		if (getSuccessor(g, current, *sIt) == nilVal) break;
-		current = getSuccessor(g, current, *sIt);
-	}
-	for(;!atEnd(sIt);goNext(sIt)) {
-		TVertexDescriptor newState = addVertex(g);
-		resize(terminalStateMap, numVertices(g), Generous());
-		assignProperty(terminalStateMap,newState,String<TPos>());
-		addEdge(g,current,newState,*sIt);
-		current = newState;
-	}
-	String<TPos> tmp = getProperty(terminalStateMap,current);
-	appendValue(tmp, keywordIndex);
-	assignProperty(terminalStateMap,current,tmp);
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    TVertexDescriptor current = getRoot(g);
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    typename Iterator<TKeyword const, Rooted>::Type sIt = begin(str, Rooted());
+    for(;!atEnd(sIt);goNext(sIt)) {
+        if (getSuccessor(g, current, *sIt) == nilVal) break;
+        current = getSuccessor(g, current, *sIt);
+    }
+    for(;!atEnd(sIt);goNext(sIt)) {
+        TVertexDescriptor newState = addVertex(g);
+        resize(terminalStateMap, numVertices(g), Generous());
+        assignProperty(terminalStateMap,newState,String<TPos>());
+        addEdge(g,current,newState,*sIt);
+        current = newState;
+    }
+    String<TPos> tmp = getProperty(terminalStateMap,current);
+    appendValue(tmp, keywordIndex);
+    assignProperty(terminalStateMap,current,tmp);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -130,40 +104,21 @@ _addStringToTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
  * @see Automaton#createTrieOnReverse
  */
 
-/**
-.Function.createTrie
-..class:Spec.Trie
-..cat:Graph
-..summary:Creates a trie.
-..signature:createTrie(g, terminalStateMap, keywords)
-..param.g:Out-parameter: An automaton.
-...type:Spec.Trie
-..param.terminalStateMap:Out-parameter: An external property map.
-...type:Class.External Property Map
-...remarks:The external property map must be a String<String<unsigned int> > because
-in every vertex of the trie a number of keywords can end. This is the case in the Aho-Corasick
-algorithm if one pattern is a suffix of another pattern! Hence, we must associate with every vertex a set of indices that correspond to keywords.
-..param.keywords:In-parameter: A set of strings.
-...type:Class.String
-..returns:void
-..see:Function.createTrieOnReverse
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TTerminalStateMap, typename TKeywords>
 inline void
 createTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-		   TTerminalStateMap& terminalStateMap,
-		   TKeywords const& keywords)
+           TTerminalStateMap& terminalStateMap,
+           TKeywords const& keywords)
 {
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Position<TKeywords>::Type TPos;
-	TVertexDescriptor root = addVertex(g);
-	assignRoot(g,root);
-	resize(terminalStateMap, numVertices(g), Generous());
-	assignProperty(terminalStateMap,root,String<TPos>());
-	typename Iterator<TKeywords const, Rooted>::Type it = begin(keywords);
-	for(;!atEnd(it);goNext(it)) _addStringToTrie(g,terminalStateMap,*it,position(it));
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Position<TKeywords>::Type TPos;
+    TVertexDescriptor root = addVertex(g);
+    assignRoot(g,root);
+    resize(terminalStateMap, numVertices(g), Generous());
+    assignProperty(terminalStateMap,root,String<TPos>());
+    typename Iterator<TKeywords const, Rooted>::Type it = begin(keywords, Rooted());
+    for(;!atEnd(it);goNext(it)) _addStringToTrie(g,terminalStateMap,*it,position(it));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -185,49 +140,30 @@ createTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
  * @see Automaton#createTrie
  */
 
-/**
-.Function.createTrieOnReverse
-..class:Spec.Trie
-..cat:Graph
-..summary:Creates a trie for all reversed keywords.
-..signature:createTrieOnReverse(g, terminalStateMap, keywords)
-..returns.param.g:Out-parameter: An automaton.
-...type:Spec.Trie
-..returns.param.terminalStateMap:Out-parameter: An external property map.
-...type:Class.External Property Map
-...remarks:The external property map must be a String<String<unsigned int> > because
-in every vertex of the trie a number of keywords can end. This is the case in the Aho-Corasick
-algorithm if one pattern is a suffix of another pattern! Hence, we must associate with every vertex a set of indices that correspond to keywords.
-..param.keywords:In-parameter: A set of strings.
-...type:Class.String
-..returns:void
-..see:Function.createTrie
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TCargo, typename TSpec, typename TTerminalStateMap, typename TKeywords>
 inline void
 createTrieOnReverse(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-					TTerminalStateMap& terminalStateMap,
-					TKeywords const& keywords)
+                    TTerminalStateMap& terminalStateMap,
+                    TKeywords const& keywords)
 {
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Position<TKeywords>::Type TPos;
-	TVertexDescriptor root = addVertex(g);
-	assignRoot(g,root);
-	resize(terminalStateMap, numVertices(g), Generous());
-	assignProperty(terminalStateMap,root,String<TPos>());
-	typename Iterator<TKeywords const, Rooted>::Type it = begin(keywords);
-	for(;!atEnd(it);goNext(it)) {
-		typedef typename Value<TKeywords>::Type TKeyword;
-		TKeyword tmp;
-		typename Iterator<TKeyword const, Rooted>::Type sIt = end(*it);
-		while(!atBegin(sIt)) {
-			goPrevious(sIt);
-			appendValue(tmp,getValue(sIt));
-		}
-		_addStringToTrie(g,terminalStateMap,tmp,position(it));
-	}
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Position<TKeywords>::Type TPos;
+    TVertexDescriptor root = addVertex(g);
+    assignRoot(g,root);
+    resize(terminalStateMap, numVertices(g), Generous());
+    assignProperty(terminalStateMap,root,String<TPos>());
+    typename Iterator<TKeywords const, Rooted>::Type it = begin(keywords);
+    for(;!atEnd(it);goNext(it)) {
+        typedef typename Value<TKeywords>::Type TKeyword;
+        TKeyword tmp;
+        typename Iterator<TKeyword const, Rooted>::Type sIt = end(*it);
+        while(!atBegin(sIt)) {
+            goPrevious(sIt);
+            appendValue(tmp,getValue(sIt));
+        }
+        _addStringToTrie(g,terminalStateMap,tmp,position(it));
+    }
 }
 
 /*!
@@ -240,44 +176,26 @@ createTrieOnReverse(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
  * @param[out] terminalStateMap An external property map; of type <tt>String&lt;String&lt;unsigned&gt; &gt;</tt>.
  * @param[in]  text             A @link TextConcept @endlink object.
  */
- 
-/**
-.Function.createSuffixTrie
-..class:Spec.Trie
-..cat:Graph
-..summary:Creates a trie of all suffixes of a text.
-..signature:createSuffixTrie(g, terminalStateMap, text)
-..param.g:Out-parameter: An automaton.
-...type:Spec.Trie
-..param.terminalStateMap:Out-parameter: An external property map.
-...type:Class.External Property Map
-...remarks:The external property map must be a String<String<unsigned int> >.
-..param.text:In-parameter: A text.
-...type:Class.String
-..returns:void
-..see:Function.createTrie
-..see:Function.createTrieOnReverse
-..include:seqan/graph_types.h
-*/
+
 template <typename TAlphabet, typename TCargo, typename TSpec, typename TTerminalStateMap, typename TText>
 inline void
 createSuffixTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-				 TTerminalStateMap& terminalStateMap,
-				 TText const& text)
+                 TTerminalStateMap& terminalStateMap,
+                 TText const& text)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Position<TText const>::Type TPosition;
-	TVertexDescriptor root = addVertex(g);
-	assignRoot(g,root);
-	resize(terminalStateMap, numVertices(g), Generous());
-	assignProperty(terminalStateMap,root,String<TPosition>());
-
-	for (TPosition i = 0; i < length(text); ++i)
-	{
-		_addStringToTrie(g,terminalStateMap,suffix(text, i),i);
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Position<TText const>::Type TPosition;
+    TVertexDescriptor root = addVertex(g);
+    assignRoot(g,root);
+    resize(terminalStateMap, numVertices(g), Generous());
+    assignProperty(terminalStateMap,root,String<TPosition>());
+
+    for (TPosition i = 0; i < length(text); ++i)
+    {
+        _addStringToTrie(g,terminalStateMap,suffix(text, i),i);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -286,29 +204,29 @@ createSuffixTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
 template <typename TAlphabet, typename TCargo, typename TSpec, typename TTerminalStateMap, typename TTexts>
 inline void
 createSetSuffixTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
-					TTerminalStateMap& terminalStateMap,
-					TTexts const& texts)
+                    TTerminalStateMap& terminalStateMap,
+                    TTexts const& texts)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Position<TTexts const>::Type TTextsPosition;
-	typedef typename Value<TTexts const>::Type TText;
-	typedef typename Position<TText const>::Type TPosition;
-
-	TVertexDescriptor root = addVertex(g);
-	assignRoot(g,root);
-	resize(terminalStateMap, numVertices(g), Generous());
-	assignProperty(terminalStateMap,root,String<TPosition>());
-
-	for (TTextsPosition j = 0; j < length(texts); ++j)
-	{
-		TText const & text = texts[j];
-		for (TPosition i = 0; i < length(text); ++i)
-		{
-			_addStringToTrie(g,terminalStateMap,suffix(text, i),j);
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Position<TTexts const>::Type TTextsPosition;
+    typedef typename Value<TTexts const>::Type TText;
+    typedef typename Position<TText const>::Type TPosition;
+
+    TVertexDescriptor root = addVertex(g);
+    assignRoot(g,root);
+    resize(terminalStateMap, numVertices(g), Generous());
+    assignProperty(terminalStateMap,root,String<TPosition>());
+
+    for (TTextsPosition j = 0; j < length(texts); ++j)
+    {
+        TText const & text = texts[j];
+        for (TPosition i = 0; i < length(text); ++i)
+        {
+            _addStringToTrie(g,terminalStateMap,suffix(text, i),j);
+        }
+    }
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_impl_undirected.h b/seqan/graph_types/graph_impl_undirected.h
index b745a2c..b33f86c 100644
--- a/seqan/graph_types/graph_impl_undirected.h
+++ b/seqan/graph_types/graph_impl_undirected.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -57,67 +57,48 @@ namespace SEQAN_NAMESPACE_MAIN
  *                property maps do not work.
  */
 
-/**
-.Spec.Undirected Graph:
-..cat:Graph
-..general:Class.Graph
-..summary:An undirected graph that stores the edges in an adjacency list.
-..description:
-...image:undirectedGraph|An undirected graph with multiple components.
-..signature:Graph<Undirected<TCargo, TSpec> >
-..param.TCargo:The cargo type that can be attached to the edges.
-...metafunction:Metafunction.Cargo
-...remarks:Use @Metafunction.Cargo@ to get the cargo type of an undirected graph.
-...default:$void$
-..param.TSpec:The specializing type for the graph.
-...metafunction:Metafunction.Spec
-...remarks:Use WithoutEdgeId here to omit edge ids.
-Note: If edges do not store ids external property maps do not work.
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
 template<typename TCargo,typename TSpec>
-class Graph<Undirected<TCargo, TSpec> > 
+class Graph<Undirected<TCargo, TSpec> >
 {
-	public:
-		typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
-		typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
-		typedef typename EdgeType<Graph>::Type TEdgeStump_;	
-		typedef Allocator<SinglePool<sizeof(TEdgeStump_)> > TAllocator_;
-		
-		String<TEdgeStump_*> data_vertex;			// Pointers to EdgeStump lists
-		TVertexIdManager_ data_id_managerV;
-		TEdgeIdManager_ data_id_managerE;		
-		TAllocator_ data_allocator;
+    public:
+        typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
+        typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
+        typedef typename EdgeType<Graph>::Type TEdgeStump_;
+        typedef Allocator<SinglePool<sizeof(TEdgeStump_)> > TAllocator_;
+
+        String<TEdgeStump_*> data_vertex;            // Pointers to EdgeStump lists
+        TVertexIdManager_ data_id_managerV;
+        TEdgeIdManager_ data_id_managerE;
+        TAllocator_ data_allocator;
 
 //____________________________________________________________________________
 
 
-		Graph() {
-			SEQAN_CHECKPOINT
-		}
-
-
-		~Graph() {
-			SEQAN_CHECKPOINT
-			clear(*this);
-		}
-
-		Graph(Graph const & _other) :
-			data_allocator(_other.data_allocator)
-		{
-			SEQAN_CHECKPOINT
-			_copyGraph(_other, *this);		
-		}
-	
-		Graph const& operator = (Graph const & _other) {
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			clear(*this);
-			data_allocator = _other.data_allocator;
-			_copyGraph(_other, *this);
-			return *this;
-		}
+        Graph() {
+            SEQAN_CHECKPOINT
+        }
+
+
+        ~Graph() {
+            SEQAN_CHECKPOINT
+            clear(*this);
+        }
+
+        Graph(Graph const & _other) :
+            data_allocator(_other.data_allocator)
+        {
+            SEQAN_CHECKPOINT
+            _copyGraph(_other, *this);
+        }
+
+        Graph const& operator = (Graph const & _other) {
+            SEQAN_CHECKPOINT
+            if (this == &_other) return *this;
+            clear(*this);
+            data_allocator = _other.data_allocator;
+            _copyGraph(_other, *this);
+            return *this;
+        }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -129,10 +110,10 @@ class Graph<Undirected<TCargo, TSpec> >
 template<typename TCargo, typename TSpec>
 inline String<typename EdgeType<Graph<Undirected<TCargo, TSpec> > >::Type*>&
 _getVertexString(Graph<Undirected<TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	return const_cast<String<TEdgeStump*>&>(g.data_vertex);
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    return const_cast<String<TEdgeStump*>&>(g.data_vertex);
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -140,10 +121,10 @@ _getVertexString(Graph<Undirected<TCargo, TSpec> > const& g) {
 template<typename TCargo, typename TSpec>
 inline typename VertexIdHandler<Graph<Undirected<TCargo, TSpec> > >::Type&
 _getVertexIdManager(Graph<Undirected<TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
-	return const_cast<TVertexIdManager&>(g.data_id_managerV);
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexIdHandler<TGraph>::Type TVertexIdManager;
+    return const_cast<TVertexIdManager&>(g.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -151,10 +132,10 @@ _getVertexIdManager(Graph<Undirected<TCargo, TSpec> > const& g) {
 template<typename TCargo, typename TSpec>
 inline typename EdgeIdHandler<Graph<Undirected<TCargo, TSpec> > >::Type&
 _getEdgeIdManager(Graph<Undirected<TCargo, TSpec> > const& g) {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
-	return const_cast<TEdgeIdManager&>(g.data_id_managerE);
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeIdHandler<TGraph>::Type TEdgeIdManager;
+    return const_cast<TEdgeIdManager&>(g.data_id_managerE);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -162,56 +143,56 @@ _getEdgeIdManager(Graph<Undirected<TCargo, TSpec> > const& g) {
 template<typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Undirected<TCargo, TSpec> > const& source,
-		   Graph<Undirected<TCargo, TSpec> >& dest,
-		   bool) 
+           Graph<Undirected<TCargo, TSpec> >& dest,
+           bool)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
-	clear(dest);
-	resize(dest.data_vertex, length(_getVertexString(source)));
-	TIter itInit = begin(dest.data_vertex, Standard());
-	TIter itInitEnd = end(dest.data_vertex, Standard());
-	for(;itInit!=itInitEnd; ++itInit) *itInit = (TEdgeStump*) 0;
-	TIterConst it = begin(source.data_vertex, Standard());
-	TIterConst itEnd = end(source.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		TEdgeStump* current = *it;
-		TVertexDescriptor sourceVertex = pos;
-		while(current != (TEdgeStump*) 0) {
-			TVertexDescriptor targetVertex = getTarget(current);
-
-			if (targetVertex != sourceVertex) {
-				// Create missing vertices, targetVertex is always bigger than sourceVertex
-				_createVertices(dest,targetVertex);
-			
-				// Add edge
-				TEdgeDescriptor e = addEdge(dest, sourceVertex, targetVertex);
-				_assignId(e, _getId(current));
-				assignCargo(e, getCargo(current));
-				current = getNextS(current);  // Follow the link belonging to the source id
-			} else {
-				// Do nothing here because we don't want to create edges twice!!!
-				current = getNextT(current);
-			}
-		}
-	}
-	dest.data_id_managerV = source.data_id_managerV;
-	dest.data_id_managerE = source.data_id_managerE;
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+    clear(dest);
+    resize(dest.data_vertex, length(_getVertexString(source)));
+    TIter itInit = begin(dest.data_vertex, Standard());
+    TIter itInitEnd = end(dest.data_vertex, Standard());
+    for(;itInit!=itInitEnd; ++itInit) *itInit = (TEdgeStump*) 0;
+    TIterConst it = begin(source.data_vertex, Standard());
+    TIterConst itEnd = end(source.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        TEdgeStump* current = *it;
+        TVertexDescriptor sourceVertex = pos;
+        while(current != (TEdgeStump*) 0) {
+            TVertexDescriptor targetVertex = getTarget(current);
+
+            if (targetVertex != sourceVertex) {
+                // Create missing vertices, targetVertex is always bigger than sourceVertex
+                _createVertices(dest,targetVertex);
+
+                // Add edge
+                TEdgeDescriptor e = addEdge(dest, sourceVertex, targetVertex);
+                _assignId(e, _getId(current));
+                assignCargo(e, getCargo(current));
+                current = getNextS(current);  // Follow the link belonging to the source id
+            } else {
+                // Do nothing here because we don't want to create edges twice!!!
+                current = getNextT(current);
+            }
+        }
+    }
+    dest.data_id_managerV = source.data_id_managerV;
+    dest.data_id_managerE = source.data_id_managerE;
 }
 
 
 template<typename TCargo, typename TSpec>
 inline void
 _copyGraph(Graph<Undirected<TCargo, TSpec> > const& source,
-		   Graph<Undirected<TCargo, TSpec> >& dest) 
+           Graph<Undirected<TCargo, TSpec> >& dest)
 {
-	_copyGraph(source, dest, false); // Never transpose because undirected and transposed undirected graph are equal
+    _copyGraph(source, dest, false); // Never transpose because undirected and transposed undirected graph are equal
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -223,12 +204,12 @@ _copyGraph(Graph<Undirected<TCargo, TSpec> > const& source,
 template<typename TCargo, typename TSpec>
 inline void
 transpose(Graph<Undirected<TCargo, TSpec> > const& source,
-		  Graph<Undirected<TCargo, TSpec> >& dest)
+          Graph<Undirected<TCargo, TSpec> >& dest)
 {
-	SEQAN_CHECKPOINT
-	// Undirected graph, no transpose just copy
-	_copyGraph(source, dest, false);
-	
+    SEQAN_CHECKPOINT
+    // Undirected graph, no transpose just copy
+    _copyGraph(source, dest, false);
+
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -237,464 +218,464 @@ template<typename TCargo, typename TSpec>
 inline void
 transpose(Graph<Undirected<TCargo, TSpec> > const&)
 {
-	// Nothing to do
+    // Nothing to do
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type 
-numEdges(Graph<Undirected<TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type
+numEdges(Graph<Undirected<TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return idCount(g.data_id_managerE);
+    SEQAN_CHECKPOINT
+    return idCount(g.data_id_managerE);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type 
-numVertices(Graph<Undirected<TCargo, TSpec> > const& g) 
+inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type
+numVertices(Graph<Undirected<TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return idCount(g.data_id_managerV);
+    SEQAN_CHECKPOINT
+    return idCount(g.data_id_managerV);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline bool 
-empty(Graph<Undirected<TCargo, TSpec> > const& g) 
+inline bool
+empty(Graph<Undirected<TCargo, TSpec> > const& g)
 {
-	SEQAN_CHECKPOINT
-	return (!(idCount(g.data_id_managerV)));
+    SEQAN_CHECKPOINT
+    return (!(idCount(g.data_id_managerV)));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 inline void
-clearEdges(Graph<Undirected<TCargo, TSpec> >& g) 
+clearEdges(Graph<Undirected<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
-
-	// Collect all edges
-	String<TEdgeDescriptor> edges;
-	TIter it = begin(g.data_vertex, Standard());
-	TIter itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd; ++it, ++pos) {
-		TEdgeStump* current = *it;
-		TVertexDescriptor sourceVertex = pos;
-		while(current != (TEdgeStump*) 0) {
-			if (getTarget(current) != sourceVertex) {
-				appendValue(edges, current, Generous());
-				current = getNextS(current);
-			}
-			// Do nothing here because we don't want to create edges twice!!!
-			else current = getNextT(current);
-		}
-		*it = (TEdgeStump*) 0;
-	}
-	SEQAN_ASSERT(numEdges(g) == length(edges));
-
-	// Release all edges
-	typedef typename Iterator<String<TEdgeDescriptor>, Standard>::Type TStringIter;
-	TStringIter edgeIt = begin(edges, Standard());
-	TStringIter edgeEndIt = end(edges, Standard());
-	for(; edgeIt != edgeEndIt; ++edgeIt) {
-		valueDestruct(*edgeIt);
-		deallocate(g.data_allocator, *edgeIt, 1);	
-	}
-	releaseAll(g.data_id_managerE);
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*>, Standard>::Type TIter;
+
+    // Collect all edges
+    String<TEdgeDescriptor> edges;
+    TIter it = begin(g.data_vertex, Standard());
+    TIter itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd; ++it, ++pos) {
+        TEdgeStump* current = *it;
+        TVertexDescriptor sourceVertex = pos;
+        while(current != (TEdgeStump*) 0) {
+            if (getTarget(current) != sourceVertex) {
+                appendValue(edges, current, Generous());
+                current = getNextS(current);
+            }
+            // Do nothing here because we don't want to create edges twice!!!
+            else current = getNextT(current);
+        }
+        *it = (TEdgeStump*) 0;
+    }
+    SEQAN_ASSERT(numEdges(g) == length(edges));
+
+    // Release all edges
+    typedef typename Iterator<String<TEdgeDescriptor>, Standard>::Type TStringIter;
+    TStringIter edgeIt = begin(edges, Standard());
+    TStringIter edgeEndIt = end(edges, Standard());
+    for(; edgeIt != edgeEndIt; ++edgeIt) {
+        valueDestruct(*edgeIt);
+        deallocate(g.data_allocator, *edgeIt, 1);
+    }
+    releaseAll(g.data_id_managerE);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 inline void
-clearVertices(Graph<Undirected<TCargo, TSpec> >& g) 
+clearVertices(Graph<Undirected<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearEdges(g);
-	releaseAll(g.data_id_managerV);
-	clear(g.data_vertex);
+    SEQAN_CHECKPOINT
+    clearEdges(g);
+    releaseAll(g.data_id_managerV);
+    clear(g.data_vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
-inline void 
-clear(Graph<Undirected<TCargo, TSpec> >& g) 
+inline void
+clear(Graph<Undirected<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	clearVertices(g);
+    SEQAN_CHECKPOINT
+    clearVertices(g);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type 
-outDegree(Graph<Undirected<TCargo, TSpec> > const& g, 
-		  TVertexDescriptor const vertex) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type
+outDegree(Graph<Undirected<TCargo, TSpec> > const& g,
+          TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TGraph>::Type TSize;
-	TSize count=0;
-	TEdgeStump* current = g.data_vertex[vertex];
-	while(current!=0) {
-		if ( (TVertexDescriptor) getTarget(current)==vertex) current = getNextT(current);
-		else current = getNextS(current);
-		++count;
-	}
-	return count;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TGraph>::Type TSize;
+    TSize count=0;
+    TEdgeStump* current = g.data_vertex[vertex];
+    while(current!=0) {
+        if ( (TVertexDescriptor) getTarget(current)==vertex) current = getNextT(current);
+        else current = getNextS(current);
+        ++count;
+    }
+    return count;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type 
-inDegree(Graph<Undirected<TCargo, TSpec> > const& g, 
-		 TVertexDescriptor const vertex) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type
+inDegree(Graph<Undirected<TCargo, TSpec> > const& g,
+         TVertexDescriptor const vertex)
 {
-	SEQAN_CHECKPOINT
-	// In-degree and out-degree are equal for undirected graphs
-	return outDegree(g,vertex);
+    SEQAN_CHECKPOINT
+    // In-degree and out-degree are equal for undirected graphs
+    return outDegree(g,vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename Size<Graph<Undirected<TCargo, TSpec> > >::Type
 degree(Graph<Undirected<TCargo, TSpec> > const& g,
-	   TVertexDescriptor const vertex) 
+       TVertexDescriptor const vertex)
 {
-	return outDegree(g,vertex);
+    return outDegree(g,vertex);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec> 
-inline typename VertexDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type 
-addVertex(Graph<Undirected<TCargo, TSpec> >& g) 
+template<typename TCargo, typename TSpec>
+inline typename VertexDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type
+addVertex(Graph<Undirected<TCargo, TSpec> >& g)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	TVertexDescriptor vd = obtainId(g.data_id_managerV);
-	if (vd == length(g.data_vertex)) appendValue(g.data_vertex, (TEdgeStump*) 0, Generous()); 
-	else g.data_vertex[vd] = (TEdgeStump*) 0;
-	return vd;
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    TVertexDescriptor vd = obtainId(g.data_id_managerV);
+    if (vd == length(g.data_vertex)) appendValue(g.data_vertex, (TEdgeStump*) 0, Generous());
+    else g.data_vertex[vd] = (TEdgeStump*) 0;
+    return vd;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeVertex(Graph<Undirected<TCargo, TSpec> >& g, 
-			 TVertexDescriptor const v) 
+inline void
+removeVertex(Graph<Undirected<TCargo, TSpec> >& g,
+             TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
 
-	removeOutEdges(g,v); // Remove all outgoing edges
-	releaseId(g.data_id_managerV, v); // Release id
+    removeOutEdges(g,v); // Remove all outgoing edges
+    releaseId(g.data_id_managerV, v); // Release id
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline typename EdgeDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type 
-addEdge(Graph<Undirected<TCargo, TSpec> >& g, 
-		TVertexDescriptor source, 
-		TVertexDescriptor target) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline typename EdgeDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type
+addEdge(Graph<Undirected<TCargo, TSpec> >& g,
+        TVertexDescriptor source,
+        TVertexDescriptor target)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT_NEQ(source, target);
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
-
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Id<TGraph>::Type TId;
-
-	// Source must be the smaller vertex id
-	if (source > target) {TVertexDescriptor tmp = target; target = source; source = tmp; }
-
-	TEdgeStump* edge_ptr;
-	allocate(g.data_allocator, edge_ptr, 1);
-	valueConstruct(edge_ptr);
-	assignSource(edge_ptr, source);
-	assignTarget(edge_ptr, target);
-	assignNextS(edge_ptr, (TEdgeStump*) 0);
-	assignNextT(edge_ptr, (TEdgeStump*) 0);
-	TId id = obtainId(g.data_id_managerE);
-	_assignId(edge_ptr, id);
-	if (g.data_vertex[source]!=0) assignNextS(edge_ptr, g.data_vertex[source]);
-	if (g.data_vertex[target]!=0) assignNextT(edge_ptr, g.data_vertex[target]);
-	g.data_vertex[source]=edge_ptr;
-	g.data_vertex[target]=edge_ptr;
-	return edge_ptr;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT_NEQ(source, target);
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Id<TGraph>::Type TId;
+
+    // Source must be the smaller vertex id
+    if (source > target) {TVertexDescriptor tmp = target; target = source; source = tmp; }
+
+    TEdgeStump* edge_ptr;
+    allocate(g.data_allocator, edge_ptr, 1);
+    valueConstruct(edge_ptr);
+    assignSource(edge_ptr, source);
+    assignTarget(edge_ptr, target);
+    assignNextS(edge_ptr, (TEdgeStump*) 0);
+    assignNextT(edge_ptr, (TEdgeStump*) 0);
+    TId id = obtainId(g.data_id_managerE);
+    _assignId(edge_ptr, id);
+    if (g.data_vertex[source]!=0) assignNextS(edge_ptr, g.data_vertex[source]);
+    if (g.data_vertex[target]!=0) assignNextT(edge_ptr, g.data_vertex[target]);
+    g.data_vertex[source]=edge_ptr;
+    g.data_vertex[target]=edge_ptr;
+    return edge_ptr;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor, typename TCargo2> 
-inline typename EdgeDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type 
-addEdge(Graph<Undirected<TCargo, TSpec> >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target,
-		TCargo2 const cargo) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor, typename TCargo2>
+inline typename EdgeDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type
+addEdge(Graph<Undirected<TCargo, TSpec> >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target,
+        TCargo2 const cargo)
 {
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT_NEQ(source, target);
-	
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor e = addEdge(g,source,target);
-	assignCargo(e,cargo);
-	return e;
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT_NEQ(source, target);
+
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor e = addEdge(g,source,target);
+    assignCargo(e,cargo);
+    return e;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline void 
-removeEdge(Graph<Undirected<TCargo, TSpec> >& g, 
-		   TVertexDescriptor const source, 
-		   TVertexDescriptor const target) 
+inline void
+removeEdge(Graph<Undirected<TCargo, TSpec> >& g,
+           TVertexDescriptor const source,
+           TVertexDescriptor const target)
 {
-	SEQAN_CHECKPOINT;
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
-	
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-
-	// Find edge and source predecessor
-	TEdgeStump* predSource = 0;
-	TEdgeStump* current = g.data_vertex[source];
-	while(current != (TEdgeStump*) 0) {
-		TVertexDescriptor adjV = (TVertexDescriptor) getTarget(current);
-		if (adjV != source) {
-			if ( adjV == target) break;
-			predSource = current;
-			current = getNextS(current);
-		} else {
-			adjV = (TVertexDescriptor) getSource(current);
-			if ( adjV == target) break;
-			predSource = current;
-			current = getNextT(current);
-		}
-	}
-	
-	// Not found?
-	if (current == (TEdgeStump*) 0) return;
-
-	// Find edge and target predecessor
-	TEdgeStump* predTarget = 0;
-	current = g.data_vertex[target];
-	while(current != (TEdgeStump*) 0) {
-		TVertexDescriptor adjV = (TVertexDescriptor) getTarget(current);
-		if (adjV != target) {
-			if ( adjV == source) break;
-			predTarget = current;
-			current = getNextS(current);
-		} else {
-			adjV = (TVertexDescriptor) getSource(current);
-			if ( adjV == source) break;
-			predTarget = current;
-			current = getNextT(current);
-		}
-	}
-
-	
-	// Relink the next pointer of source predecessor
-	if (predSource != (TEdgeStump*) 0) {
-		if (source != (TVertexDescriptor) getTarget(current)) {
-			if (source != (TVertexDescriptor) getTarget(predSource)) assignNextS(predSource, getNextS(current));
-			else assignNextT(predSource, getNextS(current));
-		} else {
-			if (source != (TVertexDescriptor) getTarget(predSource)) assignNextS(predSource, getNextT(current));
-			else assignNextT(predSource, getNextT(current));
-		}
-	}
-	else {
-		if (source != (TVertexDescriptor) getTarget(current)) value(g.data_vertex, source) = getNextS(current);
-		else value(g.data_vertex, source) = getNextT(current);
-	}
-
-	// Relink the next pointer of target predecessor
-	if (predTarget != (TEdgeStump*) 0) {
-		if (target != (TVertexDescriptor) getTarget(current)) {
-			if (target != (TVertexDescriptor) getTarget(predTarget)) assignNextS(predTarget, getNextS(current));
-			else assignNextT(predTarget, getNextS(current));
-		} else {
-			if (target != (TVertexDescriptor) getTarget(predTarget)) assignNextS(predTarget, getNextT(current));
-			else assignNextT(predTarget, getNextT(current));
-		}
-	}
-	else {
-		if (target != (TVertexDescriptor) getTarget(current)) value(g.data_vertex, target) = getNextS(current);
-		else value(g.data_vertex, target) = getNextT(current);
-	}
-
-	// Deallocate
-	releaseId(g.data_id_managerE, _getId(current));
-	valueDestruct(current);
-	deallocate(g.data_allocator, current, 1);	
+    SEQAN_CHECKPOINT;
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    // Find edge and source predecessor
+    TEdgeStump* predSource = 0;
+    TEdgeStump* current = g.data_vertex[source];
+    while(current != (TEdgeStump*) 0) {
+        TVertexDescriptor adjV = (TVertexDescriptor) getTarget(current);
+        if (adjV != source) {
+            if ( adjV == target) break;
+            predSource = current;
+            current = getNextS(current);
+        } else {
+            adjV = (TVertexDescriptor) getSource(current);
+            if ( adjV == target) break;
+            predSource = current;
+            current = getNextT(current);
+        }
+    }
+
+    // Not found?
+    if (current == (TEdgeStump*) 0) return;
+
+    // Find edge and target predecessor
+    TEdgeStump* predTarget = 0;
+    current = g.data_vertex[target];
+    while(current != (TEdgeStump*) 0) {
+        TVertexDescriptor adjV = (TVertexDescriptor) getTarget(current);
+        if (adjV != target) {
+            if ( adjV == source) break;
+            predTarget = current;
+            current = getNextS(current);
+        } else {
+            adjV = (TVertexDescriptor) getSource(current);
+            if ( adjV == source) break;
+            predTarget = current;
+            current = getNextT(current);
+        }
+    }
+
+
+    // Relink the next pointer of source predecessor
+    if (predSource != (TEdgeStump*) 0) {
+        if (source != (TVertexDescriptor) getTarget(current)) {
+            if (source != (TVertexDescriptor) getTarget(predSource)) assignNextS(predSource, getNextS(current));
+            else assignNextT(predSource, getNextS(current));
+        } else {
+            if (source != (TVertexDescriptor) getTarget(predSource)) assignNextS(predSource, getNextT(current));
+            else assignNextT(predSource, getNextT(current));
+        }
+    }
+    else {
+        if (source != (TVertexDescriptor) getTarget(current)) value(g.data_vertex, source) = getNextS(current);
+        else value(g.data_vertex, source) = getNextT(current);
+    }
+
+    // Relink the next pointer of target predecessor
+    if (predTarget != (TEdgeStump*) 0) {
+        if (target != (TVertexDescriptor) getTarget(current)) {
+            if (target != (TVertexDescriptor) getTarget(predTarget)) assignNextS(predTarget, getNextS(current));
+            else assignNextT(predTarget, getNextS(current));
+        } else {
+            if (target != (TVertexDescriptor) getTarget(predTarget)) assignNextS(predTarget, getNextT(current));
+            else assignNextT(predTarget, getNextT(current));
+        }
+    }
+    else {
+        if (target != (TVertexDescriptor) getTarget(current)) value(g.data_vertex, target) = getNextS(current);
+        else value(g.data_vertex, target) = getNextT(current);
+    }
+
+    // Deallocate
+    releaseId(g.data_id_managerE, _getId(current));
+    valueDestruct(current);
+    deallocate(g.data_allocator, current, 1);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline void 
+inline void
 removeEdge(Graph<Undirected<TCargo, TSpec> >& g,
-		   TEdgeDescriptor const edge)
+           TEdgeDescriptor const edge)
 {
-	
-	SEQAN_CHECKPOINT
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, sourceVertex(g,edge)));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, targetVertex(g,edge)));
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor source = sourceVertex(g,edge);
-	TVertexDescriptor target = targetVertex(g,edge);
-
-	// Find edge and source predecessor
-	TEdgeStump* predSource = 0;
-	TEdgeStump* current = g.data_vertex[source];
-	while(current != (TEdgeStump*) 0) {
-		TVertexDescriptor adjV = (TVertexDescriptor) getTarget(current);
-		if (adjV != source) {
-			if ((adjV == target) && (current == edge)) break;
-			predSource = current;
-			current = getNextS(current);
-		} else {
-			adjV = (TVertexDescriptor) getSource(current);
-			if ((adjV == target) && (current == edge)) break;
-			predSource = current;
-			current = getNextT(current);
-		}
-	}
-	
-	// Not found?
-	if (current == (TEdgeStump*) 0) return;
-
-	// Find edge and target predecessor
-	TEdgeStump* predTarget = 0;
-	current = g.data_vertex[target];
-	while(current != (TEdgeStump*) 0) {
-		TVertexDescriptor adjV = (TVertexDescriptor) getTarget(current);
-		if (adjV != target) {
-			if ((adjV == source) && (current == edge)) break;
-			predTarget = current;
-			current = getNextS(current);
-		} else {
-			adjV = (TVertexDescriptor) getSource(current);
-			if ((adjV == source) && (current == edge)) break;
-			predTarget = current;
-			current = getNextT(current);
-		}
-	}
-
-	
-	// Relink the next pointer of source predecessor
-	if (predSource != (TEdgeStump*) 0) {
-		if (source != (TVertexDescriptor) getTarget(current)) {
-			if (source != (TVertexDescriptor) getTarget(predSource)) assignNextS(predSource, getNextS(current));
-			else assignNextT(predSource, getNextS(current));
-		} else {
-			if (source != (TVertexDescriptor) getTarget(predSource)) assignNextS(predSource, getNextT(current));
-			else assignNextT(predSource, getNextT(current));
-		}
-	}
-	else {
-		if (source != (TVertexDescriptor) getTarget(current)) value(g.data_vertex, source) = getNextS(current);
-		else value(g.data_vertex, source) = getNextT(current);
-	}
-
-	// Relink the next pointer of target predecessor
-	if (predTarget != (TEdgeStump*) 0) {
-		if (target != (TVertexDescriptor) getTarget(current)) {
-			if (target != (TVertexDescriptor) getTarget(predTarget)) assignNextS(predTarget, getNextS(current));
-			else assignNextT(predTarget, getNextS(current));
-		} else {
-			if (target != (TVertexDescriptor) getTarget(predTarget)) assignNextS(predTarget, getNextT(current));
-			else assignNextT(predTarget, getNextT(current));
-		}
-	}
-	else {
-		if (target != (TVertexDescriptor) getTarget(current)) value(g.data_vertex, target) = getNextS(current);
-		else value(g.data_vertex, target) = getNextT(current);
-	}
-
-	// Deallocate
-	releaseId(g.data_id_managerE, _getId(current));
-	valueDestruct(current);
-	deallocate(g.data_allocator, current, 1);
+
+    SEQAN_CHECKPOINT
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, sourceVertex(g,edge)));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, targetVertex(g,edge)));
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor source = sourceVertex(g,edge);
+    TVertexDescriptor target = targetVertex(g,edge);
+
+    // Find edge and source predecessor
+    TEdgeStump* predSource = 0;
+    TEdgeStump* current = g.data_vertex[source];
+    while(current != (TEdgeStump*) 0) {
+        TVertexDescriptor adjV = (TVertexDescriptor) getTarget(current);
+        if (adjV != source) {
+            if ((adjV == target) && (current == edge)) break;
+            predSource = current;
+            current = getNextS(current);
+        } else {
+            adjV = (TVertexDescriptor) getSource(current);
+            if ((adjV == target) && (current == edge)) break;
+            predSource = current;
+            current = getNextT(current);
+        }
+    }
+
+    // Not found?
+    if (current == (TEdgeStump*) 0) return;
+
+    // Find edge and target predecessor
+    TEdgeStump* predTarget = 0;
+    current = g.data_vertex[target];
+    while(current != (TEdgeStump*) 0) {
+        TVertexDescriptor adjV = (TVertexDescriptor) getTarget(current);
+        if (adjV != target) {
+            if ((adjV == source) && (current == edge)) break;
+            predTarget = current;
+            current = getNextS(current);
+        } else {
+            adjV = (TVertexDescriptor) getSource(current);
+            if ((adjV == source) && (current == edge)) break;
+            predTarget = current;
+            current = getNextT(current);
+        }
+    }
+
+
+    // Relink the next pointer of source predecessor
+    if (predSource != (TEdgeStump*) 0) {
+        if (source != (TVertexDescriptor) getTarget(current)) {
+            if (source != (TVertexDescriptor) getTarget(predSource)) assignNextS(predSource, getNextS(current));
+            else assignNextT(predSource, getNextS(current));
+        } else {
+            if (source != (TVertexDescriptor) getTarget(predSource)) assignNextS(predSource, getNextT(current));
+            else assignNextT(predSource, getNextT(current));
+        }
+    }
+    else {
+        if (source != (TVertexDescriptor) getTarget(current)) value(g.data_vertex, source) = getNextS(current);
+        else value(g.data_vertex, source) = getNextT(current);
+    }
+
+    // Relink the next pointer of target predecessor
+    if (predTarget != (TEdgeStump*) 0) {
+        if (target != (TVertexDescriptor) getTarget(current)) {
+            if (target != (TVertexDescriptor) getTarget(predTarget)) assignNextS(predTarget, getNextS(current));
+            else assignNextT(predTarget, getNextS(current));
+        } else {
+            if (target != (TVertexDescriptor) getTarget(predTarget)) assignNextS(predTarget, getNextT(current));
+            else assignNextT(predTarget, getNextT(current));
+        }
+    }
+    else {
+        if (target != (TVertexDescriptor) getTarget(current)) value(g.data_vertex, target) = getNextS(current);
+        else value(g.data_vertex, target) = getNextT(current);
+    }
+
+    // Deallocate
+    releaseId(g.data_id_managerE, _getId(current));
+    valueDestruct(current);
+    deallocate(g.data_allocator, current, 1);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
-removeOutEdges(Graph<Undirected<TCargo, TSpec> >& g, 
-			   TVertexDescriptor const v) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeOutEdges(Graph<Undirected<TCargo, TSpec> >& g,
+               TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	TEdgeDescriptor eD = g.data_vertex[v];
-	while(eD != (TEdgeStump*) 0) {
-		removeEdge(g,eD);
-		eD = g.data_vertex[v];
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    TEdgeDescriptor eD = g.data_vertex[v];
+    while(eD != (TEdgeStump*) 0) {
+        removeEdge(g,eD);
+        eD = g.data_vertex[v];
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TCargo, typename TSpec, typename TVertexDescriptor> 
-inline void 
-removeInEdges(Graph<Undirected<TCargo, TSpec> >& g, 
-			   TVertexDescriptor const v) 
+template<typename TCargo, typename TSpec, typename TVertexDescriptor>
+inline void
+removeInEdges(Graph<Undirected<TCargo, TSpec> >& g,
+               TVertexDescriptor const v)
 {
-	SEQAN_CHECKPOINT
-	removeOutEdges(g,v);
+    SEQAN_CHECKPOINT
+    removeOutEdges(g,v);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type
 targetVertex(Graph<Undirected<TCargo, TSpec> > const&,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return getTarget(edge);
+    SEQAN_CHECKPOINT
+    return getTarget(edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TEdgeDescriptor>
-inline typename VertexDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type
 sourceVertex(Graph<Undirected<TCargo, TSpec> > const&,
-			 TEdgeDescriptor const edge) 
+             TEdgeDescriptor const edge)
 {
-	SEQAN_CHECKPOINT
-	return getSource(edge);
+    SEQAN_CHECKPOINT
+    return getSource(edge);
 }
 
 
@@ -702,132 +683,130 @@ sourceVertex(Graph<Undirected<TCargo, TSpec> > const&,
 
 template<typename TCargo, typename TSpec, typename TMatrix>
 inline void
-getAdjacencyMatrix(Graph<Undirected<TCargo, TSpec> > const& g, 
-				   TMatrix& mat) 
+getAdjacencyMatrix(Graph<Undirected<TCargo, TSpec> > const& g,
+                   TMatrix& mat)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Size<TMatrix>::Type TSize;
-	TSize len = getIdUpperBound(g.data_id_managerV);
-	resize(mat, len*len, 0);
-
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	TVertexDescriptor pos = 0;
-	for(;it!=itEnd;++it, ++pos) {
-		TVertexDescriptor sourceV = pos;
-		TEdgeStump* current = *it;
-		while(current!=0) {
-			TVertexDescriptor adjV = getTarget(current);
-			if (adjV != sourceV) {
-				++mat[sourceV*len+adjV];
-				current=getNextS(current);
-			} else {
-				adjV = getSource(current);
-				++mat[sourceV*len+adjV];
-				current=getNextT(current);
-			}
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Size<TMatrix>::Type TSize;
+    TSize len = getIdUpperBound(g.data_id_managerV);
+    resize(mat, len*len, 0);
+
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    TVertexDescriptor pos = 0;
+    for(;it!=itEnd;++it, ++pos) {
+        TVertexDescriptor sourceV = pos;
+        TEdgeStump* current = *it;
+        while(current!=0) {
+            TVertexDescriptor adjV = getTarget(current);
+            if (adjV != sourceV) {
+                ++mat[sourceV*len+adjV];
+                current=getNextS(current);
+            } else {
+                adjV = getSource(current);
+                ++mat[sourceV*len+adjV];
+                current=getNextT(current);
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec, typename TVertexDescriptor>
-inline typename EdgeDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type 
+inline typename EdgeDescriptor<Graph<Undirected<TCargo, TSpec> > >::Type
 findEdge(Graph<Undirected<TCargo, TSpec> > const& g,
-		 TVertexDescriptor const v,
-		 TVertexDescriptor const w)
+         TVertexDescriptor const v,
+         TVertexDescriptor const w)
 {
-	SEQAN_CHECKPOINT;
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, w));
-	
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	
-	TEdgeStump* current = g.data_vertex[v];
-	while(current != (TEdgeStump*) 0) {
-		TVertexDescriptor adjV = getTarget(current);
-		if (adjV != v) {
-			if ( adjV == w) return current;
-			current=getNextS(current);
-		} else {
-			adjV = getSource(current);
-			if ( adjV == w) return current;
-			current=getNextT(current);
-		}
-	}
-	return 0;
+    SEQAN_CHECKPOINT;
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, v));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, w));
+
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+
+    TEdgeStump* current = g.data_vertex[v];
+    while(current != (TEdgeStump*) 0) {
+        TVertexDescriptor adjV = getTarget(current);
+        if (adjV != v) {
+            if ( adjV == w) return current;
+            current=getNextS(current);
+        } else {
+            adjV = getSource(current);
+            if ( adjV == w) return current;
+            current=getNextT(current);
+        }
+    }
+    return 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TFile, typename TCargo, typename TSpec, typename TIDString>
+template <typename TFile, typename TCargo, typename TSpec>
 inline void
 write(TFile & target,
-	  Graph<Undirected<TCargo, TSpec> > const& g,
-	  TIDString const &,
-	  Raw)
+      Graph<Undirected<TCargo, TSpec> > const& g)
 {
 //IOREV _nodoc_
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
-	TIterConst it = begin(g.data_vertex, Standard());
-	TIterConst itEnd = end(g.data_vertex, Standard());
-	streamPut(target,"Adjacency list:\n");
-	TVertexDescriptor pos = 0;
-	for(;it != itEnd; ++it, ++pos) {
-		TVertexDescriptor sourceV = pos;
-		streamPut(target, (int)sourceV);
-		streamPut(target," -> ");
-		TEdgeStump* current = *it;
-		while(current!=0) {
-			TVertexDescriptor adjV = getTarget(current);
-			if (adjV != sourceV) {
-				streamPut(target, (int)adjV);
-				streamPut(target, ',');
-				current=getNextS(current);
-			} else {
-				adjV = getSource(current);
-				streamPut(target, (int)adjV);
-				streamPut(target, ',');
-				current=getNextT(current);
-			}
-		}
-		streamPut(target, '\n');
-	}
-	it = begin(g.data_vertex, Standard());
-	pos = 0;
-	streamPut(target,"Edge list:\n");
-	for(; it != itEnd; ++it, ++pos) {
-		TVertexDescriptor sourceV = pos;
-		TEdgeStump* current = *it;
-		while(current!=0) {
-			TVertexDescriptor targetV = getTarget(current);
-			if (sourceV != targetV) {
-				streamPut(target,"Source: ");
-				streamPut(target, (int)sourceV);		
-				streamPut(target, ',');
-				streamPut(target,"Target: ");
-				streamPut(target, (int)targetV);
-				streamPut(target, ' ');
-				streamPut(target,"(Id: ");
-				streamPut(target, (int)_getId(current));
-				streamPut(target, ')');
-				streamPut(target, '\n');
-				current=getNextS(current);
-			} else {
-				current=getNextT(current);
-			}
-		}
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    typedef typename Iterator<String<TEdgeStump*> const, Standard>::Type TIterConst;
+    TIterConst it = begin(g.data_vertex, Standard());
+    TIterConst itEnd = end(g.data_vertex, Standard());
+    write(target, "Adjacency list:\n");
+    TVertexDescriptor pos = 0;
+    for(;it != itEnd; ++it, ++pos) {
+        TVertexDescriptor sourceV = pos;
+        appendNumber(target, (int)sourceV);
+        write(target, " -> ");
+        TEdgeStump* current = *it;
+        while(current!=0) {
+            TVertexDescriptor adjV = getTarget(current);
+            if (adjV != sourceV) {
+                appendNumber(target, (int)adjV);
+                writeValue(target, ',');
+                current=getNextS(current);
+            } else {
+                adjV = getSource(current);
+                appendNumber(target, (int)adjV);
+                writeValue(target, ',');
+                current=getNextT(current);
+            }
+        }
+        writeValue(target, '\n');
+    }
+    it = begin(g.data_vertex, Standard());
+    pos = 0;
+    write(target, "Edge list:\n");
+    for(; it != itEnd; ++it, ++pos) {
+        TVertexDescriptor sourceV = pos;
+        TEdgeStump* current = *it;
+        while(current!=0) {
+            TVertexDescriptor targetV = getTarget(current);
+            if (sourceV != targetV) {
+                write(target, "Source: ");
+                appendNumber(target, (int)sourceV);
+                writeValue(target, ',');
+                write(target, "Target: ");
+                appendNumber(target, (int)targetV);
+                writeValue(target, ' ');
+                write(target, "(Id: ");
+                appendNumber(target, (int)_getId(current));
+                writeValue(target, ')');
+                writeValue(target, '\n');
+                current=getNextS(current);
+            } else {
+                current=getNextT(current);
+            }
+        }
+    }
 }
 
 
diff --git a/seqan/graph_types/graph_impl_wordgraph.h b/seqan/graph_types/graph_impl_wordgraph.h
index b999b99..bed9639 100644
--- a/seqan/graph_types/graph_impl_wordgraph.h
+++ b/seqan/graph_types/graph_impl_wordgraph.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -58,116 +58,101 @@ struct WordGraph;
  * @tparam TSpec     The specializing types.
  */
 
-/**
-.Spec.Word Graph:
-..cat:Graph
-..general:Spec.Automaton
-..summary:A special automaton that stores words instead of single characters along its edges.
-..signature:Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >
-..param.TAlphabet:The alphabet type that is used for the words.
-...metafunction:Metafunction.Alphabet
-...remarks:Use @Metafunction.Alphabet@ to get the value type of the words.
-...default:$char$
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:$Default$, see @Tag.Default@.
-..include:seqan/graph_types.h
-*/
 template<typename TAlphabet, typename TSpec>
-class Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > 
+class Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >
 {
-	public:
-		typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
-		typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
-		typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
-		typedef typename EdgeType<Graph>::Type TEdge_;	
+    public:
+        typedef typename VertexIdHandler<Graph>::Type TVertexIdManager_;
+        typedef typename EdgeIdHandler<Graph>::Type TEdgeIdManager_;
+        typedef typename VertexDescriptor<Graph>::Type TVertexDescriptor_;
+        typedef typename EdgeType<Graph>::Type TEdge_;
 
-		String<AutomatonEdgeArray<TEdge_, TAlphabet> > data_vertex;		// List of tables
-		TVertexIdManager_ data_id_managerV;
-		TEdgeIdManager_ data_id_managerE;
-		TVertexDescriptor_ data_root;
+        String<AutomatonEdgeArray<TEdge_, TAlphabet> > data_vertex;        // List of tables
+        TVertexIdManager_ data_id_managerV;
+        TEdgeIdManager_ data_id_managerE;
+        TVertexDescriptor_ data_root;
 
 
 //____________________________________________________________________________
 
 
-		Graph() : data_root(0) {
-			SEQAN_CHECKPOINT
-		}
-
-
-		~Graph() {
-			SEQAN_CHECKPOINT
-			clear(*this);
-		}
-
-		Graph(Graph const & _other) 
-		{
-			SEQAN_CHECKPOINT
-			_copyGraph(_other, *this);
-		}
-	
-		Graph const& operator = (Graph const & _other) {
-			SEQAN_CHECKPOINT
-			if (this == &_other) return *this;
-			_copyGraph(_other, *this);
-			return *this;
-		}
+        Graph() : data_root(0) {
+            SEQAN_CHECKPOINT
+        }
+
+
+        ~Graph() {
+            SEQAN_CHECKPOINT
+            clear(*this);
+        }
+
+        Graph(Graph const & _other)
+        {
+            SEQAN_CHECKPOINT
+            _copyGraph(_other, *this);
+        }
+
+        Graph const& operator = (Graph const & _other) {
+            SEQAN_CHECKPOINT
+            if (this == &_other) return *this;
+            _copyGraph(_other, *this);
+            return *this;
+        }
 };
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TSpec, typename TVertexDescriptor>
-inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type 
-addEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target,
-		String<TAlphabet> const & label) 
+inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type
+addEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target,
+        String<TAlphabet> const & label)
 {
-	SEQAN_CHECKPOINT;
+    SEQAN_CHECKPOINT;
     SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
-	
-	typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename Id<TGraph>::Type TId;
-	
-	TAlphabet firstChar = getValue(label, 0);
-	TEdgeDescriptor e = findEdge(g, source, firstChar);
-	TId id = obtainId(g.data_id_managerE);
-	_assignId(e, id);
-	assignTarget(e, target);
-	String<TAlphabet> suf(suffix(label,1));
-	assignCargo(e, suf);
-	return e;
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+
+    typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename Id<TGraph>::Type TId;
+
+    TAlphabet firstChar = getValue(label, 0);
+    TEdgeDescriptor e = findEdge(g, source, firstChar);
+    TId id = obtainId(g.data_id_managerE);
+    _assignId(e, id);
+    assignTarget(e, target);
+    String<TAlphabet> suf(suffix(label,1));
+    assignCargo(e, suf);
+    return e;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TSpec, typename TVertexDescriptor, typename TChars>
-inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type 
-addEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target,
-		TChars const* chars) 
+inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type
+addEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target,
+        TChars const* chars)
 {
-	SEQAN_CHECKPOINT
-	return addEdge(g,source,target,String<TAlphabet>(chars));
+    SEQAN_CHECKPOINT
+    return addEdge(g,source,target,String<TAlphabet>(chars));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TSpec, typename TVertexDescriptor, typename TLabel, typename TEdgeCargo>
-inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type 
-addEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& /*g*/, 
-		TVertexDescriptor const /*source*/, 
-		TVertexDescriptor const /*target*/,
-		TLabel const /*label*/,
-		TEdgeCargo const /*cargo*/)
+inline typename EdgeDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type
+addEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& /*g*/,
+        TVertexDescriptor const /*source*/,
+        TVertexDescriptor const /*target*/,
+        TLabel const /*label*/,
+        TEdgeCargo const /*cargo*/)
 {
-	// No additional cargo allowed. Cargo is used for the words in the graph.
-	// Use external property map.
+    // No additional cargo allowed. Cargo is used for the words in the graph.
+    // Use external property map.
     SEQAN_ASSERT_FAIL("No additional cargo allowed. Cargo is used for the words in the graph. Use external property map.");
 }
 
@@ -175,56 +160,54 @@ addEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& /*g*
 
 template<typename TAlphabet, typename TSpec, typename TVertexDescriptor>
 inline void
-removeEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& g, 
-		TVertexDescriptor const source, 
-		TVertexDescriptor const target,
-		String<TAlphabet> const& label) 
+removeEdge(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >& g,
+        TVertexDescriptor const source,
+        TVertexDescriptor const target,
+        String<TAlphabet> const& label)
 {
-	SEQAN_CHECKPOINT;
-	(void)target;  // In case it is compiled without assertions.
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
+    SEQAN_CHECKPOINT;
+    (void)target;  // In case it is compiled without assertions.
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, source));
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, target));
 
-	TAlphabet firstChar = getValue(label, 0);
-	removeEdge(g, findEdge(g,source, firstChar));
+    TAlphabet firstChar = getValue(label, 0);
+    removeEdge(g, findEdge(g,source, firstChar));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template<typename TFile, typename TAlphabet, typename TCargo, typename TSpec, typename TIDString>
+template<typename TFile, typename TAlphabet, typename TCargo, typename TSpec>
 inline void
 write(TFile & target,
-	  Graph<Automaton<TAlphabet, TCargo, WordGraph<TSpec> > > const& g,
-	  TIDString const &,
-	  Raw)
+      Graph<Automaton<TAlphabet, TCargo, WordGraph<TSpec> > > const& g)
 {
 //IOREV _nodoc_
-	typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	typedef typename Size<TAlphabet>::Type TSize;
-	TSize table_length = ValueSize<TAlphabet>::VALUE;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-
-	streamPut(target,"WordGraph - Directed:\n");
-	typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Rooted>::Type TIterConst;
-	for(TIterConst it = begin(g.data_vertex);!atEnd(it);goNext(it)) {
-		if (!idInUse(g.data_id_managerV, position(it))) continue;
-		TVertexDescriptor sourceVertex = position(it);
-		for(TSize i=0;i<table_length;++i) {
-			TEdge const* ed = &g.data_vertex[sourceVertex].data_edge[i];
-			if (getTarget(ed) ==  nilVal) continue;
-			streamPut(target, (int)sourceVertex);
-			streamPut(target,"->");
-			streamPut(target, (int)getTarget(ed));
-			streamPut(target, ' ');
-			streamPut(target, ' ');
-			streamPut(target, "Label: ");
-			streamPut(target, TAlphabet(i));
-			streamPut(target, CharString(getCargo(ed)));
-			streamPut(target, '\n');
-		}
-	}
+    typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    typedef typename Size<TAlphabet>::Type TSize;
+    TSize table_length = ValueSize<TAlphabet>::VALUE;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+
+    write(target, "WordGraph - Directed:\n");
+    typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> > const, Rooted>::Type TIterConst;
+    for(TIterConst it = begin(g.data_vertex);!atEnd(it);goNext(it)) {
+        if (!idInUse(g.data_id_managerV, position(it))) continue;
+        TVertexDescriptor sourceVertex = position(it);
+        for(TSize i=0;i<table_length;++i) {
+            TEdge const* ed = &g.data_vertex[sourceVertex].data_edge[i];
+            if (getTarget(ed) ==  nilVal) continue;
+            appendNumber(target, (int)sourceVertex);
+            write(target, "->");
+            appendNumber(target, (int)getTarget(ed));
+            writeValue(target, ' ');
+            writeValue(target, ' ');
+            write(target, "Label: ");
+            writeValue(target, TAlphabet(i));
+            write(target, CharString(getCargo(ed)));
+            writeValue(target, '\n');
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -246,32 +229,32 @@ write(TFile & target,
  */
 
 template<typename TAlphabet, typename TSpec, typename TVertexDescriptor, typename TCharacters>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type
 getSuccessor(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > const& g,
-			 TVertexDescriptor vertex,
-			 TCharacters const& chars)
+             TVertexDescriptor vertex,
+             TCharacters const& chars)
 {
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-	typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdgeStump;
-	TEdgeStump* ed = findEdge(g, vertex, getValue(chars, 0));
-	if (getCargo(ed) == suffix(chars, 1)) {
-		return getTarget(ed);
-	} else {
-		return getNil<TVertexDescriptor>();
-	}
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+    typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdgeStump;
+    TEdgeStump* ed = findEdge(g, vertex, getValue(chars, 0));
+    if (getCargo(ed) == suffix(chars, 1)) {
+        return getTarget(ed);
+    } else {
+        return getNil<TVertexDescriptor>();
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TSpec, typename TVertexDescriptor, typename TCharacters>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type
 getSuccessor(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > const& g,
-			 TVertexDescriptor vertex,
-			 TCharacters const* chars)
+             TVertexDescriptor vertex,
+             TCharacters const* chars)
 {
-	SEQAN_CHECKPOINT
-	return getSuccessor(g,vertex,String<TAlphabet>(chars));
+    SEQAN_CHECKPOINT
+    return getSuccessor(g,vertex,String<TAlphabet>(chars));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -285,7 +268,7 @@ getSuccessor(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >
  *
  * @param[in]     a       An WordGraph.
  * @param[in]     v       The descriptor of the vertex to start at.
- * @param[in]     str     The @link SequenceConcept @endlink to parse.
+ * @param[in]     str     The @link ContainerConcept @endlink to parse.
  * @param[in,out] beginIt Begin iterator to sequence to parse.  Set to the first character that could not be parsed
  *                        or to the value of endIt if all of the string was parsed.
  * @param[in]     endIt   End iterator to sequence to parse.
@@ -297,34 +280,34 @@ getSuccessor(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > >
  */
 
 template<typename TAlphabet, typename TSpec, typename TVertexDescriptor, typename TIterator>
-inline typename VertexDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type 
+inline typename VertexDescriptor<Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > >::Type
 parseString(Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > const& g,
-			TVertexDescriptor const vertex,
-			TIterator beginIt,
-			TIterator endIt)
+            TVertexDescriptor const vertex,
+            TIterator beginIt,
+            TIterator endIt)
 {
-	SEQAN_CHECKPOINT;
-	SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
-	typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > TGraph;
-	typedef typename Size<TGraph>::Type TSize;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	TVertexDescriptor succ = vertex;
-	while (beginIt!=endIt) {
-		String<TAlphabet> label(*beginIt);
-		TSize range = 1;
-		TVertexDescriptor tmp = getSuccessor(g,succ,label);
-		while ((tmp == nilVal) &&
-				(beginIt+range != endIt))
-		{
-			appendValue(label, *(beginIt + range));
-			tmp = getSuccessor(g,succ,label);
-			++range;
-		}
-		if (tmp == nilVal) break;
-		succ = tmp;
-		beginIt = beginIt+range;
-	}
-	return succ;
+    SEQAN_CHECKPOINT;
+    SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex));
+    typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec> > > TGraph;
+    typedef typename Size<TGraph>::Type TSize;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    TVertexDescriptor succ = vertex;
+    while (beginIt!=endIt) {
+        String<TAlphabet> label(*beginIt);
+        TSize range = 1;
+        TVertexDescriptor tmp = getSuccessor(g,succ,label);
+        while ((tmp == nilVal) &&
+                (beginIt+range != endIt))
+        {
+            appendValue(label, *(beginIt + range));
+            tmp = getSuccessor(g,succ,label);
+            ++range;
+        }
+        if (tmp == nilVal) break;
+        succ = tmp;
+        beginIt = beginIt+range;
+    }
+    return succ;
 }
 
 /*!
diff --git a/seqan/graph_types/graph_interface.h b/seqan/graph_types/graph_interface.h
index 5557c54..2a4d6f9 100644
--- a/seqan/graph_types/graph_interface.h
+++ b/seqan/graph_types/graph_interface.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,6 +33,8 @@
 #ifndef SEQAN_HEADER_GRAPH_INTERFACE_H
 #define SEQAN_HEADER_GRAPH_INTERFACE_H
 
+// TODO(holtgrew): The documentation needs some improvements, possibly together with a refactoring of the module.
+
 namespace SEQAN_NAMESPACE_MAIN
 {
 
@@ -63,7 +65,7 @@ struct Hmm;
 
 /*!
  * @class Graph
- * @extends ContainerConcept
+ * @implements ContainerConcept
  * @headerfile <seqan/graph_types.h>
  * @brief Graph class.
  *
@@ -77,48 +79,37 @@ struct Hmm;
  * This is an example for Dijktra's algorithm on a directed graph with an external property map.  The property map
  * labels the edges with weights.  The xample only outputs distances, not th edetails of the paths.
  *
- * @include demos/graph/graph_algo_dijkstra.cpp
+ * @include demos/dox/graph_types/graph_algo_dijkstra.cpp
  *
  * The output of the distances is as follows:
  *
- * @include demos/graph/graph_algo_dijkstra.cpp.stdout
+ * @include demos/dox/graph_types/graph_algo_dijkstra.cpp.stdout
  */
 
-/**
-.Class.Graph:
-..cat:Graph
-..summary:Generic graph.
-..signature:Graph<TSpec>
-..param.TSpec:The specializing type determines the kind of graph, e.g., directed, undirected, tree, or automaton.
-...remarks:The default Graph<> corresponds to a directed graph.
-...default:Directed<>
-..include:seqan/graph_types.h
-..example:This is an example for Dijkstra's algorithm on a directed graph with an external property map. The property map adds weights to the edges. The example only outputs distances, not the details of the paths.
-...file:demos/graph/graph_algo_dijkstra.cpp
-...text:The output of the distances is as follows:
-...output:Distance from 0 to 0: 0
-Distance from 0 to 1: 8
-Distance from 0 to 2: 9
-Distance from 0 to 3: 5
-Distance from 0 to 4: 7
-
-*/
 template<typename TSpec = Directed<> >
 class Graph;
 
+/*!
+ * @mfn Graph#Size
+ * @brief Size type of the Graph.
+ *
+ * @signature Size<TGraph>::Type;
+ *
+ * @tparam TGraph The graph type to query for its size type.
+ *
+ * @return Type The size type.
+ */
+
 //////////////////////////////////////////////////////////////////////////////
 // General Graph Metafunction
 //////////////////////////////////////////////////////////////////////////////
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Spec.param.T.type:Class.Graph
-///.Metafunction.Spec.class:Class.Graph
-
 template<typename TSpec>
-struct Spec<Graph<TSpec> > 
+struct Spec<Graph<TSpec> >
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -126,116 +117,123 @@ struct Spec<Graph<TSpec> >
 template<typename TSpec>
 struct Spec<Graph<TSpec> const>
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.EdgeDescriptor.param.T.type:Class.Graph
-///.Metafunction.EdgeDescriptor.class:Class.Graph
-
 template<typename TSpec>
-struct EdgeDescriptor<Graph<TSpec> > 
+struct EdgeDescriptor<Graph<TSpec> >
 {
-	typedef typename EdgeType<Graph<TSpec> >::Type* Type;
+    typedef typename EdgeType<Graph<TSpec> >::Type* Type;
 };
 
 template<typename TSpec>
 struct EdgeDescriptor<Graph<TSpec> const>
 {
-	typedef typename EdgeType<Graph<TSpec> const>::Type* Type;
+    typedef typename EdgeType<Graph<TSpec> const>::Type* Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.VertexDescriptor.param.T.type:Class.Graph
-///.Metafunction.VertexDescriptor.class:Class.Graph
-
 template<typename TSpec>
-struct VertexDescriptor<Graph<TSpec> > 
+struct VertexDescriptor<Graph<TSpec> >
 {
-	typedef typename Id<Graph<TSpec> >::Type Type;
+    typedef typename Id<Graph<TSpec> >::Type Type;
 };
 
 template<typename TSpec>
 struct VertexDescriptor<Graph<TSpec> const>
 {
-	typedef typename Id<Graph<TSpec> >::Type Type;
+    typedef typename Id<Graph<TSpec> >::Type Type;
 };
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.EdgeType.param.T.type:Class.Graph
-///.Metafunction.EdgeType.class:Class.Graph
-
 template<typename TCargo, typename TSpec>
 struct EdgeType<Graph<Directed<TCargo, TSpec> > > {
-	typedef EdgeStump<TCargo, true, false, true, TSpec> Type;
+    typedef EdgeStump<TCargo, true, false, true, TSpec> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 struct EdgeType<Graph<Directed<TCargo, TSpec> > const> {
-	typedef EdgeStump<TCargo, true, false, true, TSpec> const Type;
+    typedef EdgeStump<TCargo, true, false, true, TSpec> const Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo>
 struct EdgeType<Graph<Directed<TCargo, WithoutEdgeId> > > {
-	typedef EdgeStump<TCargo, true, false, false, WithoutEdgeId> Type;
+    typedef EdgeStump<TCargo, true, false, false, WithoutEdgeId> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo>
 struct EdgeType<Graph<Directed<TCargo, WithoutEdgeId> > const> {
-	typedef EdgeStump<TCargo, true, false, false, WithoutEdgeId> const Type;
+    typedef EdgeStump<TCargo, true, false, false, WithoutEdgeId> const Type;
 };
 
-
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 struct EdgeType<Graph<Tree<TCargo, TSpec> > > {
-	typedef EdgeStump<TCargo, true, false, false, TreeTag> Type;
+    typedef EdgeStump<TCargo, true, false, false, TreeTag> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 struct EdgeType<Graph<Tree<TCargo, TSpec> > const> {
-	typedef EdgeStump<TCargo, true, false, false, TreeTag> const Type;
+    typedef EdgeStump<TCargo, true, false, false, TreeTag> const Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TCargo>
+struct EdgeType<Graph<Directed<TCargo, WithSourceId> > >
+{
+    typedef EdgeStump<TCargo, true, true, true, WithSourceId> Type;
+};
+
+//////////////////////////////////////////////////////////////////////////////
+
+template<typename TCargo>
+struct EdgeType<Graph<Directed<TCargo, WithSourceId> > const>
+{
+    typedef EdgeStump<TCargo, true, true, true, WithSourceId> const Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 struct EdgeType<Graph<Undirected<TCargo, TSpec> > > {
-	typedef EdgeStump<TCargo, true, true, true, TSpec> Type;
+    typedef EdgeStump<TCargo, true, true, true, TSpec> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TSpec>
 struct EdgeType<Graph<Undirected<TCargo, TSpec> > const> {
-	typedef EdgeStump<TCargo, true, true, true, TSpec> const Type;
+    typedef EdgeStump<TCargo, true, true, true, TSpec> const Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo>
-struct EdgeType<Graph<Undirected<TCargo, WithoutEdgeId> > > {
-	typedef EdgeStump<TCargo, true, true, false, WithoutEdgeId> Type;
+struct EdgeType<Graph<Undirected<TCargo, WithoutEdgeId> > >
+{
+    typedef EdgeStump<TCargo, true, true, false, WithoutEdgeId> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo>
 struct EdgeType<Graph<Undirected<TCargo, WithoutEdgeId> > const> {
-	typedef EdgeStump<TCargo, true, true, false, WithoutEdgeId> const Type;
+    typedef EdgeStump<TCargo, true, true, false, WithoutEdgeId> const Type;
 };
 
 
@@ -243,77 +241,71 @@ struct EdgeType<Graph<Undirected<TCargo, WithoutEdgeId> > const> {
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
 struct EdgeType<Graph<Automaton<TAlphabet, TCargo, TSpec> > > {
-	typedef EdgeStump<TCargo, false, false, true, TSpec> Type;
+    typedef EdgeStump<TCargo, false, false, true, TSpec> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
 struct EdgeType<Graph<Automaton<TAlphabet, TCargo, TSpec> > const> {
-	typedef EdgeStump<TCargo, false, false, true, TSpec> const Type;
+    typedef EdgeStump<TCargo, false, false, true, TSpec> const Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo>
 struct EdgeType<Graph<Automaton<TAlphabet, TCargo, WithoutEdgeId> > > {
-	typedef EdgeStump<TCargo, false, false, false, WithoutEdgeId> Type;
+    typedef EdgeStump<TCargo, false, false, false, WithoutEdgeId> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo>
 struct EdgeType<Graph<Automaton<TAlphabet, TCargo, WithoutEdgeId> > const> {
-	typedef EdgeStump<TCargo, false, false, false, WithoutEdgeId> const Type;
+    typedef EdgeStump<TCargo, false, false, false, WithoutEdgeId> const Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
 struct EdgeType<Graph<Hmm<TAlphabet, TCargo, TSpec> > const> {
-	typedef typename EdgeType<Graph<Directed<TCargo, TSpec> > const>::Type Type;
+    typedef typename EdgeType<Graph<Directed<TCargo, TSpec> > const>::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
 struct EdgeType<Graph<Hmm<TAlphabet, TCargo, TSpec> > > {
-	typedef typename EdgeType<Graph<Directed<TCargo, TSpec> > >::Type Type;
+    typedef typename EdgeType<Graph<Directed<TCargo, TSpec> > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Cargo.param.T.type:Class.Graph
-///.Metafunction.Cargo.class:Class.Graph
-
 template<typename TSpec>
 struct Cargo<Graph<TSpec> > {
-	typedef typename Cargo<typename EdgeType<Graph<TSpec> >::Type>::Type Type;
+    typedef typename Cargo<typename EdgeType<Graph<TSpec> >::Type>::Type Type;
 };
 
 
 template<typename TSpec>
 struct Cargo<Graph<TSpec> const> {
-	typedef typename Cargo<typename EdgeType<Graph<TSpec> const>::Type>::Type Type;
+    typedef typename Cargo<typename EdgeType<Graph<TSpec> const>::Type>::Type Type;
 };
 
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.EdgeIdHandler.param.T.type:Class.Graph
-///.Metafunction.EdgeIdHandler.class:Class.Graph
-
 template<typename TSpec>
 struct EdgeIdHandler<Graph<TSpec> const> {
-	typedef typename EdgeIdHandler<typename EdgeType<Graph<TSpec> const>::Type>::Type Type;
+    typedef typename EdgeIdHandler<typename EdgeType<Graph<TSpec> const>::Type>::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TSpec>
 struct EdgeIdHandler<Graph<TSpec> > {
-	typedef typename EdgeIdHandler<typename EdgeType<Graph<TSpec> >::Type>::Type Type;
+    typedef typename EdgeIdHandler<typename EdgeType<Graph<TSpec> >::Type>::Type Type;
 };
 
 
@@ -321,33 +313,30 @@ struct EdgeIdHandler<Graph<TSpec> > {
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Alphabet.param.T.type:Class.Graph
-///.Metafunction.Alphabet.class:Class.Graph
-
 template<typename TAlphabet, typename TCargo, typename TSpec>
 struct Alphabet<Graph<Automaton<TAlphabet, TCargo, TSpec> > > {
-	typedef TAlphabet Type;
+    typedef TAlphabet Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
 struct Alphabet<Graph<Automaton<TAlphabet, TCargo, TSpec> > const> {
-	typedef TAlphabet Type;
+    typedef TAlphabet Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
 struct Alphabet<Graph<Hmm<TAlphabet, TCargo, TSpec> > > {
-	typedef TAlphabet Type;
+    typedef TAlphabet Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TSpec>
 struct Alphabet<Graph<Hmm<TAlphabet, TCargo, TSpec> > const> {
-	typedef TAlphabet Type;
+    typedef TAlphabet Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -396,7 +385,9 @@ struct Alphabet<Graph<Hmm<TAlphabet, TCargo, TSpec> > const> {
  *
  * @signature bool empty(g);
  *
- * @param[in] g true if g is empty and valse if not.
+ * @param[in] g The Graph to query.
+ *
+ * @return bool <tt>true</tt> if g is empty and <tt>false</tt> if not.
  */
 
 /*!
@@ -479,8 +470,8 @@ struct Alphabet<Graph<Hmm<TAlphabet, TCargo, TSpec> > const> {
  * @fn Graph#addEdge
  * @brief Adds a new edge to a graph, either with or without cargo.
  *
- * @signatures TEdgeDescriptor addEdge(g, source, target, label[, cargo]);
- * @signatures TEdgeDescriptor addEdge(g, source, target, cargo);
+ * @signature TEdgeDescriptor addEdge(g, source, target, label[, cargo]);
+ * @signature TEdgeDescriptor addEdge(g, source, target, cargo);
  *
  * @param[in,out] g      The Graph to add the edge to.
  * @param[in]     source Descriptor of the source vertex.
@@ -571,7 +562,9 @@ struct Alphabet<Graph<Hmm<TAlphabet, TCargo, TSpec> > const> {
  * @signature void getAdjacencyMatrix(g, matrix);
  *
  * @param[in]  g      The Graph to compute ajacency matrix for.
- * @param[out] matrix The Matrix to fill with the adjacency matrix values.
+ * @param[out] matrix A @link String @endlink filled with <tt>n * n</tt> elements of @link IntegerConcept @endlink
+ *                    where <tt>matrix[i + n * j]</tt> gives the edge count between vertices <tt>i</tt> and
+ *                    <tt>j</tt>.
  */
 
 /*!
@@ -618,21 +611,11 @@ struct Alphabet<Graph<Hmm<TAlphabet, TCargo, TSpec> > const> {
  * @return T Pseudo nil value for type T.
  */
 
-/**
-.Function.getNil
-..class:Class.Graph
-..cat:Graph
-..summary:Utility function returning a value that represents nil.
-Useful for various graph algorithms, e.g., missing predecessors, vertices that have not been visited, etc.
-..signature:getNil<T>()
-..returns:Pseudo nil value for type T.
-..include:seqan/graph_types.h
-*/
 template <typename T>
 inline T
 getNil(T *)
 {
-	return ~0;
+    return ~0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -641,8 +624,8 @@ template <typename T>
 inline T
 getNil()
 {
-	T * _tag = 0;
-	return getNil(_tag);
+    T * _tag = 0;
+    return getNil(_tag);
 }
 
 
@@ -655,8 +638,8 @@ template <typename T>
 inline T
 _getInfinity()
 {
-	T * _tag = 0;
-	return supremumValueImpl(_tag);
+    T * _tag = 0;
+    return supremumValueImpl(_tag);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -665,7 +648,7 @@ template <>
 inline double
 _getInfinity()
 {
-	return 1000000000;
+    return 1000000000;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -674,8 +657,8 @@ template<typename TWeightMap>
 inline typename Value<TWeightMap>::Type
 _getInfinityDistance(TWeightMap const&)
 {
-	// We need to divide by 2 because of addition in some graph algorithms: infinity + something
-	return (_getInfinity<typename Value<TWeightMap>::Type>()/2);
+    // We need to divide by 2 because of addition in some graph algorithms: infinity + something
+    return (_getInfinity<typename Value<TWeightMap>::Type>()/2);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -684,7 +667,7 @@ template <typename T>
 inline T
 _getInfinityDistance()
 {
-	return (_getInfinity<T>() / 2);
+    return (_getInfinity<T>() / 2);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -694,8 +677,8 @@ template<typename TId>
 inline TId
 _getId(TId const id)
 {
-	SEQAN_CHECKPOINT
-	return id;
+    SEQAN_CHECKPOINT
+    return id;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -703,10 +686,10 @@ _getId(TId const id)
 template<typename TSpec, typename TVertexDescriptor>
 inline void
 _createVertices(Graph<TSpec>& g,
-				TVertexDescriptor const maxId) 
+                TVertexDescriptor const maxId)
 {
-		// Create missing vertices
-		while (maxId >= getIdUpperBound(g.data_id_managerV)) addVertex(g);
+    // Create missing vertices
+    while (maxId >= getIdUpperBound(g.data_id_managerV)) addVertex(g);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -726,43 +709,24 @@ _createVertices(Graph<TSpec>& g,
  * child, parent, child</tt>.
  */
 
-/**
-.Function.addEdges
-..class:Class.Graph
-..cat:Graph
-..summary:Shortcut to add multiple edges at once.
-Creates vertices implicitly.
-..signature:addEdges(g, edges, size)
-..param.g:A graph.
-...type:Class.Graph
-..param.edges:An array of vertex descriptors. It is assumed that the
-edges are stored in the following way: Source1, Target1, Source2, Target2, Source3, ...
-For a tree the root must be the first vertex in this array and the enumeration is Parent, Child, Parent, Child, ...
-...type:Metafunction.VertexDescriptor
-..param.size:Size of the array. Must be a multiple of 2.
-...type:Metafunction.Size
-..returns:void
-..see:Function.addEdge
-..include:seqan/graph_types.h
-*/
 template<typename TSpec, typename TEdgeArray, typename TSize>
 inline void
 addEdges(Graph<TSpec>& dest,
-		 TEdgeArray const & edges,
-		 TSize const size) 
+         TEdgeArray const & edges,
+         TSize const size)
 {
-	typedef typename VertexDescriptor<Graph<TSpec> >::Type TVertexDescriptor;
-	for(TSize i=0;i<size;++i) {
-		TVertexDescriptor source = edges[2*i];
-		TVertexDescriptor target = edges[2*i+1];
-		// Create missing vertices
-		if (source>target) _createVertices(dest,source);
-		else _createVertices(dest,target);
-		// Add edge
-		SEQAN_ASSERT(idInUse(dest.data_id_managerV, source));
-		SEQAN_ASSERT(idInUse(dest.data_id_managerV, target));
-		addEdge(dest, source, target);
-	}
+    typedef typename VertexDescriptor<Graph<TSpec> >::Type TVertexDescriptor;
+    for(TSize i=0;i<size;++i) {
+        TVertexDescriptor source = edges[2*i];
+        TVertexDescriptor target = edges[2*i+1];
+        // Create missing vertices
+        if (source>target) _createVertices(dest,source);
+        else _createVertices(dest,target);
+        // Add edge
+        SEQAN_ASSERT(idInUse(dest.data_id_managerV, source));
+        SEQAN_ASSERT(idInUse(dest.data_id_managerV, target));
+        addEdge(dest, source, target);
+    }
 }
 
 
@@ -770,11 +734,12 @@ addEdges(Graph<TSpec>& dest,
 
 template <typename TStream, typename TSpec>
 inline TStream &
-operator << (TStream & target, 
-			 Graph<TSpec> const& source)
+operator << (TStream & target,
+             Graph<TSpec> const& source)
 {
-	write(target, source);
-	return target;
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
+    return target;
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_iterator.h b/seqan/graph_types/graph_iterator.h
index 107e151..2efef28 100644
--- a/seqan/graph_types/graph_iterator.h
+++ b/seqan/graph_types/graph_iterator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,29 +45,29 @@ namespace SEQAN_NAMESPACE_MAIN
 template <typename TSpec>
 struct GraphIterator;
 
-	// Vertex iterator
-	template <typename TSpec = Default>
-	struct InternalVertexIterator;
+    // Vertex iterator
+    template <typename TSpec = Default>
+    struct InternalVertexIterator;
 
-	// Edge iterator
-	template <typename TSpec = Default>
-	struct InternalEdgeIterator;
+    // Edge iterator
+    template <typename TSpec = Default>
+    struct InternalEdgeIterator;
 
-	// OutEdge iterator
-	template <typename TSpec = Default>
-	struct InternalOutEdgeIterator;
+    // OutEdge iterator
+    template <typename TSpec = Default>
+    struct InternalOutEdgeIterator;
 
-	// Adjacency iterator
-	template <typename TSpec = Default>
-	struct InternalAdjacencyIterator;
+    // Adjacency iterator
+    template <typename TSpec = Default>
+    struct InternalAdjacencyIterator;
 
-	// Bfs iterator
-	template <typename TSpec = Default>
-	struct InternalBfsIterator;
+    // Bfs iterator
+    template <typename TSpec = Default>
+    struct InternalBfsIterator;
 
-	// Dfs iterator
-	template <typename TSpec = Default>
-	struct InternalDfsIterator;
+    // Dfs iterator
+    template <typename TSpec = Default>
+    struct InternalDfsIterator;
 
 //////////////////////////////////////////////////////////////////////////////
 // Graph Iterators - Metafunctions
@@ -75,21 +75,18 @@ struct GraphIterator;
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Host.param.T.type:Class.Graph
-///.Metafunction.Host.class:Class.Graph
-
 template<typename TGraph, typename TIteratorSpec>
 struct Host<Iter<TGraph, GraphIterator<TIteratorSpec> > >
-{	
-	typedef TGraph Type;
+{
+    typedef TGraph Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TGraph, typename TIteratorSpec>
 struct Host<Iter<TGraph const, GraphIterator<TIteratorSpec> > >
-{	
-	typedef TGraph const Type;
+{
+    typedef TGraph const Type;
 };
 
 
diff --git a/seqan/graph_types/graph_iterator_adjacency.h b/seqan/graph_types/graph_iterator_adjacency.h
index 9ad6897..936b822 100644
--- a/seqan/graph_types/graph_iterator_adjacency.h
+++ b/seqan/graph_types/graph_iterator_adjacency.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -70,67 +70,40 @@ namespace SEQAN_NAMESPACE_MAIN
  * @param[in] v     The descriptor of the vertex to iterate adjacent edges of.
  */
 
-/**
-.Spec.Adjacency Iterator:
-..cat:Graph
-..summary:Adjacency iterator for @Class.Graph@.
-..signature:Iterator<TGraph, AdjacencyIterator>
-..param.TGraph:A graph.
-...type:Class.Graph
-..general:Class.Iter
-..see:Spec.Vertex Iterator
-..see:Spec.Out-Edge Iterator
-..see:Spec.Edge Iterator
-..see:Spec.Bfs Iterator
-..include:seqan/graph_types.h
-
-.Memfunc.Adjacency Iterator#Iter
-..summary:Constructor
-..class:Spec.Adjacency Iterator
-..signature:Iter()
-..signature:Iter(graph, v)
-..signature:Iter(iter)
-..param.graph:The graph to iterate edges of.
-...type:Class.Graph
-..param.v:Vertex descriptor of vertex to iterate adjacent edges of.
-...type:Metafunction.VertexDescriptor
-..param.iter:Other iterator to copy-construct from.
-...type:Spec.Adjacency Iterator
-*/
 template<typename TGraph, typename TSpec>
-class Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > 
+class Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >
 {
 public:
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator_;
-	TOutEdgeIterator_ data_edge_it;
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph const& _graph, TVertexDescriptor_ const v) : 
-		data_edge_it(_graph, v)
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter(Iter const& _iter) : data_edge_it(_iter.data_edge_it)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_edge_it = _other.data_edge_it;
-		return *this;
-	}
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator_;
+    TOutEdgeIterator_ data_edge_it;
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph const& _graph, TVertexDescriptor_ const v) :
+        data_edge_it(_graph, v)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    ~Iter() {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(Iter const& _iter) : data_edge_it(_iter.data_edge_it)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_edge_it = _other.data_edge_it;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -143,14 +116,14 @@ class Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >
 
 template<typename TGraph>
 struct Iterator<TGraph, AdjacencyIterator>
-{	
-	typedef Iter<TGraph, GraphIterator<InternalAdjacencyIterator<AdjacencyIterator> > > Type;
+{
+    typedef Iter<TGraph, GraphIterator<InternalAdjacencyIterator<AdjacencyIterator> > > Type;
 };
 
 template<typename TGraph>
 struct Iterator<TGraph const, AdjacencyIterator>
-{	
-	typedef Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<AdjacencyIterator> > > Type;
+{
+    typedef Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<AdjacencyIterator> > > Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -158,13 +131,13 @@ struct Iterator<TGraph const, AdjacencyIterator>
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -172,13 +145,13 @@ struct Value<Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<TIterato
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TIteratorSpec> > > >
 {
-	typedef typename Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<TIteratorSpec> > > >
 {
-	typedef typename Reference<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Reference<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -186,13 +159,13 @@ struct Reference<Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<TIte
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TIteratorSpec> > > >
 {
-	typedef typename GetValue<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename GetValue<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<TIteratorSpec> > > >
 {
-	typedef typename GetValue<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename GetValue<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -200,13 +173,13 @@ struct GetValue<Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<TIter
 template<typename TGraph, typename TIteratorSpec>
 struct Spec<Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TIteratorSpec> > > >
 {
-	typedef TIteratorSpec Type;
+    typedef TIteratorSpec Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Spec<Iter<TGraph const, GraphIterator<InternalAdjacencyIterator<TIteratorSpec> > > >
 {
-	typedef TIteratorSpec Type;
+    typedef TIteratorSpec Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -219,8 +192,8 @@ template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > >::Type
 getValue(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return targetVertex(it.data_edge_it);
+    SEQAN_CHECKPOINT
+    return targetVertex(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -229,8 +202,8 @@ template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > >::Type
 value(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return getValue(it);
+    SEQAN_CHECKPOINT
+    return getValue(it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -239,8 +212,8 @@ template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > >::Type
 operator * (Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return value(it);
+    SEQAN_CHECKPOINT
+    return value(it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -249,9 +222,9 @@ template<typename TGraph, typename TSpec>
 inline typename Host<Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > >::Type const&
 hostGraph(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return hostGraph(it.data_edge_it);
-} 
+    SEQAN_CHECKPOINT
+    return hostGraph(it.data_edge_it);
+}
 
 //////////////////////////////////////////////////////////////////////////////
 
@@ -259,8 +232,8 @@ template<typename TGraph, typename TSpec>
 inline bool
 atBegin(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return atBegin(it.data_edge_it);
+    SEQAN_CHECKPOINT
+    return atBegin(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -269,8 +242,8 @@ template<typename TGraph, typename TSpec>
 inline void
 goBegin(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	goBegin(it.data_edge_it);
+    SEQAN_CHECKPOINT
+    goBegin(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -279,8 +252,8 @@ template<typename TGraph, typename TSpec>
 inline bool
 atEnd(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (atEnd(it.data_edge_it));
+    SEQAN_CHECKPOINT
+    return (atEnd(it.data_edge_it));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -289,8 +262,8 @@ template<typename TGraph, typename TSpec>
 inline void
 goEnd(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	goEnd(it.data_edge_it);
+    SEQAN_CHECKPOINT
+    goEnd(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -299,8 +272,8 @@ template<typename TGraph, typename TSpec>
 inline void
 goNext(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	goNext(it.data_edge_it);
+    SEQAN_CHECKPOINT
+    goNext(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -310,8 +283,8 @@ inline Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >&
 operator ++(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	goNext(it);
-	return it;
+    goNext(it);
+    return it;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -320,10 +293,10 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >
 operator ++(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > ret = it;
-	goNext(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > ret = it;
+    goNext(it);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -332,8 +305,8 @@ template<typename TGraph, typename TSpec>
 inline void
 goPrevious(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	goPrevious(it.data_edge_it);
+    SEQAN_CHECKPOINT
+    goPrevious(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -342,9 +315,9 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >&
 operator --(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	goPrevious(it);
-	return it;
+    SEQAN_CHECKPOINT
+    goPrevious(it);
+    return it;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -353,10 +326,10 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >
 operator --(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > ret = it;
-	goPrevious(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > > ret = it;
+    goPrevious(it);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -364,10 +337,10 @@ operator --(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it,
 template<typename TGraph, typename TSpec>
 inline bool
 operator ==(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it2)
 {
 SEQAN_CHECKPOINT
-	return (it1.data_edge_it==it2.data_edge_it);
+    return (it1.data_edge_it==it2.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -375,10 +348,10 @@ SEQAN_CHECKPOINT
 template<typename TGraph, typename TSpec>
 inline bool
 operator !=(Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalAdjacencyIterator<TSpec> > >& it2)
 {
 SEQAN_CHECKPOINT
-	return (it1.data_edge_it!=it2.data_edge_it);
+    return (it1.data_edge_it!=it2.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/graph_types/graph_iterator_bfs.h b/seqan/graph_types/graph_iterator_bfs.h
index 12c94de..2010a49 100644
--- a/seqan/graph_types/graph_iterator_bfs.h
+++ b/seqan/graph_types/graph_iterator_bfs.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -69,92 +69,64 @@ namespace SEQAN_NAMESPACE_MAIN
  * @param[in] v     The descriptor of the vertex to start BFS iteration.
  */
 
-/**
-.Spec.Bfs Iterator:
-..cat:Graph
-..summary:Breath-first search iterator for @Class.Graph@.
-..signature:Iterator<TGraph, BfsIterator>
-..param.TGraph:A graph.
-...type:Class.Graph
-..general:Class.Iter
-..see:Spec.Vertex Iterator
-..see:Spec.Out-Edge Iterator
-..see:Spec.Edge Iterator
-..see:Spec.Adjacency Iterator
-..see:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-
-.Memfunc.Bfs Iterator#Iter
-..summary:Constructor
-..class:Spec.Bfs Iterator
-..signature:Iter()
-..signature:Iter(graph, v)
-..signature:Iter(iter)
-..param.graph:The graph to iterate edges of.
-...type:Class.Graph
-..param.v:Vertex descriptor of vertex to start BFS from.
-...type:Metafunction.VertexDescriptor
-..param.iter:Other iterator to copy-construct from.
-...type:Spec.Bfs Iterator
-*/
 template<typename TGraph, typename TSpec>
-class Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > > 
+class Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >
 {
 public:
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
-	TGraph const* data_host;
-	TVertexDescriptor_ data_source;
-	String<bool> data_tokenMap;
-	std::deque<TVertexDescriptor_> data_queue;
-
-	void _init() {
-		resizeVertexMap(*data_host,data_tokenMap);
-		typedef typename Iterator<String<bool>, Rooted>::Type TIter;
-		TIter it = begin(data_tokenMap);
-		for(;!atEnd(it);goNext(it)) {
-			assignValue(it,false);
-		}
-		assignProperty(data_tokenMap, data_source, true);
-		data_queue.clear();
-		data_queue.push_back(data_source);
-	}
-
-	Iter()
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph const& _graph, TVertexDescriptor_ v) : 
-		data_host(&_graph),
-		data_source(v)
-	{
-		SEQAN_CHECKPOINT
-		_init();
-	}
-	
-	
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter(Iter const& _iter) :
-		data_host(_iter.data_host),
-		data_source(_iter.data_source),
-		data_tokenMap(_iter.data_tokenMap),
-		data_queue(_iter.data_queue)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host=_other.data_host;
-		data_source=_other.data_source;
-		data_tokenMap=_other.data_tokenMap;
-		data_queue=_other.data_queue;
-		return *this;
-	}
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
+    TGraph const* data_host;
+    TVertexDescriptor_ data_source;
+    String<bool> data_tokenMap;
+    std::deque<TVertexDescriptor_> data_queue;
+
+    void _init() {
+        resizeVertexMap(data_tokenMap, *data_host);
+        typedef typename Iterator<String<bool>, Rooted>::Type TIter;
+        TIter it = begin(data_tokenMap);
+        for(;!atEnd(it);goNext(it)) {
+            assignValue(it,false);
+        }
+        assignProperty(data_tokenMap, data_source, true);
+        data_queue.clear();
+        data_queue.push_back(data_source);
+    }
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph const& _graph, TVertexDescriptor_ v) :
+        data_host(&_graph),
+        data_source(v)
+    {
+        SEQAN_CHECKPOINT
+        _init();
+    }
+
+
+    ~Iter() {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_source(_iter.data_source),
+        data_tokenMap(_iter.data_tokenMap),
+        data_queue(_iter.data_queue)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host=_other.data_host;
+        data_source=_other.data_source;
+        data_tokenMap=_other.data_tokenMap;
+        data_queue=_other.data_queue;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -164,50 +136,50 @@ class Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >
 //////////////////////////////////////////////////////////////////////////////
 template<typename TGraph>
 struct Iterator<TGraph, BfsIterator>
-{	
-	typedef Iter<TGraph, GraphIterator<InternalBfsIterator<BfsIterator> > > Type;
+{
+    typedef Iter<TGraph, GraphIterator<InternalBfsIterator<BfsIterator> > > Type;
 };
 
 template<typename TGraph>
 struct Iterator<TGraph const, BfsIterator>
-{	
-	typedef Iter<TGraph const, GraphIterator<InternalBfsIterator<BfsIterator> > > Type;
+{
+    typedef Iter<TGraph const, GraphIterator<InternalBfsIterator<BfsIterator> > > Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph, GraphIterator<InternalBfsIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph const, GraphIterator<InternalBfsIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph, GraphIterator<InternalBfsIterator<TIteratorSpec> > > >
 {
-	typedef typename Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph const, GraphIterator<InternalBfsIterator<TIteratorSpec> > > >
 {
-	typedef typename Reference<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Reference<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph, GraphIterator<InternalBfsIterator<TIteratorSpec> > > >
 {
-	typedef typename GetValue<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename GetValue<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph const, GraphIterator<InternalBfsIterator<TIteratorSpec> > > >
 {
-	typedef typename GetValue<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename GetValue<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -217,85 +189,85 @@ template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > > >::Type
 getValue(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_queue.front();
+    SEQAN_CHECKPOINT
+    return it.data_queue.front();
 }
 
 template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > > >::Type
 value(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return getValue(it);
+    SEQAN_CHECKPOINT
+    return getValue(it);
 }
 
 template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > > >::Type
 operator * (Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return value(it);
+    SEQAN_CHECKPOINT
+    return value(it);
 }
 
 template<typename TGraph, typename TSpec>
 inline typename Host<Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > > >::Type const&
 hostGraph(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return *it.data_host;
+    SEQAN_CHECKPOINT
+    return *it.data_host;
 }
 
 template<typename TGraph, typename TSpec>
 inline bool
 atBegin(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (it.data_queue.empty()) return false;
-	else return (it.data_queue.front() == it.data_source);
+    SEQAN_CHECKPOINT
+    if (it.data_queue.empty()) return false;
+    else return (it.data_queue.front() == it.data_source);
 }
 
 template<typename TGraph, typename TSpec>
 inline void
 goBegin(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it._init();
+    SEQAN_CHECKPOINT
+    it._init();
 }
 
 template<typename TGraph, typename TSpec>
 inline bool
 atEnd(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_queue.empty());
+    SEQAN_CHECKPOINT
+    return (it.data_queue.empty());
 }
 
 template<typename TGraph, typename TSpec>
 inline void
 goEnd(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_queue.clear();
+    SEQAN_CHECKPOINT
+    it.data_queue.clear();
 }
 
 template<typename TGraph, typename TSpec>
 inline void
 goNext(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (it.data_queue.empty()) return;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor u = it.data_queue.front();
-	it.data_queue.pop_front();
-	typedef typename Iterator<TGraph, AdjacencyIterator>::Type TAdjacencyIterator;
-	TAdjacencyIterator itad(*it.data_host,u);
-	for(;!atEnd(itad);goNext(itad)) {
-		TVertexDescriptor v = getValue(itad);
-		if (getProperty(it.data_tokenMap, v) == false) {
-			assignProperty(it.data_tokenMap, v, true);
-			it.data_queue.push_back(v);
-		}
-	}
+    SEQAN_CHECKPOINT
+    if (it.data_queue.empty()) return;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor u = it.data_queue.front();
+    it.data_queue.pop_front();
+    typedef typename Iterator<TGraph, AdjacencyIterator>::Type TAdjacencyIterator;
+    TAdjacencyIterator itad(*it.data_host,u);
+    for(;!atEnd(itad);goNext(itad)) {
+        TVertexDescriptor v = getValue(itad);
+        if (getProperty(it.data_tokenMap, v) == false) {
+            assignProperty(it.data_tokenMap, v, true);
+            it.data_queue.push_back(v);
+        }
+    }
 }
 
 template<typename TGraph, typename TSpec>
@@ -303,40 +275,40 @@ inline Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >&
 operator ++(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	goNext(it);
-	return it;
+    goNext(it);
+    return it;
 }
 
 template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >
 operator ++(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > > ret = it;
-	goNext(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > > ret = it;
+    goNext(it);
+    return ret;
 }
 
 template<typename TGraph, typename TSpec>
 inline bool
 operator ==(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_source==it2.data_source) &&
-			(it1.data_tokenMap==it2.data_tokenMap) &&
-			(it1.data_queue==it2.data_queue));
+    SEQAN_CHECKPOINT
+    return ((it1.data_source==it2.data_source) &&
+            (it1.data_tokenMap==it2.data_tokenMap) &&
+            (it1.data_queue==it2.data_queue));
 }
 
 template<typename TGraph, typename TSpec>
 inline bool
 operator !=(Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalBfsIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_source!=it2.data_source) ||
-			(it1.data_tokenMap!=it2.data_tokenMap) ||
-			(it1.data_queue!=it2.data_queue));
+    SEQAN_CHECKPOINT
+    return ((it1.data_source!=it2.data_source) ||
+            (it1.data_tokenMap!=it2.data_tokenMap) ||
+            (it1.data_queue!=it2.data_queue));
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_iterator_dfs.h b/seqan/graph_types/graph_iterator_dfs.h
index bca2dbc..ec85b89 100644
--- a/seqan/graph_types/graph_iterator_dfs.h
+++ b/seqan/graph_types/graph_iterator_dfs.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -71,93 +71,64 @@ namespace SEQAN_NAMESPACE_MAIN
  * @param[in] v     The descriptor of the vertex to start DFS preorder iteration.
  */
 
-/**
-.Spec.Dfs Preorder Iterator:
-..cat:Graph
-..summary:Depth-first search iterator for @Class.Graph@.
-..remarks:Preorder means that a vertex is enumerated before its adjacent vertices have been explored.
-..signature:Iterator<TGraph, DfsPreorder>
-..param.TGraph:A graph.
-...type:Class.Graph
-..general:Class.Iter
-..see:Spec.Vertex Iterator
-..see:Spec.Out-Edge Iterator
-..see:Spec.Edge Iterator
-..see:Spec.Adjacency Iterator
-..see:Spec.Bfs Iterator
-..include:seqan/graph_types.h
-
-.Memfunc.Dfs Preorder Iterator#Iter
-..summary:Constructor
-..class:Spec.Dfs Preorder Iterator
-..signature:Iter()
-..signature:Iter(graph, v)
-..signature:Iter(iter)
-..param.graph:The graph to iterate edges of.
-...type:Class.Graph
-..param.v:Vertex descriptor of vertex to start DFS from.
-...type:Metafunction.VertexDescriptor
-..param.iter:Other iterator to copy-construct from.
-...type:Spec.Dfs Preorder Iterator
-*/
 template<typename TGraph, typename TSpec>
-class Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > > 
+class Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >
 {
 public:
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
-	TGraph const* data_host;
-	TVertexDescriptor_ data_source;
-	String<bool> data_tokenMap;			// Which vertices have been visited
-	String<TVertexDescriptor_> data_stack;
-	
-	void _init() {
-		resizeVertexMap(*data_host,data_tokenMap);
-		typedef typename Iterator<String<bool>, Rooted>::Type TIter;
-		TIter it = begin(data_tokenMap);
-		for(;!atEnd(it);goNext(it)) {
-			assignValue(it,false);
-		}
-		assignProperty(data_tokenMap, data_source, true);
-		clear(data_stack);
-		appendValue(data_stack, data_source, Generous());
-	}
-
-	Iter()
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph& _graph, TVertexDescriptor_ v) : 
-		data_host(&_graph),
-		data_source(v)
-	{
-		SEQAN_CHECKPOINT
-		_init();
-	}
-	
-	
-	Iter(Iter const& _iter) :
-		data_host(_iter.data_host),
-		data_source(_iter.data_source),
-		data_tokenMap(_iter.data_tokenMap),
-		data_stack(_iter.data_stack)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host=_other.data_host;
-		data_source=_other.data_source;
-		data_tokenMap=_other.data_tokenMap;
-		data_stack=_other.data_stack;
-		return *this;
-	}
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
+    TGraph const* data_host;
+    TVertexDescriptor_ data_source;
+    String<bool> data_tokenMap;            // Which vertices have been visited
+    String<TVertexDescriptor_> data_stack;
+
+    void _init() {
+        resizeVertexMap(data_tokenMap, *data_host);
+        typedef typename Iterator<String<bool>, Rooted>::Type TIter;
+        TIter it = begin(data_tokenMap);
+        for(;!atEnd(it);goNext(it)) {
+            assignValue(it,false);
+        }
+        assignProperty(data_tokenMap, data_source, true);
+        clear(data_stack);
+        appendValue(data_stack, data_source, Generous());
+    }
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph& _graph, TVertexDescriptor_ v) :
+        data_host(&_graph),
+        data_source(v)
+    {
+        SEQAN_CHECKPOINT
+        _init();
+    }
+
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_source(_iter.data_source),
+        data_tokenMap(_iter.data_tokenMap),
+        data_stack(_iter.data_stack)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    ~Iter() {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host=_other.data_host;
+        data_source=_other.data_source;
+        data_tokenMap=_other.data_tokenMap;
+        data_stack=_other.data_stack;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -167,50 +138,50 @@ class Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >
 //////////////////////////////////////////////////////////////////////////////
 template<typename TGraph>
 struct Iterator<TGraph, DfsPreorder>
-{	
-	typedef Iter<TGraph, GraphIterator<InternalDfsIterator<DfsPreorder> > > Type;
+{
+    typedef Iter<TGraph, GraphIterator<InternalDfsIterator<DfsPreorder> > > Type;
 };
 
 template<typename TGraph>
 struct Iterator<TGraph const, DfsPreorder>
-{	
-	typedef Iter<TGraph const, GraphIterator<InternalDfsIterator<DfsPreorder> > > Type;
+{
+    typedef Iter<TGraph const, GraphIterator<InternalDfsIterator<DfsPreorder> > > Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph, GraphIterator<InternalDfsIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph const, GraphIterator<InternalDfsIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph, GraphIterator<InternalDfsIterator<TIteratorSpec> > > >
 {
-	typedef typename Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph const, GraphIterator<InternalDfsIterator<TIteratorSpec> > > >
 {
-	typedef typename Reference<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Reference<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph, GraphIterator<InternalDfsIterator<TIteratorSpec> > > >
 {
-	typedef typename GetValue<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename GetValue<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph const, GraphIterator<InternalDfsIterator<TIteratorSpec> > > >
 {
-	typedef typename GetValue<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename GetValue<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 
@@ -221,86 +192,86 @@ template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > > >::Type
 getValue(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return getValue(it.data_stack, length(it.data_stack) - 1);
+    SEQAN_CHECKPOINT
+    return getValue(it.data_stack, length(it.data_stack) - 1);
 }
 
 template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > > >::Type
 value(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	// We don't want vertex ids to be changed
-	return getValue(it);
+    SEQAN_CHECKPOINT
+    // We don't want vertex ids to be changed
+    return getValue(it);
 }
 
 template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > > >::Type
 operator * (Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return value(it);
+    SEQAN_CHECKPOINT
+    return value(it);
 }
 
 template<typename TGraph, typename TSpec>
 inline typename Host<Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > > >::Type const&
 hostGraph(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return *it.data_host;
+    SEQAN_CHECKPOINT
+    return *it.data_host;
 }
 
 template<typename TGraph, typename TSpec>
 inline bool
 atBegin(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (empty(it.data_stack)) return false;
-	else return (getValue(it.data_stack, length(it.data_stack) - 1) == it.data_source);
+    SEQAN_CHECKPOINT
+    if (empty(it.data_stack)) return false;
+    else return (getValue(it.data_stack, length(it.data_stack) - 1) == it.data_source);
 }
 
 template<typename TGraph, typename TSpec>
 inline void
 goBegin(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it._init();
+    SEQAN_CHECKPOINT
+    it._init();
 }
 
 template<typename TGraph, typename TSpec>
 inline bool
 atEnd(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (empty(it.data_stack));
+    SEQAN_CHECKPOINT
+    return (empty(it.data_stack));
 }
 
 template<typename TGraph, typename TSpec>
 inline void
 goEnd(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	clear(it.data_stack);
+    SEQAN_CHECKPOINT
+    clear(it.data_stack);
 }
 
 template<typename TGraph, typename TSpec>
 inline void
 goNext(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (empty(it.data_stack)) return;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor u = getValue(it.data_stack, length(it.data_stack) - 1);
-	resize(it.data_stack, length(it.data_stack) - 1);
-	typedef typename Iterator<TGraph, AdjacencyIterator>::Type TAdjacencyIterator;
-	TAdjacencyIterator itad(*it.data_host,u);
-	for(;!atEnd(itad);goNext(itad)) {
-		TVertexDescriptor v = getValue(itad);
-		if (getProperty(it.data_tokenMap, v) == false) {
-			assignProperty(it.data_tokenMap, v, true);
-			appendValue(it.data_stack, v, Generous());
-		}
-	}
+    SEQAN_CHECKPOINT
+    if (empty(it.data_stack)) return;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor u = getValue(it.data_stack, length(it.data_stack) - 1);
+    resize(it.data_stack, length(it.data_stack) - 1);
+    typedef typename Iterator<TGraph, AdjacencyIterator>::Type TAdjacencyIterator;
+    TAdjacencyIterator itad(*it.data_host,u);
+    for(;!atEnd(itad);goNext(itad)) {
+        TVertexDescriptor v = getValue(itad);
+        if (getProperty(it.data_tokenMap, v) == false) {
+            assignProperty(it.data_tokenMap, v, true);
+            appendValue(it.data_stack, v, Generous());
+        }
+    }
 }
 
 template<typename TGraph, typename TSpec>
@@ -308,40 +279,40 @@ inline Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >&
 operator ++(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	goNext(it);
-	return it;
+    goNext(it);
+    return it;
 }
 
 template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >
 operator ++(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > > ret = it;
-	goNext(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > > ret = it;
+    goNext(it);
+    return ret;
 }
 
 template<typename TGraph, typename TSpec>
 inline bool
 operator ==(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_source==it2.data_source) &&
-			(it1.data_tokenMap==it2.data_tokenMap) &&
-			(it1.data_stack==it2.data_stack));
+    SEQAN_CHECKPOINT
+    return ((it1.data_source==it2.data_source) &&
+            (it1.data_tokenMap==it2.data_tokenMap) &&
+            (it1.data_stack==it2.data_stack));
 }
 
 template<typename TGraph, typename TSpec>
 inline bool
 operator !=(Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalDfsIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_source!=it2.data_source) ||
-			(it1.data_tokenMap!=it2.data_tokenMap) ||
-			(it1.data_stack!=it2.data_stack));
+    SEQAN_CHECKPOINT
+    return ((it1.data_source!=it2.data_source) ||
+            (it1.data_tokenMap!=it2.data_tokenMap) ||
+            (it1.data_stack!=it2.data_stack));
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_iterator_edge.h b/seqan/graph_types/graph_iterator_edge.h
index e91d31c..a07545d 100644
--- a/seqan/graph_types/graph_iterator_edge.h
+++ b/seqan/graph_types/graph_iterator_edge.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,6 +43,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
 /*!
  * @class EdgeIterator
+ * @extends Iter
  * @headerfile <seqan/graph_types.h>
  * @brief Edge iterator for @link Graph @endlink.
  *
@@ -68,85 +69,52 @@ namespace SEQAN_NAMESPACE_MAIN
  * @param[in] graph The @link Graph @endlink to iterate edges of.
  */
 
-/**
-.Spec.Edge Iterator:
-..cat:Graph
-..summary:Edge iterator for @Class.Graph@.
-..signature:Iterator<TGraph, EdgeIterator>
-..param.TGraph:A graph.
-...type:Class.Graph
-..general:Class.Iter
-..see:Spec.Vertex Iterator
-..see:Spec.Out-Edge Iterator
-..see:Spec.Adjacency Iterator
-..see:Spec.Bfs Iterator
-..see:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-
-.Memfunc.Edge Iterator#Iter
-..summary:Constructor
-..class:Spec.Edge Iterator
-..signature:Iter()
-..signature:Iter(graph)
-..signature:Iter(iter)
-..param.graph:The graph to iterate edges of.
-...type:Class.Graph
-..param.iter:Other iterator to copy-construct from.
-...type:Spec.Edge Iterator
-*/
-
 template<typename TGraph, typename TSpec>
-class Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > > 
+class Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >
 {
 public:
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator_;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator_;
-	TVertexIterator_ data_vertex_it;
-	TOutEdgeIterator_ data_edge_it;
-	TVertexDescriptor_ data_first_slot;
-
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph const& _graph) : 
-		data_vertex_it(_graph),
-		data_edge_it(_graph, getIdLowerBound(_getVertexIdManager(_graph)))  
-	{
-		SEQAN_CHECKPOINT
-		while((atEnd(data_edge_it)) && (!atEnd(data_vertex_it))) 
-		{
-				goNext(data_vertex_it);
-				typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator_;
-				if(!atEnd(data_vertex_it))
-					data_edge_it = TOutEdgeIterator_(hostGraph(*this), value(data_vertex_it));			
-		}
-		data_first_slot = value(data_vertex_it);
-	}
-
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter(Iter const& _iter) : 
-		data_vertex_it(_iter.data_vertex_it),
-		data_edge_it(_iter.data_edge_it),
-		data_first_slot(_iter.data_first_slot)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_vertex_it = _other.data_vertex_it;
-		data_edge_it = _other.data_edge_it;
-		data_first_slot = _other.data_first_slot;
-		return *this;
-	}
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator_;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator_;
+    TVertexIterator_ data_vertex_it;
+    TOutEdgeIterator_ data_edge_it;
+    TVertexDescriptor_ data_first_slot;
+
+
+    Iter() : data_vertex_it(), data_edge_it(), data_first_slot()
+    {}
+
+    Iter(TGraph const& _graph) :
+        data_vertex_it(_graph),
+        data_edge_it(_graph, getIdLowerBound(_getVertexIdManager(_graph)))  ,
+        data_first_slot()
+    {
+        while((atEnd(data_edge_it)) && (!atEnd(data_vertex_it)))
+        {
+                goNext(data_vertex_it);
+                typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator_;
+                if(!atEnd(data_vertex_it))
+                    data_edge_it = TOutEdgeIterator_(hostGraph(*this), value(data_vertex_it));
+        }
+        data_first_slot = value(data_vertex_it);
+    }
+
+    Iter(Iter const& _iter) :
+        data_vertex_it(_iter.data_vertex_it),
+        data_edge_it(_iter.data_edge_it),
+        data_first_slot(_iter.data_first_slot)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_vertex_it = _other.data_vertex_it;
+        data_edge_it = _other.data_edge_it;
+        data_first_slot = _other.data_first_slot;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -158,14 +126,14 @@ class Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >
 
 template<typename TGraph>
 struct Iterator<TGraph, EdgeIterator>
-{	
-	typedef Iter<TGraph, GraphIterator<InternalEdgeIterator<EdgeIterator> > > Type;
+{
+    typedef Iter<TGraph, GraphIterator<InternalEdgeIterator<EdgeIterator> > > Type;
 };
 
 template<typename TGraph>
 struct Iterator<TGraph const, EdgeIterator>
-{	
-	typedef Iter<TGraph const, GraphIterator<InternalEdgeIterator<EdgeIterator> > > Type;
+{
+    typedef Iter<TGraph const, GraphIterator<InternalEdgeIterator<EdgeIterator> > > Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -173,13 +141,13 @@ struct Iterator<TGraph const, EdgeIterator>
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph, GraphIterator<InternalEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph const, GraphIterator<InternalEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -187,13 +155,13 @@ struct Value<Iter<TGraph const, GraphIterator<InternalEdgeIterator<TIteratorSpec
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph, GraphIterator<InternalEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename Reference<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Reference<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph const, GraphIterator<InternalEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename Reference<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Reference<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -201,13 +169,13 @@ struct Reference<Iter<TGraph const, GraphIterator<InternalEdgeIterator<TIterator
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph, GraphIterator<InternalEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename GetValue<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename GetValue<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph const, GraphIterator<InternalEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename GetValue<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename GetValue<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -215,13 +183,13 @@ struct GetValue<Iter<TGraph const, GraphIterator<InternalEdgeIterator<TIteratorS
 template<typename TGraph, typename TIteratorSpec>
 struct Spec<Iter<TGraph, GraphIterator<InternalEdgeIterator<TIteratorSpec> > > >
 {
-	typedef TIteratorSpec Type;
+    typedef TIteratorSpec Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Spec<Iter<TGraph const, GraphIterator<InternalEdgeIterator<TIteratorSpec> > > >
 {
-	typedef TIteratorSpec Type;
+    typedef TIteratorSpec Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -235,7 +203,7 @@ inline typename GetValue<Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec>
 getValue(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	return getValue(it.data_edge_it);
+    return getValue(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -245,7 +213,7 @@ inline typename Reference<Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec>
 value(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	return value(it.data_edge_it);
+    return value(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -254,8 +222,8 @@ template<typename TGraph, typename TSpec>
 inline typename Reference<Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > > >::Type
 operator * (Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return value(it);
+    SEQAN_CHECKPOINT
+    return value(it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -264,9 +232,9 @@ template<typename TGraph, typename TSpec>
 inline typename Host<Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > > >::Type const&
 hostGraph(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return hostGraph(it.data_vertex_it);
-} 
+    SEQAN_CHECKPOINT
+    return hostGraph(it.data_vertex_it);
+}
 
 //////////////////////////////////////////////////////////////////////////////
 
@@ -274,9 +242,9 @@ template<typename TGraph, typename TSpec>
 inline bool
 atBegin(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return ((it.data_first_slot == getValue(it.data_vertex_it)) &&
-			atBegin(it.data_edge_it));
+    SEQAN_CHECKPOINT
+    return ((it.data_first_slot == getValue(it.data_vertex_it)) &&
+            atBegin(it.data_edge_it));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -285,11 +253,11 @@ template<typename TGraph, typename TSpec>
 inline void
 goBegin(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	goBegin(it.data_vertex_it);
-	while (it.data_first_slot != getValue(it.data_vertex_it)) ++it.data_vertex_it;
-	it.data_edge_it = TOutEdgeIterator(hostGraph(it), getValue(it.data_vertex_it));	
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    goBegin(it.data_vertex_it);
+    while (it.data_first_slot != getValue(it.data_vertex_it)) ++it.data_vertex_it;
+    it.data_edge_it = TOutEdgeIterator(hostGraph(it), getValue(it.data_vertex_it));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -298,8 +266,8 @@ template<typename TGraph, typename TSpec>
 inline bool
 atEnd(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return atEnd(it.data_vertex_it);
+    SEQAN_CHECKPOINT
+    return atEnd(it.data_vertex_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -308,9 +276,9 @@ template<typename TGraph, typename TSpec>
 inline void
 goEnd(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	goEnd(it.data_edge_it);
-	goEnd(it.data_vertex_it);
+    SEQAN_CHECKPOINT
+    goEnd(it.data_edge_it);
+    goEnd(it.data_vertex_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -319,20 +287,20 @@ template<typename TGraph, typename TSpec>
 inline void
 _goNextInternal(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atEnd(it)) {
-		goNext(it.data_edge_it);
-		if(!atEnd(it.data_edge_it)) return;
-		else {
-			while ((atEnd(it.data_edge_it)) && (!atEnd(it.data_vertex_it))) {
-				goNext(it.data_vertex_it);
-				if ((atEnd(it.data_vertex_it)) ||
-					(!idInUse(_getVertexIdManager(hostGraph(it)), getValue(it.data_vertex_it)))) continue;
-				typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-				it.data_edge_it = TOutEdgeIterator(hostGraph(it), getValue(it.data_vertex_it));			
-			}
-		}
-	}
+    SEQAN_CHECKPOINT
+    if (!atEnd(it)) {
+        goNext(it.data_edge_it);
+        if(!atEnd(it.data_edge_it)) return;
+        else {
+            while ((atEnd(it.data_edge_it)) && (!atEnd(it.data_vertex_it))) {
+                goNext(it.data_vertex_it);
+                if ((atEnd(it.data_vertex_it)) ||
+                    (!idInUse(_getVertexIdManager(hostGraph(it)), getValue(it.data_vertex_it)))) continue;
+                typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+                it.data_edge_it = TOutEdgeIterator(hostGraph(it), getValue(it.data_vertex_it));
+            }
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -341,8 +309,8 @@ template<typename TGraph, typename TSpec>
 inline void
 goNext(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	_goNextInternal(it);
+    SEQAN_CHECKPOINT
+    _goNextInternal(it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -351,14 +319,14 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goNext(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	_goNextInternal(it);
-	TVertexDescriptor sourceV = sourceVertex(it.data_edge_it);
-	while((!atEnd(it)) && (targetVertex(hostGraph(it), getValue(it.data_edge_it)) == sourceV)) {
-		_goNextInternal(it);
-		sourceV = sourceVertex(it.data_edge_it);
-	}
+    typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    _goNextInternal(it);
+    TVertexDescriptor sourceV = sourceVertex(it.data_edge_it);
+    while((!atEnd(it)) && (targetVertex(hostGraph(it), getValue(it.data_edge_it)) == sourceV)) {
+        _goNextInternal(it);
+        sourceV = sourceVertex(it.data_edge_it);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -367,9 +335,9 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >&
 operator ++(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	goNext(it);
-	return it;
+    SEQAN_CHECKPOINT
+    goNext(it);
+    return it;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -378,10 +346,10 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >
 operator ++(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > > ret = it;
-	goNext(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > > ret = it;
+    goNext(it);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -390,24 +358,24 @@ template<typename TGraph, typename TSpec>
 inline void
 _goPreviousInternal(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atBegin(it)) {
-		if ((atEnd(it)) ||
-			(atBegin(it.data_edge_it))) 
-		{
-			--it.data_vertex_it;
-			typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-			it.data_edge_it = TOutEdgeIterator(hostGraph(it), getValue(it.data_vertex_it));
-			while((!atBegin(it.data_vertex_it)) && 
-					(atEnd(it.data_edge_it))) {
-				--it.data_vertex_it;
-				typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-				it.data_edge_it = TOutEdgeIterator(hostGraph(it), getValue(it.data_vertex_it));			
-			}
-			goEnd(it.data_edge_it);
-		}
-		--it.data_edge_it;
-	}
+    SEQAN_CHECKPOINT
+    if (!atBegin(it)) {
+        if ((atEnd(it)) ||
+            (atBegin(it.data_edge_it)))
+        {
+            --it.data_vertex_it;
+            typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+            it.data_edge_it = TOutEdgeIterator(hostGraph(it), getValue(it.data_vertex_it));
+            while((!atBegin(it.data_vertex_it)) &&
+                    (atEnd(it.data_edge_it))) {
+                --it.data_vertex_it;
+                typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+                it.data_edge_it = TOutEdgeIterator(hostGraph(it), getValue(it.data_vertex_it));
+            }
+            goEnd(it.data_edge_it);
+        }
+        --it.data_edge_it;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -416,8 +384,8 @@ template<typename TGraph, typename TSpec>
 inline void
 goPrevious(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	_goPreviousInternal(it);
+    SEQAN_CHECKPOINT
+    _goPreviousInternal(it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -426,14 +394,14 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goPrevious(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	_goPreviousInternal(it);
-	TVertexDescriptor sourceV = sourceVertex(it.data_edge_it);
-	while((!atBegin(it)) && (targetVertex(hostGraph(it), getValue(it.data_edge_it)) == sourceV)) {
-		_goPreviousInternal(it);
-		sourceV = sourceVertex(it.data_edge_it);
-	}
+    typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    _goPreviousInternal(it);
+    TVertexDescriptor sourceV = sourceVertex(it.data_edge_it);
+    while((!atBegin(it)) && (targetVertex(hostGraph(it), getValue(it.data_edge_it)) == sourceV)) {
+        _goPreviousInternal(it);
+        sourceV = sourceVertex(it.data_edge_it);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -443,8 +411,8 @@ inline Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >&
 operator --(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	goPrevious(it);
-	return it;
+    goPrevious(it);
+    return it;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -453,10 +421,10 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >
 operator --(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > > ret = it;
-	goPrevious(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > > ret = it;
+    goPrevious(it);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -464,11 +432,11 @@ operator --(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it, int)
 template<typename TGraph, typename TSpec>
 inline bool
 operator ==(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it2)
 {
 SEQAN_CHECKPOINT
-	return ((it1.data_vertex_it==it2.data_vertex_it) && 
-			(it1.data_edge_it==it2.data_edge_it));
+    return ((it1.data_vertex_it==it2.data_vertex_it) &&
+            (it1.data_edge_it==it2.data_edge_it));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -476,31 +444,31 @@ SEQAN_CHECKPOINT
 template<typename TGraph, typename TSpec>
 inline bool
 operator !=(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it2)
 {
 SEQAN_CHECKPOINT
-	return ((it1.data_vertex_it!=it2.data_vertex_it) || 
-			(it1.data_edge_it!=it2.data_edge_it));
+    return ((it1.data_vertex_it!=it2.data_vertex_it) ||
+            (it1.data_edge_it!=it2.data_edge_it));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TGraph, typename TSpec>
-inline typename VertexDescriptor<TGraph>::Type 
+inline typename VertexDescriptor<TGraph>::Type
 sourceVertex(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return sourceVertex(it.data_edge_it);
+    SEQAN_CHECKPOINT
+    return sourceVertex(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TGraph, typename TSpec>
-inline typename VertexDescriptor<TGraph>::Type 
+inline typename VertexDescriptor<TGraph>::Type
 targetVertex(Iter<TGraph, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return targetVertex(it.data_edge_it);
+    SEQAN_CHECKPOINT
+    return targetVertex(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -509,7 +477,7 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline typename Alphabet<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > >::Type
 label(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalEdgeIterator<TSpec> > >& it)
 {
-	return label(it.data_edge_it);
+    return label(it.data_edge_it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/graph_types/graph_iterator_outedge.h b/seqan/graph_types/graph_iterator_outedge.h
index 4e53187..e87144a 100644
--- a/seqan/graph_types/graph_iterator_outedge.h
+++ b/seqan/graph_types/graph_iterator_outedge.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -69,84 +69,55 @@ namespace SEQAN_NAMESPACE_MAIN
  * @param[in] v     The descriptor of the vertex to iterate out edges of.
  */
 
-/**
-.Spec.Out-Edge Iterator:
-..cat:Graph
-..summary:Out-edge iterator for @Class.Graph@.
-..signature:Iterator<TGraph, OutEdgeIterator>
-..param.TGraph:A graph.
-...type:Class.Graph
-..general:Class.Iter
-..see:Spec.Vertex Iterator
-..see:Spec.Edge Iterator
-..see:Spec.Adjacency Iterator
-..see:Spec.Bfs Iterator
-..see:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-
-.Memfunc.Out-Edge Iterator#Iter
-..summary:Constructor
-..class:Spec.Out-Edge Iterator
-..signature:Iter()
-..signature:Iter(graph, v)
-..signature:Iter(iter)
-..param.graph:The graph to iterate edges of.
-...type:Class.Graph
-..param.v:Vertex descriptor of vertex to iterate out-edges from.
-...type:Metafunction.VertexDescriptor
-..param.iter:Other iterator to copy-construct from.
-...type:Spec.Out-Edge Iterator
-*/
-
 
 //////////////////////////////////////////////////////////////////////////////
 // InternalOutEdgeIterator for Directed Graph
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TGraphSpec, typename TSpec>
-class Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > 
+class Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >
 {
 public:
-	typedef Graph<Directed<TCargo, TGraphSpec> > TGraph_;
-	typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
-	typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;
-	TGraph_ const* data_host;
-	TVertexDescriptor_ data_source;
-	TEdgeDescriptor_ data_edge;
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) : 
-		data_host(&_graph),
-		data_source(v),
-		data_edge(getValue(_graph.data_vertex,v))
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(Iter const& _iter) : 
-		data_host(_iter.data_host),
-		data_source(_iter.data_source),
-		data_edge(_iter.data_edge)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host = _other.data_host;
-		data_source = _other.data_source;
-		data_edge = _other.data_edge;
-		return *this;
-	}
+    typedef Graph<Directed<TCargo, TGraphSpec> > TGraph_;
+    typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
+    typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;
+    TGraph_ const* data_host;
+    TVertexDescriptor_ data_source;
+    TEdgeDescriptor_ data_edge;
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) :
+        data_host(&_graph),
+        data_source(v),
+        data_edge(getValue(_graph.data_vertex,v))
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_source(_iter.data_source),
+        data_edge(_iter.data_edge)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    ~Iter() {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host = _other.data_host;
+        data_source = _other.data_source;
+        data_edge = _other.data_edge;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -158,8 +129,8 @@ class Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIt
 
 template<typename TCargo, typename TGraphSpec>
 struct Iterator<Graph<Directed<TCargo, TGraphSpec> >, OutEdgeIterator>
-{	
-	typedef Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
+{
+    typedef Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
 };
 
 template<typename TCargo, typename TGraphSpec>
@@ -172,49 +143,49 @@ struct Iterator<Graph<Directed<TCargo, TGraphSpec> > const, OutEdgeIterator> :
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TGraphSpec, typename TSpec>
-class Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > 
+class Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >
 {
 public:
-	typedef Graph<Tree<TCargo, TGraphSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TGraph const* data_host;
-	TVertexDescriptor data_source;
-	TEdgeDescriptor data_edge;
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-	
+    typedef Graph<Tree<TCargo, TGraphSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TGraph const* data_host;
+    TVertexDescriptor data_source;
+    TEdgeDescriptor data_edge;
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
     Iter(TGraph const& _graph, TVertexDescriptor const v) :
-		data_host(&_graph),
-		data_source(v),
-		data_edge(getValue(_graph.data_vertex,v))
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(Iter const& _iter) :
-		data_host(_iter.data_host),
-		data_source(_iter.data_source),
-		data_edge(_iter.data_edge)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host = _other.data_host;
-		data_source = _other.data_source;
-		data_edge = _other.data_edge;
-		return *this;
-	}
+        data_host(&_graph),
+        data_source(v),
+        data_edge(getValue(_graph.data_vertex,v))
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_source(_iter.data_source),
+        data_edge(_iter.data_edge)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    ~Iter() {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host = _other.data_host;
+        data_source = _other.data_source;
+        data_edge = _other.data_edge;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -226,8 +197,8 @@ class Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterat
 
 template<typename TCargo, typename TGraphSpec>
 struct Iterator<Graph<Tree<TCargo, TGraphSpec> >, OutEdgeIterator>
-{	
-	typedef Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
+{
+    typedef Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
 };
 
 template<typename TCargo, typename TGraphSpec>
@@ -240,49 +211,49 @@ struct Iterator<Graph<Tree<TCargo, TGraphSpec> > const, OutEdgeIterator> :
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TGraphSpec, typename TSpec>
-class Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > 
+class Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >
 {
 public:
-	typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
-	typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TGraph const* data_host;
-	TVertexDescriptor data_source;
-	TEdgeDescriptor data_edge;
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph const& _graph, TVertexDescriptor const v) : 
-		data_host(&_graph),
-		data_source(v),
-		data_edge(getValue(_graph.data_vertex,v))
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(Iter const& _iter) : 
-		data_host(_iter.data_host),
-		data_source(_iter.data_source),
-		data_edge(_iter.data_edge)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host = _other.data_host;
-		data_source = _other.data_source;
-		data_edge = _other.data_edge;
-		return *this;
-	}
+    typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
+    typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TGraph const* data_host;
+    TVertexDescriptor data_source;
+    TEdgeDescriptor data_edge;
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph const& _graph, TVertexDescriptor const v) :
+        data_host(&_graph),
+        data_source(v),
+        data_edge(getValue(_graph.data_vertex,v))
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_source(_iter.data_source),
+        data_edge(_iter.data_edge)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    ~Iter() {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host = _other.data_host;
+        data_source = _other.data_source;
+        data_edge = _other.data_edge;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -294,8 +265,8 @@ class Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdge
 
 template<typename TCargo, typename TGraphSpec>
 struct Iterator<Graph<Undirected<TCargo, TGraphSpec> >, OutEdgeIterator>
-{	
-	typedef Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
+{
+    typedef Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
 };
 
 template<typename TCargo,typename TGraphSpec>
@@ -309,68 +280,68 @@ struct Iterator<Graph<Undirected<TCargo, TGraphSpec> > const, OutEdgeIterator> :
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TIteratorSpec>
-class Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > 
+class Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > >
 {
 public:
-	typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph_;
-	typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
-	typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;
-	typedef typename Size<TAlphabet>::Type TSize_;
-	TGraph_ const* data_host;
-	TVertexDescriptor_ data_source;
-	TSize_ data_pos;
-	TSize_ data_begin;
-	TSize_ data_end;
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) : 
-		data_host(&_graph),
-		data_source(v)
-	{
-		SEQAN_CHECKPOINT
-		TVertexDescriptor_ nilVal = getNil<TVertexDescriptor_>();
-		TSize_ table_length = ValueSize<TAlphabet>::VALUE;
-		TSize_ pos = 0;
-		while (	(pos < table_length) &&
-				(_graph.data_vertex[v].data_edge[pos].data_target == nilVal))
-		{
-				++pos;
-		}
-		data_pos = pos;
-		data_begin = pos;
-		data_end = table_length;
-	}
-
-	Iter(Iter const& _iter) : 
-		data_host(_iter.data_host),
-		data_source(_iter.data_source),
-		data_pos(_iter.data_pos),
-		data_begin(_iter.data_begin),
-		data_end(_iter.data_end)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	~Iter() 
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) 
-	{
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host = _other.data_host;
-		data_source = _other.data_source;
-		data_pos = _other.data_pos;
-		data_begin = _other.data_begin;
-		data_end = _other.data_end;
-		return *this;
-	}
+    typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph_;
+    typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
+    typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;
+    typedef typename Size<TAlphabet>::Type TSize_;
+    TGraph_ const* data_host;
+    TVertexDescriptor_ data_source;
+    TSize_ data_pos;
+    TSize_ data_begin;
+    TSize_ data_end;
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) :
+        data_host(&_graph),
+        data_source(v)
+    {
+        SEQAN_CHECKPOINT
+        TVertexDescriptor_ nilVal = getNil<TVertexDescriptor_>();
+        TSize_ table_length = ValueSize<TAlphabet>::VALUE;
+        TSize_ pos = 0;
+        while (    (pos < table_length) &&
+                (_graph.data_vertex[v].data_edge[pos].data_target == nilVal))
+        {
+                ++pos;
+        }
+        data_pos = pos;
+        data_begin = pos;
+        data_end = table_length;
+    }
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_source(_iter.data_source),
+        data_pos(_iter.data_pos),
+        data_begin(_iter.data_begin),
+        data_end(_iter.data_end)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    ~Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other)
+    {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host = _other.data_host;
+        data_source = _other.data_source;
+        data_pos = _other.data_pos;
+        data_begin = _other.data_begin;
+        data_end = _other.data_end;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -383,8 +354,8 @@ class Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<Inter
 
 template<typename TAlphabet, typename TCargo, typename TGraphSpec>
 struct Iterator<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, OutEdgeIterator>
-{	
-	typedef Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
+{
+    typedef Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
 };
 
 template<typename TAlphabet, typename TCargo, typename TGraphSpec>
@@ -397,49 +368,49 @@ struct Iterator<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > const, OutEdgeI
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpec>
-class Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > 
+class Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >
 {
 public:
-	typedef Graph<Hmm<TAlphabet, TCargo, TGraphSpec> > TGraph_;
-	typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
-	typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;
-	TGraph_ const* data_host;
-	TVertexDescriptor_ data_source;
-	TEdgeDescriptor_ data_edge;
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) : 
-		data_host(&_graph),
-		data_source(v),
-		data_edge(getValue(_graph.data_model.data_vertex,v))
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(Iter const& _iter) : 
-		data_host(_iter.data_host),
-		data_source(_iter.data_source),
-		data_edge(_iter.data_edge)
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host = _other.data_host;
-		data_source = _other.data_source;
-		data_edge = _other.data_edge;
-		return *this;
-	}
+    typedef Graph<Hmm<TAlphabet, TCargo, TGraphSpec> > TGraph_;
+    typedef typename EdgeDescriptor<TGraph_>::Type TEdgeDescriptor_;
+    typedef typename VertexDescriptor<TGraph_>::Type TVertexDescriptor_;
+    TGraph_ const* data_host;
+    TVertexDescriptor_ data_source;
+    TEdgeDescriptor_ data_edge;
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph_ const& _graph, TVertexDescriptor_ const v) :
+        data_host(&_graph),
+        data_source(v),
+        data_edge(getValue(_graph.data_model.data_vertex,v))
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_source(_iter.data_source),
+        data_edge(_iter.data_edge)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    ~Iter() {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host = _other.data_host;
+        data_source = _other.data_source;
+        data_edge = _other.data_edge;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -451,8 +422,8 @@ class Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOut
 
 template<typename TAlphabet, typename TCargo, typename TGraphSpec>
 struct Iterator<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, OutEdgeIterator>
-{	
-	typedef Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
+{
+    typedef Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > Type;
 };
 
 template<typename TAlphabet, typename TCargo, typename TGraphSpec>
@@ -469,13 +440,13 @@ struct Iterator<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> > const, OutEdgeIterato
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename EdgeDescriptor<TGraph>::Type Type;
+    typedef typename EdgeDescriptor<TGraph>::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename EdgeDescriptor<TGraph const>::Type Type;
+    typedef typename EdgeDescriptor<TGraph const>::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -483,13 +454,13 @@ struct Value<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorS
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -497,13 +468,13 @@ struct Reference<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TItera
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -511,13 +482,13 @@ struct GetValue<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIterat
 template<typename TGraph, typename TIteratorSpec>
 struct Spec<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >
 {
-	typedef TIteratorSpec Type;
+    typedef TIteratorSpec Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Spec<Iter<TGraph const, GraphIterator<InternalOutEdgeIterator<TIteratorSpec> > > >
 {
-	typedef TIteratorSpec Type;
+    typedef TIteratorSpec Type;
 };
 
 
@@ -532,8 +503,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline typename GetValue<Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 getValue(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -542,8 +513,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline typename GetValue<Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 getValue(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -552,8 +523,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline typename GetValue<Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 getValue(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -562,8 +533,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline typename GetValue<Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 getValue(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -572,10 +543,10 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline typename GetValue<Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 getValue(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph;
-	TGraph * g = const_cast<TGraph*>(it.data_host);
-	return (&g->data_vertex[it.data_source].data_edge[it.data_pos]);
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph;
+    TGraph * g = const_cast<TGraph*>(it.data_host);
+    return (&g->data_vertex[it.data_source].data_edge[it.data_pos]);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -584,8 +555,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline typename Reference<Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 value(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 
@@ -595,8 +566,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline typename Reference<Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 value(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -605,8 +576,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline typename Reference<Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 value(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 
@@ -616,8 +587,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline typename Reference<Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 value(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_edge;
+    SEQAN_CHECKPOINT
+    return it.data_edge;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -626,10 +597,10 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline typename Reference<Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 value(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph;
-	TGraph * g = const_cast<TGraph*>(it.data_host);
-	return (&g->data_vertex[it.data_source].data_edge[it.data_pos]);
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph;
+    TGraph * g = const_cast<TGraph*>(it.data_host);
+    return (&g->data_vertex[it.data_source].data_edge[it.data_pos]);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -638,8 +609,8 @@ template<typename TGraph, typename TSpec>
 inline typename Reference<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type
 operator * (Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return value(it);
+    SEQAN_CHECKPOINT
+    return value(it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -648,8 +619,8 @@ template<typename TGraph, typename TSpec>
 inline typename Host<Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > > >::Type const&
 hostGraph(Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return *it.data_host;
+    SEQAN_CHECKPOINT
+    return *it.data_host;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -658,8 +629,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 atBegin(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == getValue(it.data_host->data_vertex, it.data_source));
+    SEQAN_CHECKPOINT
+    return (it.data_edge == getValue(it.data_host->data_vertex, it.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -668,8 +639,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline bool
 atBegin(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == getValue(it.data_host->data_model.data_vertex, it.data_source));
+    SEQAN_CHECKPOINT
+    return (it.data_edge == getValue(it.data_host->data_model.data_vertex, it.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -678,8 +649,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 atBegin(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == getValue(it.data_host->data_vertex, it.data_source));
+    SEQAN_CHECKPOINT
+    return (it.data_edge == getValue(it.data_host->data_vertex, it.data_source));
 }
 
 
@@ -689,8 +660,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 atBegin(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == getValue(it.data_host->data_vertex, it.data_source));
+    SEQAN_CHECKPOINT
+    return (it.data_edge == getValue(it.data_host->data_vertex, it.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -699,8 +670,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline bool
 atBegin(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_begin == it.data_pos);
+    SEQAN_CHECKPOINT
+    return (it.data_begin == it.data_pos);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -709,8 +680,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goBegin(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = getValue(it.data_host->data_vertex,it.data_source);
+    SEQAN_CHECKPOINT
+    it.data_edge = getValue(it.data_host->data_vertex,it.data_source);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -719,8 +690,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline void
 goBegin(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = getValue(it.data_host->data_model.data_vertex,it.data_source);
+    SEQAN_CHECKPOINT
+    it.data_edge = getValue(it.data_host->data_model.data_vertex,it.data_source);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -729,8 +700,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goBegin(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = getValue(it.data_host->data_vertex,it.data_source);
+    SEQAN_CHECKPOINT
+    it.data_edge = getValue(it.data_host->data_vertex,it.data_source);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -739,8 +710,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goBegin(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = getValue(it.data_host->data_vertex,it.data_source);
+    SEQAN_CHECKPOINT
+    it.data_edge = getValue(it.data_host->data_vertex,it.data_source);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -749,8 +720,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline void
 goBegin(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_pos = it.data_begin;
+    SEQAN_CHECKPOINT
+    it.data_pos = it.data_begin;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -759,8 +730,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 atEnd(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == 0);
+    SEQAN_CHECKPOINT
+    return (it.data_edge == 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -769,8 +740,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline bool
 atEnd(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == 0);
+    SEQAN_CHECKPOINT
+    return (it.data_edge == 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -779,8 +750,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 atEnd(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == 0);
+    SEQAN_CHECKPOINT
+    return (it.data_edge == 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -789,8 +760,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 atEnd(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_edge == 0);
+    SEQAN_CHECKPOINT
+    return (it.data_edge == 0);
 }
 
 /////////////////////////////////////////////////////////////////////////////
@@ -799,8 +770,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline bool
 atEnd(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return (it.data_end == it.data_pos);
+    SEQAN_CHECKPOINT
+    return (it.data_end == it.data_pos);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -809,8 +780,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goEnd(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = 0;
+    SEQAN_CHECKPOINT
+    it.data_edge = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -819,8 +790,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline void
 goEnd(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = 0;
+    SEQAN_CHECKPOINT
+    it.data_edge = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -829,8 +800,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goEnd(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = 0;
+    SEQAN_CHECKPOINT
+    it.data_edge = 0;
 }
 
 
@@ -840,8 +811,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goEnd(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_edge = 0;
+    SEQAN_CHECKPOINT
+    it.data_edge = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -850,8 +821,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline void
 goEnd(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_pos = it.data_end;
+    SEQAN_CHECKPOINT
+    it.data_pos = it.data_end;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -860,8 +831,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goNext(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atEnd(it)) it.data_edge = getNextT(it.data_edge);
+    SEQAN_CHECKPOINT
+    if (!atEnd(it)) it.data_edge = getNextT(it.data_edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -870,8 +841,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline void
 goNext(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atEnd(it)) it.data_edge = getNextT(it.data_edge);
+    SEQAN_CHECKPOINT
+    if (!atEnd(it)) it.data_edge = getNextT(it.data_edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -880,8 +851,8 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goNext(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atEnd(it)) it.data_edge = getNextT(it.data_edge);
+    SEQAN_CHECKPOINT
+    if (!atEnd(it)) it.data_edge = getNextT(it.data_edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -890,11 +861,11 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goNext(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atEnd(it)) {
-		if (it.data_source == getSource(it.data_edge)) it.data_edge = getNextS(it.data_edge);
-		else it.data_edge = getNextT(it.data_edge);
-	}
+    SEQAN_CHECKPOINT
+    if (!atEnd(it)) {
+        if (it.data_source == getSource(it.data_edge)) it.data_edge = getNextS(it.data_edge);
+        else it.data_edge = getNextT(it.data_edge);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -903,16 +874,16 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline void
 goNext(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	if (it.data_pos < it.data_end) ++it.data_pos;
-	while (	(it.data_pos < it.data_end) &&
-			(it.data_host->data_vertex[it.data_source].data_edge[it.data_pos].data_target == nilVal))
-	{
-				++it.data_pos;
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    if (it.data_pos < it.data_end) ++it.data_pos;
+    while (    (it.data_pos < it.data_end) &&
+            (it.data_host->data_vertex[it.data_source].data_edge[it.data_pos].data_target == nilVal))
+    {
+                ++it.data_pos;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -922,8 +893,8 @@ inline Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >&
 operator ++(Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	goNext(it);
-	return it;
+    goNext(it);
+    return it;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -932,10 +903,10 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >
 operator ++(Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > > ret = it;
-	goNext(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > > ret = it;
+    goNext(it);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -944,12 +915,12 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goPrevious(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef typename EdgeType<Graph<Directed<TCargo, TGraphSpec> > >::Type TEdge;
-	TEdge* current = getValue(it.data_host->data_vertex, it.data_source);
-	if (current == it.data_edge) return;
-	while ((current != 0) && (getNextT(current) != it.data_edge)) current = getNextT(current);
-	it.data_edge = current;
+    SEQAN_CHECKPOINT
+    typedef typename EdgeType<Graph<Directed<TCargo, TGraphSpec> > >::Type TEdge;
+    TEdge* current = getValue(it.data_host->data_vertex, it.data_source);
+    if (current == it.data_edge) return;
+    while ((current != 0) && (getNextT(current) != it.data_edge)) current = getNextT(current);
+    it.data_edge = current;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -958,12 +929,12 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline void
 goPrevious(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef typename EdgeType<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> > >::Type TEdge;
-	TEdge* current = getValue(it.data_host->data_model.data_vertex, it.data_source);
-	if (current == it.data_edge) return;
-	while ((current != 0) && (getNextT(current) != it.data_edge)) current = getNextT(current);
-	it.data_edge = current;
+    SEQAN_CHECKPOINT
+    typedef typename EdgeType<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> > >::Type TEdge;
+    TEdge* current = getValue(it.data_host->data_model.data_vertex, it.data_source);
+    if (current == it.data_edge) return;
+    while ((current != 0) && (getNextT(current) != it.data_edge)) current = getNextT(current);
+    it.data_edge = current;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -972,12 +943,12 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goPrevious(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef typename EdgeType<Graph<Tree<TCargo, TGraphSpec> > >::Type TEdge;
-	TEdge* current = getValue(it.data_host->data_vertex, it.data_source);
-	if (current == it.data_edge) return;
-	while ((current != 0) && (getNextT(current) != it.data_edge)) current = getNextT(current);
-	it.data_edge = current;
+    SEQAN_CHECKPOINT
+    typedef typename EdgeType<Graph<Tree<TCargo, TGraphSpec> > >::Type TEdge;
+    TEdge* current = getValue(it.data_host->data_vertex, it.data_source);
+    if (current == it.data_edge) return;
+    while ((current != 0) && (getNextT(current) != it.data_edge)) current = getNextT(current);
+    it.data_edge = current;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -986,21 +957,21 @@ template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline void
 goPrevious(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
-	typedef typename EdgeType<TGraph>::Type TEdge;
-	TEdge* current = getValue(it.data_host->data_vertex, it.data_source);
-	if (current == it.data_edge) return;
-	while (current != 0) {
-		if (it.data_source == getSource(current)) {
-			if (it.data_edge == getNextS(current)) break;
-			else current = getNextS(current);
-		} else {
-			if (it.data_edge == getNextT(current)) break;
-			else current = getNextT(current);
-		}
-	}
-	it.data_edge = current;
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
+    typedef typename EdgeType<TGraph>::Type TEdge;
+    TEdge* current = getValue(it.data_host->data_vertex, it.data_source);
+    if (current == it.data_edge) return;
+    while (current != 0) {
+        if (it.data_source == getSource(current)) {
+            if (it.data_edge == getNextS(current)) break;
+            else current = getNextS(current);
+        } else {
+            if (it.data_edge == getNextT(current)) break;
+            else current = getNextT(current);
+        }
+    }
+    it.data_edge = current;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1009,16 +980,16 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline void
 goPrevious(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
-	if (it.data_pos != it.data_begin) --it.data_pos;
-	while (	(it.data_pos != it.data_begin) &&
-			(it.data_host->data_vertex[it.data_source].data_edge[it.data_pos].data_target == nilVal))
-	{
-				--it.data_pos;
-	}
+    SEQAN_CHECKPOINT
+    typedef Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
+    if (it.data_pos != it.data_begin) --it.data_pos;
+    while (    (it.data_pos != it.data_begin) &&
+            (it.data_host->data_vertex[it.data_source].data_edge[it.data_pos].data_target == nilVal))
+    {
+                --it.data_pos;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1027,9 +998,9 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >&
 operator --(Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	goPrevious(it);
-	return it;
+    SEQAN_CHECKPOINT
+    goPrevious(it);
+    return it;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1038,10 +1009,10 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >
 operator --(Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > > ret = it;
-	goPrevious(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > > ret = it;
+    goPrevious(it);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1049,11 +1020,11 @@ operator --(Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it, i
 template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator ==(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge==it2.data_edge) && 
-			(it1.data_source==it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge==it2.data_edge) &&
+            (it1.data_source==it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1061,11 +1032,11 @@ operator ==(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOut
 template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator ==(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge==it2.data_edge) && 
-			(it1.data_source==it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge==it2.data_edge) &&
+            (it1.data_source==it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1073,11 +1044,11 @@ operator ==(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<Inter
 template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator ==(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge==it2.data_edge) && 
-			(it1.data_source==it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge==it2.data_edge) &&
+            (it1.data_source==it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1085,11 +1056,11 @@ operator ==(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdge
 template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator ==(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge==it2.data_edge) && 
-			(it1.data_source==it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge==it2.data_edge) &&
+            (it1.data_source==it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1097,11 +1068,11 @@ operator ==(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalO
 template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator ==(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_pos==it2.data_pos) && 
-			(it1.data_source==it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_pos==it2.data_pos) &&
+            (it1.data_source==it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1109,11 +1080,11 @@ operator ==(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator
 template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator !=(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge!=it2.data_edge) || 
-			(it1.data_source!=it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge!=it2.data_edge) ||
+            (it1.data_source!=it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1121,11 +1092,11 @@ operator !=(Iter<Graph<Directed<TCargo, TGraphSpec> >, GraphIterator<InternalOut
 template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator !=(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge!=it2.data_edge) || 
-			(it1.data_source!=it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge!=it2.data_edge) ||
+            (it1.data_source!=it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1133,11 +1104,11 @@ operator !=(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<Inter
 template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator !=(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge!=it2.data_edge) || 
-			(it1.data_source!=it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge!=it2.data_edge) ||
+            (it1.data_source!=it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1145,11 +1116,11 @@ operator !=(Iter<Graph<Tree<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdge
 template<typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator !=(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_edge!=it2.data_edge) || 
-			(it1.data_source!=it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_edge!=it2.data_edge) ||
+            (it1.data_source!=it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1157,21 +1128,21 @@ operator !=(Iter<Graph<Undirected<TCargo, TGraphSpec> >, GraphIterator<InternalO
 template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpec>
 inline bool
 operator !=(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it1,
-			Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
+            Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return ((it1.data_pos!=it2.data_pos) || 
-			(it1.data_source!=it2.data_source));
+    SEQAN_CHECKPOINT
+    return ((it1.data_pos!=it2.data_pos) ||
+            (it1.data_source!=it2.data_source));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TGraph, typename TSpec>
-inline typename VertexDescriptor<TGraph>::Type 
+inline typename VertexDescriptor<TGraph>::Type
 sourceVertex(Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_source;
+    SEQAN_CHECKPOINT
+    return it.data_source;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1202,71 +1173,55 @@ sourceVertex(Iter<TGraph, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
  * @return TAlphabet The current label (Alphabe is the alphabet of the automaton).
  */
 
-/**
-.Function.Automaton#label
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..cat:Graph
-..summary:Returns the label of the out-edge this iterator points to (for automatons).
-..signature:label(it)
-..param.it:An out-edge iterator.
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-..returns:A label.
-...type:Metafunction.Alphabet.
-..remarks:The label function only works for out-edge iterators on automatons.
-..include:seqan/graph_types.h
-*/
-
 template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpec>
 inline typename Alphabet<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > >::Type
 label(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	return TAlphabet(it.data_pos);
+    return TAlphabet(it.data_pos);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TGraphSpec, typename TSpec>
-inline typename VertexDescriptor<Graph<Directed<TCargo, TGraphSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Directed<TCargo, TGraphSpec> > >::Type
 targetVertex(Iter<Graph<Directed<TCargo, TGraphSpec> > , GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return targetVertex(*it.data_host, it.data_edge);
+    SEQAN_CHECKPOINT
+    return targetVertex(*it.data_host, it.data_edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpec>
-inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> > >::Type
 targetVertex(Iter<Graph<Hmm<TAlphabet, TCargo, TGraphSpec> > , GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return targetVertex(*it.data_host, it.data_edge);
+    SEQAN_CHECKPOINT
+    return targetVertex(*it.data_host, it.data_edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TGraphSpec, typename TSpec>
-inline typename VertexDescriptor<Graph<Tree<TCargo, TGraphSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Tree<TCargo, TGraphSpec> > >::Type
 targetVertex(Iter<Graph<Tree<TCargo, TGraphSpec> > , GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return targetVertex(*it.data_host, it.data_edge);
+    SEQAN_CHECKPOINT
+    return targetVertex(*it.data_host, it.data_edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template<typename TCargo, typename TGraphSpec, typename TSpec>
-inline typename VertexDescriptor<Graph<Undirected<TCargo, TGraphSpec> > >::Type 
+inline typename VertexDescriptor<Graph<Undirected<TCargo, TGraphSpec> > >::Type
 targetVertex(Iter<Graph<Undirected<TCargo, TGraphSpec> > , GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	TVertexDescriptor target = targetVertex(*it.data_host, it.data_edge);
-	if (target != it.data_source) return target;
-	else return sourceVertex(*it.data_host, it.data_edge);
+    SEQAN_CHECKPOINT
+    typedef Graph<Undirected<TCargo, TGraphSpec> > TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    TVertexDescriptor target = targetVertex(*it.data_host, it.data_edge);
+    if (target != it.data_source) return target;
+    else return sourceVertex(*it.data_host, it.data_edge);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1275,8 +1230,8 @@ template<typename TAlphabet, typename TCargo, typename TGraphSpec, typename TSpe
 inline typename VertexDescriptor<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> > >::Type
 targetVertex(Iter<Graph<Automaton<TAlphabet, TCargo, TGraphSpec> >, GraphIterator<InternalOutEdgeIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return it.data_host->data_vertex[it.data_source].data_edge[it.data_pos].data_target;
+    SEQAN_CHECKPOINT
+    return it.data_host->data_vertex[it.data_source].data_edge[it.data_pos].data_target;
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_iterator_vertex.h b/seqan/graph_types/graph_iterator_vertex.h
index a23638f..3411d14 100644
--- a/seqan/graph_types/graph_iterator_vertex.h
+++ b/seqan/graph_types/graph_iterator_vertex.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -69,70 +69,44 @@ namespace SEQAN_NAMESPACE_MAIN
  * @param[in] graph The @link Graph @endlink to iterate vertices of.
  */
 
-/**
-.Spec.Vertex Iterator:
-..cat:Graph
-..summary:Vertex iterator for @Class.Graph@.
-..signature:Iterator<TGraph, VertexIterator>
-..param.TGraph:A graph.
-...type:Class.Graph
-..general:Class.Iter
-..see:Spec.Edge Iterator
-..see:Spec.Out-Edge Iterator
-..see:Spec.Adjacency Iterator
-..see:Spec.Bfs Iterator
-..see:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-
-.Memfunc.Vertex Iterator#Iter
-..summary:Constructor
-..class:Spec.Vertex Iterator
-..signature:Iter()
-..signature:Iter(graph)
-..signature:Iter(iter)
-..param.graph:The graph to iterate vertices of.
-...type:Class.Graph
-..param.iter:Other iterator to copy-construct from.
-...type:Spec.Vertex Iterator
-*/
 template<typename TGraph, typename TSpec>
-class Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > 
+class Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >
 {
 public:
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
-	TGraph const* data_host;
-	TVertexDescriptor_ data_pos;
-
-	Iter()	
-	{
-		SEQAN_CHECKPOINT
-	}
-	
-	Iter(TGraph const& _graph) : 
-		data_host(&_graph), 
-		data_pos(getIdLowerBound(_getVertexIdManager(*data_host))) 
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	Iter(Iter const& _iter) : 
-		data_host(_iter.data_host), 
-		data_pos(_iter.data_pos) 
-	{
-		SEQAN_CHECKPOINT
-	}
-
-	~Iter() {
-		SEQAN_CHECKPOINT
-	}
-
-	Iter const&	operator = (Iter const & _other) {
-		SEQAN_CHECKPOINT
-		if (this == &_other) return *this;
-		data_host = _other.data_host;
-		data_pos = _other.data_pos;
-		return *this;
-	}
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor_;
+    TGraph const* data_host;
+    TVertexDescriptor_ data_pos;
+
+    Iter()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(TGraph const& _graph) :
+        data_host(&_graph),
+        data_pos(getIdLowerBound(_getVertexIdManager(*data_host)))
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter(Iter const& _iter) :
+        data_host(_iter.data_host),
+        data_pos(_iter.data_pos)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    ~Iter() {
+        SEQAN_CHECKPOINT
+    }
+
+    Iter const&    operator = (Iter const & _other) {
+        SEQAN_CHECKPOINT
+        if (this == &_other) return *this;
+        data_host = _other.data_host;
+        data_pos = _other.data_pos;
+        return *this;
+    }
 //____________________________________________________________________________
 };
 
@@ -142,18 +116,16 @@ class Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Iterator.param.T.type:Class.Graph
-
 template<typename TGraph>
 struct Iterator<TGraph, VertexIterator>
-{	
-	typedef Iter<TGraph, GraphIterator<InternalVertexIterator<VertexIterator> > > Type;
+{
+    typedef Iter<TGraph, GraphIterator<InternalVertexIterator<VertexIterator> > > Type;
 };
 
 template<typename TGraph>
 struct Iterator<TGraph const, VertexIterator>
-{	
-	typedef Iter<TGraph const, GraphIterator<InternalVertexIterator<VertexIterator> > > Type;
+{
+    typedef Iter<TGraph const, GraphIterator<InternalVertexIterator<VertexIterator> > > Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -161,13 +133,13 @@ struct Iterator<TGraph const, VertexIterator>
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >
 {
-	typedef typename VertexDescriptor<TGraph>::Type Type;
+    typedef typename VertexDescriptor<TGraph>::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >
 {
-	typedef typename VertexDescriptor<TGraph const>::Type Type;
+    typedef typename VertexDescriptor<TGraph const>::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -175,13 +147,13 @@ struct Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSp
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type& Type;
+    typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type& Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Reference<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type& Type;
+    typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type& Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -189,13 +161,13 @@ struct Reference<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIterat
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct GetValue<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >
 {
-	typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
+    typedef typename Value<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -203,13 +175,13 @@ struct GetValue<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIterato
 template<typename TGraph, typename TIteratorSpec>
 struct Spec<Iter<TGraph, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >
 {
-	typedef TIteratorSpec Type;
+    typedef TIteratorSpec Type;
 };
 
 template<typename TGraph, typename TIteratorSpec>
 struct Spec<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpec> > > >
 {
-	typedef TIteratorSpec Type;
+    typedef TIteratorSpec Type;
 };
 
 
@@ -219,60 +191,22 @@ struct Spec<Iter<TGraph const, GraphIterator<InternalVertexIterator<TIteratorSpe
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.getValue
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..class:Spec.Bfs Iterator
-..class:Spec.Dfs Preorder Iterator
-..cat:Graph
-..param.object
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-...type:Spec.Bfs Iterator
-...type:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-*/
-
 template<typename TGraph, typename TSpec>
 inline typename GetValue<Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > >::Type
 getValue(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	return it.data_pos;
+    return it.data_pos;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.value:
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..class:Spec.Bfs Iterator
-..class:Spec.Dfs Preorder Iterator
-..cat:Graph
-..param.object
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-...type:Spec.Bfs Iterator
-...type:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-*/
-
 template<typename TGraph, typename TSpec>
 inline typename Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > >::Type
 value(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	return it.data_pos;
+    return it.data_pos;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -281,189 +215,71 @@ template<typename TGraph, typename TSpec>
 inline typename Reference<Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > >::Type
 operator * (Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return value(it);
+    SEQAN_CHECKPOINT
+    return value(it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 // TODO(holtgrew): Add GraphIterator class that has hostGraph() function?
 
-/**
-.Function.hostGraph
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..class:Spec.Bfs Iterator
-..class:Spec.Dfs Preorder Iterator
-..cat:Graph
-..summary:The graph this iterator is working on.
-..signature:hostGraph(it)
-..param.it:A vertex or edge iterator.
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-...type:Spec.Bfs Iterator
-...type:Spec.Dfs Preorder Iterator
-..returns:A pointer to the host graph.
-..include:seqan/graph_types.h
-*/
-
 template<typename TGraph, typename TSpec>
 inline typename Host<Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > >::Type const&
 hostGraph(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	return *it.data_host;
-} 
+    SEQAN_CHECKPOINT
+    return *it.data_host;
+}
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.atBegin
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..class:Spec.Bfs Iterator
-..class:Spec.Dfs Preorder Iterator
-..cat:Graph
-..param.iterator
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-...type:Spec.Bfs Iterator
-...type:Spec.Dfs Preorder Iterator
-..see:Function.goBegin
-..include:seqan/graph_types.h
-*/
-
 template<typename TGraph, typename TSpec>
 inline bool
 atBegin(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	return (getValue(it) == getIdLowerBound(_getVertexIdManager(*it.data_host)));	
+    return (getValue(it) == getIdLowerBound(_getVertexIdManager(*it.data_host)));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.goBegin
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..class:Spec.Bfs Iterator
-..class:Spec.Dfs Preorder Iterator
-..cat:Graph
-..param.iterator
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-...type:Spec.Bfs Iterator
-...type:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-*/
-
 template<typename TGraph, typename TSpec>
 inline void
 goBegin(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_pos = getIdLowerBound(_getVertexIdManager(*it.data_host));
+    SEQAN_CHECKPOINT
+    it.data_pos = getIdLowerBound(_getVertexIdManager(*it.data_host));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.atEnd
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..class:Spec.Bfs Iterator
-..class:Spec.Dfs Preorder Iterator
-..cat:Graph
-..param.iterator
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-...type:Spec.Bfs Iterator
-...type:Spec.Dfs Preorder Iterator
-..see:Function.goEnd
-..include:seqan/graph_types.h
-*/
-
 template<typename TGraph, typename TSpec>
 inline bool
 atEnd(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	return (getValue(it) >= getIdUpperBound(_getVertexIdManager(*it.data_host)));	
+    return (getValue(it) >= getIdUpperBound(_getVertexIdManager(*it.data_host)));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.goEnd
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..class:Spec.Bfs Iterator
-..class:Spec.Dfs Preorder Iterator
-..cat:Graph
-..param.iterator
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-...type:Spec.Bfs Iterator
-...type:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-*/
 template<typename TGraph, typename TSpec>
 inline void
 goEnd(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	it.data_pos = getIdUpperBound(_getVertexIdManager(*it.data_host));
+    SEQAN_CHECKPOINT
+    it.data_pos = getIdUpperBound(_getVertexIdManager(*it.data_host));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.goNext
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..class:Spec.Bfs Iterator
-..class:Spec.Dfs Preorder Iterator
-..cat:Graph
-..param.iterator
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-...type:Spec.Bfs Iterator
-...type:Spec.Dfs Preorder Iterator
-..include:seqan/graph_types.h
-*/
-
 template<typename TGraph, typename TSpec>
 inline void
 goNext(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atEnd(it)) ++it.data_pos;
-	while ((!atEnd(it)) && (!idInUse(_getVertexIdManager(*it.data_host), it.data_pos))) ++it.data_pos;
+    SEQAN_CHECKPOINT
+    if (!atEnd(it)) ++it.data_pos;
+    while ((!atEnd(it)) && (!idInUse(_getVertexIdManager(*it.data_host), it.data_pos))) ++it.data_pos;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -473,8 +289,8 @@ inline Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >&
 operator ++(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	goNext(it);
-	return it;
+    goNext(it);
+    return it;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -483,36 +299,21 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >
 operator ++(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > ret = it;
-	goNext(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > ret = it;
+    goNext(it);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.goPrevious
-..class:Spec.Vertex Iterator
-..class:Spec.Out-Edge Iterator
-..class:Spec.Edge Iterator
-..class:Spec.Adjacency Iterator
-..cat:Graph
-..param.iterator
-...type:Spec.Vertex Iterator
-...type:Spec.Out-Edge Iterator
-...type:Spec.Edge Iterator
-...type:Spec.Adjacency Iterator
-..include:seqan/graph_types.h
-*/
-
 template<typename TGraph, typename TSpec>
 inline void
 goPrevious(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
-	SEQAN_CHECKPOINT
-	if (!atBegin(it)) --it.data_pos;
-	while ((!atBegin(it)) && (!idInUse(_getVertexIdManager(*it.data_host), it.data_pos))) --it.data_pos;
+    SEQAN_CHECKPOINT
+    if (!atBegin(it)) --it.data_pos;
+    while ((!atBegin(it)) && (!idInUse(_getVertexIdManager(*it.data_host), it.data_pos))) --it.data_pos;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -522,8 +323,8 @@ inline Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >&
 operator --(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it)
 {
 SEQAN_CHECKPOINT
-	goPrevious(it);
-	return it;
+    goPrevious(it);
+    return it;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -532,10 +333,10 @@ template<typename TGraph, typename TSpec>
 inline Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >
 operator --(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it, int)
 {
-	SEQAN_CHECKPOINT
-	Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > ret = it;
-	goPrevious(it);
-	return ret;
+    SEQAN_CHECKPOINT
+    Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > > ret = it;
+    goPrevious(it);
+    return ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -543,10 +344,10 @@ operator --(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it, in
 template<typename TGraph, typename TSpec>
 inline bool
 operator ==(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return (it1.data_pos==it2.data_pos);
+    SEQAN_CHECKPOINT
+    return (it1.data_pos==it2.data_pos);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -554,10 +355,10 @@ operator ==(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it1,
 template<typename TGraph, typename TSpec>
 inline bool
 operator !=(Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it1,
-			Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it2)
+            Iter<TGraph, GraphIterator<InternalVertexIterator<TSpec> > >& it2)
 {
-	SEQAN_CHECKPOINT
-	return (it1.data_pos!=it2.data_pos);
+    SEQAN_CHECKPOINT
+    return (it1.data_pos!=it2.data_pos);
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/graph_types/graph_property.h b/seqan/graph_types/graph_property.h
deleted file mode 100644
index 5479c35..0000000
--- a/seqan/graph_types/graph_property.h
+++ /dev/null
@@ -1,865 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_GRAPH_PROPERTY_H
-#define SEQAN_HEADER_GRAPH_PROPERTY_H
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-//	Graph - External property map
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Class.External Property Map
-..cat:Graph
-..summary:An external property map.
-..remarks:The external property map is assumed to be an instance of @Class.String@.
-It is indexed via VertexDescriptors or EdgeDescriptors.
-..signature:String<TValue, TSpec>
-..param.TValue:The value type. That is the type of information stored in the property map.
-...metafunction:Metafunction.Value
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:$Alloc<>$, see @Spec.Alloc String@.
-..include:seqan/graph_types.h
-*/
-
-
-//////////////////////////////////////////////////////////////////////////////
-// FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.resizeVertexMap
-..class:Class.Graph
-..cat:Graph
-..summary:Initializes a vertex map. 
-..signature:resizeVertexMap(g, pm [, prototype])
-..param.g:A Graph.
-...type:Class.Graph
-..param.pm:An External Property Map.
-...type:Class.External Property Map
-..param.prototype:An optional prototype that is used for initializing the property map.
-..returns:void
-..see:Function.resizeEdgeMap
-..include:seqan/graph_types.h
-*/
-
-template<typename TSpec, typename TPropertyMap>
-inline void
-resizeVertexMap(Graph<TSpec> const & g,
-                TPropertyMap & pm)
-{
-	SEQAN_CHECKPOINT;
-    typedef typename Value<TPropertyMap>::Type TValue;
-	resize(pm, getIdUpperBound(_getVertexIdManager(g)), TValue(), Generous());
-}
-
-template<typename TSpec, typename TPropertyMap, typename TPrototype>
-inline void
-resizeVertexMap(Graph<TSpec> const & g,
-                TPropertyMap & pm,
-                TPrototype const & prototype)
-{
-	SEQAN_CHECKPOINT;
-	resize(pm, getIdUpperBound(_getVertexIdManager(g)), prototype, Generous());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.resizeEdgeMap:
-..cat:Graph
-..summary:Initializes an edge map
-..signature:resizeEdgeMap(g, pm [, prototype])
-..param.g:A Graph.
-...type:Class.Graph
-..param.pm:An External or Internal Property Map.
-...type:Class.External Property Map
-...type:Class.InternalMap
-...type:Class.InternalPointerMap
-...type:Class.InternalRawMap
-..param.prototype:An optional prototype that is used for initializing the property map.
-..returns:void
-..see:Function.resizeVertexMap
-..include:seqan/graph_types.h
-*/
-
-template<typename TSpec, typename TPropertyMap>
-inline void
-resizeEdgeMap(Graph<TSpec> const & g,
-			  TPropertyMap & pm)
-{
-	SEQAN_CHECKPOINT;
-    typedef typename Value<TPropertyMap>::Type TValue;
-	resize(pm, getIdUpperBound(_getEdgeIdManager(g)), TValue(), Generous());
-}
-
-template<typename TSpec, typename TPropertyMap, typename TPrototype>
-inline void
-resizeEdgeMap(Graph<TSpec> const & g,
-              TPropertyMap & pm,
-              TPrototype const & prototype)
-{
-	SEQAN_CHECKPOINT;
-	resize(pm, getIdUpperBound(_getEdgeIdManager(g)), prototype, Generous());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.assignProperty:
-..class:Class.External Property Map
-..class:Class.InternalMap
-..class:Class.InternalPointerMap
-..class:Class.InternalRawMap
-..cat:Graph
-..summary:Assigns a property to an item in the property map.
-..signature:assignProperty(pm, d, val)
-..param.pm:An External or Internal Property Map.
-...type:Class.External Property Map
-...type:Class.InternalMap
-...type:Class.InternalPointerMap
-...type:Class.InternalRawMap
-..param.d:A vertex or edge descriptor.
-...remarks:Identifies the item in the property map.
-...type:Metafunction.VertexDescriptor
-...type:Metafunction.EdgeDescriptor
-..param.val:The new value.
-...remarks:Type of the new value must match the value type of the property map.
-See @Metafunction.Value@.
-..returns:void
-..see:Function.getProperty
-..see:Function.property
-..include:seqan/graph_types.h
-*/
-
-template<typename TPropertyMap, typename TDescriptor, typename TValue>
-inline void
-assignProperty(TPropertyMap& pm,
-			   TDescriptor const d,
-			   TValue const val)
-{
-	SEQAN_CHECKPOINT
-	assignValue(pm, _getId(d), val);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.property
-..class:Class.External Property Map
-..class:Class.InternalMap
-..class:Class.InternalPointerMap
-..class:Class.InternalRawMap
-..cat:Graph
-..summary:Accesses the property of an item in the property map.
-..signature:property(pm, d)
-..param.pm:An External or Internal Property Map.
-...type:Class.External Property Map
-...type:Class.InternalMap
-...type:Class.InternalPointerMap
-...type:Class.InternalRawMap
-..param.d:A vertex or edge descriptor.
-...remarks:Identifies the item in the property map.
-...type:Metafunction.VertexDescriptor
-...type:Metafunction.EdgeDescriptor
-..returns:Reference to the item in the property map.
-..see:Function.getProperty
-..see:Function.assignProperty
-..include:seqan/graph_types.h
-*/
-
-template<typename TPropertyMap, typename TDescriptor>
-inline typename Reference<TPropertyMap>::Type
-property(TPropertyMap& pm,
-		TDescriptor const d)
-{
-	SEQAN_CHECKPOINT
-	return value(pm, _getId(d));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TPropertyMap, typename TDescriptor>
-inline typename Reference<TPropertyMap const>::Type
-property(TPropertyMap const& pm,
-		TDescriptor const d)
-{
-	SEQAN_CHECKPOINT
-	return value(pm, _getId(d));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.getProperty
-..class:Class.External Property Map
-..class:Class.InternalMap
-..class:Class.InternalPointerMap
-..class:Class.InternalRawMap
-..cat:Graph
-..summary:Get method for an item's property.
-..signature:getProperty(pm, d)
-..param.pm:An External or Internal Property Map.
-...type:Class.External Property Map
-...type:Class.InternalMap
-...type:Class.InternalPointerMap
-...type:Class.InternalRawMap
-..param.d:A vertex or edge descriptor.
-...remarks:Identifies the item in the property map.
-...type:Metafunction.VertexDescriptor
-...type:Metafunction.EdgeDescriptor
-..returns:Value of the item in the property map.
-..see:Function.property
-..see:Function.assignProperty
-..include:seqan/graph_types.h
-*/
-
-template<typename TPropertyMap, typename TDescriptor>
-inline typename GetValue<TPropertyMap const>::Type
-getProperty(TPropertyMap const& pm,
-			TDescriptor const d)
-{
-	SEQAN_CHECKPOINT
-	return getValue(pm, _getId(d));
-}
-
-
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Graph - Internal Property Manager using member ids (only for edges!!!)
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Class.InternalMap:
-..cat:Graph
-..summary:An internal property map using member ids.
-..remarks:Internal property maps are used to access internal edge cargos.
-..signature:InternalMap<TContainer, MemberId>
-..param.TContainer:The cargo type.
-...metafunction:Metafunction.Cargo
-..param.MemberId:An unsigned int.
-...remarks:Specifies the position of the member in the cargo.
-Note: If zero it is assumed that the cargo is a simple type (e.g., int).
-...default:$0$.
-..include:seqan/graph_types.h
-..see:Class.External Property Map
-..see:Class.InternalPointerMap
-..see:Class.InternalRawMap
-*/
-template<typename TContainer, unsigned int const MemberId = 0>
-struct InternalMap 
-{
-};
-
-
-//////////////////////////////////////////////////////////////////////////////
-//	Internal Property Manager using member Ids - Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Metafunction.Value.param.T.type:Class.InternalMap
-///.Metafunction.Value.class:Class.InternalMap
-
-template<typename T1, typename T2>
-struct Value<InternalMap<Pair<T1, T2>, 1> const> {
-	typedef T1 const Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2>
-struct Value<InternalMap<Pair<T1, T2>, 1> > {
-	typedef T1 Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2>
-struct Value<InternalMap<Pair<T1, T2>, 2> const> {
-	typedef T2 const Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2>
-struct Value<InternalMap<Pair<T1, T2>, 2> > {
-	typedef T2 Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T>
-struct Value<InternalMap<T, 0> const> {
-	typedef T const Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T>
-struct Value<InternalMap<T, 0> > {
-	typedef T Type;
-};
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Internal Property Manager using member Ids - FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TContainer, unsigned int const MemberId>
-inline void
-resizeEdgeMap(Graph<TSpec> const&,
-			  InternalMap<TContainer, MemberId>&)
-{
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TContainer, unsigned int const MemberId>
-inline void
-resizeEdgeMap(Graph<TSpec>&,
-			  InternalMap<TContainer, MemberId>&)
-{
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TContainer, unsigned int const MemberId, typename TSource>
-inline void
-assignEdgeMap(Graph<TSpec> const &,
-			  InternalMap<TContainer, MemberId> &,
-              TSource const &)
-{
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TContainer, unsigned int const MemberId, typename TSource>
-inline void
-assignEdgeMap(Graph<TSpec> &,
-			  InternalMap<TContainer, MemberId> &,
-              TSource const &)
-{
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor, typename TValue>
-inline void
-assignProperty(InternalMap<Pair<T1, T2>, 1>&,
-			   TEdgeDescriptor const e,
-			   TValue const val)
-{
-	SEQAN_CHECKPOINT
-	(cargo(e)).i1 = val;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor, typename TValue>
-inline void
-assignProperty(InternalMap<Pair<T1, T2>, 2>&,
-			   TEdgeDescriptor const e,
-			   TValue const val)
-{
-	SEQAN_CHECKPOINT
-	(cargo(e)).i2 = val;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T, typename TEdgeDescriptor, typename TValue>
-inline void
-assignProperty(InternalMap<T, 0>&,
-			   TEdgeDescriptor const e,
-			   TValue const val)
-{
-	SEQAN_CHECKPOINT
-	assignCargo(e, val);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor>
-inline typename Value<InternalMap<Pair<T1, T2>, 2> >::Type&
-property(InternalMap<Pair<T1, T2>, 2>&,
-		 TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return (cargo(e)).i2;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor>
-inline typename Value<InternalMap<Pair<T1, T2>, 2> const>::Type&
-property(InternalMap<Pair<T1, T2>, 2> const&,
-		 TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return (cargo(e)).i2;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor>
-inline typename Value<InternalMap<Pair<T1, T2>, 1> >::Type&
-property(InternalMap<Pair<T1, T2>, 1>&,
-		 TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return (cargo(e)).i1;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor>
-inline typename Value<InternalMap<Pair<T1, T2>, 1> const>::Type&
-property(InternalMap<Pair<T1, T2>, 1> const&,
-		 TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return (cargo(e)).i1;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T, typename TEdgeDescriptor>
-inline typename Value<InternalMap<T, 0> >::Type&
-property(InternalMap<T, 0>&,
-		 TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return cargo(e);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T, typename TEdgeDescriptor>
-inline typename Value<InternalMap<T, 0> const>::Type&
-property(InternalMap<T, 0> const&,
-		 TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return cargo(e);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor>
-inline typename Value<InternalMap<Pair<T1, T2>, 1> >::Type
-getProperty(InternalMap<Pair<T1, T2>, 1> const&,
-			TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return (getCargo(e)).i1;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor>
-inline typename Value<InternalMap<Pair<T1, T2>, 1> >::Type
-getProperty(InternalMap<Pair<T1, T2>, 1>&,
-			TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return (getCargo(e)).i1;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor>
-inline typename Value<InternalMap<Pair<T1, T2>, 2> >::Type
-getProperty(InternalMap<Pair<T1, T2>, 2> const&,
-			TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return (getCargo(e)).i2;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T1, typename T2, typename TEdgeDescriptor>
-inline typename Value<InternalMap<Pair<T1, T2>, 2> >::Type
-getProperty(InternalMap<Pair<T1, T2>, 2>&,
-			TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return (getCargo(e)).i2;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T, typename TEdgeDescriptor>
-inline typename Value<InternalMap<T, 0> >::Type
-getProperty(InternalMap<T, 0> const&,
-			TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return getCargo(e);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename T, typename TEdgeDescriptor>
-inline typename Value<InternalMap<T, 0> >::Type
-getProperty(InternalMap<T, 0>&,
-			TEdgeDescriptor e)
-{
-	SEQAN_CHECKPOINT
-	return getCargo(e);
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Graph - Internal Property Manager using pointer to members (only for edges!!!)
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Class.InternalPointerMap:
-..cat:Graph
-..summary:An internal property map using pointer to members.
-..remarks:Internal property maps are used to access internal edge cargos.
-..signature:InternalPointerMap<TPropmap, Instance>
-..param.TPropmap:A pointer to member type.
-..param.Instance:A pointer to a member of type TPropmap.
-..include:seqan/graph_types.h
-..see:Class.External Property Map
-..see:Class.InternalMap
-..see:Class.InternalRawMap
-*/
-template <typename TPropmap, TPropmap const Instance> 
-struct InternalPointerMap 
-{
-}; 
-
-//////////////////////////////////////////////////////////////////////////////
-//	Internal Property Manager using member Ids - Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Metafunction.Value.param.T.type:Class.InternalPointerMap
-///.Metafunction.Value.class:Class.InternalMap
-
-template<typename TClass, typename TValue, TValue TClass:: * TPMember>
-struct Value<InternalPointerMap<TValue TClass::*, TPMember> const> {
-	typedef TValue const Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TClass, typename TValue, TValue TClass:: * TPMember>
-struct Value<InternalPointerMap<TValue TClass::*, TPMember> > {
-	typedef TValue Type;
-};
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Internal Property Manager using pointer to members - FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TPropmap, TPropmap const Instance>
-inline void
-resizeEdgeMap(Graph<TSpec>&,
-			  InternalPointerMap<TPropmap, Instance>&)
-{
-	SEQAN_CHECKPOINT
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TSpec, typename TPropmap, TPropmap const Instance>
-inline void
-resizeEdgeMap(Graph<TSpec> const&,
-			  InternalPointerMap<TPropmap, Instance>&)
-{
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TClass, typename TValue, TValue TClass:: * TPMember, typename TEdgeDescriptor>
-inline void
-assignProperty(InternalPointerMap<TValue TClass::*, TPMember>&,
-			TEdgeDescriptor const e,
-			TValue const val)
-{
-	SEQAN_CHECKPOINT
-	(cargo(e)).*TPMember = val;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TClass, typename TValue, TValue TClass:: * TPMember, typename TEdgeDescriptor>
-inline typename Value<InternalPointerMap<TValue TClass::*, TPMember> >::Type&
-property(InternalPointerMap<TValue TClass::*, TPMember>&,
-		 TEdgeDescriptor const e)
-{
-	SEQAN_CHECKPOINT
-	return (cargo(e)).*TPMember;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TClass, typename TValue, TValue TClass:: * TPMember, typename TEdgeDescriptor>
-inline typename Value<InternalPointerMap<TValue TClass::*, TPMember> const>::Type&
-property(InternalPointerMap<TValue TClass::*, TPMember> const&,
-		 TEdgeDescriptor const e)
-{
-	SEQAN_CHECKPOINT
-	return (cargo(e)).*TPMember;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TClass, typename TValue, TValue TClass:: * TPMember, typename TEdgeDescriptor>
-inline typename Value<InternalPointerMap<TValue TClass::*, TPMember> >::Type
-getProperty(InternalPointerMap<TValue TClass::*, TPMember> const&,
-			TEdgeDescriptor const e)
-{
-	SEQAN_CHECKPOINT
-	return (getCargo(e)).*TPMember;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-template<typename TClass, typename TValue, TValue TClass:: * TPMember, typename TEdgeDescriptor>
-inline typename Value<InternalPointerMap<TValue TClass::*, TPMember> >::Type
-getProperty(InternalPointerMap<TValue TClass::*, TPMember>&,
-			TEdgeDescriptor const e)
-{
-	SEQAN_CHECKPOINT
-	return (getCargo(e)).*TPMember;
-}
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Graph - Internal Property Manager using raw pointer to member (only for edges!!!)
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Class.InternalRawMap:
-..cat:Graph
-..summary:An internal property map using raw pointer to members.
-..remarks:Internal property maps are used to access internal edge cargos.
-..include:seqan/graph_types.h
-..see:Class.External Property Map
-..see:Class.InternalMap
-..see:Class.InternalPointerMap
-*/
-
-//////////////////////////////////////////////////////////////////////////////
-// Internal Property Manager using raw pointer to member - Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-///.Metafunction.Value.param.T.type:Class.InternalRawMap
-///.Metafunction.Value.class:Class.InternalRawMap
-
-template <typename TClass, typename TValue> 
-struct Value<TValue TClass:: *> {
-	typedef TValue Type;
-};
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TClass, typename TValue> 
-struct Value<TValue TClass:: * const> {
-	typedef TValue const Type;
-};
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Raw pointer to member - FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TSpec, typename TClass, typename TValue> 
-inline void
-resizeEdgeMap(Graph<TSpec> const&,
-			  TValue TClass:: *)
-{
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TSpec, typename TClass, typename TValue> 
-inline void
-resizeEdgeMap(Graph<TSpec>&,
-			  TValue TClass:: *)
-{
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-template <typename TClass, typename TValue, typename TEdgeDescriptor> 
-inline void 
-assignProperty(TValue TClass:: * ptr_to_member, 
-			TEdgeDescriptor const e, 
-			TValue const val) 
-{
-	SEQAN_CHECKPOINT
-	(cargo(e)).*ptr_to_member=val; 
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TClass, typename TValue, typename TEdgeDescriptor> 
-inline TValue& 
-property(TValue TClass:: * const ptr_to_member, 
-		 TEdgeDescriptor const e) 
-{
-	SEQAN_CHECKPOINT
-	return (cargo(e)).*ptr_to_member; 
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TClass, typename TValue, typename TEdgeDescriptor> 
-inline TValue
-getProperty(TValue TClass:: * const ptr_to_member, 
-			TEdgeDescriptor const e) 
-{
-	SEQAN_CHECKPOINT
-	return (getCargo(e)).*ptr_to_member; 
-} 
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Init functions for all Maps - FUNCTIONS
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.assignVertexMap
-..class:Class.External Property Map
-..class:Class.InternalMap
-..class:Class.InternalPointerMap
-..class:Class.InternalRawMap
-..cat:Graph
-..summary:Initializes a vertex map with values of an array.
-..signature:assignVertexMap(g, pm, prop)
-..param.g:A Graph.
-...type:Class.Graph
-..param.pm:An External Property Map.
-...type:Class.External Property Map
-..param.prop:An array with properties that are to be assigned to the items in the property map.
-...remarks:For every vertex descriptor there must be an entry in the array.
-..returns:void
-..see:Function.assignEdgeMap
-..include:seqan/graph_types.h
-*/
-
-template<typename TSpec, typename TPropertyMap, typename TProperties>
-inline void
-assignVertexMap(Graph<TSpec> const & g,
-                TPropertyMap & pm,
-                TProperties const & prop)
-{
-	SEQAN_CHECKPOINT
-	resize(pm, getIdUpperBound(_getVertexIdManager(g)), Generous());
-	typedef Graph<TSpec> TGraph;
-	typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
-	TVertexIterator it(g);
-	for (; !atEnd(it); goNext(it))
-		assignProperty(pm,getValue(it), getValue(prop, _getId(value(it))));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.assignEdgeMap
-..class:Class.External Property Map
-..class:Class.InternalMap
-..class:Class.InternalPointerMap
-..class:Class.InternalRawMap
-..cat:Graph
-..summary:Initializes a vertex map with values of an array.
-..signature:assignEdgeMap(g, pm, prop)
-..param.g:A Graph.
-...type:Class.Graph
-..param.pm:An External or Internal Property Map.
-...type:Class.External Property Map
-...type:Class.InternalMap
-...type:Class.InternalPointerMap
-...type:Class.InternalRawMap
-..param.prop:An array with properties that are to be assigned to the items in the property map.
-...remarks:For every edge id there must be an entry in the array.
-..returns:void
-..see:Function.assignVertexMap
-..include:seqan/graph_types.h
-*/
-
-template<typename TSpec, typename TPropertyMap, typename TProperties>
-inline void
-assignEdgeMap(Graph<TSpec> const & g,
-              TPropertyMap & pm,
-              TProperties const & prop)
-{
-	SEQAN_CHECKPOINT
-	resize(pm, getIdUpperBound(_getEdgeIdManager(g)), Generous());
-	typedef Graph<TSpec> TGraph;
-	typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
-	TEdgeIterator it(g);
-	for (; !atEnd(it); goNext(it))
-		assignProperty(pm,*it,prop[_getId(*it)]);
-}
-
-}// namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/graph_types/graph_utility_parsing.h b/seqan/graph_types/graph_utility_parsing.h
index 8b88d47..5e9a196 100644
--- a/seqan/graph_types/graph_utility_parsing.h
+++ b/seqan/graph_types/graph_utility_parsing.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -48,44 +48,46 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 
 // This is unused and a deletion candidate.
+// TODO(singer): Remove this!
+/*
 template<typename TPath, typename TStringSet, typename TNames>
 inline unsigned int
 _loadSequences(TPath const& in_path,
-			   TStringSet& origStrSet,
-			   TNames& names)
+               TStringSet& origStrSet,
+               TNames& names)
 {
 //IOREV _nodoc_ uses custom IO, with ifstream, should be adapted to File()
-	typedef typename Size<TStringSet>::Type TSize;
-	
-	// Count sequences and read names
-	TSize seqCount = 0;
-	std::ifstream file;
-	std::stringstream input;
-	input << in_path;
-	file.open(input.str().c_str(), std::ios_base::in | std::ios_base::binary);
-	if (!file.is_open()) return 0;
-	while (!file.eof()) {
-		String<char> id;
-		readID(file, id, Fasta());
-		appendValue(names, id);
-		goNext(file, Fasta());
-		++seqCount;
-	}
+    typedef typename Size<TStringSet>::Type TSize;
 
-	// Load sequences
-	file.clear();
-	file.seekg(0, std::ios_base::beg);
-	resize(origStrSet, seqCount);
-	TSize count = 0;
-	for(TSize i = 0; (i < seqCount) && !file.eof(); ++i) 	{
-		read(file, origStrSet[i], Fasta());
-		count += length(origStrSet[i]);
-	}
+    // Count sequences and read names
+    TSize seqCount = 0;
+    std::ifstream file;
+    std::stringstream input;
+    input << in_path;
+    file.open(input.str().c_str(), std::ios_base::in | std::ios_base::binary);
+    if (!file.is_open()) return 0;
+    while (!file.eof()) {
+        String<char> id;
+        readID(file, id, Fasta());
+        appendValue(names, id);
+        goNext(file, Fasta());
+        ++seqCount;
+    }
+
+    // Load sequences
+    file.clear();
+    file.seekg(0, std::ios_base::beg);
+    resize(origStrSet, seqCount);
+    TSize count = 0;
+    for(TSize i = 0; (i < seqCount) && !file.eof(); ++i)     {
+        read(file, origStrSet[i], Fasta());
+        count += length(origStrSet[i]);
+    }
     file.close();
 
-	return count;
+    return count;
 }
-
+*/
 
 }// namespace SEQAN_NAMESPACE_MAIN
 
diff --git a/seqan/graph_types/property_map_generic.h b/seqan/graph_types/property_map_generic.h
new file mode 100644
index 0000000..e292043
--- /dev/null
+++ b/seqan/graph_types/property_map_generic.h
@@ -0,0 +1,223 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Tobias Rausch <rausch@embl.de>
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Graph-related property map functions, defaults are used for general types
+// implementing the PropertyMapConcept, e.g. containers such as SeqAn
+// Strings.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_GENERIC_H_
+#define INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_GENERIC_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Class Graph#resizeVertexMap
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn Graph#resizeVertexMap
+ * @brief Initializes a vertex map.
+ * @signature void resizeVertexMap(pm, g[, prototype]);
+ *
+ * @param[in,out] pm        A @link PropertyMapConcept property map @endlink.
+ * @param[in]     g         A Graph.
+ * @param[in]     prototype An optional prototype that is used for initializing the property map.
+ */
+
+template <typename TPropertyMap, typename TSpec>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >, void)
+resizeVertexMap(TPropertyMap & pm, Graph<TSpec> const & g)
+{
+    typedef typename Value<TPropertyMap>::Type TValue;
+    resize(pm, getIdUpperBound(_getVertexIdManager(g)), TValue(), Generous());
+}
+
+template <typename TPropertyMap, typename TSpec, typename TPrototype>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >, void)
+resizeVertexMap(TPropertyMap & pm, Graph<TSpec> const & g, TPrototype const & prototype)
+{
+    resize(pm, getIdUpperBound(_getVertexIdManager(g)), prototype, Generous());
+}
+
+// --------------------------------------------------------------------------
+// Class Graph#resizeEdgeMap
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn Graph#resizeEdgeMap
+ * @brief Initializes an edge map.
+ * @signature void resizeEdgeMap(pm, g[, prototype]);;
+ * @param[in,out] pm        A @link PropertyMapConcept property map @endlink.
+ * @param[in]     g         A Graph.
+ * @param[in]     prototype An optional prototype that is used for initializing the property map.
+ */
+
+template <typename TPropertyMap, typename TSpec>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >, void)
+resizeEdgeMap(TPropertyMap & pm, Graph<TSpec> const & g)
+{
+    typedef typename Value<TPropertyMap>::Type TValue;
+    resize(pm, getIdUpperBound(_getEdgeIdManager(g)), TValue(), Generous());
+}
+
+template <typename TPropertyMap, typename TSpec, typename TPrototype>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >, void)
+resizeEdgeMap(TPropertyMap & pm, Graph<TSpec> const & g, TPrototype const & prototype)
+{
+    resize(pm, getIdUpperBound(_getEdgeIdManager(g)), prototype, Generous());
+}
+
+// --------------------------------------------------------------------------
+// Function Graph#assignVertexMap()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn Graph#assignVertexMap
+ * @brief Initializes a vertex map with values of an array.
+ * @signature void assignVertexMap(g, pm, prop);
+ *
+ * @param[out] pm   A @link PropertyMapConcept property map @endlink.
+ * @param[in]  g    A Graph.
+ * @param[in]  prop An array with properties that are to be assigned to the items in the property map.
+ *
+ * For every vertex descriptor there must be an entry in the array.
+ */
+
+template <typename TSpec, typename TPropertyMap, typename TProperties>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >, void)
+assignVertexMap(TPropertyMap & pm,
+                Graph<TSpec> const & g,
+                TProperties const & prop)
+{
+    resize(pm, getIdUpperBound(_getVertexIdManager(g)), Generous());
+    typedef Graph<TSpec> TGraph;
+    typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+    TVertexIterator it(g);
+    for (; !atEnd(it); goNext(it))
+        assignProperty(pm, getValue(it), getValue(prop, _getId(value(it))));
+}
+
+// --------------------------------------------------------------------------
+// Function Graph#assignEdgeMap()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn Graph#assignEdgeMap
+ * @brief Initializes a vertex map with values of an array.
+ * @signature void assignEdgeMap(g, pm, prop);
+ *
+ * @param[in]  pm   An @link PropertyMapConcept property map @endlink.
+ * @param[out] prop An array with properties that are to be assigned to the items in the property map.
+ * @param[in]  g    A Graph.
+ *
+ * For every edge id there must be an entry in the array.
+ */
+
+template <typename TSpec, typename TPropertyMap, typename TProperties>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >, void)
+assignEdgeMap(TPropertyMap & pm,
+              Graph<TSpec> const & g,
+              TProperties const & prop)
+{
+    resize(pm, getIdUpperBound(_getEdgeIdManager(g)), Generous());
+    typedef Graph<TSpec> TGraph;
+    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+    TEdgeIterator it(g);
+    for (; !atEnd(it); goNext(it))
+        assignProperty(pm, *it, prop[_getId(*it)]);
+}
+
+// --------------------------------------------------------------------------
+// Class PropertyMapConcept#assignProperty
+// --------------------------------------------------------------------------
+
+template <typename TPropertyMap, typename TDescriptor, typename TValue>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >, void)
+assignProperty(TPropertyMap & pm, TDescriptor const d, TValue const val)
+{
+    assignValue(pm, _getId(d), val);
+}
+
+// --------------------------------------------------------------------------
+// Class PropertyMapConcept#property
+// --------------------------------------------------------------------------
+
+template <typename TPropertyMap, typename TDescriptor>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >,
+                     typename Reference<TPropertyMap>::Type)
+property(TPropertyMap & pm, TDescriptor const d)
+{
+    return value(pm, _getId(d));
+}
+
+template <typename TPropertyMap, typename TDescriptor>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >,
+                     typename Reference<TPropertyMap const>::Type)
+property(TPropertyMap const & pm, TDescriptor const d)
+{
+    return value(pm, _getId(d));
+}
+
+// --------------------------------------------------------------------------
+// Class PropertyMapConcept#getProperty
+// --------------------------------------------------------------------------
+
+template <typename TPropertyMap, typename TDescriptor>
+SEQAN_FUNC_ENABLE_IF(Is<PropertyMapConcept<TPropertyMap> >,
+                     typename GetValue<TPropertyMap const>::Type)
+getProperty(TPropertyMap const & pm, TDescriptor const d)
+{
+    return getValue(pm, _getId(d));
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_GENERIC_H_
diff --git a/seqan/graph_types/property_map_internal.h b/seqan/graph_types/property_map_internal.h
new file mode 100644
index 0000000..291e928
--- /dev/null
+++ b/seqan/graph_types/property_map_internal.h
@@ -0,0 +1,227 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Tobias Rausch <rausch@embl.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_INTERNAL_H_
+#define INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_INTERNAL_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Class InternalPropertyMap
+// --------------------------------------------------------------------------
+
+/*!
+ * @class InternalPropertyMap InternalPropertyMap
+ * @implements PropertyMapConcept
+ * @headerfile <seqan/graph_types.h>
+ * @brief An internal property map with direct access to members.
+ *
+ * @signature template <typename TMember>
+ *            class InternalPropertyMap;
+ *
+ * @tparam TMember The member type.
+ *
+ * Internal property maps are used to access internal edge cargos.
+ */
+
+template <typename TMember>
+struct InternalPropertyMap
+{};
+
+template <typename TMember>
+SEQAN_CONCEPT_IMPL((InternalPropertyMap<TMember>), (PropertyMapConcept));
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction InternalPropertyMap#Value
+// --------------------------------------------------------------------------
+
+template <typename TValue>
+struct Value<InternalPropertyMap<TValue> >
+{
+    typedef TValue Type;
+};
+
+template <typename TValue>
+struct Value<InternalPropertyMap<TValue> const> : Value<InternalPropertyMap<TValue> >
+{};
+
+// --------------------------------------------------------------------------
+// Metafunction PropertyMapConcept#GetValue
+// --------------------------------------------------------------------------
+
+template <typename TValue>
+struct GetValue<InternalPropertyMap<TValue> >
+{
+    typedef TValue Type;
+};
+
+template <typename TValue>
+struct GetValue<InternalPropertyMap<TValue> const>
+{
+    typedef TValue Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction InternalPropertyMap#Reference
+// --------------------------------------------------------------------------
+
+template <typename TValue>
+struct Reference<InternalPropertyMap<TValue> const>
+{
+    typedef TValue const & Type;
+};
+
+template <typename TValue>
+struct Reference<InternalPropertyMap<TValue> >
+{
+    typedef TValue & Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function Graph#resizeEdgeMap()
+// --------------------------------------------------------------------------
+
+// Overload for InternalPropertyMap.
+
+template <typename TPropMap, typename TSpec>
+void resizeEdgeMap(InternalPropertyMap<TPropMap> &, Graph<TSpec> const &)
+{}
+
+// --------------------------------------------------------------------------
+// Function InternalPropertyMap#resize()
+// --------------------------------------------------------------------------
+
+template <typename TPropertyMap, typename TSize, typename TPrototype>
+void resize(InternalPropertyMap<TPropertyMap> &, TSize, TPrototype)
+{}
+
+// --------------------------------------------------------------------------
+// Function InternalPropertyMap#assignProperty()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn InternalPropertyMap#assignProperty:
+ * @brief Assigns a property to an item in the property map.
+ * @signature void assignProperty(pm, d, val)
+ *
+ * @param[in,out] pm  The InternalPropertyMap to assign into.
+ * @param[in]     d   A vertex or edge descriptor that identifies the item in the property map.
+ *                    Types: @link VertexDescriptor @endlink, @link Graph#EdgeDescriptor @endlink
+ * @param[in]     val The new value, where thg type of the new value must match the value type of the property map.
+ */
+
+template <typename TValue, typename TEdgeDescriptor>
+void assignProperty(InternalPropertyMap<TValue> &,
+                    TEdgeDescriptor const e,
+                    TValue const val)
+{
+    cargo(e) = val;
+}
+
+// --------------------------------------------------------------------------
+// Function InternalPropertyMap#property()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn InternalPropertyMap#property:
+ * @brief Accesses the property of an item in the property map.
+ *
+ * @signature TReference property(pm, d)
+ *
+ * @param[in,out] pm  The property map.
+ * @param[in]     d   A vertex or edge descriptor that identifies the item in the property map.
+ *                    Types: @link VertexDescriptor @endlink, @link Graph#EdgeDescriptor @endlink
+ *
+ * @return TReference @link PropertyMapConcept#Reference Reference @endlink to the item in the property map of type
+ *                    @link Reference @endlink.
+ */
+
+template <typename TValue, typename TEdgeDescriptor>
+typename Reference<InternalPropertyMap<TValue> const>::Type
+property(InternalPropertyMap<TValue> const &, TEdgeDescriptor const e)
+{
+    return cargo(e);
+}
+
+template <typename TValue, typename TEdgeDescriptor>
+typename Reference<InternalPropertyMap<TValue> >::Type
+property(InternalPropertyMap<TValue>&, TEdgeDescriptor const e)
+{
+    return cargo(e);
+}
+
+// --------------------------------------------------------------------------
+// Function InternalPropertyMap#getProperty()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn InternalPropertyMap#getProperty
+ * @brief Get method for an item's property.
+ *
+ * @signature TGetValue getProperty(pm, d)
+ *
+ * @param[in] pm  The property map.
+ * @param[in] d   A vertex or edge descriptor that identifies the item in the property map.
+ *               Types: @link VertexDescriptor @endlink, @link Graph#EdgeDescriptor @endlink
+ *
+ * @return TValue Get-value of the item in the property map of type @link PropertyMapConcept#GetValue GetValue @endlink.
+ */
+
+template <typename TValue, typename TEdgeDescriptor>
+typename GetValue<InternalPropertyMap<TValue> >::Type
+getProperty(InternalPropertyMap<TValue> const &, TEdgeDescriptor const e)
+{
+    return getCargo(e);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_INTERNAL_H_
diff --git a/seqan/graph_types/property_map_internal_pointer.h b/seqan/graph_types/property_map_internal_pointer.h
new file mode 100644
index 0000000..27ef8cf
--- /dev/null
+++ b/seqan/graph_types/property_map_internal_pointer.h
@@ -0,0 +1,232 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Tobias Rausch <rausch@embl.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_INTERNAL_POINTER_H_
+#define INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_INTERNAL_POINTER_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Class InternalPointerPropertyMap
+// --------------------------------------------------------------------------
+
+/*!
+ * @class InternalPointerPropertyMap InternalPointerPropertyMap
+ * @implements PropertyMapConcept
+ * @headerfile <seqan/graph_types.h>
+ * @brief An internal property map using pointer to members.
+ *
+ * @signature template <typename TMemberPointer, TMemberPointer const MEMBER_POINTER>
+ *            class InternalPointerPropertyMap;
+ *
+ * @tparam TMemberPointer  A pointer to a member type.
+ * @tparam MEMBER_POINTER  A pointer to a type member of type <tt>TMemberPointer</tt>.
+ *
+ * Internal property maps are used to access internal edge cargos that are structs or classes.
+ */
+
+template <typename TPointer, TPointer const MEMBER_POINTER>
+struct InternalPointerPropertyMap
+{};
+
+template <typename TPointer, TPointer const MEMBER_POINTER>
+SEQAN_CONCEPT_IMPL((InternalPointerPropertyMap<TPointer, MEMBER_POINTER>), (PropertyMapConcept));
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction InternalPointerPropertyMap#Value
+// --------------------------------------------------------------------------
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER>
+struct Value<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> >
+{
+    typedef TValue Type;
+};
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER>
+struct Value<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> const> :
+    Value<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> >
+{};
+
+// --------------------------------------------------------------------------
+// Metafunction InternalPointerPropertyMap#GetValue
+// --------------------------------------------------------------------------
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER>
+struct GetValue<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> >
+{
+    typedef TValue Type;
+};
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER>
+struct GetValue<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> const>
+{
+    typedef TValue Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction InternalPointerPropertyMap#Reference
+// --------------------------------------------------------------------------
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER>
+struct Reference<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> const>
+{
+    typedef TValue const & Type;
+};
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER>
+struct Reference<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> >
+{
+    typedef TValue & Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function Graph#resizeEdgeMap()
+// --------------------------------------------------------------------------
+
+// Overload for InternalPointerPropertyMap.
+
+template <typename TPropMap, TPropMap const INSTANCE, typename TSpec>
+void resizeEdgeMap(InternalPointerPropertyMap<TPropMap, INSTANCE> &, Graph<TSpec> const &)
+{}
+
+// --------------------------------------------------------------------------
+// Function InternalPointerPropertyMap#resize()
+// --------------------------------------------------------------------------
+
+template <typename TPropertyMap, TPropertyMap INSTANCE, typename TSize, typename TPrototype>
+void resize(InternalPointerPropertyMap<TPropertyMap, INSTANCE> &, TSize, TPrototype)
+{}
+
+// --------------------------------------------------------------------------
+// Function InternalPointerPropertyMap#assignProperty()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn InternalPointerPropertyMap#assignProperty:
+ * @brief Assigns a property to an item in the property map.
+ * @signature void assignProperty(pm, d, val)
+ *
+ * @param[in,out] pm  The InternalPointerPropertyMap to assign into.
+ * @param[in]     d   A vertex or edge descriptor that identifies the item in the property map.
+ *                    Types: @link VertexDescriptor @endlink, @link Graph#EdgeDescriptor @endlink
+ * @param[in]     val The new value, where thg type of the new value must match the value type of the property map.
+ */
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER, typename TEdgeDescriptor>
+void assignProperty(InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> &,
+                    TEdgeDescriptor const e,
+                    TValue const val)
+{
+    (cargo(e)).*MEMBER_POINTER = val;
+}
+
+// --------------------------------------------------------------------------
+// Function InternalPointerPropertyMap#property()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn InternalPointerPropertyMap#property:
+ * @brief Accesses the property of an item in the property map.
+ *
+ * @signature TReference property(pm, d)
+ *
+ * @param[in,out] pm  The property map.
+ * @param[in]     d   A vertex or edge descriptor that identifies the item in the property map.
+ *                    Types: @link VertexDescriptor @endlink, @link Graph#EdgeDescriptor @endlink
+ *
+ * @return TReference @link PropertyMapConcept#Reference Reference @endlink to the item in the property map of type
+ *                    @link Reference @endlink.
+ */
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER, typename TEdgeDescriptor>
+typename Reference<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> >::Type
+property(InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER>&,
+         TEdgeDescriptor const e)
+{
+    return (cargo(e)).*MEMBER_POINTER;
+}
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER, typename TEdgeDescriptor>
+typename Reference<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> const>::Type
+property(InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> const &,
+         TEdgeDescriptor const e)
+{
+    return (cargo(e)).*MEMBER_POINTER;
+}
+
+// --------------------------------------------------------------------------
+// Function InternalPointerPropertyMap#getProperty()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn InternalPointerPropertyMap#getProperty
+ * @brief Get method for an item's property.
+ *
+ * @signature TGetValue getProperty(pm, d)
+ *
+ * @param[in] pm  The property map.
+ * @param[in] d   A vertex or edge descriptor that identifies the item in the property map.
+ *               Types: @link VertexDescriptor @endlink, @link Graph#EdgeDescriptor @endlink
+ *
+ * @return TValue Get-value of the item in the property map of type @link PropertyMapConcept#GetValue GetValue @endlink.
+ */
+
+template <typename TClass, typename TValue, TValue TClass::* MEMBER_POINTER, typename TEdgeDescriptor>
+typename GetValue<InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> >::Type
+getProperty(InternalPointerPropertyMap<TValue TClass::*, MEMBER_POINTER> const &,
+            TEdgeDescriptor const e)
+{
+    return (getCargo(e)).*MEMBER_POINTER;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_GRAPH_TYPES_PROPERTY_MAP_INTERNAL_POINTER_H_
diff --git a/seqan/hts_io.h b/seqan/hts_io.h
new file mode 100644
index 0000000..134f919
--- /dev/null
+++ b/seqan/hts_io.h
@@ -0,0 +1,18 @@
+#ifndef INCLUDE_SEQAN_HTS_IO_H_
+#define INCLUDE_SEQAN_HTS_IO_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/bam_io.h>
+
+// ===========================================================================
+// HTS I/O
+// ===========================================================================
+
+#include <seqan/hts_io/hts_alignment_record.h>
+#include <seqan/hts_io/hts_file.h>
+#include <seqan/hts_io/hts_alignment_record_utils.h>
+
+#endif // INCLUDE_SEQAN_HTS_IO_H_
diff --git a/seqan/hts_io/bam_alignment_record.h b/seqan/hts_io/bam_alignment_record.h
new file mode 100644
index 0000000..5e4d9cf
--- /dev/null
+++ b/seqan/hts_io/bam_alignment_record.h
@@ -0,0 +1,313 @@
+#ifndef INCLUDE_SEQAN_HTS_IO_BAM_ALIGNMENT_RECORD_H_
+#define INCLUDE_SEQAN_HTS_IO_BAM_ALIGNMENT_RECORD_H_
+
+#include <seqan/bam_io/bam_alignment_record.h>
+
+#include <htslib/hfile.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/kstring.h>
+
+namespace seqan
+{
+
+inline void
+syncCores(bam1_t * hts_record, BamAlignmentRecord const & record)
+{
+  hts_record->core.tid     = record.rID;
+  hts_record->core.pos     = record.beginPos;
+  hts_record->core.l_qname = record._l_qname;
+  hts_record->core.qual    = record.mapQ;
+  hts_record->core.bin     = record.bin;
+  hts_record->core.n_cigar = record._n_cigar;
+  hts_record->core.flag    = record.flag;
+  hts_record->core.l_qseq  = record._l_qseq;
+  hts_record->core.mtid    = record.rNextId;
+  hts_record->core.mpos    = record.pNext;
+  hts_record->core.isize   = record.tLen;
+}
+
+inline void
+syncCores(BamAlignmentRecord & record, bam1_t * hts_record)
+{
+  record.rID      = hts_record->core.tid;
+  record.beginPos = hts_record->core.pos;
+  record._l_qname = hts_record->core.l_qname;
+  record.mapQ     = hts_record->core.qual;
+  record.bin      = hts_record->core.bin;
+  record._n_cigar = hts_record->core.n_cigar;
+  record.flag     = hts_record->core.flag;
+  record._l_qseq  = hts_record->core.l_qseq;
+  record.rNextId  = hts_record->core.mtid;
+  record.pNext    = hts_record->core.mpos;
+  record.tLen     = hts_record->core.isize;
+}
+
+inline std::vector<std::string>
+split(std::string const & s, char const & delimiter)
+{
+  std::vector<std::string> splitted_str(0);
+  std::string item;
+  std::size_t pos = 0;
+
+  while (true)
+  {
+    std::size_t new_pos = s.find(delimiter, pos);
+    std::string item(s, pos, new_pos - pos);
+    // std::cerr << "pos = " << pos << " " << " new_pos = " << new_pos << std::endl;
+    // std::cerr << "item = '" << item << "'" << std::endl;
+
+    splitted_str.push_back(item);
+
+    if (new_pos == std::string::npos)
+    {
+      break;
+    }
+    else
+    {
+      pos = new_pos + 1;
+    }
+  }
+
+  return splitted_str;
+}
+
+inline std::string
+join(std::vector<std::string> const & splitted_str, char const & delimiter)
+{
+  // std::string s;
+  std::stringstream ss;
+
+  ss << splitted_str.front();
+
+  for (auto it = splitted_str.begin()+1; it != splitted_str.end(); ++it)
+  {
+    ss << delimiter << *it;
+  }
+
+  return ss.str();
+}
+
+
+template<typename TTagType>
+inline void
+printTag(TTagType & read_int, CharString const & tags, unsigned & i, std::stringstream & ss)
+{
+  memcpy(&read_int, &tags[i], sizeof(TTagType));
+  ss << static_cast<int64_t>(read_int);
+  i += sizeof(TTagType);
+}
+
+
+inline std::string
+toString(BamAlignmentRecord const & record, bam_hdr_t * hdr)
+{
+  std::stringstream ss;
+
+  if (!hdr)
+  {
+    std::cerr << "ERROR: No header. Did you forget to read header?" << std::endl;
+    std::exit(1);
+  }
+  else if (record.rID >= hdr->n_targets)
+  {
+    std::cerr << "ERROR: Invalid contig in BamAlignmentRecord with rID " << record.rID << std::endl;
+    std::exit(1);
+  }
+
+  std::string const chrom = record.rID == -1 ? "*" : hdr->target_name[record.rID];
+  ss << record.qName << '\t' << record.flag << '\t' << chrom << '\t' << record.beginPos+1 << '\t' << record.mapQ << '\t';
+
+  if (length(record.cigar) > 0)
+  {
+    for (auto print_it = begin(record.cigar); print_it != end(record.cigar); ++ print_it)
+      ss << print_it->count << print_it->operation;
+  }
+  else
+  {
+    ss << "*";
+  }
+
+  if (record.rNextId == -1)
+    ss << "\t*\t";
+  else if (record.rNextId == record.rID)
+    ss << "\t=\t";
+  else
+    ss << '\t' << hdr->target_name[record.rNextId] << '\t';
+
+  ss << record.pNext+1 << '\t' << record.tLen << '\t' << record.seq << '\t' << record.qual;
+
+  for (unsigned i = 0; i < length(record.tags);)
+  {
+    ss << '\t' << record.tags[i] << record.tags[i+1] << ':';
+    i += 3;
+
+    switch(record.tags[i-1])
+    {
+      case 'A':
+      {
+        /* A printable character */
+        ss << "A:" << record.tags[i];
+        ++i;
+        break;
+      }
+
+      case 'Z':
+      {
+        ss << "Z:";
+
+        /* A string! Let's loop it until qNULL */
+        while (record.tags[i] != '\0' && record.tags[i] != '\t' && record.tags[i] != '\n')
+        {
+          ss << record.tags[i];
+          ++i;
+        }
+
+        ++i;
+        break;
+      }
+
+      case 'c':
+      {
+        ss << "i:";
+        int8_t read_int8 = 0;
+        printTag(read_int8, record.tags, i, ss);
+        break;
+      }
+
+      case 'C':
+      {
+        ss << "i:";
+        uint8_t read_uint8 = 0;
+        printTag(read_uint8, record.tags, i, ss);
+        break;
+      }
+
+      case 's':
+      {
+        ss << "i:";
+        int16_t read_int16 = 0;
+        printTag(read_int16, record.tags, i, ss);
+        break;
+      }
+
+      case 'S':
+      {
+        ss << "i:";
+        uint16_t read_uint16 = 0;
+        printTag(read_uint16, record.tags, i, ss);
+        break;
+      }
+
+      case 'i':
+      {
+        ss << "i:";
+        int32_t read_int32 = 0;
+        printTag(read_int32, record.tags, i, ss);
+        break;
+      }
+
+      case 'I':
+      {
+        ss << "I:";
+        uint32_t read_uint32 = 0;
+        printTag(read_uint32, record.tags, i, ss);
+        break;
+      }
+
+      case 'f':
+      {
+        ss << "f:";
+        float read_float = 0.0;
+        memcpy(&read_float, &record.tags[i], sizeof(float));
+        ss << read_float;
+        i += sizeof(float);
+        break;
+      }
+
+      default:
+      {
+        i = length(record.tags); // Unkown tag, stop
+        break;
+      }
+    }
+  }
+
+  return ss.str();
+}
+
+
+inline bool
+parse(BamAlignmentRecord & record, bam1_t * hts_record)
+{
+  syncCores(record, hts_record);
+
+  // Parse qName
+  record.qName = hts_record->data;
+  auto it = hts_record->data + record._l_qname;
+
+  // Parse CIGAR
+  resize(record.cigar, record._n_cigar, Exact());
+  static char const * CIGAR_MAPPING = "MIDNSHP=X*******";
+
+  for (auto cig = begin(record.cigar, Standard()); cig != end(record.cigar, Standard()); ++cig)
+  {
+    uint32_t opAndCnt;
+    memcpy(&opAndCnt, it, sizeof(uint32_t));
+    it += sizeof(uint32_t);
+    SEQAN_ASSERT_LEQ(opAndCnt & 15, 8u);
+    cig->operation = CIGAR_MAPPING[opAndCnt & 15];
+    cig->count = opAndCnt >> 4;
+  }
+
+  // Parse sequence
+  resize(record.seq, record._l_qseq, Exact());
+
+  for (int i = 0; i < record._l_qseq; ++i)
+  {
+    record.seq[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(it, i)];
+  }
+
+  it += (hts_record->core.l_qseq + 1) >> 1;
+
+  // Parse qualities
+  resize(record.qual, record._l_qseq, Exact());
+
+  for (int i = 0; i < record._l_qseq; ++i, ++it)
+  {
+    record.qual[i] = static_cast<char>(*it + 33);
+  }
+
+  it = bam_get_aux(hts_record);
+  resize(record.tags, bam_get_l_aux(hts_record), Exact());
+  arrayCopyForward(it, it + bam_get_l_aux(hts_record), begin(record.tags, Standard()));
+
+  return true;
+}
+
+
+inline bool
+parse(bam1_t * hts_record, bam_hdr_t * hdr, BamAlignmentRecord const & record)
+{
+  kstring_t * s = static_cast<kstring_t*>(calloc(1, sizeof(kstring_t)));
+  std::string str = toString(record, hdr);
+  ksprintf(s, "%s", str.data());
+  int ret = sam_parse1(s, hdr, hts_record);
+
+  free(s->s);
+  free(s);
+
+  if (ret != 0)
+  {
+    std::cerr << "[seqan::hts_io.bam_alignment_record] ERROR parsing record:\n";
+    std::cerr << str << std::endl;
+    return false;
+  }
+
+  return true;
+}
+
+} // namespace seqan
+
+
+#endif // INCLUDE_SEQAN_HTS_IO_BAM_ALIGNMENT_RECORD_H_
diff --git a/seqan/hts_io/hts_alignment_record.h b/seqan/hts_io/hts_alignment_record.h
new file mode 100644
index 0000000..ed9ac1c
--- /dev/null
+++ b/seqan/hts_io/hts_alignment_record.h
@@ -0,0 +1,58 @@
+#ifndef SEQAN_HTS_IO_HTS_ALIGNMENT_RECORD_H_
+#define SEQAN_HTS_IO_HTS_ALIGNMENT_RECORD_H_
+
+#include <seqan/basic.h>
+
+#include <cstdio>
+
+#include <htslib/hfile.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+
+namespace seqan {
+
+class HtsSequenceRecord
+{
+  public:
+    String<char> qName;
+    String<Iupac> seq;
+    String<char> qual;
+
+    static __int32 const INVALID_POS = -1;
+    static __int32 const INVALID_REF_ID = -1;
+    static __int32 const INVALID_LEN = 0;
+    static __uint32 const INVALID_QID = 4294967295u;
+
+    HtsSequenceRecord()
+      : qName(), seq(), qual() {}
+
+    HtsSequenceRecord(bam1_t * hts_record)
+    {
+        HtsSequenceRecord::parse(hts_record);
+    }
+
+    void parse(bam1_t * hts_record)
+    {
+        qName = bam_get_qname(hts_record);
+        int32_t lqseq = hts_record->core.l_qseq;
+        resize(seq, lqseq, Exact());
+        uint8_t* seqptr = bam_get_seq(hts_record);
+
+        for (int i = 0; i < lqseq; ++i)
+        {
+          seq[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, i)];
+        }
+
+        uint8_t* qualptr = bam_get_qual(hts_record);
+        resize(qual, lqseq, Exact());
+
+        for (int i = 0; i < lqseq; ++i, ++qualptr)
+        {
+            qual[i] = static_cast<char>(*qualptr + 33);
+        }
+    }
+};
+
+} // namespace seqan
+
+#endif // SEQAN_HTS_IO_HTS_ALIGNMENT_RECORD_H_
diff --git a/seqan/hts_io/hts_alignment_record_utils.h b/seqan/hts_io/hts_alignment_record_utils.h
new file mode 100644
index 0000000..9986545
--- /dev/null
+++ b/seqan/hts_io/hts_alignment_record_utils.h
@@ -0,0 +1,24 @@
+#ifndef INCLUDE_SEQAN_HTS_IO_HTS_ALIGNMENT_RECORD_UTILS_H_
+#define INCLUDE_SEQAN_HTS_IO_HTS_ALIGNMENT_RECORD_UTILS_H_
+
+#include <seqan/bam_io/bam_alignment_record.h>
+#include <seqan/hts_io/hts_file.h>
+
+namespace seqan {
+
+
+CharString inline
+getContigName(int32_t const rID, HtsFile const & file)
+{
+    SEQAN_ASSERT(file.hdr);
+
+    if (rID < 0 || rID >= file.hdr->n_targets)
+        return CharString("");
+
+    return CharString(file.hdr->target_name[rID]);
+}
+
+
+} // namespace seqan
+
+#endif // INCLUDE_SEQAN_HTS_IO_HTS_ALIGNMENT_RECORD_UTILS_H_
diff --git a/seqan/hts_io/hts_file.h b/seqan/hts_io/hts_file.h
new file mode 100644
index 0000000..a3bfe4f
--- /dev/null
+++ b/seqan/hts_io/hts_file.h
@@ -0,0 +1,463 @@
+#ifndef SEQAN_HTS_IO_HTS_FILE_IN_H_
+#define SEQAN_HTS_IO_HTS_FILE_IN_H_
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <fcntl.h>
+#include <iostream>
+#include <sys/types.h>
+
+#include <seqan/basic.h>
+
+#include <htslib/hfile.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+// #include <htslib/vcf.h>
+#include <htslib/bgzf.h>
+
+#include <seqan/hts_io/bam_alignment_record.h>
+#include <seqan/hts_io/hts_alignment_record.h>
+
+
+namespace seqan
+{
+
+class HtsFile
+{
+  public:
+    const char * filename;  /** @brief The filename of the current file. */
+    htsFile * fp;           /** @brief Pointer to the file. */
+    bam_hdr_t * hdr;        /** @brief The header of the current file. */
+    bam1_t * hts_record;    /** @brief The current HTS record. */
+    hts_idx_t * hts_index;  /** @brief The index of the file. */
+    hts_itr_t * hts_iter;   /** @brief An iterator that iterates through a certain region in the HTS file. */
+    const char * file_mode; /** @brief Which file mode to use. E.g. "r" for reading and "wb" for writing binaries. */
+    bool at_end = false;
+    bool read_all = true;
+
+    /**
+     * @brief Empty HTS file constructor
+     */
+    HtsFile(const char * mode = "r")
+      : filename(""), fp(nullptr), hdr(nullptr), hts_record(nullptr), hts_index(nullptr), hts_iter(nullptr), file_mode(mode), at_end(false)
+    {
+        // Don't call open() yet, file name is not known
+    }
+
+    /**
+     * @brief Constructs a new HtsFile object.
+     *
+     * @param f The filename of the file.
+     * @param mode The file mode to use when opening the file.
+     * @param reference Reference FASTA file. Used for reading CRAM files.
+     * @return A new HtsFile object.
+     */
+    HtsFile(const char * f, const char * mode, const char * reference = "")
+      : filename(f), fp(nullptr), hdr(nullptr), hts_record(nullptr), hts_index(nullptr), hts_iter(nullptr), file_mode(mode), at_end(false)
+    {
+        open(reference);
+    }
+
+    /**
+     * @brief Destructs an HtsFile object.
+     */
+    ~HtsFile()
+    {
+        if (hdr)
+            bam_hdr_destroy(hdr);
+
+        if (hts_record)
+            bam_destroy1(hts_record);
+
+        if (fp)
+            hts_close(fp);
+    }
+
+    inline bool
+    open(const char * reference = "")
+    {
+        const char * read_mode = "r";
+        fp = hts_open(filename, file_mode);
+
+        if (fp == nullptr)
+        {
+            SEQAN_FAIL("Could not open file with filename %s", filename);
+            // return false;
+        }
+
+        // Use a specific reference FASTA file (needed for reading CRAM with no reference in @SQ tags in header)
+        if (reference != nullptr && reference[0] != '\0')
+        {
+            int ret = hts_set_fai_filename(fp, reference);
+
+            if (ret < 0)
+            {
+                SEQAN_FAIL("Could not open reference FASTA file with filename %s", reference);
+            }
+        }
+
+        if (strcmp(file_mode, read_mode) == 0)
+        {
+            hdr = sam_hdr_read(fp);
+        }
+
+        // if (hdr == nullptr)
+        // {
+        //   return false;
+        // }
+
+        hts_record = bam_init1();
+        return true;
+    }
+};
+
+class HtsFileIn : public HtsFile
+{
+  public:
+    HtsFileIn()
+      : HtsFile("r") {}
+
+    HtsFileIn(const char * f)
+      : HtsFile(f, "r") {}
+};
+
+class HtsFileOut : public HtsFile
+{
+  public:
+    HtsFileOut(const char * mode = "wb")
+      : HtsFile(mode) {}
+
+    HtsFileOut(const char * f, const char * mode = "wb")
+      : HtsFile(f, mode) {}
+};
+
+
+/* For backwards compability */
+typedef HtsFileIn BamFileIn;
+typedef HtsFileOut BamFileOut;
+
+
+/**
+ * @brief Opens a HTS file from filename.
+ *
+ * @param target An empty HtsFile object.
+ * @param f The filename to open from.
+ */
+inline bool
+open(HtsFile & target, const char * f)
+{
+    target.filename = f;
+    return target.open();
+}
+
+/**
+ * @brief Opens a HTS from stream (e.g. std::cin).
+ *
+ * @param target An empty HtsFile object.
+ * @param s The stream to read from.
+ */
+inline bool
+open(HtsFile & target, std::istream &)
+{
+    return open(target, "-");
+}
+
+
+/**
+ * @brief Copies a header from a source HTS file and replaces the header of the target.
+ *
+ * @param target Target HTS file.
+ * @param source Source HTS file.
+ */
+inline void
+copyHeader(HtsFile & target, HtsFile const & source)
+{
+    target.hdr = bam_hdr_dup(source.hdr);
+}
+
+/**
+ * @brief Copies a record from a source HTS file and replaces the record of the target.
+ *
+ * @param target Target HTS file.
+ * @param source Source HTS file.
+ */
+inline void
+copyRecord(HtsFile & target, HtsFile const & source)
+{
+    target.hts_record = bam_dup1(source.hts_record);
+}
+
+/**
+ * @brief Loads an index for a HTS file using the default filename.
+ *
+ * @param file HTS file to load index for.
+ * @returns True on success, otherwise false.
+ */
+inline bool
+loadIndex(HtsFile & file)
+{
+    file.hts_index = sam_index_load(file.fp, file.filename);
+    return file.hts_index != nullptr;
+}
+
+/**
+ * @brief Loads an index for a HTS file with a specific filename.
+ *
+ * @param file HTS file to load index for.
+ * @param indexFileName The filename of the index.
+ */
+inline bool
+loadIndex(HtsFile & file, const char * indexFileName)
+{
+    file.hts_index = sam_index_load2(file.fp, file.filename, indexFileName);
+    return file.hts_index != nullptr;
+}
+
+/**
+ * @brief Builds an index for BAM or CRAM files using the default filename.
+ *
+ * @param file The file to build index for.
+ * @param min_shift Force a certain minimum amount of shift. (I think) smaller shifts mean more accurate queries at the cost of index size.
+ *                  The default value is 0, which means the default value of htslib will be used.
+ * @returns True on success, otherwise false.
+ */
+inline bool
+buildIndex(HtsFile & file, int min_shift = 0)
+{
+    return !sam_index_build(file.filename, min_shift);
+}
+
+/**
+ * @brief Builds an index for BAM or CRAM files using a specific filename.
+ *
+ * @param file The file to build index for.
+ * @param min_shift Force a certain minimum amount of shift. (I think) smaller shifts mean more accurate queries at the cost of index size.
+ *                  The default value is 0, which means the default value of htslib will be used.
+ * @returns True on success, otherwise false.
+ */
+inline bool
+buildIndex(HtsFile & file, const char * indexFileName, int min_shift = 0)
+{
+    return !sam_index_build2(file.filename, indexFileName, min_shift);
+}
+
+/**
+ * @brief Uses the index to go to a certain region of the HTS file.
+ *
+ * @param file HTS file to change index on.
+ * @param region The region to go to. Should be on one of these formats: chrX, chrX:A, or chrX:A-B.
+ */
+inline bool
+setRegion(HtsFile & file, const char * region)
+{
+    if (strncmp(region, ".", 1) == 0)
+    {
+      file.read_all = true;
+      return true;
+    }
+    else
+    {
+      file.read_all = false;
+    }
+
+    if (file.hts_iter != nullptr)
+        sam_itr_destroy(file.hts_iter);
+
+    if (file.hdr == nullptr)
+    {
+      if (!file.open())
+        return false;
+    }
+
+    file.hts_iter = sam_itr_querys(file.hts_index, file.hdr, region);
+    return file.hts_iter;
+}
+
+inline bool
+setRegion(HtsFile & file, const char * chromosome, int start, int end)
+{
+    file.read_all = false;
+    if (file.hts_iter != nullptr)
+        sam_itr_destroy(file.hts_iter);
+
+    char region[50];
+    sprintf(region, "%s:%d-%d", chromosome, start, end);
+
+    if (file.hdr == nullptr)
+    {
+      if (!file.open())
+        return false;
+    }
+
+    file.hts_iter = sam_itr_querys(file.hts_index, file.hdr, region);
+    return file.hts_iter != nullptr;
+}
+
+inline bool
+setRegion(HtsFile & file, int32_t tid, int32_t start, int32_t end)
+{
+    file.read_all = false;
+    if (file.hts_iter != nullptr)
+        sam_itr_destroy(file.hts_iter);
+
+    file.hts_iter = sam_itr_queryi(file.hts_index, tid, start, end);
+    return file.hts_iter;
+}
+
+/**
+ * @brief Check if the have read the last of record of an input file.
+ *
+ * @param file An input file.
+ * @return True if we have read the last record.
+ */
+inline bool
+atEnd(HtsFileIn const & file)
+{
+    return file.at_end;
+}
+
+/**
+ * @brief Read the next record from a HTS file.
+ *
+ * @param file HTS file to read from.
+ * @returns True on success, otherwise false.
+ */
+inline bool
+readRecord(HtsFile & file)
+{
+    if (sam_read1(file.fp, file.hdr, file.hts_record) >= 0)
+    {
+        return true;
+    }
+
+    file.at_end = true;
+    return false;
+}
+
+/**
+ * @brief Read the next record from a HTS file and parse it to a sequence record.
+ *
+ * @param record Sequencing record to write to.
+ * @param file HTS file to read from.
+ * @returns True on success, otherwise false.
+ */
+inline bool
+readRecord(HtsSequenceRecord & record, HtsFile & file)
+{
+    if (readRecord(file))
+    {
+        record.parse(file.hts_record);
+        return true;
+    }
+    else
+    {
+        // We've reached the end of the file, or an error occured.
+        return false;
+    }
+}
+
+/**
+ * @brief Reads an alignment record.
+ *
+ * @param record The record to insert data into.
+ * @param file The file to read from.
+ */
+inline bool
+readRecord(BamAlignmentRecord & record, HtsFile & file)
+{
+    if (readRecord(file))
+    {
+        parse(record, file.hts_record);
+        return true;
+    }
+    else
+    {
+        // We've reached the end of the file, or an error occured.
+        return false;
+    }
+}
+
+/**
+ * @brief Read the next record from a region and parse it to a sequence record.
+ *
+ * @param record Sequencing record to write to.
+ * @param file HTS file to read from.
+ * @returns True on success, otherwise false.
+ */
+inline bool
+readRegion(HtsSequenceRecord & record, HtsFile & file)
+{
+    if (file.read_all)
+    {
+        return readRecord(record, file);
+    }
+
+    if (sam_itr_next(file.fp, file.hts_iter, file.hts_record) >= 0)
+    {
+        record.parse(file.hts_record);
+        return true;
+    }
+    else
+    {
+        // We've reached the end of the file, or an error occured.
+        return false;
+    }
+}
+
+inline bool
+readRegion(BamAlignmentRecord & record, HtsFile & file)
+{
+    if (file.read_all)
+    {
+        return readRecord(record, file);
+    }
+
+    if (sam_itr_next(file.fp, file.hts_iter, file.hts_record) >= 0)
+    {
+        parse(record, file.hts_record);
+        return true;
+    }
+    else
+    {
+        // We've reached the end of the file, or an error occured.
+        return false;
+    }
+}
+
+/**
+ * @brief Writes a HTS header to disk.
+ *
+ * @param file HTS file to get the header from.
+ * @returns True on success, otherwise false.
+ */
+inline bool
+writeHeader(HtsFile & file)
+{
+    return sam_hdr_write(file.fp, file.hdr) >= 0;
+}
+
+/**
+ * @brief Writes a record to file.
+ *
+ * @param file The file to write to.
+ * @param record The record to write.
+ *
+ * @returns True on success, otherwise false.
+ */
+inline bool
+writeRecord(HtsFile & file, BamAlignmentRecord const & record)
+{
+    int ret = parse(file.hts_record, file.hdr, record);
+
+    if (ret < 0)
+      return false;
+
+    return sam_write1(file.fp, file.hdr, file.hts_record) >= 0;
+}
+
+
+} // namespace seqan
+
+#endif  // SEQAN_HTS_IO_HTS_FILE_IN_H_
diff --git a/seqan/index.h b/seqan/index.h
index ec27b61..291dde4 100644
--- a/seqan/index.h
+++ b/seqan/index.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -33,8 +34,9 @@
 #ifndef SEQAN_HEADER_INDEX_H
 #define SEQAN_HEADER_INDEX_H
 
-//____________________________________________________________________________
-// prerequisites
+// ==========================================================================
+// Prerequisites.
+// ==========================================================================
 
 #include <seqan/sequence.h>
 #include <seqan/pipe.h>
@@ -42,8 +44,9 @@
 #include <seqan/parallel.h>
 
 #include <seqan/find.h>
-#include <seqan/misc/misc_set.h>
-#include <seqan/misc/misc_memset.h>
+#include <seqan/misc/set.h>
+#include <seqan/misc/memset.h>
+#include <seqan/misc/bit_twiddling.h>
 
 #include <climits>
 #include <functional>
@@ -56,10 +59,13 @@
 #include <cmath>    // isnan, isinf
 #include <string.h> // memset
 
-//////////////////////////////////////////////////////////////////////////////
-// INDEX CONSTRUCTION
-//////////////////////////////////////////////////////////////////////////////
+#ifdef __SSE4_2__
+#include <nmmintrin.h>
+#endif
 
+// ==========================================================================
+// Index construction.
+// ==========================================================================
 
 #include <seqan/index/index_forwards.h>
 
@@ -69,20 +75,24 @@
 
 #include <seqan/index/index_base.h>
 
-//____________________________________________________________________________
-// q-gram index creator
+#include <seqan/index/find_index_binary.h>
+
+// ----------------------------------------------------------------------------
+// q-Gram index creator.
+// ----------------------------------------------------------------------------
 
 #include <seqan/index/shape_base.h>
 #include <seqan/index/shape_gapped.h>
 #include <seqan/index/shape_onegapped.h>
 #include <seqan/index/shape_predefined.h>
 #include <seqan/index/shape_threshold.h>
+#include <seqan/index/shape_minimizer.h>
 #include <seqan/index/index_qgram.h>
 #include <seqan/index/index_qgram_openaddressing.h>
-//#include <seqan/index/index_qgram_nested.h>
 
-//____________________________________________________________________________
-// suffix array creators
+// ----------------------------------------------------------------------------
+// Suffix array creators.
+// ----------------------------------------------------------------------------
 
 #include <seqan/index/radix.h>
 #include <seqan/index/index_sa_btree.h>
@@ -102,8 +112,9 @@
 #include <seqan/index/pump_separator7.h>
 #include <seqan/index/index_skew7_multi.h>
 
-//____________________________________________________________________________
-// enhanced table creators
+// ----------------------------------------------------------------------------
+// Enhanced table creators.
+// ----------------------------------------------------------------------------
 
 #include <seqan/index/pump_lcp_core.h>
 #include <seqan/index/index_lcp.h>
@@ -112,47 +123,91 @@
 #include <seqan/index/index_childtab.h>
 #include <seqan/index/index_bwt.h>
 
-
-//////////////////////////////////////////////////////////////////////////////
-// INDEX USAGE
-//////////////////////////////////////////////////////////////////////////////
+// ==========================================================================
+// Index usage.
+// ==========================================================================
 
 #include <seqan/index/index_shims.h>
 
-//____________________________________________________________________________
-// (virtual) string trees
+// ----------------------------------------------------------------------------
+// Virtual string trees.
+// ----------------------------------------------------------------------------
 
 #include <seqan/index/index_esa_base.h>
 #include <seqan/index/index_esa_stree.h>
 #include <seqan/index/index_wotd.h>
 #include <seqan/index/index_dfi.h>
+#include <seqan/index/index_sa_stree.h>
+#include <seqan/index/index_sa_truncated.h>
+#include <seqan/index/index_qgram_stree.h>
+#include <seqan/index/index_qgram_bucketrefinement.h>
+
+// ----------------------------------------------------------------------------
+// Rank dictionaries.
+// ----------------------------------------------------------------------------
+
+#include <seqan/index/index_fm_rank_dictionary_base.h>
+#include <seqan/index/index_fm_rank_dictionary_naive.h>
+#include <seqan/index/index_fm_rank_dictionary_levels.h>
+#include <seqan/index/index_fm_right_array_binary_tree.h>
+#include <seqan/index/index_fm_right_array_binary_tree_iterator.h>
+#include <seqan/index/index_fm_rank_dictionary_wt.h>
+
+// ----------------------------------------------------------------------------
+// Sparse strings.
+// ----------------------------------------------------------------------------
+
+#include <seqan/index/index_fm_sparse_string.h>
+
+// ----------------------------------------------------------------------------
+// FM index.
+// ----------------------------------------------------------------------------
+
+#include <seqan/index/index_fm_lf_table.h>
+#include <seqan/index/index_fm_compressed_sa.h>
+#include <seqan/index/index_fm_compressed_sa_iterator.h>
+#include <seqan/index/index_fm.h>
+#include <seqan/index/index_fm_stree.h>
 
-//____________________________________________________________________________
-// suffix tree algorithms
+// ----------------------------------------------------------------------------
+// Suffix tree algorithms.
+// ----------------------------------------------------------------------------
 
 #include <seqan/index/index_esa_algs.h>
 #include <seqan/index/index_esa_algs_multi.h>
 #include <seqan/index/index_esa_drawing.h>
 #include <seqan/index/repeat_base.h>
 
-//____________________________________________________________________________
-// Pizza & Chili interface (compressed indices)
+// ----------------------------------------------------------------------------
+// Pizza & Chili interface (compressed indices).
+// ----------------------------------------------------------------------------
 
 #include <seqan/index/index_pizzachili.h>
 #include <seqan/index/index_pizzachili_find.h>
 
-//____________________________________________________________________________
-// Shawarma interface (suffix array creators)
+// ----------------------------------------------------------------------------
+// Shawarma interface (suffix array creators).
+// ----------------------------------------------------------------------------
 
 #include <seqan/index/index_shawarma.h>
 
+// ----------------------------------------------------------------------------
+// View and device indices.
+// ----------------------------------------------------------------------------
 
-//////////////////////////////////////////////////////////////////////////////
-// FINDER INTERFACE
-//////////////////////////////////////////////////////////////////////////////
+#include <seqan/index/index_view.h>
+// NOTE(esiragusa): CUDA FM-index is broken.
+//#ifdef PLATFORM_CUDA
+//#include <seqan/index/index_device.h>
+//#endif
 
-//____________________________________________________________________________
-// index based finders
+// ==========================================================================
+// Finder interface.
+// ==========================================================================
+
+// ----------------------------------------------------------------------------
+// Index based finders.
+// ----------------------------------------------------------------------------
 
 #include <seqan/index/find_index_esa.h>
 #include <seqan/index/find_index_approx.h>
@@ -160,24 +215,26 @@
 #include <seqan/index/find_index.h>
 #include <seqan/index/find_quasar.h>
 #include <seqan/index/find_swift.h>
-
-//////////////////////////////////////////////////////////////////////////////
-// FM INDEX
-//////////////////////////////////////////////////////////////////////////////
-#include <seqan/index/index_fm_rank_support_bit_string.h>
-#include <seqan/index/index_fm_rank_support_bit_string_iterator.h>
-#include <seqan/index/index_fm_sparse_string.h>
-#include <seqan/index/index_fm_compressed_sa.h>
-#include <seqan/index/index_fm_compressed_sa_iterator.h>
-#include <seqan/index/index_fm_prefix_sum_table.h>
-#include <seqan/index/index_fm_right_array_binary_tree.h>
-#include <seqan/index/index_fm_right_array_binary_tree_iterator.h>
-// #include <seqan/index/index_fm_wavelet_tree.h>
-#include <seqan/index/index_fm_rank_dictionary_wt.h>
-#include <seqan/index/index_fm_rank_dictionary_bms.h>
-#include <seqan/index/index_fm_sentinel_rank_dictionary.h>
-#include <seqan/index/index_fm_lf_table.h>
-#include <seqan/index/index_fm.h>
-#include <seqan/index/index_fm_stree.h>
+#include <seqan/index/find_pigeonhole.h>
+#include <seqan/index/find_backtracking.h>
+
+// ----------------------------------------------------------------------------
+// Non-standard index based finders.
+// ----------------------------------------------------------------------------
+
+#include <seqan/index/find2_base.h>
+#include <seqan/index/find2_index.h>
+#include <seqan/index/find2_backtracking.h>
+#include <seqan/index/find2_vstree_factory.h>
+#include <seqan/index/find2_index_multi.h>
+#include <seqan/index/find2_functors.h>
+
+// ----------------------------------------------------------------------------
+// Lambda interface.
+// ----------------------------------------------------------------------------
+
+#ifdef SEQAN_CXX11_STANDARD
+#include <seqan/index/find_index_lambda.h>
+#endif
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/index/INFO b/seqan/index/INFO
deleted file mode 100644
index 5fcb371..0000000
--- a/seqan/index/INFO
+++ /dev/null
@@ -1,12 +0,0 @@
-Name: seqan-index
-Author: David Weese <david.weese@fu-berlin.de>
-Author: Birte Kehr <birte.kehr@fu-berlin.de>
-Author: Jochen Singer <jochen.singer@fu-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Index data structures.
- This module contains index data structures such as q-gram indices, and extended
- suffix arrays as well as algorithms for building and using them.  It also
- contains the semiglobal and local SWIFT implementations.
diff --git a/seqan/index/find2_backtracking.h b/seqan/index/find2_backtracking.h
new file mode 100644
index 0000000..5cffb7e
--- /dev/null
+++ b/seqan/index/find2_backtracking.h
@@ -0,0 +1,1359 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Approximate string matching via backtracking on two substring indices.
+// ==========================================================================
+
+#ifndef SEQAN_FIND_BACKTRACKING_MULTIPLE_H_
+#define SEQAN_FIND_BACKTRACKING_MULTIPLE_H_
+
+//#define SEQAN_DEBUG
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TDistance, typename TSpec>
+struct Backtracking;
+
+struct StageInitial_;
+struct StageUpper_;
+struct StageDiagonal_;
+struct StageLower_;
+struct StageFinal_;
+struct StageExact_;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction TextIterator_
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec>
+struct TextIterator_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> >
+{
+    typedef typename Iterator<Index<TText, TTextIndexSpec>, TopDown<> >::Type   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction PatternIterator_
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec>
+struct PatternIterator_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> >
+{
+    typedef typename Iterator<Index<TPattern, TPatternIndexSpec>, TopDown<> >::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction VertexScore_
+// ----------------------------------------------------------------------------
+
+template <typename TBacktracking>
+struct VertexScore_ {};
+
+template <typename TSpec>
+struct VertexScore_<Backtracking<HammingDistance, TSpec> >
+{
+    typedef unsigned char           Type;
+};
+
+template <typename TSpec>
+struct VertexScore_<Backtracking<EditDistance, TSpec> >
+{
+    typedef String<unsigned char>                   TString;
+    typedef Segment<TString, InfixSegment>          Type;
+    typedef Segment<const TString, InfixSegment>    ConstType;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction VertexScoreStack_
+// ----------------------------------------------------------------------------
+
+template <typename TBacktracking>
+struct VertexScoreStack_ {};
+
+template <typename TSpec>
+struct VertexScoreStack_<Backtracking<HammingDistance, TSpec> >
+{
+    typedef String<typename VertexScore_<Backtracking<HammingDistance, TSpec> >::Type> Type;
+};
+
+template <typename TSpec>
+struct VertexScoreStack_<Backtracking<EditDistance, TSpec> >
+{
+    typedef StringSet<typename VertexScore_<Backtracking<EditDistance, TSpec> >::TString, Owner<ConcatDirect<> > > Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction NextStage_
+// ----------------------------------------------------------------------------
+
+template <typename TBacktracking, typename TStage>
+struct NextStage_
+{
+    typedef Nothing         Type;
+};
+
+// HammingDistance: StageInitial|StageExact -> StageFinal
+
+template <typename TSpec>
+struct NextStage_<Backtracking<HammingDistance, TSpec>, StageInitial_>
+{
+    typedef StageFinal_     Type;
+};
+
+template <typename TSpec>
+struct NextStage_<Backtracking<HammingDistance, TSpec>, StageExact_>
+{
+    typedef StageFinal_     Type;
+};
+
+// EditDistance: StageInitial -> StageUpper -> StageDiagonal -> StageLower -> StageFinal
+
+template <typename TSpec>
+struct NextStage_<Backtracking<EditDistance, TSpec>, StageInitial_>
+{
+    typedef StageUpper_     Type;
+};
+
+template <typename TSpec>
+struct NextStage_<Backtracking<EditDistance, TSpec>, StageUpper_>
+{
+    typedef StageDiagonal_  Type;
+};
+
+template <typename TSpec>
+struct NextStage_<Backtracking<EditDistance, TSpec>, StageDiagonal_>
+{
+    typedef StageLower_     Type;
+};
+
+template <typename TSpec>
+struct NextStage_<Backtracking<EditDistance, TSpec>, StageLower_>
+{
+    typedef StageFinal_     Type;
+};
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tags for backtracking stages
+// ----------------------------------------------------------------------------
+
+struct StageInitial_ {};
+struct StageUpper_ {};
+struct StageDiagonal_ {};
+struct StageLower_ {};
+struct StageFinal_ {};
+struct StageExact_ {};
+
+// ----------------------------------------------------------------------------
+// Class Finder_
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec,
+          typename TDistance, typename TSpec>
+struct Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> >
+{
+    typedef Index<TText, TTextIndexSpec>                                                TTextIndex;
+    typedef Index<TPattern, TPatternIndexSpec>                                          TPatternIndex;
+    typedef Backtracking<TDistance, TSpec>                                              TBacktracking;
+    typedef typename TextIterator_<TTextIndex, TPatternIndex, TBacktracking>::Type      TTextIterator;
+    typedef typename PatternIterator_<TTextIndex, TPatternIndex, TBacktracking>::Type   TPatternIterator;
+    typedef String<TTextIterator>                                                       TTextStack;
+    typedef String<TPatternIterator>                                                    TPatternStack;
+    typedef typename VertexScoreStack_<TBacktracking>::Type                             TVertexScoreStack;
+    typedef typename Score_<TBacktracking>::Type                                        TScore;
+
+    TTextStack              textStack;
+    TPatternStack           patternStack;
+    TVertexScoreStack       scoreStack;
+    TScore                  maxScore;
+
+    Finder_() :
+        textStack(),
+        patternStack(),
+        scoreStack(),
+        maxScore(0)
+    {}
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _min3()
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+inline TValue
+_min3(TValue a, TValue b, TValue c)
+{
+    TValue m = a;
+    if (m > b) m = b;
+    if (m > c) m = c;
+    return m;
+}
+
+// ----------------------------------------------------------------------------
+// Function _updateVertexScore()
+// ----------------------------------------------------------------------------
+
+template <typename TVertexScore>
+inline void
+_updateVertexScore(TVertexScore current,
+                   TVertexScore const previous,
+                   StageInitial_ const & /* tag */)
+{
+    // Update last cell.
+    // C[i,0] = C[i-1,0] + 1 [Upper]
+    back(current) = back(previous) + 1;
+}
+
+template <typename TVertexScore, typename TTextValue, typename TPatternIterator, typename TStage>
+inline void
+_updateVertexScore(TVertexScore current,
+                   TVertexScore const previous,
+                   TTextValue textChar,
+                   TPatternIterator patternIt,
+                   TStage const & /* tag */)
+{
+    typedef typename Iterator<TVertexScore, Standard>::Type         TVertexScoreIterator;
+    typedef typename Iterator<TVertexScore const, Standard>::Type   TVertexScoreConstIterator;
+    typedef typename Value<TVertexScore>::Type                      TScore;
+
+    TVertexScoreIterator currentIt = begin(current, Standard());
+    TVertexScoreIterator columnEnd = end(current, Standard());
+    TVertexScoreConstIterator previousIt = begin(previous, Standard());
+
+    // Update first cell.
+    if (IsSameType<TStage, StageUpper_>::VALUE)
+    {
+        // C[0,j] = C[0,j-1] + 1 [Left]
+        value(currentIt) = value(previousIt) + 1;
+    }
+    else
+    {
+        TScore score = ordEqual(textChar, value(patternIt)) ? 0 : 1;
+
+        // C[i,j] = min { C[i-1,j-1] + d(t,p), C[i-1,j] + 1 } [Diagonal, Left]
+        value(currentIt) = _min(value(previousIt) + score, value(previousIt + 1) + 1);
+
+        ++previousIt;
+        ++patternIt;
+    }
+
+    // Update central cells.
+    for (++currentIt; currentIt != columnEnd - 1; ++currentIt, ++previousIt, ++patternIt)
+    {
+        TScore score = ordEqual(textChar, value(patternIt)) ? 0 : 1;
+
+        // C[i,j] = min { C[i-1,j-1] + d(t,p), C[i-1,j] + 1, C[i,j-1] + 1 } [Diagonal, Left, Upper]
+        value(currentIt) = _min3(value(previousIt) + score, value(previousIt + 1) + 1, value(currentIt - 1) + 1);
+    }
+
+    // Update last cell.
+    if (IsSameType<TStage, StageLower_>::VALUE)
+    {
+        TScore score = ordEqual(textChar, value(patternIt)) ? 0 : 1;
+
+        // C[i,j] = min { C[i-1,j-1] + d(t,p), C[i-1,j] + 1, C[i,j-1] + 1 } [Diagonal, Left, Upper]
+        value(currentIt) = _min3(value(previousIt) + score, value(previousIt + 1) + 1, value(currentIt - 1) + 1);
+
+        ++previousIt;
+    }
+    else
+    {
+        TScore score = ordEqual(textChar, value(patternIt)) ? 0 : 1;
+
+        // C[i,j] = min { C[i-1,j-1] + d(t,p), C[i,j-1] + 1 } [Diagonal, Upper]
+        value(currentIt) = _min(value(previousIt) + score, value(currentIt - 1) + 1);
+    }
+
+    // Assert end of columns.
+    SEQAN_ASSERT_EQ(currentIt + 1, end(current, Standard()));
+    SEQAN_ASSERT_EQ(previousIt + 1, end(previous, Standard()));
+}
+
+template <typename TVertexScore, typename TTextValue, typename TPatternValue>
+inline void
+_updateVertexScore(TVertexScore current,
+                   TVertexScore const previous,
+                   TTextValue textChar,
+                   TPatternValue patternChar,
+                   StageFinal_ const & /* tag */)
+{
+    typedef typename Iterator<TVertexScore, Standard>::Type         TVertexScoreIterator;
+    typedef typename Iterator<TVertexScore const, Standard>::Type   TVertexScoreConstIterator;
+    typedef typename Value<TVertexScore>::Type                      TScore;
+
+    TVertexScoreIterator currentIt = begin(current, Standard());
+    TVertexScoreConstIterator previousIt = begin(previous, Standard());
+
+    // Update last cell.
+    TScore score = ordEqual(textChar, patternChar) ? 0 : 1;
+
+    // C[i,j] = min { C[i-1,j-1] + d(t,p), C[i-1,j] + 1 } [Diagonal, Left]
+    value(currentIt) = _min(value(previousIt) + score, value(previousIt + 1) + 1);
+
+    // Assert end of columns.
+    SEQAN_ASSERT_EQ(currentIt + 1, end(current, Standard()));
+    SEQAN_ASSERT_EQ(previousIt + 2, end(previous, Standard()));
+}
+
+// ----------------------------------------------------------------------------
+// Function copyBackAndResize()                                     [StringSet]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSSetSpec, typename TDelta>
+inline void
+copyBackAndResize(StringSet<TString, TSSetSpec> & stringSet, TDelta delta)
+{
+    // Copy last element to the back.
+    appendValue(stringSet, back(stringSet));
+
+    // Update limits.
+    back(stringSet.limits) += delta;
+
+    // Resize concat.
+    resize(stringSet.concat, length(stringSet.concat) + delta);
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec>
+inline void
+clear(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder)
+{
+    clear(finder.textStack);
+    clear(finder.patternStack);
+    clear(finder.scoreStack);
+}
+
+// ----------------------------------------------------------------------------
+// Function _initState()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TTextIterator, typename TPatternIterator>
+inline void
+_initState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+           TTextIterator const & textIt, TPatternIterator const & patternIt)
+{
+    // Init iterators.
+    appendValue(finder.textStack, textIt);
+    appendValue(finder.patternStack, patternIt);
+
+    _initScore(finder);
+
+#ifdef SEQAN_DEBUG
+        _printState(finder, StageInitial_());
+#endif
+}
+
+// ----------------------------------------------------------------------------
+// Function _initScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec>
+inline void
+_initScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder)
+{
+    typedef Backtracking<TDistance, TSpec>              TBacktracking;
+    typedef typename Score_<TBacktracking>::Type        TScore;
+
+    // Push zero.
+    appendValue(finder.scoreStack, TScore());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_initScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder)
+{
+    typedef Backtracking<EditDistance, TSpec>           TBacktracking;
+    typedef typename Score_<TBacktracking>::Type        TScore;
+
+    // Push a column with one zero cell.
+    append(finder.scoreStack.limits, 1);
+    appendValue(finder.scoreStack.concat, TScore());
+}
+
+// ----------------------------------------------------------------------------
+// Function _pushState()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_pushState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+           TStage const & /* tag */)
+{
+    _pushIterators(finder, TStage());
+    _pushScore(finder, TStage());
+
+    if (_moveIteratorsDown(finder, TStage()))
+    {
+        _updateScore(finder, TStage());
+
+#ifdef SEQAN_DEBUG
+        _printPush(finder, TStage());
+#endif
+        return true;
+    }
+
+    _popIterators(finder, TStage());
+    _popScore(finder, TStage());
+
+    return false;
+}
+
+// ----------------------------------------------------------------------------
+// Function _pushIterators()
+// ----------------------------------------------------------------------------
+// TODO(esiragusa): Specialize _pushIterators() for StageInitial_ and StageFinal_ of EditDistance
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_pushIterators(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+               TStage const & /* tag */)
+{
+    appendValue(finder.patternStack, back(finder.patternStack));
+    appendValue(finder.textStack, back(finder.textStack));
+}
+
+// ----------------------------------------------------------------------------
+// Function _pushScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_pushScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+           TStage const & /* tag */)
+{
+    // Copy the last score on top of the stack.
+    appendValue(finder.scoreStack, back(finder.scoreStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_pushScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > & /* finder */,
+           StageExact_ const & /* tag */)
+{
+    // Do nothing.
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_pushScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+           StageInitial_ const & /* tag */)
+{
+    // Copy the last column on top of the stack and add one cell.
+    copyBackAndResize(finder.scoreStack, 1);
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_pushScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+           StageUpper_ const & /* tag */)
+{
+    _pushScore(finder, StageInitial_());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_pushScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+           StageLower_ const & /* tag */)
+{
+    // Copy the last column on top of the stack and remove one cell.
+    copyBackAndResize(finder.scoreStack, -1);
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_pushScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+           StageFinal_ const & /* tag */)
+{
+    _pushScore(finder, StageLower_());
+}
+
+// ----------------------------------------------------------------------------
+// Function _moveIteratorsDown()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_moveIteratorsDown(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+                   TStage const & /* tag */)
+{
+    // Go down in text and pattern.
+    return goDown(back(finder.textStack)) && goDown(back(finder.patternStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveIteratorsDown(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > & finder,
+                   StageExact_ const & /* tag */)
+{
+    typedef Index<TText, TTextIndexSpec>                                                TTextIndex;
+    typedef Index<TPattern, TPatternIndexSpec>                                          TPatternIndex;
+    typedef Backtracking<HammingDistance, TSpec>                                        TBacktracking;
+    typedef typename TextIterator_<TTextIndex, TPatternIndex, TBacktracking>::Type      TTextIterator;
+    typedef typename PatternIterator_<TTextIndex, TPatternIndex, TBacktracking>::Type   TPatternIterator;
+
+    TTextIterator & textIt = back(finder.textStack);
+    TPatternIterator & patternIt = back(finder.patternStack);
+
+    // Go down in pattern and search pattern label in text.
+    if (goDown(patternIt) && goDown(textIt, parentEdgeLabel(patternIt)))
+        return true;
+
+    // Otherwise go right in pattern.
+    return _moveIteratorsRight(finder, StageExact_());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveIteratorsDown(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+                   StageInitial_ const & /* tag */)
+{
+    // Go down in pattern.
+    return goDown(back(finder.patternStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveIteratorsDown(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+                   StageLower_ const & /* tag */)
+{
+    // Go down in text.
+    return goDown(back(finder.textStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveIteratorsDown(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+                   StageFinal_ const & /* tag */)
+{
+    return _moveIteratorsDown(finder, StageLower_());
+}
+
+// ----------------------------------------------------------------------------
+// Function _nextState()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_nextState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+           TStage const & /* tag */)
+{
+    if (_moveIteratorsRight(finder, TStage()))
+    {
+        _updateScore(finder, TStage());
+
+#ifdef SEQAN_DEBUG
+        _printState(finder, TStage());
+#endif
+        return true;
+    }
+
+    return false;
+}
+
+// ----------------------------------------------------------------------------
+// Function _moveIteratorsRight()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_moveIteratorsRight(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+                    TStage const & /* tag */)
+{
+    // Try to go right in the pattern.
+    if (goRight(back(finder.patternStack)))
+    {
+        return true;
+    }
+    // Try to go right in the text.
+    else if (goRight(back(finder.textStack)))
+    {
+        // Move to the leftmost pattern.
+//        back(finder.patternStack) = finder.patternLeftmost;
+
+        eraseBack(finder.patternStack);
+        appendValue(finder.patternStack, back(finder.patternStack));
+        goDown(back(finder.patternStack));
+        return true;
+    }
+
+    return false;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveIteratorsRight(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > & finder,
+                    StageExact_ const & /* tag */)
+{
+    typedef Index<TText, TTextIndexSpec>                                                TTextIndex;
+    typedef Index<TPattern, TPatternIndexSpec>                                          TPatternIndex;
+    typedef Backtracking<HammingDistance, TSpec>                                        TBacktracking;
+    typedef typename TextIterator_<TTextIndex, TPatternIndex, TBacktracking>::Type      TTextIterator;
+    typedef typename PatternIterator_<TTextIndex, TPatternIndex, TBacktracking>::Type   TPatternIterator;
+
+    // TODO(esiragusa): Implement goRight(it, pattern).
+//    TTextIterator & textIt = back(finder.textStack);
+//    TPatternIterator & patternIt = back(finder.patternStack);
+//    return goRight(patternIt) && goRight(textIt, parentEdgeLabel(patternIt));
+
+    TPatternIterator & patternIt = back(finder.patternStack);
+
+    // Try to go right in the pattern.
+    while (goRight(patternIt))
+    {
+        // Move up in the text.
+        back(finder.textStack) = finder.textStack[length(finder.textStack) - 2];
+
+        // Search pattern label in text.
+        TTextIterator & textIt = back(finder.textStack);
+        if (goDown(textIt, parentEdgeLabel(patternIt)))
+            return true;
+    }
+
+    return false;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveIteratorsRight(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+                    StageInitial_ const & /* tag */)
+{
+    // Try to go right in the pattern.
+    return goRight(back(finder.patternStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveIteratorsRight(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+                    StageLower_ const & /* tag */)
+{
+    // Try to go right in the text.
+    return goRight(back(finder.textStack));
+}
+
+// ----------------------------------------------------------------------------
+// Function _popState()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_popState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+          TStage const & /* tag */)
+{
+    _popIterators(finder, TStage());
+    _popScore(finder, TStage());
+
+#ifdef SEQAN_DEBUG
+    _printPop(finder, TStage());
+#endif
+}
+
+// ----------------------------------------------------------------------------
+// Function _popIterators()
+// ----------------------------------------------------------------------------
+// TODO(esiragusa): Specialize _popIterators() for StageInitial_ and StageFinal_ of EditDistance
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_popIterators(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+              TStage const & /* tag */)
+{
+    eraseBack(finder.textStack);
+    eraseBack(finder.patternStack);
+}
+
+// ----------------------------------------------------------------------------
+// Function _popScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_popScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+          TStage const & /* tag */)
+{
+    eraseBack(finder.scoreStack);
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_popScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > & /* finder */,
+          StageExact_ const & /* tag */)
+{
+    // Do nothing.
+}
+
+// ----------------------------------------------------------------------------
+// Function _updateScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_updateScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & /* finder */,
+             TStage const & /* tag */)
+{}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec, typename TStage>
+inline void
+_updateScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > & finder,
+             TStage const & /* tag */)
+{
+    typedef Backtracking<HammingDistance, TSpec>    TBacktracking;
+    typedef typename Score_<TBacktracking>::Type    TScore;
+
+    // Compute score of text and pattern.
+    TScore score = ordEqual(parentEdgeLabel(back(finder.textStack)), parentEdgeLabel(back(finder.patternStack))) ? 0 : 1;
+
+    // Add score to previous score.
+    back(finder.scoreStack) = value(finder.scoreStack, length(finder.scoreStack) - 2) + score;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_updateScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > & /* finder */,
+             StageExact_ const & /* tag */)
+{
+    // Do nothing.
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_updateScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+             StageInitial_ const & /* tag */)
+{
+    _updateVertexScore(back(finder.scoreStack), value(finder.scoreStack, length(finder.scoreStack) - 2), StageInitial_());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_updateScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+             StageUpper_ const & /* tag */)
+{
+    typedef Index<TPattern, TPatternIndexSpec>                              TPatternIndex;
+    typedef typename Fibre<TPatternIndex, FibreText>::Type const            TPatternFibreText;
+    typedef typename Infix<TPatternFibreText>::Type                         TPatternRepr;
+    typedef typename Iterator<TPatternRepr, Standard>::Type                 TPatternReprIterator;
+
+    // Get pattern read so far.
+    TPatternRepr pattern = representative(back(finder.patternStack));
+    TPatternReprIterator patternIt = begin(pattern, Standard());
+
+    _updateVertexScore(back(finder.scoreStack),
+                       value(finder.scoreStack, length(finder.scoreStack) - 2),
+                       parentEdgeLabel(back(finder.textStack)),
+                       patternIt,
+                       StageUpper_());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_updateScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+             StageDiagonal_ const & /* tag */)
+{
+    typedef Index<TPattern, TPatternIndexSpec>                              TPatternIndex;
+    typedef typename Fibre<TPatternIndex, FibreText>::Type const            TPatternFibreText;
+    typedef typename Infix<TPatternFibreText>::Type                         TPatternRepr;
+    typedef typename Iterator<TPatternRepr, Standard>::Type                 TPatternReprIterator;
+
+    // Get last 2k + 1 pattern symbols.
+    TPatternRepr pattern = representative(back(finder.patternStack));
+    TPatternReprIterator patternIt = end(pattern, Standard()) - (2 * finder.maxScore + 1);
+
+    _updateVertexScore(back(finder.scoreStack),
+                       value(finder.scoreStack, length(finder.scoreStack) - 2),
+                       parentEdgeLabel(back(finder.textStack)),
+                       patternIt,
+                       StageDiagonal_());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_updateScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+             StageLower_ const & /* tag */)
+{
+    typedef Index<TPattern, TPatternIndexSpec>                              TPatternIndex;
+    typedef typename Fibre<TPatternIndex, FibreText>::Type const            TPatternFibreText;
+    typedef typename Infix<TPatternFibreText>::Type                         TPatternRepr;
+    typedef typename Iterator<TPatternRepr, Standard>::Type                 TPatternReprIterator;
+
+    // Get last pattern symbols.
+    TPatternRepr pattern = representative(back(finder.patternStack));
+    TPatternReprIterator patternIt = end(pattern, Standard()) - (length(back(finder.scoreStack)));
+
+    _updateVertexScore(back(finder.scoreStack),
+                       value(finder.scoreStack, length(finder.scoreStack) - 2),
+                       parentEdgeLabel(back(finder.textStack)),
+                       patternIt,
+                       StageLower_());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_updateScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > & finder,
+             StageFinal_ const & /* tag */)
+{
+    _updateVertexScore(back(finder.scoreStack),
+                       value(finder.scoreStack, length(finder.scoreStack) - 2),
+                       parentEdgeLabel(back(finder.textStack)),
+                       parentEdgeLabel(back(finder.patternStack)),
+                       StageFinal_());
+}
+
+// ----------------------------------------------------------------------------
+// Function _setScoreThreshold()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TMaxScore>
+inline void
+_setScoreThreshold(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+                  TMaxScore maxScore)
+{
+    finder.maxScore = maxScore;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getMinScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline typename Score_<Backtracking<HammingDistance, TSpec> >::Type
+_getMinScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & finder)
+{
+    return _getScore(finder);
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline typename Score_<Backtracking<EditDistance, TSpec> >::Type
+_getMinScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder)
+{
+    typedef Backtracking<EditDistance, TSpec>                       TBacktracking;
+    typedef typename VertexScore_<TBacktracking>::ConstType         TVertexScore;
+
+    TVertexScore column = back(finder.scoreStack);
+
+    // Return the min value in column.
+    return value(std::min_element(begin(column, Standard()), end(column, Standard())));
+}
+
+// ----------------------------------------------------------------------------
+// Function _getScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline typename Score_<Backtracking<HammingDistance, TSpec> >::Type
+_getScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & finder)
+{
+    // Return the last value.
+    return back(finder.scoreStack);
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline typename Score_<Backtracking<EditDistance, TSpec> >::Type
+_getScore(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder)
+{
+    // Return the value of last cell in column.
+    return back(back(finder.scoreStack));
+}
+
+// ----------------------------------------------------------------------------
+// Function _textIterator()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename TextIterator_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> >::Type &
+_textIterator(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder)
+{
+    return back(finder.textStack);
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename TextIterator_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> >::Type const &
+_textIterator(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & finder)
+{
+    return back(finder.textStack);
+}
+
+// ----------------------------------------------------------------------------
+// Function _patternIterator()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename PatternIterator_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> >::Type &
+_patternIterator(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder)
+{
+    return back(finder.patternStack);
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename PatternIterator_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> >::Type const &
+_patternIterator(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & finder)
+{
+    return back(finder.patternStack);
+}
+
+// ----------------------------------------------------------------------------
+// Function _inTerminalState()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_inTerminalState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & /* finder */,
+                 TStage const & /* tag */)
+{
+    // The current state is not terminal by default.
+    return false;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_inTerminalState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & finder,
+                 StageFinal_ const & /* tag */)
+{
+    // Is the score within the max score?
+    return _getScore(finder) <= finder.maxScore;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_inTerminalState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                 StageLower_ const & /* tag */)
+{
+    // Is the score within the max score?
+    return _getScore(finder) <= finder.maxScore;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_inTerminalState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                 StageFinal_ const & /* tag */)
+{
+    // Is the score within the max score?
+    return _getScore(finder) <= finder.maxScore;
+}
+
+// ----------------------------------------------------------------------------
+// Function _inActiveState()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_inActiveState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & finder,
+               TStage const & /* tag */)
+{
+    // Is the minimum score within the max score?
+    return _getMinScore(finder) <= finder.maxScore;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_inActiveState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & /* finder */,
+               StageExact_ const & /* tag */)
+{
+    // Exact search only walks through active states.
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function _moveToExactStage()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_moveToStageExact(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & /* finder */,
+                  TStage const & /* tag */)
+{
+    // By default there is no exact stage.
+    return false;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveToStageExact(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & finder,
+                  StageInitial_ const & /* tag */)
+{
+    // Was the maximum score attained?
+    return _getMinScore(finder) == finder.maxScore;
+}
+
+//template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec, typename TStage>
+//inline bool
+//_moveToStageExact(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+//                  TStage const & /* tag */)
+//{
+//    // TODO(esiragusa): Implement exact search speedup for EditDistance.
+//    return _getMinScore(finder) == finder.maxScore;
+//}
+
+// ----------------------------------------------------------------------------
+// Function _moveToNextStage()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_moveToNextStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & /* finder */,
+                 TStage const & /* tag */)
+{
+    // By default there is no next stage.
+    return false;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveToNextStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & finder,
+                 StageInitial_ const & /* tag */)
+{
+    return isRightTerminal(back(finder.patternStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveToNextStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & finder,
+                 StageExact_ const & /* tag */)
+{
+    return isRightTerminal(back(finder.patternStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveToNextStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                 StageInitial_ const & /* tag */)
+{
+    // Move to upper stage when k pattern symbols have been consumed.
+    return (repLength(back(finder.patternStack)) >= finder.maxScore) || isRightTerminal(back(finder.patternStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveToNextStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                 StageUpper_ const & /* tag */)
+{
+    // Move to diagonal stage when the diagonal has size 2k + 1.
+    return (length(back(finder.scoreStack)) >= 2u * finder.maxScore + 1u) || isRightTerminal(back(finder.patternStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveToNextStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                 StageDiagonal_ const & /* tag */)
+{
+    // Move to lower stage when all pattern symbols have been consumed.
+    return isRightTerminal(back(finder.patternStack));
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_moveToNextStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                 StageLower_ const & /* tag */)
+{
+    // Move to final stage when there is only one cell left to compute.
+    return length(back(finder.scoreStack)) <= 2;
+}
+
+// ----------------------------------------------------------------------------
+// Function _stayInCurrentStage()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline bool
+_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & /* finder */,
+                    TStage const & /* tag */)
+{
+    // Stay in the current stage by default.
+    return true;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                    StageInitial_ const & /* tag */)
+{
+    return repLength(back(finder.patternStack)) < finder.maxScore;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                    StageUpper_ const & /* tag */)
+{
+    return length(back(finder.scoreStack)) < 2u * finder.maxScore + 1u;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline bool
+_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+                    StageLower_ const & /* tag */)
+{
+    return length(back(finder.scoreStack)) > 2;
+}
+
+// ----------------------------------------------------------------------------
+// Functions _print*()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): Debug functions.
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_printCall(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & finder,
+           TStage const & /* tag */)
+{
+    std::cout << "call:           "; _printFindSignature(finder, TStage());
+    std::cout << "past text:      " << representative(back(finder.textStack)) << std::endl;
+    std::cout << "past pattern:   " << representative(back(finder.patternStack)) << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_printReturn(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & finder,
+             TStage const & /* tag */)
+{
+    std::cout << "return:         "; _printFindSignature(finder, TStage());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_printPush(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & finder,
+           TStage const & /* tag */)
+{
+    std::cout << "push:           "; _printFindSignature(finder, TStage());
+    _printState(finder, TStage());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_printPop(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & finder,
+          TStage const & /* tag */)
+{
+    std::cout << "pop:            "; _printFindSignature(finder, TStage());
+    _printState(finder, TStage());
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > const & /* finder */,
+                    TStage const & /* tag */)
+{
+    std::cout << "<TDistance, TStage>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & /* finder */,
+                    StageInitial_ const & /* tag */)
+{
+    std::cout << "<HammingDistance, StageInitial>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & /* finder */,
+                    StageFinal_ const & /* tag */)
+{
+    std::cout << "<HammingDistance, StageFinal>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & /* finder */,
+                    StageExact_ const & /* tag */)
+{
+    std::cout << "<HammingDistance, StageExact>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & /* finder */,
+                    StageInitial_ const & /* tag */)
+{
+    std::cout << "<EditDistance, StageInitial>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & /* finder */,
+                    StageUpper_ const & /* tag */)
+{
+    std::cout << "<EditDistance, StageUpper>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & /* finder */,
+                    StageDiagonal_ const & /* tag */)
+{
+    std::cout << "<EditDistance, StageDiagonal>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & /* finder */,
+                    StageLower_ const & /* tag */)
+{
+    std::cout << "<EditDistance, StageLower>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec>
+inline void
+_printFindSignature(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & /* finder */,
+                    StageFinal_ const & /* tag */)
+{
+    std::cout << "<EditDistance, StageFinal>" << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec, typename TStage>
+inline void
+_printState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, TSpec> > const & finder,
+            TStage const & /* tag */)
+{
+    std::cout << "text:           " << parentEdgeLabel(back(finder.textStack)) << std::endl;
+    std::cout << "pattern:        " << parentEdgeLabel(back(finder.patternStack)) << std::endl;
+    std::cout << "errors:         " << static_cast<unsigned>(_getScore(finder)) << std::endl;
+}
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TSpec, typename TStage>
+inline void
+_printState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, TSpec> > const & finder,
+            TStage const & /* tag */)
+{
+    std::cout << "text:           " << parentEdgeLabel(back(finder.textStack)) << std::endl;
+    std::cout << "pattern:        " << parentEdgeLabel(back(finder.patternStack)) << std::endl;
+    std::cout << "column:         " << "|";
+    std::copy(begin(back(finder.scoreStack), Standard()),
+              end(back(finder.scoreStack), Standard()),
+              std::ostream_iterator<int>(std::cout, "|"));
+    std::cout << std::endl;
+}
+
+// ----------------------------------------------------------------------------
+// Function _find()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TStage, typename TDelegate>
+inline void
+_find(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+      TDelegate & delegate,
+      TStage const & /* tag */)
+{
+    typedef Backtracking<TDistance, TSpec>                      TBacktracking;
+    typedef typename NextStage_<TBacktracking, TStage>::Type    TNextStage;
+
+#ifdef SEQAN_DEBUG
+    _printCall(finder, TStage());
+#endif
+
+    if (_moveToStageExact(finder, TStage()))
+    {
+        _find(finder, delegate, StageExact_());
+    }
+    else
+    {
+        if (_moveToNextStage(finder, TStage()))
+        {
+            _find(finder, delegate, TNextStage());
+        }
+        if (_stayInCurrentStage(finder, TStage()))
+        {
+            if (_inTerminalState(finder, TStage()))
+            {
+                // Inversion of control.
+                delegate(finder);
+            }
+            else if (_inActiveState(finder, TStage()))
+            {
+                if (_pushState(finder, TStage()))
+                {
+                    do
+                    {
+                        _find(finder, delegate, TStage());
+                    }
+                    while (_nextState(finder, TStage()));
+
+                    _popState(finder, TStage());
+                }
+            }
+        }
+    }
+
+#ifdef SEQAN_DEBUG
+    _printReturn(finder, TStage());
+#endif
+}
+
+// ----------------------------------------------------------------------------
+// Function _find()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec, typename TDistance, typename TSpec, typename TValue, typename TDelegate>
+inline void
+_find(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<TDistance, TSpec> > & finder,
+      Index<TText, TTextIndexSpec> & text,
+      Index<TPattern, TPatternIndexSpec> & pattern,
+      TValue maxScore,
+      TDelegate & delegate)
+{
+    typedef Index<TText, TTextIndexSpec>                                                TTextIndex;
+    typedef Index<TPattern, TPatternIndexSpec>                                          TPatternIndex;
+    typedef Backtracking<TDistance, TSpec>                                              TBacktracking;
+    typedef typename TextIterator_<TTextIndex, TPatternIndex, TBacktracking>::Type      TTextIterator;
+    typedef typename PatternIterator_<TTextIndex, TPatternIndex, TBacktracking>::Type   TPatternIterator;
+
+    TTextIterator textIt(text);
+    TPatternIterator patternIt(pattern);
+
+    _setScoreThreshold(finder, maxScore);
+    _initState(finder, textIt, patternIt);
+    _find(finder, delegate, StageInitial_());
+    _popState(finder, StageInitial_());
+}
+
+}
+
+#endif  // #ifndef SEQAN_FIND_BACKTRACKING_MULTIPLE_H_
diff --git a/seqan/index/find2_base.h b/seqan/index/find2_base.h
new file mode 100644
index 0000000..3856e0c
--- /dev/null
+++ b/seqan/index/find2_base.h
@@ -0,0 +1,241 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_FIND_FIND_BASE_H_
+#define SEQAN_FIND_FIND_BASE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TText, typename TPattern, typename TSpec = void>
+struct Finder_;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction View                                                   [Finder]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+struct View<Finder_<TText, TPattern, TSpec> >
+{
+    typedef Finder_<typename View<TText>::Type, typename View<TPattern>::Type, TSpec>   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RemoveView                                             [Finder]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+struct RemoveView<Finder_<TText, TPattern, TSpec> >
+{
+    typedef Finder_<typename RemoveView<TText>::Type, typename RemoveView<TPattern>::Type, TSpec>   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView                                                 [Finder]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+struct IsView<Finder_<TText, TPattern, TSpec> > : IsView<TText> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsDevice                                               [Finder]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+struct IsDevice<Finder_<TText, TPattern, TSpec> > : IsDevice<TText> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction View                                                  [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedle, typename TSpec>
+struct View<Pattern<TNeedle, TSpec> >
+{
+    typedef Pattern<typename View<TNeedle>::Type, TSpec>    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RemoveView                                            [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedle, typename TSpec>
+struct RemoveView<Pattern<TNeedle, TSpec> >
+{
+    typedef Pattern<typename RemoveView<TNeedle>::Type, TSpec>    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView                                                [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedle, typename TSpec>
+struct IsView<Pattern<TNeedle, TSpec> > : IsView<TNeedle> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsDevice                                              [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedle, typename TSpec>
+struct IsDevice<Pattern<TNeedle, TSpec> > : IsDevice<TNeedle> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction TextIterator_
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+struct TextIterator_
+{
+    typedef typename Iterator<TText>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction PatternIterator_
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+struct PatternIterator_
+{
+    typedef typename Iterator<TPattern const, Rooted>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Score_
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+struct Score_
+{
+    typedef unsigned char   Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _textIterator()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline typename TextIterator_<TText, TPattern, TSpec>::Type &
+_textIterator(Finder_<TText, TPattern, TSpec> & finder)
+{
+    return finder._textIt;
+}
+
+template <typename TText, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline typename TextIterator_<TText, TPattern, TSpec>::Type const &
+_textIterator(Finder_<TText, TPattern, TSpec> const & finder)
+{
+    return finder._textIt;
+}
+
+// ----------------------------------------------------------------------------
+// Function _patternIterator()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline typename PatternIterator_<TText, TPattern, TSpec>::Type &
+_patternIterator(Finder_<TText, TPattern, TSpec> & finder)
+{
+    return finder._patternIt;
+}
+
+template <typename TText, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline typename PatternIterator_<TText, TPattern, TSpec>::Type const &
+_patternIterator(Finder_<TText, TPattern, TSpec> const & finder)
+{
+    return finder._patternIt;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Score_<TSpec>::Type
+_getScore(Finder_<TText, TPattern, TSpec> const & finder)
+{
+    return finder._score;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getScoreThreshold()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Score_<TSpec>::Type
+_getScoreThreshold(Finder_<TText, TPattern, TSpec> const & finder)
+{
+    return finder._scoreThreshold;
+}
+
+// ----------------------------------------------------------------------------
+// Function _setScoreThreshold()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec, typename TScore>
+SEQAN_HOST_DEVICE inline void
+_setScoreThreshold(Finder_<TText, TPattern, TSpec> & finder, TScore score)
+{
+    finder._scoreThreshold = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline void
+clear(Finder_<TText, TPattern, TSpec> & finder)
+{
+    // NOTE(esiragusa): if find wasn't called yet, _textIterator is uninitialized.
+//    goBegin(_textIterator(finder));
+    // NOTE(esiragusa): if find wasn't called yet, _patternIterator is uninitialized.
+//    goBegin(_patternIterator(finder));
+    finder._score = typename Score_<TSpec>::Type();
+}
+
+
+}
+
+#endif  // #ifndef SEQAN_FIND_FIND_BASE_H_
diff --git a/seqan/index/find2_functors.h b/seqan/index/find2_functors.h
new file mode 100644
index 0000000..52fcbd6
--- /dev/null
+++ b/seqan/index/find2_functors.h
@@ -0,0 +1,217 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Some useful functors to be used along with the Finder class.
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_FIND_FUNCTORS_H_
+#define SEQAN_INDEX_FIND_FUNCTORS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag Counts_
+// ----------------------------------------------------------------------------
+
+struct Counts_;
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class OccurrencesCounter_
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec = typename ExecSpec<TIndex>::Type>
+struct OccurrencesCounter_
+{
+    typename Member<OccurrencesCounter_, Counts_>::Type    counts;
+
+    OccurrencesCounter_() {}
+
+    template <typename TPattern>
+    OccurrencesCounter_(TPattern const & pattern)
+    {
+        _init(*this, pattern);
+    }
+
+    template <typename TFinder>
+    inline SEQAN_HOST_DEVICE void
+    operator() (TFinder const & finder)
+    {
+        counts[getThreadId()] += countOccurrences(_textIterator(finder));
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Member Counts_; Count
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct Member<OccurrencesCounter_<TIndex, TSpec>, Counts_>
+{
+    typedef String<typename Size<TIndex>::Type> Type;
+};
+
+#ifdef PLATFORM_CUDA
+template <typename TIndex, typename TSpec>
+struct Member<OccurrencesCounter_<TIndex, Device<TSpec> >, Counts_>
+{
+    typedef thrust::device_vector<typename Size<TIndex>::Type>  Type;
+};
+#endif
+
+template <typename TIndex, typename TSpec>
+struct Member<OccurrencesCounter_<TIndex, View<Device<TSpec> > >, Counts_>
+{
+    typedef typename View<typename Member<OccurrencesCounter_<TIndex, Device<TSpec> >, Counts_>::Type>::Type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction View
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct View<OccurrencesCounter_<TIndex, TSpec> >
+{
+    typedef OccurrencesCounter_<TIndex, View<TSpec> >  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Device
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct Device<OccurrencesCounter_<TIndex, TSpec> >
+{
+    typedef OccurrencesCounter_<TIndex, Device<TSpec> >  Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _init()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec, typename TPattern>
+inline void
+_init(OccurrencesCounter_<TIndex, TSpec> & counter, TPattern const & /* pattern */)
+{
+    resize(counter.counts, omp_get_max_threads(), 0, Exact());
+}
+
+template <typename TIndex, typename TSpec, typename TPattern>
+inline void
+_init(OccurrencesCounter_<TIndex, Device<TSpec> > & counter, TPattern const & pattern)
+{
+    resize(counter.counts, length(needle(pattern)), Exact());
+}
+
+// ----------------------------------------------------------------------------
+// Function view()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+typename View<OccurrencesCounter_<TIndex, TSpec> >::Type
+view(OccurrencesCounter_<TIndex, TSpec> & counter)
+{
+    typename View<OccurrencesCounter_<TIndex, TSpec> >::Type counterView;
+
+    counterView.counts = view(counter.counts);
+
+    return counterView;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getCount()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+inline typename Size<TIndex>::Type
+_getCount(OccurrencesCounter_<TIndex, TSpec> & counter)
+{
+    return sum(counter.counts);
+}
+
+#ifdef PLATFORM_CUDA
+template <typename TIndex, typename TSpec>
+inline typename Size<TIndex>::Type
+_getCount(OccurrencesCounter_<TIndex, Device<TSpec> > & counter)
+{
+    return thrust::reduce(begin(counter.counts, Standard()), end(counter.counts, Standard()));
+}
+#endif
+
+// --------------------------------------------------------------------------
+// Function countOccurrences()
+// --------------------------------------------------------------------------
+// Count the occurrences of a set of needles in a indexed haystack.
+
+template <typename TText, typename TSpec, typename TNeedle, typename TSSetSpec>
+typename Size<Index<TText, TSpec> >::Type
+countOccurrences(Index<TText, TSpec> & index, StringSet<TNeedle, TSSetSpec> & needles)
+{
+    typedef Index<TText, TSpec>                         TIndex;
+    typedef StringSet<TNeedle, TSSetSpec>               TNeedles;
+    typedef Multiple<FinderSTree>                       TAlgorithmSpec;
+    typedef Pattern<TNeedles, TAlgorithmSpec>           TPattern;
+    typedef Finder_<TIndex, TPattern, TAlgorithmSpec>   TFinder;
+    typedef OccurrencesCounter_<TIndex>                  TCounter;
+
+    // Instantiate a finder object holding the context of the search algorithm.
+    TFinder finder(index);
+
+    // Instantiate a pattern object holding the needles.
+    TPattern pattern(needles);
+
+    // Instantiate a functor object counting the number of occurrences.
+    TCounter counter(pattern);
+
+    // Find all needles in haystack and call counter() on match.
+    _find(finder, pattern, counter);
+
+    // Return the number of occurrences.
+    return _getCount(counter);
+}
+
+}
+
+#endif  // #ifndef SEQAN_INDEX_FIND_FUNCTORS_H_
diff --git a/seqan/index/find2_index.h b/seqan/index/find2_index.h
new file mode 100644
index 0000000..04742f4
--- /dev/null
+++ b/seqan/index/find2_index.h
@@ -0,0 +1,266 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Approximate string matching via backtracking on a substring index.
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_FIND_INDEX_H_
+#define SEQAN_INDEX_FIND_INDEX_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tags for backtracking specializations
+// ----------------------------------------------------------------------------
+
+struct BacktrackingSemiGlobal_;
+typedef Tag<BacktrackingSemiGlobal_>    BacktrackingSemiGlobal;
+
+struct BacktrackingGlobal_;
+typedef Tag<BacktrackingGlobal_>        BacktrackingGlobal;
+
+// ----------------------------------------------------------------------------
+// Tag Backtracking
+// ----------------------------------------------------------------------------
+
+template <typename TDistance = HammingDistance, typename TSpec = BacktrackingSemiGlobal>
+struct Backtracking {};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction TextIterator_
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TSpec>
+struct TextIterator_<Index<TText, TIndexSpec>, TPattern, TSpec>
+{
+    typedef typename Iterator<Index<TText, TIndexSpec>, TopDown<> >::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction TextIterator_
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TDistance, typename TSpec>
+struct TextIterator_<Index<TText, TIndexSpec>, TPattern, Backtracking<TDistance, TSpec> >
+{
+    typedef typename Iterator<Index<TText, TIndexSpec>, TopDown<ParentLinks<> > >::Type  Type;
+};
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class Finder
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TSpec>
+struct Finder_<Index<TText, TIndexSpec>, TPattern, TSpec>
+{
+    typedef Index<TText, TIndexSpec>                                    TIndex;
+    typedef typename TextIterator_<TIndex, TPattern, TSpec>::Type       TTextIterator;
+    typedef typename PatternIterator_<TIndex, TPattern, TSpec>::Type    TPatternIterator;
+    typedef typename Score_<TSpec>::Type                                TScore;
+
+    TTextIterator       _textIt;
+    TPatternIterator    _patternIt;
+    TScore              _scoreThreshold;
+    TScore              _score;
+
+    SEQAN_HOST_DEVICE
+    Finder_() :
+        _scoreThreshold(),
+        _score()
+    {}
+
+    SEQAN_HOST_DEVICE
+    Finder_(TIndex /* const */ & index) :
+        _textIt(index),
+        _scoreThreshold(),
+        _score()
+    {}
+
+    SEQAN_HOST_DEVICE
+    Finder_(TTextIterator const & textIt) :
+        _textIt(textIt),
+        _scoreThreshold(),
+        _score()
+    {}
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline void
+clear(Finder_<Index<TText, TIndexSpec>, TPattern, TSpec> & finder)
+{
+    // NOTE(esiragusa): should clear() be called on text/patternIt?
+    goRoot(_textIterator(finder));
+    // NOTE(esiragusa): if find wasn't called yet, _patternIterator is uninitialized.
+//    goBegin(_patternIterator(finder));
+    finder._score = typename Score_<TSpec>::Type();
+}
+
+// ----------------------------------------------------------------------------
+// Function find_()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TDelegate>
+SEQAN_HOST_DEVICE inline void
+_find(Finder_<Index<TText, TIndexSpec>, TPattern, FinderSTree> & finder,
+      TPattern const & pattern,
+      TDelegate & delegate)
+{
+    if (goDown(_textIterator(finder), pattern))
+    {
+        // TODO(esiragusa): update _patternIterator.
+        delegate(finder);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function _getVertexScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Score_<Backtracking<HammingDistance, TSpec> >::Type
+_getVertexScore(Finder_<TText, TPattern, Backtracking<HammingDistance, TSpec> > const & finder)
+{
+    return !ordEqual(parentEdgeLabel(_textIterator(finder)), value(_patternIterator(finder)));
+}
+
+// ----------------------------------------------------------------------------
+// Function _printState()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TSpec>
+SEQAN_HOST_DEVICE inline void
+_printState(Finder_<Index<TText, TIndexSpec>, TPattern, Backtracking<HammingDistance, TSpec> > & finder)
+{
+    std::cout << "Text:        " << parentEdgeLabel(_textIterator(finder)) << std::endl;
+    std::cout << "Pattern:     " << value(_patternIterator(finder)) << std::endl;
+    std::cout << "Text Len:    " << repLength(_textIterator(finder)) << std::endl;
+    std::cout << "Pattern Len: " << position(_patternIterator(finder)) + 1 << std::endl;
+    std::cout << "Errors:      " << static_cast<unsigned>(_getScore(finder)) << std::endl;
+    std::cout << "Max errors:  " << static_cast<unsigned>(finder._scoreThreshold) << std::endl;
+}
+
+// ----------------------------------------------------------------------------
+// Function _find()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TSpec, typename TDelegate>
+SEQAN_HOST_DEVICE inline void
+_find(Finder_<Index<TText, TIndexSpec>, TPattern, Backtracking<HammingDistance, TSpec> > & finder,
+      TPattern const & pattern,
+      TDelegate & delegate)
+{
+    typedef Index<TText, TIndexSpec>                                        TIndex;
+    typedef Backtracking<HammingDistance, TSpec>                            TFinderSpec;
+    typedef typename TextIterator_<TIndex, TPattern, TFinderSpec>::Type     TTextIterator;
+    typedef typename PatternIterator_<TIndex, TPattern, TFinderSpec>::Type  TPatternIterator;
+
+    _patternIterator(finder) = begin(pattern);
+
+    TTextIterator & textIt = _textIterator(finder);
+    TPatternIterator & patternIt = _patternIterator(finder);
+
+    do
+    {
+        // Exact case.
+        if (finder._score == finder._scoreThreshold)
+        {
+            if (goDown(textIt, suffix(pattern, position(patternIt))))
+            {
+                delegate(finder);
+            }
+
+            goUp(textIt);
+        }
+
+        // Approximate case.
+        else if (finder._score < finder._scoreThreshold)
+        {
+            // Base case.
+            if (atEnd(patternIt))
+            {
+                delegate(finder);
+            }
+
+            // Recursive case.
+            else if (goDown(textIt))
+            {
+                finder._score += _getVertexScore(finder);
+                goNext(patternIt);
+                continue;
+            }
+        }
+
+        // Backtrack.
+        do
+        {
+            // Termination.
+            if (isRoot(textIt)) break;
+
+            goPrevious(patternIt);
+            finder._score -= _getVertexScore(finder);
+        }
+        while (!goRight(textIt) && goUp(textIt));
+
+        // Termination.
+        if (isRoot(textIt)) break;
+
+        finder._score += _getVertexScore(finder);
+        goNext(patternIt);
+    }
+    while (true);
+}
+
+}
+
+#endif  // #ifndef SEQAN_INDEX_FIND_INDEX_H_
diff --git a/seqan/index/find2_index_multi.h b/seqan/index/find2_index_multi.h
new file mode 100644
index 0000000..bc5fcb7
--- /dev/null
+++ b/seqan/index/find2_index_multi.h
@@ -0,0 +1,611 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_FIND_INDEX_MULTIPLE_H
+#define SEQAN_INDEX_FIND_INDEX_MULTIPLE_H
+
+#ifdef PLATFORM_CUDA
+#include <thrust/sort.h>
+#include <thrust/reduce.h>
+#endif
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag Multiple
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+struct Multiple;
+
+// ----------------------------------------------------------------------------
+// Finder Member Tags
+// ----------------------------------------------------------------------------
+
+struct Factory_;
+
+// ----------------------------------------------------------------------------
+// Pattern Member Tags
+// ----------------------------------------------------------------------------
+
+struct Needles_;
+struct Hashes_;
+struct Permutation_;
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class Finder; Multiple
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+struct Finder_<TText, TPattern, Multiple<TSpec> >
+{
+    typename Member<Finder_, Factory_>::Type    _factory;
+
+    Finder_() {}
+
+    Finder_(TText & text) :
+        _factory(text)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class Finder; Index, Multiple
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TPattern, typename TSpec>
+struct Finder_<Index<TText, TIndexSpec>, TPattern, Multiple<TSpec> >
+{
+    typedef Index<TText, TIndexSpec>            TIndex;
+
+    typename Member<Finder_, Factory_>::Type    _factory;
+    typename Score_<TSpec>::Type                _scoreThreshold;
+
+    Finder_() :
+        _scoreThreshold()
+    {}
+
+    Finder_(TIndex & index) :
+        _factory(index),
+        _scoreThreshold()
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class Pattern; Multiple
+// ----------------------------------------------------------------------------
+
+template <typename TNeedles, typename TSpec>
+class Pattern<TNeedles, Multiple<TSpec> >
+{
+public:
+    typename Member<Pattern, Needles_>::Type        data_host;
+    typename Member<Pattern, Hashes_>::Type         _hashes;
+    typename Member<Pattern, Permutation_>::Type    _permutation;
+
+    Pattern() {}
+
+    Pattern(TNeedles const & needles) :
+        data_host(needles)
+    {
+        _preprocess(*this);
+    }
+
+//    Pattern(TNeedles const & needles)
+//    {
+//        setHost(*this, needles);
+//    }
+};
+
+// ----------------------------------------------------------------------------
+// Class FinderContext_
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+struct FinderContext_;
+
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+struct FinderContext_<TText, TPattern, Multiple<TSpec>, TDelegate>
+{
+    typedef typename Needle<TPattern>::Type                 TNeedles;
+    typedef typename Value<TPattern>::Type                  TNeedle;
+    typedef Finder_<TText, TNeedle, TSpec>                  TBaseFinder;
+    typedef Finder_<TText, TPattern, Multiple<TSpec> >      TFinder;
+    typedef typename Iterator<TNeedles, Standard>::Type     TPatternIterator;
+
+    TFinder &      finder;
+    TDelegate &    delegate;
+    TBaseFinder    baseFinder;
+//    TPatternIterator _patternIt;
+    unsigned        _patternIt;
+
+    explicit SEQAN_HOST_DEVICE
+    FinderContext_(TFinder & finder, TDelegate & delegate) :
+        finder(finder),
+        delegate(delegate),
+        baseFinder(getObject(finder._factory, getThreadId()))
+    {}
+
+    // NOTE(esiragusa): This is called on firstprivate.
+    FinderContext_(FinderContext_ & ctx) :
+        finder(ctx.finder),
+        delegate(ctx.delegate),
+        baseFinder(getObject(finder._factory, getThreadId()))
+    {}
+
+    template <typename TOther>
+    SEQAN_HOST_DEVICE inline void
+    operator()(TOther & /* other */)
+    {
+        delegate(*this);
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Score_; Multiple
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+struct Score_<Multiple<TSpec> >
+{
+    typedef typename Score_<TSpec>::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Host                                                  [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedles, typename TSpec>
+struct Host<Pattern<TNeedles, Multiple<TSpec> > >
+{
+    typedef TNeedles Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction PatternShape_                                         [Pattern]
+// ----------------------------------------------------------------------------
+// TODO(esiragusa): Automatically select a good shape.
+
+template <typename TPattern>
+struct PatternShape_
+{
+    typedef typename Host<TPattern>::Type                               TNeedles_;
+    typedef typename Value<TNeedles_>::Type                             TNeedle_;
+    typedef typename Value<TNeedle_>::Type                              TAlphabet_;
+    typedef UngappedShape<Max<MinLength<TNeedles_>::VALUE, 1>::VALUE>   TShapeSpec_;
+
+    typedef Shape<TAlphabet_, TShapeSpec_>                              Type;
+};
+
+// ----------------------------------------------------------------------------
+// Member Needles_                                                    [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedles, typename TSpec>
+struct Member<Pattern<TNeedles, Multiple<TSpec> >, Needles_>
+{
+    typedef typename IfView<TNeedles, TNeedles, Holder<TNeedles> >::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Member Hashes_                                                     [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedles, typename TSpec>
+struct Member<Pattern<TNeedles, Multiple<TSpec> >, Hashes_>
+{
+    typedef Nothing Type;
+};
+
+#ifdef PLATFORM_CUDA
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec>
+struct Member<Pattern<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, Multiple<TSpec> >, Hashes_>
+{
+    typedef thrust::device_vector<TValue, TAlloc>   TNeedle_;
+    typedef StringSet<TNeedle_, TSSetSpec>          TNeedles_;
+    typedef Pattern<TNeedles_, Multiple<TSpec> >    TPattern_;
+    typedef typename PatternShape_<TPattern_>::Type TShape_;
+    typedef typename Value<TShape_>::Type           THash_;
+
+    typedef thrust::device_vector<THash_>           Type;
+};
+#endif
+
+template <typename TNeedle, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Member<Pattern<StringSet<ContainerView<TNeedle, TViewSpec>, TSSetSpec>, Multiple<TSpec> >, Hashes_>
+{
+    typedef Pattern<StringSet<TNeedle, TSSetSpec>, Multiple<TSpec> >        TPattern_;
+    typedef typename View<typename Member<TPattern_, Hashes_>::Type>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Member Permutation_                                                [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedles, typename TSpec>
+struct Member<Pattern<TNeedles, Multiple<TSpec> >, Permutation_>
+{
+    typedef Nothing Type;
+};
+
+#ifdef PLATFORM_CUDA
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec>
+struct Member<Pattern<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, Multiple<TSpec> >, Permutation_>
+{
+    typedef thrust::device_vector<TValue, TAlloc>   TNeedle_;
+    typedef StringSet<TNeedle_, TSSetSpec>          TNeedles_;
+    typedef typename Size<TNeedles_>::Type          TSize_;
+
+    typedef thrust::device_vector<TSize_>           Type;
+};
+#endif
+
+template <typename TNeedle, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Member<Pattern<StringSet<ContainerView<TNeedle, TViewSpec>, TSSetSpec>, Multiple<TSpec> >, Permutation_>
+{
+    typedef Pattern<StringSet<TNeedle, TSSetSpec>, Multiple<TSpec> >            TPattern_;
+    typedef typename View<typename Member<TPattern_, Permutation_>::Type>::Type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Member Factory_                                                     [Finder]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+struct Member<Finder_<TText, TPattern, Multiple<TSpec> >, Factory_>
+{
+    typedef Factory<typename TextIterator_<TText, TPattern, TSpec>::Type>   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Delegated                                              [Finder]
+// ----------------------------------------------------------------------------
+
+//template <typename TText, typename TPattern, typename TSpec>
+//struct Delegated<Finder_<TText, TPattern, Multiple<TSpec> > >
+//{
+//    typedef Proxy<Finder_<TText, TPattern, Multiple<TSpec> > > Type;
+//};
+
+// ============================================================================
+// Kernels
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Kernel _preprocessKernel()                                         [Pattern]
+// ----------------------------------------------------------------------------
+
+#ifdef PLATFORM_CUDA
+template <typename TNeedles, typename TSpec>
+SEQAN_GLOBAL void
+_preprocessKernel(Pattern<TNeedles, Multiple<TSpec> > pattern)
+{
+    typedef Pattern<TNeedles, Multiple<TSpec> >     TPattern;
+    typedef typename PatternShape_<TPattern>::Type  TShape;
+
+    unsigned threadId = getThreadId();
+
+    // Return silently if there is no job left.
+    if (threadId >= length(pattern.data_host)) return;
+
+    // Compute the hash of a needle.
+    TShape shape;
+    SEQAN_ASSERT_LEQ(weight(shape), length(pattern.data_host[threadId]));
+    pattern._hashes[threadId] = hash(shape, begin(pattern.data_host[threadId], Standard()));
+
+    // Fill with the identity permutation.
+    pattern._permutation[threadId] = threadId;
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Kernel _findKernel()                                                [Finder]
+// ----------------------------------------------------------------------------
+
+#ifdef PLATFORM_CUDA
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+SEQAN_GLOBAL void
+_findKernel(Finder_<TText, TPattern, Multiple<TSpec> > finder, TPattern pattern, TDelegate delegate)
+{
+    typedef FinderContext_<TText, TPattern, Multiple<TSpec>, TDelegate> TFinderContext;
+
+    unsigned threadId = getThreadId();
+
+    // Return if there is no job left.
+    if (threadId >= length(pattern.data_host)) return;
+
+    // Instantiate a thread context.
+    TFinderContext ctx(finder, delegate);
+
+    // Get the sorted needle id.
+    ctx._patternIt = pattern._permutation[threadId];
+
+    // Find a single needle.
+    clear(ctx.baseFinder);
+    _setScoreThreshold(ctx.baseFinder, _getScoreThreshold(finder));
+    _find(ctx.baseFinder, pattern.data_host[ctx._patternIt], ctx);
+}
+#endif
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _preprocess()                                   [Pattern; ExecHost]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedles, typename TSpec>
+inline void
+_preprocess(Pattern<TNeedles, Multiple<TSpec> > & /* pattern */, ExecHost const & /* tag */) {}
+
+// ----------------------------------------------------------------------------
+// Function _preprocess()                                 [Pattern; ExecDevice]
+// ----------------------------------------------------------------------------
+
+#ifdef PLATFORM_CUDA
+template <typename TNeedles, typename TSpec>
+inline void
+_preprocess(Pattern<TNeedles, Multiple<TSpec> > & pattern, ExecDevice const & /* tag */)
+{
+    typedef Pattern<TNeedles, Multiple<TSpec> > TPattern;
+    typedef typename Size<TNeedles>::Type       TSize;
+
+    TSize needlesCount = length(needle(pattern));
+
+    resize(pattern._hashes, needlesCount, Exact());
+    resize(pattern._permutation, needlesCount, Exact());
+
+    // Compute grid size.
+    unsigned ctaSize = CtaSize<TPattern>::VALUE;
+    unsigned activeBlocks = (needlesCount + ctaSize - 1) / ctaSize;
+
+    // Launch the preprocessing kernel.
+    _preprocessKernel<<<activeBlocks, ctaSize>>>(view(pattern));
+    SEQAN_ASSERT_EQ(cudaGetLastError(), cudaSuccess);
+
+    // Sort the pattern.
+    thrust::sort_by_key(pattern._hashes.begin(), pattern._hashes.end(), pattern._permutation.begin());
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function _preprocess()                                             [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedles, typename TSpec>
+inline void
+_preprocess(Pattern<TNeedles, Multiple<TSpec> > & pattern)
+{
+    typedef Pattern<TNeedles, Multiple<TSpec> > TPattern;
+
+    _preprocess(pattern, typename ExecSpace<TPattern>::Type());
+}
+
+// ----------------------------------------------------------------------------
+// Function setHost()                                                 [Pattern]
+// ----------------------------------------------------------------------------
+
+//template <typename TNeedles, typename TSpec, typename TOtherNeedles>
+//SEQAN_HOST_DEVICE inline void
+//setHost(Pattern<TNeedles, Multiple<TSpec> > & pattern, TOtherNeedles const & needles)
+//{
+//}
+
+// ----------------------------------------------------------------------------
+// Function _initFactory()                                             [Finder]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec, typename THistorySize, typename TObjectsSize>
+inline void
+_initFactory(Finder_<TText, TPattern, Multiple<TSpec> > & finder,
+             THistorySize maxHistoryLength,
+             TObjectsSize maxObjects)
+{
+    // Initialize the iterator factory.
+    setMaxHistoryLength(finder._factory, maxHistoryLength);
+    setMaxObjects(finder._factory, maxObjects);
+    build(finder._factory);
+}
+
+// ----------------------------------------------------------------------------
+// Function _find()                                          [Finder; ExecHost]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+inline void
+_find(Finder_<TText, TPattern, Multiple<TSpec> > & finder,
+      TPattern & pattern,
+      TDelegate & delegate,
+      ExecHost const & /* tag */)
+{
+    typedef Finder_<TText, TPattern,  Multiple<TSpec> >                         TFinder;
+    typedef typename View<TText>::Type                                          TTextView;
+    typedef typename View<TPattern>::Type                                       TPatternView;
+    typedef typename View<TFinder>::Type                                        TFinderView;
+    typedef typename Needle<TPattern>::Type                                     TNeedles;
+    typedef typename View<TNeedles>::Type                                       TNeedlesView;
+    typedef typename Size<TNeedles>::Type                                       TSize;
+    typedef FinderContext_<TTextView, TPatternView, Multiple<TSpec>, TDelegate> TFinderContext;
+
+    // Initialize the iterator factory.
+    _initFactory(finder, maxLength(needle(pattern), Parallel()) + 1, omp_get_max_threads());
+
+    TNeedles & needles = needle(pattern);
+    TSize needlesCount = length(needles);
+
+    // Use a finder view.
+    TFinderView finderView = view(finder);
+    TNeedlesView needlesView = view(needles);
+
+    // Instantiate a thread context.
+    // NOTE(esiragusa): Each thread initializes its private context on firstprivate.
+    TFinderContext ctx(finderView, delegate);
+
+    // Find all needles in parallel.
+    SEQAN_OMP_PRAGMA(parallel for schedule(dynamic) firstprivate(ctx))
+    for (TSize needleId = 0; needleId < needlesCount; ++needleId)
+    {
+        clear(ctx.baseFinder);
+        _setScoreThreshold(ctx.baseFinder, _getScoreThreshold(finder));
+        ctx._patternIt = needleId;
+        _find(ctx.baseFinder, needlesView[ctx._patternIt], ctx);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function _find()                                        [Finder; ExecDevice]
+// ----------------------------------------------------------------------------
+
+#ifdef PLATFORM_CUDA
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+inline void
+_find(Finder_<TText, TPattern, Multiple<TSpec> > & finder,
+      TPattern /* const */ & pattern,
+      TDelegate & delegate,
+      ExecDevice const & /* tag */)
+{
+    typedef Finder_<TText, TPattern, Multiple<TSpec> >  TFinder;
+    typedef typename View<TFinder>::Type                TFinderView;
+
+    // NOTE(esiragusa): Use this to switch to persistent threads.
+//    unsigned activeBlocks = cudaMaxActiveBlocks(_findKernel<TTextView, TPatternsView, TSpec, TDelegateView>, ctaSize, 0);
+//    setMaxObjects(finder._factory, activeBlocks * ctaSize);
+
+    // Compute grid size.
+    unsigned ctaSize = CtaSize<TFinderView>::VALUE;
+    unsigned activeBlocks = (length(needle(pattern)) + ctaSize - 1) / ctaSize;
+
+    // Initialize the iterator factory.
+    _initFactory(finder, 33 + 1, length(needle(pattern)));
+    // TODO(esiragusa): Compute the longest pattern.
+    // NOTE(esiragusa): back/value do not work on thrust::device_vector.
+//    _initFactory(finder, length(back(needle(pattern))) + 1, length(needle(pattern)));
+
+    // Launch the find kernel.
+    _findKernel<<<activeBlocks, ctaSize>>>(view(finder), view(pattern), view(delegate));
+    SEQAN_ASSERT_EQ(cudaGetLastError(), cudaSuccess);
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function _find()                                                    [Finder]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+inline void
+_find(Finder_<TText, TPattern, Multiple<TSpec> > & finder, TPattern & pattern, TDelegate & delegate)
+{
+    typedef Finder_<TText, TPattern,  Multiple<TSpec> > TFinder;
+
+    if (empty(needle(pattern))) return;
+
+    _find(finder, pattern, delegate, typename ExecSpace<TFinder>::Type());
+}
+
+// ----------------------------------------------------------------------------
+// Function view()                                                    [Pattern]
+// ----------------------------------------------------------------------------
+
+template <typename TNeedles, typename TSpec>
+inline typename View<Pattern<TNeedles, Multiple<TSpec> > >::Type
+view(Pattern<TNeedles, Multiple<TSpec> > & pattern)
+{
+    typename View<Pattern<TNeedles, Multiple<TSpec> > >::Type   patternView;
+
+    patternView.data_host = view(needle(pattern));
+    patternView._hashes = view(pattern._hashes);
+    patternView._permutation = view(pattern._permutation);
+
+    return patternView;
+}
+
+// ----------------------------------------------------------------------------
+// Function view()                                                     [Finder]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec>
+inline typename View<Finder_<TText, TPattern, Multiple<TSpec> > >::Type
+view(Finder_<TText, TPattern, Multiple<TSpec> > & finder)
+{
+    typename View<Finder_<TText, TPattern, Multiple<TSpec> > >::Type finderView;
+
+    finderView._factory = view(finder._factory);
+
+    return finderView;
+}
+
+// ----------------------------------------------------------------------------
+// Function _textIterator()                                     [Finder Context]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+inline SEQAN_HOST_DEVICE typename TextIterator_<TText, TPattern, Multiple<TSpec> >::Type &
+_textIterator(FinderContext_<TText, TPattern, Multiple<TSpec>, TDelegate> & ctx)
+{
+    return _textIterator(ctx.baseFinder);
+}
+
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+inline SEQAN_HOST_DEVICE typename TextIterator_<TText, TPattern, Multiple<TSpec> >::Type const &
+_textIterator(FinderContext_<TText, TPattern, Multiple<TSpec>, TDelegate> const & ctx)
+{
+    return _textIterator(ctx.baseFinder);
+}
+
+// ----------------------------------------------------------------------------
+// Function _getScore()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TPattern, typename TSpec, typename TDelegate>
+SEQAN_HOST_DEVICE inline typename Score_<TSpec>::Type
+_getScore(FinderContext_<TText, TPattern, Multiple<TSpec>, TDelegate> const & ctx)
+{
+    return _getScore(ctx.baseFinder);
+}
+
+}
+
+#endif  // #ifndef SEQAN_INDEX_FIND_INDEX_MULTIPLE_H
diff --git a/seqan/index/find2_vstree_factory.h b/seqan/index/find2_vstree_factory.h
new file mode 100644
index 0000000..0baee27
--- /dev/null
+++ b/seqan/index/find2_vstree_factory.h
@@ -0,0 +1,325 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_ITER_VSTREE_FACTORY_H
+#define SEQAN_INDEX_ITER_VSTREE_FACTORY_H
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class Factory
+// ----------------------------------------------------------------------------
+
+template <typename TObject, typename TSpec = void>
+struct Factory;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction View
+// ----------------------------------------------------------------------------
+
+template <typename TObject, typename TSpec>
+struct View<Factory<TObject, TSpec> >
+{
+    typedef Factory<typename View<TObject>::Type, TSpec>    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView
+// ----------------------------------------------------------------------------
+
+template <typename TObject, typename TSpec>
+struct IsView<Factory<TObject, TSpec> > : IsView<TObject> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Host
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct Host<Factory<Iter<TIndex, VSTree<TSpec> > > >
+{
+    typedef TIndex  Type;
+};
+
+template <typename TIndex, typename TSpec>
+struct Host<Factory<Iter<TIndex, VSTree<TSpec> > > const>
+{
+    typedef TIndex const    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Member Index_
+// ----------------------------------------------------------------------------
+
+struct Index_;
+
+template <typename TIndex, typename TSpec>
+struct Member<Factory<Iter<TIndex, VSTree<TSpec> > >, Index_>
+{
+    typedef typename IfView<TIndex, TIndex, Holder<TIndex> >::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Member History_
+// ----------------------------------------------------------------------------
+
+struct History_;
+
+template <typename TIndex, typename TSpec>
+struct Member<Factory<Iter<TIndex, TSpec> >, History_>
+{
+    typedef typename HistoryStack_<Iter<TIndex, TSpec> >::Type   Type;
+};
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class Factory
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct Factory<Iter<TIndex, VSTree<TSpec> > >
+{
+    typename Member<Factory, Index_>::Type  _index;
+
+    Factory() {}
+
+    Factory(TIndex & index) :
+        _index(index)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class Factory
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct Factory<Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > > :
+    Factory<Iter<TIndex, VSTree<TSpec> > >
+{
+    typedef Factory<Iter<TIndex, VSTree<TSpec> > >  TBase;
+
+    typename Member<Factory, History_>::Type    _history;
+    typename Size<TIndex>::Type                 _maxHistoryLength;
+    typename Size<Factory>::Type                _maxObjects;
+
+    Factory() :
+        TBase(),
+        _maxHistoryLength(0),
+        _maxObjects(0)
+    {}
+
+    Factory(TIndex & index) :
+        TBase(index)
+    {}
+
+    template <typename TSize, typename THistorySize>
+    Factory(TIndex & index, TSize maxObjects, THistorySize maxHistoryLength) :
+        TBase(index)
+    {
+        setMaxObjects(*this, maxObjects);
+        setMaxHistoryLength(*this, maxHistoryLength);
+        build(*this);
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function host()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+inline typename Host<Factory<Iter<TIndex, VSTree<TSpec> > > >::Type &
+host(Factory<Iter<TIndex, VSTree<TSpec> > > & factory)
+{
+    return _host(factory, typename IsView<TIndex>::Type());
+}
+
+template <typename TIndex, typename TSpec>
+inline SEQAN_HOST_DEVICE typename Host<Factory<Iter<TIndex, VSTree<TSpec> > > >::Type &
+_host(Factory<Iter<TIndex, VSTree<TSpec> > > & factory, True const & /* isView */)
+{
+    return factory._index;
+}
+
+template <typename TIndex, typename TSpec>
+inline typename Host<Factory<Iter<TIndex, VSTree<TSpec> > > >::Type &
+_host(Factory<Iter<TIndex, VSTree<TSpec> > > & factory, False const & /* isView */)
+{
+    return value(factory._index);
+}
+
+template <typename TIndex, typename TSpec>
+inline typename Host<Factory<Iter<TIndex, VSTree<TSpec> > > const>::Type &
+host(Factory<Iter<TIndex, VSTree<TSpec> > > const & factory)
+{
+    return _host(factory, typename IsView<TIndex>::Type());
+}
+
+template <typename TIndex, typename TSpec>
+inline SEQAN_HOST_DEVICE typename Host<Factory<Iter<TIndex, VSTree<TSpec> > > const>::Type &
+_host(Factory<Iter<TIndex, VSTree<TSpec> > > const & factory, True const & /* isView */)
+{
+    return factory._index;
+}
+
+template <typename TIndex, typename TSpec>
+inline typename Host<Factory<Iter<TIndex, VSTree<TSpec> > > const>::Type &
+_host(Factory<Iter<TIndex, VSTree<TSpec> > > const & factory, False const & /* isView */)
+{
+    return value(factory._index);
+}
+
+// ----------------------------------------------------------------------------
+// Function view()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+inline typename View<Factory<Iter<TIndex, VSTree<TSpec> > > >::Type
+view(Factory<Iter<TIndex, VSTree<TSpec> > > & factory)
+{
+    typename View<Factory<Iter<TIndex, VSTree<TSpec> > > >::Type factoryView;
+
+    host(factoryView) = view(_host(factory, typename IsView<TIndex>::Type()));
+
+    return factoryView;
+}
+
+template <typename TIndex, typename TSpec>
+inline typename View<Factory<Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > > >::Type
+view(Factory<Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > > & factory)
+{
+    typename View<Factory<Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > > >::Type factoryView;
+
+    host(factoryView) = view(_host(factory, typename IsView<TIndex>::Type()));
+    factoryView._history = view(factory._history);
+    factoryView._maxHistoryLength = factory._maxHistoryLength;
+    factoryView._maxObjects = factory._maxObjects;
+
+    return factoryView;
+}
+
+// ----------------------------------------------------------------------------
+// Function setMaxHistoryLength()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec, typename TSize>
+inline void
+setMaxHistoryLength(Factory<Iter<TIndex, VSTree<TSpec> > > & /* factory */, TSize /* maxHistoryLength */)
+{}
+
+template <typename TIndex, typename TSpec, typename TSize>
+inline void
+setMaxHistoryLength(Factory<Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > > & factory, TSize maxHistoryLength)
+{
+    factory._maxHistoryLength = maxHistoryLength;
+}
+
+// ----------------------------------------------------------------------------
+// Function setMaxObjects()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec, typename TSize>
+inline void
+setMaxObjects(Factory<Iter<TIndex, VSTree<TSpec> > > & /* factory */, TSize /* maxObjects */)
+{}
+
+template <typename TIndex, typename TSpec, typename TSize>
+inline void
+setMaxObjects(Factory<Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > > & factory, TSize maxObjects)
+{
+    factory._maxObjects = maxObjects;
+}
+
+// ----------------------------------------------------------------------------
+// Function build()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+inline void
+build(Factory<Iter<TIndex, VSTree<TSpec> > > & /* factory */)
+{}
+
+template <typename TIndex, typename TSpec>
+inline void
+build(Factory<Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > > & factory)
+{
+    resize(factory._history, factory._maxObjects * factory._maxHistoryLength, Exact());
+}
+
+// ----------------------------------------------------------------------------
+// Function getObject()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec, typename TId>
+inline SEQAN_HOST_DEVICE Iter<TIndex, VSTree<TSpec> >
+getObject(Factory<Iter<TIndex, VSTree<TSpec> > > & factory, TId /* objectId */)
+{
+    return Iter<TIndex, VSTree<TSpec> >(_host(factory, typename IsView<TIndex>::Type()));
+}
+
+// ----------------------------------------------------------------------------
+// Function getObject()
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec, typename TId>
+inline SEQAN_HOST_DEVICE Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > >
+getObject(Factory<Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > > & factory, TId objectId)
+{
+    SEQAN_ASSERT_LT(objectId, factory._maxObjects);
+
+    Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > it(_host(factory, typename IsView<TIndex>::Type()));
+
+    it.history._begin = begin(factory._history, Standard()) + objectId * factory._maxHistoryLength;
+    it.history._end = it.history._begin;
+    it.history._capacity = factory._maxHistoryLength;
+
+    return it;
+}
+
+}
+
+#endif  // #ifndef SEQAN_INDEX_ITER_VSTREE_FACTORY_H
diff --git a/seqan/index/find_backtracking.h b/seqan/index/find_backtracking.h
new file mode 100644
index 0000000..28a7f71
--- /dev/null
+++ b/seqan/index/find_backtracking.h
@@ -0,0 +1,1399 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Approximate string matching via backtracking on VSTrees
+// ==========================================================================
+
+#ifndef SEQAN_FIND_BACKTRACKING_H_
+#define SEQAN_FIND_BACKTRACKING_H_
+
+//#define SEQAN_DEBUG
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TDistance, typename TSpec>
+struct Backtracking;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TPrefix, typename TDistance>
+struct BacktrackingState_ {};
+
+// ============================================================================
+
+template <typename TSuffix, typename TDistance>
+struct SuffixAligner_
+{};
+
+template <typename TSuffix>
+struct SuffixAligner_<TSuffix, HammingDistance>
+{
+    typedef typename Size<TSuffix>::Type    TSize;
+
+    TSize               suffix_length;
+    TSize               suffix_position;
+
+    SuffixAligner_() :
+        suffix_length(0),
+        suffix_position(0)
+    {}
+};
+
+// ============================================================================
+
+template <typename TPrefix, typename TDistance>
+struct PrefixAligner_
+{};
+
+template <typename TPrefix>
+struct PrefixAligner_<TPrefix, HammingDistance>
+{
+    typedef typename Size<TPrefix>::Type    TSize;
+
+    TSize               prefix_length;
+    TSize               prefix_position;
+    TSize               global_position;
+    unsigned            errors;
+
+    PrefixAligner_() :
+        prefix_length(0),
+        prefix_position(0),
+        global_position(0),
+        errors(0)
+    {}
+};
+
+// ============================================================================
+
+template <typename TText, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+class Finder<Index<TText, TSpec>, Backtracking<TDistance, TBacktrackingSpec> >
+{
+protected:
+    typedef Index<TText, TSpec>                                         TIndex;
+    typedef typename Iterator<TIndex, TopDown<> >::Type                 TIndexIterator;
+    typedef String<TIndexIterator>                                      TParentStack;
+
+    typedef typename Fibre<TIndex, FibreSA>::Type                       TSA;
+    typedef typename Iterator<TSA const, Standard>::Type                TIterator;
+    typedef typename Size<TIndex>::Type                                 TSize;
+
+    typedef typename EdgeLabel<TIndexIterator>::Type                    TSuffix;
+    typedef SuffixAligner_<TSuffix, TDistance>                           TSuffixAligner;
+
+public:
+    bool                index_iterator_at_root;
+
+    Holder<TIndex>      index;
+    TIndexIterator      index_iterator;
+    TParentStack        index_parents;
+    Pair<TSize>         index_range;
+
+    TIterator           data_iterator;
+    TSize               data_length;
+    Pair<TIterator>     range;
+
+    TSuffixAligner      suffix_aligner;
+
+    Finder() {}
+
+    Finder(TIndex & index) :
+        index(index),
+        index_iterator(index)
+    {
+        clear(*this);
+    }
+
+    Finder(TIndex const & index) :
+        index(index),
+        index_iterator(index)
+    {
+        clear(*this);
+    }
+
+    ~Finder()
+    {
+#ifdef SEQAN_DEBUG
+        std::cout << "Finder Parents Height: " << length(this->index_parents) << std::endl;
+#endif
+    }
+
+};
+
+// ============================================================================
+
+template <typename TNeedle, typename TDistance, typename TBacktrackingSpec>
+class Pattern<TNeedle, Backtracking<TDistance, TBacktrackingSpec> >
+{
+protected:
+    typedef TNeedle                                     TPrefix;
+    typedef PrefixAligner_<TPrefix, TDistance>           TPrefixAligner;
+
+    typedef typename BacktrackingState_<TPrefix, TDistance>::Type    TState;
+    typedef String<TState>                              TStateStack;
+
+public:
+    Holder<TNeedle>         data_host;
+    TPrefixAligner          prefix_aligner;
+    TStateStack             state;
+
+    Pattern() {}
+
+#ifdef SEQAN_CXX11_STANDARD
+    Pattern(TNeedle && needle,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle>::type const &, Pattern const &>))
+    {
+        ignoreUnusedVaraiableWarning(dummy);
+        setHost(*this, std::forward<TNeedle>(needle));
+    }
+#else
+    Pattern(TNeedle const & needle)
+    {
+        setHost(*this, needle);
+    }
+#endif  // SEQAN_CXX11_STANDARD
+    ~Pattern()
+    {
+        // Empty stack
+        clear(this->state);
+    }
+
+};
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+class Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> >
+{
+protected:
+    typedef Index<TNeedle, TSpec>                                       TIndex;
+    typedef typename Iterator<TIndex, TopDown<> >::Type                 TIndexIterator;
+    typedef String<TIndexIterator>                                      TParentStack;
+
+    typedef typename Fibre<TIndex, FibreSA>::Type                       TSA;
+    typedef typename Iterator<TSA const, Standard>::Type                TIterator;
+    typedef typename Size<TIndex>::Type                                 TSize;
+
+    typedef typename EdgeLabel<TIndexIterator>::Type                    TPrefix;
+    typedef PrefixAligner_<TPrefix, TDistance>                           TPrefixAligner;
+
+    typedef typename BacktrackingState_<TPrefix, TDistance>::Type                    TState;
+    typedef String<TState>                                              TStateStack;
+
+    typedef String<bool>                                                TEndStack;
+
+public:
+    bool                index_iterator_at_root;
+
+    Holder<TIndex>      data_host;
+    TIndexIterator      index_iterator;
+    TParentStack        index_parents;
+    Pair<TSize>         index_range;
+
+    TIterator           data_iterator;
+    TSize               data_length;
+    Pair<TIterator>     range;
+
+    TPrefixAligner      prefix_aligner;
+    TStateStack         state;
+    TEndStack           atEnd;
+
+    unsigned            exact;
+    bool                search;
+
+    // TODO(esiragusa): Remove depth, isLeaf(it) should return true when repLength(it) >= depth
+    TSize               depth;
+
+    Pattern() {}
+
+
+#ifdef SEQAN_CXX11_STANDARD
+    Pattern(TIndex && index, TSize depth) :
+        data_host(std::forward<TIndex>(index)),
+        index_iterator(index),
+        depth(depth)
+    {
+        setHost(*this, std::forward<TIndex>(index));
+    }
+
+#else
+    Pattern(TIndex & index, TSize depth) :
+        data_host(index),
+        index_iterator(index),
+        depth(depth)
+    {
+        setHost(*this, index);
+    }
+
+    Pattern(TIndex const & index, TSize depth) :
+        data_host(index),
+        index_iterator(index),
+        depth(depth)
+    {
+        setHost(*this, index);
+    }
+#endif  // SEQAN_CXX11_STANDARD
+    ~Pattern()
+    {
+#ifdef SEQAN_DEBUG
+        std::cout << "BacktrackingState_ Height: " << length(this->state) << std::endl;
+        std::cout << "atEnd Height: " << length(this->atEnd) << std::endl;
+        std::cout << "Pattern Parents Height: " << length(this->index_parents) << std::endl;
+#endif
+
+        // Empty stacks
+        clear(this->index_parents);
+        clear(this->state);
+        clear(this->atEnd);
+    }
+
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+template <typename TPrefix>
+struct BacktrackingState_<TPrefix, HammingDistance>
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+    typedef Pair<TSize, unsigned>                   Type;
+};
+
+// ============================================================================
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+struct Position<Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > >:
+    SAValue<Index<TNeedle, TSpec> >
+{};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TPrefix>
+inline unsigned
+getScore(PrefixAligner_<TPrefix, HammingDistance> const & me, bool atEnd)
+{
+    return atEnd ? me.errors : MaxValue<unsigned>::VALUE;
+}
+
+template <typename TPrefix>
+inline unsigned
+getMinScore(PrefixAligner_<TPrefix, HammingDistance> const & me)
+{
+    return me.errors;
+}
+
+template <typename TPrefix>
+inline typename BacktrackingState_<TPrefix, HammingDistance>::Type
+getInitialState(PrefixAligner_<TPrefix, HammingDistance> &)
+{
+    typedef typename BacktrackingState_<TPrefix, HammingDistance>::Type  TState;
+    return TState(0, 0);
+}
+
+template <typename TPrefix>
+inline typename BacktrackingState_<TPrefix, HammingDistance>::Type
+getState(PrefixAligner_<TPrefix, HammingDistance> & me)
+{
+    typedef typename BacktrackingState_<TPrefix, HammingDistance>::Type  TState;
+    return TState(me.global_position, me.errors);
+}
+
+template <typename TPrefix, typename TState>
+inline void
+setState(PrefixAligner_<TPrefix, HammingDistance> & me, TState const & state)
+{
+    me.global_position = state.i1;
+    me.errors = state.i2;
+#ifdef SEQAN_DEBUG
+    std::cout << "Old BacktrackingState_:      " << "(" << state.i1 << ", " << state.i2 << ")" << std::endl;
+#endif
+}
+
+template <typename TSuffix, typename TState>
+inline void
+setState(SuffixAligner_<TSuffix, HammingDistance> &, TState const &)
+{
+//    me.global_position = state.i1;
+}
+
+template <typename TSuffix, typename TSize>
+inline void setLength(SuffixAligner_<TSuffix, HammingDistance> & me, TSize suffix_length)
+{
+    me.suffix_length = suffix_length;
+}
+
+template <typename TPrefix, typename TSize>
+inline void setLength(PrefixAligner_<TPrefix, HammingDistance> & me, TSize prefix_length)
+{
+    me.prefix_length = prefix_length;
+}
+
+template <typename TSuffix, typename TSize>
+inline void setPosition(SuffixAligner_<TSuffix, HammingDistance> & me, TSize suffix_position)
+{
+    me.suffix_position = suffix_position;
+}
+
+template <typename TPrefix, typename TSize>
+inline void setPosition(PrefixAligner_<TPrefix, HammingDistance> & me, TSize prefix_position)
+{
+    me.prefix_position = prefix_position;
+}
+
+// ============================================================================
+
+template <typename TSuffix, typename TPrefix, typename TErrors>
+inline bool align(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                  PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                  TSuffix & suffix,
+                  TPrefix & prefix,
+                  TErrors errors)
+{
+    return _align(suffix_aligner, prefix_aligner, suffix, prefix, errors,
+                  typename IsSequence<TSuffix>::Type(), typename IsSequence<TPrefix>::Type());
+}
+
+template <typename TSuffix, typename TPrefix, typename TErrors>
+inline bool _align(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                   PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                   TSuffix & suffix,
+                   TPrefix & prefix,
+                   TErrors errors,
+                   False const & /* tag */,
+                   False const & /* tag */)
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+
+    TSize extension = _min(suffix_aligner.suffix_length - suffix_aligner.suffix_position,
+                           prefix_aligner.prefix_length - prefix_aligner.prefix_position);
+
+    if (extension > 0)
+    {
+        if (suffix != prefix)
+            if (++prefix_aligner.errors > errors)
+                return false;
+
+        suffix_aligner.suffix_position++;
+        prefix_aligner.prefix_position++;
+        prefix_aligner.global_position++;
+    }
+
+    return true;
+}
+
+template <typename TSuffix, typename TPrefix, typename TErrors>
+inline bool _align(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                   PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                   TSuffix & suffix,
+                   TPrefix & prefix,
+                   TErrors errors,
+                   True const & /* tag */,
+                   False const & /* tag */)
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+
+    TSize extension = _min(suffix_aligner.suffix_length - suffix_aligner.suffix_position,
+                           prefix_aligner.prefix_length - prefix_aligner.prefix_position);
+
+    if (extension > 0)
+    {
+        if (suffix[suffix_aligner.suffix_position] != prefix)
+            if (++prefix_aligner.errors > errors)
+                return false;
+
+        suffix_aligner.suffix_position++;
+        prefix_aligner.prefix_position++;
+        prefix_aligner.global_position++;
+    }
+
+    return true;
+}
+
+template <typename TSuffix, typename TPrefix, typename TErrors>
+inline bool _align(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                   PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                   TSuffix & suffix,
+                   TPrefix & prefix,
+                   TErrors errors,
+                   False const & /* tag */,
+                   True const & /* tag */)
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+
+    TSize extension = _min(suffix_aligner.suffix_length - suffix_aligner.suffix_position,
+                           prefix_aligner.prefix_length - prefix_aligner.prefix_position);
+
+    if (extension > 0)
+    {
+        if (suffix != prefix[prefix_aligner.prefix_position])
+            if (++prefix_aligner.errors > errors)
+                return false;
+
+        suffix_aligner.suffix_position++;
+        prefix_aligner.prefix_position++;
+        prefix_aligner.global_position++;
+    }
+
+    return true;
+}
+
+template <typename TSuffix, typename TPrefix, typename TErrors>
+inline bool _align(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                   PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                   TSuffix & suffix,
+                   TPrefix & prefix,
+                   TErrors errors,
+                   True const & /* tag */,
+                   True const & /* tag */)
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+
+    TSize extension = _min(suffix_aligner.suffix_length - suffix_aligner.suffix_position,
+                           prefix_aligner.prefix_length - prefix_aligner.prefix_position);
+
+    TSize endPosition = prefix_aligner.global_position + extension;
+
+    while (prefix_aligner.global_position < endPosition)
+    {
+        if (suffix[suffix_aligner.suffix_position] != prefix[prefix_aligner.prefix_position])
+            if (++prefix_aligner.errors > errors)
+                return false;
+
+        suffix_aligner.suffix_position++;
+        prefix_aligner.prefix_position++;
+        prefix_aligner.global_position++;
+    }
+
+    return true;
+}
+
+// ============================================================================
+
+template <typename TSuffix, typename TPrefix>
+inline bool match(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                  PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                  TSuffix const & suffix,
+                  TPrefix const & prefix)
+{
+    return _match(suffix_aligner, prefix_aligner, suffix, prefix,
+                  typename IsSequence<TSuffix>::Type(), typename IsSequence<TPrefix>::Type());
+}
+
+template <typename TSuffix, typename TPrefix>
+inline bool _match(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                   PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                   TSuffix const & suffix,
+                   TPrefix const & prefix,
+                   False const & /* tag */,
+                   False const & /* tag */)
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+
+    TSize extension = _min(suffix_aligner.suffix_length - suffix_aligner.suffix_position,
+                           prefix_aligner.prefix_length - prefix_aligner.prefix_position);
+
+    if (extension > 0)
+    {
+        if (suffix != prefix)
+            return false;
+
+        suffix_aligner.suffix_position++;
+        prefix_aligner.prefix_position++;
+        prefix_aligner.global_position++;
+    }
+
+    return true;
+}
+
+template <typename TSuffix, typename TPrefix>
+inline bool _match(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                   PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                   TSuffix const & suffix,
+                   TPrefix const & prefix,
+                   True const & /* tag */,
+                   False const & /* tag */)
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+
+    TSize extension = _min(suffix_aligner.suffix_length - suffix_aligner.suffix_position,
+                           prefix_aligner.prefix_length - prefix_aligner.prefix_position);
+
+    if (extension > 0)
+    {
+        if (suffix[suffix_aligner.suffix_position] != prefix)
+            return false;
+
+        suffix_aligner.suffix_position++;
+        prefix_aligner.prefix_position++;
+        prefix_aligner.global_position++;
+    }
+
+    return true;
+}
+
+template <typename TSuffix, typename TPrefix>
+inline bool _match(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                   PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                   TSuffix const & suffix,
+                   TPrefix const & prefix,
+                   False const & /* tag */,
+                   True const & /* tag */)
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+
+    TSize extension = _min(suffix_aligner.suffix_length - suffix_aligner.suffix_position,
+                           prefix_aligner.prefix_length - prefix_aligner.prefix_position);
+
+    if (extension > 0)
+    {
+        if (suffix != prefix[prefix_aligner.prefix_position])
+            return false;
+
+        suffix_aligner.suffix_position++;
+        prefix_aligner.prefix_position++;
+        prefix_aligner.global_position++;
+    }
+
+    return true;
+}
+
+template <typename TSuffix, typename TPrefix>
+inline bool _match(SuffixAligner_<TSuffix, HammingDistance> & suffix_aligner,
+                   PrefixAligner_<TPrefix, HammingDistance> & prefix_aligner,
+                   TSuffix const & suffix,
+                   TPrefix const & prefix,
+                   True const & /* tag */,
+                   True const & /* tag */)
+{
+    typedef typename Size<TPrefix>::Type            TSize;
+
+    TSize extension = _min(suffix_aligner.suffix_length - suffix_aligner.suffix_position,
+                           prefix_aligner.prefix_length - prefix_aligner.prefix_position);
+
+    TSize endPosition = prefix_aligner.global_position + extension;
+
+    while (prefix_aligner.global_position < endPosition)
+    {
+        if (suffix[suffix_aligner.suffix_position] != prefix[prefix_aligner.prefix_position])
+            return false;
+
+        suffix_aligner.suffix_position++;
+        prefix_aligner.prefix_position++;
+        prefix_aligner.global_position++;
+    }
+
+    return true;
+}
+
+// ============================================================================
+
+template <typename TPrefix>
+inline bool _atEnd(PrefixAligner_<TPrefix, HammingDistance> const & me)
+{
+    return me.prefix_position == me.prefix_length;
+}
+
+template <typename TSuffix>
+inline bool _atEnd(SuffixAligner_<TSuffix, HammingDistance> const & me)
+{
+    return me.suffix_position == me.suffix_length;
+}
+
+// ============================================================================
+
+template <typename TText, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline void
+clear(Finder<Index<TText, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    typedef Index<TText, TSpec>                                         TIndex;
+    typedef typename Iterator<TIndex, TopDown<> >::Type                 TIndexIterator;
+
+    typedef typename Fibre<TIndex, FibreSA>::Type                       TSA;
+    typedef typename Iterator<TSA const, Standard>::Type                TIterator;
+
+    typedef typename EdgeLabel<TIndexIterator>::Type                    TSuffix;
+    typedef SuffixAligner_<TSuffix, TDistance>                           TSuffixAligner;
+
+    // Init backtracking on root node
+    me.index_iterator = TIndexIterator(host(me));
+    me.index_iterator_at_root = true;
+
+    // Empty parent stack
+    clear(me.index_parents);
+
+    // Init data iterator on empty range
+    hostIterator(me) = begin(indexSA(host(me)), Standard());
+    me.range.i1 = me.range.i2 = TIterator();
+    me.data_length = 0;
+
+    // Call SuffixAligner_ constructor
+    me.suffix_aligner = TSuffixAligner();
+}
+
+// ============================================================================
+
+template <typename TNeedle, typename TDistance, typename TBacktrackingSpec>
+void _reinitPattern(Pattern<TNeedle, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    typedef TNeedle                                     TPrefix;
+    typedef PrefixAligner_<TPrefix, TDistance>           TPrefixAligner;
+    //typedef typename BacktrackingState_<TPrefix, TDistance>::Type    TState;
+
+    // Call PrefixAligner_ constructor
+    me.prefix_aligner = TPrefixAligner();
+
+    // Init stack on empty word
+    clear(me.state);
+    appendValue(me.state, getInitialState(me.prefix_aligner));
+}
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+void _moveIteratorAtRoot(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    typedef Index<TNeedle, TSpec>                                       TIndex;
+    typedef typename Iterator<TIndex, TopDown<> >::Type                 TIndexIterator;
+    me.index_iterator = TIndexIterator(host(me));
+}
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+void _reinitPattern(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    typedef Index<TNeedle, TSpec>                                       TIndex;
+    typedef typename Iterator< TIndex, TopDown<> >::Type                TIndexIterator;
+    typedef typename Fibre<TIndex, FibreSA>::Type                       TSA;
+    typedef typename Iterator<TSA const, Standard>::Type                TIterator;
+
+    typedef typename EdgeLabel<TIndexIterator>::Type                    TPrefix;
+    typedef PrefixAligner_<TPrefix, TDistance>                           TPrefixAligner;
+    //typedef typename BacktrackingState_<TPrefix, TDistance>::Type                    TState;
+
+    // Init backtracking on root node
+    _moveIteratorAtRoot(me);
+//    me.index_iterator = TIndexIterator(host(me));
+    me.index_iterator_at_root = true;
+
+    // Empty parent stack
+    clear(me.index_parents);
+
+    // Init data iterator on empty range
+    hostIterator(me) = begin(indexSA(host(me)), Standard());
+    me.range.i1 = me.range.i2 = TIterator();
+    me.data_length = 0;
+
+    // Init stack on empty word
+    clear(me.state);
+    appendValue(me.state, getInitialState(me.prefix_aligner));
+
+    // Empty atEnd stack
+    clear(me.atEnd);
+//    appendValue(me.atEnd, true);
+
+    // Empty exact search stack
+    me.exact = 0;
+    me.search = false;
+
+    // Call PrefixAligner_ constructor
+    me.prefix_aligner = TPrefixAligner();
+}
+
+// ============================================================================
+
+template < typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec >
+inline typename Iterator< typename Fibre<Index<TNeedle, TSpec>, FibreSA>::Type const, Standard>::Type const &
+hostIterator(Pattern< Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > const & me)
+{
+    return me.data_iterator;
+}
+
+template < typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec >
+inline typename Iterator< typename Fibre<Index<TNeedle, TSpec>, FibreSA>::Type const, Standard >::Type &
+hostIterator(Pattern< Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    return me.data_iterator;
+}
+
+// ============================================================================
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline bool
+empty(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    return me.range.i1 == me.range.i2;
+}
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline bool
+atBegin(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    return (empty(me) || hostIterator(me) == me.range.i1);
+}
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline bool
+atEnd(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    return (empty(me) || hostIterator(me) == me.range.i2);
+}
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline void
+goBegin(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    hostIterator(me) = me.range.i1;
+}
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline void
+goEnd(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    hostIterator(me) = me.range.i2;
+}
+
+// ============================================================================
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline typename Position<Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > >::Type
+beginPosition(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    SEQAN_ASSERT_NOT(empty(me));
+    return *me.data_iterator;
+}
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline typename Position<Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > >::Type
+endPosition(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    return posAdd(beginPosition(me), me.data_length);
+}
+
+template <typename TNeedle, typename TSpec, typename TDistance, typename TBacktrackingSpec>
+inline typename Position<Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > >::Type
+position(Pattern<Index<TNeedle, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & me)
+{
+    return beginPosition(me);
+}
+
+// ============================================================================
+
+template <typename TText, typename TSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle>
+inline bool
+_resume(Finder<Index<TText, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+        Pattern<TNeedle, Backtracking<TDistance, TBacktrackingSpec> > & pattern)
+{
+    // Resume positively from root only the first time
+    if (finder.index_iterator_at_root)
+    {
+        finder.index_iterator_at_root = false;
+        return true;
+    }
+
+    return _cut(finder, pattern);
+}
+
+template <typename TText, typename TSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle, typename TErrors>
+inline bool
+_backtrack(Finder<Index<TText, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+           Pattern<TNeedle, Backtracking<TDistance, TBacktrackingSpec> > & pattern,
+           TErrors errors)
+{
+    typedef Index<TText, TSpec>                             TIndex;
+    typedef typename Iterator<TIndex, TopDown<> >::Type     TIndexIterator;
+    typedef typename EdgeLabel<TIndexIterator>::Type        TSuffix;
+    typedef typename Size<TIndex>::Type                     TSuffixSize;
+
+    typedef typename BacktrackingState_<TNeedle, TDistance>::Type        TState;
+
+    setLength(pattern.prefix_aligner, length(needle(pattern)));
+    setPosition(pattern.prefix_aligner, 0);
+
+    do
+    {
+        SEQAN_ASSERT_NOT(empty(pattern.state));
+
+#ifdef SEQAN_DEBUG
+        std::cout << "Stack Height:   " << length(pattern.state) << std::endl;
+        std::cout << "Suffix:         " <<
+        prefix(representative(finder.index_iterator),
+               _min(repLength(finder.index_iterator), length(needle(pattern))))
+        << std::endl;
+#endif
+        // Restore last state
+        setState(finder.suffix_aligner, back(pattern.state));
+        setState(pattern.prefix_aligner, back(pattern.state));
+
+        // Update current prefix
+        setPosition(pattern.prefix_aligner, pattern.prefix_aligner.global_position);
+
+        // Update current suffix
+        TSuffix suffixEdge = parentEdgeLabel(finder.index_iterator);
+        TSuffixSize suffixLength = parentEdgeLength(finder.index_iterator);
+        TSuffixSize suffixPos = pattern.prefix_aligner.global_position - parentRepLength(finder.index_iterator);
+        setLength(finder.suffix_aligner, suffixLength);
+        setPosition(finder.suffix_aligner, suffixPos);
+
+        // Align suffix with pattern
+        align(finder.suffix_aligner, pattern.prefix_aligner, suffixEdge, needle(pattern), errors);
+
+        // A complete match was found
+        if (getScore(pattern.prefix_aligner, _atEnd(pattern.prefix_aligner)) <= errors)
+        {
+            finder.index_range = range(finder.index_iterator);
+            return true;
+        }
+        // Reduce to exact suffix search (speedup)
+        else if (getMinScore(pattern.prefix_aligner) == errors)
+        {
+            TIndexIterator index_iterator(finder.index_iterator);
+
+            // A complete match was found
+            if (goDown(index_iterator, suffix(needle(pattern), pattern.prefix_aligner.global_position)))
+            {
+                // Move aligners to end of pattern
+                pattern.prefix_aligner.global_position = length(needle(pattern));
+
+                finder.index_range = range(index_iterator);
+                return true;
+            }
+            else
+                _cut(finder, pattern);
+        }
+        // Walk down text index only if an alignment is still possible
+        else if (getMinScore(pattern.prefix_aligner) <= errors && !isLeaf(finder.index_iterator))
+        {
+            appendValue(finder.index_parents, finder.index_iterator);
+            goDown(finder.index_iterator);
+//            appendValue(pattern.state, getState(pattern.prefix_aligner));
+            appendValue(pattern.state, TState(pattern.prefix_aligner.global_position, pattern.prefix_aligner.errors));
+        }
+        // Otherwise cut branch
+        else
+            _cut(finder, pattern);
+    }
+    while (!isRoot(finder.index_iterator));
+
+    return false;
+}
+
+template <typename TText, typename TSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle>
+inline bool
+_cut(Finder<Index<TText, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+     Pattern<TNeedle, Backtracking<TDistance, TBacktrackingSpec> > & pattern)
+{
+    // Walk to next node
+    if (!goRight(finder.index_iterator))
+        while (!isRoot(finder.index_iterator))
+        {
+            SEQAN_ASSERT_NOT(empty(finder.index_parents));
+            finder.index_iterator = back(finder.index_parents);
+            eraseBack(finder.index_parents);
+
+            SEQAN_ASSERT_NOT(empty(pattern.state));
+            eraseBack(pattern.state);
+            if (goRight(finder.index_iterator))
+                break;
+        }
+
+    return !isRoot(finder.index_iterator);
+}
+
+// ============================================================================
+
+template <typename TText, typename TTextSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle, typename TNeedleSpec, typename TErrors>
+inline bool
+_resume(Finder<Index<TText, TTextSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+        Pattern<Index<TNeedle, TNeedleSpec>, Backtracking<TDistance, TBacktrackingSpec> > & pattern,
+        TErrors errors)
+{
+    // Resume positively from root only the first time
+    if (finder.index_iterator_at_root)
+    {
+        finder.index_iterator_at_root = false;
+        return _backtrack(finder, pattern, errors);
+    }
+
+    if (pattern.search)
+    {
+        if (_cut_exact(finder, pattern) && _search(finder, pattern))
+            return true;
+
+        SEQAN_ASSERT_NOT(pattern.exact);
+
+        SEQAN_ASSERT_NOT(empty(finder.index_parents));
+        finder.index_iterator = back(finder.index_parents);
+        eraseBack(finder.index_parents);
+        SEQAN_ASSERT_NOT(empty(pattern.index_parents));
+        pattern.index_iterator = back(pattern.index_parents);
+        eraseBack(pattern.index_parents);
+        SEQAN_ASSERT_NOT(empty(pattern.state));
+        eraseBack(pattern.state);
+
+        pattern.search = false;
+    }
+
+    return _cut(finder, pattern) && _backtrack(finder, pattern, errors);
+}
+
+template <typename TText, typename TTextSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle, typename TNeedleSpec, typename TErrors>
+inline bool
+_backtrack(Finder<Index<TText, TTextSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+           Pattern<Index<TNeedle, TNeedleSpec>, Backtracking<TDistance, TBacktrackingSpec> > & pattern,
+           TErrors errors)
+{
+    typedef Index<TText, TTextSpec>                                     TTextIndex;
+    typedef typename Iterator<TTextIndex, TopDown<> >::Type             TTextIndexIterator;
+    typedef typename EdgeLabel<TTextIndexIterator>::Type                TSuffix;
+    typedef typename Size<TTextIndex>::Type                             TSuffixSize;
+
+    typedef Index<TNeedle, TNeedleSpec>                                 TNeedleIndex;
+    typedef typename Iterator<TNeedleIndex, TopDown<> >::Type           TNeedleIndexIterator;
+    typedef typename EdgeLabel<TNeedleIndexIterator>::Type              TPrefix;
+    //typedef typename Size<TNeedleIndex>::Type                           TPrefixSize;
+
+    typedef typename BacktrackingState_<TNeedle, TDistance>::Type                    TState;
+
+    SEQAN_ASSERT_NOT(pattern.exact);
+
+    do
+    {
+        SEQAN_ASSERT_NOT(empty(pattern.state));
+
+#ifdef SEQAN_DEBUG
+        std::cout << "Stack Height:   " << length(pattern.state) << std::endl;
+        std::cout << "Suffix:         "    << representative(finder.index_iterator) << std::endl;
+        std::cout << "Prefix:         " << representative(pattern.index_iterator) << std::endl;
+#endif
+
+        // Lookup last state
+        setState(finder.suffix_aligner, back(pattern.state));
+        setState(pattern.prefix_aligner, back(pattern.state));
+
+        // Update current suffix
+        TSuffix suffixEdge = parentEdgeLabel(finder.index_iterator);
+        TSuffixSize suffixLength = parentEdgeLength(finder.index_iterator);
+        TSuffixSize suffixPos = pattern.prefix_aligner.global_position - parentRepLength(finder.index_iterator);
+        setLength(finder.suffix_aligner, suffixLength);
+        setPosition(finder.suffix_aligner, suffixPos);
+
+        // Update current prefix
+        TPrefix prefixEdge = parentEdgeLabel(pattern.index_iterator);
+        TSuffixSize prefixLength = parentEdgeLength(pattern.index_iterator);
+        TSuffixSize prefixPos = pattern.prefix_aligner.global_position - parentRepLength(pattern.index_iterator);
+        setLength(pattern.prefix_aligner, _min(prefixLength, pattern.depth - parentRepLength(pattern.index_iterator)));
+        setPosition(pattern.prefix_aligner, prefixPos);
+
+        // Align suffix with prefix
+        align(finder.suffix_aligner, pattern.prefix_aligner, suffixEdge, prefixEdge, errors);
+
+        // A complete match was found
+//        if (getScore(pattern.prefix_aligner, isLeaf(pattern.index_iterator)) <= errors)
+        if (getScore(pattern.prefix_aligner, (pattern.prefix_aligner.global_position >= pattern.depth)) <= errors)
+        {
+            finder.index_range = range(finder.index_iterator);
+            pattern.index_range = range(pattern.index_iterator);
+            return true;
+        }
+        // Reduce to exact suffix search (speedup)
+        else if (getMinScore(pattern.prefix_aligner) == errors)
+        {
+            pattern.search = true;
+
+            appendValue(finder.index_parents, finder.index_iterator);
+            appendValue(pattern.index_parents, pattern.index_iterator);
+//            appendValue(pattern.state, getState(pattern.prefix_aligner));
+            appendValue(pattern.state, TState(pattern.prefix_aligner.global_position, pattern.prefix_aligner.errors));
+
+            if (_search(finder, pattern))
+                return true;
+
+            SEQAN_ASSERT_NOT(pattern.exact);
+
+            SEQAN_ASSERT_NOT(empty(finder.index_parents));
+            finder.index_iterator = back(finder.index_parents);
+            eraseBack(finder.index_parents);
+            SEQAN_ASSERT_NOT(empty(pattern.index_parents));
+            pattern.index_iterator = back(pattern.index_parents);
+            eraseBack(pattern.index_parents);
+            SEQAN_ASSERT_NOT(empty(pattern.state));
+            eraseBack(pattern.state);
+
+            pattern.search = false;
+
+            _cut(finder, pattern);
+        }
+        else if (getMinScore(pattern.prefix_aligner) <= errors)
+        {
+            if (_atEnd(finder.suffix_aligner))
+            {
+                if (!isLeaf(finder.index_iterator))
+                {
+                    appendValue(finder.index_parents, finder.index_iterator);
+                    appendValue(pattern.index_parents, pattern.index_iterator);
+//                    appendValue(pattern.state, getState(pattern.prefix_aligner));
+                    appendValue(pattern.state, TState(pattern.prefix_aligner.global_position, pattern.prefix_aligner.errors));
+                    appendValue(pattern.atEnd, false);
+
+                    goDown(finder.index_iterator);
+                }
+                else
+                    _cut(finder, pattern);
+            }
+            else if (_atEnd(pattern.prefix_aligner))
+            {
+                if (prefixLength < pattern.depth && !isLeaf(pattern.index_iterator))
+                {
+                    appendValue(finder.index_parents, finder.index_iterator);
+                    appendValue(pattern.index_parents, pattern.index_iterator);
+//                    appendValue(pattern.state, getState(pattern.prefix_aligner));
+                    appendValue(pattern.state, TState(pattern.prefix_aligner.global_position, pattern.prefix_aligner.errors));
+                    appendValue(pattern.atEnd, true);
+
+                    goDown(pattern.index_iterator);
+                }
+                else
+                    _cut(finder, pattern);
+            }
+        }
+        else
+            _cut(finder, pattern);
+    }
+    while (!(isRoot(pattern.index_iterator) && isRoot(finder.index_iterator)));
+
+    return false;
+}
+
+template <typename TText, typename TTextSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle, typename TNeedleSpec>
+inline bool
+_cut(Finder<Index<TText, TTextSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+     Pattern<Index<TNeedle, TNeedleSpec>, Backtracking<TDistance, TBacktrackingSpec> > & pattern)
+{
+    SEQAN_ASSERT_NOT(pattern.exact);
+
+    if (empty(pattern.atEnd))
+        return false;
+
+    do
+    {
+        SEQAN_ASSERT_NOT(empty(pattern.atEnd));
+
+        if (!back(pattern.atEnd))
+        {
+            if (goRight(finder.index_iterator))
+            {
+                SEQAN_ASSERT_NOT(empty(pattern.index_parents));
+                pattern.index_iterator = back(pattern.index_parents);
+                break;
+            }
+        }
+        else
+        {
+            if (goRight(pattern.index_iterator))
+            {
+                SEQAN_ASSERT_NOT(empty(finder.index_parents));
+                finder.index_iterator = back(finder.index_parents);
+                break;
+            }
+        }
+
+        SEQAN_ASSERT_NOT(empty(finder.index_parents));
+        finder.index_iterator = back(finder.index_parents);
+        eraseBack(finder.index_parents);
+        SEQAN_ASSERT_NOT(empty(pattern.index_parents));
+        pattern.index_iterator = back(pattern.index_parents);
+        eraseBack(pattern.index_parents);
+        SEQAN_ASSERT_NOT(empty(pattern.state));
+        eraseBack(pattern.state);
+        SEQAN_ASSERT_NOT(empty(pattern.atEnd));
+        eraseBack(pattern.atEnd);
+    }
+    while (!(isRoot(pattern.index_iterator) && isRoot(finder.index_iterator)));
+
+    return !(isRoot(pattern.index_iterator) && isRoot(finder.index_iterator));
+}
+
+template <typename TText, typename TTextSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle, typename TNeedleSpec>
+inline unsigned
+_search(Finder<Index<TText, TTextSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+        Pattern<Index<TNeedle, TNeedleSpec>, Backtracking<TDistance, TBacktrackingSpec> > & pattern)
+{
+    typedef Index<TText, TTextSpec>                                     TTextIndex;
+    typedef typename Iterator<TTextIndex, TopDown<> >::Type             TTextIndexIterator;
+    typedef typename EdgeLabel<TTextIndexIterator>::Type                TSuffix;
+    typedef typename Size<TTextIndex>::Type                             TSuffixSize;
+
+    typedef Index<TNeedle, TNeedleSpec>                                 TNeedleIndex;
+    typedef typename Iterator<TNeedleIndex, TopDown<> >::Type           TNeedleIndexIterator;
+    typedef typename EdgeLabel<TNeedleIndexIterator>::Type              TPrefix;
+    typedef typename Size<TNeedleIndex>::Type                           TPrefixSize;
+
+    typedef typename BacktrackingState_<TNeedle, TDistance>::Type                    TState;
+
+    do
+    {
+        SEQAN_ASSERT_NOT(empty(pattern.state));
+
+#ifdef SEQAN_DEBUG
+        std::cout << "Stack Height:   " << length(pattern.state) << std::endl;
+        std::cout << "Exact Height:   " << pattern.exact << std::endl;
+        std::cout << "Suffix:         "    << representative(finder.index_iterator) << std::endl;
+        std::cout << "Prefix:         " << representative(pattern.index_iterator) << std::endl;
+#endif
+
+        // Lookup last state
+        setState(finder.suffix_aligner, back(pattern.state));
+        setState(pattern.prefix_aligner, back(pattern.state));
+
+        // Update current suffix
+        TSuffix suffixEdge = parentEdgeLabel(finder.index_iterator);
+        TSuffixSize suffixLength = parentEdgeLength(finder.index_iterator);
+        TSuffixSize suffixPos = pattern.prefix_aligner.global_position - parentRepLength(finder.index_iterator);
+        setLength(finder.suffix_aligner, suffixLength);
+        setPosition(finder.suffix_aligner, suffixPos);
+
+        // Update current prefix
+        TPrefix prefixEdge = parentEdgeLabel(pattern.index_iterator);
+        TSuffixSize prefixLength = parentEdgeLength(pattern.index_iterator);
+        TSuffixSize prefixPos = pattern.prefix_aligner.global_position - parentRepLength(pattern.index_iterator);
+        setLength(pattern.prefix_aligner, _min(prefixLength, pattern.depth - parentRepLength(pattern.index_iterator)));
+        setPosition(pattern.prefix_aligner, prefixPos);
+
+        // Align exactly suffix with prefix
+        if (match(finder.suffix_aligner, pattern.prefix_aligner, suffixEdge, prefixEdge))
+        {
+            if (!_atEnd(pattern.prefix_aligner) && _atEnd(finder.suffix_aligner))
+            {
+                TPrefixSize extension = pattern.prefix_aligner.prefix_length - pattern.prefix_aligner.prefix_position;
+
+                TTextIndexIterator index_iterator(finder.index_iterator);
+                // NOTE(esiragusa): This works if prefixEdge is a sequence, not if it is a simple type.
+                if (!goDown(finder.index_iterator,
+                            infixWithLength(prefixEdge, pattern.prefix_aligner.prefix_position, extension)))
+                {
+                    finder.index_iterator = index_iterator;
+                    if (!_cut_exact(finder, pattern))
+                        break;
+
+                    continue;
+                }
+
+                pattern.prefix_aligner.global_position += extension;
+                // NOTE(esiragusa): It is not necessary to update length and position as long as they are not used below.
+//                suffixEdge = parentEdgeLabel(finder.index_iterator);
+//                suffixLength = parentEdgeLength(finder.index_iterator);
+//                suffixPos = pattern.prefix_aligner.global_position - parentRepLength(finder.index_iterator);
+//                setLength(finder.suffix_aligner, suffixLength);
+//                setPosition(finder.suffix_aligner, suffixPos);
+            }
+
+            // A complete match was found
+            if (pattern.prefix_aligner.global_position >= pattern.depth)
+            {
+                finder.index_range = range(finder.index_iterator);
+                pattern.index_range = range(pattern.index_iterator);
+                return true;
+            }
+            else if (prefixLength < pattern.depth && !isLeaf(pattern.index_iterator))
+            {
+                ++pattern.exact;
+
+                appendValue(finder.index_parents, finder.index_iterator);
+                appendValue(pattern.index_parents, pattern.index_iterator);
+//                appendValue(pattern.state, getState(pattern.prefix_aligner));
+                appendValue(pattern.state, TState(pattern.prefix_aligner.global_position, pattern.prefix_aligner.errors));
+
+                goDown(pattern.index_iterator);
+            }
+        }
+        else if (!_cut_exact(finder, pattern))
+            break;
+
+    }
+    while (!(isRoot(pattern.index_iterator) && isRoot(finder.index_iterator)));
+
+    SEQAN_ASSERT_NOT(pattern.exact);
+
+    return false;
+}
+
+template <typename TText, typename TTextSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle, typename TNeedleSpec>
+inline bool
+_cut_exact(Finder<Index<TText, TTextSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+           Pattern<Index<TNeedle, TNeedleSpec>, Backtracking<TDistance, TBacktrackingSpec> > & pattern)
+{
+    do
+    {
+        if (!pattern.exact)
+            return false;
+
+        if (goRight(pattern.index_iterator))
+        {
+            SEQAN_ASSERT_NOT(empty(finder.index_parents));
+            finder.index_iterator = back(finder.index_parents);
+            break;
+        }
+
+        SEQAN_ASSERT_NOT(empty(finder.index_parents));
+        finder.index_iterator = back(finder.index_parents);
+        eraseBack(finder.index_parents);
+        SEQAN_ASSERT_NOT(empty(pattern.index_parents));
+        pattern.index_iterator = back(pattern.index_parents);
+        eraseBack(pattern.index_parents);
+        SEQAN_ASSERT_NOT(empty(pattern.state));
+        eraseBack(pattern.state);
+
+        --pattern.exact;
+    }
+    while (!(isRoot(pattern.index_iterator) && isRoot(finder.index_iterator)));
+
+    return !(isRoot(pattern.index_iterator) && isRoot(finder.index_iterator));
+}
+
+// ============================================================================
+
+template <typename TText, typename TSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle, typename TErrors>
+inline bool
+find(Finder<Index<TText, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+     Pattern<TNeedle, Backtracking<TDistance, TBacktrackingSpec> > & pattern,
+     TErrors errors)
+{
+
+    // Try to get another match from current node
+    if (!atEnd(finder))
+        goNext(hostIterator(finder));
+
+    // Try to get more matches by backtracking some more
+    if (atEnd(finder))
+    {
+        // Resume from last matching node and backtrack until next match
+        if (_resume(finder, pattern) && _backtrack(finder, pattern, errors))
+        {
+            // Set data iterator range to the interval containing matches
+            hostIterator(finder) = begin(indexSA(host(finder)), Standard());
+            finder.range.i1 = hostIterator(finder) + finder.index_range.i1;
+            finder.range.i2 = hostIterator(finder) + finder.index_range.i2;
+            hostIterator(finder) = finder.range.i1;
+
+            // Set match length
+            _setFinderLength(finder, pattern.prefix_aligner.global_position);
+        }
+        // No more matches
+        else
+        {
+            hostIterator(finder) = begin(indexSA(host(finder)), Standard());
+            finder.range.i1 = hostIterator(finder);
+            finder.range.i2 = hostIterator(finder);
+        }
+    }
+
+    return !atEnd(finder);
+}
+
+template <typename TText, typename TTextSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle, typename TNeedleSpec, typename TErrors>
+inline bool
+find(Finder<Index<TText, TTextSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+     Pattern<Index<TNeedle, TNeedleSpec>, Backtracking<TDistance, TBacktrackingSpec> > & pattern,
+     TErrors errors)
+{
+
+    // Try to get another match from current pattern node
+    goNext(hostIterator(pattern));
+
+    // Try to get another match from current text node
+    if (atEnd(pattern))
+    {
+        goNext(hostIterator(finder));
+
+        if (!atEnd(finder))
+        {
+            // Set data iterator range to the interval containing matches
+            hostIterator(pattern) = begin(indexSA(host(pattern)), Standard());
+            pattern.range.i1 = hostIterator(pattern) + pattern.index_range.i1;
+            pattern.range.i2 = hostIterator(pattern) + pattern.index_range.i2;
+            hostIterator(pattern) = pattern.range.i1;
+        }
+        // Try to get more matches by backtracking some more
+        else
+        {
+            // Resume from last matching node and backtrack until next match
+//                if (_resume(finder, pattern) && _backtrack(finder, pattern, errors))
+            if (_resume(finder, pattern, errors))
+            {
+                // Set data iterator range to the interval containing matches
+                hostIterator(finder) = begin(indexSA(host(finder)), Standard());
+                finder.range.i1 = hostIterator(finder) + finder.index_range.i1;
+                finder.range.i2 = hostIterator(finder) + finder.index_range.i2;
+                hostIterator(finder) = finder.range.i1;
+
+                hostIterator(pattern) = begin(indexSA(host(pattern)), Standard());
+                pattern.range.i1 = hostIterator(pattern) + pattern.index_range.i1;
+                pattern.range.i2 = hostIterator(pattern) + pattern.index_range.i2;
+                hostIterator(pattern) = pattern.range.i1;
+
+                // Set match length
+                _setFinderLength(finder, pattern.prefix_aligner.global_position);
+                pattern.data_length = pattern.prefix_aligner.global_position;
+            }
+            // No more matches
+            else
+            {
+                hostIterator(finder) = begin(indexSA(host(finder)), Standard());
+                finder.range.i1 = hostIterator(finder);
+                finder.range.i2 = hostIterator(finder);
+
+                hostIterator(pattern) = begin(indexSA(host(pattern)), Standard());
+                pattern.range.i1 = hostIterator(pattern);
+                pattern.range.i2 = hostIterator(pattern);
+            }
+        }
+
+    }
+
+    return !(atEnd(finder) && atEnd(pattern));
+}
+
+//template <typename TText, typename TSpec, typename TDistance, typename TBacktrackingSpec, typename TNeedle>
+//inline bool
+//find(Finder<Index<TText, TSpec>, Backtracking<TDistance, TBacktrackingSpec> > & finder,
+//     Pattern<TNeedle, Backtracking<TDistance, TBacktrackingSpec> > & pattern)
+//{
+//    return find(finder, pattern, 0u);
+//}
+
+}
+
+#endif  // #ifndef SEQAN_FIND_BACKTRACKING_H_
diff --git a/seqan/index/find_index.h b/seqan/index/find_index.h
index 46361f6..8da3aca 100644
--- a/seqan/index/find_index.h
+++ b/seqan/index/find_index.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,270 +40,270 @@ namespace SEQAN_NAMESPACE_MAIN
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	struct Position< Finder< Index<TText, TSpec>, TSpecFinder > >:
-		SAValue< Index<TText, TSpec> > {};
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    struct Position< Finder< Index<TText, TSpec>, TSpecFinder > >:
+        SAValue< Index<TText, TSpec> > {};
 
 
 //////////////////////////////////////////////////////////////////////////////
-// generic Finder class for all indices containing a suffix array or 
+// generic Finder class for all indices containing a suffix array or
 // similar table, where a query result is an interval in this table
 //
 // your index must specialize the function _findFirstIndex and set
 // finder.range to the interval containing the query hits. See:
 //
-//	template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
-//	inline void _findFirstIndex(
-//		Finder< Index<TText, TSpec>, TSpecFinder > &finder,
-//		TPattern const &pattern,
-//		EsaFindMlr const)
-//	{
-//		Index<TText, TSpec> &index = haystack(finder);
-//		indexRequire(index, EsaSA());
-//		finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern);
-//	}
-
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	class Finder< Index<TText, TSpec>, TSpecFinder >
-	{
+//    template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+//    inline void _findFirstIndex(
+//        Finder< Index<TText, TSpec>, TSpecFinder > &finder,
+//        TPattern const &pattern,
+//        FinderMlr const)
+//    {
+//        Index<TText, TSpec> &index = haystack(finder);
+//        indexRequire(index, EsaSA());
+//        finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern);
+//    }
+
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    class Finder< Index<TText, TSpec>, TSpecFinder >
+    {
     protected:
-		typedef Index<TText, TSpec>								TIndex;
-		typedef typename Fibre<TIndex, FibreSA>::Type			TSA;
-		typedef typename Iterator<TSA const, Standard>::Type	TIterator;
-		typedef typename Size<TIndex>::Type						TSize;
-
-	public:
-		Holder<TIndex>	index;
-		Pair<TIterator>	range;
-		TIterator		data_iterator;
-		TSize			data_length;
-
-		Finder() : data_iterator(), data_length(0)
-		{
-			clear(*this);
-		}
-		Finder(TIndex &_index): index(_index), data_iterator(), data_length(0)
-		{
-			clear(*this);
-		}
-		Finder(TIndex const &_index): index(_index), data_iterator(), data_length(0)
-		{
-			clear(*this);
-		}
-	};
+        typedef Index<TText, TSpec>                                TIndex;
+        typedef typename Fibre<TIndex, FibreSA>::Type            TSA;
+        typedef typename Iterator<TSA const, Standard>::Type    TIterator;
+        typedef typename Size<TIndex>::Type                        TSize;
+
+    public:
+        Holder<TIndex>    index;
+        Pair<TIterator>    range;
+        TIterator        data_iterator;
+        TSize            data_length;
+
+        Finder() : data_iterator(), data_length(0)
+        {
+            clear(*this);
+        }
+        Finder(TIndex &_index): index(_index), data_iterator(), data_length(0)
+        {
+            clear(*this);
+        }
+        Finder(TIndex const &_index): index(_index), data_iterator(), data_length(0)
+        {
+            clear(*this);
+        }
+    };
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Parameter_< Index<TText, TSpec> >::Type 
-	host(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Parameter_< Index<TText, TSpec> >::Type
+    host(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		return value(me.index);
-	}
+        return value(me.index);
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Parameter_< Index<TText, TSpec> >::Type 
-	host(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Parameter_< Index<TText, TSpec> >::Type
+    host(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+    {
 SEQAN_CHECKPOINT
-		return value(me.index);
-	}
+        return value(me.index);
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Parameter_< Index<TText, TSpec> >::Type 
-	container(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Parameter_< Index<TText, TSpec> >::Type
+    container(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		return value(me.index);
-	}
+        return value(me.index);
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Parameter_< Index<TText, TSpec> >::Type 
-	container(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Parameter_< Index<TText, TSpec> >::Type
+    container(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+    {
 SEQAN_CHECKPOINT
-		return value(me.index);
-	}
+        return value(me.index);
+    }
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline void
-	setHost(
-		Finder< Index<TText, TSpec>, TSpecFinder > & me, 
-		typename Parameter_<Index<TText, TSpec> >::Type container_)
-	{
-		me.index = container_;
-	}
-
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline void
-	setContainer(
-		Finder< Index<TText, TSpec>, TSpecFinder > & me, 
-		typename Parameter_<Index<TText, TSpec> >::Type container_)
-	{
-		me.index = container_;
-	}
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline void
+    setHost(
+        Finder< Index<TText, TSpec>, TSpecFinder > & me,
+        typename Parameter_<Index<TText, TSpec> >::Type container_)
+    {
+        me.index = container_;
+    }
+
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline void
+    setContainer(
+        Finder< Index<TText, TSpec>, TSpecFinder > & me,
+        typename Parameter_<Index<TText, TSpec> >::Type container_)
+    {
+        me.index = container_;
+    }
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Iterator< typename Fibre<Index<TText, TSpec>, FibreSA>::Type const, Standard>::Type &
-	hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Iterator< typename Fibre<Index<TText, TSpec>, FibreSA>::Type const, Standard>::Type &
+    hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		return me.data_iterator;
-	}
+        return me.data_iterator;
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Iterator< typename Fibre<Index<TText, TSpec>, FibreSA>::Type const, Standard>::Type const &
-	hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Iterator< typename Fibre<Index<TText, TSpec>, FibreSA>::Type const, Standard>::Type const &
+    hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+    {
 SEQAN_CHECKPOINT
-		return me.data_iterator;
-	}
+        return me.data_iterator;
+    }
 
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline bool
-	empty(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline bool
+    empty(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		return me.range.i1 == me.range.i2;
-	}
+        return me.range.i1 == me.range.i2;
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline void
-	clear(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline void
+    clear(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		typedef Index<TText, TSpec>								TIndex;
-		typedef typename Fibre<TIndex, FibreSA>::Type			TSA;
-		typedef typename Iterator<TSA const, Standard>::Type	TIterator;
-		me.range.i1 = me.range.i2 = TIterator();
-		me.data_length = 0;
-	}
+        typedef Index<TText, TSpec>                                TIndex;
+        typedef typename Fibre<TIndex, FibreSA>::Type            TSA;
+        typedef typename Iterator<TSA const, Standard>::Type    TIterator;
+        me.range.i1 = me.range.i2 = TIterator();
+        me.data_length = 0;
+    }
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline bool
-	atBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline bool
+    atBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		return (empty(me) || hostIterator(me) == me.range.i1);
-	}
+        return (empty(me) || hostIterator(me) == me.range.i1);
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline bool
-	atEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline bool
+    atEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		return (empty(me) || hostIterator(me) == me.range.i2);
-	}
+        return (empty(me) || hostIterator(me) == me.range.i2);
+    }
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline void
-	goBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline void
+    goBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		hostIterator(me) = me.range.i1;
-	}
+        hostIterator(me) = me.range.i1;
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline void
-	goEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline void
+    goEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		hostIterator(me) = me.range.i2;
-	}
+        hostIterator(me) = me.range.i2;
+    }
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
-	beginPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
+    beginPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
         SEQAN_CHECKPOINT;
-		SEQAN_ASSERT_NOT(empty(me));
-		return *me.data_iterator;
-	}
-
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
-	beginPosition(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
-	{
+        SEQAN_ASSERT_NOT(empty(me));
+        return *me.data_iterator;
+    }
+
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
+    beginPosition(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+    {
         SEQAN_CHECKPOINT;
-		SEQAN_ASSERT_NOT(empty(me));
-		return *me.data_iterator;
-	}
+        SEQAN_ASSERT_NOT(empty(me));
+        return *me.data_iterator;
+    }
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
-	endPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
+    endPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		return posAdd(beginPosition(me), me.data_length);
-	}
+        return posAdd(beginPosition(me), me.data_length);
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
-	endPosition(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
+    endPosition(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+    {
 SEQAN_CHECKPOINT
-		return posAdd(beginPosition(me), me.data_length);
-	}
+        return posAdd(beginPosition(me), me.data_length);
+    }
 
 //____________________________________________________________________________
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
-	position(Finder< Index<TText, TSpec>, TSpecFinder > & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
+    position(Finder< Index<TText, TSpec>, TSpecFinder > & me)
+    {
 SEQAN_CHECKPOINT
-		return beginPosition(me);
-	}
+        return beginPosition(me);
+    }
 
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
-	position(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
+    position(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
+    {
 SEQAN_CHECKPOINT
-		return beginPosition(me);
-	}
+        return beginPosition(me);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // find
 
-	template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
-	inline bool find(
-		Finder<Index<TText, TSpec>, TSpecFinder> &finder,
-		TPattern const &pattern)
-	{
-		if (empty(finder)) 
-		{
-			_findFirstIndex(finder, needle(pattern), TSpecFinder());
-			_setFinderLength(finder, length(needle(pattern)));
-			hostIterator(finder) = finder.range.i1;
-		} else
-			++hostIterator(finder);
-		return !atEnd(finder);
-	}
-
-	template < typename TText, typename TSpec, typename TSpecFinder >
-	inline bool find(Finder<Index<TText, TSpec>, TSpecFinder> &finder)
-	{
-		if (empty(finder)) return false;
-		++hostIterator(finder);
-		return !atEnd(finder);
-	}
+    template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+    inline bool find(
+        Finder<Index<TText, TSpec>, TSpecFinder> &finder,
+        TPattern const &pattern)
+    {
+        if (empty(finder))
+        {
+            _findFirstIndex(finder, needle(pattern), TSpecFinder());
+            _setFinderLength(finder, length(needle(pattern)));
+            hostIterator(finder) = finder.range.i1;
+        } else
+            ++hostIterator(finder);
+        return !atEnd(finder);
+    }
+
+    template < typename TText, typename TSpec, typename TSpecFinder >
+    inline bool find(Finder<Index<TText, TSpec>, TSpecFinder> &finder)
+    {
+        if (empty(finder)) return false;
+        ++hostIterator(finder);
+        return !atEnd(finder);
+    }
 
 }
 
diff --git a/seqan/index/find_index_approx.h b/seqan/index/find_index_approx.h
index e953a5a..d8cc3ec 100644
--- a/seqan/index/find_index_approx.h
+++ b/seqan/index/find_index_approx.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,37 +41,37 @@ namespace SEQAN_NAMESPACE_MAIN
 template <typename TSAValue1, typename TSAValue2>
 struct AddResultsFunctor
 {
-	String<Pair<TSAValue1, String<TSAValue2> > > results;
-    
+    String<Pair<TSAValue1, String<TSAValue2> > > results;
+
     template <typename TIter1, typename TIter2>
     void operator() (TIter1 &iter1, TIter2 &iter2)
     {
-		unsigned ofs = length(results);
-		resize(results, ofs + countOccurrences(iter1));
-		for (unsigned i = 0; i < countOccurrences(iter1); ++i)
-		{
-			results[ofs + i].i1 = getOccurrences(iter1)[i];
-			results[ofs + i].i2 = getOccurrences(iter2);
-		}
+        unsigned ofs = length(results);
+        resize(results, ofs + countOccurrences(iter1));
+        for (unsigned i = 0; i < countOccurrences(iter1); ++i)
+        {
+            results[ofs + i].i1 = getOccurrences(iter1)[i];
+            results[ofs + i].i2 = getOccurrences(iter2);
+        }
     }
 };
 
 template <
-	bool enumerateA,
-	bool enumerateB,
-	typename TOnFoundFunctor, 
-	typename TTreeIteratorA, 
-	typename TIterPosA, 
-	typename TTreeIteratorB, 
-	typename TIterPosB, 
-	typename TErrors >
-inline void 
+    bool enumerateA,
+    bool enumerateB,
+    typename TOnFoundFunctor,
+    typename TTreeIteratorA,
+    typename TIterPosA,
+    typename TTreeIteratorB,
+    typename TIterPosB,
+    typename TErrors >
+inline void
 _exactTreeSearch(
-	TOnFoundFunctor	&onFoundFunctor,    // functor to store matches
-	TTreeIteratorA	iterA,              // pattern tree iterator
-	TIterPosA		iterPosA,           // position in representative
-	TTreeIteratorB	iterB,              // text suffix tree iterator
-	TIterPosB		iterPosB)           // position in representative
+    TOnFoundFunctor    &onFoundFunctor,    // functor to store matches
+    TTreeIteratorA    iterA,              // pattern tree iterator
+    TIterPosA        iterPosA,           // position in representative
+    TTreeIteratorB    iterB,              // text suffix tree iterator
+    TIterPosB        iterPosB)           // position in representative
 {
     while (true)
     {
@@ -132,7 +132,7 @@ _exactTreeSearch(
                 if (!goRight(iterA))
                     return;
             }
-            
+
             // search pairs of edges with the same character
             while (true)
             {
@@ -158,73 +158,73 @@ _exactTreeSearch(
 }
 
 template <
-	bool enumerateA,
-	bool enumerateB,
-	typename TOnFoundFunctor, 
-	typename TTreeIteratorA, 
-	typename TIterPosA, 
-	typename TTreeIteratorB, 
-	typename TIterPosB, 
-	typename TErrors >
-inline void 
+    bool enumerateA,
+    bool enumerateB,
+    typename TOnFoundFunctor,
+    typename TTreeIteratorA,
+    typename TIterPosA,
+    typename TTreeIteratorB,
+    typename TIterPosB,
+    typename TErrors >
+inline void
 _approximateTreeSearch(
-	TOnFoundFunctor	&onFoundFunctor,    // functor to store matches
-	TTreeIteratorA	iterA,              // pattern tree iterator
-	TIterPosA		iterPosA,           // position in representative
-	TTreeIteratorB	iterB_,             // text suffix tree iterator
-	TIterPosB		iterPosB,           // position in representative
-	TErrors			errorsLeft)         // tolerated errors left
+    TOnFoundFunctor    &onFoundFunctor,    // functor to store matches
+    TTreeIteratorA    iterA,              // pattern tree iterator
+    TIterPosA        iterPosA,           // position in representative
+    TTreeIteratorB    iterB_,             // text suffix tree iterator
+    TIterPosB        iterPosB,           // position in representative
+    TErrors            errorsLeft)         // tolerated errors left
 {
-	if (enumerateA && !goDown(iterA)) 
-	{
+    if (enumerateA && !goDown(iterA))
+    {
         onFoundFunctor(iterA, iterB_);
-		return;
-	}
-	if (enumerateB && !goDown(iterB_)) return;
-	
-	do 
-	{
-		TTreeIteratorB iterB = iterB_;
-		do 
-		{
-			TErrors e = errorsLeft;
-			TIterPosA ipA = iterPosA;
-			TIterPosB ipB = iterPosB;
-			
-			if (ipB == repLength(iterB)) continue;
-			
-			while (true)
-			{
-				if (ipA == repLength(iterA))
-				{
-					if (ipB == repLength(iterB))
-						_approximateTreeSearch<true,true>(onFoundFunctor, iterA, ipA, iterB, ipB, e);
-					else
-						_approximateTreeSearch<true,false>(onFoundFunctor, iterA, ipA, iterB, ipB, e);
-					break;
-				} 
-				else if (ipB == repLength(iterB))
-				{
-					_approximateTreeSearch<false,true>(onFoundFunctor, iterA, ipA, iterB, ipB, e);
-					break;
-				}
+        return;
+    }
+    if (enumerateB && !goDown(iterB_)) return;
+
+    do
+    {
+        TTreeIteratorB iterB = iterB_;
+        do
+        {
+            TErrors e = errorsLeft;
+            TIterPosA ipA = iterPosA;
+            TIterPosB ipB = iterPosB;
+
+            if (ipB == repLength(iterB)) continue;
+
+            while (true)
+            {
+                if (ipA == repLength(iterA))
+                {
+                    if (ipB == repLength(iterB))
+                        _approximateTreeSearch<true,true>(onFoundFunctor, iterA, ipA, iterB, ipB, e);
+                    else
+                        _approximateTreeSearch<true,false>(onFoundFunctor, iterA, ipA, iterB, ipB, e);
+                    break;
+                }
+                else if (ipB == repLength(iterB))
+                {
+                    _approximateTreeSearch<false,true>(onFoundFunctor, iterA, ipA, iterB, ipB, e);
+                    break;
+                }
+
+                if (representative(iterA)[ipA] != representative(iterB)[ipB])
+                    if (e-- == 0) break;
 
-				if (representative(iterA)[ipA] != representative(iterB)[ipB])
-					if (e-- == 0) break;
-				
-				++ipA;
-				++ipB;
-			}
-		} while (enumerateB && goRight(iterB));
-	} while (enumerateA && goRight(iterA));
+                ++ipA;
+                ++ipB;
+            }
+        } while (enumerateB && goRight(iterB));
+    } while (enumerateA && goRight(iterA));
 }
 
 
 template <typename TSAValue>
 struct AddSingleResultsFunctor
 {
-	String<TSAValue> results;
-    
+    String<TSAValue> results;
+
     template <typename TPattern, typename TIter>
     void operator() (TPattern & /*pattern*/, TIter &iter)
     {
@@ -234,95 +234,95 @@ struct AddSingleResultsFunctor
 
 
 template <
-	typename TOnFoundFunctor, 
-	typename TString, 
-	typename TStringPos, 
-	typename TTreeIterator, 
-	typename TIterPos, 
-	typename TErrors >
-inline void 
+    typename TOnFoundFunctor,
+    typename TString,
+    typename TStringPos,
+    typename TTreeIterator,
+    typename TIterPos,
+    typename TErrors >
+inline void
 _approximateStringSearch(
-	TOnFoundFunctor	&onFoundFunctor,    // functor to store matches
-	TString const &string,              // search pattern 
-	TStringPos stringPos,               // position in pattern
-	TTreeIterator iter,                 // text suffix tree iterator
-	TIterPos iterPos,                   // position in representative
-	TErrors errorsLeft)                 // tolerated errors left
+    TOnFoundFunctor    &onFoundFunctor,    // functor to store matches
+    TString const &string,              // search pattern
+    TStringPos stringPos,               // position in pattern
+    TTreeIterator iter,                 // text suffix tree iterator
+    TIterPos iterPos,                   // position in representative
+    TErrors errorsLeft)                 // tolerated errors left
 {
-	if (errorsLeft == 0)
-	{
-		if (goDown(iter, suffix(string, stringPos)))
-			onFoundFunctor(string, iter);
-		return;
-	}
-	
-	if (!goDown(iter)) return;
-	do 
-	{
-		TErrors e = errorsLeft;
-		TStringPos sp = stringPos;
-		TIterPos ip = iterPos;
-		
-		if (ip == repLength(iter)) continue;
-		
-		while (true)
-		{
-			if (representative(iter)[ip] != string[sp])
-				if (e-- == 0) break;
-			
-			if (++sp == length(string))
-			{
+    if (errorsLeft == 0)
+    {
+        if (goDown(iter, suffix(string, stringPos)))
+            onFoundFunctor(string, iter);
+        return;
+    }
+
+    if (!goDown(iter)) return;
+    do
+    {
+        TErrors e = errorsLeft;
+        TStringPos sp = stringPos;
+        TIterPos ip = iterPos;
+
+        if (ip == repLength(iter)) continue;
+
+        while (true)
+        {
+            if (representative(iter)[ip] != string[sp])
+                if (e-- == 0) break;
+
+            if (++sp == length(string))
+            {
                 onFoundFunctor(string, iter);
-				break;
-			}
-			
-			if (++ip == repLength(iter))
-			{
-				_approximateStringSearch(onFoundFunctor, string, sp, iter, ip, e);
-				break;
-			}
-		}
-	} while (goRight(iter));
+                break;
+            }
+
+            if (++ip == repLength(iter))
+            {
+                _approximateStringSearch(onFoundFunctor, string, sp, iter, ip, e);
+                break;
+            }
+        }
+    } while (goRight(iter));
 }
 
 template <
-    typename TOnFoundFunctor, 
-    typename TString, 
-    typename TTreeIterator, 
+    typename TOnFoundFunctor,
+    typename TString,
+    typename TTreeIterator,
     typename TErrors>
-inline void 
+inline void
 approximateStringSearch(
-    TOnFoundFunctor &onFoundFunctor, 
-    TString const &string, 
-    TTreeIterator &iter, 
+    TOnFoundFunctor &onFoundFunctor,
+    TString const &string,
+    TTreeIterator &iter,
     TErrors errorsLeft)
 {
-	if (length(string) <= errorsLeft)
-	{
+    if (length(string) <= errorsLeft)
+    {
         onFoundFunctor(string, iter);
-		return;
-	}	
-	_approximateStringSearch(onFoundFunctor, string, 0u, iter, repLength(iter), errorsLeft);
+        return;
+    }
+    _approximateStringSearch(onFoundFunctor, string, 0u, iter, repLength(iter), errorsLeft);
 }
 
 template <
-    typename TOnFoundFunctor, 
-    typename TTreeIteratorA, 
-    typename TTreeIteratorB, 
+    typename TOnFoundFunctor,
+    typename TTreeIteratorA,
+    typename TTreeIteratorB,
     typename TErrors>
-inline void 
+inline void
 approximateTreeSearch(
-    TOnFoundFunctor &onFoundFunctor, 
-    TTreeIteratorA const &iterA, 
-    TTreeIteratorB const &iterB, 
+    TOnFoundFunctor &onFoundFunctor,
+    TTreeIteratorA const &iterA,
+    TTreeIteratorB const &iterB,
     TErrors errorsLeft)
 {
-	_approximateTreeSearch<true,true>(
-        onFoundFunctor, 
-        iterA, 
-        repLength(iterA), 
-        iterB, 
-        repLength(iterB), 
+    _approximateTreeSearch<true,true>(
+        onFoundFunctor,
+        iterA,
+        repLength(iterA),
+        iterB,
+        repLength(iterB),
         errorsLeft);
 }
 
diff --git a/seqan/index/find_index_binary.h b/seqan/index/find_index_binary.h
new file mode 100644
index 0000000..e926109
--- /dev/null
+++ b/seqan/index/find_index_binary.h
@@ -0,0 +1,1912 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_HEADER_INDEX_FIND_BINARY_H
+#define SEQAN_HEADER_INDEX_FIND_BINARY_H
+
+namespace seqan
+{
+    //////////////////////////////////////////////////////////////////////////////
+    // different layouts of a suffix array or lcp table
+
+    struct SortedList {};            // classical sorted list (suffix array, sorted list, ...)
+    struct LeftCompleteTree {};        // flattened search tree root, left child, right child, left child's left child, left child's right child, ...
+
+    template < unsigned BlockSize = 4096 >
+    struct BTree {};                // b-tree compacts nodes and its children to blocks of BlockSize
+
+    template < typename TString, typename TSpec >
+    class SearchTreeIterator {};
+
+    //////////////////////////////////////////////////////////////////////////////
+    // class to access a flat search tree like a real tree
+    //
+
+    template <typename TString>
+    class SearchTreeIterator< TString, SortedList >
+    {
+    public:
+
+        typedef typename Value<TString>::Type                TValue;
+        typedef typename Size<TString>::Type                TSize;
+        typedef typename Iterator<TString, Standard>::Type    TIterator;
+
+        inline SearchTreeIterator(TString &string):
+            first(begin(string, Standard())),
+            count(length(string))
+        {
+            count2 = count / 2;
+            _mid = first;
+            goFurther(_mid, count2);
+        }
+
+        inline SearchTreeIterator(TIterator &first, TSize count):
+            first(first),
+            count(count)
+        {
+            count2 = count / 2;
+            _mid = first;
+            goFurther(_mid, count2);
+        }
+
+        inline const TValue& operator*() const {
+            return *_mid;
+        }
+
+        inline const TValue* operator->() const {
+            return &*_mid;
+        }
+
+        inline TSize mid() {
+            return count2;
+        }
+
+        // descend left
+        inline SearchTreeIterator & left()
+        {
+            count = count2;
+            count2 /= 2;
+            _mid = first;
+            goFurther(_mid, count2);
+            return *this;
+        }
+
+        // descend right
+        inline SearchTreeIterator & right()
+        {
+            first = ++_mid, count -= count2 + 1;
+            count2 = count / 2;
+            goFurther(_mid, count2);
+            return *this;
+        }
+
+        inline SearchTreeIterator leftChild() const {
+            return SearchTreeIterator(*this).left();
+        }
+
+        inline SearchTreeIterator rightChild() const {
+            return SearchTreeIterator(*this).right();
+        }
+
+        inline bool atEnd() {
+            return !count;
+        }
+
+        inline operator TIterator & () {
+            return _mid;
+        }
+
+    private:
+        TIterator    first, _mid;
+        TSize        count, count2;
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // class to access a flat search tree like a real tree
+    //
+
+    template <typename TString>
+    class SearchTreeIterator< TString, LeftCompleteTree >
+    {
+    public:
+        typedef typename Value<TString>::Type                TValue;
+        typedef typename Size<TString>::Type                TSize;
+        typedef typename Iterator<TString, Standard>::Type    TIterator;
+
+        TIterator    it;
+        TSize        size;
+
+        inline SearchTreeIterator(TString &string, TSize _size):
+            it(begin(string, Standard())),
+            size(_size)
+        {
+            _left = 0;
+            _lSize = 1;
+            _iSize = size;
+            for (_xSize = 1; _xSize < size; _xSize <<= 1)
+                continue;  // Create smallest 2^k that is >= size.
+            if (!size) _xSize = 0;
+        }
+
+        inline SearchTreeIterator():
+            it(),
+            size(0),
+            _xSize(0) {}
+
+        inline const TValue& operator*() const {
+            return *it;
+        }
+
+        inline const TValue* operator->() const {
+            return &*it;
+        }
+
+        inline TSize mid() {
+            return _xSize >> 1;
+        }
+
+        inline TSize leftSize() {
+            return mid();
+        }
+
+        inline TSize rightSize() {
+            return _iSize - mid();
+        }
+
+        // descend left
+        inline SearchTreeIterator & left()
+        {
+            if (_xSize <= 1) {
+                _xSize = 0;
+                return *this;
+            }
+            _descendLeft();
+            _iSize = _xSize;        // = mid();
+            return *this;
+        }
+
+        // descend right
+        inline SearchTreeIterator & right()
+        {
+            if (_xSize <= 1) {
+                _xSize = 0;
+                return *this;
+            }
+            _iSize -= mid();
+            SEQAN_ASSERT_NEQ(_iSize, 0u);    // _xSize/2 is less than _iSize by invariant
+
+            // step down right
+            _descendRight();
+
+            // step down left until we have two sons or are a leaf
+            while (_iSize <= (_xSize >> 1))
+                _descendLeft();
+
+            return *this;
+        }
+
+        inline SearchTreeIterator leftChild() const {
+            return SearchTreeIterator(*this).left();
+        }
+
+        inline SearchTreeIterator rightChild() const {
+            return SearchTreeIterator(*this).right();
+        }
+
+        inline SearchTreeIterator& operator--() {
+            --it;
+            return *this;
+        }
+
+        inline SearchTreeIterator operator--(int) {
+            SearchTreeIterator before = *this;
+            --it;
+            return before;
+        }
+
+        inline SearchTreeIterator & operator++() {
+            ++it;
+            return *this;
+        }
+
+        inline SearchTreeIterator operator++(int) {
+            SearchTreeIterator before = *this;
+            ++it;
+            return before;
+        }
+
+        inline bool operator==(SearchTreeIterator const &I) {
+            return (_xSize == I._xSize) && (_xSize == 0 || it == I.it);
+        }
+
+        //operator FlatFwdIt() {
+        //    return it;
+        //}
+
+        inline bool atEnd() {
+            return !_xSize;
+        }
+
+        inline operator TIterator & () {
+            return it;
+        }
+
+    private:
+        TSize _left;        // left iterator offset of current interval
+        TSize _lSize;        // iterator elements of current level
+        TSize _xSize;        // max interval size of current level
+        TSize _iSize;        // current interval size
+
+        inline void _descendLeft()
+        {
+            goFurther(it, _left + _lSize);
+            _left <<= 1;
+            _xSize >>= 1;
+            _lSize = (size + _xSize - 1) / _xSize;
+        }
+
+        inline void _descendRight()
+        {
+            goFurther(it, _left + 1 + _lSize);
+            _left = (_left << 1) + 1;
+            _xSize >>= 1;
+            _lSize = (size + _xSize - 1) / _xSize;
+        }
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // class to access a flat search b-tree like a real tree
+    //
+
+    template <typename TString, unsigned BlockSize>
+    class SearchTreeIterator< TString, BTree<BlockSize> >
+    {
+    public:
+        typedef typename Value<TString>::Type                TValue;
+        typedef typename Size<TString>::Type                TSize;
+        typedef typename Iterator<TString, Standard>::Type    TIterator;
+
+        enum { BlockHeight = Log2Floor<BlockSize>::VALUE };
+        enum { BlockElements = (1 << BlockHeight) - 1 };
+        enum { BlockInnerElements = (1 << (BlockHeight - 1)) - 1 };
+        enum { BlockLeafs = 1 << (BlockHeight - 1) };
+
+        TIterator    it;
+        TSize        size;
+
+        inline SearchTreeIterator(TString &string):
+            it(begin(string, Standard())),
+            size(length(string))
+        {
+            //_left = 0;
+            //_lSize = 0;
+   //         _iSize = size;
+
+            _heightHigh = 1;
+            _stepSizeLow = 1;
+            for(TSize _xSizeLow = 2; _xSizeLow <= size; _xSizeLow <<= 1) {
+                if (_stepSizeLow == BlockLeafs) {
+                    _stepSizeLow = 1;
+                    ++_heightHigh;
+                } else
+                    _stepSizeLow <<= 1;
+            }
+
+            _stepSizeLow >>= 1;
+            for(_xSizeHigh = 1; _xSizeHigh * BlockSize <= size; _xSizeHigh *= BlockSize) ;
+
+            _leftLow = (_stepSizeLow << 1) - 1;        // point to the middle
+            _leftHigh = 0;
+            _lSizeHigh = 1;
+
+            it += _leftLow;
+
+            _updateElements();
+
+            //if (!size) _xSizeLow = 0;
+   //         if (!size) _xSizeHigh = 0;
+        }
+
+        inline SearchTreeIterator():
+            it() {}
+
+        inline const TValue& operator*() const {
+            return *it;
+        }
+
+        inline const TValue* operator->() const {
+            return &*it;
+        }
+
+        // descend left
+        inline SearchTreeIterator & left()
+        {
+            if (_heightHigh == 1 && !_stepSizeLow) {
+                _heightHigh = 0;
+                return *this;
+            }
+            _descendLeft();
+            return *this;
+        }
+
+        // descend right
+        inline SearchTreeIterator & right()
+        {
+            if (_heightHigh == 1 && !_stepSizeLow) {
+                ++it;
+                _heightHigh = 0;
+                return *this;
+            }
+
+            // step down right
+            _descendRight();
+
+            // step down left until we have two sons or are a leaf
+            while (_elements <= _leftLow)
+                _descendLeft();
+
+            return *this;
+        }
+
+        inline SearchTreeIterator leftChild() const {
+            return SearchTreeIterator(*this).left();
+        }
+
+        inline SearchTreeIterator rightChild() const {
+            return SearchTreeIterator(*this).right();
+        }
+
+        inline SearchTreeIterator& operator--() {
+            --it;
+            return *this;
+        }
+
+        inline SearchTreeIterator operator--(int) {
+            SearchTreeIterator before = *this;
+            --it;
+            return before;
+        }
+
+        inline SearchTreeIterator& operator++() {
+            ++it;
+            return *this;
+        }
+
+        inline SearchTreeIterator operator++(int) {
+            SearchTreeIterator before = *this;
+            ++it;
+            return before;
+        }
+
+        inline bool operator==(SearchTreeIterator const &I) {
+            return (it == I.it) || (atEnd() && I.atEnd());
+        }
+
+        //operator FlatFwdIt() {
+        //    return it;
+        //}
+
+        inline bool atEnd() const {
+            return !_heightHigh;
+        }
+
+        inline operator TIterator & () {
+            return it;
+        }
+
+    private:
+        TSize _heightHigh;    // height measured in BBlocks
+        unsigned _elements;        // elements in current BBlock
+
+        unsigned _leftLow;        // left iterator offset of current interval
+        unsigned _stepSizeLow;    // left/right step size of current level
+
+        TSize _leftHigh;        // left BBlock offset of current interval
+        TSize _lSizeHigh;    // BBlocks of current level
+        TSize _xSizeHigh;    // max BBlocks of current level
+
+        inline void _descendLeft()
+        {
+            if (_stepSizeLow) {
+                it -= _stepSizeLow;
+                _leftLow -= _stepSizeLow;
+                _stepSizeLow >>= 1;
+            } else
+                if (--_heightHigh) {
+                    _descendBBlock(_leftLow);
+
+                    _leftLow = BlockInnerElements;        // point to the middle
+                    _stepSizeLow = BlockLeafs / 2;        // with step size of half an interval length
+                }
+        }
+
+        inline void _descendRight()
+        {
+            if (_stepSizeLow) {
+                it += _stepSizeLow;
+                _leftLow += _stepSizeLow;
+                _stepSizeLow >>= 1;
+            } else
+                if (--_heightHigh) {
+                    _descendBBlock(_leftLow + 1);
+
+                    _leftLow = BlockInnerElements;        // point to the middle
+                    _stepSizeLow = BlockLeafs / 2;        // with step size of half an interval length
+                }
+        }
+
+        inline void _updateElements()
+        {
+            TSize firstElement = (1 + _leftHigh * BlockSize) * _xSizeHigh - 1;
+            TSize lastElement = (1 + (_leftHigh + 1) * BlockSize) * _xSizeHigh - 2;
+
+            if (lastElement >= size)
+                _elements = (size - firstElement) / _xSizeHigh;
+            else
+                _elements = BlockElements;
+        }
+
+        inline void _descendBBlock(TSize _childIndex)
+        {
+            // goFurther to the begin of the current BBlock and further to the destination BBlock
+            goFurther(it, BlockSize * (_leftHigh * (BlockSize - 1) + _childIndex + _lSizeHigh) + BlockInnerElements - _leftLow);
+
+            _leftHigh = _leftHigh * BlockSize + _childIndex;
+            _xSizeHigh /= BlockSize;
+            _lSizeHigh = (size / _xSizeHigh + BlockSize - 1) / BlockSize;
+
+            _updateElements();
+        }
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // substring search with SA table and w/o LCP-table or enhancement
+    //
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TSpec,
+        typename TQuery
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    _lowerBoundSANaive(
+        TText &text,
+        SearchTreeIterator< TSA, TSpec > treeIter,
+        TQuery &query,
+        typename Difference<TText>::Type parentRepLen = 0)
+    {    // find first element not before query, using operator<
+        //typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+
+        for (; !treeIter.atEnd(); )
+        {    // divide and conquer, find half that contains answer
+
+            TSuffix        suf = suffix(text, *treeIter);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+
+            goFurther(t, parentRepLen);
+            while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
+                ++t;
+                ++q;
+            }
+
+            // is text < query ?
+            if (q != qEnd && (t == tEnd || lessLex(*t, *q))) {
+                treeIter.right();
+            } else {
+                treeIter.left();
+            }
+        }
+        return treeIter;
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TSpec,
+        typename TQuery
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    _lowerBoundSA(
+        TText &text,
+        SearchTreeIterator< TSA, TSpec > treeIter,
+        TQuery &query,
+        typename Difference<TText>::Type parentRepLen = 0)
+    {    // find first element not before query, using operator<
+        typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TDiff lcpLower = 0;
+        TDiff lcpUpper = 0;
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+
+        for (; !treeIter.atEnd(); )
+        {    // divide and conquer, find half that contains answer
+
+            TSuffix        suf = suffix(text, *treeIter);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+            TDiff        lcp = _min(lcpLower, lcpUpper);
+
+            goFurther(t, lcp + parentRepLen);
+            goFurther(q, lcp);
+            while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
+                ++t;
+                ++q;
+                ++lcp;
+            }
+
+            // is text < query ?
+            if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q)))) {
+                treeIter.right();
+                lcpLower = lcp;
+            } else {
+                treeIter.left();
+                lcpUpper = lcp;
+            }
+        }
+        return treeIter;
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TSpec,
+        typename TQuery
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    _upperBoundSANaive(
+        TText &text,
+        SearchTreeIterator< TSA, TSpec > treeIter,
+        TQuery &query,
+        typename Difference<TText>::Type parentRepLen = 0)
+    {    // find first element that query is before, using operator<
+        //typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+
+        for (; !treeIter.atEnd(); )
+        {    // divide and conquer, find half that contains answer
+
+            TSuffix        suf = suffix(text, *treeIter);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+
+            goFurther(t, parentRepLen);
+            while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
+                ++t;
+                ++q;
+            }
+
+            // is text <= query ?
+            if (q == qEnd || t == tEnd || !ordGreater(*t, convert<TTextAlphabet>(*q))) {
+                treeIter.right();
+            } else {
+                treeIter.left();
+            }
+        }
+        return treeIter;
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TSpec,
+        typename TQuery
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    _upperBoundSA(
+        TText &text,
+        SearchTreeIterator< TSA, TSpec > treeIter,
+        TQuery &query,
+        typename Difference<TText>::Type parentRepLen = 0)
+    {    // find first element that query is before, using operator<
+        typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TDiff lcpLower = 0;
+        TDiff lcpUpper = 0;
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+
+        for (; !treeIter.atEnd(); )
+        {    // divide and conquer, find half that contains answer
+
+            TSuffix        suf = suffix(text, *treeIter);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+            TDiff        lcp = _min(lcpLower, lcpUpper);
+
+            goFurther(t, lcp + parentRepLen);
+            goFurther(q, lcp);
+            while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
+                ++t;
+                ++q;
+                ++lcp;
+            }
+
+            // is text <= query ?
+            if (q == qEnd || t == tEnd || !ordGreater(*t, convert<TTextAlphabet>(*q))) {
+                treeIter.right();
+                lcpLower = lcp;
+            } else {
+                treeIter.left();
+                lcpUpper = lcp;
+            }
+        }
+        return treeIter;
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // binary search without mlr-heuristic
+    template <
+        typename TText,
+        typename TSA,
+        typename TSpec,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA, Standard>::Type >
+    _equalRangeSANaive(
+        TText &text,
+        SearchTreeIterator< TSA, TSpec > treeIter,
+        TQuery &query,
+        typename Difference<TText>::Type parentRepLen = 0)
+    {    // find range equivalent to query, using operator<
+        //typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Iterator<TSA, Standard>::Type        TSAIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+
+        for (; !treeIter.atEnd(); )
+        {    // divide and conquer, check midpoint
+
+            TSuffix        suf = suffix(text, *treeIter);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+
+            goFurther(t, parentRepLen);
+            while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
+                ++t;
+                ++q;
+            }
+
+            // is text < query ?
+            if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q))))
+            {    // range begins above mid, loop
+                treeIter.right();
+            }
+            // is text > query ?
+            else if (q != qEnd && (t != tEnd && ordGreater(*t, convert<TTextAlphabet>(*q))))
+            {    // range in first half, loop
+                treeIter.left();
+            } else
+            // is text == query ?
+            {    // range straddles mid, find each end and return
+                return Pair<TSAIter> (
+                    _lowerBoundSANaive(text, treeIter.leftChild(), query, parentRepLen),
+                    _upperBoundSANaive(text, treeIter.rightChild(), query, parentRepLen)
+                );
+            }
+        }
+        return Pair<TSAIter> (treeIter, treeIter);    // empty range
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // binary search with mlr-heuristic
+    template <
+        typename TText,
+        typename TSA,
+        typename TSpec,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA, Standard>::Type >
+    _equalRangeSA(
+        TText &text,
+        SearchTreeIterator< TSA, TSpec > treeIter,
+        TQuery &query,
+        typename Difference<TText>::Type parentRepLen = 0)
+    {    // find range equivalent to query, using operator<
+        typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Iterator<TSA, Standard>::Type        TSAIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TDiff lcpLower = 0;
+        TDiff lcpUpper = 0;
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+
+        for (; !treeIter.atEnd(); )
+        {    // divide and conquer, check midpoint
+
+            TSuffix        suf = suffix(text, *treeIter);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+            TDiff        lcp = _min(lcpLower, lcpUpper);
+
+            goFurther(t, lcp + parentRepLen);
+            goFurther(q, lcp);
+            while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
+                ++t;
+                ++q;
+                ++lcp;
+            }
+
+            // is text < query ?
+            if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q))))
+            {    // range begins above mid, loop
+                treeIter.right();
+                lcpLower = lcp;
+            }
+            // is text > query ?
+            else if (q != qEnd && (t != tEnd && ordGreater(*t, convert<TTextAlphabet>(*q))))
+            {    // range in first half, loop
+                treeIter.left();
+                lcpUpper = lcp;
+            } else
+            // is text == query ?
+            {    // range straddles mid, find each end and return
+                return Pair<TSAIter> (
+                    _lowerBoundSA(text, treeIter.leftChild(), query, parentRepLen),
+                    _upperBoundSA(text, treeIter.rightChild(), query, parentRepLen)
+                );
+            }
+        }
+        return Pair<TSAIter> (treeIter, treeIter);    // empty range
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Finder wrappers (return iterators instead of positions)
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Iterator<TSA const, Standard>::Type
+    lowerBoundSANaiveIterator(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query)
+    {    // find range equivalent to query, using operator<
+        return _lowerBoundSANaive(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Iterator<TSA const, Standard>::Type
+    lowerBoundSAIterator(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query)
+    {    // find range equivalent to query, using operator<
+        return _lowerBoundSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Iterator<TSA const, Standard>::Type
+    upperBoundSAIterator(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query)
+    {    // find range equivalent to query, using operator<
+        return _upperBoundSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA const, Standard>::Type >
+    equalRangeSAIterator(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query)
+    {    // find range equivalent to query, using operator<
+        return _equalRangeSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA const, Standard>::Type >
+    equalRangeSANaiveIterator(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query)
+    {    // find range equivalent to query, using operator<
+        return _equalRangeSANaive(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // workarounds for the Visual Studio array problem
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Iterator<TSA const, Standard>::Type
+    lowerBoundSAIterator(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query)
+    {    // find range equivalent to query, using operator<
+        return _lowerBoundSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Iterator<TSA const, Standard>::Type
+    upperBoundSAIterator(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query)
+    {    // find range equivalent to query, using operator<
+        return _upperBoundSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA const, Standard>::Type >
+    equalRangeSAIterator(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query)
+    {    // find range equivalent to query, using operator<
+        return _equalRangeSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // wrappers with nice interfaces
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery,
+        typename TFlatTreeSpec
+    >
+    inline typename Position<TSA>::Type
+    lowerBoundSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query,
+        TFlatTreeSpec const)
+    {    // find first element not before query, using operator<
+        return _lowerBoundSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Position<TSA>::Type
+    lowerBoundSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query)
+    {    // find first element not before query, using operator<
+        return lowerBoundSA(text, sa, query, SortedList());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery,
+        typename TFlatTreeSpec
+    >
+    inline typename Position<TSA>::Type
+    upperBoundSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query,
+        TFlatTreeSpec const)
+    {    // find first element that query is before, using operator<
+        return _upperBoundSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Position<TSA>::Type
+    upperBoundSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query)
+    {    // find first element that query is before, using operator<
+        return upperBoundSA(text, sa, query, SortedList());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery,
+        typename TFlatTreeSpec
+    >
+    inline Pair< typename Position<TSA>::Type >
+    equalRangeSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query,
+        TFlatTreeSpec const)
+    {    // find range equivalent to query, using operator<
+        Pair< typename Iterator<TSA const, Standard>::Type > itPair =
+            _equalRangeSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query);
+        return Pair< typename Position<TSA>::Type >
+            (itPair.i1 - begin(sa, Standard()), itPair.i2 - begin(sa, Standard()));
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline Pair< typename Position<TSA>::Type >
+    equalRangeSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery const &query)
+    {    // find first element that query is before, using operator<
+        return equalRangeSA(text, sa, query, SortedList());
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // workarounds for the Visual Studio array problem
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery,
+        typename TFlatTreeSpec
+    >
+    inline typename Position<TSA>::Type
+    lowerBoundSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query,
+        TFlatTreeSpec const)
+    {    // find first element not before query, using operator<
+        return _lowerBoundSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Position<TSA>::Type
+    lowerBoundSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query)
+    {    // find first element not before query, using operator<
+        return lowerBoundSA(text, sa, query, SortedList());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery,
+        typename TFlatTreeSpec
+    >
+    inline typename Position<TSA>::Type
+    upperBoundSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query,
+        TFlatTreeSpec const)
+    {    // find first element that query is before, using operator<
+        return _upperBoundSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline typename Position<TSA>::Type
+    upperBoundSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query)
+    {    // find first element that query is before, using operator<
+        return upperBoundSA(text, sa, query, SortedList());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery,
+        typename TFlatTreeSpec
+    >
+    inline Pair< typename Position<TSA>::Type >
+    equalRangeSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query,
+        TFlatTreeSpec const)
+    {    // find range equivalent to query, using operator<
+        Pair< typename Iterator<TSA const, Standard>::Type > itPair =
+            _equalRangeSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query);
+        return Pair< typename Position<TSA>::Type >
+            (itPair.i1 - begin(sa, Standard()), itPair.i2 - begin(sa, Standard()));
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TQuery
+    >
+    inline Pair< typename Position<TSA>::Type >
+    equalRangeSA(
+        TText const &text,
+        TSA const &sa,
+        TQuery *query)
+    {    // find first element that query is before, using operator<
+        return equalRangeSA(text, sa, query, SortedList());
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // substring search with enhanced LCP-table
+    //
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCP,
+        typename TSpec,
+        typename TQuery,
+        typename TDiff_
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    _lowerBoundLcpe(
+        TText &text,
+        TSA &sa,
+        SearchTreeIterator< TLCP, TSpec > treeIter,
+        TQuery &query,
+        TDiff_ lcpLower,
+        TDiff_ lcpUpper)
+    {    // find first element not before query, using operator<
+        typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TSA, Standard>::Type        TSAIter;
+        typedef SearchTreeIterator< TLCP, TSpec >            TLCPTreeIt;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TDiff delta = length(sa) - 1;
+        TDiff lcp;
+        #ifdef SEQAN_PROFILE_LCPEFIND
+            TDiff skippedCompares = 0;    // difference of char compares related to xxx_bound_sa
+        #endif
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+        TSAIter first = begin(sa, Standard());
+
+        // binary search with intervals >= 3 elements
+        for (; 1 < delta; )
+        {    // divide and conquer, find half that contains answer
+            TDiff delta2 = treeIter.leftSize();
+            TSAIter mid = first;
+            goFurther(mid, delta2);
+
+            if (lcpLower > lcpUpper)
+            {
+                TLCPTreeIt leftChild = treeIter;
+                leftChild.left();
+                TDiff lcpMidLower = *leftChild;
+
+                if (lcpMidLower > lcpLower)
+                {
+                    // second half
+                    #ifdef SEQAN_PROFILE_LCPEFIND
+                        skippedCompares += lcpLower - lcpUpper;
+                    #endif
+                    first = mid;
+                    treeIter.right();
+                    if ((delta -= delta2) == 1) {
+                        ++first;
+                        delta = 0;
+                    }
+                    continue;
+                }
+                else if (lcpMidLower < lcpLower)
+                {
+                    // first half
+                    #ifdef SEQAN_PROFILE_LCPEFIND
+                        skippedCompares += lcpMidLower - lcpUpper;
+                    #endif
+                    lcpUpper = lcpMidLower;
+                    treeIter = leftChild;
+                    if ((delta = delta2) == 1)
+                        delta = 0;
+                    continue;
+                }
+                lcp = lcpLower;
+            }
+            else if (lcpLower < lcpUpper)
+            {
+                TLCPTreeIt rightChild = treeIter;
+                rightChild.right();
+                TDiff lcpMidUpper = *rightChild;
+
+                if (lcpMidUpper > lcpUpper)
+                {
+                    // first half
+                    #ifdef SEQAN_PROFILE_LCPEFIND
+                        skippedCompares += lcpUpper - lcpLower;
+                    #endif
+                    treeIter.left();
+                    if ((delta = delta2) == 1)
+                        delta = 0;
+                    continue;
+                }
+                else if (lcpMidUpper < lcpUpper)
+                {
+                    // second half
+                    #ifdef SEQAN_PROFILE_LCPEFIND
+                        skippedCompares += lcpMidUpper - lcpLower;
+                    #endif
+                    lcpLower = lcpMidUpper;
+                    first = mid;
+                    treeIter = rightChild;
+                    if ((delta -= delta2) == 1) {
+                        ++first;
+                        delta = 0;
+                    }
+                    continue;
+                }
+                lcp = lcpUpper;
+            } else
+                lcp = lcpUpper;
+
+
+            TSuffix        suf = suffix(text, *mid);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+
+            // lcp search changes MIN to MAX here
+//            TDiff lcp = _max(lcpLower, lcpUpper);
+            #ifdef SEQAN_PROFILE_LCPEFIND
+                skippedCompares += lcp - _min(lcpLower, lcpUpper);
+            #endif
+            goFurther(t, lcp);
+            goFurther(q, lcp);
+            for(TDiff i = _min(difference(t, tEnd), difference(q, qEnd));
+                i && ordEqual(*t, convert<TTextAlphabet>(*q));
+                --i, ++t, ++q, ++lcp) ;
+
+            // is text < query ?
+            if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q))))
+            {
+                // second half
+                lcpLower = lcp;
+                first = mid;
+                treeIter.right();
+                if ((delta -= delta2) == 1) {
+                    ++first;
+                    delta = 0;
+                }
+            } else {
+                // first half
+                lcpUpper = lcp;
+                treeIter.left();
+                if ((delta = delta2) == 1)
+                    delta = 0;
+            }
+        }
+
+        #ifdef SEQAN_PROFILE_LCPEFIND
+            SEQAN_PROADD(SEQAN_PROEXTRA3, skippedCompares);
+        #endif
+
+        // binary search for intervals of 2 or less elements
+        lcp = _min(lcpLower, lcpUpper);
+        TQueryIter q = qBegin;
+        goFurther(q, lcp);
+
+        while (true) {
+            TSuffix        suf = suffix(text, *first);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+
+            goFurther(t, lcp);
+            for(TDiff i = _min(difference(t, tEnd), difference(q, qEnd));
+                i && ordEqual(*t, convert<TTextAlphabet>(*q));
+                 --i, ++t, ++q) ;
+
+            // is text < query ?
+            if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q)))) {
+                // second half
+                ++first;
+                if (!delta) return first;
+                --delta;
+            } else {
+                // first half -> end
+                return first;
+            }
+        }
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCP,
+        typename TSpec,
+        typename TQuery
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    _lowerBoundLcpe(
+        TText &text,
+        TSA &sa,
+        SearchTreeIterator< TLCP, TSpec > &treeIter,
+        TQuery &query)
+    {
+        return _lowerBoundLcpe(text, sa, treeIter, query, 0, 0);
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCP,
+        typename TSpec,
+        typename TQuery,
+        typename TDiff_
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    _upperBoundLcpe(
+        TText &text,
+        TSA &sa,
+        SearchTreeIterator< TLCP, TSpec > treeIter,
+        TQuery &query,
+        TDiff_ lcpLower,
+        TDiff_ lcpUpper)
+    {    // find first element not before query, using operator<
+        typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TSA, Standard>::Type        TSAIter;
+        typedef SearchTreeIterator< TLCP, TSpec >            TLCPTreeIt;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TDiff delta = length(sa) - 1;
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+        TSAIter first = begin(sa, Standard());
+
+        // binary search with intervals >= 3 elements
+        for (; 1 < delta; )
+        {    // divide and conquer, find half that contains answer
+            TDiff delta2 = treeIter.leftSize();
+            TSAIter mid = first;
+            goFurther(mid, delta2);
+
+            if (lcpLower > lcpUpper)
+            {
+                TLCPTreeIt leftChild = treeIter;
+                leftChild.left();
+                TDiff lcpMidLower = *leftChild;
+
+                if (lcpMidLower > lcpLower)
+                {
+                    // second half
+                    first = mid;
+                    treeIter.right();
+                    if ((delta -= delta2) == 1) {
+                        ++first;
+                        delta = 0;
+                    }
+                    continue;
+                }
+                else if (lcpMidLower < lcpLower)
+                {
+                    // first half
+                    lcpUpper = lcpMidLower;
+                    treeIter = leftChild;
+                    if ((delta = delta2) == 1)
+                        delta = 0;
+                    continue;
+                }
+            }
+            else if (lcpLower < lcpUpper)
+            {
+                TLCPTreeIt rightChild = treeIter;
+                rightChild.right();
+                TDiff lcpMidUpper = *rightChild;
+
+                if (lcpMidUpper > lcpUpper)
+                {
+                    // first half
+                    treeIter.left();
+                    if ((delta = delta2) == 1)
+                        delta = 0;
+                    continue;
+                }
+                else if (lcpMidUpper < lcpUpper)
+                {
+                    // second half
+                    lcpLower = lcpMidUpper;
+                    first = mid;
+                    treeIter = rightChild;
+                    if ((delta -= delta2) == 1) {
+                        ++first;
+                        delta = 0;
+                    }
+                    continue;
+                }
+            }
+
+            TSuffix        suf = suffix(text, *mid);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+
+            // lcp search changes MIN to MAX here
+            TDiff lcp = _max(lcpLower, lcpUpper);
+            goFurther(t, lcp);
+            goFurther(q, lcp);
+            TDiff max = _min(difference(t, tEnd), difference(q, qEnd));
+            TDiff i = max;
+            for(; i && ordEqual(*t, convert<TTextAlphabet>(*q)); --i, ++t, ++q) ;
+            lcp += max - i;
+
+            // is text <= query ?
+            if (q == qEnd || t == tEnd || !ordGreater(*t, convert<TTextAlphabet>(*q)))
+            {
+                // second half
+                lcpLower = lcp;
+                first = mid;
+                treeIter.right();
+                if ((delta -= delta2) == 1) {
+                    ++first;
+                    delta = 0;
+                }
+            } else {
+                // first half
+                lcpUpper = lcp;
+                treeIter.left();
+                if ((delta = delta2) == 1)
+                    delta = 0;
+            }
+        }
+
+        // binary search for intervals of 2 or less elements
+        TDiff lcp = _min(lcpLower, lcpUpper);
+        TQueryIter q = qBegin;
+        goFurther(q, lcp);
+
+        while (true) {
+            TSuffix        suf = suffix(text, *first);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+
+            goFurther(t, lcp);
+            TDiff i = _min(difference(t, tEnd), difference(q, qEnd));
+            for(; i && ordEqual(*t, convert<TTextAlphabet>(*q)); --i, ++t, ++q) ;
+
+            // is text <= query ?
+            if (q == qEnd || t == tEnd || !ordGreater(*t, convert<TTextAlphabet>(*q))) {
+                // second half
+                ++first;
+                if (!delta) return first;
+                --delta;
+            } else {
+                // first half -> end
+                return first;
+            }
+        }
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCP,
+        typename TSpec,
+        typename TQuery
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    _upperBoundLcpe(
+        TText &text,
+        TSA &sa,
+        SearchTreeIterator< TLCP, TSpec > &treeIter,
+        TQuery &query)
+    {
+        return _upperBoundLcpe(text, sa, treeIter, query, 0, 0);
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCP,
+        typename TSpec,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA, Standard>::Type >
+    _equalRangeLcpe(
+        TText &text,
+        TSA &sa,
+        SearchTreeIterator< TLCP, TSpec > treeIter,
+        TQuery &query)
+    {    // find first element not before query, using operator<
+        typedef typename Difference<TText>::Type            TDiff;
+        typedef typename Suffix<TText>::Type                TSuffix;
+        typedef typename Iterator<TSuffix, Standard>::Type    TTextIter;
+        typedef typename Iterator<TSA, Standard>::Type        TSAIter;
+        typedef SearchTreeIterator< TLCP, TSpec >            TLCPTreeIt;
+        typedef typename Iterator<TQuery, Standard>::Type    TQueryIter;
+        typedef typename Value<TSuffix>::Type               TTextAlphabet;
+
+        TDiff lcpLower = 0;
+        TDiff lcpUpper = 0;
+        TDiff delta = length(sa) - 1;
+
+        TQueryIter qBegin = begin(query, Standard());
+        TQueryIter qEnd = end(query, Standard());
+        TSAIter first = begin(sa, Standard());
+        TSAIter last = end(sa, Standard());
+
+        // binary search with intervals >= 3 elements
+        for (; 1 < delta; )
+        {    // divide and conquer, find half that contains answer
+            TDiff delta2 = treeIter.leftSize();
+            TSAIter mid = first;
+            goFurther(mid, delta2);
+
+            if (lcpLower > lcpUpper)
+            {
+                TLCPTreeIt leftChild = treeIter;
+                leftChild.left();
+                TDiff lcpMidLower = *leftChild;
+
+                if (lcpMidLower > lcpLower)
+                {
+                    // second half
+                    first = mid;
+                    treeIter.right();
+                    if ((delta -= delta2) == 1) {
+                        ++first;
+                        delta = 0;
+                    }
+                    continue;
+                }
+                else if (lcpMidLower < lcpLower)
+                {
+                    // first half
+                    lcpUpper = lcpMidLower;
+                    treeIter = leftChild;
+                    if ((delta = delta2) == 1)
+                        delta = 0;
+                    continue;
+                }
+            }
+            else if (lcpLower < lcpUpper)
+            {
+                TLCPTreeIt rightChild = treeIter;
+                rightChild.right();
+                TDiff lcpMidUpper = *rightChild;
+
+                if (lcpMidUpper > lcpUpper)
+                {
+                    // first half
+                    treeIter.left();
+                    if ((delta = delta2) == 1)
+                        delta = 0;
+                    continue;
+                }
+                else if (lcpMidUpper < lcpUpper)
+                {
+                    // second half
+                    lcpLower = lcpMidUpper;
+                    first = mid;
+                    treeIter = rightChild;
+                    if ((delta -= delta2) == 1) {
+                        ++first;
+                        delta = 0;
+                    }
+                    continue;
+                }
+            }
+
+            TSuffix        suf = suffix(text, *mid);
+            TTextIter    t = begin(suf, Standard());
+            TTextIter    tEnd = end(suf, Standard());
+            TQueryIter    q = qBegin;
+
+            // lcp search changes MIN to MAX here
+            TDiff lcp = _max(lcpLower, lcpUpper);
+            goFurther(t, lcp);
+            goFurther(q, lcp);
+            TDiff max = _min(difference(t, tEnd), difference(q, qEnd));
+            TDiff i = max;
+            for(; i && ordEqual(*t, convert<TTextAlphabet>(*q)); --i, ++t, ++q) ;
+            lcp += max - i;
+
+            // is text < query ?
+            if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q)))) {
+                // second half
+                lcpLower = lcp;
+                first = mid;
+                treeIter.right();
+                if ((delta -= delta2) == 1) {
+                    ++first;
+                    delta = 0;
+                }
+            } else
+            // is text > query ?
+            if (q != qEnd && t != tEnd && ordGreater(*t, convert<TTextAlphabet>(*q))) {
+                // first half
+                lcpUpper = lcp;
+                treeIter.left();
+                if ((delta = delta2) == 1)
+                    delta = 0;
+            }
+            else
+            {    // range straddles mid, find each end and return
+                typename Infix<TSA>::Type leftRange(sa, first, mid);
+                TSAIter First2 = _lowerBoundLcpe(
+                    text, leftRange, treeIter.leftChild(), query, lcpLower, lcp);
+
+                treeIter.right();
+                if ((delta -= delta2) == 1) {
+                    delta = 0;
+                    ++first;
+                }
+
+                typename Infix<TSA>::Type rightRange(sa, mid, last);
+                TSAIter Last2 = _upperBoundLcpe(
+                    text, rightRange, treeIter, query, lcp, lcpUpper);
+
+                return Pair<TSAIter> (First2, Last2);
+            }
+        }
+
+        // range straddles mid, find each end and return
+        typename Infix<TSA>::Type midRange(sa, first, last);
+        return Pair<TSAIter> (
+            _lowerBoundLcpe(text, midRange, treeIter, query, lcpLower, lcpUpper),
+            _upperBoundLcpe(text, midRange, treeIter, query, lcpLower, lcpUpper)
+        );
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCP,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA, Standard>::Type >
+    _equalRangeLcpe(
+        TText &text,
+        TSA &sa,
+        TLCP &lcp,
+        TQuery &query)
+    {
+        return _equalRangeLcpe(text, sa, SearchTreeIterator<TLCP, LeftCompleteTree>(lcp, (length(text)>1)?length(text)-1:0), query);
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // little helpers (not used)
+/*
+    template < typename LCPFwdIt, typename TSize >
+    TSize lcp(LCPFwdIt first, TSize count) {
+        if (count > 1) {
+            TSize lcp = *first;
+            ++first;
+            count-=2;
+            while (count) {
+                if (lcp < *first) lcp = *first;
+                ++first;
+                --count;
+            }
+            return lcp;
+        } else
+            return 0;
+    }
+*/
+
+    //////////////////////////////////////////////////////////////////////////////
+    // wrappers with nice interfaces
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline typename Position<TLCPE>::Type
+    lowerBoundLcpe(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery const &query)
+    {    // find first element not before query, using operator<
+        return _lowerBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline typename Position<TLCPE>::Type
+    upperBoundLcpe(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery const &query)
+    {    // find first element that query is before, using operator<
+        return upperBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline Pair< typename Position<TSA>::Type >
+    equalRangeLcpe(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery const &query)
+    {    // find range equivalent to query, using operator<
+        Pair< typename Iterator<TSA const, Standard>::Type > itPair =
+            _equalRangeLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query);
+        return Pair< typename Position<TSA>::Type >
+            (itPair.i1 - begin(sa, Standard()), itPair.i2 - begin(sa, Standard()));
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    lowerBoundLcpeIterator(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery const &query)
+    {    // find first element not before query, using operator<
+        return _lowerBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0);
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline typename Iterator<TSA, Standard>::Type
+    upperBoundLcpeIterator(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery const &query)
+    {    // find first element that query is before, using operator<
+        return upperBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA, Standard>::Type >
+    equalRangeLcpeIterator(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery const &query)
+    {    // find range equivalent to query, using operator<
+        return _equalRangeLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query);
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // workarounds for the Visual Studio array problem
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline typename Position<TLCPE>::Type
+    lowerBoundLcpe(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery *query)
+    {    // find first element not before query, using operator<
+        return _lowerBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline typename Position<TLCPE>::Type
+    upperBoundLcpe(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery *query)
+    {    // find first element that query is before, using operator<
+        return upperBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline Pair< typename Position<TSA>::Type >
+    equalRangeLcpe(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery *query)
+    {    // find range equivalent to query, using operator<
+        Pair< typename Iterator<TSA const, Standard>::Type > itPair =
+            _equalRangeLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query);
+        return Pair< typename Position<TSA>::Type >
+            (itPair.i1 - begin(sa, Standard()), itPair.i2 - begin(sa, Standard()));
+    }
+
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TQuery
+    >
+    inline Pair< typename Iterator<TSA, Standard>::Type >
+    equalRangeLcpeIterator(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TQuery *query)
+    {    // find range equivalent to query, using operator<
+        return _equalRangeLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query);
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // wrappers with nice interfaces
+/*
+    template <
+        typename TText,
+        typename TSA,
+        typename TLCPE,
+        typename TSubText >
+    inline Pair<typename Iterator<TSA const>::Type> equalRangeLcpe(
+        TText const &text,
+        TSA const &sa,
+        TLCPE const &lcpe,
+        TSubText const &subtext)
+    {
+        return _equalRangeLcpe(
+            begin(text), end(text),
+            begin(sa), end(sa),
+            SearchTreeIterator<typename Iterator<TLCPE const>::Type, LeftCompleteTree>(begin(lcpe, (length(text)>1)?length(text)-1:0), (length(text)>1)?length(text)-1:0),
+            begin(subtext), end(subtext));
+    }
+*/
+
+
+
+}
+#endif
+
diff --git a/seqan/index/find_index_esa.h b/seqan/index/find_index_esa.h
index 011a84c..3015e7d 100644
--- a/seqan/index/find_index_esa.h
+++ b/seqan/index/find_index_esa.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,1940 +35,70 @@
 #ifndef SEQAN_HEADER_INDEX_ESA_FIND_H
 #define SEQAN_HEADER_INDEX_ESA_FIND_H
 
-namespace SEQAN_NAMESPACE_MAIN
+namespace seqan
 {
 
 //////////////////////////////////////////////////////////////////////////////
 // ESA finders
 
-	template < typename TText, typename TSpec >
-	struct DefaultFinder< Index<TText, IndexEsa<TSpec> > > {
-        typedef EsaFindMlr Type;	// standard suffix array finder is mlr-heuristic
+    template < typename TText, typename TSpec >
+    struct DefaultFinder< Index<TText, IndexEsa<TSpec> > > {
+        typedef FinderMlr Type;    // standard suffix array finder is mlr-heuristic
     };
 
-
-	//////////////////////////////////////////////////////////////////////////////
-	// different layouts of a suffix array or lcp table
-
-	struct SortedList {};			// classical sorted list (suffix array, sorted list, ...)
-	struct LeftCompleteTree {};		// flattened search tree root, left child, right child, left child's left child, left child's right child, ...
-
-	template < unsigned BlockSize = 4096 >
-	struct BTree {};				// b-tree compacts nodes and its children to blocks of BlockSize
-
-	template < typename TString, typename TSpec >
-	class SearchTreeIterator {};
-
-	//////////////////////////////////////////////////////////////////////////////
-	// class to access a flat search tree like a real tree
-	//
-
-	template <typename TString>
-	class SearchTreeIterator< TString, SortedList >
-	{
-	public:
-
-		typedef typename Value<TString>::Type				TValue;
-		typedef typename Size<TString>::Type				TSize;
-		typedef typename Iterator<TString, Standard>::Type	TIterator;
-
-		inline SearchTreeIterator(TString &string):
-			first(begin(string, Standard())),
-			count(length(string))
-		{
-			count2 = count / 2;
-			_mid = first;
-			goFurther(_mid, count2);
-		}
-
-        inline SearchTreeIterator(TIterator &first, TSize count):
-            first(first),
-            count(count)
-		{
-			count2 = count / 2;
-			_mid = first;
-			goFurther(_mid, count2);
-		}
-
-        inline const TValue& operator*() const {
-			return *_mid;
-		}
-
-        inline const TValue* operator->() const {
-			return &*_mid;
-		}
-
-		inline TSize mid() {
-			return count2;
-		}
-
-		// descend left
-		inline SearchTreeIterator & left()
-		{
-			count = count2;
-			count2 /= 2;
-			_mid = first;
-			goFurther(_mid, count2);
-			return *this;
-		}
-
-		// descend right
-        inline SearchTreeIterator & right()
-		{
-			first = ++_mid, count -= count2 + 1;
-			count2 = count / 2;
-			goFurther(_mid, count2);
-			return *this;
-		}
-
-        inline SearchTreeIterator leftChild() const {
-            return SearchTreeIterator(*this).left();
-        }
-
-        inline SearchTreeIterator rightChild() const {
-            return SearchTreeIterator(*this).right();
-        }
-
-        inline bool atEnd() {
-            return !count;
-        }
-
-		inline operator TIterator & () {
-			return _mid;
-		}
-
-	private:
-		TIterator	first, _mid;
-		TSize		count, count2;
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// class to access a flat search tree like a real tree
-	//
-
-	template <typename TString>
-	class SearchTreeIterator< TString, LeftCompleteTree > 
-	{
-	public:
-		typedef typename Value<TString>::Type				TValue;
-		typedef typename Size<TString>::Type				TSize;
-		typedef typename Iterator<TString, Standard>::Type	TIterator;
-
-		TIterator	it;
-		TSize		size;
-
-		inline SearchTreeIterator(TString &string, TSize _size):
-			it(begin(string, Standard())),
-			size(_size)
-		{
-			_left = 0;
-			_lSize = 1;
-            _iSize = size;
-			for (_xSize = 1; _xSize < size; _xSize <<= 1)
-                continue;  // Create smallest 2^k that is >= size.
-            if (!size) _xSize = 0;
-		}
-
-		inline SearchTreeIterator():
-			it(),
-            size(0),
-            _xSize(0) {}
-
-        inline const TValue& operator*() const {
-			return *it;
-		}
-
-        inline const TValue* operator->() const {
-			return &*it;
-		}
-
-		inline TSize mid() {
-			return _xSize >> 1;
-		}
-
-		inline TSize leftSize() {
-			return mid();
-		}
-
-		inline TSize rightSize() {
-			return _iSize - mid();
-		}
-
-		// descend left
-        inline SearchTreeIterator & left()
-		{
-            if (_xSize <= 1) {
-                _xSize = 0;
-                return *this;
-            }
-            _descendLeft();
-			_iSize = _xSize;	    // = mid();
-            return *this;
-        }
-
-		// descend right
-        inline SearchTreeIterator & right()
-		{
-            if (_xSize <= 1) {
-                _xSize = 0;
-                return *this;
-            }
-			_iSize -= mid();
-            SEQAN_ASSERT_NEQ(_iSize, 0u);    // _xSize/2 is less than _iSize by invariant
-
-            // step down right
-            _descendRight();
-
-            // step down left until we have two sons or are a leaf
-            while (_iSize <= (_xSize >> 1))
-                _descendLeft();
-
-            return *this;
-        }
-
-        inline SearchTreeIterator leftChild() const {
-            return SearchTreeIterator(*this).left();
-        }
-
-        inline SearchTreeIterator rightChild() const {
-            return SearchTreeIterator(*this).right();
-        }
-
-        inline SearchTreeIterator& operator--() {
-            --it;
-            return *this;
-        }
-
-        inline SearchTreeIterator operator--(int) {
-            SearchTreeIterator before = *this;
-            --it;
-            return before;
-        }
-
-        inline SearchTreeIterator & operator++() {
-            ++it;
-            return *this;
-        }
-
-        inline SearchTreeIterator operator++(int) {
-            SearchTreeIterator before = *this;
-            ++it;
-            return before;
-        }
-
-        inline bool operator==(SearchTreeIterator const &I) {
-            return (_xSize == I._xSize) && (_xSize == 0 || it == I.it);
-        }
-
-        //operator FlatFwdIt() {
-        //    return it;
-        //}
-
-        inline bool atEnd() {
-            return !_xSize;
-        }
-
-		inline operator TIterator & () {
-			return it;
-		}
-
-	private:
-		TSize _left;		// left iterator offset of current interval
-		TSize _lSize;		// iterator elements of current level
-		TSize _xSize;		// max interval size of current level
-		TSize _iSize;		// current interval size
-
-        inline void _descendLeft() 
-		{
-			goFurther(it, _left + _lSize);
-			_left <<= 1;
-			_xSize >>= 1;
-			_lSize = (size + _xSize - 1) / _xSize;
-        }
-
-        inline void _descendRight() 
-		{
-			goFurther(it, _left + 1 + _lSize);
-			_left = (_left << 1) + 1;
-			_xSize >>= 1;
-			_lSize = (size + _xSize - 1) / _xSize;
-        }
-    };
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// class to access a flat search b-tree like a real tree
-	//
-
-	template <typename TString, unsigned BlockSize>
-	class SearchTreeIterator< TString, BTree<BlockSize> > 
-	{
-	public:
-		typedef typename Value<TString>::Type				TValue;
-		typedef typename Size<TString>::Type				TSize;
-		typedef typename Iterator<TString, Standard>::Type	TIterator;
-
-		enum { BlockHeight = Log2Floor<BlockSize>::VALUE };
-		enum { BlockElements = (1 << BlockHeight) - 1 };
-		enum { BlockInnerElements = (1 << (BlockHeight - 1)) - 1 };
-		enum { BlockLeafs = 1 << (BlockHeight - 1) };
-
-		TIterator	it;
-		TSize		size;
-
-		inline SearchTreeIterator(TString &string):
-			it(begin(string, Standard())),
-			size(length(string))
-		{
-			//_left = 0;
-			//_lSize = 0;
-   //         _iSize = size;
-
-			_heightHigh = 1;
-			_stepSizeLow = 1;
-			for(TSize _xSizeLow = 2; _xSizeLow <= size; _xSizeLow <<= 1) {
-				if (_stepSizeLow == BlockLeafs) {
-					_stepSizeLow = 1;
-					++_heightHigh;
-				} else
-					_stepSizeLow <<= 1;
-			}
-			
-			_stepSizeLow >>= 1;
-			for(_xSizeHigh = 1; _xSizeHigh * BlockSize <= size; _xSizeHigh *= BlockSize) ;
-
-			_leftLow = (_stepSizeLow << 1) - 1;		// point to the middle
-			_leftHigh = 0;
-			_lSizeHigh = 1;
-
-			it += _leftLow;
-
-			_updateElements();
-
-			//if (!size) _xSizeLow = 0;
-   //         if (!size) _xSizeHigh = 0;
-		}
-
-		inline SearchTreeIterator():
-			it() {}
-
-        inline const TValue& operator*() const {
-			return *it;
-		}
-
-		inline const TValue* operator->() const {
-			return &*it;
-		}
-
-		// descend left
-        inline SearchTreeIterator & left() 
-		{
-            if (_heightHigh == 1 && !_stepSizeLow) {
-                _heightHigh = 0;
-                return *this;
-            }
-            _descendLeft();
-            return *this;
-        }
-
-		// descend right
-        inline SearchTreeIterator & right() 
-		{
-            if (_heightHigh == 1 && !_stepSizeLow) {
-				++it;
-                _heightHigh = 0;
-                return *this;
-            }
-
-            // step down right
-            _descendRight();
-
-            // step down left until we have two sons or are a leaf
-            while (_elements <= _leftLow)
-                _descendLeft();
-
-            return *this;
-        }
-
-        inline SearchTreeIterator leftChild() const {
-            return SearchTreeIterator(*this).left();
-        }
-
-        inline SearchTreeIterator rightChild() const {
-            return SearchTreeIterator(*this).right();
-        }
-
-        inline SearchTreeIterator& operator--() {
-            --it;
-            return *this;
-        }
-
-        inline SearchTreeIterator operator--(int) {
-            SearchTreeIterator before = *this;
-            --it;
-            return before;
-        }
-
-        inline SearchTreeIterator& operator++() {
-            ++it;
-            return *this;
-        }
-
-        inline SearchTreeIterator operator++(int) {
-            SearchTreeIterator before = *this;
-            ++it;
-            return before;
-        }
-
-        inline bool operator==(SearchTreeIterator const &I) {
-			return (it == I.it) || (atEnd() && I.atEnd());
-        }
-
-        //operator FlatFwdIt() {
-        //    return it;
-        //}
-
-        inline bool atEnd() const {
-            return !_heightHigh;
-        }
-
-		inline operator TIterator & () {
-			return it;
-		}
-
-	private:
-		TSize _heightHigh;	// height measured in BBlocks
-		unsigned _elements;		// elements in current BBlock
-
-		unsigned _leftLow;		// left iterator offset of current interval
-		unsigned _stepSizeLow;	// left/right step size of current level
-
-		TSize _leftHigh;		// left BBlock offset of current interval
-		TSize _lSizeHigh;	// BBlocks of current level
-		TSize _xSizeHigh;	// max BBlocks of current level
-
-		inline void _descendLeft() 
-		{
-			if (_stepSizeLow) {
-				it -= _stepSizeLow;
-				_leftLow -= _stepSizeLow;
-				_stepSizeLow >>= 1;
-			} else
-				if (--_heightHigh) {
-					_descendBBlock(_leftLow);
-
-					_leftLow = BlockInnerElements;		// point to the middle
-					_stepSizeLow = BlockLeafs / 2;		// with step size of half an interval length
-				}
-        }
-
-		inline void _descendRight() 
-		{
-			if (_stepSizeLow) {
-				it += _stepSizeLow;
-				_leftLow += _stepSizeLow;
-				_stepSizeLow >>= 1;
-			} else
-				if (--_heightHigh) {
-					_descendBBlock(_leftLow + 1);
-
-					_leftLow = BlockInnerElements;		// point to the middle
-					_stepSizeLow = BlockLeafs / 2;		// with step size of half an interval length
-				}
-        }
-
-		inline void _updateElements() 
-		{
-			TSize firstElement = (1 + _leftHigh * BlockSize) * _xSizeHigh - 1;
-			TSize lastElement = (1 + (_leftHigh + 1) * BlockSize) * _xSizeHigh - 2;
-
-			if (lastElement >= size)
-				_elements = (size - firstElement) / _xSizeHigh;
-			else
-				_elements = BlockElements;
-		}
-
-        inline void _descendBBlock(TSize _childIndex) 
-		{
-			// goFurther to the begin of the current BBlock and further to the destination BBlock
-			goFurther(it, BlockSize * (_leftHigh * (BlockSize - 1) + _childIndex + _lSizeHigh) + BlockInnerElements - _leftLow);
-
-			_leftHigh = _leftHigh * BlockSize + _childIndex;
-			_xSizeHigh /= BlockSize;
-			_lSizeHigh = (size / _xSizeHigh + BlockSize - 1) / BlockSize;
-
-			_updateElements();
-        }
-    };
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// substring search with SA table and w/o LCP-table or enhancement
-	//
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TSpec,
-		typename TQuery
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	_lowerBoundSANaive(
-		TText &text,
-		SearchTreeIterator< TSA, TSpec > treeIter,
-		TQuery &query,
-        typename Difference<TText>::Type parentRepLen = 0)
-	{	// find first element not before query, using operator<
-		//typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-
-		for (; !treeIter.atEnd(); )
-		{	// divide and conquer, find half that contains answer
-
-			TSuffix		suf = suffix(text, *treeIter);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-            
-            goFurther(t, parentRepLen);
-			while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
-				++t;
-				++q;
-			}
-			
-            // is text < query ?
-			if (q != qEnd && (t == tEnd || lessLex(*t, *q))) {
-				treeIter.right();
-			} else {
-				treeIter.left();
-			}
-		}
-		return treeIter;
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TSpec,
-		typename TQuery
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	_lowerBoundSA(
-		TText &text,
-		SearchTreeIterator< TSA, TSpec > treeIter,
-		TQuery &query,
-        typename Difference<TText>::Type parentRepLen = 0)
-	{	// find first element not before query, using operator<
-		typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TDiff lcpLower = 0;
-		TDiff lcpUpper = 0;
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-
-		for (; !treeIter.atEnd(); )
-		{	// divide and conquer, find half that contains answer
-
-			TSuffix		suf = suffix(text, *treeIter);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-            TDiff		lcp = _min(lcpLower, lcpUpper);
-
-			goFurther(t, lcp + parentRepLen);
-			goFurther(q, lcp);
-			while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
-				++t;
-				++q;
-				++lcp;
-			}
-			
-            // is text < query ?
-			if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q)))) {
-				treeIter.right();
-				lcpLower = lcp;
-			} else {
-				treeIter.left();
-				lcpUpper = lcp;
-			}
-		}
-		return treeIter;
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TSpec,
-		typename TQuery
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	_upperBoundSANaive(
-		TText &text,
-		SearchTreeIterator< TSA, TSpec > treeIter,
-		TQuery &query,
-        typename Difference<TText>::Type parentRepLen = 0)
-	{	// find first element that query is before, using operator<
-		//typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-
-		for (; !treeIter.atEnd(); )
-		{	// divide and conquer, find half that contains answer
-
-			TSuffix		suf = suffix(text, *treeIter);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-
-            goFurther(t, parentRepLen);
-			while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
-				++t;
-				++q;
-			}
-			
-            // is text <= query ?
-			if (q == qEnd || t == tEnd || !ordGreater(*t, convert<TTextAlphabet>(*q))) {
-				treeIter.right();
-			} else {
-				treeIter.left();
-			}
-		}
-		return treeIter;
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TSpec,
-		typename TQuery
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	_upperBoundSA(
-		TText &text,
-		SearchTreeIterator< TSA, TSpec > treeIter,
-		TQuery &query,
-        typename Difference<TText>::Type parentRepLen = 0)
-	{	// find first element that query is before, using operator<
-		typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TDiff lcpLower = 0;
-		TDiff lcpUpper = 0;
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-
-		for (; !treeIter.atEnd(); )
-		{	// divide and conquer, find half that contains answer
-
-			TSuffix		suf = suffix(text, *treeIter);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-            TDiff		lcp = _min(lcpLower, lcpUpper);
-
-			goFurther(t, lcp + parentRepLen);
-			goFurther(q, lcp);
-			while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
-				++t;
-				++q;
-				++lcp;
-			}
-			
-            // is text <= query ?
-			if (q == qEnd || t == tEnd || !ordGreater(*t, convert<TTextAlphabet>(*q))) {
-				treeIter.right();
-				lcpLower = lcp;
-			} else {
-				treeIter.left();
-				lcpUpper = lcp;
-			}
-		}
-		return treeIter;
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-    // binary search without mlr-heuristic
-	template <
-		typename TText,
-		typename TSA,
-		typename TSpec,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA, Standard>::Type >
-	_equalRangeSANaive(
-		TText &text,
-		SearchTreeIterator< TSA, TSpec > treeIter,
-		TQuery &query,
-        typename Difference<TText>::Type parentRepLen = 0)
-	{	// find range equivalent to query, using operator<
-		//typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-		typedef typename Iterator<TSA, Standard>::Type		TSAIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-
-		for (; !treeIter.atEnd(); )
-		{	// divide and conquer, check midpoint
-
-			TSuffix		suf = suffix(text, *treeIter);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-            
-            goFurther(t, parentRepLen);
-			while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
-				++t;
-				++q;
-			}
-			
-            // is text < query ?
-			if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q))))
-			{	// range begins above mid, loop
-				treeIter.right();
-			}
-            // is text > query ?
-			else if (q != qEnd && (t != tEnd && ordGreater(*t, convert<TTextAlphabet>(*q))))
-			{	// range in first half, loop
-				treeIter.left();
-			} else
-            // is text == query ?
-			{	// range straddles mid, find each end and return
-				return Pair<TSAIter> (
-					_lowerBoundSANaive(text, treeIter.leftChild(), query, parentRepLen),
-					_upperBoundSANaive(text, treeIter.rightChild(), query, parentRepLen)
-				);
-			}
-		}
-		return Pair<TSAIter> (treeIter, treeIter);	// empty range
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-    // binary search with mlr-heuristic
-	template <
-		typename TText,
-		typename TSA,
-		typename TSpec,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA, Standard>::Type >
-	_equalRangeSA(
-		TText &text,
-		SearchTreeIterator< TSA, TSpec > treeIter,
-		TQuery &query,
-        typename Difference<TText>::Type parentRepLen = 0)
-	{	// find range equivalent to query, using operator<
-		typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-		typedef typename Iterator<TSA, Standard>::Type		TSAIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TDiff lcpLower = 0;
-		TDiff lcpUpper = 0;
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-
-		for (; !treeIter.atEnd(); )
-		{	// divide and conquer, check midpoint
-
-			TSuffix		suf = suffix(text, *treeIter);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-            TDiff		lcp = _min(lcpLower, lcpUpper);
-
-			goFurther(t, lcp + parentRepLen);
-			goFurther(q, lcp);
-			while (t != tEnd && q != qEnd && ordEqual(*t, convert<TTextAlphabet>(*q))) {
-				++t;
-				++q;
-				++lcp;
-			}
-			
-            // is text < query ?
-			if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q))))
-			{	// range begins above mid, loop
-				treeIter.right();
-				lcpLower = lcp;
-			}
-            // is text > query ?
-			else if (q != qEnd && (t != tEnd && ordGreater(*t, convert<TTextAlphabet>(*q))))
-			{	// range in first half, loop
-				treeIter.left();
-				lcpUpper = lcp;
-			} else
-            // is text == query ?
-			{	// range straddles mid, find each end and return
-				return Pair<TSAIter> (
-					_lowerBoundSA(text, treeIter.leftChild(), query, parentRepLen),
-					_upperBoundSA(text, treeIter.rightChild(), query, parentRepLen)
-				);
-			}
-		}
-		return Pair<TSAIter> (treeIter, treeIter);	// empty range
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Finder wrappers (return iterators instead of positions)
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Iterator<TSA const, Standard>::Type
-	lowerBoundSANaiveIterator(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query)
-	{	// find range equivalent to query, using operator<
-		return _lowerBoundSANaive(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Iterator<TSA const, Standard>::Type
-	lowerBoundSAIterator(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query)
-	{	// find range equivalent to query, using operator<
-		return _lowerBoundSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Iterator<TSA const, Standard>::Type
-	upperBoundSAIterator(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query)
-	{	// find range equivalent to query, using operator<
-		return _upperBoundSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA const, Standard>::Type >
-	equalRangeSAIterator(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query)
-	{	// find range equivalent to query, using operator<
-		return _equalRangeSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA const, Standard>::Type >
-	equalRangeSANaiveIterator(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query)
-	{	// find range equivalent to query, using operator<
-		return _equalRangeSANaive(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// workarounds for the Visual Studio array problem
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Iterator<TSA const, Standard>::Type
-	lowerBoundSAIterator(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query)
-	{	// find range equivalent to query, using operator<
-		return _lowerBoundSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Iterator<TSA const, Standard>::Type
-	upperBoundSAIterator(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query)
-	{	// find range equivalent to query, using operator<
-		return _upperBoundSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA const, Standard>::Type >
-	equalRangeSAIterator(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query)
-	{	// find range equivalent to query, using operator<
-		return _equalRangeSA(text, SearchTreeIterator<TSA const, SortedList>(sa), query);
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// wrappers with nice interfaces
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery,
-		typename TFlatTreeSpec
-	>
-	inline typename Position<TSA>::Type 
-	lowerBoundSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query,
-		TFlatTreeSpec const)
-	{	// find first element not before query, using operator<
-		return _lowerBoundSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Position<TSA>::Type 
-	lowerBoundSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query)
-	{	// find first element not before query, using operator<
-		return lowerBoundSA(text, sa, query, SortedList());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery,
-		typename TFlatTreeSpec
-	>
-	inline typename Position<TSA>::Type 
-	upperBoundSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query,
-		TFlatTreeSpec const)
-	{	// find first element that query is before, using operator<
-		return _upperBoundSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Position<TSA>::Type 
-	upperBoundSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query)
-	{	// find first element that query is before, using operator<
-		return upperBoundSA(text, sa, query, SortedList());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery,
-		typename TFlatTreeSpec
-	>
-	inline Pair< typename Position<TSA>::Type >
-	equalRangeSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query,
-		TFlatTreeSpec const)
-	{	// find range equivalent to query, using operator<
-		Pair< typename Iterator<TSA const, Standard>::Type > itPair =
-			_equalRangeSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query);
-		return Pair< typename Position<TSA>::Type >
-			(itPair.i1 - begin(sa, Standard()), itPair.i2 - begin(sa, Standard()));
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline Pair< typename Position<TSA>::Type >
-	equalRangeSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery const &query)
-	{	// find first element that query is before, using operator<
-		return equalRangeSA(text, sa, query, SortedList());
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// workarounds for the Visual Studio array problem
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery,
-		typename TFlatTreeSpec
-	>
-	inline typename Position<TSA>::Type 
-	lowerBoundSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query,
-		TFlatTreeSpec const)
-	{	// find first element not before query, using operator<
-		return _lowerBoundSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Position<TSA>::Type 
-	lowerBoundSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query)
-	{	// find first element not before query, using operator<
-		return lowerBoundSA(text, sa, query, SortedList());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery,
-		typename TFlatTreeSpec
-	>
-	inline typename Position<TSA>::Type 
-	upperBoundSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query,
-		TFlatTreeSpec const)
-	{	// find first element that query is before, using operator<
-		return _upperBoundSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline typename Position<TSA>::Type 
-	upperBoundSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query)
-	{	// find first element that query is before, using operator<
-		return upperBoundSA(text, sa, query, SortedList());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery,
-		typename TFlatTreeSpec
-	>
-	inline Pair< typename Position<TSA>::Type >
-	equalRangeSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query,
-		TFlatTreeSpec const)
-	{	// find range equivalent to query, using operator<
-		Pair< typename Iterator<TSA const, Standard>::Type > itPair =
-			_equalRangeSA(text, SearchTreeIterator<TSA const, TFlatTreeSpec>(sa), query);
-		return Pair< typename Position<TSA>::Type >
-			(itPair.i1 - begin(sa, Standard()), itPair.i2 - begin(sa, Standard()));
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TQuery
-	>
-	inline Pair< typename Position<TSA>::Type >
-	equalRangeSA(
-		TText const &text,
-		TSA const &sa,
-		TQuery *query)
-	{	// find first element that query is before, using operator<
-		return equalRangeSA(text, sa, query, SortedList());
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// substring search with enhanced LCP-table
-	//
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCP,
-		typename TSpec,
-		typename TQuery,
-		typename TDiff_
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	_lowerBoundLcpe(
-		TText &text,
-		TSA &sa,
-		SearchTreeIterator< TLCP, TSpec > treeIter,
-		TQuery &query,
-		TDiff_ lcpLower,
-		TDiff_ lcpUpper)
-	{	// find first element not before query, using operator<
-		typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TSA, Standard>::Type		TSAIter;
-		typedef SearchTreeIterator< TLCP, TSpec >			TLCPTreeIt;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TDiff delta = length(sa) - 1;
-		TDiff lcp;
-		#ifdef SEQAN_PROFILE_LCPEFIND
-			TDiff skippedCompares = 0;	// difference of char compares related to xxx_bound_sa
-		#endif
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-		TSAIter first = begin(sa, Standard());
-
-		// binary search with intervals >= 3 elements
-		for (; 1 < delta; )
-		{	// divide and conquer, find half that contains answer
-			TDiff delta2 = treeIter.leftSize();
-			TSAIter mid = first;
-			goFurther(mid, delta2);
-
-			if (lcpLower > lcpUpper) 
-			{
-                TLCPTreeIt leftChild = treeIter;
-                leftChild.left();
-				TDiff lcpMidLower = *leftChild;
-
-				if (lcpMidLower > lcpLower) 
-				{
-					// second half
-					#ifdef SEQAN_PROFILE_LCPEFIND
-						skippedCompares += lcpLower - lcpUpper;
-					#endif
-					first = mid;
-					treeIter.right();
-					if ((delta -= delta2) == 1) {
-						++first;
-						delta = 0;
-					}
-					continue;
-				} 
-				else if (lcpMidLower < lcpLower) 
-				{
-					// first half
-					#ifdef SEQAN_PROFILE_LCPEFIND
-						skippedCompares += lcpMidLower - lcpUpper;
-					#endif
-					lcpUpper = lcpMidLower;
-					treeIter = leftChild;
-					if ((delta = delta2) == 1)
-						delta = 0;
-					continue;
-				}
-				lcp = lcpLower;
-			} 
-			else if (lcpLower < lcpUpper) 
-			{
-                TLCPTreeIt rightChild = treeIter;
-                rightChild.right();
-				TDiff lcpMidUpper = *rightChild;
-
-				if (lcpMidUpper > lcpUpper) 
-				{
-					// first half
-					#ifdef SEQAN_PROFILE_LCPEFIND
-						skippedCompares += lcpUpper - lcpLower;
-					#endif
-					treeIter.left();
-					if ((delta = delta2) == 1)
-						delta = 0;
-					continue;
-				} 
-				else if (lcpMidUpper < lcpUpper) 
-				{
-					// second half
-					#ifdef SEQAN_PROFILE_LCPEFIND
-						skippedCompares += lcpMidUpper - lcpLower;
-					#endif
-					lcpLower = lcpMidUpper;
-					first = mid;
-                    treeIter = rightChild;
-					if ((delta -= delta2) == 1) {
-						++first;
-						delta = 0;
-					}
-					continue;
-				}
-				lcp = lcpUpper;
-			} else
-				lcp = lcpUpper;
-
-
-			TSuffix		suf = suffix(text, *mid);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-
-			// lcp search changes MIN to MAX here
-//			TDiff lcp = _max(lcpLower, lcpUpper);
-			#ifdef SEQAN_PROFILE_LCPEFIND
-				skippedCompares += lcp - _min(lcpLower, lcpUpper);
-			#endif
-			goFurther(t, lcp);
-			goFurther(q, lcp);
-			for(TDiff i = _min(difference(t, tEnd), difference(q, qEnd)); 
-				i && ordEqual(*t, convert<TTextAlphabet>(*q));
-				--i, ++t, ++q, ++lcp) ;
-
-            // is text < query ?
-			if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q))))
-			{
-				// second half
-				lcpLower = lcp;
-				first = mid;
-				treeIter.right();
-				if ((delta -= delta2) == 1) {
-					++first;
-					delta = 0;
-				}
-			} else {
-				// first half
-				lcpUpper = lcp;
-				treeIter.left();
-				if ((delta = delta2) == 1)
-					delta = 0;
-			}
-		}
-
-		#ifdef SEQAN_PROFILE_LCPEFIND
-			SEQAN_PROADD(SEQAN_PROEXTRA3, skippedCompares);
-		#endif
-
-        // binary search for intervals of 2 or less elements
-        lcp = _min(lcpLower, lcpUpper);
-		TQueryIter q = qBegin;
-		goFurther(q, lcp);
-
-		while (true) {
-			TSuffix		suf = suffix(text, *first);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-
-			goFurther(t, lcp);
-			for(TDiff i = _min(difference(t, tEnd), difference(q, qEnd)); 
-            	i && ordEqual(*t, convert<TTextAlphabet>(*q));
-            	 --i, ++t, ++q) ;
-
-            // is text < query ?
-			if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q)))) {
-				// second half
-				++first;
-				if (!delta) return first;
-                --delta;
-			} else {
-				// first half -> end
-				return first;
-			}
-        }
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCP,
-		typename TSpec,
-		typename TQuery
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	_lowerBoundLcpe(
-		TText &text,
-		TSA &sa,
-		SearchTreeIterator< TLCP, TSpec > &treeIter,
-		TQuery &query)
-	{
-		return _lowerBoundLcpe(text, sa, treeIter, query, 0, 0);
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCP,
-		typename TSpec,
-		typename TQuery,
-		typename TDiff_
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	_upperBoundLcpe(
-		TText &text,
-		TSA &sa,
-		SearchTreeIterator< TLCP, TSpec > treeIter,
-		TQuery &query,
-		TDiff_ lcpLower,
-		TDiff_ lcpUpper)
-	{	// find first element not before query, using operator<
-		typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TSA, Standard>::Type		TSAIter;
-		typedef SearchTreeIterator< TLCP, TSpec >			TLCPTreeIt;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TDiff delta = length(sa) - 1;
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-		TSAIter first = begin(sa, Standard());
-
-        // binary search with intervals >= 3 elements
-		for (; 1 < delta; )
-		{	// divide and conquer, find half that contains answer
-			TDiff delta2 = treeIter.leftSize();
-			TSAIter mid = first;
-			goFurther(mid, delta2);
-
-			if (lcpLower > lcpUpper) 
-			{
-                TLCPTreeIt leftChild = treeIter;
-                leftChild.left();
-				TDiff lcpMidLower = *leftChild;
-
-				if (lcpMidLower > lcpLower) 
-				{
-					// second half
-					first = mid;
-					treeIter.right();
-					if ((delta -= delta2) == 1) {
-						++first;
-						delta = 0;
-					}
-					continue;
-				} 
-				else if (lcpMidLower < lcpLower) 
-				{
-					// first half
-					lcpUpper = lcpMidLower;
-					treeIter = leftChild;
-					if ((delta = delta2) == 1)
-						delta = 0;
-					continue;
-				}
-			} 
-			else if (lcpLower < lcpUpper) 
-			{
-                TLCPTreeIt rightChild = treeIter;
-                rightChild.right();
-				TDiff lcpMidUpper = *rightChild;
-
-				if (lcpMidUpper > lcpUpper) 
-				{
-					// first half
-					treeIter.left();
-					if ((delta = delta2) == 1)
-						delta = 0;
-					continue;
-				}
-				else if (lcpMidUpper < lcpUpper) 
-				{
-					// second half
-					lcpLower = lcpMidUpper;
-					first = mid;
-                    treeIter = rightChild;
-					if ((delta -= delta2) == 1) {
-						++first;
-						delta = 0;
-					}
-					continue;
-				}
-			}
-
-			TSuffix		suf = suffix(text, *mid);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-
-			// lcp search changes MIN to MAX here
-			TDiff lcp = _max(lcpLower, lcpUpper);
-			goFurther(t, lcp);
-			goFurther(q, lcp);
-			TDiff max = _min(difference(t, tEnd), difference(q, qEnd));
-            TDiff i = max;
-			for(; i && ordEqual(*t, convert<TTextAlphabet>(*q)); --i, ++t, ++q) ;
-			lcp += max - i;
-
-            // is text <= query ?
-			if (q == qEnd || t == tEnd || !ordGreater(*t, convert<TTextAlphabet>(*q)))
-			{
-				// second half
-				lcpLower = lcp;
-				first = mid;
-				treeIter.right();
-				if ((delta -= delta2) == 1) {
-					++first;
-					delta = 0;
-				}
-			} else {
-				// first half
-				lcpUpper = lcp;
-				treeIter.left();
-				if ((delta = delta2) == 1)
-					delta = 0;
-			}
-		}
-
-        // binary search for intervals of 2 or less elements
-        TDiff lcp = _min(lcpLower, lcpUpper);
-		TQueryIter q = qBegin;
-		goFurther(q, lcp);
-
-		while (true) {
-			TSuffix		suf = suffix(text, *first);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-
-			goFurther(t, lcp);
-			TDiff i = _min(difference(t, tEnd), difference(q, qEnd));
-            for(; i && ordEqual(*t, convert<TTextAlphabet>(*q)); --i, ++t, ++q) ;
-
-            // is text <= query ?
-			if (q == qEnd || t == tEnd || !ordGreater(*t, convert<TTextAlphabet>(*q))) {
-				// second half
-				++first;
-				if (!delta) return first;
-                --delta;
-			} else {
-				// first half -> end
-				return first;
-			}
-        }
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCP,
-		typename TSpec,
-		typename TQuery
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	_upperBoundLcpe(
-		TText &text,
-		TSA &sa,
-		SearchTreeIterator< TLCP, TSpec > &treeIter,
-		TQuery &query)
-	{
-		return _upperBoundLcpe(text, sa, treeIter, query, 0, 0);
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCP,
-		typename TSpec,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA, Standard>::Type >
-	_equalRangeLcpe(
-		TText &text,
-		TSA &sa,
-		SearchTreeIterator< TLCP, TSpec > treeIter,
-		TQuery &query)
-	{	// find first element not before query, using operator<
-		typedef typename Difference<TText>::Type			TDiff;
-		typedef typename Suffix<TText>::Type				TSuffix;
-		typedef typename Iterator<TSuffix, Standard>::Type	TTextIter;
-		typedef typename Iterator<TSA, Standard>::Type		TSAIter;
-		typedef SearchTreeIterator< TLCP, TSpec >			TLCPTreeIt;
-		typedef typename Iterator<TQuery, Standard>::Type	TQueryIter;
-        typedef typename Value<TSuffix>::Type               TTextAlphabet;
-
-		TDiff lcpLower = 0;
-		TDiff lcpUpper = 0;
-        TDiff delta = length(sa) - 1;
-
-		TQueryIter qBegin = begin(query, Standard());
-		TQueryIter qEnd = end(query, Standard());
-		TSAIter first = begin(sa, Standard());
-		TSAIter last = end(sa, Standard());
-
-        // binary search with intervals >= 3 elements
-		for (; 1 < delta; )
-		{	// divide and conquer, find half that contains answer
-			TDiff delta2 = treeIter.leftSize();
-			TSAIter mid = first;
-			goFurther(mid, delta2);
-
-			if (lcpLower > lcpUpper) 
-			{
-                TLCPTreeIt leftChild = treeIter;
-                leftChild.left();
-				TDiff lcpMidLower = *leftChild;
-
-				if (lcpMidLower > lcpLower) 
-				{
-					// second half
-					first = mid;
-					treeIter.right();
-					if ((delta -= delta2) == 1) {
-						++first;
-						delta = 0;
-					}
-					continue;
-				}
-				else if (lcpMidLower < lcpLower) 
-				{
-					// first half
-					lcpUpper = lcpMidLower;
-					treeIter = leftChild;
-					if ((delta = delta2) == 1)
-						delta = 0;
-					continue;
-				}
-			} 
-			else if (lcpLower < lcpUpper) 
-			{
-                TLCPTreeIt rightChild = treeIter;
-                rightChild.right();
-				TDiff lcpMidUpper = *rightChild;
-
-				if (lcpMidUpper > lcpUpper) 
-				{
-					// first half
-					treeIter.left();
-					if ((delta = delta2) == 1)
-						delta = 0;
-					continue;
-				} 
-				else if (lcpMidUpper < lcpUpper) 
-				{
-					// second half
-					lcpLower = lcpMidUpper;
-					first = mid;
-                    treeIter = rightChild;
-					if ((delta -= delta2) == 1) {
-						++first;
-						delta = 0;
-					}
-					continue;
-				}
-			}
-
-			TSuffix		suf = suffix(text, *mid);
-			TTextIter	t = begin(suf, Standard());
-			TTextIter	tEnd = end(suf, Standard());
-			TQueryIter	q = qBegin;
-
-			// lcp search changes MIN to MAX here
-			TDiff lcp = _max(lcpLower, lcpUpper);
-			goFurther(t, lcp);
-			goFurther(q, lcp);
-			TDiff max = _min(difference(t, tEnd), difference(q, qEnd));
-            TDiff i = max;
-			for(; i && ordEqual(*t, convert<TTextAlphabet>(*q)); --i, ++t, ++q) ;
-			lcp += max - i;
-
-            // is text < query ?
-			if (q != qEnd && (t == tEnd || ordLess(*t, convert<TTextAlphabet>(*q)))) {
-				// second half
-				lcpLower = lcp;
-				first = mid;
-				treeIter.right();
-				if ((delta -= delta2) == 1) {
-					++first;
-					delta = 0;
-				}
-			} else
-            // is text > query ?
-			if (q != qEnd && t != tEnd && ordGreater(*t, convert<TTextAlphabet>(*q))) {
-				// first half
-				lcpUpper = lcp;
-				treeIter.left();
-				if ((delta = delta2) == 1)
-					delta = 0;
-			} 
-			else
-			{	// range straddles mid, find each end and return
-				typename Infix<TSA>::Type leftRange(sa, first, mid);
-				TSAIter First2 = _lowerBoundLcpe(
-					text, leftRange, treeIter.leftChild(), query, lcpLower, lcp);
-
-				treeIter.right();
-				if ((delta -= delta2) == 1) {
-					delta = 0;
-					++first;
-				}
-
-				typename Infix<TSA>::Type rightRange(sa, mid, last);
-				TSAIter Last2 = _upperBoundLcpe(
-					text, rightRange, treeIter, query, lcp, lcpUpper);
-
-				return Pair<TSAIter> (First2, Last2);
-			}
-		}
-
-		// range straddles mid, find each end and return
-		typename Infix<TSA>::Type midRange(sa, first, last);
-		return Pair<TSAIter> (
-			_lowerBoundLcpe(text, midRange, treeIter, query, lcpLower, lcpUpper),
-			_upperBoundLcpe(text, midRange, treeIter, query, lcpLower, lcpUpper)
-		);
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCP,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA, Standard>::Type >
-	_equalRangeLcpe(
-		TText &text,
-		TSA &sa,
-		TLCP &lcp,
-		TQuery &query)
-	{
-		return _equalRangeLcpe(text, sa, SearchTreeIterator<TLCP, LeftCompleteTree>(lcp, (length(text)>1)?length(text)-1:0), query);
-	}
-
-
-    //////////////////////////////////////////////////////////////////////////////
-	// little helpers (not used)
-/*
-	template < typename LCPFwdIt, typename TSize >
-	TSize lcp(LCPFwdIt first, TSize count) {
-		if (count > 1) {
-			TSize lcp = *first;
-			++first;
-			count-=2;
-			while (count) {
-				if (lcp < *first) lcp = *first;
-				++first;
-				--count;
-			}
-			return lcp;
-		} else
-			return 0;
-	}
-*/
-
-	//////////////////////////////////////////////////////////////////////////////
-	// wrappers with nice interfaces
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline typename Position<TLCPE>::Type 
-	lowerBoundLcpe(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery const &query)
-	{	// find first element not before query, using operator<
-		return _lowerBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline typename Position<TLCPE>::Type 
-	upperBoundLcpe(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery const &query)
-	{	// find first element that query is before, using operator<
-		return upperBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline Pair< typename Position<TSA>::Type >
-	equalRangeLcpe(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery const &query)
-	{	// find range equivalent to query, using operator<
-		Pair< typename Iterator<TSA const, Standard>::Type > itPair =
-			_equalRangeLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query);
-		return Pair< typename Position<TSA>::Type >
-			(itPair.i1 - begin(sa, Standard()), itPair.i2 - begin(sa, Standard()));
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	lowerBoundLcpeIterator(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery const &query)
-	{	// find first element not before query, using operator<
-		return _lowerBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0);
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline typename Iterator<TSA, Standard>::Type
-	upperBoundLcpeIterator(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery const &query)
-	{	// find first element that query is before, using operator<
-		return upperBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA, Standard>::Type >
-	equalRangeLcpeIterator(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery const &query)
-	{	// find range equivalent to query, using operator<
-		return _equalRangeLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query);
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// workarounds for the Visual Studio array problem
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline typename Position<TLCPE>::Type 
-	lowerBoundLcpe(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery *query)
-	{	// find first element not before query, using operator<
-		return _lowerBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline typename Position<TLCPE>::Type 
-	upperBoundLcpe(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery *query)
-	{	// find first element that query is before, using operator<
-		return upperBoundLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query, 0, 0) - begin(sa, Standard());
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline Pair< typename Position<TSA>::Type >
-	equalRangeLcpe(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery *query)
-	{	// find range equivalent to query, using operator<
-		Pair< typename Iterator<TSA const, Standard>::Type > itPair =
-			_equalRangeLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query);
-		return Pair< typename Position<TSA>::Type >
-			(itPair.i1 - begin(sa, Standard()), itPair.i2 - begin(sa, Standard()));
-	}
-
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TQuery
-	>
-	inline Pair< typename Iterator<TSA, Standard>::Type >
-	equalRangeLcpeIterator(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TQuery *query)
-	{	// find range equivalent to query, using operator<
-		return _equalRangeLcpe(text, sa, SearchTreeIterator<TLCPE const, LeftCompleteTree>(lcpe, (length(text)>1)?length(text)-1:0), query);
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// wrappers with nice interfaces
-/*
-	template <
-		typename TText,
-		typename TSA,
-		typename TLCPE,
-		typename TSubText >
-	inline Pair<typename Iterator<TSA const>::Type> equalRangeLcpe(
-		TText const &text,
-		TSA const &sa,
-		TLCPE const &lcpe,
-		TSubText const &subtext)
-	{
-		return _equalRangeLcpe(
-			begin(text), end(text),
-			begin(sa), end(sa),
-            SearchTreeIterator<typename Iterator<TLCPE const>::Type, LeftCompleteTree>(begin(lcpe, (length(text)>1)?length(text)-1:0), (length(text)>1)?length(text)-1:0),
-			begin(subtext), end(subtext));
-	}
-*/
-
 //////////////////////////////////////////////////////////////////////////////
 // _findFirstIndex implementation
 
-	template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
-	inline void 
-	_findFirstIndex(
-		Finder< Index<TText, TSpec>, TSpecFinder > &finder,
-		TPattern const &pattern,
-		EsaFindMlr const)
-	{
-		Index<TText, TSpec> &index = haystack(finder);
-		indexRequire(index, EsaSA());
-		finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern);
-	}
-
-	template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
-	inline void 
-	_findFirstIndex(
-		Finder< Index<TText, TSpec>, TSpecFinder > &finder,
-		TPattern const &pattern,
-		EsaFindLcpe const)
-	{
-		Index<TText, TSpec> &index = haystack(finder);
-		indexRequire(index, EsaSA());
-		indexRequire(index, EsaLcpe());
-		finder.range = equalRangeLcpeIterator(indexText(index), indexSA(index), indexLcpe(index), pattern);
-	}
-
-	template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
-	inline void
-	_findFirstIndex(
-		Finder< Index<TText, TSpec>, TSpecFinder > &finder,
-		TPattern const &pattern,
-		FinderSTree const)
-	{
+    template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+    inline void
+    _findFirstIndex(
+        Finder< Index<TText, TSpec>, TSpecFinder > &finder,
+        TPattern const &pattern,
+        FinderMlr const)
+    {
+        Index<TText, TSpec> &index = haystack(finder);
+        indexRequire(index, FibreSA());
+        finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern);
+    }
+
+    template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+    inline void
+    _findFirstIndex(
+        Finder< Index<TText, TSpec>, TSpecFinder > &finder,
+        TPattern const &pattern,
+        FinderLcpe const)
+    {
+        Index<TText, TSpec> &index = haystack(finder);
+        indexRequire(index, FibreSA());
+        indexRequire(index, FibreLcpe());
+        finder.range = equalRangeLcpeIterator(indexText(index), indexSA(index), indexLcpe(index), pattern);
+    }
+
+    template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+    inline void
+    _findFirstIndex(
+        Finder< Index<TText, TSpec>, TSpecFinder > &finder,
+        TPattern const &pattern,
+        FinderSTree const)
+    {
         typedef Index<TText, TSpec>                             TIndex;
-		typedef typename Fibre<TIndex, FibreSA>::Type			TSA;
-		typedef typename Iterator<TSA const, Standard>::Type	TIterator;
-        
-		TIndex &index = haystack(finder);
+        typedef typename Fibre<TIndex, FibreSA>::Type            TSA;
+        typedef typename Iterator<TSA const, Standard>::Type    TIterator;
+
+        TIndex &index = haystack(finder);
         typename Iterator<TIndex, TopDown<EmptyEdges> >::Type it(index);
         TIterator saIt = begin(indexSA(index), Standard());
         if (goDown(it, pattern))
         {
             Pair<typename Size<TIndex>::Type> rng = range(it);
-			finder.range.i1 = saIt + rng.i1;
-			finder.range.i2 = saIt + rng.i2;
+            finder.range.i1 = saIt + rng.i1;
+            finder.range.i2 = saIt + rng.i2;
         } else
         {
             finder.range.i1 = saIt;
             finder.range.i2 = saIt;
         }
-	}
-
+    }
 
 }
 #endif
diff --git a/seqan/index/find_index_lambda.h b/seqan/index/find_index_lambda.h
new file mode 100644
index 0000000..37aff78
--- /dev/null
+++ b/seqan/index/find_index_lambda.h
@@ -0,0 +1,276 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_FIND_INDEX_LAMBDA_H
+#define SEQAN_FIND_INDEX_LAMBDA_H
+
+namespace seqan {
+
+// ============================================================================
+// Metafunction
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultFind<Index>
+// ----------------------------------------------------------------------------
+
+template <typename THaystack, typename THaystackSpec, typename TPattern>
+struct DefaultFind<Index<THaystack, THaystackSpec>, TPattern>
+{
+    typedef Backtracking<Exact> Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _findImpl(indexText, sequenceNeedle, Backtracking<Exact>)
+// ----------------------------------------------------------------------------
+
+template <typename TState, typename TIndex, typename TNeedle,
+          typename TThreshold, typename TDelegate, typename TSpec>
+SEQAN_FUNC_ENABLE_IF(IsSequence<TNeedle>, void)
+_findImpl(TState & /* state */,
+          TIndex & index,
+          TNeedle const & needle,
+          TThreshold /* threshold */,
+          TDelegate && delegate,
+          Backtracking<Exact, TSpec>)
+{
+    typedef typename Iterator<TIndex, TopDown<> >::Type TIndexIt;
+
+    TIndexIt indexIt(index);
+
+    if (goDown(indexIt, needle))
+    {
+        delegate(indexIt, TThreshold());
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function _findImpl(trieText, sequenceNeedle, Backtracking<Edit/HammingDistance>)
+// ----------------------------------------------------------------------------
+
+template <typename TIndexIt, typename TNeedle, typename TNeedleIt,
+          typename TThreshold, typename TDelegate, typename TDistance>
+inline void
+_findBacktracking(TIndexIt indexIt,
+                  TNeedle const & needle,
+                  TNeedleIt needleIt,
+                  TThreshold errors,
+                  TThreshold threshold,
+                  TDelegate && delegate,
+                  TDistance)
+{
+    // Exact case.
+    if (errors == threshold)
+    {
+        if (goDown(indexIt, suffix(needle, position(needleIt, needle))))
+            delegate(indexIt, errors);
+    }
+    // Approximate case.
+    else if (errors < threshold)
+    {
+        // Base case.
+        if (atEnd(needleIt, needle))
+        {
+            delegate(indexIt, errors);
+        }
+        // Recursive case.
+        else
+        {
+            // Insertion.
+            if (IsSameType<TDistance, EditDistance>::VALUE)
+            {
+                _findBacktracking(indexIt, needle, needleIt + 1,
+                                  static_cast<TThreshold>(errors + 1), threshold, delegate, TDistance());
+            }
+
+            if (goDown(indexIt))
+            {
+                do
+                {
+                    // Mismatch.
+                    TThreshold delta = !ordEqual(parentEdgeLabel(indexIt), value(needleIt));
+                    _findBacktracking(indexIt, needle, needleIt + 1,
+                                      static_cast<TThreshold>(errors + delta), threshold, delegate, TDistance());
+
+                    // Deletion.
+                    if (IsSameType<TDistance, EditDistance>::VALUE)
+                    {
+                        _findBacktracking(indexIt, needle, needleIt,
+                                          static_cast<TThreshold>(errors + 1), threshold, delegate, TDistance());
+                    }
+                }
+                while (goRight(indexIt));
+            }
+        }
+    }
+}
+
+template <typename TState, typename TIndex, typename TNeedle,
+          typename TThreshold, typename TDelegate, typename TDistance, typename TSpec>
+SEQAN_FUNC_ENABLE_IF(And<Is<StringTrieConcept<TIndex> >, IsSequence<TNeedle> >, void)
+_findImpl(TState & /* indexIt */,
+          TIndex & index,
+          TNeedle const & needle,
+          TThreshold threshold,
+          TDelegate && delegate,
+          Backtracking<TDistance, TSpec>)
+{
+    typedef typename Iterator<TIndex, TopDown<> >::Type       TIndexIt;
+    typedef typename Iterator<TNeedle const, Standard>::Type  TNeedleIt;
+
+    TIndexIt indexIt(index);
+    TNeedleIt needleIt = begin(needle, Standard());
+    TThreshold errors = 0;
+
+    _findBacktracking(indexIt, needle, needleIt, errors, threshold, delegate, TDistance());
+}
+
+// ----------------------------------------------------------------------------
+// Function _findImpl(treeText, sequenceNeedle, Backtracking<HammingDistance>());
+// ----------------------------------------------------------------------------
+
+template <typename TState, typename TIndex, typename TNeedle,
+          typename TThreshold, typename TDelegate, typename TSpec>
+SEQAN_FUNC_ENABLE_IF(And<Is<StringTreeConcept<TIndex> >, IsSequence<TNeedle> >, void)
+_findImpl(TState & /* indexIt */,
+          TIndex & index,
+          TNeedle const & needle,
+          TThreshold threshold,
+          TDelegate && delegate,
+          Backtracking<HammingDistance, TSpec>)
+{
+    typedef typename Iterator<TIndex, TopDown<> >::Type     TIndexIt;
+
+    TIndexIt indexIt(index);
+
+    // This lambda is stored locally because approximateStringSearch() does not accept rvalue delegates.
+    std::function<void(TNeedle const &, TIndexIt const &)> delegator = [&](TNeedle const &, TIndexIt const & it)
+    {
+        // NOTE(esiragusa): the approximateStringSearch() functor doesn't know the score...
+        delegate(it, threshold);
+    };
+
+    approximateStringSearch(delegator, needle, indexIt, threshold);
+}
+
+// ----------------------------------------------------------------------------
+// Function find(treeText, trieNeedle, Backtracking<TDistance>());
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TNeedle,
+          typename TThreshold, typename TDelegate, typename TDistance, typename TSpec>
+SEQAN_FUNC_ENABLE_IF(And<Is<StringTreeConcept<TIndex> >, Is<StringTrieConcept<TNeedle> > >, void)
+find(TIndex & text,
+     TNeedle & needle,
+     TThreshold threshold,
+     TDelegate && delegate,
+     Backtracking<TDistance, TSpec>)
+{
+    typedef typename Iterator<TIndex, TopDown<> >::Type     TTextIt;
+    typedef typename Iterator<TNeedle, TopDown<> >::Type    TNeedleIt;
+
+    TTextIt textIt(text);
+    TNeedleIt needleIt(needle);
+
+    // This lambda is stored locally because approximateTreeSearch() does not accept rvalue delegates.
+    std::function<void(TNeedleIt const &, TTextIt const &)> delegator =
+    [&](TNeedleIt const & nIt, TTextIt const & tIt)
+    {
+        // NOTE(esiragusa): the approximateTreeSearch() functor doesn't know the score...
+        delegate(tIt, nIt, threshold);
+    };
+
+    approximateTreeSearch(delegator, needleIt, textIt, threshold);
+}
+
+// ----------------------------------------------------------------------------
+// Function find(indexText, treeNeedle, errors, [](...){}, Backtracking<TDistance>());
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TNeedle,
+          typename TThreshold, typename TDelegate, typename TDistance, typename TSpec>
+SEQAN_FUNC_ENABLE_IF(And<Is<StringIndexConcept<TIndex> >, Is<StringTreeConcept<TNeedle> > >, void)
+find(TIndex & index,
+     TNeedle & needle,
+     TThreshold threshold,
+     TDelegate && delegate,
+     Backtracking<TDistance, TSpec>)
+{
+    typedef Backtracking<TDistance, TSpec>                  TAlgorithm;
+    typedef Finder<TIndex, TAlgorithm>                      TFinder_;
+    typedef Pattern<TNeedle, TAlgorithm>                    TPattern_;
+
+    TFinder_ _finder(index);
+    TPattern_ _pattern(needle, length(back(host(needle))));
+
+    while (_resume(_finder, _pattern, threshold))
+    {
+        delegate(_finder.index_iterator, _pattern.index_iterator, _pattern.prefix_aligner.errors);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function find(trieText, trieNeedle, errors, [](...){}, Backtracking<TDistance>());
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TNeedle,
+          typename TThreshold, typename TDelegate, typename TDistance, typename TSpec>
+SEQAN_FUNC_ENABLE_IF(And<Is<StringTrieConcept<TIndex> >, Is<StringTrieConcept<TNeedle> > >, void)
+find(TIndex & index,
+     TNeedle & needle,
+     TThreshold threshold,
+     TDelegate && delegate,
+     Backtracking<TDistance, TSpec>)
+{
+    typedef Backtracking<TDistance, TSpec>                  TAlgorithm;
+    typedef Finder_<TIndex, TNeedle, TAlgorithm>            TFinder;
+
+    TFinder finder;
+
+    // This lambda is stored locally because _find() does not accept rvalue delegates.
+    std::function<void(TFinder const &)> delegator = [&](TFinder const &)
+    {
+        delegate(_textIterator(finder), _patternIterator(finder), _getScore(finder));
+    };
+
+    _find(finder, index, needle, threshold, delegator);
+}
+
+}
+
+#endif  // #ifndef SEQAN_FIND_INDEX_LAMBDA_H
diff --git a/seqan/index/find_index_qgram.h b/seqan/index/find_index_qgram.h
index f63724a..d3f1891 100644
--- a/seqan/index/find_index_qgram.h
+++ b/seqan/index/find_index_qgram.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,24 +41,16 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 // QGram finders
 
-	struct FinderQGramLookup_; //Finder that simply looks up the q-gram in the hash table
+    struct FinderQGramLookup_; //Finder that simply looks up the q-gram in the hash table
 
 // the docu is now in index_base.h
-/**
-.Tag.Index Find Algorithm
-..summary:Tags to specialise the search strategies.
-..tag.QGramFindLookup:q-gram search.
-Finds q-grams in a @Spec.IndexQGram@ index using the hash table.
-..include:seqan/index.h
-*/
-
-	typedef Tag<FinderQGramLookup_> const QGramFindLookup;
+    typedef Tag<FinderQGramLookup_> const QGramFindLookup;
 
 //____________________________________________________________________________
 
 
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	struct DefaultFinder<Index<TText, IndexQGram<TShapeSpec, TSpec> > > {
+    template < typename TText, typename TShapeSpec, typename TSpec >
+    struct DefaultFinder<Index<TText, IndexQGram<TShapeSpec, TSpec> > > {
         typedef QGramFindLookup Type;
     };
 
@@ -66,27 +58,27 @@ Finds q-grams in a @Spec.IndexQGram@ index using the hash table.
 //////////////////////////////////////////////////////////////////////////////
 // _findFirstIndex implementation
 
-	template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
-	inline void _findFirstIndex(
-		Finder< Index<TText, TSpec>, TSpecFinder > &finder,
-		TPattern const &pattern,
-		QGramFindLookup const)
-	{
-		typedef Index<TText, TSpec>									TIndex;
-		typedef typename Fibre<TIndex, QGramSA>::Type				TSA;
-		typedef typename Fibre<TIndex, QGramShape>::Type			TShape;
-		typedef typename Fibre<TIndex, QGramDir>::Type				TDir;
-		typedef typename Fibre<TIndex, QGramBucketMap>::Type		TBucketMap;
-		typedef typename Iterator<TSA const, Standard>::Type		TSAIterator;
-		typedef typename Iterator<TPattern const, Standard>::Type	TPatternIterator;
-
-		TIndex &index = haystack(finder);
-		indexRequire(index, QGramSADir());
-
-		TSAIterator saIt = begin(indexSA(index), Standard());
-		TPatternIterator pIt = begin(pattern, Standard());
-		TDir const &dir = indexDir(index);
-		TShape &shape = indexShape(index);
+    template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
+    inline void _findFirstIndex(
+        Finder< Index<TText, TSpec>, TSpecFinder > &finder,
+        TPattern const &pattern,
+        QGramFindLookup const)
+    {
+        typedef Index<TText, TSpec>                                    TIndex;
+        typedef typename Fibre<TIndex, QGramSA>::Type                TSA;
+        typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+        typedef typename Fibre<TIndex, QGramDir>::Type                TDir;
+        typedef typename Fibre<TIndex, QGramBucketMap>::Type        TBucketMap;
+        typedef typename Iterator<TSA const, Standard>::Type        TSAIterator;
+        typedef typename Iterator<TPattern const, Standard>::Type    TPatternIterator;
+
+        TIndex &index = haystack(finder);
+        indexRequire(index, QGramSADir());
+
+        TSAIterator saIt = begin(indexSA(index), Standard());
+        TPatternIterator pIt = begin(pattern, Standard());
+        TDir const &dir = indexDir(index);
+        TShape &shape = indexShape(index);
 
         if (IsSameType<TBucketMap, Nothing>::VALUE)
         {
@@ -105,7 +97,7 @@ Finds q-grams in a @Spec.IndexQGram@ index using the hash table.
             finder.range.i1 = saIt + dir[bktNo];
             finder.range.i2 = saIt + dir[bktNo + 1];
         }
-	}
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/index/find_pigeonhole.h b/seqan/index/find_pigeonhole.h
old mode 100755
new mode 100644
index a7e5448..9d46525
--- a/seqan/index/find_pigeonhole.h
+++ b/seqan/index/find_pigeonhole.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -31,7 +31,7 @@
 // ==========================================================================
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
-// This filter uses the pigeonhole principle to search k-error matches 
+// This filter uses the pigeonhole principle to search k-error matches
 // between strings in a stringset and a text.
 // The pigeonhole principle states:
 // If a string is split into k+1 pieces then in every k-error match of the
@@ -39,10 +39,10 @@
 // ==========================================================================
 
 
-#ifndef CORE_INCLUDE_SEQAN_FIND_PIGEONHOLE_H_
-#define CORE_INCLUDE_SEQAN_FIND_PIGEONHOLE_H_
+#ifndef INCLUDE_SEQAN_FIND_PIGEONHOLE_H_
+#define INCLUDE_SEQAN_FIND_PIGEONHOLE_H_
 
-namespace seqan 
+namespace seqan
 {
 
 // ==========================================================================
@@ -58,180 +58,221 @@ namespace seqan
 
     template <typename TSpec = void>
     struct Pigeonhole {
-        enum { ONE_PER_DIAGONAL = 1 };	// 1..record last seed diagonal and ignore seeds on the same diag. (heuristic)
-        enum { HAMMING_ONLY = 0 };		// 0..no indels; 1..allow indels
+        enum { ONE_PER_DIAGONAL = 1 };    // 1..record last seed diagonal and ignore seeds on the same diag. (heuristic)
+        enum { HAMMING_ONLY = 0 };        // 0..no indels; 1..allow indels
     };
 
     template <>
     struct Pigeonhole<Hamming_> {
-        enum { ONE_PER_DIAGONAL = 1 };	// 1..record last seed diagonal and ignore seeds on the same diag. (heuristic)
-        enum { HAMMING_ONLY = 1 };		// 0..no indels; 1..allow indels
+        enum { ONE_PER_DIAGONAL = 1 };    // 1..record last seed diagonal and ignore seeds on the same diag. (heuristic)
+        enum { HAMMING_ONLY = 1 };        // 0..no indels; 1..allow indels
     };
-	
+
 //////////////////////////////////////////////////////////////////////////////
 
 
 //____________________________________________________________________________
 
 
-	template <typename TSpec, typename THstkPos>
-	struct PigeonholeHit_ 
-	{
-		THstkPos	hstkPos;			// seed diagonal begin in haystack 
-		unsigned	ndlSeqNo;			// needle sequence number
-	};
-    
+    template <typename TSpec, typename THstkPos>
+    struct PigeonholeHit_
+    {
+        THstkPos    hstkPos;            // seed diagonal begin in haystack
+        unsigned    ndlSeqNo;            // needle sequence number
+    };
+
     template <typename THaystack, typename TPattern, typename TPigeonholeSpec>
     struct FindResult<Finder<THaystack, Pigeonhole<TPigeonholeSpec> >, TPattern>
     {
         typedef SwiftHitSemiGlobal_<__int64> Type;
     };
-        
-    struct PigeonholeParameters {
+
+/*!
+ * @class PigeonholeParameters
+ * @headerfile <seqan/index/find_pigeonhole.h>
+ * @brief Parameters for the pigeonhole filter algorithm.
+ *
+ * @signature struct PigeonholeParameters;
+ *
+ * @see PigeonholePattern
+ *
+ *
+ * @fn PigeonholeParameters::PigeonholeParameters
+ * @brief Default constructor.
+ *
+ * @signature PigeonholeParameters::PigeonholeParameters();
+ *
+ * Initializes all member variables, default values are given in the variable documentation.
+ *
+ *
+ * @var unsigned PigeonholeParameters::overlap;
+ * @brief Overlap length of adjacent q-grams, default is to use non-overlappling q-grams (<tt>= 0</tt>).
+ *
+ * @var unsigned PigeonholeParameters::delta;
+ * @brief Delta length, becomes index step site; defaults to <tt>0</tt>.
+ *
+ * A value of <tt>0</tt> means that the delta will be auto-detected.
+ *
+ * @var bool PigeonholeParameters::printDots;
+ * @brief Whether to print dots for the scanning progress, defaults to <tt>false</tt>.
+ *
+ * @var bool PigeonholeParameters::debug;
+ * @brief Whether to print debug information, defaults to <tt>false</tt>.
+ */
+
+
+    struct PigeonholeParameters
+    {
         unsigned overlap;           // overlap length of adjacent q-grams, default is to use non-overlapping q-grams (=0)
         unsigned delta;             // delta length (0 = automatic detection), becomes index stepSize
         bool printDots;             // the q-gram will have length q=delta+overlap
         bool debug;
-        
-        PigeonholeParameters():
+
+        PigeonholeParameters() :
             overlap(0),
             delta(0),
-            printDots(false),		// print a . for every 100kbps mapped genome
-            debug(false) {}
+            printDots(false),        // print a . for every 100kbps mapped genome
+            debug(false)
+        {}
     };
-    
+
 
 //____________________________________________________________________________
 
 
-/**
-.Spec.Pigeonhole:
-..summary:Provides a fast filter alogrithm that uses the pigeonhole lemma, i.e. if a pattern matches with k errors in the text, every partition into k+1 parts contains one part that matches without error.
-..general:Class.Pattern
-..general:Class.Finder
-..cat:Searching
-..signature:Finder<THaystack, Pigeonhole<TSpec> >
-..signature:Pattern<TIndex, Pigeonhole<TSpec> >
-..param.THaystack:The type of the sequence that should be searched.
-..param.TIndex: A q-gram index of needle(s) that should be searched for.
-...type:Spec.IndexQGram
-..param.TSpec: Specifies the type of Swift filter.
-..include:seqan/index.h
-..remarks:
- The @Class.Pattern@ must be a q-gram index over multiple patterns. The tolerated error rate must be given when @Function.find@ or @Function.windowFindBegin@ is called.
- In these functions the length of the index @Class.Shape@ is set automatically thus it must be modifiable at runtime, e.g. @Spec.OneGappedShape@.
-
-*/
+/*!
+ * @class PigeonholeFinder
+ * @extends Finder
+ * @headerfile <seqan/index/find_pigeonhole.h>
+ *
+ * @brief Pigeonhole-based finder.  Must be used together with @link PigeonholePattern @endlink.
+ *
+ * @signature template <typename THaystack, typename TSpec>
+ *            class Finder<THaystack, Pigeonhole<TSpec> >;
+ *
+ * @tparam TSpec Specifies the type of pigeonhole filter.
+ * @tparam THaystack The type of the sequence that should be searched.
+ *                   Types: @link ContainerConcept @endlink
+ *
+ * Provides a fast filter algorithm that uses the pigeonhole lemma, i.e. if a pattern matches with k errors in the text,
+ * every partition into k+1 parts contains one part that matches without error.
+ *
+ * The @link Pattern @endlink must be a q-gram index over multiple patterns.  The tolerated error rate must be given
+ * when @link Finder#find @endlink or @link PigeonholeFinder#windowFindBegin @endlink is called.  In these functions the
+ * length of the index @link Shape @endlink is set automatically thus it must be modifiable at runtime, e.g. @link
+ * OneGappedShape @endlink.
+ *
+ * @see PigeonholePattern
+ *
+ * @var PigeonholeParameters PigeonholePattern::parameters;
+ * @brief The pigeonhole parameters to use for configuration.
+ */
 
 /*!
- * @class Pigeonhole
- * 
+ * @class PigeonholePattern
  * @extends Pattern
- * @extends Finder
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Provides a fast filter algorithm that uses the pigeonhole lemma, i.e. if a pattern matches with k errors
- *        in the text, every partition into k+1 parts contains one part that matches without error.
- * 
- * @signature Finder<THaystack, Pigeonhole<TSpec> >
- * @signature Pattern<TIndex, Pigeonhole<TSpec> >
- * 
- * @tparam TSpec Specifies the type of Swift filter.
+ * @headerfile <seqan/index/find_pigeonhole.h>
+ *
+ * @brief Pigeonhole-based pattern.  Must be used together with @link PigeonholeFinder @endlink.
+ *
+ * See @link PigeonholeFinder @endlink for more information on the algorithm.
+ *
+ * @signature template <typename THaystack, typename TSpec>
+ *            class Pattern<TIndex, Pigeonhole<TSpec> >;
+ *
+ * @tparam TSpec Specifies the type of pigeonhole filter.
  * @tparam TIndex A q-gram index of needle(s) that should be searched for.
  *                Types: @link IndexQGram @endlink
- * @tparam THaystack The type of the sequence that should be searched. 
- *                   Types: @link SequenceConcept @endlink
- * 
- * @section Remarks
- * 
- * The @link Pattern @endlink must be a q-gram index over multiple patterns. The tolerated error rate must be given when
- * @link Finder#find @endlink or @link windowFindBegin @endlink is called.  In these functions the length of the index @link
- * Shape @endlink is set automatically thus it must be modifiable at runtime, e.g. @link OneGappedShape @endlink.
+ *
+ * @see PigeonholeFinder
+ */
+
+/*!
+ * @typedef PigeonholeFinder::THitString
+ * @brief The type to use for the hit string returned in @link PigeonholeFinder#getWindowFindHits @endlink.
+ *
+ * @signature typedef (...) PigeonholeFinder::THitString;
  */
 
 // docu is now in find_pattern_base.h
-///.Class.Pattern.param.TSpec.type:Spec.Pigeonhole
-///.Class.Finder.param.TSpec.type:Spec.Pigeonhole
-
-	template <typename THaystack, typename TSpec>
-	class Finder<THaystack, Pigeonhole<TSpec> >
-	{
-	public:
-		typedef typename Iterator<THaystack, Rooted>::Type			TIterator;
-		typedef typename Position<THaystack>::Type					THstkPos;
-//		typedef PigeonholeHit_<TSpec, __int64>						TPigeonholeHit;
-		typedef typename FindResult<Finder>::Type                   TPigeonholeHit;
-		typedef typename WindowFindResult<Finder>::Type				THitString;
-		typedef typename Iterator<THitString, Standard>::Type		THitIterator;
-		typedef typename SAValue<THaystack>::Type					TSAValue;
-		typedef Repeat<TSAValue, unsigned>							TRepeat;
+    template <typename THaystack, typename TSpec>
+    class Finder<THaystack, Pigeonhole<TSpec> >
+    {
+    public:
+        typedef typename Iterator<THaystack, Rooted>::Type            TIterator;
+        typedef typename Position<THaystack>::Type                    THstkPos;
+//        typedef PigeonholeHit_<TSpec, __int64>                        TPigeonholeHit;
+        typedef typename FindResult<Finder>::Type                   TPigeonholeHit;
+        typedef typename WindowFindResult<Finder>::Type                THitString;
+        typedef typename Iterator<THitString, Standard>::Type        THitIterator;
+        typedef typename SAValue<THaystack>::Type                    TSAValue;
+        typedef Repeat<TSAValue, unsigned>                            TRepeat;
         // TODO(holtgrew): Make this a holder so we can share the actual string when copying.
-		typedef String<TRepeat>										TRepeatString;
-		typedef typename Iterator<TRepeatString, Standard>::Type	TRepeatIterator;
-
-		TIterator		data_iterator;
-		TIterator		haystackEnd;
-		bool			_needReinit;	// if true, the Pattern needs to be reinitialized
-		THitString		hits;
-		THitIterator	curHit, endHit;
-		THstkPos		startPos, curPos, endPos;
+        typedef String<TRepeat>                                        TRepeatString;
+        typedef typename Iterator<TRepeatString, Standard>::Type    TRepeatIterator;
+
+        TIterator        data_iterator;
+        TIterator        haystackEnd;
+        bool            _needReinit;    // if true, the Pattern needs to be reinitialized
+        THitString        hits;
+        THitIterator    curHit, endHit;
+        THstkPos        startPos, curPos, endPos;
         THstkPos        windowStart;
-		THstkPos		dotPos, dotPos2;
-		TRepeatString	data_repeats;
-		TRepeatIterator	curRepeat, endRepeat;
-
-		Finder():
-			_needReinit(true) { }
-
-		Finder(THaystack &haystack):
-			data_iterator(begin(haystack, Rooted())),
-			_needReinit(true) { }
-
-		template <typename TRepeatSize, typename TPeriodSize>
-		Finder(THaystack &haystack, TRepeatSize minRepeatLen, TPeriodSize maxPeriod):
-			data_iterator(begin(haystack, Rooted())),
-			_needReinit(true) 
-		{
-			findRepeats(data_repeats, haystack, minRepeatLen, maxPeriod);
-		}
-
-		Finder(TIterator &iter):
-			data_iterator(iter),
-			_needReinit(true) { }
-
-		Finder(TIterator const &iter):
-			data_iterator(iter),
-			_needReinit(true) { }
-
-		Finder(Finder const &orig):
-			data_iterator(orig.data_iterator),
-			haystackEnd(orig.haystackEnd),
-			_needReinit(orig._needReinit),
-			hits(orig.hits),
+        THstkPos        dotPos, dotPos2;
+        TRepeatString    data_repeats;
+        TRepeatIterator    curRepeat, endRepeat;
+
+        Finder():
+            _needReinit(true) { }
+
+        Finder(THaystack &haystack):
+            data_iterator(begin(haystack, Rooted())),
+            _needReinit(true) { }
+
+        template <typename TRepeatSize, typename TPeriodSize>
+        Finder(THaystack &haystack, TRepeatSize minRepeatLen, TPeriodSize maxPeriod):
+            data_iterator(begin(haystack, Rooted())),
+            _needReinit(true)
+        {
+            findRepeats(data_repeats, haystack, minRepeatLen, maxPeriod);
+        }
+
+        Finder(TIterator &iter):
+            data_iterator(iter),
+            _needReinit(true) { }
+
+        Finder(TIterator const &iter):
+            data_iterator(iter),
+            _needReinit(true) { }
+
+        Finder(Finder const &orig):
+            data_iterator(orig.data_iterator),
+            haystackEnd(orig.haystackEnd),
+            _needReinit(orig._needReinit),
+            hits(orig.hits),
             startPos(orig.startPos),
             curPos(orig.curPos),
             endPos(orig.endPos),
             windowStart(orig.windowStart),
             dotPos(orig.dotPos),
             dotPos2(orig.dotPos2),
-			data_repeats(orig.data_repeats)
-		{
-			curHit = begin(hits, Standard()) + (orig.curHit - begin(orig.hits, Standard()));
-			endHit = end(hits, Standard());
-			curRepeat = begin(data_repeats, Standard()) + (orig.curRepeat - begin(orig.data_repeats, Standard()));
-			endRepeat = end(data_repeats, Standard());
-		}
-
-		inline typename Reference<TIterator>::Type 
-		operator* () { return value(hostIterator(*this)); }
-
-		inline typename Reference<TIterator const>::Type 
-		operator* () const { return value(hostIterator(*this)); }
-
-		operator TIterator () const	{ return data_iterator;	}
-        
-        Finder & operator = (Finder const &orig) 
+            data_repeats(orig.data_repeats)
+        {
+            curHit = begin(hits, Standard()) + (orig.curHit - begin(orig.hits, Standard()));
+            endHit = end(hits, Standard());
+            curRepeat = begin(data_repeats, Standard()) + (orig.curRepeat - begin(orig.data_repeats, Standard()));
+            endRepeat = end(data_repeats, Standard());
+        }
+
+        inline typename Reference<TIterator>::Type
+        operator* () { return value(hostIterator(*this)); }
+
+        inline typename Reference<TIterator const>::Type
+        operator* () const { return value(hostIterator(*this)); }
+
+        operator TIterator () const    { return data_iterator;    }
+
+        Finder & operator = (Finder const &orig)
         {
             data_iterator = orig.data_iterator;
             haystackEnd = orig.haystackEnd;
@@ -254,63 +295,63 @@ namespace seqan
 
 //____________________________________________________________________________
 
-	
-	template <typename THaystack, typename TSpec>
-	inline bool
-	atEnd(Finder<THaystack, Pigeonhole<TSpec> > & me)
-	{
-		return hostIterator(hostIterator(me)) == hostIterator(me.haystackEnd);
-	}
 
-	template <typename THaystack, typename TSpec>
-	inline void
-	goEnd(Finder<THaystack, Pigeonhole<TSpec> > & me)
-	{
-		hostIterator(me) = me.haystackEnd;
-	}
+    template <typename THaystack, typename TSpec>
+    inline bool
+    atEnd(Finder<THaystack, Pigeonhole<TSpec> > & me)
+    {
+        return hostIterator(hostIterator(me)) == hostIterator(me.haystackEnd);
+    }
+
+    template <typename THaystack, typename TSpec>
+    inline void
+    goEnd(Finder<THaystack, Pigeonhole<TSpec> > & me)
+    {
+        hostIterator(me) = me.haystackEnd;
+    }
 
 
 //____________________________________________________________________________
 
 
-	template <typename TIndex, typename TSpec>
-	class Pattern<TIndex, Pigeonhole<TSpec> >
-	{
-	public:
-		typedef typename Size<TIndex>::Type								TSize;
-		typedef unsigned												TShortSize;
-		typedef typename Fibre<TIndex, Tag<FibreSA_> const >::Type		TSA;
-		typedef typename Fibre<TIndex, Tag<Fibre_Shape_> const >::Type	TShape;
-		typedef typename Iterator<TSA const, Standard>::Type			TIterator;
-				
-		TShape					shape;
+    template <typename TIndex, typename TSpec>
+    class Pattern<TIndex, Pigeonhole<TSpec> >
+    {
+    public:
+        typedef typename Size<TIndex>::Type                                TSize;
+        typedef unsigned                                                TShortSize;
+        typedef typename Fibre<TIndex, Tag<FibreSA_> const >::Type        TSA;
+        typedef typename Fibre<TIndex, Tag<Fibre_Shape_> const >::Type    TShape;
+        typedef typename Iterator<TSA const, Standard>::Type            TIterator;
+
+        TShape                    shape;
         __int64                 curBeginPos, curEndPos;
-		__int64					finderLength;
-		__int64					seqDisabled;
-		TSize					finderPosOffset;						// these must be of
-		TSize					finderPosNextOffset;					// type TSize of TBucket
+        __int64                    finderLength;
+        __int64                    seqDisabled;
+        TSize                    finderPosOffset;                        // these must be of
+        TSize                    finderPosNextOffset;                    // type TSize of TBucket
         TSize                   maxSeqLen;
-		unsigned				curSeqNo;
-		String<__int64>         lastSeedDiag;
-		PigeonholeParameters    params;
-		double					_currentErrorRate;
-
-		Holder<TIndex>	data_host;
-
-		Pattern() 
-		{
-			clear(*this);
-		}
-		Pattern(TIndex &_index): data_host(_index) 
-		{
-			clear(*this);
-		}
-		Pattern(TIndex const &_index): data_host(_index)
-		{
-			clear(*this);
-		}
-	};
-	
+        unsigned                curSeqNo;
+        String<__int64>         lastSeedDiag;
+        PigeonholeParameters    params;
+        double                    _currentErrorRate;
+
+        Holder<TIndex>    data_host;
+
+        Pattern()
+        {
+            clear(*this);
+        }
+        Pattern(TIndex &_index): data_host(_index)
+        {
+            clear(*this);
+        }
+        Pattern(TIndex const &_index): data_host(_index)
+        {
+            clear(*this);
+        }
+    };
+
 //____________________________________________________________________________
 
 
@@ -335,9 +376,9 @@ _pigeonholeUpdateShapeLength(Shape<TValue, SimpleShape> &shape, TSize newLength)
 {
     TSize weight = _pigeonholeMaxShapeWeight(shape);
 
-    if (weight > newLength) 
-		weight = newLength;
-		
+    if (weight > newLength)
+        weight = newLength;
+
     if (weight == length(shape))
         return false;
 
@@ -351,17 +392,17 @@ _pigeonholeUpdateShapeLength(Shape<TValue, OneGappedShape> &shape, TSize newLeng
 {
     if (length(shape) == newLength)
         return false;
-    
+
     TSize weight = _pigeonholeMaxShapeWeight(shape);
 
     if (weight > newLength)
-		weight = newLength;
+        weight = newLength;
 
-	CharString str;
-	resize(str, weight / 2, '1');
-	resize(str, newLength - (weight + 1) / 2, '0');
-	resize(str, newLength, '1');
-	stringToShape(shape, str);
+    CharString str;
+    resize(str, weight / 2, '1');
+    resize(str, newLength - (weight + 1) / 2, '0');
+    resize(str, newLength, '1');
+    stringToShape(shape, str);
     return true;
 }
 
@@ -371,12 +412,12 @@ _pigeonholeUpdateShapeLength(Shape<TValue, GenericShape> &shape, TSize newLength
 {
     if (length(shape) == newLength)
         return false;
-    
+
     TSize weight = _pigeonholeMaxShapeWeight(shape);
-    
+
     if (weight >= newLength)
         weight = newLength;
-    
+
     CharString str;
     resize(str, weight / 2, '1');
     resize(str, newLength - (weight + 1) / 2, '0');
@@ -386,74 +427,89 @@ _pigeonholeUpdateShapeLength(Shape<TValue, GenericShape> &shape, TSize newLength
     return true;
 }
 
+/*!
+ * @fn PigeonholePattern#maskPatternSequence
+ * @headerfile <seqan/index/find_pigeonhole.h>
+ * @brief Mask and unmask pattern sequence.
+ *
+ * @note Disabling sequences in the pigeonhole filter requires the <tt>ONE_PER_DIAGONAL</tt> heuristic.
+ *
+ * @signature void maskPatternSequence(pattern, seqNo, enable);
+ *
+ * @param[in,out] pattern The PigeonholePattern to update.
+ * @param[in]     seqNo   Index of the sequence to disable/enable.
+ * @param[in]     enable  A <tt>bool</tt> that indicates whether hits are to be generated for the given sequence.
+ */
+
 template <typename TIndex, typename TSpec, typename TSeqNo>
 inline void
-maskPatternSequence(Pattern<TIndex, Pigeonhole<TSpec> > & pattern, TSeqNo seqNo, bool enable) 
+maskPatternSequence(Pattern<TIndex, Pigeonhole<TSpec> > & pattern, TSeqNo seqNo, bool enable)
 {
-    SEQAN_ASSERT_NEQ_MSG((int)Pigeonhole<TSpec>::ONE_PER_DIAGONAL, 0, "Disabling sequences in the pigeonhole filter requires the ONE_PER_DIAGONAL heuristic.");
-	
-	if (enable)
-		pattern.lastSeedDiag[seqNo] = -(__int64)pattern.maxSeqLen;
-	else
-		pattern.lastSeedDiag[seqNo] = pattern.seqDisabled;
+    SEQAN_ASSERT_NEQ_MSG((int)Pigeonhole<TSpec>::ONE_PER_DIAGONAL, 0,
+                         "Disabling sequences in the pigeonhole filter requires the ONE_PER_DIAGONAL heuristic.");
+
+    if (enable)
+        pattern.lastSeedDiag[seqNo] = -(__int64)pattern.maxSeqLen;
+    else
+        pattern.lastSeedDiag[seqNo] = pattern.seqDisabled;
 }
 
 template <typename TIndex, typename TFloat, typename TSpec>
-inline void _patternInit(Pattern<TIndex, Pigeonhole<TSpec> > &pattern, TFloat errorRate) 
+inline void _patternInit(Pattern<TIndex, Pigeonhole<TSpec> > &pattern, TFloat errorRate)
 {
-	typedef typename Size<TIndex>::Type TSize;
+    typedef typename Size<TIndex>::Type TSize;
+
+    double _newErrorRate = errorRate;
+    TSize seqCount = countSequences(host(pattern));
 
-	double _newErrorRate = errorRate;
-	TSize seqCount = countSequences(host(pattern));
+    if (pattern._currentErrorRate != _newErrorRate)
+    {
+        // settings have been changed -> initialize bucket parameters
 
-	if (pattern._currentErrorRate != _newErrorRate)
-	{
-		// settings have been changed -> initialize bucket parameters
-	
-		pattern._currentErrorRate = _newErrorRate;
+        pattern._currentErrorRate = _newErrorRate;
 
         TSize minDelta = MaxValue<TSize>::VALUE;
         TSize maxDelta = 3;
         TSize maxSeqLen = 0;
-        for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) 
+        for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
         {
             // get pattern length and max. allowed errors
             TSize length = sequenceLength(seqNo, host(pattern));
             if (maxSeqLen < length) maxSeqLen = length;
-			
-			// sequence must have sufficient length
-			if (length <= pattern.params.overlap) continue;
-			
-			// cut overlap many characters from the end
+
+            // sequence must have sufficient length
+            if (length <= pattern.params.overlap) continue;
+
+            // cut overlap many characters from the end
             TSize errors = (TSize) floor(errorRate * length);
-			length -= pattern.params.overlap;
+            length -= pattern.params.overlap;
             TSize delta = length / (errors + 1);
-			
-			
-			// ignore too short q-grams
-			if (delta < 3) continue;
+
+
+            // ignore too short q-grams
+            if (delta < 3) continue;
             if (minDelta > delta) minDelta = delta;
             if (maxDelta < delta) maxDelta = delta;
         }
         pattern.maxSeqLen = maxSeqLen;
         if (minDelta < 3) minDelta = maxDelta;
-		
+
         TIndex &index = host(pattern);
-		pattern.finderPosOffset = 0;
-		pattern.finderPosNextOffset = pattern.maxSeqLen + pattern.finderLength;
-		
+        pattern.finderPosOffset = 0;
+        pattern.finderPosNextOffset = pattern.maxSeqLen + pattern.finderLength;
+
         if (pattern.params.delta != 0)
-		{
-			// use user-defined delta
+        {
+            // use user-defined delta
             minDelta = pattern.params.delta;
         }
 
-		if (minDelta == MaxValue<TSize>::VALUE)
-		{
-			// disable index
-			minDelta = pattern.maxSeqLen + 1;
-		}
-        		
+        if (minDelta == MaxValue<TSize>::VALUE)
+        {
+            // disable index
+            minDelta = pattern.maxSeqLen + 1;
+        }
+
         if (_pigeonholeUpdateShapeLength(pattern.shape, minDelta + pattern.params.overlap) || getStepSize(index) != minDelta)
         {
             clear(index);
@@ -468,55 +524,55 @@ inline void _patternInit(Pattern<TIndex, Pigeonhole<TSpec> > &pattern, TFloat er
         clear(pattern.lastSeedDiag);
         if (Pigeonhole<TSpec>::ONE_PER_DIAGONAL)
             resize(pattern.lastSeedDiag, seqCount, -(__int64)maxSeqLen);
-		pattern.seqDisabled = -(__int64)maxSeqLen - 1;
+        pattern.seqDisabled = -(__int64)maxSeqLen - 1;
     }
-	else
-	{
-		// settings are unchanged -> reset buckets
+    else
+    {
+        // settings are unchanged -> reset buckets
 
-		// finderPosOffset is used to circumvent expensive resetting of all buckets
-		pattern.finderPosOffset = pattern.finderPosNextOffset;
-		pattern.finderPosNextOffset += pattern.maxSeqLen + pattern.finderLength;
+        // finderPosOffset is used to circumvent expensive resetting of all buckets
+        pattern.finderPosOffset = pattern.finderPosNextOffset;
+        pattern.finderPosNextOffset += pattern.maxSeqLen + pattern.finderLength;
     }
 }
 
 template <
-	typename TFinder,
-	typename TIndex, 
-	typename TSpec,
-	typename THValue
+    typename TFinder,
+    typename TIndex,
+    typename TSpec,
+    typename THValue
 >
 inline bool _pigeonholeProcessQGram(
-	TFinder &finder, 
-	Pattern<TIndex, Pigeonhole<TSpec> > &pattern,
-	THValue hash)
+    TFinder &finder,
+    Pattern<TIndex, Pigeonhole<TSpec> > &pattern,
+    THValue hash)
 {
-	//typedef Pattern<TIndex, Pigeonhole<TSpec> >         TPattern;
-	//typedef typename TFinder::THstkPos					THstkPos;
+    //typedef Pattern<TIndex, Pigeonhole<TSpec> >         TPattern;
+    //typedef typename TFinder::THstkPos                    THstkPos;
 
     typedef typename Fibre<TIndex, QGramSA>::Type const TSA;
     typedef typename Iterator<TSA, Standard>::Type      TSAIter;
     typedef typename TFinder::TPigeonholeHit            THit;
-    
-	TIndex const &index = host(pattern);	
-    
-	// all previous matches reported -> search new ones
-	clear(finder.hits);
-    
+
+    TIndex const &index = host(pattern);
+
+    // all previous matches reported -> search new ones
+    clear(finder.hits);
+
     TSAIter saBegin = begin(indexSA(index), Standard());
     Pair<unsigned> ndlPos;
     THit hit;
 
-    register unsigned bktNo = getBucket(index.bucketMap, hash);
-    register TSAIter occ = saBegin + indexDir(index)[bktNo];
-    register TSAIter occEnd = saBegin + indexDir(index)[bktNo + 1];
-    
-    for(; occ != occEnd; ++occ) 
+    unsigned bktNo = getBucket(index.bucketMap, hash);
+    TSAIter occ = saBegin + indexDir(index)[bktNo];
+    TSAIter occEnd = saBegin + indexDir(index)[bktNo + 1];
+
+    for(; occ != occEnd; ++occ)
     {
         posLocalize(ndlPos, *occ, stringSetLimits(index));
         hit.hstkPos = finder.curPos;
         hit.hstkPos -= getSeqOffset(ndlPos);                    // bucket begin in haystack
-        hit.ndlSeqNo = getSeqNo(ndlPos);						// needle seq. number
+        hit.ndlSeqNo = getSeqNo(ndlPos);                        // needle seq. number
         if (Pigeonhole<TSpec>::ONE_PER_DIAGONAL)
         {
             __int64 diag = hit.hstkPos + (__int64)pattern.finderPosOffset;
@@ -524,44 +580,44 @@ inline bool _pigeonholeProcessQGram(
                 continue;
             pattern.lastSeedDiag[hit.ndlSeqNo] = diag;
         }
-		unsigned ndlLength = sequenceLength(hit.ndlSeqNo, host(pattern));
-
-		if (Pigeonhole<TSpec>::HAMMING_ONLY != 0)
-		{
-			hit.bucketWidth = ndlLength;
-		}
-		else
-		{
-			unsigned indels = (unsigned)floor(pattern._currentErrorRate * ndlLength);
-			hit.bucketWidth = ndlLength + (indels << 1);
-			hit.hstkPos -= indels;
-		}
+        unsigned ndlLength = sequenceLength(hit.ndlSeqNo, host(pattern));
+
+        if (Pigeonhole<TSpec>::HAMMING_ONLY != 0)
+        {
+            hit.bucketWidth = ndlLength;
+        }
+        else
+        {
+            unsigned indels = (unsigned)floor(pattern._currentErrorRate * ndlLength);
+            hit.bucketWidth = ndlLength + (indels << 1);
+            hit.hstkPos -= indels;
+        }
         appendValue(finder.hits, hit);
     }
 
-	finder.curHit = begin(finder.hits, Standard());
-	finder.endHit = end(finder.hits, Standard());
+    finder.curHit = begin(finder.hits, Standard());
+    finder.endHit = end(finder.hits, Standard());
 
-	return !empty(finder.hits);
+    return !empty(finder.hits);
 }
 
 
 template <typename TIndex, typename TSpec>
-inline bool 
-empty(Pattern<TIndex, Pigeonhole<TSpec> > & me) 
+inline bool
+empty(Pattern<TIndex, Pigeonhole<TSpec> > & me)
 {
-	return me._currentErrorRate == -1;
+    return me._currentErrorRate == -1;
 }
 
 template <typename TIndex, typename TSpec>
-inline void 
-clear(Pattern<TIndex, Pigeonhole<TSpec> > & me) 
+inline void
+clear(Pattern<TIndex, Pigeonhole<TSpec> > & me)
 {
-	me.finderPosOffset = 0;
-	me.finderPosNextOffset = 0;
-	me.finderLength = 0;
-	me._currentErrorRate = -1;
-	clear(me.lastSeedDiag);
+    me.finderPosOffset = 0;
+    me.finderPosNextOffset = 0;
+    me.finderLength = 0;
+    me._currentErrorRate = -1;
+    clear(me.lastSeedDiag);
 }
 
 //____________________________________________________________________________
@@ -570,15 +626,15 @@ template <typename THaystack, typename TSpec>
 inline typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type
 position(Finder<THaystack, Pigeonhole<TSpec> > const & finder)
 {
-	typename Finder<THaystack, Pigeonhole<TSpec> >::TPigeonholeHit &hit = *finder.curHit;
-	return hit.hstkPos + hit.bucketWidth;
+    typename Finder<THaystack, Pigeonhole<TSpec> >::TPigeonholeHit &hit = *finder.curHit;
+    return hit.hstkPos + hit.bucketWidth;
 }
 
 template <typename THaystack, typename TSpec>
 inline typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type
 position(Finder<THaystack, Pigeonhole<TSpec> > & finder)
 {
-	return position(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
+    return position(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
 }
 
 //____________________________________________________________________________
@@ -587,17 +643,17 @@ template <typename TIndex, typename TSpec>
 inline typename SAValue<TIndex>::Type
 position(Pattern<TIndex, Pigeonhole<TSpec> > const & pattern)
 {
-	typedef typename Size<TIndex>::Type TSize;
+    typedef typename Size<TIndex>::Type TSize;
     typename SAValue<TIndex >::Type pos;
-	posLocalToX(pos, Pair<unsigned, TSize>(pattern.curSeqNo, length(needle(pattern))), stringSetLimits(host(pattern)));
-	return pos;
+    posLocalToX(pos, Pair<unsigned, TSize>(pattern.curSeqNo, length(needle(pattern))), stringSetLimits(host(pattern)));
+    return pos;
 }
 
 template <typename TIndex, typename TSpec>
 inline typename SAValue<TIndex>::Type
 position(Pattern<TIndex, Pigeonhole<TSpec> > & pattern)
 {
-	return position(const_cast<Pattern<TIndex, Pigeonhole<TSpec> > const &>(pattern));
+    return position(const_cast<Pattern<TIndex, Pigeonhole<TSpec> > const &>(pattern));
 }
 
 //____________________________________________________________________________
@@ -606,14 +662,14 @@ template <typename THaystack, typename TSpec>
 inline __int64
 beginPosition(Finder<THaystack, Pigeonhole<TSpec> > const & finder)
 {
-	return (*finder.curHit).hstkPos;
+    return (*finder.curHit).hstkPos;
 }
 
 template <typename THaystack, typename TSpec>
 inline __int64
 beginPosition(Finder<THaystack, Pigeonhole<TSpec> > & finder)
 {
-	return beginPosition(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
+    return beginPosition(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
 }
 
 //____________________________________________________________________________
@@ -623,15 +679,15 @@ inline typename SAValue<TIndex >::Type
 beginPosition(Pattern<TIndex, Pigeonhole<TSpec> > const & pattern)
 {
     typename SAValue<TIndex >::Type pos;
-	posLocalToX(pos, Pair<unsigned>(pattern.curSeqNo, 0), stringSetLimits(host(pattern)));
-	return pos;
+    posLocalToX(pos, Pair<unsigned>(pattern.curSeqNo, 0), stringSetLimits(host(pattern)));
+    return pos;
 }
 
 template <typename TIndex, typename TSpec>
 inline typename SAValue<TIndex>::Type
 beginPosition(Pattern<TIndex, Pigeonhole<TSpec> > & pattern)
 {
-	return beginPosition(const_cast<Pattern<TIndex, Pigeonhole<TSpec> > const &>(pattern));
+    return beginPosition(const_cast<Pattern<TIndex, Pigeonhole<TSpec> > const &>(pattern));
 }
 
 //____________________________________________________________________________
@@ -640,15 +696,15 @@ template <typename THaystack, typename TSpec>
 inline typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type
 endPosition(Finder<THaystack, Pigeonhole<TSpec> > const & finder)
 {
-	typename Finder<THaystack, Pigeonhole<TSpec> >::TPigeonholeHit &hit = *finder.curHit;
-	return hit.hstkPos + hit.bucketWidth;
+    typename Finder<THaystack, Pigeonhole<TSpec> >::TPigeonholeHit &hit = *finder.curHit;
+    return hit.hstkPos + hit.bucketWidth;
 }
 
 template <typename THaystack, typename TSpec>
 inline typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type
 endPosition(Finder<THaystack, Pigeonhole<TSpec> > & finder)
 {
-	return endPosition(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
+    return endPosition(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
 }
 
 //____________________________________________________________________________
@@ -657,66 +713,58 @@ template <typename TIndex, typename TSpec>
 inline typename SAValue<TIndex >::Type
 endPosition(Pattern<TIndex, Pigeonhole<TSpec> > const & pattern)
 {
-	typedef typename Size<TIndex>::Type TSize;
-	typename SAValue<TIndex >::Type pos;
-	posLocalToX(pos, Pair<unsigned, TSize>(pattern.curSeqNo, length(needle(pattern))), stringSetLimits(host(pattern)));
-	return pos;
+    typedef typename Size<TIndex>::Type TSize;
+    typename SAValue<TIndex >::Type pos;
+    posLocalToX(pos, Pair<unsigned, TSize>(pattern.curSeqNo, length(needle(pattern))), stringSetLimits(host(pattern)));
+    return pos;
 }
 
 template <typename TIndex, typename TSpec>
 inline typename SAValue<TIndex>::Type
 endPosition(Pattern<TIndex, Pigeonhole<TSpec> > & pattern)
 {
-	return endPosition(const_cast<Pattern<TIndex, Pigeonhole<TSpec> > const &>(pattern));
+    return endPosition(const_cast<Pattern<TIndex, Pigeonhole<TSpec> > const &>(pattern));
 }
 
-///.Function.positionRangeNoClip.param.finder.type:Spec.Pigeonhole
-///.Function.positionRangeNoClip.class:Spec.Pigeonhole
-///.Function.positionRangeNoClip.param.pattern.type:Spec.Pigeonhole
-
 template <typename THaystack, typename TSpec>
 inline Pair<typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type>
 positionRangeNoClip(Finder<THaystack, Pigeonhole<TSpec> > const & finder)
 {
-	typedef typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type TPosition;
-	typedef Pair<TPosition> TPair;
-	typename Finder<THaystack, Pigeonhole<TSpec> >::TPigeonholeHit &hit = *finder.curHit;
-	return TPair((TPosition)hit.hstkPos, (TPosition)(hit.hstkPos + hit.bucketWidth));
+    typedef typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type TPosition;
+    typedef Pair<TPosition> TPair;
+    typename Finder<THaystack, Pigeonhole<TSpec> >::TPigeonholeHit &hit = *finder.curHit;
+    return TPair((TPosition)hit.hstkPos, (TPosition)(hit.hstkPos + hit.bucketWidth));
 }
 
 template <typename THaystack, typename TSpec>
 inline Pair<typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type>
 positionRangeNoClip(Finder<THaystack, Pigeonhole<TSpec> > & finder)
 {
-	return positionRangeNoClip(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
+    return positionRangeNoClip(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
 }
 
-///.Function.positionRange.param.finder.type:Spec.Pigeonhole
-///.Function.positionRange.class:Spec.Pigeonhole
-///.Function.positionRange.param.pattern.type:Spec.Pigeonhole
-
 template <typename THaystack, typename TSpec>
 inline Pair<typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type>
 positionRange(Finder<THaystack, Pigeonhole<TSpec> > const & finder)
 {
-	typedef typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type TPosition;
-	typedef Pair<TPosition> TPair;
-	typename Finder<THaystack, Pigeonhole<TSpec> >::TPigeonholeHit &hit = *finder.curHit;
+    typedef typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type TPosition;
+    typedef Pair<TPosition> TPair;
+    typename Finder<THaystack, Pigeonhole<TSpec> >::TPigeonholeHit &hit = *finder.curHit;
 
-	__int64 hitBegin = hit.hstkPos;
-	__int64 hitEnd = hit.hstkPos + hit.bucketWidth;
-	__int64 textEnd = length(haystack(finder));
+    __int64 hitBegin = hit.hstkPos;
+    __int64 hitEnd = hit.hstkPos + hit.bucketWidth;
+    __int64 textEnd = length(haystack(finder));
 
-	if (hitBegin < 0) hitBegin = 0;
-	if (hitEnd > textEnd) hitEnd = textEnd;
-	return TPair((TPosition)hitBegin, (TPosition)hitEnd);
+    if (hitBegin < 0) hitBegin = 0;
+    if (hitEnd > textEnd) hitEnd = textEnd;
+    return TPair((TPosition)hitBegin, (TPosition)hitEnd);
 }
 
 template <typename THaystack, typename TSpec>
 inline Pair<typename Position<Finder<THaystack, Pigeonhole<TSpec> > >::Type>
 positionRange(Finder<THaystack, Pigeonhole<TSpec> > & finder)
 {
-	return positionRange(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
+    return positionRange(const_cast<Finder<THaystack, Pigeonhole<TSpec> > const &>(finder));
 }
 
 //____________________________________________________________________________
@@ -725,7 +773,7 @@ template <typename TIndex, typename TSpec>
 inline Pair<typename SAValue<TIndex>::Type>
 positionRange(Pattern<TIndex, Pigeonhole<TSpec> > & pattern)
 {
-	return Pair<typename SAValue<TIndex>::Type> (beginPosition(pattern), endPosition(pattern));
+    return Pair<typename SAValue<TIndex>::Type> (beginPosition(pattern), endPosition(pattern));
 }
 
 //____________________________________________________________________________
@@ -734,41 +782,38 @@ template <typename TPigeonholeHit, typename TText>
 inline typename Infix<TText>::Type
 pigeonholeInfixNoClip(TPigeonholeHit const &hit, TText &text)
 {
-	return infix(text, hit.hstkPos, hit.hstkPos + hit.bucketWidth);
+    return infix(text, hit.hstkPos, hit.hstkPos + hit.bucketWidth);
 }
 
 template <typename TPigeonholeHit, typename TText>
 inline typename Infix<TText>::Type
 pigeonholeInfix(TPigeonholeHit const &hit, TText &text)
 {
-	__int64 hitBegin = hit.hstkPos;
-	__int64 hitEnd = hit.hstkPos + hit.bucketWidth;
-	__int64 textEnd = length(text);
-
-	if (hitBegin < 0) hitBegin = 0;
-	if (hitEnd > textEnd) hitEnd = textEnd;
-	SEQAN_ASSERT_LEQ(hitBegin, hitEnd);
-	return infix(text, hitBegin, hitEnd);
+    __int64 hitBegin = hit.hstkPos;
+    __int64 hitEnd = hit.hstkPos + hit.bucketWidth;
+    __int64 textEnd = length(text);
+
+    if (hitBegin < 0) hitBegin = 0;
+    if (hitEnd > textEnd) hitEnd = textEnd;
+    SEQAN_ASSERT_LEQ(hitBegin, hitEnd);
+    return infix(text, hitBegin, hitEnd);
 }
 
 //____________________________________________________________________________
 
-///.Function.Finder#infix.param.finder.type:Spec.Pigeonhole
-///.Function.Finder#infix.class:Spec.Pigeonhole
-
 template <typename THaystack, typename TSpec>
 inline typename Infix<THaystack>::Type
 infix(Finder<THaystack, Pigeonhole<TSpec> > &finder)
 {
     typename Parameter_<THaystack>::Type tmpHaystack = haystack(finder);
-	return swiftInfix(*finder.curHit, tmpHaystack);
+    return swiftInfix(*finder.curHit, tmpHaystack);
 }
 
 template <typename THaystack, typename TSpec, typename TText>
 inline typename Infix<TText>::Type
 infix(Finder<THaystack, Pigeonhole<TSpec> > &finder, TText &text)
 {
-	return swiftInfix(*finder.curHit, text);
+    return swiftInfix(*finder.curHit, text);
 }
 
 //____________________________________________________________________________
@@ -777,14 +822,14 @@ template <typename THaystack, typename TSpec>
 inline typename Infix<THaystack>::Type
 infixNoClip(Finder<THaystack, Pigeonhole<TSpec> > &finder)
 {
-	return swiftInfixNoClip(*finder.curHit, haystack(finder));
+    return swiftInfixNoClip(*finder.curHit, haystack(finder));
 }
 
 template <typename THaystack, typename TSpec, typename TText>
 inline typename Infix<TText>::Type
 infixNoClip(Finder<THaystack, Pigeonhole<TSpec> > &finder, TText &text)
 {
-	return swiftInfixNoClip(*finder.curHit, text);
+    return swiftInfixNoClip(*finder.curHit, text);
 }
 
 //____________________________________________________________________________
@@ -794,296 +839,323 @@ inline typename Infix<TText>::Type
 infix(Pattern<TIndex, Pigeonhole<TSpec> > const & pattern, TText &text)
 {
     __int64 hitBegin = pattern.curBeginPos;
-	__int64 hitEnd = pattern.curEndPos;
-	__int64 textLength = sequenceLength(pattern.curSeqNo, needle(pattern));
+    __int64 hitEnd = pattern.curEndPos;
+    __int64 textLength = sequenceLength(pattern.curSeqNo, needle(pattern));
 
-	if (hitEnd > textLength) hitEnd = textLength;
+    if (hitEnd > textLength) hitEnd = textLength;
     if (hitBegin < 0) hitBegin = 0;
 
-	return infix(text, hitBegin, hitEnd);
+    return infix(text, hitBegin, hitEnd);
 }
 
 template <typename TIndex, typename TSpec>
 inline typename Infix< typename GetSequenceByNo< TIndex const >::Type >::Type
 infix(Pattern<TIndex, Pigeonhole<TSpec> > const & pattern)
 {
-	return infix(getSequenceByNo(pattern.curSeqNo, needle(pattern)), 0, sequenceLength(pattern.curSeqNo, needle(pattern)));
+    return infix(getSequenceByNo(pattern.curSeqNo, needle(pattern)), 0, sequenceLength(pattern.curSeqNo, needle(pattern)));
 }
 
 template <typename TIndex, typename TSpec>
 inline typename Infix< typename GetSequenceByNo< TIndex const >::Type >::Type
 infix(Pattern<TIndex, Pigeonhole<TSpec> > & pattern)
 {
-	return infix(const_cast<Pattern<TIndex, Pigeonhole<TSpec> > const &>(pattern));
+    return infix(const_cast<Pattern<TIndex, Pigeonhole<TSpec> > const &>(pattern));
 }
 
 //____________________________________________________________________________
 
 template <typename THaystack, typename TSpec>
-inline void 
+inline void
 _printDots(Finder<THaystack, Pigeonhole<TSpec> > &finder)
 {
-	while (finder.curPos >= finder.dotPos) 
-	{
-		finder.dotPos += 100000;
-		if (finder.dotPos >= finder.dotPos2)
-		{
-			::std::cerr << (finder.dotPos2 / 1000000) << "M" << ::std::flush;
-			finder.dotPos2 += 1000000;
-		} else
-			::std::cerr << "." << ::std::flush;
-	}
+    while (finder.curPos >= finder.dotPos)
+    {
+        finder.dotPos += 100000;
+        if (finder.dotPos >= finder.dotPos2)
+        {
+            std::cerr << (finder.dotPos2 / 1000000) << "M" << std::flush;
+            finder.dotPos2 += 1000000;
+        } else
+            std::cerr << "." << std::flush;
+    }
 }
 
 template <typename TFinder, typename TIndex, typename TSpec>
-inline bool 
+inline bool
 _nextNonRepeatRange(
-	TFinder &finder,
-	Pattern<TIndex, Pigeonhole<TSpec> > &pattern)
+    TFinder &finder,
+    Pattern<TIndex, Pigeonhole<TSpec> > &pattern)
 {
-	//typedef typename TFinder::TRepeat		TRepeat;
-	//typedef typename Value<TRepeat>::Type	TPos;
-
-	if (finder.curRepeat == finder.endRepeat) return false;
-
-	do 
-	{
-		finder.startPos = (*finder.curRepeat).endPosition;
-		if (++finder.curRepeat == finder.endRepeat) 
-		{
-			finder.endPos = length(host(finder));
-			if (finder.startPos + length(pattern.shape) > finder.endPos)
-				return false;
-			else
-				break;
-		} else
-			finder.endPos = (*finder.curRepeat).beginPosition;
-		// repeat until the shape fits in non-repeat range
-	} while (finder.startPos + length(pattern.shape) > finder.endPos);
-
-	finder.curPos = finder.startPos;
-	hostIterator(finder) = begin(host(finder)) + finder.startPos;
-	finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1);
-
-//	if (pattern.params.printDots)
-//		::std::cerr << ::std::endl << "  scan range (" << finder.startPos << ", " << finder.endPos << ") " << std::flush;
-
-	return true;
+    //typedef typename TFinder::TRepeat        TRepeat;
+    //typedef typename Value<TRepeat>::Type    TPos;
+
+    if (finder.curRepeat == finder.endRepeat) return false;
+
+    do
+    {
+        finder.startPos = (*finder.curRepeat).endPosition;
+        if (++finder.curRepeat == finder.endRepeat)
+        {
+            finder.endPos = length(host(finder));
+            if (finder.startPos + length(pattern.shape) > finder.endPos)
+                return false;
+            else
+                break;
+        } else
+            finder.endPos = (*finder.curRepeat).beginPosition;
+        // repeat until the shape fits in non-repeat range
+    } while (finder.startPos + length(pattern.shape) > finder.endPos);
+
+    finder.curPos = finder.startPos;
+    hostIterator(finder) = begin(host(finder)) + finder.startPos;
+    finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1);
+
+//    if (pattern.params.printDots)
+//        std::cerr << std::endl << "  scan range (" << finder.startPos << ", " << finder.endPos << ") " << std::flush;
+
+    return true;
 }
 
 template <typename TFinder, typename TIndex, typename TSpec>
-inline bool 
+inline bool
 _firstNonRepeatRange(
-	TFinder &finder,
-	Pattern<TIndex, Pigeonhole<TSpec> > &pattern)
+    TFinder &finder,
+    Pattern<TIndex, Pigeonhole<TSpec> > &pattern)
 {
-	//typedef typename TFinder::TRepeat		TRepeat;
-	//typedef typename Value<TRepeat>::Type	TPos;
+    //typedef typename TFinder::TRepeat        TRepeat;
+    //typedef typename Value<TRepeat>::Type    TPos;
 
-	finder.curRepeat = begin(finder.data_repeats, Standard());
-	finder.endRepeat = end(finder.data_repeats, Standard());
+    finder.curRepeat = begin(finder.data_repeats, Standard());
+    finder.endRepeat = end(finder.data_repeats, Standard());
 
-	if (finder.curRepeat == finder.endRepeat)
-		finder.endPos = length(host(finder));
-	else
-		finder.endPos = (*finder.curRepeat).beginPosition;
+    if (finder.curRepeat == finder.endRepeat)
+        finder.endPos = length(host(finder));
+    else
+        finder.endPos = (*finder.curRepeat).beginPosition;
 
-	if (length(pattern.shape) > finder.endPos)
-		return _nextNonRepeatRange(finder, pattern);
+    if (length(pattern.shape) > finder.endPos)
+        return _nextNonRepeatRange(finder, pattern);
 
-	finder.curPos = finder.startPos = 0;
-	hostIterator(finder) = begin(host(finder));
-	finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1);
+    finder.curPos = finder.startPos = 0;
+    hostIterator(finder) = begin(host(finder));
+    finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1);
 
-//	if (pattern.params.printDots)
-//		::std::cerr << ::std::endl << "  scan range (" << finder.startPos << ", " << finder.endPos << ") " << std::flush;
+//    if (pattern.params.printDots)
+//        std::cerr << std::endl << "  scan range (" << finder.startPos << ", " << finder.endPos << ") " << std::flush;
 
-	return true;
+    return true;
 }
 
 template <typename TFinder, typename TIndex, typename TSpec>
-inline void 
+inline void
 _copyPigeonholeHit(
-	TFinder &finder,
-	Pattern<TIndex, Pigeonhole<TSpec> > &pattern)
+    TFinder &finder,
+    Pattern<TIndex, Pigeonhole<TSpec> > &pattern)
 {
-	pattern.curSeqNo = (*finder.curHit).ndlSeqNo;
-	pattern.curBeginPos = 0;
-	pattern.curEndPos = length(indexText(needle(pattern))[pattern.curSeqNo]);
+    pattern.curSeqNo = (*finder.curHit).ndlSeqNo;
+    pattern.curBeginPos = 0;
+    pattern.curEndPos = length(indexText(needle(pattern))[pattern.curSeqNo]);
 }
 
 template <typename THaystack, typename TIndex, typename TSpec>
-inline bool 
+inline bool
 find(
-	Finder<THaystack, Pigeonhole<TSpec> > &finder,
-	Pattern<TIndex, Pigeonhole<TSpec> > &pattern, 
-	double errorRate)
+    Finder<THaystack, Pigeonhole<TSpec> > &finder,
+    Pattern<TIndex, Pigeonhole<TSpec> > &pattern,
+    double errorRate)
 {
-	if (empty(finder)) 
-	{
-		pattern.finderLength = length(container(finder));
-		_patternInit(pattern, errorRate);
-		_finderSetNonEmpty(finder);
-		finder.dotPos = 100000;
-		finder.dotPos2 = 10 * finder.dotPos;
-
-		if (!_firstNonRepeatRange(finder, pattern)) return false;
-		if (_pigeonholeProcessQGram(finder, pattern, hash(pattern.shape, hostIterator(hostIterator(finder)))))
-		{
-			_copyPigeonholeHit(finder, pattern);
-			return true;
-		}
-	} 
-	else
-	{
-		if (++finder.curHit < finder.endHit) 
-		{
-			_copyPigeonholeHit(finder, pattern);
-			return true;
-		}
-	}
-
-	// all previous matches reported -> search new ones
-	clear(finder.hits);
-
-	// are we at the end of the text?
-	if (atEnd(finder) && finder.curRepeat == finder.endRepeat) 
-	{
-		finder.curHit = finder.endHit;
-		return false;
-	}
-
-	do 
-	{
-		if (pattern.params.printDots) _printDots(finder);
-		if (atEnd(++finder)) 
-		{
-			if (!_nextNonRepeatRange(finder, pattern)) 
+    if (empty(finder))
+    {
+        pattern.finderLength = length(container(finder));
+        _patternInit(pattern, errorRate);
+        _finderSetNonEmpty(finder);
+        finder.dotPos = 100000;
+        finder.dotPos2 = 10 * finder.dotPos;
+
+        if (!_firstNonRepeatRange(finder, pattern)) return false;
+        if (_pigeonholeProcessQGram(finder, pattern, hash(pattern.shape, hostIterator(hostIterator(finder)))))
+        {
+            _copyPigeonholeHit(finder, pattern);
+            return true;
+        }
+    }
+    else
+    {
+        if (++finder.curHit < finder.endHit)
+        {
+            _copyPigeonholeHit(finder, pattern);
+            return true;
+        }
+    }
+
+    // all previous matches reported -> search new ones
+    clear(finder.hits);
+
+    // are we at the end of the text?
+    if (atEnd(finder) && finder.curRepeat == finder.endRepeat)
+    {
+        finder.curHit = finder.endHit;
+        return false;
+    }
+
+    do
+    {
+        if (pattern.params.printDots) _printDots(finder);
+        if (atEnd(++finder))
+        {
+            if (!_nextNonRepeatRange(finder, pattern))
                 return false;
-			hash(pattern.shape, hostIterator(hostIterator(finder)));
-		}
-		else
-		{
-			++finder.curPos;
-			hashNext(pattern.shape, hostIterator(hostIterator(finder)));
-		}
-		
-		if (_pigeonholeProcessQGram(finder, pattern, value(pattern.shape)))
-		{
-			_copyPigeonholeHit(finder, pattern);
-			return true;
-		}
-
-	} while (true);
+            hash(pattern.shape, hostIterator(hostIterator(finder)));
+        }
+        else
+        {
+            ++finder.curPos;
+            hashNext(pattern.shape, hostIterator(hostIterator(finder)));
+        }
+
+        if (_pigeonholeProcessQGram(finder, pattern, value(pattern.shape)))
+        {
+            _copyPigeonholeHit(finder, pattern);
+            return true;
+        }
+
+    } while (true);
 }
 
-/**
-.Function.windowFindBegin:
-..class:Spec.Pigeonhole
-..param.finder.type:Spec.Pigeonhole
-..param.pattern.type:Spec.Pigeonhole
-*/
+/*!
+ * @fn PigeonholeFinder#windowFindBegin
+ * @headerfile <seqan/index/find_pigeonhole.h>
+ *
+ * @brief Initializes the pattern. Sets the finder on the begin position.  Gets the first non-repeat range and sets it
+ * in the finder.  Used together with @link PigeonholeFinder#windowFindEnd @endlink.
+ *
+ * @signature windowFindBegin(finder, pattern, errorRate)
+ *
+ * @param[in,out] finder    The PigeonholeFinder to use.
+ * @param[in,out] pattern   The PigeonholePattern to use.
+ * @param[in]     errorRate Error rate that is allowed between reads and reference.  Should be the same in as in @link
+ *                          PigeonholeFinder#windowFindNext @endlink.  Types: <tt>double</tt>
+ *
+ * @see PigeonholeFinder#windowFindNext
+ * @see PigeonholeFinder#windowFindEnd
+ */
 
 template <typename THaystack, typename TIndex, typename TSpec>
-inline bool 
+inline bool
 windowFindBegin(
-	Finder<THaystack, Pigeonhole<TSpec> > &finder,
-	Pattern<TIndex, Pigeonhole<TSpec> > &pattern, 
-	double errorRate)
+    Finder<THaystack, Pigeonhole<TSpec> > &finder,
+    Pattern<TIndex, Pigeonhole<TSpec> > &pattern,
+    double errorRate)
 {
-	SEQAN_CHECKPOINT
-	
-	pattern.finderLength = pattern.maxSeqLen + length(container(finder));
-	_patternInit(pattern, errorRate);
-	_finderSetNonEmpty(finder);
-	finder.dotPos = 100000;
-	finder.dotPos2 = 10 * finder.dotPos;
+    SEQAN_CHECKPOINT
+
+    pattern.finderLength = pattern.maxSeqLen + length(container(finder));
+    _patternInit(pattern, errorRate);
+    _finderSetNonEmpty(finder);
+    finder.dotPos = 100000;
+    finder.dotPos2 = 10 * finder.dotPos;
     finder.windowStart = 0;
 
-	if (!_firstNonRepeatRange(finder, pattern)) return false;
-    
+    if (!_firstNonRepeatRange(finder, pattern)) return false;
+
     return true;
 }
 
 
-/**
-.Function.windowFindNext:
-..class:Spec.Pigeonhole
-..param.finder.type:Spec.Pigeonhole
-..param.pattern.type:Spec.Pigeonhole
-*/
+/*!
+ * @fn PigeonholeFinder#windowFindNext
+ * @headerfile <seqan/index/find_pigeonhol.h>
+ * @brief Searches over the next window with the finder.  The found hits can be retrieved with @link
+ *        PigeonholeFinder#getWindowFindHits @endlink Used together with @link PigeonholeFinder#windowFindBegin @endlink
+ *        and @link PigeonholeFinder#windowFindEnd @endlink.
+ *
+ * @signature bool windowFindNext(finder, pattern, finderWindowLength)
+ *
+ * @param[in,out] finder             The PigeonholeFinder to use.
+ * @param[in,out] pattern            The PigeonholePattern to use.
+ * @param[in]     finderWindowLength Number of bases that are scanned beginning from the position the finder is at.
+ *                                   Including bases that are marked as repeats and that are skipped. Types: <tt>unsigned</tt>.
+ *
+ * @return bool <tt>true</tt>, if there are bases that can be scanned, <tt>false</tt> otherwise.
+ *
+ * @see PigeonholeFinder#windowFindBegin
+ * @see PigeonholeFinder#windowFindEnd
+ * @see PigeonholeFinder#getWindowFindHits
+ */
+
+
 
 template <typename THaystack, typename TIndex, typename TSpec, typename TSize>
-inline bool 
+inline bool
 windowFindNext(
-	Finder<THaystack, Pigeonhole<TSpec> > &finder,
-	Pattern<TIndex, Pigeonhole<TSpec> > &pattern, 
-	TSize finderWindowLength)
+    Finder<THaystack, Pigeonhole<TSpec> > &finder,
+    Pattern<TIndex, Pigeonhole<TSpec> > &pattern,
+    TSize finderWindowLength)
 {
-	SEQAN_CHECKPOINT
-	
-	typedef typename Fibre<TIndex, QGramShape>::Type        TShape;
-	typedef Finder<THaystack, Pigeonhole<TSpec> >           TFinder;
-	typedef typename TFinder::THstkPos                      THstkPos;
-    
+    SEQAN_CHECKPOINT
+
+    typedef typename Fibre<TIndex, QGramShape>::Type        TShape;
+    typedef Finder<THaystack, Pigeonhole<TSpec> >           TFinder;
+    typedef typename TFinder::THstkPos                      THstkPos;
+
     typedef typename Fibre<TIndex, QGramSA>::Type           TSA;
     typedef typename Iterator<TSA const, Standard>::Type    TSAIter;
     typedef typename TFinder::TPigeonholeHit                THit;
 
-    TIndex const &index = host(pattern);	
+    TIndex const &index = host(pattern);
+
+    // all previous matches reported -> search new ones
+    clear(finder.hits);
 
-	// all previous matches reported -> search new ones
-	clear(finder.hits);
-    
-	THstkPos windowEnd = finder.windowStart + finderWindowLength;
+    THstkPos windowEnd = finder.windowStart + finderWindowLength;
     TSAIter saBegin = begin(indexSA(index), Standard());
     Pair<unsigned> ndlPos;
     THit hit;
-	double errorRate = pattern._currentErrorRate;
-	__int64 seqDisabled = pattern.seqDisabled;
-        
+    double errorRate = pattern._currentErrorRate;
+    __int64 seqDisabled = pattern.seqDisabled;
+
     // iterate over all non-repeat regions within the window
     for (; finder.curPos < windowEnd; )
     {
         THstkPos nonRepeatEnd = finder.endPos - length(pattern.shape) + 1;
         THstkPos localEnd = _min(windowEnd, nonRepeatEnd);
-        
+
         // filter a non-repeat region within the window
         if (finder.curPos < localEnd)
         {
             TShape &shape = pattern.shape;
-            
+
             hashInit(shape, hostIterator(hostIterator(finder)));
             for (; finder.curPos < localEnd; ++finder.curPos, ++finder)
             {
                 hashNext(shape, hostIterator(hostIterator(finder)));
-                
-                register unsigned bktNo = getBucket(index.bucketMap, value(shape));
-                register TSAIter occ = saBegin + indexDir(index)[bktNo];
-                register TSAIter occEnd = saBegin + indexDir(index)[bktNo + 1];
-
-				for(; occ != occEnd; ++occ) 
-				{
-					posLocalize(ndlPos, *occ, stringSetLimits(index));
-					hit.hstkPos = finder.curPos;
+
+                unsigned bktNo = getBucket(index.bucketMap, value(shape));
+                TSAIter occ = saBegin + indexDir(index)[bktNo];
+                TSAIter occEnd = saBegin + indexDir(index)[bktNo + 1];
+
+                for(; occ != occEnd; ++occ)
+                {
+                    posLocalize(ndlPos, *occ, stringSetLimits(index));
+                    hit.hstkPos = finder.curPos;
                     hit.hstkPos -= getSeqOffset(ndlPos);                    // bucket begin in haystack
-					hit.ndlSeqNo = getSeqNo(ndlPos);						// needle seq. number
-
-					if (Pigeonhole<TSpec>::ONE_PER_DIAGONAL)
-					{
-						register __int64 lastDiag = pattern.lastSeedDiag[hit.ndlSeqNo];
-						if (lastDiag == seqDisabled) continue;
-						
-						register __int64 diag = hit.hstkPos + (__int64)pattern.finderPosOffset;
-						if (lastDiag == diag)
-						{
-//							std::cout<<"double hit"<<std::endl;
-							continue;
-						}
-						pattern.lastSeedDiag[hit.ndlSeqNo] = diag;
-					}
+                    hit.ndlSeqNo = getSeqNo(ndlPos);                        // needle seq. number
+
+                    if (Pigeonhole<TSpec>::ONE_PER_DIAGONAL)
+                    {
+                        __int64 lastDiag = pattern.lastSeedDiag[hit.ndlSeqNo];
+                        if (lastDiag == seqDisabled) continue;
+
+                        __int64 diag = hit.hstkPos + (__int64)pattern.finderPosOffset;
+                        if (lastDiag == diag)
+                        {
+//                            std::cout<<"double hit"<<std::endl;
+                            continue;
+                        }
+                        pattern.lastSeedDiag[hit.ndlSeqNo] = diag;
+                    }
 //                     std::cout<<"hit at:\thpos="<<finder.curPos<<"\tnpos="<<getSeqOffset(ndlPos)<<"\treadNo="<<hit.ndlSeqNo<<"\thash="<<value(shape)<<std::endl;
-					unsigned ndlLength = sequenceLength(hit.ndlSeqNo, host(pattern));
+                    unsigned ndlLength = sequenceLength(hit.ndlSeqNo, host(pattern));
                     if (Pigeonhole<TSpec>::HAMMING_ONLY != 0)
                     {
                         hit.bucketWidth = ndlLength;
@@ -1094,13 +1166,13 @@ windowFindNext(
                         hit.bucketWidth = ndlLength + (indels << 1);
                         hit.hstkPos -= indels;
                     }
-					appendValue(finder.hits, hit);
-				}
+                    appendValue(finder.hits, hit);
+                }
             }
         }
-        
+
         if (pattern.params.printDots) _printDots(finder);
-        
+
         if (finder.curPos >= nonRepeatEnd)
             if (!_nextNonRepeatRange(finder, pattern))
             {
@@ -1109,47 +1181,80 @@ windowFindNext(
             }
     }
     finder.windowStart = windowEnd;
-	return true;
+    return true;
 }
 
-/**
-.Function.windowFindEnd:
-..class:Spec.Pigeonhole
-..param.finder.type:Spec.Pigeonhole
-..param.pattern.type:Spec.Pigeonhole
-*/
+
+/*!
+ * @fn PigeonholeFinder#windowFindEnd
+ * @headerfile <seqan/index/find_pigeonhole.h>
+ * @brief Flushes the pattern.  Used together with @link PigeonholeFinder#windowFindBegin @endlink and @link
+ *        PigeonholeFinder#windowFindNext @endlink.
+ *
+ * @signature void windowFindEnd(finder, pattern);
+ *
+ * @param[in,out] pattern A pattern with window interface.
+ * @param[in,out] finder  A finder with window interface. Types: @link PigeonholeFinder @endlink
+ *
+ * @see PigeonholeFinder#windowFindBegin
+ * @see PigeonholeFinder#windowFindNext
+ */
+
 
 template <typename THaystack, typename TIndex, typename TSpec>
-inline void 
+inline void
 windowFindEnd(
-	Finder<THaystack, Pigeonhole<TSpec> > &,
-	Pattern<TIndex, Pigeonhole<TSpec> > &)
+    Finder<THaystack, Pigeonhole<TSpec> > &,
+    Pattern<TIndex, Pigeonhole<TSpec> > &)
 {
 }
 
-///.Function.getWindowFindHits.param.finder.type:Spec.Pigeonhole
+/*!
+ * @fn PigeonholeFinder#getWindowFindHits
+ * @headerfile <seqan/index/find_pigeonhole.h>
+ * @brief Returns the string of hits from the finder.
+ *
+ * @signature THitString getWindowFindHits(finder);
+ *
+ * @param[in] finder     A PigeonFinder.
+ * @return    THitString @link String @endlink of Hits, see @link PigeonholeFinder::THitString @endlink.
+ *
+ * @see PigeonholeFinder#windowFindNext
+ */
+
+
 
 template <typename THaystack, typename TSpec>
 inline typename Finder<THaystack, Pigeonhole<TSpec> >::THitString &
 getWindowFindHits(Finder<THaystack, Pigeonhole<TSpec> > &finder)
 {
-	SEQAN_CHECKPOINT
-	
-	return finder.hits;
+    SEQAN_CHECKPOINT
+
+    return finder.hits;
 }
 
-///.Function.getMaxDeviationOfOrder.param.pattern.type:Spec.Pigeonhole
+/*!
+ * @fn PigeonholePattern#getMaxDeviationOfOrder
+ * @headerfile <seqan/index/find_pigeonhole.h>
+ * @brief Returns the maximal out-of-order distance of adjacent hits.
+ *
+ * @signature TSize getMaxDeviationOfOrder(pattern);
+ *
+ * @param[in] pattern A PigeonholeFinder.
+ * @return    TSize   Returns the maximal distance two adjacent hits can have which are not in increasing order.
+ *                    <tt>TSize</tt> is the size type of the underlying index.
+ */
 
 template <typename TIndex, typename TSpec>
 inline typename Size<TIndex>::Type
 getMaxDeviationOfOrder(Pattern<TIndex, Pigeonhole<TSpec> > &pattern)
 {
-	SEQAN_CHECKPOINT;
-   
-	return (pattern.maxSeqLen <= length(indexShape(host(pattern))))? 0: pattern.maxSeqLen - length(indexShape(host(pattern)));
+    SEQAN_CHECKPOINT;
+
+    return (pattern.maxSeqLen <= length(indexShape(host(pattern))))? 0: pattern.maxSeqLen - length(indexShape(host(pattern)));
 }
 
 }// namespace seqan
 
-#endif //#ifndef CORE_INCLUDE_SEQAN_FIND_PIGEONHOLE_H_
+#endif //#ifndef INCLUDE_SEQAN_FIND_PIGEONHOLE_H_
 
diff --git a/seqan/index/find_quasar.h b/seqan/index/find_quasar.h
index a45d7a7..1265abd 100644
--- a/seqan/index/find_quasar.h
+++ b/seqan/index/find_quasar.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -53,73 +53,48 @@ template <typename TNeedle>
 class Pattern<TNeedle, Quasar> {
 //____________________________________________________________________________
 private:
-	Pattern(Pattern const& other);
-	Pattern const& operator=(Pattern const & other);
+    Pattern(Pattern const& other);
+    Pattern const& operator=(Pattern const & other);
 
 //____________________________________________________________________________
 public:
-	Holder<TNeedle> data_host;
+    Holder<TNeedle> data_host;
 
 
 //____________________________________________________________________________
 
-	Pattern() {	
-	}
-
-	template <typename TNeedle2>
-	Pattern(TNeedle2 const & ndl)
-	{
+    Pattern() {
+    }
+
+#ifdef SEQAN_CXX11_STANDARD
+    template <typename TNeedle2>
+    Pattern(TNeedle2 && ndl,
+            SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
+    {
+        ignoreUnusedVariableWarning(dummy);
+        setHost(*this, std::forward<TNeedle2>(ndl));
+    }
+#else
+    template <typename TNeedle2>
+    Pattern(TNeedle2 const & ndl)
+    {
 SEQAN_CHECKPOINT
-		setHost(*this, ndl);
-	}
-
-	~Pattern() {
-		SEQAN_CHECKPOINT
-	}
+        setHost(*this, ndl);
+    }
+#endif  // SEQAN_CXX11_STANDARD
 //____________________________________________________________________________
 };
 
-//////////////////////////////////////////////////////////////////////////////
-// Host Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, Quasar> >
-{
-	typedef TNeedle Type;
-};
-
-template <typename TNeedle>
-struct Host< Pattern<TNeedle, Quasar> const>
-{
-	typedef TNeedle const Type;
-};
-
 
 //////////////////////////////////////////////////////////////////////////////
 // Functions
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost (Pattern<TNeedle, Quasar> & me, TNeedle2 const& needle) 
-{
-	SEQAN_CHECKPOINT
-	setValue(me.data_host, needle);
-}
-
-template <typename TNeedle, typename TNeedle2>
-inline void 
-setHost (Pattern<TNeedle, Quasar> & me, TNeedle2 & needle)
-{
-	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
-}
-
 //____________________________________________________________________________
 
 
 template <typename TNeedle>
-inline void _patternInit (Pattern<TNeedle, Quasar> & /*me*/) 
+inline void _patternInit (Pattern<TNeedle, Quasar> & /*me*/)
 {
 SEQAN_CHECKPOINT
 }
@@ -127,39 +102,21 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, Quasar>const>::Type & 
-host(Pattern<TNeedle, Quasar> & me)
-{
-SEQAN_CHECKPOINT
-	return value(me.data_host);
-}
 
-template <typename TNeedle>
-inline typename Host<Pattern<TNeedle, Quasar>const>::Type & 
-host(Pattern<TNeedle, Quasar> const & me)
+template <typename TFinder, typename TNeedle>
+inline bool
+find(TFinder & finder, Pattern<TNeedle, Quasar> & me)
 {
-SEQAN_CHECKPOINT
-	return value(me.data_host);
-}
+    SEQAN_CHECKPOINT
 
-//____________________________________________________________________________
+    if (empty(finder)) {
+        _patternInit(me);
+        _finderSetNonEmpty(finder);
+    } else {
+        finder+=4;
+    }
 
-
-template <typename TFinder, typename TNeedle>
-inline bool 
-find(TFinder & finder, Pattern<TNeedle, Quasar> & me) 
-{
-	SEQAN_CHECKPOINT
-	
-	if (empty(finder)) {
-		_patternInit(me);
-		_finderSetNonEmpty(finder);
-	} else {
-		finder+=4;
-	}
-
-	return true;
+    return true;
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/index/find_swift.h b/seqan/index/find_swift.h
index 130e6b9..68035fc 100644
--- a/seqan/index/find_swift.h
+++ b/seqan/index/find_swift.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,125 +46,98 @@ namespace SEQAN_NAMESPACE_MAIN
 
 // TODO(bkehr): Is this documentatin right? Should the Specializations be Tags?
 // weese: of minimal length?
-/**
-.Spec.Swift:
-..summary:Provides a fast filter alogrithm that guarantees to find all regions overlapping with potential \epsilon-matches.
-An \epsilon-match is a matching region of minimal length and an error rate of at most \epsilon.
-..general:Class.Pattern
-..general:Class.Finder
-..cat:Searching
-..signature:Finder<THaystack, Swift<TSpec> >
-..signature:Pattern<TIndex, Swift<TSpec> >
-..param.THaystack: A haystack type.
-...type:Class.Index
-...type:Class.String
-...type:Class.StringSet
-..param.TIndex: A q-gram index of needle(s).
-...type:Spec.IndexQGram
-..param.TSpec: Specifies the type of Swift filter.
-..include:seqan/index.h
-..remarks:
-The @Class.Pattern@ must be a q-gram index over multiple patterns. The allowed error rate must be given when @Function.find@ or @Function.windowFindBegin@ is called.
-*/
-
 /*!
- * @class Swift
- * 
+ * @class SwiftPattern
  * @extends Pattern
+ * @headerfile <seqan/index.h>
+ * @brief Pattern for SWIFT search, must be used together with @link SwiftFinder @endlink.
+ *
+ * @signature template <typename TIndex, typename TSpec>
+ *            class Pattern<TIndex, Swift<TSpec> >;
+ *
+ * @tparam TSpec  Specifies the type of Swift filter.
+ * @tparam TIndex A q-gram index of needle(s).  Types: @link IndexQGram @endlink
+ *
+ * The @link Pattern @endlink must be a @link IndexQGram @endlink over multiple patterns.  The allowed error rate must
+ * be given when @link Finder#find @endlink or @link SwiftFinder#windowFindBegin @endlink is called.
+ *
+ * Provides a fast filter alogrithm that guarantees to find all regions overlapping with potential &epsilon;-matches.
+ * An &epsilon;-match is a matching region of minimal length and an error rate of at most &epsilon;.
+ *
+ * @see SwiftFinder
+ *
+ * @var SwiftParameters SwiftPattern::parameters;
+ * @brief The SWIFT parameters to use for configuration.
+ */
+
+/*!
+ * @class SwiftFinder
  * @extends Finder
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Provides a fast filter alogrithm that guarantees to find all regions overlapping with potential
- *        \epsilon-matches. An \epsilon-match is a matching region of minimal length and an error rate of at most
- *        \epsilon.
- * 
- * @signature Finder<THaystack, Swift<TSpec> >
- * @signature Pattern<TIndex, Swift<TSpec> >
- * 
- * @tparam TSpec Specifies the type of Swift filter. Types: @link SwiftLocal @endlink, @link SwiftSemiGlobal @endlink
- * @tparam TIndex A q-gram index of needle(s). Types: @link IndexQGram @endlink
- * @tparam THaystack A haystack type. Types: @link Index @endlink, @link String @endlink, @link StringSet @endlink
- * 
- * @section Remarks
- * 
- * The @link Pattern @endlink must be a @link IndexQGram @endlink over multiple patterns. The allowed error rate must
- * be given when @link Finder#find @endlink or @link Swift#windowFindBegin @endlink is called.
+ * @headerfile <seqan/index.h>
+ * @brief Finder for SWIFT search, must be used together with @link SwiftPattern @endlink.
+ *
+ * @signature template <typename THaystack, typename TSpec>
+ *            class Finder<THaystack, Swift<TSpec> >;
+ *
+ * @tparam TSpec     Specifies the type of Swift filter.
+ * @tparam THaystack A haystack type.  Types: @link Index @endlink, @link String @endlink, @link StringSet @endlink.
+ *
+ * See @link SwiftPattern @endlink for an overview of the SWIFT algorithm.
+ *
+ * @see SwiftPattern
  */
 
-///.Class.Pattern.param.TSpec.type:Spec.Swift
-///.Class.Finder.param.TSpec.type:Spec.Swift
-
-/**
-.Spec.SwiftLocal:
-..summary:The specialization for the general swift filter that finds epsilon matches between haystack and needle.
-..general:Spec.Swift
-..cat:Searching
-..signature:Finder<THaystack, Swift<SwiftLocal> >
-..signature:Pattern<TIndex, Swift<SwiftLocal> >
-..param.THaystack: A haystack type.
-...type:Class.Index
-...type:Class.String
-...type:Class.StringSet
-..param.TIndex: A q-gram index of needle(s).
-...type:Spec.IndexQGram
-..include:seqan/index.h
-*/
+/*!
+ * @class SwiftLocalPattern
+ * @extends SwiftPattern
+ * @headerfile <seqan/index.h>
+ *
+ * @brief The specialization for the general SWIFT filter that finds &epsilon;-matches between haystack and needle.
+ *
+ * @signature template <typename THaystack>
+ *            class Finder<THaystack, Swift<SwiftLocal> >;
+ *
+ * @tparam THaystack A haystack type. Types: @link Index @endlink, @link String @endlink, @link StringSet @endlink.
+ */
 
 /*!
- * @class SwiftLocal
- * 
- * @extends Swift
- * 
- * @headerfile seqan/index.h
- * 
- * @brief The specialization for the general swift filter that finds epsilon matches between haystack and needle.
- * 
- * @signature Finder<THaystack, Swift<SwiftLocal> >
- * @signature Pattern<TIndex, Swift<SwiftLocal> >
- * 
- * @tparam TIndex A q-gram index of needle(s). Types: @link IndexQGram @endlink
- * @tparam THaystack A haystack type. Types: @link Index @endlink, @link String @endlink, @link StringSet @endlink
+ * @class SwiftLocalFinder
+ * @extends SwiftFinder
+ * @headerfile <seqan/index.h>
+ * @brief The specialization for the general SWIFT filter that finds &epsilon;-matches between haystack and needle.
+ *
+ * @signature template <typename THaystack>
+ *            class Finder<THaystack, Swift<SwiftLocal> >;
+ *
+ * @tparam THaystack A haystack type. Types: @link Index @endlink, @link String @endlink, @link StringSet @endlink.
  */
 
-///.Spec.Swift.param.TSpec.type:Spec.SwiftLocal
-
-/**
-.Spec.SwiftSemiGlobal:
-..summary:The specialization for the semi-global swift filter that finds regions of the haystack where a needle matches with an error rate less than \epsilon.
-..general:Spec.Swift
-..cat:Searching
-..signature:Finder<THaystack, Swift<SwiftSemiGlobal> >
-..signature:Pattern<TIndex, Swift<SwiftSemiGlobal> >
-..param.THaystack: A haystack type.
-...type:Class.Index
-...type:Class.String
-...type:Class.StringSet
-..param.TIndex: A q-gram index of needle(s).
-...type:Spec.IndexQGram
-..include:seqan/index.h
-*/
+/*!
+ * @class SwiftSemiGlobalPattern
+ * @extends SwiftPattern
+ * @headerfile <seqan/index.h>
+ * @brief The specialization for the semi-global swift filter that finds regions of the haystack where a needle matches
+ *        with an error rate less than \epsilon.
+ *
+ * @signature template <typename TIndex>
+ *            class Pattern<TIndex, Swift<SwiftSemiGlobal> >;
+ *
+ * @tparam TIndex A @link IndexQGram q-gram index @endlink of needle(s).
+ */
 
 /*!
- * @class SwiftSemiGlobal
- * 
- * @extends Swift
- * 
- * @headerfile seqan/index.h
- * 
- * @brief The specialization for the semi-global swift filter that finds regions
- *        of the haystack where a needle matches with an error rate less than
- *        \epsilon.
- * 
- * @signature Finder<THaystack, Swift<SwiftSemiGlobal> >
- * @signature Pattern<TIndex, Swift<SwiftSemiGlobal> >
- * 
- * @tparam TIndex A q-gram index of needle(s). Types: @link IndexQGram @endlink
+ * @class SwiftSemiGlobalFinder
+ * @extends SwiftFinder
+ * @headerfile <seqan/index.h>
+ * @brief The specialization for the semi-global swift filter that finds regions of the haystack where a needle matches
+ *        with an error rate less than \epsilon.
+ *
+ * @signature template <typename THaystack>
+ *            class Finder<THaystack, Swift<SwiftSemiGlobal> >;
+ *
  * @tparam THaystack A haystack type. Types: @link Index @endlink, @link String @endlink, @link StringSet @endlink
  */
 
-///.Spec.Swift.param.TSpec.type:Spec.SwiftSemiGlobal
-
 template < typename TObject, typename TSpec > class Index;
 template < typename TObject > struct SAValue;
 
@@ -209,25 +182,61 @@ struct Swift<SwiftLocal> {
     enum { PARAMS_BY_LENGTH = 0 };  // params are determined by seq.no.
 };
 
-struct SwiftParameters {
+/*!
+ * @class SwiftParameters
+ * @headerfile <seqan/index.h>
+ * @brief Parameters for the SWIFT algorithm.
+ *
+ * @signature struct SwiftParameters;
+ *
+ * @see SwiftPattern
+ *
+ *
+ * @fn SwiftParameters::SwiftParameters
+ * @brief Default constructor.
+ *
+ * @signature SwiftParameters::SwiftParameters();
+ *
+ * Initializes all member variables, default values are given in the variable documentation.
+ *
+ *
+ * @var int SwiftParameters::minThreshold;
+ * @brief Minimal threshold to use initially, defaults to <tt>1</tt>.
+ *
+ * @var int SwiftParameters::minLog2Delta;
+ * @brief Minimal delta to use, defaults to <tt>16</tt>.
+ *
+ * @var int SwiftParameters::tabooLength;
+ * @brief Taboo length to use, defaults to <tt>1</tt>.
+ *
+ * @var bool SwiftParameters::printDots;
+ * @brief Whether to print dots for the scanning progress, defaults to <tt>false</tt>.
+ *
+ * @var bool SwiftParameters::debug;
+ * @brief Whether to print debug information, defaults to <tt>false</tt>.
+ */
+
+struct SwiftParameters
+{
     int minThreshold;
     int minLog2Delta;
     int tabooLength;
     bool printDots;
     bool debug;
 
-    SwiftParameters():
+    SwiftParameters() :
         minThreshold(1),        // set minimal threshold to 1
         minLog2Delta(4),        // set minimal delta to 16
         tabooLength(1),         // minimal genomic distance between q-gram hits
         printDots(false),       // print a . for every 100kbps mapped genome
-        debug(false) {}
+        debug(false)
+    {}
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
     template <typename TSpec, typename TSize_, typename TShortSize_ = unsigned short>
-    struct SwiftBucket_ 
+    struct SwiftBucket_
     {
         typedef TSize_          TSize;
         typedef TShortSize_ TShortSize;
@@ -257,7 +266,7 @@ struct SwiftParameters {
     };
 
     template <typename TSpec, typename TSize_, typename TShortSize_ = unsigned short>
-    struct SwiftBucketParams_ 
+    struct SwiftBucketParams_
     {
         typedef TSize_          TSize;
         typedef TShortSize_     TShortSize;
@@ -291,9 +300,9 @@ struct SwiftParameters {
 
 
     template <typename THstkPos>
-    struct SwiftHit_ 
+    struct SwiftHit_
     {
-        THstkPos    hstkPos;            // parallelogram begin in haystack 
+        THstkPos    hstkPos;            // parallelogram begin in haystack
         unsigned    ndlSeqNo;           // needle sequence number
         THstkPos    ndlPos;             // begin position of hit in needle
         unsigned    bucketWidth;        // (non-diagonal) bucket width (hitLengthNeedle + delta + overlap (for diagonals))
@@ -303,11 +312,11 @@ struct SwiftParameters {
     template <typename THstkPos>
     struct SwiftHitSemiGlobal_
     {
-        THstkPos    hstkPos;            // parallelogram begin in haystack 
+        THstkPos    hstkPos;            // parallelogram begin in haystack
         unsigned    ndlSeqNo;           // needle sequence number
         unsigned    bucketWidth;        // (non-diagonal) bucket width (bktHeight + delta + overlap (for diagonals))
     };
-    
+
 
     template <typename TFinder, typename TPattern = void>
     struct FindResult
@@ -319,24 +328,31 @@ struct SwiftParameters {
         typedef String<typename FindResult<TFinder, TPattern>::Type> Type;
     };
 
-    
-    
+
+
     template <typename THaystack, typename TPattern, typename TSwiftSpec>
     struct FindResult<Finder<THaystack, Swift<TSwiftSpec> >, TPattern>
     {
         typedef SwiftHit_<__int64> Type;
     };
-    
+
     template <typename THaystack, typename TPattern, typename TSpec>
     struct FindResult<Finder<THaystack, Swift<Tag<SwiftSemiGlobal_<TSpec> > > >, TPattern>
     {
         typedef SwiftHitSemiGlobal_<__int64> Type;
     };
-    
+
 
 //____________________________________________________________________________
 
 
+/*!
+ * @typedef SwiftFinder::THitString
+ * @brief The type to use for the hit string returned in @link SwiftFinder#getWindowFindHits @endlink.
+ *
+ * @signature typedef (...) SwiftFinder::THitString;
+ */
+
     template <typename THaystack, typename TSpec>
     class Finder<THaystack, Swift<TSpec> >
     {
@@ -363,30 +379,36 @@ struct SwiftParameters {
         TRepeatString   data_repeats;
         TRepeatIterator curRepeat, endRepeat;
 
-        Finder():
-            _needReinit(true) { }
+        Finder() :
+            data_iterator(), haystackEnd(), _needReinit(true), curHit(), endHit(),
+            startPos(), curPos(), endPos(), windowStart(), dotPos(), dotPos2(),
+            curRepeat(), endRepeat()
+        {}
 
-        Finder(THaystack &haystack):
-            data_iterator(begin(haystack, Rooted())),
-            _needReinit(true) { }
+        Finder(THaystack & haystack) :
+            data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(),
+            startPos(), curPos(), endPos(), windowStart(), dotPos(), dotPos2(), curRepeat(), endRepeat()
+        {}
 
         template <typename TRepeatSize, typename TPeriodSize>
-        Finder(THaystack &haystack, TRepeatSize minRepeatLen, TPeriodSize maxPeriod):
-            data_iterator(begin(haystack, Rooted())),
-            _needReinit(true) 
+        Finder(THaystack &haystack, TRepeatSize minRepeatLen, TPeriodSize maxPeriod) :
+            data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(),
+            startPos(), curPos(), endPos(), windowStart(), dotPos(), dotPos2(), curRepeat(), endRepeat()
         {
             findRepeats(data_repeats, haystack, minRepeatLen, maxPeriod);
         }
 
-        Finder(TIterator &iter):
-            data_iterator(iter),
-            _needReinit(true) { }
+        Finder(TIterator &iter) :
+            data_iterator(iter), haystackEnd(), _needReinit(true), curHit(), endHit(),
+            startPos(), curPos(), endPos(), windowStart(), dotPos(), dotPos2(), curRepeat(), endRepeat()
+        {}
 
-        Finder(TIterator const &iter):
-            data_iterator(iter),
-            _needReinit(true) { }
+        Finder(TIterator const & iter):
+            data_iterator(iter), haystackEnd(), _needReinit(true), curHit(), endHit(),
+            startPos(), curPos(), endPos(), windowStart(), dotPos(), dotPos2(), curRepeat(), endRepeat()
+        {}
 
-        Finder(Finder const &orig):
+        Finder(Finder const & orig):
             data_iterator(orig.data_iterator),
             haystackEnd(orig.haystackEnd),
             _needReinit(orig._needReinit),
@@ -405,15 +427,15 @@ struct SwiftParameters {
             endRepeat = end(data_repeats, Standard());
         }
 
-        inline typename Reference<TIterator>::Type 
+        inline typename Reference<TIterator>::Type
         operator* () { return value(hostIterator(*this)); }
 
-        inline typename Reference<TIterator const>::Type 
+        inline typename Reference<TIterator const>::Type
         operator* () const { return value(hostIterator(*this)); }
 
         operator TIterator () const { return data_iterator; }
-        
-        Finder & operator = (Finder const &orig) 
+
+        Finder & operator = (Finder const &orig)
         {
             data_iterator = orig.data_iterator;
             haystackEnd = orig.haystackEnd;
@@ -464,7 +486,7 @@ struct SwiftParameters {
         Finder(Finder const &orig):
             in(orig.in),
             hits(orig.hits),
-            _needReinit(orig._needReinit) 
+            _needReinit(orig._needReinit)
         {
             curHit = begin(hits, Standard()) + (orig.curHit - begin(orig.hits, Standard()));
             endHit = end(hits, Standard());
@@ -474,7 +496,7 @@ struct SwiftParameters {
 
 //____________________________________________________________________________
 
-    
+
     template <typename THaystack, typename TSpec>
     inline bool
     atEnd(Finder<THaystack, Swift<TSpec> > & me)
@@ -502,13 +524,13 @@ struct SwiftParameters {
         typedef typename Fibre<TIndex, Tag<FibreSA_> const >::Type      TSA;
         typedef typename Fibre<TIndex, Tag<Fibre_Shape_> const >::Type  TShape;
         typedef typename Iterator<TSA const, Standard>::Type            TIterator;
-        
+
         typedef SwiftBucket_<TSpec, TSize, TShortSize>                  TBucket;
         typedef String<TBucket>                                         TBucketString;
         typedef SwiftBucketParams_<TSpec, TSize, TShortSize>            TBucketParams;
         typedef String<TBucketParams>                                   TBucketParamsString;
         typedef String<Pair<unsigned> >                                 TVerifyList;
-        
+
         TShape                  shape;
         TBucketString           buckets;
         TBucketParamsString     bucketParams;
@@ -520,50 +542,52 @@ struct SwiftParameters {
         TSize                   finderPosNextOffset;                    // type TSize of TBucket
         __int64                 finderLength;
         __int64                 maxPatternLength;
-        
+
         double                  _currentErrorRate;
         int                     _currentMinLengthForAll;
 
         Holder<TIndex>  data_host;
 
-        Pattern() 
+        Pattern()
         {
             clear(*this);
         }
-        Pattern(TIndex &_index): data_host(_index) 
+
+        Pattern(TIndex &_index): data_host(_index)
         {
             clear(*this);
         }
+
         Pattern(TIndex const &_index): data_host(_index)
         {
             clear(*this);
         }
     };
-    
+
 //____________________________________________________________________________
 
 
 template <typename TSpec_, typename TSize, typename TShortSize>
 inline void _printSwiftParams(SwiftBucketParams_<TSpec_, TSize, TShortSize > &bucketParams)
 {
-    ::std::cout << "  firstBucket: " << bucketParams.firstBucket << ::std::endl;
-    ::std::cout << "  reuseMask:   " << bucketParams.reuseMask << ::std::endl;
-    ::std::cout << "  distanceCut: " << bucketParams.distanceCut << ::std::endl;
-    ::std::cout << "  delta:       " << bucketParams.delta << ::std::endl;
-    ::std::cout << "  threshold:   " << bucketParams.threshold << ::std::endl;
-    ::std::cout << "  overlap:     " << bucketParams.overlap << ::std::endl;
-    ::std::cout << "  logDelta:    " << (int)bucketParams.logDelta << ::std::endl << ::std::endl;
+    std::cout << "  firstBucket: " << bucketParams.firstBucket << std::endl;
+    std::cout << "  reuseMask:   " << bucketParams.reuseMask << std::endl;
+    std::cout << "  distanceCut: " << bucketParams.distanceCut << std::endl;
+    std::cout << "  delta:       " << bucketParams.delta << std::endl;
+    std::cout << "  threshold:   " << bucketParams.threshold << std::endl;
+    std::cout << "  overlap:     " << bucketParams.overlap << std::endl;
+    std::cout << "  logDelta:    " << (int)bucketParams.logDelta << std::endl << std::endl;
 }
 
 template <typename TSpec_, typename TSize, typename TShortSize>
 inline void _printSwiftParams(SwiftBucketParams_<Tag<SwiftSemiGlobal_<TSpec_> >, TSize, TShortSize > &bucketParams)
 {
-    ::std::cout << "  firstBucket: " << bucketParams.firstBucket << ::std::endl;
-    ::std::cout << "  reuseMask:   " << bucketParams.reuseMask << ::std::endl;
-    ::std::cout << "  delta:       " << bucketParams.delta << ::std::endl;
-    ::std::cout << "  threshold:   " << bucketParams.threshold << ::std::endl;
-    ::std::cout << "  overlap:     " << bucketParams.overlap << ::std::endl;
-    ::std::cout << "  logDelta:    " << (int)bucketParams.logDelta << ::std::endl << ::std::endl;
+    std::cout << "  firstBucket: " << bucketParams.firstBucket << std::endl;
+    std::cout << "  reuseMask:   " << bucketParams.reuseMask << std::endl;
+    std::cout << "  delta:       " << bucketParams.delta << std::endl;
+    std::cout << "  threshold:   " << bucketParams.threshold << std::endl;
+    std::cout << "  overlap:     " << bucketParams.overlap << std::endl;
+    std::cout << "  logDelta:    " << (int)bucketParams.logDelta << std::endl << std::endl;
 }
 
 template <typename TIndex, typename TSpec>
@@ -574,25 +598,25 @@ inline void _printSwiftBuckets(Pattern< TIndex, Swift<TSpec> > &p)
     unsigned j = 0;
     TParams *bucketParams = &_swiftBucketParams(p, 0);
 
-    for(unsigned i=0; i<length(p.buckets) && i<10; ++i) 
+    for(unsigned i=0; i<length(p.buckets) && i<10; ++i)
     {
         if ((i & bucketParams->reuseMask) == 0)
         {
-            ::std::cout << ::std::endl << "ReadBucket #" << j << "    " << '"';
-            ::std::cout << indexText(host(p))[j] << '"' << ::std::endl;
-            ::std::cout << "  length:      " << sequenceLength(j, host(p)) << ::std::endl;
+            std::cout << std::endl << "ReadBucket #" << j << "    " << '"';
+            std::cout << indexText(host(p))[j] << '"' << std::endl;
+            std::cout << "  length:      " << sequenceLength(j, host(p)) << std::endl;
             bucketParams = &_swiftBucketParams(p, j++);
             _printSwiftParams(*bucketParams);
         }
 
-        ::std::cout << "    lastInc: " << (int)p.buckets[i].lastIncrement;
-        ::std::cout << "  \tCounter: " << p.buckets[i].counter << ::std::endl;
+        std::cout << "    lastInc: " << (int)p.buckets[i].lastIncrement;
+        std::cout << "  \tCounter: " << p.buckets[i].counter << std::endl;
     }
 }
 
 template <typename TIndex, typename TSpec, typename TSize>
 inline typename Pattern<TIndex, Swift<TSpec> >::TBucketParams &
-_swiftBucketParams(Pattern<TIndex, Swift<TSpec> > & pattern, TSize seqNo) 
+_swiftBucketParams(Pattern<TIndex, Swift<TSpec> > & pattern, TSize seqNo)
 {
     if (Swift<TSpec>::PARAMS_BY_LENGTH)
         return pattern.bucketParams[sequenceLength(seqNo, host(pattern))];
@@ -602,7 +626,7 @@ _swiftBucketParams(Pattern<TIndex, Swift<TSpec> > & pattern, TSize seqNo)
 
 template <typename TIndex, typename TSpec, typename TParams, typename TSize>
 inline unsigned
-_swiftBucketNo(Pattern<TIndex, Swift<TSpec> > const &, TParams &bucketParams, TSize seqNo) 
+_swiftBucketNo(Pattern<TIndex, Swift<TSpec> > const &, TParams &bucketParams, TSize seqNo)
 {
     if (Swift<TSpec>::PARAMS_BY_LENGTH)
         return (bucketParams.reuseMask + 1) * seqNo;    // assumes the same reuseMask for all reads
@@ -619,9 +643,24 @@ _qgramLemma(Pattern<TIndex, Swift<TSpec> > const & pattern, TSeqNo seqNo, int er
     return qgramThreshold(indexShape(host(pattern)), sequenceLength(seqNo, host(pattern)), errors, EditDistance(), ThreshQGramLemma());
 }
 
+/*!
+ * @fn SwiftPattern#setMinThreshold
+ * @headerfile <seqan/index.h>
+ * @brief Set minimal threshold (<i>t</i>) for a given needle.
+ *
+ * This function can be used to make the filter allow less errors for a given needle.
+ *
+ * @signature void setMinThreshold(pattern, seqNo, thresh);
+ *
+ * @param[in,out] pattern The SwiftPattern to modify.
+ * @param[in]     seqNo   The number to set the threshold for.
+ * @param[in]     tresh   The threshold to use.
+ */
+
+
 template <typename TIndex, typename TSpec, typename TSeqNo, typename TThreshold>
 inline void
-setMinThreshold(Pattern<TIndex, Swift<TSpec> > & pattern, TSeqNo seqNo, TThreshold thresh) 
+setMinThreshold(Pattern<TIndex, Swift<TSpec> > & pattern, TSeqNo seqNo, TThreshold thresh)
 {
     typedef Pattern<TIndex, Swift<TSpec> >                      TPattern;
     typedef typename TPattern::TBucketParams                    TBucketParams;
@@ -634,7 +673,7 @@ setMinThreshold(Pattern<TIndex, Swift<TSpec> > & pattern, TSeqNo seqNo, TThresho
 
     for (; it != itEnd; ++it)
     {
-        
+
         // increase the threshold if it is less than the minimal threshold
         if ((*it).threshold < thresh)
         {
@@ -685,7 +724,7 @@ _resetBucket(SwiftBucket_<SwiftSemiGlobal_<TSpec_>, TSize, TShortSize> & bkt, TP
 }
 
 template <typename TIndex, typename TFloat, typename TSize_, typename TSpec>
-inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRate, TSize_ minLengthForAll) 
+inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRate, TSize_ minLengthForAll)
 {
     typedef Pattern<TIndex, Swift<TSpec> >                      TPattern;
     typedef typename Size<TIndex>::Type                         TSize;
@@ -701,11 +740,11 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
     TSize seqCount = countSequences(host(pattern));
 
     clear(pattern.verifyList);
-    
+
     if (pattern._currentErrorRate != _newErrorRate || pattern._currentMinLengthForAll != minLengthForAll)
     {
         // settings have been changed -> initialize bucket parameters
-    
+
         pattern._currentErrorRate = _newErrorRate;
         pattern._currentMinLengthForAll = minLengthForAll;
 
@@ -716,7 +755,7 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
         TSize count = 0;
         TSize bucketsPerCol2Max = 0;
         TSize maxLength = 0;
-        
+
         if (Swift<TSpec>::PARAMS_BY_LENGTH) {
             for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) {
                 TSize length = sequenceLength(seqNo, host(pattern));
@@ -730,12 +769,12 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
         pattern.maxPatternLength = maxLength;
         pattern.finderPosOffset = 0;
         pattern.finderPosNextOffset = pattern.finderLength + pattern.maxPatternLength;
-        
-        if (Swift<TSpec>::SEMIGLOBAL == 0) 
+
+        if (Swift<TSpec>::SEMIGLOBAL == 0)
         {
             // global matches
             TSize minLength = minLengthForAll;
-            for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) 
+            for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
             {
                 // swift q-gram lemma
                 TBucketParams &bucketParams = _swiftBucketParams(pattern, seqNo);
@@ -753,8 +792,8 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
 
                 SEQAN_ASSERT_GT_MSG((1 / errorRate), span, "SWIFT only works if span < 1 / error rate!");
                 TSize errors = (TSize) floor((2 * bucketParams.threshold + span - 3) / (1 / errorRate - span));
-            
-            
+
+
                 // a bucket has distanceCut different positions of q-grams
                 // if a q-gram is this far or further away it can't belong to the
                 // same bucket
@@ -762,17 +801,17 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
 
                 // from now, errors is the maximal number of indels
                 if (Swift<TSpec>::HAMMING_ONLY != 0)
-                    errors = 0;         
+                    errors = 0;
 
                 TSize bucketsPerCol2;
-                if(Swift<TSpec>::DIAGONAL == 1) 
+                if(Swift<TSpec>::DIAGONAL == 1)
                 {
                     // Use overlapping parallelograms
                     bucketParams.overlap = errors;
-    
+
                     // delta must be a power of 2 and greater than errors
                     bucketParams.logDelta = (TSize) ceil(log((double)errors + 1) / log(2.0));
-                    if (bucketParams.logDelta < pattern.params.minLog2Delta) 
+                    if (bucketParams.logDelta < pattern.params.minLog2Delta)
                         bucketParams.logDelta = pattern.params.minLog2Delta;
                     bucketParams.delta = 1 << bucketParams.logDelta;
                     bucketParams.tabooLength = pattern.params.tabooLength;
@@ -789,28 +828,28 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
 
                     // delta must be a power of 2 greater than seq.length + errors (define a minimal delta of 32)
                     //bucketParams.logDelta = ;
-                    //if (bucketParams.logDelta < pattern.params.minLog2Delta) 
+                    //if (bucketParams.logDelta < pattern.params.minLog2Delta)
                     //  bucketParams.logDelta = pattern.params.minLog2Delta;
                     //bucketParams.delta = 1 << bucketParams.logDelta;
                     bucketsPerCol2 = 1;
                 }
-            
+
                 bucketParams.firstBucket = count; // firstBucket is only used if Swift<TSpec>::PARAMS_BY_LENGTH == 0
                 bucketParams.reuseMask = bucketsPerCol2 - 1;
                 bucketParams.tabooLength = pattern.params.tabooLength;
-            
+
                 if (Swift<TSpec>::PARAMS_BY_LENGTH) {
                     ++count;
                     if (bucketsPerCol2Max < bucketsPerCol2)
                         bucketsPerCol2Max = bucketsPerCol2;
                 } else
                     count += bucketsPerCol2;
-        
+
                 /*if (seqNo<3)
                     _printSwiftParams(bucketParams);*/
             }
         } else
-            for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) 
+            for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
             {
                 // get pattern length and max. allowed errors
                 TBucketParams &bucketParams = _swiftBucketParams(pattern, seqNo);
@@ -829,10 +868,10 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
                     bucketParams.threshold = threshold;
                 else
                     bucketParams.threshold = pattern.params.minThreshold;
-                
+
                 // from now, errors is the maximal number of indels
                 if (Swift<TSpec>::HAMMING_ONLY != 0)
-                    errors = 0;         
+                    errors = 0;
 
                 // a bucket has distanceCut different positions of q-grams
                 // if a q-gram is this far or farer away it can't belong to the
@@ -842,12 +881,12 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
                 TSize bucketsPerCol2;
                 if (Swift<TSpec>::DIAGONAL == 1)
                 {
-                    // Use overlapping parallelograms               
+                    // Use overlapping parallelograms
                     bucketParams.overlap = errors;
-                    
+
                     // delta must be a power of 2 greater then errors (define a minimal delta of 8)
                     bucketParams.logDelta = (TSize) ceil(log((double)(errors + 1)) / log(2.0));
-                    if (bucketParams.logDelta < pattern.params.minLog2Delta) 
+                    if (bucketParams.logDelta < pattern.params.minLog2Delta)
                         bucketParams.logDelta = pattern.params.minLog2Delta;
                     bucketParams.delta = 1 << bucketParams.logDelta;
 
@@ -864,7 +903,7 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
 
                     // delta must be a power of 2 greater then seq.length + errors (define a minimal delta of 32)
                     bucketParams.logDelta = (TSize) ceil(log((double)(length - span + 1 + errors)) / log(2.0));
-                    if (bucketParams.logDelta < pattern.params.minLog2Delta) 
+                    if (bucketParams.logDelta < pattern.params.minLog2Delta)
                         bucketParams.logDelta = pattern.params.minLog2Delta;
                     bucketParams.delta = 1 << bucketParams.logDelta;
 
@@ -876,14 +915,14 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
                 bucketParams.firstBucket = count;
                 bucketParams.reuseMask = bucketsPerCol2 - 1;
                 bucketParams.tabooLength = pattern.params.tabooLength;
-                
+
                 if (Swift<TSpec>::PARAMS_BY_LENGTH) {
                     ++count;
                     if (bucketsPerCol2Max < bucketsPerCol2)
                         bucketsPerCol2Max = bucketsPerCol2;
                 } else
                     count += bucketsPerCol2;
-                
+
 /*              if (seqNo<3)
                     _printSwiftParams(bucketParams);
 */          }
@@ -900,7 +939,7 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
         {
             TBucketParams &bucketParams = _swiftBucketParams(pattern, seqNo);
             TBucketSize lastIncrement = (TBucketSize)0 - (TBucketSize)bucketParams.tabooLength;
-            for(bktEnd = bkt + bucketParams.reuseMask + 1; bkt != bktEnd; ++bkt) 
+            for(bktEnd = bkt + bucketParams.reuseMask + 1; bkt != bktEnd; ++bkt)
             {
                 _resetBucket(*bkt, lastIncrement, bucketParams.threshold);
             }
@@ -914,16 +953,16 @@ inline void _patternInit(Pattern<TIndex, Swift<TSpec> > &pattern, TFloat errorRa
         __int64 clearance = pattern.finderLength + pattern.maxPatternLength;
         pattern.finderPosOffset = pattern.finderPosNextOffset;
         pattern.finderPosNextOffset += clearance;
-        
+
         // reset buckets only if an overflow of the finder position would occur
         // we would not detect an overflow if clearance is larger than the largest TBucketSize value
         if (pattern.finderPosNextOffset <= pattern.finderPosOffset || (__int64)(TBucketSize)clearance < (__int64)clearance)
         {
             pattern.finderPosOffset = 0;
             pattern.finderPosNextOffset = pattern.finderLength + pattern.maxPatternLength;
-            
+
             TBucketIterator bktEnd, bkt = begin(pattern.buckets, Standard());
-            for (TSize ndlSeqNo = 0; ndlSeqNo < seqCount; ++ndlSeqNo) 
+            for (TSize ndlSeqNo = 0; ndlSeqNo < seqCount; ++ndlSeqNo)
             {
                 TBucketParams &bucketParams = _swiftBucketParams(pattern, ndlSeqNo);
                 TBucketSize lastIncrement = (TBucketSize)0 - (TBucketSize)bucketParams.tabooLength;
@@ -965,9 +1004,9 @@ inline void _createHit(
     __int64 lastInc = (__int64)bkt.lastIncrement - pattern.finderPosOffset;
     __int64 firstInc = (__int64)bkt.firstIncrement - pattern.finderPosOffset;
 
-    if(diag > lastInc) 
+    if(diag > lastInc)
     {
-        // bucket is reused since last increment 
+        // bucket is reused since last increment
         TSize reusePos = (bucketParams.reuseMask + 1) << bucketParams.logDelta;
         diag -= (__int64)ceil((diag-lastInc)/(double)reusePos) * reusePos;
     }
@@ -983,7 +1022,7 @@ inline void _createHit(
         ndlSeqNo,               // needle seq. number           *   *
         ndlBegin,               // bucket begin in needle       *     *
         width,                  // bucket width (non-diagonal)    *   *
-        height                  // bucket height                    * * 
+        height                  // bucket height                    * *
     };                          //                                    *
 
     // append the hit to the finders hit list
@@ -1053,10 +1092,10 @@ inline bool _swiftMultiProcessQGram(
         unsigned bktNo = (diag >> bucketParams.logDelta) & bucketParams.reuseMask; // bucket no of diagonal
         unsigned bktOfs = diag & (bucketParams.delta - 1); // offset of diagonal to bucket begin
         __int64  bktBeginHstk = diag & ~(__int64)(bucketParams.delta - 1); // haystack position of bucket begin diagonal
-        
+
         // global (over all pattern sequences) number of current bucket
         TBucketIter bkt = bktBegin + (_swiftBucketNo(pattern, bucketParams, getSeqNo(ndlPos)) + bktNo);
-        
+
         TShortSize hitCount;
 
         do {
@@ -1065,7 +1104,7 @@ inline bool _swiftMultiProcessQGram(
             {
                 // last increment was before the beginning of the current bucket => bucket is reused
                 // Or last increment was in the same bucket but lies more than distanceCut away
-                
+
                 if ((*bkt).counter >= (*bkt).threshold)
                 {
                     // create a new hit and append it to the finders hit list
@@ -1133,12 +1172,12 @@ inline bool _swiftMultiProcessQGram(
 // Returns true if the hit-list of the finder is not empty after this call.
 template <
     typename TFinder,
-    typename TIndex, 
+    typename TIndex,
     typename TSpec_,
     typename THValue
 >
 inline bool _swiftMultiProcessQGram(
-    TFinder &finder, 
+    TFinder &finder,
     Pattern<TIndex, Swift<Tag<SwiftSemiGlobal_<TSpec_> > > > &pattern,
     THValue hash)
 {
@@ -1153,29 +1192,29 @@ inline bool _swiftMultiProcessQGram(
     typedef typename TBucket::TShortSize                        TShortSize;
     typedef typename TPattern::TBucketParams                    TBucketParams;
     typedef typename FindResult<TFinder, TPattern>::Type        THit;
-    
-    TIndex const & index = host(pattern);    
-    
+
+    TIndex const & index = host(pattern);
+
     // create an iterator over the positions of the q-gram occurrences in pattern
     TSAIter saBegin = begin(indexSA(index), Standard());
     TSAIter occ = saBegin + indexDir(index)[getBucket(index.bucketMap, hash)];
     TSAIter occEnd = saBegin + indexDir(index)[getBucket(index.bucketMap, hash) + 1];
     TBucketIter bktBegin = begin(pattern.buckets, Standard());
     Pair<unsigned> ndlPos;
-    
+
 /*  std::cerr<<"\t["<<(occEnd-occ)<<"]"<< std::flush;
-    
+
     if ((occEnd-occ)>100)
     {
         std::cerr<<" ";
         for(int i=0;i<length(indexShape(host(pattern)));++i)
             std::cerr<<*(hostIterator(hostIterator(finder))+i);
     }
-*/  
+*/
     // iterate over all q-gram occurrences and do the processing
     __int64 curPos = finder.curPos + pattern.finderPosOffset;
 //    bool dbg=pattern.params.debug && (finder.curPos > 496 && finder.curPos < 591);
-    for(; occ != occEnd; ++occ) 
+    for(; occ != occEnd; ++occ)
     {
         posLocalize(ndlPos, *occ, stringSetLimits(index));
         TBucketParams &bucketParams = _swiftBucketParams(pattern, getSeqNo(ndlPos));
@@ -1187,13 +1226,13 @@ inline bool _swiftMultiProcessQGram(
         unsigned bktOfs = diag & (bucketParams.delta - 1);
         __int64  bktBeginHstk = diag & ~(__int64)(bucketParams.delta - 1);
 
-        TBucketIter bkt = bktBegin + (_swiftBucketNo(pattern, bucketParams, getSeqNo(ndlPos)) + bktNo);     
+        TBucketIter bkt = bktBegin + (_swiftBucketNo(pattern, bucketParams, getSeqNo(ndlPos)) + bktNo);
         TShortSize hitCount;
 
 //        if (dbg && (*occ).i1==15)
 //            std::cout << finder.curPos << '\t' << *occ << '\t' << (*bkt).counter<<std::endl;
-//      
-        do 
+//
+        do
         {
             if ((__int64)(*bkt).lastIncrement < bktBeginHstk + (__int64)pattern.finderPosOffset)
             {
@@ -1204,7 +1243,7 @@ inline bool _swiftMultiProcessQGram(
             else
             {
                 if ((__int64)((*bkt).lastIncrement + bucketParams.tabooLength) > curPos)
-                    goto checkOverlap;  // increment only once per sequence         
+                    goto checkOverlap;  // increment only once per sequence
                 hitCount = (*bkt).counter + 1;
             }
 
@@ -1226,15 +1265,15 @@ inline bool _swiftMultiProcessQGram(
                 __int64 upperBktNo = ((*bkt).lastIncrement - pattern.finderPosOffset) >> bucketParams.logDelta;
 
                 // we must decrement bucket no. until (no. mod reuse == bktNo)
-                __int64 _bktBeginHstk = 
+                __int64 _bktBeginHstk =
                      (upperBktNo - ((upperBktNo - bktNo) & bucketParams.reuseMask)) << bucketParams.logDelta;
 
                 if ((*bkt)._lastIncDiag - _bktBeginHstk >= bucketParams.delta + bucketParams.overlap || (*bkt)._lastIncDiag < _bktBeginHstk) {
-                    ::std::cerr << "qgram stored in wrong bucket (diag:" << (*bkt)._lastIncDiag << ", begin:" << _bktBeginHstk;
-                    ::std::cerr << ", delta:" << bucketParams.delta << ", overlap:" << bucketParams.overlap << ")" << ::std::endl;
+                    std::cerr << "qgram stored in wrong bucket (diag:" << (*bkt)._lastIncDiag << ", begin:" << _bktBeginHstk;
+                    std::cerr << ", delta:" << bucketParams.delta << ", overlap:" << bucketParams.overlap << ")" << std::endl;
                 }
 #endif
-//              if (bktBeginHstk >= 0) 
+//              if (bktBeginHstk >= 0)
 //              {
                     THit hit = {
                         bktBeginHstk,                                       // bucket begin in haystack
@@ -1281,7 +1320,7 @@ inline bool _swiftMultiProcessQGram(
 // resets counter and lastIncrement of all buckets listed in patterns verify list
 template <
     typename TFinder,
-    typename TIndex, 
+    typename TIndex,
     typename TSpec
 >
 inline bool _swiftMultiFlushBuckets(
@@ -1340,11 +1379,11 @@ inline bool _swiftMultiFlushBuckets(
 // no resetting is needed for the semiglobal version
 template <
     typename TFinder,
-    typename TIndex, 
+    typename TIndex,
     typename TSpec_
 >
 inline bool _swiftMultiFlushBuckets(
-    TFinder &, 
+    TFinder &,
     Pattern<TIndex, Swift<Tag<SwiftSemiGlobal_<TSpec_> > > > &)
 {
     // there is nothing to be done here as we dump matches immediately after reaching the threshold
@@ -1352,15 +1391,15 @@ inline bool _swiftMultiFlushBuckets(
 }
 
 template <typename TIndex, typename TSpec>
-inline bool 
-empty(Pattern<TIndex, Swift<TSpec> > & me) 
+inline bool
+empty(Pattern<TIndex, Swift<TSpec> > & me)
 {
     return empty(me.bucketParams);
 }
 
 template <typename TIndex, typename TSpec>
-inline void 
-clear(Pattern<TIndex, Swift<TSpec> > & me) 
+inline void
+clear(Pattern<TIndex, Swift<TSpec> > & me)
 {
     me.finderPosOffset = 0;
     me.finderPosNextOffset = 0;
@@ -1368,6 +1407,9 @@ clear(Pattern<TIndex, Swift<TSpec> > & me)
     me.maxPatternLength = 0;
     me._currentErrorRate = -1;
     me._currentMinLengthForAll = -1;
+    me.curSeqNo = 0;
+    me.curBeginPos = 0;
+    me.curEndPos = 0;
     clear(me.bucketParams);
     clear(me.buckets);
 }
@@ -1439,13 +1481,24 @@ beginPosition(Finder<THaystack, Swift<TSpec> > & finder)
 
 //____________________________________________________________________________
 
+/*!
+ * @fn SwiftPattern#beginPosition
+ * @headerfile <seqan/index.h>
+ * @brief Returns the begin position of the local match in the pattern.
+ *
+ * @signature TPosition beginPosition(pattern);
+ *
+ * @param[in] pattern   The SwiftPattern to query.
+ * @return    TPosition The @link TextConcept#SAValue SA value @endlink of the pattern text.
+ */
+
 template <typename TIndex, typename TSpec>
 inline typename SAValue<TIndex>::Type
 beginPosition(Pattern<TIndex, Swift<TSpec> > const & pattern)
 {
     __int64 hitBegin = pattern.curBeginPos;
     if (hitBegin < 0) hitBegin = 0;
-    
+
     typename SAValue<TIndex >::Type pos;
     posLocalToX(pos, Pair<unsigned, __int64>(pattern.curSeqNo, hitBegin), stringSetLimits(host(pattern)));
     return pos;
@@ -1469,6 +1522,17 @@ beginPosition(Pattern<TIndex, Swift<TSpec> > & pattern)
 
 //____________________________________________________________________________
 
+/*!
+ * @fn SwiftPattern#endPosition
+ * @headerfile <seqan/index.h>
+ * @brief Returns the end position of the local match in the pattern.
+ *
+ * @signature TPosition endPosition(pattern);
+ *
+ * @param[in] pattern   The SwiftPattern to query.
+ * @return    TPosition The @link TextConcept#SAValue SA value @endlink of the pattern text.
+ */
+
 template <typename THaystack, typename TSpec>
 inline typename Position<Finder<THaystack, Swift<TSpec> > >::Type
 endPosition(Finder<THaystack, Swift<TSpec> > const & finder)
@@ -1517,44 +1581,40 @@ endPosition(Pattern<TIndex, Swift<TSpec> > & pattern)
 }
 
 //____________________________________________________________________________
-/**
-.Function.positionRangeNoClip
-..cat:Searching
-..summary:Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.
-..signature:positionRangeNoClip(finder)
-..class:Class.Finder
-..signature:positionRangeNoClip(pattern)
-..param.finder:A @Class.Finder@ object.
-...type:Spec.Swift
-..param.pattern:A @Class.Pattern@ object.
-...type:Spec.Swift
-..returns:A pair of the begin and end position in the haystack or needle for the last hit found. These positions could
-be negative or beyond the end of $finder$ or $pattern$ when using filter algorithms.
-...remarks:The return type is $Pair<typename SAValue<THost>::Type>$ if $THost$ is the type of haystack or needle.
-..see:Function.positionRange
-..include:seqan/index.h
-*/
+/*!
+ * @fn SwiftFinder#positionRangeNoClip
+ * @headerfile <seqan/index.h>
+ * @brief Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.
+ *
+ * @signature TPair positionRangeNoClip(finder);
+ *
+ * @param[in] finder A SwiftFinder object to query.
+ *
+ * @return TPair A pair of the begin and end position in the haystack or needle for the last hit found.  These positions
+ *               could be negative or beyond the end of <tt>finder</tt> or <tt>pattern</tt> when using filter
+ *               algorithms.  The return type is <tt>Pair&lt;typename SAValue&lt;THost&gt;::Type&gt;</tt> if
+ *               <tt>THost</tt> is the type of haystack or needle.
+ *
+ * @see SwiftFinder#positionRange
+ * @see SwiftPattern#positionRangeNoClip
+ */
 
 /*!
- * @fn Finder#positionRangeNoClip
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a pair of the begin and end position in or beyond the haystack
- *        or needle for the last hit found.
- * 
- * @signature positionRangeNoClip(finder)
- * @signature positionRangeNoClip(pattern)
- * 
- * @param pattern A @link Pattern @endlink object. Types: @link Pigeonhole @endlink, @link Swift @endlink
- * @param finder A @link Finder @endlink object. Types: @link Pigeonhole @endlink, @link Swift @endlink
- * 
- * @return TReturn A pair of the begin and end position in the haystack or needle for the last hit found. These
- *                 positions could be negative or beyond the end of <tt>finder</tt> or <tt>pattern</tt> when using 
- *                 filter algorithms. The return type is <tt>Pair&lt;typename SAValue&lt;THost&gt;::Type&gt;</tt> if <tt>THost</tt>
- *                 is the type of haystack or needle.
- * 
- * @see Finder#positionRange
+ * @fn SwiftPattern#positionRangeNoClip
+ * @headerfile <seqan/index.h>
+ * @brief Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.
+ *
+ * @signature TPair positionRangeNoClip(pattern)
+ *
+ * @param[in] pattern SwiftPattern object to query.
+ *
+ * @return TPair A pair of the begin and end position in the haystack or needle for the last hit found.  These positions
+ *               could be negative or beyond the end of <tt>finder</tt> or <tt>pattern</tt> when using filter
+ *               algorithms.  The return type is <tt>Pair&lt;typename SAValue&lt;THost&gt;::Type&gt;</tt> if
+ *               <tt>THost</tt> is the type of haystack or needle.
+ *
+ * @see SwiftPattern#positionRange
+ * @see SwiftFinder#positionRangeNoClip
  */
 
 template <typename THaystack, typename TSpec>
@@ -1575,44 +1635,38 @@ positionRangeNoClip(Finder<THaystack, Swift<TSpec> > & finder)
 }
 
 //____________________________________________________________________________
-/**
-.Function.positionRange
-..cat:Searching
-..summary:Returns a pair of the begin and end position in the haystack or needle for the last hit found.
-..signature:positionRange(finder)
-..class:Class.Finder
-..signature:positionRange(pattern)
-..param.finder:A @Class.Finder@ object.
-...type:Spec.Swift
-..param.pattern:A @Class.Pattern@ object.
-...type:Spec.Swift
-..returns:A pair of the begin and end position in the haystack or needle for the last hit found.
-...remarks:The return type is $Pair<typename SAValue<THost>::Type>$ if $THost$ is the type of haystack or needle.
-..see:Function.beginPosition
-..see:Function.endPosition
-..include:seqan/index.h
-*/
+/*!
+ * @fn SwiftFinder#positionRange
+ * @headerfile <seqan/index.h>
+ * @brief Returns a pair of the begin and end position in the haystack or needle for the last hit found.
+ *
+ * @signature TPair positionRange(finder);
+ *
+ * @param[in] finder A @link Finder @endlink object.
+ *
+ * @return TPair A @link Pair @endlink of the begin and end position in the haystack or needle for the last
+ *               hit found.  The return type is <tt>Pair&lt;typename SAValue&ltTHost&g;::Type&gt;</tt> if
+ *               <tt>THost</tt> is the type of haystack or needle.
+ *
+ * @see Finder#beginPosition
+ * @see Finder#endPosition
+ * @see SwiftFinder#positionRangeNoClip
+ */
 
 /*!
- * @fn Finder#positionRange
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a pair of the begin and end position in the haystack or needle
- *        for the last hit found.
- * 
- * @signature positionRange(finder)
- * @signature positionRange(pattern)
- * 
- * @param pattern A @link Pattern @endlink object. Types: @link Pigeonhole @endlink, @link Swift @endlink
- * @param finder A @link Finder @endlink object. Types: @link Pigeonhole @endlink, @link Swift @endlink
- * 
- * @return TReturn A pair of the begin and end position in the haystack or needle for the last hit found.The return type
- *                 is <tt>Pair&lt;typename SAValue&ltTHost&g;::Type&gt;</tt> if <tt>THost</tt> is the type of haystack or needle.
- * 
- * @see beginPosition
- * @see endPosition
- * @see Finder#positionRangeNoClip
+ * @fn SwiftPattern#positionRange
+ * @headerfile <seqan/index.h>
+ * @brief Returns a pair of the begin and end position in the haystack or needle for the last hit found.
+ *
+ * @signature TPair positionRange(pattern);
+ *
+ * @param[in] pattern A @link Pattern @endlink object.
+ *
+ * @return TPair A @link Pair @endlink of the begin and end position in the haystack or needle for the last
+ *               hit found.  The return type is <tt>Pair&lt;typename SAValue&ltTHost&g;::Type&gt;</tt> if
+ *               <tt>THost</tt> is the type of haystack or needle.
+ *
+ * @see SwiftPattern#positionRangeNoClip
  */
 
 template <typename THaystack, typename TSpec>
@@ -1650,6 +1704,8 @@ positionRange(Pattern<TIndex, Swift<TSpec> > & pattern)
 
 //____________________________________________________________________________
 
+// TODO(holtgrew): Document this properly.
+
 template <typename TSwiftHit, typename TText>
 inline typename Infix<TText>::Type
 swiftInfixNoClip(TSwiftHit const &hit, TText &text)
@@ -1674,9 +1730,6 @@ swiftInfix(TSwiftHit const & hit, TText & text)
 //____________________________________________________________________________
 
 // now in find_base.h
-///.Function.Finder#infix.remarks:For finders or patterns of filtering algorithms (e.g. @Spec.Swift@) the returned infix is a potential match.
-///.Function.Finder#infix.param.finder.type:Spec.Swift
-
 template <typename THaystack, typename TSpec>
 inline typename Infix<THaystack>::Type
 infix(Finder<THaystack, Swift<TSpec> > &finder)
@@ -1748,18 +1801,18 @@ infix(Pattern<TIndex, Swift<TSpec> > & pattern)
 //____________________________________________________________________________
 
 template <typename THaystack, typename TSpec>
-inline void 
+inline void
 _printDots(Finder<THaystack, Swift<TSpec> > &finder)
 {
-    while (finder.curPos >= finder.dotPos) 
+    while (finder.curPos >= finder.dotPos)
     {
         finder.dotPos += 100000;
         if (finder.dotPos >= finder.dotPos2)
         {
-            ::std::cerr << (finder.dotPos2 / 1000000) << "M" << ::std::flush;
+            std::cerr << (finder.dotPos2 / 1000000) << "M" << std::flush;
             finder.dotPos2 += 1000000;
         } else
-            ::std::cerr << "." << ::std::flush;
+            std::cerr << "." << std::flush;
     }
 }
 
@@ -1793,7 +1846,7 @@ _nextNonRepeatRange(
     finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1);
 
 //  if (pattern.params.printDots)
-//      ::std::cerr << ::std::endl << "  scan range (" << finder.startPos << ", " << finder.endPos << ") " << std::flush;
+//      std::cerr << std::endl << "  scan range (" << finder.startPos << ", " << finder.endPos << ") " << std::flush;
 
     return true;
 }
@@ -1823,7 +1876,7 @@ _firstNonRepeatRange(
     finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1);
 
 //  if (pattern.params.printDots)
-//      ::std::cerr << ::std::endl << "  scan range (" << finder.startPos << ", " << finder.endPos << ") " << std::flush;
+//      std::cerr << std::endl << "  scan range (" << finder.startPos << ", " << finder.endPos << ") " << std::flush;
 
     return true;
 }
@@ -1840,7 +1893,7 @@ _copySwiftHit(
 }
 
 template <typename TFinder, typename TIndex, typename TSpec>
-inline void 
+inline void
 _copySwiftHit(
     TFinder &finder,
     Pattern<TIndex, Swift<Tag<SwiftSemiGlobal_<TSpec> > > > &pattern)
@@ -1851,26 +1904,26 @@ _copySwiftHit(
 }
 
 template <typename TFinder, typename TIndex, typename TSpec>
-inline bool 
+inline bool
 find(
     TFinder &finder,
-    Pattern<TIndex, Swift<Tag<SwiftSemiGlobal_<TSpec> > > > &pattern, 
+    Pattern<TIndex, Swift<Tag<SwiftSemiGlobal_<TSpec> > > > &pattern,
     double errorRate)
 {
     return find(finder, pattern, errorRate, 0);
 }
 
 template <typename THaystack, typename TIndex, typename TSpec, typename TSize>
-inline bool 
+inline bool
 find(
     Finder<THaystack, Swift<TSpec> > &finder,
-    Pattern<TIndex, Swift<TSpec> > &pattern, 
+    Pattern<TIndex, Swift<TSpec> > &pattern,
     double errorRate,
     TSize minLength)
 {
     //typedef typename Fibre<TIndex, QGramShape>::Type    TShape;
 
-    if (empty(finder)) 
+    if (empty(finder))
     {
         pattern.finderLength = pattern.params.tabooLength + length(container(finder));
         _patternInit(pattern, errorRate, minLength);
@@ -1884,10 +1937,10 @@ find(
             _copySwiftHit(finder, pattern);
             return true;
         }
-    } 
+    }
     else
     {
-        if (++finder.curHit < finder.endHit) 
+        if (++finder.curHit < finder.endHit)
         {
             _copySwiftHit(finder, pattern);
             return true;
@@ -1898,18 +1951,18 @@ find(
     clear(finder.hits);
 
     // are we at the end of the text?
-    if (atEnd(finder) && finder.curRepeat == finder.endRepeat) 
+    if (atEnd(finder) && finder.curRepeat == finder.endRepeat)
     {
         finder.curHit = finder.endHit;
         return false;
     }
 
-    do 
+    do
     {
         if (pattern.params.printDots) _printDots(finder);
-        if (atEnd(++finder)) 
+        if (atEnd(++finder))
         {
-            if (!_nextNonRepeatRange(finder, pattern)) 
+            if (!_nextNonRepeatRange(finder, pattern))
             {
                 if(_swiftMultiFlushBuckets(finder, pattern))
                 {
@@ -1926,7 +1979,7 @@ find(
             ++finder.curPos;
             hashNext(pattern.shape, hostIterator(hostIterator(finder)));
         }
-        
+
         if (_swiftMultiProcessQGram(finder, pattern, value(pattern.shape)))
         {
             _copySwiftHit(finder, pattern);
@@ -1937,13 +1990,13 @@ find(
 }
 
 template <typename THashes, typename TPipeSpec, typename TIndex, typename TSpec>
-inline bool 
+inline bool
 find(
     Finder<Pipe<THashes, TPipeSpec>, Swift<TSpec> > &finder,
-    Pattern<TIndex, Swift<TSpec> > &pattern, 
+    Pattern<TIndex, Swift<TSpec> > &pattern,
     double errorRate)
 {
-    if (empty(finder)) 
+    if (empty(finder))
     {
         pattern.finderLength = 0;
         _patternInit(pattern, errorRate, 0);
@@ -1952,7 +2005,7 @@ find(
         finder.dotPos2 = 10 * finder.dotPos;
 
         beginRead(finder.in);
-        if (eof(finder.in)) 
+        if (eof(finder.in))
         {
             endRead(finder.in);
             return false;
@@ -1964,7 +2017,7 @@ find(
             return true;
         }
     } else
-        if (++finder.curHit != finder.endHit) 
+        if (++finder.curHit != finder.endHit)
         {
             _copySwiftHit(finder, pattern);
             return true;
@@ -1973,10 +2026,10 @@ find(
     clear(finder.hits);
     if (eof(finder.in)) return false;
 
-    do 
+    do
     {
         ++finder.in;
-        if (eof(finder.in)) 
+        if (eof(finder.in))
         {
             endRead(finder.in);
 #ifdef SEQAN_DEBUG_SWIFT
@@ -1987,7 +2040,7 @@ find(
                 _copySwiftHit(finder, pattern);
                 return true;
             }
-            else 
+            else
                 return false;
         }
         finder.curPos = (*finder.in).i1;
@@ -1999,51 +2052,33 @@ find(
     return true;
 }
 
-/**
-.Function.windowFindBegin:
-..cat:Searching
-..summary:Initializes the pattern. Sets the finder on the begin position.
- Gets the first non-repeat range and sets it in the finder.
- Used together with @Function.windowFindBegin@ and @Function.windowFindEnd@.
-..signature:windowFindBegin(finder, pattern, errorRate)
-..class:Spec.Swift
-..param.finder:A finder with window interface.
-...type:Spec.Swift
-..param.pattern: A pattern with window interface.
-...type:Spec.Swift
-..param.errorRate:Error rate that is allowed between reads and reference.
- Should be the same in as in @Function.windowFindNext@.
-...type:nolink:double
-..include:seqan/index.h
-*/
-
 /*!
- * @fn Swift#windowFindBegin
- * 
- * @headerfile seqan/index.h
- * 
+ * @fn SwiftFinder#windowFindBegin
+ * @headerfile <seqan/index.h>
  * @brief Initializes the pattern. Sets the finder on the begin position.  Gets the first non-repeat range and sets it
- * in the finder.  Used together with @link Swift#windowFindEnd @endlink.
- * 
- * @signature windowFindBegin(finder, pattern, errorRate)
- * 
- * @param pattern A pattern with window interface. Types: @link Pigeonhole @endlink, @link Swift @endlink
- * @param errorRate Error rate that is allowed between reads and reference. Should be the same in as in @link
- *                  Swift#windowFindNext @endlink.  Types: <tt>double</tt>
- * @param finder A finder with window interface. Types: @link Pigeonhole @endlink, @link Swift @endlink
- * 
- * @see Swift#windowFindNext
- * @see Swift#windowFindEnd
+ *        in the finder.  Used together with @link SwiftFinder#windowFindEnd @endlink.
+ *
+ * @signature bool windowFindBegin(finder, pattern, errorRate);
+ *
+ * @param[in,out] finder    A finder with window interface.
+ * @param[in,out] pattern   A pattern with window interface. Types: @link SwiftPattern @endlink.
+ * @param[in]     errorRate Error rate that is allowed between reads and reference.  Should be the same in as in
+ *                          @link SwiftFinder#windowFindNext @endlink.  Types: <tt>double</tt>
+ *
+ * @return bool <tt>true</tt> if there were bases to be scanned and <tt>false</tt> otherwise.
+ *
+ * @see SwiftFinder#windowFindNext
+ * @see SwiftFinder#windowFindEnd
  */
 template <typename THaystack, typename TIndex, typename TSpec>
-inline bool 
+inline bool
 windowFindBegin(
     Finder<THaystack, Swift<TSpec> > &finder,
-    Pattern<TIndex, Swift<TSpec> > &pattern, 
+    Pattern<TIndex, Swift<TSpec> > &pattern,
     double errorRate)
 {
     SEQAN_CHECKPOINT
-    
+
     pattern.finderLength = pattern.params.tabooLength + length(container(finder));
     _patternInit(pattern, errorRate, 0);
     _finderSetNonEmpty(finder);
@@ -2052,54 +2087,31 @@ windowFindBegin(
     finder.windowStart = 0;
 
     if (!_firstNonRepeatRange(finder, pattern)) return false;
-    
+
     return true;
 }
 
 
-/**
-.Function.windowFindNext:
-..cat:Searching
-..summary:Searches over the next window with the finder. The found hits can be retrieved with @Function.getWindowFindHits@
- Used together with @Function.windowFindBegin@ and @Function.windowFindEnd@.
-..signature:windowFindNext(finder, pattern, finderWindowLength)
-..param.finder:A finder with window interface.
-..class:Spec.Swift
-...type:Spec.Swift
-..param.pattern: A pattern with window interface.
-...type:Spec.Swift
-..param.finderWindowLength:Number of bases that are scanned beginning from the position the finder is at.
- Including bases that are marked as repeats and that are skipped.
-...type:nolink:unsigned int
-..returns:true, if there are bases that can be scanned. false, otherwise
-..see:Function.windowFindBegin
-..see:Function.windowFindEnd
-..see:Function.getWindowFindHits
-..include:seqan/index.h
-*/
-
 /*!
- * @fn Swift#windowFindNext
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Searches over the next window with the finder. The found hits can be retrieved with @link 
- *        Swift#getWindowFindHits @endlink  Used together with @link Swift#windowFindBegin @endlink and @link
- *        Swift#windowFindEnd @endlink.
- * 
- * @signature windowFindNext(finder, pattern, finderWindowLength)
- * 
- * @param pattern A pattern with window interface. Types: Pigeonhole, Swift
- * @param finderWindowLength Number of bases that are scanned beginning from the position the finder is at.  Including
- * bases that are marked as repeats and that are skipped. Types: nolink:unsigned int
- * @param finder A finder with window interface. Types: Pigeonhole
- * 
- * @return TReturn true, if there are bases that can be scanned. false,
- *                 otherwise
- * 
- * @see Swift#windowFindBegin
- * @see Swift#windowFindEnd
- * @see Swift#getWindowFindHits
+ * @fn SwiftFinder#windowFindNext
+ * @headerfile <seqan/index.h>
+ * @brief Searches over the next window with the finder. The found hits can be retrieved with @link
+ *        SwiftFinder#getWindowFindHits @endlink.  Used together with @link SwiftFinder#windowFindBegin @endlink and
+ *        @link SwiftFinder#windowFindEnd @endlink.
+ *
+ * @signature bool windowFindNext(finder, pattern, finderWindowLength)
+ *
+ * @param[in,out] finder             A SwiftFinder.
+ * @param[in,out] pattern            A SwiftPattern.
+ * @param[in] finderWindowLength     Number of bases that are scanned beginning from the position the finder is at.
+ *                                   Including bases that are marked as repeats and that are skipped. Types:
+ *                                   nolink:unsigned int
+ *
+ * @return bool <tt>true</tt>, if there are bases that can be scanned, <tt>false</tt> otherwise.
+ *
+ * @see SwiftFinder#windowFindBegin
+ * @see SwiftFinder#windowFindEnd
+ * @see SwiftFinder#getWindowFindHits
  */
 
 template <typename THaystack, typename TIndex, typename TSpec, typename TSize>
@@ -2153,37 +2165,22 @@ windowFindNext(
 }
 
 /*!
- * @fn Swift#windowFindEnd
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Flushes the pattern. Used together with @link Swift#windowFindBegin @endlink
- *        and @link Swift#windowFindNext @endlink.
- * 
- * @signature windowFindEnd(finder, pattern)
- * 
- * @param pattern A pattern with window interface. Types: @link Swift @endlink
- * @param finder A finder with window interface. Types: @link Pigeonhole @endlink
- * 
- * @see Swift#windowFindBegin
- * @see Swift#windowFindNext
+ * @fn SwiftFinder#windowFindEnd
+ * @headerfile <seqan/index.h>
+ * @brief Flushes the finder.  Used together with @link SwiftFinder#windowFindBegin @endlink and @link
+ *        SwiftFinder#windowFindNext @endlink.
+ *
+ * @signature void windowFindEnd(finder, pattern);
+ *
+ * @param[in,out] finder  A finder with window interface.
+ * @param[in,out] pattern A pattern with window interface. Types: @link SwiftPattern @endlink
+ *
+ * @see SwiftFinder#windowFindBegin
+ * @see SwiftFinder#windowFindNext
  */
 
-/**
-.Function.windowFindEnd:
-..cat:Searching
-..summary:Flushes the pattern. Used together with @Function.windowFindBegin@ and @Function.windowFindNext@.
-..signature:windowFindNext(finder, pattern)
-..param.finder:A finder with window interface.
-..class:Spec.Swift
-...type:Spec.Swift
-..param.pattern: A pattern with window interface.
-...type:Spec.Swift
-..see:Function.windowFindBegin
-..include:seqan/index.h
-*/
 template <typename THaystack, typename TIndex, typename TSpec>
-inline void 
+inline void
 windowFindEnd(
     Finder<THaystack, Swift<TSpec> > & finder,
     Pattern<TIndex, Swift<TSpec> > &pattern)
@@ -2193,73 +2190,44 @@ windowFindEnd(
 }
 
 /*!
- * @fn Swift#getWindowFindHits
- * 
- * @headerfile seqan/index.h
- * 
+ * @fn SwiftFinder#getWindowFindHits
+ * @headerfile <seqan/index.h>
  * @brief Returns the string of hits from the finder.
- * 
- * @signature getWindowFindHits(finder)
- * 
- * @param finder A finder with window interface. Types: @link Swift @endlink
- * 
- * @return TReturn @link String @endlink of Hits (use Finder<...>::THitString as Type).
- * 
- * @see Swift#windowFindNext
+ *
+ * @signature THitString getWindowFindHits(finder);
+
+ * @param[in] finder     A finder with window interface.
+ * @return    THitString @link String @endlink of hits, see @link SwiftFinder::THitString @endlink.
+ *
+ * @see SwiftFinder#windowFindNext
  */
 
-/**
-.Function.getWindowFindHits:
-..cat:Searching
-..summary:Returns the string of hits from the finder.
-..signature:getWindowFindHits(finder)
-..class:Spec.Swift
-..param.finder:A finder with window interface.
-...type:Spec.Swift
-..returns:@Class.String@ of Hits (use Finder<...>::THitString as Type).
-..include:seqan/index.h
-*/
 template <typename THaystack, typename TSpec>
 inline typename WindowFindResult<Finder<THaystack, Swift<TSpec> >, void>::Type &
 getWindowFindHits(Finder<THaystack, Swift<TSpec> > &finder)
 {
     SEQAN_CHECKPOINT
-    
+
     return finder.hits;
 }
 
 /*!
- * @fn Pattern#getMaxDeviationOfOrder
- * 
- * @headerfile seqan/index.h
- * 
+ * @fn SwiftPattern#getMaxDeviationOfOrder
+ * @headerfile <seqan/index.h>
  * @brief Returns the maximal out-of-order distance of adjacent hits.
- * 
- * @signature getMaxDeviationOfOrder(pattern)
- * 
- * @param pattern A pattern with window interface. Types: @link Swift @endlink, @link Pigeonhole @endlink
-
- * 
- * @return TReturn Returns the maximal distance two adjacent hits can have which are not in increasing order.
+ *
+ * @signature TSize getMaxDeviationOfOrder(pattern);
+ *
+ * @param[in] pattern A SwiftPattern.
+ * @return    TSize   Returns the maximal distance two adjacent hits can have which are not in increasing order.
+ *                    <tt>TSize</tt> is the size type of the underlying index.
  */
 
-/**
-.Function.getMaxDeviationOfOrder:
-..cat:Searching
-..summary:Returns the maximal out-of-order distance of adjacent hits.
-..signature:getMaxDeviationOfOrder(pattern)
-..class:Class.Pattern
-..param.pattern:A pattern with window interface.
-...type:Spec.Swift
-..returns:Returns the maximal distance two adjacent hits can have which are not in increasing order.
-..include:seqan/index.h
-*/
 template <typename TIndex, typename TSpec>
 inline typename Size<TIndex>::Type
 getMaxDeviationOfOrder(Pattern<TIndex, Swift<TSpec> > &pattern)
 {
-    SEQAN_CHECKPOINT
-    
+    // TODO(holtgrew): Can pattern be made const?
     return back(pattern.bucketParams).delta + back(pattern.bucketParams).overlap + length(pattern.bucketParams) - 2;
 }
 
diff --git a/seqan/index/index_base.h b/seqan/index/index_base.h
index 2b9b966..a91b9d6 100644
--- a/seqan/index/index_base.h
+++ b/seqan/index/index_base.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,455 +38,368 @@
 
 //#define SEQAN_TEST_INDEX
 
-namespace SEQAN_NAMESPACE_MAIN {
+namespace SEQAN_NAMESPACE_MAIN
+{
 
-//////////////////////////////////////////////////////////////////////////////
-// needful forward declarations
+// ============================================================================
+// Forwards
+// ============================================================================
 
-// suffix array construction specs
-struct Skew3;
-struct Skew7;
-struct LarssonSadakane;
-struct ManberMyers;
-struct SAQSort;
-struct QGramAlg;
+    // suffix array construction specs
+    struct Skew3;
+    struct Skew7;
+    struct LarssonSadakane;
+    struct ManberMyers;
+    struct SAQSort;
+    struct QGramAlg;
 
-// lcp table construction algorithms
-struct Kasai;
-struct KasaiOriginal;       // original, but more space-consuming algorithm
+    // inverse suffix array construction specs
+    template <typename TParallel>
+    struct FromSortedSa{};
 
-// enhanced suffix array construction algorithms
-struct Childtab;
-struct Bwt;
+    // lcp table construction algorithms
+    struct Kasai;
+    struct KasaiOriginal;    // original, but more space-consuming algorithm
 
-/*
-.Tag.Index Find Algorithm
-..summary:Tag to specify the index search algorithm.
-..remarks:These tag can be used to specify the @Function.find@ algorithm
-for @Class.Index@ based substring searches.
-..cat:Index
+    // enhanced suffix array construction algorithms
+    struct Childtab;
+    struct Bwt;
 
-..tag.EsaFindMlr:Binary search with mlr-heuristic.
-...remarks:Exact string matching using a suffix array binary search with the mlr-heuristic.
+// ============================================================================
+// Concepts
+// ============================================================================
 
-..tag.EsaFindLcpe:Binary search using lcp values.
-...remarks:Exact string matching using a suffix array binary search and a lcp-interval tree.
+/*!
+ * @concept StringIndexConcept
+ * @brief An index that can be traversed top-down.
+ * @headerfile <seqan/index.h>
+ *
+ * @signature StringIndexConcept<T>
+ */
 
-..tag.FinderSTree:Suffix tree search.
-...remarks:Exact string matching using a suffix tree.
+SEQAN_CONCEPT(StringIndexConcept, (TIndex))
+{
+//    typedef typename Iterator<TIndex, TopDown<> >::Type     TTopDownIterator;
+    typedef typename VertexDescriptor<TIndex>::Type         TVertexDescriptor;
+    typedef String<int>                                     TPropertyMap;
+
+    TIndex          index;
+    TPropertyMap    pm;
+
+    SEQAN_CONCEPT_USAGE(StringIndexConcept)
+    {
+        // property map interface
+        resizeVertexMap(pm, index);
+
+        // iteration
+//        TTopDownIterator iter = begin(index, TopDown<>());
+    }
+};
+
+/*!
+ * @concept StringTreeConcept
+ * @brief An index that can be traversed top-down as a tree.
+ * @headerfile <seqan/index.h>
+ *
+ * @signature StringTreeConcept<T>
+ */
+
+SEQAN_CONCEPT_REFINE(StringTreeConcept, (TIndex), (StringIndexConcept)) {};
+
+/*!
+ * @concept StringTrieConcept
+ * @brief An index that can be traversed top-down as a trie.
+ * @headerfile <seqan/index.h>
+ *
+ * @signature StringTrieConcept<T>
+ */
+
+SEQAN_CONCEPT_REFINE(StringTrieConcept, (TIndex), (StringIndexConcept)) {};
 
-..see:Class.Finder
-..see:Spec.IndexEsa
-..see:Spec.IndexQGram
-..include:seqan/index.h
-*/
 
 /*!
  * @defgroup IndexFindAlgorithm Index Find Algorithm
  * @brief Tag to specify the index search algorithm.
- * @section Remarks
+ *
  * These tags can be used to specify the @link Finder#find @endlink algorithm for @link
  * Index @endlink based substring searches.
+ *
  * @see Finder
+ *
  * @tag IndexFindAlgorithm#FinderSTree
  * @brief Suffix tree search.
- * @section Remarks
+ *
  * Exact string matching using a suffix tree.
+ *
  * @tag IndexFindAlgorithm#PizzaChiliFinder
- * @brief Finds an occurrence in a @link Pizza & Chili Index @endlink index.
- * @section Remarks
+ * @brief Finds an occurrence in a @link PizzaChiliIndex @endlink index.
+ *
  * The actual algorithm used for searching depends on the @link PizzaChiliIndexTags @endlink used.
+ *
  * @tag IndexFindAlgorithm#QGramFindLookup
- * @brief q-gram search. Finds q-grams in a @link IndexQGram @endlink index
- *        using the hash table.
- * @tag IndexFindAlgorithm#EsaFindLcpe
+ * @brief q-gram search. Finds q-grams in a @link IndexQGram @endlink index using the hash table.
+ *
+ * @tag IndexFindAlgorithm#FinderLcpe
  * @brief Binary search using lcp values.
- * @section Remarks
- * Exact string matching using a suffix array binary search and a lcp-interval
- * tree.
- * @tag IndexFindAlgorithm#EsaFindMlr
+ *
+ *
+ * Exact string matching using a suffix array binary search and a lcp-interval tree.
+ *
+ * @tag IndexFindAlgorithm#FinderMlr
  * @brief Binary search with mlr-heuristic.
- * @section Remarks
- * Exact string matching using a suffix array binary search with the mlr-
- * heuristic.
+ *
+ * Exact string matching using a suffix array binary search with the mlr-heuristic.
  */
-// finder tags
-struct FinderMlr_;         // simple Suffix Array finder with mlr-heuristic
-struct FinderLcpe_;        // Suffix Array finder using an enhanced LCP-Table
-struct FinderSTree_;        // Suffix Array finder using an enhanced LCP-Table
+    // finder tags
+    struct FinderMlr_;     // simple Suffix Array finder with mlr-heuristic
+    struct FinderLcpe_;    // Suffix Array finder using an enhanced LCP-Table
+    struct FinderSTree_;    // Suffix Array finder using an enhanced LCP-Table
 
-typedef Tag<FinderMlr_> const EsaFindMlr;
-typedef Tag<FinderLcpe_> const EsaFindLcpe;
-typedef Tag<FinderSTree_> const FinderSTree;
+    typedef Tag<FinderMlr_> const FinderMlr;
+    typedef Tag<FinderLcpe_> const FinderLcpe;
+    typedef Tag<FinderSTree_> const FinderSTree;
 
-template <typename TSpec = void>
-struct IndexEsa {};
+    template <typename TSpec = void>
+    struct IndexEsa {};
 
 
 // ----------------------------------------------------------------------------
 // Metafunction DefaultIndexSpec
 // ----------------------------------------------------------------------------
-/**
-.Metafunction.DefaultIndexSpec:
-..cat:Index
-..summary:Default @Class.Index@ specialization type.
-..signature:DefaultIndexSpec<TText>::Type
-..class:Class.Index
-..param.TText:The given text type.
-..returns:Can be @Spec.IndexEsa@ or $IndexQGram$, etc.
-..remarks:Currently @Spec.IndexEsa@ is default if $TText$ is a @Class.String@.
-..include:seqan/index.h
-*/
 /*!
  * @mfn Index#DefaultIndexSpec
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Default @link Index @endlink specialization type.
- * @signature template <typename TText>
- *            DefaultIndexSpec<TText>::Type
+ *
+ * @signature DefaultIndexSpec<TText>::Type;
+ *
  * @tparam TText The given text type.
+ *
  * @return TReturn Currently the return type is @link IndexEsa @endlink.
- * @section Example The following will define <tt>TIndex</tt> to be of type @link IndexEsa @endlink, because the
- *          default index type for @link String @endlink or @link StringSet @endlink is @link IndexEsa @endlink.
+ *
+ * @section Examples
+ *
+ * The following will define <tt>TIndex</tt> to be of type @link IndexEsa @endlink, because the
+ * default index type for @link String @endlink or @link StringSet @endlink is @link IndexEsa @endlink.
+ *
  * @code{.cpp}
  * typedef DefaultIndexSpec<String<Dna> >::Type TIndex;
  * @endcode
  */
-template <typename TObject>
-struct DefaultIndexSpec
-{
-    typedef IndexEsa<> Type;
-};
+    template < typename TObject >
+    struct DefaultIndexSpec {
+        typedef IndexEsa<> Type;
+    };
 
 // ----------------------------------------------------------------------------
 // Metafunction DefaultIndexStringSpec
 // ----------------------------------------------------------------------------
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Metafunction.DefaultIndexStringSpec:
-..cat:Index
-..summary:Default @Class.String@ specialization type of the @Metafunction.Fibre@ of an @Class.Index@.
-..signature:DefaultIndexStringSpec<TIndex>::Type
-..class:Class.Index
-..param.TIndex:An @Class.Index@ Type.
-..returns:If the underlying text is a @Class.String@ or a set of Strings (see @Class.StringSet@) the String's spec. type is returned.
-..remarks:Most of the @Class.Index@ fibres are strings. The @Class.String@ specialization type is chosen by this meta-function.
-..include:seqan/index.h
-*/
+//NOTE(esiragusa): Deprecated in favor of StringSpec.
 
-//TODO(singer): Does not belong here but to the text concept
 /*!
  * @mfn Index#DefaultIndexStringSpec
- * @headerfile seqan/index.h
- * @brief Default @link String @endlink specialization type of the @link Index#Fibre
+ * @headerfile <seqan/index.h>
+ * @brief Default @link String @endlink specialization type of the @link Fibre
  *        @endlink of an @link Index @endlink.
- * @signature template <typename TIndex>
- *            DefaultIndexStringSpec<TIndex>::Type
+ *
+ * @signature DefaultIndexStringSpec<TIndex>::Type;
+ *
  * @tparam TIndex An @link Index @endlink Type.
+ *
  * @return TReturn If the underlying text is a @link String @endlink or a set of
  *                 Strings (see @link StringSet @endlink) the String's spec.
  *                 type is returned.
+ *
  * @section Remarks
  *
  * Most of the @link Index @endlink fibres are strings. The @link String
  * @endlink specialization type is chosen by this meta-function.
  */
-// default which should actually never been used
-template <typename TIndex>
-struct DefaultIndexStringSpec
-{
-    typedef Alloc<> Type;
-};
 
-template <typename TValue, typename TSpec>
-struct DefaultIndexStringSpec<String<TValue, External<TSpec> > >
-{
-    typedef External<TSpec> Type;
-};
+    template <typename TObject>
+    struct DefaultIndexStringSpec : StringSpec<TObject> {};
 
-template <typename TString, typename TSpec>
-struct DefaultIndexStringSpec<StringSet<TString, TSpec> >:
-    DefaultIndexStringSpec<TString>{};
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Class.Index:
-..summary:Contains preprocessing data of a fixed text. In combination with a @Class.Finder@ or a @Spec.VSTree Iterator@ it allows fast dictionary look-up and advanced computations.
-..cat:Index
-..signature:Index<TText[, TSpec]>
-..param.TText:The text type.
-...type:Class.String
-...type:Class.StringSet
-...metafunction:Metafunction.Host
-..param.TSpec:The index type.
-...type:Spec.IndexEsa
-...type:Spec.IndexWotd
-...type:Spec.IndexQGram
-...type:Spec.FMIndex
-...default:The result of @Metafunction.DefaultIndexSpec@: @Spec.IndexEsa@
-...metafunction:Metafunction.Spec
-..remarks:Indices allow fast dictionary look-ups and other advanced computations because they contain pre-computated
-information about the underlying text. These information are stored in so called fibres (see @Metafunction.Fibre@).
-..remarks:In order to search for a pattern one can use a @Class.Finder@ or a @Spec.VSTree Iterator@. The @Class.Finder@
-is especially useful when searching for exact matches while the @Spec.VSTree Iterator@ allows to iterate an index as if
-traversing a tree/trie.
-..remarks:These fibres are created on demand depending on the requirements of an algorithm.
-..include:seqan/index.h
-..example
-...text:The following code shows how to search for exact matches between the reference "tobeornottobe" and the
-pattern "to" with the means of a Finder.
-...file:demos/index/index_finder.cpp
-...output:Hit at position: 9
-Hit at position: 0
-...text:This code shows how an index can be used with iterators to achieve a pre-order tree like traversal
-in DFS of the text "tobeornottobe". In order to do so a Top-Down History iterator is used.
-...file:demos/index/index_iterator.cpp
-...output:
-
-be
-beornottobe
-e
-eornottobe
-nottobe
-o
-obe
-obeornottobe
-ornottobe
-ottobe
-rnottobe
-t
-tobe
-tobeornottobe
-ttobe
-...text:
-Note that you can also use specialised iterators such as:
-...code:Iterator<TIndex, TopDown<ParentLinks<PreOrder> > >::Type
-...text:or
-...code:Iterator<TIndex, TopDown<ParentLinks<PostOrder> > >::Type
-...text:You can achieve a post-order traversal like this:
-...snippet:demos/index/index_iterator_short.cpp|iteration
-...output:beornottobe
-be
-eornottobe
-e
-nottobe
-obeornottobe
-obe
-ornottobe
-ottobe
-o
-rnottobe
-tobeornottobe
-tobe
-ttobe
-t
-
-*/
-
 template <
-    typename TObject,
-    typename TSpec = typename DefaultIndexSpec<TObject>::Type>
-class Index;
+        typename TObject,
+        typename TSpec = typename DefaultIndexSpec<TObject>::Type >
+    class Index;
 
 /*!
  * @class Index
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Indices are data structures which contain preprocessing data of a fixed text (or set of texts). In combination
  *        with a @link Finder @endlink or an @link VSTreeIterator @endlink it allows fast dictionary look-up and advanced computations.
- * @signature template <typename TText, typename TSpec>
- *            Index<TText[, TSpec]>
+ *
+ * @signature class Index<TText[, TSpec]>;
+ *
  * @tparam TSpec The index type.
  * @tparam TText The text type. Types: @link String @endlink, @link StringSet @endlink
- * @section Remarks
  *
- * An index contains various arrays or objects, also called fibres (see @link Index#Fibre @endlink).
+ *
+ * An index contains various arrays or objects, also called fibres (see @link Fibre @endlink).
  * These fibres are created on demand depending on the requirements of an algorithm. To force the fibre creation you can
  * use the function @link Index#indexCreate @endlink.
- * The list of fibres is available in @link Index#Fibre @endlink
- * @section Example
+ * The list of fibres is available in @link Fibre @endlink
+ *
+ * @section Examples
  *
  * The following code shows how to search for exact matches between the reference "tobeornottobe" and the
  * pattern "to" with the means of a Finder.
- * @include demos/index/index_finder.cpp
- * @include demos/index/index_finder.cpp.stdout
- 
+ *
+ * @include demos/dox/index/finder.cpp
+ *
+ * The result is as follows
+ *
+ * @include demos/dox/index/finder.cpp.stdout
+ *
  * This code shows how an index can be used with iterators to achieve a pre-order tree like traversal
  * in DFS of the text "tobeornottobe". In order to do so a Top-Down History iterator is used.
- * @include demos/index/index_iterator.cpp
+ *
+ * @include demos/dox/index/iterator.cpp
  *
  * The result is as follows
  *
- * @include demos/index/index_iterator.cpp.stdout
+ * @include demos/dox/index/iterator.cpp.stdout
  *
  * Note that you can also use specialized iterators such as:
+ *
  * @code{.cpp}
  * Iterator<TIndex, TopDown<ParentLinks<PreOrder> > >::Type
  * @endcode
+ *
  * or
+ *
  * @code{.cpp}
  * Iterator<TIndex, TopDown<ParentLinks<PostOrder> > >::Type
  * @endcode
  *
  * You can achieve a post-order traversal like this:
  *
- * @snippet demos/index/index_iterator_short.cpp iteration
- * @include demos/index/index_iterator_short.cpp.stdout
+ * @snippet demos/dox/index/iterator_short.cpp iteration
+ *
+ * The result is as follows
+ *
+ * @include demos/dox/index/iterator_short.cpp.stdout
  */
 
-template <typename TObject, typename TSpec>
-struct Host<Index<TObject, TSpec> >
-{
-    typedef TObject Type;
-};
-
-template <typename TObject, typename TSpec>
-struct Spec<Index<TObject, TSpec> >
-{
-    typedef TSpec Type;
-};
-/**
-.Metafunction.Fibre:
-..summary:Type of a specific container member (fibre).
-..signature:Fibre<TContainer, TSpec>::Type
-..class:Class.Index
-..cat:Index
-..param.TContainer:The container type.
-...type:Class.Index
-..param.TSpec:Tag to specify the fibre.
-..returns:Fibre type.
-..remarks:Some containers, such as @Class.Index@, can be seen as a bundle consisting of various fibres. Because not every table is a fibre we did not call them tables, however, in many cases one can think of fibres as tables. The fibre interface was designed to unify the access to the members of the different fibres.
-To get a reference or the type of a specific fibre use @Function.getFibre@ or @Metafunction.Fibre@.
-..remarks:A @Metafunction.Fibre@ does not need to be a real container. It can also be a view (see @Tag.ESA Index Fibres.EsaRawText@).
-..include:seqan/index.h
-*/
+    template <typename TObject, typename TSpec>
+    struct Host< Index<TObject, TSpec> > {
+        typedef TObject Type;
+    };
 
+    template <typename TObject, typename TSpec>
+    struct Spec< Index<TObject, TSpec> > {
+        typedef TSpec Type;
+    };
 /*!
- * @mfn Index#Fibre
- * @headerfile seqan/index.h
+ * @mfn Fibre
+ * @headerfile <seqan/index.h>
  * @brief Type of a specific container member (fibre).
- * @signature template <typename TIndex, TSpec>
- *            Fibre<TIndex, TSpec>::Type
- * @tparam TSpec Tag to specify the fibre. Types: @link IndexEsaFibres @endlink, @link WaveletTreeFibres @endlink,
- *               @link RightArrayBinaryTreeFibres @endlink, @link SentinelRankDictionaryFibres @endlink
- * @tparam TContainer The container type. Types: Index, RankDictionary,
- *                    RightArrayBinaryTree
+ *
+ * @signature Fibre<TObject, TSpec>::Type;
+ *
+ * @tparam TSpec Tag to specify the fibre. Types: @link IndexEsaFibres @endlink, @link FMIndexFibres @endlink, @link
+ *               QGramIndexFibres @endlink, @link WOTDIndexFibres @endlink, @link WaveletTreeFibres @endlink, @link
+ *               RightArrayBinaryTreeFibres @endlink, @link RankDictionaryFibres @endlink, @link
+ *               SentinelRankDictionaryFibres @endlink
+ * @tparam TObject The container type. Types: @link Index @endlink, @link RankDictionary @endlink, @link SparseString
+ *                 @endlink, @link CompressedSA @endlink
+ *
  * @return Type Fibre type.
- * @section Remarks
  *
- * Some containers, such as @link Index @endlink, can be seen as a bundle consisting of various fibres.  Because not
- * every table is a fibre we did not call them tables, however, in many cases one can think of fibres as tables.  The
- * fibre interface was designed to unify the access to the members of the different fibres.  To get a reference or the
- * type of a specific fibre use @link Index#getFibre @endlink or @link Index#Fibre @endlink.  A @link Index#Fibre @endlink does not need
- * to be a real container.
- * @see Index#getFibre
+ * @section Naming
+ *
+ * Some containers, such as the @link Index @endlink or the @link RankDictionary @endlink, can be seen as a collection
+ * of tables.  However, each table alone is just a collection of information.  They only become powerful if used
+ * together.  Therefore, a more appropriate label for the tables is fibre, like the fibres of a rope.
+ *
+ * In addition, sometimes a fibre can be a single value and calling it a table would be misleading.
  */
 
-// meta function to get the type of a bundle fibre
-template <typename TIndex, typename TSpec>
-struct Fibre
-{
-    typedef String<typename Size<TIndex>::Type> Type;
-};
-
-template <typename TIndex, typename TSpec>
-struct Fibre<TIndex const, TSpec>
-{
-    typedef typename Fibre<TIndex, TSpec>::Type const Type;
-};
+    // meta function to get the type of a bundle fibre
+    template < typename TIndex, typename TSpec >
+    struct Fibre {
+        typedef String< typename Size<TIndex>::Type > Type;
+    };
 
-struct FibreRecord
-{
-    unsigned    id;
-    void * ptr;
-    bool        owner;
-};
+    template < typename TIndex, typename TSpec >
+    struct Fibre<TIndex const, TSpec> {
+        typedef typename Fibre<TIndex, TSpec>::Type const Type;
+    };
 
-// less function to search in sorted list for fibre id
-struct FibreLess :
-    public::std::binary_function<FibreRecord, unsigned, bool> // functor for operator>
-{
-    inline bool operator()(FibreRecord const & _Left, unsigned const Right_) const // apply operator> to operands
-    {
-        return _Left.id < Right_;
-    }
+    struct FibreRecord {
+        unsigned    id;
+        void*        ptr;
+        bool        owner;
+    };
 
-};
+    // less function to search in sorted list for fibre id
+    struct FibreLess: public std::binary_function<FibreRecord, unsigned, bool>
+    {    // functor for operator>
+        inline bool operator()(FibreRecord const & _Left, unsigned const Right_) const
+        {    // apply operator> to operands
+            return (_Left.id < Right_);
+        }
+    };
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Metafunction.DefaultIndexCreator:
-..cat:Index
-..summary:Default algorithm to create a demanded and not yet existing @Metafunction.Fibre@.
-..signature:DefaultIndexCreator<TIndex, TFibre>::Type
-..class:Class.Index
-..param.TIndex:An @Class.Index@ Type.
-..param.TFibre:A tag specifying the fibre (e.g. @Tag.ESA Index Fibres.EsaSA@).
-..returns:A tag specifying the default algorithm to create the fibre with.
-..include:seqan/index.h
-*/
-
 /*!
  * @mfn Index#DefaultIndexCreator
- * @headerfile seqan/index.h
- * @deprecated advanced
- * @brief Default algorithm to create a demanded and not yet existing @link Index#Fibre @endlink.
- * @signature template <typename TIndex>
- *            DefaultIndexCreator<TIndex, TFibre>::Type
+ * @headerfile <seqan/index.h>
+ * @note Advanced functionality, not commonly used.
+ * @brief Default algorithm to create a demanded and not yet existing @link Fibre @endlink.
+ *
+ * @signature DefaultIndexCreator<TIndex, TFibre>::Type;
+ *
  * @tparam TIndex An @link Index @endlink Type.
- * @tparam TFibre A tag specifying the fibre (e.g. @link ESAIndexFibres.EsaSA
+ * @tparam TFibre A tag specifying the fibre (e.g. @link IndexEsaFibres#EsaSA
  *                @endlink).
- * @return TReturn A tag specifying the default algorithm to create the fibre
- *                 with.    // standard algorithm for indices creation
+ *
+ * @return Type A tag specifying the default algorithm to create the fibre with.
  */
 
-template <typename TIndex, typename TFibre>
-struct DefaultIndexCreator
-{
-    typedef Default Type;
-};
+    template < typename TIndex, typename TFibre >
+    struct DefaultIndexCreator {
+        typedef Default Type;
+    };
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <
-    typename TSA,
-    typename TText,
-    typename TAlgSpec>
-struct SACreatorRandomAccess_
-{
-    typedef typename AllowsFastRandomAccess<TSA>::Type   TRandomSA;
-    typedef typename AllowsFastRandomAccess<TText>::Type TRandomText;
-    typedef typename And<TRandomText, TRandomSA>::Type Type;
-};
+    template <
+        typename TSA,
+        typename TText,
+        typename TAlgSpec >
+    struct SACreatorRandomAccess_
+    {
+        typedef typename AllowsFastRandomAccess<TSA>::Type   TRandomSA;
+        typedef typename AllowsFastRandomAccess<TText>::Type TRandomText;
+        typedef typename And<TRandomText,TRandomSA>::Type Type;
+    };
 
-template <
-    typename TLCP,
-    typename TText,
-    typename TSA,
-    typename TAlgSpec>
-struct LcpCreatorRandomAccess_
-{
-    typedef typename AllowsFastRandomAccess<TText>::Type TRandomText;
-    typedef typename AllowsFastRandomAccess<TLCP>::Type  TRandomLCP;
-    typedef typename AllowsFastRandomAccess<TSA>::Type   TRandomSA;
-    typedef typename And<TRandomLCP, typename And<TRandomText, TRandomSA>::Type>::Type Type;
-};
+    template <
+        typename TLCP,
+        typename TText,
+        typename TSA,
+        typename TAlgSpec >
+    struct LcpCreatorRandomAccess_
+    {
+        typedef typename AllowsFastRandomAccess<TText>::Type TRandomText;
+        typedef typename AllowsFastRandomAccess<TLCP>::Type  TRandomLCP;
+        typedef typename AllowsFastRandomAccess<TSA>::Type   TRandomSA;
+        typedef typename And<TRandomLCP, typename And<TRandomText,TRandomSA>::Type>::Type Type;
+    };
 
 
 //////////////////////////////////////////////////////////////////////////////
-/*
-    .Class.Bundle:
-    ..summary:General purpose container of various members.
-    ..signature:Bundle<TValue, TSize>
-    ..param.TValue:The value type, that is the type of the items/characters stored in the string.
-    ...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-    ..param.TSpec:The specializing type.
-    ...default:$Alloc<>$, see @Spec.Alloc String@.
-*/
+
 /*
     template < typename TSpec = void >
     truct Bundle {
-        typedef ::std::vector<FibreRecord>	TFibreRecords;
-        TFibreRecords						fibres;
+        typedef std::vector<FibreRecord>    TFibreRecords;
+        TFibreRecords                        fibres;
     };
 
     template < typename TBundleSpec, typename TFibreSpec >
@@ -527,73 +441,45 @@ struct LcpCreatorRandomAccess_
 //////////////////////////////////////////////////////////////////////////////
 // various fibre specs for enhanced suffix arrays
 
-struct FibreText_;          // Original text. Can be a String or a StringSet
-struct FibreRawText_;       // Concatenation of the strings above
-struct FibreSA_;            // suffix array (of raw text with virtual $-delimiters) with Pair entries
-struct FibreRawSA_;     // suffix array with integer entries
-struct FibreSae_;           // suffix array reordered in a b-tree
-struct FibreLcp_;           // lcp table of raw text
-struct FibreLcpe_;          // lcp interval tree
-struct FibreChildtab_;      // childtab (Kurtz et al.) of raw text
-struct FibreBwt_;           // burrows wheeler table of raw text
-
-typedef Tag<FibreText_> const       FibreText;
-typedef Tag<FibreRawText_> const    FibreRawText;
-typedef Tag<FibreSA_> const         FibreSA;
-typedef Tag<FibreRawSA_> const      FibreRawSA;
-typedef Tag<FibreSae_> const        FibreSae;
-typedef Tag<FibreLcp_> const        FibreLcp;
-typedef Tag<FibreLcpe_> const       FibreLcpe;
-typedef Tag<FibreChildtab_> const   FibreChildtab;
-typedef Tag<FibreBwt_> const        FibreBwt;
+    struct FibreText_;      // Original text. Can be a String or a StringSet
+    struct FibreRawText_;   // Concatenation of the strings above
+    struct FibreSA_;        // suffix array (of raw text with virtual $-delimiters) with Pair entries
+    struct FibreRawSA_;     // suffix array with integer entries
+    struct FibreIsa_;       // inverse suffix array.
+    struct FibreSae_;       // suffix array reordered in a b-tree
+    struct FibreLcp_;       // lcp table of raw text
+    struct FibreLcpe_;      // lcp interval tree
+    struct FibreChildtab_;  // childtab (Kurtz et al.) of raw text
+    struct FibreBwt_;       // burrows wheeler table of raw text
+
+    typedef Tag<FibreText_> const      FibreText;
+    typedef Tag<FibreRawText_> const   FibreRawText;
+    typedef Tag<FibreSA_> const        FibreSA;
+    typedef Tag<FibreRawSA_> const     FibreRawSA;
+    typedef Tag<FibreIsa_> const       FibreIsa;
+    typedef Tag<FibreSae_> const       FibreSae;
+    typedef Tag<FibreLcp_> const       FibreLcp;
+    typedef Tag<FibreLcpe_> const      FibreLcpe;
+    typedef Tag<FibreChildtab_> const  FibreChildtab;
+    typedef Tag<FibreBwt_> const       FibreBwt;
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Metafunction.SAValue:
-..cat:Index
-..summary:The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set.
-..signature:SAValue<TObject>::Type
-..class:Class.Index
-..param.TObject:A string, string set, or index type.
-...type:Class.String
-...type:Class.StringSet
-...type:Class.Index
-..returns:A type to store a position.
-...text:If $TObject$ is a @Class.String@, it is a single integer value. By default this is the @Metafunction.Size@ type of $TObject$.
-...text:If $TObject$ is a @Class.StringSet@, it could be a single integer too (called global position, see @Spec.ConcatDirect@) or a @Class.Pair@ (called local position, see @Spec.Owner@).
-Currently SeqAn defaults to a local position for @Class.StringSet@ classes (index_base.h).
-..example.code:template < typename TString, typename TSpec >
-struct SAValue< StringSet<TString, TSpec> > {
-    typedef Pair<
-        typename Size< StringSet<TString, TSpec> >::Type,
-        typename SAValue<TString>::Type,
-        Pack
-    > Type;
-};
-..remarks.note:SAValue is the return type of various function, e.g. @Function.position@ for the @Class.Index@ @Class.Finder@ class, @Function.getOccurrence@, @Function.getOccurrences@ etc.
-You should always use the type of this meta-function to store the return values.
-If you want to write algorithms for both variants (local and global positions) you
-should use the functions @Function.posLocalize@, @Function.posGlobalize@, @Function.getSeqNo@ and @Function.getSeqOffset@.
-..remarks.note:If $TObject$ is an @Class.Index@, @Metafunction.Position@ returns the same value as $SAValue$. You can change the position type of an index by overloading $SAValue$, not @Metafunction.Position@.
-..include:seqan/index.h
-*/
-
 /*!
  * @mfn SAValue
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief The default alphabet type of a suffix array, i.e. the type to store a
  *        position of a string or string set.
- * @signature template <typename TObject>
- *            SAValue<TObject>::Type
+ *
+ * @signature SAValue<TObject>::Type;
+ *
  * @tparam TObject A string, string set, or index type. Types: @link String @endlink, @link StringSet @endlink,
  *                 @link Index @endlink
  * @return TReturn A type to store a position.If <tt>TObject</tt> is a @link String @endlink, it is a single integer
  *                 value. By default this is the @link Size @endlink type of <tt>TObject</tt>.If <tt>TObject</tt> is a
  *                 @link StringSet @endlink, it could be a single integer too (called global position, see @link
- *                 ConcatDirect @endlink) or a @link Pair @endlink (called local position, see @link Owner @endlink).
- *                 Currently SeqAn defaults to a local position for @link StringSet @endlink classes (index_base.h).
- *
- * @section Remark
+ *                 ConcatDirectStringSet @endlink) or a @link Pair @endlink (called local position, see
+ *                 @link OwnerStringSet @endlink).  Currently SeqAn defaults to a local position for @link StringSet
+ *                 @endlink classes (index_base.h).
  *
  * SAValue is the return type of various functions, e.g. @link Finder#position @endlink for the Index @link Finder @endlink
  * class, @link VSTreeIterator#getOccurrence @endlink, @link VSTreeIterator#getOccurrences @endlink, @link IndexQGram#getOccurrences
@@ -601,10 +487,8 @@ should use the functions @Function.posLocalize@, @Function.posGlobalize@, @Funct
  * algorithms for both variants (local and global positions) you should use the functions @link TextConcept#posLocalize @endlink,
  * @link TextConcept#posGlobalize @endlink, @link TextConcept#getSeqNo @endlink and @link TextConcept#getSeqOffset @endlink.
  *
- * @section Note
- *
- * If <tt>TObject</tt> is an @link Index @endlink, @link Position @endlink returns the same value as <tt>SAValue</tt>.
- * You can change the position type of an index by overloading <tt>SAValue</tt>, not @link Position @endlink.
+ * @note If <tt>TObject</tt> is an @link Index @endlink, @link Position @endlink returns the same value as <tt>SAValue</tt>.
+ *       You can change the position type of an index by overloading <tt>SAValue</tt>, not @link Position @endlink.
  *
  * @section Examples
  *
@@ -612,35 +496,29 @@ should use the functions @Function.posLocalize@, @Function.posGlobalize@, @Funct
  * @code{.cpp}
  * template < typename TString, typename TSpec >
  * struct SAValue< StringSet<TString, TSpec> > {
- *  typedef Pair<
- *      typename Size< StringSet<TString, TSpec> >::Type,
- *      typename SAValue<TString>::Type,
- *      Pack
- *  > Type;
+ *     typedef Pair<
+ *         typename Size< StringSet<TString, TSpec> >::Type,
+ *         typename SAValue<TString>::Type,
+ *         Pack
+ *     > Type;
  * };
  * @endcode
  * @see orderOccurrences
  */
 
-template <typename TObject>
-struct SAValue :
-    Size<TObject>{};
+    template <typename TObject>
+    struct SAValue:
+        Position<TObject> {};
 
-template <typename TObject>
-struct SAValue<TObject const>:
-    SAValue<TObject>{};
+    template <typename TObject>
+    struct SAValue<TObject const>:
+        SAValue<TObject> {};
 
-// to speed up sequence number computation
-// we use a pair of seqNo and localPosition
-template <typename TString, typename TSpec>
-struct SAValue<StringSet<TString, TSpec> >
-{
-    typedef Pair<
-        typename Size<StringSet<TString, TSpec> >::Type,
-        typename SAValue<TString>::Type,
-        Pack
-        > Type;
-};
+    // to speed up sequence number computation
+    // we use a pair of seqNo and localPosition
+    template <typename TString, typename TSpec>
+    struct SAValue<StringSet<TString, TSpec> > :
+        StringSetPosition<StringSet<TString, TSpec> > {};
 
 /*
     template < typename TString, typename TSpec >
@@ -648,126 +526,146 @@ struct SAValue<StringSet<TString, TSpec> >
         typedef Pair<
             typename Size< StringSet<TString, TSpec> >::Type,
             typename SAValue<TString>::Type,
-            BitPacked<2,30>						    // max. 4 sequences
-        > Type;										// max. 2^30 characters each
+            BitPacked<2,30>                            // max. 4 sequences
+        > Type;                                        // max. 2^30 characters each
     };
 */
-template <typename TText, typename TSpec>
-struct SAValue<Index<TText, TSpec> >:
-    SAValue<TText>{};
+    template < typename TText, typename TSpec >
+    struct SAValue< Index<TText, TSpec> >:
+        SAValue<TText> {};
 
-template <typename TObject, typename TSpec>
-struct DefaultIndexStringSpec<Index<TObject, TSpec> >:
-    DefaultIndexStringSpec<TObject>{};
+    template <typename TText, typename TSpec>
+    struct StringSpec<Index<TText, TSpec> > : StringSpec<TText> {};
 
 //////////////////////////////////////////////////////////////////////////////
 // value and size type of an index
 
-template <typename TText, typename TSpec>
-struct Value<Index<TText, TSpec> >
-{
-    typedef typename Value<
-        typename Fibre<Index<TText, TSpec>, FibreRawText>::Type
+    template < typename TText, typename TSpec >
+    struct Value< Index<TText, TSpec> > {
+        typedef typename Value<
+            typename Fibre< Index<TText, TSpec>, FibreRawText>::Type
         >::Type Type;
-};
+    };
 
-template <typename TText, typename TSpec>
-struct Size<Index<TText, TSpec> >
-{
-    typedef typename Size<
-        typename Fibre<Index<TText, TSpec>, FibreRawText>::Type
-        >::Type Type;
-};
+/*!
+ * @mfn Index#Size
+ * @headerfile <seqan/index.h>
+ * @brief Returns the size type of an Index.
+ *
+ * @signature Size<TIndex>::Type;
+ *
+ * @tparam TIndex The Index specialization.
+ *
+ * @return Type The resulting size type of the index.
+ */
+
+    template < typename TText, typename TSpec >
+    struct Size< Index<TText, TSpec> > {
+        typedef typename LengthSum<TText>::Type Type;
+    };
 
-template <typename TText, typename TSpec>
-struct Position<Index<TText, TSpec> >:
-    SAValue<Index<TText, TSpec> >{};
+    template < typename TText, typename TSpec >
+    struct Position< Index<TText, TSpec> >:
+        SAValue< Index<TText, TSpec> > {};
 
 //////////////////////////////////////////////////////////////////////////////
 // infix of an index
 
-template <typename TText, typename TSpec>
-struct Infix<Index<TText, TSpec> >:
-    public Infix<TText>{};
+    template < typename TText, typename TSpec >
+    struct Infix< Index<TText, TSpec> >:
+        public Infix<TText> {};
 
-template <typename TText, typename TSpec>
-struct Infix<Index<TText, TSpec> const>:
-    public Infix<TText>{};
+    template < typename TText, typename TSpec >
+    struct Infix< Index<TText, TSpec> const >:
+        public Infix<TText> {};
 
 //////////////////////////////////////////////////////////////////////////////
 // default table type
 
-template <typename TObject, typename TSpec, typename TFibre>
-struct Fibre<Index<TObject, TSpec>, Tag<TFibre> const>
-{
-    typedef String<
-        typename Size<Index<TObject, TSpec> >::Type,
-        typename DefaultIndexStringSpec<Index<TObject, TSpec> >::Type
+    template < typename TObject, typename TSpec, typename TFibre >
+    struct Fibre< Index<TObject, TSpec>, Tag<TFibre> const > {
+        typedef String<
+            typename Size< Index<TObject, TSpec> >::Type,
+            typename StringSpec< Index<TObject, TSpec> >::Type
         > Type;
-};
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 // original text
 
-template <typename TText, typename TSpec>
-struct Fibre<Index<TText, TSpec>, FibreText>
-{
-    typedef TText Type;
-};
+    template < typename TText, typename TSpec >
+    struct Fibre< Index<TText, TSpec>, FibreText> {
+        typedef TText Type;
+    };
+
+//////////////////////////////////////////////////////////////////////////////
+// type of the text member
+
+    template <typename TText, typename TSpec>
+    struct Member<Index<TText, TSpec>, FibreText>
+    {
+        typedef Holder<typename Fibre<Index<TText, TSpec>, FibreText>::Type>    Type;
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 // concatenated text
 
-template <typename TText, typename TSpec>
-struct Fibre<Index<TText, TSpec>, FibreRawText>
-{
-    typedef typename Concatenator<TText>::Type Type;
-};
+    template < typename TText, typename TSpec >
+    struct Fibre< Index<TText, TSpec>, FibreRawText> {
+        typedef typename Concatenator<TText>::Type Type;
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 // suffix array type
 
-template <typename TText, typename TSpec>
-struct Fibre<Index<TText, TSpec>, FibreSA>
-{
-    typedef String<
-        typename SAValue<Index<TText, TSpec> >::Type,
-        typename DefaultIndexStringSpec<Index<TText, TSpec> >::Type
+    template < typename TText, typename TSpec >
+    struct Fibre< Index<TText, TSpec>, FibreSA> {
+        typedef String<
+            typename SAValue< Index<TText, TSpec> >::Type,
+            typename StringSpec< Index<TText, TSpec> >::Type
         > Type;
-};
+    };
 
 //////////////////////////////////////////////////////////////////////////////
-// globalize functor
+// lcp type
 
-template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
-struct FunctorGlobalize :
-    public::std::unary_function<InType, Result>
-{
-    TLimitsString const * limits;
-    FunctorGlobalize() {}
-    FunctorGlobalize(TLimitsString const & _limits) :
-        limits(&_limits) {}
+    template <typename TText, typename TSSetSpec, typename TSpec>
+    struct Fibre<Index<StringSet<TText, TSSetSpec>, TSpec>, FibreLcp>
+    {
+        typedef String<
+            typename Size<TText>::Type,
+            typename StringSpec<Index<StringSet<TText, TSSetSpec>, TSpec> >::Type
+        > Type;
+    };
 
-    inline Result operator()(InType const & x) const
+//////////////////////////////////////////////////////////////////////////////
+// globalize functor
+
+    template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
+    struct FunctorGlobalize : public std::unary_function<InType,Result>
     {
-        return posGlobalize(x, *limits);
-    }
+        TLimitsString const * limits;
 
-};
+        FunctorGlobalize() : limits() {}
+        FunctorGlobalize(TLimitsString const &_limits) : limits(&_limits) {}
 
-template <typename InType, typename Result>
-struct FunctorGlobalize<InType, Nothing, Result>:
-    public::std::unary_function<InType, InType>
-{
-    FunctorGlobalize() {}
-    FunctorGlobalize(Nothing const &) {}
+        inline Result operator()(InType const &x) const
+        {
+            return posGlobalize(x, *limits);
+        }
+    };
 
-    inline InType operator()(InType const & x) const
+    template <typename InType, typename Result>
+    struct FunctorGlobalize<InType, Nothing, Result> : public std::unary_function<InType,InType>
     {
-        return x;
-    }
+        FunctorGlobalize() {}
+        FunctorGlobalize(Nothing const &) {}
 
-};
+        inline InType operator()(InType const &x) const
+        {
+            return x;
+        }
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 // raw suffix array contains integer offsets relative to raw text
@@ -789,158 +687,147 @@ struct FunctorGlobalize<InType, Nothing, Result>:
         > Type;
     };
 */
-template <typename TText, typename TSpec>
-struct Fibre<Index<TText, TSpec>, FibreRawSA>
-{
-    typedef Index<TText, TSpec> TIndex;
-    typedef ModifiedString<
-        typename Fibre<TIndex, FibreSA>::Type,
-        ModView<FunctorGlobalize<
-                    typename Value<typename Fibre<TIndex, FibreSA>::Type>::Type,
-                    typename StringSetLimits<TText>::Type>
-                >
+    template < typename TText, typename TSpec >
+    struct Fibre< Index<TText, TSpec>, FibreRawSA>
+    {
+        typedef Index<TText, TSpec> TIndex;
+        typedef ModifiedString<
+            typename Fibre<TIndex, FibreSA>::Type,
+            ModView< FunctorGlobalize<
+                typename Value< typename Fibre<TIndex, FibreSA>::Type >::Type,
+                typename StringSetLimits<TText>::Type >
+            >
         > Type;
-};
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 // default burrows-wheeler table
 
-template <typename TText, typename TSpec>
-struct Fibre<Index<TText, TSpec>, FibreBwt>
-{
-    typedef String<
-        typename Value<Index<TText, TSpec> >::Type,
-        typename DefaultIndexStringSpec<Index<TText, TSpec> >::Type
+    template < typename TText, typename TSpec >
+    struct Fibre< Index<TText, TSpec>, FibreBwt> {
+        typedef String <
+            typename Value< Index<TText, TSpec> >::Type,
+            typename StringSpec< Index<TText, TSpec> >::Type
         > Type;
-};
+    };
 
 
 //////////////////////////////////////////////////////////////////////////////
 // default fibre creators
 
-template <typename TText, typename TSpec>
-struct DefaultIndexCreator<Index<TText, TSpec>, FibreSA>
-{
-    typedef Skew7 Type;                             // standard suffix array creator is skew7
-};
-
-template <typename TText, typename TSpec>
-struct DefaultIndexCreator<Index<TText, TSpec>, FibreLcp>
-{
-    typedef Kasai Type;
-};
+    template < typename TText, typename TSpec >
+    struct DefaultIndexCreator<Index<TText, TSpec>, FibreSA> {
+        typedef Skew7 Type;                            // standard suffix array creator is skew7
+    };
 
-template <typename TText, typename TSpec>
-struct DefaultIndexCreator<Index<TText, TSpec>, FibreBwt>
-{
-    typedef Bwt Type;
-};
+    template < typename TText, typename TSpec >
+    struct DefaultIndexCreator<Index<TText, TSpec>, FibreIsa> {
+        typedef FromSortedSa<Serial> Type;
+    };
 
-template <typename TText, typename TSpec>
-struct DefaultIndexCreator<Index<TText, TSpec>, FibreChildtab>
-{
-    typedef Childtab Type;
-};
+    template < typename TText, typename TSpec >
+    struct DefaultIndexCreator<Index<TText, TSpec>, FibreLcp> {
+        typedef Kasai Type;
+    };
 
+    template < typename TText, typename TSpec >
+    struct DefaultIndexCreator<Index<TText, TSpec>, FibreBwt> {
+        typedef Bwt Type;
+    };
 
-template <typename TText, typename TSpec>
-inline Holder<TText> & _dataHost(Index<TText, TSpec> & index)
-{
-    return index.text;
-}
+    template < typename TText, typename TSpec >
+    struct DefaultIndexCreator<Index<TText, TSpec>, FibreChildtab> {
+        typedef Childtab Type;
+    };
 
-template <typename TText, typename TSpec>
-inline Holder<TText> const & _dataHost(Index<TText, TSpec> const & index)
-{
-    return index.text;
-}
+    template <typename TText, typename TSpec>
+    inline typename Member<Index<TText, TSpec>, FibreText>::Type &
+    _dataHost(Index<TText, TSpec> & index) {
+        return index.text;
+    }
+    template <typename TText, typename TSpec>
+    inline typename Member<Index<TText, TSpec> const, FibreText>::Type &
+    _dataHost(Index<TText, TSpec> const &index) {
+        return index.text;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.getFibre:
-..summary:Returns a specific fibre of a container.
-..signature: TObject getFibre(index, fibreTag)
-..class:Class.Index
-..cat:Index
-..param.index:The index holding the fibre.
-...type:Class.Index
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.ESA Index Fibres
-...type:Tag.QGram Index Fibres
-...type:Tag.WOTD Index Fibres
-...type:Tag.FM Index Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-..example
-...text:The following code shows a simple example how the function @Function.getFibre@ is used.
-...file:demos/index/index_begin_range_goDown_representative_repLength.cpp
-...output:The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-*/
-
 /*!
  * @fn Index#getFibre
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Returns a specific fibre of a container.
- * @signature TFibre getFibre(index, fibreTag)
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types: @link IndexEsaFibres Index Esa Fibres
- *        @endlink, @link FMIndexFibres FM Index Fibres @endlink, @link WOTDIndexFibres Index Wotd Fibres @endlink,
- *        and @link QGramIndexFibres Index QGram Fibres @endlink.
  *
- * @param index The container holding the fibre.
+ * @signature TFibre getFibre(index, fibreTag);
  *
- * @return TFibre A reference to the @link Index#Fibre @endlink object.
+ * @param[in] index    The container holding the fibre.
+ * @param[in] fibreTag A tag that identifies the @link Fibre @endlink. Types: @link IndexEsaFibres Index Esa Fibres
+ *                     @endlink, @link FMIndexFibres FM Index Fibres @endlink, @link WOTDIndexFibres Index Wotd Fibres @endlink,
+ *                     and @link QGramIndexFibres Index QGram Fibres @endlink.
  *
- * @section Example
+ * @return TFibre A reference to the @link Fibre @endlink object.
+ *
+ * @section Examples
  *
  * The following example shows how to search for a pattern in a string.
- * @include demos/index/index_getOccurrences_getFrequency_range_getFibre.cpp
- * @include demos/index/index_getOccurrences_getFrequency_range_getFibre.cpp.stdout
- * @see Index#Fibre
+ *
+ * @include demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.stdout
+ *
+ * @see Fibre
  */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreText>::Type &
-getFibre(Index<TText, TSpec>&index, FibreText)
-{
-    return value(index.text);
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreText>::Type &
-getFibre(Index<TText, TSpec> const & index, FibreText)
-{
-    return value(index.text);
-}
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec>, FibreText>::Type &
+    getFibre(Index<TText, TSpec> &index, FibreText) {
+        return value(index.text);
+    }
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec> const, FibreText>::Type &
+    getFibre(Index<TText, TSpec> const &index, FibreText) {
+        return value(index.text);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreRawText>::Type &
-getFibre(Index<TText, TSpec>&index, FibreRawText)
-{
-    return concat(value(index.text));
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreRawText>::Type &
-getFibre(Index<TText, TSpec> const & index, FibreRawText)
-{
-    return concat(value(index.text));
-}
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec>, FibreRawText>::Type &
+    getFibre(Index<TText, TSpec> &index, FibreRawText) {
+        return concat(getFibre(index, FibreText()));
+    }
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec> const, FibreRawText>::Type &
+    getFibre(Index<TText, TSpec> const &index, FibreRawText) {
+        return concat(getFibre(index, FibreText()));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreSA>::Type &
-getFibre(Index<TText, TSpec>&index, FibreSA)
-{
-    return index.sa;
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreSA>::Type &
-getFibre(Index<TText, TSpec> const & index, FibreSA)
-{
-    return index.sa;
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreSA>::Type &
+    getFibre(Index<TText, TSpec> &index, FibreSA) {
+        return index.sa;
+    }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreSA>::Type &
+    getFibre(Index<TText, TSpec> const &index, FibreSA) {
+        return index.sa;
+    }
+
+//////////////////////////////////////////////////////////////////////////////
+
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreIsa>::Type &
+    getFibre(Index<TText, TSpec> &index, FibreIsa) {
+        return index.isa;
+    }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreIsa>::Type &
+    getFibre(Index<TText, TSpec> const &index, FibreIsa) {
+        return index.isa;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 /*
@@ -970,1087 +857,734 @@ getFibre(Index<TText, TSpec> const & index, FibreSA)
     }
 */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreRawSA>::Type
-getFibre(Index<TText, TSpec> & index, FibreRawSA)
-{
-    typedef Index<TText, TSpec> TIndex;
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec>, FibreRawSA>::Type
+    getFibre(Index<TText, TSpec> &index, FibreRawSA)
+    {
+        typedef Index<TText, TSpec> TIndex;
 
-    typedef FunctorGlobalize<
-        typename Value<typename Fibre<TIndex, FibreSA>::Type>::Type,
-        typename StringSetLimits<TText>::Type
+        typedef FunctorGlobalize<
+            typename Value< typename Fibre<TIndex, FibreSA>::Type >::Type,
+            typename StringSetLimits<TText>::Type
         > TFunctor;
 
-    typedef ModifiedString<
-        typename Fibre<Index<TText, TSpec>, FibreSA>::Type,
-        ModView<TFunctor>
+        typedef ModifiedString<
+            typename Fibre<Index<TText, TSpec>, FibreSA>::Type,
+            ModView< TFunctor >
         > ModString;
 
-    return ModString(indexSA(index), TFunctor(stringSetLimits(indexText(index))));
-}
-
+        return ModString(indexSA(index), TFunctor(stringSetLimits(indexText(index))));
+    }
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreLcp>::Type &
-getFibre(Index<TText, TSpec>&index, FibreLcp)
-{
-    return index.lcp;
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreLcp>::Type &
-getFibre(Index<TText, TSpec> const & index, FibreLcp)
-{
-    return index.lcp;
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreLcp>::Type &
+    getFibre(Index<TText, TSpec> &index, FibreLcp) {
+        return index.lcp;
+    }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreLcp>::Type &
+    getFibre(Index<TText, TSpec> const &index, FibreLcp) {
+        return index.lcp;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreLcpe>::Type &
-getFibre(Index<TText, TSpec>&index, FibreLcpe)
-{
-    return index.lcpe;
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreLcpe>::Type &
-getFibre(Index<TText, TSpec> const & index, FibreLcpe)
-{
-    return index.lcpe;
-}
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec>, FibreLcpe>::Type &
+    getFibre(Index<TText, TSpec> &index, FibreLcpe) {
+        return index.lcpe;
+    }
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec> const, FibreLcpe>::Type &
+    getFibre(Index<TText, TSpec> const &index, FibreLcpe) {
+        return index.lcpe;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreChildtab>::Type &
-getFibre(Index<TText, TSpec>&index, FibreChildtab)
-{
-    return index.childtab;
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreChildtab>::Type &
-getFibre(Index<TText, TSpec> const & index, FibreChildtab)
-{
-    return index.childtab;
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreChildtab>::Type &
+    getFibre(Index<TText, TSpec> &index, FibreChildtab) {
+        return index.childtab;
+    }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreChildtab>::Type &
+    getFibre(Index<TText, TSpec> const &index, FibreChildtab) {
+        return index.childtab;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreBwt>::Type &
-getFibre(Index<TText, TSpec>&index, FibreBwt)
-{
-    return index.bwt;
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreBwt>::Type &
-getFibre(Index<TText, TSpec> const & index, FibreBwt)
-{
-    return index.bwt;
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreBwt>::Type &
+    getFibre(Index<TText, TSpec> &index, FibreBwt) {
+        return index.bwt;
+    }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreBwt>::Type &
+    getFibre(Index<TText, TSpec> const &index, FibreBwt) {
+        return index.bwt;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.Index#length
-..cat:Index
-..summary:The number of characters in the underlying text of the index is returned.
-..signature:length(index)
-..class:Class.Index
-..param.index:The index to return the number of characters of.
-...type:Class.Index
-..returns:The number of characters in the raw underlying text of the index is returned.
-...metafunction:Metafunction.Size
-..remarks:If the underlying text is a @Class.StringSet@ then the sum of all characters of the sequneces in the string
-set is returned.
-..include:seqan/index.h
-..example
-...text:The following code shows how @Function.length@ can be used on an index in order to determine the number of characters in the underlying text.
-...file:demos/index/index_length_countSequences.cpp
-...output:Hit at position: < 1 , 2 >
-Hit at position: < 0 , 0 >
- */
-
 /*!
  * @fn Index#length
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Returns the number of characters in the underlying text of the index.
- * @signature TSize length(index)
- * @param index An index of a text.
+ *
+ * @signature TSize length(index);
+ *
+ * @param[in] index An index of a text.
+ *
  * @return TSize Returns the number of characters in the raw underlying text of the
- *        index with TSize being the result of the @link Size @endlink meta-function
- *        of @link Index @endlink.
- * @section Example
+ *               index with TSize being the result of the @link Size @endlink meta-function
+ *               of @link Index @endlink.
+ *
+ * @section Examples
  *
  * The following example shows how to count characters of an index, determine the number of sequences involved and how
  * to search for a pattern.
- * @include demos/index/index_length_countSequences.cpp
- * @include demos/index/index_length_countSequences.cpp.stdout
+ *
+ * @include demos/dox/index/length_countSequences.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/index/length_countSequences.cpp.stdout
  */
 
-template <typename TText, typename TSpec>
-inline typename Size<Index<TText, TSpec> >::Type
-length(Index<TText, TSpec> const & index)
-{
-    return length(indexRawText(index));
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Size<Index<TText, TSpec> >::Type
+    length(Index<TText, TSpec> const &index) {
+        return length(indexRawText(index));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.countSequences
-..cat:Index
-..summary:Return the number of sequences in an index' underlying text.
-..signature:countSequences(index)
-..class:Class.Index
-..param.index:The index to return the number of sequences of.
-...type:Class.Index
-..returns:The number of sequences in the index' underlying text.
-...metafunction:Metafunction.Size
-..include:seqan/index.h
-..example
-...text:The following code shows how @Function.countSequences@ can be used on an index in order to determine the number of sequences in the underlying text (which can be a @Class.StringSet@).
-...file:demos/index/index_length_countSequences.cpp
-...output:Hit at position: < 1 , 2 >
-Hit at position: < 0 , 0 >
-
- */
-
 /*!
  * @fn Index#countSequences
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Return the number of sequences in an index' underlying text.
- * @signature TSize countSequences(index)
- * @param index The index to return the number of sequences of.
+ *
+ * @signature TSize countSequences(index);
+ *
+ * @param[in] index The index to return the number of sequences of.
+ *
  * @return TSize The number of sequences in the index' underlying text with TSize being the result @link Size @endlink.
- * @section Example
+ *
+ * @section Examples
  *
  * The following example shows how to count characters of an index, determine the number of sequences involved and how
  * to search for a pattern.
  *
- * @include demos/index/index_length_countSequences.cpp
- * @code{.txt}
+ * @include demos/dox/index/length_countSequences.cpp
+ *
+ * The output is as follows:
+ *
+ * @code{.output}
  * The text has 25 characters and consists of 2 sequences.
  * Hit at position: < 1 , 2 >
  * Hit at position: < 0 , 0 >
  * @endcode
  */
 
-template <typename TText, typename TSpec>
-inline typename Size<TText>::Type
-countSequences(Index<TText, TSpec> const & index)
-{
-    return countSequences(indexText(index));
-}
+    template <typename TText, typename TSpec>
+    inline typename Size<TText>::Type
+    countSequences(Index<TText, TSpec> const &index) {
+        return countSequences(indexText(index));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // TODO(singer): Since this is a public function it should be documented
-template <typename TText, typename TSpec>
-struct GetSequenceByNo<Index<TText, TSpec> >
-{
-    typedef typename GetSequenceByNo<TText>::Type Type;
-};
+    template <typename TText, typename TSpec>
+    struct GetSequenceByNo< Index<TText, TSpec> >
+    {
+        typedef typename GetSequenceByNo<TText>::Type Type;
+    };
 
-template <typename TText, typename TSpec>
-struct GetSequenceByNo<Index<TText, TSpec> const>
-{
-    typedef typename GetSequenceByNo<TText const>::Type Type;
-};
+    template <typename TText, typename TSpec>
+    struct GetSequenceByNo< Index<TText, TSpec> const>
+    {
+        typedef typename GetSequenceByNo<TText const>::Type Type;
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 // TODO(singer): Since this is a public function it should be documented
-template <typename TSeqNo, typename TText, typename TSpec>
-inline typename GetSequenceByNo<Index<TText, TSpec> >::Type
-getSequenceByNo(TSeqNo seqNo, Index<TText, TSpec> & index)
-{
-    return getSequenceByNo(seqNo, indexText(index));
-}
+    template <typename TSeqNo, typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename GetSequenceByNo< Index<TText, TSpec> >::Type
+    getSequenceByNo(TSeqNo seqNo, Index<TText, TSpec> &index)
+    {
+        return getSequenceByNo(seqNo, indexText(index));
+    }
 
-template <typename TSeqNo, typename TText, typename TSpec>
-inline typename GetSequenceByNo<Index<TText, TSpec> const>::Type
-getSequenceByNo(TSeqNo seqNo, Index<TText, TSpec> const & index)
-{
-    return getSequenceByNo(seqNo, indexText(index));
-}
+    template <typename TSeqNo, typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename GetSequenceByNo< Index<TText, TSpec> const>::Type
+    getSequenceByNo(TSeqNo seqNo, Index<TText, TSpec> const &index)
+    {
+        return getSequenceByNo(seqNo, indexText(index));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // TODO(singer): Since this is a public function it should be documented
-template <typename TSeqNo, typename TText, typename TSpec>
-inline typename Size<Index<TText, TSpec> >::Type
-sequenceLength(TSeqNo seqNo, Index<TText, TSpec> const & index)
-{
-    return sequenceLength(seqNo, indexText(index));
-}
+    template <typename TSeqNo, typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Size<Index<TText, TSpec> >::Type
+    sequenceLength(TSeqNo seqNo, Index<TText, TSpec> const &index) {
+        return sequenceLength(seqNo, indexText(index));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // TODO(singer): Since this is a public function it should be documented
-template <typename TPos, typename TText, typename TSpec>
-inline typename Size<Index<TText, TSpec> >::Type
-suffixLength(TPos pos, Index<TText, TSpec> const & index)
-{
-    return length(indexText(index)) - pos;
-}
+    template <typename TPos, typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Size<Index<TText, TSpec> >::Type
+    suffixLength(TPos pos, Index<TText, TSpec> const &index)
+    {
+        return length(indexText(index)) - pos;
+    }
 
-template <typename TPos, typename TString, typename TSSetSpec, typename TSpec>
-inline typename Size<Index<StringSet<TString, TSSetSpec>, TSpec> >::Type
-suffixLength(TPos pos, Index<StringSet<TString, TSSetSpec>, TSpec> const & index)
-{
-    typename StringSetLimits<StringSet<TString, TSSetSpec> >::Type const & limits = stringSetLimits(index);
-    return sequenceLength(getSeqNo(pos, limits), index) - getSeqOffset(pos, limits);
-}
+    template <typename TPos, typename TString, typename TSSetSpec, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Size<Index<StringSet<TString, TSSetSpec>, TSpec> >::Type
+    suffixLength(TPos pos, Index<StringSet<TString, TSSetSpec>, TSpec> const &index)
+    {
+        typename StringSetLimits<StringSet<TString, TSSetSpec> >::Type const &limits = stringSetLimits(index);
+        return sequenceLength(getSeqNo(pos, limits), index) - getSeqOffset(pos, limits);
+    }
 
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Function.textAt:
-..summary:Shortcut for $value(indexText(..), ..)$.
-..cat:Index
-..signature:textAt(position, index)
-..class:Class.Index
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-..example
-...text:The following code shows how the BWT of a text can be computed.
-...file:demos/index/index_textAt_indexText_saAt_indexRequire.cpp
-...output:BWT	Suffices
-P	PI
-S	SIPPI
-S	SISSIPPI
-M	MISSISSIPPI
-I	I
-P	PPI
-I	IPPI
-S	SSIPPI
-S	SSISSIPPI
-I	ISSIPPI
-I	ISSISSIPPI*/
 
+//////////////////////////////////////////////////////////////////////////////
 /*!
- * @fn Index#textAt
- * @headerfile seqan/index.h
+ * @fn IndexEsa#textAt
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>value(indexText(..), ..)</tt>.
- * @signature TValue textAt(position, index)
- * @param index The @link Index @endlink object. Types: @link Index @endlink
- * @param position A position in the array on which the value should be accessed.
- * @return TValue A reference or proxy to the value. The type is the result if the meta-function @link Reference
- *                @endlink.
- *
- * @section Note
  *
- * The result of this function when used on an Index<TText, FMIndex<TOccSpec, Compress> > is not defined.
+ * @signature TValue textAt(position, index);
  *
- * @section Example
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ * @param[in] position A position in the fibre on which the value should be accessed.
  *
- * The following code shows how the BWT of a text can be computed.
- * @include demos/index/index_textAt_indexText_saAt_indexRequire.cpp
- * @include demos/index/index_textAt_indexText_saAt_indexRequire.cpp.stdout
+ * @return TValue A reference or proxy to the value in the text.
  */
 
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex, FibreRawText>::Type>::Type
-textAt(TPos i, TIndex & index)
-{
-    return value(getFibre(index, FibreRawText()), i);
-}
-
-template <typename TPos, typename TString, typename TSSetSpec, typename TSpec>
-inline typename Reference<typename Fibre<Index<StringSet<TString, TSSetSpec>, TSpec>, FibreRawText>::Type>::Type
-textAt(TPos i, Index<StringSet<TString, TSSetSpec>, TSpec> & index)
-{
-    return value(getFibre(index, FibreRawText()), posGlobalize(i, stringSetLimits(index)));
-}
-
-template <typename TPos, typename TString, typename TSSetSpec, typename TSpec>
-inline typename Reference<typename Fibre<Index<StringSet<TString, TSSetSpec>, TSpec> const, FibreRawText>::Type>::Type
-textAt(TPos i, Index<StringSet<TString, TSSetSpec>, TSpec> const & index)
-{
-    return value(getFibre(index, FibreRawText()), posGlobalize(i, stringSetLimits(index)));
-}
-
-template <typename TPos, typename TString, typename TSpec>
-inline typename Reference<typename Fibre<Index<StringSet<TString, Owner<Default> >, TSpec>, FibreRawText>::Type>::Type
-textAt(TPos i, Index<StringSet<TString, Owner<Default> >, TSpec> & index)
-{
-    Pair<
-        typename Size<StringSet<TString, Owner<Default> > >::Type,
-        typename Size<TString>::Type> locPos;
-    posLocalize(locPos, i, stringSetLimits(index));
-    return value(value(getFibre(index, FibreText()), getValueI1(locPos)), getValueI2(locPos));
-}
-
-template <typename TPos, typename TString, typename TSpec>
-inline typename Reference<typename Fibre<Index<StringSet<TString, Owner<Default> >, TSpec> const, FibreRawText>::Type>::Type
-textAt(TPos i, Index<StringSet<TString, Owner<Default> >, TSpec> const & index)
-{
-    Pair<
-        typename Size<StringSet<TString, Owner<Default> > >::Type,
-        typename Size<TString>::Type> locPos;
-    posLocalize(locPos, i, stringSetLimits(index));
-    return value(value(getFibre(index, FibreText()), getValueI1(locPos)), getValueI2(locPos));
-}
+    template <typename TPos, typename TIndex>
+    inline typename Reference<typename Fibre<TIndex, FibreRawText>::Type>::Type
+    textAt(TPos i, TIndex &index) {
+        return value(getFibre(index, FibreRawText()), i);
+    }
+    template <typename TPos, typename TString, typename TSSetSpec, typename TSpec>
+    inline typename Reference<typename Fibre< Index< StringSet<TString, TSSetSpec>, TSpec>, FibreRawText>::Type>::Type
+    textAt(TPos i, Index< StringSet<TString, TSSetSpec>, TSpec> &index) {
+        return value(getFibre(index, FibreRawText()), posGlobalize(i, stringSetLimits(index)));
+    }
+    template <typename TPos, typename TString, typename TSSetSpec, typename TSpec>
+    inline typename Reference<typename Fibre< Index< StringSet<TString, TSSetSpec>, TSpec> const, FibreRawText>::Type>::Type
+    textAt(TPos i, Index< StringSet<TString, TSSetSpec>, TSpec> const &index) {
+        return value(getFibre(index, FibreRawText()), posGlobalize(i, stringSetLimits(index)));
+    }
+    template <typename TPos, typename TString, typename TSpec>
+    inline typename Reference<typename Fibre< Index< StringSet<TString, Owner<Default> >, TSpec>, FibreRawText>::Type>::Type
+    textAt(TPos i, Index< StringSet<TString, Owner<Default> >, TSpec> &index) {
+        Pair <
+            typename Size< StringSet<TString, Owner<Default> > >::Type,
+            typename Size< TString >::Type > locPos;
+        posLocalize(locPos, i, stringSetLimits(index));
+        return value(value(getFibre(index, FibreText()), getValueI1(locPos)), getValueI2(locPos));
+    }
+    template <typename TPos, typename TString, typename TSpec>
+    inline typename Reference<typename Fibre< Index< StringSet<TString, Owner<Default> >, TSpec> const, FibreRawText>::Type>::Type
+    textAt(TPos i, Index< StringSet<TString, Owner<Default> >, TSpec> const &index) {
+        Pair <
+        typename Size< StringSet<TString, Owner<Default> > >::Type,
+        typename Size< TString >::Type > locPos;
+        posLocalize(locPos, i, stringSetLimits(index));
+        return value(value(getFibre(index, FibreText()), getValueI1(locPos)), getValueI2(locPos));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // infix
 
-template <typename TText, typename TSpec, typename TPosBegin, typename TPosEnd>
-inline typename Infix<TText>::Type
-infix(Index<TText, TSpec> & index, TPosBegin pos_begin, TPosEnd pos_end)
-{
-    return infix(indexText(index), pos_begin, pos_end);
-}
+    template <typename TText, typename TSpec, typename TPosBegin, typename TPosEnd>
+    inline typename Infix<TText>::Type
+    infix(Index<TText, TSpec> &index, TPosBegin pos_begin, TPosEnd pos_end)
+    {
+        return infix(indexText(index), pos_begin, pos_end);
+    }
 
-template <typename TText, typename TSpec, typename TPosBegin, typename TPosEnd>
-inline typename Infix<TText>::Type
-infix(Index<TText, TSpec> const & index, TPosBegin pos_begin, TPosEnd pos_end)
-{
-    return infix(indexText(index), pos_begin, pos_end);
-}
+    template <typename TText, typename TSpec, typename TPosBegin, typename TPosEnd>
+    inline typename Infix<TText>::Type
+    infix(Index<TText, TSpec> const &index, TPosBegin pos_begin, TPosEnd pos_end)
+    {
+        return infix(indexText(index), pos_begin, pos_end);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.rawtextAt:
-..summary:Shortcut for $value(indexRawText(..), ..)$.
-..cat:Index
-..signature:rawtextAt(position, index)
-..class:Class.Index
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-*/
 /*!
  * @fn Index#rawtextAt
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>value(indexRawText(..), ..)</tt>.
- * @signature TValue rawtextAt(position, index)
- * @param index The @link Index @endlink object. Types: @link Index @endlink
  *
- * @param position A position in the array on which the value should be
- *                 accessed.
+ * @signature TValue rawtextAt(position, index);
+ *
+ * @param[in] index    The @link Index @endlink object. Types: @link Index @endlink
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
  * @return TValue A reference or proxy to the value. The type is the result if the meta-function @link Reference
  *                @endlink.
  *
- * @section Note
- *
- * The result of this function when used on an Index<TText, FMIndex<TOccSpec, Compress> > is not defined.
+ * @note The result of this function when used on an Index&lt;TText, FMIndex&lt;TOccSpec, Compress&gt; &gt; is not
+ *       defined.
  */
 
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex, FibreRawText>::Type>::Type rawtextAt(TPos i, TIndex & index)
-{
-    return value(getFibre(index, FibreRawText()), i);
-}
-
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex const, FibreRawText>::Type>::Type rawtextAt(TPos i, TIndex const & index)
-{
-    return value(getFibre(index, FibreRawText()), i);
-}
+    template <typename TPos, typename TIndex>
+    inline typename Reference<typename Fibre<TIndex, FibreRawText>::Type>::Type rawtextAt(TPos i, TIndex &index) {
+        return value(getFibre(index, FibreRawText()), i);
+    }
+    template <typename TPos, typename TIndex>
+    inline typename Reference<typename Fibre<TIndex const, FibreRawText>::Type>::Type rawtextAt(TPos i, TIndex const &index) {
+        return value(getFibre(index, FibreRawText()), i);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.saAt:
-..summary:Shortcut for $value(indexSA(..), ..)$.
-..cat:Index
-..signature:saAt(position, index)
-..class:Class.Index
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-..example
-...text:The following code shows how the BWT of a text can be computed.
-...file:demos/index/index_textAt_indexText_saAt_indexRequire.cpp
-...output:BWT	Suffices
-P	PI
-S	SIPPI
-S	SISSIPPI
-M	MISSISSIPPI
-I	I
-P	PPI
-I	IPPI
-S	SSIPPI
-S	SSISSIPPI
-I	ISSIPPI
-I	ISSISSIPPI*/
 /*!
  * @fn IndexEsa#saAt
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>value(indexSA(..), ..)</tt>.
  *
- * @deprecated advanced
- * @signature TValue saAt(position, index)
- * @param index The @link Index @endlink object holding the fibre.
- * @param position A position in the array on which the value should be accessed.
- * @return TValue A reference or proxy to the value in the suffix array. To be more precise, a reference to a poistion
- * containing a value of type @link SAValue @endlink is returned (or a proxy).
- * SAValue
- * @section Example
+ * @signature TValue saAt(position, index);
  *
- * The following code shows how the BWT of a text can be computed.
- * @include demos/index/index_textAt_indexText_saAt_indexRequire.cpp
- * @code{.txt}
- * BWT	Suffices
- * P	PI
- * S	SIPPI
- * S	SISSIPPI
- * M	MISSISSIPPI
- * I	I
- * P	PPI
- * I	IPPI
- * S	SSIPPI
- * S	SSISSIPPI
- * I	ISSIPPI
- * I	ISSISSIPPI
- * @endcode
-
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TValue A reference or proxy to the value in the suffix array.
  */
 
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex, FibreSA>::Type>::Type saAt(TPos i, TIndex & index)
-{
-    return value(getFibre(index, FibreSA()), i);
-}
-
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex const, FibreSA>::Type>::Type saAt(TPos i, TIndex const & index)
-{
-    return value(getFibre(index, FibreSA()), i);
-}
+    template <typename TPos, typename TIndex>
+    SEQAN_HOST_DEVICE inline typename Reference<typename Fibre<TIndex, FibreSA>::Type>::Type saAt(TPos i, TIndex &index) {
+        return value(getFibre(index, FibreSA()), i);
+    }
+    template <typename TPos, typename TIndex>
+    SEQAN_HOST_DEVICE inline typename Reference<typename Fibre<TIndex const, FibreSA>::Type>::Type saAt(TPos i, TIndex const &index) {
+        return value(getFibre(index, FibreSA()), i);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.rawsaAt:
-..summary:Shortcut for $value(indexRawSA(..), ..)$.
-..cat:Index
-..signature:saAt(position, index)
-..class:Class.Index
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-*/
+// TODO(weese): I disabled the doc, as we don't want to encourage users to use it
 
-/*!
+/*
  * @fn IndexEsa#rawsaAt
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
+ * @note Advanced functionality, not commonly used.
  * @brief Shortcut for <tt>value(indexRawSA(..), ..)</tt>.
- * @deprecated. advanced
  *
- * @signature TValue rawsaAt(position, index)
- * @param index The @link Index @endlink object holding the fibre.
- * @param position A position in the array on which the value should be
- *                 accessed.
- * @return TValue A reference or proxy to the value. To be more precise, a reference to a poistion
+ * @signature TValue rawsaAt(position, index);
+ *
+ * @param[in] index    The @link Index @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TValue A reference or proxy to the value.  To be more precise, a reference to a position
  *                containing a value of type @link SAValue @endlink is returned (or a proxy).
  */
 
-template <typename TPos, typename TIndex>
-inline typename Value<typename Fibre<TIndex const, FibreRawSA>::Type>::Type rawsaAt(TPos i, TIndex const & index)
-{
-    return posGlobalize(saAt(i, index), stringSetLimits(indexText(index)));
-}
+    template <typename TPos, typename TIndex>
+    inline typename Value<typename Fibre<TIndex const, FibreRawSA>::Type>::Type rawsaAt(TPos i, TIndex const &index) {
+        return posGlobalize(saAt(i, index), stringSetLimits(indexText(index)));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.IndexEsa#lcpAt:
-..summary:Shortcut for $value(indexLcp(..), ..)$.
-..cat:Index
-..signature:lcpAt(position, index)
-..class:Spec.IndexEsa
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Spec.IndexEsa@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-*/
+/*!
+ * @fn IndexEsa#isaAt
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>value(indexIsa(..), ..)</tt>.
+ *
+ * @signature TValue isaAt(position, index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TValue A reference or proxy to the value in the inverse suffix array.
+ */
+
+    template <typename TPos, typename TIndex>
+    SEQAN_HOST_DEVICE inline typename Reference<typename Fibre<TIndex, FibreIsa>::Type>::Type isaAt(TPos i, TIndex &index) {
+        return value(getFibre(index, FibreIsa()), i);
+    }
+    template <typename TPos, typename TIndex>
+    SEQAN_HOST_DEVICE inline typename Reference<typename Fibre<TIndex const, FibreIsa>::Type>::Type isaAt(TPos i, TIndex const &index) {
+        return value(getFibre(index, FibreIsa()), i);
+    }
+//////////////////////////////////////////////////////////////////////////////
 /*!
  * @fn IndexEsa#lcpAt
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>value(indexLcp(..), ..)</tt>.
- * @signature TValue lcpAt(position, index)
- * @param index The @link Index @endlink object holding the fibre.
- * @param position A position in the array on which the value should be accessed.
+ *
+ * @signature TValue lcpAt(position, index);
+ *
+ * @param[in] index    The @link Index @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
  * @return TValue A reference or proxy to the value.
  */
 
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex, FibreLcp>::Type>::Type lcpAt(TPos i, TIndex & index)
-{
-    return value(getFibre(index, FibreLcp()), i);
-}
-
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex const, FibreLcp>::Type>::Type lcpAt(TPos i, TIndex const & index)
-{
-    return value(getFibre(index, FibreLcp()), i);
-}
+    template <typename TPos, typename TIndex>
+    SEQAN_HOST_DEVICE inline typename Reference<typename Fibre<TIndex, FibreLcp>::Type>::Type lcpAt(TPos i, TIndex &index) {
+        return value(getFibre(index, FibreLcp()), i);
+    }
+    template <typename TPos, typename TIndex>
+    SEQAN_HOST_DEVICE inline typename Reference<typename Fibre<TIndex const, FibreLcp>::Type>::Type lcpAt(TPos i, TIndex const &index) {
+        return value(getFibre(index, FibreLcp()), i);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.IndexEsa#lcpeAt:
-..summary:Shortcut for $value(indexLcpe(..), ..)$.
-..cat:Index
-..signature:lcpeAt(position, index)
-..class:Spec.IndexEsa
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Spec.IndexEsa@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexEsa#lcpeAt
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>value(indexLcpe(..), ..)</tt>.
- * @signature TValue lcpeAt(position, index)
- * @param index The @link Index @endlink object holding the fibre.
- * @param position A position in the array on which the value should be accessed.
+ *
+ * @signature TValue lcpeAt(position, index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
  * @return TValue A reference or proxy to the value.
  */
 
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex, FibreLcpe>::Type>::Type lcpeAt(TPos i, TIndex & index)
-{
-    return value(getFibre(index, FibreLcpe()), i);
-}
-
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex const, FibreLcpe>::Type>::Type lcpeAt(TPos i, TIndex const & index)
-{
-    return value(getFibre(index, FibreLcpe()), i);
-}
+    template <typename TPos, typename TIndex>
+    inline typename Reference<typename Fibre<TIndex, FibreLcpe>::Type>::Type lcpeAt(TPos i, TIndex &index) {
+        return value(getFibre(index, FibreLcpe()), i);
+    }
+    template <typename TPos, typename TIndex>
+    inline typename Reference<typename Fibre<TIndex const, FibreLcpe>::Type>::Type lcpeAt(TPos i, TIndex const &index) {
+        return value(getFibre(index, FibreLcpe()), i);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.IndexEsa#childAt:
-..summary:Shortcut for $value(indexChildtab(..), ..)$.
-..cat:Index
-..signature:childAt(position, index)
-..class:Spec.IndexEsa
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Spec.IndexEsa@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexEsa#childAt
- *
- * @headerfile seqan/index.h
- *
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>value(indexChildtab(..), ..)</tt>.
  *
- * @signature TValue childAt(position, index)
+ * @signature TValue childAt(position, index);
+ *
+ * @param[in] position A position in the array on which the value should be accessed.
+ * @param[in] index    The @link IndexEsa @endlink object holding the fibre.
  *
- * @param index The @link IndexEsa @endlink object holding the fibre.
- * @param position A position in the array on which the value should be accessed.
  * @return TValue A reference or proxy to the value.
  */
 
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex, FibreChildtab>::Type>::Type childAt(TPos i, TIndex & index)
-{
-    return value(getFibre(index, FibreChildtab()), i);
-}
-
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex const, FibreChildtab>::Type>::Type childAt(TPos i, TIndex const & index)
-{
-    return value(getFibre(index, FibreChildtab()), i);
-}
+    template <typename TPos, typename TIndex>
+    SEQAN_HOST_DEVICE inline typename Reference<typename Fibre<TIndex, FibreChildtab>::Type>::Type childAt(TPos i, TIndex &index) {
+        return value(getFibre(index, FibreChildtab()), i);
+    }
+    template <typename TPos, typename TIndex>
+    SEQAN_HOST_DEVICE inline typename Reference<typename Fibre<TIndex const, FibreChildtab>::Type>::Type childAt(TPos i, TIndex const &index) {
+        return value(getFibre(index, FibreChildtab()), i);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.IndexEsa#bwtAt:
-..summary:Shortcut for $value(indexBwt(..), ..)$.
-..cat:Index
-..signature:bwtAt(position, index)
-..class:Spec.IndexEsa
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Spec.IndexEsa@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexEsa#bwtAt
- *
- * @headerfile seqan/index.h
- *
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>value(indexBwt(..), ..)</tt>.
  *
- * @signature TVlaue bwtAt(position, index)
+ * @signature TValue bwtAt(position, index);
  *
- * @param index The @link IndexEsa @endlink object holding the fibre.
- * @param position A position in the array on which the value should be accessed.
+ * @param[in] index    The @link IndexEsa @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
  *
- * @return TReturn A reference or proxy to the value.
+ * @return TValue A reference or proxy to the value.
  */
 
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex, FibreBwt>::Type>::Type bwtAt(TPos i, TIndex & index)
-{
-    return value(getFibre(index, FibreBwt()), i);
-}
-
-template <typename TPos, typename TIndex>
-inline typename Reference<typename Fibre<TIndex const, FibreBwt>::Type>::Type bwtAt(TPos i, TIndex const & index)
-{
-    return value(getFibre(index, FibreBwt()), i);
-}
+    template <typename TPos, typename TIndex>
+    inline typename Reference<typename Fibre<TIndex, FibreBwt>::Type>::Type bwtAt(TPos i, TIndex &index) {
+        return value(getFibre(index, FibreBwt()), i);
+    }
+    template <typename TPos, typename TIndex>
+    inline typename Reference<typename Fibre<TIndex const, FibreBwt>::Type>::Type bwtAt(TPos i, TIndex const &index) {
+        return value(getFibre(index, FibreBwt()), i);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TIndex, typename TPos, typename TSize>
-inline typename SAValue<TIndex>::Type toSuffixPosition(TIndex &, TPos i, TSize)
-{
-    return i;
-}
-
-template <typename TIndex, typename TPos, typename TSize>
-inline typename SAValue<TIndex const>::Type toSuffixPosition(TIndex const &, TPos i, TSize)
-{
-    return i;
-}
+    template <typename TIndex, typename TPos, typename TSize>
+    inline typename SAValue<TIndex>::Type toSuffixPosition(TIndex &, TPos i, TSize) {
+        return i;
+    }
+    template <typename TIndex, typename TPos, typename TSize>
+    inline typename SAValue<TIndex const>::Type toSuffixPosition(TIndex const &, TPos i, TSize) {
+        return i;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // interface for infinity/invalid values
 
-template <typename TValue>
-inline void _setSizeInval(TValue & v)
-{
-    v = MaxValue<TValue>::VALUE;
-}
+    template <typename TValue>
+    SEQAN_HOST_DEVICE inline void _setSizeInval(TValue &v) {
+        v = MaxValue<TValue>::VALUE;
+    }
 
-template <typename TValue>
-inline bool _isSizeInval(TValue const & v)
-{
+    template <typename TValue>
+    SEQAN_HOST_DEVICE inline bool _isSizeInval(TValue const &v) {
 //IOREV _notio_
-    return v == MaxValue<TValue>::VALUE;
-}
+        return v == MaxValue<TValue>::VALUE;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexText:
-..summary:Shortcut for $getFibre(index, FibreText())$.
-..cat:Index
-..signature:indexText(index)
-..class:Class.Index
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Class.Index
-..returns:A reference to the text fibre (original text).
-..include:seqan/index.h
-..example
-...text:The following code shows how the BWT of a text can be computed.
-...file:demos/index/index_textAt_indexText_saAt_indexRequire.cpp
-...output:BWT	Suffices
-P	PI
-S	SIPPI
-S	SISSIPPI
-M	MISSISSIPPI
-I	I
-P	PPI
-I	IPPI
-S	SSIPPI
-S	SSISSIPPI
-I	ISSIPPI
-I	ISSISSIPPI
-*/
 /*!
  * @fn Index#indexText
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>getFibre(.., EsaText)</tt>.
- * @signature TValue indexText(index)
- * @param index The @link Index @endlink object holding the fibre.
- * @return TValue A reference to the text of the index.
  *
- * @section Note
+ * @signature TFibre indexText(index);
  *
- * The result of this function when used on an Index<TText, FMIndex<TOccSpec, CompressText> > is not defined.
+ * @param[in] index The @link Index @endlink object holding the fibre.
  *
- * @section Example
+ * @return TFibre A reference to the text of the index.
+ *
+ * @note The result of this function when used on an <tt>Index&lt;TText, FMIndex&lt;TOccSpec, CompressText&gt; &gt;
+ *       is not defined.
+ *
+ * @section Examples
  *
  * The following code shows how the BWT of a text can be computed.
- * @include demos/index/index_textAt_indexText_saAt_indexRequire.cpp
- * @include demos/index/index_textAt_indexText_saAt_indexRequire.cpp.stdout
+ *
+ * @include demos/dox/index/textAt_indexText_saAt_indexRequire.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/index/textAt_indexText_saAt_indexRequire.cpp.stdout
  */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreText>::Type & indexText(Index<TText, TSpec>&index)
-{
-    return getFibre(index, FibreText());
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreText>::Type & indexText(Index<TText, TSpec> const & index)
-{
-    return getFibre(index, FibreText());
-}
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec>, FibreText>::Type & indexText(Index<TText, TSpec> &index) { return getFibre(index, FibreText()); }
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec> const, FibreText>::Type & indexText(Index<TText, TSpec> const &index) { return getFibre(index, FibreText()); }
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TText, typename TSpec>
-inline typename StringSetLimits<TText const>::Type
-stringSetLimits(Index<TText, TSpec> &)
-{
-    return Nothing();
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename StringSetLimits<TText const>::Type
+    stringSetLimits(Index<TText, TSpec> &) {
+        return Nothing();
+    }
 
-template <typename TText, typename TSpec>
-inline typename StringSetLimits<TText const>::Type
-stringSetLimits(Index<TText, TSpec> const &)
-{
-    return Nothing();
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename StringSetLimits<TText const>::Type
+    stringSetLimits(Index<TText, TSpec> const &) {
+        return Nothing();
+    }
 
-template <typename TString, typename TSSetSpec, typename TSpec>
-inline typename StringSetLimits<StringSet<TString, TSSetSpec> const>::Type &
-stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec>&index)
-{
-    return stringSetLimits(indexText(index));
-}
+    template <typename TString, typename TSSetSpec, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type &
+    stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> &index) {
+        return stringSetLimits(indexText(index));
+    }
 
-template <typename TString, typename TSSetSpec, typename TSpec>
-inline typename StringSetLimits<StringSet<TString, TSSetSpec> const>::Type &
-stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> const & index)
-{
-    return stringSetLimits(indexText(index));
-}
+    template <typename TString, typename TSSetSpec, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type &
+    stringSetLimits(Index<StringSet<TString, TSSetSpec>, TSpec> const &index) {
+        return stringSetLimits(indexText(index));
+    }
 
-template <typename TString, typename TSSetSpec, typename TSpec>
-inline typename StringSetLimits<StringSet<TString, TSSetSpec> const>::Type &
-stringSetLimits(Index<StringSet<TString, TSSetSpec> const, TSpec>&index)
-{
-    return stringSetLimits(indexText(index));
-}
+    template <typename TString, typename TSSetSpec, typename TSpec>
+    inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type &
+    stringSetLimits(Index<StringSet<TString, TSSetSpec> const, TSpec> &index) {
+        return stringSetLimits(indexText(index));
+    }
 
-template <typename TString, typename TSSetSpec, typename TSpec>
-inline typename StringSetLimits<StringSet<TString, TSSetSpec> const>::Type &
-stringSetLimits(Index<StringSet<TString, TSSetSpec> const, TSpec> const & index)
-{
-    return stringSetLimits(indexText(index));
-}
+    template <typename TString, typename TSSetSpec, typename TSpec>
+    inline typename StringSetLimits< StringSet<TString, TSSetSpec> const >::Type &
+    stringSetLimits(Index<StringSet<TString, TSSetSpec> const, TSpec> const &index) {
+        return stringSetLimits(indexText(index));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexRawText:
-..summary:Shortcut for $getFibre(.., EsaRawText)$.
-..cat:Index
-..signature:indexRawText(index)
-..class:Class.Index
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference to the @Tag.ESA Index Fibres.EsaRawText@ fibre (concatenated input text).
-..include:seqan/index.h
-*/
-//TODO(singer) The RawText Fibre exist for more then the Esa index
 /*!
- * @fn IndexEsa#indexRawText
- * @headerfile seqan/index.h
- * @brief Shortcut for <tt>$getFibre(.., EsaRawText)</tt>.
- * @signature TVlaue rawtextAt(position, index)
- * @param index The @link Index @endlink object.
- * @param position A position in the array on which the value should be accessed.
- * @return TValue A reference or proxy to the value.
+ * @fn Index#indexRawText
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>$getFibre(.., FibreRawText)</tt>.
+ *
+ * @signature TFibre indexRawText(position, index);
+ *
+ * @param[in] position A position in the array on which the value should be accessed.
+ * @param[in] index The @link Index @endlink object.
+ *
+ * @return TFibre A reference or proxy to the value.
  */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreRawText>::Type & indexRawText(Index<TText, TSpec>&index)
-{
-    return getFibre(index, FibreRawText());
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreRawText>::Type & indexRawText(Index<TText, TSpec> const & index)
-{
-    return getFibre(index, FibreRawText());
-}
+    template <typename TText, typename TSpec>
+    inline SEQAN_HOST_DEVICE
+    typename Fibre<Index<TText, TSpec>, FibreRawText>::Type &
+    indexRawText(Index<TText, TSpec> &index)
+    {
+        return getFibre(index, FibreRawText());
+    }
+
+    template <typename TText, typename TSpec>
+    inline SEQAN_HOST_DEVICE
+    typename Fibre<Index<TText, TSpec> const, FibreRawText>::Type &
+    indexRawText(Index<TText, TSpec> const &index)
+    {
+        return getFibre(index, FibreRawText());
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexSA:
-..summary:Shortcut for $getFibre(.., FibreSA)$.
-..cat:Index
-..signature:indexSA(index)
-..class:Class.Index
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Class.Index
-..returns:A reference to the suffix array fibre.
-..include:seqan/index.h
-..example
-...text:The following code shows how the BWT of a text can be computed.
-...file:demos/index/index_textAt_indexText_saAt_indexRequire.cpp
-...output:BWT	Suffices
-P	PI
-S	SIPPI
-S	SISSIPPI
-M	MISSISSIPPI
-I	I
-P	PPI
-I	IPPI
-S	SSIPPI
-S	SSISSIPPI
-I	ISSIPPI
-I	ISSISSIPPI*/
-//TODO(singer) The function in not only defined for the esa index
+
 /*!
  * @fn IndexEsa#indexSA
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>getFibre(.., EsaSA)</tt>.
- * @signature TSa indexSA(index)
- * @param index The @link Index @endlink object holding the fibre.
- * @return TReturn A reference to the @link IndexEsaFibres#EsaSA @endlink
- *                 fibre (suffix array).
- * @return TSa A reference to the suffix array fibre.
- * @section Example
  *
- * The following code shows how the BWT of a text can be computed.
- * @include demos/index/index_textAt_indexText_saAt_indexRequire.cpp
- * @code{.txt}
- * BWT	Suffices
- * P	PI
- * S	SIPPI
- * S	SISSIPPI
- * M	MISSISSIPPI
- * I	I
- * P	PPI
- * I	IPPI
- * S	SSIPPI
- * S	SSISSIPPI
- * I	ISSIPPI
- * I	ISSISSIPPI
- * @endcode
+ * @signature TSA indexSA(index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ *
+ * @return TSA A reference to the @link IndexEsaFibres#EsaSA @endlink fibre (suffix array).
  */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreSA>::Type & indexSA(Index<TText, TSpec>&index)
-{
-    return getFibre(index, FibreSA());
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreSA>::Type & indexSA(Index<TText, TSpec> const & index)
-{
-    return getFibre(index, FibreSA());
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreSA>::Type & indexSA(Index<TText, TSpec> &index) { return getFibre(index, FibreSA()); }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreSA>::Type & indexSA(Index<TText, TSpec> const &index) { return getFibre(index, FibreSA()); }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexRawSA:
-..summary:Shortcut for $getFibre(.., EsaRawSA)$.
-..cat:Index
-..signature:indexRawSA(index)
-..class:Class.Index
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference to the @Tag.ESA Index Fibres.EsaRawSA@ fibre (suffix array).
-..include:seqan/index.h
-*/
 
-// TODO(singer): should this be documented? 
+// NOTE(esiragusa): indexRawSA() is internal and must stay invisible in the doc.
+
 /*
- * @fn Index#indexRawSA
- * @headerfile seqan/index.h
+ * @fn IndexEsa#indexRawSA
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>getFibre(.., EsaRawSA)</tt>.
- * @signature TSa & indexRawSA(index)
- * @param index The @link Index @endlink object holding the fibre.
- * @return TSa A reference to the @link IndexEsaFibres#EsaRawSA @endlink fibre (suffix array).
+ *
+ * @signature TSA indexRawSA(index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ *
+ * @return TSA A reference to the @link IndexEsaFibres#EsaRawSA @endlink fibre (suffix array).
  */
 
-/*
     template <typename TText, typename TSpec>
-    inline typename Fibre<Index<TText, TSpec>, FibreRawSA>::Type const & indexRawSA(Index<TText, TSpec> &index) { return getFibre(index, FibreRawSA()); }
+    inline typename Fibre<Index<TText, TSpec>, FibreRawSA>::Type indexRawSA(Index<TText, TSpec> &index) { return getFibre(index, FibreRawSA()); }
     template <typename TText, typename TSpec>
-    inline typename Fibre<Index<TText, TSpec> const, FibreRawSA>::Type const & indexRawSA(Index<TText, TSpec> const &index) { return getFibre(index, FibreRawSA()); }
-*/
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreRawSA>::Type indexRawSA(Index<TText, TSpec> & index)
-{
-    return getFibre(index, FibreRawSA());
-}
+    inline typename Fibre<Index<TText, TSpec> const, FibreRawSA>::Type indexRawSA(Index<TText, TSpec> const &index) { return getFibre(index, FibreRawSA()); }
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreRawSA>::Type indexRawSA(Index<TText, TSpec> const & index)
-{
-    return getFibre(index, FibreRawSA());
-}
+//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn IndexEsa#indexIsa
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(.., EsaIsa)</tt>.
+ *
+ * @signature TIsa indexIsa(index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ *
+ * @return TIsa A reference to the inverse suffix array fibre.
+ */
+
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreIsa>::Type & indexIsa(Index<TText, TSpec> &index) { return getFibre(index, FibreIsa()); }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreIsa>::Type & indexIsa(Index<TText, TSpec> const &index) { return getFibre(index, FibreIsa()); }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.IndexEsa#indexLcp:
-..summary:Shortcut for $getFibre(.., EsaLcp)$.
-..cat:Index
-..signature:indexLcp(index)
-..class:Spec.IndexEsa
-..param.index:The @Spec.IndexEsa@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference to the @Tag.ESA Index Fibres.EsaLcp@ fibre (lcp table).
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexEsa#indexLcp
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>getFibre(.., EsaLcp)</tt>.
- * @signature TLcp indexLcp(index)
- * @param index The @link Index @endlink object holding the fibre.
- * @return TLcp A reference to the @link IndexEsaFibres#EsaLcp @endlink
- *                 fibre (lcp table).
+ *
+ * @signature TLcp indexLcp(index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ *
+ * @return TLcp A reference to the @link IndexEsaFibres#EsaLcp @endlink fibre (lcp table).
  */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreLcp>::Type & indexLcp(Index<TText, TSpec>&index)
-{
-    return getFibre(index, FibreLcp());
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreLcp>::Type & indexLcp(Index<TText, TSpec> const & index)
-{
-    return getFibre(index, FibreLcp());
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreLcp>::Type & indexLcp(Index<TText, TSpec> &index) { return getFibre(index, FibreLcp()); }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreLcp>::Type & indexLcp(Index<TText, TSpec> const &index) { return getFibre(index, FibreLcp()); }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.IndexEsa#indexLcpe:
-..summary:Shortcut for $getFibre(.., EsaLcpe)$.
-..cat:Index
-..signature:indexLcpe(index)
-..class:Spec.IndexEsa
-..param.index:The @Spec.IndexEsa@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference to the @Tag.IndexEsaFibres.EsaLcpe@ fibre (enhanced lcp table).
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexEsa#indexLcpe
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>getFibre(.., EsaLcpe)</tt>.
- * @signature TLcpe indexLcpe(index)
- * @param index The @link Index @endlink object holding the fibre.
+ *
+ * @signature TLcpe indexLcpe(index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ *
  * @return TLcpe A reference to the @link IndexEsaFibres#EsaLcpe @endlink fibre (enhanced lcp table).
  */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreLcpe>::Type & indexLcpe(Index<TText, TSpec>&index)
-{
-    return getFibre(index, FibreLcpe());
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreLcpe>::Type & indexLcpe(Index<TText, TSpec> const & index)
-{
-    return getFibre(index, FibreLcpe());
-}
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec>, FibreLcpe>::Type & indexLcpe(Index<TText, TSpec> &index) { return getFibre(index, FibreLcpe()); }
+    template <typename TText, typename TSpec>
+    inline typename Fibre<Index<TText, TSpec> const, FibreLcpe>::Type & indexLcpe(Index<TText, TSpec> const &index) { return getFibre(index, FibreLcpe()); }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.IndexEsa#indexBwt:
-..summary:Shortcut for $getFibre(.., EsaBwt)$.
-..cat:Index
-..signature:indexBwt(index)
-..class:Spec.IndexEsa
-..param.index:The @Spec.IndexEsa@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference to the @Tag.ESA Index Fibres.EsaBwt@ fibre (Burrows-Wheeler table).
-..include:seqan/index.h
-*/
-/*
+/*!
  * @fn IndexEsa#indexBwt
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>getFibre(.., EsaBwt)</tt>.
- * @signature TBwt indexBwt(index)
- * @param index The @link IndexEsa @endlink object holding the fibre.
- * @return TBwt A reference to the @link IndexEsaFibres.EsaBwt @endlink fibre (Burrows-Wheeler table).
+ *
+ * @signature TBwt indexBwt(index);
+ *
+ * @param[in] index The @link IndexEsa @endlink object holding the fibre.
+ *
+ * @return TBwt A reference to the @link IndexEsaFibres#EsaBwt @endlink fibre (Burrows-Wheeler table).
  */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreBwt>::Type & indexBwt(Index<TText, TSpec>&index)
-{
-    return getFibre(index, FibreBwt());
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreBwt>::Type & indexBwt(Index<TText, TSpec> const & index)
-{
-    return getFibre(index, FibreBwt());
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreBwt>::Type & indexBwt(Index<TText, TSpec> &index) { return getFibre(index, FibreBwt()); }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreBwt>::Type & indexBwt(Index<TText, TSpec> const &index) { return getFibre(index, FibreBwt()); }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.IndexEsa#indexChildtab:
-..summary:Shortcut for $getFibre(.., EsaChildtab)$.
-..cat:Index
-..signature:indexChildtab(index)
-..class:Spec.IndexEsa
-..param.index:The @Spec.IndexEsa@ object holding the fibre.
-...type:Spec.IndexEsa
-..returns:A reference to the @Tag.ESA Index Fibres.EsaChildtab@ fibre (child table).
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexEsa#indexChildtab
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief Shortcut for <tt>getFibre(.., EsaChildtab)</tt>.
- * @signature TchildTab indexChildtab(index)
- * @param index The @link Index @endlink object holding the fibre.
+ *
+ * @signature TChildTab indexChildtab(index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre.
+ *
  * @return TChildTab A reference to the @link IndexEsaFibres#EsaChildtab @endlink fibre (child table).
  */
 
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec>, FibreChildtab>::Type & indexChildtab(Index<TText, TSpec>&index)
-{
-    return getFibre(index, FibreChildtab());
-}
-template <typename TText, typename TSpec>
-inline typename Fibre<Index<TText, TSpec> const, FibreChildtab>::Type & indexChildtab(Index<TText, TSpec> const & index)
-{
-    return getFibre(index, FibreChildtab());
-}
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec>, FibreChildtab>::Type & indexChildtab(Index<TText, TSpec> &index) { return getFibre(index, FibreChildtab()); }
+    template <typename TText, typename TSpec>
+    SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, TSpec> const, FibreChildtab>::Type & indexChildtab(Index<TText, TSpec> const &index) { return getFibre(index, FibreChildtab()); }
 
 
 // ----------------------------------------------------------------------------
 // Function open
 // ----------------------------------------------------------------------------
-/**
-.Function.Index#open
-..class:Class.Index
-..summary:This functions opens an index from disk.
-..signature:open(index, fileName [, mode])
-..param.index:The index to be opened.
-...type:Class.Index
-..param.fileName:C-style character string containing the file name.
-..param.mode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-..example
-...text:The following code shows how the function @Function.open@ is used with indices.
-...file:demos/index/index_open_save.cpp
-...output:1
-1
-*/
 /*!
  * @fn Index#open
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief This functions opens an index from disk.
- * @signature bool open(index, fileName [, mode])
- * @param mode The combination of flags defining how the file should be opened.To open a file read-only, write-only or
- *             to read and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or <tt>OPEN_RDWR</tt>.To create or
- *             overwrite a file add <tt>OPEN_CREATE</tt>.To append a file if existing add <tt>OPEN_APPEND</tt>.To
- *             circumvent problems, files are always opened in binary mode.
- *             Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>
  *
- * @param index The index to be opened.
+ * @signature bool open(index, fileName[, mode]);
+ *
+ * @param[in,out]  index The index to be opened.
+ * @param[in]      fileName C-style character string containing the file name.
+ * @param[in] mode The combination of flags defining how the file should be opened.To open a file read-only, write-only or
+ *                 to read and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or <tt>OPEN_RDWR</tt>.To create or
+ *                 overwrite a file add <tt>OPEN_CREATE</tt>.To append a file if existing add <tt>OPEN_APPEND</tt>.To
+ *                 circumvent problems, files are always opened in binary mode.
+ *                 Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>.
  *
- * @param fileName C-style character string containing the file name.
  * @return bool <tt>true</tt> on success and <tt>false</tt> otherwise.
- * @section Example
  *
- * The following code shows how the function @Function.open@ is used with indices.
- * @include demos/index/index_open_save.cpp
- * @include demos/index/index_open_save.cpp.stdout
+ * @section Examples
+ *
+ * The following code shows how the function @link Index#open @endlink is used with indices.
+ *
+ * @include demos/dox/index/open_save.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/index/open_save.cpp.stdout
  */
 
 // ----------------------------------------------------------------------------
@@ -2059,48 +1593,32 @@ inline typename Fibre<Index<TText, TSpec> const, FibreChildtab>::Type & indexChi
 
 /*!
  * @fn Index#save
- * @headerfile seqan/index.h
+ * @headerfile <seqan/index.h>
  * @brief This functions saves an index to disk.
- * @signature bool save(index, fileName [, mode])
- * @param mode The combination of flags defining how the file should be opened.To open a file read-only, write-only or
- *             to read and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or <tt>OPEN_RDWR</tt>.To create or
- *             overwrite a file add <tt>OPEN_CREATE</tt>.To append a file if existing add <tt>OPEN_APPEND</tt>.To
- *             circumvent problems, files are always opened in binary mode.
- *             Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>
  *
- * @param index The index to be saved to disk.
+ * @signature bool save(index, fileName[, mode]);
+ *
+ * @param[in,out]  index The index to be opened.
+ * @param[in]      fileName C-style character string containing the file name.
+ * @param[in] mode The combination of flags defining how the file should be opened.To open a file read-only, write-only or
+ *                 to read and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or <tt>OPEN_RDWR</tt>.To create or
+ *                 overwrite a file add <tt>OPEN_CREATE</tt>.To append a file if existing add <tt>OPEN_APPEND</tt>.To
+ *                 circumvent problems, files are always opened in binary mode.
+ *                 Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>.
  *
- * @param fileName C-style character string containing the file name.
  * @return bool <tt>true</tt> on success and <tt>false</tt> otherwise.
- * @section Example
  *
- * The following code shows how the function @Function.save@ is used with indices.
- * @include demos/index/index_open_save.cpp
- * @include demos/index/index_open_save.cpp.stdout
+ * @section Examples
+ *
+ * The following code shows how the function @link Index#save @endlink is used with indices.
+ *
+ * @include demos/dox/index/open_save.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/index/open_save.cpp.stdout
  */
-/**
-.Function.Index#save
-..class:Class.Index
-..summary:This functions saves an index to disk.
-..signature:save(index, fileName [, mode])
-..param.index:The index to be saved to disk.
-...type:Class.Index
-..param.fileName:C-style character string containing the file name.
-..param.mode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-..example
-...text:The following code shows how the function @Function.open@ is used with indices.
-...file:demos/index/index_open_save.cpp
-...output:1
-1
-*/
-
 }
 
 #endif
+
diff --git a/seqan/index/index_bwt.h b/seqan/index/index_bwt.h
index 9a1f715..490b95d 100644
--- a/seqan/index/index_bwt.h
+++ b/seqan/index/index_bwt.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,11 +37,11 @@
 
 namespace SEQAN_NAMESPACE_MAIN
 {
-	
+
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct Bwt {};
+    struct Bwt {};
 
 
     //////////////////////////////////////////////////////////////////////////////
@@ -54,7 +54,7 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef typename Value<TTextInput>::Type Type;
     };
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // bwt class
     template < typename TTextInput, typename TSuffixArrayInput >
     struct Pipe< Bundle2< TTextInput, TSuffixArrayInput >, Bwt >
@@ -62,50 +62,50 @@ namespace SEQAN_NAMESPACE_MAIN
         // *** SPECIALIZATION ***
 
         typedef Pipe< TSuffixArrayInput, Counter > TSA;
-		                                typedef typename Size<TTextInput>::Type	TSize;
-		typedef Pool< TypeOf_(TSA), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TSA)>, TSize> > > TInverter;
+                                        typedef typename Size<TTextInput>::Type    TSize;
+        typedef Pool< TypeOf_(TSA), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TSA)>, TSize> > > TInverter;
         typedef Pipe< TInverter, Filter< filterI2<TypeOf_(TInverter)> > > TCounterFilter;
-		typedef Pipe< TTextInput, Shifter< -1, false > > TShiftText;
+        typedef Pipe< TTextInput, Shifter< -1, false > > TShiftText;
 
-		typedef Pipe< Bundle2< TCounterFilter, TShiftText >, Joiner > TJoiner;
-		typedef Pool< TypeOf_(TJoiner), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TJoiner)>, TSize> > > TLinearMapper;
+        typedef Pipe< Bundle2< TCounterFilter, TShiftText >, Joiner > TJoiner;
+        typedef Pool< TypeOf_(TJoiner), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TJoiner)>, TSize> > > TLinearMapper;
         typedef Pipe< TLinearMapper, Filter< filterI2<TypeOf_(TLinearMapper)> > > TFilter;
 
-        TLinearMapper		mapper;
-		TFilter				in;
-        
+        TLinearMapper        mapper;
+        TFilter                in;
+
         Pipe():
             in(mapper) {}
 
         Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn):
             in(mapper)
-		{
-			process(_bundleIn.in1, _bundleIn.in2);
-		}
+        {
+            process(_bundleIn.in1, _bundleIn.in2);
+        }
 
-		template < typename TTextInput_, typename TSuffixArrayInput_ >
+        template < typename TTextInput_, typename TSuffixArrayInput_ >
         bool process(TTextInput_ &textIn, TSuffixArrayInput_ &suffixArrayIn) {
 
             // *** INSTANTIATION ***
 
-			TSA							sa(suffixArrayIn);
-			TInverter					inverter;
-			TCounterFilter				filter(inverter);
-			
+            TSA                            sa(suffixArrayIn);
+            TInverter                    inverter;
+            TCounterFilter                filter(inverter);
+
             #ifdef SEQAN_DEBUG_INDEX
-				::std::cerr << "  invert suffix array" << ::std::endl;
+                std::cerr << "  invert suffix array" << std::endl;
             #endif
-			inverter << sa;
-			SEQAN_PROMARK("Suffix-Array invertiert");
+            inverter << sa;
+            SEQAN_PROMARK("Suffix-Array invertiert");
+
+            TShiftText                    shifter(textIn);
+            TJoiner                        joiner(bundle2(filter, shifter));
 
-			TShiftText					shifter(textIn);
-			TJoiner						joiner(bundle2(filter, shifter));
-			
             #ifdef SEQAN_DEBUG_INDEX
-                ::std::cerr << "  de-invert suffix array" << ::std::endl;
+                std::cerr << "  de-invert suffix array" << std::endl;
             #endif
-			mapper << joiner;
-			SEQAN_PROMARK("Suffix-Array linearisiert");
+            mapper << joiner;
+            SEQAN_PROMARK("Suffix-Array linearisiert");
 
             return true;
         }
@@ -113,19 +113,19 @@ namespace SEQAN_NAMESPACE_MAIN
         inline typename Value<Pipe>::Type const operator*() const {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
         }
-	};
+    };
 
     // not sure which interface is more intuitive, we support both
     // you can call "skew << pipe" or "skew_t skew(pipe); skew.process()"
     // for the first we would need no _in member
-	template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_ >
+    template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_ >
     inline bool operator<<(Pipe< TInput, Bwt > &me, Bundle2< TTextInput_, TSuffixArrayInput_ > const &bundleIn) {
- 	    return me.process(bundleIn.in1, bundleIn.in2);
+         return me.process(bundleIn.in1, bundleIn.in2);
     }
 
 
@@ -140,88 +140,88 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef typename Value<TTextInput>::Type Type;
     };
 
-	template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
-	struct _filterGlobalizer : public ::std::unary_function<InType,Result> {
-		TLimitsString const &limits;
-		_filterGlobalizer(TLimitsString const &_limits) : limits(_limits) {}
+    template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
+    struct _filterGlobalizer : public std::unary_function<InType,Result> {
+        TLimitsString const &limits;
+        _filterGlobalizer(TLimitsString const &_limits) : limits(_limits) {}
         inline Result operator()(const InType& x) const
         {
-			return posGlobalize(x, limits);
-		}
+            return posGlobalize(x, limits);
+        }
     };
 
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // bwt class
     template < typename TTextInput, typename TSuffixArrayInput, typename TPair, typename TLimitsString >
     struct Pipe< Bundle2< TTextInput, TSuffixArrayInput >, Multi<Bwt, TPair, TLimitsString> >
     {
         // *** SPECIALIZATION ***
 
-										typedef _filterGlobalizer<TypeOf_(TSuffixArrayInput), TLimitsString, TSizeOf_(TSuffixArrayInput)> filter_globalizer_t;
-		typedef Pipe< TSuffixArrayInput, Filter<filter_globalizer_t> > TGlobalizer;
+                                        typedef _filterGlobalizer<TypeOf_(TSuffixArrayInput), TLimitsString, TSizeOf_(TSuffixArrayInput)> filter_globalizer_t;
+        typedef Pipe< TSuffixArrayInput, Filter<filter_globalizer_t> > TGlobalizer;
         typedef Pipe< TGlobalizer, Counter > TSA;
-		                                typedef typename Size<TTextInput>::Type	TSize;
-		typedef Pool< TypeOf_(TSA), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TSA)>, TSize> > > TInverter;
+                                        typedef typename Size<TTextInput>::Type    TSize;
+        typedef Pool< TypeOf_(TSA), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TSA)>, TSize> > > TInverter;
         typedef Pipe< TInverter, Filter< filterI2<TypeOf_(TInverter)> > > TCounterFilter;
-		typedef Pipe< TTextInput, Shifter< -1, false > > TShiftText;
+        typedef Pipe< TTextInput, Shifter< -1, false > > TShiftText;
 
-		typedef Pipe< Bundle2< TCounterFilter, TShiftText >, Joiner > TJoiner;
-		typedef Pool< TypeOf_(TJoiner), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TJoiner)>, TSize> > > TLinearMapper;
+        typedef Pipe< Bundle2< TCounterFilter, TShiftText >, Joiner > TJoiner;
+        typedef Pool< TypeOf_(TJoiner), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TJoiner)>, TSize> > > TLinearMapper;
         typedef Pipe< TLinearMapper, Filter< filterI2<TypeOf_(TLinearMapper)> > > TFilter;
 
-		TTextInput			*textIn;
-		TSuffixArrayInput	*suffixArrayIn;
-        TLinearMapper		mapper;
-		TFilter				in;
+        TTextInput            *textIn;
+        TSuffixArrayInput    *suffixArrayIn;
+        TLinearMapper        mapper;
+        TFilter                in;
+
+        TLimitsString const    &limits;
 
-		TLimitsString const	&limits;
-        
         Pipe(TLimitsString const &_limits):
             in(mapper),
-			limits(_limits)	{}
+            limits(_limits)    {}
 
         Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn, TLimitsString const &_limits):
             textIn(&_bundleIn.in1),
-			suffixArrayIn(&_bundleIn.in2),
+            suffixArrayIn(&_bundleIn.in2),
             in(mapper),
-			limits(_limits)
-		{
-			process();
-		}
+            limits(_limits)
+        {
+            process();
+        }
 
         inline void process() {
             process(*textIn, *suffixArrayIn);
         }
 
-		template < typename TTextInput_, typename TSuffixArrayInput_ >
+        template < typename TTextInput_, typename TSuffixArrayInput_ >
         bool process(TTextInput_ &textIn, TSuffixArrayInput_ &suffixArrayIn) {
 
             // *** INSTANTIATION ***
 
-			for(int i=0;i<length(limits);++i)
-				::std::cout << limits[i]<<"  ";
-			::std::cout<<::std::endl;
-			
-			TGlobalizer					globalizer(suffixArrayIn, limits);
-			TSA							sa(globalizer);
-			TInverter					inverter;
-			TCounterFilter				filter(inverter);
-			
+            for(int i=0;i<length(limits);++i)
+                std::cout << limits[i]<<"  ";
+            std::cout<<std::endl;
+
+            TGlobalizer                    globalizer(suffixArrayIn, limits);
+            TSA                            sa(globalizer);
+            TInverter                    inverter;
+            TCounterFilter                filter(inverter);
+
             #ifdef SEQAN_DEBUG_INDEX
-                ::std::cerr << "  invert suffix array" << ::std::endl;
+                std::cerr << "  invert suffix array" << std::endl;
             #endif
-			inverter << sa;
-			SEQAN_PROMARK("Suffix-Array invertiert");
+            inverter << sa;
+            SEQAN_PROMARK("Suffix-Array invertiert");
+
+            TShiftText                    shifter(textIn);
+            TJoiner                        joiner(bundle2(filter, shifter));
 
-			TShiftText					shifter(textIn);
-			TJoiner						joiner(bundle2(filter, shifter));
-			
             #ifdef SEQAN_DEBUG_INDEX
-                ::std::cerr << "  de-invert suffix array" << ::std::endl;
+                std::cerr << "  de-invert suffix array" << std::endl;
             #endif
-			mapper << joiner;
-			SEQAN_PROMARK("Suffix-Array linearisiert");
+            mapper << joiner;
+            SEQAN_PROMARK("Suffix-Array linearisiert");
 
             return true;
         }
@@ -229,19 +229,19 @@ namespace SEQAN_NAMESPACE_MAIN
         inline typename Value<Pipe>::Type const operator*() const {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
         }
-	};
+    };
 
     // not sure which interface is more intuitive, we support both
     // you can call "bwt << pipe" or "bwt_t bwt(pipe); bwt.process()"
     // for the first we would need no _in member
-	template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_, typename TPair, typename TLimitsString >
+    template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_, typename TPair, typename TLimitsString >
     inline bool operator<<(Pipe< TInput, Multi<Bwt, TPair, TLimitsString> > &me, Bundle2< TTextInput_, TSuffixArrayInput_ > const &bundleIn) {
- 	    return me.process(bundleIn.in1, bundleIn.in2);
+         return me.process(bundleIn.in1, bundleIn.in2);
     }
 
 
@@ -255,55 +255,55 @@ namespace SEQAN_NAMESPACE_MAIN
                typename TText,
                typename TSA >
     void createBWTableInt(
-		TBWT &bwt,
-		TText const &s,
-		TSA const &SA)
-	{
-		typedef typename Value<TBWT>::Type		TValue;
-		typedef typename GetValue<TSA>::Type	TSAValue;
-		typedef typename Size<TSA>::Type		TSize;
-
-		TSize n = length(s);
-
-		for (TSize i = 0; i < n; ++i)
-		{
-			TSAValue sa = getValue(SA, i);
-			if (sa != 0)
-				bwt[i] = getValue(s, sa - 1);
-			else
-				bwt[i] = TValue();
-//				bwt[i] = getValue(s, n - 1);
-		}
-	}
+        TBWT &bwt,
+        TText const &s,
+        TSA const &SA)
+    {
+        typedef typename Value<TBWT>::Type        TValue;
+        typedef typename GetValue<TSA>::Type    TSAValue;
+        typedef typename Size<TSA>::Type        TSize;
+
+        TSize n = length(s);
+
+        for (TSize i = 0; i < n; ++i)
+        {
+            TSAValue sa = getValue(SA, i);
+            if (sa != 0)
+                bwt[i] = getValue(s, sa - 1);
+            else
+                bwt[i] = TValue();
+//                bwt[i] = getValue(s, n - 1);
+        }
+    }
 
     template < typename TBWT,
                typename TString,
-			   typename TSpec,
+               typename TSpec,
                typename TSA >
     void createBWTableInt(
-		TBWT &bwt,
-		StringSet<TString, TSpec> const &s,
-		TSA const &SA)
-	{
-		typedef typename Value<TBWT>::Type		TValue;
-		typedef typename Size<TSA>::Type		TSize;
-
-		TSize n = lengthSum(s);
-		Pair<unsigned, typename Size<TString>::Type> loc;
-
-		for (TSize i = 0; i < n; ++i)
-		{
-			posLocalize(loc, getValue(SA, i), stringSetLimits(s));
-			if (loc.i2 != 0)
-				bwt[i] = s[loc.i1][loc.i2 - 1];
-			else
-				if (loc.i1 != 0)
-					bwt[i] = s[loc.i1 - 1][length(s[loc.i1 - 1]) - 1];
-				else
-					bwt[i] = TValue();
-//					bwt[i] = getValue(s, n - 1);
-		}
-	}
+        TBWT &bwt,
+        StringSet<TString, TSpec> const &s,
+        TSA const &SA)
+    {
+        typedef typename Value<TBWT>::Type        TValue;
+        typedef typename Size<TSA>::Type        TSize;
+
+        TSize n = lengthSum(s);
+        Pair<unsigned, typename Size<TString>::Type> loc;
+
+        for (TSize i = 0; i < n; ++i)
+        {
+            posLocalize(loc, getValue(SA, i), stringSetLimits(s));
+            if (loc.i2 != 0)
+                bwt[i] = s[loc.i1][loc.i2 - 1];
+            else
+                if (loc.i1 != 0)
+                    bwt[i] = s[loc.i1 - 1][length(s[loc.i1 - 1]) - 1];
+                else
+                    bwt[i] = TValue();
+//                    bwt[i] = getValue(s, n - 1);
+        }
+    }
 
 //}
 
diff --git a/seqan/index/index_childtab.h b/seqan/index/index_childtab.h
index 3ded596..40e1e89 100644
--- a/seqan/index/index_childtab.h
+++ b/seqan/index/index_childtab.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,7 +41,7 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct Childtab {};
+    struct Childtab {};
 
     //////////////////////////////////////////////////////////////////////////////
     // external childtab algorithm
@@ -53,260 +53,241 @@ namespace SEQAN_NAMESPACE_MAIN
     };
 
 
-	template < typename TLCPInput, typename TDest >
-	inline void _childtabProcess(TLCPInput &lcpIn, TDest &dest)
-	{
-		typedef typename Value<TLCPInput>::Type				TValue;
-		typedef typename Size<TLCPInput>::Type				TSize;
+    template < typename TLCPInput, typename TDest >
+    inline void _childtabProcess(TLCPInput &lcpIn, TDest &dest)
+    {
+        typedef typename Value<TLCPInput>::Type                TValue;
+        typedef typename Size<TLCPInput>::Type                TSize;
 
-		typedef Pair<TSize, TValue, Pack>				TPair;		// (i, lcptab[i])
-		typedef ::std::stack<TPair> 						TStack;
+        typedef Pair<TSize, TValue, Pack>                TPair;        // (i, lcptab[i])
+        typedef std::stack<TPair>                         TStack;
 
-		TStack stack_updown;
-		TStack stack_nextl;
+        TStack stack_updown;
+        TStack stack_nextl;
 
         #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "--- CREATE CHILD TABLE ---" << std::endl;
             std::cerr << "Start stack-processing [pipelining]" << std::endl;
         #endif
 
-		stack_updown.push(TPair(0, 0));
-		stack_nextl.push(TPair(0, 0));
-
-		dest.undefinedValue = TPair(MaxValue<TSize>::VALUE, 0);		// undefined value for unused entries
-		resize(dest, length(lcpIn));
-		beginRead(lcpIn);
-		beginWrite(dest);
-
-		TSize n = length(lcpIn);
-		TSize undef = n + 1;
-		TSize lastIndex_nextl;
-		TPair lastIndex_updown = TPair(undef, 0);
-
-		TValue lcp_i;
-		for(TSize i = 0; i < n; ++i) {
-			lcp_i = *lcpIn; ++lcpIn;
-
-			//////////////////////////////////////////////////////////////////////////////
-			// nextlIndex part
-			lastIndex_nextl = undef;
-			while (lcp_i < stack_nextl.top().i2)
-				stack_nextl.pop();
-
-			if (lcp_i == stack_nextl.top().i2) {
-				lastIndex_nextl = stack_nextl.top().i1;
-				push(dest, TPair(lastIndex_nextl, i + 1));					// childtab[top].nextl
-
-//				::std::cerr << "nextl:\t\t\t" << TPair(lastIndex_nextl, i + 1) << ::std::endl;
-				stack_nextl.pop();
-			}
-			stack_nextl.push(TPair(i + 1, lcp_i));
-
-
-			//////////////////////////////////////////////////////////////////////////////
-			// up/down part
-			TPair top;
-			while (lcp_i < stack_updown.top().i2) {
-				lastIndex_updown = stack_updown.top();
-				stack_updown.pop();
-				
-				top = stack_updown.top();
-				if (lcp_i <= top.i2 && top.i2 != lastIndex_updown.i2 && top.i1 != lastIndex_nextl) {
-					push(dest, TPair(top.i1, lastIndex_updown.i1));			// childtab[top].down
-
-//					::std::cerr << "down:\t\t" << TPair(top.i1, lastIndex_updown.i1) << ::std::endl;			// childtab[top].down
-				}
-			}
-			if (lastIndex_updown.i1 != undef) {
-				push(dest, TPair(i, lastIndex_updown.i1));			// childtab[top].up goes to [top - 1]
-
-//				::std::cerr << "up:\t" << TPair(i, lastIndex_updown.i1) << ::std::endl;
-				lastIndex_updown.i1 = undef;
-			}
-			stack_updown.push(TPair(i + 1, lcp_i));
-		}
-
-		endRead(lcpIn);
-		endWrite(dest);
+        stack_updown.push(TPair(0, 0));
+        stack_nextl.push(TPair(0, 0));
+
+        dest.undefinedValue = TPair(MaxValue<TSize>::VALUE, 0);        // undefined value for unused entries
+        resize(dest, length(lcpIn));
+        beginRead(lcpIn);
+        beginWrite(dest);
+
+        TSize n = length(lcpIn);
+        TSize undef = n + 1;
+        TSize lastIndex_nextl;
+        TPair lastIndex_updown = TPair(undef, 0);
+
+        TValue lcp_i;
+        for(TSize i = 0; i < n; ++i) {
+            lcp_i = *lcpIn; ++lcpIn;
+
+            //////////////////////////////////////////////////////////////////////////////
+            // nextlIndex part
+            lastIndex_nextl = undef;
+            while (lcp_i < stack_nextl.top().i2)
+                stack_nextl.pop();
+
+            if (lcp_i == stack_nextl.top().i2) {
+                lastIndex_nextl = stack_nextl.top().i1;
+                push(dest, TPair(lastIndex_nextl, i + 1));                    // childtab[top].nextl
+
+//                std::cerr << "nextl:\t\t\t" << TPair(lastIndex_nextl, i + 1) << std::endl;
+                stack_nextl.pop();
+            }
+            stack_nextl.push(TPair(i + 1, lcp_i));
+
+
+            //////////////////////////////////////////////////////////////////////////////
+            // up/down part
+            TPair top;
+            while (lcp_i < stack_updown.top().i2) {
+                lastIndex_updown = stack_updown.top();
+                stack_updown.pop();
+
+                top = stack_updown.top();
+                if (lcp_i <= top.i2 && top.i2 != lastIndex_updown.i2 && top.i1 != lastIndex_nextl) {
+                    push(dest, TPair(top.i1, lastIndex_updown.i1));            // childtab[top].down
+
+//                    std::cerr << "down:\t\t" << TPair(top.i1, lastIndex_updown.i1) << std::endl;            // childtab[top].down
+                }
+            }
+            if (lastIndex_updown.i1 != undef) {
+                push(dest, TPair(i, lastIndex_updown.i1));            // childtab[top].up goes to [top - 1]
+
+//                std::cerr << "up:\t" << TPair(i, lastIndex_updown.i1) << std::endl;
+                lastIndex_updown.i1 = undef;
+            }
+            stack_updown.push(TPair(i + 1, lcp_i));
+        }
+
+        endRead(lcpIn);
+        endWrite(dest);
     }
 
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // Enhanced class (outputs only the childtab (3rd) column of the Enhanced Suffix Array)
     template < typename TLCPInput >
     struct Pipe< TLCPInput, Childtab >
     {
         // *** SPECIALIZATION ***
 
-		typedef typename Value<TLCPInput>::Type		TValue;
-		typedef typename Size<TLCPInput>::Type		TSize;
+        typedef typename Value<TLCPInput>::Type        TValue;
+        typedef typename Size<TLCPInput>::Type        TSize;
 
-		typedef Pair<TSize, TValue, Pack>		TCoreType;		// (i, lcptab[i])
+        typedef Pair<TSize, TValue, Pack>        TCoreType;        // (i, lcptab[i])
 
-		typedef Pool< TCoreType, MapperSpec< MapperConfigSize< filterI1<TCoreType>, TSize > > > TLinearMapper;
+        typedef Pool< TCoreType, MapperSpec< MapperConfigSize< filterI1<TCoreType>, TSize > > > TLinearMapper;
         typedef Pipe< TLinearMapper, Filter< filterI2<TCoreType> > > TFilter;
 
         TLinearMapper   mapper;
-		TFilter			in;
-        
+        TFilter            in;
+
         Pipe():
             in(mapper) {}
 
         Pipe(TLCPInput &_in):
             in(mapper)
-		{
-			process(_in);
-		}
+        {
+            process(_in);
+        }
 
-		template < typename TLcpInput_ >
+        template < typename TLcpInput_ >
         inline bool process(TLcpInput_ &_lcpIn) {
 
             // *** INSTANTIATION ***
-			
-			_childtabProcess(_lcpIn, mapper);
+
+            _childtabProcess(_lcpIn, mapper);
             return true;
         }
 
         inline typename Value<Pipe>::Type const operator*() const {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
         }
-	};
+    };
 
-	template < typename TInput, typename TLcpInput_ >
+    template < typename TInput, typename TLcpInput_ >
     inline bool operator<<(Pipe< TInput, Childtab > &me, TLcpInput_ const &in) {
- 	    return me.process(in);
+         return me.process(in);
     }
 
-	template < typename TLCPTable,
+    template < typename TLCPTable,
                typename TChildTable >
     void createChildtabExt(
-		TChildTable &childtab,
-		TLCPTable &lcp)
-	{
-		typedef Pipe< TLCPTable, Source<> >	TSource;
-		typedef Pipe< TSource, Childtab >	TESA;
-
-		TSource source(lcp);
-		TESA	esa(source);
-
-		childtab << esa;
-	}
-
-/**
-.Function.createChildtab:
-..summary:Creates a child table from a given lcp table.
-..cat:Index
-..signature:createChildtab(childTab, lcp[, algo_tag])
-..class:Class.Index
-..param.childTab:A reference to the resulting child table.
-..param.lcp:A given lcp table.
-..param.algo_tag:A tag that identifies the algorithm which is used for creation.
-..remarks:The size of $childTab$ must be at least $length(text)$ before calling this function.
-..include:seqan/index.h
-*/
+        TChildTable &childtab,
+        TLCPTable &lcp)
+    {
+        typedef Pipe< TLCPTable, Source<> >    TSource;
+        typedef Pipe< TSource, Childtab >    TESA;
+
+        TSource source(lcp);
+        TESA    esa(source);
+
+        childtab << esa;
+    }
 
 /*!
  * @fn IndexEsa#createChildtab
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Creates a child table from a given lcp table.
- * 
- * @signature createChildtab(childTab, lcp[, algoTag])
- * 
- * @param algoTag A tag that identifies the algorithm which is used for
- *                the creation.
- * @param lcp A given lcp table.
- * @param childTab A reference to the resulting child table.
- * 
- * @section Remarks
- * 
- * The size of <tt>childTab</tt> must be at least <tt>length(text)</tt> before
- * calling this function.
+ *
+ * @signature void createChildtab(childTab, lcp[, algoTag]);
+ *
+ * @param[out] childTab A reference to the resulting child table.
+ * @param[in]  lcp      A given lcp table.
+ * @param[in]  algoTag  A tag that identifies the algorithm which is used for the creation.
+ *
+ * The size of <tt>childTab</tt> must be at least <tt>length(text)</tt> before calling this function.
  */
-	template < typename TLCPTable,
+    template < typename TLCPTable,
                typename TValue,
-			   typename TConfig >
+               typename TConfig >
     inline void createChildtab(
-		String<TValue, External<TConfig> > &childtab,
-		TLCPTable &lcp)
-	{
-		createChildtabExt(childtab, lcp);
-	}
-
-	
-	
+        String<TValue, External<TConfig> > &childtab,
+        TLCPTable &lcp)
+    {
+        createChildtabExt(childtab, lcp);
+    }
+
+
+
     //////////////////////////////////////////////////////////////////////////////
     // internal childtab algorithm
     //////////////////////////////////////////////////////////////////////////////
-	
-	template < typename TLCPInput, typename TDest >
-	inline void createChildtab(TDest &dest, TLCPInput const &lcpIn)
-	{
-		typedef typename Value<TLCPInput>::Type				TValue;
-		typedef typename Size<TLCPInput>::Type				TSize;
-		typedef typename Iterator<TLCPInput const>::Type	TIter;
 
-		typedef Pair<TSize, TValue>							TPair;		// (i, lcptab[i])
-		typedef String<TPair>								TStack;
+    template < typename TLCPInput, typename TDest >
+    inline void createChildtab(TDest &dest, TLCPInput const &lcpIn)
+    {
+        typedef typename Value<TLCPInput>::Type                TValue;
+        typedef typename Size<TLCPInput>::Type                TSize;
+        typedef typename Iterator<TLCPInput const>::Type    TIter;
+
+        typedef Pair<TSize, TValue>                            TPair;        // (i, lcptab[i])
+        typedef String<TPair>                                TStack;
 
         #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "--- CREATE CHILD TABLE ---" << std::endl;
             std::cerr << "Start stack-processing [random access]" << std::endl;
         #endif
 
-		TStack stack;
-
-		appendValue(stack, TPair(0, 0));
-
-		resize(dest, length(lcpIn));
-
-		TSize n = length(lcpIn);
-		TSize undef = n + 1;
-		TPair lastIndex = TPair(undef, 0);
-
-		TValue lcp_i;
-		TIter lcpI = begin(lcpIn);
-
-		for(TSize i = 0; i < n; ++i, ++lcpI)
-		{
-			lcp_i = *lcpI;
-
-			TPair top;
-			while (lcp_i < back(stack).i2)
-			{
-				lastIndex = back(stack);
-				pop(stack);
-
-				top = back(stack);
-				if (lcp_i < top.i2 && top.i2 != lastIndex.i2 /*&& top.i1 != lastIndex_nextl*/) {
-					dest[top.i1] = lastIndex.i1;			// childtab[top].down
-//					::std::cerr << "down:\t" << TPair(top.i1, lastIndex.i1) << ::std::endl;			// childtab[top].down
-				}
-//				else
-//					if (lcp_i == top.i2 && top.i2 != lastIndex.i2 /*&& top.i1 != lastIndex_nextl*/)
-//						::std::cerr << "down:\t" << TPair(top.i1, lastIndex.i1) << ::std::endl;			// childtab[top].down
-
-			}
-			if (lastIndex.i1 != undef)
-			{
-				dest[i] = lastIndex.i1;						// childtab[top].up goes to [top - 1]
-
-//				::std::cerr << "up:  \t" << TPair(i+1, lastIndex.i1) << ::std::endl;
-				lastIndex.i1 = undef;
-			}
-			if (lcp_i == back(stack).i2)
-			{
-				dest[back(stack).i1] = i + 1;				// childtab[top].nextl
-//				::std::cerr << "nextl:\t\t\t" << TPair(back(stack).i1, i + 1) << ::std::endl;
-			}
-			appendValue(stack, TPair(i + 1, lcp_i));
-		}
+        TStack stack;
+
+        appendValue(stack, TPair(0, 0));
+
+        resize(dest, length(lcpIn));
+
+        TSize n = length(lcpIn);
+        TSize undef = n + 1;
+        TPair lastIndex = TPair(undef, 0);
+
+        TValue lcp_i;
+        TIter lcpI = begin(lcpIn);
+
+        for(TSize i = 0; i < n; ++i, ++lcpI)
+        {
+            lcp_i = *lcpI;
+
+            TPair top;
+            while (lcp_i < back(stack).i2)
+            {
+                lastIndex = back(stack);
+                eraseBack(stack);
+
+                top = back(stack);
+                if (lcp_i < top.i2 && top.i2 != lastIndex.i2 /*&& top.i1 != lastIndex_nextl*/) {
+                    dest[top.i1] = lastIndex.i1;            // childtab[top].down
+//                    std::cerr << "down:\t" << TPair(top.i1, lastIndex.i1) << std::endl;            // childtab[top].down
+                }
+//                else
+//                    if (lcp_i == top.i2 && top.i2 != lastIndex.i2 /*&& top.i1 != lastIndex_nextl*/)
+//                        std::cerr << "down:\t" << TPair(top.i1, lastIndex.i1) << std::endl;            // childtab[top].down
+
+            }
+            if (lastIndex.i1 != undef)
+            {
+                dest[i] = lastIndex.i1;                        // childtab[top].up goes to [top - 1]
+
+//                std::cerr << "up:  \t" << TPair(i+1, lastIndex.i1) << std::endl;
+                lastIndex.i1 = undef;
+            }
+            if (lcp_i == back(stack).i2)
+            {
+                dest[back(stack).i1] = i + 1;                // childtab[top].nextl
+//                std::cerr << "nextl:\t\t\t" << TPair(back(stack).i1, i + 1) << std::endl;
+            }
+            appendValue(stack, TPair(i + 1, lcp_i));
+        }
     }
 
 //}
diff --git a/seqan/index/index_device.h b/seqan/index/index_device.h
new file mode 100644
index 0000000..76f837a
--- /dev/null
+++ b/seqan/index/index_device.h
@@ -0,0 +1,430 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// This file contains Index specializations for thrust::device_vector.
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_DEVICE_H_
+#define SEQAN_INDEX_DEVICE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Device                                                  [Index]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec>
+struct Device<Index<TText, TSpec> >
+{
+    typedef Index<typename Device<TText>::Type, TSpec>          Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsDevice                                                [Index]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec>
+struct IsDevice<Index<TText, TSpec> > : IsDevice<TText> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsDevice                                                 [Iter]
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct IsDevice<Iter<TIndex, VSTree<TSpec> > > : IsDevice<TIndex> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreSA                                          [Device Index]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+struct Fibre<Index<thrust::device_vector<TValue, TAlloc>, TSpec>, FibreSA>
+{
+    typedef thrust::device_vector<typename SAValue<Index<thrust::device_vector<TValue, TAlloc>, TSpec> >::Type> Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec>, FibreSA>
+{
+    typedef thrust::device_vector<typename SAValue<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec> >::Type>   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreLcp                                         [Device Index]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+struct Fibre<Index<thrust::device_vector<TValue, TAlloc>, TSpec>, FibreLcp>
+{
+    typedef thrust::device_vector<typename Size<Index<thrust::device_vector<TValue, TAlloc>, TSpec> >::Type>    Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec>, FibreLcp>
+{
+    typedef thrust::device_vector<typename Size<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec> >::Type>  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreChildtab                                    [Device Index]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+struct Fibre<Index<thrust::device_vector<TValue, TAlloc>, TSpec>, FibreChildtab>
+{
+    typedef thrust::device_vector<typename Size<Index<thrust::device_vector<TValue, TAlloc>, TSpec> >::Type>    Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec>, FibreChildtab>
+{
+    typedef thrust::device_vector<typename Size<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec> >::Type>  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreBwt                                         [Device Index]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+struct Fibre<Index<thrust::device_vector<TValue, TAlloc>, TSpec>, FibreBwt>
+{
+    typedef thrust::device_vector<typename Value<Index<thrust::device_vector<TValue, TAlloc>, TSpec> >::Type>   Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec>, FibreBwt>
+{
+    typedef thrust::device_vector<typename Value<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec> >::Type> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreSA                                        [Device FMIndex]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec, typename TConfig>
+struct Fibre<Index<thrust::device_vector<TValue, TAlloc>, FMIndex<TSpec, TConfig> >, FibreSA>
+{
+    typedef CompressedSA<thrust::device_vector<TValue, TAlloc>, TSpec, TConfig>      Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, FMIndex<TSpec, TConfig> >, FibreSA>
+{
+    typedef CompressedSA<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec, TConfig>    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibrePrefixSums                                     [Device LF]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec, typename TConfig>
+struct Fibre<LF<thrust::device_vector<TValue, TAlloc>, TSpec, TConfig>, FibrePrefixSums>
+{
+    typedef thrust::device_vector<TValue, TAlloc>               TText_;
+    typedef typename Size<LF<TText_, TSpec, TConfig> >::Type    TSize_;
+//    typedef typename Value<LF<TText_, TSpec, TConfig> >::Type  TValue_;
+//    typedef Tuple<TSize_, ValueSize<TValue_>::VALUE>                Type;
+
+    typedef thrust::device_vector<TSize_>                       Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec, TConfig>, FibrePrefixSums>
+{
+    typedef StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec> TText_;
+    typedef typename Size<LF<TText_, TSpec, TConfig> >::Type            TSize_;
+//    typedef typename Value<LF<TText_, TSpec, TConfig> >::Type           TValue_;
+//    typedef Tuple<TSize_, ValueSize<TValue_>::VALUE>                    Type;
+
+    typedef thrust::device_vector<TSize_>                               Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreBwt                                            [Device LF]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec, typename TConfig>
+struct Fibre<LF<thrust::device_vector<TValue, TAlloc>, TSpec, TConfig>, FibreBwt>
+{
+    typedef thrust::device_vector<TValue, TAlloc>               TText_;
+    typedef typename Value<LF<TText_, TSpec, TConfig> >::Type   TValue_;
+
+    typedef RankDictionary<TValue_, TwoLevels<Device<TSpec> > > Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec, TConfig>, FibreBwt>
+{
+    typedef StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec> TText_;
+    typedef typename Value<LF<TText_, TSpec, TConfig> >::Type           TValue_;
+
+    typedef RankDictionary<TValue_, TwoLevels<Device<TSpec> > >         Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreSentinels                                      [Device LF]
+// ----------------------------------------------------------------------------
+
+// NOTE(esiragusa): Single text sentinel rank dictionary is an integer.
+//template <typename TText, typename TViewSpec, typename TSpec>
+//struct Fibre<LF<thrust::device_vector<TValue, TAlloc>, TSpec>, FibreSentinels>
+//{
+//    typedef typename Fibre<LF<TText, TSpec, TConfig>, FibreSentinels>::Type   Type;
+//};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec, TConfig>, FibreSentinels>
+{
+//    typedef RankDictionary<bool, TwoLevels<Device<TSpec> > >    Type;
+    typedef RankDictionary<bool, Naive<Device<TSpec> > >    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreRanks                              [Device RankDictionary]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct Fibre<RankDictionary<TValue, TwoLevels<Device<TSpec> > >, FibreRanks>
+{
+    typedef thrust::device_vector<RankDictionaryEntry_<TValue, TwoLevels<TSpec> > > Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Fibre<RankDictionary<TValue, Naive<Device<TSpec> > >, FibreRanks>
+{
+    typedef RankDictionary<TValue, Naive<TSpec> >               TRankDictionary_;
+    typedef typename Size<TRankDictionary_>::Type               TSize_;
+
+    typedef thrust::device_vector<TSize_>                       Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreSparseString                         [Device CompressedSA]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec, typename TConfig>
+struct Fibre<CompressedSA<thrust::device_vector<TValue, TAlloc>, TSpec, TConfig>, FibreSparseString>
+{
+    typedef thrust::device_vector<TValue/*, TAlloc*/>       TText_;
+    typedef typename SAValue<TText_>::Type                  TSAValue_;
+    typedef thrust::device_vector<TSAValue_/*, TAlloc*/>    TString_;
+
+    typedef SparseString<TString_, TSpec>                   Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<CompressedSA<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TSpec, TConfig>, FibreSparseString>
+{
+    typedef StringSet<thrust::device_vector<TValue/*, TAlloc*/>, TSSetSpec> TText_;
+    typedef typename SAValue<TText_>::Type                                  TSAValue_;
+    typedef thrust::device_vector<TSAValue_/*, TAlloc*/>                    TString_;
+
+    typedef SparseString<TString_, TSpec>                                   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreIndicators                           [Device SparseString]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+struct Fibre<SparseString<thrust::device_vector<TValue, TAlloc>, TSpec>, FibreIndicators>
+{
+    typedef RankDictionary<bool, TwoLevels<Device<TSpec> > >        Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreValues                               [Device SparseString]
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): FibreValues is already defined as below.
+
+//template <typename TValue, typename TAlloc, typename TSpec>
+//struct Fibre<SparseString<thrust::device_vector<TValue, TAlloc>, TSpec>, FibreValues>
+//{
+//    typedef thrust::device_vector<TValue, TAlloc>       Type;
+//};
+
+// ----------------------------------------------------------------------------
+// Metafunction HistoryStack_                              [Device VSTree Iter]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TIndexSpec, typename TSpec>
+struct HistoryStack_<Iter<Index<thrust::device_vector<TValue, TAlloc>, TIndexSpec>, VSTree<TSpec> > >
+{
+    typedef thrust::device_vector<TValue, TAlloc>       TText_;
+    typedef Index<TText_, TIndexSpec>                   TIndex_;
+    typedef Iter<TIndex_, VSTree<TSpec> >               TIter_;
+    typedef typename HistoryStackEntry_<TIter_>::Type   TEntry_;
+    typedef thrust::device_vector<TEntry_>              Type;
+};
+
+template <typename TValue, typename TAlloc, typename TSSetSpec, typename TIndexSpec, typename TSpec>
+struct HistoryStack_<Iter<Index<StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>, TIndexSpec>, VSTree<TSpec> > >
+{
+    typedef StringSet<thrust::device_vector<TValue, TAlloc>, TSSetSpec>     TText_;
+    typedef Index<TText_, TIndexSpec>                                       TIndex_;
+    typedef Iter<TIndex_, VSTree<TSpec> >                                   TIter_;
+    typedef typename HistoryStackEntry_<TIter_>::Type                       TEntry_;
+    typedef thrust::device_vector<TEntry_>                                  Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+// NOTE(esiragusa): Functions assign() are not specific to Device Index.
+
+// ----------------------------------------------------------------------------
+// Function assign()                                                  [FMIndex]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig, typename TText2, typename TOccSpec2, typename TSpec2>
+inline void
+assign(Index<TText, FMIndex<TSpec, TConfig> > & index, Index<TText2, FMIndex<TOccSpec2, TSpec2> > const & source)
+{
+    assign(indexText(index), indexText(source));
+    assign(indexLF(index), indexLF(source));
+    assign(indexSA(index), indexSA(source));
+
+    // Set the pointer.
+    setFibre(indexSA(index), indexLF(index), FibreLF());
+}
+
+template <typename TText, typename TSpec, typename TConfig, typename TText2, typename TOccSpec2, typename TSpec2>
+inline void
+assign(Index<TText, FMIndex<TSpec, TConfig> > & index, Index<TText2, FMIndex<TOccSpec2, TSpec2> > & source)
+{
+    assign(index, reinterpret_cast<Index<TText2, FMIndex<TOccSpec2, TSpec2> > const &>(source));
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()                                                       [LF]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TText2, typename TSpec2, typename TConfig>
+inline void
+assign(LF<TText, TSpec, TConfig> & lf, LF<TText2, TSpec2, TConfig> const & source)
+{
+    assign(getFibre(lf, FibrePrefixSums()), getFibre(source, FibrePrefixSums()));
+    assign(getFibre(lf, FibreBwt()), getFibre(source, FibreBwt()));
+    assign(getFibre(lf, FibreSentinels()), getFibre(source, FibreSentinels()));
+    assign(lf.sentinelSubstitute, source.sentinelSubstitute);
+}
+
+template <typename TText, typename TSpec, typename TText2, typename TSpec2, typename TConfig>
+inline void
+assign(LF<TText, TSpec, TConfig> & lf, LF<TText2, TSpec2, TConfig> & source)
+{
+    assign(lf, reinterpret_cast<LF<TText2, TSpec2, TConfig> const &>(source));
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()                                           [RankDictionary]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TValue2, typename TSpec2>
+inline void
+assign(RankDictionary<TValue, TwoLevels<TSpec> > & dict, RankDictionary<TValue2, TwoLevels<TSpec2> > const & source)
+{
+    assign(getFibre(dict, FibreRanks()), getFibre(source, FibreRanks()));
+    assign(dict._length, source._length);
+}
+
+template <typename TValue, typename TSpec, typename TValue2, typename TSpec2>
+inline void
+assign(RankDictionary<TValue, TwoLevels<TSpec> > & dict, RankDictionary<TValue2, TwoLevels<TSpec2> > & source)
+{
+    assign(dict, reinterpret_cast<RankDictionary<TValue2, TwoLevels<TSpec2> > const &>(source));
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()                                           [RankDictionary]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TValue2, typename TSpec2>
+inline void
+assign(RankDictionary<TValue, Naive<TSpec> > & dict, RankDictionary<TValue2, Naive<TSpec2> > const & source)
+{
+    assign(getFibre(dict, FibreRanks()), getFibre(source, FibreRanks()));
+}
+
+template <typename TValue, typename TSpec, typename TValue2, typename TSpec2>
+inline void
+assign(RankDictionary<TValue, Naive<TSpec> > & dict, RankDictionary<TValue2, Naive<TSpec2> > & source)
+{
+    assign(dict, reinterpret_cast<RankDictionary<TValue2, Naive<TSpec2> > const &>(source));
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()                                             [CompressedSA]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TText2, typename TSpec2, typename TConfig>
+inline void
+assign(CompressedSA<TText, TSpec, TConfig> & sa, CompressedSA<TText2, TSpec2, TConfig> const & source)
+{
+    assign(getFibre(sa, FibreSparseString()), getFibre(source, FibreSparseString()));
+}
+
+template <typename TText, typename TSpec, typename TText2, typename TSpec2, typename TConfig>
+inline void
+assign(CompressedSA<TText, TSpec, TConfig> & sa, CompressedSA<TText2, TSpec2, TConfig> & source)
+{
+    assign(getFibre(sa, FibreSparseString()), getFibre(source, FibreSparseString()));
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()                                             [SparseString]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec, typename TString2, typename TSpec2>
+inline void
+assign(SparseString<TString, TSpec> & sparseString, SparseString<TString2, TSpec2> const & source)
+{
+    assign(getFibre(sparseString, FibreValues()), getFibre(source, FibreValues()));
+    assign(getFibre(sparseString, FibreIndicators()), getFibre(source, FibreIndicators()));
+    assign(sparseString._length, source._length);
+}
+
+template <typename TString, typename TSpec, typename TString2, typename TSpec2>
+inline void
+assign(SparseString<TString, TSpec> & sparseString, SparseString<TString2, TSpec2> & source)
+{
+    assign(sparseString, reinterpret_cast<SparseString<TString2, TSpec2> const &>(source));
+}
+
+}
+
+#endif  // #ifndef SEQAN_INDEX_DEVICE_H_
diff --git a/seqan/index/index_dfi.h b/seqan/index/index_dfi.h
index dd939dd..b32c75e 100644
--- a/seqan/index/index_dfi.h
+++ b/seqan/index/index_dfi.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,579 +42,636 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 // simple struct to store frequency vectors
 
-	struct DfiEntry_
-	{
-		unsigned						lastSeqSeen;
-//		String<unsigned, Array<2> >		freq;
-		String<unsigned>				freq;
-	};
+    struct DfiEntry_
+    {
+        unsigned                        lastSeqSeen;
+//        String<unsigned, Array<2> >        freq;
+        String<unsigned>                freq;
+    };
 
 
 //////////////////////////////////////////////////////////////////////////////
 // constant frequency predicate
 
-	template <bool Result>
-	struct DfiPredDefault_ 
-	{
+    template <bool Result>
+    struct DfiPredDefault_
+    {
         inline bool operator()(DfiEntry_ const &) const {
-			return Result;
-		}
+            return Result;
+        }
     };
 
 
-///.Spec.VSTree Iterator.param.TContainer.type:Spec.IndexDfi
-///.Spec.TopDown Iterator.param.TContainer.type:Spec.IndexDfi
-///.Spec.TopDownHistory Iterator.param.TContainer.type:Spec.IndexDfi
-
 //////////////////////////////////////////////////////////////////////////////
 // Dfi - The Deferred Frequency Index
 
-/**
-.Spec.IndexDfi:
-..summary:The Deferred Frequency Index (see Weese and Schulz, "Efficient string mining under constraints via the
-deferred frequency index").
-..cat:Index
-..general:Spec.IndexWotd
-..signature:Index<TText, IndexWotd< Dfi<TPredHull, TPred> > >
-..param.TText:The text type.
-...type:Class.String
-..param.TPred:An arbitrary frequency predicate
-..param.TPredHull:A monotonic hull of $TPred$
-..remarks:This index is based on a lazy suffix tree (see @Spec.IndexWotd@).
-All $TPredHull$ sufficing nodes can be iterated using a @Spec.TopDown Iterator@.
-To iterate the exact solution set of $TPred$, use a $Spec.TopDownHistory Iterator$ of this index.
-..include:seqan/index.h
-*/
 /*!
  * @class IndexDfi
- * 
  * @extends IndexWotd
- * 
- * @headerfile seqan/index.h
- * 
- * @brief The Deferred Frequency Index (see Weese and Schulz, "Efficient string
- *        mining under constraints via the deferred frequency index").
- * 
- * @signature Index<TText, IndexWotd< Dfi<TPredHull, TPred> > >
- * 
- * @tparam TText The text type. Types: @link String @endlink, @link StringSet @endlink
- * @tparam TPred An arbitrary frequency predicate
+ * @headerfile <seqan/index.h>
+ *
+ * @brief The Deferred Frequency Index (see Weese and Schulz, "Efficient string mining under constraints via
+ *        the deferred frequency index").
+ *
+ * @signature template <typename TText, typename TPredHull, typename TPred>
+ *            class Index<TText, IndexWotd< Dfi<TPredHull, TPred> > >;
+ *
+ * @tparam TText     The @link TextConcept text @endlink.
+ * @tparam TPred     An arbitrary frequency predicate.
  * @tparam TPredHull A monotonic hull of <tt>TPred</tt>
- * 
- * @section Remarks
- * 
- * This index is based on a lazy suffix tree (see @link IndexWotd @endlink). All
- * <tt>TPredHull</tt> sufficing nodes can be iterated using a @link TopDownIterator @endlink. To iterate the exact solution set of <tt>TPred</tt>, use a
- * <tt>Spec.TopDownHistory Iterator</tt> of this index.
+ *
+ * This index is based on a lazy suffix tree (see @link IndexWotd @endlink).  All <tt>TPredHull</tt> sufficing
+ * nodes can be iterated using a @link TopDownIterator @endlink.  To iterate the exact solution set of <tt>TPred</tt>,
+ * use a @link TopDownHistoryIterator @endlink of this index.
+ */
+
+/*!
+ * @defgroup DfiIndexFibres Dfi Index Fibres
+ * @brief Tag to select a specific fibre (e.g. table, object, ...) of an @link
+ *        IndexDfi @endlink index.
+ *
+ * These tags can be used to get @link Fibre @endlink of an @link IndexDfi @endlink.
+ *
+ * @see Fibre
+ * @see Index#getFibre
+ * @see IndexDfi
+ *
+ * @tag DfiIndexFibres#DfiDir
+ * @brief The child table.
+ *
+ * @tag DfiIndexFibres#DfiRawSA
+ * @brief The raw suffix array.
+ *
+ * @tag DfiIndexFibres#DfiText
+ * @brief The original text the index should be based on.
+ *
+ * @tag DfiIndexFibres#DfiRawText
+ * @brief The raw text the index is really based on.
+ *
+ * @tag DfiIndexFibres#DfiSA
+ * @brief The suffix array.
+ */
+
+//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn IndexDfi#indexSA
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(.., DfiSA)</tt>.
+ *
+ * @signature TSa indexSA(index);
+ *
+ * @param[in] index The @link IndexDfi @endlink object holding the fibre.
+ *
+ * @return TSa A reference to the @link DfiIndexFibres#DfiSA @endlink fibre (partially sorted suffix array).
+ */
+
+/*!
+ * @fn IndexDfi#indexDir
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(.., DfiDir())</tt>.
+ * @signature TFibre indexDir(index);
+ *
+ * @param[in] index The @link IndexDfi @endlink object holding the fibre.
+ *
+ * @return TFibre A reference to the @link DfiIndexFibres#DfiDir @endlink fibre (tree structure).
+ */
+
+/*!
+ * @fn IndexDfi#saAt
+ * @headerfile <seqan/index.h>
+ * @note Advanced functionality, not commonly used.
+ * @brief Shortcut for <tt>value(indexSA(..), ..)</tt>.
+ *
+ * @signature TValue saAt(position, index);
+ *
+ * @param[in] index The @link IndexDfi @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TValue A reference or proxy to the value in the @link DfiIndexFibres#DfiSA @endlink fibre.
+ *                To be more precise, a reference to a position containing a value of type
+ *                @link SAValue @endlink is returned (or a proxy).
  */
 
-	template < 
-		typename TPredHull = DfiPredDefault_<true>,
-		typename TPred = DfiPredDefault_<true>
-	>
-	struct Dfi;
-
-	template < 
-		typename TObject,
-		typename TPredHull,
-		typename TPred
-	>
-	class Index<TObject, IndexWotd< Dfi<TPredHull, TPred> > >:
-		public Index<TObject, IndexWotd<> > 
-	{
-	public:
-		
-		typedef Index<TObject, IndexWotd<> >	TBase;
-
-		// extending base class
-		typedef typename TBase::TText	TText;
-		typedef typename TBase::TValue	TValue;
-		typedef typename TBase::TSize	TSize;
-		
-		using TBase::LEAF;
-		using TBase::LAST_CHILD;
-		using TBase::UNEVALUATED;
-		using TBase::SENTINELS;
-
-		// frequency strings for Dfi
-		typedef DfiEntry_						TDFIEntry;
-		typedef String<
-			TDFIEntry, 
-			Array<ValueSize<TValue>::VALUE> >	TDFIEntries;
-		typedef String<unsigned>				TDFIDatasets;
-
-		// 1st word flags
-		static TSize const DFI_PRED_HULL	= (TSize)1 << (BitsPerValue<TSize>::VALUE - 3); // this node fulfills all monotonic frequency predicates (e.g. min_freq)
-		static TSize const DFI_PRED			= (TSize)1 << (BitsPerValue<TSize>::VALUE - 4); // this node fulfills all frequency predicates (e.g. emerging, minmax_freq)
-		static TSize const DFI_PARENT_FREQ	= (TSize)1 << (BitsPerValue<TSize>::VALUE - 5); // this node has the same frequency as its parent
-
-		static TSize const BITMASK0			= ~(LEAF | LAST_CHILD | DFI_PRED_HULL | DFI_PRED | DFI_PARENT_FREQ);
-		static TSize const BITMASK1			= ~(UNEVALUATED | SENTINELS);
-
-		TDFIEntry		nodeEntry;			// current nodes frequencies
-		TDFIEntries		childEntry;			// child frequencies for each first letter of outgoing edges
-		TDFIDatasets	ds;
-
-		TPredHull		predHull;
-		TPred			pred;
-		
-		Index() {}
-
-		Index(Index &other):
-			TBase((TBase &)other),
-			childEntry(other.childEntry),
-			ds(other.ds),
-			predHull(other.predHull),
-			pred(other.pred) {}
-
-		Index(Index const &other):
-			TBase((TBase const &)other),
-			childEntry(other.childEntry),
-			ds(other.ds),
-			predHull(other.predHull),
-			pred(other.pred) {}
-
-		template <typename TText_>
-		Index(TText_ &_text):
-			TBase(_text) {}
-
-		template <typename TText_>
-		Index(TText_ &_text, TPredHull const &_predHull):
-			TBase(_text),
-			predHull(_predHull) {}
-
-		template <typename TText_>
-		Index(TText_ &_text, TPredHull const &_predHull, TPred const &_pred):
-			TBase(_text),
-			predHull(_predHull),
-			pred(_pred) {}
-	};
-
-	
-	template < 
-		typename TText, 
-		typename TPredHull,
-		typename TPred,
-		typename TSpec
-	>
-	inline bool nodePredicate(
-		Iter<Index<TText, IndexWotd< Dfi<TPredHull, TPred> > >, TSpec> &it)
-	{
-		typedef Index<TText, IndexWotd< Dfi<TPredHull, TPred> > > TIndex;
-		return (dirAt(value(it).node, container(it)) & TIndex::DFI_PRED) != 0;
-	}
-
-	template < 
-		typename TText, 
-		typename TPredHull,
-		typename TPred,
-		typename TSpec
-	>
-	inline bool nodeHullPredicate(
-		Iter<Index<TText, IndexWotd< Dfi<TPredHull, TPred> > >, TSpec> &it)
-	{
-		typedef Index<TText, IndexWotd< Dfi<TPredHull, TPred> > > TIndex;
-		return (dirAt(value(it).node, container(it)) & TIndex::DFI_PRED_HULL) != 0;
-	}
+/*!
+ * @fn IndexDfi#dirAt
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>value(indexDir(index), position)</tt>.
+ *
+ * @signature TFibre dirAt(position, index);
+ *
+ * @param[in] index    The @link IndexDfi @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TFibre A reference to the @link DfiIndexFibres#DfiDir @endlink fibre.
+ */
+
+        template <
+        typename TPredHull = DfiPredDefault_<true>,
+        typename TPred = DfiPredDefault_<true>
+    >
+    struct Dfi;
+
+    template <
+        typename TObject,
+        typename TPredHull,
+        typename TPred
+    >
+    class Index<TObject, IndexWotd< Dfi<TPredHull, TPred> > >:
+        public Index<TObject, IndexWotd<> >
+    {
+    public:
+
+        typedef Index<TObject, IndexWotd<> >    TBase;
+
+        // extending base class
+        typedef typename TBase::TText    TText;
+        typedef typename TBase::TValue    TValue;
+        typedef typename TBase::TSize    TSize;
+
+        using TBase::LEAF;
+        using TBase::LAST_CHILD;
+        using TBase::UNEVALUATED;
+        using TBase::SENTINELS;
+
+        // frequency strings for Dfi
+        typedef DfiEntry_                        TDFIEntry;
+        typedef String<
+            TDFIEntry,
+            Array<ValueSize<TValue>::VALUE> >    TDFIEntries;
+        typedef String<unsigned>                TDFIDatasets;
+
+        // 1st word flags
+        static TSize const DFI_PRED_HULL    = (TSize)1 << (BitsPerValue<TSize>::VALUE - 3); // this node fulfills all monotonic frequency predicates (e.g. min_freq)
+        static TSize const DFI_PRED            = (TSize)1 << (BitsPerValue<TSize>::VALUE - 4); // this node fulfills all frequency predicates (e.g. emerging, minmax_freq)
+        static TSize const DFI_PARENT_FREQ    = (TSize)1 << (BitsPerValue<TSize>::VALUE - 5); // this node has the same frequency as its parent
+
+        static TSize const BITMASK0            = ~(LEAF | LAST_CHILD | DFI_PRED_HULL | DFI_PRED | DFI_PARENT_FREQ);
+        static TSize const BITMASK1            = ~(UNEVALUATED | SENTINELS);
+
+        TDFIEntry        nodeEntry;            // current nodes frequencies
+        TDFIEntries        childEntry;            // child frequencies for each first letter of outgoing edges
+        TDFIDatasets    ds;
+
+        TPredHull        predHull;
+        TPred            pred;
+
+        Index() {}
+
+        Index(Index &other):
+            TBase((TBase &)other),
+            childEntry(other.childEntry),
+            ds(other.ds),
+            predHull(other.predHull),
+            pred(other.pred) {}
+
+        Index(Index const &other):
+            TBase((TBase const &)other),
+            childEntry(other.childEntry),
+            ds(other.ds),
+            predHull(other.predHull),
+            pred(other.pred) {}
+
+        template <typename TText_>
+        Index(TText_ &_text):
+            TBase(_text) {}
+
+        template <typename TText_>
+        Index(TText_ &_text, TPredHull const &_predHull):
+            TBase(_text),
+            predHull(_predHull) {}
+
+        template <typename TText_>
+        Index(TText_ &_text, TPredHull const &_predHull, TPred const &_pred):
+            TBase(_text),
+            predHull(_predHull),
+            pred(_pred) {}
+    };
+
+
+    template <
+        typename TText,
+        typename TPredHull,
+        typename TPred,
+        typename TSpec
+    >
+    inline bool nodePredicate(
+        Iter<Index<TText, IndexWotd< Dfi<TPredHull, TPred> > >, TSpec> &it)
+    {
+        typedef Index<TText, IndexWotd< Dfi<TPredHull, TPred> > > TIndex;
+        return (dirAt(value(it).node, container(it)) & TIndex::DFI_PRED) != 0;
+    }
+
+    template <
+        typename TText,
+        typename TPredHull,
+        typename TPred,
+        typename TSpec
+    >
+    inline bool nodeHullPredicate(
+        Iter<Index<TText, IndexWotd< Dfi<TPredHull, TPred> > >, TSpec> &it)
+    {
+        typedef Index<TText, IndexWotd< Dfi<TPredHull, TPred> > > TIndex;
+        return (dirAt(value(it).node, container(it)) & TIndex::DFI_PRED_HULL) != 0;
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 // we modify counting sort used in the wotd-index
 // to count the frequencies in passing
 
-	template < typename TText, typename TSpec, typename TPredHull, typename TPred >
-	typename Size< Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > > >::Type
-	_sortFirstWotdBucket(Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > > &index)
-	{
-	SEQAN_CHECKPOINT
-		typedef Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > >	TIndex;
-		typedef typename Fibre<TIndex, WotdSA >::Type			TSA;
-		typedef typename TIndex::TCounter						TCounter;
-
-		typedef typename TIndex::TDFIEntry						TDFIEntry;
-		typedef typename TIndex::TDFIDatasets					TDFIDatasets;
-		typedef typename Iterator<TDFIDatasets, Standard>::Type	TDFIDatasetsIterator;
-
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA, Standard>::Type			TSAIterator;
-		typedef typename Iterator<TCounter, Standard>::Type		TCntIterator;
-		typedef typename Size<TText>::Type						TSize;
-		typedef typename Value<TText>::Type						TValue;
-		
-		StringSet<TText, TSpec> const &stringSet = indexText(index);
-		TCounter &occ = index.tempOcc;
-		TCounter &bound = index.tempBound;
-
-		// 1. clear counters and copy SA to temporary SA
-		arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
-
-		index.nodeEntry.lastSeqSeen = -1;
-		for(unsigned j = 0; j < length(index.nodeEntry.freq); ++j)
-			index.nodeEntry.freq[j] = 0;
-		for(unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i) 
-		{
-			TDFIEntry &childEntry = index.childEntry[i];
-			childEntry.lastSeqSeen = -1;
-			for(unsigned j = 0; j < length(childEntry.freq); ++j)
-				childEntry.freq[j] = 0;
-		}
-
-		// 2. count characters
-		_wotdCountChars(occ, stringSet);
-
-		// 3. cummulative sum
-		TSize requiredSize = _wotdCummulativeSum(bound, occ);
-
-		// 4. fill suffix array
-		unsigned dsNo = 0;
-		TDFIDatasetsIterator currentDS = begin(index.ds, Standard()) + 1;
-		for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-		{
-			// search for surrounding dataset
-			while (seqNo >= *currentDS) {
-				++dsNo;
-				++currentDS;
-			}
-
-			TSA &sa = indexSA(index);
-			TSAIterator saBeg = begin(sa, Standard());
-			TCntIterator boundBeg = begin(bound, Standard());
-
-			typename Value<TSA>::Type localPos;
-			assignValueI1(localPos, seqNo);
-			assignValueI2(localPos, 0);
-
-			TText const &text = value(stringSet, seqNo);
-			TTextIterator itText = begin(text, Standard());
-			TTextIterator itTextEnd = end(text, Standard());
-			for(; itText != itTextEnd; ++itText) 
-			{
-				unsigned ord = ordValue(*itText);
-				TDFIEntry &childEntry = index.childEntry[ord];
-				// new sequence is seen for <ord> character
-				// -> increment frequency of current dataset
-				if (childEntry.lastSeqSeen != seqNo) 
-				{
-					childEntry.lastSeqSeen = seqNo;
-					++childEntry.freq[dsNo];
-				}
-
-				*(saBeg + (*(boundBeg + ord))++) = localPos;
-				assignValueI2(localPos, getValueI2(localPos) + 1);
-			}
-		}
-		index.sentinelOcc = 0;
-		index.sentinelBound = 0;
-
-		return requiredSize;
-	}
-
-	// sort bucket using radixsort
-	// - all buckets are in lexicographical order
-	// - SA[left,right) contains real SA entries (the beginning positions of the suffices)
-	template < typename TText, typename TSpec, typename TPredHull, typename TPred, typename TBeginPos, typename TEndPos, typename TSize >
-	TSize _sortWotdBucket(
-		Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > > &index,
-		TBeginPos left, 
-		TEndPos right,
-		TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > >	TIndex;
-		typedef typename Fibre<TIndex, WotdSA >::Type				TSA;
-		typedef typename TIndex::TCounter							TCounter;
-		typedef typename TIndex::TTempSA							TTempSA;
-		typedef typename TIndex::TDFIEntry							TDFIEntry;
-		typedef typename TIndex::TDFIDatasets						TDFIDatasets;
-		typedef typename Iterator<TDFIDatasets, Standard>::Type		TDFIDatasetsIterator;
-
-		typedef typename Iterator<TText const, Standard>::Type		TTextIterator;
-		typedef typename Iterator<TSA, Standard>::Type				TSAIterator;
-		typedef typename Iterator<TTempSA const, Standard>::Type    TTempSAIterator;
-		typedef typename Iterator<TCounter, Standard>::Type			TCntIterator;
-		typedef typename Size<TText>::Type							TTextSize;
-		typedef typename Value<TText>::Type							TValue;
-
-		StringSet<TText, TSpec> const &stringSet = indexText(index);
-		TTempSA const &tempSA = index.tempSA;
-		TCounter &occ = index.tempOcc;
-		TCounter &bound = index.tempBound;
-
-		// 1. clear counters and copy SA to temporary SA
-		TCntIterator occBeg = begin(occ, Standard());
-
-		arrayFill(occBeg, end(occ, Standard()), 0);
-		index.tempSA = infix(indexSA(index), left, right);
-
-		index.nodeEntry.lastSeqSeen = -1;
-		for(unsigned j = 0; j < length(index.nodeEntry.freq); ++j)
-			index.nodeEntry.freq[j] = 0;
-		for(unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i) {
-			TDFIEntry &childEntry = index.childEntry[i];
-			childEntry.lastSeqSeen = -1;
-			for(unsigned  j = 0; j < length(childEntry.freq); ++j)
-				childEntry.freq[j] = 0;
-		}
-
-		index.sentinelOcc = 0;
-		index.sentinelBound = 0;
-
-		// 2. count characters
-		{
-			TDFIDatasetsIterator currentDS = begin(index.ds, Standard()) + 1;
-			TTextIterator itText = TTextIterator();
-			TTempSAIterator itSA = begin(tempSA, Standard());
-			TTempSAIterator itSAEnd = end(tempSA, Standard());
-			TTextSize textLength = 0;
-			unsigned lastSeqSeen = (unsigned)-1;
-			unsigned dsNo = 0;
-			Pair<unsigned, TTextSize> lPos;
-			for (; itSA != itSAEnd; ++itSA) 
-			{
-				posLocalize(lPos, *itSA, stringSetLimits(index));
-				if (lastSeqSeen != getSeqNo(lPos))
-				{
-					lastSeqSeen = getSeqNo(lPos);
-
-					// search for surrounding dataset
-					while (lastSeqSeen >= *currentDS) 
-					{
-						++dsNo;
-						++currentDS;
-					}
-					++index.nodeEntry.freq[dsNo];
-
-					// shift textBegin and textLength by prefixLen
-					textLength = length(stringSet[lastSeqSeen]) - prefixLen;
-					itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
-				}
-				if (textLength > getSeqOffset(lPos)) 
-				{
-					unsigned ord = ordValue(*(itText + getSeqOffset(lPos)));
-					TDFIEntry &childEntry = index.childEntry[ord];
-					// new sequence is seen for <ord> character
-					// -> increment frequency of current dataset
-					if (childEntry.lastSeqSeen != lastSeqSeen) 
-					{
-						childEntry.lastSeqSeen = lastSeqSeen;
-						++childEntry.freq[dsNo];
-					}
-					++*(occBeg + ord);
-				} else
-					if (textLength == getSeqOffset(lPos)) ++index.sentinelOcc;
-			}
-		}
-
-		// 3. cumulative sum
-		TSize requiredSize = 0;
-		if (index.interSentinelNodes) {
-			if (index.sentinelOcc != 0)
-				requiredSize = (index.sentinelOcc > 1)? 2: 1;	// insert *one* $-edge for all $_i suffices
-		} else
-			requiredSize = index.sentinelOcc;					// insert each $_i suffix one-by-one
-
-		requiredSize += _wotdCummulativeSum(bound, occ, left + index.sentinelOcc);
-		index.sentinelBound = left;
+    template < typename TText, typename TSpec, typename TPredHull, typename TPred >
+    typename Size< Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > > >::Type
+    _sortFirstWotdBucket(Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > > &index)
+    {
+    SEQAN_CHECKPOINT
+        typedef Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > >    TIndex;
+        typedef typename Fibre<TIndex, WotdSA >::Type            TSA;
+        typedef typename TIndex::TCounter                        TCounter;
+
+        typedef typename TIndex::TDFIEntry                        TDFIEntry;
+        typedef typename TIndex::TDFIDatasets                    TDFIDatasets;
+        typedef typename Iterator<TDFIDatasets, Standard>::Type    TDFIDatasetsIterator;
+
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA, Standard>::Type            TSAIterator;
+        typedef typename Iterator<TCounter, Standard>::Type        TCntIterator;
+        typedef typename Size<TText>::Type                        TSize;
+        typedef typename Value<TText>::Type                        TValue;
+
+        StringSet<TText, TSpec> const &stringSet = indexText(index);
+        TCounter &occ = index.tempOcc;
+        TCounter &bound = index.tempBound;
+
+        // 1. clear counters and copy SA to temporary SA
+        arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
+
+        index.nodeEntry.lastSeqSeen = -1;
+        for(unsigned j = 0; j < length(index.nodeEntry.freq); ++j)
+            index.nodeEntry.freq[j] = 0;
+        for(unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
+        {
+            TDFIEntry &childEntry = index.childEntry[i];
+            childEntry.lastSeqSeen = -1;
+            for(unsigned j = 0; j < length(childEntry.freq); ++j)
+                childEntry.freq[j] = 0;
+        }
+
+        // 2. count characters
+        _wotdCountChars(occ, stringSet);
+
+        // 3. cummulative sum
+        TSize requiredSize = _wotdCummulativeSum(bound, occ);
+
+        // 4. fill suffix array
+        unsigned dsNo = 0;
+        TDFIDatasetsIterator currentDS = begin(index.ds, Standard()) + 1;
+        for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+        {
+            // search for surrounding dataset
+            while (seqNo >= *currentDS) {
+                ++dsNo;
+                ++currentDS;
+            }
+
+            TSA &sa = indexSA(index);
+            TSAIterator saBeg = begin(sa, Standard());
+            TCntIterator boundBeg = begin(bound, Standard());
+
+            typename Value<TSA>::Type localPos;
+            assignValueI1(localPos, seqNo);
+            assignValueI2(localPos, 0);
+
+            TText const &text = value(stringSet, seqNo);
+            TTextIterator itText = begin(text, Standard());
+            TTextIterator itTextEnd = end(text, Standard());
+            for(; itText != itTextEnd; ++itText)
+            {
+                unsigned ord = ordValue(*itText);
+                TDFIEntry &childEntry = index.childEntry[ord];
+                // new sequence is seen for <ord> character
+                // -> increment frequency of current dataset
+                if (childEntry.lastSeqSeen != seqNo)
+                {
+                    childEntry.lastSeqSeen = seqNo;
+                    ++childEntry.freq[dsNo];
+                }
+
+                *(saBeg + (*(boundBeg + ord))++) = localPos;
+                assignValueI2(localPos, getValueI2(localPos) + 1);
+            }
+        }
+        index.sentinelOcc = 0;
+        index.sentinelBound = 0;
+
+        return requiredSize;
+    }
+
+    // sort bucket using radixsort
+    // - all buckets are in lexicographical order
+    // - SA[left,right) contains real SA entries (the beginning positions of the suffices)
+    template < typename TText, typename TSpec, typename TPredHull, typename TPred, typename TBeginPos, typename TEndPos, typename TSize >
+    TSize _sortWotdBucket(
+        Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > > &index,
+        TBeginPos left,
+        TEndPos right,
+        TSize prefixLen)
+    {
+    SEQAN_CHECKPOINT
+        typedef Index<StringSet<TText, TSpec>, IndexWotd<Dfi<TPredHull, TPred> > >    TIndex;
+        typedef typename Fibre<TIndex, WotdSA >::Type                TSA;
+        typedef typename TIndex::TCounter                            TCounter;
+        typedef typename TIndex::TTempSA                            TTempSA;
+        typedef typename TIndex::TDFIEntry                            TDFIEntry;
+        typedef typename TIndex::TDFIDatasets                        TDFIDatasets;
+        typedef typename Iterator<TDFIDatasets, Standard>::Type        TDFIDatasetsIterator;
+
+        typedef typename Iterator<TText const, Standard>::Type        TTextIterator;
+        typedef typename Iterator<TSA, Standard>::Type                TSAIterator;
+        typedef typename Iterator<TTempSA const, Standard>::Type    TTempSAIterator;
+        typedef typename Iterator<TCounter, Standard>::Type            TCntIterator;
+        typedef typename Size<TText>::Type                            TTextSize;
+        typedef typename Value<TText>::Type                            TValue;
+
+        StringSet<TText, TSpec> const &stringSet = indexText(index);
+        TTempSA const &tempSA = index.tempSA;
+        TCounter &occ = index.tempOcc;
+        TCounter &bound = index.tempBound;
+
+        // 1. clear counters and copy SA to temporary SA
+        TCntIterator occBeg = begin(occ, Standard());
+
+        arrayFill(occBeg, end(occ, Standard()), 0);
+        index.tempSA = infix(indexSA(index), left, right);
+
+        index.nodeEntry.lastSeqSeen = -1;
+        for(unsigned j = 0; j < length(index.nodeEntry.freq); ++j)
+            index.nodeEntry.freq[j] = 0;
+        for(unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i) {
+            TDFIEntry &childEntry = index.childEntry[i];
+            childEntry.lastSeqSeen = -1;
+            for(unsigned  j = 0; j < length(childEntry.freq); ++j)
+                childEntry.freq[j] = 0;
+        }
+
+        index.sentinelOcc = 0;
+        index.sentinelBound = 0;
+
+        // 2. count characters
+        {
+            TDFIDatasetsIterator currentDS = begin(index.ds, Standard()) + 1;
+            TTextIterator itText = TTextIterator();
+            TTempSAIterator itSA = begin(tempSA, Standard());
+            TTempSAIterator itSAEnd = end(tempSA, Standard());
+            TTextSize textLength = 0;
+            unsigned lastSeqSeen = (unsigned)-1;
+            unsigned dsNo = 0;
+            Pair<unsigned, TTextSize> lPos;
+            for (; itSA != itSAEnd; ++itSA)
+            {
+                posLocalize(lPos, *itSA, stringSetLimits(index));
+                if (lastSeqSeen != getSeqNo(lPos))
+                {
+                    lastSeqSeen = getSeqNo(lPos);
+
+                    // search for surrounding dataset
+                    while (lastSeqSeen >= *currentDS)
+                    {
+                        ++dsNo;
+                        ++currentDS;
+                    }
+                    ++index.nodeEntry.freq[dsNo];
+
+                    // shift textBegin and textLength by prefixLen
+                    textLength = length(stringSet[lastSeqSeen]) - prefixLen;
+                    itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
+                }
+                if (textLength > getSeqOffset(lPos))
+                {
+                    unsigned ord = ordValue(*(itText + getSeqOffset(lPos)));
+                    TDFIEntry &childEntry = index.childEntry[ord];
+                    // new sequence is seen for <ord> character
+                    // -> increment frequency of current dataset
+                    if (childEntry.lastSeqSeen != lastSeqSeen)
+                    {
+                        childEntry.lastSeqSeen = lastSeqSeen;
+                        ++childEntry.freq[dsNo];
+                    }
+                    ++*(occBeg + ord);
+                } else
+                    if (textLength == getSeqOffset(lPos)) ++index.sentinelOcc;
+            }
+        }
+
+        // 3. cumulative sum
+        TSize requiredSize = 0;
+        if (index.interSentinelNodes) {
+            if (index.sentinelOcc != 0)
+                requiredSize = (index.sentinelOcc > 1)? 2: 1;    // insert *one* $-edge for all $_i suffices
+        } else
+            requiredSize = index.sentinelOcc;                    // insert each $_i suffix one-by-one
+
+        requiredSize += _wotdCummulativeSum(bound, occ, left + index.sentinelOcc);
+        index.sentinelBound = left;
 /*
-		::std::cout << "$=" << index.sentinelOcc<<"@"<<index.sentinelBound << "\t";
-		for(int i=0; i<length(occ);++i)
-			if (occ[i])
-				::std::cout << i << "=" << occ[i]<<"@"<<bound[i] << "\t";
+        std::cout << "$=" << index.sentinelOcc<<"@"<<index.sentinelBound << "\t";
+        for(int i=0; i<length(occ);++i)
+            if (occ[i])
+                std::cout << i << "=" << occ[i]<<"@"<<bound[i] << "\t";
 */
-		// 4. fill suffix array
-		{
-			TSA &sa = indexSA(index);
-			TSAIterator saBeg = begin(sa, Standard());
-			TCntIterator boundBeg = begin(bound, Standard());
-
-			TTextIterator itText = TTextIterator();
-			TTempSAIterator itSA = begin(tempSA, Standard());
-			TTempSAIterator itSAEnd = end(tempSA, Standard());
-			TTextSize textLength = 0;
-			unsigned lastSeqSeen = (unsigned)-1;
-			Pair<unsigned, TTextSize> lPos;
-			for(; itSA != itSAEnd; ++itSA)
-			{
-				posLocalize(lPos, *itSA, stringSetLimits(index));
-				if (lastSeqSeen != getSeqNo(lPos))
-				{
-					lastSeqSeen = getSeqNo(lPos);
-
-					// shift textBegin and textLength by prefixLen
-					textLength = length(stringSet[lastSeqSeen]) - prefixLen;
-					itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
-				}
-				if (textLength > getSeqOffset(lPos))
-					*(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA;
-				else
-					if (textLength == getSeqOffset(lPos))
-						*(saBeg + index.sentinelBound++) = *itSA;
-			}
-		}
-
-		return requiredSize;
-	}
-
-
-	// store buckets into directory
-	// storing SA links and topology links in Dir
-	template <typename TText, typename TPredHull, typename TPred, typename TSize>
-	inline void 
-	_storeWotdChildren(
-		Index<TText, IndexWotd<Dfi<TPredHull, TPred> > > &index,
-		TSize dirOfs,
-		TSize lcp)
-	{
-	SEQAN_CHECKPOINT
-		typedef Index<TText, IndexWotd<Dfi<TPredHull, TPred> > >	TIndex;
-
-		typedef typename Fibre<TIndex, WotdDir>::Type		TDir;
-		typedef typename TIndex::TCounter					TCounter;
-		typedef typename TIndex::TDFIEntries				TEntries;
-
-		typedef typename Iterator<TDir, Standard>::Type		TDirIterator;
-		typedef typename Size<TDir>::Type					TDirSize;
-		typedef typename Iterator<TCounter, Standard>::Type	TCntIterator;
-		typedef typename Iterator<TEntries, Standard>::Type	TEntriesIterator;
-
-		typedef typename Value<TCounter>::Type				TCntValue;
-		typedef typename Value<TDir>::Type					TDirValue;
-
-		TDirIterator itDirBegin = begin(indexDir(index), Standard()) + dirOfs;
-		TDirIterator itDirEnd = end(indexDir(index), Standard());
-		TDirIterator itDir = itDirBegin;
-		TDirIterator itPrev = itDirEnd;
-
-		TCntIterator it = begin(index.tempOcc, Standard());
-		TCntIterator bit = begin(index.tempBound, Standard());
-		TCntIterator itEnd = end(index.tempOcc, Standard());
-		TEntriesIterator itEntry = begin(index.childEntry, Standard());
-
-		TCntValue occ;
-		if (index.sentinelOcc != 0)
-		{
-			TDirValue orMask = (index.predHull(*itEntry))? index.DFI_PRED_HULL: 0;
-			if (index.pred(*itEntry)) orMask |= index.DFI_PRED;
-
-			if (index.sentinelOcc > 1 && index.interSentinelNodes)	// occurs on multiseqs
-			{
-				itPrev = itDir;
-				*itDir = (index.sentinelBound - index.sentinelOcc) | orMask;	++itDir;
-				*itDir = index.sentinelBound | index.UNEVALUATED;				++itDir;
-			} else
-				orMask |= index.LEAF;
-				for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d)
-				{
-					itPrev = itDir;
-					*itDir = d | orMask;										++itDir;
-				}
-		}
-
-		for (; it != itEnd; ++it, ++bit, ++itEntry)
-		{
-			if ((occ = *it) == 0) continue;
-
-			TDirValue orMask = (index.predHull(*itEntry))? index.DFI_PRED_HULL: 0;
-			if (index.pred(*itEntry)) orMask |= index.DFI_PRED;
-			if ((*itEntry).freq == index.nodeEntry.freq) orMask |= index.DFI_PARENT_FREQ;
-
-			if (occ > 1) {
-				itPrev = itDir;
-				*itDir = (*bit - occ) | orMask;					++itDir;
-				*itDir = *bit | index.UNEVALUATED;				++itDir;
-			} else {
-				itPrev = itDir;
-				*itDir = (*bit - occ) | index.LEAF | orMask;	++itDir;
-			}
-		}
-
-		// first child gets the mutual lcp value of the children (== parent repLength)
-		*itDirBegin = ((*itDirBegin) & ~index.BITMASK0) | lcp;
-
-		// mark the last child
-		if (itPrev != itDirEnd)
-			*itPrev |= index.LAST_CHILD;
-	}
+        // 4. fill suffix array
+        {
+            TSA &sa = indexSA(index);
+            TSAIterator saBeg = begin(sa, Standard());
+            TCntIterator boundBeg = begin(bound, Standard());
+
+            TTextIterator itText = TTextIterator();
+            TTempSAIterator itSA = begin(tempSA, Standard());
+            TTempSAIterator itSAEnd = end(tempSA, Standard());
+            TTextSize textLength = 0;
+            unsigned lastSeqSeen = (unsigned)-1;
+            Pair<unsigned, TTextSize> lPos;
+            for(; itSA != itSAEnd; ++itSA)
+            {
+                posLocalize(lPos, *itSA, stringSetLimits(index));
+                if (lastSeqSeen != getSeqNo(lPos))
+                {
+                    lastSeqSeen = getSeqNo(lPos);
+
+                    // shift textBegin and textLength by prefixLen
+                    textLength = length(stringSet[lastSeqSeen]) - prefixLen;
+                    itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
+                }
+                if (textLength > getSeqOffset(lPos))
+                    *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA;
+                else
+                    if (textLength == getSeqOffset(lPos))
+                        *(saBeg + index.sentinelBound++) = *itSA;
+            }
+        }
+
+        return requiredSize;
+    }
+
+
+    // store buckets into directory
+    // storing SA links and topology links in Dir
+    template <typename TText, typename TPredHull, typename TPred, typename TSize>
+    inline void
+    _storeWotdChildren(
+        Index<TText, IndexWotd<Dfi<TPredHull, TPred> > > &index,
+        TSize dirOfs,
+        TSize lcp)
+    {
+    SEQAN_CHECKPOINT
+        typedef Index<TText, IndexWotd<Dfi<TPredHull, TPred> > >    TIndex;
+
+        typedef typename Fibre<TIndex, WotdDir>::Type        TDir;
+        typedef typename TIndex::TCounter                    TCounter;
+        typedef typename TIndex::TDFIEntries                TEntries;
+
+        typedef typename Iterator<TDir, Standard>::Type        TDirIterator;
+        typedef typename Size<TDir>::Type                    TDirSize;
+        typedef typename Iterator<TCounter, Standard>::Type    TCntIterator;
+        typedef typename Iterator<TEntries, Standard>::Type    TEntriesIterator;
+
+        typedef typename Value<TCounter>::Type                TCntValue;
+        typedef typename Value<TDir>::Type                    TDirValue;
+
+        TDirIterator itDirBegin = begin(indexDir(index), Standard()) + dirOfs;
+        TDirIterator itDirEnd = end(indexDir(index), Standard());
+        TDirIterator itDir = itDirBegin;
+        TDirIterator itPrev = itDirEnd;
+
+        TCntIterator it = begin(index.tempOcc, Standard());
+        TCntIterator bit = begin(index.tempBound, Standard());
+        TCntIterator itEnd = end(index.tempOcc, Standard());
+        TEntriesIterator itEntry = begin(index.childEntry, Standard());
+
+        TCntValue occ;
+        if (index.sentinelOcc != 0)
+        {
+            TDirValue orMask = (index.predHull(*itEntry))? index.DFI_PRED_HULL: 0;
+            if (index.pred(*itEntry)) orMask |= index.DFI_PRED;
+
+            if (index.sentinelOcc > 1 && index.interSentinelNodes)    // occurs on multiseqs
+            {
+                itPrev = itDir;
+                *itDir = (index.sentinelBound - index.sentinelOcc) | orMask;    ++itDir;
+                *itDir = index.sentinelBound | index.UNEVALUATED;                ++itDir;
+            } else
+                orMask |= index.LEAF;
+                for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d)
+                {
+                    itPrev = itDir;
+                    *itDir = d | orMask;                                        ++itDir;
+                }
+        }
+
+        for (; it != itEnd; ++it, ++bit, ++itEntry)
+        {
+            if ((occ = *it) == 0) continue;
+
+            TDirValue orMask = (index.predHull(*itEntry))? index.DFI_PRED_HULL: 0;
+            if (index.pred(*itEntry)) orMask |= index.DFI_PRED;
+            if ((*itEntry).freq == index.nodeEntry.freq) orMask |= index.DFI_PARENT_FREQ;
+
+            if (occ > 1) {
+                itPrev = itDir;
+                *itDir = (*bit - occ) | orMask;                    ++itDir;
+                *itDir = *bit | index.UNEVALUATED;                ++itDir;
+            } else {
+                itPrev = itDir;
+                *itDir = (*bit - occ) | index.LEAF | orMask;    ++itDir;
+            }
+        }
+
+        // first child gets the mutual lcp value of the children (== parent repLength)
+        *itDirBegin = ((*itDirBegin) & ~index.BITMASK0) | lcp;
+
+        // mark the last child
+        if (itPrev != itDirEnd)
+            *itPrev |= index.LAST_CHILD;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // debug output
 
-	template <typename TText, typename TPredHull, typename TPred>
-	inline void
-	_dump(Index<TText, IndexWotd< Dfi<TPredHull, TPred> > > &index)
-	{
-		typedef IndexWotd< Dfi<TPredHull, TPred> >		TSpec;
-		typedef Index<TText, TSpec>							TIndex;
-		typedef typename Fibre<TIndex, WotdDir>::Type		TDir;
-		typedef typename Value<TDir>::Type					TDirValue;
-
-		::std::cout << "  Dir (wotd/Dfi)" << ::std::endl;
-		for(unsigned i=0; i < length(indexDir(index)); ++i) {
-			TDirValue d = indexDir(index)[i];
-			::std::cout << i << ":  " << (d & index.BITMASK0);
-			if (d & index.LEAF)				::std::cout << "  (Leaf/Uneval)";
-			if (d & index.LAST_CHILD)		::std::cout << "  (LastChild/SENTINELS)";
-			if (d & index.DFI_PRED_HULL)	::std::cout << "  (PRED_HULL)";
-			if (d & index.DFI_PRED)			::std::cout << "  (PRED)";
-			if (d & index.DFI_PARENT_FREQ)	::std::cout << "  (PARENT_FREQ)";
-			::std::cout << ::std::endl;
-		}
-
-		::std::cout << ::std::endl << "  SA" << ::std::endl;
-		for(unsigned i=0; i < length(indexSA(index)); ++i)
-			::std::cout << i << ":  " << indexSA(index)[i] << "  " << suffix(indexText(index), indexSA(index)[i]) << ::std::endl;
-
-		::std::cout << ::std::endl;
-	}
-
-	template <typename TText, typename TPredHull, typename TPred>
-	inline void
-	_dumpFreq(Index<TText, IndexWotd< Dfi<TPredHull, TPred> > > &index)
-	{
-		typedef Dfi<TPredHull, TPred> TSpec;
-		typedef Index<TText, IndexWotd<TSpec> >				TIndex;
-		typedef typename Value<TIndex>::Type					TValue;
-
-		::std::cout << "  ParentF = (";
-		for(unsigned d=0; d<length(index.nodeEntry.freq); ++d) {
-			if (d>0) ::std::cout << ",";
-			::std::cout << index.nodeEntry.freq[d];
-		}
-		::std::cout << ")" << ::std::endl;
-
-		for(unsigned i=0; i<length(index.tempOcc); ++i)
-			if (index.tempOcc[i] != 0) {
-				::std::cout << "  Freq[" << (TValue)i << "] = (";
-				for(unsigned d=0; d<length(index.childEntry[i].freq); ++d) {
-					if (d>0) ::std::cout << ",";
-					::std::cout << index.childEntry[i].freq[d];
-				}
-				::std::cout << ")" << ::std::endl;
-			}
-	}
+    template <typename TText, typename TPredHull, typename TPred>
+    inline void
+    _dump(Index<TText, IndexWotd< Dfi<TPredHull, TPred> > > &index)
+    {
+        typedef IndexWotd< Dfi<TPredHull, TPred> >        TSpec;
+        typedef Index<TText, TSpec>                            TIndex;
+        typedef typename Fibre<TIndex, WotdDir>::Type        TDir;
+        typedef typename Value<TDir>::Type                    TDirValue;
+
+        std::cout << "  Dir (wotd/Dfi)" << std::endl;
+        for(unsigned i=0; i < length(indexDir(index)); ++i) {
+            TDirValue d = indexDir(index)[i];
+            std::cout << i << ":  " << (d & index.BITMASK0);
+            if (d & index.LEAF)                std::cout << "  (Leaf/Uneval)";
+            if (d & index.LAST_CHILD)        std::cout << "  (LastChild/SENTINELS)";
+            if (d & index.DFI_PRED_HULL)    std::cout << "  (PRED_HULL)";
+            if (d & index.DFI_PRED)            std::cout << "  (PRED)";
+            if (d & index.DFI_PARENT_FREQ)    std::cout << "  (PARENT_FREQ)";
+            std::cout << std::endl;
+        }
+
+        std::cout << std::endl << "  SA" << std::endl;
+        for(unsigned i=0; i < length(indexSA(index)); ++i)
+            std::cout << i << ":  " << indexSA(index)[i] << "  " << suffix(indexText(index), indexSA(index)[i]) << std::endl;
+
+        std::cout << std::endl;
+    }
+
+    template <typename TText, typename TPredHull, typename TPred>
+    inline void
+    _dumpFreq(Index<TText, IndexWotd< Dfi<TPredHull, TPred> > > &index)
+    {
+        typedef Dfi<TPredHull, TPred> TSpec;
+        typedef Index<TText, IndexWotd<TSpec> >                TIndex;
+        typedef typename Value<TIndex>::Type                    TValue;
+
+        std::cout << "  ParentF = (";
+        for(unsigned d=0; d<length(index.nodeEntry.freq); ++d) {
+            if (d>0) std::cout << ",";
+            std::cout << index.nodeEntry.freq[d];
+        }
+        std::cout << ")" << std::endl;
+
+        for(unsigned i=0; i<length(index.tempOcc); ++i)
+            if (index.tempOcc[i] != 0) {
+                std::cout << "  Freq[" << (TValue)i << "] = (";
+                for(unsigned d=0; d<length(index.childEntry[i].freq); ++d) {
+                    if (d>0) std::cout << ",";
+                    std::cout << index.childEntry[i].freq[d];
+                }
+                std::cout << ")" << std::endl;
+            }
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-// interface for automatic index creation 
-
-	template <typename TText, typename TPredHull, typename TPred>
-	inline bool indexCreate(Index<TText, IndexWotd<Dfi<TPredHull, TPred> > > &index, WotdDir const, Default const)
-	{
-		typedef Index<TText, IndexWotd<Dfi<TPredHull, TPred> > >	TIndex;
-		typedef typename Value<TIndex>::Type							TValue;
-
-		resize(index.childEntry, (unsigned) ValueSize<TValue>::VALUE);
-		if (empty(index.ds)) {
-			resize(index.ds, 2);
-			index.ds[0] = 0;
-			index.ds[1] = countSequences(index);
-		}
-		resize(index.nodeEntry.freq, length(index.ds) - 1, Exact());
-		for(unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
-			resize(index.childEntry[i].freq, length(index.ds) - 1, Exact());
-
-		_wotdCreateFirstLevel(index);
-		return true;
-	}
+// interface for automatic index creation
+
+    template <typename TText, typename TPredHull, typename TPred>
+    inline bool indexCreate(Index<TText, IndexWotd<Dfi<TPredHull, TPred> > > &index, WotdDir const, Default const)
+    {
+        typedef Index<TText, IndexWotd<Dfi<TPredHull, TPred> > >    TIndex;
+        typedef typename Value<TIndex>::Type                            TValue;
+
+        resize(index.childEntry, (unsigned) ValueSize<TValue>::VALUE);
+        if (empty(index.ds)) {
+            resize(index.ds, 2);
+            index.ds[0] = 0;
+            index.ds[1] = countSequences(index);
+        }
+        resize(index.nodeEntry.freq, length(index.ds) - 1, Exact());
+        for(unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
+            resize(index.childEntry[i].freq, length(index.ds) - 1, Exact());
+
+        _wotdCreateFirstLevel(index);
+        return true;
+    }
 }
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/index/index_esa_algs.h b/seqan/index/index_esa_algs.h
index 7f1f0c2..30e24e1 100644
--- a/seqan/index/index_esa_algs.h
+++ b/seqan/index/index_esa_algs.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,222 +37,168 @@
 
 namespace SEQAN_NAMESPACE_MAIN
 {
-	
-	//////////////////////////////////////////////////////////////////////////////
-	// more sophisticated algorithms on enhanced suffix arrays of 1 sequence
-	// (also called virtual suffix trees)
-	//////////////////////////////////////////////////////////////////////////////
-
-
-/**
-.Spec.SuperMaxRepeats Iterator:
-..cat:Index
-..general:Spec.BottomUp Iterator
-..summary:Iterator to search for all supermaximal repeats.
-..signature:Iterator<TContainer, SuperMaxRepeats>::Type
-..signature:Iter<TContainer, VSTree< BottomUp<SuperMaxRepeats> > >
-..param.TContainer:Type of an index that can be iterated with a bottom-up iterator.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..include:seqan/index.h
-
-.Memfunc.SuperMaxRepeats Iterator#Iterator
-..class:Spec.SuperMaxRepeats Iterator
-..summary:Constructor
-..signature:Iterator(index[, minLength])
-..signature:Iterator(iterator)
-..param.index:An index object.
-..param.minLength:Minimum length of the supermaximal repeats, default value is 1.
-..param.iterator:Another SuperMaxRepeats iterator. (copy constructor)
-...type:Spec.SuperMaxRepeats Iterator
-*/
+
+    //////////////////////////////////////////////////////////////////////////////
+    // more sophisticated algorithms on enhanced suffix arrays of 1 sequence
+    // (also called virtual suffix trees)
+    //////////////////////////////////////////////////////////////////////////////
+
 
 /*!
  * @class SuperMaxRepeatsIterator Super Max Repeats Iterator
- * 
  * @extends BottomUpIterator
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief Iterator to search for all supermaximal repeats.
  *
- * @signature Iter<TContainer, VSTree< BottomUp<SuperMaxRepeats> > >
- * @signature Iter<TContainer, VSTree< BottomUp<SuperMaxRepeats> > >
- * 
+ * @signature Iterator<TContainer, SuperMaxRepeats>::Type;
+ * @signature template <typename TContainer>
+ *            class Iter<TContainer, VSTree<BottomUp<SuperMaxRepeats> > >;
+ *
  * @tparam TContainer Type of an index that can be iterated with a bottom-up
  *                    iterator. Types: @link IndexEsa @endlink
  *
  *
- * @section Note Instead of using the class Iter directly we recommend to use the result of the metafunction 
+ * @note Note Instead of using the class Iter directly we recommend to use the result of the metafunction
  *               Iterator&lt;TContainer, SuperMaxRepeats&gt;::Type (which is Iter&lt;TContainer, VSTree&lt;BottomUp&lt;SuperMaxRepeats&gt; &g;t &gt;).
- * 
- * Demo: Demo.Supermaximal Repeats
+ *
+ * @see DemoSupermaximalRepeats
  */
 
 /*!
- * @fn Iter<TContainer, VSTree< BottomUp<SuperMaxRepeats> > >::Iter<TContainer, VSTree< BottomUp<SuperMaxRepeats> > >
- *
- * brief The constructor
- *
- * @signature Iter<TContainer, VSTree< BottomUp<SuperMaxRepeats> > >(index [, minLength]) 
- * @signature Iter<TContainer, VSTree< BottomUp<SuperMaxRepeats> > >(iterator) 
+ * @fn SuperMaxRepeatsIterator::Iter
+ * @brief The constructor
  *
- * @param index The index to be used for the iteration. Types: @link IndexEsa @endlink
+ * @signature Iter::Iter(index[, minLength]);
+ * @signature Iter::Iter(iterator);
  *
- * @param minLength Minimum length of the supermaximal repeats, default value is 1.
- *
- * @param iterator Another SuperMaxRepeats iterator. Types: @link SuperMaxRepeatsIterator @endlink
+ * @param[in] index     The index to be used for the iteration. Types: @link IndexEsa @endlink
+ * @param[in] minLength Minimum length of the supermaximal repeats, default value is 1.
+ * @param[in] iterator  Another SuperMaxRepeats iterator. Types: @link SuperMaxRepeatsIterator @endlink
  */
-	//////////////////////////////////////////////////////////////////////////////
-	// super-maximal repeats - suffix tree version
-	//////////////////////////////////////////////////////////////////////////////
-
-	template < typename TSTree >
-	struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > > > {
-		typedef PostorderEmptyEdges	Type;
-	};
-
-	template < typename TSTree >
-	class Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > >:
-		public Iter< TSTree, VSTree< BottomUp<> > > 
-	{
-	public:
-		typedef Iter< TSTree, VSTree< BottomUp<> > >	TBase;
-		typedef typename Size<TSTree>::Type				TSize;
-		typedef typename Value<TSTree>::Type			TValue;
+    //////////////////////////////////////////////////////////////////////////////
+    // super-maximal repeats - suffix tree version
+    //////////////////////////////////////////////////////////////////////////////
+
+    template < typename TSTree >
+    struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > > > {
+        typedef PostorderEmptyEdges    Type;
+    };
+
+    template < typename TSTree >
+    class Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > >:
+        public Iter< TSTree, VSTree< BottomUp<> > >
+    {
+    public:
+        typedef Iter< TSTree, VSTree< BottomUp<> > >    TBase;
+        typedef typename Size<TSTree>::Type                TSize;
+        typedef typename Value<TSTree>::Type            TValue;
 //____________________________________________________________________________
 
-		TSize						minLength;
-		typename Set<TValue>::Type	charSet;
+        TSize                        minLength;
+        typename Set<TValue>::Type    charSet;
 //____________________________________________________________________________
 
         Iter() :
             TBase(),
             minLength(0)
         {}
-        
-		Iter(TSTree &_tree):
-			TBase(_tree),
-			minLength(1)
-		{
-			indexRequire(_tree, EsaChildtab());
-			indexRequire(_tree, EsaBwt());
-			goNext(*this);	// the iterator starts in a suffix, i.e. not a repeat
-		}
-
-		Iter(TSTree &_tree, MinimalCtor):
-			TBase(_tree, MinimalCtor()) {}
-
-		Iter(TSTree &_tree, TSize _minLength):
-			TBase(_tree),
-			minLength(_minLength)
-		{
-			indexRequire(_tree, EsaChildtab());
-			indexRequire(_tree, EsaBwt());
-			goNext(*this);	// the iterator starts in a suffix, i.e. not a repeat
-		}
-
-		Iter(Iter const &_origin):
-			TBase((TBase const &)_origin),
-			minLength(_origin.minLength),
-			charSet(_origin.charSet) {}
-	};
-
-	template < typename TSTree >
-	inline void goNext(Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > > &it) {
-		do {
-			goNext(it, PostorderEmptyEdges());
-		} while (!atEnd(it) && 
-			     !(	childrenAreLeaves(it) && 
-					(repLength(it) >= it.minLength) &&
-					!isPartiallyLeftExtensible(it, it.charSet)) );
-	}
-		
-
-/**
-.Spec.SuperMaxRepeatsFast Iterator:
-..cat:Index
-..general:Spec.BottomUp Iterator
-..summary:Iterator to search for all supermaximal repeats (for enh. suffix arrays only).
-..signature:Iterator<TContainer, SuperMaxRepeatsFast>::Type
-..signature:Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast> > >
-..param.TContainer:Type of an index based on enhanced suffix array.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..include:seqan/index.h
-
-.Memfunc.SuperMaxRepeatsFast Iterator#Iterator
-..class:Spec.SuperMaxRepeatsFast Iterator
-..summary:Constructor
-..signature:Iterator(index[, minLength])
-..signature:Iterator(iterator)
-..param.index:An index object.
-..param.minLength:Minimum length of the supermaximal repeats, default value is 1.
-..param.iterator:Another SuperMaxRepeatsFast iterator. (copy constructor)
-...type:Spec.SuperMaxRepeatsFast Iterator
-*/
-/*H
+
+        Iter(TSTree &_tree):
+            TBase(_tree),
+            minLength(1)
+        {
+            indexRequire(_tree, EsaChildtab());
+            indexRequire(_tree, EsaBwt());
+            goNext(*this);    // the iterator starts in a suffix, i.e. not a repeat
+        }
+
+        Iter(TSTree &_tree, MinimalCtor):
+            TBase(_tree, MinimalCtor()) {}
+
+        Iter(TSTree &_tree, TSize _minLength):
+            TBase(_tree),
+            minLength(_minLength)
+        {
+            indexRequire(_tree, EsaChildtab());
+            indexRequire(_tree, EsaBwt());
+            goNext(*this);    // the iterator starts in a suffix, i.e. not a repeat
+        }
+
+        Iter(Iter const &_origin):
+            TBase((TBase const &)_origin),
+            minLength(_origin.minLength),
+            charSet(_origin.charSet) {}
+    };
+
+    template < typename TSTree >
+    inline void goNext(Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > > &it) {
+        do {
+            goNext(it, PostorderEmptyEdges());
+        } while (!atEnd(it) &&
+                 !(    childrenAreLeaves(it) &&
+                    (repLength(it) >= it.minLength) &&
+                    !isPartiallyLeftExtensible(it, it.charSet)) );
+    }
+
+
+/*!
  * @class SuperMaxRepeatsFastIterator Super Max Repeats Fast Iterator
- *
  * @extends BottomUpIterator
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Iterator to search for all supermaximal repeats (for enh. suffix
- *        arrays only).
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Iterator to search for all supermaximal repeats (for enh. suffix arrays only).
+ *
+ * @signature Iterator<TContainer, SuperMaxRepeatsFast>::Type;
+ * @signature template <typename TContainer>
+ *            class Iter<TContainer, VSTree<BottomUp<SuperMaxRepeatsFast> > >;
  *
- * @signature Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast> > >
- * @signature Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast> > >
- * 
  * @tparam TContainer Type of an index based on enhanced suffix array. Types:
  *                    @link IndexEsa @endlink
- * 
- * @section Note Instead of using the class Iter directly we recommend to use the result of the metafunction 
- *               Iterator<TContainer, SuperMaxRepeatsFast>::Type (which is Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast> > >).
+ *
+ * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
+ *       Iterator&lt;TContainer, SuperMaxRepeatsFast&gt;::Type (which is Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast&gt; &gt; &gt;).
  */
 
-/*H
- * @fn Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast> > >::Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast> > >
- *
- * brief The constructor
- *
- * @signature Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast> > >(index[, minLength])
- * @signature Iter<TContainer, VSTree< BottomUp<SuperMaxRepeatsFast> > >(iterator)
- *
- * @param index The index to be used for the iteration. Types: @link IndexEsa @endlink
+/*!
+ * @fn SuperMaxRepeatsFastIterator::Iter
+ * @brief The constructor
  *
- * @param minLength Minimum length of the supermaximal repeats, default value is 1.
+ * @signature Iter::Iter(index[, minLength]);
+ * @signature Iter::Iter(iterator);
  *
- * @param iterator Another SuperMaxRepeatsFast iterator. Types: @link SuperMaxRepeatsFastIterator @endlink
+ * @param[in] index     The index to be used for the iteration. Types: @link IndexEsa @endlink
+ * @param[in] minLength Minimum length of the supermaximal repeats, default value is 1.
+ * @param[in] iterator  Another SuperMaxRepeatsFast iterator. Types: @link SuperMaxRepeatsFastIterator @endlink
  */
 
-	//////////////////////////////////////////////////////////////////////////////
-	// supermaximal repeats - specialized for Enhanced Suffix Arrays
-	//////////////////////////////////////////////////////////////////////////////
-
-	template < typename TSTree >
-	struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<SuperMaxRepeatsFast> > > > {
-		typedef PostorderEmptyEdges	Type;
-	};
-
-	template < typename TText, typename TSpec >
-	class Iter< Index<TText, IndexEsa<TSpec> >, VSTree< BottomUp<SuperMaxRepeatsFast> > >:
-		public Iter< Index<TText, IndexEsa<TSpec> >, VSTree< BottomUp<> > > 
-	{
-	public:
-		typedef Index< TText, IndexEsa<TSpec> >		TIndex;
-		typedef Iter< TIndex, VSTree< BottomUp<> > >	TBase;
-		typedef typename Size<TIndex>::Type				TSize;
-		typedef typename Value<TIndex>::Type			TValue;
-
-		typedef typename Iterator<typename Fibre<TIndex, EsaLcp>::Type const>::Type	TLCPIter;
+    //////////////////////////////////////////////////////////////////////////////
+    // supermaximal repeats - specialized for Enhanced Suffix Arrays
+    //////////////////////////////////////////////////////////////////////////////
+
+    template < typename TSTree >
+    struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<SuperMaxRepeatsFast> > > > {
+        typedef PostorderEmptyEdges    Type;
+    };
+
+    template < typename TText, typename TSpec >
+    class Iter< Index<TText, IndexEsa<TSpec> >, VSTree< BottomUp<SuperMaxRepeatsFast> > >:
+        public Iter< Index<TText, IndexEsa<TSpec> >, VSTree< BottomUp<> > >
+    {
+    public:
+        typedef Index< TText, IndexEsa<TSpec> >        TIndex;
+        typedef Iter< TIndex, VSTree< BottomUp<> > >    TBase;
+        typedef typename Size<TIndex>::Type                TSize;
+        typedef typename Value<TIndex>::Type            TValue;
+
+        typedef typename Iterator<typename Fibre<TIndex, EsaLcp>::Type const>::Type    TLCPIter;
 //____________________________________________________________________________
 
-		TSize		minLength;
-		TLCPIter	lIter, lEnd;	// lcp table iterators (optimization)
-		TSize		lValueLast;		// current l-value of interval
-		bool 		rising;			// is the left interval border valid
-		typename Set<TValue>::Type	charSet;
+        TSize        minLength;
+        TLCPIter    lIter, lEnd;    // lcp table iterators (optimization)
+        TSize        lValueLast;        // current l-value of interval
+        bool         rising;            // is the left interval border valid
+        typename Set<TValue>::Type    charSet;
 //____________________________________________________________________________
 
         Iter() :
@@ -261,244 +207,218 @@ namespace SEQAN_NAMESPACE_MAIN
             lValueLast(0),
             rising(false)
         {}
-        
-		Iter(TIndex &_index):
-			TBase(_index),
-			minLength(1),
-			lValueLast(0),
-			rising(true)
-		{
-			this->vDesc.range = Pair<TSize>(0,0);
-			indexRequire(_index, EsaBwt());
-			lIter = begin(indexLcp(container(*this)));
-			lEnd  = end(indexLcp(container(*this)));
-			goNext(*this);
-		}
-
-		Iter(TIndex &_index, MinimalCtor):
-			TBase(_index, MinimalCtor()) {}
-
-		Iter(TIndex &_index, TSize _minLength):
-			TBase(_index),
-			minLength(_minLength),
-			lValueLast(0),
-			rising(true)
-		{
-			this->vDesc.i1 = Pair<TSize>(0,0);
-			indexRequire(_index, EsaBwt());
-			lIter = begin(indexLcp(container(*this)));
-			lEnd  = end(indexLcp(container(*this)));
-			goNext(*this);
-		}
-
-		Iter(Iter const &_origin):
-			TBase((TBase const &)_origin),
-			minLength(_origin.minLength),
-			lIter(_origin.lIter),
-			lEnd(_origin.lEnd),
-			lValueLast(_origin.lValueLast),
-			rising(_origin.rising) {}
-	};
-
-	template < typename TText, typename TSpec >
-	inline void goNext(Iter< Index<TText, IndexEsa<TSpec> >, VSTree< BottomUp<SuperMaxRepeatsFast> > > &it) 
-	{
-		typedef Index<TText, IndexEsa<TSpec> >		TIndex;
-		typename Size<TIndex>::Type					lcp;
-
-		while (it.lIter != it.lEnd) {
-			lcp = *it.lIter;
-
-			if (lcp < it.lValueLast) {
-				if (it.rising) {
-					if (it.lValueLast > it.minLength) {
-						_dfsLcp(it) = it.lValueLast;
-						++_dfsRange(it).i2;
-						++it.lIter;
-						it.lValueLast = lcp;
-						if (!isPartiallyLeftExtensible(it, it.charSet)) return;
-						continue;
-					}
-					it.rising = false;
-				}
-			} else
-			if (lcp > it.lValueLast) {
-				_dfsRange(it).i1 = _dfsRange(it).i2;
-				it.rising = true;
-			}
-
-			++_dfsRange(it).i2;
-			++it.lIter;
-			it.lValueLast = lcp;
-		}
-		_dfsRange(it).i2 = 0;
-		return;
-	}
-
-	
-/**
-.Spec.MaxRepeats Iterator:
-..cat:Index
-..general:Spec.BottomUp Iterator
-..summary:Iterator to search for all maximal repeats.
-..signature:Iterator<TContainer, MaxRepeats>::Type
-..signature:Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >
-..param.TContainer:Type of an index that can be iterated with a bottom-up iterator.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..include:seqan/index.h
-
-.Memfunc.MaxRepeats Iterator#Iterator
-..class:Spec.MaxRepeats Iterator
-..summary:Constructor
-..signature:Iterator(index[, minLength])
-..signature:Iterator(iterator)
-..param.index:An index object.
-..param.minLength:Minimum length of the maximal repeats, default value is 1.
-..param.iterator:Another MaxRepeats iterator. (copy constructor)
-...type:Spec.MaxRepeats Iterator
-*/
-/*H
+
+        Iter(TIndex &_index):
+            TBase(_index),
+            minLength(1),
+            lValueLast(0),
+            rising(true)
+        {
+            this->vDesc.range = Pair<TSize>(0,0);
+            indexRequire(_index, EsaBwt());
+            lIter = begin(indexLcp(container(*this)));
+            lEnd  = end(indexLcp(container(*this)));
+            goNext(*this);
+        }
+
+        Iter(TIndex &_index, MinimalCtor):
+            TBase(_index, MinimalCtor()) {}
+
+        Iter(TIndex &_index, TSize _minLength):
+            TBase(_index),
+            minLength(_minLength),
+            lValueLast(0),
+            rising(true)
+        {
+            this->vDesc.i1 = Pair<TSize>(0,0);
+            indexRequire(_index, EsaBwt());
+            lIter = begin(indexLcp(container(*this)));
+            lEnd  = end(indexLcp(container(*this)));
+            goNext(*this);
+        }
+
+        Iter(Iter const &_origin):
+            TBase((TBase const &)_origin),
+            minLength(_origin.minLength),
+            lIter(_origin.lIter),
+            lEnd(_origin.lEnd),
+            lValueLast(_origin.lValueLast),
+            rising(_origin.rising) {}
+    };
+
+    template < typename TText, typename TSpec >
+    inline void goNext(Iter< Index<TText, IndexEsa<TSpec> >, VSTree< BottomUp<SuperMaxRepeatsFast> > > &it)
+    {
+        typedef Index<TText, IndexEsa<TSpec> >        TIndex;
+        typename Size<TIndex>::Type                    lcp;
+
+        while (it.lIter != it.lEnd) {
+            lcp = *it.lIter;
+
+            if (lcp < it.lValueLast) {
+                if (it.rising) {
+                    if (it.lValueLast > it.minLength) {
+                        _dfsLcp(it) = it.lValueLast;
+                        ++_dfsRange(it).i2;
+                        ++it.lIter;
+                        it.lValueLast = lcp;
+                        if (!isPartiallyLeftExtensible(it, it.charSet)) return;
+                        continue;
+                    }
+                    it.rising = false;
+                }
+            } else
+            if (lcp > it.lValueLast) {
+                _dfsRange(it).i1 = _dfsRange(it).i2;
+                it.rising = true;
+            }
+
+            ++_dfsRange(it).i2;
+            ++it.lIter;
+            it.lValueLast = lcp;
+        }
+        _dfsRange(it).i2 = 0;
+        return;
+    }
+
+
+/*!
  * @class MaxRepeatsIterator Max Repeats Iterator
- * 
  * @extends BottomUpIterator
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief Iterator to search for all maximal repeats.
- * 
- * @signature Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >(index[, minLength])
- * @signature Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >(iterator)
- * 
+ *
+ * @signature Iterator<TContainer, MaxRepeats>::Type;
+ * @signature template <typename TContainer>
+ *            class Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >;
+ *
  * @tparam TContainer Type of an index that can be iterated with a bottom-up
  *                    iterator. Types: IndexEsa
- * 
- * @section Note Instead of using the class Iter directly we recommend to use the result of the metafunction 
- *               Iterator<TContainer, MaxRepeats>::Type (which is Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >).
- * 
- * Demo: Demo.Maximal Repeats
- */
-
-/*H
- * @fn Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >::Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >
  *
- * brief The constructor
+ * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
+ *       Iterator&lt;TContainer, MaxRepeats&gt;::Type (which is Iter<TContainer, VSTree< BottomUp<MaxRepeats&gt; &gt; &gt;).
  *
- * @signature Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >(index[, minLength])
- * @signature Iter<TContainer, VSTree< BottomUp<MaxRepeats> > >(iterator)
- *
- * @param index The index to be used for the iteration. Types: @link IndexEsa @endlink
+ * @see DemoMaximalRepeats
+ */
+
+/*!
+ * @fn MaxRepeatsIterator::Iter
+ * @brief The constructor
  *
- * @param minLength Minimum length of the supermaximal repeats, default value is 1.
+ * @signature Iter::Iter(index[, minLength]);
+ * @signature Iter::Iter(iterator);
  *
- * @param iterator Another MaxRepeats iterator. Types: @link MaxRepeatsIterator @endlink
+ * @param[in] index     The index to be used for the iteration. Types: @link IndexEsa @endlink
+ * @param[in] minLength Minimum length of the supermaximal repeats, default value is 1.
+ * @param[in] iterator  Another MaxRepeats iterator. Types: @link MaxRepeatsIterator @endlink
  */
 
-	//////////////////////////////////////////////////////////////////////////////
-	// maximal repeats - suffix tree version
-	//////////////////////////////////////////////////////////////////////////////
-
-	// contains a list of indices of the same bwt value (fraction)
-	template <typename TSize>
-	struct FractionHeader_ {
-		TSize	begin, end;
-		TSize	size;
-		FractionHeader_() {}
-		FractionHeader_(TSize _begin, TSize _end, TSize _size):
-			begin(_begin), end(_end), size(_size) {}
-	};
-
-	// contains a set of fractions (one for each bwt value) 
-	// and a fraction for the undefined bwt value (for the virtual character at position -1)
-	template <typename TValue, typename TSize>
-	struct FractionCompound_ {
-		typedef FractionHeader_<TSize>			TFractionHeader;
-		typedef Pair<TValue, TFractionHeader>	TFraction;	// TFraction = (c,(begin,end))
-		typedef typename Set<TFraction>::Type	TSet;		// c..char, begin/end indices in posList
-
-		TSet			set;
-		TFractionHeader	leftmost;
-
-		FractionCompound_():
-			leftmost(0,0,0) {}
-	};
-
-	// tests existence of left maximal repeats
-	// right maximality is implicitly given
-	template <typename TValue, typename TSize>
-	int _haveMaximalRepeats(
-		FractionCompound_<TValue, TSize> const &a,
-		FractionCompound_<TValue, TSize> const &b)
-	{
-		TSize cs = length(a.set), ps = length(b.set);
-
-		if (a.leftmost.size > 0) ++cs;
-		if (b.leftmost.size > 0) ++ps;
-
-		if (cs == 0 || ps == 0) return false;
-		if (cs  > 1 || ps  > 1) return true;
-
-		if (a.leftmost.size > 0 || b.leftmost.size > 0)
-			return true;
-
-		return (keyOf(begin(a.set)) != keyOf(begin(b.set)));
-	}
-
-
-	template <typename TValue, typename TSize>
-	int _haveMaximalRepeats(
-		FractionCompound_<TValue, TSize> const &a,
-		FractionCompound_<TValue, TSize> const &b,
-		TValue &equalKey)
-	{
-		TSize cs = length(a.set), ps = length(b.set);
-
-		if (a.leftmost.size > 0) ++cs;
-		if (b.leftmost.size > 0) ++ps;
-
-		if (cs == 0 || ps == 0) return 0;
-		if (cs  > 1 || ps  > 1) return 2;	// more than 2
-
-		if (a.leftmost.size > 0 || b.leftmost.size > 0)
-			return 2;
-
-		if ((equalKey = keyOf(begin(a.set))) != keyOf(begin(b.set)))
-			return 2;
-		else
-			return 1;
-	}
-
-
-	template < typename TSTree, typename TSpec >
-	struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > > {
-		typedef PostorderEmptyEdges	Type;
-	};
-
-	template < typename TSTree, typename TSpec >
-	class Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > >:
-		public Iter< TSTree, VSTree< BottomUp<> > > 
-	{
-	public:
-		typedef Iter< TSTree, VSTree< BottomUp<> > >	TBase;
-		typedef typename Value<TSTree>::Type			TValue;
-		typedef typename Size<TSTree>::Type				TSize;
-
-		typedef FractionCompound_<TValue, TSize>		TFractionCompound;
-		typedef String<TFractionCompound>               TSetStack;
-		typedef String<TSize>							TPositionList;
-		
-		typedef typename TFractionCompound::TSet		TSet;
-		typedef typename Iterator<TSet>::Type			TSetIterator;
-		typedef typename Iterator<TSet const>::Type		TConstSetIterator;
-
-		typedef typename TBase::TStackEntry				TStackEntry;
+    //////////////////////////////////////////////////////////////////////////////
+    // maximal repeats - suffix tree version
+    //////////////////////////////////////////////////////////////////////////////
+
+    // contains a list of indices of the same bwt value (fraction)
+    template <typename TSize>
+    struct FractionHeader_ {
+        TSize    begin, end;
+        TSize    size;
+        FractionHeader_() : begin(0), end(0), size(0) {}
+        FractionHeader_(TSize _begin, TSize _end, TSize _size):
+            begin(_begin), end(_end), size(_size) {}
+    };
+
+    // contains a set of fractions (one for each bwt value)
+    // and a fraction for the undefined bwt value (for the virtual character at position -1)
+    template <typename TValue, typename TSize>
+    struct FractionCompound_ {
+        typedef FractionHeader_<TSize>            TFractionHeader;
+        typedef Pair<TValue, TFractionHeader>    TFraction;    // TFraction = (c,(begin,end))
+        typedef typename Set<TFraction>::Type    TSet;        // c..char, begin/end indices in posList
+
+        TSet            set;
+        TFractionHeader    leftmost;
+
+        FractionCompound_():
+            leftmost(0,0,0) {}
+    };
+
+    // tests existence of left maximal repeats
+    // right maximality is implicitly given
+    template <typename TValue, typename TSize>
+    int _haveMaximalRepeats(
+        FractionCompound_<TValue, TSize> const &a,
+        FractionCompound_<TValue, TSize> const &b)
+    {
+        TSize cs = length(a.set), ps = length(b.set);
+
+        if (a.leftmost.size > 0) ++cs;
+        if (b.leftmost.size > 0) ++ps;
+
+        if (cs == 0 || ps == 0) return false;
+        if (cs  > 1 || ps  > 1) return true;
+
+        if (a.leftmost.size > 0 || b.leftmost.size > 0)
+            return true;
+
+        return (keyOf(begin(a.set)) != keyOf(begin(b.set)));
+    }
+
+
+    template <typename TValue, typename TSize>
+    int _haveMaximalRepeats(
+        FractionCompound_<TValue, TSize> const &a,
+        FractionCompound_<TValue, TSize> const &b,
+        TValue &equalKey)
+    {
+        TSize cs = length(a.set), ps = length(b.set);
+
+        if (a.leftmost.size > 0) ++cs;
+        if (b.leftmost.size > 0) ++ps;
+
+        if (cs == 0 || ps == 0) return 0;
+        if (cs  > 1 || ps  > 1) return 2;    // more than 2
+
+        if (a.leftmost.size > 0 || b.leftmost.size > 0)
+            return 2;
+
+        if ((equalKey = keyOf(begin(a.set))) != keyOf(begin(b.set)))
+            return 2;
+        else
+            return 1;
+    }
+
+
+    template < typename TSTree, typename TSpec >
+    struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > > {
+        typedef PostorderEmptyEdges    Type;
+    };
+
+    template < typename TSTree, typename TSpec >
+    class Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > >:
+        public Iter< TSTree, VSTree< BottomUp<> > >
+    {
+    public:
+        typedef Iter< TSTree, VSTree< BottomUp<> > >    TBase;
+        typedef typename Value<TSTree>::Type            TValue;
+        typedef typename Size<TSTree>::Type                TSize;
+
+        typedef FractionCompound_<TValue, TSize>        TFractionCompound;
+        typedef String<TFractionCompound>               TSetStack;
+        typedef String<TSize>                            TPositionList;
+
+        typedef typename TFractionCompound::TSet        TSet;
+        typedef typename Iterator<TSet>::Type            TSetIterator;
+        typedef typename Iterator<TSet const>::Type        TConstSetIterator;
+
+        typedef typename HistoryStackEntry_<TBase>::Type TStackEntry;
 
 //____________________________________________________________________________
 
-		TSize			minLength;
-		TSetStack		setStack;
-		TPositionList	posList;	// this list is indexed just as SA is and contains the next entry's index
-		bool			canMerge;	// is false, if parent node appears after its first child on stack
+        TSize            minLength;
+        TSetStack        setStack;
+        TPositionList    posList;    // this list is indexed just as SA is and contains the next entry's index
+        bool            canMerge;    // is false, if parent node appears after its first child on stack
 //____________________________________________________________________________
 
         Iter() :
@@ -506,634 +426,641 @@ namespace SEQAN_NAMESPACE_MAIN
             minLength(0),
             canMerge(false)
         {}
-        
-		Iter(TSTree &_index):
-			TBase(_index, MinimalCtor()),
-			minLength(1),
-			canMerge(true)
-		{
-			indexRequire(_index, EsaSA());
-			indexRequire(_index, EsaLcp());
-			indexRequire(_index, EsaBwt());
-			resize(posList, length(_index));
-
-			if (!empty(indexSA(_index))) 
-			{
-				TStackEntry e;
-				e.range.i1 = 0;
-				e.range.i2 = 0;
-				_dfsOnPush(*this, e);
-				goNext(*this);
-			}
-		}
-
-		Iter(TSTree &_tree, MinimalCtor):
-			TBase(_tree, MinimalCtor()) {}
-
-		Iter(TSTree &_index, TSize _minLength):
-			TBase(_index, MinimalCtor()),
-			minLength(_minLength),
-			canMerge(true)
-		{
-			indexRequire(_index, EsaSA());
-			indexRequire(_index, EsaLcp());
-			indexRequire(_index, EsaBwt());
-			resize(posList, length(_index));
-
-			if (!empty(indexSA(_index))) 
-			{
-				TStackEntry e;
-				e.range.i1 = 0;
-				e.range.i2 = 0;
-				_dfsOnPush(*this, e);
-				goNext(*this);
-			}
-		}
-
-		Iter(Iter const &_origin):
-			TBase((TBase const &)_origin),
-			minLength(_origin.minLength),
-			setStack(_origin.setStack),
-			posList(_origin.posList),
-			canMerge(_origin.canMerge) {}
+
+        Iter(TSTree &_index):
+            TBase(_index, MinimalCtor()),
+            minLength(1),
+            canMerge(true)
+        {
+            indexRequire(_index, EsaSA());
+            indexRequire(_index, EsaLcp());
+            indexRequire(_index, EsaBwt());
+            resize(posList, length(_index));
+
+            if (!empty(indexSA(_index)))
+            {
+                TStackEntry e;
+                e.range.i1 = 0;
+                e.range.i2 = 0;
+                _dfsOnPush(*this, e);
+                goNext(*this);
+            }
+        }
+
+        Iter(TSTree &_tree, MinimalCtor):
+            TBase(_tree, MinimalCtor()) {}
+
+        Iter(TSTree &_index, TSize _minLength):
+            TBase(_index, MinimalCtor()),
+            minLength(_minLength),
+            canMerge(true)
+        {
+            indexRequire(_index, EsaSA());
+            indexRequire(_index, EsaLcp());
+            indexRequire(_index, EsaBwt());
+            resize(posList, length(_index));
+
+            if (!empty(indexSA(_index)))
+            {
+                TStackEntry e;
+                e.range.i1 = 0;
+                e.range.i2 = 0;
+                _dfsOnPush(*this, e);
+                goNext(*this);
+            }
+        }
+
+        Iter(Iter const &_origin):
+            TBase((TBase const &)_origin),
+            minLength(_origin.minLength),
+            setStack(_origin.setStack),
+            posList(_origin.posList),
+            canMerge(_origin.canMerge) {}
 
 //____________________________________________________________________________
 
-		inline bool hasRepeats() 
-		{
-			if (length(setStack) < 2) return false;
-			return _haveMaximalRepeats(back(setStack), setStack[length(setStack) - 2]) > 0;
-		}
-
-		inline TSize countRepeats() const
-		{
-			if (length(setStack) < 2) return 0;
-
-			TFractionCompound const &child  = back(setStack);
-			TFractionCompound const &parent = topPrev(setStack);
-
-			TConstSetIterator childFraction	= begin(child.set);
-			TConstSetIterator childEnd		= end(child.set);
-			TConstSetIterator parentFraction	= begin(parent.set);
-			TConstSetIterator parentEnd		= end(parent.set);
-
-			TSize sum = 0;
-			for(; childFraction != childEnd; ++childFraction) {
-				for(; parentFraction != parentEnd; ++parentFraction) {
-					if (keyOf(childFraction) != keyOf(parentFraction))
-						sum += objectOf(childFraction).size * objectOf(parentFraction).size;
-
-					sum += child.leftmost.size * objectOf(parentFraction).size;
-				}
-				sum += objectOf(childFraction).size * parent.leftmost.size;
-			}
-			sum += child.leftmost.size * parent.leftmost.size;
-			return sum;
-		}
+        inline bool hasRepeats()
+        {
+            if (length(setStack) < 2) return false;
+            return _haveMaximalRepeats(back(setStack), setStack[length(setStack) - 2]) > 0;
+        }
+
+        inline TSize countRepeats() const
+        {
+            if (length(setStack) < 2) return 0;
+
+            TFractionCompound const &child  = back(setStack);
+            TFractionCompound const &parent = backPrev(setStack);
+
+            TConstSetIterator childFraction    = begin(child.set);
+            TConstSetIterator childEnd        = end(child.set);
+            TConstSetIterator parentFraction    = begin(parent.set);
+            TConstSetIterator parentEnd        = end(parent.set);
+
+            TSize sum = 0;
+            for(; childFraction != childEnd; ++childFraction) {
+                for(; parentFraction != parentEnd; ++parentFraction) {
+                    if (keyOf(childFraction) != keyOf(parentFraction))
+                        sum += objectOf(childFraction).size * objectOf(parentFraction).size;
+
+                    sum += child.leftmost.size * objectOf(parentFraction).size;
+                }
+                sum += objectOf(childFraction).size * parent.leftmost.size;
+            }
+            sum += child.leftmost.size * parent.leftmost.size;
+            return sum;
+        }
 //____________________________________________________________________________
 
-		inline void _dump() const {
-			::std::cerr << "SETSTACK of " << representative(*this) << ":" << ::std::endl;
-			typename Iterator<TSetStack const>::Type it = begin(setStack), itEnd = end(setStack);
-			while (it != itEnd) {
-				TSet const &set = (*it).set;
-				typename Iterator<TSet const>::Type sit = begin(set), sitEnd = end(set);
-
-				while (sit != sitEnd) {
-					::std::cerr << keyOf(sit) << "::";
-					typename TFractionCompound::TFractionHeader head = objectOf(sit);
-					TSize i = head.begin;
-					while (!_isSizeInval(i)) {
-						::std::cerr << saAt(i,container(*this)) << "  ";
-						i = posList[i];
-					}
-					::std::cerr << ::std::endl;
-					++sit;
-				}
-				
-				if ((*it).leftmost.size > 0)
-				{
-					::std::cerr << "\"\"::";
-					TSize i = (*it).leftmost.begin;
-					while (!_isSizeInval(i)) {
-						::std::cerr << saAt(i,container(*this)) << "  ";
-						i = posList[i];
-					}
-					::std::cerr << ::std::endl;
-				}
-				
-				::std::cerr << "_________________________" << ::std::endl;
-				++it;
-			}
-		}
-	};
+        inline void _dump() const {
+            std::cerr << "SETSTACK of " << representative(*this) << ":" << std::endl;
+            typename Iterator<TSetStack const>::Type it = begin(setStack), itEnd = end(setStack);
+            while (it != itEnd) {
+                TSet const &set = (*it).set;
+                typename Iterator<TSet const>::Type sit = begin(set), sitEnd = end(set);
+
+                while (sit != sitEnd) {
+                    std::cerr << keyOf(sit) << "::";
+                    typename TFractionCompound::TFractionHeader head = objectOf(sit);
+                    TSize i = head.begin;
+                    while (!_isSizeInval(i)) {
+                        std::cerr << saAt(i,container(*this)) << "  ";
+                        i = posList[i];
+                    }
+                    std::cerr << std::endl;
+                    ++sit;
+                }
+
+                if ((*it).leftmost.size > 0)
+                {
+                    std::cerr << "\"\"::";
+                    TSize i = (*it).leftmost.begin;
+                    while (!_isSizeInval(i)) {
+                        std::cerr << saAt(i,container(*this)) << "  ";
+                        i = posList[i];
+                    }
+                    std::cerr << std::endl;
+                }
+
+                std::cerr << "_________________________" << std::endl;
+                ++it;
+            }
+        }
+    };
 //____________________________________________________________________________
 
-	// add bwt partitions of child to parent node
-	template < typename TSTree, typename TSpec, typename TValue, typename TSize >
-	inline void _fractionMerge(
-		Iter<TSTree, VSTree< BottomUp<TSpec> > > &it, 
-		FractionCompound_<TValue, TSize> &parent,
-		FractionCompound_<TValue, TSize> &child)
-	{
-		typedef FractionCompound_<TValue, TSize>	TCompound;
-		typedef typename TCompound::TFraction		TFraction;
-		typedef typename TCompound::TFractionHeader	TFractionHeader;
-		typedef typename TCompound::TSet			TSet;
-		typedef typename Iterator<TSet>::Type		TSetIterator;
-
-		TSetIterator _end = end(child.set);
-		for(TSetIterator i = begin(child.set); i != _end; ++i) {
-			if (in(keyOf(i), parent.set)) {	// append child fraction to parent's fraction
-				TFractionHeader &parent_header = objectOf(find(keyOf(i), parent.set));
-				TFractionHeader const &child_header = objectOf(i);
-				it.posList[parent_header.end] = child_header.begin;
-				parent_header.end = child_header.end;
-				parent_header.size += child_header.size;
-			} else
-				insert(TFraction(keyOf(i), objectOf(i)), parent.set);	// insert child fraction in parent's set
-		}
-		if (parent.leftmost.size > 0) {
-			if (child.leftmost.size > 0) {
-				it.posList[parent.leftmost.end] = child.leftmost.begin;
-				parent.leftmost.end = child.leftmost.end;
-				parent.leftmost.size += child.leftmost.size;
-			}
-		} else
-			parent.leftmost = child.leftmost;
-	}
-
-	// maximal repeat push/leaf handlers of lcp-dfs-traversal
-	template < typename TSTree, typename TElement, typename TSpec >
-	inline void _dfsOnPush(Iter<TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it, TElement const &e) 
-	{
-		typedef Iter<TSTree, VSTree< BottomUp<> > > TBase;
-		_dfsOnPush((TBase&)it, e);
-
-		if (it.canMerge)
-			resize(it.setStack, length(it.setStack) + 1);
+    // add bwt partitions of child to parent node
+    template < typename TSTree, typename TSpec, typename TValue, typename TSize >
+    inline void _fractionMerge(
+        Iter<TSTree, VSTree< BottomUp<TSpec> > > &it,
+        FractionCompound_<TValue, TSize> &parent,
+        FractionCompound_<TValue, TSize> &child)
+    {
+        typedef FractionCompound_<TValue, TSize>    TCompound;
+        typedef typename TCompound::TFraction        TFraction;
+        typedef typename TCompound::TFractionHeader    TFractionHeader;
+        typedef typename TCompound::TSet            TSet;
+        typedef typename Iterator<TSet>::Type        TSetIterator;
+
+        TSetIterator _end = end(child.set);
+        for(TSetIterator i = begin(child.set); i != _end; ++i) {
+            if (in(keyOf(i), parent.set)) {    // append child fraction to parent's fraction
+                TFractionHeader &parent_header = objectOf(find(keyOf(i), parent.set));
+                TFractionHeader const &child_header = objectOf(i);
+                it.posList[parent_header.end] = child_header.begin;
+                parent_header.end = child_header.end;
+                parent_header.size += child_header.size;
+            } else
+                insert(TFraction(keyOf(i), objectOf(i)), parent.set);    // insert child fraction in parent's set
+        }
+        if (parent.leftmost.size > 0) {
+            if (child.leftmost.size > 0) {
+                it.posList[parent.leftmost.end] = child.leftmost.begin;
+                parent.leftmost.end = child.leftmost.end;
+                parent.leftmost.size += child.leftmost.size;
+            }
+        } else
+            parent.leftmost = child.leftmost;
+    }
+
+    // maximal repeat push/leaf handlers of lcp-dfs-traversal
+    template < typename TSTree, typename TElement, typename TSpec >
+    inline void _dfsOnPush(Iter<TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it, TElement const &e)
+    {
+        typedef Iter<TSTree, VSTree< BottomUp<> > > TBase;
+        _dfsOnPush((TBase&)it, e);
+
+        if (it.canMerge)
+            resize(it.setStack, length(it.setStack) + 1);
 /*
-		::std::cerr << "PUSH ";
-		_dumpHistoryStack(it);
-		it._dump();
-*/	}
-
-	template < typename TSTree, typename TSpec >
-	inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it) 
-	{
-		typedef Iter<TSTree, VSTree< BottomUp<> > > TBase;
-		_dfsOnLeaf((TBase&)it);
-
-		typedef typename Value<TSTree>::Type	TValue;
-		typedef typename Size<TSTree>::Type		TSize;
-		typedef typename SAValue<TSTree>::Type	TSAValue;
-		typedef FractionHeader_<TSize>			TFractionHeader;
-		typedef Pair<TValue, TFractionHeader>	TFraction;
-
-		resize(it.setStack, length(it.setStack) + 1);
-
-		TSTree &index = container(it);
-
-		TSize       i = _dfsRange(it).i1;
-		TSAValue	lPos;
-		posLocalize(lPos, getOccurrence(it), stringSetLimits(index));
-
-		if (!posAtFirstLocal(lPos))
-			insert(
-				TFraction(
-					bwtAt(i, container(it)),
-					TFractionHeader(i, i, 1)), 
-				back(it.setStack).set);
-		else
-			back(it.setStack).leftmost = TFractionHeader(i, i, 1);
-
-		_setSizeInval(it.posList[i]);
+        std::cerr << "PUSH ";
+        _dumpHistoryStack(it);
+        it._dump();
+*/    }
+
+    template < typename TSTree, typename TSpec >
+    inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it)
+    {
+        typedef Iter<TSTree, VSTree< BottomUp<> > > TBase;
+        _dfsOnLeaf((TBase&)it);
+
+        typedef typename Value<TSTree>::Type    TValue;
+        typedef typename Size<TSTree>::Type        TSize;
+        typedef typename SAValue<TSTree>::Type    TSAValue;
+        typedef FractionHeader_<TSize>            TFractionHeader;
+        typedef Pair<TValue, TFractionHeader>    TFraction;
+
+        resize(it.setStack, length(it.setStack) + 1);
+
+        TSTree &index = container(it);
+
+        TSize       i = _dfsRange(it).i1;
+        TSAValue    lPos;
+        posLocalize(lPos, getOccurrence(it), stringSetLimits(index));
+
+        if (!posAtFirstLocal(lPos))
+            insert(
+                TFraction(
+                    bwtAt(i, container(it)),
+                    TFractionHeader(i, i, 1)),
+                back(it.setStack).set);
+        else
+            back(it.setStack).leftmost = TFractionHeader(i, i, 1);
+
+        _setSizeInval(it.posList[i]);
 /*
-		::std::cerr << "LEAF ";
-		_dumpHistoryStack(it);
-		it._dump();
-*/	}
+        std::cerr << "LEAF ";
+        _dumpHistoryStack(it);
+        it._dump();
+*/    }
 
 //____________________________________________________________________________
 
-	template < typename TSTree, typename TSpec >
-	inline void goNext(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it) 
+    template < typename TSTree, typename TSpec >
+    inline void goNext(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it)
     {
         typedef Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > TIter;
-		do {
-			if (it.canMerge && length(it.setStack) >= 2) 
+        do {
+            if (it.canMerge && length(it.setStack) >= 2)
             {
                 typename Size<typename TIter::TSetStack>::Type len = length(it.setStack);
-				_fractionMerge(it, it.setStack[len - 2], back(it.setStack));
-				resize(it.setStack, len - 1);
-			}
-			goNext(it, PostorderEmptyEdges());
-			if (empty(it.history))
-				it.canMerge = false;
-			else
-				it.canMerge = !_dfsReversedOrder(it);
-		} while (!eof(it) && !(it.canMerge && (repLength(it) >= it.minLength) && it.hasRepeats()));
-	}
+                _fractionMerge(it, it.setStack[len - 2], back(it.setStack));
+                resize(it.setStack, len - 1);
+            }
+            goNext(it, PostorderEmptyEdges());
+            if (empty(it.history))
+                it.canMerge = false;
+            else
+                it.canMerge = !_dfsReversedOrder(it);
+        } while (!eof(it) && !(it.canMerge && (repLength(it) >= it.minLength) && it.hasRepeats()));
+    }
 //____________________________________________________________________________
 
-	template < typename TSTree, typename TSpec >
-	inline typename VertexDescriptor<TSTree>::Type 
-	value(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > const &it) 
-	{
-		if (empty(it.history))
-			return it.vDesc;
-		typedef typename VertexDescriptor<TSTree>::Type TDesc;
-		return TDesc(back(it.history).range.i1, it.vDesc.range.i2, 0);
-	}
+    template < typename TSTree, typename TSpec >
+    inline typename VertexDescriptor<TSTree>::Type
+    value(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > const &it)
+    {
+        if (empty(it.history))
+            return it.vDesc;
+        typedef typename VertexDescriptor<TSTree>::Type TDesc;
+        return TDesc(back(it.history).range.i1, it.vDesc.range.i2, 0);
+    }
 //____________________________________________________________________________
 
-	template < typename TSTree, typename TSpec >
-	inline typename Size<TSTree>::Type 
-	repLength(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > const &it) 
-	{
-		return back(it.history).range.i2;
-	}
+    template < typename TSTree, typename TSpec >
+    inline typename Size<TSTree>::Type
+    repLength(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > const &it)
+    {
+        return back(it.history).range.i2;
+    }
 //____________________________________________________________________________
 
-///.Function.length.param.object.type:Spec.MaxRepeats Iterator
-///.Function.length.class:Spec.MaxRepeats Iterator
-	template < typename TSTree, typename TSpec >
-	inline typename Size<TSTree>::Type 
-	length(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > const &it) {
-		return it.countRepeats();
-	}
+/*!
+ * @fn MaxRepeatsIterator#length
+ * @headerfile <seqan/index.h>
+ * @brief Return the number of repeats.
+ *
+ * @signature TSize length(it);
+ *
+ * @param[in] it The MaxRepeatsIterator to query.
+ *
+ * @return TSize The number of found repeats.
+ */
+
+
+    template < typename TSTree, typename TSpec >
+    inline typename Size<TSTree>::Type
+    length(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > const &it) {
+        return it.countRepeats();
+    }
 //____________________________________________________________________________
 
-///.Function.begin.param.object.type:Spec.MaxRepeats Iterator
-///.Function.begin.class:Spec.MaxRepeats Iterator
-	template < typename TSTree, class TSpec >
-	inline typename Iterator< Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > >::Type
-	begin(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it) 
-	{
-		typedef Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > >	TIter;
-		return typename Iterator<TIter>::Type(it);
-	}
+    template < typename TSTree, class TSpec >
+    inline typename Iterator< Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > >::Type
+    begin(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it)
+    {
+        typedef Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > >    TIter;
+        return typename Iterator<TIter>::Type(it);
+    }
 //____________________________________________________________________________
 
-///.Function.end.param.object.type:Spec.MaxRepeats Iterator
-///.Function.end.class:Spec.MaxRepeats Iterator
-	template < typename TSTree, class TSpec >
-	inline typename Iterator< Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > >::Type
-	end(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it) 
-	{
-		typedef Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > >	TIter;
-		return typename Iterator<TIter>::Type(it, MinimalCtor());
-	}
+    template < typename TSTree, class TSpec >
+    inline typename Iterator< Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > >::Type
+    end(Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > &it)
+    {
+        typedef Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > >    TIter;
+        return typename Iterator<TIter>::Type(it, MinimalCtor());
+    }
 
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// maximal repeat representation
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // maximal repeat representation
+    //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TSTree>
-	struct MaxRepeat {
-//		Iter< TSTree, VSTree<BottomUp<MaxRepeats> > > &it;
-	};
+    template <typename TSTree>
+    struct MaxRepeat {
+//        Iter< TSTree, VSTree<BottomUp<MaxRepeats> > > &it;
+    };
 
-	template <typename TSTree>
-	struct Value< MaxRepeat<TSTree> > {
-		typedef Pair< typename SAValue<TSTree>::Type > Type;
-	};
+    template <typename TSTree>
+    struct Value< MaxRepeat<TSTree> > {
+        typedef Pair< typename SAValue<TSTree>::Type > Type;
+    };
 
-	template <typename TSTree>
-	struct Size< MaxRepeat<TSTree> > {
-		typedef typename Size<TSTree>::Type Type;
-	};
+    template <typename TSTree>
+    struct Size< MaxRepeat<TSTree> > {
+        typedef typename Size<TSTree>::Type Type;
+    };
 
 
-	template <typename TSTree>
-	inline typename Size< MaxRepeat<TSTree> >::Type 
-	length(MaxRepeat<TSTree> const &repeat) {
-		return repeat.it.countRepeats();
-	}
+    template <typename TSTree>
+    inline typename Size< MaxRepeat<TSTree> >::Type
+    length(MaxRepeat<TSTree> const &repeat) {
+        return repeat.it.countRepeats();
+    }
 
 /*
-	template <typename TSTree>
-	inline typename Iterator< MaxRepeat<TSTree> >::Type 
-	begin(MaxRepeat<TSTree> &repeat) {
-		return Iterator< MaxRepeat<TSTree> >::Type(repeat.it);
-	}
-
-	template <typename TSTree>
-	inline typename Iterator< MaxRepeat<TSTree> const >::Type 
-	begin(MaxRepeat<TSTree> const &repeat) {
-		return Iterator< MaxRepeat<TSTree> >::Type(repeat.it);
-	}
+    template <typename TSTree>
+    inline typename Iterator< MaxRepeat<TSTree> >::Type
+    begin(MaxRepeat<TSTree> &repeat) {
+        return Iterator< MaxRepeat<TSTree> >::Type(repeat.it);
+    }
+
+    template <typename TSTree>
+    inline typename Iterator< MaxRepeat<TSTree> const >::Type
+    begin(MaxRepeat<TSTree> const &repeat) {
+        return Iterator< MaxRepeat<TSTree> >::Type(repeat.it);
+    }
 */
 
 
-	template <typename TSTree>
-	class Iter< MaxRepeat<TSTree>, MaxRepeatOccurrences > {
-	public:
-
-		typedef typename Value<TSTree>::Type	TValue;
-		typedef typename Size<TSTree>::Type		TSize;
-		typedef	Pair<TSize>						TPair;
-
-		typedef FractionCompound_<TValue, TSize>	TFractionCompound;
-		typedef typename TFractionCompound::TSet	TSet;
-		typedef typename Iterator<TSet const>::Type	TSetIterator;
-
-		TSize			childPtr, parentPtr;
-		TSetIterator	childFraction, childEnd;
-		TSetIterator	parentFraction, parentEnd;
-		bool			_atEnd;
-		TPair			tmp;
-		bool			leftmostChild, leftmostParent;
-		
-		Iter<TSTree, VSTree<BottomUp<MaxRepeats> > > const *maxIt;
-        
-		inline Iter():
-			childPtr(0), parentPtr(0),
-			_atEnd(true),
-			tmp(TPair(0, 0)),
-			leftmostChild(false), leftmostParent(false) {}
-
-		inline Iter(Iter<TSTree, VSTree<BottomUp<MaxRepeats> > > const &_maxIt):
-			childPtr(0), parentPtr(0),
-			_atEnd(true), 
-			tmp(TPair(0, 0)),
-			leftmostChild(false), leftmostParent(false),
-			maxIt(&_maxIt)
-		{
-			_init();
-		}
-		
-		inline Iter(Iter<TSTree, VSTree<BottomUp<MaxRepeats> > > const &_maxIt, MinimalCtor):
-			maxIt(&_maxIt),
-			_atEnd(true) {}
-		
-		inline void _reinitParentFraction() 
+    template <typename TSTree>
+    class Iter< MaxRepeat<TSTree>, MaxRepeatOccurrences > {
+    public:
+
+        typedef typename Value<TSTree>::Type    TValue;
+        typedef typename Size<TSTree>::Type        TSize;
+        typedef    Pair<TSize>                        TPair;
+
+        typedef FractionCompound_<TValue, TSize>    TFractionCompound;
+        typedef typename TFractionCompound::TSet    TSet;
+        typedef typename Iterator<TSet const>::Type    TSetIterator;
+
+        TSize            childPtr, parentPtr;
+        TSetIterator    childFraction, childEnd;
+        TSetIterator    parentFraction, parentEnd;
+        bool            _atEnd;
+        TPair            tmp;
+        bool            leftmostChild, leftmostParent;
+
+        Iter<TSTree, VSTree<BottomUp<MaxRepeats> > > const *maxIt;
+
+        inline Iter():
+            childPtr(0), parentPtr(0),
+            _atEnd(true),
+            tmp(TPair(0, 0)),
+            leftmostChild(false), leftmostParent(false) {}
+
+        inline Iter(Iter<TSTree, VSTree<BottomUp<MaxRepeats> > > const &_maxIt):
+            childPtr(0), parentPtr(0),
+            _atEnd(true),
+            tmp(TPair(0, 0)),
+            leftmostChild(false), leftmostParent(false),
+            maxIt(&_maxIt)
+        {
+            _init();
+        }
+
+        inline Iter(Iter<TSTree, VSTree<BottomUp<MaxRepeats> > > const &_maxIt, MinimalCtor):
+            maxIt(&_maxIt),
+            _atEnd(true) {}
+
+        inline void _reinitParentFraction()
+        {
+            if (leftmostParent)
+            {
+                TFractionCompound const &parent = maxIt->setStack[length(maxIt->setStack) - 2];
+                parentPtr = parent.leftmost.begin;
+            } else
+                parentPtr = objectOf(parentFraction).begin;
+        }
+
+        inline bool _innerStep() {
+            if (_isSizeInval(childPtr = maxIt->posList[childPtr])) {
+                if (_isSizeInval(parentPtr = maxIt->posList[parentPtr]))
+                {
+                    _reinitParentFraction();
+                    return false;
+                }
+                childPtr = objectOf(childFraction).begin;
+            }
+            return true;
+        }
+
+        inline void _firstParentFraction() {
+            TFractionCompound const &parent = maxIt->setStack[length(maxIt->setStack) - 2];
+
+            parentFraction    = begin(parent.set);
+            parentEnd        = end(parent.set);
+
+            if (parentFraction != parentEnd) {
+                leftmostParent = false;
+                parentPtr = objectOf(parentFraction).begin;
+            } else {
+                leftmostParent = true;
+                parentPtr = parent.leftmost.begin;
+            }
+        }
+
+        inline void _firstChildFraction() {
+            TFractionCompound const &child = back(maxIt->setStack);
+
+            childFraction    = begin(child.set);
+            childEnd        = end(child.set);
+
+            if (childFraction != childEnd) {
+                leftmostChild = false;
+                childPtr = objectOf(childFraction).begin;
+            } else {
+                leftmostChild = true;
+                childPtr = child.leftmost.begin;
+            }
+        }
+
+        inline bool _nextParentFraction()
         {
-			if (leftmostParent)
-			{
-				TFractionCompound const &parent = maxIt->setStack[length(maxIt->setStack) - 2];
-				parentPtr = parent.leftmost.begin;
-			} else
-				parentPtr = objectOf(parentFraction).begin;
-		}
-
-		inline bool _innerStep() {
-			if (_isSizeInval(childPtr = maxIt->posList[childPtr])) {
-				if (_isSizeInval(parentPtr = maxIt->posList[parentPtr]))
-				{
-					_reinitParentFraction();
-					return false;
-				}
-				childPtr = objectOf(childFraction).begin;
-			}
-			return true;
-		}
-
-		inline void _firstParentFraction() {
-			TFractionCompound const &parent = maxIt->setStack[length(maxIt->setStack) - 2];
-
-			parentFraction	= begin(parent.set);
-			parentEnd		= end(parent.set);
-
-			if (parentFraction != parentEnd) {
-				leftmostParent = false;
-				parentPtr = objectOf(parentFraction).begin;
-			} else {
-				leftmostParent = true;
-				parentPtr = parent.leftmost.begin;
-			}
-		}
-
-		inline void _firstChildFraction() {
-			TFractionCompound const &child = back(maxIt->setStack);
-
-			childFraction	= begin(child.set);
-			childEnd		= end(child.set);
-
-			if (childFraction != childEnd) {
-				leftmostChild = false;
-				childPtr = objectOf(childFraction).begin;
-			} else {
-				leftmostChild = true;
-				childPtr = child.leftmost.begin;
-			}
-		}
-
-		inline bool _nextParentFraction() 
+            if (leftmostParent)
+                return false;
+
+            if (++parentFraction == parentEnd) {
+                if (maxIt->setStack[length(maxIt->setStack) - 2].leftmost.size > 0) {
+                    leftmostParent = true;
+                    parentPtr = maxIt->setStack[length(maxIt->setStack) - 2].leftmost.begin;
+                } else
+                    return false;
+            } else
+                parentPtr = objectOf(parentFraction).begin;
+
+            return true;
+        }
+
+        inline bool _nextChildFraction() {
+            if (leftmostChild)
+                return false;
+
+            if (++childFraction == childEnd) {
+                if (back(maxIt->setStack).leftmost.size > 0) {
+                    leftmostChild = true;
+                    childPtr = back(maxIt->setStack).leftmost.begin;
+                } else
+                    return false;
+            } else
+                childPtr = objectOf(childFraction).begin;
+
+            return true;
+        }
+
+        inline bool _outerStep() {
+            do {
+                if (!_nextChildFraction()) {
+                    _firstChildFraction();
+                    if (!_nextParentFraction()) {
+                        _atEnd = true;
+                        return false;
+                    }
+                }
+                if (leftmostChild || leftmostParent) break;
+            } while (keyOf(childFraction) == keyOf(parentFraction));        // ignore occurrences with equal bwt entries
+            return true;
+        }
+
+        inline void _init()
         {
-			if (leftmostParent)
-				return false;
-
-			if (++parentFraction == parentEnd) {
-				if (maxIt->setStack[length(maxIt->setStack) - 2].leftmost.size > 0) {
-					leftmostParent = true;
-					parentPtr = maxIt->setStack[length(maxIt->setStack) - 2].leftmost.begin;
-				} else
-					return false;
-			} else
-				parentPtr = objectOf(parentFraction).begin;
-
-			return true;
-		}
-
-		inline bool _nextChildFraction() {
-			if (leftmostChild)
-				return false;
-
-			if (++childFraction == childEnd) {
-				if (back(maxIt->setStack).leftmost.size > 0) {
-					leftmostChild = true;
-					childPtr = back(maxIt->setStack).leftmost.begin;
-				} else
-					return false;
-			} else
-				childPtr = objectOf(childFraction).begin;
-
-			return true;
-		}
-
-		inline bool _outerStep() {
-			do {
-				if (!_nextChildFraction()) {
-					_firstChildFraction();
-					if (!_nextParentFraction()) {
-						_atEnd = true;
-						return false;
-					}
-				}
-				if (leftmostChild || leftmostParent) break;
-			} while (keyOf(childFraction) == keyOf(parentFraction));		// ignore occurrences with equal bwt entries
-			return true;
-		}
-
-		inline void _init() 
-		{
-			if (length(maxIt->setStack) < 2) {
-				_atEnd = true;
-				return;
-			}
-
-			_firstChildFraction();
-			_firstParentFraction();
-
-			if (!leftmostChild && !leftmostParent &&
-				(keyOf(childFraction) == keyOf(parentFraction)))
-				_atEnd = !_outerStep();
-			else
-				_atEnd = false;
-
-			if (!_atEnd) {
-				tmp.i1 = saAt(parentPtr, container(*maxIt));
-				tmp.i2 = saAt(childPtr, container(*maxIt));
-			}
-		}
-	};
+            if (length(maxIt->setStack) < 2) {
+                _atEnd = true;
+                return;
+            }
+
+            _firstChildFraction();
+            _firstParentFraction();
+
+            if (!leftmostChild && !leftmostParent &&
+                (keyOf(childFraction) == keyOf(parentFraction)))
+                _atEnd = !_outerStep();
+            else
+                _atEnd = false;
+
+            if (!_atEnd) {
+                tmp.i1 = saAt(parentPtr, container(*maxIt));
+                tmp.i2 = saAt(childPtr, container(*maxIt));
+            }
+        }
+    };
 
 //____________________________________________________________________________
 
-	template < typename TRepeat >
-	inline typename Value< Iter<TRepeat, MaxRepeatOccurrences> >::Type &
-	value(Iter<TRepeat, MaxRepeatOccurrences> const &it)  {
-		return it.tmp;
-	}
-
-	template < typename TRepeat >
-	inline typename Value< Iter<TRepeat, MaxRepeatOccurrences> >::Type &
-	value(Iter<TRepeat, MaxRepeatOccurrences> &it)  {
-		return it.tmp;
-	}
+    template < typename TRepeat >
+    inline typename Value< Iter<TRepeat, MaxRepeatOccurrences> >::Type &
+    value(Iter<TRepeat, MaxRepeatOccurrences> const &it)  {
+        return it.tmp;
+    }
+
+    template < typename TRepeat >
+    inline typename Value< Iter<TRepeat, MaxRepeatOccurrences> >::Type &
+    value(Iter<TRepeat, MaxRepeatOccurrences> &it)  {
+        return it.tmp;
+    }
 //____________________________________________________________________________
 
-	template < typename TRepeat >
-	inline Iter<TRepeat, MaxRepeatOccurrences> &
-	goNext(Iter<TRepeat, MaxRepeatOccurrences> &it)  {
-		if (it._innerStep()) {
-			it.tmp.i1 = saAt(it.parentPtr, container(*it.maxIt));
-			it.tmp.i2 = saAt(it.childPtr, container(*it.maxIt));
-			return it;
-		}
-		if (it._outerStep()) {
-			it.tmp.i1 = saAt(it.parentPtr, container(*it.maxIt));
-			it.tmp.i2 = saAt(it.childPtr, container(*it.maxIt));
-		}
-		return it;
-	}
+    template < typename TRepeat >
+    inline Iter<TRepeat, MaxRepeatOccurrences> &
+    goNext(Iter<TRepeat, MaxRepeatOccurrences> &it)  {
+        if (it._innerStep()) {
+            it.tmp.i1 = saAt(it.parentPtr, container(*it.maxIt));
+            it.tmp.i2 = saAt(it.childPtr, container(*it.maxIt));
+            return it;
+        }
+        if (it._outerStep()) {
+            it.tmp.i1 = saAt(it.parentPtr, container(*it.maxIt));
+            it.tmp.i2 = saAt(it.childPtr, container(*it.maxIt));
+        }
+        return it;
+    }
 //____________________________________________________________________________
 
-	template < typename TRepeat >
-	inline void
-	goBegin(Iter<TRepeat, MaxRepeatOccurrences> &it) 
-	{
-		it._init;
-	}
+    template < typename TRepeat >
+    inline void
+    goBegin(Iter<TRepeat, MaxRepeatOccurrences> &it)
+    {
+        it._init;
+    }
 
 //____________________________________________________________________________
 
-	template < typename TRepeat >
-	inline void
-	goEnd(Iter<TRepeat, MaxRepeatOccurrences> &it) 
-	{
-		it._atEnd = true;
-	}
+    template < typename TRepeat >
+    inline void
+    goEnd(Iter<TRepeat, MaxRepeatOccurrences> &it)
+    {
+        it._atEnd = true;
+    }
 
-	template < typename TRepeat >
-	inline bool atEnd(Iter<TRepeat, MaxRepeatOccurrences> const &it) {
-		return it._atEnd;
-	}
+    template < typename TRepeat >
+    inline bool atEnd(Iter<TRepeat, MaxRepeatOccurrences> const &it) {
+        return it._atEnd;
+    }
 
-	template < typename TRepeat >
-	inline bool atEnd(Iter<TRepeat, MaxRepeatOccurrences> &it) {
-		return it._atEnd;
-	}
+    template < typename TRepeat >
+    inline bool atEnd(Iter<TRepeat, MaxRepeatOccurrences> &it) {
+        return it._atEnd;
+    }
 
 //____________________________________________________________________________
 
-	template < typename TRepeat >
-	inline bool
-	operator == (
-		Iter<TRepeat, MaxRepeatOccurrences> const &itA,
-		Iter<TRepeat, MaxRepeatOccurrences> const &itB)
-	{
-		if (itA._atEnd && itB._atEnd) return true;
-		if (itA._atEnd || itB._atEnd) return false;
-		return (itA.childPtr == itB.childPtr) && (itA.parentPtr == itB.parentPtr);
-	}
-
-	template < typename TRepeat >
-	inline bool
-	operator != (
-		Iter<TRepeat, MaxRepeatOccurrences> const &itA,
-		Iter<TRepeat, MaxRepeatOccurrences> const &itB)
-	{
-		if (itA._atEnd && itB._atEnd) return false;
-		if (itA._atEnd || itB._atEnd) return true;
-		return (itA.childPtr != itB.childPtr) || (itA.parentPtr != itB.parentPtr);
-	}
+    template < typename TRepeat >
+    inline bool
+    operator == (
+        Iter<TRepeat, MaxRepeatOccurrences> const &itA,
+        Iter<TRepeat, MaxRepeatOccurrences> const &itB)
+    {
+        if (itA._atEnd && itB._atEnd) return true;
+        if (itA._atEnd || itB._atEnd) return false;
+        return (itA.childPtr == itB.childPtr) && (itA.parentPtr == itB.parentPtr);
+    }
+
+    template < typename TRepeat >
+    inline bool
+    operator != (
+        Iter<TRepeat, MaxRepeatOccurrences> const &itA,
+        Iter<TRepeat, MaxRepeatOccurrences> const &itB)
+    {
+        if (itA._atEnd && itB._atEnd) return false;
+        if (itA._atEnd || itB._atEnd) return true;
+        return (itA.childPtr != itB.childPtr) || (itA.parentPtr != itB.parentPtr);
+    }
 //____________________________________________________________________________
 
 
-	template <typename TSTree, typename TSpec>
-	struct Size< Iter<TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > > {
-		typedef typename Size<TSTree>::Type Type;
-	};
+    template <typename TSTree, typename TSpec>
+    struct Size< Iter<TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > > {
+        typedef typename Size<TSTree>::Type Type;
+    };
 
-	template <typename TSTree>
-	struct Size< Iter<MaxRepeat<TSTree>, MaxRepeatOccurrences> > {
-		typedef typename Size<TSTree>::Type Type;
-	};
+    template <typename TSTree>
+    struct Size< Iter<MaxRepeat<TSTree>, MaxRepeatOccurrences> > {
+        typedef typename Size<TSTree>::Type Type;
+    };
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Iterator wrappers
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // Iterator wrappers
+    //////////////////////////////////////////////////////////////////////////////
 
-	// iterates over all supermaximal repeats
-	template <typename TSTree>
-	struct Iterator< TSTree, SuperMaxRepeats > {
-		typedef Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > > Type;
-	};
+    // iterates over all supermaximal repeats
+    template <typename TSTree>
+    struct Iterator< TSTree, SuperMaxRepeats > {
+        typedef Iter< TSTree, VSTree< BottomUp<SuperMaxRepeats> > > Type;
+    };
 //____________________________________________________________________________
 
-	// iterates over all maximal unique matches
-	template <typename TSTree>
-	struct Iterator< TSTree, SuperMaxRepeatsFast > {
-		typedef Iter< TSTree, VSTree< BottomUp<SuperMaxRepeatsFast> > > Type;
-	};
+    // iterates over all maximal unique matches
+    template <typename TSTree>
+    struct Iterator< TSTree, SuperMaxRepeatsFast > {
+        typedef Iter< TSTree, VSTree< BottomUp<SuperMaxRepeatsFast> > > Type;
+    };
 //____________________________________________________________________________
 
-	// iterates over all maximal repeat structures
-	template <typename TSTree, typename TSpec>
-	struct Iterator< TSTree, MaxRepeats_<TSpec> > {
-		typedef Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > Type;
-	};
+    // iterates over all maximal repeat structures
+    template <typename TSTree, typename TSpec>
+    struct Iterator< TSTree, MaxRepeats_<TSpec> > {
+        typedef Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > Type;
+    };
 //____________________________________________________________________________
 
-	// iterates over all maximal repeat pairs of a repeat structure
-
-	// Iterator of Iterator<TIndex, MaxRepeats>
-	template <typename TSTree, typename TSpec>
-	struct Iterator< Iter< TSTree, TSpec >, MaxRepeatOccurrences > {
-		typedef Iter< MaxRepeat<TSTree>, MaxRepeatOccurrences > Type;
-	};
-
-	template <typename TSTree, typename TSpec>
-	struct DefaultIteratorSpec< Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > > {
-		typedef MaxRepeatOccurrences Type;
-	};
-
-	// alternative (use MaxRepeat<TIndex> as a wrapper in between)
-	template <typename TSTree>
-	struct Iterator< MaxRepeat<TSTree>, MaxRepeatOccurrences > {
-		typedef Iter <MaxRepeat<TSTree>, MaxRepeatOccurrences > Type;
-	};
-
-	template <typename TSTree>
-	struct DefaultIteratorSpec< MaxRepeat<TSTree> > {
-		typedef MaxRepeatOccurrences Type;
-	};
+    // iterates over all maximal repeat pairs of a repeat structure
+
+    // Iterator of Iterator<TIndex, MaxRepeats>
+    template <typename TSTree, typename TSpec>
+    struct Iterator< Iter< TSTree, TSpec >, MaxRepeatOccurrences > {
+        typedef Iter< MaxRepeat<TSTree>, MaxRepeatOccurrences > Type;
+    };
+
+    template <typename TSTree, typename TSpec>
+    struct DefaultIteratorSpec< Iter< TSTree, VSTree< BottomUp<MaxRepeats_<TSpec> > > > > {
+        typedef MaxRepeatOccurrences Type;
+    };
+
+    // alternative (use MaxRepeat<TIndex> as a wrapper in between)
+    template <typename TSTree>
+    struct Iterator< MaxRepeat<TSTree>, MaxRepeatOccurrences > {
+        typedef Iter <MaxRepeat<TSTree>, MaxRepeatOccurrences > Type;
+    };
+
+    template <typename TSTree>
+    struct DefaultIteratorSpec< MaxRepeat<TSTree> > {
+        typedef MaxRepeatOccurrences Type;
+    };
 
 //}
 
diff --git a/seqan/index/index_esa_algs_multi.h b/seqan/index/index_esa_algs_multi.h
index 89a9838..abe2cc1 100644
--- a/seqan/index/index_esa_algs_multi.h
+++ b/seqan/index/index_esa_algs_multi.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,95 +35,65 @@
 
 namespace SEQAN_NAMESPACE_MAIN
 {
-	
-	//////////////////////////////////////////////////////////////////////////////
-	// more sophisticated algorithms on suffix trees of
-	// multiple sequences (generalized suffix tree)
-	//////////////////////////////////////////////////////////////////////////////
-
-
-/**
-.Spec.Mums Iterator:
-..cat:Index
-..general:Spec.BottomUp Iterator
-..summary:Iterator to search for all maximum unique matches.
-..signature:Iterator<TContainer, Mums>::Type
-..signature:Iter<TContainer, VSTree< BottomUp<Mums> > >
-..param.TContainer:Type of an index that can be iterated with a bottom-up iterator.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..include:seqan/index.h
-
-.Memfunc.Mums Iterator#Iterator
-..class:Spec.Mums Iterator
-..summary:Constructor
-..signature:Iterator(index[, minLength])
-..signature:Iterator(iterator)
-..param.index:An index object.
-..param.minLength:Minimum length of the maximal unique matches, default value is 1.
-..param.iterator:Another Mums iterator. (copy constructor)
-...type:Spec.Mums Iterator
-*/
-/*H
+
+    //////////////////////////////////////////////////////////////////////////////
+    // more sophisticated algorithms on suffix trees of
+    // multiple sequences (generalized suffix tree)
+    //////////////////////////////////////////////////////////////////////////////
+
+
+/*!
  * @class MumsIterator Mums Iterator
- * 
- * @extends vIterator
- * 
- * @headerfile seqan/index.h
- * 
+ * @extends BottomUpIterator
+ * @headerfile <seqan/index.h>
+ *
  * @brief Iterator to search for all maximum unique matches.
- * 
- * @signature Iterator<TContainer, Mums>::Type
- * @signature Iter<TContainer, VSTree< BottomUp<Mums> > >(index[, minLength])
- * @signature Iter<TContainer, VSTree< BottomUp<Mums> > >(iterator)
- * 
+ *
+ * @signature Iterator<TContainer, Mums>::Type;
+ * @signature template <typename TContainer>
+ *            class Iter<TContainer, VSTree< BottomUp<Mums> > >;
+ *
  * @tparam TContainer Type of an index that can be iterated with a bottom-up
  *                    iterator. Types: @link IndexEsa @endlink
  *
- * Demo: Demo.Mummy
- * 
- * Demo: Demo.Maximal Unique Matches
- *
- * @section Note Instead of using the class Iter directly we recommend to use the result of the metafunction 
- *               Iterator<TContainer, Mums>::Type (which is Iter<TContainer, VSTree< BottomUp<Mums> > >).
+ * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
+ *       Iterator&lt;TContainer, Mums>::Type (which is Iter&lt;TContainer, VSTree&lt; BottomUp&lt;Mums> > >).
  */
-/*H
- * @fn Iter<TContainer, VSTree< BottomUp<Mums> > >::Iter<TContainer, VSTree< BottomUp<Mums> > >
- *
- * brief The constructor
- *
- * @signature Iter<TContainer, VSTree< BottomUp<Mums> > >(index[, minLength])
- * @signature Iter<TContainer, VSTree< BottomUp<Mums> > >(iterator)
+/*!
+ * @fn MumsIterator::Iter
  *
- * @param index The index to be used for the iteration. Types: @link IndexEsa @endlink
+ * @brief The constructor.
  *
- * @param minLength Minimum length of the supermaximal repeats, default value is 1.
+ * @signature Iter::Iter(index[, minLength]);
+ * @signature Iter::Iter(iterator);
  *
- * @param iterator Another MultiMems iterator. Types: @link MultiMemsIterator @endlink
+ * @param[in] index     The index to be used for the iteration. Types: @link IndexEsa @endlink
+ * @param[in] minLength Minimum length of the supermaximal repeats, default value is 1.
+ * @param[in] iterator  Another MultiMems iterator. Types: @link MultiMemsIterator @endlink
  */
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Mums - generalized suffix tree version
-	//////////////////////////////////////////////////////////////////////////////
-
-	template < typename TSTree >
-	struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<Mums> > > > {
-		typedef PostorderEmptyEdges	Type;
-	};
-
-	template < typename TSTree >
-	class Iter< TSTree, VSTree< BottomUp<Mums> > >:
-		public Iter< TSTree, VSTree< BottomUp<> > > 
-	{
-	public:
-		typedef Iter< TSTree, VSTree< BottomUp<> > >	TBase;
-		typedef typename Size<TSTree>::Type				TSize;
-		typedef VectorSet_<TSize, Alloc<> >				TSeqSet;
+    //////////////////////////////////////////////////////////////////////////////
+    // Mums - generalized suffix tree version
+    //////////////////////////////////////////////////////////////////////////////
+
+    template < typename TSTree >
+    struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<Mums> > > > {
+        typedef PostorderEmptyEdges    Type;
+    };
+
+    template < typename TSTree >
+    class Iter< TSTree, VSTree< BottomUp<Mums> > >:
+        public Iter< TSTree, VSTree< BottomUp<> > >
+    {
+    public:
+        typedef Iter< TSTree, VSTree< BottomUp<> > >    TBase;
+        typedef typename Size<TSTree>::Type                TSize;
+        typedef VectorSet_<TSize, Alloc<> >                TSeqSet;
 //____________________________________________________________________________
 
-		TSize		minLength;
-		TSize		seqCount;
-		TSeqSet		seqSet;
+        TSize        minLength;
+        TSize        seqCount;
+        TSeqSet        seqSet;
 //____________________________________________________________________________
 
         Iter() :
@@ -131,148 +101,121 @@ namespace SEQAN_NAMESPACE_MAIN
             minLength(0),
             seqCount(0)
         {}
-        
-		Iter(TSTree &_tree):
-			TBase(_tree),
-			minLength(1),
-			seqCount(countSequences(_tree)),
-			seqSet(countSequences(_tree))
-		{
-			indexRequire(_tree, EsaBwt());
-			goNext(*this);	// the iterator starts in a suffix, i.e. not a MUM node (length(occ)<2<=seqCount)
-		}
-
-		Iter(TSTree &_tree, MinimalCtor):
-			TBase(_tree, MinimalCtor()) {}
-
-		Iter(TSTree &_tree, TSize _minLength):
-			TBase(_tree),
-			minLength(_minLength),
-			seqCount(countSequences(_tree)),
-			seqSet(countSequences(_tree))
-		{
-			indexRequire(_tree, EsaBwt());
-			goNext(*this);	// the iterator starts in a suffix, i.e. not a MUM node (length(occ)<2<=seqCount)
-		}
-
-		Iter(Iter const &_origin):
-			TBase((TBase const &)_origin),
-			minLength(_origin.minLength),
-			seqCount(countSequences(container(_origin))),
-			seqSet(countSequences(container(_origin))) {}
-	};
-
-	template < typename TSTree >
-	inline void goNext(Iter< TSTree, VSTree< BottomUp<Mums> > > &it) {
-		do {
-			goNext(it, PostorderEmptyEdges());
-		} while (!atEnd(it) && 
-			     !(	(countOccurrences(it) == it.seqCount) && 
-					(repLength(it) >= it.minLength) &&
-					isUnique(it, it.seqSet) && 
-					isLeftMaximal(it)) );
-	}
-
-
-
-	
-/**
-.Spec.MultiMems Iterator:
-..cat:Index
-..general:Spec.BottomUp Iterator
-..summary:Iterator to search for MultiMems.
-..signature:Iterator<TContainer, MultiMems>::Type
-..signature:Iter<TContainer, VSTree< BottomUp<MultiMems> > >
-..param.TContainer:Type of an index that can be iterated with a bottom-up iterator.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..include:seqan/index.h
-
-.Memfunc.MultiMems Iterator#Iterator
-..class:Spec.MultiMems Iterator
-..summary:Constructor
-..signature:Iterator(index[, minLength])
-..signature:Iterator(iterator)
-..param.index:An index object.
-..param.minLength:Minimum length of the multiple maximal exact matches, default value is 1.
-..param.iterator:Another MultiMems iterator. (copy constructor)
-...type:Spec.MultiMems Iterator
-*/
-/*H
+
+        Iter(TSTree &_tree):
+            TBase(_tree),
+            minLength(1),
+            seqCount(countSequences(_tree)),
+            seqSet(countSequences(_tree))
+        {
+            indexRequire(_tree, EsaBwt());
+            goNext(*this);    // the iterator starts in a suffix, i.e. not a MUM node (length(occ)<2<=seqCount)
+        }
+
+        Iter(TSTree &_tree, MinimalCtor):
+            TBase(_tree, MinimalCtor()) {}
+
+        Iter(TSTree &_tree, TSize _minLength):
+            TBase(_tree),
+            minLength(_minLength),
+            seqCount(countSequences(_tree)),
+            seqSet(countSequences(_tree))
+        {
+            indexRequire(_tree, EsaBwt());
+            goNext(*this);    // the iterator starts in a suffix, i.e. not a MUM node (length(occ)<2<=seqCount)
+        }
+
+        Iter(Iter const &_origin):
+            TBase((TBase const &)_origin),
+            minLength(_origin.minLength),
+            seqCount(countSequences(container(_origin))),
+            seqSet(countSequences(container(_origin))) {}
+    };
+
+    template < typename TSTree >
+    inline void goNext(Iter< TSTree, VSTree< BottomUp<Mums> > > &it) {
+        do {
+            goNext(it, PostorderEmptyEdges());
+        } while (!atEnd(it) &&
+                 !(    (countOccurrences(it) == it.seqCount) &&
+                    (repLength(it) >= it.minLength) &&
+                    isUnique(it, it.seqSet) &&
+                    isLeftMaximal(it)) );
+    }
+
+
+
+
+/*!
  * @class MultiMemsIterator Multi Mems Iterator
- * 
  * @extends BottomUpIterator
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief Iterator to search for MultiMems.
- * 
- * @signature Iterator<TContainer, MultiMems>::Type
- * @signature Iter<TContainer, VSTree< BottomUp<MultiMems> > >(index[, minLength])
- * @signature Iter<TContainer, VSTree< BottomUp<MultiMems> > >(iterator)
- * 
+ *
+ * @signature Iterator<TContainer, MultiMems>::Type;
+ * @signature template <typename TContainer>
+ *            class Iter<TContainer, VSTree< BottomUp<MultiMems> > >;
+ *
  * @tparam TContainer Type of an index that can be iterated with a bottom-up
  *                    iterator. Types: IndexEsa
  *
- * @section Note Instead of using the class Iter directly we recommend to use the result of the metafunction 
- *               Iterator<TContainer, MultiMems>::Type (which is Iter<TContainer, VSTree< BottomUp<MultiMems> > >).
+ * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
+ *       Iterator&lt;TContainer, MultiMems&gt;::Type (which is Iter<TContainer, VSTree< BottomUp<MultiMems&gt; &gt; &gt;).
  */
-/*H
- * @fn Iter<TContainer, VSTree< BottomUp<MultiMems> > >::Iter<TContainer, VSTree< BottomUp<MultiMems> > >
- *
- * brief The constructor
+/*!
+ * @fn MultiMemsIterator::Iter
+ * @brief The constructor
  *
- * @signature Iter<TContainer, VSTree< BottomUp<MultiMems> > >(index[, minLength])
- * @signature Iter<TContainer, VSTree< BottomUp<MultiMems> > >(iterator)
+ * @signature Iter::Iter(index[, minLength]);
+ * @signature Iter::Iter(iterator);
  *
- * @param index The index to be used for the iteration. Types: @link IndexEsa @endlink
- *
- * @param minLength Minimum length of the supermaximal repeats, default value is 1.
- *
- * @param iterator Another MultiMemsIterator iterator. Types: @link MultiMemsIterator @endlink
+ * @param[in] index     The index to be used for the iteration. Types: @link IndexEsa @endlink
+ * @param[in] minLength Minimum length of the supermaximal repeats, default value is 1.
+ * @param[in] iterator  Another MultiMemsIterator iterator. Types: @link MultiMemsIterator @endlink
  */
 
-	//////////////////////////////////////////////////////////////////////////////
-	// MultiMems
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // MultiMems
+    //////////////////////////////////////////////////////////////////////////////
+
+    // contains a set of fraction compounds
+    // one compound for each sequence
+    template <typename TValue, typename TSize>
+    struct FractionMultiCompound_ {
+        typedef FractionCompound_<TValue, TSize>    TCompound;
+        typedef String<TCompound>                    TSet;    // seqNo..unsigned, compound: bwt character->suffixes
 
-	// contains a set of fraction compounds
-	// one compound for each sequence
-	template <typename TValue, typename TSize>
-	struct FractionMultiCompound_ {
-		typedef FractionCompound_<TValue, TSize>	TCompound;
-		typedef String<TCompound>					TSet;	// seqNo..unsigned, compound: bwt character->suffixes
+        TSet    set;
+    };
 
-		TSet	set;
-	};
 
+    template < typename TSTree >
+    class Iter< TSTree, VSTree< BottomUp<MultiMems> > >:
+        public Iter< TSTree, VSTree< BottomUp<> > >
+    {
+    public:
+        typedef Iter< TSTree, VSTree< BottomUp<> > >    TBase;
+        typedef typename Value<TSTree>::Type            TValue;
+        typedef typename Size<TSTree>::Type                TSize;
 
-	template < typename TSTree >
-	class Iter< TSTree, VSTree< BottomUp<MultiMems> > >:
-		public Iter< TSTree, VSTree< BottomUp<> > > 
-	{
-	public:
-		typedef Iter< TSTree, VSTree< BottomUp<> > >	TBase;
-		typedef typename Value<TSTree>::Type			TValue;
-		typedef typename Size<TSTree>::Type				TSize;
+        typedef FractionMultiCompound_<TValue, TSize>    TMultiCompound;
+        typedef String<TMultiCompound, Block<> >        TSetStack;
+        typedef String<TSize>                            TPositionList;
 
-		typedef FractionMultiCompound_<TValue, TSize>	TMultiCompound;
-		typedef String<TMultiCompound, Block<> >		TSetStack;
-		typedef String<TSize>							TPositionList;
-		
-		typedef typename TMultiCompound::TSet			TSet;
-		typedef typename Iterator<TSet>::Type			TSetIterator;
+        typedef typename TMultiCompound::TSet            TSet;
+        typedef typename Iterator<TSet>::Type            TSetIterator;
 
-		typedef typename TBase::TStackEntry				TStackEntry;
+        typedef typename HistoryStackEntry_<TBase>::Type TStackEntry;
 
 //____________________________________________________________________________
 
-		TSize			minLength;
-		unsigned		minSupport;	// the support is the number of distinct sequences
-		unsigned		maxSupport;	// a repeat/match occurs in
-		TSetStack		setStack;
-		TPositionList	posList;	// this list is indexed just as SA is and contains the next entry's index
-		bool			canMerge;	// is false, if parent node appears after its first child on stack
+        TSize            minLength;
+        unsigned        minSupport;    // the support is the number of distinct sequences
+        unsigned        maxSupport;    // a repeat/match occurs in
+        TSetStack        setStack;
+        TPositionList    posList;    // this list is indexed just as SA is and contains the next entry's index
+        bool            canMerge;    // is false, if parent node appears after its first child on stack
 //____________________________________________________________________________
 
         Iter() :
@@ -282,525 +225,525 @@ namespace SEQAN_NAMESPACE_MAIN
             maxSupport(0),
             canMerge(0)
         {}
-        
-		Iter(TSTree &_index):
-			TBase(_index, MinimalCtor()),
-			minSupport(countSequences(_index)),
-			maxSupport(countSequences(_index)),
-			canMerge(true)
-		{
-			indexRequire(_index, EsaSA());
-			indexRequire(_index, EsaLcp());
-			indexRequire(_index, EsaBwt());
-			resize(posList, length(_index));
-
-			if (!empty(indexSA(_index))) 
-			{
-				TStackEntry e;
-				e.range.i1 = 0;
-				e.range.i2 = 0;
-				_dfsOnPush(*this, e);
-				goNext(*this);
-			}
-		}
-
-		Iter(TSTree &_tree, MinimalCtor):
-			TBase(_tree, MinimalCtor()) {}
-
-		Iter(TSTree &_index, TSize _minLength):
-			TBase(_index, MinimalCtor()),
-			minLength(_minLength),
-			minSupport(countSequences(_index)),
-			maxSupport(countSequences(_index)),
-			canMerge(true)
-		{
-			indexRequire(_index, EsaSA());
-			indexRequire(_index, EsaLcp());
-			indexRequire(_index, EsaBwt());
-			resize(posList, length(_index));
-
-			if (!empty(indexSA(_index))) 
-			{
-				TStackEntry e;
-				e.range.i1 = 0;
-				e.range.i2 = 0;
-				_dfsOnPush(*this, e);
-				goNext(*this);
-			}
-		}
-
-		Iter(Iter const &_origin):
-			TBase((TBase const &)_origin),
-			minLength(_origin.minLength),
-			minSupport(_origin.minSupport),
-			maxSupport(_origin.maxSupport),
-			setStack(_origin.setStack),
-			posList(_origin.posList),
-			canMerge(_origin.canMerge) {}
+
+        Iter(TSTree &_index):
+            TBase(_index, MinimalCtor()),
+            minSupport(countSequences(_index)),
+            maxSupport(countSequences(_index)),
+            canMerge(true)
+        {
+            indexRequire(_index, EsaSA());
+            indexRequire(_index, EsaLcp());
+            indexRequire(_index, EsaBwt());
+            resize(posList, length(_index));
+
+            if (!empty(indexSA(_index)))
+            {
+                TStackEntry e;
+                e.range.i1 = 0;
+                e.range.i2 = 0;
+                _dfsOnPush(*this, e);
+                goNext(*this);
+            }
+        }
+
+        Iter(TSTree &_tree, MinimalCtor):
+            TBase(_tree, MinimalCtor()) {}
+
+        Iter(TSTree &_index, TSize _minLength):
+            TBase(_index, MinimalCtor()),
+            minLength(_minLength),
+            minSupport(countSequences(_index)),
+            maxSupport(countSequences(_index)),
+            canMerge(true)
+        {
+            indexRequire(_index, EsaSA());
+            indexRequire(_index, EsaLcp());
+            indexRequire(_index, EsaBwt());
+            resize(posList, length(_index));
+
+            if (!empty(indexSA(_index)))
+            {
+                TStackEntry e;
+                e.range.i1 = 0;
+                e.range.i2 = 0;
+                _dfsOnPush(*this, e);
+                goNext(*this);
+            }
+        }
+
+        Iter(Iter const &_origin):
+            TBase((TBase const &)_origin),
+            minLength(_origin.minLength),
+            minSupport(_origin.minSupport),
+            maxSupport(_origin.maxSupport),
+            setStack(_origin.setStack),
+            posList(_origin.posList),
+            canMerge(_origin.canMerge) {}
 
 //____________________________________________________________________________
 
-		inline bool hasRepeats() 
-		{
-			if (length(setStack) < 2) return false;
-
-			TMultiCompound &child  = top(setStack);
-			TMultiCompound &parent = topPrev(setStack);
-
-			TValue prevKey = TValue();
-			TValue equalKey = TValue();
-
-			unsigned distinctSeqs = 0;
-			bool distinctKeys = false;
-
-			TSetIterator parentCompound	= begin(parent.set);
-			TSetIterator parentEnd		= end(parent.set);
-			TSetIterator childCompound	= begin(child.set);
-			TSetIterator childEnd		= end(child.set);
-
-			while (childCompound != childEnd && parentCompound != parentEnd)
-			{
-				int result = _haveMaximalRepeats(*childCompound, *parentCompound, equalKey);
-				if (result > 0) {
-					if (!distinctKeys && result == 1) {
-						if (distinctSeqs > 0 && prevKey != equalKey)
-							distinctKeys = true;						// there is a left maximal repeat
-						prevKey = equalKey;
-					} else
-						distinctKeys = true;
-
-					if (++distinctSeqs > minSupport && distinctKeys)	// if it is also a  repeat in at least
-						return true;									// minSequences distinct sequences then
-				}														// we have at least one repeat
-				++childCompound;
-				++parentCompound;
-			}
-			return false;
-		}
+        inline bool hasRepeats()
+        {
+            if (length(setStack) < 2) return false;
+
+            TMultiCompound &child  = back(setStack);
+            TMultiCompound &parent = backPrev(setStack);
+
+            TValue prevKey = TValue();
+            TValue equalKey = TValue();
+
+            unsigned distinctSeqs = 0;
+            bool distinctKeys = false;
+
+            TSetIterator parentCompound    = begin(parent.set);
+            TSetIterator parentEnd        = end(parent.set);
+            TSetIterator childCompound    = begin(child.set);
+            TSetIterator childEnd        = end(child.set);
+
+            while (childCompound != childEnd && parentCompound != parentEnd)
+            {
+                int result = _haveMaximalRepeats(*childCompound, *parentCompound, equalKey);
+                if (result > 0) {
+                    if (!distinctKeys && result == 1) {
+                        if (distinctSeqs > 0 && prevKey != equalKey)
+                            distinctKeys = true;                        // there is a left maximal repeat
+                        prevKey = equalKey;
+                    } else
+                        distinctKeys = true;
+
+                    if (++distinctSeqs > minSupport && distinctKeys)    // if it is also a  repeat in at least
+                        return true;                                    // minSequences distinct sequences then
+                }                                                        // we have at least one repeat
+                ++childCompound;
+                ++parentCompound;
+            }
+            return false;
+        }
 /*
-		inline TSize countRepeats() 
-		{
-			if (length(setStack) < 2) return 0;
-
-			TFractionCompound &child  = top(setStack);
-			TFractionCompound &parent = topPrev(setStack);
-
-			TSetIterator childFraction	= begin(child.set);
-			TSetIterator childEnd		= end(child.set);
-			TSetIterator parentFraction	= begin(parent.set);
-			TSetIterator parentEnd		= end(parent.set);
-
-			TSize sum = 0;
-			for(; childFraction != childEnd; ++childFraction) {
-				for(; parentFraction != parentEnd; ++parentFraction) {
-					if (keyOf(childFraction) != keyOf(parentFraction))
-						sum += (*childFraction).size * (*parentFraction).size;
-
-					sum += child.leftmost.size * (*parentFraction).size;
-				}
-				sum += (*childFraction).size * parent.leftmost.size;
-			}
-			sum += child.leftmost.size * parent.leftmost.size;
-			return sum;
-		}
+        inline TSize countRepeats()
+        {
+            if (length(setStack) < 2) return 0;
+
+            TFractionCompound &child  = back(setStack);
+            TFractionCompound &parent = backPrev(setStack);
+
+            TSetIterator childFraction    = begin(child.set);
+            TSetIterator childEnd        = end(child.set);
+            TSetIterator parentFraction    = begin(parent.set);
+            TSetIterator parentEnd        = end(parent.set);
+
+            TSize sum = 0;
+            for(; childFraction != childEnd; ++childFraction) {
+                for(; parentFraction != parentEnd; ++parentFraction) {
+                    if (keyOf(childFraction) != keyOf(parentFraction))
+                        sum += (*childFraction).size * (*parentFraction).size;
+
+                    sum += child.leftmost.size * (*parentFraction).size;
+                }
+                sum += (*childFraction).size * parent.leftmost.size;
+            }
+            sum += child.leftmost.size * parent.leftmost.size;
+            return sum;
+        }
 */
 //____________________________________________________________________________
 /*
-		inline void _dump() const {
-			::std::cerr << "SETSTACK of " << representative(*this) << ":" << ::std::endl;
-			typename Iterator<TSetStack const>::Type it = begin(setStack), itEnd = end(setStack);
-			while (it != itEnd) {
-				TSet const &set = (*it).set;
-				typename Iterator<TSet const>::Type sit = begin(set), sitEnd = end(set);
-
-				while (sit != sitEnd) {
-					::std::cerr << keyOf(sit) << "::";
-					typename TFractionCompound::TFractionHeader head = objectOf(sit);
-					TSize i = head.begin;
-					while (!_isSizeInval(i)) {
-						::std::cerr << i << "  ";
-						i = posList[i];
-					}
-					::std::cerr << ::std::endl;
-					++sit;
-				}
-
-				::std::cerr << "_________________________" << ::std::endl;
-				++it;
-			}
-		}
+        inline void _dump() const {
+            std::cerr << "SETSTACK of " << representative(*this) << ":" << std::endl;
+            typename Iterator<TSetStack const>::Type it = begin(setStack), itEnd = end(setStack);
+            while (it != itEnd) {
+                TSet const &set = (*it).set;
+                typename Iterator<TSet const>::Type sit = begin(set), sitEnd = end(set);
+
+                while (sit != sitEnd) {
+                    std::cerr << keyOf(sit) << "::";
+                    typename TFractionCompound::TFractionHeader head = objectOf(sit);
+                    TSize i = head.begin;
+                    while (!_isSizeInval(i)) {
+                        std::cerr << i << "  ";
+                        i = posList[i];
+                    }
+                    std::cerr << std::endl;
+                    ++sit;
+                }
+
+                std::cerr << "_________________________" << std::endl;
+                ++it;
+            }
+        }
 */
-	};
-
-	// add bwt partitions of child to parent node
-	template < typename TSTree, typename TSpec, typename TValue, typename TSize >
-	inline void _fractionMerge(
-		Iter<TSTree, VSTree< BottomUp<TSpec> > > &it, 
-		FractionMultiCompound_<TValue, TSize> &parent,
-		FractionMultiCompound_<TValue, TSize> &child)
-	{
-		typedef FractionMultiCompound_<TValue, TSize>	TCompound;
-		typedef typename TCompound::TSet				TSet;
-		typedef typename Iterator<TSet, Standard>::Type	TSetIterator;
-
-		TSetIterator parentCompound	= begin(parent.set, Standard());
-		TSetIterator parentEnd		= end(parent.set, Standard());
-		TSetIterator childCompound	= begin(child.set, Standard());
-		TSetIterator childEnd		= end(child.set, Standard());
-
-		while (childCompound != childEnd && parentCompound != parentEnd)
-		{
-			// append child compound to parent compound
-			_fractionMerge(it, *parentCompound, *childCompound);
-			++childCompound;
-			++parentCompound;
-		}
-	}
-
-	template < typename TSTree >
-	inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<MultiMems> > > &it) 
-	{
-		typedef Iter<TSTree, VSTree< BottomUp<> > > TBase;
-		_dfsOnLeaf((TBase&)it);
-
-		typedef typename Value<TSTree>::Type		TValue;
-		typedef typename Size<TSTree>::Type			TSize;
-		typedef typename SAValue<TSTree>::Type		TSAValue;
-		typedef FractionHeader_<TSize>				TFractionHeader;
-		typedef Pair<TValue, TFractionHeader>		TFraction;
-		//typedef typename Set<TFraction>::Type		TFractionSet;
-
-		typedef FractionCompound_<TValue, TSize>	TCompound;
-		//typedef Pair<unsigned, TCompound>			TCompoundPair;
-		//typedef typename Set<TCompoundPair>::Type	TSet;
-
-		push(it.setStack);
-
-		TSTree &index = container(it);
-
-		TSize		gPos = posGlobalize(_dfsRange(it).i1, stringSetLimits(index));
-		TSAValue	lPos;
-		posLocalize(lPos, _dfsRange(it).i1, stringSetLimits(index));
-
-		TCompound &compound = top(it.setStack).set[getValueI1(lPos)];
-		if (!posAtFirstLocal(lPos))
-			insert(
-				TFraction(
-					bwtAt(gPos, container(it)),
-					TFractionHeader(gPos, gPos, 1)), 
-				compound.set);
-		else
-			compound.leftmost = TFractionHeader(gPos, gPos, 1);
-
-		_setSizeInval(it.posList[gPos]);
+    };
+
+    // add bwt partitions of child to parent node
+    template < typename TSTree, typename TSpec, typename TValue, typename TSize >
+    inline void _fractionMerge(
+        Iter<TSTree, VSTree< BottomUp<TSpec> > > &it,
+        FractionMultiCompound_<TValue, TSize> &parent,
+        FractionMultiCompound_<TValue, TSize> &child)
+    {
+        typedef FractionMultiCompound_<TValue, TSize>    TCompound;
+        typedef typename TCompound::TSet                TSet;
+        typedef typename Iterator<TSet, Standard>::Type    TSetIterator;
+
+        TSetIterator parentCompound    = begin(parent.set, Standard());
+        TSetIterator parentEnd        = end(parent.set, Standard());
+        TSetIterator childCompound    = begin(child.set, Standard());
+        TSetIterator childEnd        = end(child.set, Standard());
+
+        while (childCompound != childEnd && parentCompound != parentEnd)
+        {
+            // append child compound to parent compound
+            _fractionMerge(it, *parentCompound, *childCompound);
+            ++childCompound;
+            ++parentCompound;
+        }
+    }
+
+    template < typename TSTree >
+    inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<MultiMems> > > &it)
+    {
+        typedef Iter<TSTree, VSTree< BottomUp<> > > TBase;
+        _dfsOnLeaf((TBase&)it);
+
+        typedef typename Value<TSTree>::Type        TValue;
+        typedef typename Size<TSTree>::Type            TSize;
+        typedef typename SAValue<TSTree>::Type        TSAValue;
+        typedef FractionHeader_<TSize>                TFractionHeader;
+        typedef Pair<TValue, TFractionHeader>        TFraction;
+        //typedef typename Set<TFraction>::Type        TFractionSet;
+
+        typedef FractionCompound_<TValue, TSize>    TCompound;
+        //typedef Pair<unsigned, TCompound>            TCompoundPair;
+        //typedef typename Set<TCompoundPair>::Type    TSet;
+
+        push(it.setStack);
+
+        TSTree &index = container(it);
+
+        TSize        gPos = posGlobalize(_dfsRange(it).i1, stringSetLimits(index));
+        TSAValue    lPos;
+        posLocalize(lPos, _dfsRange(it).i1, stringSetLimits(index));
+
+        TCompound &compound = back(it.setStack).set[getValueI1(lPos)];
+        if (!posAtFirstLocal(lPos))
+            insert(
+                TFraction(
+                    bwtAt(gPos, container(it)),
+                    TFractionHeader(gPos, gPos, 1)),
+                compound.set);
+        else
+            compound.leftmost = TFractionHeader(gPos, gPos, 1);
+
+        _setSizeInval(it.posList[gPos]);
 /*
-		::std::cerr << "LEAF ";
-		_dumpHistoryStack(it);
-		it._dump();
-*/	}
+        std::cerr << "LEAF ";
+        _dumpHistoryStack(it);
+        it._dump();
+*/    }
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// maximal repeat representation
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // maximal repeat representation
+    //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TSTree>
-	struct MultiMem {
-//		Iter< TSTree, VSTree<BottomUp<MultiMems> > > &it;
-	};
+    template <typename TSTree>
+    struct MultiMem {
+//        Iter< TSTree, VSTree<BottomUp<MultiMems> > > &it;
+    };
 
-	template <typename TSTree>
-	struct Value< MultiMem<TSTree> > {
-		typedef Pair< typename SAValue<TSTree>::Type > Type;
-	};
+    template <typename TSTree>
+    struct Value< MultiMem<TSTree> > {
+        typedef Pair< typename SAValue<TSTree>::Type > Type;
+    };
 
-	template <typename TSTree>
-	struct Size< MultiMem<TSTree> > {
-		typedef typename Size<TSTree>::Type Type;
-	};
+    template <typename TSTree>
+    struct Size< MultiMem<TSTree> > {
+        typedef typename Size<TSTree>::Type Type;
+    };
 
 
-	template <typename TSTree>
-	inline typename Size< MultiMem<TSTree> >::Type 
-	length(MultiMem<TSTree> const &repeat) {
-		return repeat.it.countRepeats();
-	}
+    template <typename TSTree>
+    inline typename Size< MultiMem<TSTree> >::Type
+    length(MultiMem<TSTree> const &repeat) {
+        return repeat.it.countRepeats();
+    }
 
 /*
-	template <typename TSTree>
-	inline typename Iterator< MultiMem<TSTree> >::Type 
-	begin(MultiMem<TSTree> &repeat) {
-		return Iterator< MultiMem<TSTree> >::Type(repeat.it);
-	}
-
-	template <typename TSTree>
-	inline typename Iterator< MultiMem<TSTree> const >::Type 
-	begin(MultiMem<TSTree> const &repeat) {
-		return Iterator< MultiMem<TSTree> >::Type(repeat.it);
-	}
+    template <typename TSTree>
+    inline typename Iterator< MultiMem<TSTree> >::Type
+    begin(MultiMem<TSTree> &repeat) {
+        return Iterator< MultiMem<TSTree> >::Type(repeat.it);
+    }
+
+    template <typename TSTree>
+    inline typename Iterator< MultiMem<TSTree> const >::Type
+    begin(MultiMem<TSTree> const &repeat) {
+        return Iterator< MultiMem<TSTree> >::Type(repeat.it);
+    }
 */
 
 
-	template <typename TSTree>
-	class Iter< MultiMem<TSTree>, MultiMemOccurences > {
-	public:
-
-		typedef typename Value<TSTree>::Type	TValue;
-		typedef typename Size<TSTree>::Type		TSize;
-		typedef typename SAValue<TSTree>::Type	TSAValue;
-		typedef	Pair<TSAValue>					TPair;
-
-		typedef FractionCompound_<TValue, TSize> const	TFractionCompound;
-		typedef typename TFractionCompound::TSet const	TSet;
-		typedef typename Iterator<TSet>::Type			TSetIterator;
-
-		typedef Iter<TSTree, VSTree<BottomUp<MultiMems> > >	const	TIterator;
-		typedef typename TIterator::TPositionList const				TPositionList;
-
-		TIterator	*mmemIt;
-		bool		_atEnd;
-		unsigned	seqCount;
-		TPair		tmp;
-	
-		
-		// for every sequence there is a SubState stucture
-		// storing the current enumeration state
-		// that is necessary to enumerate every combination
-		// of left maximal multi match
-
-		struct SubState 
-		{
-			SubState			*prevState;
-			TPositionList		*posList;
-			TFractionCompound	*child, *parent;
-			TSize				childPtr, parentPtr;			// per seq. suffix iterators
-			TSetIterator		childFraction,  childBegin,  childEnd;
-			TSetIterator		parentFraction, parentBegin, parentEnd;	
-			bool				leftmostChild, leftmostParent;	// use undef. bwt (leftmost) set
-			TValue				leftChar;						// are the keys of seq[1..i] equal?
-			bool				charsEqual;
-
-			inline void _updateLeftMaximality() {
-				if (prevState)
-					charsEqual = prevState->charsEqual && (leftChar == keyOf(childFraction));
-			}
-
-			inline bool _innerStep()
-			{
-				if (_isSizeInval(childPtr = ((*posList)[childPtr]))) {
-					if (_isSizeInval(parentPtr = (*posList)[parentPtr])) {
-						parentPtr = objectOf(parentFraction).begin;
-						return false;
-					}
-					childPtr = objectOf(childFraction).begin;
-				}
-				return true;
-			}
-
-			inline void _firstParentFraction()
-			{
-				parentBegin		= parentFraction	= begin(parent->set);
-				parentEnd		= end(parent->set);
-
-				if (parentFraction != parentEnd) {
-					leftmostParent = false;
-					parentPtr = objectOf(parentFraction).begin;
-				} else {
-					leftmostParent = true;
-					parentPtr = parent->leftmost.begin;
-				}
-
-				leftChar = keyOf(parentFraction);
-			}
-
-			inline void _firstChildFraction() 
-			{
-				childBegin		= childFraction		= begin(child->set);
-				childEnd		= end(child->set);
-
-				if (childFraction != childEnd) {
-					leftmostChild = false;
-					childPtr = objectOf(childFraction).begin;
-				} else {
-					leftmostChild = true;
-					childPtr = child->leftmost.begin;
-				}
-			}
-
-			inline bool _nextParentFraction() 
-			{
-				if (leftmostParent) return false;
-
-				if (++parentFraction == parentEnd) {
-					if (parent->leftmost.size > 0) {
-						leftmostParent = true;
-						parentPtr = parent->leftmost.begin;
-					} else
-						return false;
-				} else
-					parentPtr = objectOf(parentFraction).begin;
-
-				return true;
-			}
-
-			inline bool _nextChildFraction() 
-			{
-				if (leftmostChild) return false;
-
-				if (++childFraction == childEnd) {
-					if (child->leftmost.size > 0) {
-						leftmostChild = true;
-						childPtr = child->leftmost.begin;
-					} else
-						return false;
-				} else
-					childPtr = objectOf(childFraction).begin;
-
-				return true;
-			}
-
-			// single per-sequence enumeration step
-			inline bool _outerStep() 
-			{
-				if (!_nextChildFraction()) {
-					_firstChildFraction();
-					if (!_nextParentFraction()) {
-						_firstParentFraction();
-						return false;
-					}
-				}
-				return true;
-			}
-
-		};
-
-		String<SubState>	subState;
+    template <typename TSTree>
+    class Iter< MultiMem<TSTree>, MultiMemOccurences > {
+    public:
+
+        typedef typename Value<TSTree>::Type    TValue;
+        typedef typename Size<TSTree>::Type        TSize;
+        typedef typename SAValue<TSTree>::Type    TSAValue;
+        typedef    Pair<TSAValue>                    TPair;
+
+        typedef FractionCompound_<TValue, TSize> const    TFractionCompound;
+        typedef typename TFractionCompound::TSet const    TSet;
+        typedef typename Iterator<TSet>::Type            TSetIterator;
+
+        typedef Iter<TSTree, VSTree<BottomUp<MultiMems> > >    const    TIterator;
+        typedef typename TIterator::TPositionList const                TPositionList;
+
+        TIterator    *mmemIt;
+        bool        _atEnd;
+        unsigned    seqCount;
+        TPair        tmp;
+
+
+        // for every sequence there is a SubState stucture
+        // storing the current enumeration state
+        // that is necessary to enumerate every combination
+        // of left maximal multi match
+
+        struct SubState
+        {
+            SubState            *prevState;
+            TPositionList        *posList;
+            TFractionCompound    *child, *parent;
+            TSize                childPtr, parentPtr;            // per seq. suffix iterators
+            TSetIterator        childFraction,  childBegin,  childEnd;
+            TSetIterator        parentFraction, parentBegin, parentEnd;
+            bool                leftmostChild, leftmostParent;    // use undef. bwt (leftmost) set
+            TValue                leftChar;                        // are the keys of seq[1..i] equal?
+            bool                charsEqual;
+
+            inline void _updateLeftMaximality() {
+                if (prevState)
+                    charsEqual = prevState->charsEqual && (leftChar == keyOf(childFraction));
+            }
+
+            inline bool _innerStep()
+            {
+                if (_isSizeInval(childPtr = ((*posList)[childPtr]))) {
+                    if (_isSizeInval(parentPtr = (*posList)[parentPtr])) {
+                        parentPtr = objectOf(parentFraction).begin;
+                        return false;
+                    }
+                    childPtr = objectOf(childFraction).begin;
+                }
+                return true;
+            }
+
+            inline void _firstParentFraction()
+            {
+                parentBegin        = parentFraction    = begin(parent->set);
+                parentEnd        = end(parent->set);
+
+                if (parentFraction != parentEnd) {
+                    leftmostParent = false;
+                    parentPtr = objectOf(parentFraction).begin;
+                } else {
+                    leftmostParent = true;
+                    parentPtr = parent->leftmost.begin;
+                }
+
+                leftChar = keyOf(parentFraction);
+            }
+
+            inline void _firstChildFraction()
+            {
+                childBegin        = childFraction        = begin(child->set);
+                childEnd        = end(child->set);
+
+                if (childFraction != childEnd) {
+                    leftmostChild = false;
+                    childPtr = objectOf(childFraction).begin;
+                } else {
+                    leftmostChild = true;
+                    childPtr = child->leftmost.begin;
+                }
+            }
+
+            inline bool _nextParentFraction()
+            {
+                if (leftmostParent) return false;
+
+                if (++parentFraction == parentEnd) {
+                    if (parent->leftmost.size > 0) {
+                        leftmostParent = true;
+                        parentPtr = parent->leftmost.begin;
+                    } else
+                        return false;
+                } else
+                    parentPtr = objectOf(parentFraction).begin;
+
+                return true;
+            }
+
+            inline bool _nextChildFraction()
+            {
+                if (leftmostChild) return false;
+
+                if (++childFraction == childEnd) {
+                    if (child->leftmost.size > 0) {
+                        leftmostChild = true;
+                        childPtr = child->leftmost.begin;
+                    } else
+                        return false;
+                } else
+                    childPtr = objectOf(childFraction).begin;
+
+                return true;
+            }
+
+            // single per-sequence enumeration step
+            inline bool _outerStep()
+            {
+                if (!_nextChildFraction()) {
+                    _firstChildFraction();
+                    if (!_nextParentFraction()) {
+                        _firstParentFraction();
+                        return false;
+                    }
+                }
+                return true;
+            }
+
+        };
+
+        String<SubState>    subState;
 
         Iter() :
             mmemIt(),
             _atEnd(true),
             seqCount(0)
         {}
-        
-		inline Iter(Iter<TSTree, VSTree<BottomUp<MultiMems> > > const &_maxIt):
-			mmemIt(&_maxIt),
-			seqCount(countSequences(container(_maxIt)))
-		{
-			_init();
-		}
-
-		inline bool _isLeftMaximal() {
-			return !subState[seqCount - 1].charsEqual;
-		}
-		
-		// inner enumeration
-		inline bool _innerStep() {
-			for(unsigned seq = 0; seq < seqCount; ++seq)
-				if (subState[seq]._innerStep()) return true;
-			return false;
-		}
-
-		inline bool _outerStepNoCheck() {
-			for(unsigned seq = 0; seq < seqCount; ++seq)
-				if (subState[seq]._outerStep()) return true;
-			return false;
-		}
-
-		// outer enumeration
-		inline bool _outerStep() {
-			while (!((_atEnd = !_outerStepNoCheck()) || _isLeftMaximal())) ;
-			return !_atEnd;
-		}
-
-		inline void _init() 
-		{
-			if (length(mmemIt->setStack) < 2) {
-				_atEnd = true;
-				return;
-			}
-
-			resize(subState, seqCount);
-			SubState *prev = NULL;
-			for(unsigned seq = 0; seq < seqCount; ++seq)
-			{
-				SubState &state = subState[seq];
-
-				state.prevState = prev;
-				state.posList = &(mmemIt->posList);
-				state.parent = &(topPrev(mmemIt->setStack).set[seq]);
-				state.child = &(top(mmemIt->setStack).set[seq]);
-
-				state._firstChildFraction();
-				state._firstParentFraction();
-
-				prev = &state;
-			}
-
-			_atEnd = false;
-			while (!(_isLeftMaximal() || (_atEnd = !_outerStep()))) ;
-		}
-	};
-
-
-	template < typename TRepeat >
-	inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type &
-	value(Iter<TRepeat, MultiMemOccurences> const &it)  {
-		return it.tmp;
-	}
-
-	template < typename TRepeat >
-	inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type &
-	value(Iter<TRepeat, MultiMemOccurences> &it)  {
-		return it.tmp;
-	}
+
+        inline Iter(Iter<TSTree, VSTree<BottomUp<MultiMems> > > const &_maxIt):
+            mmemIt(&_maxIt),
+            seqCount(countSequences(container(_maxIt)))
+        {
+            _init();
+        }
+
+        inline bool _isLeftMaximal() {
+            return !subState[seqCount - 1].charsEqual;
+        }
+
+        // inner enumeration
+        inline bool _innerStep() {
+            for(unsigned seq = 0; seq < seqCount; ++seq)
+                if (subState[seq]._innerStep()) return true;
+            return false;
+        }
+
+        inline bool _outerStepNoCheck() {
+            for(unsigned seq = 0; seq < seqCount; ++seq)
+                if (subState[seq]._outerStep()) return true;
+            return false;
+        }
+
+        // outer enumeration
+        inline bool _outerStep() {
+            while (!((_atEnd = !_outerStepNoCheck()) || _isLeftMaximal())) ;
+            return !_atEnd;
+        }
+
+        inline void _init()
+        {
+            if (length(mmemIt->setStack) < 2) {
+                _atEnd = true;
+                return;
+            }
+
+            resize(subState, seqCount);
+            SubState *prev = NULL;
+            for(unsigned seq = 0; seq < seqCount; ++seq)
+            {
+                SubState &state = subState[seq];
+
+                state.prevState = prev;
+                state.posList = &(mmemIt->posList);
+                state.parent = &(backPrev(mmemIt->setStack).set[seq]);
+                state.child = &(back(mmemIt->setStack).set[seq]);
+
+                state._firstChildFraction();
+                state._firstParentFraction();
+
+                prev = &state;
+            }
+
+            _atEnd = false;
+            while (!(_isLeftMaximal() || (_atEnd = !_outerStep()))) ;
+        }
+    };
+
+
+    template < typename TRepeat >
+    inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type &
+    value(Iter<TRepeat, MultiMemOccurences> const &it)  {
+        return it.tmp;
+    }
+
+    template < typename TRepeat >
+    inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type &
+    value(Iter<TRepeat, MultiMemOccurences> &it)  {
+        return it.tmp;
+    }
 
 //TODO:fix me
-	template < typename TRepeat >
-	inline Iter<TRepeat, MultiMemOccurences> &
-	goNext(Iter<TRepeat, MultiMemOccurences> &it)  {
-		if (it._innerStep()) {
-//			it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
-//			it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
-			return it;
-		}
-		if (it._outerStep()) {
-//			it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
-//			it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
-		}
-		return it;
-	}
-
-	template < typename TRepeat >
-	inline bool atEnd(Iter<TRepeat, MultiMemOccurences> const &it) {
-		return it._atEnd;
-	}
-
-	template < typename TRepeat >
-	inline bool atEnd(Iter<TRepeat, MultiMemOccurences> &it) {
-		return it._atEnd;
-	}
-
-
-	template <typename TSTree>
-	struct Iterator< MultiMem<TSTree> > {
-		typedef Iter<MultiMem<TSTree>, MultiMemOccurences> Type;
-	};
-
-	template <typename TSTree>
-	struct Size< Iter<MultiMem<TSTree>, MultiMemOccurences> > {
-		typedef typename Size<TSTree>::Type Type;
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Iterator wrappers
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <typename TObject>
-	struct Iterator< TObject, Mums > {
-		typedef Iter< TObject, VSTree< BottomUp<Mums> > > Type;
-	};
+    template < typename TRepeat >
+    inline Iter<TRepeat, MultiMemOccurences> &
+    goNext(Iter<TRepeat, MultiMemOccurences> &it)  {
+        if (it._innerStep()) {
+//            it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
+//            it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
+            return it;
+        }
+        if (it._outerStep()) {
+//            it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
+//            it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
+        }
+        return it;
+    }
+
+    template < typename TRepeat >
+    inline bool atEnd(Iter<TRepeat, MultiMemOccurences> const &it) {
+        return it._atEnd;
+    }
+
+    template < typename TRepeat >
+    inline bool atEnd(Iter<TRepeat, MultiMemOccurences> &it) {
+        return it._atEnd;
+    }
+
+
+    template <typename TSTree>
+    struct Iterator< MultiMem<TSTree> > {
+        typedef Iter<MultiMem<TSTree>, MultiMemOccurences> Type;
+    };
+
+    template <typename TSTree>
+    struct Size< Iter<MultiMem<TSTree>, MultiMemOccurences> > {
+        typedef typename Size<TSTree>::Type Type;
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Iterator wrappers
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <typename TObject>
+    struct Iterator< TObject, Mums > {
+        typedef Iter< TObject, VSTree< BottomUp<Mums> > > Type;
+    };
 
 //}
 
diff --git a/seqan/index/index_esa_base.h b/seqan/index/index_esa_base.h
index 08a6fd4..e321b43 100644
--- a/seqan/index/index_esa_base.h
+++ b/seqan/index/index_esa_base.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,114 +39,69 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	// dfs order
-	struct Preorder_;
-	struct Postorder_;
-
-	template <typename TDfsOrder = Postorder_, typename THideEmptyEdges = True>
-	struct VSTreeIteratorTraits {
-		typedef TDfsOrder DfsOrder;
-		typedef THideEmptyEdges HideEmptyEdges;
-	};
-
-/**
-.Tag.DFS Order
-..summary:Pre/postorder selection for depth-first search.
-..cat:Index
-..description:
-These tags are given to @Function.goNext@ and trigger post-order or pre-order traversal of a suffix tree.
-In case of $PreorderEmptyEdges$ and $PostorderEmptyEdges$, the empty edges are also traversed.
-..tag.Preorder:Visit the node before its children.
-..tag.Postorder:Visit the node after its children.
-..tag.PreorderEmptyEdges:Visit the node before its children, visit empty edges.
-..tag.PostorderEmptyEdges:Visit the node after its children, visit empty edges.
-..include:seqan/index.h
-*/
+    // dfs order
+    struct Preorder_;
+    struct Postorder_;
+
+    template <typename TDfsOrder = Postorder_, typename THideEmptyEdges = True>
+    struct VSTreeIteratorTraits {
+        typedef TDfsOrder DfsOrder;
+        typedef THideEmptyEdges HideEmptyEdges;
+    };
+
 /*!
  * @defgroup DfsOrder DFS Order
- * 
  * @brief Pre/postorder selection for depth-first search.
- * 
- * These tags are given to @link goNext @endlink and trigger post-order or pre-
+ *
+ * These tags are given to @link InputIteratorConcept#goNext @endlink and trigger post-order or pre-
  * order traversal of a suffix tree. In case of <tt>PreorderEmptyEdges</tt> and
  * <tt>PostorderEmptyEdges</tt>, the empty edges are also traversed.
- * 
+ *
  * @tag DfsOrder#Preorder
- * 
  * @brief Visit the node before its children.
- * 
+ *
  * @tag DfsOrder#PostorderEmptyEdges
- * 
  * @brief Visit the node after its children, visit empty edges.
- * 
+ *
  * @tag DfsOrder#PreorderEmptyEdges
- * 
  * @brief Visit the node before its children, visit empty edges.
- * 
+ *
  * @tag DfsOrder#Postorder
- * 
  * @brief Visit the node after its children.
  */
-	// predefined iterator traits
-	struct Preorder:			VSTreeIteratorTraits<Preorder_,  True> {};
-	struct Postorder:			VSTreeIteratorTraits<Postorder_, True> {};
-	struct PreorderEmptyEdges:	VSTreeIteratorTraits<Preorder_,  False> {};	// also iterate over
-	struct PostorderEmptyEdges:	VSTreeIteratorTraits<Postorder_, False> {};	// empty edges (with $-label)
-
-	// traits for TopDown iterators (w/o ParentLinks) for which postorder/preorder is ignored
-	struct HideEmptyEdges:		VSTreeIteratorTraits<Postorder_, True> {};
-	struct EmptyEdges:			VSTreeIteratorTraits<Postorder_, False> {};	// empty edges (with $-label)
-	
-	// MultiMems are more specialized MaxRepeats
-	template <typename TSpec = void>
-	struct MaxRepeats_;	// base class
-	struct MultiMems_;	// subclass tag
-
-
-
-	// virtual suffix tree iterators
-	template <typename TSpec = void>
-	struct VSTree;
-
-/**
-.Tag.TopDown
-..summary:Tag that specifies a @Spec.VSTree Iterator@ to traverse the virtual string tree from the root towards the leafs.
-..cat:Index
-..tag.Preorder:Pre-order traversal of the virtual string tree.
-..tag.Postorder:Post-order traversal of the virtual string tree.
-..tag.ParentLinks:A top down iterator with the possibility to go back up again.
-..example
-...text:The following example shows how a the @Tag.TopDown@ tag is used.
-...file:demos/index/index_begin_atEnd_representative.cpp
-...output:
-A
-AA
-ATAA
-TA
-TAA
-TATAA
---------------------------------
-AA
-ATAA
-A
-TAA
-TATAA
-TA
+    // predefined iterator traits
+    struct Preorder:            VSTreeIteratorTraits<Preorder_,  True> {};
+    struct Postorder:            VSTreeIteratorTraits<Postorder_, True> {};
+    struct PreorderEmptyEdges:    VSTreeIteratorTraits<Preorder_,  False> {};    // also iterate over
+    struct PostorderEmptyEdges:    VSTreeIteratorTraits<Postorder_, False> {};    // empty edges (with $-label)
+
+    // traits for TopDown iterators (w/o ParentLinks) for which postorder/preorder is ignored
+    struct HideEmptyEdges:        VSTreeIteratorTraits<Postorder_, True> {};
+    struct EmptyEdges:            VSTreeIteratorTraits<Postorder_, False> {};    // empty edges (with $-label)
+
+    // MultiMems are more specialized MaxRepeats
+    template <typename TSpec = void>
+    struct MaxRepeats_;    // base class
+    struct MultiMems_;    // subclass tag
+
+
+
+    // virtual suffix tree iterators
+    template <typename TSpec = void>
+    struct VSTree;
 
-*/
 /*!
- * @defgroup TopDown
- * 
+ * @defgroup TopDown Top-Down Iteration
  * @brief Tag that specifies a @link VSTreeIterator @endlink to traverse the virtual string tree from the root towards
  *        the leafs.
- * 
+ *
  * @section Examples
- * 
+ *
  * The following example shows how a the @link TopDown @endlink tag is used.
- * 
- * @include demos/index/index_begin_atEnd_representative.cpp
- * 
- * @code{.txt}
+ *
+ * @include demos/dox/index/begin_atEnd_representative.cpp
+ *
+ * @code{.output}
  * A
  * AA
  * ATAA
@@ -159,56 +115,37 @@ TA
  * TAA
  * TATAA
  * TA
- * 
  * @endcode
  *
  * @tag TopDown#ParentLinks
- * 
  * @brief A top down iterator with the possibility to go back up again.
- * 
+ *
  * @tag TopDown#Preorder
- * 
  * @brief Pre-order traversal of the virtual string tree.
- * 
+ *
  * @tag TopDown#Postorder
- * 
  * @brief Post-order traversal of the virtual string tree.
  */
 
-		// top down traversal iterators
-		template <typename TSpec = Preorder>
-		struct TopDown {};					// starts in the suffix tree root and can go down and go right
-
-			// allows an top-down iterator to go up
-			template < typename TSpec = Preorder >
-			struct ParentLinks {};			// .. can also go up
-
-/**
-.Tag.BottomUp
-..summary:Tag that specifies a @Spec.VSTree Iterator@ to traverse the virtual string tree from the root towards the leafs.
-..cat:Index
-..tag.Postorder:Post-order traversal of the virtual string tree.
-..example
-...text:The following example shows how a the @Tag.BottomUp@ tag is used.
-...file:demos/index/index_begin_atEnd_representative_bottomUp.cpp
-...output:
-AA
-ATAA
-A
-TAA
-TATAA
-TA
-*/
+        // top down traversal iterators
+        template <typename TSpec = Preorder>
+        struct TopDown {};                    // starts in the suffix tree root and can go down and go right
+
+            // allows an top-down iterator to go up
+            template < typename TSpec = Preorder >
+            struct ParentLinks {};            // .. can also go up
+
 /*!
- * @defgroup BottomUp Bottom Up
- * 
+ * @defgroup BottomUp Bottom-Up Iteration
  * @brief Tag that specifies a @link VSTreeIterator @endlink to traverse the
  *        virtual string tree from the root towards the leafs.
- * 
+ *
  * @section Examples
  *
- * The following example shows how the @link Bottom Up @endlink tag is used.
- * @include demos/index/index_begin_atEnd_representative_bottomUp.cpp
+ * The following example shows how the @link BottomUp @endlink tag is used.
+ *
+ * @include demos/dox/index/begin_atEnd_representative_bottomUp.cpp
+ *
  * @code{.txt}
  * AA
  * ATAA
@@ -219,454 +156,400 @@ TA
  * @endcode
  *
  * @tag BottomUp#Postorder
- * 
  * @brief Post-order traversal of the virtual string tree.
  */
-		// bottom up traversal iterators
-		template <typename TSpec = Postorder>
-		struct BottomUp {};					// starts in the first node of a depth-first-search and can go next
-
-			struct	SuperMaxRepeats;					// maximal repeat and not part of a longer repeat
-			struct	SuperMaxRepeatsFast;
-			struct	Mums;								// Maximal Unique Match (unique in every sequence)
-
-			typedef MaxRepeats_<void>		MaxRepeats;	// maximal repeat
-			struct	MaxRepeatOccurrences;
-			typedef MaxRepeats_<MultiMems_> MultiMems;	// Multiple Maximal Exact Match
-			struct	MultiMemOccurences;					// i.e. maximal match over different sequences
-
-
-/**
-.Metafunction.GetVSTreeIteratorTraits:
-..cat:Index
-..summary:Default behaviour of @Function.goNext@ when no second parameter is given.
-..signature:GetVSTreeIteratorTraits<TIterator>::Type
-..class:Class.Index
-..param.TIterator:A @Spec.VSTree Iterator@.
-..returns:$Tag.Postorder$ by default and $Tag.Preorder$ if $TIterator$ is $VSTree<TopDown<ParentLinks<> > >$ or $VSTree<TopDown<ParentLinks<Preorder> > >$.
-..include:seqan/index.h
-*/
+        // bottom up traversal iterators
+        template <typename TSpec = Postorder>
+        struct BottomUp {};                    // starts in the first node of a depth-first-search and can go next
+
+            struct    SuperMaxRepeats;                    // maximal repeat and not part of a longer repeat
+            struct    SuperMaxRepeatsFast;
+            struct    Mums;                                // Maximal Unique Match (unique in every sequence)
+
+            typedef MaxRepeats_<void>        MaxRepeats;    // maximal repeat
+            struct    MaxRepeatOccurrences;
+            typedef MaxRepeats_<MultiMems_> MultiMems;    // Multiple Maximal Exact Match
+            struct    MultiMemOccurences;                    // i.e. maximal match over different sequences
+
+
 /*!
  * @mfn Index#GetVSTreeIteratorTraits
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Default behaviour of @link VSTreeIterator#goNext @endlink when no second parameter is given.
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Default behaviour of @link InputIteratorConcept#goNext @endlink when no second parameter is given.
+ *
  * @signature GetVSTreeIteratorTraits<TIterator>::Type
- * 
+ *
  * @tparam TIterator A @link VSTreeIterator @endlink.
- * 
- * @return TReturn @link DfsOrder#Postorder @endlink by default and @link DfsOrde#Preorder @endlink
+ *
+ * @return TReturn @link DfsOrder#Postorder @endlink by default and @link DfsOrder#Preorder @endlink
  *                 if <tt>TIterator</tt> is <tt>VSTree&lt;TopDown&lt;ParentLinks&lt;&gt; &gt; &gt;</tt>
  *                 or <tt>VSTree&lt;TopDown&lt;ParentLinks&lt;Preorder&gt; &gt; &gt;</tt>.
  */
 
-	template <typename TIterator>
-	struct GetVSTreeIteratorTraits:
-		DeepestSpec<TIterator> {};
+    template <typename TIterator>
+    struct GetVSTreeIteratorTraits:
+        DeepestSpec<TIterator> {};
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TSize>
-	struct VertexEsa {
-		Pair<TSize> range;			// current SA interval of hits (unique node identifier)
-		TSize		parentRight;	// right boundary of parent node's range (allows to go right)
-
-		VertexEsa() : range(0, 0), parentRight(0) {}
-
-		VertexEsa(MinimalCtor):
-			range(0,0),
-			parentRight(0) {}
-
-		VertexEsa(TSize otherRangeLeft, TSize otherRangeRight, TSize otherParentRight):
-			range(Pair<TSize>(otherRangeLeft, otherRangeRight)),
-			parentRight(otherParentRight) {}
-
-		VertexEsa(Pair<TSize> const &otherRange, TSize otherParentRight):
-			range(otherRange),
-			parentRight(otherParentRight) {}
-
-		VertexEsa(VertexEsa const &other):
-			range(other.range),
-			parentRight(other.parentRight) {}
-	};
-	
-	template <typename TSize>
-	inline bool operator==(VertexEsa<TSize> const &a, VertexEsa<TSize> const &b)
-	{
-		return a.range == b.range;
-	}
-
-	template <typename TSize>
-	inline bool operator!=(VertexEsa<TSize> const &a, VertexEsa<TSize> const &b)
-	{
-		return a.range != b.range;
-	}
+    template <typename TSize>
+    struct VertexEsa {
+        Pair<TSize> range;            // current SA interval of hits (unique node identifier)
+        TSize        parentRight;    // right boundary of parent node's range (allows to go right)
+
+        SEQAN_HOST_DEVICE
+        VertexEsa() : range(0, 0), parentRight(0) {}
+
+        SEQAN_HOST_DEVICE
+        VertexEsa(MinimalCtor):
+            range(0,0),
+            parentRight(0) {}
+
+        SEQAN_HOST_DEVICE
+        VertexEsa(TSize otherRangeLeft, TSize otherRangeRight, TSize otherParentRight):
+            range(Pair<TSize>(otherRangeLeft, otherRangeRight)),
+            parentRight(otherParentRight) {}
+
+        SEQAN_HOST_DEVICE
+        VertexEsa(Pair<TSize> const &otherRange, TSize otherParentRight):
+            range(otherRange),
+            parentRight(otherParentRight) {}
+
+        SEQAN_HOST_DEVICE
+        VertexEsa(VertexEsa const &other):
+            range(other.range),
+            parentRight(other.parentRight) {}
+    };
+
+    template <typename TSize>
+    SEQAN_HOST_DEVICE inline bool operator==(VertexEsa<TSize> const &a, VertexEsa<TSize> const &b)
+    {
+        return a.range == b.range;
+    }
+
+    template <typename TSize>
+    SEQAN_HOST_DEVICE inline bool operator!=(VertexEsa<TSize> const &a, VertexEsa<TSize> const &b)
+    {
+        return a.range != b.range;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Metafunction.VertexDescriptor.param.T.type:Spec.IndexEsa
-///.Metafunction.VertexDescriptor.class:Spec.IndexEsa
+/*!
+ * @mfn StringTreeConcept#VertexDescriptor
+ * @headerfile <seqan/index.h>
+ * @brief Returns the type of an object that represents a string tree node.
+ *
+ * @signature VertexDescriptor<TIndex>::Type;
+ *
+ * @tparam TIndex The index type.
+ *
+ * @return Type The resulting vertex descriptor type.
+ */
 
-	template < typename TText, typename TSpec >
-	struct VertexDescriptor< Index<TText, IndexEsa<TSpec> > > {
-		typedef typename Size< Index<TText, IndexEsa<TSpec> > >::Type TSize;
-		typedef VertexEsa<TSize> Type;
-	};
+    template < typename TText, typename TSpec >
+    struct VertexDescriptor< Index<TText, IndexEsa<TSpec> > > {
+        typedef typename Size< Index<TText, IndexEsa<TSpec> > >::Type TSize;
+        typedef VertexEsa<TSize> Type;
+    };
 
 
 //////////////////////////////////////////////////////////////////////////////
 // needful forward declarations
 
-	struct ArrayGaps_;
+    struct ArrayGaps_;
     typedef Tag<ArrayGaps_> ArrayGaps;
 
-	template <typename TSource, typename TSpec>
-	class Align;
+    template <typename TSource, typename TSpec>
+    class Align;
 
 
 //////////////////////////////////////////////////////////////////////////////
 // ESA fibres
 
-/**
-.Tag.ESA Index Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of an @Spec.IndexEsa.ESA@ index.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of an Enhanced Suffix Array based @Spec.IndexEsa.Index@.
-..cat:Index
-
-..tag.EsaText:The original text the index should be based on.
-
-..tag.EsaRawText:The raw text the index is really based on.
-...remarks:$EsaText$ and $EsaRawText$ fibres are equal by default.
-They differ if the index text is a set of strings. Then, raw text is the concatenation of all strings in this set.
-
-..tag.EsaSA:The suffix array.
-...remarks:The suffix array contains the indices of all suffices of $EsaRawText$ in lexicographical order.
-...remarks:@Metafunction.Fibre@ returns a @Class.String@ over the alphabet of the @Metafunction.SAValue@ of $TIndex$.
-
-..tag.EsaLcp:The lcp table.
-...remarks:The lcp table contains the lcp-value of two adjacent suffices in the suffix array $EsaSA$.
-...remarks:@Metafunction.Fibre@ returns a @Class.String@ over the alphabet of a size type.
-
-..tag.EsaChildtab:The child table.
-...remarks:The child table contains structural information of the suffix tree (see Abhouelda et al.).
-...remarks:@Metafunction.Fibre@ returns a @Class.String@ over the alphabet of a size type.
-
-..tag.EsaBwt:The Burrows-Wheeler table.
-...remarks:The Burrows-Wheeler table contains the Burrows-Wheeler transformation of $EsaRawText$.
-The entries are the characters left of the corresponding suffix in the suffix array $EsaSA$.
-...remarks:@Metafunction.Fibre@ returns the same type for $EsaRawText$ and for $EsaBwt$.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..see:Spec.IndexEsa
-..include:seqan/index.h
-*/
-
 /*!
  * @defgroup IndexEsaFibres Index Esa Fibres
- * 
  * @brief Tag to select a specific fibre (e.g. table, object, ...) of an @link
  *        IndexEsa @endlink index.
- * 
- * @section Remarks
- * 
- * These tags can be used to get @link Index#Fibre Fibres @endlink of an Enhanced
+ *
+ * These tags can be used to get @link Fibre Fibres @endlink of an Enhanced
  * Suffix Array based @link IndexEsa @endlink.
- * 
- * @see Index#Fibre
+ *
+ * @see Fibre
  * @see Index#getFibre
  * @see IndexEsa
- * 
- * @tag IndexEsaFibres#EsaSA
- * 
- * @headerfile seqan/index.h
  *
+ * @tag IndexEsaFibres#EsaSA
+ * @headerfile <seqan/index.h>
  * @brief The suffix array.
- * 
- * @section Remarks
- * 
+ *
  * The suffix array contains the indices of all suffices of <tt>EsaRawText</tt>
  * in lexicographical order.
- * 
- * @link Index#Fibre @endlink returns a @link String @endlink over the alphabet of the
+ *
+ * @link Fibre @endlink returns a @link String @endlink over the alphabet of the
  * @link SAValue @endlink of <tt>TIndex</tt>.
- * 
- * @tag IndexEsaFibres#EsaChildtab
- * 
- * @headerfile seqan/index.h
  *
+ * @tag IndexEsaFibres#EsaIsa
+ * @headerfile <seqan/index.h>
+ * @brief The inverse suffix array.
+ *
+ * The inverse suffix array stores the lexicographic rank of each suffix of <tt>EsaRawText</tt>.
+ *
+ * @link Fibre @endlink returns a @link String @endlink over the alphabet of a
+ * size type.
+ *
+ * @tag IndexEsaFibres#EsaChildtab
+ * @headerfile <seqan/index.h>
  * @brief The child table.
- * 
- * @section Remarks
- * 
+ *
  * The child table contains structural information of the suffix tree (see
  * Abhouelda et al.).
- * 
- * @link Index#Fibre @endlink returns a @link String @endlink over the alphabet of a
+ *
+ * @link Fibre @endlink returns a @link String @endlink over the alphabet of a
  * size type.
- * 
- * @tag IndexEsaFibres#EsaRawText
- * 
- * @headerfile seqan/index.h
  *
+ * @tag IndexEsaFibres#EsaRawText
+ * @headerfile <seqan/index.h>
  * @brief The raw text the index is really based on.
- * 
- * @section Remarks
- * 
+ *
  * <tt>EsaText</tt> and <tt>EsaRawText</tt> fibres are equal by default. They
  * differ if the index text is a set of strings. Then, raw text is the
  * concatenation of all strings in this set.
- * 
- * @tag IndexEsaFibres#EsaText
- * 
- * @headerfile seqan/index.h
  *
+ * @tag IndexEsaFibres#EsaText
+ * @headerfile <seqan/index.h>
  * @brief The original text the index should be based on.
- * 
- * @tag IndexEsaFibres#EsaBwt
- * 
- * @headerfile seqan/index.h
  *
+ * @tag IndexEsaFibres#EsaBwt
+ * @headerfile <seqan/index.h>
  * @brief The Burrows-Wheeler table.
- * 
- * @section Remarks
- * 
+ *
  * The Burrows-Wheeler table contains the Burrows-Wheeler transformation of
  * <tt>EsaRawText</tt>. The entries are the characters left of the corresponding
  * suffix in the suffix array <tt>EsaSA</tt>.
- * 
- * @link Index#Fibre @endlink returns the same type for <tt>EsaRawText</tt> and for
+ *
+ * @link Fibre @endlink returns the same type for <tt>EsaRawText</tt> and for
  * <tt>EsaBwt</tt>.
- * 
- * @tag IndexEsaFibres#EsaLcp
- * 
- * @headerfile seqan/index.h
  *
+ * @tag IndexEsaFibres#EsaLcp
+ * @headerfile <seqan/index.h>
  * @brief The lcp table.
- * 
- * @section Remarks
- * 
+ *
  * The lcp table contains the lcp-value of two adjacent suffices in the suffix
  * array <tt>EsaSA</tt>.
- * 
- * @link Index#Fibre @endlink returns a @link String @endlink over the alphabet of a
+ *
+ * @link Fibre @endlink returns a @link String @endlink over the alphabet of a
  * size type.
  *
  * @tag IndexEsaFibres#EsaLcpe
- * 
- * @headerfile seqan/index.h
- *
+ * @headerfile <seqan/index.h>
  * @brief The lcpe table.
  */
 
-///.Metafunction.Fibre.param.TSpec.type:Tag.ESA Index Fibres
-
-	typedef FibreText		EsaText;
-	typedef FibreRawText	EsaRawText;
-	typedef FibreSA         EsaSA;
-	typedef FibreRawSA		EsaRawSA;
-	typedef FibreSae		EsaSae;
-	typedef FibreLcp		EsaLcp;
-	typedef FibreLcpe		EsaLcpe;
-	typedef FibreChildtab	EsaChildtab;
-	typedef FibreBwt		EsaBwt;
-
+    typedef FibreText       EsaText;
+    typedef FibreRawText    EsaRawText;
+    typedef FibreSA         EsaSA;
+    typedef FibreIsa        EsaIsa;
+    typedef FibreRawSA      EsaRawSA;
+    typedef FibreSae        EsaSae;
+    typedef FibreLcp        EsaLcp;
+    typedef FibreLcpe       EsaLcpe;
+    typedef FibreChildtab   EsaChildtab;
+    typedef FibreBwt        EsaBwt;
 
 //////////////////////////////////////////////////////////////////////////////
 // ESA index
 
-/**
-.Spec.IndexEsa:
-..summary:The enhanced suffix array index is very fast index, requiring more memory than other indices.
-In addition to the suffix array an lcp (longest common prefix) table and a child table (containing structural 
-information of the suffix tree) are provided.
-..cat:Index
-..general:Class.Index
-..signature:Index<TText, IndexEsa<> >
-..param.TText:The text type.
-...type:Class.String
-...type:Class.StringSet
-..remarks:The main fibres (see @Class.Index@ and @Metafunction.Fibre@) of this index are a suffix array
-(see @Tag.ESA Index Fibres.EsaSA@), a lcp table (see @Tag.ESA Index Fibres.EsaLcp@) and a child table (see @Tag.ESA Index Fibres.EsaChildtab@).
-..remarks:This index can be accessed as a Suffix Tree using the @Spec.VSTree Iterator@ classes.  ..include:seqan/index.h
-*/
 /*!
  * @class IndexEsa
- * 
  * @extends Index
- * 
- * @headerfile seqan/index.h
- * 
+ * @implements StringTreeConcept
+ * @headerfile <seqan/index.h>
  * @brief An index based on an enhanced suffix array.
- * 
+ *
  * @signature template <typename TText, typename TSpec>
- *            Index<TText, IndexEsa<TSpec> >
- * 
- * @tparam TText The text type. Types: @link SequenceConcept @endlink, @link StringSet @endlink
- * @tparam TSpec The specialization which is <tt>void</tt> by default.
- * 
- * @section Remarks
- * 
- * The fibres (see @link Index @endlink and @link Index#Fibre @endlink) of this index are a suffix array (see @link
+ *            class Index<TText, IndexEsa<TSpec> >;
+ *
+ * @tparam TText The @link TextConcept text type @endlink.
+ * @tparam TSpec The specialization, defaults to <tt>void</tt>.
+ *
+ * The fibres (see @link Index @endlink and @link Fibre @endlink) of this index are a suffix array (see @link
  * IndexEsaFibres#EsaSA @endlink), a lcp table (see @link IndexEsaFibres#EsaLcp @endlink), etc.
- * 
+ *
  * This index can be accessed as a Suffix Tree using the @link VSTreeIterator @endlink classes.
- * 
+ *
  * @see IndexEsaFibres
  */
 
 /*
-	already defined in index_base.h
+    already defined in index_base.h
 
-	template <typename TSpec = void>
-	struct IndexEsa;
+    template <typename TSpec = void>
+    struct IndexEsa;s
 */
 
-	template < typename TText, typename TSpec >
-	class Index<TText, IndexEsa<TSpec> > {
-	public:
-		Holder<typename Fibre<Index, EsaText>::Type>	text;
-		typename Fibre<Index, EsaSA>::Type				sa;			// suffix array 
-		typename Fibre<Index, EsaLcp>::Type			lcp;		// longest-common-prefix table
-		typename Fibre<Index, EsaLcpe>::Type			lcpe;		// extended lcp table
-		typename Fibre<Index, EsaChildtab>::Type		childtab;	// child table (tree topology)
-		typename Fibre<Index, EsaBwt>::Type			bwt;		// burrows-wheeler table
-		typename Cargo<Index>::Type						cargo;		// user-defined cargo
-
-		Index() {}
-
-		Index(Index &other):
-			text(other.text),
-			sa(other.sa),
-			lcp(other.lcp),
-			lcpe(other.lcpe),
-			childtab(other.childtab),
-			bwt(other.bwt),
-			cargo(other.cargo) {}
-
-		Index(Index const &other):
-			text(other.text),
-			sa(other.sa),
-			lcp(other.lcp),
-			lcpe(other.lcpe),
-			childtab(other.childtab),
-			bwt(other.bwt),
-			cargo(other.cargo) {}
-
-		template <typename TText_>
-		Index(TText_ &_text):
-			text(_text) {}
-
-		template <typename TText_>
-		Index(TText_ const &_text):
-			text(_text) {}
-	};
+    template < typename TText, typename TSpec >
+    class Index<TText, IndexEsa<TSpec> > {
+    public:
+        typename Member<Index, EsaText>::Type       text;
+        typename Fibre<Index, EsaSA>::Type          sa;            // suffix array
+        typename Fibre<Index, EsaIsa>::Type         isa;        // inverse suffix array
+        typename Fibre<Index, EsaLcp>::Type         lcp;        // longest-common-prefix table
+        typename Fibre<Index, EsaLcpe>::Type        lcpe;        // extended lcp table
+        typename Fibre<Index, EsaChildtab>::Type    childtab;    // child table (tree topology)
+        typename Fibre<Index, EsaBwt>::Type         bwt;        // burrows-wheeler table
+        typename Cargo<Index>::Type                 cargo;        // user-defined cargo
+
+        Index() {}
+
+        Index(Index &other):
+            text(other.text),
+            sa(other.sa),
+            isa(other.isa),
+            lcp(other.lcp),
+            lcpe(other.lcpe),
+            childtab(other.childtab),
+            bwt(other.bwt),
+            cargo(other.cargo) {}
+
+        Index(Index const &other):
+            text(other.text),
+            sa(other.sa),
+            isa(other.isa),
+            lcp(other.lcp),
+            lcpe(other.lcpe),
+            childtab(other.childtab),
+            bwt(other.bwt),
+            cargo(other.cargo) {}
+
+        template <typename TText_>
+        Index(TText_ &_text):
+            text(_text) {}
+
+        template <typename TText_>
+        Index(TText_ const &_text):
+            text(_text) {}
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template < typename TText, typename TSpec >
-	void _indexRequireTopDownIteration(Index<TText, IndexEsa<TSpec> > &index) 
-	{
-		indexRequire(index, EsaSA());
-		indexRequire(index, EsaLcp());
-		indexRequire(index, EsaChildtab());
-	}
-
-	template < typename TText, typename TSpec >
-	void _indexRequireBottomUpIteration(Index<TText, IndexEsa<TSpec> > &index) 
-	{
-		indexRequire(index, EsaSA());
-		indexRequire(index, EsaLcp());
-	}
+    template < typename TText, typename TSpec >
+    SEQAN_HOST_DEVICE inline void _indexRequireTopDownIteration(Index<TText, IndexEsa<TSpec> > &index)
+    {
+        indexRequire(index, EsaSA());
+        indexRequire(index, EsaLcp());
+        indexRequire(index, EsaChildtab());
+    }
+
+    template < typename TText, typename TSpec >
+    void _indexRequireBottomUpIteration(Index<TText, IndexEsa<TSpec> > &index)
+    {
+        indexRequire(index, EsaSA());
+        indexRequire(index, EsaLcp());
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.clear.param.object.type:Class.Index
+/*!
+ * @fn Index#clear
+ * @brief Resets all fibres of an index.
+ *
+ * @signature void clear(index);
+ *
+ * @param[in,out] index The index to be cleared.
+ */
 
-	template <typename TText, typename TSpec>
-	inline void clear(Index<TText, IndexEsa<TSpec> > &index) {
-		clear(getFibre(index, EsaSA()));
-		clear(getFibre(index, EsaLcp()));
-		clear(getFibre(index, EsaLcpe()));
-		clear(getFibre(index, EsaChildtab()));
-		clear(getFibre(index, EsaBwt()));
-	}
+    template <typename TText, typename TSpec>
+    inline void clear(Index<TText, IndexEsa<TSpec> > &index) {
+        clear(getFibre(index, EsaSA()));
+        clear(getFibre(index, EsaIsa()));
+        clear(getFibre(index, EsaLcp()));
+        clear(getFibre(index, EsaLcpe()));
+        clear(getFibre(index, EsaChildtab()));
+        clear(getFibre(index, EsaBwt()));
+    }
 
 // ----------------------------------------------------------------------------
 // Function open
 // ----------------------------------------------------------------------------
 
-	template < typename TObject, typename TSpec >
-	inline bool open(
-		Index< TObject, IndexEsa<TSpec> > &index, 
-		const char *fileName,
-		int openMode)
-	{
-		String<char> name;
+    template < typename TObject, typename TSpec >
+    inline bool open(
+        Index< TObject, IndexEsa<TSpec> > &index,
+        const char *fileName,
+        int openMode)
+    {
+        String<char> name;
 
-		name = fileName;	append(name, ".txt");
-		if ((!open(getFibre(index, EsaText()), toCString(name), openMode)) && 
-			(!open(getFibre(index, EsaText()), fileName, openMode))) return false;
+        name = fileName;    append(name, ".txt");
+        if ((!open(getFibre(index, EsaText()), toCString(name), openMode)) &&
+            (!open(getFibre(index, EsaText()), fileName, openMode))) return false;
 
-		name = fileName;	append(name, ".sa");
+        name = fileName;    append(name, ".sa");
         if (!open(getFibre(index, EsaSA()), toCString(name), openMode)) return false;
 
-		name = fileName;	append(name, ".lcp");
+        name = fileName;    append(name, ".isa");
+        if (!open(getFibre(index, EsaIsa()), toCString(name), openMode)) return false;
+
+        name = fileName;    append(name, ".lcp");
         if (!open(getFibre(index, EsaLcp()), toCString(name), openMode)) return false;
 
-		name = fileName;	append(name, ".child");
+        name = fileName;    append(name, ".child");
         if (!open(getFibre(index, EsaChildtab()), toCString(name), openMode)) return false;
 
-		name = fileName;	append(name, ".bwt");
+        name = fileName;    append(name, ".bwt");
         if (!open(getFibre(index, EsaBwt()), toCString(name), openMode)) return false;
 
-		return true;
-	}
-	template < typename TObject, typename TSpec >
-	inline bool open(
-		Index< TObject, IndexEsa<TSpec> > &index, 
-		const char *fileName) 
-	{
-		return open(index, fileName, DefaultOpenMode<Index< TObject, IndexEsa<TSpec> > >::VALUE);
-	}
+        return true;
+    }
+    template < typename TObject, typename TSpec >
+    inline bool open(
+        Index< TObject, IndexEsa<TSpec> > &index,
+        const char *fileName)
+    {
+        return open(index, fileName, DefaultOpenMode<Index< TObject, IndexEsa<TSpec> > >::VALUE);
+    }
 
 // ----------------------------------------------------------------------------
 // Function save
 // ----------------------------------------------------------------------------
 
-	template < typename TObject, typename TSpec >
-	inline bool save(
-		Index< TObject, IndexEsa<TSpec> > &index, 
-		const char *fileName,
-		int openMode)
-	{
-		String<char> name;
+    template < typename TObject, typename TSpec >
+    inline bool save(
+        Index< TObject, IndexEsa<TSpec> > const &index,
+        const char *fileName,
+        int openMode)
+    {
+        String<char> name;
 
-		name = fileName;	append(name, ".txt");	
-		if ((!save(getFibre(index, EsaText()), toCString(name), openMode)) && 
-			(!save(getFibre(index, EsaText()), fileName, openMode))) return false;
+        name = fileName;    append(name, ".txt");
+        if ((!save(getFibre(index, EsaText()), toCString(name), openMode)) &&
+            (!save(getFibre(index, EsaText()), fileName, openMode))) return false;
 
-		name = fileName;	append(name, ".sa");
+        name = fileName;    append(name, ".sa");
         if (!save(getFibre(index, EsaSA()), toCString(name), openMode)) return false;
 
-		name = fileName;	append(name, ".lcp");
+        name = fileName;    append(name, ".isa");
+        if (!save(getFibre(index, EsaIsa()), toCString(name), openMode)) return false;
+
+        name = fileName;    append(name, ".lcp");
         if (!save(getFibre(index, EsaLcp()), toCString(name), openMode)) return false;
 
-		name = fileName;	append(name, ".child");
+        name = fileName;    append(name, ".child");
         if (!save(getFibre(index, EsaChildtab()), toCString(name), openMode)) return false;
 
-		name = fileName;	append(name, ".bwt");
+        name = fileName;    append(name, ".bwt");
         if (!save(getFibre(index, EsaBwt()), toCString(name), openMode)) return false;
 
-		return true;
-	}
-	template < typename TObject, typename TSpec >
-	inline bool save(
-		Index< TObject, IndexEsa<TSpec> > &index, 
-		const char *fileName)
-	{
-		return save(index, fileName, DefaultOpenMode<Index< TObject, IndexEsa<TSpec> > >::VALUE);
-	}
+        return true;
+    }
+    template < typename TObject, typename TSpec >
+    inline bool save(
+        Index< TObject, IndexEsa<TSpec> > const &index,
+        const char *fileName)
+    {
+        return save(index, fileName, DefaultOpenMode<Index< TObject, IndexEsa<TSpec> > >::VALUE);
+    }
 
 }
 
diff --git a/seqan/index/index_esa_drawing.h b/seqan/index/index_esa_drawing.h
index 1322800..5a33156 100644
--- a/seqan/index/index_esa_drawing.h
+++ b/seqan/index/index_esa_drawing.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,69 +39,73 @@ namespace SEQAN_NAMESPACE_MAIN
 {
 
 template <typename TFile, typename TText, typename TESASpec>
-void write(TFile & file, 
-	   Index<TText, IndexEsa<TESASpec> > & stree,
-	   DotDrawing) 
+void writeRecords(
+    TFile & file,
+    Index<TText, IndexEsa<TESASpec> > & stree,
+    DotDrawing)
 {
 //IOREV _nodoc_
-	SEQAN_CHECKPOINT
-	typedef Index<TText, IndexEsa<TESASpec> > TIndex;
-	
-	streamPut(file, "digraph G {\n");
-	streamPut(file, '\n');
-	streamPut(file, "/* Graph Attributes */\n");
-	streamPut(file, "graph [rankdir = LR];\n");
-	streamPut(file, '\n');
-	streamPut(file, "/* Node Attributes */\n");
-	streamPut(file, "node [shape = ellipse, fillcolor = lightgrey, style = filled, fontname = \"Times-Italic\"];\n");
-	streamPut(file, '\n');
-	streamPut(file, "/* Edge Attributes */\n");
-	streamPut(file, "edge [fontname = \"Times-Italic\", arrowsize = 0.75, fontsize = 16];\n");
-	streamPut(file, '\n');
+    SEQAN_CHECKPOINT
+    typedef Index<TText, IndexEsa<TESASpec> > TIndex;
 
-	streamPut(file, "/* Edges */\n");
-	typedef typename Iterator<TIndex, TopDown<ParentLinks<Preorder> > >::Type TIterator;
-	typedef typename Iterator<TIndex, TopDown<> >::Type TIteratorSimple;
-	TIterator it(stree);
+    typename DirectionIterator<TFile, Output>::Type iter = directionIterator(file, Output());
 
-	for(;!atEnd(it);++it) 
-	{
-		// dump node
-       		streamPut(file, "\"[");
- 		streamPut(file, (int)value(it).range.i1);
-		streamPut(file, ':');
-		streamPut(file, (int)value(it).range.i2);
-       		streamPut(file, ")\"");
-       		if (!isRightTerminal(it))
-			streamPut(file, " [style = dashed]");
-       		streamPut(file, ";\n");
+    write(iter, "digraph G {\n");
+    writeValue(iter, '\n');
+    write(iter, "/* Graph Attributes */\n");
+    write(iter, "graph [rankdir = LR];\n");
+    writeValue(iter, '\n');
+    write(iter, "/* Node Attributes */\n");
+    write(iter, "node [shape = ellipse, fillcolor = lightgrey, style = filled, fontname = \"Times-Italic\"];\n");
+    writeValue(iter, '\n');
+    write(iter, "/* Edge Attributes */\n");
+    write(iter, "edge [fontname = \"Times-Italic\", arrowsize = 0.75, fontsize = 16];\n");
+    writeValue(iter, '\n');
 
-		// dump edge from parent (if not root)
-		if (!isRoot(it)) {
-			TIteratorSimple src(container(it), nodeUp(it));
+    write(iter, "/* Edges */\n");
+    typedef typename Iterator<TIndex, TopDown<ParentLinks<Preorder> > >::Type TIterator;
+    typedef typename Iterator<TIndex, TopDown<> >::Type TIteratorSimple;
+    TIterator it(stree);
 
-			streamPut(file, "\"[");
-			streamPut(file, (int)value(src).range.i1);
-			streamPut(file, ':');
-			streamPut(file, (int)value(src).range.i2);
-			streamPut(file, ")\"");
+    for(;!atEnd(it);++it)
+    {
+        // dump node
+        write(iter, "\"[");
+         appendNumber(iter, range(it).i1);
+        writeValue(iter, ':');
+        appendNumber(iter, range(it).i2);
+        write(iter, ")\"");
+        if (!isRightTerminal(it))
+            write(iter, " [style = dashed]");
+        write(iter, ";\n");
 
-			streamPut(file, " -> ");
+        // dump edge from parent (if not root)
+        if (!isRoot(it))
+        {
+            TIteratorSimple src(container(it), nodeUp(it));
 
-			streamPut(file, "\"[");
-			streamPut(file, (int)value(it).range.i1);
-			streamPut(file, ':');
-			streamPut(file, (int)value(it).range.i2);
-			streamPut(file, ")\"");
+            write(iter, "\"[");
+            appendNumber(iter, range(src).i1);
+            writeValue(iter, ':');
+            appendNumber(iter, range(src).i2);
+            write(iter, ")\"");
 
-			streamPut(file, " [label = \"");
-			streamPut(file, parentEdgeLabel(it));
-			streamPut(file, "\"];\n");
-		}
-	}
-	streamPut(file, '\n');
+            write(iter, " -> ");
 
-	streamPut(file, "}\n");
+            write(iter, "\"[");
+            appendNumber(iter, range(it).i1);
+            writeValue(iter, ':');
+            appendNumber(iter, range(it).i2);
+            write(iter, ")\"");
+
+            write(iter, " [label = \"");
+            write(iter, parentEdgeLabel(it));
+            write(iter, "\"];\n");
+        }
+    }
+    writeValue(iter, '\n');
+
+    write(iter, "}\n");
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/index/index_esa_stree.h b/seqan/index/index_esa_stree.h
index 09934ad..984d287 100644
--- a/seqan/index/index_esa_stree.h
+++ b/seqan/index/index_esa_stree.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,63 +39,31 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-/**
-.Spec.VSTree Iterator:
-..cat:Index
-..summary:Abstract iterator for suffix trees.
-..signature:Iter<TContainer, VSTree<TSpec> >
-..general:Class.Iter
-..param.TContainer:Type of the container that can be iterated.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..param.TSpec:The specialization type.
-..remarks:This iterator is a pointer to a node in the suffix tree (given by the enhanced suffix array @Spec.IndexEsa@).
-Every node can uniquely be mapped to an interval of the suffix array containing all suffixes of the node's subtree.
-This interval and some extra information constitute the @Metafunction.VertexDescriptor@ returned by the @Function.value@ function of the iterator.
-..include:seqan/index.h
-..example
-...text:This code shows how an index can be used with iterators to achieve a pre-order tree like traversal
-in DFS of the text "tobeornottobe". In order to do so a Top-Down History iterator is used.
-...file:demos/index/index_iterator.cpp
-...output:
-
-be
-beornottobe
-e
-eornottobe
-nottobe
-o
-obe
-obeornottobe
-ornottobe
-ottobe
-rnottobe
-t
-tobe
-tobeornottobe
-ttobe
-*/
+template <typename TText, typename TSpec>
+SEQAN_CONCEPT_IMPL((Index<TText, IndexEsa<TSpec> >), (StringTreeConcept));
+
+template <typename TText, typename TSpec>
+SEQAN_CONCEPT_IMPL((Index<TText, IndexEsa<TSpec> > const), (StringTreeConcept));
+
 /*!
  * @class VSTreeIterator VSTree Iterator
- * 
  * @extends Iter
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief Abstract iterator for string trees, where string trees are trees constructed from a string.
- * 
- * @signature Iter<TContainer, VSTree<TSpec> >
- * 
- * @tparam TSpec The specialization type.
- * @tparam TContainer Type of the container that can be iterated. Types:
- *                    @link IndexDfi @endlink, @link IndexEsa @endlink, @link IndexWotd @endlink, @link FMindex @endlink
- * 
- * @section Remarks
- * 
+ *
+ * @signature template <typename TContainer, typename TSpec>
+ *            class Iter<TContainer, VSTree<TSpec> >;
+ *
+ * @tparam TSpec      The specialization type.
+ * @tparam TContainer Type of the container that can be iterated.  Types: @link IndexDfi @endlink,
+ *                    @link IndexEsa @endlink, @link IndexWotd @endlink, @link FMIndex @endlink
+ *
  * This iterator is a pointer to a node in the string tree of a given text. Depending on the index this can either be a
  * suffix or prefix tree/trie.  Every node can uniquely be mapped to an interval of suffices or prefixes.
  *
  * Default virtual string tree iterators depending on the @link Index @endlink
+ *
  * <table border="1">
  * <tr>
  *   <td>IndexSa</td>
@@ -118,14 +87,15 @@ ttobe
  * </tr>
  * </table>
  *
- * @section Example 
+ * @section Examples
  *
  * This code shows how an index can be used with iterators to achieve a pre-order tree like traversal
  * in DFS of the text "tobeornottobe". In order to do so a Top-Down History iterator is used.
  *
- * @include demos/index/index_iterator.cpp
- * @code{.txt}
- * 
+ * @include demos/dox/index/iterator.cpp
+ *
+ * @code{.output}
+ *
  * be
  * beornottobe
  * e
@@ -143,301 +113,261 @@ ttobe
  * ttobe
  */
 
-	template < typename TIndex, typename TSpec >
+    template < typename TIndex, typename TSpec >
     struct Value< Iter< TIndex, VSTree<TSpec> > > {
-		typedef typename VertexDescriptor<TIndex>::Type Type;
-	};
- 
-	template < typename TIndex, typename TSpec >
-	struct Size< Iter< TIndex, VSTree<TSpec> > > {
-		typedef typename Size<TIndex>::Type Type;
-	};
- 
-	template < typename TIndex, typename TSpec >
-	struct Position< Iter< TIndex, VSTree<TSpec> > > {
-		typedef typename Position<TIndex>::Type Type;
-	};
+        typedef typename VertexDescriptor<TIndex>::Type Type;
+    };
+
+    template < typename TIndex, typename TSpec >
+    struct Size< Iter< TIndex, VSTree<TSpec> > > {
+        typedef typename Size<TIndex>::Type Type;
+    };
+
+    template < typename TIndex, typename TSpec >
+    struct Position< Iter< TIndex, VSTree<TSpec> > > {
+        typedef typename Position<TIndex>::Type Type;
+    };
 
+/*!
+ * @mfn VSTreeIterator#EdgeLabel
+ * @headerfile <seqan/index.h>
+ * @brief Type of a string representing the characters of edges.
+ *
+ * @signature EdgeLabel<TSpec>::Type;
+ *
+ * @tparam TSpec Tag to specify the object of which the type of the edge labels is requested.
+ *
+ * @return Type of a string representing the characters of edges.
+ */
     template < typename TSpec >
     struct EdgeLabel {};
 
     template < typename TIndex, typename TSpec >
     struct EdgeLabel< Iter< TIndex, VSTree<TSpec> > > {
-		typedef typename Infix< typename Fibre<TIndex, FibreText>::Type const >::Type Type;
-	};
-
-/**
-.Spec.TopDown Iterator:
-..cat:Index
-..general:Spec.VSTree Iterator
-..summary:Iterator for virtual trees that can go down and right beginning from the root.
-..signature:Iterator<TContainer, TopDown<TSpec> >::Type
-..signature:Iter<TContainer, VSTree< TopDown<TSpec> > >
-..param.TContainer:Type of the container that can be iterated.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..param.TSpec:The specialization type.
-..remarks:If not copy-constructed the @Spec.TopDown Iterator@ starts in the root node of the virtual tree.
-..remarks:Note that the virtual tree can either be a virtual suffix tree or a virtual prefix tree. The suffix tree is shown in Figure 1 and is implemented with the @Spec.IndexDfi@, @Spec.IndexEsa@ and @Spec.IndexWotd@. In contrast the @Spec.FMIndex@ implements a prefix trie shown in Figure 2.
-..include:seqan/index.h
-
-.Memfunc.TopDown Iterator#Iterator
-..class:Spec.TopDown Iterator
-..summary:Constructor
-..signature:Iterator(index[, vertexDesc])
-..signature:Iterator(iterator)
-..param.index:An index object.
-..param.vertexDesc:The vertex descriptor of a node the iterator should start in.
-The iterator starts in the root node by default.
-..param.iterator:Another TopDown iterator. (copy constructor)
-...type:Spec.TopDown Iterator
-...type:Spec.TopDownHistory Iterator
-..remarks:If not copy-constructed the @Spec.TopDown Iterator@ starts in the root node of the virtual tree.
-..remarks:Note that the virtual tree can either be a virtual suffix tree or a virtual prefix tree. The suffix tree is shown in Figure 1 and is implemented with the @Spec.IndexDfi@, @Spec.IndexEsa@ and @Spec.IndexWotd@. In contrast the @Spec.FMIndex@ implements a prefix trie shown in Figure 2.
-*/
+        typedef typename Infix< typename Fibre<TIndex, FibreText>::Type const >::Type Type;
+    };
+
 /*!
  * @class TopDownIterator Top Down Iterator
- * 
  * @extends VSTreeIterator
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief Iterator for virtual trees/tries that can go down and right beginning from the root.
- * 
+ *
  * @signature template <typename TIndex, typename TSpec>
- *            Iter<TContainer, VSTree< TopDown<TSpec> > >
- * 
+ *            class Iter<TContainer, VSTree< TopDown<TSpec> > >;
+ *
  * @tparam TSpec The specialization type.
  * @tparam TIndex Type of the container that can be iterated. Types: @link IndexDfi @endlink, @link IndexEsa @endlink,
  *                @link IndexWotd @endlink, @link FMIndex @endlink, @link IndexSa @endlink
- * 
- * @section Remarks
- * 
+ *
  * If not copy-constructed the @link TopDownIterator @endlink starts in the root node of the virtual tree/trie.
- * 
- * @section Note 
  *
- * Instead of using the class Iter directly we recommend to use the result of the metafunction 
- * Iterator&t;TContainer, TopDown&lt;TSpec&gt; &gt;::Type (which is Iter&lt;TContainer, VSTree&lt;TopDown&lt;TSpec&gt; &gt; &gt;).
+ * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
+ *       Iterator&t;TContainer, TopDown&lt;TSpec&gt; &gt;::Type (which is Iter&lt;TContainer,
+ *       VSTree&lt;TopDown&lt;TSpec&gt; &gt; &gt;).
  */
 /*!
  * @fn TopDownIterator::Iterator
- * 
  * @brief Constructor
- * 
- * @signature Iterator(index[, vertexDesc])
- * @signature Iterator(iterator)
- * 
- * @param index An index object.
- * @param iterator Another TopDown iterator. (copy constructor) Types: TopDown
- *                 Iterator, TopDownHistory Iterator
- * @param vertexDesc The vertex descriptor of a node the iterator should start
- *                   in. The iterator starts in the root node by default.
- * 
- * @section Remarks
- * 
+ *
+ * @signature Iter::Iter(index[, vertexDesc]);
+ * @signature Iter::Iter(iterator);
+ *
+ * @param[in] index An index object.
+ * @param[in] iterator Another TopDown iterator. (copy constructor) Types: TopDown
+ *                    Iterator, TopDownHistory Iterator
+ * @param[in] vertexDesc The vertex descriptor of a node the iterator should start
+ *                       in. The iterator starts in the root node by default.
+ *
  * If not copy-constructed the @link TopDownIterator @endlink starts in the
  * root node of the virtual tree.
  */
 
-	template < typename TIndex, class TSpec >
-	class Iter< TIndex, VSTree< TopDown<TSpec> > > 
-	{
-	public:
+    template < typename TIndex, class TSpec >
+    class Iter< TIndex, VSTree< TopDown<TSpec> > >
+    {
+    public:
 
-		typedef typename VertexDescriptor<TIndex>::Type	TVertexDesc;
-		typedef Iter									iterator;
+        typedef typename VertexDescriptor<TIndex>::Type    TVertexDesc;
+        typedef Iter                                    iterator;
 
-		TIndex const	*index;		// container of all necessary tables
-		TVertexDesc		vDesc;		// current interval in suffix array and
-									// right border of parent interval (needed in goRight)
+        TIndex const    *index;        // container of all necessary tables
+        TVertexDesc        vDesc;        // current interval in suffix array and
+                                    // right border of parent interval (needed in goRight)
 
-		// pseudo history stack (to go up at most one node)
-		TVertexDesc		_parentDesc;
+        // pseudo history stack (to go up at most one node)
+        TVertexDesc        _parentDesc;
 
 //____________________________________________________________________________
 
+        SEQAN_HOST_DEVICE
         Iter() : index() {}
-        
-		Iter(TIndex &_index):
-			index(&_index)
-		{
-			_indexRequireTopDownIteration(_index);
-			goRoot(*this);
-		}
-
-		Iter(TIndex &_index, MinimalCtor):
-			index(&_index),
-			vDesc(MinimalCtor()),
+
+        SEQAN_HOST_DEVICE
+        Iter(TIndex &_index):
+            index(&_index)
+        {
+            _indexRequireTopDownIteration(_index);
+            goRoot(*this);
+        }
+
+        SEQAN_HOST_DEVICE
+        Iter(TIndex &_index, MinimalCtor):
+            index(&_index),
+            vDesc(MinimalCtor()),
             _parentDesc(MinimalCtor()) {}
 
         // NOTE(esiragusa): _parentDesc is unitialized
-		Iter(TIndex &_index, TVertexDesc const &_vDesc):
-			index(&_index),
-			vDesc(_vDesc)
-		{
-			_indexRequireTopDownIteration(_index);
-		}
+        SEQAN_HOST_DEVICE
+        Iter(TIndex &_index, TVertexDesc const &_vDesc):
+            index(&_index),
+            vDesc(_vDesc)
+        {
+            _indexRequireTopDownIteration(_index);
+        }
 
         template <typename TSpec2>
-		Iter(Iter<TIndex, VSTree<TopDown<TSpec2> > > const &_origin):
-			index(&container(_origin)),
-			vDesc(value(_origin)),
-			_parentDesc(nodeUp(_origin)) {}
+        SEQAN_HOST_DEVICE
+        Iter(Iter<TIndex, VSTree<TopDown<TSpec2> > > const &_origin):
+            index(&container(_origin)),
+            vDesc(value(_origin)),
+            _parentDesc(nodeUp(_origin)) {}
 
 //____________________________________________________________________________
 
         template <typename TSpec2>
-		inline Iter const &
-		operator = (Iter<TIndex, VSTree<TopDown<TSpec2> > > const &_origin)
-		{
-			index = &container(_origin);
-			vDesc = value(_origin);
-			_parentDesc = nodeUp(_origin);
-			return *this;
-		}
-	};
-
-
-/**
-.Spec.TopDownHistory Iterator:
-..cat:Index
-..general:Spec.TopDown Iterator
-..summary:String tree iterator that can go down, right, and up. Supports depth-first search.
-..signature:Iterator<TContainer, TopDown< ParentLinks<TSpec> > >::Type
-..signature:Iter<TContainer, VSTree< TopDown< ParentLinks<TSpec> > > >
-..param.TContainer:Type of the container that can be iterated.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..implements:Concept.ForwardIteratorConcept
-..param.TSpec:The specialization type. Specifies the depth-first search mode.
-...type:Tag.DFS Order.tag.Preorder
-...type:Tag.DFS Order.tag.PreorderEmptyEdges
-...type:Tag.DFS Order.tag.Postorder
-...type:Tag.DFS Order.tag.PostorderEmptyEdges
-..remarks:If not copy-constructed the @Spec.TopDownHistory Iterator@ starts in the root node of the string tree.
-Depending on the depth-first search mode the root is not the first DFS node. To go to the first DFS node use @Function.goBegin@.
-..remarks:Note that the virtual tree can either be a virtual suffix tree or a virtual prefix tree. The suffix tree is shown in Figure 1 and is implemented with the @Spec.IndexDfi@, @Spec.IndexEsa@ and @Spec.IndexWotd@. In contrast the @Spec.FMIndex@ implements a prefix trie shown in Figure 2.
-..include:seqan/index.h
-
-.Memfunc.TopDownHistory Iterator#Iterator
-..class:Spec.TopDownHistory Iterator
-..summary:Constructor
-..signature:Iterator(index)
-..signature:Iterator(iterator)
-..param.index:An index object.
-..param.iterator:Another TopDownHistory iterator. (copy constructor)
-...type:Spec.TopDownHistory Iterator
-..remarks:If not copy-constructed the @Spec.TopDownHistory Iterator@ starts in the root node of the suffix tree.
-..remarks:Note that the virtual tree can either be a virtual suffix tree or a virtual prefix tree. The suffix tree is shown in Figure 1 and is implemented with the @Spec.IndexDfi@, @Spec.IndexEsa@ and @Spec.IndexWotd@. In contrast the @Spec.FMIndex@ implements a prefix trie shown in Figure 2.
-*/
+        SEQAN_HOST_DEVICE inline Iter const &
+        operator = (Iter<TIndex, VSTree<TopDown<TSpec2> > > const &_origin)
+        {
+            index = &container(_origin);
+            vDesc = value(_origin);
+            _parentDesc = nodeUp(_origin);
+            return *this;
+        }
+    };
+
+
 /*!
  * @class TopDownHistoryIterator Top Down History Iterator
- * 
  * @implements ForwardIteratorConcept
- * 
  * @extends TopDownIterator
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief String tree iterator that can go down, right, and up. Supports depth-
  *        first search.
- * 
- * @signature template <typename TIndex, typename TSpec> 
- *            Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > >
- * 
- * @tparam TSpec Specifies the depth-first search mode.  Types: @link DFS Order @endlink
+ *
+ * @signature template <typename TIndex, typename TSpec>
+ *            class Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > >;
+ *
+ * @tparam TSpec Specifies the depth-first search mode.  Types: @link DfsOrder @endlink
  * @tparam TIndex Type of the container that can be iterated. Types: @link IndexDfi @endlink, @link IndexEsa @endlink,
  *                @link IndexWotd @endlink, @link FMIndex @endlink, @link IndexSa @endlink
  *
- * @section Note Instead of using the class Iter directly we recommend to use the result of the metafunction 
- *               Iterator&lt;TContainer, TopDown&lt;ParentLinks&lt;TSpec&gt; &gt; &gt;::Type (which is Iter&lt;TContainer, VSTree&lt;ParentLinks&lt;TopDown&lt;TSpec&gt; &gt; &gt; &gt;).
+ * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
+ *       Iterator&lt;TContainer, TopDown&lt;ParentLinks&lt;TSpec&gt; &gt; &gt;::Type (which is Iter&lt;TContainer,
+ *       VSTree&lt;ParentLinks&lt;TopDown&lt;TSpec&gt; &gt; &gt; &gt;).
  *
- * 
- * @section Remarks
- * 
  * If not copy-constructed the @link TopDownHistoryIterator @endlink starts in the root node of the string tree.
  * Depending on the depth-first search mode the root is not the first DFS node. To go to the first DFS node use @link
  * VSTreeIterator#goBegin @endlink.
+ *
  * @section Example
  *
  * @link DemoConstraintIterator @endlink
  */
 /*!
  * @fn TopDownHistoryIterator::Iterator
- * 
  * @brief Constructor
- * 
- * @signature Iterator(index)
- * @signature Iterator(iterator)
- * 
- * @param index An index object.
- * @param iterator Another TopDownHistory iterator. (copy constructor) Types:
- *                 TopDownHistory Iterator
- * 
- * @section Remarks
- * 
+ *
+ * @signature Iter::Iter(index);
+ * @signature Iter::Iter(iterator);
+ *
+ * @param[in] index    An index object.
+ * @param[in] iterator Another TopDownHistory iterator. (copy constructor) Types:
+ *                     TopDownHistory Iterator
+ *
  * If not copy-constructed the @link TopDownHistoryIterator @endlink starts in
  * the root node of the string tree.
  */
 
-	template < typename TVSTreeIter >
-	struct HistoryStackEntry_;
-	
-	template <typename TSize>
-	struct HistoryStackEsa_
-	{
-		Pair<TSize> range;		// current SA interval of hits
-		HistoryStackEsa_() {}
-		template <typename TSize_>
-		HistoryStackEsa_(Pair<TSize_> const &_range): range(_range) {}
-	};
-
-	template < typename TIndex, typename TSpec >
-	struct HistoryStackEntry_< Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > >
-	{
-		typedef HistoryStackEsa_<typename Size<TIndex>::Type>	Type;
-	};
-
-	template < typename TIndex, class TSpec >
-	class Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > >:
-		public Iter< TIndex, VSTree< TopDown<> > >
-	{
-	public:
-
-		typedef Iter< TIndex, VSTree< TopDown<> > >		TBase;
-		typedef	typename HistoryStackEntry_<Iter>::Type	TStackEntry;
-		typedef String<TStackEntry, Block<> >			TStack;
-		typedef Iter									iterator;
-
-		TStack			history;	// contains all previously visited intervals (allows to go up)
+    template < typename TVSTreeIter >
+    struct HistoryStackEntry_;
+
+    template <typename TSize>
+    struct HistoryStackEsa_
+    {
+        Pair<TSize> range;        // current SA interval of hits
+
+        SEQAN_HOST_DEVICE inline
+        HistoryStackEsa_() {}
+
+        template <typename TSize_>
+        SEQAN_HOST_DEVICE inline
+        HistoryStackEsa_(Pair<TSize_> const &_range): range(_range) {}
+    };
+
+    template < typename TIndex, typename TSpec >
+    struct HistoryStackEntry_< Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > >
+    {
+        typedef HistoryStackEsa_<typename Size<TIndex>::Type>    Type;
+    };
+
+    template <typename TVSTreeIter>
+    struct HistoryStack_;
+
+    template <typename TIndex, typename TSpec>
+    struct HistoryStack_<Iter<TIndex, VSTree<TSpec> > >
+    {
+        typedef Iter<TIndex, VSTree<TSpec> >                        TIter_;
+        typedef String<typename HistoryStackEntry_<TIter_>::Type>   Type;
+
+//        typedef String<typename HistoryStackEntry_<TIter_>::Type, Block<> > Type;
+    };
+
+    template < typename TIndex, class TSpec >
+    class Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > >:
+        public Iter< TIndex, VSTree< TopDown<> > >
+    {
+    public:
+
+        typedef Iter< TIndex, VSTree< TopDown<> > >        TBase;
+        typedef    typename HistoryStack_<Iter>::Type      TStack;
+        typedef Iter                                    iterator;
+
+        TStack            history;    // contains all previously visited intervals (allows to go up)
 
 //____________________________________________________________________________
 
+        SEQAN_HOST_DEVICE
         Iter() :
             TBase()
         {}
 
-		Iter(TIndex &_index):
-			TBase(_index) {}
+        SEQAN_HOST_DEVICE
+        Iter(TIndex &_index):
+            TBase(_index) {}
 
-		Iter(TIndex &_index, MinimalCtor):
-			TBase(_index, MinimalCtor()) {}
+        SEQAN_HOST_DEVICE
+        Iter(TIndex &_index, MinimalCtor):
+            TBase(_index, MinimalCtor()) {}
 
-		Iter(Iter const &_origin):
-			TBase((TBase const &)_origin),
-			history(_origin.history) {}
+        SEQAN_HOST_DEVICE
+        Iter(Iter const &_origin):
+            TBase((TBase const &)_origin),
+            history(_origin.history) {}
 
 //____________________________________________________________________________
 
-		inline Iter const &
-		operator = (Iter const &_origin)
-		{
-			*(TBase*)(this) = _origin;
-			history = _origin.history;
-			return *this;
-		}
-	};
+        SEQAN_HOST_DEVICE inline
+        Iter const &
+        operator = (Iter const &_origin)
+        {
+            *(TBase*)(this) = _origin;
+            history = _origin.history;
+            return *this;
+        }
+    };
 
 //    //TODO(weese): define concepts somewhere else
 //    SEQAN_CONCEPT(ParentLinksConcepts,(T))
@@ -449,94 +379,63 @@ Depending on the depth-first search mode the root is not the first DFS node. To
 //    private:
 //        T a;
 //    };
-//    
+//
 //    template <typename TIndex, class TSpec>
-//    SEQAN_CONCEPT_IMPL(Iter<TIndex,VSTree<TopDown<ParentLinks<TSpec> > > >, (ParentLinksConcepts));
-
-/**
-.Spec.BottomUp Iterator:
-..cat:Index
-..general:Spec.VSTree Iterator
-..summary:Iterator for an efficient postorder depth-first search in a suffix tree.
-..signature:Iterator<TContainer, BottomUp<TSpec> >::Type
-..signature:Iter<TContainer, VSTree< BottomUp<TSpec> > >
-..param.TContainer:Type of the container that can be iterated.
-...type:Spec.IndexEsa
-...metafunction:Metafunction.Container
-..implements:Concept.ForwardIteratorConcept
-..param.TSpec:The specialization type.
-..include:seqan/index.h
-
-.Memfunc.BottomUp Iterator#Iterator
-..class:Spec.BottomUp Iterator
-..summary:Constructor
-..signature:Iterator(index)
-..signature:Iterator(iterator)
-..param.index:An index object.
-..param.iterator:Another BottomUp iterator. (copy constructor)
-...type:Spec.BottomUp Iterator
-..remarks:If not copy-constructed the @Spec.BottomUp Iterator@ starts in the first DFS node, which is the left-most leaf of the suffix tree.
-*/
+//    SEQAN_CONCEPT_IMPL((ParentLinksConcepts), Iter<TIndex,VSTree<TopDown<ParentLinks<TSpec> > > >);
+
 /*!
  * @class BottomUpIterator Bottom Up Iterator
- * 
  * @implements ForwardIteratorConcept
- * 
  * @extends VSTreeIterator
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Iterator for an efficient postorder depth-first search in a virtual string tree.
- * 
+ *
  * @signature template <typename TIndex, typename TSpec>
- *            Iter<TContainer, VSTree< BottomUp<TSpec> > >
- * 
+ *            class Iter<TContainer, VSTree< BottomUp<TSpec> > >;
+ *
  * @tparam TSpec The specialization type.
  * @tparam TIndex Type of the container that can be iterated.
  *
- * @section Note 
- *
- * Instead of using the class Iter directly we recommend to use the result of the metafunction 
- * Iterator&lt;TContainer, BottomUp&lt;TSpec&gt; &gt;::Type (which is Iter&lt;TContainer, VSTree&lt;BottomUp&lt;TSpec&gt; &gt; &gt;).
- * 
- * @fn Bottom Up Iterator::Iterator
- * 
+ * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
+ *       Iterator&lt;TContainer, BottomUp&lt;TSpec&gt; &gt;::Type (which is Iter&lt;TContainer,
+ *       VSTree&lt;BottomUp&lt;TSpec&gt; &gt; &gt;).
+ */
+
+/*!
+ * @fn BottomUpIterator::Iter
  * @brief Constructor
- * 
- * @signature Iterator(index)
- * @signature Iterator(iterator)
- * 
- * @param index An index object.
- * @param iterator A Bottom Up Iterator.
- * 
- * @section Remarks
- * 
+ *
+ * @signature Iter::Iter(index);
+ * @signature Iter::Iter(iterator);
+ *
+ * @param[in] index    An index object.
+ * @param[in] iterator A Bottom Up Iterator.
+ *
  * If not copy-constructed the @link BottomUpIterator @endlink starts in the first DFS node, which is the left-most leaf
  * of the virtual string tree.
  */
 
-	template < typename TIndex, typename TSpec >
-	struct HistoryStackEntry_< Iter< TIndex, VSTree< BottomUp<TSpec> > > >
-	{
-		typedef HistoryStackEsa_<typename Size<TIndex>::Type>	Type;
-	};
-
-	template < typename TIndex, typename TSpec >
-	class Iter< TIndex, VSTree< BottomUp<TSpec> > > 
-	{
-	public:
-
-		typedef typename VertexDescriptor<TIndex>::Type	TVertexDesc;
-		typedef typename Size<TIndex>::Type				TSize;
-		typedef	typename HistoryStackEntry_<Iter>::Type	TStackEntry;
-		typedef String<TStackEntry, Block<> >			TStack;
-		typedef Iter									iterator;
-
-		TIndex	const	*index;			// container of all necessary tables
-		TVertexDesc		vDesc;			// current interval in suffix array and
-										// right border of parent interval (unused here)
-		TSize			lValue;			// current l-value
-		TStack			history;		// contains all left borders of current l-intervals (== left borders of history intervals)
+    template < typename TIndex, typename TSpec >
+    struct HistoryStackEntry_< Iter< TIndex, VSTree< BottomUp<TSpec> > > >
+    {
+        typedef HistoryStackEsa_<typename Size<TIndex>::Type>    Type;
+    };
+
+    template < typename TIndex, typename TSpec >
+    class Iter< TIndex, VSTree< BottomUp<TSpec> > >
+    {
+    public:
+
+        typedef typename VertexDescriptor<TIndex>::Type    TVertexDesc;
+        typedef typename Size<TIndex>::Type                TSize;
+        typedef    typename HistoryStack_<Iter>::Type      TStack;
+        typedef Iter                                    iterator;
+
+        TIndex    const    *index;            // container of all necessary tables
+        TVertexDesc        vDesc;            // current interval in suffix array and
+                                        // right border of parent interval (unused here)
+        TSize            lValue;            // current l-value
+        TStack            history;        // contains all left borders of current l-intervals (== left borders of history intervals)
 
 //____________________________________________________________________________
 
@@ -545,786 +444,665 @@ Depending on the depth-first search mode the root is not the first DFS node. To
             lValue(0)
         {}
 
-		Iter(TIndex &_index):
-			index(&_index),
-			vDesc(MinimalCtor()),
-			lValue(0)
-		{
-			_indexRequireBottomUpIteration(_index);
-			goBegin(*this);
-		}
-
-		Iter(TIndex &_index, MinimalCtor):
-			index(&_index),
-			vDesc(MinimalCtor()),
-			lValue(0) {}
-
-		Iter(Iter const &_origin):
-			index(&container(_origin)),
-			vDesc(value(_origin)),
-			lValue(_dfsLcp(_origin)),
-			history(_origin.history) {}
+        Iter(TIndex &_index):
+            index(&_index),
+            vDesc(MinimalCtor()),
+            lValue(0)
+        {
+            _indexRequireBottomUpIteration(_index);
+            goBegin(*this);
+        }
+
+        Iter(TIndex &_index, MinimalCtor):
+            index(&_index),
+            vDesc(MinimalCtor()),
+            lValue(0) {}
+
+        Iter(Iter const &_origin):
+            index(&container(_origin)),
+            vDesc(value(_origin)),
+            lValue(_dfsLcp(_origin)),
+            history(_origin.history) {}
 
 //____________________________________________________________________________
 
-		inline Iter const &
-		operator = (Iter const &_origin)
-		{
-			index = &container(_origin);
-			vDesc = _origin.vDesc;
-			lValue = _origin.lValue;
-			history = _origin.history;
-			return *this;
-		}
-	};
+        inline Iter const &
+        operator = (Iter const &_origin)
+        {
+            index = &container(_origin);
+            vDesc = _origin.vDesc;
+            lValue = _origin.lValue;
+            history = _origin.history;
+            return *this;
+        }
+    };
+
 
+    //////////////////////////////////////////////////////////////////////////////
+    // Iterator wrappers
+    //////////////////////////////////////////////////////////////////////////////
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Iterator wrappers
-	//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @mfn StringTreeConcept#Iterator
+ * @headerfile <seqan/index.h>
+ * @brief Returns the type of an iterator to traverse the nodes of a string tree.
+ *
+ * @signature Iterator<TIndex, TSpec>::Type;
+ *
+ * @tparam TIndex The index type.
+ * @tparam TSpec The spec type of a @link VSTreeIterator @endlink, e.g. @link TopDownIterator TopDown<>@endlink or @link BottomUpIterator BottomUp<>@endlink.
+ *
+ * @return Type The resulting string tree iterator type.
+ */
 
-	template <typename TObject, typename TSpec>
-	struct Iterator< TObject, BottomUp<TSpec> > {
-		typedef Iter< TObject, VSTree< BottomUp<TSpec> > > Type;
-	};
+    template <typename TObject, typename TSpec>
+    struct Iterator< TObject, BottomUp<TSpec> > {
+        typedef Iter< TObject, VSTree< BottomUp<TSpec> > > Type;
+    };
 
-	template <typename TObject, typename TSpec>
-	struct Iterator< TObject, TopDown<TSpec> > {
-		typedef Iter< TObject, VSTree< TopDown<TSpec> > > Type;
-	};
+    template <typename TObject, typename TSpec>
+    struct Iterator< TObject, TopDown<TSpec> > {
+        typedef Iter< TObject, VSTree< TopDown<TSpec> > > Type;
+    };
 
 
 
 
-	template < typename TIndex, typename TSpec >
-	inline void _dumpHistoryStack(Iter<TIndex, VSTree<TSpec> > &it) {
-		for(typename Size<TIndex>::Type i = 0; i < length(it.history); ++i)
-			::std::cerr << it.history[i].range << '\t';
-		::std::cerr << value(it) << ::std::endl;
-	}
+    template < typename TIndex, typename TSpec >
+    inline void _dumpHistoryStack(Iter<TIndex, VSTree<TSpec> > &it) {
+        for(typename Size<TIndex>::Type i = 0; i < length(it.history); ++i)
+            std::cerr << it.history[i].range << '\t';
+        std::cerr << value(it) << std::endl;
+    }
 
-	template <typename TText, typename TSpec>
-	inline void
-	_dump(Index<TText, IndexEsa<TSpec> > &index)
-	{
-		::std::cout << "  SA" << ::std::endl;
-		for(unsigned i=0; i < length(indexSA(index)); ++i)
-			::std::cout << i << ":  " << indexSA(index)[i] << "  " << suffix(indexText(index), indexSA(index)[i]) << ::std::endl;
+    template <typename TText, typename TSpec>
+    inline void
+    _dump(Index<TText, IndexEsa<TSpec> > &index)
+    {
+        std::cout << "  SA" << std::endl;
+        for(unsigned i=0; i < length(indexSA(index)); ++i)
+            std::cout << i << ":  " << indexSA(index)[i] << "  " << suffix(indexText(index), indexSA(index)[i]) << std::endl;
 
-		::std::cout << ::std::endl << "  LCP" << ::std::endl;
-		for(unsigned i=0; i < length(indexLcp(index)); ++i)
-			::std::cout << i << ":  " << indexLcp(index)[i] << ::std::endl;
+        std::cout << std::endl << "  LCP" << std::endl;
+        for(unsigned i=0; i < length(indexLcp(index)); ++i)
+            std::cout << i << ":  " << indexLcp(index)[i] << std::endl;
 
-		::std::cout << ::std::endl << "  Childtab" << ::std::endl;
-		for(unsigned i=0; i < length(indexChildtab(index)); ++i)
-			::std::cout << i << ":  " << indexChildtab(index)[i] << ::std::endl;
+        std::cout << std::endl << "  Childtab" << std::endl;
+        for(unsigned i=0; i < length(indexChildtab(index)); ++i)
+            std::cout << i << ":  " << indexChildtab(index)[i] << std::endl;
 
-		::std::cout << ::std::endl;
-	}
+        std::cout << std::endl;
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template < typename TIndex, typename TSpec >
-	inline bool _dfsReversedOrder(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it) {
+    template < typename TIndex, typename TSpec >
+    inline bool _dfsReversedOrder(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it) {
         return lcpAt(_dfsRange(it).i2 - 1, container(it)) > back(it.history).range.i2;
-	}
+    }
 
-	// standard push/pop handlers of lcp-dfs-traversal
-	template < typename TIndex, typename TSpec, typename TSize >
-	inline void _dfsOnPop(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, TSize const) {
+    // standard push/pop handlers of lcp-dfs-traversal
+    template < typename TIndex, typename TSpec, typename TSize >
+    inline void _dfsOnPop(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, TSize const) {
         _dfsRange(it).i1 = back(it.history).range.i1;
-		_dfsLcp(it) = back(it.history).range.i2;
-		pop(it.history);
-	}
+        _dfsLcp(it) = back(it.history).range.i2;
+        eraseBack(it.history);
+    }
 
-	template < typename TIndex, typename TSpec, typename TElement >
-	inline void _dfsOnPush(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, TElement const &e) {
-		appendValue(it.history, e);
-	}
+    template < typename TIndex, typename TSpec, typename TElement >
+    inline void _dfsOnPush(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, TElement const &e) {
+        appendValue(it.history, e);
+    }
 
-	template < typename TIndex, typename TSpec >
-	inline void _dfsOnLeaf(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it) {
-		_setSizeInval(_dfsLcp(it));
-	}
+    template < typename TIndex, typename TSpec >
+    inline void _dfsOnLeaf(Iter<TIndex, VSTree< BottomUp<TSpec> > > &it) {
+        _setSizeInval(_dfsLcp(it));
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 // postorder bottom up iterator (dfs)
 
-	template < typename TIndex, typename TSpec, typename THideEmptyEdges >
-	inline void goNextImpl(
-		Iter<TIndex, VSTree< BottomUp<TSpec> > > &it, 
-		VSTreeIteratorTraits<Postorder_, THideEmptyEdges> const) 
-	{
-		TIndex const &index = container(it);
-		do {
-			// postorder dfs via lcp-table
-			if (isRoot(it)) {
-				_dfsClear(it);
-				return;
-			}
-			
-			if (_dfsRange(it).i2)
-			{
-				typedef typename Size<TIndex>::Type TSize;
-				typedef typename Iter<TIndex, VSTree< BottomUp<TSpec> > >::TStackEntry TStackEntry;
-				TStackEntry	_top_ = back(it.history);
-				TSize		lcp_i = lcpAt(_dfsRange(it).i2 - 1, index);
-
-				if (lcp_i < _top_.range.i2) {
-					_dfsOnPop(it, lcp_i);
-					if (nodePredicate(it)) return;
-					else continue;
-				}
-
-				if (lcp_i > _top_.range.i2) {
-					_top_.range.i1 = _dfsRange(it).i1;
-					_top_.range.i2 = lcp_i;
-					_dfsOnPush(it, _top_);
-				}
-
-	// innerer Knoten:
-	// wenn kein Pop, aber Push -> begehe mind. 2. Teilbaum irgendeines Vorfahrs
-	// wenn kein Pop, kein Push -> verlasse mind. zweites Kindblatt
-	// wenn Pop, aber kein Push -> verlasse Wurzel des mind. 2.Teilbaums
-	// wenn Pop und Push        -> verlasse ersten Teilbaum (sieht Vater zum ersten Mal und pusht jenen)
-
-	// wenn nach Pop ein Pop folgen wuerde	-> Vater ist Top of Stack
-	// wenn nach Pop ein Push folgen wuerde	-> Vater erst beim Push auf Stack (-> zwischenspeichern)
-			}
-
-			// last lcp entry (== 0) causes removal of toplevel interval
-			if ((_dfsRange(it).i1 = _dfsRange(it).i2++) == length(index)) {
-				_dfsOnPop(it, 0);
-				_dfsRange(it).i2 = _dfsRange(it).i1;
-			} else {
-				// skip $ leafs (empty edges)
-				if (THideEmptyEdges::VALUE &&
-					suffixLength(saAt(_dfsRange(it).i1, index), index) == lcpAt(_dfsRange(it).i1, index))
-					continue;
-
-				_dfsOnLeaf(it);
-	// Blatt:
-	// wenn danach kein Pop, aber Push -> Vater wird erst noch gepusht
-	// wenn danach Pop				   -> Vater ist Top des Stack
-			}
-			if (nodePredicate(it)) return;
-		} while (true);
-	}
+    template < typename TIndex, typename TSpec, typename THideEmptyEdges >
+    inline void goNextImpl(
+        Iter<TIndex, VSTree< BottomUp<TSpec> > > &it,
+        VSTreeIteratorTraits<Postorder_, THideEmptyEdges> const)
+    {
+        typedef Iter<TIndex, VSTree< BottomUp<TSpec> > >    TIter;
+        typedef typename Size<TIndex>::Type                 TSize;
+        typedef typename HistoryStackEntry_<TIter>::Type    TStackEntry;
+
+        TIndex const &index = container(it);
+        do {
+            // postorder dfs via lcp-table
+            if (isRoot(it)) {
+                _dfsClear(it);
+                return;
+            }
+
+            if (_dfsRange(it).i2)
+            {
+                TStackEntry    _top_ = back(it.history);
+                TSize        lcp_i = lcpAt(_dfsRange(it).i2 - 1, index);
+
+                if (lcp_i < _top_.range.i2) {
+                    _dfsOnPop(it, lcp_i);
+                    if (nodePredicate(it)) return;
+                    else continue;
+                }
+
+                if (lcp_i > _top_.range.i2) {
+                    _top_.range.i1 = _dfsRange(it).i1;
+                    _top_.range.i2 = lcp_i;
+                    _dfsOnPush(it, _top_);
+                }
+
+    // innerer Knoten:
+    // wenn kein Pop, aber Push -> begehe mind. 2. Teilbaum irgendeines Vorfahrs
+    // wenn kein Pop, kein Push -> verlasse mind. zweites Kindblatt
+    // wenn Pop, aber kein Push -> verlasse Wurzel des mind. 2.Teilbaums
+    // wenn Pop und Push        -> verlasse ersten Teilbaum (sieht Vater zum ersten Mal und pusht jenen)
+
+    // wenn nach Pop ein Pop folgen wuerde    -> Vater ist Top of Stack
+    // wenn nach Pop ein Push folgen wuerde    -> Vater erst beim Push auf Stack (-> zwischenspeichern)
+            }
+
+            // last lcp entry (== 0) causes removal of toplevel interval
+            if ((_dfsRange(it).i1 = _dfsRange(it).i2++) == length(index)) {
+                _dfsOnPop(it, 0);
+                _dfsRange(it).i2 = _dfsRange(it).i1;
+            } else {
+                // skip $ leafs (empty edges)
+                if (THideEmptyEdges::VALUE &&
+                    suffixLength(saAt(_dfsRange(it).i1, index), index) == lcpAt(_dfsRange(it).i1, index))
+                    continue;
+
+                _dfsOnLeaf(it);
+    // Blatt:
+    // wenn danach kein Pop, aber Push -> Vater wird erst noch gepusht
+    // wenn danach Pop                   -> Vater ist Top des Stack
+            }
+            if (nodePredicate(it)) return;
+        } while (true);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.repLength:
-..summary:Returns the length of the substring representing the path from root to $iterator$ node.
-..cat:Index
-..signature:repLength(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:The length of the sequence returned by @Function.representative@
-...type:Metafunction.Size|Size type of the underlying index
-..include:seqan/index.h
-..example
-...text:The following code shows a simple example how the function @Function.repLength@ is used.
-...file:demos/index/index_begin_range_goDown_representative_repLength.cpp
-...output:The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-*/
 /*!
  * @fn VSTreeIterator#repLength
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the length of the substring representing the path from root to <tt>iterator</tt> node.
- * 
- * @signature TSize repLength(iterator)
- * 
- * @param iterator An iterator of a string tree. Types: @link VSTreeIterator @endlink
- * 
+ *
+ * @signature TSize repLength(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree. Types: @link VSTreeIterator @endlink
+ *
  * @return TSize The length of the sequence returned by @link VSTreeIterator#representative
- *               @endlink The return type is the result of the metafunction @link Size @endlink of the underlying 
+ *               @endlink The return type is the result of the metafunction @link Size @endlink of the underlying
  *               index.
- * 
+ *
  * @link DemoMummy @endlink
  * @link DemoSupermaximalRepeats @endlink
  * @link DemoMaximalUniqueMatches @endlink
  */
-	template < typename TIndex, typename TSpec >
-	inline typename Size<TIndex>::Type 
-	repLength(Iter< TIndex, VSTree<BottomUp<TSpec> > > const &it) 
-	{
-		typename Size<TIndex>::Type lcp;
-		if (!_isSizeInval(lcp = it.lValue))
-			return lcp;
-		else
-			return suffixLength(getOccurrence(it), container(it));
-	}
-
-
-	template < typename TIndex, typename TSize >
-	inline typename Size<TIndex>::Type
-	repLength(TIndex const &index, VertexEsa<TSize> const &vDesc) 
-	{
-		if (_isLeaf(vDesc)) return suffixLength(saAt(vDesc.range.i1, index), index);
-		if (_isRoot(vDesc)) return 0;
-
-		// get l-value of suffix array range
-		TSize lval = _getUp(vDesc.range.i2, index);
-		if (!(vDesc.range.i1 < lval && lval < vDesc.range.i2))
-			lval = _getDown(vDesc.range.i1, index);
-		
-		// retrieve the longest-common-prefix length of suffices in range
-		return lcpAt(lval - 1, index);
-	}
-
-	template < typename TIndex, typename TSpec >
-	inline typename Size<TIndex>::Type
-	repLength(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it) 
-	{
-		return repLength(container(it), value(it));
-	}
+    template < typename TIndex, typename TSpec >
+    inline typename Size<TIndex>::Type
+    repLength(Iter< TIndex, VSTree<BottomUp<TSpec> > > const &it)
+    {
+        typename Size<TIndex>::Type lcp;
+        if (!_isSizeInval(lcp = it.lValue))
+            return lcp;
+        else
+            return suffixLength(getOccurrence(it), container(it));
+    }
+
+
+    template < typename TIndex, typename TSize >
+    SEQAN_HOST_DEVICE inline typename Size<TIndex>::Type
+    repLength(TIndex const &index, VertexEsa<TSize> const &vDesc)
+    {
+        if (_isLeaf(vDesc)) return suffixLength(saAt(vDesc.range.i1, index), index);
+        if (_isRoot(vDesc)) return 0;
+
+        // get l-value of suffix array range
+        TSize lval = _getUp(vDesc.range.i2, index);
+        if (!(vDesc.range.i1 < lval && lval < vDesc.range.i2))
+            lval = _getDown(vDesc.range.i1, index);
+
+        // retrieve the longest-common-prefix length of suffices in range
+        return lcpAt(lval - 1, index);
+    }
+
+    template < typename TIndex, typename TSpec >
+    SEQAN_HOST_DEVICE inline typename Size<TIndex>::Type
+    repLength(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it)
+    {
+        return repLength(container(it), value(it));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.nodeDepth:
-..summary:Returns the zero-based node depth of the $iterator$ node.
-..cat:Index
-..signature:nodeDepth(iterator)
-..class:Spec.TopDownHistory Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDownHistory Iterator
-..returns:The length of the path from root to $iterator$ node, e.g. 0 is returned for the root node.
-...type:Metafunction.Size|Size type of the underlying index
-..include:seqan/index.h
-*/
 /*!
  * @fn TopDownHistoryIterator#nodeDepth
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns the zero-based node depth of the <tt>iterator</tt> node.
- * 
- * @signature TSize nodeDepth(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
+ *
+ * @signature TSize nodeDepth(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
  * @return TSize The length of the path from root to <tt>iterator</tt> node,
  *               e.g. 0 is returned for the root node. The type of the result
  *               is the result of the metafunction @link Size @endlink of the underlying index.
  */
 
-	template < typename TIndex, typename TSpec >
-	inline typename Size<TIndex>::Type
-	nodeDepth(Iter< TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > const &it) 
-	{
-		return length(it.history);
-	}
+    template < typename TIndex, typename TSpec >
+    inline typename Size<TIndex>::Type
+    nodeDepth(Iter< TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > const &it)
+    {
+        return length(it.history);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.parentRepLength:
-..summary:Returns the length of the substring representing the path from root to $iterator$'s parent node.
-..cat:Index
-..signature:parentRepLength(iterator)
-..class:Spec.TopDown Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..returns:The length of the sequence returned by @Function.representative@ of the parent node.
-...type:Metafunction.Size|Size type of the underlying index
-..include:seqan/index.h
-*/
 /*!
  * @fn TopDownIterator#parentRepLength
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the length of the substring representing the path from root to <tt>iterator</tt>'s parent node.
- * 
- * @signature TSize parentRepLength(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
+ *
+ * @signature TSize parentRepLength(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
  * @return TReturn The length of the sequence returned by @link VSTreeIterator#representative @endlink of the parent node. The result
  *                 type is the resultof the metafunction @link Size @endlink of the underlying index.
  */
 
-	template < typename TIndex, typename TSpec >
-	inline typename Size<TIndex>::Type
-	parentRepLength(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it) 
-	{
-		return repLength(container(it), nodeUp(it));
-	}
+    template < typename TIndex, typename TSpec >
+    SEQAN_HOST_DEVICE inline typename Size<TIndex>::Type
+    parentRepLength(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it)
+    {
+        return repLength(container(it), nodeUp(it));
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.emptyParentEdge:
-..summary:Returns $true$ iff the edge label from the $iterator$ node to its parent is empty.
-..cat:Index
-..signature:bool emptyParentEdge(iterator)
-..classSpec.TopDown Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..returns:$true$ if @Function.parentEdgeLength@$ returns 0, otherwise $false$.
-...type:Metafunction.Size|Size type of the underlying index
-..include:seqan/index.h
-*/
 /*!
  * @fn TopDownIterator#emptyParentEdge
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns <tt>true</tt> iff the edge label from the <tt>iterator</tt>
  *        node to its parent is empty.
- * 
- * @signature bool emptyParentEdge(iterator)
- * 
- * @param iterator An iterator of a string tree. Types: @link TopDownIterator @endlink
- * 
- * @return TReturn <tt>true</tt> if @link TopDownIterator#parentEdgeLength @endlink<tt> returns 0, otherwise </tt>false$. 
+ *
+ * @signature bool emptyParentEdge(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree. Types: @link TopDownIterator @endlink
+ *
+ * @return bool <tt>true</tt> if @link TopDownIterator#parentEdgeLength @endlink<tt> returns 0, otherwise </tt>false$.
  */
 
-	template < typename TIndex, typename TSpec >
-	inline bool
-	emptyParentEdge(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it) 
-	{
-		// the following is more efficient than 
-		// return parentEdgeLength(it) == 0;
-		TIndex const &index = container(it);
-		typename SAValue<TIndex>::Type pos = getOccurrence(it);
-		return getSeqOffset(pos, stringSetLimits(index)) + parentRepLength(it)
-			== sequenceLength(getSeqNo(pos, stringSetLimits(index)), index);
-	}
+    template < typename TIndex, typename TSpec >
+    SEQAN_HOST_DEVICE inline bool
+    emptyParentEdge(Iter< TIndex, VSTree<TopDown<TSpec> > > const &it)
+    {
+        // the following is more efficient than
+        // return parentEdgeLength(it) == 0;
+        TIndex const &index = container(it);
+        typename SAValue<TIndex>::Type pos = getOccurrence(it);
+        return getSeqOffset(pos, stringSetLimits(index)) + parentRepLength(it)
+            == sequenceLength(getSeqNo(pos, stringSetLimits(index)), index);
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.lca:
-..summary:Returns the last common ancestor of two tree nodes.
-..cat:Index
-..signature:bool lca(a, b, result)
-..class:Spec.TopDownHistory Iterator
-..param.a:The first node.
-...type:Spec.TopDownHistory Iterator
-..param.b:The second node.
-...type:Spec.TopDownHistory Iterator
-..param.result:A reference to the resulting lca node.
-...type:Spec.TopDownHistory Iterator
-..returns:$false$ if the lca of $a$ and $b$ is the root node, otherwise $true$.
-..include:seqan/index.h
-*/
 /*!
  * @fn TopDownHistoryIterator#lca
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the last common ancestor of two tree nodes.
- * 
- * @signature bool lca(a, b, result)
- * 
- * @param a The first node. Types: @link TopDownHistoryIterator @endlink
- * @param b The second node. Types: @link TopDownHistoryIterator @endlink
- * @param result A reference to the resulting lca node. Types: @link TopDownHistoryIterator @endlink 
- * 
+ *
+ * @signature bool lca(a, b, result);
+ *
+ * @param[in]  a      The first node. Types: @link TopDownHistoryIterator @endlink
+ * @param[in]  b      The second node. Types: @link TopDownHistoryIterator @endlink
+ * @param[out] result A reference to the resulting lca node. Types: @link TopDownHistoryIterator @endlink
+ *
  * @return TReturn <tt>false</tt> if the lca of <tt>a</tt> and <tt>b</tt> is the root node, otherwise <tt>true</tt>.
  */
 
-	template < typename TIndex, class TSpec1, class TSpec2 >
-	inline bool lca(
-		Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &a, 
-		Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec2> > > > &b, 
-		Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &_lca)
-	{
-		typedef Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > TIter;
-		typename TIter::TStack::const_iterator iA;
-		typename TIter::TStack::const_iterator iB;
-
-		typedef typename Size<TIndex>::Type TSize;
-
-		typename HistoryStackEntry_<TIter>::Type hA, hB;
-
-		// push current intervals
-		hA = value(a).range;
-		hB = value(b).range;
-		appendValue(a.history, hA);
-		appendValue(b.history, hB);
-
-		TSize s = min(length(a.history), length(b.history)), i0 = 0;
-		
-		while (s) {
-			TSize m = s / 2;
-			iA = begin(a.history, Standard()) + i0 + m;
-			iB = begin(b.history, Standard()) + i0 + m;
-			if ((*iA).range == (*iB).range) {
-				i0 += m + 1;
-				s -= m + 1;
-			} else
-				s = m;
-		}
-
-		_lca.history = prefix(a.history, i0);
-
-		// pop current intervals
-		pop(a.history);
-		pop(b.history);
-		goUp(_lca);
-
-		return i0;
-	}
+    template < typename TIndex, class TSpec1, class TSpec2 >
+    inline bool lca(
+        Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &a,
+        Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec2> > > > &b,
+        Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &_lca)
+    {
+        typedef Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > TIter;
+        typename TIter::TStack::const_iterator iA;
+        typename TIter::TStack::const_iterator iB;
+
+        typedef typename Size<TIndex>::Type TSize;
+
+        typename HistoryStackEntry_<TIter>::Type hA, hB;
+
+        // push current intervals
+        hA = value(a).range;
+        hB = value(b).range;
+        appendValue(a.history, hA);
+        appendValue(b.history, hB);
+
+        TSize s = min(length(a.history), length(b.history)), i0 = 0;
+
+        while (s) {
+            TSize m = s / 2;
+            iA = begin(a.history, Standard()) + i0 + m;
+            iB = begin(b.history, Standard()) + i0 + m;
+            if ((*iA).range == (*iB).range) {
+                i0 += m + 1;
+                s -= m + 1;
+            } else
+                s = m;
+        }
+
+        _lca.history = prefix(a.history, i0);
+
+        // pop current intervals
+        eraseBack(a.history);
+        eraseBack(b.history);
+        goUp(_lca);
+
+        return i0;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.lcp:
-..summary:Returns the length of the longest-common-prefix of two suffix tree nodes.
-..cat:Index
-..signature:lcp(a, b)
-..class:Spec.TopDownHistory Iterator
-..param.a:The first node.
-...type:Spec.TopDownHistory Iterator
-..param.b:The second node.
-...type:Spec.TopDownHistory Iterator
-..returns:The lcp-length of $a$ and $b$.
-..include:seqan/index.h
-*/
-/*! 
+/*!
  * @fn TopDownHistoryIterator#lcp
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the length of the longest-common-prefix of two suffix tree
  *        nodes.
- * 
- * @signature TSize lcp(a, b)
- * 
- * @param a The first node. Types: @link TopDownHistoryIterator @endlink
- * @param b The second node. Types: @link TopDownHistoryIterator @endlink
- * 
+ *
+ * @signature TSize lcp(a, b);
+ *
+ * @param[in] a The first node. Types: @link TopDownHistoryIterator @endlink
+ * @param[in] b The second node. Types: @link TopDownHistoryIterator @endlink
+ *
  * @return TSize The lcp-length of <tt>a</tt> and <tt>b</tt>. The type of the result is the result of the metafunction
  *               @link Size @endlink of the @link Index @endlink of the iterator
  */
-	// return the lcp of a and b by seeking the lca of them
-	template < typename TIndex, class TSpec1, class TSpec2 >
-	inline typename Size<TIndex>::Type lcp(
-		Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &a, 
-		Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec2> > > > &b) 
-	{
-		typedef Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > TIter;
-		typename TIter::TStack::const_iterator iA;
-		typename TIter::TStack::const_iterator iB;
-
-		typedef typename Size<TIndex>::Type TSize;
-
-		typename HistoryStackEntry_<TIter>::Type hA, hB;
-
-		// push current intervals
-		hA = value(a).range;
-		hB = value(b).range;
-		appendValue(a.history, hA);
-		appendValue(b.history, hB);
-
-		TSize s = min(length(a.history), length(b.history)), i0 = 0;
-		
-		while (s) {
-			TSize m = s / 2;
-			iA = begin(a.history, Standard()) + i0 + m;
-			iB = begin(b.history, Standard()) + i0 + m;
-			if ((*iA).range == (*iB).range) {
-				i0 += m + 1;
-				s -= m + 1;
-			} else
-				s = m;
-		}
-
-		TSize _lcp = (i0 > 0)? repLength(container(a), TDesc(a.history[i0 - 1], 0)): 0;
-
-		// pop current intervals
-		pop(a.history);
-		pop(b.history);
-
-		return _lcp;
-	}
+    // return the lcp of a and b by seeking the lca of them
+    template < typename TIndex, class TSpec1, class TSpec2 >
+    inline typename Size<TIndex>::Type lcp(
+        Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > &a,
+        Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec2> > > > &b)
+    {
+        typedef Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec1> > > > TIter;
+        typename TIter::TStack::const_iterator iA;
+        typename TIter::TStack::const_iterator iB;
+
+        typedef typename Size<TIndex>::Type TSize;
+
+        typename HistoryStackEntry_<TIter>::Type hA, hB;
+
+        // push current intervals
+        hA = value(a).range;
+        hB = value(b).range;
+        appendValue(a.history, hA);
+        appendValue(b.history, hB);
+
+        TSize s = min(length(a.history), length(b.history)), i0 = 0;
+
+        while (s) {
+            TSize m = s / 2;
+            iA = begin(a.history, Standard()) + i0 + m;
+            iB = begin(b.history, Standard()) + i0 + m;
+            if ((*iA).range == (*iB).range) {
+                i0 += m + 1;
+                s -= m + 1;
+            } else
+                s = m;
+        }
 
-//////////////////////////////////////////////////////////////////////////////
-///.Function.container.param.iterator.type:Spec.VSTree Iterator
+        TSize _lcp = (i0 > 0)? repLength(container(a), TDesc(a.history[i0 - 1], 0)): 0;
+
+        // pop current intervals
+        eraseBack(a.history);
+        eraseBack(b.history);
 
-	template < typename TIndex, class TSpec >
-	inline TIndex const & 
-	container(Iter< TIndex, VSTree<TSpec> > const &it) { 
-		return *it.index; 
-	}
+        return _lcp;
+    }
+
+//////////////////////////////////////////////////////////////////////////////
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline TIndex const &
+    container(Iter< TIndex, VSTree<TSpec> > const &it) {
+        return *it.index;
+    }
 
-	template < typename TIndex, class TSpec >
-	inline TIndex & 
-	container(Iter< TIndex, VSTree<TSpec> > &it) { 
-		return *const_cast<TIndex*>(it.index); 
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline TIndex &
+    container(Iter< TIndex, VSTree<TSpec> > &it) {
+        return *const_cast<TIndex*>(it.index);
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.value.param.object.type:Spec.VSTree Iterator
+/*!
+ * @fn VSTreeIterator#value
+ * @headerfile <seqan/index.h>
+ * @brief Returns a vertex descriptor of the current node.
+ *
+ * @signature TDesc value(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree. Types: @link VSTreeIterator @endlink
+ *
+ * @return TDesc An object of type @link StringTreeConcept#VertexDescriptor @endlink that
+ *               uniquely identifies the current node. The vertex descriptor can be used to
+ *               store node specific values in an @link PropertyMapConcept @endlink.
+ */
+
+/*!
+ * @fn VSTreeIterator#assignProperty
+ * @brief Assigns a property to an item in the property map.
+ * @signature void assignProperty(pm, value(iterator), val)
+ * @param[in,out] pm        An @link PropertyMapConcept @endlink.
+ * @param[in]     iterator  An iterator of a string tree. Types: @link VSTreeIterator @endlink
+ * @param[in]     val       The new value, where the type of the new value must match the value type of the property map.
+*/
+
+/*!
+ * @fn VSTreeIterator#property
+ * @brief Accesses the property of an item in the property map.
+ * @signature TRef property(pm, value(iterator))
+ * @param[in,out] pm        An @link PropertyMapConcept @endlink.
+ * @param[in]     iterator  An iterator of a string tree. Types: @link VSTreeIterator @endlink
+ * @return TRef Reference to the item in the property map of type @link Reference @endlink.
+ */
+
+/*!
+ * @fn VSTreeIterator#getProperty
+ * @brief Get method for an item's property.
+ * @signature TValue getProperty(pm, value(iterator))
+ * @param[in,out] pm        An @link PropertyMapConcept @endlink.
+ * @param[in]     iterator  An iterator of a string tree. Types: @link VSTreeIterator @endlink
+ * @return TValue Reference to the item in the property map of type @link GetValue @endlink.
+ */
 
-	template < typename TIndex, class TSpec >
-	inline typename VertexDescriptor<TIndex>::Type & 
-	value(Iter< TIndex, VSTree<TSpec> > &it) { 
-		return it.vDesc;
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename VertexDescriptor<TIndex>::Type &
+    value(Iter< TIndex, VSTree<TSpec> > &it) {
+        return it.vDesc;
+    }
 
-	template < typename TIndex, class TSpec >
-	inline typename VertexDescriptor<TIndex>::Type const & 
-	value(Iter< TIndex, VSTree<TSpec> > const &it) { 
-		return it.vDesc;
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename VertexDescriptor<TIndex>::Type const &
+    value(Iter< TIndex, VSTree<TSpec> > const &it) {
+        return it.vDesc;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // property map interface
 
-/**
-.Function.resizeVertexMap:
-..cat:Index
-..signature:resizeVertexMap(index, pm)
-..param.index:An index with a suffix tree interface.
-...type:Spec.IndexEsa
-..include:seqan/index.h
-*/
-//TODO (singer): Ask Manuel what to do with resizeEdgeMap and ExternalPropertyMap
 /*!
- * @fn Index#resizeVertexMap
- * 
- * @headerfile seqan/index.h
- * 
+ * @fn StringTreeConcept#resizeVertexMap
+ * @headerfile <seqan/index.h>
  * @brief Initializes a vertex map.
- * 
- * @signature void resizeVertexMap(index, pm)
- * 
- * @param index An index with a suffix tree interface. Types: @link IndexEsa @endlink, @link IndexWotd @endlink
- * @param pm An External Property Map. Types: @link ExternalPropertyMap @endlink
- * 
- * @see ExternalPropertyMap#resizeEdgeMap
+ *
+ * @signature void resizeVertexMap(pm, index);
+ *
+ * @param[in,out] pm    An External Property Map.
+ * @param[in]     index An index with a string tree interface. Types: @link IndexEsa @endlink, @link IndexWotd @endlink
  */
-	template < typename TText, typename TSpec, typename TPropertyMap >
-	inline void
-	resizeVertexMap(
-		Index<TText, TSpec> const& index, 
-		TPropertyMap & pm)
-	{
-		resize(pm, 2 * length(index), Generous());
-	}
+    template < typename TText, typename TSpec, typename TPropertyMap >
+    inline void
+    resizeVertexMap(
+        TPropertyMap & pm,
+        Index<TText, TSpec> const & index)
+    {
+        resize(pm, 2 * length(index), Generous());
+    }
 /* // different interface compared to resizeVertexMap(graph, ...)
-	template < typename TText, typename TSpec, typename TPropertyMap, typename TProperty >
-	inline void
-	resizeVertexMap(
-		Index<TText, TSpec> const& index, 
-		TPropertyMap & pm,
-		TProperty const & prop)
-	{
-		resize(pm, 2 * length(index), prop, Generous());
-	}
+    template < typename TText, typename TSpec, typename TPropertyMap, typename TProperty >
+    inline void
+    resizeVertexMap(
+        Index<TText, TSpec> const& index,
+        TPropertyMap & pm,
+        TProperty const & prop)
+    {
+        resize(pm, 2 * length(index), prop, Generous());
+    }
 */
-	template < typename TSize >
-	inline typename Id< VertexEsa<TSize> const >::Type
-	_getId(VertexEsa<TSize> const &desc) 
-	{
-		TSize i2 = getValueI2(desc.range);
-		if (_isSizeInval(i2) || i2 == desc.parentRight)
-			// desc is the right-most child -> use left interval border
-			return 2 * getValueI1(desc.range);
-		else
-			// desc is not the right-most child -> use right interval border
-			// ensure that it doesn't collide with the left borders
-			return 2 * getValueI2(desc.range) - 1;
-	}
-
-	template < typename TSize >
-	inline typename Id< VertexEsa<TSize> >::Type
-	_getId(VertexEsa<TSize> &desc) 
-	{
-		return _getId(const_cast<VertexEsa<TSize> const &>(desc));
-	}
+    template < typename TSize >
+    inline typename Id< VertexEsa<TSize> const >::Type
+    _getId(VertexEsa<TSize> const &desc)
+    {
+        TSize i2 = getValueI2(desc.range);
+        if (_isSizeInval(i2) || i2 == desc.parentRight)
+            // desc is the right-most child -> use left interval border
+            return 2 * getValueI1(desc.range);
+        else
+            // desc is not the right-most child -> use right interval border
+            // ensure that it doesn't collide with the left borders
+            return 2 * getValueI2(desc.range) - 1;
+    }
+
+    template < typename TSize >
+    inline typename Id< VertexEsa<TSize> >::Type
+    _getId(VertexEsa<TSize> &desc)
+    {
+        return _getId(const_cast<VertexEsa<TSize> const &>(desc));
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.getOccurrence:
-..summary:Returns an occurrence of the @Function.representative@ substring or a q-gram in the index text.
-..cat:Index
-..signature:getOccurrence(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:A position where the @Function.representative@ of $iterator$ occurs in the text (see @Tag.ESA Index Fibres.EsaText@).
-If $iterator$'s container type is $TIndex$ the return type is $SAValue<TIndex>::Type$.
-..include:seqan/index.h
-*/
 /*!
  * @fn VSTreeIterator#getOccurrence
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns an occurrence of the @link VSTreeIterator#representative @endlink substring in the index text.
  *
- * @signature TSAValue getOccurrence(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
- * @return TSAValue A position where the @link VSTreeIterator#representative @endlink of <tt>iterator</tt> occurs in the text. The
- * return type is the result of the metafunction @link SAValue @endlink of the index type of the iterator.
+ * @signature TSAValue getOccurrence(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
+ * @return TSAValue A position where the @link VSTreeIterator#representative @endlink of <tt>iterator</tt> occurs in
+ *         the text.  The return type is the result of the metafunction @link SAValue @endlink of the index type of
+ *         the iterator.
  */
 
-	template < typename TIndex, class TSpec >
-	inline typename SAValue<TIndex>::Type 
-	getOccurrence(Iter< TIndex, VSTree<TSpec> > const &it)
-	{
-		return saAt(value(it).range.i1, container(it));
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename SAValue<TIndex>::Type
+    getOccurrence(Iter< TIndex, VSTree<TSpec> > const &it)
+    {
+        return saAt(value(it).range.i1, container(it));
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.countOccurrences:
-..summary:Returns the number of occurrences of @Function.representative@ substring or a q-gram in the index text.
-..cat:Index
-..signature:countOccurrences(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:The number of positions where the @Function.representative@ of $iterator$ occurs in the text (see @Tag.ESA Index Fibres.EsaText@).
-If $iterator$'s container type is $TIndex$ the return type is $Size<TIndex>::Type$.
-..include:seqan/index.h
-*/
 /*!
  * @fn VSTreeIterator#countOccurrences
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the number of occurrences of @link VSTreeIterator#representative @endlink
  *        substring in the index text.
  *
- * @signature TSize countOccurrences(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
+ * @signature TSize countOccurrences(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
  * @return TSize The number of positions where the @link VSTreeIterator#representative @endlink of <tt>iterator</tt> occurs in the
  *               text. The return type is the result of the metafunction @link Size @endlink of the index type of the
  *               iterator.
 
- * @section Remarks
- * 
  * The necessary index tables are built on-demand via @link Index#indexRequire @endlink if index is not <tt>const</tt>.
- * 
+ *
  * @section Examples
  *
- * @include demos/index/index_counting.cpp
+ * @include demos/dox/index/counting.cpp
  *
  * The result is as follows:
  *
- * @include demos/index/index_counting.cpp.stdout
+ * @include demos/dox/index/counting.cpp.stdout
  */
 
-	template < typename TIndex, class TSpec >
-	inline typename Size<TIndex>::Type 
-	countOccurrences(Iter< TIndex, VSTree<TSpec> > const &it) 
-	{
-		if (_isSizeInval(value(it).range.i2))
-			return length(indexSA(container(it))) - value(it).range.i1;
-		else
-			return value(it).range.i2 - value(it).range.i1;
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename Size<TIndex>::Type
+    countOccurrences(Iter< TIndex, VSTree<TSpec> > const &it)
+    {
+        if (_isSizeInval(value(it).range.i2))
+            return length(indexSA(container(it))) - value(it).range.i1;
+        else
+            return value(it).range.i2 - value(it).range.i1;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.range:
-..summary:Returns the suffix array interval borders of occurrences of @Function.representative@ substring or a q-gram in the index text.
-..cat:Index
-..signature:range(iterator)
-..class:Spec.VSTree Iterator
-..class:Class.Index
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:All positions where a substring occurs in the text (see @Tag.ESA Index Fibres.EsaText@) 
-are stored in a contiguous range of the suffix array.
-$range$ returns begin and end position of this range for occurrences of @Function.representative@.
-If $iterator$'s container type is $TIndex$ the return type is $Pair<Size<TIndex>::Type>.
-..include:seqan/index.h
-..example
-...text:The following code shows a simple example how the function @Function.range@ is used.
-...file:demos/index/index_begin_range_goDown_representative_repLength.cpp
-...output:The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-*/
 /*!
  * @fn VSTreeIterator#range
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the suffix array interval borders of occurrences of @link VSTreeIterator#representative @endlink substring in the
  *        index text.
- * 
- * @signature Pair<TSize> range(iterator)
- * 
- * @param iterator An iterator of a string tree/trie.
- * 
- * @return TReturn All positions where a substring occurs in the text are stored in a contiguous range of the suffix
- *                 array. <tt>range</tt> returns begin and end position of this range for occurrences of @link 
- *                 VSTreeIterator#representative @endlink. The type is @link Pair @endlink<@link Size @endlink< <tt>TIndex<tt> > >
- *                 with TIndex being the index type of the iterator.
- *
- * @section Remarks
- * 
+ *
+ * @signature TPair range(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree/trie.
+ *
+ * @return TPair All positions where a substring occurs in the text are stored in a contiguous range of the suffix
+ *               array. <tt>range</tt> returns begin and end position of this range for occurrences of @link
+ *               VSTreeIterator#representative @endlink. The type is @link Pair @endlink<@link Size @endlink< <tt>TIndex<tt> > >
+ *               with TIndex being the index type of the iterator.
+ *
  * The necessary index tables are built on-demand via @link Index#indexRequire @endlink if index is not <tt>const</tt>.
  */
-	template < typename TText, typename TSpec, typename TDesc >
-	inline Pair<typename Size<Index<TText, TSpec> >::Type>
-	range(Index<TText, TSpec> const &index, TDesc const &desc)
-	{
-		if (_isSizeInval(desc.range.i2))
-			return Pair<typename Size<Index<TText, TSpec> >::Type>(desc.range.i1, length(indexSA(index)));
-		else
-			return desc.range;
-	}
-
-	template < typename TIndex, typename TSpec >
-	inline Pair<typename Size<TIndex>::Type>
-	range(Iter<TIndex, VSTree<TSpec> > const &it)
-	{
-		if (_isSizeInval(value(it).range.i2))
-			return Pair<typename Size<TIndex>::Type>(value(it).range.i1, length(indexSA(container(it))));
-		else
-			return value(it).range;
-	}
+    template < typename TText, typename TSpec, typename TDesc >
+    SEQAN_HOST_DEVICE inline Pair<typename Size<Index<TText, TSpec> >::Type>
+    range(Index<TText, TSpec> const &index, TDesc const &desc)
+    {
+        if (_isSizeInval(desc.range.i2))
+            return Pair<typename Size<Index<TText, TSpec> >::Type>(desc.range.i1, length(indexSA(index)));
+        else
+            return desc.range;
+    }
 
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Function.getOccurrences:
-..summary:Returns all occurrences of the @Function.representative@ substring or a q-gram in the index text.
-..cat:Index
-..signature:getOccurrences(iterator)
-..classSpec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:All positions where the @Function.representative@ of $iterator$ occurs in the text (see @Tag.ESA Index Fibres.EsaText@).
-If $iterator$'s container type is $TIndex$ the return type is $Infix<Fibre<TIndex, EsaSA>::Type const>::Type$.
-..include:seqan/index.h
-*/
-/*!
- * @fn VSTreeIterator#getOccurrences
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns all occurrences of the @link VSTreeIterator#representative @endlink substring in the index text.
- * 
- * @signature Infix<TSA> getOccurrences(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
- * @return Infix&lt;TSA&gt; All positions where the @link VSTreeIterator#representative @endlink of <tt>iterator</tt> occurs in the text.
- *                    Type @link SequenceConcept#Infix @endlink&lt;@link Index#Fibre @endlink&lt;TIndex, FibreSA&gt;::Type&gt;. 
- * 
- * @section Remarks
- * 
+    template < typename TIndex, typename TSpec >
+    SEQAN_HOST_DEVICE inline Pair<typename Size<TIndex>::Type>
+    range(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        if (_isSizeInval(value(it).range.i2))
+            return Pair<typename Size<TIndex>::Type>(value(it).range.i1, length(indexSA(container(it))));
+        else
+            return value(it).range;
+    }
+
+//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn VSTreeIterator#getOccurrences
+ * @headerfile <seqan/index.h>
+ * @brief Returns all occurrences of the @link VSTreeIterator#representative @endlink substring in the index text.
+ *
+ * @signature TInfix getOccurrences(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
+ * @return TInfix All positions where the @link VSTreeIterator#representative @endlink of <tt>iterator</tt> occurs in the text.
+ *                Type @link SegmentableConcept#Infix @endlink&lt;@link Fibre @endlink&lt;TIndex, FibreSA&gt;::Type&gt;.
+ *
  * The necessary index tables are built on-demand via @link Index#indexRequire @endlink if index is not <tt>const</tt>.
- * 
+ *
  * @section Example
  *
  * @link DemoMummy @endlink
@@ -1338,190 +1116,140 @@ If $iterator$'s container type is $TIndex$ the return type is $Infix<Fibre<TInde
  * @see orderOccurrences
  */
 
-	template < typename TIndex, class TSpec >
-	inline typename Infix< typename Fibre<TIndex, FibreSA>::Type const >::Type 
-	getOccurrences(Iter< TIndex, VSTree<TSpec> > const &it) 
-	{
-		if (_isSizeInval(value(it).range.i2))
-			return infix(indexSA(container(it)), value(it).range.i1, length(indexSA(container(it))));
-		else
-			return infix(indexSA(container(it)), value(it).range.i1, value(it).range.i2);
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename Infix< typename Fibre<TIndex, FibreSA>::Type const >::Type
+    getOccurrences(Iter< TIndex, VSTree<TSpec> > const &it)
+    {
+        if (_isSizeInval(value(it).range.i2))
+            return infix(indexSA(container(it)), value(it).range.i1, length(indexSA(container(it))));
+        else
+            return infix(indexSA(container(it)), value(it).range.i1, value(it).range.i2);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.alignment:
-..summary:Returns an alignment of the occurrences of the @Function.representative@ substring in the index text.
-..cat:internal
-..signature:alignment(iterator)
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:A local alignment corresponding to the seed of the $iterator$.
-..remarks:The @Function.representative@ must uniquely occur in every sequence (e.g. in Mums), 
-otherwise the seed returned is one many.
-..include:seqan/index.h
-*/
 /*!
  * @fn VSTreeIterator#alignment
- *
  * @brief Returns an alignment of the occurrences of the @link VSTreeIterator#representative @endlink substring in the index text.
+ * @note Internal function.
  *
- * @deprecated Internal
+ * @signature TAlign alignment(iterator);
  *
- * @signature Align alignment(iterator)
+ * @param[in] iterator An iterator of a string tree.
  *
- * @param iterator An iterator of a string tree.
- * 
- * @return Align A local alignment corresponding to the seed of the <tt>iterator<tt>.
+ * @return TAlign A local alignment corresponding to the seed of the <tt>iterator<tt>.
  *
- * @section Remark 
- *
- * The function @link VSTreeIterator#representative @endlink must uniquely occur in every sequence (e.g. in Mums), 
+ * The function @link VSTreeIterator#representative @endlink must uniquely occur in every sequence (e.g. in Mums),
  * otherwise the seed returned is one many. The return type is a @link Align @endlink object.
  */
 
-	template < typename TString, typename TSSetSpec, typename TIndexSpec, class TSpec >
-	inline Align<TString, ArrayGaps>
-	alignment(Iter< Index< StringSet<TString, TSSetSpec>, TIndexSpec >, VSTree<TSpec> > &it) 
-	{
-		typedef Index< StringSet<TString, TSSetSpec>, TIndexSpec > TIndex;
-		typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
-		typedef typename Iterator<TOccs, Standard>::Type TIter;
-
-		Align<TString, ArrayGaps> align;
-		TIndex &index = container(it);
-		resize(rows(align), length(indexText(index)));	// resize alignment to number of sequences
-		TOccs occs = getOccurrences(it);
-		typename Size<TIndex>::Type repLen = repLength(it);
-		TIter occ = begin(occs, Standard()), occEnd = end(occs, Standard());
-		while (occ != occEnd) {
-			typename Size<TIndex>::Type seqNo = getSeqNo(*occ, stringSetLimits((TIndex const&)index));
-			typename Size<TIndex>::Type seqOfs = getSeqOffset(*occ, stringSetLimits((TIndex const&)index));
-			setSource(row(align, seqNo), value(indexText(index), seqNo), seqOfs, seqOfs + repLen);
-			++occ;
-		}
-		return align;
-	}
+    template < typename TString, typename TSSetSpec, typename TIndexSpec, class TSpec >
+    inline Align<TString, ArrayGaps>
+    alignment(Iter< Index< StringSet<TString, TSSetSpec>, TIndexSpec >, VSTree<TSpec> > &it)
+    {
+        typedef Index< StringSet<TString, TSSetSpec>, TIndexSpec > TIndex;
+        typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
+        typedef typename Iterator<TOccs, Standard>::Type TIter;
+
+        Align<TString, ArrayGaps> align;
+        TIndex &index = container(it);
+        resize(rows(align), length(indexText(index)));    // resize alignment to number of sequences
+        TOccs occs = getOccurrences(it);
+        typename Size<TIndex>::Type repLen = repLength(it);
+        TIter occ = begin(occs, Standard()), occEnd = end(occs, Standard());
+        while (occ != occEnd) {
+            typename Size<TIndex>::Type seqNo = getSeqNo(*occ, stringSetLimits((TIndex const&)index));
+            typename Size<TIndex>::Type seqOfs = getSeqOffset(*occ, stringSetLimits((TIndex const&)index));
+            setSource(row(align, seqNo), value(indexText(index), seqNo), seqOfs, seqOfs + repLen);
+            ++occ;
+        }
+        return align;
+    }
 /*
-	template < typename TString, typename TConcSpec, typename TIndexSpec, class TSpec >
-	inline typename Align<TString const, ArrayGaps>
-	alignment(Iter< Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec >, VSTree<TSpec> > const &it) 
-	{
-		typedef Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec > TIndex;
-		typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
-		typedef typename Iterator<TOccs, Standard>::Type TIter;
-
-		Align<TString const, ArrayGaps> align;
-		TIndex const &index = container(it);
-		resize(rows(align), length(indexText(index)));	// resize alignment to number of sequences
-		TOccs occs = getOccurrences(it);
-		typename Size<TIndex>::Type repLen = repLength(it);
-		TIter occ = begin(occs, Standard()), occEnd = end(occs, Standard());
-		while (occ != occEnd) {
-			typename Size<TIndex>::Type seqNo = getSeqNo(*occ, stringSetLimits(index));
-			typename Size<TIndex>::Type globOfs = posGlobalize(*occ, stringSetLimits(index));
-			setSource(row(align, seqNo), concat(indexText(index)), globOfs, globOfs + repLen);
-			++occ;
-		}
-		return align;
-	}
+    template < typename TString, typename TConcSpec, typename TIndexSpec, class TSpec >
+    inline typename Align<TString const, ArrayGaps>
+    alignment(Iter< Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec >, VSTree<TSpec> > const &it)
+    {
+        typedef Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec > TIndex;
+        typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
+        typedef typename Iterator<TOccs, Standard>::Type TIter;
+
+        Align<TString const, ArrayGaps> align;
+        TIndex const &index = container(it);
+        resize(rows(align), length(indexText(index)));    // resize alignment to number of sequences
+        TOccs occs = getOccurrences(it);
+        typename Size<TIndex>::Type repLen = repLength(it);
+        TIter occ = begin(occs, Standard()), occEnd = end(occs, Standard());
+        while (occ != occEnd) {
+            typename Size<TIndex>::Type seqNo = getSeqNo(*occ, stringSetLimits(index));
+            typename Size<TIndex>::Type globOfs = posGlobalize(*occ, stringSetLimits(index));
+            setSource(row(align, seqNo), concat(indexText(index)), globOfs, globOfs + repLen);
+            ++occ;
+        }
+        return align;
+    }
 */
-	template < typename TString, typename TConcSpec, typename TIndexSpec, class TSpec >
-	inline Align<TString, ArrayGaps>
-	alignment(Iter< Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec >, VSTree<TSpec> > &it) 
-	{
-		typedef Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec > TIndex;
-		typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
-		typedef typename Iterator<TOccs, Standard>::Type TIter;
-
-		Align<TString, ArrayGaps> align;
-		TIndex &index = container(it);
-		resize(rows(align), length(indexText(index)));	// resize alignment to number of sequences
-		TOccs occs = getOccurrences(it);
-		typename Size<TIndex>::Type repLen = repLength(it);
-		TIter occ = begin(occs, Standard()), occEnd = end(occs, Standard());
-		while (occ != occEnd) {
-			typename Size<TIndex>::Type seqNo = getSeqNo(*occ, stringSetLimits((TIndex const&)index));
-			typename Size<TIndex>::Type globOfs = posGlobalize(*occ, stringSetLimits((TIndex const&)index));
-			setSource(row(align, seqNo), concat(indexText(index)), globOfs, globOfs + repLen);
-			++occ;
-		}
-		return align;
-	}
+    template < typename TString, typename TConcSpec, typename TIndexSpec, class TSpec >
+    inline Align<TString, ArrayGaps>
+    alignment(Iter< Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec >, VSTree<TSpec> > &it)
+    {
+        typedef Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec > TIndex;
+        typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
+        typedef typename Iterator<TOccs, Standard>::Type TIter;
+
+        Align<TString, ArrayGaps> align;
+        TIndex &index = container(it);
+        resize(rows(align), length(indexText(index)));    // resize alignment to number of sequences
+        TOccs occs = getOccurrences(it);
+        typename Size<TIndex>::Type repLen = repLength(it);
+        TIter occ = begin(occs, Standard()), occEnd = end(occs, Standard());
+        while (occ != occEnd) {
+            typename Size<TIndex>::Type seqNo = getSeqNo(*occ, stringSetLimits((TIndex const&)index));
+            typename Size<TIndex>::Type globOfs = posGlobalize(*occ, stringSetLimits((TIndex const&)index));
+            setSource(row(align, seqNo), concat(indexText(index)), globOfs, globOfs + repLen);
+            ++occ;
+        }
+        return align;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.getOccurrencesBwt:
-..summary:Returns the characters left beside all occurrence of the @Function.representative@ substring in the index text.
-..cat:Index
-..signature:getOccurrencesBwt(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:All positions where the @Function.representative@ of $iterator$ occurs in the text (see @Tag.ESA Index Fibres.EsaText@).
-If $iterator$'s container type is $TIndex$ the return type is $Infix<Fibre<TIndex, EsaBwt>::Type const>::Type$.
-..include:seqan/index.h
-*/
 /*!
  * @fn VSTreeIterator#getOccurrencesBwt
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the characters left beside all occurrence of the @link
  *        VSTreeIterator#representative @endlink substring in the index text.
- * 
- * @signature getOccurrencesBwt(iterator)
- * 
- * @param iterator An iterator of a suffix tree.
- * 
+ *
+ * @signature TReturn getOccurrencesBwt(iterator);
+ *
+ * @param[in] iterator An iterator of a suffix tree.
+ *
  * @return TReturn All positions where the @link VSTreeIterator#representative @endlink of
  *                 <tt>iterator</tt> occurs in the text.
  *
- *                 If <tt>iterator</tt>'s container
- *                 type is <tt>TIndex</tt> the return type is
+ *                 If <tt>iterator</tt>'s container type is <tt>TIndex</tt> the return type is
  *                 <tt>Infix<Fibre<TIndex, EsaBwt>::Type const>::Type</tt>.
  */
-	template < typename TIndex, class TSpec >
-	inline typename Infix< typename Fibre<TIndex, EsaBwt>::Type const >::Type 
-	getOccurrencesBwt(Iter< TIndex, VSTree<TSpec> > const &it) 
-	{
-		if (_isSizeInval(value(it).range.i2))
-			return infix(indexBwt(container(it)), value(it).range.i1, length(indexSA(container(it))));
-		else
-			return infix(indexBwt(container(it)), value(it).range.i1, value(it).range.i2);
-	}
+    template < typename TIndex, class TSpec >
+    inline typename Infix< typename Fibre<TIndex, EsaBwt>::Type const >::Type
+    getOccurrencesBwt(Iter< TIndex, VSTree<TSpec> > const &it)
+    {
+        if (_isSizeInval(value(it).range.i2))
+            return infix(indexBwt(container(it)), value(it).range.i1, length(indexSA(container(it))));
+        else
+            return infix(indexBwt(container(it)), value(it).range.i1, value(it).range.i2);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.representative:
-..summary:Returns a substring representing the path from root to $iterator$ node.
-..cat:Index
-..signature:representative(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a string tree.
-...type:Spec.VSTree Iterator
-..returns:An @Spec.InfixSegment@ of the text of an index (see @Tag.ESA Index Fibres.EsaText@).
-If $iterator$'s container type is $TIndex$ the return type is $Infix<Fibre<TIndex, EsaText>::Type const>::Type$.
-..include:seqan/index.h
-..example
-...text:The following code shows a simple example how the @Function.range@ is used.
-...file:demos/index/index_begin_range_goDown_representative_repLength.cpp
-...output:The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-*/
 /*!
  * @fn VSTreeIterator#representative
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns a substring representing the path from root to <tt>iterator</tt> node.
- * 
- * @signature Infix<TSting> representative(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
- * @return Infix&lt;TSting&gt; An @link InfixSegment @endlink of the text of an index. The type is <tt>Infix&lt;Fibre&lt;TIndex, FibreText&gt;::Type&gt;::Type</tt>.
- * 
+ *
+ * @signature TInfix representative(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
+ * @return TInfix Infix&lt;TSting&gt; An @link InfixSegment @endlink of the text of an index. The type is <tt>Infix&lt;Fibre&lt;TIndex, FibreText&gt;::Type&gt;::Type</tt>.
+ *
  * @section Examples
  *
  * @link DemoMummy @endlink
@@ -1531,63 +1259,29 @@ The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
  * @link DemoMaximalUniqueMatches @endlink
  */
 
-	template < typename TIndex, class TSpec >
-	inline typename Infix< typename Fibre<TIndex, FibreText>::Type const >::Type 
-	representative(Iter< TIndex, VSTree<TSpec> > const &it) 
-	{
-		return infixWithLength(indexText(container(it)), getOccurrence(it), repLength(it));
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename Infix< typename Fibre<TIndex, FibreText>::Type const >::Type
+    representative(Iter< TIndex, VSTree<TSpec> > const &it)
+    {
+        return infixWithLength(indexText(container(it)), getOccurrence(it), repLength(it));
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.countChildren:
-..summary:Count the number of children of a tree node.
-..cat:Index
-..signature:countChildren(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:The number of children of a tree node.
-If $iterator$'s container type is $TIndex$, the return type is $Size<TIndex>::Type$.
-..include:seqan/index.h
-..example.code:
- 
- // this code is in seqan/index/index_esa_stree.h
- 
- typedef Index< String<char> > TMyIndex;
- TMyIndex myIndex(myString);
- 
- Iterator< TMyIndex, TopDown<ParentLinks<PreorderEmptyEdges> > >::Type tdIterator(myIndex);
- Size<TMyIndex>::Type count;
- 
- while (!atEnd(tdIterator)) {
- // We print out the representatives of all nodes that have more than 3 children and the number of occurrences.
- count = countChildren(tdIterator);
- if (count >= 3)
- {
-     ::std::cout << "Representative " << representative(tdIterator) << " has " <<  count << " children  and " << countOccurrences(tdIterator) << " Occurrences " << ::std::endl;
- 
-     ++tdIterator;
- }
-
-*/
 /*!
  * @fn VSTreeIterator#countChildren
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Count the number of children of a tree node.
- * 
- * @signature TSize countChildren(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
+ *
+ * @signature TSize countChildren(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
  * @return TSize The number of children of a tree node. The type is the result of @link Size @endlink of the index type
  *               of the iterator.
- *  
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * // this code is in seqan/index/index_esa_stree.h
  *
@@ -1602,311 +1296,240 @@ If $iterator$'s container type is $TIndex$, the return type is $Size<TIndex>::Ty
  *  count = countChildren(tdIterator);
  *  if (count >= 3)
  *  {
- *      ::std::cout << "Representative " << representative(tdIterator) << " has " <<  count << " children  and " << countOccurrences(tdIterator) << " Occurrences " << ::std::endl;
+ *      std::cout << "Representative " << representative(tdIterator) << " has " <<  count << " children  and " << countOccurrences(tdIterator) << " Occurrences " << std::endl;
  *
  *      ++tdIterator;
  *  }
  * @endcode
+ *
  * @link DemoIndexCountChildren @endlink
  */
-	template < typename TIndex, typename TSpec >
-	inline typename Size<TIndex>::Type 
-	countChildren(Iter<TIndex, VSTree<TSpec> > const &it) 
-	{
-		typedef Iter<TIndex, VSTree<TSpec> >					TIter;
-		typedef typename GetVSTreeIteratorTraits<TIter>::Type	TTraits;
-		
-		Iter<TIndex, VSTree<TopDown<TTraits> > > temp(it);
-		typename Size<TIndex>::Type numChildren = 0; 
-		if (goDown(temp))
-		{
-			++numChildren;
-			while (goRight(temp)) ++numChildren;
-		}
-		return numChildren;
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline typename Size<Index<TText, IndexEsa<TIndexSpec> > >::Type 
-	countChildren(Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > const &it) 
-	{
-		typedef Index<TText, IndexEsa<TIndexSpec> >			TIndex;
-		typedef Iter<TIndex, VSTree<TSpec> >					TIter;
-		typedef typename GetVSTreeIteratorTraits<TIter>::Type	TTraits;
-		typedef typename TTraits::HideEmptyEdges				THideEmptyEdges;
-
-		if (_isLeaf(it, EmptyEdges())) return 0;
-
-		typedef typename Size<TIndex>::Type TSize;
-		TIndex const &index = container(it);
-		TSize lcp = repLength(it);
-		TSize result = (isRoot(it))? 0: 1;
-
-		// check if child has an empty edge (same representative as its parent)
-		typename SAValue<TIndex>::Type pos = getOccurrence(it);
-		if (THideEmptyEdges::VALUE && getSeqOffset(pos, stringSetLimits(index)) + lcp == sequenceLength(getSeqNo(pos, stringSetLimits(index)), index))
-			--result;	// if so, don't count
-
-		// get l-Value between first and second child
-		TSize i = _getUp(value(it).range.i2, index);
-		if (!(value(it).range.i1 < i && i < value(it).range.i2))
-			i = _getDown(value(it).range.i1, index);
-
-		if (THideEmptyEdges::VALUE)
-		{
-			// only count children with non-empty parent edges (different representative than its parent)
-			pos = saAt(i, index);
-			if (getSeqOffset(pos, stringSetLimits(index)) + lcp != sequenceLength(getSeqNo(pos, stringSetLimits(index)), index))
-				++result;
-		} else
-			++result;
-
-		// try to get next l-Value
-		while (_isNextl(i, index)) 
-		{
-			i = _getNextl(i, index);
-			if (THideEmptyEdges::VALUE)
-			{
-				// only count children with non-empty parent edges (different representative than its parent)
-				pos = saAt(i, index);
-				if (getSeqOffset(pos, stringSetLimits(index)) + lcp != sequenceLength(getSeqNo(pos, stringSetLimits(index)), index))
-					++result;
-			} else
-				++result;
-		}
-		return result;
-	}
-    
-	// get the interval of SA of the subtree under the edge beginning with character c
-	template < typename TText, class TIndexSpec, class TSpec, typename TValue >
-	inline bool 
-	_getNodeByChar(
-		Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > const &it, 
-		TValue c, 
-		typename VertexDescriptor< Index<TText, IndexEsa<TIndexSpec> > >::Type &childDesc)
-	{
-		typedef Index<TText, IndexEsa<TIndexSpec> >		TIndex;
-		typedef typename Size<TIndex>::Type					TSize;
+    template < typename TIndex, typename TSpec >
+    inline typename Size<TIndex>::Type
+    countChildren(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        typedef Iter<TIndex, VSTree<TSpec> >                    TIter;
+        typedef typename GetVSTreeIteratorTraits<TIter>::Type    TTraits;
+
+        Iter<TIndex, VSTree<TopDown<TTraits> > > temp(it);
+        typename Size<TIndex>::Type numChildren = 0;
+        if (goDown(temp))
+        {
+            ++numChildren;
+            while (goRight(temp)) ++numChildren;
+        }
+        return numChildren;
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline typename Size<Index<TText, IndexEsa<TIndexSpec> > >::Type
+    countChildren(Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > const &it)
+    {
+        typedef Index<TText, IndexEsa<TIndexSpec> >            TIndex;
+        typedef Iter<TIndex, VSTree<TSpec> >                    TIter;
+        typedef typename GetVSTreeIteratorTraits<TIter>::Type    TTraits;
+        typedef typename TTraits::HideEmptyEdges                THideEmptyEdges;
+
+        if (_isLeaf(it, EmptyEdges())) return 0;
+
+        typedef typename Size<TIndex>::Type TSize;
+        TIndex const &index = container(it);
+        TSize lcp = repLength(it);
+        TSize result = (isRoot(it))? 0: 1;
+
+        // check if child has an empty edge (same representative as its parent)
+        typename SAValue<TIndex>::Type pos = getOccurrence(it);
+        if (THideEmptyEdges::VALUE && getSeqOffset(pos, stringSetLimits(index)) + lcp == sequenceLength(getSeqNo(pos, stringSetLimits(index)), index))
+            --result;    // if so, don't count
+
+        // get l-Value between first and second child
+        TSize i = _getUp(value(it).range.i2, index);
+        if (!(value(it).range.i1 < i && i < value(it).range.i2))
+            i = _getDown(value(it).range.i1, index);
+
+        if (THideEmptyEdges::VALUE)
+        {
+            // only count children with non-empty parent edges (different representative than its parent)
+            pos = saAt(i, index);
+            if (getSeqOffset(pos, stringSetLimits(index)) + lcp != sequenceLength(getSeqNo(pos, stringSetLimits(index)), index))
+                ++result;
+        } else
+            ++result;
+
+        // try to get next l-Value
+        while (_isNextl(i, index))
+        {
+            i = _getNextl(i, index);
+            if (THideEmptyEdges::VALUE)
+            {
+                // only count children with non-empty parent edges (different representative than its parent)
+                pos = saAt(i, index);
+                if (getSeqOffset(pos, stringSetLimits(index)) + lcp != sequenceLength(getSeqNo(pos, stringSetLimits(index)), index))
+                    ++result;
+            } else
+                ++result;
+        }
+        return result;
+    }
+
+    // get the interval of SA of the subtree under the edge beginning with character c
+    template < typename TText, class TIndexSpec, class TSpec, typename TValue >
+    SEQAN_HOST_DEVICE inline bool
+    _getNodeByChar(
+        Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > const &it,
+        TValue c,
+        typename VertexDescriptor< Index<TText, IndexEsa<TIndexSpec> > >::Type &childDesc)
+    {
+        typedef Index<TText, IndexEsa<TIndexSpec> >        TIndex;
+        typedef typename Size<TIndex>::Type                    TSize;
         typedef typename Fibre<TIndex, EsaSA>::Type const  TSA;
-		typedef typename Value<TSA>::Type                   TSAValue;
+        typedef typename Value<TSA>::Type                   TSAValue;
 
-		if (_isLeaf(it, EmptyEdges())) return false;
+        if (_isLeaf(it, EmptyEdges())) return false;
 
-		Pair<TSize> child(value(it).range.i1, _getUp(value(it).range.i2, container(it)));
-		if (!(value(it).range.i1 < child.i2 && child.i2 < value(it).range.i2))
-			child.i2 = _getDown(value(it).range.i1, container(it));
+        Pair<TSize> child(value(it).range.i1, _getUp(value(it).range.i2, container(it)));
+        if (!(value(it).range.i1 < child.i2 && child.i2 < value(it).range.i2))
+            child.i2 = _getDown(value(it).range.i1, container(it));
 
-		TSize _lcp = lcpAt(child.i2 - 1, container(it));
+        TSize _lcp = lcpAt(child.i2 - 1, container(it));
         TIndex const &index = container(it);
         TText const &text = indexText(index);
 
         TSAValue pos = saAt(child.i1, container(it));
-		if (posAddAndCheck(pos, _lcp, text) && (textAt(pos, container(it)) == c)) 
+        if (posAddAndCheck(pos, _lcp, text) && (textAt(pos, container(it)) == c))
         {
-			childDesc.range = child;
-			childDesc.parentRight = value(it).range.i2;
-			return true;
-		}
-		child.i1 = child.i2;
-		while (_isNextl(child.i2, container(it))) 
-		{
-			child.i2 = _getNextl(child.i2, container(it));
+            childDesc.range = child;
+            childDesc.parentRight = value(it).range.i2;
+            return true;
+        }
+        child.i1 = child.i2;
+        while (_isNextl(child.i2, container(it)))
+        {
+            child.i2 = _getNextl(child.i2, container(it));
             pos = saAt(child.i1, container(it));
-			if (posAddAndCheck(pos, _lcp, text) && (textAt(pos, container(it)) == c)) 
+            if (posAddAndCheck(pos, _lcp, text) && (textAt(pos, container(it)) == c))
             {
-				childDesc.range = child;
-				childDesc.parentRight = value(it).range.i2;
-				return true;
-			}
-			child.i1 = child.i2;
-		}
-
-		if (!isRoot(it)) {
+                childDesc.range = child;
+                childDesc.parentRight = value(it).range.i2;
+                return true;
+            }
+            child.i1 = child.i2;
+        }
+
+        if (!isRoot(it)) {
             pos = saAt(child.i1, container(it));
-			if (posAddAndCheck(pos, _lcp, text) && (textAt(pos, container(it)) == c))
+            if (posAddAndCheck(pos, _lcp, text) && (textAt(pos, container(it)) == c))
             {
-				childDesc.range.i1 = child.i1;
-				childDesc.range.i2 = childDesc.parentRight = value(it).range.i2;
-				return true;
-			}
-		}
-		return false;
-	}
-
-
-/**
-.Function.nodePredicate:
-..summary:If $false$ this node will be skipped during the bottom-up traversal.
-..cat:Index
-..signature:bool nodePredicate(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:
-..include:seqan/index.h
-*/
+                childDesc.range.i1 = child.i1;
+                childDesc.range.i2 = childDesc.parentRight = value(it).range.i2;
+                return true;
+            }
+        }
+        return false;
+    }
+
+
 //TODO(singer): Why only bottom-up???
 /*!
  * @fn VSTreeIterator#nodePredicate
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief If <tt>false</tt> this node will be skipped during the bottom-up traversal.
- * 
- * @signature bool nodePredicate(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
- * @return bool Returns whether or not the node will be skipped. 
- * 
- * @link DemoConstraintIterator @endlink
+ *
+ * @signature bool nodePredicate(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
+ * @return bool Returns whether or not the node will be skipped.
+ *
+ * @see DemoConstraintIterator
  */
 
-	template < typename TIndex, class TSpec >
-	inline bool
-	nodePredicate(Iter<TIndex, TSpec> &)
-	{
-		return true;
-	}
-
-
-/**
-.Function.nodeHullPredicate:
-..summary:If $false$ this node and its subtree is concealed.
-..cat:Index
-..signature:bool nodeHullPredicate(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:
-..include:seqan/index.h
-*/
+    template < typename TIndex, class TSpec >
+    inline bool
+    nodePredicate(Iter<TIndex, TSpec> &)
+    {
+        return true;
+    }
+
+
 /*!
  * @fn VSTreeIterator#nodeHullPredicate
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief If <tt>false</tt> this node and its subtree is concealed.
- * 
- * @signature bool nodeHullPredicate(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
+ *
+ * @signature bool nodeHullPredicate(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
  * @return bool Returns whether or not a subtree is concealed.
- * 
+ *
  * @link DemoConstraintIterator @endlink
  */
 
-	template < typename TIndex, class TSpec >
-	inline bool
-	nodeHullPredicate(Iter<TIndex, TSpec> &)
-	{
-		return true;
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool
+    nodeHullPredicate(Iter<TIndex, TSpec> &)
+    {
+        return true;
+    }
 
 //____________________________________________________________________________
 
-/**
-.Function.goRoot:
-..summary:Move iterator to the root node.
-..cat:Index
-..signature:goRoot(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..include:seqan/index.h
-..example
-...text:The following code shows a simple example how the @Function.range@ is used.
-...file:demos/index/index_begin_range_goDown_representative_repLength.cpp
-...output:The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-*/
 /*!
  * @fn VSTreeIterator#goRoot
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Move iterator to the root node.
- * 
- * @signature void goRoot(iterator)
- * 
- * @param iterator An iterator of a suffix tree.
+ *
+ * @signature void goRoot(iterator);
+ *
+ * @param[in,out] iterator An iterator of a suffix tree.
  */
 
-	template < typename TText, typename TIndexSpec, class TSpec >
-	inline void goRoot(Iter<Index<TText, TIndexSpec>, VSTree<TSpec> > &it) 
-	{
-		_historyClear(it);
-		clear(it);							// start in root node with range (0,infty)
-		if (!empty(indexSA(container(it))))
-            _setSizeInval(value(it).range.i2);	// infty is equivalent to length(index) and faster to compare
-	}
+    template < typename TText, typename TIndexSpec, class TSpec >
+    SEQAN_HOST_DEVICE inline void goRoot(Iter<Index<TText, TIndexSpec>, VSTree<TSpec> > &it)
+    {
+        _historyClear(it);
+        clear(it);                            // start in root node with range (0,infty)
+        if (!empty(indexSA(container(it))))
+            _setSizeInval(value(it).range.i2);    // infty is equivalent to length(index) and faster to compare
+    }
 
 //____________________________________________________________________________
 
-/**
-.Function.Index#begin
-..summary:Returns an iterator pointing to the root node of the virtual string tree/trie of an index. The only exception are @Tag.DFS Order.Postorder@ iterators, where begin returns an iterator pointing to the leftmost node in the tree/trie.
-..signature:begin(index, tag)
-..class:Class.Index
-..param.index:The index to be traversed
-...type:Spec.IndexEsa
-...type:Spec.IndexDfi
-...type:Spec.IndexWotd
-...type:Spec.FMIndex
-...type:Spec.IndexSa
-..param.tag:The specialisation of the iterator to be returned by the function.
-...type:Spec.VSTree Iterator
-..returns:Returns an iterator pointing to the root not of the virtual suffix tree of the index.
-...type:nolink:$The result of Iterator<Index<TText, TIndexSpec>, TSpec >::Type$
-..example
-...text:The following example shows the usage of the @Function.begin@ function. Note that in the first case @Function.begin@ returns an iterator pointing to the root node, while in the second case @Function.begin@ returns a pointer to the left most node.
-...file:demos/index/index_begin_atEnd_representative.cpp
-...output:
-A
-AA
-ATAA
-TA
-TAA
-TATAA
---------------------------------
-AA
-ATAA
-A
-TAA
-TATAA
-TA
-
-*/
 //TODO(singer): The summary is not entirely true!!!
 /*!
- * @fn Index#begin
- * 
- * @brief Returns an iterator pointing to the root not of the virtual string tree of the index.
- * 
- * @signature TIterator begin(index, tag)
- * 
- * @param index The index to be traversed. Types: @link IndexEsa @endlink, @link IndexDfi @endlink, @link IndexWotd
- *              @endlink, @link FMIndex @endlink
- * @param tag The specialisation of the iterator to be returned by the function.
- *            Types: @link VSTreeIterator @endlink
- * 
- * @return TIterator Returns an iterator pointing to the root not of the virtual string tree of the index. The type is
- * the result of Iterator<Index<TText, TIndexSpec>, TSpec >::Type
- * @section Example
- * 
- * The following example shows the usage of the @Function.begin@ function. Note that in the first case @link Index#begin @endlink
- * returns an iterator pointing to the root node, while in the second case @link Index#begin @endlink returns a pointer to the
+ * @fn StringTreeConcept#begin
+ * @headerfile <seqan/index.h>
+ * @brief Returns an iterator pointing to the root node of a string tree index.
+ *
+ * @signature TIterator begin(index, tag);
+ *
+ * @param[in] index An index that implements the @link StringTreeConcept @endlink.  Types: @link IndexEsa @endlink, @link IndexDfi @endlink,
+ *                  @link IndexWotd @endlink, @link FMIndex @endlink.
+ * @param[in] tag   The specialisation of the iterator to be returned by the function.
+ *                  Types: @link VSTreeIterator @endlink
+ *
+ * @return TIterator Returns an iterator pointing to the root node of the virtual string tree of the index. The type is
+ *                   the result of <tt>Iterator<Index<TText, TIndexSpec>, TSpec >::Type</tt>
+ *
+ * @section Examples
+ *
+ * The following example shows the usage of the @link StringTreeConcept#begin @endlink function. Note that in the first case @link StringTreeConcept#begin @endlink
+ * returns an iterator pointing to the root node, while in the second case @link StringTreeConcept#begin @endlink returns a pointer to the
  * left most node.
- * @include demos/index/index_begin_atEnd_representative.cpp
- * @include demos/index/index_begin_atEnd_representative.cpp.stdout
+ *
+ * @include demos/dox/index/begin_atEnd_representative.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/index/begin_atEnd_representative.cpp.stdout
  */
-	template < typename TText, typename TIndexSpec, class TSpec >
-	inline typename Iterator<Index<TText, TIndexSpec>, TSpec >::Type
-	begin(Index<TText, TIndexSpec> &index, TSpec const)
-	{
-		typedef Iter<Index<TText, TIndexSpec>, VSTree<TSpec> >	TIter;
-		typedef typename GetVSTreeIteratorTraits<TIter>::Type	TTraits;
+    template < typename TText, typename TIndexSpec, class TSpec >
+    inline typename Iterator<Index<TText, TIndexSpec>, TSpec >::Type
+    begin(Index<TText, TIndexSpec> &index, TSpec const)
+    {
+        typedef Iter<Index<TText, TIndexSpec>, VSTree<TSpec> >    TIter;
+        typedef typename GetVSTreeIteratorTraits<TIter>::Type    TTraits;
 
         typename Iterator<Index<TText, TIndexSpec>, TSpec>::Type it(index);
 
@@ -1914,10 +1537,10 @@ TA
             while (goDown(it)) ;
         }
 
-		return it;
-	}
+        return it;
+    }
 
-	template < typename TText, typename TIndexSpec, class TSpec >
+    template < typename TText, typename TIndexSpec, class TSpec >
     inline typename Iterator<Index<TText, TIndexSpec>, BottomUp<TSpec> >::Type
     begin(Index<TText, TIndexSpec> &index, BottomUp<TSpec> const)
     {
@@ -1925,294 +1548,255 @@ TA
     }
 /*!
  * @fn VSTreeIterator#goBegin
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Iterates to the first position of a container.
- * 
- * @signature goBegin(iterator)
- * 
- * @param iterator Object that iterates through
- * 
- * @section Remarks
- * 
+ *
+ * @signature void goBegin(iterator);
+ *
+ * @param[in,out] iterator Object that iterates through
+ *
  * This function is equivalent to <tt>iterator = begin(container)</tt>.
- * 
- * @see Index#begin
+ *
+ * @see StringTreeConcept#begin
  */
 
 /*!
  * @fn BottomUpIterator#goBegin
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Iterates to the first position of a container.
- * 
- * @signature goBegin(iterator)
- * 
- * @param iterator Object that iterates through
- * 
- * @section Remarks
- * 
+ *
+ * @signature void goBegin(iterator);
+ *
+ * @param[in,out] iterator Object that iterates through.
+ *
  * This function is equivalent to <tt>iterator = begin(container)</tt>.
- * 
- * @see DemoIteratorBasics
- * 
- * @see Index#begin
+ *
+ * @see StringTreeConcept#begin
  */
-///.Function.goBegin.param.iterator.type:Spec.BottomUp Iterator
-///.Function.goBegin.class:Spec.BottomUp Iterator
-///.Function.goBegin.param.iterator.type:Spec.TopDownHistory Iterator
-///.Function.goBegin.class:Spec.TopDownHistory Iterator
-	template < typename TText, typename TIndexSpec, class TSpec >
-	inline void goBegin(Iter<Index<TText, TIndexSpec>, VSTree<TSpec> > &it) 
-	{
-		typedef Iter<Index<TText, TIndexSpec>, VSTree<TSpec> >	TIter;
-		typedef typename GetVSTreeIteratorTraits<TIter>::Type	TTraits;
-		typedef typename TTraits::HideEmptyEdges				THideEmptyEdges;
-
-		goRoot(it);
-
-		if (IsSameType<typename TTraits::DfsOrder, Postorder_>::VALUE) {
-			while (goDown(it)) ;
-			return;
-		}
-
-		// if root doesn't suffice predicate, do a dfs-step
-		if ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it))
-			goNext(it);
-	}
-
-	template < typename TText, typename TIndexSpec, class TSpec >
-	inline void goBegin(Iter<Index<TText, IndexEsa<TIndexSpec> >, VSTree< BottomUp<TSpec> > > &it) 
-	{
-		typedef Index<TText, IndexEsa<TIndexSpec> >		TIndex;
-		typedef Iter<TIndex, VSTree< BottomUp<TSpec> > >	TIter;
-		//typedef typename VertexDescriptor<TIndex>::Type		TVertexDesc;
-		typedef typename Size<TIndex>::Type					TSize;
-		typedef	Pair<TSize>									TStackEntry;
-
-		_dfsClear(it);
-		clear(it);							// start in root node with range (0,infty)
-		if (!empty(indexSA(container(it)))) {
-			_dfsOnPush(it, TStackEntry(0,0));
-			goNextImpl(it, typename GetVSTreeIteratorTraits< TIter >::Type());
-		}
-	}
+    template < typename TText, typename TIndexSpec, class TSpec >
+    inline void goBegin(Iter<Index<TText, TIndexSpec>, VSTree<TSpec> > &it)
+    {
+        typedef Iter<Index<TText, TIndexSpec>, VSTree<TSpec> >    TIter;
+        typedef typename GetVSTreeIteratorTraits<TIter>::Type    TTraits;
+        typedef typename TTraits::HideEmptyEdges                THideEmptyEdges;
+
+        goRoot(it);
+
+        if (IsSameType<typename TTraits::DfsOrder, Postorder_>::VALUE) {
+            while (goDown(it)) ;
+            return;
+        }
+
+        // if root doesn't suffice predicate, do a dfs-step
+        if ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it))
+            goNext(it);
+    }
+
+    template < typename TText, typename TIndexSpec, class TSpec >
+    inline void goBegin(Iter<Index<TText, IndexEsa<TIndexSpec> >, VSTree< BottomUp<TSpec> > > &it)
+    {
+        typedef Index<TText, IndexEsa<TIndexSpec> >        TIndex;
+        typedef Iter<TIndex, VSTree< BottomUp<TSpec> > >    TIter;
+        //typedef typename VertexDescriptor<TIndex>::Type        TVertexDesc;
+        typedef typename Size<TIndex>::Type                    TSize;
+        typedef    Pair<TSize>                                    TStackEntry;
+
+        _dfsClear(it);
+        clear(it);                            // start in root node with range (0,infty)
+        if (!empty(indexSA(container(it)))) {
+            _dfsOnPush(it, TStackEntry(0,0));
+            goNextImpl(it, typename GetVSTreeIteratorTraits< TIter >::Type());
+        }
+    }
 
 //____________________________________________________________________________
 
 // TODO(singer) ask Dave
-///.Function.end.param.object.type:Class.Index
-///.Function.end.class:Class.Index
-	template < typename TText, typename TIndexSpec, class TSpec >
-	inline typename Iterator<Index<TText, TIndexSpec>, TSpec >::Type
-	end(Index<TText, TIndexSpec> &index, TSpec const) 
-	{
-		return typename Iterator< 
-			Index<TText, TIndexSpec>, 
-			TSpec
-		>::Type (index, MinimalCtor());
-	}
+    template < typename TText, typename TIndexSpec, class TSpec >
+    inline typename Iterator<Index<TText, TIndexSpec>, TSpec >::Type
+    end(Index<TText, TIndexSpec> &index, TSpec const)
+    {
+        return typename Iterator<
+            Index<TText, TIndexSpec>,
+            TSpec
+        >::Type (index, MinimalCtor());
+    }
 
 // TODO(singer) ask Dave
-///.Function.goEnd.param.iterator.type:Spec.BottomUp Iterator
-///.Function.goEnd.class:Spec.BottomUp Iterator
-///.Function.goEnd.param.iterator.type:Spec.TopDownHistory Iterator
-///.Function.goEnd.class:Spec.TopDownHistory Iterator
-	template < typename TText, typename TIndexSpec, class TSpec >
-	inline void goEnd(Iter<Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > &it) 
-	{
-		_historyClear(it);
-		clear(it);
-	}
-
-	template < typename TText, typename TIndexSpec, class TSpec >
-	inline void goEnd(Iter<Index<TText, IndexEsa<TIndexSpec> >, VSTree< BottomUp<TSpec> > > &it) 
-	{
-		_dfsClear(it);
-		clear(it);
-	}
+    template < typename TText, typename TIndexSpec, class TSpec >
+    inline void goEnd(Iter<Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > &it)
+    {
+        _historyClear(it);
+        clear(it);
+    }
+
+    template < typename TText, typename TIndexSpec, class TSpec >
+    inline void goEnd(Iter<Index<TText, IndexEsa<TIndexSpec> >, VSTree< BottomUp<TSpec> > > &it)
+    {
+        _dfsClear(it);
+        clear(it);
+    }
 
 //____________________________________________________________________________
 
 // TODO(singer) ask Dave
-///.Function.goNext.param.iterator.type:Spec.BottomUp Iterator
-///.Function.goNext.class:Spec.BottomUp Iterator
-///.Function.goNext.param.iterator.type:Spec.TopDownHistory Iterator
-///.Function.goNext.class:Spec.TopDownHistory Iterator
-
-	template < typename TIndex, typename TSpec >
-	inline void goNext(Iter<TIndex, VSTree<TSpec> > &it) {
-		goNext(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree<TSpec> > >::Type());
-	}
-
-	template < typename TIndex, typename TSpec, typename TTraits >
-	inline void goNext(Iter<TIndex, VSTree<TSpec> > &it, TTraits const traits) {
-		goNextImpl(it, traits);
-	}
-
-	template < typename TIndex, typename TSpec >
-	inline void goNextRight(Iter<TIndex, VSTree<TSpec> > &it) {
-		goNextRight(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree<TSpec> > >::Type());
-	}
-
-	template < typename TIndex, typename TSpec, typename TTraits >
-	inline void goNextRight(Iter<TIndex, VSTree<TSpec> > &it, TTraits const traits) {
-		goNextRightImpl(it, traits);
-	}
-
-	template < typename TIndex, typename TSpec >
-	inline void goNextUp(Iter<TIndex, VSTree<TSpec> > &it) {
-		goNextUp(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree<TSpec> > >::Type());
-	}
-
-	template < typename TIndex, typename TSpec, typename TTraits >
-	inline void goNextUp(Iter<TIndex, VSTree<TSpec> > &it, TTraits const traits) {
-		goNextUpImpl(it, traits);
-	}
-
-
-/**
-.Function.goDown:
-..summary:Iterates down one edge or a path in a tree.
-..cat:Index
-..signature:bool goDown(iterator)
-..signature:bool goDown(iterator, char)
-..signature:bool goDown(iterator, text[, lcp])
-..class:Spec.TopDown Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..param.char:$iterator$ goes down the edge beginning with $char$.
-..param.text:$iterator$ goes down the path representing $text$. If $text$ ends within an edge, $iterator$ will point to the child-end of this edge.
-..param.lcp:A reference of a size type. When $goDown$ returns, $lcp$ contains the length of the longest-common-prefix of $text$ and a path beginning at the $iterator$ node.
-...type:Class.String
-...type:Class.Segment
-..remarks:$goDown(iterator)$ goes down the leftmost edge in the suffix tree, i.e. the edge beginning with the lexicographically smallest character.
-..returns:$true$ if the edge or path to go down exists, otherwise $false$.
-...type:nolink:bool
-..include:seqan/index.h
-..example
-...text:The following code shows a simple example how the function @Function.goDown@ is used.
-...file:demos/index/index_begin_range_goDown_representative_repLength.cpp
-...output:The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
-*/
+// TODO(holtgrew): Dave needs to update this.
+/*!
+ * @fn VSTreeIterator#goNext
+ * @brief Go to next tree node.
+ *
+ * @signature void goNext(it);
+ *
+ * @param[in,out] it VSTreeIterator to advance.
+ */
+
+    template < typename TIndex, typename TSpec >
+    inline void goNext(Iter<TIndex, VSTree<TSpec> > &it) {
+        goNext(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree<TSpec> > >::Type());
+    }
+
+    template < typename TIndex, typename TSpec, typename TTraits >
+    inline void goNext(Iter<TIndex, VSTree<TSpec> > &it, TTraits const traits) {
+        goNextImpl(it, traits);
+    }
+
+    template < typename TIndex, typename TSpec >
+    inline void goNextRight(Iter<TIndex, VSTree<TSpec> > &it) {
+        goNextRight(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree<TSpec> > >::Type());
+    }
+
+    template < typename TIndex, typename TSpec, typename TTraits >
+    inline void goNextRight(Iter<TIndex, VSTree<TSpec> > &it, TTraits const traits) {
+        goNextRightImpl(it, traits);
+    }
+
+    template < typename TIndex, typename TSpec >
+    inline void goNextUp(Iter<TIndex, VSTree<TSpec> > &it) {
+        goNextUp(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree<TSpec> > >::Type());
+    }
+
+    template < typename TIndex, typename TSpec, typename TTraits >
+    inline void goNextUp(Iter<TIndex, VSTree<TSpec> > &it, TTraits const traits) {
+        goNextUpImpl(it, traits);
+    }
+
+
 //TODO(singer): The lcp stuff needs to be adapted
 /*!
  * @fn TopDownIterator#goDown
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Iterates down one edge or a path in a tree.
- * 
- * @signature bool goDown(iterator)
- * @signature bool goDown(iterator, char)
- * @signature bool goDown(iterator, text[, lcp])
- * 
- * @param char <tt>iterator</tt> goes down the edge beginning with <tt>char</tt>.
- * @param text <tt>iterator</tt> goes down the path representing <tt>text</tt>.  If <tt>text</tt> ends within an edge,
- *             <tt>iterator</tt> will point to the child-end of this edge.
- * @param lcp A reference of a size type. When <tt>goDown</tt> returns, <tt>lcp</tt> contains the length of the
- *            longest-common-prefix of <tt>text</tt> and a path beginning at the <tt>iterator</tt> node.  Types: @link String @endlink, @link Segment @endlink
- * @param iterator An iterator of a tree.
- * @return TReturn <tt>true</tt> if the edge or path to go down exists, otherwise <tt>false</tt>.
- * 
- * @section Remarks
- * 
+ *
+ * @signature bool goDown(iterator);
+ * @signature bool goDown(iterator, char);
+ * @signature bool goDown(iterator, text[, lcp]);
+ *
+ * @param[in] char <tt>iterator</tt> goes down the edge beginning with <tt>char</tt>.
+ * @param[in] text <tt>iterator</tt> goes down the path representing <tt>text</tt>.  If <tt>text</tt> ends within
+ *                 an edge, <tt>iterator</tt> will point to the child-end of this edge.
+ * @param[in] lcp  A reference of a size type. When <tt>goDown</tt> returns, <tt>lcp</tt> contains the length of the
+ *                 longest-common-prefix of <tt>text</tt> and a path beginning at the <tt>iterator</tt> node.
+ *                 Types: @link String @endlink, @link Segment @endlink
+ * @param[in] iterator
+ *                 An iterator of a tree.
+ *
+ * @return bool <tt>true</tt> if the edge or path to go down exists, otherwise <tt>false</tt>.
+ *
  * <tt>goDown(iterator)</tt> goes down the leftmost edge in the tree, i.e. the edge beginning with the lexicographically
  * smallest character.
- * 
+ *
  * @section Example
  *
  * The following code shows a simple example how the function @link TopDownIterator#goDown @endlink is used.
- * @include demos/index/index_begin_range_goDown_representative_repLength.cpp
- * @code{.txt}
+ *
+ * @include demos/dox/index/begin_range_goDown_representative_repLength.cpp
+ *
+ * @code{.output}
  * The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
  * The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
  * @endcode
  */
     //////////////////////////////////////////////////////////////////////////////
-	// unified history stack access for goDown(..)
+    // unified history stack access for goDown(..)
 
-	template < typename TIndex, class TSpec >
-	inline void 
-	_historyClear(Iter< TIndex, VSTree<TSpec> > &) {}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline void
+    _historyClear(Iter< TIndex, VSTree<TSpec> > &) {}
 
 
     template < typename TIndex, class TSpec >
-    inline void
+    SEQAN_HOST_DEVICE inline void
     _historyClear(Iter< TIndex, VSTree< TopDown<TSpec> > > &it)
     {
         it._parentDesc = value(it);
     }
 
     template < typename TIndex, class TSpec >
-    inline void
+    SEQAN_HOST_DEVICE inline void
     _historyClear(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it)
     {
         clear(it.history);
     }
 /*
-	template < typename TText, class TIndexSpec, class TSpec >
-	inline void 
-	_historyPush(Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > &it) 
-	{
-		value(it).parentRight = value(it).range.i2;
-	}
-*/	template < typename TText, class TIndexSpec, class TSpec >
-	inline void 
-	_historyPush(Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it) 
-	{
-		it._parentDesc = value(it);
-		value(it).parentRight = value(it).range.i2;
-	}
-	template < typename TText, class TIndexSpec, class TSpec >
-	inline void 
-	_historyPush(Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it) 
-	{
-		typedef Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > TIter;
-		typename HistoryStackEntry_<TIter>::Type h;
-		h.range = value(it).range;
-
-		value(it).parentRight = value(it).range.i2;
-		appendValue(it.history, h);
-	}
-
-
-	// standard down/right/up handlers of top-down-traversal
-	template < typename TIndex, typename TSpec >
-	inline void _onGoDown(Iter<TIndex, VSTree< TopDown<TSpec> > > &) {}
-
-	template < typename TIndex, typename TSpec >
-	inline void _onGoRight(Iter<TIndex, VSTree< TopDown<TSpec> > > &) {}
-
-	template < typename TIndex, typename TSpec >
-	inline void _onGoUp(Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &) {}
+    template < typename TText, class TIndexSpec, class TSpec >
+    inline void
+    _historyPush(Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > &it)
+    {
+        value(it).parentRight = value(it).range.i2;
+    }
+*/    template < typename TText, class TIndexSpec, class TSpec >
+    SEQAN_HOST_DEVICE inline void
+    _historyPush(Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it)
+    {
+        it._parentDesc = value(it);
+        value(it).parentRight = value(it).range.i2;
+    }
+    template < typename TText, class TIndexSpec, class TSpec >
+    SEQAN_HOST_DEVICE inline void
+    _historyPush(Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it)
+    {
+        typedef Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > TIter;
+        typename HistoryStackEntry_<TIter>::Type h;
+        h.range = value(it).range;
+
+        value(it).parentRight = value(it).range.i2;
+        appendValue(it.history, h);
+    }
+
+
+    // standard down/right/up handlers of top-down-traversal
+    template < typename TIndex, typename TSpec >
+    SEQAN_HOST_DEVICE inline void _onGoDown(Iter<TIndex, VSTree< TopDown<TSpec> > > &) {}
+
+    template < typename TIndex, typename TSpec >
+    SEQAN_HOST_DEVICE inline void _onGoRight(Iter<TIndex, VSTree< TopDown<TSpec> > > &) {}
+
+    template < typename TIndex, typename TSpec >
+    SEQAN_HOST_DEVICE inline void _onGoUp(Iter<TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &) {}
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// goDown
+    // goDown
 
-	// go down the leftmost edge (including empty $-edges)
-	template < typename TText, class TIndexSpec, class TSpec, typename TDfsOrder >
-	inline bool _goDown(
-		Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
-		VSTreeIteratorTraits<TDfsOrder, False> const)
-	{
-		typedef Index<TText, IndexEsa<TIndexSpec> >	TIndex;
+    // go down the leftmost edge (including empty $-edges)
+    template < typename TText, class TIndexSpec, class TSpec, typename TDfsOrder >
+    SEQAN_HOST_DEVICE inline bool _goDown(
+        Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
+        VSTreeIteratorTraits<TDfsOrder, False> const)
+    {
+        typedef Index<TText, IndexEsa<TIndexSpec> >    TIndex;
 
-		if (_isLeaf(it, EmptyEdges())) return false;
-		_historyPush(it);
+        if (_isLeaf(it, EmptyEdges())) return false;
+        _historyPush(it);
 
-		TIndex const &index = container(it);
+        TIndex const &index = container(it);
 
-		typename Size<TIndex>::Type lval = _getUp(value(it).range.i2, index);
-		if (!(value(it).range.i1 < lval && lval < value(it).range.i2))
-			lval = _getDown(value(it).range.i1, index);
-		value(it).range.i2 = lval;
-		return true;
-	}
+        typename Size<TIndex>::Type lval = _getUp(value(it).range.i2, index);
+        if (!(value(it).range.i1 < lval && lval < value(it).range.i2))
+            lval = _getDown(value(it).range.i1, index);
+        value(it).range.i2 = lval;
+        return true;
+    }
 
     template <typename TIterator>
     struct IsParentLinks_: public False {};
@@ -2220,9 +1804,9 @@ The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
     template <typename TIndex, typename TSpec>
     struct IsParentLinks_< Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > >: public True {};
 
-    
+
     template <typename TIndex, typename TSpec, typename TVertexDesc>
-    inline void
+    SEQAN_HOST_DEVICE inline void
     _setParentNodeDescriptor(Iter<TIndex, VSTree< TopDown<TSpec> > > &it,
                              TVertexDesc const &desc)
     {
@@ -2235,18 +1819,18 @@ The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
                              TVertexDesc const &)
     {
     }
-    
-	// go down the leftmost edge (skip empty $-edges)
-	template < typename TText, class TIndexSpec, class TSpec, typename TDfsOrder >
-	inline bool _goDown(
-		Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
-		VSTreeIteratorTraits<TDfsOrder, True> const)
-	{
+
+    // go down the leftmost edge (skip empty $-edges)
+    template < typename TText, class TIndexSpec, class TSpec, typename TDfsOrder >
+    SEQAN_HOST_DEVICE inline bool _goDown(
+        Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
+        VSTreeIteratorTraits<TDfsOrder, True> const)
+    {
         typedef Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > >   TIter;
-		typedef Index<TText, IndexEsa<TIndexSpec> >                                     TIndex;
+        typedef Index<TText, IndexEsa<TIndexSpec> >                                     TIndex;
         typedef typename VertexDescriptor<TIndex>::Type                                 TVertexDesc;
-		
-		if (_isLeaf(it, HideEmptyEdges())) return false;
+
+        if (_isLeaf(it, HideEmptyEdges())) return false;
 
         // save parent descriptor if we need to restore it
         TVertexDesc oldParentDesc;
@@ -2255,15 +1839,15 @@ The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
 
         _historyPush(it);
 
-		TIndex const &index = container(it);
+        TIndex const &index = container(it);
 
         typename Size<TIndex>::Type rangeLeft = value(it).range.i1;
-		typename Size<TIndex>::Type lval = _getUp(value(it).range.i2, index);
-		if (!(rangeLeft < lval && lval < value(it).range.i2))
-			lval = _getDown(rangeLeft, index);
+        typename Size<TIndex>::Type lval = _getUp(value(it).range.i2, index);
+        if (!(rangeLeft < lval && lval < value(it).range.i2))
+            lval = _getDown(rangeLeft, index);
 
         // skip the all empty edges
-		typename Size<TIndex>::Type lcp = lcpAt(lval - 1, index);
+        typename Size<TIndex>::Type lcp = lcpAt(lval - 1, index);
         while (suffixLength(saAt(rangeLeft, index), index) <= lcp)
             ++rangeLeft;
 
@@ -2272,9 +1856,9 @@ The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
         {
             value(it).range.i1 = rangeLeft;
             if (_isNextl(rangeLeft, index))
-				lval = _getNextl(rangeLeft, index);
-			else
-				lval = value(it).parentRight;
+                lval = _getNextl(rangeLeft, index);
+            else
+                lval = value(it).parentRight;
         }
         value(it).range.i2 = lval;
 
@@ -2287,180 +1871,150 @@ The string ISSI occurs 2 times in MISSISSIPPI and has 4 characters.
                 return false;
             }
         }
-		return true;
-	}
+        return true;
+    }
 
-	// go down the leftmost edge
-	template < typename TIndex, class TSpec >
-	inline bool goDown(Iter< TIndex, VSTree< TopDown<TSpec> > > &it) {
-		if (_goDown(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree< TopDown<TSpec> > > >::Type())) {
-			_onGoDown(it);
-			return true;
-		} else
-			return false;
-	}
+    // go down the leftmost edge
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool goDown(Iter< TIndex, VSTree< TopDown<TSpec> > > &it) {
+        if (_goDown(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree< TopDown<TSpec> > > >::Type())) {
+            _onGoDown(it);
+            return true;
+        } else
+            return false;
+    }
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// goDown a specific edge (chosen by the first character)
-
-	// go down the edge beginning with c (returns false iff this edge doesn't exists)
-	template < typename TIndex, class TSpec, typename TValue >
-	inline bool _goDownChar(Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TValue c) 
-	{
-		typename VertexDescriptor<TIndex>::Type nodeDesc;
-		if (_getNodeByChar(it, c, nodeDesc)) {
-			_historyPush(it);
-			value(it) = nodeDesc;
-			return true;
-		}
-		return false;
-	}
-
-	// go down the path corresponding to pattern
-	// lcp is the longest prefix of pattern and path
-	template < typename TIndex, typename TSpec, typename TString, typename TSize >
-	inline bool
-	_goDownString(
-		Iter< TIndex, VSTree< TopDown<TSpec> > > &node,
-		TString const &pattern, 
-		TSize &lcp) 
-	{
-		typedef typename Fibre<TIndex, FibreText>::Type const		TText;
-		typedef typename Infix<TText>::Type							TInfix;
-		typedef typename Iterator<TInfix, Standard>::Type			IText;
-		typedef typename Iterator<TString const, Standard>::Type	IPattern;
-		
-		IPattern p_begin = begin(pattern, Standard()), p_end = end(pattern, Standard());
-		IText t_begin, t_end;
-
-		if (p_begin == p_end) {
-			lcp = 0;
-			return true;
-		}
-
-		TSize parentRepLen = repLength(node);
-		// go down the edge beginning with a pattern character
-		while (_goDownChar(node, *p_begin))
-		{
-			TInfix t = representative(node);
-			t_begin = begin(t, Standard()) + parentRepLen;
-			t_end = end(t, Standard());
-
-			while (t_begin != t_end && p_begin != p_end) 
-			{
-				// compare each character along the edge
-				if (*p_begin != *t_begin) {
-					lcp = p_begin - begin(pattern, Standard());
-					return false;
-				}
-				++t_begin;
-				++p_begin;
-			}
-
-			// was the whole pattern found?
-			if (p_begin == p_end) {
-				lcp = length(pattern);
-				return true;
-			}
-			parentRepLen = length(t);
-		}
-		lcp = p_begin - begin(pattern, Standard());
-		return false;
-	}
-
-	template < typename TIndex, typename TSpec, typename TObject >
-	inline bool 
-	_goDownObject(
-		Iter< TIndex, VSTree< TopDown<TSpec> > > &it, 
-		TObject const &obj,
-		False)
-	{
-		return _goDownChar(it, obj);
-	}
-
-	template < typename TIndex, typename TSpec, typename TObject >
-	inline bool 
-	_goDownObject(
-		Iter< TIndex, VSTree< TopDown<TSpec> > > &it, 
-		TObject const &obj,
-		True)
-	{
-		typename Size<TIndex>::Type dummy;
-		return _goDownString(it, obj, dummy);
-	}
-
-
-	// public interface for goDown(it, ...)
-	template < typename TIndex, typename TSpec, typename TObject >
-	inline bool
-	goDown(
-		Iter< TIndex, VSTree< TopDown<TSpec> > > &it, 
-		TObject const &obj) 
-	{
-		return _goDownObject(it, obj, typename IsSequence<TObject>::Type());
-	}
-
-	template < typename TIndex, typename TSpec, typename TString, typename TSize >
-	inline bool 
-	goDown(
-		Iter< TIndex, VSTree< TopDown<TSpec> > > &it, 
-		TString const &pattern,
-		TSize &lcp)
-	{
-		return _goDownString(it, pattern, lcp);
-	}
-
-		
-/**
-.Function.goUp:
-..summary:Iterates up one edge to the parent in a tree.
-..cat:Index
-..signature:goUp(iterator)
-..class:Spec.TopDownHistory Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDownHistory Iterator
-..returns:$true$ if the iterator could be moved, otherwise $false$.
-...type:nolink:bool
-..include:seqan/index.h
-..example
-...text:The following code shows how the function @Function.goUp@ is used.
-...file:demos/index/index_iterator.cpp
-...output:be
-beornottobe
-e
-eornottobe
-nottobe
-o
-obe
-obeornottobe
-ornottobe
-ottobe
-rnottobe
-t
-tobe
-tobeornottobe
-ttobe
-*/
+    // goDown a specific edge (chosen by the first character)
+
+    // go down the edge beginning with c (returns false iff this edge doesn't exists)
+    template < typename TIndex, class TSpec, typename TValue >
+    SEQAN_HOST_DEVICE inline bool _goDownChar(Iter< TIndex, VSTree< TopDown<TSpec> > > &it, TValue c)
+    {
+        typename VertexDescriptor<TIndex>::Type nodeDesc;
+        if (_getNodeByChar(it, c, nodeDesc)) {
+            _historyPush(it);
+            value(it) = nodeDesc;
+            return true;
+        }
+        return false;
+    }
+
+    // go down the path corresponding to pattern
+    // lcp is the longest prefix of pattern and path
+    template < typename TIndex, typename TSpec, typename TString, typename TSize >
+    SEQAN_HOST_DEVICE inline bool
+    _goDownString(
+        Iter< TIndex, VSTree< TopDown<TSpec> > > &node,
+        TString const &pattern,
+        TSize &lcp)
+    {
+        typedef typename Fibre<TIndex, FibreText>::Type const        TText;
+        typedef typename Infix<TText>::Type                            TInfix;
+        typedef typename Iterator<TInfix, Standard>::Type            IText;
+        typedef typename Iterator<TString const, Standard>::Type    IPattern;
+
+        IPattern p_begin = begin(pattern, Standard()), p_end = end(pattern, Standard());
+        IText t_begin, t_end;
+
+        if (p_begin == p_end) {
+            lcp = 0;
+            return true;
+        }
+
+        TSize parentRepLen = repLength(node);
+        // go down the edge beginning with a pattern character
+        while (_goDownChar(node, *p_begin))
+        {
+            TInfix t = representative(node);
+            t_begin = begin(t, Standard()) + parentRepLen;
+            t_end = end(t, Standard());
+
+            while (t_begin != t_end && p_begin != p_end)
+            {
+                // compare each character along the edge
+                if (*p_begin != *t_begin) {
+                    lcp = p_begin - begin(pattern, Standard());
+                    return false;
+                }
+                ++t_begin;
+                ++p_begin;
+            }
+
+            // was the whole pattern found?
+            if (p_begin == p_end) {
+                lcp = length(pattern);
+                return true;
+            }
+            parentRepLen = length(t);
+        }
+        lcp = p_begin - begin(pattern, Standard());
+        return false;
+    }
+
+    template < typename TIndex, typename TSpec, typename TObject >
+    SEQAN_HOST_DEVICE inline bool
+    _goDownObject(
+        Iter< TIndex, VSTree< TopDown<TSpec> > > &it,
+        TObject const &obj,
+        False)
+    {
+        return _goDownChar(it, obj);
+    }
+
+    template < typename TIndex, typename TSpec, typename TObject >
+    SEQAN_HOST_DEVICE inline bool
+    _goDownObject(
+        Iter< TIndex, VSTree< TopDown<TSpec> > > &it,
+        TObject const &obj,
+        True)
+    {
+        typename Size<TIndex>::Type dummy;
+        return _goDownString(it, obj, dummy);
+    }
+
+
+    // public interface for goDown(it, ...)
+    template < typename TIndex, typename TSpec, typename TObject >
+    SEQAN_HOST_DEVICE inline bool
+    goDown(
+        Iter< TIndex, VSTree< TopDown<TSpec> > > &it,
+        TObject const &obj)
+    {
+        return _goDownObject(it, obj, typename IsSequence<TObject>::Type());
+    }
+
+    template < typename TIndex, typename TSpec, typename TString, typename TSize >
+    SEQAN_HOST_DEVICE inline bool
+    goDown(
+        Iter< TIndex, VSTree< TopDown<TSpec> > > &it,
+        TString const &pattern,
+        TSize &lcp)
+    {
+        return _goDownString(it, pattern, lcp);
+    }
+
+
 /*!
  * @fn TopDownHistoryIterator#goUp
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Iterates up one edge to the parent in a tree/trie.
- * 
- * @signature bool goUp(iterator)
- * 
- * @param iterator An iterator of a string tree/trie.
- * 
+ *
+ * @signature bool goUp(iterator);
+ *
+ * @param[in,out] iterator An iterator of a string tree/trie.
+ *
  * @return bool <tt>true</tt> if the iterator could be moved, otherwise <tt>false</tt>.
  *
  * @section Example
  *
  * The following code shows how the function @link TopDownHistoryIterator#goUp @endlink is used.
- * @include demos/index/index_iterator.cpp
- * @code{.txt}
- * be
+ *
+ * @include demos/dox/index/iterator.cpp
+ *
+ * @code{.output}
+ * be
  * beornottobe
  * e
  * eornottobe
@@ -2475,312 +2029,243 @@ ttobe
  * tobe
  * tobeornottobe
  * ttobe
- * 
+ *
  * @endcode
  */
-	// go up one edge (returns false if in root node)
-	// can be used at most once, as no history stack is available
-	template < typename TIndex, class TSpec >
-	inline bool 
-	_goUp(Iter< TIndex, VSTree< TopDown<TSpec> > > &it) 
-	{
-		if (!isRoot(it)) {
-			value(it) = it._parentDesc;
-			return true;
-		}
-		return false;
-	}
-
-	// go up one edge (returns false if in root node)
-	template < typename TIndex, class TSpec >
-	inline bool 
-	_goUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it) 
-	{
-		if (!empty(it.history)) {
-			value(it).range = back(it.history).range;
-			pop(it.history);
-			if (!empty(it.history))
-				value(it).parentRight = back(it.history).range.i2;	// copy right boundary of parent's range
-			return true;
-		}
-		return false;
-	}
-
-	// go up one edge
-	template < typename TIndex, class TSpec >
-	inline bool goUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it) {
-		if (_goUp(it)) {
-			_onGoUp(it);
-			return true;
-		} else
-			return false;
-	}
-
-/**
-.Function.nodeUp:
-..summary:Returns the vertex descriptor of the parent node.
-..cat:Index
-..signature:nodeUp(iterator)
-..class:Spec.TopDown Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..returns:The vertex descriptor of the parent node. The type is $VertexDescriptor<TIndex>::Type$.
-If $iterator$ points at the root node, the vertex descriptor of $iterator$ ($value(iterator)$) is returned.
-...type:Metafunction.VertexDescriptor
-..include:seqan/index.h
-*/
+    // go up one edge (returns false if in root node)
+    // can be used at most once, as no history stack is available
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool
+    _goUp(Iter< TIndex, VSTree< TopDown<TSpec> > > &it)
+    {
+        if (!isRoot(it)) {
+            value(it) = it._parentDesc;
+            return true;
+        }
+        return false;
+    }
+
+    // go up one edge (returns false if in root node)
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool
+    _goUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it)
+    {
+        if (!empty(it.history)) {
+            value(it).range = back(it.history).range;
+            eraseBack(it.history);
+            if (!empty(it.history))
+                value(it).parentRight = back(it.history).range.i2;    // copy right boundary of parent's range
+            return true;
+        }
+        return false;
+    }
+
+    // go up one edge
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool goUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it) {
+        if (_goUp(it)) {
+            _onGoUp(it);
+            return true;
+        } else
+            return false;
+    }
+
 /*!
  * @fn TopDownIterator#nodeUp
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the vertex descriptor of the parent node.
- * 
- * @signature TVertexDiscriptor nodeUp(iterator)
- * 
- * @param iterator An iterator of a string tree/trie.
- * 
- * @return TReturn The vertex descriptor of the parent node. The type is @link VertexDescriptor @endlink of TIndex. If
- *                 <tt>iterator</tt> points at the root node, the vertex descriptor of it is returned.
+ *
+ * @signature TVertexDiscriptor nodeUp(iterator);
+ *
+ * @param[in,out] iterator An iterator of a string tree/trie.
+ *
+ * @return TVertexDescriptor The vertex descriptor of the parent node. The type is @link VertexDescriptor @endlink of TIndex. If
+ *                           <tt>iterator</tt> points at the root node, the vertex descriptor of it is returned.
  */
 
-	// return vertex descriptor of parent's node
-	template < typename TIndex, class TSpec >
-	inline typename VertexDescriptor<TIndex>::Type
-	nodeUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > const &it) 
-	{
-		if (!empty(it.history))
+    // return vertex descriptor of parent's node
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename VertexDescriptor<TIndex>::Type
+    nodeUp(Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > const &it)
+    {
+        if (!empty(it.history))
         {
-			typename Size<TIndex>::Type parentRight = 0;
-			if (length(it.history) >= 2)
-				parentRight = topPrev(it.history).range.i2;
-			return typename VertexDescriptor<TIndex>::Type(back(it.history).range, parentRight);
-		} else
-			return value(it);
-	}
-
-	// nodeUp adaption for non-history iterators
-	// ATTENTION: Do not call nodeUp after a goDown that returned false (or after _goUp)!
-	template < typename TIndex, class TSpec >
-	inline typename VertexDescriptor<TIndex>::Type const &
-	nodeUp(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it) 
-	{
-		return it._parentDesc;
-	}
-
-/**
-.Function.goRight:
-..summary:Iterates to the next sibling in a tree.
-..cat:Index
-..signature:goRight(iterator)
-..class:Spec.TopDown Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..returns:$true$ if the iterator could be moved, otherwise $false$.
-...type:nolink:bool
-..include:seqan/index.h
-*/
+            typename Size<TIndex>::Type parentRight = 0;
+            if (length(it.history) >= 2)
+                parentRight = backPrev(it.history).range.i2;
+            return typename VertexDescriptor<TIndex>::Type(back(it.history).range, parentRight);
+        } else
+            return value(it);
+    }
+
+    // nodeUp adaption for non-history iterators
+    // ATTENTION: Do not call nodeUp after a goDown that returned false (or after _goUp)!
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename VertexDescriptor<TIndex>::Type const &
+    nodeUp(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it)
+    {
+        return it._parentDesc;
+    }
+
 /*!
  * @fn TopDownIterator#goRight
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Iterates to the next sibling in a tree.
- * 
- * @signature bool goRight(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
+ *
+ * @signature bool goRight(iterator);
+ *
+ * @param[in,out] iterator An iterator of a string tree.
+ *
  * @return bool <tt>true</tt> if the iterator could be moved, otherwise <tt>false</tt>.
  */
-	// go right to the lexic. next sibling
-	template < typename TText, class TIndexSpec, class TSpec, typename TDfsOrder, typename THideEmptyEdges >
-	inline bool _goRight(
-		Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it, 
-		VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const) 
-	{
-		typedef Index<TText, IndexEsa<TIndexSpec> > TIndex;
-
-		if (isRoot(it)) return false;		
-
-		typename Size<TIndex>::Type right = value(it).parentRight;
-		if (_isSizeInval(right)) right = length(indexSA(container(it)));
-
-		do {
-			if (value(it).range.i2 == right)				// not the right-most child?
-				return false;
-
-			if (_isNextl(value(it).range.i2, container(it))) 
-			{
-				value(it).range.i1 = value(it).range.i2;	// go right
-				value(it).range.i2 = _getNextl(value(it).range.i2, container(it));
-			} else {
-				value(it).range.i1 = value(it).range.i2;	// now it is the right-most child
-				value(it).range.i2 = value(it).parentRight;
-			}
-
-		} while ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it));
-		return true;
-	}
-
-	// go down the leftmost edge
-	template < typename TIndex, class TSpec >
-	inline bool goRight(Iter< TIndex, VSTree< TopDown<TSpec> > > &it) {
-		if (_goRight(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree< TopDown<TSpec> > > >::Type())) {
-			_onGoRight(it);
-			return true;
-		} else
-			return false;
-	}
-
-/**
-.Function.parentEdgeLength:
-..summary:Returns the length of the edge from the $iterator$ node to its parent.
-..cat:Index
-..signature:parentEdgeLength(iterator)
-..class:Spec.TopDown Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..returns:The returned value is equal to $length(parentEdgeLabel(iterator))$.
-..include:seqan/index.h
-*/
+    // go right to the lexic. next sibling
+    template < typename TText, class TIndexSpec, class TSpec, typename TDfsOrder, typename THideEmptyEdges >
+    SEQAN_HOST_DEVICE inline bool _goRight(
+        Iter< Index<TText, IndexEsa<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
+        VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
+    {
+        typedef Index<TText, IndexEsa<TIndexSpec> > TIndex;
+
+        if (isRoot(it)) return false;
+
+        typename Size<TIndex>::Type right = value(it).parentRight;
+        if (_isSizeInval(right)) right = length(indexSA(container(it)));
+
+        do {
+            if (value(it).range.i2 == right)                // not the right-most child?
+                return false;
+
+            if (_isNextl(value(it).range.i2, container(it)))
+            {
+                value(it).range.i1 = value(it).range.i2;    // go right
+                value(it).range.i2 = _getNextl(value(it).range.i2, container(it));
+            } else {
+                value(it).range.i1 = value(it).range.i2;    // now it is the right-most child
+                value(it).range.i2 = value(it).parentRight;
+            }
+
+        } while ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it));
+        return true;
+    }
+
+    // go down the leftmost edge
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool goRight(Iter< TIndex, VSTree< TopDown<TSpec> > > &it) {
+        if (_goRight(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree< TopDown<TSpec> > > >::Type())) {
+            _onGoRight(it);
+            return true;
+        } else
+            return false;
+    }
+
 /*!
  * @fn TopDownIterator#parentEdgeLength
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the length of the edge from the <tt>iterator</tt> node to its parent.
- * 
- * @signature TSize parentEdgeLength(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
+ *
+ * @signature TSize parentEdgeLength(iterator);
+ *
+ * @param[in,out] iterator An iterator of a string tree.
+ *
  * @return TSize The returned value is equal to <tt>length(parentEdgeLabel(iterator))</tt> and its type is the result of
  *               the metafunction @link Size @endlink of the underlying index.
  */
-	template < typename TIndex, class TSpec >
-	inline typename Size< TIndex >::Type
-	parentEdgeLength(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it) 
-	{
-		return repLength(it) - parentRepLength(it);
-	}
-
-/**
-.Function.parentEdgeLabel:
-..summary:Returns a substring representing the edge from an $iterator$ node to its parent.
-..cat:Index
-..signature:parentEdgeLabel(iterator)
-..class:Spec.TopDown Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..returns:An @Spec.InfixSegment@ of the text of an index (see @Tag.ESA Index Fibres.EsaText@).
-If $iterator$'s container type is $TIndex$ the return type is $Infix<Fibre<TIndex, EsaText>::Type const>::Type$.
-..include:seqan/index.h
-*/
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename Size< TIndex >::Type
+    parentEdgeLength(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it)
+    {
+        return repLength(it) - parentRepLength(it);
+    }
+
 /*!
  * @fn TopDownIterator#parentEdgeLabel
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns a substring representing the edge from an <tt>iterator</tt> node to its parent.
- * 
- * @signature TEdgeLabel parentEdgeLabel(iterator)
- * 
- * @param iterator An iterator of a string tree/trie.
- * 
+ *
+ * @signature TEdgeLabel parentEdgeLabel(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree/trie.
+ *
  * @return TEdgeLabel Returns a substring representing the edge from an <tt>iterator</tt> node to its parent.
- *                    and its type is the result of the metafunction @link TopDownIterator#EdgeLabel @endlink of the iterator.
+ *                    and its type is the result of the metafunction @link VSTreeIterator#EdgeLabel @endlink of the iterator.
  */
 
-	template < typename TIndex, class TSpec >
-    inline typename EdgeLabel< Iter< TIndex, VSTree<TSpec> > >::Type
-	parentEdgeLabel(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it)
-	{
-		return infixWithLength(
-			indexText(container(it)), 
-			posAdd(getOccurrence(it), parentRepLength(it)),
-			parentEdgeLength(it));
-	}
-
-/**
-.Function.parentEdgeFirstChar:
-..summary:Returns the first character of the edge from an $iterator$ node to its parent.
-..cat:Index
-..signature:parentEdgeFirstChar(iterator)
-..class:Spec.TopDown Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.TopDown Iterator
-..returns:A single character of type $Value<TIndex>::Type$ which is identical to $Value<Fibre<TIndex, EsaRawText>::Type>::Type$.
-..include:seqan/index.h
-*/
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline typename EdgeLabel< Iter< TIndex, VSTree<TSpec> > >::Type
+    parentEdgeLabel(Iter< TIndex, VSTree< TopDown<TSpec> > > const &it)
+    {
+        return infixWithLength(
+            indexText(container(it)),
+            posAdd(getOccurrence(it), parentRepLength(it)),
+            parentEdgeLength(it));
+    }
+
 //TODO(singer): EsaRawText
 /*!
  * @fn TopDownIterator#parentEdgeFirstChar
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the first character of the edge from an <tt>iterator</tt> node to its parent.
- * 
- * @signature TValue parentEdgeFirstChar(iterator)
- * 
- * @param iterator An iterator of a string tree.
- * 
+ *
+ * @signature TValue parentEdgeFirstChar(iterator);
+ *
+ * @param[in] iterator An iterator of a string tree.
+ *
  * @return TValue A single character of type <tt>Value&lt;TIndex&gt;::Type</tt> which is identical to
  *                 <tt>Value&lt;Fibre&lt;TIndex, EsaRawText&gt;::Type&gt;::Type</tt>.
  */
 
-	template < typename TIndex, class TSpec >
-	inline typename Value<TIndex>::Type 
-	parentEdgeFirstChar(Iter< TIndex, VSTree<TSpec> > const &it) 
-	{
-		return infixWithLength(
-			indexText(container(it)),
-			posAdd(getOccurrence(it), parentRepLength(it)),
-			1)[0];
-	}
+    template < typename TIndex, class TSpec >
+    inline typename Value<TIndex>::Type
+    parentEdgeFirstChar(Iter< TIndex, VSTree<TSpec> > const &it)
+    {
+        return infixWithLength(
+            indexText(container(it)),
+            posAdd(getOccurrence(it), parentRepLength(it)),
+            1)[0];
+    }
 
     template < typename TIndex, class TSpec >
-	inline void _clear(Iter<TIndex, VSTree<TSpec> > &it) 
-	{
-		value(it) = typename VertexDescriptor<TIndex>::Type(MinimalCtor());
+    SEQAN_HOST_DEVICE inline void _clear(Iter<TIndex, VSTree<TSpec> > &it)
+    {
+        value(it) = typename VertexDescriptor<TIndex>::Type(MinimalCtor());
     }
 
-	template < typename TIndex, class TSpec >
-	inline void clear(Iter<TIndex, VSTree<TSpec> > &it) 
-	{
-		_clear(it);
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline void clear(Iter<TIndex, VSTree<TSpec> > &it)
+    {
+        _clear(it);
     }
 
-	template < typename TIndex, class TSpec >
-	inline void _dfsClear(Iter<TIndex, VSTree<TSpec> > &it) 
-	{
-		clear(it.history);
+    template < typename TIndex, class TSpec >
+    inline void _dfsClear(Iter<TIndex, VSTree<TSpec> > &it)
+    {
+        clear(it.history);
     }
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// dfs traversal for ParentLink iterators
-
-	template < typename TIndex, typename TSpec, typename THideEmptyEdges >
-	inline void goNextImpl(
-		Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it, 
-		VSTreeIteratorTraits<Preorder_, THideEmptyEdges> const)
-	{
-		// preorder dfs
-		do {
-			if (!goDown(it) && !goRight(it))
-				while (goUp(it) && !goRight(it)) {}
-			if (isRoot(it)) {
-				clear(it);
-				return;
-			}
-		} while (!nodePredicate(it));
-	}
-
-	template < typename TIndex, typename TSpec, typename THideEmptyEdges >
+    // dfs traversal for ParentLink iterators
+
+    template < typename TIndex, typename TSpec, typename THideEmptyEdges >
+    inline void goNextImpl(
+        Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it,
+        VSTreeIteratorTraits<Preorder_, THideEmptyEdges> const)
+    {
+        // preorder dfs
+        do {
+            if (!goDown(it) && !goRight(it))
+                while (goUp(it) && !goRight(it)) {}
+            if (isRoot(it)) {
+                clear(it);
+                return;
+            }
+        } while (!nodePredicate(it));
+    }
+
+    template < typename TIndex, typename TSpec, typename THideEmptyEdges >
     inline void goNextRightImpl(
-		Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it, 
-		VSTreeIteratorTraits<Preorder_, THideEmptyEdges> const tag)
+        Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it,
+        VSTreeIteratorTraits<Preorder_, THideEmptyEdges> const tag)
     {
         // preorder dfs
         if (!goRight(it))
@@ -2793,10 +2278,10 @@ If $iterator$'s container type is $TIndex$ the return type is $Infix<Fibre<TInde
             goNextImpl(it, tag);
     }
 
-	template < typename TIndex, typename TSpec, typename THideEmptyEdges >
+    template < typename TIndex, typename TSpec, typename THideEmptyEdges >
     inline void goNextUpImpl(
-		Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it, 
-		VSTreeIteratorTraits<Preorder_, THideEmptyEdges> const tag)
+        Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it,
+        VSTreeIteratorTraits<Preorder_, THideEmptyEdges> const tag)
     {
         // preorder dfs
         while (goUp(it) && !goRight(it)) {}
@@ -2811,104 +2296,71 @@ If $iterator$'s container type is $TIndex$ the return type is $Infix<Fibre<TInde
 
 
 
-	template < typename TIndex, typename TSpec, typename THideEmptyEdges >
-	inline void goNextImpl(
-		Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it, 
-		VSTreeIteratorTraits<Postorder_, THideEmptyEdges> const)
-	{
-		// postorder dfs
-		do {
-			if (goRight(it))
-				while (goDown(it)) ;
-			else
-				if (!goUp(it)) {
-					clear(it);
-					return;
-				}
-		} while (!nodePredicate(it));
-	}
+    template < typename TIndex, typename TSpec, typename THideEmptyEdges >
+    inline void goNextImpl(
+        Iter< TIndex, VSTree< TopDown< ParentLinks<TSpec> > > > &it,
+        VSTreeIteratorTraits<Postorder_, THideEmptyEdges> const)
+    {
+        // postorder dfs
+        do {
+            if (goRight(it))
+                while (goDown(it)) ;
+            else
+                if (!goUp(it)) {
+                    clear(it);
+                    return;
+                }
+        } while (!nodePredicate(it));
+    }
 
     //////////////////////////////////////////////////////////////////////////////
-	// boolean functions
-
-	template < typename TIndex, class TSpec >
-	inline bool eof(Iter<TIndex, VSTree<TSpec> > &it) 
-	{
-		return !value(it).range.i2;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline bool eof(Iter<TIndex, VSTree<TSpec> > const &it) 
-	{
-		return !value(it).range.i2;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline bool empty(Iter<TIndex, VSTree<TSpec> > &it) 
-	{
-		return !value(it).range.i2;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline bool empty(Iter<TIndex, VSTree<TSpec> > const &it) 
-	{
-		return !value(it).range.i2;
-	}
+    // boolean functions
 
-//..concept:Concept.ContainerConcept
-/**
-.Function.VSTree Iterator#atEnd
-..class:Spec.VSTree Iterator
-..concept:Concept.RootedIteratorConcept
-..cat:Iteration
-..summary:Determines whether an virtual string tree iterator is at the end position.
-..signature:bool atEnd(iterator)
-..param.iterator:An iterator.
-...type:Spec.BottomUp Iterator
-...type:Spec.TopDownHistory Iterator
-...concept:Concept.RootedIteratorConcept
-..returns:$true$ if $iterator$ points behind the last item of the container, otherwise $false$.
-..include:seqan/index.h
-..example
-...text:The following example shows the usage of the @Function.atEnd@ function. 
-...file:demos/index/index_begin_atEnd_representative.cpp
-...output:
-A
-AA
-ATAA
-TA
-TAA
-TATAA
---------------------------------
-AA
-ATAA
-A
-TAA
-TATAA
-TA
+    template < typename TIndex, class TSpec >
+    inline bool eof(Iter<TIndex, VSTree<TSpec> > &it)
+    {
+        return !value(it).range.i2;
+    }
 
-*/
+    template < typename TIndex, class TSpec >
+    inline bool eof(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        return !value(it).range.i2;
+    }
 
+    template < typename TIndex, class TSpec >
+    inline bool empty(Iter<TIndex, VSTree<TSpec> > &it)
+    {
+        return !value(it).range.i2;
+    }
+
+    template < typename TIndex, class TSpec >
+    inline bool empty(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        return !value(it).range.i2;
+    }
+
+//..concept:Concept.ContainerConcept
 /*!
  * @fn VSTreeIterator#atEnd
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Determines whether an virtual string tree iterator is at the end position.
- * 
- * @signature bool atEnd(iterator)
- * 
- * @param iterator An iterator.
- * 
- * @return TReturn <tt>true</tt> if <tt>iterator</tt> points behind the last item of the container, otherwise
- *                 <tt>false</tt>.
- * 
+ *
+ * @signature bool atEnd(iterator);
+ *
+ * @param[in] iterator An iterator.
+ *
+ * @return bool <tt>true</tt> if <tt>iterator</tt> points behind the last item of the container, otherwise
+ *              <tt>false</tt>.
+ *
  * @section Examples
- * 
+ *
  * The following example shows the usage of the @link VSTreeIterator#atEnd @endlink function.
- * @include demos/index/index_begin_atEnd_representative.cpp
- * @code{.txt}
- * A 
+ *
+ * @include demos/dox/index/begin_atEnd_representative.cpp
+ *
+ * @code{.output}
+ * A
  * AA
  * ATAA
  * TA
@@ -2926,24 +2378,24 @@ TA
 
 /*!
  * @fn BottomUp#atEnd
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Determines whether an virtual string tree iterator is at the end position.
- * 
- * @signature bool atEnd(iterator)
- * 
- * @param iterator An iterator.
- * 
- * @return TReturn <tt>true</tt> if <tt>iterator</tt> points behind the last item of the container, otherwise
- *                 <tt>false</tt>.
- * 
+ *
+ * @signature bool atEnd(iterator);
+ *
+ * @param[in] iterator An iterator.
+ *
+ * @return bool <tt>true</tt> if <tt>iterator</tt> points behind the last item of the container, otherwise
+ *              <tt>false</tt>.
+ *
  * @section Examples
- * 
+ *
  * The following example shows the usage of the @link BottomUp#atEnd @endlink function.
- * @include demos/index/index_begin_atEnd_representative.cpp
- * @code{.txt}
- * A 
+ *
+ * @include demos/dox/index/begin_atEnd_representative.cpp
+ *
+ * @code{.output}
+ * A
  * AA
  * ATAA
  * TA
@@ -2959,61 +2411,36 @@ TA
  *
  */
 
-///.Function.atEnd.param.iterator.type:Spec.BottomUp Iterator
-///.Function.atEnd.class:Spec.BottomUp Iterator
-///.Function.atEnd.param.iterator.type:Spec.TopDownHistory Iterator
-///.Function.atEnd.class:Spec.TopDownHistory Iterator
-
-	template < typename TIndex, class TSpec >
-	inline bool atEnd(Iter<TIndex, VSTree<TSpec> > &it) 
-	{
-		return !value(it).range.i2;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline bool atEnd(Iter<TIndex, VSTree<TSpec> > const &it) 
-	{
-		return !value(it).range.i2;
-	}
-
-/**
-.Function.isRoot:
-..summary:Test whether a tree iterator points to the root node.
-..cat:Index
-..signature:bool isRoot(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a tree.
-...type:Spec.VSTree Iterator
-..returns:$true$ if $iterator$ points to the root of the tree, otherwise $false$.
-...type:nolink:bool
-..include:seqan/index.h
-..example
-...text:The following example shows the usage of the @Function.isRoot@ function. 
-...file:demos/index/index_begin_atEnd_representative_bottomUp.cpp
-...output:AA
-ATAA
-A
-TAA
-TATAA
-TA
-*/
+    template < typename TIndex, class TSpec >
+    inline bool atEnd(Iter<TIndex, VSTree<TSpec> > &it)
+    {
+        return !value(it).range.i2;
+    }
+
+    template < typename TIndex, class TSpec >
+    inline bool atEnd(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        return !value(it).range.i2;
+    }
+
 /*!
  * @fn VSTreeIterator#isRoot
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Test whether a tree iterator points to the root node.
- * 
- * @signature bool isRoot(iterator)
- * 
- * @param iterator An iterator of a tree.
- * 
- * @return TReturn <tt>true</tt> if <tt>iterator</tt> points to the root of the tree, otherwise <tt>false</tt>.
+ *
+ * @signature bool isRoot(iterator);
+ *
+ * @param[in] iterator An iterator of a tree.
+ *
+ * @return bool <tt>true</tt> if <tt>iterator</tt> points to the root of the tree, otherwise <tt>false</tt>.
+ *
  * @section Example
  *
- * The following example shows the usage of the @Function.isRoot@ function. 
- * @include demos/index/index_begin_atEnd_representative_bottomUp.cpp
- * code{.txt}
+ * The following example shows the usage of the @Function.isRoot@ function.
+ *
+ * @include demos/dox/index/begin_atEnd_representative_bottomUp.cpp
+ *
+ * code{.output}
  * output:AA
  * ATAA
  * A
@@ -3022,313 +2449,229 @@ TA
  * TA
  * @endcode
  */
-	template < typename TIndex, class TSpec >
-	inline bool isRoot(Iter<TIndex, VSTree< BottomUp<TSpec> > > const &it) 
-	{
-		return empty(it.history);
-	}
-
-	template < typename TIndex, class TSpec >
-	inline bool isRoot(Iter<TIndex, VSTree<TSpec> > const &it) 
-	{
-		return _isRoot(value(it));
-	}
-
-	template < typename TSize >
-	inline bool _isRoot(VertexEsa<TSize> const &value) 
-	{
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool isRoot(Iter<TIndex, VSTree< BottomUp<TSpec> > > const &it)
+    {
+        return empty(it.history);
+    }
+
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool isRoot(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        return _isRoot(value(it));
+    }
+
+    template < typename TSize >
+    SEQAN_HOST_DEVICE inline bool _isRoot(VertexEsa<TSize> const &value)
+    {
 //IOREV _notio_
-		return _isSizeInval(value.range.i2);
-	}
-
-/**
-.Function.isRightTerminal:
-..summary:Test whether iterator points to a suffix.
-..cat:Index
-..signature:bool isRightTerminal(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:$true$ if $iterator$ points to the node representing a suffix, otherwise $false$.
-...type:nolink:bool
-..remarks:Every leaf is also a right terminal (see @Function.isLeaf@), but not vice versa.
-..include:seqan/index.h
-*/
+        return _isSizeInval(value.range.i2);
+    }
+
 //TODO(singer): Note the case for trie or FM Index
 /*!
  * @fn VSTreeIterator#isRightTerminal
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Test whether iterator points to a suffix.
- * 
- * @signature bool isRightTerminal(iterator)
- * 
- * @param iterator An iterator of a suffix tree.
- * 
- * @return TReturn <tt>true</tt> if <tt>iterator</tt> points to the node representing a suffix, otherwise
- *                 <tt>false</tt>. Types: <tt>bool<tt>
- * 
- * @section Remarks
- * 
+ *
+ * @signature bool isRightTerminal(iterator);
+ *
+ * @param[in] iterator An iterator of a suffix tree.
+ *
+ * @return bool <tt>true</tt> if <tt>iterator</tt> points to the node representing a suffix, otherwise
+ *              <tt>false</tt>.
+ *
  * Every leaf is also a right terminal (see @link VSTreeIterator#isLeaf @endlink), but not vice versa.
  */
 
-	template < typename TIndex, class TSpec >
-	inline bool isRightTerminal(Iter<TIndex, VSTree<TSpec> > const &it) 
-	{
-		// do we reach a leaf in a suffix tree with trailing '$'
-		typename SAValue<TIndex>::Type pos = getOccurrence(it);
-		TIndex const &index = container(it);
-		typename StringSetLimits<typename Host<TIndex>::Type const>::Type &limits = stringSetLimits(index);
-
-		return (getSeqOffset(pos, limits) + repLength(it) 
-			== sequenceLength(getSeqNo(pos, limits), index));
-	}
-
-/**
-.Function.isLeftMaximal:
-..summary:Test whether the occurrences of an iterator's @Function.representative@ mutually differ in the character left of the hits.
-..cat:Index
-..signature:bool isLeftMaximal(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:$true$ if there are at least two different characters left of the occurrences, otherwise $false$.
-...type:nolink:bool
-..see:Function.getOccurrences
-..include:seqan/index.h
-*/
+    template < typename TIndex, class TSpec >
+    inline bool isRightTerminal(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        // do we reach a leaf in a suffix tree with trailing '$'
+        typename SAValue<TIndex>::Type pos = getOccurrence(it);
+        TIndex const &index = container(it);
+        typename StringSetLimits<typename Host<TIndex>::Type const>::Type &limits = stringSetLimits(index);
+
+        return (getSeqOffset(pos, limits) + repLength(it)
+            == sequenceLength(getSeqNo(pos, limits), index));
+    }
+
 /*!
  * @fn VSTreeIterator#isLeftMaximal
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Test whether the occurrences of an iterator's @link VSTreeIterator#representative @endlink mutually differ in the character
  *        left of the hits.
- * 
- * @signature bool isLeftMaximal(iterator)
- * 
- * @param iterator An iterator of a suffix tree.
- * 
- * @return TReturn <tt>true</tt> if there are at least two different characters left of the occurrences, otherwise
- *                 <tt>false</tt>. Types: <tt>bool<tt>
- * 
+ *
+ * @signature bool isLeftMaximal(iterator);
+ *
+ * @param[in] iterator An iterator of a suffix tree.
+ *
+ * @return bool <tt>true</tt> if there are at least two different characters left of the occurrences, otherwise
+ *              <tt>false</tt>.
+ *
  * @see VSTreeIterator#getOccurrences
  */
 
-	template < typename TIndex, class TSpec >
-	inline bool isLeftMaximal(Iter<TIndex, VSTree<TSpec> > const &it)
-	{
-		typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type	TOccs;
-		typedef typename Infix< typename Fibre<TIndex, EsaBwt>::Type const >::Type	TOccsBWT;
-		typedef typename Value< typename Fibre<TIndex, EsaBwt>::Type const >::Type	TValue;
-
-		typedef typename Iterator<TOccs, Standard>::Type	TIter;
-		typedef typename Iterator<TOccsBWT, Standard>::Type TIterBWT;
-		
-		TIndex const &index = container(it);
-		typename StringSetLimits<typename Host<TIndex>::Type const>::Type &limits = stringSetLimits(index);
-
-		TOccs occs = getOccurrences(it);
-		TOccsBWT bwts = getOccurrencesBwt(it);
-
-		TIter oc = begin(occs, Standard()), ocEnd = end(occs, Standard());
-		TIterBWT bw = begin(bwts, Standard());
-
-		if (oc == ocEnd) return true;
-		if (posAtFirstLocal(*oc, limits)) return true;
-
-		TValue seen = *bw;
-		++oc; 
-		++bw;
-		if (oc == ocEnd) return true;
-
-		do {
-			if (posAtFirstLocal(*oc, limits)) return true;
-			if (seen != *bw) return true;
-			++oc;
-			++bw;
-		} while (oc != ocEnd);
-
-		return false;
-	}
-
-/**
-.Function.isPartiallyLeftExtensible:
-..summary:Test whether the characters left of the two occurrences of @Function.representative@ are equal.
-..cat:Index
-..signature:bool isPartiallyLeftExtensible(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:$true$ if there are at least two different characters left of the occurrences, otherwise $false$.
-..see:Function.getOccurrences
-..include:seqan/index.h
-*/
+    template < typename TIndex, class TSpec >
+    inline bool isLeftMaximal(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type    TOccs;
+        typedef typename Infix< typename Fibre<TIndex, EsaBwt>::Type const >::Type    TOccsBWT;
+        typedef typename Value< typename Fibre<TIndex, EsaBwt>::Type const >::Type    TValue;
+
+        typedef typename Iterator<TOccs, Standard>::Type    TIter;
+        typedef typename Iterator<TOccsBWT, Standard>::Type TIterBWT;
+
+        TIndex const &index = container(it);
+        typename StringSetLimits<typename Host<TIndex>::Type const>::Type &limits = stringSetLimits(index);
+
+        TOccs occs = getOccurrences(it);
+        TOccsBWT bwts = getOccurrencesBwt(it);
+
+        TIter oc = begin(occs, Standard()), ocEnd = end(occs, Standard());
+        TIterBWT bw = begin(bwts, Standard());
+
+        if (oc == ocEnd) return true;
+        if (posAtFirstLocal(*oc, limits)) return true;
+
+        TValue seen = *bw;
+        ++oc;
+        ++bw;
+        if (oc == ocEnd) return true;
+
+        do {
+            if (posAtFirstLocal(*oc, limits)) return true;
+            if (seen != *bw) return true;
+            ++oc;
+            ++bw;
+        } while (oc != ocEnd);
+
+        return false;
+    }
+
 /*!
  * @fn VSTreeIterator#isPartiallyLeftExtensible
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Test whether the characters left of the two occurrences of @link VSTreeIterator#representative @endlink are equal.
- * 
- * @signature bool isPartiallyLeftExtensible(iterator)
- * 
- * @param iterator An iterator of a suffix tree.
- * 
- * @return TReturn <tt>true</tt> if there are at least two different characters left of the occurrences, otherwise
- *                 <tt>false</tt>.
- * 
+ *
+ * @signature bool isPartiallyLeftExtensible(iterator);
+ *
+ * @param[in] iterator An iterator of a suffix tree.
+ *
+ * @return bool <tt>true</tt> if there are at least two different characters left of the occurrences, otherwise
+ *              <tt>false</tt>.
+ *
  * @see VSTreeIterator#getOccurrences
  */
-	template < typename TIndex, class TSpec, typename TSet >
-	inline bool isPartiallyLeftExtensible(Iter<TIndex, VSTree<TSpec> > const &it, TSet &charSet)
-	{
-		typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type	TOccs;
-		typedef typename Infix< typename Fibre<TIndex, EsaBwt>::Type const >::Type	TOccsBWT;
-		typedef typename Value< typename Fibre<TIndex, EsaBwt>::Type const >::Type	TValue;
-
-		typedef typename Iterator<TOccs, Standard>::Type	TIter;
-		typedef typename Iterator<TOccsBWT, Standard>::Type TIterBWT;
-		
-		TIndex const &index = container(it);
-		typename StringSetLimits<typename Host<TIndex>::Type const>::Type &limits = stringSetLimits(index);
-
-		clear(charSet);
-
-		TOccs occs = getOccurrences(it);
-		TOccsBWT bwts = getOccurrencesBwt(it);
-
-		TIter oc = begin(occs, Standard()), ocEnd = end(occs, Standard());
-		TIterBWT bw = begin(bwts, Standard());
-
-		while (oc != ocEnd) {
-			if (!posAtFirstLocal(*oc, limits)) {
-				TValue c = *bw;
-				if (in(c, charSet)) return true;
-				insert(c, charSet);
-			}
-			++oc;
-			++bw;
-		}
-
-		return false;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline bool isPartiallyLeftExtensible(Iter<TIndex, VSTree<TSpec> > const &it)
-	{
-		typename Set<typename Value<TIndex>::Type>::Type set;
-		return isPartiallyLeftExtensible(it, set);
-	}
-
-/**
-.Function.isUnique:
-..summary:Test whether the @Function.representative@ occurs only once in every sequence.
-..cat:Index
-..signature:bool isUnique(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:$true$ if there are at least two different characters left of the occurrences, otherwise $false$.
-...type:nolink:bool
-..see:Function.getOccurrences
-..include:seqan/index.h
-*/
+    template < typename TIndex, class TSpec, typename TSet >
+    inline bool isPartiallyLeftExtensible(Iter<TIndex, VSTree<TSpec> > const &it, TSet &charSet)
+    {
+        typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type    TOccs;
+        typedef typename Infix< typename Fibre<TIndex, EsaBwt>::Type const >::Type    TOccsBWT;
+        typedef typename Value< typename Fibre<TIndex, EsaBwt>::Type const >::Type    TValue;
+
+        typedef typename Iterator<TOccs, Standard>::Type    TIter;
+        typedef typename Iterator<TOccsBWT, Standard>::Type TIterBWT;
+
+        TIndex const &index = container(it);
+        typename StringSetLimits<typename Host<TIndex>::Type const>::Type &limits = stringSetLimits(index);
+
+        clear(charSet);
+
+        TOccs occs = getOccurrences(it);
+        TOccsBWT bwts = getOccurrencesBwt(it);
+
+        TIter oc = begin(occs, Standard()), ocEnd = end(occs, Standard());
+        TIterBWT bw = begin(bwts, Standard());
+
+        while (oc != ocEnd) {
+            if (!posAtFirstLocal(*oc, limits)) {
+                TValue c = *bw;
+                if (in(c, charSet)) return true;
+                insert(c, charSet);
+            }
+            ++oc;
+            ++bw;
+        }
+
+        return false;
+    }
+
+    template < typename TIndex, class TSpec >
+    inline bool isPartiallyLeftExtensible(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        typename Set<typename Value<TIndex>::Type>::Type set;
+        return isPartiallyLeftExtensible(it, set);
+    }
+
 /*!
  * @fn VSTreeIterator#isUnique
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Test whether the @link VSTreeIterator#representative @endlink occurs only once in every sequence.
- * 
- * @signature bool isUnique(iterator)
- * 
- * @param iterator An iterator of a suffix tree.
- * 
- * @return TReturn <tt>true</tt> if there are at least two different characters left of the occurrences, otherwise
- *                 <tt>false</tt>. Types: <tt> bool <tt>
- * 
+ *
+ * @signature bool isUnique(iterator);
+ *
+ * @param[in] iterator An iterator of a suffix tree.
+ *
+ * @return bool <tt>true</tt> if there are at least two different characters left of the occurrences, otherwise
+ *              <tt>false</tt>.
+ *
  * @see VSTreeIterator#getOccurrences
  */
 
-	template < typename TIndex, class TSpec, typename TSet >
-	inline bool isUnique(Iter<TIndex, VSTree<TSpec> > const &it, TSet &set)
-	{
-		typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
-		typedef typename Iterator<TOccs, Standard>::Type TIter;
-		typedef typename Size<TIndex>::Type TSize;
-
-		TIndex const &index = container(it);
-
-		clear(set);
-
-		TOccs occs = getOccurrences(it);
-		TIter oc = begin(occs, Standard()), ocEnd = end(occs, Standard());
-
-		while (oc != ocEnd) {
-			TSize seqNo = getSeqNo(*oc, stringSetLimits(index));
-			if (in(seqNo, set)) return false;
-			insert(seqNo, set);
-			++oc;
-		}
-
-		return true;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline bool isUnique(Iter<TIndex, VSTree<TSpec> > const &it) {
-		VectorSet_<
-			typename Size<TIndex>::Type,
-			Alloc<> 
-		> set(countSequences(container(it)));
-		return isUnique(it, set);
-	}
-
-/**
-.Function.getFrequency:
-..summary:Returns the number of sequences, which contain the @Function.representative@ as a substring.
-..cat:Index
-..signature:int getFrequency(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:The number of different sequences containing the @Function.representative@.
-..see:Function.getOccurrences
-..include:seqan/index.h
-..example
-...text:The following code how @Function.getFrequency@ is used. Note that the result of alternative 1 and 2 is the same, however alternative one copies a string which requires more memory.
-...file:demos/index/index_getOccurrences_getFrequency_range_getFibre.cpp
-...output:SSI occurs in 2 sequences.
-Hit in sequence 0 at position 5
-Hit in sequence 1 at position 4
-Hit in sequence 0 at position 2
-----------------------------
-Hit in sequence 0 at position 5
-Hit in sequence 1 at position 4
-Hit in sequence 0 at position 2
-*/
+    template < typename TIndex, class TSpec, typename TSet >
+    inline bool isUnique(Iter<TIndex, VSTree<TSpec> > const &it, TSet &set)
+    {
+        typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
+        typedef typename Iterator<TOccs, Standard>::Type TIter;
+        typedef typename Size<TIndex>::Type TSize;
+
+        TIndex const &index = container(it);
+
+        clear(set);
+
+        TOccs occs = getOccurrences(it);
+        TIter oc = begin(occs, Standard()), ocEnd = end(occs, Standard());
+
+        while (oc != ocEnd) {
+            TSize seqNo = getSeqNo(*oc, stringSetLimits(index));
+            if (in(seqNo, set)) return false;
+            insert(seqNo, set);
+            ++oc;
+        }
+
+        return true;
+    }
+
+    template < typename TIndex, class TSpec >
+    inline bool isUnique(Iter<TIndex, VSTree<TSpec> > const &it) {
+        VectorSet_<
+            typename Size<TIndex>::Type,
+            Alloc<>
+        > set(countSequences(container(it)));
+        return isUnique(it, set);
+    }
+
 /*!
  * @fn VSTreeIterator#getFrequency
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the number of sequences, which contain the @link
  *        VSTreeIterator#representative @endlink as a substring.
- * 
- * @signature int getFrequency(iterator)
- * 
- * @param iterator An iterator of a suffix tree. Types: @link VSTreeIterator @endlink
- * 
- * @return TReturn The number of different sequences containing the @link
- *                 VSTreeIterator#representative @endlink.
+ *
+ * @signature int getFrequency(iterator);
+ *
+ * @param[in] iterator An iterator of a suffix tree. Types: @link VSTreeIterator @endlink
+ *
+ * @return int The number of different sequences containing the @link VSTreeIterator#representative @endlink.
+ *
  * @section Example
  *
  * The following code how @link VSTreeIterator#getFrequency @endlink is used. Note that the result of alternative 1 and 2 is the same,
  * however alternative one copies a string which requires more memory.
- * @include demos/index/index_getOccurrences_getFrequency_range_getFibre.cpp
- * @code{.txt}
+ *
+ * @include demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp
+ *
+ * @code{.output}
  * SSI occurs in 2 sequences.
  * Hit in sequence 0 at position 5
  * Hit in sequence 1 at position 4
@@ -3341,234 +2684,207 @@ Hit in sequence 0 at position 2
  * @see VSTreeIterator#getOccurrences
  */
 
-	template < typename TIndex, class TSpec, typename TSet >
-	inline typename Size<TIndex>::Type
-	getFrequency(Iter<TIndex, VSTree<TSpec> > const &it, TSet &set)
-	{
-		typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
-		typedef typename Iterator<TOccs, Standard>::Type TIter;
-		typedef typename Size<TIndex>::Type TSize;
-
-		TIndex const &index = container(it);
-
-		clear(set);
-
-		TOccs occs = getOccurrences(it);
-		TIter oc = begin(occs, Standard()), ocEnd = end(occs, Standard());
-
-		int counter = 0;
-		while (oc != ocEnd) {
-			TSize seqNo = getSeqNo(*oc, stringSetLimits(index));
-			if (!in(seqNo, set)) {
-				++counter;
-				insert(seqNo, set);
-			}
-			++oc;
-		}
-
-		return counter;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline typename Size<TIndex>::Type
-	getFrequency(Iter<TIndex, VSTree<TSpec> > const &it) 
-	{
-		VectorSet_<
-			typename Size<TIndex>::Type,
-			Alloc<> 
-		> set(countSequences(container(it)));
-		return getFrequency(it, set);
-	}
-
-/**
-.Function.childrenAreLeaves:
-..summary:Test whether iterator points to a node with only leaf-children.
-..cat:Index
-..signature:bool childrenAreLeaves(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a suffix tree.
-...type:Spec.VSTree Iterator
-..returns:$true$ if $iterator$ points to an inner node of the tree, whose children are leaves. Otherwise it is $false$.
-..include:seqan/index.h
-*/
+    template < typename TIndex, class TSpec, typename TSet >
+    inline typename Size<TIndex>::Type
+    getFrequency(Iter<TIndex, VSTree<TSpec> > const &it, TSet &set)
+    {
+        typedef typename Infix< typename Fibre<TIndex, EsaSA>::Type const >::Type TOccs;
+        typedef typename Iterator<TOccs, Standard>::Type TIter;
+        typedef typename Size<TIndex>::Type TSize;
+
+        TIndex const &index = container(it);
+
+        clear(set);
+
+        TOccs occs = getOccurrences(it);
+        TIter oc = begin(occs, Standard()), ocEnd = end(occs, Standard());
+
+        int counter = 0;
+        while (oc != ocEnd) {
+            TSize seqNo = getSeqNo(*oc, stringSetLimits(index));
+            if (!in(seqNo, set)) {
+                ++counter;
+                insert(seqNo, set);
+            }
+            ++oc;
+        }
+
+        return counter;
+    }
+
+    template < typename TIndex, class TSpec >
+    inline typename Size<TIndex>::Type
+    getFrequency(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        VectorSet_<
+            typename Size<TIndex>::Type,
+            Alloc<>
+        > set(countSequences(container(it)));
+        return getFrequency(it, set);
+    }
+
 /*!
  * @fn VSTreeIterator#childrenAreLeaves
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Test whether iterator points to a node with only leaf-children.
- * 
- * @signature bool childrenAreLeaves(iterator)
- * 
- * @param iterator An iterator of a suffix tree.
- * 
- * @return TReturn <tt>true</tt> if <tt>iterator</tt> points to an inner node of the tree, whose children are leaves.
- *                 Otherwise it is <tt>false</tt>.
+ *
+ * @signature bool childrenAreLeaves(iterator);
+ *
+ * @param[in] iterator An iterator of a suffix tree.
+ *
+ * @return bool <tt>true</tt> if <tt>iterator</tt> points to an inner node of the tree, whose children are leaves.
+ *              Otherwise it is <tt>false</tt>.
  */
-	template < typename TIndex, class TSpec >
-	inline bool childrenAreLeaves(Iter<TIndex, VSTree<TSpec> > const &it) 
-	{
-		return countChildren(it) == countOccurrences(it);
-	}
-
-/**
-.Function.isLeaf:
-..summary:Test whether a tree iterator points to a leaf.
-..cat:Index
-..signature:bool isLeaf(iterator)
-..class:Spec.VSTree Iterator
-..param.iterator:An iterator of a tree.
-...type:Spec.VSTree Iterator
-..returns:$true$ if $iterator$ points to a leaf of the tree, otherwise $false$.
-...type:nolink:bool
-..include:seqan/index.h
-*/
+    template < typename TIndex, class TSpec >
+    inline bool childrenAreLeaves(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        return countChildren(it) == countOccurrences(it);
+    }
+
 /*!
  * @fn VSTreeIterator#isLeaf
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Test whether a tree iterator points to a leaf.
- * 
- * @signature bool isLeaf(iterator)
- * 
- * @param iterator An iterator of a tree.
- * 
- * @return TReturn <tt>true</tt> if <tt>iterator</tt> points to a leaf of the tree, otherwise <tt>false</tt>.
- * 
+ *
+ * @signature bool isLeaf(iterator);
+ *
+ * @param[in] iterator An iterator of a tree.
+ *
+ * @return bool <tt>true</tt> if <tt>iterator</tt> points to a leaf of the tree, otherwise <tt>false</tt>.
+ *
  * @link DemoIndexCountChildren @endlink
  */
-	template < typename TSize >
-	inline bool _isLeaf(VertexEsa<TSize> const &vDesc)
-	{
+    template < typename TSize >
+    SEQAN_HOST_DEVICE inline bool _isLeaf(VertexEsa<TSize> const &vDesc)
+    {
 //IOREV _notio_
-		// is this a leaf?
-		return vDesc.range.i1 + 1 >= vDesc.range.i2;
-	}
+        // is this a leaf?
+        return vDesc.range.i1 + 1 >= vDesc.range.i2;
+    }
 
-	// is this a leaf? (including empty $-edges)
-	template < typename TIndex, class TSpec, typename TDfsOrder >
-	inline bool _isLeaf(
-		Iter<TIndex, VSTree<TSpec> > const &it,
-		VSTreeIteratorTraits<TDfsOrder, False> const)
-	{
-		return _isLeaf(value(it));
-	}
+    // is this a leaf? (including empty $-edges)
+    template < typename TIndex, class TSpec, typename TDfsOrder >
+    SEQAN_HOST_DEVICE inline bool _isLeaf(
+        Iter<TIndex, VSTree<TSpec> > const &it,
+        VSTreeIteratorTraits<TDfsOrder, False> const)
+    {
+        return _isLeaf(value(it));
+    }
 
 
     template <typename TIndex, typename TSpec>
-    inline typename SAValue<TIndex>::Type
+    SEQAN_HOST_DEVICE inline typename SAValue<TIndex>::Type
     _lastOccurrence(Iter<TIndex, VSTree<TSpec> > const &it)
     {
-		return back(getOccurrences(it));
+        return back(getOccurrences(it));
     }
 
     template <typename TText, typename TIndexSpec, typename TSpec>
-    inline typename SAValue<Index<TText, IndexEsa<TIndexSpec> > >::Type
+    SEQAN_HOST_DEVICE inline typename SAValue<Index<TText, IndexEsa<TIndexSpec> > >::Type
     _lastOccurrence(Iter<Index<TText, IndexEsa<TIndexSpec> >, VSTree<TSpec> > const &it)
     {
         if (_isSizeInval(value(it).range.i2))
             return back(indexSA(container(it)));
         else
-			return saAt(value(it).range.i2 - 1, container(it));
+            return saAt(value(it).range.i2 - 1, container(it));
     }
 
-	// is this a leaf? (hide empty $-edges)
-	template < typename TIndex, class TSpec, typename TDfsOrder >
-	inline bool _isLeaf(Iter<TIndex, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDfsOrder, True> const)
-	{
+    // is this a leaf? (hide empty $-edges)
+    template < typename TIndex, class TSpec, typename TDfsOrder >
+    SEQAN_HOST_DEVICE inline bool _isLeaf(Iter<TIndex, VSTree<TSpec> > const &it, VSTreeIteratorTraits<TDfsOrder, True> const)
+    {
         typedef typename SAValue<TIndex>::Type  TOcc;
 
-		if (_isLeaf(value(it))) return true;
+        if (_isLeaf(value(it))) return true;
 
-		TIndex const &index = container(it);
+        TIndex const &index = container(it);
 
-		// get representative length (see repLength)
-		typename Size<TIndex>::Type lcp = repLength(it);
-        
-		// if the last suffix in the interval is larger than the lcp,
+        // get representative length (see repLength)
+        typename Size<TIndex>::Type lcp = repLength(it);
+
+        // if the last suffix in the interval is larger than the lcp,
         // not all outgoing edges are empty (uses lex. sorting)
-		TOcc oc = _lastOccurrence(it);
+        TOcc oc = _lastOccurrence(it);
         return getSeqOffset(oc, stringSetLimits(index)) + lcp == sequenceLength(getSeqNo(oc, stringSetLimits(index)), index);
-	}
+    }
 
-	template < typename TIndex, class TSpec >
-	inline bool isLeaf(Iter<TIndex, VSTree<TSpec> > const &it)
-	{
-		return _isLeaf(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree<TSpec> > >::Type());
-	}
+    template < typename TIndex, class TSpec >
+    SEQAN_HOST_DEVICE inline bool isLeaf(Iter<TIndex, VSTree<TSpec> > const &it)
+    {
+        return _isLeaf(it, typename GetVSTreeIteratorTraits< Iter<TIndex, VSTree<TSpec> > >::Type());
+    }
 
-	//////////////////////////////////////////////////////////////////////////////
-	// (more or less) internal functions for accessing the childtab
+    //////////////////////////////////////////////////////////////////////////////
+    // (more or less) internal functions for accessing the childtab
 
-	template < typename TSize, typename TIndex >
-	inline bool _isNextl(TSize i, TIndex const &index) 
-	{
+    template < typename TSize, typename TIndex >
+    SEQAN_HOST_DEVICE inline bool _isNextl(TSize i, TIndex const &index)
+    {
 //IOREV _notio_
-		if (i >= length(index)) return false;
-		TSize j = childAt(i, index);
-		return (j > i) && lcpAt(j - 1, index) == lcpAt(i - 1, index);
-	}
-
-	template < typename TSize, typename TIndex >
-	inline bool _isUp(TSize i, TIndex const &index) 
-	{
+        if (i >= length(index)) return false;
+        TSize j = childAt(i, index);
+        return (j > i) && lcpAt(j - 1, index) == lcpAt(i - 1, index);
+    }
+
+    template < typename TSize, typename TIndex >
+    SEQAN_HOST_DEVICE inline bool _isUp(TSize i, TIndex const &index)
+    {
 //IOREV _notio_
-		if (i >= length(index)) return false;
-		TSize j = childAt(i, index);
-		return (j <= i) && lcpAt(j - 1, index) > lcpAt(i - 1, index);
-	}
-
-	template < typename TSize, typename TIndex >
-	inline TSize _getNextl(TSize i, TIndex const &index) 
-	{
-		return childAt(i, index);
-	}
-
-	template < typename TSize, typename TIndex >
-	inline TSize _getUp(TSize i, TIndex const &index) 
-	{
-		if (!_isSizeInval(i))
-			return childAt(i - 1, index);
-		else
-			return childAt(0, index);
-	}
-
-	template < typename TSize, typename TIndex >
-	inline TSize _getDown(TSize i, TIndex const &index) 
-	{
-		return childAt(i, index);
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// depth-first search 
-
-	template < typename TIndex, class TSpec >
-	inline Pair<typename Size<TIndex>::Type> &
-	_dfsRange(Iter< TIndex, VSTree< BottomUp<TSpec> > > &it)
-	{
-		return value(it).range;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline Pair<typename Size<TIndex>::Type> const & 
-	_dfsRange(Iter< TIndex, VSTree< BottomUp<TSpec> > > const &it) 
-	{
-		return value(it).range;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline typename Size<TIndex>::Type & _dfsLcp(Iter< TIndex, VSTree< BottomUp<TSpec> > > &it)
-	{
-		return it.lValue;
-	}
-
-	template < typename TIndex, class TSpec >
-	inline typename Size<TIndex>::Type _dfsLcp(Iter< TIndex, VSTree< BottomUp<TSpec> > > const &it)
-	{
-		return it.lValue;
-	}
+        if (i >= length(index)) return false;
+        TSize j = childAt(i, index);
+        return (j <= i) && lcpAt(j - 1, index) > lcpAt(i - 1, index);
+    }
+
+    template < typename TSize, typename TIndex >
+    SEQAN_HOST_DEVICE inline TSize _getNextl(TSize i, TIndex const &index)
+    {
+        return childAt(i, index);
+    }
+
+    template < typename TSize, typename TIndex >
+    SEQAN_HOST_DEVICE inline TSize _getUp(TSize i, TIndex const &index)
+    {
+        if (!_isSizeInval(i))
+            return childAt(i - 1, index);
+        else
+            return childAt(0, index);
+    }
+
+    template < typename TSize, typename TIndex >
+    SEQAN_HOST_DEVICE inline TSize _getDown(TSize i, TIndex const &index)
+    {
+        return childAt(i, index);
+    }
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // depth-first search
+
+    template < typename TIndex, class TSpec >
+    inline Pair<typename Size<TIndex>::Type> &
+    _dfsRange(Iter< TIndex, VSTree< BottomUp<TSpec> > > &it)
+    {
+        return value(it).range;
+    }
+
+    template < typename TIndex, class TSpec >
+    inline Pair<typename Size<TIndex>::Type> const &
+    _dfsRange(Iter< TIndex, VSTree< BottomUp<TSpec> > > const &it)
+    {
+        return value(it).range;
+    }
+
+    template < typename TIndex, class TSpec >
+    inline typename Size<TIndex>::Type & _dfsLcp(Iter< TIndex, VSTree< BottomUp<TSpec> > > &it)
+    {
+        return it.lValue;
+    }
+
+    template < typename TIndex, class TSpec >
+    inline typename Size<TIndex>::Type _dfsLcp(Iter< TIndex, VSTree< BottomUp<TSpec> > > const &it)
+    {
+        return it.lValue;
+    }
 
 
 }
diff --git a/seqan/index/index_fm.h b/seqan/index/index_fm.h
index 5f03983..b8ed184 100644
--- a/seqan/index/index_fm.h
+++ b/seqan/index/index_fm.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,6 +31,7 @@
 //
 // ==========================================================================
 // Author: Jochen Singer <jochen.singer@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
 // ==========================================================================
 
 //SEQAN_NO_DDDOC:do not generate documentation for this file
@@ -39,874 +41,452 @@
 
 namespace seqan {
 
-// ==========================================================================
-// Forwards
-// ==========================================================================
-
-template <typename TChar, typename TSpec>
-class PrefixSumTable;
-
-// WT = WaveletTree
-/**
-.Tag.WT
-..summary:Tag that specifies the @Spec.FMIndex@ to use a wavelet tree as the occurrence table.
-..cat:Index
-*/
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction FMIndexConfig
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class FMIndexConfig
+ * @headerfile <seqan/index.h>
+ * @brief A configuration object that determines the data types of certain fibres of the @link FMIndex @endlink.
+ *
+ * @signature template <[typename TSpec]>
+ *            struct FMIndexConfig;
+ *
+ * @tparam TSpec The specializating type, defaults to <tt>void</tt>.
+ *
+ * @var unsigned FMIndexConfig::SAMPLING;
+ * @brief The sampling rate determines how many suffix array entries are represented with one entry in the
+ *        @link CompressedSA @endlink.
+ *
+ * @typedef FMIndexConfig::TValuesSpec
+ * @signature typedef WaveletTree<TSpec, TConfig> TValuesSpec;
+ * @brief The <tt>TValuesSpec</tt> determines the type of the occurrence table. In the default @link FMIndexConfig
+ *        @endlink object the type of <tt>TValuesSpec</tt> is a wavelet tree (@link WaveletTree @endlink).
+ *
+ * @typedef FMIndexConfig::TSentinelsSpec
+ * @signature typedef Levels<TSpec, TConfig> TSentinelsSpec;
+ * @brief The <tt>TSentinelsSpec</tt> determines the type of the sentinels in the @link FMIndex @endlink.  In the
+ *        default @link FMIndexConfig @endlink object the type of <tt>TSentinelsSpec</tt> is a two level
+ *        @link RankDictionary @endlink.
+ */
+template <typename TSpec = void, typename TLengthSum = size_t>
+struct FMIndexConfig
+{
+    typedef TLengthSum                                  LengthSum;
+    typedef WaveletTree<TSpec, WTRDConfig<LengthSum> >  Bwt;
+    typedef Levels<TSpec, LevelsRDConfig<LengthSum> >   Sentinels;
+
+    static const unsigned SAMPLING =                    10;
+};
 
-template <typename TSpec = void>
-class WT;
+// ============================================================================
+// Forwards
+// ============================================================================
 
-template <typename TOccSpec = WT<>, typename TSpec = void>
+template <typename TSpec = void, typename TConfig = FMIndexConfig<TSpec> >
 class FMIndex;
 
-struct FinderFMIndex_;
-typedef Tag<FinderFMIndex_> FinderFMIndex;
-
-template <typename TText, typename TOccSpec, typename TSpec>
-struct DefaultFinder<Index<TText, FMIndex<TOccSpec, TSpec> > >
-{
-	typedef FinderFMIndex Type;
-};
-
-// ==========================================================================
-// Tags, Classes, Enums
-// ==========================================================================
+// ============================================================================
+// Tags
+// ============================================================================
 
-struct FibrePrefixSumTable_;
-struct FibreSA_;
+// FM index fibres
 struct FibreTempSA_;
-struct FibreText_;
-struct FibreLfTable_;
-struct FibreSaLfTable_;
-struct CompressText_;
-struct Sentinel_;
-struct Sentinels_;
-
-typedef Tag<FibrePrefixSumTable_> const FibrePrefixSumTable;
-typedef Tag<FibreSA_> const             FibreSA;
-typedef Tag<FibreTempSA_> const         FibreTempSA;
-typedef Tag<FibreText_> const           FibreText;
-typedef Tag<FibreLfTable_> const        FibreLfTable;
-typedef Tag<FibreSaLfTable_> const      FibreSaLfTable;
-typedef Tag<CompressText_> const        CompressText;
-typedef Tag<Sentinel_> const            Sentinel;
-typedef Tag<Sentinels_> const           Sentinels;
-
+struct FibreLF_;
+struct FibreSALF_;
 
-// FM index fibres
-/**
-.Tag.FM Index Fibres
-..summary:Tag to select a specific fibre of a @Spec.FMIndex@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a FM index.
-..cat:Index
-
-..tag.FibrePrefixSumTable:The prefix sum table of the index.
-..tag.FibreSA:The compressed suffix array of the text.
-..tag.FibreText:The original text of the index.
-..tag.FibreLfTable:The lf table.
-..tag.FibreSaLfTable:The lf table as well as the compressed suffix array.
-...remarks:This tag can only be used with the functions @Function.indexRequire@ or @Function.indexSupplied@.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index_fm.h
-*/
-
-/**
-.Tag.CompressText
-..cat:Index
-..summary:Tag to select a FM index variant that can be used such that it is 
-not necessary to store the text after index construction. This index is very
-space efficient.
-*/
+typedef Tag<FibreTempSA_> const         FibreTempSA;
+typedef Tag<FibreLF_> const             FibreLF;
+typedef Tag<FibreSALF_> const           FibreSALF;
 
-// ==========================================================================
+// ============================================================================
 // Metafunctions
-// ==========================================================================
+// ============================================================================
 
 // ----------------------------------------------------------------------------
 // Metafunction Fibre
 // ----------------------------------------------------------------------------
-    
-/*
-.Metafunction.Fibre:
-..summary:Type of a specific FMIndex member (fibre).
-..signature:Fibre<Index<TText, FMIndex<TSentinelRankDictionary, TSpec> >, TFibreSpec>::Type
-..class:Spec.FMIndex
-..cat:Index
-..param.TText:The text type.
-...type:Class.String
-...type:Class.StringSet
-..param.TSentinelRankDictionary:The type of the sentinel rank dictionary.
-...type:Class.SentinelRankDictionary
-..param.TSpec:Tag to specify a certain variant of the FM index.
-...type:Tag.CompressText
-...default;$void$
-..param.TFibreSpec:Tag to specify the fibre.
-...type:Tag.FM Index Fibres
-..returns:Fibre type.
-..remarks:Some containers, such as @Spec.FMIndex@, can be seen as a bundle consisting of various fibres. Because not 
-every table is a fibre we did not call them tables, however, in many cases one can think of fibres as tables. The 
-fibre interface was designed to unify the access to the members of the different fibres.
-To get a reference or the type of a specific fibre use @Function.getFibre@ or @Metafunction.Fibre@.		
-..include:seqan/index.h
-*/
-
-template <typename TText, typename TWaveletTreeSpec, typename TSpec>
-struct Fibre<Index<TText, FMIndex<WT<TWaveletTreeSpec>, TSpec> >, FibreOccTable>
-{
-    typedef typename Value<TText>::Type TValue_;
-	typedef SentinelRankDictionary<RankDictionary<WaveletTree<TValue_> >, Sentinel> Type;
-};
-
-template <typename TText, typename TStringSetSpec, typename TWaveletTreeSpec, typename TSpec>
-struct Fibre<Index<StringSet<TText, TStringSetSpec>, FMIndex<WT<TWaveletTreeSpec>, TSpec > >, FibreOccTable>
-{
-    typedef typename Value<TText>::Type TValue_;
-    typedef SentinelRankDictionary<RankDictionary<WaveletTree<TValue_> >, Sentinels> Type;
-};
-
-template <typename TText, typename TWaveletTreeSpec, typename TSpec>
-struct Fibre<Index<TText, FMIndex<SBM<TWaveletTreeSpec>, TSpec> >, FibreOccTable>
-{
-    typedef typename Value<Index<TText, FMIndex<WT<TWaveletTreeSpec>, TSpec> > >::Type TValue_;
-	typedef SentinelRankDictionary<RankDictionary<SequenceBitMask<TValue_> >, Sentinel> Type;
-};
-
-template <typename TText, typename TStringSetSpec, typename TWaveletTreeSpec, typename TSpec>
-struct Fibre<Index<StringSet<TText, TStringSetSpec>, FMIndex<SBM<TWaveletTreeSpec>, TSpec > >, FibreOccTable>
-{
-    typedef typename Value<TText>::Type TValue_;
-    typedef SentinelRankDictionary<RankDictionary<SequenceBitMask<TValue_> >, Sentinels> Type;
-};
-
-template <typename TText, typename TOccSpec, typename TSpec>
-struct Fibre<Index<TText, FMIndex<TOccSpec, TSpec> >, FibreLfTable>
-{
-    typedef typename Fibre<Index<TText, FMIndex<TOccSpec, TSpec> >, FibreOccTable>::Type        TOccTable_;
-	typedef typename Fibre<Index<TText, FMIndex<TOccSpec, TSpec> >, FibrePrefixSumTable>::Type  TPrefixSumTable_;
-	typedef LfTable<TOccTable_, TPrefixSumTable_>   	                                        Type;
-};
 
-template <typename TText, typename TOccSpec, typename TSpec>
-struct Fibre<Index<TText, FMIndex<TOccSpec, TSpec> > const, FibreLfTable>
-{
-    typedef typename Fibre<Index<TText, FMIndex<TOccSpec, TSpec> > const, FibreOccTable>::Type          TOccTable_;
-	typedef typename Fibre<Index<TText, FMIndex<TOccSpec, TSpec> > const, FibrePrefixSumTable>::Type    TPrefixSumTable_;
-	typedef LfTable<TOccTable_, TPrefixSumTable_>   	                                                Type;
+/*!
+ * @defgroup FMIndexFibres FM Index Fibres
+ * @brief Tag to select a specific fibre of a @link FMIndex @endlink.
+ *
+ * These tags can be used to get @link Fibre Fibres @endlink of a FM index.
+ *
+ * @see Fibre
+ * @see Index#getFibre
+ *
+ * @tag FMIndexFibres#FibreText
+ * @brief The original text of the index.
+ *
+ * @tagFMIndexFibres#FibreSA
+ * @brief The compressed suffix array of the text.
+ *
+ * @tag FMIndexFibres#FibreLF
+ * @brief The lf table.
+ */
+
+
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<Index<TText, FMIndex<TSpec, TConfig> >, FibreLF>
+{
+    typedef LF<TText, TSpec, TConfig>  Type;
 };
 
-template <typename TText, typename TOccSpec, typename TSpec>
-struct Fibre<Index<TText, FMIndex<TOccSpec, TSpec> >, FibrePrefixSumTable>
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<Index<TText, FMIndex<TSpec, TConfig> >, FibreSA>
 {
-    typedef typename Value<Index<TText, FMIndex<TOccSpec, TSpec> > >::Type  TChar_;
-    typedef typename MakeUnsigned<TChar_>::Type                             TUChar_;
-	typedef PrefixSumTable<TUChar_, void>                                   Type;
+    typedef CompressedSA<TText, TSpec, TConfig> Type;
 };
 
-template <typename TText, typename TOccSpec, typename TSpec>
-struct Fibre<Index<TText, FMIndex<TOccSpec, TSpec> > const, FibrePrefixSumTable>
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<Index<TText, FMIndex<TSpec, TConfig> >, FibreTempSA>
 {
-    typedef typename Value<Index<TText, FMIndex<TOccSpec, TSpec> > const>::Type TChar_;
-    typedef typename MakeUnsigned<TChar_>::Type                                 TUChar_;
-	typedef PrefixSumTable<TUChar_, void>                                       Type;
-};
-
-template <typename TText, typename TOccSpec, typename TSpec>
-struct Fibre<Index<TText, FMIndex<TOccSpec, TSpec> >, FibreSA>
-{
-	typedef typename SAValue<Index<TText, FMIndex<TOccSpec, TSpec> > >::Type                TSAValue_;
-	typedef SparseString<String<TSAValue_>, void>                                           TSparseString_;
-	typedef typename Fibre<Index<TText, FMIndex<TOccSpec, TSpec> >, FibreLfTable>::Type     TLfTable_;
-	typedef CompressedSA<TSparseString_, TLfTable_, void>                                   Type;
-};
+    typedef Index<TText, FMIndex<TSpec, TConfig> >          TIndex_;
+    typedef typename SAValue<TIndex_>::Type                 TSAValue_;
 
-template <typename TText, typename TOccSpec, typename TSpec>
-struct Fibre<Index<TText, FMIndex<TOccSpec, TSpec> >, FibreTempSA>
-{
-	typedef typename SAValue<Index<TText, FMIndex<TOccSpec, TSpec> > >::Type    TSAValue;
-	typedef String<TSAValue, External<ExternalConfigLarge<> > >                 Type;
+    // NOTE(esiragusa): External causes problems on device code.
+#ifndef PLATFORM_CUDA
+    typedef String<TSAValue_, External<ExternalConfigLarge<> > >                Type;
+#else
+    typedef String<TSAValue_, typename DefaultIndexStringSpec<TText>::Type>     Type;
+#endif
 };
 
-// ==========================================================================
-// Classes
-// ==========================================================================
-
 // ----------------------------------------------------------------------------
-// Class FmIndexInfo_ 
+// Metafunction DefaultFinder
 // ----------------------------------------------------------------------------
 
-// Stores the information about an FM index file bundle and is written to the .fma file.
-
-#ifdef PLATFORM_WINDOWS
-    #pragma pack(push,1)
-#endif
-
-struct FmIndexInfo_
+template <typename TText, typename TSpec, typename TConfig>
+struct DefaultFinder<Index<TText, FMIndex<TSpec, TConfig> > >
 {
-    // The compression factor.
-    __uint32 compressionFactor;
-    // The sizeof(TSAEntry) values for suffix array entries.
-    __uint32 sizeOfSAEntry;
-    // The length of the genome.
-    __uint64 genomeLength;
-}
+    typedef FinderSTree Type;
+};
 
-#ifndef PLATFORM_WINDOWS
-    __attribute__((packed))
-#endif
-    ;
-#ifdef PLATFORM_WINDOWS
-      #pragma pack(pop)
-#endif
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class FMIndex
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class FMIndex
+ * @extends Index
+ * @implements StringTrieConcept
+ * @headerfile <seqan/index.h>
+ * @brief An index based on the Burrows-Wheeler transform.
+ *
+ * @signature template <typename TText[, typename TSpec[, typename TConfig]]>
+ *            class Index<TText, FMIndex<TSpec, TConfig> >;
+ *
+ * @tparam TText   The text type. Types: @link String @endlink, @link StringSet @endlink
+ * @tparam TSpec   FM index specialisation, defaults to <tt>void</tt>.
+ * @tparam TConfig A config object which determines the data types of the different fibres, defaults to
+ *                 <tt>FMIndexConfig&lt;TSpec&gt;</tt>.
+ *
+ * @section Structure
+ *
+ * The FM index consists of various @link Fibre @endlink of which the most important ones are the compressed
+ * suffix array and the LF table, which provides all necessary information for the LF mapping.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+class Index<TText, FMIndex<TSpec, TConfig> >
+{
+public:
+    typename Member<Index, FibreText>::Type         text;
+    typename Fibre<Index, FibreLF>::Type            lf;
+    typename Fibre<Index, FibreSA>::Type            sa;
+
+    Index() {};
+
+    Index(TText & text) :
+        text(text)
+    {}
+};
 
-// ----------------------------------------------------------------------------
-// Spec FMIndex 
-// ----------------------------------------------------------------------------
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_CONCEPT_IMPL((Index<TText, FMIndex<TSpec, TConfig> >), (StringTrieConcept));
 
-/**
-.Spec.FMIndex:
-..summary:An index based on the Burrows-Wheeler transform.
-..cat:Index
-..general:Class.Index
-..signature:Index<TText, FMIndex<TOccSpec, TSpec> >
-..param.TText:The text type.
-...type:Class.String
-...type:Class.StringSet
-..param.TOccSpec:Occurrence table specialisation. 
-...type:Tag.WT
-...type:Tag.SBM
-...remarks:The tags are really shortcuts for the different @Class.SentinelRankDictionary@s
-...default:Tag.WT
-..param.TSpec:FM index specialisation.
-...type:Tag.CompressText
-...default:void
-..include:seqan/index.h
-*/
-
-template <typename TText, typename TOccSpec, typename TSpec>
-class Index<TText, FMIndex<TOccSpec, TSpec> >
-{
-    public:
-    Holder<typename Fibre<Index, FibreText>::Type>  text;
-	typename Fibre<Index, FibreLfTable>::Type       lfTable;
-	typename Fibre<Index, FibreSA>::Type            compressedSA;
-	typename Size<TText>::Type                      n;
-    unsigned                                        compressionFactor; 
-
-	Index() :
-		n(0)
-	{}
-
-	Index(TText & text, unsigned compressionFactor = 10) :
-	    text(text),
-		n(_computeBwtLength(text)),
-		compressionFactor(compressionFactor)
-	{}
-
-	inline bool operator==(const Index & b) const
-    {
-        return lfTable == b.lfTable &&
-               compressedSA == b.compressedSA &&
-               n == b.n &&
-               compressionFactor == b.compressionFactor;
-    }
-};
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_CONCEPT_IMPL((Index<TText, FMIndex<TSpec, TConfig> > const), (StringTrieConcept));
 
-// ==========================================================================
+// ============================================================================
 // Functions
-// ==========================================================================
+// ============================================================================
+
 // ----------------------------------------------------------------------------
-// Function clear
+// Function clear()
 // ----------------------------------------------------------------------------
 
 // Already documented
-template <typename TText, typename TOccSpec, typename TSpec>
-inline void clear(Index<TText, FMIndex<TOccSpec, TSpec> > & index)
+template <typename TText, typename TSpec, typename TConfig>
+inline void clear(Index<TText, FMIndex<TSpec, TConfig> > & index)
 {
-    clear(getFibre(index, FibreLfTable()));
+    clear(getFibre(index, FibreText()));
+    clear(getFibre(index, FibreLF()));
     clear(getFibre(index, FibreSA()));
 }
 
 // ----------------------------------------------------------------------------
-// Helper function _computeBwtLength
-// ----------------------------------------------------------------------------
-
-// This function computes the length of the bwt string.
-template <typename TText>
-inline typename Size<TText>::Type
-_computeBwtLength(TText const & text)
-{
-    return length(text) + 1;
-}
-
-// This function computes the length of the bwt string.
-template <typename TText, typename TSetSpec>
-inline typename Size<typename StringSetLimits<TText>::Type>::Type
-_computeBwtLength(StringSet<TText, TSetSpec> const & text)
-{
-    return lengthSum(text) + countSequences(text);
-}
-
-// ----------------------------------------------------------------------------
-// Helper function _createBwTable
-// ----------------------------------------------------------------------------
-
-// This function computes the BWT of a text. Note that the sentinel sign is substituted and its position stored.
-// The function is tested implicitly in lfTableLfMapping() in test_index_fm.h
-template <typename TBwt, typename TSentinelPosition, typename TText, typename TSA, typename TSentinelSub>
-inline void _createBwTable(TBwt & bwt, TSentinelPosition & sentinelPos, TText const & text, TSA const & sa,
-		                   TSentinelSub const sentinelSub)
-{
-	//typedefs
-	typedef typename GetValue<TSA>::Type                    TSAValue;
-    typedef typename Iterator<TSA const, Standard>::Type    TSAIter;
-    typedef typename Iterator<TBwt, Standard>::Type         TBwtIter;
-
-	//little helpers
-    TSAIter saIt = begin(sa, Standard());
-    TSAIter saItEnd = end(sa, Standard());
-    TBwtIter bwtIt = begin(bwt, Standard());
-    
-	assignValue(bwtIt, back(text));
-	for (; saIt != saItEnd; ++saIt)
-	{
-        ++bwtIt;
-		TSAValue pos = getValue(saIt);
-		if (pos != 0)
-			assignValue(bwtIt, getValue(text, pos - 1));
-		else
-		{
-			assignValue(bwtIt, sentinelSub);
-			sentinelPos = bwtIt - begin(bwt, Standard());
-		}
-	}
-}
-
-// This function computes the BWT of a text. Note that the sentinel sign is substituted and its position stored.
-// The function is tested implicitly in lfTableLfMapping() in test_index_fm.h
-template <typename TBwt, typename TSentinelPosition, typename TText, typename TSetSpec, typename TSA, typename TSentinelSub>
-inline void _createBwTable(TBwt & bwt, TSentinelPosition & sentinelPos, StringSet<TText, TSetSpec> const & text,
-		                   TSA const & sa, TSentinelSub const sentinelSub)
-{
-    typedef typename Value<TSA>::Type                       TSAValue;
-    typedef typename Size<TSA>::Type                        TSize;
-    typedef typename Iterator<TSA const, Standard>::Type    TSAIter;
-    typedef typename Iterator<TBwt, Standard>::Type         TBwtIter;
-
-    // little Helpers
-    TSize seqNum = countSequences(text);
-    TSize totalLen = lengthSum(text);
-
-    resize(sentinelPos, seqNum + totalLen, Exact());
-    
-    TSAIter saIt = begin(sa, Standard());
-    TSAIter saItEnd = end(sa, Standard());
-    TBwtIter bwtItBeg = begin(bwt, Standard());
-    TBwtIter bwtIt = bwtItBeg;
-
-    // fill the sentinel positions (they are all at the beginning of the bwt)
-    for (TSize i = 1; i <= seqNum; ++i, ++bwtIt)
-        assignValue(bwtIt, back(text[seqNum - i]));
-
-    // compute the rest of the bwt
-    for (; saIt != saItEnd; ++saIt, ++bwtIt)
-    {
-        TSAValue pos;    // = SA[i];
-        posLocalize(pos, getValue(saIt), stringSetLimits(text));
-        if (getSeqOffset(pos) != 0)
-            assignValue(bwtIt, getValue(getValue(text, getSeqNo(pos)), getSeqOffset(pos) - 1));
-        else
-        {
-            assignValue(bwtIt, sentinelSub);
-            setBit(sentinelPos, bwtIt - bwtItBeg);
-        }
-    }
-
-    // update the auxiliary rank support bit string information.
-    _updateRanks(sentinelPos);
-}
-
-// ----------------------------------------------------------------------------
-// Helper function _determineSentinelSubstitute
+// Function empty()
 // ----------------------------------------------------------------------------
 
-// This function determines the '$' substitute.
-// The character with the smallest number of occurrences greater 0 is chosen.
-template <typename TPrefixSumTable, typename TChar>
-inline void _determineSentinelSubstitute(TPrefixSumTable const & pst, TChar & sub)
+// This function checks whether the index is empty. Its already documented.
+template <typename TText, typename TSpec, typename TConfig>
+inline bool empty(Index<TText, FMIndex<TSpec, TConfig> > const & index)
 {
-    typedef typename RemoveConst<TPrefixSumTable>::Type TNonConstPrefixSumTable;
-	typedef typename Value<TNonConstPrefixSumTable>::Type TValue;
-
-	TValue min = getPrefixSum(pst, length(pst) - 1);
-	unsigned pos = length(pst) - 1;
-	for (unsigned i = 0; i < length(pst) - 1; ++i)
-	{
-		unsigned diff = pst[i + 1] - pst[i];
-		if (diff != 0 && diff < min)
-		{
-			min = diff;
-			pos = i;
-		}
-	}
-	sub = getCharacter(pst, pos);
+    return empty(getFibre(index, FibreText())) &&
+           empty(getFibre(index, FibreLF())) &&
+           empty(getFibre(index, FibreSA()));
 }
 
 // ----------------------------------------------------------------------------
-// Function empty
+// Function getFibre()
 // ----------------------------------------------------------------------------
 
-// This function checks whether the index is empty. Its already documented.
-template <typename TText, typename TIndexSpec, typename TFMISpeedEnhancement>
-inline bool empty(Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> > const & index)
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, FMIndex<TSpec, TConfig> >, FibreLF>::Type &
+getFibre(Index<TText, FMIndex<TSpec, TConfig> > & index, FibreLF /*tag*/)
 {
-    return empty(getFibre(index, FibreLfTable()))
-            && empty(getFibre(index, FibreSA()));
+    return index.lf;
 }
 
-// ----------------------------------------------------------------------------
-// Function _findFirstIndex
-// ----------------------------------------------------------------------------
-
-// This function is used by the finder interface. It initializes the range of the finder.
-template <typename TText, typename TPattern, typename TIndexSpec, typename TFMISpeedEnhancement>
-inline void
-_findFirstIndex(Finder<Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> >, FinderFMIndex> & finder,
-		        TPattern const & pattern, FinderFMIndex const &)
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, FMIndex<TSpec, TConfig> >, FibreLF>::Type const &
+getFibre(Index<TText, FMIndex<TSpec, TConfig> > const & index, FibreLF /*tag*/)
 {
-	typedef Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> >    TIndex;
-
-	TIndex & index = haystack(finder);
-
-	indexRequire(index, FibreSaLfTable());
-    setContainer(finder.range.i1, getFibre(container(finder), FibreSA()));
-    setContainer(finder.range.i2, getFibre(container(finder), FibreSA()));
-
-	_range(index, pattern, finder.range);
+    return index.lf;
 }
 
 // ----------------------------------------------------------------------------
-// Function getFibre
+// Function indexLF()
 // ----------------------------------------------------------------------------
+/*!
+ * @fn FMIndex#indexLF
+ * @headerfile <seqan/index.h>
+ * @brief A shortcut for <tt>getFibre(index, FibreLF())</tt>.
+ *
+ * @signature TFibre indexLF(index);
+ *
+ * @param[in] index The FM index.
+ *
+ * @return TFibre A reference to the @link FMIndexFibres#FibreLF @endlink.
+ */
 
-/**
-.Function.FMIndex#getFibre:
-..summary:Returns a specific fibre of a fm index.
-..signature:getFibre(index, fibreTag)
-..class:Spec.FMIndex
-..cat:Index
-..param.index:The index holding the fibre.
-...type:Spec.FMIndex
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.FM Index Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-
-template <typename TText, typename TIndexSpec, typename TFMISpeedEnhancement>
-typename Fibre<Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> >, FibreLfTable >::Type &
-getFibre(Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> > & index, FibreLfTable /*tag*/)
-{
-	return index.lfTable;
-}
-
-template <typename TText, typename TIndexSpec, typename TFMISpeedEnhancement>
-typename Fibre<Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> >, FibreLfTable >::Type const &
-getFibre(Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> > const & index, FibreLfTable /*tag*/)
-{
-	return index.lfTable;
-}
-
-template <typename TText, typename TIndexSpec, typename TFMISpeedEnhancement>
-typename Fibre<Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> >, FibreSA >::Type &
-getFibre(Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> > & index, FibreSA /*tag*/)
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, FMIndex<TSpec, TConfig> >, FibreLF>::Type &
+indexLF(Index<TText, FMIndex<TSpec, TConfig> > & index)
 {
-	return index.compressedSA;
+    return getFibre(index, FibreLF());
 }
 
-template <typename TText, typename TIndexSpec, typename TFMISpeedEnhancement>
-typename Fibre<Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> >, FibreSA >::Type const &
-getFibre(Index<TText, FMIndex<TIndexSpec, TFMISpeedEnhancement> > const & index, FibreSA /*tag*/)
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<TText, FMIndex<TSpec, TConfig> >, FibreLF>::Type const &
+indexLF(Index<TText, FMIndex<TSpec, TConfig> > const & index)
 {
-	return index.compressedSA;
+    return getFibre(index, FibreLF());
 }
 
 // ----------------------------------------------------------------------------
-// Function toSuffixPosition
-// ----------------------------------------------------------------------------
-
-/**
-.Function.FMIndex#toSuffixPosition
-..class:Spec.FMIndex
-..summary:This function computes the position of a specified position in the suffix array (additionally containing 
-entries for the sentinels. The returned position correspond to the suffix array of the original text without sentinels.
-..signature:toSuffixPosition(fmIndex, pos, offset)
-..param.fmIndex:The FM index.
-...type:Spec.FMIndex
-..param.pos:The position in the suffix array of the fm index (with sentinels).
-...type:Concept.UnsignedIntegerConcept
-..param.offset:The number of sequences in the original text.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-
-template <typename TText, typename TOccSpec, typename TIndexSpec, typename TPos, typename TSize>
-inline typename SAValue<Index<TText, FMIndex<TOccSpec, TIndexSpec > > >::Type
-toSuffixPosition(Index<TText, FMIndex<TOccSpec, TIndexSpec > > & index, TPos i, TSize offset)
+// Function toSuffixPosition()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FMIndex#toSuffixPosition
+ * @headerfile <seqan/index.h>
+ * @brief This function computes the position of a specified position in the compressed suffix array (additionally
+ *        containing entries for the sentinels). The returned position corresponds to the suffix array of the original
+ *        text without sentinels.
+ *
+ * @signature TSAValue toSuffixPosition(index, pos, offset);
+ *
+ * @param[in] index  The FM index.
+ * @param[in] pos    The position in the suffix array of the FM index (with sentinels).
+ *                   Types: @link UnsignedIntegerConcept @endlink
+ * @param[in] offset The number of sequences in the original text.  Types: @link UnsignedIntegerConcept @endlink
+ *
+ * @return TSAValue The function function computes the position of a specified position in the compressed suffix array
+ *                  (additionally containing entries for the sentinels).  The returned position corresponds to the
+ *                  suffix array of the original text without sentinels.  The return type is @link SAValue
+ *                  @endlink&lt;@link Index @endlink&lt;TText, FMIndex&lt;TSpec, TConfig&gt; &gt; &gt;::Type
+ */
+
+template <typename TText, typename TSpec, typename TConfig, typename TPos, typename TSize>
+inline typename SAValue<Index<TText, FMIndex<TSpec, TConfig> > >::Type
+toSuffixPosition(Index<TText, FMIndex<TSpec, TConfig> > & index, TPos i, TSize offset)
 {
     SEQAN_ASSERT_GEQ(suffixLength(i, index), offset);
     setSeqOffset(i, suffixLength(i, index) - offset);
     return i;
 }
 
-template <typename TText, typename TOccSpec, typename TIndexSpec, typename TPos, typename TSize>
-inline typename SAValue<Index<TText, FMIndex<TOccSpec, TIndexSpec > > const>::Type
-toSuffixPosition(Index<TText, FMIndex<TOccSpec, TIndexSpec > > const & index, TPos i, TSize offset)
+template <typename TText, typename TSpec, typename TConfig, typename TPos, typename TSize>
+inline typename SAValue<Index<TText, FMIndex<TSpec, TConfig> > const>::Type
+toSuffixPosition(Index<TText, FMIndex<TSpec, TConfig> > const & index, TPos i, TSize offset)
 {
     SEQAN_ASSERT_GEQ(suffixLength(i, index), offset);
     setSeqOffset(i, suffixLength(i, index) - offset);
     return i;
 }
 
-// ----------------------------------------------------------------------------
-// Helper function _getFrequencies
-// ----------------------------------------------------------------------------
-
-// This function determines the number of the different characters in the text.
-template <typename TText, typename TSetSpec, typename TFreq>
-inline void _getFrequencies(TFreq & freq,
-						    StringSet<TText, TSetSpec> const & text)
-{
-	typedef typename Value<TText>::Type TChar;
-	resize(freq, ValueSize<TChar>::VALUE, 0, Exact());
-
-    typedef typename Size<TText>::Type TSize;
-	for (TSize i = 0; i < length(text); ++i)
-	    for (TSize j = 0; j < length(text[i]); ++j)
-		    ++freq[getCharacterPosition(freq, text[i][j])];
-}
-
-// This function determines the number of the different characters in the text.
-template <typename TText, typename TFreq>
-inline void _getFrequencies(TFreq & freq,
-		   	   	   	   	   TText const & text)
-{
-	typedef typename Value<TText>::Type TChar;
-	resize(freq, ValueSize<TChar>::VALUE, 0, Exact());
-
-    typedef typename Size<TText>::Type TSize;
-	for (TSize i = 0; i < length(text); ++i)
-		++freq[getCharacterPosition(freq, text[i])];
-}
-
-// ----------------------------------------------------------------------------
-// Function _indexCreateSA
-// ----------------------------------------------------------------------------
-
-// This function computes the full and compressed suffix array. 
-// Note, in contrast to indexCreate(index, FibreSA()) the full suffix array is also computed.
-template <typename TText, typename TIndexSpec, typename TSpec, typename TSA>
-inline bool _indexCreateSA(Index<TText, FMIndex<TIndexSpec, TSpec> > & index, TSA & fullSa, TText const & text)
+template <typename TText, typename TSpec, typename TConfig, typename TSpecFinder, typename TPattern>
+inline void
+_findFirstIndex(Finder<Index<TText, FMIndex<TSpec, TConfig> >, TSpecFinder> & finder,
+                TPattern const & pattern,
+                FinderSTree const)
 {
-	typedef Index<TText, FMIndex<TIndexSpec, TSpec> > TIndex;
-	typedef typename Fibre<TIndex, FibreSA>::Type TCompressedSA;
+    typedef Index<TText, FMIndex<TSpec, TConfig> >          TIndex;
+    typedef typename Fibre<TIndex, FibreSA>::Type           TSA;
+    typedef typename Iterator<TSA const, Standard>::Type    TIterator;
 
-    // TODO(singer): If there is a lfTable we do not need the Skew7
-	// create the fulle sa
+    TIndex & index = haystack(finder);
+    TIterator saIt = begin(indexSA(index), Standard());
+    typename Iterator<TIndex, TopDown<EmptyEdges> >::Type it(index);
 
-    // create the compressed sa
-	TCompressedSA & compressedSA = getFibre(index, FibreSA());
-    setLfTable(compressedSA, getFibre(index, FibreLfTable()));
+    ModifiedString<TPattern const, ModReverse> revPattern(pattern);
 
-    unsigned numSentinel = countSequences(text);
-    createCompressedSa(compressedSA, fullSa, index.compressionFactor, numSentinel); 
-
-	return true;
+    if (goDown(it, revPattern))
+    {
+        Pair<typename Size<TIndex>::Type> rng = range(it);
+        finder.range.i1 = saIt + rng.i1;
+        finder.range.i2 = saIt + rng.i2;
+    }
+    else
+    {
+        finder.range.i1 = saIt;
+        finder.range.i2 = saIt;
+    }
 }
 
 // ----------------------------------------------------------------------------
-// Function _indexCreateLfTables
+// Function indexCreate()
 // ----------------------------------------------------------------------------
 
-// This function creates all table of the lf table given a text and a suffix array.
-template <typename TIndexSpec, typename TSpec, typename TText, typename TSA>
-inline bool _indexCreateLfTables(Index<TText, FMIndex<TIndexSpec, TSpec> > & index, TText & text, TSA const & sa)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool indexCreate(Index<TText, FMIndex<TSpec, TConfig> > & index, FibreSALF)
 {
-	typedef Index<TText, FMIndex<TIndexSpec, TSpec> >		        TIndex;
-	typedef typename Fibre<TIndex, FibreLfTable>::Type              TLfTable;
-	typedef typename Fibre<TLfTable, FibreOccTable>::Type           TOccTable;
-	typedef typename Fibre<TOccTable, FibreSentinelPosition>::Type  TSentinelPosition;
-	typedef typename Value<TIndex>::Type						    TAlphabet;
-
-	createPrefixSumTable(index.lfTable.prefixSumTable, text);
-
-	TAlphabet sentinelSub(0);
-	_determineSentinelSubstitute(index.lfTable.prefixSumTable, sentinelSub);
-
-	String<TAlphabet> bwt;
-	resize(bwt, index.n, Exact());
-	TSentinelPosition sentinelPos = _setDefaultSentinelPosition(length(bwt), TSentinelPosition());
-
-	_createBwTable(bwt, sentinelPos, text, sa, sentinelSub);
-
-    createSentinelRankDictionary(index.lfTable, bwt, sentinelSub, sentinelPos);
-
-	_insertSentinel(index.lfTable.prefixSumTable, countSequences(text));
-
-	return true;
-}
+    typedef Index<TText, FMIndex<TSpec, TConfig> >               TIndex;
+    typedef typename Fibre<TIndex, FibreTempSA>::Type            TTempSA;
+    typedef typename Size<TIndex>::Type                          TSize;
+    typedef typename DefaultIndexCreator<TIndex, FibreSA>::Type  TAlgo;
 
-// ----------------------------------------------------------------------------
-// Function indexCreate
-// ----------------------------------------------------------------------------
-
-/**
-.Function.FMIndex#indexCreate
-..summary:Creates a specific @Metafunction.Fibre@.
-..signature:indexCreate(index, fibreTag)
-..param.index:The index to be created.
-...type:Spec.FMIndex
-..param.fibreTag:The fibre of the index to be computed.
-...type:Tag.FM Index Fibres.tag.FibreSaLfTable
-..remarks:If you call this function on the compressed text version of the FM index
-you will get an error message: "Logic error. It is not possible to create this index without a text."
-*/
-
-// This function creates the index.
-template <typename TText, typename TIndexSpec, typename TSpec>
-inline bool _indexCreate(Index<TText, FMIndex<TIndexSpec, TSpec > > & index, TText & text)
-{
-	typedef Index<TText, FMIndex<TIndexSpec, TSpec> >   TIndex;
-	typedef typename Fibre<TIndex, FibreTempSA>::Type   TTempSA;
+    TText const & text = indexText(index);
 
     if (empty(text))
         return false;
 
     TTempSA tempSA;
-    
-	resize(tempSA, lengthSum(text), Exact());
-	createSuffixArray(tempSA,
-			text,
-			Skew7());
 
+    // Create the full SA.
+    resize(tempSA, lengthSum(text), Exact());
+    createSuffixArray(tempSA, text, TAlgo());
 
-	// create the compressed SA
-	_indexCreateSA(index, tempSA, text);
+    // Create the LF table.
+    createLF(indexLF(index), text, tempSA);
 
-	// create the lf table
-	_indexCreateLfTables(index, text, tempSA);
+    // Set the FMIndex LF as the CompressedSA LF.
+    setFibre(indexSA(index), indexLF(index), FibreLF());
 
-	return true;
-}
+    // Create the compressed SA.
+    TSize numSentinel = countSequences(text);
+    createCompressedSa(indexSA(index), tempSA, numSentinel);
 
+    return true;
+}
 
-template <typename TText, typename TIndexSpec, typename TSpec>
-inline bool indexCreate(Index<TText, FMIndex<TIndexSpec, TSpec> > & index, FibreSaLfTable const)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool indexCreate(Index<TText, FMIndex<TSpec, TConfig> > & index, FibreSA)
 {
-    return _indexCreate(index, getFibre(index, FibreText()));
+    return indexCreate(index, FibreSALF());
 }
 
-template <typename TText, typename TIndexSpec, typename TSpec>
-inline bool indexCreate(Index<TText, FMIndex<TIndexSpec, TSpec> > & index)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool indexCreate(Index<TText, FMIndex<TSpec, TConfig> > & index)
 {
-    return indexCreate(index, FibreSaLfTable());
+    return indexCreate(index, FibreSALF());
 }
 
 // ----------------------------------------------------------------------------
-// Function indexSupplied
+// Function indexSupplied()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.FMIndex#indexSupplied:
-..summary:Returns whether a specific @Metafunction.Fibre@ is present.
-..param.fibreTag:
-...type:Tag.FM Index Fibres
-*/
-template <typename TText, typename TIndexSpec, typename TSpec>
-inline bool indexSupplied(Index<TText, FMIndex<TIndexSpec, TSpec > > & index, FibreSaLfTable const)
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline bool indexSupplied(Index<TText, FMIndex<TSpec, TConfig> > & index, FibreSALF const)
 {
-    return !(empty(getFibre(index, FibreSA())) || empty(getFibre(index, FibreLfTable())));
+    return !(empty(getFibre(index, FibreSA())) || empty(getFibre(index, FibreLF())));
 }
 
-template <typename TText, typename TIndexSpec, typename TSpec>
-inline bool indexSupplied(Index<TText, FMIndex<TIndexSpec, TSpec > > const & index, FibreSaLfTable const)
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline bool indexSupplied(Index<TText, FMIndex<TSpec, TConfig> > const & index, FibreSALF const)
 {
-    return !(empty(getFibre(index, FibreSA())) || empty(getFibre(index, FibreLfTable())));
+    return !(empty(getFibre(index, FibreSA())) || empty(getFibre(index, FibreLF())));
 }
 
 // ----------------------------------------------------------------------------
-// Function _range
+// Function open()
 // ----------------------------------------------------------------------------
 
-// This function computes a range in the suffix array whose entries point to location
-// in the text where the pattern occurs. 
-template <typename TText, typename TOccSpec, typename TSpec, typename TPattern, typename TIter, typename TPairSpec>
-inline void _range(const Index<TText, FMIndex<TOccSpec, TSpec> > & index, const TPattern & pattern, 
-                   Pair<TIter, TPairSpec> & range)
-{
-    typedef Index<TText, FMIndex<TOccSpec, TSpec> >             TIndex;
-    typedef typename Value<TIndex>::Type                        TAlphabet;
-    typedef typename ValueSize<TAlphabet>::Type                 TAlphabetSize;
-    typedef typename Size<TIndex>::Type                         TSize;
- 	typedef typename Value<TPattern>::Type                      TChar;
-
-    if (empty(pattern))
-    {
-	    setPosition(range.i1, countSequences(index));
-	    setPosition(range.i2, index.n);
-    }
-
-	TSize i = length(pattern) - 1;
-	TChar letter = pattern[i];
-
-    // initilization
-	TAlphabetSize letterPosition = getCharacterPosition(index.lfTable.prefixSumTable, letter);
-	TSize sp = getPrefixSum(index.lfTable.prefixSumTable, letterPosition);
-	TSize ep = getPrefixSum(index.lfTable.prefixSumTable, letterPosition + 1) - 1;
-
-	// the search as proposed by Ferragina and Manzini
-	while ((sp <= ep) && (i > 0))
-	{
-	    --i;
-		letter = pattern[i];
-		letterPosition = getCharacterPosition(index.lfTable.prefixSumTable, letter);
-		TSize prefixSum = getPrefixSum(index.lfTable.prefixSumTable, letterPosition);
-		sp = prefixSum + countOccurrences(index.lfTable.occTable, letter, sp - 1);
-		ep = prefixSum + countOccurrences(index.lfTable.occTable, letter, ep) - 1;
-	}
-
-    setPosition(range.i1, sp);
-	setPosition(range.i2, ep + 1);
-}
-
-// ----------------------------------------------------------------------------
-// Function open
-// ----------------------------------------------------------------------------
-
-/**
-.Function.Index#open
-..class:Class.Index
-..summary:This functions loads a dictionary from disk.
-..signature:open(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
 // This function can be used to open a previously saved index.
-template <typename TText, typename TOccSpec, typename TSpec>
-inline bool open(Index<TText, FMIndex<TOccSpec, TSpec> > & index, const char * fileName, int openMode)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool open(Index<TText, FMIndex<TSpec, TConfig> > & index, const char * fileName, int openMode)
 {
     String<char> name;
 
-//    typedef Index<TText, FMIndex<TOccSpec, TSpec> > TIndex;
-//    typedef typename Fibre<TIndex, FibreSA>::Type TSAFibre;
-//    typedef typename Value<TSAFibre>::Type TSAValue;
-
-    String<FmIndexInfo_> infoString;
-
-    if (!(IsSameType<TSpec, CompressText>::VALUE))
-    {
-        name = fileName;    append(name, ".txt");
-        if (!open(getFibre(index, FibreText()), toCString(name), openMode)) return false;
-    }
+    name = fileName;    append(name, ".txt");
+    if (!open(getFibre(index, FibreText()), toCString(name), openMode)) return false;
 
     name = fileName;    append(name, ".sa");
     if (!open(getFibre(index, FibreSA()), toCString(name), openMode)) return false;
 
     name = fileName;    append(name, ".lf");
-    if (!open(getFibre(index, FibreLfTable()), toCString(name), openMode)) return false;
-
-    name = fileName;    append(name, ".fma");
-    if (!open(infoString, toCString(name), openMode)) return false;
-
-    // TODO(weese): Why do we check the SA size here? Everywhere else we require the types being the same for reading and writing
-    //              Moreover a correct size is not indicating a correct type
-    // Check that the size of the SA entries is correct.
-//    if (infoString[0].sizeOfSAEntry != 0 && infoString[0].sizeOfSAEntry != sizeof(TSAValue))
-//        return false;
+    if (!open(getFibre(index, FibreLF()), toCString(name), openMode)) return false;
 
-    index.compressionFactor = infoString[0].compressionFactor;
-    index.n = infoString[0].genomeLength;
-    getFibre(index, FibreSA()).lfTable = & getFibre(index, FibreLfTable());
+    setFibre(getFibre(index, FibreSA()), getFibre(index, FibreLF()), FibreLF());
 
     return true;
 }
 
 // This function can be used to open a previously saved index.
-template <typename TText, typename TOccSpec, typename TSpec>
-inline bool open(Index<TText, FMIndex<TOccSpec, TSpec> > & index, const char * fileName)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool open(Index<TText, FMIndex<TSpec, TConfig> > & index, const char * fileName)
 {
-    return open(index, fileName, DefaultOpenMode<Index<TText, FMIndex<TOccSpec, TSpec> > >::VALUE);
+    return open(index, fileName, DefaultOpenMode<Index<TText, FMIndex<TSpec, TConfig> > >::VALUE);
 }
 
 // ----------------------------------------------------------------------------
-// Function save
+// Function save()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.Index#save
-..class:Class.Index
-..summary:This functions saves an index to disk.
-..signature:save(index, fileName [, openMode])
-..param.index:The index.
-...type:Class.RankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TText, typename TOccSpec, typename TSpec>
-inline bool save(Index<TText, FMIndex<TOccSpec, TSpec> > const & index, const char * fileName, int openMode)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool save(Index<TText, FMIndex<TSpec, TConfig> > const & index, const char * fileName, int openMode)
 {
     String<char> name;
 
-    typedef Index<TText, FMIndex<TOccSpec, TSpec> > TIndex;
-    typedef typename Fibre<TIndex, FibreSA>::Type TSAFibre;
-    typedef typename Value<TSAFibre>::Type TSAValue;
-
-    String<FmIndexInfo_> infoString;
-    FmIndexInfo_ info = { index.compressionFactor, sizeof(TSAValue), index.n };
-    appendValue(infoString, info);
-    
-    if (!(IsSameType<TSpec, CompressText>::VALUE))
-    {
-        name = fileName;    append(name, ".txt");
-        if (!save(getFibre(index, FibreText()), toCString(name), openMode)) return false;
-    }
+    name = fileName;    append(name, ".txt");
+    if (!save(getFibre(index, FibreText()), toCString(name), openMode)) return false;
 
     name = fileName;    append(name, ".sa");
     if (!save(getFibre(index, FibreSA()), toCString(name), openMode)) return false;
 
     name = fileName;    append(name, ".lf");
-    if (!save(getFibre(index, FibreLfTable()), toCString(name), openMode)) return false;
-
-    name = fileName;    append(name, ".fma");
-    if (!save(infoString, toCString(name), openMode)) return false;
+    if (!save(getFibre(index, FibreLF()), toCString(name), openMode)) return false;
 
     return true;
 }
 
 // This function can be used to save an index on disk.
-template <typename TText, typename TOccSpec, typename TSpec>
-inline bool save(Index<TText, FMIndex<TOccSpec, TSpec> > const & index, const char * fileName)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool save(Index<TText, FMIndex<TSpec, TConfig> > const & index, const char * fileName)
 {
-    return save(index, fileName, DefaultOpenMode<Index<TText, FMIndex<TOccSpec, TSpec> > >::VALUE);
+    return save(index, fileName, DefaultOpenMode<Index<TText, FMIndex<TSpec, TConfig> > >::VALUE);
 }
 
 }
diff --git a/seqan/index/index_fm_compressed_sa.h b/seqan/index/index_fm_compressed_sa.h
old mode 100755
new mode 100644
index 2df6a7b..952759e
--- a/seqan/index/index_fm_compressed_sa.h
+++ b/seqan/index/index_fm_compressed_sa.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,502 +41,546 @@
 
 namespace seqan {
 
-// ==========================================================================
+// ============================================================================
 // Forwards
-// ==========================================================================
-
-/**
-.Tag.CompressedSA Fibres
-..summary:Tag to select a specific fibre of a @Class.CompressedSA@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a sparse string.
-..cat:Index
-
-..tag.FibreSparseString:The sparse string.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
+// ============================================================================
+
+template <typename TText, typename TSpec, typename TConfig>
+struct CompressedSA;
+
+template <typename TText, typename TSpec, typename TConfig>
+struct LF;
+
+struct FibreLF_;
+typedef Tag<FibreLF_> const     FibreLF;
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+/*!
+ * @defgroup CompressedSAFibres CompressedSA Fibres
+ * @brief Tag to select a specific fibre of a @link CompressedSA @endlink.
+ *
+ * @tag CompressedSAFibres#FibreSparseString
+ * @brief The sparse string.
+ *
+ * @tag CompressedSAFibres#FibreLF
+ * @brief A @link LF @endlink to recompute the missing values of the compressed suffix array.
+ *
+ * @see Fibre
+ * @see CompressedSA#getFibre
+ */
+// TODO(esiragusa): Rename FibreSparseString as FibreSparseValues.
 struct FibreSparseString_;
 typedef Tag<FibreSparseString_> const FibreSparseString;
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-class CompressedSA;
-
-// ==========================================================================
+// ============================================================================
 // Metafunctions
-// ==========================================================================
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultIndexStringSpec
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig>
+struct DefaultIndexStringSpec<CompressedSA<TText, TSpec, TConfig> > :
+    DefaultIndexStringSpec<TText> {};
 
 // ----------------------------------------------------------------------------
 // Metafunction Fibre
 // ----------------------------------------------------------------------------
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Fibre<CompressedSA<TSparseString, TLfTable, TSpec>, FibreSparseString>
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>
 {
-    typedef TSparseString Type;
+    // TODO(esiragusa): Change SparseString spec to be SparseString<TValue, TSpec, TConfig>.
+    typedef CompressedSA<TText, TSpec, TConfig>         TCSA;
+    typedef typename SAValue<TText>::Type               TSAValue_;
+    typedef typename DefaultIndexStringSpec<TCSA>::Type TSASpec_;
+    typedef String<TSAValue_, TSASpec_>                 TSA_;
+    typedef SparseString<TSA_, TConfig>                 Type;
 };
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Fibre<CompressedSA<TSparseString, TLfTable, TSpec> const, FibreSparseString>
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<CompressedSA<TText, TSpec, TConfig>, FibreLF>
 {
-    typedef TSparseString Type;
+    typedef LF<TText, TSpec, TConfig>   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig>
+struct Member<CompressedSA<TText, TSpec, TConfig>, FibreLF>
+{
+    typedef typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreLF>::Type *    Type;
 };
 
 // ----------------------------------------------------------------------------
 // Metafunction Reference
 // ----------------------------------------------------------------------------
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Reference<CompressedSA<TSparseString, TLfTable, TSpec> >
+template <typename TText, typename TSpec, typename TConfig>
+struct Reference<CompressedSA<TText, TSpec, TConfig> >
 {
     // TODO(singer): We actually need a proxy here.
-    typedef typename Value<CompressedSA<TSparseString, TLfTable, TSpec> >::Type Type;
+    typedef typename Value<CompressedSA<TText, TSpec, TConfig> >::Type Type;
 };
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Reference<const CompressedSA<TSparseString, TLfTable, TSpec> >
+template <typename TText, typename TSpec, typename TConfig>
+struct Reference<CompressedSA<TText, TSpec, TConfig> const>
 {
     // TODO(singer): We actually need a proxy here.
-    typedef typename Value<CompressedSA<TSparseString, TLfTable, TSpec> >::Type /*const*/ Type;
+    typedef typename Value<CompressedSA<TText, TSpec, TConfig> >::Type /*const*/ Type;
 };
 
 // ----------------------------------------------------------------------------
 // Metafunction Value
 // ----------------------------------------------------------------------------
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Value<CompressedSA<TSparseString, TLfTable, TSpec> >
+template <typename TText, typename TSpec, typename TConfig>
+struct Value<CompressedSA<TText, TSpec, TConfig> >
 {
-    typedef typename Value<TSparseString>::Type Type;
+    typedef typename Value<typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>::Type>::Type   Type;
 };
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Value<CompressedSA<TSparseString, TLfTable, TSpec> const>
+template <typename TText, typename TSpec, typename TConfig>
+struct Value<CompressedSA<TText, TSpec, TConfig> const>
 {
-    typedef typename Value<TSparseString>::Type const Type;
+    typedef typename Value<typename Fibre<CompressedSA<TText, TSpec, TConfig> const, FibreSparseString>::Type>::Type    Type;
 };
 
-// ==========================================================================
+// ============================================================================
 // Classes
-// ==========================================================================
-
-// forwards
-template <typename TPos, typename TOffSet>
-TPos _addGapDistance(TPos const & value, TOffSet const & offSet);
-
-template <typename TSeqId, typename TSpec, typename TPos, typename TOffSet>
-Pair<TSeqId, TPos> _addGapDistance(Pair<TSeqId, TPos, TSpec> const & value, TOffSet const & offSet);
+// ============================================================================
 
 // ----------------------------------------------------------------------------
 // Class CompressedSA
 // ----------------------------------------------------------------------------
 
-/**
-.Class.CompressedSA:
-..cat:Index
-..summary:A suffix array storing only a few suffix array entries and computing the remaining on demand.
-..signature:CompressedSA<TSparseString, TLfTable, TSpec>
-..param.TSparseString:The string containing specific suffix array entries.
-...type:Class.SparseString
-..param.TLfTable:The lfTable containg an occurrence table and a prefix sum table.
-...type:Class.LfTable
-..param.TSpec:Possibility to specialise a compressed suffix array.
-...default:void.
-..remarks:The compressed suffix array can only be used with the FM index.
-..include:seqan/index.h
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec>
-class CompressedSA
+/*!
+ * @class CompressedSA
+ * @implements ContainerConcept
+ * @headerfile <seqan/index.h>
+ *
+ * @brief A suffix array storing only a few suffix array entries and computing the remaining on demand.
+ *
+ * @signature template <typename TText, typename TSpec, typename TConfig>
+ *            class CompressedSA;
+ *
+ * @tparam TSpec Possibility to specialize a compressed suffix array. Default: void.
+ * @tparam TText The type of the text the compressed suffix array is created from. Types: @link String @endlink, @link
+ *               StringSet @endlink
+ * @tparam TConfig A configuration object that can be used to change the types of the fibres easily. This possibility is
+ *                 provided for convenience.
+ *
+ * @section Remarks
+ *
+ * The compressed suffix array can only be used together with a @link LF @endlink.
+ */
+template <typename TText, typename TSpec, typename TConfig>
+struct CompressedSA
 {
-public:
-    TSparseString   sparseString;
-    TLfTable *      lfTable;
-
-    CompressedSA(){};
+    typename Fibre<CompressedSA, FibreSparseString>::Type   sparseString;
+    typename Member<CompressedSA, FibreLF>::Type            lf;
 
-    CompressedSA(TLfTable & lfTable) :
-        lfTable(&lfTable)
+    CompressedSA() :
+        lf()
     {}
 
-    inline CompressedSA & operator=(CompressedSA const & other)
+    template <typename TLF>
+    CompressedSA(TLF & lf)
     {
-        sparseString = other.sparseString;
-        lfTable = other.lfTable;
-        return *this;
+        setFibre(*this, lf, FibreLF());
     }
 
-    typedef typename Value<typename Fibre<TSparseString, FibreValueString>::Type>::Type TCompressedSaValue;
-    typedef typename Fibre<TSparseString, FibreIndicatorString>::Type TIndicatorString;
-
     template <typename TPos>
-    inline TCompressedSaValue const operator[](TPos pos)
+    SEQAN_HOST_DEVICE inline typename Value<CompressedSA>::Type const
+    operator[](TPos pos)
     {
-        TIndicatorString const & indicatorString = getFibre(sparseString, FibreIndicatorString());
-        TPos counter = 0;
-
-        while (!isBitSet(indicatorString, pos))
-        {
-            pos = lfMapping(*lfTable, pos);
-            ++counter;
-        }
-        return _addGapDistance(getValue(sparseString.valueString, getRank(indicatorString, pos) - 1), counter);
+        return value(*this, pos);
     }
 
     template <typename TPos>
-    inline TCompressedSaValue operator[](TPos pos) const
-    {
-        TIndicatorString const & indicatorString = getFibre(sparseString, FibreIndicatorString());
-        TPos counter = 0;
-        while (!isBitSet(indicatorString, pos))
-        {
-            pos = lfMapping(*lfTable, pos);
-            ++counter;
-        }
-        return _addGapDistance(getValue(sparseString.valueString, getRank(indicatorString, pos) - 1), counter);
-    }
-
-    inline bool operator==(const CompressedSA & other) const
+    SEQAN_HOST_DEVICE inline typename Value<CompressedSA>::Type
+    operator[](TPos pos) const
     {
-        return sparseString == other.sparseString &&
-               *lfTable == *(other.lfTable);
+        return value(*this, pos);
     }
-
 };
 
-// ==========================================================================
+// ============================================================================
 // Functions
-// ==========================================================================
+// ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function _addGapDistance
+// Function clear()
 // ----------------------------------------------------------------------------
 
-template <typename TPos, typename TOffSet>
-TPos _addGapDistance(TPos const & value, TOffSet const & offSet)
-{
-    return value + offSet;
-}
-
-template <typename TSeqId, typename TSpec, typename TPos, typename TOffSet>
-Pair<TSeqId, TPos> _addGapDistance(Pair<TSeqId, TPos, TSpec> const & value, TOffSet const & offSet)
-{
-    return Pair<TSeqId, TPos>(value.i1, value.i2 + offSet);
-}
-
-// ==========================================================================
-/*
-.Function.assignValue
-..param.object
-...type:Class.CompressedSA
-..remarks:In the case of the compressed suffix array the new value only influences the sparse string and not the indicator string.
-..include:seqan/index.h
-*/
-// template <typename TSparseString, typename TLfTable, typename TSpec, typename TPos, typename TValue>
-// void assignValue(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, TPos pos, TValue value)
-// {
-//     assignValue(getFibre(compressedSA, FibreSparseString()), pos, value);
-// }
-
-// ==========================================================================
-/**
-.Function.clear.param.object.type:Class.CompressedSA
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline void clear(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA)
+/*!
+ * @fn CompressedSA#clear
+ * @headerfile <seqan/index.h>
+ * @brief Resets the compressed suffix array.
+ *
+ * @signature void clear(compressedSA);
+ *
+ * @param[in,out] compressesSA The compressed suffix array to be cleared.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+inline void clear(CompressedSA<TText, TSpec, TConfig> & compressedSA)
 {
     clear(getFibre(compressedSA, FibreSparseString()));
+//    clear(getFibre(compressedSA, FibreLF()));
 }
 
-// ==========================================================================
-/**
-.Function.empty.param.object.type:Class.CompressedSA
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline bool empty(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA)
-{
-    return empty(getFibre(compressedSA, FibreSparseString()));
-}
-
-// ==========================================================================
-// TODO (singer): How to name this function?
-/*
-.Function.entryStored
-..summary:Determines whether the requested position contains a value different from the default value.
-..signature:bool entryStored(object, pos)
-..param.object
-...type:Class.CompressedSA
-..param.pos:The position of an item in object.
-...Remarks:pos should be convertible to Position<T>::Type for container-type T.
-..include:seqan/index.h
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec, typename TPos>
-inline bool entryStored(CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA, TPos const & pos)
-{
-    return entryStored(getFibre(compressedSA, FibreSparseString()), pos);
-}
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
 
-template <typename TSparseString, typename TLfTable, typename TSpec, typename TPos>
-inline bool entryStored(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, TPos const & pos)
+/*!
+ * @fn CompressedSA#empty
+ * @headerfile <seqan/index.h>
+ * @brief Checks whether or not a compressed suffix array contains any elements.
+ *
+ * @signature bool empty(compressedSA);
+ *
+ * @param[in] compressesSA The compressed suffix array to be cleared.
+ *
+ * @return bool Returns true if the compressed suffix array is empty and false otherwise.
+ */
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline bool empty(CompressedSA<TText, TSpec, TConfig> & compressedSA)
 {
-    return entryStored(getFibre(compressedSA, FibreSparseString()), pos);
+    return empty(getFibre(compressedSA, FibreSparseString()));
+    //    && empty(getFibre(compressedSA, FibreLF()));
 }
 
-// ==========================================================================
+// ----------------------------------------------------------------------------
+// Function createCompressedSa()
+// ----------------------------------------------------------------------------
 // This function creates a compressed suffix array using a normal one.
-/**
-.Function.CompressedSA#createCompressedSa
-..summary:This functions creates a compressed suffix array with a specified compression factor.
-..signature:void createCompressedSa(compressedSA, completeSA, compressionFactor [,offset])
-..param.compressedSA:The compressed suffix array
-...type:Class.CompressedSA
-..param.completeSA:A complete suffix array containing all values
-..param.compressionFactor:The compression factor.
-...type:Concept.UnsignedIntegerConcept
-...remarks:A compression factor of x means that the compressed suffix array specifically stores a value for every x values in the complete suffix array.
-..param:offset:Number of elements at the beginning which should contain the default value.
-..include:seqan/index.h
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec, typename TSA, typename TCompression, typename TSize>
-void createCompressedSa(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, 
-        TSA const & sa,
-        TCompression const compressionFactor, 
-        TSize offset)
+
+// TODO(holtgrew): Rename to createCompressedSA
+/*!
+ * @fn CompressedSA#createCompressedSa
+ * @headerfile <seqan/index.h>
+ * @brief This function creates a compressed suffix array with a specified compression factor.
+ *
+ * @signature void createCompressedSa(compressedSA, completeSA, compressionFactor[, offset]);
+ *
+ * @param[out] compressedSA      The compressed suffix array.
+ * @param[in]  completeSA        A complete suffix array containing all values. Types: @link String @endlink
+ * @param[in]  compressionFactor The compression factor. A compression factor of x means that the compressed suffix array
+ *                               specifically stores a value for every x values in the complete suffix array. Types: @link
+ *                               UnsignedIntegerConcept @endlink
+ * @param[in] offset             The offset determines how many empty values should be inserted into the compressed suffix array at the
+ *                               beginning. This possibility accounts for the sentinel positions of the @link FMIndex @endlink.
+ */
+
+template <typename TText, typename TSpec, typename TConfig, typename TSA, typename TSize>
+void createCompressedSa(CompressedSA<TText, TSpec, TConfig> & compressedSA, TSA const & sa, TSize offset)
 {
-    typedef CompressedSA<TSparseString, TLfTable, TSpec>            TCompressedSA;
+    typedef CompressedSA<TText, TSpec, TConfig>                     TCompressedSA;
     typedef typename Size<TSA>::Type                                TSASize;
     typedef typename Fibre<TCompressedSA, FibreSparseString>::Type  TSparseSA;
-    typedef typename Fibre<TSparseSA, FibreIndicatorString>::Type   TIndicatorString;
+    typedef typename Fibre<TSparseSA, FibreIndicators>::Type        TIndicators;
+    typedef typename Fibre<TSparseSA, FibreValues>::Type            TValues;
     typedef typename Iterator<TSA const, Standard>::Type            TSAIter;
 
     TSparseSA & sparseString = getFibre(compressedSA, FibreSparseString());
-    TIndicatorString & indicatorString = getFibre(sparseString, FibreIndicatorString());
+    TIndicators & indicators = getFibre(sparseString, FibreIndicators());
+    TValues & values = getFibre(sparseString, FibreValues());
 
     TSASize saLen = length(sa);
     resize(compressedSA, saLen + offset, Exact());
-    
+
     TSAIter saIt = begin(sa, Standard());
     TSAIter saItEnd = end(sa, Standard());
 
+    for (TSASize pos = 0; pos < offset; ++pos)
+        setValue(indicators, pos, false);
+
     for (TSASize pos = offset; saIt != saItEnd; ++saIt, ++pos)
     {
-        if (getSeqOffset(getValue(saIt)) % compressionFactor == 0)
-            setBit(indicatorString, pos);
+        if (getSeqOffset(getValue(saIt)) % TConfig::SAMPLING == 0)
+            setValue(indicators, pos, true);
         else
-            clearBit(indicatorString, pos);
+            setValue(indicators, pos, false);
     }
-    _updateRanks(indicatorString);
+    updateRanks(indicators);
 
-    resize(sparseString.valueString, getRank(indicatorString, length(indicatorString) - 1), Exact());
+    resize(values, getRank(indicators, length(sparseString) - 1), Exact());
 
     saIt = begin(sa, Standard());
     for (TSASize pos = offset, counter = 0; saIt != saItEnd; ++saIt, ++pos)
     {
-        if (isBitSet(indicatorString, pos))
+        if (getValue(indicators, pos))
         {
-            assignValue(compressedSA.sparseString.valueString, counter, getValue(saIt));
+            assignValue(values, counter, getValue(saIt));
             ++counter;
         }
     }
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec, typename TSA, typename TCompression>
-void createCompressedSa(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, TSA const & completeSA, TCompression const compressionFactor)
+template <typename TText, typename TSpec, typename TConfig, typename TSA>
+void createCompressedSa(CompressedSA<TText, TSpec, TConfig> & compressedSA, TSA const & sa)
 {
-    createCompressedSa(compressedSA, completeSA, compressionFactor, 0);
+    createCompressedSa(compressedSA, sa, 0);
 }
 
-// ==========================================================================
-/**
-.Function.CompressedSA#getFibre:
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(container, fibreTag)
-..class:Class.CompressedSA
-..cat:Index
-..param.container:The container holding the fibre.
-...type:Class.CompressedSA
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.CompressedSA Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-..example.code:
-Index< String<char> > index_esa("tobeornottobe");
-
-String<char> & text = getFibre(indexEsa, EsaText());
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Fibre<CompressedSA<TSparseString, TLfTable, TSpec>, FibreSparseString>::Type const &
-getFibre(CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA, FibreSparseString)
+// ----------------------------------------------------------------------------
+// Function getFibre()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn CompressedSA#getFibre
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Returns a specific fibre of a compressed suffix array.
+ *
+ * @signature TFibre getFibre(compressedSA, fibreTag);
+ *
+ * @param[in]  fibreTag A tag that identifies the @link Fibre @endlink.  Types: @link CompressedSAFibres @endlink.
+ * @param[out] compressedSA The container holding the fibre.
+ *
+ * @return TFibre A reference to the specified fibre of type @link Fibre @endlink&lt;CompressedSA&lt;TText, TSpec, TConfig&gt;, FibreSparseString&gt;::Type.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>::Type const &
+getFibre(CompressedSA<TText, TSpec, TConfig> const & compressedSA, FibreSparseString)
 {
     return compressedSA.sparseString;
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Fibre<CompressedSA<TSparseString, TLfTable, TSpec>, FibreSparseString>::Type &
-getFibre(CompressedSA<TSparseString, TLfTable, TSpec>&compressedSA, FibreSparseString)
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>::Type &
+getFibre(CompressedSA<TText, TSpec, TConfig> & compressedSA, FibreSparseString)
 {
     return compressedSA.sparseString;
 }
 
-// ==========================================================================
-// This functions computes the position in the suffix array of text[sa[pos] - 1]
-// iff the current position is not present in the compressed suffix array.
-template <typename TSparseString, typename TLfTable, typename TSpec, typename TPos>
-inline bool _getNextPos(CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA, TPos & pos)
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreLF>::Type const &
+getFibre(CompressedSA<TText, TSpec, TConfig> const & compressedSA, FibreLF)
 {
-    typedef typename Fibre<TSparseString, FibreIndicatorString>::Type TIndicatorString;
-    TIndicatorString const & indicatorString = compressedSA.sparseString.indicatorString;
+    return value(compressedSA.lf);
+}
 
-    if (isBitSet(indicatorString, pos))
-    {
-        return true;
-    }
-    pos = lfMapping(*compressedSA.lfTable, pos);
-    return false;
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreLF>::Type &
+getFibre(CompressedSA<TText, TSpec, TConfig> & compressedSA, FibreLF)
+{
+    return value(compressedSA.lf);
 }
 
-// ==========================================================================
-/**
-.Function.length.param.object.type:Class.CompressedSA
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Size<typename Fibre<CompressedSA<TSparseString, TLfTable, TSpec>, FibreSparseString>::Type>::Type
-length(CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA)
+// ----------------------------------------------------------------------------
+// Function setFibre()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn CompressedSA#setFibre
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Set the LF of the compressed suffix array. *
+ * @signature void setFibre(compressedSa, lf, fibreLF);
+ *
+ * @param[in] compressesSa The compressed suffix array.
+ * @param[in] lf The LF table to be used by the compressed suffix array.
+ * @param[in] fibreLF A tag to specify the LF table Fibre
+ */
+
+template <typename TText, typename TSpec, typename TConfig, typename TLF>
+void setFibre(CompressedSA<TText, TSpec, TConfig> & compressedSA, TLF & lf, FibreLF)
+{
+    setValue(compressedSA.lf, lf);
+}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn CompressedSA#length
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Returns the number of elements in the compressed suffix array.
+ *
+ * @signature TSize length(compressedSA);
+ *
+ * @param[in] compressesSA The compressed suffix array.
+ *
+ * @return TSize The number of elements in the compressed suffix array.  Types: The result of @link Size @endlink
+ *               of the compressed suffix array.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Size<typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>::Type>::Type
+length(CompressedSA<TText, TSpec, TConfig> const & compressedSA)
 {
     return length(getFibre(compressedSA, FibreSparseString()));
 }
 
-// ==========================================================================
-/**
-.Function.resize.param.object.type:Class.CompressedSA
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec, typename TSize, typename TExpand>
-inline typename Size<typename Fibre<CompressedSA<TSparseString, TLfTable, TSpec>, FibreSparseString>::Type>::Type
-resize(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA,
-                   TSize size,
-                   Tag<TExpand> tag)
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn CompressedSA#resize
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Resets the number of elements in the compressed suffix array.
+ *
+ * @signature TSize resize(compressedSA, newLength);
+ *
+ * @param[in,out] compressesSA The compressed suffix array.
+ * @param[in]     newLength    The number of elements which should be stored in the compressed suffix array.
+ *                             Types: @link UnsignedIntegerConcept @endlink.
+ *
+ * @return TSize The number of elements in the compressed suffix array.  Types: The result of @link Size @endlink
+ *               of the compressed suffix array.
+ *
+ * If the new length is smaller than the actual one then the last <tt>x<tt> items of the compressed suffix array
+ * are deleted with <tt>x = oldLength - newLength</tt>.
+ */
+
+template <typename TText, typename TSpec, typename TConfig, typename TSize, typename TExpand>
+inline typename Size<typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>::Type>::Type
+resize(CompressedSA<TText, TSpec, TConfig> & compressedSA, TSize size, Tag<TExpand> tag)
 {
     return resize(getFibre(compressedSA, FibreSparseString()), size, tag);
 }
 
-// template <typename TSparseString, typename TLfTable, typename TSpec, typename TSize>
-// inline void resize(CompressedSA<String<TSparseString>, TLfTable, TSpec> & compressedSA, TSize size)
-// {
-//     resize(getFibre(compressedSA, FibreSparseString()), size);
-// }
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
 
-// ==========================================================================
-/**
-.Function.open
-..param.object:
-...type:Class.CompressedSA
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline bool open(
-    CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA,
-    const char * fileName,
-    int openMode)
+/*!
+ * @fn CompressedSA#value
+ *
+ * @brief Returns the value stored at a specified position in the compressed suffix-array.
+ *
+ * @signature TValue value(compressedSA, pos);
+ *
+ * @param[in] compressedSA The compressed suffix array to access.
+ * @param[in] pos          Position at which to access the suffix array. Types: @link UnsignedIntegerConcept @endlink.
+ *
+ * Note that the compressed suffix array is read only. Therefore a const reference is return by this function.
+ */
+
+template <typename TText, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Value<CompressedSA<TText, TSpec, TConfig> >::Type
+value(CompressedSA<TText, TSpec, TConfig> & compressedSA, TPos pos)
 {
-    String<char> name;
-    name = fileName;
-    if (!open(getFibre(compressedSA, FibreSparseString()), toCString(name), openMode))
-    {
-        return false;
-    }
-    return true;
+    typedef typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>::Type     TSparseString;
+    typedef typename Fibre<TSparseString, FibreIndicators>::Type    TIndicators;
+    typedef typename Fibre<TSparseString, FibreValues>::Type        TValues;
 
-}
+    TIndicators const & indicators = getFibre(compressedSA.sparseString, FibreIndicators());
+    TValues const & values = getFibre(compressedSA.sparseString, FibreValues());
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline bool open(
-    CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA,
-    const char * fileName)
-{
-    return open(compressedSA, fileName, DefaultOpenMode<CompressedSA<TSparseString, TLfTable, TSpec> >::VALUE);
+    TPos counter = 0;
+    for (; !getValue(indicators, pos); ++counter)
+        pos = getFibre(compressedSA, FibreLF())(pos);
+
+    return posAdd(getValue(values, getRank(indicators, pos) - 1), counter);
 }
 
-// ==========================================================================
-/**
-.Function.CompressedSA#save
-..class:Class.CompressedSA
-..summary:This functions saves a compressed suffix array to disk.
-..signature:open(compressedSA, fileName [, openMode])
-..param.compressedSA:The string to be saved.
-...type:Class.CompressedSA
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline bool save(
-    CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA,
-    const char * fileName,
-    int openMode)
+template <typename TText, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Value<CompressedSA<TText, TSpec, TConfig> >::Type const
+value(CompressedSA<TText, TSpec, TConfig> const & compressedSA, TPos pos)
 {
-    String<char> name;
-    name = fileName;
-    if (!save(getFibre(compressedSA, FibreSparseString()), toCString(name), openMode))
-    {
-        return false;
-    }
-    return true;
+    typedef typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>::Type     TSparseString;
+    typedef typename Fibre<TSparseString, FibreIndicators>::Type    TIndicators;
+    typedef typename Fibre<TSparseString, FibreValues>::Type        TValues;
+
+    TIndicators const & indicators = getFibre(compressedSA.sparseString, FibreIndicators());
+    TValues const & values = getFibre(compressedSA.sparseString, FibreValues());
+
+    TPos counter = 0;
+    for (; !getValue(indicators, pos); ++counter)
+        pos = getFibre(compressedSA, FibreLF())(pos);
+
+    return posAdd(getValue(values, getRank(indicators, pos) - 1), counter);
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline bool save(
-    CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA,
-    const char * fileName)
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn CompressedSA#open
+ * @headerfile <seqan/index.h>
+ * @brief This functions opens a compressed suffix array from disk.
+ *
+ * @signature bool open(compressedSA, fileName[, mode]);
+ *
+ * @param[in,out]  compressedSA The compressed suffix array to be opened.
+ * @param[in]      fileName     <tt>char const *</tt> containing the file name.
+ * @param[in]      mode         The combination of flags defining how the file should be opened.  To open a file
+ *                              read-only, write-only or to read and write use <tt>OPEN_RDONLY</tt>,
+ *                              <tt>OPEN_WRONLY</tt>, or <tt>OPEN_RDWR</tt>.To create or overwrite a file add
+ *                              <tt>OPEN_CREATE</tt>.  To append a file if existing add <tt>OPEN_APPEND</tt>.  To
+ *                              circumvent problems, files are always opened in binary mode.
+ *                              Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>
+ *
+ * @return bool <tt>true</tt> on success.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+inline bool open(CompressedSA<TText, TSpec, TConfig> & compressedSA, const char * fileName, int openMode)
 {
-    return save(compressedSA, fileName, DefaultOpenMode<CompressedSA<TSparseString, TLfTable, TSpec> >::VALUE);
+    return open(getFibre(compressedSA, FibreSparseString()), fileName, openMode);
 }
 
-// ==========================================================================
-/**
-.Function.setLfTable
-..summary:Set the LfTable of the compressed suffix array.
-..signature:setLfTable(CompressedSA<TSparseString, TLfTable, TSpec> compressedSa, TLfTable & lfTable)
-..param.CompressedSA<TSparseString, TLfTable, TSpec>:The compressed suffix array.
-...type:Class.CompressedSA
-..param.lfTable
-...type:Class.LfTable
-..include:seqan/index.h
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec>
-void setLfTable(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, TLfTable & lfTable)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool open(CompressedSA<TText, TSpec, TConfig> & compressedSA, const char * fileName)
 {
-    compressedSA.lfTable = &lfTable;
+    return open(compressedSA, fileName, DefaultOpenMode<CompressedSA<TText, TSpec, TConfig> >::VALUE);
 }
 
-// ==========================================================================
-/**
-.Function.CompressedSA#value
-..summary:Returns the value stored at a specified position in the compressed suffix-array.
-..signature:value(compressedSA, pos)
-..param.compressedSA:The compressed suffix array to access.
-...type:Class.CompressedSA
-..param.pos:Position at which to access the suffix array.
-...type:Concept.UnsignedIntegerConcept
-..remarks:Note that the compressed suffix array is read only. Therefore a const reference is return by
-this function.
-*/
-template <typename TSparseString, typename TLfTable, typename TSpec, typename TPos>
-inline typename Value<TSparseString>::Type
-value(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, TPos pos)
+// ----------------------------------------------------------------------------
+// Function save()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn CompressedSA#save
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief This functions saves a compressed suffix array to disk.
+ *
+ * @signature bool save(compressedSA, fileName[, mode]);
+ *
+ * @param[in,out]  compressedSA The compressed suffix array to be opened.
+ * @param[in]      fileName     <tt>char const *</tt> containing the file name.
+ * @param[in]      mode         The combination of flags defining how the file should be opened.  To open a file
+ *                              read-only, write-only or to read and write use <tt>OPEN_RDONLY</tt>,
+ *                              <tt>OPEN_WRONLY</tt>, or <tt>OPEN_RDWR</tt>.To create or overwrite a file add
+ *                              <tt>OPEN_CREATE</tt>.  To append a file if existing add <tt>OPEN_APPEND</tt>.  To
+ *                              circumvent problems, files are always opened in binary mode.
+ *                              Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>
+ *
+ * @return bool <tt>true</tt> on success.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+inline bool save(CompressedSA<TText, TSpec, TConfig> const & compressedSA, const char * fileName, int openMode)
 {
-    return compressedSA[pos];
+    return save(getFibre(compressedSA, FibreSparseString()), fileName, openMode);
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec, typename TPos>
-inline typename Value<TSparseString>::Type const
-value(const CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, TPos pos)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool save(CompressedSA<TText, TSpec, TConfig> const & compressedSA, const char * fileName)
 {
-    return compressedSA[pos];
+    return save(compressedSA, fileName, DefaultOpenMode<CompressedSA<TText, TSpec, TConfig> >::VALUE);
 }
 
 }
diff --git a/seqan/index/index_fm_compressed_sa_iterator.h b/seqan/index/index_fm_compressed_sa_iterator.h
old mode 100755
new mode 100644
index f3d52ed..48b66bb
--- a/seqan/index/index_fm_compressed_sa_iterator.h
+++ b/seqan/index/index_fm_compressed_sa_iterator.h
@@ -1,7 +1,8 @@
 // ==========================================================================
-//                 seqan - the library for sequence analysis
+//                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,100 +40,127 @@
 
 namespace seqan {
 
-// ==========================================================================
-//Forwards
-// ==========================================================================
-
-struct FibreSparseString_;
-typedef Tag<FibreSparseString_> const FibreSparseString;
-
-template <typename TSparseString, typename TLfTable, typename TSpec>
-class CompressedSA;
-
-// ==========================================================================
+// ============================================================================
 // Metafunctions
-// ==========================================================================
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Standard>
+template <typename TText, typename TSpec, typename TConfig>
+struct Iterator<CompressedSA<TText, TSpec, TConfig> const, Standard>
 {
-    typedef Iter<CompressedSA<TSparseString, TLfTable, TSpec> const, PositionIterator> Type;
+    typedef Iter<CompressedSA<TText, TSpec, TConfig> const, PositionIterator> Type;
 };
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Standard>
+template <typename TText, typename TSpec, typename TConfig>
+struct Iterator<CompressedSA<TText, TSpec, TConfig>, Standard>
 {
-    typedef Iter<CompressedSA<TSparseString, TLfTable, TSpec>, PositionIterator> Type;
+    typedef Iter<CompressedSA<TText, TSpec, TConfig>, PositionIterator> Type;
 };
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Rooted>:
-    Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Standard>{};
+template <typename TText, typename TSpec, typename TConfig>
+struct Iterator<CompressedSA<TText, TSpec, TConfig>, Rooted>:
+    Iterator<CompressedSA<TText, TSpec, TConfig>, Standard>{};
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-struct Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Rooted>:
-    Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Standard>{};
+template <typename TText, typename TSpec, typename TConfig>
+struct Iterator<CompressedSA<TText, TSpec, TConfig> const, Rooted>:
+    Iterator<CompressedSA<TText, TSpec, TConfig> const, Standard>{};
 
-// ==========================================================================
+// ============================================================================
 // Functions
-// ==========================================================================
-///.Function.begin.param.object.type:Class.CompressedSA
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Standard>::Type
-begin(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, Standard const & /* dummy */)
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function begin()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn CompressedSA#begin
+ * @headerfile <seqan/index.h>
+ * @brief Returns an iterator pointing to the first position of a compresses suffix array.
+ *
+ * @signature TIterator begin(compressedSA, tag);
+ *
+ * @param[in] compressedSA The compresses suffix array to be traversed.
+ * @param[in] tag The specialisation of the iterator to be returned by the function. Types: @link
+ *                ContainerIteratorTags#Standard @endlink, @link ContainerIteratorTags#Rooted @endlink
+ *
+ * @return TIterator Returns an iterator pointing to the first position of a compresses suffix array.  Types: <tt>The
+ *                   result of Iterator&lt;Index&lt;TText, TIndexSpec&gt;, TSpec&gt;::Type</tt>
+ */
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Iterator<CompressedSA<TText, TSpec, TConfig>, Standard>::Type
+begin(CompressedSA<TText, TSpec, TConfig> & compressedSA, Standard const & /* dummy */)
 {
-    return typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Standard>::Type(compressedSA, 0);
+    return typename Iterator<CompressedSA<TText, TSpec, TConfig>, Standard>::Type(compressedSA, 0);
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Standard>::Type
-begin(CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA, Standard const & /* dummy */)
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Iterator<CompressedSA<TText, TSpec, TConfig> const, Standard>::Type
+begin(CompressedSA<TText, TSpec, TConfig> const & compressedSA, Standard const & /* dummy */)
 {
-    return typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Standard>::Type(compressedSA, 0);
+    return typename Iterator<CompressedSA<TText, TSpec, TConfig> const, Standard>::Type(compressedSA, 0);
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Rooted>::Type
-begin(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, Rooted const & /* dummy */)
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Iterator<CompressedSA<TText, TSpec, TConfig>, Rooted>::Type
+begin(CompressedSA<TText, TSpec, TConfig> & compressedSA, Rooted const & /* dummy */)
 {
-    return typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Rooted>::Type(compressedSA, 0);
+    return typename Iterator<CompressedSA<TText, TSpec, TConfig>, Rooted>::Type(compressedSA, 0);
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Rooted>::Type
-begin(CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA, Rooted const & /* dummy */)
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Iterator<CompressedSA<TText, TSpec, TConfig> const, Rooted>::Type
+begin(CompressedSA<TText, TSpec, TConfig> const & compressedSA, Rooted const & /* dummy */)
 {
-    return typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Rooted>::Type(compressedSA, 0);
+    return typename Iterator<CompressedSA<TText, TSpec, TConfig> const, Rooted>::Type(compressedSA, 0);
 }
 
-// ==========================================================================
-///.Function.end.param.object.type:Class.CompressedSA
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Rooted>::Type
-end(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, Rooted const & /* dummy */)
+// ----------------------------------------------------------------------------
+// Function end()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn CompressedSA#end
+ * @headerfile <seqan/index.h>
+ * @brief Returns an iterator pointing to the position behind the last element of a compresses suffix array.
+ *
+ * @signature TIterator end(compressedSA, tag);
+ *
+ * @param[in] compressedSA The compresses suffix array to be traversed.
+ * @param[in] tag The specialisation of the iterator to be returned by the function. Types: @link
+ *                ContainerIteratorTags#Standard @endlink, @link ContainerIteratorTags#Rooted @endlink
+ *
+ * @return TIterator Returns an iterator pointing to the position behind the last element of a compresses suffix array.
+ *                   Types: <tt>The result of Iterator&lt;Index&lt;TText, TIndexSpec&gt;, TSpec&gt;::Type</tt>
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Iterator<CompressedSA<TText, TSpec, TConfig>, Rooted>::Type
+end(CompressedSA<TText, TSpec, TConfig> & compressedSA, Rooted const & /* dummy */)
 {
-    return typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Rooted>::Type(compressedSA, length(compressedSA));
+    return typename Iterator<CompressedSA<TText, TSpec, TConfig>, Rooted>::Type(compressedSA, length(compressedSA));
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Rooted>::Type
-end(CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA, Rooted/* dummy */)
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Iterator<CompressedSA<TText, TSpec, TConfig> const, Rooted>::Type
+end(CompressedSA<TText, TSpec, TConfig> const & compressedSA, Rooted/* dummy */)
 {
-    return typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Rooted>::Type(compressedSA, length(compressedSA));
+    return typename Iterator<CompressedSA<TText, TSpec, TConfig> const, Rooted>::Type(compressedSA, length(compressedSA));
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Standard>::Type
-end(CompressedSA<TSparseString, TLfTable, TSpec> & compressedSA, Standard const & /* dummy */)
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Iterator<CompressedSA<TText, TSpec, TConfig>, Standard>::Type
+end(CompressedSA<TText, TSpec, TConfig> & compressedSA, Standard const & /* dummy */)
 {
-    return typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec>, Standard>::Type(compressedSA, length(compressedSA));
+    return typename Iterator<CompressedSA<TText, TSpec, TConfig>, Standard>::Type(compressedSA, length(compressedSA));
 }
 
-template <typename TSparseString, typename TLfTable, typename TSpec>
-inline typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Standard>::Type
-end(CompressedSA<TSparseString, TLfTable, TSpec> const & compressedSA, Standard/* dummy */)
+template <typename TText, typename TSpec, typename TConfig>
+inline typename Iterator<CompressedSA<TText, TSpec, TConfig> const, Standard>::Type
+end(CompressedSA<TText, TSpec, TConfig> const & compressedSA, Standard/* dummy */)
 {
-    return typename Iterator<CompressedSA<TSparseString, TLfTable, TSpec> const, Standard>::Type(compressedSA, length(compressedSA));
+    return typename Iterator<CompressedSA<TText, TSpec, TConfig> const, Standard>::Type(compressedSA, length(compressedSA));
 }
 
 }
diff --git a/seqan/index/index_fm_device.h b/seqan/index/index_fm_device.h
new file mode 100644
index 0000000..3f5a198
--- /dev/null
+++ b/seqan/index/index_fm_device.h
@@ -0,0 +1,151 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// This file contains Index specializations for thrust::device_vector.
+// ==========================================================================
+
+#ifndef INDEX_FM_DEVICE_H_
+#define INDEX_FM_DEVICE_H_
+
+namespace seqan {
+
+// ----------------------------------------------------------------------------
+// Typedef DnaStringSet
+// ----------------------------------------------------------------------------
+
+typedef StringSet<DnaString, Owner<ConcatDirect<> > >   DnaStringSet;
+
+// ----------------------------------------------------------------------------
+// Typedef CudaFMIndexConfig
+// ----------------------------------------------------------------------------
+
+struct CudaFMIndexConfig
+{
+    typedef TwoLevels<void>    TValuesSpec;
+    typedef Naive<void>        TSentinelsSpec;
+
+    static const unsigned SAMPLING = 10;
+};
+
+typedef FMIndex<void, CudaFMIndexConfig>        CudaFMIndexSpec;
+
+// ----------------------------------------------------------------------------
+// Typedef DnaStringSetFMIndex
+// ----------------------------------------------------------------------------
+
+typedef Index<DnaString, CudaFMIndexSpec>       DnaStringFMIndex;
+typedef Index<DnaStringSet, CudaFMIndexSpec>    DnaStringSetFMIndex;
+
+// ----------------------------------------------------------------------------
+// Metafunction SAValue
+// ----------------------------------------------------------------------------
+
+template <>
+struct SAValue<DnaStringSet>
+{
+    typedef Pair<__uint8, __uint32, Pack> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size; Index
+// ----------------------------------------------------------------------------
+
+template <>
+struct Size<DnaStringSetFMIndex>
+{
+    typedef __uint32 Type;
+};
+
+template <>
+struct Size<View<DnaStringSetFMIndex>::Type>
+{
+    typedef __uint32 Type;
+};
+
+template <>
+struct Size<Device<DnaStringSetFMIndex>::Type>
+{
+    typedef __uint32 Type;
+};
+
+template <>
+struct Size<View<Device<DnaStringSetFMIndex>::Type>::Type>
+{
+    typedef __uint32 Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size; LF
+// ----------------------------------------------------------------------------
+
+template <>
+struct Size<LF<DnaStringSet, void, CudaFMIndexConfig> >
+{
+    typedef __uint32 Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size; Rank Dictionary
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+struct Size<RankDictionary<Dna, TwoLevels<TSpec> > >
+{
+    typedef __uint32 Type;
+};
+
+template <typename TSpec>
+struct Size<RankDictionary<bool, TwoLevels<TSpec> > >
+{
+    typedef __uint32 Type;
+};
+
+template <typename TSpec>
+struct Size<RankDictionary<bool, Naive<TSpec> > >
+{
+    typedef __uint32 Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value; Shape
+// ----------------------------------------------------------------------------
+
+template <unsigned q>
+struct Value<Shape<Dna, UngappedShape<q> > >
+{
+    typedef __uint32    Type;
+};
+
+}
+
+#endif  // #ifndef INDEX_FM_DEVICE_H_
diff --git a/seqan/index/index_fm_doc.h b/seqan/index/index_fm_doc.h
deleted file mode 100644
index a6a1cce..0000000
--- a/seqan/index/index_fm_doc.h
+++ /dev/null
@@ -1,1367 +0,0 @@
-/**
-.Tag.WT
-..summary:Tag that specifies the @Spec.FMIndex@ to use a wavelet tree as the occurrence table.
-..cat:Index
-*/
-/**
-.Tag.FM Index Fibres
-..summary:Tag to select a specific fibre of a @Spec.FMIndex@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a FM index.
-..cat:Index
-
-..tag.FibrePrefixSumTable:The prefix sum table of the index.
-..tag.FibreSA:The compressed suffix array of the text.
-..tag.FibreText:The original text of the index.
-..tag.FibreLfTable:The lf table.
-..tag.FibreSaLfTable:The lf table as well as the compressed suffix array.
-...remarks:This tag can only be used with the functions @Function.indexRequire@ or @Function.indexSupplied@.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index_fm.h
-*/
-/**
-.Tag.CompressText
-..cat:Index
-..summary:Tag to select a FM index variant that can be used such that it is 
-not necessary to store the text after index construction. This index is very
-space efficient.
-*/
-/**
-.Spec.FMIndex:
-..summary:An index based on the Burrows-Wheeler transform.
-..cat:Index
-..general:Class.Index
-..signature:Index<TText, FMIndex<TOccSpec, TSpec> >
-..param.TText:The text type.
-...type:Class.String
-...type:Class.StringSet
-..param.TOccSpec:Occurrence table specialisation. 
-...type:Tag.WT
-...type:Tag.SBM
-...remarks:The tags are really shortcuts for the different @Class.SentinelRankDictionary@s
-...default:Tag.WT
-..param.TSpec:FM index specialisation.
-...type:Tag.CompressText
-...default:void
-..include:seqan/index.h
-*/
-/**
-.Function.FMIndex#getFibre:
-..summary:Returns a specific fibre of a fm index.
-..signature:getFibre(index, fibreTag)
-..class:Spec.FMIndex
-..cat:Index
-..param.index:The index holding the fibre.
-...type:Spec.FMIndex
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.FM Index Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-/**
-.Function.FMIndex#toSuffixPosition
-..class:Spec.FMIndex
-..summary:This function computes the position of a specified position in the suffix array (additionally containing 
-entries for the sentinels. The returned position correspond to the suffix array of the original text without sentinels.
-..signature:toSuffixPosition(fmIndex, pos, offset)
-..param.fmIndex:The FM index.
-...type:Spec.FMIndex
-..param.pos:The position in the suffix array of the fm index (with sentinels).
-...type:Concept.UnsignedIntegerConcept
-..param.offset:The number of sequences in the original text.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-/**
-.Function.FMIndex#indexCreate
-..summary:Creates a specific @Metafunction.Fibre@.
-..signature:indexCreate(index, fibreTag)
-..param.index:The index to be created.
-...type:Spec.FMIndex
-..param.fibreTag:The fibre of the index to be computed.
-...type:Tag.FM Index Fibres.tag.FibreSaLfTable
-..remarks:If you call this function on the compressed text version of the FM index
-you will get an error message: "Logic error. It is not possible to create this index without a text."
-*/
-/**
-.Function.FMIndex#indexSupplied:
-..summary:Returns whether a specific @Metafunction.Fibre@ is present.
-..param.fibreTag:
-...type:Tag.FM Index Fibres
-*/
-/**
-.Tag.CompressedSA Fibres
-..summary:Tag to select a specific fibre of a @Class.CompressedSA@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a sparse string.
-..cat:Index
-
-..tag.FibreSparseString:The sparse string.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-/**
-.Class.CompressedSA:
-..cat:Index
-..summary:A suffix array storing only a few suffix array entries and computing the remaining on demand.
-..signature:CompressedSA<TSparseString, TLfTable, TSpec>
-..param.TSparseString:The string containing specific suffix array entries.
-...type:Class.SparseString
-..param.TLfTable:The lfTable containg an occurrence table and a prefix sum table.
-...type:Class.LfTable
-..param.TSpec:Possibility to specialize a compressed suffix array.
-...default:void.
-..remarks:The compressed suffix array can only be used with the FM index.
-..include:seqan/index.h
-*/
-/**
-.Function.clear.param.object.type:Class.CompressedSA
-.Function.clear.class:Class.CompressedSA
-*/
-/**
-.Function.empty.param.object.type:Class.CompressedSA
-.Function.empty.class:Class.CompressedSA
-*/
-/**
-.Function.createCompressedSa
-..summary:This functions creates a compressed suffix array with a specified compression factor.
-..signature:void createCompressedSa(compressedSA, completeSA, compressionFactor [,offset])
-..class:Class.CompressedSA
-..param.compressedSA:The compressed suffix array
-...type:Class.CompressedSA
-..param.completeSA:A complete suffix array containing all values
-..param.compressionFactor:The compression factor.
-...type:Concept.UnsignedIntegerConcept
-...remarks:A compression factor of x means that the compressed suffix array specifically stores a value for every x values in the complete suffix array.
-..param:offset:Number of elements at the beginning which should contain the default value.
-..include:seqan/index.h
-*/
-/**
-.Function.CompressedSA#getFibre:
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(compressedSA, fibreTag)
-..class:Class.CompressedSA
-..cat:Index
-..param.compressedSA:The compressed suffix array holding the fibre.
-...type:Class.CompressedSA
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.CompressedSA Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-..example.code:
-Index< String<char> > index_esa("tobeornottobe");
-
-String<char> & text = getFibre(indexEsa, EsaText());
-*/
-/**
-.Function.length.param.object.type:Class.CompressedSA
-.Function.length.class:Class.CompressedSA
-*/
-/**
-.Function.resize.param.object.type:Class.CompressedSA
-.Function.resize.class:Class.CompressedSA
-*/
-/**
-.Function.CompressedSA#open
-..class:Class.CompressedSA
-..summary:This functions opens a compressed suffix array from disk.
-..signature:open(compressedSA, fileName [, openMode])
-..param.compressedSA:The compresses suffix array to be opened.
-...type:Class.CompressedSA
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/template <typename TSparseString, typename TLfTable, typename TSpec>
-/**
-.Function.CompressedSA#save
-..class:Class.CompressedSA
-..summary:This functions saves a compressed suffix array to disk.
-..signature:save(compressedSA, fileName [, openMode])
-..param.compressedSA:The compressed suffix array to be saved.
-...type:Class.CompressedSA
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Function.setLfTable
-..class:Class.CompressedSA
-..summary:Set the LfTable of the compressed suffix array.
-..signature:setLfTable(CompressedSA<TSparseString, TLfTable, TSpec> compressedSa, TLfTable & lfTable)
-..param.CompressedSA<TSparseString, TLfTable, TSpec>:The compressed suffix array.
-...type:Class.CompressedSA
-..param.lfTable
-...type:Class.LfTable
-..include:seqan/index.h
-*/
-/**
-.Function.CompressedSA#value
-..class:Class.CompressedSA
-..summary:Returns the value stored at a specified position in the compressed suffix-array.
-..signature:value(compressedSA, pos)
-..param.compressedSA:The compressed suffix array to access.
-...type:Class.CompressedSA
-..param.pos:Position at which to access the suffix array.
-...type:Concept.UnsignedIntegerConcept
-..remarks:Note that the compressed suffix array is read only. Therefore a const reference is return by
-this function.
-*/
-///.Function.begin.param.object.type:Class.CompressedSA
-///.Function.begin.class:Class.CompressedSA
-///.Function.end.param.object.type:Class.CompressedSA
-///.Function.end.class:Class.CompressedSA
-/**
-.Tag.LF Table Fibres
-..summary:Tag to select a specific fibre of a @Spec.FMIndex@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a FM index.
-..cat:Index
-
-..tag.FibreOccTable:The occurrence table of the lf table.
-..tag.FMTablePrefixSumTable:The prefix sum table of the lf table.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index_fm.h
-*/
-/**
-.Class.LfTable:
-..cat:Index
-..summary:LfTable is an object storing all necessary information for the LF-mapping.
-..signature:LfTable<TOccTable, TPrefixSumTable>
-..param.TOccTable:The occurrence table data structure.
-...type:Class.SentinelRankDictionary
-..param.TPrefixSumTable:The specialisation tag.
-...default:String
-..include:seqan/Index.h
-*/
-/**
-.Function.LfTable#clear
-..class:Class.LfTable
-..summary:Clears the LF table.
-..signature:clear(lfTable)
-..param.lfTable:The LF table to be cleared.
-...type:Class.LfTable
-..include:seqan/index.h
-*/
-/**
-.Function.LfTable#empty
-..class:Class.LfTable
-..summary:Clears the LF table.
-..signature:empty(lfTable)
-..param.lfTable:The LF table to be cleared.
-...type:Class.LfTable
-..returns:$true$ if the LF table is empty, $false$ otherwise.
-...type:nolink:$bool$
-..include:seqan/index.h
-*/
-/**
-.Function.createLfTable
-..class:Class.LfTable
-..summary:Creates the LF table
-..signature:createLfTable(lfTable, text)
-..param.lfTable:The LF table to be constructed.
-...type:Class.LfTable.
-..param.text:The underlying text
-...type:Class.String
-..returns:$true$ on successes, $false$ otherwise.
-..include:seqan/index.h
-*/
-/**
-.Function.LfTable#getFibre:
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(container, fibreTag)
-..class:Class.LfTable
-..cat:Index
-..param.container:The container holding the fibre.
-...type:Class.LfTable
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.LF Table Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-/**
-.Function.lfMapping:
-..class:Class.LfTable
-..summary:Returns the position of an character at a specified position of L in F. L corresponds to the last column of 
-the sorted cyclic rotations of the original text, while F correspond to the first column.
-..cat:Index
-..signature:lfMapping(lfTable, pos)
-..param.lfTable:The @Class.LfTable@ holding the occurrence and prefix sum table.
-...type:Class.LfTable
-..param.pos:The position in L
-..returns:Returns the position of the character L[c] in F. The returned position is of the same type as pos.
-..include:seqan/index.h
-*/
-/**
-.Function.LfTable#open
-..class:Class.LfTable
-..summary:This functions loads a LF table from disk.
-..signature:open(lfTable, fileName [, openMode])
-..param.lfTable:The lfTable.
-...type:Class.LfTable
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A nolink:$bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Function.LfTable#save
-..class:Class.LfTable
-..summary:This functions saves a LF table to disk.
-..signature:save(lfTable, fileName [, openMode])
-..param.lfTable:The dictionary.
-...type:Class.LfTable
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A nolink:$bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Tag.PrefixSumTable Fibres
-..summary:Tag to select a specific fibre of a @Class.CompressedSA@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a sparse string.
-..cat:Index
-
-..tag.FibreEntries:The entries in the prefix sum table.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-/**
-.Class.PrefixSumTable:
-..cat:Index
-..summary:The prefix-sum table is a data structure which stores for each character the number of smaller lexicographic 
-smaller characters in a given text.
-..signature:PrefixSumTable<TChar, TSpec>
-..param.TChar:The character type
-..param.TSpec:A specialisation tag.
-...default:void
-..include:seqan/Index.h
-*/
-/**
-.Function.PrefixSumTable#clear
-..class:Class.PrefixSumTable
-..summary:Clears the prefix sum table.
-..signature:clear(prefixSumTable)
-..param.prefixSumTable:The prefix sum table to be cleared.
-...type:Class.LfTable
-..include:seqan/index.h
-*/
-/**
-.Function.createPrefixSumTable
-..class:Class.PrefixSumTable
-..summary:Creates the prefix sum table
-..signature:createPrefixSumTable(prefixSumTable, text)
-..param.prefixSumTable:The prefix sum table to be constructed.
-...type:Class.PrefixSumTable
-..param.text:The underlying text.
-...type:Class.String
-...type:Class.StringSet
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#getAlphabetSize
-..class:Class.PrefixSumTable
-..summary:Returns the number of different characters in the prefix sum table.
-..signature:getAlphabetSize(prefixSumTable)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable.
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#getCharacterPosition
-..class:Class.PrefixSumTable
-..summary:Returns the position of a given character within the prefix sum table.
-..signature:getCharacterPosition(prefixSumTable, character)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.character:A character.
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#getCharacter
-..class:Class.PrefixSumTable
-..summary:Returns the character of a given position within the prefix sum table.
-..signature:getCharacter(prefixSumTable, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable.
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-/**
-.Function#getPrefixSum
-..class:Class.PrefixSumTable
-..summary:Returns the prefix sum of a given position. 
-..signature:getPrefixSum(prefixSumTable, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#getValue
-..class:Class.PrefixSumTable
-..summary:Returns the prefix sum of a given position. 
-..signature:getValue(prefixSumTable, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#getFibre:
-..class:Class.PrefixSumTable
-..summary:Returns a specific fibre of a prefix-sum table.
-..signature:getFibre(prefixSumTable, fibreTag)
-..class:Class.PrefixSumTable
-..cat:Index
-..param.prefixSumTable:The container holding the fibre.
-...type:Class.PrefixSumTable
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.PrefixSumTable Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#length
-..class:Class.PrefixSumTable
-..summary:Returns the number of different characters in the prefix-sum table.
-..signature:length(lfTable)
-..param.lfTable:The prefix-sum table.
-...type:Class.LfTable
-..returns:Returns the number of different characters in the prefix-sum table.
-...type:Metafunction.Size
-...remarks:If the type of the characters of the prefix-sum table consists of more than 8 bit only the characters
-actually occurring in the original text are accounted for when calling length.
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#prefixSum
-..class:Class.PrefixSumTable
-..summary:Returns a reference to the entry of the prefix sum table of a given position. 
-..signature:prefixSum(prefixSumTable, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#resize
-..class:Class.PrefixSumTable
-..summary:Resize the prefix sum table to be able to store more or less characters. 
-..signature:resize(prefixSumTable, size [,value, resizeTag])
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.size:The new size.
-...type:Concept.UnsignedIntegerConcept
-..param.resizeTag: Specifies the strategy that is applied if the capacity of $object$ is less than $newLength$. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowExplicit@.
-
-..param.value:The value to be used to initialize the new storage.
-..include:seqan/index.h
-*/
-/**
-.Function.setPrefixSum
-..class:Class.PrefixSumTable
-..summary:Returns a reference to the entry of the prefix-sum table of a given position. 
-..signature:setPrefixSum(prefixSumTable, value, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.value:A specified value to be inserted.
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#open
-..class:Class.PrefixSumTable
-..summary:This functions loads a prefix-sum table from disk.
-..signature:open(prefixSumTable, fileName [, openMode])
-..param.prefixSumTable:The prefix-sum table.
-...type:Class.PrefixSumTable
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Function.PrefixSumTable#save
-..class:Class.PrefixSumTable
-..summary:This functions saves a prefix-sum table to disk.
-..signature:save(prefixSumTable, fileName [, openMode])
-..param.prefixSumTable:The prefix-sum table.
-...type:Class.PrefixSumTable
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Tag.SBM
-..summary:Tag that specifies the @Spec.FMIndex@ to use a StringSet of rank support bis strings as the occurrence table.
-..cat:Index
-*/
-/**
-.Spec.SequenceBitMask Fibres
-..cat:Index
-..summary:Tag to select a specific fibre of a SequenceBitMask.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a SequenceBitMask.
-
-..DISABLED.tag.FibreBitStrings:The string set containing a bit string for each node.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-/**
-.Spec.SequenceBitMask:
-..cat:Index
-..general:Class.RankDictionary
-..summary:The string set bit string dictionary is a string set of rank support bit strings for constant time acces
-of the rank of a specified character at a specified position.
-..signature:SequenceBitMask<TValue>
-..param.TValue:The value type of the .
-..include:seqan/index.h
-..remarks:This data structure is optimized for very small alphabets, such as @Spec.Dna@ or @Spec.Dna5@. Consider using a @Spec.WaveletTree@ if your alphabet size is larger.
-*/
-///.Function.RankDictionary#getFibre.param.fibreTag.type:Spec.SequenceBitMask Fibres
-/**
-.Tag.WaveletTree Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Spec.WaveletTree@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a @Spec.WaveletTree@.
-..cat:Spec.WaveletTree
-
-..tag.FibreBitStrings:The string set containing a bit string for each node.
-
-..tag.FibreTreeStructure:The wavelet tree structure of the wavelet tree.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-/**
-.Class.RankDictionary:
-..cat:Index
-..summary:A rank dictionary is a data structure to store the rank of an element of a sequence at every position of the 
-sequence.
-..signature:RankDictionary<TSpec>
-..param.TSpec:The rank dictionary specialisation.
-...type:Spec.WaveletTree
-...type:Spec.SequenceBitMask
-...default:@Spec.WaveletTree@
-..include:seqan/index.h
-*/
-/**
-.Spec.WaveletTree:
-..general:Class.RankDictionary
-..cat:Index
-..summary:A wavelet tree is a tree like binary encoding of a text.
-..signature:WaveletTree<TValue>
-..param.TValue:The value type of the wavelet tree.
-..include:seqan/index.h
-..remarks:The nodes of a wavelet tree consist of a bit string as well as a character c. In each level of the tree, 
-characters smaller than c are represented as a 0 while character greater or equal to c are represented with a 1.
-The characters represented by a 0 form the string to be represented by the left subtree while characters represented
-by a 1 form the string of the right subtree. Therefore, only the bit string of the root node represents all characters while all other nodes represent subsets.
-*/
-/**
-.Function.RankDictionary#clear
-..class:Class.RankDictionary
-..summary:Clears the rank dictionary.
-..signature:clear(dictionary)
-..param.dictionary:The rank dictionary to be cleared.
-...type:Class.RankDictionary
-..include:seqan/index.h
-*/
-/**
-.Function.RankDictionary#empty
-..class:Class.RankDictionary
-..summary:Returns whether or not the rank dictionary is empty.
-..signature:empty(dictionary)
-..param.dictionary:The rank dictionary to be checked.
-...type:Class.RankDictionary
-..returns:$true$ if the dictionary is empty, $false$ otherwise.
-..include:seqan/index.h
-*/
-/**
-.Function.RankDictionary#getValue
-..summary:Returns the character of a specified position.
-..signature:getValue(dictionary, pos)
-..class:Class.RankDictionary
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.pos:The position
-..include:seqan/index.h
-*/
-/**
-.Function.RankDictionary#getFibre:
-..summary:Returns a specific fibre of a dictionary.
-..signature:getFibre(dictionary, fibreTag)
-..class:Class.RankDictionary
-..cat:Index
-..param.dictionary:The dictionary holding the fibre.
-...type:Class.RankDictionary
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.WaveletTree Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-/**
-.Function.RankDictionary#countOccurrences:
-..summary:Returns the rank (number of occurrences) of a specified character up to a specified position. 
-..signature:countOccurrences(dictionary, character, pos)
-..class:Class.RankDictionary
-..cat:Index
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.character:The character of interest.
-..param.pos:The position (which is also included in the rank computation).
-..returns:The rank (number of occurrences) of a specified character up to a specified position. 
-...type:nolink:$unsigned$
-..include:seqan/index.h
-*/
-/**
-.Function.createRankDictionary
-..class:Class.RankDictionary
-..summary:This functions creates the dictionary.
-..signature:createRankDictionary(dictionary, text)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.text:A text to be transfered into a wavelet tree.
-...type:Class.String
-..include:seqan/index.h
-*/
-/**
-.Function.RankDictionary#open
-..class:Class.RankDictionary
-..summary:This functions loads a dictionary from disk.
-..signature:open(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Function.RankDictionary#save
-..class:Class.RankDictionary
-..summary:This functions saves a dictionary to disk.
-..signature:open(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-///.Metafunction.Fibre.param.TContainer.type:Class.RankDictionary
-///.Metafunction.Fibre.param.TSpec.type:Tag.WaveletTree Fibres
-/**
-.Tag.RankSupportBitString Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Class.RankSupportBitString@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a rank support bit string.
-..cat:Index
-
-..tag.FibreBits:The bit string.
-..tag.FibreBlocks:The block string.
-..tag.FibreSuperBlocks:The super block string.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-/**
-.Class.RankSupportBitString:
-..summary:A bit string supporting rank queries in constant time.
-..cat:Index
-..signature:RankSupportBitString<TSpec>
-..param.TSpec:Specialisation tag.
-...default:void
-..remarks:The constant rank query time is achieved by evaluating precomputed subsolutions. In order to do so, the bit string is divided into blocks of length l. A super block string stores for each block of l blocks the number of bits set from the beginning. In addition a block string stores the number of bits set in each block from the start of the last super block block. Therefore it is possible to compute the result of a rank query in constant time by adding information from the bit, block and super block string.
-..include:seqan/index.h
-*/
-/**
-.Function.RankSupportBitString#appendValue:
-..signature:appendValue(ranKSupportBitString, value)
-..cat:Index
-..summary:Appends a value to a container.
-..param.ranKSupportBitString:A @Class.RankSupportBitString@.
-...type:Class.RankSupportBitString
-..param.value:Value that is appended to $target$.
-...type:Concept.UnsignedIntegerConcept
-...type:nolink:bool
-...remarks:If the value is different from 0 it is interpreted as 1.
-..include:seqan/sequence.h
-*/
-/**
-.Function.clear.param.object.type:Class.RankSupportBitString
-.Function.clear.class:Class.RankSupportBitString
-*/
-/**
-.Function.getRank
-..class:Class.RankSupportBitString
-..summary:Returns the rank (the number of bits set from the start of the bit string) of a specified position.
-..signature:getRank(bitString, pos)
-..param.bitString:The bit string.
-...type:Class.RankSupportBitString
-..param.pos:Position of a bit.
-..returns:Value type of the super block fibre (default unsigned long).
-..include:seqan/index.h
-..example.code:
-*/
-/**
-.Function.empty.param.object.type:Class.RankSupportBitString
-.Function.empty:Class.RankSupportBitString
-*/
-/**
-.Function.isSetBit
-..class:Class.RankSupportBitString
-..summary:Returns whether the bit with the given index is set to 1.
-..signature:isSetBit(bitString, pos)
-..param.bitString:The bit string.
-...type:Class.RankSupportBitString
-..param.pos:Position of the bit.
-..returns:Returns whether a specified bit is set or not.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-
-RankSupportBitString<> bitString;
-resize(bitString, length(genome));
-...
-mark all 'a's
-...
-
-for (unsigned i = 0; i < length(bitString); ++i)
-    if(isSetBit(bitString, i))
-        std::cout << "a found at: " << i << std::endl;
-*/
-/**
-.Function.RankSupportBitString#getFibre:
-..class:Class.RankSupportBitString
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(container, fibreTag)
-..class:Class.RankSupportBitString
-..cat:Index
-..param.container:The container holding the fibre.
-...type:Class.RankSupportBitString
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.RankSupportBitString Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-..example.code:
-Index< String<char> > index_esa("tobeornottobe");
-
-String<char> & text = getFibre(indexEsa, EsaText());
-*/
-/**
-.Function.length.param.object.type:Class.RankSupportBitString
-.Function.length.class:Class.RankSupportBitString
-*/
-/**
-.Function.resize.param.object.type:Class.RankSupportBitString
-.Function.resize.class:Class.RankSupportBitString
-*/
-/**
-.Function.setBitTo
-..class:Class.RankSupportBitString
-..signature:setBitTo(bitString, pos, bit)
-..param.bitString:The bit string.
-...type:Class.RankSupportBitString
-..param.pos:Position of the bit.
-..param.bit:The value of the bit.
-...remarks:Note that values different from 0 are interpreted as 1.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-
-RankSupportBitString<> bitString;
-resize(bitString, length(genome));
-
-for (unsigned i = 0; i < length(genome); ++i)
-    if(genome[i] < Dna5('c'))
-        setBitTo(bitString, 1);
-
-updateRanks_(bitString);
-*/
-/**
-.Function.RankSupportBitString#open
-..class:Class.RankSupportBitString
-..summary:This functions saves a @Class.RankSupportBitString@ to disk.
-..signature:open(bitString, fileName [, openMode])
-..param.bitString:The bit string to be saved.
-...type:Class.RankSupportBitString
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Function.RankSupportBitString#save
-..class:Class.RankSupportBitString
-..summary:This functions saves a @Class.RankSupportBitString@ to disk.
-..signature:save(bitString, fileName [, openMode])
-..param.bitString:The bit string to be saved.
-...type:Class.RankSupportBitString
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Tag.RightArrayBinaryTree Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Class.RightArrayBinaryTree@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a RightArrayBinaryTree.
-..cat:RightArrayBinaryTree
-..tag.FibreTreeStructureEncoding:The string encoding the wavelet tree structure.
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-/**
-.Class.RightArrayBinaryTree:
-..cat:WaveletTree
-..summary:A special format to encode the structure of a wavelet tree. The structure is very space efficient because only one position is stored which encodes where the left and right subtree of a given node exist.
-..signature:RightArrayBinaryTree<TValue, TSpec>
-..param.TSpec:The value type, that is the type of the stored characters.
-..param.TSpec:The wavelet tree structure specialisation.
-...default:void.
-..include:seqan/index.h
-*/
-/**
-.Function.clear.param.object.type:Class.RightArrayBinaryTree
-.Function.clear.class:Class.RightArrayBinaryTree
-*/
-/**
-.Function.createRightArrayBinaryTree
-..class:Class.RightArrayBinaryTree
-..summary:Computes the wavelet tree structure of a text.
-..signature:createRightArrayBinaryTree(waveletTreeStructure, text)
-..param.waveletTreeStructure:A wavelet tree structure.
-...type:Class.RightArrayBinaryTree
-..param.text:A text.
-...type:Class.String
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-
-RightArrayBinaryTree<Dna5> waveletTreeStructure;
-computeRightArrayBinaryTree(genome);
-*/
-/**
-.Function.empty.param.object.type:Class.RightArrayBinaryTree
-.Function.empty.class:Class.RightArrayBinaryTree
-*/
-/**
-.Function.RightArrayBinaryTree#getFibre:
-..class:Class.RightArrayBinaryTree
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(container, fibreTag)
-..class:Class.RightArrayBinaryTree
-..cat:Index
-..param.container:The container holding the fibre.
-...type:Class.RightArrayBinaryTree
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.RightArrayBinaryTree Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-/**
-.Function.RightArrayBinaryTree#open
-..class:Class.RightArrayBinaryTree
-..summary:This functions loads a @Class.RightArrayBinaryTree@ from disk.
-..signature:open(rightArrayBinaryTree, fileName [, openMode])
-..param.rightArrayBinaryTree:The rightArrayBinaryTree.
-...type:Class.RightArrayBinaryTree
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Function.RightArrayBinaryTree#save
-..class:Class.RightArrayBinaryTree
-..summary:This functions saves a @Class.RightArrayBinaryTree@ to disk.
-..signature:save(rightArrayBinaryTree, fileName [, openMode])
-..param.rightArrayBinaryTree:The rightArrayBinaryTree.
-...type:Class.RightArrayBinaryTree
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-///.Metafunction.Fibre.param.TContainer.type:Class.RightArrayBinaryTree
-///.Metafunction.Fibre.param.TSpec.type:Tag.RightArrayBinaryTree Fibres
-/**
-.Spec.RightArrayBinaryTree Iterator:
-..summary:An iterator for @Class.RightArrayBinaryTree@.
-..cat:Iter
-..general:Class.Iter
-..signature:Iter<RightArrayBinaryTree, TSpec >
-..param.RightArrayBinaryTree:The @Class.RightArrayBinaryTree@.
-...type:Class.RightArrayBinaryTree
-..param.TSpec:Specialisation Tag.
-...type:Spec.TopDown Iterator
-..include:seqan/index.h
-*/
-/**
-.Function.getCharacter
-..class:Spec.RightArrayBinaryTree Iterator
-..summary:This function returns the pivot character of the node the iterator currently points to.
-..signature:getCharacter(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator
-..include:seqan/index.h
-*/
-/**
-.Function.getLeftChildPos
-..class:Spec.RightArrayBinaryTree Iterator
-..summary:Returns the position in @Class.RightArrayBinaryTree@ of the left child vertex.
-..signature:getLeftChildPos(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator.
-..include:seqan/index.h
-*/
-/**
-.Function.getSubTreeSize
-..class:Spec.RightArrayBinaryTree Iterator
-..summary:Returns the number of vertices in the subtree starting at the position an iterator points to.
-..signature:getSubTreeSize(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator.
-..include:seqan/index.h
-*/
-/**
-.Function.RightArrayBinaryTree Iterator#getPosition
-..class:Spec.RightArrayBinaryTree Iterator
-..summary:Returns the position of the iterator in the host.
-..signature:getPosition(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator.
-..include:seqan/index.h
-*/
-/**
-.Function.getRightChildPos
-..class:Spec.RightArrayBinaryTree Iterator
-..summary:Returns the position in @Class.RightArrayBinaryTree@ of the right child vertex.
-..signature:getLeftChildPos(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator.
-..include:seqan/index.h
-*/
-/**
-.Function.goLeftChild
-..class:Spec.RightArrayBinaryTree Iterator
-..summary:Sets the iterator to the left child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false.
-..signature:bool goLeftChild(iterator)
-..param.iterator:An iterator of a wavelet tree structure.
-...type:Spec.RightArrayBinaryTree Iterator
-..remarks:$goLeftChild(iterator)$ goes down the left edge if it exist.
-..returns:$true$ if the edge or path to go down exists, otherwise $false$.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goLeftChild(it); // go to left child of root node
-*/
-/**
-.Function.RightArrayBinaryTree Iterator#goRight
-..class:Spec.RightArrayBinaryTree Iterator
-..summary:Iterates to the next sibling in a tree.
-..signature:bool goRight(iterator)
-..param.iterator:
-...type:Spec.RightArrayBinaryTree Iterator
-*/
-/**
-.Function.goRightChild
-..class:Spec.RightArrayBinaryTree Iterator
-..summary:Sets the iterator to the right child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false.
-..signature:bool goRightChild(iterator)
-..param.iterator:An iterator of a wavelet tree structure.
-...type:Spec.RightArrayBinaryTree Iterator
-..remarks:$goRightChild(iterator)$ goes down the right edge if it exist.
-..returns:$true$ if the edge or path to go down exists, otherwise $false$.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goRightChild(it); // go to right child of root node
-*/
-/**
-.Function.goUp.param.iterator.type:Spec.TopDownHistory Iterator
-.Function.goUp.class:Spec.RightArrayBinaryTree Iterator
-*/
-/**
-.Function.isLeaf
-..class:Spec.RightArrayBinaryTree Iterator
-..param.iterator.type:Spec.RightArrayBinaryTree Iterator
-*/
-/**
-.Function.RightArrayBinaryTree Iterator#setCharacter
-..class:Spec.RightArrayBinaryTree Iterator
-..signature:bool setCharacter(iterator, character)
-..param.iterator:An iterator of a wavelet tree structure.
-...type:Spec.RightArrayBinaryTree Iterator
-..param.character:The character to be assigned to a node.
-..summary:$setCharacter(iterator, character)$ sets the character of the node the iterator points to to character.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goRightChild(it); // go to right child of root node
-setCharacter(it,'T'); // sets the character of the root's
-                      // right child to 'T'
-*/
-/**
-.Function#isRoot
-..class:Spec.RightArrayBinaryTree Iterator
-..param.iterator.type:Spec.RightArrayBinaryTree Iterator
-*/
-///.Function.begin.param.object.type:Class.RightArrayBinaryTree
-///.Function.begin.class:Spec.RightArrayBinaryTree Iterator
-///.Function.container.param.iterator.type:Class.RightArrayBinaryTree
-///.Function.container.class:Spec.RightArrayBinaryTree Iterator
-///.Function.end.param.object.type:Class.RightArrayBinaryTree
-///.Function.end.class:Spec.RightArrayBinaryTree Iterator
-///.Function.goDown.param.iterator.type:Spec.RightArrayBinaryTree Iterator
-///.Function.goDown.class:Spec.RightArrayBinaryTree Iterator
-/**
-.Tag.SentinelRankDictionary Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Class.SentinelRankDictionary@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a SentinelRankDictionary.
-..cat:SentinelRankDictionary
-
-..tag.FibreRankDictionary:The rank dictionary.
-
-..tag.FibreSentinelPosition:The bit string encoding the position of the sentinel sign.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-/**
-.Class.SentinelRankDictionary:
-..cat:Index
-..summary:A rank dictionary, additional storing sentinel character which are not accounted for in a rank querry.
-..signature:SentinelRankDictionary<TRankDictionary, TSpec>
-..param.TRankDictionary:The rank dictionary of a text.
-...type:Class.RankDictionary
-..param.TSpec:Specialisation
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#clear
-..class:Class.SentinelRankDictionary
-..summary:Clears the dictionary.
-..signature:clear(dictionary)
-..param.dictionary:The rank dictionary to be cleared.
-...type:Class.SentinelRankDictionary
-..include:seqan/index.h
-*/
-/**
-.Function.sentinelPosition
-..class:Class.SentinelRankDictionary
-..summary:Returns whether a specified position is a sentinel position.
-..signature:sentinelPosition(dictionary, pos)
-..param.dictionary:The dictionary.
-...type:Class.SentinelRankDictionary
-..param.pos:The position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#empty
-..class:Class.SentinelRankDictionary
-..summary:Returns whether or not the dictionary is empty.
-..signature:empty(dictionary)
-..param.dictionary:The rank dictionary to be checked.
-...type:Class.SentinelRankDictionary
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#getValue
-..class:Class.SentinelRankDictionary
-..summary:Returns the character of a specified position.
-..signature:getCharacter(dictionary, pos)
-..param.dictionary:The rank dictionary.
-...type:Class.RankDictionary
-..param.pos:The position
-..include:seqan/index.h
-..example.code:
-*/
-/**
-.Function.SentinelRankDictionary#getFibre:
-..class:Class.SentinelRankDictionary
-..summary:Returns a specific fibre of a dictionary.
-..signature:getFibre(dictionary, fibreTag)
-..class:Class.RankDictionary
-..cat:Index
-..param.dictionary:The dictionary holding the fibre.
-...type:Class.RankDictionary
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.SentinelRankDictionary Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#countOccurrences
-..class:Class.SentinelRankDictionary
-..summary:Returns the number of occurrences of a specified character from the start
-to a specified position.
-..signature:countOccurrences(dictionary, character, pos)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.character:The character.
-..param.pos:The position (which is included in the counting).
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RankDictionary<String<Dna5> > dictionary(genome);
-
-std::cout << countOccurrences(dictionary, 'a', 3) << std::endl; // 1
-std::cout << countOccurrences(dictionary, 'a', 4) << std::endl; // 2
-*/
-/**
-.Function.SentinelRankDictionary#getSentinelSubstitute
-..class:Class.SentinelRankDictionary
-..summary:Returns the character used to substitute the sentinel sign.
-..signature:getSentinelSubstitute(dictionary)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#setSentinelSubstitute
-..class:Class.SentinelRankDictionary
-..summary:Sets the character used to substitute the sentinel sign.
-..signature:setSentinelSubstitute(dictionary, character)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.character:The sentinel substitute.
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#setSentinelPosition
-..class:Class.SentinelRankDictionary
-..summary:Sets the sentinel position..
-..signature:setSentinelPosition(dictionary, pos)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.pos:The sentinel position.
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#createSentinelRankDictionary
-..class:Class.SentinelRankDictionary
-..summary:This functions creates the dictionary structure.
-..signature:void createSentinelRankDictionary(dictionary, text)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary.
-..param.text:A text to be transfered into a dictionary.
-...type:Class.String
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#open
-..class:Class.SentinelRankDictionary
-..summary:This functions loads a dictionary from disk.
-..signature:open(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.SentinelRankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Function.SentinelRankDictionary#save
-..class:Class.SentinelRankDictionary
-..summary:This functions saves a dictionary to disk.
-..signature:save(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.SentinelRankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-///.Metafunction.Fibre.param.TSpec.type:Tag.SentinelRankDictionary Fibres
-/**
-.Tag.SparseString Fibres
-..summary:Tag to select a specific fibre of a @Class.SparseString@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a sparse string.
-..cat:Index
-
-..tag.FibreValueString:The string storing values different from a default value.
-..tag.FibreIndicatorString:The bit string indicating if the value of a given position is different from the default
-value.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-/**
-.Class.SparseString:
-..cat:Index
-..summary:A string storing only a fraction of the values of the original string..
-..signature:SparseString<TValueString, TSpec>
-..param.TValueString:The string containing the values.
-..param.TSpec:The specialisation tag.
-...default:void.
-..include:seqan/String.h
-*/
-/**
-.Function.SparseString#getFibre:
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(sparseString, fibreTag)
-..class:Class.SparseString
-..cat:Index
-..param.sparseString:The compressed suffix array holding the fibre.
-...type:Class.SparseString
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.SparseString Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-*/
-/**
-.Function.SparseString#open
-..class:Class.SparseString
-..summary:This functions saves a sparse string to disk.
-..signature:open(string, fileName [, openMode])
-..param.string:The string to be saved.
-...type:Class.SparseString
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-/**
-.Function.SparseString#save
-..class:Class.SparseString
-..summary:This functions saves a sparse string to disk.
-..signature:save(string, fileName [, openMode])
-..param.string:The string to be saved.
-...type:Class.SparseString
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-///.Function.clear.param.object.type:Class.SparseString
-///.Function.clear.class:Class.SparseString
-///.Function.empty.param.object.type:Class.SparseString
-///.Function.empty.class:Class.SparseString
-///.Function.assignValue.param.container.type:Class.SparseString
-///.Function.assignValue.class:Class.SparseString
-///.Function.getValue.param.container.type:Class.SparseString
-///.Function.getValue.class:Class.SparseString
-///.Function.value.param.container.type:Class.SparseString
-///.Function.value.class:Class.SparseString
-///.Function.length.param.object.type:Class.SparseString
-///.Function.length.class:Class.SparseString
-///.Function.resize.param.object.type:Class.SparseString
-///.Function.resize.class:Class.SparseString
-///.Spec.VSTree Iterator.param.TContainer.type:Spec.FMIndex
-///.Function.begin.param.object.type:Spec.FMIndex
diff --git a/seqan/index/index_fm_dox.h b/seqan/index/index_fm_dox.h
index 8bb94a2..c9669d9 100644
--- a/seqan/index/index_fm_dox.h
+++ b/seqan/index/index_fm_dox.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -57,997 +57,77 @@
  * @brief The text is kept and not cleared. This FM Index version is faster but more memory is required.
  */
 
-/*!
- * @defgroup FMIndexFibres FM Index Fibres
- * 
- * @brief Tag to select a specific fibre of a @link FMIndex @endlink.
- * 
- * @section Remarks
- * 
- * These tags can be used to get @link Index#Fibre Fibres @endlink of a FM index.
- * 
- * @see Index#Fibre
- * @see Index#getFibre
- * 
- * @tag FMIndexFibres#FibreText
- * 
- * @brief The original text of the index.
- * 
- * @tag FMIndexFibres#FibreSaLfTable
- * 
- * @brief The lf table as well as the compressed suffix array.
- * 
- * @section Remarks
- * 
- * This tag can only be used with the functions @link Index#indexRequire @endlink or
- * @link Index#indexSupplied @endlink.
- * 
- * @tagFMIndexFibres#FibreSA
- * 
- * @brief The compressed suffix array of the text.
- * 
- * @tag FMIndexFibres#FibrePrefixSumTable
- * 
- * @brief The prefix sum table of the index.
- * 
- * @tag FMIndexFibres#FibreLfTable
- * 
- * @brief The lf table.
- */
-
-/*!
- * @class FMIndex
- * 
- * @extends Index
- * 
- * @headerfile seqan/index.h
- * 
- * @brief An index based on the Burrows-Wheeler transform.
- * 
- * @signature Index<TText, FMIndex<TOccSpec, TSpec> >
- * 
- * @tparam TOccSpec Occurrence table specialisation.The tags are really
- *                  shortcuts for the different @link SentinelRankDictionary
- *                  @endlinks Types: @link FMIndexRankDictionarySpec#WT @endlink, @link FMIndexRankDictionarySpec#SBM @endlink, Default: @link FMIndexRankDictionarySpec#WT @endlink
- *
- * @tparam TSpec FM index specialisation. Types: @link FMIndexCompressionSpec#CompressText @endlink, @link FMIndexCompressionSpec#void @endlink, Default: @link FMIndexCompressionSpec#void @endlink
- *
- * @tparam TText The text type. Types: @link String @endlink, @link StringSet @endlink
- */
 
 /*!
  * @fn FMIndex#begin
- * 
- * @brief Returns an iterator pointing to the root not of the virtual prefix
- *        trie of the reversed text of the index.
- * 
- * @signature Iterator begin(index, tag)
- * 
- * @param index The index to be traversed.
- * @param tag The specialisation of the iterator to be returned by the function.
- *            Types: VSTree Iterator
- * 
- * @return TReturn Returns an iterator pointing to the root not of the virtual
- *                 prefix trie of the reversed text of the the index. Types:
- *                 nolink:<tt>The result of Iterator<Index<TText, TIndexSpec>,
- *                 TSpec >::Type</tt>
- */
-
-/*!
- * @fn FMIndex#toSuffixPosition
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This function computes the position of a specified position in the
- *        suffix array (additionally containing entries for the sentinels. The
- *        returned position correspond to the suffix array of the original text
- *        without sentinels.
- * 
- * @signature toSuffixPosition(fmIndex, pos, offset)
- * 
- * @param pos The position in the suffix array of the fm index (with sentinels).
- *            Types: @link UnsignedIntegerConcept @endlink
- * @param fmIndex The FM index.
- * @param offset The number of sequences in the original text. Types:
- *               @link UnsignedIntegerConcept @endlink
- */
-
-/*!
- * @defgroup CompressedSAFibres  CompressedSA Fibres
- * 
- * @brief Tag to select a specific fibre of a @link CompressedSA @endlink.
- * 
- * @see Index#Fibre
- * @see Index#getFibre
- * 
- * @tag CompressedSAFibres#FibreSparseString
- * 
- * @brief The sparse string.
- */
-
-/*!
- * @class CompressedSA
- * 
- * @headerfile seqan/index.h
- * 
- * @brief A suffix array storing only a few suffix array entries and computing
- *        the remaining on demand.
- * 
- * @signature CompressedSA<TSparseString, TLfTable, TSpec>
- * 
- * @tparam TSpec Possibility to specialise a compressed suffix array. Default:
- *               void.
- * @tparam TLfTable The lfTable containg an occurrence table and a prefix sum
- *                  table. Types: @link LfTable @endlink
- * @tparam TSparseString The string containing specific suffix array entries.
- *                       Types: @link SparseString @endlink
- * 
- * @section Remarks
- * 
- * The compressed suffix array can only be used together with the @link LfTable @endlink.
- */
-
-/*!
- * @fn CompressedSA#clear
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Resets an object.
- * 
- * @signature clear(compressedSA)
- * 
- * @param compressesSA The compressed suffix array to be cleared.
- */
-
-/*!
- * @fn CompressedSA#empty
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Checks whether or not a compressed suffix array contains any elements.
- * 
- * @signature bool empty (compressedSA)
- * 
- * @param compressesSA The compressed suffix array to be cleared.
- *
- * @return bool Returns true if the compressed suffix array is empty and false otherwise.
- */
-
-/*!
- * @fn CompressedSA#createCompressedSa
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions creates a compressed suffix array with a specified
- *        compression factor.
- * 
- * @signature void createCompressedSa(compressedSA, completeSA,
- *            compressionFactor [,offset])
- * 
- * @param compressedSA The compressed suffix array.
- *
- * @param compressionFactor The compression factor. A compression factor of x
- *                          means that the compressed suffix array specifically
- *                          stores a value for every x values in the complete
- *                          suffix array. Types: @link UnsignedIntegerConcept @endlink
- * @param completeSA A complete suffix array containing all values. Types: @link String @endlink
- */
-
-/*!
- * @fn CompressedSA#getFibre
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a specific fibre of a compressed suffix array.
- * 
- * @signature getFibre(compressedSA, fibreTag)
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types:
- *                 @link CompressedSAFibres CompressedSA Fibres @endlink
- * @param compressedSA The container holding the fibre.
- * 
- * @return TReturn A reference to the @link Index#Fibre @endlink object.
- */
-
-/*!
- * @fn CompressedSA#length
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the number of elements in the compressed suffix array.
- * 
- * @signature TSize length(compressedSA)
- * 
- * @param compressesSA The compressed suffix array.
- *
- * @return TSize The number of elements in the compressed suffix array. Types: The result of @link Size @endlink of the
- * compressed suffix array.
- */
-/*!
- * @fn CompressedSA#resize
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Resets the number of elements in the compressed suffix array.
- * 
- * @signature TSize resize(compressedSA, newLenght)
- * 
- * @param compressesSA The compressed suffix array.
- * @param newLength The number of elements which should be stored in the compressed suffix array. Types: @link
- * UnsignedIntegerConcept @endlink.
+ * @headerfile <seqan/index.h>
+ * @brief Returns an iterator pointing to the root node of the virtual prefix trie of the reversed text of the index.
  *
- * @return TSize The number of elements in the compressed suffix array. Types: The result of @link Size @endlink of the
- * compressed suffix array.
+ * @signature TIterator begin(index, tag);
  *
- * @section Note If the new length is smaller than the actual one then the last <tt>x<tt> items of the compressed suffix array
- * are deleted with x = oldLength - newLength.
- */
-
-/*!
- * @fn CompressedSA#open
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions opens a compressed suffix array from disk.
- * 
- * @signature open(compressedSA, fileName [, mode])
- * 
- * @param mode The combination of flags defining how the file should be
- *             opened.To open a file read-only, write-only or to read and write
- *             use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *             <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *             <tt>OPEN_CREATE</tt>.To append a file if existing add
- *             <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *             opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *             OPEN_APPEND</tt>
- * @param compressedSA The compressed suffix array to be opened.
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
-
-
-/*!
- * @fn CompressedSA#save
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions saves a compressed suffix array to disk.
- * 
- * @signature save(compressedSA, fileName [, mode])
- * 
- * @param mode The combination of flags defining how the file should be
- *             opened.To open a file read-only, write-only or to read and write
- *             use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *             <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *             <tt>OPEN_CREATE</tt>.To append a file if existing add
- *             <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *             opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *             OPEN_APPEND</tt>
- * @param compressedSA The compressed suffix array to be opened.
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
-
-/*!
- * @fn CompressedSA#setLfTable
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Set the LfTable of the compressed suffix array.
- * 
- * @signature setLfTable(compressedSa, lfTable)
- * 
- * @param lfTable The LfTable Types: LfTable
- * @param compressedSA The compressed suffix array.
- */
-
-/*!
- * @fn CompressedSA#value
- * 
- * @brief Returns the value stored at a specified position in the compressed
- *        suffix-array.
- * 
- * @signature Value value(compressedSA, pos)
- * 
- * @param pos Position at which to access the suffix array. Types:
- *            @link UnsignedIntegerConcept @endlink
- * @param compressedSA The compressed suffix array to access.
- * 
- * @section Remarks
- * 
- * Note that the compressed suffix array is read only. Therefore a const
- * reference is return by this function.
- */
-
-/*!
- * @defgroup LFTableFibres LF Table Fibres
- * 
- * @brief Tag to select a specific fibre of a @link LfTable @endlink.
- * 
- * @section Remarks
- * 
- * These tags can be used to get @link Index#Fibre Fibres @endlink of a @link LfTable @endlink.
- * 
- * @see Index#Fibre
- * @see Index#getFibre
- * 
- * @tag LFTableFibres#FMTablePrefixSumTable
- * 
- * @brief The prefix sum table of the lf table.
- * 
- * @tag LFTableFibres#FibreOccTable
- * 
- * @brief The occurrence table of the lf table.
- */
-
-/*!
- * @class LfTable
- * 
- * @headerfile seqan/Index.h
- * 
- * @brief LfTable is an object storing all necessary information for the LF-
- *        mapping.
- * 
- * @signature LfTable<TOccTable, TPrefixSumTable>
- * 
- * @tparam TPrefixSumTable The specialisation tag. Default: @link String @endlink
- * @tparam TOccTable The occurrence table data structure. Types: @link RankDictionary @endlink, @link SentinelRankDictionary @endlink.
- */
-
-/*!
- * @fn LfTable#clear
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Resets the LF table.
- * 
- * @signature clear(lfTable)
- * 
- * @param lfTable The LF table to be cleared.
- */
-
-/*!
-  * @fn LfTable#empty
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Clears the LF table.
- * 
- * @signature empty(lfTable)
- * 
- * @param lfTable The LF table to be checked.
- * 
- * @return TReturn <tt>true</tt> if the LF table is empty, <tt>false</tt>
- *                 otherwise. Types: nolink:<tt>bool</tt>
- */
-
-/*!
- * @fn createLfTable
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Creates the LF table
- * 
- * @signature createLfTable(lfTable, text)
- * 
- * @param lfTable The LF table to be constructed.
- * @param text The underlying text Types: @link String @endlink.
- * 
- * @return TReturn <tt>true</tt> on successes, <tt>false</tt> otherwise.
- */
-
-/*!
- * @fn LfTable#getFibre
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a specific fibre of a LF table.
- * 
- * @signature getFibre(lfTable, fibreTag)
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types: @link LFTableFibres @endlink
- * @param container The container holding the fibre.
- * 
- * @return TReturn A reference to the @link Index#Fibre @endlink object.
+ * @param[in] index The index to be traversed.
+ * @param[in] tag   The specialisation of the iterator to be returned by the function. Types: VSTree Iterator
+ *
+ * @return TIterator Returns an iterator pointing to the root node of the virtual prefix trie of the reversed text
+ *                   of the the index.  Types: <tt>The result of Iterator&lt;Index&lt;TText, TIndexSpec&gt;,
+ *                   TSpec&gt;::Type</tt>
  */
 
 /*!
- * @fn LfTable#lfMapping
- * 
- * @headerfile seqan/index.h
- * 
+ * @fn LF#lfMapping
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns the position of an character at a specified position of L in
  *        F. L corresponds to the last column of the sorted cyclic rotations of
  *        the original text, while F correspond to the first column.
- * 
+ *
  * @signature lfMapping(lfTable, pos)
- * 
- * @param lfTable The @link LfTable @endlink holding the occurrence and prefix
+ *
+ * @param lfTable The @link LF @endlink holding the occurrence and prefix
  *                sum table.
  *
  * @param pos The position in L. Types: @link UnsignedIntegerConcept @endlink
- * 
+ *
  * @return TReturn Returns the position of the character L[c] in F. The returned
  *                 position is of the same type as pos. Types: The type of the position.
  */
 
-/*!
- * @fn LfTable#open
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions loads a LF table from disk.
- * 
- * @signature open(lfTable, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param lfTable The lfTable. Types: LfTable
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A nolink:<tt>bool</tt> which is <tt>true</tt> on success.
- */
-
-/*!
- * @fn LfTable#save
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions saves a LF table to disk.
- * 
- * @signature save(lfTable, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param lfTable The dictionary. Types: LfTable
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A nolink:<tt>bool</tt> which is <tt>true</tt> on success.
- */
-
-/*!
- * @defgroup PrefixSumTableFibres PrefixSumTable Fibres
- * 
- * @brief Tag to select a specific fibre of a @link PrefixSumTableFibres @endlink.
- * 
- * @see Index#Fibre
- * @see Index#getFibre
- * 
- * @tag PrefixSumTableFibres#FibreEntries
- * 
- * @brief The entries in the prefix sum table.
- */
-
-/*!
- * @class PrefixSumTable
- * 
- * @headerfile seqan/Index.h
- * 
- * @brief The prefix-sum table is a data structure which stores for each
- *        character the number of smaller lexicographic smaller characters in a
- *        given text.
- * 
- * @signature PrefixSumTable<TChar, TSpec>
- * 
- * @tparam TSpec A specialisation tag. Default: void
- * @tparam TChar The character type
- */
-
-/*!
- * @fn PrefixSumTable#clear
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Resets the prefix sum table.
- * 
- * @signature clear(prefixSumTable)
- * @param prefixSumTable The prefix sum table to be cleared.
- */
-
-/*!
- * @fn PrefixSumTable#createPrefixSumTable
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Creates the prefix sum table
- * 
- * @signature createPrefixSumTable(prefixSumTable, text)
- * 
- * @param text The underlying text. Types: @link String @endlink, @link StringSet @endlink
- * @param prefixSumTable The prefix sum table to be constructed.
- */
-
-/*!
- * @fn PrefixSumTable#getAlphabetSize
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the number of different characters in the prefix sum table.
- * 
- * @signature getAlphabetSize(prefixSumTable)
- * 
- * @param prefixSumTable A prefix sum table.
- */
-
-/*!
- * @fn PrefixSumTable#getCharacterPosition
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the position of a given character within the prefix sum table.
- * 
- * @signature getCharacterPosition(prefixSumTable, character)
- * 
- * @param character A character.
- * @param prefixSumTable A prefix sum table.
- */
-
-/*!
- * @fn PrefixSumTable#getCharacter
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the character of a given position within the prefix sum table.
- * 
- * @signature getCharacter(prefixSumTable, pos)
- * 
- * @param pos A position. Types: @link UnsignedIntegerConcept @endlink
- * @param prefixSumTable A prefix sum table.
- */
-
-/*!
- * @fn PrefixSumTable#getPrefixSum
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the prefix sum of a given position.
- * 
- * @signature getPrefixSum(prefixSumTable, pos)
- * 
- * @param pos A position. Types: @link UnsignedIntegerConcept @endlink
- * @param prefixSumTable A prefix sum table.
- */
-
-/*!
- * @fn PrefixSumTable#getValue
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the prefix sum of a given position.
- * 
- * @signature getValue(prefixSumTable, pos)
- * 
- * @param pos A position. Types: @link UnsignedIntegerConcept @endlink
- * @param prefixSumTable A prefix sum table.
- */
-
-/*!
- * @fn PrefixSumTable#getFibre
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a specific fibre of a prefix-sum table.
- * 
- * @signature getFibre(prefixSumTable, fibreTag)
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types:
- *                 @link PrefixSumTableFibres PrefixSumTanble Fibres @endlink.
- * @param prefixSumTable The prefix sum table.
- * 
- * @return TReturn A reference to the @link Index#Fibre @endlink object.
- */
-
-/*!
- * @fn PrefixSumTable#length
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the number of different characters in the prefix-sum table.
- * 
- * @signature length(lfTable)
- * 
- * @param lfTable The prefix-sum table.
- * 
- * @return TReturn Returns the number of different characters in the prefix-sum
- *                 table.If the type of the characters of the prefix-sum table
- *                 consists of more than 8 bit only the characters actually
- *                 occurring in the original text are accounted for when calling
- *                 length. Types: @link Size @endlink of the prefix-sum table.
- */
-
-/*!
- * @fn PrefixSumTable#prefixSum
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a reference to the entry of the prefix sum table of a given
- *        position.
- * 
- * @signature prefixSum(prefixSumTable, pos)
- * 
- * @param pos A position. Types: @link UnsignedIntegerConcept @endlink.
- * @param prefixSumTable A prefix sum table.
- */
-
-/*!
- * @fn PrefixSumTable#resize
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Resize the prefix-sum table to be able to store more or less
- *        characters.
- * 
- * @signature resize(prefixSumTable, size [,value, resizeTag])
- * 
- * @param resizeTag Specifies the strategy that is applied if the capacity of
- *                  <tt>object</tt> is less than <tt>newLength</tt>. (optional)
- *                  Types: @link OverflowStrategyTags @endlink Default: Specified by @link
- *                  DefaultOverflowExplicit @endlink.
- * @param prefixSumTable A prefix sum table. Types: PrefixSumTable
- * @param value The value to be used to initialize the new storage.
- * @param size The new size. Types: @link UnsignedIntegerConcept @endlink
- */
-
-/*!
- * @fn PrefixSumTable#setPrefixSum
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a reference to the entry of the prefix-sum table of a given
- *        position.
- * 
- * @signature setPrefixSum(prefixSumTable, value, pos)
- * 
- * @param pos A position. Types: @link UnsignedIntegerConcept @endlink
- * @param value A specified value to be inserted.
- * @param prefixSumTable A prefix sum table.
- */
-
-/*!
-  * @fn PrefixSumTable#open
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions loads a prefix-sum table from disk.
- * 
- * @signature open(prefixSumTable, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param prefixSumTable The prefix-sum table.
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
-
-/*!
- * @fn PrefixSumTable#save
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions saves a prefix-sum table to disk.
- * 
- * @signature save(prefixSumTable, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param prefixSumTable The prefix-sum table.
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
-
-/*!
- * @class RankDictionary
- * 
- * @headerfile seqan/index.h
- * 
- * @brief A rank dictionary is a data structure to store the rank of an element
- *        of a sequence at every position of the sequence.
- * 
- * @signature RankDictionary<TSpec>
- * 
- * @tparam TSpec The rank dictionary specialisation. Types: WaveletTree,
- *               SequenceBitMask Default: @link WaveletTree @endlink
- */
-
-/*!
- * @class WaveletTree
- *
- * @extends RankDictionary
- * 
- * @headerfile seqan/index.h
- * 
- * @brief A wavelet tree is a tree like binary encoding of a text.
- * 
- * @signature template <typename TValue>
- *            RankDictionary<WaveletTree<TValue> >
- * 
- * @tparam TValue The value type of the wavelet tree.
- * 
- * @section Remarks
- * 
- * The nodes of a wavelet tree consist of a bit string as well as a character c.
- * In each level of the tree, characters smaller than c are represented as a 0
- * while character greater or equal to c are represented with a 1. The
- * characters represented by a 0 form the string to be represented by the left
- * subtree while characters represented by a 1 form the string of the right
- * subtree. Therefore, only the bit string of the root node represents all
- * characters while all other nodes represent subsets.
- */
-
-/*!
- * @defgroup WaveletTreeFibres WaveletTree Fibres
- * 
- * @brief Tag to select a specific fibre (e.g. table, object, ...) of a @link
- *        WaveletTree @endlink.
- * 
- * @section Remarks
- * 
- * These tags can be used to get @link Index#Fibre Fibres @endlink of a @link
- * WaveletTree @endlink.
- * 
- * @see Index#Fibre
- * @see Index#getFibre
- * 
- * @tag WaveletTreeFibres#FibreTreeStructure
- * 
- * @brief The wavelet tree structure of the wavelet tree.
- * 
- * @tag WaveletTreeFibres#FibreBitStrings
- * 
- * @brief The string set containing a bit string for each node.
- */
-
-/*!
- * @class SequenceBitMask
- *
- * @extends RankDictionary
- * 
- * @headerfile seqan/index.h
- * 
- * @brief The string set bit string dictionary is a string set of rank support
- *        bit strings for constant time acces of the rank of a specified
- *        character at a specified position.
- * 
- * @signature template <typename TValue>
- *            RankDictionary<SequenceBitMask<TValue> >
- * 
- * @tparam TValue The value type of the .
- * 
- * @section Remarks
- * 
- * This data structure is optimized for very small alphabets, such as @link Dna @endlink
- * or  @link Dna5 @endlink.  Consider using a @link WaveletTree @endlink if
- * your alphabet size is larger.
- */
-
-/*!
- * @class SequenceBitMaskFibres SequenceBitMask Fibres
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Tag to select a specific fibre of a SequenceBitMask.
- *
- * @tag SequenceBitMaskFibres#FibreBitStrings The string set containing a bit string for each character.
- * 
- * @see Index#Fibre
- * @see Index#getFibre
- */
-
-/*!
- * @mfn RankDictionary#Fibre
- *
- * @brief Returns the type of a specified fibre of a @link RankDictionary @endlink.
- *
- * signature Fibre<RankDictionary, FibreSpec>::Type
- *
- * @tparam FibreSpec The Fibre of interest. Types: @link WaveletTreeFibres @endlink, @link SequenceBitMaskFibres @endlink.
- *
- */
-
-/*!
- * @fn RankDictionary#clear
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Resets the rank dictionary.
- * 
- * @signature clear(dictionary)
- * 
- * @param dictionary The rank dictionary to be cleared.
- */
-
-/*!
- * @fn RankDictionary#empty
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns whether or not the rank dictionary is empty.
- * 
- * @signature empty(dictionary)
- * 
- * @param dictionary The rank dictionary to be checked.
- * 
- * @return TReturn <tt>true</tt> if the dictionary is empty, <tt>false</tt>
- *                 otherwise.
- */
-
-/*!
- * @fn RankDictionary#getValue
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the character of a specified position.
- * 
- * @signature getValue(dictionary, pos)
- * 
- * @param pos The position. Types: @link UnsignedIntegerConcept @endlink.
- * @param dictionary The dictionary.
- */
-
-/*!
-  * @fn RankDictionary#getFibre
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a specific fibre of a dictionary.
- * 
- * @signature getFibre(dictionary, fibreTag)
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types:
- *                 @link SequenceBitMaskFibres SequenceBitMask Fibres @endlink, @link WaveletTreeFibres WaveletTree Fibres @endlink.
- * @param dictionary The dictionary holding the fibre.
- * 
- * @return TReturn A reference to the @link Index#Fibre @endlink object.
- */
-
-/*!
- * @fn RankDictionary#countOccurrences
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the rank (number of occurrences) of a specified character up
- *        to a specified position.
- * 
- * @signature countOccurrences(dictionary, character, pos)
- * 
- * @param character The character of interest.
- * @param pos The position (which is also included in the rank computation).
- * @param dictionary The dictionary. 
- *
- * @return TReturn The rank (number of occurrences) of a specified character up
- *                 to a specified position. Types: <tt>unsigned</tt>
- */
-
-/*!
- * @fn RankDictionary#createRankDictionary
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions creates the dictionary.
- * 
- * @signature createRankDictionary(dictionary, text)
- * 
- * @param text A text to be transfered into a wavelet tree. Types: @link String @endlink
- * @param dictionary The dictionary.
- */
-
-/*!
- * @fn RankDictionary#open
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions loads a rank dictionary from disk.
- * 
- * @signature open(dictionary, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param dictionary The dictionary.
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
-
-/*!
- * @fn RankDictionary#save
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions saves a dictionary to disk.
- * 
- * @signature save(dictionary, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param dictionary The dictionary.
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
-
 /*!
  * @defgroup RankSupportBitStringFibres RankSupportBitString Fibres
- * 
+ *
  * @brief Tag to select a specific fibre (e.g. table, object, ...) of a @link
  *        RankSupportBitString @endlink.
- * 
- * @section Remarks
- * 
- * These tags can be used to get @link Index#Fibre Fibres @endlink of a rank support
+ *
+ * These tags can be used to get @link Fibre Fibres @endlink of a rank support
  * bit string.
- * 
- * @see Index#Fibre
+ *
+ * @see Fibre
  * @see Index#getFibre
- * 
+ *
  * @tag RankSupportBitStringFibres#FibreSuperBlocks
- * 
  * @brief The super block string.
- * 
+ *
  * @tag RankSupportBitStringFibres#FibreBits
- * 
  * @brief The bit string.
- * 
+ *
  * @tag RankSupportBitStringFibres#FibreBlocks
- * 
  * @brief The block string.
  */
 
 /*!
  * @class RankSupportBitString
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief A bit string supporting rank queries in constant time.
- * 
- * @signature RankSupportBitString<TSpec>
- * 
- * @tparam TSpec Specialisation tag. Default: void
- * 
- * @section Remarks
- * 
+ *
+ * @signature template <typename TSpec>
+ *            class RankSupportBitString;
+ *
+ * @tparam TSpec Specialisation tag.  Default: void
+ *
  * The constant rank query time is achieved by evaluating precomputed
- * subsolutions. In order to do so, the bit string is divided into blocks of
- * length l. A super block string stores for each block of l blocks the number
+ * subsolutions.  In order to do so, the bit string is divided into blocks of
+ * length l.  A super block string stores for each block of l blocks the number
  * of bits set from the beginning. In addition a block string stores the number
  * of bits set in each block from the start of the last super block block.
  * Therefore it is possible to compute the result of a rank query in constant
@@ -1056,13 +136,13 @@
 
 /*!
  * @fn RankSupportBitString#appendValue
- * 
- * @headerfile seqan/sequence.h
- * 
+ *
+ * @headerfile <seqan/sequence.h>
+ *
  * @brief Appends a bit to a @link RankSupportBitString @endlink.
- * 
+ *
  * @signature appendValue(bitString, bit)
- * 
+ *
  * @param target A container. Types: RankSupportBitString
  * @param bit Value that is appended to <tt>target</tt>.If the value is
  *              different from 0 it is interpreted as 1. Types: @link UnsignedIntegerConcept @endlink, bool
@@ -1070,41 +150,41 @@
 
 /*!
  * @fn RankSupportBitString#clear
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Resets an rank-support-bit string.
- * 
+ *
  * @signature clear(bitString)
- * 
+ *
  * @param bitString The bit string to be cleared.
  */
 
 /*!
  * @fn RankSupportBitString#getRank
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns the rank (the number of bits set from the start of the bit
  *        string) of a specified position.
- * 
+ *
  * @signature getRank(bitString, pos)
- * 
+ *
  * @param bitString The bit string. Types: @link RankSupportBitString @endlink
  * @param pos Position of a bit.
- * 
- * @return TReturn @link Value @endlink of @link Index#Fibre @endlink of the rank-support-bit string.
+ *
+ * @return TReturn @link Value @endlink of @link Fibre @endlink of the rank-support-bit string.
  */
 
 /*!
  * @fn RankSupportBitString#empty
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Checks whether or not a rank-support-bit string contains any elements.
- * 
+ *
  * @signature bool empty(bitString)
- * 
+ *
  * @param bitString The rank-support-bit string to be checked.
  *
  * @return bool Returns true if the rank-support-bit string is empty and false otherwise.
@@ -1112,58 +192,58 @@
 
 /*!
  * @fn RankSupportBitString#isBitSet
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns whether the bit with the given index is set to 1.
- * 
+ *
  * @signature isSetBit(bitString, pos)
- * 
+ *
  * @param bitString The bit string.
  * @param pos Position of the bit. Types: @link UnsignedIntegerConcept @endlink
- * 
+ *
  * @return TReturn Returns whether a specified bit is set or not.
  */
 
 /*!
  * @fn RankSupportBitString#getFibre
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns a specific fibre of a rank-support-bit string.
- * 
+ *
  * @signature getFibre(bitString, fibreTag)
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types:
+ *
+ * @param fibreTag A tag that identifies the @link Fibre @endlink. Types:
  *                 @link RankSupportBitStringFibres RankSupportBitString Fibres @endlink.
  * @param bitString The rank-support-bit string holding the fibre.
- * 
- * @return TReturn A reference to the @link Index#Fibre @endlink object.
+ *
+ * @return TReturn A reference to the @link Fibre @endlink object.
  */
 
 /*!
  * @fn RankSupportBitString#length
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns the number of bits in the rank-support-bit string.
- * 
+ *
  * @signature length(bitString)
- * 
+ *
  * @param bitString The rank-support-bit string.
- * 
- * @return TReturn Types: @link Value @endlink of @link Index#Fibre @endlink of the rank-support-bit string.
+ *
+ * @return TReturn Types: @link Value @endlink of @link Fibre @endlink of the rank-support-bit string.
  */
 
 /*!
  * @fn RankSupportBitString#resize
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Resets the number of bits in the rank-support-bit string.
- * 
+ *
  * @signature TSize resize(bitString, newLenght)
- * 
+ *
  * @param bitString The rank-support-bit string.
  * @param newLength The number of elements which should be stored in the compressed suffix array. Types: @link
  * UnsignedIntegerConcept @endlink.
@@ -1177,34 +257,34 @@
 
 /*!
  * @fn RankSupportBitString#setBitTo
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Set the bit with the given position to the given value.
- * 
+ *
  * @signature setBitTo(bitString, pos, value)
- * 
+ *
  * @param pos Position of the bit. Types: @link UnsignedIntegerConcept @endlink
- * @param bitString The bit string. 
+ * @param bitString The bit string.
  * @param bit The value of the bit. Note that values different from 0 are
  *            interpreted as 1.
- * 
+ *
  * @return TReturn <tt>void</tt>
- * 
+ *
  * @section Examples
- * 
+ *
  * @see RankSupportBitString#isBitSet
  */
 
 /*!
  * @fn RankSupportBitString#open
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief This functions opens a @link RankSupportBitString @endlink from disk.
- * 
+ *
  * @signature open(bitString, fileName [, openMode])
- * 
+ *
  * @param openMode The combination of flags defining how the file should be
  *                 opened.To open a file read-only, write-only or to read and
  *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
@@ -1215,19 +295,19 @@
  *                 OPEN_APPEND</tt>
  * @param bitString The bit string to be opened.
  * @param fileName C-style character string containing the file name.
- * 
+ *
  * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
  */
 
 /*!
  * @fn RankSupportBitString#save
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief This functions saves a @link RankSupportBitString @endlink to disk.
- * 
+ *
  * @signature save(bitString, fileName [, openMode])
- * 
+ *
  * @param openMode The combination of flags defining how the file should be
  *                 opened.To open a file read-only, write-only or to read and
  *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
@@ -1238,569 +318,226 @@
  *                 OPEN_APPEND</tt>
  * @param bitString The bit string to be saved.
  * @param fileName C-style character string containing the file name.
- * 
+ *
  * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
  */
 
-/*!
- * @class RightArrayBinaryTree
- * 
- * @headerfile seqan/index.h
- * 
- * @brief A special format to encode the structure of a wavelet tree. The
- *        structure is very space efficient because only one position is stored
- *        which encodes where the left and right subtree of a given node exist.
- * 
- * @signature RightArrayBinaryTree<TValue, TSpec>
- * 
- * @tparam TValue The value type - type of the stored characters.
- *
- * @tparam TSpec The wavelet tree structure specialisation. Default: void.
- */
 
-/*!
- * @defgroup RightArrayBinaryTreeFibres RightArrayBinaryTree Fibres
- * 
- * @brief Tag to select a specific fibre (e.g. table, object, ...) of a @link
- *        RightArrayBinaryTree @endlink.
- * 
- * @section Remarks
- * 
- * These tags can be used to get @link Index#Fibre Fibres @endlink of a @link RightArrayBinaryTree @endlink.
- * 
- * @see Index#Fibre
- * @see Index#getFibre
- * 
- * @tag RightArrayBinaryTreeFibres#FibreTreeStructureEncoding
- * 
- * @brief The string encoding the wavelet tree structure.
- */
 
-/*!
- * @fn RightArrayBinaryTree#clear
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Resets a right-array-binary tree.
- * 
- * @signature clear(rightArrayBinaryTree)
- * 
- * @param rightArrayBinaryTree The right-array-binary tree to be cleared.
- */
 
-/*!
- * @fn RightArrayBinaryTree#createRightArrayBinaryTree
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Computes the right-array-binary tree of a text.
- * 
- * @signature createRightArrayBinaryTree(rightArrayBinaryTree, text)
- * 
- * @param text A text. Types: @link String @endlink
- * @param rightArrayBinaryTree A wavelet tree structure.
- */
 
-/*!
- * @fn RightArrayBinaryTree#empty
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Checks whether or not a right-array-binary tree contains any elements.
- * 
- * @signature bool empty(rightArrayBinaryTree)
- * 
- * @param rightArrayBinaryTree The right-array-binary tree to be checked.
- *
- * @return bool Returns true if the rank-support-bit string is empty and false otherwise.
- */
 
-/*!
- * @fn RightArrayBinaryTree#getFibre
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a specific fibre of a right-array-binary tree.
- * 
- * @signature getFibre(rightArrayBinaryTree, fibreTag)
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types:
- *                 @link RightArrayBinaryTreeFibres RightArrayBinaryTree Fibres @endlink.
- * @param container The container holding the fibre.
- * 
- * @return TReturn A reference to the @link Index#Fibre @endlink object.
- */
 
-/*!
- * @fn RightArrayBinaryTree#open
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions loads a @link RightArrayBinaryTree @endlink from disk.
- * 
- * @signature open(rightArrayBinaryTree, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param rightArrayBinaryTree The rightArrayBinaryTree. 
- *
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
 
-/*!
- * @fn RightArrayBinaryTree#save
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions saves a @link RightArrayBinaryTree @endlink to disk.
- * 
- * @signature save(rightArrayBinaryTree, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param rightArrayBinaryTree The rightArrayBinaryTree. 
- *
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
 
-/*!
- * @class RightArrayBinaryTreeIterator RightArrayBinaryTree Iterator
- * 
- * @extends Iter
- * 
- * @headerfile seqan/index.h
- * 
- * @brief An iterator for @link RightArrayBinaryTree @endlink.
- * 
- * @signature Iter<RightArrayBinaryTree, TSpec >
- * 
- * @tparam TSpec Specialisation Tag. Types: TopDownIterator
- * @tparam RightArrayBinaryTree The @link RightArrayBinaryTree @endlink. Types:
- *                              @link RightArrayBinaryTree @endlink
- */
 
-/*!
- * @fn RightArrayBinaryTree#begin
- * 
- * @headerfile seqan/index.h
- * 
- * @brief The begin (root) of a @link RightArrayBinaryTree @endlink.
- * 
- * @signature Iterator begin(rightArrayBinaryTree, iterSpec)
- * 
- * @param rightArrayBinaryTree The right-array-binary tree.
- *
- * @param iterSpec A specialisation tag. Types: TopDown<>, TopDown<ParentLinks<> >
- * 
- * @return TReturn An iterator to the first item in <tt>object</tt>.
- *                 Metafunctions: Metafunction.Iterator
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#container
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Container of an iterator.
- * 
- * @signature Container container(iterator)
- * 
- * @param iterator An iterator.
- * 
- * @return TReturn The container that <tt>iterator</tt> traverses.
- */
 
-/*!
- * @fn RightArrayBinaryTree#end
- * 
- * @headerfile seqan/index.h
- * 
- * @brief The end (rigthmost laef) of a @link RightArrayBinaryTree @endlink.
- * 
- * @signature Iterator end(rightArrayBinaryTree, iterSpec)
- * 
- * @param rightArrayBinaryTree The right-array-binary tree.
- *
- * @param iterSpec A specialisation tag. Types: TopDown<>, TopDown<ParentLinks<> >
- * 
- * @return TReturn An iterator to the first item in <tt>object</tt>.
- *                 Metafunctions: Metafunction.Iterator
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#getCharacter
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This function returns the pivot character of the node the iterator
- *        currently points to.
- * 
- * @signature getCharacter(iterator)
- * 
- * @param iterator The iterator.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#getLeftChildPos
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the position in @link RightArrayBinaryTree @endlink of the
- *        left child node.
- * 
- * @signature getLeftChildPos(iterator)
- * 
- * @param iterator The iterator.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#getSubTreeSize
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the number of vertices in the subtree starting at the position
- *        an iterator points to.
- * 
- * @signature getSubTreeSize(iterator)
- * 
- * @param iterator The iterator.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#getPosition
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the position of the iterator in the host.
- * 
- * @signature getPosition(iterator)
- * 
- * @param iterator The iterator.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#getRightChildPos
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the position in @link RightArrayBinaryTree @endlink of the
- *        right child node.
- * 
- * @signature getLeftChildPos(iterator)
- * 
- * @param iterator The iterator.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#goDown
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Iterates down the leftmost edge in a @link RightArrayBinaryTree @endlink.
- * 
- * @signature bool goDown(iterator)
- *
- * @param iterator The iterator
- * 
- * @return TReturn <tt>true</tt> if an edge to go down exists,
- *                 otherwise <tt>false</tt>. Types: bool
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#goLeftChild
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Sets the iterator to the left child of the current node if it exists
- *        and returns true, otherwise the iterator does not change position and
- *        the function returns false.
- * 
- * @signature bool goLeftChild(iterator)
- * 
- * @param iterator The iterator
- * 
- * @return TReturn <tt>true</tt> if the edge to go down exists,
- *                 otherwise <tt>false</tt>.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#goRight
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Iterates to the next sibling in a @link RightArrayBinaryTree @endlink.
- * 
- * @signature goRight(iterator)
- * 
- * @param iterator The iterator
- * 
- * @return TReturn <tt>true</tt> if the iterator could be moved, otherwise
- *                 <tt>false</tt>. Types: nolink:bool
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#goRightChild
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Sets the iterator to the right child of the current node if it exists
- *        and returns true, otherwise the iterator does not change position and
- *        the function returns false.
- * 
- * @signature bool goRightChild(iterator)
- * 
- * @param iterator The iterator.
- * 
- * @return TReturn <tt>true</tt> if the edge to go down exists,
- *                 otherwise <tt>false</tt>.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#goUp
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Iterates up one edge to the parent in a @link RightArrayBinaryTree @endlink.
- * 
- * @signature goUp(iterator)
- * 
- * @param iterator The iterator.
- * 
- * @return TReturn <tt>true</tt> if the iterator could be moved, otherwise
- *                 <tt>false</tt>. Types: nolink:bool
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#isLeaf
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Tests whether a given node is a leaf or not.
- * 
- * @signature isLeaf(iterator)
- * 
- * @param iterator The iterator.
- * 
- * @return TReturn True if the node is a leaf.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#setCharacter
- * 
- * @headerfile seqan/index.h
- * 
- * @brief The function sets the character of the
- *        node the iterator points to to character.
- * 
- * @signature void setCharacter(iterator, character)
- * 
- * @param character The character to be assigned to a node.
- * @param iterator The iterator.
- */
 
-/*!
- * @fn RightArrayBinaryTreeIterator#isRoot
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Test whether a iterator points to the root node.
- * 
- * @signature bool isRoot(iterator)
- * 
- * @param iterator The iterator.
- * 
- * @return TReturn <tt>true</tt> if <tt>iterator</tt> points to the root of the
- *                 tree, otherwise <tt>false</tt>. Types: nolink:bool
- */
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 
 /*!
  * @defgroup SentinelRankDictionaryFibres SentinelRankDictionary Fibres
- * 
+ *
  * @brief Tag to select a specific fibre of a @link
  *        SentinelRankDictionary @endlink.
- *  
- * @see Index#Fibre
+ *
+ * @see Fibre
  * @see Index#getFibre
- * 
+ *
  * @tag SentinelRankDictionaryFibres#FibreSentinelPosition
- * 
  * @brief The bit string encoding the position of the sentinel sign.
- * 
+ *
  * @tag SentinelRankDictionaryFibres#FibreRankDictionary
- * 
  * @brief The rank dictionary.
  */
 
 /*!
  * @class SentinelRankDictionary
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief A rank dictionary, additional storing sentinel character which are not
  *        accounted for in a rank query.
- * 
- * @signature SentinelRankDictionary<TRankDictionary, TSpec>
- * 
+ *
+ * @signature template <typename TRankDictionary, typename TSpec>
+ *            class SentinelRankDictionary;
+ *
  * @tparam TSpec Specialisation
  * @tparam TRankDictionary The rank dictionary of a text.
  */
 
 /*!
  * @fn SentinelRankDictionary#clear
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief Clears the dictionary.
- * 
+ *
  * @signature clear(dictionary)
- * 
+ *
  * @param dictionary The rank dictionary to be cleared.
  */
 
 /*!
  * @fn SentinelRankDictionary#sentinelPosition
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns whether a specified position is a sentinel position.
- * 
+ *
  * @signature sentinelPosition(dictionary, pos)
- * 
+ *
  * @param pos The position. Types: @link UnsignedIntegerConcept @endlink
  * @param dictionary The dictionary.
  */
 
 /*!
  * @fn SentinelRankDictionary#empty
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns whether or not the dictionary is empty.
- * 
+ *
  * @signature empty(dictionary)
- * 
- * @param dictionary The rank dictionary to be checked. 
+ *
+ * @param dictionary The rank dictionary to be checked.
  */
 
 /*!
  * @fn SentinelRankDictionary#getValue
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns the character of a specified position.
- * 
+ *
  * @signature getCharacter(dictionary, pos)
- * 
+ *
  * @param pos The position
  * @param dictionary The rank dictionary.
  */
 
 /*!
  * @fn SentinelRankDictionary#getFibre
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns a specific fibre of a dictionary.
- * 
+ *
  * @signature getFibre(dictionary, fibreTag)
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types:
+ *
+ * @param fibreTag A tag that identifies the @link Fibre @endlink. Types:
  *                 @link SentinelRankDictionaryFibres SentinelRankDictionary Fibres @endlink.
  * @param dictionary The dictionary holding the fibre.
- * 
- * @return TReturn A reference to the @link Index#Fibre @endlink object.
+ *
+ * @return TReturn A reference to the @link Fibre @endlink object.
  */
 
 /*!
  * @fn SentinelRankDictionary#countOccurrences
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the number of occurrences of a specified character from the
- *        start to a specified position.
- * 
- * @signature countOccurrences(dictionary, character, pos)
- * 
- * @param character The character.
- * @param pos The position (which is included in the counting).
- * @param dictionary The dictionary.
+ * @headerfile <seqan/index.h>
+ * @brief Returns the number of occurrences of a specified character from the start to a specified position.
+ *
+ * @signature TSize countOccurrences(dictionary, character, pos);
+ *
+ * @param[in] dictionary The dictionary.
+ * @param[in] character  The character.
+ * @param[in] pos        The position (which is included in the counting).
+ *
+ * @return TSize The number of occurences  (Metafunction: @link Index#Size @endlink).
  */
 
 /*!
  * @fn SentinelRankDictionary#getSentinelSubstitute
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Returns the character used to substitute the sentinel sign.
- * 
+ *
  * @signature getSentinelSubstitute(dictionary)
- * 
+ *
  * @param dictionary The dictionary.
  */
 
 /*!
  * @fn SentinelRankDictionary#setSentinelSubstitute
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Sets the character used to substitute the sentinel sign.
- * 
+ *
  * @signature setSentinelSubstitute(dictionary, character)
- * 
+ *
  * @param character The sentinel substitute.
  * @param dictionary The dictionary.
  */
 
 /*!
  * @fn SentinelRankDictionary#setSentinelPosition
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief Sets the sentinel position..
- * 
+ *
  * @signature setSentinelPosition(dictionary, pos)
- * 
+ *
  * @param pos The sentinel position. Types: @link UnsignedIntegerConcept @endlink
  * @param dictionary The dictionary.
  */
 
 /*!
  * @fn SentinelRankDictionary#createSentinelRankDictionary
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief This functions creates the dictionary structure.
- * 
+ *
  * @signature void createSentinelRankDictionary(dictionary, text)
- * 
+ *
  * @param text A text to be transfered into a dictionary. Types: @link String @endlink
- * @param dictionary The dictionary. 
+ * @param dictionary The dictionary.
  */
 
 /*!
  * @fn SentinelRankDictionary#save
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief This functions saves a dictionary to disk.
- * 
+ *
  * @signature save(dictionary, fileName [, openMode])
- * 
+ *
  * @param openMode The combination of flags defining how the file should be
  *                 opened.To open a file read-only, write-only or to read and
  *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
@@ -1811,19 +548,19 @@
  *                 OPEN_APPEND</tt>
  * @param dictionary The dictionary. Types: SentinelRankDictionary
  * @param fileName C-style character string containing the file name.
- * 
+ *
  * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
  */
 
 /*!
  * @fn SentinelRankDictionary#open
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief This functions loads a dictionary from disk.
- * 
+ *
  * @signature open(dictionary, fileName [, openMode])
- * 
+ *
  * @param openMode The combination of flags defining how the file should be
  *                 opened.To open a file read-only, write-only or to read and
  *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
@@ -1834,193 +571,6 @@
  *                 OPEN_APPEND</tt>
  * @param dictionary The dictionary. Types: SentinelRankDictionary
  * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
-
-/*!
- * @class SparseString
- * 
- * @headerfile seqan/index.h
- * 
- * @brief A string storing only a fraction of the values of the original
- *        string.
- * 
- * @signature SparseString<TValueString, TSpec>
- * 
- * @tparam TSpec The specialisation tag. Default: void.
- * @tparam TValueString The type of the string containing the values. Types: @link String @endlink
- */
-
-/*!
- * @defgroup SparseStringFibres FM Index Fibres
- * 
- * @brief Tag to select a specific fibre of a @link FMIndex @endlink.
- * 
- * @section Remarks
- * 
- * These tags can be used to get @link Index#Fibre Fibres @endlink of a FM index.
- * 
- * @see Index#Fibre
- * @see Index#getFibre
- * 
- * @tag SparseStringFibres#FibreValueString
- * 
- * @brief The String containing the stored values.
- * 
- * @tag SparseStringFibres#FibreIndicatorString
- * 
- * @brief The string storing for each position if a value different from a default value is stored.
- */
-
-/*!
- * @fn SparseString#clear
- *
- * @headerfile seqan/index.h
- * 
- * @brief Clears the @link SparseString @endlink.
- * 
- * @signature clear(sparseString)
- * 
- * @param sparseString The  @link SparseString @endlink to be cleared.
- */
-
-/*!
- * @fn SparseString#empty
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns whether or not the @link SparseString @endlink is empty.
- * 
- * @signature empty(sparseString)
- * 
- * @param sparseString The @link SparseString @endlink to be checked. 
- */
-
-/*!
- * @fn SparseString#getValue
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the value of a @link SparseString @endlink.
- * 
- * @signature getValue(sparseString, pos)
- * 
- * @param sparseString The @link SparseString @endlink. 
- * @param pos The position at which a value should be assign to the sparse string. 
- *        Types: @link UnsignedIntegerConcept @endlink
- *
- * @return TValue The type @link GetValue @endlink of @link SparseString @endlink is returned.
- */
-
-/*!
- * @fn SparseString#value
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the value of a @link SparseString @endlink.
- * 
- * @signature value(sparseString, pos)
- * 
- * @param sparseString The @link SparseString @endlink. 
- * @param pos The position at which a value should be assign to the sparse string. 
- *        Types: @link UnsignedIntegerConcept @endlink
- *
- * @return TValue The type @link Reference @endlink of @link SparseString @endlink is returned.
- */
-
-/*!
- * @fn SparseString#getFibre
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns a specific fibre of a @link SparseString @endlink.
- * 
- * @signature getFibre(sparseString, fibreTag)
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. Types:
- *                 @link SparseStringFibres SparseString Fibres @endlink
- * @param sparseString The sparseString holding the fibre.
- * 
- * @return TReturn A reference to the @link Index#Fibre @endlink object.
- */
-
-/*!
- * @fn SparseString#length
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the number of elements in the @link SparseString @endlink.
- * 
- * @signature TSize length(sparseString)
- * 
- * @param sparseString The sparse string suffix array.
- *
- * @return TSize The number of elements in the sparse string array. Types: The result of @link Size @endlink of the
- * sparse string.
- */
-
-/*!
- * @fn SparseString#resize
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Resets the number of elements in the compressed suffix array.
- * 
- * @signature TSize resize(sparseString, newLenght)
- * 
- * @param sparseString The sparse string.
- * @param newLength The number of elements which should be stored in the  sparse string. Types: @link
- * UnsignedIntegerConcept @endlink.
  *
- * @return TSize The number of elements in the  sparse string. Types: The result of @link Size @endlink of the
- * sparse string.
- *
- * @section Note If the new length is smaller than the actual one then the last <tt>x<tt> items of the compressed suffix array
- * are deleted with x = oldLength - newLength.
- */
-
-/*!
- * @fn SparseString#open
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions open a sparse string from disk.
- * 
- * @signature open(string, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param string The string to be saved. Types: SparseString
- * @param fileName C-style character string containing the file name.
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
- */
-/*!
- * @fn SparseString#save
- * 
- * @headerfile seqan/index.h
- * 
- * @brief This functions saves a sparse string to disk.
- * 
- * @signature open(string, fileName [, openMode])
- * 
- * @param openMode The combination of flags defining how the file should be
- *                 opened.To open a file read-only, write-only or to read and
- *                 write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
- *                 <tt>OPEN_RDWR</tt>.To create or overwrite a file add
- *                 <tt>OPEN_CREATE</tt>.To append a file if existing add
- *                 <tt>OPEN_APPEND</tt>.To circumvent problems, files are always
- *                 opened in binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE |
- *                 OPEN_APPEND</tt>
- * @param string The string to be saved. Types: SparseString
- * @param fileName C-style character string containing the file name.
- * 
  * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
  */
diff --git a/seqan/index/index_fm_lf_table.h b/seqan/index/index_fm_lf_table.h
old mode 100755
new mode 100644
index 71cc619..47b5ab1
--- a/seqan/index/index_fm_lf_table.h
+++ b/seqan/index/index_fm_lf_table.h
@@ -1,7 +1,8 @@
 // ==========================================================================
-//                 seqan - the library for sequence analysis
+//                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,7 +31,10 @@
 //
 // ==========================================================================
 // Author: Jochen Singer <jochen.singer@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
 // ==========================================================================
+// LF stores all necessary information for the LF-mapping.
+// ============================================================================
 
 //SEQAN_NO_DDDOC:do not generate documentation for this file
 
@@ -39,407 +43,705 @@
 
 namespace seqan {
 
-// ==========================================================================
-// LfTable is an object storing all necessary information for the LF-mapping.
-// To be more precise, the occurrence-table data structure as well as the
-// prefix-sum table are stored.
-// ==========================================================================
-
-// ==========================================================================
+// ============================================================================
 // Forwards
-// ==========================================================================
+// ============================================================================
 
-template <typename TValue>
-struct WaveletTree;
+template <typename TText, typename TSpec, typename TConfig>
+struct LF;
 
-template<typename TValue> 
-class RankDictionary;
+// ============================================================================
+// Tags
+// ============================================================================
+
+/*!
+ * @defgroup LFTableFibres LF Table Fibres
+ * @brief Tag to select a specific fibre of a @link LF @endlink.
+ *
+ * These tags can be used to get @link Fibre Fibres @endlink of a @link LF @endlink.
+ *
+ * @see Fibre
+ * @see Index#getFibre
+ *
+ * @tag LFTableFibres#FibrePrefixSums
+ * @brief The prefix sum table of the lf table.
+ *
+ * @tag LFTableFibres#FibreBwt
+ * @brief The occurrence table of the lf table.
+ *
+ * @tag LFTableFibres#FibreSentinels
+ * @brief The type of the senitnels.
+ */
+
+struct FibrePrefixSums_;
+struct FibreSentinels_;
+struct FibreTempBwt_;
+
+typedef Tag<FibrePrefixSums_>   const FibrePrefixSums;
+typedef Tag<FibreSentinels_>    const FibreSentinels;
+typedef Tag<FibreTempBwt_>      const FibreTempBwt;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
 
-template<typename TRankDirectorySpec, typename TSpec> 
-class SentinelRankDictionary;
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
 
-/**
-.Tag.LF Table Fibres
-..summary:Tag to select a specific fibre of a @Spec.FMIndex@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a FM index.
-..cat:Index
+template <typename TText, typename TSpec, typename TConfig>
+struct Size<LF<TText, TSpec, TConfig> >
+{
+    typedef typename TConfig::LengthSum    Type;
+};
 
-..tag.FibreOccTable:The occurrence table of the lf table.
-..tag.FMTablePrefixSumTable:The prefix sum table of the lf table.
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+// TODO(esiragusa): define Value<LF> == Size<LF> because LF[pos-i] = pos-j
 
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index_fm.h
-*/
-struct FibreOccTable_;
-struct FibrePrefixSumTable_;
+template <typename TText, typename TSpec, typename TConfig>
+struct Value<LF<TText, TSpec, TConfig> > : Value<TText> {};
 
-typedef Tag<FibreOccTable_> const FibreOccTable;
-typedef Tag<FibrePrefixSumTable_> const FMTablePrefixSumTable;
+template <typename TText, typename TSpec, typename TConfig>
+struct Value<LF<TText, TSpec, TConfig> const> :
+    public Value<LF<TText, TSpec, TConfig> > {};
 
-template <typename TOccTable, typename TPrefixSumTable>
-struct LfTable;
+template <typename TText, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Value<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> > : Value<TText> {};
 
-// ==========================================================================
-// Tags
-// ==========================================================================
+template <typename TText, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Value<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> const> :
+    public Value<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> > {};
 
-struct FibreRankDictionary_;
-typedef Tag<FibreRankDictionary_> const FibreRankDictionary;
+// ----------------------------------------------------------------------------
+// Metafunction Fibre<FibrePrefixSums>
+// ----------------------------------------------------------------------------
 
-struct FibreSentinentalPosition_;
-typedef Tag<FibreSentinentalPosition_> const FibreSentinentalPosition;
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<LF<TText, TSpec, TConfig>, FibrePrefixSums>
+{
+//    typedef typename Value<LF<TText, TSpec, TConfig> >::Type  TValue_;
+//    typedef Tuple<TSize_, ValueSize<TValue_>::VALUE>          Type;
 
-// ==========================================================================
-// Metafunctions
-// ==========================================================================
+    typedef typename Size<LF<TText, TSpec, TConfig> >::Type TSize_;
+    typedef typename DefaultIndexStringSpec<TText>::Type    TSpec_;
+    typedef String<TSize_,  TSpec_>                         Type;
+};
 
 // ----------------------------------------------------------------------------
-// Metafunction Fibre
+// Metafunction Fibre<FibreBwt>
 // ----------------------------------------------------------------------------
 
-template <typename TOccTable, typename TPrefixSumTable>
-struct Fibre<LfTable<TOccTable, TPrefixSumTable>, FibreOccTable>
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<LF<TText, TSpec, TConfig>, FibreBwt>
 {
-    typedef TOccTable Type;
+    typedef typename Value<LF<TText, TSpec, TConfig> >::Type    TValue_;
+    typedef RankDictionary<TValue_, typename TConfig::Bwt>      Type;
 };
 
-template <typename TOccTable, typename TPrefixSumTable>
-struct Fibre<LfTable<TOccTable, TPrefixSumTable> const, FibreOccTable>
-{
-    typedef TOccTable const Type;
-};
+// ----------------------------------------------------------------------------
+// Metafunction Fibre<FibreSentinels>
+// ----------------------------------------------------------------------------
 
-template <typename TOccTable, typename TPrefixSumTable>
-struct Fibre<LfTable<TOccTable, TPrefixSumTable>, FMTablePrefixSumTable>
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<LF<TText, TSpec, TConfig>, FibreSentinels>
 {
-    typedef TPrefixSumTable Type;
+    typedef typename Size<TText>::Type   Type;
 };
 
-template <typename TOccTable, typename TPrefixSumTable>
-struct Fibre<LfTable<TOccTable, TPrefixSumTable> const, FMTablePrefixSumTable>
+template <typename TText, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig>, FibreSentinels>
 {
-    typedef TPrefixSumTable const Type;
+    typedef RankDictionary<bool, typename TConfig::Sentinels>   Type;
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction Reference
+// Metafunction Fibre<FibreTempBwt>
 // ----------------------------------------------------------------------------
 
-template <typename TOccTable, typename TPrefixSumTable>
-struct Reference<LfTable<TOccTable, TPrefixSumTable> >
+template <typename TText, typename TSpec, typename TConfig>
+struct Fibre<LF<TText, TSpec, TConfig>, FibreTempBwt>
 {
-    typedef TPrefixSumTable & Type;
+    typedef typename Value<LF<TText, TSpec, TConfig> >::Type        TValue_;
+    typedef String<TValue_, External<ExternalConfigLarge<> > >      Type;
 };
 
-// ==========================================================================
+// ============================================================================
 // Classes
-// ==========================================================================
+// ============================================================================
 
 // ----------------------------------------------------------------------------
-// Class LfTable
+// Class LF
 // ----------------------------------------------------------------------------
 
-/**
-.Class.LfTable:
-..cat:Index
-..summary:LfTable is an object storing all necessary information for the LF-mapping.
-..signature:LfTable<TOccTable, TPrefixSumTable>
-..param.TOccTable:The occurrence table data structure.
-...type:Spec.WaveletTree
-..param.TPrefixSumTable:The specialisation tag.
-...default:String
-..include:seqan/Index.h
-*/
-template <typename TOccTable, typename TPrefixSumTable>
-struct LfTable
+/*!
+ * @class LF
+ *
+ * @headerfile <seqan/Index.h>
+ *
+ * @signature template <typename TText, typename TSpec, typename TConfig>
+ *            struct LF;
+ *
+ * @brief LF is an object storing all necessary information for the LF-mapping.
+ *
+ * @tparam TText The type of the text the LF table is constructed from.
+ * @tparam TSpec A possibility to specialize the LF table. Default: <tt>void</tt>
+ * @tparam TConfig A configuration object for easily defining the LF table fibres.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+struct LF
 {
-    TOccTable occTable;
-    TPrefixSumTable prefixSumTable;
+    typename Fibre<LF, FibrePrefixSums>::Type   sums;
+    typename Fibre<LF, FibreBwt>::Type          bwt;
+    typename Fibre<LF, FibreSentinels>::Type    sentinels;
+    typename Value<LF>::Type                    sentinelSubstitute;
 
-    LfTable() :
-        occTable(),
-        prefixSumTable()
+    LF() : sentinels(), sentinelSubstitute(0)
     {}
 
-    LfTable(TOccTable const & occTable, TPrefixSumTable const & prefixSumTable) :
-        occTable(occTable),
-        prefixSumTable(prefixSumTable)
-    {}
+    LF(TText const & text) : sentinels(), sentinelSubstitute(0)
+    {
+        createLF(text);
+    }
 
-    inline LfTable & operator=(LfTable const & other)
+    template <typename TPos>
+    SEQAN_HOST_DEVICE typename Size<LF const>::Type
+    operator[] (TPos pos) const
     {
-        occTable = other.occTable;
-        prefixSumTable = other.prefixSumTable;
-        return *this;
+        return _getBwtRank(*this, pos);
     }
 
-    inline bool operator==(const LfTable & b) const
+    template <typename TPos>
+    SEQAN_HOST_DEVICE typename Size<LF const>::Type
+    operator() (TPos pos) const
     {
-        return occTable == b.occTable &&
-               prefixSumTable == b.prefixSumTable;
+        return _getBwtRank(*this, pos);
     }
 
+    template <typename TPos, typename TValue>
+    SEQAN_HOST_DEVICE typename Size<LF const>::Type
+    operator() (TPos pos, TValue val) const
+    {
+        return _getBwtRank(*this, pos, val);
+    }
 };
 
-// ==========================================================================
+// ============================================================================
 // Functions
-// ==========================================================================
+// ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function clear
+// Function bwtLength()
 // ----------------------------------------------------------------------------
+// This function returns the length of the BWT of a text or a text collection.
 
-/**
-.Function.LfTable#clear
-..class:Class.LfTable
-..summary:Clears the LF table.
-..signature:clear(lfTable)
-..param.lfTable:The LF table to be cleared.
-...type:Class.LfTable
-..include:seqan/index.h
-*/
-
-template <typename TOccTable, typename TPrefixSumTable>
-inline void clear(LfTable<TOccTable, TPrefixSumTable> & lfTable)
+template <typename TText>
+inline typename LengthSum<TText>::Type
+bwtLength(TText const & text)
 {
-    clear(lfTable.occTable);
-    clear(lfTable.prefixSumTable);
+    return lengthSum(text) + countSequences(text);
 }
 
 // ----------------------------------------------------------------------------
-// Function empty
+// Function getFibre()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.LfTable#empty
-..class:Class.LfTable
-..summary:Clears the LF table.
-..signature:empty(lfTable)
-..param.lfTable:The LF table to be cleared.
-...type:Class.LfTable
-..returns:$true$ if the LF table is empty, $false$ otherwise.
-...type:nolink:$bool$
-..include:seqan/index.h
-*/
+/*!
+ * @fn LF#getFibre
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Returns a specific fibre of a LF table.
+ *
+ * @signature TFibre getFibre(lfTable, fibreTag);
+ *
+ * @param[in] fibreTag A tag that identifies the @link Fibre @endlink. Types: @link LFTableFibres @endlink
+ * @param[in] lfTable  The LF table.
+ *
+ * @return TFibre A reference to the @link Fibre @endlink object of type @link Fibre @endlink&lt;@link LF @endlink&lt;TText, TSpec, TConfig&gt;, FibrePrefixSums&gt;::Type
+ */
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<LF<TText, TSpec, TConfig>, FibrePrefixSums>::Type &
+getFibre(LF<TText, TSpec, TConfig> & lf, FibrePrefixSums)
+{
+    return lf.sums;
+}
 
-template <typename TOccTable, typename TPrefixSumTable>
-inline bool empty(LfTable<TOccTable, TPrefixSumTable> & lfTable)
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<LF<TText, TSpec, TConfig>, FibrePrefixSums>::Type const &
+getFibre(LF<TText, TSpec, TConfig> const & lf, FibrePrefixSums)
 {
-    return empty(lfTable.occTable)
-           && empty(lfTable.prefixSumTable);
+    return lf.sums;
+}
+
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<LF<TText, TSpec, TConfig>, FibreBwt>::Type &
+getFibre(LF<TText, TSpec, TConfig> & lf, FibreBwt)
+{
+    return lf.bwt;
+}
+
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<LF<TText, TSpec, TConfig>, FibreBwt>::Type const &
+getFibre(LF<TText, TSpec, TConfig> const & lf, FibreBwt)
+{
+    return lf.bwt;
+}
+
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<LF<TText, TSpec, TConfig>, FibreSentinels>::Type &
+getFibre(LF<TText, TSpec, TConfig> & lf, FibreSentinels)
+{
+    return lf.sentinels;
+}
+
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<LF<TText, TSpec, TConfig>, FibreSentinels>::Type const &
+getFibre(LF<TText, TSpec, TConfig> const & lf, FibreSentinels)
+{
+    return lf.sentinels;
 }
 
 // ----------------------------------------------------------------------------
-// Function createLfTable
+// Function empty()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.createLfTable
-..summary:Creates the LF table
-..signature:createLfTable(lfTable, text)
-..param.lfTable:The LF table to be constructed.
-...type:Class.LfTable.
-..param.text:The underlying text
-...type:Class.String
-..returns:$true$ on successes, $false$ otherwise.
-..include:seqan/index.h
-*/
+/*!
+ * @fn LF#empty
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Clears the LF table.
+ *
+ * @signature bool empty(lfTable);
+ *
+ * @param[in] lfTable The LF table to be checked.
+ *
+ * @return bool <tt>true</tt> if the LF table is empty, <tt>false</tt> otherwise.
+ */
+
+
+template <typename TText, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline bool empty(LF<TText, TSpec, TConfig> const & lf)
+{
+    return empty(lf.bwt) &&
+           empty(lf.sums);
+}
 
-template <typename TValue, typename TSpec, typename TPrefixSumTable, typename TText>
-inline bool createLfTable(LfTable<SentinelRankDictionary<RankDictionary<WaveletTree<TValue> >, TSpec>, TPrefixSumTable> & lfTable, TText const text)
+template <typename TText, typename TSSetSpec, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline bool empty(LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> const & lf)
 {
-    typedef typename SAValue<TText>::Type   TSAValue;
-    typedef TValue                          TAlphabet;
-    typedef typename Fibre<SentinelRankDictionary<RankDictionary<WaveletTree<TValue> >, TSpec>, FibreSentinentalPosition>::Type TDollarPos;
+    return empty(lf.bwt) &&
+           empty(lf.sentinels) &&
+           empty(lf.sums);
+}
 
-    String<TSAValue> sa;
-    resize(sa, length(text), Exact());
-    createSuffixArray(sa, text, Skew7());
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
 
-    createPrefixSumTable(lfTable.prefixSumTable, text);
+/*!
+ * @fn LF#clear
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Resets the LF table.
+ *
+ * @signature void clear(lfTable);
+ *
+ * @param[in,out] lfTable The LF table to be cleared.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+inline void clear(LF<TText, TSpec, TConfig> & lf)
+{
+    clear(lf.bwt);
+    _clearSentinels(lf);
+    clear(lf.sums);
+    lf.sentinelSubstitute = 0;
+}
 
-    TAlphabet dollarSub;
-    _determineDollarSubstitute(lfTable.prefixSumTable, dollarSub);
+// ----------------------------------------------------------------------------
+// Function _clearSentinels()
+// ----------------------------------------------------------------------------
 
-    String<TAlphabet> bwt;
-    TDollarPos dollarPos = 0;
-    resize(bwt, _computeBwtLength(text), Exact());
-    _createBwTable(bwt, dollarPos, text, sa, dollarSub);
+template <typename TText, typename TSpec, typename TConfig>
+inline void _clearSentinels(LF<TText, TSpec, TConfig> & lf)
+{
+    lf.sentinels = 0;
+}
 
-    clear(sa);
+template <typename TText, typename TSSetSpec, typename TSpec, typename TConfig>
+inline void _clearSentinels(LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> & lf)
+{
+    clear(lf.sentinels);
+}
 
-    createOccurrenceTable(lfTable, bwt, dollarSub, dollarPos);
-    clear(bwt);
+// ----------------------------------------------------------------------------
+// Function _getSentinelsRank()
+// ----------------------------------------------------------------------------
 
-    _insertDollar(lfTable.prefixSumTable, countSequences(text));
+template <typename TText, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<LF<TText, TSpec, TConfig> const>::Type
+_getSentinelsRank(LF<TText, TSpec, TConfig> const & lf, TPos pos)
+{
+    return pos >= lf.sentinels;
+}
 
-    //here comes the dollar modification
-    //addDollarNode(index.lfTable.occTable, dollarSub, dollarPos);
-    return true;
+template <typename TText, typename TSSetSpec, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> const>::Type
+_getSentinelsRank(LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> const & lf, TPos pos)
+{
+    return getRank(lf.sentinels, pos);
 }
 
 // ----------------------------------------------------------------------------
-// Function getFibre
+// Function isSentinel()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.LfTable#getFibre:
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(container, fibreTag)
-..class:Class.LfTable
-..cat:Index
-..param.container:The container holding the fibre.
-...type:Class.LfTable
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.LF Table Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
+template <typename TText, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline bool isSentinel(LF<TText, TSpec, TConfig> const & lf, TPos pos)
+{
+    return lf.sentinels == pos;
+}
 
-template <typename TOccTable, typename TPrefixSumTable>
-inline typename Fibre<LfTable<TOccTable, TPrefixSumTable>, FMTablePrefixSumTable>::Type &
-getFibre(LfTable<TOccTable, TPrefixSumTable>&lfTable, FMTablePrefixSumTable)
+template <typename TText, typename TSSetSpec, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline bool isSentinel(LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> const & lf, TPos pos)
 {
-    return lfTable.prefixSumTable;
+    return getValue(lf.sentinels, pos);
 }
 
-template <typename TOccTable, typename TPrefixSumTable>
-inline typename Fibre<LfTable<TOccTable, TPrefixSumTable>, FMTablePrefixSumTable>::Type const &
-getFibre(LfTable<TOccTable, TPrefixSumTable> const & lfTable, FMTablePrefixSumTable)
+// ----------------------------------------------------------------------------
+// Function _getPrefixSum()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig, typename TValue>
+SEQAN_HOST_DEVICE inline
+typename Size<LF<TText, TSpec, TConfig> const>::Type
+_getPrefixSum(LF<TText, TSpec, TConfig> const & lf, TValue val)
 {
-    return lfTable.prefixSumTable;
+    typedef LF<TText, TSpec, TConfig> const             TLF;
+    typedef typename Value<TLF>::Type                   TTextValue;
+
+    return getValue(lf.sums, ordValue(static_cast<TTextValue>(val)));
 }
 
-template <typename TOccTable, typename TPrefixSumTable>
-inline typename Fibre<LfTable<TOccTable, TPrefixSumTable>, FibreOccTable>::Type &
-getFibre(LfTable<TOccTable, TPrefixSumTable>&lfTable, FibreOccTable)
+// ----------------------------------------------------------------------------
+// Function _getBwtRank(pos, val)
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig, typename TPos, typename TValue>
+SEQAN_HOST_DEVICE inline
+typename Size<LF<TText, TSpec, TConfig> >::Type
+_getBwtRank(LF<TText, TSpec, TConfig> const & lf, TPos pos, TValue val)
 {
-    return lfTable.occTable;
+    typedef LF<TText, TSpec, TConfig> const                TLF;
+    typedef typename Size<TLF>::Type                       TSize;
+
+    TSize rank = _getPrefixSum(lf, val);
+
+    if (pos > 0)
+    {
+        rank += getRank(lf.bwt, pos - 1, val);
+
+        if (ordEqual(lf.sentinelSubstitute, val))
+            rank -= _getSentinelsRank(lf, pos - 1);
+    }
+
+    return rank;
 }
 
-template <typename TOccTable, typename TPrefixSumTable>
-inline typename Fibre<LfTable<TOccTable, TPrefixSumTable>, FibreOccTable>::Type const &
-getFibre(LfTable<TOccTable, TPrefixSumTable> const & lfTable, FibreOccTable )
+// ----------------------------------------------------------------------------
+// Function _getBwtRank(pos)
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline
+typename Size<LF<TText, TSpec, TConfig> const>::Type
+_getBwtRank(LF<TText, TSpec, TConfig> const & lf, TPos pos)
 {
-    return lfTable.occTable;
+    return _getBwtRank(lf, pos, getValue(lf.bwt, pos));
 }
 
 // ----------------------------------------------------------------------------
-// Function lfMapping
+// Function _setSentinelSubstitute()
 // ----------------------------------------------------------------------------
+// This function determines the '$' substitute.
+// The character with the smallest number of occurrences greater 0 is chosen.
+
+template <typename TText, typename TSpec, typename TConfig>
+inline void _setSentinelSubstitute(LF<TText, TSpec, TConfig> & lf)
+{
+    typedef LF<TText, TSpec, TConfig>                   TLF;
+    typedef typename Fibre<TLF, FibrePrefixSums>::Type  TPrefixSums;
+    typedef typename Value<TPrefixSums>::Type           TValue;
+    typedef typename Size<TPrefixSums>::Type            TSize;
+
+    TValue minOcc = MaxValue<TValue>::VALUE;
+    TSize ordVal = 0;
+
+    for (TSize i = 0; i < length(lf.sums) - 1; ++i)
+    {
+        TSize occ = getValue(lf.sums, i + 1) - getValue(lf.sums, i);
+        if (occ > 0 && occ < minOcc)
+        {
+            minOcc = occ;
+            ordVal = i;
+        }
+    }
 
-/**
-.Function.LfTable#lfMapping:
-..summary:Returns the position of an character at a specified position of L in F. L corresponds to the last column of 
-the sorted cyclic rotations of the original text, while F correspond to the first column.
-..cat:Index
-..signature:lfMapping(lfTable, pos)
-..param.lfTable:The @Class.LfTable@ holding the occurrence and prefix sum table.
-...type:Class.LfTable
-..param.pos:The position in L
-..returns:Returns the position of the character L[c] in F. The returned position is of the same type as pos.
-..include:seqan/index.h
-*/
+    lf.sentinelSubstitute = ordVal;
+}
 
-template <typename TLfTable, typename TPos>
-inline TPos lfMapping(TLfTable & lfTable,
-                      TPos pos)
+// ----------------------------------------------------------------------------
+// Function _createBwt()
+// ----------------------------------------------------------------------------
+// This function computes the BWT of a text. Note that the sentinel sign is substituted and its position stored.
+
+template <typename TText, typename TSpec, typename TConfig, typename TBwt, typename TOtherText, typename TSA>
+inline void
+_createBwt(LF<TText, TSpec, TConfig> & lf, TBwt & bwt, TOtherText const & text, TSA const & sa)
 {
-    typedef typename Fibre<TLfTable, FibreOccTable>::Type TOccTable;
-    typedef typename Value<TOccTable>::Type TChar;
-    TChar c = getValue(lfTable.occTable, pos);
-    return countOccurrences(getFibre(lfTable, FibreOccTable()), c, pos) + getPrefixSum(lfTable.prefixSumTable, getCharacterPosition(lfTable.prefixSumTable, c)) - 1;
+    typedef typename GetValue<TSA>::Type                    TSAValue;
+    typedef typename Iterator<TSA const, Standard>::Type    TSAIter;
+    typedef typename Iterator<TBwt, Standard>::Type         TBwtIter;
+
+    TSAIter saIt = begin(sa, Standard());
+    TSAIter saItEnd = end(sa, Standard());
+    TBwtIter bwtIt = begin(bwt, Standard());
+
+    assignValue(bwtIt, back(text));
+    ++bwtIt;
+
+    for (; saIt != saItEnd; ++saIt, ++bwtIt)
+    {
+        TSAValue pos = getValue(saIt);
+
+        if (pos != 0)
+        {
+            assignValue(bwtIt, getValue(text, pos - 1));
+        }
+        else
+        {
+            assignValue(bwtIt, lf.sentinelSubstitute);
+            lf.sentinels = bwtIt - begin(bwt, Standard());
+        }
+    }
 }
 
 // ----------------------------------------------------------------------------
-// Function open
-// ----------------------------------------------------------------------------
-
-/**
-.Function.LfTable#open
-..class:Class.LfTable
-..summary:This functions loads a LF table from disk.
-..signature:open(lfTable, fileName [, openMode])
-..param.lfTable:The lfTable.
-...type:Class.LfTable
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A nolink:$bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TOccTable, typename TPrefixSumTable>
-inline bool open(
-    LfTable<TOccTable, TPrefixSumTable> & lfTable,
-    const char * fileName,
-    int openMode)
+// Function _createBwt()
+// ----------------------------------------------------------------------------
+// This function computes the BWT of a text collection. Note that the sentinel sign is substituted and its position stored.
+
+template <typename TText, typename TSSetSpec, typename TSpec, typename TConfig, typename TBwt, typename TOtherText, typename TSA>
+inline void
+_createBwt(LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> & lf, TBwt & bwt, TOtherText const & text, TSA const & sa)
 {
-    String<char> name;
-    name = fileName; 
-    if (!open(getFibre(lfTable, FibreOccTable()), toCString(name), openMode))
+    typedef typename Value<TSA>::Type                       TSAValue;
+    typedef typename Size<TSA>::Type                        TSize;
+    typedef typename Iterator<TSA const, Standard>::Type    TSAIter;
+    typedef typename Iterator<TBwt, Standard>::Type         TBwtIter;
+
+    TSize seqNum = countSequences(text);
+    TSize totalLen = lengthSum(text);
+
+    resize(lf.sentinels, seqNum + totalLen, Exact());
+
+    TSAIter saIt = begin(sa, Standard());
+    TSAIter saItEnd = end(sa, Standard());
+    TBwtIter bwtItBeg = begin(bwt, Standard());
+    TBwtIter bwtIt = bwtItBeg;
+
+    // Fill the sentinel positions (they are all at the beginning of the bwt).
+    for (TSize i = 1; i <= seqNum; ++i, ++bwtIt)
     {
-        return false;
+        assignValue(bwtIt, back(text[seqNum - i]));
+        setValue(lf.sentinels, bwtIt - bwtItBeg, false);
     }
-    name = fileName;    open(getFibre(lfTable, FMTablePrefixSumTable()), toCString(name), openMode);
-    return true;
 
+    // Compute the rest of the bwt.
+    for (; saIt != saItEnd; ++saIt, ++bwtIt)
+    {
+        TSAValue pos;    // = SA[i];
+        posLocalize(pos, getValue(saIt), stringSetLimits(text));
+
+        if (getSeqOffset(pos) != 0)
+        {
+            assignValue(bwtIt, getValue(getValue(text, getSeqNo(pos)), getSeqOffset(pos) - 1));
+            setValue(lf.sentinels, bwtIt - bwtItBeg, false);
+        }
+        else
+        {
+            assignValue(bwtIt, lf.sentinelSubstitute);
+            setValue(lf.sentinels, bwtIt - bwtItBeg, true);
+        }
+    }
+
+    // Update the auxiliary RankDictionary of sentinel positions.
+    updateRanks(lf.sentinels);
 }
 
-template <typename TOccTable, typename TPrefixSumTable>
-inline bool open(
-    LfTable<TOccTable, TPrefixSumTable> & lfTable,
-    const char * fileName)
+// ----------------------------------------------------------------------------
+// Function createLF()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn LF#createLF
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief Creates the LF table
+ *
+ * @signature void createLF(lfTable, text, sa);
+ *
+ * @param[out] lfTable The LF table to be constructed.
+ * @param[in]  text    The underlying text Types: @link String @endlink.
+ * @param[in]  sa      The suffix array of the LF table underlying text. Types: @link String @endlink,
+ *                     @link StringSet @endlink.
+ *
+ * @return TReturn Returns a <tt>bool</tt> which is <tt>true</tt> on successes and <tt>false</tt> otherwise.
+ */
+// This function creates all table of the lf table given a text and a suffix array.
+template <typename TText, typename TSpec, typename TConfig, typename TOtherText, typename TSA>
+inline void createLF(LF<TText, TSpec, TConfig> & lf, TOtherText const & text, TSA const & sa)
 {
-    return open(lfTable, fileName, DefaultOpenMode<LfTable<TOccTable, TPrefixSumTable> >::VALUE);
+    typedef LF<TText, TSpec, TConfig>                          TLF;
+    typedef typename Fibre<TLF, FibreTempBwt>::Type            TBwt;
+    typedef typename Value<TLF>::Type                          TValue;
+    typedef typename Size<TLF>::Type                           TSize;
+
+    // Clear assuming undefined state.
+    clear(lf);
+
+    // Compute prefix sum.
+    prefixSums<TValue>(lf.sums, text);
+
+    // Choose the sentinel substitute.
+    _setSentinelSubstitute(lf);
+
+    // Create BWT and mark sentinels.
+    TBwt bwt;
+    resize(bwt, bwtLength(text), Exact());
+    _createBwt(lf, bwt, text, sa);
+
+    // Index BWT bwt for rank queries.
+    createRankDictionary(lf.bwt, bwt);
+
+    // Add sentinels to prefix sum.
+    TSize sentinelsCount = countSequences(text);
+    for (TSize i = 0; i < length(lf.sums); ++i)
+        lf.sums[i] += sentinelsCount;
 }
 
-/**
-.Function.LfTable#save
-..class:Class.LfTable
-..summary:This functions saves a LF table to disk.
-..signature:save(lfTable, fileName [, openMode])
-..param.lfTable:The dictionary.
-...type:Class.LfTable
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A nolink:$bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TOccTable, typename TPrefixSumTable>
-inline bool save(
-    LfTable<TOccTable, TPrefixSumTable> const & lfTable,
-    const char * fileName,
-    int openMode)
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn LF#open
+ * @headerfile <seqan/index.h>
+ * @brief This functions loads a LF table from disk.
+ *
+ * @signature bool open(lfTable, fileName[, openMode]);
+ *
+ * @param[in,out] lfTable  The LF object.
+ * @param[in]     fileName C-style character string containing the file name.
+ * @param[in]      openMode
+ *                     The combination of flags defining how the file should be opened.  To open a file
+ *                     read-only, write-only or to read and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>,
+ *                     or <tt>OPEN_RDWR</tt>.  To create or overwrite a file add <tt>OPEN_CREATE</tt>.  To append
+ *                     a file if existing add <tt>OPEN_APPEND</tt>.  To circumvent problems, files are always
+ *                     opened in binary mode.  Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>.
+ *
+ * @return bool <tt>true</tt> on success.
+ */
+
+
+template <typename TText, typename TSpec, typename TConfig>
+inline bool open(LF<TText, TSpec, TConfig> & lf, const char * fileName, int openMode)
 {
     String<char> name;
 
     name = fileName;
-    if (!save(getFibre(lfTable, FibreOccTable()), toCString(name), openMode))
-    {
-        return false;
-    }
-    name = fileName;    save(getFibre(lfTable, FMTablePrefixSumTable()), toCString(name), openMode);
+    append(name, ".pst");
+    if (!open(lf.sums, toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".drv");
+    if (!open(lf.bwt, toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".drp");
+    if (!open(lf.sentinels, toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".drs");
+    if (!open(lf.sentinelSubstitute, toCString(name), openMode)) return false;
+
+    return true;
+}
+
+template <typename TText, typename TSpec, typename TConfig>
+inline bool open(LF<TText, TSpec, TConfig> & lf, const char * fileName)
+{
+    return open(lf, fileName, DefaultOpenMode<LF<TText, TSpec, TConfig> >::VALUE);
+}
+
+// ----------------------------------------------------------------------------
+// Function save()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn LF#save
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief This functions saves a LF table to disk.
+ *
+ * @signature bool save(lfTable, fileName[, openMode]);
+ *
+ * @param[in] lfTable  The LF object to save.
+ * @param[in] fileName C-style character string containing the file name.
+ * @param[in] openMode
+ *                     The combination of flags defining how the file should be opened.  To open a file
+ *                     read-only, write-only or to read and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>,
+ *                     or <tt>OPEN_RDWR</tt>.  To create or overwrite a file add <tt>OPEN_CREATE</tt>.  To append
+ *                     a file if existing add <tt>OPEN_APPEND</tt>.  To circumvent problems, files are always
+ *                     opened in binary mode.  Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>.
+ *
+ * @return bool <tt>true</tt> on success.
+ */
+
+template <typename TText, typename TSpec, typename TConfig>
+inline bool save(LF<TText, TSpec, TConfig> const & lf, const char * fileName, int openMode)
+{
+    String<char> name;
+
+    name = fileName;
+    append(name, ".pst");
+    if (!save(lf.sums, toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".drv");
+    if (!save(lf.bwt, toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".drp");
+    if (!save(lf.sentinels, toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".drs");
+    if (!save(lf.sentinelSubstitute, toCString(name), openMode)) return false;
+
     return true;
 }
 
-template <typename TOccTable, typename TPrefixSumTable>
-inline bool save(
-    LfTable<TOccTable, TPrefixSumTable> const & lfTable,
-    const char * fileName)
+template <typename TText, typename TSpec, typename TConfig>
+inline bool save(LF<TText, TSpec, TConfig> const & lf, const char * fileName)
 {
-    return save(lfTable, fileName, DefaultOpenMode<LfTable<TOccTable, TPrefixSumTable> >::VALUE);
+    return save(lf, fileName, DefaultOpenMode<LF<TText, TSpec, TConfig> >::VALUE);
 }
 
 }
diff --git a/seqan/index/index_fm_prefix_sum_table.h b/seqan/index/index_fm_prefix_sum_table.h
deleted file mode 100755
index 227bbed..0000000
--- a/seqan/index/index_fm_prefix_sum_table.h
+++ /dev/null
@@ -1,740 +0,0 @@
-// ==========================================================================
-//                 seqan - the library for sequence analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Jochen Singer <jochen.singer@fu-berlin.de>
-// ==========================================================================
-
-//SEQAN_NO_DDDOC:do not generate documentation for this file
-
-#ifndef INDEX_FM_PREFIX_SUM_TABLE_H_
-#define INDEX_FM_PREFIX_SUM_TABLE_H_
-
-namespace seqan {
-
-// ==========================================================================
-// Forwards
-// ==========================================================================
-
-template <typename TChar, typename TSpec>
-class PrefixSumTable;
-
-/**
-.Tag.PrefixSumTable Fibres
-..summary:Tag to select a specific fibre of a @Class.CompressedSA@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a sparse string.
-..cat:Index
-
-..tag.FibreEntries:The entries in the prefix sum table.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-struct FibreEntries_;
-typedef Tag<FibreEntries_> const FibreEntries;
-
-// ==========================================================================
-// Metafunctions
-// ==========================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction GetValue
-// ----------------------------------------------------------------------------
-
-template <typename TChar, typename TSpec>
-struct GetValue<PrefixSumTable<TChar, TSpec> >
-{
-    typedef typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type TEntries;
-    typedef typename Value<TEntries>::Type Type;
-};
-
-template <typename TChar, typename TSpec>
-struct GetValue<PrefixSumTable<TChar, TSpec> const>
-{
-    typedef typename Fibre<PrefixSumTable<TChar, TSpec> const, FibreEntries>::Type TEntries;
-    typedef typename Value<TEntries>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction clear
-// ----------------------------------------------------------------------------
-// TODO(singer): change the type to be dependent on a template argument
-template <typename TChar, typename TSpec>
-struct Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>
-{
-    typedef String<unsigned long long> Type;
-};
-
-template <typename TChar, typename TSpec>
-struct Fibre<PrefixSumTable<TChar, TSpec> const, FibreEntries>
-{
-    typedef String<unsigned long long> const Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <typename TChar, typename TSpec>
-struct Size<PrefixSumTable<TChar, TSpec> >
-{
-    typedef typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type TEntries;
-    typedef typename Size<TEntries>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Infix
-// ----------------------------------------------------------------------------
-
-template <typename TChar, typename TSpec>
-struct Infix<PrefixSumTable<TChar, TSpec> >
-{
-    typedef typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type TEntries;
-    typedef typename Infix<TEntries>::Type Type;
-};
-
-template <typename TChar, typename TSpec>
-struct Infix<PrefixSumTable<TChar, TSpec> const>
-{
-    typedef typename Fibre<PrefixSumTable<TChar, TSpec> const, FibreEntries>::Type TEntries;
-    typedef typename Infix<TEntries>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction CharacterValue
-// ----------------------------------------------------------------------------
-
-template <typename TSpec>
-struct CharacterValue;
-
-template <typename TChar, typename TSpec>
-struct CharacterValue<PrefixSumTable<TChar, TSpec> >
-{
-    typedef typename MakeUnsigned<TChar>::Type TUChar;
-    typedef TUChar Type;
-};
-
-template <typename TChar, typename TSpec>
-struct CharacterValue<PrefixSumTable<TChar, TSpec> const>
-{
-    typedef typename MakeUnsigned<TChar>::Type TUChar;
-    typedef TUChar Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Reference
-// ----------------------------------------------------------------------------
-
-template <typename TChar, typename TSpec>
-struct Reference<PrefixSumTable<TChar, TSpec> >
-{
-    typedef typename Value<PrefixSumTable<TChar, TSpec> >::Type & Type;
-};
-
-template <typename TChar, typename TSpec>
-struct Reference<PrefixSumTable<TChar, TSpec> const>
-{
-    typedef typename Value<PrefixSumTable<TChar, TSpec> >::Type const & Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <typename TChar, typename TSpec>
-struct Value<PrefixSumTable<TChar, TSpec> >
-{
-    typedef typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type TEntries;
-    typedef typename Value<TEntries>::Type Type;
-};
-
-template <typename TChar, typename TSpec>
-struct Value<PrefixSumTable<TChar, TSpec> const>
-{
-    typedef typename Fibre<PrefixSumTable<TChar, TSpec> const, FibreEntries>::Type TEntries;
-    typedef typename Value<TEntries>::Type const Type;
-};
-
-// ==========================================================================
-// Classes
-// ==========================================================================
-
-// ----------------------------------------------------------------------------
-// Class PrefixSumTable
-// ----------------------------------------------------------------------------
-
-/**
-.Class.PrefixSumTable:
-..cat:Index
-..summary:The prefix-sum table is a data structure which stores for each character the number of smaller lexicographic 
-smaller characters in a given text.
-..signature:PrefixSumTable<TChar, TSpec>
-..param.TChar:The character type
-..param.TSpec:A specialisation tag.
-...default:void
-..include:seqan/Index.h
-*/
-template <typename TChar, typename TSpec = void>
-class PrefixSumTable
-{
-    typedef typename Fibre<PrefixSumTable, FibreEntries>::Type TEntries;
-    typedef typename Value<TEntries>::Type TEntry;
-
-public:
-    TEntries entries;
-
-    PrefixSumTable() :
-        entries()
-    {}
-
-    PrefixSumTable(String<TChar> const & text) :
-        entries()
-    {
-        createPrefixSumTable(*this, text);
-    }
-
-    template <typename TPos>
-    inline TEntry & operator[](TPos pos)
-    {
-        return value(*this, pos);
-    }
-
-    template <typename TPos>
-    inline TEntry const & operator[](TPos pos) const
-    {
-        return value(*this, pos);
-    }
-
-    inline bool operator==(PrefixSumTable const & other)
-    {
-        return entries == other.entries;
-    }
-
-    inline bool operator==(PrefixSumTable const & other) const
-    {
-        return entries == other.entries;
-    }
-};
-
-// ==========================================================================
-// Functions
-// ==========================================================================
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#clear
-..class:Class.PrefixSumTable
-..summary:Clears the prefix sum table.
-..signature:clear(prefixSumTable)
-..param.prefixSumTable:The prefix sum table to be cleared.
-...type:Class.LfTable
-..include:seqan/index.h
-*/
-
-    template <typename TChar, typename TSpec>
-inline void clear(PrefixSumTable<TChar, TSpec> & prefixSumTable)
-{
-    clear(prefixSumTable.entries);
-}
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-/**
-.Function.PrefixSumTable#createPrefixSumTable
-..class:Class.PrefixSumTable
-..summary:Creates the prefix sum table
-..signature:createPrefixSumTable(prefixSumTable, text)
-..param.prefixSumTable:The prefix sum table to be constructed.
-...type:Class.PrefixSumTable
-..param.text:The underlying text.
-...type:Class.String
-...type:Class.StringSet
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec, typename TText>
-inline void createPrefixSumTable(PrefixSumTable<TChar, TSpec> & prefixSumTable, TText const & text)
-{
-    typedef PrefixSumTable<TChar, TSpec> TPrefixSumTable;
-    typedef typename Value<typename Fibre<TPrefixSumTable, FibreEntries>::Type>::Type TPrefixSumValue;
-
-    TPrefixSumTable freq;
-    _getFrequencies(freq, text);
-
-    unsigned alpSize = length(freq);
-    resize(prefixSumTable, alpSize + 1, 0, Exact());
-
-
-    TPrefixSumValue temp = 0;
-    TPrefixSumValue sum = 0;
-    for (TPrefixSumValue i = 0; i < alpSize; ++i)
-    {
-        temp = getPrefixSum(freq, i);
-        setPrefixSum(prefixSumTable, sum, i);
-        sum += temp;
-    }
-    setPrefixSum(prefixSumTable, sum, alpSize);
-}
-
-// ----------------------------------------------------------------------------
-// Function getAlphabetSize
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#getAlphabetSize
-..class:Class.PrefixSumTable
-..summary:Returns the number of different characters in the prefix sum table.
-..signature:getAlphabetSize(prefixSumTable)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable.
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec>
-unsigned getAlphabetSize(PrefixSumTable<TChar, TSpec> const & pst)
-{
-    return length(pst.entries) - 1;
-}
-
-// ----------------------------------------------------------------------------
-// Function getCharacterPosition
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#getCharacterPosition
-..class:Class.PrefixSumTable
-..summary:Returns the position of a given character within the prefix sum table.
-..signature:getCharacterPosition(prefixSumTable, character)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.character:A character.
-..include:seqan/index.h
-*/
-
-// TODO(esiragusa): Remove TDummy specialization.
-template <typename TDummy, typename TChar>
-inline unsigned getCharacterPosition(TDummy const & /*tag*/, TChar character)
-{
-    return ordValue(character);
-}
-
-template <typename TChar, typename TSpec, typename TChar2>
-inline unsigned getCharacterPosition(PrefixSumTable<TChar, TSpec> const & /*tag*/, TChar2 character)
-{
-    return ordValue(static_cast<TChar>(character));
-}
-
-// ----------------------------------------------------------------------------
-// Function getCharacter
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#getCharacter
-..class:Class.PrefixSumTable
-..summary:Returns the character of a given position within the prefix sum table.
-..signature:getCharacter(prefixSumTable, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable.
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec, typename TPos>
-inline typename CharacterValue<PrefixSumTable<TChar, TSpec> const>::Type
-getCharacter(PrefixSumTable<TChar, TSpec> const & /*tag*/, TPos const pos)
-{
-    return static_cast<TChar>(pos);
-}
-
-// ----------------------------------------------------------------------------
-// Function _getPivotPosition
-// ----------------------------------------------------------------------------
-
-// This function returns the position of the character which ensures that the sum of occurrences of the characters from
-// beginPos to the computed pos and the sum of occurrences from the computed pos to endPos are about the same.
-template <typename TChar, typename TSpec, typename TBeginPos, typename TEndPos>
-unsigned _getPivotPosition(PrefixSumTable<TChar, TSpec> const & pst, TBeginPos beginPos, TEndPos endPos)
-{
-    TBeginPos realBeginPos = beginPos + 1;
-    TEndPos realEndPos = endPos + 1;
-    unsigned lengthRange = realEndPos - realBeginPos + 1;
-    unsigned pivotPos = realBeginPos + lengthRange / 2 - 1;
-
-    unsigned tooSmallValues = pst[beginPos];
-    long currentMin = pst[realEndPos] + 1;
-
-    if (pst[pivotPos] - tooSmallValues >= pst[realEndPos] - pst[pivotPos])
-    {
-        while ((pivotPos >= realBeginPos) && std::abs((long)(pst[pivotPos] - tooSmallValues) - (long)((pst[realEndPos] - pst[pivotPos]))) <= currentMin)
-        {
-            currentMin = std::abs((long)((pst[pivotPos] - tooSmallValues)) - (long)((pst[realEndPos] - pst[pivotPos])));
-            --pivotPos;
-        }
-        ++pivotPos;
-    }
-    else
-    {
-        while (std::abs((long)((pst[pivotPos] - tooSmallValues)) - (long)((pst[realEndPos] - pst[pivotPos]))) < currentMin && (pivotPos < realEndPos))
-        {
-            currentMin = std::abs((long)((pst[pivotPos] - tooSmallValues)) - (long)((pst[realEndPos] - pst[pivotPos])));
-            ++pivotPos;
-        }
-        --pivotPos;
-    }
-
-    return pivotPos;
-}
-
-// ----------------------------------------------------------------------------
-// Function getPrefixSum
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#getPrefixSum
-..class:Class.PrefixSumTable
-..summary:Returns the prefix sum of a given position. 
-..signature:getPrefixSum(prefixSumTable, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec, typename TPos>
-typename Value<typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type>::Type
-getPrefixSum(PrefixSumTable<TChar, TSpec> const & pst, TPos const pos)
-{
-    return getValue(pst, pos);
-}
-
-// ----------------------------------------------------------------------------
-// Function getValue
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#getvalue
-..class:Class.PrefixSumTable
-..summary:Returns the prefix sum of a given position. 
-..signature:getValue(prefixSumTable, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec, typename TPos>
-inline typename GetValue<typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type>::Type
-getValue(PrefixSumTable<TChar, TSpec> & pst, TPos const pos)
-{
-    return pst.entries[pos];
-}
-
-template <typename TChar, typename TSpec, typename TPos>
-inline typename GetValue<typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type>::Type const
-getValue(PrefixSumTable<TChar, TSpec> const & pst, TPos const pos)
-{
-    return pst.entries[pos];
-}
-
-// ----------------------------------------------------------------------------
-// Function getFibre
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#getFibre:
-..class:Class.PrefixSumTable
-..summary:Returns a specific fibre of a prefix-sum table.
-..signature:getFibre(prefixSumTable, fibreTag)
-..class:Class.PrefixSumTable
-..cat:Index
-..param.prefixSumTable:The container holding the fibre.
-...type:Class.PrefixSumTable
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.PrefixSumTable Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec>
-inline typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type const &
-getFibre(PrefixSumTable<TChar, TSpec> const & pst, FibreEntries const /*tag*/)
-{
-    return pst.entries;
-}
-
-template <typename TChar, typename TSpec>
-inline typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type &
-getFibre(PrefixSumTable<TChar, TSpec> & pst, FibreEntries const /*tag*/)
-{
-    return pst.entries;
-}
-
-// ----------------------------------------------------------------------------
-// Function _insertSentinel
-// ----------------------------------------------------------------------------
-
-template <typename TChar, typename TSpec, typename TNumSentinel>
-void _insertSentinel(PrefixSumTable<TChar, TSpec> & pst, TNumSentinel const numSentinel)
-{
-    for (unsigned i = 0; i < length(pst); ++i)
-        prefixSum(pst, i) = getPrefixSum(pst, i) + numSentinel;
-}
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#length
-..class:Class.PrefixSumTable
-..summary:Returns the number of different characters in the prefix-sum table.
-..signature:length(lfTable)
-..param.lfTable:The prefix-sum table.
-...type:Class.LfTable
-..returns:Returns the number of different characters in the prefix-sum table.
-...type:Metafunction.Size
-...remarks:If the type of the characters of the prefix-sum table consists of more than 8 bit only the characters
-actually occurring in the original text are accounted for when calling length.
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec>
-inline typename Size<PrefixSumTable<TChar, TSpec> >::Type
-length(PrefixSumTable<TChar, TSpec> const & pst)
-{
-    return length(pst.entries);
-}
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#prefixSum
-..class:Class.PrefixSumTable
-..summary:Returns a reference to the entry of the prefix sum table of a given position. 
-..signature:prefixSum(prefixSumTable, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec, typename TPos>
-typename Value<typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type>::Type &
-prefixSum(PrefixSumTable<TChar, TSpec>&pst, TPos const pos)
-{
-    return value(pst, pos);
-}
-
-template <typename TChar, typename TSpec, typename TPos>
-typename Value<typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type>::Type const &
-prefixSum(PrefixSumTable<TChar, TSpec> const & pst, TPos const pos)
-{
-    return value(pst, pos);
-}
-
-// ----------------------------------------------------------------------------
-// Function resize
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#resize
-..class:Class.PrefixSumTable
-..summary:Resize the prefix sum table to be able to store more or less characters. 
-..signature:resize(prefixSumTable, size [,value, resizeTag])
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.size:The new size.
-...type:Concept.UnsignedIntegerConcept
-..param.resizeTag: Specifies the strategy that is applied if the capacity of $object$ is less than $newLength$. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowExplicit@.
-
-..param.value:The value to be used to initialize the new storage.
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec, typename TSize, typename TExpand>
-inline typename Size<PrefixSumTable<TChar, TSpec> >::Type
-resize(PrefixSumTable<TChar, TSpec> & pst, TSize size, Tag<TExpand> tag)
-{
-    return resize(pst.entries, size, tag);
-}
-
-template <typename TChar, typename TSpec, typename TSize, typename TValue, typename TExpand>
-inline typename Size<PrefixSumTable<TChar, TSpec> >::Type
-resize(PrefixSumTable<TChar, TSpec> & pst, TSize size, TValue value, Tag<TExpand> tag)
-{
-    return resize(pst.entries, size, value, tag);
-}
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-
-/**
-.Function.setPrefixSum
-..class:Class.PrefixSumTable
-..summary:Returns a reference to the entry of the prefix-sum table of a given position. 
-..signature:setPrefixSum(prefixSumTable, value, pos)
-..param.prefixSumTable:A prefix sum table.
-...type:Class.PrefixSumTable
-..param.value:A specified value to be inserted.
-..param.pos:A position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec, typename TValue, typename TPos>
-inline void setPrefixSum(PrefixSumTable<TChar, TSpec> & pst, TValue value, TPos const pos)
-{
-    pst.entries[pos] = value;
-}
-
-// ----------------------------------------------------------------------------
-// Function value
-// ----------------------------------------------------------------------------
-
-template <typename TChar, typename TSpec, typename TPos>
-inline typename Value<typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type>::Type &
-value(PrefixSumTable<TChar, TSpec>&pst, TPos const pos)
-{
-    return pst.entries[pos];
-}
-
-template <typename TChar, typename TSpec, typename TPos>
-inline typename Value<typename Fibre<PrefixSumTable<TChar, TSpec>, FibreEntries>::Type>::Type const &
-value(PrefixSumTable<TChar, TSpec> const & pst, TPos const pos)
-{
-    return pst.entries[pos];
-}
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#open
-..class:Class.PrefixSumTable
-..summary:This functions loads a prefix-sum table from disk.
-..signature:open(prefixSumTable, fileName [, openMode])
-..param.prefixSumTable:The prefix-sum table.
-...type:Class.PrefixSumTable
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec>
-inline bool open(
-    PrefixSumTable<TChar, TSpec> & pst,
-    const char * fileName,
-    int openMode)
-{
-    String<char> name;
-    name = fileName;    append(name, ".pst");
-    if (!open(getFibre(pst, FibreEntries()), toCString(name), openMode))
-    {
-        return false;
-    }
-    return true;
-
-}
-
-template <typename TChar, typename TSpec>
-inline bool open(
-    PrefixSumTable<TChar, TSpec> & pst,
-    const char * fileName)
-{
-    return open(pst, fileName, DefaultOpenMode<PrefixSumTable<TChar, TSpec> >::VALUE);
-}
-// ----------------------------------------------------------------------------
-// Function save
-// ----------------------------------------------------------------------------
-
-/**
-.Function.PrefixSumTable#save
-..class:Class.PrefixSumTable
-..summary:This functions saves a prefix-sum table to disk.
-..signature:save(prefixSumTable, fileName [, openMode])
-..param.prefixSumTable:The prefix-sum table.
-...type:Class.PrefixSumTable
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TChar, typename TSpec>
-inline bool save(
-    PrefixSumTable<TChar, TSpec> const & pst,
-    const char * fileName,
-    int openMode)
-{
-    String<char> name;
-    name = fileName;    append(name, ".pst");
-    if (!save(getFibre(pst, FibreEntries()), toCString(name), openMode))
-    {
-        return false;
-    }
-    return true;
-}
-
-template <typename TChar, typename TSpec>
-inline bool save(
-    PrefixSumTable<TChar, TSpec> const & pst,
-    const char * fileName)
-{
-    return save(pst, fileName, DefaultOpenMode<PrefixSumTable<TChar, TSpec> >::VALUE);
-}
-
-}
-#endif // SANDBOX_MY_SANDBOX_APPS_FMINDEX_PREFIX_SUM_TABLE_H_
diff --git a/seqan/index/index_fm_rank_dictionary_base.h b/seqan/index/index_fm_rank_dictionary_base.h
new file mode 100644
index 0000000..80ff7cb
--- /dev/null
+++ b/seqan/index/index_fm_rank_dictionary_base.h
@@ -0,0 +1,444 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INDEX_FM_RANK_DICTIONARY_BASE_H_
+#define INDEX_FM_RANK_DICTIONARY_BASE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag FibreRanks
+// ----------------------------------------------------------------------------
+
+/*!
+ * @defgroup RankDictionaryFibres RankDictionary Fibres
+ * @brief Tag to select a specific fibre of a SequenceBitMask.
+ *
+ * @see Fibre
+ * @see RankDictionary#getFibre
+ *
+ * @tag RankDictionaryFibres#FibreRanks
+ * @brief The string set containing a bit string for each character.
+ */
+
+struct FibreRanks_;
+
+typedef Tag<FibreRanks_>
+const FibreRanks;
+
+// ----------------------------------------------------------------------------
+// Tag RDConfig
+// ----------------------------------------------------------------------------
+
+template <typename TSize = size_t, typename TFibre = Alloc<> >
+struct RDConfig
+{
+    typedef TFibre  Fibre;
+    typedef TSize   Size;
+};
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class RankDictionary
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class RankDictionary
+ * @headerfile <seqan/index.h>
+ * @brief A rank dictionary is a data structure storing the rank of an element in a sequence at every position of
+ *        the sequence.
+ *
+ * @signature template <typename TValue, typename TSpec>
+ *            struct RankDictionary;
+ *
+ * @tparam TSpec The rank dictionary specialisation. Default: @link WaveletTree @endlink, @link TwoLevelRankDictionary @endlink.
+ */
+template <typename TValue, typename TSpec>
+struct RankDictionary;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultIndexStringSpec
+// ----------------------------------------------------------------------------
+
+template <typename TValue, template <typename, typename> class TRankDictionary, typename TSpec, typename TConfig>
+struct DefaultIndexStringSpec<RankDictionary<TValue, TRankDictionary<TSpec, TConfig> > >
+{
+    typedef typename TConfig::Fibre Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+template <typename TValue, template <typename, typename> class TRankDictionary, typename TSpec, typename TConfig>
+struct Size<RankDictionary<TValue, TRankDictionary<TSpec, TConfig> > >
+{
+    typedef typename TConfig::Size  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct Value<RankDictionary<TValue, TSpec> >
+{
+    typedef TValue  Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Value<RankDictionary<TValue, TSpec> const> :
+    Value<RankDictionary<TValue, TSpec> > {};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function getFibre()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RankDictionary#getFibre
+ * @headerfile <seqan/index.h>
+ * @brief Returns a specific fibre of a dictionary.
+ *
+ * @signature TFibre getFibre(dictionary, fibreTag);
+ *
+ * @param[in] dictionary The dictionary holding the fibre.
+ * @param[in] fibreTag   A tag that identifies the @link Fibre @endlink. Types: @link RankDictionaryFibres @endlink.
+ *
+ * @return TFibre A reference to the @link Fibre @endlink object.
+ */
+
+
+template <typename TValue, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<RankDictionary<TValue, TSpec>, FibreRanks>::Type &
+getFibre(RankDictionary<TValue, TSpec> & dict, FibreRanks)
+{
+    return dict.ranks;
+}
+
+template <typename TValue, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<RankDictionary<TValue, TSpec>, FibreRanks>::Type const &
+getFibre(RankDictionary<TValue, TSpec> const & dict, FibreRanks)
+{
+    return dict.ranks;
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RankDictionary#clear
+ * @headerfile <seqan/index.h>
+ * @brief Resets the rank dictionary.
+ *
+ * @signature void clear(dictionary);
+ *
+ * @param[in,out] dictionary The rank dictionary to be cleared.
+ */
+
+template <typename TValue, typename TSpec>
+inline void clear(RankDictionary<TValue, TSpec> & dict)
+{
+    clear(getFibre(dict, FibreRanks()));
+}
+
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RankDictionary#empty
+ * @headerfile <seqan/index.h>
+ * @brief Returns whether or not the rank dictionary is empty.
+ *
+ * @signature bool empty(dictionary);
+ *
+ * @param[in] dictionary The rank dictionary to be checked.
+ *
+ * @return bool <tt>true</tt> if the dictionary is empty, <tt>false</tt> otherwise.
+ */
+
+template <typename TValue, typename TSpec>
+SEQAN_HOST_DEVICE inline bool empty(RankDictionary<TValue, TSpec> const & dict)
+{
+    return empty(getFibre(dict, FibreRanks()));
+}
+
+// ----------------------------------------------------------------------------
+// Function createRankDictionary()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RankDictionary#createRankDictionary
+ * @headerfile <seqan/index.h>
+ * @brief This functions creates the dictionary.
+ *
+ * @signature void createRankDictionary(dictionary, text);
+ *
+ * @param[in]  text       A text to be transfered into a rank dictionary. Types: @link ContainerConcept @endlink
+ * @param[out] dictionary The dictionary.
+ */
+
+template <typename TValue, typename TSpec, typename TText>
+inline void
+createRankDictionary(RankDictionary<TValue, TSpec> & dict, TText const & text)
+{
+    typedef typename Iterator<TText const, Standard>::Type      TTextIterator;
+
+    // Resize the RankDictionary.
+    resize(dict, length(text), Exact());
+
+    // Assign the text value by value.
+    TTextIterator textBegin = begin(text, Standard());
+    TTextIterator textEnd = end(text, Standard());
+    for (TTextIterator textIt = textBegin; textIt != textEnd; ++textIt)
+        setValue(dict, textIt - textBegin, value(textIt));
+
+    // Update all ranks.
+    updateRanks(dict);
+}
+
+// ----------------------------------------------------------------------------
+// Function getRank()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RankDictionary#getRank
+ * @headerfile <seqan/index.h>
+ * @brief Returns the rank of a specified character up to a specified position.
+ *
+ * @signature TSize countOccurrences(dictionary, pos[, character]);
+ *
+ * @param[in] dictionary The dictionary.
+ * @param[in] pos The position (which is also included in the rank computation).
+ * @param[in] character The character of interest. Default: <tt>true</tt>
+ *
+ * @return TSize The rank of a specified character up to a specified position.
+ *               The result of the metafunction Size&lt;RankDictionary&gt;::Type
+ */
+
+
+// ----------------------------------------------------------------------------
+// Function getValue()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RankDictionary#getValue
+ * @headerfile <seqan/index.h>
+ * @brief Returns the character of a specified position.
+ *
+ * @signature TValue getValue(dictionary, pos);
+ *
+ * @param[in] dictionary The dictionary.
+ * @param[in] pos        The position. Types: @link UnsignedIntegerConcept @endlink.
+ *
+ * @return TValue Returns the character of a specified position. The result is of type
+ *                Value&lt;RankDictionary&gt;::Type;
+ */
+
+// ----------------------------------------------------------------------------
+// Function setValue()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RankDictionary#setValue
+ * @headerfile <seqan/index.h>
+ * @brief Sets the character at a specified position.
+ *
+ * @signature void setValue(dictionary, pos, character);
+ *
+ * @param[in] dictionary The dictionary.
+ * @param[in] pos        The position. Types: @link UnsignedIntegerConcept @endlink.
+ * @param[in] character  The character to be set.
+ */
+
+// ----------------------------------------------------------------------------
+// Function updateRanks()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RankDictionary#updateRanks
+ *
+ * @brief Updates the rank information.
+ *
+ * @signature void updateRanks(dict)
+ *
+ * @param dict The @link RankDictionary @endlink.
+ */
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RankDictionary#length
+ *
+ * @brief Retruns the number of element in the rank dictionary.
+ *
+ * @signature TSize length(dict)
+ *
+ * @param dict The @link RankDictionary @endlink.
+ *
+ * @return TSize The number of element in the rank dictionary. The result of the metafunction
+ *               Size&lt;RankDictionary&gt;::Type
+ */
+
+
+// ----------------------------------------------------------------------------
+// Function reserve()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RankDictionary#reserve
+ *
+ * @brief Reserves memory for a specified number of elements in the rank dictionary
+ *
+ * @signature TSize reserve(dict, newCapacity, tag)
+ *
+ * @param dict The @link RankDictionary @endlink.
+ * @param newCapacity The number of elements one wants to reserve memory for.
+ * @param tag The tag that specifies the memory allocation strategy. Types: @link OverflowStrategyTags @endlink.
+ *
+ * @section Remarks
+ *
+ * This operation does not changes the content of object.
+ *
+ * This operation may invalidate iterators of object.
+ *
+ * @return TSize Retruns the number of element that could be reserved. The result of the metafunction
+ *               Size&lt;RankDictionary&gt;::Type
+ */
+
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RankDictionary#resize
+ *
+ * @brief Increases the length of a rank dictionary to a specified value.
+ *
+ * @signature TSize resize(dict, newLength, tag)
+ *
+ * @param dict The @link RankDictionary @endlink.
+ * @param newLength The number of elements the rank dictionaru contains after resizing.
+ * @param tag The tag that specifies the memory allocation strategy. Types: @link OverflowStrategyTags @endlink.
+ *
+ * @section Remarks
+ *
+ * This operation may invalidate iterators of object.
+ *
+ * @return TSize Retruns the number of element that could be reserved. The result of the metafunction
+ *               Size&lt;RankDictionary&gt;::Type
+ */
+
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RankDictionary#open
+ * @headerfile <seqan/index.h>
+ * @brief This functions loads a rank dictionary from disk.
+ *
+ * @signature bool open(dictionary, fileName[, openMode]);
+ *
+ * @param[in,out] dictionary The dictionary.
+ * @param[in]     fileName   C-style character string containing the file name.
+ * @param[in]     openMode   The combination of flags defining how the file should be opened.To open a file read-only,
+ *                           write-only or to read and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
+ *                           <tt>OPEN_RDWR</tt>.To create or overwrite a file add <tt>OPEN_CREATE</tt>.To append a file
+ *                           if existing add <tt>OPEN_APPEND</tt>.To circumvent problems, files are always opened in
+ *                           binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>
+ *
+ * @return bool <tt>true</tt> on success.
+ */
+
+template <typename TValue, typename TSpec>
+inline bool open(RankDictionary<TValue, TSpec> & dict, const char * fileName, int openMode)
+{
+    return open(getFibre(dict, FibreRanks()), fileName, openMode);
+}
+
+template <typename TValue, typename TSpec>
+inline bool open(RankDictionary<TValue, TSpec> & dict, const char * fileName)
+{
+    return open(dict, fileName, DefaultOpenMode<RankDictionary<TValue, TSpec> >::VALUE);
+}
+
+// ----------------------------------------------------------------------------
+// Function save()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RankDictionary#save
+ * @headerfile <seqan/index.h>
+ * @brief This functions saves a dictionary to disk.
+ *
+ * @signature bool save(dictionary, fileName[, openMode]);
+ *
+ * @param[in] dictionary The dictionary.
+ * @param[in] fileName   C-style character string containing the file name.
+ * @param[in] openMode   The combination of flags defining how the file should be opened.To open a file read-only,
+ *                       write-only or to read and write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
+ *                       <tt>OPEN_RDWR</tt>.To create or overwrite a file add <tt>OPEN_CREATE</tt>.To append a file
+ *                       if existing add <tt>OPEN_APPEND</tt>.To circumvent problems, files are always opened in
+ *                       binary mode. Default: <tt>OPEN_RDWR | OPEN_CREATE | OPEN_APPEND</tt>
+ *
+ * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on success.
+ */
+template <typename TValue, typename TSpec>
+inline bool save(RankDictionary<TValue, TSpec> const & dict, const char * fileName, int openMode)
+{
+    return save(getFibre(dict, FibreRanks()), fileName, openMode);
+}
+
+template <typename TValue, typename TSpec>
+inline bool save(RankDictionary<TValue, TSpec> const & dict, const char * fileName)
+{
+    return save(dict, fileName, DefaultOpenMode<RankDictionary<TValue, TSpec> >::VALUE);
+}
+
+}
+
+#endif  // INDEX_FM_RANK_DICTIONARY_BASE_H_
diff --git a/seqan/index/index_fm_rank_dictionary_bms.h b/seqan/index/index_fm_rank_dictionary_bms.h
deleted file mode 100644
index 3d555e5..0000000
--- a/seqan/index/index_fm_rank_dictionary_bms.h
+++ /dev/null
@@ -1,354 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Jochen Singer <jochen.singer@fu-berlin.de>
-// ==========================================================================
-
-//SEQAN_NO_DDDOC:do not generate documentation for this file
-
-#ifndef INDEX_FM_RANKDICTIONARY_SBM
-#define INDEX_FM_RANKDICTIONARY_SBM
-
-namespace seqan {
-
-// ==========================================================================
-// Forwards
-// ==========================================================================
-
-template <typename TValue>
-class SequenceBitMask;
-
-template<typename TSpec> 
-class RankDictionary;
-
-// ==========================================================================
-// Tags
-// ==========================================================================
-
-struct FibreBitStrings_;
-typedef Tag<FibreBitStrings_> const FibreBitStrings;
-
-/**
-.Tag.SBM
-..summary:Tag that specifies the @Spec.FMIndex@ to use a StringSet of rank support bis strings as the occurrence table.
-..cat:Index
-*/
-template <typename TSpec = void>
-class SBM;
-
-// ==========================================================================
-// Metafunctions
-// ==========================================================================
-
-/**
-.Spec.SequenceBitMask Fibres
-..cat:Index
-..summary:Tag to select a specific fibre of a SequenceBitMask.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a SequenceBitMask.
-
-..DISABLED.tag.FibreBitStrings:The string set containing a bit string for each node.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-
-// ----------------------------------------------------------------------------
-// Metafunction Fibre
-// ----------------------------------------------------------------------------
-
-template <typename TValue>
-struct Fibre<RankDictionary<SequenceBitMask<TValue> >, FibreBitStrings>
-{
-    typedef StringSet<RankSupportBitString<void> > Type;
-};
-
-template <typename TValue>
-struct Fibre<RankDictionary<SequenceBitMask<TValue> > const, FibreBitStrings>
-{
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreBitStrings>::Type const Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <typename TValue>
-struct Size<RankDictionary<SequenceBitMask<TValue> > >
-{
-    typedef typename Size<String<TValue> >::Type Type;
-};
-
-template <typename TValue>
-struct Size<RankDictionary<SequenceBitMask<TValue> > const> :
-    public Size<RankDictionary<SequenceBitMask<TValue> > > {};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <typename TValue>
-struct Value<RankDictionary<SequenceBitMask<TValue> > >
-{
-    typedef TValue Type;
-};
-
-template <typename TValue>
-struct Value<RankDictionary<SequenceBitMask<TValue> > const> :
-    public Value<RankDictionary<SequenceBitMask<TValue> > > {};
-
-// ==========================================================================
-// Classes
-// ==========================================================================
-
-// ----------------------------------------------------------------------------
-// Spec SequenceBitMask
-// ----------------------------------------------------------------------------
-
-/**
-.Spec.SequenceBitMask:
-..cat:Index
-..summary:The string set bit string dictionary is a string set of rank support bit strings for constant time acces
-of the rank of a specified character at a specified position.
-..signature:SequenceBitMask<TValue>
-..param.TValue:The value type of the .
-..include:seqan/index.h
-..remarks:This data structure is optimized for very small alphabets, such as @Spec.Dna@ or @Spec.Dna5@. Consider using a @Spec.WaveletTree@ if your alphabet size is larger.
-*/
-template <typename TValue>
-class RankDictionary<SequenceBitMask<TValue> >
-{
-    typedef typename Fibre<RankDictionary<SequenceBitMask<TValue> >, FibreBitStrings>::Type    TBitStrings;
-
-public:
-    TBitStrings bitStrings;
-
-    RankDictionary() {}
-
-    template <typename TText>
-    RankDictionary(TText const & text)
-    {
-        createRankDictionary(*this, text);
-    }
-
-    template <typename TText, typename TFreqTable>
-    RankDictionary(TText const & text, TFreqTable const & freqTable)
-    {
-        createRankDictionary(*this, text, freqTable);
-    }
-
-    template <typename TText, typename TFreqTable, typename TPrefixSumTable>
-    RankDictionary(TText const & text, TFreqTable const & freqTable, TPrefixSumTable const & prefixSumTable)
-    {
-        createRankDictionary(*this, text, freqTable, prefixSumTable);
-    }
-
-    RankDictionary & operator=(RankDictionary const & other)
-    {
-        bitStrings = other.bitStrings;
-        return *this;
-    }
-
-    bool operator==(RankDictionary const & b) const
-    {
-        typedef typename Size<typename Fibre<RankDictionary<SequenceBitMask<TValue> >, FibreBitStrings>::Type>::Type TSize;
-        
-        if (length(bitStrings) != length(b.bitStrings))
-            return false;
-        
-        for (TSize i = 0; i < length(bitStrings); ++i)
-            if (!(bitStrings[i] == b.bitStrings[i]))
-                return false;
-        
-        return true;
-    }
-};
-
-// ==========================================================================
-//Functions
-// ==========================================================================
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-
-template <typename TValue>
-inline void clear(RankDictionary<SequenceBitMask<TValue> > & dictionary)
-{
-    clear(getFibre(dictionary, FibreBitStrings()));
-}
-
-// ----------------------------------------------------------------------------
-// Function empty
-// ----------------------------------------------------------------------------
-
-template <typename TValue>
-inline bool empty(RankDictionary<SequenceBitMask<TValue> > const & dictionary)
-{
-    return empty(getFibre(dictionary, FibreBitStrings()));
-}
-
-// ----------------------------------------------------------------------------
-// Function getValue
-// ----------------------------------------------------------------------------
-
-template <typename TValue, typename TPos>
-inline TValue
-getValue(RankDictionary<SequenceBitMask<TValue> > const & dictionary, TPos pos)
-{
-    typedef typename Fibre<RankDictionary<SequenceBitMask<TValue> > const, FibreBitStrings>::Type TBitStrings;
-
-    TBitStrings & bitStrings = getFibre(dictionary, FibreBitStrings());
-    for (unsigned i = 0; i < ValueSize<TValue>::VALUE - 1; ++i)
-        if (isBitSet(bitStrings[i], pos))
-            return i;
-
-    return maxValue<TValue>();
-}
-
-template <typename TValue, typename TPos>
-inline TValue
-getValue(RankDictionary<SequenceBitMask<TValue> > & dictionary, TPos pos)
-{
-    return getValue(const_cast<RankDictionary<SequenceBitMask<TValue> > const &>(dictionary), pos);
-}
-
-// ----------------------------------------------------------------------------
-// Function getFibre
-// ----------------------------------------------------------------------------
-
-///.Function.RankDictionary#getFibre.param.fibreTag.type:Spec.SequenceBitMask Fibres
-template <typename TValue>
-inline typename Fibre<RankDictionary<SequenceBitMask<TValue> >, FibreBitStrings>::Type &
-getFibre(RankDictionary<SequenceBitMask<TValue> >& dictionary, FibreBitStrings)
-{
-    return dictionary.bitStrings;
-}
-
-template <typename TValue>
-inline typename Fibre<RankDictionary<SequenceBitMask<TValue> >, FibreBitStrings>::Type const &
-getFibre(RankDictionary<SequenceBitMask<TValue> > const &dictionary, FibreBitStrings)
-{
-    return dictionary.bitStrings;
-}
-
-// ----------------------------------------------------------------------------
-// Function countOccurrences
-// ----------------------------------------------------------------------------
-
-// This functions computes the number of occurrences of a specified character
-// up to a specified position.
-template <typename TValue, typename TCharIn, typename TPos>
-inline typename Size<RankDictionary<SequenceBitMask<TValue> > const>::Type
-countOccurrences(RankDictionary<SequenceBitMask<TValue> > const & dictionary,
-                                 TCharIn const character, TPos const pos)
-{
-    return getRank(dictionary.bitStrings[ordValue(character)], pos);
-}
-
-template < typename TValue, typename TCharIn, typename TPos>
-inline typename Size<RankDictionary<SequenceBitMask<TValue> > >::Type
-countOccurrences(RankDictionary<SequenceBitMask<TValue> > & dictionary, TCharIn const character,
-                                 TPos const pos)
-{
-    return countOccurrences(const_cast<RankDictionary<SequenceBitMask<TValue> > const &>(dictionary), character, pos);
-
-    //return getRank(dictionary.bitStrings[ordValue(character)], pos);
-}
-
-// ----------------------------------------------------------------------------
-// Function createRankDictionary
-// ----------------------------------------------------------------------------
-
-// TODO(singer): createRankDictionary
-template <typename TValue, typename TText> 
-inline void createRankDictionary(RankDictionary<SequenceBitMask<TValue> > & dictionary, TText const & text)
-{ 
-    typedef typename Fibre<RankDictionary<SequenceBitMask<TValue> >, FibreBitStrings>::Type TBitStrings;
-
-    TBitStrings & bitStrings = getFibre(dictionary, FibreBitStrings());
-    resize(bitStrings, ValueSize<TValue>::VALUE, Exact());
-
-    for (unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
-        resize(bitStrings[i], length(text), 0, Exact());
-    
-    for (unsigned i = 0; i < length(text); ++i)
-        setBitTo(bitStrings[ordValue(text[i])], i, 1);
-
-    for (unsigned i = 0; i < ValueSize<TValue>::VALUE; ++i)
-        _updateRanks(bitStrings[i]);
-}
-
-template <typename TValue, typename TSpec, typename TPrefixSumTable, typename TText> 
-inline void createRankDictionary(LfTable<SentinelRankDictionary<RankDictionary<SequenceBitMask<TValue> >, TSpec >, TPrefixSumTable> & lfTable,
-                              TText const & text)
-{
-    createRankDictionary(getFibre(getFibre(lfTable, FibreOccTable()), FibreRankDictionary()), text);
-}
-
-// ----------------------------------------------------------------------------
-// Function open
-// ----------------------------------------------------------------------------
-
-template <typename TValue>
-inline bool open(RankDictionary<SequenceBitMask<TValue> > & dictionary, const char * fileName, int openMode)
-{
-    String<char> name;
-    name = fileName;    append(name, ".rd"); if (!open(getFibre(dictionary, FibreBitStrings()), toCString(name), openMode)) return false;
-    return true;
-}
-
-template <typename TValue>
-inline bool open(RankDictionary<SequenceBitMask<TValue> > & dictionary, const char * fileName)
-{
-    return open(dictionary, fileName, DefaultOpenMode<RankDictionary<SequenceBitMask<TValue> > >::VALUE);
-}
-
-// ----------------------------------------------------------------------------
-// Function save
-// ----------------------------------------------------------------------------
-
-template <typename TValue>
-inline bool save(RankDictionary<SequenceBitMask<TValue> > const & dictionary, const char * fileName, int openMode)
-{
-    String<char> name;
-    name = fileName;    append(name, ".rd");   if (!save(getFibre(dictionary, FibreBitStrings()), toCString(name), openMode)) return false;
-    
-    return true;
-}
-
-template <typename TValue>
-inline bool save(RankDictionary<SequenceBitMask<TValue> > const & dictionary, const char * fileName)
-{
-    return save(dictionary, fileName, DefaultOpenMode<RankDictionary<SequenceBitMask<TValue> > >::VALUE);
-}
-}
-#endif  // INDEX_FM_RANKDICTIONARY_SBM
diff --git a/seqan/index/index_fm_rank_dictionary_levels.h b/seqan/index/index_fm_rank_dictionary_levels.h
new file mode 100644
index 0000000..6cb4027
--- /dev/null
+++ b/seqan/index/index_fm_rank_dictionary_levels.h
@@ -0,0 +1,898 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INDEX_FM_RANK_DICTIONARY_LEVELS_H_
+#define INDEX_FM_RANK_DICTIONARY_LEVELS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryBitMask_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec = void>
+struct RankDictionaryBitMask_;
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryWordSize_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct RankDictionaryWordSize_;
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryBitsPerBlock_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct RankDictionaryBitsPerBlock_;
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryBlock_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct RankDictionaryBlock_;
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryValues_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct RankDictionaryValues_;
+
+// ----------------------------------------------------------------------------
+// Struct RankDictionaryEntry_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct RankDictionaryEntry_;
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag LevelsRDConfig
+// ----------------------------------------------------------------------------
+
+template <typename TSize = size_t, typename TFibre = Alloc<>, unsigned LEVELS_ = 1>
+struct LevelsRDConfig : RDConfig<TSize, TFibre>
+{
+    static const unsigned LEVELS =  LEVELS_;
+};
+
+// ----------------------------------------------------------------------------
+// Tag Levels
+// ----------------------------------------------------------------------------
+
+template <typename TSpec = void, typename TConfig = LevelsRDConfig<> >
+struct Levels {};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryBitMask_
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+struct RankDictionaryBitMask_<__uint32, TSpec>
+{
+    static const __uint32 VALUE = 0x55555555;
+};
+
+template <typename TSpec>
+struct RankDictionaryBitMask_<__uint64, TSpec>
+{
+    static const __uint64 VALUE = 0x5555555555555555ull;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryWordSize_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionaryWordSize_<TValue, Levels<TSpec, TConfig> > :
+    BitsPerValue<__uint64> {};
+
+// NOTE(esiragusa): This is required on CUDA devices.
+//template <typename TValue, typename TSpec, typename TConfig>
+//struct RankDictionaryWordSize_<TValue, Levels<TSpec, TConfig> > :
+//    BitsPerValue<__uint32> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryBitsPerBlock_
+// ----------------------------------------------------------------------------
+// The number of bits per block equals the number of bits of the block summary.
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionaryBitsPerBlock_<TValue, Levels<TSpec, TConfig> > :
+    BitsPerValue<typename RankDictionaryBlock_<TValue, Levels<TSpec, TConfig> >::Type> {};
+
+// NOTE(esiragusa): This lets a Dna block to have the size of one word - one popcount per block.
+//template <typename TSpec, typename TConfig>
+//struct RankDictionaryBitsPerBlock_<Dna, Levels<TSpec, TConfig> > :
+//    RankDictionaryWordSize_<Dna, Levels<TSpec, TConfig> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryBlock_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionaryBlock_<TValue, Levels<TSpec, TConfig> >
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >         TRankDictionary_;
+    typedef typename Size<TRankDictionary_>::Type                   TSize_;
+
+    typedef Tuple<TSize_, ValueSize<TValue>::VALUE>                 Type;
+};
+
+template <typename TSpec, typename TConfig>
+struct RankDictionaryBlock_<bool, Levels<TSpec, TConfig> >
+{
+    typedef RankDictionary<bool, Levels<TSpec, TConfig> >           TRankDictionary_;
+
+    typedef typename Size<TRankDictionary_>::Type                   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RankDictionaryValues_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionaryValues_<TValue, Levels<TSpec, TConfig> >
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >                 TRankDictionary_;
+
+    typedef Tuple<TValue, TRankDictionary_::_VALUES_PER_WORD, BitPacked<> > TValues;
+    typedef typename TValues::TBitVector                                    TWord;
+    typedef Tuple<TValues, TRankDictionary_::_WORDS_PER_BLOCK>              Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Fibre
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct Fibre<RankDictionary<TValue, Levels<TSpec, TConfig> >, FibreRanks>
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >         TRankDictionary_;
+    typedef RankDictionaryEntry_<TValue, Levels<TSpec, TConfig> >   TEntry_;
+    typedef typename DefaultIndexStringSpec<TRankDictionary_>::Type TFibreSpec_;
+
+    typedef String<TEntry_, TFibreSpec_>                            Type;
+};
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Struct RankDictionaryEntry_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec = Levels<> >
+struct RankDictionaryEntry_ {};
+
+// ----------------------------------------------------------------------------
+// Struct Levels RankDictionaryEntry_
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionaryEntry_<TValue, Levels<TSpec, TConfig> >
+{
+    // A bit-compressed block of TValue symbols.
+    typename RankDictionaryValues_<TValue, Levels<TSpec, TConfig> >::Type   values;
+
+    // A summary of counts for each block of TValue symbols.
+    typename RankDictionaryBlock_<TValue, Levels<TSpec, TConfig> >::Type    block;
+};
+
+// ----------------------------------------------------------------------------
+// Class Levels RankDictionary
+// ----------------------------------------------------------------------------
+// TODO(esiragusa): update doc
+/*!
+ * @class TwoLevelRankDictionary
+ * @extends RankDictionary
+ * @headerfile <seqan/index.h>
+ *
+ * @brief A TwoLevelRankDictionary is a @link RankDictionary @endlink consisting of two levels.
+ *
+ * @signature template <typename TValue, typename TSpec, typename TConfig>
+ *            class RankDictionary<TValue, WaveletTree<TSpec> >;
+ *
+ * @tparam TValue The alphabet type of the wavelet tree.
+ * @tparam TSpec  A tag for specialization purposes. Default: <tt>void</tt>
+ *
+ * This @link RankDictionary @endlink consists of two levels of rank
+ * infromation, in which one stores information of blocks and the other
+ * information until a specified block. Combining those two informations
+ * leads to constant rank dictionary look ups.
+ */
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionary<TValue, Levels<TSpec, TConfig> >
+{
+    // ------------------------------------------------------------------------
+    // Constants
+    // ------------------------------------------------------------------------
+
+    static const unsigned _BITS_PER_VALUE   = BitsPerValue<TValue>::VALUE;
+    static const unsigned _BITS_PER_BLOCK   = RankDictionaryBitsPerBlock_<TValue, Levels<TSpec, TConfig> >::VALUE;
+    static const unsigned _BITS_PER_WORD    = Min<RankDictionaryWordSize_<TValue, Levels<TSpec, TConfig> >::VALUE, _BITS_PER_BLOCK>::VALUE;
+    static const unsigned _VALUES_PER_WORD  = _BITS_PER_WORD  / _BITS_PER_VALUE;
+    static const unsigned _VALUES_PER_BLOCK = _BITS_PER_BLOCK / _BITS_PER_VALUE;
+    static const unsigned _WORDS_PER_BLOCK  = _BITS_PER_BLOCK / _BITS_PER_WORD;
+
+    // ------------------------------------------------------------------------
+    // Fibres
+    // ------------------------------------------------------------------------
+
+    typename Fibre<RankDictionary, FibreRanks>::Type    ranks;
+    typename Size<RankDictionary>::Type                 _length;
+    // TODO(esiragusa): open/save _length or remove it.
+
+    // ------------------------------------------------------------------------
+    // Constructors
+    // ------------------------------------------------------------------------
+
+    RankDictionary() :
+        _length(0)
+    {}
+
+    template <typename TText>
+    RankDictionary(TText const & text) :
+        _length(0)
+    {
+        createRankDictionary(*this, text);
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function loadAndCache()
+// ----------------------------------------------------------------------------
+// TODO(esiragusa): move loadAndCache() in misc_cuda.h
+
+template <typename TValue>
+SEQAN_HOST_DEVICE inline TValue
+loadAndCache(TValue const & value)
+{
+#if __CUDA_ARCH__ >= 350
+    return __ldg(&value);
+#else
+    return value;
+#endif
+}
+
+// ----------------------------------------------------------------------------
+// Function loadAndCache()                                              [Tuple]
+// ----------------------------------------------------------------------------
+// TODO(esiragusa): move loadAndCache() in misc_cuda.h
+
+template <typename TValue, unsigned SIZE, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline Tuple<TValue, SIZE, TSpec>
+loadAndCache(Tuple<TValue, SIZE, TSpec> const & tuple)
+{
+#if __CUDA_ARCH__ >= 350
+    typedef Tuple<TValue, SIZE, TSpec>  TTuple;
+
+    const unsigned UINTS = BytesPerValue<TTuple>::VALUE / 4;
+
+    union { TTuple x; uint4 y[UINTS]; } tmp;
+
+    for (unsigned u = 0; u < UINTS; ++u)
+        tmp.y[u] = __ldg(reinterpret_cast<uint4 const *>(&tuple) + u);
+
+    return tmp.x;
+#else
+    return tuple;
+#endif
+}
+
+// ----------------------------------------------------------------------------
+// Function loadAndCache()                               [RankDictionaryEntry_]
+// ----------------------------------------------------------------------------
+//
+//template <typename TValue, typename TSpec, typename TConfig>
+//SEQAN_HOST_DEVICE inline RankDictionaryEntry_<TValue, Levels<TSpec, TConfig> >
+//loadAndCache(RankDictionaryEntry_<TValue, Levels<TSpec, TConfig> > const & entry)
+//{
+//#if __CUDA_ARCH__ >= 350
+//    typedef RankDictionaryEntry_<TValue, Levels<TSpec, TConfig> >   TEntry;
+//
+//    const unsigned UINTS = BytesPerValue<TEntry>::VALUE / 4;
+//
+//    union { TEntry x; uint4 y[UINTS]; } tmp;
+//
+//    for (unsigned u = 0; u < UINTS; ++u)
+//        tmp.y[u] = __ldg(reinterpret_cast<uint4 const *>(&entry) + u);
+//
+//    return tmp.x;
+//#else
+//    return entry;
+//#endif
+//}
+
+//template <unsigned SIZE, typename TSpec, typename TConfig>
+//SEQAN_HOST_DEVICE inline Tuple<Tuple<Dna, SIZE, BitPacked<> >, 4, TSpec>
+//loadAndCache(Tuple<Tuple<Dna, SIZE, BitPacked<> >, 4, TSpec> const & values)
+//{
+//#if __CUDA_ARCH__ >= 350
+//    Tuple<Tuple<Dna, SIZE, BitPacked<> >, 4, TSpec> tmp;
+//
+//    uint4 t = __ldg((uint4 *)values.i);
+//    tmp.i[0].i = t.x;
+//    tmp.i[1].i = t.y;
+//    tmp.i[2].i = t.z;
+//    tmp.i[3].i = t.w;
+//
+//    return tmp;
+//#else
+//    return values;
+//#endif
+//}
+
+//template <unsigned SIZE, typename TSpec, typename TConfig>
+//SEQAN_HOST_DEVICE inline Tuple<Tuple<bool, SIZE, BitPacked<> >, 1, TSpec>
+//loadAndCache(Tuple<Tuple<bool, SIZE, BitPacked<> >, 1, TSpec> const & values)
+//{
+//#if __CUDA_ARCH__ >= 350
+//    Tuple<Tuple<bool, SIZE, BitPacked<> >, 1, TSpec> tmp;
+//
+//    uint2 t = __ldg((uint2 *)values.i);
+//    tmp.i[0].i = t.x;
+//    tmp.i[1].i = t.y;
+//
+//    return tmp;
+//#else
+//    return values;
+//#endif
+//}
+
+// ----------------------------------------------------------------------------
+// Function _toPosInWord()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+_toPosInWord(RankDictionary<TValue, Levels<TSpec, TConfig> > const & /* dict */, TPos posInBlock)
+{
+    return posInBlock % RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_WORD;
+}
+
+// ----------------------------------------------------------------------------
+// Function _toWordPos()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+_toWordPos(RankDictionary<TValue, Levels<TSpec, TConfig> > const & /* dict */, TPos posInBlock)
+{
+    return posInBlock / RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_WORD;
+}
+
+// ----------------------------------------------------------------------------
+// Function _toPosInBlock()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+_toPosInBlock(RankDictionary<TValue, Levels<TSpec, TConfig> > const & /* dict */, TPos pos)
+{
+    return pos % RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_BLOCK;
+}
+
+// ----------------------------------------------------------------------------
+// Function _toBlockPos()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+_toBlockPos(RankDictionary<TValue, Levels<TSpec, TConfig> > const & /* dict */, TPos pos)
+{
+    return pos / RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_BLOCK;
+}
+
+// ----------------------------------------------------------------------------
+// Function _toPos()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TBlockPos>
+inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+_toPos(RankDictionary<TValue, Levels<TSpec, TConfig> > const & /* dict */, TBlockPos blockPos)
+{
+    return blockPos * RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_BLOCK;
+}
+
+// ----------------------------------------------------------------------------
+// Function _valuesAt()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TBlockPos, typename TWordPos>
+SEQAN_HOST_DEVICE inline typename RankDictionaryValues_<TValue, Levels<TSpec, TConfig> >::TValues &
+_valuesAt(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TBlockPos blockPos, TWordPos wordPos)
+{
+    return dict.ranks[blockPos].values[wordPos];
+}
+
+template <typename TValue, typename TSpec, typename TConfig, typename TBlockPos, typename TWordPos>
+SEQAN_HOST_DEVICE inline typename RankDictionaryValues_<TValue, Levels<TSpec, TConfig> >::TValues const &
+_valuesAt(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict, TBlockPos blockPos, TWordPos wordPos)
+{
+    return dict.ranks[blockPos].values[wordPos];
+}
+
+// ----------------------------------------------------------------------------
+// Function _valuesAt()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename RankDictionaryValues_<TValue, Levels<TSpec, TConfig> >::Type &
+_valuesAt(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TPos pos)
+{
+    return dict.ranks[_toBlockPos(dict, pos)].values;
+}
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename RankDictionaryValues_<TValue, Levels<TSpec, TConfig> >::Type const &
+_valuesAt(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict, TPos pos)
+{
+    return dict.ranks[_toBlockPos(dict, pos)].values;
+}
+
+// ----------------------------------------------------------------------------
+// Function _blockAt()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename RankDictionaryBlock_<TValue, Levels<TSpec, TConfig> >::Type &
+_blockAt(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TPos pos)
+{
+    return dict.ranks[_toBlockPos(dict, pos)].block;
+}
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename RankDictionaryBlock_<TValue, Levels<TSpec, TConfig> >::Type const &
+_blockAt(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict, TPos pos)
+{
+    return dict.ranks[_toBlockPos(dict, pos)].block;
+}
+
+// ----------------------------------------------------------------------------
+// Function _padValues()
+// ----------------------------------------------------------------------------
+// Set values beyond length(dict) but still within the end of the ranks fibre.
+
+template <typename TValue, typename TSpec, typename TConfig>
+inline void _padValues(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict)
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >         TRankDictionary;
+    typedef typename Size<TRankDictionary>::Type                    TSize;
+
+    TSize beginPos = length(dict);
+    TSize endPos   = length(dict.ranks) * TRankDictionary::_VALUES_PER_BLOCK;
+
+    for (TSize pos = beginPos; pos < endPos; ++pos)
+        setValue(dict, pos, TValue());
+}
+
+// ----------------------------------------------------------------------------
+// Function _clearBlockAt()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+inline void _clearBlockAt(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TPos pos)
+{
+    clear(_blockAt(dict, pos));
+}
+
+// ----------------------------------------------------------------------------
+// Function _clearBlockAt(bool)
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TPos>
+inline void _clearBlockAt(RankDictionary<bool, Levels<TSpec, TConfig> > & dict, TPos pos)
+{
+    _blockAt(dict, pos) = 0u;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getBlockRank()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TBlock, typename TPos, typename TChar>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > const>::Type
+_getBlockRank(RankDictionary<TValue, Levels<TSpec, TConfig> > const & /* dict */, TBlock const & block, TPos /* pos */, TChar c)
+{
+    return loadAndCache(block[ordValue(c)]);
+//    return block[ordValue(c)];
+}
+
+// ----------------------------------------------------------------------------
+// Function _getBlockRank(bool)
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TBlock, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<bool, Levels<TSpec, TConfig> > const>::Type
+_getBlockRank(RankDictionary<bool, Levels<TSpec, TConfig> > const & dict, TBlock const & block, TPos pos, bool c)
+{
+    TBlock rank = loadAndCache(block);
+
+    // If c == false then return the complementary rank.
+    return c ? rank : pos - _toPosInBlock(dict, pos) - rank;
+
+//    return c ? block : pos - _toPosInBlock(dict, pos) - block;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getWordRank()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): This version is generic but absymally slow - only for testing purposes.
+
+template <typename TValue, typename TSpec, typename TConfig, typename TWord, typename TPosInWord>
+inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > const>::Type
+_getWordRank(RankDictionary<TValue, Levels<TSpec, TConfig> > const & /* dict */,
+             TWord const & word,
+             TPosInWord posInWord,
+             TValue c)
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >                           TRankDictionary;
+    typedef typename RankDictionaryValues_<TValue, Levels<TSpec, TConfig> >::TValues  TRankDictionaryValues;
+    typedef typename Size<TRankDictionary>::Type                                TSize;
+
+    TRankDictionaryValues values;
+    values.i = word;
+
+    TSize valueRank = 0;
+
+    for (TSize i = 0; i <= posInWord; ++i)
+        valueRank += isEqual(values[i], c);
+
+    return valueRank;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getWordRank(Dna)
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TWord, typename TPosInWord>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<Dna, Levels<TSpec, TConfig> > const>::Type
+_getWordRank(RankDictionary<Dna, Levels<TSpec, TConfig> > const & /* dict */,
+             TWord const & values,
+             TPosInWord posInWord,
+             Dna c)
+{
+    typedef RankDictionary<Dna, Levels<TSpec, TConfig> >                TRankDictionary;
+    typedef typename Size<TRankDictionary>::Type                        TSize;
+
+    // Clear the last positions.
+    TWord word = hiBits(values, TRankDictionary::_BITS_PER_VALUE * (posInWord + 1));
+
+    // And matches when c == G|T.
+    TWord odd  = ((ordValue(c) & ordValue(Dna('G'))) ? word : ~word) >> 1;
+
+    // And matches when c == C|T.
+    TWord even = ((ordValue(c) & ordValue(Dna('C'))) ? word : ~word);
+
+    // Apply the interleaved mask.
+    TWord mask = odd & even & RankDictionaryBitMask_<TWord>::VALUE;
+
+    // The rank is the sum of the bits on.
+    TSize valueRank = popCount(mask);
+
+    // If c == A then masked character positions must be subtracted from the count.
+    if (c == Dna('A')) valueRank -= TRankDictionary::_VALUES_PER_WORD - (posInWord + 1);
+
+    return valueRank;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getWordRank(bool)
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TWord, typename TPosInWord>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<bool, Levels<TSpec, TConfig> > const>::Type
+_getWordRank(RankDictionary<bool, Levels<TSpec, TConfig> > const & /* dict */,
+             TWord const & values,
+             TPosInWord posInWord,
+             bool c)
+{
+    // Negate the values to compute the rank of zero.
+    TWord word = c ? values : ~values;
+
+    // Clear the last positions.
+    TWord mask = hiBits(word, posInWord + 1);
+
+    // Get the sum of the bits on.
+    return popCount(mask);
+}
+
+// ----------------------------------------------------------------------------
+// Function _getWordRank()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TWord>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > const>::Type
+_getWordRank(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict, TWord const & values, TValue c)
+{
+    return _getWordRank(dict, values, RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_WORD - 1, c);
+}
+
+// ----------------------------------------------------------------------------
+// Function _getValueRank()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TValues, typename TPosInBlock>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > const>::Type
+_getValueRank(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict,
+              TValues const & values,
+              TPosInBlock posInBlock,
+              TValue c)
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> > TRankDictionary;
+    typedef typename Size<TRankDictionary>::Type            TSize;
+
+    TSize wordPos    = _toWordPos(dict, posInBlock);
+    TSize posInWord  = _toPosInWord(dict, posInBlock);
+
+    TSize valueRank = 0;
+
+    // NOTE(esiragusa): writing the loop in this form prevents the compiler from unrolling it.
+//    for (TSize wordPrevPos = 0; wordPrevPos < wordPos; ++wordPrevPos)
+//      valueRank += _getWordRank(dict, values[wordPrevPos].i, c);
+
+    for (TSize wordPrevPos = 0; wordPrevPos < TRankDictionary::_WORDS_PER_BLOCK; ++wordPrevPos)
+      if (wordPrevPos < wordPos) valueRank += _getWordRank(dict, values[wordPrevPos].i, c);
+
+    valueRank += _getWordRank(dict, values[wordPos].i, posInWord, c);
+
+    return valueRank;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getValuesRanks()
+// ----------------------------------------------------------------------------
+// TODO(esiragusa): Specialize _getValuesRanks() for Dna.
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+inline typename RankDictionaryBlock_<TValue, Levels<TSpec, TConfig> >::Type
+_getValuesRanks(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict, TPos pos)
+{
+    typedef typename RankDictionaryBlock_<TValue, Levels<TSpec, TConfig> >::Type    TBlock;
+    typedef typename ValueSize<TValue>::Type                                        TValueSize;
+
+    TBlock blockRank;
+
+    for (TValueSize c = 0; c < ValueSize<TValue>::VALUE; ++c)
+        assignValue(blockRank, c, _getValueRank(dict, _valuesAt(dict, pos), _toPosInBlock(dict, pos), TValue(c)));
+
+    return blockRank;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getValuesRanks(bool)
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TPos>
+inline typename RankDictionaryBlock_<bool, Levels<TSpec, TConfig> >::Type
+_getValuesRanks(RankDictionary<bool, Levels<TSpec, TConfig> > const & dict, TPos pos)
+{
+    return _getValueRank(dict, _valuesAt(dict, pos), _toPosInBlock(dict, pos), true);
+}
+
+// ----------------------------------------------------------------------------
+// Function getRank()
+// ----------------------------------------------------------------------------
+template <typename TValue, typename TSpec, typename TConfig, typename TPos, typename TChar>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > const>::Type
+getRank(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict, TPos pos, TChar c)
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> > const           TRankDictionary;
+    typedef typename Fibre<TRankDictionary, FibreRanks>::Type               TFibreRanks;
+    typedef typename Value<TFibreRanks>::Type                               TRankEntry;
+//    typedef typename RankDictionaryBlock_<TValue, Levels<TSpec, TConfig> >::Type  TRankBlock;
+    typedef typename RankDictionaryValues_<TValue, Levels<TSpec, TConfig> >::Type TRankValues;
+    typedef typename Size<TRankDictionary>::Type                            TSize;
+
+    TSize blockPos   = _toBlockPos(dict, pos);
+    TSize posInBlock = _toPosInBlock(dict, pos);
+
+//    TRankEntry entry = loadAndCache(dict.ranks[blockPos]);
+    TRankEntry const & entry = dict.ranks[blockPos];
+
+//    TRankBlock block = loadAndCache(entry.block);
+    TRankValues values = loadAndCache(entry.values);
+
+    return _getBlockRank(dict, entry.block, pos, static_cast<TValue>(c)) +
+           _getValueRank(dict, values, posInBlock, static_cast<TValue>(c));
+}
+
+// ----------------------------------------------------------------------------
+// Function getRank(bool)
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<bool, Levels<TSpec, TConfig> > const>::Type
+getRank(RankDictionary<bool, Levels<TSpec, TConfig> > const & dict, TPos pos)
+{
+    return getRank(dict, pos, true);
+}
+
+// ----------------------------------------------------------------------------
+// Function getValue()
+// ----------------------------------------------------------------------------
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Value<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+getValue(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TPos pos)
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >             TRankDictionary;
+    typedef typename Size<TRankDictionary>::Type                        TSize;
+
+    TSize blockPos   = _toBlockPos(dict, pos);
+    TSize posInBlock = _toPosInBlock(dict, pos);
+    TSize wordPos    = _toWordPos(dict, posInBlock);
+    TSize posInWord  = _toPosInWord(dict, posInBlock);
+
+    return _valuesAt(dict, blockPos, wordPos)[posInWord];
+}
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Value<RankDictionary<TValue, Levels<TSpec, TConfig> > const>::Type
+getValue(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict, TPos pos)
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >             TRankDictionary;
+    typedef typename Size<TRankDictionary>::Type                        TSize;
+
+    TSize blockPos   = _toBlockPos(dict, pos);
+    TSize posInBlock = _toPosInBlock(dict, pos);
+    TSize wordPos    = _toWordPos(dict, posInBlock);
+    TSize posInWord  = _toPosInWord(dict, posInBlock);
+
+    return _valuesAt(dict, blockPos, wordPos)[posInWord];
+}
+
+// ----------------------------------------------------------------------------
+// Function setValue()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos, typename TChar>
+inline void setValue(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TPos pos, TChar c)
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >             TRankDictionary;
+    typedef typename Size<TRankDictionary>::Type                        TSize;
+
+    TSize blockPos   = _toBlockPos(dict, pos);
+    TSize posInBlock = _toPosInBlock(dict, pos);
+    TSize wordPos    = _toWordPos(dict, posInBlock);
+    TSize posInWord  = _toPosInWord(dict, posInBlock);
+
+    assignValue(_valuesAt(dict, blockPos, wordPos), posInWord, static_cast<TValue>(c));
+}
+
+// ----------------------------------------------------------------------------
+// Function appendValue()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): Better not to have appendValue() - it is not efficient - and thus neither length().
+
+template <typename TValue, typename TSpec, typename TConfig, typename TChar, typename TExpand>
+inline void appendValue(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TChar c, Tag<TExpand> const tag)
+{
+    resize(dict, length(dict) + 1, tag);
+    setValue(dict, length(dict) - 1, c);
+}
+
+// ----------------------------------------------------------------------------
+// Function updateRanks()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+inline void updateRanks(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict)
+{
+    typedef RankDictionary<TValue, Levels<TSpec, TConfig> >         TRankDictionary;
+    typedef typename Size<TRankDictionary>::Type                    TSize;
+    typedef typename Fibre<TRankDictionary, FibreRanks>::Type       TFibreRanks;
+    typedef typename Iterator<TFibreRanks, Standard>::Type          TFibreRanksIter;
+
+    if (empty(dict)) return;
+
+    TFibreRanksIter ranksBegin = begin(dict.ranks, Standard());
+    TFibreRanksIter ranksEnd = end(dict.ranks, Standard());
+
+    // Insures the first block ranks start from zero.
+    _clearBlockAt(dict, 0u);
+
+    // Clear the uninitialized values.
+    _padValues(dict);
+
+    // Iterate through the blocks.
+    for (TFibreRanksIter ranksIt = ranksBegin; ranksIt != ranksEnd - 1; ++ranksIt)
+    {
+        TSize blockPos = ranksIt - ranksBegin;
+        TSize curr = _toPos(dict, blockPos);
+        TSize next = _toPos(dict, blockPos + 1);
+
+        _blockAt(dict, next) = _blockAt(dict, curr) + _getValuesRanks(dict, next - 1);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+length(RankDictionary<TValue, Levels<TSpec, TConfig> > const & dict)
+{
+    return dict._length;
+}
+
+// ----------------------------------------------------------------------------
+// Function reserve()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TSize, typename TExpand>
+inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+reserve(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TSize newCapacity, Tag<TExpand> const tag)
+{
+    return reserve(dict.ranks, (newCapacity + RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_BLOCK - 1) /
+                               RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_BLOCK, tag);
+}
+
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TSize, typename TExpand>
+inline typename Size<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+resize(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, TSize newLength, Tag<TExpand> const tag)
+{
+    dict._length = newLength;
+    return resize(dict.ranks, (newLength + RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_BLOCK - 1) /
+                              RankDictionary<TValue, Levels<TSpec, TConfig> >::_VALUES_PER_BLOCK, tag);
+}
+
+}
+
+#endif  // INDEX_FM_RANK_DICTIONARY_LEVELS_H_
diff --git a/seqan/index/index_fm_rank_dictionary_naive.h b/seqan/index/index_fm_rank_dictionary_naive.h
new file mode 100644
index 0000000..c4c19f1
--- /dev/null
+++ b/seqan/index/index_fm_rank_dictionary_naive.h
@@ -0,0 +1,236 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INDEX_FM_RANK_DICTIONARY_NAIVE_H_
+#define INDEX_FM_RANK_DICTIONARY_NAIVE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag Naive
+// ----------------------------------------------------------------------------
+
+template <typename TSpec = void, typename TConfig = RDConfig<> >
+struct Naive {};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Fibre
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct Fibre<RankDictionary<TValue, Naive<TSpec, TConfig> >, FibreRanks>
+{
+    typedef RankDictionary<TValue, Naive<TSpec, TConfig> >          TRankDictionary_;
+    typedef typename Size<TRankDictionary_>::Type                   TSize_;
+    typedef typename DefaultIndexStringSpec<TRankDictionary_>::Type TFibreSpec_;
+
+    typedef String<TSize_, TFibreSpec_>                             Type;
+};
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class Naive RankDictionary
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionary<TValue, Naive<TSpec, TConfig> >
+{
+    // ------------------------------------------------------------------------
+    // Fibres
+    // ------------------------------------------------------------------------
+
+    typename Fibre<RankDictionary, FibreRanks>::Type    ranks;
+
+    // ------------------------------------------------------------------------
+    // Constructors
+    // ------------------------------------------------------------------------
+
+    RankDictionary() {}
+
+    template <typename TText>
+    RankDictionary(TText const & text)
+    {
+        createRankDictionary(*this, text);
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function getRank()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Size<RankDictionary<bool, Naive<TSpec, TConfig> > const>::Type
+getRank(RankDictionary<bool, Naive<TSpec, TConfig> > const & dict, TPos pos, bool c = true)
+{
+    typedef RankDictionary<bool, Naive<TSpec, TConfig> > const                       TRankDictionary;
+    typedef typename Fibre<TRankDictionary, FibreRanks>::Type               TFibreRanks;
+    typedef typename Iterator<TFibreRanks, Standard>::Type                  TFibreRanksIterator;
+
+    TFibreRanksIterator ranksBegin = begin(dict.ranks, Standard());
+    TFibreRanksIterator ranksEnd   = end(dict.ranks, Standard());
+    TFibreRanksIterator ranksIt    = ranksBegin;
+
+    for (; ranksIt != ranksEnd && value(ranksIt) <= pos; ++ranksIt) ;
+
+    return c ? ranksIt - ranksBegin : pos + 1 - (ranksIt - ranksBegin);
+}
+
+// ----------------------------------------------------------------------------
+// Function getValue()
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Value<RankDictionary<bool, Naive<TSpec, TConfig> > >::Type
+getValue(RankDictionary<bool, Naive<TSpec, TConfig> > & dict, TPos pos)
+{
+    typedef RankDictionary<bool, Naive<TSpec, TConfig> > const                       TRankDictionary;
+    typedef typename Fibre<TRankDictionary, FibreRanks>::Type               TFibreRanks;
+    typedef typename Iterator<TFibreRanks, Standard>::Type                  TFibreRanksIterator;
+
+    TFibreRanksIterator ranksBegin = begin(dict.ranks, Standard());
+    TFibreRanksIterator ranksEnd   = end(dict.ranks, Standard());
+    TFibreRanksIterator ranksIt    = ranksBegin;
+
+    for (; ranksIt != ranksEnd && value(ranksIt) < pos; ++ranksIt) ;
+
+    return ranksIt != ranksEnd && value(ranksIt) == pos;
+}
+
+template <typename TSpec, typename TConfig, typename TPos>
+SEQAN_HOST_DEVICE inline typename Value<RankDictionary<bool, Naive<TSpec, TConfig> > const>::Type
+getValue(RankDictionary<bool, Naive<TSpec, TConfig> > const & dict, TPos pos)
+{
+    typedef RankDictionary<bool, Naive<TSpec, TConfig> > const                       TRankDictionary;
+    typedef typename Fibre<TRankDictionary, FibreRanks>::Type               TFibreRanks;
+    typedef typename Iterator<TFibreRanks, Standard>::Type                  TFibreRanksIterator;
+
+    TFibreRanksIterator ranksBegin = begin(dict.ranks, Standard());
+    TFibreRanksIterator ranksEnd   = end(dict.ranks, Standard());
+    TFibreRanksIterator ranksIt    = ranksBegin;
+
+    for (; ranksIt != ranksEnd && value(ranksIt) < pos; ++ranksIt) ;
+
+    return ranksIt != ranksEnd && value(ranksIt) == pos;
+}
+
+// ----------------------------------------------------------------------------
+// Function setValue()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TPos, typename TChar>
+inline void setValue(RankDictionary<TValue, Naive<TSpec, TConfig> > & dict, TPos pos, TChar c)
+{
+//    SEQAN_ASSERT_GT(pos, (TPos)back(dict.ranks));
+
+    if (c == false) return;
+
+    appendValue(dict.ranks, pos);
+}
+
+// ----------------------------------------------------------------------------
+// Function appendValue()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): Better not to have appendValue() - it is not efficient - and thus neither length().
+
+template <typename TSpec, typename TConfig, typename TChar, typename TExpand>
+inline void appendValue(RankDictionary<bool, Naive<TSpec, TConfig> > & dict, TChar c, Tag<TExpand> const tag)
+{
+    if (c == false) return;
+
+// NOTE(esiragusa): RankDictionary's resize() is desabled.
+//    resize(dict, length(dict) + 1, tag);
+    resize(dict.ranks, length(dict) + 1, tag);
+    setValue(dict, length(dict) - 1, c);
+}
+
+// ----------------------------------------------------------------------------
+// Function updateRanks()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+inline void updateRanks(RankDictionary<TValue, Naive<TSpec, TConfig> > & /* dict */) {}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+inline typename Size<RankDictionary<TValue, Naive<TSpec, TConfig> > >::Type
+length(RankDictionary<TValue, Naive<TSpec, TConfig> > const & dict)
+{
+    return length(dict.ranks);
+}
+
+// ----------------------------------------------------------------------------
+// Function reserve()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig, typename TSize, typename TExpand>
+inline typename Size<RankDictionary<TValue, Naive<TSpec, TConfig> > >::Type
+reserve(RankDictionary<TValue, Naive<TSpec, TConfig> > & dict, TSize newCapacity, Tag<TExpand> const tag)
+{
+   return reserve(dict.ranks, newCapacity, tag);
+}
+
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): disabled because LF::_createBwt() resizes the rank dict to the bwt length.
+
+template <typename TValue, typename TSpec, typename TConfig, typename TSize, typename TExpand>
+inline typename Size<RankDictionary<TValue, Naive<TSpec, TConfig> > >::Type
+resize(RankDictionary<TValue, Naive<TSpec, TConfig> > & dict, TSize /* newLength */, Tag<TExpand> const /* tag */)
+{
+    return length(dict);
+//    return resize(dict.ranks, newLength, tag);
+}
+
+}
+
+#endif  // INDEX_FM_RANK_DICTIONARY_NAIVE_H_
diff --git a/seqan/index/index_fm_rank_dictionary_wt.h b/seqan/index/index_fm_rank_dictionary_wt.h
old mode 100755
new mode 100644
index 5139aab..4d956a3
--- a/seqan/index/index_fm_rank_dictionary_wt.h
+++ b/seqan/index/index_fm_rank_dictionary_wt.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,172 +41,132 @@
 namespace seqan {
 
 // ==========================================================================
-//Forwards
+// Tags
 // ==========================================================================
 
-struct FibreBitStrings_;
-struct FibreTreeStructure_;
-struct FibreDollarPosition_;
-struct FibreOccTable_;
-struct FibreRankDictionary_;
+// --------------------------------------------------------------------------
+// Tag WaveletTreeConfig
+// --------------------------------------------------------------------------
 
-template <typename TValue>
-struct WaveletTree;
+template <typename TSize = size_t, typename TFibre = Alloc<>, unsigned LEVELS = 1, unsigned ARITY_ = 2>
+struct WTRDConfig : LevelsRDConfig<TSize, TFibre, LEVELS>
+{
+    static const unsigned ARITY = ARITY_;
+};
 
-// ==========================================================================
-// Tags
-// ==========================================================================
+// --------------------------------------------------------------------------
+// Tag WaveletTree
+// --------------------------------------------------------------------------
+
+template <typename TSpec = void, typename TConfig = WTRDConfig<> >
+struct WaveletTree {};
 
-typedef Tag<FibreTreeStructure_> const FibreTreeStructure;
-typedef Tag<FibreBitStrings_> const FibreBitStrings;
-typedef Tag<FibreDollarPosition_> const FibreDollarPosition;
-typedef Tag<FibreOccTable_> const FibreOccTable;
-typedef Tag<FibreRankDictionary_> const FibreRankDictionary;
+struct FibreTreeStructure_;
+typedef Tag<FibreTreeStructure_>    const FibreTreeStructure;
 
 // ==========================================================================
 // Metafunctions
 // ==========================================================================
-/**
-.Tag.WaveletTree Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Spec.WaveletTree@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a @Spec.WaveletTree@.
-..cat:Spec.WaveletTree
-
-..tag.FibreBitStrings:The string set containing a bit string for each node.
-
-..tag.FibreTreeStructure:The wavelet tree structure of the wavelet tree.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
+/*!
+ * @defgroup WaveletTreeFibres WaveletTree Fibres
+ * @brief Tag to select a specific fibre (e.g. table, object, ...) of a @link WaveletTree @endlink.
+ *
+ * These tags can be used to get @link Fibre Fibres @endlink of a @link WaveletTree @endlink.
+ *
+ * @see Fibre
+ * @see Index#getFibre
+ *
+ * @tag WaveletTreeFibres#FibreTreeStructure
+ * @brief The wavelet tree structure of the wavelet tree.
+ *
+ * @tag WaveletTreeFibres#FibreRanks
+ * @brief A string set containing a rank support bit string for each node in the tree.
+ *
+ */
 
 // ----------------------------------------------------------------------------
 // Metafunction Fibre
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Fibre.param.TContainer.type:Class.RankDictionary
-///.Metafunction.Fibre.param.TSpec.type:Tag.WaveletTree Fibres
-/*
-.Metafunction.Fibre:
-..summary:Type of a specific FMIndex member (fibre).
-..signature:Fibre<RankDictionary<WaveletTree<TValue> >, TFibreSpec>::Type
-..class:Spec.FMIndex
-..cat:Index
-..param.TValue:The character type of the @Class.String@ the wavelet tree represents.
-..param.TFibreSpec:Tag to specify the fibre.
-...type:Tag.WaveletTree Fibres
-..returns:Fibre type.
-..remarks:Some containers, such as @Spec.FMIndex@, can be seen as a bundle consisting of various fibres. Because not 
-every table is a fibre we did not call them tables, however, in many cases one can think of fibres as tables. The 
-fibre interface was designed to unify the access to the members of the different fibres.
-To get a reference or the type of a specific fibre use @Function.getFibre@ or @Metafunction.Fibre@.		
-..include:seqan/index.h
-*/
-
-template <typename TValue>
-struct Fibre<RankDictionary<WaveletTree<TValue> >, FibreBitStrings>
+/*!
+ * @class WaveletTree
+ * @extends RankDictionary
+ * @headerfile <seqan/index.h>
+ *
+ * @brief A WaveletTree is a hierarchical @link RankDictionary @endlink.
+ *
+ * @signature template <typename TValue, typename TSpec, typename TConfig>
+ *            class RankDictionary<TValue, WaveletTree<TSpec, TConfig> >;
+ *
+ * @tparam TValue The alphabet type of the wavelet tree.
+ * @tparam TSpec A tag for specialization purposes. Default: <tt>void</tt>
+ *
+ * The nodes of a wavelet tree consist of a bit string as well as a character c.
+ * In each level of the tree, characters smaller than c are represented as a 0
+ * while character greater or equal to c are represented with a 1. The
+ * characters represented by a 0 form the string to be represented by the left
+ * subtree while characters represented by a 1 form the string of the right
+ * subtree. Therefore, only the bit string of the root node represents all
+ * characters while all other nodes represent subsets.
+ */
+// TODO(esiragusa): update doc
+
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct Fibre<RankDictionary<TValue, WaveletTree<TSpec, TConfig> >, FibreRanks>
 {
-    typedef StringSet<RankSupportBitString<void> > Type;
+    // TODO(esiragusa): use String and investigate issues with open/save() and valgrind.
+    typedef StringSet<RankDictionary<bool, Levels<TSpec, TConfig> > > Type;
 };
 
-template <typename TValue>
-struct Fibre<RankDictionary<WaveletTree<TValue> > const, FibreBitStrings>
-{
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreBitStrings>::Type const Type;
-};
-
-template <typename TValue>
-struct Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>
+template <typename TValue, typename TSpec, typename TConfig>
+struct Fibre<RankDictionary<TValue, WaveletTree<TSpec, TConfig> >, FibreTreeStructure>
 {
     typedef typename MakeUnsigned<TValue>::Type TUChar_;
     typedef RightArrayBinaryTree<TUChar_, void>  Type;
 };
 
-template <typename TValue>
-struct Fibre<RankDictionary<WaveletTree<TValue> > const, FibreTreeStructure>
-{
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>::Type const Type;
-};
-
 // ----------------------------------------------------------------------------
-// Metafunction Size
+// Metafunction Value
 // ----------------------------------------------------------------------------
- 
-template <typename TValue>
-struct Size<RankDictionary<WaveletTree<TValue> > >
+// TODO(esiragusa): remove this - const version should be Value const (as by default)
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct Value<RankDictionary<TValue, WaveletTree<TSpec, TConfig> > >
 {
-    typedef typename Size<String<TValue> >::Type Type;
+    typedef TValue Type;
 };
 
-template <typename TValue>
-struct Size<RankDictionary<WaveletTree<TValue> > const> :
-    public Size<RankDictionary<WaveletTree<TValue> > > {};
+template <typename TValue, typename TSpec, typename TConfig>
+struct Value<RankDictionary<TValue, WaveletTree<TSpec, TConfig> > const> :
+    public Value<RankDictionary<TValue, WaveletTree<TSpec, TConfig> > > {};
 
 // ----------------------------------------------------------------------------
-// Metafunction Value
+// Metafunction RankDictionaryBlock_
 // ----------------------------------------------------------------------------
 
-template <typename TValue>
-struct Value<RankDictionary<WaveletTree<TValue> > >
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionaryBlock_<TValue, WaveletTree<TSpec, TConfig> >
 {
-    typedef TValue Type;
+    typedef RankDictionary<TValue, WaveletTree<TSpec, TConfig> >    TRankDictionary_;
+    typedef typename Size<TRankDictionary_>::Type                   TSize_;
+//    typedef Tuple<TSize_, ValueSize<TValue>::VALUE>                 Type;
+    typedef String<TSize_>                                          Type;
 };
 
-template <typename TValue>
-struct Value<RankDictionary<WaveletTree<TValue> > const> :
-    public Value<RankDictionary<WaveletTree<TValue> > > {};
-
-
 // ==========================================================================
 // Classes
 // ==========================================================================
 
-// ----------------------------------------------------------------------------
-// Class RankDictionary
-// ----------------------------------------------------------------------------
-
-/**
-.Class.RankDictionary:
-..cat:Index
-..summary:A rank dictionary is a data structure to store the rank of an element of a sequence at every position of the 
-sequence.
-..signature:RankDictionary<TSpec>
-..param.TSpec:The rank dictionary specialisation.
-...type:Spec.WaveletTree
-...type:Spec.SequenceBitMask
-...default:@Spec.WaveletTree@
-..include:seqan/index.h
-*/
-template<typename TSpec> 
-class RankDictionary;
-
 // ----------------------------------------------------------------------------
 // Spec WaveletTree
 // ----------------------------------------------------------------------------
 
-/**
-.Spec.WaveletTree:
-..cat:Index
-..summary:A wavelet tree is a tree like binary encoding of a text.
-..signature:WaveletTree<TValue>
-..param.TValue:The value type of the wavelet tree.
-..include:seqan/index.h
-..remarks:The nodes of a wavelet tree consist of a bit string as well as a character c. In each level of the tree, 
-characters smaller than c are represented as a 0 while character greater or equal to c are represented with a 1.
-The characters represented by a 0 form the string to be represented by the left subtree while characters represented
-by a 1 form the string of the right subtree. Therefore, only the bit string of the root node represents all characters while all other nodes represent subsets.
-*/
-
-template <typename TValue>
-class RankDictionary<WaveletTree<TValue> >
+template <typename TValue, typename TSpec, typename TConfig>
+struct RankDictionary<TValue, WaveletTree<TSpec, TConfig> >
 {
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreBitStrings>::Type    TBitStrings;
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>::Type TWaveletTreeStructure;
-
-public:
-    TBitStrings bitStrings;
-    TWaveletTreeStructure waveletTreeStructure;
+    typename Fibre<RankDictionary, FibreRanks>::Type            ranks;
+    typename Fibre<RankDictionary, FibreTreeStructure>::Type    waveletTreeStructure;
 
     RankDictionary() {}
 
@@ -214,127 +175,78 @@ class RankDictionary<WaveletTree<TValue> >
     {
         createRankDictionary(*this, text);
     }
-
-    template <typename TText, typename TFreqTable>
-    RankDictionary(TText const & text, TFreqTable const & freqTable)
-    {
-        createRankDictionary(*this, text, freqTable);
-    }
-
-    template <typename TText, typename TFreqTable, typename TPrefixSumTable>
-    RankDictionary(TText const & text, TFreqTable const & freqTable, TPrefixSumTable const & prefixSumTable)
-    {
-        createRankDictionary(*this, text, freqTable, prefixSumTable);
-    }
-
-    RankDictionary & operator=(RankDictionary const & other)
-    {
-        bitStrings = other.bitStrings;
-        waveletTreeStructure = other.waveletTreeStructure;
-        return *this;
-    }
-
-    bool operator==(RankDictionary const & b) const
-    {
-        typedef typename Size<typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreBitStrings>::Type>::Type TSize;
-        
-        if (length(bitStrings) != length(b.bitStrings))
-            return false;
-
-        for (TSize i = 0; i < length(bitStrings); ++i)
-            if (!(bitStrings[i] == b.bitStrings[i]))
-                return false;
-
-        return waveletTreeStructure == b.waveletTreeStructure;
-    }
 };
 
 // ==========================================================================
-//Functions
+// Functions
 // ==========================================================================
 
 // ----------------------------------------------------------------------------
-// Function clear
+// Function getFibre()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+inline typename Fibre<RankDictionary<TValue, WaveletTree<TSpec, TConfig> >, FibreTreeStructure>::Type &
+getFibre(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict, FibreTreeStructure)
+{
+    return dict.waveletTreeStructure;
+}
+
+template <typename TValue, typename TSpec, typename TConfig>
+inline typename Fibre<RankDictionary<TValue, WaveletTree<TSpec, TConfig> >, FibreTreeStructure>::Type const &
+getFibre(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > const & dict, FibreTreeStructure)
+{
+    return dict.waveletTreeStructure;
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.RankDictionary#clear
-..class:Class.RankDictionary
-..summary:Clears the rank dictionary.
-..signature:clear(dictionary)
-..param.dictionary:The rank dictionary to be cleared.
-...type:Class.RankDictionary
-..include:seqan/index.h
-*/
-
-template <typename TValue>
-inline void clear(RankDictionary<WaveletTree<TValue> > & dictionary)
+template <typename TValue, typename TSpec, typename TConfig>
+inline void clear(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict)
 {
-    clear(getFibre(dictionary, FibreBitStrings()));
-    clear(getFibre(dictionary, FibreTreeStructure()));
+    clear(getFibre(dict, FibreRanks()));
+    clear(getFibre(dict, FibreTreeStructure()));
 }
 
 // ----------------------------------------------------------------------------
-// Function empty
+// Function empty()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.RankDictionary#empty
-..class:Class.RankDictionary
-..summary:Returns whether or not the rank dictionary is empty.
-..signature:empty(dictionary)
-..param.dictionary:The rank dictionary to be checked.
-...type:Class.RankDictionary
-..returns:$true$ if the dictionary is empty, $false$ otherwise.
-..include:seqan/index.h
-*/
-
-template <typename TValue>
-inline bool empty(RankDictionary<WaveletTree<TValue> > const & dictionary)
+template <typename TValue, typename TSpec, typename TConfig>
+inline bool empty(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > const & dict)
 {
-    return empty(getFibre(dictionary, FibreTreeStructure()));
+    return empty(getFibre(dict, FibreRanks())) && empty(getFibre(dict, FibreTreeStructure()));
 }
 
 // ----------------------------------------------------------------------------
-// Function getValue
+// Function getValue()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.RankDictionary#getValue
-..summary:Returns the character of a specified position.
-..signature:getCharacter(dictionary, pos)
-..class:Class.RankDictionary
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.pos:The position
-..include:seqan/index.h
-*/
-
-template <typename TValue, typename TPos>
-inline TValue
-getValue(RankDictionary<WaveletTree<TValue> > & dictionary,
-                 TPos pos)
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+inline TValue getValue(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict, TPos pos)
 {
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>::Type const    TWaveletTreeStructure;
+    typedef typename Fibre<RankDictionary<TValue, WaveletTree<TSpec, TConfig> >, FibreTreeStructure>::Type const    TWaveletTreeStructure;
     typedef typename Fibre<TWaveletTreeStructure, FibreTreeStructureEncoding>::Type                 TWaveletTreeStructureString;
     typedef typename Value<TWaveletTreeStructureString>::Type                                       TWaveletTreeStructureEntry;
     typedef typename Value<TWaveletTreeStructureEntry, 1>::Type                                     TChar;
 
     unsigned treePos = 0;
-    typename Iterator<TWaveletTreeStructure, TopDown<> >::Type iter(dictionary.waveletTreeStructure, treePos);
-    
+    typename Iterator<TWaveletTreeStructure, TopDown<> >::Type iter(dict.waveletTreeStructure, treePos);
+
     // initialize the return value with the smallest possible value
-    TChar character = dictionary.waveletTreeStructure.minCharValue;
+    TChar character = dict.waveletTreeStructure.minCharValue;
 
     // while the current node is not a leaf, go right if the bit at the current position is 1
     // go left otherwise
     // note that when going right the return value changes
     while (true)
     {
-        TPos rank1 = getRank(dictionary.bitStrings[treePos], pos);
-        if (isBitSet(dictionary.bitStrings[treePos], pos))
+        TPos rank1 = getRank(dict.ranks[treePos], pos);
+        if (getValue(dict.ranks[treePos], pos))
         {
-            character = getCharacter(iter); 
+            character = getCharacter(iter);
             pos = rank1 - 1;  // -1 because strings start at 0
             if (!goRightChild(iter))
                 break;
@@ -351,97 +263,36 @@ getValue(RankDictionary<WaveletTree<TValue> > & dictionary,
     return character;
 }
 
-// TODO(singer): We would like to have only one variant BUT there is a getValue() with const.
-template <typename TValue, typename TPos>
-inline TValue
-getValue(RankDictionary<WaveletTree<TValue> > const & tree, TPos pos)
+template <typename TValue, typename TSpec, typename TConfig, typename TPos>
+inline TValue getValue(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > const & dict, TPos pos)
 {
-    return getValue(const_cast<RankDictionary<WaveletTree<TValue> > &>(tree), pos);
+    return getValue(const_cast<RankDictionary<TValue, WaveletTree<TSpec, TConfig> > &>(dict), pos);
 }
 
 // ----------------------------------------------------------------------------
-// Function getFibre
+// Function getRank()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.RankDictionary#getFibre:
-..summary:Returns a specific fibre of a dictionary.
-..signature:getFibre(dictionary, fibreTag)
-..class:Class.RankDictionary
-..cat:Index
-..param.dictionary:The dictionary holding the fibre.
-...type:Class.RankDictionary
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.WaveletTree Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-template <typename TValue>
-inline typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreBitStrings>::Type &
-getFibre(RankDictionary<WaveletTree<TValue> >& dictionary, const FibreBitStrings)
+template <typename TValue, typename TSpec, typename TConfig, typename TPos, typename TChar>
+inline typename Size<RankDictionary<TValue, WaveletTree<TSpec, TConfig> > >::Type
+getRank(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > const & dict, TPos pos, TChar character)
 {
-    return dictionary.bitStrings;
-}
-
-template <typename TValue>
-inline typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreBitStrings>::Type const &
-getFibre(RankDictionary<WaveletTree<TValue> > const & dictionary, const FibreBitStrings)
-{
-    return dictionary.bitStrings;
-}
-
-template <typename TValue>
-inline typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>::Type &
-getFibre(RankDictionary<WaveletTree<TValue> >& dictionary, FibreTreeStructure)
-{
-    return dictionary.waveletTreeStructure;
-}
-
-template <typename TValue>
-inline typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>::Type const &
-getFibre(RankDictionary<WaveletTree<TValue> > const & dictionary, const FibreTreeStructure)
-{
-    return dictionary.waveletTreeStructure;
-}
-
-// ----------------------------------------------------------------------------
-// Function countOccurrences
-// ----------------------------------------------------------------------------
-
-/**
-.Function.RankDictionary#countOccurrences:
-..summary:Returns the rank (number of occurrences) of a specified character up to a specified position. 
-..signature:countOccurrences(dictionary, character, pos)
-..class:Class.RankDictionary
-..cat:Index
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.character:The character of interest.
-..param.pos:The position (which is also included in the rank computation).
-..returns:The rank (number of occurrences) of a specified character up to a specified position. 
-...type:nolink:$unsigned$
-..include:seqan/index.h
-*/
-
-template < typename TValue, typename TCharIn, typename TPos>
-inline unsigned countOccurrences(RankDictionary<WaveletTree<TValue> > const & tree, TCharIn const character,
-                                   TPos const pos)
-{
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>::Type TWaveletTreeStructure;
-    typedef typename Fibre<TWaveletTreeStructure, FibreTreeStructureEncoding>::Type TWaveletTreeStructureString;
-    typedef typename Value<TWaveletTreeStructureString>::Type TWaveletTreeStructureEntry;
-    typedef typename Value<TWaveletTreeStructureEntry, 1>::Type TChar;
+    typedef typename Fibre<RankDictionary<TValue, WaveletTree<TSpec, TConfig> >, FibreTreeStructure>::Type  TWaveletTreeStructure;
+    typedef typename Fibre<TWaveletTreeStructure, FibreTreeStructureEncoding>::Type         TWaveletTreeStructureString;
+    typedef typename Value<TWaveletTreeStructureString>::Type                               TWaveletTreeStructureEntry;
+    typedef typename Value<TWaveletTreeStructureEntry, 1>::Type                             TChar_;
 
     TPos sum = pos;
     TPos treePos = 0;
 
     // determine the leaf containing the character
     // count the number of 1 or 0 up to the computed position
-    typename Iterator<TWaveletTreeStructure const, TopDown<> >::Type it(tree.waveletTreeStructure, treePos);
-    TChar charInTree = tree.waveletTreeStructure.minCharValue;
+    typename Iterator<TWaveletTreeStructure const, TopDown<> >::Type it(dict.waveletTreeStructure, treePos);
+    TChar_ charInTree = dict.waveletTreeStructure.minCharValue;
+
     while (true)
     {
-        TPos addValue = getRank(tree.bitStrings[treePos], sum);
+        TPos addValue = getRank(dict.ranks[treePos], sum);
         if (ordGreater(getCharacter(it), character))
         {
             if (addValue > sum) return 0;
@@ -469,158 +320,125 @@ inline unsigned countOccurrences(RankDictionary<WaveletTree<TValue> > const & tr
 }
 
 // ----------------------------------------------------------------------------
-// Function _fillWaveletTree
+// Function _fillStructure()
 // ----------------------------------------------------------------------------
 
 // This function is used to fill the bit strings of the wavelet tree.
-template <typename TValue, typename TText>
-inline void _fillWaveletTree(RankDictionary<WaveletTree<TValue> > & tree, TText const & text)
+template <typename TValue, typename TSpec, typename TConfig, typename TText>
+inline void _fillStructure(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict, TText const & text)
 {
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreBitStrings>::Type     TFibreRankSupportBitStrings;
-    typedef typename Value<TFibreRankSupportBitStrings>::Type                               TFibreRankSupportBitString;
-    typedef typename Fibre<TFibreRankSupportBitString, FibreBits>::Type                     TFibreBitString;
-    typedef typename Size<TFibreBitString>::Type                                            TSize;
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>::Type  TWaveletTreeStructure;
+    typedef RankDictionary<TValue, WaveletTree<TSpec, TConfig> >        TRankDictionary;
+    typedef typename Fibre<TRankDictionary, FibreTreeStructure>::Type   TWaveletTreeStructure;
+    typedef typename Iterator<TWaveletTreeStructure, TopDown<> >::Type  TWaveletTreeIterator;
+    typedef typename Size<TRankDictionary>::Type                        TSize;
+    typedef typename Iterator<TText const, Standard>::Type              TTextIterator;
+
+    resize(dict.ranks, length(dict.waveletTreeStructure), Exact());
 
-    resize(tree.bitStrings, _length(tree.waveletTreeStructure), Exact());
+    for (TSize i = 0; i < length(dict.ranks); ++i)
+        resize(dict.ranks[i], 0);
 
-    for (TSize i = 0; i < length(text); ++i)
+    TTextIterator textBegin = begin(text, Standard());
+    TTextIterator textEnd = end(text, Standard());
+
+    for (TTextIterator textIt = textBegin; textIt != textEnd; ++textIt)
     {
-        typename Iterator<TWaveletTreeStructure, TopDown<> >::Type it(tree.waveletTreeStructure, 0);
-        bool bit;
+        TWaveletTreeIterator it(dict.waveletTreeStructure, 0);
 
         while (true)
         {
-            // decide whether the character is smaller then the pivot element of the current node 
-            if (ordGreater(getCharacter(it), getValue(text, i)))
+            // decide whether the character is smaller then the pivot element of the current node
+            if (ordGreater(getCharacter(it), value(textIt)))
             {
-                bit = 0;
-                appendValue(getFibre(tree, FibreBitStrings())[getPosition(it)], bit);
+                // TODO(esiragusa): use resize() & setValue() instead of appendValue().
+                appendValue(dict.ranks[getPosition(it)], false);
                 if (!goLeftChild(it))
                     break;
             }
             else
             {
-                bit = 1;
-                appendValue(getFibre(tree, FibreBitStrings())[getPosition(it)], bit);
+                appendValue(dict.ranks[getPosition(it)], true);
                 if (!goRightChild(it))
                     break;
             }
         }
     }
-
-    TFibreRankSupportBitStrings & bitStrings = getFibre(tree, FibreBitStrings());
-    for (TSize i = 0; i < length(bitStrings); ++i)
-        _updateRanks(bitStrings[i]);
 }
 
 // ----------------------------------------------------------------------------
-// Function createRankDictionary
+// Function updateRanks()                                      [RankDictionary]
 // ----------------------------------------------------------------------------
-/**
-.Function.RankDictionary#createRankDictionary
-..class:Class.RankDictionary
-..summary:This functions creates the dictionary.
-..signature:createRankDictionary(dictionary, text)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.text:A text to be transfered into a wavelet tree.
-...type:Class.String
-..include:seqan/index.h
-*/
-
-// TODO(singer): change to createRankDictionary
-template <typename TValue, typename TText> 
-inline void createRankDictionary(RankDictionary<WaveletTree<TValue> > & dictionary, TText const & text)
-{
-    createRightArrayBinaryTree(getFibre(dictionary, FibreTreeStructure()), text);
-    _fillWaveletTree(dictionary, text);
-}
 
-template <typename TValue, typename TSpec, typename TPrefixSumTable, typename TText> 
-inline void createRankDictionary(LfTable<SentinelRankDictionary<RankDictionary<WaveletTree<TValue> >, TSpec >, TPrefixSumTable> & lfTable,
-                              TText const & text)
+template <typename TValue, typename TSpec, typename TConfig>
+inline void updateRanks(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict)
 {
-    createRightArrayBinaryTree(lfTable);
-    _fillWaveletTree(getFibre(getFibre(lfTable, FibreOccTable()), FibreRankDictionary()), text);
+    typedef RankDictionary<TValue, WaveletTree<TSpec, TConfig> >        TRankDictionary;
+    typedef typename Size<TRankDictionary>::Type                        TSize;
+
+    for (TSize i = 0; i < length(getFibre(dict, FibreRanks())); ++i)
+        updateRanks(getFibre(dict, FibreRanks())[i]);
 }
 
 // ----------------------------------------------------------------------------
-// Function open
+// Function createRankDictionary()
 // ----------------------------------------------------------------------------
-
-/**
-.Function.RankDictionary#open
-..class:Class.RankDictionary
-..summary:This functions loads a dictionary from disk.
-..signature:open(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TValue>
-inline bool open(RankDictionary<WaveletTree<TValue> > & dictionary, const char * fileName, int openMode)
+template <typename TValue, typename TSpec, typename TConfig, typename TText, typename TPrefixSums>
+inline void
+createRankDictionary(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict, TText const & text, TPrefixSums const & sums)
 {
-    String<char> name;
-    name = fileName;    append(name, ".wtc"); if (!open(getFibre(dictionary, FibreBitStrings()), toCString(name), openMode)) return false;
-    name = fileName;    append(name, ".wts"); if (!open(getFibre(dictionary, FibreTreeStructure()), toCString(name), openMode)) return false;
-    return true;
+    createRightArrayBinaryTree(getFibre(dict, FibreTreeStructure()), sums);
+//    _resizeStructure(dict, text);
+    _fillStructure(dict, text);
+    updateRanks(dict);
 }
 
-    template <typename TValue>
-inline bool open(RankDictionary<WaveletTree<TValue> > & tree, const char * fileName)
+template <typename TValue, typename TSpec, typename TConfig, typename TText>
+inline void
+createRankDictionary(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict, TText const & text)
 {
-    return open(tree, fileName, DefaultOpenMode<RankDictionary<WaveletTree<TValue> > >::VALUE);
+    typename RankDictionaryBlock_<TValue, WaveletTree<TSpec, TConfig> >::Type sums;
+    prefixSums<TValue>(sums, text);
+    createRankDictionary(dict, text, sums);
 }
 
 // ----------------------------------------------------------------------------
-// Function save
+// Function open()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.RankDictionary#save
-..class:Class.RankDictionary
-..summary:This functions saves a dictionary to disk.
-..signature:open(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TValue>
-inline bool save(RankDictionary<WaveletTree<TValue> > const & dictionary, const char * fileName, int openMode)
+template <typename TValue, typename TSpec, typename TConfig>
+inline bool open(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict, const char * fileName, int openMode)
 {
     String<char> name;
-    name = fileName;    append(name, ".wtc");   
-    if (!save(getFibre(dictionary, FibreBitStrings()), toCString(name), openMode)) return false;
-    
-    name = fileName;    append(name, ".wts");   
-    if (!save(getFibre(dictionary, FibreTreeStructure()), toCString(name), openMode)) return false;
-    
+
+    name = fileName;
+    append(name, ".wtc");
+    if (!open(getFibre(dict, FibreRanks()), toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".wts");
+    if (!open(getFibre(dict, FibreTreeStructure()), toCString(name), openMode)) return false;
+
     return true;
 }
 
-template <typename TValue>
-inline bool save(RankDictionary<WaveletTree<TValue> > const & tree, const char * fileName)
+// ----------------------------------------------------------------------------
+// Function save()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+inline bool save(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > const & dict, const char * fileName, int openMode)
 {
-    return save(tree, fileName, DefaultOpenMode<RankDictionary<WaveletTree<TValue> > >::VALUE);
+    String<char> name;
+
+    name = fileName;
+    append(name, ".wtc");
+    if (!save(getFibre(dict, FibreRanks()), toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".wts");
+    if (!save(getFibre(dict, FibreTreeStructure()), toCString(name), openMode)) return false;
+
+    return true;
 }
 
 }
diff --git a/seqan/index/index_fm_rank_support_bit_string.h b/seqan/index/index_fm_rank_support_bit_string.h
deleted file mode 100755
index 23371c1..0000000
--- a/seqan/index/index_fm_rank_support_bit_string.h
+++ /dev/null
@@ -1,834 +0,0 @@
-// ==========================================================================
-//                 seqan - the library for sequence analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Jochen Singer <jochen.singer@fu-berlin.de>
-// ==========================================================================
-
-//SEQAN_NO_DDDOC:do not generate documentation for this file
-
-#ifndef INDEX_FM_RANK_SUPPORT_BIT_STRING_H_
-#define INDEX_FM_RANK_SUPPORT_BIT_STRING_H_
-
-#include <seqan/misc/misc_bit_twiddling.h>
-
-namespace seqan {
-
-//Rank Support Bit String
-template <typename TSpec = void>
-struct RankSupportBitString;
-
-// ==========================================================================
-// Tags
-// ==========================================================================
-
-// FM index fibres
-
-/**
-.Tag.RankSupportBitString Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Class.RankSupportBitString@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a rank support bit string.
-..cat:Index
-
-..tag.FibreBits:The bit string.
-..tag.FibreBlocks:The block string.
-..tag.FibreSuperBlocks:The super block string.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-
-struct FibreBits_;
-struct FibreBlocks_;
-struct FibreSuperBlocks_;
-
-typedef Tag<FibreBits_> const           FibreBits;         
-typedef Tag<FibreBlocks_> const         FibreBlocks;      
-typedef Tag<FibreSuperBlocks_> const    FibreSuperBlocks; 
-
-typedef FibreBits           RankSupportBitStringBits;
-typedef FibreBlocks         RankSupportBitStringBlocks;
-typedef FibreSuperBlocks    RankSupportBitStringSuperBlocks;
-
-// ==========================================================================
-// Metafunctions
-// ==========================================================================
-
-template <typename TSpec>
-struct DefaultOverflowImplicit<RankSupportBitString<TSpec> >
-{
-    typedef Generous Type;
-};
-
-//The limiting factor of the size is the underlying data type of the super block string
-template <typename TSpec>
-struct Size<RankSupportBitString<TSpec> >
-{
-    typedef unsigned long long Type;
-};
-
-template <typename TSpec>
-struct Position<RankSupportBitString<TSpec> > :
-	Size<RankSupportBitString<TSpec> > {};
-
-template <typename TSpec>
-struct Fibre<RankSupportBitString<TSpec>, FibreBits>
-{
-    typedef String<unsigned long long> Type;
-};
-
-template <typename TSpec>
-struct Fibre<RankSupportBitString<TSpec>, FibreBlocks>
-{
-    typedef String<unsigned short> Type;
-};
-
-template <typename TSpec>
-struct Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>
-{
-    typedef String<typename Size<RankSupportBitString<TSpec> >::Type> Type;
-};
-
-// ==========================================================================
-// Classes
-// ==========================================================================
-
-/**
-.Class.RankSupportBitString:
-..summary:A bit string supporting rank queries in constant time.
-..cat:Index
-..signature:RankSupportBitString<TSpec>
-..param.TSpec:Specialisation tag.
-...default:void
-..remarks:The constant rank query time is achieved by evaluating precomputed subsolutions. In order to do so, the bit string is divided into blocks of length l. A super block string stores for each block of l blocks the number of bits set from the beginning. In addition a block string stores the number of bits set in each block from the start of the last super block block. Therefore it is possible to compute the result of a rank query in constant time by adding information from the bit, block and super block string.
-..include:seqan/index.h
-*/
-
-// Forward declaration because setBit is used in constructor
-template <typename TSpec, typename TPos>
-inline void setBitTo(RankSupportBitString<TSpec> & bitString, TPos pos, bool setBit);
-
-template <typename TSpec>
-struct RankSupportBitString
-{
-    typedef typename Fibre<RankSupportBitString, FibreBits>::Type         TBitString;
-    typedef typename Fibre<RankSupportBitString, FibreBlocks>::Type       TBlockString;
-    typedef typename Fibre<RankSupportBitString, FibreSuperBlocks>::Type  TSuperBlockString;
-
-    TBitString                                  bits;
-    TBlockString                                blocks;
-    TSuperBlockString                           superBlocks;
-    typename Size<RankSupportBitString>::Type   _length;
-
-    RankSupportBitString() :
-        _length(0)
-    {}
-
-    // TODO(singer): Use concept sequence when available
-    template <typename TValue, typename TStringSpec>
-    RankSupportBitString(String<TValue, TStringSpec> const & input) :
-        _length(length(input))
-    {
-        typedef typename Iterator<String<TValue, TStringSpec> const>::Type TIter_;
-
-        resize(*this, _length, Exact());
-        typename Position<RankSupportBitString>::Type i = 0;
-        for (TIter_ it = begin(input, Standard()); it != end(input, Standard()); ++it, ++i)
-            setBitTo(*this, i, getValue(it));
-        _updateRanks(*this);
-    }
-    
-    template <typename THost, typename TStringSpec>
-    RankSupportBitString(Segment<THost, TStringSpec> const & input) :
-        _length(length(input))
-    {
-        typedef typename Iterator<Segment<THost, TStringSpec> const>::Type TIter_;
-
-        resize(*this, _length, Exact());
-        typename Position<RankSupportBitString>::Type i = 0;
-        for (TIter_ it = begin(input, Standard()); it != end(input, Standard()); ++it, ++i)
-            setBitTo(*this, i, getValue(it));
-        _updateRanks(*this);
-    }
-
-    inline bool operator==(const RankSupportBitString & other) const
-    {
-        return _length == other._length &&
-               bits == other.bits &&
-               blocks == other.blocks &&
-               superBlocks == other.superBlocks;
-    }
-};
-
-// ==========================================================================
-// Functions
-// ==========================================================================
-
-/**
-.Function.RankSupportBitString#appendValue:
-..signature:appendValue(target, value)
-..cat:Index
-..summary:Appends a value to a container.
-..param.target:A container.
-...type:Class.RankSupportBitString
-..param.value:Value that is appended to $target$.
-...type:Concept.UnsignedIntegerConcept
-...type:nolink:bool
-...remarks:If the value is different from 0 it is interpreted as 1.
-..include:seqan/sequence.h
-*/
-template <typename TSpec>
-inline void appendValue(RankSupportBitString<TSpec> & bitString, bool bit)
-{
-	typename Size<RankSupportBitString<TSpec> >::Type len = length(bitString);
-    resize(bitString, len + 1);
-    setBitTo(bitString, len, bit);
-    _updateLastRank(bitString); 
-}
-
-// ==========================================================================
-/**
-.Function.clear
-..param.object:
-...type:Class.RankSupportBitString
-*/
-template <typename TSpec>
-inline void clear(RankSupportBitString<TSpec> & bitString)
-{
-    clear(bitString.bits);
-    clear(bitString.blocks);
-    clear(bitString.superBlocks);
-    bitString._length = 0;
-}
-
-// ==========================================================================
-// This function returns the number of bits set in a block until a specified position
-template <typename TValue>
-inline unsigned _getRankInBlock(TValue const value, False)
-{
-    return popCount(value);
-}
-
-template <typename TValue>
-inline unsigned _getRankInBlock(TValue const value, True)
-{
-    return popCount(value);
-}
-
-template <typename TValue>
-inline unsigned _getRankInBlock(TValue const value)
-{
-    return _getRankInBlock(value, typename Eval<(BitsPerValue<TValue>::VALUE > 32)>::Type());
-}
-
-template <typename TSpec, typename TPos>
-inline typename Value<typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type>::Type
-_getRankInBlock(RankSupportBitString<TSpec> const & bitString, TPos const pos)
-{
-    //typedef RankSupportBitString<TSpec>                                     TRankSupportBitString;
-    typedef typename Fibre<RankSupportBitString<TSpec>, FibreBits>::Type    TFibreBits;
-    typedef typename Value<TFibreBits>::Type                                TFibreBitsValue;
-
-    TFibreBitsValue const mask = ((TFibreBitsValue)2u << _getPosInBlock(bitString, pos)) - 1;
-    return _getRankInBlock(bitString.bits[_getBlockPos(bitString, pos)] & mask);
-}
-
-// ==========================================================================
-// This function returns the number of bits set in a block until a specified position
-template <typename TSpec, typename TPos>
-inline typename Value<typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type>::Type
-_getSuperBlockPos(RankSupportBitString<TSpec> const & /*bitString*/, TPos const pos)
-{
-    typedef RankSupportBitString<TSpec>                                 TRankSupportBitString;
-    typedef typename Fibre<TRankSupportBitString, FibreBits>::Type      TFibreBits;
-    typedef typename Fibre<TRankSupportBitString, FibreBlocks>::Type    TFibrelocks;
-    typedef typename Value<TFibreBits>::Type                            TFibreBitsValue;
-    typedef typename Value<TFibrelocks>::Type                     		TFibreBlocksValue;
-
-    TFibreBlocksValue const _bitsPerValue = BitsPerValue<TFibreBitsValue>::VALUE;
-    return pos / (_bitsPerValue * _bitsPerValue);
-}
-
-// ==========================================================================
-/**
-.Function.getRank
-..summary:Returns the rank (the number of bits set from the start of the bit string) of a specified position.
-..signature:getRank(bitString, pos)
-..param.bitString:The bit string.
-...type:Class.RankSupportBitString
-..param.pos:Position of a bit.
-..returns:Value type of the super block fibre (default unsigned long).
-..include:seqan/index.h
-..example.code:
-*/
-template <typename TSpec, typename TPos>
-inline typename Value<typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type>::Type
-getRank(RankSupportBitString<TSpec> const & bitString, TPos const pos)
-{
-    return bitString.superBlocks[_getSuperBlockPos(bitString, pos)]
-         + bitString.blocks[_getBlockPos(bitString, pos)]
-         + _getRankInBlock(bitString, pos);
-}
-
-
-/**
-.Function.empty
-..param.object:
-...type:Class.RankSupportBitString
-*/
-
-// ==========================================================================
-/**
-.Function.isSetBit
-..summary:Returns whether the bit with the given index is set to 1.
-..signature:isSetBit(bitString, pos)
-..param.bitString:The bit string.
-...type:Class.RankSupportBitString
-..param.pos:Position of the bit.
-..returns:Returns whether a specified bit is set or not.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-
-RankSupportBitString<> bitString;
-resize(bitString, length(genome));
-...
-mark all 'a's
-...
-
-for (unsigned i = 0; i < length(bitString); ++i)
-    if(isSetBit(bitString, i))
-        std::cout << "a found at: " << i << std::endl;
-*/
-
-template <typename TSpec, typename TPos>
-inline bool isBitSet(RankSupportBitString<TSpec> const & bitString, TPos const pos)
-{
-    return isBitSet(bitString.bits[_getBlockPos(bitString, pos)], _getPosInBlock(bitString, pos));
-}
-
-// ==========================================================================
-// This function returns the position in the block string of the corresponding block.
-template <typename TSpec, typename TPos>
-inline typename Value<typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type>::Type
-_getBlockPos(RankSupportBitString<TSpec> const & /*bitString*/, TPos const pos)
-{
-    typedef RankSupportBitString<TSpec>                             TRankSupportBitString;
-    typedef typename Fibre<TRankSupportBitString, FibreBits>::Type  TFibreBits;
-    typedef typename Value<TFibreBits>::Type                        TFibreBitsValue;
-
-    return pos / BitsPerValue<TFibreBitsValue>::VALUE;
-}
-
-// ==========================================================================
-/**
-.Function.RankSupportBitString#getFibre:
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(container, fibreTag)
-..class:Class.RankSupportBitString
-..cat:Index
-..param.container:The container holding the fibre.
-...type:Class.RankSupportBitString
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.RankSupportBitString Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-..example.code:
-Index< String<char> > index_esa("tobeornottobe");
-
-String<char> & text = getFibre(indexEsa, EsaText());
-*/
-template <typename TSpec>
-inline typename Fibre<RankSupportBitString<TSpec>, FibreBits>::Type &
-getFibre(RankSupportBitString<TSpec>&string, const FibreBits)
-{
-    return string.bits;
-}
-
-template <typename TSpec>
-inline typename Fibre<RankSupportBitString<TSpec>, FibreBits>::Type const &
-getFibre(RankSupportBitString<TSpec> const & string, const FibreBits)
-{
-    return string.bits;
-}
-
-template <typename TSpec>
-inline typename Fibre<RankSupportBitString<TSpec>, FibreBlocks>::Type &
-getFibre(RankSupportBitString<TSpec>&string, const FibreBlocks)
-{
-    return string.blocks;
-}
-
-template <typename TSpec>
-inline typename Fibre<RankSupportBitString<TSpec>, FibreBlocks>::Type const &
-getFibre(RankSupportBitString<TSpec> const & string, const FibreBlocks)
-{
-    return string.blocks;
-}
-
-template <typename TSpec>
-inline typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type &
-getFibre(RankSupportBitString<TSpec>&string, const FibreSuperBlocks)
-{
-    return string.superBlocks;
-}
-
-template <typename TSpec>
-inline typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type const &
-getFibre(const RankSupportBitString<TSpec>&string, const FibreSuperBlocks)
-{
-    return string.superBlocks;
-}
-
-// ==========================================================================
-// This function returns the position of a specified bit within a block.
-template <typename TSpec, typename TPos>
-inline typename Value<typename Fibre<RankSupportBitString<TSpec>, FibreBlocks>::Type>::Type
-_getPosInBlock(RankSupportBitString<TSpec> const & /*bitString*/, TPos const pos)
-{
-    typedef RankSupportBitString<TSpec>                             TRankSupportBitString;
-    typedef typename Fibre<TRankSupportBitString, FibreBits>::Type  TFibreBits;
-    typedef typename Value<TFibreBits>::Type                        TFibreBitsValue;
-
-    return pos % BitsPerValue<TFibreBitsValue>::VALUE;
-}
-
-// ==========================================================================
-/**
-.Function.length
-..param.object:
-...type:Class.RankSupportBitString
-*/
-template <typename TSpec>
-inline typename Value<typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type>::Type
-length(RankSupportBitString<TSpec> const & bitString)
-{
-    return bitString._length;
-}
-
-
-// ==========================================================================
-/*
-.Function._updateRanks
-..summary:Adds the block and super block information to the bit string.
-..signature:_updateRanks(bitString)
-..param.bitString:The bit string to be completed.
-...type:Class.RankSupportBitString
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-
-RankSupportBitString<> bitString;
-resize(bitString, length(genome));
-
-for (unsigned i = 0; i < length(genome); ++i)
-    if(genome[i] < Dna5('c'))
-        setBitTo(bitString, 1);
-
-_updateRanks(bitString);
-*/
-
-template <typename TSpec, typename TPos>
-inline void _updateRanksImpl(RankSupportBitString<TSpec> & bitString, TPos pos)
-{
-    if (!empty(bitString))
-    {
-        typedef RankSupportBitString<TSpec>                                     TRankSupportBitString;
-        typedef typename Fibre<RankSupportBitString<TSpec>, FibreBits>::Type    TFibreBits;
-        typedef typename Fibre<TRankSupportBitString, FibreBlocks>::Type        TFibreBlocks;
-        typedef typename Fibre<TRankSupportBitString, FibreSuperBlocks>::Type   TFibreSuperBlocks;
-        typedef typename Value<TFibreBits>::Type                                TFibreBitsValue;
-        typedef typename Value<TFibreBlocks>::Type                              TFibreBlocksValue;
-        typedef typename Value<TFibreSuperBlocks>::Type                         TFibreSuperBlocksValue;
-
-        TFibreSuperBlocksValue i = _getBlockPos(bitString, pos);
-
-        TFibreBlocksValue _blockSum;
-        if (i == 0)
-            _blockSum = 0;
-        else
-            _blockSum = bitString.blocks[i - 1];
-
-        TFibreSuperBlocksValue _sBlockSum;
-        TFibreSuperBlocksValue superBlockPos = _getSuperBlockPos(bitString, pos);
-        if (superBlockPos != 0)
-        {
-            _sBlockSum = bitString.superBlocks[superBlockPos];
-        }
-        else
-            _sBlockSum = 0;
-        
-        if (i == 0)
-            ++i;
-        for (; i < length(bitString.bits); ++i)
-        {
-        	_blockSum += _getRankInBlock(bitString.bits[i - 1]);
-            if ((i % BitsPerValue<TFibreBitsValue>::VALUE) == 0u)
-            {
-                _sBlockSum += _blockSum;
-                bitString.superBlocks[++superBlockPos] = _sBlockSum;
-                _blockSum = 0;
-            }
-            bitString.blocks[i] = _blockSum;
-       }
-    }
-}
-
-template <typename TSpec, typename TPos>
-inline void _updateRanks(RankSupportBitString<TSpec> & bitString, TPos pos)
-{
-    _updateRanksImpl(bitString, pos);
-}
-
-template <typename TSpec>
-inline void _updateRanks(RankSupportBitString<TSpec> & bitString)
-{
-    _updateRanksImpl(bitString, 0u);
-}
-
-// This function update the rank information of the last block.
-// ==========================================================================
-template <typename TSpec>
-inline void _updateLastRank(RankSupportBitString<TSpec> & bitString)
-{
-    typedef RankSupportBitString<TSpec>                                     TRankSupportBitString;
-    typedef typename Fibre<TRankSupportBitString, FibreSuperBlocks>::Type   TFibreSuperBlocks;
-    typedef typename Value<TFibreSuperBlocks>::Type                         TFibreSuperBlocksValue;
-
-    // It is only necessary to update the rank at the start of a new block
-    TFibreSuperBlocksValue pos = length(bitString) - 1;
-    if (_getPosInBlock(bitString, pos) != 0u) return;
-
-    // Here we compute the new rank if the last bit does not reside in the 
-    // first block and the last as well as the second last bit are in the 
-    // same block.
-    TFibreSuperBlocksValue superBlockPos = _getSuperBlockPos(bitString, pos);
-    TFibreSuperBlocksValue blockPos = _getBlockPos(bitString, pos);
-    if (blockPos > 0u && superBlockPos == _getSuperBlockPos(bitString, pos - 1))
-        getFibre(bitString, FibreBlocks())[blockPos] = getFibre(bitString, FibreBlocks())[blockPos - 1]
-                + _getRankInBlock(bitString.bits[blockPos - 1]);
-
-    // Here we compute the new rank if the last and second last bit are in
-    // different blocks.
-    if ((superBlockPos > _getSuperBlockPos(bitString, pos - 1)) && superBlockPos > 0u)
-        getFibre(bitString, FibreSuperBlocks())[superBlockPos] = getFibre(bitString, FibreSuperBlocks())[superBlockPos - 1]
-                + getFibre(bitString, FibreBlocks())[blockPos - 1]
-                + _getRankInBlock(bitString.bits[blockPos - 1]);
-}
-
-
-// ==========================================================================
-template <typename TSpec, typename TSize, typename TExpand>
-inline typename Size<RankSupportBitString<TSpec> >::Type
-reserve(RankSupportBitString<TSpec> & bitString, TSize const size, Tag<TExpand> const tag)
-{
-    typedef RankSupportBitString<TSpec>                                     TRankSupportBitString;
-    typedef typename Fibre<TRankSupportBitString, FibreBits>::Type          TFibreBits;
-    typedef typename Fibre<TRankSupportBitString, FibreBlocks>::Type        TFibreBlocks;
-    typedef typename Fibre<TRankSupportBitString, FibreSuperBlocks>::Type   TFibreSuperBlocks;
-    typedef typename Value<TFibreBits>::Type                                TFibreBitsValue;
-    typedef typename Value<TFibreBlocks>::Type                              TFibreBlocksValue;
-    typedef typename Value<TFibreSuperBlocks>::Type                         TFibreSuperBlocksValue;
-
-    TFibreBlocksValue _bitsPerBlock = BitsPerValue<TFibreBitsValue>::VALUE;
-    TFibreSuperBlocksValue _numberOfBlocks = (size + _bitsPerBlock - 1) / _bitsPerBlock;
-
-    resserve(bitString.blocks, _numberOfBlocks, tag);
-    reserve(bitString.superBlocks, (_numberOfBlocks + _bitsPerBlock - 1) / _bitsPerBlock, tag);
-    return reserve(bitString.bits, _numberOfBlocks, tag) * _bitsPerBlock;
-}
-
-// ==========================================================================
-/**
-.Function.resize
-..param.object:
-...type:Class.RankSupportBitString
-*/
-template <typename TSpec, typename TLength, typename TValue, typename TExpand>
-inline typename Size<RankSupportBitString<TSpec> >::Type
-resize(RankSupportBitString<TSpec> & bitString, TLength const _length, TValue const _value, Tag<TExpand> const tag)
-{
-    typedef RankSupportBitString<TSpec>                                     TRankSupportBitString;
-    typedef typename Fibre<TRankSupportBitString, FibreBits>::Type          TFibreBits;
-    typedef typename Fibre<TRankSupportBitString, FibreBlocks>::Type        TFibreBlocks;
-    typedef typename Fibre<TRankSupportBitString, FibreSuperBlocks>::Type   TFibreSuperBlocks;
-    typedef typename Value<TFibreBits>::Type                                TFibreBitsValue;
-    typedef typename Value<TFibreBlocks>::Type                              TFibreBlocksValue;
-    typedef typename Value<TFibreSuperBlocks>::Type                         TFibreSuperBlocksValue;
-
-    TFibreBlocksValue _bitsPerBlock = BitsPerValue<TFibreBitsValue>::VALUE;
-    TFibreSuperBlocksValue _numberOfBlocks = (_length + _bitsPerBlock - 1) / _bitsPerBlock;
-
-    TLength currentLength = length(bitString);
-
-    resize(bitString.bits, _numberOfBlocks, 0, tag);
-    resize(bitString.blocks, _numberOfBlocks, 0, tag);
-    resize(bitString.superBlocks, (_numberOfBlocks + _bitsPerBlock - 1) / _bitsPerBlock, 0, tag);
-
-    if (_value != 0 && currentLength < _length)
-    {
-        for (unsigned i = currentLength; i < (typename MakeUnsigned<TLength const>::Type)_length; ++i)
-            setBit(bitString, i);
-        _updateRanks(bitString, currentLength);
-    }
-
-    return bitString._length = _length;
-}
-
-template <typename TSpec, typename TLength, typename TExpand>
-inline typename Size<RankSupportBitString<TSpec> >::Type
-resize(RankSupportBitString<TSpec> & bitString, TLength const _length, Tag<TExpand> const tag)
-{
-    return resize(bitString, _length, 0, tag);
-}
-
-// ==========================================================================
-/**
-.Function.setBitTo
-..signature:setBitTo(bitString, pos, bit)
-..param.bitString:The bit string.
-...type:Class.RankSupportBitString
-..param.pos:Position of the bit.
-..param.bit:The value of the bit.
-...remarks:Note that values different from 0 are interpreted as 1.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-
-RankSupportBitString<> bitString;
-resize(bitString, length(genome));
-
-for (unsigned i = 0; i < length(genome); ++i)
-    if(genome[i] < Dna5('c'))
-        setBitTo(bitString, 1);
-
-updateRanks_(bitString);
-*/
-template <typename TSpec, typename TPos>
-inline void setBit(RankSupportBitString<TSpec> & bitString, TPos pos)
-{
-    //typedef RankSupportBitString<TSpec>                                     TRankSupportBitString;
-    typedef typename Fibre<RankSupportBitString<TSpec>, FibreBits>::Type    TFibreBits;
-    typedef typename Value<TFibreBits>::Type                                TFibreBitsValue;
-
-    TFibreBitsValue const shiftValue = (TFibreBitsValue)1u << _getPosInBlock(bitString, pos);
-    bitString.bits[_getBlockPos(bitString, pos)] |= shiftValue;
-}
-
-template <typename TSpec, typename TPos>
-inline void clearBit(RankSupportBitString<TSpec> & bitString, TPos pos)
-{
-    //typedef RankSupportBitString<TSpec>                                     TRankSupportBitString;
-    typedef typename Fibre<RankSupportBitString<TSpec>, FibreBits>::Type    TFibreBits;
-    typedef typename Value<TFibreBits>::Type                                TFibreBitsValue;
-
-    TFibreBitsValue const shiftValue = (TFibreBitsValue)1u << _getPosInBlock(bitString, pos);
-    bitString.bits[_getBlockPos(bitString, pos)] &= ~shiftValue;
-}
-
-template <typename TSpec, typename TPos>
-inline void setBitTo(RankSupportBitString<TSpec> & bitString, TPos pos, bool value)
-{
-    if (value)
-        setBit(bitString, pos);
-    else
-        clearBit(bitString, pos);
-}
-
-// ==========================================================================
-/**
-.Function.open
-..signature:open(object, filename[ ,openMode])
-..param.object:The object to be opened.
-...type:Class.RankSupportBitString
-*/
-
-template <typename TSpec>
-inline bool open(
-    RankSupportBitString<TSpec> & string,
-    const char * fileName,
-    int openMode)
-{
-    typedef typename Value<typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type>::Type TValue;
-    String<TValue> lengthString;
-    resize(lengthString, 1, Exact());
-
-    String<char> name;
-    name = fileName;    append(name, ".bit");
-    if (!open(getFibre(string, FibreBits()), toCString(name), openMode))
-        return false;
-
-    name = fileName;    append(name, ".bl");    open(getFibre(string, FibreBlocks()), toCString(name), openMode);
-    name = fileName;    append(name, ".sbl");   open(getFibre(string, FibreSuperBlocks()), toCString(name), openMode);
-    name = fileName;    append(name, ".len");    open(lengthString, toCString(name), openMode);
-    string._length = lengthString[0];
-    return true;
-}
-
-template <typename TSpec>
-inline bool open(
-    RankSupportBitString<TSpec> & string,
-    const char * fileName)
-{
-    return open(string, fileName, OPEN_RDONLY);
-}
-
-template <typename TSpec, typename TSetSpec>
-inline bool open(
-    StringSet<RankSupportBitString<TSpec>, TSetSpec> & strings,
-    const char * fileName)
-{
-    return open(strings, fileName, OPEN_RDONLY);
-}
-
-// ==========================================================================
-/**
-.Function.RankSupportBitString#save
-..class:Class.RankSupportBitString
-..summary:This functions saves a @Class.RankSupportBitString@ to disk.
-..signature:save(bitString, fileName [, openMode])
-..param.bitString:The bit string to be saved.
-...type:Class.RightArrayBinaryTree
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-template <typename TSpec>
-inline bool save(
-    RankSupportBitString<TSpec> const & string,
-    const char * fileName,
-    int openMode)
-{
-    typedef typename Value<typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type>::Type TValue;
-    String<TValue> lengthString;
-    resize(lengthString, 1, Exact());
-    lengthString[0] = length(string);
-    String<char> name;
-    name = fileName;    append(name, ".len");   save(lengthString, toCString(name), openMode);
-    name = fileName;    append(name, ".bit");   save(getFibre(string, FibreBits()), toCString(name), openMode);
-    name = fileName;    append(name, ".bl");    save(getFibre(string, FibreBlocks()), toCString(name), openMode);
-    name = fileName;    append(name, ".sbl");   save(getFibre(string, FibreSuperBlocks()), toCString(name), openMode);
-    return true;
-}
-
-template <typename TSpec>
-inline bool save(
-    RankSupportBitString<TSpec> const & string,
-    const char * fileName)
-{
-    return save(string, fileName, DefaultOpenMode<RankSupportBitString<TSpec> >::VALUE);
-}
-
-template <typename TSpec, typename TSetSpec>
-inline bool save(
-    StringSet<RankSupportBitString<TSpec>, TSetSpec> const & strings,
-    const char * fileName)
-{
-    return save(strings, fileName, DefaultOpenMode<RankSupportBitString<TSpec> >::VALUE);
-}
-
-// ==========================================================================
-template <typename TValue>
-inline void printBits(TValue entrie)
-{
-    unsigned bitsPerValue = BitsPerValue<TValue>::VALUE;
-    TValue one = 1;
-    std::cout << "entrie: " << entrie << std::endl;
-    std::cout << bitsPerValue << std::endl;
-    for (TValue i = 0; i < bitsPerValue; ++i)
-    {
-        std::cout << ((entrie >> i) & one);
-    }
-    std::cout << std::endl;
-}
-
-template <typename TValue, typename TSize>
-inline std::ostream & printBits(std::ostream & stream, TValue entrie, TSize blockSize)
-{
-    unsigned bitsPerValue = BitsPerValue<TValue>::VALUE;
-    bool temp;
-    for (int i = bitsPerValue - 1; i >= 0; --i)
-    {
-        temp = (entrie >> i) & 1;
-        stream << temp;
-        if ((bitsPerValue - i) % blockSize == 0)
-            stream << " ";
-    }
-    return stream;
-}
-
-template <typename TSpec>
-inline std::ostream & operator<<(std::ostream & stream, const RankSupportBitString<TSpec> & rankSupportBitString)
-{
-    typedef typename Fibre<RankSupportBitString<TSpec>, FibreBits>::Type                TBitString;
-    typedef typename Fibre<RankSupportBitString<TSpec>, FibreBlocks>::Type             TBlockString;
-    typedef typename Fibre<RankSupportBitString<TSpec>, FibreSuperBlocks>::Type        TSuperBlockString;
-
-    typedef typename Value<TBitString>::Type          TBitStringValue;
-    typedef typename Value<TBlockString>::Type       TBlockStringValue;
-    typedef typename Value<TSuperBlockString>::Type  TSuperBlockStringValue;
-
-    unsigned bitsPerBlock = BitsPerValue<typename Value<TBitString>::Type>::VALUE;
-
-    TBitString const & bits = rankSupportBitString.bits;
-    TBlockString const & blockString = rankSupportBitString.blocks;
-    TSuperBlockString const & superBlocks = rankSupportBitString.superBlocks;
-
-    stream << "  ";
-    for (TBitStringValue i = 0; i < length(bits); i++)
-    {
-        printBits(stream, bits[i], bitsPerBlock);
-    }
-    stream << std::endl;
-
-    for (TBlockStringValue i = 0; i < length(blockString); i++)
-    {
-        stream << blockString[i] << " ";
-    }
-    stream << std::endl;
-
-    for (TSuperBlockStringValue i = 0; i < length(superBlocks); i++)
-    {
-        stream << superBlocks[i] << " ";
-    }
-    return stream;
-}
-
-}
-
-
-#endif  // INDEX_FM_BRANK_SUPPORT_BIT_STRING_H_
diff --git a/seqan/index/index_fm_rank_support_bit_string_iterator.h b/seqan/index/index_fm_rank_support_bit_string_iterator.h
deleted file mode 100755
index 3a4fb55..0000000
--- a/seqan/index/index_fm_rank_support_bit_string_iterator.h
+++ /dev/null
@@ -1,173 +0,0 @@
-// ==========================================================================
-//                 seqan - the library for sequence analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Jochen Singer <jochen.singer@fu-berlin.de>
-// ==========================================================================
-
-//SEQAN_NO_DDDOC:do not generate documentation for this file
-
-#ifndef INDEX_FM_RANK_SUPPORT_BIT_STRING_ITERATOR_H_
-#define INDEX_FM_RANK_SUPPORT_BIT_STRING_ITERATOR_H_
-
-namespace seqan {
-// ==========================================================================
-// Metafunctions
-// ==========================================================================
-
-template <typename TSpec>
-struct Iterator<RankSupportBitString<TSpec> const, Standard>
-{
-    typedef Iter<RankSupportBitString<TSpec> const, PositionIterator> Type;
-};
-
-template <typename TSpec>
-struct Iterator<RankSupportBitString<TSpec>, Standard>
-{
-    typedef Iter<RankSupportBitString<TSpec>, PositionIterator> Type;
-};
-
-template <typename TSpec>
-struct Iterator<RankSupportBitString<TSpec>, Rooted>:
-    Iterator<RankSupportBitString<TSpec>, Standard>{};
-
-template <typename TSpec>
-struct Iterator<RankSupportBitString<TSpec> const, Rooted>:
-    Iterator<RankSupportBitString<TSpec> const, Standard>{};
-
-// ==========================================================================
-// Functions
-// ==========================================================================
-template <typename TSpec>
-inline typename Iterator<RankSupportBitString<TSpec>, Standard>::Type
-begin(RankSupportBitString<TSpec> & rsbs, Standard)
-{
-    return typename Iterator<RankSupportBitString<TSpec>, Standard>::Type(rsbs, 0u);
-}
-
-template <typename TSpec>
-inline typename Iterator<RankSupportBitString<TSpec>, Standard>::Type
-begin(RankSupportBitString<TSpec> const & rsbs, Standard)
-{
-    return typename Iterator<RankSupportBitString<TSpec> const, Standard>::Type(rsbs, 0u);
-}
-
-template <typename TSpec>
-inline typename Iterator<RankSupportBitString<TSpec>, Rooted>::Type
-begin(RankSupportBitString<TSpec> & rsbs, Rooted)
-{
-    return typename Iterator<RankSupportBitString<TSpec>, Rooted>::Type(rsbs, 0u);
-}
-
-template <typename TSpec>
-inline typename Iterator<RankSupportBitString<TSpec>, Rooted>::Type
-begin(RankSupportBitString<TSpec> const & rsbs, Rooted)
-{
-    return typename Iterator<RankSupportBitString<TSpec> const, Rooted>::Type(rsbs, 0u);
-}
-
-// ==========================================================================
-template <typename TSpec>
-inline typename Iterator<RankSupportBitString<TSpec>, Standard>::Type
-end(RankSupportBitString<TSpec> & rsbs, Standard)
-{
-    return typename Iterator<RankSupportBitString<TSpec>, Standard >::Type(rsbs, length(rsbs));
-}
-
-template <typename TSpec>
-inline typename Iterator<RankSupportBitString<TSpec> const, Standard>::Type
-end(RankSupportBitString<TSpec> const & rsbs, Standard)
-{
-    return typename Iterator<RankSupportBitString<TSpec> const, Standard >::Type(rsbs, length(rsbs));
-}
-
-template <typename TSpec>
-inline typename Iterator<RankSupportBitString<TSpec>, Rooted>::Type
-end(RankSupportBitString<TSpec> & rsbs, Rooted)
-{
-    return typename Iterator<RankSupportBitString<TSpec>, Rooted >::Type(rsbs, length(rsbs));
-}
-
-template <typename TSpec>
-inline typename Iterator<RankSupportBitString<TSpec> const, Rooted>::Type
-end(RankSupportBitString<TSpec> const & rsbs, Rooted)
-{
-    return typename Iterator<RankSupportBitString<TSpec> const, Rooted >::Type(rsbs, length(rsbs));
-}
-
-// ==========================================================================
-struct Bit_;
-struct Rank_;
-
-typedef Tag<Bit_>   const Bit;
-typedef Tag<Rank_>  const Rank;
-
-template <typename TSpec>
-inline bool getValue(Iter<RankSupportBitString<TSpec>, PositionIterator> const & it)
-{
-    return isBitSet(value(it), position(it));
-}
-
-template <typename TSpec>
-inline bool getValue(Iter<RankSupportBitString<TSpec>, PositionIterator> & it)
-{
-    return isBitSet(value(it), position(it));
-}
-
-template <typename TSpec>
-inline bool getValue(Iter<RankSupportBitString<TSpec>, PositionIterator> const & it, Bit)
-{
-    return getValue(it);
-}
-
-template <typename TSpec>
-inline bool getValue(Iter<RankSupportBitString<TSpec>, PositionIterator> & it, Bit)
-{
-    return getValue(it);
-}
-
-// ==========================================================================
-template <typename TSpec>
-inline typename Size<RankSupportBitString<TSpec> >::Type
-getValue(Iter<RankSupportBitString<TSpec>, PositionIterator> const & it, Rank)
-{
-    return getRank(value(it), position(it));
-}
-
-template <typename TSpec>
-inline typename Size<RankSupportBitString<TSpec> >::Type
-getValue(Iter<RankSupportBitString<TSpec>, PositionIterator> & it, Rank)
-{
-    return getRank(value(it), position(it));
-}
-
-}
-#endif // INDEX_FM_COMPRESSED_SA_ITERATOR_H_
-
diff --git a/seqan/index/index_fm_right_array_binary_tree.h b/seqan/index/index_fm_right_array_binary_tree.h
old mode 100755
new mode 100644
index 9266d44..14d1f63
--- a/seqan/index/index_fm_right_array_binary_tree.h
+++ b/seqan/index/index_fm_right_array_binary_tree.h
@@ -1,7 +1,8 @@
 // ==========================================================================
-//                 seqan - the library for sequence analysis
+//                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,50 +40,46 @@
 
 namespace seqan {
 
-// ==========================================================================
+// ============================================================================
 // Forwards
-// ==========================================================================
-template <typename TOccTable, typename TPrefixSumTable>
-struct LfTable;
-
-template <typename TValue>
-struct WaveletTree;
-
-template<typename TValue> 
-class RankDictionary;
-
-template<typename TRankDictionarySpec, typename TSpec> 
-class SentinelRankDictionary;
-
-struct FibreTreeStructure_;
-typedef Tag<FibreTreeStructure_> const FibreTreeStructure;
+// ============================================================================
 
 template <typename TChar, typename TSpec = void>
 class RightArrayBinaryTree;
 
-// ==========================================================================
-// Tags 
-// ==========================================================================
+// ============================================================================
+// Tags
+// ============================================================================
 //
-/**
-.Tag.RightArrayBinaryTree Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Class.RightArrayBinaryTree@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a RightArrayBinaryTree.
-..cat:RightArrayBinaryTree
-..tag.FibreTreeStructureEncoding:The string encoding the wavelet tree structure.
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-
-///.Metafunction.Fibre.param.TContainer.type:Class.RightArrayBinaryTree
-///.Metafunction.Fibre.param.TSpec.type:Tag.RightArrayBinaryTree Fibres
+/*!
+ * @defgroup RightArrayBinaryTreeFibres RightArrayBinaryTree Fibres
+ * @brief Tag to select a specific fibre (e.g. table, object, ...) of a @link
+ *        RightArrayBinaryTree @endlink.
+ *
+ * These tags can be used to get @link Fibre Fibres @endlink of a @link RightArrayBinaryTree @endlink.
+ *
+ * @see Fibre
+ * @see Index#getFibre
+ *
+ * @tag RightArrayBinaryTreeFibres#FibreTreeStructureEncoding
+ *
+ * @brief The string encoding the wavelet tree structure.
+ */
+
 struct FibreTreeStructureEncoding_;
 typedef Tag<FibreTreeStructureEncoding_> const FibreTreeStructureEncoding;
 
-// ==========================================================================
+struct FibreTreeStructure_;
+typedef Tag<FibreTreeStructure_> const FibreTreeStructure;
+
+// ============================================================================
 // Metafunctions
-// ==========================================================================
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Fibre
+// ----------------------------------------------------------------------------
+
 template <typename TChar, typename TSpec>
 struct Fibre<RightArrayBinaryTree<TChar, TSpec>, FibreTreeStructureEncoding>
 {
@@ -91,26 +88,10 @@ struct Fibre<RightArrayBinaryTree<TChar, TSpec>, FibreTreeStructureEncoding>
     typedef String<Pair<TChar, TPos> > Type;
 };
 
-// template <typename TChar, typename TSpec>
-// struct Fibre<RightArrayBinaryTree<TChar, TSpec> const, FibreTreeStructureEncoding>
-// {
-//     typedef typename Fibre<RightArrayBinaryTree<TChar, TSpec>, FibreTreeStructureEncoding>::Type const Type;
-// };
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
 
-// ==========================================================================
-template <typename TChar, typename TSpec>
-struct Reference<RightArrayBinaryTree<TChar, TSpec> >
-{
-    typedef typename Value<RightArrayBinaryTree<TChar, TSpec> >::Type & Type;
-};
-
-template <typename TChar, typename TSpec>
-struct Reference<const RightArrayBinaryTree<TChar, TSpec> >
-{
-    typedef typename Value<RightArrayBinaryTree<TChar, TSpec> >::Type const & Type;
-};
-
-// ==========================================================================
 template <typename TChar, typename TSpec>
 struct Value<RightArrayBinaryTree<TChar, TSpec> >
 {
@@ -122,36 +103,36 @@ struct Value<RightArrayBinaryTree<TChar, TSpec> >
 };
 
 template <typename TChar, typename TSpec>
-struct Value<RightArrayBinaryTree<TChar, TSpec> const>
-{
-    typedef typename Fibre<RightArrayBinaryTree<TChar, TSpec>, FibreTreeStructureEncoding>::Type TWaveletTreeVertices_;
-    typedef typename Value<TWaveletTreeVertices_>::Type TWaveletTreeVertex_;
-    typedef typename Value<TWaveletTreeVertex_, 2>::Type TPos;
-
-    typedef Pair<TChar, TPos> Type;
-};
+struct Value<RightArrayBinaryTree<TChar, TSpec> const> :
+    Value<RightArrayBinaryTree<TChar, TSpec> > {};
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class RightArrayBinaryTree
+// ----------------------------------------------------------------------------
+/*!
+ * @class RightArrayBinaryTree
+ * @headerfile <seqan/index.h>
+ * @brief A special format to encode the structure of a wavelet tree.  The structure is very space efficient because
+ *        only one position is stored which encodes where the left and right subtree of a given node exist.
+ *
+ * @signature template <typename TChar, typename TSpec>
+ *            class RightArrayBinaryTree;
+ *
+ * @tparam TValue The type of the stored characters.
+ * @tparam TSpec  The wavelet tree structure specialisation. Default: void.
+ */
 
-// ==========================================================================
-//Tags, Classes, Enums
-// ==========================================================================
-
-/**
-.Class.RightArrayBinaryTree:
-..cat:WaveletTree
-..summary:A special format to encode the structure of a wavelet tree. The structure is very space efficient because only one position is stored which encodes where the left and right subtree of a given node exist.
-..signature:RightArrayBinaryTree<TValue, TSpec>
-..param.TSpec:The value type, that is the type of the stored characters.
-..param.TSpec:The wavelet tree structure specialisation.
-...default:void.
-..include:seqan/index.h
-*/
 template <typename TChar, typename TSpec>
 class RightArrayBinaryTree
 {
 public:
     typename Fibre<RightArrayBinaryTree, FibreTreeStructureEncoding>::Type treeVertices;
     TChar minCharValue;
- 
+
     RightArrayBinaryTree() :
         treeVertices(),
         minCharValue()
@@ -162,134 +143,138 @@ class RightArrayBinaryTree
         treeVertices(),
         minCharValue()
     {
-        createRightArrayBinaryTree(*this,
-                                    text);
-    }
-
-    inline bool operator==(const RightArrayBinaryTree & b) const
-    {
-        return treeVertices == b.treeVertices;
+        createRightArrayBinaryTree(*this, text);
     }
 };
 
-// ==========================================================================
+// ============================================================================
 // Functions
-// ==========================================================================
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTree#clear
+ * @headerfile <seqan/index.h>
+ * @brief Resets a right-array-binary tree.
+ *
+ * @signature void clear(rightArrayBinaryTree);
+ *
+ * @param[in,out] rightArrayBinaryTree The RightArrayBinaryTree to be cleared.
+ */
 
-/**
-.Function.clear
-..param.object:
-...type:Class.RightArrayBinaryTree
-*/
 template <typename TChar, typename TSpec>
 inline void clear(RightArrayBinaryTree<TChar, TSpec> & treeStructure)
 {
     clear(treeStructure.treeVertices);
 }
 
-// ==========================================================================
-/**
-.Function.createRightArrayBinaryTree
-..summary:Computes the wavelet tree structure of a text.
-..signature:createRightArrayBinaryTree(waveletTreeStructure, text)
-..param.waveletTreeStructure:A wavelet tree structure.
-...type:Class.RightArrayBinaryTree
-..param.text:A text.
-...type:Class.String
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-
-RightArrayBinaryTree<Dna5> waveletTreeStructure;
-computeRightArrayBinaryTree(genome);
-*/
+// ----------------------------------------------------------------------------
+// Function createRightArrayBinaryTree()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTree#createRightArrayBinaryTree
+ * @headerfile <seqan/index.h>
+ * @brief Computes the right-array-binary tree of a text.
+ *
+ * @signature void createRightArrayBinaryTree(rightArrayBinaryTree, text);
+ *
+ * @param[in] rightArrayBinaryTree A wavelet tree structure.
+ * @param[in] text                 A @link TextConcept text @endlink.
+ */
+
 // This function computes the wavelet tree structure.
-template <typename TChar, typename TSpec, typename TBorderString, typename TPrefixSumTable, typename TIterSpec>
-inline void createRightArrayBinaryTree(Iter<RightArrayBinaryTree<TChar, TSpec>, TIterSpec> & it,
-                                        TBorderString & borderString,
-                                        TPrefixSumTable & pst)
+template <typename TChar, typename TSpec, typename TIterSpec, typename TBorderString, typename TPrefixSums>
+inline void _createRightArrayBinaryTreeImpl(Iter<RightArrayBinaryTree<TChar, TSpec>, TIterSpec> & it,
+                                            TBorderString & borderString,
+                                            TPrefixSums const & sums)
 {
     do
     {
         // TODO (singer): Comment this
         if (back(borderString).i2 - back(borderString).i1 + 1 < 3 ||
-            getPrefixSum(pst, back(borderString).i1) == getPrefixSum(pst, back(borderString).i2 + 1))
+            sums[back(borderString).i1] == sums[back(borderString).i2 + 1])
         {
-            setCharacter(it, getCharacter(pst, back(borderString).i1 + 1));
+            setCharacter(it, back(borderString).i1 + 1);
             SEQAN_ASSERT_MSG(isLeaf(it), "You just deleted a subtree.");
         }
         else
-            _setChildVertices(it, borderString, pst);
+            _setChildVertices(it, borderString, sums);
 
-        if (!_goDownConstruction(it) && !_setAndGoRight(it, borderString, pst))
-            while (_goUpStructureConstruction(it, borderString) && !_setAndGoRight(it, borderString, pst))
-                ;
+        if (!_goDownConstruction(it) && !_setAndGoRight(it, borderString))
+            while (_goUpStructureConstruction(it, borderString) && !_setAndGoRight(it, borderString)) ;
     }
     while (!isRoot(it));
 }
 
-// ==========================================================================
 // This function computes the wavelet tree structure.
-template <typename TChar, typename TSpec, typename TIterSpec, typename TPrefixSumTable>
-inline void createRightArrayBinaryTree(Iter<RightArrayBinaryTree<TChar, TSpec>, TIterSpec> & it,
-                                        TPrefixSumTable & pst)
+template <typename TChar, typename TSpec, typename TIterSpec, typename TPrefixSums>
+inline void _createRightArrayBinaryTreeImpl(Iter<RightArrayBinaryTree<TChar, TSpec>, TIterSpec> & it,
+                                            TPrefixSums const & sums)
 {
-    typedef RightArrayBinaryTree<TChar, TSpec> TRightArrayBinaryTree;
+    typedef RightArrayBinaryTree<TChar, TSpec>                       TRightArrayBinaryTree;
+    typedef typename Size<RightArrayBinaryTree<TChar, TSpec> >::Type TSize;
+
     TRightArrayBinaryTree & waveletTreeStructure = container(it);
 
-    unsigned alpSize = getAlphabetSize(pst);
-    String<Pair<unsigned> > borderString;
-    appendValue(borderString, Pair<unsigned>(0, alpSize - 1));
+    String<Pair<TSize> > borderString;
+    appendValue(borderString, Pair<TSize>(0, ValueSize<TChar>::VALUE - 1));
     _resize(waveletTreeStructure, 1, Exact());
-    createRightArrayBinaryTree(it, borderString, pst);
+    _createRightArrayBinaryTreeImpl(it, borderString, sums);
 }
 
-// This function computes the wavelet tree structure contained in the lfTable.
-template < typename TValue, typename TSpec, typename TPrefixSumTable>
-inline void createRightArrayBinaryTree(LfTable<SentinelRankDictionary<RankDictionary<WaveletTree<TValue> >, TSpec>, TPrefixSumTable> & lfTable)
-{
-    typedef typename Fibre<RankDictionary<WaveletTree<TValue> >, FibreTreeStructure>::Type TRightArrayBinaryTree;
-    TRightArrayBinaryTree & rightArrayBinaryTree = lfTable.occTable.rankDictionary.waveletTreeStructure;
-
-    typename Iterator<TRightArrayBinaryTree, TopDown<ParentLinks<void> > >::Type it(rightArrayBinaryTree, 0u);
-    createRightArrayBinaryTree(it, lfTable.prefixSumTable);
-}
+// ----------------------------------------------------------------------------
+// Function createRightArrayBinaryTree()
+// ----------------------------------------------------------------------------
 
-template <typename TChar, typename TSpec, typename TText>
-inline void createRightArrayBinaryTree(RightArrayBinaryTree<TChar, TSpec> & waveletTreeStructure, TText const & text)
+template <typename TChar, typename TSpec, typename TPrefixSums>
+inline void
+createRightArrayBinaryTree(RightArrayBinaryTree<TChar, TSpec> & waveletTreeStructure, TPrefixSums const & sums)
 {
-    PrefixSumTable<TChar, void> pst(text);
-
     typename Iterator<RightArrayBinaryTree<TChar, TSpec>, TopDown<ParentLinks<> > >::Type it(waveletTreeStructure, 0u);
-    createRightArrayBinaryTree(it, pst);
+    _createRightArrayBinaryTreeImpl(it, sums);
 }
 
-// ==========================================================================
-/**
-.Function.empty
-..param.object:
-...type:Class.RightArrayBinaryTree
-*/
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RightArrayBinaryTree#empty
+ * @headerfile <seqan/index.h>
+ * @brief Checks whether or not a right-array-binary tree contains any elements.
+ *
+ * @signature bool empty(rightArrayBinaryTree);
+ *
+ * @param[in] rightArrayBinaryTree The right-array-binary tree to be queried.
+ *
+ * @return bool Returns <tt>true</tt> if the rank-support-bit string is empty and <tt>false</tt> otherwise.
+ */
+
 template <typename TChar, typename TSpec>
 inline bool empty(RightArrayBinaryTree<TChar, TSpec> const & treeStructure)
 {
     return empty(getFibre(treeStructure, FibreTreeStructureEncoding()));
 }
 
-// ==========================================================================
-/**
-.Function.RightArrayBinaryTree#getFibre:
-..summary:Returns a specific fibre of a container.
-..signature:getFibre(container, fibreTag)
-..class:Class.RightArrayBinaryTree
-..cat:Index
-..param.container:The container holding the fibre.
-...type:Class.RightArrayBinaryTree
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.RightArrayBinaryTree Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
+// ----------------------------------------------------------------------------
+// Function getFibre()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTree#getFibre
+ * @headerfile <seqan/index.h>
+ * @brief Returns a specific fibre of a right-array-binary tree.
+ *
+ * @signature TFibre getFibre(rightArrayBinaryTree, fibreTag);
+ *
+ * @param[in] rightArrayBinaryTree
+ *                      The container holding the fibre.
+ * @param[in] fibreTag  A tag that identifies the @link Fibre @endlink.  Types: @link RightArrayBinaryTreeFibres
+ *                      RightArrayBinaryTree Fibres @endlink.
+ *
+ * @return TFibre A reference to the @link Fibre @endlink object.
+ */
 template <typename TChar, typename TSpec>
 inline typename Fibre<RightArrayBinaryTree<TChar, TSpec>, FibreTreeStructureEncoding>::Type &
 getFibre(RightArrayBinaryTree<TChar, TSpec> & treeStructure, FibreTreeStructureEncoding)
@@ -304,15 +289,32 @@ getFibre(RightArrayBinaryTree<TChar, TSpec> const & treeStructure, FibreTreeStru
     return treeStructure.treeVertices;
 }
 
-// ==========================================================================
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
 // This function returns the number of different entries in the wavelet tree structure.
+/*!
+ * @fn RightArrayBinaryTree#length
+ * @brief Returns the number of nodes in the right-array-binary-tree.
+ *
+ * @signature TSize length(rightArrayBinaryTree);
+ *
+ * @param[in] tree The right-array-binary-tree to query for its size.
+ *
+ * @return TSize The number of nodes in the right-array-binary-tree.
+ */
 template <typename TChar, typename TSpec>
-inline unsigned _length(RightArrayBinaryTree<TChar, TSpec> const & tree)
+inline typename Size<RightArrayBinaryTree<TChar, TSpec> >::Type
+length(RightArrayBinaryTree<TChar, TSpec> const & tree)
 {
     return length(tree.treeVertices);
 }
 
-// ==========================================================================
+// ----------------------------------------------------------------------------
+// Function _resize()
+// ----------------------------------------------------------------------------
+
 // This function resizes the string holding the nodes of the wavelet tree structure.
 template <typename TChar, typename TSpec, typename TSize, typename TExpand>
 inline typename Size<RightArrayBinaryTree<TChar, TSpec> >::Type
@@ -325,90 +327,106 @@ _resize(RightArrayBinaryTree<TChar, TSpec> & treeStructure, TSize size, Tag<TExp
 template <typename TChar, typename TSpec, typename TSize, typename TExpand>
 inline typename Size<RightArrayBinaryTree<TChar, TSpec> >::Type
 _resize(RightArrayBinaryTree<TChar, TSpec> & treeStructure, TSize size,
-                   typename Value<typename Fibre<RightArrayBinaryTree<TChar, TSpec>, FibreTreeStructureEncoding>::Type>::Type value,
-                   Tag<TExpand> tag)
+        typename Value<typename Fibre<RightArrayBinaryTree<TChar, TSpec>, FibreTreeStructureEncoding>::Type>::Type value,
+        Tag<TExpand> tag)
 {
     return resize(treeStructure.treeVertices, size, value, tag);
 }
 
-// ==========================================================================
-/**
-.Function.RightArrayBinaryTree#open
-..class:Class.RightArrayBinaryTree
-..summary:This functions loads a @Class.RightArrayBinaryTree@ from disk.
-..signature:open(rightArrayBinaryTree, fileName [, openMode])
-..param.rightArrayBinaryTree:The rightArrayBinaryTree.
-...type:Class.RightArrayBinaryTree
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTree#open
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief This functions loads a @link RightArrayBinaryTree @endlink from disk.
+ *
+ * @signature bool open(rightArrayBinaryTree, fileName [, openMode])
+ *
+ * @param[in,out] rightArrayBinaryTree
+ *                               The RightArrayBinaryTree.
+ * @param[in]     fileName       C-style character string containing the file name.
+ * @param[in]     openMode       The combination of flags defining how the file should be
+ *                               opened.  To open a file read-only, write-only or to read and
+ *                               write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
+ *                               <tt>OPEN_RDWR</tt>.  To create or overwrite a file add
+ *                               <tt>OPEN_CREATE</tt>.  To append a file if existing add
+ *                               <tt>OPEN_APPEND</tt>.  To circumvent problems, files are always
+ *                               opened in binary mode.  Default: <tt>OPEN_RDWR | OPEN_CREATE |
+ *                               OPEN_APPEND</tt>.
+ *
+ * @return bool A <tt>bool</tt> which is <tt>true</tt> on success.
+ */
+
 template <typename TChar, typename TSpec>
-inline bool open(
-    RightArrayBinaryTree<TChar, TSpec> & treeStructure,
-    const char * fileName,
-    int openMode)
+inline bool open(RightArrayBinaryTree<TChar, TSpec> & treeStructure, const char * fileName, int openMode)
 {
     String<char> name;
 
-    String<TChar> minString;
-    name = fileName;    append(name, ".rtv");   if(!open(getFibre(treeStructure, FibreTreeStructureEncoding()), toCString(name), openMode)) return false;
-    name = fileName;    append(name, ".rtm");   if(!open(minString, toCString(name), openMode)) return false;
-    treeStructure.minCharValue = minString[0];
+    name = fileName;
+    append(name, ".rtv");
+    if (!open(getFibre(treeStructure, FibreTreeStructureEncoding()), toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".rtm");
+    if (!open(treeStructure.minCharValue, toCString(name), openMode)) return false;
+
     return true;
 }
 
 template <typename TChar, typename TSpec>
-inline bool open(
-    RightArrayBinaryTree<TChar, TSpec> & treeStructure,
-    const char * fileName)
+inline bool open(RightArrayBinaryTree<TChar, TSpec> & treeStructure, const char * fileName)
 {
     return open(treeStructure, fileName, DefaultOpenMode<RightArrayBinaryTree<TChar, TSpec> >::VALUE);
 }
 
-// ==========================================================================
-/**
-.Function.RightArrayBinaryTree#save
-..class:Class.RightArrayBinaryTree
-..summary:This functions saves a @Class.RightArrayBinaryTree@ to disk.
-..signature:save(rightArrayBinaryTree, fileName [, openMode])
-..param.rightArrayBinaryTree:The rightArrayBinaryTree.
-...type:Class.RightArrayBinaryTree
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
+// ----------------------------------------------------------------------------
+// Function save()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTree#save
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief This functions saves a @link RightArrayBinaryTree @endlink to disk.
+ *
+ * @signature bool save(rightArrayBinaryTree, fileName [, openMode])
+ *
+ * @param[in,out] rightArrayBinaryTree
+ *                               The RightArrayBinaryTree.
+ * @param[in]     fileName       C-style character string containing the file name.
+ * @param[in]     openMode       The combination of flags defining how the file should be
+ *                               opened.  To open a file read-only, write-only or to read and
+ *                               write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
+ *                               <tt>OPEN_RDWR</tt>.  To create or overwrite a file add
+ *                               <tt>OPEN_CREATE</tt>.  To append a file if existing add
+ *                               <tt>OPEN_APPEND</tt>.  To circumvent problems, files are always
+ *                               opened in binary mode.  Default: <tt>OPEN_RDWR | OPEN_CREATE |
+ *                               OPEN_APPEND</tt>.
+ *
+ * @return bool A <tt>bool</tt> which is <tt>true</tt> on success.
+ */
+
 template <typename TChar, typename TSpec>
-inline bool save(
-    RightArrayBinaryTree<TChar, TSpec> const & treeStructure,
-    const char * fileName,
-    int openMode)
+inline bool save(RightArrayBinaryTree<TChar, TSpec> const & treeStructure, const char * fileName, int openMode)
 {
     String<char> name;
 
-    String<TChar> minString;
-    appendValue(minString, treeStructure.minCharValue);
-    name = fileName;    append(name, ".rtv");   if (!save(getFibre(treeStructure, FibreTreeStructureEncoding()), toCString(name), openMode)) return false;
-    name = fileName;    append(name, ".rtm");   if (!save(minString, toCString(name), openMode)) return false;
+    name = fileName;
+    append(name, ".rtv");
+    if (!save(getFibre(treeStructure, FibreTreeStructureEncoding()), toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".rtm");
+    if (!save(treeStructure.minCharValue, toCString(name), openMode)) return false;
+
     return true;
 }
 
 template <typename TChar, typename TSpec>
-inline bool save(
-    RightArrayBinaryTree<TChar, TSpec> const & treeStructure,
-    const char * fileName)
+inline bool save(RightArrayBinaryTree<TChar, TSpec> const & treeStructure, const char * fileName)
 {
     return save(treeStructure, fileName, DefaultOpenMode<RightArrayBinaryTree<TChar, TSpec> >::VALUE);
 }
diff --git a/seqan/index/index_fm_right_array_binary_tree_iterator.h b/seqan/index/index_fm_right_array_binary_tree_iterator.h
old mode 100755
new mode 100644
index 2a270fa..54752e8
--- a/seqan/index/index_fm_right_array_binary_tree_iterator.h
+++ b/seqan/index/index_fm_right_array_binary_tree_iterator.h
@@ -1,7 +1,8 @@
 // ==========================================================================
-//                 seqan - the library for sequence analysis
+//                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,15 +40,22 @@
 
 namespace seqan {
 
-// ==========================================================================
+// ============================================================================
 // Forwards
-// ==========================================================================
+// ============================================================================
+
 template <typename TSpec>
 struct RightArrayBinaryTreeIterator;
 
-// ==========================================================================
+
+// ============================================================================
 // Metafunctions
-// ==========================================================================
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
+
 template <typename TChar, typename TSpec, typename TIterSpec>
 struct Iterator<RightArrayBinaryTree<TChar, TSpec>, TopDown<TIterSpec> >
 {
@@ -60,7 +68,10 @@ struct Iterator<RightArrayBinaryTree<TChar, TSpec> const, TopDown<TIterSpec> >
     typedef Iter<RightArrayBinaryTree<TChar, TSpec> const, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > Type;
 };
 
-// ==========================================================================
+// ----------------------------------------------------------------------------
+// Metafunction Spec
+// ----------------------------------------------------------------------------
+
 template <typename TChar, typename TSpec, typename TIterSpec>
 struct Spec<Iter<RightArrayBinaryTree<TChar, TSpec>, RightArrayBinaryTreeIterator<TIterSpec> > >
 {
@@ -73,23 +84,21 @@ struct Spec<Iter<RightArrayBinaryTree<TChar, TSpec> const, RightArrayBinaryTreeI
     typedef TIterSpec Type;
 };
 
-// ==========================================================================
+// ============================================================================
 // Classes
-// ==========================================================================
-
-/**
-.Spec.RightArrayBinaryTree Iterator:
-..summary:An iterator for @Class.RightArrayBinaryTree@.
-..cat:Iter
-..general:Class.Iter
-..signature:Iter<RightArrayBinaryTree, TSpec >
-..param.RightArrayBinaryTree:The @Class.RightArrayBinaryTree@.
-...type:Class.RightArrayBinaryTree
-..param.TSpec:Specialisation Tag.
-...type:Spec.TopDown Iterator
-..include:seqan/index.h
-*/
-
+// ============================================================================
+/*!
+ * @class RightArrayBinaryTreeIterator RightArrayBinaryTree Iterator
+ * @extends Iter
+ * @headerfile <seqan/index.h>
+ * @brief An iterator for @link RightArrayBinaryTree @endlink.
+ *
+ * @signature template <typename TSpec>
+ *            class Iter<TRightArrayBinaryTree, TSpec >;
+ *
+ * @tparam TSpec                 Specialisation Tag. Types: TopDownIterator
+ * @tparam TRightArrayBinaryTree The @link RightArrayBinaryTree @endlink.
+ */
 template <typename TTree, typename TIterSpec>
 class Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > >
 {
@@ -128,7 +137,7 @@ class Iter<TTree, RightArrayBinaryTreeIterator<TopDown<ParentLinks<TSpec> > > >
         TBase(),
         history()
     {}
-    
+
     Iter(TTree & treeStructure, TPos pos = 0) :
         TBase(treeStructure,  pos),
         history()
@@ -138,11 +147,25 @@ class Iter<TTree, RightArrayBinaryTreeIterator<TopDown<ParentLinks<TSpec> > > >
 
 };
 
-// ==========================================================================
+// ============================================================================
 // Functions
-// ==========================================================================
-
-///.Function.begin.param.object.type:Class.RightArrayBinaryTree
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function begin()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTree#begin
+ * @headerfile <seqan/index.h>
+ * @brief The begin (root) of a @link RightArrayBinaryTree @endlink.
+ *
+ * @signature TIterator begin(rightArrayBinaryTree, iterSpec);
+ *
+ * @param[in] rightArrayBinaryTree The right-array-binary tree.
+ * @param[in] iterSpec             A specialisation tag. Types: TopDown&lt;&gt;, TopDown&lt;ParentLinks&lt;&gt; &gt;.
+ *
+ * @return TIterator An iterator to the first item in <tt>object</tt>. Metafunctions: Metafunction.Iterator
+ */
 template <typename TChar, typename TSpec, typename TIterSpec>
 inline typename Iterator<RightArrayBinaryTree<TChar, TSpec> const, TIterSpec>::Type
 begin(RightArrayBinaryTree<TChar, TSpec> const & waveletTreeStructure, TIterSpec const &)
@@ -157,7 +180,19 @@ begin(RightArrayBinaryTree<TChar, TSpec> & waveletTreeStructure, TIterSpec const
     return typename Iterator<RightArrayBinaryTree<TChar, TSpec>, TIterSpec>::Type(waveletTreeStructure);
 }
 
-///.Function.container.param.iterator.type:Class.RightArrayBinaryTree
+// ----------------------------------------------------------------------------
+// Function container()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#container
+ * @headerfile <seqan/index.h>
+ * @brief Container of an iterator.
+ * @signature TContainer container(iterator)
+ *
+ * @param[in] iterator An iterator.
+ *
+ * @return TContainer The container that <tt>iterator</tt> traverses.
+ */
 template <typename TTree, typename TIterSpec>
 inline TTree &
 container(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it)
@@ -172,29 +207,49 @@ container(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const
     return *it.waveletTreeStructure;
 }
 
-///.Function.end.param.object.type:Class.RightArrayBinaryTree
+// ----------------------------------------------------------------------------
+// Function end()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTree#end
+ * @headerfile <seqan/index.h>
+ * @brief The end (rigthmost leaf) of a @link RightArrayBinaryTree @endlink.
+ *
+ * @signature TIterator end(rightArrayBinaryTree, iterSpec);
+ *
+ * @param[in] rightArrayBinaryTree The right-array-binary tree.
+ * @param[in] iterSpec             A specialisation tag. Types: TopDown&lt;&gt;, TopDown&lt;ParentLinks&lt;&gt; &gt;.
+ *
+ * @return TIterator An iterator to the first item in <tt>object</tt>.  Metafunctions: Metafunction.Iterator
+ */
 template <typename TChar, typename TSpec, typename TIterSpec>
 inline typename Iterator<RightArrayBinaryTree<TChar, TSpec> const, TIterSpec>::Type
 end(RightArrayBinaryTree<TChar, TSpec> const & waveletTreeStructure, TIterSpec const &)
 {
-    return typename Iterator<RightArrayBinaryTree<TChar, TSpec> const, TIterSpec>::Type(waveletTreeStructure, _length(waveletTreeStructure));
+    return typename Iterator<RightArrayBinaryTree<TChar, TSpec> const, TIterSpec>::Type(waveletTreeStructure, length(waveletTreeStructure));
 }
 
 template <typename TChar, typename TSpec, typename TIterSpec>
 inline typename Iterator<RightArrayBinaryTree<TChar, TSpec>, TIterSpec>::Type
 end(RightArrayBinaryTree<TChar, TSpec> & waveletTreeStructure, TIterSpec const &)
 {
-    return typename Iterator<RightArrayBinaryTree<TChar, TSpec>, TIterSpec>::Type(waveletTreeStructure, _length(waveletTreeStructure));
+    return typename Iterator<RightArrayBinaryTree<TChar, TSpec>, TIterSpec>::Type(waveletTreeStructure, length(waveletTreeStructure));
 }
 
-/**
-.Function.getCharacter
-..summary:This function returns the pivot character of the node the iterator currently points to.
-..signature:getCharacter(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator
-..include:seqan/index.h
-*/
+// ----------------------------------------------------------------------------
+// Function getCharacter()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#getCharacter
+ * @headerfile <seqan/index.h>
+ * @brief This function returns the pivot character of the node the iterator currently points to.
+ *
+ * @signature TChar getCharacter(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return TChar The resulting character.
+ */
 template <typename TTree, typename TIterSpec>
 inline typename Value<typename Value<TTree>::Type, 1>::Type
 getCharacter(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & iter)
@@ -202,14 +257,20 @@ getCharacter(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > con
     return iter.waveletTreeStructure->treeVertices[getPosition(iter)].i1;
 }
 
-/**
-.Function.getLeftChildPos
-..summary:Returns the position in @Class.RightArrayBinaryTree@ of the left child vertex.
-..signature:getLeftChildPos(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator.
-..include:seqan/index.h
-*/
+// ----------------------------------------------------------------------------
+// Function getLeftChildPos()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#getLeftChildPos
+ * @headerfile <seqan/index.h>
+ * @brief Returns the position in @link RightArrayBinaryTree @endlink of the left child node.
+ *
+ * @signature unsigned getLeftChildPos(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return unsigned The left child position.
+ */
 template <typename TTree, typename TIterSpec>
 inline unsigned int getLeftChildPos(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & iter)
 {
@@ -220,19 +281,29 @@ inline unsigned int getLeftChildPos(Iter<TTree, RightArrayBinaryTreeIterator<Top
     return 0;
 }
 
-/**
-.Function.getSubTreeSize
-..summary:Returns the number of vertices in the subtree starting at the position an iterator points to.
-..signature:getSubTreeSize(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator.
-..include:seqan/index.h
-*/
+// ----------------------------------------------------------------------------
+// Function getSubTreeSize()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#getSubTreeSize
+ * @headerfile <seqan/index.h>
+ * @brief Returns the number of vertices in the subtree starting at the position
+ *        an iterator points to.
+ *
+ * @signature unsigned getSubTreeSize(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return unsigned The subtree size.
+ */
 template <typename TTree, typename TIterSpec>
-inline unsigned getSubTreeSize(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & it)
+inline typename Size<TTree>::Type
+getSubTreeSize(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & it)
 {
+    typedef typename Size<TTree>::Type TSize;
+
     Iter<TTree, RightArrayBinaryTreeIterator<TopDown<> > > _it(container(it));
-    unsigned originalPos = getPosition(it);
+    TSize originalPos = getPosition(it);
     goToPosition(_it, originalPos);
     while (goRightChild(_it) || goLeftChild(_it))
         continue;
@@ -240,30 +311,44 @@ inline unsigned getSubTreeSize(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<
     return getPosition(_it) - originalPos;
 }
 
-/**
-.Function.getPosition
-..summary:Returns the position of the iterator in the host.
-..signature:getPosition(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator.
-..include:seqan/index.h
-*/
+// ----------------------------------------------------------------------------
+// Function getPosition()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#getPosition
+ * @headerfile <seqan/index.h>
+ * @brief Returns the position of the iterator in the host.
+ *
+ * @signature unsigned getPosition(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return unsigned The position.
+ */
 template <typename TTree, typename TIterSpec>
-inline unsigned int getPosition(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & it)
+inline typename Size<TTree>::Type
+getPosition(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & it)
 {
     return it.position;
 }
 
-/**
-.Function.getRightChildPos
-..summary:Returns the position in @Class.RightArrayBinaryTree@ of the right child vertex.
-..signature:getLeftChildPos(it)
-..param.it:The iterator.
-...type:Spec.RightArrayBinaryTree Iterator.
-..include:seqan/index.h
-*/
+// ----------------------------------------------------------------------------
+// Function getRightChildPos()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#getRightChildPos
+ * @headerfile <seqan/index.h>
+ * @brief Returns the position in @link RightArrayBinaryTree @endlink of the right child node.
+ *
+ * @signature unsigned getLeftChildPos(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return unsigned The left child position.
+ */
 template <typename TTree, typename TIterSpec>
-inline unsigned int getRightChildPos(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & it)
+inline typename Size<TTree>::Type
+getRightChildPos(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & it)
 {
     if (it.waveletTreeStructure->treeVertices[getPosition(it)].i2 > 2)
     {
@@ -276,6 +361,10 @@ inline unsigned int getRightChildPos(Iter<TTree, RightArrayBinaryTreeIterator<To
     return 0;
 }
 
+// ----------------------------------------------------------------------------
+// Function _historyPush()
+// ----------------------------------------------------------------------------
+
 template <typename TTree, typename TIterSpec, typename TPos>
 inline void _historyPush(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & /*tag*/ , TPos /*tag*/)
 {}
@@ -286,7 +375,20 @@ inline void _historyPush(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<Parent
     appendValue(it.history, pos);
 }
 
-///.Function.goDown.param.iterator.type:Spec.RightArrayBinaryTree Iterator
+// ----------------------------------------------------------------------------
+// Function goDown()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#goDown
+ * @headerfile <seqan/index.h>
+ * @brief Iterates down the leftmost edge in a @link RightArrayBinaryTree @endlink.
+ *
+ * @signature bool goDown(iterator);
+ *
+ * @param[in] iterator The iterator
+ *
+ * @return bool <tt>true</tt> if an edge to go down exists, otherwise <tt>false</tt>.
+ */
 template <typename TTree, typename TIterSpec>
 inline bool goDown(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & iter)
 {
@@ -295,6 +397,10 @@ inline bool goDown(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> >
     return false;
 }
 
+// ----------------------------------------------------------------------------
+// Function _goDownConstruction()
+// ----------------------------------------------------------------------------
+
 template <typename TTree, typename TIterSpec>
 inline bool _goDownConstruction(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it)
 {
@@ -306,31 +412,31 @@ inline bool _goDownConstruction(Iter<TTree, RightArrayBinaryTreeIterator<TopDown
     return false;
 }
 
-/**
-.Function.goLeftChild
-..summary:Sets the iterator to the left child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false.
-..signature:bool goLeftChild(iterator)
-..param.iterator:An iterator of a wavelet tree structure.
-...type:Spec.RightArrayBinaryTree Iterator
-..remarks:$goLeftChild(iterator)$ goes down the left edge if it exist.
-..returns:$true$ if the edge or path to go down exists, otherwise $false$.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goLeftChild(it); // go to left child of root node
-*/
+// ----------------------------------------------------------------------------
+// Function goLeftChild()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn RightArrayBinaryTreeIterator#goLeftChild
+ * @headerfile <seqan/index.h>
+ * @brief Sets the iterator to the left child of the current node if it exists and returns true, otherwise the
+ *        iterator does not change position and the function returns false.
+ *
+ * @signature bool goLeftChild(iterator);
+ *
+ * @param[in] iterator The iterator
+ *
+ * @return bool <tt>true</tt> if the edge to go down exists, otherwise <tt>false</tt>.
+ */
 template <typename TTree, typename TIterSpec>
 inline bool goLeftChild(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it)
 {
-    unsigned leftChildPos = getLeftChildPos(it);
+    typedef typename Size<TTree>::Type TSize;
+
+    TSize leftChildPos = getLeftChildPos(it);
     if (leftChildPos == 0)
         return false;
-    
+
     if (!goToPosition(it, leftChildPos))
         return false;
 
@@ -338,24 +444,26 @@ inline bool goLeftChild(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSp
     return true;
 }
 
-/**
-.Function.goRight
-..param.iterator:
-...type:Spec.RightArrayBinaryTree Iterator
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goDown(it); // go to left child of root node
-goRight(it); // go to right child of root node
-*/
+// ----------------------------------------------------------------------------
+// Function goRight()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#goRight
+ * @headerfile <seqan/index.h>
+ * @brief Iterates to the next sibling in a @link RightArrayBinaryTree @endlink.
+ *
+ * @signature bool goRight(iterator);
+ *
+ * @param[in] iterator The iterator
+ *
+ * @return bool <tt>true</tt> if the iterator could be moved, otherwise <tt>false</tt>.
+ */
 template <typename TTree, typename TIterSpec>
 inline bool goRight(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it)
 {
-    unsigned pos = getPosition(it);
+    typedef typename Size<TTree>::Type TSize;
+
+    TSize pos = getPosition(it);
     if (goUp(it))
     {
         if (goRightChild(it))
@@ -370,28 +478,27 @@ inline bool goRight(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec>
     return false;
 }
 
-/**
-.Function.goRightChild
-..summary:Sets the iterator to the right child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false.
-..signature:bool goRightChild(iterator)
-..param.iterator:An iterator of a wavelet tree structure.
-...type:Spec.RightArrayBinaryTree Iterator
-..remarks:$goRightChild(iterator)$ goes down the right edge if it exist.
-..returns:$true$ if the edge or path to go down exists, otherwise $false$.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goRightChild(it); // go to right child of root node
-*/
+// ----------------------------------------------------------------------------
+// Function goRightChild()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#goRightChild
+ * @headerfile <seqan/index.h>
+ * @brief Sets the iterator to the right child of the current node if it exists and returns true, otherwise the
+ *        iterator does not change position and the function returns false.
+ *
+ * @signature bool goRightChild(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return bool <tt>true</tt> if the edge to go down exists, otherwise <tt>false</tt>.
+ */
 template <typename TTree, typename TIterSpec>
 inline bool goRightChild(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it)
 {
-    unsigned rightChildPos = getRightChildPos(it);
+    typedef typename Size<TTree>::Type TSize;
+
+    TSize rightChildPos = getRightChildPos(it);
     if (rightChildPos == 0)
         return false;
 
@@ -408,31 +515,17 @@ inline bool goRightChild(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterS
 //     unsigned rightChildPos = getRightChildPos(iter);
 //     if (rightChildPos == 0)
 //         return false;
-// 
+//
 //     appendValue(iter.position, rightChildPos);
 //     return true;
 // }
 
+// ----------------------------------------------------------------------------
+// Function goToPosition()
+// ----------------------------------------------------------------------------
+
 // TODO(singer): Make this work!
-/*
-.Function.goToPosition
-..summary:Move the iterator to a specified position.
-..signature:bool goToPosition(iterator, pos)
-..param.iterator:An iterator of a wavelet tree structure.
-...type:Spec.RightArrayBinaryTree Iterator
-..param.pos:A position.
-..remarks:$goToPosition(iterator)$ goes to position pos regardless of pos being a valid position.
-..returns:$true$ if the edge or path to go down exists, otherwise $false$.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goToPosition(it, 2); // go to right child of root node
-*/
+
 template <typename TTree, typename TIterSpec, typename TPos>
 inline bool goToPosition(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it, TPos pos)
 {
@@ -440,43 +533,41 @@ inline bool goToPosition(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterS
     return true;
 }
 
-/**
-.Function.goUp.param.iterator.type:Spec.TopDownHistory Iterator
-*/
-/*
-..returns:$true$ if the current node is not the root node.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
+// ----------------------------------------------------------------------------
+// Function goUp()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#goUp
+ * @headerfile <seqan/index.h>
+ * @brief Iterates up one edge to the parent in a @link RightArrayBinaryTree @endlink.
+ *
+ * @signature bool goUp(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return bool <tt>true</tt> if the iterator could be moved, otherwise <tt>false</tt>.
+ */
 
-goRightChild(it); // go to right child of root node
-goUp(it); // go to root node
-*/
 template <typename TTree, typename TIterSpec>
 inline bool goUp(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<ParentLinks<TIterSpec> > > > & it)
 {
-    unsigned treeLevel = length(it.history);
+    typedef typename Size<TTree>::Type TSize;
+
+    TSize treeLevel = length(it.history);
 
     if (isRoot(it))
         return false;
 
-//     for (unsigned i = 0; i < length(it.history); ++i)
-//         std::cerr << (int)it.history[i] << " ";
-//     std::cerr << std::endl;
     resize(it.history, treeLevel - 1);
-//     for (unsigned i = 0; i < length(it.history); ++i)
-//         std::cerr << (int)it.history[i] << " ";
-//     std::cerr << std::endl;
     goToPosition(it, back(it.history));
-//     std::cerr << "done" << std::endl;
 
     return true;
 }
 
+// ----------------------------------------------------------------------------
+// Function _goUpStructureConstruction()
+// ----------------------------------------------------------------------------
+
 // This function implements the functionality of go up and
 // resizes the borderString of the structure construction.
 template <typename TTree, typename TIterSpec, typename TBorderString>
@@ -490,33 +581,35 @@ inline bool _goUpStructureConstruction(Iter<TTree, RightArrayBinaryTreeIterator<
     return false;
 }
 
-/**
-.Function.isLeaf
-..class:Spec.RightArrayBinaryTree Iterator
-..param.iterator.type:Spec.RightArrayBinaryTree Iterator
-..example:
-...text:Code example for the @Spec.RightArrayBinaryTree Iterator@:
-...code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goRightChild(it); // go to right child of root node
-goUp(it); // go to root node
-*/
+// ----------------------------------------------------------------------------
+// Function isLeaf()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#isLeaf
+ * @headerfile <seqan/index.h>
+ * @brief Tests whether a given node is a leaf or not.
+ *
+ * @signature bool isLeaf(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return bool <tt>true</tt> if the node is a leaf.
+ */
 template <typename TTree, typename TIterSpec>
 inline bool isLeaf(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & iter)
 {
     return container(iter).treeVertices[getPosition(iter)].i2 == 0;
 }
 
+// ----------------------------------------------------------------------------
+// Function _setAndGoRight()
+// ----------------------------------------------------------------------------
+
 // This function creates the right sibling of the current node
 // and goes to that one.
 // Note: It acn only be called, if the right sibling really exists!
-template <typename TTree, typename TIterSpec, typename TBorderString, typename TPrefixSumTable>
-inline bool _setAndGoRight(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it, TBorderString & borderString, TPrefixSumTable & pst)
+template <typename TTree, typename TIterSpec, typename TBorderString>
+inline bool _setAndGoRight(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it, TBorderString & borderString)
 {
     typedef typename Value<typename Value<TTree>::Type, 1>::Type TChar;
 
@@ -535,31 +628,25 @@ inline bool _setAndGoRight(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIte
     TChar pivot = getCharacter(it);
     _setRightChildPos(it, length(container(it).treeVertices) - 1);
     goRightChild(it);
-    back(borderString).i1 = getCharacterPosition(pst, pivot);
+    back(borderString).i1 = ordValue(pivot);
     back(borderString).i2 = borderString[length(borderString) - 2].i2;
 
     return true;
 }
 
-/**
-.Function.setCharacter
-..signature:bool setCharacter(iterator, character)
-..param.iterator:An iterator of a wavelet tree structure.
-...type:Spec.RightArrayBinaryTree Iterator
-..param.character:The character to be assigned to a node.
-..summary:$setCharacter(iterator, character)$ sets the character of the node the iterator points to to character.
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-goRightChild(it); // go to right child of root node
-setCharacter(it,'T'); // sets the character of the root's
-                      // right child to 'T'
-*/
+// ----------------------------------------------------------------------------
+// Function setCharacter()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#setCharacter
+ * @headerfile <seqan/index.h>
+ * @brief The function sets the character of the node the iterator points to to character.
+ *
+ * @signature void setCharacter(iterator, character);
+ *
+ * @param[in,out] iterator  The iterator.
+ * @param[in]     character The character to be assigned to a node.
+ */
 template <typename TTree, typename TIterSpec, typename TChar2>
 inline void setCharacter(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & iter,
                          TChar2 character)
@@ -567,18 +654,66 @@ inline void setCharacter(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterS
     container(iter).treeVertices[getPosition(iter)].i1 = character;
 }
 
+// ----------------------------------------------------------------------------
+// Function _getPivotPosition()
+// ----------------------------------------------------------------------------
+
+// This function returns the position of the character which ensures that the sum of occurrences of the characters from
+// beginPos to the computed pos and the sum of occurrences from the computed pos to endPos are about the same.
+template <typename TPrefixSums, typename TBeginPos, typename TEndPos>
+TBeginPos
+_getPivotPosition(TPrefixSums const & sums, TBeginPos beginPos, TEndPos endPos)
+{
+    typedef typename Value< TPrefixSums >::Type TValue;
+
+    TBeginPos realBeginPos = beginPos + 1;
+    TEndPos realEndPos = endPos + 1;
+    TBeginPos lengthRange = realEndPos - realBeginPos + 1;
+    TBeginPos pivotPos = realBeginPos + lengthRange / 2 - 1;
+
+    TValue tooSmallValues = sums[beginPos];
+    long currentMin = sums[realEndPos] + 1;
+
+    if (sums[pivotPos] - tooSmallValues >= sums[realEndPos] - sums[pivotPos])
+    {
+        while ((pivotPos >= realBeginPos) && std::abs((long)(sums[pivotPos] - tooSmallValues) - (long)((sums[realEndPos] - sums[pivotPos]))) <= currentMin)
+        {
+            currentMin = std::abs((long)((sums[pivotPos] - tooSmallValues)) - (long)((sums[realEndPos] - sums[pivotPos])));
+            --pivotPos;
+        }
+        ++pivotPos;
+    }
+    else
+    {
+        while (std::abs((long)((sums[pivotPos] - tooSmallValues)) - (long)((sums[realEndPos] - sums[pivotPos]))) < currentMin && (pivotPos < realEndPos))
+        {
+            currentMin = std::abs((long)((sums[pivotPos] - tooSmallValues)) - (long)((sums[realEndPos] - sums[pivotPos])));
+            ++pivotPos;
+        }
+        --pivotPos;
+    }
+
+    return pivotPos;
+}
+
+// ----------------------------------------------------------------------------
+// Function _setChildVertices()
+// ----------------------------------------------------------------------------
+
 // This function sets the left child of the current node, or the right if there is no left child.
-template <typename TTree, typename TIterSpec, typename TBorderString, typename TCharPST, typename TSpecPST>
+template <typename TTree, typename TIterSpec, typename TBorderString, typename TPrefixSums>
 void _setChildVertices(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & it,
-                        TBorderString & borderString,
-                        PrefixSumTable<TCharPST, TSpecPST> & pst)
+                       TBorderString & borderString,
+                       TPrefixSums & sums)
 {
+    typedef typename Size<TTree>::Type TSize;
     typedef typename Value<TBorderString>::Type TBorderStringValue;
-    unsigned leftBorder = back(borderString).i1;
-    unsigned rightBorder = back(borderString).i2;
-    unsigned pivotPosition = _getPivotPosition(pst, leftBorder, rightBorder);
 
-    setCharacter(it, getCharacter(pst, pivotPosition));
+    TSize leftBorder = back(borderString).i1;
+    TSize rightBorder = back(borderString).i2;
+    TSize pivotPosition = _getPivotPosition(sums, leftBorder, rightBorder);
+
+    setCharacter(it, pivotPosition);
 
     if (leftBorder == pivotPosition - 1)
     {
@@ -593,17 +728,21 @@ void _setChildVertices(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpe
     appendValue(borderString, TBorderStringValue(back(borderString).i1, pivotPosition - 1));
 }
 
+// ----------------------------------------------------------------------------
+// Function _setLeftChildPos()
+// ----------------------------------------------------------------------------
+
 // This functions sets the pointer to the left child.
 template <typename TTree, typename TIterSpec>
 inline bool _setLeftChildPos(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & iter)
 {
     switch (iter.waveletTreeStructure->treeVertices[getPosition(iter)].i2)
     {
-    case (0):
+    case 0:
         iter.waveletTreeStructure->treeVertices[getPosition(iter)].i2 = 2;
         return true;
 
-    case (2):
+    case 2:
         return true;
 
     default:
@@ -611,22 +750,26 @@ inline bool _setLeftChildPos(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TI
     }
 }
 
+// ----------------------------------------------------------------------------
+// Function _setRightChildPos()
+// ----------------------------------------------------------------------------
+
 // This functions sets the pointer to the left child.
 template <typename TTree, typename TPos, typename TIterSpec>
 inline bool _setRightChildPos(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > & iter, TPos rightChildPosition)
 {
     switch (iter.waveletTreeStructure->treeVertices[getPosition(iter)].i2)
     {
-    case (0):
+    case 0:
         SEQAN_ASSERT_EQ_MSG(rightChildPosition, 0u, "Wrong right child position!");
         iter.waveletTreeStructure->treeVertices[getPosition(iter)].i2 = 1;
         return true;
 
-    case (2):
+    case 2:
         iter.waveletTreeStructure->treeVertices[getPosition(iter)].i2 = rightChildPosition + 2;
         return true;
 
-    case (1):
+    case 1:
         SEQAN_ASSERT_MSG(rightChildPosition == 0u, "Wrong right child position!");
         return true;
 
@@ -635,21 +778,20 @@ inline bool _setRightChildPos(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<T
     }
 }
 
-/**
-.Function.isRoot
-..class:Spec.RightArrayBinaryTree Iterator
-..param.iterator.type:Spec.RightArrayBinaryTree Iterator
-..example
-...text:Code example for the @Spec.RightArrayBinaryTree Iterator@:
-...code:
-String<Dna5> genome = "ACGTACGT";
-RightArrayBinaryTree<Dna5> waveletTreeStructure(genome);
-
-Iterator<RightArrayBinaryTree<Dna5>, TopDown<> >::Type it;
-it = begin(waveletTreeStructure); // go to root node
-
-isRoot(it) // returns true
-*/
+// ----------------------------------------------------------------------------
+// Function isRoot()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn RightArrayBinaryTreeIterator#isRoot
+ * @headerfile <seqan/index.h>
+ * @brief Test whether a iterator points to the root node.
+ *
+ * @signature bool isRoot(iterator);
+ *
+ * @param[in] iterator The iterator.
+ *
+ * @return bool <tt>true</tt> if <tt>iterator</tt> points to the root of the tree, otherwise <tt>false</tt>.
+ */
 template <typename TTree, typename TIterSpec>
 inline bool isRoot(Iter<TTree, RightArrayBinaryTreeIterator<TopDown<TIterSpec> > > const & it)
 {
diff --git a/seqan/index/index_fm_sentinel_rank_dictionary.h b/seqan/index/index_fm_sentinel_rank_dictionary.h
deleted file mode 100644
index 07bdd8f..0000000
--- a/seqan/index/index_fm_sentinel_rank_dictionary.h
+++ /dev/null
@@ -1,777 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Jochen Singer <jochen.singer@fu-berlin.de>
-// ==========================================================================
-
-// TODO(singer): sentinel
-
-//SEQAN_NO_DDDOC:do not generate documentation for this file
-
-#ifndef INDEX_FM_Sentinel_RANK_DICTIONARY_H_
-#define INDEX_FM_Sentinel_RANK_DICTIONARY_H_
-
-namespace seqan {
-
-// ==========================================================================
-//Forwards
-// ==========================================================================
-
-template <typename TValue>
-class RankDictionary;
-
-template<typename TRankDictionarySpec, typename TSpec> 
-class SentinelRankDictionary;
-
-// ==========================================================================
-// Tags
-// ==========================================================================
-
-struct Sentinel_;
-struct Sentinels_;
-struct FibreRankDictionary_;
-struct FibreSentinelPosition_;
-
-typedef Tag<Sentinel_> const                Sentinel;
-typedef Tag<Sentinels_> const               Sentinels;
-typedef Tag<FibreRankDictionary_> const     FibreRankDictionary;
-typedef Tag<FibreSentinelPosition_> const   FibreSentinelPosition;
-
-// ----------------------------------------------------------------------------
-// Spec SentinelRankDictionary Fibres
-// ----------------------------------------------------------------------------
-
-/**
-.Tag.SentinelRankDictionary Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Class.SentinelRankDictionary@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a SentinelRankDictionary.
-..cat:SentinelRankDictionary
-
-..tag.FibreRankDictionary:The rank dictionary.
-
-..tag.FibreSentinelPosition:The bit string encoding the position of the sentinel sign.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..include:seqan/index.h
-*/
-
-// ==========================================================================
-// Metafunctions
-// ==========================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Fibre
-// ----------------------------------------------------------------------------
-
-// TODO(DOC)
-///.Metafunction.Fibre.param.TSpec.type:Tag.SentinelRankDictionary Fibres
-
-template <typename TValue, typename TSpec>
-struct Fibre<SentinelRankDictionary<RankDictionary<WaveletTree<TValue> >, TSpec>, FibreRankDictionary>
-{
-    typedef RankDictionary<WaveletTree<TValue> > Type;
-};
-
-template <typename TValue, typename TSpec>
-struct Fibre<SentinelRankDictionary<RankDictionary<SequenceBitMask<TValue> >, TSpec>, FibreRankDictionary>
-{
-    typedef RankDictionary<SequenceBitMask<TValue> > Type;
-};
-
-template <typename TRankDictionary, typename TSpec>
-struct Fibre<SentinelRankDictionary<TRankDictionary, TSpec> const, FibreRankDictionary>
-{
-    typedef typename Fibre<SentinelRankDictionary<TRankDictionary, TSpec>, FibreRankDictionary>::Type const Type;
-};
-
-template <typename TRankDictionary>
-struct Fibre<SentinelRankDictionary<TRankDictionary, Sentinel>, FibreSentinelPosition>
-{
-    typedef typename Size<TRankDictionary>::Type Type;
-};
-
-template <typename TRankDictionary>
-struct Fibre<SentinelRankDictionary<TRankDictionary, Sentinel> const, FibreSentinelPosition>
-{
-    typedef typename Fibre<SentinelRankDictionary<TRankDictionary, Sentinel>, FibreSentinelPosition>::Type const Type;
-};
-
-template <typename TRankDictionary>
-struct Fibre<SentinelRankDictionary<TRankDictionary, Sentinels>, FibreSentinelPosition>
-{
-    typedef RankSupportBitString<void> Type;
-};
-
-template <typename TRankDictionary>
-struct Fibre<SentinelRankDictionary<TRankDictionary, Sentinels> const, FibreSentinelPosition>
-{
-    typedef typename Fibre<SentinelRankDictionary<TRankDictionary, Sentinels>, FibreSentinelPosition>::Type const Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <typename TRankDictionary, typename TSpec>
-struct Value<SentinelRankDictionary<TRankDictionary, TSpec> > :
-    public Value<TRankDictionary> {};
-
-template <typename TRankDictionary, typename TSpec>
-struct Value<SentinelRankDictionary<TRankDictionary, TSpec> const> :    
-    public Value<TRankDictionary const> {};
-
-// ==========================================================================
-// Classes
-// ==========================================================================
-
-// ----------------------------------------------------------------------------
-// Class SentinelRankDictionary
-// ----------------------------------------------------------------------------
-
-/**
-.Class.SentinelRankDictionary:
-..cat:Index
-..summary:A rank dictionary, additional storing sentinel character which are not accounted for in a rank querry.
-..signature:SentinelRankDictionary<TRankDictionary, TSpec>
-..param.TRankDictionary:The rank dictionary of a text.
-...type:Class.RankDictionary
-..param.TSpec:Specialisation
-..include:seqan/index.h
-*/
-
-template <typename TLength, typename TTag>
-TTag
-_setDefaultSentinelPosition(TLength const _length, TTag const & /*tag*/)
-{
-    return _length;
-}
-
-template <typename TLength, typename TBitStringSpec>
-RankSupportBitString<TBitStringSpec>
-_setDefaultSentinelPosition(TLength const _length, RankSupportBitString<TBitStringSpec> const & /*tag*/)
-{
-
-    RankSupportBitString<TBitStringSpec> bitString;
-    resize(bitString, _length, 0, Exact());
-    return bitString;
-}
-
-template <typename TRankDictionary, typename TSpec>
-class SentinelRankDictionary
-{
-public:
-    typedef typename Value<SentinelRankDictionary>::Type TChar;
-    typedef typename Fibre<SentinelRankDictionary<TRankDictionary, TSpec>, FibreSentinelPosition>::Type TSentinelPosition;
-
-    TRankDictionary rankDictionary;
-    TSentinelPosition sentinelPosition;
-    TChar sentinelSubstitute;
-
-    SentinelRankDictionary() :
-        sentinelPosition(_setDefaultSentinelPosition(0u, TSentinelPosition())),
-        sentinelSubstitute()
-    {}
-   
-    // TODO(singer): Use concept sequence when available
-    template <typename TValue, typename TStringSpec>
-    SentinelRankDictionary(String<TValue, TStringSpec> const & text) :
-        rankDictionary(text),
-        sentinelPosition(_setDefaultSentinelPosition(length(text), TSentinelPosition())),
-        sentinelSubstitute()
-    {}
-    
-    template <typename THost, typename TSegmentSpec>
-    SentinelRankDictionary(Segment<THost, TSegmentSpec> const & text) :
-        rankDictionary(text),
-        sentinelPosition(_setDefaultSentinelPosition(length(text), TSentinelPosition())),
-        sentinelSubstitute()
-    {}
-
-    bool operator==(const SentinelRankDictionary & b) const
-    {
-        return rankDictionary == b.rankDictionary &&
-               sentinelPosition == b.sentinelPosition &&
-               sentinelSubstitute == b.sentinelSubstitute;
-    }
-};
-
-//     // TODO(singer): Use concept sequence when available
-//     template <typename TRankDictionary, typename TValue, typename TStringSpec>
-//     SentinelRankDictionary<TRankDictionary, Sentinel>::SentinelRankDictionary(String<TValue, TStringSpec> const & text) :
-//         rankDictionary(text),
-//         sentinelPosition(length(text)),
-//         sentinelSubstitute()
-//     {}
-//     
-//     template <typename TRankDictionary, typename THost, typename TSegmentSpec>
-//     SentinelRankDictionary::SentinelRankDictionary<TRankDictionary, Sentinel>(Segment<THost, TSegmentSpec> const & text) :
-//         rankDictionary(text),
-//         sentinelPosition(length(text)),
-//         sentinelSubstitute()
-//     {}
-// 
-//     template <typename TRankDictionary, typename TValue, typename TStringSpec>
-//     SentinelRankDictionary::SentinelRankDictionary<TRankDictionary, Sentinels>(String<TValue, TStringSpec> const & text) :
-//         rankDictionary(text),
-//         sentinelPosition(),
-//         sentinelSubstitute()
-//     {}
-//     
-//     template <typename TRankDictionary, typename THost, typename TSegmentSpec>
-//     SentinelRankDictionary::SentinelRankDictionary<TRankDictionary, Sentinels>(Segment<THost, TSegmentSpec> const & text) :
-//         rankDictionary(text),
-//         sentinelPosition(length(text)),
-//         sentinelSubstitute()
-//     {}
-
-// ==========================================================================
-//Functions
-// ==========================================================================
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#clear
-..class:Class.SentinelRankDictionary
-..summary:Clears the dictionary.
-..signature:clear(dictionary)
-..param.dictionary:The rank dictionary to be cleared.
-...type:Class.SentinelRankDictionary
-..include:seqan/index.h
-*/
-
-template <typename TRankDictionary>
-inline void _clearSentinental(SentinelRankDictionary<TRankDictionary, Sentinel> &)
-{}
-
-template <typename TRankDictionary>
-inline void _clearSentinental(SentinelRankDictionary<TRankDictionary, Sentinels> & dictionary)
-{
-    clear(getFibre(dictionary, FibreSentinelPosition()));
-}
-
-template <typename TRankDictionary, typename TSpec>
-inline void clear(SentinelRankDictionary<TRankDictionary, TSpec> & dictionary)
-{
-    clear(getFibre(dictionary, FibreRankDictionary()));
-    _clearSentinental(dictionary);
-}
-
-// ----------------------------------------------------------------------------
-// Function sentinelPosition
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#sentinelPosition
-..class:Class.SentinelRankDictionary
-..summary:Returns whether a specified position is a sentinel position.
-..signature:sentinelPosition(dictionary, pos)
-..param.dictionary:The dictionary.
-...type:Class.SentinelRankDictionary
-..param.pos:The position.
-...type:Concept.UnsignedIntegerConcept
-..include:seqan/index.h
-*/
-
-//.Function.sentinelPosition.param.type:Class.RankDictionary
-template <typename TRankDictionary, typename TPos>
-inline bool sentinelPosition(SentinelRankDictionary<TRankDictionary, Sentinel> const & dictionary, TPos pos)
-{
-    return dictionary.sentinelPosition == pos;
-}
-
-template <typename TRankDictionary, typename TPos>
-inline bool sentinelPosition(SentinelRankDictionary<TRankDictionary, Sentinels> const & dictionary, TPos pos)
-{
-    return isBitSet(getFibre(dictionary, FibreSentinelPosition()), pos);
-}
-
-// ----------------------------------------------------------------------------
-// Function empty
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#empty
-..class:Class.SentinelRankDictionary
-..summary:Returns whether or not the dictionary is empty.
-..signature:empty(dictionary)
-..param.dictionary:The rank dictionary to be checked.
-...type:Class.SentinelRankDictionary
-..include:seqan/index.h
-*/
-template <typename TRankDictionary, typename TSpec>
-inline bool empty(SentinelRankDictionary<TRankDictionary, TSpec> const & dictionary)
-{
-    return empty(getFibre(dictionary, FibreRankDictionary()));
-}
-
-// ----------------------------------------------------------------------------
-// Function getValue
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#getValue
-..class:Class.SentinelRankDictionary
-..summary:Returns the character of a specified position.
-..signature:getCharacter(dictionary, pos)
-..param.dictionary:The rank dictionary.
-...type:Class.RankDictionary
-..param.pos:The position
-..include:seqan/index.h
-..example.code:
-*/
-template <typename TRankDictionary, typename TSpec, typename TPos>
-inline typename Value<TRankDictionary>::Type
-getValue(SentinelRankDictionary<TRankDictionary, TSpec > const & dictionary,
-                 TPos pos)
-{
-    SEQAN_ASSERT_NEQ(sentinelPosition(dictionary, pos), true);
-    return getValue(getFibre(dictionary, FibreRankDictionary()), pos);
-}
-
-template <typename TRankDictionary, typename TSpec, typename TPos>
-inline typename Value<TRankDictionary>::Type
-getValue(SentinelRankDictionary<TRankDictionary, TSpec > & dictionary,
-                 TPos pos)
-{
-    SEQAN_ASSERT_NEQ(sentinelPosition(dictionary, pos), true);
-    return getValue(getFibre(dictionary, FibreRankDictionary()), pos);
-}
-
-// ----------------------------------------------------------------------------
-// Function getSentinelPosition
-// ----------------------------------------------------------------------------
-
-/*
-.Function.SentinelRankDictionary#_getSentinelPosition
-..class:Class.SentinelRankDictionary
-..summary:Returns the position(s) of sentinel(s).
-..signature:getSentinelPosition(dictionary)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..remark:If there are several sentinels, a string containing the sentinel positions is returned.
- Should be used for debugging only.
-..include:seqan/index.h
-*/
-
-template <typename TRankDictionary>
-inline typename Size<SentinelRankDictionary<TRankDictionary, Sentinel> >::Type
-_getSentinelPosition(SentinelRankDictionary<TRankDictionary, Sentinel> const & dictionary)
-{
-    return dictionary.sentinelPosition;
-}
-
-template <typename TRankDictionary>
-inline String<typename Size<SentinelRankDictionary<TRankDictionary, Sentinel> >::Type > 
-_getSentinelPosition(SentinelRankDictionary<TRankDictionary, Sentinels> const & dictionary)
-{
-    String<unsigned long> sentinelPositions;
-
-    for (unsigned i = 0; i < length(dictionary.sentinelPosition); ++i)
-        if (isBitSet(dictionary.sentinelPosition, i))
-            appendValue(sentinelPositions, i);
-    return sentinelPositions;
-}
-
-// ----------------------------------------------------------------------------
-// Function getFibre
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#getFibre:
-..class:Class.SentinelRankDictionary
-..summary:Returns a specific fibre of a dictionary.
-..signature:getFibre(dictionary, fibreTag)
-..class:Class.RankDictionary
-..cat:Index
-..param.dictionary:The dictionary holding the fibre.
-...type:Class.RankDictionary
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.SentinelRankDictionary Fibres
-..returns:A reference to the @Metafunction.Fibre@ object.
-..include:seqan/index.h
-*/
-template <typename TRankDictionary, typename TSpec>
-inline typename Fibre<SentinelRankDictionary<TRankDictionary, TSpec>, FibreRankDictionary>::Type &
-getFibre(SentinelRankDictionary<TRankDictionary, TSpec>& dictionary, FibreRankDictionary)
-{
-    return dictionary.rankDictionary;
-}
-
-template <typename TRankDictionary, typename TSpec>
-inline typename Fibre<SentinelRankDictionary<TRankDictionary, TSpec>, FibreRankDictionary>::Type const &
-getFibre(SentinelRankDictionary<TRankDictionary, TSpec> const & dictionary, FibreRankDictionary)
-{
-    return dictionary.rankDictionary;
-}
-
-template <typename TRankDictionary, typename TSpec>
-inline typename Fibre<SentinelRankDictionary<TRankDictionary, TSpec>, FibreSentinelPosition>::Type &
-getFibre(SentinelRankDictionary<TRankDictionary, TSpec>& dictionary, FibreSentinelPosition)
-{
-    return dictionary.sentinelPosition;
-}
-
-template <typename TRankDictionary, typename TSpec>
-inline typename Fibre<SentinelRankDictionary<TRankDictionary, TSpec>, FibreSentinelPosition>::Type const &
-getFibre(SentinelRankDictionary<TRankDictionary, TSpec> const & dictionary, FibreSentinelPosition)
-{
-    return dictionary.sentinelPosition;
-}
-
-// ----------------------------------------------------------------------------
-// Function countOccurrences
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#countOccurrences
-..class:Class.SentinelRankDictionary
-..summary:Returns the number of occurrences of a specified character from the start
-to a specified position.
-..signature:countOccurrences(dictionary, character, pos)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.character:The character.
-..param.pos:The position (which is included in the counting).
-..include:seqan/index.h
-..example.code:
-String<Dna5> genome = "ACGTACGT";
-RankDictionary<String<Dna5> > dictionary(genome);
-
-std::cout << countOccurrences(dictionary, 'a', 3) << std::endl; // 1
-std::cout << countOccurrences(dictionary, 'a', 4) << std::endl; // 2
-*/
-
-template <typename TRankDictionary, typename TChar, typename TPos>
-inline unsigned countOccurrences(SentinelRankDictionary<TRankDictionary, Sentinel> const & dictionary,
-                               TChar const character,
-                               TPos const pos)
-{
-    unsigned occ = countOccurrences(getFibre(dictionary, FibreRankDictionary()), character, pos);
-    if (ordEqual(getSentinelSubstitute(dictionary), character) && pos >= dictionary.sentinelPosition)
-         --occ;
-    return occ;
-}
-
-template <typename TRankDictionary, typename TChar, typename TPos>
-inline unsigned countOccurrences(SentinelRankDictionary<TRankDictionary, Sentinels> const & dictionary,
-                                TChar const character,
-                                TPos const pos)
-{
-    unsigned occ = countOccurrences(getFibre(dictionary, FibreRankDictionary()), character, pos);
-    if (ordEqual(getSentinelSubstitute(dictionary), character))
-        return occ - getRank(getFibre(dictionary, FibreSentinelPosition()), pos);
-
-    return occ;
-}
-
-// ----------------------------------------------------------------------------
-// Function getSentinelSubstitute
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#getSentinelSubstitute
-..class:Class.SentinelRankDictionary
-..summary:Returns the character used to substitute the sentinel sign.
-..signature:getSentinelSubstitute(dictionary)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..include:seqan/index.h
-*/
-template <typename TRankDictionary, typename TSpec>
-inline typename Value<TRankDictionary>::Type
-getSentinelSubstitute(SentinelRankDictionary<TRankDictionary, TSpec> const & dictionary /*tag*/)
-{
-    return dictionary.sentinelSubstitute;
-}
-
-// ----------------------------------------------------------------------------
-// Function setSentinelSubstitute
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#setSentinelSubstitute
-..class:Class.SentinelRankDictionary
-..summary:Sets the character used to substitute the sentinel sign.
-..signature:setSentinelSubstitute(dictionary, character)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.character:The sentinel substitute.
-..include:seqan/index.h
-*/
-
-template <typename TRankDictionary, typename TSpec, typename TChar>
-inline void setSentinelSubstitute(SentinelRankDictionary<TRankDictionary, TSpec> & dictionary,
-                                TChar sentinelSubstitute)
-{
-    dictionary.sentinelSubstitute = sentinelSubstitute;
-}
-
-// ----------------------------------------------------------------------------
-// Function setSentinelPosition
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#setSentinelPosition
-..class:Class.SentinelRankDictionary
-..summary:Sets the sentinel position..
-..signature:setSentinelPosition(dictionary, pos)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary
-..param.pos:The sentinel position.
-..include:seqan/index.h
-*/
-
-template <typename TRankDictionary, typename TSpec, typename TPos>
-inline void setSentinelPosition(SentinelRankDictionary<TRankDictionary, TSpec> & dictionary,
-                              TPos const & position)
-{
-    dictionary.sentinelPosition = position;
-}
-
-// ----------------------------------------------------------------------------
-// Function sentinelRankDictionaryCreate
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#createSentinelRankDictionary
-..class:Class.SentinelRankDictionary
-..summary:This functions creates the dictionary structure.
-..signature:void createSentinelRankDictionary(dictionary, text)
-..param.dictionary:The dictionary.
-...type:Class.RankDictionary.
-..param.text:A text to be transfered into a dictionary.
-...type:Class.String
-..include:seqan/index.h
-*/
-
-template <typename TRankDictionary, typename TSpec, typename TText, typename TSentinelSub, typename TSentinelPos>
-inline void createSentinelRankDictionary(SentinelRankDictionary<TRankDictionary, TSpec> & dictionary,
-                              TText const & text,
-                              TSentinelSub const & sentinelSub,
-                              TSentinelPos const & sentinelPos)
-{
-    setSentinelSubstitute(dictionary, sentinelSub);
-    setSentinelPosition(dictionary, sentinelPos);
-
-    createRankDictionary(getFibre(dictionary, FibreRankDictionary()), text);
-}
-
-template <typename TRankDictionary, typename TSpec, typename TPrefixSumTable, typename TText, typename TDollarSub, typename TDollarPos>
-inline void createSentinelRankDictionary(LfTable<SentinelRankDictionary<TRankDictionary, TSpec>, TPrefixSumTable> & lfTable,
-                              TText const & text,
-                              TDollarSub const & dollarSub,
-                              TDollarPos const & dollarPos)
-{
-    setSentinelSubstitute(getFibre(lfTable, FibreOccTable()), dollarSub);
-    setSentinelPosition(getFibre(lfTable, FibreOccTable()), dollarPos);
-
-    createRankDictionary(lfTable, text);
-}
-
-// ----------------------------------------------------------------------------
-// Function open
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#open
-..class:Class.SentinelRankDictionary
-..summary:This functions loads a dictionary from disk.
-..signature:open(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.SentinelRankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TRankDictionary>
-inline bool _openSentinelInformation(
-    SentinelRankDictionary<TRankDictionary, Sentinel> & dictionary,
-    const char * fileName,
-    int openMode)
-{
-    String<char> name;
-
-    typedef typename Fibre<SentinelRankDictionary<TRankDictionary, Sentinel>, FibreSentinelPosition>::Type TSentinelString;
-    typedef typename Value<SentinelRankDictionary<TRankDictionary, Sentinel> >::Type TChar;
-
-    String<Pair<TChar, TSentinelString, Pack> > sentinelValues;
-
-    name = fileName;    append(name, ".dr");
-    if (!open(sentinelValues, toCString(name), openMode) || empty(sentinelValues))
-    {
-        return false;
-    }
-    dictionary.sentinelSubstitute = sentinelValues[0].i1;
-    dictionary.sentinelPosition = sentinelValues[0].i2;
-    return true;
-}
-
-template <typename TRankDictionary>
-inline bool _openSentinelInformation(
-    SentinelRankDictionary<TRankDictionary, Sentinels> & dictionary,
-    const char * fileName,
-    int openMode)
-{
-    String<char> name;
-
-    typedef typename Value<SentinelRankDictionary<TRankDictionary, Sentinels> >::Type TChar;
-    String<TChar> sentinelSub;
-    
-    name = fileName;    append(name, ".drs"); if (!open(sentinelSub, toCString(name), openMode)) return false;
-    name = fileName;    append(name, ".drp"); if (!open(dictionary.sentinelPosition, toCString(name), openMode)) return false;
-    
-    if (empty(sentinelSub))
-        return false;
-
-    dictionary.sentinelSubstitute = sentinelSub[0];
-    
-    return true;
-}
-
-template <typename TRankDictionary, typename TSpec>
-inline bool open(
-    SentinelRankDictionary<TRankDictionary, TSpec> & dictionary,
-    const char * fileName,
-    int openMode)
-{
-    if (!open(getFibre(dictionary, FibreRankDictionary()), fileName, openMode)) return false;
-    if (!_openSentinelInformation(dictionary, fileName, openMode)) return false;
-    return true;
-}
-
-
-    template <typename TRankDictionary, typename TSpec>
-inline bool open(
-    SentinelRankDictionary<TRankDictionary, TSpec> & dictionary,
-    const char * fileName)
-{
-    return open(dictionary, fileName, DefaultOpenMode<SentinelRankDictionary<TRankDictionary, Sentinel> >::VALUE);
-}
-
-// ----------------------------------------------------------------------------
-// Function save
-// ----------------------------------------------------------------------------
-
-/**
-.Function.SentinelRankDictionary#save
-..class:Class.SentinelRankDictionary
-..summary:This functions saves a dictionary to disk.
-..signature:open(dictionary, fileName [, openMode])
-..param.dictionary:The dictionary.
-...type:Class.SentinelRankDictionary
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-
-template <typename TRankDictionary>
-inline bool _saveSentinelInformation(
-    SentinelRankDictionary<TRankDictionary, Sentinel> const & dictionary,
-    const char * fileName,
-    int openMode)
-{
-    String<char> name;
-
-    typedef typename Value<SentinelRankDictionary<TRankDictionary, Sentinel> >::Type TChar;
-    typedef typename Fibre<SentinelRankDictionary<TRankDictionary, Sentinel>, FibreSentinelPosition>::Type TSentinelString;
-
-    String<Pair<TChar, TSentinelString, Pack> > sentinelValues;
-    appendValue(sentinelValues, Pair<TChar, TSentinelString>(dictionary.sentinelSubstitute, dictionary.sentinelPosition));
-    
-    name = fileName;    append(name, ".dr"); if (!save(sentinelValues, toCString(name), openMode)) return false;
-    return true;
-}
-
-template <typename TRankDictionary>
-inline bool _saveSentinelInformation(
-    SentinelRankDictionary<TRankDictionary, Sentinels> const & dictionary,
-    const char * fileName,
-    int openMode)
-{
-    String<char> name;
-
-    typedef typename Value<SentinelRankDictionary<TRankDictionary, Sentinels> >::Type TChar;
-    String<TChar> sentinelSub;
-    appendValue(sentinelSub, dictionary.sentinelSubstitute);
-
-    name = fileName;    append(name, ".drs"); if(!save(sentinelSub, toCString(name), openMode)) return false;
-    name = fileName;    append(name, ".drp"); if(!save(dictionary.sentinelPosition, toCString(name), openMode)) return false;
-    return true;
-}
-
-template <typename TRankDictionary, typename TSpec>
-inline bool save(
-    SentinelRankDictionary<TRankDictionary, TSpec> const & dictionary,
-    const char * fileName,
-    int openMode)
-{
-    if (!save(getFibre(dictionary, FibreRankDictionary()), fileName, openMode)) return false;
-    if (!_saveSentinelInformation(dictionary, fileName, openMode)) return false;
-    
-    return true;
-}
-
-template <typename TRankDictionary, typename TSpec>
-inline bool save(
-    SentinelRankDictionary<TRankDictionary, TSpec> const & dictionary,
-    const char * fileName)
-{
-    return save(dictionary, fileName, DefaultOpenMode<SentinelRankDictionary<TRankDictionary, Sentinel> >::VALUE);
-}
-
-template <typename TRankDictionary, typename TSpec>
-inline bool save(
-    SentinelRankDictionary<TRankDictionary, TSpec> & dictionary,
-    const char * fileName)
-{
-    return save(dictionary, fileName, DefaultOpenMode<SentinelRankDictionary<TRankDictionary, Sentinel> >::VALUE);
-}
-
-}
-#endif  // INDEX_FM_Sentinel_RANK_DICTIONARY_H_
-
diff --git a/seqan/index/index_fm_sparse_string.h b/seqan/index/index_fm_sparse_string.h
old mode 100755
new mode 100644
index 1b0b546..f4a0eb4
--- a/seqan/index/index_fm_sparse_string.h
+++ b/seqan/index/index_fm_sparse_string.h
@@ -1,7 +1,8 @@
 // ==========================================================================
-//                 seqan - the library for sequence analysis
+//                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,6 +31,7 @@
 //
 // ==========================================================================
 // Author: Jochen Singer <jochen.singer@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
 // ==========================================================================
 
 //SEQAN_NO_DDDOC:do not generate documentation for this file
@@ -46,365 +48,546 @@ namespace seqan {
 template <typename TString, typename TSpec>
 struct SparseString;
 
-struct FibreValueString_;
-struct FibreIndicatorString_;
-
-typedef Tag<FibreValueString_>       const FibreValueString;
-typedef Tag<FibreIndicatorString_>    const FibreIndicatorString;
+// ==========================================================================
+// Tags
+// ==========================================================================
+/*!
+ * @defgroup SparseStringFibres Sparse String Fibres
+ * @brief Tag to select a specific fibre of a @link FMIndex @endlink.
+ *
+ * These tags can be used to get @link Fibre Fibres @endlink of a FM index.
+ *
+ * @see Fibre
+ * @see SparseString#getFibre
+ *
+ * @tag SparseStringFibres#FibreValueString
+ * @brief The String containing the stored values.
+ *
+ * @tag SparseStringFibres#FibreIndicatorString
+ * @brief The string storing for each position if a value different from a default value is stored.
+ */
+// ----------------------------------------------------------------------------
+// Tag FibreValues
+// ----------------------------------------------------------------------------
+
+struct FibreValues_;
+typedef Tag<FibreValues_>       const FibreValues;
+
+// ----------------------------------------------------------------------------
+// Tag FibreIndicators
+// ----------------------------------------------------------------------------
+
+struct FibreIndicators_;
+typedef Tag<FibreIndicators_>   const FibreIndicators;
 
 // ==========================================================================
 // Metafunctions
 // ==========================================================================
 
-template <typename TFibreValueString, typename TSpec>
-struct Value<SparseString<TFibreValueString, TSpec> >
-{
-    typedef typename Value<TFibreValueString>::Type Type;
-};
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+template <typename TFibreValues, typename TSpec>
+struct Size<SparseString<TFibreValues, TSpec> > : Size<TFibreValues> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
 
-template <typename TFibreValueString, typename TSpec>
-struct Value<SparseString<TFibreValueString, TSpec> const>
+template <typename TFibreValues, typename TSpec>
+struct Value<SparseString<TFibreValues, TSpec> >
 {
-    typedef typename Value<TFibreValueString>::Type Type;
+    typedef typename Value<TFibreValues>::Type Type;
 };
 
-// ==========================================================================
-template <typename TFibreValueString, typename TSpec>
-struct GetValue<SparseString<TFibreValueString, TSpec> > :
-    Value<SparseString<TFibreValueString, TSpec> > {};
+template <typename TFibreValues, typename TSpec>
+struct Value<SparseString<TFibreValues, TSpec> const> :
+    Value<SparseString<TFibreValues, TSpec> > {};
 
-template <typename TFibreValueString, typename TSpec>
-struct GetValue<SparseString<TFibreValueString, TSpec> const> :
-    Value<SparseString<TFibreValueString, TSpec> const> {};
+// ----------------------------------------------------------------------------
+// Metafunction GetValue
+// ----------------------------------------------------------------------------
 
-// ==========================================================================
-template <typename TFibreValueString, typename TSpec>
-struct Reference<SparseString<TFibreValueString, TSpec> >
-{
-    typedef typename Value<SparseString<TFibreValueString, TSpec> >::Type Type;
-};
+template <typename TFibreValues, typename TSpec>
+struct GetValue<SparseString<TFibreValues, TSpec> > :
+    Value<SparseString<TFibreValues, TSpec> > {};
+
+template <typename TFibreValues, typename TSpec>
+struct GetValue<SparseString<TFibreValues, TSpec> const> :
+    Value<SparseString<TFibreValues, TSpec> const> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Reference
+// ----------------------------------------------------------------------------
 
-template <typename TFibreValueString, typename TSpec>
-struct Reference<SparseString<TFibreValueString, TSpec> const>
+template <typename TFibreValues, typename TSpec>
+struct Reference<SparseString<TFibreValues, TSpec> >
 {
-    typedef typename Value<SparseString<TFibreValueString, TSpec> >::Type const Type;
+    typedef typename Value<SparseString<TFibreValues, TSpec> >::Type Type;
 };
 
-// ==========================================================================
+// ----------------------------------------------------------------------------
+// Metafunction DefaultValue
+// ----------------------------------------------------------------------------
+
 template <typename TSpec>
-struct DefaultValue {};
+struct DefaultValue;
 
-template <typename TFibreValueString, typename TSpec>
-struct DefaultValue<SparseString<TFibreValueString, TSpec> const>
-{
-    typedef typename GetValue<SparseString<TFibreValueString, TSpec> const>::Type Type;
-    static const Type VALUE = -1;
-};
+template <typename TSpec>
+struct DefaultValue<TSpec const> :
+    DefaultValue<TSpec> {};
 
-template <typename TFibreValueString, typename TSpec>
-struct DefaultValue<SparseString<TFibreValueString, TSpec> >
+template <typename TFibreValues, typename TSpec>
+struct DefaultValue<SparseString<TFibreValues, TSpec> >
 {
-    typedef typename GetValue<SparseString<TFibreValueString, TSpec> const>::Type Type;
+    typedef typename GetValue<SparseString<TFibreValues, TSpec> const>::Type Type;
     static const Type VALUE = -1;
 };
 
-// ==========================================================================
-template <typename TFibreValueString, typename TSpec>
-struct Fibre<SparseString<TFibreValueString, TSpec>, FibreValueString>
-{
-    typedef TFibreValueString Type;
-};
+// ----------------------------------------------------------------------------
+// Metafunction Fibre
+// ----------------------------------------------------------------------------
 
-template <typename TFibreValueString, typename TSpec>
-struct Fibre<SparseString<TFibreValueString, TSpec> const, FibreValueString>
+template <typename TFibreValues, typename TSpec>
+struct Fibre<SparseString<TFibreValues, TSpec>, FibreValues>
 {
-    typedef TFibreValueString const Type;
+    typedef TFibreValues Type;
 };
 
-template <typename TFibreValueString, typename TSpec>
-struct Fibre<SparseString<TFibreValueString, TSpec>, FibreIndicatorString>
+template <typename TFibreValues, typename TSpec>
+struct Fibre<SparseString<TFibreValues, TSpec>, FibreIndicators>
 {
-    typedef RankSupportBitString<void> Type;
+    // NOTE(esiragusa): the CSA TConfig is not passed to the RD.
+    typedef RankDictionary<bool, Levels<TSpec> > Type;
 };
 
-template <typename TFibreValueString, typename TSpec>
-struct Fibre<SparseString<TFibreValueString, TSpec> const, FibreIndicatorString>
-{
-    typedef RankSupportBitString<void> const Type;
-};
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
 
-// ==========================================================================
-template <typename TFibreValueString, typename TSpec>
-struct Iterator<SparseString<TFibreValueString, TSpec> const, Standard>
+template <typename TFibreValues, typename TSpec>
+struct Iterator<SparseString<TFibreValues, TSpec>, Standard>
 {
-    typedef Iter<SparseString<TFibreValueString, TSpec> const, PositionIterator> Type;
+    typedef Iter<SparseString<TFibreValues, TSpec>, PositionIterator> Type;
 };
 
-template <typename TFibreValueString, typename TSpec>
-struct Iterator<SparseString<TFibreValueString, TSpec>, Standard>
+template <typename TFibreValues, typename TSpec>
+struct Iterator<SparseString<TFibreValues, TSpec> const, Standard>
 {
-    typedef Iter<SparseString<TFibreValueString, TSpec>, PositionIterator> Type;
+    typedef Iter<SparseString<TFibreValues, TSpec> const, PositionIterator> Type;
 };
 
-template <typename TFibreValueString, typename TSpec>
-struct Iterator<SparseString<TFibreValueString, TSpec>, Rooted>:
-    Iterator<SparseString<TFibreValueString, TSpec>, Standard>{};
-
-template <typename TFibreValueString, typename TSpec>
-struct Iterator<SparseString<TFibreValueString, TSpec> const, Rooted>:
-    Iterator<SparseString<TFibreValueString, TSpec> const, Standard>{};
-
+template <typename TFibreValues, typename TSpec>
+struct Iterator<SparseString<TFibreValues, TSpec>, Rooted>:
+    Iterator<SparseString<TFibreValues, TSpec>, Standard>{};
 
+template <typename TFibreValues, typename TSpec>
+struct Iterator<SparseString<TFibreValues, TSpec> const, Rooted>:
+    Iterator<SparseString<TFibreValues, TSpec> const, Standard>{};
 
 // ==========================================================================
 // Classes
 // ==========================================================================
 
-/**
-.Class.SparseString:
-..cat:Index
-..summary:A string storing only a fraction of the values of the original string..
-..signature:SparseString<TValueString, TSpec>
-..param.TValueString:The string containing the values.
-..param.TSpec:The specialisation tag.
-...default:void.
-..include:seqan/String.h
-*/
+// ----------------------------------------------------------------------------
+// Class SparseString
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): Why is SparseString not a specialization of String?
+
+/*!
+ * @class SparseString
+ * @headerfile <seqan/index.h>
+ * @brief A string storing only a fraction of the values of the original string.
+ *
+ * @signature template <typename TValueString, typename TSpec>
+ *            class SparseString;
+ *
+ * @tparam TSpec        The specialisation tag. Default: void.
+ * @tparam TValueString The type of the @link String string @endlink containing the values.
+ */
+
 template <typename TValueString, typename TSpec = void>
 struct SparseString
 {
-    typedef typename Fibre<SparseString, FibreValueString>::Type TFibreValueString_;
-    typedef typename Fibre<SparseString, FibreIndicatorString>::Type TFibreIndicatorString;
+    typedef typename Fibre<SparseString, FibreValues>::Type         TFibreValues_;
+    typedef typename Fibre<SparseString, FibreIndicators>::Type     TFibreIndicators_;
+    typedef typename Size<SparseString>::Type                       TSize;
 
-    TFibreValueString_              	valueString;
-    TFibreIndicatorString               indicatorString;
+    TFibreValues_           values;
+    TFibreIndicators_       indicators;
+    TSize                   _length;
 
-    inline bool operator==(const SparseString & b) const
-    {
-        return valueString == b.valueString &&
-            indicatorString == b.indicatorString;
-    }
+    SparseString() :
+        _length(0)
+    {}
 };
 
 // ==========================================================================
 // Functions
 // ==========================================================================
 
-/*
-.Function._assignValueInValueString
-..param.container:
-...type:Class.CompressedSA
-*/
-template <typename TFibreValueString, typename TSpec, typename TPos, typename TValue>
-inline void _assignValueInValueString(SparseString<TFibreValueString, TSpec> & string, TPos pos, TValue value)
+template <typename TFibreValues, typename TSpec, typename TPos, typename TValue>
+inline void _assignValueInValueString(SparseString<TFibreValues, TSpec> & string, TPos pos, TValue value)
 {
-    getFibre(string, FibreValueString())[pos] = value;
+    getFibre(string, FibreValues())[pos] = value;
 }
 
-///.Function.clear.param.object.type:Class.SparseString
-template <typename TFibreValueString, typename TSpec>
-inline void clear(SparseString<TFibreValueString, TSpec> & string)
-{
-    clear(getFibre(string, FibreValueString()));
-    clear(getFibre(string, FibreIndicatorString()));
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn SparseString#clear
+ * @headerfile <seqan/index.h>
+ * @brief Resets the @link SparseString @endlink.
+ *
+ * @signature void clear(sparseString);
+ *
+ * @param[in,out] sparseString The @link SparseString @endlink to be cleared.
+ */
+
+template <typename TFibreValues, typename TSpec>
+inline void clear(SparseString<TFibreValues, TSpec> & string)
+{
+    string._length = 0;
+    clear(getFibre(string, FibreValues()));
+    clear(getFibre(string, FibreIndicators()));
 }
 
-///.Function.empty.param.object.type:Class.SparseString
-template <typename TFibreValueString, typename TSpec>
-inline bool empty(SparseString<TFibreValueString, TSpec> const & string)
-{
-    return empty(getFibre(string, FibreIndicatorString()));
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn SparseString#empty
+ * @headerfile <seqan/index.h>
+ * @brief Returns whether or not the @link SparseString @endlink is empty.
+ *
+ * @signature bool empty(sparseString);
+ *
+ * @param[in] sparseString The SparseString to be checked.
+ *
+ * @return bool <tt>true</tt> if there are no elements in the sparse string and <tt>false</tt> otherwise.
+ */
+
+template <typename TFibreValues, typename TSpec>
+SEQAN_HOST_DEVICE inline bool empty(SparseString<TFibreValues, TSpec> const & string)
+{
+//    return empty(getFibre(string, FibreIndicators()));
+    return length(string) == 0;
 }
 
-template <typename TFibreValueString, typename TSpec, typename TPos>
-inline bool _isContained(SparseString<TFibreValueString, TSpec> const & string, TPos const & pos)
+template <typename TFibreValues, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline bool _isContained(SparseString<TFibreValues, TSpec> const & string, TPos const & pos)
 {
-    return isBitSet(getFibre(string, FibreIndicatorString()), pos);
+    return getValue(getFibre(string, FibreIndicators()), pos);
 }
 
-///.Function.assignValue.param.container.type:Class.SparseString
-template <typename TFibreValueString, typename TSpec, typename TPos, typename TValue>
+// ----------------------------------------------------------------------------
+// Function assignValue()
+// ----------------------------------------------------------------------------
+
+template <typename TFibreValues, typename TSpec, typename TPos, typename TValue>
 inline void
-assignValue(SparseString<TFibreValueString, TSpec> & string, TPos pos, TValue value)
+assignValue(SparseString<TFibreValues, TSpec> & string, TPos pos, TValue value)
 {
     if (!_isContained(string, pos))
-    {
-        setBit(getFibre(string, FibreIndicatorString()), pos, 0);    
-    }
-    getFibre(string, FibreValueString())[getRank(getFibre(string, FibreIndicatorString()), pos) - 1] = value;
+        setValue(getFibre(string, FibreIndicators()), pos, false);
+
+    getFibre(string, FibreValues())[getRank(getFibre(string, FibreIndicators()), pos) - 1] = value;
 }
 
-///.Function.getValue.param.container.type:Class.SparseString
-template <typename TFibreValueString, typename TSpec, typename TPos>
-inline typename GetValue<SparseString<TFibreValueString, TSpec> >::Type
-getValue(SparseString<TFibreValueString, TSpec> & string, TPos pos)
+// ----------------------------------------------------------------------------
+// Function getValue()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn SparseString#getValue
+ * @headerfile <seqan/index.h>
+ * @brief Returns the value of a SparseString.
+ *
+ * @signature TValue getValue(sparseString, pos);
+ *
+ * @param[in] sparseString The @link SparseString @endlink.
+ * @param[in] pos          The position at which a value should be assign to the sparse string.
+ *                         Types: @link UnsignedIntegerConcept @endlink
+ *
+ * @return TValue The type @link GetValue @endlink of @link SparseString @endlink is returned.
+ */
+
+template <typename TFibreValues, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline typename GetValue<SparseString<TFibreValues, TSpec> >::Type
+getValue(SparseString<TFibreValues, TSpec> & string, TPos pos)
 {
     if (_isContained(string, pos))
-        return getValue(getFibre(string, FibreValueString()), getRank(getFibre(string, FibreIndicatorString()), pos) - 1);
-    else 
-        return DefaultValue<SparseString<TFibreValueString, TSpec> >::VALUE;
+        return getValue(getFibre(string, FibreValues()), getRank(getFibre(string, FibreIndicators()), pos) - 1);
+    else
+        return DefaultValue<SparseString<TFibreValues, TSpec> >::VALUE;
 }
 
-template <typename TFibreValueString, typename TSpec, typename TPos>
-inline typename GetValue<SparseString<TFibreValueString, TSpec> const>::Type
-getValue(SparseString<TFibreValueString, TSpec> const & string, TPos pos)
+template <typename TFibreValues, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline typename GetValue<SparseString<TFibreValues, TSpec> const>::Type
+getValue(SparseString<TFibreValues, TSpec> const & string, TPos pos)
 {
     if (_isContained(string, pos))
-        return getValue(getFibre(string, FibreValueString()), getRank(getFibre(string, FibreIndicatorString()), pos) - 1);
-    else 
-        return DefaultValue<SparseString<TFibreValueString, TSpec> const>::VALUE;
+        return getValue(getFibre(string, FibreValues()), getRank(getFibre(string, FibreIndicators()), pos) - 1);
+    else
+        return DefaultValue<SparseString<TFibreValues, TSpec> const>::VALUE;
 }
 
-
-///.Function.value.param.container.type:Class.SparseString
-template <typename TFibreValueString, typename TSpec, typename TPos>
-inline typename Reference<SparseString<TFibreValueString, TSpec> >::Type 
-value(SparseString<TFibreValueString, TSpec>&string, TPos pos)
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn SparseString#value
+ * @headerfile <seqan/index.h>
+ * @brief Returns the value of a @link SparseString @endlink.
+ *
+ * @signature TReference value(sparseString, pos);
+ *
+ * @param[in] sparseString The @link SparseString @endlink.
+ * @param[in] pos          The position at which a value should be assign to the sparse string.
+ *                         Types: @link UnsignedIntegerConcept @endlink
+ *
+ * @return TReference The type @link Reference @endlink of @link SparseString @endlink is returned.
+ */
+
+template <typename TFibreValues, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline typename Reference<SparseString<TFibreValues, TSpec> >::Type
+value(SparseString<TFibreValues, TSpec> & string, TPos pos)
 {
     return getValue(string, pos);
 }
 
-template <typename TFibreValueString, typename TSpec, typename TPos>
-inline typename Reference<SparseString<TFibreValueString, TSpec> >::Type
-value(SparseString<TFibreValueString, TSpec> const & string, TPos pos)
+template <typename TFibreValues, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline typename Reference<SparseString<TFibreValues, TSpec> >::Type
+value(SparseString<TFibreValues, TSpec> const & string, TPos pos)
 {
     return getValue(string, pos);
 }
 
-///.Function.getFibre.param.container.type:Class.CompressedSA
-template <typename TFibreValueString, typename TSpec>
-inline typename Fibre<SparseString<TFibreValueString, TSpec>, FibreValueString>::Type const &
-getFibre(SparseString<TFibreValueString, TSpec> const & sparseString, FibreValueString)
-{
-    return sparseString.valueString;
+// ----------------------------------------------------------------------------
+// Function getFibre()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn SparseString#getFibre
+ * @headerfile <seqan/index.h>
+ * @brief Returns a specific fibre of a @link SparseString @endlink.
+ *
+ * @signature TFibre getFibre(sparseString, fibreTag);
+ *
+ * @param[in] sparseString The sparseString holding the fibre.
+ * @param[in] fibreTag     A tag that identifies the @link Fibre @endlink. Types:
+ *                         @link SparseStringFibres SparseString Fibres @endlink
+ *
+ * @return TFibre A reference to the @link Fibre @endlink object.
+ */
+
+template <typename TFibreValues, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<SparseString<TFibreValues, TSpec>, FibreValues>::Type const &
+getFibre(SparseString<TFibreValues, TSpec> const & sparseString, FibreValues)
+{
+    return sparseString.values;
 }
 
-template <typename TFibreValueString, typename TSpec>
-inline typename Fibre<SparseString<TFibreValueString, TSpec>, FibreValueString>::Type &
-getFibre(SparseString<TFibreValueString, TSpec>&sparseString, FibreValueString)
+template <typename TFibreValues, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<SparseString<TFibreValues, TSpec>, FibreValues>::Type &
+getFibre(SparseString<TFibreValues, TSpec> & sparseString, FibreValues)
 {
-    return sparseString.valueString;
+    return sparseString.values;
 }
 
-template <typename TFibreValueString, typename TSpec>
-inline typename Fibre<SparseString<TFibreValueString, TSpec>, FibreIndicatorString>::Type const &
-getFibre(SparseString<TFibreValueString, TSpec> const & sparseString, FibreIndicatorString)
+template <typename TFibreValues, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<SparseString<TFibreValues, TSpec>, FibreIndicators>::Type const &
+getFibre(SparseString<TFibreValues, TSpec> const & sparseString, FibreIndicators)
 {
-    return sparseString.indicatorString;
+    return sparseString.indicators;
 }
 
-template <typename TFibreValueString, typename TSpec>
-inline typename Fibre<SparseString<TFibreValueString, TSpec>, FibreIndicatorString>::Type &
-getFibre(SparseString<TFibreValueString, TSpec>&sparseString, FibreIndicatorString)
+template <typename TFibreValues, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<SparseString<TFibreValues, TSpec>, FibreIndicators>::Type &
+getFibre(SparseString<TFibreValues, TSpec> & sparseString, FibreIndicators)
 {
-    return sparseString.indicatorString;
+    return sparseString.indicators;
 }
 
-///.Function.length.param.object.type:Class.SparseString
-template <typename TFibreValueString, typename TSpec>
-inline typename Size<typename Fibre<SparseString<TFibreValueString, TSpec>, FibreValueString>::Type>::Type
-length(SparseString<TFibreValueString, TSpec> const & string)
-{
-    return length(getFibre(string, FibreIndicatorString()));
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn SparseString#length
+ * @headerfile <seqan/index.h>
+ * @brief Returns the number of elements in the @link SparseString @endlink.
+ *
+ * @signature TSize length(sparseString);
+ *
+ * @param[in] sparseString The sparse string suffix array.
+ *
+ * @return TSize The number of elements in the sparse string array. Types: The result of @link Size @endlink of the
+ *               sparse string.
+ */
+
+
+template <typename TFibreValues, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Size<SparseString<TFibreValues, TSpec> const>::Type
+length(SparseString<TFibreValues, TSpec> const & string)
+{
+    return string._length;
 }
 
-///.Function.resize.param.object.type:Class.SparseString
-template <typename TFibreValueString, typename TSpec, typename TSize, typename TValue, typename TExpand>
-inline typename Size<typename Fibre<SparseString<TFibreValueString, TSpec>, FibreValueString>::Type>::Type
-resize(SparseString<TFibreValueString, TSpec> & string,
-                   TSize const size,
-                   TValue const value,
-                   Tag<TExpand> const tag)
-{
-    if (value != DefaultValue<SparseString<TFibreValueString, TSpec> >::VALUE)
-    {
-        TSize _length = length(getFibre(string, FibreIndicatorString()));
-        if (_length < size)
-            resize(getFibre(string, FibreValueString()), length(getFibre(string, FibreValueString())) + (size - length), value, tag);
-        else
-            resize(getFibre(string, FibreValueString()), getRank(string, size), value, tag);
-        resize(getFibre(string, FibreIndicatorString()), size, 1, tag);            
-    }
-    return resize(getFibre(string, FibreIndicatorString()), size, 0);
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): This version of resize() was now working, therefore it was commented out.
+
+//template <typename TFibreValues, typename TSpec, typename TSize, typename TValue, typename TExpand>
+//inline typename Size<typename Fibre<SparseString<TFibreValues, TSpec>, FibreValues>::Type>::Type
+//resize(SparseString<TFibreValues, TSpec> & string, TSize size, TValue value, Tag<TExpand> const tag)
+//{
+//    if (value != DefaultValue<SparseString<TFibreValues, TSpec> >::VALUE)
+//    {
+//        if (length(string) < size)
+//            resize(getFibre(string, FibreValues()), length(getFibre(string, FibreValues())) + (size - length(string)), value, tag);
+//        else
+//            resize(getFibre(string, FibreValues()), getRank(getFibre(string, FibreIndicators()), size), value, tag);
+//
+//        resize(getFibre(string, FibreIndicators()), size, true, tag);
+//    }
+//
+//    string._length = size;
+//
+//    return resize(getFibre(string, FibreIndicators()), size, false);
+//}
+
+/*!
+ * @fn SparseString#resize
+ * @headerfile <seqan/index.h>
+ * @brief Resets the number of elements in the compressed suffix array.
+ *
+ * @signature TSize resize(sparseString, newLength);
+ *
+ * @param[in,out] sparseString The sparse string.
+ * @param[in]     newLength    The number of elements which should be stored in the  sparse string.  Types:
+ *                             @link UnsignedIntegerConcept @endlink.
+ *
+ * @return TSize The number of elements in the  sparse string. Types: The result of @link Size @endlink of the
+ *               sparse string.
+ *
+ * @note If the new length is smaller than the actual one then the last <tt>x<tt> items of the compressed suffix array
+ *       are deleted with <tt>x = oldLength - newLength</tt>.
+ */
+
+template <typename TFibreValues, typename TSpec, typename TSize, typename TExpand>
+inline typename Size<typename Fibre<SparseString<TFibreValues, TSpec>, FibreValues>::Type>::Type
+resize(SparseString<TFibreValues, TSpec> & string, TSize size, Tag<TExpand> tag)
+{
+//    return resize(string, size, DefaultValue<SparseString<TFibreValues, TSpec> >::VALUE, tag);
+
+    string._length = size;
+    return resize(getFibre(string, FibreIndicators()), size, tag);
 }
 
-template <typename TFibreValueString, typename TSpec, typename TSize, typename TExpand>
-inline typename Size<typename Fibre<SparseString<TFibreValueString, TSpec>, FibreValueString>::Type>::Type
-resize(SparseString<TFibreValueString, TSpec> & string,
-                   TSize const size,
-                   Tag<TExpand> tag)
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn SparseString#open
+ * @headerfile <seqan/index.h>
+ * @brief This functions open a sparse string from disk.
+ *
+ * @signature bool open(string, fileName[, openMode]);
+ *
+ * @param[in] string   The string to be opened. Types: SparseString
+ * @param[in] fileName C-style character string containing the file name.
+ * @param[in] openMode The combination of flags defining how the file should be
+ *                     opened.  To open a file read-only, write-only or to read and
+ *                     write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
+ *                     <tt>OPEN_RDWR</tt>.To create or overwrite a file add
+ *                     <tt>OPEN_CREATE</tt>.  To append a file if existing add
+ *                     <tt>OPEN_APPEND</tt>.  To circumvent problems, files are always
+ *                     opened in binary mode.  Default: <tt>OPEN_RDWR | OPEN_CREATE |
+ *                     OPEN_APPEND</tt>
+ *
+ * @return bool <tt>true</tt> on success.
+ */
+
+template <typename TFibreValues, typename TSpec>
+inline bool open(SparseString<TFibreValues, TSpec> & sparseString, const char * fileName, int openMode)
 {
-    return resize(getFibre(string, FibreIndicatorString()), size, 0, tag);
-}
+    String<char> name;
 
+    // Length saved inside a .len file.
+    name = fileName;
+    append(name, ".len");
+    if (!open(sparseString._length, toCString(name), openMode)) return false;
+
+    // Values saved inside a .val file.
+    name = fileName;
+    append(name, ".val");
+    if (!open(getFibre(sparseString, FibreValues()), toCString(name), openMode)) return false;
+
+    // Indicators saved inside a .ind file.
+    name = fileName;
+    append(name, ".ind");
+    if (!open(getFibre(sparseString, FibreIndicators()), toCString(name), openMode)) return false;
 
-/**
-.Function.open
-..param.string:
-...type:Class.SparseString
-*/
-template <typename TFibreValueString, typename TSpec>
-inline bool open(
-    SparseString<TFibreValueString, TSpec> & sparseString,
-    const char * fileName,
-    int openMode)
-{
-    String<char> name;
-    name = fileName;    append(name, ".val");
-    if (!open(getFibre(sparseString, FibreValueString()), toCString(name), openMode)) // val = value string
-    {
-        return false;
-    }
-    name = fileName;    append(name, ".ind");   open(getFibre(sparseString, FibreIndicatorString()), toCString(name), openMode); // ind = indicator string
     return true;
 }
 
-template <typename TFibreValueString, typename TSpec>
-inline bool open(
-    SparseString<TFibreValueString, TSpec> & sparseString,
-    const char * fileName)
+template <typename TFibreValues, typename TSpec>
+inline bool open(SparseString<TFibreValues, TSpec> & sparseString, const char * fileName)
 {
-    return open(sparseString, fileName, DefaultOpenMode<SparseString<TFibreValueString, TSpec> >::VALUE);
+    return open(sparseString, fileName, DefaultOpenMode<SparseString<TFibreValues, TSpec> >::VALUE);
 }
 
-/**
-.Function.SparseString#save
-..class:Class.SparseString
-..summary:This functions saves a sparse string to disk.
-..signature:open(string, fileName [, openMode])
-..param.string:The string to be saved.
-...type:Class.SparseString
-..param.fileName:C-style character string containing the file name.
-..param.openMode:The combination of flags defining how the file should be opened.
-...remarks:To open a file read-only, write-only or to read and write use $OPEN_RDONLY$, $OPEN_WRONLY$, or $OPEN_RDWR$.
-...remarks:To create or overwrite a file add $OPEN_CREATE$.
-...remarks:To append a file if existing add $OPEN_APPEND$.
-...remarks:To circumvent problems, files are always opened in binary mode.
-...default:$OPEN_RDWR | OPEN_CREATE | OPEN_APPEND$
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/index.h
-*/
-template <typename TFibreValueString, typename TSpec>
-inline bool save(
-    SparseString<TFibreValueString, TSpec> const & sparseString,
-    const char * fileName)
-{
-    return save(sparseString, fileName, DefaultOpenMode<SparseString<TFibreValueString, TSpec> >::VALUE);
+// ----------------------------------------------------------------------------
+// Function save()
+// ----------------------------------------------------------------------------
+/*!
+ * @fn SparseString#save
+ *
+ * @headerfile <seqan/index.h>
+ *
+ * @brief This functions saves a sparse string to disk.
+ *
+ * @signature bool save(string, fileName[, openMode]);
+ *
+ * @param[in] string   The string to be saved.  Types: SparseString
+ * @param[in] fileName C-style character string containing the file name.
+ * @param[in] openMode The combination of flags defining how the file should be
+ *                     opened.  To open a file read-only, write-only or to read and
+ *                     write use <tt>OPEN_RDONLY</tt>, <tt>OPEN_WRONLY</tt>, or
+ *                     <tt>OPEN_RDWR</tt>.To create or overwrite a file add
+ *                     <tt>OPEN_CREATE</tt>.  To append a file if existing add
+ *                     <tt>OPEN_APPEND</tt>.  To circumvent problems, files are always
+ *                     opened in binary mode.  Default: <tt>OPEN_RDWR | OPEN_CREATE |
+ *                     OPEN_APPEND</tt>
+ *
+ * @return bool <tt>true</tt> on success.
+ */
+template <typename TFibreValues, typename TSpec>
+inline bool save(SparseString<TFibreValues, TSpec> const & sparseString, const char * fileName)
+{
+    return save(sparseString, fileName, DefaultOpenMode<SparseString<TFibreValues, TSpec> >::VALUE);
 }
 
-template <typename TFibreValueString, typename TSpec>
-inline bool save(
-    SparseString<TFibreValueString, TSpec> const & sparseString,
-    const char * fileName,
-    int openMode)
+template <typename TFibreValues, typename TSpec>
+inline bool save(SparseString<TFibreValues, TSpec> const & sparseString, const char * fileName, int openMode)
 {
     String<char> name;
-    name = fileName;    append(name, ".val");
-    if (!save(getFibre(sparseString, FibreValueString()), toCString(name), openMode))
-    {
-        return false;
-    }
-    name = fileName;    append(name, ".ind");   save(getFibre(sparseString, FibreIndicatorString()), toCString(name), openMode);
+
+    name = fileName;
+    append(name, ".len");
+    if (!save(length(sparseString), toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".val");
+    if (!save(getFibre(sparseString, FibreValues()), toCString(name), openMode)) return false;
+
+    name = fileName;
+    append(name, ".ind");
+    if (!save(getFibre(sparseString, FibreIndicators()), toCString(name), openMode)) return false;
+
     return true;
 }
 // TODO(singer): setValue function
diff --git a/seqan/index/index_fm_stree.h b/seqan/index/index_fm_stree.h
index c85c7dc..e22540f 100644
--- a/seqan/index/index_fm_stree.h
+++ b/seqan/index/index_fm_stree.h
@@ -1,7 +1,8 @@
 // ==========================================================================
-//                 seqan - the library for sequence analysis
+//                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,6 +31,7 @@
 //
 // ==========================================================================
 // Author: Jochen Singer <jochen.singer@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
 // ==========================================================================
 
 //SEQAN_NO_DDDOC:do not generate documentation for this file
@@ -44,42 +46,80 @@ namespace seqan {
 // ==========================================================================
 
 // ----------------------------------------------------------------------------
-// Class VertexFmi
+// Class HistoryStackFM_
 // ----------------------------------------------------------------------------
 
-template <typename TAlphabet, typename TSize>
-struct VertexFmi
+template <typename TSize, typename TAlphabet>
+struct HistoryStackFM_
+{
+    Pair<TSize> range;
+    TSize       repLen;
+    TAlphabet   lastChar;
+
+    SEQAN_HOST_DEVICE
+    HistoryStackFM_() {}
+
+    template <typename TSize_, typename TAlphabet_>
+    SEQAN_HOST_DEVICE
+    HistoryStackFM_(Pair<TSize_> const &_range, TSize_ _repLen, TAlphabet_ _lastChar):
+        range(_range),
+        repLen(_repLen),
+        lastChar(_lastChar)
+    {}
+
+    SEQAN_HOST_DEVICE
+    HistoryStackFM_ const &
+    operator=(HistoryStackFM_ const & _origin)
+    {
+        range = _origin.range;
+        repLen = _origin.repLen;
+        lastChar = _origin.lastChar;
+        return _origin;
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class VertexFM
+// ----------------------------------------------------------------------------
+
+template <typename TSize, typename TAlphabet>
+struct VertexFM
 {
     Pair<TSize> range;
     TSize       repLen;
     TAlphabet   lastChar;
 
-    VertexFmi() :
+    SEQAN_HOST_DEVICE
+    VertexFM() :
         range(0, 0),
         repLen(0),
         lastChar(0)
     {}
 
-    VertexFmi(MinimalCtor) :
+    SEQAN_HOST_DEVICE
+    VertexFM(MinimalCtor) :
         range(0, 0),
         repLen(0),
         lastChar(0)
     {}
 
-    VertexFmi(Pair<TSize> newCurrentRange, TSize newRepLen, TAlphabet newChar) :
+    SEQAN_HOST_DEVICE
+    VertexFM(Pair<TSize> newCurrentRange, TSize newRepLen, TAlphabet newChar) :
         range(newCurrentRange),
         repLen(newRepLen),
         lastChar(newChar)
     {}
 
-    VertexFmi(VertexFmi const & other) :
+    SEQAN_HOST_DEVICE
+    VertexFM(VertexFM const & other) :
         range(other.range),
         repLen(other.repLen),
         lastChar(other.lastChar)
     {}
 
-    inline VertexFmi &
-    operator = (VertexFmi const & _origin)
+    SEQAN_HOST_DEVICE inline
+    VertexFM &
+    operator = (VertexFM const & _origin)
     {
         range = _origin.range;
         repLen = _origin.repLen;
@@ -88,34 +128,6 @@ struct VertexFmi
     }
 };
 
-// ----------------------------------------------------------------------------
-// Class HistoryStackFmi_
-// ----------------------------------------------------------------------------
-
-template <typename TAlphabet, typename TSize>
-struct HistoryStackFmi_
-{
-    Pair<TSize> range;		// current SA interval of hits
-    TAlphabet   lastChar;
-
-    HistoryStackFmi_() {}
-
-    template <typename TAlphabet_, typename TSize_>
-    HistoryStackFmi_(TAlphabet_ const _lastChar, Pair<TSize_> const &_range):
-        range(_range),
-        lastChar(_lastChar)
-    {}
-
-    inline HistoryStackFmi_ const &
-    operator=(HistoryStackFmi_ const & _origin)
-    {
-        range = _origin.range;
-        lastChar = _origin.lastChar;
-        return _origin;
-    }
-};
-
-
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -127,11 +139,11 @@ struct HistoryStackFmi_
 template < typename TText, typename TOccSpec, typename TIndexSpec>
 struct VertexDescriptor<Index<TText, FMIndex<TOccSpec, TIndexSpec> > >
 {
-    typedef Index<TText,FMIndex<TOccSpec, TIndexSpec> >     TIndex;
-    typedef typename Value<TIndex>::Type                    TAlphabet;
-    typedef typename Size<TIndex>::Type                     TSize;
+    typedef Index<TText,FMIndex<TOccSpec, TIndexSpec> >     TIndex_;
+    typedef typename Size<TIndex_>::Type                    TSize_;
+    typedef typename Value<TIndex_>::Type                   TAlphabet_;
 
-    typedef VertexFmi<TAlphabet, TSize> Type;
+    typedef VertexFM<TSize_, TAlphabet_>                    Type;
 };
 
 // ----------------------------------------------------------------------------
@@ -142,8 +154,8 @@ template <typename TText, typename TOccSpec, typename TSpec, typename TIterSpec>
 struct HistoryStackEntry_<Iter<Index<TText, FMIndex<TOccSpec, TSpec> >,
                                VSTree< TopDown< ParentLinks<TIterSpec> > > > >
 {
-    typedef HistoryStackFmi_<typename Value<Index<TText, FMIndex<TOccSpec, TSpec> > >::Type,
-                             typename Size<Index<TText, FMIndex<TOccSpec, TSpec> > >::Type>     Type;
+    typedef HistoryStackFM_<typename Size<Index<TText, FMIndex<TOccSpec, TSpec> > >::Type,
+                             typename Value<Index<TText, FMIndex<TOccSpec, TSpec> > >::Type>    Type;
 };
 
 // ----------------------------------------------------------------------------
@@ -166,28 +178,23 @@ struct EdgeLabel<Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TSpec
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec>
-void _indexRequireTopDownIteration(Index<TText, FMIndex<TOccSpec, TIndexSpec> > & index)
+SEQAN_HOST_DEVICE inline void _indexRequireTopDownIteration(Index<TText, FMIndex<TOccSpec, TIndexSpec> > & index)
 {
-    indexRequire(index, FibreSaLfTable());
+    indexRequire(index, FibreSALF());
 }
 
 // ----------------------------------------------------------------------------
 // Function begin()                                                  [Iterator]
 // ----------------------------------------------------------------------------
 
-// ==========================================================================
-///.Function.begin.param.object.type:Spec.FMIndex
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
 inline
 typename Iterator<Index<TText,FMIndex<TOccSpec, TIndexSpec> >, TSpec>::Type
 begin(Index<TText, FMIndex<TOccSpec, TIndexSpec> > & index, TSpec const /*Tag*/)
 {
-	typedef typename Iterator<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, TSpec>::Type TIter;
-
-	TIter it(index);
-	value(it).range.i1 = index.lfTable.prefixSumTable[0];
+    typedef typename Iterator<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, TSpec>::Type TIter;
 
-	return it;
+    return TIter(index);
 }
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
@@ -195,12 +202,9 @@ inline
 typename Iterator<Index<TText,FMIndex<TOccSpec, TIndexSpec> > const, TSpec>::Type
 begin(Index<TText, FMIndex<TOccSpec, TIndexSpec> > const & index, TSpec const /*Tag*/)
 {
-	typedef typename Iterator<Index<TText, FMIndex<TOccSpec, TIndexSpec> > const, TSpec>::Type TIter;
-
-	TIter it(index);
-	value(it).range.i1 = index.lfTable.prefixSumTable[0];
+    typedef typename Iterator<Index<TText, FMIndex<TOccSpec, TIndexSpec> > const, TSpec>::Type TIter;
 
-	return it;
+    return TIter(index);
 }
 
 // ----------------------------------------------------------------------------
@@ -208,7 +212,7 @@ begin(Index<TText, FMIndex<TOccSpec, TIndexSpec> > const & index, TSpec const /*
 // ----------------------------------------------------------------------------
 
 template <typename TAlphabet, typename TSize>
-inline bool _isRoot(VertexFmi<TAlphabet, TSize> const & value)
+SEQAN_HOST_DEVICE inline bool _isRoot(VertexFM<TAlphabet, TSize> const & value)
 {
     return _isSizeInval(value.range.i2);
 }
@@ -218,33 +222,20 @@ inline bool _isRoot(VertexFmi<TAlphabet, TSize> const & value)
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder>
-inline bool _isLeaf(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TSpec> > const & it,
-                    VSTreeIteratorTraits<TDfsOrder, False> const)
+SEQAN_HOST_DEVICE inline bool
+_isLeaf(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TSpec> > const & it,
+        VSTreeIteratorTraits<TDfsOrder, False> const)
 {
-    return _isLeaf(it, VSTreeIteratorTraits<TDfsOrder, True>());
+    return value(it).range.i1 >= value(it).range.i2;
 }
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder>
-inline bool _isLeaf(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TSpec> > const & it,
-                    VSTreeIteratorTraits<TDfsOrder, True> const)
-{
-    return (value(it).range.i1 + 1 >= value(it).range.i2 &&
-            value(it).range.i1 == _getSentinelPosition(container(it).lfTable.occTable));
-}
-
-template <typename TText, typename TSetSpec, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder>
-inline bool _isLeaf(Iter<Index<StringSet<TText, TSetSpec>, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TSpec> > const & it,
-                    VSTreeIteratorTraits<TDfsOrder, False> const)
-{
-    return _isLeaf(it, VSTreeIteratorTraits<TDfsOrder, True>());
-}
-
-template <typename TText, typename TSetSpec, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder>
-inline bool _isLeaf(Iter<Index<StringSet<TText, TSetSpec>, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TSpec> > const & it,
-                    VSTreeIteratorTraits<TDfsOrder, True> const)
+SEQAN_HOST_DEVICE inline bool
+_isLeaf(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TSpec> > const & it,
+        VSTreeIteratorTraits<TDfsOrder, True> const)
 {
-    return (value(it).range.i1 + 1 >= value(it).range.i2 &&
-            sentinelPosition(getFibre(getFibre(container(it), FibreLfTable()), FibreOccTable()), value(it).range.i1));
+    return _isLeaf(it, VSTreeIteratorTraits<TDfsOrder, False>()) &&
+           isSentinel(indexLF(container(it)), value(it).range.i1);
 }
 
 // ----------------------------------------------------------------------------
@@ -252,37 +243,24 @@ inline bool _isLeaf(Iter<Index<StringSet<TText, TSetSpec>, FMIndex<TOccSpec, TIn
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TChar>
-inline bool _getNodeByChar(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > const & it,
-                           typename VertexDescriptor<Index<TText, FMIndex<TOccSpec, TIndexSpec> > >::Type const & vDesc,
-                           Pair<typename Size<Index<TText, FMIndex<TOccSpec, TIndexSpec> > >::Type> & _range,
-                           TChar c)
+SEQAN_HOST_DEVICE inline bool
+_getNodeByChar(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > const & it,
+               typename VertexDescriptor<Index<TText, FMIndex<TOccSpec, TIndexSpec> > >::Type const & vDesc,
+               Pair<typename Size<Index<TText, FMIndex<TOccSpec, TIndexSpec> > >::Type> & _range,
+               TChar c)
 {
     typedef Index<TText, FMIndex<TOccSpec, TIndexSpec> >        TIndex;
-    typedef typename Value<TIndex>::Type                        TAlphabet;
-    typedef typename ValueSize<TAlphabet>::Type                 TAlphabetSize;
-    typedef typename Size<TIndex>::Type                         TSize;
-
-    typedef typename Fibre<TIndex, FibreLfTable>::Type          TLfTable;
-    typedef typename Fibre<TLfTable, FibrePrefixSumTable>::Type TPrefixSumTable;
+    typedef typename Fibre<TIndex, FibreLF>::Type               TLF;
 
-    TIndex const & _index = container(it);
-    TPrefixSumTable const & pst = getFibre(getFibre(_index, FibreLfTable()), FibrePrefixSumTable());
+    TIndex const & index = container(it);
+    TLF const & lf = indexLF(index);
 
-    TAlphabetSize cPosition = getCharacterPosition(pst, c);
+    _range = range(index, vDesc);
 
-    if (_isRoot(vDesc))
-    {
-        _range.i1 = getPrefixSum(pst, cPosition);
-        _range.i2 = getPrefixSum(pst, cPosition + 1);
-    }
-    else
-    {
-        TSize prefixSum = getPrefixSum(pst, cPosition);
-        _range.i1 = prefixSum + countOccurrences(_index.lfTable.occTable, c, vDesc.range.i1 - 1);
-        _range.i2 = prefixSum + countOccurrences(_index.lfTable.occTable, c, vDesc.range.i2 - 1);
-    }
+    _range.i1 = lf(_range.i1, c);
+    _range.i2 = lf(_range.i2, c);
 
-    return _range.i1 + 1 <= _range.i2;
+    return _range.i1 < _range.i2;
 }
 
 // ----------------------------------------------------------------------------
@@ -290,7 +268,8 @@ inline bool _getNodeByChar(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VS
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TChar>
-inline bool _goDownChar(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it, TChar c)
+SEQAN_HOST_DEVICE inline bool
+_goDownChar(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it, TChar c)
 {
     typedef Index<TText, FMIndex<TOccSpec, TIndexSpec> >        TIndex;
     typedef Pair<typename Size<TIndex>::Type>                   TRange;
@@ -317,23 +296,31 @@ inline bool _goDownChar(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTre
 
 // TODO(esiragusa): Implement this.
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder>
-inline bool _goDown(Iter<Index<TText, FMIndex<TOccSpec,TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
-                    VSTreeIteratorTraits<TDfsOrder, False> const)
+SEQAN_HOST_DEVICE inline bool
+_goDown(Iter<Index<TText, FMIndex<TOccSpec,TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+        VSTreeIteratorTraits<TDfsOrder, False> const)
 {
     return _goDown(it, VSTreeIteratorTraits<TDfsOrder, True>());
 }
 
 template <typename TText, typename TOccSpec, typename TSpec, typename TIndexSpec, typename TDfsOrder>
-inline bool _goDown(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
-                    VSTreeIteratorTraits<TDfsOrder, True> const)
+SEQAN_HOST_DEVICE inline bool
+_goDown(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+        VSTreeIteratorTraits<TDfsOrder, True> const)
 {
     typedef Index<TText, FMIndex<TOccSpec, TIndexSpec> >    TIndex;
     typedef typename Value<TIndex>::Type                    TAlphabet;
-    typedef typename ValueSize<TAlphabet>::Type             TAlphabetSize;
+//    typedef typename ValueSize<TAlphabet>::Type             TAlphabetSize;
 
+    // NOTE(esiragusa): isLeaf() early exit is slower on CUDA.
+    // NOTE(esiragusa): this should be faster only for texts over small alphabets consisting of few/long sequences.
+#ifndef __CUDA_ARCH__
     if (isLeaf(it)) return false;
+#endif
 
-    for (TAlphabetSize c = 0; c < ValueSize<TAlphabet>::VALUE; ++c)
+    // TODO(esiragusa): Fix increment for alphabets with qualities.
+//    for (TAlphabetSize c = 0; c < ValueSize<TAlphabet>::VALUE; ++c)
+    for (TAlphabet c = 0; ordValue(c) < ValueSize<TAlphabet>::VALUE; ++c)
         if (_goDownChar(it, c)) return true;
 
     return false;
@@ -343,52 +330,41 @@ inline bool _goDown(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<To
 // Function _goDownString()                                          [Iterator]
 // ----------------------------------------------------------------------------
 
-//template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TString, typename TSize>
-//inline bool _goDownString(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
-//                          TString const & string,
-//                          TSize & lcp)
-//{
-//    typedef Index<TText, FMIndex<TOccSpec, TIndexSpec> >        TIndex;
-//    typedef Pair<typename Size<TIndex>::Type>                   TRange;
-//
-//    typedef typename Iterator<TString const, Standard>::Type    TIterator;
-//
-//    _historyPush(it);
-//
-//    lcp = 0;
-//
-//    for (TIterator stringIt = begin(string, Standard()); stringIt != end(string, Standard()); ++stringIt)
-//    {
-//        TRange _range;
-//
-//        if (isLeaf(it) || !_getNodeByChar(it, value(it), _range, value(stringIt)))
-//            return false;
-//
-//        value(it).range = _range;
-//        value(it).lastChar = value(stringIt);
-//        value(it).repLen++;
-//        lcp++;
-//    }
-//
-//    return true;
-//}
-
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TString, typename TSize>
-inline bool _goDownString(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > &it,
-                          TString const & string,
-                          TSize & lcp)
+SEQAN_HOST_DEVICE inline bool
+_goDownString(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > &it,
+              TString const & string,
+              TSize & lcp)
 {
-    //typedef Index<TText, FMIndex<TOccSpec, TIndexSpec> >        TIndex;
-    //typedef typename Value<TIndex>::Type                        TAlphabet;
+    typedef Index<TText, FMIndex<TOccSpec, TIndexSpec> >        TIndex;
+    typedef Pair<typename Size<TIndex>::Type>                   TRange;
     typedef typename Iterator<TString const, Standard>::Type    TStringIter;
 
-    lcp = 0;
+    _historyPush(it);
 
-    for (TStringIter stringIt = begin(string, Standard()); stringIt != end(string, Standard()); ++stringIt, ++lcp)
-        if (isLeaf(it) || !_goDownChar(it, value(stringIt)))
-            return false;
+    TStringIter stringIt = begin(string, Standard());
+    TStringIter stringEnd = end(string, Standard());
 
-    return true;
+    for (lcp = 0; stringIt != stringEnd; ++stringIt, ++lcp)
+    {
+        TRange _range;
+
+        // NOTE(esiragusa): isLeaf() early exit is slower on CUDA.
+        // NOTE(esiragusa): this should be faster only for texts over small alphabets consisting of few/long sequences.
+#ifdef __CUDA_ARCH__
+        if (!_getNodeByChar(it, value(it), _range, value(stringIt))) break;
+#else
+        if (isLeaf(it) || !_getNodeByChar(it, value(it), _range, value(stringIt))) break;
+#endif
+
+        value(it).range = _range;
+    }
+
+    value(it).repLen += lcp;
+
+    if (lcp) value(it).lastChar = value(stringIt - 1);
+
+    return stringIt == stringEnd;
 }
 
 // ----------------------------------------------------------------------------
@@ -397,19 +373,20 @@ inline bool _goDownString(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VST
 
 // TODO(esiragusa): Implement this.
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder>
-inline bool _goRight(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
-                     VSTreeIteratorTraits<TDfsOrder, False> const)
+SEQAN_HOST_DEVICE inline bool
+_goRight(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+         VSTreeIteratorTraits<TDfsOrder, False> const)
 {
     return _goRight(it, VSTreeIteratorTraits<TDfsOrder, True>());
 }
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder>
-inline bool _goRight(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
-                     VSTreeIteratorTraits<TDfsOrder, True> const)
+SEQAN_HOST_DEVICE inline bool
+_goRight(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+         VSTreeIteratorTraits<TDfsOrder, True> const)
 {
     typedef Index<TText, FMIndex<TOccSpec, TIndexSpec> >        TIndex;
     typedef typename Value<TIndex>::Type                        TAlphabet;
-    typedef typename ValueSize<TAlphabet>::Type                 TAlphabetSize;
     typedef Pair<typename Size<TIndex>::Type>                   TRange;
 
     typedef typename VertexDescriptor<TIndex>::Type             TVertexDescriptor;
@@ -419,15 +396,18 @@ inline bool _goRight(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<T
     TVertexDescriptor parentDesc = nodeUp(it);
     TRange _range;
 
-    for (TAlphabetSize c = ordValue(value(it).lastChar) + 1; c < ValueSize<TAlphabet>::VALUE; ++c)
-        if (_getNodeByChar(it, parentDesc, _range, c))
+    // TODO(esiragusa): Fix increment for alphabets with qualities.
+//    for (TAlphabetSize c = ordValue(value(it).lastChar) + 1; c < ValueSize<TAlphabet>::VALUE; ++c)
+    for (value(it).lastChar++; ordValue(value(it).lastChar) < ValueSize<TAlphabet>::VALUE; value(it).lastChar++)
+    {
+        if (_getNodeByChar(it, parentDesc, _range, value(it).lastChar))
         {
             value(it).range = _range;
-            value(it).lastChar = c;
 
             return true;
         }
-    
+    }
+
     return false;
 }
 
@@ -436,32 +416,23 @@ inline bool _goRight(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<T
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
-bool _goUp(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it)
+SEQAN_HOST_DEVICE inline bool
+_goUp(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it)
 {
-	if (!isRoot(it))
-	{
-        value(it).range = it._parentDesc.range;
-        value(it).lastChar = it._parentDesc.lastChar;
-        --value(it).repLen;
-        return true;
-    }
-    
-    return false;
+    if (isRoot(it)) return false;
+
+    _historyPop(it);
+    return true;
 }
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
-bool _goUp(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
+SEQAN_HOST_DEVICE inline bool
+_goUp(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
 {
-	if (!isRoot(it))
-	{
-        value(it).range = back(it.history).range;
-        value(it).lastChar = back(it.history).lastChar;
-        --value(it).repLen;
-        pop(it.history);
-        return true;
-    }
-    
-    return false;
+    if (isRoot(it)) return false;
+
+    _historyPop(it);
+    return true;
 }
 
 // ----------------------------------------------------------------------------
@@ -469,14 +440,14 @@ bool _goUp(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree<TopDown<Par
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, class TSpec>
-inline typename VertexDescriptor<Index<TText, FMIndex<TOccSpec, TIndexSpec> > >::Type
+SEQAN_HOST_DEVICE inline typename VertexDescriptor<Index<TText, FMIndex<TOccSpec, TIndexSpec> > >::Type
 nodeUp(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > const & it)
 {
     typedef Index<TText, FMIndex<TOccSpec, TIndexSpec> >    TIndex;
     typedef typename VertexDescriptor<TIndex>::Type         TVertexDescriptor;
 
     if (!empty(it.history))
-        return TVertexDescriptor(back(it.history).range, value(it).repLen - 1, back(it.history).lastChar);
+        return TVertexDescriptor(back(it.history).range, back(it.history).repLen, back(it.history).lastChar);
     else
         return value(it);
 }
@@ -486,13 +457,14 @@ nodeUp(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec> >, VSTree< TopDown< Paren
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
-inline void _historyPush(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<TSpec> > > & it)
+SEQAN_HOST_DEVICE inline void
+_historyPush(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<TSpec> > > & it)
 {
     it._parentDesc = value(it);
 }
 
 template < typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
-inline void
+SEQAN_HOST_DEVICE inline void
 _historyPush(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
 {
     typedef Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<ParentLinks<TSpec> > > > TIter;
@@ -500,20 +472,44 @@ _historyPush(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<
     typename HistoryStackEntry_<TIter>::Type h;
 
     h.range = value(it).range;
+    h.repLen = value(it).repLen;
     h.lastChar = value(it).lastChar;
 
     appendValue(it.history, h);
 }
 
+// ----------------------------------------------------------------------------
+// Function _historyPop()                                            [Iterator]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline void
+_historyPop(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<TSpec> > > & it)
+{
+    value(it).range = back(it.history).range;
+    value(it).repLen = back(it.history).repLen;
+    value(it).lastChar = back(it.history).lastChar;
+}
+
+template < typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline void
+_historyPop(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
+{
+    value(it).range = back(it.history).range;
+    value(it).repLen = back(it.history).repLen;
+    value(it).lastChar = back(it.history).lastChar;
+    eraseBack(it.history);
+}
+
 // ----------------------------------------------------------------------------
 // Function repLength()                                              [Iterator]
 // ----------------------------------------------------------------------------
 
 template <typename TIndex, typename TAlphabet, typename TSize>
-inline typename Size<TIndex>::Type
-repLength(TIndex const &, VertexFmi<TAlphabet, TSize> const & vDesc)
+SEQAN_HOST_DEVICE inline typename Size<TIndex>::Type
+repLength(TIndex const &, VertexFM<TAlphabet, TSize> const & vDesc)
 {
-	return vDesc.repLen;
+    return vDesc.repLen;
 }
 
 // ----------------------------------------------------------------------------
@@ -521,7 +517,7 @@ repLength(TIndex const &, VertexFmi<TAlphabet, TSize> const & vDesc)
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
-inline typename EdgeLabel<Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<TSpec> > > >::Type
+SEQAN_HOST_DEVICE inline typename EdgeLabel<Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<TSpec> > > >::Type
 parentEdgeLabel(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<TSpec> > > const & it)
 {
     return value(it).lastChar;
@@ -532,7 +528,7 @@ parentEdgeLabel(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDo
 // ----------------------------------------------------------------------------
 
 template <typename TText, typename TOccSpec, typename TIndexSpec, typename TSpec>
-inline typename Value<Index<TText, FMIndex<TOccSpec, TIndexSpec > > >::Type
+SEQAN_HOST_DEVICE inline typename Value<Index<TText, FMIndex<TOccSpec, TIndexSpec > > >::Type
 parentEdgeFirstChar(Iter<Index<TText, FMIndex<TOccSpec, TIndexSpec > >, VSTree<TopDown<TSpec> > > const & it)
 {
     return value(it).lastChar;
diff --git a/seqan/index/index_forwards.h b/seqan/index/index_forwards.h
index 74ab9fd..25b012b 100644
--- a/seqan/index/index_forwards.h
+++ b/seqan/index/index_forwards.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_INDEX_MANUAL_FORWARDS_H 
-#define SEQAN_HEADER_INDEX_MANUAL_FORWARDS_H 
+#ifndef SEQAN_HEADER_INDEX_MANUAL_FORWARDS_H
+#define SEQAN_HEADER_INDEX_MANUAL_FORWARDS_H
 
 //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
 
@@ -43,25 +43,25 @@
 
 namespace SEQAN_NAMESPACE_MAIN {
 
-	struct FibreText_;		// Original text. Can be a String or a StringSet
-	struct FibreRawText_;	// Concatenation of the strings above
-	struct FibreSA_;		// suffix array (of raw text with virtual $-delimiters) with Pair entries
-	struct FibreRawSA_;	// suffix array with integer entries
-	struct FibreSae_;		// suffix array reordered in a b-tree
-	struct FibreLcp_;		// lcp table of raw text
-	struct FibreLcpe_;		// lcp interval tree
-	struct FibreChildtab_;	// childtab (Kurtz et al.) of raw text
-	struct FibreBwt_;		// burrows wheeler table of raw text
+    struct FibreText_;        // Original text. Can be a String or a StringSet
+    struct FibreRawText_;    // Concatenation of the strings above
+    struct FibreSA_;        // suffix array (of raw text with virtual $-delimiters) with Pair entries
+    struct FibreRawSA_;    // suffix array with integer entries
+    struct FibreSae_;        // suffix array reordered in a b-tree
+    struct FibreLcp_;        // lcp table of raw text
+    struct FibreLcpe_;        // lcp interval tree
+    struct FibreChildtab_;    // childtab (Kurtz et al.) of raw text
+    struct FibreBwt_;        // burrows wheeler table of raw text
 
-	typedef Tag<FibreText_> const		FibreText;
-	typedef Tag<FibreRawText_> const	FibreRawText;
-	typedef Tag<FibreSA_> const		FibreSA;
-	typedef Tag<FibreRawSA_> const		FibreRawSA;
-	typedef Tag<FibreSae_> const		FibreSae;
-	typedef Tag<FibreLcp_> const		FibreLcp;
-	typedef Tag<FibreLcpe_> const		FibreLcpe;
-	typedef Tag<FibreChildtab_> const	FibreChildtab;
-	typedef Tag<FibreBwt_> const		FibreBwt;
+    typedef Tag<FibreText_> const        FibreText;
+    typedef Tag<FibreRawText_> const    FibreRawText;
+    typedef Tag<FibreSA_> const        FibreSA;
+    typedef Tag<FibreRawSA_> const        FibreRawSA;
+    typedef Tag<FibreSae_> const        FibreSae;
+    typedef Tag<FibreLcp_> const        FibreLcp;
+    typedef Tag<FibreLcpe_> const        FibreLcpe;
+    typedef Tag<FibreChildtab_> const    FibreChildtab;
+    typedef Tag<FibreBwt_> const        FibreBwt;
 
 }
 
diff --git a/seqan/index/index_lcp.h b/seqan/index/index_lcp.h
index 3236e4c..bb59134 100644
--- a/seqan/index/index_lcp.h
+++ b/seqan/index/index_lcp.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,12 +37,12 @@
 
 namespace SEQAN_NAMESPACE_MAIN
 {
-	
+
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct Kasai {};
-	struct KasaiOriginal {};	// original, but more space-consuming algorithm
+    struct Kasai {};
+    struct KasaiOriginal {};    // original, but more space-consuming algorithm
 
 
     //////////////////////////////////////////////////////////////////////////////
@@ -55,13 +55,13 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef typename Size<TTextInput>::Type Type;
     };
 
-	template <typename InType, typename Result = typename Value< typename Value<InType, 2>::Type>::Type>
-	struct _mapInverse : public std::unary_function<InType,Result> {
+    template <typename InType, typename Result = typename Value< typename Value<InType, 2>::Type>::Type>
+    struct _mapInverse : public std::unary_function<InType,Result> {
         inline Result operator()(const InType& x) const
         { return x.i2[0]; }
     };
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // lcp class
     template < typename TTextInput, typename TSuffixArrayInput >
     struct Pipe< Bundle2< TTextInput, TSuffixArrayInput >, Kasai >
@@ -70,82 +70,82 @@ namespace SEQAN_NAMESPACE_MAIN
 
         typedef Pipe< TSuffixArrayInput, Echoer<2,false> > TEchoer;
                                         typedef _mapInverse<TypeOf_(TEchoer)> map_inverse_t;
-		                                typedef typename Size<TTextInput>::Type	TSize;
-		typedef Pool< TypeOf_(TEchoer), MapperSpec< MapperConfigSize< map_inverse_t, TSize> > > TInverter;
-		                                typedef Pair<TSize> TCoreType;
-		typedef Pool< TCoreType, MapperSpec< MapperConfigSize< filterI1<TCoreType>, TSize > > > TLinearMapper;
+                                        typedef typename Size<TTextInput>::Type    TSize;
+        typedef Pool< TypeOf_(TEchoer), MapperSpec< MapperConfigSize< map_inverse_t, TSize> > > TInverter;
+                                        typedef Pair<TSize> TCoreType;
+        typedef Pool< TCoreType, MapperSpec< MapperConfigSize< filterI1<TCoreType>, TSize > > > TLinearMapper;
         typedef Pipe< TLinearMapper, Filter< filterI2<TCoreType> > > TFilter;
 
-		TTextInput				*textIn;
-        TSuffixArrayInput		*suffixArrayIn;
+        TTextInput                *textIn;
+        TSuffixArrayInput        *suffixArrayIn;
         TLinearMapper           mapper;
-		TFilter					in;
-        const LcpConfig			conf;
-        
+        TFilter                    in;
+        const LcpConfig            conf;
+
         Pipe():
             in(mapper) {}
 
         Pipe(const LcpConfig &_conf):
             in(mapper),
-			conf(_conf) {}
+            conf(_conf) {}
 
         Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn):
             textIn(&_bundleIn.in1),
-			suffixArrayIn(&_bundleIn.in2),
+            suffixArrayIn(&_bundleIn.in2),
             in(mapper)
-		{
-			process();
-		}
+        {
+            process();
+        }
 
         Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn, LcpConfig const &_conf):
             textIn(&_bundleIn.in1),
-			suffixArrayIn(&_bundleIn.in2),
+            suffixArrayIn(&_bundleIn.in2),
             in(mapper),
-			conf(_conf)
-		{
-			process();
-		}
-        
+            conf(_conf)
+        {
+            process();
+        }
+
         inline void process() {
             process(*textIn, *suffixArrayIn);
         }
 
-		template < typename TTextInput_, typename TSuffixArrayInput_ >
+        template < typename TTextInput_, typename TSuffixArrayInput_ >
         bool process(TTextInput_ &textIn, TSuffixArrayInput_ &suffixArrayIn) {
 
             // *** INSTANTIATION ***
-			
-			TEchoer						echoer(suffixArrayIn);
-			TInverter					inverter(echoer);
+
+            TEchoer                        echoer(suffixArrayIn);
+            TInverter                    inverter(echoer);
 
             #ifdef SEQAN_DEBUG_INDEX
                 std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
                 std::cerr << "Start Kasai [pipelining]" << std::endl;
                 std::cerr << "  invert suffix array" << std::endl;
             #endif
-			inverter << echoer;
-			SEQAN_PROMARK("Suffix-Array invertiert");
+            inverter << echoer;
+            SEQAN_PROMARK("Suffix-Array invertiert");
 
-			_lcpProcess(textIn, inverter, mapper);
+            _lcpProcess(textIn, inverter, mapper);
             return true;
         }
 
         inline typename Value<Pipe>::Type const operator*() const {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
         }
-	};
+    };
 
     // not sure which interface is more intuitive, we support both
     // you can call "skew << pipe" or "skew_t skew(pipe); skew.process()"
     // for the first we would need no _in member
-	template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_ >
+    template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_ >
     inline bool operator<<(Pipe< TInput, Kasai > &me, Bundle2< TTextInput_, TSuffixArrayInput_ > const &bundleIn) {
- 	    return me.process(bundleIn.in1, bundleIn.in2);
+         return me.process(bundleIn.in1, bundleIn.in2);
     }
 
 
@@ -160,14 +160,14 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef typename Value<TLimitsString>::Type Type;
     };
 
-	template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
-	struct _mapInverseMulti : public std::unary_function<InType,Result> {
-		TLimitsString const &limits;
-		_mapInverseMulti(TLimitsString const &_limits) : limits(_limits) {}
+    template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
+    struct _mapInverseMulti : public std::unary_function<InType,Result> {
+        TLimitsString const &limits;
+        _mapInverseMulti(TLimitsString const &_limits) : limits(_limits) {}
         inline Result operator()(const InType& x) const
         {
-			return posGlobalize(x.i2[0], limits);
-		}
+            return posGlobalize(x.i2[0], limits);
+        }
     };
 
     //////////////////////////////////////////////////////////////////////////////
@@ -179,90 +179,90 @@ namespace SEQAN_NAMESPACE_MAIN
 
         typedef Pipe< TSuffixArrayInput, Echoer<2,false> > TEchoer;
                                         typedef _mapInverseMulti<TypeOf_(TEchoer), TLimitsString, TSizeOf_(TEchoer)> map_inverse_t;
-		                                typedef typename Size<TTextInput>::Type	TSize;
-		typedef Pool< TypeOf_(TEchoer), MapperSpec< MapperConfigSize< map_inverse_t, TSize> > > TInverter;
-		                                typedef Pair<TSize> TCoreType;
-		typedef Pool< TCoreType, MapperSpec< MapperConfigSize< filterI1<TCoreType>, TSize > > > TLinearMapper;
+                                        typedef typename Size<TTextInput>::Type    TSize;
+        typedef Pool< TypeOf_(TEchoer), MapperSpec< MapperConfigSize< map_inverse_t, TSize> > > TInverter;
+                                        typedef Pair<TSize> TCoreType;
+        typedef Pool< TCoreType, MapperSpec< MapperConfigSize< filterI1<TCoreType>, TSize > > > TLinearMapper;
         typedef Pipe< TLinearMapper, Filter< filterI2<TCoreType> > > TFilter;
 
         TLinearMapper           mapper;
-		TFilter					in;
-		TLimitsString const		&limits;
-        const LcpConfig			conf;
-        
+        TFilter                    in;
+        TLimitsString const        &limits;
+        const LcpConfig            conf;
+
         Pipe(TLimitsString const &_limits):
             in(mapper),
-			limits(_limits)	{}
+            limits(_limits)    {}
 
         Pipe(TLimitsString const &_limits, LcpConfig const &_conf):
             in(mapper),
-			limits(_limits),
-			conf(_conf) {}
+            limits(_limits),
+            conf(_conf) {}
 
         Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn, TLimitsString const &_limits):
             in(mapper),
-			limits(_limits)
-		{
-			process(_bundleIn.in1, _bundleIn.in2);
-		}
+            limits(_limits)
+        {
+            process(_bundleIn.in1, _bundleIn.in2);
+        }
 
         Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn, TLimitsString const &_limits, LcpConfig const &_conf):
             in(mapper),
-			limits(_limits),
-			conf(_conf)
-		{
-			process(_bundleIn.in1, _bundleIn.in2);
-		}
-        
-		template < typename TTextInput_, typename TSuffixArrayInput_ >
+            limits(_limits),
+            conf(_conf)
+        {
+            process(_bundleIn.in1, _bundleIn.in2);
+        }
+
+        template < typename TTextInput_, typename TSuffixArrayInput_ >
         bool process(TTextInput_ &textIn, TSuffixArrayInput_ &suffixArrayIn) {
 
             // *** INSTANTIATION ***
-			
-			TEchoer						echoer(suffixArrayIn);
-			map_inverse_t				_mapInverse(limits);
-			TInverter					inverter(echoer, _mapInverse);
+
+            TEchoer                        echoer(suffixArrayIn);
+            map_inverse_t                _mapInverse(limits);
+            TInverter                    inverter(echoer, _mapInverse);
 
             #ifdef SEQAN_DEBUG_INDEX
                 std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
                 std::cerr << "Start Kasai [pipelining,stringset]" << std::endl;
                 std::cerr << "  invert suffix array" << std::endl;
             #endif
-			inverter << echoer;
-			SEQAN_PROMARK("Suffix-Array invertiert");
+            inverter << echoer;
+            SEQAN_PROMARK("Suffix-Array invertiert");
 
-			_lcpProcessMulti(textIn, limits, inverter, mapper);
+            _lcpProcessMulti(textIn, limits, inverter, mapper);
             return true;
         }
 
         inline typename Value<Pipe>::Type const operator*() const {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
         }
-	};
+    };
 
     // not sure which interface is more intuitive, we support both
     // you can call "skew << pipe" or "skew_t skew(pipe); skew.process()"
     // for the first we would need no _in member
-	template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_, typename TPair, typename TLimitsString >
+    template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_, typename TPair, typename TLimitsString >
     inline bool operator<<(Pipe< TInput, Multi<Kasai, TPair, TLimitsString> > &me, Bundle2< TTextInput_, TSuffixArrayInput_ > const &bundleIn) {
- 	    return me.process(bundleIn.in1, bundleIn.in2);
+         return me.process(bundleIn.in1, bundleIn.in2);
     }
 
-	
-	
-	//////////////////////////////////////////////////////////////////////////////
+
+
+    //////////////////////////////////////////////////////////////////////////////
     // internal Kasai algorithm
     //////////////////////////////////////////////////////////////////////////////
 
-	template < 
+    template <
         typename TLCP,
-		typename TText,
-		typename TSA >
+        typename TText,
+        typename TSA >
     struct LcpCreatorRandomAccess_<TLCP, TText, TSA, Kasai>
     {
         typedef typename AllowsFastRandomAccess<TLCP>::Type  TRandomLCP;
@@ -275,139 +275,139 @@ namespace SEQAN_NAMESPACE_MAIN
                typename TText,
                typename TSA >
     void _createLCPTableRandomAccess(
-		TLCPTable &LCP,
-		TText const &s,
-		TSA const &SA,
-		KasaiOriginal const)
-	{
-		typedef typename Value<TSA>::Type TSize;
-
-		#ifdef SEQAN_DEBUG_INDEX
+        TLCPTable &LCP,
+        TText const &s,
+        TSA const &SA,
+        KasaiOriginal const)
+    {
+        typedef typename Value<TSA>::Type TSize;
+
+        #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
             std::cerr << "Start Kasai [random access]" << std::endl;
-			if (sizeof(TSize) > 4)
-				std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
+            if (sizeof(TSize) > 4)
+                std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
         #endif
 
-		TSize n = length(s);
+        TSize n = length(s);
         if (n == 0) return;
 
         #ifdef SEQAN_DEBUG_INDEX
-            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;	// for lcpMax, lcpMean, |Sigma|
+            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;    // for lcpMax, lcpMean, |Sigma|
         #endif
 
         String<TSize, Alloc<> > ISA;
-		resize(ISA, n, Exact());
+        resize(ISA, n, Exact());
+
+        for(TSize i = 0; i < n; ++i)
+            ISA[SA[i]] = i;
 
-		for(TSize i = 0; i < n; ++i)
-			ISA[SA[i]] = i;
-		
-		SEQAN_PROMARK("Suffix-Array invertiert");
+        SEQAN_PROMARK("Suffix-Array invertiert");
 
-		typename Iterator<TText const>::Type Ibegin = begin(s);
+        typename Iterator<TText const>::Type Ibegin = begin(s);
         typename Iterator<TText const>::Type I = Ibegin, J;
         for(TSize i = 0, h = 0, j, isa; i < n; ++i) {
-			if ((isa = ISA[i])) {
-				J = Ibegin + h + (j = SA[isa - 1]);
+            if ((isa = ISA[i])) {
+                J = Ibegin + h + (j = SA[isa - 1]);
                 for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ;
-				LCP[isa - 1] = h;
+                LCP[isa - 1] = h;
                 #ifdef SEQAN_DEBUG_INDEX
                     if ((lcpNumer += h) > n) {
                         lcpNumer -= n;
                         ++lcpAvrg;
                     }
                     if (lcpMax < h) lcpMax = h;
-					if (!h) ++sigma;
+                    if (!h) ++sigma;
                 #endif
-			}
-			if (h) --h;
+            }
+            if (h) --h;
             else ++I;
         }
-		LCP[n - 1] = 0;
+        LCP[n - 1] = 0;
         #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "  n: " << n;
             std::cerr << "  lcpMax: " << lcpMax;
             std::cerr << "  lcpAvrg: " << (TSize)(lcpAvrg + (lcpNumer + n/2) / n);
             std::cerr << "  sigma: " << sigma << std::endl;
         #endif
-	}
+    }
 
-	// HINT:
-	// In contrast to the upper functions 
-	// createLCPTableInPlace expects the lcp table to be of size n
+    // HINT:
+    // In contrast to the upper functions
+    // createLCPTableInPlace expects the lcp table to be of size n
     template < typename TLCPTable,
                typename TText,
                typename TSA >
     void _createLCPTableRandomAccess(
-		TLCPTable &LCP,
-		TText const &s,
-		TSA const &SA,
-		Kasai const)
-	{
-		typedef typename Value<TSA>::Type TSize;
-
-		#ifdef SEQAN_DEBUG_INDEX
+        TLCPTable &LCP,
+        TText const &s,
+        TSA const &SA,
+        Kasai const)
+    {
+        typedef typename Value<TSA>::Type TSize;
+
+        #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
             std::cerr << "Start Kasai [random access,inplace]" << std::endl;
-			if (sizeof(TSize) > 4)
-				std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
+            if (sizeof(TSize) > 4)
+                std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
         #endif
 
-		TSize n = length(s);
+        TSize n = length(s);
         if (n == 0) return;
 
         #ifdef SEQAN_DEBUG_INDEX
-            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;	// for lcpMax, lcpMean, |Sigma|
+            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;    // for lcpMax, lcpMean, |Sigma|
         #endif
 
-		TSize mark = ~(~0u>>1);
-		TSize mask =   ~0u>>1;
+        TSize mark = ~(~0u>>1);
+        TSize mask =   ~0u>>1;
+
+        for(TSize i = 0; i < n; ++i)
+            LCP[SA[i]] = i;
 
-		for(TSize i = 0; i < n; ++i)
-			LCP[SA[i]] = i;
-		
-		SEQAN_PROMARK("Suffix-Array invertiert");
+        SEQAN_PROMARK("Suffix-Array invertiert");
         #ifdef SEQAN_DEBUG_INDEX
-			std::cerr << "Suffix-Array invertiert" << std::endl;
-		#endif
+            std::cerr << "Suffix-Array invertiert" << std::endl;
+        #endif
 
-		typename Iterator<TText const>::Type Ibegin = begin(s);
+        typename Iterator<TText const>::Type Ibegin = begin(s);
         typename Iterator<TText const>::Type I = Ibegin, J;
         for(TSize i = 0, h = 0, j, isa; i < n; ++i) {
-			if ((isa = LCP[i] + 1) < n) {
-				J = Ibegin + h + (j = SA[isa]);
+            if ((isa = LCP[i] + 1) < n) {
+                J = Ibegin + h + (j = SA[isa]);
                 for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ;
-				LCP[i] = h | mark;
+                LCP[i] = h | mark;
                 #ifdef SEQAN_DEBUG_INDEX
                     if ((lcpNumer += h) > n) {
                         lcpNumer -= n;
                         ++lcpAvrg;
                     }
                     if (lcpMax < h) lcpMax = h;
-					if (!h) ++sigma;
+                    if (!h) ++sigma;
                 #endif
-			}
-			if (h) --h;
+            }
+            if (h) --h;
             else ++I;
         }
-		LCP[SA[n - 1]] = mark;
-		SEQAN_PROMARK("permutierte LCP-Tabelle erzeugt");
+        LCP[SA[n - 1]] = mark;
+        SEQAN_PROMARK("permutierte LCP-Tabelle erzeugt");
         #ifdef SEQAN_DEBUG_INDEX
-			std::cerr << "permutierte LCP-Tabelle erzeugt" << std::endl;
-		#endif
+            std::cerr << "permutierte LCP-Tabelle erzeugt" << std::endl;
+        #endif
         for(TSize i = 0, j, tmp; i < n; ++i)
-			if (LCP[i] & mark) {
-				j = i;
-				tmp = LCP[j];
-				while (SA[j] != i) {
-					LCP[j] = LCP[SA[j]] & mask;
-					j = SA[j];
-				}
-				LCP[j] = tmp & mask;
-			}
+            if (LCP[i] & mark) {
+                j = i;
+                tmp = LCP[j];
+                while (SA[j] != i) {
+                    LCP[j] = LCP[SA[j]] & mask;
+                    j = SA[j];
+                }
+                LCP[j] = tmp & mask;
+            }
         #ifdef SEQAN_DEBUG_INDEX
-			std::cerr << "LCP-Tabelle erzeugt" << std::endl;
-		#endif
+            std::cerr << "LCP-Tabelle erzeugt" << std::endl;
+        #endif
 
         #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "  n: " << n;
@@ -415,109 +415,109 @@ namespace SEQAN_NAMESPACE_MAIN
             std::cerr << "  lcpAvrg: " << (TSize)(lcpAvrg + (lcpNumer + n/2) / n);
             std::cerr << "  sigma: " << sigma << std::endl;
         #endif
-	}
+    }
 
 
-	// Kasai in-place for multiple sequences
+    // Kasai in-place for multiple sequences
     template < typename TLCPTable,
-			   typename TString,
-			   typename TSpec,
+               typename TString,
+               typename TSpec,
                typename TSA >
     void _createLCPTableRandomAccess(
-		TLCPTable &LCP,
-		StringSet<TString, TSpec> const &sset,
-		TSA const &SA,
-		Kasai const)
-	{
-        typedef StringSet<TString, TSpec>							TStringSet;
-		typedef typename Concatenator<TStringSet const>::Type		TText;
-		typedef typename StringSetLimits<TStringSet const>::Type	TLimitsString;
-//		typedef typename Value<TSA>::Type							TPair;
-		typedef Pair<
-			typename Size<TStringSet>::Type,
-			typename Size<TString>::Type>							TPair;
-		typedef PairDecrementer_<TPair, TLimitsString>				TDecrementer;
-		typedef typename Value<TLCPTable>::Type						TSize;
-
-		#ifdef SEQAN_DEBUG_INDEX
+        TLCPTable &LCP,
+        StringSet<TString, TSpec> const &sset,
+        TSA const &SA,
+        Kasai const)
+    {
+        typedef StringSet<TString, TSpec>                            TStringSet;
+        typedef typename Concatenator<TStringSet const>::Type        TText;
+        typedef typename StringSetLimits<TStringSet const>::Type    TLimitsString;
+//        typedef typename Value<TSA>::Type                            TPair;
+        typedef Pair<
+            typename Size<TStringSet>::Type,
+            typename Size<TString>::Type>                            TPair;
+        typedef PairDecrementer_<TPair, TLimitsString>                TDecrementer;
+        typedef typename Value<TLCPTable>::Type                        TSize;
+
+        #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
             std::cerr << "Start Kasai [random access,inplace,stringset]" << std::endl;
-			if (sizeof(TSize) > 4)
-				std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
+            if (sizeof(TSize) > 4)
+                std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
         #endif
 
-		TText &s = concat(sset);
-		TSize n = length(s);
-		
+        TText &s = concat(sset);
+        TSize n = length(s);
+
         if (n == 0) return;
 
         #ifdef SEQAN_DEBUG_INDEX
-            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;	// for lcpMax, lcpMean, |Sigma|
+            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;    // for lcpMax, lcpMean, |Sigma|
         #endif
 
-		TSize mark = ~(~0u>>1);
-		TSize mask =   ~0u>>1;
-
-		TLimitsString const &limits = stringSetLimits(sset);
-		{
-			typename Iterator<TSA const>::Type itSA = begin(SA);
-			for(TSize i = 0; i < n; ++i, ++itSA)
-				LCP[posGlobalize(*itSA, limits)] = i;
-		}
-		
-		SEQAN_PROMARK("Suffix-Array invertiert");
+        TSize mark = ~(~(TSize)0ul >> 1);
+        TSize mask =   ~(TSize)0ul >> 1;
+
+        TLimitsString const &limits = stringSetLimits(sset);
+        {
+            typename Iterator<TSA const>::Type itSA = begin(SA);
+            for(TSize i = 0; i < n; ++i, ++itSA)
+                LCP[posGlobalize(*itSA, limits)] = i;
+        }
+
+        SEQAN_PROMARK("Suffix-Array invertiert");
         #ifdef SEQAN_DEBUG_INDEX
-			std::cerr << "Suffix-Array invertiert" << std::endl;
-		#endif
+            std::cerr << "Suffix-Array invertiert" << std::endl;
+        #endif
 
-		typename Iterator<TText const>::Type Ibegin = begin(s);
+        typename Iterator<TText const>::Type Ibegin = begin(s);
         typename Iterator<TText const>::Type I = Ibegin, J;
 
-		TDecrementer dec(limits);
+        TDecrementer dec(limits);
 
-		for(TSize i = 0, h = 0, j, isa; i < n; ++i, --dec) {
-			if ((isa = LCP[i] + 1) < n) {
-				j = posGlobalize(SA[isa], limits);
-				J = Ibegin + h + j;
+        for(TSize i = 0, h = 0, j, isa; i < n; ++i, --dec) {
+            if ((isa = LCP[i] + 1) < n) {
+                j = posGlobalize(SA[isa], limits);
+                J = Ibegin + h + j;
 
                 for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ;
-				LCP[i] = h | mark;
+                LCP[i] = h | mark;
                 #ifdef SEQAN_DEBUG_INDEX
                     if ((lcpNumer += h) > n) {
                         lcpNumer -= n;
                         ++lcpAvrg;
                     }
                     if (lcpMax < h) lcpMax = h;
-					if (!h) ++sigma;
+                    if (!h) ++sigma;
                 #endif
-			}
-			if (h) 
-				--h;
-			else 
-				++I;
+            }
+            if (h)
+                --h;
+            else
+                ++I;
         }
 
-		LCP[posGlobalize(SA[n - 1], limits)] = mark;
+        LCP[posGlobalize(SA[n - 1], limits)] = mark;
 
-		SEQAN_PROMARK("permutierte LCP-Tabelle erzeugt");
+        SEQAN_PROMARK("permutierte LCP-Tabelle erzeugt");
         #ifdef SEQAN_DEBUG_INDEX
-			std::cerr << "permutierte LCP-Tabelle erzeugt" << std::endl;
-		#endif
+            std::cerr << "permutierte LCP-Tabelle erzeugt" << std::endl;
+        #endif
         for(TSize sa_j, i = 0, j, tmp; i < n; ++i)
-			if (LCP[i] & mark) {
-				j = i;
-				tmp = LCP[j];
-				sa_j = posGlobalize(SA[j], limits);
-				while (sa_j != i) {
-					LCP[j] = LCP[sa_j] & mask;
-					j = sa_j;
-					sa_j = posGlobalize(SA[j], limits);
-				}
-				LCP[j] = tmp & mask;
-			}
+            if (LCP[i] & mark) {
+                j = i;
+                tmp = LCP[j];
+                sa_j = posGlobalize(SA[j], limits);
+                while (sa_j != i) {
+                    LCP[j] = LCP[sa_j] & mask;
+                    j = sa_j;
+                    sa_j = posGlobalize(SA[j], limits);
+                }
+                LCP[j] = tmp & mask;
+            }
         #ifdef SEQAN_DEBUG_INDEX
-			std::cerr << "LCP-Tabelle erzeugt" << std::endl;
-		#endif
+            std::cerr << "LCP-Tabelle erzeugt" << std::endl;
+        #endif
 
         #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "  n: " << n;
@@ -525,7 +525,7 @@ namespace SEQAN_NAMESPACE_MAIN
             std::cerr << "  lcpAvrg: " << (TSize)(lcpAvrg + (lcpNumer + n/2) / n);
             std::cerr << "  sigma: " << sigma << std::endl;
         #endif
-	}
+    }
 
 
 //}
diff --git a/seqan/index/index_lcp_tree.h b/seqan/index/index_lcp_tree.h
index 0d7af7c..cb8bb71 100644
--- a/seqan/index/index_lcp_tree.h
+++ b/seqan/index/index_lcp_tree.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,116 +37,116 @@
 
 namespace SEQAN_NAMESPACE_MAIN
 {
-	
-	template <
-		class LCPFwdIt,		// lcp table input iterator
-		class FlatOutIt >	// flat tree output iterator
-	inline FlatOutIt createLcpBinTree(
-		LCPFwdIt First_, LCPFwdIt _Last,
-		FlatOutIt Dest_)
-	{
+
+    template <
+        class LCPFwdIt,        // lcp table input iterator
+        class FlatOutIt >    // flat tree output iterator
+    inline FlatOutIt createLcpBinTree(
+        LCPFwdIt First_, LCPFwdIt _Last,
+        FlatOutIt Dest_)
+    {
         typedef typename Value<LCPFwdIt>::Type  TValue;
         typedef typename Size<LCPFwdIt>::Type   TSize;
 
         TSize size = difference(First_, _Last);
         if (size <= 1) return Dest_;
-		--size;
+        --size;
 
         // calculate the depth of the lcp tree
-		unsigned treeLevels = 1;
-		TSize _xSize = 1;
-		for(; size > _xSize; _xSize *= 2, ++treeLevels) ;
-	
-		// get output iterators for every level in the flat tree
-		FlatOutIt *level = new FlatOutIt[treeLevels];
-		for(unsigned i = treeLevels - 1; _xSize; --i, _xSize /= 2) {
-			level[i] = Dest_;
-			goFurther(Dest_, (size + _xSize - 1) / _xSize);
-		}
-
-		// fields to keep track of minimum elements and state
-		TValue *minVal = new TValue[treeLevels];
-		bool *half = new bool[treeLevels];
-		for(unsigned i = 0; i < treeLevels; ++i)
-			half[i] = false;
-
-		// it works like a binary counter of half[n]...half[1]half[0]
-		for(TSize j = 0; j < size; ++j, ++First_) {
-			*(level[0]) = minVal[0] = *First_;
-			++(level[0]);
-			for(unsigned i = 1; i < treeLevels; ++i) {
-				if (half[i]) {
-					if (minVal[i-1] < minVal[i]) minVal[i] = minVal[i-1];
-					*(level[i]) = minVal[i];	// min[i] is the minimum of last 2 values in min[i-1]
-					++(level[i]);
-					half[i] = false;
-				} else {
-					minVal[i] = minVal[i-1];
-					half[i] = true;
-					break;
-				}
-			}
-		}
-
-		// complete half filled nodes
-		bool carry = false;
-		for(unsigned i = 1; i < treeLevels; ++i)
-			if (half[i] || carry) {
-				if (half[i]) {
-					if (minVal[i-1] < minVal[i]) minVal[i] = minVal[i-1];
-				} else
-					minVal[i] = minVal[i-1];
-				*(level[i]) = minVal[i];
-				++(level[i]);
-				carry = true;
-			}
-
-		// trailing zero
-		*Dest_ = 0;
-		++Dest_;
-
-		delete[] half;
-		delete[] minVal;
-		delete[] level;
-
-		return Dest_;
+        unsigned treeLevels = 1;
+        TSize _xSize = 1;
+        for(; size > _xSize; _xSize *= 2, ++treeLevels) ;
+
+        // get output iterators for every level in the flat tree
+        FlatOutIt *level = new FlatOutIt[treeLevels];
+        for(unsigned i = treeLevels - 1; _xSize; --i, _xSize /= 2) {
+            level[i] = Dest_;
+            goFurther(Dest_, (size + _xSize - 1) / _xSize);
+        }
+
+        // fields to keep track of minimum elements and state
+        TValue *minVal = new TValue[treeLevels];
+        bool *half = new bool[treeLevels];
+        for(unsigned i = 0; i < treeLevels; ++i)
+            half[i] = false;
+
+        // it works like a binary counter of half[n]...half[1]half[0]
+        for(TSize j = 0; j < size; ++j, ++First_) {
+            *(level[0]) = minVal[0] = *First_;
+            ++(level[0]);
+            for(unsigned i = 1; i < treeLevels; ++i) {
+                if (half[i]) {
+                    if (minVal[i-1] < minVal[i]) minVal[i] = minVal[i-1];
+                    *(level[i]) = minVal[i];    // min[i] is the minimum of last 2 values in min[i-1]
+                    ++(level[i]);
+                    half[i] = false;
+                } else {
+                    minVal[i] = minVal[i-1];
+                    half[i] = true;
+                    break;
+                }
+            }
+        }
+
+        // complete half filled nodes
+        bool carry = false;
+        for(unsigned i = 1; i < treeLevels; ++i)
+            if (half[i] || carry) {
+                if (half[i]) {
+                    if (minVal[i-1] < minVal[i]) minVal[i] = minVal[i-1];
+                } else
+                    minVal[i] = minVal[i-1];
+                *(level[i]) = minVal[i];
+                ++(level[i]);
+                carry = true;
+            }
+
+        // trailing zero
+        *Dest_ = 0;
+        ++Dest_;
+
+        delete[] half;
+        delete[] minVal;
+        delete[] level;
+
+        return Dest_;
+    }
+
+
+
+    template < typename TSize >
+    inline TSize sizeofLcpe(TSize n)
+    {
+        if (n < 2) return n;    // 0 -> 0, 1 -> 1, 2 -> 2, 3 -> 4
+        --n;
+        TSize size = 2;
+        for(TSize _xSize = 1; _xSize < n; _xSize *= 2)
+            size += (n + _xSize - 1) / _xSize;
+        return size;
     }
 
+    template < typename TSize >
+    inline TSize sizeofLcph(TSize n)
+    {
+        return sizeofLcpe(n);
+    }
 
+    template <
+        class LCPFwdIt,        // lcp table input iterator
+        typename TSize >
+    inline void sizeofLcpe(LCPFwdIt First_, LCPFwdIt _Last, TSize &Size_)
+    {
+        Size_ = sizeofLcpe(difference(First_, _Last));
+    }
 
-	template < typename TSize >
-	inline TSize sizeofLcpe(TSize n)
-	{
-		if (n < 2) return n;	// 0 -> 0, 1 -> 1, 2 -> 2, 3 -> 4
-		--n;
-		TSize size = 2;
-		for(TSize _xSize = 1; _xSize < n; _xSize *= 2)
-			size += (n + _xSize - 1) / _xSize;
-		return size;
-	}
-
-	template < typename TSize >
-	inline TSize sizeofLcph(TSize n)
-	{
-		return sizeofLcpe(n);
-	}
-
-	template <
-		class LCPFwdIt,		// lcp table input iterator
-		typename TSize >
-	inline void sizeofLcpe(LCPFwdIt First_, LCPFwdIt _Last, TSize &Size_)
-	{
-		Size_ = sizeofLcpe(difference(First_, _Last));
-	}
-
-	template <
-		class LCPFwdIt,		// lcp table input iterator
-		typename TSize >
-	inline void sizeofLcph(LCPFwdIt First_, LCPFwdIt _Last, TSize &Size_)
-	{
-		sizeofLcpe(First_, _Last, Size_);
-		return;
-	}
+    template <
+        class LCPFwdIt,        // lcp table input iterator
+        typename TSize >
+    inline void sizeofLcph(LCPFwdIt First_, LCPFwdIt _Last, TSize &Size_)
+    {
+        sizeofLcpe(First_, _Last, Size_);
+        return;
+    }
 
 
     template < typename TLCPE, typename TLCP >
@@ -155,13 +155,13 @@ namespace SEQAN_NAMESPACE_MAIN
     }
 
 
-	template < typename TSize >
+    template < typename TSize >
     inline unsigned _treeLevels(TSize lcpSize)
-	{
-		unsigned treeLevels = 1;
-		--lcpSize;
-		TSize _xSize = 1;
-		for (; lcpSize > _xSize; _xSize *= 2, ++treeLevels)
+    {
+        unsigned treeLevels = 1;
+        --lcpSize;
+        TSize _xSize = 1;
+        for (; lcpSize > _xSize; _xSize *= 2, ++treeLevels)
             continue;  // Get smallest 2^k that is <= lcpSize.
         return treeLevels;
     }
diff --git a/seqan/index/index_pizzachili.h b/seqan/index/index_pizzachili.h
index 74da187..6b87a53 100644
--- a/seqan/index/index_pizzachili.h
+++ b/seqan/index/index_pizzachili.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,40 +40,24 @@
 
 namespace SEQAN_NAMESPACE_MAIN {
 
-/**
-.Tag.Pizza & Chili Index Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Spec.Pizza & Chili Index@ index.
-..cat:Index
-..tag.PizzaChiliText:The original text the index is based on.
-..tag.PizzaChiliCompressed:The compressed suffix array.
-...remarks:Pizza & Chili indices are compressed indices. Hence, this fibre is used for searching in the index.
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..see:Spec.Pizza & Chili Index
-..include:seqan/index.h
-*/
 /*!
  * @defgroup PizzaChiliIndexFibres Pizza &amp; Chili Index Fibres
- * 
+ *
  * @brief Tag to select a specific fibre (e.g. table, object, ...) of a @link
  *        PizzaChiliIndex @endlink index.
- * 
- * @see Index#Fibre
+ *
+ * Pizza &amp; Chili indices are compressed indices. Hence, this fibre is used for
+ * searching in the index.
+ *
+ * @see Fibre
  * @see Index#getFibre
  * @see PizzaChiliIndex
- * 
+ *
  * @tag PizzaChiliIndexFibres#PizzaChiliText
- * 
  * @brief The original text the index is based on.
- * 
+ *
  * @tag PizzaChiliIndexFibres#PizzaChiliCompressed
- * 
  * @brief The compressed suffix array.
- * 
- * @section Remarks
- * 
- * Pizza &amp; Chili indices are compressed indices. Hence, this fibre is used for
- * searching in the index.
  */
 
 struct FibrePizzaChiliCompressed_;
@@ -84,39 +68,22 @@ typedef Tag<FibrePizzaChiliCompressed_> const FibrePizzaChiliCompressed;
 typedef FibrePizzaChiliText PizzaChiliText;
 typedef FibrePizzaChiliCompressed PizzaChiliCompressed;
 
-/**
-.Spec.Pizza & Chili Index:
-..summary:An adapter for the Pizza & Chili index API.
-..remarks:
-..cat:Index
-..general:Class.Index
-..signature:Index<TText, PizzaChili<TSpec> >
-..param.TText:The text type.
-...type:Class.String
-..param.TSpec:Tag specifying the Pizza & Chili index library to use.
-...type:Tag.Pizza & Chili Index Tags
-..see:Spec.Pizza & Chili String
-..see:Tag.Pizza & Chili Index Fibres
-..see:Tag.Index Find Algorithm
-..include:seqan/index.h
-*/
 /*!
- * @class PizzaChiliIndex Pizza &amp; Chili Index
- * 
+ * @class PizzaChiliIndex Pizza & Chili Index
+ *
  * @extends Index
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief An adapter for the Pizza &amp; Chili index API.
- * 
- * @signature Index<TText, PizzaChili<TSpec> >
- * 
+ *
+ * @signature template <typename TText, typename TSpec>
+ *            class Index<TText, PizzaChili<TSpec> >;
+ *
  * @tparam TSpec Tag specifying the Pizza &amp; Chili index library to use. Types:
  *               @link PizzaChiliIndexTags @endlink
  * @tparam TText The text type. Types: @link String @endlink
- * 
- * @section Remarks
- * 
+ *
  * @see PizzaChiliString
  * @see PizzaChiliIndexFibres
  * @see IndexFindAlgorithm
diff --git a/seqan/index/index_pizzachili_find.h b/seqan/index/index_pizzachili_find.h
index 0ea3b08..ab3c873 100644
--- a/seqan/index/index_pizzachili_find.h
+++ b/seqan/index/index_pizzachili_find.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,15 +39,6 @@ namespace SEQAN_NAMESPACE_MAIN {
 
 struct PizzaChiliFinder_;
 
-/**
-.Tag.Index Find Algorithm
-..cat:Searching
-..tag.PizzaChiliFinder:Finds an occurrence in a @Spec.Pizza & Chili Index@ index.
-...remarks:The actual algorithm used for searching depends on the @Tag.Pizza & Chili Index Tags@ used.
-..see:Spec.Pizza & Chili Index
-..include:seqan/index.h
-*/
-
 typedef Tag<PizzaChiliFinder_> const PizzaChiliFinder;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -96,7 +87,7 @@ class Finder<Index<TText, PizzaChili<TSpec> >, PizzaChiliFinder>
     ~Finder() {
 SEQAN_CHECKPOINT
         if (range.i1 != 0)
-            ::std::free(range.i1);
+            std::free(range.i1);
     }
 };
 
@@ -141,7 +132,7 @@ SEQAN_CHECKPOINT
     typedef typename PizzaChiliCodeProvider<TSpec>::Type TCodeProvider;
 
     if (finder.range.i1 != 0)
-        ::std::free(finder.range.i1);
+        std::free(finder.range.i1);
 
     TIndex& index = haystack(finder);
     indexRequire(index, PizzaChiliCompressed());
diff --git a/seqan/index/index_pizzachili_string.h b/seqan/index/index_pizzachili_string.h
index a3409d7..b8a39d1 100644
--- a/seqan/index/index_pizzachili_string.h
+++ b/seqan/index/index_pizzachili_string.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,46 +41,29 @@
 
 namespace SEQAN_NAMESPACE_MAIN {
 
-/**
-.Spec.Pizza & Chili String:
-..summary:String used by the Pizza & Chili indices.
-..remarks:The string is lazy in the sense that it holds a reference to the
-compressed index structure it is associated with. Only when the text is
-actually read, the index is queried for the text. If only a substring is
-needed, this string tries to query only a substring.
-..cat:Strings
-..general:Class.String
-..signature:String<TValue, PizzaChili<TSpec> >
-..param.TValue:The value type, that is the type of them items/characters stored in the string.
-...remarks:This type must be a simple type and it must hold that $sizeof(TValue) == 1$.
-..param.TSpec:Tag specifying the Pizza & Chili index library to use.
-...type:Tag.Pizza & Chili Index Tags
-..include:seqan/index.h
-*/
 /*!
  * @class PizzaChiliString Pizza &amp; Chili String
- * 
+ *
  * @extends String
- * 
- * @headerfile seqan/index.h
- * 
+ *
+ * @headerfile <seqan/index.h>
+ *
  * @brief String used by the Pizza &amp; Chili indices.
- * 
- * @signature String<TValue, PizzaChili<TSpec> >
- * 
+ *
+ * @signature template <typename TValue, typename TSpec>
+ *            class String<TValue, PizzaChili<TSpec> >;
+ *
  * @tparam TSpec Tag specifying the Pizza &amp; Chili index library to use. Types:
  *               PizzaChiliIndexTags
  * @tparam TValue The value type, that is the type of them items/characters
  *                stored in the string.This type must be a simple type and it
  *                must hold that <tt>sizeof(TValue) == 1</tt>.
- * 
- * @section Remarks
- * 
+ *
  * The string is lazy in the sense that it holds a reference to the compressed
  * index structure it is associated with. Only when the text is actually read,
  * the index is queried for the text. If only a substring is needed, this string
  * tries to query only a substring.
- * 
+ *
  * @see PizzaChiliIndex
  * @see PizzaChiliIndexTags
  */
@@ -279,7 +262,7 @@ _pizzaChiliAllocate(
 ) {
 SEQAN_ CHECKPOINT
     TValue* old = me.data_begin;
-    me.data_begin = static_cast<TValue*>(::std::malloc(new_capacity));
+    me.data_begin = static_cast<TValue*>(std::malloc(new_capacity));
     return old == me.data_begin ? 0 : old;
 }
 */
@@ -299,8 +282,8 @@ SEQAN_CHECKPOINT
     //    return _pizzaChiliAllocate(me, new_capacity);
 
     me.data_begin =
-        static_cast<TValue*>(::std::realloc(me.data_begin, new_capacity));
-    // ::std::realloc does the cleanup itself.
+        static_cast<TValue*>(std::realloc(me.data_begin, new_capacity));
+    // std::realloc does the cleanup itself.
     return 0;
 }
 
@@ -309,7 +292,7 @@ inline void
 _pizzaChiliDeallocate(TValue* begin) {
 SEQAN_CHECKPOINT
     if (begin != 0)
-        ::std::free(begin);
+        std::free(begin);
 }
 
 template <typename TValue, typename TSpec>
@@ -458,7 +441,7 @@ SEQAN_CHECKPOINT
         }
         if (me.index_handle == 0) {
 SEQAN_CHECKPOINT
-            me.data_begin = static_cast<TValue*>(::std::malloc(1));
+            me.data_begin = static_cast<TValue*>(std::malloc(1));
             me.data_begin[0] = '\0';
             me.data_end = me.data_begin;
         }
@@ -490,7 +473,7 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TSpec, typename TTag>
-inline typename Iterator<String<TValue, PizzaChili<TSpec> >, Tag<TSpec> const>::Type 
+inline typename Iterator<String<TValue, PizzaChili<TSpec> >, Tag<TSpec> const>::Type
 begin(
     String<TValue, PizzaChili<TSpec> >& me,
     Tag<TTag> const
@@ -501,7 +484,7 @@ SEQAN_CHECKPOINT
 }
 
 template <typename TValue, typename TSpec, typename TTag>
-inline typename Iterator<String<TValue, PizzaChili<TSpec> > const, Tag<TSpec> const>::Type 
+inline typename Iterator<String<TValue, PizzaChili<TSpec> > const, Tag<TSpec> const>::Type
 begin(
     String<TValue, PizzaChili<TSpec> > const& me,
     Tag<TTag> const
@@ -512,7 +495,7 @@ SEQAN_CHECKPOINT
 }
 
 template <typename TValue, typename TSpec, typename TTag>
-inline typename Iterator<String<TValue, PizzaChili<TSpec> >, Tag<TSpec> const>::Type 
+inline typename Iterator<String<TValue, PizzaChili<TSpec> >, Tag<TSpec> const>::Type
 end(
     String<TValue, PizzaChili<TSpec> >& me,
     Tag<TTag> const
@@ -523,7 +506,7 @@ SEQAN_CHECKPOINT
 }
 
 template <typename TValue, typename TSpec, typename TTag>
-inline typename Iterator<String<TValue, PizzaChili<TSpec> > const, Tag<TSpec> const>::Type 
+inline typename Iterator<String<TValue, PizzaChili<TSpec> > const, Tag<TSpec> const>::Type
 end(
     String<TValue, PizzaChili<TSpec> > const& me,
     Tag<TTag> const
diff --git a/seqan/index/index_qgram.h b/seqan/index/index_qgram.h
index c89b90f..2d38c4a 100644
--- a/seqan/index/index_qgram.h
+++ b/seqan/index/index_qgram.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,284 +42,188 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 // q-gram index fibres
 
-/**
-.Tag.QGram Index Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of a @Spec.IndexQGram.q-gram Index@.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of a @Spec.IndexQGram.q-gram Index@.
-..cat:Index
-
-..tag.QGramText:The original text the index should be based on.
-
-..tag.QGram_RawText:The concatenation of all text sequences.
-...remarks:$QGramText$ and $QGram_RawText$ fibres are equal by default.
-They differ if the index text is a set of strings. Then, raw text is the concatenation of all strings in this set.
-
-..tag.QGramSA:The suffix array.
-...remarks:Contains all occurrences of q-grams, s.t. the occurrences of a single q-gram are stored in a contiguous block (q-gram bucket).
-q-grams exceeding the end of the text are ignored.
-The beginning of each bucket can be determined by the q-gram directory ($QGramDir$, see below).
-...remarks:It corresponds to a suffix array which is sorted by the first q-gram.
-...remarks:@Metafunction.Fibre@ returns a @Class.String@ over the alphabet of the @Metafunction.SAValue@ of $TIndex$.
-
-..tag.QGramDir:The directory/hash table.
-...remarks:The directory contains for every possible q-gram hash value the start index of the q-gram bucket.
-A q-gram bucket is a contiguous interval in the suffix array ($QGramSA$, see above).
-Each suffix in this interval begins with the same q-gram.
-The end index is the start index of the next bucket.
-...remarks:@Metafunction.Fibre@ returns a @Class.String@ over the alphabet of a size type.
-
-..tag.QGramBucketMap:Maps q-gram hashes to buckets.
-This fibre is used by the @Spec.OpenAddressing@ index and stores all parameters of the open addressing hash function and hash value occupancy in the QGramDir fibre.
-In contrast to @Spec.OpenAddressing@, @Spec.IndexQGram@ uses a trivial 1-to-1 mapping from q-gram hash values to buckets.
-For that index the fibre is of type @Tag.Nothing@.
-
-..tag.QGramCounts:The counts array.
-...remarks:Contains the numbers of occurrences per sequence of each q-gram, s.t. the numbers of the same q-gram are stored in a contiguous block (q-gram count bucket).
-A bucket contains entries (seqNo,count) of sequences with at least one q-gram occurrence. q-grams exceeding the end of the text are ignored.
-The beginning of each count bucket can be determined by the q-gram counts directory ($QGramCountsDir$, see below).
-...remarks:@Metafunction.Fibre@ returns a @Class.String@ over the alphabet of the @Metafunction.SAValue@ of $TIndex$.
-
-..tag.QGramCountsDir:The counts directory.
-...remarks:The counts directory contains for every possible q-gram hash value the start index of the q-gram count bucket.
-A q-gram count bucket is a contiguous interval in the counts array ($QGramCounts$, see above).
-The end index is the start index of the next bucket.
-...remarks:@Metafunction.Fibre@ returns a @Class.String@ over the alphabet of a size type.
-
-..tag.QGramShape:The shape the index is based on.
-...remarks:The q-gram index needs an underlying @Class.Shape@. This shape can be gapped or ungapped.
-The number of '1's (relevant positions) in the shape determines $q$ and the size of the directory table.
-...remarks:Dynamic shapes (@Spec.SimpleShape@, @Spec.GenericShape@, ...) must be initialized before the index can be used.
-
-..tag.QGramSADir:The union of suffix array and directory.
-...remarks:In most applications a q-gram index consisting of both of these table is required.
-To efficiently create them at once use this tag for @Function.indexRequire@ or @Function.indexCreate@.
- 
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..see:Spec.IndexQGram
-..include:seqan/index.h
-*/
 /*!
  * @defgroup QGramIndexFibres Index QGram Fibres
- * 
  * @brief Tag to select a specific fibre (e.g. table, object, ...) of a @link
  *        IndexQGram @endlink.
- * 
- * @see Index#Fibre
+ *
+ * @see Fibre
  * @see Index#getFibre
  * @see IndexQGram
- * 
+ *
  * @tag QGramIndexFibres#QGramDir
- * 
  * @brief The directory/hash table.
- * 
- * @section Remarks
- * 
+ *
  * The directory contains for every possible q-gram hash value the start index
  * of the q-gram bucket. A q-gram bucket is a contiguous interval in the suffix
  * array (<tt>QGramSA</tt>, see above). Each suffix in this interval begins with
  * the same q-gram. The end index is the start index of the next bucket.
- * 
- * @link Index#Fibre @endlink returns a @link String @endlink over the alphabet of a
+ *
+ * @link Fibre @endlink returns a @link String @endlink over the alphabet of a
  * size type.
- * 
+ *
  * @tag QGramIndexFibres#QGramBucketMap
- * 
  * @brief Maps q-gram hashes to buckets. This fibre is used by the @link
- *        OpenAddressing @endlink index and stores all parameters of the open
+ *        OpenAddressingQGramIndex @endlink index and stores all parameters of the open
  *        addressing hash function and hash value occupancy in the QGramDir
- *        fibre. In contrast to @link OpenAddressing @endlink, @link IndexQGram
+ *        fibre. In contrast to @link OpenAddressingQGramIndex @endlink, @link IndexQGram
  *        @endlink uses a trivial 1-to-1 mapping from q-gram hash values to
  *        buckets. For that index the fibre is of type @link Nothing @endlink.
- * 
+ *
  * @tag QGramIndexFibres#QGramCountsDir
- * 
  * @brief The counts directory.
- * 
- * @section Remarks
- * 
+ *
  * The counts directory contains for every possible q-gram hash value the start
  * index of the q-gram count bucket. A q-gram count bucket is a contiguous
  * interval in the counts array (<tt>QGramCounts</tt>, see above). The end index
  * is the start index of the next bucket.
- * 
- * @link Index#Fibre @endlink returns a @link String @endlink over the alphabet of a
+ *
+ * @link Fibre @endlink returns a @link String @endlink over the alphabet of a
  * size type.
- * 
+ *
  * @tag QGramIndexFibres#QGramText
- * 
  * @brief The original text the index should be based on.
- * 
+ *
  * @tag QGramIndexFibres#QGramShape
- * 
  * @brief The shape the index is based on.
- * 
- * @section Remarks
- * 
+ *
  * The q-gram index needs an underlying @link Shape @endlink. This shape can be
  * gapped or ungapped. The number of '1's (relevant positions) in the shape
  * determines <tt>q</tt> and the size of the directory table.
- * 
+ *
  * Dynamic shapes (@link SimpleShape @endlink, @link GenericShape @endlink, ...)
  * must be initialized before the index can be used.
- * 
+ *
  * @tag QGramIndexFibres#QGramSADir
- * 
  * @brief The union of suffix array and directory.
- * 
- * @section Remarks
- * 
+ *
  * In most applications a q-gram index consisting of both of these table is
  * required. To efficiently create them at once use this tag for @link
  * Index#indexRequire @endlink or @link Index#indexCreate @endlink.
- * 
+ *
  * @tag QGramIndexFibres#QGram_RawText
- * 
  * @brief The concatenation of all text sequences.
- * 
- * @section Remarks
- * 
+ *
  * <tt>QGramText</tt> and <tt>QGram_RawText</tt> fibres are equal by default.
  * They differ if the index text is a set of strings. Then, raw text is the
  * concatenation of all strings in this set.
- * 
+ *
  * @tag QGramIndexFibres#QGramCounts
- * 
  * @brief The counts array.
- * 
- * @section Remarks
- * 
+ *
  * Contains the numbers of occurrences per sequence of each q-gram, s.t. the
  * numbers of the same q-gram are stored in a contiguous block (q-gram count
  * bucket). A bucket contains entries (seqNo,count) of sequences with at least
  * one q-gram occurrence. q-grams exceeding the end of the text are ignored. The
  * beginning of each count bucket can be determined by the q-gram counts
  * directory (<tt>QGramCountsDir</tt>, see below).
- * 
- * @link Index#Fibre @endlink returns a @link String @endlink over the alphabet of the
+ *
+ * @link Fibre @endlink returns a @link String @endlink over the alphabet of the
  * @link SAValue @endlink of <tt>TIndex</tt>.
- * 
+ *
  * @tag QGramIndexFibres#QGramSA
- * 
  * @brief The suffix array.
- * 
- * @section Remarks
- * 
+ *
  * Contains all occurrences of q-grams, s.t. the occurrences of a single q-gram
  * are stored in a contiguous block (q-gram bucket). q-grams exceeding the end
  * of the text are ignored. The beginning of each bucket can be determined by
  * the q-gram directory (<tt>QGramDir</tt>, see below).
- * 
+ *
  * It corresponds to a suffix array which is sorted by the first q-gram.
- * 
- * @link Index#Fibre @endlink returns a @link String @endlink over the alphabet of the
+ *
+ * @link Fibre @endlink returns a @link String @endlink over the alphabet of the
  * @link SAValue @endlink of <tt>TIndex</tt>.
  */
 
-	struct FibreDir_;			// directory/hash table, contains start indices of buckets
-	struct FibreSADir_;		// identifies algorithm to construct both SA and directory at once
-	struct Fibre_Shape_;		// underlying shape
-	struct FibreCounts_;		// counts each q-gram
-	struct FibreCountsDir_;	// directory for counts buckets
-	struct FibreBucketMap_;	// stores a q-gram hash value for each directory entry (-1 if empty)
+struct FibreDir_;            // directory/hash table, contains start indices of buckets
+struct FibreSADir_;        // identifies algorithm to construct both SA and directory at once
+struct Fibre_Shape_;        // underlying shape
+struct FibreCounts_;        // counts each q-gram
+struct FibreCountsDir_;    // directory for counts buckets
+struct FibreBucketMap_;    // stores a q-gram hash value for each directory entry (-1 if empty)
 
-	typedef Tag<FibreDir_> const		FibreDir;
-	typedef Tag<FibreSADir_> const		FibreSADir;
-	typedef Tag<Fibre_Shape_> const		FibreShape;
-	typedef Tag<FibreCounts_> const	FibreCounts;
-	typedef Tag<FibreCountsDir_> const	FibreCountsDir;
-	typedef Tag<FibreBucketMap_> const	FibreBucketMap;
+typedef Tag<FibreDir_> const        FibreDir;
+typedef Tag<FibreSADir_> const        FibreSADir;
+typedef Tag<Fibre_Shape_> const        FibreShape;
+typedef Tag<FibreCounts_> const    FibreCounts;
+typedef Tag<FibreCountsDir_> const    FibreCountsDir;
+typedef Tag<FibreBucketMap_> const    FibreBucketMap;
 
 //////////////////////////////////////////////////////////////////////////////
 
-	typedef FibreText		QGramText;
-	typedef FibreRawText	QGram_RawText;
-	typedef FibreSA         QGramSA;
-	typedef FibreRawSA		QGramRawSA;
-	typedef FibreDir		QGramDir;
-	typedef FibreSADir		QGramSADir;
-	typedef FibreShape		QGramShape;
-	typedef FibreCounts     QGramCounts;
-	typedef FibreCountsDir	QGramCountsDir;
-	typedef FibreBucketMap	QGramBucketMap;
+typedef FibreText        QGramText;
+typedef FibreRawText    QGram_RawText;
+typedef FibreSA         QGramSA;
+typedef FibreRawSA        QGramRawSA;
+typedef FibreDir        QGramDir;
+typedef FibreSADir        QGramSADir;
+typedef FibreShape        QGramShape;
+typedef FibreCounts     QGramCounts;
+typedef FibreCountsDir    QGramCountsDir;
+typedef FibreBucketMap    QGramBucketMap;
 
 //////////////////////////////////////////////////////////////////////////////
 // q-gram index
 
-/**
-.Spec.IndexQGram:
-..summary:An index based on an array of sorted q-grams. Especially useful for q-gram/k-mer searches.
-..cat:Index
-..general:Class.Index
-..signature:Index<TText, IndexQGram<TShapeSpec[, TSpec]> >
-..param.TText:The text type.
-...type:Class.String
-..param.TShapeSpec:The @Class.Shape@ specialization type.
-...note:This can be either a $TSpec$ argument (e.g. $SimpleShape$) or a complete @Class.Shape@ class (e.g. Shape<Dna, SimpleShape>).
-..param.TSpec:The specializing type.
-...default:Default
-...type:Spec.OpenAddressing
-..remarks:The fibres (see @Class.Index@ and @Metafunction.Fibre@) of this index are a suffix array sorted by the first q characters (see @Tag.QGram Index Fibres.QGramSA@) and a q-gram directory (see @Tag.QGram Index Fibres.QGramDir@).
-The size of the q-gram directory is |\Sigma|^q.
-On a 32bit system the q-gram length is limited to 3 for $char$ alphabets or 13-14 for @Spec.Dna@ alphabets.
-Consider to use the @Spec.OpenAddressing@ q-gram index for longer q-grams if you don't need q-grams to be sorted.
-..include:seqan/index.h
-..example
-...text:The following code prints all occurrences of the gapped q-gram "AT-A" in "CATGATTACATA".
-...file:demos/index/index_qgram.cpp
-...output:1
-4
-*/
+/*!
+ * @defgroup OpenAdressingTags Open Adressing Tags
+ * @brief Tags for selecting open adressing.
+ *
+ * @tag OpenAdressingTags#OpenAdressing
+ * @brief Tag for enabling open adressing.
+ */
+
 /*!
  * @class IndexQGram
- * 
  * @extends Index
- * 
- * @headerfile seqan/index.h
- * 
+ * @implements StringTrieConcept
+ * @headerfile <seqan/index.h>
+ *
  * @brief An index based on an array of sorted q-grams.
- * 
- * @signature Index<TText, IndexQGram<TShapeSpec[, TSpec]> >
- * 
- * @tparam TSpec The specializing type. Types: @link OpenAddressing @endlink, Default: Default
+ *
+ * @signature template <typename TIndex, typename TShapeSpec, typename TSpec>
+ *            class Index<TText, IndexQGram<TShapeSpec[, TSpec]> >;
+ *
+ * @tparam TSpec The specializing type. Types: @link OpenAdressingTags#OpenAdressing @endlink, Default: void
  * @tparam TText The text type. Types: @link String @endlink
  * @tparam TShapeSpec The @link Shape @endlink specialization type.
- * 
- * @section Remarks
- * 
- * The fibres (see @link Index @endlink and @link Index#Fibre @endlink) of this index
- * are a suffix array sorted by the first q characters (see @link QGramIndexFibres#QGramSA @endlink) and a q-gram directory (see @link QGramIndexFibres#QGramDir @endlink). The size of the q-gram directory is |\Sigma|^q. On
- * a 32bit system the q-gram length is limited to 3 for <tt>char</tt> alphabets
- * or 13-14 for @link Dna @endlink alphabets. Consider to use the @link
- * OpenAddressing @endlink q-gram index for longer q-grams if you don't need
- * q-grams to be sorted.
- * 
+ *
+ * The fibres (see @link Index @endlink and @link Fibre @endlink) of this index are a suffix array sorted by the first
+ * <i>q</i> characters (see @link QGramIndexFibres#QGramSA @endlink) and a <i>q</i>-gram directory (see @link
+ * QGramIndexFibres#QGramDir @endlink).
+ *
+ * The size of the q-gram directory is <i>&Sigma;<sup>q</sup></i>.  On a 32 bit system the <i>q</i>-gram length is
+ * limited to 3 for <tt>char</tt> alphabets or 13-14 for @link Dna @endlink alphabets.
+ *
+ * Consider to use the @link OpenAddressingQGramIndex @endlink for longer <i>q</i>-grams if you don't need
+ * <i>q</i>-grams to be sorted.
+ *
  * @see QGramIndexFibres
  */
 
-	template < typename TShapeSpec, typename TSpec = Default >
-	struct IndexQGram {};
-
-	// use the index value type as shape value type
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	struct Fibre< Index<TText, IndexQGram<TShapeSpec, TSpec> >, FibreShape> 
-	{
-		typedef Index< TText, IndexQGram<TShapeSpec, TSpec> >	TIndex;
-		typedef Shape< typename Value<TIndex>::Type, TShapeSpec >	Type;
-	};
-
-	// allow different value types for the shape
-	template < typename TText, typename TShapeValue, typename TShapeSpec, typename TSpec >
-	struct Fibre< Index<TText, IndexQGram<Shape<TShapeValue, TShapeSpec>, TSpec> >, FibreShape> 
-	{
-		typedef Shape<TShapeValue, TShapeSpec>	Type;
-	};
-
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	struct Fibre< Index<TText, IndexQGram<TShapeSpec, TSpec> >, FibreBucketMap>
-	{
-		typedef Nothing Type;
-	};
+template < typename TShapeSpec, typename TSpec = Default >
+struct IndexQGram {};
+
+// use the index value type as shape value type
+template < typename TText, typename TShapeSpec, typename TSpec >
+struct Fibre< Index<TText, IndexQGram<TShapeSpec, TSpec> >, FibreShape>
+{
+    typedef Index< TText, IndexQGram<TShapeSpec, TSpec> >    TIndex;
+    typedef Shape< typename Value<TIndex>::Type, TShapeSpec >    Type;
+};
+
+// allow different value types for the shape
+template < typename TText, typename TShapeValue, typename TShapeSpec, typename TSpec >
+struct Fibre< Index<TText, IndexQGram<Shape<TShapeValue, TShapeSpec>, TSpec> >, FibreShape>
+{
+    typedef Shape<TShapeValue, TShapeSpec>    Type;
+};
+
+template < typename TText, typename TShapeSpec, typename TSpec >
+struct Fibre< Index<TText, IndexQGram<TShapeSpec, TSpec> >, FibreBucketMap>
+{
+    typedef Nothing Type;
+};
 
 #ifdef PLATFORM_WINDOWS_VS
 #pragma warning( push )
@@ -329,2929 +233,2670 @@ Consider to use the @Spec.OpenAddressing@ q-gram index for longer q-grams if you
 #pragma warning( disable: 4522 )
 #endif  // PLATFORM_WINDOWS_VS
 
-	template < typename TText_, typename TShapeSpec, typename TSpec >
-	class Index<TText_, IndexQGram<TShapeSpec, TSpec> > {
-	public:
-		typedef typename Fibre<Index, QGramText>::Type			TText;
-		typedef typename Fibre<Index, QGramSA>::Type			TSA;
-		typedef typename Fibre<Index, QGramDir>::Type			TDir;
-		typedef typename Fibre<Index, QGramCounts>::Type		TCounts;
-		typedef typename Fibre<Index, QGramCountsDir>::Type     TCountsDir;
-		typedef typename Fibre<Index, QGramShape>::Type         TShape;
-		typedef typename Fibre<Index, QGramBucketMap>::Type     TBucketMap;
-		typedef typename Cargo<Index>::Type						TCargo;
-		typedef typename Size<Index>::Type						TSize;
-
-		Holder<TText>	text;		// underlying text
-		TSA				sa;			// suffix array sorted by the first q chars
-		TDir			dir;		// bucket directory
-		TCounts			counts;		// counts each q-gram per sequence
-		TCountsDir		countsDir;	// directory for count buckets
-		TShape			shape;		// underlying shape
-		TCargo			cargo;		// user-defined cargo
-		TBucketMap		bucketMap;	// bucketMap table (used by open-addressing index)
-		TSize			stepSize;	// store every <stepSize>'th q-gram in the index
-
-		Index():
-			stepSize(1) {}
-
-		Index(Index &other):
-			text(other.text),
-			sa(other.sa),
-			dir(other.dir),
-			counts(other.counts),
-			countsDir(other.countsDir),
-			shape(other.shape),
-			cargo(other.cargo),
-			stepSize(1) {}
-
-		Index(Index const &other):
-			text(other.text),
-			sa(other.sa),
-			dir(other.dir),
-			counts(other.counts),
-			countsDir(other.countsDir),
-			shape(other.shape),
-			cargo(other.cargo),
-			stepSize(1) {}
-
-		template <typename TText__>
-		Index(TText__ &_text):
-			text(_text),
-			stepSize(1) {}
-
-		template <typename TText__>
-		Index(TText__ const &_text):
-			text(_text),
-			stepSize(1) {}
-
-		template <typename TText__, typename TShape_>
-		Index(TText__ &_text, TShape_ const &_shape):
-			text(_text),
-			shape(_shape),
-			stepSize(1) {}
-
-		template <typename TText__, typename TShape_>
-		Index(TText__ const &_text, TShape_ const &_shape):
-			text(_text),
-			shape(_shape),
-			stepSize(1) {}
-	};
+template < typename TText_, typename TShapeSpec, typename TSpec >
+class Index<TText_, IndexQGram<TShapeSpec, TSpec> > {
+public:
+    typedef typename Member<Index, QGramText>::Type         TTextMember;
+    typedef typename Fibre<Index, QGramText>::Type            TText;
+    typedef typename Fibre<Index, QGramSA>::Type            TSA;
+    typedef typename Fibre<Index, QGramDir>::Type            TDir;
+    typedef typename Fibre<Index, QGramCounts>::Type        TCounts;
+    typedef typename Fibre<Index, QGramCountsDir>::Type     TCountsDir;
+    typedef typename Fibre<Index, QGramShape>::Type         TShape;
+    typedef typename Fibre<Index, QGramBucketMap>::Type     TBucketMap;
+    typedef typename Cargo<Index>::Type                        TCargo;
+    typedef typename Size<Index>::Type                        TSize;
+
+    TTextMember     text;        // underlying text
+    TSA                sa;            // suffix array sorted by the first q chars
+    TDir            dir;        // bucket directory
+    TCounts            counts;        // counts each q-gram per sequence
+    TCountsDir        countsDir;    // directory for count buckets
+    TShape            shape;        // underlying shape
+    TCargo            cargo;        // user-defined cargo
+    TBucketMap        bucketMap;    // bucketMap table (used by open-addressing index)
+    TSize            stepSize;    // store every <stepSize>'th q-gram in the index
+
+    Index():
+    stepSize(1) {}
+
+    Index(Index &other):
+    text(other.text),
+    sa(other.sa),
+    dir(other.dir),
+    counts(other.counts),
+    countsDir(other.countsDir),
+    shape(other.shape),
+    cargo(other.cargo),
+    stepSize(1) {}
+
+    Index(Index const &other):
+    text(other.text),
+    sa(other.sa),
+    dir(other.dir),
+    counts(other.counts),
+    countsDir(other.countsDir),
+    shape(other.shape),
+    cargo(other.cargo),
+    stepSize(1) {}
+
+    template <typename TText__>
+    Index(TText__ &_text):
+    text(_text),
+    stepSize(1) {}
+
+    template <typename TText__>
+    Index(TText__ const &_text):
+    text(_text),
+    stepSize(1) {}
+
+    template <typename TText__, typename TShape_>
+    Index(TText__ &_text, TShape_ const &_shape):
+    text(_text),
+    shape(_shape),
+    stepSize(1) {}
+
+    template <typename TText__, typename TShape_>
+    Index(TText__ const &_text, TShape_ const &_shape):
+    text(_text),
+    shape(_shape),
+    stepSize(1) {}
+};
 
 #ifdef PLATFORM_WINDOWS_VS
 // Reset warning state to previous values for C4521, C4522.
 #pragma warning( pop )
 #endif  // PLATFORM_WINDOWS_VS
 
-    template < typename TText, typename TShapeSpec, typename TSpec >
-    struct Value< Index<TText, IndexQGram<TShapeSpec, TSpec> > > {
-		typedef typename Value< typename Fibre< Index<TText, IndexQGram<TShapeSpec, TSpec> >, QGram_RawText >::Type >::Type Type;
-    };
+template <typename TText, typename TShapeSpec, typename TSpec>
+SEQAN_CONCEPT_IMPL((Index<TText, IndexQGram<TShapeSpec, TSpec> >), (StringTrieConcept));
 
-	template < typename TText, typename TShapeSpec, typename TSpec >
-    struct Size< Index<TText, IndexQGram<TShapeSpec, TSpec> > > {
-		typedef typename Size< typename Fibre< Index<TText, IndexQGram<TShapeSpec, TSpec> >, QGram_RawText >::Type >::Type Type;
-    };
+template <typename TText, typename TShapeSpec, typename TSpec>
+SEQAN_CONCEPT_IMPL((Index<TText, IndexQGram<TShapeSpec, TSpec> > const), (StringTrieConcept));
 
 
+template < typename TText, typename TShapeSpec, typename TSpec >
+struct Value< Index<TText, IndexQGram<TShapeSpec, TSpec> > > {
+    typedef typename Value< typename Fibre< Index<TText, IndexQGram<TShapeSpec, TSpec> >, QGram_RawText >::Type >::Type Type;
+};
+
+template < typename TText, typename TShapeSpec, typename TSpec >
+struct Size< Index<TText, IndexQGram<TShapeSpec, TSpec> > > {
+    typedef typename Size< typename Fibre< Index<TText, IndexQGram<TShapeSpec, TSpec> >, QGram_RawText >::Type >::Type Type;
+};
+
 //////////////////////////////////////////////////////////////////////////////
 // default fibre creators
 
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	struct DefaultIndexCreator<Index<TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA> {
-        typedef Default Type;
-    };
+template < typename TText, typename TShapeSpec, typename TSpec >
+struct DefaultIndexCreator<Index<TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA> {
+    typedef Default Type;
+};
 
 //////////////////////////////////////////////////////////////////////////////
 // counts array type
 
-	template < typename TText, typename TSpec >
-	struct Fibre< Index<TText, TSpec>, FibreCounts> {
-		typedef String<
-				Pair<
-					typename Size< TText >::Type,
-					typename Size< Index<TText, TSpec> >::Type
-				>,
-				typename DefaultIndexStringSpec< Index<TText, TSpec> >::Type 
-		> Type;
-	};
+template < typename TText, typename TSpec >
+struct Fibre< Index<TText, TSpec>, FibreCounts> {
+    typedef String<
+    Pair<
+    typename Size< TText >::Type,
+    typename Size< Index<TText, TSpec> >::Type
+    >,
+    typename DefaultIndexStringSpec< Index<TText, TSpec> >::Type
+    > Type;
+};
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreDir>::Type &
+getFibre(Index<TText, TSpec> &index, FibreDir) {
+    return index.dir;
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreDir>::Type &
+getFibre(Index<TText, TSpec> const &index, FibreDir) {
+    return index.dir;
+}
+
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreCounts>::Type &
+getFibre(Index<TText, TSpec> &index, FibreCounts) {
+    return index.counts;
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreCounts>::Type &
+getFibre(Index<TText, TSpec> const &index, FibreCounts) {
+    return index.counts;
+}
+
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreCountsDir>::Type &
+getFibre(Index<TText, TSpec> &index, FibreCountsDir) {
+    return index.countsDir;
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreCountsDir>::Type &
+getFibre(Index<TText, TSpec> const &index, FibreCountsDir) {
+    return index.countsDir;
+}
+
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreBucketMap>::Type &
+getFibre(Index<TText, TSpec> &index, FibreBucketMap) {
+    return index.bucketMap;
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreBucketMap>::Type &
+getFibre(Index<TText, TSpec> const &index, FibreBucketMap) {
+    return index.bucketMap;
+}
 
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreShape>::Type &
+getFibre(Index<TText, TSpec> &index, FibreShape) {
+    return index.shape;
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreShape>::Type &
+getFibre(Index<TText, TSpec> const &index, FibreShape) {
+    return index.shape;
+}
 
 //////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn IndexQGram#indexSA
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(.., QGramSA)</tt>.
+ *
+ * @signature TSa indexSA(index);
+ *
+ * @param[in] index The @link IndexQGram @endlink object holding the fibre.
+ *
+ * @return TSa A reference to the @link QGramIndexFibres#QGramSA @endlink fibre (q-gram positions).
+ */
 
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreDir>::Type & 
-	getFibre(Index<TText, TSpec> &index, FibreDir) {
-		return index.dir;
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreDir>::Type & 
-	getFibre(Index<TText, TSpec> const &index, FibreDir) {
-		return index.dir;
-	}
-
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreCounts>::Type & 
-	getFibre(Index<TText, TSpec> &index, FibreCounts) {
-		return index.counts;
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreCounts>::Type & 
-	getFibre(Index<TText, TSpec> const &index, FibreCounts) {
-		return index.counts;
-	}
-
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreCountsDir>::Type & 
-	getFibre(Index<TText, TSpec> &index, FibreCountsDir) {
-		return index.countsDir;
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreCountsDir>::Type & 
-	getFibre(Index<TText, TSpec> const &index, FibreCountsDir) {
-		return index.countsDir;
-	}
-
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreBucketMap>::Type & 
-	getFibre(Index<TText, TSpec> &index, FibreBucketMap) {
-		return index.bucketMap;
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreBucketMap>::Type & 
-	getFibre(Index<TText, TSpec> const &index, FibreBucketMap) {
-		return index.bucketMap;
-	}
-
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreShape>::Type & 
-	getFibre(Index<TText, TSpec> &index, FibreShape) {
-		return index.shape;
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreShape>::Type & 
-	getFibre(Index<TText, TSpec> const &index, FibreShape) {
-		return index.shape;
-	}
+/*!
+ * @fn IndexQGram#saAt
+ * @headerfile <seqan/index.h>
+ * @note Advanced functionality, not commonly used.
+ * @brief Shortcut for <tt>value(indexSA(..), ..)</tt>.
+ *
+ * @signature TValue saAt(position, index);
+ *
+ * @param[in] index The @link IndexQGram @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TValue A reference or proxy to the value in the @link QGramIndexFibres#QGramSA @endlink fibre.
+ *                To be more precise, a reference to a position containing a value of type
+ *                @link SAValue @endlink is returned (or a proxy).
+ */
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexDir
-..summary:Shortcut for $getFibre(.., QGramDir)$.
-..cat:Index
-..signature:indexDir(index)
-..class:Spec.IndexQGram
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexQGram
-..returns:A reference to the @Tag.QGram Index Fibres.QGramDir@ fibre (q-gram directory).
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#indexDir
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Shortcut for <tt>getFibre(.., QGramDir)</tt>.
- * 
- * @signature indexDir(index)
- * 
- * @param index The @link Index @endlink object holding the fibre. Types:
- *              IndexQGram
- * 
- * @return TReturn A reference to the @link QGramIndexFibres#QGramDir @endlink
- *                 fibre (q-gram directory).
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(.., QGramDir())</tt>.
+ * @signature TFibre indexDir(index);
+ *
+ * @param[in] index The @link IndexQGram @endlink object holding the fibre.
+ *
+ * @return TFibre A reference to the @link QGramIndexFibres#QGramDir @endlink fibre (q-gram directory).
  */
 
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreDir>::Type & 
-	indexDir(Index<TText, TSpec> &index) { 
-		return getFibre(index, FibreDir()); 
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreDir>::Type & 
-	indexDir(Index<TText, TSpec> const &index) { 
-		return getFibre(index, FibreDir()); 
-	}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreDir>::Type &
+indexDir(Index<TText, TSpec> &index) {
+    return getFibre(index, FibreDir());
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreDir>::Type &
+indexDir(Index<TText, TSpec> const &index) {
+    return getFibre(index, FibreDir());
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.dirAt
-..summary:Shortcut for $value(indexDir(..), ..)$.
-..cat:Index
-..signature:dirAt(position, index)
-..class:Spec.IndexQGram
-..param.position:A position in the array on which the value should be accessed.
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexQGram
-..returns:A reference or proxy to the value.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#dirAt
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Shortcut for <tt>value(indexDir(..), ..)</tt>.
- * 
- * @signature dirAt(position, index)
- * 
- * @param index The @link Index @endlink object holding the fibre. Types: @link
- *              IndexQGram @endlink
- * @param position A position in the array on which the value should be
- *                 accessed.
- * 
- * @return TReturn A reference or proxy to the value.
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>value(indexDir(index), position)</tt>.
+ *
+ * @signature TFibre dirAt(position, index);
+ *
+ * @param[in] index    The IndexQGram object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TFibre A reference to the @link QGramIndexFibres#QGramDir @endlink fibre.
  */
 
-	template <typename TPos, typename TIndex>
-	inline typename Reference<typename Fibre<TIndex, FibreDir>::Type>::Type 
-	dirAt(TPos i, TIndex &index) {
-		return value(getFibre(index, FibreDir()), i);
-	}
-	template <typename TPos, typename TIndex>
-	inline typename Reference<typename Fibre<TIndex const, FibreDir>::Type>::Type 
-	dirAt(TPos i, TIndex const &index) {
-		return value(getFibre(index, FibreDir()), i);
-	}
+template <typename TPos, typename TIndex>
+inline typename Reference<typename Fibre<TIndex, FibreDir>::Type>::Type
+dirAt(TPos i, TIndex &index) {
+    return value(getFibre(index, FibreDir()), i);
+}
+template <typename TPos, typename TIndex>
+inline typename Reference<typename Fibre<TIndex const, FibreDir>::Type>::Type
+dirAt(TPos i, TIndex const &index) {
+    return value(getFibre(index, FibreDir()), i);
+}
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexCounts
-..summary:Shortcut for $getFibre(.., QGramCounts)$.
-..cat:Index
-..signature:indexCounts(index)
-..class:Spec.IndexQGram
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexQGram
-..returns:A reference to the @Tag.QGram Index Fibres.QGramCounts@ fibre (counts array).
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#indexCounts
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Shortcut for <tt>getFibre(.., QGramCounts)</tt>.
- * 
- * @signature indexCounts(index)
- * 
- * @param index The @link Index @endlink object holding the fibre. Types: @link
- *              IndexQGram @endlink
- * 
- * @return TReturn A reference to the @link QGramIndexFibres#QGramCounts
- *                 @endlink fibre (counts array).
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(index, QGramCounts())</tt>.
+ *
+ * @signature TFibre indexCounts(index);
+ *
+ * @param[in] index The @link IndexQGram @endlink object holding the fibre.
+ *
+ * @return TFibre A reference to the @link QGramIndexFibres#QGramCounts @endlink fibre (counts array).
  */
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreCounts>::Type & 
-	indexCounts(Index<TText, TSpec> &index) {
-		return getFibre(index, FibreCounts()); 
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreCounts>::Type & 
-	indexCounts(Index<TText, TSpec> const &index) {
-		return getFibre(index, FibreCounts()); 
-	}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreCounts>::Type &
+indexCounts(Index<TText, TSpec> &index) {
+    return getFibre(index, FibreCounts());
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreCounts>::Type &
+indexCounts(Index<TText, TSpec> const &index) {
+    return getFibre(index, FibreCounts());
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexCountsDir
-..summary:Shortcut for $getFibre(.., QGramCountsDir)$.
-..cat:Index
-..signature:indexCountsDir(index)
-..class:Spec.IndexQGram
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexQGram
-..returns:A reference to the @Tag.QGram Index Fibres.QGramCountsDir@ fibre (counts directory).
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#indexCountsDir
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Shortcut for <tt>getFibre(.., QGramCountsDir)</tt>.
- * 
- * @signature indexCountsDir(index)
- * 
- * @param index The @link Index @endlink object holding the fibre. Types: @link
- *              IndexQGram @endlink
- * 
- * @return TReturn A reference to the @link QGramIndexFibres#QGramCountsDir
- *                 @endlink fibre (counts directory).
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(index, QGramCountsDir())</tt>.
+ *
+ * @signature TFibre indexCountsDir(index);
+ *
+ * @param[in] index The IndexQGram object holding the fibre.
+ *
+ * @return TFibre A reference to the @link QGramIndexFibres#QGramCountsDir @endlink fibre (counts directory).
  */
 
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreCountsDir>::Type & 
-	indexCountsDir(Index<TText, TSpec> &index) {
-		return getFibre(index, FibreCountsDir()); 
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreCountsDir>::Type & 
-	indexCountsDir(Index<TText, TSpec> const &index) {
-		return getFibre(index, FibreCountsDir()); 
-	}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreCountsDir>::Type &
+indexCountsDir(Index<TText, TSpec> &index) {
+    return getFibre(index, FibreCountsDir());
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreCountsDir>::Type &
+indexCountsDir(Index<TText, TSpec> const &index) {
+    return getFibre(index, FibreCountsDir());
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexBucketMap
-..summary:Shortcut for $getFibre(.., QGramBucketMap)$.
-..cat:Index
-..signature:indexBucketMap(index)
-..class:Spec.IndexQGram
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexQGram
-..returns:A reference to the @Tag.QGram Index Fibres.QGramBucketMap@ fibre (maps q-gram hashes to buckets).
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#indexBucketMap
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Shortcut for <tt>getFibre(.., QGramBucketMap)</tt>.
- * 
- * @signature indexBucketMap(index)
- * 
- * @param index The @link Index @endlink object holding the fibre. Types: @link
- *              IndexQGram @endlink
- * 
- * @return TReturn A reference to the @link QGramIndexFibres#QGramBucketMap
- *                 @endlink fibre (maps q-gram hashes to buckets).
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(index, QGramBucketMap())</tt>.
+ *
+ * @signature TFibre indexBucketMap(index);
+ *
+ * @param[in] index The IndexQGram object holding the fibre.
+ *
+ * @return TFibre A reference to the @link QGramIndexFibres#QGramBucketMap @endlink fibre (maps q-gram hashes to
+ *                buckets).
  */
 
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreBucketMap>::Type & 
-	indexBucketMap(Index<TText, TSpec> &index) {
-		return getFibre(index, FibreBucketMap()); 
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreBucketMap>::Type & 
-	indexBucketMap(Index<TText, TSpec> const &index) {
-		return getFibre(index, FibreBucketMap()); 
-	}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreBucketMap>::Type &
+indexBucketMap(Index<TText, TSpec> &index) {
+    return getFibre(index, FibreBucketMap());
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreBucketMap>::Type &
+indexBucketMap(Index<TText, TSpec> const &index) {
+    return getFibre(index, FibreBucketMap());
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexShape
-..summary:Shortcut for $getFibre(.., QGramShape)$.
-..cat:Index
-..signature:indexShape(index)
-..class:Spec.IndexQGram
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Spec.IndexQGram
-..returns:Returns a reference to the @Class.Shape@ object of a q-gram index.
-Formally, this is a reference to the @Tag.QGram Index Fibres.QGramShape@ fibre.
-...type:Class.Shape
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#indexShape
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Shortcut for <tt>getFibre(.., QGramShape)</tt>.
- * 
- * @signature indexShape(index)
- * 
- * @param index The @link Index @endlink object holding the fibre. Types: @link
- *              IndexQGram @endlink
- * 
- * @return TReturn Returns a reference to the @link Shape @endlink object of a
- *                 q-gram index. Formally, this is a reference to the @link
- *                 QGramIndexFibres#QGramShape @endlink fibre. Types: @link Shape @endlink
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(index, QGramShape())</tt>.
+ * @signature TFibre indexShape(index);
+ *
+ * @param[in] index The @link Index @endlink object holding the fibre. Types: @link IndexQGram @endlink
+ *
+ * @return TFibre Returns a reference to the @link Shape @endlink object of a q-gram index.  Formally, this is a
+ *                reference to the @link QGramIndexFibres#QGramShape @endlink fibre.
  */
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec>, FibreShape>::Type & 
-	indexShape(Index<TText, TSpec> &index) { 
-		return getFibre(index, FibreShape()); 
-	}
-	template <typename TText, typename TSpec>
-	inline typename Fibre<Index<TText, TSpec> const, FibreShape>::Type & 
-	indexShape(Index<TText, TSpec> const &index) { 
-		return getFibre(index, FibreShape()); 
-	}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec>, FibreShape>::Type &
+indexShape(Index<TText, TSpec> &index) {
+    return getFibre(index, FibreShape());
+}
+template <typename TText, typename TSpec>
+inline typename Fibre<Index<TText, TSpec> const, FibreShape>::Type &
+indexShape(Index<TText, TSpec> const &index) {
+    return getFibre(index, FibreShape());
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.getStepSize
-..summary:Return the q-gram step size used for index creation.
-..cat:Index
-..signature:getStepSize(index)
-..class:Spec.IndexQGram
-..param.index:A q-gram index.
-...type:Spec.IndexQGram
-..returns:The step size. If $x$ is returned every $x$'th q-gram is stored in the index.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#getStepSize
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Return the q-gram step size used for index creation.
- * 
- * @signature getStepSize(index)
- * 
- * @param index A q-gram index. Types: @link IndexQGram @endlink
- * 
- * @return TReturn The step size. If <tt>x</tt> is returned every <tt>x</tt>'th
- *                 q-gram is stored in the index.
- * 
+ * @headerfile <seqan/index.h>
+ * @brief Return the <i>q</i>-gram step size used for index creation.
+ * @signature TSize getStepSize(index);
+ *
+ * @param[in] index A IndexQGram object.
+ *
+ * @return TSize The step size of type @link Index#Size @endlink.  If <i>x</i> is returned every <i>x</i><sup>th</sup>
+ *               <i>q</i>-gram is stored in the index.
+ *
  * @see IndexQGram#setStepSize
  */
-	template <typename TText, typename TShapeSpec, typename TSpec>
-	inline typename Size<TText>::Type 
-	getStepSize(Index<TText, IndexQGram<TShapeSpec, TSpec> > const &index)
-	{
-		return (index.stepSize != 0)? index.stepSize: length(indexShape(index));
-	}
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Size<Index<TText, IndexQGram<TShapeSpec, TSpec> > const>::Type
+getStepSize(Index<TText, IndexQGram<TShapeSpec, TSpec> > const &index)
+{
+    return (index.stepSize != 0)? index.stepSize: length(indexShape(index));
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.setStepSize
-..summary:Change the q-gram step size used for index creation.
-..cat:Index
-..signature:setStepSize(index, stepSize)
-..class:Spec.IndexQGram
-..param.index:A q-gram index.
-...type:Spec.IndexQGram
-..param.stepSize:Store every $stepSize$'th q-gram in the index.
-..remarks:The default step size of a q-gram index is 1, which corresponds to all overlapping q-grams.
-To take effect of changing the $stepSize$ the q-gram index should be empty or recreated. 
-..remarks:A $stepSize$ of 0 corresponds to $stepSize=length(indexShape(index))$, i.e. all non-overlapping q-grams.
-..see:Function.getStepSize
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#setStepSize
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Change the q-gram step size used for index creation.
- * 
- * @signature setStepSize(index, stepSize)
- * 
- * @param index A q-gram index. Types: @link IndexQGram @endlink
- * @param stepSize Store every <tt>stepSize</tt>'th q-gram in the index.
- * 
- * @section Remarks
- * 
- * The default step size of a q-gram index is 1, which corresponds to all
- * overlapping q-grams. To take effect of changing the <tt>stepSize</tt> the
- * q-gram index should be empty or recreated.
- * 
- * A <tt>stepSize</tt> of 0 corresponds to
- * <tt>stepSize=length(indexShape(index))</tt>, i.e. all non-overlapping
+ * @headerfile <seqan/index.h>
+ * @brief Change the <i>q</i>-gram step size used for index creation.
+ *
+ * @signature void setStepSize(index, stepSize);
+ *
+ * @param[in,out] index    The IndexQGram to modify.
+ * @param[in]     stepSize The step size, @link IntegerConcept @endlink;  Each <tt>stepSize</tt><sup>th</sup>
+ *                         <i>q</i>-gram will be stored.
+ *
+ * The default step size of a <i>q</i>-gram index is 1, which corresponds to all overlapping <i>q</i>-grams.  To take
+ * effect of changing the <tt>stepSize</tt> the <i>q</i>-gram index should be empty or recreated.
+ *
+ * A <tt>stepSize</tt> of 0 corresponds to <tt>stepSize = length(indexShape(index))</tt>, i.e. all non-overlapping
  * q-grams.
- * 
+ *
  * @see IndexQGram#getStepSize
  */
 
-	template <typename TText, typename TShapeSpec, typename TSpec, typename TSize>
-	inline void
-	setStepSize(Index<TText, IndexQGram<TShapeSpec, TSpec> > &index, TSize stepSize)
-	{
-		index.stepSize = stepSize;
-	}
+template <typename TText, typename TShapeSpec, typename TSpec, typename TSize>
+inline void
+setStepSize(Index<TText, IndexQGram<TShapeSpec, TSpec> > &index, TSize stepSize)
+{
+    index.stepSize = stepSize;
+}
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TValue, typename TSpec>
-	inline __int64 _fullDirLength(Shape<TValue, TSpec> const &shape)
-	{
-		return _intPow((__int64)ValueSize<TValue>::VALUE, weight(shape)) + 1;
-	}
-
-	template <typename TValue, typename TSpec>
-	inline __int64 _fullDir2Length(Shape<TValue, TSpec> const &shape)
-	{
-		return (_intPow(
-					(__int64)ValueSize<TValue>::VALUE,
-					weight(shape) + 1) - 1)
-				/ ((unsigned)ValueSize<TValue>::VALUE - 1) + 1;
-	}
-
-	template <typename TIndex>
-	inline __int64 _fullDirLength(TIndex const &index)
-	{
-		return _fullDirLength(indexShape(index));
-	}
-
-	template <typename TIndex>
-	inline __int64 _fullDir2Length(TIndex const &index)
-	{
-		return _fullDir2Length(indexShape(index));
-	}
-
-
-    //////////////////////////////////////////////////////////////////////////////
-    // QGramLess
-	//
-	// compare two q-grams of a given text (q-grams can be smaller than q)
-    template < typename TSAValue, typename TText >
-	struct QGramLess_ : 
-		public ::std::binary_function < TSAValue, TSAValue, bool >
-    {
-		typedef typename Iterator<TText, Standard>::Type TIter;
-		TIter _begin, _end;
-		typename Size<TText>::Type _q;
-
-		template <typename TSize>
-		QGramLess_(TText &text, TSize q): 
-			_begin(begin(text, Standard())),
-			_end(end(text, Standard())),
-			_q(q) {}
-
-		// skip the first <offset> characters
-		template <typename TSize1, typename TSize2>
-		QGramLess_(TText &text, TSize1 q, TSize2 offset): 
-			_begin(begin(text, Standard()) + offset),
-			_end(end(text, Standard())),
-			_q(q) {}
-
-		inline bool operator() (TSAValue const a, TSAValue const b) const 
-		{
-			if (a == b) return false;
-			TIter itA = _begin + a;
-			TIter itB = _begin + b;
-			if (a <= b) {
-				TIter itEnd = itB + _q;
-				if (itEnd > _end)
-					itEnd = _end;
-				for(; itB != itEnd; ++itB, ++itA) {
-					if (ordLess(*itA, *itB)) return true;
-					if (ordLess(*itB, *itA)) return false;
-				}
-				return false;
-			} else {
-				TIter itEnd = itA + _q;
-				if (itEnd > _end)
-					itEnd = _end;
-				for(; itA != itEnd; ++itA, ++itB) {
-					if (ordLess(*itA, *itB)) return true;
-					if (ordLess(*itB, *itA)) return false;
-				}
-				return true;
-			}
-		}
-	};
-
-	template < typename TSAValue, typename TString, typename TSpec >
-	struct QGramLess_<TSAValue, StringSet<TString, TSpec> const> : 
-		public ::std::binary_function < TSAValue, TSAValue, bool >
-    {
-		typedef typename Iterator<TString const, Standard>::Type TIter;
-		typedef typename Size<TString>::Type                     TSize;
-        typedef StringSet<TString, TSpec>                        TStringSet;
-		TStringSet const &_stringSet;
-		typename Size<TString>::Type _q;
-
-		template <typename TSize>
-		QGramLess_(StringSet<TString, TSpec> const &text, TSize q): 
-			_stringSet(text),
-			_q(q) {}
-
-		inline bool operator() (TSAValue const &a, TSAValue const &b) const 
-		{
-			if (a == b) return false;
-            
-            typename Size<TStringSet>::Type seqNoA = getSeqNo(a, stringSetLimits(_stringSet));
-            typename Size<TStringSet>::Type seqNoB = getSeqNo(b, stringSetLimits(_stringSet));
-			TIter itA = begin(_stringSet[seqNoA], Standard()) + getSeqOffset(a, stringSetLimits(_stringSet));
-			TIter itB = begin(_stringSet[seqNoB], Standard()) + getSeqOffset(b, stringSetLimits(_stringSet));
-            TIter itAEnd = end(_stringSet[seqNoA], Standard());
-            TIter itBEnd = end(_stringSet[seqNoB], Standard());
-            
-            if (itAEnd - itA < itBEnd - itB)
-            {
-                TIter itQEnd = itA + _q;
-                TIter itEnd = _min(itQEnd, itAEnd);
-                for(; itA < itEnd; ++itA, ++itB) {
-                    if (ordLess(*itA, *itB)) return true;
-                    if (ordLess(*itB, *itA)) return false;
-                }
-                // if qgram a is shorter than b => a < b
-                if (itA != itQEnd) return true;
-            }
-            else
-            {
-                TIter itQEnd = itB + _q;
-                TIter itEnd = _min(itQEnd, itBEnd);
-                for(; itB < itEnd; ++itA, ++itB) {
-                    if (ordLess(*itA, *itB)) return true;
-                    if (ordLess(*itB, *itA)) return false;
-                }
-                // if qgram b is shorter or equal than a => a >= b
-                if (itB != itQEnd) return false;
-            }
-            if (seqNoA < seqNoB) return true;
-            if (seqNoA > seqNoB) return false;
-			return suffixLength(a, _stringSet) > suffixLength(b, _stringSet);
-		}
-	};
-
-
-    //////////////////////////////////////////////////////////////////////////////
-    // QGramLessOffset
-	//
-	// compare two q-grams of a given text and skip the first <offset> characters
-    template < typename TSAValue, typename TText >
-	struct QGramLessOffset_ :
-		QGramLess_<TSAValue, TText>
-	{
-		template <typename TSize1, typename TSize2>
-		QGramLessOffset_(TText &text, TSize1 q, TSize2 offset): 
-			QGramLess_<TSAValue, TText> (text, q, offset) {}
-	};
-
-	template < typename TSAValue, typename TString, typename TSpec >
-	struct QGramLessOffset_<TSAValue, StringSet<TString, TSpec> const> : 
-		public ::std::binary_function < TSAValue, TSAValue, bool >
-    {
-		typedef typename Iterator<TString const, Standard>::Type TIter;
-		typedef typename Size<TString>::Type                     TSize;
-        typedef StringSet<TString, TSpec>                        TStringSet;
-        typedef typename StringSetLimits<TStringSet>::Type       TLimits;
-
-		TStringSet const &_stringSet;
-        TLimits const &limits;
-		TSize _q, _offset;
-
-		template <typename TSize1, typename TSize2>
-		QGramLessOffset_(StringSet<TString, TSpec> const &text, TSize1 q, TSize2 offset): 
-			_stringSet(text),
-            limits(stringSetLimits(text)),
-			_q(q),
-			_offset(offset) {}
-
-		inline bool operator() (TSAValue const &a, TSAValue const &b) const 
-		{
-			if (a == b) return false;
-            
-            typename Size<TStringSet const>::Type seqNoA = getSeqNo(a, limits);
-            typename Size<TStringSet const>::Type seqNoB = getSeqNo(b, limits);
-
-			TIter itA    = begin(_stringSet[seqNoA], Standard()) + getSeqOffset(a, limits);
-            TIter itAEnd =   end(_stringSet[seqNoA], Standard());
-			TIter itB    = begin(_stringSet[seqNoB], Standard()) + getSeqOffset(b, limits);
-            TIter itBEnd =   end(_stringSet[seqNoB], Standard());
-            
-            if (itAEnd - itA < itBEnd - itB)
-            {
-                itA += _offset;
-                itB += _offset;
-                TIter itQEnd = itA + _q;
-                TIter itEnd = _min(itQEnd, itAEnd);
-                for(; itA < itEnd; ++itA, ++itB) {
-                    if (ordLess(*itA, *itB)) return true;
-                    if (ordLess(*itB, *itA)) return false;
-                }
-                // if qgram a is shorter than b => a < b
-                if (itA != itQEnd) return true;
-            }
-            else
-            {
-                itA += _offset;
-                itB += _offset;
-                TIter itQEnd = itB + _q;
-                TIter itEnd = _min(itQEnd, itBEnd);
-                for(; itB < itEnd; ++itA, ++itB) {
-                    if (ordLess(*itA, *itB)) return true;
-                    if (ordLess(*itB, *itA)) return false;
-                }
-                // if qgram b is shorter or equal than a => a >= b
-                if (itB != itQEnd) return false;
-            }
-            if (seqNoA < seqNoB) return true;
-            if (seqNoA > seqNoB) return false;
-			return suffixLength(a, _stringSet) > suffixLength(b, _stringSet);
-		}
-	};
-
-
-    //////////////////////////////////////////////////////////////////////////////
-    // QGramLessNoCheck
-	//
-	// compare two q-grams of a given text (no check for q-grams smaller than q)
-    template < typename TSAValue, typename TText >
-	struct QGramLessNoCheck_ : 
-		public ::std::binary_function < TSAValue, TSAValue, bool >
-    {
-		typedef typename Iterator<TText, Standard>::Type TIter;
-		TIter _begin;
-		typename Size<TText>::Type _q;
-
-		template <typename TSize>
-		QGramLessNoCheck_(TText &text, TSize q): 
-			_begin(begin(text, Standard())),
-			_q(q) {}
-
-		// skip the first <offset> characters
-		template <typename TSize>
-		QGramLessNoCheck_(TText &text, TSize q, TSize offset): 
-			_begin(begin(text, Standard()) + offset),
-			_q(q) {}
-
-		inline bool operator() (TSAValue const a, TSAValue const b) const 
-		{
-			if (a == b) return false;
-			TIter itA = _begin + a;
-			TIter itB = _begin + b;
+template <typename TValue, typename TSpec>
+inline __int64 _fullDirLength(Shape<TValue, TSpec> const &shape)
+{
+    return _intPow((__int64)ValueSize<TValue>::VALUE, weight(shape)) + 1;
+}
 
-            TIter itEnd = itA + _q;
-            for(; itA != itEnd; ++itA, ++itB) {
+template <typename TValue, typename TSpec>
+inline __int64 _fullDir2Length(Shape<TValue, TSpec> const &shape)
+{
+    return (_intPow(
+                    (__int64)ValueSize<TValue>::VALUE,
+                    weight(shape) + 1) - 1)
+    / ((unsigned)ValueSize<TValue>::VALUE - 1) + 1;
+}
+
+template <typename TIndex>
+inline __int64 _fullDirLength(TIndex const &index)
+{
+    return _fullDirLength(indexShape(index));
+}
+
+template <typename TIndex>
+inline __int64 _fullDir2Length(TIndex const &index)
+{
+    return _fullDir2Length(indexShape(index));
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// QGramLess
+//
+// compare two q-grams of a given text (q-grams can be smaller than q)
+template < typename TSAValue, typename TText >
+struct QGramLess_ :
+public std::binary_function < TSAValue, TSAValue, bool >
+{
+    typedef typename Iterator<TText, Standard>::Type TIter;
+    TIter _begin, _end;
+    typename Size<TText>::Type _q;
+
+    template <typename TSize>
+    QGramLess_(TText &text, TSize q):
+    _begin(begin(text, Standard())),
+    _end(end(text, Standard())),
+    _q(q) {}
+
+    // skip the first <offset> characters
+    template <typename TSize1, typename TSize2>
+    QGramLess_(TText &text, TSize1 q, TSize2 offset):
+    _begin(begin(text, Standard()) + offset),
+    _end(end(text, Standard())),
+    _q(q) {}
+
+    inline bool operator() (TSAValue const a, TSAValue const b) const
+    {
+        if (a == b) return false;
+        TIter itA = _begin + a;
+        TIter itB = _begin + b;
+        if (a <= b) {
+            TIter itEnd = itB + _q;
+            if (itEnd > _end)
+                itEnd = _end;
+            for(; itB != itEnd; ++itB, ++itA) {
                 if (ordLess(*itA, *itB)) return true;
                 if (ordLess(*itB, *itA)) return false;
             }
-			return a < b;
-		}
-	};
-
-    template < typename TSAValue, typename TString, typename TSpec >
-	struct QGramLessNoCheck_<TSAValue, StringSet<TString, TSpec> const> : 
-		public ::std::binary_function < TSAValue, TSAValue, bool >
-    {
-		typedef typename Iterator<TString, Standard>::Type  TIter;
-        typedef StringSet<TString, TSpec>                   TStringSet;
-		TStringSet const &_stringSet;
-		typename Size<TString>::Type _q;
-
-		template <typename TSize>
-		QGramLessNoCheck_(StringSet<TString, TSpec> const &text, TSize q): 
-			_stringSet(text),
-			_q(q) {}
-
-		inline bool operator() (TSAValue const &a, TSAValue const &b) const 
-		{
-			if (a == b) return false;
-            
-            typename Size<TStringSet>::Type seqNoA = getSeqNo(a, stringSetLimits(_stringSet));
-            typename Size<TStringSet>::Type seqNoB = getSeqNo(b, stringSetLimits(_stringSet));
-            
-			TIter itA = begin(_stringSet[seqNoA], Standard()) + getSeqOffset(a, stringSetLimits(_stringSet));
-			TIter itB = begin(_stringSet[seqNoB], Standard()) + getSeqOffset(b, stringSetLimits(_stringSet));
-            
+            return false;
+        } else {
             TIter itEnd = itA + _q;
+            if (itEnd > _end)
+                itEnd = _end;
             for(; itA != itEnd; ++itA, ++itB) {
                 if (ordLess(*itA, *itB)) return true;
                 if (ordLess(*itB, *itA)) return false;
             }
-            if (seqNoA < seqNoB) return true;
-            if (seqNoA > seqNoB) return false;
-			return suffixLength(a, _stringSet) > suffixLength(b, _stringSet);
-		}
-	};
-
-
-    //////////////////////////////////////////////////////////////////////////////
-    // QGramLessNoCheckOffset_
-	//
-	// compare two q-grams of a given text and skip the first <offset> characters
-    template < typename TSAValue, typename TText >
-	struct QGramLessNoCheckOffset_: QGramLessNoCheck_<TSAValue, TText> 
-	{
-		template <typename TSize1, typename TSize2>
-		QGramLessNoCheckOffset_(TText &text, TSize1 q, TSize2 offset): 
-			QGramLessNoCheck_<TSAValue, TText> (text, q, offset) {}
-	};
-
-	template < typename TSAValue, typename TString, typename TSpec >
-	struct QGramLessNoCheckOffset_<TSAValue, StringSet<TString, TSpec> const> : 
-		public ::std::binary_function < TSAValue, TSAValue, bool >
-    {
-		typedef typename Iterator<TString, Standard>::Type TIter;
-		StringSet<TString, TSpec> const &_stringSet;
-		typename Size<TString>::Type _q, _offset;
-
-		template <typename TSize1, typename TSize2>
-		QGramLessNoCheckOffset_(StringSet<TString, TSpec> const &text, TSize1 q, TSize2 offset): 
-			_stringSet(text),
-			_q(q),
-			_offset(offset) {}
-
-		inline bool operator() (TSAValue const &a, TSAValue const &b) const 
-		{
-			if (a == b) return false;
-			TIter itA = begin(_stringSet[getValueI1(a)], Standard()) + getValueI2(a) + _offset;
-			TIter itB = begin(_stringSet[getValueI1(b)], Standard()) + getValueI2(b) + _offset;
-			if (a <= b) {
-				TIter itEnd = itB + _q;
-				for(; itB != itEnd; ++itB, ++itA) {
-					if (ordLess(*itA, *itB)) return true;
-					if (ordLess(*itB, *itA)) return false;
-				}
-				return false;
-			} else {
-				TIter itEnd = itA + _q;
-				for(; itA != itEnd; ++itA, ++itB) {
-					if (ordLess(*itA, *itB)) return true;
-					if (ordLess(*itB, *itA)) return false;
-				}
-				return true;
-			}
-		}
-	};
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Counting sort - little helpers
-	//
-	
-	// map hashes 1:1 to directory
-	template < typename THashValue, typename TParallelTag >
-	inline THashValue
-	requestBucket(Nothing &, THashValue hash, Tag<TParallelTag>)
-	{
-		return hash;
-	}
-
-	template < typename THashValue, typename TParallelTag >
-	inline THashValue
-	getBucket(Nothing const &, THashValue hash, Tag<TParallelTag>)
-	{
-		return hash;
-	}
-
-    // backward compatibility wrappers
-	template < typename TBucketMap, typename THashValue >
-	inline THashValue
-	requestBucket(TBucketMap &bucketMap, THashValue hash)
-	{
-		return requestBucket(bucketMap, hash, Serial());
-	}
-
-	template < typename TBucketMap, typename THashValue >
-	inline THashValue
-	getBucket(TBucketMap const &bucketMap, THashValue hash)
-	{
-		return getBucket(bucketMap, hash, Serial());
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Counting sort - Step 1: Clear directory
-	template < typename TDir, typename TParallelTag >
-	inline void
-	_qgramClearDir(TDir &dir, Nothing &, Tag<TParallelTag> parallelTag)
-	{
-		arrayFill(begin(dir, Standard()), end(dir, Standard()), 0, parallelTag);
-	}
-
-	template < typename TDir, typename TBucketMap >
-	inline void _qgramClearDir(TDir &dir, TBucketMap &bucketMap)
-    {
-        _qgramClearDir(dir, bucketMap, Serial());
+            return true;
+        }
     }
+};
 
+template < typename TSAValue, typename TString, typename TSpec >
+struct QGramLess_<TSAValue, StringSet<TString, TSpec> const> :
+public std::binary_function < TSAValue, TSAValue, bool >
+{
+    typedef typename Iterator<TString const, Standard>::Type TIter;
+    typedef typename Size<TString>::Type                     TSize;
+    typedef StringSet<TString, TSpec>                        TStringSet;
+    TStringSet const &_stringSet;
+    typename Size<TString>::Type _q;
+
+    template <typename TSize>
+    QGramLess_(StringSet<TString, TSpec> const &text, TSize q):
+    _stringSet(text),
+    _q(q) {}
+
+    inline bool operator() (TSAValue const &a, TSAValue const &b) const
+    {
+        if (a == b) return false;
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Counting sort - Step 2: Count q-grams
-	template < typename TDir, typename TBucketMap, typename TText, typename TShape, typename TStepSize >
-	inline void
-	_qgramCountQGrams(TDir &dir, TBucketMap &bucketMap, TText const &text, TShape shape, TStepSize stepSize)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type	TIterator;
-		typedef typename Value<TDir>::Type						TSize;
-
-		if (length(text) < length(shape) || empty(shape)) return;
-		TSize num_qgrams = (length(text) - length(shape)) / stepSize + 1;
-
-		TIterator itText = begin(text, Standard());
-		++dir[requestBucket(bucketMap, hash(shape, itText))];
-		if (stepSize == 1)
-			for(TSize i = 1; i < num_qgrams; ++i)
-			{
-				++itText;
-				++dir[requestBucket(bucketMap, hashNext(shape, itText))];
-			}
-		else
-			for(TSize i = 1; i < num_qgrams; ++i)
-			{
-				itText += stepSize;
-				++dir[requestBucket(bucketMap, hash(shape, itText))];
-			}
-	}
-
-	template < typename TDir, typename TBucketMap, typename TString, typename TSpec, typename TShape, typename TStepSize >
-	inline void
-	_qgramCountQGrams(TDir &dir, TBucketMap &bucketMap, StringSet<TString, TSpec> const &stringSet, TShape shape, TStepSize stepSize)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TString const, Standard>::Type	TIterator;
-		typedef typename Value<TDir>::Type							TSize;
-
-		if (empty(shape)) return;
-		
-		if (stepSize == 1)
-			for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-			{
-				TString const &sequence = value(stringSet, seqNo);
-				if (length(sequence) < length(shape)) continue;
-				TSize num_qgrams = length(sequence) - length(shape) + 1;
-
-				TIterator itText = begin(sequence, Standard());
-				++dir[requestBucket(bucketMap, hash(shape, itText))];
-				for(TSize i = 1; i < num_qgrams; ++i)
-				{
-					++itText;
-					++dir[requestBucket(bucketMap, hashNext(shape, itText))];
-				}
-			}
-		else
-			for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-			{
-				TString const &sequence = value(stringSet, seqNo);
-				if (length(sequence) < length(shape)) continue;
-				TSize num_qgrams = (length(sequence) - length(shape)) / stepSize + 1;
-
-				TIterator itText = begin(sequence, Standard());
-				for(TSize i = 0; i < num_qgrams; ++i)
-				{
-					++dir[requestBucket(bucketMap, hash(shape, itText))];
-					itText += stepSize;
-				}
-			}
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Counting sort - Step 3: Cumulative sum
-    //
-    // a disabled bucket 3,2,x,4   (x = disabled)               y_i=sum_{j<=i} x_j
-    // results in        0,0,3,x,5 (_qgramCummulativeSum)       z_i=y_{i-2}
-    // or in             0,3,5,5,9 (_qgramCummulativeSumAlt)    z_i=y_{i-1}
-
-    //    3 2 1 x x 5
-    // 0 0 3 5 x x 6 11
-    //   0 3 5 6 6 6 11
-
-	// First two entries are 0.
-	// Step 4 increments the entries hash(qgram)+1 on-the-fly while filling the SA table.
-	// After step 4 each entry (0..n-1) is the beginning of a qgram bucket.
-	template < typename TDir, typename TWithConstraints >
-	inline typename Value<TDir>::Type
-	_qgramCummulativeSum(TDir &dir, TWithConstraints)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TDir, Standard>::Type TDirIterator;
-		typedef typename Value<TDir>::Type              TSize;
-
-		TDirIterator it = begin(dir, Standard());
-		TDirIterator itEnd = end(dir, Standard());
-		TSize prevDiff = 0, prev2Diff = 0, sum = 0;
-		while (it != itEnd) 
-		{
-			if (TWithConstraints::VALUE && prevDiff == (TSize)-1)
-			{
-				sum += prev2Diff;
-				prev2Diff = 0;
-				prevDiff = *it;
-				*it = (TSize)-1;								// disable bucket
-			} else {
-				sum += prev2Diff;
-				prev2Diff = prevDiff;
-				prevDiff = *it;
-				*it = sum;
-			}
-			++it;
-		}
-		return sum + prev2Diff;
-	}
-
-	// The first entry is 0.
-	// This function is used when Steps 4 and 5 (fill SA, correct disabled buckets) are ommited.
-	template < typename TDir, typename TWithConstraints >
-	inline typename Value<TDir>::Type
-	_qgramCummulativeSumAlt(TDir &dir, TWithConstraints const)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TDir, Standard>::Type TDirIterator;
-		typedef typename Value<TDir>::Type              TSize;
-
-		TDirIterator it = begin(dir, Standard());
-		TDirIterator itEnd = end(dir, Standard());
-		TSize prevDiff = 0, sum = 0;
-		for (; it != itEnd; ++it)
-		{
-			if (!TWithConstraints::VALUE || prevDiff != (TSize)-1)
-            {
-                sum += prevDiff;
-                prevDiff = *it;
-                *it = sum;
+        typename Size<TStringSet>::Type seqNoA = getSeqNo(a, stringSetLimits(_stringSet));
+        typename Size<TStringSet>::Type seqNoB = getSeqNo(b, stringSetLimits(_stringSet));
+        TIter itA = begin(_stringSet[seqNoA], Standard()) + getSeqOffset(a, stringSetLimits(_stringSet));
+        TIter itB = begin(_stringSet[seqNoB], Standard()) + getSeqOffset(b, stringSetLimits(_stringSet));
+        TIter itAEnd = end(_stringSet[seqNoA], Standard());
+        TIter itBEnd = end(_stringSet[seqNoB], Standard());
+
+        if (itAEnd - itA < itBEnd - itB)
+        {
+            TIter itQEnd = itA + _q;
+            TIter itEnd = _min(itQEnd, itAEnd);
+            for(; itA < itEnd; ++itA, ++itB) {
+                if (ordLess(*itA, *itB)) return true;
+                if (ordLess(*itB, *itA)) return false;
             }
-            else
-            {
-                prevDiff = *it; 
-                *it = (TSize)-1;    // disable bucket
+            // if qgram a is shorter than b => a < b
+            if (itA != itQEnd) return true;
+        }
+        else
+        {
+            TIter itQEnd = itB + _q;
+            TIter itEnd = _min(itQEnd, itBEnd);
+            for(; itB < itEnd; ++itA, ++itB) {
+                if (ordLess(*itA, *itB)) return true;
+                if (ordLess(*itB, *itA)) return false;
             }
-		}
-		return sum + prevDiff;
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Counting sort - Step 4: Fill suffix array
-	// w/o constraints
-	template <
-		typename TSA,
-		typename TText, 
-		typename TShape, 
-		typename TDir, 
-		typename TBucketMap, 
-		typename TWithConstraints, 
-		typename TStepSize >
-	inline void
-	_qgramFillSuffixArray(
-		TSA &sa, 
-		TText const &text, 
-		TShape shape, 
-		TDir &dir, 
-		TBucketMap &bucketMap, 
-		TStepSize stepSize,
-		TWithConstraints const)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type	TIterator;
-		typedef typename Value<TDir>::Type						TSize;
-
-		if (empty(shape) || length(text) < length(shape)) return;
-
-		TSize num_qgrams = length(text) - length(shape) + 1;
-		TIterator itText = begin(text, Standard());
-
-		if (TWithConstraints::VALUE) {
-			TSize bktNo = getBucket(bucketMap, hash(shape, itText)) + 1;			// first hash
-			if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = 0;						// if bucket is enabled
-		} else
-			sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = 0;			// first hash
-
-		if (stepSize == 1)
-			for(TSize i = 1; i < num_qgrams; ++i)
-			{
-				++itText;
-				if (TWithConstraints::VALUE) {
-					TSize bktNo = getBucket(bucketMap, hashNext(shape, itText)) + 1;	// next hash
-					if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = i;					// if bucket is enabled
-				} else
-					sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = i;	// next hash
-			}
-		else
-			for(TSize i = stepSize; i < num_qgrams; i += stepSize)
-			{
-				itText += stepSize;
-				if (TWithConstraints::VALUE) {
-					TSize bktNo = getBucket(bucketMap, hash(shape, itText)) + 1;		// next hash (we mustn't use hashNext here)
-					if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = i;					// if bucket is enabled
-				} else
-					sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = i;		// next hash
-			}
-	}
-
-	// multiple sequences
-	template <
-		typename TSA, 
-		typename TString, 
-		typename TSpec, 
-		typename TShape, 
-		typename TDir,
-		typename TBucketMap,
-		typename TStepSize,
-		typename TWithConstraints >
-	inline void
-	_qgramFillSuffixArray(
-		TSA &sa, 
-		StringSet<TString, TSpec> const &stringSet,
-		TShape shape, 
-		TDir &dir,
-		TBucketMap &bucketMap,
-		TStepSize stepSize,
-		TWithConstraints const)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TString const, Standard>::Type	TIterator;
-		typedef typename Value<TDir>::Type							TSize;
-
-		if (empty(shape)) return;
-
-		if (stepSize == 1)
-			for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-			{
-				TString const &sequence = value(stringSet, seqNo);
-				if (length(sequence) < length(shape)) continue;
-				TSize num_qgrams = length(sequence) - length(shape) + 1;
-
-				typename Value<TSA>::Type localPos;
-				assignValueI1(localPos, seqNo);
-				assignValueI2(localPos, 0);
-
-				TIterator itText = begin(sequence, Standard());
-				if (TWithConstraints::VALUE) {
-					TSize bktNo = getBucket(bucketMap, hash(shape, itText)) + 1;					// first hash
-					if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos;						// if bucket is enabled
-				} else
-					sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos;			// first hash
-
-				for(TSize i = 1; i < num_qgrams; ++i)
-				{
-					++itText;
-					assignValueI2(localPos, i);
-					if (TWithConstraints::VALUE) {
-						TSize bktNo = getBucket(bucketMap, hashNext(shape, itText)) + 1;			// next hash
-						if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos;					// if bucket is enabled
-					} else
-						sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos;	// next hash
-				}
-			}
-		else
-			for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-			{
-				TString const &sequence = value(stringSet, seqNo);
-				if (length(sequence) < length(shape)) continue;
-				TSize num_qgrams = length(sequence) - length(shape) + 1;
-
-				typename Value<TSA>::Type localPos;
-				assignValueI1(localPos, seqNo);
-				assignValueI2(localPos, 0);
-
-				TIterator itText = begin(sequence, Standard());
-				for(TSize i = 0; i < num_qgrams; i += stepSize)
-				{
-					assignValueI2(localPos, i);
-					if (TWithConstraints::VALUE) {
-						TSize bktNo = getBucket(bucketMap, hash(shape, itText)) + 1;				// hash
-						if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos;					// if bucket is enabled
-					} else
-						sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos;		// hash
-					itText += stepSize;
-				}
-			}
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Step 5: Correct disabled buckets
-	template < typename TDir >
-	inline void
-	_qgramPostprocessBuckets(TDir &dir)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TDir, Standard>::Type			TDirIterator;
-		typedef typename Value<TDir>::Type						TSize;
-
-		TDirIterator it = begin(dir, Standard());
-		TDirIterator itEnd = end(dir, Standard());
-		TSize prev = 0;
-		for (; it != itEnd; ++it) 
-			if (*it == (TSize)-1)   // end positions
-				*it = prev;
-			else
-				prev = *it;
-	}
+            // if qgram b is shorter or equal than a => a >= b
+            if (itB != itQEnd) return false;
+        }
+        if (seqNoA < seqNoB) return true;
+        if (seqNoA > seqNoB) return false;
+        return suffixLength(a, _stringSet) > suffixLength(b, _stringSet);
+    }
+};
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.createQGramIndex:
-..summary:Builds a q-gram index on a sequence. 
-..cat:Index
-..signature:createQGramIndex(index)
-..signature:createQGramIndex(sa, dir, bucketMap, text, shape, stepSize) [DEPRECATED]
-..class:Spec.IndexQGram
-..param.index:The q-gram index.
-...type:Spec.IndexQGram
-..param.sa:The resulting list in which all q-grams are sorted alphabetically.
-..param.dir:The resulting array that indicates at which position in index the corresponding q-grams can be found.
-..param.bucketMap:Stores the q-gram hashes for the openaddressing hash maps, see @Function.indexBucketMap@.
-If bucketMap is of the type @Tag.Nothing@ the q-gram hash determines the bucket address in the index.
-..param.text:The sequence.
-..param.shape:The shape to be used.
-...type:Class.Shape
-..param.stepSize:Store every $stepSize$'th q-gram in the index.
-..returns:Index contains the sorted list of qgrams. For each q-gram $dir$ contains the first position in index that corresponds to this q-gram.
-..remarks:This function should not be called directly. Please use @Function.indexCreate@ or @Function.indexRequire@.
-The resulting tables must have appropriate size before calling this function.
-..include:seqan/index.h
-*/
-/*!
- * @fn IndexQGram#createQGramIndex
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Builds a q-gram index on a sequence.
- * 
- * @signature createQGramIndex(index)
- * @signature createQGramIndex(sa, dir, bucketMap, text, shape, stepSize)
- *            [DEPRECATED]
- * 
- * @param index The q-gram index. Types: @link IndexQGram @endlink
- * @param stepSize Store every <tt>stepSize</tt>'th q-gram in the index.
- * @param text The sequence.
- * @param bucketMap Stores the q-gram hashes for the openaddressing hash maps,
- *                  see @link IndexQGram#indexBucketMap @endlink. If bucketMap is of the
- *                  type @link Nothing @endlink the q-gram hash determines the
- *                  bucket address in the index.
- * @param shape The shape to be used. Types: @link Shape @endlink
- * @param sa The resulting list in which all q-grams are sorted alphabetically.
- * @param dir The resulting array that indicates at which position in index the
- *            corresponding q-grams can be found.
- * 
- * @return TReturn Index contains the sorted list of qgrams. For each q-gram
- *                 <tt>dir</tt> contains the first position in index that
- *                 corresponds to this q-gram.
- * 
- * @section Remarks
- * 
- * This function should not be called directly. Please use @link Index#indexCreate
- * @endlink or @link Index#indexRequire @endlink. The resulting tables must have
- * appropriate size before calling this function.
- */
-	template < typename TIndex >
-	inline bool _qgramDisableBuckets(TIndex &)
-	{
-		return false;	// we disable no buckets by default
-	}
-
-	template < typename TIndex >
-	void createQGramIndex(TIndex &index)
-	{
-	SEQAN_CHECKPOINT
-		typename Fibre<TIndex, QGramText>::Type const &text      = indexText(index);
-		typename Fibre<TIndex, QGramSA>::Type         &sa        = indexSA(index);
-		typename Fibre<TIndex, QGramDir>::Type        &dir       = indexDir(index);
-		typename Fibre<TIndex, QGramShape>::Type      &shape     = indexShape(index);
-		typename Fibre<TIndex, QGramBucketMap>::Type  &bucketMap = index.bucketMap;
-		
-		// 1. clear counters
-		_qgramClearDir(dir, bucketMap);
-
-		// 2. count q-grams
-		_qgramCountQGrams(dir, bucketMap, text, shape, getStepSize(index));
-
-		if (_qgramDisableBuckets(index))
-		{
-			// 3. cumulative sum
-			_qgramCummulativeSum(dir, True());
-			
-			// 4. fill suffix array
-			_qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True());
-
-			// 5. correct disabled buckets
-			_qgramPostprocessBuckets(dir);
-		}
-		else
-		{
-			// 3. cumulative sum
-			_qgramCummulativeSum(dir, False());
-			
-			// 4. fill suffix array
-			_qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False());
-		} 
-	}
-
-	// DEPRECATED
-	// better use createQGramIndex(index) (above)
-	template <
-        typename TSA,
-		typename TDir,
-		typename TBucketMap,
-		typename TText,
-		typename TShape,
-		typename TStepSize >
-	void createQGramIndex(
-		TSA &sa,
-		TDir &dir,
-		TBucketMap &bucketMap,
-		TText const &text,
-		TShape &shape,
-		TStepSize stepSize)	
-	{
-	SEQAN_CHECKPOINT
-		
-		// 1. clear counters
-		_qgramClearDir(dir, bucketMap);
-
-		// 2. count q-grams
-		_qgramCountQGrams(dir, bucketMap, text, shape, stepSize);
-
-		// 3. cumulative sum
-        __int64 res = _qgramCummulativeSum(dir, False());
-        SEQAN_ASSERT_EQ(res, static_cast<__int64>(length(sa)));
-        ignoreUnusedVariableWarning(res);
-
-		// 4. fill suffix array
-		_qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False());
-	}
-
-	// DEPRECATED
-	// better use createQGramIndex(index) (above)
-	template <
-        typename TSA,
-		typename TDir,
-		typename TBucketMap,
-		typename TText,
-		typename TShape,
-		typename TStepSize >
-	void createQGramIndex(
-		TSA &sa,
-		TDir &dir,
-		TBucketMap &bucketMap,
-		TText const &text,
-		TShape &shape)	
-	{
-		createQGramIndex(sa, dir, bucketMap, text, shape, 1);
-	}
+// QGramLessOffset
+//
+// compare two q-grams of a given text and skip the first <offset> characters
+template < typename TSAValue, typename TText >
+struct QGramLessOffset_ :
+QGramLess_<TSAValue, TText>
+{
+    template <typename TSize1, typename TSize2>
+    QGramLessOffset_(TText &text, TSize1 q, TSize2 offset):
+    QGramLess_<TSAValue, TText> (text, q, offset) {}
+};
+
+template < typename TSAValue, typename TString, typename TSpec >
+struct QGramLessOffset_<TSAValue, StringSet<TString, TSpec> const> :
+public std::binary_function < TSAValue, TSAValue, bool >
+{
+    typedef typename Iterator<TString const, Standard>::Type TIter;
+    typedef typename Size<TString>::Type                     TSize;
+    typedef StringSet<TString, TSpec>                        TStringSet;
+    typedef typename StringSetLimits<TStringSet>::Type       TLimits;
+
+    TStringSet const &_stringSet;
+    TLimits const &limits;
+    TSize _q, _offset;
+
+    template <typename TSize1, typename TSize2>
+    QGramLessOffset_(StringSet<TString, TSpec> const &text, TSize1 q, TSize2 offset):
+    _stringSet(text),
+    limits(stringSetLimits(text)),
+    _q(q),
+    _offset(offset) {}
+
+    inline bool operator() (TSAValue const &a, TSAValue const &b) const
+    {
+        if (a == b) return false;
 
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Function.createQGramIndexSAOnly:
-..summary:Builds the suffix array of a q-gram index on a sequence. 
-..cat:Index
-..signature:createQGramIndexSAOnly(sa, text, shape, stepSize)
-..class:Spec.IndexQGram
-..param.sa:The resulting list in which all q-grams are sorted alphabetically.
-..param.text:The sequence.
-..param.shape:The shape to be used. q is the length of this shape
-...type:Class.Shape
-..param.stepSize:Store every $stepSize$'th q-gram in the index.
-..remarks:This function should not be called directly. Please use @Function.indexCreate@ or @Function.indexRequire@.
-The resulting tables must have appropriate size before calling this function.
-..include:seqan/index.h
-*/
-/*!
- * @fn IndexQGram#createQGramIndexSAOnly
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Builds the suffix array of a q-gram index on a sequence.
- * 
- * @signature createQGramIndexSAOnly(sa, text, shape, stepSize)
- * 
- * @param stepSize Store every <tt>stepSize</tt>'th q-gram in the index.
- * @param sa The resulting list in which all q-grams are sorted alphabetically.
- * @param shape The shape to be used. q is the length of this shape Types: @link Shape @endlink
- * @param text The sequence.
- * 
- * @section Remarks
- * 
- * This function should not be called directly. Please use @link Index#indexCreate
- * @endlink or @link Index#indexRequire @endlink. The resulting tables must have
- * appropriate size before calling this function.
- */
-	template < 
-		typename TSA, 
-		typename TText,
-		typename TShape,
-		typename TStepSize >
-	void createQGramIndexSAOnly(
-		TSA &sa,
-		TText const &text,
-		TShape &shape,
-		TStepSize stepSize)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Size<TSA>::Type TSize;
-		typedef typename Iterator<TSA, Standard>::Type TIter;
-
-		// 1. Fill suffix array with a permutation (the identity)
-		TIter it = begin(sa, Standard());
-		TIter itEnd = end(sa, Standard());
-		TSize i = 0;
-		for(; it != itEnd; ++it, i += stepSize)
-			*it = i;
-
-		// 2. Sort suffix array with quicksort
-		TSize span = length(shape);
-		if (i + span > length(text) + 1)
-			::std::sort(
-				begin(sa, Standard()), 
-				end(sa, Standard()), 
-				QGramLess_<typename Value<TSA>::Type, TText const>(text, span));
-		else
-			::std::sort(
-				begin(sa, Standard()), 
-				end(sa, Standard()), 
-				QGramLessNoCheck_<typename Value<TSA>::Type, TText const>(text, span));
-	}
-
-	template < 
-		typename TSA, 
-		typename TString,
-		typename TSpec,
-		typename TShape,
-		typename TStepSize >
-	void createQGramIndexSAOnly(
-		TSA &sa,
-		StringSet<TString, TSpec> const &stringSet,
-		TShape &shape,
-		TStepSize stepSize)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TSA, Standard>::Type	TIter;
-		typedef typename Value<TSA>::Type				TValue;
-		typedef typename Size<TString>::Type			TSize;
-		typedef StringSet<TString, TSpec>				TStringSet;
-		
-		// 1. Fill suffix array with a permutation (the identity)
-		TIter it = begin(sa, Standard());
-		TValue pair;
-		unsigned int const q1 = length(shape) - 1;
-		for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-		{
-			unsigned int const strlen = length(stringSet[seqNo]);
-			if (strlen > q1) {
-				assignValueI1(pair, seqNo);
-				for (TSize i = 0; i < strlen - q1; ++it, i += stepSize) {
-					assignValueI2(pair, i);
-					*it = pair;
-				}
-			}
-		}
-        SEQAN_ASSERT_EQ(it, end(sa, Standard()));
-
-		// 2. Sort suffix array with quicksort
-		TSize q = length(shape);
-		if (lengthSum(stringSet) == length(sa))
-			::std::sort(
-				begin(sa, Standard()), 
-				end(sa, Standard()), 
-				QGramLess_<typename Value<TSA>::Type, TStringSet const>(stringSet, q));
-		else
-			::std::sort(
-				begin(sa, Standard()), 
-				end(sa, Standard()), 
-				QGramLessNoCheck_<typename Value<TSA>::Type, TStringSet const>(stringSet, q));
-	}
-
-	template < 
-		typename TSA, 
-		typename TText,
-		typename TSize1,
-		typename TSize2 >
-	inline void
-    _refineQGramIndexBucket(
-		TSA &sa,
-		TText const &text,
-		TSize1 oldQ,
-		TSize2 newQ)
-	{
-	SEQAN_CHECKPOINT
-        if (length(sa) <= 1)
-            return;
-
-        ::std::sort(
-            begin(sa, Standard()), 
-            end(sa, Standard()),
-            QGramLessOffset_<typename Value<TSA>::Type, TText const>(text, newQ - oldQ, oldQ));
-	}
-
-	template <
-		typename TSA,
-		typename TDir,
-		typename TText,
-		typename TSize1,
-		typename TSize2 >
-	inline void _refineQGramIndex(
-		TSA &sa,
-		TDir const &dir,
-		TText const &text,
-		TSize1 oldQ,
-		TSize2 newQ)
-	{
-		//typedef typename Size<TSA>::Type                        TSize;
-		typedef typename Iterator<TSA, Standard>::Type          TIter;
-		typedef typename Iterator<TDir const, Standard>::Type   TDirIter;
-
-		if (newQ <= (TSize2)oldQ) return;
-
-		if (length(dir) < 2) {
-			::std::sort(
-				begin(sa, Standard()),
-				end(sa, Standard()),
-				QGramLess_<typename Value<TSA>::Type, TText const>(text, newQ));
-			return;
-		}
-
-		// 1. Sort each bucket with quicksort and compare substrings s[i+oldQ..i+newQ)
-		TDirIter dirIt = begin(dir, Standard());
-		TDirIter dirItEnd = end(dir, Standard());
-		TIter itBegin = begin(sa, Standard());
-		TIter itBktBegin = itBegin + *dirIt;
-		TIter itBktEnd;
-		++dirIt;
-		for(; dirIt != dirItEnd; ++dirIt, itBktBegin = itBktEnd) {
-			itBktEnd = itBegin + *dirIt;
-			if (itBktEnd - itBktBegin < 2) continue;
-			::std::sort(
-				itBktBegin,
-				itBktEnd,
-				QGramLessOffset_<typename Value<TSA>::Type, TText const>(text, newQ - oldQ, oldQ));
-		}
-	}
+        typename Size<TStringSet const>::Type seqNoA = getSeqNo(a, limits);
+        typename Size<TStringSet const>::Type seqNoB = getSeqNo(b, limits);
+
+        TIter itA    = begin(_stringSet[seqNoA], Standard()) + getSeqOffset(a, limits);
+        TIter itAEnd =   end(_stringSet[seqNoA], Standard());
+        TIter itB    = begin(_stringSet[seqNoB], Standard()) + getSeqOffset(b, limits);
+        TIter itBEnd =   end(_stringSet[seqNoB], Standard());
+
+        if (itAEnd - itA < itBEnd - itB)
+        {
+            itA += _offset;
+            itB += _offset;
+            TIter itQEnd = itA + _q;
+            TIter itEnd = _min(itQEnd, itAEnd);
+            for(; itA < itEnd; ++itA, ++itB) {
+                if (ordLess(*itA, *itB)) return true;
+                if (ordLess(*itB, *itA)) return false;
+            }
+            // if qgram a is shorter than b => a < b
+            if (itA != itQEnd) return true;
+        }
+        else
+        {
+            itA += _offset;
+            itB += _offset;
+            TIter itQEnd = itB + _q;
+            TIter itEnd = _min(itQEnd, itBEnd);
+            for(; itB < itEnd; ++itA, ++itB) {
+                if (ordLess(*itA, *itB)) return true;
+                if (ordLess(*itB, *itA)) return false;
+            }
+            // if qgram b is shorter or equal than a => a >= b
+            if (itB != itQEnd) return false;
+        }
+        if (seqNoA < seqNoB) return true;
+        if (seqNoA > seqNoB) return false;
+        return suffixLength(a, _stringSet) > suffixLength(b, _stringSet);
+    }
+};
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.createQGramIndexDirOnly:
-..summary:Builds the directory of a q-gram index on a sequence. 
-..cat:Index
-..signature:createQGramIndexDirOnly(dir, bucketMap, text, shape, stepSize)
-..class:Spec.IndexQGram
-..param.dir:The resulting array that indicates at which position in index the corresponding q-grams can be found.
-..param.bucketMap:Stores the q-gram hashes for the openaddressing hash maps, see @Function.indexBucketMap@.
-If bucketMap is of the type @Tag.Nothing@ the q-gram hash determines the bucket address in the index.
-..param.text:The sequence.
-..param.shape:The shape to be used.
-...type:Class.Shape
-..param.stepSize:Store every $stepSize$'th q-gram in the index.
-..returns:Index contains the sorted list of qgrams. For each possible q-gram pos contains the first position in index that corresponds to this q-gram. 
-..remarks:This function should not be called directly. Please use @Function.indexCreate@ or @Function.indexRequire@.
-The resulting tables must have appropriate size before calling this function.
-..include:seqan/index.h
-*/
-/*!
- * @fn IndexQGram#createQGramIndexDirOnly
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Builds the directory of a q-gram index on a sequence.
- * 
- * @signature createQGramIndexDirOnly(dir, bucketMap, text, shape, stepSize)
- * 
- * @param bucketMap Stores the q-gram hashes for the openaddressing hash maps,
- *                  see @link IndexQGram#indexBucketMap @endlink. If bucketMap is of the
- *                  type @link Nothing @endlink the q-gram hash determines the
- *                  bucket address in the index.
- * @param shape The shape to be used. Types: @link Shape @endlink
- * @param text The sequence.
- * @param dir The resulting array that indicates at which position in index the
- *            corresponding q-grams can be found.
- * @param stepSize Store every <tt>stepSize</tt>'th q-gram in the index.
- * 
- * @return TReturn Index contains the sorted list of qgrams. For each possible
- *                 q-gram pos contains the first position in index that
- *                 corresponds to this q-gram.
- * 
- * @section Remarks
- * 
- * This function should not be called directly. Please use @link Index#indexCreate
- * @endlink or @link Index#indexRequire @endlink. The resulting tables must have
- * appropriate size before calling this function.
- */
+// QGramLessNoCheck
+//
+// compare two q-grams of a given text (no check for q-grams smaller than q)
+template < typename TSAValue, typename TText >
+struct QGramLessNoCheck_ :
+public std::binary_function < TSAValue, TSAValue, bool >
+{
+    typedef typename Iterator<TText, Standard>::Type TIter;
+    TIter _begin;
+    typename Size<TText>::Type _q;
+
+    template <typename TSize>
+    QGramLessNoCheck_(TText &text, TSize q):
+    _begin(begin(text, Standard())),
+    _q(q) {}
+
+    // skip the first <offset> characters
+    template <typename TSize>
+    QGramLessNoCheck_(TText &text, TSize q, TSize offset):
+    _begin(begin(text, Standard()) + offset),
+    _q(q) {}
+
+    inline bool operator() (TSAValue const a, TSAValue const b) const
+    {
+        if (a == b) return false;
+        TIter itA = _begin + a;
+        TIter itB = _begin + b;
+
+        TIter itEnd = itA + _q;
+        for(; itA != itEnd; ++itA, ++itB) {
+            if (ordLess(*itA, *itB)) return true;
+            if (ordLess(*itB, *itA)) return false;
+        }
+        return a < b;
+    }
+};
 
-	template <
-		typename TDir,
-		typename TBucketMap,
-		typename TText,
-		typename TShape,
-		typename TStepSize >
-	void createQGramIndexDirOnly(
-		TDir &dir,
-		TBucketMap &bucketMap,
-		TText const &text,
-		TShape &shape,
-		TStepSize stepSize)
-	{
-	SEQAN_CHECKPOINT
+template < typename TSAValue, typename TString, typename TSpec >
+struct QGramLessNoCheck_<TSAValue, StringSet<TString, TSpec> const> :
+public std::binary_function < TSAValue, TSAValue, bool >
+{
+    typedef typename Iterator<TString, Standard>::Type  TIter;
+    typedef StringSet<TString, TSpec>                   TStringSet;
+    TStringSet const &_stringSet;
+    typename Size<TString>::Type _q;
 
-		// 1. clear counters
-		_qgramClearDir(dir, bucketMap);
+    template <typename TSize>
+    QGramLessNoCheck_(StringSet<TString, TSpec> const &text, TSize q):
+    _stringSet(text),
+    _q(q) {}
 
-		// 2. count q-grams
-		_qgramCountQGrams(dir, bucketMap, text, shape, stepSize);
+    inline bool operator() (TSAValue const &a, TSAValue const &b) const
+    {
+        if (a == b) return false;
 
-		// 3. cumulative sum (Step 4 is ommited)
-		_qgramCummulativeSumAlt(dir, False());
-	}
+        typename Size<TStringSet>::Type seqNoA = getSeqNo(a, stringSetLimits(_stringSet));
+        typename Size<TStringSet>::Type seqNoB = getSeqNo(b, stringSetLimits(_stringSet));
 
+        TIter itA = begin(_stringSet[seqNoA], Standard()) + getSeqOffset(a, stringSetLimits(_stringSet));
+        TIter itB = begin(_stringSet[seqNoB], Standard()) + getSeqOffset(b, stringSetLimits(_stringSet));
 
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Function.createCountArray:
-..summary:Builds an index on a StringSet storing how often a q-gram occurs in each sequence.
-..cat:Index
-..signature:createCountsArray(counts, dir, bucketMap, stringSet, shape, stepSize)
-..param.counts:The resulting list of pairs (seqNo,count).
-..param.dir:The resulting array that indicates at which position in the count table the corresponding a certain q-gram can be found.
-..param.bucketMap:Stores the q-gram hashes for the openaddressing hash maps, see @Function.indexBucketMap@.
-If bucketMap is of the type @Tag.Nothing@ the q-gram hash determines the bucket address in the index.
-..param.stringSet:The StringSet.
-...type:Class.StringSet
-..param.shape:The shape to be used.
-...type:Class.Shape
-..param.stepSize:Store every $stepSize$'th q-gram in the index.
-..remarks:This function should not be called directly. Please use @Function.indexCreate@ or @Function.indexRequire@.
-The resulting tables must have appropriate size before calling this function.
-..include:seqan/index.h
-*/
-/*!
- * @fn IndexQGram#createCountArray
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Builds an index on a StringSet storing how often a q-gram occurs in
- *        each sequence.
- * 
- * @signature createCountsArray(counts, dir, bucketMap, stringSet, shape,
- *            stepSize)
- * 
- * @param stepSize Store every <tt>stepSize</tt>'th q-gram in the index.
- * @param bucketMap Stores the q-gram hashes for the openaddressing hash maps,
- *                  see @link IndexQGram#indexBucketMap @endlink. If bucketMap is of the
- *                  type @link Nothing @endlink the q-gram hash determines the
- *                  bucket address in the index.
- * @param shape The shape to be used. Types: @link Shape @endlink
- * @param counts The resulting list of pairs (seqNo,count).
- * @param stringSet The StringSet. Types: @link StringSet @endlink
- * @param dir The resulting array that indicates at which position in the count
- *            table the corresponding a certain q-gram can be found.
- * 
- * @section Remarks
- * 
- * This function should not be called directly. Please use @link Index#indexCreate
- * @endlink or @link Index#indexRequire @endlink. The resulting tables must have
- * appropriate size before calling this function.
- */
-	template < 
-		typename TCounts, 
-		typename TDir,
-		typename TBucketMap,
-		typename TString,
-		typename TSpec,
-		typename TShape,
-		typename TStepSize >
-	void createCountsArray(
-		TCounts &counts,
-		TDir &dir,
-		TBucketMap &bucketMap,
-		StringSet<TString, TSpec> const &stringSet,
-		TShape shape,
-		TStepSize stepSize)
-	{
-		typedef typename Iterator<TString const, Standard>::Type	TIterator;
-		//typedef typename Iterator<TDir, Standard>::Type				TDirIterator;
-		typedef typename Value<TShape>::Type						TValue;
-		typedef typename Size<TString>::Type						TSize;
-
-		TDir lastSeqSeen;
-		resize(lastSeqSeen, length(dir), Exact());
-		
-		// 1. clear counters
-		_qgramClearDir(dir, bucketMap);
-		if (empty(shape))
-		{
-			clear(counts);
-			return;
-		}
-		arrayFill(begin(lastSeqSeen, Standard()), end(lastSeqSeen, Standard()), -1);
-		
-		// 2. count distinct sequences for each q-gram
-		for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-		{
-			TString const &sequence = value(stringSet, seqNo);
-			if (length(sequence) < length(shape)) continue;
-			TSize num_qgrams = (length(sequence) - length(shape)) / stepSize + 1;
-
-			TIterator itText = begin(sequence, Standard());
-			TValue bktNo = requestBucket(bucketMap, hash(shape, itText));
-			lastSeqSeen[bktNo] = seqNo;
-			++dir[bktNo];
-			if (stepSize == 1)
-				for(TSize i = 1; i < num_qgrams; ++i)
-				{
-					++itText;
-					bktNo = requestBucket(bucketMap, hashNext(shape, itText));
-					if (seqNo != lastSeqSeen[bktNo]) {
-						lastSeqSeen[bktNo] = seqNo;
-						++dir[bktNo];
-					}
-				}
-			else
-				for(TSize i = 1; i < num_qgrams; ++i)
-				{
-					itText += stepSize;
-					bktNo = requestBucket(bucketMap, hash(shape, itText));
-					if (seqNo != lastSeqSeen[bktNo]) {
-						lastSeqSeen[bktNo] = seqNo;
-						++dir[bktNo];
-					}
-				}
-		}
-
-		// 3. cumulative sum
-		resize(counts, _qgramCummulativeSum(dir, False()), Exact());
-
-		// 4. fill count array
-		arrayFill(begin(lastSeqSeen, Standard()), end(lastSeqSeen, Standard()), -1);
-		for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-		{
-			TString const &sequence = value(stringSet, seqNo);
-			if (length(sequence) < length(shape)) continue;
-			TSize num_qgrams = (length(sequence) - length(shape)) / stepSize + 1;
-
-			TIterator itText = begin(sequence, Standard());
-			TValue bktNo = getBucket(bucketMap, hash(shape, itText));
-			lastSeqSeen[bktNo] = seqNo;
-			TSize pos = dir[bktNo + 1]++;
-			counts[pos].i1 = seqNo;				// first hash
-			counts[pos].i2 = 1;
-
-			if (stepSize == 1)
-				for(TSize i = 1; i < num_qgrams; ++i)
-				{
-					++itText;
-					bktNo = getBucket(bucketMap, hashNext(shape, itText));
-					if (seqNo == lastSeqSeen[bktNo])
-						++(counts[dir[bktNo + 1] - 1].i2);
-					else {
-						lastSeqSeen[bktNo] = seqNo;
-						pos = dir[bktNo + 1]++;
-						counts[pos].i1 = seqNo;				// next hash
-						counts[pos].i2 = 1;
-					}
-				}
-			else
-				for(TSize i = 1; i < num_qgrams; ++i)
-				{
-					itText += stepSize;
-					bktNo = getBucket(bucketMap, hash(shape, itText));
-					if (seqNo == lastSeqSeen[bktNo])
-						++(counts[dir[bktNo + 1] - 1].i2);
-					else {
-						lastSeqSeen[bktNo] = seqNo;
-						pos = dir[bktNo + 1]++;
-						counts[pos].i1 = seqNo;				// next hash
-						counts[pos].i2 = 1;
-					}
-				}
-		}
-	}
+        TIter itEnd = itA + _q;
+        for(; itA != itEnd; ++itA, ++itB) {
+            if (ordLess(*itA, *itB)) return true;
+            if (ordLess(*itB, *itA)) return false;
+        }
+        if (seqNoA < seqNoB) return true;
+        if (seqNoA > seqNoB) return false;
+        return suffixLength(a, _stringSet) > suffixLength(b, _stringSet);
+    }
+};
 
 
 //////////////////////////////////////////////////////////////////////////////
-// create q-gram index of *one* sequence in external memory 
+// QGramLessNoCheckOffset_
+//
+// compare two q-grams of a given text and skip the first <offset> characters
+template < typename TSAValue, typename TText >
+struct QGramLessNoCheckOffset_: QGramLessNoCheck_<TSAValue, TText>
+{
+    template <typename TSize1, typename TSize2>
+    QGramLessNoCheckOffset_(TText &text, TSize1 q, TSize2 offset):
+    QGramLessNoCheck_<TSAValue, TText> (text, q, offset) {}
+};
+
+template < typename TSAValue, typename TString, typename TSpec >
+struct QGramLessNoCheckOffset_<TSAValue, StringSet<TString, TSpec> const> :
+public std::binary_function < TSAValue, TSAValue, bool >
+{
+    typedef typename Iterator<TString, Standard>::Type TIter;
+    StringSet<TString, TSpec> const &_stringSet;
+    typename Size<TString>::Type _q, _offset;
 
-	// *** COMPARATORS & MAPS ***
-        
-    template <typename InType, typename Result = int>
-    struct _qgramComp : public ::std::binary_function<InType,InType,Result> {
-        inline Result operator()(InType const &a, InType const &b) const
-        {
-			typedef typename Value<InType, 2>::Type TQGram;
-			typename Value<TQGram>::Type const *sa = a.i2.i;
-            typename Value<TQGram>::Type const *sb = b.i2.i;
-			typename Value<TQGram>::Type const *saEnd = sa + length(a.i2);
-
-            for(; sa != saEnd; ++sa, ++sb) {
-                if (*sa == *sb) continue;
-                return (*sa < *sb)? -1 : 1;
+    template <typename TSize1, typename TSize2>
+    QGramLessNoCheckOffset_(StringSet<TString, TSpec> const &text, TSize1 q, TSize2 offset):
+    _stringSet(text),
+    _q(q),
+    _offset(offset) {}
+
+    inline bool operator() (TSAValue const &a, TSAValue const &b) const
+    {
+        if (a == b) return false;
+        TIter itA = begin(_stringSet[getValueI1(a)], Standard()) + getValueI2(a) + _offset;
+        TIter itB = begin(_stringSet[getValueI1(b)], Standard()) + getValueI2(b) + _offset;
+        if (a <= b) {
+            TIter itEnd = itB + _q;
+            for(; itB != itEnd; ++itB, ++itA) {
+                if (ordLess(*itA, *itB)) return true;
+                if (ordLess(*itB, *itA)) return false;
             }
-			return posCompare(a.i1, b.i1);
-        }
-    };
-
-    // optimized for bitvectors
-    template <typename T1, typename TValue, unsigned _size, typename Result>
-    struct _qgramComp< Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack >, Result > :
-        public ::std::binary_function<
-            Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack >,
-            Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack >,
-            Result> {       
-        inline Result operator()(
-            const Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack > &a,
-            const Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack > &b) const
-        {
-            if (a.i2 < b.i2) return -1;
-            if (a.i2 > b.i2) return 1;
-			return posCompare(a.i1, b.i1);
+            return false;
+        } else {
+            TIter itEnd = itA + _q;
+            for(; itA != itEnd; ++itA, ++itB) {
+                if (ordLess(*itA, *itB)) return true;
+                if (ordLess(*itB, *itA)) return false;
+            }
+            return true;
         }
-    };
-
-	template < 
-		typename TText_,
-		typename TShapeSpec,
-		typename TSpec >
-	void createQGramIndexExt(Index<TText_, IndexQGram<TShapeSpec, TSpec> > &index)
-	{
-	SEQAN_CHECKPOINT
-        typedef Index<TText_, IndexQGram<TShapeSpec, TSpec> >       TIndex;
-        typedef typename Fibre<TIndex, QGramText>::Type             TText;
-        typedef typename Fibre<TIndex, QGramSA>::Type               TSA;
-        typedef typename Fibre<TIndex, QGramDir>::Type              TDir;
-        typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
-        typedef typename Fibre<TIndex, QGramBucketMap>::Type        TBucketMap;
-
-		TText const &text = indexText(index);
-		TSA &sa = indexSA(index);
-		TDir &dir = indexDir(index);
-		TShape &shape = indexShape(index);
-		TBucketMap &bucketMap = index.bucketMap;
-
-        // signed characters behave different than unsigned when compared
-        // to get the same index with signed or unsigned chars we simply cast them to unsigned
-        // before feeding them into the pipeline
-		typedef typename Value<TIndex>::Type                        TValue;
-        typedef typename MakeUnsigned_<TValue>::Type				TUValue;
-
-        // *** SPECIALIZATION ***
-
-		typedef Pipe< TText, Source<> >								TSource;
-        typedef Pipe< TSource, Caster<TUValue, CasterConvert> >		TUnsigner;
-		typedef Pipe< TUnsigner, Tupler<LENGTH<TShape>::VALUE> >	TTupler;
-						                typedef _qgramComp<TypeOf_(TTupler)> qcomp_t;
-        typedef Pool< 
-					TypeOf_(TTupler), 
-					SorterSpec< SorterConfigSize<qcomp_t, TSizeOf_(TTupler) > > 
-				> TSortTuples;
-
-        // *** INSTANTIATION ***
-
-		TSource			src(text);
-        TUnsigner		unsigner(src);
-		TTupler			tupler(unsigner);
-		TSortTuples		sorter;
-
-		// sort q-grams
-		sorter << tupler;
-
-		// fill sa and dir
-		if (!beginRead(sorter)) return;
-
-		typename Iterator<TSA>::Type itSA = begin(sa);
-		typename Iterator<TDir>::Type itDir = begin(dir);
-
-		qcomp_t	qcomp;
-
-        typename Size<TSortTuples>::Type leftToRead = length(sorter);
-        typename Value<TShape>::Type code, old_code = 0;
-        
-        if (leftToRead > 0)
-        {
-            typename Value<TSortTuples>::Type old_qgram = *sorter;
-
-            old_code = hash(shape, getValueI2(old_qgram));
-            *itSA = (*sorter).i1;
-            *itDir = 0;
-            --leftToRead, ++sorter, ++itSA, ++itDir;
-            
-            for (; leftToRead > 0; --leftToRead, ++sorter, ++itSA)
-            {
-                // copy occurrence position
-                *itSA = (*sorter).i1;
-                if (qcomp(old_qgram, *sorter) != 0) 
-                {
-                    old_qgram = *sorter;
-                    code = hash(shape, getValueI2(old_qgram));
+    }
+};
 
-                    SEQAN_ASSERT_LT(old_code, code);
+//////////////////////////////////////////////////////////////////////////////
+// Counting sort - little helpers
+//
 
-                    // copy bucket begin
-                    typename Size<TSortTuples>::Type i = length(sorter) - leftToRead;
-                    for(; old_code < code; ++old_code, ++itDir)
-                        *itDir = i;
-                }
-            }
-        }
+// map hashes 1:1 to directory
+template < typename THashValue, typename TParallelTag >
+inline THashValue
+requestBucket(Nothing &, THashValue hash, Tag<TParallelTag>)
+{
+    return hash;
+}
 
-        // fill bucket table
-        typename Size<TSortTuples>::Type i = length(sorter);
-        code = length(dir);
-        for(; old_code < code; ++old_code, ++itDir)
-            *itDir = i;
+template < typename THashValue, typename TParallelTag >
+inline THashValue
+getBucket(Nothing const &, THashValue hash, Tag<TParallelTag>)
+{
+    return hash;
+}
 
-		endRead(sorter);
-	}
+// backward compatibility wrappers
+template < typename TBucketMap, typename THashValue >
+inline THashValue
+requestBucket(TBucketMap &bucketMap, THashValue hash)
+{
+    return requestBucket(bucketMap, hash, Serial());
+}
 
+template < typename TBucketMap, typename THashValue >
+inline THashValue
+getBucket(TBucketMap const &bucketMap, THashValue hash)
+{
+    return getBucket(bucketMap, hash, Serial());
+}
 
 //////////////////////////////////////////////////////////////////////////////
-// create q-gram index of *multiple* sequences in external memory 
-
-    // uses a Sorter to (1) sort q-grams and (2) afterwards create the bucket directory
-	template < 
-		typename TString,
-		typename TSSSpec,
-		typename TShapeSpec,
-		typename TSpec >
-	void createQGramIndexExt(Index<StringSet<TString, TSSSpec>, IndexQGram<TShapeSpec, TSpec> > &index)
-	{
-	SEQAN_CHECKPOINT
-        typedef StringSet<TString, TSSSpec>                         TText_;
-        typedef Index<TText_, IndexQGram<TShapeSpec, TSpec> >       TIndex;
-        typedef typename Fibre<TIndex, QGramText>::Type             TText;
-        typedef typename Fibre<TIndex, QGramSA>::Type               TSA;
-        typedef typename Fibre<TIndex, QGramDir>::Type              TDir;
-        typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
-        typedef typename Fibre<TIndex, QGramBucketMap>::Type        TBucketMap;
-
-		TText const &stringSet = indexText(index);
-		TSA &sa = indexSA(index);
-		TDir &dir = indexDir(index);
-		TShape &shape = indexShape(index);
-		TBucketMap &bucketMap = index.bucketMap;
-
-        typedef typename Value<TDir>::Type TSize;
-        const TSize DISABLED_BUCKET = (TSize)-1;
-
-        // signed characters behave different than unsigned when compared
-        // to get the same index with signed or unsigned chars we simply cast them to unsigned
-        // before feeding them into the pipeline
-		typedef typename Concatenator<TText>::Type                  TConcat;
-		typedef typename Value<TIndex>::Type                        TValue;
-        typedef typename MakeUnsigned_<TValue>::Type                TUValue;
-		typedef Multi<
-			Tupler<LENGTH<TShape>::VALUE, true, BitPacked<> >,
-			typename Value<TSA>::Type,
-			typename StringSetLimits<TText>::Type >                 TTuplerSpec;
-
-        // *** SPECIALIZATION ***
-
-		typedef Pipe< TConcat, Source<> >							TSource;
-        typedef Pipe< TSource, Caster<TUValue, CasterConvert> >		TUnsigner;
-		typedef Pipe< TUnsigner, TTuplerSpec >						TTupler;
-						                typedef _qgramComp<TypeOf_(TTupler)> qcomp_t;
-        typedef Pool< 
-					TypeOf_(TTupler), 
-					SorterSpec< SorterConfigSize<qcomp_t, TSizeOf_(TTupler) > > 
-				> TSortTuples;
-
-        // *** INSTANTIATION ***
-
-		TSource			src(concat(stringSet));
-        TUnsigner		unsigner(src);
-		TTupler			tupler(unsigner, stringSetLimits(stringSet));
-		TSortTuples		sorter;
-
-		if (empty(shape)) return;
+// Counting sort - Step 1: Clear directory
+template < typename TDir, typename TParallelTag >
+inline void
+_qgramClearDir(TDir &dir, Nothing &, Tag<TParallelTag> parallelTag)
+{
+    arrayFill(begin(dir, Standard()), end(dir, Standard()), 0, parallelTag);
+}
 
-#ifdef _OPENMP
-std::cout << "start\n";
-double start = omp_get_wtime();
-#endif
+template < typename TDir, typename TBucketMap >
+inline void _qgramClearDir(TDir &dir, TBucketMap &bucketMap)
+{
+    _qgramClearDir(dir, bucketMap, Serial());
+}
 
-		// 1. clear counters
-		_qgramClearDir(dir, bucketMap);
 
-		// 2. count q-grams
-        if (!beginRead(tupler))
-            return;
+//////////////////////////////////////////////////////////////////////////////
+// Counting sort - Step 2: Count q-grams
+template < typename TDir, typename TBucketMap, typename TText, typename TShape, typename TStepSize >
+inline void
+_qgramCountQGrams(TDir &dir, TBucketMap &bucketMap, TText const &text, TShape shape, TStepSize stepSize)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TText const, Standard>::Type    TIterator;
+    typedef typename Value<TDir>::Type                        TSize;
 
-        for (; !eof(tupler); ++tupler)
-            ++dir[requestBucket(bucketMap, hash(shape, getValueI2(*tupler)))];
+    if (length(text) < length(shape) || empty(shape)) return;
+    TSize num_qgrams = (length(text) - length(shape)) / stepSize + 1;
 
-        endRead(tupler);
+    TIterator itText = begin(text, Standard());
+    ++dir[requestBucket(bucketMap, hash(shape, itText))];
+    if (stepSize == 1)
+        for(TSize i = 1; i < num_qgrams; ++i)
+        {
+            ++itText;
+            ++dir[requestBucket(bucketMap, hashNext(shape, itText))];
+        }
+    else
+        for(TSize i = 1; i < num_qgrams; ++i)
+        {
+            itText += stepSize;
+            ++dir[requestBucket(bucketMap, hash(shape, itText))];
+        }
+}
 
-#ifdef _OPENMP
-std::cout << "scan took " << omp_get_wtime() - start << " seconds.\n";
-#endif
+template < typename TDir, typename TBucketMap, typename TString, typename TSpec, typename TShape, typename TStepSize >
+inline void
+_qgramCountQGrams(TDir &dir, TBucketMap &bucketMap, StringSet<TString, TSpec> const &stringSet, TShape shape, TStepSize stepSize)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TString const, Standard>::Type    TIterator;
+    typedef typename Value<TDir>::Type                            TSize;
 
-        // 3a. optionally disable some buckets
-		bool bucketsDisabled = _qgramDisableBuckets(index);
+    if (empty(shape)) return;
 
-        // 3b. cumulative sum
-        TSize qgramCount;
-        if (bucketsDisabled)
-            qgramCount = _qgramCummulativeSumAlt(dir, True());
-        else
-            qgramCount = _qgramCummulativeSumAlt(dir, False());
+    if (stepSize == 1)
+        for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+        {
+            TString const &sequence = value(stringSet, seqNo);
+            if (length(sequence) < length(shape)) continue;
+            TSize num_qgrams = length(sequence) - length(shape) + 1;
+
+            TIterator itText = begin(sequence, Standard());
+            ++dir[requestBucket(bucketMap, hash(shape, itText))];
+            for(TSize i = 1; i < num_qgrams; ++i)
+            {
+                ++itText;
+                ++dir[requestBucket(bucketMap, hashNext(shape, itText))];
+            }
+        }
+    else
+        for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+        {
+            TString const &sequence = value(stringSet, seqNo);
+            if (length(sequence) < length(shape)) continue;
+            TSize num_qgrams = (length(sequence) - length(shape)) / stepSize + 1;
+
+            TIterator itText = begin(sequence, Standard());
+            for(TSize i = 0; i < num_qgrams; ++i)
+            {
+                ++dir[requestBucket(bucketMap, hash(shape, itText))];
+                itText += stepSize;
+            }
+        }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Counting sort - Step 3: Cumulative sum
+//
+// a disabled bucket 3,2,x,4   (x = disabled)               y_i=sum_{j<=i} x_j
+// results in        0,0,3,x,5 (_qgramCummulativeSum)       z_i=y_{i-2}
+// or in             0,3,5,5,9 (_qgramCummulativeSumAlt)    z_i=y_{i-1}
+
+//    3 2 1 x x 5
+// 0 0 3 5 x x 6 11
+//   0 3 5 6 6 6 11
+
+// First two entries are 0.
+// Step 4 increments the entries hash(qgram)+1 on-the-fly while filling the SA table.
+// After step 4 each entry (0..n-1) is the beginning of a qgram bucket.
+template < typename TDir, typename TWithConstraints >
+inline typename Value<TDir>::Type
+_qgramCummulativeSum(TDir &dir, TWithConstraints)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TDir, Standard>::Type TDirIterator;
+    typedef typename Value<TDir>::Type              TSize;
+
+    TDirIterator it = begin(dir, Standard());
+    TDirIterator itEnd = end(dir, Standard());
+    TSize prevDiff = 0, prev2Diff = 0, sum = 0;
+    while (it != itEnd)
+    {
+        if (TWithConstraints::VALUE && prevDiff == (TSize)-1)
+        {
+            sum += prev2Diff;
+            prev2Diff = 0;
+            prevDiff = *it;
+            *it = (TSize)-1;                                // disable bucket
+        } else {
+            sum += prev2Diff;
+            prev2Diff = prevDiff;
+            prevDiff = *it;
+            *it = sum;
+        }
+        ++it;
+    }
+    return sum + prev2Diff;
+}
+
+// The first entry is 0.
+// This function is used when Steps 4 and 5 (fill SA, correct disabled buckets) are ommited.
+template < typename TDir, typename TWithConstraints >
+inline typename Value<TDir>::Type
+_qgramCummulativeSumAlt(TDir &dir, TWithConstraints const)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TDir, Standard>::Type TDirIterator;
+    typedef typename Value<TDir>::Type              TSize;
+
+    TDirIterator it = begin(dir, Standard());
+    TDirIterator itEnd = end(dir, Standard());
+    TSize prevDiff = 0, sum = 0;
+    for (; it != itEnd; ++it)
+    {
+        if (!TWithConstraints::VALUE || prevDiff != (TSize)-1)
+        {
+            sum += prevDiff;
+            prevDiff = *it;
+            *it = sum;
+        }
+        else
+        {
+            prevDiff = *it;
+            *it = (TSize)-1;    // disable bucket
+        }
+    }
+    return sum + prevDiff;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Counting sort - Step 4: Fill suffix array
+// w/o constraints
+template <
+typename TSA,
+typename TText,
+typename TShape,
+typename TDir,
+typename TBucketMap,
+typename TWithConstraints,
+typename TStepSize >
+inline void
+_qgramFillSuffixArray(
+                      TSA &sa,
+                      TText const &text,
+                      TShape shape,
+                      TDir &dir,
+                      TBucketMap &bucketMap,
+                      TStepSize stepSize,
+                      TWithConstraints const)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TText const, Standard>::Type    TIterator;
+    typedef typename Value<TDir>::Type                        TSize;
+
+    if (empty(shape) || length(text) < length(shape)) return;
+
+    TSize num_qgrams = length(text) - length(shape) + 1;
+    TIterator itText = begin(text, Standard());
+
+    if (TWithConstraints::VALUE) {
+        TSize bktNo = getBucket(bucketMap, hash(shape, itText)) + 1;            // first hash
+        if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = 0;                        // if bucket is enabled
+    } else
+        sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = 0;            // first hash
+
+    if (stepSize == 1)
+        for(TSize i = 1; i < num_qgrams; ++i)
+        {
+            ++itText;
+            if (TWithConstraints::VALUE) {
+                TSize bktNo = getBucket(bucketMap, hashNext(shape, itText)) + 1;    // next hash
+                if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = i;                    // if bucket is enabled
+            } else
+                sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = i;    // next hash
+        }
+    else
+        for(TSize i = stepSize; i < num_qgrams; i += stepSize)
+        {
+            itText += stepSize;
+            if (TWithConstraints::VALUE) {
+                TSize bktNo = getBucket(bucketMap, hash(shape, itText)) + 1;        // next hash (we mustn't use hashNext here)
+                if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = i;                    // if bucket is enabled
+            } else
+                sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = i;        // next hash
+        }
+}
+
+// multiple sequences
+template <
+typename TSA,
+typename TString,
+typename TSpec,
+typename TShape,
+typename TDir,
+typename TBucketMap,
+typename TStepSize,
+typename TWithConstraints >
+inline void
+_qgramFillSuffixArray(
+                      TSA &sa,
+                      StringSet<TString, TSpec> const &stringSet,
+                      TShape shape,
+                      TDir &dir,
+                      TBucketMap &bucketMap,
+                      TStepSize stepSize,
+                      TWithConstraints const)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TString const, Standard>::Type    TIterator;
+    typedef typename Value<TDir>::Type                            TSize;
+
+    if (empty(shape)) return;
+
+    if (stepSize == 1)
+        for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+        {
+            TString const &sequence = value(stringSet, seqNo);
+            if (length(sequence) < length(shape)) continue;
+            TSize num_qgrams = length(sequence) - length(shape) + 1;
+
+            typename Value<TSA>::Type localPos;
+            assignValueI1(localPos, seqNo);
+            assignValueI2(localPos, 0);
+
+            TIterator itText = begin(sequence, Standard());
+            if (TWithConstraints::VALUE) {
+                TSize bktNo = getBucket(bucketMap, hash(shape, itText)) + 1;                    // first hash
+                if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos;                        // if bucket is enabled
+            } else
+                sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos;            // first hash
+
+            for(TSize i = 1; i < num_qgrams; ++i)
+            {
+                ++itText;
+                assignValueI2(localPos, i);
+                if (TWithConstraints::VALUE) {
+                    TSize bktNo = getBucket(bucketMap, hashNext(shape, itText)) + 1;            // next hash
+                    if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos;                    // if bucket is enabled
+                } else
+                    sa[dir[getBucket(bucketMap, hashNext(shape, itText)) + 1]++] = localPos;    // next hash
+            }
+        }
+    else
+        for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+        {
+            TString const &sequence = value(stringSet, seqNo);
+            if (length(sequence) < length(shape)) continue;
+            TSize num_qgrams = length(sequence) - length(shape) + 1;
+
+            typename Value<TSA>::Type localPos;
+            assignValueI1(localPos, seqNo);
+            assignValueI2(localPos, 0);
+
+            TIterator itText = begin(sequence, Standard());
+            for(TSize i = 0; i < num_qgrams; i += stepSize)
+            {
+                assignValueI2(localPos, i);
+                if (TWithConstraints::VALUE) {
+                    TSize bktNo = getBucket(bucketMap, hash(shape, itText)) + 1;                // hash
+                    if (dir[bktNo] != (TSize)-1) sa[dir[bktNo]++] = localPos;                    // if bucket is enabled
+                } else
+                    sa[dir[getBucket(bucketMap, hash(shape, itText)) + 1]++] = localPos;        // hash
+                itText += stepSize;
+            }
+        }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Step 5: Correct disabled buckets
+template < typename TDir >
+inline void
+_qgramPostprocessBuckets(TDir &dir)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TDir, Standard>::Type            TDirIterator;
+    typedef typename Value<TDir>::Type                        TSize;
+
+    TDirIterator it = begin(dir, Standard());
+    TDirIterator itEnd = end(dir, Standard());
+    TSize prev = 0;
+    for (; it != itEnd; ++it)
+        if (*it == (TSize)-1)   // end positions
+            *it = prev;
+        else
+            prev = *it;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn IndexQGram#createQGramIndex
+ * @headerfile <seqan/index.h>
+ * @brief Builds a <i>q</i>-gram index on a sequence.
+ *
+ * @signature void createQGramIndex(index);
+ * @signature void createQGramIndex(sa, dir, bucketMap, text, shape, stepSize); [DEPRECATED]
+ *
+ * @param[out] index     The IndexQGram to create.
+ * @param[out] sa        The resulting list in which all <i>q</i>-grams are sorted alphabetically.
+ * @param[out] dir       The resulting array that indicates at which position in index the corresponding <i>q</i>-grams
+ * @param[in]  bucketMap Stores the <i>q</i>-gram hashes for the openaddressing hash maps, see
+ *                       @link IndexQGram#indexBucketMap @endlink. If bucketMap is of the type @link Nothing @endlink
+ *                       the <i>q</i>-gram hash determines the bucket address in the index.
+ * @param[in]  text      The @link TextConcept @endlink object to build the index for.
+ * @param[in]  shape     The shape to be used. Types: @link Shape @endlink
+ *                       can be found.
+ * @param[in]  stepSize  Store every <tt>stepSize</tt>'th <i>q</i>-gram in the index, @link IntegerConcept @endlink.
+ *
+ * The resulting <i>q</i>-gram <tt>index</tt> contains the sorted list of qgrams. For each <i>q</i>-gram <tt>dir</tt> contains the
+ * first position in index that corresponds to this <i>q</i>-gram.
+ *
+ * @warning This function should not be called directly. Please use @link Index#indexCreate @endlink or @link
+ *          Index#indexRequire @endlink.  The resulting tables must have appropriate size before calling this function.
+ */
+template < typename TIndex >
+inline bool _qgramDisableBuckets(TIndex &)
+{
+    return false;    // we disable no buckets by default
+}
+
+template <typename TSA, typename TText, typename TShape, typename TDir>
+inline void
+_qgramRefineSuffixArray(TSA & /* sa */, TText const & /* text */, TShape const & /* shape */, TDir const & /* dir */)
+{
+}
+
+template <typename TSA, typename TText, typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec, typename TDir>
+inline void
+_qgramRefineSuffixArray(TSA & sa, TText const & text, Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > const & shape, TDir const & dir)
+{
+    _refineQGramIndex(sa, dir, text, 0, length(shape));
+}
+
+template < typename TIndex >
+void createQGramIndex(TIndex &index)
+{
+    SEQAN_CHECKPOINT
+    typename Fibre<TIndex, QGramText>::Type const &text      = indexText(index);
+    typename Fibre<TIndex, QGramSA>::Type         &sa        = indexSA(index);
+    typename Fibre<TIndex, QGramDir>::Type        &dir       = indexDir(index);
+    typename Fibre<TIndex, QGramShape>::Type      &shape     = indexShape(index);
+    typename Fibre<TIndex, QGramBucketMap>::Type  &bucketMap = index.bucketMap;
+
+    // 1. clear counters
+    _qgramClearDir(dir, bucketMap);
+
+    // 2. count q-grams
+    _qgramCountQGrams(dir, bucketMap, text, shape, getStepSize(index));
+
+    if (_qgramDisableBuckets(index))
+    {
+        // 3. cumulative sum
+        _qgramCummulativeSum(dir, True());
+
+        // 4. fill suffix array
+        _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), True());
+
+        // 5. correct disabled buckets
+        _qgramPostprocessBuckets(dir);
+    }
+    else
+    {
+        // 3. cumulative sum
+        _qgramCummulativeSum(dir, False());
+
+        // 4. fill suffix array
+        _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, getStepSize(index), False());
+    }
+
+    // 5. refine suffix array
+    _qgramRefineSuffixArray(sa, text, shape, dir);
+}
+
+// DEPRECATED
+// better use createQGramIndex(index) (above)
+template <
+typename TSA,
+typename TDir,
+typename TBucketMap,
+typename TText,
+typename TShape,
+typename TStepSize >
+void createQGramIndex(
+                      TSA &sa,
+                      TDir &dir,
+                      TBucketMap &bucketMap,
+                      TText const &text,
+                      TShape &shape,
+                      TStepSize stepSize)
+{
+    SEQAN_CHECKPOINT
+
+    // 1. clear counters
+    _qgramClearDir(dir, bucketMap);
+
+    // 2. count q-grams
+    _qgramCountQGrams(dir, bucketMap, text, shape, stepSize);
+
+    // 3. cumulative sum
+    __int64 res = _qgramCummulativeSum(dir, False());
+    SEQAN_ASSERT_EQ(res, static_cast<__int64>(length(sa)));
+    ignoreUnusedVariableWarning(res);
+
+    // 4. fill suffix array
+    _qgramFillSuffixArray(sa, text, shape, dir, bucketMap, stepSize, False());
+}
+
+// DEPRECATED
+// better use createQGramIndex(index) (above)
+template <
+typename TSA,
+typename TDir,
+typename TBucketMap,
+typename TText,
+typename TShape,
+typename TStepSize >
+void createQGramIndex(
+                      TSA &sa,
+                      TDir &dir,
+                      TBucketMap &bucketMap,
+                      TText const &text,
+                      TShape &shape)
+{
+    createQGramIndex(sa, dir, bucketMap, text, shape, 1);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn IndexQGram#createQGramIndexSAOnly
+ * @headerfile <seqan/index.h>
+ * @brief Builds the suffix array of a q-gram index on a sequence.
+ *
+ * @signature void createQGramIndexSAOnly(sa, text, shape, stepSize)
+ *
+ * @param[out] sa       The resulting list in which all q-grams are sorted alphabetically, @link String @endlink
+ *                      object of @link SAValue @endlink of the underlying @link TextConcept text @endlink.
+ * @param[in]  text     The sequence, a @link TextConcept @endlink object.
+ * @param[in]  shape    The @link Shape @endlink to be used. q is the length of this shape.
+ * @param[in]  stepSize Store every <tt>stepSize</tt>'th q-gram in the index, @link IntegerConcept @endlink.
+ *
+ * @warning This function should not be called directly. Please use @link Index#indexCreate @endlink or @link
+ *          Index#indexRequire @endlink. The resulting tables must have appropriate size before calling this function.
+ */
+template <
+typename TSA,
+typename TText,
+typename TShape,
+typename TStepSize >
+void createQGramIndexSAOnly(
+                            TSA &sa,
+                            TText const &text,
+                            TShape &shape,
+                            TStepSize stepSize)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Size<TSA>::Type TSize;
+    typedef typename Iterator<TSA, Standard>::Type TIter;
+
+    // 1. Fill suffix array with a permutation (the identity)
+    TIter it = begin(sa, Standard());
+    TIter itEnd = end(sa, Standard());
+    TSize i = 0;
+    for(; it != itEnd; ++it, i += stepSize)
+        *it = i;
+
+    // 2. Sort suffix array with quicksort
+    TSize span = length(shape);
+    if (i + span > length(text) + 1)
+        std::sort(
+                  begin(sa, Standard()),
+                  end(sa, Standard()),
+                  QGramLess_<typename Value<TSA>::Type, TText const>(text, span));
+    else
+        std::sort(
+                  begin(sa, Standard()),
+                  end(sa, Standard()),
+                  QGramLessNoCheck_<typename Value<TSA>::Type, TText const>(text, span));
+}
+
+template <
+typename TSA,
+typename TString,
+typename TSpec,
+typename TShape,
+typename TStepSize >
+void createQGramIndexSAOnly(
+                            TSA &sa,
+                            StringSet<TString, TSpec> const &stringSet,
+                            TShape &shape,
+                            TStepSize stepSize)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Iterator<TSA, Standard>::Type    TIter;
+    typedef typename Value<TSA>::Type                TValue;
+    typedef typename Size<TString>::Type            TSize;
+    typedef StringSet<TString, TSpec>                TStringSet;
+
+    // 1. Fill suffix array with a permutation (the identity)
+    TIter it = begin(sa, Standard());
+    TValue pair;
+    unsigned int const q1 = length(shape) - 1;
+    for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+    {
+        unsigned int const strlen = length(stringSet[seqNo]);
+        if (strlen > q1) {
+            assignValueI1(pair, seqNo);
+            for (TSize i = 0; i < strlen - q1; ++it, i += stepSize) {
+                assignValueI2(pair, i);
+                *it = pair;
+            }
+        }
+    }
+    SEQAN_ASSERT_EQ(it, end(sa, Standard()));
+
+    // 2. Sort suffix array with quicksort
+    TSize q = length(shape);
+    if (lengthSum(stringSet) == length(sa))
+        std::sort(
+                  begin(sa, Standard()),
+                  end(sa, Standard()),
+                  QGramLess_<typename Value<TSA>::Type, TStringSet const>(stringSet, q));
+    else
+        std::sort(
+                  begin(sa, Standard()),
+                  end(sa, Standard()),
+                  QGramLessNoCheck_<typename Value<TSA>::Type, TStringSet const>(stringSet, q));
+}
+
+template <
+typename TSA,
+typename TText,
+typename TSize1,
+typename TSize2 >
+inline void
+_refineQGramIndexBucket(
+                        TSA &sa,
+                        TText const &text,
+                        TSize1 oldQ,
+                        TSize2 newQ)
+{
+    SEQAN_CHECKPOINT
+    if (length(sa) <= 1)
+        return;
+
+    std::sort(
+              begin(sa, Standard()),
+              end(sa, Standard()),
+              QGramLessOffset_<typename Value<TSA>::Type, TText const>(text, newQ - oldQ, oldQ));
+}
+
+template <
+typename TSA,
+typename TDir,
+typename TText,
+typename TSize1,
+typename TSize2 >
+inline void _refineQGramIndex(
+                              TSA &sa,
+                              TDir const &dir,
+                              TText const &text,
+                              TSize1 oldQ,
+                              TSize2 newQ)
+{
+    //typedef typename Size<TSA>::Type                        TSize;
+    typedef typename Iterator<TSA, Standard>::Type          TIter;
+    typedef typename Iterator<TDir const, Standard>::Type   TDirIter;
+
+    if (newQ <= (TSize2)oldQ) return;
+
+    if (length(dir) < 2) {
+        std::sort(
+                  begin(sa, Standard()),
+                  end(sa, Standard()),
+                  QGramLess_<typename Value<TSA>::Type, TText const>(text, newQ));
+        return;
+    }
+
+    // 1. Sort each bucket with quicksort and compare substrings s[i+oldQ..i+newQ)
+    TDirIter dirIt = begin(dir, Standard());
+    TDirIter dirItEnd = end(dir, Standard());
+    TIter itBegin = begin(sa, Standard());
+    TIter itBktBegin = itBegin + *dirIt;
+    TIter itBktEnd;
+    ++dirIt;
+    for(; dirIt != dirItEnd; ++dirIt, itBktBegin = itBktEnd) {
+        itBktEnd = itBegin + *dirIt;
+        if (itBktEnd - itBktBegin < 2) continue;
+        std::sort(
+                  itBktBegin,
+                  itBktEnd,
+                  QGramLessOffset_<typename Value<TSA>::Type, TText const>(text, newQ - oldQ, oldQ));
+    }
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn IndexQGram#createQGramIndexDirOnly
+ * @headerfile <seqan/index.h>
+ * @brief Builds the directory of a <i>q</i>-gram index on a sequence.
+ *
+ * @signature void createQGramIndexDirOnly(dir, bucketMap, text, shape, stepSize);
+ *
+ * @param[out] dir       The resulting array that indicates at which position in index the corresponding q-grams can be
+ *                       found.
+ * @param[out] bucketMap Stores the q-gram hashes for the openaddressing hash maps, see @link IndexQGram#indexBucketMap
+ *                       @endlink.  If bucketMap is of the type @link Nothing @endlink the q-gram hash determines the
+ *                       bucket address in the index.
+ * @param[in]  text      The sequence, @link TextConcept @endlink.
+ * @param[in]  stepSize  Store every <tt>stepSize</tt>'th q-gram in the index, @link IntegerConcept @endlink.
+ * @param[in]  shape     The @link Shape @endlink to be used.
+ *
+ * The resulting <tt>index</tt> contains the sorted list of qgrams. For each possible q-gram pos contains the first
+ * position in index that corresponds to this q-gram.
+ *
+ * @warning This function should not be called directly. Please use @link Index#indexCreate @endlink or @link
+ *          Index#indexRequire @endlink. The resulting tables must have appropriate size before calling this function.
+ */
+
+template <
+typename TDir,
+typename TBucketMap,
+typename TText,
+typename TShape,
+typename TStepSize >
+void createQGramIndexDirOnly(
+                             TDir &dir,
+                             TBucketMap &bucketMap,
+                             TText const &text,
+                             TShape &shape,
+                             TStepSize stepSize)
+{
+    SEQAN_CHECKPOINT
+
+    // 1. clear counters
+    _qgramClearDir(dir, bucketMap);
+
+    // 2. count q-grams
+    _qgramCountQGrams(dir, bucketMap, text, shape, stepSize);
+
+    // 3. cumulative sum (Step 4 is ommited)
+    _qgramCummulativeSumAlt(dir, False());
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn IndexQGram#createCountArray
+ * @headerfile <seqan/index.h>
+ * @brief Builds an index on a StringSet storing how often a <i>q</i>-gram occurs in each sequence.
+ *
+ * @signature void createCountsArray(counts, dir, bucketMap, stringSet, shape, stepSize);
+ *
+ * @param[out] counts    The resulting @link String @endlink of pairs <i>(seqNo, count)</i>.
+ * @param[out] dir       The resulting array that indicates at which position in the count
+ *                       table the corresponding a certain q-gram can be found.
+ * @param[out] bucketMap Stores the q-gram hashes for the openaddressing hash maps,
+ *                       see @link IndexQGram#indexBucketMap @endlink. If bucketMap is of the
+ *                       type @link Nothing @endlink the q-gram hash determines the
+ *                       bucket address in the index.
+ * @param[in] stringSet  The @link StringSet @endlink.
+ * @param[in] shape      The @link Shape @endlink to be used.
+ * @param[in] stepSize   Store every <tt>stepSize</tt><sup>th</sup> <i>q</i>-gram in the index,
+ *                       @link IntegerConcept @endlink.
+ *
+ * @warning This function should not be called directly.  Please use @link Index#indexCreate @endlink or @link
+ *          Index#indexRequire @endlink.  The resulting tables must have appropriate size before calling this function.
+ */
+template <
+typename TCounts,
+typename TDir,
+typename TBucketMap,
+typename TString,
+typename TSpec,
+typename TShape,
+typename TStepSize >
+void createCountsArray(
+                       TCounts &counts,
+                       TDir &dir,
+                       TBucketMap &bucketMap,
+                       StringSet<TString, TSpec> const &stringSet,
+                       TShape shape,
+                       TStepSize stepSize)
+{
+    typedef typename Iterator<TString const, Standard>::Type    TIterator;
+    //typedef typename Iterator<TDir, Standard>::Type                TDirIterator;
+    typedef typename Value<TShape>::Type                        TValue;
+    typedef typename Size<TString>::Type                        TSize;
+
+    TDir lastSeqSeen;
+    resize(lastSeqSeen, length(dir), Exact());
+
+    // 1. clear counters
+    _qgramClearDir(dir, bucketMap);
+    if (empty(shape))
+    {
+        clear(counts);
+        return;
+    }
+    arrayFill(begin(lastSeqSeen, Standard()), end(lastSeqSeen, Standard()), -1);
+
+    // 2. count distinct sequences for each q-gram
+    for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+    {
+        TString const &sequence = value(stringSet, seqNo);
+        if (length(sequence) < length(shape)) continue;
+        TSize num_qgrams = (length(sequence) - length(shape)) / stepSize + 1;
+
+        TIterator itText = begin(sequence, Standard());
+        TValue bktNo = requestBucket(bucketMap, hash(shape, itText));
+        lastSeqSeen[bktNo] = seqNo;
+        ++dir[bktNo];
+        if (stepSize == 1)
+            for(TSize i = 1; i < num_qgrams; ++i)
+            {
+                ++itText;
+                bktNo = requestBucket(bucketMap, hashNext(shape, itText));
+                if (seqNo != lastSeqSeen[bktNo]) {
+                    lastSeqSeen[bktNo] = seqNo;
+                    ++dir[bktNo];
+                }
+            }
+        else
+            for(TSize i = 1; i < num_qgrams; ++i)
+            {
+                itText += stepSize;
+                bktNo = requestBucket(bucketMap, hash(shape, itText));
+                if (seqNo != lastSeqSeen[bktNo]) {
+                    lastSeqSeen[bktNo] = seqNo;
+                    ++dir[bktNo];
+                }
+            }
+    }
+
+    // 3. cumulative sum
+    resize(counts, _qgramCummulativeSum(dir, False()), Exact());
+
+    // 4. fill count array
+    arrayFill(begin(lastSeqSeen, Standard()), end(lastSeqSeen, Standard()), -1);
+    for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+    {
+        TString const &sequence = value(stringSet, seqNo);
+        if (length(sequence) < length(shape)) continue;
+        TSize num_qgrams = (length(sequence) - length(shape)) / stepSize + 1;
+
+        TIterator itText = begin(sequence, Standard());
+        TValue bktNo = getBucket(bucketMap, hash(shape, itText));
+        lastSeqSeen[bktNo] = seqNo;
+        TSize pos = dir[bktNo + 1]++;
+        counts[pos].i1 = seqNo;                // first hash
+        counts[pos].i2 = 1;
+
+        if (stepSize == 1)
+            for(TSize i = 1; i < num_qgrams; ++i)
+            {
+                ++itText;
+                bktNo = getBucket(bucketMap, hashNext(shape, itText));
+                if (seqNo == lastSeqSeen[bktNo])
+                    ++(counts[dir[bktNo + 1] - 1].i2);
+                else {
+                    lastSeqSeen[bktNo] = seqNo;
+                    pos = dir[bktNo + 1]++;
+                    counts[pos].i1 = seqNo;                // next hash
+                    counts[pos].i2 = 1;
+                }
+            }
+        else
+            for(TSize i = 1; i < num_qgrams; ++i)
+            {
+                itText += stepSize;
+                bktNo = getBucket(bucketMap, hash(shape, itText));
+                if (seqNo == lastSeqSeen[bktNo])
+                    ++(counts[dir[bktNo + 1] - 1].i2);
+                else {
+                    lastSeqSeen[bktNo] = seqNo;
+                    pos = dir[bktNo + 1]++;
+                    counts[pos].i1 = seqNo;                // next hash
+                    counts[pos].i2 = 1;
+                }
+            }
+    }
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// create q-gram index of *one* sequence in external memory
+
+// *** COMPARATORS & MAPS ***
+
+template <typename InType, typename Result = int>
+struct _qgramComp : public std::binary_function<InType,InType,Result> {
+    inline Result operator()(InType const &a, InType const &b) const
+    {
+        typedef typename Value<InType, 2>::Type TQGram;
+        typename Value<TQGram>::Type const *sa = a.i2.i;
+        typename Value<TQGram>::Type const *sb = b.i2.i;
+        typename Value<TQGram>::Type const *saEnd = sa + length(a.i2);
+
+        for(; sa != saEnd; ++sa, ++sb) {
+            if (*sa == *sb) continue;
+            return (*sa < *sb)? -1 : 1;
+        }
+        return posCompare(a.i1, b.i1);
+    }
+};
+
+// optimized for bitvectors
+template <typename T1, typename TValue, unsigned _size, typename Result>
+struct _qgramComp< Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack >, Result > :
+public std::binary_function<
+Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack >,
+Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack >,
+Result> {
+    inline Result operator()(
+                             const Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack > &a,
+                             const Pair<T1, Tuple<TValue, _size, BitPacked<> >, Pack > &b) const
+    {
+        if (a.i2 < b.i2) return -1;
+        if (a.i2 > b.i2) return 1;
+        return posCompare(a.i1, b.i1);
+    }
+};
+
+template <
+typename TText_,
+typename TShapeSpec,
+typename TSpec >
+void createQGramIndexExt(Index<TText_, IndexQGram<TShapeSpec, TSpec> > &index)
+{
+    SEQAN_CHECKPOINT
+    typedef Index<TText_, IndexQGram<TShapeSpec, TSpec> >       TIndex;
+    typedef typename Fibre<TIndex, QGramText>::Type             TText;
+    typedef typename Fibre<TIndex, QGramSA>::Type               TSA;
+    typedef typename Fibre<TIndex, QGramDir>::Type              TDir;
+    typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+    typedef typename Fibre<TIndex, QGramBucketMap>::Type        TBucketMap;
+
+    TText const &text = indexText(index);
+    TSA &sa = indexSA(index);
+    TDir &dir = indexDir(index);
+    TShape &shape = indexShape(index);
+    TBucketMap &bucketMap = index.bucketMap;
+
+    // signed characters behave different than unsigned when compared
+    // to get the same index with signed or unsigned chars we simply cast them to unsigned
+    // before feeding them into the pipeline
+    typedef typename Value<TIndex>::Type                        TValue;
+    typedef typename MakeUnsigned_<TValue>::Type                TUValue;
+
+    // *** SPECIALIZATION ***
+
+    typedef Pipe< TText, Source<> >                                TSource;
+    typedef Pipe< TSource, Caster<TUValue, CasterConvert> >        TUnsigner;
+    typedef Pipe< TUnsigner, Tupler<LENGTH<TShape>::VALUE> >    TTupler;
+    typedef _qgramComp<TypeOf_(TTupler)> qcomp_t;
+    typedef Pool<
+    TypeOf_(TTupler),
+    SorterSpec< SorterConfigSize<qcomp_t, TSizeOf_(TTupler) > >
+    > TSortTuples;
+
+    // *** INSTANTIATION ***
+
+    TSource            src(text);
+    TUnsigner        unsigner(src);
+    TTupler            tupler(unsigner);
+    TSortTuples        sorter;
+
+    // sort q-grams
+    sorter << tupler;
+
+    // fill sa and dir
+    if (!beginRead(sorter)) return;
+
+    typename Iterator<TSA>::Type itSA = begin(sa);
+    typename Iterator<TDir>::Type itDir = begin(dir);
+
+    qcomp_t    qcomp;
+
+    typename Size<TSortTuples>::Type leftToRead = length(sorter);
+    typename Value<TShape>::Type code, old_code = 0;
+
+    if (leftToRead > 0)
+    {
+        typename Value<TSortTuples>::Type old_qgram = *sorter;
+
+        old_code = hash(shape, getValueI2(old_qgram));
+        *itSA = (*sorter).i1;
+        *itDir = 0;
+        --leftToRead, ++sorter, ++itSA, ++itDir;
+
+        for (; leftToRead > 0; --leftToRead, ++sorter, ++itSA)
+        {
+            // copy occurrence position
+            *itSA = (*sorter).i1;
+            if (qcomp(old_qgram, *sorter) != 0)
+            {
+                old_qgram = *sorter;
+                code = hash(shape, getValueI2(old_qgram));
+
+                SEQAN_ASSERT_LT(old_code, code);
+
+                // copy bucket begin
+                typename Size<TSortTuples>::Type i = length(sorter) - leftToRead;
+                for(; old_code < code; ++old_code, ++itDir)
+                    *itDir = i;
+            }
+        }
+    }
+
+    // fill bucket table
+    typename Size<TSortTuples>::Type i = length(sorter);
+    code = length(dir);
+    for(; old_code < code; ++old_code, ++itDir)
+        *itDir = i;
+
+    endRead(sorter);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// create q-gram index of *multiple* sequences in external memory
+
+// uses a Sorter to (1) sort q-grams and (2) afterwards create the bucket directory
+template <
+typename TString,
+typename TSSSpec,
+typename TShapeSpec,
+typename TSpec >
+void createQGramIndexExt(Index<StringSet<TString, TSSSpec>, IndexQGram<TShapeSpec, TSpec> > &index)
+{
+    SEQAN_CHECKPOINT
+    typedef StringSet<TString, TSSSpec>                         TText_;
+    typedef Index<TText_, IndexQGram<TShapeSpec, TSpec> >       TIndex;
+    typedef typename Fibre<TIndex, QGramText>::Type             TText;
+    typedef typename Fibre<TIndex, QGramSA>::Type               TSA;
+    typedef typename Fibre<TIndex, QGramDir>::Type              TDir;
+    typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+    typedef typename Fibre<TIndex, QGramBucketMap>::Type        TBucketMap;
+
+    TText const &stringSet = indexText(index);
+    TSA &sa = indexSA(index);
+    TDir &dir = indexDir(index);
+    TShape &shape = indexShape(index);
+    TBucketMap &bucketMap = index.bucketMap;
+
+    typedef typename Value<TDir>::Type TSize;
+    const TSize DISABLED_BUCKET = (TSize)-1;
+
+    // signed characters behave different than unsigned when compared
+    // to get the same index with signed or unsigned chars we simply cast them to unsigned
+    // before feeding them into the pipeline
+    typedef typename Concatenator<TText>::Type                  TConcat;
+    typedef typename Value<TIndex>::Type                        TValue;
+    typedef typename MakeUnsigned_<TValue>::Type                TUValue;
+    typedef Multi<
+    Tupler<LENGTH<TShape>::VALUE, true, BitPacked<> >,
+    typename Value<TSA>::Type,
+    typename StringSetLimits<TText>::Type >                 TTuplerSpec;
+
+    // *** SPECIALIZATION ***
+
+    typedef Pipe< TConcat, Source<> >                            TSource;
+    typedef Pipe< TSource, Caster<TUValue, CasterConvert> >        TUnsigner;
+    typedef Pipe< TUnsigner, TTuplerSpec >                        TTupler;
+    typedef _qgramComp<TypeOf_(TTupler)> qcomp_t;
+    typedef Pool<
+    TypeOf_(TTupler),
+    SorterSpec< SorterConfigSize<qcomp_t, TSizeOf_(TTupler) > >
+    > TSortTuples;
+
+    // *** INSTANTIATION ***
+
+    TSource            src(concat(stringSet));
+    TUnsigner        unsigner(src);
+    TTupler            tupler(unsigner, stringSetLimits(stringSet));
+    TSortTuples        sorter;
+
+    if (empty(shape)) return;
+
+#ifdef _OPENMP
+    std::cout << "start\n";
+    double start = omp_get_wtime();
+#endif
+
+    // 1. clear counters
+    _qgramClearDir(dir, bucketMap);
+
+    // 2. count q-grams
+    if (!beginRead(tupler))
+        return;
 
-		// 4. fill suffix array
-        resize(sorter, qgramCount);
-        if (!beginRead(tupler) || !beginWrite(sorter))
-            return;
+    for (; !eof(tupler); ++tupler)
+        ++dir[requestBucket(bucketMap, hash(shape, getValueI2(*tupler)))];
+
+    endRead(tupler);
 
 #ifdef _OPENMP
-std::cout << "start write\n";
-start = omp_get_wtime();
+    std::cout << "scan took " << omp_get_wtime() - start << " seconds.\n";
 #endif
 
-        for (; !eof(tupler); ++tupler)
-            if (dir[getBucket(bucketMap, hash(shape, getValueI2(*tupler))) + 1] != DISABLED_BUCKET)
-                push(sorter, *tupler);
+    // 3a. optionally disable some buckets
+    bool bucketsDisabled = _qgramDisableBuckets(index);
+
+    // 3b. cumulative sum
+    TSize qgramCount;
+    if (bucketsDisabled)
+        qgramCount = _qgramCummulativeSumAlt(dir, True());
+    else
+        qgramCount = _qgramCummulativeSumAlt(dir, False());
 
-        endRead(tupler);
-        endWrite(sorter);
+    // 4. fill suffix array
+    resize(sorter, qgramCount);
+    if (!beginRead(tupler) || !beginWrite(sorter))
+        return;
 
 #ifdef _OPENMP
-std::cout << "writing took " << omp_get_wtime() - start << " seconds.\n";
-start = omp_get_wtime();
+    std::cout << "start write\n";
+    start = omp_get_wtime();
 #endif
 
-        beginRead(sorter);
-        typename Iterator<TSA, Standard>::Type saIt = begin(sa, Standard());
-        for (; !eof(sorter); ++sorter, ++saIt)
-            *saIt = getValueI1(*sorter);
-        endRead(sorter);
+    for (; !eof(tupler); ++tupler)
+        if (dir[getBucket(bucketMap, hash(shape, getValueI2(*tupler))) + 1] != DISABLED_BUCKET)
+            push(sorter, *tupler);
+
+    endRead(tupler);
+    endWrite(sorter);
 
 #ifdef _OPENMP
-std::cout << "reading took " << omp_get_wtime() - start << " seconds.\n";
+    std::cout << "writing took " << omp_get_wtime() - start << " seconds.\n";
+    start = omp_get_wtime();
 #endif
 
-        // 5. correct disabled buckets
-        if (bucketsDisabled)
-            _qgramPostprocessBuckets(dir);
+    beginRead(sorter);
+    typename Iterator<TSA, Standard>::Type saIt = begin(sa, Standard());
+    for (; !eof(sorter); ++sorter, ++saIt)
+        *saIt = getValueI1(*sorter);
+    endRead(sorter);
 
+#ifdef _OPENMP
+    std::cout << "reading took " << omp_get_wtime() - start << " seconds.\n";
+#endif
 
-/*
-		// sort q-grams
-		sorter << tupler;
+    // 5. correct disabled buckets
+    if (bucketsDisabled)
+        _qgramPostprocessBuckets(dir);
 
-		// fill sa and dir
-		if (!beginRead(sorter)) return;
 
-		typename Iterator<TSA>::Type itSA = begin(sa);
-		typename Iterator<TDir>::Type itDir = begin(dir);
+    /*
+     // sort q-grams
+     sorter << tupler;
 
-		qcomp_t	qcomp;
+     // fill sa and dir
+     if (!beginRead(sorter)) return;
 
-        typename Size<TSortTuples>::Type leftToRead = length(sorter);
-        typename Value<TShape>::Type code, old_code = 0;
-        
-        if (leftToRead > 0)
-        {
-            typename Value<TSortTuples>::Type old_qgram = *sorter;
+     typename Iterator<TSA>::Type itSA = begin(sa);
+     typename Iterator<TDir>::Type itDir = begin(dir);
 
-            old_code = hash(shape, getValueI2(old_qgram));
-            *itSA = (*sorter).i1;
-            *itDir = 0;
-            --leftToRead, ++sorter, ++itSA, ++itDir;
-            
-            for (; leftToRead > 0; --leftToRead, ++sorter, ++itSA)
-            {
-                // copy occurrence position
-                *itSA = (*sorter).i1;
-                
-                if (qcomp(old_qgram, *sorter) != 0) 
-                {
-                    old_qgram = *sorter;
-                    code = hash(shape, getValueI2(old_qgram));
-                    
-                    // copy bucket begin
-                    typename Size<TSortTuples>::Type i = length(sorter) - leftToRead;
-                    for(; old_code < code; ++old_code, ++itDir)
-                        *itDir = i;
-                }
-            }
-        }
+     qcomp_t    qcomp;
+
+     typename Size<TSortTuples>::Type leftToRead = length(sorter);
+     typename Value<TShape>::Type code, old_code = 0;
+
+     if (leftToRead > 0)
+     {
+     typename Value<TSortTuples>::Type old_qgram = *sorter;
+
+     old_code = hash(shape, getValueI2(old_qgram));
+     *itSA = (*sorter).i1;
+     *itDir = 0;
+     --leftToRead, ++sorter, ++itSA, ++itDir;
+
+     for (; leftToRead > 0; --leftToRead, ++sorter, ++itSA)
+     {
+     // copy occurrence position
+     *itSA = (*sorter).i1;
+
+     if (qcomp(old_qgram, *sorter) != 0)
+     {
+     old_qgram = *sorter;
+     code = hash(shape, getValueI2(old_qgram));
+
+     // copy bucket begin
+     typename Size<TSortTuples>::Type i = length(sorter) - leftToRead;
+     for(; old_code < code; ++old_code, ++itDir)
+     *itDir = i;
+     }
+     }
+     }
+
+     // fill bucket table
+     typename Size<TSortTuples>::Type i = length(sorter);
+     code = length(dir);
+     for(; old_code < code; ++old_code, ++itDir)
+     *itDir = i;
+
+     endRead(sorter);
+     */
+}
 
-        // fill bucket table
-        typename Size<TSortTuples>::Type i = length(sorter);
-        code = length(dir);
-        for(; old_code < code; ++old_code, ++itDir)
-            *itDir = i;
-
-		endRead(sorter);
-*/
-	}
-
-    // uses a Mapper to (1) create the bucket directory and (2) afterwards map q-grams to their final position
-    // dir must allow random accesses
-	template < typename TIndex >
-	void createQGramIndexExtSA(TIndex &index)
-	{
-	SEQAN_CHECKPOINT
-        typedef typename Fibre<TIndex, QGramText>::Type             TText;
-        typedef typename Fibre<TIndex, QGramSA>::Type               TSA;
-        typedef typename Fibre<TIndex, QGramDir>::Type              TDir;
-        typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
-        typedef typename Fibre<TIndex, QGramBucketMap>::Type        TBucketMap;
-
-		TText const &stringSet = indexText(index);
-		TSA &sa = indexSA(index);
-		TDir &dir = indexDir(index);
-		TShape &shape = indexShape(index);
-		TBucketMap &bucketMap = index.bucketMap;
-		
-        typedef typename Value<TDir>::Type TSize;
-        const TSize DISABLED_BUCKET = (TSize)-1;
-        
-        // signed characters behave different than unsigned when compared
-        // to get the same index with signed or unsigned chars we simply cast them to unsigned
-        // before feeding them into the pipeline
-		typedef typename Concatenator<TText>::Type                  TConcat;
-		typedef typename Value<TIndex>::Type                        TValue;
-        typedef typename MakeUnsigned_<TValue>::Type                TUValue;
-		typedef Multi<
-			Tupler<LENGTH<TShape>::VALUE, true, BitPacked<> >,
-			typename Value<TSA>::Type,
-			typename StringSetLimits<TText>::Type >                 TTuplerSpec;
-
-        // *** SPECIALIZATION ***
-
-		typedef Pipe< TConcat, Source<> >							TSource;
-        typedef Pipe< TSource, Caster<TUValue, CasterConvert> >		TUnsigner;
-		typedef Pipe< TUnsigner, TTuplerSpec >						TTupler;
-        typedef Pair<
-            typename Value<TSA>::Type,
-            typename Size<TSA>::Type,
-            Pack >                                                  TPosWithRank;       // (pos_pair,rank)
-
-        typedef Pool< 
-					TPosWithRank,
-					MapperSpec< MapperConfig<filterI2<TPosWithRank> > >
-				> TMapTuples;
-
-
-		if (empty(shape)) return;
-
-        // *** INSTANTIATION ***
-
-		TSource			src(concat(stringSet));
-        TUnsigner		unsigner(src);
-		TTupler			tupler(unsigner, stringSetLimits(stringSet));
-        TMapTuples      mapper;
+// uses a Mapper to (1) create the bucket directory and (2) afterwards map q-grams to their final position
+// dir must allow random accesses
+template < typename TIndex >
+void createQGramIndexExtSA(TIndex &index)
+{
+    SEQAN_CHECKPOINT
+    typedef typename Fibre<TIndex, QGramText>::Type             TText;
+    typedef typename Fibre<TIndex, QGramSA>::Type               TSA;
+    typedef typename Fibre<TIndex, QGramDir>::Type              TDir;
+    typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+    typedef typename Fibre<TIndex, QGramBucketMap>::Type        TBucketMap;
+
+    TText const &stringSet = indexText(index);
+    TSA &sa = indexSA(index);
+    TDir &dir = indexDir(index);
+    TShape &shape = indexShape(index);
+    TBucketMap &bucketMap = index.bucketMap;
+
+    typedef typename Value<TDir>::Type TSize;
+    const TSize DISABLED_BUCKET = (TSize)-1;
+
+    // signed characters behave different than unsigned when compared
+    // to get the same index with signed or unsigned chars we simply cast them to unsigned
+    // before feeding them into the pipeline
+    typedef typename Concatenator<TText>::Type                  TConcat;
+    typedef typename Value<TIndex>::Type                        TValue;
+    typedef typename MakeUnsigned_<TValue>::Type                TUValue;
+    typedef Multi<
+    Tupler<LENGTH<TShape>::VALUE, true, BitPacked<> >,
+    typename Value<TSA>::Type,
+    typename StringSetLimits<TText>::Type >                 TTuplerSpec;
+
+    // *** SPECIALIZATION ***
+
+    typedef Pipe< TConcat, Source<> >                            TSource;
+    typedef Pipe< TSource, Caster<TUValue, CasterConvert> >        TUnsigner;
+    typedef Pipe< TUnsigner, TTuplerSpec >                        TTupler;
+    typedef Pair<
+    typename Value<TSA>::Type,
+    typename Size<TSA>::Type,
+    Pack >                                                  TPosWithRank;       // (pos_pair,rank)
+
+    typedef Pool<
+    TPosWithRank,
+    MapperSpec< MapperConfig<filterI2<TPosWithRank> > >
+    > TMapTuples;
+
+
+    if (empty(shape)) return;
+
+    // *** INSTANTIATION ***
+
+    TSource            src(concat(stringSet));
+    TUnsigner        unsigner(src);
+    TTupler            tupler(unsigner, stringSetLimits(stringSet));
+    TMapTuples      mapper;
 
 #ifdef _OPENMP
-std::cout << "start\n";
-double start = omp_get_wtime();
+    std::cout << "start\n";
+    double start = omp_get_wtime();
 #endif
 
-		// 1. clear counters
-		_qgramClearDir(dir, bucketMap);
+    // 1. clear counters
+    _qgramClearDir(dir, bucketMap);
 
-		// 2. count q-grams
-        if (!beginRead(tupler))
-            return;
+    // 2. count q-grams
+    if (!beginRead(tupler))
+        return;
 
-        for (; !eof(tupler); ++tupler)
-            ++dir[requestBucket(bucketMap, hash(shape, getValueI2(*tupler)))];
+    for (; !eof(tupler); ++tupler)
+        ++dir[requestBucket(bucketMap, hash(shape, getValueI2(*tupler)))];
 
-        endRead(tupler);
+    endRead(tupler);
 
 #ifdef _OPENMP
-std::cout << "scan took " << omp_get_wtime() - start << " seconds.\n";
+    std::cout << "scan took " << omp_get_wtime() - start << " seconds.\n";
 #endif
 
-        // 3a. optionally disable some buckets
-		bool bucketsDisabled = _qgramDisableBuckets(index);
+    // 3a. optionally disable some buckets
+    bool bucketsDisabled = _qgramDisableBuckets(index);
 
-        // 3b. cumulative sum
-        TSize qgramCount;
-        if (bucketsDisabled)
-            qgramCount = _qgramCummulativeSum(dir, True());
-        else
-            qgramCount = _qgramCummulativeSum(dir, False());
+    // 3b. cumulative sum
+    TSize qgramCount;
+    if (bucketsDisabled)
+        qgramCount = _qgramCummulativeSum(dir, True());
+    else
+        qgramCount = _qgramCummulativeSum(dir, False());
 
-        
-		// 4. fill suffix array
-        resize(mapper, qgramCount);
-        if (!beginRead(tupler) || !beginWrite(mapper))
-            return;
+
+    // 4. fill suffix array
+    resize(mapper, qgramCount);
+    if (!beginRead(tupler) || !beginWrite(mapper))
+        return;
 
 #ifdef _OPENMP
-std::cout << "start write\n";
-start = omp_get_wtime();
+    std::cout << "start write\n";
+    start = omp_get_wtime();
 #endif
 
-        for (; !eof(tupler); ++tupler)
-        {
-            TSize bktNo = getBucket(bucketMap, hash(shape, getValueI2(*tupler))) + 1;
-            if (dir[bktNo] != DISABLED_BUCKET)
-                push(mapper, TPosWithRank(getValueI1(*tupler), dir[bktNo]++));
-        }
+    for (; !eof(tupler); ++tupler)
+    {
+        TSize bktNo = getBucket(bucketMap, hash(shape, getValueI2(*tupler))) + 1;
+        if (dir[bktNo] != DISABLED_BUCKET)
+            push(mapper, TPosWithRank(getValueI1(*tupler), dir[bktNo]++));
+    }
 
-        endRead(tupler);
-        endWrite(mapper);
+    endRead(tupler);
+    endWrite(mapper);
 
 #ifdef _OPENMP
-std::cout << "writing took " << omp_get_wtime() - start << " seconds.\n";
-start = omp_get_wtime();
+    std::cout << "writing took " << omp_get_wtime() - start << " seconds.\n";
+    start = omp_get_wtime();
 #endif
 
-        beginRead(mapper);
-        typename Iterator<TSA, Standard>::Type saIt = begin(sa, Standard());
-        for (; !eof(mapper); ++mapper, ++saIt)
-            *saIt = getValueI1(*mapper);
-        endRead(mapper);
+    beginRead(mapper);
+    typename Iterator<TSA, Standard>::Type saIt = begin(sa, Standard());
+    for (; !eof(mapper); ++mapper, ++saIt)
+        *saIt = getValueI1(*mapper);
+    endRead(mapper);
 
 #ifdef _OPENMP
-std::cout << "reading took " << omp_get_wtime() - start << " seconds.\n";
+    std::cout << "reading took " << omp_get_wtime() - start << " seconds.\n";
 #endif
 
-        // 5. correct disabled buckets
-        if (bucketsDisabled)
-            _qgramPostprocessBuckets(dir);
-	}
+    // 5. correct disabled buckets
+    if (bucketsDisabled)
+        _qgramPostprocessBuckets(dir);
+}
 
 
 
 //////////////////////////////////////////////////////////////////////////////
-// interface for automatic index creation 
-
-	template <typename TText, typename TShape, typename TSize>
-	inline typename LengthSum<TText const>::Type
-	_qgramQGramCount(TText const &text, TShape const &shape, TSize stepSize)
-	{
-		if (empty(shape)) return 0;
-
-		// count all overlapping q-grams
-		TSize qgramCount = 0;
-		for(unsigned i = 0; i < countSequences(text); ++i)
-			if (sequenceLength(i, text) >= length(shape))
-				qgramCount += (sequenceLength(i, text) - length(shape)) / stepSize + 1;
-		return qgramCount;
-    }
+// interface for automatic index creation
+
+template <typename TText, typename TShape, typename TStepSize>
+inline typename LengthSum<TText const>::Type
+_qgramQGramCount(TText const &text, TShape const &shape, TStepSize stepSize)
+{
+    typedef typename LengthSum<TText const>::Type   TSize;
+    typedef typename Size<TText const>::Type        TSetSize;
+
+    if (empty(shape)) return 0;
+
+    // count all overlapping q-grams
+    TSize qgramCount = 0;
+    for(TSetSize i = 0; i < countSequences(text); ++i)
+        if (sequenceLength(i, text) >= length(shape))
+            qgramCount += (sequenceLength(i, text) - length(shape)) / stepSize + 1;
+    return qgramCount;
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Size<Index<TText, IndexQGram<TShapeSpec, TSpec> > >::Type
+_qgramQGramCount(Index<TText, IndexQGram<TShapeSpec, TSpec> > const &index)
+{
+    return _qgramQGramCount(indexText(index), indexShape(index), getStepSize(index));
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool indexCreate(
+                        Index<TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                        FibreSADir,
+                        Default const)
+{
+    resize(indexSA(index), _qgramQGramCount(index), Exact());
+    resize(indexDir(index), _fullDirLength(index), Exact());
+    createQGramIndex(index);
+    resize(indexSA(index), back(indexDir(index)), Exact());     // shrink if some buckets were disabled
+    return true;
+}
+
+template <typename TText, typename TSpec>
+inline bool indexSupplied(Index<TText, TSpec> &index, FibreSADir) {
+    return !(empty(getFibre(index, FibreSA())) || empty(getFibre(index, FibreDir())));
+}
 
-	template <typename TText, typename TShapeSpec, typename TSpec>
-	inline typename Size<Index<TText, IndexQGram<TShapeSpec, TSpec> > >::Type
-	_qgramQGramCount(Index<TText, IndexQGram<TShapeSpec, TSpec> > const &index)
-	{
-        return _qgramQGramCount(indexText(index), indexShape(index), getStepSize(index));
-	}
-
-	template <typename TText, typename TShapeSpec, typename TSpec>
-	inline bool indexCreate(
-		Index<TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		FibreSADir, 
-		Default const) 
-	{		
-		resize(indexSA(index), _qgramQGramCount(index), Exact());
-		resize(indexDir(index), _fullDirLength(index), Exact());
-		createQGramIndex(index);
-		resize(indexSA(index), back(indexDir(index)), Exact());     // shrink if some buckets were disabled
-		return true;
-	}
-
-	template <typename TText, typename TSpec>
-	inline bool indexSupplied(Index<TText, TSpec> &index, FibreSADir) {
-		return !(empty(getFibre(index, FibreSA())) || empty(getFibre(index, FibreDir())));
-	}
-
-	template <typename TText, typename TShapeSpec, typename TSpec>
-	inline bool indexCreate(
-		Index<TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		FibreSA, 
-		Default const)
-	{
-		resize(indexSA(index), _qgramQGramCount(index), Exact());
-		createQGramIndexSAOnly(indexSA(index), indexText(index), indexShape(index), getStepSize(index));
-		return true;
-	}
-
-	template <typename TText, typename TShapeSpec, typename TSpec>
-	inline bool indexCreate(
-		Index<TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		FibreCounts, 
-		Default const) 
-	{
-		resize(indexCountsDir(index), _fullDirLength(index), Exact());
-		createCountsArray(indexCounts(index), indexCountsDir(index), indexBucketMap(index), indexText(index), indexShape(index), getStepSize(index));
-		return true;
-	}
-
-	template <typename TText, typename TShapeSpec, typename TSpec>
-	inline bool indexCreate(
-		Index<TText, IndexQGram<TShapeSpec, TSpec> > &index,
-		FibreDir,
-		Default const)
-	{
-		resize(indexDir(index), _fullDirLength(index), Exact());
-		createQGramIndexDirOnly(indexDir(index), indexBucketMap(index), indexText(index), indexShape(index), getStepSize(index));
-		return true;
-	}
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool indexCreate(
+                        Index<TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                        FibreSA,
+                        Default const)
+{
+    resize(indexSA(index), _qgramQGramCount(index), Exact());
+    createQGramIndexSAOnly(indexSA(index), indexText(index), indexShape(index), getStepSize(index));
+    return true;
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool indexCreate(
+                        Index<TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                        FibreCounts,
+                        Default const)
+{
+    resize(indexCountsDir(index), _fullDirLength(index), Exact());
+    createCountsArray(indexCounts(index), indexCountsDir(index), indexBucketMap(index), indexText(index), indexShape(index), getStepSize(index));
+    return true;
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool indexCreate(
+                        Index<TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                        FibreDir,
+                        Default const)
+{
+    resize(indexDir(index), _fullDirLength(index), Exact());
+    createQGramIndexDirOnly(indexDir(index), indexBucketMap(index), indexText(index), indexShape(index), getStepSize(index));
+    return true;
+}
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.getKmerSimilarityMatrix:
-..summary:Creates a matrix storing the number of common q-grams between all pairs of sequences.
-..cat:Index
-..signature:getKmerSimilarityMatrix(index, distMat[, seqSet])
-..class:Spec.IndexQGram
-..param.index:A q-gram index.
-...type:Spec.IndexQGram
-..param.distMat:The resulting q-gram similarity matrix.
-...type:Concept.ContainerConcept 
-..param.seqSet:Contains sequence numbers if only a subset of sequences should be compared.
-...type:Concept.ContainerConcept
-..remarks:$distMat$ need to be a container of a floating point type and will be resized to $seqCount*seqCount$, where $seqCount$ is the number of sequences in the index/in $seqSet$.
-The fraction of common q-grams between sequence $i$ and $j$ is stored at position $i*seqCount + j$.
-It sums up the minimum number of q-gram occurrences between both sequences for each q-gram and normalizes it.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#getKmerSimilarityMatrix
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Creates a matrix storing the number of common q-grams between all
- *        pairs of sequences.
- * 
- * @signature getKmerSimilarityMatrix(index, distMat[, seqSet])
- * 
- * @param distMat The resulting q-gram similarity matrix. Types:
- *                @link ContainerConcept @endlink
- * @param seqSet Contains sequence numbers if only a subset of sequences should
- *               be compared. Types: @link ContainerConcept @endlink
- * @param index A q-gram index. Types: @link IndexQGram @endlink
- * 
- * @section Remarks
- * 
- * <tt>distMat</tt> need to be a container of a floating point type and will be
- * resized to <tt>seqCount*seqCount</tt>, where <tt>seqCount</tt> is the number
- * of sequences in the index/in <tt>seqSet</tt>. The fraction of common q-grams
- * between sequence <tt>i</tt> and <tt>j</tt> is stored at position
- * <tt>i*seqCount + j</tt>. It sums up the minimum number of q-gram occurrences
- * between both sequences for each q-gram and normalizes it.
+ * @headerfile <seqan/index.h>
+ * @brief Creates a matrix storing the number of common q-grams between all pairs of sequences.
+ *
+ * @signature void getKmerSimilarityMatrix(index, distMat[, seqSet]);
+ *
+ * @param[out] distMat The resulting q-gram similarity matrix.  Types: @link ContainerConcept @endlink
+ * @param[in]  seqSet  Contains sequence numbers if only a subset of sequences should be compared.  Types: @link
+ *                     ContainerConcept @endlink
+ * @param[in]  index   The @link IndexQGram @endlink to use.
+ *
+ * <tt>distMat</tt> need to be a container of a floating point type and will be resized to <tt>seqCount * seqCount</tt>,
+ * where <tt>seqCount</tt> is the number of sequences in the index/in <tt>seqSet</tt>.  The fraction of common q-grams
+ * between sequence <tt>i</tt> and <tt>j</tt> is stored at position <tt>i*seqCount + j</tt>.  It sums up the minimum
+ * number of q-gram occurrences between both sequences for each q-gram and normalizes it.
  */
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TDistMatrix >
-	inline void getKmerSimilarityMatrix(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		TDistMatrix &distMat)
-	{
-		typedef Index< TText, IndexQGram<TShapeSpec,TSpec> >	TIndex;
-		typedef typename Size<TIndex>::Type						TSize;
-		typedef typename Size<TDistMatrix>::Type				TSizeMat;
-		typedef typename Value<TDistMatrix>::Type				TValueMat;
-
-		typedef typename Fibre<TIndex, QGramCountsDir>::Type	TCountsDir;
-		typedef typename Iterator<TCountsDir, Standard>::Type	TIterCountsDir;
-		typedef typename Fibre<TIndex, QGramCounts>::Type		TCounts;
-		typedef typename Iterator<TCounts, Standard>::Type		TIterCounts;
-
-		// declare requirements
-		indexRequire(index, QGramCounts());
-
-		// initialize distance matrix
-		TSizeMat seqNoLength = countSequences(index);
-		clear(distMat);
-		resize(distMat, seqNoLength * seqNoLength);
-		arrayFill(begin(distMat, Standard()), end(distMat, Standard()), 0);
-
-		TIterCountsDir itCountsDir = begin(indexCountsDir(index), Standard());
-		TIterCountsDir itCountsDirEnd = end(indexCountsDir(index), Standard());
-		TIterCounts itCountsBegin = begin(indexCounts(index), Standard());
-
-		// for each bucket count common q-grams for each sequence pair
-		TSize bucketBegin = *itCountsDir;
-		for(++itCountsDir; itCountsDir != itCountsDirEnd; ++itCountsDir) 
-		{
-			TSize bucketEnd = *itCountsDir;
-
-			// q-gram must occur in at least 2 different sequences
-			if (bucketBegin != bucketEnd) 
-			{
-				TIterCounts itA = itCountsBegin + bucketBegin;
-				TIterCounts itEnd = itCountsBegin + bucketEnd;
-				for(; itA != itEnd; ++itA) 
-				{
-					TSizeMat ofs = (*itA).i1 * seqNoLength;
-					TSize countA = (*itA).i2;
-					TIterCounts itB = itA;
-
-					for(; itB != itEnd; ++itB) 
-					{
-						TSize countB = (*itB).i2;
-						if (countA < countB)
-							distMat[ofs + (*itB).i1] += countA;
-						else
-							distMat[ofs + (*itB).i1] += countB;
-					}
-				}
-			}
-			bucketBegin = bucketEnd;
-		}
-
-		// copy upper triangle to lower triangle and scale
-		for(TSizeMat row = 0; row < seqNoLength; ++row) 
-		{
-			TValueMat maxValRow = distMat[row * (seqNoLength + 1)];
-			for(TSizeMat col = row + 1; col < seqNoLength; ++col)
-			{
-				// fractional common kmer count
-				TValueMat maxValCol = distMat[col * (seqNoLength + 1)];
-				TValueMat val = distMat[row * seqNoLength + col];
-
-				// number of common q-grams / Number of possible common q-grams
-				if (maxValRow < maxValCol) {
-					if (maxValRow != 0)
-						val /= maxValRow;
-					distMat[col * seqNoLength + row] = val;
-					distMat[row * seqNoLength + col] = val;
-				} else {
-					if (maxValCol != 0)
-						val /= maxValCol;
-					distMat[col * seqNoLength + row] = val;
-					distMat[row * seqNoLength + col] = val;
-				}
-			}
-		}
-
-		// set diagonal to 1
-		for(TSizeMat i = 0; i < seqNoLength; ++i)
-			distMat[i * (seqNoLength + 1)] = 1;
-	}
+template < typename TText, typename TShapeSpec, typename TSpec, typename TDistMatrix >
+inline void getKmerSimilarityMatrix(
+                                    Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                                    TDistMatrix &distMat)
+{
+    typedef Index< TText, IndexQGram<TShapeSpec,TSpec> >    TIndex;
+    typedef typename Size<TIndex>::Type                        TSize;
+    typedef typename Size<TDistMatrix>::Type                TSizeMat;
+    typedef typename Value<TDistMatrix>::Type                TValueMat;
+
+    typedef typename Fibre<TIndex, QGramCountsDir>::Type    TCountsDir;
+    typedef typename Iterator<TCountsDir, Standard>::Type    TIterCountsDir;
+    typedef typename Fibre<TIndex, QGramCounts>::Type        TCounts;
+    typedef typename Iterator<TCounts, Standard>::Type        TIterCounts;
+
+    // declare requirements
+    indexRequire(index, QGramCounts());
+
+    // initialize distance matrix
+    TSizeMat seqNoLength = countSequences(index);
+    clear(distMat);
+    resize(distMat, seqNoLength * seqNoLength);
+    arrayFill(begin(distMat, Standard()), end(distMat, Standard()), 0);
+
+    TIterCountsDir itCountsDir = begin(indexCountsDir(index), Standard());
+    TIterCountsDir itCountsDirEnd = end(indexCountsDir(index), Standard());
+    TIterCounts itCountsBegin = begin(indexCounts(index), Standard());
+
+    // for each bucket count common q-grams for each sequence pair
+    TSize bucketBegin = *itCountsDir;
+    for(++itCountsDir; itCountsDir != itCountsDirEnd; ++itCountsDir)
+    {
+        TSize bucketEnd = *itCountsDir;
+
+        // q-gram must occur in at least 2 different sequences
+        if (bucketBegin != bucketEnd)
+        {
+            TIterCounts itA = itCountsBegin + bucketBegin;
+            TIterCounts itEnd = itCountsBegin + bucketEnd;
+            for(; itA != itEnd; ++itA)
+            {
+                TSizeMat ofs = (*itA).i1 * seqNoLength;
+                TSize countA = (*itA).i2;
+                TIterCounts itB = itA;
+
+                for(; itB != itEnd; ++itB)
+                {
+                    TSize countB = (*itB).i2;
+                    if (countA < countB)
+                        distMat[ofs + (*itB).i1] += countA;
+                    else
+                        distMat[ofs + (*itB).i1] += countB;
+                }
+            }
+        }
+        bucketBegin = bucketEnd;
+    }
+
+    // copy upper triangle to lower triangle and scale
+    for(TSizeMat row = 0; row < seqNoLength; ++row)
+    {
+        TValueMat maxValRow = distMat[row * (seqNoLength + 1)];
+        for(TSizeMat col = row + 1; col < seqNoLength; ++col)
+        {
+            // fractional common kmer count
+            TValueMat maxValCol = distMat[col * (seqNoLength + 1)];
+            TValueMat val = distMat[row * seqNoLength + col];
+
+            // number of common q-grams / Number of possible common q-grams
+            if (maxValRow < maxValCol) {
+                if (maxValRow != 0)
+                    val /= maxValRow;
+                distMat[col * seqNoLength + row] = val;
+                distMat[row * seqNoLength + col] = val;
+            } else {
+                if (maxValCol != 0)
+                    val /= maxValCol;
+                distMat[col * seqNoLength + row] = val;
+                distMat[row * seqNoLength + col] = val;
+            }
+        }
+    }
+
+    // set diagonal to 1
+    for(TSizeMat i = 0; i < seqNoLength; ++i)
+        distMat[i * (seqNoLength + 1)] = 1;
+}
 
 
 //////////////////////////////////////////////////////////////////////////////
-// getKmerSimilarityMatrix 
+// getKmerSimilarityMatrix
 //     for a subset of the StringSet given as a sorted string of sequence numbers
 
-	template < 
-		typename TText, 
-		typename TShapeSpec, 
-		typename TSpec, 
-		typename TDistMatrix, 
-		typename TSeqNoString 
-	>
-	inline void getKmerSimilarityMatrix(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		TDistMatrix &distMat,
-		TSeqNoString const &seqNo)
-	{
-		typedef Index< TText, IndexQGram<TShapeSpec,TSpec> >	TIndex;
-		typedef typename Size<TIndex>::Type						TSize;
-		typedef typename Size<TDistMatrix>::Type				TSizeMat;
-		typedef typename Value<TDistMatrix>::Type				TValueMat;
-
-		typedef typename Fibre<TIndex, QGramCountsDir>::Type	TCountsDir;
-		typedef typename Iterator<TCountsDir, Standard>::Type	TIterCountsDir;
-		typedef typename Fibre<TIndex, QGramCounts>::Type		TCounts;
-		typedef typename Iterator<TCounts, Standard>::Type		TIterCounts;
-		typedef typename Iterator<TSeqNoString, Standard>::Type	TIterSeqNo;
-
-		// declare requirements
-		indexRequire(index, QGramCounts());
-
-		// initialize distance matrix
-		TSizeMat seqNoLength = length(seqNo);
-		clear(distMat);
-		resize(distMat, seqNoLength * seqNoLength);
-		arrayFill(begin(distMat, Standard()), end(distMat, Standard()), 0);
-
-		TIterCountsDir itCountsDir = begin(indexCountsDir(index), Standard());
-		TIterCountsDir itCountsDirEnd = end(indexCountsDir(index), Standard());
-		TIterCounts itCountsBegin = begin(indexCounts(index), Standard());
-		TIterSeqNo itSetBegin = begin(seqNo, Standard());
-		TIterSeqNo itSetEnd = end(seqNo, Standard());
-
-		// for each bucket count common q-grams for each sequence pair
-		TSize bucketBegin = *itCountsDir;
-		for(++itCountsDir; itCountsDir != itCountsDirEnd; ++itCountsDir) 
-		{
-			TSize bucketEnd = *itCountsDir;
-
-			// q-gram must occur in at least 2 different sequences
-			if (bucketBegin != bucketEnd) 
-			{
-				TIterCounts itA = itCountsBegin + bucketBegin;
-				TIterCounts itEnd = itCountsBegin + bucketEnd;
-				TIterSeqNo itSetA = itSetBegin;
-
-				while (itA != itEnd && itSetA != itSetEnd)
-				{
-					if ((*itA).i1 < *itSetA)
-						++itA;
-					else if ((*itA).i1 > *itSetA)
-						++itSetA;
-					else 
-					{
-						TSizeMat ofs = (itSetA - itSetBegin) * seqNoLength;
-						TSize countA = (*itA).i2;
-						TIterCounts itB = itA;
-						TIterSeqNo itSetB = itSetA;
-
-						while (itB != itEnd && itSetB != itSetEnd)
-						{
-							if ((*itB).i1 < *itSetB)
-								++itB;
-							else if ((*itB).i1 > *itSetB)
-								++itSetB;
-							else 
-							{
-								TSize countB = (*itB).i2;
-								if (countA < countB)
-									distMat[ofs + (itSetB - itSetBegin)] += countA;
-								else
-									distMat[ofs + (itSetB - itSetBegin)] += countB;
-								++itB;
-								++itSetB;
-							}
-						}
-						++itA;
-						++itSetA;
-					}
-				}
-			}
-			bucketBegin = bucketEnd;
-		}
-
-		// copy upper triangle to lower triangle and scale
-		for(TSizeMat row = 0; row < seqNoLength; ++row) 
-		{
-			TValueMat maxValRow = distMat[row * (seqNoLength + 1)];
-			for(TSizeMat col = row + 1; col < seqNoLength; ++col)
-			{
-				// fractional common kmer count
-				TValueMat maxValCol = distMat[col * (seqNoLength + 1)];
-				TValueMat val = distMat[row * seqNoLength + col];
-
-				// number of common q-grams / Number of possible common q-grams
-				if (maxValRow < maxValCol) {
-					if (maxValRow != 0)
-						val /= maxValRow;
-					distMat[col * seqNoLength + row] = val;
-					distMat[row * seqNoLength + col] = val;
-				} else {
-					if (maxValCol != 0)
-						val /= maxValCol;
-					distMat[col * seqNoLength + row] = val;
-					distMat[row * seqNoLength + col] = val;
-				}
-			}
-		}
-
-		// set diagonal to 1
-		for(TSizeMat i = 0; i < seqNoLength; ++i)
-			distMat[i * (seqNoLength + 1)] = 1;
-	}
-	
-	
+template <
+typename TText,
+typename TShapeSpec,
+typename TSpec,
+typename TDistMatrix,
+typename TSeqNoString
+>
+inline void getKmerSimilarityMatrix(
+                                    Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                                    TDistMatrix &distMat,
+                                    TSeqNoString const &seqNo)
+{
+    typedef Index< TText, IndexQGram<TShapeSpec,TSpec> >    TIndex;
+    typedef typename Size<TIndex>::Type                        TSize;
+    typedef typename Size<TDistMatrix>::Type                TSizeMat;
+    typedef typename Value<TDistMatrix>::Type                TValueMat;
+
+    typedef typename Fibre<TIndex, QGramCountsDir>::Type    TCountsDir;
+    typedef typename Iterator<TCountsDir, Standard>::Type    TIterCountsDir;
+    typedef typename Fibre<TIndex, QGramCounts>::Type        TCounts;
+    typedef typename Iterator<TCounts, Standard>::Type        TIterCounts;
+    typedef typename Iterator<TSeqNoString, Standard>::Type    TIterSeqNo;
+
+    // declare requirements
+    indexRequire(index, QGramCounts());
+
+    // initialize distance matrix
+    TSizeMat seqNoLength = length(seqNo);
+    clear(distMat);
+    resize(distMat, seqNoLength * seqNoLength);
+    arrayFill(begin(distMat, Standard()), end(distMat, Standard()), 0);
+
+    TIterCountsDir itCountsDir = begin(indexCountsDir(index), Standard());
+    TIterCountsDir itCountsDirEnd = end(indexCountsDir(index), Standard());
+    TIterCounts itCountsBegin = begin(indexCounts(index), Standard());
+    TIterSeqNo itSetBegin = begin(seqNo, Standard());
+    TIterSeqNo itSetEnd = end(seqNo, Standard());
+
+    // for each bucket count common q-grams for each sequence pair
+    TSize bucketBegin = *itCountsDir;
+    for(++itCountsDir; itCountsDir != itCountsDirEnd; ++itCountsDir)
+    {
+        TSize bucketEnd = *itCountsDir;
+
+        // q-gram must occur in at least 2 different sequences
+        if (bucketBegin != bucketEnd)
+        {
+            TIterCounts itA = itCountsBegin + bucketBegin;
+            TIterCounts itEnd = itCountsBegin + bucketEnd;
+            TIterSeqNo itSetA = itSetBegin;
+
+            while (itA != itEnd && itSetA != itSetEnd)
+            {
+                if ((*itA).i1 < *itSetA)
+                    ++itA;
+                else if ((*itA).i1 > *itSetA)
+                    ++itSetA;
+                else
+                {
+                    TSizeMat ofs = (itSetA - itSetBegin) * seqNoLength;
+                    TSize countA = (*itA).i2;
+                    TIterCounts itB = itA;
+                    TIterSeqNo itSetB = itSetA;
+
+                    while (itB != itEnd && itSetB != itSetEnd)
+                    {
+                        if ((*itB).i1 < *itSetB)
+                            ++itB;
+                        else if ((*itB).i1 > *itSetB)
+                            ++itSetB;
+                        else
+                        {
+                            TSize countB = (*itB).i2;
+                            if (countA < countB)
+                                distMat[ofs + (itSetB - itSetBegin)] += countA;
+                            else
+                                distMat[ofs + (itSetB - itSetBegin)] += countB;
+                            ++itB;
+                            ++itSetB;
+                        }
+                    }
+                    ++itA;
+                    ++itSetA;
+                }
+            }
+        }
+        bucketBegin = bucketEnd;
+    }
+
+    // copy upper triangle to lower triangle and scale
+    for(TSizeMat row = 0; row < seqNoLength; ++row)
+    {
+        TValueMat maxValRow = distMat[row * (seqNoLength + 1)];
+        for(TSizeMat col = row + 1; col < seqNoLength; ++col)
+        {
+            // fractional common kmer count
+            TValueMat maxValCol = distMat[col * (seqNoLength + 1)];
+            TValueMat val = distMat[row * seqNoLength + col];
+
+            // number of common q-grams / Number of possible common q-grams
+            if (maxValRow < maxValCol) {
+                if (maxValRow != 0)
+                    val /= maxValRow;
+                distMat[col * seqNoLength + row] = val;
+                distMat[row * seqNoLength + col] = val;
+            } else {
+                if (maxValCol != 0)
+                    val /= maxValCol;
+                distMat[col * seqNoLength + row] = val;
+                distMat[row * seqNoLength + col] = val;
+            }
+        }
+    }
+
+    // set diagonal to 1
+    for(TSizeMat i = 0; i < seqNoLength; ++i)
+        distMat[i * (seqNoLength + 1)] = 1;
+}
+
+
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.range:
-..signature:range(index, shape)
-..class:Spec.IndexQGram
-..param.index:A q-gram index.
-...type:Spec.IndexQGram
-..param.shape:A shape object.
-...note:The shape stores the q-gram of the last call to @Function.hash@ or @Function.hashNext@.
-...type:Class.Shape
-..returns:All positions where the q-gram stored in $shape$ occurs in the text (see @Tag.QGram Index Fibres.QGramText@)
-are stored in a contiguous range of the suffix array.
-$range$ returns begin and end position of this range.
-If the type of $index$ is $TIndex$ the return type is $Pair<Size<TIndex>::Type>.
-..note:The necessary index tables are built on-demand via @Function.indexRequire@ if index is not $const$.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#range
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the suffix array interval borders of a q-gram in the index text.
- * 
- * @signature range(index, shape)
- * 
- * @param index A q-gram index. Types: @link IndexQGram @endlink
- * @param shape A shape object. Types: @link Shape @endlink
- * 
- * @return TReturn All positions where the q-gram
- *                 stored in <tt>shape</tt> occurs in the text (see @link QGramIndexFibres#QGramText @endlink) are 
- *                 stored in a contiguous
- *                 range of the suffix array. <tt>range</tt> returns begin and
- *                 end position of this range. If the type of <tt>index</tt> is
- *                 <tt>TIndex</tt> the return type is <tt>Pair&lt;Size&lt;TIndex&gt;::Type&gt;</tt>.
- * 
- * @section Remarks
- * 
+ *
+ * @signature TPair range(index, shape);
+ *
+ * @param[in] index  The IndexQGram object to query.
+ * @param[in] shape  The @link Shape @endlink object to use for the query.
+ *
+ * @return TPair All positions where the q-gram stored in <tt>shape</tt> occurs in the text (see @link
+ *               QGramIndexFibres#QGramText @endlink) are stored in a contiguous range of the suffix
+ *               array.  <tt>range</tt> returns begin and end position of this range. If the type of <tt>index</tt> is
+ *               <tt>TIndex</tt> the return type is <tt>Pair&lt;Size&lt;TIndex&gt;::Type&gt;</tt>.
+ *
  * The necessary index tables are built on-demand via @link Index#indexRequire @endlink if index is not <tt>const</tt>.
  */
 
 
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline Pair<typename Size< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type>
-	range(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
-		Shape< TValue, TShapeSpec2 > const &shape)
-	{
-		typedef typename Size< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type TSize;
-		typedef typename Size< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreDir>::Type>::Type TDirSize;
-		TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
-		return Pair<TSize>(indexDir(index)[bucket], indexDir(index)[bucket + 1]);
-	}
-
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline Pair<typename Size< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type>
-	range(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
-		Shape< TValue, TShapeSpec2 > const &shape)
-	{
-		indexRequire(index, QGramDir());
-		return range(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
-	}
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline Pair<typename Size< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type>
+range(
+      Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
+      Shape< TValue, TShapeSpec2 > const &shape)
+{
+    typedef typename Size< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type TSize;
+    typedef typename Size< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreDir>::Type>::Type TDirSize;
+    TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
+    return Pair<TSize>(indexDir(index)[bucket], indexDir(index)[bucket + 1]);
+}
+
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline Pair<typename Size< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type>
+range(
+      Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+      Shape< TValue, TShapeSpec2 > const &shape)
+{
+    indexRequire(index, QGramDir());
+    return range(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.getOccurrence:
-..signature:getOccurrence(index, shape)
-..class:Spec.IndexQGram
-..param.index:A q-gram index.
-...type:Spec.IndexQGram
-..param.shape:A shape object.
-...note:The shape stores the q-gram of the last call to @Function.hash@ or @Function.hashNext@.
-...type:Class.Shape
-..returns:A position where the q-gram stored in $shape$ occurs in the text (see @Tag.QGram Index Fibres.QGramText@).
-If the type of $index$ is $TIndex$ the return type is $SAValue<TIndex>::Type$.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#getOccurrence
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns an occurrence a q-gram in the index text.
  *
- * @signature getOccurrence(index, shape)
- * 
- * @param index A q-gram index. Types: @link IndexQGram @endlink
- * @param shape A shape object. Types: @link Shape @endlink
- * 
- * @return TReturn A position where the q-gram
- *                 stored in <tt>shape</tt> occurs in the text (see @link QGramIndexFibres#QGramText @endlink). 
- *                 Type: @link SAValue @endlink of the index type.
+ * @signature TSAValue getOccurrence(index, shape);
+ *
+ * @param[in] index The IndexQGram object to query.
+ * @param[in] shape The @link Shape @endlink object to use for the query.  The shape stores the <i>q</i>-gram of the
+ *                  last call ot @link Shape#hash @endlink or @link Shape#hashNext @endlink.
+ *
+ * @return TSAValue A position where the <i>q</i>-gram stored in <tt>shape</tt> occurs in the text (see @link
+ *                  QGramIndexFibres#QGramText @endlink).  Type: @link SAValue @endlink of the index type.
  */
 
 
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline typename SAValue< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type
-	getOccurrence(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
-		Shape< TValue, TShapeSpec2 > const &shape) 
-	{
-		return saAt(indexDir(index)[getBucket(indexBucketMap(index), value(shape))], index);
-	}
-
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline typename SAValue< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type
-	getOccurrence(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
-		Shape< TValue, TShapeSpec2 > const &shape) 
-	{
-		indexRequire(index, QGramSADir());
-		return getOccurrence(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
-	}
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline typename SAValue< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type
+getOccurrence(
+              Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
+              Shape< TValue, TShapeSpec2 > const &shape)
+{
+    return saAt(indexDir(index)[getBucket(indexBucketMap(index), value(shape))], index);
+}
+
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline typename SAValue< Index< TText, IndexQGram<TShapeSpec, TSpec> > >::Type
+getOccurrence(
+              Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+              Shape< TValue, TShapeSpec2 > const &shape)
+{
+    indexRequire(index, QGramSADir());
+    return getOccurrence(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.getOccurrences:
-..signature:getOccurrences(index, shape)
-..class:Spec.IndexQGram
-..param.index:A q-gram index.
-...type:Spec.IndexQGram
-..param.shape:A shape object.
-...note:The shape stores the q-gram of the last call to @Function.hash@ or @Function.hashNext@.
-...type:Class.Shape
-..returns:All positions where the q-gram stored in $shape$ occurs in the text (see @Tag.QGram Index Fibres.QGramText@).
-If the type of $index$ is $TIndex$ the return type is $Infix<Fibre<TIndex, QGramSA>::Type const>::Type$.
-..remarks:The necessary index tables are built on-demand via @Function.indexRequire@ if index is not $const$.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#getOccurrences
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns all occurrences of a q-gram in the index text.
- * 
- * @signature getOccurrences(index, shape)
- * 
- * @param index A q-gram index. Types: IndexQGram
- * @param shape A shape object. Types: Shape
- * 
- * @return TReturn All
- *                 positions where the q-gram stored in <tt>shape</tt> occurs in
- *                 the text (see @link QGramIndexFibres#QGramText @endlink).
- *                 Tupes: @link SequenceConcept#Infix @endlink<@link Index#Fibre @endlink<TIndex, QGramSA>::Type>::Type>.
- * 
- * @section Remarks
- * 
- * The necessary index tables are built on-demand via @link Index#indexRequire
- * @endlink if index is not <tt>const</tt>.
- * 
+ *
+ * @signature TSAInfix getOccurrences(index, shape);
+ *
+ * @param[in] index A IndexQGram to query.
+ * @param[in] shape A @link Shape @endlink object.
+ *
+ * @return TSAInfix All positions where the q-gram stored in <tt>shape</tt> occurs in the text (see @link
+ *                 QGramIndexFibres#QGramText @endlink).  Tupes: @link SegmentableConcept#Infix @endlink<@link Fibre
+ *                 @endlink<TIndex, QGramSA>::Type>::Type>.
+ *
+ * The necessary index tables are built on-demand via @link Index#indexRequire @endlink if index is not <tt>const</tt>.
+ *
  * @see DemoMummy
  * @see DemoSupermaximalRepeats
  * @see DemoMaximalUniqueMatches
- * 
+ *
  * @see VSTreeIterator#isUnique
  * @see VSTreeIterator#getFrequency
  * @see VSTreeIterator#isPartiallyLeftExtensible
  * @see VSTreeIterator#isLeftMaximal
  */
 
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline typename Infix< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA>::Type const >::Type 
-	getOccurrences(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
-		Shape< TValue, TShapeSpec2 > const &shape) 
-	{
-		typedef typename Size<typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreDir>::Type>::Type TDirSize;
-		TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
-		return infix(indexSA(index), indexDir(index)[bucket], indexDir(index)[bucket + 1]);
-	}	
-
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline typename Infix< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA>::Type const >::Type 
-	getOccurrences(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
-		Shape< TValue, TShapeSpec2 > const &shape) 
-	{
-		indexRequire(index, QGramSADir());
-		return getOccurrences(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
-	}	
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline typename Infix< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA>::Type const >::Type
+getOccurrences(
+               Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
+               Shape< TValue, TShapeSpec2 > const &shape)
+{
+    typedef typename Size<typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreDir>::Type>::Type TDirSize;
+    TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
+    return infix(indexSA(index), indexDir(index)[bucket], indexDir(index)[bucket + 1]);
+}
+
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline typename Infix< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA>::Type const >::Type
+getOccurrences(
+               Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+               Shape< TValue, TShapeSpec2 > const &shape)
+{
+    indexRequire(index, QGramSADir());
+    return getOccurrences(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
+}
+
+// ----------------------------------------------------------------------------
+// Function getOccurrences(); MinimizerShape
+// ----------------------------------------------------------------------------
+
+template <typename TText, unsigned TSPAN, unsigned TWEIGHT, typename TShapeSpec, typename TSpec, typename TValue, typename TPattern>
+inline typename Infix<typename Fibre<Index<TText, IndexQGram<MinimizerShape<TSPAN, TWEIGHT, TShapeSpec>, TSpec> >, FibreSA>::Type const>::Type
+getOccurrences(Index<TText, IndexQGram<MinimizerShape<TSPAN, TWEIGHT, TShapeSpec>, TSpec> > const &index,
+               Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TShapeSpec> > const &shape,
+               TPattern const & pattern)
+{
+    typedef Index<TText, IndexQGram<MinimizerShape<TSPAN, TWEIGHT>, TSpec> > const  TIndex;
+    typedef typename Fibre<TIndex, FibreDir>::Type                                  TDir;
+    typedef typename Fibre<TIndex, FibreSA>::Type                                   TSA;
+    typedef typename Size<TDir>::Type                                               TDirSize;
+    typedef typename Size<TSA>::Type                                                TSASize;
+    typedef typename Iterator<TSA const, Standard>::Type                            TSAIterator;
+    typedef SearchTreeIterator<TSA const, SortedList>                               TSearchTreeIterator;
+
+    TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
+
+    TSAIterator saBegin = begin(indexSA(index), Standard()) + dirAt(bucket, index);
+    TSASize saLen = dirAt(bucket + 1, index) - dirAt(bucket, index);
+    TSearchTreeIterator node(saBegin, saLen);
+    Pair<TSAIterator> range = _equalRangeSA(indexText(index), node, pattern);
+
+    return infix(indexSA(index), range.i1, range.i2);
+}
+
+template <typename TText, unsigned TSPAN, unsigned TWEIGHT, typename TShapeSpec, typename TSpec, typename TValue, typename TPattern>
+inline typename Infix<typename Fibre<Index<TText, IndexQGram<MinimizerShape<TSPAN, TWEIGHT, TShapeSpec>, TSpec> >, FibreSA>::Type const>::Type
+getOccurrences(Index<TText, IndexQGram<MinimizerShape<TSPAN, TWEIGHT, TShapeSpec>, TSpec> > &index,
+               Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TShapeSpec> > const &shape,
+               TPattern const & pattern)
+{
+    typedef Index<TText, IndexQGram<MinimizerShape<TSPAN, TWEIGHT, TShapeSpec>, TSpec> >    TIndex;
+
+    indexRequire(index, QGramSADir());
+    return getOccurrences(const_cast<TIndex const &>(index), shape, pattern);
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.countOccurrences:
- ..cat:Index
-..signature:countOccurrences(index, shape)
-..class:Spec.IndexQGram
-..param.index:A q-gram index.
-...type:Spec.IndexQGram
-..param.shape:A shape object.
-...note:The shape stores the q-gram of the last call to @Function.hash@ or @Function.hashNext@.
-...type:Class.Shape
-..returns:The number of positions where the q-gram stored in $shape$ occurs in the text (see @Tag.QGram Index Fibres.QGramText@).
-If the type of $index$ is $TIndex$ the return type is $Size<TIndex>::Type$.
-..note:The necessary index tables are built on-demand via @Function.indexRequire@ if index is not $const$.
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#countOccurrences
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Returns the number of occurrences of a q-gram in the index text.
- * 
- * @signature countOccurrences(index, shape)
- * 
- * @param index A q-gram index. Types: @link IndexQGram @endlink
- * @param shape A shape object. Types: @link Shape @endlink
- * 
- * @return TReturn The number of positions where the
- *                 q-gram stored in <tt>shape</tt> occurs in the text (see @link
- *                 QGramIndexFibres#QGramText @endlink). Type: @link Size @endlink of the index type.
- *                  
- * @section Remarks
- * 
- * The necessary index tables are built on-demand via @link Index#indexRequire
- * @endlink if index is not <tt>const</tt>.
- * 
+ *
+ * @signature TSize countOccurrences(index, shape);
+ *
+ * @param[in] index IndexQGram object to query.
+ * @param[in] shape A @link Shape @endlink object to use for the query.
+ *
+ * @return TSize The number of positions where the q-gram stored in <tt>shape</tt> occurs in the text (see @link
+ *               QGramIndexFibres#QGramText @endlink).  Metafunction: @link Index#Size @endlink.
+ *
+ * The necessary index tables are built on-demand via @link Index#indexRequire @endlink if index is not <tt>const</tt>.
+ *
  * Demo: Demo.Supermaximal Repeats
- * 
+ *
  * Demo: Demo.Index countChildren
  */
 
-    //TODO(singer): Why Size of FibreSA and not Size<Index>?
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline typename Size< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA>::Type const >::Type 
-	countOccurrences(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
-		Shape< TValue, TShapeSpec2 > const &shape) 
-	{
-		typedef typename Size<typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreDir>::Type>::Type TDirSize;
-		TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
-		return indexDir(index)[bucket + 1] - indexDir(index)[bucket];
-	}	
-
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline typename Size< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA>::Type const >::Type 
-	countOccurrences(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
-		Shape< TValue, TShapeSpec2 > const &shape) 
-	{
-		indexRequire(index, QGramDir());
-		return countOccurrences(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
-	}
+//TODO(singer): Why Size of FibreSA and not Size<Index>?
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline typename Size< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA>::Type const >::Type
+countOccurrences(
+                 Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
+                 Shape< TValue, TShapeSpec2 > const &shape)
+{
+    typedef typename Size<typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreDir>::Type>::Type TDirSize;
+    TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
+    return indexDir(index)[bucket + 1] - indexDir(index)[bucket];
+}
+
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline typename Size< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreSA>::Type const >::Type
+countOccurrences(
+                 Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                 Shape< TValue, TShapeSpec2 > const &shape)
+{
+    indexRequire(index, QGramDir());
+    return countOccurrences(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
+}
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.countOccurrencesMultiple:
-..cat:Index
-..summary:Returns the number of occurrences of a q-gram for every sequence of a @Class.StringSet@ .
-..signature:countOccurrencesMultiple(index, shape)
-..class:Spec.IndexQGram
-..param.index:A q-gram index of a @Class.StringSet@.
-...type:Spec.IndexQGram
-..param.shape:A shape object.
-...note:The shape stores the q-gram of the last call to @Function.hash@ or @Function.hashNext@.
-...type:Class.Shape
-..returns:A sequence of @Class.Pair.pairs@ (seqNo,count), count>0.
-For every @Class.StringSet@ sequence the q-gram occurs in, seqNo is the sequence number and count the number of occurrences.
-If the type of $index$ is $TIndex$ the return type is $Infix<Fibre<TIndex, QGramCounts>::Type const>::Type$.
-..remarks:The necessary index tables are built on-demand via @Function.indexRequire@ if index is not $const$.
-..see:Function.countOccurrences
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexQGram#countOccurrencesMultiple
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns the number of occurrences of a q-gram for every sequence of a
- *        @link StringSet @endlink .
- * 
- * @signature countOccurrencesMultiple(index, shape)
- * 
- * @param index A q-gram index of a @link StringSet @endlink. Types: @link IndexQGram @endlink
- * @param shape A shape object. Types: Shape
- * 
- * @return TReturn A sequence of @link Pair pairs @endlink (seqNo,count),
- *                 count>0. For every @link StringSet @endlink sequence the
- *                 q-gram occurs in, seqNo is the sequence number and count the
- *                 number of occurrences. If the type of <tt>index</tt> is
- *                 <tt>TIndex</tt> the return type is <tt>Infix<Fibre<TIndex,
- *                 QGramCounts>::Type const>::Type</tt>.
- * 
- * @section Remarks
- * 
+ * @headerfile <seqan/index.h>
+ * @brief Returns the number of occurrences of a q-gram for every sequence of a @link StringSet @endlink .
+ *
+ * @signature TCountInfix countOccurrencesMultiple(index, shape);
+ *
+ * @param[in] index A IndexQGram of a @link StringSet @endlink.
+ * @param[in] shape A @link Shape @endlink.
+ *
+ * @return TCountInfix A sequence of @link Pair pairs @endlink (seqNo,count), count &gt; 0.  For every @link StringSet
+ *                     @endlink sequence the q-gram occurs in, seqNo is the sequence number and count the number of
+ *                     occurrences.  If the type of <tt>index</tt> is <tt>TIndex</tt> the return type is
+ *                     <tt>Infix&lt;Fibre&lt;TIndex, QGramCounts&gt;::Type const&gt;::Type</tt>.
+ *
  * The necessary index tables are built on-demand via @link Index#indexRequire @endlink if index is not <tt>const</tt>.
- * 
+ *
  * @see VSTreeIterator#countOccurrences
  */
 
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline typename Infix< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreCounts>::Type const >::Type 
-	countOccurrencesMultiple(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
-		Shape< TValue, TShapeSpec2 > const &shape) 
-	{
-		typedef typename Size<typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreCountsDir>::Type>::Type TDirSize;
-		TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
-		return infix(indexCounts(index), indexCountsDir(index)[bucket], indexCountsDir(index)[bucket + 1]);
-	}	
-
-	template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
-	inline typename Infix< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreCounts>::Type const >::Type 
-	countOccurrencesMultiple(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
-		Shape< TValue, TShapeSpec2 > const &shape) 
-	{
-		indexRequire(index, QGramCounts());
-		return countOccurrencesMultiple(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
-	}
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline typename Infix< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreCounts>::Type const >::Type
+countOccurrencesMultiple(
+                         Index< TText, IndexQGram<TShapeSpec, TSpec> > const &index,
+                         Shape< TValue, TShapeSpec2 > const &shape)
+{
+    typedef typename Size<typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreCountsDir>::Type>::Type TDirSize;
+    TDirSize bucket = getBucket(indexBucketMap(index), value(shape));
+    return infix(indexCounts(index), indexCountsDir(index)[bucket], indexCountsDir(index)[bucket + 1]);
+}
+
+template < typename TText, typename TShapeSpec, typename TSpec, typename TShapeSpec2, typename TValue >
+inline typename Infix< typename Fibre< Index< TText, IndexQGram<TShapeSpec, TSpec> >, FibreCounts>::Type const >::Type
+countOccurrencesMultiple(
+                         Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                         Shape< TValue, TShapeSpec2 > const &shape)
+{
+    indexRequire(index, QGramCounts());
+    return countOccurrencesMultiple(const_cast<Index< TText, IndexQGram<TShapeSpec, TSpec> > const &>(index), shape);
+}
 
 
 //////////////////////////////////////////////////////////////////////////////
 // clear
 
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	inline void clear(Index<TText, IndexQGram<TShapeSpec, TSpec> > &index)
-	{
-		clear(getFibre(index, QGramSA()));
-		clear(getFibre(index, QGramDir()));
-		clear(getFibre(index, QGramCounts()));
-		clear(getFibre(index, QGramCountsDir()));
-	}
+template < typename TText, typename TShapeSpec, typename TSpec >
+inline void clear(Index<TText, IndexQGram<TShapeSpec, TSpec> > &index)
+{
+    clear(getFibre(index, QGramSA()));
+    clear(getFibre(index, QGramDir()));
+    clear(getFibre(index, QGramCounts()));
+    clear(getFibre(index, QGramCountsDir()));
+}
 
 //////////////////////////////////////////////////////////////////////////////
 // open
 
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	inline bool open(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		const char *fileName,
-		int openMode)
-	{
-		String<char> name;
-
-		name = fileName;	append(name, ".txt");
-		if ((!open(getFibre(index, QGramText()), toCString(name), openMode)) &&
-			(!open(getFibre(index, QGramText()), fileName, openMode))) return false;
-
-		name = fileName;	append(name, ".sa");
-        if (!open(getFibre(index, QGramSA()), toCString(name), openMode)) return false;
-
-		name = fileName;	append(name, ".dir");
-        if (!open(getFibre(index, QGramDir()), toCString(name), openMode)) return false;
-        
-		return true;
-	}
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	inline bool open(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		const char *fileName)
-	{
-		return open(index, fileName, OPEN_RDONLY);
-	}
+template < typename TText, typename TShapeSpec, typename TSpec >
+inline bool open(
+                 Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                 const char *fileName,
+                 int openMode)
+{
+    String<char> name;
+    
+    name = fileName;    append(name, ".txt");
+    if ((!open(getFibre(index, QGramText()), toCString(name), openMode)) &&
+        (!open(getFibre(index, QGramText()), fileName, openMode))) return false;
+    
+    name = fileName;    append(name, ".sa");
+    if (!open(getFibre(index, QGramSA()), toCString(name), openMode)) return false;
+    
+    name = fileName;    append(name, ".dir");
+    if (!open(getFibre(index, QGramDir()), toCString(name), openMode)) return false;
+    
+    return true;
+}
+template < typename TText, typename TShapeSpec, typename TSpec >
+inline bool open(
+                 Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                 const char *fileName)
+{
+    return open(index, fileName, OPEN_RDONLY);
+}
 
 
 //////////////////////////////////////////////////////////////////////////////
 // save
 
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	inline bool save(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		const char *fileName,
-		int openMode)
-	{
-		String<char> name;
-
-		name = fileName;	append(name, ".txt");
-		if ((!save(getFibre(index, QGramText()), toCString(name), openMode)) && 
-			(!save(getFibre(index, QGramText()), fileName, openMode))) return false;
-
-		name = fileName;	append(name, ".sa");
-        if (!save(getFibre(index, QGramSA()), toCString(name), openMode)) return false;
-
-		name = fileName;	append(name, ".dir");
-        if (!save(getFibre(index, QGramDir()), toCString(name), openMode)) return false;
-
-		return true;
-	}
-	template < typename TText, typename TShapeSpec, typename TSpec >
-	inline bool save(
-		Index< TText, IndexQGram<TShapeSpec, TSpec> > &index, 
-		const char *fileName)
-	{
-		return save(index, fileName, OPEN_WRONLY | OPEN_CREATE);
-	}
-
+template < typename TText, typename TShapeSpec, typename TSpec >
+inline bool save(
+                 Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                 const char *fileName,
+                 int openMode)
+{
+    String<char> name;
+    
+    name = fileName;    append(name, ".txt");
+    if ((!save(getFibre(index, QGramText()), toCString(name), openMode)) &&
+        (!save(getFibre(index, QGramText()), fileName, openMode))) return false;
+    
+    name = fileName;    append(name, ".sa");
+    if (!save(getFibre(index, QGramSA()), toCString(name), openMode)) return false;
+    
+    name = fileName;    append(name, ".dir");
+    if (!save(getFibre(index, QGramDir()), toCString(name), openMode)) return false;
+    
+    return true;
+}
+template < typename TText, typename TShapeSpec, typename TSpec >
+inline bool save(
+                 Index< TText, IndexQGram<TShapeSpec, TSpec> > &index,
+                 const char *fileName)
+{
+    return save(index, fileName, OPEN_WRONLY | OPEN_CREATE);
+}
+    
 }
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/index/index_qgram_bucketrefinement.h b/seqan/index/index_qgram_bucketrefinement.h
new file mode 100644
index 0000000..93a4985
--- /dev/null
+++ b/seqan/index/index_qgram_bucketrefinement.h
@@ -0,0 +1,634 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_QGRAM_BUCKETREFINEMENT_H_
+#define SEQAN_INDEX_QGRAM_BUCKETREFINEMENT_H_
+
+//#define SEQAN_DEBUG
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TText>
+class Index<TText, IndexSa<InfixSegment> >
+{
+public:
+    typename Member<Index, FibreText>::Type       text;
+    Holder<typename Fibre<Index, FibreSA>::Type>  sa;
+
+    Index() {}
+
+    Index(Index & other) :
+        text(other.text),
+        sa(other.sa)
+    {}
+
+    Index(Index const & other) :
+        text(other.text),
+        sa(other.sa)
+    {}
+
+    template <typename TText_>
+    Index(TText_ & _text) :
+        text(_text)
+    {}
+
+    template <typename TText_>
+    Index(TText_ const & _text) :
+        text(_text)
+    {}
+};
+
+struct BucketRefinement_;
+typedef Tag<BucketRefinement_> BucketRefinement;
+
+template <typename TText, typename TShapeSpec>
+class Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >:
+    public Index<TText, IndexQGram<TShapeSpec> >
+{
+public:
+    typedef Index<TText, IndexQGram<TShapeSpec> >    TBase;
+    typedef Index<TText, IndexSa<InfixSegment> >     TIndexSa;
+
+    TIndexSa    _indexSa;
+
+    Index() :
+        TBase()
+    {
+        _setHost(*this);
+    }
+
+    Index(Index & other) :
+        TBase(static_cast<TBase &>(other)),
+        _indexSa(other._indexSA)
+    {
+        _setHost(*this);
+    }
+
+    Index(Index const & other) :
+        TBase(static_cast<TBase const &>(other)),
+        _indexSa(other._indexSa)
+    {
+        _setHost(*this);
+    }
+
+    template <typename TText_>
+    Index(TText_ & _text) :
+        TBase(_text),
+        _indexSa(_text)
+    {
+        _setHost(*this);
+    }
+
+    template <typename TText_>
+    Index(TText_ const & _text) :
+        TBase(_text),
+        _indexSa(_text)
+    {
+        _setHost(*this);
+    }
+
+    template <typename TText_, typename TShape_>
+    Index(TText_ & _text, TShape_ const & _shape) :
+        TBase(_text, _shape),
+        _indexSa(_text)
+    {
+        _setHost(*this);
+    }
+
+    template <typename TText_, typename TShape_>
+    Index(TText_ const & _text, TShape_ const & _shape) :
+        TBase(_text, _shape),
+        _indexSa(_text)
+    {
+        _setHost(*this);
+    }
+};
+
+// ============================================================================
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+class Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > >
+{
+public:
+    typedef Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >         TIndex;
+    typedef Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > >            TParentLinksIter;
+
+    typedef Index<TText, IndexQGram<TShapeSpec> >                           TTopIndex;
+    typedef typename Iterator<TTopIndex, TopDown<TSpec> >::Type             TTopIterator;
+
+    typedef Index<TText, IndexSa<InfixSegment> >                            TBottomIndex;
+    typedef typename Iterator<TBottomIndex, TopDown<TSpec> >::Type          TBottomIterator;
+
+    TTopIterator    _topIterator;
+    TBottomIterator _bottomIterator;
+
+    Iter() {}
+
+    Iter(TIndex & _index) :
+        _topIterator(),
+        _bottomIterator(_index._indexSa)
+    {
+        _indexRequireTopDownIteration(_index);
+        _topIterator = TTopIterator(static_cast<TTopIndex &>(_index));
+        goRoot(_topIterator);
+        goRoot(_bottomIterator);
+    }
+
+    Iter(Iter const & _origin) :
+        _topIterator(_origin._topIterator),
+        _bottomIterator(_origin._bottomIterator)
+    {}
+
+    Iter(TParentLinksIter const & _origin) :
+        _topIterator(_origin._topIterator),
+        _bottomIterator(_origin._bottomIterator)
+    {}
+
+    inline Iter const &
+    operator=(Iter const & _origin)
+    {
+        _bottomIterator = _origin._bottomIterator;
+        _topIterator = _origin._topIterator;
+        return *this;
+    }
+};
+
+// ============================================================================
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+class Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<ParentLinks<TSpec> > > >
+{
+public:
+    typedef Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >                 TIndex;
+    typedef Iter<TIndex, VSTree<TopDown<TSpec> > >                                  TBase;
+
+    typedef Index<TText, IndexQGram<TShapeSpec> >                                   TTopIndex;
+    typedef typename Iterator<TTopIndex, TopDown<ParentLinks<TSpec> > >::Type       TTopIterator;
+
+    typedef Index<TText, IndexSa<InfixSegment> >                                    TBottomIndex;
+    typedef typename Iterator<TBottomIndex, TopDown<ParentLinks<TSpec> > >::Type    TBottomIterator;
+
+    TTopIterator    _topIterator;
+    TBottomIterator _bottomIterator;
+
+    Iter() {}
+
+    Iter(TIndex & _index) :
+        _topIterator(),
+        _bottomIterator(_index._indexSa)
+    {
+        _indexRequireTopDownIteration(_index);
+        _topIterator = TTopIterator(static_cast<TTopIndex &>(_index));
+        goRoot(_topIterator);
+        goRoot(_bottomIterator);
+    }
+
+    Iter(Iter const & _origin) :
+        _topIterator(_origin._topIterator),
+        _bottomIterator(_origin._bottomIterator)
+    {}
+
+    inline Iter const &
+    operator=(Iter const & _origin)
+    {
+        _bottomIterator = _origin._bottomIterator;
+        _topIterator = _origin._topIterator;
+        return *this;
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreText>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreText>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreRawText>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreRawText>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreSA>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreSA>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreRawSA>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreRawSA>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreDir>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreDir>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreSADir>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreSADir>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreShape>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreShape>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreCounts>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreCounts>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreCountsDir>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreCountsDir>
+{};
+
+template <typename TText, typename TShapeSpec>
+struct Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreBucketMap>:
+    public Fibre<Index<TText, IndexQGram<TShapeSpec> >, FibreBucketMap>
+{};
+
+// ============================================================================
+
+template <typename TText, typename TShapeSpec>
+struct DefaultIndexCreator<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreSA>:
+    public DefaultIndexCreator<Index<TText, IndexSa<InfixSegment> >, FibreSA>
+{};
+
+// ============================================================================
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+struct EdgeLabel<Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > > :
+    EdgeLabel<Iter<Index<TText, IndexQGram<TShapeSpec> >, VSTree<TSpec> > > {};
+
+// ============================================================================
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+struct Iterator<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > >
+{
+    typedef Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > >     Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TText>
+inline typename Fibre<Index<TText, IndexSa<InfixSegment> >, FibreSA>::Type &
+getFibre(Index<TText, IndexSa<InfixSegment> > & index, FibreSA)
+{
+    return value(index.sa);
+}
+
+template <typename TText>
+inline typename Fibre<Index<TText, IndexSa<InfixSegment> > const, FibreSA>::Type &
+getFibre(Index<TText, IndexSa<InfixSegment> > const & index, FibreSA)
+{
+    return value(index.sa);
+}
+
+// Works by creating the full SA and removing the suffixes of length < q.
+template <typename TText, typename TShapeSpec>
+inline bool indexCreate(Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > & index, FibreSADir, Default const)
+{
+    // Create QGram directory.
+    resize(indexDir(index), _fullDirLength(index), Exact());
+    createQGramIndexDirOnly(indexDir(index), indexBucketMap(index), indexText(index), indexShape(index), getStepSize(index));
+
+    // Create full SA.
+    indexCreate(index, FibreSA());
+
+    // Remove too short suffixes from SA.
+    _pruneSA(index);
+
+    // Update indexSA host.
+    _setHost(index);
+
+    return true;
+}
+
+// Works by creating the q-gram directory and quick-sorting the SA bucket-wise.
+//template <typename TText, typename TShapeSpec>
+//inline bool indexCreate(Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > & index, FibreSADir, Default const)
+//{
+//    typedef Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >                 TIndex;
+//    typedef Index<TText, IndexQGram<TShapeSpec> >                                   TTopIndex;
+//
+////    // Create QGram directory and refine suffix array.
+//    indexCreate(static_cast<TTopIndex &>(index), FibreSADir(), Default());
+//    _refineQGramIndex(indexSA(index), indexDir(index), indexText(index),
+//                      weight(indexShape(index)), lengthSum(indexText(index)));
+//
+//    // Update indexSA host.
+//    _setHost(index);
+//
+//    return true;
+//}
+
+template <typename TText, typename TShapeSpec>
+void _setHost(Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > & index)
+{
+    setValue(index._indexSa.sa, indexSA(index));
+}
+
+template <typename TText, typename TShapeSpec>
+void _pruneSA(Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > & index)
+{
+    typedef Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >     TIndex;
+    typedef typename Fibre<TIndex, FibreSA>::Type                       TSA;
+    typedef typename Iterator<TSA, Standard>::Type                      TSAIterator;
+
+    TSA & sa = indexSA(index);
+
+    TSAIterator saBegin = begin(sa, Standard());
+    TSAIterator saEnd = end(sa, Standard());
+
+    TSAIterator saOld = saBegin;
+    TSAIterator saNew = saOld;
+
+    while (saOld != saEnd)
+    {
+        if (suffixLength(*saOld, index) < weight(indexShape(index)))
+        {
+            ++saOld;
+        }
+        else
+        {
+            *saNew = *saOld;
+            ++saOld;
+            ++saNew;
+        }
+    }
+
+    resize(sa, saNew - saBegin, Exact());
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool _implantSa(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > & it)
+{
+    //typedef Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >     TIndex;
+    //typedef typename Value<TIndex>::Type                                TAlphabet;
+
+    if (repLength(it._topIterator) < weight(indexShape(container(it._topIterator))))
+        return false;
+
+    SEQAN_ASSERT_EQ(repLength(it._bottomIterator), 0u);
+    SEQAN_ASSERT(isRoot(it._bottomIterator));
+
+    _historyPush(it._bottomIterator);
+
+    value(it._bottomIterator).repLen = value(it._topIterator).repLen;
+    value(it._bottomIterator).range = value(it._topIterator).range;
+    value(it._bottomIterator).lastChar = value(it._topIterator).lastChar;
+
+    return true;
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool _atTop(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return isRoot(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool isRoot(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > const & it)
+{
+    return isRoot(it._topIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool isLeaf(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > const & it)
+{
+    // TODO(esiragusa): Fix isLeaf: last qgram is a top leaf but there is no subtree attached
+    return isLeaf(it._topIterator) && isLeaf(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline void goRoot(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > & it)
+{
+    goRoot(it._bottomIterator);
+    goRoot(it._topIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool goDown(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > & it)
+{
+    //typedef Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >     TIndex;
+    //typedef Pair<typename Size<TIndex>::Type>                           TSARange;
+
+    if (_atTop(it))
+    {
+        if (goDown(it._topIterator))
+            return true;
+
+        if (!_implantSa(it))
+            return false;
+    }
+
+    return goDown(it._bottomIterator);
+}
+
+// NOTE(esiragusa): I should have overloaded _goDownChar() instead.
+template <typename TText, typename TShapeSpec, typename TSpec, typename TObject>
+inline bool _goDownObject(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > & it,
+                          TObject const & obj,
+                          False const & /* tag */)
+{
+    if (_atTop(it))
+    {
+        if (_goDownObject(it._topIterator, obj, False()))
+            return true;
+
+        if (!_implantSa(it))
+            return false;
+    }
+
+    return _goDownObject(it._bottomIterator, obj, False());
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec, typename TString, typename TSize>
+inline bool _goDownString(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > & it,
+                          TString const & pattern,
+                          TSize & lcp)
+{
+    TSize topLcp = 0;
+
+    if (_atTop(it))
+    {
+        if (_goDownString(it._topIterator, pattern, lcp))
+            return true;
+
+        if (!_implantSa(it))
+            return false;
+
+        topLcp = lcp;
+    }
+
+    bool wentDown = _goDownString(it._bottomIterator, suffix(pattern, topLcp), lcp);
+
+    lcp += topLcp;
+
+    return wentDown;
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool goRight(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > & it)
+{
+    return _atTop(it) ? goRight(it._topIterator) : goRight(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline bool
+goUp(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
+{
+    if (repLength(it._bottomIterator) > repLength(it._topIterator))
+    {
+        SEQAN_ASSERT_NOT(isRoot(it._bottomIterator));
+
+        goUp(it._bottomIterator);
+
+        SEQAN_ASSERT_NOT(isRoot(it._bottomIterator));
+
+        if (repLength(it._bottomIterator) <= repLength(it._topIterator))
+            goRoot(it._bottomIterator);
+
+        return true;
+    }
+
+    return goUp(it._topIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Size<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > >::Type
+countOccurrences(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > const & it)
+{
+    return _atTop(it) ? countOccurrences(it._topIterator) : countOccurrences(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename SAValue<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > >::Type
+getOccurrence(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > const & it)
+{
+    return _atTop(it) ? getOccurrence(it._topIterator) : getOccurrence(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Infix<typename Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreSA>::Type const>::Type
+getOccurrences(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > const & it)
+{
+    return _atTop(it) ? getOccurrences(it._topIterator) : getOccurrences(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Size<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > >::Type
+repLength(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return _atTop(it) ? repLength(it._topIterator) : repLength(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Infix<typename Fibre<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, FibreText>::Type const>::Type
+representative(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > const & it)
+{
+    return _atTop(it) ? representative(it._topIterator) : representative(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Size<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > >::Type
+parentRepLength(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return _atTop(it) ? parentRepLength(it._topIterator) : parentRepLength(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Size<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > >::Type
+parentEdgeLength(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return _atTop(it) ? parentEdgeLength(it._topIterator) : parentEdgeLength(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename EdgeLabel<Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > >::Type
+parentEdgeLabel(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return _atTop(it) ? parentEdgeLabel(it._topIterator) : parentEdgeLabel(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline typename Value<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > >::Type
+parentEdgeFirstChar(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return _atTop(it) ? parentEdgeFirstChar(it._topIterator) : parentEdgeFirstChar(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec, typename TSpec>
+inline Pair<typename Size<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > >::Type>
+range(Iter<Index<TText, IndexQGram<TShapeSpec, BucketRefinement> >, VSTree<TSpec> > const & it)
+{
+    return _atTop(it) ? range(it._topIterator) : range(it._bottomIterator);
+}
+
+template <typename TText, typename TShapeSpec>
+inline bool open(Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > & index, const char * fileName)
+{
+    typedef Index<TText, IndexQGram<TShapeSpec> >    TBaseIndex;
+
+    if (open(static_cast<TBaseIndex &>(index), fileName))
+    {
+        setHost(index._indexSa, indexText(index));
+        _setHost(index);
+        return true;
+    }
+
+    return false;
+}
+
+template <typename TText, typename TShapeSpec>
+inline bool save(Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > & index, const char * fileName)
+{
+    typedef Index<TText, IndexQGram<TShapeSpec> >    TBaseIndex;
+
+    return save(static_cast<TBaseIndex &>(index), fileName);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INDEX_QGRAM_BUCKETREFINEMENT_H_
diff --git a/seqan/index/index_qgram_openaddressing.h b/seqan/index/index_qgram_openaddressing.h
index 4a6c2e6..f199230 100644
--- a/seqan/index/index_qgram_openaddressing.h
+++ b/seqan/index/index_qgram_openaddressing.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,73 +38,48 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	struct OpenAddressing_;
-	typedef Tag<OpenAddressing_> OpenAddressing;
-	
-	template <typename THashValue>
-	struct BucketMap 
-	{
+    struct OpenAddressing_;
+    typedef Tag<OpenAddressing_> OpenAddressing;
+
+    template <typename THashValue>
+    struct BucketMap
+    {
         static const THashValue EMPTY;
-		String<THashValue> qgramCode;
-	};
+        String<THashValue> qgramCode;
+    };
 
-	template <typename THashValue>
+    template <typename THashValue>
     const THashValue BucketMap<THashValue>::EMPTY = (THashValue)-1;
 
-	// use the index value type as shape value type
-	template < typename TObject, typename TShapeSpec >
-	struct Fibre< Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >, FibreBucketMap>
-	{
-		typedef typename Fibre< Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >, FibreShape>::Type TShape;
-		typedef typename Value<TShape>::Type	THashValue;
-		typedef BucketMap<THashValue>			Type;
-	};
-	
-/**
-.Spec.OpenAddressing
-..summary:An index based on an array of sorted q-grams.
-..cat:Index
-..general:Spec.IndexQGram
-..signature:Index<TText, IndexQGram<TShapeSpec, OpenAddressing> >
-..param.TText:The text type.
-...type:Class.String
-..param.TShapeSpec:The @Class.Shape@ specialization type.
-...note:This can be either a $TSpec$ argument (e.g. $SimpleShape$) or a complete @Class.Shape@ class (e.g. Shape<Dna, SimpleShape>).
-..remarks:This index uses a non-trivial hashing for mapping q-gram hash values to buckets.
-This reduces the sizes of bucket directories (QGramDir, QGramCountsDir fibres) from |\Sigma|^q to min(\alpha*n,|\Sigma|^q), for a load factor \alpha>1.
-A bucket still stores occurrences (or counts) of the same q-gram, but in contrast to the @Spec.IndexQGram@ index, buckets are in random order due to the hashing.
-..include:seqan/index.h
-.Memvar.OpenAddressing#alpha
-..summary:Load factor. Controls space/time-tradeoff and must be greater 1. Default value is 1.6.
-..class:Spec.OpenAddressing
-*/	
+    // use the index value type as shape value type
+    template < typename TObject, typename TShapeSpec >
+    struct Fibre< Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >, FibreBucketMap>
+    {
+        typedef typename Fibre< Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >, FibreShape>::Type TShape;
+        typedef typename Value<TShape>::Type    THashValue;
+        typedef BucketMap<THashValue>            Type;
+    };
+
 /*!
- * @class OpenAddressing
- * 
+ * @class OpenAddressingQGramIndex
  * @extends IndexQGram
- * 
- * @headerfile seqan/index.h
- * 
- * @brief An index based on an array of sorted q-grams.
- * 
- * @signature Index<TText, IndexQGram<TShapeSpec, OpenAddressing> >
- * 
- * @tparam TText The text type. Types: @link String @endlink
+ * @headerfile <seqan/index.h>
+ * @brief A <i>q</i>-gram that uses open addressing hashing instead of an array.
+ *
+ * @signature template <typename TIndex, typename TShapeSpec>
+ *            class Index<TText, IndexQGram<TShapeSpec, OpenAddressing> >;
+ *
+ * @tparam TText      The @link TextConcept text type @endlink.
  * @tparam TShapeSpec The @link Shape @endlink specialization type.
- * 
- * @section Remarks
- * 
- * This index uses a non-trivial hashing for mapping q-gram hash values to
- * buckets. This reduces the sizes of bucket directories (QGramDir,
- * QGramCountsDir fibres) from |\Sigma|^q to min(\alpha*n,|\Sigma|^q), for a
- * load factor \alpha>1. A bucket still stores occurrences (or counts) of the
- * same q-gram, but in contrast to the @link IndexQGram @endlink index, buckets
- * are in random order due to the hashing.
- * 
- * @var VariableType OpenAddressing::alpha
- * 
- * @brief Load factor. Controls space/time-tradeoff and must be greater 1.
- *        Default value is 1.6.
+ *
+ * This index uses a non-trivial hashing for mapping q-gram hash values to buckets.  This reduces the sizes of bucket
+ * directories (QGramDir, QGramCountsDir fibres) from &Sigma;<i><sup>q</sup></i> to min(<i>&alpha; &middot; n</i>,
+ * \Sigma<i><sup>q</sup></i>), for a load factor <i>&alpha; &gt; 1</i>.  A bucket still stores occurrences (or counts)
+ * of the same <i>q</i>-gram, but in contrast to the @link IndexQGram @endlink index, buckets are in random order due to
+ * the hashing.
+ *
+ * @var double OpenAddressingQGramIndex::alpha
+ * @brief Load factor.  Controls space/time-tradeoff and must be greater 1.  Default value is 1.6.
  */
 #ifdef PLATFORM_WINDOWS_VS
 #pragma warning( push )
@@ -112,88 +87,89 @@ A bucket still stores occurrences (or counts) of the same q-gram, but in contras
 #pragma warning( disable: 4521 )
 #endif  // PLATFORM_WINDOWS_VS
 
-	template < typename TObject, typename TShapeSpec >
-	class Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >
-	{
+    template < typename TObject, typename TShapeSpec >
+    class Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >
+    {
     private:
         static const double defaultAlpha;
-	public:
-		typedef typename Fibre<Index, QGramText>::Type		TText;
-		typedef typename Fibre<Index, QGramSA>::Type		TSA;
-		typedef typename Fibre<Index, QGramDir>::Type		TDir;
-		typedef typename Fibre<Index, QGramCounts>::Type	TCounts;
-		typedef typename Fibre<Index, QGramCountsDir>::Type	TCountsDir;
-		typedef typename Fibre<Index, QGramShape>::Type		TShape;
-		typedef typename Fibre<Index, QGramBucketMap>::Type	TBucketMap;
-		typedef typename Cargo<Index>::Type					TCargo;
-		typedef typename Size<Index>::Type					TSize;
-
-		Holder<TText>	text;		// underlying text
-		TSA				sa;			// suffix array sorted by the first q chars
-		TDir			dir;		// bucket directory
-		TCounts			counts;		// counts each q-gram per sequence
-		TCountsDir		countsDir;	// directory for count buckets
-		TShape			shape;		// underlying shape
-		TCargo			cargo;		// user-defined cargo
-		TBucketMap		bucketMap;	// bucketMap table (used by open-addressing index)
-		TSize			stepSize;	// store every <stepSize>'th q-gram in the index
-
-		double			alpha;		// for m entries the hash map has at least size alpha*m
-
-		Index():
-			stepSize(1),
-			alpha(defaultAlpha) {}
-
-		Index(Index &other):
-			text(other.text),
-			sa(other.sa),
-			dir(other.dir),
-			counts(other.counts),
-			countsDir(other.countsDir),
-			shape(other.shape),
-			cargo(other.cargo),
-			bucketMap(other.bucketMap),
-			stepSize(1),
-			alpha(defaultAlpha) {}
-
-		Index(Index const &other):
-			text(other.text),
-			sa(other.sa),
-			dir(other.dir),
-			counts(other.counts),
-			countsDir(other.countsDir),
-			shape(other.shape),
-			cargo(other.cargo),
-			bucketMap(other.bucketMap),
-			stepSize(1),
-			alpha(defaultAlpha) {}
-
-		template <typename TText_>
-		Index(TText_ &_text):
-			text(_text),
-			stepSize(1),
-			alpha(defaultAlpha) {}
-
-		template <typename TText_>
-		Index(TText_ const &_text):
-			text(_text),
-			stepSize(1),
-			alpha(defaultAlpha) {}
-
-		template <typename TText_, typename TShape_>
-		Index(TText_ &_text, TShape_ const &_shape):
-			text(_text),
-			shape(_shape),
-			stepSize(1),
-			alpha(defaultAlpha) {}
-
-		template <typename TText_, typename TShape_>
-		Index(TText_ const &_text, TShape_ const &_shape):
-			text(_text),
-			shape(_shape),
-			stepSize(1),
-			alpha(defaultAlpha) {}
-	};
+    public:
+        typedef typename Member<Index, QGramText>::Type     TTextMember;
+        typedef typename Fibre<Index, QGramText>::Type        TText;
+        typedef typename Fibre<Index, QGramSA>::Type        TSA;
+        typedef typename Fibre<Index, QGramDir>::Type        TDir;
+        typedef typename Fibre<Index, QGramCounts>::Type    TCounts;
+        typedef typename Fibre<Index, QGramCountsDir>::Type    TCountsDir;
+        typedef typename Fibre<Index, QGramShape>::Type        TShape;
+        typedef typename Fibre<Index, QGramBucketMap>::Type    TBucketMap;
+        typedef typename Cargo<Index>::Type                    TCargo;
+        typedef typename Size<Index>::Type                    TSize;
+
+        TTextMember     text;        // underlying text
+        TSA                sa;            // suffix array sorted by the first q chars
+        TDir            dir;        // bucket directory
+        TCounts            counts;        // counts each q-gram per sequence
+        TCountsDir        countsDir;    // directory for count buckets
+        TShape            shape;        // underlying shape
+        TCargo            cargo;        // user-defined cargo
+        TBucketMap        bucketMap;    // bucketMap table (used by open-addressing index)
+        TSize            stepSize;    // store every <stepSize>'th q-gram in the index
+
+        double            alpha;        // for m entries the hash map has at least size alpha*m
+
+        Index():
+            stepSize(1),
+            alpha(defaultAlpha) {}
+
+        Index(Index &other):
+            text(other.text),
+            sa(other.sa),
+            dir(other.dir),
+            counts(other.counts),
+            countsDir(other.countsDir),
+            shape(other.shape),
+            cargo(other.cargo),
+            bucketMap(other.bucketMap),
+            stepSize(1),
+            alpha(defaultAlpha) {}
+
+        Index(Index const &other):
+            text(other.text),
+            sa(other.sa),
+            dir(other.dir),
+            counts(other.counts),
+            countsDir(other.countsDir),
+            shape(other.shape),
+            cargo(other.cargo),
+            bucketMap(other.bucketMap),
+            stepSize(1),
+            alpha(defaultAlpha) {}
+
+        template <typename TText_>
+        Index(TText_ &_text):
+            text(_text),
+            stepSize(1),
+            alpha(defaultAlpha) {}
+
+        template <typename TText_>
+        Index(TText_ const &_text):
+            text(_text),
+            stepSize(1),
+            alpha(defaultAlpha) {}
+
+        template <typename TText_, typename TShape_>
+        Index(TText_ &_text, TShape_ const &_shape):
+            text(_text),
+            shape(_shape),
+            stepSize(1),
+            alpha(defaultAlpha) {}
+
+        template <typename TText_, typename TShape_>
+        Index(TText_ const &_text, TShape_ const &_shape):
+            text(_text),
+            shape(_shape),
+            stepSize(1),
+            alpha(defaultAlpha) {}
+    };
 #ifdef PLATFORM_WINDOWS_VS
 // Enable warning C4521 again (multiple copy operators).
 #pragma warning( pop )
@@ -203,17 +179,17 @@ A bucket still stores occurrences (or counts) of the same q-gram, but in contras
     template < typename TObject, typename TShapeSpec >
     const double Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >::defaultAlpha = 1.6;
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Counting sort - Step 1: Clear directory
-	template < typename TDir, typename THashValue, typename TParallelTag >
-	inline void _qgramClearDir(TDir &dir, BucketMap<THashValue> &bucketMap, Tag<TParallelTag> parallelTag)
-	{
+    //////////////////////////////////////////////////////////////////////////////
+    // Counting sort - Step 1: Clear directory
+    template < typename TDir, typename THashValue, typename TParallelTag >
+    inline void _qgramClearDir(TDir &dir, BucketMap<THashValue> &bucketMap, Tag<TParallelTag> parallelTag)
+    {
         typedef BucketMap<THashValue> TBucketMap;
         if (!empty(dir))
             arrayFill(begin(dir, Standard()), end(dir, Standard()), 0, parallelTag);
         if (!empty(bucketMap.qgramCode))
             arrayFill(begin(bucketMap.qgramCode, Standard()), end(bucketMap.qgramCode, Standard()), TBucketMap::EMPTY, parallelTag);
-	}
+    }
 
     template < typename TBucketMap, typename TValue >
     inline TValue
@@ -228,37 +204,37 @@ A bucket still stores occurrences (or counts) of the same q-gram, but in contras
 #endif
     }
 
-	template < typename THashValue, typename THashValue2, typename TParallelTag >
-	inline THashValue
-	requestBucket(BucketMap<THashValue> &bucketMap, THashValue2 code, Tag<TParallelTag> parallelTag)
-	{
+    template < typename THashValue, typename THashValue2, typename TParallelTag >
+    inline THashValue
+    requestBucket(BucketMap<THashValue> &bucketMap, THashValue2 code, Tag<TParallelTag> parallelTag)
+    {
         typedef BucketMap<THashValue> TBucketMap;
-		typedef unsigned long TSize;
-		// get size of the index
+        typedef unsigned long TSize;
+        // get size of the index
 
-		// check whether bucket map is disabled and
-		// where the hash should be found if no collision took place before
-		register TSize hlen = length(bucketMap.qgramCode);
-		if (hlen == 0ul) return code;
+        // check whether bucket map is disabled and
+        // where the hash should be found if no collision took place before
+        TSize hlen = length(bucketMap.qgramCode);
+        if (hlen == 0ul) return code;
 
-        register TSize h1 = _hashFunction(bucketMap, code);
+        TSize h1 = _hashFunction(bucketMap, code);
 #ifdef SEQAN_OPENADDRESSING_COMPACT
         --hlen;
-		h1 %= hlen;
+        h1 %= hlen;
 #else
         hlen -= 2;
-		h1 &= hlen;
+        h1 &= hlen;
 #endif
-		// was the entry empty or occupied by our code?
+        // was the entry empty or occupied by our code?
         THashValue currentCode = atomicCas(bucketMap.qgramCode[h1], TBucketMap::EMPTY, code, parallelTag);
         if (currentCode == TBucketMap::EMPTY || currentCode == code)
-			return h1;
+            return h1;
 
         // if not we have a collision -> probe for our code or an empty entry
         //
         // do linear probing if we need to save memory (when SEQAN_OPENADDRESSING_COMPACT is defined)
         // otherwise do quadratic probing to avoid clustering (Cormen 1998)
-        register TSize delta = 0;
+        TSize delta = 0;
         (void)delta;
         do {
 #ifdef SEQAN_OPENADDRESSING_COMPACT
@@ -270,47 +246,47 @@ A bucket still stores occurrences (or counts) of the same q-gram, but in contras
             currentCode = atomicCas(bucketMap.qgramCode[h1], TBucketMap::EMPTY, code, parallelTag);
         } while (currentCode != TBucketMap::EMPTY && currentCode != code);
         return h1;
-	}
+    }
 
-	template < typename THashValue, typename THashValue2 >
-	inline THashValue
-	getBucket(BucketMap<THashValue> const &bucketMap, THashValue2 code)
-	{
+    template < typename THashValue, typename THashValue2 >
+    inline THashValue
+    getBucket(BucketMap<THashValue> const &bucketMap, THashValue2 code)
+    {
         typedef BucketMap<THashValue> TBucketMap;
-		typedef unsigned long TSize;
-		// get size of the index
-		
-		// check whether bucket map is disabled and
-		// where the hash should be found if no collision took place before
-		register TSize hlen = length(bucketMap.qgramCode);
-		if (hlen == 0ul) return code;
-
-        register TSize h1 = _hashFunction(bucketMap, code);
+        typedef unsigned long TSize;
+        // get size of the index
+
+        // check whether bucket map is disabled and
+        // where the hash should be found if no collision took place before
+        TSize hlen = length(bucketMap.qgramCode);
+        if (hlen == 0ul) return code;
+
+        TSize h1 = _hashFunction(bucketMap, code);
 #ifdef SEQAN_OPENADDRESSING_COMPACT
         --hlen;
         h1 %= hlen;
 #else
         hlen -= 2;
-		h1 &= hlen;
+        h1 &= hlen;
 #endif
-		
+
         // probe for our code or an empty entry
         //
         // do linear probing if we need to save memory (when SEQAN_OPENADDRESSING_COMPACT is defined)
         // otherwise do quadratic probing to avoid clustering (Cormen 1998)
-        register TSize delta = 0;
+        TSize delta = 0;
         (void)delta;
-		while (bucketMap.qgramCode[h1] != code && bucketMap.qgramCode[h1] != TBucketMap::EMPTY)
-		{
+        while (bucketMap.qgramCode[h1] != code && bucketMap.qgramCode[h1] != TBucketMap::EMPTY)
+        {
 #ifdef SEQAN_OPENADDRESSING_COMPACT
-			h1 = (h1 + 1) % hlen;               // linear probing guarantees that all entries are visited
+            h1 = (h1 + 1) % hlen;               // linear probing guarantees that all entries are visited
 #else
-			h1 = (h1 + delta + 1) & hlen;       // for power2-sized tables the (i*i+i)/2 probing guarantees the same
+            h1 = (h1 + delta + 1) & hlen;       // for power2-sized tables the (i*i+i)/2 probing guarantees the same
             ++delta;
 #endif
-		}
-		return h1;
-	}
+        }
+        return h1;
+    }
 
     template <typename TBucketMap>
     inline bool _emptyBucketMap(TBucketMap const &bucketMap)
@@ -323,40 +299,100 @@ A bucket still stores occurrences (or counts) of the same q-gram, but in contras
         return false;
     }
 
-	template <typename TObject, typename TShapeSpec>
-	inline __int64 _fullDirLength(Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> > const &index) 
-	{
-		typedef Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >	TIndex;
-		typedef typename Fibre<TIndex, QGramDir>::Type						TDir;
-		typedef typename Fibre<TIndex, FibreShape>::Type					TShape;
-		typedef typename Host<TShape>::Type									TTextValue;
-		typedef typename Value<TDir>::Type									TDirValue;
-		typedef typename Value<TShape>::Type								THashValue;
-		
-		double num_qgrams = _qgramQGramCount(index) * index.alpha;
-		double max_qgrams = pow((double)ValueSize<TTextValue>::VALUE, (double)weight(indexShape(index)));
-		__int64 qgrams;
-		
-		// compare size of open adressing with 1-1 mapping and use the smaller one
-		if (num_qgrams * (sizeof(TDirValue) + sizeof(THashValue)) < max_qgrams * sizeof(TDirValue))
-		{
-			qgrams = (__int64)ceil(num_qgrams);
+    template <typename TObject, typename TShapeSpec>
+    inline __int64 _fullDirLength(Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> > const &index)
+    {
+        typedef Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >    TIndex;
+        typedef typename Fibre<TIndex, QGramDir>::Type                        TDir;
+        typedef typename Fibre<TIndex, FibreShape>::Type                    TShape;
+        typedef typename Host<TShape>::Type                                    TTextValue;
+        typedef typename Value<TDir>::Type                                    TDirValue;
+        typedef typename Value<TShape>::Type                                THashValue;
+
+        double num_qgrams = _qgramQGramCount(index) * index.alpha;
+        double max_qgrams = pow((double)ValueSize<TTextValue>::VALUE, (double)weight(indexShape(index)));
+        __int64 qgrams;
+
+        // compare size of open adressing with 1-1 mapping and use the smaller one
+        if (num_qgrams * (sizeof(TDirValue) + sizeof(THashValue)) < max_qgrams * sizeof(TDirValue))
+        {
+            qgrams = (__int64)ceil(num_qgrams);
 #ifndef SEQAN_OPENADDRESSING_COMPACT
-			__int64 power2 = 1;
-			while (power2 < qgrams)
-				power2 <<= 1;
-			qgrams = power2;
+            __int64 power2 = 1;
+            while (power2 < qgrams)
+                power2 <<= 1;
+            qgrams = power2;
 #endif
-			resize(const_cast<TIndex &>(index).bucketMap.qgramCode, qgrams + 1, Exact());
-		} else
-		{
-			qgrams = (__int64)ceil(max_qgrams);
-			clear(const_cast<TIndex &>(index).bucketMap.qgramCode);	// 1-1 mapping, no bucket map needed
-		}
-		
-		return qgrams + 1;
-	}
-	
+            resize(const_cast<TIndex &>(index).bucketMap.qgramCode, qgrams + 1, Exact());
+        } else
+        {
+            qgrams = (__int64)ceil(max_qgrams);
+            clear(const_cast<TIndex &>(index).bucketMap.qgramCode);    // 1-1 mapping, no bucket map needed
+        }
+
+        return qgrams + 1;
+    }
+
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+template < typename TText, typename TShapeSpec>
+inline bool open(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName, int openMode)
+{
+    String<char> name;
+    
+    name = fileName;    append(name, ".txt");
+    if (!open(getFibre(index, QGramText()), toCString(name), openMode)) return false;
+    
+    name = fileName;    append(name, ".sa");
+    if (!open(getFibre(index, QGramSA()), toCString(name), openMode)) return false;
+    
+    name = fileName;    append(name, ".dir");
+    if (!open(getFibre(index, QGramDir()), toCString(name), openMode)) return false;
+
+    name = fileName;    append(name, ".bkt");
+    if (!open(getFibre(index, QGramBucketMap()).qgramCode, toCString(name), openMode)) return false;
+
+    return true;
+}
+
+template <typename TText, typename TShapeSpec>
+inline bool open(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName)
+{
+    return open(index, fileName, OPEN_RDONLY);
+}
+
+// ----------------------------------------------------------------------------
+// Function save()
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TShapeSpec>
+inline bool save(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName, int openMode)
+{
+    String<char> name;
+    
+    name = fileName;    append(name, ".txt");
+    if (!save(getFibre(index, QGramText()), toCString(name), openMode)) return false;
+    
+    name = fileName;    append(name, ".sa");
+    if (!save(getFibre(index, QGramSA()), toCString(name), openMode)) return false;
+    
+    name = fileName;    append(name, ".dir");
+    if (!save(getFibre(index, QGramDir()), toCString(name), openMode)) return false;
+
+    name = fileName;    append(name, ".bkt");
+    if (!save(getFibre(index, QGramBucketMap()).qgramCode, toCString(name), openMode)) return false;
+
+    return true;
+}
+
+template <typename TText, typename TShapeSpec>
+inline bool save(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName)
+{
+    return save(index, fileName, OPEN_WRONLY | OPEN_CREATE);
+}
+
 }
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/index/index_qgram_stree.h b/seqan/index/index_qgram_stree.h
new file mode 100644
index 0000000..3de57f1
--- /dev/null
+++ b/seqan/index/index_qgram_stree.h
@@ -0,0 +1,382 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// TopDown Iterators for the QGram Index.
+// ==========================================================================
+// Define SEQAN_INDEX_QGRAM_TREE to let the edge labels be tree-like infixes
+// of arbitrary length instead of trie-like unitary symbols.
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_QGRAM_STREE_H_
+#define SEQAN_INDEX_QGRAM_STREE_H_
+
+//#define SEQAN_DEBUG
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TSize, typename TShape>
+struct VertexQGram
+{
+    typedef typename Host<TShape>::Type                 TAlphabet;
+    typedef typename Value<TShape>::Type                THashValue;
+
+    Pair<TSize>         range;
+    Pair<THashValue>    hash;
+    TSize               repLen;
+    TAlphabet           lastChar;
+
+    VertexQGram() :
+        range(0, 0),
+        hash(0, 0),
+        repLen(0),
+        lastChar(0)
+    {}
+
+    VertexQGram(MinimalCtor) :
+        range(0, 0),
+        hash(0, 0),
+        repLen(0),
+        lastChar(0)
+    {}
+
+    VertexQGram(VertexQGram const & other) :
+        range(other.range),
+        hash(other.hash),
+        repLen(other.repLen),
+        lastChar(other.lastChar)
+    {}
+};
+
+template <typename TSize, typename TShape>
+struct HistoryStackQGram_
+{
+    typedef typename Host<TShape>::Type                 TAlphabet;
+    typedef typename Value<TShape>::Type                THashValue;
+
+    Pair<TSize>         range;
+    Pair<THashValue>    hash;
+    TAlphabet           lastChar;
+
+    HistoryStackQGram_() {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec>
+struct VertexDescriptor<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> > >
+{
+private:
+    typedef Index<TText, IndexQGram<TIndexSpec> >       TIndex;
+    typedef typename Fibre<TIndex, QGramShape>::Type    TShape;
+    typedef typename Size<TIndex>::Type                 TSize;
+
+public:
+    typedef VertexQGram<TSize, TShape>                  Type;
+};
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+struct HistoryStackEntry_<Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >,
+                               VSTree<TopDown<ParentLinks<TSpec> > > > >
+{
+private:
+    typedef Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >   TIndex;
+    typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+    typedef typename Size<TIndex>::Type                         TSize;
+
+public:
+    typedef HistoryStackQGram_<TSize, TShape>                   Type;
+};
+
+#ifndef SEQAN_INDEX_QGRAM_TREE
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+struct EdgeLabel<Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TSpec> > >
+{
+    typedef typename Value<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> > >::Type Type;
+};
+#endif
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+struct Iterator<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TSpec> >
+{
+    typedef Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TSpec> >    Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec>
+void _indexRequireTopDownIteration(Index<TText, IndexQGram<TShapeSpec, TIndexSpec> > & index)
+{
+    indexRequire(index, QGramSADir());
+}
+
+template <typename TSize, typename TShape>
+inline bool _isRoot(VertexQGram<TSize, TShape> const & value)
+{
+    return _isSizeInval(value.range.i2);
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+inline bool isLeaf(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TSpec> > const & it)
+{
+    return value(it).hash.i1 + 1 >= value(it).hash.i2;
+}
+
+template <typename TIndex, typename TSize, typename TShape>
+inline typename Size<TIndex>::Type
+repLength(TIndex const &, VertexQGram<TSize, TShape> const & vDesc)
+{
+    return vDesc.repLen;
+}
+
+#ifndef SEQAN_INDEX_QGRAM_TREE
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+inline typename EdgeLabel<Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > >::Type
+parentEdgeLabel(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return value(it).lastChar;
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+inline typename Value<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> > >::Type
+parentEdgeFirstChar(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return value(it).lastChar;
+}
+#endif
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+inline void goRoot(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TSpec> > & it)
+{
+    typedef Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >   TIndex;
+    typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+
+    _historyClear(it);
+    clear(it);
+    if (!empty(indexSA(container(it))))
+        _setSizeInval(value(it).range.i2);
+
+    value(it).hash.i1 = 0;
+    value(it).hash.i2 = ValueSize<TShape>::VALUE;
+    value(it).repLen = 0;
+
+#ifdef SEQAN_DEBUG
+    std::cout << "[" << value(it).hash.i1 << "," << value(it).hash.i2 << ")" << std::endl;
+#endif
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+inline void
+_historyPush(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it)
+{
+    it._parentDesc = value(it);
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+inline void
+_historyPush(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
+{
+    typedef Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > TIter;
+    typename HistoryStackEntry_<TIter>::Type h;
+    h.range = value(it).range;
+    h.hash = value(it).hash;
+    h.lastChar = value(it).lastChar;
+
+    appendValue(it.history, h);
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec, typename TValue>
+inline bool
+_getNodeByChar(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TSpec> > const & it,
+               TValue c,
+               typename VertexDescriptor<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> > >::Type & childDesc)
+{
+    typedef Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >   TIndex;
+    typedef typename Fibre<TIndex, QGramDir>::Type              TDir;
+    typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+    typedef typename Host<TShape>::Type                         TAlphabet;
+    typedef typename Value<TShape>::Type                        THValue;
+
+    if (isLeaf(it))
+        return false;
+
+    TIndex const & index = container(it);
+    TDir const & dir = indexDir(index);
+    TShape const & shape = indexShape(index);
+
+    childDesc = value(it);
+    childDesc.lastChar = c;
+
+    // TODO(esiragusa): Remove call to pow
+    THValue h = static_cast<THValue>(pow(static_cast<double>(ValueSize<TAlphabet>::VALUE), static_cast<int>(weight(shape) - childDesc.repLen - 1)));
+    childDesc.hash.i1 = childDesc.hash.i1 + ordValue(childDesc.lastChar) * h;
+    childDesc.hash.i2 = childDesc.hash.i2 - (ValueSize<TAlphabet>::VALUE - 1 - ordValue(childDesc.lastChar)) * h;
+
+#ifdef SEQAN_DEBUG
+    std::cout << "[" << childDesc.hash.i1 << "," << childDesc.hash.i2 << ")" << std::endl;
+#endif
+
+    childDesc.range.i1 = dir[getBucket(index.bucketMap, childDesc.hash.i1)];
+    childDesc.range.i2 = dir[getBucket(index.bucketMap, childDesc.hash.i2)];
+
+    childDesc.repLen++;
+
+#ifdef SEQAN_DEBUG
+    std::cout << "[" << childDesc.range.i1 << "," << childDesc.range.i2 << ")" << std::endl;
+#endif
+
+    return childDesc.range.i1 < childDesc.range.i2;
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+inline bool _getNextNode(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TSpec> > & it)
+{
+    typedef Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >   TIndex;
+    typedef typename Fibre<TIndex, QGramDir>::Type              TDir;
+    typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+    typedef typename Host<TShape>::Type                         TAlphabet;
+    typedef typename Value<TShape>::Type                        THValue;
+
+    TIndex const & index = container(it);
+    TDir const & dir = indexDir(index);
+    TShape const & shape = indexShape(index);
+
+    // TODO(esiragusa): Remove call to pow
+    THValue h = static_cast<THValue>(pow(static_cast<double>(ValueSize<TAlphabet>::VALUE), static_cast<int>(weight(shape) - value(it).repLen)));
+
+    // TODO(esiragusa): Remove workaround for alphabets with quality values
+    for (typename ValueSize<TAlphabet>::Type c = ordValue(value(it).lastChar) + 1; c < ValueSize<TAlphabet>::VALUE; ++c)
+    {
+        value(it).hash.i1 = value(it).hash.i2;
+        value(it).hash.i2 += h;
+        value(it).range.i1 = value(it).range.i2;
+        value(it).range.i2 = dir[getBucket(index.bucketMap, value(it).hash.i2)];
+        value(it).lastChar = c;
+
+        if (value(it).range.i1 < value(it).range.i2)
+            return true;
+    }
+
+    return false;
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec, typename TString, typename TSize>
+inline bool
+_goDownString(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & node,
+              TString const & pattern,
+              TSize & lcp)
+{
+    typedef typename Iterator<TString const, Standard>::Type    PatternIterator;
+
+    lcp = 0;
+
+    PatternIterator patternBegin = begin(pattern, Standard());
+    PatternIterator patternEnd = end(pattern, Standard());
+
+    // TODO(esiragusa): Specialize to compute the whole hash at once
+    for (PatternIterator patternIt = patternBegin; patternIt != patternEnd; ++patternIt)
+    {
+        if (!_goDownChar(node, *patternIt))
+            return false;
+
+        ++lcp;
+    }
+
+    return true;
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder, typename THideEmptyEdges>
+inline bool _goDown(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+                    VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
+{
+    typedef Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >   TIndex;
+    typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
+    typedef typename Host<TShape>::Type                         TAlphabet;
+
+    if (isLeaf(it))
+        return false;
+
+    // TODO(esiragusa): check nodeHullPredicate
+
+    typename VertexDescriptor<TIndex>::Type nodeDesc;
+
+    // TODO(esiragusa): Remove workaround for alphabets with quality values
+    for (typename ValueSize<TAlphabet>::Type c = 0; c < ValueSize<TAlphabet>::VALUE; ++c)
+    {
+        if (_getNodeByChar(it, c, nodeDesc))
+        {
+            _historyPush(it);
+            value(it) = nodeDesc;
+            return true;
+        }
+    }
+
+    return false;
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec, typename TDfsOrder, typename THideEmptyEdges>
+inline bool _goRight(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+                     VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
+{
+    if (isRoot(it))
+        return false;
+
+    return _getNextNode(it);
+}
+
+template <typename TText, typename TShapeSpec, typename TIndexSpec, typename TSpec>
+inline bool
+_goUp(Iter<Index<TText, IndexQGram<TShapeSpec, TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
+{
+    if (!empty(it.history))
+    {
+        value(it).range = back(it.history).range;
+        value(it).hash = back(it.history).hash;
+        value(it).lastChar = back(it.history).lastChar;
+        value(it).repLen--;
+        eraseBack(it.history);
+        return true;
+    }
+    return false;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INDEX_QGRAM_STREE_H_
diff --git a/seqan/index/index_sa_btree.h b/seqan/index/index_sa_btree.h
index 3a817c0..6ea4911 100644
--- a/seqan/index/index_sa_btree.h
+++ b/seqan/index/index_sa_btree.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,73 +37,73 @@
 
 namespace SEQAN_NAMESPACE_MAIN
 {
-	
-	template <
-		class SAFwdIt,		// suffix array input iterator
-		class FlatOutIt >	// flat tree output iterator
-	inline FlatOutIt createSABTree(
-		SAFwdIt First_, SAFwdIt _Last,
-		FlatOutIt Dest_, unsigned BlockSize)
-	{
-        typedef typename Value<SAFwdIt>::Type	TSize;
+
+    template <
+        class SAFwdIt,        // suffix array input iterator
+        class FlatOutIt >    // flat tree output iterator
+    inline FlatOutIt createSABTree(
+        SAFwdIt First_, SAFwdIt _Last,
+        FlatOutIt Dest_, unsigned BlockSize)
+    {
+        typedef typename Value<SAFwdIt>::Type    TSize;
 
         TSize size = difference(First_, _Last);
-		if (!size) return Dest_;
+        if (!size) return Dest_;
 
         // calculate the depth of the sa b-tree
-		TSize BlockElements = BlockSize - 1;
-
-		unsigned treeLevels = 1;
-		TSize _xSize;
-		for(_xSize = 1; _xSize * BlockSize <= size; _xSize *= BlockSize, ++treeLevels) ;
-	
-		// get output iterators for every level in the flat tree
-		FlatOutIt *level = new FlatOutIt[treeLevels];
-		for(int i = treeLevels - 1; _xSize; --i, _xSize /= BlockSize) {
-			level[i] = Dest_;
-			goFurther(Dest_, ((size / _xSize + BlockSize - 1) / BlockSize) * BlockSize);
-		}
-
-		// counter for each b-tree level
-		TSize *cnt = new TSize[treeLevels];
-		for(unsigned i = 0; i < treeLevels; ++i)
-			cnt[i] = 0;
-
-		// distribute to responsible levels
-		for(TSize j = 0; j < size; ++j, ++First_)
-			for(unsigned i = 0; i < treeLevels; ++i) {
-				*(level[i]) = *First_;
-				++(level[i]);
-				if (cnt[i] != BlockElements) {
-					++cnt[i];
-					break;
-				} else
-					cnt[i] = 0;
-			}
-
-		delete[] cnt;
-		delete[] level;
-
-		return Dest_;
+        TSize BlockElements = BlockSize - 1;
+
+        unsigned treeLevels = 1;
+        TSize _xSize;
+        for(_xSize = 1; _xSize * BlockSize <= size; _xSize *= BlockSize, ++treeLevels) ;
+
+        // get output iterators for every level in the flat tree
+        FlatOutIt *level = new FlatOutIt[treeLevels];
+        for(int i = treeLevels - 1; _xSize; --i, _xSize /= BlockSize) {
+            level[i] = Dest_;
+            goFurther(Dest_, ((size / _xSize + BlockSize - 1) / BlockSize) * BlockSize);
+        }
+
+        // counter for each b-tree level
+        TSize *cnt = new TSize[treeLevels];
+        for(unsigned i = 0; i < treeLevels; ++i)
+            cnt[i] = 0;
+
+        // distribute to responsible levels
+        for(TSize j = 0; j < size; ++j, ++First_)
+            for(unsigned i = 0; i < treeLevels; ++i) {
+                *(level[i]) = *First_;
+                ++(level[i]);
+                if (cnt[i] != BlockElements) {
+                    ++cnt[i];
+                    break;
+                } else
+                    cnt[i] = 0;
+            }
+
+        delete[] cnt;
+        delete[] level;
+
+        return Dest_;
     }
 
 
-	template < typename TSize >
-	inline TSize sizeofSABTree(TSize n, unsigned BlockSize)
-	{
-		TSize size = 0;
-		for(TSize _xSize = 1; _xSize <= n; _xSize *= BlockSize)
-			size += (n / _xSize + BlockSize - 1) / BlockSize;
-		return size * BlockSize;
-	}
+    template < typename TSize >
+    inline TSize sizeofSABTree(TSize n, unsigned BlockSize)
+    {
+        TSize size = 0;
+        for(TSize _xSize = 1; _xSize <= n; _xSize *= BlockSize)
+            size += (n / _xSize + BlockSize - 1) / BlockSize;
+        return size * BlockSize;
+    }
 
-	template <
-		class SAFwdIt,		// suffix array input iterator
-		typename TSize >
-	inline void sizeofSABTree(SAFwdIt First_, SAFwdIt _Last, TSize &Size_, unsigned BlockSize)
-	{
-		Size_ = sizeofSABTree(difference(First_, _Last), BlockSize);
-	}
+    template <
+        class SAFwdIt,        // suffix array input iterator
+        typename TSize >
+    inline void sizeofSABTree(SAFwdIt First_, SAFwdIt _Last, TSize &Size_, unsigned BlockSize)
+    {
+        Size_ = sizeofSABTree(difference(First_, _Last), BlockSize);
+    }
 
 
     template < typename TSAB, typename TSA >
@@ -112,11 +112,11 @@ namespace SEQAN_NAMESPACE_MAIN
     }
 
 
-	template < typename TSize >
+    template < typename TSize >
     inline unsigned treeLevelsSAB(TSize saSize, unsigned BlockSize)
-	{
-		unsigned treeLevels = 1;
-		for (TSize _xSize = 1; _xSize <= saSize; _xSize *= BlockSize, ++treeLevels)
+    {
+        unsigned treeLevels = 1;
+        for (TSize _xSize = 1; _xSize <= saSize; _xSize *= BlockSize, ++treeLevels)
             continue;  // Get smallest 2^k that is > saSize.
         return treeLevels;
     }
diff --git a/seqan/index/index_sa_bwtwalk.h b/seqan/index/index_sa_bwtwalk.h
index 0d897be..50c92ca 100644
--- a/seqan/index/index_sa_bwtwalk.h
+++ b/seqan/index/index_sa_bwtwalk.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -51,205 +51,205 @@
 
 namespace SEQAN_NAMESPACE_MAIN
 {
-	// Public tags
-	struct BwtWalkFast_ {};
-	typedef Tag<BwtWalkFast_> const BwtWalkFast;
-
-	struct BwtWalkInPlace_ {};
-	typedef Tag<BwtWalkInPlace_> const BwtWalkInPlace;
-
-	template <typename TSpec = BwtWalkFast >
-	struct BwtWalk {};
-
-	// Public function
-	// NOTE: This function uses the supremum value of Value<TSA>::Type as NIL symbol
-	//       for temporary calculations. Therefore, the caller must ensure that
-	//       length(s) < MaxValue<TValue>::VALUE. Otherwise, behaviour is undefined!
-	template < typename TSA, typename TText, typename TSpec >
-	inline void createSuffixArray(
-		TSA &SA,
-		TText const &s,
-		BwtWalk<TSpec> const &)
-	{
-		typedef typename AllowsFastRandomAccess<TSA>::Type TAllowsFastRandomAccess;
-		_createSuffixArray(SA, s, BwtWalk<TSpec>(), TAllowsFastRandomAccess());
-	}
-
-	// List functions, for internal use (that's why there's a '_' in front)
-
-	// Inserts p into the suffix list between the given predecessor and successor
-	// NOTE: Intentionally not using references for predecessor and successor!
-	template < typename TArray, typename TValue >
-	inline void _insertBetween(
-		TArray &lexprevpos,
-		TArray &lexnextpos,
-		TValue p,
-		TValue predecessor,
-		TValue successor)
-	{
-		value(lexprevpos, p) = predecessor;
-		value(lexnextpos, p) = successor;
-		const TValue NIL = MaxValue<TValue>::VALUE;
-		if (predecessor != NIL) value(lexnextpos, predecessor) = p;
-		if (successor != NIL) value(lexprevpos, successor) = p;
-	}
-
-	// Inserts p into the suffix list before the given successor
-	template < typename TArray, typename TValue >
-	inline void _insertBefore(
-		TArray &lexprevpos,
-		TArray &lexnextpos,
-		TValue p,
-		TValue successor)
-	{
-		_insertBetween(lexprevpos, lexnextpos, p, getValue(lexprevpos, successor), successor);
-	}
-
-	// Inserts p into the suffix list after the given predecessor
-	template < typename TArray, typename TValue >
-	inline void _insertAfter(
-		TArray &lexprevpos,
-		TArray &lexnextpos,
-		TValue p,
-		TValue predecessor)
-	{
-		_insertBetween(lexprevpos, lexnextpos, p, predecessor, getValue(lexnextpos, predecessor));
-	}
-
-	// Inserts p into the suffix list between the given predecessor and successor
-	template < typename TArray, typename TValue >
-	inline void _insertXorBetween(
-		TArray &lexxorpos,
-		TValue p,
-		TValue predecessor,
-		TValue successor)
-	{
-		const TValue NIL = MaxValue<TValue>::VALUE;
-		value(lexxorpos, p) = predecessor ^ successor;
-		if (predecessor != NIL) value(lexxorpos, predecessor) = getValue(lexxorpos, predecessor) ^ successor ^ p;
-		if (successor != NIL) value(lexxorpos, successor) = getValue(lexxorpos, successor) ^ predecessor ^ p;
-	}
-
-	// Creates a suffix array. This is the version for fast random access.
-	template < typename TSA, typename TText >
-	inline void _createSuffixArray(
-		TSA &SA,
-		TText const &s,
-		BwtWalk<BwtWalkFast> const &,
-		True const &)
-	{
-		typedef typename Value<TSA>::Type TValue;
-		typedef typename Iterator<TSA, Standard>::Type TSaIter;
-		const TValue NIL = MaxValue<TValue>::VALUE;
-		
-		if (empty(s)) return;
-		
-		TSA lexnextpos;
-		// Since SA is capable of fast random access, we can temporarily use it as lexprevpos array.
-		TSA &lexprevpos = SA;
-
-		resize(lexnextpos, length(s), NIL, Exact());
-		std::fill(begin(lexprevpos, Standard()), end(lexprevpos, Standard()), NIL);
-
-		// finally create suffix array
-		//   1) first suffix is returned...
-		TValue p = _createSuffixList(lexprevpos, lexnextpos, s);
-		//   2) sequentially write out suffix array
-		TSaIter saIt = begin(SA, Standard());
-		while (p != NIL) {
-			*saIt = p;
-			p = getValue(lexnextpos, p);
-			++saIt;
-		}
-	}
-
-	// Creates a suffix array. This is the version for external memory.
-	// (SA is written sequentially from start to finish.)
-	template < typename TSA, typename TText >
-	inline void _createSuffixArray(
-		TSA &SA,
-		TText const& s,
-		BwtWalk<BwtWalkFast> const &,
-		False const &)
-	{
-		typedef typename Value<TSA>::Type TValue;
-		typedef typename Iterator<TSA, Standard>::Type TSaIter;
-		const TValue NIL = MaxValue<TValue>::VALUE;
-		typedef String<TValue> TArray;
-
-		if (empty(s)) return;
-
-		TArray lexnextpos;
-		TArray lexprevpos;
-
-		resize(lexnextpos, length(s), NIL, Exact());
-		resize(lexprevpos, length(s), NIL, Exact());
-
-		// finally create suffix array
-		//   1) first suffix is returned...
-		TValue p = _createSuffixList(lexprevpos, lexnextpos, s);
-		//   2) sequentially write out suffix array
-		TSaIter saIt = begin(SA, Standard());
-		while (p != NIL) {
-			*saIt = p;
-			p = getValue(lexnextpos, p);
-			++saIt;
-		}
-	}
-
-	// Note: Writing to SA is done sequential only, i.e. well-suited to be directly
-	//       written to external storage.
-	template < typename TSA, typename TText >
-	inline void _createSuffixArray(
-		TSA &SA,
-		TText const &s,
-		BwtWalk<BwtWalkInPlace> const &,
-		False const &)
-	{
-		typedef typename Value<TSA>::Type TValue;
-		typedef typename Iterator<TSA, Standard>::Type TSaIter;
-		const TValue NIL = MaxValue<TValue>::VALUE;
-		typedef String<TValue> TArray;
-
-		if (empty(s)) return;
-		
-		TArray lexxorpos;
-		// invalid ^ invalid == 0
-		resize(lexxorpos, length(s), 0, Exact());
-
-		// finally create suffix array
-		//   1) first suffix is returned...
-		TValue p = _createXoredSuffixList(lexxorpos, s);
-		//   2) sequentially write out suffix array
-		TValue previous = NIL;
-		TSaIter saIt = begin(SA, Standard());
-		while (p != NIL) {
-			*saIt = p;
-			TValue tmp = p;
-			p = getValue(lexxorpos, p) ^ previous;
-			previous = tmp;
-			++saIt;
-		}
-	}
-
-	// Variant for fast random access SA
-	// This version computes the suffix array in place, but only if the text s is
-	// short enough such that the most significant bit (MSB) of the entries in the
-	// SA can be used as a flag bit, which is needed to invert a permutation in place.
-	// Otherwise, an additional length(s) bits of memory are used.
+    // Public tags
+    struct BwtWalkFast_ {};
+    typedef Tag<BwtWalkFast_> const BwtWalkFast;
+
+    struct BwtWalkInPlace_ {};
+    typedef Tag<BwtWalkInPlace_> const BwtWalkInPlace;
+
+    template <typename TSpec = BwtWalkFast >
+    struct BwtWalk {};
+
+    // Public function
+    // NOTE: This function uses the supremum value of Value<TSA>::Type as NIL symbol
+    //       for temporary calculations. Therefore, the caller must ensure that
+    //       length(s) < MaxValue<TValue>::VALUE. Otherwise, behaviour is undefined!
+    template < typename TSA, typename TText, typename TSpec >
+    inline void createSuffixArray(
+        TSA &SA,
+        TText const &s,
+        BwtWalk<TSpec> const &)
+    {
+        typedef typename AllowsFastRandomAccess<TSA>::Type TAllowsFastRandomAccess;
+        _createSuffixArray(SA, s, BwtWalk<TSpec>(), TAllowsFastRandomAccess());
+    }
+
+    // List functions, for internal use (that's why there's a '_' in front)
+
+    // Inserts p into the suffix list between the given predecessor and successor
+    // NOTE: Intentionally not using references for predecessor and successor!
+    template < typename TArray, typename TValue >
+    inline void _insertBetween(
+        TArray &lexprevpos,
+        TArray &lexnextpos,
+        TValue p,
+        TValue predecessor,
+        TValue successor)
+    {
+        value(lexprevpos, p) = predecessor;
+        value(lexnextpos, p) = successor;
+        const TValue NIL = MaxValue<TValue>::VALUE;
+        if (predecessor != NIL) value(lexnextpos, predecessor) = p;
+        if (successor != NIL) value(lexprevpos, successor) = p;
+    }
+
+    // Inserts p into the suffix list before the given successor
+    template < typename TArray, typename TValue >
+    inline void _insertBefore(
+        TArray &lexprevpos,
+        TArray &lexnextpos,
+        TValue p,
+        TValue successor)
+    {
+        _insertBetween(lexprevpos, lexnextpos, p, getValue(lexprevpos, successor), successor);
+    }
+
+    // Inserts p into the suffix list after the given predecessor
+    template < typename TArray, typename TValue >
+    inline void _insertAfter(
+        TArray &lexprevpos,
+        TArray &lexnextpos,
+        TValue p,
+        TValue predecessor)
+    {
+        _insertBetween(lexprevpos, lexnextpos, p, predecessor, getValue(lexnextpos, predecessor));
+    }
+
+    // Inserts p into the suffix list between the given predecessor and successor
+    template < typename TArray, typename TValue >
+    inline void _insertXorBetween(
+        TArray &lexxorpos,
+        TValue p,
+        TValue predecessor,
+        TValue successor)
+    {
+        const TValue NIL = MaxValue<TValue>::VALUE;
+        value(lexxorpos, p) = predecessor ^ successor;
+        if (predecessor != NIL) value(lexxorpos, predecessor) = getValue(lexxorpos, predecessor) ^ successor ^ p;
+        if (successor != NIL) value(lexxorpos, successor) = getValue(lexxorpos, successor) ^ predecessor ^ p;
+    }
+
+    // Creates a suffix array. This is the version for fast random access.
+    template < typename TSA, typename TText >
+    inline void _createSuffixArray(
+        TSA &SA,
+        TText const &s,
+        BwtWalk<BwtWalkFast> const &,
+        True const &)
+    {
+        typedef typename Value<TSA>::Type TValue;
+        typedef typename Iterator<TSA, Standard>::Type TSaIter;
+        const TValue NIL = MaxValue<TValue>::VALUE;
+
+        if (empty(s)) return;
+
+        TSA lexnextpos;
+        // Since SA is capable of fast random access, we can temporarily use it as lexprevpos array.
+        TSA &lexprevpos = SA;
+
+        resize(lexnextpos, length(s), NIL, Exact());
+        std::fill(begin(lexprevpos, Standard()), end(lexprevpos, Standard()), NIL);
+
+        // finally create suffix array
+        //   1) first suffix is returned...
+        TValue p = _createSuffixList(lexprevpos, lexnextpos, s);
+        //   2) sequentially write out suffix array
+        TSaIter saIt = begin(SA, Standard());
+        while (p != NIL) {
+            *saIt = p;
+            p = getValue(lexnextpos, p);
+            ++saIt;
+        }
+    }
+
+    // Creates a suffix array. This is the version for external memory.
+    // (SA is written sequentially from start to finish.)
+    template < typename TSA, typename TText >
+    inline void _createSuffixArray(
+        TSA &SA,
+        TText const& s,
+        BwtWalk<BwtWalkFast> const &,
+        False const &)
+    {
+        typedef typename Value<TSA>::Type TValue;
+        typedef typename Iterator<TSA, Standard>::Type TSaIter;
+        const TValue NIL = MaxValue<TValue>::VALUE;
+        typedef String<TValue> TArray;
+
+        if (empty(s)) return;
+
+        TArray lexnextpos;
+        TArray lexprevpos;
+
+        resize(lexnextpos, length(s), NIL, Exact());
+        resize(lexprevpos, length(s), NIL, Exact());
+
+        // finally create suffix array
+        //   1) first suffix is returned...
+        TValue p = _createSuffixList(lexprevpos, lexnextpos, s);
+        //   2) sequentially write out suffix array
+        TSaIter saIt = begin(SA, Standard());
+        while (p != NIL) {
+            *saIt = p;
+            p = getValue(lexnextpos, p);
+            ++saIt;
+        }
+    }
+
+    // Note: Writing to SA is done sequential only, i.e. well-suited to be directly
+    //       written to external storage.
+    template < typename TSA, typename TText >
+    inline void _createSuffixArray(
+        TSA &SA,
+        TText const &s,
+        BwtWalk<BwtWalkInPlace> const &,
+        False const &)
+    {
+        typedef typename Value<TSA>::Type TValue;
+        typedef typename Iterator<TSA, Standard>::Type TSaIter;
+        const TValue NIL = MaxValue<TValue>::VALUE;
+        typedef String<TValue> TArray;
+
+        if (empty(s)) return;
+
+        TArray lexxorpos;
+        // invalid ^ invalid == 0
+        resize(lexxorpos, length(s), 0, Exact());
+
+        // finally create suffix array
+        //   1) first suffix is returned...
+        TValue p = _createXoredSuffixList(lexxorpos, s);
+        //   2) sequentially write out suffix array
+        TValue previous = NIL;
+        TSaIter saIt = begin(SA, Standard());
+        while (p != NIL) {
+            *saIt = p;
+            TValue tmp = p;
+            p = getValue(lexxorpos, p) ^ previous;
+            previous = tmp;
+            ++saIt;
+        }
+    }
+
+    // Variant for fast random access SA
+    // This version computes the suffix array in place, but only if the text s is
+    // short enough such that the most significant bit (MSB) of the entries in the
+    // SA can be used as a flag bit, which is needed to invert a permutation in place.
+    // Otherwise, an additional length(s) bits of memory are used.
 
     // This is a helper function for the case "length(s) >= (NIL && NOTFLAGBIT)".
-	template < typename TSA, typename TText, typename TValue, typename TArray >
-	inline void _createSuffixArray(
-		TSA &SA,
+    template < typename TSA, typename TText, typename TValue, typename TArray >
+    inline void _createSuffixArray(
+        TSA &SA,
         TArray & lexxorpos,
         TValue & p,
-		TText const &s,
+        TText const &s,
         TValue const & NIL,
         TValue const &,
         TValue const &,
-		BwtWalk<BwtWalkInPlace> const &,
-		True const &,
+        BwtWalk<BwtWalkInPlace> const &,
+        True const &,
         True const &)
     {
         // If the string is too long, we cannot use the MSB of the SA entries as a flag.
@@ -288,17 +288,17 @@ namespace SEQAN_NAMESPACE_MAIN
     }
 
     // This is a helper function for the case "length(s) < (NIL && NOTFLAGBIT)".
-	template < typename TSA, typename TText, typename TValue, typename TArray >
-	inline void _createSuffixArray(
-		TSA &SA,
+    template < typename TSA, typename TText, typename TValue, typename TArray >
+    inline void _createSuffixArray(
+        TSA &SA,
         TArray & lexxorpos,
         TValue & p,
-		TText const &s,
+        TText const &s,
         TValue const & NIL,
         TValue const & FLAGBIT,
         TValue const & NOTFLAGBIT,
-		BwtWalk<BwtWalkInPlace> const &,
-		True const &,
+        BwtWalk<BwtWalkInPlace> const &,
+        True const &,
         False const &)
     {
         // The string is short enough, we can use the MSB of the SA entries as a flag.
@@ -334,17 +334,17 @@ namespace SEQAN_NAMESPACE_MAIN
 
     // This takes care of the case where the suffix array's entry type is
     // longer than the string length type to circumvent some warnings.
-	template < typename TSA, typename TText, typename TValue, typename TArray >
-	inline void _createSuffixArrayHandleTooLongSuffixArrayType(
-		TSA &SA,
+    template < typename TSA, typename TText, typename TValue, typename TArray >
+    inline void _createSuffixArrayHandleTooLongSuffixArrayType(
+        TSA &SA,
         TArray & lexxorpos,
         TValue & p,
-		TText const &s,
+        TText const &s,
         TValue const & NIL,
         TValue const & FLAGBIT,
         TValue const & NOTFLAGBIT,
-		BwtWalk<BwtWalkInPlace> const &,
-		True const &,
+        BwtWalk<BwtWalkInPlace> const &,
+        True const &,
         True const &)
     {
         _createSuffixArray(SA, lexxorpos, p, s, NIL, FLAGBIT, NOTFLAGBIT, BwtWalk<BwtWalkInPlace>(), True(), False());
@@ -352,306 +352,306 @@ namespace SEQAN_NAMESPACE_MAIN
 
     // This takes care of the case where the suffix array's entry type is NOT
     // longer than the string length type to circumvent some warnings.
-	template < typename TSA, typename TText, typename TValue, typename TArray >
-	inline void _createSuffixArrayHandleTooLongSuffixArrayType(
-		TSA &SA,
+    template < typename TSA, typename TText, typename TValue, typename TArray >
+    inline void _createSuffixArrayHandleTooLongSuffixArrayType(
+        TSA &SA,
         TArray & lexxorpos,
         TValue & p,
-		TText const &s,
+        TText const &s,
         TValue const & NIL,
         TValue const & FLAGBIT,
         TValue const & NOTFLAGBIT,
-		BwtWalk<BwtWalkInPlace> const &,
-		True const &,
+        BwtWalk<BwtWalkInPlace> const &,
+        True const &,
         False const &)
     {
         if (length(s) >= (NIL & NOTFLAGBIT))
             _createSuffixArray(SA, lexxorpos, p, s, NIL, FLAGBIT, NOTFLAGBIT, BwtWalk<BwtWalkInPlace>(), True(), True());
-        else 
+        else
             _createSuffixArray(SA, lexxorpos, p, s, NIL, FLAGBIT, NOTFLAGBIT, BwtWalk<BwtWalkInPlace>(), True(), False());
     }
 
     // This is the main entry point.
-	template < typename TSA, typename TText >
-	inline void _createSuffixArray(
-		TSA &SA,
-		TText const &s,
-		BwtWalk<BwtWalkInPlace> const &,
-		True const &)
-	{
-		typedef typename Value<TSA>::Type TValue;
-		const TValue NIL = MaxValue<TValue>::VALUE;
-
-		const TValue FLAGBIT = (TValue)1 << (BitsPerValue<TValue>::VALUE-1);
-		const TValue NOTFLAGBIT = ~FLAGBIT;
-
-		if (empty(s)) return;
-		
-		// since SA is capable of fast random access, we can temporarily use it as the lexxorpos array
-		TSA & lexxorpos = SA;
-		std::fill(begin(lexxorpos, Standard()), end(lexxorpos, Standard()), 0);
-
-		// finally create suffix array
-		//   1) first suffix is returned ...
-		TValue p = _createXoredSuffixList(lexxorpos, s);
+    template < typename TSA, typename TText >
+    inline void _createSuffixArray(
+        TSA &SA,
+        TText const &s,
+        BwtWalk<BwtWalkInPlace> const &,
+        True const &)
+    {
+        typedef typename Value<TSA>::Type TValue;
+        const TValue NIL = MaxValue<TValue>::VALUE;
+
+        const TValue FLAGBIT = (TValue)1 << (BitsPerValue<TValue>::VALUE-1);
+        const TValue NOTFLAGBIT = ~FLAGBIT;
+
+        if (empty(s)) return;
+
+        // since SA is capable of fast random access, we can temporarily use it as the lexxorpos array
+        TSA & lexxorpos = SA;
+        std::fill(begin(lexxorpos, Standard()), end(lexxorpos, Standard()), 0);
+
+        // finally create suffix array
+        //   1) first suffix is returned ...
+        TValue p = _createXoredSuffixList(lexxorpos, s);
 
         typedef typename Size<TText>::Type TSize;
         typedef typename Eval<!(sizeof(TSize) <= sizeof(TValue))>::Type TBool;
         _createSuffixArrayHandleTooLongSuffixArrayType(SA, lexxorpos, p, s, NIL, FLAGBIT, NOTFLAGBIT, BwtWalk<BwtWalkInPlace>(), True(), TBool());
-	}
-
-	template < typename TArray, typename TValue >
-	inline void _findNewCharInsertionPosition(
-		TArray &lexfirstpos,
-		TArray &lexlastpos,
-		TValue &pMinus,
-		TValue &pPlus,
-		unsigned int cOrd)
-	{
-		const TValue NIL = MaxValue<TValue>::VALUE;
-
-		// current char does not exist
-		// first find pMinus ...
-		pMinus = NIL;
-		unsigned int cMinus = cOrd;
-		while (cMinus > 0) {
-			--cMinus;
-			if (getValue(lexlastpos, cMinus) != NIL) {
-				pMinus = getValue(lexlastpos, cMinus);
-				break;
-			}
-		}
-
-		// ... and pPlus
-		pPlus = NIL;
-		for (unsigned int cPlus = cOrd+1; cPlus < length(lexfirstpos); ++cPlus) {
-			if (getValue(lexfirstpos, cPlus) != NIL) {
-				pPlus = getValue(lexfirstpos, cPlus);
-				break;
-			}
-		}
-	}
-
-	// returns begin of suffix list
-	template <typename TArray, typename TText>
-	inline typename Value<TArray>::Type _createSuffixList(
-		TArray &lexprevpos,
-		TArray &lexnextpos,
-		TText const &s)
-	{
-		typedef typename Iterator<const TText, Standard>::Type TTextIter;
-		typedef typename Value<TArray>::Type TValue;
-
-		typedef typename Value<const TText>::Type TChar;
-		const unsigned int ALPHABETSIZE = ValueSize<TChar>::VALUE;
-		const TValue NIL = MaxValue<TValue>::VALUE;
-		typedef String<TValue, Array<ALPHABETSIZE> > TAlphabetArray;
-
-		TAlphabetArray lexfirstpos, lexlastpos;
-
-		resize(lexfirstpos, ALPHABETSIZE, NIL, Exact());
-		resize(lexlastpos, ALPHABETSIZE, NIL, Exact());
-
-		// main loop
-		TTextIter it = end(s, Standard());
-		TValue p = length(s);
-		while (it != begin(s, Standard())) {
-			--it;
-			--p;
-			TChar c = *it;
-			// Instead of using c as an index, we use its ordValue.
-			unsigned int cOrd = ordValue(c);
-			if (getValue(lexfirstpos, cOrd) == NIL) {
-				TValue pMinus, pPlus;
-				_findNewCharInsertionPosition(lexfirstpos, lexlastpos, pMinus, pPlus, cOrd);
-				_insertBetween(lexprevpos, lexnextpos, p, pMinus, pPlus);
-				// this is our first suffix starting with c, remember in lexfirstpos/lexlastpos
-				value(lexfirstpos, cOrd) = p;
-				value(lexlastpos, cOrd) = p;
-			} else {
-				// current char already exists (case 2. in the paper)
-				TValue pLeft = getValue(lexprevpos, p+1); // walking left
-				TValue pRight = getValue(lexnextpos, p+1); // walking right
-				// walk along Bwt in both directions
-				while (true) {
-					// check if we have found the insertion position while walking to the left side
-					if (pLeft == NIL) {
-						if (back(s) == c) {
-							// this is the lexicographically second suffix starting with c, the first
-							// suffix starting with c consists only of one character (the last char in s)
-							// this case could be avoided by adding a $ symbol to the end of s.
-							_insertAfter(lexprevpos, lexnextpos, p, (TValue)(length(s)-1));
-							if (getValue(lexlastpos, cOrd) == length(s)-1) value(lexlastpos, cOrd) = p;
-						} else {
-							// this is the lexicographically first suffix starting with c,
-							// insert before lexfirstpos[c]
-							_insertBefore(lexprevpos, lexnextpos, p, getValue(lexfirstpos, cOrd));
-							value(lexfirstpos, cOrd) = p;
-						}
-						break;
-					} else {
-						// check if character has been found walking to the left
-						if (getValue(s, pLeft-1) == c) {
-							// insert in the middle of the list
-							_insertAfter(lexprevpos, lexnextpos, p, pLeft-1);
-							// check if just inserted suffix is now the last suffix starting with c
-							if (getValue(lexlastpos, cOrd) == pLeft-1) value(lexlastpos, cOrd) = p;
-							break;
-						}
-					}
-					pLeft = getValue(lexprevpos, pLeft);
-
-					// check if we have found the insertion position while walking to the right side
-					if (pRight == NIL) {
-						// this is the lexicographically last suffix starting with c,
-						// insert before lexfirstpos[c]
-						_insertAfter(lexprevpos, lexnextpos, p, getValue(lexlastpos, cOrd));
-						value(lexlastpos, cOrd) = p;
-						break;
-					} else {
-						// check if character has been found walking to the right
-						if (getValue(s, pRight-1) == c) {
-							// insert in the middle of the list
-							_insertBefore(lexprevpos, lexnextpos, p, pRight-1);
-							// check if just inserted suffix is now the first suffix starting with c
-							if (getValue(lexfirstpos, cOrd) == pRight-1) value(lexfirstpos, cOrd) = p;
-							break;
-						}
-					}
-					pRight = getValue(lexnextpos, pRight);
-				}
-			}
-		}
-
-		typename Iterator<TAlphabetArray, Standard>::Type fit = begin(lexfirstpos, Standard());
-		while (*fit == NIL) ++fit;
-		return *fit;
-	}
-
-	// returns beginning of suffix list
-	template <typename TArray, typename TText>
-	inline typename Value<TArray>::Type _createXoredSuffixList(
-		TArray &lexxorpos,
-		TText const &s)
-	{
-		typedef typename Iterator<const TText, Standard>::Type TTextIter;
-		typedef typename Value<TArray>::Type TValue;
-
-		typedef typename Value<const TText>::Type TChar;
-		const unsigned int ALPHABETSIZE = ValueSize<TChar>::VALUE;
-		const TValue NIL = MaxValue<TValue>::VALUE;
-		typedef String<TValue, Array<ALPHABETSIZE> > TAlphabetArray;
-
-		TAlphabetArray lexfirstpos;
-		TAlphabetArray lexlastpos;
-		resize(lexfirstpos, ALPHABETSIZE, NIL, Exact());
-		resize(lexlastpos, ALPHABETSIZE, NIL, Exact());
-
-		// main loop
-		TTextIter it = end(s, Standard());
-		TValue p = length(s);
-		// store predecessor and successor from last round (p+1)
-		TValue lastPredecessor = NIL;
-		TValue lastSuccessor = NIL;
-		while (it != begin(s, Standard())) {
-			--it;
-			--p;
-			TChar c = *it;
-			// Instead of using c as an index, we use its ordValue.
-			unsigned int cOrd = ordValue(c);
-			// to insert into xored list, we need to find predecessor _and_ successor
-			TValue predecessor = NIL;
-			TValue successor = NIL;
-			if (getValue(lexfirstpos, cOrd) == NIL) {
-				_findNewCharInsertionPosition(lexfirstpos, lexlastpos, predecessor, successor, cOrd);
-				// this is our first suffix starting with c, remember in lexfirstpos/lexlastpos
-				value(lexfirstpos, cOrd) = p;
-				value(lexlastpos, cOrd) = p;
-			} else {
-				// current char already exists
-				bool skipWalkRight = false;
-				// ----- walk left ------------------ (search for predecessor) ------
-				TValue pLast = p+1;
-				TValue pLeft = getValue(lexxorpos, p+1) ^ lastSuccessor; // walking left
-				while (true) {
-					// check if we have found the insertion position while walking to the left side
-					if (pLeft == NIL) {
-						if (back(s) == c) {
-							// this is the lexicographically second suffix starting with c, the first
-							// suffix starting with c consists only of one character (the last char in s)
-							// this case could be avoided by adding a $ symbol to the end of s.
-							predecessor = (TValue)(length(s)-1);
-							if (getValue(lexlastpos, cOrd) == length(s)-1) value(lexlastpos, cOrd) = p;
-						} else {
-							// this is the lexicographically first suffix starting with c,
-							// insert before lexfirstpos[c]
-							successor = getValue(lexfirstpos, cOrd);
-							// first find pMinus ...
-							unsigned int cMinus = cOrd;
-							while (cMinus > 0) {
-								--cMinus;
-								if (getValue(lexlastpos, cMinus) != NIL) {
-									predecessor = getValue(lexlastpos, cMinus);
-									break;
-								}
-							}
-							skipWalkRight = true;
-							value(lexfirstpos, cOrd)=p;
-						}
-						break;
-					} else {
-						// check if character has been found walking to the left
-						if (getValue(s, pLeft-1) == c) {
-							// insert in the middle of the list
-							predecessor = pLeft-1;
-							// check if just inserted suffix is now the last suffix starting with c
-							if (getValue(lexlastpos, cOrd) == pLeft-1) value(lexlastpos, cOrd) = p;
-							break;
-						}
-					}
-					TValue tmp = pLeft;
-					pLeft = getValue(lexxorpos, pLeft) ^ pLast;
-					pLast = tmp;
-				}
-
-				// ----- walk right ------------------ (search for successor) ------
-				pLast = p+1;
-				TValue pRight = getValue(lexxorpos, p+1) ^ lastPredecessor; // walking right
-				while (!skipWalkRight) {
-					// check if we have found the insertion position while walking to the right side
-					if (pRight == NIL) {
-						// this is the lexicographically last suffix starting with c,
-						for (unsigned int cPlus = cOrd+1; cPlus < length(lexfirstpos); ++cPlus) {
-							if (getValue(lexfirstpos, cPlus) != NIL) {
-								successor = getValue(lexfirstpos, cPlus);
-								break;
-							}
-						}
-						value(lexlastpos, cOrd) = p;
-						break;
-					} else {
-						// check if character has been found walking to the right
-						if (getValue(s, pRight-1) == c) {
-							successor = pRight-1;
-							// check if just inserted suffix is now the first suffix starting with c
-							if (getValue(lexfirstpos, cOrd) == pRight-1) value(lexfirstpos, cOrd) = p;
-							break;
-						}
-					}
-					TValue tmp = pRight;
-					pRight = getValue(lexxorpos, pRight) ^ pLast;
-					pLast = tmp;
-				}
-			}
-			// finally insert between predecessor and successor
-			_insertXorBetween(lexxorpos, p, predecessor, successor);
-			lastPredecessor = predecessor;
-			lastSuccessor = successor;
-		}
-
-		typename Iterator<TArray, Standard>::Type fit = begin(lexfirstpos, Standard());
-		while (*fit == NIL) ++fit;
-		return *fit;
-	}
+    }
+
+    template < typename TArray, typename TValue >
+    inline void _findNewCharInsertionPosition(
+        TArray &lexfirstpos,
+        TArray &lexlastpos,
+        TValue &pMinus,
+        TValue &pPlus,
+        unsigned int cOrd)
+    {
+        const TValue NIL = MaxValue<TValue>::VALUE;
+
+        // current char does not exist
+        // first find pMinus ...
+        pMinus = NIL;
+        unsigned int cMinus = cOrd;
+        while (cMinus > 0) {
+            --cMinus;
+            if (getValue(lexlastpos, cMinus) != NIL) {
+                pMinus = getValue(lexlastpos, cMinus);
+                break;
+            }
+        }
+
+        // ... and pPlus
+        pPlus = NIL;
+        for (unsigned int cPlus = cOrd+1; cPlus < length(lexfirstpos); ++cPlus) {
+            if (getValue(lexfirstpos, cPlus) != NIL) {
+                pPlus = getValue(lexfirstpos, cPlus);
+                break;
+            }
+        }
+    }
+
+    // returns begin of suffix list
+    template <typename TArray, typename TText>
+    inline typename Value<TArray>::Type _createSuffixList(
+        TArray &lexprevpos,
+        TArray &lexnextpos,
+        TText const &s)
+    {
+        typedef typename Iterator<const TText, Standard>::Type TTextIter;
+        typedef typename Value<TArray>::Type TValue;
+
+        typedef typename Value<const TText>::Type TChar;
+        const unsigned int ALPHABETSIZE = ValueSize<TChar>::VALUE;
+        const TValue NIL = MaxValue<TValue>::VALUE;
+        typedef String<TValue, Array<ALPHABETSIZE> > TAlphabetArray;
+
+        TAlphabetArray lexfirstpos, lexlastpos;
+
+        resize(lexfirstpos, ALPHABETSIZE, NIL, Exact());
+        resize(lexlastpos, ALPHABETSIZE, NIL, Exact());
+
+        // main loop
+        TTextIter it = end(s, Standard());
+        TValue p = length(s);
+        while (it != begin(s, Standard())) {
+            --it;
+            --p;
+            TChar c = *it;
+            // Instead of using c as an index, we use its ordValue.
+            unsigned int cOrd = ordValue(c);
+            if (getValue(lexfirstpos, cOrd) == NIL) {
+                TValue pMinus, pPlus;
+                _findNewCharInsertionPosition(lexfirstpos, lexlastpos, pMinus, pPlus, cOrd);
+                _insertBetween(lexprevpos, lexnextpos, p, pMinus, pPlus);
+                // this is our first suffix starting with c, remember in lexfirstpos/lexlastpos
+                value(lexfirstpos, cOrd) = p;
+                value(lexlastpos, cOrd) = p;
+            } else {
+                // current char already exists (case 2. in the paper)
+                TValue pLeft = getValue(lexprevpos, p+1); // walking left
+                TValue pRight = getValue(lexnextpos, p+1); // walking right
+                // walk along Bwt in both directions
+                while (true) {
+                    // check if we have found the insertion position while walking to the left side
+                    if (pLeft == NIL) {
+                        if (back(s) == c) {
+                            // this is the lexicographically second suffix starting with c, the first
+                            // suffix starting with c consists only of one character (the last char in s)
+                            // this case could be avoided by adding a $ symbol to the end of s.
+                            _insertAfter(lexprevpos, lexnextpos, p, (TValue)(length(s)-1));
+                            if (getValue(lexlastpos, cOrd) == length(s)-1) value(lexlastpos, cOrd) = p;
+                        } else {
+                            // this is the lexicographically first suffix starting with c,
+                            // insert before lexfirstpos[c]
+                            _insertBefore(lexprevpos, lexnextpos, p, getValue(lexfirstpos, cOrd));
+                            value(lexfirstpos, cOrd) = p;
+                        }
+                        break;
+                    } else {
+                        // check if character has been found walking to the left
+                        if (getValue(s, pLeft-1) == c) {
+                            // insert in the middle of the list
+                            _insertAfter(lexprevpos, lexnextpos, p, pLeft-1);
+                            // check if just inserted suffix is now the last suffix starting with c
+                            if (getValue(lexlastpos, cOrd) == pLeft-1) value(lexlastpos, cOrd) = p;
+                            break;
+                        }
+                    }
+                    pLeft = getValue(lexprevpos, pLeft);
+
+                    // check if we have found the insertion position while walking to the right side
+                    if (pRight == NIL) {
+                        // this is the lexicographically last suffix starting with c,
+                        // insert before lexfirstpos[c]
+                        _insertAfter(lexprevpos, lexnextpos, p, getValue(lexlastpos, cOrd));
+                        value(lexlastpos, cOrd) = p;
+                        break;
+                    } else {
+                        // check if character has been found walking to the right
+                        if (getValue(s, pRight-1) == c) {
+                            // insert in the middle of the list
+                            _insertBefore(lexprevpos, lexnextpos, p, pRight-1);
+                            // check if just inserted suffix is now the first suffix starting with c
+                            if (getValue(lexfirstpos, cOrd) == pRight-1) value(lexfirstpos, cOrd) = p;
+                            break;
+                        }
+                    }
+                    pRight = getValue(lexnextpos, pRight);
+                }
+            }
+        }
+
+        typename Iterator<TAlphabetArray, Standard>::Type fit = begin(lexfirstpos, Standard());
+        while (*fit == NIL) ++fit;
+        return *fit;
+    }
+
+    // returns beginning of suffix list
+    template <typename TArray, typename TText>
+    inline typename Value<TArray>::Type _createXoredSuffixList(
+        TArray &lexxorpos,
+        TText const &s)
+    {
+        typedef typename Iterator<const TText, Standard>::Type TTextIter;
+        typedef typename Value<TArray>::Type TValue;
+
+        typedef typename Value<const TText>::Type TChar;
+        const unsigned int ALPHABETSIZE = ValueSize<TChar>::VALUE;
+        const TValue NIL = MaxValue<TValue>::VALUE;
+        typedef String<TValue, Array<ALPHABETSIZE> > TAlphabetArray;
+
+        TAlphabetArray lexfirstpos;
+        TAlphabetArray lexlastpos;
+        resize(lexfirstpos, ALPHABETSIZE, NIL, Exact());
+        resize(lexlastpos, ALPHABETSIZE, NIL, Exact());
+
+        // main loop
+        TTextIter it = end(s, Standard());
+        TValue p = length(s);
+        // store predecessor and successor from last round (p+1)
+        TValue lastPredecessor = NIL;
+        TValue lastSuccessor = NIL;
+        while (it != begin(s, Standard())) {
+            --it;
+            --p;
+            TChar c = *it;
+            // Instead of using c as an index, we use its ordValue.
+            unsigned int cOrd = ordValue(c);
+            // to insert into xored list, we need to find predecessor _and_ successor
+            TValue predecessor = NIL;
+            TValue successor = NIL;
+            if (getValue(lexfirstpos, cOrd) == NIL) {
+                _findNewCharInsertionPosition(lexfirstpos, lexlastpos, predecessor, successor, cOrd);
+                // this is our first suffix starting with c, remember in lexfirstpos/lexlastpos
+                value(lexfirstpos, cOrd) = p;
+                value(lexlastpos, cOrd) = p;
+            } else {
+                // current char already exists
+                bool skipWalkRight = false;
+                // ----- walk left ------------------ (search for predecessor) ------
+                TValue pLast = p+1;
+                TValue pLeft = getValue(lexxorpos, p+1) ^ lastSuccessor; // walking left
+                while (true) {
+                    // check if we have found the insertion position while walking to the left side
+                    if (pLeft == NIL) {
+                        if (back(s) == c) {
+                            // this is the lexicographically second suffix starting with c, the first
+                            // suffix starting with c consists only of one character (the last char in s)
+                            // this case could be avoided by adding a $ symbol to the end of s.
+                            predecessor = (TValue)(length(s)-1);
+                            if (getValue(lexlastpos, cOrd) == length(s)-1) value(lexlastpos, cOrd) = p;
+                        } else {
+                            // this is the lexicographically first suffix starting with c,
+                            // insert before lexfirstpos[c]
+                            successor = getValue(lexfirstpos, cOrd);
+                            // first find pMinus ...
+                            unsigned int cMinus = cOrd;
+                            while (cMinus > 0) {
+                                --cMinus;
+                                if (getValue(lexlastpos, cMinus) != NIL) {
+                                    predecessor = getValue(lexlastpos, cMinus);
+                                    break;
+                                }
+                            }
+                            skipWalkRight = true;
+                            value(lexfirstpos, cOrd)=p;
+                        }
+                        break;
+                    } else {
+                        // check if character has been found walking to the left
+                        if (getValue(s, pLeft-1) == c) {
+                            // insert in the middle of the list
+                            predecessor = pLeft-1;
+                            // check if just inserted suffix is now the last suffix starting with c
+                            if (getValue(lexlastpos, cOrd) == pLeft-1) value(lexlastpos, cOrd) = p;
+                            break;
+                        }
+                    }
+                    TValue tmp = pLeft;
+                    pLeft = getValue(lexxorpos, pLeft) ^ pLast;
+                    pLast = tmp;
+                }
+
+                // ----- walk right ------------------ (search for successor) ------
+                pLast = p+1;
+                TValue pRight = getValue(lexxorpos, p+1) ^ lastPredecessor; // walking right
+                while (!skipWalkRight) {
+                    // check if we have found the insertion position while walking to the right side
+                    if (pRight == NIL) {
+                        // this is the lexicographically last suffix starting with c,
+                        for (unsigned int cPlus = cOrd+1; cPlus < length(lexfirstpos); ++cPlus) {
+                            if (getValue(lexfirstpos, cPlus) != NIL) {
+                                successor = getValue(lexfirstpos, cPlus);
+                                break;
+                            }
+                        }
+                        value(lexlastpos, cOrd) = p;
+                        break;
+                    } else {
+                        // check if character has been found walking to the right
+                        if (getValue(s, pRight-1) == c) {
+                            successor = pRight-1;
+                            // check if just inserted suffix is now the first suffix starting with c
+                            if (getValue(lexfirstpos, cOrd) == pRight-1) value(lexfirstpos, cOrd) = p;
+                            break;
+                        }
+                    }
+                    TValue tmp = pRight;
+                    pRight = getValue(lexxorpos, pRight) ^ pLast;
+                    pLast = tmp;
+                }
+            }
+            // finally insert between predecessor and successor
+            _insertXorBetween(lexxorpos, p, predecessor, successor);
+            lastPredecessor = predecessor;
+            lastSuccessor = successor;
+        }
+
+        typename Iterator<TArray, Standard>::Type fit = begin(lexfirstpos, Standard());
+        while (*fit == NIL) ++fit;
+        return *fit;
+    }
 }
 #endif
diff --git a/seqan/index/index_sa_lss.h b/seqan/index/index_sa_lss.h
index dae855f..2fce2b9 100644
--- a/seqan/index/index_sa_lss.h
+++ b/seqan/index/index_sa_lss.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -62,294 +62,294 @@ namespace SEQAN_NAMESPACE_MAIN
 template <typename TValue>
 struct ContextLss_
 {
-	TValue *I,                   /* group array, ultimately suffix array.*/
-	*V,                          /* inverse array, ultimately inverse of I.*/
-	r,                           /* number of symbols aggregated by transform.*/
-	h;                           /* length of already-sorted prefixes.*/
-
-	// MODIFIED: renamed defines according to SeqAn's naming conventions
-	#define SEQAN_LSSKEY(p)          (V[*(p)+(h)])
-	#define SEQAN_LSSSWAP(p, q)      (tmp=*(p), *(p)=*(q), *(q)=tmp)
-	#define SEQAN_LSSMED3(a, b, c)   (SEQAN_LSSKEY(a)<SEQAN_LSSKEY(b) ?                        \
-			(SEQAN_LSSKEY(b)<SEQAN_LSSKEY(c) ? (b) : SEQAN_LSSKEY(a)<SEQAN_LSSKEY(c) ? (c) : (a))       \
-			: (SEQAN_LSSKEY(b)>SEQAN_LSSKEY(c) ? (b) : SEQAN_LSSKEY(a)>SEQAN_LSSKEY(c) ? (c) : (a)))
-
-	/* Subroutine for select_sort_split and sort_split. Sets group numbers for a
-	   group whose lowest position in I is pl and highest position is pm.*/
-
-	inline void update_group(TValue *pl, TValue *pm)
-	{
-	   TValue g;
-
-	   g=pm-I;                      /* group number.*/
-	   V[*pl]=g;                    /* update group number of first position.*/
-	   if (pl==pm)
-		  *pl=-1;                   /* one element, sorted group.*/
-	   else
-		  do                        /* more than one element, unsorted group.*/
-			 V[*++pl]=g;            /* update group numbers.*/
-		  while (pl<pm);
-	}
-
-	/* Quadratic sorting method to use for small subarrays. To be able to update
-	   group numbers consistently, a variant of selection sorting is used.*/
-
-	inline void select_sort_split(TValue *p, TValue n) {
-	   TValue *pa, *pb, *pi, *pn;
-	   TValue f, v, tmp;
-
-	   pa=p;                        /* pa is start of group being picked out.*/
-	   pn=p+n-1;                    /* pn is last position of subarray.*/
-	   while (pa<pn) {
-		  for (pi=pb=pa+1, f=SEQAN_LSSKEY(pa); pi<=pn; ++pi)
-			 if ((v=SEQAN_LSSKEY(pi))<f) {
-				f=v;                /* f is smallest key found.*/
-				SEQAN_LSSSWAP(pi, pa);       /* place smallest element at beginning.*/
-				pb=pa+1;            /* pb is position for elements equal to f.*/
-			 } else if (v==f) {     /* if equal to smallest key.*/
-				SEQAN_LSSSWAP(pi, pb);       /* place next to other smallest elements.*/
-				++pb;
-			 }
-		  update_group(pa, pb-1);   /* update group values for new group.*/
-		  pa=pb;                    /* continue sorting rest of the subarray.*/
-	   }
-	   if (pa==pn) {                /* check if last part is single element.*/
-		  V[*pa]=pa-I;
-		  *pa=-1;                   /* sorted group.*/
-	   }
-	}
-
-	/* Subroutine for sort_split, algorithm by Bentley & McIlroy.*/
-
-	inline TValue choose_pivot(TValue *p, TValue n) {
-	   TValue *pl, *pm, *pn;
-	   TValue s;
-	   
-	   pm=p+(n>>1);                 /* small arrays, middle element.*/
-	   if (n>7) {
-		  pl=p;
-		  pn=p+n-1;
-		  if (n>40) {               /* big arrays, pseudomedian of 9.*/
-			 s=n>>3;
-			 pl=SEQAN_LSSMED3(pl, pl+s, pl+s+s);
-			 pm=SEQAN_LSSMED3(pm-s, pm, pm+s);
-			 pn=SEQAN_LSSMED3(pn-s-s, pn-s, pn);
-		  }
-		  pm=SEQAN_LSSMED3(pl, pm, pn);      /* midsize arrays, median of 3.*/
-	   }
-	   return SEQAN_LSSKEY(pm);
-	}
-
-	/* Sorting routine called for each unsorted group. Sorts the array of integers
-	   (suffix numbers) of length n starting at p. The algorithm is a ternary-split
-	   quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
-	   Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
-	   function is based on Program 7.*/
-
-	inline void sort_split(TValue *p, TValue n)
-	{
-	   TValue *pa, *pb, *pc, *pd, *pl, *pm, *pn;
-	   TValue f, v, s, t, tmp;
-
-	   if (n<7) {                   /* multi-selection sort smallest arrays.*/
-		  select_sort_split(p, n);
-		  return;
-	   }
-
-	   v=choose_pivot(p, n);
-	   pa=pb=p;
-	   pc=pd=p+n-1;
-	   while (1) {                  /* split-end partition.*/
-		  while (pb<=pc && (f=SEQAN_LSSKEY(pb))<=v) {
-			 if (f==v) {
-				SEQAN_LSSSWAP(pa, pb);
-				++pa;
-			 }
-			 ++pb;
-		  }
-		  while (pc>=pb && (f=SEQAN_LSSKEY(pc))>=v) {
-			 if (f==v) {
-				SEQAN_LSSSWAP(pc, pd);
-				--pd;
-			 }
-			 --pc;
-		  }
-		  if (pb>pc)
-			 break;
-		  SEQAN_LSSSWAP(pb, pc);
-		  ++pb;
-		  --pc;
-	   }
-	   pn=p+n;
-	   if ((s=pa-p)>(t=pb-pa))
-		  s=t;
-	   for (pl=p, pm=pb-s; s; --s, ++pl, ++pm)
-		  SEQAN_LSSSWAP(pl, pm);
-	   if ((s=pd-pc)>(t=pn-pd-1))
-		  s=t;
-	   for (pl=pb, pm=pn-s; s; --s, ++pl, ++pm)
-		  SEQAN_LSSSWAP(pl, pm);
-
-	   s=pb-pa;
-	   t=pd-pc;
-	   if (s>0)
-		  sort_split(p, s);
-	   update_group(p+s, p+n-t-1);
-	   if (t>0)
-		  sort_split(p+n-t, t);
-	}
-
-	/* Bucketsort for first iteration.
-
-	   Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
-	   at least once. x[n] is 0. (This is the corresponding output of transform.) k
-	   must be at most n+1. p is array of size n+1 whose contents are disregarded.
-
-	   Output: x is V and p is I after the initial sorting stage of the refined
-	   suffix sorting algorithm.*/
-	      
-	inline void bucketsort(TValue *x, TValue *p, TValue n, TValue k)
-	{
-	   TValue *pi, i, c, d, g;
-
-	   for (pi=p; pi<p+k; ++pi)
-		  *pi=-1;                   /* mark linked lists empty.*/
-	   for (i=0; i<=n; ++i) {
-		  x[i]=p[c=x[i]];           /* insert in linked list.*/
-		  p[c]=i;
-	   }
-	   for (pi=p+k-1, i=n; pi>=p; --pi) {
-		  d=x[c=*pi];               /* c is position, d is next in list.*/
-		  x[c]=g=i;                 /* last position equals group number.*/
-		  if (d>=0) {               /* if more than one element in group.*/
-			 p[i--]=c;              /* p is permutation for the sorted x.*/
-			 do {
-				d=x[c=d];           /* next in linked list.*/
-				x[c]=g;             /* group number in x.*/
-				p[i--]=c;           /* permutation in p.*/
-			 } while (d>=0);
-		  } else
-			 p[i--]=-1;             /* one element, sorted group.*/
-	   }
-	}
-
-	/* Transforms the alphabet of x by attempting to aggregate several symbols into
-	   one, while preserving the suffix order of x. The alphabet may also be
-	   compacted, so that x on output comprises all integers of the new alphabet
-	   with no skipped numbers.
-
-	   Input: x is an array of size n+1 whose first n elements are positive
-	   integers in the range l...k-1. p is array of size n+1, used for temporary
-	   storage. q controls aggregation and compaction by defining the maximum value
-	   for any symbol during transformation: q must be at least k-l; if q<=n,
-	   compaction is guaranteed; if k-l>n, compaction is never done; if q is
-	   INT_MAX, the maximum number of symbols are aggregated into one.
-	   
-	   Output: Returns an integer j in the range 1...q representing the size of the
-	   new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
-	   set to the number of old symbols grouped into one. Only x[n] is 0.*/
-
-	inline TValue transform(TValue *x, TValue *p, TValue n, TValue k, TValue l, TValue q)
-	{
-	   TValue b, c, d, e, i, j, m, s;
-	   TValue *pi, *pj;
-	   
-	   for (s=0, i=k-l; i; i>>=1)
-		  ++s;                      /* s is number of bits in old symbol.*/
-	   e=MaxValue<TValue>::VALUE>>s; /* e is for overflow checking.*/
-	   for (b=d=r=0; r<n && d<=e && (c=d<<s|(k-l))<=q; ++r) {
-		  b=b<<s|(x[r]-l+1);        /* b is start of x in chunk alphabet.*/
-		  d=c;                      /* d is max symbol in chunk alphabet.*/
-	   }
-	   m=(1<<(r-1)*s)-1;            /* m masks off top old symbol from chunk.*/
-	   x[n]=l-1;                    /* emulate zero terminator.*/
-	   if (d<=n) {                  /* if bucketing possible, compact alphabet.*/
-		  for (pi=p; pi<=p+d; ++pi)
-			 *pi=0;                 /* zero transformation table.*/
-		  for (pi=x+r, c=b; pi<=x+n; ++pi) {
-			 p[c]=1;                /* mark used chunk symbol.*/
-			 c=(c&m)<<s|(*pi-l+1);  /* shift in next old symbol in chunk.*/
-		  }
-		  for (i=1; i<r; ++i) {     /* handle last r-1 positions.*/
-			 p[c]=1;                /* mark used chunk symbol.*/
-			 c=(c&m)<<s;            /* shift in next old symbol in chunk.*/
-		  }
-		  for (pi=p, j=1; pi<=p+d; ++pi)
-			 if (*pi)
-				*pi=j++;            /* j is new alphabet size.*/
-		  for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
-			 *pi=p[c];              /* transform to new alphabet.*/
-			 c=(c&m)<<s|(*pj-l+1);  /* shift in next old symbol in chunk.*/
-		  }
-		  while (pi<x+n) {          /* handle last r-1 positions.*/
-			 *pi++=p[c];            /* transform to new alphabet.*/
-			 c=(c&m)<<s;            /* shift right-end zero in chunk.*/
-		  }
-	   } else {                     /* bucketing not possible, don't compact.*/
-		  for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
-			 *pi=c;                 /* transform to new alphabet.*/
-			 c=(c&m)<<s|(*pj-l+1);  /* shift in next old symbol in chunk.*/
-		  }
-		  while (pi<x+n) {          /* handle last r-1 positions.*/
-			 *pi++=c;               /* transform to new alphabet.*/
-			 c=(c&m)<<s;            /* shift right-end zero in chunk.*/
-		  }
-		  j=d+1;                    /* new alphabet size.*/
-	   }
-	   x[n]=0;                      /* end-of-string symbol is zero.*/
-	   return j;                    /* return new alphabet size.*/
-	}
-
-	/* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
-	   n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
-	   contents of x[n] is disregarded, the n-th symbol being regarded as
-	   end-of-string smaller than all other symbols.*/
-
-	void suffixsort(TValue *x, TValue *p, TValue n, TValue k, TValue l)
-	{
-	   TValue *pi, *pk;
-	   TValue i, j, s, sl;
-	   
-	   V=x;                         /* set global values.*/
-	   I=p;
-	   
-	   if (n>=k-l) {                /* if bucketing possible,*/
-		  j=transform(V, I, n, k, l, n);
-		  bucketsort(V, I, n, j);   /* bucketsort on first r positions.*/
-	   } else {
-		  transform(V, I, n, k, l, MaxValue<TValue>::VALUE);
-		  for (i=0; i<=n; ++i)
-			 I[i]=i;                /* initialize I with suffix numbers.*/
-		  h=0;
-		  sort_split(I, n+1);       /* quicksort on first r positions.*/
-	   }
-	   h=r;                         /* number of symbols aggregated by transform.*/
-	   
-	   while (*I>=-n) {
-		  pi=I;                     /* pi is first position of group.*/
-		  sl=0;                     /* sl is negated length of sorted groups.*/
-		  do {
-			 if ((s=*pi)<0) {
-				pi-=s;              /* skip over sorted group.*/
-				sl+=s;              /* add negated length to sl.*/
-			 } else {
-				if (sl) {
-				   *(pi+sl)=sl;     /* combine sorted groups before pi.*/
-				   sl=0;
-				}
-				pk=I+V[s]+1;        /* pk-1 is last position of unsorted group.*/
-				sort_split(pi, pk-pi);
-				pi=pk;              /* next group.*/
-			 }
-		  } while (pi<=I+n);
-		  if (sl)                   /* if the array ends with a sorted group.*/
-			 *(pi+sl)=sl;           /* combine sorted groups at end of I.*/
-		  h=2*h;                    /* double sorted-depth.*/
-	   }
-
-	   for (i=0; i<=n; ++i)         /* reconstruct suffix array from inverse.*/
-		  I[V[i]]=i;
-	}  
+    TValue *I,                   /* group array, ultimately suffix array.*/
+    *V,                          /* inverse array, ultimately inverse of I.*/
+    r,                           /* number of symbols aggregated by transform.*/
+    h;                           /* length of already-sorted prefixes.*/
+
+    // MODIFIED: renamed defines according to SeqAn's naming conventions
+    #define SEQAN_LSSKEY(p)          (V[*(p)+(h)])
+    #define SEQAN_LSSSWAP(p, q)      (tmp=*(p), *(p)=*(q), *(q)=tmp)
+    #define SEQAN_LSSMED3(a, b, c)   (SEQAN_LSSKEY(a)<SEQAN_LSSKEY(b) ?                        \
+            (SEQAN_LSSKEY(b)<SEQAN_LSSKEY(c) ? (b) : SEQAN_LSSKEY(a)<SEQAN_LSSKEY(c) ? (c) : (a))       \
+            : (SEQAN_LSSKEY(b)>SEQAN_LSSKEY(c) ? (b) : SEQAN_LSSKEY(a)>SEQAN_LSSKEY(c) ? (c) : (a)))
+
+    /* Subroutine for select_sort_split and sort_split. Sets group numbers for a
+       group whose lowest position in I is pl and highest position is pm.*/
+
+    inline void update_group(TValue *pl, TValue *pm)
+    {
+       TValue g;
+
+       g=pm-I;                      /* group number.*/
+       V[*pl]=g;                    /* update group number of first position.*/
+       if (pl==pm)
+          *pl=-1;                   /* one element, sorted group.*/
+       else
+          do                        /* more than one element, unsorted group.*/
+             V[*++pl]=g;            /* update group numbers.*/
+          while (pl<pm);
+    }
+
+    /* Quadratic sorting method to use for small subarrays. To be able to update
+       group numbers consistently, a variant of selection sorting is used.*/
+
+    inline void select_sort_split(TValue *p, TValue n) {
+       TValue *pa, *pb, *pi, *pn;
+       TValue f, v, tmp;
+
+       pa=p;                        /* pa is start of group being picked out.*/
+       pn=p+n-1;                    /* pn is last position of subarray.*/
+       while (pa<pn) {
+          for (pi=pb=pa+1, f=SEQAN_LSSKEY(pa); pi<=pn; ++pi)
+             if ((v=SEQAN_LSSKEY(pi))<f) {
+                f=v;                /* f is smallest key found.*/
+                SEQAN_LSSSWAP(pi, pa);       /* place smallest element at beginning.*/
+                pb=pa+1;            /* pb is position for elements equal to f.*/
+             } else if (v==f) {     /* if equal to smallest key.*/
+                SEQAN_LSSSWAP(pi, pb);       /* place next to other smallest elements.*/
+                ++pb;
+             }
+          update_group(pa, pb-1);   /* update group values for new group.*/
+          pa=pb;                    /* continue sorting rest of the subarray.*/
+       }
+       if (pa==pn) {                /* check if last part is single element.*/
+          V[*pa]=pa-I;
+          *pa=-1;                   /* sorted group.*/
+       }
+    }
+
+    /* Subroutine for sort_split, algorithm by Bentley & McIlroy.*/
+
+    inline TValue choose_pivot(TValue *p, TValue n) {
+       TValue *pl, *pm, *pn;
+       TValue s;
+
+       pm=p+(n>>1);                 /* small arrays, middle element.*/
+       if (n>7) {
+          pl=p;
+          pn=p+n-1;
+          if (n>40) {               /* big arrays, pseudomedian of 9.*/
+             s=n>>3;
+             pl=SEQAN_LSSMED3(pl, pl+s, pl+s+s);
+             pm=SEQAN_LSSMED3(pm-s, pm, pm+s);
+             pn=SEQAN_LSSMED3(pn-s-s, pn-s, pn);
+          }
+          pm=SEQAN_LSSMED3(pl, pm, pn);      /* midsize arrays, median of 3.*/
+       }
+       return SEQAN_LSSKEY(pm);
+    }
+
+    /* Sorting routine called for each unsorted group. Sorts the array of integers
+       (suffix numbers) of length n starting at p. The algorithm is a ternary-split
+       quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
+       Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
+       function is based on Program 7.*/
+
+    inline void sort_split(TValue *p, TValue n)
+    {
+       TValue *pa, *pb, *pc, *pd, *pl, *pm, *pn;
+       TValue f, v, s, t, tmp;
+
+       if (n<7) {                   /* multi-selection sort smallest arrays.*/
+          select_sort_split(p, n);
+          return;
+       }
+
+       v=choose_pivot(p, n);
+       pa=pb=p;
+       pc=pd=p+n-1;
+       while (1) {                  /* split-end partition.*/
+          while (pb<=pc && (f=SEQAN_LSSKEY(pb))<=v) {
+             if (f==v) {
+                SEQAN_LSSSWAP(pa, pb);
+                ++pa;
+             }
+             ++pb;
+          }
+          while (pc>=pb && (f=SEQAN_LSSKEY(pc))>=v) {
+             if (f==v) {
+                SEQAN_LSSSWAP(pc, pd);
+                --pd;
+             }
+             --pc;
+          }
+          if (pb>pc)
+             break;
+          SEQAN_LSSSWAP(pb, pc);
+          ++pb;
+          --pc;
+       }
+       pn=p+n;
+       if ((s=pa-p)>(t=pb-pa))
+          s=t;
+       for (pl=p, pm=pb-s; s; --s, ++pl, ++pm)
+          SEQAN_LSSSWAP(pl, pm);
+       if ((s=pd-pc)>(t=pn-pd-1))
+          s=t;
+       for (pl=pb, pm=pn-s; s; --s, ++pl, ++pm)
+          SEQAN_LSSSWAP(pl, pm);
+
+       s=pb-pa;
+       t=pd-pc;
+       if (s>0)
+          sort_split(p, s);
+       update_group(p+s, p+n-t-1);
+       if (t>0)
+          sort_split(p+n-t, t);
+    }
+
+    /* Bucketsort for first iteration.
+
+       Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
+       at least once. x[n] is 0. (This is the corresponding output of transform.) k
+       must be at most n+1. p is array of size n+1 whose contents are disregarded.
+
+       Output: x is V and p is I after the initial sorting stage of the refined
+       suffix sorting algorithm.*/
+
+    inline void bucketsort(TValue *x, TValue *p, TValue n, TValue k)
+    {
+       TValue *pi, i, c, d, g;
+
+       for (pi=p; pi<p+k; ++pi)
+          *pi=-1;                   /* mark linked lists empty.*/
+       for (i=0; i<=n; ++i) {
+          x[i]=p[c=x[i]];           /* insert in linked list.*/
+          p[c]=i;
+       }
+       for (pi=p+k-1, i=n; pi>=p; --pi) {
+          d=x[c=*pi];               /* c is position, d is next in list.*/
+          x[c]=g=i;                 /* last position equals group number.*/
+          if (d>=0) {               /* if more than one element in group.*/
+             p[i--]=c;              /* p is permutation for the sorted x.*/
+             do {
+                d=x[c=d];           /* next in linked list.*/
+                x[c]=g;             /* group number in x.*/
+                p[i--]=c;           /* permutation in p.*/
+             } while (d>=0);
+          } else
+             p[i--]=-1;             /* one element, sorted group.*/
+       }
+    }
+
+    /* Transforms the alphabet of x by attempting to aggregate several symbols into
+       one, while preserving the suffix order of x. The alphabet may also be
+       compacted, so that x on output comprises all integers of the new alphabet
+       with no skipped numbers.
+
+       Input: x is an array of size n+1 whose first n elements are positive
+       integers in the range l...k-1. p is array of size n+1, used for temporary
+       storage. q controls aggregation and compaction by defining the maximum value
+       for any symbol during transformation: q must be at least k-l; if q<=n,
+       compaction is guaranteed; if k-l>n, compaction is never done; if q is
+       INT_MAX, the maximum number of symbols are aggregated into one.
+
+       Output: Returns an integer j in the range 1...q representing the size of the
+       new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
+       set to the number of old symbols grouped into one. Only x[n] is 0.*/
+
+    inline TValue transform(TValue *x, TValue *p, TValue n, TValue k, TValue l, TValue q)
+    {
+       TValue b, c, d, e, i, j, m, s;
+       TValue *pi, *pj;
+
+       for (s=0, i=k-l; i; i>>=1)
+          ++s;                      /* s is number of bits in old symbol.*/
+       e=MaxValue<TValue>::VALUE>>s; /* e is for overflow checking.*/
+       for (b=d=r=0; r<n && d<=e && (c=d<<s|(k-l))<=q; ++r) {
+          b=b<<s|(x[r]-l+1);        /* b is start of x in chunk alphabet.*/
+          d=c;                      /* d is max symbol in chunk alphabet.*/
+       }
+       m=(1<<(r-1)*s)-1;            /* m masks off top old symbol from chunk.*/
+       x[n]=l-1;                    /* emulate zero terminator.*/
+       if (d<=n) {                  /* if bucketing possible, compact alphabet.*/
+          for (pi=p; pi<=p+d; ++pi)
+             *pi=0;                 /* zero transformation table.*/
+          for (pi=x+r, c=b; pi<=x+n; ++pi) {
+             p[c]=1;                /* mark used chunk symbol.*/
+             c=(c&m)<<s|(*pi-l+1);  /* shift in next old symbol in chunk.*/
+          }
+          for (i=1; i<r; ++i) {     /* handle last r-1 positions.*/
+             p[c]=1;                /* mark used chunk symbol.*/
+             c=(c&m)<<s;            /* shift in next old symbol in chunk.*/
+          }
+          for (pi=p, j=1; pi<=p+d; ++pi)
+             if (*pi)
+                *pi=j++;            /* j is new alphabet size.*/
+          for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
+             *pi=p[c];              /* transform to new alphabet.*/
+             c=(c&m)<<s|(*pj-l+1);  /* shift in next old symbol in chunk.*/
+          }
+          while (pi<x+n) {          /* handle last r-1 positions.*/
+             *pi++=p[c];            /* transform to new alphabet.*/
+             c=(c&m)<<s;            /* shift right-end zero in chunk.*/
+          }
+       } else {                     /* bucketing not possible, don't compact.*/
+          for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
+             *pi=c;                 /* transform to new alphabet.*/
+             c=(c&m)<<s|(*pj-l+1);  /* shift in next old symbol in chunk.*/
+          }
+          while (pi<x+n) {          /* handle last r-1 positions.*/
+             *pi++=c;               /* transform to new alphabet.*/
+             c=(c&m)<<s;            /* shift right-end zero in chunk.*/
+          }
+          j=d+1;                    /* new alphabet size.*/
+       }
+       x[n]=0;                      /* end-of-string symbol is zero.*/
+       return j;                    /* return new alphabet size.*/
+    }
+
+    /* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
+       n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
+       contents of x[n] is disregarded, the n-th symbol being regarded as
+       end-of-string smaller than all other symbols.*/
+
+    void suffixsort(TValue *x, TValue *p, TValue n, TValue k, TValue l)
+    {
+       TValue *pi, *pk;
+       TValue i, j, s, sl;
+
+       V=x;                         /* set global values.*/
+       I=p;
+
+       if (n>=k-l) {                /* if bucketing possible,*/
+          j=transform(V, I, n, k, l, n);
+          bucketsort(V, I, n, j);   /* bucketsort on first r positions.*/
+       } else {
+          transform(V, I, n, k, l, MaxValue<TValue>::VALUE);
+          for (i=0; i<=n; ++i)
+             I[i]=i;                /* initialize I with suffix numbers.*/
+          h=0;
+          sort_split(I, n+1);       /* quicksort on first r positions.*/
+       }
+       h=r;                         /* number of symbols aggregated by transform.*/
+
+       while (*I>=-n) {
+          pi=I;                     /* pi is first position of group.*/
+          sl=0;                     /* sl is negated length of sorted groups.*/
+          do {
+             if ((s=*pi)<0) {
+                pi-=s;              /* skip over sorted group.*/
+                sl+=s;              /* add negated length to sl.*/
+             } else {
+                if (sl) {
+                   *(pi+sl)=sl;     /* combine sorted groups before pi.*/
+                   sl=0;
+                }
+                pk=I+V[s]+1;        /* pk-1 is last position of unsorted group.*/
+                sort_split(pi, pk-pi);
+                pi=pk;              /* next group.*/
+             }
+          } while (pi<=I+n);
+          if (sl)                   /* if the array ends with a sorted group.*/
+             *(pi+sl)=sl;           /* combine sorted groups at end of I.*/
+          h=2*h;                    /* double sorted-depth.*/
+       }
+
+       for (i=0; i<=n; ++i)         /* reconstruct suffix array from inverse.*/
+          I[V[i]]=i;
+    }
 };
 
 
@@ -357,92 +357,92 @@ struct ContextLss_
 //////////////////////////////////////////////////////////////////////////////
 // SeqAn interface
 
-	struct LarssonSadakane {};
+    struct LarssonSadakane {};
 
-	// WARNING:
-	// 1. the content of s will be destroyed
-	// 2. s and SA have to have size n+1
-	// 3. s[n] must be unique and less than any other character in s
-	//
-	// better use LarssonSadakane as a pipe (look down)
+    // WARNING:
+    // 1. the content of s will be destroyed
+    // 2. s and SA have to have size n+1
+    // 3. s[n] must be unique and less than any other character in s
+    //
+    // better use LarssonSadakane as a pipe (look down)
 
     template < typename TSA,
                typename TText >
     void createSuffixArray(
-		TSA &SA,
-		TText const &s,
-		LarssonSadakane const &,
-		unsigned K)
-	{
-		typedef typename Value<TSA>::Type			TValue;
-		typedef typename MakeSigned_<TValue>::Type	TSValue;	// LarssonSadakane expects signed values
-		ContextLss_<TSValue> c;
-		c.suffixsort(
-			(TSValue*)begin(s, Standard()),		// text
-			(TSValue*)begin(SA, Standard()),	// SA
-			length(s) - 1,						// n
-			K,									// text[i] <  K
-			0);									// text[i] >= 0
-	}
+        TSA &SA,
+        TText const &s,
+        LarssonSadakane const &,
+        unsigned K)
+    {
+        typedef typename Value<TSA>::Type            TValue;
+        typedef typename MakeSigned_<TValue>::Type    TSValue;    // LarssonSadakane expects signed values
+        ContextLss_<TSValue> c;
+        c.suffixsort(
+            (TSValue*)begin(s, Standard()),        // text
+            (TSValue*)begin(SA, Standard()),    // SA
+            length(s) - 1,                        // n
+            K,                                    // text[i] <  K
+            0);                                    // text[i] >= 0
+    }
 
     //////////////////////////////////////////////////////////////////////////////
     // qsufsort pipe
     template < typename TInput >
     struct Pipe< TInput, LarssonSadakane >
     {
-		typedef typename SAValue<TInput>::Type	TValue;
-		typedef String<TValue, Alloc<> >		TText;
-		typedef String<TValue, Alloc<> >		TSA;
-		typedef Pipe<TSA, Source<> >			TSource;
-
-		TSA		sa;
-		TSource	in;
-
-		Pipe(TInput &_textIn):
-			in(sa)
-		{
-	        typedef typename Iterator<TText, Standard>::Type TIter;
-
-			TValue len = length(_textIn);
-			TText text;
-			resize(text, len + 1, Exact());
-
-			TIter	it = begin(text);
-			TIter	itEnd = begin(text) + len;
-			TValue	maxChar = 0;
-
-			beginRead(_textIn);
-			for(; it != itEnd; ++it, ++_textIn) {
-				TValue val = (*it = 1 + (TValue)*_textIn);
-				if (val > maxChar)
-					maxChar = val;
-			}
-			endRead(_textIn);
-
-			resize(sa, len + 1, Exact());
-			createSuffixArray(sa, text, LarssonSadakane(), maxChar + 1);
-		}
-
-		inline typename Value<TSource>::Type const & operator*() {
+        typedef typename SAValue<TInput>::Type    TValue;
+        typedef String<TValue, Alloc<> >        TText;
+        typedef String<TValue, Alloc<> >        TSA;
+        typedef Pipe<TSA, Source<> >            TSource;
+
+        TSA        sa;
+        TSource    in;
+
+        Pipe(TInput &_textIn):
+            in(sa)
+        {
+            typedef typename Iterator<TText, Standard>::Type TIter;
+
+            TValue len = length(_textIn);
+            TText text;
+            resize(text, len + 1, Exact());
+
+            TIter    it = begin(text);
+            TIter    itEnd = begin(text) + len;
+            TValue    maxChar = 0;
+
+            beginRead(_textIn);
+            for(; it != itEnd; ++it, ++_textIn) {
+                TValue val = (*it = 1 + (TValue)*_textIn);
+                if (val > maxChar)
+                    maxChar = val;
+            }
+            endRead(_textIn);
+
+            resize(sa, len + 1, Exact());
+            createSuffixArray(sa, text, LarssonSadakane(), maxChar + 1);
+        }
+
+        inline typename Value<TSource>::Type const & operator*() {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
-        }        
-	};
-
-	template < typename TInput >
-	inline bool control(Pipe< TInput, LarssonSadakane > &me, ControlBeginRead const &command) {
-		control(me.in, command);
-		++me.in;
-		return true;
-	}
-	
+        }
+    };
+
+    template < typename TInput >
+    inline bool control(Pipe< TInput, LarssonSadakane > &me, ControlBeginRead const &command) {
+        control(me.in, command);
+        ++me.in;
+        return true;
+    }
+
     template < typename TInput >
     inline typename Size< Pipe< TInput, LarssonSadakane > >::Type
-	length(Pipe< TInput, LarssonSadakane > const &me) {
+    length(Pipe< TInput, LarssonSadakane > const &me) {
         return length(me.in) - 1;
     }
 
diff --git a/seqan/index/index_sa_mm.h b/seqan/index/index_sa_mm.h
index 376ca69..9084693 100644
--- a/seqan/index/index_sa_mm.h
+++ b/seqan/index/index_sa_mm.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,7 +38,7 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	struct ManberMyers {};
+    struct ManberMyers {};
 
 
     //////////////////////////////////////////////////////////////////////////////
@@ -48,134 +48,134 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TSA,
                typename TText >
     void createSuffixArray(
-		TSA &SA,
-		TText const &s,
-		ManberMyers const &,
-		unsigned K,
+        TSA &SA,
+        TText const &s,
+        ManberMyers const &,
+        unsigned K,
         unsigned maxdepth)
-	{
-		typedef typename Value<TSA>::Type	TSize;
-		typedef typename Value<TText>::Type	TValue;
+    {
+        typedef typename Value<TSA>::Type    TSize;
+        typedef typename Value<TText>::Type    TValue;
 
-		typedef String<TSize, Alloc<> >		TString;
-		typedef String<bool, Alloc<> >		TBoolString;
+        typedef String<TSize, Alloc<> >        TString;
+        typedef String<bool, Alloc<> >        TBoolString;
 
-		typedef typename Iterator<TString, Standard>::Type	TIter;
+        typedef typename Iterator<TString, Standard>::Type    TIter;
 
-		TSize n = length(s);
+        TSize n = length(s);
 
         TString ISA;        resize(ISA, n, Exact());
         TString count;
-        TBoolString Bh;		resize(Bh, n, Exact());
-		TBoolString B2h;	resize(B2h, n, Exact());
-
-		// sort the first character (h=1)
-		{
-			resize(count, _max((TSize)K, n), Exact());
-			TIter it = begin(ISA, Standard());
-			for(TSize i = 0; i < n; ++i, ++it)
-				*it = i;
-			SEQAN_PROMARK("Suffix-Array invertiert");
-
-			radixPass(SA, ISA, s, count, length(count));
-			arrayFill(begin(Bh, Standard()), end(Bh, Standard()), false);
-		}
-
-		// update bucket borders Bh
-		{
-			TValue c = 0, d;
-			for(TSize i = 0; i < n; ++i) {
-				if (c != (d = s[SA[i]])) {
-					c = d;
-					Bh[i] = true;
-				}
-			}
-		}
-
-		// extend h-sort to 2h-sort
-		{
-			resize(count, n, Exact());
-			TSize j, k, l, Ti, cd = 0;
-
-			// set necessary number of rounds cd
-			for(TSize h = 1; h < n; h <<= 1, ++cd) ;
-			if (maxdepth > 0 && maxdepth < cd) 
-				cd = maxdepth;
-
-			for(TSize h = 1; cd > 0; h <<= 1, --cd) {
-
-				#ifdef SEQAN_DEBUG_INDEX
-					::std::cerr << "[" << cd << "] ";
-				#endif
-				SEQAN_PROADD(SEQAN_PRODEPTH, 1);
-				SEQAN_PROMARK("Beginne Durchlauf");
-				arrayFill(begin(count, Standard()), end(count, Standard()), 0);
-				arrayFill(begin(B2h, Standard()), end(B2h, Standard()), false);
-
-				l = 0;
-				for(TSize i = 0; i < n; ++i) {
-					if (Bh[i]) l = i;
-					ISA[SA[i]] = l;
-				}
-
-				SEQAN_ASSERT_GEQ(n, h);
-				Ti = n - h;
-				TIter p = begin(ISA, Standard()) + Ti;
-
-				SEQAN_ASSERT_LT(*p, n);
-				j = count[*p]++;
-				*p += j;
-
-				SEQAN_ASSERT_LT(*p, n);
-				B2h[*p] = true;
-
-				l = 0;
-				for(TSize i = 0; i < n; ++i) {
-
-					if ((Ti = SA[i]) >= h) {
-						Ti -= h;
-						p = begin(ISA) + Ti;
-
-						SEQAN_ASSERT_LT(*p, n);
-						j = count[*p]++;
-						*p += j;
-
-						SEQAN_ASSERT_LT(*p, n);
-						B2h[*p] = true;
-					}
-
-					if (i + 1 == n || Bh[i + 1]) {
-						for(j = l; j <= i; ++j)
-							if ((Ti = SA[j]) >= h) {
-								Ti -= h;
-								if (B2h[k = ISA[Ti]])
-									while (++k < n && !Bh[k] && B2h[k])
-										B2h[k] = false;
-							}
-						l = i + 1;
-					}
-				}
-
-				for(TSize i = 0; i < n; ++i) {
-					SA[ISA[i]] = i;
-					Bh[i] |= B2h[i];
-				}
-			}
-		}
+        TBoolString Bh;        resize(Bh, n, Exact());
+        TBoolString B2h;    resize(B2h, n, Exact());
+
+        // sort the first character (h=1)
+        {
+            resize(count, _max((TSize)K, n), Exact());
+            TIter it = begin(ISA, Standard());
+            for(TSize i = 0; i < n; ++i, ++it)
+                *it = i;
+            SEQAN_PROMARK("Suffix-Array invertiert");
+
+            radixPass(SA, ISA, s, count, length(count));
+            arrayFill(begin(Bh, Standard()), end(Bh, Standard()), false);
+        }
+
+        // update bucket borders Bh
+        {
+            TValue c = 0, d;
+            for(TSize i = 0; i < n; ++i) {
+                if (c != (d = s[SA[i]])) {
+                    c = d;
+                    Bh[i] = true;
+                }
+            }
+        }
+
+        // extend h-sort to 2h-sort
+        {
+            resize(count, n, Exact());
+            TSize j, k, l, Ti, cd = 0;
+
+            // set necessary number of rounds cd
+            for(TSize h = 1; h < n; h <<= 1, ++cd) ;
+            if (maxdepth > 0 && maxdepth < cd)
+                cd = maxdepth;
+
+            for(TSize h = 1; cd > 0; h <<= 1, --cd) {
+
+                #ifdef SEQAN_DEBUG_INDEX
+                    std::cerr << "[" << cd << "] ";
+                #endif
+                SEQAN_PROADD(SEQAN_PRODEPTH, 1);
+                SEQAN_PROMARK("Beginne Durchlauf");
+                arrayFill(begin(count, Standard()), end(count, Standard()), 0);
+                arrayFill(begin(B2h, Standard()), end(B2h, Standard()), false);
+
+                l = 0;
+                for(TSize i = 0; i < n; ++i) {
+                    if (Bh[i]) l = i;
+                    ISA[SA[i]] = l;
+                }
+
+                SEQAN_ASSERT_GEQ(n, h);
+                Ti = n - h;
+                TIter p = begin(ISA, Standard()) + Ti;
+
+                SEQAN_ASSERT_LT(*p, n);
+                j = count[*p]++;
+                *p += j;
+
+                SEQAN_ASSERT_LT(*p, n);
+                B2h[*p] = true;
+
+                l = 0;
+                for(TSize i = 0; i < n; ++i) {
+
+                    if ((Ti = SA[i]) >= h) {
+                        Ti -= h;
+                        p = begin(ISA) + Ti;
+
+                        SEQAN_ASSERT_LT(*p, n);
+                        j = count[*p]++;
+                        *p += j;
+
+                        SEQAN_ASSERT_LT(*p, n);
+                        B2h[*p] = true;
+                    }
+
+                    if (i + 1 == n || Bh[i + 1]) {
+                        for(j = l; j <= i; ++j)
+                            if ((Ti = SA[j]) >= h) {
+                                Ti -= h;
+                                if (B2h[k = ISA[Ti]])
+                                    while (++k < n && !Bh[k] && B2h[k])
+                                        B2h[k] = false;
+                            }
+                        l = i + 1;
+                    }
+                }
+
+                for(TSize i = 0; i < n; ++i) {
+                    SA[ISA[i]] = i;
+                    Bh[i] |= B2h[i];
+                }
+            }
+        }
         SEQAN_PROSET(SEQAN_PRODEPTH, 0);
         #ifdef SEQAN_DEBUG_INDEX
-			::std::cerr << ::std::endl;
+            std::cerr << std::endl;
         #endif
-	}
+    }
 
     // creates suffix array sorted by the first maxLCP chars of suffixes
     template < typename TSA,
                typename TText,
                typename TSize >
     inline void createSuffixArrayPart(
-		TSA &SA,
-		TText &s,
-		ManberMyers const &alg,
+        TSA &SA,
+        TText &s,
+        ManberMyers const &alg,
         TSize maxLCP,
         unsigned K)
     {
@@ -188,9 +188,9 @@ namespace SEQAN_NAMESPACE_MAIN
                typename TText,
                typename TSize >
     inline void createSuffixArrayPart(
-		TSA &SA,
-		TText &s,
-		ManberMyers const &alg,
+        TSA &SA,
+        TText &s,
+        ManberMyers const &alg,
         TSize maxLCP)
     {
         SEQAN_CHECKPOINT;
diff --git a/seqan/index/index_sa_qsort.h b/seqan/index/index_sa_qsort.h
index 7a9d21a..7317a27 100644
--- a/seqan/index/index_sa_qsort.h
+++ b/seqan/index/index_sa_qsort.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,207 +38,235 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	struct SAQSort {};
+    struct SAQSort {};
 
-	// compare two suffices of a given text
+    // compare two suffices of a given text
     template < typename TSAValue, typename TText >
-	struct SuffixLess_ : 
-		public ::std::binary_function < TSAValue, TSAValue, bool >
+    struct SuffixLess_ :
+        public std::binary_function < TSAValue, TSAValue, bool >
     {
-		typedef typename Iterator<TText const, Standard>::Type TIter;
-		TIter _begin, _end;
-
-		SuffixLess_(TText const &text):
-			_begin(begin(text, Standard())),
-			_end(end(text, Standard())) {}
-
-		// skip the first <offset> characters
-		template <typename TSize>
-		SuffixLess_(TText const &text, TSize offset):
-			_begin(begin(text, Standard()) + offset),
-			_end(end(text, Standard())) {}
-
-		inline bool operator() (TSAValue const a, TSAValue const b) const 
-		{
-			if (a == b) return false;
-			TIter itA = _begin + a;
-			TIter itB = _begin + b;
-			if (a <= b) {
-				for(; itB != _end; ++itB, ++itA) {
-					if (ordLess(*itA, *itB)) return true;
-					if (ordLess(*itB, *itA)) return false;
-				}
-				return false;
-			} else {
-				for(; itA != _end; ++itA, ++itB) {
-					if (ordLess(*itA, *itB)) return true;
-					if (ordLess(*itB, *itA)) return false;
-				}
-				return true;
-			}
-		}
-	};
-
-	// compare two suffices of a given text
+        typedef typename Iterator<TText const, Standard>::Type TIter;
+        TIter _begin, _end;
+
+        SuffixLess_(TText const &text):
+            _begin(begin(text, Standard())),
+            _end(end(text, Standard())) {}
+
+        // skip the first <offset> characters
+        template <typename TSize>
+        SuffixLess_(TText const &text, TSize offset):
+            _begin(begin(text, Standard()) + offset),
+            _end(end(text, Standard())) {}
+
+        inline bool operator() (TSAValue const a, TSAValue const b) const
+        {
+            if (a == b) return false;
+            TIter itA = _begin + a;
+            TIter itB = _begin + b;
+            if (a <= b) {
+                for(; itB != _end; ++itB, ++itA) {
+                    if (ordLess(*itA, *itB)) return true;
+                    if (ordLess(*itB, *itA)) return false;
+                }
+                return false;
+            } else {
+                for(; itA != _end; ++itA, ++itB) {
+                    if (ordLess(*itA, *itB)) return true;
+                    if (ordLess(*itB, *itA)) return false;
+                }
+                return true;
+            }
+        }
+    };
+
+    // compare two suffices of a given text
     template < typename TSAValue, typename TString, typename TSetSpec >
-	struct SuffixLess_<TSAValue, StringSet<TString, TSetSpec> const > :
-		public ::std::binary_function < TSAValue, TSAValue, bool >
+    struct SuffixLess_<TSAValue, StringSet<TString, TSetSpec> const > :
+        public std::binary_function < TSAValue, TSAValue, bool >
     {
         typedef StringSet<TString, TSetSpec> const TText;
-        
-		typename Size<TString>::Type _offset;
-		TText &_text;
-
-		SuffixLess_(TText &text):
-			_text(text) {}
-			
-		// skip the first <offset> characters
-		template <typename TSize>
-		SuffixLess_(TText &text, TSize offset):
-			_text(text),
-			_offset(offset) {}
-		
-		inline bool operator() (TSAValue const a, TSAValue const b) const 
-		{
-			typedef typename Iterator<TString const, Standard>::Type TIter;
-			if (a == b) return false;
-			TIter itA = begin(getValue(_text, getSeqNo(a)), Standard()) + getSeqOffset(a);
-			TIter itB = begin(getValue(_text, getSeqNo(b)), Standard()) + getSeqOffset(b);
-			TIter itAEnd = end(getValue(_text, getSeqNo(a)), Standard());
-			TIter itBEnd = end(getValue(_text, getSeqNo(b)), Standard());
-			if (itAEnd - itA < itBEnd - itB) {
-				for(; itA != itAEnd; ++itA, ++itB) {
-					if (ordLess(*itA, *itB)) return true;
-					if (ordLess(*itB, *itA)) return false;
-				}
-				return true;
-			} else {
-				for(; itB != itBEnd; ++itB, ++itA) {
-					if (ordLess(*itA, *itB)) return true;
-					if (ordLess(*itB, *itA)) return false;
-				}
+
+        TText &_text;
+        typename Size<TString>::Type _offset;
+
+        SuffixLess_(TText &text):
+            _text(text) {}
+
+        // skip the first <offset> characters
+        template <typename TSize>
+        SuffixLess_(TText &text, TSize offset):
+            _text(text),
+            _offset(offset) {}
+
+        inline bool operator() (TSAValue const a, TSAValue const b) const
+        {
+            typedef typename Iterator<TString const, Standard>::Type TIter;
+            if (a == b) return false;
+            TIter itA = begin(getValue(_text, getSeqNo(a)), Standard()) + getSeqOffset(a);
+            TIter itB = begin(getValue(_text, getSeqNo(b)), Standard()) + getSeqOffset(b);
+            TIter itAEnd = end(getValue(_text, getSeqNo(a)), Standard());
+            TIter itBEnd = end(getValue(_text, getSeqNo(b)), Standard());
+            if (itAEnd - itA < itBEnd - itB) {
+                for(; itA != itAEnd; ++itA, ++itB) {
+                    if (ordLess(*itA, *itB)) return true;
+                    if (ordLess(*itB, *itA)) return false;
+                }
+                return true;
+            } else {
+                for(; itB != itBEnd; ++itB, ++itA) {
+                    if (ordLess(*itA, *itB)) return true;
+                    if (ordLess(*itB, *itA)) return false;
+                }
                 if (itA != itAEnd)
                     return false;
-				return getSeqNo(a) > getSeqNo(b);
-			}
-		}	
-	};
+                return getSeqNo(a) > getSeqNo(b);
+            }
+        }
+    };
 
-	// compare two suffices of a given text and skip the first <lcp> characters
+    // compare two suffices of a given text and skip the first <lcp> characters
     template < typename TSAValue, typename TText >
-	struct SuffixLessOffset_: SuffixLess_<TSAValue, TText> 
-	{
-		// skip the first <offset> characters
-		template <typename TSize>
-		SuffixLessOffset_(TText &text, TSize offset): 
-			SuffixLess_<TSAValue, TText> (text, offset) {}
-	};
-
-		
-		
-	template < typename TSA, 
-			typename TText,
-			typename TSize>
-	void _sortBucketQuickSort(
-		TSA &sa,
-		TText &text,
-		TSize lcp)
-	{
-	SEQAN_CHECKPOINT
-		// sort bucket with quicksort
-		::std::sort(
-			begin(sa, Standard()), 
-			end(sa, Standard()), 
-			SuffixLessOffset_<typename Value<TSA>::Type, TText>(text, lcp));
-	}
-
-	template < typename TSA,
+    struct SuffixLessOffset_: SuffixLess_<TSAValue, TText>
+    {
+        // skip the first <offset> characters
+        template <typename TSize>
+        SuffixLessOffset_(TText &text, TSize offset):
+            SuffixLess_<TSAValue, TText> (text, offset) {}
+    };
+
+
+
+    template < typename TSA,
+            typename TText,
+            typename TSize>
+    void _sortBucketQuickSort(
+        TSA &sa,
+        TText &text,
+        TSize lcp)
+    {
+    SEQAN_CHECKPOINT
+        // sort bucket with quicksort
+        std::sort(
+            begin(sa, Standard()),
+            end(sa, Standard()),
+            SuffixLessOffset_<typename Value<TSA>::Type, TText>(text, lcp));
+    }
+
+    template < typename TSA,
                typename TText >
     inline void createSuffixArray(
-		TSA &SA,
-		TText const &s,
-		SAQSort const &)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Size<TSA>::Type TSize;
-		typedef typename Iterator<TSA, Standard>::Type TIter;
-
-		// 1. Fill suffix array with a permutation (the identity)
-		TIter it = begin(SA, Standard());
-		TIter itEnd = end(SA, Standard());
-		for(TSize i = 0; it != itEnd; ++it, ++i)
-			*it = i;
-
-		// 2. Sort suffix array with quicksort
-		::std::sort(
-			begin(SA, Standard()), 
-			end(SA, Standard()), 
-			SuffixLess_<typename Value<TSA>::Type, TText const>(s));
-	}
-
-	template < typename TSA,
+        TSA &SA,
+        TText const &s,
+        SAQSort const &)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Size<TSA>::Type TSize;
+        typedef typename Iterator<TSA, Standard>::Type TIter;
+
+        // 1. Fill suffix array with a permutation (the identity)
+        TIter it = begin(SA, Standard());
+        TIter itEnd = end(SA, Standard());
+        for(TSize i = 0; it != itEnd; ++it, ++i)
+            *it = i;
+
+        // 2. Sort suffix array with quicksort
+        std::sort(
+            begin(SA, Standard()),
+            end(SA, Standard()),
+            SuffixLess_<typename Value<TSA>::Type, TText const>(s));
+    }
+
+    template < typename TSA,
                typename TString,
-			   typename TSSetSpec >
+               typename TSSetSpec >
     inline void createSuffixArray(
-		TSA &SA,
-		StringSet< TString, TSSetSpec > const &s,
-		SAQSort const &)
-	{
-	SEQAN_CHECKPOINT
+        TSA &SA,
+        StringSet< TString, TSSetSpec > const &s,
+        SAQSort const &)
+    {
+    SEQAN_CHECKPOINT
         typedef StringSet< TString, TSSetSpec > TText;
-		typedef typename Size<TSA>::Type TSize;
-		typedef typename Iterator<TSA, Standard>::Type TIter;
-
-		// 1. Fill suffix array with a permutation (the identity)
-		TIter it = begin(SA, Standard());
-		for(unsigned j = 0; j < length(s); ++j)
-		{
-			TSize len = length(s[j]);
-			for(TSize i = 0; i < len; ++i, ++it)
-				*it = Pair<unsigned, TSize>(j, i);
-		}
-
-		// 2. Sort suffix array with quicksort
-		::std::sort(
-			begin(SA, Standard()), 
-			end(SA, Standard()), 
-			SuffixLess_<typename Value<TSA>::Type, TText const>(s));
-	}
+        typedef typename Size<TSA>::Type TSize;
+        typedef typename Iterator<TSA, Standard>::Type TIter;
+
+        // 1. Fill suffix array with a permutation (the identity)
+        TIter it = begin(SA, Standard());
+        for(unsigned j = 0; j < length(s); ++j)
+        {
+            TSize len = length(s[j]);
+            for(TSize i = 0; i < len; ++i, ++it)
+                *it = Pair<unsigned, TSize>(j, i);
+        }
+
+        // 2. Sort suffix array with quicksort
+        std::sort(
+            begin(SA, Standard()),
+            end(SA, Standard()),
+            SuffixLess_<typename Value<TSA>::Type, TText const>(s));
+    }
+
+    // Fill suffix array with permutation (i, 0)
+    template <typename TSA, typename TString, typename TSSetSpec>
+    inline void
+    fillSuffixArray(TSA &sa, StringSet<TString, TSSetSpec> const & /* s */, Trie const &)
+    {
+        typedef typename Iterator<TSA, Standard>::Type  TIter;
+        typedef typename Value<TSA>::Type               TSAValue;
+
+        TIter it = begin(sa, Standard());
+        TIter itEnd = end(sa, Standard());
+        for (; it != itEnd; ++it)
+            *it = TSAValue(position(it, sa), 0);
+    }
+
+    template <typename TSA, typename TString, typename TSSetSpec>
+    inline void
+    createSuffixArray(TSA &sa, StringSet<TString, TSSetSpec> const &s, Trie const &)
+    {
+        typedef StringSet<TString, TSSetSpec>           TText;
+        typedef typename Value<TSA>::Type               TSAValue;
+
+        // 1. Fill suffix array with permutation (i, 0)
+        fillSuffixArray(sa, s, Trie());
+
+        // 2. Sort suffix array with quicksort
+        sort(sa, SuffixLess_<TSAValue, TText const>(s));
+    }
 
     //////////////////////////////////////////////////////////////////////////////
     // suffix quicksort pipe
     template < typename TInput >
     struct Pipe< TInput, SAQSort >
     {
-		typedef typename Value<TInput>::Type	TValue;
-		typedef typename SAValue<TInput>::Type	TSAValue;
+        typedef typename Value<TInput>::Type    TValue;
+        typedef typename SAValue<TInput>::Type    TSAValue;
 
-		typedef String<TValue, Alloc<> >		TText;
-		typedef String<TSAValue, Alloc<> >		TSA;
-		typedef Pipe<TSA, Source<> >			TSource;
+        typedef String<TValue, Alloc<> >        TText;
+        typedef String<TSAValue, Alloc<> >        TSA;
+        typedef Pipe<TSA, Source<> >            TSource;
 
-		TSA		sa;
-		TSource	in;
+        TSA        sa;
+        TSource    in;
 
-		Pipe(TInput &_textIn):
-			in(sa)
-		{
-			TText text;
-			text << _textIn;
+        Pipe(TInput &_textIn):
+            in(sa)
+        {
+            TText text;
+            text << _textIn;
 
-			resize(sa, length(_textIn), Exact());
-			createSuffixArray(sa, text, SAQSort());
-		}
+            resize(sa, length(_textIn), Exact());
+            createSuffixArray(sa, text, SAQSort());
+        }
 
-		inline typename Value<TSource>::Type const & operator*() {
+        inline typename Value<TSource>::Type const & operator*() {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
-        }        
-	};
+        }
+    };
 
 }
 
diff --git a/seqan/index/index_sa_stree.h b/seqan/index/index_sa_stree.h
new file mode 100644
index 0000000..1352779
--- /dev/null
+++ b/seqan/index/index_sa_stree.h
@@ -0,0 +1,699 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_SA_STREE_H_
+#define SEQAN_INDEX_SA_STREE_H_
+
+//#define SEQAN_DEBUG
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TString, typename TSpec>
+class SearchTreeIterator;
+
+struct SortedList;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TSpec = void>
+struct IndexSa {};
+
+/*!
+ * @class IndexSa
+ * @extends Index
+ * @implements StringTrieConcept
+ * @headerfile <seqan/index.h>
+ * @brief An index based on a suffix array.
+ * @signature template <typename TText, typename TSpec>
+ *            class Index<TText, IndexSa<TSpec> >;
+ *
+ * @tparam TText The type of the underlying @link TextConcept text @endlink.
+ * @tparam TSpec A tag for specialization purposes.
+ */
+
+template <typename TText, typename TSpec>
+class Index<TText, IndexSa<TSpec> >
+{
+public:
+    typename Member<Index, FibreText>::Type         text;
+    typename Fibre<Index, FibreSA>::Type            sa;
+    typename Cargo<Index>::Type                     cargo;
+
+    Index() {}
+
+    Index(Index & other) :
+        text(other.text),
+        sa(other.sa)
+    {}
+
+    Index(Index const & other) :
+        text(other.text),
+        sa(other.sa)
+    {}
+
+    template <typename TText_>
+    Index(TText_ & _text) :
+        text(_text)
+    {}
+
+    template <typename TText_>
+    Index(TText_ const & _text) :
+        text(_text)
+    {}
+};
+
+template <typename TText, typename TSpec>
+SEQAN_CONCEPT_IMPL((Index<TText, IndexSa<TSpec> >), (StringTrieConcept));
+
+template <typename TText, typename TSpec>
+SEQAN_CONCEPT_IMPL((Index<TText, IndexSa<TSpec> > const), (StringTrieConcept));
+
+
+template <typename TSize, typename TAlphabet>
+struct VertexSA : public VertexEsa<TSize>
+{
+    typedef VertexEsa<TSize>                        TBase;
+
+    TSize       repLen;
+    TAlphabet   lastChar;
+
+    SEQAN_HOST_DEVICE
+    VertexSA() :
+        TBase(),
+        repLen(0),
+        lastChar(0)
+    {}
+
+    SEQAN_HOST_DEVICE
+    VertexSA(MinimalCtor) :
+        TBase(MinimalCtor()),
+        repLen(0),
+        lastChar(0)
+    {}
+
+    SEQAN_HOST_DEVICE
+    VertexSA(VertexSA const & other) :
+        TBase(other),
+        repLen(other.repLen),
+        lastChar(other.lastChar)
+    {}
+};
+
+template <typename TSize, typename TAlphabet>
+struct HistoryStackSA_
+{
+    Pair<TSize> range;
+    TSize       repLen;
+    TAlphabet   lastChar;
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+template <typename TText, typename TSpec>
+struct VertexDescriptor<Index<TText, IndexSa<TSpec> > >
+{
+    typedef Index<TText, IndexSa<TSpec> >           TIndex;
+    typedef typename Size<TIndex>::Type             TSize;
+    typedef typename Value<TIndex>::Type            TAlphabet;
+
+    typedef VertexSA<TSize, TAlphabet>              Type;
+};
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+struct HistoryStackEntry_<Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > >
+{
+private:
+    typedef Index<TText, IndexSa<TIndexSpec> >      TIndex;
+    typedef typename Size<TIndex>::Type             TSize;
+    typedef typename Value<TIndex>::Type            TAlphabet;
+
+public:
+    typedef HistoryStackSA_<TSize, TAlphabet>       Type;
+};
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+struct EdgeLabel<Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TSpec> > >
+{
+    typedef typename Value<Index<TText, IndexSa<TIndexSpec> > >::Type Type;
+};
+
+template < typename TText, typename TIndexSpec >
+struct DefaultFinder< Index<TText, IndexSa<TIndexSpec> > >
+{
+    typedef FinderMlr Type;    // standard suffix array finder is mlr-heuristic
+};
+
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TText, typename TIndexSpec>
+SEQAN_HOST_DEVICE inline void _indexRequireTopDownIteration(Index<TText, IndexSa<TIndexSpec> > & index)
+{
+    indexRequire(index, FibreSA());
+}
+
+template <typename TText>
+void _indexRequireTopDownIteration(Index<TText, IndexSa<InfixSegment> > &)
+{
+    // The SA fibre must be provided by calling setHost explicitely.
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline typename SAValue<Index<TText, IndexSa<TIndexSpec> > >::Type
+_lastOccurrence(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TSpec> > const &it)
+{
+    if (_isSizeInval(value(it).range.i2))
+        return back(indexSA(container(it)));
+    else
+        return saAt(value(it).range.i2 - 1, container(it));
+}
+
+
+// is this the first child of the parent node?
+template <typename TIndex, typename TSpec>
+inline bool
+isFirstChild(Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > const & it)
+{
+    if (!empty(it.history))
+    {
+        typename Size<TIndex>::Type parentLeft = back(it.history).range.i1;
+        if (value(it).range.i1 == parentLeft)
+            return true;
+
+        TIndex const & index = container(it);
+        return suffixLength(saAt(value(it).range.i1 - 1, index), index) + 1 == value(it).repLen;
+    }
+    else
+        return value(it).range.i1 == 0;
+
+}
+
+// is this the last child of the parent node?
+template <typename TIndex, typename TSpec>
+inline bool
+isLastChild(Iter<TIndex, VSTree<TopDown<TSpec> > > const & it)
+{
+    return value(it).range.i2 == value(it).parentRight;
+}
+
+template <typename TIndex, typename TSpec>
+inline bool
+isLastChild(Iter<TIndex, VSTree<TopDown<ParentLinks<TSpec> > > > const & it)
+{
+    if (!empty(it.history))
+        return value(it).range.i2 == back(it.history).range.i2;
+    else
+        return _isSizeInval(value(it).range.i2);
+
+}
+
+// go down and skip non-branching nodes
+// this function emulates suffix tree traversal
+template <typename TIndex, typename TSpec>
+inline bool
+goDownSkipSingletons(Iter<TIndex, VSTree< TopDown<TSpec> > > &it)
+{
+    do {
+        if (!goDown(it))
+            return false;
+    } while (isLastChild(it));
+    return true;
+}
+
+// is this a leaf? (hide empty $-edges)
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder>
+SEQAN_HOST_DEVICE inline bool
+_isLeaf(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TSpec> > const & it,
+        VSTreeIteratorTraits<TDfsOrder, True> const)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> >                      TIndex;
+    typedef typename SAValue<TIndex>::Type                          TOcc;
+
+//    if (_isLeaf(value(it))) return true;
+
+    TIndex const & index = container(it);
+
+    typename Size<TIndex>::Type lcp = repLength(it);
+
+    // if the last suffix in the interval is larger than the lcp,
+    // not all outgoing edges are empty (uses lex. sorting)
+    TOcc oc = _lastOccurrence(it);
+    return getSeqOffset(oc, stringSetLimits(index)) + lcp == sequenceLength(getSeqNo(oc, stringSetLimits(index)), index);
+}
+
+template <typename TIndex, typename TSize, typename TAlphabet>
+SEQAN_HOST_DEVICE inline typename Size<TIndex>::Type
+repLength(TIndex const &, VertexSA<TSize, TAlphabet> const & vDesc)
+{
+    return vDesc.repLen;
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+inline typename EdgeLabel<Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > >::Type
+parentEdgeLabel(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return value(it).lastChar;
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+inline typename Value<Index<TText, IndexSa<TIndexSpec> > >::Type
+parentEdgeFirstChar(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > const & it)
+{
+    return value(it).lastChar;
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline void goRoot(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TSpec> > & it)
+{
+    _historyClear(it);
+    clear(it);
+    if (!empty(indexSA(container(it))))
+        _setSizeInval(value(it).range.i2);
+    value(it).repLen = 0;
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder>
+inline bool _goDown(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+                    VSTreeIteratorTraits<TDfsOrder, False> const)
+{
+    // TODO(esiragusa): goDown including empty $-edges
+    return _goDown(it, VSTreeIteratorTraits<TDfsOrder, True>());
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder>
+inline bool _goDown(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+                    VSTreeIteratorTraits<TDfsOrder, True> const)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> >              TIndex;
+    typedef typename Fibre<TIndex, FibreSA>::Type           TSA;
+    typedef typename Size<TIndex>::Type                     TSASize;
+    typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+    typedef SearchTreeIterator<TSA const, SortedList>       TSearchTreeIterator;
+    typedef typename Value<TIndex>::Type                    TAlphabet;
+
+#ifdef SEQAN_DEBUG
+    std::cout << "goDown" << std::endl;
+#endif
+
+    if (_isLeaf(it, HideEmptyEdges()))
+        return false;
+
+    TIndex const & index = container(it);
+    TSA const & sa = indexSA(index);
+    TText const & text = indexText(index);
+
+    // TODO(esiragusa): check nodeHullPredicate
+
+#ifdef SEQAN_DEBUG
+    std::cout << "parent: " << value(it).range << std::endl;
+#endif
+
+    Pair<typename Size<TIndex>::Type> saRange = range(it);
+
+    // TODO(esiragusa): remove this check.
+    if (saRange.i1 >= saRange.i2) return false;
+
+    // Skip $-edges.
+    while (suffixLength(saAt(saRange.i1, index), index) <= value(it).repLen)
+    {
+        // TODO(esiragusa): remove this check and ++saRange.i1 in loop.
+        // Interval contains only $-edges.
+        if (++saRange.i1 >= saRange.i2)
+            return false;
+    }
+
+    // Get first and last characters in interval.
+    TAlphabet cLeft = textAt(posAdd(saAt(saRange.i1, index), value(it).repLen), index);
+    TAlphabet cRight = textAt(posAdd(saAt(saRange.i2 - 1, index), value(it).repLen), index);
+
+#ifdef SEQAN_DEBUG
+    std::cout << "char: " << Pair<TAlphabet>(cLeft, cRight) << std::endl;
+#endif
+
+    // Save vertex descriptor.
+    _historyPush(it);
+
+    // Update left range.
+    value(it).range.i1 = saRange.i1;
+
+    // Update right range.
+    // NOTE(esiragusa): I should use ordLess(cLeft, cRight) but masai redefines it for Ns.
+    if (ordValue(cLeft) != ordValue(cRight))
+    {
+        TSAIterator saBegin = begin(sa, Standard()) + saRange.i1;
+        TSASize saLen = saRange.i2 - saRange.i1;
+        TSearchTreeIterator node(saBegin, saLen);
+
+        TSAIterator upperBound = _upperBoundSA(text, node, cLeft, value(it).repLen);
+
+        value(it).range.i2 = upperBound - begin(sa, Standard());
+    }
+    else
+    {
+        value(it).range.i2 = saRange.i2;
+    }
+
+    // Update child repLen, lastChar.
+    value(it).repLen++;
+    value(it).lastChar = cLeft;
+
+#ifdef SEQAN_DEBUG
+    std::cout << "child: " <<  value(it).range << std::endl;
+#endif
+
+    return true;
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder, typename THideEmptyEdges>
+inline bool _goRight(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+                     VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> >              TIndex;
+    typedef typename Fibre<TIndex, FibreSA>::Type           TSA;
+    typedef typename Size<TIndex>::Type                     TSASize;
+    typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+    typedef SearchTreeIterator<TSA const, SortedList>       TSearchTreeIterator;
+    typedef typename Value<TIndex>::Type                    TAlphabet;
+
+#ifdef SEQAN_DEBUG
+    std::cout << "goRight" << std::endl;
+#endif
+
+    if (isRoot(it))
+        return false;
+
+    TIndex const & index = container(it);
+    TSA const & sa = indexSA(index);
+
+#ifdef SEQAN_DEBUG
+    std::cout << "current: " << value(it).range << std::endl;
+#endif
+
+    Pair<typename Size<TIndex>::Type> saRange;
+    saRange.i1 = value(it).range.i2;
+    saRange.i2 = (_isSizeInval(value(it).parentRight)) ? length(sa) : value(it).parentRight;
+
+    if (saRange.i1 >= saRange.i2) return false;
+
+    // Change repLen to parent repLen.
+    value(it).repLen--;
+
+    // TODO(esiragusa): don't check for empty edges (do it in goDown)
+    // Skip $-edges.
+    while (suffixLength(saAt(saRange.i1, index), index) <= value(it).repLen)
+    {
+        // Interval contains only $-edges.
+        if (++saRange.i1 >= saRange.i2)
+            return false;
+    }
+
+    // Get first and last characters in interval.
+    TAlphabet cLeft = textAt(posAdd(saAt(saRange.i1, index), value(it).repLen), index);
+    TAlphabet cRight = textAt(posAdd(saAt(saRange.i2 - 1, index), value(it).repLen), index);
+
+    SEQAN_ASSERT_NEQ(ordValue(cLeft), ordValue(value(it).lastChar));
+
+#ifdef SEQAN_DEBUG
+    std::cout << "char: " << Pair<TAlphabet>(cLeft, cRight) << std::endl;
+#endif
+
+    // Update left range.
+    value(it).range.i1 = saRange.i1;
+
+    // Update right range.
+    // NOTE(esiragusa): I should use ordLess(cLeft, cRight) but masai redefines it for Ns.
+    if (ordValue(cLeft) != ordValue(cRight))
+    {
+        TSAIterator saBegin = begin(sa, Standard()) + saRange.i1;
+        TSASize saLen = saRange.i2 - saRange.i1;
+        TSearchTreeIterator node(saBegin, saLen);
+
+        TText const & text = indexText(index);
+        TSAIterator upperBound = _upperBoundSA(text, node, cLeft, value(it).repLen);
+
+        value(it).range.i2 = upperBound - begin(sa, Standard());
+    }
+    else
+    {
+        value(it).range.i2 = saRange.i2;
+    }
+
+    // Update repLen, lastChar.
+    value(it).repLen++;
+    value(it).lastChar = cLeft;
+
+#ifdef SEQAN_DEBUG
+    std::cout << "sibling: " <<  value(it).range << std::endl;
+#endif
+
+    return true;
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec, typename TValue>
+inline bool _goDownChar(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > & it, TValue c)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> >              TIndex;
+    typedef typename Fibre<TIndex, FibreSA>::Type           TSA;
+    typedef typename Size<TIndex>::Type                     TSASize;
+    typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+    typedef SearchTreeIterator<TSA const, SortedList>       TSearchTreeIterator;
+
+    // Save vertex descriptor.
+    _historyPush(it);
+
+    TIndex const & index = container(it);
+    TSA const & sa = indexSA(index);
+    TText const & text = indexText(index);
+
+#ifdef SEQAN_DEBUG
+    std::cout << "parent: " << value(it).range << std::endl;
+#endif
+
+    TSAIterator saBegin = begin(sa, Standard()) + value(it).range.i1;
+    TSASize saLen = isRoot(it) ? length(sa) : value(it).range.i2 - value(it).range.i1;
+    TSearchTreeIterator node(saBegin, saLen);
+    Pair<TSAIterator> range = _equalRangeSA(text, node, c, value(it).repLen);
+
+    if (range.i1 >= range.i2)
+        return false;
+
+    // Update range, lastChar and repLen.
+    value(it).range.i1 = range.i1 - begin(sa, Standard());
+    value(it).range.i2 = range.i2 - begin(sa, Standard());
+    value(it).repLen++;
+    value(it).lastChar = c;
+
+#ifdef SEQAN_DEBUG
+    std::cout << "child: " <<  value(it).range << std::endl;
+#endif
+
+    return true;
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec, typename TString, typename TSize>
+inline bool _goDownString(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > & it,
+                          TString const & pattern, TSize & lcp)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> >              TIndex;
+    typedef typename Fibre<TIndex, FibreSA>::Type           TSA;
+    typedef typename Size<TSA const>::Type                  TSASize;
+    typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+    typedef SearchTreeIterator<TSA const, SortedList>       TSearchTreeIterator;
+
+    // Save vertex descriptor.
+    _historyPush(it);
+
+#ifdef SEQAN_DEBUG
+    std::cout << "parent: " << value(it).range << std::endl;
+#endif
+
+    if (!empty(pattern))
+    {
+        TIndex const & index = container(it);
+        TSA const & sa = indexSA(index);
+        TText const & text = indexText(index);
+
+        TSAIterator saBegin = begin(sa, Standard()) + value(it).range.i1;
+        TSASize saLen = isRoot(it) ? length(sa) : value(it).range.i2 - value(it).range.i1;
+        TSearchTreeIterator node(saBegin, saLen);
+        Pair<TSAIterator> range = _equalRangeSA(text, node, pattern, value(it).repLen);
+
+        if (range.i1 >= range.i2)
+            return false;
+
+        // Update range, lastChar and repLen.
+        value(it).range.i1 = range.i1 - begin(sa, Standard());
+        value(it).range.i2 = range.i2 - begin(sa, Standard());
+        value(it).repLen += length(pattern);
+        value(it).lastChar = back(pattern);
+    }
+
+#ifdef SEQAN_DEBUG
+    std::cout << "child: " <<  value(it).range << std::endl;
+#endif
+
+    lcp = length(pattern);
+
+    return true;
+}
+
+// return vertex descriptor of parent's node
+template <typename TText, typename TIndexSpec, typename TSpec>
+inline typename VertexDescriptor<Index<TText, IndexSa<TIndexSpec> > >::Type
+nodeUp(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > const & it)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> > TIndex;
+
+    if (!empty(it.history))
+    {
+        typename VertexDescriptor<TIndex>::Type desc;
+        desc.range = back(it.history).range;
+        desc.repLen = back(it.history).repLen;
+        desc.lastChar = back(it.history).lastChar;
+        if (length(it.history) >= 2)
+            desc.parentRight = backPrev(it.history).range.i2;
+        else
+            desc.parentRight = value(it).parentRight;
+        return desc;
+    } else
+        return value(it);
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+inline bool _goUp(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
+{
+#ifdef SEQAN_DEBUG
+    std::cout << "goUp" << std::endl;
+#endif
+
+    if (!empty(it.history))
+    {
+        value(it).range = back(it.history).range;
+        value(it).repLen = back(it.history).repLen;
+        value(it).lastChar = back(it.history).lastChar;
+        eraseBack(it.history);
+        if (!empty(it.history))
+            value(it).parentRight = back(it.history).range.i2;
+        return true;
+    }
+    return false;
+}
+
+// ============================================================================
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+inline void _historyPush(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > > & it)
+{
+    it._parentDesc = value(it);
+    value(it).parentRight = value(it).range.i2;
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+inline void _historyPush(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > & it)
+{
+    typedef Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > TIter;
+    typename HistoryStackEntry_<TIter>::Type h;
+    h.range = value(it).range;
+    h.repLen = value(it).repLen;
+    h.lastChar = value(it).lastChar;
+    appendValue(it.history, h);
+
+    value(it).parentRight = value(it).range.i2;
+}
+
+// ============================================================================
+
+template <typename TText, typename TSpec>
+inline void clear(Index<TText, IndexSa<TSpec> > & index)
+{
+    clear(getFibre(index, FibreSA()));
+}
+
+template <typename TObject, typename TSpec>
+inline bool open(Index<TObject, IndexSa<TSpec> > & index, const char * fileName, int openMode)
+{
+    String<char> name;
+
+    name = fileName;    append(name, ".txt");
+    if ((!open(getFibre(index, FibreText()), toCString(name), openMode)) &&
+        (!open(getFibre(index, FibreText()), fileName, openMode))) return false;
+
+    name = fileName;    append(name, ".sa");
+    if (!open(getFibre(index, FibreSA()), toCString(name), openMode)) return false;
+
+    return true;
+}
+
+template <typename TObject, typename TSpec>
+inline bool open(Index<TObject, IndexSa<TSpec> > & index, const char * fileName)
+{
+    return open(index, fileName, DefaultOpenMode<Index<TObject, IndexSa<TSpec> > >::VALUE);
+}
+
+template <typename TObject, typename TSpec>
+inline bool save(Index<TObject, IndexSa<TSpec> > & index, const char * fileName, int openMode)
+{
+    String<char> name;
+
+    name = fileName;    append(name, ".txt");
+    if ((!save(getFibre(index, FibreText()), toCString(name), openMode)) &&
+        (!save(getFibre(index, FibreText()), fileName, openMode))) return false;
+
+    name = fileName;    append(name, ".sa");
+    if (!save(getFibre(index, FibreSA()), toCString(name), openMode)) return false;
+
+    return true;
+}
+
+template <typename TObject, typename TSpec>
+inline bool save(Index<TObject, IndexSa<TSpec> > & index, const char * fileName)
+{
+    return save(index, fileName, DefaultOpenMode<Index<TObject, IndexSa<TSpec> > >::VALUE);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INDEX_SA_STREE_H_
diff --git a/seqan/index/index_sa_truncated.h b/seqan/index/index_sa_truncated.h
new file mode 100644
index 0000000..0d5994e
--- /dev/null
+++ b/seqan/index/index_sa_truncated.h
@@ -0,0 +1,163 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// This file contains the Truncated VSTree iterator spec for IndexSa.
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_SA_STREE_TRUNCATED_H_
+#define SEQAN_INDEX_SA_STREE_TRUNCATED_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag Truncated
+// ----------------------------------------------------------------------------
+
+template <typename TSpec = void>
+struct Truncated;
+
+// ----------------------------------------------------------------------------
+// Class Iter
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+class Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<Truncated<TSpec> > > > :
+    public Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<TSpec> > >
+{
+public:
+    typedef Index<TText, IndexSa<TIndexSpec> >          TIndex;
+    typedef Iter<TIndex, VSTree<TopDown<TSpec> > >      TBase;
+    typedef typename VertexDescriptor<TIndex>::Type     TVertexDesc;
+    typedef typename Size<TIndex>::Type                 TDepth;
+
+    TDepth depth;
+
+    Iter() :
+        TBase(),
+        depth(MaxValue<TDepth>::VALUE)
+    {}
+
+    Iter(TIndex &_index) :
+        TBase(_index),
+        depth(MaxValue<TDepth>::VALUE)
+    {}
+
+    Iter(TIndex &_index, MinimalCtor) :
+        TBase(_index, MinimalCtor()),
+        depth(MaxValue<TDepth>::VALUE)
+    {}
+
+    Iter(TIndex &_index, TVertexDesc const &_vDesc) :
+        TBase(_index, _vDesc),
+        depth(MaxValue<TDepth>::VALUE)
+    {}
+
+    Iter(Iter const &_origin):
+        TBase(_origin),
+        depth(_origin.depth)
+    {}
+
+    inline Iter const &
+    operator = (Iter const &_origin)
+    {
+        *static_cast<TBase*>(this) = _origin;
+        depth = _origin.depth;
+
+        return *this;
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder>
+inline bool _isLeaf(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<Truncated<TSpec> > > > const & it,
+                    VSTreeIteratorTraits<TDfsOrder, True> const)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> >                          TIndex;
+    typedef Iter<TIndex, VSTree<TopDown<TSpec> > >                      TBase;
+
+    return repLength(it) >= it.depth || _isLeaf(static_cast<TBase>(it), VSTreeIteratorTraits<TDfsOrder, True>());
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+inline bool isRightTerminal(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<Truncated<TSpec> > > > const & it)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> >                          TIndex;
+    typedef Iter<TIndex, VSTree<TopDown<TSpec> > >                      TBase;
+
+    return repLength(it) >= it.depth || isRightTerminal(static_cast<TBase>(it));
+}
+
+template <typename TText, typename TIndexSpec, typename TSpec>
+inline typename Infix<typename Fibre<Index<TText, IndexSa<TIndexSpec> >, FibreSA>::Type const>::Type
+getEmptyEdges(Iter<Index<TText, IndexSa<TIndexSpec> >, VSTree<TopDown<Truncated<TSpec> > > > const & it)
+{
+    typedef Index<TText, IndexSa<TIndexSpec> >                          TIndex;
+    typedef Iter<TIndex, VSTree<TopDown<TSpec> > >                      TBase;
+
+    if (repLength(it) >= it.depth)
+        return getOccurrences(it);
+    else
+        return getEmptyEdges(static_cast<TBase>(it));
+}
+
+template < typename TIndex, class TSpec >
+inline typename Infix< typename Fibre<TIndex, FibreSA>::Type const >::Type
+getEmptyEdges(Iter< TIndex, VSTree<TSpec> > const &it)
+{
+    typedef typename Size<TIndex>::Type TSize;
+
+    TIndex const &index = container(it);
+    TSize repLen = repLength(it);
+    Pair<TSize> saRange = range(it);
+
+    TSize i2 = saRange.i1;
+    while (i2 < saRange.i2 && suffixLength(saAt(i2, index), index) <= repLen)
+        ++i2;
+
+    return infix(indexSA(index), saRange.i1, i2);
+}
+
+}
+
+#endif  // #ifndef SEQAN_INDEX_SA_STREE_TRUNCATED_H_
diff --git a/seqan/index/index_shawarma.h b/seqan/index/index_shawarma.h
index f4c9955..66f1fde 100644
--- a/seqan/index/index_shawarma.h
+++ b/seqan/index/index_shawarma.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,54 +45,54 @@ extern "C" {
 
 namespace SEQAN_NAMESPACE_MAIN {
 
-/*	namespace shawarma {
+/*    namespace shawarma {
 
-		extern void ds_ssort(unsigned char *t, int *sa, int n);
-		extern int init_ds_ssort(int adist, int bs_ratio);
+        extern void ds_ssort(unsigned char *t, int *sa, int n);
+        extern int init_ds_ssort(int adist, int bs_ratio);
 
-	}
+    }
 */
 //////////////////////////////////////////////////////////////////////////////
 // SeqAn interface
 
-	template <typename TSpec>
-	struct Shawarma {};
+    template <typename TSpec>
+    struct Shawarma {};
 
-	struct MSufSort{};			// MSufSort
-	struct DivSufSort{};		// DivSufSort
-	struct DeepShallow{};		// Deep-Shallow sort
-	struct QSufSort{};			// QSufSort
+    struct MSufSort{};            // MSufSort
+    struct DivSufSort{};        // DivSufSort
+    struct DeepShallow{};        // Deep-Shallow sort
+    struct QSufSort{};            // QSufSort
 
-	// WARNING:
-	// 1. text value must have char size
-	// 2. SA value must have int size
-	// 3. Deep-Shallow sort expects overshoot bytes behind the text
-	// 4. SA must be contiguous
-	//
+    // WARNING:
+    // 1. text value must have char size
+    // 2. SA value must have int size
+    // 3. Deep-Shallow sort expects overshoot bytes behind the text
+    // 4. SA must be contiguous
+    //
 
     template < typename TSA,
                typename TText >
     void createSuffixArray(
-		TSA &SA,
-		TText const &s,
-		Shawarma<DeepShallow> const)
-	{
-		typedef typename Value<TText>::Type	TValue   SEQAN_TYPEDEF_FOR_DEBUG;
-		typedef typename Value<TSA>::Type	TSAValue SEQAN_TYPEDEF_FOR_DEBUG;
-
-		SEQAN_ASSERT_EQ(sizeof(TValue), sizeof(unsigned char));
-		SEQAN_ASSERT_EQ(sizeof(TSAValue), sizeof(int));
-//		SEQAN_ASSERT(IsContiguous<TSA>::VALUE);
-
-		int overshoot = init_ds_ssort(500, 2000);
-
-		SEQAN_ASSERT_GT(overshoot, 0);
-		reserve(s, length(s) + overshoot);
-		ds_ssort(
-			(unsigned char*)toCString(s),		// text
-			(int*)begin(SA, Standard()),		// SA
-			length(s));							// n
-	}
+        TSA &SA,
+        TText const &s,
+        Shawarma<DeepShallow> const)
+    {
+        typedef typename Value<TText>::Type    TValue   SEQAN_TYPEDEF_FOR_DEBUG;
+        typedef typename Value<TSA>::Type    TSAValue SEQAN_TYPEDEF_FOR_DEBUG;
+
+        SEQAN_ASSERT_EQ(sizeof(TValue), sizeof(unsigned char));
+        SEQAN_ASSERT_EQ(sizeof(TSAValue), sizeof(int));
+//        SEQAN_ASSERT(IsContiguous<TSA>::VALUE);
+
+        int overshoot = init_ds_ssort(500, 2000);
+
+        SEQAN_ASSERT_GT(overshoot, 0);
+        reserve(s, length(s) + overshoot);
+        ds_ssort(
+            (unsigned char*)toCString(s),        // text
+            (int*)begin(SA, Standard()),        // SA
+            length(s));                            // n
+    }
 
 
 } // namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/index/index_shims.h b/seqan/index/index_shims.h
index 3ed6fc3..f04d981 100644
--- a/seqan/index/index_shims.h
+++ b/seqan/index/index_shims.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,344 +39,352 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Suffix Array creation wrappers
-	//////////////////////////////////////////////////////////////////////////////
-
-	// build suffix array with an external pipeling algorithm (skew3, skew7, ...)
-	template < 
-		typename TSA, 
-		typename TObject, 
-		typename TAlgSpec >
-	void _createSuffixArrayPipelining(
-		TSA &suffixArray,
-		TObject const &text,
-		TAlgSpec const)
-	{
-	SEQAN_CHECKPOINT
+    //////////////////////////////////////////////////////////////////////////////
+    // Suffix Array creation wrappers
+    //////////////////////////////////////////////////////////////////////////////
+
+    // build suffix array with an external pipeling algorithm (skew3, skew7, ...)
+    template <
+        typename TSA,
+        typename TObject,
+        typename TAlgSpec >
+    void _createSuffixArrayPipelining(
+        TSA &suffixArray,
+        TObject const &text,
+        TAlgSpec const)
+    {
+    SEQAN_CHECKPOINT
         // signed characters behave different than unsigned when compared
         // to get the same index with signed or unsigned chars we simply cast them to unsigned
         // before feeding them into the pipeline
         typedef typename MakeUnsigned_< typename Value<TObject>::Type >::Type TUValue;
 
         // specialization
-		typedef Pipe< TObject, Source<> >				src_t;
+        typedef Pipe< TObject, Source<> >                src_t;
         typedef Pipe< src_t, Caster<TUValue> >          unsigner_t;
-		typedef Pipe< unsigner_t, TAlgSpec >	        creator_t;
+        typedef Pipe< unsigner_t, TAlgSpec >            creator_t;
 
-		// instantiation and processing
-		src_t		src(text);
+        // instantiation and processing
+        src_t        src(text);
         unsigner_t  unsigner(src);
-		creator_t	creator(unsigner);
-
-		suffixArray << creator;
-		#ifdef SEQAN_TEST_INDEX
-			isSuffixArray(suffixArray, text);
-		#endif
-	}
-
-
-	// build suffix array (external) for mutliple sequences
-	template < 
-		typename TSA, 
-		typename TString, 
-		typename TSpec,
-		typename TAlgSpec >
-	void _createSuffixArrayPipelining(
-		TSA &suffixArray,
-		StringSet<TString, TSpec> const &stringSet,
-		TAlgSpec const)
-	{
-	SEQAN_CHECKPOINT
+        creator_t    creator(unsigner);
+
+        suffixArray << creator;
+        #ifdef SEQAN_TEST_INDEX
+            isSuffixArray(suffixArray, text);
+        #endif
+    }
+
+
+    // build suffix array (external) for mutliple sequences
+    template <
+        typename TSA,
+        typename TString,
+        typename TSpec,
+        typename TAlgSpec >
+    void _createSuffixArrayPipelining(
+        TSA &suffixArray,
+        StringSet<TString, TSpec> const &stringSet,
+        TAlgSpec const)
+    {
+    SEQAN_CHECKPOINT
         // signed characters behave different than unsigned when compared
         // to get the same index with signed or unsigned chars we simply cast them to unsigned
         // before feeding them into the pipeline
-		typedef typename Concatenator<StringSet<TString, TSpec> >::Type			TConcat;
-        typedef typename MakeUnsigned_< typename Value<TConcat>::Type >::Type	TUValue;
-		typedef Multi<
-			TAlgSpec, 
-			typename Value<TSA>::Type, 
-			typename StringSetLimits<StringSet<TString, TSpec> >::Type >        MultiConstrSpec;
+        typedef typename Concatenator<StringSet<TString, TSpec> >::Type            TConcat;
+        typedef typename MakeUnsigned_< typename Value<TConcat>::Type >::Type    TUValue;
+        typedef Multi<
+            TAlgSpec,
+            typename Value<TSA>::Type,
+            typename StringSetLimits<StringSet<TString, TSpec> >::Type >        MultiConstrSpec;
 
         // specialization
-		typedef Pipe< TConcat, Source<> >				src_t;
+        typedef Pipe< TConcat, Source<> >                src_t;
         typedef Pipe< src_t, Caster<TUValue> >          unsigner_t;
-		typedef Pipe< unsigner_t, MultiConstrSpec >	    creator_t;
+        typedef Pipe< unsigner_t, MultiConstrSpec >        creator_t;
 
-		// instantiation and processing
-		src_t		src(concat(stringSet));
+        // instantiation and processing
+        src_t        src(concat(stringSet));
         unsigner_t  unsigner(src);
-		creator_t	creator(unsigner, stringSetLimits(stringSet));
-
-		suffixArray << creator;
-		#ifdef SEQAN_TEST_INDEX
-			//isSuffixArray(suffixArray, stringSet);
-		#endif
-	}
-
-
-/**
-.Function.createSuffixArray:
-..summary:Creates a suffix array from a given text.
-..cat:Index
-..signature:createSuffixArray(suffixArray, text[, algo_tag])
-..param.suffixArray:The resulting suffix array.
-..param.text:A given text.
-..param.algo_tag:A tag that identifies the algorithm which is used for creation.
-..remarks:This function should not be called directly. Please use @Function.indexCreate@ or @Function.indexRequire@.
-The size of $suffixArray$ must be at least $length(text)$ before calling this function.
-..include:seqan/index.h
-*/
+        creator_t    creator(unsigner, stringSetLimits(stringSet));
+
+        suffixArray << creator;
+        #ifdef SEQAN_TEST_INDEX
+            //isSuffixArray(suffixArray, stringSet);
+        #endif
+    }
+
+
 /*!
  * @fn createSuffixArray
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Creates a suffix array from a given text.
- * 
- * @signature createSuffixArray(suffixArray, text[, algo_tag])
- * 
- * @param text A given text. Types: @link SequenceConcept @endlink
- * @param algo_tag A tag that identifies the algorithm which is used for
- *                 creation.
- * @param suffixArray The resulting suffix array.
- * 
- * @section Remarks
- * 
- * This function should not be called directly. Please use @link Index#indexCreate
- * @endlink or @link Index#indexRequire @endlink. The size of <tt>suffixArray</tt>
+ *
+ * @signature void createSuffixArray(suffixArray, text[, algoTag]);
+ *
+ * @param[out] suffix  Array The resulting suffix array.
+ * @param[in]  text    A given text. Types: @link ContainerConcept @endlink
+ * @param[in]  algoTag A tag that identifies the algorithm which is used for creation.
+ *
+ * This function should not be called directly.  Please use @link Index#indexCreate
+ * @endlink or @link Index#indexRequire @endlink.  The size of <tt>suffixArray</tt>
  * must be at least <tt>length(text)</tt> before calling this function.
- * 
- * @link DemoSuffixArray @endlink
+ *
+ * @see DemoSuffixArray
  */
     template < typename TSA,
                typename TText,
-			   typename TAlgSpec >
+               typename TAlgSpec >
     inline void _createSuffixArrayRandomAccess(
-		TSA &sa,
-		TText const &s,
-		TAlgSpec const &alg)
-	{
-	SEQAN_CHECKPOINT
-		// -> call internal memory algorithm with an extended interface (+ alphabet size, max_depth)
-		if (BitsPerValue< typename Value<TText>::Type >::VALUE > 16)
-			createSuffixArray(sa, s, alg, length(s), 0);
-		else
-			createSuffixArray(sa, s, alg, ValueSize< typename Value<TText>::Type >::VALUE, 0);
-	}
-
-	template < 
-		typename TSA, 
-		typename TText, 
-		typename TAlgSpec >
-	inline void _createSuffixArrayWrapper(
-		TSA &sa,
-		TText const &s,
-		TAlgSpec const &alg,
+        TSA &sa,
+        TText const &s,
+        TAlgSpec const &alg)
+    {
+    SEQAN_CHECKPOINT
+        // -> call internal memory algorithm with an extended interface (+ alphabet size, max_depth)
+        if (BitsPerValue< typename Value<TText>::Type >::VALUE > 16)
+            createSuffixArray(sa, s, alg, length(s), 0);
+        else
+            createSuffixArray(sa, s, alg, ValueSize< typename Value<TText>::Type >::VALUE, 0);
+    }
+
+    template <
+        typename TSA,
+        typename TText,
+        typename TAlgSpec >
+    inline void _createSuffixArrayWrapper(
+        TSA &sa,
+        TText const &s,
+        TAlgSpec const &alg,
         True)
-	{
-	SEQAN_CHECKPOINT
+    {
+    SEQAN_CHECKPOINT
         _createSuffixArrayRandomAccess(sa, s, alg);
-	}
+    }
 
     // always use external Skew7 for multiple strings
-	template < 
-		typename TSA, 
-		typename TSequence, 
-		typename TSetSpec,
-		typename TAlgSpec >
-	inline void _createSuffixArrayWrapper(
-		TSA &sa,
-		StringSet<TSequence, TSetSpec> const &s,
-		TAlgSpec const &,
+    template <
+        typename TSA,
+        typename TSequence,
+        typename TSetSpec,
+        typename TAlgSpec >
+    inline void _createSuffixArrayWrapper(
+        TSA &sa,
+        StringSet<TSequence, TSetSpec> const &s,
+        TAlgSpec const &,
         True)
-	{
-	SEQAN_CHECKPOINT
+    {
+    SEQAN_CHECKPOINT
         _createSuffixArrayPipelining(sa, s, Skew7());
-	}
-
-	template < 
-		typename TSA, 
-		typename TText,
-		typename TAlgSpec >
-	inline void _createSuffixArrayWrapper(
-		TSA &sa,
-		TText const &s,
-		TAlgSpec const &alg,
+    }
+
+    template <
+        typename TSA,
+        typename TText,
+        typename TAlgSpec >
+    inline void _createSuffixArrayWrapper(
+        TSA &sa,
+        TText const &s,
+        TAlgSpec const &alg,
         False)
-	{
-	SEQAN_CHECKPOINT
+    {
+    SEQAN_CHECKPOINT
         _createSuffixArrayPipelining(sa, s, alg);
-	}
+    }
 
-	template < 
-		typename TSA,
-		typename TText,
+    template <
+        typename TSA,
+        typename TText,
         typename TAlgSpec >
-	inline void createSuffixArray(
-		TSA &sa,
-		TText const &s,
-		TAlgSpec const &alg)
-	{
-	SEQAN_CHECKPOINT
+    inline void createSuffixArray(
+        TSA &sa,
+        TText const &s,
+        TAlgSpec const &alg)
+    {
+    SEQAN_CHECKPOINT
         _createSuffixArrayWrapper(sa, s, alg, typename SACreatorRandomAccess_<TSA, TText, TAlgSpec>::Type());
     }
 
+//____________________________________________________________________________
+
+/*!
+ * @fn createInvSuffixArray
+ * @headerfile <seqan/index.h>
+ * @brief Creates the inverse suffix array from a given suffix array.
+ *
+ * @signature void createInvSuffixArray(invSuffixArray, suffixArray);
+ *
+ * @param[out] invSuffixArray  The resulting inverse suffix array.
+ * @param[in]  suffixArray     The precomputed suffix array for some text.
+ *
+ * This function should not be called directly. Please use @link Index#indexCreate
+ * @endlink or @link Index#indexRequire @endlink. The size of <tt>invSuffixArray</tt> must be at
+ * least <tt>length(suffixArray)</tt> before calling this function.
+ *
+ * The complexity is linear in size of the suffix array.
+ */
 
+    template <typename TIsa, typename TSa, typename TParallel>
+    inline void
+    createInvSuffixArray(TIsa &isa,
+                         TSa const &sa,
+                         FromSortedSa<TParallel> const &/*alg*/)
+    {
+        typedef typename Size<TSa>::Type                     TSize;
+        typedef typename MakeSigned<TSize>::Type             TSignedSize;
+        typedef typename StringSetLimits<TSa>::Type          TLimits;
+        typedef typename Iterator<TSa const, Standard>::Type TIter;
+
+        TLimits const & limits = stringSetLimits(sa);
+        Splitter<TSize> splitter(0, length(sa), TParallel());
+
+        SEQAN_OMP_PRAGMA(parallel for)
+        for (TSignedSize job = 0; job < static_cast<TSignedSize>(length(splitter)); ++job)
+        {
+            TIter saIt = begin(sa, Standard()) + splitter[job];
+            TIter saItEnd = begin(sa, Standard()) + splitter[job + 1];
+            TSize pos = splitter[job];
+
+            for (; saIt != saItEnd; ++saIt)
+                isa[posGlobalize(*saIt, limits)] = pos++;
+        }
+    }
 
 //____________________________________________________________________________
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// LCP Table creation wrappers
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // LCP Table creation wrappers
+    //////////////////////////////////////////////////////////////////////////////
 
-	template < 
+    template <
         typename TLCPTable,
-		typename TObject, 
+        typename TObject,
         typename TSA,
-		typename TAlgSpec >
-	void _createLCPTablePipelining(
-		TLCPTable &LCP,
-		TObject const &text,
-		TSA const &suffixArray,
-		TAlgSpec const)
-	{
-	SEQAN_CHECKPOINT
-		// specialization
-		typedef Pipe< TObject, Source<> >							srcText_t;
-		typedef Pipe< TSA, Source<> >   							srcSA_t;
-	    typedef Pipe< Bundle2< srcText_t, srcSA_t >, TAlgSpec >		creator_t;
-
-		// instantiation and processing
-		srcText_t	srcText(text);
-		srcSA_t		srcSA(suffixArray);
-		creator_t	creator(bundle2(srcText, srcSA));
-
-		LCP << creator;
-		#ifdef SEQAN_TEST_INDEX
-			isLCPTable(LCP, suffixArray, text);
-		#endif
-	}
-
-
-	// build lcp table (external) for mutliple sequences
-	template < 
+        typename TAlgSpec >
+    void _createLCPTablePipelining(
+        TLCPTable &LCP,
+        TObject const &text,
+        TSA const &suffixArray,
+        TAlgSpec const)
+    {
+    SEQAN_CHECKPOINT
+        // specialization
+        typedef Pipe< TObject, Source<> >                            srcText_t;
+        typedef Pipe< TSA, Source<> >                               srcSA_t;
+        typedef Pipe< Bundle2< srcText_t, srcSA_t >, TAlgSpec >        creator_t;
+
+        // instantiation and processing
+        srcText_t    srcText(text);
+        srcSA_t        srcSA(suffixArray);
+        creator_t    creator(bundle2(srcText, srcSA));
+
+        LCP << creator;
+        #ifdef SEQAN_TEST_INDEX
+            isLCPTable(LCP, suffixArray, text);
+        #endif
+    }
+
+
+    // build lcp table (external) for mutliple sequences
+    template <
         typename TLCPTable,
-		typename TString,
-		typename TSpec,
+        typename TString,
+        typename TSpec,
         typename TSA,
-		typename TAlgSpec >
-	void _createLCPTablePipelining(
-		TLCPTable &LCP,
-		StringSet<TString, TSpec> const &stringSet,
-		TSA const &suffixArray,
-		TAlgSpec const)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Concatenator<StringSet<TString, TSpec> >::Type TConcat;
-		typedef Multi<
-			TAlgSpec, 
-			typename Value<TSA>::Type, 
-			typename StringSetLimits<StringSet<TString, TSpec> >::Type > MultiConstrSpec;
-
-		// specialization
-		typedef Pipe< TConcat, Source<> >								srcText_t;
-		typedef Pipe< TSA, Source<> >   								srcSA_t;
-	    typedef Pipe< Bundle2< srcText_t, srcSA_t >, MultiConstrSpec >	creator_t;
-
-		// instantiation and processing
-		srcText_t	srcText(concat(stringSet));
-		srcSA_t		srcSA(suffixArray);
-		creator_t	creator(bundle2(srcText, srcSA), stringSetLimits(stringSet));
-
-		LCP << creator;
-		#ifdef SEQAN_TEST_INDEX
-			isLCPTable(LCP, suffixArray, text);
-		#endif
-	}
-
-
-/**
-.Function.createLcpTable:
-..summary:Creates a lcp table from a given text and suffix array.
-..cat:Index
-..signature:createLcpTable(lcp, text, suffixArray[, algo_tag])
-..param.lcp:The resulting lcp table.
-..param.text:A given text.
-..param.suffixArray:The suffix array of $text$.
-..param.algo_tag:A tag that identifies the algorithm which is used for creation.
-..remarks:This function should not be called directly. Please use @Function.indexCreate@ or @Function.indexRequire@.
-The size of $lcp$ must be at least $length(text)$ before calling this function.
-..include:seqan/index.h
-*/
+        typename TAlgSpec >
+    void _createLCPTablePipelining(
+        TLCPTable &LCP,
+        StringSet<TString, TSpec> const &stringSet,
+        TSA const &suffixArray,
+        TAlgSpec const)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Concatenator<StringSet<TString, TSpec> >::Type TConcat;
+        typedef Multi<
+            TAlgSpec,
+            typename Value<TSA>::Type,
+            typename StringSetLimits<StringSet<TString, TSpec> >::Type > MultiConstrSpec;
+
+        // specialization
+        typedef Pipe< TConcat, Source<> >                                srcText_t;
+        typedef Pipe< TSA, Source<> >                                   srcSA_t;
+        typedef Pipe< Bundle2< srcText_t, srcSA_t >, MultiConstrSpec >    creator_t;
+
+        // instantiation and processing
+        srcText_t    srcText(concat(stringSet));
+        srcSA_t        srcSA(suffixArray);
+        creator_t    creator(bundle2(srcText, srcSA), stringSetLimits(stringSet));
+
+        LCP << creator;
+        #ifdef SEQAN_TEST_INDEX
+            isLCPTable(LCP, suffixArray, text);
+        #endif
+    }
+
+
 /*!
  * @fn createLcpTable
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Creates a lcp table from a given text and suffix array.
- * 
- * @signature createLcpTable(lcp, text, suffixArray[, algo_tag])
- * 
- * @param text A given text. Types: @link SequenceConcept @endlink
- * @param algo_tag A tag that identifies the algorithm which is used for
- *                 creation.
- * @param suffixArray The suffix array of <tt>text</tt>.
- * @param lcp The resulting lcp table.
- * 
- * @section Remarks
- * 
- * This function should not be called directly. Please use @link Index#indexCreate
- * @endlink or @link Index#indexRequire @endlink. The size of <tt>lcp</tt> must be at
+ * @headerfile <seqan/index.h>
+ * @brief Creates a LCP table from a given text and suffix array.
+ *
+ * @signature void createLcpTable(lcp, text, suffixArray[, algoTag]);
+ *
+ * @param[out] lcp         The resulting lcp table.
+ * @param[in]  text        A given text. Types: @link ContainerConcept @endlink
+ * @param[in]  suffixArray The suffix array of <tt>text</tt>.
+ * @param[in]  algoTag     A tag that identifies the algorithm which is used for creation.
+ *
+ * This function should not be called directly.  Please use @link Index#indexCreate
+ * @endlink or @link Index#indexRequire @endlink.  The size of <tt>lcp</tt> must be at
  * least <tt>length(text)</tt> before calling this function.
  */
 
-	template < 
+    template <
         typename TLCP,
-		typename TText,
-		typename TSA,
+        typename TText,
+        typename TSA,
         typename TAlgSpec >
-	inline void _createLCPTableWrapper(
-		TLCP &lcp,
-		TText const &s,
-		TSA const &sa,
-		TAlgSpec const &alg,
+    inline void _createLCPTableWrapper(
+        TLCP &lcp,
+        TText const &s,
+        TSA const &sa,
+        TAlgSpec const &alg,
         True)
-	{
-	SEQAN_CHECKPOINT
+    {
+    SEQAN_CHECKPOINT
         _createLCPTableRandomAccess(lcp, s, sa, alg);
-	}
+    }
 
-	template < 
+    template <
         typename TLCP,
-		typename TText,
-		typename TSA,
+        typename TText,
+        typename TSA,
         typename TAlgSpec >
-	inline void _createLCPTableWrapper(
-		TLCP &lcp,
-		TText const &s,
-		TSA const &sa,
-		TAlgSpec const &alg,
+    inline void _createLCPTableWrapper(
+        TLCP &lcp,
+        TText const &s,
+        TSA const &sa,
+        TAlgSpec const &alg,
         False)
-	{
-	SEQAN_CHECKPOINT
+    {
+    SEQAN_CHECKPOINT
         _createLCPTablePipelining(lcp, s, sa, alg);
-	}
+    }
 
-	template < 
+    template <
         typename TLCP,
-		typename TText,
-		typename TSA,
+        typename TText,
+        typename TSA,
         typename TAlgSpec >
-	inline void createLcpTable(
-		TLCP &lcp,
-		TText const &s,
-		TSA const &sa,
-		TAlgSpec const &alg)
-	{
-	SEQAN_CHECKPOINT
+    inline void createLcpTable(
+        TLCP &lcp,
+        TText const &s,
+        TSA const &sa,
+        TAlgSpec const &alg)
+    {
+    SEQAN_CHECKPOINT
         _createLCPTableWrapper(lcp, s, sa, alg, typename LcpCreatorRandomAccess_<TLCP, TText, TSA, TAlgSpec>::Type());
     }
 
@@ -384,69 +393,69 @@ The size of $lcp$ must be at least $length(text)$ before calling this function.
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Enhanced LCP Table creation wrappers
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // Enhanced LCP Table creation wrappers
+    //////////////////////////////////////////////////////////////////////////////
 
     // build enhanced LCP table with an external pipelining algorithm (ext kasai, ...)
-	// and a dynamic programming tree construction alg
-	// (in contrast to the LCP table the enhanced LCP table contains the lcp-values 
-	// of suffix intervals used in the binary search)
-	template < 
-		typename TValue, 
+    // and a dynamic programming tree construction alg
+    // (in contrast to the LCP table the enhanced LCP table contains the lcp-values
+    // of suffix intervals used in the binary search)
+    template <
+        typename TValue,
         typename TSpec,
-		typename TObject, 
+        typename TObject,
         typename TSA,
         typename TLCP,
-		typename TAlgSpec >
-	void createLcpeTableExt(
-		String< TValue, TSpec > &LCPE,
-		TObject const &text,
-		TSA const &suffixArray,
+        typename TAlgSpec >
+    void createLcpeTableExt(
+        String< TValue, TSpec > &LCPE,
+        TObject const &text,
+        TSA const &suffixArray,
         TLCP const & /*LCP*/,
-		TAlgSpec const)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Concatenator<TObject>::Type				TConcat;
-
-		// specialization
-		typedef Pipe< TConcat, Source<> >						    srcText_t;
-		typedef Pipe< TSA, Source<> >					    	    srcSA_t;
-	    typedef Pipe< Bundle2< srcText_t, srcSA_t >, TAlgSpec >		creator_t;
-
-		// instantiation and processing
-		srcText_t	srcText(concat(text));
-		srcSA_t		srcSA(suffixArray);
-		creator_t	creator(bundle2(srcText, srcSA));
-
-		#ifdef SEQAN_TEST_INDEX
-			isLCPTable(creator, suffixArray, text);
-		#endif
-		createLcpBinTree(LCPE, creator);
-	}
+        TAlgSpec const)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Concatenator<TObject>::Type                TConcat;
+
+        // specialization
+        typedef Pipe< TConcat, Source<> >                            srcText_t;
+        typedef Pipe< TSA, Source<> >                                srcSA_t;
+        typedef Pipe< Bundle2< srcText_t, srcSA_t >, TAlgSpec >        creator_t;
+
+        // instantiation and processing
+        srcText_t    srcText(concat(text));
+        srcSA_t        srcSA(suffixArray);
+        creator_t    creator(bundle2(srcText, srcSA));
+
+        #ifdef SEQAN_TEST_INDEX
+            isLCPTable(creator, suffixArray, text);
+        #endif
+        createLcpBinTree(LCPE, creator);
+    }
 
     // build enhanced LCP table with an lcp algorithm
-	// and a dynamic programming tree construction alg
+    // and a dynamic programming tree construction alg
     template <
         typename TValue,
         typename TSpec,
         typename TText,
         typename TSA,
         typename TLCP,
-		typename TAlgSpec >
+        typename TAlgSpec >
     void createLcpeTable(
-		String< TValue, TSpec > &LCPE,
-		TText const &s,
-		TSA const &,
+        String< TValue, TSpec > &LCPE,
+        TText const &s,
+        TSA const &,
         TLCP const &LCP,
-		TAlgSpec const)
-	{
-	SEQAN_CHECKPOINT
+        TAlgSpec const)
+    {
+    SEQAN_CHECKPOINT
         //TSA LCP;
         //resize(LCP, length(s), Exact());
-		// we use LCPE[n-lcpSize..n-1] as a temporary buffer instead of allocating one
+        // we use LCPE[n-lcpSize..n-1] as a temporary buffer instead of allocating one
         typename Size<TText>::Type lcpSize = length(s) > 1? length(s) - 1: 0;
-		typename Suffix<String< TValue, TSpec > >::Type LCPcopy = suffix(LCPE, length(LCPE) - lcpSize);
+        typename Suffix<String< TValue, TSpec > >::Type LCPcopy = suffix(LCPE, length(LCPE) - lcpSize);
         LCPcopy = prefix(LCP, lcpSize);
         createLcpBinTree(LCPE, LCP);
     }
@@ -457,15 +466,15 @@ The size of $lcp$ must be at least $length(text)$ before calling this function.
         typename TText,
         typename TSA,
         typename TLCP,
-		typename TAlgSpec >
+        typename TAlgSpec >
     void createLcpeTable(
-		String< TValue, External<TConfig> > &LCPE,
-		TText const &s,
-		TSA const &SA,
+        String< TValue, External<TConfig> > &LCPE,
+        TText const &s,
+        TSA const &SA,
         TLCP const &LCP,
-		TAlgSpec const alg)
-	{
-	SEQAN_CHECKPOINT
+        TAlgSpec const alg)
+    {
+    SEQAN_CHECKPOINT
         createLcpeTableExt(LCPE, s, SA, LCP, alg);
     }
 
@@ -476,13 +485,13 @@ The size of $lcp$ must be at least $length(text)$ before calling this function.
         typename TSA,
         typename TLCP>
     inline void createLcpeTable(
-		String< TValue, TSpec > &LCPE,
-		TText &s,
-		TSA &SA,
+        String< TValue, TSpec > &LCPE,
+        TText &s,
+        TSA &SA,
         TLCP &LCP)
-	{
-	SEQAN_CHECKPOINT
-		createLcpeTable(LCPE, s, SA, LCP, Kasai());
+    {
+    SEQAN_CHECKPOINT
+        createLcpeTable(LCPE, s, SA, LCP, Kasai());
     }
 
 
@@ -490,235 +499,185 @@ The size of $lcp$ must be at least $length(text)$ before calling this function.
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Burrows-Wheeler-Table creation wrappers
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // Burrows-Wheeler-Table creation wrappers
+    //////////////////////////////////////////////////////////////////////////////
 
-	template < typename TBWT,
+    template < typename TBWT,
                typename TText,
-			   typename TSA >
+               typename TSA >
     void createBWTableExt(
-		TBWT &bwt,
-		TText const &s,
-		TSA const &SA)
-	{
-	SEQAN_CHECKPOINT
-		// specialization
-		typedef Pipe< TText, Source<> >						srcText_t;
-		typedef Pipe< TSA, Source<> >   					srcSA_t;
-	    typedef Pipe< Bundle2< srcText_t, srcSA_t >, Bwt >	creator_t;
-
-		// instantiation and processing
-		srcText_t	srcText(s);
-		srcSA_t		srcSA(SA);
-		creator_t	creator(bundle2(srcText, srcSA));
-
-		bwt << creator;
-	}
-
-/**
-.Function.createBWTable:
-..summary:Creates a Burrows-Wheeler table from a given text and suffix array.
-..cat:Index
-..signature:createBWTable(bwt, text, suffixArray[, algo_tag])
-..param.bwt:The resulting Burrows-Wheeler table.
-..param.text:A given text.
-..param.suffixArray:The suffix array of $text$.
-..param.algo_tag:A tag that identifies the algorithm which is used for creation.
-..remarks:This function should not be called directly. Please use @Function.indexCreate@ or @Function.indexRequire@.
-The size of $bwt$ must be at least $length(text)$ before calling this function.
-..include:seqan/index.h
-*/
+        TBWT &bwt,
+        TText const &s,
+        TSA const &SA)
+    {
+    SEQAN_CHECKPOINT
+        // specialization
+        typedef Pipe< TText, Source<> >                        srcText_t;
+        typedef Pipe< TSA, Source<> >                       srcSA_t;
+        typedef Pipe< Bundle2< srcText_t, srcSA_t >, Bwt >    creator_t;
+
+        // instantiation and processing
+        srcText_t    srcText(s);
+        srcSA_t        srcSA(SA);
+        creator_t    creator(bundle2(srcText, srcSA));
+
+        bwt << creator;
+    }
+
 /*!
  * @fn createBWTable
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Creates a Burrows-Wheeler table from a given text and suffix array.
- * 
- * @signature createBWTable(bwt, text, suffixArray[, algo_tag])
- * 
- * @param bwt The resulting Burrows-Wheeler table.
- * @param algo_tag A tag that identifies the algorithm which is used for
- *                 creation.
- * @param suffixArray The suffix array of <tt>text</tt>.
- * @param text A given text. Types: @link SequenceConcept @endlink
- * 
- * @section Remarks
- * 
- * This function should not be called directly. Please use @link Index#indexCreate
- * @endlink or @link Index#indexRequire @endlink. The size of <tt>bwt</tt> must be at
+ *
+ * @signature void createBWTable(bwt, text, suffixArray[, algoTag]);
+ *
+ * @param[out] bwt     The resulting Burrows-Wheeler table.
+ * @param[in]  suffix  Array The suffix array of <tt>text</tt>.
+ * @param[in]  text    A given text. Types: @link ContainerConcept @endlink
+ * @param[in]  algoTag A tag that identifies the algorithm which is used for creation.
+ *
+ * This function should not be called directly.  Please use @link Index#indexCreate
+ * @endlink or @link Index#indexRequire @endlink.  The size of <tt>bwt</tt> must be at
  * least <tt>length(text)</tt> before calling this function.
  */
-	// default
-	template < typename TBWT, typename TText, typename TSA, typename TTextRandom_ >
-    inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa,		TTextRandom_ const)
-	{
-	SEQAN_CHECKPOINT
-		createBWTableExt(bwt, concat(s), sa);
-	}
-
-	// text supports fast random access
-	template < typename TBWT, typename TText, typename TSA >
-    inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa,		True const)
-	{
-	SEQAN_CHECKPOINT
-		createBWTableInt(bwt, concat(s), sa);
-	}
-
-	template < typename TBWT, typename TText, typename TSA >
+    // default
+    template < typename TBWT, typename TText, typename TSA, typename TTextRandom_ >
+    inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa,        TTextRandom_ const)
+    {
+    SEQAN_CHECKPOINT
+        createBWTableExt(bwt, concat(s), sa);
+    }
+
+    // text supports fast random access
+    template < typename TBWT, typename TText, typename TSA >
+    inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa,        True const)
+    {
+    SEQAN_CHECKPOINT
+        createBWTableInt(bwt, concat(s), sa);
+    }
+
+    template < typename TBWT, typename TText, typename TSA >
     inline void createBWTable(TBWT &bwt, TText const &s, TSA const &sa)
-	{
-	SEQAN_CHECKPOINT
-		_createBWTableWrapper(bwt, s, sa, typename AllowsFastRandomAccess<TText>::Type());
-	}
+    {
+    SEQAN_CHECKPOINT
+        _createBWTableWrapper(bwt, s, sa, typename AllowsFastRandomAccess<TText>::Type());
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TOccValue>
-	struct SAValueLess_:
-		public ::std::less<TOccValue> {};
+    template <typename TOccValue>
+    struct SAValueLess_:
+        public std::less<TOccValue> {};
 
-	template <typename T1, typename T2, typename TPack>
-	struct SAValueLess_< Pair<T1,T2,TPack> >:
-		public ::std::binary_function< Pair<T1,T2,TPack>, Pair<T1,T2,TPack>, bool> 
-	{
-		inline bool operator()(Pair<T1,T2,TPack> const &a, Pair<T1,T2,TPack> const &b) const {
-			return	(getValueI1(a) < getValueI1(b)) ||
-					((getValueI1(a) == getValueI1(b)) && (getValueI2(a) < getValueI2(b)));
-		}
-	};
+    template <typename T1, typename T2, typename TPack>
+    struct SAValueLess_< Pair<T1,T2,TPack> >:
+        public std::binary_function< Pair<T1,T2,TPack>, Pair<T1,T2,TPack>, bool>
+    {
+        inline bool operator()(Pair<T1,T2,TPack> const &a, Pair<T1,T2,TPack> const &b) const {
+            return    (getValueI1(a) < getValueI1(b)) ||
+                    ((getValueI1(a) == getValueI1(b)) && (getValueI2(a) < getValueI2(b)));
+        }
+    };
 
 //TODO(singer): Make this internal
-/**
-.Function.orderOccurrences:
-..summary:Sorts a string of occurrences.
-..cat:Index
-..signature:orderOccurrences(occstring)
-..param.occstring:String of occurrences.
-...remarks:Contains suffix array values returned by @Function.getOccurrences@.
-..remarks:The occurrences are sorted by increasing positions.
-..see:Function.getOccurrences
-..see:Metafunction.SAValue
-..include:seqan/index.h
-*/
 /*!
  * @fn orderOccurrences
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Sorts a string of occurrences.
- * 
- * @signature orderOccurrences(occString)
- * 
- * @param occString String of occurrences.
- * 
- * @section Remarks
- * 
+ *
+ * @signature void orderOccurrences(occString);
+ *
+ * @param[in,out] occString String of occurrences.
+ *
  * The occurrences are sorted by increasing positions.
- * 
- * @link DemoMummy @endlink
- * @link DemoSuperMaximalRepeats @endlink
- * @link DemoMaximalUniqueMatches @endlink
- * 
+ *
+ * @see DemoMummy
+ * @see DemoSupermaximalRepeats
+ * @see DemoMaximalUniqueMatches
+ *
  * @see VSTreeIterator#getOccurrences
  * @see IndexQGram#getOccurrences
  * @see SAValue
  */
-	template <typename TValue, typename TSpec>
-	inline void orderOccurrences(String<TValue, TSpec> &occString)
-	{
-	SEQAN_CHECKPOINT
-		::std::sort(begin(occString, Standard()), end(occString, Standard()), SAValueLess_<TValue>());
-	}
+    template <typename TValue, typename TSpec>
+    inline void orderOccurrences(String<TValue, TSpec> &occString)
+    {
+    SEQAN_CHECKPOINT
+        std::sort(begin(occString, Standard()), end(occString, Standard()), SAValueLess_<TValue>());
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 // fibre creators
 
-/**
-.Function.indexCreate:
-..summary:Creates a specific @Metafunction.Fibre@.
-..cat:Index
-..signature:indexCreate(index, fibreTag[, algoTag])
-..class:Class.Index
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Class.Index
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.ESA Index Fibres
-...type:Tag.QGram Index Fibres
-...type:Tag.WOTD Index Fibres
-...type:Tag.FM Index Fibres
-..param.algoTag:A tag that identifies the algorithm which is used to create the fibre.
-...default:The result of @Metafunction.DefaultIndexCreator@.
-..returns:A $bool$ which is $true$ on a successful creation.
-..remarks:$indexCreate$ calls the fibre corresponding $createXXX(..)$ function (e.g. @Function.createSuffixArray@).
-..include:seqan/index.h
-*/
 /*!
  * @fn Index#indexCreate
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Creates a specific @link Index#Fibre @endlink.
- * 
- * @signature indexCreate(index, fibreTag[, algoTag])
- * 
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink
- * @param algoTag A tag that identifies the algorithm which is used to create
- *                 the fibre. Default: The result of @link Index#DefaultIndexCreator
- *                 @endlink.
- * @param index The @link Index @endlink object holding the fibre.
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on a successful
- *                 creation.
- * 
- * @section Remarks
- * 
- * <tt>indexCreate</tt> calls the fibre corresponding <tt>createXXX(..)</tt>
- * function (e.g. @link createSuffixArray @endlink).
+ * @headerfile <seqan/index.h>
+ * @brief Creates a specific @link Fibre @endlink.
+ *
+ * @signature bool indexCreate(index, fibreTag[, algoTag]);
+ *
+ * @param[in]     fibreTag A tag that identifies the @link Fibre @endlink
+ * @param[in]     algoTag  A tag that identifies the algorithm which is used to create the fibre.  Default: The
+ *                         result of @link Index#DefaultIndexCreator @endlink.
+ * @param[in,out] index    The @link Index @endlink object holding the fibre.
+ *
+ * @return bool <tt>true</tt> on a success and false <tt>otherwise</tt>
+ *
+ * <tt>indexCreate</tt> calls the fibre corresponding <tt>createXXX(..)</tt> function (e.g. @link createSuffixArray
+ * @endlink).
  */
-	template <typename TText, typename TSpec, typename TSpecAlg>
-	inline bool indexCreate(Index<TText, TSpec> &index, FibreSA, TSpecAlg const alg) {
-	SEQAN_CHECKPOINT
-		resize(indexSA(index), length(indexRawText(index)), Exact());
-		createSuffixArray(indexSA(index), indexText(index), alg);
-		return true;
-	}
-
-	template <typename TText, typename TSpec, typename TSpecAlg>
-	inline bool indexCreate(Index<TText, TSpec> &index, FibreLcp, TSpecAlg const alg) {
-	SEQAN_CHECKPOINT
-		resize(indexLcp(index), length(indexRawText(index)), Exact());
-		createLcpTable(indexLcp(index), indexText(index), indexSA(index), alg);
-		return true;
-	}
-
-	template <typename TText, typename TSpec, typename TSpecAlg>
-	inline bool indexCreate(Index<TText, TSpec> &index, FibreLcpe, TSpecAlg const alg) {
-	SEQAN_CHECKPOINT
-	//TODO: separate LCP from LCPE (for now LCPE = LCP + extra)
-		resize(indexLcpe(index), sizeofLcpe(lengthSum(index)), Exact());
-		createLcpeTable(indexLcpe(index), indexRawText(index), indexSA(index), indexLcp(index), alg);
-		return true;
-//		return false;
-	}
-
-	template <typename TText, typename TSpec>
-	inline bool indexCreate(Index<TText, TSpec> &index, FibreBwt, Bwt const) {
-	SEQAN_CHECKPOINT
-		resize(indexBwt(index), length(indexRawText(index)), Exact());
-		createBWTable(indexBwt(index), indexText(index), indexRawSA(index));
-		return true;
-	}
-
-	template <typename TText, typename TSpec>
-	inline bool indexCreate(Index<TText, TSpec> &index, FibreChildtab, Childtab const) {
-	SEQAN_CHECKPOINT
-		resize(indexChildtab(index), length(indexRawText(index)), Exact());
-		createChildtab(indexChildtab(index), indexLcp(index));
-		return true;
-	}
+    template <typename TText, typename TSpec, typename TSpecAlg>
+    inline bool indexCreate(Index<TText, TSpec> &index, FibreSA, TSpecAlg const alg) {
+    SEQAN_CHECKPOINT
+        resize(indexSA(index), length(indexRawText(index)), Exact());
+        createSuffixArray(indexSA(index), indexText(index), alg);
+        return true;
+    }
+
+    template <typename TText, typename TSpec, typename TParallel>
+    inline bool indexCreate(Index<TText, TSpec> &index, FibreIsa, FromSortedSa<TParallel> const alg)
+    {
+        resize(indexIsa(index), length(indexRawText(index)), Exact());
+        createInvSuffixArray(indexIsa(index), indexSA(index), alg);
+        return true;
+    }
+
+    template <typename TText, typename TSpec, typename TSpecAlg>
+    inline bool indexCreate(Index<TText, TSpec> &index, FibreLcp, TSpecAlg const alg) {
+    SEQAN_CHECKPOINT
+        resize(indexLcp(index), length(indexRawText(index)), Exact());
+        createLcpTable(indexLcp(index), indexText(index), indexSA(index), alg);
+        return true;
+    }
+
+    template <typename TText, typename TSpec, typename TSpecAlg>
+    inline bool indexCreate(Index<TText, TSpec> &index, FibreLcpe, TSpecAlg const alg) {
+    SEQAN_CHECKPOINT
+    //TODO: separate LCP from LCPE (for now LCPE = LCP + extra)
+        resize(indexLcpe(index), sizeofLcpe(lengthSum(index)), Exact());
+        createLcpeTable(indexLcpe(index), indexRawText(index), indexSA(index), indexLcp(index), alg);
+        return true;
+//        return false;
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexCreate(Index<TText, TSpec> &index, FibreBwt, Bwt const) {
+    SEQAN_CHECKPOINT
+        resize(indexBwt(index), length(indexRawText(index)), Exact());
+        createBWTable(indexBwt(index), indexText(index), indexRawSA(index));
+        return true;
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexCreate(Index<TText, TSpec> &index, FibreChildtab, Childtab const) {
+    SEQAN_CHECKPOINT
+        resize(indexChildtab(index), length(indexRawText(index)), Exact());
+        createChildtab(indexChildtab(index), indexLcp(index));
+        return true;
+    }
 
     template <typename TText, typename TSpec, typename TFibre>
     inline bool indexCreate(Index<TText, TSpec> &index, Tag<TFibre> const fibre) {
@@ -727,336 +686,353 @@ The size of $bwt$ must be at least $length(text)$ before calling this function.
     }
 
 
+// ----------------------------------------------------------------------------
+// Function indexCreate(FibreSA, Trie)
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec>
+inline bool indexCreate(Index<TText, TSpec> & index, FibreSA, Trie)
+{
+    resize(indexSA(index), length(indexText(index)), Exact());
+    createSuffixArray(indexSA(index), indexText(index), Trie());
+    return true;
+}
+
 //////////////////////////////////////////////////////////////////////////////
 // automatic fibre creation
 
-/**
-.Function.indexSupplied:
-..summary:Returns whether a specific @Metafunction.Fibre@ is present.
-..cat:Index
-..signature:indexSupplied(index, fibreTag)
-..class:Class.Index
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Class.Index
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.ESA Index Fibres
-..returns:A $bool$ which is $true$, iff the fibre is present.
-..include:seqan/index.h
-*/
 /*!
  * @fn Index#indexSupplied
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Returns whether a specific @link Index#Fibre @endlink is present.
- * 
- * @signature indexSupplied(index, fibreTag)
- * 
- * @param index The @link Index @endlink object holding the fibre.
- * @param fibreTag A tag that identifies the @link Index#Fibre @endlink. 
- *                 Index Fibres
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt>, iff the fibre is
- *                 present.
+ * @headerfile <seqan/index.h>
+ * @brief Returns whether a specific @link Fibre @endlink is present.
+ *
+ * @signature bool indexSupplied(index, fibreTag);
+ *
+ * @param[in] index    The @link Index @endlink object holding the fibre.
+ * @param[in] fibreTag A tag that identifies the @link Fibre @endlink Index Fibres.
+ *
+ * @return bool <tt>true</tt>, iff the fibre is present.
  */
-	template <typename TText, typename TSpec, typename TFibre>
-	inline bool indexSupplied(Index<TText, TSpec> &index, Tag<TFibre> const fibre) {
-	SEQAN_CHECKPOINT
-		return !empty(getFibre(index, fibre));
-	}
+    template <typename TText, typename TSpec, typename TFibre>
+    SEQAN_HOST_DEVICE inline bool indexSupplied(Index<TText, TSpec> &index, Tag<TFibre> const fibre) {
+    SEQAN_CHECKPOINT
+        return !empty(getFibre(index, fibre));
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
-/**
-.Function.indexRequire:
-..summary:On-demand creation of a specific @Metafunction.Fibre@.
-..cat:Index
-..signature:indexRequire(index, fibreTag)
-..class:Class.Index
-..param.index:The @Class.Index@ object holding the fibre.
-...type:Class.Index
-..param.fibreTag:A tag that identifies the @Metafunction.Fibre@.
-...type:Tag.ESA Index Fibres
-...type:Tag.QGram Index Fibres
-...type:Tag.WOTD Index Fibres
-...type:Tag.FM Index Fibres
-..returns:A $bool$ which is $true$ on a successful creation.
-..remarks:If the fibre already exists (@Function.indexSupplied@ is true) then $indexRequire$ does nothing.
-If the fibre doesn't exist then @Function.indexCreate@ is called to create it.
-..include:seqan/index.h
-..example
-...text:The following code shows how the BWT of an text can be computed.
-...file:demos/index/index_textAt_indexText_saAt_indexRequire.cpp
-...output:BWT	Suffices
-P	PI
-S	SIPPI
-S	SISSIPPI
-M	MISSISSIPPI
-I	I
-P	PPI
-I	IPPI
-S	SSIPPI
-S	SSISSIPPI
-I	ISSIPPI
-I	ISSISSIPPI
-*/
 /*!
  * @fn Index#indexRequire
- * 
- * @headerfile seqan/index.h
- * 
- * @brief On-demand creation of a specific @link Index#Fibre @endlink.
- * 
- * @signature indexRequire(index, fibre_tag)
- * 
- * @param index The @link Index @endlink object holding the fibre.
- * @param fibre_tag A tag that identifies the @link Index#Fibre @endlink
- * 
- * @return TReturn A <tt>bool</tt> which is <tt>true</tt> on a successful
- *                 creation.
- * 
- * @section Remarks
- * 
+ * @headerfile <seqan/index.h>
+ * @brief On-demand creation of a specific @link Fibre @endlink.
+ *
+ * @signature bool indexRequire(index, fibreTag);
+ *
+ * @param[in,out] index    The @link Index @endlink object holding the fibre.
+ * @param[in]     fibreTag A tag that identifies the @link Fibre @endlink
+ *
+ * @return bool <tt>true</tt> on a successful creation.
+ *
  * If the fibre already exists (@link Index#indexSupplied @endlink is true) then <tt>indexRequire</tt> does nothing. If
  * the fibre doesn't exist then @link Index#indexCreate @endlink is called to create it.
  *
- * @section Example
+ * @section Examples
  *
  * The following code shows how the BWT of an text can be computed.
- * @include demos/index/index_textAt_indexText_saAt_indexRequire.cpp
- * @include demos/index/index_textAt_indexText_saAt_indexRequire.cpp.stdout
+ *
+ * @include demos/dox/index/textAt_indexText_saAt_indexRequire.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/index/textAt_indexText_saAt_indexRequire.cpp.stdout
  */
 
-	template <typename TText, typename TSpec, typename TFibre>
-	inline bool indexRequire(Index<TText, TSpec> &index, Tag<TFibre> const fibre) {
-	SEQAN_CHECKPOINT
-		if (indexSupplied(index, fibre)) return true;				// if the table doesn't exist,
-		if (!indexSolveDependencies(index, fibre)) return false;	// fulfill requirements
-		return indexCreate(index, fibre);							// and create table
-	}
+    template <typename TText, typename TSpec, typename TFibre>
+    inline bool indexRequire(Index<TText, TSpec> &index, Tag<TFibre> const fibre) {
+    SEQAN_CHECKPOINT
+        if (indexSupplied(index, fibre)) return true;                // if the table doesn't exist,
+        if (!indexSolveDependencies(index, fibre)) return false;    // fulfill requirements
+        return indexCreate(index, fibre);                            // and create table
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 // index cargo interface
 
-	template <typename TText, typename TSpec>
-	inline typename Reference< typename Cargo<Index<TText, TSpec> >::Type >::Type
-	cargo(Index<TText, TSpec> & me)
-	{
-	SEQAN_CHECKPOINT
-		return me.cargo;
-	}
-
-	template <typename TText, typename TSpec>
-	inline typename Reference< typename Cargo<Index<TText, TSpec> const>::Type >::Type
-	cargo(Index<TText, TSpec> const & me)
-	{
-	SEQAN_CHECKPOINT
-		return me.cargo;
-	}
+    template <typename TText, typename TSpec>
+    inline typename Reference< typename Cargo<Index<TText, TSpec> >::Type >::Type
+    cargo(Index<TText, TSpec> & me)
+    {
+    SEQAN_CHECKPOINT
+        return me.cargo;
+    }
+
+    template <typename TText, typename TSpec>
+    inline typename Reference< typename Cargo<Index<TText, TSpec> const>::Type >::Type
+    cargo(Index<TText, TSpec> const & me)
+    {
+    SEQAN_CHECKPOINT
+        return me.cargo;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // solve dependencies
 
-	template <typename TText, typename TSpec, typename TFibre>
-	inline bool indexSolveDependencies(Index<TText, TSpec> &, Tag<TFibre> const) {
-	SEQAN_CHECKPOINT
-		return true;
-	}
-
-	template <typename TText, typename TSpec>
-	inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreLcp) {
-	SEQAN_CHECKPOINT
-		return indexRequire(index, FibreSA());
-	}
-
-	template <typename TText, typename TSpec>
-	inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreLcpe) {
-	SEQAN_CHECKPOINT
-		return indexRequire(index, FibreLcp());
-	}
-
-	template <typename TText, typename TSpec>
-	inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreChildtab) {
-	SEQAN_CHECKPOINT
-		return indexRequire(index, FibreLcp());
-	}
-
-	template <typename TText, typename TSpec>
-	inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreBwt) {
-	SEQAN_CHECKPOINT
-		return indexRequire(index, FibreSA());
-	}
+    template <typename TText, typename TSpec, typename TFibre>
+    inline bool indexSolveDependencies(Index<TText, TSpec> &, Tag<TFibre> const) {
+    SEQAN_CHECKPOINT
+        return true;
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreIsa) {
+    SEQAN_CHECKPOINT
+        return indexRequire(index, FibreSA());
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreLcp) {
+    SEQAN_CHECKPOINT
+        return indexRequire(index, FibreSA());
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreLcpe) {
+    SEQAN_CHECKPOINT
+        return indexRequire(index, FibreLcp());
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreChildtab) {
+    SEQAN_CHECKPOINT
+        return indexRequire(index, FibreLcp());
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexSolveDependencies(Index<TText, TSpec> &index, FibreBwt) {
+    SEQAN_CHECKPOINT
+        return indexRequire(index, FibreSA());
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 // open
 
-	template < typename TValue, typename TSpec >
-	inline bool open(String<TValue, TSpec> &string, const char *fileName, int openMode) {
-	SEQAN_CHECKPOINT
-		String<TValue, External< ExternalConfigLarge<> > > extString;
-		if (!open(extString, fileName, openMode & ~OPEN_CREATE)) return false;
-		assign(string, extString, Exact());
-		return true;
-	}
-	template < typename TValue, typename TSpec >
-	inline bool open(String<TValue, TSpec> &string, const char *fileName) {
-	SEQAN_CHECKPOINT
-		return open(string, fileName, OPEN_RDONLY);
-	}
-
-	template < typename THost, typename TSpec >
-	inline bool open(Segment<THost, TSpec> &string, const char *fileName, int openMode) {
-	SEQAN_CHECKPOINT
-		String<typename Value<THost>::Type, External< ExternalConfigLarge<> > > extString;
-		if (!open(extString, fileName, openMode & ~OPEN_CREATE)) return false;
-		assign(string, extString, Exact());
-		return true;
-	}
-	template < typename THost, typename TSpec >
-	inline bool open(Segment<THost, TSpec> &string, const char *fileName) {
-	SEQAN_CHECKPOINT
-		return open(string, fileName, OPEN_RDONLY);
-	}
-
-	// ATTENTION:
-	// This implementation of open doesn't work with external memory StringSets (External<>, MMap<>)
-	// If you need a persistent external StringSet you have to use a Owner<ConcatDirect<> > StringSet.
-	template < typename TString, typename TSSSpec >
-	inline bool open(StringSet<TString, TSSSpec> &multi, const char *fileName, int openMode) {
-	SEQAN_CHECKPOINT
-		char id[12]; // 2^32 has 10 decimal digits + 1 (0x00)
-		unsigned i = 0;
-		clear(multi);
-		CharString name;
-		while (true)
-		{
-			sprintf(id, ".%u", i);
-			name = fileName;
-			append(name, id);
-			{
-				resize(multi, i + 1);
-				if (!open(multi[i], toCString(name), (openMode & ~OPEN_CREATE) | OPEN_QUIET))
-				{
-					resize(multi, i);
-					break;
-				}
-			}
-			++i;
-		}
-		return i > 0;
-	}
-
-	template < typename TValue, typename TSpec, typename TSSSpec >
+    // TODO(esiragusa): Move open() / save() to respective String/StringSet classes.
+
+    template <typename TValue>
+    inline bool open(TValue & value, const char *fileName, int openMode)
+    {
+        String<TValue, External< ExternalConfigLarge<> > > extString;
+        if (!open(extString, fileName, openMode & ~OPEN_CREATE)) return false;
+        if (!empty(extString)) assign(value, front(extString));
+        return true;
+    }
+
+    template <typename TValue>
+    inline bool open(TValue & value, const char *fileName)
+    {
+        return open(value, fileName, OPEN_RDONLY);
+    }
+
+    template < typename TValue, typename TSpec >
+    inline bool open(String<TValue, TSpec> &string, const char *fileName, int openMode) {
+    SEQAN_CHECKPOINT
+        String<TValue, External< ExternalConfigLarge<> > > extString;
+        if (!open(extString, fileName, openMode & ~OPEN_CREATE)) return false;
+        assign(string, extString, Exact());
+        return true;
+    }
+    template < typename TValue, typename TSpec >
+    inline bool open(String<TValue, TSpec> &string, const char *fileName) {
+    SEQAN_CHECKPOINT
+        return open(string, fileName, OPEN_RDONLY);
+    }
+
+    template < typename THost, typename TSpec >
+    inline bool open(Segment<THost, TSpec> &string, const char *fileName, int openMode) {
+    SEQAN_CHECKPOINT
+        String<typename Value<THost>::Type, External< ExternalConfigLarge<> > > extString;
+        if (!open(extString, fileName, openMode & ~OPEN_CREATE)) return false;
+        assign(string, extString, Exact());
+        return true;
+    }
+    template < typename THost, typename TSpec >
+    inline bool open(Segment<THost, TSpec> &string, const char *fileName) {
+    SEQAN_CHECKPOINT
+        return open(string, fileName, OPEN_RDONLY);
+    }
+
+#ifdef PLATFORM_CUDA
+    template <typename TChar, typename TAlloc>
+    inline bool open(thrust::device_vector<TChar, TAlloc> & me, const char *fileName, int openMode)
+    {
+        String<TChar> str;
+        if (!open(str, fileName, openMode)) return false;
+        assign(me, str);
+        return true;
+    }
+
+    template <typename TChar, typename TAlloc>
+    inline bool open(thrust::device_vector<TChar, TAlloc> & me, const char *fileName)
+    {
+        return open(me, fileName, OPEN_RDONLY);
+    }
+#endif
+
+    // ATTENTION:
+    // This implementation of open doesn't work with external memory StringSets (External<>, MMap<>)
+    // If you need a persistent external StringSet you have to use a Owner<ConcatDirect<> > StringSet.
+    template < typename TString, typename TSSSpec >
+    inline bool open(StringSet<TString, TSSSpec> &multi, const char *fileName, int openMode) {
+    SEQAN_CHECKPOINT
+        char id[12]; // 2^32 has 10 decimal digits + 1 (0x00)
+        unsigned i = 0;
+        clear(multi);
+        CharString name;
+        while (true)
+        {
+            sprintf(id, ".%u", i);
+            name = fileName;
+            append(name, id);
+            {
+                resize(multi, i + 1);
+                if (!open(multi[i], toCString(name), (openMode & ~OPEN_CREATE) | OPEN_QUIET))
+                {
+                    resize(multi, i);
+                    break;
+                }
+            }
+            ++i;
+        }
+        return i > 0;
+    }
+
+    template < typename TValue, typename TSpec, typename TSSSpec >
         inline bool open(StringSet<String<TValue, TSpec>, Dependent<TSSSpec> > &, const char *, int) {
         SEQAN_CHECKPOINT
         // Do nothing for dependent string sets
         return true;
     }
 
-	template < typename TString, typename TSSSpec >
-	inline bool open(StringSet<TString, Owner<ConcatDirect<TSSSpec> > > &multi, const char *fileName, int openMode) {
-	SEQAN_CHECKPOINT
-		CharString name;
-		name = fileName;
-		append(name, ".concat");
-		if (!open(multi.concat, toCString(name), openMode | OPEN_QUIET)) return false;
-		name = fileName;
-		append(name, ".limits");
-		if (!open(multi.limits, toCString(name), openMode | OPEN_QUIET) && !empty(multi.concat))
-		{
-			clear(multi);
-			return false;
-		}
-		// limits file was just created
-		if (empty(multi.limits))
-			appendValue(multi.limits, 0);
-		return true;
-	}
-
-	template < typename TValue, typename TSpec, typename TSSSpec>
-	inline bool open(StringSet<String<TValue, TSpec>, TSSSpec> &multi, const char *fileName) {
-	SEQAN_CHECKPOINT
-		return open(multi, fileName, OPEN_RDONLY);
-	}
+    template < typename TString, typename TSSSpec >
+    inline bool open(StringSet<TString, Owner<ConcatDirect<TSSSpec> > > &multi, const char *fileName, int openMode) {
+    SEQAN_CHECKPOINT
+        CharString name;
+        name = fileName;
+        append(name, ".concat");
+        if (!open(multi.concat, toCString(name), openMode | OPEN_QUIET)) return false;
+        name = fileName;
+        append(name, ".limits");
+        if (!open(multi.limits, toCString(name), openMode | OPEN_QUIET) && !empty(multi.concat))
+        {
+            clear(multi);
+            return false;
+        }
+        // limits file was just created
+        if (empty(multi.limits))
+            appendValue(multi.limits, 0);
+        return true;
+    }
+
+    template < typename TValue, typename TSpec, typename TSSSpec>
+    inline bool open(StringSet<String<TValue, TSpec>, TSSSpec> &multi, const char *fileName) {
+    SEQAN_CHECKPOINT
+        return open(multi, fileName, OPEN_RDONLY);
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 // save
 
-	template < typename TValue, typename TSpec >
-	inline bool save(String<TValue, TSpec> const &string, const char *fileName, int openMode) {
-	SEQAN_CHECKPOINT
+    template <typename TValue>
+    inline bool save(TValue const &val, const char *fileName, int openMode)
+    {
+        String<TValue, External< ExternalConfigLarge<> > > extString;
+        if (!open(extString, fileName, openMode)) return false;
+        clear(extString);
+        appendValue(extString, val);
+        return true;
+    }
+
+    template <typename TValue>
+    inline bool save(TValue const &val, const char *fileName)
+    {
+        return save(val, fileName, OPEN_WRONLY | OPEN_CREATE);
+    }
+
+    template < typename TValue, typename TSpec >
+    inline bool save(String<TValue, TSpec> const &string, const char *fileName, int openMode) {
+    SEQAN_CHECKPOINT
 //
-//		if (length(string) == 0) return true;
-		String<TValue, External< ExternalConfigLarge<> > > extString;
-		if (!open(extString, fileName, openMode)) return false;
-		assign(extString, string, Exact());
-		return true;
-	}
-	template < typename TValue, typename TSpec >
-	inline bool save(String<TValue, TSpec> const &string, const char *fileName) {
-	SEQAN_CHECKPOINT
-		return save(string, fileName, OPEN_WRONLY | OPEN_CREATE);
-	}
-
-	template < typename THost, typename TSpec >
-	inline bool save(Segment<THost, TSpec> const &string, const char *fileName, int openMode) {
-	SEQAN_CHECKPOINT
-		if (length(string) == 0) return true;
-		String<typename Value<THost>::Type, External< ExternalConfigLarge<> > > extString;
-		if (!open(extString, fileName, openMode)) return false;
-		assign(extString, string, Exact());
-		return true;
-	}
-	template < typename THost, typename TSpec >
-	inline bool save(Segment<THost, TSpec> const &string, const char *fileName) {
-	SEQAN_CHECKPOINT
-		return save(string, fileName, OPEN_WRONLY | OPEN_CREATE);
-	}
-
-	template < typename TString, typename TSSSpec>
-	inline bool save(StringSet<TString, TSSSpec> const &multi, const char *fileName, int openMode) {
-	SEQAN_CHECKPOINT
-		if (length(multi) == 0) return true;
-		char id[12]; // 2^32 has 10 decimal digits + 2 ('.' and 0x00)
-		CharString name;
-		for(unsigned i = 0; i < length(multi); ++i)
-		{
-			sprintf(id, ".%u", i);
-			name = fileName;
-			append(name, &(id[0]));
-			if (!save(multi[i], toCString(name), openMode))
-				return false;
-		}
-		return true;
-	}
-
-	template < typename TValue, typename TSpec, typename TSSSpec >
+//        if (length(string) == 0) return true;
+        String<TValue, External< ExternalConfigLarge<> > > extString;
+        if (!open(extString, fileName, openMode)) return false;
+        assign(extString, string, Exact());
+        return true;
+    }
+    template < typename TValue, typename TSpec >
+    inline bool save(String<TValue, TSpec> const &string, const char *fileName) {
+    SEQAN_CHECKPOINT
+        return save(string, fileName, OPEN_WRONLY | OPEN_CREATE);
+    }
+
+    template < typename THost, typename TSpec >
+    inline bool save(Segment<THost, TSpec> const &string, const char *fileName, int openMode) {
+    SEQAN_CHECKPOINT
+        if (length(string) == 0) return true;
+        String<typename Value<THost>::Type, External< ExternalConfigLarge<> > > extString;
+        if (!open(extString, fileName, openMode)) return false;
+        assign(extString, string, Exact());
+        return true;
+    }
+    template < typename THost, typename TSpec >
+    inline bool save(Segment<THost, TSpec> const &string, const char *fileName) {
+    SEQAN_CHECKPOINT
+        return save(string, fileName, OPEN_WRONLY | OPEN_CREATE);
+    }
+
+    template < typename TString, typename TSSSpec>
+    inline bool save(StringSet<TString, TSSSpec> const &multi, const char *fileName, int openMode) {
+    SEQAN_CHECKPOINT
+        if (length(multi) == 0) return true;
+        char id[12]; // 2^32 has 10 decimal digits + 2 ('.' and 0x00)
+        CharString name;
+        for(unsigned i = 0; i < length(multi); ++i)
+        {
+            sprintf(id, ".%u", i);
+            name = fileName;
+            append(name, &(id[0]));
+            if (!save(multi[i], toCString(name), openMode))
+                return false;
+        }
+        return true;
+    }
+
+    template < typename TValue, typename TSpec, typename TSSSpec >
     inline bool save(StringSet<String<TValue, TSpec>, Dependent<TSSSpec> > const &, const char *, int) {
         SEQAN_CHECKPOINT
         // Do nothing for dependent string sets
         return true;
     }
 
-	template < typename TString, typename TSSSpec >
-	inline bool save(StringSet<TString, Owner<ConcatDirect<TSSSpec> > > const &multi, const char *fileName, int openMode) {
-	SEQAN_CHECKPOINT
-		CharString name;
-		name = fileName;
-		append(name, ".concat");
-		if (!save(multi.concat, toCString(name), openMode)) return false;
-		name = fileName;
-		append(name, ".limits");
-		if (!save(multi.limits, toCString(name), openMode)) return false;
-		return true;
-	}
-	template < typename TValue, typename TSpec, typename TSSSpec>
-	inline bool save(StringSet<String<TValue, TSpec>, TSSSpec> const &multi, const char *fileName) {
-	SEQAN_CHECKPOINT
-		return save(multi, fileName, OPEN_WRONLY | OPEN_CREATE);
-	}
+    template < typename TString, typename TSSSpec >
+    inline bool save(StringSet<TString, Owner<ConcatDirect<TSSSpec> > > const &multi, const char *fileName, int openMode) {
+    SEQAN_CHECKPOINT
+        CharString name;
+        name = fileName;
+        append(name, ".concat");
+        if (!save(multi.concat, toCString(name), openMode)) return false;
+        name = fileName;
+        append(name, ".limits");
+        if (!save(multi.limits, toCString(name), openMode)) return false;
+        return true;
+    }
+    template < typename TValue, typename TSpec, typename TSSSpec>
+    inline bool save(StringSet<String<TValue, TSpec>, TSSSpec> const &multi, const char *fileName) {
+    SEQAN_CHECKPOINT
+        return save(multi, fileName, OPEN_WRONLY | OPEN_CREATE);
+    }
 
 }
 
diff --git a/seqan/index/index_skew3.h b/seqan/index/index_skew3.h
index 79b844c..540677a 100644
--- a/seqan/index/index_skew3.h
+++ b/seqan/index/index_skew3.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,24 +41,24 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct Skew3 {};
+    struct Skew3 {};
 
 
     //////////////////////////////////////////////////////////////////////////////
     // external Skew3 algorithm
     //////////////////////////////////////////////////////////////////////////////
 
-	template <typename T>
-	struct SkewDC_<3, T>
+    template <typename T>
+    struct SkewDC_<3, T>
     {
-		static const unsigned VALUE[];
-	};
+        static const unsigned VALUE[];
+    };
 
-	template <typename T>
-	const unsigned SkewDC_<3, T>::VALUE[] = { 2,   1, 2 };
+    template <typename T>
+    const unsigned SkewDC_<3, T>::VALUE[] = { 2,   1, 2 };
 
 
-	// *** COMPARATORS & MAPS ***
+    // *** COMPARATORS & MAPS ***
 
     template <typename TValue, typename TResult = int>
     struct _skew3NComp :
@@ -66,18 +66,18 @@ namespace SEQAN_NAMESPACE_MAIN
     {
         inline TResult operator() (const TValue &a, const TValue &b) const
         {
-			typedef typename Value<TValue, 1>::Type                 TSize;
+            typedef typename Value<TValue, 1>::Type                 TSize;
             typedef typename Value<TValue, 2>::Type                 TTriplet;
             typedef typename Value<TTriplet>::Type                  TTripletValue;
             typedef typename StoredTupleValue_<TTripletValue>::Type TStoredValue;
 
             const TStoredValue *sa = a.i2.i;
             const TStoredValue *sb = b.i2.i;
-            
+
             TSize n = LENGTH<TTriplet>::VALUE;
             if (a.i1 < n) n = a.i1;
             if (b.i1 < n) n = b.i1;
-            
+
             // compare the overlap of septets (the first n bases)
             for (TSize i = 0; i < n; i++, ++sa, ++sb)
             {
@@ -176,10 +176,10 @@ namespace SEQAN_NAMESPACE_MAIN
         // *** SPECIALIZATION ***
 
         // step 1
-		typedef Pipe< TInput, Sampler<3> >  TSamplerDC3;
+        typedef Pipe< TInput, Sampler<3> >  TSamplerDC3;
                                         typedef _skew3NComp<TypeOf_(TSamplerDC3)> ncomp_t;
         typedef Pool< TypeOf_(TSamplerDC3), SorterSpec< SorterConfigSize<ncomp_t, TSizeOf_(TSamplerDC3) > > > TSortTuples;
-		typedef Pipe< TSortTuples, Namer<ncomp_t> > TNamer;
+        typedef Pipe< TSortTuples, Namer<ncomp_t> > TNamer;
                                         typedef _skew3NMapSliced<TypeOf_(TNamer)> nmap_sliced_t;
                                         typedef _skew3NMapLinear<TypeOf_(TNamer)> nmap_linear_t;
         typedef Pool< TypeOf_(TNamer), MapperSpec< MapperConfigSize< nmap_sliced_t, TSizeOf_(TNamer) > > > TNames_Sliced;
@@ -202,7 +202,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
         // step 3
                                         typedef _skew3NMapExtended<TypeOf_(typename TExtender::Out12)> nmap_extended_t;
-		typedef Pool< TypeOf_(typename TExtender::Out12), MapperSpec< MapperConfigSize< nmap_extended_t, TSizeOf_(typename TExtender::Out12) > > > TSorterS12;
+        typedef Pool< TypeOf_(typename TExtender::Out12), MapperSpec< MapperConfigSize< nmap_extended_t, TSizeOf_(typename TExtender::Out12) > > > TSorterS12;
         typedef Pipe< Bundle2< TSorterS0, TSorterS12 >, Merger3 > TMerger;
 
         TSorterS0   sortedS0;
@@ -210,15 +210,15 @@ namespace SEQAN_NAMESPACE_MAIN
         TMerger     in;
 
         Pipe() :
-			in(bundle2(sortedS0, sortedS12)) {}
+            in(bundle2(sortedS0, sortedS12)) {}
 
         Pipe(TInput& _textIn) :
-			in(bundle2(sortedS0, sortedS12))
-		{
-			process(_textIn);
-		}
+            in(bundle2(sortedS0, sortedS12))
+        {
+            process(_textIn);
+        }
 
-	    template < typename TInput_ >
+        template < typename TInput_ >
         bool process(TInput_ &textIn)
         {
 
@@ -262,7 +262,7 @@ namespace SEQAN_NAMESPACE_MAIN
                     std::cerr << "  make names linear" << std::endl;
                 #endif
                 names_linear << names_sliced;
-				clear(names_sliced);
+                clear(names_sliced);
                 SEQAN_PROMARK("Mapper (10) - ISA12 konstruieren");
 
                 // step 2
@@ -287,8 +287,8 @@ namespace SEQAN_NAMESPACE_MAIN
                 }
                 #endif
 
-				clear(filter);
-				unslicer_func_t             func(length(textIn));
+                clear(filter);
+                unslicer_func_t             func(length(textIn));
                 TUnslicer                   unslicer(recurse, func);
                 TRenamer                    renamer(unslicer);
 
@@ -297,14 +297,14 @@ namespace SEQAN_NAMESPACE_MAIN
                     std::cerr << "  rename names" << std::endl;
                 #endif
                 names_linear << renamer;
-				clear(renamer);
+                clear(renamer);
                 SEQAN_PROMARK("Mapper (10) - ISA12 konstruieren");
 
                 // step 2
                 #ifdef SEQAN_DEBUG_INDEX
                     std::cerr << "  prepare merge" << std::endl;
                 #endif
-				_skew3Extend(textIn, names_linear, sortedS0, sortedS12);
+                _skew3Extend(textIn, names_linear, sortedS0, sortedS12);
                 SEQAN_PROMARK("Mapper (12), Sorter (13) - SA12 und SA0 verschmelzen");
             }
 
@@ -334,25 +334,25 @@ namespace SEQAN_NAMESPACE_MAIN
     // not sure which interface is more intuitive, we support both
     // you can call "skew << pipe" or "skew_t skew(pipe); skew.process()"
     // for the first we would need no _in member
-	template < typename TInput, typename TObject >
+    template < typename TInput, typename TObject >
     inline bool operator<<(Pipe< TInput, Skew3 > &me, TObject &textIn)
     {
         return me.process(textIn);
     }
 
-	template <
-		typename TSA,
-		typename TValue,
-		typename TConfig >
-	inline void createSuffixArray(
-		TSA &SA,
-		String< TValue, External<TConfig> > &s,
-		Skew3 const &spec,
-		unsigned /*K*/,
+    template <
+        typename TSA,
+        typename TValue,
+        typename TConfig >
+    inline void createSuffixArray(
+        TSA &SA,
+        String< TValue, External<TConfig> > &s,
+        Skew3 const &spec,
+        unsigned /*K*/,
         unsigned /*maxdepth*/)
-	{
+    {
         createSuffixArrayExt(SA, s, spec);
-	}
+    }
 
 
     //////////////////////////////////////////////////////////////////////////////
@@ -360,7 +360,7 @@ namespace SEQAN_NAMESPACE_MAIN
     //////////////////////////////////////////////////////////////////////////////
 
     //////////////////////////////////////////////////////////////////////////////
-	// typedefs and helpers
+    // typedefs and helpers
 
     template <typename T, typename ST> inline
     bool _leqSkew3(T a1, ST a2,   T b1, ST b2)
@@ -387,22 +387,22 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TSA,
                typename TText >
     void createSuffixArray(
-		TSA &SA,
-		TText &s,
-		Skew3 const &,
-		unsigned K,
+        TSA &SA,
+        TText &s,
+        Skew3 const &,
+        unsigned K,
         unsigned maxdepth,
         unsigned depth)
     {
-		typedef typename Value<TSA>::Type TSize;
-		typedef typename Value<TText>::Type TValue;
+        typedef typename Value<TSA>::Type TSize;
+        typedef typename Value<TText>::Type TValue;
 
         #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "--- CREATE SUFFIX ARRAY ---" << std::endl;
             std::cerr << "Skew3 [random access]" << std::endl;
         #endif
 
-		TSize n = length(s);
+        TSize n = length(s);
         if (n < 1) return;
 
         TSize n0=n/3, n1=(n+2)/3, n2=(n+1)/3, n12=n1+n2;
@@ -412,131 +412,131 @@ namespace SEQAN_NAMESPACE_MAIN
         SEQAN_PROSET(SEQAN_PROEXTRA1, K);
         SEQAN_PROMARK("Rekursionsabstieg");
         #ifdef SEQAN_DEBUG_INDEX
-			std::cerr << "enter level " << depth << " (" << n << ")" << std::endl;
+            std::cerr << "enter level " << depth << " (" << n << ")" << std::endl;
         #endif
 
         String<TSize, Alloc<> > s12;
         resize(s12, n12, Exact());
-		// we use SA[n0..n-1] as a temporary buffer instead of allocating one;
-		typename Suffix<TSA>::Type SA12 = suffix(SA, n0);
+        // we use SA[n0..n-1] as a temporary buffer instead of allocating one;
+        typename Suffix<TSA>::Type SA12 = suffix(SA, n0);
 
 
-		// generate positions of mod 1 and mod 2 suffixes
-		{
-			//for (TSize i=0, j=0;  i < n;  i++) if ((n-i)%3) s12[j++] = i;
-			s12[0] = o1;
-			for (TSize i=o2, j=n1-n2;  i < n;  i++)
+        // generate positions of mod 1 and mod 2 suffixes
+        {
+            //for (TSize i=0, j=0;  i < n;  i++) if ((n-i)%3) s12[j++] = i;
+            s12[0] = o1;
+            for (TSize i=o2, j=n1-n2;  i < n;  i++)
             {
-				s12[j++] = i++;
-				s12[j++] = i++;
-			}
-		}
+                s12[j++] = i++;
+                s12[j++] = i++;
+            }
+        }
 
 
-		// lsb radix sort the mod 1 and mod 2 triples
-		{
-			String<TSize, Alloc<> > cnt;
-			resize(cnt, K, Exact());	// counter array
+        // lsb radix sort the mod 1 and mod 2 triples
+        {
+            String<TSize, Alloc<> > cnt;
+            resize(cnt, K, Exact());    // counter array
 
-			radixPass(SA12, s12, s, cnt, K, 2);
-			radixPass(s12, SA12, s, cnt, K, 1);
-			radixPass(SA12, s12, s, cnt, K);
-		}
+            radixPass(SA12, s12, s, cnt, K, 2);
+            radixPass(s12, SA12, s, cnt, K, 1);
+            radixPass(SA12, s12, s, cnt, K);
+        }
         SEQAN_PROMARK("Triplets sortiert");
 
         // find lexicographic names of triples
-		TSize name = 0;
+        TSize name = 0;
 
         bool differ = true;
-		TValue c0 = TValue(), c1 = TValue(), c2 = TValue();
-		for (TSize i = 0, clip = _max(n, (TSize)2) - 2, l;  i < n12;  i++)
+        TValue c0 = TValue(), c1 = TValue(), c2 = TValue();
+        for (TSize i = 0, clip = _max(n, (TSize)2) - 2, l;  i < n12;  i++)
         {
-			if ((l = SA12[i]) < clip)
+            if ((l = SA12[i]) < clip)
             {
-				if (differ || s[l] != c0 || s[l+1] != c1 || s[l+2] != c2)
+                if (differ || s[l] != c0 || s[l+1] != c1 || s[l+2] != c2)
                 {
-					name++;  c0 = s[l];  c1 = s[l+1];  c2 = s[l+2];
-					differ = false;
-				}
-			}
+                    name++;  c0 = s[l];  c1 = s[l+1];  c2 = s[l+2];
+                    differ = false;
+                }
+            }
             else
             {
-				name++;
-				differ = true;  // the last 2 triples always differ from the rest
-			}
-			s12[(n-l) % 3 == 2 ? l/3 : l/3 + n2] = name - 1;    // left or right half
-		}
+                name++;
+                differ = true;  // the last 2 triples always differ from the rest
+            }
+            s12[(n-l) % 3 == 2 ? l/3 : l/3 + n2] = name - 1;    // left or right half
+        }
         SEQAN_PROMARK("s12 konstruiert");
 
-		// recurse if names are not yet unique
-		if (name < n12)
+        // recurse if names are not yet unique
+        if (name < n12)
         {
             if (depth != maxdepth)
             {
-			    createSuffixArray(SA12, s12, Skew3(), name, maxdepth, depth + 1);
+                createSuffixArray(SA12, s12, Skew3(), name, maxdepth, depth + 1);
                 #ifdef SEQAN_TEST_SKEW3
                     SEQAN_ASSERT(isSuffixArray(SA12, s12));
                 #endif
             }
-			// store unique names in s12 using the suffix array
-			for (TSize i = 0;  i < n12;  i++) s12[SA12[i]] = i;
-		}
+            // store unique names in s12 using the suffix array
+            for (TSize i = 0;  i < n12;  i++) s12[SA12[i]] = i;
+        }
         else // generate the suffix array of s12 directly
-			for (TSize i = 0;  i < n12;  i++) SA12[s12[i]] = i;
-
+            for (TSize i = 0;  i < n12;  i++) SA12[s12[i]] = i;
 
 
-		// use SA[0...n0-1] as a temporary buffer instead of s0
-		// and allocate SA0
 
-		{
-			String<TSize, Alloc<> > SA0;
-			resize(SA0, n0, Exact());
-			typename Infix<TSA>::Type s0 = infix(SA, 0, n0);
+        // use SA[0...n0-1] as a temporary buffer instead of s0
+        // and allocate SA0
 
-			// stably sort the mod 0 suffixes from SA12 by their first character
-			{
-				String<TSize, Alloc<> > cnt;
-				resize(cnt, K, Exact());	// counter array
+        {
+            String<TSize, Alloc<> > SA0;
+            resize(SA0, n0, Exact());
+            typename Infix<TSA>::Type s0 = infix(SA, 0, n0);
 
-				for (TSize i=0, j=0, l;  i < n12;  i++)
-					if ((l = SA12[i]) < n2)
-						if ((l = o2 + (3 * l) ) > 0)
-							s0[j++] = l - 1;
-				radixPass(SA0, s0, s, cnt, K);
-			}
+            // stably sort the mod 0 suffixes from SA12 by their first character
+            {
+                String<TSize, Alloc<> > cnt;
+                resize(cnt, K, Exact());    // counter array
+
+                for (TSize i=0, j=0, l;  i < n12;  i++)
+                    if ((l = SA12[i]) < n2)
+                        if ((l = o2 + (3 * l) ) > 0)
+                            s0[j++] = l - 1;
+                radixPass(SA0, s0, s, cnt, K);
+            }
             SEQAN_PROMARK("SA0 konstruiert");
 
-			// merge sorted SA0 suffixes and sorted SA12 suffixes
-			#define SEQAN_GET_ISKEW3(ii) (ii < n2 ? ii * 3 + o2 : (ii - n2) * 3 + o1)
-			if (n0)
-			{
-				for (TSize p=0,  t=0,  k=0,  clip = n - 1;  k < n;  k++)
+            // merge sorted SA0 suffixes and sorted SA12 suffixes
+            #define SEQAN_GET_ISKEW3(ii) (ii < n2 ? ii * 3 + o2 : (ii - n2) * 3 + o1)
+            if (n0)
+            {
+                for (TSize p=0,  t=0,  k=0,  clip = n - 1;  k < n;  k++)
                 {
-					TSize ii = SA12[t];					// pos of current interleave offset 12 suffix
-					TSize i  = SEQAN_GET_ISKEW3(ii);	// pos of current offset 12 suffix
-					TSize j  = SA0[p];					// pos of current offset 0  suffix
-					if (ii < n2 ?
-						_leqSkew3<TValue, TSize> (s[i],       s12[ii + n1],     s[j],        s12[j/3 + n2  - n0]) :
-					(i < clip) ?     // clip if 12 suffix is the last
-						_leqSkew3<TValue, TSize> (s[i],s[i+1],s12[ii + 1 - n1], s[j],s[j+1], s12[j/3 + n12 - n0]) :
-						s[i] <= s[j])
-
-					{ // suffix from SA12 is smaller
-						SA[k] = i;
-						if (++t == n12) // done --- only SA0 suffixes left
-							for (;  p < n0;  p++) SA[++k] = SA0[p];
-					}
+                    TSize ii = SA12[t];                    // pos of current interleave offset 12 suffix
+                    TSize i  = SEQAN_GET_ISKEW3(ii);    // pos of current offset 12 suffix
+                    TSize j  = SA0[p];                    // pos of current offset 0  suffix
+                    if (ii < n2 ?
+                        _leqSkew3<TValue, TSize> (s[i],       s12[ii + n1],     s[j],        s12[j/3 + n2  - n0]) :
+                    (i < clip) ?     // clip if 12 suffix is the last
+                        _leqSkew3<TValue, TSize> (s[i],s[i+1],s12[ii + 1 - n1], s[j],s[j+1], s12[j/3 + n12 - n0]) :
+                        s[i] <= s[j])
+
+                    { // suffix from SA12 is smaller
+                        SA[k] = i;
+                        if (++t == n12) // done --- only SA0 suffixes left
+                            for (;  p < n0;  p++) SA[++k] = SA0[p];
+                    }
                     else
                     {
-						SA[k] = j;
-						if (++p == n0)  // done --- only SA12 suffixes left
-							for (;  t < n12;  t++) { ii = SA12[t]; SA[++k] = SEQAN_GET_ISKEW3(ii); }
-					}
-				}
-			} else
-				for (TSize t = 0;  t < n12;  t++) { TSize ii = SA12[t]; SA[t] = SEQAN_GET_ISKEW3(ii); }
-		}
+                        SA[k] = j;
+                        if (++p == n0)  // done --- only SA12 suffixes left
+                            for (;  t < n12;  t++) { ii = SA12[t]; SA[++k] = SEQAN_GET_ISKEW3(ii); }
+                    }
+                }
+            } else
+                for (TSize t = 0;  t < n12;  t++) { TSize ii = SA12[t]; SA[t] = SEQAN_GET_ISKEW3(ii); }
+        }
         SEQAN_PROMARK("SA12 und SA0 verschmolzen");
 
         #ifdef SEQAN_DEBUG_INDEX
@@ -549,23 +549,23 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TSA,
                typename TText >
     inline void createSuffixArray(
-		TSA &SA,
-		TText &s,
-		Skew3 const &alg,
-		unsigned K,
+        TSA &SA,
+        TText &s,
+        Skew3 const &alg,
+        unsigned K,
         unsigned maxdepth)
-	{
-		createSuffixArray(SA, s, alg, K, maxdepth, 1);
-	}
+    {
+        createSuffixArray(SA, s, alg, K, maxdepth, 1);
+    }
 
     // creates suffix array sorted by the first maxLCP chars of suffixes
     template < typename TSA,
                typename TText,
                typename TSize >
     inline void createSuffixArrayPart(
-		TSA &SA,
-		TText &s,
-		Skew3 const &_dummy,
+        TSA &SA,
+        TText &s,
+        Skew3 const &_dummy,
         TSize maxLCP,
         unsigned K)
     {
@@ -579,13 +579,13 @@ namespace SEQAN_NAMESPACE_MAIN
                typename TText,
                typename TSize >
     inline void createSuffixArrayPart(
-		TSA &SA,
-		TText &s,
-		Skew3 const &_dummy,
+        TSA &SA,
+        TText &s,
+        Skew3 const &_dummy,
         TSize maxLCP)
     {
-    	SEQAN_CHECKPOINT;
-    	createSuffixArrayPart(SA, s, _dummy, maxLCP, ValueSize< typename Value<TText>::Type >::VALUE);
+        SEQAN_CHECKPOINT;
+        createSuffixArrayPart(SA, s, _dummy, maxLCP, ValueSize< typename Value<TText>::Type >::VALUE);
     }
 
 //}
diff --git a/seqan/index/index_skew7.h b/seqan/index/index_skew7.h
index d9d3840..93521c7 100644
--- a/seqan/index/index_skew7.h
+++ b/seqan/index/index_skew7.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,39 +41,39 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct Skew7 {};
+    struct Skew7 {};
 
 
     //////////////////////////////////////////////////////////////////////////////
     // external Skew7 algorithm
     //////////////////////////////////////////////////////////////////////////////
 
-	template <typename T>
-	struct SkewDC_<7, T>
+    template <typename T>
+    struct SkewDC_<7, T>
     {
-		static const unsigned VALUE[];
-	};
+        static const unsigned VALUE[];
+    };
+
+    template <typename T>
+    const unsigned SkewDC_<7, T>::VALUE[] = { 3,   1, 2, 4 };
 
-	template <typename T>
-	const unsigned SkewDC_<7, T>::VALUE[] = { 3,   1, 2, 4 };
 
+    // *** COMPARATORS & MAPS ***
 
-	// *** COMPARATORS & MAPS ***
-        
     template <typename TValue, typename TResult = int>
     struct _skew7NComp :
         public std::binary_function<TValue, TValue, TResult>
     {
         inline TResult operator() (const TValue &a, const TValue &b) const
         {
-			typedef typename Value<TValue, 1>::Type                 TSize;
+            typedef typename Value<TValue, 1>::Type                 TSize;
             typedef typename Value<TValue, 2>::Type                 TSeptet;
             typedef typename Value<TSeptet>::Type                   TSeptetValue;
             typedef typename StoredTupleValue_<TSeptetValue>::Type  TStoredValue;
 
             const TStoredValue *sa = a.i2.i;
             const TStoredValue *sb = b.i2.i;
-            
+
             TSize n = LENGTH<TSeptet>::VALUE;
             if (a.i1 < n) n = a.i1;
             if (b.i1 < n) n = b.i1;
@@ -107,7 +107,7 @@ namespace SEQAN_NAMESPACE_MAIN
         {
             if (a.i2 < b.i2) return -1;
             if (a.i2 > b.i2) return 1;
-            if (a.i1 < 7 || b.i1 < 7) 
+            if (a.i1 < 7 || b.i1 < 7)
                 return (a.i1 < b.i1)? -1 : 1;
             return 0;
         }
@@ -122,7 +122,7 @@ namespace SEQAN_NAMESPACE_MAIN
         _skew7NMapLinear(TResult BN_): BN4(BN_+1), BN(BN_) {}
 
         inline TResult operator() (const TValue& x) const
-		{
+        {
             TResult i = x.i1; return (i%7 == 4)? BN4-(i-(i/7)*4): BN-(i-(i/7)*4);
         }
     };
@@ -132,15 +132,15 @@ namespace SEQAN_NAMESPACE_MAIN
         public std::unary_function<TValue, TResult>
     {
         TResult off[5];
-        
+
         _skew7NMapSliced(TResult BN_)
-        { 
-			off[0] = 0;
-			off[1] = BN_ - 1; 
-			off[2] = (2*BN_)/3 - 1; 
-			off[3] = 0;
-			off[4] = BN_/3 - 1; 
-		}
+        {
+            off[0] = 0;
+            off[1] = BN_ - 1;
+            off[2] = (2*BN_)/3 - 1;
+            off[3] = 0;
+            off[4] = BN_/3 - 1;
+        }
 
         inline TResult operator() (const TValue& x) const
         {
@@ -154,14 +154,14 @@ namespace SEQAN_NAMESPACE_MAIN
         public std::unary_function<TValue, TResult>
     {
         TResult o1, o2, o4, n4, n24;
-        
+
         _skew7UnslicerFunc(TResult N) :
             o1(N - (N + 6) % 7),
             o2(N - (N + 5) % 7),
             o4(N - (N + 3) % 7),
             n4((N + 3) / 7),
             n24((N + 5) / 7 + n4) {}
-        
+
         inline TResult operator() (const TValue& x) const
         {
             return (x < n4)  ? o4 -  x        * 7:
@@ -202,7 +202,7 @@ namespace SEQAN_NAMESPACE_MAIN
         public std::binary_function<
             Triple<T1,T2,Tuple<T,_size, BitPacked<> >, Pack>,
             Triple<T1,T2,Tuple<T,_size, BitPacked<> >, Pack>,
-            TResult> 
+            TResult>
     {
         inline TResult operator() (
             const Triple<T1,T2,Tuple<T,_size, BitPacked<> >, Pack> &a,
@@ -215,7 +215,7 @@ namespace SEQAN_NAMESPACE_MAIN
     };
     */
 
-	template < typename TInput >
+    template < typename TInput >
     struct Value< Pipe< TInput, Skew7 > > :
         public Size<TInput> {};
 
@@ -225,9 +225,9 @@ namespace SEQAN_NAMESPACE_MAIN
 
     template <typename T, typename TStringSpec>
     struct Skew7StringSpec_<String<T, TStringSpec> >
-	{
+    {
         typedef TStringSpec Type;
-	};
+    };
 
     template <typename T, typename TSegmentSpec>
     struct Skew7StringSpec_<Segment<T, TSegmentSpec> >:
@@ -246,17 +246,17 @@ namespace SEQAN_NAMESPACE_MAIN
         // *** SPECIALIZATION ***
 
         // use packing if lessorequal 16 different values per char
-        typedef typename IfC< 
+        typedef typename IfC<
             (BitsPerValue<TypeOf_(TInput)>::VALUE > 0) &&
             (BitsPerValue<TypeOf_(TInput)>::VALUE <= 4),
             BitPacked<>,
             Pack>::Type TPack;
 
         // step 1
-		typedef Pipe< TInput, Sampler<7, TPack> >  TSamplerDC7;
+        typedef Pipe< TInput, Sampler<7, TPack> >  TSamplerDC7;
                                         typedef _skew7NComp<TypeOf_(TSamplerDC7)> ncomp_t;
         typedef Pool< TypeOf_(TSamplerDC7), SorterSpec< SorterConfigSize<ncomp_t, TSizeOf_(TSamplerDC7) > > > TSortTuples;
-		typedef Pipe< TSortTuples, Namer<ncomp_t> > TNamer;
+        typedef Pipe< TSortTuples, Namer<ncomp_t> > TNamer;
                                         typedef _skew7NMapSliced<TypeOf_(TNamer)> nmap_sliced_t;
                                         typedef _skew7NMapLinear<TypeOf_(TNamer)> nmap_linear_t;
         typedef Pool< TypeOf_(TNamer), MapperSpec< MapperConfigSize< nmap_sliced_t, TSizeOf_(TNamer) > > > TNames_Sliced;
@@ -267,19 +267,19 @@ namespace SEQAN_NAMESPACE_MAIN
         // non-unique names
         typedef Pipe< TNames_Sliced, Filter< filterI2<TypeOf_(TNames_Sliced)> > > TFilter;
 
-			// recursion
-			typedef Pipe< TFilter, Skew3 > TRecurse;
-										typedef _skew7UnslicerFunc<TypeOf_(TRecurse)> unslicer_func_t;
-			typedef Pipe< TRecurse, Filter<unslicer_func_t> > TUnslicer;
-			typedef Pipe< TUnslicer, Counter > TRenamer;
+            // recursion
+            typedef Pipe< TFilter, Skew3 > TRecurse;
+                                        typedef _skew7UnslicerFunc<TypeOf_(TRecurse)> unslicer_func_t;
+            typedef Pipe< TRecurse, Filter<unslicer_func_t> > TUnslicer;
+            typedef Pipe< TUnslicer, Counter > TRenamer;
 
-			// no recursion inMemory shortcut
-			typedef Pipe< TFilter, LarssonSadakane > TInMem;
-			typedef Pipe< TInMem, Filter<unslicer_func_t> > TUnslicerInMem;
-			typedef Pipe< TUnslicerInMem, Counter > TRenamerInMem;
+            // no recursion inMemory shortcut
+            typedef Pipe< TFilter, LarssonSadakane > TInMem;
+            typedef Pipe< TInMem, Filter<unslicer_func_t> > TUnslicerInMem;
+            typedef Pipe< TUnslicerInMem, Counter > TRenamerInMem;
 
         typedef Pool< TypeOf_(TRenamer), MapperSpec< MapperConfigSize< nmap_linear_t, TSizeOf_(TRenamer) > > > TNames_Linear;
-        
+
         // step 2
         typedef Pipe< Bundle2< TInput, TNames_Linear >, Extender7<TPack> > TExtender;
                                         typedef _skew7ExtendComp<TypeOf_(typename TExtender::Out0),3> extend0_comp_t;
@@ -293,7 +293,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
         // step 3
                                         typedef _skew7NMapExtended<TypeOf_(typename TExtender::Out124)> nmap_extended_t;
-		typedef Pool< TypeOf_(typename TExtender::Out124), MapperSpec< MapperConfigSize< nmap_extended_t, TSizeOf_(typename TExtender::Out124) > > > TSorterS124;
+        typedef Pool< TypeOf_(typename TExtender::Out124), MapperSpec< MapperConfigSize< nmap_extended_t, TSizeOf_(typename TExtender::Out124) > > > TSorterS124;
         typedef Pipe< Bundle5< TSorterS0, TSorterS3, TSorterS5, TSorterS6, TSorterS124 >, Merger7 > TMerger;
 
         TSorterS0   sortedS0;
@@ -302,24 +302,24 @@ namespace SEQAN_NAMESPACE_MAIN
         TSorterS6   sortedS6;
         TSorterS124 sortedS124;
         TMerger     in;
-            
+
         Pipe():
-			in(bundle5(sortedS0, sortedS3, sortedS5, sortedS6, sortedS124)) {}
-
-		Pipe(TInput& _textIn):
-			in(bundle5(sortedS0, sortedS3, sortedS5, sortedS6, sortedS124))
-		{
-			process(_textIn);
-		}
-        
-	    template < typename TInput_ >
+            in(bundle5(sortedS0, sortedS3, sortedS5, sortedS6, sortedS124)) {}
+
+        Pipe(TInput& _textIn):
+            in(bundle5(sortedS0, sortedS3, sortedS5, sortedS6, sortedS124))
+        {
+            process(_textIn);
+        }
+
+        template < typename TInput_ >
         bool process(TInput_ &textIn) {
 
             SEQAN_PROADD(SEQAN_PRODEPTH, 1);
             SEQAN_PROMARK("Enter recursion");
             #ifdef SEQAN_DEBUG_INDEX
                 std::cerr << "enter level " << SEQAN_PROVAL(SEQAN_PRODEPTH) << " bit-packing: ";
-				std::cerr << IsSameType<TPack, BitPacked<> >::VALUE << " " << BitsPerValue<TypeOf_(TInput)>::VALUE << std::endl;
+                std::cerr << IsSameType<TPack, BitPacked<> >::VALUE << " " << BitsPerValue<TypeOf_(TInput)>::VALUE << std::endl;
             #endif
             {
 
@@ -355,7 +355,7 @@ namespace SEQAN_NAMESPACE_MAIN
                     std::cerr << "  make names linear" << std::endl;
                 #endif
                 names_linear << names_sliced;
-				clear(names_sliced);
+                clear(names_sliced);
                 SEQAN_PROMARK("Mapper (10) - construct ISA124");
 
                 // step 2
@@ -368,50 +368,50 @@ namespace SEQAN_NAMESPACE_MAIN
                 SEQAN_PROMARK("Mapper (4) - construct s124");
 
                 TFilter                     filter(names_sliced);
-				TNames_Linear               names_linear(map_linear);
-
-				if (length(filter) > 128*1024*1024) 
-				{
-					// recursion
-					TRecurse                    recurse(filter);
-
-					#ifdef SEQAN_TEST_SKEW7
-					{
-						String<typename Value<TFilter>::Type, Alloc<> > _text;
-						_text << filter;
-						SEQAN_ASSERT(isSuffixArray(recurse, _text));
-					}
-					#endif
-
-					clear(filter);
-					unslicer_func_t             func(length(textIn));
-					TUnslicer                   unslicer(recurse, func);
-					TRenamer                    renamer(unslicer);
-
-					#ifdef SEQAN_DEBUG_INDEX
-						std::cerr << "  rename names" << std::endl;
-					#endif
-
-					names_linear << renamer;
-				}
-				else
-				{
-					TInMem						inMem(filter);
-
-					clear(filter);
-					unslicer_func_t				func(length(textIn));
-					TUnslicerInMem              unslicer(inMem, func);
-					TRenamerInMem               renamer(unslicer);
-
-					#ifdef SEQAN_DEBUG_INDEX
-						std::cerr << "  rename names" << std::endl;
-					#endif
-
-					names_linear << renamer;
-				} 
+                TNames_Linear               names_linear(map_linear);
+
+                if (length(filter) > 128*1024*1024)
+                {
+                    // recursion
+                    TRecurse                    recurse(filter);
+
+                    #ifdef SEQAN_TEST_SKEW7
+                    {
+                        String<typename Value<TFilter>::Type, Alloc<> > _text;
+                        _text << filter;
+                        SEQAN_ASSERT(isSuffixArray(recurse, _text));
+                    }
+                    #endif
+
+                    clear(filter);
+                    unslicer_func_t             func(length(textIn));
+                    TUnslicer                   unslicer(recurse, func);
+                    TRenamer                    renamer(unslicer);
+
+                    #ifdef SEQAN_DEBUG_INDEX
+                        std::cerr << "  rename names" << std::endl;
+                    #endif
+
+                    names_linear << renamer;
+                }
+                else
+                {
+                    TInMem                        inMem(filter);
+
+                    clear(filter);
+                    unslicer_func_t                func(length(textIn));
+                    TUnslicerInMem              unslicer(inMem, func);
+                    TRenamerInMem               renamer(unslicer);
+
+                    #ifdef SEQAN_DEBUG_INDEX
+                        std::cerr << "  rename names" << std::endl;
+                    #endif
+
+                    names_linear << renamer;
+                }
 
                 SEQAN_PROMARK("Mapper (10) - ISA124 konstruieren");
-               
+
                 // step 2
                 #ifdef SEQAN_DEBUG_INDEX
                     std::cerr << "  prepare merge" << std::endl;
@@ -419,7 +419,7 @@ namespace SEQAN_NAMESPACE_MAIN
                 _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124);
                 SEQAN_PROMARK("Mapper (12), Sorter (13-16) - merge SA124, SA3, SA5, SA6, SA0");
             }
-            
+
             // step 3
             // ... is done on-demand by merger
             }
@@ -435,17 +435,17 @@ namespace SEQAN_NAMESPACE_MAIN
         inline typename Value<Pipe>::Type const operator*() {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
-        }        
+        }
     };
 
     // not sure which interface is more intuitive, we support both
     // you can call "skew << pipe" or "skew_t skew(pipe); skew.process()"
     // for the first we would need no _in member
-	template < typename TInput, typename TObject >
+    template < typename TInput, typename TObject >
     inline bool operator<<(Pipe< TInput, Skew7 > &me, TObject &textIn) {
         return me.process(textIn);
     }
@@ -456,9 +456,9 @@ namespace SEQAN_NAMESPACE_MAIN
     //////////////////////////////////////////////////////////////////////////////
 
     //////////////////////////////////////////////////////////////////////////////
-	// typedefs and helpers
+    // typedefs and helpers
 
-	// compares n characters and in case of equality the names a2 and b2 (no clipping)
+    // compares n characters and in case of equality the names a2 and b2 (no clipping)
     template <typename TTextIter, typename TSize> inline
     bool _leqSkew7(TTextIter a1, TSize a2,   TTextIter b1, TSize b2,   TSize n)
     {
@@ -470,7 +470,7 @@ namespace SEQAN_NAMESPACE_MAIN
         return (a2 <= b2);
     }
 
-	// compares at most the last n characters (a) with b (clipping)
+    // compares at most the last n characters (a) with b (clipping)
     template <typename TTextIter, typename TSize> inline
     bool _leqSkew7(TTextIter a,   TTextIter b,   TSize n)
     { // lexic. order for n-tupels
@@ -478,16 +478,16 @@ namespace SEQAN_NAMESPACE_MAIN
             if (ordLess(*a, *b)) return true;
             if (ordLess(*b, *a)) return false;
         }
-        return true;	// a is shorter than b
+        return true;    // a is shorter than b
     }
 
-	// compares two suffixes of residue classes a and b
+    // compares two suffixes of residue classes a and b
     template <typename TTextIter, typename TSize, typename TString> inline
     bool _leqSkew7(unsigned a, unsigned b,   TTextIter spos[], const TSize tpos[], const bool islast[], const TString &s124, const TSize adjust[7][7])
     {
         TTextIter sa = spos[a];
         TTextIter sb = spos[b];
-		TSize shft = SkewShift_<7>::VALUE[a][b];
+        TSize shft = SkewShift_<7>::VALUE[a][b];
         if (sa > sb) {
             if ((a != 0) && (a < shft) && islast[a]) // do we need to clip?
                 return _leqSkew7 (sa,   sb,   a);
@@ -497,7 +497,7 @@ namespace SEQAN_NAMESPACE_MAIN
         }
         return _leqSkew7 (sa, s124[tpos[a] + adjust[a][b]],   sb, s124[tpos[b] + adjust[b][a]],   shft);
     }
-    
+
     template <typename TSAOut, typename TText, typename TSAIn, typename TEnable>
     inline bool _fastTupleSortSkew7(TSAOut &, TText const &, TSAIn const &, TEnable)
     {
@@ -508,20 +508,20 @@ namespace SEQAN_NAMESPACE_MAIN
     inline bool _fastTupleSortSkew7(TSAOut &SA124, TText const &s, TSAIn const &s124, True)
     {
         typedef typename Value<TText>::Type TValue;
-		typedef typename Value<TSAOut>::Type TSize;
-		typedef typename Iterator<TText const, Standard>::Type TValueIter;
-		typedef typename Iterator<TSAIn const, Standard>::Type TSAIter;
-        
+        typedef typename Value<TSAOut>::Type TSize;
+        typedef typename Iterator<TText const, Standard>::Type TValueIter;
+        typedef typename Iterator<TSAIn const, Standard>::Type TSAIter;
+
         // optimized tuple sort for short alphabets
         Shape<TValue, UngappedShape<7> > shape;
         String<TSize, Alloc<> > cnt;
         resize(cnt, _fullDir2Length(shape), 0, Exact());
-        
-        TValueIter textBegin = begin(s, Standard());            
+
+        TValueIter textBegin = begin(s, Standard());
         TSAIter it = begin(s124, Standard());
         TSAIter itEnd = end(s124, Standard());
 
-		register TSize n = length(s);
+        TSize n = length(s);
         for(; it != itEnd; ++it)
             ++cnt[hash2(shape, textBegin + *it, n - *it)];
 
@@ -530,344 +530,344 @@ namespace SEQAN_NAMESPACE_MAIN
         it = begin(s124, Standard());
         for(; it != itEnd; ++it)
             SA124[cnt[hash2(shape, textBegin + *it, n - *it) + 1]++] = *it;
-        
+
         return true;
     }
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Skew algorithm with difference cover of Z_7
-	//
-	// Construct the suffix array SA of s[0..n-1], where s is a string over
-	// the alphabet {0..K}.
-	//
-	// The following algorithm divides the suffixes in seven residue classes
-	// according to their lengths and uses a difference cover {1,2,4}. 
-	// That approach results in an algorithm that is more space and time efficient
-	// than the original skew algorithm with a difference cover {1,2} of Z_3.
-	//
-	// * no trailing 0's required
-	// * no dummy triples in special cases
+    //////////////////////////////////////////////////////////////////////////////
+    // Skew algorithm with difference cover of Z_7
+    //
+    // Construct the suffix array SA of s[0..n-1], where s is a string over
+    // the alphabet {0..K}.
+    //
+    // The following algorithm divides the suffixes in seven residue classes
+    // according to their lengths and uses a difference cover {1,2,4}.
+    // That approach results in an algorithm that is more space and time efficient
+    // than the original skew algorithm with a difference cover {1,2} of Z_3.
+    //
+    // * no trailing 0's required
+    // * no dummy triples in special cases
 
     template < typename TSA,
                typename TText >
     void createSuffixArray(
-		TSA &SA,
-		TText &s,
-		Skew7 const &,
-		unsigned K,
+        TSA &SA,
+        TText &s,
+        Skew7 const &,
+        unsigned K,
         unsigned maxdepth,
-		unsigned depth)
+        unsigned depth)
     {
-		typedef typename Value<TSA>::Type TSize;
-		typedef typename Value<TText>::Type TValue;
+        typedef typename Value<TSA>::Type TSize;
+        typedef typename Value<TText>::Type TValue;
         typedef String<TSize, Alloc<> > TBuffer;
-		typedef typename Iterator<TSA, Standard>::Type TSAIter;
-		//typedef typename Iterator<TBuffer, Standard>::Type TBufferIter;
-		typedef typename Iterator<TText const, Standard>::Type TValueIter;
+        typedef typename Iterator<TSA, Standard>::Type TSAIter;
+        //typedef typename Iterator<TBuffer, Standard>::Type TBufferIter;
+        typedef typename Iterator<TText const, Standard>::Type TValueIter;
 
-		SEQAN_ASSERT(IsContiguous<TText>::VALUE == true);
-		SEQAN_ASSERT(IsContiguous<TSA>::VALUE == true);
+        SEQAN_ASSERT(AllowsFastRandomAccess<TText>::VALUE == true);
+        SEQAN_ASSERT(AllowsFastRandomAccess<TSA>::VALUE == true);
 
         #ifdef SEQAN_DEBUG_INDEX
             std::cerr << "--- CREATE SUFFIX ARRAY ---" << std::endl;
             std::cerr << "Skew7 [random access]" << std::endl;
         #endif
 
-		TSize n = length(s);
+        TSize n = length(s);
         if (n < 1) return;
 
-		TSize _n[7];
-		TSize _o[7];
+        TSize _n[7];
+        TSize _o[7];
 
-		_n[0] = n/7;
-		_o[0] = n%7;
-		TSize j = n + 6;
-		for(int i = 1; i < 7; ++i, --j) {
-			_n[i] = j/7;
-			_o[i] = j%7;
-		}
+        _n[0] = n/7;
+        _o[0] = n%7;
+        TSize j = n + 6;
+        for(int i = 1; i < 7; ++i, --j) {
+            _n[i] = j/7;
+            _o[i] = j%7;
+        }
 
-		TSize _n24  = _n[2]+_n[4];
-		TSize _n124 = _n[1]+_n24;
+        TSize _n24  = _n[2]+_n[4];
+        TSize _n124 = _n[1]+_n24;
 
         SEQAN_PROSET(SEQAN_PRODEPTH, depth);
         SEQAN_PROSET(SEQAN_PROEXTRA1, K);
         SEQAN_PROMARK("Rekursionsabstieg");
         #ifdef SEQAN_DEBUG_INDEX
-			std::cerr << "enter level " << depth << " (" << n << ")" << std::endl;
+            std::cerr << "enter level " << depth << " (" << n << ")" << std::endl;
         #endif
 
         TBuffer s124;
         resize(s124, _n124, Exact());
-		// we use SA[n-n124..n-1] as a temporary buffer instead of allocating one
-		typename Suffix<TSA>::Type SA124 = suffix(SA, n - _n124);
-
+        // we use SA[n-n124..n-1] as a temporary buffer instead of allocating one
+        typename Suffix<TSA>::Type SA124 = suffix(SA, n - _n124);
 
-		// generate positions of mod 3, mod 5 and mod 6 suffixes
-		{
-			TSize j = 0;
-			if (_n[2] > _n[4]) s124[j++] = _o[2];
-			if (_n[1] > _n[4]) s124[j++] = _o[1];
 
-			for (TSize i=_o[4];  i < n;  i+=7) {
-				s124[j++] = i;
-				s124[j++] = i + 2;
-				s124[j++] = i + 3;
-			}
-		}
+        // generate positions of mod 3, mod 5 and mod 6 suffixes
+        {
+            TSize j = 0;
+            if (_n[2] > _n[4]) s124[j++] = _o[2];
+            if (_n[1] > _n[4]) s124[j++] = _o[1];
+
+            for (TSize i=_o[4];  i < n;  i+=7) {
+                s124[j++] = i;
+                s124[j++] = i + 2;
+                s124[j++] = i + 3;
+            }
+        }
 
 
-		// lsb radix sort the mod 3, mod 5 and mod 6 7-tupels
+        // lsb radix sort the mod 3, mod 5 and mod 6 7-tupels
         if (!_fastTupleSortSkew7(SA124, s, s124, typename Eval<BitsPerValue<TValue>::VALUE < 4>::Type()))
-		{
-			String<TSize, Alloc<> > cnt;
-			resize(cnt, K, Exact());	// counter array
-
-			radixPass(SA124, s124,  s, cnt, K, 6);
-			radixPass(s124,  SA124, s, cnt, K, 5);
-			radixPass(SA124, s124,  s, cnt, K, 4);
-			radixPass(s124,  SA124, s, cnt, K, 3);
-			radixPass(SA124, s124,  s, cnt, K, 2);
-			radixPass(s124,  SA124, s, cnt, K, 1);
-			radixPass(SA124, s124,  s, cnt, K);
-		}
+        {
+            String<TSize, Alloc<> > cnt;
+            resize(cnt, K, Exact());    // counter array
+
+            radixPass(SA124, s124,  s, cnt, K, 6);
+            radixPass(s124,  SA124, s, cnt, K, 5);
+            radixPass(SA124, s124,  s, cnt, K, 4);
+            radixPass(s124,  SA124, s, cnt, K, 3);
+            radixPass(SA124, s124,  s, cnt, K, 2);
+            radixPass(s124,  SA124, s, cnt, K, 1);
+            radixPass(SA124, s124,  s, cnt, K);
+        }
         SEQAN_PROMARK("7-lets sortiert");
 
-		// find lexicographic names of 7-tupel
-		TSize name = 0;
-		{
-			TSize ofs[7] = {0, _n24, _n[4], 0, 0, 0, 0};
-			bool differ = true;
-			TValue c0 = TValue(0), c1 = TValue(0), c2 = TValue(0), c3 = TValue(0), c4 = TValue(0), c5 = TValue(0), c6 = TValue(0);
-			for (TSize i = 0, clip = _max(n, (TSize)6) - 6, l;  i < _n124;  i++) {
-				if ((l = SA124[i]) < clip) {
-					if (differ || s[l] != c0 || s[l+1] != c1 || s[l+2] != c2 || s[l+3] != c3 ||
-												s[l+4] != c4 || s[l+5] != c5 || s[l+6] != c6) {
-						name++;  c0 = s[l];  c1 = s[l+1];  c2 = s[l+2];  c3 = s[l+3];
-											 c4 = s[l+4];  c5 = s[l+5];  c6 = s[l+6];
-						differ = false;
-					}
-				} else {
-					name++;
-					differ = true;  // the last 6 7-tupels always differ from the rest
-				}
-				s124[(l/7) + ofs[(n-l) % 7]] = name - 1;   // select a third
-			}
-		}
+        // find lexicographic names of 7-tupel
+        TSize name = 0;
+        {
+            TSize ofs[7] = {0, _n24, _n[4], 0, 0, 0, 0};
+            bool differ = true;
+            TValue c0 = TValue(0), c1 = TValue(0), c2 = TValue(0), c3 = TValue(0), c4 = TValue(0), c5 = TValue(0), c6 = TValue(0);
+            for (TSize i = 0, clip = _max(n, (TSize)6) - 6, l;  i < _n124;  i++) {
+                if ((l = SA124[i]) < clip) {
+                    if (differ || s[l] != c0 || s[l+1] != c1 || s[l+2] != c2 || s[l+3] != c3 ||
+                                                s[l+4] != c4 || s[l+5] != c5 || s[l+6] != c6) {
+                        name++;  c0 = s[l];  c1 = s[l+1];  c2 = s[l+2];  c3 = s[l+3];
+                                             c4 = s[l+4];  c5 = s[l+5];  c6 = s[l+6];
+                        differ = false;
+                    }
+                } else {
+                    name++;
+                    differ = true;  // the last 6 7-tupels always differ from the rest
+                }
+                s124[(l/7) + ofs[(n-l) % 7]] = name - 1;   // select a third
+            }
+        }
         SEQAN_PROMARK("s12 konstruiert");
 
-		// recurse if names are not yet unique
-		if (name < _n124) {
+        // recurse if names are not yet unique
+        if (name < _n124) {
             if (depth != maxdepth)
             {
-			    createSuffixArray(SA124, s124, Skew7(), name, maxdepth, depth + 1);
-			    #ifdef SEQAN_TEST_SKEW7
-				    SEQAN_ASSERT(isSuffixArray(SA124, s124));
-			    #endif
+                createSuffixArray(SA124, s124, Skew7(), name, maxdepth, depth + 1);
+                #ifdef SEQAN_TEST_SKEW7
+                    SEQAN_ASSERT(isSuffixArray(SA124, s124));
+                #endif
             }
-			// store unique names in s124 using the suffix array
-			for (TSize i = 0;  i < _n124;  i++) s124[SA124[i]] = i;
-		} else // generate the suffix array of s124 directly
-			for (TSize i = 0;  i < _n124;  i++) SA124[s124[i]] = i;
-
-
-		// use SA[0...n3-1] and SA[n3...n3+n5-1] as a temporary buffers instead of allocating some
-		// and allocate SA0, SA3, SA5 and SA6
-
-		{
-			typename Infix<TSA>::Type s3 = infix(SA, 0, _n[3]), s5 = infix(SA, _n[3], _n[3] + _n[5]);
-			String<TSize, typename Skew7StringSpec_<TSA>::Type> SA0, SA3, SA5, SA6;
-
-			resize(SA0, _n[0], Exact());
-			resize(SA3, _n[3], Exact());
-			resize(SA5, _n[5], Exact());
-			resize(SA6, _n[6], Exact());
-
-			// stably sort the mod 5 and mod 3 suffixes from SA124 by their first character
-			{
-				for (TSize i=0, j3=0, j5=0, l;  i < _n124;  i++) {
-					l = SA124[i];
-					if (l < _n[4]) {
-						if ((l = _o[4] + (7 * l)) > 0)
-							s5[j5++] = l - 1;
-					} else if (l < _n24) {
-						if ((l = _o[2] + (7 * (l - _n[4]))) > 0)
-							s3[j3++] = l - 1;
-					}
-				}
-
-				{
-					String<TSize, Alloc<> > cnt;
-					resize(cnt, K, Exact());	// counter array
-
-					radixPass(SA3, s3, s, cnt, K);
+            // store unique names in s124 using the suffix array
+            for (TSize i = 0;  i < _n124;  i++) s124[SA124[i]] = i;
+        } else // generate the suffix array of s124 directly
+            for (TSize i = 0;  i < _n124;  i++) SA124[s124[i]] = i;
+
+
+        // use SA[0...n3-1] and SA[n3...n3+n5-1] as a temporary buffers instead of allocating some
+        // and allocate SA0, SA3, SA5 and SA6
+
+        {
+            typename Infix<TSA>::Type s3 = infix(SA, 0, _n[3]), s5 = infix(SA, _n[3], _n[3] + _n[5]);
+            String<TSize, typename Skew7StringSpec_<TSA>::Type> SA0, SA3, SA5, SA6;
+
+            resize(SA0, _n[0], Exact());
+            resize(SA3, _n[3], Exact());
+            resize(SA5, _n[5], Exact());
+            resize(SA6, _n[6], Exact());
+
+            // stably sort the mod 5 and mod 3 suffixes from SA124 by their first character
+            {
+                for (TSize i=0, j3=0, j5=0, l;  i < _n124;  i++) {
+                    l = SA124[i];
+                    if (l < _n[4]) {
+                        if ((l = _o[4] + (7 * l)) > 0)
+                            s5[j5++] = l - 1;
+                    } else if (l < _n24) {
+                        if ((l = _o[2] + (7 * (l - _n[4]))) > 0)
+                            s3[j3++] = l - 1;
+                    }
+                }
+
+                {
+                    String<TSize, Alloc<> > cnt;
+                    resize(cnt, K, Exact());    // counter array
+
+                    radixPass(SA3, s3, s, cnt, K);
                     SEQAN_PROMARK("SA3 konstruiert");
 
-					radixPass(SA5, s5, s, cnt, K);
+                    radixPass(SA5, s5, s, cnt, K);
                     SEQAN_PROMARK("SA5 konstruiert");
-	    
-					// stably sort the mod 6 suffixes from SA5 by their first character
 
-					if (_n[5] == _n[6]) radixExtend    (SA6, SA5, s, cnt, K);
-					else                radixExtendClip(SA6, SA5, s, cnt, K);
+                    // stably sort the mod 6 suffixes from SA5 by their first character
+
+                    if (_n[5] == _n[6]) radixExtend    (SA6, SA5, s, cnt, K);
+                    else                radixExtendClip(SA6, SA5, s, cnt, K);
                     SEQAN_PROMARK("SA6 konstruiert");
 
-					// stably sort the mod 0 suffixes from SA6 by their first character
+                    // stably sort the mod 0 suffixes from SA6 by their first character
 
-					if (_n[6] == _n[0]) radixExtend    (SA0, SA6, s, cnt, K);
-					else                radixExtendClip(SA0, SA6, s, cnt, K);	    
+                    if (_n[6] == _n[0]) radixExtend    (SA0, SA6, s, cnt, K);
+                    else                radixExtendClip(SA0, SA6, s, cnt, K);
                     SEQAN_PROMARK("SA0 konstruiert");
-				}
-			}
-
-			// MULTIWAY MERGE all SA_ streams
-			{
-				// a helper matrix to lex-name-compare every combination of suffixes
-				TSize adjust[7][7] =
-					//      0               1              2             3             4              5               6
-				   {{0             , _n124-_n[0]   , _n24-_n[0]  , _n124-_n[0] , _n[4]-_n[0] , _n[4]-_n[0]   , _n24-_n[0]    },  // 0
-					{1-_n[1]       , 0             , 0           , 1-_n[1]     , 0           , 1-_n[1]-_n[2] , 1-_n[1]-_n[2] },  // 1*
-					{1-_n[2]       , 0             , 0           , _n[1]       , 0           , _n[1]         , 1-_n[2]       },  // 2*
-					{1+_n[4]-_n[3] , 1+_n[4]-_n[3] , _n24-_n[3]  , 0           , _n124-_n[3] , _n24-_n[3]    , _n124-_n[3]   },  // 3
-					{_n[1]+_n[2]   , 0             , 0           ,_n[2]        , 0           , _n[1]+_n[2]   , _n[2]         },  // 4*
-					{_n24-_n[5]    , _n124-_n[5]   , _n[4]-_n[5] , _n[4]-_n[5] , _n24-_n[5]  , 0             , _n124-_n[5]   },  // 5
-					{_n124-_n[6]   , _n24-_n[6]    , _n124-_n[6] , _n[4]-_n[6] , _n[4]-_n[6] , _n24-_n[6]    , 0             }}; // 6
-
-				TSAIter pos[7] = {begin(SA0)      , begin(SA124)      , begin(SA124)      , 
-								  begin(SA3)      , begin(SA124)      , begin(SA5)        , begin(SA6)      };
-				TSAIter max[7] = {begin(SA0)+_n[0], begin(SA124)+_n124, begin(SA124)+_n124,
-								  begin(SA3)+_n[3], begin(SA124)+_n124, begin(SA5)+_n[5]  , begin(SA6)+_n[6]};
-				TValueIter spos[7];
-				TSize tpos[7];
-				bool islast[7];
-
-				int a, b, rank[5];
-				int fill = 0;
-				TSize k = 0;
-
-				#define SEQAN_GET_ISKEW7(ii) (ii < _n[4] ? (ii * 7) + _o[4] : (ii < _n24 ? ((ii - _n[4]) * 7) + _o[2] : ((ii - _n24) * 7) + _o[1]))
-				#define SEQAN_GET_ASKEW7(ii) (ii < _n[4] ? 4 : (ii < _n24 ? 2 : 1))
-
-				// fill the stream ranking list
-				for(int i = 0; i < 7; ++i) {
-					if (!_n[i]) continue;
-					if (i == 2 || i == 4) continue; // insert only the least suffix of SA124
-
-					if (i == 1) {
-
-						TSize ii  = *(pos[1]);
-						a         = SEQAN_GET_ASKEW7(ii);
-						TSize j	  = SEQAN_GET_ISKEW7(ii);
-
-						tpos[a]   = ii;
-						spos[a]   = begin(s) + j;
-						islast[a] = (j + 7 >= n);
-
-					} else {
-
-						a = i;
-						TSize j   = *(pos[a]);
-
-						tpos[a]   = j / 7;
-						spos[a]   = begin(s) + j;
-						islast[a] = (j + 7 >= n);
-
-					}
-
-					// get the rank of stream a's suffix
-					int j;
-					for(j = 0;  j < fill;  ++j) {
-						b = rank[j];
-						if (_leqSkew7 (a,  b,   spos, tpos, islast, s124, adjust)) break;
-					}
-
-					// insert the suffix
-					for(int i = fill; i > j; --i)
-						rank[i] = rank[i-1];
-					rank[j] = a;
-					fill++;
-				}
-
-				// main merge loop
-				// in order to find the least suffix in every step we use a stream ranking list
-				// so we only need to keep up the ordering and thus rank[0] is always the least suffix
-				while (fill > 1) {
-
-					// add the least suffix to SA and get the next of the corresponding stream
-					a = rank[0];
-					SA[k++] = spos[a] - begin(s);
-					if (a == 1 || a == 2 || a == 4)
-						pos[4] = pos[2] = ++pos[1];
-					else
-						++pos[a];
-
-					if (pos[a] < max[a]) {
-
-						// set corresponding spos, tpos, islast values and adapt a if necessary
-						if (a == 1 || a == 2 || a == 4) {
-
-							TSize ii  = *(pos[1]);
-							a		  = SEQAN_GET_ASKEW7(ii);
-							TSize j   = SEQAN_GET_ISKEW7(ii);
-
-							tpos[a]   = ii;
-							spos[a]   = begin(s) + j;
-							islast[a] = (j + 7 >= n);
-
-						} else {
-
-							TSize j   = *(pos[a]);
-
-							tpos[a]   = j / 7;
-							spos[a]   = begin(s) + j;
-							islast[a] = (j + 7 >= n);
-
-						}
-
-						// get the rank of stream a's suffix
-
-						// linear search
-						int right;
-						for(right = 1;  right < fill;  right++) {
-							b = rank[right];
-							if (_leqSkew7 (a,  b,   spos, tpos, islast, s124, adjust)) break;
-						}
+                }
+            }
+
+            // MULTIWAY MERGE all SA_ streams
+            {
+                // a helper matrix to lex-name-compare every combination of suffixes
+                TSize adjust[7][7] =
+                    //      0               1              2             3             4              5               6
+                   {{0             , _n124-_n[0]   , _n24-_n[0]  , _n124-_n[0] , _n[4]-_n[0] , _n[4]-_n[0]   , _n24-_n[0]    },  // 0
+                    {1-_n[1]       , 0             , 0           , 1-_n[1]     , 0           , 1-_n[1]-_n[2] , 1-_n[1]-_n[2] },  // 1*
+                    {1-_n[2]       , 0             , 0           , _n[1]       , 0           , _n[1]         , 1-_n[2]       },  // 2*
+                    {1+_n[4]-_n[3] , 1+_n[4]-_n[3] , _n24-_n[3]  , 0           , _n124-_n[3] , _n24-_n[3]    , _n124-_n[3]   },  // 3
+                    {_n[1]+_n[2]   , 0             , 0           ,_n[2]        , 0           , _n[1]+_n[2]   , _n[2]         },  // 4*
+                    {_n24-_n[5]    , _n124-_n[5]   , _n[4]-_n[5] , _n[4]-_n[5] , _n24-_n[5]  , 0             , _n124-_n[5]   },  // 5
+                    {_n124-_n[6]   , _n24-_n[6]    , _n124-_n[6] , _n[4]-_n[6] , _n[4]-_n[6] , _n24-_n[6]    , 0             }}; // 6
+
+                TSAIter pos[7] = {begin(SA0, Standard())      , begin(SA124, Standard())      , begin(SA124, Standard())      ,
+                                  begin(SA3, Standard())      , begin(SA124, Standard())      , begin(SA5, Standard())        , begin(SA6, Standard())      };
+                TSAIter max[7] = {begin(SA0, Standard())+_n[0], begin(SA124, Standard())+_n124, begin(SA124, Standard())+_n124,
+                                  begin(SA3, Standard())+_n[3], begin(SA124, Standard())+_n124, begin(SA5, Standard())+_n[5]  , begin(SA6, Standard())+_n[6]};
+                TValueIter spos[7];
+                TSize tpos[7];
+                bool islast[7];
+
+                int a, b, rank[5];
+                int fill = 0;
+                TSize k = 0;
+
+                #define SEQAN_GET_ISKEW7(ii) (ii < _n[4] ? (ii * 7) + _o[4] : (ii < _n24 ? ((ii - _n[4]) * 7) + _o[2] : ((ii - _n24) * 7) + _o[1]))
+                #define SEQAN_GET_ASKEW7(ii) (ii < _n[4] ? 4 : (ii < _n24 ? 2 : 1))
+
+                // fill the stream ranking list
+                for(int i = 0; i < 7; ++i) {
+                    if (!_n[i]) continue;
+                    if (i == 2 || i == 4) continue; // insert only the least suffix of SA124
+
+                    if (i == 1) {
+
+                        TSize ii  = *(pos[1]);
+                        a         = SEQAN_GET_ASKEW7(ii);
+                        TSize j      = SEQAN_GET_ISKEW7(ii);
+
+                        tpos[a]   = ii;
+                        spos[a]   = begin(s, Standard()) + j;
+                        islast[a] = (j + 7 >= n);
+
+                    } else {
+
+                        a = i;
+                        TSize j   = *(pos[a]);
+
+                        tpos[a]   = j / 7;
+                        spos[a]   = begin(s, Standard()) + j;
+                        islast[a] = (j + 7 >= n);
+
+                    }
+
+                    // get the rank of stream a's suffix
+                    int j;
+                    for(j = 0;  j < fill;  ++j) {
+                        b = rank[j];
+                        if (_leqSkew7 (a,  b,   spos, tpos, islast, s124, adjust)) break;
+                    }
+
+                    // insert the suffix
+                    for(int i = fill; i > j; --i)
+                        rank[i] = rank[i-1];
+                    rank[j] = a;
+                    fill++;
+                }
+
+                // main merge loop
+                // in order to find the least suffix in every step we use a stream ranking list
+                // so we only need to keep up the ordering and thus rank[0] is always the least suffix
+                while (fill > 1) {
+
+                    // add the least suffix to SA and get the next of the corresponding stream
+                    a = rank[0];
+                    SA[k++] = spos[a] - begin(s, Standard());
+                    if (a == 1 || a == 2 || a == 4)
+                        pos[4] = pos[2] = ++pos[1];
+                    else
+                        ++pos[a];
+
+                    if (pos[a] < max[a]) {
+
+                        // set corresponding spos, tpos, islast values and adapt a if necessary
+                        if (a == 1 || a == 2 || a == 4) {
+
+                            TSize ii  = *(pos[1]);
+                            a          = SEQAN_GET_ASKEW7(ii);
+                            TSize j   = SEQAN_GET_ISKEW7(ii);
+
+                            tpos[a]   = ii;
+                            spos[a]   = begin(s, Standard()) + j;
+                            islast[a] = (j + 7 >= n);
+
+                        } else {
+
+                            TSize j   = *(pos[a]);
+
+                            tpos[a]   = j / 7;
+                            spos[a]   = begin(s, Standard()) + j;
+                            islast[a] = (j + 7 >= n);
+
+                        }
+
+                        // get the rank of stream a's suffix
+
+                        // linear search
+                        int right;
+                        for(right = 1;  right < fill;  right++) {
+                            b = rank[right];
+                            if (_leqSkew7 (a,  b,   spos, tpos, islast, s124, adjust)) break;
+                        }
 /*
-						// binary search
-						int left = 0;
-						int right = fill;
-						while (left + 1 != right) {
-							int middle = (left + right) >> 2;
-							if (leq<TValue, TSize> (a,  rank[middle],   spos, tpos, islast, s124, adjust))
-								right = middle;
-							else
-								left = middle;
-						}*/
-
-						// remove the least suffix ...
-						for(int i = 1; i < right; ++i)
-							rank[i-1] = rank[i];
-
-						// ... and insert the new one
-						rank[right-1] = a;
-
-					} else {
-						// only remove the least suffix
-						fill--;
-						for(int i = 0; i < fill; ++i)
-							rank[i] = rank[i+1];
-					}
-				}
-
-				// only one (or less) stream left to fill SA with
-				a = rank[0];
-				if (a == 1 || a == 2 || a == 4)
-					for (;  k < n;  ++k) { TSize ii = *(pos[1]++); SA[k] = SEQAN_GET_ISKEW7(ii); }
-				else
-					for (;  k < n;  ++k) SA[k] = *(pos[a]++);
-			}	    
-		}
+                        // binary search
+                        int left = 0;
+                        int right = fill;
+                        while (left + 1 != right) {
+                            int middle = (left + right) >> 2;
+                            if (leq<TValue, TSize> (a,  rank[middle],   spos, tpos, islast, s124, adjust))
+                                right = middle;
+                            else
+                                left = middle;
+                        }*/
+
+                        // remove the least suffix ...
+                        for(int i = 1; i < right; ++i)
+                            rank[i-1] = rank[i];
+
+                        // ... and insert the new one
+                        rank[right-1] = a;
+
+                    } else {
+                        // only remove the least suffix
+                        fill--;
+                        for(int i = 0; i < fill; ++i)
+                            rank[i] = rank[i+1];
+                    }
+                }
+
+                // only one (or less) stream left to fill SA with
+                a = rank[0];
+                if (a == 1 || a == 2 || a == 4)
+                    for (;  k < n;  ++k) { TSize ii = *(pos[1]++); SA[k] = SEQAN_GET_ISKEW7(ii); }
+                else
+                    for (;  k < n;  ++k) SA[k] = *(pos[a]++);
+            }
+        }
         SEQAN_PROMARK("SA124, SA3, SA5, SA6, SA0 verschmolzen");
 
         #ifdef SEQAN_DEBUG_INDEX
@@ -875,28 +875,28 @@ namespace SEQAN_NAMESPACE_MAIN
         #endif
         SEQAN_PROMARK("Rekursionsaufstieg");
         SEQAN_PROSUB(SEQAN_PRODEPTH, 1);
-	}
+    }
 
     template < typename TSA,
                typename TText >
     inline void createSuffixArray(
-		TSA &SA,
-		TText &s,
-		Skew7 const &alg,
-		unsigned K,
+        TSA &SA,
+        TText &s,
+        Skew7 const &alg,
+        unsigned K,
         unsigned maxdepth)
-	{
-		createSuffixArray(SA, s, alg, K, maxdepth, 1);
-	}
+    {
+        createSuffixArray(SA, s, alg, K, maxdepth, 1);
+    }
 
     // creates suffix array sorted by the first maxLCP chars of suffixes
     template < typename TSA,
                typename TText,
                typename TSize >
     inline void createSuffixArrayPart(
-		TSA &SA,
-		TText &s,
-		Skew7 const &_dummy,
+        TSA &SA,
+        TText &s,
+        Skew7 const &_dummy,
         TSize maxLCP,
         unsigned K)
     {
@@ -911,13 +911,13 @@ namespace SEQAN_NAMESPACE_MAIN
                typename TText,
                typename TSize >
     inline void createSuffixArrayPart(
-		TSA &SA,
-		TText &s,
-		Skew7 const &_dummy,
+        TSA &SA,
+        TText &s,
+        Skew7 const &_dummy,
         TSize maxLCP)
     {
-    	SEQAN_CHECKPOINT;
-    	createSuffixArrayPart(SA, s, _dummy, maxLCP, ValueSize< typename Value<TText>::Type >::VALUE);
+        SEQAN_CHECKPOINT;
+        createSuffixArrayPart(SA, s, _dummy, maxLCP, ValueSize< typename Value<TText>::Type >::VALUE);
     }
 //}
 
diff --git a/seqan/index/index_skew7_multi.h b/seqan/index/index_skew7_multi.h
index 6a90f7b..99ccaba 100644
--- a/seqan/index/index_skew7_multi.h
+++ b/seqan/index/index_skew7_multi.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,11 +40,11 @@ namespace SEQAN_NAMESPACE_MAIN
 
     //////////////////////////////////////////////////////////////////////////////
     // external Skew7 algorithm (optimized for multiple sequences)
-	//  - creates a suffix array of pairs (seqNo,seqPos)
+    //  - creates a suffix array of pairs (seqNo,seqPos)
     //////////////////////////////////////////////////////////////////////////////
 
 
-	template < typename TInput, typename TPair, typename TLimitsString >
+    template < typename TInput, typename TPair, typename TLimitsString >
     struct Value< Pipe< TInput, Multi<Skew7, TPair, TLimitsString> > >
     {
         typedef TPair Type;
@@ -52,23 +52,23 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
     // *** COMPARATORS & MAPS ***
-        
+
     template <typename TValue, typename TResult = int>
     struct _skew7NCompMulti : public std::binary_function<TValue, TValue, TResult> {
         inline TResult operator() (const TValue &a, const TValue &b) const
         {
-			typedef typename Value<TValue, 1>::Type                 TPos;
-			typedef typename Value<TPos, 2>::Type                   TSize;
+            typedef typename Value<TValue, 1>::Type                 TPos;
+            typedef typename Value<TPos, 2>::Type                   TSize;
             typedef typename Value<TValue, 2>::Type                 TSeptet;
             typedef typename Value<TSeptet>::Type                   TSeptetValue;
             typedef typename StoredTupleValue_<TSeptetValue>::Type  TStoredValue;
-            
+
             const TStoredValue *sa = a.i2.i;
             const TStoredValue *sb = b.i2.i;
 
             TSize n = LENGTH<TSeptet>::VALUE;
-			TSize aLeft = getValueI2(getValueI1(a));
-			TSize bLeft = getValueI2(getValueI1(b));
+            TSize aLeft = getValueI2(getValueI1(a));
+            TSize bLeft = getValueI2(getValueI1(b));
             if (aLeft < n) n = aLeft;
             if (bLeft < n) n = bLeft;
 
@@ -82,9 +82,9 @@ namespace SEQAN_NAMESPACE_MAIN
             if (n < LENGTH<TSeptet>::VALUE)
             {
                 // overlap is equal, now suffix lengths decide
-				if (aLeft < bLeft) return -1;
-				if (aLeft > bLeft) return 1;
-				return (getValueI1(getValueI1(a)) > getValueI1(getValueI1(b)))? -1 : 1;
+                if (aLeft < bLeft) return -1;
+                if (aLeft > bLeft) return 1;
+                return (getValueI1(getValueI1(a)) > getValueI1(getValueI1(b)))? -1 : 1;
             }
 
             return 0;
@@ -97,117 +97,117 @@ namespace SEQAN_NAMESPACE_MAIN
         public std::binary_function<
             Pair<T1, Tuple<TValue, 7, BitPacked<> >, Pack >,
             Pair<T1, Tuple<TValue, 7, BitPacked<> >, Pack >,
-            TResult> {       
+            TResult> {
         inline TResult operator() (
             const Pair<T1, Tuple<TValue, 7, BitPacked<> >, Pack > &a,
             const Pair<T1, Tuple<TValue, 7, BitPacked<> >, Pack > &b) const
         {
             typedef typename Value<T1, 2>::Type TSize;
-			TSize aLeft = getValueI2(getValueI1(a));
-			TSize bLeft = getValueI2(getValueI1(b));
+            TSize aLeft = getValueI2(getValueI1(a));
+            TSize bLeft = getValueI2(getValueI1(b));
 
-			if (aLeft >= 7 && bLeft >= 7)
+            if (aLeft >= 7 && bLeft >= 7)
             {
-				if (a.i2 < b.i2) return -1;
-				if (a.i2 > b.i2) return 1;
-				return 0;
-			}
+                if (a.i2 < b.i2) return -1;
+                if (a.i2 > b.i2) return 1;
+                return 0;
+            }
 
             TSize n = 7;
-			if (aLeft < n) n = aLeft;
+            if (aLeft < n) n = aLeft;
             if (bLeft < n) n = bLeft;
 
             // compare the overlap of septets (the first n bases)
             for(TSize i = 0; i < n; i++)
             {
-				if (a.i2[i] == b.i2[i]) continue;
-				return (a.i2[i] < b.i2[i])? -1 : 1;
-			}
+                if (a.i2[i] == b.i2[i]) continue;
+                return (a.i2[i] < b.i2[i])? -1 : 1;
+            }
 
             // overlap is equal, now suffix lengths decide
-			if (aLeft < bLeft) return -1;
-			if (aLeft > bLeft) return 1;
-			return (getValueI1(getValueI1(a)) > getValueI1(getValueI1(b)))? -1 : 1;
+            if (aLeft < bLeft) return -1;
+            if (aLeft > bLeft) return 1;
+            return (getValueI1(getValueI1(a)) > getValueI1(getValueI1(b)))? -1 : 1;
         }
     };
 
-	template <
-		typename TValue,
+    template <
+        typename TValue,
         typename TLimitsString,
         typename TResultSize = typename Value<TLimitsString>::Type,
-		typename TResult = Pair<TResultSize, typename Value<TValue,2>::Type, typename Spec<TValue>::Type>
+        typename TResult = Pair<TResultSize, typename Value<TValue,2>::Type, typename Spec<TValue>::Type>
     >
     struct _skew7GlobalSlicedMulti :
-		public std::unary_function<TValue, TResult>
+        public std::unary_function<TValue, TResult>
     {
-    
-		typedef TResultSize TSize;
-
-		TSize			n4, n2, n1;
-		TSize			n24;
-		TLimitsString	off[5];
-
-		_skew7GlobalSlicedMulti(TLimitsString const &limits)
-		{
-			typename Iterator<TLimitsString const>::Type it = begin(limits), itEnd = end(limits);
-
-			n4 = n2 = n1 = n24 = 0;
-
-			if (it == itEnd) return;
-
-			// count the numbers of septets in residue class 1, 2, and 4
-			
-			TSize size, cur;
-			TSize old = *it; ++it;
-
-			while (it != itEnd) {
-				cur = *it;
-				size = cur - old;
-				old = cur;
-				
-				n4 += (size + 3) / 7;
-				n2 += (size + 5) / 7;
-				n1 += (size + 6) / 7;
-
-				++it;
-			}
-
-			n24 = n2 + n4;
-
-			// precompute the begin positions (off) of septet names 
-			// in the sliced string for every sequence and every residue class
-
-			resize(off[1], length(limits) - 1);
-			resize(off[2], length(limits) - 1);
-			resize(off[4], length(limits) - 1);
-
-			it = begin(limits);
-			old = *it; ++it;
-
-			TSize seqNo = 0;
-			TSize off4 = 0, off2 = n4, off1 = n24;
-			while (it != itEnd) {
-				cur = *it;
-				size = cur - old;
-				old = cur;
-				
-				off4 += (size + 3) / 7;
-				off2 += (size + 5) / 7;
-				off1 += (size + 6) / 7;
-
-				off[4][seqNo] = (off4)? off4-1 : 0;
-				off[2][seqNo] = (off2)? off2-1 : 0;
-				off[1][seqNo] = (off1)? off1-1 : 0;
-
-				++it; ++seqNo;
-			}
-		}
-
-		inline TResult operator() (const TValue &x) const {
-			typename Value<TValue,1>::Type x_i1 = x.i1;
-			TSize seqOfs = getValueI2(x_i1);
-			return TResult(off[seqOfs % 7][getValueI1(x_i1)] - seqOfs/7, x.i2);
-		}
+
+        typedef TResultSize TSize;
+
+        TSize            n4, n2, n1;
+        TSize            n24;
+        TLimitsString    off[5];
+
+        _skew7GlobalSlicedMulti(TLimitsString const &limits)
+        {
+            typename Iterator<TLimitsString const, Standard>::Type it = begin(limits, Standard()), itEnd = end(limits, Standard());
+
+            n4 = n2 = n1 = n24 = 0;
+
+            if (it == itEnd) return;
+
+            // count the numbers of septets in residue class 1, 2, and 4
+
+            TSize size, cur;
+            TSize old = *it; ++it;
+
+            while (it != itEnd) {
+                cur = *it;
+                size = cur - old;
+                old = cur;
+
+                n4 += (size + 3) / 7;
+                n2 += (size + 5) / 7;
+                n1 += (size + 6) / 7;
+
+                ++it;
+            }
+
+            n24 = n2 + n4;
+
+            // precompute the begin positions (off) of septet names
+            // in the sliced string for every sequence and every residue class
+
+            resize(off[1], length(limits) - 1);
+            resize(off[2], length(limits) - 1);
+            resize(off[4], length(limits) - 1);
+
+            it = begin(limits, Standard());
+            old = *it; ++it;
+
+            TSize seqNo = 0;
+            TSize off4 = 0, off2 = n4, off1 = n24;
+            while (it != itEnd) {
+                cur = *it;
+                size = cur - old;
+                old = cur;
+
+                off4 += (size + 3) / 7;
+                off2 += (size + 5) / 7;
+                off1 += (size + 6) / 7;
+
+                off[4][seqNo] = (off4)? off4-1 : 0;
+                off[2][seqNo] = (off2)? off2-1 : 0;
+                off[1][seqNo] = (off1)? off1-1 : 0;
+
+                ++it; ++seqNo;
+            }
+        }
+
+        inline TResult operator() (const TValue &x) const {
+            typename Value<TValue,1>::Type x_i1 = x.i1;
+            TSize seqOfs = getValueI2(x_i1);
+            return TResult(off[seqOfs % 7][getValueI1(x_i1)] - seqOfs/7, x.i2);
+        }
     };
 
 
@@ -217,39 +217,39 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TInput, typename TPair_, typename TLimitsString >
     struct Pipe< TInput, Multi<Skew7, TPair_, TLimitsString> >
     {
-  
+
         // *** SPECIALIZATION ***
 
         // use packing if lessorequal 16 different values per char
         typedef typename MakePacked<TPair_>::Type TPair;
-        typedef typename IfC< 
-            (BitsPerValue<TypeOf_(TInput)>::VALUE > 0) && 
+        typedef typename IfC<
+            (BitsPerValue<TypeOf_(TInput)>::VALUE > 0) &&
             (BitsPerValue<TypeOf_(TInput)>::VALUE <= 4),
             BitPacked<>,
             Pack>::Type TPack;
 
         // step 1
-		typedef Pipe< TInput, Multi<Sampler<7, TPack>, TPair, TLimitsString> >  TSamplerDC7;
+        typedef Pipe< TInput, Multi<Sampler<7, TPack>, TPair, TLimitsString> >  TSamplerDC7;
                                         typedef _skew7NCompMulti<TypeOf_(TSamplerDC7)> ncomp_t;
         typedef Pool< TypeOf_(TSamplerDC7), SorterSpec< SorterConfigSize<ncomp_t, TSizeOf_(TSamplerDC7) > > > TSortTuples;
-		typedef Pipe< TSortTuples, Namer<ncomp_t> > TNamer;
+        typedef Pipe< TSortTuples, Namer<ncomp_t> > TNamer;
                                         typedef _skew7GlobalSlicedMulti<TypeOf_(TNamer), TLimitsString, TSizeOf_(TNamer)> func_slice_t;
 
-		typedef Pipe< TNamer, Filter<func_slice_t> > TSlicedPos;
+        typedef Pipe< TNamer, Filter<func_slice_t> > TSlicedPos;
         typedef Pool< TypeOf_(TSlicedPos), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TSlicedPos)>, TSizeOf_(TSlicedPos) > > > TNames_Sliced;
 
         // non-unique names
         typedef Pipe< TNames_Sliced, Filter< filterI2<TypeOf_(TNames_Sliced)> > > TFilter;
 
-			// recursion
-			typedef Pipe< TFilter, Skew7 > TRecurse;
-			typedef Pipe< TRecurse, Counter > TRenamer;
+            // recursion
+            typedef Pipe< TFilter, Skew7 > TRecurse;
+            typedef Pipe< TRecurse, Counter > TRenamer;
 
-			// no recursion inMemory shortcut
-			typedef Pipe< TFilter, LarssonSadakane > TInMem;
-			typedef Pipe< TInMem, Counter > TRenamerInMem;
+            // no recursion inMemory shortcut
+            typedef Pipe< TFilter, LarssonSadakane > TInMem;
+            typedef Pipe< TInMem, Counter > TRenamerInMem;
 
-		typedef Pool< TypeOf_(TRenamer), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TRenamer)>, TSizeOf_(TRenamer) > > > TNames_Linear;
+        typedef Pool< TypeOf_(TRenamer), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TRenamer)>, TSizeOf_(TRenamer) > > > TNames_Linear;
 
         // step 2
         typedef Pipe< Bundle2< TInput, TNames_Linear >, Extender7Multi<TPair, TPack> > TExtender;
@@ -264,37 +264,37 @@ namespace SEQAN_NAMESPACE_MAIN
 
         // step 3
                                         typedef _skew7NMapExtended<TypeOf_(typename TExtender::Out124)> nmap_extended_t;
-		typedef Pool< TypeOf_(typename TExtender::Out124), MapperSpec< MapperConfigSize< nmap_extended_t, TSizeOf_(typename TExtender::Out124) > > > TSorterS124;
+        typedef Pool< TypeOf_(typename TExtender::Out124), MapperSpec< MapperConfigSize< nmap_extended_t, TSizeOf_(typename TExtender::Out124) > > > TSorterS124;
         typedef Pipe< Bundle5< TSorterS0, TSorterS3, TSorterS5, TSorterS6, TSorterS124 >, Merger7Multi<TLimitsString> > TMerger;
 
-        TSorterS0			sortedS0;
-        TSorterS3			sortedS3;
-        TSorterS5			sortedS5;
-        TSorterS6			sortedS6;
-        TSorterS124			sortedS124;
-        TMerger				in;
-		TLimitsString       const &limits;
+        TSorterS0            sortedS0;
+        TSorterS3            sortedS3;
+        TSorterS5            sortedS5;
+        TSorterS6            sortedS6;
+        TSorterS124            sortedS124;
+        TMerger                in;
+        TLimitsString       const &limits;
 
         // (weese): The SEQAN_CTOR_ENABLE_IF is necessary to avoid implicit casts and references to temporaries
 
         template <typename TLimitsString_>
         Pipe(TLimitsString_ const &_limits, SEQAN_CTOR_ENABLE_IF(IsSameType<TLimitsString, TLimitsString_>)) :
-			in(bundle5(sortedS0, sortedS3, sortedS5, sortedS6, sortedS124), _limits),
-			limits(_limits)
+            in(bundle5(sortedS0, sortedS3, sortedS5, sortedS6, sortedS124), _limits),
+            limits(_limits)
         {
             ignoreUnusedVariableWarning(dummy);
         }
 
         template <typename TLimitsString_>
         Pipe(TInput& _textIn, TLimitsString_ const &_limits, SEQAN_CTOR_ENABLE_IF(IsSameType<TLimitsString, TLimitsString_>)) :
-			in(bundle5(sortedS0, sortedS3, sortedS5, sortedS6, sortedS124), _limits),
-			limits(_limits)
-		{
+            in(bundle5(sortedS0, sortedS3, sortedS5, sortedS6, sortedS124), _limits),
+            limits(_limits)
+        {
             ignoreUnusedVariableWarning(dummy);
-			process(_textIn);
-		}
-        
-	    template < typename TInput_ >
+            process(_textIn);
+        }
+
+        template < typename TInput_ >
         bool process(TInput_ &textIn) {
 
             SEQAN_PROADD(SEQAN_PRODEPTH, 1);
@@ -317,40 +317,40 @@ namespace SEQAN_NAMESPACE_MAIN
             sorter << sampler;
             SEQAN_PROMARK("Sorter (2) - sort 7-mers");
 
-			TNamer                      namer(sorter);
-            func_slice_t				func_slice(limits);
+            TNamer                      namer(sorter);
+            func_slice_t                func_slice(limits);
 
-			TSlicedPos					slicedPos(namer, func_slice);
+            TSlicedPos                    slicedPos(namer, func_slice);
             TNames_Sliced               names_sliced;
             #ifdef SEQAN_DEBUG_INDEX
                 std::cerr << "  slice names" << std::endl;
             #endif
             names_sliced << slicedPos;
 
-			if (namer.unique() || empty(names_sliced)) {
+            if (namer.unique() || empty(names_sliced)) {
                 // unique names
 
                 clear(sorter);
                 SEQAN_PROMARK("Mapper (4) - construct s124");
 
-				TNames_Linear               names_S1, names_S2, names_S4;
+                TNames_Linear               names_S1, names_S2, names_S4;
 
                 #ifdef SEQAN_DEBUG_INDEX
                     std::cerr << "  make names linear" << std::endl;
                 #endif
 
-				_skew7SeparateSlices(
-					names_sliced, func_slice, 
-					names_S1, names_S2, names_S4);
+                _skew7SeparateSlices(
+                    names_sliced, func_slice,
+                    names_S1, names_S2, names_S4);
 
-				clear(names_sliced);
+                clear(names_sliced);
                 SEQAN_PROMARK("Mapper (10) - construct ISA124");
 
                 // step 2
                 _skew7ExtendMulti(
-					textIn, limits, 
-					names_S1, names_S2, names_S4, 
-					sortedS0, sortedS3, sortedS5, sortedS6, sortedS124);
+                    textIn, limits,
+                    names_S1, names_S2, names_S4,
+                    sortedS0, sortedS3, sortedS5, sortedS6, sortedS124);
 
             } else {
                 // non-unique names
@@ -359,58 +359,58 @@ namespace SEQAN_NAMESPACE_MAIN
                 SEQAN_PROMARK("Mapper (4) - construct s124");
 
                 TFilter                     filter(names_sliced);
-				TNames_Linear               names_S1, names_S2, names_S4;
-
-//				if (length(filter) > 128*1024*1024) 
-				{
-					// recursion
-					TRecurse                    recurse(filter);
-
-					#ifdef SEQAN_TEST_SKEW7
-					{
-						String<typename Value<TFilter>::Type, Alloc<> > _text;
-						_text << filter;
-						SEQAN_ASSERT(isSuffixArray(recurse, _text));
-					}
-					#endif
-
-					clear(filter);
-					TRenamer                    renamer(recurse);
-
-					// partition SA by residue classes
-
-					#ifdef SEQAN_DEBUG_INDEX
-						std::cerr << "  rename names" << std::endl;
-					#endif
-
-					_skew7SeparateSlices(
-						renamer, func_slice, 
-						names_S1, names_S2, names_S4);
-				} 
-/*				else
-				{
-					TInMem						inMem(filter);
-					clear(filter);
-					TRenamerInMem               renamer(inMem);
-					_skew7SeparateSlices(
-						renamer, func_slice, 
-						names_S1, names_S2, names_S4);
-				} 
+                TNames_Linear               names_S1, names_S2, names_S4;
+
+//                if (length(filter) > 128*1024*1024)
+                {
+                    // recursion
+                    TRecurse                    recurse(filter);
+
+                    #ifdef SEQAN_TEST_SKEW7
+                    {
+                        String<typename Value<TFilter>::Type, Alloc<> > _text;
+                        _text << filter;
+                        SEQAN_ASSERT(isSuffixArray(recurse, _text));
+                    }
+                    #endif
+
+                    clear(filter);
+                    TRenamer                    renamer(recurse);
+
+                    // partition SA by residue classes
+
+                    #ifdef SEQAN_DEBUG_INDEX
+                        std::cerr << "  rename names" << std::endl;
+                    #endif
+
+                    _skew7SeparateSlices(
+                        renamer, func_slice,
+                        names_S1, names_S2, names_S4);
+                }
+/*                else
+                {
+                    TInMem                        inMem(filter);
+                    clear(filter);
+                    TRenamerInMem               renamer(inMem);
+                    _skew7SeparateSlices(
+                        renamer, func_slice,
+                        names_S1, names_S2, names_S4);
+                }
 */
                 SEQAN_PROMARK("Mapper (10) - construct ISA124");
-               
+
                 // step 2
                 #ifdef SEQAN_DEBUG_INDEX
                     std::cerr << "  prepare merge" << std::endl;
                 #endif
                 _skew7ExtendMulti(
-					textIn, limits, 
-					names_S1, names_S2, names_S4, 
-					sortedS0, sortedS3, sortedS5, sortedS6, sortedS124);
+                    textIn, limits,
+                    names_S1, names_S2, names_S4,
+                    sortedS0, sortedS3, sortedS5, sortedS6, sortedS124);
 
                 SEQAN_PROMARK("Mapper (12), Sorter (13-16) - merge SA124, SA3, SA5, SA6, SA0");
             }
- 
+
             // step 3
             // ... is done on-demand by merger
             }
@@ -426,17 +426,17 @@ namespace SEQAN_NAMESPACE_MAIN
         inline typename Value<Pipe>::Type const operator*() {
             return *in;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             return *this;
-        }        
+        }
     };
 
     // not sure which interface is more intuitive, we support both
     // you can call "skew << pipe" or "skew_t skew(pipe); skew.process()"
     // for the first we would need no _in member
-	template < typename TInput, typename TObject, typename TPair, typename TLimitsString >
+    template < typename TInput, typename TObject, typename TPair, typename TLimitsString >
     inline bool operator<<(Pipe< TInput, Multi<Skew7, TPair, TLimitsString> > &me, TObject &textIn) {
         return me.process(textIn);
     }
diff --git a/seqan/index/index_view.h b/seqan/index/index_view.h
new file mode 100644
index 0000000..d12a3ab
--- /dev/null
+++ b/seqan/index/index_view.h
@@ -0,0 +1,860 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// This file contains Index specializations for Views.
+// ==========================================================================
+
+#ifndef SEQAN_INDEX_VIEW_H_
+#define SEQAN_INDEX_VIEW_H_
+
+namespace seqan {
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction View                                                    [Index]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec>
+struct View<Index<TText, TSpec> >
+{
+    typedef Index<typename View<TText>::Type, TSpec>        Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RemoveView                                              [Index]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec>
+struct RemoveView<Index<TText, TSpec> >
+{
+    typedef Index<typename RemoveView<TText>::Type, TSpec>  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView                                                  [Index]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec>
+struct IsView<Index<TText, TSpec> > : IsView<TText> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction View                                                       [LF]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig>
+struct View<LF<TText, TSpec, TConfig> >
+{
+    typedef LF<typename View<TText>::Type, TSpec, TConfig>     Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction View                                             [CompressedSA]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig>
+struct View<CompressedSA<TText, TSpec, TConfig> >
+{
+    typedef CompressedSA<typename View<TText>::Type, TSpec, TConfig>    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction View                                           [RankDictionary]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct View<RankDictionary<TValue, Levels<TSpec, TConfig> > >
+{
+    typedef RankDictionary<TValue, Levels<View<TSpec>, TConfig> >        Type;
+};
+
+template <typename TValue, typename TSpec>
+struct View<RankDictionary<TValue, Naive<TSpec> > >
+{
+    typedef RankDictionary<TValue, Naive<View<TSpec> > >            Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction View                                             [SparseString]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+struct View<SparseString<TString, TSpec> >
+{
+    typedef SparseString<typename View<TString>::Type, TSpec>       Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction View                                                     [Iter]
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct View<Iter<TIndex, VSTree<TSpec> > >
+{
+    typedef Iter<typename View<TIndex>::Type, VSTree<TSpec> >       Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RemoveView                                               [Iter]
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct RemoveView<Iter<TIndex, VSTree<TSpec> > >
+{
+    typedef Iter<typename RemoveView<TIndex>::Type, VSTree<TSpec> > Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView                                                   [Iter]
+// ----------------------------------------------------------------------------
+
+template <typename TIndex, typename TSpec>
+struct IsView<Iter<TIndex, VSTree<TSpec> > > : IsView<TIndex> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreSA                                            [Index View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, TSpec>, FibreSA>
+{
+    typedef typename View<typename Fibre<Index<TText, TSpec>, FibreSA>::Type>::Type         Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, TSpec> const, FibreSA>
+{
+    typedef typename View<typename Fibre<Index<TText, TSpec> const, FibreSA>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec>, FibreSA>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, TSpec>, FibreSA>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const, FibreSA>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, TSpec> const, FibreSA>::Type>::Type     Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreLcp                                           [Index View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, TSpec>, FibreLcp>
+{
+    typedef typename View<typename Fibre<Index<TText, TSpec>, FibreLcp>::Type>::Type        Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, TSpec> const, FibreLcp>
+{
+    typedef typename View<typename Fibre<Index<TText, TSpec> const, FibreLcp>::Type>::Type  Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec>, FibreLcp>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, TSpec>, FibreLcp>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const, FibreLcp>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, TSpec> const, FibreLcp>::Type>::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreChildtab                                      [Index View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, TSpec>, FibreChildtab>
+{
+    typedef typename View<typename Fibre<Index<TText, TSpec>, FibreChildtab>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, TSpec> const, FibreChildtab>
+{
+    typedef typename View<typename Fibre<Index<TText, TSpec> const, FibreChildtab>::Type>::Type Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec>, FibreChildtab>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, TSpec>, FibreChildtab>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const, FibreChildtab>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, TSpec> const, FibreChildtab>::Type>::Type   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreBwt                                           [Index View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, TSpec>, FibreBwt>
+{
+    typedef typename View<typename Fibre<Index<TText, TSpec>, FibreBwt>::Type>::Type        Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, TSpec> const, FibreBwt>
+{
+    typedef typename View<typename Fibre<Index<TText, TSpec> const, FibreBwt>::Type>::Type  Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec>, FibreBwt>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, TSpec>, FibreBwt>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const, FibreBwt>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, TSpec> const, FibreBwt>::Type>::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member                                             [Index View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Member<Index<ContainerView<TText, TViewSpec>, TSpec>, FibreText>
+{
+    typedef typename Fibre<Index<ContainerView<TText, TViewSpec>, TSpec>, FibreText>::Type      Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec>
+struct Member<Index<ContainerView<TText, TViewSpec>, TSpec> const, FibreText>
+{
+    typedef typename Fibre<Index<ContainerView<TText, TViewSpec>, TSpec> const, FibreText>::Type    Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Member<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec>, FibreText>
+{
+    typedef typename Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec>, FibreText>::Type      Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+struct Member<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const, FibreText>
+{
+    typedef typename Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const, FibreText>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreSA                                          [FMIndex View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, FMIndex<TSpec, TConfig> >, FibreSA>
+{
+    typedef typename View<typename Fibre<Index<TText, FMIndex<TSpec, TConfig> >, FibreSA>::Type>::Type    Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<Index<ContainerView<TText, TViewSpec>, FMIndex<TSpec, TConfig> > const, FibreSA>
+{
+    typedef typename View<typename Fibre<Index<TText, FMIndex<TSpec, TConfig> > const, FibreSA>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, FMIndex<TSpec, TConfig> >, FibreSA>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, FMIndex<TSpec, TConfig> >, FibreSA>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, FMIndex<TSpec, TConfig> > const, FibreSA>
+{
+    typedef typename View<typename Fibre<Index<StringSet<TText, TSSetSpec>, FMIndex<TSpec, TConfig> > const, FibreSA>::Type>::Type     Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibrePrefixSums                                       [LF View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<ContainerView<TText, TViewSpec>, TSpec, TConfig>, FibrePrefixSums>
+{
+    typedef typename View<typename Fibre<LF<TText, TSpec, TConfig>, FibrePrefixSums>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<ContainerView<TText, TViewSpec>, TSpec, TConfig> const, FibrePrefixSums>
+{
+    typedef typename View<typename Fibre<LF<TText, TSpec, TConfig> const, FibrePrefixSums>::Type>::Type  Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig>, FibrePrefixSums>
+{
+    typedef typename View<typename Fibre<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig>, FibrePrefixSums>::Type>::Type  Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig> const, FibrePrefixSums>
+{
+    typedef typename View<typename Fibre<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> const, FibrePrefixSums>::Type>::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreBwt                                              [LF View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<ContainerView<TText, TViewSpec>, TSpec, TConfig>, FibreBwt>
+{
+    typedef typename View<typename Fibre<LF<TText, TSpec, TConfig>, FibreBwt>::Type>::Type   Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<ContainerView<TText, TViewSpec>, TSpec, TConfig> const, FibreBwt>
+{
+    typedef typename View<typename Fibre<LF<TText, TSpec, TConfig> const, FibreBwt>::Type>::Type     Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig>, FibreBwt>
+{
+    typedef typename View<typename Fibre<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig>, FibreBwt>::Type>::Type  Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig> const, FibreBwt>
+{
+    typedef typename View<typename Fibre<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> const, FibreBwt>::Type>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreSentinels                                        [LF View]
+// ----------------------------------------------------------------------------
+
+// NOTE(esiragusa): Single text sentinel rank dictionary is an integer.
+//template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+//struct Fibre<LF<ContainerView<TText, TViewSpec>, TSpec>, FibreSentinels>
+//{
+//    typedef typename Fibre<LF<TText, TSpec, TConfig>, FibreSentinels>::Type   Type;
+//};
+
+template <typename TText, typename TSSetSpec, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig>, FibreSentinels>
+{
+    typedef typename View<typename Fibre<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig>, FibreSentinels>::Type>::Type  Type;
+};
+
+template <typename TText, typename TSSetSpec, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<LF<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig> const, FibreSentinels>
+{
+    typedef typename View<typename Fibre<LF<StringSet<TText, TSSetSpec>, TSpec, TConfig> const, FibreSentinels>::Type>::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Fibre                                     [RankDictionary View]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct Fibre<RankDictionary<TValue, Levels<View<TSpec>, TConfig> >, FibreRanks>
+{
+    typedef typename View<typename Fibre<RankDictionary<TValue, Levels<TSpec, TConfig> >, FibreRanks>::Type>::Type    Type;
+};
+
+template <typename TValue, typename TSpec, typename TConfig>
+struct Fibre<RankDictionary<TValue, Levels<View<TSpec>, TConfig> > const, FibreRanks>
+{
+    typedef typename View<typename Fibre<RankDictionary<TValue, Levels<TSpec, TConfig> > const, FibreRanks>::Type>::Type  Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Fibre<RankDictionary<TValue, Naive<View<TSpec> > >, FibreRanks>
+{
+    typedef typename View<typename Fibre<RankDictionary<TValue, Naive<TSpec> >, FibreRanks>::Type>::Type    Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Fibre<RankDictionary<TValue, Naive<View<TSpec> > > const, FibreRanks>
+{
+    typedef typename View<typename Fibre<RankDictionary<TValue, Naive<TSpec> > const, FibreRanks>::Type>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Fibre                                       [CompressedSA View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig>, FibreSparseString>
+{
+    typedef typename View<typename Fibre<CompressedSA<TText, TSpec, TConfig>, FibreSparseString>::Type>::Type    Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Fibre<CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig> const, FibreSparseString>
+{
+    typedef typename View<typename Fibre<CompressedSA<TText, TSpec, TConfig> const, FibreSparseString>::Type>::Type  Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig>, FibreSparseString>
+{
+    typedef typename View<typename Fibre<CompressedSA<StringSet<TText, TSSetSpec>, TSpec, TConfig>, FibreSparseString>::Type>::Type  Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Fibre<CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig> const, FibreSparseString>
+{
+    typedef typename View<typename Fibre<CompressedSA<StringSet<TText, TSSetSpec>, TSpec, TConfig> const, FibreSparseString>::Type>::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member                                      [CompressedSA View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+struct Member<CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig>, FibreLF>
+{
+    typedef typename Fibre<CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig>, FibreLF>::Type     Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+struct Member<CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig>, FibreLF>
+{
+    typedef typename Fibre<CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig>, FibreLF>::Type   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreIndicators                             [SparseString View]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+struct Fibre<SparseString<ContainerView<TString>, TSpec>, FibreIndicators>
+{
+    typedef typename View<typename Fibre<SparseString<TString, TSpec>, FibreIndicators>::Type>::Type        Type;
+};
+
+template <typename TString, typename TSpec>
+struct Fibre<SparseString<ContainerView<TString>, TSpec> const, FibreIndicators>
+{
+    typedef typename View<typename Fibre<SparseString<TString, TSpec> const, FibreIndicators>::Type>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FibreValues                                 [SparseString View]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+struct Fibre<SparseString<ContainerView<TString>, TSpec>, FibreValues>
+{
+    typedef typename View<typename Fibre<SparseString<TString, TSpec>, FibreValues>::Type>::Type        Type;
+};
+
+template <typename TString, typename TSpec>
+struct Fibre<SparseString<ContainerView<TString>, TSpec> const, FibreValues>
+{
+    typedef typename View<typename Fibre<SparseString<TString, TSpec> const, FibreValues>::Type>::Type  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction HistoryStack_                                [VSTree Iter View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TIndexSpec, typename TSpec>
+struct HistoryStack_<Iter<Index<ContainerView<TText, TViewSpec>, TIndexSpec>, VSTree<TSpec> > >
+{
+    typedef Index<TText, TIndexSpec>                        TIndex_;
+    typedef Iter<TIndex_, VSTree<TSpec> >                   TIter_;
+    typedef typename HistoryStack_<TIter_>::Type            THistory_;
+    typedef ContainerView<THistory_, Resizable<TViewSpec> > Type;
+};
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TIndexSpec, typename TSpec>
+struct HistoryStack_<Iter<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TIndexSpec>, VSTree<TSpec> > >
+{
+    typedef Index<StringSet<TText, TSSetSpec>, TIndexSpec>  TIndex_;
+    typedef Iter<TIndex_, VSTree<TSpec> >                   TIter_;
+    typedef typename HistoryStack_<TIter_>::Type            THistory_;
+    typedef ContainerView<THistory_, Resizable<TViewSpec> > Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function getFibre()                                             [Index View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<ContainerView<TText, TViewSpec>, TSpec>, FibreText>::Type &
+getFibre(Index<ContainerView<TText, TViewSpec>, TSpec> & index, FibreText)
+{
+    return index.text;
+}
+
+template <typename TText, typename TViewSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<ContainerView<TText, TViewSpec>, TSpec> const, FibreText>::Type &
+getFibre(Index<ContainerView<TText, TViewSpec>, TSpec> const & index, FibreText)
+{
+    return index.text;
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec>, FibreText>::Type &
+getFibre(Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> & index, FibreText)
+{
+    return index.text;
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const, FibreText>::Type &
+getFibre(Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const & index, FibreText)
+{
+    return index.text;
+}
+
+template <typename TText, typename TViewSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<ContainerView<TText, TViewSpec>, TSpec>, FibreRawText>::Type &
+getFibre(Index<ContainerView<TText, TViewSpec>, TSpec> & index, FibreRawText)
+{
+    return concat(getFibre(index, FibreText()));
+}
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<ContainerView<TText, TViewSpec>, TSpec> const, FibreRawText>::Type &
+getFibre(Index<ContainerView<TText, TViewSpec>, TSpec> const & index, FibreRawText)
+{
+    return concat(getFibre(index, FibreText()));
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec>, FibreRawText>::Type &
+getFibre(Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> & index, FibreRawText)
+{
+    return concat(getFibre(index, FibreText()));
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Fibre<Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const, FibreRawText>::Type &
+getFibre(Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> const & index, FibreRawText)
+{
+    return concat(getFibre(index, FibreText()));
+}
+
+// ----------------------------------------------------------------------------
+// Function indexRequire()                                         [Index View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TFibre>
+SEQAN_HOST_DEVICE inline bool
+indexRequire(Index<ContainerView<TText, TViewSpec>, TSpec> & index, Tag<TFibre> const fibre)
+{
+    bool supplied = indexSupplied(index, fibre);
+    SEQAN_ASSERT_MSG(supplied, "Fibre must be supplied on a view.");
+    return supplied;
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TFibre>
+SEQAN_HOST_DEVICE inline bool
+indexRequire(Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> & index, Tag<TFibre> const fibre)
+{
+    bool supplied = indexSupplied(index, fibre);
+    SEQAN_ASSERT_MSG(supplied, "Fibre must be supplied on a view.");
+    return supplied;
+}
+
+// ----------------------------------------------------------------------------
+// Function indexRequire()                                       [FMIndex View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig, typename TFibre>
+SEQAN_HOST_DEVICE inline bool
+indexRequire(Index<ContainerView<TText, TViewSpec>, FMIndex<TSpec, TConfig> > & index, Tag<TFibre> const fibre)
+{
+    bool supplied = indexSupplied(index, fibre);
+    SEQAN_ASSERT_MSG(supplied, "Fibre must be supplied on a view.");
+    return supplied;
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig, typename TFibre>
+SEQAN_HOST_DEVICE inline bool
+indexRequire(Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, FMIndex<TSpec, TConfig> > & index, Tag<TFibre> const fibre)
+{
+    bool supplied = indexSupplied(index, fibre);
+    SEQAN_ASSERT_MSG(supplied, "Fibre must be supplied on a view.");
+    return supplied;
+}
+
+// ----------------------------------------------------------------------------
+// Function indexCreate()                                          [Index View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TFibre>
+SEQAN_HOST_DEVICE inline bool
+indexCreate(Index<ContainerView<TText, TViewSpec>, TSpec> & /* index */, Tag<TFibre> const /* fibre */)
+{
+    SEQAN_ASSERT_MSG(false, "Fibre cannot be created on a view.");
+    return false;
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TFibre>
+SEQAN_HOST_DEVICE inline bool
+indexCreate(Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec> & /* index */, Tag<TFibre> const /* fibre */)
+{
+    SEQAN_ASSERT_MSG(false, "Fibre cannot be created on a view.");
+    return false;
+}
+
+// ----------------------------------------------------------------------------
+// Function indexCreate()                                        [FMIndex View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig, typename TFibre>
+SEQAN_HOST_DEVICE inline bool
+indexCreate(Index<ContainerView<TText, TViewSpec>, FMIndex<TSpec, TConfig> > & /* index */, Tag<TFibre> const /* fibre */)
+{
+    SEQAN_ASSERT_MSG(false, "Fibre cannot be created on a view.");
+    return false;
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig, typename TFibre>
+SEQAN_HOST_DEVICE inline bool
+indexCreate(Index<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, FMIndex<TSpec, TConfig> > & /* index */, Tag<TFibre> const /* fibre */)
+{
+    SEQAN_ASSERT_MSG(false, "Fibre cannot be created on a view.");
+    return false;
+}
+
+// ----------------------------------------------------------------------------
+// Function getFibre()                                      [CompressedSA View]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig>, FibreLF>::Type &
+getFibre(CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig> & sa, FibreLF)
+{
+    return sa.lf;
+}
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig> const, FibreLF>::Type &
+getFibre(CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig> const & sa, FibreLF)
+{
+    return sa.lf;
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig>, FibreLF>::Type &
+getFibre(CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig> & sa, FibreLF)
+{
+    return sa.lf;
+}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig>
+SEQAN_HOST_DEVICE inline typename Fibre<CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig> const, FibreLF>::Type &
+getFibre(CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig> const & sa, FibreLF)
+{
+    return sa.lf;
+}
+
+// ----------------------------------------------------------------------------
+// Function setFibre()                                      [CompressedSA View]
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): setFibre() sets the same pointer of view().
+
+template <typename TText, typename TViewSpec, typename TSpec, typename TConfig, typename TLF>
+void setFibre(CompressedSA<ContainerView<TText, TViewSpec>, TSpec, TConfig> & /* sa */, TLF & /* lf */, FibreLF)
+{}
+
+template <typename TText, typename TViewSpec, typename TSSetSpec, typename TSpec, typename TConfig, typename TLF>
+void setFibre(CompressedSA<StringSet<ContainerView<TText, TViewSpec>, TSSetSpec>, TSpec, TConfig> & /* sa */, TLF & /* lf */, FibreLF)
+{}
+
+// ----------------------------------------------------------------------------
+// Function view()                                                      [Index]
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): view() of a generic Index is not useful and potentially dangerous.
+
+//template <typename TText, typename TSpec, typename TConfig>
+//Index<ContainerView<TText>, TSpec>
+//view(Index<TText, TSpec> & index)
+//{
+//    Index<ContainerView<TText>, TSpec> indexView;
+//
+//    indexText(indexView) = view(indexText(index));
+//
+//    return indexView;
+//}
+
+// ----------------------------------------------------------------------------
+// Function view()                                                    [IndexSa]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec>
+typename View<Index<TText, IndexSa<TSpec> > >::Type
+view(Index<TText, IndexSa<TSpec> > & index)
+{
+    typename View<Index<TText, IndexSa<TSpec> > >::Type indexView;
+
+    indexText(indexView) = view(indexText(index));
+    indexSA(indexView) = view(indexSA(index));
+
+    return indexView;
+}
+
+// ----------------------------------------------------------------------------
+// Function view()                                                   [IndexEsa]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec>
+typename View<Index<TText, IndexEsa<TSpec> > >::Type
+view(Index<TText, IndexEsa<TSpec> > & index)
+{
+    typename View<Index<TText, IndexEsa<TSpec> > >::Type indexView;
+
+    indexText(indexView) = view(indexText(index));
+    indexSA(indexView) = view(indexSA(index));
+    indexLcp(indexView) = view(indexLcp(index));
+    indexChildtab(indexView) = view(indexChildtab(index));
+    // TODO(esiragusa): View of cargo?
+
+    return indexView;
+}
+
+// ----------------------------------------------------------------------------
+// Function view()                                                    [FMIndex]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig>
+typename View<Index<TText, FMIndex<TSpec, TConfig> > >::Type
+view(Index<TText, FMIndex<TSpec, TConfig> > & index)
+{
+    typename View<Index<TText, FMIndex<TSpec, TConfig> > >::Type indexView;
+
+    indexText(indexView) = view(indexText(index));
+    indexLF(indexView) = view(indexLF(index));
+    indexSA(indexView) = view(indexSA(index));
+
+    return indexView;
+}
+
+// ----------------------------------------------------------------------------
+// Function view()                                                         [LF]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig>
+typename View<LF<TText, TSpec, TConfig> >::Type
+view(LF<TText, TSpec, TConfig> & lf)
+{
+    typename View<LF<TText, TSpec, TConfig> >::Type lfView;
+
+    getFibre(lfView, FibrePrefixSums()) = view(getFibre(lf, FibrePrefixSums()));
+    getFibre(lfView, FibreBwt()) = view(getFibre(lf, FibreBwt()));
+    getFibre(lfView, FibreSentinels()) = view(getFibre(lf, FibreSentinels()));
+    lfView.sentinelSubstitute = view(lf.sentinelSubstitute);
+
+    return lfView;
+}
+
+// ----------------------------------------------------------------------------
+// Function view()                                             [RankDictionary]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TConfig>
+typename View<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type
+view(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict)
+{
+    typename View<RankDictionary<TValue, Levels<TSpec, TConfig> > >::Type dictView;
+
+    getFibre(dictView, FibreRanks()) = view(getFibre(dict, FibreRanks()));
+    dictView._length = dict._length;
+
+    return dictView;
+}
+
+template <typename TValue, typename TSpec, typename TConfig>
+typename View<RankDictionary<TValue, Naive<TSpec> > >::Type
+view(RankDictionary<TValue, Naive<TSpec> > & dict)
+{
+    typename View<RankDictionary<TValue, Naive<TSpec> > >::Type dictView;
+
+    getFibre(dictView, FibreRanks()) = view(getFibre(dict, FibreRanks()));
+
+    return dictView;
+}
+
+// ----------------------------------------------------------------------------
+// Function view()                                               [CompressedSA]
+// ----------------------------------------------------------------------------
+
+template <typename TText, typename TSpec, typename TConfig>
+typename View<CompressedSA<TText, TSpec, TConfig> >::Type
+view(CompressedSA<TText, TSpec, TConfig> & sa)
+{
+    typename View<CompressedSA<TText, TSpec, TConfig> >::Type saView;
+
+    getFibre(saView, FibreLF()) = view(getFibre(sa, FibreLF()));
+    getFibre(saView, FibreSparseString()) = view(getFibre(sa, FibreSparseString()));
+
+    return saView;
+}
+
+// ----------------------------------------------------------------------------
+// Function view()                                               [SparseString]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec, typename TConfig>
+typename View<SparseString<TString, TSpec> >::Type
+view(SparseString<TString, TSpec> & sparseString)
+{
+    typename View<SparseString<TString, TSpec> >::Type sparseStringView;
+
+    getFibre(sparseStringView, FibreValues()) = view(getFibre(sparseString, FibreValues()));
+    getFibre(sparseStringView, FibreIndicators()) = view(getFibre(sparseString, FibreIndicators()));
+    sparseStringView._length = sparseString._length;
+
+    return sparseStringView;
+}
+
+}
+
+#endif  // #ifndef SEQAN_INDEX_VIEW_H_
diff --git a/seqan/index/index_wotd.h b/seqan/index/index_wotd.h
index 57d97c8..c24b7d2 100644
--- a/seqan/index/index_wotd.h
+++ b/seqan/index/index_wotd.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,2051 +42,2023 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 // wotd tree index fibres
 
-/**
-.Tag.WOTD Index Fibres
-..summary:Tag to select a specific fibre (e.g. table, object, ...) of an @Spec.IndexWotd@ index.
-..remarks:These tags can be used to get @Metafunction.Fibre.Fibres@ of an WOTD based @Spec.IndexWotd@.
-..remarks:TODO(holtgrew): Ask David.
-..cat:Index
-
-..tag.WotdText:The original text the index should be based on.
-...remarks:TODO(holtgrew): Ask David.
-
-..tag.WotdRawText:The raw text the index is really based on.
-...remarks:TODO(holtgrew): Ask David.
-
-..tag.WotdSA:The suffix array.
-...remarks:TODO(holtgrew): Ask David.
-
-..tag.WotdRawSA:The raw suffix array.
-...remarks:TODO(holtgrew): Ask David.
-
-..tag.WotdDir:The child table.
-...remarks:TODO(holtgrew): Ask David.
-
-..see:Metafunction.Fibre
-..see:Function.getFibre
-..see:Spec.IndexWotd
-..include:seqan/index.h
-*/
-/*! 
+/*!
  * @defgroup WOTDIndexFibres WOTD Index Fibres
- * 
  * @brief Tag to select a specific fibre (e.g. table, object, ...) of an @link
  *        IndexWotd @endlink index.
- * 
- * @section Remarks
- * 
- * These tags can be used to get @link Index#Fibre @endlink of an @link IndexWotd @endlink.
- * 
- * TODO(holtgrew): Ask David.
- * 
- * @see Index#Fibre
+ *
+ * These tags can be used to get @link Fibre @endlink of an @link IndexWotd @endlink.
+ *
+ * @see Fibre
  * @see Index#getFibre
  * @see IndexWotd
- * 
+ *
  * @tag WOTDIndexFibres#WotdDir
- * 
  * @brief The child table.
- * 
- * @section Remarks
- * 
- * TODO(holtgrew): Ask David.
- * 
+ *
  * @tag WOTDIndexFibres#WotdRawSA
- * 
  * @brief The raw suffix array.
- * 
- * @section Remarks
- * 
- * TODO(holtgrew): Ask David.
- * 
+ *
  * @tag WOTDIndexFibres#WotdText
- * 
  * @brief The original text the index should be based on.
- * 
- * @section Remarks
- * 
- * TODO(holtgrew): Ask David.
- * 
+ *
  * @tag WOTDIndexFibres#WotdRawText
- * 
  * @brief The raw text the index is really based on.
- * 
- * @section Remarks
- * 
- * TODO(holtgrew): Ask David.
- * 
+ *
  * @tag WOTDIndexFibres#WotdSA
- * 
  * @brief The suffix array.
- * 
- * @section Remarks
- * 
- * TODO(holtgrew): Ask David.
  */
-	typedef FibreText		WotdText;
-	typedef FibreRawText	WotdRawText;
-	typedef FibreSA         WotdSA;
-	typedef FibreRawSA		WotdRawSA;
-	typedef FibreDir		WotdDir;
 
-///.Spec.VSTree Iterator.param.TContainer.type:Spec.IndexWotd
-///.Spec.TopDown Iterator.param.TContainer.type:Spec.IndexWotd
-///.Spec.TopDownHistory Iterator.param.TContainer.type:Spec.IndexWotd
+//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn IndexWotd#indexSA
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(.., WotdSA)</tt>.
+ *
+ * @signature TSa indexSA(index);
+ *
+ * @param[in] index The @link IndexWotd @endlink object holding the fibre.
+ *
+ * @return TSa A reference to the @link WOTDIndexFibres#WotdSA @endlink fibre (partially sorted suffix array).
+ */
+
+/*!
+ * @fn IndexWotd#indexDir
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>getFibre(.., WotdDir())</tt>.
+ * @signature TFibre indexDir(index);
+ *
+ * @param[in] index The @link IndexWotd @endlink object holding the fibre.
+ *
+ * @return TFibre A reference to the @link WOTDIndexFibres#WotdDir @endlink fibre (tree structure).
+ */
+
+/*!
+ * @fn IndexWotd#saAt
+ * @headerfile <seqan/index.h>
+ * @note Advanced functionality, not commonly used.
+ * @brief Shortcut for <tt>value(indexSA(..), ..)</tt>.
+ *
+ * @signature TValue saAt(position, index);
+ *
+ * @param[in] index The @link IndexWotd @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TValue A reference or proxy to the value in the @link WOTDIndexFibres#WotdSA @endlink fibre.
+ *                To be more precise, a reference to a position containing a value of type
+ *                @link SAValue @endlink is returned (or a proxy).
+ */
+
+/*!
+ * @fn IndexWotd#dirAt
+ * @headerfile <seqan/index.h>
+ * @brief Shortcut for <tt>value(indexDir(index), position)</tt>.
+ *
+ * @signature TFibre dirAt(position, index);
+ *
+ * @param[in] index    The @link IndexWotd @endlink object holding the fibre.
+ * @param[in] position A position in the array on which the value should be accessed.
+ *
+ * @return TFibre A reference to the @link WOTDIndexFibres#WotdDir @endlink fibre.
+ */
+
+    typedef FibreText        WotdText;
+    typedef FibreRawText    WotdRawText;
+    typedef FibreSA         WotdSA;
+    typedef FibreRawSA        WotdRawSA;
+    typedef FibreDir        WotdDir;
 
 //////////////////////////////////////////////////////////////////////////////
 // wotd tree index
 
-/**
-.Spec.IndexWotd:
-..summary:This index represents a lazy suffix tree, meaning that a path from the tree of the index in only computed,
-if it is traversed. For details see Giegerich et al., "Efficient implementation of lazy suffix trees".
-..cat:Index
-..general:Class.Index
-..signature:Index<TText, IndexWotd<> >
-..param.TText:The text type.
-...type:Class.String
-..remarks:The fibres (see @Class.Index@ and @Metafunction.Fibre@) of this index are a partially sorted suffix array (see @Tag.WOTD Index Fibres.WotdSA@) and the wotd tree (see @Tag.WOTD Index Fibres.WotdDir@).
-..include:seqan/index.h
-*/
 /*!
  * @class IndexWotd
- * 
  * @extends Index
- * 
- * @headerfile seqan/index.h
- * 
- * @brief An index based on a lazy suffix tree (see Giegerich et al., "Efficient
- *        implementation of lazy suffix trees").
- * 
- * @signature Index<TText, IndexWotd<> >
- * 
- * @tparam TText The text type. Types: @link SequenceConcept @endlink
- * 
- * @section Remarks
- * 
- * The fibres (see @link Index @endlink and @link Index#Fibre @endlink) of this index
- * are a partially sorted suffix array (see @link WOTDIndexFibres#WotdSA
- * @endlink) and the wotd tree (see @link WOTDIndexFibres#WotdDir @endlink).
- * 
+ * @implements StringTreeConcept
+ * @headerfile <seqan/index.h>
+ * @brief An index based on a lazy suffix tree (see Giegerich et al., "Efficient implementation of lazy suffix
+ *        trees").
+ *
+ * @signature template <typename TText, typename TSpec>
+ *            class Index<TText, IndexWotd<TSpec> >;
+ *
+ * @tparam TText The @link TextConcept @endlink text type.
+ * @tparam TSpec The type for further specialization of the Index type.
+ *
+ * The fibres (see @link Index @endlink and @link Fibre @endlink) of this index are a partially sorted suffix array
+ * (see @link WOTDIndexFibres#WotdSA @endlink) and the wotd tree (see @link WOTDIndexFibres#WotdDir @endlink).
+ *
  * Demo: Demo.Constraint Iterator
- * 
+ *
  * @see WOTDIndexFibres
- */ 
+ */
 
-	struct WotdOriginal_;
-	typedef Tag<WotdOriginal_> const WotdOriginal;
+    struct WotdOriginal_;
+    typedef Tag<WotdOriginal_> const WotdOriginal;
 
-	template < typename TSpec = void >
-	struct IndexWotd {};
+    template < typename TSpec = void >
+    struct IndexWotd {};
 
 /*
-	template < typename TObject, typename TSpec >
-	struct Fibre< Index<TObject, IndexWotd<TSpec> >, FibreDir> 
-	{
-		typedef Index<TObject, IndexWotd<TSpec> > TIndex;
-		typedef String< 
-			typename typename Size<TIndex>::Type,
-			Alloc<>
-		> Type;
-	};
+    template < typename TObject, typename TSpec >
+    struct Fibre< Index<TObject, IndexWotd<TSpec> >, FibreDir>
+    {
+        typedef Index<TObject, IndexWotd<TSpec> > TIndex;
+        typedef String<
+            typename typename Size<TIndex>::Type,
+            Alloc<>
+        > Type;
+    };
 */
-	
-	template < typename TObject, typename TSpec >
-	class Index<TObject, IndexWotd<TSpec> > {
-	public:
-		typedef typename Fibre<Index, WotdText>::Type		TText;
-		typedef typename Fibre<Index, WotdSA>::Type         TSA;
-		typedef typename Fibre<Index, WotdDir>::Type		TDir;
-
-		typedef typename Value<Index>::Type					TValue;
-		typedef typename Value<TDir>::Type					TDirValue;
-		typedef typename Size<TText>::Type					TSize;
-		typedef String<TSize, Alloc<> >						TCounter;
-		typedef String<typename Value<TSA>::Type, Alloc<> >	TTempSA;
-		typedef typename Cargo<Index>::Type					TCargo;
-
-		// 1st word flags
-		static TDirValue const LEAF          = (TDirValue)1 << (BitsPerValue<TDirValue>::VALUE - 1); // this node is a leaf
-		static TDirValue const LAST_CHILD    = (TDirValue)1 << (BitsPerValue<TDirValue>::VALUE - 2); // this node is the last child
-		// 2nd word flag
-		static TDirValue const UNEVALUATED   = (TDirValue)1 << (BitsPerValue<TDirValue>::VALUE - 1); // this node is partially evalutated and has no evaluated children
-		static TDirValue const SENTINELS     = (TDirValue)1 << (BitsPerValue<TDirValue>::VALUE - 2); // the children of this node have solely $-edges
-
-		static TDirValue const BITMASK0      = ~(LEAF | LAST_CHILD);
-		static TDirValue const BITMASK1      = ~(UNEVALUATED | SENTINELS);
-
-
-		Holder<TText>	text;	// underlying text
-		TSA				sa;		// suffix array sorted by the first q chars
-		TDir			dir;	// bucket directory
-		TCargo			cargo;	// user-defined cargo
-
-
-		TTempSA			tempSA;
-		TCounter		tempOcc;
-		TCounter		tempBound;
-
-		TSize			sentinelOcc;
-		TSize			sentinelBound;
-		bool			interSentinelNodes;	// should virtually one (true) $-sign or many (false) $_i-signs be appended to the strings in text 
-
-		Index():
-			interSentinelNodes(false) {}
-
-		Index(Index &other):
-			text(other.text),
-			sa(other.sa),
-			dir(other.dir),
-			cargo(other.cargo),
-			tempSA(other.tempSA),
-			tempBound(other.tempBound),
-			sentinelOcc(other.sentinelOcc),
-			sentinelBound(other.sentinelBound),
-			interSentinelNodes(other.interSentinelNodes) {}
-
-		Index(Index const &other):
-			text(other.text),
-			sa(other.sa),
-			dir(other.dir),
-			cargo(other.cargo),
-			tempSA(other.tempSA),
-			tempBound(other.tempBound),
-			sentinelOcc(other.sentinelOcc),
-			sentinelBound(other.sentinelBound),
-			interSentinelNodes(other.interSentinelNodes) {}
-
-		template <typename TText_>
-		Index(TText_ &_text):
-			text(_text),
-			interSentinelNodes(false) {}
-
-		template <typename TText_>
-		Index(TText_ const &_text):
-			text(_text),
-			interSentinelNodes(false) {}
-	};
+
+    template < typename TObject, typename TSpec >
+    class Index<TObject, IndexWotd<TSpec> > {
+    public:
+        typedef typename Fibre<Index, WotdText>::Type        TText;
+        typedef typename Fibre<Index, WotdSA>::Type         TSA;
+        typedef typename Fibre<Index, WotdDir>::Type        TDir;
+
+        typedef typename Value<Index>::Type                    TValue;
+        typedef typename Value<TDir>::Type                    TDirValue;
+        typedef typename Size<Index>::Type                    TSize;
+        typedef String<TSize, Alloc<> >                        TCounter;
+        typedef String<typename Value<TSA>::Type, Alloc<> >    TTempSA;
+        typedef typename Cargo<Index>::Type                    TCargo;
+
+        // 1st word flags
+        static TDirValue const LEAF          = (TDirValue)1 << (BitsPerValue<TDirValue>::VALUE - 1); // this node is a leaf
+        static TDirValue const LAST_CHILD    = (TDirValue)1 << (BitsPerValue<TDirValue>::VALUE - 2); // this node is the last child
+        // 2nd word flag
+        static TDirValue const UNEVALUATED   = (TDirValue)1 << (BitsPerValue<TDirValue>::VALUE - 1); // this node is partially evalutated and has no evaluated children
+        static TDirValue const SENTINELS     = (TDirValue)1 << (BitsPerValue<TDirValue>::VALUE - 2); // the children of this node have solely $-edges
+
+        static TDirValue const BITMASK0      = ~(LEAF | LAST_CHILD);
+        static TDirValue const BITMASK1      = ~(UNEVALUATED | SENTINELS);
+
+
+        Holder<TText>    text;    // underlying text
+        TSA                sa;        // suffix array sorted by the first q chars
+        TDir            dir;    // bucket directory
+        TCargo            cargo;    // user-defined cargo
+
+
+        TTempSA            tempSA;
+        TCounter        tempOcc;
+        TCounter        tempBound;
+
+        TSize            sentinelOcc;
+        TSize            sentinelBound;
+        bool            interSentinelNodes;    // should virtually one (true) $-sign or many (false) $_i-signs be appended to the strings in text
+
+        Index():
+            interSentinelNodes(false) {}
+
+        Index(Index &other) :
+            text(other.text),
+            sa(other.sa),
+            dir(other.dir),
+            cargo(other.cargo),
+            tempSA(other.tempSA),
+            tempBound(other.tempBound),
+            sentinelOcc(other.sentinelOcc),
+            sentinelBound(other.sentinelBound),
+            interSentinelNodes(other.interSentinelNodes) {}
+
+        Index(Index const &other) :
+            text(other.text),
+            sa(other.sa),
+            dir(other.dir),
+            cargo(other.cargo),
+            tempSA(other.tempSA),
+            tempBound(other.tempBound),
+            sentinelOcc(other.sentinelOcc),
+            sentinelBound(other.sentinelBound),
+            interSentinelNodes(other.interSentinelNodes) {}
+
+        template <typename TText_>
+        Index(TText_ &_text) :
+            text(_text),
+            sentinelOcc(0),
+            sentinelBound(0),
+            interSentinelNodes(false) {}
+
+        template <typename TText_>
+        Index(TText_ const &_text):
+            text(_text),
+            sentinelOcc(0),
+            sentinelBound(0),
+            interSentinelNodes(false) {}
+    };
 /*
     template < typename TText, typename TSpec >
     struct Value< Index<TText, IndexWotd<TSpec> > > {
-		typedef typename Value< typename Fibre< Index<TText, IndexWotd<TSpec> >, WotdRawText >::Type >::Type Type;
+        typedef typename Value< typename Fibre< Index<TText, IndexWotd<TSpec> >, WotdRawText >::Type >::Type Type;
     };
 
-	template < typename TText, typename TSpec >
+    template < typename TText, typename TSpec >
     struct Size< Index<TText, IndexWotd<TSpec> > > {
-		typedef typename Size< typename Fibre< Index<TText, IndexWotd<TSpec> >, WotdRawText >::Type >::Type Type;
+        typedef typename Size< typename Fibre< Index<TText, IndexWotd<TSpec> >, WotdRawText >::Type >::Type Type;
     };
 */
 
+template <typename TText, typename TSpec>
+SEQAN_CONCEPT_IMPL((Index<TText, IndexWotd<TSpec> >), (StringTreeConcept));
+
+template <typename TText, typename TSpec>
+SEQAN_CONCEPT_IMPL((Index<TText, IndexWotd<TSpec> > const), (StringTreeConcept));
 
 //////////////////////////////////////////////////////////////////////////////
 // default fibre creators
 
-	template < typename TText, typename TSpec >
-	struct DefaultIndexCreator<Index<TText, IndexWotd<TSpec> >, FibreDir> {
+    template < typename TText, typename TSpec >
+    struct DefaultIndexCreator<Index<TText, IndexWotd<TSpec> >, FibreDir> {
         typedef Default Type;
     };
 
-	template < typename TText, typename TSSetSpec, typename TSpec >
-	struct DefaultIndexCreator<Index<StringSet<TText, TSSetSpec>, IndexWotd<TSpec> >, FibreDir> {
+    template < typename TText, typename TSSetSpec, typename TSpec >
+    struct DefaultIndexCreator<Index<StringSet<TText, TSSetSpec>, IndexWotd<TSpec> >, FibreDir> {
         typedef Default Type;
     };
 
 //////////////////////////////////////////////////////////////////////////////
 // default finder
 
-	template < typename TText, typename TSpec >
-	struct DefaultFinder< Index<TText, IndexWotd<TSpec> > > {
-        typedef FinderSTree Type;	// standard suffix array finder is mlr-heuristic
+    template < typename TText, typename TSpec >
+    struct DefaultFinder< Index<TText, IndexWotd<TSpec> > >
+    {
+        typedef FinderSTree Type;    // standard wotd finder is tree based search
     };
 
 //////////////////////////////////////////////////////////////////////////////
 
 
-	template <typename TSize>
-	struct VertexWotdOriginal_ {
-		TSize		node;			// position of current node entry in directory
-		TSize		parentRepLen;	// representative length of parent node
-		TSize		edgeLen;		// length of edge above current node
-
-		VertexWotdOriginal_() {}
-		VertexWotdOriginal_(MinimalCtor):
-			parentRepLen(0),
-			edgeLen(0) 
-		{
-			_setSizeInval(node);
-		}
-	};
-
-	template <typename TSize>
-	struct VertexWotdModified_ {
-		TSize		node;			// position of current node entry in directory
-		TSize		parentRepLen;	// representative length of parent node
-		TSize		edgeLen;		// length of edge above current node
-		Pair<TSize> range;			// current SA interval of hits
-		TSize		parentRight;	// right boundary of parent node's range (allows to go right)
-
-		VertexWotdModified_() {}
-		VertexWotdModified_(MinimalCtor):
-			node(0),
-			parentRepLen(0),
-			edgeLen(0),
-			range(0,0),
-			parentRight(0) {}
-		VertexWotdModified_(Pair<TSize> const &otherRange, TSize otherParentRight):
-			node(0),
-			parentRepLen(0),
-			edgeLen(0),
-			range(otherRange),
-			parentRight(otherParentRight) {}
-	};
+    template <typename TSize>
+    struct VertexWotdOriginal_ {
+        TSize        node;            // position of current node entry in directory
+        TSize        parentRepLen;    // representative length of parent node
+        TSize        edgeLen;        // length of edge above current node
+
+        VertexWotdOriginal_() : node(0), parentRepLen(0), edgeLen(0) {}
+        VertexWotdOriginal_(MinimalCtor) : node(0), parentRepLen(0), edgeLen(0)
+        {
+            _setSizeInval(node);
+        }
+    };
+
+    template <typename TSize>
+    struct VertexWotdModified_ {
+        TSize        node;            // position of current node entry in directory
+        TSize        parentRepLen;    // representative length of parent node
+        TSize        edgeLen;        // length of edge above current node
+        Pair<TSize> range;            // current SA interval of hits
+        TSize        parentRight;    // right boundary of parent node's range (allows to go right)
+
+        VertexWotdModified_() :
+            node(0),
+            parentRepLen(0),
+            edgeLen(0),
+            range(0,0),
+            parentRight(0)
+        {}
+        VertexWotdModified_(MinimalCtor) :
+            node(0),
+            parentRepLen(0),
+            edgeLen(0),
+            range(0,0),
+            parentRight(0)
+        {}
+        VertexWotdModified_(Pair<TSize> const &otherRange, TSize otherParentRight) :
+            node(0),
+            parentRepLen(0),
+            edgeLen(0),
+            range(otherRange),
+            parentRight(otherParentRight)
+        {}
+    };
 
 //////////////////////////////////////////////////////////////////////////////
-///.Metafunction.VertexDescriptor.param.T.type:Spec.IndexWotd
-
-	template < typename TText >
-	struct VertexDescriptor< Index<TText, IndexWotd<WotdOriginal> > > {
-		typedef typename Size< Index<TText, IndexWotd<WotdOriginal> > >::Type TSize;
-		typedef VertexWotdOriginal_<TSize> Type;
-	};
-
-	template < typename TText, typename TSpec >
-	struct VertexDescriptor< Index<TText, IndexWotd<TSpec> > > {
-		typedef typename Size< Index<TText, IndexWotd<TSpec> > >::Type TSize;
-		typedef VertexWotdModified_<TSize> Type;
-	};
-
-	template < typename TText, typename TSpec >
-	void _indexRequireTopDownIteration(Index<TText, IndexWotd<TSpec> > &index) 
-	{
-		indexRequire(index, WotdDir());
-	}
+    template < typename TText >
+    struct VertexDescriptor< Index<TText, IndexWotd<WotdOriginal> > > {
+        typedef typename Size< Index<TText, IndexWotd<WotdOriginal> > >::Type TSize;
+        typedef VertexWotdOriginal_<TSize> Type;
+    };
+
+    template < typename TText, typename TSpec >
+    struct VertexDescriptor< Index<TText, IndexWotd<TSpec> > > {
+        typedef typename Size< Index<TText, IndexWotd<TSpec> > >::Type TSize;
+        typedef VertexWotdModified_<TSize> Type;
+    };
+
+    template < typename TText, typename TSpec >
+    void _indexRequireTopDownIteration(Index<TText, IndexWotd<TSpec> > &index)
+    {
+        indexRequire(index, WotdDir());
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // history stack functions
 
-	template <typename TSize>
-	struct HistoryStackWotdOriginal_
-	{
-		TSize		node;		// position of current node entry in directory
-		TSize		edgeLen;	// length of edge above current node
-	};
-
-	template <typename TSize>
-	struct HistoryStackWotdModified_
-	{
-		TSize		node;		// position of current node entry in directory
-		TSize		edgeLen;	// length of edge above current node
-		Pair<TSize> range;		// current SA interval of hits
-	};
-
-	template < typename TText, typename TSpec >
-	struct HistoryStackEntry_< Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > > 
-	{
-		typedef Index<TText, IndexWotd<WotdOriginal> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-		typedef HistoryStackWotdOriginal_<TSize>		Type;
-	};
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	struct HistoryStackEntry_< Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > >
-	{
-		typedef Index<TText, IndexWotd<TIndexSpec> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-		typedef HistoryStackWotdModified_<TSize>		Type;
-	};
-
-
-	template < typename TText, typename TSpec >
-	inline void 
-	_historyPush(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it) 
-	{
-		it._parentDesc = value(it);
-		value(it).parentRepLen += parentEdgeLength(it);
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline void 
-	_historyPush(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it) 
-	{
-		it._parentDesc = value(it);
-		value(it).parentRepLen += parentEdgeLength(it);
-		value(it).parentRight = value(it).range.i2;
-	}
-
-	template < typename TText, typename TSpec >
-	inline void 
-	_historyPush(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it) 
-	{
-		typedef typename Size< Index<TText, IndexWotd<WotdOriginal> > >::Type TSize;
-		TSize edgeLen = parentEdgeLength(it);
-		HistoryStackWotdOriginal_<TSize> entry = { value(it).node, edgeLen };
-		appendValue(it.history, entry);
-		value(it).parentRepLen += edgeLen;
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline void 
-	_historyPush(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it) 
-	{
-		typedef typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type TSize;
-		TSize edgeLen = parentEdgeLength(it);
-		HistoryStackWotdModified_<TSize> entry = { value(it).node, edgeLen, value(it).range };
-		appendValue(it.history, entry);
-		value(it).parentRepLen += edgeLen;
-		value(it).parentRight = value(it).range.i2;
-	}
+    template <typename TSize>
+    struct HistoryStackWotdOriginal_
+    {
+        TSize        node;        // position of current node entry in directory
+        TSize        edgeLen;    // length of edge above current node
+    };
+
+    template <typename TSize>
+    struct HistoryStackWotdModified_
+    {
+        TSize        node;        // position of current node entry in directory
+        TSize        edgeLen;    // length of edge above current node
+        Pair<TSize> range;        // current SA interval of hits
+    };
+
+    template < typename TText, typename TSpec >
+    struct HistoryStackEntry_< Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > >
+    {
+        typedef Index<TText, IndexWotd<WotdOriginal> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+        typedef HistoryStackWotdOriginal_<TSize>        Type;
+    };
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    struct HistoryStackEntry_< Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > >
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+        typedef HistoryStackWotdModified_<TSize>        Type;
+    };
+
+
+    template < typename TText, typename TSpec >
+    inline void
+    _historyPush(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it)
+    {
+        it._parentDesc = value(it);
+        value(it).parentRepLen += parentEdgeLength(it);
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline void
+    _historyPush(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it)
+    {
+        it._parentDesc = value(it);
+        value(it).parentRepLen += parentEdgeLength(it);
+        value(it).parentRight = value(it).range.i2;
+    }
+
+    template < typename TText, typename TSpec >
+    inline void
+    _historyPush(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it)
+    {
+        typedef typename Size< Index<TText, IndexWotd<WotdOriginal> > >::Type TSize;
+        TSize edgeLen = parentEdgeLength(it);
+        HistoryStackWotdOriginal_<TSize> entry = { value(it).node, edgeLen };
+        appendValue(it.history, entry);
+        value(it).parentRepLen += edgeLen;
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline void
+    _historyPush(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it)
+    {
+        typedef typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type TSize;
+        TSize edgeLen = parentEdgeLength(it);
+        HistoryStackWotdModified_<TSize> entry = { value(it).node, edgeLen, value(it).range };
+        appendValue(it.history, entry);
+        value(it).parentRepLen += edgeLen;
+        value(it).parentRight = value(it).range.i2;
+    }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.resizeVertexMap.param.index.type:Spec.IndexWotd
-///.Function.resizeVertexMap.class:Spec.IndexWotd
-
-	template < typename TText, typename TIndexSpec, typename TPropertyMap >
-	inline void
-	resizeVertexMap(
-		Index<TText, IndexWotd<TIndexSpec> > const& index,
-		TPropertyMap & pm)
-	{
-		resize(pm, length(indexDir(index)), Generous());
-	}
+    template < typename TText, typename TIndexSpec, typename TPropertyMap >
+    inline void
+    resizeVertexMap(
+        TPropertyMap & pm,
+        Index<TText, IndexWotd<TIndexSpec> > const& index)
+    {
+        resize(pm, length(indexDir(index)), Generous());
+    }
 
 /* // different interface compared to resizeVertexMap(graph, ...)
-	template < typename TText, typename TIndexSpec, typename TPropertyMap, typename TProperty >
-	inline void
-	resizeVertexMap(
-		Index<TText, IndexWotd<TIndexSpec> > const& index,
-		TPropertyMap & pm,
-		TProperty const & prop)
-	{
-		resize(pm, length(indexDir(index)), prop, Generous());
-	}
+    template < typename TText, typename TIndexSpec, typename TPropertyMap, typename TProperty >
+    inline void
+    resizeVertexMap(
+        Index<TText, IndexWotd<TIndexSpec> > const& index,
+        TPropertyMap & pm,
+        TProperty const & prop)
+    {
+        resize(pm, length(indexDir(index)), prop, Generous());
+    }
 */
-	template < typename TSize >
-	inline typename Id< VertexWotdOriginal_<TSize> const >::Type
-	_getId(VertexWotdOriginal_<TSize> const &desc) 
-	{
-		return desc.node;
-	}
-
-	template < typename TSize >
-	inline typename Id< VertexWotdOriginal_<TSize> >::Type
-	_getId(VertexWotdOriginal_<TSize> &desc) 
-	{
-		return _getId(const_cast<VertexWotdOriginal_<TSize> const &>(desc));
-	}
-
-	template < typename TSize >
-	inline typename Id< VertexWotdModified_<TSize> const >::Type
-	_getId(VertexWotdModified_<TSize> const &desc) 
-	{
-		return desc.node;
-	}
-
-	template < typename TSize >
-	inline typename Id< VertexWotdModified_<TSize> >::Type
-	_getId(VertexWotdModified_<TSize> &desc) 
-	{
-		return _getId(const_cast<VertexWotdModified_<TSize> const &>(desc));
-	}
+    template < typename TSize >
+    inline typename Id< VertexWotdOriginal_<TSize> const >::Type
+    _getId(VertexWotdOriginal_<TSize> const &desc)
+    {
+        return desc.node;
+    }
+
+    template < typename TSize >
+    inline typename Id< VertexWotdOriginal_<TSize> >::Type
+    _getId(VertexWotdOriginal_<TSize> &desc)
+    {
+        return _getId(const_cast<VertexWotdOriginal_<TSize> const &>(desc));
+    }
+
+    template < typename TSize >
+    inline typename Id< VertexWotdModified_<TSize> const >::Type
+    _getId(VertexWotdModified_<TSize> const &desc)
+    {
+        return desc.node;
+    }
+
+    template < typename TSize >
+    inline typename Id< VertexWotdModified_<TSize> >::Type
+    _getId(VertexWotdModified_<TSize> &desc)
+    {
+        return _getId(const_cast<VertexWotdModified_<TSize> const &>(desc));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template < typename TSize >
-	inline bool _isRoot(VertexWotdOriginal_<TSize> const &value) {
-//IOREV_notio_
-		return value.node == 0;
-	}
-
-	template < typename TSize >
-	inline bool _isRoot(VertexWotdModified_<TSize> const &value) {
-//IOREV_notio_
-		return value.node == 0; 
-	}
-
-	// is this a leaf? (including empty $-edges)
-	template < typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder >
-	inline bool _isLeaf(
-		Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TSpec> > const &it,
-		VSTreeIteratorTraits<TDfsOrder, False> const)
-	{
-//IOREV_notio_
-		typedef Index<TText, IndexWotd<TIndexSpec> > TIndex;
-		TIndex const &index = container(it);
-		return (dirAt(value(it).node, index) & index.LEAF) != 0;
-	}
-
-	// is this a leaf? (excluding empty $-edges)
-	template < typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder >
-	inline bool _isLeaf(
-		Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TSpec> > const &it,
-		VSTreeIteratorTraits<TDfsOrder, True> const)
-	{
-//IOREV_notio_
-		typedef Index<TText, IndexWotd<TIndexSpec> >	TIndex;
-
-		TIndex const &index = container(it);
-		if (dirAt(value(it).node, index) & index.LEAF)
-			return true;
-
-		// ensure node evaluation and test for sentinel child edges?
-		return _wotdEvaluate(it) & index.SENTINELS;
-	}
-
-
-	// parentEdgeLength - ORIGINAL VERSION
-	template < typename TIndex, typename TSize >
-	inline typename Size<TIndex>::Type
-	parentEdgeLength(TIndex const &index, VertexWotdOriginal_<TSize> &vDesc)
-	{
-		TSize edgeLen = vDesc.edgeLen;
-		if (edgeLen != (TSize)-1)
-			return edgeLen;
-
-		TSize pos = vDesc.node;
-		TSize w0 = dirAt(pos, index);
-		if (w0 & index.LEAF)
-			return vDesc.edgeLen = suffixLength(w0 & index.BITMASK0, index);
-
-		TSize w1 = dirAt(pos + 1, index);
-		if (w1 & index.UNEVALUATED)
-			return vDesc.edgeLen = _bucketLcp(
-				infix(indexSA(index), w0 & index.BITMASK0, w1 & index.BITMASK1),
-				indexText(index));
-		else
-			return vDesc.edgeLen = _getNodeLP(index, w1) - (w0 & index.BITMASK0);
-	}
-
-	// parentEdgeLength - MODIFIED VERSION
-	template < typename TIndex, typename TSize >
-	inline typename Size<TIndex>::Type
-	parentEdgeLength(TIndex const &index, VertexWotdModified_<TSize> &vDesc)
-	{
-		TSize edgeLen = vDesc.edgeLen;
-		if (edgeLen != (TSize)-1)
-			return edgeLen;
-
-		TSize pos = vDesc.node;
-		TSize w0 = dirAt(pos, index);
-		if (w0 & index.LEAF)
-			return vDesc.edgeLen =
-				suffixLength(saAt(vDesc.range.i1, index), index) - vDesc.parentRepLen;
-
-		TSize w1 = dirAt(pos + 1, index);
-		if (w1 & index.UNEVALUATED)
-			if (_isSizeInval(vDesc.range.i2))
-				return vDesc.edgeLen = _bucketLcp(
-					suffix(indexSA(index), vDesc.range.i1),
-					indexText(index),
-					vDesc.parentRepLen) - vDesc.parentRepLen;
-			else
-				return vDesc.edgeLen = _bucketLcp(
-					infix(indexSA(index), vDesc.range.i1, vDesc.range.i2),
-					indexText(index),
-					vDesc.parentRepLen) - vDesc.parentRepLen;
-		else
-			return (dirAt(w1 & index.BITMASK1, index) & index.BITMASK0) - vDesc.parentRepLen;
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
-	parentEdgeLength(Iter<
-		Index<TText, IndexWotd<TIndexSpec> >, 
-		VSTree< TopDown<TSpec> > > const &it)
-	{
-		typedef Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > TIter;
-		return parentEdgeLength(container(it), value(const_cast<TIter&>(it)));
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
-	parentRepLength(Iter<
-		Index<TText, IndexWotd<TIndexSpec> >, 
-		VSTree< TopDown<TSpec> > > const &it)
-	{
-		return value(it).parentRepLen;
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
-	parentRepLength(Iter<
-		Index<TText, IndexWotd<TIndexSpec> >, 
-		VSTree< TopDown< ParentLinks<TSpec> > > > const &it)
-	{
-		return value(it).parentRepLen;
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
-	repLength(Iter<
-		Index<TText, IndexWotd<TIndexSpec> >, 
-		VSTree< TopDown<TSpec> > > const &it) 
-	{
-		return parentRepLength(it) + parentEdgeLength(it);
-	}
-
-
-	// parentEdgeLabel - ORIGINAL VERSION (doesn't work if TText is a StringSet)
-	template < typename TText, typename TSpec >
-	inline typename Infix< typename Fibre<Index<TText, IndexWotd<WotdOriginal> >, EsaText>::Type const >::Type 
-	parentEdgeLabel(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > const &it) 
-	{
-		typedef Index<TText, IndexWotd<WotdOriginal> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-
-		TIndex const &index = container(it);
-
-		if (isRoot(it))
-			return infix(indexText(index), 0, 0);
-		else {
-			TSize occ = _getNodeLP(index, value(it).node);
-			return infix(indexText(index), occ, occ + parentEdgeLength(it));
-		}
-	}
-
-	// getOccurrence - ORIGINAL VERSION
-	template < typename TText, typename TSpec >
-	inline typename SAValue<Index<TText, IndexWotd<WotdOriginal> > >::Type 
-	getOccurrence(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree<TSpec> > const &it) {
-		return _getNodeLP(container(it), value(it).node) - value(it).parentRepLen;
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline bool
-	emptyParentEdge(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TopDown<TSpec> > > const &it) 
-	{
-		typedef Index<TText, IndexWotd<TIndexSpec> > TIndex;
-
-		TIndex const &index = container(it);
-		typename SAValue<TIndex>::Type pos = getOccurrence(it);
-		return getSeqOffset(pos, stringSetLimits(index)) + value(it).parentRepLen
-			== sequenceLength(getSeqNo(pos, stringSetLimits(index)), index);
-	}
-
-	// to avoid ambiguity
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline bool
-	emptyParentEdge(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > const &it) 
-	{
-		typedef Index<TText, IndexWotd<TIndexSpec> > TIndex;
-
-		TIndex const &index = container(it);
-		typename SAValue<TIndex>::Type pos = getOccurrence(it);
-		return getSeqOffset(pos, stringSetLimits(index)) + value(it).parentRepLen
-			== sequenceLength(getSeqNo(pos, stringSetLimits(index)), index);
-	}
-
-
-
-	template < typename TText, typename TSpec >
-	inline void 
-	goRoot(Iter<
-		Index<TText, IndexWotd<WotdOriginal> >, 
-		VSTree<TSpec> > &it) 
-	{
-		_historyClear(it);
-		value(it).node = 0;			// start in root node (first entry in dir)
-		value(it).parentRepLen = 0;	// parent prefix length is 0
-		value(it).edgeLen = 0;		// edge length is 0
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline void 
-	goRoot(Iter<
-		Index<TText, IndexWotd<TIndexSpec> >, 
-		VSTree<TSpec> > &it) 
-	{
-		_historyClear(it);
-		value(it).range.i1 = 0;		// start in root node with range (0,infty)
-		_setSizeInval(value(it).range.i2);	// infty is equivalent to length(index) and faster to compare
-		value(it).node = 0;			// start in root node (first entry in dir)
-		value(it).parentRepLen = 0;	// parent prefix length is 0
-		value(it).edgeLen = 0;		// edge length is 0
-	}
-
-	template < typename TText, typename TSpec >
-	inline bool atEnd(Iter<Index<TText, IndexWotd<WotdOriginal> >, VSTree<TSpec> > &it) 
-	{
-		return _isSizeInval(value(it).node);
-	}
-
-	template < typename TText, typename TSpec >
-	inline bool atEnd(Iter<Index<TText, IndexWotd<WotdOriginal> >, VSTree<TSpec> > const &it) 
-	{
-		return _isSizeInval(value(it).node);
-	}
-
-		
-	// adjust iterator's right border of SA range
-	template < typename TText, typename TSpec >
-	inline void
-	_adjustRightBorder(
-		Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &) 
-	{}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline void
-	_adjustRightBorder(
-		Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it)
-	{
-		typedef Index<TText, IndexWotd<TIndexSpec> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-
-		TIndex	const &index = container(it);
-		TSize	pos = value(it).node;
-
-		TSize w0 = dirAt(pos, index);
-		if (w0 & index.LEAF)
-			value(it).range.i2 = value(it).range.i1 + 1;
-		else
-			if (w0 & index.LAST_CHILD)
-				value(it).range.i2 = value(it).parentRight;
-			else {
-				w0 = dirAt(pos + 2, index);
-				value(it).range.i2 = w0 & index.BITMASK0;
-			}
-	}
-
-	// go down the leftmost edge (including empty $-edges)
-	template < typename TText, typename TSpec, typename TDfsOrder, typename THideEmptyEdges >
-	inline bool 
-	_goDown(
-		Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it,
-		VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
-	{
-		typedef Index<TText, IndexWotd<WotdOriginal> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-
-		if (_isLeaf(it, EmptyEdges())) return false;
-
-		TIndex &index = container(it);
-		_historyPush(it);
-
-		// ensure node evaluation
-		TSize childNode = _wotdEvaluate(it);
-
-		if (THideEmptyEdges::VALUE && (childNode & index.SENTINELS) != 0)
-			return false;
-
-		// go down
-		value(it).node = childNode & index.BITMASK1;
-		value(it).edgeLen = -1;
-
-		// go right if parent edge is empty 
-		// or hull predicate is false
-		if ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it))
-			if (!goRight(it)) {
-				_goUp(it);
-				return false;
-			}
-
-		return true;
-	}
-
-	// go down the leftmost edge (excluding empty $-edges)
-	template < typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder, typename THideEmptyEdges >
-	inline bool 
-	_goDown(
-		Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
-		VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
-	{
-		typedef Index<TText, IndexWotd<TIndexSpec> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-
-		if (_isLeaf(it, EmptyEdges())) return false;
-		TIndex const &index = container(it);
-
-		// ensure node evaluation
-		TSize childNode = _wotdEvaluate(it);
-
-		if (THideEmptyEdges::VALUE && (childNode & index.SENTINELS) != 0)
-			return false;
-
-		// go down
-		_historyPush(it);
-		value(it).node = childNode & index.BITMASK1;
-		value(it).edgeLen = -1;
-		_adjustRightBorder(it);
-
-		// go right if parent edge is empty
-		// or hull predicate is false
-		if ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it))
-			if (!goRight(it)) {
-				_goUp(it);
-				return false;
-			}
-
-		return true;
-	}
-
-	// go right to the lexic. next sibling
-	template < typename TText, typename TSpec, typename TDfsOrder, typename THideEmptyEdges >
-	inline bool 
-	_goRight(
-		Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it,
-		VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const) 
-	{
-		typedef Index<TText, IndexWotd<WotdOriginal> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-
-		TIndex const &index = container(it);
-
-		do {
-			TSize w0 = dirAt(value(it).node, index);
-			if (w0 & index.LAST_CHILD)
-				return false;
-
-			value(it).node += (w0 & index.LEAF)? 1: 2;
-			value(it).edgeLen = -1;
-
-			_adjustRightBorder(it);
-		} while ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it));
-		return true;
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder, typename THideEmptyEdges >
-	inline bool 
-	_goRight(
-		Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
-		VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const) 
-	{
-		typedef Index<TText, IndexWotd<TIndexSpec> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-
-		TIndex const &index = container(it);
-
-		do {
-			TSize w0 = dirAt(value(it).node, index);
-			if (w0 & index.LAST_CHILD)
-				return false;
-
-			value(it).node += (w0 & index.LEAF)? 1: 2;
-			value(it).edgeLen = -1;
-
-			value(it).range.i1 = value(it).range.i2;
-			_adjustRightBorder(it);
-		} while ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it));
-		return true;
-	}
-
-	// go up one edge (returns false if in root node)
-	// can be used at most once, as no history stack is available
-	template < typename TText, typename TWotdSpec, typename TSpec >
-	inline bool 
-	_goUp(Iter< Index<TText, IndexWotd<TWotdSpec> >, VSTree< TopDown<TSpec> > > &it) 
-	{
-		if (!isRoot(it)) {
-			value(it) = it._parentDesc;
-			return true;
-		}
-		return false;
-	}
-
-	// go up one edge (returns false if in root node)
-	template < typename TText, typename TSpec >
-	inline bool 
-	_goUp(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it) 
-	{
-		typedef typename Size< Index<TText, IndexWotd<WotdOriginal> > >::Type TSize;
-
-		if (!empty(it.history)) {
-			HistoryStackWotdOriginal_<TSize> const &entry = back(it.history);
-			value(it).node = entry.node;
-			value(it).parentRepLen -= entry.edgeLen;
-			value(it).edgeLen = entry.edgeLen;
-			pop(it.history);
-			return true;
-		}
-		return false;
-	}
-
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline bool 
-	_goUp(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it) 
-	{
-		typedef typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type TSize;
-
-		if (!empty(it.history)) 
-		{
-			HistoryStackWotdModified_<TSize> const &entry = back(it.history);
-			value(it).node = entry.node;
-			value(it).parentRepLen -= entry.edgeLen;
-			value(it).edgeLen = entry.edgeLen;
-			value(it).range = entry.range;
-			pop(it.history);
-			if (!empty(it.history))
-				value(it).parentRight = back(it.history).range.i2;	// copy right boundary of parent's range
-			return true;
-		}
-		return false;
-	}
-
-	// return vertex descriptor of parent's node
-	template < typename TText, typename TSpec >
-	inline typename VertexDescriptor< Index<TText, IndexWotd<WotdOriginal> > >::Type
-	nodeUp(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > const &it) 
-	{
-		typedef Index<TText, IndexWotd<WotdOriginal> > TIndex;
-		typedef typename Size<TIndex>::Type TSize;
-
-		if (!empty(it.history))
-		{
-			HistoryStackWotdOriginal_<TSize> const &entry = back(it.history);
-			typename VertexDescriptor<TIndex>::Type desc;
-
-			desc.node = entry.node;
-			desc.parentRepLen = value(it).parentRepLen - entry.edgeLen;
-			desc.edgeLen = entry.edgeLen;
-			TSize h = length(it.history) - 1;
-			if (h != 0) --h;
-			return desc;
-		} else
-			return value(it);
-	}
-
-	// return vertex descriptor of parent's node
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline typename VertexDescriptor< Index<TText, IndexWotd<TIndexSpec> > >::Type
-	nodeUp(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > const &it) 
-	{
-		typedef Index<TText, IndexWotd<TIndexSpec> > TIndex;
-		typedef typename Size<TIndex>::Type TSize;
-
-		if (!empty(it.history))
-		{
-			HistoryStackWotdModified_<TSize> const &entry = back(it.history);
-			typename VertexDescriptor<TIndex>::Type desc;
-
-			desc.node = entry.node;
-			desc.parentRepLen = value(it).parentRepLen - entry.edgeLen;
-			desc.edgeLen = entry.edgeLen;
-			return desc;
-		} else
-			return value(it);
-	}
+    template < typename TSize >
+    inline bool _isRoot(VertexWotdOriginal_<TSize> const &value)
+    {
+        return value.node == 0;
+    }
+
+    template < typename TSize >
+    inline bool _isRoot(VertexWotdModified_<TSize> const &value)
+    {
+        return value.node == 0;
+    }
+
+    // is this a leaf? (including empty $-edges)
+    template < typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder >
+    inline bool _isLeaf(
+        Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TSpec> > const &it,
+        VSTreeIteratorTraits<TDfsOrder, False> const)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> > TIndex;
+        TIndex const &index = container(it);
+        return (dirAt(value(it).node, index) & index.LEAF) != 0;
+    }
+
+    // is this a leaf? (excluding empty $-edges)
+    template < typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder >
+    inline bool _isLeaf(
+        Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TSpec> > const &it,
+        VSTreeIteratorTraits<TDfsOrder, True> const)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> >    TIndex;
+
+        TIndex const &index = container(it);
+        if (dirAt(value(it).node, index) & index.LEAF)
+            return true;
+
+        // ensure node evaluation and test for sentinel child edges?
+        return _wotdEvaluate(it) & index.SENTINELS;
+    }
+
+
+    // parentEdgeLength - ORIGINAL VERSION
+    template < typename TIndex, typename TSize >
+    inline typename Size<TIndex>::Type
+    parentEdgeLength(TIndex const &index, VertexWotdOriginal_<TSize> &vDesc)
+    {
+        TSize edgeLen = vDesc.edgeLen;
+        if (edgeLen != (TSize)-1)
+            return edgeLen;
+
+        TSize pos = vDesc.node;
+        TSize w0 = dirAt(pos, index);
+        if (w0 & index.LEAF)
+            return vDesc.edgeLen = suffixLength(w0 & index.BITMASK0, index);
+
+        TSize w1 = dirAt(pos + 1, index);
+        if (w1 & index.UNEVALUATED)
+            return vDesc.edgeLen = _bucketLcp(
+                infix(indexSA(index), w0 & index.BITMASK0, w1 & index.BITMASK1),
+                indexText(index));
+        else
+            return vDesc.edgeLen = _getNodeLP(index, w1) - (w0 & index.BITMASK0);
+    }
+
+    // parentEdgeLength - MODIFIED VERSION
+    template < typename TIndex, typename TSize >
+    inline typename Size<TIndex>::Type
+    parentEdgeLength(TIndex const &index, VertexWotdModified_<TSize> &vDesc)
+    {
+        TSize edgeLen = vDesc.edgeLen;
+        if (edgeLen != (TSize)-1)
+            return edgeLen;
+
+        TSize pos = vDesc.node;
+        TSize w0 = dirAt(pos, index);
+        if (w0 & index.LEAF)
+            return vDesc.edgeLen =
+                suffixLength(saAt(vDesc.range.i1, index), index) - vDesc.parentRepLen;
+
+        TSize w1 = dirAt(pos + 1, index);
+        if (w1 & index.UNEVALUATED)
+            if (_isSizeInval(vDesc.range.i2))
+                return vDesc.edgeLen = _bucketLcp(
+                    suffix(indexSA(index), vDesc.range.i1),
+                    indexText(index),
+                    vDesc.parentRepLen) - vDesc.parentRepLen;
+            else
+                return vDesc.edgeLen = _bucketLcp(
+                    infix(indexSA(index), vDesc.range.i1, vDesc.range.i2),
+                    indexText(index),
+                    vDesc.parentRepLen) - vDesc.parentRepLen;
+        else
+            return (dirAt(w1 & index.BITMASK1, index) & index.BITMASK0) - vDesc.parentRepLen;
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
+    parentEdgeLength(Iter<
+        Index<TText, IndexWotd<TIndexSpec> >,
+        VSTree< TopDown<TSpec> > > const &it)
+    {
+        typedef Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > TIter;
+        return parentEdgeLength(container(it), value(const_cast<TIter&>(it)));
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
+    parentRepLength(Iter<
+        Index<TText, IndexWotd<TIndexSpec> >,
+        VSTree< TopDown<TSpec> > > const &it)
+    {
+        return value(it).parentRepLen;
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
+    parentRepLength(Iter<
+        Index<TText, IndexWotd<TIndexSpec> >,
+        VSTree< TopDown< ParentLinks<TSpec> > > > const &it)
+    {
+        return value(it).parentRepLen;
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
+    repLength(Iter<
+        Index<TText, IndexWotd<TIndexSpec> >,
+        VSTree< TopDown<TSpec> > > const &it)
+    {
+        return parentRepLength(it) + parentEdgeLength(it);
+    }
+
+
+    // parentEdgeLabel - ORIGINAL VERSION (doesn't work if TText is a StringSet)
+    template < typename TText, typename TSpec >
+    inline typename Infix< typename Fibre<Index<TText, IndexWotd<WotdOriginal> >, EsaText>::Type const >::Type
+    parentEdgeLabel(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > const &it)
+    {
+        typedef Index<TText, IndexWotd<WotdOriginal> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+
+        TIndex const &index = container(it);
+
+        if (isRoot(it))
+            return infix(indexText(index), 0, 0);
+        else {
+            TSize occ = _getNodeLP(index, value(it).node);
+            return infix(indexText(index), occ, occ + parentEdgeLength(it));
+        }
+    }
+
+    // getOccurrence - ORIGINAL VERSION
+    template < typename TText, typename TSpec >
+    inline typename SAValue<Index<TText, IndexWotd<WotdOriginal> > >::Type
+    getOccurrence(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree<TSpec> > const &it) {
+        return _getNodeLP(container(it), value(it).node) - value(it).parentRepLen;
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline bool
+    emptyParentEdge(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TopDown<TSpec> > > const &it)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> > TIndex;
+
+        TIndex const &index = container(it);
+        typename SAValue<TIndex>::Type pos = getOccurrence(it);
+        return getSeqOffset(pos, stringSetLimits(index)) + value(it).parentRepLen
+            == sequenceLength(getSeqNo(pos, stringSetLimits(index)), index);
+    }
+
+    // to avoid ambiguity
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline bool
+    emptyParentEdge(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TopDown<ParentLinks<TSpec> > > > const &it)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> > TIndex;
+
+        TIndex const &index = container(it);
+        typename SAValue<TIndex>::Type pos = getOccurrence(it);
+        return getSeqOffset(pos, stringSetLimits(index)) + value(it).parentRepLen
+            == sequenceLength(getSeqNo(pos, stringSetLimits(index)), index);
+    }
+
+
+
+    template < typename TText, typename TSpec >
+    inline void
+    goRoot(Iter<
+        Index<TText, IndexWotd<WotdOriginal> >,
+        VSTree<TSpec> > &it)
+    {
+        _historyClear(it);
+        value(it).node = 0;            // start in root node (first entry in dir)
+        value(it).parentRepLen = 0;    // parent prefix length is 0
+        value(it).edgeLen = 0;        // edge length is 0
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline void
+    goRoot(Iter<
+        Index<TText, IndexWotd<TIndexSpec> >,
+        VSTree<TSpec> > &it)
+    {
+        _historyClear(it);
+        value(it).range.i1 = 0;        // start in root node with range (0,infty)
+        _setSizeInval(value(it).range.i2);    // infty is equivalent to length(index) and faster to compare
+        value(it).node = 0;            // start in root node (first entry in dir)
+        value(it).parentRepLen = 0;    // parent prefix length is 0
+        value(it).edgeLen = 0;        // edge length is 0
+    }
+
+    template < typename TText, typename TSpec >
+    inline bool atEnd(Iter<Index<TText, IndexWotd<WotdOriginal> >, VSTree<TSpec> > &it)
+    {
+        return _isSizeInval(value(it).node);
+    }
+
+    template < typename TText, typename TSpec >
+    inline bool atEnd(Iter<Index<TText, IndexWotd<WotdOriginal> >, VSTree<TSpec> > const &it)
+    {
+        return _isSizeInval(value(it).node);
+    }
+
+
+    // adjust iterator's right border of SA range
+    template < typename TText, typename TSpec >
+    inline void
+    _adjustRightBorder(
+        Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &)
+    {}
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline void
+    _adjustRightBorder(
+        Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+
+        TIndex    const &index = container(it);
+        TSize    pos = value(it).node;
+
+        TSize w0 = dirAt(pos, index);
+        if (w0 & index.LEAF)
+            value(it).range.i2 = value(it).range.i1 + 1;
+        else
+            if (w0 & index.LAST_CHILD)
+                value(it).range.i2 = value(it).parentRight;
+            else {
+                w0 = dirAt(pos + 2, index);
+                value(it).range.i2 = w0 & index.BITMASK0;
+            }
+    }
+
+    // go down the leftmost edge (including empty $-edges)
+    template < typename TText, typename TSpec, typename TDfsOrder, typename THideEmptyEdges >
+    inline bool
+    _goDown(
+        Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it,
+        VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
+    {
+        typedef Index<TText, IndexWotd<WotdOriginal> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+
+        if (_isLeaf(it, EmptyEdges())) return false;
+
+        TIndex &index = container(it);
+        _historyPush(it);
+
+        // ensure node evaluation
+        TSize childNode = _wotdEvaluate(it);
+
+        if (THideEmptyEdges::VALUE && (childNode & index.SENTINELS) != 0)
+            return false;
+
+        // go down
+        value(it).node = childNode & index.BITMASK1;
+        value(it).edgeLen = -1;
+
+        // go right if parent edge is empty
+        // or hull predicate is false
+        if ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it))
+            if (!goRight(it)) {
+                _goUp(it);
+                return false;
+            }
+
+        return true;
+    }
+
+    // go down the leftmost edge (excluding empty $-edges)
+    template < typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder, typename THideEmptyEdges >
+    inline bool
+    _goDown(
+        Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
+        VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+
+        if (_isLeaf(it, EmptyEdges())) return false;
+        TIndex const &index = container(it);
+
+        // ensure node evaluation
+        TSize childNode = _wotdEvaluate(it);
+
+        if (THideEmptyEdges::VALUE && (childNode & index.SENTINELS) != 0)
+            return false;
+
+        // go down
+        _historyPush(it);
+        value(it).node = childNode & index.BITMASK1;
+        value(it).edgeLen = -1;
+        _adjustRightBorder(it);
+
+        // go right if parent edge is empty
+        // or hull predicate is false
+        if ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it))
+            if (!goRight(it)) {
+                _goUp(it);
+                return false;
+            }
+
+        return true;
+    }
+
+    // go right to the lexic. next sibling
+    template < typename TText, typename TSpec, typename TDfsOrder, typename THideEmptyEdges >
+    inline bool
+    _goRight(
+        Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it,
+        VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
+    {
+        typedef Index<TText, IndexWotd<WotdOriginal> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+
+        TIndex const &index = container(it);
+
+        do {
+            TSize w0 = dirAt(value(it).node, index);
+            if (w0 & index.LAST_CHILD)
+                return false;
+
+            value(it).node += (w0 & index.LEAF)? 1: 2;
+            value(it).edgeLen = -1;
+
+            _adjustRightBorder(it);
+        } while ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it));
+        return true;
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec, typename TDfsOrder, typename THideEmptyEdges >
+    inline bool
+    _goRight(
+        Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
+        VSTreeIteratorTraits<TDfsOrder, THideEmptyEdges> const)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+
+        TIndex const &index = container(it);
+
+        do {
+            TSize w0 = dirAt(value(it).node, index);
+            if (w0 & index.LAST_CHILD)
+                return false;
+
+            value(it).node += (w0 & index.LEAF)? 1: 2;
+            value(it).edgeLen = -1;
+
+            value(it).range.i1 = value(it).range.i2;
+            _adjustRightBorder(it);
+        } while ((THideEmptyEdges::VALUE && emptyParentEdge(it)) || !nodeHullPredicate(it));
+        return true;
+    }
+
+    // go up one edge (returns false if in root node)
+    // can be used at most once, as no history stack is available
+    template < typename TText, typename TWotdSpec, typename TSpec >
+    inline bool
+    _goUp(Iter< Index<TText, IndexWotd<TWotdSpec> >, VSTree< TopDown<TSpec> > > &it)
+    {
+        if (!isRoot(it)) {
+            value(it) = it._parentDesc;
+            return true;
+        }
+        return false;
+    }
+
+    // go up one edge (returns false if in root node)
+    template < typename TText, typename TSpec >
+    inline bool
+    _goUp(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it)
+    {
+        typedef typename Size< Index<TText, IndexWotd<WotdOriginal> > >::Type TSize;
+
+        if (!empty(it.history)) {
+            HistoryStackWotdOriginal_<TSize> const &entry = back(it.history);
+            value(it).node = entry.node;
+            value(it).parentRepLen -= entry.edgeLen;
+            value(it).edgeLen = entry.edgeLen;
+            eraseBack(it.history);
+            return true;
+        }
+        return false;
+    }
+
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline bool
+    _goUp(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > &it)
+    {
+        typedef typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type TSize;
+
+        if (!empty(it.history))
+        {
+            HistoryStackWotdModified_<TSize> const &entry = back(it.history);
+            value(it).node = entry.node;
+            value(it).parentRepLen -= entry.edgeLen;
+            value(it).edgeLen = entry.edgeLen;
+            value(it).range = entry.range;
+            eraseBack(it.history);
+            if (!empty(it.history))
+                value(it).parentRight = back(it.history).range.i2;    // copy right boundary of parent's range
+            return true;
+        }
+        return false;
+    }
+
+    // return vertex descriptor of parent's node
+    template < typename TText, typename TSpec >
+    inline typename VertexDescriptor< Index<TText, IndexWotd<WotdOriginal> > >::Type
+    nodeUp(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown< ParentLinks<TSpec> > > > const &it)
+    {
+        typedef Index<TText, IndexWotd<WotdOriginal> > TIndex;
+        typedef typename Size<TIndex>::Type TSize;
+
+        if (!empty(it.history))
+        {
+            HistoryStackWotdOriginal_<TSize> const &entry = back(it.history);
+            typename VertexDescriptor<TIndex>::Type desc;
+
+            desc.node = entry.node;
+            desc.parentRepLen = value(it).parentRepLen - entry.edgeLen;
+            desc.edgeLen = entry.edgeLen;
+            TSize h = length(it.history) - 1;
+            if (h != 0) --h;
+            return desc;
+        } else
+            return value(it);
+    }
+
+    // return vertex descriptor of parent's node
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline typename VertexDescriptor< Index<TText, IndexWotd<TIndexSpec> > >::Type
+    nodeUp(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown< ParentLinks<TSpec> > > > const &it)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> > TIndex;
+        typedef typename Size<TIndex>::Type TSize;
+
+        if (!empty(it.history))
+        {
+            HistoryStackWotdModified_<TSize> const &entry = back(it.history);
+            typename VertexDescriptor<TIndex>::Type desc;
+
+            desc.node = entry.node;
+            desc.parentRepLen = value(it).parentRepLen - entry.edgeLen;
+            desc.edgeLen = entry.edgeLen;
+            return desc;
+        } else
+            return value(it);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
 
-	// Counting sort - Step 2a: Count characters
-	template < typename TBuckets, typename TText >
-	inline void
-	_wotdCountChars(TBuckets &buckets, TText const &text)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type TTextIterator;
-
-		TTextIterator itText = begin(text, Standard());
-		TTextIterator itTextEnd = end(text, Standard());
-		for (; itText != itTextEnd; ++itText)
-			++buckets[ordValue(getValue(itText))];
-	}
-
-
-	template < typename TBuckets, typename TText, typename TSpec >
-	inline void
-	_wotdCountChars(TBuckets &buckets, StringSet<TText, TSpec> const &stringSet)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type TTextIterator;
-
-		for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-		{
-			TText const &text = value(stringSet, seqNo);
-			TTextIterator itText = begin(text, Standard());
-			TTextIterator itTextEnd = end(text, Standard());
-			for (; itText != itTextEnd; ++itText)
-				++buckets[ordValue(getValue(itText))];
-		}
-	}
-
-	// Counting sort - Step 2b: Count the prefixLen'th characters of suffices
-	template < typename TBuckets, typename TText, typename TSA, typename TSize >
-	inline typename Size<TText>::Type
-	_wotdCountCharsWotdOriginal(
-		TBuckets &buckets, 
-		TText const &text, 
-		TSA &sa,
-		TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA, Standard>::Type          TSAIterator;
-		typedef typename Size<TText>::Type						TTextSize;
-
-		TTextIterator itText = begin(text, Standard());
-		TSAIterator itSA = begin(sa, Standard());
-		TSAIterator itSAEnd = end(sa, Standard());
-
-		TTextSize sentinels = 0;
-		TTextSize textLength = length(text);
-		for (; itSA != itSAEnd; ++itSA) 
-		{
-			// add prefix on entries in sa
-			TTextSize saValue = (*itSA += prefixLen);
-			if (textLength > saValue)
-				++buckets[ordValue(*(itText + saValue))];
-			else
-				if (textLength == saValue) ++sentinels;
-		}
-		return sentinels;
-	}
-
-	template < typename TBuckets, typename TText, typename TSA, typename TSize >
-	inline typename Size<TText>::Type
-	_wotdCountChars(
-		TBuckets &buckets, 
-		TText const &text, 
-		TSA const &sa,
-		TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA const, Standard>::Type	TSAIterator;
-		typedef typename Size<TText>::Type						TTextSize;
-
-		TTextIterator itText = begin(text, Standard()) + prefixLen;
-		TSAIterator itSA = begin(sa, Standard());
-		TSAIterator itSAEnd = end(sa, Standard());
-
-		TTextSize sentinels = 0;
-		TTextSize textLength = length(text) - prefixLen;
-		for (; itSA != itSAEnd; ++itSA) 
-		{
-			TTextSize saValue = *itSA;
-			if (textLength > saValue)
-				++buckets[ordValue(*(itText + saValue))];
-			else
-				if (textLength == saValue) ++sentinels;
-		}
-		return sentinels;
-	}
-
-	template < 
-		typename TBuckets, 
-		typename TText, 
-		typename TSpec, 
-		typename TSA, 
-		typename TSize 
-	>
-	inline typename Size<TText>::Type
-	_wotdCountChars(
-		TBuckets &buckets, 
-		StringSet<TText, TSpec> const &stringSet,
-		TSA const &sa,
-		TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA const, Standard>::Type	TSAIterator;
-		typedef typename Size<TText>::Type						TTextSize;
-
-		TTextIterator itText = TTextIterator();
-		TSAIterator itSA = begin(sa, Standard());
-		TSAIterator itSAEnd = end(sa, Standard());
-
-		TTextSize sentinels = 0;
-		TTextSize textLength = 0;
-		unsigned lastSeqSeen = (unsigned)-1;
-		Pair<unsigned, TTextSize> lPos;
-		for (; itSA != itSAEnd; ++itSA) 
-		{
-			posLocalize(lPos, *itSA, stringSetLimits(stringSet));
-			if (lastSeqSeen != getSeqNo(lPos))
-			{
-				lastSeqSeen = getSeqNo(lPos);
-
-				// shift textBegin and textLength by prefixLen
-				textLength = length(stringSet[lastSeqSeen]) - prefixLen;
-				itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
-			}
-			if (textLength > getSeqOffset(lPos))
-				++buckets[ordValue(*(itText + getSeqOffset(lPos)))];
-			else
-				if (textLength == getSeqOffset(lPos)) ++sentinels;
-		}
-		return sentinels;
-	}
+    // Counting sort - Step 2a: Count characters
+    template < typename TBuckets, typename TText >
+    inline void
+    _wotdCountChars(TBuckets &buckets, TText const &text)
+    {
+        typedef typename Iterator<TText const, Standard>::Type TTextIterator;
+
+        TTextIterator itText = begin(text, Standard());
+        TTextIterator itTextEnd = end(text, Standard());
+        for (; itText != itTextEnd; ++itText)
+            ++buckets[ordValue(getValue(itText))];
+    }
+
+
+    template < typename TBuckets, typename TText, typename TSpec >
+    inline void
+    _wotdCountChars(TBuckets &buckets, StringSet<TText, TSpec> const &stringSet)
+    {
+        typedef typename Iterator<TText const, Standard>::Type TTextIterator;
+
+        for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+        {
+            TText const &text = value(stringSet, seqNo);
+            TTextIterator itText = begin(text, Standard());
+            TTextIterator itTextEnd = end(text, Standard());
+            for (; itText != itTextEnd; ++itText)
+                ++buckets[ordValue(getValue(itText))];
+        }
+    }
+
+    // Counting sort - Step 2b: Count the prefixLen'th characters of suffices
+    template < typename TBuckets, typename TText, typename TSA, typename TSize >
+    inline typename Size<TText>::Type
+    _wotdCountCharsWotdOriginal(
+        TBuckets &buckets,
+        TText const &text,
+        TSA &sa,
+        TSize prefixLen)
+    {
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA, Standard>::Type          TSAIterator;
+        typedef typename Size<TText>::Type                        TTextSize;
+
+        TTextIterator itText = begin(text, Standard());
+        TSAIterator itSA = begin(sa, Standard());
+        TSAIterator itSAEnd = end(sa, Standard());
+
+        TTextSize sentinels = 0;
+        TTextSize textLength = length(text);
+        for (; itSA != itSAEnd; ++itSA)
+        {
+            // add prefix on entries in sa
+            TTextSize saValue = (*itSA += prefixLen);
+            if (textLength > saValue)
+                ++buckets[ordValue(*(itText + saValue))];
+            else
+                if (textLength == saValue) ++sentinels;
+        }
+        return sentinels;
+    }
+
+    template < typename TBuckets, typename TText, typename TSA, typename TSize >
+    inline typename Size<TText>::Type
+    _wotdCountChars(
+        TBuckets &buckets,
+        TText const &text,
+        TSA const &sa,
+        TSize prefixLen)
+    {
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+        typedef typename Size<TText>::Type                        TTextSize;
+
+        TTextIterator itText = begin(text, Standard()) + prefixLen;
+        TSAIterator itSA = begin(sa, Standard());
+        TSAIterator itSAEnd = end(sa, Standard());
+
+        TTextSize sentinels = 0;
+        TTextSize textLength = length(text) - prefixLen;
+        for (; itSA != itSAEnd; ++itSA)
+        {
+            TTextSize saValue = *itSA;
+            if (textLength > saValue)
+                ++buckets[ordValue(*(itText + saValue))];
+            else
+                if (textLength == saValue) ++sentinels;
+        }
+        return sentinels;
+    }
+
+    template <
+        typename TBuckets,
+        typename TText,
+        typename TSpec,
+        typename TSA,
+        typename TSize
+    >
+    inline typename Size<TText>::Type
+    _wotdCountChars(
+        TBuckets &buckets,
+        StringSet<TText, TSpec> const &stringSet,
+        TSA const &sa,
+        TSize prefixLen)
+    {
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+        typedef typename Size<TText>::Type                        TTextSize;
+
+        if (empty(stringSet))
+            return 0;
+
+        TTextIterator itText = begin(front(stringSet), Standard());
+        TSAIterator itSA = begin(sa, Standard());
+        TSAIterator itSAEnd = end(sa, Standard());
+
+        TTextSize sentinels = 0;
+        TTextSize textLength = 0;
+        unsigned lastSeqSeen = (unsigned)-1;
+        Pair<unsigned, TTextSize> lPos;
+        for (; itSA != itSAEnd; ++itSA)
+        {
+            posLocalize(lPos, *itSA, stringSetLimits(stringSet));
+            if (lastSeqSeen != getSeqNo(lPos))
+            {
+                lastSeqSeen = getSeqNo(lPos);
+
+                // shift textBegin and textLength by prefixLen
+                textLength = length(stringSet[lastSeqSeen]) - prefixLen;
+                itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
+            }
+            if (textLength > getSeqOffset(lPos))
+                ++buckets[ordValue(*(itText + getSeqOffset(lPos)))];
+            else
+                if (textLength == getSeqOffset(lPos)) ++sentinels;
+        }
+        return sentinels;
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 
-	// Counting sort - Step 3: Cumulative sum
-	template < typename TBounds, typename TBuckets, typename TSize >
-	inline typename Size<TBuckets>::Type
-	_wotdCummulativeSum(TBounds &bounds, TBuckets const &buckets, TSize offset)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TBounds, Standard>::Type          TBoundIterator;
-		typedef typename Iterator<TBuckets const, Standard>::Type   TBucketsIterator;
-
-		TBucketsIterator it = begin(buckets, Standard());
-		TBucketsIterator itEnd = end(buckets, Standard());
-		TBoundIterator bit = begin(bounds, Standard());
-
-		typename Value<TBounds>::Type	sum = offset;
-		typename Size<TBuckets>::Type	requiredSize = 0;
-		typename Value<TBuckets>::Type	diff;
-
-		for (; it != itEnd; ++it, ++bit)
-			if ((diff = *it) != 0) {
-				requiredSize += (diff > 1)? 2: 1;
-				*bit = sum;
-				sum += diff;
-			}
-
-		return requiredSize;
-	}
-
-	template < typename TBounds, typename TBuckets >
-	inline typename Size<TBuckets>::Type
-	_wotdCummulativeSum(TBounds &bounds, TBuckets const &buckets)
-	{
-		return _wotdCummulativeSum(bounds, buckets, 0);
-	}
+    // Counting sort - Step 3: Cumulative sum
+    template < typename TBounds, typename TBuckets, typename TSize >
+    inline typename Size<TBuckets>::Type
+    _wotdCummulativeSum(TBounds &bounds, TBuckets const &buckets, TSize offset)
+    {
+        typedef typename Iterator<TBounds, Standard>::Type          TBoundIterator;
+        typedef typename Iterator<TBuckets const, Standard>::Type   TBucketsIterator;
+
+        TBucketsIterator it = begin(buckets, Standard());
+        TBucketsIterator itEnd = end(buckets, Standard());
+        TBoundIterator bit = begin(bounds, Standard());
+
+        typename Value<TBounds>::Type    sum = offset;
+        typename Size<TBuckets>::Type    requiredSize = 0;
+        typename Value<TBuckets>::Type    diff;
+
+        for (; it != itEnd; ++it, ++bit)
+            if ((diff = *it) != 0) {
+                requiredSize += (diff > 1)? 2: 1;
+                *bit = sum;
+                sum += diff;
+            }
+
+        return requiredSize;
+    }
+
+    template < typename TBounds, typename TBuckets >
+    inline typename Size<TBuckets>::Type
+    _wotdCummulativeSum(TBounds &bounds, TBuckets const &buckets)
+    {
+        return _wotdCummulativeSum(bounds, buckets, 0);
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 //TODO(singer): The function createWotdIndex in never defined!
-/**
-.Function.createWotdIndex:
-..summary:Builds a q-gram index on a sequence. 
-..cat:Index
-..signature:createWotdIndex(sa, dir, text)
-..class:Spec.IndexWotd
-..param.text:The sequence.
-..param.sa:The resulting list in which all q-grams are sorted alphabetically.
-..param.dir:The resulting array that indicates at which position in index the corresponding q-grams can be found.
-..returns:Index contains the sorted list of qgrams. For each possible q-gram pos contains the first position in index that corresponds to this q-gram. 
-..include:seqan/index.h
-*/
 /*!
  * @fn IndexWotd#createWotdIndex
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Builds a q-gram index on a sequence.
- * 
- * @signature createWotdIndex(sa, dir, text)
- * 
- * @param text The sequence. Types: @link SequenceConcept @endlink
- * @param sa The resulting list in which all q-grams are sorted alphabetically. 
- * @param dir The resulting array that indicates at which position in index the
- *            corresponding q-grams can be found.
- * 
- * @return TReturn Index contains the sorted list of qgrams. For each possible
- *                 q-gram pos contains the first position in index that
- *                 corresponds to this q-gram.
+ * @headerfile <seqan/index.h>
+ * @brief Builds a the WOTD index.
+ *
+ * @signature void createWotdIndex(sa, dir, text);
+ *
+ * @param[out] sa  The resulting list in which all <i>q</i>-grams are sorted alphabetically.
+ * @param[out] dir The resulting array that indicates at which position in index the corresponding <i>q</i>-grams
+ *                 can be found.
+ * @param[in] text The sequence. Types: @link ContainerConcept @endlink
+ *
+ * The resulting <tt>index</tt> contains the sorted list of qgrams.  For each possible <i>q</i>-gram pos contains
+ * the first position in index that corresponds to this <i>q</i>-gram.
  */
 
-	// single sequence
-	template < typename TIndex >
-	typename Size<TIndex>::Type
-	_sortFirstWotdBucket(TIndex &index)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Fibre<TIndex, WotdText >::Type		TText;
-		typedef typename Fibre<TIndex, WotdSA >::Type			TSA;
-		typedef typename TIndex::TCounter						TCounter;
-
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA, Standard>::Type			TSAIterator;
-		typedef typename Iterator<TCounter, Standard>::Type		TCntIterator;
-		typedef typename Size<TText>::Type						TSize;
-		
-		TText const &text = indexText(index);
-		TCounter &occ = index.tempOcc;
-		TCounter &bound = index.tempBound;
-
-		// 1. clear counters and copy SA to temporary SA
-		arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
-
-		// 2. count characters
-		_wotdCountChars(occ, text);
-
-		// 3. cumulative sum
-		TSize requiredSize = _wotdCummulativeSum(bound, occ);
-
-		// 4. fill suffix array
-		{
-			TSA &sa = indexSA(index);
-			TSAIterator saBeg = begin(sa, Standard());
-			TCntIterator boundBeg = begin(bound, Standard());
-
-			TTextIterator itText = begin(text, Standard());
-			TTextIterator itTextEnd = end(text, Standard());
-			for(TSize i = 0; itText != itTextEnd; ++itText, ++i)
-				*(saBeg + (*(boundBeg + ordValue(getValue(itText))))++) = i;
-		}
-		index.sentinelOcc = 0;
-		index.sentinelBound = 0;
-
-		return requiredSize;
-	}
-
-	// multiple sequences
-	template < typename TText, typename TSpec, typename TIndexSpec >
-	typename Size< Index<StringSet<TText, TSpec>, TIndexSpec> >::Type
-	_sortFirstWotdBucket(Index<StringSet<TText, TSpec>, TIndexSpec> &index)
-	{
-	SEQAN_CHECKPOINT
-		typedef Index<StringSet<TText, TSpec>, TIndexSpec>		TIndex;
-		typedef typename Fibre<TIndex, WotdSA >::Type			TSA;
-		typedef typename TIndex::TCounter						TCounter;
-
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA, Standard>::Type			TSAIterator;
-		typedef typename Iterator<TCounter, Standard>::Type		TCntIterator;
-		typedef typename Size<TText>::Type						TSize;
-
-		StringSet<TText, TSpec> const &stringSet = indexText(index);
-		TCounter &occ = index.tempOcc;
-		TCounter &bound = index.tempBound;
-
-		// 1. clear counters and copy SA to temporary SA
-		arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
-
-		// 2. count characters
-		_wotdCountChars(occ, stringSet);
-
-		// 3. cummulative sum
-		TSize requiredSize = _wotdCummulativeSum(bound, occ);
-
-		// 4. fill suffix array
-		for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo) 
-		{
-			TSA &sa = indexSA(index);
-			TSAIterator saBeg = begin(sa, Standard());
-			TCntIterator boundBeg = begin(bound, Standard());
-
-			typename Value<TSA>::Type localPos;
-			assignValueI1(localPos, seqNo);
-			assignValueI2(localPos, 0);
-
-			TText const &text = value(stringSet, seqNo);
-			TTextIterator itText = begin(text, Standard());
-			TTextIterator itTextEnd = end(text, Standard());
-			for(; itText != itTextEnd; ++itText) 
-			{
-				*(saBeg + (*(boundBeg + ordValue(getValue(itText))))++) = localPos;
-				assignValueI2(localPos, getValueI2(localPos) + 1);
-			}
-		}
-		index.sentinelOcc = 0;
-		index.sentinelBound = 0;
-
-		return requiredSize;
-	}
-
-
-
-	// sort bucket using counting sort
-	// (nearly) ORIGINAL VERSION:
-	// - brings the bucket with the longest suffix (lpBucket) to front
-	// - all other buckets are in lexicographical order
-	// - adds prefixLen to all SA entries in SA[left,right)
-	template < typename TText, typename TBeginPos, typename TEndPos, typename TSize >
-	TSize _sortWotdBucket(
-		Index<TText, IndexWotd<WotdOriginal> > &index,
-		TBeginPos left, 
-		TEndPos right,
-		TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef Index<TText, IndexWotd<WotdOriginal> >              TIndex;
-		typedef typename Fibre<TIndex, WotdSA >::Type               TSA;
-		typedef typename TIndex::TCounter                           TCounter;
-
-		typedef typename Iterator<TText const, Standard>::Type      TTextIterator;
-		typedef typename Iterator<TSA, Standard>::Type              TSAIterator;
-		typedef typename Iterator<TCounter, Standard>::Type         TCntIterator;
-		typedef typename Iterator<TCounter const, Standard>::Type   TConstCntIterator;
-		typedef typename Size<TText>::Type                          TTextSize;
-
-		TText const &text = indexText(index);
-		TCounter const &tempSA = index.tempSA;
-		TCounter &occ = index.tempOcc;
-		TCounter &bound = index.tempBound;
-
-		// 1. clear counters and copy SA to temporary SA
-		arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
-
-		// 2. count characters
-		index.tempSA = infix(indexSA(index), left, right);
-		index.sentinelBound = 0;
-		index.sentinelOcc =
-			_wotdCountCharsWotdOriginal(occ, text, index.tempSA, prefixLen);
-
-		// 3. cumulative sum
-		TSize requiredSize = 0;
-
-		// actually, here sentinelOcc<=1 holds (this is the original wotd)
-		if (index.interSentinelNodes) {
-			if (index.sentinelOcc != 0)
-				requiredSize = (index.sentinelOcc > 1)? 2: 1;	// insert *one* $-edge for all $_i suffices
-		} else
-			requiredSize = index.sentinelOcc;					// insert each $_i suffix one-by-one
-
-		requiredSize += _wotdCummulativeSum(bound, occ, left + index.sentinelOcc);
-		index.sentinelBound = left;
-
-		// 4. fill suffix array
-		{
-			TSA &sa = indexSA(index);
-			TSAIterator saBeg = begin(sa, Standard());
-			TCntIterator boundBeg = begin(bound, Standard());
-
-			TTextIterator itText = begin(text, Standard());
-			TConstCntIterator itSA = begin(tempSA, Standard());
-			TConstCntIterator itSAEnd = end(tempSA, Standard());
-			TTextSize textLength = length(text);
-			for(; itSA != itSAEnd; ++itSA)
-			{
-				TTextSize saValue = *itSA;
-				if (textLength > saValue)
-					*(saBeg + (*(boundBeg + ordValue(*(itText + saValue))))++) = saValue;
-				else
-					if (textLength == saValue)
-						*(saBeg + index.sentinelBound++) = saValue;
-			}
-		}
-
-		// 5. move lpBucket to front and add saOffset to hash directory entries
-		{
-			TSize lpBucket = ordValue(text[tempSA[0]]);
-			if (lpBucket != 0) {
-				TSize lpBucketOcc = occ[lpBucket];
-				TSize lpBucketBound = bound[lpBucket];
-
-				TCntIterator itOcc = begin(occ, Standard()) + lpBucket;
-				TCntIterator itBound = begin(bound, Standard()) + lpBucket;
-				TCntIterator itBeg = begin(bound, Standard());
-				for(; itBound != itBeg; --itBound, --itOcc) {
-					*itOcc = *(itOcc - 1);
-					*itBound = *(itBound - 1);
-				}
-				if (index.sentinelOcc != 0) {
-					// bring first bucket before sentinel bucket
-					*itOcc = index.sentinelOcc;
-					*itBound = index.sentinelBound;
-					index.sentinelOcc = lpBucketOcc;
-					index.sentinelBound = lpBucketBound;
-				} else {
-					*itOcc = lpBucketOcc;
-					*itBound = lpBucketBound;
-				}
-			} else
-				if (index.sentinelOcc != 0) {
-					// bring first bucket before sentinel bucket
-					TSize swap = index.sentinelOcc;
-					index.sentinelOcc = occ[0];
-					occ[0] = swap;
-					swap = index.sentinelBound;
-					index.sentinelBound = bound[0];
-					bound[0] = swap;
-				}
-		}
-
-		return requiredSize;
-	}
-
-
-
-
-
-	// sort bucket using counting sort
-	// MODIFIED VERSION:
-	// - all buckets are in lexicographical order
-	// - SA[left,right) contains real SA entries (the beginning positions of the suffices)
-
-	// single sequence
-	template < typename TIndex, typename TBeginPos, typename TEndPos, typename TSize >
-	TSize _sortWotdBucket(
-		TIndex &index,
-		TBeginPos left, 
-		TEndPos right,
-		TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Fibre<TIndex, WotdText >::Type             TText;
-		typedef typename Fibre<TIndex, WotdSA >::Type               TSA;
-		typedef typename TIndex::TCounter                           TCounter;
-
-		typedef typename Iterator<TText const, Standard>::Type      TTextIterator;
-		typedef typename Iterator<TSA, Standard>::Type              TSAIterator;
-		typedef typename Iterator<TCounter, Standard>::Type         TCntIterator;
-		typedef typename Iterator<TCounter const, Standard>::Type   TConstCntIterator;
-		typedef typename Size<TText>::Type                          TTextSize;
-
-		TText const &text = indexText(index);
-		TCounter const &tempSA = index.tempSA;
-		TCounter &occ = index.tempOcc;
-		TCounter &bound = index.tempBound;
-
-		// 1. clear counters and copy SA to temporary SA
-		arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
-		index.tempSA = infix(indexSA(index), left, right);
-
-		// 2. count characters
-		index.sentinelBound = 0;
-		index.sentinelOcc = _wotdCountChars(occ, text, tempSA, prefixLen);
-
-		// 3. cumulative sum
-		TSize requiredSize = 0;
-		if (index.interSentinelNodes) {
-			if (index.sentinelOcc != 0)
-				requiredSize = (index.sentinelOcc > 1)? 2: 1;	// insert *one* $-edge for all $_i suffices
-		} else
-			requiredSize = index.sentinelOcc;					// insert each $_i suffix one-by-one
-
-		requiredSize += _wotdCummulativeSum(bound, occ, left + index.sentinelOcc);
-		index.sentinelBound = left;
-
-		// 4. fill suffix array
-		{
-			TSA &sa = indexSA(index);
-			TSAIterator saBeg = begin(sa, Standard());
-			TCntIterator boundBeg = begin(bound, Standard());
-
-			TTextIterator itText = begin(text, Standard()) + prefixLen;
-			TConstCntIterator itSA = begin(tempSA, Standard());
-			TConstCntIterator itSAEnd = end(tempSA, Standard());
-			TTextSize textLength = length(text) - prefixLen;
-			for(; itSA != itSAEnd; ++itSA)
-			{
-				TTextSize saValue = *itSA;
-				if (textLength > saValue)
-					*(saBeg + (*(boundBeg + ordValue(*(itText + saValue))))++) = saValue;
-				else
-					if (textLength == saValue)
-						*(saBeg + index.sentinelBound++) = saValue;
-			}
-		}
-
-		return requiredSize;
-	}
-
-	// multiple sequences
-	template < typename TText, typename TSpec, typename TIndexSpec, typename TBeginPos, typename TEndPos, typename TSize >
-	TSize _sortWotdBucket(
-		Index<StringSet<TText, TSpec>, TIndexSpec> &index,
-		TBeginPos left, 
-		TEndPos right,
-		TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef Index<StringSet<TText, TSpec>, TIndexSpec>			TIndex;
-		typedef typename Fibre<TIndex, WotdSA >::Type				TSA;
-		typedef typename TIndex::TCounter							TCounter;
-		typedef typename TIndex::TTempSA							TTempSA;
-
-		typedef typename Iterator<TText const, Standard>::Type		TTextIterator;
-		typedef typename Iterator<TSA, Standard>::Type				TSAIterator;
-		typedef typename Iterator<TTempSA const, Standard>::Type    TTempSAIterator;
-		typedef typename Iterator<TCounter, Standard>::Type			TCntIterator;
-		typedef typename Size<TText>::Type							TTextSize;
-
-		StringSet<TText, TSpec> const &stringSet = indexText(index);
-		TTempSA const &tempSA = index.tempSA;
-		TCounter &occ = index.tempOcc;
-		TCounter &bound = index.tempBound;
-
-		// 1. clear counters and copy SA to temporary SA
-		TCntIterator occBeg = begin(occ, Standard());
-
-		arrayFill(occBeg, end(occ, Standard()), 0);
-		index.tempSA = infix(indexSA(index), left, right);
-
-		// 2. count characters
-		index.sentinelBound = 0;
-		index.sentinelOcc = _wotdCountChars(occ, stringSet, tempSA, prefixLen);
-
-		// 3. cumulative sum
-		TSize requiredSize = 0;
-		if (index.interSentinelNodes) {
-			if (index.sentinelOcc != 0)
-				requiredSize = (index.sentinelOcc > 1)? 2: 1;	// insert *one* $-edge for all $_i suffices
-		} else
-			requiredSize = index.sentinelOcc;					// insert each $_i suffix one-by-one
-
-		requiredSize += _wotdCummulativeSum(bound, occ, left + index.sentinelOcc);
-		index.sentinelBound = left;
-
-		// 4. fill suffix array
-		{
-			TSA &sa = indexSA(index);
-			TSAIterator saBeg = begin(sa, Standard());
-			TCntIterator boundBeg = begin(bound, Standard());
-
-			TTextIterator itText = TTextIterator();
-			TTempSAIterator itSA = begin(tempSA, Standard());
-			TTempSAIterator itSAEnd = end(tempSA, Standard());
-			TTextSize textLength = 0;
-			unsigned lastSeqSeen = (unsigned)-1;
-			Pair<unsigned, TTextSize> lPos;
-			for(; itSA != itSAEnd; ++itSA)
-			{
-				posLocalize(lPos, *itSA, stringSetLimits(index));
-				if (lastSeqSeen != getSeqNo(lPos))
-				{
-					lastSeqSeen = getSeqNo(lPos);
-
-					// shift textBegin and textLength by prefixLen
-					textLength = length(stringSet[lastSeqSeen]) - prefixLen;
-					itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
-				}
-				if (textLength > getSeqOffset(lPos))
-					*(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA;
-				else
-					if (textLength == getSeqOffset(lPos))
-						*(saBeg + index.sentinelBound++) = *itSA;
-			}
-		}
-
-		return requiredSize;
-	}
-
-
-
-
-
-	template < typename TSA, typename TText >
-	typename Size<TText>::Type 
-	_bucketLcp(TSA const &sa, TText const &text)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA const, Standard>::Type	TSAIterator;
-		typedef typename Value<TText>::Type						TValue;
-		typedef typename Size<TText>::Type						TTextSize;
-
-		TTextSize prefixLen = 0;
-		
-		if (length(sa) < 2) return prefixLen;
-
-		TTextIterator itText = begin(text, Standard());
-		TSAIterator itSAEnd = end(sa, Standard());
-		TTextSize textLength = length(text);
-
-		do {
-			TSAIterator itSA = begin(sa, Standard());
-			TTextSize sa = *itSA;
-			if (textLength == sa) return prefixLen;
-
-			TValue c = *(itText + sa);
-			for(++itSA; itSA != itSAEnd; ++itSA) {
-				sa = *itSA;
-				if (textLength == sa || c != *(itText + sa))
-					return prefixLen;
-			}
-			++prefixLen; --textLength;
-			++itText;
-		} while (true);
-	}
-
-	template < typename TSA, typename TText, typename TSize >
-	typename Size<TText>::Type 
-	_bucketLcp(TSA const &sa, TText const &text, TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA const, Standard>::Type	TSAIterator;
-		typedef typename Value<TText>::Type						TValue;
-		typedef typename Size<TText>::Type						TTextSize;
-
-		if (length(sa) < 2) return prefixLen;
-
-		TTextIterator itText = begin(text, Standard()) + prefixLen;
-		TSAIterator itSAEnd = end(sa, Standard());
-		TTextSize textLength = length(text) - prefixLen;
-
-		do {
-			TSAIterator itSA = begin(sa, Standard());
-			TTextSize sa = *itSA;
-			if (textLength == sa) return prefixLen;
-
-			TValue c = *(itText + sa);
-			for(++itSA; itSA != itSAEnd; ++itSA) {
-				sa = *itSA;
-				if (textLength == sa || *(itText + sa) != c)
-					return prefixLen;
-			}
-			++prefixLen; --textLength;
-			++itText;
-		} while (true);
-	}
-
-	template < typename TSA, typename TText, typename TSpec, typename TSize >
-	typename Size<TText>::Type 
-	_bucketLcp(TSA const &sa, StringSet<TText, TSpec> const &stringSet, TSize prefixLen)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TText const, Standard>::Type	TTextIterator;
-		typedef typename Iterator<TSA const, Standard>::Type	TSAIterator;
-		typedef typename Value<TText>::Type						TValue;
-		typedef typename Size<TText>::Type						TTextSize;
-
-		if (length(sa) < 2) return prefixLen;
-
-		TSAIterator itSAEnd = end(sa, Standard());
-		TTextIterator itText;
-		TTextSize textLength;
-
-		Pair<unsigned, TTextSize> lPos;
-		do {
-			TSAIterator itSA = begin(sa, Standard());
-			posLocalize(lPos, *itSA, stringSetLimits(stringSet));
-
-			unsigned lastSeqSeen = getSeqNo(*itSA);
-			textLength = length(stringSet[lastSeqSeen]) - prefixLen;
-			if (textLength == getSeqOffset(lPos)) return prefixLen;
-
-			itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
-			TValue c = *(itText + getSeqOffset(*itSA));
-			for(++itSA; itSA != itSAEnd; ++itSA)
-			{
-				posLocalize(lPos, *itSA, stringSetLimits(stringSet));
-
-				if (lastSeqSeen != getSeqNo(lPos))
-				{
-					lastSeqSeen = getSeqNo(lPos);
-
-					// shift textBegin and textLength by prefixLen
-					textLength = length(stringSet[lastSeqSeen]) - prefixLen;
-					itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
-				}
-
-				if (textLength == getSeqOffset(lPos) || c != *(itText + getSeqOffset(lPos)))
-					return prefixLen;
-			}
-			++prefixLen; --textLength;
-			++itText;
-		} while (true);
-	}
-
-
-	template <typename TText, typename TSpec, typename TPos>
-	inline TPos
-	_getNodeLP(
-		Index<TText, IndexWotd<TSpec> > const &index, 
-		TPos pos)
-	{
-		TPos w0 = dirAt(pos, index);
-		if (w0 & index.LEAF)
-			return w0 & index.BITMASK0;
-
-		TPos w1 = dirAt(pos + 1, index);
-		if (w1 & index.UNEVALUATED)
-			return saAt(w0 & index.BITMASK0, index);
-		else
-			return w0 & index.BITMASK0;
-	}
-
-	// store buckets into directory 
-	// ORIGINAL VERSION: storing SA entries and topology links in Dir
-	template <typename TText, typename TPos>
-	inline void 
-	_storeWotdChildren(
-		Index<TText, IndexWotd<WotdOriginal> > &index,
-		TPos dirOfs)
-	{
-	SEQAN_CHECKPOINT
-		typedef Index<TText, IndexWotd<WotdOriginal> >		TIndex;
-		typedef typename Fibre<TIndex, WotdDir>::Type		TDir;
-		typedef typename Iterator<TDir, Standard>::Type		TDirIterator;
-		typedef typename Size<TDir>::Type					TDirSize;
-		typedef typename TIndex::TCounter					TCounter;
-		typedef typename Iterator<TCounter, Standard>::Type	TCntIterator;
-
-		typedef typename Value<TCounter>::Type				TValue;
-
-		TDirIterator itDir = begin(indexDir(index), Standard()) + dirOfs;
-		TDirIterator itDirEnd = end(indexDir(index), Standard());
-		TDirIterator itPrev = itDirEnd;
-
-		TCntIterator it = begin(index.tempOcc, Standard());
-		TCntIterator bit = begin(index.tempBound, Standard());
-		TCntIterator itEnd = end(index.tempOcc, Standard());
-
-		TValue occ;
-		if (index.sentinelOcc != 0)
-		{
-			if (index.sentinelOcc > 1 && index.interSentinelNodes)	// occurs on multiseqs
-			{
-				itPrev = itDir;
-				*itDir = index.sentinelBound - index.sentinelOcc;	++itDir;
-				*itDir = index.sentinelBound | index.UNEVALUATED;	++itDir;
-			} else
-				for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d)
-				{
-					itPrev = itDir;
-					*itDir = saAt(d, index) | index.LEAF;			++itDir;
-				}
-		}
-		for (; it != itEnd; ++it, ++bit)
-		{
-			if ((occ = *it) == 0) continue;
-			if (occ > 1) {
-				itPrev = itDir;
-				*itDir = *bit - occ; 							++itDir;
-				*itDir = *bit | index.UNEVALUATED;				++itDir;
-			} else {
-				itPrev = itDir;
-				*itDir = saAt(*bit - occ, index) | index.LEAF;	++itDir;
-			}
-		}
-
-		// mark the last child
-		if (itPrev != itDirEnd)
-			*itPrev |= index.LAST_CHILD;
-	}
-
-	// store buckets into directory
-	// MODIFIED VERSION: storing SA links and topology links in Dir
-	template <typename TText, typename TSpec, typename TSize>
-	inline void 
-	_storeWotdChildren(
-		Index<TText, IndexWotd<TSpec> > &index,
-		TSize dirOfs,
-		TSize lcp)
-	{
-	SEQAN_CHECKPOINT
-		typedef Index<TText, IndexWotd<TSpec> >			TIndex;
-		typedef typename Fibre<TIndex, WotdDir>::Type		TDir;
-		typedef typename Iterator<TDir, Standard>::Type		TDirIterator;
-		typedef typename Size<TDir>::Type					TDirSize;
-		typedef typename TIndex::TCounter					TCounter;
-		typedef typename Iterator<TCounter, Standard>::Type	TCntIterator;
-
-		typedef typename Value<TCounter>::Type				TValue;
-
-		TDirIterator itDirBegin = begin(indexDir(index), Standard()) + dirOfs;
-		TDirIterator itDirEnd = end(indexDir(index), Standard());
-		TDirIterator itDir = itDirBegin;
-		TDirIterator itPrev = itDirEnd;
-
-		TCntIterator it = begin(index.tempOcc, Standard());
-		TCntIterator bit = begin(index.tempBound, Standard());
-		TCntIterator itEnd = end(index.tempOcc, Standard());
-
-		TValue occ;
-		if (index.sentinelOcc != 0)
-		{
-			if (index.sentinelOcc > 1 && index.interSentinelNodes)	// occurs on multiseqs
-			{ 
-				itPrev = itDir;
-				*itDir = index.sentinelBound - index.sentinelOcc;	++itDir;
-				*itDir = index.sentinelBound | index.UNEVALUATED;	++itDir;
-			} else
-				for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d)
-				{
-					itPrev = itDir;
-					*itDir = d | index.LEAF;						++itDir;
-				}
-		}
-		for (; it != itEnd; ++it, ++bit)
-		{
-			if ((occ = *it) == 0) continue;
-			if (occ > 1) {
-				itPrev = itDir;
-				*itDir = *bit - occ; 				++itDir;
-				*itDir = *bit | index.UNEVALUATED;	++itDir;
-			} else {
-				itPrev = itDir;
-				*itDir = (*bit - occ) | index.LEAF;	++itDir;
-			}
-		}
-
-		// first child gets the mutual lcp value of the children (== parent repLength)
-		*itDirBegin = ((*itDirBegin) & ~index.BITMASK0) | lcp;
-
-		// mark the last child
-		if (itPrev != itDirEnd)
-			*itPrev |= index.LAST_CHILD;
-	}
-
-
-	template < typename TText, typename TSpec >
-	inline typename Size< Index<TText, IndexWotd<WotdOriginal> > >::Type 
-	_wotdEvaluate(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree<TSpec> > const &it)
-	{
-		typedef Index<TText, IndexWotd<WotdOriginal> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
-
-		TIndex &index = const_cast<TIndex&>(container(it));
-		TSize pos = value(it).node;
-		TSize w1 = dirAt(pos + 1, index);
-
-		// test for evaluation
-		if (w1 & index.UNEVALUATED)
-		{
-			TSize w0 = dirAt(pos, index);
-			TSize lp = saAt(w0 & index.BITMASK0, index);
-			TSize dst = length(indexDir(index));
-
-			TSize size = _sortWotdBucket(
-				index, 
-				w0 & index.BITMASK0, 
-				w1 & index.BITMASK1, 
-				parentEdgeLength(it));
-
-			resize(indexDir(index), dst + size, Generous());
-			_storeWotdChildren(index, dst);
-
-			// mark nodes with solely empty child edges
-			w1 = dst;
-			if (index.sentinelOcc > 0)
+    // single sequence
+    template < typename TIndex >
+    typename Size<TIndex>::Type
+    _sortFirstWotdBucket(TIndex &index)
+    {
+        typedef typename Fibre<TIndex, WotdText >::Type        TText;
+        typedef typename Fibre<TIndex, WotdSA >::Type            TSA;
+        typedef typename TIndex::TCounter                        TCounter;
+
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA, Standard>::Type            TSAIterator;
+        typedef typename Iterator<TCounter, Standard>::Type        TCntIterator;
+        typedef typename Size<TText>::Type                        TSize;
+
+        TText const &text = indexText(index);
+        TCounter &occ = index.tempOcc;
+        TCounter &bound = index.tempBound;
+
+        // 1. clear counters and copy SA to temporary SA
+        arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
+
+        // 2. count characters
+        _wotdCountChars(occ, text);
+
+        // 3. cumulative sum
+        TSize requiredSize = _wotdCummulativeSum(bound, occ);
+
+        // 4. fill suffix array
+        {
+            TSA &sa = indexSA(index);
+            TSAIterator saBeg = begin(sa, Standard());
+            TCntIterator boundBeg = begin(bound, Standard());
+
+            TTextIterator itText = begin(text, Standard());
+            TTextIterator itTextEnd = end(text, Standard());
+            for(TSize i = 0; itText != itTextEnd; ++itText, ++i)
+                *(saBeg + (*(boundBeg + ordValue(getValue(itText))))++) = i;
+        }
+        index.sentinelOcc = 0;
+        index.sentinelBound = 0;
+
+        return requiredSize;
+    }
+
+    // multiple sequences
+    template < typename TText, typename TSpec, typename TIndexSpec >
+    typename Size< Index<StringSet<TText, TSpec>, TIndexSpec> >::Type
+    _sortFirstWotdBucket(Index<StringSet<TText, TSpec>, TIndexSpec> &index)
+    {
+        typedef Index<StringSet<TText, TSpec>, TIndexSpec>        TIndex;
+        typedef typename Fibre<TIndex, WotdSA >::Type            TSA;
+        typedef typename TIndex::TCounter                        TCounter;
+
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA, Standard>::Type            TSAIterator;
+        typedef typename Iterator<TCounter, Standard>::Type        TCntIterator;
+        typedef typename Size<TText>::Type                        TSize;
+
+        StringSet<TText, TSpec> const &stringSet = indexText(index);
+        TCounter &occ = index.tempOcc;
+        TCounter &bound = index.tempBound;
+
+        // 1. clear counters and copy SA to temporary SA
+        arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
+
+        // 2. count characters
+        _wotdCountChars(occ, stringSet);
+
+        // 3. cummulative sum
+        TSize requiredSize = _wotdCummulativeSum(bound, occ);
+
+        // 4. fill suffix array
+        for(unsigned seqNo = 0; seqNo < length(stringSet); ++seqNo)
+        {
+            TSA &sa = indexSA(index);
+            TSAIterator saBeg = begin(sa, Standard());
+            TCntIterator boundBeg = begin(bound, Standard());
+
+            typename Value<TSA>::Type localPos;
+            assignValueI1(localPos, seqNo);
+            assignValueI2(localPos, 0);
+
+            TText const &text = value(stringSet, seqNo);
+            TTextIterator itText = begin(text, Standard());
+            TTextIterator itTextEnd = end(text, Standard());
+            for(; itText != itTextEnd; ++itText)
+            {
+                *(saBeg + (*(boundBeg + ordValue(getValue(itText))))++) = localPos;
+                assignValueI2(localPos, getValueI2(localPos) + 1);
+            }
+        }
+        index.sentinelOcc = 0;
+        index.sentinelBound = 0;
+
+        return requiredSize;
+    }
+
+
+
+    // sort bucket using counting sort
+    // (nearly) ORIGINAL VERSION:
+    // - brings the bucket with the longest suffix (lpBucket) to front
+    // - all other buckets are in lexicographical order
+    // - adds prefixLen to all SA entries in SA[left,right)
+    template < typename TText, typename TBeginPos, typename TEndPos, typename TSize >
+    TSize _sortWotdBucket(
+        Index<TText, IndexWotd<WotdOriginal> > &index,
+        TBeginPos left,
+        TEndPos right,
+        TSize prefixLen)
+    {
+        typedef Index<TText, IndexWotd<WotdOriginal> >              TIndex;
+        typedef typename Fibre<TIndex, WotdSA >::Type               TSA;
+        typedef typename TIndex::TCounter                           TCounter;
+
+        typedef typename Iterator<TText const, Standard>::Type      TTextIterator;
+        typedef typename Iterator<TSA, Standard>::Type              TSAIterator;
+        typedef typename Iterator<TCounter, Standard>::Type         TCntIterator;
+        typedef typename Iterator<TCounter const, Standard>::Type   TConstCntIterator;
+        typedef typename Size<TText>::Type                          TTextSize;
+
+        TText const &text = indexText(index);
+        TCounter const &tempSA = index.tempSA;
+        TCounter &occ = index.tempOcc;
+        TCounter &bound = index.tempBound;
+
+        // 1. clear counters and copy SA to temporary SA
+        arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
+
+        // 2. count characters
+        index.tempSA = infix(indexSA(index), left, right);
+        index.sentinelBound = 0;
+        index.sentinelOcc =
+            _wotdCountCharsWotdOriginal(occ, text, index.tempSA, prefixLen);
+
+        // 3. cumulative sum
+        TSize requiredSize = 0;
+
+        // actually, here sentinelOcc<=1 holds (this is the original wotd)
+        if (index.interSentinelNodes) {
+            if (index.sentinelOcc != 0)
+                requiredSize = (index.sentinelOcc > 1)? 2: 1;    // insert *one* $-edge for all $_i suffices
+        } else
+            requiredSize = index.sentinelOcc;                    // insert each $_i suffix one-by-one
+
+        requiredSize += _wotdCummulativeSum(bound, occ, left + index.sentinelOcc);
+        index.sentinelBound = left;
+
+        // 4. fill suffix array
+        {
+            TSA &sa = indexSA(index);
+            TSAIterator saBeg = begin(sa, Standard());
+            TCntIterator boundBeg = begin(bound, Standard());
+
+            TTextIterator itText = begin(text, Standard());
+            TConstCntIterator itSA = begin(tempSA, Standard());
+            TConstCntIterator itSAEnd = end(tempSA, Standard());
+            TTextSize textLength = length(text);
+            for(; itSA != itSAEnd; ++itSA)
+            {
+                TTextSize saValue = *itSA;
+                if (textLength > saValue)
+                    *(saBeg + (*(boundBeg + ordValue(*(itText + saValue))))++) = saValue;
+                else
+                    if (textLength == saValue)
+                        *(saBeg + index.sentinelBound++) = saValue;
+            }
+        }
+
+        // 5. move lpBucket to front and add saOffset to hash directory entries
+        {
+            TSize lpBucket = ordValue(text[tempSA[0]]);
+            if (lpBucket != 0) {
+                TSize lpBucketOcc = occ[lpBucket];
+                TSize lpBucketBound = bound[lpBucket];
+
+                TCntIterator itOcc = begin(occ, Standard()) + lpBucket;
+                TCntIterator itBound = begin(bound, Standard()) + lpBucket;
+                TCntIterator itBeg = begin(bound, Standard());
+                for(; itBound != itBeg; --itBound, --itOcc) {
+                    *itOcc = *(itOcc - 1);
+                    *itBound = *(itBound - 1);
+                }
+                if (index.sentinelOcc != 0) {
+                    // bring first bucket before sentinel bucket
+                    *itOcc = index.sentinelOcc;
+                    *itBound = index.sentinelBound;
+                    index.sentinelOcc = lpBucketOcc;
+                    index.sentinelBound = lpBucketBound;
+                } else {
+                    *itOcc = lpBucketOcc;
+                    *itBound = lpBucketBound;
+                }
+            } else
+                if (index.sentinelOcc != 0) {
+                    // bring first bucket before sentinel bucket
+                    TSize swap = index.sentinelOcc;
+                    index.sentinelOcc = occ[0];
+                    occ[0] = swap;
+                    swap = index.sentinelBound;
+                    index.sentinelBound = bound[0];
+                    bound[0] = swap;
+                }
+        }
+
+        return requiredSize;
+    }
+
+
+
+
+
+    // sort bucket using counting sort
+    // MODIFIED VERSION:
+    // - all buckets are in lexicographical order
+    // - SA[left,right) contains real SA entries (the beginning positions of the suffices)
+
+    // single sequence
+    template < typename TIndex, typename TBeginPos, typename TEndPos, typename TSize >
+    TSize _sortWotdBucket(
+        TIndex &index,
+        TBeginPos left,
+        TEndPos right,
+        TSize prefixLen)
+    {
+        typedef typename Fibre<TIndex, WotdText >::Type             TText;
+        typedef typename Fibre<TIndex, WotdSA >::Type               TSA;
+        typedef typename TIndex::TCounter                           TCounter;
+
+        typedef typename Iterator<TText const, Standard>::Type      TTextIterator;
+        typedef typename Iterator<TSA, Standard>::Type              TSAIterator;
+        typedef typename Iterator<TCounter, Standard>::Type         TCntIterator;
+        typedef typename Iterator<TCounter const, Standard>::Type   TConstCntIterator;
+        typedef typename Size<TText>::Type                          TTextSize;
+
+        TText const &text = indexText(index);
+        TCounter const &tempSA = index.tempSA;
+        TCounter &occ = index.tempOcc;
+        TCounter &bound = index.tempBound;
+
+        // 1. clear counters and copy SA to temporary SA
+        arrayFill(begin(occ, Standard()), end(occ, Standard()), 0);
+        index.tempSA = infix(indexSA(index), left, right);
+
+        // 2. count characters
+        index.sentinelBound = 0;
+        index.sentinelOcc = _wotdCountChars(occ, text, tempSA, prefixLen);
+
+        // 3. cumulative sum
+        TSize requiredSize = 0;
+        if (index.interSentinelNodes) {
+            if (index.sentinelOcc != 0)
+                requiredSize = (index.sentinelOcc > 1)? 2: 1;    // insert *one* $-edge for all $_i suffices
+        } else
+            requiredSize = index.sentinelOcc;                    // insert each $_i suffix one-by-one
+
+        requiredSize += _wotdCummulativeSum(bound, occ, left + index.sentinelOcc);
+        index.sentinelBound = left;
+
+        // 4. fill suffix array
+        {
+            TSA &sa = indexSA(index);
+            TSAIterator saBeg = begin(sa, Standard());
+            TCntIterator boundBeg = begin(bound, Standard());
+
+            TTextIterator itText = begin(text, Standard()) + prefixLen;
+            TConstCntIterator itSA = begin(tempSA, Standard());
+            TConstCntIterator itSAEnd = end(tempSA, Standard());
+            TTextSize textLength = length(text) - prefixLen;
+            for(; itSA != itSAEnd; ++itSA)
+            {
+                TTextSize saValue = *itSA;
+                if (textLength > saValue)
+                    *(saBeg + (*(boundBeg + ordValue(*(itText + saValue))))++) = saValue;
+                else
+                    if (textLength == saValue)
+                        *(saBeg + index.sentinelBound++) = saValue;
+            }
+        }
+
+        return requiredSize;
+    }
+
+    // multiple sequences
+    template < typename TText, typename TSpec, typename TIndexSpec, typename TBeginPos, typename TEndPos, typename TSize >
+    TSize _sortWotdBucket(
+        Index<StringSet<TText, TSpec>, TIndexSpec> &index,
+        TBeginPos left,
+        TEndPos right,
+        TSize prefixLen)
+    {
+        typedef Index<StringSet<TText, TSpec>, TIndexSpec>            TIndex;
+        typedef typename Fibre<TIndex, WotdSA >::Type                TSA;
+        typedef typename TIndex::TCounter                            TCounter;
+        typedef typename TIndex::TTempSA                            TTempSA;
+
+        typedef typename Iterator<TText const, Standard>::Type        TTextIterator;
+        typedef typename Iterator<TSA, Standard>::Type                TSAIterator;
+        typedef typename Iterator<TTempSA const, Standard>::Type    TTempSAIterator;
+        typedef typename Iterator<TCounter, Standard>::Type            TCntIterator;
+        typedef typename Size<TText>::Type                            TTextSize;
+
+        StringSet<TText, TSpec> const &stringSet = indexText(index);
+        TTempSA const &tempSA = index.tempSA;
+        TCounter &occ = index.tempOcc;
+        TCounter &bound = index.tempBound;
+
+        // 1. clear counters and copy SA to temporary SA
+        TCntIterator occBeg = begin(occ, Standard());
+
+        arrayFill(occBeg, end(occ, Standard()), 0);
+        index.tempSA = infix(indexSA(index), left, right);
+
+        // 2. count characters
+        index.sentinelBound = 0;
+        index.sentinelOcc = _wotdCountChars(occ, stringSet, tempSA, prefixLen);
+
+        // 3. cumulative sum
+        TSize requiredSize = 0;
+        if (index.interSentinelNodes) {
+            if (index.sentinelOcc != 0)
+                requiredSize = (index.sentinelOcc > 1)? 2: 1;    // insert *one* $-edge for all $_i suffices
+        } else
+            requiredSize = index.sentinelOcc;                    // insert each $_i suffix one-by-one
+
+        requiredSize += _wotdCummulativeSum(bound, occ, left + index.sentinelOcc);
+        index.sentinelBound = left;
+
+        // 4. fill suffix array
+        {
+            if (empty(stringSet))
+                return requiredSize;
+
+            TSA &sa = indexSA(index);
+            TSAIterator saBeg = begin(sa, Standard());
+            TCntIterator boundBeg = begin(bound, Standard());
+
+            TTextIterator itText = begin(front(stringSet), Standard());
+            TTempSAIterator itSA = begin(tempSA, Standard());
+            TTempSAIterator itSAEnd = end(tempSA, Standard());
+            TTextSize textLength = 0;
+            unsigned lastSeqSeen = (unsigned)-1;
+            Pair<unsigned, TTextSize> lPos;
+            for(; itSA != itSAEnd; ++itSA)
+            {
+                posLocalize(lPos, *itSA, stringSetLimits(index));
+                if (lastSeqSeen != getSeqNo(lPos))
+                {
+                    lastSeqSeen = getSeqNo(lPos);
+
+                    // shift textBegin and textLength by prefixLen
+                    textLength = length(stringSet[lastSeqSeen]) - prefixLen;
+                    itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
+                }
+                if (textLength > getSeqOffset(lPos))
+                    *(saBeg + (*(boundBeg + ordValue(*(itText + getSeqOffset(lPos)))))++) = *itSA;
+                else
+                    if (textLength == getSeqOffset(lPos))
+                        *(saBeg + index.sentinelBound++) = *itSA;
+            }
+        }
+
+        return requiredSize;
+    }
+
+
+
+
+
+    template < typename TSA, typename TText >
+    typename Size<TText>::Type
+    _bucketLcp(TSA const &sa, TText const &text)
+    {
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+        typedef typename Value<TText>::Type                        TValue;
+        typedef typename Size<TText>::Type                        TTextSize;
+
+        TTextSize prefixLen = 0;
+
+        if (length(sa) < 2) return prefixLen;
+
+        TTextIterator itText = begin(text, Standard());
+        TSAIterator itSAEnd = end(sa, Standard());
+        TTextSize textLength = length(text);
+
+        do {
+            TSAIterator itSA = begin(sa, Standard());
+            TTextSize sa = *itSA;
+            if (textLength == sa) return prefixLen;
+
+            TValue c = *(itText + sa);
+            for(++itSA; itSA != itSAEnd; ++itSA) {
+                sa = *itSA;
+                if (textLength == sa || c != *(itText + sa))
+                    return prefixLen;
+            }
+            ++prefixLen; --textLength;
+            ++itText;
+        } while (true);
+    }
+
+    template < typename TSA, typename TText, typename TSize >
+    typename Size<TText>::Type
+    _bucketLcp(TSA const &sa, TText const &text, TSize prefixLen)
+    {
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+        typedef typename Value<TText>::Type                        TValue;
+        typedef typename Size<TText>::Type                        TTextSize;
+
+        if (length(sa) < 2) return prefixLen;
+
+        TTextIterator itText = begin(text, Standard()) + prefixLen;
+        TSAIterator itSAEnd = end(sa, Standard());
+        TTextSize textLength = length(text) - prefixLen;
+
+        do {
+            TSAIterator itSA = begin(sa, Standard());
+            TTextSize sa = *itSA;
+            if (textLength == sa) return prefixLen;
+
+            TValue c = *(itText + sa);
+            for(++itSA; itSA != itSAEnd; ++itSA) {
+                sa = *itSA;
+                if (textLength == sa || *(itText + sa) != c)
+                    return prefixLen;
+            }
+            ++prefixLen; --textLength;
+            ++itText;
+        } while (true);
+    }
+
+    template < typename TSA, typename TText, typename TSpec, typename TSize >
+    typename Size<TText>::Type
+    _bucketLcp(TSA const &sa, StringSet<TText, TSpec> const &stringSet, TSize prefixLen)
+    {
+        typedef typename Iterator<TText const, Standard>::Type    TTextIterator;
+        typedef typename Iterator<TSA const, Standard>::Type    TSAIterator;
+        typedef typename Value<TText>::Type                        TValue;
+        typedef typename Size<TText>::Type                        TTextSize;
+
+        if (length(sa) < 2) return prefixLen;
+
+        TSAIterator itSAEnd = end(sa, Standard());
+        TTextIterator itText;
+        TTextSize textLength;
+
+        Pair<unsigned, TTextSize> lPos;
+        do {
+            TSAIterator itSA = begin(sa, Standard());
+            posLocalize(lPos, *itSA, stringSetLimits(stringSet));
+
+            unsigned lastSeqSeen = getSeqNo(*itSA);
+            textLength = length(stringSet[lastSeqSeen]) - prefixLen;
+            if (textLength == getSeqOffset(lPos)) return prefixLen;
+
+            itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
+            TValue c = *(itText + getSeqOffset(*itSA));
+            for(++itSA; itSA != itSAEnd; ++itSA)
+            {
+                posLocalize(lPos, *itSA, stringSetLimits(stringSet));
+
+                if (lastSeqSeen != getSeqNo(lPos))
+                {
+                    lastSeqSeen = getSeqNo(lPos);
+
+                    // shift textBegin and textLength by prefixLen
+                    textLength = length(stringSet[lastSeqSeen]) - prefixLen;
+                    itText = begin(stringSet[lastSeqSeen], Standard()) + prefixLen;
+                }
+
+                if (textLength == getSeqOffset(lPos) || c != *(itText + getSeqOffset(lPos)))
+                    return prefixLen;
+            }
+            ++prefixLen; --textLength;
+            ++itText;
+        } while (true);
+    }
+
+
+    template <typename TText, typename TSpec, typename TPos>
+    inline TPos
+    _getNodeLP(
+        Index<TText, IndexWotd<TSpec> > const &index,
+        TPos pos)
+    {
+        TPos w0 = dirAt(pos, index);
+        if (w0 & index.LEAF)
+            return w0 & index.BITMASK0;
+
+        TPos w1 = dirAt(pos + 1, index);
+        if (w1 & index.UNEVALUATED)
+            return saAt(w0 & index.BITMASK0, index);
+        else
+            return w0 & index.BITMASK0;
+    }
+
+    // store buckets into directory
+    // ORIGINAL VERSION: storing SA entries and topology links in Dir
+    template <typename TText, typename TPos>
+    inline void
+    _storeWotdChildren(
+        Index<TText, IndexWotd<WotdOriginal> > &index,
+        TPos dirOfs)
+    {
+        typedef Index<TText, IndexWotd<WotdOriginal> >        TIndex;
+        typedef typename Fibre<TIndex, WotdDir>::Type        TDir;
+        typedef typename Iterator<TDir, Standard>::Type        TDirIterator;
+        typedef typename Size<TDir>::Type                    TDirSize;
+        typedef typename TIndex::TCounter                    TCounter;
+        typedef typename Iterator<TCounter, Standard>::Type    TCntIterator;
+
+        typedef typename Value<TCounter>::Type                TValue;
+
+        TDirIterator itDir = begin(indexDir(index), Standard()) + dirOfs;
+        TDirIterator itDirEnd = end(indexDir(index), Standard());
+        TDirIterator itPrev = itDirEnd;
+
+        TCntIterator it = begin(index.tempOcc, Standard());
+        TCntIterator bit = begin(index.tempBound, Standard());
+        TCntIterator itEnd = end(index.tempOcc, Standard());
+
+        TValue occ;
+        if (index.sentinelOcc != 0)
+        {
+            if (index.sentinelOcc > 1 && index.interSentinelNodes)    // occurs on multiseqs
+            {
+                itPrev = itDir;
+                *itDir = index.sentinelBound - index.sentinelOcc;    ++itDir;
+                *itDir = index.sentinelBound | index.UNEVALUATED;    ++itDir;
+            } else
+                for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d)
+                {
+                    itPrev = itDir;
+                    *itDir = saAt(d, index) | index.LEAF;            ++itDir;
+                }
+        }
+        for (; it != itEnd; ++it, ++bit)
+        {
+            if ((occ = *it) == 0) continue;
+            if (occ > 1) {
+                itPrev = itDir;
+                *itDir = *bit - occ;                             ++itDir;
+                *itDir = *bit | index.UNEVALUATED;                ++itDir;
+            } else {
+                itPrev = itDir;
+                *itDir = saAt(*bit - occ, index) | index.LEAF;    ++itDir;
+            }
+        }
+
+        // mark the last child
+        if (itPrev != itDirEnd)
+            *itPrev |= index.LAST_CHILD;
+    }
+
+    // store buckets into directory
+    // MODIFIED VERSION: storing SA links and topology links in Dir
+    template <typename TText, typename TSpec, typename TSize>
+    inline void
+    _storeWotdChildren(
+        Index<TText, IndexWotd<TSpec> > &index,
+        TSize dirOfs,
+        TSize lcp)
+    {
+        typedef Index<TText, IndexWotd<TSpec> >            TIndex;
+        typedef typename Fibre<TIndex, WotdDir>::Type        TDir;
+        typedef typename Iterator<TDir, Standard>::Type        TDirIterator;
+        typedef typename Size<TDir>::Type                    TDirSize;
+        typedef typename TIndex::TCounter                    TCounter;
+        typedef typename Iterator<TCounter, Standard>::Type    TCntIterator;
+
+        typedef typename Value<TCounter>::Type                TValue;
+
+        TDirIterator itDirBegin = begin(indexDir(index), Standard()) + dirOfs;
+        TDirIterator itDirEnd = end(indexDir(index), Standard());
+        TDirIterator itDir = itDirBegin;
+        TDirIterator itPrev = itDirEnd;
+
+        TCntIterator it = begin(index.tempOcc, Standard());
+        TCntIterator bit = begin(index.tempBound, Standard());
+        TCntIterator itEnd = end(index.tempOcc, Standard());
+
+        TValue occ;
+        if (index.sentinelOcc != 0)
+        {
+            if (index.sentinelOcc > 1 && index.interSentinelNodes)    // occurs on multiseqs
+            {
+                itPrev = itDir;
+                *itDir = index.sentinelBound - index.sentinelOcc;    ++itDir;
+                *itDir = index.sentinelBound | index.UNEVALUATED;    ++itDir;
+            } else
+                for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d)
+                {
+                    itPrev = itDir;
+                    *itDir = d | index.LEAF;                        ++itDir;
+                }
+        }
+        for (; it != itEnd; ++it, ++bit)
+        {
+            if ((occ = *it) == 0) continue;
+            if (occ > 1) {
+                itPrev = itDir;
+                *itDir = *bit - occ;                 ++itDir;
+                *itDir = *bit | index.UNEVALUATED;    ++itDir;
+            } else {
+                itPrev = itDir;
+                *itDir = (*bit - occ) | index.LEAF;    ++itDir;
+            }
+        }
+
+        // first child gets the mutual lcp value of the children (== parent repLength)
+        *itDirBegin = ((*itDirBegin) & ~index.BITMASK0) | lcp;
+
+        // mark the last child
+        if (itPrev != itDirEnd)
+            *itPrev |= index.LAST_CHILD;
+    }
+
+
+    template < typename TText, typename TSpec >
+    inline typename Size< Index<TText, IndexWotd<WotdOriginal> > >::Type
+    _wotdEvaluate(Iter< Index<TText, IndexWotd<WotdOriginal> >, VSTree<TSpec> > const &it)
+    {
+        typedef Index<TText, IndexWotd<WotdOriginal> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
+
+        TIndex &index = const_cast<TIndex&>(container(it));
+        TSize pos = value(it).node;
+        TSize w1 = dirAt(pos + 1, index);
+
+        // test for evaluation
+        if (w1 & index.UNEVALUATED)
+        {
+            TSize w0 = dirAt(pos, index);
+            TSize lp = saAt(w0 & index.BITMASK0, index);
+            TSize dst = length(indexDir(index));
+
+            TSize size = _sortWotdBucket(
+                index,
+                w0 & index.BITMASK0,
+                w1 & index.BITMASK1,
+                parentEdgeLength(it));
+
+            resize(indexDir(index), dst + size, Generous());
+            _storeWotdChildren(index, dst);
+
+            // mark nodes with solely empty child edges
+            w1 = dst;
+            if (index.sentinelOcc > 0)
             {
                 TSize sentinelSize = index.sentinelOcc;
                 if (index.interSentinelNodes && sentinelSize > 2)
                     sentinelSize = 2;
-				if (size == sentinelSize) w1 |= index.SENTINELS;
+                if (size == sentinelSize) w1 |= index.SENTINELS;
             }
 
-			assert(!(index.sentinelOcc == 1 && size == 1));
+            assert(!(index.sentinelOcc == 1 && size == 1));
 
-			dirAt(pos, index)     = (w0 & ~index.BITMASK0) | lp;
-			dirAt(pos + 1, index) = w1;
-		}
+            dirAt(pos, index)     = (w0 & ~index.BITMASK0) | lp;
+            dirAt(pos + 1, index) = w1;
+        }
 
-		return w1;
-	}
+        return w1;
+    }
 
-	template < typename TText, typename TIndexSpec, typename TSpec >
-	inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type 
-	_wotdEvaluate(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TSpec> > const &it)
-	{
-		typedef Index<TText, IndexWotd<TIndexSpec> >	TIndex;
-		typedef typename Size<TIndex>::Type				TSize;
+    template < typename TText, typename TIndexSpec, typename TSpec >
+    inline typename Size< Index<TText, IndexWotd<TIndexSpec> > >::Type
+    _wotdEvaluate(Iter< Index<TText, IndexWotd<TIndexSpec> >, VSTree<TSpec> > const &it)
+    {
+        typedef Index<TText, IndexWotd<TIndexSpec> >    TIndex;
+        typedef typename Size<TIndex>::Type                TSize;
 
-		TIndex &index = const_cast<TIndex&>(container(it));
-		TSize pos = value(it).node;
-		TSize w1 = dirAt(pos + 1, index);
+        TIndex &index = const_cast<TIndex&>(container(it));
+        TSize pos = value(it).node;
+        TSize w1 = dirAt(pos + 1, index);
 
-		// test for evaluation
-		if (w1 & index.UNEVALUATED) 
-		{
-			TSize dst = length(indexDir(index));
+        // test for evaluation
+        if (w1 & index.UNEVALUATED)
+        {
+            TSize dst = length(indexDir(index));
 
-			TSize size = _sortWotdBucket(
-				index, 
-				value(it).range.i1, 
-				w1 & index.BITMASK1, 
-				repLength(it));
+            TSize size = _sortWotdBucket(
+                index,
+                value(it).range.i1,
+                w1 & index.BITMASK1,
+                repLength(it));
 /*
-			if (globalDumpFlag) 
-			{
-				::std::cerr << '"' << representative(it) << '"' << ::std::endl;
+            if (globalDumpFlag)
+            {
+                std::cerr << '"' << representative(it) << '"' << std::endl;
                 for (int i=0;i<length(getOccurrences(it));++i)
-                    ::std::cerr << getOccurrences(it)[i]<<'\t'<<suffix(indexText(index),getOccurrences(it)[i])<<std::endl;
-//				_dumpFreq(index);
-			}
+                    std::cerr << getOccurrences(it)[i]<<'\t'<<suffix(indexText(index),getOccurrences(it)[i])<<std::endl;
+//                _dumpFreq(index);
+            }
 */
-			resize(indexDir(index), dst + size, Generous());
-			_storeWotdChildren(index, dst, repLength(it));
+            resize(indexDir(index), dst + size, Generous());
+            _storeWotdChildren(index, dst, repLength(it));
 
-			// mark nodes with solely empty child edges
-			w1 = dst;
-			if (index.sentinelOcc > 0)
+            // mark nodes with solely empty child edges
+            w1 = dst;
+            if (index.sentinelOcc > 0)
             {
                 TSize sentinelSize = index.sentinelOcc;
                 if (index.interSentinelNodes && sentinelSize > 2)
                     sentinelSize = 2;
-				if (size == sentinelSize) w1 |= index.SENTINELS;
+                if (size == sentinelSize) w1 |= index.SENTINELS;
             }
 
-			dirAt(pos + 1, index) = w1;
-		}
-
-		return w1;
-	}
-
-
-	template <typename TText, typename TSpec>
-	inline void
-	_dump(Index<TText, IndexWotd<TSpec> > &index)
-	{
-		typedef Index<TText, IndexWotd<TSpec> >			TIndex;
-		typedef typename Fibre<TIndex, WotdDir>::Type		TDir;
-		typedef typename Value<TDir>::Type					TDirValue;
+            dirAt(pos + 1, index) = w1;
+        }
 
-		::std::cout << "  Dir (wotd)" << ::std::endl;
-		for(unsigned i=0; i < length(indexDir(index)); ++i) {
-			TDirValue d = indexDir(index)[i];
-			::std::cout << i << ":  " << (d & index.BITMASK0);
-			if (d & index.LEAF)			::std::cout << "  (Leaf/Uneval)";
-			if (d & index.LAST_CHILD)	::std::cout << "  (LastChild/SENTINELS)";
-			::std::cout << ::std::endl;
-		}
+        return w1;
+    }
+
+
+    template <typename TText, typename TSpec>
+    inline void
+    _dump(Index<TText, IndexWotd<TSpec> > &index)
+    {
+        typedef Index<TText, IndexWotd<TSpec> >            TIndex;
+        typedef typename Fibre<TIndex, WotdDir>::Type        TDir;
+        typedef typename Value<TDir>::Type                    TDirValue;
+
+        std::cout << "  Dir (wotd)" << std::endl;
+        for(unsigned i=0; i < length(indexDir(index)); ++i) {
+            TDirValue d = indexDir(index)[i];
+            std::cout << i << ":  " << (d & index.BITMASK0);
+            if (d & index.LEAF)            std::cout << "  (Leaf/Uneval)";
+            if (d & index.LAST_CHILD)    std::cout << "  (LastChild/SENTINELS)";
+            std::cout << std::endl;
+        }
 
-		::std::cout << ::std::endl << "  SA" << ::std::endl;
-		for(unsigned i=0; i < length(indexSA(index)); ++i)
-			::std::cout << i << ":  " << indexSA(index)[i] << "  " << suffix(indexText(index), indexSA(index)[i]) << ::std::endl;
+        std::cout << std::endl << "  SA" << std::endl;
+        for(unsigned i=0; i < length(indexSA(index)); ++i)
+            std::cout << i << ":  " << indexSA(index)[i] << "  " << suffix(indexText(index), indexSA(index)[i]) << std::endl;
 
-		::std::cout << ::std::endl;
+        std::cout << std::endl;
 
-	}
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // _goDownChar
 
-	template < typename TText, class TSpec, typename TValue >
-	inline bool _goDownChar(
-		Iter<Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it,
-		TValue c)
-	{
-		typedef Index<TText, IndexWotd<TSpec> >	TIndex;
-		typedef typename Value<TIndex>::Type		TIndexValue;
-
-		bool sorted = false;
-		if (!goDown(it)) return false;
-		do {
-			if (parentEdgeLength(it) != 0) {
-				TIndexValue edgeChar = parentEdgeLabel(it)[0];
-				if (edgeChar == c) return true;		// the edge is found
-				if (sorted && edgeChar > c) break;	// too far (except the first one,
-			}										// child edges are sorted)
-			sorted = true;
-		} while (goRight(it));
-		_goUp(it);
-		return false;
-	}
-
-	template < typename TText, class TIndexSpec, class TSpec, typename TValue >
-	inline bool _goDownChar(
-		Iter<Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
-		TValue c)
-	{
-		typedef Index<TText, IndexWotd<TSpec> >	TIndex;
-		typedef typename Value<TIndex>::Type		TIndexValue;
-
-		if (!goDown(it)) return false;
-		do {
-			if (parentEdgeLength(it) != 0) {
-				TIndexValue edgeChar = parentEdgeLabel(it)[0];
-				if (edgeChar == c) return true;	// the edge is found
-				if (edgeChar > c) break;		// too far (child edges are sorted)
-			}
-		} while (goRight(it));
-		_goUp(it);
-		return false;
-	}
+    template < typename TText, class TSpec, typename TValue >
+    inline bool _goDownChar(
+        Iter<Index<TText, IndexWotd<WotdOriginal> >, VSTree< TopDown<TSpec> > > &it,
+        TValue c)
+    {
+        typedef Index<TText, IndexWotd<TSpec> >    TIndex;
+        typedef typename Value<TIndex>::Type        TIndexValue;
+
+        bool sorted = false;
+        if (!goDown(it)) return false;
+        do {
+            if (parentEdgeLength(it) != 0) {
+                TIndexValue edgeChar = parentEdgeLabel(it)[0];
+                if (edgeChar == c) return true;        // the edge is found
+                if (sorted && edgeChar > c) break;    // too far (except the first one,
+            }                                        // child edges are sorted)
+            sorted = true;
+        } while (goRight(it));
+        _goUp(it);
+        return false;
+    }
+
+    template < typename TText, class TIndexSpec, class TSpec, typename TValue >
+    inline bool _goDownChar(
+        Iter<Index<TText, IndexWotd<TIndexSpec> >, VSTree< TopDown<TSpec> > > &it,
+        TValue c)
+    {
+        typedef Index<TText, IndexWotd<TSpec> >    TIndex;
+        typedef typename Value<TIndex>::Type        TIndexValue;
+
+        if (!goDown(it)) return false;
+        do {
+            if (parentEdgeLength(it) != 0) {
+                TIndexValue edgeChar = parentEdgeLabel(it)[0];
+                if (edgeChar == c) return true;    // the edge is found
+                if (edgeChar > c) break;        // too far (child edges are sorted)
+            }
+        } while (goRight(it));
+        _goUp(it);
+        return false;
+    }
 
 /*
-	template < typename TText, typename TSpec, typename TValue >
-	inline bool
-	_getNodeByChar(
-		Iter< Index<TText, IndexWotd<TSpec> >, VSTree<TSpec> > const &it,
-		TValue c, 
-		typename VertexDescriptor< Index<TText, IndexWotd<TSpec> > >::Type &childDesc)
-	{
-		typedef Index<TText, IndexWotd<TSpec> >			TIndex;
-		typedef typename Fibre<TIndex, WotdDir>::Type		TDir;
-		typedef typename Fibre<TIndex, WotdSA>::Type		TSA;
-
-		typedef typename Value<TSA>::Type					TSAValue;
-		typedef typename Value<TDir>::Type					TDirValue;
-
-		typename Size<TIndex>::Type len = length(index);
-		typename VertexDescriptor<TIndex>::Type	desc;
-
-		TSAValue pos = _firstSuffixOfBucket(index, value(it).node);
-		while (pos == len || value < (c = textAt(index, pos + value.i2))) {
-			value.node += (dirAt(value.node, index) & index.LEAF)? 1: 2;
-			pos = _firstSuffixOfBucket(index, value.node);
-		}
-		assert(pos != len);
-
-		return c == value;
-	}
+    template < typename TText, typename TSpec, typename TValue >
+    inline bool
+    _getNodeByChar(
+        Iter< Index<TText, IndexWotd<TSpec> >, VSTree<TSpec> > const &it,
+        TValue c,
+        typename VertexDescriptor< Index<TText, IndexWotd<TSpec> > >::Type &childDesc)
+    {
+        typedef Index<TText, IndexWotd<TSpec> >            TIndex;
+        typedef typename Fibre<TIndex, WotdDir>::Type        TDir;
+        typedef typename Fibre<TIndex, WotdSA>::Type        TSA;
+
+        typedef typename Value<TSA>::Type                    TSAValue;
+        typedef typename Value<TDir>::Type                    TDirValue;
+
+        typename Size<TIndex>::Type len = length(index);
+        typename VertexDescriptor<TIndex>::Type    desc;
+
+        TSAValue pos = _firstSuffixOfBucket(index, value(it).node);
+        while (pos == len || value < (c = textAt(index, pos + value.i2))) {
+            value.node += (dirAt(value.node, index) & index.LEAF)? 1: 2;
+            pos = _firstSuffixOfBucket(index, value.node);
+        }
+        assert(pos != len);
+
+        return c == value;
+    }
 */
 
 //////////////////////////////////////////////////////////////////////////////
-// interface for automatic index creation 
+// interface for automatic index creation
 
-	template <typename TText, typename TSpec>
-	inline void _wotdCreateFirstLevel(Index<TText, IndexWotd<TSpec> > &index)
-	{
+    template <typename TText, typename TSpec>
+    inline void _wotdCreateFirstLevel(Index<TText, IndexWotd<TSpec> > &index)
+    {
         typedef Index<TText, IndexWotd<TSpec> > TIndex;
         typedef typename Value<TIndex>::Type    TValue;
         typedef typename Size<TIndex>::Type     TSize;
 
-		resize(index.tempOcc, ValueSize<TValue>::VALUE + 1, Exact());
-		resize(index.tempBound, ValueSize<TValue>::VALUE + 1, Exact());
-
-		TSize size;
-		if (empty(indexSA(index)))
-		{
-			resize(indexSA(index), length(indexRawText(index)), Exact());
-			size = _sortFirstWotdBucket(index);
-		} else
-		{
-			size = _sortWotdBucket(index, 0, length(indexSA(index)), 0);
-		}
-		
-		if (size > 0) 
-		{
-			resize(indexDir(index), size + 2, Generous());
-			_storeWotdChildren(index, 2, 0);
-
-			// mark nodes with solely empty child edges
-			TSize w1 = 2;
-			if (index.sentinelOcc > 0)
+        resize(index.tempOcc, ValueSize<TValue>::VALUE + 1, Exact());
+        resize(index.tempBound, ValueSize<TValue>::VALUE + 1, Exact());
+
+        TSize size;
+        if (empty(indexSA(index)))
+        {
+            resize(indexSA(index), length(indexRawText(index)), Exact());
+            size = _sortFirstWotdBucket(index);
+        } else
+        {
+            size = _sortWotdBucket(index, 0, length(indexSA(index)), 0);
+        }
+
+        if (size > 0)
+        {
+            resize(indexDir(index), size + 2, Generous());
+            _storeWotdChildren(index, 2, 0);
+
+            // mark nodes with solely empty child edges
+            TSize w1 = 2;
+            if (index.sentinelOcc > 0)
             {
                 TSize sentinelSize = index.sentinelOcc;
                 if (index.interSentinelNodes && sentinelSize > 2)
                     sentinelSize = 2;
-				if (size == sentinelSize) w1 |= index.SENTINELS;
+                if (size == sentinelSize) w1 |= index.SENTINELS;
             }
 
 
-			dirAt(0, index) = 0 | index.LAST_CHILD;
-			dirAt(1, index) = w1;
+            dirAt(0, index) = 0 | index.LAST_CHILD;
+            dirAt(1, index) = w1;
 
-		} else {
-			resize(indexDir(index), 1);
-			dirAt(0, index) = 0 | index.LAST_CHILD | index.LEAF;
-		}
-	}
+        } else {
+            resize(indexDir(index), 1);
+            dirAt(0, index) = 0 | index.LAST_CHILD | index.LEAF;
+        }
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexCreate(Index<TText, IndexWotd<TSpec> > &index, WotdDir const, Default const)
+    {
+        _wotdCreateFirstLevel(index);
+        return true;
+    }
+
+    template <typename TText, typename TSpec>
+    inline bool indexCreate(Index<TText, IndexWotd<TSpec> > &index, WotdDir const, Trie const)
+    {
+        resize(indexSA(index), length(indexText(index)), Exact());
+        fillSuffixArray(indexSA(index), indexText(index), Trie());
+        _wotdCreateFirstLevel(index);
+        return true;
+    }
 
-	template <typename TText, typename TSpec>
-	inline bool indexCreate(Index<TText, IndexWotd<TSpec> > &index, WotdDir const, Default const)
-	{
-		_wotdCreateFirstLevel(index);
-		return true;
-	}
 
 //////////////////////////////////////////////////////////////////////////////
 // clear
 
-	template < typename TText, typename TSpec >
-	inline void clear(Index<TText, IndexWotd<TSpec> > &index)
-	{
-		clear(getFibre(index, WotdSA()));
-		clear(getFibre(index, WotdDir()));
-	}
+    template < typename TText, typename TSpec >
+    inline void clear(Index<TText, IndexWotd<TSpec> > &index)
+    {
+        clear(getFibre(index, WotdSA()));
+        clear(getFibre(index, WotdDir()));
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 // open
 
-	template < typename TText, typename TSpec >
-	inline bool open(
-		Index< TText, IndexWotd<TSpec> > &index, 
-		const char *fileName,
-		int openMode)
-	{
+    template < typename TText, typename TSpec >
+    inline bool open(
+        Index< TText, IndexWotd<TSpec> > &index,
+        const char *fileName,
+        int openMode)
+    {
         typedef Index<TText, IndexWotd<TSpec> > TIndex;
         typedef typename Value<TIndex>::Type    TValue;
 
-		String<char> name;
+        String<char> name;
 
-		name = fileName;	append(name, ".txt");
-		if ((!open(getFibre(index, WotdText()), toCString(name), openMode)) && 
-			(!open(getFibre(index, WotdText()), fileName, openMode))) return false;
+        name = fileName;    append(name, ".txt");
+        if ((!open(getFibre(index, WotdText()), toCString(name), openMode)) &&
+            (!open(getFibre(index, WotdText()), fileName, openMode))) return false;
 
-		name = fileName;	append(name, ".sa");
+        name = fileName;    append(name, ".sa");
         if (!open(getFibre(index, WotdSA()), toCString(name), openMode)) return false;
-		name = fileName;	append(name, ".dir");
+        name = fileName;    append(name, ".dir");
 
         if (!open(getFibre(index, WotdDir()), toCString(name), openMode)) return false;
 
@@ -2096,47 +2068,47 @@ if it is traversed. For details see Giegerich et al., "Efficient implementation
             resize(index.tempBound, ValueSize<TValue>::VALUE + 1);
         }
 
-		return true;
-	}
-	template < typename TText, typename TSpec >
-	inline bool open(
-		Index< TText, IndexWotd<TSpec> > &index, 
-		const char *fileName) 
-	{
-		return open(index, fileName, OPEN_RDONLY);
-	}
+        return true;
+    }
+    template < typename TText, typename TSpec >
+    inline bool open(
+        Index< TText, IndexWotd<TSpec> > &index,
+        const char *fileName)
+    {
+        return open(index, fileName, OPEN_RDONLY);
+    }
 
 
 //////////////////////////////////////////////////////////////////////////////
 // save
 
-	template < typename TText, typename TSpec >
-	inline bool save(
-		Index< TText, IndexWotd<TSpec> > &index, 
-		const char *fileName,
-		int openMode)
-	{
-		String<char> name;
-
-		name = fileName;	append(name, ".txt");
-		if ((!save(getFibre(index, WotdText()), toCString(name), openMode)) && 
-			(!save(getFibre(index, WotdText()), fileName, openMode))) return false;
-
-		name = fileName;	append(name, ".sa");
+    template < typename TText, typename TSpec >
+    inline bool save(
+        Index< TText, IndexWotd<TSpec> > &index,
+        const char *fileName,
+        int openMode)
+    {
+        String<char> name;
+
+        name = fileName;    append(name, ".txt");
+        if ((!save(getFibre(index, WotdText()), toCString(name), openMode)) &&
+            (!save(getFibre(index, WotdText()), fileName, openMode))) return false;
+
+        name = fileName;    append(name, ".sa");
         if (!save(getFibre(index, WotdSA()), toCString(name), openMode)) return false;
-		name = fileName;	append(name, ".dir");
+        name = fileName;    append(name, ".dir");
 
         if (!save(getFibre(index, WotdDir()), toCString(name), openMode)) return false;
-        
-		return true;
-	}
-	template < typename TText, typename TSpec >
-	inline bool save(
-		Index< TText, IndexWotd<TSpec> > &index, 
-		const char *fileName)
-	{
-		return save(index, fileName, OPEN_WRONLY | OPEN_CREATE);
-	}
+
+        return true;
+    }
+    template < typename TText, typename TSpec >
+    inline bool save(
+        Index< TText, IndexWotd<TSpec> > &index,
+        const char *fileName)
+    {
+        return save(index, fileName, OPEN_WRONLY | OPEN_CREATE);
+    }
 }
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/index/pipe_merger3.h b/seqan/index/pipe_merger3.h
index 2622c97..d6af45c 100644
--- a/seqan/index/pipe_merger3.h
+++ b/seqan/index/pipe_merger3.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,7 +41,7 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct Merger3;
+    struct Merger3;
 
     template < typename TInput0, typename TInput12 >
     struct Value< Pipe< Bundle2< TInput0, TInput12 >, Merger3 > >
@@ -68,7 +68,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
         Pipe(Bundle2< TInput0, TInput12 > _in):
             in(_in) {}
-        
+
         static inline bool less1(const InType0& i0, const InType12& i12)
         { // lexic. order for pairs
             return (i0.i3[0] <  i12.i3[0] ||
@@ -102,7 +102,7 @@ namespace SEQAN_NAMESPACE_MAIN
         inline typename Value<Pipe>::Type const & operator*() const {
             return tmp;
         }
-        
+
         inline Pipe& operator++() {
             if (minStream) {
                 #ifdef SEQAN_TEST_SKEW3
@@ -146,15 +146,15 @@ namespace SEQAN_NAMESPACE_MAIN
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
     template < typename TInput >
-	inline bool control(Pipe< TInput, Merger3 > &me, ControlBeginRead const &command) {
+    inline bool control(Pipe< TInput, Merger3 > &me, ControlBeginRead const &command) {
         if (!control(me.in, command)) return false;
         me.twoStreams = !eof(me.in.in1);
         me.minStream = eof(me.in.in2)? -1: 1;
         me.N = length(me);
         me.getMin();
-		return true;
-	}
-    
+        return true;
+    }
+
     template < typename TInput >
     inline typename Size< Pipe< TInput, Merger3 > >::Type
     length(Pipe< TInput, Merger3 > const &me) {
diff --git a/seqan/index/pipe_merger7.h b/seqan/index/pipe_merger7.h
index 243f3b7..59f2c3a 100644
--- a/seqan/index/pipe_merger7.h
+++ b/seqan/index/pipe_merger7.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,29 +41,29 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	template <int I, typename T = void>
-	struct SkewShift_;
+    template <int I, typename T = void>
+    struct SkewShift_;
 
-	template <int I, typename T = void>
-	struct SkewNIndex_;
+    template <int I, typename T = void>
+    struct SkewNIndex_;
 
 
-	template <typename T>
-	struct SkewShift_<7, T>
+    template <typename T>
+    struct SkewShift_<7, T>
     {
-		static const unsigned VALUE[7][7];
-	};
+        static const unsigned VALUE[7][7];
+    };
 
-	template <typename T>
-	struct SkewNIndex_<7, T>
+    template <typename T>
+    struct SkewNIndex_<7, T>
     {
-		static const unsigned VALUE[7][7];
-	};
+        static const unsigned VALUE[7][7];
+    };
 
 
-	template <typename T>
-	const unsigned SkewShift_<7, T>::VALUE[7][7] =
-								  {{0,6,5,6,3,3,5},
+    template <typename T>
+    const unsigned SkewShift_<7, T>::VALUE[7][7] =
+                                  {{0,6,5,6,3,3,5},
                                    {6,0,0,6,0,4,4},
                                    {5,0,0,1,0,1,5},
                                    {6,6,1,0,2,1,2},
@@ -72,9 +72,9 @@ namespace SEQAN_NAMESPACE_MAIN
                                    {5,4,5,2,2,4,0}};
 
 
-	template <typename T>
-	const unsigned SkewNIndex_<7, T>::VALUE[7][7] =
-								  {{0,0,0,0,0,1,2},
+    template <typename T>
+    const unsigned SkewNIndex_<7, T>::VALUE[7][7] =
+                                  {{0,0,0,0,0,1,2},
                                    {0,0,0,0,1,1,2},
                                    {0,1,1,1,1,2,2},
                                    {0,0,1,1,1,1,2},
@@ -89,30 +89,30 @@ namespace SEQAN_NAMESPACE_MAIN
         TValue      i;
         unsigned    stream;
     };
-    
+
     template <typename TValue>
-	std::ostream& operator<<(std::ostream &out, const SkewDCStream<TValue> &s)
+    std::ostream& operator<<(std::ostream &out, const SkewDCStream<TValue> &s)
     {
-		out << "< " << s.i.i1 << " , [ ";
-		for(unsigned i = 0; i < 3; ++i)
-			out << s.i.i2[i] << " ";
-		out << "] , [ ";
-		for(unsigned i = 0; i < 6; ++i)
-			out << s.i.i3[i] << " ";
-		out << "] , " << s.stream << " >";
-		return out;
-	}
-
-
-	// greater-operator for two SkewDCStreams
+        out << "< " << s.i.i1 << " , [ ";
+        for(unsigned i = 0; i < 3; ++i)
+            out << s.i.i2[i] << " ";
+        out << "] , [ ";
+        for(unsigned i = 0; i < 6; ++i)
+            out << s.i.i3[i] << " ";
+        out << "] , " << s.stream << " >";
+        return out;
+    }
+
+
+    // greater-operator for two SkewDCStreams
     template <typename TValue>
     struct CompareSkewDCStream :
-        public ::std::binary_function < SkewDCStream<TValue>,
+        public std::binary_function < SkewDCStream<TValue>,
                                         SkewDCStream<TValue>,
                                         bool >
     {
         inline bool operator()(const SkewDCStream<TValue> &a,
-			                   const SkewDCStream<TValue> &b) const 
+                               const SkewDCStream<TValue> &b) const
         {
             typedef typename Value<TValue, 2>::Type     TNameTuple;
             typedef typename Value<TNameTuple>::Type    TName;
@@ -124,33 +124,33 @@ namespace SEQAN_NAMESPACE_MAIN
                 if (a.i.i3[i] < b.i.i3[i]) return false;
                 if (a.i.i3[i] > b.i.i3[i]) return true;
             }
-            
+
             TName na = a.i.i2[SkewNIndex_<7>::VALUE[a.stream][shft]];
             TName nb = b.i.i2[SkewNIndex_<7>::VALUE[b.stream][shft]];
             if (na < nb) return false;
             if (na > nb) return true;
 
-			// we get here, only if a septet crosses the border of
-			// the single text or a sequence in a multiple sequence text
-			return a.stream - 1 > b.stream - 1; // this is NOT the same as a.stream > b.stream, 0 should be bigger than 6
+            // we get here, only if a septet crosses the border of
+            // the single text or a sequence in a multiple sequence text
+            return a.stream - 1 > b.stream - 1; // this is NOT the same as a.stream > b.stream, 0 should be bigger than 6
         }
     };
 
 
-	// greater-operator for two SkewDCStreams (optimized for bit-packed character tuples)
+    // greater-operator for two SkewDCStreams (optimized for bit-packed character tuples)
     template <typename T1, typename T2, typename T, unsigned SIZE>
     struct CompareSkewDCStream< Triple<T1, T2, Tuple<T, SIZE, BitPacked<> >, Pack> > :
-        public ::std::binary_function < SkewDCStream<Triple<T1, T2, Tuple<T, SIZE, BitPacked<> >, Pack> >,
+        public std::binary_function < SkewDCStream<Triple<T1, T2, Tuple<T, SIZE, BitPacked<> >, Pack> >,
                                         SkewDCStream<Triple<T1, T2, Tuple<T, SIZE, BitPacked<> >, Pack> >,
                                         bool >
     {
         typedef Tuple<T,SIZE, BitPacked<> > T3;
         inline bool operator()(const SkewDCStream<Triple<T1, T2, T3, Pack> > &a,
-			                   const SkewDCStream<Triple<T1, T2, T3, Pack> > &b) const 
+                               const SkewDCStream<Triple<T1, T2, T3, Pack> > &b) const
         {
             typedef typename Value<T2>::Type TName;
             typedef typename Value<T3>::Type TValue3;
-            
+
             int shft = SkewShift_<7>::VALUE[a.stream][b.stream];
             typename T3::TBitVector mask = ~((1 << ((SIZE - shft) * BitsPerValue<TValue3>::VALUE)) - 1);
 
@@ -162,32 +162,32 @@ namespace SEQAN_NAMESPACE_MAIN
             if (na < nb) return false;
             if (na > nb) return true;
 
-			// we get here, only if a septet crosses the border of
-			// the single text or a sequence in a multiple sequence text
-			return a.stream - 1 > b.stream - 1; // this is NOT the same as a.stream > b.stream, 0 should be bigger than 6
-		}
+            // we get here, only if a septet crosses the border of
+            // the single text or a sequence in a multiple sequence text
+            return a.stream - 1 > b.stream - 1; // this is NOT the same as a.stream > b.stream, 0 should be bigger than 6
+        }
     };
 
 
 
 
-	struct Merger7;
+    struct Merger7;
 
     template < typename TInput0, typename TInput3, typename TInput5, typename TInput6, typename TInput124 >
     struct Value< Pipe< Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 >, Merger7 > >
     {
-		typedef typename Value<TInput0>::Type       TInValue0;
+        typedef typename Value<TInput0>::Type       TInValue0;
         typedef typename Value<TInValue0, 1>::Type  Type;
     };
 
 
-	template <typename TLimitsString>
-	struct Merger7Multi;
+    template <typename TLimitsString>
+    struct Merger7Multi;
 
     template < typename TInput0, typename TInput3, typename TInput5, typename TInput6, typename TInput124, typename TLimitsString >
     struct Value< Pipe< Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 >, Merger7Multi<TLimitsString> > >
     {
-		typedef typename Value<TInput0>::Type       TInValue0;
+        typedef typename Value<TInput0>::Type       TInValue0;
         typedef typename Value<TInValue0, 1>::Type  Type;
     };
 
@@ -209,10 +209,10 @@ namespace SEQAN_NAMESPACE_MAIN
 
         typedef SkewDCStream<TInValue0>             TSkewDCStream;
 
-		TSkewDCStream								inValue[7];
-		unsigned									rank[5];
-		unsigned									first;
-        CompareSkewDCStream<TInValue0>				streamGreater;
+        TSkewDCStream                                inValue[7];
+        unsigned                                    rank[5];
+        unsigned                                    first;
+        CompareSkewDCStream<TInValue0>                streamGreater;
 
         Bundle5 <
             TInput0,
@@ -221,9 +221,10 @@ namespace SEQAN_NAMESPACE_MAIN
             TInput6,
             TInput124 > in;
         TSize N;
-        
+
         Pipe(Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 > _in):
-            in(_in) {}
+            first(0), in(_in), N(0)
+        {}
 
         template <typename T1, typename T2, typename T3>
         inline static void _copy(TSkewDCStream &dst, Triple<T1,T2,T3, Pack> const &src)
@@ -234,8 +235,8 @@ namespace SEQAN_NAMESPACE_MAIN
 
         template <typename T1, typename T2, typename T, unsigned SIZE>
         inline static void _copy(TSkewDCStream &dst, Triple<T1,T2,Tuple<T,SIZE, BitPacked<> >, Pack> const &src)
-		{
-			typedef typename Value<TInValue0, 3>::Type TCharTuple;
+        {
+            typedef typename Value<TInValue0, 3>::Type TCharTuple;
             memcpy(&dst.i.i2, &src.i2, sizeof(T2));
             dst.i.i3 = src.i3;
             dst.i.i3 <<= LENGTH<TCharTuple>::VALUE - SIZE;
@@ -246,95 +247,95 @@ namespace SEQAN_NAMESPACE_MAIN
             return getValueI1(inValue[rank[first]].i);
         }
 
-		inline void insertStream(unsigned stream)
+        inline void insertStream(unsigned stream)
         {
             switch (stream) {
                 case 0:
-					if (eof(in.in1)) {
-						++first;
-						return;
-					}
-					inValue[0].i.i1 = N - (*in.in1).i1;
-					_copy(inValue[0], *in.in1);
-					++in.in1;
+                    if (eof(in.in1)) {
+                        ++first;
+                        return;
+                    }
+                    inValue[0].i.i1 = N - (*in.in1).i1;
+                    _copy(inValue[0], *in.in1);
+                    ++in.in1;
                     break;
 
                 case 3:
-					if (eof(in.in2)) {
-						++first;
-						return;
-					}
-					inValue[3].i.i1 = N - (*in.in2).i1;
-					_copy(inValue[3], *in.in2);
-					++in.in2;
+                    if (eof(in.in2)) {
+                        ++first;
+                        return;
+                    }
+                    inValue[3].i.i1 = N - (*in.in2).i1;
+                    _copy(inValue[3], *in.in2);
+                    ++in.in2;
                     break;
 
                 case 5:
-					if (eof(in.in3)) {
-						++first;
-						return;
-					}
-					inValue[5].i.i1 = N - (*in.in3).i1;
-					_copy(inValue[5], *in.in3);
-					++in.in3;
+                    if (eof(in.in3)) {
+                        ++first;
+                        return;
+                    }
+                    inValue[5].i.i1 = N - (*in.in3).i1;
+                    _copy(inValue[5], *in.in3);
+                    ++in.in3;
                     break;
 
                 case 6:
-					if (eof(in.in4)) {
-						++first;
-						return;
-					}
-					inValue[6].i.i1 = N - (*in.in4).i1;
-					_copy(inValue[6], *in.in4);
-					++in.in4;
-					break;
-
-				default:	// case 1, 2, or 4
-					if (eof(in.in5)) {
-						++first;
-						return;
-					}
-					// calculate residue class from the suffix length
-					inValue[1].stream = (*in.in5).i1 % 7;
-					inValue[1].i.i1 = N - (*in.in5).i1;
-					_copy(inValue[1], *in.in5);
-					++in.in5;
+                    if (eof(in.in4)) {
+                        ++first;
+                        return;
+                    }
+                    inValue[6].i.i1 = N - (*in.in4).i1;
+                    _copy(inValue[6], *in.in4);
+                    ++in.in4;
+                    break;
+
+                default:    // case 1, 2, or 4
+                    if (eof(in.in5)) {
+                        ++first;
+                        return;
+                    }
+                    // calculate residue class from the suffix length
+                    inValue[1].stream = (*in.in5).i1 % 7;
+                    inValue[1].i.i1 = N - (*in.in5).i1;
+                    _copy(inValue[1], *in.in5);
+                    ++in.in5;
             }
 
-			// linear search
-			int right;
-			for(right = first + 1;  right < 5;  ++right)
-				if (!streamGreater(inValue[stream],inValue[rank[right]])) break;
+            // linear search
+            int right;
+            for(right = first + 1;  right < 5;  ++right)
+                if (!streamGreater(inValue[stream],inValue[rank[right]])) break;
 
-			// remove the least suffix ...
-			for(int i = first + 1;  i < right;  ++i)
-				rank[i-1] = rank[i];
+            // remove the least suffix ...
+            for(int i = first + 1;  i < right;  ++i)
+                rank[i-1] = rank[i];
+
+            // ... and insert the new one
+            rank[right-1] = stream;
+        }
 
-			// ... and insert the new one
-			rank[right-1] = stream;
-		}
-        
         Pipe& operator++()
         {
-			insertStream(rank[first]);
+            insertStream(rank[first]);
             return *this;
         }
 
         void fill()
         {
-			inValue[0].stream = 0;
-			inValue[3].stream = 3;
-			inValue[5].stream = 5;
-			inValue[6].stream = 6;
-
-			first = 4;	insertStream(0);
-			--first;    insertStream(3);
-			--first;    insertStream(5);
-			--first;    insertStream(6);
-			--first;	insertStream(1);
+            inValue[0].stream = 0;
+            inValue[3].stream = 3;
+            inValue[5].stream = 5;
+            inValue[6].stream = 6;
+
+            first = 4;    insertStream(0);
+            --first;    insertStream(3);
+            --first;    insertStream(5);
+            --first;    insertStream(6);
+            --first;    insertStream(1);
         }
-	};
-    
+    };
+
 
     //////////////////////////////////////////////////////////////////////////////
     // merger7 class for multiple sequences
@@ -353,10 +354,10 @@ namespace SEQAN_NAMESPACE_MAIN
 
         typedef SkewDCStream<TInValue0>             TSkewDCStream;
 
-		TSkewDCStream								inValue[7];
-		unsigned									rank[5];
-		unsigned									first;
-        CompareSkewDCStream<TInValue0>				streamGreater;
+        TSkewDCStream                                inValue[7];
+        unsigned                                    rank[5];
+        unsigned                                    first;
+        CompareSkewDCStream<TInValue0>                streamGreater;
 
         Bundle5 <
             TInput0,
@@ -364,11 +365,11 @@ namespace SEQAN_NAMESPACE_MAIN
             TInput5,
             TInput6,
             TInput124 > in;
-		TLimitsString const &limits;
-        
+        TLimitsString const &limits;
+
         Pipe(Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 > _in, TLimitsString const &_limits):
-            in(_in),
-			limits(_limits) {}
+            in(_in), limits(_limits)
+        {}
 
         template <typename T1, typename T2, typename T3>
         inline static void _copy(TSkewDCStream &dst, Triple<T1,T2,T3, Pack> const &src)
@@ -380,8 +381,8 @@ namespace SEQAN_NAMESPACE_MAIN
 
         template <typename T1, typename T2, typename T, unsigned SIZE>
         inline static void _copy(TSkewDCStream &dst, Triple<T1,T2,Tuple<T,SIZE, BitPacked<> >, Pack> const &src)
-		{
-			typedef typename Value<TInValue0, 3>::Type TCharTuple;
+        {
+            typedef typename Value<TInValue0, 3>::Type TCharTuple;
             memcpy(&dst.i.i1, &src.i1, sizeof(T1));
             memcpy(&dst.i.i2, &src.i2, sizeof(T2));
             dst.i.i3 = src.i3;
@@ -393,115 +394,115 @@ namespace SEQAN_NAMESPACE_MAIN
             return getValueI1(inValue[rank[first]].i);
         }
 
-		inline void insertStream(unsigned stream)
+        inline void insertStream(unsigned stream)
         {
             switch (stream) {
                 case 0:
-					if (eof(in.in1)) {
-						++first;
-						return;
-					}
-					_copy(inValue[0], *in.in1);
-					++in.in1;
+                    if (eof(in.in1)) {
+                        ++first;
+                        return;
+                    }
+                    _copy(inValue[0], *in.in1);
+                    ++in.in1;
                     break;
 
                 case 3:
-					if (eof(in.in2)) {
-						++first;
-						return;
-					}
-					_copy(inValue[3], *in.in2);
-					++in.in2;
+                    if (eof(in.in2)) {
+                        ++first;
+                        return;
+                    }
+                    _copy(inValue[3], *in.in2);
+                    ++in.in2;
                     break;
 
                 case 5:
-					if (eof(in.in3)) {
-						++first;
-						return;
-					}
-					_copy(inValue[5], *in.in3);
-					++in.in3;
+                    if (eof(in.in3)) {
+                        ++first;
+                        return;
+                    }
+                    _copy(inValue[5], *in.in3);
+                    ++in.in3;
                     break;
 
                 case 6:
-					if (eof(in.in4)) {
-						++first;
-						return;
-					}
-					_copy(inValue[6], *in.in4);
-					++in.in4;
-					break;
-
-				default:	// case 1, 2, or 4
-					if (eof(in.in5)) {
-						++first;
-						return;
-					}
-					// calculate residue class from the suffix length
-					typename Value<TInValue124,1>::Type in_in5_i1 = getValueI1(*in.in5);
-					unsigned seqNo = getValueI1(in_in5_i1);
-					inValue[1].stream = ((limits[seqNo + 1] - limits[seqNo]) - getValueI2(in_in5_i1)) % 7;
-
-					_copy(inValue[1], *in.in5);
-					++in.in5;
+                    if (eof(in.in4)) {
+                        ++first;
+                        return;
+                    }
+                    _copy(inValue[6], *in.in4);
+                    ++in.in4;
+                    break;
+
+                default:    // case 1, 2, or 4
+                    if (eof(in.in5)) {
+                        ++first;
+                        return;
+                    }
+                    // calculate residue class from the suffix length
+                    typename Value<TInValue124,1>::Type in_in5_i1 = getValueI1(*in.in5);
+                    unsigned seqNo = getValueI1(in_in5_i1);
+                    inValue[1].stream = ((limits[seqNo + 1] - limits[seqNo]) - getValueI2(in_in5_i1)) % 7;
+
+                    _copy(inValue[1], *in.in5);
+                    ++in.in5;
             }
 
-			// linear search
-			int right;
-			for(right = first + 1;  right < 5;  ++right)
-				if (!streamGreater(inValue[stream],inValue[rank[right]])) break;
+            // linear search
+            int right;
+            for(right = first + 1;  right < 5;  ++right)
+                if (!streamGreater(inValue[stream],inValue[rank[right]])) break;
 
-			// remove the least suffix ...
-			for(int i = first + 1;  i < right;  ++i)
-				rank[i-1] = rank[i];
+            // remove the least suffix ...
+            for(int i = first + 1;  i < right;  ++i)
+                rank[i-1] = rank[i];
+
+            // ... and insert the new one
+            rank[right-1] = stream;
+        }
 
-			// ... and insert the new one
-			rank[right-1] = stream;
-		}
-        
         Pipe& operator++()
         {
-			insertStream(rank[first]);
+            insertStream(rank[first]);
             return *this;
         }
 
         void fill()
         {
-			inValue[0].stream = 0;
-			inValue[3].stream = 3;
-			inValue[5].stream = 5;
-			inValue[6].stream = 6;
-
-			first = 4;	insertStream(0);
-			--first;    insertStream(3);
-			--first;    insertStream(5);
-			--first;    insertStream(6);
-			--first;	insertStream(1);
+            inValue[0].stream = 0;
+            inValue[3].stream = 3;
+            inValue[5].stream = 5;
+            inValue[6].stream = 6;
+
+            first = 4;    insertStream(0);
+            --first;    insertStream(3);
+            --first;    insertStream(5);
+            --first;    insertStream(6);
+            --first;    insertStream(1);
         }
-	};
-    
+    };
+
 
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
     template < typename TInput >
-	inline bool control(Pipe< TInput, Merger7 > &me, ControlBeginRead const &command)
+    inline bool control(Pipe< TInput, Merger7 > &me, ControlBeginRead const &command)
     {
         if (!control(me.in, command)) return false;
         me.N = length(me);
         me.fill();
-		return true;
-	}
-    
+        return true;
+    }
+
     template < typename TInput >
-	inline bool control(Pipe< TInput, Merger7 > &me, ControlEof const &)
+    inline bool control(Pipe< TInput, Merger7 > &me, ControlEof const &)
     {
-		return me.first == 5;
+        return me.first == 5;
     }
 
     template < typename TInput >
-	inline bool control(Pipe< TInput, Merger7 > &me, ControlEos const &)
+    inline bool control(Pipe< TInput, Merger7 > &me, ControlEos const &)
     {
-		return control(me, ControlEof());
+        return control(me, ControlEof());
     }
 
     template < typename TInput >
@@ -509,7 +510,7 @@ namespace SEQAN_NAMESPACE_MAIN
     length(Pipe< TInput, Merger7 > const &me)
     {
         return length(me.in.in1) +
-               length(me.in.in2) + 
+               length(me.in.in2) +
                length(me.in.in3) +
                length(me.in.in4) +
                length(me.in.in5);
@@ -519,30 +520,30 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
     template < typename TInput, typename TLimitsString >
-	inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlBeginRead const &command)
+    inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlBeginRead const &command)
     {
         if (!control(me.in, command)) return false;
         me.fill();
-		return true;
-	}
-    
+        return true;
+    }
+
     template < typename TInput, typename TLimitsString >
-	inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEof const &)
+    inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEof const &)
     {
-		return me.first == 5;
+        return me.first == 5;
     }
 
     template < typename TInput, typename TLimitsString >
-	inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEos const &)
+    inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEos const &)
     {
-		return control(me, ControlEof());
+        return control(me, ControlEof());
     }
 
     template < typename TInput, typename TLimitsString >
     inline typename Size< Pipe< TInput, Merger7Multi<TLimitsString> > >::Type
     length(Pipe< TInput, Merger7Multi<TLimitsString> > const &me) {
         return length(me.in.in1) +
-               length(me.in.in2) + 
+               length(me.in.in2) +
                length(me.in.in3) +
                length(me.in.in4) +
                length(me.in.in5);
diff --git a/seqan/index/pizzachili_api.h b/seqan/index/pizzachili_api.h
old mode 100755
new mode 100644
index aea124c..b19046a
--- a/seqan/index/pizzachili_api.h
+++ b/seqan/index/pizzachili_api.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -55,74 +55,52 @@ struct PizzaChiliCodeProvider {
     typedef InvalidPizzaChiliSpec Type;
 };
 
-/**
-.Tag.Pizza & Chili Index Tags
-..summary:Tag specifying the Pizza & Chili library to use.
-..remarks:More information for all the index libraries can be found in the
-@http://pizzachili.dcc.uchile.cl|original documentation@ (or the
-@http://pizzachili.di.unipi.it|Italian mirror@).
-..cat:Index
-..tag.PizzaChiliAF:The alphabet-friendly FM index.
-..tag.PizzaChiliCcsa:The compressed compact suffix array index.
-..tag.PizzaChiliFM: The FM (full-text in minute space) index.
-..tag.PizzaChiili_RSA:The repair suffix array index.
-...remarks:The index cannot be saved and loaded.
-..tag.PizzaChiliSA: The simple suffix array index.
-...remarks:The index cannot be saved and loaded.
-..tag.PizzaChiliSada: the compressed suffix array index.
-...remarks:The index cannot be saved and loaded.
-..see:Spec.Pizza & Chili Index
-..see:Spec.Pizza & Chili String
-..include:seqan/index.h
-*/
 /*!
  * @defgroup PizzaChiliIndexTags Pizza &amp; Chili Index Tags
- * 
+ *
  * @brief Tag specifying the Pizza &amp; Chili library to use.
- * 
+ *
  * @section Remarks
- * 
- * More information for all the index libraries can be found in the @link
- * dcc.uchile.cl original documentation @endlink (or the @link di.unipi.it
- * Italian mirror @endlink).
- * 
+ *
+ * More information for all the index libraries can be found at <a href="dcc.uchile.cl">original documentation</a> (or the <a href="di.unipi.it">Italian mirror</a>).
+ *
  * @see PizzaChiliIndex
  * @see PizzaChiliString
- * 
+ *
  * @tag PizzaChiliIndexTags#PizzaChiliSada
- * 
+ *
  * @brief the compressed suffix array index.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The index cannot be saved and loaded.
- * 
+ *
  * @tag PizzaChiliIndexTags#PizzaChiliAF
- * 
+ *
  * @brief The alphabet-friendly FM index.
- * 
+ *
  * @tag PizzaChiliIndexTags#PizzaChiili_RSA
- * 
+ *
  * @brief The repair suffix array index.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The index cannot be saved and loaded.
- * 
+ *
  * @tag PizzaChiliIndexTags#PizzaChiliSA
- * 
+ *
  * @brief The simple suffix array index.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The index cannot be saved and loaded.
- * 
+ *
  * @tag PizzaChiliIndexTags#PizzaChiliFM
- * 
+ *
  * @brief The FM (full-text in minute space) index.
- * 
+ *
  * @tag PizzaChiliIndexTags#PizzaChiliCcsa
- * 
+ *
  * @brief The compressed compact suffix array index.
  */
 
diff --git a/seqan/index/pump_extender3.h b/seqan/index/pump_extender3.h
index 5b7f198..a134241 100644
--- a/seqan/index/pump_extender3.h
+++ b/seqan/index/pump_extender3.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,7 +46,7 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TTextInput, typename TNameInput >
     struct Pipe< Bundle2< TTextInput, TNameInput >, Extender3 >
     {
-		enum { maxShift = 2 };
+        enum { maxShift = 2 };
         typedef typename Size<Pipe>::Type                   TSize;
         typedef typename Value<TTextInput>::Type            TValue;
         typedef typename Value<TNameInput>::Type            TNameInputValue;
@@ -61,60 +61,60 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef Pipe< void, AbstractSource< OutType0, TSize > > Out0;
         typedef Pipe< void, AbstractSource< OutType12, TSize > > Out12;
     };
-        
+
     template < typename TTextInput, typename TNameInput, typename TOut0, typename TOut12 >
     static bool _skew3Extend(TTextInput &textIn, TNameInput &nameIn, TOut0 &out0, TOut12 &out12)
     {
         resize(out0, length(textIn) / 3);
         resize(out12, length(nameIn));
         if (!(
-            beginRead(textIn) && 
+            beginRead(textIn) &&
             beginRead(nameIn) &&
-            beginWrite(out0) && 
+            beginWrite(out0) &&
             beginWrite(out12))) return false;
-		
-		typename Value<TOut0>::Type  o0 = typename Value<TOut0>::Type();
-		typename Value<TOut12>::Type o1 = typename Value<TOut12>::Type();
-		typename Value<TOut12>::Type o2 = typename Value<TOut12>::Type();
+
+        typename Value<TOut0>::Type  o0 = typename Value<TOut0>::Type();
+        typename Value<TOut12>::Type o1 = typename Value<TOut12>::Type();
+        typename Value<TOut12>::Type o2 = typename Value<TOut12>::Type();
 
         unsigned r = (unsigned)(length(textIn) % 3);
         bool filled = (r != 0);
-        
+
         if (r == 2)
         {
             o2.i1 = (*nameIn).i1;
             o2.i2[0] = (*nameIn).i2; ++nameIn;
             o2.i3[0] = *textIn; ++textIn;
         }
-            
+
         if (r >= 1)
         {
             o1.i1 = (*nameIn).i1;
             o1.i2[0] = (*nameIn).i2; ++nameIn;
             o1.i3[0] = *textIn; ++textIn;
         }
-        
+
         if (r == 2)
         {
             o2.i2[1] = o1.i2[0];
             o2.i3[1] = o1.i3[0];
             push(out12, o2);
         }
-        
+
         while (!eof(nameIn))
         {
             o1.i3[1] = o0.i3[0] = *textIn; ++textIn;
             o2.i3[0] = o0.i3[1] = *textIn; ++textIn;
-            
+
             o2.i1 = (*nameIn).i1;
             o0.i2[0] = o2.i2[0] = o1.i2[1] = (*nameIn).i2; ++nameIn;
             o2.i3[1] = *textIn; ++textIn;
-            
+
             if (filled)
                 push(out12, o1);
             else
                 filled = true;
-            
+
             o1.i1 = (*nameIn).i1;
             o0.i2[1] = o2.i2[1] = o1.i2[0] = (*nameIn).i2; ++nameIn;
             o1.i3[0] = o2.i3[1];
@@ -133,7 +133,7 @@ namespace SEQAN_NAMESPACE_MAIN
         endRead(textIn);
         return true;
     }
-    
+
 //}
 
 }
diff --git a/seqan/index/pump_extender7.h b/seqan/index/pump_extender7.h
index 0c70189..666279e 100644
--- a/seqan/index/pump_extender7.h
+++ b/seqan/index/pump_extender7.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,7 +46,7 @@ namespace SEQAN_NAMESPACE_MAIN
     template <typename TPack = void>
     struct Extender7;
 
-	template <typename TTextInput, typename TNameInput, typename TPack >
+    template <typename TTextInput, typename TNameInput, typename TPack >
     struct Pipe< Bundle2< TTextInput, TNameInput >, Extender7<TPack> >
     {
         typedef typename Size<Pipe>::Type                   TSize;
@@ -76,13 +76,13 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 
 
-	// little copy helper
-	// which is needed for bitpacked structs (no =sign possible)
-	template <typename Dest, typename Ofs, typename Src>
-	static finline Src const cp___(Dest &dst, Ofs const ofs, Src const src) {
-		return dst.i3.assignValue(ofs, src);
-	}
-        
+    // little copy helper
+    // which is needed for bitpacked structs (no =sign possible)
+    template <typename Dest, typename Ofs, typename Src>
+    static finline Src const cp___(Dest &dst, Ofs const ofs, Src const src) {
+        return dst.i3.assignValue(ofs, src);
+    }
+
     template < typename TTextInput, typename TNameInput,
                typename TOut0, typename TOut3, typename TOut5, typename TOut6, typename TOut124 >
     static bool _skew7Extend(TTextInput &textIn, TNameInput &nameIn,
@@ -102,36 +102,36 @@ namespace SEQAN_NAMESPACE_MAIN
             beginWrite(out6) &&
             beginWrite(out124))) return false;
 
-		// not necessary, but this hides an 'uninitialized' warning...
-		typename Value<TOut0>::Type   o0;
-		typename Value<TOut124>::Type o1;
-		o1.i1 = typename Value<typename Value<TOut124>::Type, 1>::Type();
-		o1.i2 = typename Value<typename Value<TOut124>::Type, 2>::Type();
-		o1.i3 = typename Value<typename Value<TOut124>::Type, 3>::Type();
-
-		typename Value<TOut124>::Type o2 = o1;
-		typename Value<TOut3>::Type   o3;
-		typename Value<TOut124>::Type o4 = o1;
-		typename Value<TOut5>::Type   o5;
-		typename Value<TOut6>::Type   o6;
-		
-		o0.i1 = typename Value<typename Value<TOut0>::Type, 1>::Type();
-		o0.i2 = typename Value<typename Value<TOut0>::Type, 2>::Type();
-		o0.i3 = typename Value<typename Value<TOut0>::Type, 3>::Type();
-
-		o3.i1 = typename Value<typename Value<TOut3>::Type, 1>::Type();
-		o3.i2 = typename Value<typename Value<TOut3>::Type, 2>::Type();
-		o3.i3 = typename Value<typename Value<TOut3>::Type, 3>::Type();
-
-		o5.i1 = typename Value<typename Value<TOut5>::Type, 1>::Type();
-		o5.i2 = typename Value<typename Value<TOut5>::Type, 2>::Type();
-		o5.i3 = typename Value<typename Value<TOut5>::Type, 3>::Type();
-
-		o6.i1 = typename Value<typename Value<TOut6>::Type, 1>::Type();
-		o6.i2 = typename Value<typename Value<TOut6>::Type, 2>::Type();
-		o6.i3 = typename Value<typename Value<TOut6>::Type, 3>::Type();
-
-		typename Size<TTextInput>::Type p = length(textIn);
+        // not necessary, but this hides an 'uninitialized' warning...
+        typename Value<TOut0>::Type   o0;
+        typename Value<TOut124>::Type o1;
+        o1.i1 = typename Value<typename Value<TOut124>::Type, 1>::Type();
+        o1.i2 = typename Value<typename Value<TOut124>::Type, 2>::Type();
+        o1.i3 = typename Value<typename Value<TOut124>::Type, 3>::Type();
+
+        typename Value<TOut124>::Type o2 = o1;
+        typename Value<TOut3>::Type   o3;
+        typename Value<TOut124>::Type o4 = o1;
+        typename Value<TOut5>::Type   o5;
+        typename Value<TOut6>::Type   o6;
+
+        o0.i1 = typename Value<typename Value<TOut0>::Type, 1>::Type();
+        o0.i2 = typename Value<typename Value<TOut0>::Type, 2>::Type();
+        o0.i3 = typename Value<typename Value<TOut0>::Type, 3>::Type();
+
+        o3.i1 = typename Value<typename Value<TOut3>::Type, 1>::Type();
+        o3.i2 = typename Value<typename Value<TOut3>::Type, 2>::Type();
+        o3.i3 = typename Value<typename Value<TOut3>::Type, 3>::Type();
+
+        o5.i1 = typename Value<typename Value<TOut5>::Type, 1>::Type();
+        o5.i2 = typename Value<typename Value<TOut5>::Type, 2>::Type();
+        o5.i3 = typename Value<typename Value<TOut5>::Type, 3>::Type();
+
+        o6.i1 = typename Value<typename Value<TOut6>::Type, 1>::Type();
+        o6.i2 = typename Value<typename Value<TOut6>::Type, 2>::Type();
+        o6.i3 = typename Value<typename Value<TOut6>::Type, 3>::Type();
+
+        typename Size<TTextInput>::Type p = length(textIn);
         unsigned r = (unsigned)(p % 7);
 
 
@@ -147,14 +147,14 @@ namespace SEQAN_NAMESPACE_MAIN
         case 4:
 /* 4 */                                                 o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 = p--;
                                                      cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))); ++textIn;
-            
+
         case 3:
 /* 3 */                                   cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,   *textIn)))); ++textIn; o3.i1 = p--;
-                
+
         case 2:
 /* 2 */                           o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn).i2; ++nameIn; o2.i1 = p--;
                                cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn))))); ++textIn;
-                
+
         case 1:
 /* 1 */                o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn).i2; ++nameIn; o1.i1 = p--;
                     cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
@@ -169,51 +169,51 @@ namespace SEQAN_NAMESPACE_MAIN
 
         if (!eof(nameIn)) {
 /* 0 */  cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3,                                     *textIn)))); ++textIn; o0.i1 = p--;
-                
+
 /* 6 */  cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4,                      cp___(o6,0,    *textIn))))); ++textIn; o6.i1 = p--;
-                
+
 /* 5 */  cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5,           cp___(o5,0,cp___(o6,1,    *textIn)))))); ++textIn; o5.i1 = p--;
 
 /* 4 */     o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 = p--;
          cp___(o0,3,cp___(o1,4,                      cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))))); ++textIn;
             if (r >= 3) push(out3, o3);
             if (r >= 2) push(out124, o2);
-                
+
 /* 3 */  cp___(o0,4,cp___(o1,5,           cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,    *textIn)))))); ++textIn; o3.i1 = p--;
-                
+
 /* 2 */     o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn).i2; ++nameIn; o2.i1 = p--;
          cp___(o0,5,           cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn)))))); ++textIn;
             if (r >= 1) push(out124, o1);
-                
+
 /* 1 */     o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn).i2; ++nameIn; o1.i1 = p--;
                     cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
             push(out0, o0);
             push(out6, o6);
             push(out5, o5);
-			push(out124, o4);
+            push(out124, o4);
             r = 7;
         }
 
         // MAIN Loop: PUSH FULLY FILLED TRIPLES
-        
+
         while (!eof(nameIn)) {
 /* 0 */  cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3,                                     *textIn)))); ++textIn; o0.i1 -= 7;
-                
+
 /* 6 */  cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4,                      cp___(o6,0,    *textIn))))); ++textIn; o6.i1 -= 7;
-                
+
 /* 5 */  cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5,           cp___(o5,0,cp___(o6,1,    *textIn)))))); ++textIn; o5.i1 -= 7;
 
 /* 4 */     o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn).i2; ++nameIn; o4.i1 -= 7;
          cp___(o0,3,cp___(o1,4,                      cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))))); ++textIn;
             push(out3, o3);
             push(out124, o2);
-                
+
 /* 3 */  cp___(o0,4,cp___(o1,5,           cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,    *textIn)))))); ++textIn; o3.i1 -= 7;
-                
+
 /* 2 */     o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn).i2; ++nameIn; o2.i1 -= 7;
          cp___(o0,5,           cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn)))))); ++textIn;
             push(out124, o1);
-                
+
 /* 1 */     o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn).i2; ++nameIn; o1.i1 -= 7;
                     cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
             push(out0, o0);
@@ -226,7 +226,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
         {
 /* 0 */             cp___(o1,1,cp___(o2,2,cp___(o3,3,   0)));
-                
+
 /* 6 */             cp___(o1,2,cp___(o2,3,cp___(o3,4,   0)));
 
 /* 5 */             cp___(o1,3,cp___(o2,4,cp___(o3,5,   0)));
@@ -238,11 +238,11 @@ namespace SEQAN_NAMESPACE_MAIN
 
 /* 3 */             cp___(o1,5,                         0);
 
-/* 2 */                o1.i2[2] =						0;
+/* 2 */                o1.i2[2] =                        0;
             if (r >= 1) push(out124, o1);
-        
+
         }
-                
+
         endWrite(out124);
         endWrite(out6);
         endWrite(out5);
@@ -292,42 +292,42 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TTextInput, typename TLimitsString, typename TNameInput,
                typename TOut0, typename TOut3, typename TOut5, typename TOut6, typename TOut124 >
     static bool _skew7ExtendMulti(
-		TTextInput &textIn, TLimitsString const &limits, 
-		TNameInput &nameIn1, TNameInput &nameIn2, TNameInput &nameIn4, 
-		TOut0 &out0, TOut3 &out3, TOut5 &out5, TOut6 &out6, TOut124 &out124)
+        TTextInput &textIn, TLimitsString const &limits,
+        TNameInput &nameIn1, TNameInput &nameIn2, TNameInput &nameIn4,
+        TOut0 &out0, TOut3 &out3, TOut5 &out5, TOut6 &out6, TOut124 &out124)
     {
-		typedef typename Value<TLimitsString>::Type TSize;
-		typename Iterator<TLimitsString const>::Type it = begin(limits), itEnd = end(limits);
+        typedef typename Value<TLimitsString>::Type TSize;
+        typename Iterator<TLimitsString const>::Type it = begin(limits), itEnd = end(limits);
 
-		if (it == itEnd) return true;
+        if (it == itEnd) return true;
 
-		{
-			TSize n0 = 0, n3 = 0, n5 = 0, n6 = 0, n124 = 0;
+        {
+            TSize n0 = 0, n3 = 0, n5 = 0, n6 = 0, n124 = 0;
 
-			// count the numbers of septets in residue class 1, 2, and 4
-			
-			TSize size;
-			TSize old = *it; ++it;
+            // count the numbers of septets in residue class 1, 2, and 4
 
-			while (it != itEnd) {
-				size = *it - old;
-				old = *it;
-				
-				n0   +=  size      / 7;
-				n3   += (size + 4) / 7;
-				n5   += (size + 2) / 7;
-				n6   += (size + 1) / 7;
-				n124 += (size + 6) / 7 + (size + 5) / 7 + (size + 3) / 7;
+            TSize size;
+            TSize old = *it; ++it;
 
-				++it;
-			}
+            while (it != itEnd) {
+                size = *it - old;
+                old = *it;
 
-			resize(out0, n0);
-			resize(out3, n3);
-			resize(out5, n5);
-			resize(out6, n6);
-			resize(out124, n124);
-		}
+                n0   +=  size      / 7;
+                n3   += (size + 4) / 7;
+                n5   += (size + 2) / 7;
+                n6   += (size + 1) / 7;
+                n124 += (size + 6) / 7 + (size + 5) / 7 + (size + 3) / 7;
+
+                ++it;
+            }
+
+            resize(out0, n0);
+            resize(out3, n3);
+            resize(out5, n5);
+            resize(out6, n6);
+            resize(out124, n124);
+        }
 
 
         if (!(
@@ -341,164 +341,164 @@ namespace SEQAN_NAMESPACE_MAIN
             beginWrite(out6) &&
             beginWrite(out124))) return false;
 
-		// not necessary, but this hides an 'uninitialized' warning...
-		typename Value<TOut0>::Type   o0;
-		typename Value<TOut124>::Type o1;
-		o1.i1 = typename Value<typename Value<TOut124>::Type, 1>::Type();
-		o1.i2 = typename Value<typename Value<TOut124>::Type, 2>::Type();
-		o1.i3 = typename Value<typename Value<TOut124>::Type, 3>::Type();
-
-		typename Value<TOut124>::Type o2 = o1;
-		typename Value<TOut3>::Type   o3;
-		typename Value<TOut124>::Type o4 = o1;
-		typename Value<TOut5>::Type   o5;
-		typename Value<TOut6>::Type   o6;
-		
-		o0.i1 = typename Value<typename Value<TOut0>::Type, 1>::Type();
-		o0.i2 = typename Value<typename Value<TOut0>::Type, 2>::Type();
-		o0.i3 = typename Value<typename Value<TOut0>::Type, 3>::Type();
-
-		o3.i1 = typename Value<typename Value<TOut3>::Type, 1>::Type();
-		o3.i2 = typename Value<typename Value<TOut3>::Type, 2>::Type();
-		o3.i3 = typename Value<typename Value<TOut3>::Type, 3>::Type();
-
-		o5.i1 = typename Value<typename Value<TOut5>::Type, 1>::Type();
-		o5.i2 = typename Value<typename Value<TOut5>::Type, 2>::Type();
-		o5.i3 = typename Value<typename Value<TOut5>::Type, 3>::Type();
-
-		o6.i1 = typename Value<typename Value<TOut6>::Type, 1>::Type();
-		o6.i2 = typename Value<typename Value<TOut6>::Type, 2>::Type();
-		o6.i3 = typename Value<typename Value<TOut6>::Type, 3>::Type();
-
-		it = begin(limits);
-
-		TSize rounds, cur;
-		TSize old = *it; ++it;
-
-		typedef typename Value<TOut0>::Type         TOutValue0;
+        // not necessary, but this hides an 'uninitialized' warning...
+        typename Value<TOut0>::Type   o0;
+        typename Value<TOut124>::Type o1;
+        o1.i1 = typename Value<typename Value<TOut124>::Type, 1>::Type();
+        o1.i2 = typename Value<typename Value<TOut124>::Type, 2>::Type();
+        o1.i3 = typename Value<typename Value<TOut124>::Type, 3>::Type();
+
+        typename Value<TOut124>::Type o2 = o1;
+        typename Value<TOut3>::Type   o3;
+        typename Value<TOut124>::Type o4 = o1;
+        typename Value<TOut5>::Type   o5;
+        typename Value<TOut6>::Type   o6;
+
+        o0.i1 = typename Value<typename Value<TOut0>::Type, 1>::Type();
+        o0.i2 = typename Value<typename Value<TOut0>::Type, 2>::Type();
+        o0.i3 = typename Value<typename Value<TOut0>::Type, 3>::Type();
+
+        o3.i1 = typename Value<typename Value<TOut3>::Type, 1>::Type();
+        o3.i2 = typename Value<typename Value<TOut3>::Type, 2>::Type();
+        o3.i3 = typename Value<typename Value<TOut3>::Type, 3>::Type();
+
+        o5.i1 = typename Value<typename Value<TOut5>::Type, 1>::Type();
+        o5.i2 = typename Value<typename Value<TOut5>::Type, 2>::Type();
+        o5.i3 = typename Value<typename Value<TOut5>::Type, 3>::Type();
+
+        o6.i1 = typename Value<typename Value<TOut6>::Type, 1>::Type();
+        o6.i2 = typename Value<typename Value<TOut6>::Type, 2>::Type();
+        o6.i3 = typename Value<typename Value<TOut6>::Type, 3>::Type();
+
+        it = begin(limits);
+
+        TSize rounds, cur;
+        TSize old = *it; ++it;
+
+        typedef typename Value<TOut0>::Type         TOutValue0;
         typedef typename Value<TOutValue0, 1>::Type TPair;
-        
-		PairIncrementer_<TPair, TLimitsString> p;
-		setHost(p, limits);
-
-		while (it != itEnd) {
-			cur = *it; ++it;
-			unsigned r = (unsigned)((cur - old) % 7);
-			rounds = (cur - old) / 7;
-			old = cur;
-
-
-			// BEGIN I: PREFILL
-
-			switch (r) {
-			case 6:
-	/* 6 */                                                                    cp___(o6,0,    *textIn); ++textIn; o6.i1 = p; ++p;
-
-			case 5:
-	/* 5 */                                                         cp___(o5,0,cp___(o6,1,    *textIn)); ++textIn; o5.i1 = p; ++p;
-
-			case 4:
-	/* 4 */                                                 o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
-														cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))); ++textIn;
-	            
-			case 3:
-	/* 3 */                                   cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,   *textIn)))); ++textIn; o3.i1 = p; ++p;
-	                
-			case 2:
-	/* 2 */                           o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
-								cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn))))); ++textIn;
-	                
-			case 1:
-	/* 1 */                o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
-						cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
-				if (r >= 6) push(out6, o6);
-				if (r >= 5) push(out5, o5);
-				if (r >= 4) push(out124, o4);
-
-			case 0:;
-			}
-
-				// BEGIN II: PREFILL And PUSH FULLY FILLED TRIPLES
-
-			if (rounds != 0) {
-	/* 0 */  cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3,                                     *textIn)))); ++textIn; o0.i1 = p; ++p;
-	                
-	/* 6 */  cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4,                      cp___(o6,0,    *textIn))))); ++textIn; o6.i1 = p; ++p;
-	                
-	/* 5 */  cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5,           cp___(o5,0,cp___(o6,1,    *textIn)))))); ++textIn; o5.i1 = p; ++p;
-
-	/* 4 */     o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
-			cp___(o0,3,cp___(o1,4,                      cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))))); ++textIn;
-				if (r >= 3) push(out3, o3);
-				if (r >= 2) push(out124, o2);
-	                
-	/* 3 */  cp___(o0,4,cp___(o1,5,           cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,    *textIn)))))); ++textIn; o3.i1 = p; ++p;
-	                
-	/* 2 */     o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
-			cp___(o0,5,           cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn)))))); ++textIn;
-				if (r >= 1) push(out124, o1);
-	                
-	/* 1 */     o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
-						cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
-				push(out0, o0);
-				push(out6, o6);
-				push(out5, o5);
-				push(out124, o4);
-				r = 7;
-				--rounds;
-			}
-
-			// MAIN Loop: PUSH FULLY FILLED TRIPLES
-	        
-			while (rounds != 0) {
-	/* 0 */  cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3,                                     *textIn)))); ++textIn; o0.i1 = p; ++p;
-	                
-	/* 6 */  cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4,                      cp___(o6,0,    *textIn))))); ++textIn; o6.i1 = p; ++p;
-	                
-	/* 5 */  cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5,           cp___(o5,0,cp___(o6,1,    *textIn)))))); ++textIn; o5.i1 = p; ++p;
-
-	/* 4 */     o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
-			cp___(o0,3,cp___(o1,4,                      cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))))); ++textIn;
-				push(out3, o3);
-				push(out124, o2);
-	                
-	/* 3 */  cp___(o0,4,cp___(o1,5,           cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,    *textIn)))))); ++textIn; o3.i1 = p; ++p;
-	                
-	/* 2 */     o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
-			cp___(o0,5,           cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn)))))); ++textIn;
-				push(out124, o1);
-	                
-	/* 1 */     o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
-						cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
-				push(out0, o0);
-				push(out6, o6);
-				push(out5, o5);
-				push(out124, o4);
-				--rounds;
-			}
-
-			// END: FLUSH PARTIALLY FILLED TRIPLES
-
-			{
-	/* 0 */             cp___(o1,1,cp___(o2,2,cp___(o3,3,   0)));
-	                
-	/* 6 */             cp___(o1,2,cp___(o2,3,cp___(o3,4,   0)));
-
-	/* 5 */             cp___(o1,3,cp___(o2,4,cp___(o3,5,   0)));
-
-	/* 4 */                o1.i2[1] = o2.i2[2] = o3.i2[2] = 0;
-						cp___(o1,4,                         0);
-				if (r >= 3) push(out3, o3);
-				if (r >= 2) push(out124, o2);
-
-	/* 3 */             cp___(o1,5,                         0);
-
-	/* 2 */                o1.i2[2] =						0;
-				if (r >= 1) push(out124, o1);
-	        
-			}
-		}
-	                
+
+        PairIncrementer_<TPair, TLimitsString> p;
+        setHost(p, limits);
+
+        while (it != itEnd) {
+            cur = *it; ++it;
+            unsigned r = (unsigned)((cur - old) % 7);
+            rounds = (cur - old) / 7;
+            old = cur;
+
+
+            // BEGIN I: PREFILL
+
+            switch (r) {
+            case 6:
+    /* 6 */                                                                    cp___(o6,0,    *textIn); ++textIn; o6.i1 = p; ++p;
+
+            case 5:
+    /* 5 */                                                         cp___(o5,0,cp___(o6,1,    *textIn)); ++textIn; o5.i1 = p; ++p;
+
+            case 4:
+    /* 4 */                                                 o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
+                                                        cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))); ++textIn;
+
+            case 3:
+    /* 3 */                                   cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,   *textIn)))); ++textIn; o3.i1 = p; ++p;
+
+            case 2:
+    /* 2 */                           o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
+                                cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn))))); ++textIn;
+
+            case 1:
+    /* 1 */                o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
+                        cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
+                if (r >= 6) push(out6, o6);
+                if (r >= 5) push(out5, o5);
+                if (r >= 4) push(out124, o4);
+
+            case 0:;
+            }
+
+                // BEGIN II: PREFILL And PUSH FULLY FILLED TRIPLES
+
+            if (rounds != 0) {
+    /* 0 */  cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3,                                     *textIn)))); ++textIn; o0.i1 = p; ++p;
+
+    /* 6 */  cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4,                      cp___(o6,0,    *textIn))))); ++textIn; o6.i1 = p; ++p;
+
+    /* 5 */  cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5,           cp___(o5,0,cp___(o6,1,    *textIn)))))); ++textIn; o5.i1 = p; ++p;
+
+    /* 4 */     o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
+            cp___(o0,3,cp___(o1,4,                      cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))))); ++textIn;
+                if (r >= 3) push(out3, o3);
+                if (r >= 2) push(out124, o2);
+
+    /* 3 */  cp___(o0,4,cp___(o1,5,           cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,    *textIn)))))); ++textIn; o3.i1 = p; ++p;
+
+    /* 2 */     o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
+            cp___(o0,5,           cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn)))))); ++textIn;
+                if (r >= 1) push(out124, o1);
+
+    /* 1 */     o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
+                        cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
+                push(out0, o0);
+                push(out6, o6);
+                push(out5, o5);
+                push(out124, o4);
+                r = 7;
+                --rounds;
+            }
+
+            // MAIN Loop: PUSH FULLY FILLED TRIPLES
+
+            while (rounds != 0) {
+    /* 0 */  cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3,                                     *textIn)))); ++textIn; o0.i1 = p; ++p;
+
+    /* 6 */  cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4,                      cp___(o6,0,    *textIn))))); ++textIn; o6.i1 = p; ++p;
+
+    /* 5 */  cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5,           cp___(o5,0,cp___(o6,1,    *textIn)))))); ++textIn; o5.i1 = p; ++p;
+
+    /* 4 */     o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
+            cp___(o0,3,cp___(o1,4,                      cp___(o4,0,cp___(o5,1,cp___(o6,2,    *textIn))))); ++textIn;
+                push(out3, o3);
+                push(out124, o2);
+
+    /* 3 */  cp___(o0,4,cp___(o1,5,           cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3,    *textIn)))))); ++textIn; o3.i1 = p; ++p;
+
+    /* 2 */     o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
+            cp___(o0,5,           cp___(o2,0,cp___(o3,1,cp___(o4,2,cp___(o5,3,cp___(o6,4,    *textIn)))))); ++textIn;
+                push(out124, o1);
+
+    /* 1 */     o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
+                        cp___(o1,0,cp___(o2,1,cp___(o3,2,                                     *textIn))); ++textIn;
+                push(out0, o0);
+                push(out6, o6);
+                push(out5, o5);
+                push(out124, o4);
+                --rounds;
+            }
+
+            // END: FLUSH PARTIALLY FILLED TRIPLES
+
+            {
+    /* 0 */             cp___(o1,1,cp___(o2,2,cp___(o3,3,   0)));
+
+    /* 6 */             cp___(o1,2,cp___(o2,3,cp___(o3,4,   0)));
+
+    /* 5 */             cp___(o1,3,cp___(o2,4,cp___(o3,5,   0)));
+
+    /* 4 */                o1.i2[1] = o2.i2[2] = o3.i2[2] = 0;
+                        cp___(o1,4,                         0);
+                if (r >= 3) push(out3, o3);
+                if (r >= 2) push(out124, o2);
+
+    /* 3 */             cp___(o1,5,                         0);
+
+    /* 2 */                o1.i2[2] =                        0;
+                if (r >= 1) push(out124, o1);
+
+            }
+        }
+
         endWrite(out124);
         endWrite(out6);
         endWrite(out5);
diff --git a/seqan/index/pump_lcp_core.h b/seqan/index/pump_lcp_core.h
index ee8051a..2d13d16 100644
--- a/seqan/index/pump_lcp_core.h
+++ b/seqan/index/pump_lcp_core.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_PUMP_LCP_CORE_H
-#define SEQAN_HEADER_PUMP_LCP_CORE_H
+#ifndef SEQAN_HEADER_PUMP_LCP_H
+#define SEQAN_HEADER_PUMP_LCP_H
 
 namespace SEQAN_NAMESPACE_MAIN
 {
@@ -43,15 +43,15 @@ namespace SEQAN_NAMESPACE_MAIN
 
     struct LcpConfig
     {
-		unsigned long   windowSize;
+        unsigned long   windowSize;
         bool            absoluteSizes;  // if false, sizes are measured in units of TValue
                                         // if true, sizes are measured in bytes
 
-		LcpConfig():
+        LcpConfig():
             windowSize((sizeof(long) == 4)? 1ul << 30: 1ul << 31),
             absoluteSizes(true) {}
 
-		template < typename TValue >
+        template < typename TValue >
         void absolutize(TValue *) {
             if (!absoluteSizes) return;
             windowSize /= sizeof(TValue);
@@ -61,16 +61,16 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
 
-	template < typename TTextInput, typename TInvertedSAInput, typename TDest >
-	static void _lcpProcess(TTextInput &textIn, TInvertedSAInput &invertedSAIn, 
-						    TDest &dest, LcpConfig conf)
-	{
-		typedef typename Value<TTextInput>::Type			TValue;
-		typedef typename Size<TTextInput>::Type				TSize;
-		typedef typename BufReadHandler<TTextInput>::Type	TBufReader;
+    template < typename TTextInput, typename TInvertedSAInput, typename TDest >
+    static void _lcpProcess(TTextInput &textIn, TInvertedSAInput &invertedSAIn,
+                            TDest &dest, LcpConfig conf)
+    {
+        typedef typename Value<TTextInput>::Type            TValue;
+        typedef typename Size<TTextInput>::Type                TSize;
+        typedef typename BufReadHandler<TTextInput>::Type    TBufReader;
 
         SEQAN_PROSET(SEQAN_PRODEPTH, 0);
-		TSize rest = length(textIn);
+        TSize rest = length(textIn);
         if (rest < 2) {
             resize(dest, 0);
             return;
@@ -78,39 +78,39 @@ namespace SEQAN_NAMESPACE_MAIN
 
         // buffer is a window of textIn
         conf.absolutize((TValue*)NULL);
-		TBufReader reader(textIn, conf.windowSize);
+        TBufReader reader(textIn, conf.windowSize);
 
         Pair<TSize> out;
-		TSize windowBegin = 0;
-		TSize overlap = 0;
+        TSize windowBegin = 0;
+        TSize overlap = 0;
         TSize _pushes = 0;
         //TSize _olaps = 0;
         //char *seenISA = new bool[n];
         //memset(seenISA, 0, length(invertedSAIn));
-		
+
         #ifdef SEQAN_DEBUG_INDEX
             TSize n = rest;
-            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;	// for lcpMax, lcpMean, |Sigma|
+            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;    // for lcpMax, lcpMean, |Sigma|
         #endif
 
         resize(dest, rest);
-		beginWrite(dest);
-		// read the first block of textIn
-		typename Value<TBufReader>::Type buffer = reader.first();
-		while (length(buffer))
+        beginWrite(dest);
+        // read the first block of textIn
+        typename Value<TBufReader>::Type buffer = reader.first();
+        while (length(buffer))
         {
             SEQAN_PROADD(SEQAN_PRODEPTH, 1);
             SEQAN_PROMARK("LCP-Durchlauf beginnen");
             beginRead(textIn);
-			beginRead(invertedSAIn);
+            beginRead(invertedSAIn);
 
             out.i2 = 0;                                             // out.i2 == h
             TSize windowSize = length(buffer);
-			TSize windowEnd = windowBegin + windowSize;
-			TSize newOverlap = windowEnd;
+            TSize windowEnd = windowBegin + windowSize;
+            TSize newOverlap = windowEnd;
             #ifdef SEQAN_DEBUG_INDEX
-				::std::cerr << ::std::hex << "  read window[" << windowBegin << "," << windowEnd;
-				::std::cerr << ") overlay " << overlap << " rest " << rest << ::std::dec << ::std::endl;
+                std::cerr << std::hex << "  read window[" << windowBegin << "," << windowEnd;
+                std::cerr << ") overlay " << overlap << " rest " << rest << std::dec << std::endl;
             #endif
             rest -= windowSize;
 
@@ -118,32 +118,32 @@ namespace SEQAN_NAMESPACE_MAIN
 
             while (!eof(invertedSAIn)) {
 
-				if ((*invertedSAIn).i1 != 0) {
-
-					TSize left = (*invertedSAIn).i2[1] + out.i2;        // left == j + h
-
-					if (overlap <= (*invertedSAIn).i2[1] && left <= windowEnd) {
-	//                        ::std::cerr << "* ";
-						for(; left < windowBegin; ++left) {
-							++textIn;
-							++out.i2;
-						}
-
-						TSize k = left - windowBegin;                   // k is relative to window
-						while (k < windowSize && (!eof(textIn)) && *textIn == buffer[k]) {
-							++textIn;
-							++k;
-						}
-						TSize hAdd = k - (left - windowBegin);
-						out.i2 += hAdd;                                 // increase h by successful compares
-						left += hAdd;
-
-						if (k != windowSize || rest == 0) {
-							out.i1 = (*invertedSAIn).i1 - 1;
-							push(dest, out);
-							//SEQAN_ASSERT(!seenISA[out.i1] && 0 <= out.i1 && out.i1 < n);
-							//seen[out.i1] = true;
-							++_pushes;
+                if ((*invertedSAIn).i1 != 0) {
+
+                    TSize left = (*invertedSAIn).i2[1] + out.i2;        // left == j + h
+
+                    if (overlap <= (*invertedSAIn).i2[1] && left <= windowEnd) {
+    //                        std::cerr << "* ";
+                        for(; left < windowBegin; ++left) {
+                            ++textIn;
+                            ++out.i2;
+                        }
+
+                        TSize k = left - windowBegin;                   // k is relative to window
+                        while (k < windowSize && (!eof(textIn)) && *textIn == buffer[k]) {
+                            ++textIn;
+                            ++k;
+                        }
+                        TSize hAdd = k - (left - windowBegin);
+                        out.i2 += hAdd;                                 // increase h by successful compares
+                        left += hAdd;
+
+                        if (k != windowSize || rest == 0) {
+                            out.i1 = (*invertedSAIn).i1 - 1;
+                            push(dest, out);
+                            //SEQAN_ASSERT(!seenISA[out.i1] && 0 <= out.i1 && out.i1 < n);
+                            //seen[out.i1] = true;
+                            ++_pushes;
 
                             #ifdef SEQAN_DEBUG_INDEX
                                 if ((lcpNumer += out.i2) > n) {
@@ -151,80 +151,80 @@ namespace SEQAN_NAMESPACE_MAIN
                                     ++lcpAvrg;
                                 }
                                 if (lcpMax < out.i2) lcpMax = out.i2;
-								if (!out.i2) ++sigma;
+                                if (!out.i2) ++sigma;
                             #endif
-						}
-					}
+                        }
+                    }
 
-					if (left >= windowEnd && (*invertedSAIn).i2[1] < newOverlap) {
-						#ifdef SEQAN_VERBOSE
-							::std::cerr << "crossing border @ " << (*invertedSAIn).i2[1] << " len " << out.i2 << ::std::endl;
-						#endif
-						newOverlap = (*invertedSAIn).i2[1];    //++_olaps;
-					}
-				}
+                    if (left >= windowEnd && (*invertedSAIn).i2[1] < newOverlap) {
+                        #ifdef SEQAN_VERBOSE
+                            std::cerr << "crossing border @ " << (*invertedSAIn).i2[1] << " len " << out.i2 << std::endl;
+                        #endif
+                        newOverlap = (*invertedSAIn).i2[1];    //++_olaps;
+                    }
+                }
 
-				if (out.i2) --out.i2;                               // if (h > 0) h = h - 1
-				else ++textIn;
+                if (out.i2) --out.i2;                               // if (h > 0) h = h - 1
+                else ++textIn;
 
                 ++invertedSAIn; //++_pops;
-			}
+            }
 
-			endRead(invertedSAIn);
-			endRead(textIn);
+            endRead(invertedSAIn);
+            endRead(textIn);
 
-			windowBegin = windowEnd;
-			overlap = newOverlap;
-			buffer = reader.next();                                 // read the following block
+            windowBegin = windowEnd;
+            overlap = newOverlap;
+            buffer = reader.next();                                 // read the following block
 
-			//::std::cerr << "pops:" << _pops << " pushes:" << _pushes << " overlaps:" << _olaps << ::std::endl;
-		}
-		// trailing zero
-		push(dest, Pair<TSize>(length(textIn) - 1, 0));
+            //std::cerr << "pops:" << _pops << " pushes:" << _pushes << " overlaps:" << _olaps << std::endl;
+        }
+        // trailing zero
+        push(dest, Pair<TSize>(length(textIn) - 1, 0));
 
-		//::std::cerr << "pushes:" << _pushes << " length:" << length(textIn) << ::std::endl;
+        //std::cerr << "pushes:" << _pushes << " length:" << length(textIn) << std::endl;
         //SEQAN_ASSERT_EQ(_pushes, length(textIn));
         //for (unsigned i = 0; i < n; ++i)
         //    if (!seen[i])
-        //        ::std::cerr << "___" << i << "______HUH?" << ::std::endl;
+        //        std::cerr << "___" << i << "______HUH?" << std::endl;
         //delete[] seenISA;
 
         #ifdef SEQAN_DEBUG_INDEX
-            ::std::cerr << "  n: " << n;
-            ::std::cerr << "  lcpMax: " << lcpMax;
-            ::std::cerr << "  lcpAvrg: " << lcpAvrg + lcpNumer / (double)n;
-            ::std::cerr << "  sigma: " << sigma << ::std::endl;
+            std::cerr << "  n: " << n;
+            std::cerr << "  lcpMax: " << lcpMax;
+            std::cerr << "  lcpAvrg: " << lcpAvrg + lcpNumer / (double)n;
+            std::cerr << "  sigma: " << sigma << std::endl;
         #endif
 
 //TODO: uncomment this line
-//		reader.end();
-		endWrite(dest);
+//        reader.end();
+        endWrite(dest);
         SEQAN_PROSET(SEQAN_PRODEPTH, 0);
     }
 
-	template < typename TTextInput, typename TInvertedSAInput, typename TDest >
-	static inline void _lcpProcess(TTextInput &textIn, TInvertedSAInput &invertedSAIn, TDest &dest)
-	{
-		_lcpProcess(textIn, invertedSAIn, dest, LcpConfig());
-	}
+    template < typename TTextInput, typename TInvertedSAInput, typename TDest >
+    static inline void _lcpProcess(TTextInput &textIn, TInvertedSAInput &invertedSAIn, TDest &dest)
+    {
+        _lcpProcess(textIn, invertedSAIn, dest, LcpConfig());
+    }
 
 //////////////////////////////////////////////////////////////////////////////
 
 
-	template < typename TTextInput, typename TLimitsString, typename TInvertedSAInput, typename TDest >
-	static void _lcpProcessMulti(
-		TTextInput &textIn, TLimitsString const &limits, 
-		TInvertedSAInput &invertedSAIn, 
-		TDest &dest, LcpConfig conf)
-	{
-		typedef typename Value<TTextInput>::Type			TValue;
-		typedef typename Size<TTextInput>::Type				TSize;
-		typedef typename BufReadHandler<TTextInput>::Type	TBufReader;
+    template < typename TTextInput, typename TLimitsString, typename TInvertedSAInput, typename TDest >
+    static void _lcpProcessMulti(
+        TTextInput &textIn, TLimitsString const &limits,
+        TInvertedSAInput &invertedSAIn,
+        TDest &dest, LcpConfig conf)
+    {
+        typedef typename Value<TTextInput>::Type            TValue;
+        typedef typename Size<TTextInput>::Type                TSize;
+        typedef typename BufReadHandler<TTextInput>::Type    TBufReader;
 
-		//typedef typename Value<typename Value<typename Value<TInvertedSAInput>::Type, 2>::Type>::Type TPair;
+        //typedef typename Value<typename Value<typename Value<TInvertedSAInput>::Type, 2>::Type>::Type TPair;
 
         SEQAN_PROSET(SEQAN_PRODEPTH, 0);
-		TSize rest = length(textIn);
+        TSize rest = length(textIn);
         if (rest < 2) {
             resize(dest, 0);
             return;
@@ -232,11 +232,11 @@ namespace SEQAN_NAMESPACE_MAIN
 
         // buffer is a window of textIn
         conf.absolutize((TValue*)NULL);
-		TBufReader reader(textIn, conf.windowSize);
+        TBufReader reader(textIn, conf.windowSize);
 
         Pair<TSize> out;
-		TSize windowBegin = 0;
-		TSize overlap = 0;
+        TSize windowBegin = 0;
+        TSize overlap = 0;
         TSize _pushes = 0;
         //TSize _olaps = 0;
         //char *seenISA = new bool[n];
@@ -244,72 +244,72 @@ namespace SEQAN_NAMESPACE_MAIN
 
         #ifdef SEQAN_DEBUG_INDEX
             TSize n = rest;
-            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;	// for lcpMax, lcpMean, |Sigma|
+            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;    // for lcpMax, lcpMean, |Sigma|
         #endif
 
         resize(dest, rest);
-		beginWrite(dest);
-		// read the first block of textIn
-		typename Value<TBufReader>::Type buffer = reader.first();
-		while (length(buffer))
+        beginWrite(dest);
+        // read the first block of textIn
+        typename Value<TBufReader>::Type buffer = reader.first();
+        while (length(buffer))
         {
             SEQAN_PROADD(SEQAN_PRODEPTH, 1);
             SEQAN_PROMARK("LCP-Durchlauf beginnen");
 
             beginRead(textIn);
-			beginRead(invertedSAIn);
+            beginRead(invertedSAIn);
 
             out.i2 = 0;                                             // out.i2 == h
             TSize windowSize = length(buffer);
-			TSize windowEnd = windowBegin + windowSize;
-			TSize newOverlap = windowEnd;
+            TSize windowEnd = windowBegin + windowSize;
+            TSize newOverlap = windowEnd;
             #ifdef SEQAN_DEBUG_INDEX
-				::std::cerr << ::std::hex << "  read window[" << windowBegin << "," << windowEnd;
-				::std::cerr << ") overlay " << overlap << " rest " << rest << ::std::dec << " size:"<< sizeof(TSize)<<::std::endl;
+                std::cerr << std::hex << "  read window[" << windowBegin << "," << windowEnd;
+                std::cerr << ") overlay " << overlap << " rest " << rest << std::dec << " size:"<< sizeof(TSize)<<std::endl;
             #endif
             rest -= windowSize;
 
             //unsigned _pops = 0;
 
-			TSize leftOrig, left;		// begin and begin + seen_lcp of the lower string (global)
+            TSize leftOrig, left;        // begin and begin + seen_lcp of the lower string (global)
 
             while (!eof(invertedSAIn)) {
 
-				if ((*invertedSAIn).i1 != 0) {
+                if ((*invertedSAIn).i1 != 0) {
 
-					leftOrig = posGlobalize((*invertedSAIn).i2[1], limits);
-					left = leftOrig + out.i2;        // left == j + h
+                    leftOrig = posGlobalize((*invertedSAIn).i2[1], limits);
+                    left = leftOrig + out.i2;        // left == j + h
 
-					if (overlap <= leftOrig && left <= windowEnd) {
-	//                        ::std::cerr << "* ";
-						for(; left < windowBegin; ++left) {
-							++textIn;
-							++out.i2;
-						}
+                    if (overlap <= leftOrig && left <= windowEnd) {
+    //                        std::cerr << "* ";
+                        for(; left < windowBegin; ++left) {
+                            ++textIn;
+                            ++out.i2;
+                        }
 
-						// end of lower string relative to window
-						TSize kEnd = limits[getValueI1((*invertedSAIn).i2[1]) + 1] - windowBegin;
-						if (kEnd > windowSize) kEnd = windowSize;
+                        // end of lower string relative to window
+                        TSize kEnd = limits[getValueI1((*invertedSAIn).i2[1]) + 1] - windowBegin;
+                        if (kEnd > windowSize) kEnd = windowSize;
 
-						TSize k = left - windowBegin;						// k is relative to window
+                        TSize k = left - windowBegin;                        // k is relative to window
 
-						// comparision will break before the end of the upper string
-						// -> only lower string needs a clipping
+                        // comparision will break before the end of the upper string
+                        // -> only lower string needs a clipping
 
-						while (k < kEnd && (!eof(textIn)) && *textIn == buffer[k]) {
-							++textIn;
-							++k;
-						}
-						TSize hAdd = k - (left - windowBegin);
-						out.i2 += hAdd;                                 // increase h by successful compares
-						left += hAdd;
+                        while (k < kEnd && (!eof(textIn)) && *textIn == buffer[k]) {
+                            ++textIn;
+                            ++k;
+                        }
+                        TSize hAdd = k - (left - windowBegin);
+                        out.i2 += hAdd;                                 // increase h by successful compares
+                        left += hAdd;
 
-						if (k != windowSize || rest == 0) {
-							out.i1 = (*invertedSAIn).i1 - 1;
-							push(dest, out);
-							//SEQAN_ASSERT(!seenISA[out.i1] && 0 <= out.i1 && out.i1 < n);
-							//seen[out.i1] = true;
-							++_pushes;
+                        if (k != windowSize || rest == 0) {
+                            out.i1 = (*invertedSAIn).i1 - 1;
+                            push(dest, out);
+                            //SEQAN_ASSERT(!seenISA[out.i1] && 0 <= out.i1 && out.i1 < n);
+                            //seen[out.i1] = true;
+                            ++_pushes;
 
                             #ifdef SEQAN_DEBUG_INDEX
                                 if ((lcpNumer += out.i2) > n) {
@@ -317,67 +317,67 @@ namespace SEQAN_NAMESPACE_MAIN
                                     ++lcpAvrg;
                                 }
                                 if (lcpMax < out.i2) lcpMax = out.i2;
-								if (!out.i2) ++sigma;
+                                if (!out.i2) ++sigma;
                             #endif
-						}
-					}
-
-					if (left >= windowEnd && leftOrig < newOverlap) {
-						#ifdef SEQAN_VERBOSE
-							::std::cerr << "crossing border @ " << (*invertedSAIn).i2[1] << " len " << out.i2 << ::std::endl;
-						#endif
-						newOverlap = leftOrig;    //++_olaps;
-					}
-				}
-
-				if (out.i2) 
-					--out.i2;                               // if (h > 0) h = h - 1
-				else 
-					++textIn; 
+                        }
+                    }
+
+                    if (left >= windowEnd && leftOrig < newOverlap) {
+                        #ifdef SEQAN_VERBOSE
+                            std::cerr << "crossing border @ " << (*invertedSAIn).i2[1] << " len " << out.i2 << std::endl;
+                        #endif
+                        newOverlap = leftOrig;    //++_olaps;
+                    }
+                }
+
+                if (out.i2)
+                    --out.i2;                               // if (h > 0) h = h - 1
+                else
+                    ++textIn;
 
                 ++invertedSAIn; //++_pops;
-			}
+            }
 
-			endRead(invertedSAIn);
-			endRead(textIn);
+            endRead(invertedSAIn);
+            endRead(textIn);
 
-			windowBegin = windowEnd;
-			overlap = newOverlap;
-			buffer = reader.next();                                 // read the following block
+            windowBegin = windowEnd;
+            overlap = newOverlap;
+            buffer = reader.next();                                 // read the following block
 
-			//::std::cerr << "pops:" << _pops << " pushes:" << _pushes << " overlaps:" << _olaps << ::std::endl;
-		}
-		// trailing zero
-		push(dest, Pair<TSize>(length(textIn) - 1, 0));
+            //std::cerr << "pops:" << _pops << " pushes:" << _pushes << " overlaps:" << _olaps << std::endl;
+        }
+        // trailing zero
+        push(dest, Pair<TSize>(length(textIn) - 1, 0));
 
-		//::std::cerr << "pushes:" << _pushes << " length:" << length(textIn) << ::std::endl;
+        //std::cerr << "pushes:" << _pushes << " length:" << length(textIn) << std::endl;
         //SEQAN_ASSERT_EQ(_pushes, length(textIn));
         //for (unsigned i = 0; i < n; ++i)
         //    if (!seen[i])
-        //        ::std::cerr << "___" << i << "______HUH?" << ::std::endl;
+        //        std::cerr << "___" << i << "______HUH?" << std::endl;
         //delete[] seenISA;
 
         #ifdef SEQAN_DEBUG_INDEX
-            ::std::cerr << "  n: " << n;
-            ::std::cerr << "  lcpMax: " << lcpMax;
-            ::std::cerr << "  lcpAvrg: " << lcpAvrg + lcpNumer / (double)n;
-            ::std::cerr << "  sigma: " << sigma << ::std::endl;
+            std::cerr << "  n: " << n;
+            std::cerr << "  lcpMax: " << lcpMax;
+            std::cerr << "  lcpAvrg: " << lcpAvrg + lcpNumer / (double)n;
+            std::cerr << "  sigma: " << sigma << std::endl;
         #endif
 
 //TODO: uncomment this line
-//		reader.end();
-		endWrite(dest);
+//        reader.end();
+        endWrite(dest);
         SEQAN_PROSET(SEQAN_PRODEPTH, 0);
     }
 
-	template < typename TTextInput, typename TLimitsString, typename TInvertedSAInput, typename TDest >
-	static void _lcpProcessMulti(
-		TTextInput &textIn, TLimitsString const &limits, 
-		TInvertedSAInput &invertedSAIn, 
-		TDest &dest)
-	{
-		_lcpProcessMulti(textIn, limits, invertedSAIn, dest, LcpConfig());
-	}
+    template < typename TTextInput, typename TLimitsString, typename TInvertedSAInput, typename TDest >
+    static void _lcpProcessMulti(
+        TTextInput &textIn, TLimitsString const &limits,
+        TInvertedSAInput &invertedSAIn,
+        TDest &dest)
+    {
+        _lcpProcessMulti(textIn, limits, invertedSAIn, dest, LcpConfig());
+    }
 
 
 
diff --git a/seqan/index/pump_separator7.h b/seqan/index/pump_separator7.h
index 4a62087..aab88be 100644
--- a/seqan/index/pump_separator7.h
+++ b/seqan/index/pump_separator7.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,45 +39,45 @@ namespace SEQAN_NAMESPACE_MAIN
 {
 
 
-    template < 
-		typename TInput, typename TFunctor,
-		typename TOut1, typename TOut2, typename TOut4 
-	>
+    template <
+        typename TInput, typename TFunctor,
+        typename TOut1, typename TOut2, typename TOut4
+    >
     static void _skew7SeparateSlices(
-		TInput &in, TFunctor const &funcSlice,
-		TOut1 &out1, TOut2 &out2, TOut4 &out4)
+        TInput &in, TFunctor const &funcSlice,
+        TOut1 &out1, TOut2 &out2, TOut4 &out4)
     {
-		beginRead(in);
+        beginRead(in);
 
-		resize(out1, funcSlice.n1);
-		resize(out2, funcSlice.n2);
-		resize(out4, funcSlice.n4);
+        resize(out1, funcSlice.n1);
+        resize(out2, funcSlice.n2);
+        resize(out4, funcSlice.n4);
 
-		beginWrite(out1);
-		beginWrite(out2);
-		beginWrite(out4);
+        beginWrite(out1);
+        beginWrite(out2);
+        beginWrite(out4);
 
-		typename Value<TInput>::Type i;
-		while (!eof(in)) {
-			pop(in, i);
-			if (i.i1 < funcSlice.n4) {
-				push(out4, i);
-			} else 
-				if (i.i1 < funcSlice.n24) {
-					i.i1 -= funcSlice.n4;
-					push(out2, i);
-				} else {
-					i.i1 -= funcSlice.n24;
-					push(out1, i);
-				}
-		}
+        typename Value<TInput>::Type i;
+        while (!eof(in)) {
+            pop(in, i);
+            if (i.i1 < funcSlice.n4) {
+                push(out4, i);
+            } else
+                if (i.i1 < funcSlice.n24) {
+                    i.i1 -= funcSlice.n4;
+                    push(out2, i);
+                } else {
+                    i.i1 -= funcSlice.n24;
+                    push(out1, i);
+                }
+        }
 
-		endWrite(out4);
-		endWrite(out2);
-		endWrite(out1);
-		endRead(in);
+        endWrite(out4);
+        endWrite(out2);
+        endWrite(out1);
+        endRead(in);
     }
-    
+
 //}
 
 }
diff --git a/seqan/index/radix.h b/seqan/index/radix.h
index 8d854c7..a7fdb63 100644
--- a/seqan/index/radix.h
+++ b/seqan/index/radix.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,157 +38,157 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	// stably sort a[0..n-1] to b[0..n-1] with keys in 0..K-1 from r
-	template <
-		typename TSortedArray, 
-		typename TUnsortedArray, 
-		typename TCountArray, 
-		typename TText >
-	void radixPass(
-		TSortedArray &b,			// result array (sorted by 1 character)
-		TUnsortedArray const &a,	// source array (unsorted)
-		TText const &r,				// text to compare with
-		TCountArray &c,				// temp. counter array
-		unsigned K)					// alphabet size
-	{
-		typedef typename Value<TCountArray>::Type TSize;
-
-		TSize i, sum = 0, n = length(a);
-		arrayFill(begin(c, Standard()), begin(c, Standard()) + K, 0);	// reset counters
-		
-		for (i = 0;  i < n;  i++)										// count occurrences
-			c[ordValue(getValue(r,getValue(a,i)))]++;
-			
-		for (i = 0;  i < K;  i++)
-		{																// exclusive prefix sums
-			TSize t = getValue(c,i);
-			c[i] = sum;
-			sum += t;
-		}
-		
-		for (i = 0;  i < n;  i++)
-		{
-			TSize j = getValue(a,i);									// sort
-			b[c[ordValue(getValue(r,j))]++] = j;
-		}
-	}
-
-	template <
-		typename TSortedArray, 
-		typename TUnsortedArray, 
-		typename TCountArray, 
-		typename TText, 
-		typename TShift >
-	void radixPass(
-		TSortedArray &b,			// result array (sorted by 1 character)
-		TUnsortedArray const &a,	// source array (unsorted)
-		TText const &r,				// text to compare with
-		TCountArray &c,				// temp. counter array
-		unsigned K,					// alphabet size
-		TShift shift)				// shift value
-	{
-		typedef typename Value<TCountArray>::Type TSize;
-
-		TSize i, sum = 0, n = length(a), sn = length(r);
-		arrayFill(begin(c, Standard()), begin(c, Standard()) + K, 0);	// reset counters
-		
-		for (i = 0;  i < n;  i++)
-		{
-			TSize j = getValue(a,i) + shift;							// count occurrences
-			if (j < sn) c[ordValue(getValue(r,j))]++;
-			else        sum++;
-		}
-		
-		for (i = 0;  i < K;  i++)
-		{																// exclusive prefix sums
-			TSize t = getValue(c,i);
-			c[i] = sum;
-			sum += t;
-		}
-		
-		for (i = 0, sum = 0;  i < n;  i++)
-		{																// sort
-			TSize j = getValue(a,i);
-			TSize k = j + shift;
-			if (k < sn) 
-				b[c[ordValue(getValue(r,k))]++] = j;	// On Exception: Make sure, you have resized your sufarray
-			else
-				b[sum++] = j;							// before calling createSuffixArray(..) to length(text)?
-		}
-	}
+    // stably sort a[0..n-1] to b[0..n-1] with keys in 0..K-1 from r
+    template <
+        typename TSortedArray,
+        typename TUnsortedArray,
+        typename TCountArray,
+        typename TText >
+    void radixPass(
+        TSortedArray &b,            // result array (sorted by 1 character)
+        TUnsortedArray const &a,    // source array (unsorted)
+        TText const &r,                // text to compare with
+        TCountArray &c,                // temp. counter array
+        unsigned K)                    // alphabet size
+    {
+        typedef typename Value<TCountArray>::Type TSize;
+
+        TSize i, sum = 0, n = length(a);
+        arrayFill(begin(c, Standard()), begin(c, Standard()) + K, 0);    // reset counters
+
+        for (i = 0;  i < n;  i++)                                        // count occurrences
+            c[ordValue(getValue(r,getValue(a,i)))]++;
+
+        for (i = 0;  i < K;  i++)
+        {                                                                // exclusive prefix sums
+            TSize t = getValue(c,i);
+            c[i] = sum;
+            sum += t;
+        }
+
+        for (i = 0;  i < n;  i++)
+        {
+            TSize j = getValue(a,i);                                    // sort
+            b[c[ordValue(getValue(r,j))]++] = j;
+        }
+    }
+
+    template <
+        typename TSortedArray,
+        typename TUnsortedArray,
+        typename TCountArray,
+        typename TText,
+        typename TShift >
+    void radixPass(
+        TSortedArray &b,            // result array (sorted by 1 character)
+        TUnsortedArray const &a,    // source array (unsorted)
+        TText const &r,                // text to compare with
+        TCountArray &c,                // temp. counter array
+        unsigned K,                    // alphabet size
+        TShift shift)                // shift value
+    {
+        typedef typename Value<TCountArray>::Type TSize;
+
+        TSize i, sum = 0, n = length(a), sn = length(r);
+        arrayFill(begin(c, Standard()), begin(c, Standard()) + K, 0);    // reset counters
+
+        for (i = 0;  i < n;  i++)
+        {
+            TSize j = getValue(a,i) + shift;                            // count occurrences
+            if (j < sn) c[ordValue(getValue(r,j))]++;
+            else        sum++;
+        }
+
+        for (i = 0;  i < K;  i++)
+        {                                                                // exclusive prefix sums
+            TSize t = getValue(c,i);
+            c[i] = sum;
+            sum += t;
+        }
+
+        for (i = 0, sum = 0;  i < n;  i++)
+        {                                                                // sort
+            TSize j = getValue(a,i);
+            TSize k = j + shift;
+            if (k < sn)
+                b[c[ordValue(getValue(r,k))]++] = j;    // On Exception: Make sure, you have resized your sufarray
+            else
+                b[sum++] = j;                            // before calling createSuffixArray(..) to length(text)?
+        }
+    }
 
     // stably sort a[0..n-1] to b[0..n-1] with keys in 0..K-1 from r
-	template <
-		typename TSortedArray, 
-		typename TUnsortedArray, 
-		typename TCountArray, 
-		typename TText >
-	void radixExtend(
-		TSortedArray &b,			// result array (sorted by 1 character)
-		TUnsortedArray const &a,	// source array (unsorted)
-		TText const &r,				// text to compare with
-		TCountArray &c,				// temp. counter array
-		unsigned K)					// alphabet size
-	{
-		typedef typename Value<TCountArray>::Type TSize;
-
-		TSize i, sum = 0, n = length(a);
-		arrayFill(begin(c, Standard()), begin(c, Standard()) + K, 0);	// reset counters
-		
-		for (i = 0;  i < n;  i++)										// count occurrences
-			c[ordValue(getValue(r,getValue(a,i)-1))]++;
-			
-		for (i = 0;  i < K;  i++) 
-		{																// exclusive prefix sums
-			TSize t = getValue(c,i);
-			c[i] = sum;
-			sum += t;
-		}
-		
-		for (i = 0;  i < n;  i++)
-		{
-			TSize j = getValue(a,i);									// sort
-			b[c[ordValue(getValue(r,j-1))]++] = j - 1;
-		}
-	}
+    template <
+        typename TSortedArray,
+        typename TUnsortedArray,
+        typename TCountArray,
+        typename TText >
+    void radixExtend(
+        TSortedArray &b,            // result array (sorted by 1 character)
+        TUnsortedArray const &a,    // source array (unsorted)
+        TText const &r,                // text to compare with
+        TCountArray &c,                // temp. counter array
+        unsigned K)                    // alphabet size
+    {
+        typedef typename Value<TCountArray>::Type TSize;
+
+        TSize i, sum = 0, n = length(a);
+        arrayFill(begin(c, Standard()), begin(c, Standard()) + K, 0);    // reset counters
+
+        for (i = 0;  i < n;  i++)                                        // count occurrences
+            c[ordValue(getValue(r,getValue(a,i)-1))]++;
+
+        for (i = 0;  i < K;  i++)
+        {                                                                // exclusive prefix sums
+            TSize t = getValue(c,i);
+            c[i] = sum;
+            sum += t;
+        }
+
+        for (i = 0;  i < n;  i++)
+        {
+            TSize j = getValue(a,i);                                    // sort
+            b[c[ordValue(getValue(r,j-1))]++] = j - 1;
+        }
+    }
 
     // stably sort a[0..n-1] to b[0..n-1] with keys in 0..K-1 from r
-	template <
-		typename TSortedArray, 
-		typename TUnsortedArray, 
-		typename TCountArray, 
-		typename TText >
-	void radixExtendClip(
-		TSortedArray &b,			// result array (sorted by 1 character)
-		TUnsortedArray const &a,	// source array (unsorted)
-		TText const &r,				// text to compare with
-		TCountArray &c,				// temp. counter array
-		unsigned K)					// alphabet size
-	{
-		typedef typename Value<TCountArray>::Type TSize;
-
-		TSize i, sum = 0, n = length(a);
-		arrayFill(begin(c, Standard()), begin(c, Standard()) + K, 0);	// reset counters
-		
-		for (i = 0;  i < n;  i++)
-		{																// count occurrences
-	        TSize j = getValue(a,i);
-			if (j > 0) c[ordValue(getValue(r,j-1))]++;
-		}
-		
-		for (i = 0;  i < K;  i++)
-		{																// exclusive prefix sums
-			TSize t = getValue(c,i);
-			c[i] = sum;
-			sum += t;
-		}
-		
-		for (i = 0;  i < n;  i++)
-		{
-			TSize j = getValue(a,i);									// sort
-			if (j > 0) b[c[ordValue(getValue(r,j-1))]++] = j - 1;
-		}
-	}
+    template <
+        typename TSortedArray,
+        typename TUnsortedArray,
+        typename TCountArray,
+        typename TText >
+    void radixExtendClip(
+        TSortedArray &b,            // result array (sorted by 1 character)
+        TUnsortedArray const &a,    // source array (unsorted)
+        TText const &r,                // text to compare with
+        TCountArray &c,                // temp. counter array
+        unsigned K)                    // alphabet size
+    {
+        typedef typename Value<TCountArray>::Type TSize;
+
+        TSize i, sum = 0, n = length(a);
+        arrayFill(begin(c, Standard()), begin(c, Standard()) + K, 0);    // reset counters
+
+        for (i = 0;  i < n;  i++)
+        {                                                                // count occurrences
+            TSize j = getValue(a,i);
+            if (j > 0) c[ordValue(getValue(r,j-1))]++;
+        }
+
+        for (i = 0;  i < K;  i++)
+        {                                                                // exclusive prefix sums
+            TSize t = getValue(c,i);
+            c[i] = sum;
+            sum += t;
+        }
+
+        for (i = 0;  i < n;  i++)
+        {
+            TSize j = getValue(a,i);                                    // sort
+            if (j > 0) b[c[ordValue(getValue(r,j-1))]++] = j - 1;
+        }
+    }
 
 }
 
diff --git a/seqan/index/repeat_base.h b/seqan/index/repeat_base.h
index 17fecf3..f2605c4 100644
--- a/seqan/index/repeat_base.h
+++ b/seqan/index/repeat_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,202 +41,140 @@
 
 namespace seqan {
 
-/**
-.Class.Repeat
-..summary:Store information about a repeat.
-..cat:Index
-..signature:Repeat<TPos, TPeriod>
-..param.TPos:Type to use for storing positions.
-...metafunction:Metafunction.Value
-..param.TPeriod:Type to use for storing the repeat period.
-...default:1
-...metafunction:Metafunction.Size
-..include:seqan/index.h
-..see:Function.findRepeats
-
-.Memvar.Repeat#beginPosition
-..summary:The begin position of the repeat of type $TPos$.
-..class:Class.Repeat
-
-.Memvar.Repeat#endPosition
-..summary:The end position of the repeat of type $TPos$.
-..class:Class.Repeat
-
-.Memvar.Repeat#period
-..summary:The period of the repeat of type $TSize$.
-..class:Class.Repeat
- */
 /*!
  * @class Repeat
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Store information about a repeat.
- * 
- * @signature Repeat<TPos, TPeriod>
- * 
+ *
+ * @signature template <typename TPos, typename TPeriod>
+ *            struct Repeat;
+ *
  * @tparam TPeriod Type to use for storing the repeat period. Default: 1
  * @tparam TPos Type to use for storing positions.
- * 
+ *
  * @see findRepeats
- * 
- * @var VariableType Repeat::endPosition
- * 
+ *
+ * @var TPos Repeat::endPosition;
  * @brief The end position of the repeat of type <tt>TPos</tt>.
- * 
- * @var VariableType Repeat::beginPosition
- * 
+ *
+ * @var TPos Repeat::beginPosition;
  * @brief The begin position of the repeat of type <tt>TPos</tt>.
- * 
- * @var VariableType Repeat::period
- * 
- * @brief The period of the repeat of type <tt>TSize</tt>.
+ *
+ * @var TPeriod Repeat::period;
+ * @brief The period of the repeat of type <tt>TPeriod</tt>.
  */
 
-	template <typename TPos, typename TPeriod>
-	struct Repeat {
-		TPos		beginPosition;
-		TPos		endPosition;
-		TPeriod		period;
-	};
-
-	template <typename TPos, typename TPeriod>
-	struct Value< Repeat<TPos, TPeriod> > {
-		typedef TPos Type;
-	};
-
-	template <typename TPos, typename TPeriod>
-	struct Size< Repeat<TPos, TPeriod> > {
-		typedef TPeriod Type;
-	};
-
-
-	template <typename TSize>
-	struct RepeatFinderParams {
-		TSize minRepeatLen;
-		TSize maxPeriod;
-	};
-
-	// custom TSpec for our customized wotd-Index
-	struct TRepeatFinder;
-
-	template <typename TText>
-	struct Cargo<Index<TText, IndexWotd<TRepeatFinder> > > 
-	{
-		typedef Index<TText, IndexWotd<TRepeatFinder> >	TIndex;
-		typedef typename Size<TIndex>::Type					TSize;
-		typedef RepeatFinderParams<TSize>					Type;
-	};
-
-
-	// node predicate
-	template <typename TText, typename TSpec>
-	bool nodePredicate(Iter<Index<TText, IndexWotd<TRepeatFinder> >, TSpec> &it) 
-	{
-//		return countOccurrences(it) * nodeDepth(it) >= cargo(container(it)).minRepeatLen;
-		return countOccurrences(it) * repLength(it) >= cargo(container(it)).minRepeatLen;
-	}
-
-	// monotonic hull
-	template <typename TText, typename TSpec>
-	bool nodeHullPredicate(Iter<Index<TText, IndexWotd<TRepeatFinder> >, TSpec> &it) 
-	{
-//		return nodeDepth(it) <= cargo(container(it)).maxPeriod;
-		return repLength(it) <= cargo(container(it)).maxPeriod;
-	}
-
-	template <typename TPos>
-	struct RepeatLess_ : public ::std::binary_function<TPos, TPos, bool>
-	{
-		// key less
-		inline bool operator() (TPos const &a, TPos const &b) const {
-			return posLess(a, b);
-		}
-	};
-
-	template <typename TValue>
-	inline bool _repeatMaskValue(TValue const &) 
-	{
+    template <typename TPos, typename TPeriod>
+    struct Repeat {
+        TPos        beginPosition;
+        TPos        endPosition;
+        TPeriod        period;
+    };
+
+    template <typename TPos, typename TPeriod>
+    struct Value< Repeat<TPos, TPeriod> > {
+        typedef TPos Type;
+    };
+
+    template <typename TPos, typename TPeriod>
+    struct Size< Repeat<TPos, TPeriod> > {
+        typedef TPeriod Type;
+    };
+
+
+    template <typename TSize>
+    struct RepeatFinderParams {
+        TSize minRepeatLen;
+        TSize maxPeriod;
+    };
+
+    // custom TSpec for our customized wotd-Index
+    struct TRepeatFinder;
+
+    template <typename TText>
+    struct Cargo<Index<TText, IndexWotd<TRepeatFinder> > >
+    {
+        typedef Index<TText, IndexWotd<TRepeatFinder> >    TIndex;
+        typedef typename Size<TIndex>::Type                    TSize;
+        typedef RepeatFinderParams<TSize>                    Type;
+    };
+
+
+    // node predicate
+    template <typename TText, typename TSpec>
+    bool nodePredicate(Iter<Index<TText, IndexWotd<TRepeatFinder> >, TSpec> &it)
+    {
+//        return countOccurrences(it) * nodeDepth(it) >= cargo(container(it)).minRepeatLen;
+        return countOccurrences(it) * repLength(it) >= cargo(container(it)).minRepeatLen;
+    }
+
+    // monotonic hull
+    template <typename TText, typename TSpec>
+    bool nodeHullPredicate(Iter<Index<TText, IndexWotd<TRepeatFinder> >, TSpec> &it)
+    {
+//        return nodeDepth(it) <= cargo(container(it)).maxPeriod;
+        return repLength(it) <= cargo(container(it)).maxPeriod;
+    }
+
+    template <typename TPos>
+    struct RepeatLess_ : public std::binary_function<TPos, TPos, bool>
+    {
+        // key less
+        inline bool operator() (TPos const &a, TPos const &b) const {
+            return posLess(a, b);
+        }
+    };
+
+    template <typename TValue>
+    inline bool _repeatMaskValue(TValue const &)
+    {
         // TODO(holtgrew): Maybe use unknownValue<TValue>() instead of specializing for all alphabets, especially since we have Rna5 now and might want Rna5Q later.
-		return false;
-	}
-
-	template <>
-	inline bool _repeatMaskValue(Dna5 const &val) 
-	{
-		return val == unknownValue<Dna5>(); // 'N'
-	}
-
-	template <>
-	inline bool _repeatMaskValue(Dna5Q const &val) 
-	{
-		return val == unknownValue<Dna5Q>(); // 'N'
-	}
-
-	template <>
-	inline bool _repeatMaskValue(Iupac const &val) 
-	{
-		return val == unknownValue<Iupac>(); // 'N'
-	}
+        return false;
+    }
+
+    template <>
+    inline bool _repeatMaskValue(Dna5 const &val)
+    {
+        return val == unknownValue<Dna5>(); // 'N'
+    }
+
+    template <>
+    inline bool _repeatMaskValue(Dna5Q const &val)
+    {
+        return val == unknownValue<Dna5Q>(); // 'N'
+    }
+
+    template <>
+    inline bool _repeatMaskValue(Iupac const &val)
+    {
+        return val == unknownValue<Iupac>(); // 'N'
+    }
 /*
-	template <>
-	inline bool _repeatMaskValue(AminoAcid val) 
-	{
-		return val == 'X';
-	}
+    template <>
+    inline bool _repeatMaskValue(AminoAcid val)
+    {
+        return val == 'X';
+    }
 */
-/**
-.Function.findRepeats
-..summary:Search for repeats in a text.
-..cat:Index
-..signature:findRepeats(repeatString, text, minRepeatLength[, maxPeriod])
-..param.repeatString:A @Class.String@ of @Class.Repeat@ objects.
-..param.text:The text to search repeats in.
-...type:Class.String
-...type:Class.StringSet
-..param.minRepeatLength:The minimum length each reported repeat must have.
-..param.maxPeriod:Optionally, the maximal period that reported repeats can have.
-...default:1
-..remarks:Subsequences of undefined values/$N$s will always be reported.
-..example.text:The following demonstrates finding repeats of period 1.
-..example.code:
-String<Repeat<unsigned, unsigned> > repeats;
-Dna5String text = "CGATAAAACTNN";
-// repeat 0            AAAA
-// repeat 1                  NN
-
-findRepeats(repeats, text, 3);
-// ==> length(repeats) == 2
-// ==> repeats[0] == {beginPosition:  4, endPosition:  8, period: 1}
-// ==> repeats[1] == {beginPosition: 11, endPosition: 13, period: 1}
-..see:Function.unknownValue
-..include:seqan/index.h
-..see:Class.Repeat
- */
 /*!
  * @fn findRepeats
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Search for repeats in a text.
- * 
- * @signature findRepeats(repeatString, text, minRepeatLength[, maxPeriod])
- * 
- * @param text The text to search repeats in. Types: @link SequenceConcept @endlink
- * @param repeatString A @link String @endlink of @link Repeat @endlink objects.
- * @param maxPeriod Optionally, the maximal period that reported repeats can
- *                  have. Default: 1
- * @param minRepeatLength The minimum length each reported repeat must have.
- * 
- * @section Remarks
- * 
+ *
+ * @signature void findRepeats(repeatString, text, minRepeatLength[, maxPeriod]);
+ *
+ * @param[out] repeatString    A @link String @endlink of @link Repeat @endlink objects.
+ * @param[in]  text            The text to search repeats in.  Types: @link ContainerConcept @endlink
+ * @param[in]  minRepeatLength The minimum length each reported repeat must have.
+ * @param[in]  maxPeriod       Optionally, the maximal period that reported repeats can have. Default: 1
+ *
  * Subsequences of undefined values/<tt>N</tt>s will always be reported.
- * 
+ *
  * @section Examples
- * 
+ *
  * The following demonstrates finding repeats of period 3.
  *
- * @include demos/index/find_repeats.cpp
+ * @include demos/dox/index/find_repeats.cpp
  *
  * @code{.console}
  * # of repeats: 15
@@ -262,16 +200,16 @@ findRepeats(repeats, text, 3);
  */
 // TODO(holtgrew): minRepeatLength is 1-off.
 
-	// period-1 optimization
-	template <typename TRepeatStore, typename TString, typename TRepeatSize>
-	inline void findRepeats(TRepeatStore &repString, TString const &text, TRepeatSize minRepeatLen) 
-	{
-		typedef typename Value<TRepeatStore>::Type	TRepeat;
-		typedef typename Iterator<TString const>::Type	TIterator;
-		typedef typename Size<TString>::Type		TSize;
+    // period-1 optimization
+    template <typename TRepeatStore, typename TString, typename TRepeatSize>
+    inline void findRepeats(TRepeatStore &repString, TString const &text, TRepeatSize minRepeatLen)
+    {
+        typedef typename Value<TRepeatStore>::Type    TRepeat;
+        typedef typename Iterator<TString const>::Type    TIterator;
+        typedef typename Size<TString>::Type        TSize;
 
 #if SEQAN_ENABLE_PARALLELISM
-		typedef typename Value<TString>::Type		TValue;
+        typedef typename Value<TString>::Type        TValue;
 
         if (length(text) > (TSize)(omp_get_max_threads() * 2 * minRepeatLen)) {
             // std::cerr << ">>> PARALLEL WABOOGIE!" << std::endl;
@@ -286,7 +224,7 @@ findRepeats(repeats, text, 3);
             String<TRepeatStore> threadLocalStores;
 
             // Each threads finds repeats on its chunk in parallel.
-            #pragma omp parallel 
+            #pragma omp parallel
             {
                 // We have to determine the number of available threads at this point.  We will use the number of thread
                 // local stores to determin the number of available threads later on.
@@ -320,7 +258,7 @@ findRepeats(repeats, text, 3);
                     TSize repLeft = 0;
                     TSize repRight = 1;
 
-                    for (++it; it != itEnd; ++it, ++repRight) 
+                    for (++it; it != itEnd; ++it, ++repRight)
                     {
                         if (*it != last)
                         {
@@ -386,7 +324,7 @@ findRepeats(repeats, text, 3);
                 {
                     if (fromPositions[i].i1 == fromPositions[i].i2)
                         continue;  // Skip empty buckets.
-                    
+
                     if (lastNonEmpty != -1)
                     {
                         bool const adjacent = back(threadLocalStores[lastNonEmpty]).endPosition == front(threadLocalStores[i]).beginPosition;
@@ -398,7 +336,7 @@ findRepeats(repeats, text, 3);
                             fromPositions[i].i1 += 1;
                         }
                     }
-                    
+
                     if (fromPositions[i].i1 != fromPositions[i].i2)
                         lastNonEmpty = i;
                 }
@@ -463,8 +401,8 @@ findRepeats(repeats, text, 3);
             TIterator itEnd = end(text, Standard());
             if (it == itEnd) return;
 
-			TSize repLen = 1;
-            for (++it; it != itEnd; ++it) 
+            TSize repLen = 1;
+            for (++it; it != itEnd; ++it)
             {
                 if (*it != *(it-1))
                 {
@@ -473,19 +411,19 @@ findRepeats(repeats, text, 3);
                         // insert repeat
                         rep.endPosition = it - begin(text, Standard());
                         rep.beginPosition = rep.endPosition - repLen;
-                        //					::std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<::std::endl;
+                        //                    std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<std::endl;
                         appendValue(repString, rep);
                     }
-					repLen = 1;
+                    repLen = 1;
                 } else
-					++repLen;
+                    ++repLen;
             }
             if (_repeatMaskValue(*(it-1)) || repLen > (TSize)minRepeatLen)
             {
                 // insert repeat
-				rep.endPosition = length(text);
-				rep.beginPosition = rep.endPosition - repLen;
-                //			::std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<::std::endl;
+                rep.endPosition = length(text);
+                rep.beginPosition = rep.endPosition - repLen;
+                //            std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<std::endl;
                 appendValue(repString, rep);
             }
 #if SEQAN_ENABLE_PARALLELISM
@@ -499,158 +437,158 @@ findRepeats(repeats, text, 3);
         //     }
         //     std::cerr << std::endl;
         // }
-	}
+    }
 
     // TODO(holtgrew): Why for TString const and StringSet<> const?
-	template <typename TRepeatStore, typename TString, typename TSpec, typename TRepeatSize>
-	inline void findRepeats(TRepeatStore &repString, StringSet<TString, TSpec> const &text, TRepeatSize minRepeatLen) 
-	{
-		typedef typename Value<TRepeatStore>::Type	TRepeat;
-		typedef typename Iterator<TString>::Type	TIterator;
-		typedef typename Value<TString>::Type		TValue;
-		typedef typename Size<TString>::Type		TSize;
-
-		TRepeat rep;
-		rep.period = 1;
-		clear(repString);
-
-		for (unsigned i = 0; i < length(text); ++i)
-		{
-			TIterator it = begin(text[i], Standard());
-			TIterator itEnd = end(text[i], Standard());
-			if (it == itEnd) continue;
-
-			TValue last = *it;
-			TSize repLeft = 0;
-			TSize repRight = 1;
-			rep.beginPosition.i1 = i;
-			rep.endPosition.i1 = i;
-
-			for (++it; it != itEnd; ++it, ++repRight) 
-			{
-				if (last != *it)
-				{
-					if (_repeatMaskValue(last) || (TRepeatSize)(repRight - repLeft) > minRepeatLen)
-					{
-						// insert repeat
-						rep.beginPosition.i2 = repLeft;
-						rep.endPosition.i2 = repRight;
-//						::std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<::std::endl;
-						appendValue(repString, rep);
-					}
-					repLeft = repRight;
-					last = *it;
-				}
-			}
-			if (_repeatMaskValue(last) || (TRepeatSize)(repRight - repLeft) > minRepeatLen)
-			{
-				// insert repeat
-				rep.beginPosition.i2 = repLeft;
-				rep.endPosition.i2 = repRight;
-//				::std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<::std::endl;
-				appendValue(repString, rep);
-			}
-		}
-	}
-
-	// main function
-	template <typename TRepeatStore, typename TText, typename TRepeatSize, typename TPeriodSize>
-	void findRepeats(TRepeatStore &repString, TText const &text, TRepeatSize minRepeatLen, TPeriodSize maxPeriod) 
-	{
-		typedef Index<TText, IndexWotd<TRepeatFinder> >					TIndex;
-		typedef typename Size<TIndex>::Type									TSize;
-		typedef typename Iterator<TIndex, TopDown<ParentLinks<> > >::Type	TNodeIterator;
-		typedef typename Fibre<TIndex, FibreSA>::Type const				TSA;
-		typedef typename Infix<TSA>::Type									TOccString;
-		typedef typename Iterator<TOccString>::Type							TOccIterator;
-
-		typedef typename Value<TRepeatStore>::Type							TRepeat;
-		typedef typename Value<TOccString>::Type							TOcc;
-
-		typedef ::std::map<TOcc,TRepeat,RepeatLess_<TOcc> >					TRepeatList;
-
-		if (maxPeriod < 1) return;
-		if (maxPeriod == 1) 
-		{
-			findRepeats(repString, text, minRepeatLen);
-			return;
-		}
-
-		TIndex		index(text);
-		TRepeatList list;
-
-		// set repeat finder parameters
-		cargo(index).minRepeatLen = minRepeatLen;
-		cargo(index).maxPeriod = maxPeriod;
-
-		TNodeIterator nodeIt(index);
-		TOccIterator itA, itB, itRepBegin, itEnd;
-		TRepeat rep;
-		for (; !atEnd(nodeIt); goNext(nodeIt))
-		{
-			if (isRoot(nodeIt)) continue;
-
-			// get occurrences
-			TOccString occ = getOccurrences(nodeIt);
-			itA = begin(occ, Standard());
-			itEnd = end(occ, Standard());
-			itRepBegin = itB = itA;
-
-			TSize repLen = repLength(nodeIt);		// representative length
-			if ((TSize)minRepeatLen <= repLen) continue;
-
-			TSize diff, period = 0;					// period of current repeat
-			TSize repeatLen = 0;					// overall length of current repeat
-			TSize minLen = minRepeatLen - repLen;	// minimum repeat length minus length of representative
-
-			for (++itB; itB != itEnd; ++itB)
-			{
-				diff = posSub(*itB, *itA);
-				if (diff != period || getSeqNo(*itA) != getSeqNo(*itB))
-				{
-					// is the repeat long enough?
-					if (repeatLen >= minLen)
-						// is the repeat self overlapping or connected?
-						if (parentRepLength(nodeIt) < period && period <= repLen)
-						{
-							// insert repeat
-							rep.beginPosition = *itRepBegin;
-							rep.endPosition = posAdd(*itA, period);
-							rep.period = period;
-//							::std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<::std::endl;
-							list.insert(::std::pair<TOcc,TRepeat>(rep.beginPosition, rep));
-						}
-					itRepBegin = itA;
-					period = diff;
-					repeatLen = 0;
-				}
-				repeatLen += period;
-				itA = itB;
-			}
-
-			// is the last repeat long enough?
-			if (repeatLen >= minLen)
-				// is the repeat self overlapping or connected?
-				if (parentRepLength(nodeIt) < period && period <= repLen)
-				{
-					// insert repeat
-					rep.beginPosition = *itRepBegin;
-					rep.endPosition = posAdd(*itA, period);
-					rep.period = period;
-//					::std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<::std::endl;
-					list.insert(::std::pair<TOcc,TRepeat>(rep.beginPosition, rep));
-				}
-		}
-
-		// copy low-complex regions to result string
+    template <typename TRepeatStore, typename TString, typename TSpec, typename TRepeatSize>
+    inline void findRepeats(TRepeatStore &repString, StringSet<TString, TSpec> const &text, TRepeatSize minRepeatLen)
+    {
+        typedef typename Value<TRepeatStore>::Type    TRepeat;
+        typedef typename Iterator<TString>::Type    TIterator;
+        typedef typename Value<TString>::Type        TValue;
+        typedef typename Size<TString>::Type        TSize;
+
+        TRepeat rep;
+        rep.period = 1;
+        clear(repString);
+
+        for (unsigned i = 0; i < length(text); ++i)
+        {
+            TIterator it = begin(text[i], Standard());
+            TIterator itEnd = end(text[i], Standard());
+            if (it == itEnd) continue;
+
+            TValue last = *it;
+            TSize repLeft = 0;
+            TSize repRight = 1;
+            rep.beginPosition.i1 = i;
+            rep.endPosition.i1 = i;
+
+            for (++it; it != itEnd; ++it, ++repRight)
+            {
+                if (last != *it)
+                {
+                    if (_repeatMaskValue(last) || (TRepeatSize)(repRight - repLeft) > minRepeatLen)
+                    {
+                        // insert repeat
+                        rep.beginPosition.i2 = repLeft;
+                        rep.endPosition.i2 = repRight;
+//                        std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<std::endl;
+                        appendValue(repString, rep);
+                    }
+                    repLeft = repRight;
+                    last = *it;
+                }
+            }
+            if (_repeatMaskValue(last) || (TRepeatSize)(repRight - repLeft) > minRepeatLen)
+            {
+                // insert repeat
+                rep.beginPosition.i2 = repLeft;
+                rep.endPosition.i2 = repRight;
+//                std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<std::endl;
+                appendValue(repString, rep);
+            }
+        }
+    }
+
+    // main function
+    template <typename TRepeatStore, typename TText, typename TRepeatSize, typename TPeriodSize>
+    void findRepeats(TRepeatStore &repString, TText const &text, TRepeatSize minRepeatLen, TPeriodSize maxPeriod)
+    {
+        typedef Index<TText, IndexWotd<TRepeatFinder> >                    TIndex;
+        typedef typename Size<TIndex>::Type                                    TSize;
+        typedef typename Iterator<TIndex, TopDown<ParentLinks<> > >::Type    TNodeIterator;
+        typedef typename Fibre<TIndex, FibreSA>::Type const                TSA;
+        typedef typename Infix<TSA>::Type                                    TOccString;
+        typedef typename Iterator<TOccString>::Type                            TOccIterator;
+
+        typedef typename Value<TRepeatStore>::Type                            TRepeat;
+        typedef typename Value<TOccString>::Type                            TOcc;
+
+        typedef std::map<TOcc,TRepeat,RepeatLess_<TOcc> >                    TRepeatList;
+
+        if (maxPeriod < 1) return;
+        if (maxPeriod == 1)
+        {
+            findRepeats(repString, text, minRepeatLen);
+            return;
+        }
+
+        TIndex        index(text);
+        TRepeatList list;
+
+        // set repeat finder parameters
+        cargo(index).minRepeatLen = minRepeatLen;
+        cargo(index).maxPeriod = maxPeriod;
+
+        TNodeIterator nodeIt(index);
+        TOccIterator itA, itB, itRepBegin, itEnd;
+        TRepeat rep;
+        for (; !atEnd(nodeIt); goNext(nodeIt))
+        {
+            if (isRoot(nodeIt)) continue;
+
+            // get occurrences
+            TOccString occ = getOccurrences(nodeIt);
+            itA = begin(occ, Standard());
+            itEnd = end(occ, Standard());
+            itRepBegin = itB = itA;
+
+            TSize repLen = repLength(nodeIt);        // representative length
+            if ((TSize)minRepeatLen <= repLen) continue;
+
+            TSize diff, period = 0;                    // period of current repeat
+            TSize repeatLen = 0;                    // overall length of current repeat
+            TSize minLen = minRepeatLen - repLen;    // minimum repeat length minus length of representative
+
+            for (++itB; itB != itEnd; ++itB)
+            {
+                diff = posSub(*itB, *itA);
+                if (diff != period || getSeqNo(*itA) != getSeqNo(*itB))
+                {
+                    // is the repeat long enough?
+                    if (repeatLen >= minLen)
+                        // is the repeat self overlapping or connected?
+                        if (parentRepLength(nodeIt) < period && period <= repLen)
+                        {
+                            // insert repeat
+                            rep.beginPosition = *itRepBegin;
+                            rep.endPosition = posAdd(*itA, period);
+                            rep.period = period;
+//                            std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<std::endl;
+                            list.insert(std::pair<TOcc,TRepeat>(rep.beginPosition, rep));
+                        }
+                    itRepBegin = itA;
+                    period = diff;
+                    repeatLen = 0;
+                }
+                repeatLen += period;
+                itA = itB;
+            }
+
+            // is the last repeat long enough?
+            if (repeatLen >= minLen)
+                // is the repeat self overlapping or connected?
+                if (parentRepLength(nodeIt) < period && period <= repLen)
+                {
+                    // insert repeat
+                    rep.beginPosition = *itRepBegin;
+                    rep.endPosition = posAdd(*itA, period);
+                    rep.period = period;
+//                    std::cerr<<"left:"<<rep.beginPosition<<"  right:"<<rep.endPosition<<"  length:"<<posSub(rep.endPosition,rep.beginPosition)<<"  period:"<<rep.period<<std::endl;
+                    list.insert(std::pair<TOcc,TRepeat>(rep.beginPosition, rep));
+                }
+        }
+
+        // copy low-complex regions to result string
         clear(repString);
-		reserve(repString, list.size(), Exact());
-		typename TRepeatList::const_iterator lit = list.begin();
-		typename TRepeatList::const_iterator litEnd = list.end();
-		for (TSize i = 0; lit != litEnd; ++lit, ++i)
-			appendValue(repString, (*lit).second);
-	}
-
-}	// namespace seqan
+        reserve(repString, list.size(), Exact());
+        typename TRepeatList::const_iterator lit = list.begin();
+        typename TRepeatList::const_iterator litEnd = list.end();
+        for (TSize i = 0; lit != litEnd; ++lit, ++i)
+            appendValue(repString, (*lit).second);
+    }
+
+}    // namespace seqan
 
 #endif
diff --git a/seqan/index/shape_base.h b/seqan/index/shape_base.h
index eb4ffe6..93fcb32 100644
--- a/seqan/index/shape_base.h
+++ b/seqan/index/shape_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,1135 +40,947 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	template <unsigned q>
-	struct UngappedShape {};
-	typedef UngappedShape<0> SimpleShape;
-
-	template <typename TSpec>
-	struct GappedShape {};
-	typedef GappedShape<Default> GenericShape;
-
-
-/**
-.Class.Shape
-..cat:Index
-..summary:Stores hash value and shape for an ungapped or gapped q-gram.
-..signature:Shape<TValue, TSpec>
-..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
-..param.TSpec:The specializing type.
-...default:@Spec.SimpleShape@, for ungapped q-grams.
-..remarks:The @Metafunction.ValueSize@ of Shape is the ValueSize of TValue which is the alphabet size.
-..remarks:To get the span or the weight of a shape call @Function.length@ or @Function.weight@.
-..example
-...text:The following code shows how one can use a gapped shape to search for the pattern "ACxA" in a reference. First
-we assign a form to the shape and then compute the corresponding hash value. The hash value of a string and a Shape 
-object is unique, such that one can retrieve the string from a shape if the hash value is known.
-...file:demos/index/shape.cpp
-...output:The hash is: 4
-Hit at position: 0
-Hit at position: 14
-Hit at position: 17
-.Memfunc.Shape#Shape:
-..class:Class.Shape
-..summary:Constructor
-..signature:Shape<TValue, TSpec> ()
-..signature:Shape<TValue, TSpec> (shape)
-..param.shape:Other Shape object. (copy constructor)
-..include:seqan/index.h
-*/
+    template <unsigned q>
+    struct UngappedShape {};
+    typedef UngappedShape<0> SimpleShape;
+
+    template <typename TSpec>
+    struct GappedShape {};
+    typedef GappedShape<Default> GenericShape;
+
+
 /*!
  * @class Shape
- * 
+ * @headerfile <seqan/index.h>
  * @brief Stores hash value and shape for an ungapped or gapped q-gram.
- * 
- * @signature Shape<TValue, TSpec>
- * 
+ *
+ * @signature template <typename TValue, typename TSpec>
+ *            class Shape;
+ *
  * @tparam TSpec The specializing type. Default: @link SimpleShape @endlink, for
  *               ungapped q-grams.
  * @tparam TValue The @link Value @endlink type of the string the shape is
  *                applied to (e.g. <tt>Dna</tt>).
- * 
- * @section Remarks
- * 
+ *
  * The @link FiniteOrderedAlphabetConcept#ValueSize @endlink of Shape is the ValueSize of TValue which is the
  * alphabet size.
- * 
- * To get the span or the weight of a shape call @link length @endlink or @link
- * Shape#weight @endlink.
+ *
+ * To get the span or the weight of a shape call @link Shape#length @endlink or @link Shape#weight @endlink.
  */
-	template <typename TValue = Dna, typename TSpec = SimpleShape>
-	class Shape;
+    template <typename TValue = Dna, typename TSpec = SimpleShape>
+    class Shape;
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Value.param.T.type:Class.Shape
-///.Metafunction.Value.class:Class.Shape
-	template <typename TValue, typename TSpec>
-	struct Value<Shape<TValue,TSpec> >
-	{
-		typedef __uint64 Type;
-	};
-
-///.Metafunction.Size.param.T.type:Class.Shape
-///.Metafunction.Size.class:Class.Shape
-	template <typename TValue, typename TSpec>
-	struct Size<Shape<TValue,TSpec> >
-	{
-		typedef unsigned long Type;
-	};
-
-///.Metafunction.LENGTH.param.T.type:Class.Shape
-///.Metafunction.LENGTH.class:Class.Shape
+/*!
+ * @mfn Shape#Value
+ * @brief Returns the value type for a shape.
+ *
+ * @signature Value<TShape>::Type;
+ *
+ * @tparam TShape The Shape to query for its value type.
+ *
+ * @return Type The value type of the shape.
+ */
+
+    template <typename TValue, typename TSpec>
+    struct Value<Shape<TValue,TSpec> >
+    {
+        typedef __uint64 Type;
+    };
+
+/*!
+ * @mfn Shape#Size
+ * @brief Returns the size type for a shape.
+ *
+ * @signature Size<TShape>::Type;
+ *
+ * @tparam TShape The Shape to query for its size type.
+ *
+ * @return Type The size type of the shape.
+ */
+
+    template <typename TValue, typename TSpec>
+    struct Size<Shape<TValue,TSpec> >
+    {
+        typedef unsigned long Type;
+    };
+
+/*!
+ * @mfn Shape#LENGTH
+ * @brief Returns the length (span) of a shape.
+ *
+ * @signature LENGTH<TShape>::VALUE;
+ *
+ * @tparam TShape The Shape to query for its length (span).
+ *
+ * @return VALUE The length (span) of the shape.
+ */
+
     template <typename TValue, unsigned q>
-	struct LENGTH< Shape<TValue, UngappedShape<q> > >
-	{
-		enum { VALUE = q };
-	};
+    struct LENGTH< Shape<TValue, UngappedShape<q> > >
+    {
+        enum { VALUE = q };
+    };
+
+/*!
+ * @mfn Shape#WEIGHT
+ * @brief Returns the weight (number of 1's) of a shape.
+ *
+ * @signature WEIGHT<TShape>::VALUE;
+ *
+ * @tparam TShape The Shape to query for its weight (number of 1's).
+ *
+ * @return VALUE The weight (number of 1's) of the shape.
+ */
 
-///.Metafunction.WEIGHT.param.T.type:Class.Shape
-///.Metafunction.WEIGHT.class:Class.Shape
     template <typename TValue, unsigned q>
-	struct WEIGHT< Shape<TValue, UngappedShape<q> > >
-	{
-		enum { VALUE = q };
-	};
-
-///.Metafunction.ValueSize.param.T.type:Class.Shape
-///.Metafunction.ValueSize.class:Class.Shape
-	template <typename TValue, typename TSpec>
-	struct ValueSize< Shape<TValue, TSpec> > 
-	{
-		typedef typename Value<Shape<TValue, TSpec> >::Type THashValue;
-		static const THashValue VALUE = Power<
-						ValueSize<TValue>::VALUE, 
-						WEIGHT< Shape<TValue, TSpec> >::VALUE >::VALUE;
-	};
-
-///.Metafunction.Host.param.T.type:Class.Shape
-///.Metafunction.Host.class:Class.Shape
-
-	template <typename TValue, typename TSpec>
-	struct Host<Shape<TValue,TSpec> >
-	{
-		typedef TValue Type;
-	};
+    struct WEIGHT< Shape<TValue, UngappedShape<q> > >
+    {
+        enum { VALUE = q };
+    };
+
+/*!
+ * @mfn Shape#ValueSize
+ * @brief Returns the type to use for the value size.
+ *
+ * @signature ValueSize<TShape>::Type;
+ *
+ * @tparam TShape The Shape to query for value size type.
+ *
+ * @return Type Type to use for the value size.
+ */
+
+    template <typename TValue, typename TSpec>
+    struct ValueSize< Shape<TValue, TSpec> >
+    {
+        typedef typename Value<Shape<TValue, TSpec> >::Type THashValue;
+        static const THashValue VALUE = Power<
+                        ValueSize<TValue>::VALUE,
+                        WEIGHT< Shape<TValue, TSpec> >::VALUE >::VALUE;
+    };
+
+/*!
+ * @mfn Shape#Host
+ * @brief Returns the host (= value) type to use.
+ *
+ * @signature Host<TShape>::Type;
+ *
+ * @tparam TShape The Shape to query for host (= value) type.
+ *
+ * @return Type Type to use for the host (= value) size.
+ */
+
+    template <typename TValue, typename TSpec>
+    struct Host<Shape<TValue,TSpec> >
+    {
+        typedef TValue Type;
+    };
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Spec.SimpleShape:
-..cat:Index
-..summary:A variable length ungapped shape (also called q-gram or k-mer).
-..general:Class.Shape
-..signature:Shape<TValue, SimpleShape>
-..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
-..remarks:A SimpleShape must be resized first to a valid length. To do so, call @Function.resize@.
-..see:Spec.UngappedShape
-..include:seqan/index.h
-*/
 /*!
  * @class SimpleShape
- * 
  * @extends Shape
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief A variable length ungapped shape (also called q-gram or k-mer).
- * 
- * @signature Shape<TValue, SimpleShape>
- * 
+ *
+ * @signature template <typename TValue>
+ *            class Shape<TValue, SimpleShape>;
+ *
  * @tparam TValue The @link Value @endlink type of the string the shape is
  *                applied to (e.g. <tt>Dna</tt>).
- * 
+ *
  * @section Remarks
- * 
- * A SimpleShape must be resized first to a valid length. To do so, call @link
- * resize @endlink.
- * 
+ *
+ * A SimpleShape must be resized first to a valid length.  To do so, call @link
+ * Shape#resize @endlink.
+ *
  * @see UngappedShape
  */
 
-	//////////////////////////////////////////////////////////////////////////////
-	// ungapped shape with variable length
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // ungapped shape with variable length
+    //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TValue>
-	class Shape<TValue, SimpleShape>
-	{
-	public:
+    template <typename TValue>
+    class Shape<TValue, SimpleShape>
+    {
+    public:
 //____________________________________________________________________________
 
-		unsigned					span;
-		typename Value<Shape>::Type	hValue;
-		typename Value<Shape>::Type	XValue;
-		typename Value<Shape>::Type	leftFactor;
-		typename Value<Shape>::Type	leftFactor2;
-		TValue						leftChar;
+        unsigned                    span;
+        typename Value<Shape>::Type    hValue;
+        typename Value<Shape>::Type    XValue;
+        typename Value<Shape>::Type    leftFactor;
+        typename Value<Shape>::Type    leftFactor2;
+        TValue                        leftChar;
 //____________________________________________________________________________
-		
-/**
-.Memfunc.SimpleShape#Shape:
-..class:Spec.SimpleShape
-..summary:Constructor
-..signature:Shape<TValue, SimpleShape> ()
-..signature:Shape<TValue, SimpleShape> (shape)
-..signature:Shape<TValue, SimpleShape> (q)
-..param.shape:Other Shape object. (copy constructor)
-..param.q:Length of the ungapped q-gram.
-*/
+
 /*!
  * @fn SimpleShape::Shape
- * 
- * @brief Constructor
- * 
- * @signature Shape<TValue, SimpleShape> ()
- * @signature Shape<TValue, SimpleShape> (shape)
- * @signature Shape<TValue, SimpleShape> (q)
- * 
- * @param q Length of the ungapped q-gram.
- * @param shape Other Shape object. (copy constructor)
- */ 
-		Shape():
-			span(0),
-			hValue(0),
-			XValue(0),
-			leftFactor(0),
-			leftFactor2(0),
+ *
+ * @brief Constructor.
+ *
+ * @signature Shape::Shape();
+ * @signature Shape::Shape(shape);
+ * @signature Shape::Shape(q);
+ *
+ * @param[in] shape Other Shape object (copy constructor).
+ * @param[in] q     Length of the ungapped q-gram (@link IntegerConcept @endlink).
+ */
+        Shape():
+            span(0),
+            hValue(0),
+            XValue(0),
+            leftFactor(0),
+            leftFactor2(0),
             leftChar(0) {}
-		
-		Shape(unsigned _span):
-			hValue(0),
-			XValue(0),
-			leftFactor(0),
-			leftFactor2(0),
-			leftChar(0)
-		{
-			resize(*this, _span);
-		}
-
-		template <unsigned q>
-		Shape(Shape<TValue, UngappedShape<q> > const &other)
-		{
-			*this = other;
-		}	
+
+        Shape(unsigned _span):
+            hValue(0),
+            XValue(0),
+            leftFactor(0),
+            leftFactor2(0),
+            leftChar(0)
+        {
+            resize(*this, _span);
+        }
+
+        template <unsigned q>
+        Shape(Shape<TValue, UngappedShape<q> > const &other)
+        {
+            *this = other;
+        }
 
 //____________________________________________________________________________
 
-		template <unsigned q>
-		inline Shape &
-		operator=(Shape<TValue, UngappedShape<q> > const &other)
-		{
-			span = other.span;
-			hValue = other.hValue;
-			XValue = other.XValue;
-			leftFactor = other.leftFactor;
-			leftFactor2 = other.leftFactor2;
-			leftChar = other.leftChar;
-			return *this;
-		}
-	};
-
-	//////////////////////////////////////////////////////////////////////////////
-	// ungapped shape with fixed length q
-	//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Spec.UngappedShape:
-..cat:Index
-..summary:A fixed length ungapped shape (also called q-gram or k-mer).
-..general:Class.Shape
-..signature:Shape<TValue, UngappedShape<q> >
-..param.TValue:The @Metafunction.Value@ type of the sequence the shape is applied to (e.g. $Dna$).
-..param.q:The length of the shape.
-..include:seqan/index.h
-*/
+        template <unsigned q>
+        inline Shape &
+        operator=(Shape<TValue, UngappedShape<q> > const &other)
+        {
+            span = other.span;
+            hValue = other.hValue;
+            XValue = other.XValue;
+            leftFactor = other.leftFactor;
+            leftFactor2 = other.leftFactor2;
+            leftChar = other.leftChar;
+            return *this;
+        }
+    };
+
+    //////////////////////////////////////////////////////////////////////////////
+    // ungapped shape with fixed length q
+    //////////////////////////////////////////////////////////////////////////////
+
 /*!
  * @class UngappedShape
- * 
  * @extends Shape
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief A fixed length ungapped shape (also called q-gram or k-mer).
- * 
- * @signature Shape<TValue, UngappedShape<q> >
- * 
- * @tparam q The length of the shape.
+ *
+ * @signature template <typename TValue, unsigned Q>
+ *            class Shape<TValue, UngappedShape<Q> >;
+ *
+ * @tparam Q      The length of the shape (@link IntegerConcept @endlink).
  * @tparam TValue The @link Value @endlink type of the sequence the shape is
  *                applied to (e.g. <tt>Dna</tt>).
- * 
+ *
  * @see SimpleShape
  */
 
-	template <typename TValue, unsigned q>
-	class Shape<TValue, UngappedShape<q> >
-	{
-	public:
-		typedef typename Value<Shape>::Type THashValue;
+    template <typename TValue, unsigned q>
+    class Shape<TValue, UngappedShape<q> >
+    {
+    public:
+        typedef typename Value<Shape>::Type THashValue;
 //____________________________________________________________________________
 
-		static const unsigned span = q;
-		static const THashValue leftFactor = Power<ValueSize<TValue>::VALUE, q - 1>::VALUE;
-		static const THashValue leftFactor2 = (Power<ValueSize<TValue>::VALUE, q>::VALUE - 1) / (ValueSize<TValue>::VALUE - 1);
-		// Sigma^(q-1) + Sigma^(q-2) + ... + Sigma + 1
+        static const unsigned span = q;
+        static const THashValue leftFactor = Power<ValueSize<TValue>::VALUE, q - 1>::VALUE;
+        static const THashValue leftFactor2 = (Power<ValueSize<TValue>::VALUE, q>::VALUE - 1) / (ValueSize<TValue>::VALUE - 1);
+        // Sigma^(q-1) + Sigma^(q-2) + ... + Sigma + 1
 
-		THashValue	hValue;		// current hash value
-		THashValue	XValue;		// Sum_{i=0..q-1} (x_i + 1)
-		TValue		leftChar;	// leftmost character
+        THashValue    hValue;        // current hash value
+        THashValue    XValue;        // Sum_{i=0..q-1} (x_i + 1)
+        TValue        leftChar;    // leftmost character
 //____________________________________________________________________________
-		Shape():
-			hValue(0),
-			XValue(0),
+
+        SEQAN_HOST_DEVICE
+        Shape():
+            hValue(0),
+            XValue(0),
             leftChar(0) {}
-	};
+    };
 
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.value.param.object.type:Class.Shape
-///.Function.value.class:Class.Shape
-	template <typename TValue, typename TSpec>
-	inline typename Value< Shape<TValue, TSpec> >::Type
-	value(Shape<TValue, TSpec> &me)
-	{
-		return me.hValue;
-	}
+/*!
+ * @fn Shape#value
+ * @headerfile <seqan/index.h>
+ * @brief Returns the current hash value of the Shape.
+ *
+ * @signature TValue value(shape);
+ *
+ * @param[in] shape The Shape to query for its value.
+ *
+ * @return TValue The hash value of the shape.
+ */
 
-	template <typename TValue, typename TSpec>
-	inline typename Value< Shape<TValue, TSpec> >::Type
-	value(Shape<TValue, TSpec> const &me)
-	{
-		return me.hValue;
-	}
+    template <typename TValue, typename TSpec>
+    inline typename Value< Shape<TValue, TSpec> >::Type
+    value(Shape<TValue, TSpec> &me)
+    {
+        return me.hValue;
+    }
+
+    template <typename TValue, typename TSpec>
+    inline typename Value< Shape<TValue, TSpec> >::Type
+    value(Shape<TValue, TSpec> const &me)
+    {
+        return me.hValue;
+    }
 
 
 //____________________________________________________________________________
 /*!
  * @fn Shape#length
- * 
  * @brief Returns the number of elements of the shape (span).
- * 
- * @signature length(shape)
- * 
- * @param shape Shape object for which the number of relevant positions is determined.
- * 
- * @return TReturn The number of elements of the shape (span). The return type is 
- *         <tt>Size< Shape<TValue, TSpec> >::Type </tt>
+ *
+ * @signature TSize length(shape);
+ *
+ * @param[in] shape Shape object for which the number of relevant positions is determined.
+ *
+ * @return TSize The number of elements of the shape (span) (Metafunction: @link Shape#Size @endlink).
  */
-///.Function.length.param.object.type:Class.Shape
-///.Function.length.class:Class.Shape
-	template <typename TValue, typename TSpec>
-	inline typename Size< Shape<TValue, TSpec> >::Type
-	length(Shape<TValue, TSpec> const &me)
-	{
-	SEQAN_CHECKPOINT
-		return me.span;
-	}
+    template <typename TValue, typename TSpec>
+    inline SEQAN_HOST_DEVICE
+    typename Size< Shape<TValue, TSpec> >::Type
+    length(Shape<TValue, TSpec> const &me)
+    {
+    SEQAN_CHECKPOINT
+        return me.span;
+    }
 
 //____________________________________________________________________________
 
-/**.Function.weight:
-..cat:Index
-..summary:Number of relevant positions in a shape.
-..signature:weight(shape)
-..class:Class.Shape
-..param.shape:Shape object for which the number of relevant positions is determined.
-...type:Class.Shape
-..returns:Number of relevant positions.
-..remarks.text:For ungapped shapes the return value is the result of the @Function.length@ function.
-For gapped shapes this is the number of '1's.
-*/
 /*!
  * @fn Shape#weight
- * 
  * @brief Number of relevant positions in a shape.
- * 
- * @signature weight(shape)
- * 
- * @param shape Shape object for which the number of relevant positions is determined.
- * 
- * @return TReturn Number of relevant positions.
- * 
- * @section Remarks
- * 
+ *
+ * @signature TSize weight(shape);
+ *
+ * @param[in] shape Shape object for which the number of relevant positions is determined.
+ *
+ * @return TSize Number of relevant positions  (Metafunction: @link Shape#Size @endlink).
+ *
  * For ungapped shapes the return value is the result of the @link Shape#length
- * @endlink function. For gapped shapes this is the number of '1's.
+ * @endlink function.  For gapped shapes this is the number of '1's.
  */
-	template <typename TValue, typename TSpec>
-	inline typename Size< Shape<TValue, TSpec> >::Type
-	weight(Shape<TValue, TSpec> const &me)
-	{
-	SEQAN_CHECKPOINT
-		return length(me);
-	}
+    template <typename TValue, typename TSpec>
+    inline SEQAN_HOST_DEVICE
+    typename Size< Shape<TValue, TSpec> >::Type
+    weight(Shape<TValue, TSpec> const &me)
+    {
+    SEQAN_CHECKPOINT
+        return length(me);
+    }
 
 //____________________________________________________________________________
 
-///.Function.resize.param.object.type:Spec.SimpleShape
-///.Function.resize.class:Spec.SimpleShape
 /*!
- * @fn SimpleShape#resize
- * 
+ * @fn Shape#resize
  * @brief Resize a shape to a specified span.
- * 
- * @signature resize(shape, length)
- * 
- * @param shape Shape object for which the number of relevant positions is determined
- * @param length The new length (span) of the shape. 
- * 
- * @return TReturn The new span of type <tt> Size< Shape<TValue, SimpleShape> >::Type </tt>
+ *
+ * @signature TSize resize(shape, length)
+ *
+ * @param[in,out] shape  Shape object for which the number of relevant positions is determined
+ * @param[in]     length The new length (span) of the shape.
+ *
+ * @return TSize The new span of type  (Metafunction: @link Shape#Size @endlink).
  */
-	template <typename TValue, typename TSize>
-	inline typename Size< Shape<TValue, SimpleShape> >::Type
-	resize(Shape<TValue, SimpleShape> & me, TSize new_length)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Value< Shape<TValue, SimpleShape> >::Type	THValue;
-		me.leftFactor = _intPow((THValue)ValueSize<TValue>::VALUE, new_length - 1);
-		me.leftFactor2 = (_intPow((THValue)ValueSize<TValue>::VALUE, new_length) - 1) / (ValueSize<TValue>::VALUE - 1);
-		return me.span = new_length;
-	}
+    template <typename TValue, typename TSize>
+    inline typename Size< Shape<TValue, SimpleShape> >::Type
+    resize(Shape<TValue, SimpleShape> & me, TSize new_length)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Value< Shape<TValue, SimpleShape> >::Type    THValue;
+        me.leftFactor = _intPow((THValue)ValueSize<TValue>::VALUE, new_length - 1);
+        me.leftFactor2 = (_intPow((THValue)ValueSize<TValue>::VALUE, new_length) - 1) / (ValueSize<TValue>::VALUE - 1);
+        return me.span = new_length;
+    }
 
 //____________________________________________________________________________
 
-/**
-.Function.hash:
-..cat:Index
-..summary:Computes a (lower) hash value for a shape applied to a sequence.
-..description:The hash value (a.k.a. code) of a q-gram is the lexicographical rank of this q-gram in the set of all possible q-grams.
-For example, the hash value of the @Spec.Dna@ 3-gram AAG is 2 as there are only two 3-grams (AAA and AAC) having a smaller lexicographical rank.
-If @Function.hash@ is called with a gapped shape, the q-gram is the text subsequence of no-gap shape positions relative to the text iterator, e.g. a shape 1101 at the beginning of text ACGT corresponds to the 3-gram ACT.
-
-..signature:hash(shape, it)
-..signature:hash(shape, it, charsLeft)
-..class:Class.Shape
-..param.shape:Shape to be used for hashing.
-...type:Class.Shape
-..param.it:Sequence iterator pointing to the first character of the shape.
-..param.charsLeft:The distance of $it$ to the string end. 
-If $charsLeft$ is smaller than the shape's span, the hash value corresponds to the lexicographically smallest shape beginning with $charsLeft$ characters. The hash value of such a truncated shape corresponds to the shape applied to a text padded with the smallest alphabet characters.
-..returns:Hash value of the shape.
-..see:Function.hashNext
-..see:Function.hashUpper
-..see:Function.hash2
-..example:
-...text:Code example that computes hash values of 4-grams with different shapes starting at the beginning of a text.
-...file:demos/index/shape_hash.cpp
-...text:The resulting hexadecimal hash values of the three 4-mers GATT, GATC and GATA are:
-...output:
-0x8f
-0x8d
-0x8c
-..include:seqan/index.h
-*/
 /*!
  * @fn Shape#hash
- * 
  * @brief Computes a (lower) hash value for a shape applied to a sequence.
- * 
- * @signature hash(shape, it)
- * @signature hash(shape, it, charsLeft)
- * 
- * @param charsLeft The distance of <tt>it</tt> to the string end. If
- *                  <tt>charsLeft</tt> is smaller than the shape's span, the
- *                  hash value corresponds to the smallest shape beginning with
- *                  <tt>charsLeft</tt> characters.
- * @param shape Shape to be used for hashing. Types: @link Shape @endlink
- * @param it Sequence iterator pointing to the first character of the shape.
- * 
- * @return TReturn Hash value of the shape.
- * 
+ *
+ * @signature TValue hash(shape, it[, charsLeft]);
+ *
+ * @param[in,out] shape     Shape to be used for hashing. Types: @link Shape @endlink
+ * @param[in]     it        Sequence iterator pointing to the first character of the shape.
+ * @param[in]     charsLeft The distance of <tt>it</tt> to the string end. If
+ *                          <tt>charsLeft</tt> is smaller than the shape's span, the
+ *                          hash value corresponds to the smallest shape beginning with
+ *                          <tt>charsLeft</tt> characters.
+ *
+ * @return TValue Hash value of the shape  (Metafunction: @link Shape#Value @endlink).
+ *
  * @see Shape#hashNext
  * @see Shape#hashUpper
  * @see Shape#hash2
  * @see Shape#unhash
  */
-	template <typename TValue, typename TIter>
-	inline typename Value< Shape<TValue, SimpleShape> >::Type
-	hash(Shape<TValue, SimpleShape> &me, TIter it)
-	{
-		//typedef typename Value< Shape<TValue, SimpleShape> >::Type	THValue;
-		typedef typename Size< Shape<TValue, SimpleShape> >::Type	TSize;
-
-		SEQAN_ASSERT_GT((unsigned)me.span, 0u);
-
-		me.hValue = ordValue(me.leftChar = *it);
-		for(TSize i = 1; i < me.span; ++i) {
-			++it;
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-		return me.hValue;
-	}
-
-/**
-.Function.hashInit:
-..cat:Index
-..summary:Preprocessing step of a pure @Function.hashNext@ loop.
-..description:Overlapping q-grams can efficiently be hashed by calling @Function.hash@ on the first text position and @Function.hashNext@ on succeeding, adjacent positions. One drawback of this scenario is that for-loops cannot start with the first position directly and become more complicated. As a remedy, @Function.hashInit@ was introduced which initializes the @Class.Shape@ to be used with @Function.hashNext@ on the first position directly.
-..signature:hashInit(shape, it)
-..class:Class.Shape
-..param.shape:Shape to be used for hashing.
-...type:Class.Shape
-..param.it:Sequence iterator pointing to the first text character of the shape.
-..see:Function.hashNext
-..example:
-...text:Two hash loop examples. The first loop uses @Function.hash@/@Function.hashNext@ while the second use @Function.hashInit@/@Function.hashNext@ and can process all hashes within the loop.
-...file:demos/index/shape_hash_init.cpp
-...text:The two loops produce the same hash values:
-...output:
-0	0	1	4	17	4	18	11	47	63	62	56	
-0	0	1	4	17	4	18	11	47	63	62	56
-..include:seqan/index.h
-*/
-	template <typename TValue, typename TIter>
-	inline void
-	hashInit(Shape<TValue, SimpleShape> &me, TIter it)
-	{
-		//typedef typename Value< Shape<TValue, SimpleShape> >::Type	THValue;
-		typedef typename Size< Shape<TValue, SimpleShape> >::Type	TSize;
-
-		SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+    template <typename TValue, typename TIter>
+    inline typename Value< Shape<TValue, SimpleShape> >::Type
+    hash(Shape<TValue, SimpleShape> &me, TIter it)
+    {
+        //typedef typename Value< Shape<TValue, SimpleShape> >::Type    THValue;
+        typedef typename Size< Shape<TValue, SimpleShape> >::Type    TSize;
+
+        SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+
+        me.hValue = ordValue(me.leftChar = *it);
+        for(TSize i = 1; i < me.span; ++i) {
+            ++it;
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+        return me.hValue;
+    }
+
+/*!
+ * @fn Shape#hashInit
+ *
+ * @brief Preprocessing step of a pure @link Shape#hashNext @endlink loop.
+ *
+ * Overlapping q-grams can efficiently be hashed by calling @link Shape#hash @endlink on the first text position and @link Shape#hashNext @endlink on succeeding, adjacent positions.
+ * One drawback of this scenario is that for-loops cannot start with the first position directly and become more complicated.
+ * As a remedy, @link Shape#hashInit @endlink was introduced which initializes the Shape to be used with @link Shape#hashNext @endlink on the first position directly.
+ *
+ * @signature void hashInit(shape, it);
+ *
+ * @param[in,out] shape Shape to be used for hasing.
+ * @param[in]     it    The @link IteratorAssociatedTypesConcept iterator @endlink to use for initializing the shape.
+ *
+ * @section Example
+ *
+ * Two hash loop examples.
+ * The first loop uses @link Shape#hash @endlink/@link Shape#hashNext @endlink while the second use @link Shape#hashInit @endlink/@link Shape#hashNext @endlink and can process all hashes within the loop.
+ *
+ * @include demos/dox/index/shape_hash_init.cpp
+ *
+ * @code{.stdout}
+ * 0    0    1    4    17    4    18    11    47    63    62    56
+ * 0    0    1    4    17    4    18    11    47    63    62    56
+ * @endcode
+ */
+
+    template <typename TValue, typename TIter>
+    inline void
+    hashInit(Shape<TValue, SimpleShape> &me, TIter it)
+    {
+        //typedef typename Value< Shape<TValue, SimpleShape> >::Type    THValue;
+        typedef typename Size< Shape<TValue, SimpleShape> >::Type    TSize;
+
+        SEQAN_ASSERT_GT((unsigned)me.span, 0u);
 
         me.leftChar = 0;
-		me.hValue = ordValue(*it);
-		for(TSize i = 2; i < me.span; ++i) {
-			++it;
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-	}
+        me.hValue = ordValue(*it);
+        for(TSize i = 2; i < me.span; ++i) {
+            ++it;
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+    }
 
 //____________________________________________________________________________
 // fixed ungapped shapes
 
-	// loop unrolling ...
-	template <typename THValue, typename TValue, typename TIter>
-	inline THValue
-	_hashFixedShape(THValue hash, TIter &, TValue const, UngappedShape<1> const) {
-		return hash;
-	}
-
-	template <typename THValue, typename TValue, typename TIter, unsigned q>
-	inline THValue
-	_hashFixedShape(THValue hash, TIter &it, TValue const, UngappedShape<q> const) {
-		++it;
-		return _hashFixedShape(
-			hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
-			it, TValue(), UngappedShape<q - 1>());
-	}
-
-	// ... for fixed ungapped shapes
-	template <typename TValue, unsigned q, typename TIter>
-	inline typename Value< Shape<TValue, UngappedShape<q> > >::Type
-	hash(Shape<TValue, UngappedShape<q> > &me, TIter it)
-	{
-		//typedef typename Value< Shape<TValue, UngappedShape<q> > >::Type	THValue;
-		//typedef typename Size< Shape<TValue, UngappedShape<q> > >::Type     TSize;
-
-		me.hValue = ordValue(me.leftChar = *it);
-		return me.hValue = _hashFixedShape(me.hValue, it, TValue(), UngappedShape<q>());
-	}
-
-	template <typename TValue, unsigned q, typename TIter>
-	inline typename Value< Shape<TValue, UngappedShape<q> > >::Type
-	hashInit(Shape<TValue, UngappedShape<q> > &me, TIter it)
-	{
-		//typedef typename Value< Shape<TValue, UngappedShape<q> > >::Type	THValue;
-		//typedef typename Size< Shape<TValue, UngappedShape<q> > >::Type	TSize;
+    // loop unrolling ...
+    template <typename THValue, typename TValue, typename TIter>
+    SEQAN_HOST_DEVICE inline THValue
+    _hashFixedShape(THValue hash, TIter &, TValue const, UngappedShape<1> const) {
+        return hash;
+    }
+
+    template <typename THValue, typename TValue, typename TIter, unsigned q>
+    SEQAN_HOST_DEVICE inline THValue
+    _hashFixedShape(THValue hash, TIter &it, TValue const, UngappedShape<q> const) {
+        ++it;
+        return _hashFixedShape(
+            hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
+            it, TValue(), UngappedShape<q - 1>());
+    }
+
+    // ... for fixed ungapped shapes
+    template <typename TValue, unsigned q, typename TIter>
+    SEQAN_HOST_DEVICE inline typename Value< Shape<TValue, UngappedShape<q> > >::Type
+    hash(Shape<TValue, UngappedShape<q> > &me, TIter it)
+    {
+        //typedef typename Value< Shape<TValue, UngappedShape<q> > >::Type    THValue;
+        //typedef typename Size< Shape<TValue, UngappedShape<q> > >::Type     TSize;
+
+        me.hValue = ordValue(me.leftChar = *it);
+        return me.hValue = _hashFixedShape(me.hValue, it, TValue(), UngappedShape<q>());
+    }
+
+    template <typename TValue, unsigned q, typename TIter>
+    inline typename Value< Shape<TValue, UngappedShape<q> > >::Type
+    hashInit(Shape<TValue, UngappedShape<q> > &me, TIter it)
+    {
+        //typedef typename Value< Shape<TValue, UngappedShape<q> > >::Type    THValue;
+        //typedef typename Size< Shape<TValue, UngappedShape<q> > >::Type    TSize;
 
         me.leftChar = 0;
-		me.hValue = ordValue(*it);
+        me.hValue = ordValue(*it);
 
         if (q > 1)
             me.hValue = _hashFixedShape(me.hValue, it, TValue(), UngappedShape<q-1>());
 
-		return me.hValue;
+        return me.hValue;
     }
 
-	template <typename TValue, typename TSpec, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, TSpec> >::Type
-	hash(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
-	{
-		//typedef typename Value< Shape<TValue, TSpec> >::Type	THValue;
-
-		SEQAN_ASSERT_GT((unsigned)me.span, 0u);
-
-		TSize iEnd = me.span;
-		if (iEnd > charsLeft) iEnd = charsLeft;
-
-		TSize i = 0;
-		if (iEnd > 0) {
-			me.hValue = ordValue(me.leftChar = *it);
-			for(i = 1; i < iEnd; ++i) {
-				++it;
-				me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-			}
-		} else
-			return me.hValue = 0;
-
-		// fill shape with zeros
-		for(; i < (TSize)me.span; ++i)
-			me.hValue *= ValueSize<TValue>::VALUE;
-		return me.hValue;
-	}
+    template <typename TValue, typename TSpec, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, TSpec> >::Type
+    hash(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
+    {
+        //typedef typename Value< Shape<TValue, TSpec> >::Type    THValue;
+
+        SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+
+        TSize iEnd = me.span;
+        if (iEnd > charsLeft) iEnd = charsLeft;
+
+        TSize i = 0;
+        if (iEnd > 0) {
+            me.hValue = ordValue(me.leftChar = *it);
+            for(i = 1; i < iEnd; ++i) {
+                ++it;
+                me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+            }
+        } else
+            return me.hValue = 0;
+
+        // fill shape with zeros
+        for(; i < (TSize)me.span; ++i)
+            me.hValue *= ValueSize<TValue>::VALUE;
+        return me.hValue;
+    }
 
 //____________________________________________________________________________
 // Tuple -> fixed ungapped shapes
 
-	template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TPack>
-	inline THValue
-	_hashTuple2FixedShape(
-		THValue const, 
-		Tuple<TTValue, SIZE, TPack> const &tuple,
-		TValue const,
-		UngappedShape<1> const) 
-	{
-		return ordValue(tuple[0]);
-	}
-
-	template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TPack, unsigned q>
-	inline THValue
-	_hashTuple2FixedShape(
-		THValue const, 
-		Tuple<TTValue, SIZE, TPack> const &tuple,
-		TValue const,
-		UngappedShape<q> const) 
-	{
-		return _hashTuple2FixedShape(THValue(), tuple, TValue(), UngappedShape<q - 1>()) 
-			* ValueSize<TValue>::VALUE + ordValue(tuple[q-1]);
-	}
-
-	// ... for fixed ungapped shapes
-	template <
-		typename TValue,
-		typename TTValue, 
-		unsigned SIZE, 
-		unsigned q>
-	typename Value< Shape<TValue, UngappedShape<q> > >::Type
-	hash(
-		Shape<TValue, UngappedShape<q> > &me, 
-		Tuple<TTValue, SIZE, BitPacked<> > /*const &*/tuple)
-	{
-	SEQAN_CHECKPOINT
-		if (ValueSize<TValue>::VALUE == (1 << BitsPerValue<TTValue>::VALUE))
-			if (q == SIZE)
-				return tuple.i;
-			else
-				return tuple >> (q - SIZE);
-		else
-			return me.hValue = _hashTuple2FixedShape(me.hValue, tuple, TValue(), UngappedShape<q>());
-	}
-
-	template <
-		typename TValue,
-		typename TTValue, 
-		unsigned SIZE, 
-		typename TPack, 
-		unsigned q>
-	typename Value< Shape<TValue, UngappedShape<q> > >::Type
-	hash(
-		Shape<TValue, UngappedShape<q> > &me, 
-		Tuple<TTValue, SIZE, TPack> /*const &*/tuple)
-	{
-	SEQAN_CHECKPOINT
-		return me.hValue = _hashTuple2FixedShape(me.hValue, tuple, TValue(), UngappedShape<q>());
-	}
+    template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TPack>
+    inline THValue
+    _hashTuple2FixedShape(
+        THValue const,
+        Tuple<TTValue, SIZE, TPack> const &tuple,
+        TValue const,
+        UngappedShape<1> const)
+    {
+        return ordValue(tuple[0]);
+    }
+
+    template <typename THValue, typename TValue, typename TTValue, unsigned SIZE, typename TPack, unsigned q>
+    inline THValue
+    _hashTuple2FixedShape(
+        THValue const,
+        Tuple<TTValue, SIZE, TPack> const &tuple,
+        TValue const,
+        UngappedShape<q> const)
+    {
+        return _hashTuple2FixedShape(THValue(), tuple, TValue(), UngappedShape<q - 1>())
+            * ValueSize<TValue>::VALUE + ordValue(tuple[q-1]);
+    }
+
+    // ... for fixed ungapped shapes
+    template <
+        typename TValue,
+        typename TTValue,
+        unsigned SIZE,
+        unsigned q>
+    typename Value< Shape<TValue, UngappedShape<q> > >::Type
+    hash(
+        Shape<TValue, UngappedShape<q> > &me,
+        Tuple<TTValue, SIZE, BitPacked<> > /*const &*/tuple)
+    {
+    SEQAN_CHECKPOINT
+        if (ValueSize<TValue>::VALUE == (1 << BitsPerValue<TTValue>::VALUE))
+            if (q == SIZE)
+                return tuple.i;
+            else
+                return tuple >> (q - SIZE);
+        else
+            return me.hValue = _hashTuple2FixedShape(me.hValue, tuple, TValue(), UngappedShape<q>());
+    }
+
+    template <
+        typename TValue,
+        typename TTValue,
+        unsigned SIZE,
+        typename TPack,
+        unsigned q>
+    typename Value< Shape<TValue, UngappedShape<q> > >::Type
+    hash(
+        Shape<TValue, UngappedShape<q> > &me,
+        Tuple<TTValue, SIZE, TPack> /*const &*/tuple)
+    {
+    SEQAN_CHECKPOINT
+        return me.hValue = _hashTuple2FixedShape(me.hValue, tuple, TValue(), UngappedShape<q>());
+    }
 
 //____________________________________________________________________________
 
-/**.Function.hashUpper:
-..cat:Index
-..summary:Computes an upper hash value for a shape applied to a sequence.
-..signature:hashUpper(shape, it, charsLeft)
-..class:Class.Shape
-..param.shape:Shape to be used for hashing.
-...type:Class.Shape
-..param.it:Sequence iterator pointing to the first character of the shape.
-..param.charsLeft:The distance of $it$ to the string end. 
-..returns:Upper hash value of the shape.
-The hash value corresponds to the maximal @Function.hash@ value of a shape beginning with $min(charsLeft,length(shape))$ characters + 1.
-..remarks:This function in conjunction with @Function.hash@ is useful to search a q-gram index for p-grams with p<q.
-*/
 /*!
  * @fn Shape#hashUpper
- * 
  * @brief Computes an upper hash value for a shape applied to a sequence.
- * 
- * @signature hashUpper(shape, it, charsLeft)
- * 
- * @param charsLeft The distance of <tt>it</tt> to the string end.
- * @param shape Shape to be used for hashing. Types: @link Shape @endlink
- * @param it Sequence iterator pointing to the first character of the shape.
- * 
- * @return TReturn Upper hash value of the shape. The hash value corresponds to
- *                 the maximal @link Shape#hash @endlink value of a shape beginning
- *                 with <tt>min(charsLeft,length(shape))</tt> characters + 1.
- * 
- * @section Remarks
- * 
- * This function in conjunction with @link Shape#hash @endlink is useful to search a
- * q-gram index for p-grams with p<q.
- * 
+ *
+ * @signature TValue hashUpper(shape, it, charsLeft);
+ *
+ * @param[in,out] shape     Shape to be used for hashing. Types: @link Shape @endlink
+ * @param[in]     it        Sequence iterator pointing to the first character of the shape.
+ * @param[in]     charsLeft The distance of <tt>it</tt> to the string end.
+ *
+ * @return TValue Upper hash value of the shape. The hash value corresponds to
+ *                the maximal @link Shape#hash @endlink value of a shape beginning
+ *                with <tt>min(charsLeft,length(shape))</tt> characters + 1  (Metafunction:
+ *                @link Shape#Value @endlink).
+ *
+ * This function in conjunction with @link Shape#hash @endlink is useful to search a q-gram index for p-grams with
+ * p &lt; q.
+ *
  * @see Shape#hash
  */
 
-	template <typename TValue, typename TSpec, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, TSpec> >::Type
-	hashUpper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
-	{
-		//typedef typename Value< Shape<TValue, TSpec> >::Type	THValue;
-
-		SEQAN_ASSERT_GT((unsigned)me.span, 0u);
-
-		TSize iEnd = me.span;
-		if (iEnd > charsLeft) iEnd = charsLeft;
-
-		TSize i = 0;
-		if (iEnd > 0) {
-			me.hValue = ordValue(me.leftChar = *it);
-			for(i = 1; i < iEnd; ++i) {
-				++it;
-				me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-			}
-			++me.hValue;
-		} else
-			me.hValue = 1;
-
-		// fill shape with zeros
-		for(; i < (TSize)me.span; ++i)
-			me.hValue *= ValueSize<TValue>::VALUE;
-		return me.hValue;
-	}
+    template <typename TValue, typename TSpec, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, TSpec> >::Type
+    hashUpper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
+    {
+        //typedef typename Value< Shape<TValue, TSpec> >::Type    THValue;
+
+        SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+
+        TSize iEnd = me.span;
+        if (iEnd > charsLeft) iEnd = charsLeft;
+
+        TSize i = 0;
+        if (iEnd > 0) {
+            me.hValue = ordValue(me.leftChar = *it);
+            for(i = 1; i < iEnd; ++i) {
+                ++it;
+                me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+            }
+            ++me.hValue;
+        } else
+            me.hValue = 1;
+
+        // fill shape with zeros
+        for(; i < (TSize)me.span; ++i)
+            me.hValue *= ValueSize<TValue>::VALUE;
+        return me.hValue;
+    }
 
 //____________________________________________________________________________
 
-/**
-.Function.hashNext:
-..cat:Index
-..summary:Computes the hash value for the adjacent shape.
-..description:Overlapping q-grams can efficiently be hashed by calling @Function.hash@ on the first text position and @Function.hashNext@ on succeeding, adjacent positions. Alternatively, @Function.hashInit@ can be used to replace the first @Function.hash@ call by another @Function.hashNext@ call and hence ease loops iterating all overlapping q-grams.
-..signature:hashNext(shape, it)
-..class:Class.Shape
-..param.shape:Shape to be used for hashing.
-...type:Class.Shape
-..param.it:Sequence iterator pointing to the first character of the adjacent shape.
-..returns:Hash value of the q-gram.
-..remarks:@Function.hash@ has to be called before.
-..example:Hash loop example that outputs the hash values of all overlapping 3-grams using @Function.hash@ and @Function.hashNext@.
-...file:demos/index/shape_hash_next.cpp
-...text:The overlapping hash values are:
-...output:
-0	0	1	4	17	4	18	11	47	63	62	56	
-..include:seqan/index.h
-*/
 /*!
  * @fn Shape#hashNext
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Computes the hash value for the adjacent shape.
- * 
- * @signature hashNext(shape, it)
- * 
- * @param shape Shape to be used for hashing. Types: @link Shape @endlink
- * @param it Sequence iterator pointing to the first character of the adjacent
- *           shape.
- * 
- * @return TReturn Hash value of the q-gram.
- * 
- * @section Remarks
- * 
+ *
+ * @signature TValue hashNext(shape, it);
+ *
+ * @param[in,out] shape Shape to be used for hashing. Types: @link Shape @endlink
+ * @param[in]     it    Sequence iterator pointing to the first character of the adjacent shape.
+ *
+ * @return TValue Hash value of the q-gram (Metafunction: @link Shape#Value @endlink).
+ *
  * @link Shape#hash @endlink has to be called before.
- * 
+ *
  * @see Shape#hash
  */
-	template <typename TValue, typename TSpec, typename TIter>
-	inline typename Value< Shape<TValue, TSpec> >::Type
-	hashNext(Shape<TValue, TSpec> &me, TIter const &it)
-	{
-	SEQAN_CHECKPOINT
-		// remove first, shift left, and add next character
-		typedef typename Value< Shape<TValue, TSpec> >::Type	THValue;
-		typedef typename Size< Shape<TValue, TSpec> >::Type		TSize;
-
-		SEQAN_ASSERT_GT((unsigned)me.span, 0u);
-
-		me.hValue = 
-			(me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor) * ValueSize<TValue>::VALUE
-			+ ordValue((TValue)*(it + ((TSize)me.span - 1)));
-		me.leftChar = *it;
-		return me.hValue;
-	}
+    template <typename TValue, typename TSpec, typename TIter>
+    inline typename Value< Shape<TValue, TSpec> >::Type
+    hashNext(Shape<TValue, TSpec> &me, TIter const &it)
+    {
+    SEQAN_CHECKPOINT
+        // remove first, shift left, and add next character
+        typedef typename Value< Shape<TValue, TSpec> >::Type    THValue;
+        typedef typename Size< Shape<TValue, TSpec> >::Type        TSize;
+
+        SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+
+        me.hValue =
+            (me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor) * ValueSize<TValue>::VALUE
+            + ordValue((TValue)*(it + ((TSize)me.span - 1)));
+        me.leftChar = *it;
+        return me.hValue;
+    }
 
 //____________________________________________________________________________
 
-/**.Function.hash2:
-..cat:Index
-..summary:Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span
-..signature:hash2(shape, it, charsLeft)
-..class:Class.Shape
-..param.shape:Shape to be used for hashing.
-...type:Class.Shape
-..param.it:Sequence iterator pointing to the first character of the shape.
-..param.charsLeft:The distance of $it$ to the string end. 
-..returns:Hash value of the shape.
-..see:Function.hash2Next
-..see:Function.hash2Upper
-*/
 /*!
  * @fn Shape#hash2
- * 
- * @brief Computes an unique hash value of a shape applied to a sequence, even
- *        if the sequence is shorter than the shape span
- * 
- * @signature hash2(shape, it, charsLeft)
- * 
- * @param charsLeft The distance of <tt>it</tt> to the string end.
- * @param shape Shape to be used for hashing. Types: @link Shape @endlink
- * @param it Sequence iterator pointing to the first character of the shape.
- * 
- * @return TReturn Hash value of the shape.
- * 
+ * @brief Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than
+ *        the shape span.
+ *
+ * @signature TValue hash2(shape, it, charsLeft);
+ *
+ * @param[in,out] shape     Shape to be used for hashing. Types: @link Shape @endlink
+ * @param[in]     it        Sequence iterator pointing to the first character of the shape.
+ * @param[in]     charsLeft The distance of <tt>it</tt> to the string end.
+ *
+ * @return TValue Hash value of the shape (Metafunction: @link Shape#Value @endlink).
+ *
  * @see Shape#hash2Next
  * @see Shape#hash2Upper
  * @see Shape#unhash
  * @see Shape#hash
  */
 
-	template <typename TValue, typename TSpec, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, TSpec> >::Type
-	hash2(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
-	{
-		//typedef typename Value< Shape<TValue, TSpec> >::Type	THValue;
-
-		SEQAN_ASSERT_GT((unsigned)me.span, 0u);
-
-		TSize iEnd = me.span;
-		if (iEnd > charsLeft) iEnd = charsLeft;
-
-		TSize i = 0;
-		if (iEnd > 0) {
-			me.hValue = me.XValue = ordValue(me.leftChar = *it);
-			for(i = 1; i < iEnd; ++i) {
-				++it;
-				// update sum of x_i
-				me.XValue += ordValue((TValue)*it);
-				// shift hash
-				me.hValue = me.hValue * ValueSize<TValue>::VALUE + me.XValue;
-			}
-		} else
-			return me.hValue = me.XValue = 0;
-
-		// fill shape with zeros
-		for(; i < (TSize)me.span; ++i)
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + me.XValue;
-		return me.hValue += iEnd;
-	}
-
-/**.Function.hash2Upper:
-..cat:Index
-..summary:Computes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span.
-..signature:hash2Upper(shape, it, charsLeft)
-..class:Class.Shape
-..param.shape:Shape to be used for hashing.
-...type:Class.Shape
-..param.it:Sequence iterator pointing to the first character of the shape.
-..param.charsLeft:The distance of $it$ to the string end. 
-..returns:Upper hash value of the shape.
-The hash value corresponds to the maximal @Function.hash2@ value of a shape beginning with the $min(charsLeft,length(shape))$ characters + 1
-..remarks:This function in conjunction with @Function.hash2@ is useful to search a q-gram index for p-grams with p<q.
-*/
+    template <typename TValue, typename TSpec, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, TSpec> >::Type
+    hash2(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
+    {
+        //typedef typename Value< Shape<TValue, TSpec> >::Type    THValue;
+
+        SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+
+        TSize iEnd = me.span;
+        if (iEnd > charsLeft) iEnd = charsLeft;
+
+        TSize i = 0;
+        if (iEnd > 0) {
+            me.hValue = me.XValue = ordValue(me.leftChar = *it);
+            for(i = 1; i < iEnd; ++i) {
+                ++it;
+                // update sum of x_i
+                me.XValue += ordValue((TValue)*it);
+                // shift hash
+                me.hValue = me.hValue * ValueSize<TValue>::VALUE + me.XValue;
+            }
+        } else
+            return me.hValue = me.XValue = 0;
+
+        // fill shape with zeros
+        for(; i < (TSize)me.span; ++i)
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + me.XValue;
+        return me.hValue += iEnd;
+    }
+
 /*!
  * @fn Shape#hash2Upper
- * 
  * @brief Computes an upper unique hash value of a shape applied to a sequence,
  *        even if the sequence is shorter than the shape span.
- * 
- * @signature hash2Upper(shape, it, charsLeft)
- * 
- * @param charsLeft The distance of <tt>it</tt> to the string end.
- * @param shape Shape to be used for hashing. Types: @link Shape @endlink
- * @param it Sequence iterator pointing to the first character of the shape.
- * 
- * @return TReturn Upper hash value of the shape. The hash value corresponds to
- *                 the maximal @link Shape#hash2 @endlink value of a shape beginning
- *                 with the <tt>min(charsLeft,length(shape))</tt> characters + 1
- * 
- * @section Remarks
- * 
+ *
+ * @signature TValue hash2Upper(shape, it, charsLeft);
+ *
+ * @param[in] shape     Shape to be used for hashing. Types: @link Shape @endlink
+ * @param[in] it        Sequence iterator pointing to the first character of the shape.
+ * @param[in] charsLeft The distance of <tt>it</tt> to the string end.
+ *
+ * @return TValue Upper hash value of the shape. The hash value corresponds to
+ *                the maximal @link Shape#hash2 @endlink value of a shape beginning
+ *                with the <tt>min(charsLeft,length(shape))</tt> characters + 1
+ *                (Metafunction: @link Shape#Value @endlink).
+ *
  * This function in conjunction with @link Shape#hash2 @endlink is useful to search a
- * q-gram index for p-grams with p<q.
- * 
+ * q-gram index for p-grams with <i>p &lt; q</i>.
+ *
  * @see Shape#hash2
  */
-	template <typename TValue, typename TSpec, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, TSpec> >::Type
-	hash2Upper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Value< Shape<TValue, TSpec> >::Type	THValue;
-
-		SEQAN_ASSERT_GT((unsigned)me.span, 0u);
-
-		TSize iEnd = me.span;
-		if (iEnd > charsLeft) iEnd = charsLeft;
-
-		THValue hValue, XValue;
-		TSize i = 0;
-		if (iEnd > 0) {
-			hValue = XValue = ordValue((TValue)*it);
-			for(i = 1; i < iEnd; ++i) {
-				++it;
-				// update sum of x_i
-				XValue += ordValue((TValue)*it);
-				// shift hash
-				hValue = hValue * ValueSize<TValue>::VALUE + XValue;
-			}
-		} else
-			hValue = XValue = 0;
-
-		if (charsLeft <= me.span) {
-			++XValue;
-			++hValue;
-		}
-
-		// fill shape with zeros
-		for(; i < (TSize)me.span; ++i)
-			hValue = hValue * ValueSize<TValue>::VALUE + XValue;
-		return hValue += iEnd;
-	}
+    template <typename TValue, typename TSpec, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, TSpec> >::Type
+    hash2Upper(Shape<TValue, TSpec> &me, TIter it, TSize charsLeft)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Value< Shape<TValue, TSpec> >::Type    THValue;
+
+        SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+
+        TSize iEnd = me.span;
+        if (iEnd > charsLeft) iEnd = charsLeft;
+
+        THValue hValue, XValue;
+        TSize i = 0;
+        if (iEnd > 0) {
+            hValue = XValue = ordValue((TValue)*it);
+            for(i = 1; i < iEnd; ++i) {
+                ++it;
+                // update sum of x_i
+                XValue += ordValue((TValue)*it);
+                // shift hash
+                hValue = hValue * ValueSize<TValue>::VALUE + XValue;
+            }
+        } else
+            hValue = XValue = 0;
+
+        if (charsLeft <= me.span) {
+            ++XValue;
+            ++hValue;
+        }
+
+        // fill shape with zeros
+        for(; i < (TSize)me.span; ++i)
+            hValue = hValue * ValueSize<TValue>::VALUE + XValue;
+        return hValue += iEnd;
+    }
 
 //____________________________________________________________________________
 
-/**
-.Function.hash2Next:
-..cat:Index
-..summary:Computes a unique hash value for the adjacent shape, even if it is shorter than q.
-..signature:hash2Next(shape, it)
-..class:Class.Shape
-..param.shape:Shape to be used for hashing the q-gram.
-...type:Class.Shape
-..param.it:Sequence iterator pointing to the first character of the adjacent shape.
-..returns:Hash value of the shape.
-..remarks:@Function.hash@ has to be called before with $shape$ on the left adjacent q-gram.
-..include:seqan/index.h
-*/
 /*!
  * @fn Shape#hash2Next
- * 
- * @headerfile seqan/index.h
- * 
- * @brief Computes a unique hash value for the adjacent shape, even if it is
- *        shorter than q.
- * 
- * @signature hash2Next(shape, it)
- * 
- * @param shape Shape to be used for hashing the q-gram. Types: @link Shape @endlink
- * @param it Sequence iterator pointing to the first character of the adjacent
- *           shape.
- * 
- * @return TReturn Hash value of the shape.
- * 
- * @section Remarks
- * 
- * @link Shape#hash @endlink has to be called before with <tt>shape</tt> on the left
- * adjacent q-gram.
- * 
+ * @headerfile <seqan/index.h>
+ * @brief Computes a unique hash value for the adjacent shape, even if it is shorter than q.
+ *
+ * @signature TValue hash2Next(shape, it);
+ *
+ * @param[in,out] shape Shape to be used for hashing the q-gram. Types: @link Shape @endlink
+ * @param[in,out] it    Sequence iterator pointing to the first character of the adjacent shape.
+ *
+ * @return TValue Hash value of the shape (Metafunction: @link Shape#Value @endlink).
+ *
+ * @link Shape#hash @endlink has to be called before with <tt>shape</tt> on the left adjacent q-gram.
+ *
  * @see Shape#hash2
  */
 
-	template <typename TValue, typename TSpec, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, TSpec> >::Type
-	hash2Next(Shape<TValue, TSpec> &me, TIter &it, TSize charsLeft)
-	{
-	SEQAN_CHECKPOINT
-		// remove first, shift left, and add next character
-		typedef typename Value< Shape<TValue, TSpec> >::Type	THValue;
-
-		SEQAN_ASSERT_GT((unsigned)me.span, 0u);
-
-		if (charsLeft >= me.span) {
-			// update sum of x_i
-			me.XValue = me.XValue + ordValue((TValue)*(it + me.span - 1)) - ordValue(me.leftChar);
-			// shift hash
-			me.hValue = (me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor2) * ValueSize<TValue>::VALUE + me.XValue
-						- me.span * (ValueSize<TValue>::VALUE - 1);
-		} else {
-			// update sum of x_i
-			me.XValue -= ordValue(me.leftChar);
-			// shift hash
-			me.hValue = (me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor2) * ValueSize<TValue>::VALUE + me.XValue
-				        - charsLeft * (ValueSize<TValue>::VALUE - 1) - ValueSize<TValue>::VALUE;
-		}
-
-		me.leftChar = *it;
-		return me.hValue;
-	}
-
-/**
-.Function.unhash:
-..cat:Index
-..summary:Inverse of the @Function.hash@ function; for ungapped shapes.
-..signature:unhash(result, hash, q)
-..class:Class.Shape
-..param.result:String to write the result to.
-...type:Class.String
-..param.hash:The hash value previously computed with @Function.hash@.
-...type:nolink:A number.
-..param.q:The $q$-gram length.
-...type:nolink:$unsigned$
-..remarks:
-..see:Function.hash
-..see:Function.hash2
-..include:seqan/index.h
-*/
+    template <typename TValue, typename TSpec, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, TSpec> >::Type
+    hash2Next(Shape<TValue, TSpec> &me, TIter &it, TSize charsLeft)
+    {
+    SEQAN_CHECKPOINT
+        // remove first, shift left, and add next character
+        typedef typename Value< Shape<TValue, TSpec> >::Type    THValue;
+
+        SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+
+        if (charsLeft >= me.span) {
+            // update sum of x_i
+            me.XValue = me.XValue + ordValue((TValue)*(it + me.span - 1)) - ordValue(me.leftChar);
+            // shift hash
+            me.hValue = (me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor2) * ValueSize<TValue>::VALUE + me.XValue
+                        - me.span * (ValueSize<TValue>::VALUE - 1);
+        } else {
+            // update sum of x_i
+            me.XValue -= ordValue(me.leftChar);
+            // shift hash
+            me.hValue = (me.hValue - ordValue(me.leftChar) * (THValue)me.leftFactor2) * ValueSize<TValue>::VALUE + me.XValue
+                        - charsLeft * (ValueSize<TValue>::VALUE - 1) - ValueSize<TValue>::VALUE;
+        }
+
+        me.leftChar = *it;
+        return me.hValue;
+    }
+
 /*!
  * @fn Shape#unhash
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief Inverse of the @link Shape#hash @endlink function; for ungapped shapes.
- * 
- * @signature unhash(result, hash, q)
- * 
- * @param q The <tt>q</tt>-gram length. Types: nolink:<tt>unsigned</tt>
- * @param hash The hash value previously computed with @link Shape#hash @endlink.
- *             Types:
- * @param result String to write the result to. Types: @link String @endlink
- * 
- * @section Remarks
- * 
+ *
+ * @signature void unhash(result, hash, q);
+ *
+ * @param[out] result @link String @endlink to write the result to. Types: @link String @endlink.
+ * @param[in]  hash   The hash value previously computed with @link Shape#hash @endlink.
+ * @param[in]  q      The <tt>q</tt>-gram length. Types: <tt>unsigned</tt>
+ *
  * @see Shape#hash
  * @see Shape#hash2
  */
-	template <typename TString, typename THash>
-	inline void unhash(TString &result, THash hash, unsigned q)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Value<TString>::Type	TValue;
-
-		resize(result, q);
-		for (unsigned i = q; i > 0; ) 
-		{
-			result[--i] = (TValue)(hash % ValueSize<TValue>::VALUE);
-			hash /= ValueSize<TValue>::VALUE;
-		}
-	}
+    template <typename TString, typename THash>
+    inline void unhash(TString &result, THash hash, unsigned q)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Value<TString>::Type    TValue;
+
+        resize(result, q);
+        for (unsigned i = q; i > 0; )
+        {
+            result[--i] = (TValue)(hash % ValueSize<TValue>::VALUE);
+            hash /= ValueSize<TValue>::VALUE;
+        }
+    }
 
 //____________________________________________________________________________
 
-/**.Function.stringToShape:
-..cat:Index
-..summary:Takes a shape given as a string of '1' (relevant position) and '0' 
-(irrelevant position) and converts it into a Shape object.
-..signature:stringToShape(shape, bitmap)
-..class:Class.Shape
-..param.shape:Shape object that is manipulated.
-...type:Spec.SimpleShape
-..param.bitmap:A character string of '1' and '0' representing relevant and irrelevant positions (blanks) respectively.
-...remarks:This string must begin with a '1'. Trailing '0's are ignored.
-...remarks:If $shape$ is a @Spec.SimpleShape@ at most one contiguous sequences of $1$s is allowed.
-...type:Class.String
-..see:Function.shapeToString
-..see:Function.reverse
-*/
 /*!
  * @fn Shape#stringToShape
- * 
  * @brief Takes a shape given as a string of '1' (relevant position) and '0'
  *        (irrelevant position) and converts it into a Shape object.
- * 
- * @signature stringToShape(shape, bitmap)
- * 
- * @param shape Shape object that is manipulated. Types: SimpleShape,
- *              GenericShape, OneGappedShape
- * @param bitmap A character string of '1' and '0' representing relevant and
- *               irrelevant positions (blanks) respectively.This string must
- *               begin with a '1'. Trailing '0's are ignored.If <tt>shape</tt>
- *               is a @link SimpleShape @endlink at most one contiguous
- *               sequences of <tt>1</tt>s is allowed.If <tt>shape</tt> is a
- *               @link OneGappedShape @endlink at most two contiguous sequences
- *               of '1's are allowed. Types: @link String @endlink
- * 
+ *
+ * @signature bool stringToShape(shape, bitmap);
+ *
+ * @param[in,out] shape Shape object that is manipulated.
+ * @param[in]     bitmap A character string of '1' and '0' representing relevant and irrelevant positions (blanks)
+ *                respectively.  This string must begin with a '1'.  Trailing '0's are ignored.  If <tt>shape</tt>
+ *                is a @link SimpleShape @endlink at most one contiguous sequences of <tt>1</tt>s is allowed.  If
+ *                <tt>shape</tt> is a @link OneGappedShape @endlink at most two contiguous sequences of '1's are
+ *                allowed (@link String @endlink of <tt>char</tt>).
+ *
+ * @return bool <tt>true</tt> if the conversion was successful.
+ *
  * @see Shape#shapeToString
  * @see reverse
  */
-	template <typename TValue, typename TShapeString>
-	inline bool
-	stringToShape(
-		Shape<TValue, SimpleShape> &me, 
-		TShapeString const &bitmap)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TShapeString const>::Type		TIter;
-		typedef typename Size<TShapeString const>::Type			TSize;
-
-		TIter it = begin(bitmap, Standard());
-		TIter itEnd = end(bitmap, Standard());
-
-		TSize ones = 0;
-		for(; it != itEnd && *it == '0' ; ++it) ;
-		for(; it != itEnd && *it == '1' ; ++it)	++ones;
-		for(; it != itEnd && *it == '0' ; ++it) ;
-
-		resize(me, ones);
-
-		return it == itEnd;
-	}
+    template <typename TValue, typename TShapeString>
+    inline bool
+    stringToShape(
+        Shape<TValue, SimpleShape> &me,
+        TShapeString const &bitmap)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Iterator<TShapeString const>::Type        TIter;
+        typedef typename Size<TShapeString const>::Type            TSize;
+
+        TIter it = begin(bitmap, Standard());
+        TIter itEnd = end(bitmap, Standard());
+
+        TSize ones = 0;
+        for(; it != itEnd && *it == '0' ; ++it) ;
+        for(; it != itEnd && *it == '1' ; ++it)    ++ones;
+        for(; it != itEnd && *it == '0' ; ++it) ;
+
+        resize(me, ones);
+
+        return it == itEnd;
+    }
 
 //____________________________________________________________________________
 
-/**.Function.shapeToString:
-..cat:Index
-..class:Class.Shape
-..summary:Converts a given shape into a sequence of '1' (relevant position) and '0' 
-(irrelevant position).
-..signature:shapeToString(bitmap, shape)
-..class:Class.Shape
-..param.bitmap:The resulting sequence object.
-...type:Class.String
-..param.shape:Shape object.
-...type:Class.Shape
-..see:Function.stringToShape
-*/
 /*!
  * @fn Shape#shapeToString
- * 
- * @brief Converts a given shape into a sequence of '1' (relevant position) and
- *        '0' (irrelevant position).
- * 
- * @signature shapeToString(bitmap, shape)
- * 
- * @param shape Shape object. Types: @link Shape @endlink
- * @param bitmap The resulting sequence object. Types: @link String @endlink
- * 
+ * @brief Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position).
+ *
+ * @signature void shapeToString(bitmap, shape);
+ *
+ * @param[in,out] bitmap The resulting sequence object. Types: @link String @endlink
+ * @param[in]     shape Shape object. Types: @link Shape @endlink
+ *
  * @see Shape#stringToShape
  */
 
-	template <typename TShapeString, typename TValue, unsigned q>
-	inline void
-	shapeToString(
-		TShapeString &bitmap,
-		Shape<TValue, UngappedShape<q> > const &me)
-	{
-	SEQAN_CHECKPOINT
+    template <typename TShapeString, typename TValue, unsigned q>
+    inline void
+    shapeToString(
+        TShapeString &bitmap,
+        Shape<TValue, UngappedShape<q> > const &me)
+    {
+    SEQAN_CHECKPOINT
 
-		clear(bitmap);
-		resize(bitmap, length(me), '1');
-	}
+        clear(bitmap);
+        resize(bitmap, length(me), '1');
+    }
 
 //____________________________________________________________________________
-	
-///.Function.reverse.param.object.type:Spec.SimpleShape
-///.Function.reverse.class:Spec.SimpleShape
-
-	template <typename TValue, typename TSpec>
-	inline void
-	reverse(Shape<TValue, TSpec> &)
-	{
-	}
-	
-}	// namespace seqan
+
+    template <typename TValue, typename TSpec>
+    inline void
+    reverse(Shape<TValue, TSpec> &)
+    {
+    }
+
+}    // namespace seqan
 
 #endif
diff --git a/seqan/index/shape_gapped.h b/seqan/index/shape_gapped.h
index f268b78..cb49c74 100644
--- a/seqan/index/shape_gapped.h
+++ b/seqan/index/shape_gapped.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,736 +41,665 @@ namespace SEQAN_NAMESPACE_MAIN
 //////////////////////////////////////////////////////////////////////////////
 // HardwiredShape allows compiler-time defined gapped shape
 
-/**
-.Class.HardwiredShape:
-..cat:Index
-..summary:A structure to define a fixed gapped shape.
-..signature:HardwiredShape<P1, P2, ..., Pn>
-..param.Pi:Pi is the distance of the i'th '1' to the next '1' in the shape.
-...nowarn:unknown param
-...remarks:At most 20 parameters are allowed, so the maximal shape weight is 21.
-..remarks:You can use this structure to define your one gapped shapes in conjunction with @Spec.GappedShape@.
-...note:The shape $1100101$ corresponds to $HardwiredShape<1,3,2>$.
-...note:The following predefined shapes are already available in $seqan/index/shape_predefined.h$:
-..file:include/seqan/index/shape_predefined.h
-..include:seqan/index.h
-*/
 /*!
  * @class HardwiredShape
- * 
- * @headerfile seqan/index.h
- * 
+ * @extends GappedShape
+ * @headerfile <seqan/index.h>
  * @brief A structure to define a fixed gapped shape.
- * 
- * @signature HardwiredShape<P1, P2, ..., Pn>
- * 
- * @tparam Pi Pi is the distance of the i'th '1' to the next '1' in the shape.At
- *            most 20 parameters are allowed, so the maximal shape weight is 21.
- * 
- * @section Remarks
- * 
+ *
+ * @signature template <typename TValue, typename P1[, typename P2[, ..., typename Pn]]>
+ *            class Shape<TValue, HardwiredShape<P1[, P2[, ..., Pn]]> >;
+ *
+ * @tparam TValue The type to use for the values.
+ * @tparam Pi     Pi is the distance of the i'th '1' to the next '1' in the shape.At
+ *                most 20 parameters are allowed, so the maximal shape weight is 21.
+ *
  * You can use this structure to define your one gapped shapes in conjunction
  * with @link GappedShape @endlink.
- * 
- * @section Note The shape <tt>1100101</tt> corresponds to
- * <tt>HardwiredShape<1,3,2></tt>.
- * 
- * @section Note The following predefined shapes are already available in
- * <tt>seqan/index/shape_predefined.h</tt>:
- * 
+ *
+ * The shape <tt>1100101</tt> corresponds to <tt>HardwiredShape<1,3,2></tt>.
+ *
+ * Note The following predefined shapes are already available in <tt>seqan/index/shape_predefined.h</tt>:
+ *
  * @include include/seqan/index/shape_predefined.h
- * 
+ *
  * @see GappedShape
  * @see GenericShape
  */
 
-	// Pxx = spaces between '1's
-	template <
-		int P00 = 0, int P01 = 0, int P02 = 0, int P03 = 0, int P04 = 0, 
-		int P05 = 0, int P06 = 0, int P07 = 0, int P08 = 0, int P09 = 0,
-		int P10 = 0, int P11 = 0, int P12 = 0, int P13 = 0, int P14 = 0,
-		int P15 = 0, int P16 = 0, int P17 = 0, int P18 = 0, int P19 = 0	
-	>
-	struct HardwiredShape {
-		static const int DIFFS[];
-	};
-
-	template <
-		int P00, int P01, int P02, int P03, int P04, 
-		int P05, int P06, int P07, int P08, int P09,
-		int P10, int P11, int P12, int P13, int P14,
-		int P15, int P16, int P17, int P18, int P19	
-	>
-	const int HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 
-	>::DIFFS[] = {
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19, 0 
-	};
+    // Pxx = spaces between '1's
+    template <
+        int P00 = 0, int P01 = 0, int P02 = 0, int P03 = 0, int P04 = 0,
+        int P05 = 0, int P06 = 0, int P07 = 0, int P08 = 0, int P09 = 0,
+        int P10 = 0, int P11 = 0, int P12 = 0, int P13 = 0, int P14 = 0,
+        int P15 = 0, int P16 = 0, int P17 = 0, int P18 = 0, int P19 = 0
+    >
+    struct HardwiredShape {
+        static const int DIFFS[];
+    };
+
+    template <
+        int P00, int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19
+    >
+    const int HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19
+    >::DIFFS[] = {
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19, 0
+    };
 
 
 //////////////////////////////////////////////////////////////////////////////
 // LENGTH meta-function for fixed gapped shapes
 
-	template <>
-	struct LENGTH< HardwiredShape<
-		0,0,0,0,0,
-		0,0,0,0,0,
-		0,0,0,0,0,
-		0,0,0,0,0> >
-	{
-		enum { VALUE = 1 };
-	};
-
-	template <
-		int P00, int P01, int P02, int P03, int P04, 
-		int P05, int P06, int P07, int P08, int P09,
-		int P10, int P11, int P12, int P13, int P14,
-		int P15, int P16, int P17, int P18, int P19	
-	>
-	struct LENGTH< HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19> >
-	{
-		enum { VALUE = LENGTH< HardwiredShape<
-			P01,P02,P03,P04,P05,
-			P06,P07,P08,P09,P10,
-			P11,P12,P13,P14,P15,
-			P16,P17,P18,P19, 0 > >::VALUE + P00 };
-	};
-
-	template <
-	    typename TValue,
-		int P00, int P01, int P02, int P03, int P04, 
-		int P05, int P06, int P07, int P08, int P09,
-		int P10, int P11, int P12, int P13, int P14,
-		int P15, int P16, int P17, int P18, int P19	
-	>
-	struct LENGTH< Shape<TValue, GappedShape< HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 
-	> > > >:
-	LENGTH< HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 
-	> > {};
+    template <>
+    struct LENGTH< HardwiredShape<
+        0,0,0,0,0,
+        0,0,0,0,0,
+        0,0,0,0,0,
+        0,0,0,0,0> >
+    {
+        enum { VALUE = 1 };
+    };
+
+    template <
+        int P00, int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19
+    >
+    struct LENGTH< HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19> >
+    {
+        enum { VALUE = LENGTH< HardwiredShape<
+            P01,P02,P03,P04,P05,
+            P06,P07,P08,P09,P10,
+            P11,P12,P13,P14,P15,
+            P16,P17,P18,P19, 0 > >::VALUE + P00 };
+    };
+
+    template <
+        typename TValue,
+        int P00, int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19
+    >
+    struct LENGTH< Shape<TValue, GappedShape< HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19
+    > > > >:
+    LENGTH< HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19
+    > > {};
 
 
 //////////////////////////////////////////////////////////////////////////////
 // WEIGHT meta-function for fixed gapped shapes
 
-	template <>
-	struct WEIGHT< HardwiredShape<
-		0,0,0,0,0,
-		0,0,0,0,0,
-		0,0,0,0,0,
-		0,0,0,0,0> >
-	{
-		enum { VALUE = 1 };
-	};
-
-	template <
-		int P00, int P01, int P02, int P03, int P04, 
-		int P05, int P06, int P07, int P08, int P09,
-		int P10, int P11, int P12, int P13, int P14,
-		int P15, int P16, int P17, int P18, int P19	
-	>
-	struct WEIGHT< HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19> >
-	{
-		enum { VALUE = WEIGHT< HardwiredShape<
-			P01,P02,P03,P04,P05,
-			P06,P07,P08,P09,P10,
-			P11,P12,P13,P14,P15,
-			P16,P17,P18,P19, 0 > >::VALUE + 1 };
-	};
-
-	template <
-	    typename TValue,
-		int P00, int P01, int P02, int P03, int P04, 
-		int P05, int P06, int P07, int P08, int P09,
-		int P10, int P11, int P12, int P13, int P14,
-		int P15, int P16, int P17, int P18, int P19	
-	>
-	struct WEIGHT< Shape<TValue, GappedShape< HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 
-	> > > >:
-	WEIGHT< HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 
-	> > {};
+    template <>
+    struct WEIGHT< HardwiredShape<
+        0,0,0,0,0,
+        0,0,0,0,0,
+        0,0,0,0,0,
+        0,0,0,0,0> >
+    {
+        enum { VALUE = 1 };
+    };
+
+    template <
+        int P00, int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19
+    >
+    struct WEIGHT< HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19> >
+    {
+        enum { VALUE = WEIGHT< HardwiredShape<
+            P01,P02,P03,P04,P05,
+            P06,P07,P08,P09,P10,
+            P11,P12,P13,P14,P15,
+            P16,P17,P18,P19, 0 > >::VALUE + 1 };
+    };
+
+    template <
+        typename TValue,
+        int P00, int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19
+    >
+    struct WEIGHT< Shape<TValue, GappedShape< HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19
+    > > > >:
+    WEIGHT< HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19
+    > > {};
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Spec.GenericShape:
-..cat:Index
-..summary:A variable gapped shape.
-..general:Class.Shape
-..signature:Shape<TValue, GenericShape>
-..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
-..remarks:A GenericShape must be initialized first with a valid shape. To do so, call @Function.stringToShape@.
-..see:Spec.GappedShape
-..include:seqan/index.h
-*/
 /*!
  * @class GenericShape
- * 
  * @extends Shape
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
  * @brief A variable gapped shape.
- * 
- * @signature Shape<TValue, GenericShape>
- * 
+ *
+ * @signature template <typename TValue>
+ *            class Shape<TValue, GenericShape>;
+ *
  * @tparam TValue The @link Value @endlink type of the string the shape is
  *                applied to (e.g. <tt>Dna</tt>).
- * 
- * @section Remarks
- * 
- * A GenericShape must be initialized first with a valid shape. To do so, call
+ *
+ * A GenericShape must be initialized first with a valid shape.  To do so, call
  * @link Shape#stringToShape @endlink.
- * 
+ *
  * @see GappedShape
  * @see OneGappedShape
  */
-	//////////////////////////////////////////////////////////////////////////////
-	// variable gapped shape
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <typename TValue>
-	class Shape<TValue, GenericShape>
-	{
-	public:
+    //////////////////////////////////////////////////////////////////////////////
+    // variable gapped shape
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <typename TValue>
+    class Shape<TValue, GenericShape>
+    {
+    public:
 //____________________________________________________________________________
 
-		unsigned span;
-		unsigned weight;
-		String<int> diffs;
-	
-		typename Value<Shape>::Type	hValue;		// current hash value
+        unsigned span;
+        unsigned weight;
+        String<int> diffs;
+
+        typename Value<Shape>::Type    hValue;        // current hash value
 //____________________________________________________________________________
 
-/**
-.Memfunc.GenericShape#Shape:
-..class:Spec.GenericShape
-..summary:Constructor
-..signature:Shape<TValue, GenericShape> ()
-..signature:Shape<TValue, GenericShape> (q)
-..signature:Shape<TValue, GenericShape> (shape)
-..signature:Shape<TValue, GenericShape> (bitmap)
-..signature:Shape<TValue, GenericShape> (predefined)
-..param.q:Creates an ungapped q-gram.
-..param.shape:Any other gapped/ungapped shape.
-..param.bitmap:Bitmap string. Sequence of '0's and '1's.
-...see:Function.stringToShape
-..param.predefined:Any instance of a predefined shape spec (e.g. $ShapePatternHunter$).
-..see:Class.HardwiredShape
-*/
 /*!
  * @fn GenericShape::Shape
- * 
+ *
  * @brief Constructor
- * 
- * @signature Shape<TValue, GenericShape> ()
- * @signature Shape<TValue, GenericShape> (q)
- * @signature Shape<TValue, GenericShape> (shape)
- * @signature Shape<TValue, GenericShape> (bitmap)
- * @signature Shape<TValue, GenericShape> (predefined)
- * 
+ *
+ * @signature Shape::Shape();
+ * @signature Shape::Shape(q);
+ * @signature Shape::Shape(shape);
+ * @signature Shape::Shape(bitmap);
+ * @signature Shape::Shape(predefined);
+ *
  * @param predefined Any instance of a predefined shape spec (e.g.
  *                   <tt>ShapePatternHunter</tt>).
  * @param q Creates an ungapped q-gram.
  * @param shape Any other gapped/ungapped shape.
  * @param bitmap Bitmap string. Sequence of '0's and '1's. See @link Shape#stringToShape @endlink
- * 
+ *
  * @see HardwiredShape
  */
-		Shape():
-			span(0),
-			weight(0),
-			hValue(0) {}
-
-		// c'tor for ungapped shapes
-		Shape(unsigned _span):
-			span(_span),
-			weight(_span),
-			hValue(0)
-		{
-		SEQAN_CHECKPOINT
-			if (_span > 0)
-			{
-				resize(diffs, _span - 1);
-				for(unsigned i = 0; i < _span - 1; ++i)
-					diffs[i] = 1;
-			}
-		}
-
-		Shape(Shape const &other):
-			span(other.span),
-			weight(other.weight),
-			diffs(other.diffs),
-			hValue(other.hValue) {}	
-
-		template <typename TSpec>
-		Shape(Shape<TValue, TSpec> const &other)
-		{
-			*this = other;
-		}	
-
-		template <typename TSpec>
-		Shape(GappedShape<TSpec> const &other)
-		{
-			*this = other;
-		}
-
-		template <typename TStringValue, typename TSpec>
-		Shape(String<TStringValue, TSpec> const &bitmap)
-		{
-			*this = bitmap;
-		}	
+        Shape():
+            span(0),
+            weight(0),
+            hValue(0) {}
+
+        // c'tor for ungapped shapes
+        Shape(unsigned _span):
+            span(_span),
+            weight(_span),
+            hValue(0)
+        {
+        SEQAN_CHECKPOINT
+            if (_span > 0)
+            {
+                resize(diffs, _span - 1);
+                for(unsigned i = 0; i < _span - 1; ++i)
+                    diffs[i] = 1;
+            }
+        }
+
+        Shape(Shape const &other):
+            span(other.span),
+            weight(other.weight),
+            diffs(other.diffs),
+            hValue(other.hValue) {}
+
+        template <typename TSpec>
+        Shape(Shape<TValue, TSpec> const &other)
+        {
+            *this = other;
+        }
+
+        template <typename TSpec>
+        Shape(GappedShape<TSpec> const &other)
+        {
+            *this = other;
+        }
+
+        template <typename TStringValue, typename TSpec>
+        Shape(String<TStringValue, TSpec> const &bitmap)
+        {
+            *this = bitmap;
+        }
 
 //____________________________________________________________________________
 
-		template <unsigned q>
-		inline Shape &
-		operator=(Shape<TValue, UngappedShape<q> > const &other)
-		{
-			span = length(other);
-			weight = seqan::weight(other);
-			if (weight > 0)
-			{
-				resize(diffs, weight - 1);
-				for(unsigned i = 0; i < weight - 1; ++i)
-					diffs[i] = 1;
-			}
-			else
-				clear(diffs);
-			hValue = other.hValue;
-			return *this;
-		}
-
-		template <typename TSpec>
-		inline Shape &
-		operator=(Shape<TValue, GappedShape<TSpec> > const &other)
-		{
-			span = other.span;
-			weight = other.weight;
-			diffs = other.diffs;
-			hValue = other.hValue;
-			return *this;
-		}
-
-		template <typename TSpec>
-		inline Shape &
-		operator=(GappedShape<TSpec> const)
-		{
-			typedef Shape<TValue, GappedShape<TSpec> > TShape;
-			return *this = TShape();
-		}
-
-		template <typename TStringValue, typename TSpec>
-		inline Shape &
-		operator=(String<TStringValue, TSpec> const &bitmap)
-		{
-			stringToShape(*this, bitmap);
-			return *this;
-		}
-	};
+        template <unsigned q>
+        inline Shape &
+        operator=(Shape<TValue, UngappedShape<q> > const &other)
+        {
+            span = length(other);
+            weight = seqan::weight(other);
+            if (weight > 0)
+            {
+                resize(diffs, weight - 1);
+                for(unsigned i = 0; i < weight - 1; ++i)
+                    diffs[i] = 1;
+            }
+            else
+                clear(diffs);
+            hValue = other.hValue;
+            return *this;
+        }
+
+        template <typename TSpec>
+        inline Shape &
+        operator=(Shape<TValue, GappedShape<TSpec> > const &other)
+        {
+            span = other.span;
+            weight = other.weight;
+            diffs = other.diffs;
+            hValue = other.hValue;
+            return *this;
+        }
+
+        template <typename TSpec>
+        inline Shape &
+        operator=(GappedShape<TSpec> const)
+        {
+            typedef Shape<TValue, GappedShape<TSpec> > TShape;
+            return *this = TShape();
+        }
+
+        template <typename TStringValue, typename TSpec>
+        inline Shape &
+        operator=(String<TStringValue, TSpec> const &bitmap)
+        {
+            stringToShape(*this, bitmap);
+            return *this;
+        }
+    };
 
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Spec.GappedShape:
-..cat:Index
-..summary:A fixed gapped shape.
-..general:Class.Shape
-..signature:Shape<TValue, GappedShape<TSpec> >
-..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
-..param.TSpec:A structure to store the shape at compile-time.
-...type:Class.HardwiredShape
-..remarks:There are predefined shapes in $index/shape_predefined.h$.
-You can simply use them with $Shape<TValue, ShapePatternHunter>$ for example.
-..see:Class.HardwiredShape
-..include:seqan/index.h
-*/
 /*!
  * @class GappedShape
- * 
  * @extends Shape
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief A fixed gapped shape.
- * 
- * @signature Shape<TValue, GappedShape<TSpec> >
- * 
+ *
+ * @signature template <typename TValue, typename TSpec>
+ *            class Shape<TValue, GappedShape<TSpec> >;
+ *
  * @tparam TSpec A structure to store the shape at compile-time. Types:
  *               @link HardwiredShape @endlink
  * @tparam TValue The @link Value @endlink type of the string the shape is
  *                applied to (e.g. <tt>Dna</tt>).
- * 
- * @section Remarks
- * 
+ *
  * There are predefined shapes in <tt>index/shape_predefined.h</tt>. You can
  * simply use them with <tt>Shape<TValue, ShapePatternHunter></tt> for example.
- * 
+ *
  * @see HardwiredShape
  * @see GenericShape
  */
 
-	//////////////////////////////////////////////////////////////////////////////
-	// fixed gapped shape
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // fixed gapped shape
+    //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TValue, typename TSpec>
-	class Shape<TValue, GappedShape<TSpec> >
-	{
-	public:
+    template <typename TValue, typename TSpec>
+    class Shape<TValue, GappedShape<TSpec> >
+    {
+    public:
 //____________________________________________________________________________
 
-		typedef GappedShape<TSpec>	TShapeSpec;
+        typedef GappedShape<TSpec>    TShapeSpec;
+
+        enum { span = LENGTH<Shape>::VALUE };
+        enum { weight = WEIGHT<Shape>::VALUE };
+        const int *diffs;
 
-		enum { span = LENGTH<Shape>::VALUE };
-		enum { weight = WEIGHT<Shape>::VALUE };
-		const int *diffs;
-	
-		typename Value<Shape>::Type	hValue;		// current hash value
+        typename Value<Shape>::Type    hValue;        // current hash value
 //____________________________________________________________________________
 
-		Shape():
-			diffs(TSpec::DIFFS),
-			hValue(0) {}
+        Shape():
+            diffs(TSpec::DIFFS),
+            hValue(0) {}
 
-		Shape(Shape const &other):
-			diffs(other.diffs),	
-			hValue(other.hValue) {}
+        Shape(Shape const &other):
+            diffs(other.diffs),
+            hValue(other.hValue) {}
 //____________________________________________________________________________
 
-		inline Shape &
-		operator=(Shape const &other)
-		{
-			hValue = other.hValue;
+        inline Shape &
+        operator=(Shape const &other)
+        {
+            hValue = other.hValue;
       return *this;
-		}
-	};
+        }
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TValue, typename TSpec>
-	inline typename Size< Shape<TValue, GappedShape<TSpec> > >::Type
-	weight(Shape<TValue, GappedShape<TSpec> > const & me)
-	{
-	SEQAN_CHECKPOINT
-		return me.weight;
-	}
+    template <typename TValue, typename TSpec>
+    inline typename Size< Shape<TValue, GappedShape<TSpec> > >::Type
+    weight(Shape<TValue, GappedShape<TSpec> > const & me)
+    {
+    SEQAN_CHECKPOINT
+        return me.weight;
+    }
 
 //____________________________________________________________________________
 
-	template <typename TValue, typename TIter>
-	inline typename Value< Shape<TValue, GenericShape> >::Type
-	hash(Shape<TValue, GenericShape> &me, TIter it)
-	{
-		//typedef typename Value< Shape<TValue, GenericShape> >::Type	THValue;
-		typedef typename Size< Shape<TValue, GenericShape> >::Type	TSize;
-
-		SEQAN_ASSERT_GT((unsigned)me.weight, 0u);
-
-		me.hValue = ordValue((TValue)*it);
-		TSize iEnd = me.weight - 1;
-		for(TSize i = 0; i < iEnd; ++i) {
-			goFurther(it, me.diffs[i]);
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-		return me.hValue;
-	}
-
-	template <typename TValue, typename TSpec, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, GappedShape<TSpec> > >::Type
-	hash(Shape<TValue, GappedShape<TSpec> > &me, TIter it, TSize charsLeft)
-	{
-		//typedef typename Value< Shape<TValue, GappedShape<TSpec> > >::Type	THValue;
-
-		if (charsLeft >= (TSize)me.span)
-			return hash(me, it);
-
-		SEQAN_ASSERT_GT((unsigned)me.weight, 0u);
-
-		TSize i = 0;
-		if (charsLeft > 0) {
-			me.hValue = ordValue((TValue)*it);
-			TSize d;
-			while (charsLeft > (d = me.diffs[i])) {
-				charsLeft -= d;
-				goFurther(it, d);
-				me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-				++i;
-			}
-			++i;
-		} else
-			return me.hValue = 0;
-
-		// fill shape with zeros
-		for(; i < (TSize)me.weight; ++i)
-			me.hValue *= ValueSize<TValue>::VALUE;
-		return me.hValue;
-	}
-
-	template <typename TValue, typename TSpec, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, GappedShape<TSpec> > >::Type
-	hashUpper(Shape<TValue, GappedShape<TSpec> > &me, TIter it, TSize charsLeft)
-	{
-		//typedef typename Value< Shape<TValue, GappedShape<TSpec> > >::Type	THValue;
-
-		if (charsLeft >= (TSize)me.span) {
-			hash(me, it);
-			return ++me.hValue;
-		}
-
-		SEQAN_ASSERT_GT((unsigned)me.weight, 0u);
-
-		TSize i = 0;
-		if (charsLeft > 0) {
-			me.hValue = ordValue((TValue)*it);
-			TSize d;
-			while (charsLeft > (d = me.diffs[i])) {
-				charsLeft -= d;
-				goFurther(it, d);
-				me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-				++i;
-			}
-			++i;
-			++me.hValue;
-		} else
-			me.hValue = 1;
-
-		// fill shape with zeros
-		for(; i < (TSize)me.weight; ++i)
-			me.hValue *= ValueSize<TValue>::VALUE;
-		return me.hValue;
-	}
+    template <typename TValue, typename TIter>
+    inline typename Value< Shape<TValue, GenericShape> >::Type
+    hash(Shape<TValue, GenericShape> &me, TIter it)
+    {
+        //typedef typename Value< Shape<TValue, GenericShape> >::Type    THValue;
+        typedef typename Size< Shape<TValue, GenericShape> >::Type    TSize;
+
+        SEQAN_ASSERT_GT((unsigned)me.weight, 0u);
+
+        me.hValue = ordValue((TValue)*it);
+        TSize iEnd = me.weight - 1;
+        for(TSize i = 0; i < iEnd; ++i) {
+            goFurther(it, me.diffs[i]);
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+        return me.hValue;
+    }
+
+    template <typename TValue, typename TSpec, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, GappedShape<TSpec> > >::Type
+    hash(Shape<TValue, GappedShape<TSpec> > &me, TIter it, TSize charsLeft)
+    {
+        //typedef typename Value< Shape<TValue, GappedShape<TSpec> > >::Type    THValue;
+
+        if (charsLeft >= (TSize)me.span)
+            return hash(me, it);
+
+        SEQAN_ASSERT_GT((unsigned)me.weight, 0u);
+
+        TSize i = 0;
+        if (charsLeft > 0) {
+            me.hValue = ordValue((TValue)*it);
+            TSize d;
+            while (charsLeft > (d = me.diffs[i])) {
+                charsLeft -= d;
+                goFurther(it, d);
+                me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+                ++i;
+            }
+            ++i;
+        } else
+            return me.hValue = 0;
+
+        // fill shape with zeros
+        for(; i < (TSize)me.weight; ++i)
+            me.hValue *= ValueSize<TValue>::VALUE;
+        return me.hValue;
+    }
+
+    template <typename TValue, typename TSpec, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, GappedShape<TSpec> > >::Type
+    hashUpper(Shape<TValue, GappedShape<TSpec> > &me, TIter it, TSize charsLeft)
+    {
+        //typedef typename Value< Shape<TValue, GappedShape<TSpec> > >::Type    THValue;
+
+        if (charsLeft >= (TSize)me.span) {
+            hash(me, it);
+            return ++me.hValue;
+        }
+
+        SEQAN_ASSERT_GT((unsigned)me.weight, 0u);
+
+        TSize i = 0;
+        if (charsLeft > 0) {
+            me.hValue = ordValue((TValue)*it);
+            TSize d;
+            while (charsLeft > (d = me.diffs[i])) {
+                charsLeft -= d;
+                goFurther(it, d);
+                me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+                ++i;
+            }
+            ++i;
+            ++me.hValue;
+        } else
+            me.hValue = 1;
+
+        // fill shape with zeros
+        for(; i < (TSize)me.weight; ++i)
+            me.hValue *= ValueSize<TValue>::VALUE;
+        return me.hValue;
+    }
 
 //____________________________________________________________________________
 
-	template <typename THValue, typename TValue, typename TIter>
-	inline THValue
-	_hashHardwiredShape(THValue hash, TIter &, TValue const, HardwiredShape<
-		0,0,0,0,0,
-		0,0,0,0,0,
-		0,0,0,0,0,
-		0,0,0,0,0 > const)
-	{
-		return hash;
-	}
-
-	template <
-		         int P01, int P02, int P03, int P04,
-		int P05, int P06, int P07, int P08, int P09,
-		int P10, int P11, int P12, int P13, int P14,
-		int P15, int P16, int P17, int P18, int P19,
-		typename THValue, typename TValue, typename TIter
-	>
-	inline THValue
-	_hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape<
-		 1 ,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 > const)
-	{
-		++it;
-		return _hashHardwiredShape(hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
-			it, TValue(), HardwiredShape<
-				P01,P02,P03,P04,P05,
-				P06,P07,P08,P09,P10,
-				P11,P12,P13,P14,P15,
-				P16,P17,P18,P19, 0 >());
-	}
-
-	template <
-		int P00, int P01, int P02, int P03, int P04,
-		int P05, int P06, int P07, int P08, int P09,
-		int P10, int P11, int P12, int P13, int P14,
-		int P15, int P16, int P17, int P18, int P19,
-		typename THValue, typename TValue, typename TIter
-	>
-	inline THValue
-	_hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 > const)
-	{
-		it += P00;
-		return _hashHardwiredShape(hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
-			it, TValue(), HardwiredShape<
-				P01,P02,P03,P04,P05,
-				P06,P07,P08,P09,P10,
-				P11,P12,P13,P14,P15,
-				P16,P17,P18,P19, 0 >());
-	}
-
-	template <
-		int P00, int P01, int P02, int P03, int P04,
-		int P05, int P06, int P07, int P08, int P09,
-		int P10, int P11, int P12, int P13, int P14,
-		int P15, int P16, int P17, int P18, int P19,
-		typename TValue, typename TIter
-	>
-	inline typename Value< Shape<TValue, GappedShape< HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 
-	> > > >::Type
-	hash(Shape<TValue, GappedShape< HardwiredShape<
-		P00,P01,P02,P03,P04,
-		P05,P06,P07,P08,P09,
-		P10,P11,P12,P13,P14,
-		P15,P16,P17,P18,P19 
-	> > > &me, TIter it)
-	{
-	SEQAN_CHECKPOINT
-		typedef HardwiredShape<
-			P00,P01,P02,P03,P04,
-			P05,P06,P07,P08,P09,
-			P10,P11,P12,P13,P14,
-			P15,P16,P17,P18,P19 >								TSpec;
-		typedef GappedShape<TSpec>							TShape;
-		typedef typename Value< Shape<TValue, TShape> >::Type	THValue;
-
-		me.hValue = (THValue)ordValue((TValue)*it);
-		return me.hValue = _hashHardwiredShape(me.hValue, it, TValue(), TSpec());
-	}
+    template <typename THValue, typename TValue, typename TIter>
+    inline THValue
+    _hashHardwiredShape(THValue hash, TIter &, TValue const, HardwiredShape<
+        0,0,0,0,0,
+        0,0,0,0,0,
+        0,0,0,0,0,
+        0,0,0,0,0 > const)
+    {
+        return hash;
+    }
+
+    template <
+                 int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19,
+        typename THValue, typename TValue, typename TIter
+    >
+    inline THValue
+    _hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape<
+         1 ,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19 > const)
+    {
+        ++it;
+        return _hashHardwiredShape(hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
+            it, TValue(), HardwiredShape<
+                P01,P02,P03,P04,P05,
+                P06,P07,P08,P09,P10,
+                P11,P12,P13,P14,P15,
+                P16,P17,P18,P19, 0 >());
+    }
+
+    template <
+        int P00, int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19,
+        typename THValue, typename TValue, typename TIter
+    >
+    inline THValue
+    _hashHardwiredShape(THValue hash, TIter &it, TValue const, HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19 > const)
+    {
+        it += P00;
+        return _hashHardwiredShape(hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),
+            it, TValue(), HardwiredShape<
+                P01,P02,P03,P04,P05,
+                P06,P07,P08,P09,P10,
+                P11,P12,P13,P14,P15,
+                P16,P17,P18,P19, 0 >());
+    }
+
+    template <
+        int P00, int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19,
+        typename TValue, typename TIter
+    >
+    inline typename Value< Shape<TValue, GappedShape< HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19
+    > > > >::Type
+    hash(Shape<TValue, GappedShape< HardwiredShape<
+        P00,P01,P02,P03,P04,
+        P05,P06,P07,P08,P09,
+        P10,P11,P12,P13,P14,
+        P15,P16,P17,P18,P19
+    > > > &me, TIter it)
+    {
+    SEQAN_CHECKPOINT
+        typedef HardwiredShape<
+            P00,P01,P02,P03,P04,
+            P05,P06,P07,P08,P09,
+            P10,P11,P12,P13,P14,
+            P15,P16,P17,P18,P19 >                                TSpec;
+        typedef GappedShape<TSpec>                            TShape;
+        typedef typename Value< Shape<TValue, TShape> >::Type    THValue;
+
+        me.hValue = (THValue)ordValue((TValue)*it);
+        return me.hValue = _hashHardwiredShape(me.hValue, it, TValue(), TSpec());
+    }
 
 //____________________________________________________________________________
 
-	template <typename TValue, typename TSpec, typename TIter>
-	inline void
-	hashInit(Shape<TValue, GappedShape<TSpec> > &, TIter &)
-	{
-	}
-    
-	template <typename TValue, typename TSpec, typename TIter>
-	inline typename Value< Shape<TValue, GappedShape<TSpec> > >::Type
-	hashNext(Shape<TValue, GappedShape<TSpec> > &me, TIter &it)
-	{
-	SEQAN_CHECKPOINT
-		return hash(me, it);
-	}
+    template <typename TValue, typename TSpec, typename TIter>
+    inline void
+    hashInit(Shape<TValue, GappedShape<TSpec> > &, TIter &)
+    {
+    }
+
+    template <typename TValue, typename TSpec, typename TIter>
+    inline typename Value< Shape<TValue, GappedShape<TSpec> > >::Type
+    hashNext(Shape<TValue, GappedShape<TSpec> > &me, TIter &it)
+    {
+    SEQAN_CHECKPOINT
+        return hash(me, it);
+    }
 
 
 //____________________________________________________________________________
-///.Function.stringToShape.param.shape.type:Spec.GenericShape
-///.Function.stringToShape.class:Spec.GenericShape
-
-	template <typename TValue, typename TSpec, typename TShapeString>
-	inline bool
-	stringToShape(
-		Shape<TValue, GappedShape<TSpec> > &me, 
-		TShapeString const &bitmap)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TShapeString const>::Type		TIter;
-		typedef typename Iterator<String<int> >::Type			TShapeIter;
-
-		unsigned oneCount = 0;
-		TIter it = begin(bitmap, Standard());
-		TIter itEnd = end(bitmap, Standard());
-		for(; it != itEnd; ++it)
-			if (*it == '1')
-				++oneCount;
-
-		if ((me.weight = oneCount) == 0) {
-			me.span = 0;
-			return false;
-		}
-		
-		resize(me.diffs, oneCount - 1);
-
-		unsigned diff = 1;
-		me.span = 1;
-		TShapeIter itS = begin(me.diffs, Standard());
-
-		it = begin(bitmap, Standard());
-		
-		// skip leading zeros
-		for(; it != itEnd && *it == '0' ; ++it) ;
-
-		if (*it != '1')
-			return false;
-
-		for(++it; it != itEnd; ++it) 
-		{
-			if (*it == '1') 
-			{
-				me.span += diff;
-				*itS = diff;
-				++itS;
-				diff = 0;
-			}
-			++diff;
-		}
-
-		return true;
-	}
+    template <typename TValue, typename TSpec, typename TShapeString>
+    inline bool
+    stringToShape(
+        Shape<TValue, GappedShape<TSpec> > &me,
+        TShapeString const &bitmap)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Iterator<TShapeString const>::Type        TIter;
+        typedef typename Iterator<String<int> >::Type            TShapeIter;
+
+        unsigned oneCount = 0;
+        TIter it = begin(bitmap, Standard());
+        TIter itEnd = end(bitmap, Standard());
+        for(; it != itEnd; ++it)
+            if (*it == '1')
+                ++oneCount;
+
+        if ((me.weight = oneCount) == 0) {
+            me.span = 0;
+            return false;
+        }
+
+        resize(me.diffs, oneCount - 1);
+
+        unsigned diff = 1;
+        me.span = 1;
+        TShapeIter itS = begin(me.diffs, Standard());
+
+        it = begin(bitmap, Standard());
+
+        // skip leading zeros
+        for(; it != itEnd && *it == '0' ; ++it) ;
+
+        if (*it != '1')
+            return false;
+
+        for(++it; it != itEnd; ++it)
+        {
+            if (*it == '1')
+            {
+                me.span += diff;
+                *itS = diff;
+                ++itS;
+                diff = 0;
+            }
+            ++diff;
+        }
+
+        return true;
+    }
 
 //____________________________________________________________________________
 
-	template <typename TShapeString, typename TValue, typename TSpec>
-	inline void
-	shapeToString(
-		TShapeString &bitmap,
-		Shape<TValue, GappedShape<TSpec> > const &me)
-	{
-	SEQAN_CHECKPOINT
-
-		clear(bitmap);
-		if (weight(me) == 0) return;
-		
-		reserve(bitmap, length(me));	
-		appendValue(bitmap, '1');
-		for (unsigned i = 0; i < weight(me) - 1; ++i)
-		{
-			for (int j = 1; j < me.diffs[i]; ++j)
-				appendValue(bitmap, '0');
-			appendValue(bitmap, '1');
-		}
-	}
+    template <typename TShapeString, typename TValue, typename TSpec>
+    inline void
+    shapeToString(
+        TShapeString &bitmap,
+        Shape<TValue, GappedShape<TSpec> > const &me)
+    {
+    SEQAN_CHECKPOINT
+
+        clear(bitmap);
+        if (weight(me) == 0) return;
+
+        reserve(bitmap, length(me));
+        appendValue(bitmap, '1');
+        for (unsigned i = 0; i < weight(me) - 1; ++i)
+        {
+            for (int j = 1; j < me.diffs[i]; ++j)
+                appendValue(bitmap, '0');
+            appendValue(bitmap, '1');
+        }
+    }
 
 //____________________________________________________________________________
-///.Function.reverse.param.object.type:Spec.GenericShape
-///.Function.reverse.class:Spec.GenericShape
-
-	template <typename TValue, typename TSpec>
-	inline void
-	reverse(Shape<TValue, GappedShape<TSpec> > &me)
-	{
-	SEQAN_CHECKPOINT
-		reverse(me.diffs);
-	}
-
-}	// namespace seqan
+    template <typename TValue, typename TSpec>
+    inline void
+    reverse(Shape<TValue, GappedShape<TSpec> > &me)
+    {
+    SEQAN_CHECKPOINT
+        reverse(me.diffs);
+    }
+
+}    // namespace seqan
 
 #endif
diff --git a/seqan/index/shape_minimizer.h b/seqan/index/shape_minimizer.h
new file mode 100644
index 0000000..2807442
--- /dev/null
+++ b/seqan/index/shape_minimizer.h
@@ -0,0 +1,179 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+
+#ifndef SEQAN_HEADER_SHAPE_MINIMIZER_H
+#define SEQAN_HEADER_SHAPE_MINIMIZER_H
+
+namespace seqan
+{
+
+struct ReverseComplementTag_;
+typedef Tag<ReverseComplementTag_> const   ReverseComplement;
+
+// ----------------------------------------------------------------------------
+// Struct MinimizerShape
+// ----------------------------------------------------------------------------
+
+template <unsigned TSPAN, unsigned TWEIGHT, typename TSpec = void>
+struct MinimizerShape;
+
+// ----------------------------------------------------------------------------
+// Class Shape<MinimizerShape>
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec>
+class Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> >
+{
+public:
+    typedef typename Value<Shape>::Type THashValue;
+
+    unsigned span;
+    unsigned weight;
+    THashValue hValue;      //current minimizer hash
+
+    Shape():
+        span(TSPAN),
+        weight(TWEIGHT)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction LENGTH
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec>
+struct LENGTH<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >
+{
+    enum { VALUE = TSPAN };
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction WEIGHT
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec>
+struct WEIGHT<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >
+{
+    enum { VALUE = TWEIGHT };
+};
+
+// ----------------------------------------------------------------------------
+// Function weight()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec>
+inline SEQAN_HOST_DEVICE
+typename Size< Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >::Type
+weight(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > const &me)
+{
+    return me.weight;
+}
+
+// ----------------------------------------------------------------------------
+// Function _minHash()
+// ----------------------------------------------------------------------------
+// return lexicographically smaller hash as the minimizer
+
+template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec, typename TString>
+inline typename Value< Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >::Type 
+_minHash(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > &me, TString const & str)
+{
+    typedef typename Iterator<TString const, Standard>::Type                TIter;
+    typedef typename Value<Shape<TValue, UngappedShape<TWEIGHT> > >::Type   THValue;
+  
+    SEQAN_ASSERT_GT((unsigned)me.span, 0u);
+    SEQAN_ASSERT_GT((unsigned)me.span, (unsigned)me.weight); 
+
+    Shape<TValue, UngappedShape<TWEIGHT> > tmpShape;
+
+    TIter strIt = begin(str, Standard());
+    TIter strEnd = end(str, Standard()) - weight(me) + 1;
+
+    THValue miniTmp = hash(tmpShape, strIt);
+    for (strIt++; strIt != strEnd; strIt++)
+        miniTmp = _min(miniTmp, hashNext(tmpShape, strIt));
+
+    return miniTmp;
+}
+
+// ----------------------------------------------------------------------------
+// Function hash()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec, typename TIter>
+inline typename Value<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >::Type
+hash(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > &me, TIter const &it)
+{
+    Range<TIter> range(it, it + length(me));
+
+    me.hValue = _minHash(me, range);
+    return me.hValue;
+}
+
+// ----------------------------------------------------------------------------
+// Function hash(); ReverseComplement
+// ----------------------------------------------------------------------------
+// Uses the lexicographically smaller of S and the reverse complement of S as the minimizer
+
+template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TIter>
+inline typename Value<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, ReverseComplement> > >::Type
+hash(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, ReverseComplement> > &me, TIter const &it)
+{
+    typedef Range<TIter>                        TContainer;
+    typedef typename Value<TContainer>::Type    TAlphabet;
+    typedef typename RemoveConst<TAlphabet>::Type TNCAlphabet;
+    typedef ModifiedString<TContainer, ModView<FunctorComplement<TNCAlphabet> > > TComplement;
+    typedef ModifiedString<TComplement, ModReverse>                             TRC;
+
+    Range<TIter> range(it, it + length(me));
+    TRC revComplRange(range);
+
+    me.hValue = _min(_minHash(me, range), _minHash(me, revComplRange));
+
+    return me.hValue;
+}
+
+// ----------------------------------------------------------------------------
+// Function hashNext()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec, typename TIter>
+inline typename Value<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >::Type
+hashNext(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > &me, TIter const &it)
+{
+    return hash(me, it);
+}
+
+
+}	// namespace seqan
+
+#endif
diff --git a/seqan/index/shape_onegapped.h b/seqan/index/shape_onegapped.h
index 2b0c802..28df66c 100644
--- a/seqan/index/shape_onegapped.h
+++ b/seqan/index/shape_onegapped.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,398 +39,364 @@ namespace SEQAN_NAMESPACE_MAIN
 {
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// shape with one gap
-	//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Spec.OneGappedShape:
-..cat:Index
-..summary:A variable shape with one optional gap.
-..general:Class.Shape
-..signature:Shape<TValue, OneGappedShape>
-..param.TValue:The @Metafunction.Value@ type of the string the shape is applied to (e.g. $Dna$).
-..remarks:A OneGappedShape must be initialized first with a valid shape. To do so, call @Function.stringToShape@.
-..see:Spec.GenericShape
-..include:seqan/index.h
-.Memfunc.OneGappedShape#Shape:
-..class:Spec.OneGappedShape
-..summary:Constructor
-..signature:Shape<TValue, OneGappedShape> ()
-..signature:Shape<TValue, OneGappedShape> (shape)
-..signature:Shape<TValue, OneGappedShape> (bitmap)
-..signature:Shape<TValue, OneGappedShape> (blockLen1, gapLen, blockLen2)
-..param.shape:Other Shape object. (copy constructor)
-..param.bitmap:Bitmap string. Sequence of '0's and '1's.
-...see:Function.stringToShape
-..param.blockLen1:Number of '1's in the first block.
-..param.gapLen:Number of '0's in the second block.
-..param.blockLen2:Number of '1's in the third block.
-*/
+    //////////////////////////////////////////////////////////////////////////////
+    // shape with one gap
+    //////////////////////////////////////////////////////////////////////////////
+
 /*!
  * @class OneGappedShape
- * 
  * @extends Shape
- * 
- * @headerfile seqan/index.h
- * 
+ * @headerfile <seqan/index.h>
+ *
  * @brief A variable shape with one optional gap.
- * 
- * @signature Shape<TValue, OneGappedShape>
- * 
+ *
+ * @signature template <typename TValue>
+ *            class Shape<TValue, OneGappedShape>;
+ *
  * @tparam TValue The @link Value @endlink type of the string the shape is
  *                applied to (e.g. <tt>Dna</tt>).
- * 
- * @section Remarks
- * 
+ *
  * A OneGappedShape must be initialized first with a valid shape. To do so, call
  * @link Shape#stringToShape @endlink.
- * 
+ *
  * @see GenericShape
  */
 
-	struct OneGappedShape;
+    struct OneGappedShape;
 
-	template <typename TValue>
-	class Shape<TValue, OneGappedShape>
-	{
-	public:
+    template <typename TValue>
+    class Shape<TValue, OneGappedShape>
+    {
+    public:
 //____________________________________________________________________________
 
-		unsigned blockLen1;
-		unsigned gapLen;
-		unsigned blockLen2;
-	
-		typename Value<Shape>::Type	hValue;		// current hash value
+        unsigned blockLen1;
+        unsigned gapLen;
+        unsigned blockLen2;
+
+        typename Value<Shape>::Type    hValue;        // current hash value
 
-		TValue						leftChar;
-		typename Value<Shape>::Type	factor1;
-		typename Value<Shape>::Type	factor2;
+        TValue                        leftChar;
+        typename Value<Shape>::Type    factor1;
+        typename Value<Shape>::Type    factor2;
 
 //____________________________________________________________________________
 
-		Shape():
-			blockLen1(0),
-			gapLen(0),
-			blockLen2(0),
-			hValue(0),
-			leftChar(0),
-			factor1(0),
-			factor2(0) {}
-
-		// c'tor for ungapped shapes
-		Shape(unsigned _blockLen1, unsigned _gapLen, unsigned _blockLen2):
-			blockLen1(_blockLen1),
-			gapLen(_gapLen),
-			blockLen2(_blockLen2),
-			hValue(0),
-			leftChar(0)
-		{
-		SEQAN_CHECKPOINT
-			typedef typename Value< Shape<TValue, OneGappedShape> >::Type	THValue;
-			factor1 = _intPow((THValue)ValueSize<TValue>::VALUE, weight(*this) - 1);
-			factor2 = _intPow((THValue)ValueSize<TValue>::VALUE, blockLen2);
-		}
-
-		Shape(Shape const &other):
-			blockLen1(other.blockLen1),
-			gapLen(other.gapLen),
-			blockLen2(other.blockLen2),
-			hValue(other.hValue),
-			leftChar(other.leftChar),
-			factor1(other.factor1), 
-			factor2(other.factor2) {}
-
-		template <typename TSpec>
-		Shape(Shape<TValue, TSpec> const &other) :
+        Shape():
+            blockLen1(0),
+            gapLen(0),
+            blockLen2(0),
+            hValue(0),
+            leftChar(0),
+            factor1(0),
+            factor2(0) {}
+
+        // c'tor for ungapped shapes
+        Shape(unsigned _blockLen1, unsigned _gapLen, unsigned _blockLen2):
+            blockLen1(_blockLen1),
+            gapLen(_gapLen),
+            blockLen2(_blockLen2),
+            hValue(0),
+            leftChar(0)
+        {
+        SEQAN_CHECKPOINT
+            typedef typename Value< Shape<TValue, OneGappedShape> >::Type    THValue;
+            factor1 = _intPow((THValue)ValueSize<TValue>::VALUE, weight(*this) - 1);
+            factor2 = _intPow((THValue)ValueSize<TValue>::VALUE, blockLen2);
+        }
+
+        Shape(Shape const &other):
+            blockLen1(other.blockLen1),
+            gapLen(other.gapLen),
+            blockLen2(other.blockLen2),
+            hValue(other.hValue),
+            leftChar(other.leftChar),
+            factor1(other.factor1),
+            factor2(other.factor2) {}
+
+        template <typename TSpec>
+        Shape(Shape<TValue, TSpec> const &other) :
                 hValue(0), leftChar(0)
-		{
-			*this = other;
-		}	
+        {
+            *this = other;
+        }
 
-		template <typename TSpec>
-		Shape(GappedShape<TSpec> const &other) :
+        template <typename TSpec>
+        Shape(GappedShape<TSpec> const &other) :
                 hValue(0), leftChar(0)
-		{
-			*this = other;
-		}
+        {
+            *this = other;
+        }
 
-		template <typename TStringValue, typename TSpec>
-		Shape(String<TStringValue, TSpec> const &bitmap) :
+        template <typename TStringValue, typename TSpec>
+        Shape(String<TStringValue, TSpec> const &bitmap) :
                 hValue(0), leftChar(0)
-		{
-			*this = bitmap;
-		}	
+        {
+            *this = bitmap;
+        }
 
 //____________________________________________________________________________
 
 
-		template <typename TStringValue, typename TSpec>
-		inline Shape &
-		operator=(String<TStringValue, TSpec> const &bitmap)
-		{
-			stringToShape(*this, bitmap);
-			return *this;
-		}
-	};
+        template <typename TStringValue, typename TSpec>
+        inline Shape &
+        operator=(String<TStringValue, TSpec> const &bitmap)
+        {
+            stringToShape(*this, bitmap);
+            return *this;
+        }
+    };
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TValue>
-	inline typename Size< Shape<TValue, OneGappedShape> >::Type
-	length(Shape<TValue, OneGappedShape> const &me)
-	{
-	SEQAN_CHECKPOINT
-		return me.blockLen1 + me.gapLen + me.blockLen2;
-	}
+    template <typename TValue>
+    inline typename Size< Shape<TValue, OneGappedShape> >::Type
+    length(Shape<TValue, OneGappedShape> const &me)
+    {
+    SEQAN_CHECKPOINT
+        return me.blockLen1 + me.gapLen + me.blockLen2;
+    }
 
 //____________________________________________________________________________
 
-	template <typename TValue>
-	inline typename Size< Shape<TValue, OneGappedShape> >::Type
-	weight(Shape<TValue, OneGappedShape> const & me)
-	{
-	SEQAN_CHECKPOINT
-		return me.blockLen1 + me.blockLen2;
-	}
+    template <typename TValue>
+    inline typename Size< Shape<TValue, OneGappedShape> >::Type
+    weight(Shape<TValue, OneGappedShape> const & me)
+    {
+    SEQAN_CHECKPOINT
+        return me.blockLen1 + me.blockLen2;
+    }
 
 //____________________________________________________________________________
 
-	template <typename TValue, typename TIter>
-	inline typename Value< Shape<TValue, OneGappedShape> >::Type
-	hash(Shape<TValue, OneGappedShape> &me, TIter it)
-	{
-		//typedef typename Value< Shape<TValue, OneGappedShape> >::Type	THValue;
-		typedef typename Size< Shape<TValue, OneGappedShape> >::Type	TSize;
-
-		SEQAN_ASSERT_GT(me.blockLen1, 0u);
-
-		me.hValue = ordValue(me.leftChar = *it);
-		for(TSize i = 1; i < me.blockLen1; ++i) {
-			goNext(it);
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-		goFurther(it, me.gapLen);
-		for(TSize i = 0; i < me.blockLen2; ++i) {
-			goNext(it);
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-		return me.hValue;
-	}
-
-	template <typename TValue, typename TIter>
-	inline typename Value< Shape<TValue, OneGappedShape> >::Type
-	hashInit(Shape<TValue, OneGappedShape> &me, TIter it)
-	{
-		//typedef typename Value< Shape<TValue, OneGappedShape> >::Type	THValue;
-		typedef typename Size< Shape<TValue, OneGappedShape> >::Type	TSize;
-
-		SEQAN_ASSERT_GT(me.blockLen1, 0u);
+    template <typename TValue, typename TIter>
+    inline typename Value< Shape<TValue, OneGappedShape> >::Type
+    hash(Shape<TValue, OneGappedShape> &me, TIter it)
+    {
+        //typedef typename Value< Shape<TValue, OneGappedShape> >::Type    THValue;
+        typedef typename Size< Shape<TValue, OneGappedShape> >::Type    TSize;
+
+        SEQAN_ASSERT_GT(me.blockLen1, 0u);
+
+        me.hValue = ordValue(me.leftChar = *it);
+        for(TSize i = 1; i < me.blockLen1; ++i) {
+            goNext(it);
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+        goFurther(it, me.gapLen);
+        for(TSize i = 0; i < me.blockLen2; ++i) {
+            goNext(it);
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+        return me.hValue;
+    }
+
+    template <typename TValue, typename TIter>
+    inline typename Value< Shape<TValue, OneGappedShape> >::Type
+    hashInit(Shape<TValue, OneGappedShape> &me, TIter it)
+    {
+        //typedef typename Value< Shape<TValue, OneGappedShape> >::Type    THValue;
+        typedef typename Size< Shape<TValue, OneGappedShape> >::Type    TSize;
+
+        SEQAN_ASSERT_GT(me.blockLen1, 0u);
 
         me.leftChar = 0;
-		me.hValue = ordValue(*it);
-		for(TSize i = 2; i < me.blockLen1; ++i) {
-			goNext(it);
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-		goFurther(it, me.gapLen);
-		for(TSize i = 0; i < me.blockLen2; ++i) {
-			goNext(it);
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-		return me.hValue;
-	}
-
-	template <typename TValue, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, OneGappedShape> >::Type
-	hash(Shape<TValue, OneGappedShape> &me, TIter it, TSize charsLeft)
-	{
-		//typedef typename Value< Shape<TValue, OneGappedShape> >::Type	THValue;
-		TSize blockLen1 = me.blockLen1;
-		TSize blockLen2 = me.blockLen2;
-
-		SEQAN_ASSERT_GT(me.blockLen1, 0u);
-
-		if ((TSize)length(me) > charsLeft)
-		{
-			if (blockLen1 > charsLeft)
-			{
-				blockLen1 = charsLeft;
-				blockLen2 = 0;
-				if (blockLen1 == 0) return me.hValue = 0;
-			} else
-				if (blockLen1 + (TSize)me.gapLen > charsLeft)
-					blockLen2 = 0;
-				else
-					blockLen2 = charsLeft - (blockLen1 + me.gapLen);
-		}
-
-		me.hValue = ordValue(me.leftChar = *it);
-		for(TSize i = 1; i < blockLen1; ++i) {
-			goNext(it);
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-		goFurther(it, me.gapLen);
-		for(TSize i = 0; i < blockLen2; ++i) {
-			goNext(it);
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-		}
-		// fill shape with zeros
-		TSize w = (TSize)weight(me);
-		for(TSize i = blockLen1 + blockLen2; i < w; ++i)
-			me.hValue *= ValueSize<TValue>::VALUE;
-		return me.hValue;
-	}
-
-	template <typename TValue, typename TIter, typename TSize>
-	inline typename Value< Shape<TValue, OneGappedShape> >::Type
-	hashUpper(Shape<TValue, OneGappedShape> &me, TIter it, TSize charsLeft)
-	{
-		//typedef typename Value< Shape<TValue, OneGappedShape> >::Type	THValue;
-		TSize blockLen1 = me.blockLen1;
-		TSize blockLen2 = me.blockLen2;
-
-		SEQAN_ASSERT_GT(me.blockLen1, 0u);
-
-		if ((TSize)length(me) > charsLeft)
-		{
-			if (blockLen1 > charsLeft)
-			{
-				blockLen1 = charsLeft;
-				blockLen2 = 0;
-			} else
-				if (blockLen1 + (TSize)me.gapLen > charsLeft)
-					blockLen2 = 0;
-				else
-					blockLen2 = charsLeft - (blockLen1 + me.gapLen);
-		}
-
-		me.hValue = 0;
-		me.leftChar = *it;
-		for(TSize i = 0; i < blockLen1; ++i) {
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-			goNext(it);
-		}
-		goFurther(it, me.gapLen);
-		for(TSize i = 0; i < blockLen2; ++i) {
-			me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
-			goNext(it);
-		}
-		++me.hValue;
-
-		// fill shape with zeros
-		TSize w = (TSize)weight(me);
-		for(TSize i = blockLen1 + blockLen2; i < w; ++i)
-			me.hValue *= ValueSize<TValue>::VALUE;
-		return me.hValue;
-	}
-
-	template <typename TValue, typename TIter>
-	inline typename Value< Shape<TValue, OneGappedShape> >::Type
-	hashNext(Shape<TValue, OneGappedShape> &me, TIter &_it)
-	{
-		//typedef typename Value< Shape<TValue, OneGappedShape> >::Type	THValue;
-		TIter it(_it);
-
-		SEQAN_ASSERT_GT(me.blockLen1, 0u);
-
-		// remove leftmost character
-		me.hValue -= ordValue(me.leftChar) * me.factor1;
-		me.leftChar = *it;
-
-		// shift
-		me.hValue *= ValueSize<TValue>::VALUE;
-
-		// add emerging character
-		goFurther(it, me.blockLen1 - 1);
-		me.hValue += ordValue((TValue)*it) * me.factor2;
-
-		// subtract vanishing character
-		goFurther(it, me.gapLen);
-		me.hValue -= ordValue((TValue)*it) * me.factor2;
-
-		// add rightmost emerging character
-		goFurther(it, me.blockLen2);
-		me.hValue += ordValue((TValue)*it);
-
-		return me.hValue;
-	}
+        me.hValue = ordValue(*it);
+        for(TSize i = 2; i < me.blockLen1; ++i) {
+            goNext(it);
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+        goFurther(it, me.gapLen);
+        for(TSize i = 0; i < me.blockLen2; ++i) {
+            goNext(it);
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+        return me.hValue;
+    }
+
+    template <typename TValue, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, OneGappedShape> >::Type
+    hash(Shape<TValue, OneGappedShape> &me, TIter it, TSize charsLeft)
+    {
+        //typedef typename Value< Shape<TValue, OneGappedShape> >::Type    THValue;
+        TSize blockLen1 = me.blockLen1;
+        TSize blockLen2 = me.blockLen2;
+
+        SEQAN_ASSERT_GT(me.blockLen1, 0u);
+
+        if ((TSize)length(me) > charsLeft)
+        {
+            if (blockLen1 > charsLeft)
+            {
+                blockLen1 = charsLeft;
+                blockLen2 = 0;
+                if (blockLen1 == 0) return me.hValue = 0;
+            } else
+                if (blockLen1 + (TSize)me.gapLen > charsLeft)
+                    blockLen2 = 0;
+                else
+                    blockLen2 = charsLeft - (blockLen1 + me.gapLen);
+        }
+
+        me.hValue = ordValue(me.leftChar = *it);
+        for(TSize i = 1; i < blockLen1; ++i) {
+            goNext(it);
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+        goFurther(it, me.gapLen);
+        for(TSize i = 0; i < blockLen2; ++i) {
+            goNext(it);
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+        }
+        // fill shape with zeros
+        TSize w = (TSize)weight(me);
+        for(TSize i = blockLen1 + blockLen2; i < w; ++i)
+            me.hValue *= ValueSize<TValue>::VALUE;
+        return me.hValue;
+    }
+
+    template <typename TValue, typename TIter, typename TSize>
+    inline typename Value< Shape<TValue, OneGappedShape> >::Type
+    hashUpper(Shape<TValue, OneGappedShape> &me, TIter it, TSize charsLeft)
+    {
+        //typedef typename Value< Shape<TValue, OneGappedShape> >::Type    THValue;
+        TSize blockLen1 = me.blockLen1;
+        TSize blockLen2 = me.blockLen2;
+
+        SEQAN_ASSERT_GT(me.blockLen1, 0u);
+
+        if ((TSize)length(me) > charsLeft)
+        {
+            if (blockLen1 > charsLeft)
+            {
+                blockLen1 = charsLeft;
+                blockLen2 = 0;
+            } else
+                if (blockLen1 + (TSize)me.gapLen > charsLeft)
+                    blockLen2 = 0;
+                else
+                    blockLen2 = charsLeft - (blockLen1 + me.gapLen);
+        }
+
+        me.hValue = 0;
+        me.leftChar = *it;
+        for(TSize i = 0; i < blockLen1; ++i) {
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+            goNext(it);
+        }
+        goFurther(it, me.gapLen);
+        for(TSize i = 0; i < blockLen2; ++i) {
+            me.hValue = me.hValue * ValueSize<TValue>::VALUE + ordValue((TValue)*it);
+            goNext(it);
+        }
+        ++me.hValue;
+
+        // fill shape with zeros
+        TSize w = (TSize)weight(me);
+        for(TSize i = blockLen1 + blockLen2; i < w; ++i)
+            me.hValue *= ValueSize<TValue>::VALUE;
+        return me.hValue;
+    }
+
+    template <typename TValue, typename TIter>
+    inline typename Value< Shape<TValue, OneGappedShape> >::Type
+    hashNext(Shape<TValue, OneGappedShape> &me, TIter &_it)
+    {
+        //typedef typename Value< Shape<TValue, OneGappedShape> >::Type    THValue;
+        TIter it(_it);
+
+        SEQAN_ASSERT_GT(me.blockLen1, 0u);
+
+        // remove leftmost character
+        me.hValue -= ordValue(me.leftChar) * me.factor1;
+        me.leftChar = *it;
+
+        // shift
+        me.hValue *= ValueSize<TValue>::VALUE;
+
+        // add emerging character
+        goFurther(it, me.blockLen1 - 1);
+        me.hValue += ordValue((TValue)*it) * me.factor2;
+
+        // subtract vanishing character
+        goFurther(it, me.gapLen);
+        me.hValue -= ordValue((TValue)*it) * me.factor2;
+
+        // add rightmost emerging character
+        goFurther(it, me.blockLen2);
+        me.hValue += ordValue((TValue)*it);
+
+        return me.hValue;
+    }
 
 
 //____________________________________________________________________________
-///.Function.stringToShape.param.shape.type:Spec.OneGappedShape
-///.Function.stringToShape.class:Spec.OneGappedShape
-///.Function.stringToShape.param.bitmap.remarks:If $shape$ is a @Spec.OneGappedShape@ at most two contiguous sequences of '1's are allowed.
-
-	template <typename TValue, typename TShapeString>
-	inline bool
-	stringToShape(
-		Shape<TValue, OneGappedShape> &me, 
-		TShapeString const &bitmap)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Iterator<TShapeString const>::Type				TIter;
-		typedef typename Value< Shape<TValue, OneGappedShape> >::Type	THValue;
+    template <typename TValue, typename TShapeString>
+    inline bool
+    stringToShape(
+        Shape<TValue, OneGappedShape> &me,
+        TShapeString const &bitmap)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Iterator<TShapeString const>::Type                TIter;
+        typedef typename Value< Shape<TValue, OneGappedShape> >::Type    THValue;
 
-		TIter it = begin(bitmap, Standard());
-		TIter itEnd = end(bitmap, Standard());
+        TIter it = begin(bitmap, Standard());
+        TIter itEnd = end(bitmap, Standard());
 
-		me.blockLen1 = 0;
-		me.gapLen = 0;
-		me.blockLen2 = 0;
+        me.blockLen1 = 0;
+        me.gapLen = 0;
+        me.blockLen2 = 0;
 
-		for(; it != itEnd && *it == '0' ; ++it) ;
+        for(; it != itEnd && *it == '0' ; ++it) ;
 
-		for(; it != itEnd && *it == '1' ; ++it)
-			++me.blockLen1;
+        for(; it != itEnd && *it == '1' ; ++it)
+            ++me.blockLen1;
 
-		for(; it != itEnd && *it == '0' ; ++it)
-			++me.gapLen;
+        for(; it != itEnd && *it == '0' ; ++it)
+            ++me.gapLen;
 
-		for(; it != itEnd && *it == '1' ; ++it)
-			++me.blockLen2;
+        for(; it != itEnd && *it == '1' ; ++it)
+            ++me.blockLen2;
 
-		for(; it != itEnd && *it == '0' ; ++it) ;
+        for(; it != itEnd && *it == '0' ; ++it) ;
 
-		me.factor1 = _intPow((THValue)ValueSize<TValue>::VALUE, weight(me) - 1);
-		me.factor2 = _intPow((THValue)ValueSize<TValue>::VALUE, me.blockLen2);
+        me.factor1 = _intPow((THValue)ValueSize<TValue>::VALUE, weight(me) - 1);
+        me.factor2 = _intPow((THValue)ValueSize<TValue>::VALUE, me.blockLen2);
 
-		return it == itEnd && me.blockLen1 > 0;
-	}
+        return it == itEnd && me.blockLen1 > 0;
+    }
 
 //____________________________________________________________________________
 
-	template <typename TShapeString, typename TValue>
-	inline void
-	shapeToString(
-		TShapeString &bitmap,
-		Shape<TValue, OneGappedShape> const &me)
-	{
-	SEQAN_CHECKPOINT
+    template <typename TShapeString, typename TValue>
+    inline void
+    shapeToString(
+        TShapeString &bitmap,
+        Shape<TValue, OneGappedShape> const &me)
+    {
+    SEQAN_CHECKPOINT
 
-		clear(bitmap);
-		resize(bitmap, me.blockLen1, '1');
-		resize(bitmap, me.blockLen1 + me.gapLen, '0');
-		resize(bitmap, me.blockLen1 + me.gapLen + me.blockLen2, '1');
-	}
+        clear(bitmap);
+        resize(bitmap, me.blockLen1, '1');
+        resize(bitmap, me.blockLen1 + me.gapLen, '0');
+        resize(bitmap, me.blockLen1 + me.gapLen + me.blockLen2, '1');
+    }
 
 //____________________________________________________________________________
-///.Function.reverse.param.object.type:Spec.OneGappedShape
-///.Function.reverse.class:Spec.OneGappedShape
-
-	template <typename TValue>
-	inline void
-	reverse(Shape<TValue, OneGappedShape> &me)
-	{
-	SEQAN_CHECKPOINT
-		typedef typename Value< Shape<TValue, OneGappedShape> >::Type	THValue;
-
-		unsigned temp = me.blockLen1;
-		me.blockLen1 = me.blockLen2;
-		me.blockLen2 = temp;
-		me.factor2 = _intPow((THValue)ValueSize<TValue>::VALUE, me.blockLen2);
-	}
-	
-}	// namespace seqan
+    template <typename TValue>
+    inline void
+    reverse(Shape<TValue, OneGappedShape> &me)
+    {
+    SEQAN_CHECKPOINT
+        typedef typename Value< Shape<TValue, OneGappedShape> >::Type    THValue;
+
+        unsigned temp = me.blockLen1;
+        me.blockLen1 = me.blockLen2;
+        me.blockLen2 = temp;
+        me.factor2 = _intPow((THValue)ValueSize<TValue>::VALUE, me.blockLen2);
+    }
+
+}    // namespace seqan
 
 #endif
diff --git a/seqan/index/shape_predefined.h b/seqan/index/shape_predefined.h
index c952751..2c35d75 100644
--- a/seqan/index/shape_predefined.h
+++ b/seqan/index/shape_predefined.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,89 +40,89 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	//////////////////////////////////////////////////////////////////////////////
-	// some predefined gapped shapes
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Single seed of
-	// B.Ma and J.Tromp and M.Li, 
-	// "PatternHunter: faster and more sensitive homology search"
-	// Bioinformatics 18, 2002
-	//
-	// weight:11 
-	// length:18
-	// 
-	// shape:
-	// 111010010100110111
-
-	typedef GappedShape< 
-		HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 > 
-	> ShapePatternHunter;
-
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Multiple seeds of
-	// L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
-	// WABI, 2007
-	//
-	// weight:9 
-	// length:15 
-	//
-	// shapes:
-	// 111010100100111
-	// 110100110011101
-	// 111010001011011
-	//
-	// sensitivity:
-	// 65% 0.747975		70% 0.897741
-	// 75% 0.973134		80% 0.996226
-
-	typedef GappedShape< 
-		HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 > 
-	> ShapeIlieA1;
-
-	typedef GappedShape< 
-		HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 > 
-	> ShapeIlieA2;
-
-	typedef GappedShape< 
-		HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 > 
-	> ShapeIlieA3;
-
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Multiple seeds of
-	// L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
-	// WABI 2007
-	//
-	// weight:9 
-	// length:13..23 
-	//
-	// shapes:
-	// 1110110100111
-	// 11010000110010111
-	// 11100010010000101011
-	//
-	// sensitivity:
-	// 65% 0.767413		70% 0.910949
-	// 75% 0.978558		80% 0.997357
-
-	typedef GappedShape< 
-		HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 > 
-	> ShapeIlieB1;
-
-	typedef GappedShape< 
-		HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 > 
-	> ShapeIlieB2;
-
-	typedef GappedShape< 
-		HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 > 
-	> ShapeIlieB3;
-
-
-}	// namespace seqan
+    //////////////////////////////////////////////////////////////////////////////
+    // some predefined gapped shapes
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Single seed of
+    // B.Ma and J.Tromp and M.Li,
+    // "PatternHunter: faster and more sensitive homology search"
+    // Bioinformatics 18, 2002
+    //
+    // weight:11
+    // length:18
+    //
+    // shape:
+    // 111010010100110111
+
+    typedef GappedShape<
+        HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 >
+    > ShapePatternHunter;
+
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Multiple seeds of
+    // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
+    // WABI, 2007
+    //
+    // weight:9
+    // length:15
+    //
+    // shapes:
+    // 111010100100111
+    // 110100110011101
+    // 111010001011011
+    //
+    // sensitivity:
+    // 65% 0.747975        70% 0.897741
+    // 75% 0.973134        80% 0.996226
+
+    typedef GappedShape<
+        HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 >
+    > ShapeIlieA1;
+
+    typedef GappedShape<
+        HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 >
+    > ShapeIlieA2;
+
+    typedef GappedShape<
+        HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 >
+    > ShapeIlieA3;
+
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Multiple seeds of
+    // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
+    // WABI 2007
+    //
+    // weight:9
+    // length:13..23
+    //
+    // shapes:
+    // 1110110100111
+    // 11010000110010111
+    // 11100010010000101011
+    //
+    // sensitivity:
+    // 65% 0.767413        70% 0.910949
+    // 75% 0.978558        80% 0.997357
+
+    typedef GappedShape<
+        HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 >
+    > ShapeIlieB1;
+
+    typedef GappedShape<
+        HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 >
+    > ShapeIlieB2;
+
+    typedef GappedShape<
+        HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 >
+    > ShapeIlieB3;
+
+
+}    // namespace seqan
 
 #endif
diff --git a/seqan/index/shape_threshold.h b/seqan/index/shape_threshold.h
old mode 100755
new mode 100644
index 2b268be..05dd8e4
--- a/seqan/index/shape_threshold.h
+++ b/seqan/index/shape_threshold.h
@@ -1,7 +1,8 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,9 +43,9 @@ struct ThreshQGramLemma_;
 struct ThreshExact_;
 struct ThreshHeuristic_;
 
-typedef Tag<ThreshQGramLemma_> const	ThreshQGramLemma;
-typedef Tag<ThreshHeuristic_> const		ThreshHeuristic;
-typedef Tag<ThreshExact_> const			ThreshExact;
+typedef Tag<ThreshQGramLemma_> const    ThreshQGramLemma;
+typedef Tag<ThreshHeuristic_> const        ThreshHeuristic;
+typedef Tag<ThreshExact_> const            ThreshExact;
 
 
 //////////////////////////////////////////////////////////////////////////////
@@ -57,8 +58,8 @@ typedef Tag<ThreshExact_> const			ThreshExact;
 template <typename TShape, typename TPatternLength, typename TErrors, typename TDistance>
 inline int qgramThreshold(TShape const & shape, TPatternLength patternLength, TErrors errors, TDistance const, ThreshQGramLemma const)
 {
-	int t = (int)patternLength - (int)length(shape) + 1 - (int)errors * (int)weight(shape);
-	return (t > 0)? t: 0;
+    int t = (int)patternLength - (int)length(shape) + 1 - (int)errors * (int)weight(shape);
+    return (t > 0)? t: 0;
 }
 
 
@@ -72,58 +73,58 @@ inline int qgramThreshold(TShape const & shape, TPatternLength patternLength, TE
 template <typename TShape, typename TPatternSize, typename TErrors, typename TDistance>
 int qgramThreshold(TShape const & shape, TPatternSize patternLength, TErrors errors, TDistance const, ThreshHeuristic const)
 {
-	String<unsigned char> coverage;
-	String<bool> preserved;
-	String<unsigned> ones;
-	CharString bitString;
-
-	// initialize coverage map and bitmap of preserved q-grams
-	resize(preserved, patternLength - length(shape) + 1, true);
-	resize(coverage, patternLength, 0);
-
-	shapeToString(bitString, shape);
-	for (unsigned i = 0; i < length(bitString); ++i)
-		if (bitString[i] == '1')
-		{
-			appendValue(ones, i);
-			for (unsigned j = 0; j < length(preserved); ++j)
-				++coverage[i + j];
-		}
-
-	// greedily destroy a maximum number of q-grams
-	for (; errors > 0; --errors)
-	{
-		// find position that destroys a maximum number of q-grams
-		unsigned maxCoverage = 0;
-		unsigned maxCoveragePos = 0;
-		for (unsigned i = 0; i < length(coverage); ++i)
-			if (maxCoverage < coverage[i])
-			{
-				maxCoverage = coverage[i];
-				maxCoveragePos = i;
-			}
-
-		// destroy q-grams
-		for (unsigned k = 0; k < length(ones); ++k)
-			if (ones[k] <= maxCoveragePos)
-			{
-				unsigned startPos = maxCoveragePos - ones[k];
-				if (startPos < length(preserved) && preserved[startPos])
-				{
-					preserved[startPos] = false;
-					for (unsigned l = 0; l < length(ones); ++l)
-						--coverage[startPos + ones[l]];
-				}
-			}
-	}
-
-	unsigned thresh = 0;
-	for (unsigned i = 0; i < length(preserved); ++i)
-		if (preserved[i])
-			++thresh;
-
-	return thresh;
-}	
+    String<unsigned char> coverage;
+    String<bool> preserved;
+    String<unsigned> ones;
+    CharString bitString;
+
+    // initialize coverage map and bitmap of preserved q-grams
+    resize(preserved, patternLength - length(shape) + 1, true);
+    resize(coverage, patternLength, 0);
+
+    shapeToString(bitString, shape);
+    for (unsigned i = 0; i < length(bitString); ++i)
+        if (bitString[i] == '1')
+        {
+            appendValue(ones, i);
+            for (unsigned j = 0; j < length(preserved); ++j)
+                ++coverage[i + j];
+        }
+
+    // greedily destroy a maximum number of q-grams
+    for (; errors > 0; --errors)
+    {
+        // find position that destroys a maximum number of q-grams
+        unsigned maxCoverage = 0;
+        unsigned maxCoveragePos = 0;
+        for (unsigned i = 0; i < length(coverage); ++i)
+            if (maxCoverage < coverage[i])
+            {
+                maxCoverage = coverage[i];
+                maxCoveragePos = i;
+            }
+
+        // destroy q-grams
+        for (unsigned k = 0; k < length(ones); ++k)
+            if (ones[k] <= maxCoveragePos)
+            {
+                unsigned startPos = maxCoveragePos - ones[k];
+                if (startPos < length(preserved) && preserved[startPos])
+                {
+                    preserved[startPos] = false;
+                    for (unsigned l = 0; l < length(ones); ++l)
+                        --coverage[startPos + ones[l]];
+                }
+            }
+    }
+
+    unsigned thresh = 0;
+    for (unsigned i = 0; i < length(preserved); ++i)
+        if (preserved[i])
+            ++thresh;
+
+    return thresh;
+}
 
 
 
@@ -132,286 +133,286 @@ int qgramThreshold(TShape const & shape, TPatternSize patternLength, TErrors err
 //____________________________________________________________________________
 // Extensions to SeqAn
 
-	struct ErrorAlphabet_ {};
-	typedef SimpleType<unsigned char, ErrorAlphabet_> ErrorAlphabet;
+    struct ErrorAlphabet_ {};
+    typedef SimpleType<unsigned char, ErrorAlphabet_> ErrorAlphabet;
 
-	template <> struct ValueSize< ErrorAlphabet >    { enum { VALUE = 4 }; };
-	template <> struct BitsPerValue< ErrorAlphabet > { enum { VALUE = 2 }; };
+    template <> struct ValueSize< ErrorAlphabet >    { enum { VALUE = 4 }; };
+    template <> struct BitsPerValue< ErrorAlphabet > { enum { VALUE = 2 }; };
 
-	template <typename T = void>
-	struct TranslateTableErrorToAscii_
-	{
-		static char const VALUE[4];
-	};
-	template <typename T>
-	char const TranslateTableErrorToAscii_<T>::VALUE[4] = {'.', 'M', 'I', 'D'};
+    template <typename T = void>
+    struct TranslateTableErrorToChar_
+    {
+        static char const VALUE[4];
+    };
+    template <typename T>
+    char const TranslateTableErrorToChar_<T>::VALUE[4] = {'.', 'M', 'I', 'D'};
 
-	inline void assign(Ascii & c_target, 
-					   ErrorAlphabet const & source)
-	{
-	SEQAN_CHECKPOINT
-		c_target = TranslateTableErrorToAscii_<>::VALUE[source.value];
-	}
+    inline void assign(char & c_target,
+                       ErrorAlphabet const & source)
+    {
+    SEQAN_CHECKPOINT
+        c_target = TranslateTableErrorToChar_<>::VALUE[source.value];
+    }
 
 
-	struct ErrorPackedString;
+    struct ErrorPackedString;
 
-	template <typename TValue>
-	struct Host<String<TValue, Packed<ErrorPackedString> > >
-	{
-		typedef String<__int64, Array<1> > Type;
-	};
+    template <typename TValue>
+    struct Host<String<TValue, Packed<ErrorPackedString> > >
+    {
+        typedef String<__int64, Array<1> > Type;
+    };
 
-	template <typename TValue>
-	struct Host<String<TValue, Packed<ErrorPackedString> > const >
-	{
-		typedef String<__int64, Array<1> > const Type;
-	};
+    template <typename TValue>
+    struct Host<String<TValue, Packed<ErrorPackedString> > const >
+    {
+        typedef String<__int64, Array<1> > const Type;
+    };
 
 
 //____________________________________________________________________________
 
-	enum ErrorType {
-		SEQAN_MATCH    = 0,
-		SEQAN_MISMATCH = 1,
-		SEQAN_INSERT   = 2,
-		SEQAN_DELETE   = 3
-	};
-	
-	template <typename TDistance>
-	struct ErrorTypes {
-		enum { VALUE = 4 };
-	};
-
-	template <>
-	struct ErrorTypes<HammingDistance> {
-		enum { VALUE = 2 };
-	};
-
-	// descriptor of the modification pattern
-	// in the recursion it modifies the last q-gram of a read sequence
-	template <typename TDistance, typename TFloat>
-	struct SensitivityDPState_
-	{
-		enum { TRANSITIONS = ErrorTypes<TDistance>::VALUE };
-		TFloat prob;				// probability of this state
-		int transition[ErrorTypes<TDistance>::VALUE];	// returns previous state
-		unsigned char len;			// length of this pattern (shapeSpan-errors <= this value <= shapeSpan+errors)
-		unsigned char errors:4;		// errors in this state
-		bool skipFirst:1;			// skip this pattern if it is the first
-		bool skipLast:1;			// skip this pattern if it is the last
-		bool intermediate:1;		// this is an intermediate result (beginning with INSERT)
-		bool qgramHit:1;			// is this a q-gram hit? (result of the former delta function)
-	}
+    enum ErrorType {
+        SEQAN_MATCH    = 0,
+        SEQAN_MISMATCH = 1,
+        SEQAN_INSERT   = 2,
+        SEQAN_DELETE   = 3
+    };
+
+    template <typename TDistance>
+    struct ErrorTypes {
+        enum { VALUE = 4 };
+    };
+
+    template <>
+    struct ErrorTypes<HammingDistance> {
+        enum { VALUE = 2 };
+    };
+
+    // descriptor of the modification pattern
+    // in the recursion it modifies the last q-gram of a read sequence
+    template <typename TDistance, typename TFloat>
+    struct SensitivityDPState_
+    {
+        enum { TRANSITIONS = ErrorTypes<TDistance>::VALUE };
+        TFloat prob;                // probability of this state
+        int transition[ErrorTypes<TDistance>::VALUE];    // returns previous state
+        unsigned char len;            // length of this pattern (shapeSpan-errors <= this value <= shapeSpan+errors)
+        unsigned char errors:4;        // errors in this state
+        bool skipFirst:1;            // skip this pattern if it is the first
+        bool skipLast:1;            // skip this pattern if it is the last
+        bool intermediate:1;        // this is an intermediate result (beginning with INSERT)
+        bool qgramHit:1;            // is this a q-gram hit? (result of the former delta function)
+    }
 #ifndef PLATFORM_WINDOWS
-	__attribute__((packed))
+    __attribute__((packed))
 #endif
-	;
-
-	// descriptor of the modification pattern
-	// in the recursion it modifies the last q-gram of a read sequence
-	template <typename TDistance>
-	struct ThreshDPState_
-	{
-		enum { TRANSITIONS = ErrorTypes<TDistance>::VALUE };
-		int transition[ErrorTypes<TDistance>::VALUE];	// returns previous state
-		unsigned char len;			// length of this pattern (shapeSpan-errors <= this value <= shapeSpan+errors)
-		unsigned char errors:4;		// errors in this state
-		bool skipFirst:1;			// skip this pattern if it is the first
-		bool skipLast:1;			// skip this pattern if it is the last
-		bool intermediate:1;		// this is an intermediate result (beginning with INSERT)
-		bool qgramHit:1;			// is this a q-gram hit? (result of the former delta function)
-	}
+    ;
+
+    // descriptor of the modification pattern
+    // in the recursion it modifies the last q-gram of a read sequence
+    template <typename TDistance>
+    struct ThreshDPState_
+    {
+        enum { TRANSITIONS = ErrorTypes<TDistance>::VALUE };
+        int transition[ErrorTypes<TDistance>::VALUE];    // returns previous state
+        unsigned char len;            // length of this pattern (shapeSpan-errors <= this value <= shapeSpan+errors)
+        unsigned char errors:4;        // errors in this state
+        bool skipFirst:1;            // skip this pattern if it is the first
+        bool skipLast:1;            // skip this pattern if it is the last
+        bool intermediate:1;        // this is an intermediate result (beginning with INSERT)
+        bool qgramHit:1;            // is this a q-gram hit? (result of the former delta function)
+    }
 #ifndef PLATFORM_WINDOWS
-	__attribute__((packed))
+    __attribute__((packed))
 #endif
-	;
+    ;
 
-#ifdef PLATFORM_WINDOWS
+#if defined(PLATFORM_WINDOWS) | defined(PLATFORM_CUDA)
 
-	template<typename TValue>
-	inline bool isNan(TValue value)
-	{
-		return value != value;
-	}
+    template<typename TValue>
+    inline bool isNan(TValue value)
+    {
+        return value != value;
+    }
 
-	template<typename TValue>
-	inline bool isInf(TValue value)
-	{
-		return value == log(0.0);
-	}
+    template<typename TValue>
+    inline bool isInf(TValue value)
+    {
+        return value == log(0.0);
+    }
 
 #else
 
-	template<typename TValue>
-	inline bool isNan(TValue value)
-	{
-		return std::isnan(value);
-	}
+    template<typename TValue>
+    inline bool isNan(TValue value)
+    {
+        return std::isnan(value);
+    }
 
-	template<typename TValue>
-	inline bool isInf(TValue value)
-	{
-		return std::isinf(value);
-	}
+    template<typename TValue>
+    inline bool isInf(TValue value)
+    {
+        return std::isinf(value);
+    }
 
 #endif
 
 
-	template <typename TValue>
-	inline long double
-	_transform(TValue a)
-	{
+    template <typename TValue>
+    inline long double
+    _transform(TValue a)
+    {
 #ifdef USE_LOGVALUES
-		return log(a);
+        return log(a);
 #else
-		return a;
+        return a;
 #endif
-	}
+    }
 
-	template <typename TValue>
-	inline long double
-	_transformBack(TValue a)
-	{
+    template <typename TValue>
+    inline long double
+    _transformBack(TValue a)
+    {
 #ifdef USE_LOGVALUES
-		return exp(a);
+        return exp(a);
 #else
-		return a;
+        return a;
 #endif
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Returns the sum of two probability values in log space
-	template <typename TValue>
-	inline void
-	_probAdd(TValue &a, TValue b)
-	{
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Returns the sum of two probability values in log space
+    template <typename TValue>
+    inline void
+    _probAdd(TValue &a, TValue b)
+    {
 #ifdef USE_LOGVALUES
-		if (isInf(a)) {
-			a = b;
-			return;
-		}
-		if (isInf(b)) return;
-		if (isNan(a + log(1 + exp(b - a)))) return;
-		a += log(1 + exp(b - a));
+        if (isInf(a)) {
+            a = b;
+            return;
+        }
+        if (isInf(b)) return;
+        if (isNan(a + log(1 + exp(b - a)))) return;
+        a += log(1 + exp(b - a));
 #else
-		a += b;
+        a += b;
 #endif
-	}
+    }
 
-	template <typename TValue>
-	inline TValue
-	_probMul(TValue a, TValue b)
-	{
+    template <typename TValue>
+    inline TValue
+    _probMul(TValue a, TValue b)
+    {
 #ifdef USE_LOGVALUES
-		return a + b;
+        return a + b;
 #else
-		return a * b;
+        return a * b;
 #endif
-	}
+    }
 
-	template <typename TValue>
-	inline TValue
-	_probDiv(TValue a, TValue b)
-	{
+    template <typename TValue>
+    inline TValue
+    _probDiv(TValue a, TValue b)
+    {
 #ifdef USE_LOGVALUES
-		return a - b;
+        return a - b;
 #else
-		return a / b;
+        return a / b;
 #endif
-	}
+    }
 
 
 struct ErrorPatternLess
 {
-	template <typename TPattern>
-	bool operator() (TPattern const &a, TPattern const &b) const
-	{
-		typedef typename Iterator<TPattern const>::Type TIter;
-		TIter itA = end(a, Standard());
-		TIter itB = end(b, Standard());
-		TIter itEnd;
-		if (length(a) <= length(b))
-		{
-			itEnd = begin(a, Standard());
-			for (; itA != itEnd;) 
-			{
-				--itA;
-				--itB;
-				if (*itA < *itB) return true;
-				if (*itA > *itB) return false;
-			}
-			return false;
-		} else 
-		{
-			itEnd = begin(b, Standard());
-			for (; itB != itEnd;) 
-			{
-				--itA;
-				--itB;
-				if (*itA < *itB) return true;
-				if (*itA > *itB) return false;
-			}
-			return true;
-		}
-	}
+    template <typename TPattern>
+    bool operator() (TPattern const &a, TPattern const &b) const
+    {
+        typedef typename Iterator<TPattern const>::Type TIter;
+        TIter itA = end(a, Standard());
+        TIter itB = end(b, Standard());
+        TIter itEnd;
+        if (length(a) <= length(b))
+        {
+            itEnd = begin(a, Standard());
+            for (; itA != itEnd;)
+            {
+                --itA;
+                --itB;
+                if (*itA < *itB) return true;
+                if (*itA > *itB) return false;
+            }
+            return false;
+        } else
+        {
+            itEnd = begin(b, Standard());
+            for (; itB != itEnd;)
+            {
+                --itA;
+                --itB;
+                if (*itA < *itB) return true;
+                if (*itA > *itB) return false;
+            }
+            return true;
+        }
+    }
 };
 
 template <typename TPatternStore, typename TPattern>
-inline int 
+inline int
 _getErrorPatternIndex(TPatternStore const &patternStore, TPattern const &pattern)
 {
-	typedef typename Iterator<TPatternStore const>::Type TIter;
-	TIter lb = std::lower_bound(begin(patternStore, Standard()), end(patternStore, Standard()), pattern, ErrorPatternLess());
-	TIter invalid = end(patternStore, Standard());
-	if (lb != invalid && *lb == pattern) {
-//		std::cout << pattern;
-		return lb - begin(patternStore, Standard());
-	} else {
-/*		std::cerr << "  !Pattern Not Found! " << pattern;
-		if (lb != invalid) std::cerr << "\tnext is " << *lb;
-		std::cerr << std::endl;
-*/		return -1;
-	}
+    typedef typename Iterator<TPatternStore const>::Type TIter;
+    TIter lb = std::lower_bound(begin(patternStore, Standard()), end(patternStore, Standard()), pattern, ErrorPatternLess());
+    TIter invalid = end(patternStore, Standard());
+    if (lb != invalid && *lb == pattern) {
+//        std::cout << pattern;
+        return lb - begin(patternStore, Standard());
+    } else {
+/*        std::cerr << "  !Pattern Not Found! " << pattern;
+        if (lb != invalid) std::cerr << "\tnext is " << *lb;
+        std::cerr << std::endl;
+*/        return -1;
+    }
 }
 
 // Cut 1 read character and trailing INSERTs of the pattern
 template <typename TPattern>
-inline int 
+inline int
 _cutErrorPattern(TPattern &_pattern)
 {
-	typedef typename Iterator<TPattern const, Standard>::Type TIter;
-	TPattern const & pattern = const_cast<TPattern const&>(_pattern);
-	TIter it = end(pattern, Standard());
-	int cuttedErrors = -2;
-
-	// cut trailing INSERTs
-	do {
-		--it;
-		++cuttedErrors;
-	} while ((int)getValue(it) == SEQAN_INSERT);
-
-	// cut non INSERT
-	if ((int)getValue(it) != SEQAN_MATCH)
-		++cuttedErrors;
-
-	//  and all adjacent INSERTs
-	do {
-		--it;
-		++cuttedErrors;
-	} while ((int)getValue(it) == SEQAN_INSERT);
-
-	resize(_pattern, 1 + (it - begin(pattern, Standard())));
-	return cuttedErrors;
+    typedef typename Iterator<TPattern const, Standard>::Type TIter;
+    TPattern const & pattern = const_cast<TPattern const&>(_pattern);
+    TIter it = end(pattern, Standard());
+    int cuttedErrors = -2;
+
+    // cut trailing INSERTs
+    do {
+        --it;
+        ++cuttedErrors;
+    } while ((int)getValue(it) == SEQAN_INSERT);
+
+    // cut non INSERT
+    if ((int)getValue(it) != SEQAN_MATCH)
+        ++cuttedErrors;
+
+    //  and all adjacent INSERTs
+    do {
+        --it;
+        ++cuttedErrors;
+    } while ((int)getValue(it) == SEQAN_INSERT);
+
+    resize(_pattern, 1 + (it - begin(pattern, Standard())));
+    return cuttedErrors;
 }
 
 template < typename TLogErrorDistr >
-typename Value<TLogErrorDistr>::Type 
+typename Value<TLogErrorDistr>::Type
 _getProb(TLogErrorDistr const &logError, int errorType, int readPos)
 {
-	int maxN = length(logError) / 4;
-	SEQAN_ASSERT(readPos >= 0 && readPos < maxN);
-	return logError[maxN * (int)errorType + readPos];
+    int maxN = length(logError) / 4;
+    SEQAN_ASSERT(readPos >= 0 && readPos < maxN);
+    return logError[maxN * (int)errorType + readPos];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -420,15 +421,15 @@ template < typename TState, typename TLogErrorDistr, typename TPattern >
 inline void
 _getLastPatternProb(TState &state, TLogErrorDistr const &logError, TPattern const &pattern, int span)
 {
-	int maxN = length(logError) / 4;
-	typename Value<TLogErrorDistr>::Type prob = _transform(1.0);
-	for (int i = 0, j = 0; j < (int)length(pattern); ++j)
-	{
-		prob = _probMul(prob, _getProb(logError, getValue(pattern, j), maxN - span + i));
-		if ((int)getValue(pattern, j) != SEQAN_INSERT)
-			++i;
-	}
-	state.prob = prob;
+    int maxN = length(logError) / 4;
+    typename Value<TLogErrorDistr>::Type prob = _transform(1.0);
+    for (int i = 0, j = 0; j < (int)length(pattern); ++j)
+    {
+        prob = _probMul(prob, _getProb(logError, getValue(pattern, j), maxN - span + i));
+        if ((int)getValue(pattern, j) != SEQAN_INSERT)
+            ++i;
+    }
+    state.prob = prob;
 }
 
 template < typename TState, typename TPattern >
@@ -441,631 +442,631 @@ _getLastPatternProb(TState &, Nothing const &, TPattern const &, int)
 //////////////////////////////////////////////////////////////////////////////
 // Initialize states-string for edit/hamming-distance filters
 template <
-	typename TStateString,
-	typename TShape,
-	typename TLogErrorDistr,
-	typename TDistance >
+    typename TStateString,
+    typename TShape,
+    typename TLogErrorDistr,
+    typename TDistance >
 void initPatterns(
-	TStateString &states,				// resulting states-string
-	TShape const &bitShape,				// bit-string of the shape
-	int maxErrors,						// allowed errors per pattern
-	TLogErrorDistr const &logError,		// error distribution (Nothing or string of 4*patternLen floats)
-	TDistance,							// enumerate hamming or edit distance patterns
-	bool optionMinOutput)				// omit output
+    TStateString &states,                // resulting states-string
+    TShape const &bitShape,                // bit-string of the shape
+    int maxErrors,                        // allowed errors per pattern
+    TLogErrorDistr const &logError,        // error distribution (Nothing or string of 4*patternLen floats)
+    TDistance,                            // enumerate hamming or edit distance patterns
+    bool optionMinOutput)                // omit output
 {
 #ifndef DEBUG_RECOG_DP
-//	typedef String<ErrorAlphabet, Packed<ErrorPackedString> >	TPattern;
-	typedef String<ErrorAlphabet>								TPattern;
+//    typedef String<ErrorAlphabet, Packed<ErrorPackedString> >    TPattern;
+    typedef String<ErrorAlphabet>                                TPattern;
 #endif
 
-	typedef typename Iterator<TPattern, Standard>::Type			TIter;
-	typedef typename Value<TStateString>::Type					TState;
-	
-	ErrorType lastErrorType = (IsSameType<TDistance, HammingDistance>::VALUE)? SEQAN_MISMATCH: SEQAN_DELETE;
+    typedef typename Iterator<TPattern, Standard>::Type            TIter;
+    typedef typename Value<TStateString>::Type                    TState;
+
+    ErrorType lastErrorType = (IsSameType<TDistance, HammingDistance>::VALUE)? SEQAN_MISMATCH: SEQAN_DELETE;
 
-	SEQAN_ASSERT_EQ(SEQAN_MATCH, 0);
-	SEQAN_ASSERT((IsSameType<TLogErrorDistr,Nothing>::VALUE || (length(logError) % 4) == 0u));
+    SEQAN_ASSERT_EQ(SEQAN_MATCH, 0);
+    SEQAN_ASSERT((IsSameType<TLogErrorDistr,Nothing>::VALUE || (length(logError) % 4) == 0u));
 
 #ifndef DEBUG_RECOG_DP
-	String<TPattern> patternStore;
+    String<TPattern> patternStore;
 #endif
 
-	// a modifier is a pair of position and error type
-	String<Pair<int, ErrorType> > mods;
-	resize(mods, maxErrors, Pair<int, ErrorType> (0, SEQAN_MATCH));
-
-	TPattern pattern;
-	int span = length(bitShape);
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Enumerate all edit-modification patterns with up to k errors
-	if (maxErrors == 0) 
-	{
-		resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH);
-		appendValue(patternStore, pattern, Generous());
-	}
-	else
-	do 
-	{
-		clear(pattern);
-		resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH);
-
-		// place errors in the pattern
-		bool skip = false;
-		for (int i = 0; (i < maxErrors) && !skip; ++i)
-		{
-//			std::cout << mods[i].i1 << " " << (ErrorAlphabet)mods[i].i2 << "\t";
-			switch (mods[i].i2)
-			{
-			case SEQAN_MISMATCH:
-			case SEQAN_DELETE:
-				if (pattern[mods[i].i1] != (ErrorAlphabet)SEQAN_MATCH)
-				{
-					skip = true;
-					break;
-				}
-				pattern[mods[i].i1] = (ErrorAlphabet)mods[i].i2;
-				break;
-
-			case SEQAN_INSERT:
-				insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT);
-				break;
-				
-			case SEQAN_MATCH:
-				break;
-			}
-		}
-
-		// remove redundant patterns
-		if (!skip) 
-		{
-			TIter it = begin(pattern, Standard());
-			TIter itEnd = end(pattern, Standard());
-			int left = getValue(it);
-			int right;
-			for (++it; (it != itEnd) && !skip; ++it, left = right) 
-			{
-				right = getValue(it);
+    // a modifier is a pair of position and error type
+    String<Pair<int, ErrorType> > mods;
+    resize(mods, maxErrors, Pair<int, ErrorType> (0, SEQAN_MATCH));
+
+    TPattern pattern;
+    int span = length(bitShape);
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Enumerate all edit-modification patterns with up to k errors
+    if (maxErrors == 0)
+    {
+        resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH);
+        appendValue(patternStore, pattern, Generous());
+    }
+    else
+    do
+    {
+        clear(pattern);
+        resize(pattern, span, (ErrorAlphabet)SEQAN_MATCH);
+
+        // place errors in the pattern
+        bool skip = false;
+        for (int i = 0; (i < maxErrors) && !skip; ++i)
+        {
+//            std::cout << mods[i].i1 << " " << (ErrorAlphabet)mods[i].i2 << "\t";
+            switch (mods[i].i2)
+            {
+            case SEQAN_MISMATCH:
+            case SEQAN_DELETE:
+                if (pattern[mods[i].i1] != (ErrorAlphabet)SEQAN_MATCH)
+                {
+                    skip = true;
+                    break;
+                }
+                pattern[mods[i].i1] = (ErrorAlphabet)mods[i].i2;
+                break;
+
+            case SEQAN_INSERT:
+                insertValue(pattern, mods[i].i1, (ErrorAlphabet)SEQAN_INSERT);
+                break;
+
+            case SEQAN_MATCH:
+                break;
+            }
+        }
+
+        // remove redundant patterns
+        if (!skip)
+        {
+            TIter it = begin(pattern, Standard());
+            TIter itEnd = end(pattern, Standard());
+            int left = getValue(it);
+            int right;
+            for (++it; (it != itEnd) && !skip; ++it, left = right)
+            {
+                right = getValue(it);
 
 #ifdef NON_REDUNDANT
-				if (left == SEQAN_MISMATCH && right == SEQAN_DELETE) 
-					skip = true;	// MISMATCH before DELETE is DELETE before MISMATCH (already enumerated)
+                if (left == SEQAN_MISMATCH && right == SEQAN_DELETE)
+                    skip = true;    // MISMATCH before DELETE is DELETE before MISMATCH (already enumerated)
+
+                if (left == SEQAN_MISMATCH && right == SEQAN_INSERT)
+                    skip = true;    // MISMATCH before INSERT is INSERT before MISMATCH (already enumerated)
 
-				if (left == SEQAN_MISMATCH && right == SEQAN_INSERT) 
-					skip = true;	// MISMATCH before INSERT is INSERT before MISMATCH (already enumerated)
+                if (left == SEQAN_INSERT && right == SEQAN_DELETE)
+                    skip = true;    // INSERT before DELETE is one MISMATCH (already enumerated)
 
-				if (left == SEQAN_INSERT && right == SEQAN_DELETE) 
-					skip = true;	// INSERT before DELETE is one MISMATCH (already enumerated)
-				
-				if (left == SEQAN_DELETE && right == SEQAN_INSERT) 
-					skip = true;	// DELETE before INSERT is one MISMATCH (already enumerated)
+                if (left == SEQAN_DELETE && right == SEQAN_INSERT)
+                    skip = true;    // DELETE before INSERT is one MISMATCH (already enumerated)
 #endif
-			}
-			if (left == SEQAN_INSERT)
-				skip = true;		// no trailing INSERT allowed
-		}
-
-		if (!skip)
-		{
-			appendValue(patternStore, pattern, Generous());
-//			std::cout << pattern << std::endl;
-		}
-
-		// reposition modifiers
-		int i = 0;
-		for (; i < maxErrors; ++i)
-		{
-			if (mods[i].i2 == SEQAN_MATCH) continue;
-			int endPos = (mods[i].i2 == SEQAN_INSERT)? span + 1: span;
-			if (++mods[i].i1 < endPos) 
-			{
-				for(--i; i >= 0; --i)
-					mods[i].i1 = mods[i + 1].i1;
-				break;
-			}
-		}
-
-		if (i < maxErrors) continue;
-
-		for (i = 0; i < maxErrors; ++i)
-			mods[i].i1 = 0;
-		
-		// next state combination
-		for (i = 0; i < maxErrors; ++i)
-		{
-			if (mods[i].i2 == lastErrorType) continue;
-			mods[i].i2 = (ErrorType)(mods[i].i2 + 1);
-			for(--i; i >= 0; --i)
-				mods[i].i2 = SEQAN_MISMATCH;
-			break;
-		}
-		
-		if (i == maxErrors) break;
-
-	} while (true);
-	
-	if (!optionMinOutput) 
-		std::cout << "Stored " << length(patternStore) << " modification patterns" << std::flush;
-
-	reserve(patternStore, length(patternStore), Exact());
-	std::sort(begin(patternStore, Standard()), end(patternStore, Standard()), ErrorPatternLess());
-	for (int p = 1; p < (int)length(patternStore); ++p)
-	{
-		if (patternStore[p-1] == patternStore[p])
-			std::cerr << "  !Found duplicate! " << patternStore[p] << std::endl;
-	}
-
-	if (!optionMinOutput) 
-		std::cout << " and sorted them." << std::endl;
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Calculate transitions
-	resize(states, length(patternStore));
-	for (int p = 0; p < (int)length(patternStore); ++p)
-	{
-		pattern = patternStore[p];
-		TState &state = states[p];
-
-//		std::cout << pattern << "\t";
-
-		// count errors of current pattern
-		int errors = 0;
-		for (int i = 0; i < (int)length(pattern); ++i)
-			if ((int)getValue(pattern, i) != SEQAN_MATCH)
-				++errors;
-				
-		state.len = length(pattern);
-		state.errors = errors;
-		state.intermediate = (int)getValue(pattern, 0) == SEQAN_INSERT;
-		_getLastPatternProb(state, logError, pattern, span);
-//		std::cout << pattern << "\t";
-
-		state.skipFirst = false;
-		state.skipLast = false;
+            }
+            if (left == SEQAN_INSERT)
+                skip = true;        // no trailing INSERT allowed
+        }
+
+        if (!skip)
+        {
+            appendValue(patternStore, pattern, Generous());
+//            std::cout << pattern << std::endl;
+        }
+
+        // reposition modifiers
+        int i = 0;
+        for (; i < maxErrors; ++i)
+        {
+            if (mods[i].i2 == SEQAN_MATCH) continue;
+            int endPos = (mods[i].i2 == SEQAN_INSERT)? span + 1: span;
+            if (++mods[i].i1 < endPos)
+            {
+                for(--i; i >= 0; --i)
+                    mods[i].i1 = mods[i + 1].i1;
+                break;
+            }
+        }
+
+        if (i < maxErrors) continue;
+
+        for (i = 0; i < maxErrors; ++i)
+            mods[i].i1 = 0;
+
+        // next state combination
+        for (i = 0; i < maxErrors; ++i)
+        {
+            if (mods[i].i2 == lastErrorType) continue;
+            mods[i].i2 = (ErrorType)(mods[i].i2 + 1);
+            for(--i; i >= 0; --i)
+                mods[i].i2 = SEQAN_MISMATCH;
+            break;
+        }
+
+        if (i == maxErrors) break;
+
+    } while (true);
+
+    if (!optionMinOutput)
+        std::cout << "Stored " << length(patternStore) << " modification patterns" << std::flush;
+
+    reserve(patternStore, length(patternStore), Exact());
+    std::sort(begin(patternStore, Standard()), end(patternStore, Standard()), ErrorPatternLess());
+    for (int p = 1; p < (int)length(patternStore); ++p)
+    {
+        if (patternStore[p-1] == patternStore[p])
+            std::cerr << "  !Found duplicate! " << patternStore[p] << std::endl;
+    }
+
+    if (!optionMinOutput)
+        std::cout << " and sorted them." << std::endl;
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Calculate transitions
+    resize(states, length(patternStore));
+    for (int p = 0; p < (int)length(patternStore); ++p)
+    {
+        pattern = patternStore[p];
+        TState &state = states[p];
+
+//        std::cout << pattern << "\t";
+
+        // count errors of current pattern
+        int errors = 0;
+        for (int i = 0; i < (int)length(pattern); ++i)
+            if ((int)getValue(pattern, i) != SEQAN_MATCH)
+                ++errors;
+
+        state.len = length(pattern);
+        state.errors = errors;
+        state.intermediate = (int)getValue(pattern, 0) == SEQAN_INSERT;
+        _getLastPatternProb(state, logError, pattern, span);
+//        std::cout << pattern << "\t";
+
+        state.skipFirst = false;
+        state.skipLast = false;
 
 #ifdef NON_REDUNDANT
-		int err = 0, del = 0;
-		for (int j = 0; j < (int)length(pattern); ++j)
-		{
-			switch ((int)getValue(pattern, j)) {
-				case SEQAN_MATCH:
-					++del;
-					break;
-
-				case SEQAN_DELETE:
-					++del;
-	
-				case SEQAN_INSERT:
-					++err;
-					break;
-
-				default:;
-			}
-			if (del > 0 && del <= err)
-				state.skipFirst = true;
-		}
-		err = del = 0;
-		for (int j = (int)length(pattern) - 1; j >= 0; --j)
-		{
-			switch ((int)getValue(pattern, j)) {
-				case SEQAN_MATCH:
-					++del;
-					break;
-
-				case SEQAN_DELETE:
-					++del;
-	
-				case SEQAN_INSERT:
-					++err;
-					break;
-			
-				default:;
-			}
-			if (del > 0 && del <= err)
-				state.skipLast = true;
-		}
+        int err = 0, del = 0;
+        for (int j = 0; j < (int)length(pattern); ++j)
+        {
+            switch ((int)getValue(pattern, j)) {
+                case SEQAN_MATCH:
+                    ++del;
+                    break;
+
+                case SEQAN_DELETE:
+                    ++del;
+
+                case SEQAN_INSERT:
+                    ++err;
+                    break;
+
+                default:;
+            }
+            if (del > 0 && del <= err)
+                state.skipFirst = true;
+        }
+        err = del = 0;
+        for (int j = (int)length(pattern) - 1; j >= 0; --j)
+        {
+            switch ((int)getValue(pattern, j)) {
+                case SEQAN_MATCH:
+                    ++del;
+                    break;
+
+                case SEQAN_DELETE:
+                    ++del;
+
+                case SEQAN_INSERT:
+                    ++err;
+                    break;
+
+                default:;
+            }
+            if (del > 0 && del <= err)
+                state.skipLast = true;
+        }
 #else
-		state.skipFirst = (int)getValue(pattern, 0) == SEQAN_INSERT;
+        state.skipFirst = (int)getValue(pattern, 0) == SEQAN_INSERT;
 #endif
-		// apply pattern to read q-gram
-		// and check if shape is recognized in the genome
-		state.qgramHit = false;
-		int delta = 0;
-		for (int j = 0, readPos = 0, genomePos = 0; j < (int)length(pattern); ++j) 
-		{
-			switch ((int)getValue(pattern, j))
-			{
-				case SEQAN_MATCH:
-					if (readPos == 0) {
-						// SEQAN_ASSERT_EQ(bitShape[0], '1')
-						delta = genomePos;
-						state.qgramHit = true;
-					} else
-						if (bitShape[readPos] == '1')
-							state.qgramHit &= (readPos + delta == genomePos);
-//					std::cout << readPos;
-					++readPos; ++genomePos;
-					break;
-				case SEQAN_MISMATCH:
-					// was it a relevant read position?
-					if (bitShape[readPos] == '1')
-						state.qgramHit = false;
-//					std::cout << 'x';
-					++readPos; ++genomePos;
-					break;
-				case SEQAN_DELETE:
-					// was it a relevant read position?
-					if (bitShape[readPos] == '1')
-						state.qgramHit = false;
-					++readPos;
-					break;
-				case SEQAN_INSERT:
-					++genomePos;
-//					std::cout << 'x';
-			}				
-		}
-//		std::cout << std::endl;
-
-		// prepend INSERT
-		++errors;
-		insertValue(pattern, 0, SEQAN_INSERT);
-		if ((int)SEQAN_INSERT < (int)state.TRANSITIONS)
-		{
-			if (errors <= maxErrors)
-				state.transition[SEQAN_INSERT] = _getErrorPatternIndex(patternStore, pattern);
-			else
-				state.transition[SEQAN_INSERT] = -1;
-		}
-
-		// prepend MISMATCH and cut INSERTS
-		errors -= _cutErrorPattern(pattern);
-		if ((int)SEQAN_MISMATCH < (int)state.TRANSITIONS)
-		{
-			pattern[0] = SEQAN_MISMATCH;
-			if (errors <= maxErrors)
-				state.transition[SEQAN_MISMATCH] = _getErrorPatternIndex(patternStore, pattern);
-			else
-				state.transition[SEQAN_MISMATCH] = -1;
-		}
-		
-		// prepend DELETE
-		if ((int)SEQAN_DELETE < (int)state.TRANSITIONS)
-		{
-			pattern[0] = SEQAN_DELETE;
-			if (errors <= maxErrors)
-				state.transition[SEQAN_DELETE] = _getErrorPatternIndex(patternStore, pattern);
-			else
-				state.transition[SEQAN_DELETE] = -1;
-		}
-
-		// prepend MATCH
-		if ((int)SEQAN_MATCH < (int)state.TRANSITIONS)
-		{
-			--errors;
-			pattern[0] = SEQAN_MATCH;
-			if (errors <= maxErrors)
-				state.transition[SEQAN_MATCH] = _getErrorPatternIndex(patternStore, pattern);
-			else
-				state.transition[SEQAN_MATCH] = -1;
-		}
-/*		
-		std::cout << "\t" << state.errors;
-		std::cout << "\t" << state.qgramHit;
-		std::cout << "\t" << state.leftError;
-		std::cout << "\t" << state.rightError;
-		std::cout << "\t" << state.transition[0];
-		std::cout << "\t" << state.transition[1];
-		std::cout << "\t" << state.transition[2];
-		std::cout << "\t" << state.transition[3];
-		std::cout << std::endl;
-*/	}
-	if (!optionMinOutput) 
-		std::cout << "Preprocessing finished." << std::endl;
+        // apply pattern to read q-gram
+        // and check if shape is recognized in the genome
+        state.qgramHit = false;
+        int delta = 0;
+        for (int j = 0, readPos = 0, genomePos = 0; j < (int)length(pattern); ++j)
+        {
+            switch ((int)getValue(pattern, j))
+            {
+                case SEQAN_MATCH:
+                    if (readPos == 0) {
+                        // SEQAN_ASSERT_EQ(bitShape[0], '1')
+                        delta = genomePos;
+                        state.qgramHit = true;
+                    } else
+                        if (bitShape[readPos] == '1')
+                            state.qgramHit &= (readPos + delta == genomePos);
+//                    std::cout << readPos;
+                    ++readPos; ++genomePos;
+                    break;
+                case SEQAN_MISMATCH:
+                    // was it a relevant read position?
+                    if (bitShape[readPos] == '1')
+                        state.qgramHit = false;
+//                    std::cout << 'x';
+                    ++readPos; ++genomePos;
+                    break;
+                case SEQAN_DELETE:
+                    // was it a relevant read position?
+                    if (bitShape[readPos] == '1')
+                        state.qgramHit = false;
+                    ++readPos;
+                    break;
+                case SEQAN_INSERT:
+                    ++genomePos;
+//                    std::cout << 'x';
+            }
+        }
+//        std::cout << std::endl;
+
+        // prepend INSERT
+        ++errors;
+        insertValue(pattern, 0, SEQAN_INSERT);
+        if ((int)SEQAN_INSERT < (int)state.TRANSITIONS)
+        {
+            if (errors <= maxErrors)
+                state.transition[SEQAN_INSERT] = _getErrorPatternIndex(patternStore, pattern);
+            else
+                state.transition[SEQAN_INSERT] = -1;
+        }
+
+        // prepend MISMATCH and cut INSERTS
+        errors -= _cutErrorPattern(pattern);
+        if ((int)SEQAN_MISMATCH < (int)state.TRANSITIONS)
+        {
+            pattern[0] = SEQAN_MISMATCH;
+            if (errors <= maxErrors)
+                state.transition[SEQAN_MISMATCH] = _getErrorPatternIndex(patternStore, pattern);
+            else
+                state.transition[SEQAN_MISMATCH] = -1;
+        }
+
+        // prepend DELETE
+        if ((int)SEQAN_DELETE < (int)state.TRANSITIONS)
+        {
+            pattern[0] = SEQAN_DELETE;
+            if (errors <= maxErrors)
+                state.transition[SEQAN_DELETE] = _getErrorPatternIndex(patternStore, pattern);
+            else
+                state.transition[SEQAN_DELETE] = -1;
+        }
+
+        // prepend MATCH
+        if ((int)SEQAN_MATCH < (int)state.TRANSITIONS)
+        {
+            --errors;
+            pattern[0] = SEQAN_MATCH;
+            if (errors <= maxErrors)
+                state.transition[SEQAN_MATCH] = _getErrorPatternIndex(patternStore, pattern);
+            else
+                state.transition[SEQAN_MATCH] = -1;
+        }
+/*
+        std::cout << "\t" << state.errors;
+        std::cout << "\t" << state.qgramHit;
+        std::cout << "\t" << state.leftError;
+        std::cout << "\t" << state.rightError;
+        std::cout << "\t" << state.transition[0];
+        std::cout << "\t" << state.transition[1];
+        std::cout << "\t" << state.transition[2];
+        std::cout << "\t" << state.transition[3];
+        std::cout << std::endl;
+*/    }
+    if (!optionMinOutput)
+        std::cout << "Preprocessing finished." << std::endl;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 // Compute filtering loss of any q-gram filter (given a states-string)
 template <
-	typename TThreshString, 
-	typename TStateString >
+    typename TThreshString,
+    typename TStateString >
 void computeExactQGramThreshold(
-	TThreshString &treshPerError,
-	TStateString const &states,
-	int span,
-	int maxErrors,
-	int maxN,
-	bool optionMinOutput)
+    TThreshString &treshPerError,
+    TStateString const &states,
+    int span,
+    int maxErrors,
+    int maxN,
+    bool optionMinOutput)
 {
-	typedef typename Value<TStateString>::Type		TState;
-	typedef unsigned								TThresh;
-	typedef String<TThresh>							TMatrixCol;
-
-	int statesCount = length(states);
-//	int span = length(bitShape);
-
-	// columns n-1 and n for recursion 
-	TMatrixCol col0;	// addressing is colx[errors * statesCount + state]
-	TMatrixCol col1;
-	const TThresh infty = MaxValue<TThresh>::VALUE >> 1;
-	
-	resize(col0, maxErrors * statesCount, infty);
-	resize(col1, maxErrors * statesCount);
-
-	// RECURSION BEGIN
-	for (int s = 0; s < statesCount; ++s)
-	{
-		TState const &state = states[s];
-		if (state.skipFirst) continue;
-
-		// threshold is 1 iff we have a q-gram hit at the end
-		col0[s] = (state.qgramHit)? 1: 0;
-	}
-
-	// iterate over sequence length n
-	TMatrixCol *col = &col1;
-	TMatrixCol *colPrev = &col0;
+    typedef typename Value<TStateString>::Type        TState;
+    typedef unsigned                                TThresh;
+    typedef String<TThresh>                            TMatrixCol;
+
+    int statesCount = length(states);
+//    int span = length(bitShape);
+
+    // columns n-1 and n for recursion
+    TMatrixCol col0;    // addressing is colx[errors * statesCount + state]
+    TMatrixCol col1;
+    const TThresh infty = MaxValue<TThresh>::VALUE >> 1;
+
+    resize(col0, maxErrors * statesCount, infty);
+    resize(col1, maxErrors * statesCount);
+
+    // RECURSION BEGIN
+    for (int s = 0; s < statesCount; ++s)
+    {
+        TState const &state = states[s];
+        if (state.skipFirst) continue;
+
+        // threshold is 1 iff we have a q-gram hit at the end
+        col0[s] = (state.qgramHit)? 1: 0;
+    }
+
+    // iterate over sequence length n
+    TMatrixCol *col = &col1;
+    TMatrixCol *colPrev = &col0;
 
 #ifdef DEBUG_RECOG_DP
-	std::cout << span << ":0";
-	dump(col0, 0,statesCount);
-	std::cout << " :1";
-	dump(col0, 1,statesCount);
+    std::cout << span << ":0";
+    dump(col0, 0,statesCount);
+    std::cout << " :1";
+    dump(col0, 1,statesCount);
 #endif
-	
-
-	// RECURSION
-	//
-	// thresh(n,q,e) = min(thresh(n-1,0|(q>>1),e),              delta=1/0 <-> q hat 0/>0 error
-	//                     thresh(n-1,1|(q>>1),e-1)) + delta
-		
-	for (int n = span; n < maxN; ++n)
-	{
-		for (int e = 0; e < maxErrors * statesCount; e += statesCount)
-		{		
-			for (int s = 0; s < statesCount; ++s)
-			{
-				TState const &state = states[s];				
-
-				// MATCH
-				TThresh t = (*colPrev)[e + state.transition[SEQAN_MATCH]];
-
-				// MISMATCH, INSERT, DELETE
-				if (e > 0)
-					for (int m = SEQAN_MISMATCH; m < TState::TRANSITIONS; ++m)
-					{
-						int prevState = state.transition[m];
-						if (prevState >= 0)
-						{
-							if (m == SEQAN_INSERT)
-								t = _min(t, (*col)[(e - statesCount) + prevState]);
-							else
-								t = _min(t, (*colPrev)[(e - statesCount) + prevState]);
-						}
-					}
-
-				(*col)[e + s] = t + state.qgramHit;
-			}
-			if (!optionMinOutput)
-				std::cout << '.' << std::flush;
-		}
-
-		TMatrixCol *tmp = col;
-		col = colPrev;
-		colPrev = tmp;
+
+
+    // RECURSION
+    //
+    // thresh(n,q,e) = min(thresh(n-1,0|(q>>1),e),              delta=1/0 <-> q hat 0/>0 error
+    //                     thresh(n-1,1|(q>>1),e-1)) + delta
+
+    for (int n = span; n < maxN; ++n)
+    {
+        for (int e = 0; e < maxErrors * statesCount; e += statesCount)
+        {
+            for (int s = 0; s < statesCount; ++s)
+            {
+                TState const &state = states[s];
+
+                // MATCH
+                TThresh t = (*colPrev)[e + state.transition[SEQAN_MATCH]];
+
+                // MISMATCH, INSERT, DELETE
+                if (e > 0)
+                    for (int m = SEQAN_MISMATCH; m < TState::TRANSITIONS; ++m)
+                    {
+                        int prevState = state.transition[m];
+                        if (prevState >= 0)
+                        {
+                            if (m == SEQAN_INSERT)
+                                t = _min(t, (*col)[(e - statesCount) + prevState]);
+                            else
+                                t = _min(t, (*colPrev)[(e - statesCount) + prevState]);
+                        }
+                    }
+
+                (*col)[e + s] = t + state.qgramHit;
+            }
+            if (!optionMinOutput)
+                std::cout << '.' << std::flush;
+        }
+
+        TMatrixCol *tmp = col;
+        col = colPrev;
+        colPrev = tmp;
 
 #ifdef DEBUG_RECOG_DP
-		std::cout << n+1 << ":0";
-		dump(*colPrev, 0,statesCount);
-		std::cout << " :1";
-		dump(*colPrev, 1,statesCount);
-		std::cout << " :2";
-		dump(*colPrev, 2,statesCount);
+        std::cout << n+1 << ":0";
+        dump(*colPrev, 0,statesCount);
+        std::cout << " :1";
+        dump(*colPrev, 1,statesCount);
+        std::cout << " :2";
+        dump(*colPrev, 2,statesCount);
 #endif
-	}
-	
-	if (!optionMinOutput)
-		std::cout << std::endl;
-
-	resize(treshPerError, maxErrors);
-	
-	// RECURSION END
-	for (int eSum = 0; eSum < maxErrors; ++eSum)
-	{
-		TThresh t = infty;
-		for (int s = 0; s < statesCount; ++s)
-		{
-			TState const &state = states[s];
-
-			// skip intermediate results
-			if (state.intermediate || state.skipLast) continue;
-			if (state.errors <= eSum)
-			{
-				int e = eSum - state.errors;
-				// multiply probability for the trailing pattern
-				t = _min(t, (*colPrev)[e * statesCount + s]);
-			}
-		}
-
-		if (t >= infty) t = 0;
-		treshPerError[eSum] = t;
-	}
+    }
+
+    if (!optionMinOutput)
+        std::cout << std::endl;
+
+    resize(treshPerError, maxErrors);
+
+    // RECURSION END
+    for (int eSum = 0; eSum < maxErrors; ++eSum)
+    {
+        TThresh t = infty;
+        for (int s = 0; s < statesCount; ++s)
+        {
+            TState const &state = states[s];
+
+            // skip intermediate results
+            if (state.intermediate || state.skipLast) continue;
+            if (state.errors <= eSum)
+            {
+                int e = eSum - state.errors;
+                // multiply probability for the trailing pattern
+                t = _min(t, (*colPrev)[e * statesCount + s]);
+            }
+        }
+
+        if (t >= infty) t = 0;
+        treshPerError[eSum] = t;
+    }
 }
 
 
 //////////////////////////////////////////////////////////////////////////////
 // Compute filtering loss of any q-gram filter (given a states-string)
 template <
-	typename TLossString, 
-	typename TLogErrorDistr, 
-	typename TStateString >
+    typename TLossString,
+    typename TLogErrorDistr,
+    typename TStateString >
 void computeQGramFilteringSensitivity(
-	TLossString &found,
-	TStateString const &states,
-	int span,
-	int maxT,
-	int maxErrors,
-	TLogErrorDistr const &logError,
-//	bool optionAbsolute = false,
-	bool optionMinOutput)
+    TLossString &found,
+    TStateString const &states,
+    int span,
+    int maxT,
+    int maxErrors,
+    TLogErrorDistr const &logError,
+//    bool optionAbsolute = false,
+    bool optionMinOutput)
 {
-	typedef typename Value<TLossString>::Type		TFloat;
-	//typedef typename Value<TLogErrorDistr>::Type	TProbValue;
-	typedef typename Value<TStateString>::Type		TState;
+    typedef typename Value<TLossString>::Type        TFloat;
+    //typedef typename Value<TLogErrorDistr>::Type    TProbValue;
+    typedef typename Value<TStateString>::Type        TState;
 
-	typedef String<TFloat>							TMatrixCol;
-	//typedef String<int>								TIntCol;
+    typedef String<TFloat>                            TMatrixCol;
+    //typedef String<int>                                TIntCol;
 
-	SEQAN_ASSERT_EQ((length(logError) % 4), 0u);
+    SEQAN_ASSERT_EQ((length(logError) % 4), 0u);
 
-	int maxN = length(logError) / 4;
-	int statesCount = length(states);
-	const bool optionAbsolute = false;
-//	int span = length(bitShape);
+    int maxN = length(logError) / 4;
+    int statesCount = length(states);
+    const bool optionAbsolute = false;
+//    int span = length(bitShape);
 
-	// columns n-1 and n for recursion 
-	TMatrixCol col0;
-	TMatrixCol col1;
-	resize(col0, maxErrors * statesCount * maxT, (TFloat)_transform(0.0));
-	resize(col1, maxErrors * statesCount * maxT);
+    // columns n-1 and n for recursion
+    TMatrixCol col0;
+    TMatrixCol col1;
+    resize(col0, maxErrors * statesCount * maxT, (TFloat)_transform(0.0));
+    resize(col1, maxErrors * statesCount * maxT);
 
 #ifdef COUNT_LOSSES
-	TFloat positive = _transform(0.0);
-	TFloat negative = _transform(1.0);
+    TFloat positive = _transform(0.0);
+    TFloat negative = _transform(1.0);
 #else
-	TFloat positive = _transform(1.0);
-	TFloat negative = _transform(0.0);
+    TFloat positive = _transform(1.0);
+    TFloat negative = _transform(0.0);
 #endif
 
-	// RECURSION BEGIN
-	for (int s = 0; s < statesCount; ++s) 
-	{
-		TState const &state = states[s];
-
-		if (state.skipFirst) continue;
-
-		// we miss no match if threshold t is 0
-		col0[s*maxT] = positive;
-
-		// for n==0
-		if (state.qgramHit)
-		{
-			// we miss no match if read q-gram is recognized
-			// --> probability of finding this MMP is 1, if t=1
-			col0[s*maxT+1] = positive;
-			// --> probability of finding this MMP is 0, if t>1
-			for (int t = 2; t < maxT; ++t)
-				col0[s*maxT+t] = negative;
-		} else
-		{
-			// we miss 1 match if t>0 and read q-gram is not recognized
-			// --> probability of finding this MMP is 0, if t>=1
-			for (int t = 1; t < maxT; ++t)
-				col0[s*maxT+t] = negative;
-		}
-	}
-
-	// iterate over sequence length n
-	TMatrixCol *col = &col1;
-	TMatrixCol *colPrev = &col0;
+    // RECURSION BEGIN
+    for (int s = 0; s < statesCount; ++s)
+    {
+        TState const &state = states[s];
+
+        if (state.skipFirst) continue;
+
+        // we miss no match if threshold t is 0
+        col0[s*maxT] = positive;
+
+        // for n==0
+        if (state.qgramHit)
+        {
+            // we miss no match if read q-gram is recognized
+            // --> probability of finding this MMP is 1, if t=1
+            col0[s*maxT+1] = positive;
+            // --> probability of finding this MMP is 0, if t>1
+            for (int t = 2; t < maxT; ++t)
+                col0[s*maxT+t] = negative;
+        } else
+        {
+            // we miss 1 match if t>0 and read q-gram is not recognized
+            // --> probability of finding this MMP is 0, if t>=1
+            for (int t = 1; t < maxT; ++t)
+                col0[s*maxT+t] = negative;
+        }
+    }
+
+    // iterate over sequence length n
+    TMatrixCol *col = &col1;
+    TMatrixCol *colPrev = &col0;
 
 #ifdef DEBUG_RECOG_DP
-	::std::cout << span << ":0";
-	dump(col0, 0,statesCount);
-	::std::cout << " :1";
-	dump(col0, 1,statesCount);
+    std::cout << span << ":0";
+    dump(col0, 0,statesCount);
+    std::cout << " :1";
+    dump(col0, 1,statesCount);
 #endif
-	
-
-	// RECURSION
-	//
-	// found(n,q,t,e) = (1-errorProb[n-span]) * found(n-1,0|(q>>1),t-delta,e) delta=1/0 <-> q hat 0/>0 fehler
-	//               + errorProb[n-span] * found(n-1,1|(q>>1),t-delta,e-1)
-	
-	// rekursion (fuer q-gram matches <=1 fehler)
-	// found(n,q,t,e) = (1-errorProb[n-span]) * found(n-1,0|(q>>1),t-delta,e) delta=1/0 <-> q hat <=1/>1 fehler
-	//               + errorProb[n-span] * found(n-1,1|(q>>1),t-delta,e-1)
-	
-	for (int n = span; n < maxN; ++n)
-	{
-		for (int e = 0; e < maxErrors * statesCount; e += statesCount)
-		{		
-			for (int s = 0; s < statesCount; ++s)
-			{
-				TState const &state = states[s];				
-				for (int t = 0; t < maxT; ++t)
-				{
-					int _t = t;
-					if (_t > 0 && state.qgramHit) --_t;
-
-					// MATCH
-					TFloat recovered = _probMul(
-						_getProb(logError, SEQAN_MATCH, n-span),
-						(*colPrev)[(e+state.transition[SEQAN_MATCH])*maxT+_t]);
-
-					// MISMATCH, INSERT, DELETE
-					for (int m = SEQAN_MISMATCH; m < (int)state.TRANSITIONS; ++m)
-						if (e > 0)
-						{
-							int prevState = state.transition[m];
-							if (prevState >= 0)
-							{
-								if (m == SEQAN_INSERT)
-									_probAdd(recovered, _probMul(_getProb(logError,m,n-span), (*col)[((e-statesCount)+prevState)*maxT+t]));
-								else
-									_probAdd(recovered, _probMul(_getProb(logError,m,n-span), (*colPrev)[((e-statesCount)+prevState)*maxT+_t]));
-							}
-						}
-					(*col)[(e+s)*maxT+t] = recovered;
-				}
-			}
-			if (!optionMinOutput)
-				::std::cout << '.' << ::std::flush;
-		}
-
-		TMatrixCol *tmp = col;
-		col = colPrev;
-		colPrev = tmp;
+
+
+    // RECURSION
+    //
+    // found(n,q,t,e) = (1-errorProb[n-span]) * found(n-1,0|(q>>1),t-delta,e) delta=1/0 <-> q hat 0/>0 fehler
+    //               + errorProb[n-span] * found(n-1,1|(q>>1),t-delta,e-1)
+
+    // rekursion (fuer q-gram matches <=1 fehler)
+    // found(n,q,t,e) = (1-errorProb[n-span]) * found(n-1,0|(q>>1),t-delta,e) delta=1/0 <-> q hat <=1/>1 fehler
+    //               + errorProb[n-span] * found(n-1,1|(q>>1),t-delta,e-1)
+
+    for (int n = span; n < maxN; ++n)
+    {
+        for (int e = 0; e < maxErrors * statesCount; e += statesCount)
+        {
+            for (int s = 0; s < statesCount; ++s)
+            {
+                TState const &state = states[s];
+                for (int t = 0; t < maxT; ++t)
+                {
+                    int _t = t;
+                    if (_t > 0 && state.qgramHit) --_t;
+
+                    // MATCH
+                    TFloat recovered = _probMul(
+                        _getProb(logError, SEQAN_MATCH, n-span),
+                        (*colPrev)[(e+state.transition[SEQAN_MATCH])*maxT+_t]);
+
+                    // MISMATCH, INSERT, DELETE
+                    for (int m = SEQAN_MISMATCH; m < (int)state.TRANSITIONS; ++m)
+                        if (e > 0)
+                        {
+                            int prevState = state.transition[m];
+                            if (prevState >= 0)
+                            {
+                                if (m == SEQAN_INSERT)
+                                    _probAdd(recovered, _probMul(_getProb(logError,m,n-span), (*col)[((e-statesCount)+prevState)*maxT+t]));
+                                else
+                                    _probAdd(recovered, _probMul(_getProb(logError,m,n-span), (*colPrev)[((e-statesCount)+prevState)*maxT+_t]));
+                            }
+                        }
+                    (*col)[(e+s)*maxT+t] = recovered;
+                }
+            }
+            if (!optionMinOutput)
+                std::cout << '.' << std::flush;
+        }
+
+        TMatrixCol *tmp = col;
+        col = colPrev;
+        colPrev = tmp;
 
 #ifdef DEBUG_RECOG_DP
-		::std::cout << n+1 << ":0";
-		dump(*colPrev, 0,statesCount);
-		::std::cout << " :1";
-		dump(*colPrev, 1,statesCount);
-		::std::cout << " :2";
-		dump(*colPrev, 2,statesCount);
+        std::cout << n+1 << ":0";
+        dump(*colPrev, 0,statesCount);
+        std::cout << " :1";
+        dump(*colPrev, 1,statesCount);
+        std::cout << " :2";
+        dump(*colPrev, 2,statesCount);
 #endif
-	}
-	
-	if (!optionMinOutput)
-		::std::cout << ::std::endl;
-
-	// RECURSION END
-	for (int eSum = 0; eSum < maxErrors; ++eSum)
-		for (int t = 0; t < maxT; ++t) 
-		{
-			TFloat recovered = _transform(0.0);
-			for (int s = 0; s < statesCount; ++s)
-			{
-				TState const &state = states[s];
-
-				// skip intermediate results
-				if (state.intermediate || state.skipLast) continue;
-				if (state.errors <= eSum)
-				{
-					int e = eSum - state.errors;
-					// multiply probability for the trailing pattern
-					_probAdd(recovered, _probMul(state.prob, (*colPrev)[(e*statesCount+s)*maxT+t]));
-				}
-			}
+    }
+
+    if (!optionMinOutput)
+        std::cout << std::endl;
+
+    // RECURSION END
+    for (int eSum = 0; eSum < maxErrors; ++eSum)
+        for (int t = 0; t < maxT; ++t)
+        {
+            TFloat recovered = _transform(0.0);
+            for (int s = 0; s < statesCount; ++s)
+            {
+                TState const &state = states[s];
+
+                // skip intermediate results
+                if (state.intermediate || state.skipLast) continue;
+                if (state.errors <= eSum)
+                {
+                    int e = eSum - state.errors;
+                    // multiply probability for the trailing pattern
+                    _probAdd(recovered, _probMul(state.prob, (*colPrev)[(e*statesCount+s)*maxT+t]));
+                }
+            }
 
 #ifndef COUNT_LOSSES
-			// we can only normalize probs if t==0 contains all k-pattern probs
-			if (t > 0 && !optionAbsolute)
-				recovered = _probDiv(recovered, found[eSum*maxT]);
+            // we can only normalize probs if t==0 contains all k-pattern probs
+            if (t > 0 && !optionAbsolute)
+                recovered = _probDiv(recovered, found[eSum*maxT]);
 #endif
 
-			found[eSum*maxT+t] = recovered;
-		}
+            found[eSum*maxT+t] = recovered;
+        }
 }
 
 
@@ -1078,15 +1079,15 @@ void computeQGramFilteringSensitivity(
 template <typename TShape, typename TPatternSize, typename TErrors, typename TDistance>
 int qgramThreshold(TShape const & shape, TPatternSize patternLength, TErrors errors, TDistance const dist, ThreshExact const)
 {
-	String<ThreshDPState_<TDistance> > states;
-	String<unsigned> thresh;
-	String<char> bitString;
-	
-	shapeToString(bitString, shape);
-	initPatterns(states, bitString, errors, Nothing(), dist, true);
-	computeExactQGramThreshold(thresh, states, length(bitString), errors + 1, patternLength, true);
-	
-	return thresh[errors];
+    String<ThreshDPState_<TDistance> > states;
+    String<unsigned> thresh;
+    String<char> bitString;
+
+    shapeToString(bitString, shape);
+    initPatterns(states, bitString, errors, Nothing(), dist, true);
+    computeExactQGramThreshold(thresh, states, length(bitString), errors + 1, patternLength, true);
+
+    return thresh[errors];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1097,28 +1098,28 @@ int qgramThreshold(TShape const & shape, TPatternSize patternLength, TErrors err
 
 template <typename TSensitivityMatrix, typename TShape, typename TPatternSize, typename TErrors, typename TThresh, typename TDistance, typename TErrorDist>
 void qgramFilteringSensitivity(
-	TSensitivityMatrix & sensMat, 
-	TShape const & shape, 
-	TPatternSize patternLength, 
-	TErrors errors, 
-	TThresh maxThresh, 
-	TDistance const dist, 
-	ThreshExact const,
-	TErrorDist const & logErrorDistribution)
+    TSensitivityMatrix & sensMat,
+    TShape const & shape,
+    TPatternSize patternLength,
+    TErrors errors,
+    TThresh maxThresh,
+    TDistance const dist,
+    ThreshExact const,
+    TErrorDist const & logErrorDistribution)
 {
-	typedef typename Value<TSensitivityMatrix>::Type TFloat;
-	String<SensitivityDPState_<TDistance, TFloat> > states;
-	String<unsigned> thresh;
-	String<char> bitString;
-	
-	maxThresh = _min(maxThresh, patternLength - length(shape) + 1);
-	resize(sensMat, (maxThresh + 1) * (errors + 1));
-	shapeToString(bitString, shape);
-
-	initPatterns(states, bitString, errors, logErrorDistribution, dist, true);
-	computeQGramFilteringSensitivity(sensMat, states, length(bitString), maxThresh + 1, errors + 1, logErrorDistribution, true);
+    typedef typename Value<TSensitivityMatrix>::Type TFloat;
+    String<SensitivityDPState_<TDistance, TFloat> > states;
+    String<unsigned> thresh;
+    String<char> bitString;
+
+    maxThresh = _min(maxThresh, patternLength - length(shape) + 1);
+    resize(sensMat, (maxThresh + 1) * (errors + 1));
+    shapeToString(bitString, shape);
+
+    initPatterns(states, bitString, errors, logErrorDistribution, dist, true);
+    computeQGramFilteringSensitivity(sensMat, states, length(bitString), maxThresh + 1, errors + 1, logErrorDistribution, true);
 }
 
-}	// namespace seqan
+}    // namespace seqan
 
 #endif
diff --git a/seqan/journaled_set.h b/seqan/journaled_set.h
new file mode 100644
index 0000000..bd5558e
--- /dev/null
+++ b/seqan/journaled_set.h
@@ -0,0 +1,79 @@
+// ==========================================================================
+//                               journaled_set
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Facade header for module journaled_set.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/basic.h>  // Include the basics.
+#include <seqan/align.h>  // Include the alignment interface.
+#include <seqan/score.h>
+#include <seqan/journaled_set/score_biaffine.h>
+#include <seqan/sequence.h>
+#include <seqan/sequence_journaled.h>
+#include <seqan/seq_io.h>
+
+
+// ===========================================================================
+// First Header Group.
+// ===========================================================================
+
+#include <seqan/journaled_set/journaled_set_base.h>
+
+#include <seqan/journaled_set/journaled_set_impl.h>
+
+#include <seqan/journaled_set/journaled_set_journal_trace_descriptor.h>
+
+// ----------------------------------------------------------------------------
+// Alignment Extension for Journaled Sequences
+// ----------------------------------------------------------------------------
+
+#include <seqan/journaled_set/journal_alignment_interface.h>
+#include <seqan/journaled_set/journal_alignment_traceback_adaptor.h>
+
+// ----------------------------------------------------------------------------
+// Journaled Set Interfaces
+// ----------------------------------------------------------------------------
+
+#include <seqan/journaled_set/journaled_set_join_config.h>
+#include <seqan/journaled_set/journaled_set_join.h>
+#include <seqan/journaled_set/journaled_set_join_global_align_manhatten.h>
+#include <seqan/journaled_set/journaled_set_join_global_align_compact.h>
+
+#endif  // INCLUDE_SEQAN_JOURNALED_SET_H_
diff --git a/seqan/journaled_set/journal_alignment_interface.h b/seqan/journaled_set/journal_alignment_interface.h
new file mode 100644
index 0000000..1db9676
--- /dev/null
+++ b/seqan/journaled_set/journal_alignment_interface.h
@@ -0,0 +1,254 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Global alignment interface for journaled strings.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNAL_ALIGNMENT_INTERFACE_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNAL_ALIGNMENT_INTERFACE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function globalAlignment()                  [unbanded, String<Journaled<> >]
+// ----------------------------------------------------------------------------
+
+// Full interface.
+
+template <typename TValue, typename THostSpec, typename TJournalSpec,
+          typename TBuffSpec, typename TReference, typename TSource,
+          typename TScoreValue, typename TScoreSpec,
+          bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
+          typename TAlgoTag>
+TScoreValue globalAlignment(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString,
+                            TReference const & reference,
+                            TSource const & source,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
+                            TAlgoTag const & /*tag*/)
+{
+    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;
+    typedef typename Position<TJournalString>::Type TPosition;
+    typedef typename Size<TJournalString>::Type TSize;
+    typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps, TracebackOn<TracebackConfig_<SingleTrace, GapsLeft> > > TDPConfig;
+
+    String<TTraceSegment> traceSegments;
+    DPScoutState_<Default> dpScoutState;
+    // We need to do that in order to build journal strings from two simple sequences.
+    TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringScheme, TDPConfig(),
+                                            IsSameType<TAlgoTag, NeedlemanWunsch>());
+    _adaptTraceSegmentsTo(journaledString, reference, source, traceSegments);
+    return res;
+}
+
+// Interface without AlignConfig<>.
+
+template <typename TValue, typename THostSpec, typename TJournalSpec,
+          typename TBuffSpec, typename TReference, typename TSource,
+          typename TScoreValue, typename TScoreSpec,
+          typename TAlgoTag>
+TScoreValue globalAlignment(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString,
+                            TReference const & reference,
+                            TSource const & source,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                            TAlgoTag const & algoTag)
+{
+    AlignConfig<> alignConfig;
+    return globalAlignment(journaledString, reference, source, scoringScheme, alignConfig, algoTag);
+}
+
+// Interface without algorithm tag.
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec,
+          typename TReference, typename TSource,
+          typename TScoreValue, typename TScoreSpec,
+          bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
+TScoreValue globalAlignment(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString,
+                            TReference const & reference,
+                            TSource const & source,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig)
+{
+    typedef typename SequenceEntryForScore<Score<TScoreValue, TScoreSpec>, TReference>::Type TReferenceEntryForScore;
+    typedef typename SequenceEntryForScore<Score<TScoreValue, TScoreSpec>, TSource>::Type TSourceEntryForScore;
+
+    TReferenceEntryForScore entryRef = sequenceEntryForScore(scoringScheme, reference, 0);
+    TSourceEntryForScore entrySource = sequenceEntryForScore(scoringScheme, source, 0);
+    if (scoreGapOpenHorizontal(scoringScheme, entryRef, entrySource) ==
+        scoreGapExtendHorizontal(scoringScheme, entryRef, entrySource) ||
+        scoreGapOpenVertical(scoringScheme, entryRef, entrySource) ==
+        scoreGapExtendVertical(scoringScheme, entryRef, entrySource))
+        return globalAlignment(journaledString, reference, source, scoringScheme, alignConfig, NeedlemanWunsch());
+    else
+        return globalAlignment(journaledString, reference, source, scoringScheme, alignConfig, Gotoh());
+}
+
+// Interface without AlignConfig<> and algorithm tag.
+
+template <typename TValue, typename THostSpec, typename TJournalSpec,
+          typename TBuffSpec, typename TReference, typename TSource,
+          typename TScoreValue, typename TScoreSpec>
+TScoreValue globalAlignment(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString,
+                            TReference const & reference,
+                            TSource const & source,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme)
+{
+    AlignConfig<> alignConfig;
+    return globalAlignment(journaledString, reference, source, scoringScheme, alignConfig);
+}
+
+// ----------------------------------------------------------------------------
+// Function globalAlignment()                    [banded, String<Journaled<> >]
+// ----------------------------------------------------------------------------
+
+// Full interface.
+
+template <typename TValue, typename THostSpec, typename TJournalSpec,
+          typename TBuffSpec, typename TReference, typename TSource,
+          typename TScoreValue, typename TScoreSpec,
+          bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
+          typename TAlgoTag>
+TScoreValue globalAlignment(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString,
+                            TReference const & reference,
+                            TSource const & source,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
+                            int lowerDiag,
+                            int upperDiag,
+                            TAlgoTag const & /*algoTag*/)
+{
+    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;
+    typedef typename Position<TJournalString>::Type TPosition;
+    typedef typename Size<TJournalString>::Type TSize;
+    typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOn<TracebackConfig_<SingleTrace, GapsLeft> > > TDPConfig;
+
+    String<TTraceSegment> traceSegments;
+    DPScoutState_<Default> dpScoutState;
+    // We need to do that in order to build journal strings from two simple sequences.
+    TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, reference, source, scoringScheme,
+                                            TDPConfig(lowerDiag, upperDiag),
+                                            IsSameType<TAlgoTag, NeedlemanWunsch>());
+    _adaptTraceSegmentsTo(journaledString, reference, source, traceSegments);
+    return res;
+}
+
+// Interface without AlignConfig<>.
+
+template <typename TValue, typename THostSpec, typename TJournalSpec,
+          typename TBuffSpec, typename TReference, typename TSource,
+          typename TScoreValue, typename TScoreSpec,
+          typename TAlgoTag>
+TScoreValue globalAlignment(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString,
+                            TReference const & reference,
+                            TSource const & source,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                            int lowerDiag,
+                            int upperDiag,
+                            TAlgoTag const & algoTag)
+{
+    AlignConfig<> alignConfig;
+    return globalAlignment(journaledString, reference, source, scoringScheme, alignConfig, lowerDiag, upperDiag,
+                           algoTag);
+}
+
+// Interface without algorithm tag.
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec,
+          typename TReference, typename TSource,
+          typename TScoreValue, typename TScoreSpec,
+          bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
+TScoreValue globalAlignment(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString,
+                            TReference const & reference,
+                            TSource const & source,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                            AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
+                            int lowerDiag,
+                            int upperDiag)
+{
+    typedef typename SequenceEntryForScore<Score<TScoreValue, TScoreSpec>, TReference>::Type TReferenceEntryForScore;
+    typedef typename SequenceEntryForScore<Score<TScoreValue, TScoreSpec>, TSource>::Type TSourceEntryForScore;
+
+    TReferenceEntryForScore entryRef = sequenceEntryForScore(scoringScheme, reference, 0);
+    TSourceEntryForScore entrySource = sequenceEntryForScore(scoringScheme, source, 0);
+    if (scoreGapOpenHorizontal(scoringScheme, entryRef, entrySource) ==
+        scoreGapExtendHorizontal(scoringScheme, entryRef, entrySource) ||
+        scoreGapOpenVertical(scoringScheme, entryRef, entrySource) ==
+        scoreGapExtendVertical(scoringScheme, entryRef, entrySource))
+        return globalAlignment(journaledString, reference, source, scoringScheme, alignConfig, lowerDiag, upperDiag,
+                               NeedlemanWunsch());
+    else
+        return globalAlignment(journaledString, reference, source, scoringScheme, alignConfig, lowerDiag, upperDiag,
+                               Gotoh());
+}
+
+// Interface without AlignConfig<> and algorithm tag.
+
+template <typename TValue, typename THostSpec, typename TJournalSpec,
+          typename TBuffSpec, typename TReference, typename TSource,
+          typename TScoreValue, typename TScoreSpec>
+TScoreValue globalAlignment(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString,
+                            TReference const & reference,
+                            TSource const & source,
+                            Score<TScoreValue, TScoreSpec> const & scoringScheme,
+                            int lowerDiag,
+                            int upperDiag)
+{
+    AlignConfig<> alignConfig;
+    return globalAlignment(journaledString, reference, source, scoringScheme, alignConfig, lowerDiag, upperDiag);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNAL_ALIGNMENT_INTERFACE_H_
diff --git a/seqan/journaled_set/journal_alignment_traceback_adaptor.h b/seqan/journaled_set/journal_alignment_traceback_adaptor.h
new file mode 100644
index 0000000..3dc356a
--- /dev/null
+++ b/seqan/journaled_set/journal_alignment_traceback_adaptor.h
@@ -0,0 +1,126 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Adapts traceback to a journaled string using SortedArray specialization.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNAL_ALIGNMENT_TRACEBACK_ADAPTOR_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNAL_ALIGNMENT_TRACEBACK_ADAPTOR_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _adaptTraceSegmentsTo()           [String<Journaled<SortedArray> >]
+// ----------------------------------------------------------------------------
+
+
+template <typename TValue, typename THostSpec, typename TBuffSpec, typename TReference,
+          typename TSource, typename TPosition, typename TSize, typename TStringSpec>
+inline void
+_adaptTraceSegmentsTo(String<TValue, Journaled<THostSpec, SortedArray, TBuffSpec> > & targetJournal,
+                      TReference const & /*reference*/, //TODO(rmaerker): What if the TSequenceH is a journal string.
+                      TSource const & source,
+                      String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments)
+{
+
+    typedef String<TValue, Journaled<THostSpec, SortedArray, TBuffSpec> > TJournalString;
+    typedef typename JournalType<TJournalString>::Type TJournalEntries;
+    typedef typename Value<TJournalEntries>::Type TJournalEntry;
+
+//    typedef typename Position<TReference>::Type TPhysicalPosition;
+    typedef typename Position<TSource>::Type TVirtualPosition;
+
+    typedef TraceSegment_<TPosition, TSize> TTraceSegment;
+    typedef typename Iterator<String<TTraceSegment, TStringSpec> const>::Type TTraceIterator;
+
+    SEQAN_ASSERT_NOT_MSG(empty(host(targetJournal)), "No reference sequence set!");
+
+    // TODO(rmaerker): Hot-fix for new alignment module.
+    clear(targetJournal._journalEntries._journalNodes);
+    clear(targetJournal._insertionBuffer);
+    targetJournal._journalEntries._originalStringLength = length(host(targetJournal));
+
+    TVirtualPosition virtualPos = 0;
+
+    TTraceIterator traceSegIter = end(traceSegments, Standard()) - 1;
+    TTraceIterator traceSegIterEnd = begin(traceSegments, Standard()) - 1;
+
+    for (; traceSegIter != traceSegIterEnd; --traceSegIter)
+    {
+        switch (value(traceSegIter)._traceValue)
+        {
+        case TraceBitMap_::DIAGONAL: //matching area
+        {
+            appendValue(targetJournal._journalEntries._journalNodes, TJournalEntry(SOURCE_ORIGINAL, value(traceSegIter)._horizontalBeginPos,
+                                                                                   virtualPos, value(traceSegIter)._horizontalBeginPos, value(traceSegIter)._length));
+            virtualPos += value(traceSegIter)._length;
+            break;
+        }
+
+        case TraceBitMap_::VERTICAL: //insertion
+        {
+            appendValue(targetJournal._journalEntries._journalNodes, TJournalEntry(SOURCE_PATCH, length(targetJournal._insertionBuffer),
+                                                                                   virtualPos, 0, value(traceSegIter)._length));
+            append(targetJournal._insertionBuffer,
+                   infix(source, value(traceSegIter)._verticalBeginPos, value(traceSegIter)._verticalBeginPos +
+                         value(traceSegIter)._length));
+            virtualPos += value(traceSegIter)._length;
+            break;
+        }
+
+        default:
+            break;  // Otherwise we are in a deletion and do nothing.
+        }
+    }
+    _setLength(targetJournal, virtualPos);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNAL_ALIGNMENT_TRACEBACK_ADAPTOR_H_
diff --git a/seqan/journaled_set/journaled_set_base.h b/seqan/journaled_set/journaled_set_base.h
new file mode 100644
index 0000000..537c516
--- /dev/null
+++ b/seqan/journaled_set/journaled_set_base.h
@@ -0,0 +1,205 @@
+// ==========================================================================
+//                               journaled_set
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_BASE_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_BASE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Spec JournaledSet
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class JournaledSet
+ * @extends StringSet
+ * @headerfile <seqan/journaled_set.h>
+ *
+ * @signature template <typename TString>
+ *            class StringSet<TString, Owner<JournaledSet> >;
+ * @tparam TString The string type. Types: @link String @endlink, @link JournaledString @endlink
+ *
+ * @brief A @link StringSet @endlink storing the strings as members.  It can store a global reference sequence to which all members can
+ * be journaled if they are of type @link JournaledString @endlink.
+ *
+ * The strings are internally stored in a <tt>String&lt;TString&gt;</tt> object and the character position type is a @link
+ * Pair @endlink <tt>(seqNo, seqOfs)</tt> where seqNo identifies the string within the string set and seqOfs identifies
+ * the position within this string.
+ *
+ * The global reference is of type <tt>Host&lt;TString&gt;</tt>. Only strings of type @link JournaledString @endlink or
+ * <tt>Host&lt;</tt>@link JournaledString @endlink<tt>&gt;</tt> can be used for the advanced functionality supported by
+ * this string set.
+ */
+
+struct JournaledSet_;
+typedef Tag<JournaledSet_> JournaledSet;
+
+
+// ----------------------------------------------------------------------------
+// Class JournalTraceBuffer
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+class JournalTraceBuffer;
+
+/*!
+ * @defgroup JoinStrategiesTags Join Strategies Tags
+ * @brief Tags used for selecting journaling strategies when joining a JournaledString to a global reference sequence.
+ *
+ *
+ * @tag JoinStrategiesTags#JournaledManhattan
+ * @headerfile <seqan/sequence_journaled.h>
+ * @brief Constructs a @link JournaledString @endlink based on Manhattan distance.
+ *
+ * This strategy is very fast on the cost of memory.
+ *
+ * @signature typedef Tag<JournaledManhattan_> JournaledManhattan.
+ *
+ *
+ * @tag JoinStrategiesTags#JournaledCompact
+ * @headerfile <seqan/sequence_journaled.h>
+ * @brief Computes an optimal alignment to construct a @link JournaledString @endlink.
+ *
+ * This strategy is slow but depending on the scoring function minimizes the memory requirements for the computed @link
+ * JournaledSet @endlink.
+ *
+ * @signature typedef Tag<JournaledCompact_> JournaledCompact;
+ */
+
+// ----------------------------------------------------------------------------
+// Tag JournaledManhatten
+// ----------------------------------------------------------------------------
+
+struct JournaledManhatten_;
+typedef Tag<JournaledManhatten_> JournaledManhatten;
+
+// ----------------------------------------------------------------------------
+// Tag JournaledCompact
+// ----------------------------------------------------------------------------
+
+struct JournaledCompact_;
+typedef Tag<JournaledCompact_> JournaledCompact;
+
+
+// ----------------------------------------------------------------------------
+// Spec GlobalAlign
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class GlobalAlign
+ * @extends JoinConfig
+ *
+ * @headerfile <seqan/journaled_set.h>
+ * @brief Selects a global alignment method to join a @link JournaledString @endlink to a global reference sequence.
+ *
+ * @signature template <[typename TStrategy]>
+ *            struct GlobalAlign;
+ *
+ * @tparam TStrategy The strategy used to compute the journal (can be one of @link JoinStrategiesTags#JournaledCompact
+ *                   @endlink and @link JoinStrategiesTags#JournaledManhattan @endlink, defaults to @link
+ *                   JoinStrategiesTags#JournaledManhattan @endlink).
+ *
+ * If @link JoinStrategiesTags#JournaledManhattan @endlink is selected, then the resulting @link JournaledString
+ * @endlink consists of one insertion node covering the complete joined sequence.
+ */
+
+template <typename TSpec = JournaledManhatten>
+struct GlobalAlign{};
+
+// ----------------------------------------------------------------------------
+// Spec GlobalChain
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class GlobalChain
+ * @extends JoinConfig
+ *
+ * @headerfile <seqan/journaled_set.h>
+ * @brief Selects an anchor-based method to join a @link JournaledString @endlink to a global reference sequence.
+ *
+ * @signature template <[typename TStrategy]>
+ *            struct GlobalChain;
+ *
+ * @tparam TStrategy The strategy used to compute the journal (can be one of @link JoinStrategiesTags#JournaledCompact
+ *                   @endlink and @link JoinStrategiesTags#JournaledManhattan @endlink, defaults to @link
+ *                   JoinStrategiesTags#JournaledManhattan @endlink).
+ *
+ * The @link JoinStrategiesTags#JournaledManhattan @endlink strategy fills the gaps between the anchors with a single
+ * insertion node whil the corresponding part of the reference sequence is deleted.
+ */
+
+template <typename TSpec = JournaledManhatten>
+struct GlobalChain{};
+
+// ----------------------------------------------------------------------------
+// Class JoinConfig
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class JoinConfig
+ * @headerfile <seqan/journaled_set.h>
+ * @brief Specifies the strategy and all necessary parameters used to journal a sequence to a reference sequence.
+ *
+ * @signature template <[typename TMethod]>
+ *            struct JoinConfig;
+ *
+ * @tparam TMethod The method type. Types: @link GlobalAlign @endlink, @link GlobalChain @endlink
+ *
+ * SeqAn offers two general methods to compute the journal.  The first one uses a @link globalAlignment @endlink
+ * function and the second one uses an anchor based approach.
+ */
+
+template <typename TSpec = GlobalAlign<JournaledManhatten> >
+struct JoinConfig{};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+
+}  // namespace seqan
+
+#endif  // INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_BASE_H_
diff --git a/seqan/journaled_set/journaled_set_impl.h b/seqan/journaled_set/journaled_set_impl.h
new file mode 100644
index 0000000..fb4c453
--- /dev/null
+++ b/seqan/journaled_set/journaled_set_impl.h
@@ -0,0 +1,280 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_IMPL_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_IMPL_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class StringSet                                        [Owner<JournaledSet>]
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+class StringSet<TString, Owner<JournaledSet> >
+{
+public:
+    typedef typename Position<StringSet>::Type TPosition_;
+    typedef typename Host<TString>::Type THostString_;
+    typedef String<TString>  TStrings_;
+    typedef typename StringSetLimits<StringSet>::Type TLimits_;
+
+    Holder<THostString_> _globalRefHolder;
+    TStrings_   strings;
+    TLimits_    limits;
+    bool        limitsValid;
+
+    StringSet() : limitsValid(true)
+    {
+        appendValue(limits,0);
+    }
+
+    ~StringSet() {}
+
+    template <typename TPosition>
+    inline typename Reference<StringSet>::Type
+    operator[](TPosition const pos)
+    {
+        return value(*this, pos);
+    }
+
+    template <typename TPosition>
+    inline typename Reference<StringSet const>::Type
+    operator[](TPosition const pos) const
+    {
+        return value(*this, pos);
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Host
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+struct Host<StringSet<TString, Owner<JournaledSet> > >
+{
+    typedef typename Host<TString>::Type Type;
+};
+
+template <typename TString>
+struct Host<StringSet<TString, Owner<JournaledSet> > const >
+{
+    typedef typename Host<TString>::Type const Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TPosition>
+inline typename Reference<StringSet<TString, Owner<JournaledSet> > >::Type
+value(StringSet<TString, Owner<JournaledSet> > & me,
+      TPosition const pos)
+{
+    return me.strings[pos];
+}
+
+template <typename TString, typename TPosition>
+inline typename Reference<StringSet<TString, Owner<JournaledSet> > const >::Type
+value(StringSet<TString, Owner<JournaledSet> > const & me,
+      TPosition const pos)
+{
+    return me.strings[pos];
+}
+
+// ----------------------------------------------------------------------------
+// Function appendValue()
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TString2, typename TExpand>
+void
+appendValue(StringSet<TString, Owner<JournaledSet> > & journalSet,
+            TString2 const & newElement,
+            Tag<TExpand> tag)
+{
+    resize(journalSet, length(journalSet) + 1, tag);
+    assignValue(journalSet, length(journalSet) - 1 , newElement);
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+inline void
+clear(StringSet<TString, Owner<JournaledSet> > & journalSet)
+{
+    clear(journalSet._globalRefHolder);
+    clear(journalSet.strings);
+    resize(journalSet.limits, 1, Exact());
+    journalSet.limitsValid = true;
+}
+
+// ----------------------------------------------------------------------------
+// Function erase()
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TPos>
+inline typename Size<StringSet<TString, Owner<JournaledSet> > >::Type
+erase(StringSet<TString, Owner<JournaledSet> > & journalSet, TPos pos)
+{
+    erase(journalSet.strings, pos);
+    journalSet.limitsValid = false;
+    return length(journalSet);
+}
+
+template <typename TString, typename TPos, typename TPosEnd>
+inline typename Size<StringSet<TString, Owner<JournaledSet> > >::Type
+erase(StringSet<TString, Owner<JournaledSet> > & journalSet, TPos pos, TPosEnd posEnd)
+{
+    erase(journalSet.strings, pos, posEnd);
+    journalSet.limitsValid = false;
+    return length(journalSet);
+}
+
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSize, typename TValue, typename TExpandTag>
+inline typename Size<StringSet<TString, Owner<JournaledSet> > >::Type
+resize(StringSet<TString, Owner<JournaledSet> > & journalSet,
+       TSize const & newSize,
+       TValue const & fillValue,
+       Tag<TExpandTag> const & expansionTag)
+{
+    resize(journalSet.strings, newSize, fillValue, expansionTag);
+    resize(journalSet.limits, newSize + 1);
+    journalSet.limitsValid = true;
+    return length(journalSet);
+}
+
+// --------------------------------------------------------------------------
+// Function assignValue()
+// --------------------------------------------------------------------------
+
+// No journaled strings as values.
+template <typename TString, typename TPos,  typename TString2>
+inline void assignValue(
+    StringSet<TString, Owner<JournaledSet> > & journalSet,
+    TPos pos,
+    TString2 const & newElement)
+{
+    SEQAN_ASSERT_GEQ(pos, static_cast<TPos>(0));
+    SEQAN_ASSERT_LT(pos, static_cast<TPos>(length(journalSet)));
+
+    assign(journalSet[pos], newElement);
+}
+
+// ----------------------------------------------------------------------------
+// Function host()
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+inline Holder<typename Host<StringSet<TString, Owner<JournaledSet> > >::Type> const &
+_dataHost(StringSet<TString, Owner<JournaledSet> > const & set)
+{
+    return set._globalRefHolder;
+}
+
+template <typename TString>
+inline Holder<typename Host<StringSet<TString, Owner<JournaledSet> > >::Type>  &
+_dataHost(StringSet<TString, Owner<JournaledSet> > & set)
+{
+    return set._globalRefHolder;
+}
+
+/*!
+ * @fn JournaledSet#host
+ * @brief Returns the global reference sequence of a @link JournaledSet @endlink.
+ *
+ * @signature THost host(stringSet);
+ *
+ * @param[in] stringSet The JournaledStringSet that stores the sequences. Types: @link  JournaledSet  @endlink
+ *
+ * @return THost Reference to the host.
+ */
+
+// ----------------------------------------------------------------------------
+// Function setHost()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledSet#setHost
+ * @brief Sets the global reference of a @link JournaledSet @endlink.
+ *
+ * @signature void setHost(stringSet, ref);
+ *
+ * @param[in,out] stringSet The string set that stores the sequences. Types: @link JournaledSet @endlink
+ * @param[in]     ref       The new reference sequence of the @link JournaledSet  @endlink.
+ *
+ * @section Remarks
+ *
+ * Uses an @link Holder @endlink to store a reference to the new global reference sequence instead of copying it.
+ */
+
+// ----------------------------------------------------------------------------
+// Function createHost()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledSet#createHost
+ * @brief Creates the global reference of a @link JournaledSet @endlink.
+ *
+ * @signature void createHost(stringSet, ref);
+ *
+ * @param[in,out] stringSet The JournaledStringSet that stores the sequences.
+ * @param[in]     ref       The new reference sequence of the JournaledSet.  Stores a copy of the passed global
+ *                          reference sequence.
+ */
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_IMPL_H_
diff --git a/seqan/journaled_set/journaled_set_join.h b/seqan/journaled_set/journaled_set_join.h
new file mode 100644
index 0000000..eb55408
--- /dev/null
+++ b/seqan/journaled_set/journaled_set_join.h
@@ -0,0 +1,130 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+/*!
+ * @fn JournaledSet#join
+ * @brief Joins a @link JournaledString @endlink to a @link JournaledSet @endlink by computing and journaling
+ *        differences to the global reference sequence.
+ *
+ * @signature void join(stringSet, pos, joinConfig);
+ *
+ * @param[in,out] stringSet  The JournaledSet to join to.
+ * @param[in]     pos        The position of the JournaledString within the string set.
+ * @param[in]     joinConfig A @link JoinConfig @endlink object that specifies the method and the method's strategy
+ *                           to compute the differences.
+ */
+
+// ----------------------------------------------------------------------------
+// Function join()                                                [GlobalAlign]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TPosition, typename TSpec>
+inline void
+join(StringSet<TString, Owner<JournaledSet> > & journalSet,
+     TPosition journalIdx,
+     JoinConfig<GlobalAlign<TSpec> > const & joinConfig)
+{
+   SEQAN_ASSERT_LT(journalIdx, static_cast<TPosition>(length(journalSet)));
+   if (empty(host(journalSet)))
+   {
+       std::cerr << "No reference set! Join aborted!" << std::endl;
+   }
+   _joinInternal(value(journalSet, journalIdx), journalSet, joinConfig);
+}
+
+// ----------------------------------------------------------------------------
+// Function join                                                  [GlobalChain]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TPosition, typename TSpec>
+inline void
+join(StringSet<TString, Owner<JournaledSet> > & journalSet,
+     TPosition journalIdx,
+     JoinConfig<GlobalChain<TSpec> > const & joinConfig)
+{
+   SEQAN_ASSERT_LT(journalIdx, static_cast<TPosition>(length(journalSet)));
+
+   if (empty(host(journalSet)))
+   {
+       std::cerr << "No reference set! Join aborted!" << std::endl;
+   }
+   _joinInternal(value(journalSet, journalIdx), journalSet, joinConfig);
+}
+
+
+// ----------------------------------------------------------------------------
+// Function join                                                  [Simple Join]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TPosition, typename TSpec>
+inline void
+join(StringSet<TString, Owner<JournaledSet> > & journalSet,
+     TPosition journalIdx,
+     TSpec const &)
+{
+   join(journalSet, journalIdx, JoinConfig<GlobalAlign<JournaledManhatten> >());
+}
+
+template <typename TString, typename TPosition>
+inline void
+join(StringSet<TString, Owner<JournaledSet> > & journalSet,
+     TPosition journalIdx)
+{
+   join(journalSet, journalIdx, JoinConfig<GlobalAlign<JournaledManhatten> >());
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_H_
diff --git a/seqan/bam_io/bam_writer.h b/seqan/journaled_set/journaled_set_join_config.h
similarity index 62%
rename from seqan/bam_io/bam_writer.h
rename to seqan/journaled_set/journaled_set_join_config.h
index 65e5fbb..b5497f3 100644
--- a/seqan/bam_io/bam_writer.h
+++ b/seqan/journaled_set/journaled_set_join_config.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,11 +29,11 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_WRITER_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_WRITER_H_
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_CONFIG_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_CONFIG_H_
 
 namespace seqan {
 
@@ -45,36 +45,32 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-// TODO(holtgrew): Allow writing BAM to stdout? Extend Stream<Bgzf>?
+// ----------------------------------------------------------------------------
+// Class JoinConfig
+// ----------------------------------------------------------------------------
 
-class BamWriter_ :
-    public XamWriter_
+template <>
+struct JoinConfig<GlobalAlign<JournaledManhatten> > {};
+
+template <>
+struct JoinConfig<GlobalAlign<JournaledCompact> >
 {
-public:
-    // The BGZF stream to write to.
-    Stream<Bgzf> _stream;
-    // Flag indicating whether there was an error or not.
-    // TODO(holtgrew): Could we also use streamError()?
-    bool _isGood;
-
-    BamWriter_() :
-        XamWriter_()
+    typedef Score<int, BiAffine> TScoringScheme;
+    TScoringScheme _score;
+    int  _lowerDiagonal;
+    int  _upperDiagonal;
+    bool _isBandSet;
+    AlignConfig<true, false, false, true> _alignConfig;
+
+    JoinConfig() : _score(0, -100000, 0, -12, -1, -25),
+                   _lowerDiagonal(0),
+                   _upperDiagonal(0),
+                   _isBandSet(false),
+                   _alignConfig()
     {}
-
-    BamWriter_(CharString const & filename);
-
-    // XamWriter_ interface.
-
-    virtual int open(CharString const & filename);
-    virtual bool isGood();
-    virtual int writeHeader(BamHeader const & header,
-                            BamIOContext<StringSet<CharString> > const & context);
-    virtual int writeRecord(BamAlignmentRecord const & record,
-                            BamIOContext<StringSet<CharString> > const & context);
-    virtual int flush();
-    virtual int close();
 };
 
+
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -84,78 +80,81 @@ class BamWriter_ :
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Member Function BamWriter_::BamWriter_()
+// Function isBandSet()
 // ----------------------------------------------------------------------------
 
-inline BamWriter_::BamWriter_(CharString const & filename) :
-    XamWriter_(filename)
+template <typename TSpec>
+inline bool isBandSet(JoinConfig<TSpec> const & joinConfig)
 {
-    this->open(filename);
+    return joinConfig._isBandSet;
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamWriter_::open()
+// Function lowerDiagonal()
 // ----------------------------------------------------------------------------
 
-inline int BamWriter_::open(CharString const & filename)
+template <typename TSpec>
+inline int lowerDiagonal(JoinConfig<TSpec> const & joinConfig)
 {
-    if (!seqan::open(this->_stream, toCString(filename), "w"))
-    {
-        _isGood = false;
-        return 1;
-    }
-
-    return 0;
+    return joinConfig._lowerDiagonal;
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamWriter_::isGood()
+// Function setLowerDiagonal()
 // ----------------------------------------------------------------------------
 
-inline bool BamWriter_::isGood()
+template <typename TSpec>
+inline void setLowerDiagonal(JoinConfig<TSpec> & joinConfig, int lowerDiagonal)
 {
-    return this->_isGood;
+    joinConfig._isBandSet = true;
+    joinConfig._lowerDiagonal = lowerDiagonal;
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamWriter_::writeHeader()
+// Function setLowerDiagonal()
 // ----------------------------------------------------------------------------
 
-inline int BamWriter_::writeHeader(BamHeader const & header,
-                            BamIOContext<StringSet<CharString> > const & context)
+template <typename TSpec>
+inline int upperDiagonal(JoinConfig<TSpec> const & joinConfig)
 {
-    return write2(this->_stream, header, context, Bam());
+    return joinConfig._upperDiagonal;
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamWriter_::writeRecord()
+// Function setUpperDiagonal()
 // ----------------------------------------------------------------------------
 
-inline int BamWriter_::writeRecord(BamAlignmentRecord const & record,
-                                   BamIOContext<StringSet<CharString> > const & context)
+template <typename TSpec>
+inline void setUpperDiagonal(JoinConfig<TSpec> & joinConfig, int upperDiagonal)
 {
-    return write2(this->_stream, record, context, Bam());
+    joinConfig._isBandSet = true;
+    joinConfig._upperDiagonal = upperDiagonal;
 }
 
-// ----------------------------------------------------------------------------
-// Member Function BamWriter_::flush()
-// ----------------------------------------------------------------------------
 
-inline int BamWriter_::flush()
+inline Score<int, BiAffine> &
+scoringScheme(JoinConfig<GlobalAlign<JournaledCompact> > & joinConfig)
+{
+    return joinConfig._score;
+}
+
+inline Score<int, BiAffine> const &
+scoringScheme(JoinConfig<GlobalAlign<JournaledCompact> > const & joinConfig)
 {
-    return streamFlush(this->_stream);
+    return joinConfig._score;
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamWriter_::close()
+// Function setScoringScheme()
 // ----------------------------------------------------------------------------
 
-inline int BamWriter_::close()
+inline void
+setScoringScheme(JoinConfig<GlobalAlign<JournaledCompact> > & joinConfig, Score<int, BiAffine> const & scoringScheme)
 {
-    seqan::close(this->_stream);
-    return 0;
+    joinConfig._score = scoringScheme;
+    setScoreMismatch(joinConfig._score, -100000);   // Explicitly forbid mis matches in context with journaling.
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_WRITER_H_
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_CONFIG_H_
diff --git a/seqan/journaled_set/journaled_set_join_global_align_compact.h b/seqan/journaled_set/journaled_set_join_global_align_compact.h
new file mode 100644
index 0000000..40fb7bf
--- /dev/null
+++ b/seqan/journaled_set/journaled_set_join_global_align_compact.h
@@ -0,0 +1,85 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_COMPACT_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_COMPACT_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _joinInternal()                     [GlobalAlign<JournaledCompact>]
+// ----------------------------------------------------------------------------
+
+// TODO(rmaerker): Change the orientation of reference and journal.
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec, typename TJournalString2>
+inline void
+_joinInternal(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journal,
+              StringSet<TJournalString2, Owner<JournaledSet> > const & journalSet,
+              JoinConfig<GlobalAlign<JournaledCompact> > const & joinConfig)
+{
+    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;
+
+    // TODO(rmaerker): Check the correct behavior here.
+    TJournalString tmpJournal;
+    setHost(tmpJournal, value(journalSet._globalRefHolder));
+
+    if (isBandSet(joinConfig))
+        globalAlignment(tmpJournal, host(journalSet), journal, scoringScheme(joinConfig), joinConfig._alignConfig,
+                        lowerDiagonal(joinConfig), upperDiagonal(joinConfig));
+    else
+        globalAlignment(tmpJournal, host(journalSet), journal, scoringScheme(joinConfig), joinConfig._alignConfig);
+
+    // Apply the alignment to the journal.
+    set(journal, tmpJournal);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_COMPACT_H_
diff --git a/seqan/bam_io/xam_reader.h b/seqan/journaled_set/journaled_set_join_global_align_manhatten.h
similarity index 63%
rename from seqan/bam_io/xam_reader.h
rename to seqan/journaled_set/journaled_set_join_global_align_manhatten.h
index c8beccb..b61e32b 100644
--- a/seqan/bam_io/xam_reader.h
+++ b/seqan/journaled_set/journaled_set_join_global_align_manhatten.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,11 +29,11 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_XAM_READER_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_XAM_READER_H_
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_MANHATTEN_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_MANHATTEN_H_
 
 namespace seqan {
 
@@ -45,51 +45,6 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-// Base class implementing reading of SAM and BAM files.
-
-class XamReader_
-{
-public:
-    CharString _filename;
-
-    XamReader_()
-    {}
-
-    XamReader_(CharString const & filename) :
-        _filename(filename)
-    {}
-
-    virtual ~XamReader_()
-    {}
-
-    // Those of the following functions that return integers return status codes.  As usual, a status code of 0 means
-    // "OK", one != 0 means that there was an error.
-
-    // Open file with given name.
-    virtual int open(CharString const & filename) = 0;
-
-    // Return true if there is no error, false otherwise.
-    virtual bool isGood() = 0;
-
-    // Return true if read is at end.
-    virtual bool atEnd() = 0;
-
-    // Read the BAM header from the wrapped file.
-    virtual int readHeader(BamHeader & header, BamIOContext<StringSet<CharString> > & context) = 0;
-
-    // Read the next BAM record from the wrapped file.
-    virtual int readRecord(BamAlignmentRecord & record, BamIOContext<StringSet<CharString> > & context) = 0;
-
-    // Close the file again.
-    virtual int close() = 0;
-
-    // Return file size in bytes.
-    virtual __int64 fileSize() const = 0;
-
-    // Return approximate position in file.  For BAM, position of previous chunk is returned.
-    virtual __int64 positionInFile() const = 0;
-};
-
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -98,6 +53,29 @@ class XamReader_
 // Functions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Function _joinInternal()                   [GlobalAlign<JournaledManhatten>]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec, typename TJournalString2>
+inline void
+_joinInternal(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journal,
+              StringSet<TJournalString2, Owner<JournaledSet> > const & journalSet,
+              JoinConfig<GlobalAlign<JournaledManhatten> > const &)
+{
+
+    typedef String <TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;
+    typedef typename TJournalString::TJournalEntry TJounralEntry;
+//    typedef typename Size<TJournalString>::Type TSize;
+
+    JournalTraceBuffer<TJournalString> traceDescriptor;
+    std::stringstream stream;
+    stream << journal;
+    appendValue(getTrace(traceDescriptor), TJounralEntry(SOURCE_PATCH, 0, 0, 0,length(journal)));
+    append(getInsertionBuffer(traceDescriptor), stream.str());
+    _applyTraceOperations(journal, host(journalSet), traceDescriptor);
+}
+
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_XAM_READER_H_
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOIN_GLOBAL_ALIGN_MANHATTEN_H_
diff --git a/seqan/journaled_set/journaled_set_journal_trace_descriptor.h b/seqan/journaled_set/journaled_set_journal_trace_descriptor.h
new file mode 100644
index 0000000..c8d8e51
--- /dev/null
+++ b/seqan/journaled_set/journaled_set_journal_trace_descriptor.h
@@ -0,0 +1,463 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOURNAL_TRACE_DESCRIPTOR_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOURNAL_TRACE_DESCRIPTOR_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Enum TraceDirection
+// ----------------------------------------------------------------------------
+
+enum TraceDirection
+{
+        DIAGONAL,
+        HORIZONTAL,
+        VERTICAL
+};
+
+// ----------------------------------------------------------------------------
+// Class JournalTraceBuffer
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+class JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > >
+{
+public:
+    typedef String<TValue, Journaled< THostSpec, TJournalSpec, TBuffSpec> > TString;
+    typedef typename Position<TString>::Type TPos;
+    typedef typename Size<TString>::Type TSize;
+    typedef JournalEntry<TPos, TSize> TJournalNode;
+
+    // Stores the journal operations received from the trace back in reverse order.
+    String<TJournalNode> revSortedOperation_;
+    String<TValue, TBuffSpec> insertionBuffer_;
+
+    JournalTraceBuffer()
+    {
+    }
+
+    template <typename TPos>
+    inline typename Reference<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > >::Type
+    operator[](TPos const pos)
+    {
+        return value(*this, pos);
+    }
+
+    template <typename TPos>
+    inline typename Reference<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > const>::Type
+    operator[](TPos const pos) const
+    {
+        return value(*this, pos);
+    }
+
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Value<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > >
+{
+    typedef String<TValue, Journaled< THostSpec, TJournalSpec, TBuffSpec> > TString_;
+    typedef typename Position<TString_>::Type TPos_;
+    typedef typename Size<TString_>::Type TSize_;
+    typedef JournalEntry<TPos_, TSize_> Type;
+};
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Value<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > const>
+{
+    typedef String<TValue, Journaled< THostSpec, TJournalSpec, TBuffSpec> > TString_;
+    typedef typename Position<TString_>::Type TPos_;
+    typedef typename Size<TString_>::Type TSize_;
+    typedef JournalEntry<TPos_, TSize_> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Reference
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Reference<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > >
+{
+    typedef String<TValue, Journaled< THostSpec, TJournalSpec, TBuffSpec> > TString_;
+    typedef typename Value<JournalTraceBuffer<TString_> >::Type & Type;
+};
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Reference<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > const>
+{
+    typedef String<TValue, Journaled< THostSpec, TJournalSpec, TBuffSpec> > TString_;
+    typedef typename Value<JournalTraceBuffer<TString_> >::Type const & Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Size<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > >
+{
+    typedef String<TValue, Journaled< THostSpec, TJournalSpec, TBuffSpec> > TString_;
+    typedef typename Size<TString_>::Type Type;
+};
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Size<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > const>
+    : Size<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > >{};
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Position<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > >
+{
+    typedef String<TValue, Journaled< THostSpec, TJournalSpec, TBuffSpec> > TString_;
+    typedef typename Position<TString_>::Type Type;
+};
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Position<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > const>
+    : Position<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Iterator<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > >, Standard >
+{
+    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString_;
+    typedef typename TJournalString_::TJournalEntry TJournalEntry_;
+    typedef typename Iterator< String<TJournalEntry_>, Standard >::Type Type;
+};
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+struct Iterator<JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > const, Standard >
+{
+    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString_;
+    typedef typename TJournalString_::TJournalEntry TJournalEntry_;
+    typedef typename Iterator< String<TJournalEntry_> const, Standard >::Type Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function begin()
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+inline typename Iterator<JournalTraceBuffer<TString>, Standard >::Type
+begin(JournalTraceBuffer<TString> & me)
+{
+    SEQAN_CHECKPOINT;
+
+    return begin(getTrace(me));
+}
+
+template <typename TString>
+inline typename Iterator<JournalTraceBuffer<TString> const, Standard >::Type
+begin(JournalTraceBuffer<TString> const & me)
+{
+    return begin(getTrace(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function end()
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+inline typename Iterator<JournalTraceBuffer<TString>, Standard >::Type
+end(JournalTraceBuffer<TString> & me)
+{
+    return end(getTrace(me));
+}
+
+template <typename TString>
+inline typename Iterator<JournalTraceBuffer<TString> const, Standard >::Type
+end(JournalTraceBuffer<TString> const & me)
+{
+    return end(getTrace(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function operator<<()
+// ----------------------------------------------------------------------------
+
+template <typename TStream, typename TJournal>
+TStream &
+operator <<(TStream & stream,
+            JournalTraceBuffer<TJournal> const & obj)
+{
+    for (unsigned int i = 0; i < length(obj);++i)
+    {
+        if (obj[i].segmentSource == SOURCE_PATCH)
+        {
+            stream << obj[i] << " " <<infix(obj.insertionBuffer_,obj[i].physicalPosition, obj[i].physicalPosition + obj[i].length)<< std::endl;
+        } else
+        {
+            stream << obj[i] << std::endl;
+        }
+    }
+    return stream;
+}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+template <typename TJournal>
+inline typename Size<JournalTraceBuffer<TJournal> >::Type
+length(JournalTraceBuffer<TJournal> const & me)
+{
+    return length(me.revSortedOperation_);
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TJournalString>
+inline void
+clear(JournalTraceBuffer<TJournalString> & traceBuff)
+{
+    clear(traceBuff.revSortedOperation_);
+    clear(traceBuff.insertionBuffer_);
+}
+
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+template <typename TJournalString>
+inline typename Reference<JournalTraceBuffer<TJournalString> >::Type
+value(JournalTraceBuffer<TJournalString> & me,
+      typename Position<JournalTraceBuffer<TJournalString> >::Type const pos)
+{
+    SEQAN_CHECKPOINT;
+    return me.revSortedOperation_[pos];
+}
+
+template <typename TJournalString>
+inline typename Reference<JournalTraceBuffer<TJournalString> const>::Type
+value(JournalTraceBuffer<TJournalString> const & me,
+      typename Position<JournalTraceBuffer<TJournalString> >::Type const pos)
+{
+    return me.revSortedOperation_[pos];
+}
+
+// ----------------------------------------------------------------------------
+// Function getTrace()
+// ----------------------------------------------------------------------------
+
+template <typename TString>
+inline String <typename Value<JournalTraceBuffer<TString> >::Type> &
+getTrace(JournalTraceBuffer<TString > & me)
+{
+    return me.revSortedOperation_;
+}
+
+
+template <typename TString>
+inline String<typename Value<JournalTraceBuffer<TString> >::Type> const &
+getTrace(JournalTraceBuffer<TString> const & me)
+{
+    return me.revSortedOperation_;
+}
+
+// ----------------------------------------------------------------------------
+// Function reverseTrace()
+// ----------------------------------------------------------------------------
+
+// TODO(rmaerker): Use modifier instead.
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+void inline
+reverseTrace(JournalTraceBuffer<String< TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > & me)
+{
+    reverse(me.revSortedOperation_);
+}
+
+// ----------------------------------------------------------------------------
+// Function getTraceReverse()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+inline String <typename Value<JournalTraceBuffer<String< TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > >::Type>
+getTraceReverse(JournalTraceBuffer<String< TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > & me)
+{
+    SEQAN_CHECKPOINT;
+
+    typedef String< TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournal;
+    typedef typename Value<JournalTraceBuffer<TJournal> >::Type  TEntry;
+    typedef String<TEntry> TJournalEntries;
+
+    TJournalEntries cpy(me.revSortedOperation_);
+    reverse(cpy);
+    return cpy;
+}
+
+template <typename TString>
+inline String <typename Value<JournalTraceBuffer<TString> const>::Type> const
+getTraceReverse(JournalTraceBuffer<TString> const & me)
+{
+    SEQAN_CHECKPOINT;
+    return getTraceReverse(const_cast<JournalTraceBuffer<TString> &>(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function getInsertionBuffer()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+inline String<TValue, TBuffSpec> &
+getInsertionBuffer(JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > & me)
+{
+    SEQAN_CHECKPOINT;
+    return me.insertionBuffer_;
+}
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+inline String<TValue, TBuffSpec> const &
+getInsertionBuffer(JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > const & me)
+
+{
+    SEQAN_CHECKPOINT;
+    return me.insertionBuffer_;
+}
+
+
+// ----------------------------------------------------------------------------
+// Function _applyTraceOperations()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
+void
+_applyTraceOperations(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journal,
+                      String<TValue, THostSpec> const & newHost,
+                      JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > const & traceDescr)
+{
+    typedef String<TValue, THostSpec> THost;
+
+    setValue(journal._holder, const_cast<THost &>(newHost));
+    reinit(journal._journalEntries, length(newHost));
+    _constructAndSetJournalTree(journal, getTrace(traceDescr), getInsertionBuffer(traceDescr));
+}
+
+// ----------------------------------------------------------------------------
+// Function _alignTracePrint()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec, typename TSequenceH,
+    typename TSequenceV, typename TId, typename TPos, typename TTraceValue>
+inline void
+_alignTracePrint(JournalTraceBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > > & me,
+         TSequenceH const & /*seqH*/,
+         TSequenceV const & seqV,
+         TId,
+         TPos const pos1,
+         TId,
+         TPos const pos2,
+         TPos const segLen,
+         TTraceValue const tv)
+ {
+    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TString;
+    typedef typename Value<JournalTraceBuffer<TString> >::Type TEntryString;
+    typedef typename Value<TEntryString>::Type TJournalEntry;
+
+    enum SegmentSource segmentSrc = SOURCE_NULL;
+    TPos physicalPos = 0;
+    TPos physicalOriginPos = 0;
+
+    if (segLen == 0)
+    {
+        return;
+    }
+    switch (tv)
+    {
+    case DIAGONAL://matching area
+    {
+        segmentSrc = SOURCE_ORIGINAL;
+        physicalPos = pos1;
+        physicalOriginPos = pos1;
+        break;
+    }
+    case VERTICAL://insertion
+    {
+        segmentSrc = SOURCE_PATCH;
+        physicalPos = length(me.insertionBuffer_);
+        append(me.insertionBuffer_, infix(seqV,pos2, pos2 + segLen));
+        break;
+    }
+    case HORIZONTAL://deletion - nothing to be done here
+        return;
+        break;
+    }
+    // TODO(rmaerker): Change computation of physicalOrigin position when porting to new alignment module.
+    appendValue(getTrace(me), TJournalEntry(segmentSrc, physicalPos, pos2, physicalOriginPos, segLen));
+ }
+
+// ----------------------------------------------------------------------------
+// Function _constructAndSetJournalTree()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TBuffSpec, typename TCargo, typename THostSpec2>
+void
+_constructAndSetJournalTree(String<TValue, Journaled<THostSpec, SortedArray, TBuffSpec> > & journalSeq,
+                            String<TCargo, THostSpec2> const & cargoArray,
+                            String<TValue, TBuffSpec> const & insertionBuffer)
+{
+    assign(journalSeq._journalEntries._journalNodes, cargoArray);
+    assign(journalSeq._insertionBuffer, insertionBuffer);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_JOURNALED_SET_JOURNAL_TRACE_DESCRIPTOR_H_
diff --git a/seqan/journaled_set/score_biaffine.h b/seqan/journaled_set/score_biaffine.h
new file mode 100644
index 0000000..53648e4
--- /dev/null
+++ b/seqan/journaled_set/score_biaffine.h
@@ -0,0 +1,284 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_SET_SBIAFFINE_H_
+#define INCLUDE_SEQAN_JOURNALED_SET_SBIAFFINE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct BiAffine_;
+typedef Tag<BiAffine_> const BiAffine;
+
+template <typename TScoreValue>
+class Score<TScoreValue, BiAffine>
+{
+    public:
+    TScoreValue _match;
+    TScoreValue _mismatch;
+    TScoreValue _gapExtendHorizontal;
+    TScoreValue _gapOpenHorizontal;
+    TScoreValue _gapExtendVertical;
+    TScoreValue _gapOpenVertical;
+
+
+    Score() : _match(0),
+              _mismatch(0),
+              _gapExtendHorizontal(0),
+              _gapOpenHorizontal(0),
+              _gapExtendVertical(0),
+              _gapOpenVertical(0) {}
+
+    Score(TScoreValue match, TScoreValue mismatch, TScoreValue gap) :
+                                    _match(match),
+                                    _mismatch(mismatch),
+                                    _gapExtendHorizontal(gap),
+                                    _gapOpenHorizontal(gap),
+                                    _gapExtendVertical(gap),
+                                    _gapOpenVertical(gap) {}
+
+    Score(TScoreValue match, TScoreValue mismatch, TScoreValue gapExtend, TScoreValue gapOpen) :
+                                    _match(match),
+                                    _mismatch(mismatch),
+                                    _gapExtendHorizontal(gapExtend),
+                                    _gapOpenHorizontal(gapOpen),
+                                    _gapExtendVertical(gapExtend),
+                                    _gapOpenVertical(gapOpen) {}
+
+    Score(TScoreValue match, TScoreValue mismatch, TScoreValue gapExtendHorizontal, TScoreValue gapOpenHorizontal,
+          TScoreValue gapExtendVertical, TScoreValue gapOpenVertical) : _match(match),
+                                                                        _mismatch(mismatch),
+                                                                        _gapExtendHorizontal(gapExtendHorizontal),
+                                                                        _gapOpenHorizontal(gapOpenHorizontal),
+                                                                        _gapExtendVertical(gapExtendVertical),
+                                                                        _gapOpenVertical(gapOpenVertical) {}
+
+    Score(Score const & other) : _match(other._match),
+                                 _mismatch(other._mismatch),
+                                 _gapExtendHorizontal(other._gapExtendHorizontal),
+                                 _gapOpenHorizontal(other._gapOpenHorizontal),
+                                 _gapExtendVertical(other._gapExtendVertical),
+                                 _gapOpenVertical(other._gapOpenVertical) {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function score()
+// ----------------------------------------------------------------------------
+
+
+template <typename TScoreValue, typename TSeqEntry1, typename TSeqEntry2>
+inline TScoreValue
+score(Score<TScoreValue, BiAffine> const & me,
+      TSeqEntry1 const & seqEntry1,
+      TSeqEntry2 const & seqEntry2)
+{
+    if (seqEntry1 == static_cast<TSeqEntry1>(seqEntry2))
+        return me._match;
+    return me._mismatch;
+}
+
+// ----------------------------------------------------------------------------
+// Function scoreGapExtendHorizontal()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSeqEntry1, typename TSeqEntry2>
+inline TScoreValue
+scoreGapExtendHorizontal(Score<TScoreValue, BiAffine> const & me,
+                         TSeqEntry1 const & /*seqEntry1*/,
+                         TSeqEntry2 const & /*seqEntry2*/)
+{
+    return me._gapExtendHorizontal;
+}
+
+// ----------------------------------------------------------------------------
+// Function scoreGapOpenHorizontal()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSeqEntry1, typename TSeqEntry2>
+inline TScoreValue
+scoreGapOpenHorizontal(Score<TScoreValue, BiAffine> const & me,
+                       TSeqEntry1 const & /*seqEntry1*/,
+                       TSeqEntry2 const & /*seqEntry2*/)
+{
+    return me._gapOpenHorizontal;
+}
+
+// ----------------------------------------------------------------------------
+// Function scoreGapExtendVertical()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSeqEntry1, typename TSeqEntry2>
+inline TScoreValue
+scoreGapExtendVertical(Score<TScoreValue, BiAffine> const & me,
+                       TSeqEntry1 const & /*seqEntry1*/,
+                       TSeqEntry2 const & /*seqEntry2*/)
+{
+    return me._gapExtendVertical;
+}
+
+// ----------------------------------------------------------------------------
+// Function scoreGapOpenVertical()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue, typename TSeqEntry1, typename TSeqEntry2>
+inline TScoreValue
+scoreGapOpenVertical(Score<TScoreValue, BiAffine> const & me,
+                     TSeqEntry1 const & /*seqEntry1*/,
+                     TSeqEntry2 const & /*seqEntry2*/)
+{
+    return me._gapOpenVertical;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreMatch()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreMatch(Score<TScoreValue, BiAffine> & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._match = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreMismatch()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreMismatch(Score<TScoreValue, BiAffine>  & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._mismatch = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreGap()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreGap(Score<TScoreValue, BiAffine> & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._gapOpenHorizontal = score;
+    scoringScheme._gapOpenVertical = score;
+    scoringScheme._gapExtendHorizontal = score;
+    scoringScheme._gapExtendVertical = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreGapOpen()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreGapOpen(Score<TScoreValue, BiAffine> & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._gapOpenHorizontal = score;
+    scoringScheme._gapOpenVertical = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreGapExtend()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreGapExtend(Score<TScoreValue, BiAffine> & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._gapExtendHorizontal = score;
+    scoringScheme._gapExtendVertical = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreGapOpenHorizontal()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreGapOpenHorizontal(Score<TScoreValue, BiAffine> & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._gapOpenHorizontal = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreGapExtendHorizontal()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreGapExtendHorizontal(Score<TScoreValue, BiAffine> & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._gapExtendHorizontal = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreGapOpenVertical()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreGapOpenVertical(Score<TScoreValue, BiAffine> & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._gapOpenVertical = score;
+}
+
+// ----------------------------------------------------------------------------
+// Function setScoreGapExtendVertical()
+// ----------------------------------------------------------------------------
+
+template <typename TScoreValue>
+inline void
+setScoreGapExtendVertical(Score<TScoreValue, BiAffine> & scoringScheme, TScoreValue const & score)
+{
+    scoringScheme._gapExtendVertical = score;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_SET_SBIAFFINE_H_
diff --git a/seqan/journaled_string_tree.h b/seqan/journaled_string_tree.h
new file mode 100644
index 0000000..73a680f
--- /dev/null
+++ b/seqan/journaled_string_tree.h
@@ -0,0 +1,83 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Facade header for the journaled string tree.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_H_
+#define INCLUDE_SEQAN_JOURNALED_STRING_TREE_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#ifdef SEQAN_CXX11_STANDARD
+
+#include <seqan/basic.h>
+#include <seqan/sequence.h>
+#include <seqan/modifier.h>
+#include <seqan/sequence_journaled.h>
+#include <seqan/journaled_set.h>
+#include <seqan/parallel.h>
+#include <seqan/stream.h>
+
+// TODO(rrahn): Might put this to basic.
+#include <seqan/journaled_string_tree/observable.h>
+
+// ===========================================================================
+// Delta Map.
+// ===========================================================================
+
+#include <seqan/journaled_string_tree/delta_store.h>
+#include <seqan/journaled_string_tree/delta_map_entry.h>
+#include <seqan/journaled_string_tree/delta_map.h>
+#include <seqan/journaled_string_tree/delta_map_iterator.h>
+
+// ===========================================================================
+// Journaled String Tree.
+// ===========================================================================
+
+#include <seqan/journaled_string_tree/journaled_string_tree_base.h>
+#include <seqan/journaled_string_tree/journaled_string_tree_impl.h>
+
+// ===========================================================================
+// Journaled String Tree Traverser.
+// ===========================================================================
+
+#include <seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h>
+#include <seqan/journaled_string_tree/journaled_string_tree_traverser_node.h>
+#include <seqan/journaled_string_tree/journaled_string_tree_traverser_util.h>
+#include <seqan/journaled_string_tree/journaled_string_tree_traverser.h>
+
+#endif // SEQAN_CXX11_STANDARD
+#endif // INCLUDE_SEQAN_JOURNALED_STRING_TREE_H_
diff --git a/seqan/journaled_string_tree/delta_map.h b/seqan/journaled_string_tree/delta_map.h
new file mode 100644
index 0000000..2c4b247
--- /dev/null
+++ b/seqan/journaled_string_tree/delta_map.h
@@ -0,0 +1,1060 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements the delta map to efficiently store delta entries ordered by
+// their position within the base sequence in ascending order.
+// ==========================================================================
+
+#ifndef EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_H_
+#define EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag DeltaMapIteratorSpec
+// ----------------------------------------------------------------------------
+
+struct SpecDeltaMapIterator_;
+typedef Tag<SpecDeltaMapIterator_> DeltaMapIteratorSpec;
+
+// ----------------------------------------------------------------------------
+// Tag DeltaMapEntriesMember
+// ----------------------------------------------------------------------------
+
+struct DeltaMapEntriesMember_;
+typedef Tag<DeltaMapEntriesMember_> DeltaMapEntriesMember;
+
+// ----------------------------------------------------------------------------
+// Tag DeltaStoreMember
+// ----------------------------------------------------------------------------
+
+struct DeltaMapStoreMember_;
+typedef Tag<DeltaMapStoreMember_> DeltaMapStoreMember;
+
+// ----------------------------------------------------------------------------
+// Class DeltaMap
+// ----------------------------------------------------------------------------
+
+
+// TODO(rrahn): Add demo.
+/*!
+ * @class DeltaMap
+ *
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @brief Stores delta information and maps them to a common coordinate system.
+ *
+ * @signature template <typename TConfig>
+ *            class DeltaMap
+ * @tparam TConfig   A config type to set the types for the different delta values.
+ *
+ * This map stores delta events, i.e. replacements, insertions and deletions, for multiple sequences
+ * based on a common reference sequence. A bitvector is used to store the coverage of a delta.
+ * The types of the corresponding delta values must be set with the <tt>TConfig<\tt> object, which can be any
+ * object which defines the following types: 
+ * 
+ * <tt>TDeltaPos<\tt>: The value type used to store the position of the delta within the reference.
+ * <tt>TDeltaSnp<\tt>: The value type used to store SNPs.
+ * <tt>TDeltaDel<\tt>: The value type used to store deletions.
+ * <tt>TDeltaIns<\tt>: The value type used to store insertions.
+ * <tt>TDeltaSV<\tt>:  The value type used to store structural variants.
+ *
+ * The delta values are stored in a multi-container. To access a delta value at any given iterator position
+ * of the delta map the delta type (see @link DeltaTypeTags @endlink) must be known.
+ * The function @link DeltaMapIterator#deltaType @endlink can be used to access the id of the corresponding delta event. 
+ * Given the delta type the function @link DeltaMapIterator#deltaValue @endlink can be used to access the corresponding 
+ * value.
+ *
+ * The delta map implements the interfaces of the <b>AssociativeContainerConcept<\b> and is a multi-map.
+ */
+
+template <typename TConfig, typename TSpec = Default>
+class DeltaMap
+{
+public:
+
+    typedef typename Member<DeltaMap, DeltaMapEntriesMember>::Type TDeltaEntries;
+    typedef typename Member<DeltaMap, DeltaMapStoreMember>::Type TDeltaStore;
+
+    TDeltaEntries  _entries;
+    TDeltaStore    _deltaStore;
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Member                                  [DeltaMapEntriesMember]
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec>
+struct Member<DeltaMap<TConfig, TSpec>, DeltaMapEntriesMember>
+{
+    typedef typename Value<DeltaMap<TConfig, TSpec> >::Type TValue_;
+    typedef String<TValue_> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member                                    [DeltaMapStoreMember]
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec>
+struct Member<DeltaMap<TConfig, TSpec>, DeltaMapStoreMember>
+{
+    typedef typename TConfig::TSnpValue TSnpValue_;
+    typedef typename TConfig::TInsValue TInsValue_;
+    typedef typename TConfig::TDelValue TDelValue_;
+    typedef typename TConfig::TSVValue TSVValue_;
+    typedef impl::DeltaStore<TSnpValue_, TDelValue_, TInsValue_, TSVValue_> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member
+// ----------------------------------------------------------------------------
+
+// Const version.
+template <typename TConfig, typename TSpec, typename TTag>
+struct Member<DeltaMap<TConfig, TSpec> const, TTag>
+{
+    typedef typename Member<DeltaMap<TConfig, TSpec>, TTag>::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn DeltaMap#Value
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns value type for the delta map.
+ *
+ * @signature Value<TDeltaMap>::Type
+ * @tparam TDeltaMap The type to query the value type for.
+ * @return TValue The value type to use for <tt>TDeltaMap</tt>.
+ */
+
+template <typename TConfig, typename TSpec>
+struct Value<DeltaMap<TConfig, TSpec> >
+{
+    typedef typename Member<DeltaMap<TConfig, TSpec>, DeltaMapStoreMember>::Type TDeltaStore_;
+    typedef typename Size<TDeltaStore_>::Type TSize_;
+    typedef DeltaMapEntry<typename TConfig::TDeltaPos, TSize_> Type;
+};
+
+template <typename TConfig, typename TSpec>
+struct Value<DeltaMap<TConfig, TSpec> const>
+{
+    typedef typename Value<DeltaMap<TConfig, TSpec> >::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn DeltaMap#Size
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns size type for a delta map.
+ *
+ * @signature Size<TDeltaMap>::Type
+ * @tparam TDeltaMap The type to query the size type for.
+ * @return TSize The size type to use for <tt>TDeltaMap</tt>.
+ */
+
+template <typename TConfig, typename TSpec>
+struct Size<DeltaMap<TConfig, TSpec> >
+{
+    typedef typename Member<DeltaMap<TConfig, TSpec>, DeltaMapEntriesMember>::Type TEntries;
+    typedef typename Size<TEntries>::Type Type;
+};
+
+template <typename TConfig, typename TSpec>
+struct Size<DeltaMap<TConfig, TSpec> const > :
+    Size<DeltaMap<TConfig, TSpec> >{};
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator                                             [Standard]
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn DeltaMap#Iterator
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns iterator type for a delta map.
+ *
+ * @signature Iterator<TDeltaMap, Standard>::Type
+ * @tparam TDeltaMap The type to query the iterator type for.
+ * @return TIterator The iterator type to use for <tt>TDeltaMap</tt>. @link DeltaMapIterator @endlink.
+ */
+
+//template <typename TConfig, typename TSpec>
+//struct Iterator<DeltaMap<TConfig, TSpec>, Standard>
+//{
+//    typedef DeltaMap<TConfig, TSpec> TDeltaMap_;
+//    typedef Iter<TDeltaMap_, DeltaMapIteratorSpec> Type;
+//};
+//
+//template <typename TConfig, typename TSpec>
+//struct Iterator<DeltaMap<TConfig, TSpec> const, Standard>
+//{
+//    typedef DeltaMap<TConfig, TSpec> TDeltaMap_;
+//    typedef Iter<TDeltaMap_ const, DeltaMapIteratorSpec> Type;
+//};
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec, typename TIteratorSpec>
+struct Iterator<DeltaMap<TConfig, TSpec>, Tag<TIteratorSpec> const>
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap_;
+    typedef Iter<TDeltaMap_, DeltaMapIteratorSpec> Type;
+};
+
+template <typename TConfig, typename TSpec, typename TIteratorSpec>
+struct Iterator<DeltaMap<TConfig, TSpec> const, Tag<TIteratorSpec> const>
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap_;
+    typedef Iter<TDeltaMap_ const, DeltaMapIteratorSpec> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaValue
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn DeltaMap#DeltaValue
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns value type for a specific delta.
+ *
+ * @signature DeltaValue<TDeltaMap, TType>::Type
+ * @tparam TDeltaMap The type of the delta map.
+ * @tparam TType     The type of the delta value. One of @link DeltaTypeTags @endlink.
+ *
+ * The delta map stores four different delta events: SNPs, insertions, deletions and variable replacements.
+ * This metafunction returns the correct type for the specified event given the delta type tag.
+ */
+
+template <typename TConfig, typename TSpec, typename TDeltaType>
+struct DeltaValue<DeltaMap<TConfig, TSpec>, TDeltaType>
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap_;
+    typedef typename Member<TDeltaMap_, DeltaMapStoreMember>::Type TDeltaStore_;
+    typedef typename DeltaValue<TDeltaStore_, TDeltaType>::Type Type;
+};
+
+template <typename TConfig, typename TSpec, typename TDeltaType>
+struct DeltaValue<DeltaMap<TConfig, TSpec> const, TDeltaType>
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap_;
+    typedef typename Member<TDeltaMap_, DeltaMapStoreMember>::Type TDeltaStore_;
+    typedef typename DeltaValue<TDeltaStore_ const, TDeltaType>::Type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaCoverage
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn DeltaMap#DeltaCoverage
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns coverage type for a delta map.
+ *
+ * @signature DeltaCoverage<TDeltaMap>::Type
+ * @tparam TDeltaMap The type of the delta map.
+ */
+
+template <typename TConfig, typename TSpec>
+struct DeltaCoverage<DeltaMap<TConfig, TSpec> >
+{
+    typedef typename Value<DeltaMap<TConfig, TSpec> >::Type TEntry_;
+    typedef typename DeltaCoverage<TEntry_>::Type Type;
+};
+
+template <typename TConfig, typename TSpec>
+struct DeltaCoverage<DeltaMap<TConfig, TSpec> const>
+{
+    typedef typename Value<DeltaMap<TConfig, TSpec> >::Type TEntry_;
+    typedef typename DeltaCoverage<TEntry_ const>::Type Type;
+};
+
+
+// ============================================================================
+// Private Functions
+// ============================================================================
+
+namespace impl
+{
+
+// ----------------------------------------------------------------------------
+// Function impl::lbWrapper
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec, typename TEntry, typename TFunctor>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type
+lbWrapper(DeltaMap<TConfig, TSpec> const & deltaMap, TEntry const & entry, TFunctor const & f)
+{
+    return std::lower_bound(begin(deltaMap, Standard()), end(deltaMap, Standard()), entry, f);
+}
+
+template <typename TConfig, typename TSpec, typename TEntry, typename TFunctor>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Standard>::Type
+lbWrapper(DeltaMap<TConfig, TSpec> & deltaMap, TEntry const & entry, TFunctor const & f)
+{
+    return std::lower_bound(begin(deltaMap, Standard()), end(deltaMap, Standard()), entry, f);
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::ubWrapper
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec, typename TEntry, typename TFunctor>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type
+ubWrapper(DeltaMap<TConfig, TSpec> const & deltaMap, TEntry const & entry, TFunctor const & f)
+{
+    return std::upper_bound(begin(deltaMap, Standard()), end(deltaMap, Standard()), entry, f);
+}
+
+template <typename TConfig, typename TSpec, typename TEntry, typename TFunctor>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Standard>::Type
+ubWrapper(DeltaMap<TConfig, TSpec> & deltaMap, TEntry const & entry, TFunctor const & f)
+{
+    return std::upper_bound(begin(deltaMap, Standard()), end(deltaMap, Standard()), entry, f);
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::lowerBound();
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type
+lowerBound(DeltaMap<TConfig, TSpec> const & deltaMap,
+           TPosition const refPosition,
+           DeltaEndType const endType,
+           TDeltaType /*deltaType*/)
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap;
+    typedef typename Value<TDeltaMap>::Type TEntry;
+
+    TEntry entry;
+    entry.deltaPosition = refPosition;
+    entry.deltaRecord.i1 = selectDeltaType(TDeltaType());
+    entry.deltaTypeEnd = endType;
+    return impl::lbWrapper(deltaMap, entry, DeltaMapEntryPosAndTypeLessThanComparator_());
+}
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Standard>::Type
+lowerBound(DeltaMap<TConfig, TSpec> & deltaMap,
+           TPosition const refPosition,
+           DeltaEndType const endType,
+           TDeltaType /*deltaType*/)
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap;
+    typedef typename Value<TDeltaMap>::Type TEntry;
+
+    TEntry entry;
+    entry.deltaPosition = refPosition;
+    entry.deltaRecord.i1 = selectDeltaType(TDeltaType());
+    entry.deltaTypeEnd = endType;
+    return impl::lbWrapper(deltaMap, entry, DeltaMapEntryPosAndTypeLessThanComparator_());
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::upperBound();
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type
+upperBound(DeltaMap<TConfig, TSpec> const & deltaMap,
+           TPosition const refPosition,
+           DeltaEndType const endType,
+           TDeltaType /*deltaType*/)
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap;
+    typedef typename Value<TDeltaMap>::Type TEntry;
+
+    TEntry entry;
+    entry.deltaPosition = refPosition;
+    entry.deltaRecord.i1 = selectDeltaType(TDeltaType());
+    entry.deltaTypeEnd = endType;
+    return impl::ubWrapper(deltaMap, entry, DeltaMapEntryPosAndTypeLessThanComparator_());
+}
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Standard>::Type
+upperBound(DeltaMap<TConfig, TSpec> & deltaMap,
+           TPosition refPosition,
+           DeltaEndType const endType,
+           TDeltaType /*deltaType*/)
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap;
+    typedef typename Value<TDeltaMap>::Type TEntry;
+
+    TEntry entry;
+    entry.deltaPosition = refPosition;
+    entry.deltaRecord.i1 = selectDeltaType(TDeltaType());
+    entry.deltaTypeEnd = endType;
+    return impl::ubWrapper(deltaMap, entry, DeltaMapEntryPosAndTypeLessThanComparator_());
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::find();
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type
+find(DeltaMap<TConfig, TSpec> const & deltaMap,
+     TPosition const refPosition,
+     DeltaEndType const endType,
+     TDeltaType /*deltaType*/)
+{
+    auto it = lowerBound(deltaMap, refPosition, endType, TDeltaType());
+    if (it != end(deltaMap, Standard()) &&
+        static_cast<TPosition>(getDeltaPosition(*it)) == refPosition &&
+        getDeltaRecord(*it).i1 == selectDeltaType(TDeltaType()))
+        return it;
+    return end(deltaMap, Standard());
+}
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Standard>::Type
+find(DeltaMap<TConfig, TSpec> & deltaMap,
+     TPosition const refPosition,
+     DeltaEndType const endType,
+     TDeltaType /*deltaType*/)
+{
+    auto it = lowerBound(deltaMap, refPosition, endType, TDeltaType());
+    if (it != end(deltaMap, Standard()) &&
+        static_cast<TPosition>(getDeltaPosition(*it)) == refPosition &&
+        getDeltaRecord(*it).i1 == selectDeltaType(TDeltaType()))
+        return it;
+    return end(deltaMap, Standard());
+}
+
+
+// ----------------------------------------------------------------------------
+// Function impl::checkNoDuplicate()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap, typename TDeltaPos, typename TTag>
+inline bool
+checkNoDuplicate(TDeltaMap const & map, TDeltaPos pos, TTag /*deltaType*/)
+{
+    typedef typename Value<TDeltaMap>::Type TEntry;
+    typedef typename DeltaPosition<TEntry>::Type TEntryPos;
+
+    auto it = lowerBound(map, pos, TTag());
+    if (it != end(map, Standard()))
+        if (getDeltaPosition(*it) == static_cast<TEntryPos>(pos))
+            return getDeltaRecord(*it).i1 != selectDeltaType(TTag());
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::insert()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap, typename TDeltaPos, typename TDeltaValue, typename TCoverage, typename TTag>
+inline void
+insert(Iter<TDeltaMap, DeltaMapIteratorSpec> const & mapIt,
+       TDeltaPos deltaPos,
+       TDeltaValue const & deltaValue,
+       TCoverage const & coverage,
+       TTag const & deltaType)
+{
+    typedef typename Value<TDeltaMap>::Type TEntry;
+    typedef typename DeltaRecord<TEntry>::Type TDeltaRecord;
+
+    insertValue(mapIt._mapPtr->_entries, mapIt - begin(*mapIt._mapPtr, Standard()),
+                TEntry(deltaPos, TDeltaRecord(selectDeltaType(deltaType),
+                                              addDeltaValue(mapIt._mapPtr->_deltaStore, deltaValue, deltaType)),
+                                              coverage,
+                                              DeltaEndType::IS_BOTH));
+}
+
+template <typename TDeltaMap, typename TDeltaPos, typename TDeltaValue, typename TCoverage>
+inline void
+insert(Iter<TDeltaMap, DeltaMapIteratorSpec> mapIt,
+       TDeltaPos deltaPos,
+       TDeltaValue const & deltaValue,
+       TCoverage const & coverage,
+       DeltaTypeDel const & /*deltaType*/)
+{
+    typedef typename Value<TDeltaMap>::Type TEntry;
+    typedef typename DeltaRecord<TEntry>::Type TDeltaRecord;
+
+    DeltaEndType endType = DeltaEndType::IS_BOTH;
+    if (deltaValue > 1)
+        endType = DeltaEndType::IS_LEFT;
+
+    auto storePos = addDeltaValue(mapIt._mapPtr->_deltaStore, deltaValue, DeltaTypeDel());
+    insertValue(mapIt._mapPtr->_entries, mapIt - begin(*mapIt._mapPtr, Standard()),
+                TEntry(deltaPos, TDeltaRecord(DELTA_TYPE_DEL, storePos), coverage, endType));
+
+    if (endType == DeltaEndType::IS_LEFT)
+    {
+        deltaPos += deltaValue - 1;
+        mapIt = lowerBound(*mapIt._mapPtr, deltaPos, DeltaTypeDel());
+        insertValue(mapIt._mapPtr->_entries, mapIt - begin(*mapIt._mapPtr, Standard()),
+                    TEntry(deltaPos, TDeltaRecord(DELTA_TYPE_DEL, storePos), coverage, DeltaEndType::IS_RIGHT));
+    }
+}
+
+template <typename TDeltaMap, typename TDeltaPos, typename TDeltaValue, typename TCoverage>
+inline void
+insert(Iter<TDeltaMap, DeltaMapIteratorSpec> mapIt,
+       TDeltaPos deltaPos,
+       TDeltaValue const & deltaValue,
+       TCoverage const & coverage,
+       DeltaTypeSV const & /*deltaType*/)
+{
+    typedef typename Value<TDeltaMap>::Type TEntry;
+    typedef typename DeltaRecord<TEntry>::Type TDeltaRecord;
+
+    DeltaEndType endType = DeltaEndType::IS_BOTH;
+    if (deltaValue.i1 > 1)
+        endType = DeltaEndType::IS_LEFT;
+
+    auto storePos = addDeltaValue(mapIt._mapPtr->_deltaStore, deltaValue, DeltaTypeSV());
+    insertValue(mapIt._mapPtr->_entries, mapIt - begin(*mapIt._mapPtr, Standard()),
+                TEntry(deltaPos, TDeltaRecord(DELTA_TYPE_SV, storePos), coverage, endType));
+
+    if (endType == DeltaEndType::IS_LEFT)
+    {
+        deltaPos += deltaValue.i1 - 1;
+        mapIt = lowerBound(*mapIt._mapPtr, deltaPos, DeltaTypeSV());
+        insertValue(mapIt._mapPtr->_entries, mapIt - begin(*mapIt._mapPtr, Standard()),
+                    TEntry(deltaPos, TDeltaRecord(DELTA_TYPE_SV, storePos), coverage, DeltaEndType::IS_RIGHT));
+    }
+}
+
+}
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function lowerBound()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#lowerBound
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Finds the first element that compares not less than the specified key.
+ *
+ * @signature TIterator lowerBound(deltaMap, pos, type)
+ *
+ * @param[in] deltaMap  The delta map that is searched for the element.
+ * @param[in] pos       The delta position to be searched for.
+ * @param[in] type      The type of the delta operation. Must be of type @link DeltaTypeTags @endlink.
+ *
+ * @return TIterator An @link DeltaMap#Iterator @endlink pointing to the corresponding element.
+ *  If the key is not contained @link DeltaMap#end @endlink is returned.
+ *
+ * @remark The runtime is logarithmic in the size of the map.
+ */
+
+// Searches for the position and the delta type.
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type
+lowerBound(DeltaMap<TConfig, TSpec> const & deltaMap,
+           TPosition const refPosition,
+           TDeltaType /*deltaType*/)
+{
+    return impl::lowerBound(deltaMap, refPosition, DeltaEndType::IS_LEFT, TDeltaType());
+}
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Standard>::Type
+lowerBound(DeltaMap<TConfig, TSpec> & deltaMap,
+           TPosition const refPosition,
+           TDeltaType /*deltaType*/)
+{
+    return impl::lowerBound(deltaMap, refPosition, DeltaEndType::IS_LEFT, TDeltaType());
+}
+
+// ----------------------------------------------------------------------------
+// Function upperBound()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#upperBound
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Finds the first element that compares not less or equal to the specified key.
+ *
+ * @signature TIterator upperBound(deltaMap, pos, type)
+ *
+ * @param[in] deltaMap  The delta map that is searched for the element.
+ * @param[in] pos       The delta position to be searched for.
+ * @param[in] type      The type of the delta operation. Must be of type @link DeltaTypeTags @endlink.
+ *
+ * @return TIterator An @link DeltaMap#Iterator @endlink pointing to the corresponding element.
+ *  If the key is not contained @link DeltaMap#end @endlink is returned.
+ *
+ * @remark The runtime is logarithmic in the size of the map.
+ */
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type
+upperBound(DeltaMap<TConfig, TSpec> const & deltaMap,
+           TPosition const refPosition,
+           TDeltaType /*deltaType*/)
+{
+    return impl::upperBound(deltaMap, refPosition, DeltaEndType::IS_BOTH, TDeltaType());
+}
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Standard>::Type
+upperBound(DeltaMap<TConfig, TSpec> & deltaMap,
+           TPosition const refPosition,
+           TDeltaType /*deltaType*/)
+{
+    return impl::upperBound(deltaMap, refPosition, DeltaEndType::IS_BOTH, TDeltaType());
+}
+
+// ----------------------------------------------------------------------------
+// Function find()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#find
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Finds the element specified by the given delta position and delta type.
+ *
+ * @signature TIterator find(deltaMap, pos, type)
+ *
+ * @param[in] deltaMap  The delta map that is searched for the element.
+ * @param[in] pos       The delta position to be searched for.
+ * @param[in] type      The type of the delta operation. Must be of type @link DeltaTypeTags @endlink.
+ *
+ * @return TIterator An @link DeltaMap#Iterator @endlink pointing to the corresponding element.
+ *  If the key is not contained @link DeltaMap#end @endlink is returned.
+ *
+ * @remark The runtime is logarithmic in the size of the map.
+ */
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type
+find(DeltaMap<TConfig, TSpec> const & deltaMap,
+     TPosition const refPosition,
+     TDeltaType /*deltaType*/)
+{
+    return impl::find(deltaMap, refPosition, DeltaEndType::IS_LEFT, TDeltaType());
+}
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Standard>::Type
+find(DeltaMap<TConfig, TSpec> & deltaMap,
+     TPosition const refPosition,
+     TDeltaType /*deltaType*/)
+{
+    return impl::find(deltaMap, refPosition, DeltaEndType::IS_LEFT, TDeltaType());
+}
+
+// ----------------------------------------------------------------------------
+// Function count()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#count
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Counts the number of elements that compare equal to the specified key.
+ *
+ * @signature TSize count(deltaMap, pos, type)
+ *
+ * @param[in] deltaMap  The delta map that is searched for the element.
+ * @param[in] pos       The delta position to be searched for.
+ * @param[in] type      The type of the delta operation. Must be of type @link DeltaTypeTags @endlink.
+ *
+ * @return TSize the number of elements with the specified key. Of type @link DeltaMap#Size @endlink.
+ *
+ * @remark The runtime is logarithmic in the size of the map.
+ */
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline typename Size<DeltaMap<TConfig, TSpec> >::Type
+count(DeltaMap<TConfig, TSpec> const & deltaMap,
+      TPosition refPosition,
+      Tag<TDeltaType> /*deltaType*/)
+{
+    auto itB = lowerBound(deltaMap, refPosition, Tag<TDeltaType>());
+    auto count = 0;
+    while (itB != end(deltaMap, Standard()) &&
+           static_cast<TPosition>(getDeltaPosition(*itB)) == refPosition &&
+           getDeltaRecord(*itB).i1 == selectDeltaType(Tag<TDeltaType>()))
+    {
+        ++count;
+        ++itB;
+    }
+    return count;
+}
+
+// ----------------------------------------------------------------------------
+// Function equalRange()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#equalRange
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns the range over all elements comparing equal to the specified key.
+ *
+ * @signature Pair<TIterator> equalRange(deltaMap, pos, type)
+ *
+ * @param[in] deltaMap  The delta map that is searched for the element.
+ * @param[in] pos       The delta position to be searched for.
+ * @param[in] type      The type of the delta operation. Must be of type @link DeltaTypeTags @endlink.
+ *
+ * @return Pair<TIterator> A @link Pair @endlink of iterator types @link DeltaMap#Iterator @endlink. The first value points
+ *  to the first element that compares not less than the specified key or to the @link DeltaMap#end @endlink if such an elment could not be found.
+ * The second value points to the first element that does not compare less than or equal to the specified key or to the @link DeltaMap#end @endlink if such an elment could not be found.
+ *
+ * @remark The runtime is logarithmic in the size of the map.
+ */
+
+template <typename TConfig, typename TSpec, typename TPosition, typename TDeltaType>
+inline Pair<typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type>
+equalRange(DeltaMap<TConfig, TSpec> const & deltaMap, TPosition refPosition, TDeltaType /*deltaType*/)
+{
+    auto rBeg = lowerBound(deltaMap, refPosition, TDeltaType());
+    auto rEnd = upperBound(deltaMap, refPosition, TDeltaType());
+    return Pair<typename Iterator<DeltaMap<TConfig, TSpec> const, Standard>::Type>(rBeg, rEnd);
+}
+
+// ----------------------------------------------------------------------------
+// Function insert()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#insert
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Inserts a new delta entry.
+ *
+ * @signature bool insert(deltaMap, pos, val, cov, type);
+ *
+ * @param[in,out] deltaMap  The map to insert the new delta operation. Of type @link DeltaMap @endlink.
+ * @param[in]     pos       The position of the inserted delta entry.
+ * @param[in]     deltaVal  The value of the delta operation.
+ * @param[in]     cov       The coverage of the delta operation.
+ * @param[in]     type      A specifier to select the correct delta type. One of @link DeltaTypeTags @endlink.
+ *
+ *
+ * @remark The map is implemented as a vector and the insertion time is linear in worst case.
+ */
+
+// TODO(rrahn): Change to return iterator as specified for insert of associative containers of the STL.
+template <typename TConfig, typename TSpec, typename TDeltaPos, typename TDeltaValue,
+          typename TCoverage, typename TDeltaType>
+inline void
+insert(DeltaMap<TConfig, TSpec> & deltaMap,
+       TDeltaPos deltaPos,
+       TDeltaValue const & value,
+       TCoverage const & coverage,
+       TDeltaType const & /*deltaType*/)
+{
+    if (SEQAN_UNLIKELY(empty(deltaMap)))
+        reserve(deltaMap._entries, 1);
+
+    auto it = upperBound(deltaMap, deltaPos, TDeltaType());
+    impl::insert(it, deltaPos, value, coverage, TDeltaType());
+}
+
+// ----------------------------------------------------------------------------
+// Function erase()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#erase
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Erases an existing delta entry.
+ *
+ * @signature bool erase(deltaMap, pos, type);
+ *
+ * @param[in,out] deltaMap  The map to erase the delta from. Of type @link DeltaMap @endlink.
+ * @param[in]     pos       The position of the targeted delta entry.
+ * @param[in]     type      The type of the targeted delta entry. One of @link DeltaTypeTags @endlink.
+ *
+ * @return bool <tt>false<\tt> if such an entry does not exist, <tt>true<\tt> otherwise.
+ *
+ * @remark The map is implemented as a vector and the insertion time is linear in worst case.
+ */
+
+// TODO(rrahn): Change to return iterator as specified for insert of associative containers of the STL.
+// This is the key based method.
+// Also implement the iterator base method.
+// TODO(rrahn): Put position and delta type into a key type.
+template <typename TConfig, typename TSpec, typename TDeltaPos, typename TDeltaType>
+inline typename Size<DeltaMap<TConfig, TSpec> >::Type
+erase(DeltaMap<TConfig, TSpec> & deltaMap,
+      TDeltaPos deltaPos,
+      TDeltaType /*deltaType*/)
+{
+    typedef DeltaMap<TConfig, TSpec> TDeltaMap;
+    typedef typename Member<TDeltaMap, DeltaMapStoreMember>::Type TStore;
+    typedef typename Value<TDeltaMap>::Type TEntry;
+    typedef typename Size<TStore>::Type TStoreSize;
+
+    if (SEQAN_UNLIKELY(empty(deltaMap)))  // Check for empty deltaMap.
+        return false;
+
+    auto itRange = equalRange(deltaMap, deltaPos, TDeltaType());
+    auto count = itRange.i2 - itRange.i1;
+    if (itRange.i1 == end(deltaMap, Standard()))
+        return count;  // If lower bound is at end, there is no element with the given key.
+
+    for (auto it = itRange.i1; it != itRange.i2; ++it)
+    {
+        // Find potential right end of this delta.
+        if (!IsSameType<TDeltaType, DeltaTypeIns>::VALUE)
+        {
+            auto itR = impl::find(deltaMap,
+                                  deltaPos + deletionSize(deltaMap._deltaStore, getDeltaRecord(*it).i2, TDeltaType()) - 1,
+                                  DeltaEndType::IS_RIGHT,
+                                  TDeltaType());
+
+            SEQAN_ASSERT_LEQ(position(it, deltaMap), position(itR, deltaMap));
+            if (it != itR)
+            {
+                erase(deltaMap._entries, itR - begin(deltaMap, Standard()));
+                ++count;  // Increase count number by removed entry.
+            }
+        }
+
+        // Erase the delta record from the corresponding delta store.
+        TStoreSize storePos = getDeltaRecord(*it).i2;
+        SEQAN_ASSERT_LT(storePos, length(getDeltaStore(deltaMap._deltaStore, TDeltaType())));
+        eraseDeltaValue(deltaMap._deltaStore, storePos, TDeltaType());
+        // Update record position for all entries.
+        forEach(deltaMap, [storePos](TEntry & entry)
+        {
+            if (getDeltaRecord(entry).i1 == selectDeltaType(TDeltaType()) && getDeltaRecord(entry).i2 > storePos)
+                --getDeltaRecord(entry).i2;  // Decrease record position by one.
+        });
+    }
+
+    // Erase all entries in the range of equal values.
+    erase(deltaMap._entries, position(itRange.i1, deltaMap), position(itRange.i2, deltaMap));
+
+    return count;
+}
+
+// ----------------------------------------------------------------------------
+// Function begin()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#begin
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns an iterator pointing to the beginning of the map.
+ *
+ * @signature TIterator begin(deltaMap, tag)
+ *
+ * @param[in] deltaMap  The map to get the iterator for.
+ * @param[in] tag       The iterator tag. Of type @link ContainerIteratorTags @endlink.
+ *
+ * @return TIterator An iterator of type @link DeltaMap#Iterator @endlink pointing to the beginning of the map.
+ */
+
+template <typename TConfig, typename TSpec, typename TIteratorSpec>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Tag<TIteratorSpec> const>::Type
+begin(DeltaMap<TConfig, TSpec> & deltaMap, Tag<TIteratorSpec> const /*tag*/)
+{
+    return typename Iterator<DeltaMap<TConfig, TSpec>, Tag<TIteratorSpec> const>::Type(deltaMap, 0);
+}
+
+template <typename TConfig, typename TSpec, typename TIteratorSpec>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Tag<TIteratorSpec> const>::Type
+begin(DeltaMap<TConfig, TSpec> const & deltaMap, Tag<TIteratorSpec> const/*tag*/)
+{
+    return typename Iterator<DeltaMap<TConfig, TSpec> const, Tag<TIteratorSpec> const>::Type(deltaMap, 0);
+}
+
+// ----------------------------------------------------------------------------
+// Function iter()
+// ----------------------------------------------------------------------------
+
+template <typename TConfig, typename TSpec, typename TIteratorSpec, typename TPos>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Tag<TIteratorSpec> const>::Type
+iter(DeltaMap<TConfig, TSpec> & deltaMap,
+     TPos const & pos,
+     Tag<TIteratorSpec> const /*tag*/)
+{
+    return typename Iterator<DeltaMap<TConfig, TSpec>, Tag<TIteratorSpec> const>::Type(deltaMap, pos);
+}
+
+template <typename TConfig, typename TSpec, typename TIteratorSpec, typename TPos>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Tag<TIteratorSpec> const>::Type
+iter(DeltaMap<TConfig, TSpec> const & deltaMap,
+     TPos const & pos,
+     Tag<TIteratorSpec> const &/*tag*/)
+{
+    return typename Iterator<DeltaMap<TConfig, TSpec> const, Tag<TIteratorSpec> const>::Type(deltaMap, pos);
+}
+
+// ----------------------------------------------------------------------------
+// Function end()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#end
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns an iterator pointing to the end of the map.
+ *
+ * @signature TIterator end(deltaMap, tag)
+ *
+ * @param[in] deltaMap  The map to get the iterator for.
+ * @param[in] tag       The iterator tag. Of type @link ContainerIteratorTags @endlink.
+ *
+ * @return TIterator An iterator of type @link DeltaMap#Iterator @endlink pointing to the end of the map.
+ */
+
+template <typename TConfig, typename TSpec, typename TIteratorSpec>
+inline typename Iterator<DeltaMap<TConfig, TSpec>, Tag<TIteratorSpec> const>::Type
+end(DeltaMap<TConfig, TSpec> & deltaMap, Tag<TIteratorSpec> const /*tag*/)
+{
+    return typename Iterator<DeltaMap<TConfig, TSpec>, Tag<TIteratorSpec> const>::Type(deltaMap, size(deltaMap));
+}
+
+template <typename TConfig, typename TSpec, typename TIteratorSpec>
+inline typename Iterator<DeltaMap<TConfig, TSpec> const, Tag<TIteratorSpec> const>::Type
+end(DeltaMap<TConfig, TSpec> const & deltaMap, Tag<TIteratorSpec> const /*tag*/)
+{
+    return typename Iterator<DeltaMap<TConfig, TSpec> const, Tag<TIteratorSpec> const>::Type(deltaMap, size(deltaMap));
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#clear
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Clears the delta map.
+ *
+ * @signature clear(deltaMap)
+ *
+ * @param[in,out] deltaMap  The map to be cleared.
+ */
+
+template <typename TConfig, typename TSpec>
+inline void
+clear(DeltaMap<TConfig, TSpec> & deltaMap)
+{
+    clear(deltaMap._entries);
+    clear(deltaMap._deltaStore);
+}
+
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#empty
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Checks if the delta map is empty.
+ *
+ * @signature bool empty(deltaMap)
+ *
+ * @param[in] deltaMap  The map to be checked for.
+ *
+ * @return bool <tt>true</tt> if empty, otherwise <tt>false</tt>
+ */
+
+template <typename TConfig, typename TSpec>
+inline bool
+empty(DeltaMap<TConfig, TSpec> const & deltaMap)
+{
+    return empty(deltaMap._entries);
+}
+
+// ----------------------------------------------------------------------------
+// Function size()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#size
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns the number of mapped delta events.
+ *
+ * @signature TSize size(deltaMap)
+ *
+ * @param[in] deltaMap  The map to get the size for.
+ *
+ * @return TSize The number of delta events stored in the map.
+ */
+
+template <typename TConfig, typename TSpec>
+inline auto
+size(DeltaMap<TConfig, TSpec> const & deltaMap) -> decltype(length(deltaMap._entries))
+{
+    return length(deltaMap._entries);
+}
+
+// ----------------------------------------------------------------------------
+// Function maxSize()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMap#maxSize
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns the number of mapped delta events.
+ *
+ * @signature TSize size(deltaMap)
+ *
+ * @param[in] deltaMap  The map to get the size for.
+ *
+ * @return TSize The number of delta events stored in the map.
+ */
+
+template <typename TConfig, typename TSpec>
+constexpr typename Size<DeltaMap<TConfig, TSpec> >::Type
+maxSize(DeltaMap<TConfig, TSpec> const & /*deltaMap*/)
+{
+    return MaxValue<typename Size<DeltaMap<TConfig, TSpec> >::Type>::VALUE;
+}
+
+}
+
+#endif // EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_H_
diff --git a/seqan/journaled_string_tree/delta_map_entry.h b/seqan/journaled_string_tree/delta_map_entry.h
new file mode 100644
index 0000000..54f31e4
--- /dev/null
+++ b/seqan/journaled_string_tree/delta_map_entry.h
@@ -0,0 +1,459 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements the delta map entry.
+// ==========================================================================
+
+#ifndef EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_ENTRY_H_
+#define EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_ENTRY_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename T>
+struct DeltaCoverage;
+
+template <typename T>
+struct DeltaPosition;
+
+template <typename T>
+struct DeltaRecord;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+enum class DeltaEndType : __uint8
+{
+    IS_RIGHT = 1,   // 0x01
+    IS_LEFT  = 2,   // 0x10
+    IS_BOTH  = 3    // 0x11
+};
+
+// ----------------------------------------------------------------------------
+// Tag DeltaMapEntryCoverage
+// ----------------------------------------------------------------------------
+
+struct DeltaMapEntryCoverage_;
+typedef Tag<DeltaMapEntryCoverage_> DeltaMapEntryCoverage;
+
+// ----------------------------------------------------------------------------
+// Tag DeltaMapEntryDeltaStoreValue
+// ----------------------------------------------------------------------------
+
+struct DeltaMapEntryDeltaPosition_;
+typedef Tag<DeltaMapEntryDeltaPosition_> DeltaMapEntryDeltaPosition;
+
+// ----------------------------------------------------------------------------
+// Class DeltaMapEntry
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+class DeltaMapEntry
+{
+public:
+
+    typedef typename DeltaCoverage<DeltaMapEntry>::Type TCoverage;
+    typedef typename DeltaPosition<DeltaMapEntry>::Type TDeltaPos;
+    typedef typename DeltaRecord<DeltaMapEntry>::Type TDeltaRecord;
+
+    TDeltaPos    deltaPosition;
+    TDeltaRecord deltaRecord;
+    TCoverage    deltaCoverage;
+    DeltaEndType deltaTypeEnd;
+
+    // Default C'tor.
+    DeltaMapEntry()
+    {}
+
+    // Custom C'tor.
+    DeltaMapEntry(TDeltaPos _deltaPos, TDeltaRecord _deltaRecord, TCoverage const & _coverage) :
+    deltaPosition(_deltaPos),
+    deltaRecord(_deltaRecord),
+    deltaCoverage(_coverage),
+    deltaTypeEnd(DeltaEndType::IS_BOTH)
+    {}
+
+    DeltaMapEntry(TDeltaPos _deltaPos, TDeltaRecord _deltaRecord, TCoverage const & _coverage, DeltaEndType endType) :
+        deltaPosition(_deltaPos),
+        deltaRecord(_deltaRecord),
+        deltaCoverage(_coverage),
+        deltaTypeEnd(endType)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class DeltaMapEntryPosAndTypeLessThanComparator_
+// ----------------------------------------------------------------------------
+
+struct DeltaMapEntryPosAndTypeLessThanComparator_
+{
+
+    template <typename TEntry>
+    bool operator()(TEntry const & lhs, TEntry const & rhs)
+    {
+        if (lhs.deltaPosition == rhs.deltaPosition)
+        {
+            if (lhs.deltaRecord.i1 == rhs.deltaRecord.i1)
+            {
+                return lhs.deltaTypeEnd < rhs.deltaTypeEnd;  // Order: IS_RIGHT, IS_LEFT, IS_BOTH
+            }
+            return lhs.deltaRecord.i1 > rhs.deltaRecord.i1;  // Switch the comaprison in descending order to match ordering of DeltaTypeSelector.
+        }
+        return lhs.deltaPosition < rhs.deltaPosition;
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class DeltaMapEntryPosLessThanComparator_
+// ----------------------------------------------------------------------------
+
+struct DeltaMapEntryPosLessThanComparator_
+{
+
+    template <typename TEntry>
+    bool operator()(TEntry const & lhs, TEntry const & rhs)
+    {
+        return lhs.deltaPosition < rhs.deltaPosition;
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaPosition
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+struct DeltaPosition<DeltaMapEntry<TRefPos, TStorePos> >
+{
+    typedef TRefPos Type;
+};
+
+template <typename TRefPos, typename TStorePos>
+struct DeltaPosition<DeltaMapEntry<TRefPos, TStorePos> const>
+{
+    typedef TRefPos const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaCoverage
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+struct DeltaCoverage<DeltaMapEntry<TRefPos, TStorePos> >
+{
+    typedef String<bool, Packed<> > Type;
+};
+
+template <typename TRefPos, typename TStorePos>
+struct DeltaCoverage<DeltaMapEntry<TRefPos, TStorePos> const>
+{
+    typedef typename DeltaCoverage<DeltaMapEntry<TRefPos, TStorePos> >::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaRecord
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+struct DeltaRecord<DeltaMapEntry<TRefPos, TStorePos> >
+{
+    static const unsigned REMAINING_BITS = BitsPerValue<TStorePos>::VALUE - BitsPerValue<DeltaType>::VALUE;
+    typedef Pair<TStorePos, TStorePos, BitPacked<BitsPerValue<DeltaType>::VALUE, REMAINING_BITS> > Type;
+};
+
+template <typename TRefPos, typename TStorePos>
+struct DeltaRecord<DeltaMapEntry<TRefPos, TStorePos> const>
+{
+    typedef typename DeltaRecord<DeltaMapEntry<TRefPos, TStorePos> >::Type const Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function setRefPosition()
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos, typename TPosition>
+inline void
+setDeltaPosition(DeltaMapEntry<TRefPos, TStorePos> & deltaEntry, TPosition newRefPos)
+{
+    deltaEntry.refPos = newRefPos;
+}
+
+// ----------------------------------------------------------------------------
+// Function getRefPosition()
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+inline typename DeltaPosition<DeltaMapEntry<TRefPos, TStorePos> >::Type &
+getDeltaPosition(DeltaMapEntry<TRefPos, TStorePos> & deltaEntry)
+{
+    return deltaEntry.deltaPosition;
+}
+
+template <typename TRefPos, typename TStorePos>
+inline typename DeltaPosition<DeltaMapEntry<TRefPos, TStorePos> const>::Type &
+getDeltaPosition(DeltaMapEntry<TRefPos, TStorePos> const & deltaEntry)
+{
+    return deltaEntry.deltaPosition;
+}
+
+// ----------------------------------------------------------------------------
+// Function setDeltaCoverage()
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos, typename TCoverage>
+inline void
+setDeltaCoverage(DeltaMapEntry<TRefPos, TStorePos> & deltaEntry, TCoverage newDeltaCoverage)
+{
+    deltaEntry.deltaCoverage = newDeltaCoverage;
+}
+
+// ----------------------------------------------------------------------------
+// Function getDeltaCoverage()
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+inline typename DeltaCoverage<DeltaMapEntry<TRefPos, TStorePos> >::Type &
+getDeltaCoverage(DeltaMapEntry<TRefPos, TStorePos> & deltaEntry)
+{
+    return deltaEntry.deltaCoverage;
+}
+
+template <typename TRefPos, typename TStorePos>
+inline typename DeltaCoverage<DeltaMapEntry<TRefPos, TStorePos> const>::Type &
+getDeltaCoverage(DeltaMapEntry<TRefPos, TStorePos> const & deltaEntry)
+{
+    return deltaEntry.deltaCoverage;
+}
+
+// ----------------------------------------------------------------------------
+// Function setDeltaRecord()
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos, typename TRecord>
+inline void
+setDeltaRecord(DeltaMapEntry<TRefPos, TStorePos> & deltaEntry, TRecord newDeltaRecord)
+{
+    deltaEntry.deltaRecord = newDeltaRecord;
+}
+
+// ----------------------------------------------------------------------------
+// Function getDeltaCoverage()
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+inline typename DeltaRecord<DeltaMapEntry<TRefPos, TStorePos> >::Type &
+getDeltaRecord(DeltaMapEntry<TRefPos, TStorePos> & deltaEntry)
+{
+    return deltaEntry.deltaRecord;
+}
+
+template <typename TRefPos, typename TStorePos>
+inline typename DeltaRecord<DeltaMapEntry<TRefPos, TStorePos> const>::Type &
+getDeltaRecord(DeltaMapEntry<TRefPos, TStorePos> const & deltaEntry)
+{
+    return deltaEntry.deltaRecord;
+}
+
+/*
+ * @fn getStorePosition
+ *
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @brief Returns the id of the delta event the current iterator points to.
+ *
+ * @signature TId deltaType(it)
+ * @param[in]   it  The iterator to query the delta event key for.
+ *
+ * @return TId The id for the current delta event of type <tt>DeltaType</tt>.
+ */
+
+template <typename TRefPos, typename TStorePos>
+inline TStorePos
+getStorePosition(DeltaMapEntry<TRefPos, TStorePos> const & deltaEntry)
+{
+    return getDeltaRecord(deltaEntry).i2;
+}
+
+/*
+ * @fn getDeltaType
+ *
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @brief Returns the id of the delta event the current iterator points to.
+ *
+ * @signature TId deltaType(it)
+ * @param[in]   it  The iterator to query the delta event key for.
+ *
+ * @return TId The id for the current delta event of type <tt>DeltaType</tt>.
+ */
+
+template <typename TRefPos, typename TStorePos>
+inline DeltaType
+getDeltaType(DeltaMapEntry<TRefPos, TStorePos> const & deltaEntry)
+{
+    return static_cast<DeltaType>(getDeltaRecord(deltaEntry).i1);
+}
+
+// ----------------------------------------------------------------------------
+// Function isLeftEnd();
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+inline bool
+isLeftEnd(DeltaMapEntry<TRefPos, TStorePos> const & deltaEntry)
+{
+    return deltaEntry.deltaEndType == DeltaEndType::IS_LEFT;
+}
+
+// ----------------------------------------------------------------------------
+// Function isRightEnd();
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+inline bool
+isRightEnd(DeltaMapEntry<TRefPos, TStorePos> const & deltaEntry)
+{
+    return deltaEntry.deltaTypeEnd == DeltaEndType::IS_RIGHT;
+}
+
+// ----------------------------------------------------------------------------
+// Function applyOnDelta()
+// ----------------------------------------------------------------------------
+
+template <typename TFunctor>
+inline bool
+applyOnDelta(TFunctor & /*func*/,
+             DeltaType const & /*type*/,
+             TagSelector<void> const & /*selector*/)
+{
+    return false;
+}
+
+template <typename TFunctor, typename TTag, typename TSubList>
+inline bool
+applyOnDelta(TFunctor & func,
+             DeltaType const & deltaType,
+             TagSelector<TagList<TTag, TSubList> > const & selector)
+{
+    typedef TagSelector<TagList<TTag, TSubList> >   TTagSelector;
+    if (isDeltaType(deltaType, TTag()))
+    {
+        func(TTag());
+        return true;
+    }
+    return applyOnDelta(func, deltaType, static_cast<typename TTagSelector::Base>(selector));
+}
+
+// ----------------------------------------------------------------------------
+// Function operator==()
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+inline bool operator==(DeltaMapEntry<TRefPos, TStorePos> const & lhs, DeltaMapEntry<TRefPos, TStorePos> const & rhs)
+{
+    return (lhs.deltaPosition == rhs.deltaPosition) && (lhs.deltaRecord == rhs.deltaRecord) &&
+           (lhs.deltaCoverage == rhs.deltaCoverage);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator!=()
+// ----------------------------------------------------------------------------
+
+template <typename TRefPos, typename TStorePos>
+inline bool operator!=(DeltaMapEntry<TRefPos, TStorePos> const & lhs, DeltaMapEntry<TRefPos, TStorePos> const & rhs)
+{
+    return !(lhs == rhs);
+}
+
+// ----------------------------------------------------------------------------
+// Function _printCoverage()
+// ----------------------------------------------------------------------------
+
+template <typename TCoverage>
+inline String<char>
+_printCoverage(TCoverage const & cov)
+{
+    String<char> tmp;
+    for (bool elem : cov)
+        if (elem)
+            appendValue(tmp, '1');
+        else
+            appendValue(tmp, '0');
+    return tmp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator<<()
+// ----------------------------------------------------------------------------
+
+template <typename TStream, typename TRefPos, typename TStorePos>
+inline TStream & operator<<(TStream & stream, DeltaMapEntry<TRefPos, TStorePos> const & entry)
+{
+    stream << "<" << entry.deltaPosition << ", ";
+    switch (entry.deltaRecord.i1)
+    {
+        case DELTA_TYPE_SNP: stream << "SNP ("; break;
+        case DELTA_TYPE_DEL: stream << "DEL ("; break;
+        case DELTA_TYPE_INS: stream << "INS ("; break;
+        case DELTA_TYPE_SV: stream << "SV ("; break;
+        default: stream << "NA ("; break;
+    }
+    stream << entry.deltaRecord.i2 << "), " << _printCoverage(entry.deltaCoverage) << ", ";
+    switch (entry.deltaTypeEnd)
+    {
+        case DeltaEndType::IS_LEFT: stream << "IS_LEFT";
+            break;
+        case DeltaEndType::IS_RIGHT: stream << "IS_RIGHT";
+            break;
+        case DeltaEndType::IS_BOTH: stream << "IS_BOTH";
+            break;
+    }
+    stream << ">";
+    return stream;
+}
+
+}
+
+#endif // EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_ENTRY_H_
diff --git a/seqan/journaled_string_tree/delta_map_iterator.h b/seqan/journaled_string_tree/delta_map_iterator.h
new file mode 100644
index 0000000..915c493
--- /dev/null
+++ b/seqan/journaled_string_tree/delta_map_iterator.h
@@ -0,0 +1,600 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements the iterator over the delta map.
+// ==========================================================================
+
+#ifndef EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_ITERATOR_H_
+#define EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_ITERATOR_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TType, typename TOtherType> struct IsConstructible;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+/*!
+ * @class DeltaMapIterator
+ * @implements BidirectionalIteratorConcept
+ * @extends Iter
+ *
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @brief Bidirectional iterator over a @link DeltaMap @endlink.
+ *
+ * @signature template <typename TDeltaMap>
+ *            class Iter<TDeltaMap, DeltaMapIteratorSpec>;
+ *
+ * @tparam TDeltaMap The delta map to iterate.
+ */
+
+template <typename TDeltaMap>
+class Iter<TDeltaMap, DeltaMapIteratorSpec>
+{
+public:
+    typedef typename RemoveConst<TDeltaMap>::Type TNonConstDeltaMap_;
+
+    typedef typename Member<TDeltaMap, DeltaMapEntriesMember>::Type TMapEntries_;
+    typedef typename Iterator<TMapEntries_, Standard>::Type TMapIterator;
+
+    TDeltaMap*   _mapPtr;
+    TMapIterator _mapIter;
+
+    //Default C'tor.
+    Iter() : _mapPtr(NULL), _mapIter()
+    {}
+
+    // Copy C'tor.
+    template <typename TDeltaMapOther>
+    Iter(Iter<TDeltaMapOther, DeltaMapIteratorSpec> const & other,
+         SEQAN_CTOR_ENABLE_IF(IsConstructible<TDeltaMap, TDeltaMapOther>)) :
+        _mapPtr(other._mapPtr),
+        _mapIter(other._mapIter)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    // Custom C'tor.
+    template <typename TPos>
+    Iter(TDeltaMap & container, TPos pos) : _mapPtr(&container), _mapIter()
+    {
+        _mapIter = begin(_mapPtr->_entries, Standard()) + pos;
+    }
+
+    // Assignment Operator.
+    template <typename TDeltaMapOther>
+    SEQAN_FUNC_DISABLE_IF(IsConstructible<TDeltaMap, TDeltaMapOther>, Iter<TDeltaMap, DeltaMapIteratorSpec> &)
+    operator=(Iter<TDeltaMapOther, DeltaMapIteratorSpec> const & other)
+    {
+        _mapPtr = other._mapPtr;
+        _mapIter = other._mapIter;
+        return *this;
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Difference
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+struct Difference<Iter<TDeltaMap, DeltaMapIteratorSpec> >
+{
+    typedef Iter<TDeltaMap, DeltaMapIteratorSpec> TIter_;
+    typedef typename TIter_::TMapIterator TMapIterator_;
+    typedef typename Difference<TMapIterator_>::Type Type;
+};
+
+template <typename TDeltaMap>
+struct Difference<Iter<TDeltaMap, DeltaMapIteratorSpec> const > :
+    Difference<Iter<TDeltaMap, DeltaMapIteratorSpec> >{};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function container()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline typename Container<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type &
+container(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter)
+{
+    return *iter._mapPtr;
+}
+
+template <typename TDeltaMap>
+inline typename Container<Iter<TDeltaMap, DeltaMapIteratorSpec> const>::Type &
+container(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter)
+{
+    return *iter._mapPtr;
+}
+
+// ----------------------------------------------------------------------------
+// Function deltaType()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn DeltaMapIterator#deltaType
+ *
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @brief Returns the delta type associated with the current value the iterator is pointing to.
+ *
+ * @signature DeltaType deltaType(it);
+ * @param[in]   it   The iterator pointing to the value for which the delta type should be determined.
+ *
+ * @return DeltaType The type of the current value. Of type @link DeltaType @endlink.
+ */
+
+template <typename TDeltaMap>
+inline DeltaType
+deltaType(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter)
+{
+    return getDeltaType(*iter);
+}
+
+// ----------------------------------------------------------------------------
+// Function deltaValue()
+// ----------------------------------------------------------------------------
+
+// TODO(rrahn): Let iterator return proxy and access values using the proxy.
+/*!
+ * @fn DeltaMapIterator#deltaValue
+ *
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @brief Returns the delta value associated with the current iterator position.
+ *
+ * @signature TDeltaValue deltaValue(it, tag);
+ * @param[in]   it  The iterator to query the delta event for.
+ * @param[in]   tag The tag used to select the requested delta type.
+ *
+ * @return TDeltaValue A reference to the delta at the current iterator position of type @link DeltaMap#DeltaValue @endlink.
+ * @remark Note the expression <tt>isDeltaType(deltaType(it), tag)<\tt> must evaluate to <tt>true<\tt>, otherwise the result is undefined.
+ */
+
+template <typename TDeltaMap, typename TTag>
+inline typename DeltaValue<typename Container<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type, TTag>::Type &
+deltaValue(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter, TTag const & tag)
+{
+    SEQAN_ASSERT(isDeltaType(deltaType(iter), TTag()));
+    return deltaValue(container(iter)._deltaStore, getDeltaRecord(value(iter)).i2, tag);
+}
+
+template <typename TDeltaMap, typename TTag>
+inline typename DeltaValue<typename Container<Iter<TDeltaMap, DeltaMapIteratorSpec> const>::Type, TTag>::Type &
+deltaValue(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter, TTag const & tag)
+{
+    return deltaValue(container(iter)._deltaStore, getDeltaRecord(value(iter)).i2, tag);
+}
+
+namespace impl
+{
+
+template <typename TIter>
+struct GetInsSizeFunctor
+{
+    TIter & _it;
+    decltype(impl::insertionSize(container(_it)._deltaStore, getStorePosition(*_it), DeltaTypeIns())) val;
+
+    GetInsSizeFunctor()
+    {}
+
+    GetInsSizeFunctor(TIter & it) : _it(it)
+    {}
+
+    template <typename TDeltaType>
+    inline void
+    operator()(TDeltaType)
+    {
+        val = impl::insertionSize(container(_it)._deltaStore, getStorePosition(*_it), TDeltaType());
+    }
+};
+
+template <typename TIter>
+struct GetDelSizeFunctor
+{
+    TIter & _it;
+    decltype(impl::deletionSize(container(_it)._deltaStore, getStorePosition(*_it), DeltaTypeDel())) val;
+
+    GetDelSizeFunctor()
+    {}
+
+    GetDelSizeFunctor(TIter & it) : _it(it)
+    {}
+
+    template <typename TDeltaType>
+    inline void
+    operator()(TDeltaType)
+    {
+        val = impl::deletionSize(container(_it)._deltaStore, getStorePosition(*_it), TDeltaType());
+    }
+};
+
+template <typename TIter>
+struct GetNetSizeFunctor
+{
+    TIter & _it;
+    decltype(impl::netSize(container(_it)._deltaStore, getStorePosition(*_it), DeltaTypeSV())) val;
+
+    GetNetSizeFunctor()
+    {}
+
+    GetNetSizeFunctor(TIter & it) : _it(it)
+    {}
+
+    template <typename TDeltaType>
+    inline void
+    operator()(TDeltaType)
+    {
+        val = impl::netSize(container(_it)._deltaStore, getStorePosition(*_it), TDeltaType());
+    }
+};
+
+}  // namespace impl
+
+// ----------------------------------------------------------------------------
+// Function insSize();
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline auto
+insSize(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter) -> decltype(impl::GetInsSizeFunctor<Iter<TDeltaMap, DeltaMapIteratorSpec> >().val)
+{
+    impl::GetInsSizeFunctor<Iter<TDeltaMap, DeltaMapIteratorSpec> const> f(iter);
+    DeltaTypeSelector deltaTypes;
+    applyOnDelta(f, getDeltaType(*iter), deltaTypes);
+    return f.val;
+}
+
+// ----------------------------------------------------------------------------
+// Function delSize();
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline auto
+delSize(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter) -> decltype(impl::GetDelSizeFunctor<Iter<TDeltaMap, DeltaMapIteratorSpec> >().val)
+{
+    impl::GetDelSizeFunctor<Iter<TDeltaMap, DeltaMapIteratorSpec> const> f(iter);
+    DeltaTypeSelector deltaTypes;
+    applyOnDelta(f, getDeltaType(*iter), deltaTypes);
+    return f.val;
+}
+
+// ----------------------------------------------------------------------------
+// Function netSize();
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline auto
+netSize(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter) -> decltype(impl::GetNetSizeFunctor<Iter<TDeltaMap, DeltaMapIteratorSpec> >().val)
+{
+    impl::GetNetSizeFunctor<Iter<TDeltaMap, DeltaMapIteratorSpec> const> f(iter);
+    DeltaTypeSelector deltaTypes;
+    applyOnDelta(f, getDeltaType(*iter), deltaTypes);
+    return f.val;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator*()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline typename Reference<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type
+operator*(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter)
+{
+    return *iter._mapIter;
+}
+
+template <typename TDeltaMap>
+inline typename Reference<Iter<TDeltaMap, DeltaMapIteratorSpec> const>::Type
+operator*(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter)
+{
+    return *iter._mapIter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator++()                                               [prefix]
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline Iter<TDeltaMap, DeltaMapIteratorSpec> &
+operator++(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter)
+{
+    ++iter._mapIter;
+    return iter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator++()                                              [postfix]
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline Iter<TDeltaMap, DeltaMapIteratorSpec>
+operator++(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter,  int /*postfix*/)
+{
+    Iter<TDeltaMap, DeltaMapIteratorSpec> temp(iter);
+    ++iter;
+    return temp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator+=()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap, typename TSize>
+inline Iter<TDeltaMap, DeltaMapIteratorSpec> &
+operator+=(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter,  TSize const & len)
+{
+    iter._mapIter += len;
+    return iter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator+()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap, typename TSize>
+inline Iter<TDeltaMap, DeltaMapIteratorSpec>
+operator+(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter,  TSize const & len)
+{
+    Iter<TDeltaMap, DeltaMapIteratorSpec> temp(iter);
+    temp += len;
+    return temp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator--()                                              [postfix]
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline Iter<TDeltaMap, DeltaMapIteratorSpec> &
+operator--(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter)
+{
+    --iter._mapIter;
+    return iter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator--()                                               [prefix]
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline Iter<TDeltaMap, DeltaMapIteratorSpec>
+operator--(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter,  int /*postfix*/)
+{
+    Iter<TDeltaMap, DeltaMapIteratorSpec> temp(iter);
+    --iter;
+    return temp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator-=()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap, typename TSize>
+inline Iter<TDeltaMap, DeltaMapIteratorSpec> &
+operator-=(Iter<TDeltaMap, DeltaMapIteratorSpec> & iter,  TSize const & len)
+{
+    iter._mapIter -= len;
+    return iter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator-()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap, typename TSize>
+inline Iter<TDeltaMap, DeltaMapIteratorSpec>
+operator-(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter,  TSize const & len)
+{
+    Iter<TDeltaMap, DeltaMapIteratorSpec> temp(iter);
+    temp -= len;
+    return temp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator-()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline typename Difference<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type
+operator-(Iter<TDeltaMap, DeltaMapIteratorSpec> const & lhs,
+          Iter<TDeltaMap, DeltaMapIteratorSpec> const & rhs)
+{
+    return lhs._mapIter - rhs._mapIter;
+}
+
+template <typename TDeltaMap>
+inline typename Difference<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type
+operator-(Iter<TDeltaMap, DeltaMapIteratorSpec> const & lhs,
+          typename IterComplementConst<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type const & rhs)
+{
+    return lhs._mapIter - rhs._mapIter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator==()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline bool
+operator==(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           Iter<TDeltaMap, DeltaMapIteratorSpec> const & b)
+{
+    return a._mapIter == b._mapIter;
+}
+
+template <typename TDeltaMap>
+inline bool
+operator==(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           typename IterComplementConst<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type const & b)
+{
+    return a._mapIter == b._mapIter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator!=()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline bool
+operator!=(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           Iter<TDeltaMap, DeltaMapIteratorSpec> const & b)
+{
+    return !(a == b);
+}
+
+template <typename TDeltaMap>
+inline bool
+operator!=(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           typename IterComplementConst<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type const & b)
+{
+    return !(a == b);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator<()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline bool
+operator<(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           Iter<TDeltaMap, DeltaMapIteratorSpec> const & b)
+{
+    return a._mapIter < b._mapIter;
+}
+
+template <typename TDeltaMap>
+inline bool
+operator<(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+          typename IterComplementConst<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type const & b)
+{
+    return a._mapIter < b._mapIter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator<=()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline bool
+operator<=(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           Iter<TDeltaMap, DeltaMapIteratorSpec> const & b)
+{
+    return a._mapIter <= b._mapIter;
+}
+
+template <typename TDeltaMap>
+inline bool
+operator<=(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           typename IterComplementConst<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type const & b)
+{
+    return a._mapIter <= b._mapIter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator>()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline bool
+operator>(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           Iter<TDeltaMap, DeltaMapIteratorSpec> const & b)
+{
+    return a._mapIter > b._mapIter;
+}
+
+template <typename TDeltaMap>
+inline bool
+operator>(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           typename IterComplementConst<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type const & b)
+{
+    return a._mapIter > b._mapIter;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator>=()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline bool
+operator>=(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           Iter<TDeltaMap, DeltaMapIteratorSpec> const & b)
+{
+    return a._mapIter >= b._mapIter;
+}
+
+template <typename TDeltaMap>
+inline bool
+operator>=(Iter<TDeltaMap, DeltaMapIteratorSpec> const & a,
+           typename IterComplementConst<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type const & b)
+{
+    return a._mapIter >= b._mapIter;
+}
+
+// ----------------------------------------------------------------------------
+// Function position()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMap>
+inline typename Position<Iter<TDeltaMap, DeltaMapIteratorSpec> >::Type
+position(Iter<TDeltaMap, DeltaMapIteratorSpec> const & iter)
+{
+    return iter - begin(*iter._mapPtr, Standard());
+}
+
+//template <typename TDeltaMapLhs, typename TDeltaMapRhs>
+//inline void
+//swap(Iter<TDeltaMapLhs, DeltaMapIteratorSpec> & lhs,
+//     Iter<TDeltaMapRhs, DeltaMapIteratorSpec> & rhs)
+//{
+//    swap(lhs._mapPtr, rhs._mapPtr);
+//    swap(lhs._mapIter, rhs._mapIter);
+//}
+
+}  // namespace seqan
+
+#endif  // EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_MAP_ITERATOR_H_
diff --git a/seqan/journaled_string_tree/delta_store.h b/seqan/journaled_string_tree/delta_store.h
new file mode 100644
index 0000000..7450c24
--- /dev/null
+++ b/seqan/journaled_string_tree/delta_store.h
@@ -0,0 +1,574 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements a data structure to store deltas efficiently.
+// ==========================================================================
+
+#ifndef EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_STORE_H_
+#define EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_STORE_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TDeltaStore, typename TDeltaType>
+struct DeltaValue;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+/*!
+ * @defgroup DeltaTypeTags Delta Type Tags
+ * @brief Tags used for the different delta types.
+ */
+
+/*!
+ * @tag DeltaTypeTags#DeltaTypeSnp
+ * @brief Tag used to select SNPs.
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @signature struct DeltaTypeSnp_;
+ *            typedef Tag<DeltaTypeSnp_> DeltaTypeSnp;
+ */
+struct DeltaTypeSnp_;
+typedef Tag<DeltaTypeSnp_> DeltaTypeSnp;
+
+/*!
+ * @tag DeltaTypeTags#DeltaTypeDel
+ * @brief Tag used to select deletions.
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @signature struct DeltaTypeDel_;
+ *            typedef Tag<DeltaTypeDel_> DeltaTypeDel;
+ */
+struct DeltaTypeDel_;
+typedef Tag<DeltaTypeDel_> DeltaTypeDel;
+
+/*!
+ * @tag DeltaTypeTags#DeltaTypeIns
+ * @brief Tag used to select insertions.
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @signature struct DeltaTypeIns_;
+ *            typedef Tag<DeltaTypeIns_> DeltaTypeIns;
+ */
+struct DeltaTypeIns_;
+typedef Tag<DeltaTypeIns_> DeltaTypeIns;
+
+/*!
+ * @tag DeltaTypeTags#DeltaTypeSV
+ * @brief Tag used to select SVs.
+ * @headerfile <seqan/journaled_string_tree.h>
+ *
+ * @signature struct DeltaTypeSV_;
+ *            typedef Tag<DeltaTypeSV_> DeltaTypeSV;
+ */
+struct DeltaTypeSV_;
+typedef Tag<DeltaTypeSV_> DeltaTypeSV;
+
+typedef TagList<DeltaTypeSnp,
+        TagList<DeltaTypeDel,
+        TagList<DeltaTypeIns,
+        TagList<DeltaTypeSV> > > > DeltaTypeTagList;
+
+// ----------------------------------------------------------------------------
+// Class DeltaTypeSelector
+// ----------------------------------------------------------------------------
+
+typedef TagSelector<DeltaTypeTagList> DeltaTypeSelector;
+
+
+// ----------------------------------------------------------------------------
+// Enum DeltaType
+// ----------------------------------------------------------------------------
+
+/*!
+ * @enum DeltaType
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Keys for specifying the delta type to be accessed.
+ *
+ * @val DeltaType DELTA_TYPE_SNP
+ * @brief Id to denote SNP events.
+ *
+ * @val DeltaType DELTA_TYPE_DEL
+ * @brief Id to denote deletion events.
+ *
+ * @val DeltaType DELTA_TYPE_INS
+ * @brief Id to denote insertion events.
+ *
+ * @val DeltaType DElTA_TYPE_INDEL
+ * @brief Id to denote replacement events.
+ */
+
+enum DeltaType
+{
+    DELTA_TYPE_SNP = Find<DeltaTypeSelector, DeltaTypeSnp>::VALUE,
+    DELTA_TYPE_DEL = Find<DeltaTypeSelector, DeltaTypeDel>::VALUE,
+    DELTA_TYPE_INS = Find<DeltaTypeSelector, DeltaTypeIns>::VALUE,
+    DELTA_TYPE_SV = Find<DeltaTypeSelector, DeltaTypeSV>::VALUE
+};
+
+
+namespace impl
+{
+
+// ----------------------------------------------------------------------------
+// Class DeltaStore
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel = uint32_t, typename TIns = String<TSnp>, typename TSV = Pair<TDel, TIns> >
+class DeltaStore
+{
+public:
+    typedef typename Member<DeltaStore, DeltaTypeSnp>::Type TSnpData;
+    typedef typename Member<DeltaStore, DeltaTypeDel>::Type TDelData;
+    typedef typename Member<DeltaStore, DeltaTypeIns>::Type TInsData;
+    typedef typename Member<DeltaStore, DeltaTypeSV>::Type  TSVData;
+
+    // TODO(rmaerker): Elaborate on these ideas!
+    // Idea a) Use ConcatStringSet for insertions. Use as global insertion buffer for all journal sequences.
+    // Idea b) Use bit encoding for DNA alphabet.
+    // Idea c) Instead of insertion buffer, we append the inserted strings to the reference and only use original nodes.
+
+    TSnpData    _snpData;
+    TDelData    _delData;
+    TInsData    _insData;
+    TSVData     _svData;
+
+    DeltaStore()
+    {}
+};
+
+}  // namespace impl
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction BitsPerValue
+// ----------------------------------------------------------------------------
+
+template <>
+struct BitsPerValue<DeltaType>
+{
+    static const unsigned VALUE = 2;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member
+// ----------------------------------------------------------------------------
+
+// DeltaTypeSnp.
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct Member<impl::DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeSnp>
+{
+    typedef String<TSnp> Type;
+};
+
+// DeltaTypeDel.
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct Member<impl::DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeDel>
+{
+    typedef String<TDel> Type;
+};
+
+// DeltaTypeIns.
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct Member<impl::DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeIns>
+{
+    typedef String<TIns> Type;
+};
+
+// DeltaTypeSV.
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct Member<impl::DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeSV>
+{
+    typedef String<TSV> Type;
+};
+
+// Generic const version.
+template <typename TSnp, typename TDel, typename TIns, typename TSV, typename TDeltaType>
+struct Member<impl::DeltaStore<TSnp, TDel, TIns, TSV> const, TDeltaType>
+{
+    typedef impl::DeltaStore<TSnp, TDel, TIns, TSV> TStore_;
+    typedef typename Member<TStore_, TDeltaType>::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaValue                                     [DELTA_TYPE_SNP]
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct DeltaValue<impl::DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeSnp>
+{
+    typedef TSnp Type;
+};
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct DeltaValue<impl::DeltaStore<TSnp, TDel, TIns, TSV> const, DeltaTypeSnp>
+{
+    typedef TSnp const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaValue                                     [DELTA_TYPE_DEL]
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct DeltaValue<impl::DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeDel>
+{
+    typedef TDel Type;
+};
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct DeltaValue<impl::DeltaStore<TSnp, TDel, TIns, TSV> const, DeltaTypeDel>
+{
+    typedef TDel const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaValue                                     [DELTA_TYPE_INS]
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct DeltaValue<impl::DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeIns>
+{
+    typedef TIns Type;
+};
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct DeltaValue<impl::DeltaStore<TSnp, TDel, TIns, TSV> const, DeltaTypeIns>
+{
+    typedef TIns const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DeltaValue                                   [DELTA_TYPE_SV]
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct DeltaValue<impl::DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeSV>
+{
+    typedef TSV Type;
+};
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+struct DeltaValue<impl::DeltaStore<TSnp, TDel, TIns, TSV> const, DeltaTypeSV>
+{
+    typedef TSV const Type;
+};
+
+// ============================================================================
+// Punlic Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function isDeltaType()
+// ----------------------------------------------------------------------------
+
+template <typename TTag>
+inline bool
+isDeltaType(DeltaType type, TTag const & /*tag*/)
+{
+    return type == static_cast<DeltaType>(Find<DeltaTypeSelector, TTag>::VALUE);
+}
+
+// ----------------------------------------------------------------------------
+// Function selectDeltaType()                                    [DeltaTypeSnp]
+// ----------------------------------------------------------------------------
+
+template <typename TTag>
+constexpr inline DeltaType
+selectDeltaType(TTag const & /*tag*/)
+{
+    return static_cast<DeltaType>(Find<DeltaTypeSelector, TTag>::VALUE);
+}
+
+// ----------------------------------------------------------------------------
+// Function setDeltaType()
+// ----------------------------------------------------------------------------
+
+inline void
+setDeltaType(DeltaTypeSelector & selector, DeltaType const deltaType)
+{
+    value(selector) = deltaType;
+}
+
+// ============================================================================
+// Private Functions
+// ============================================================================
+
+namespace impl
+{
+
+// ----------------------------------------------------------------------------
+// Function getDeltaStore()                                     [DeltaTypeSnp]
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline typename Member<DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeSnp>::Type &
+getDeltaStore(DeltaStore<TSnp, TDel, TIns, TSV> & store, DeltaTypeSnp /*tag*/)
+{
+    return store._snpData;
+}
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline typename Member<DeltaStore<TSnp, TDel, TIns, TSV> const, DeltaTypeSnp>::Type &
+getDeltaStore(DeltaStore<TSnp, TDel, TIns, TSV> const & store, DeltaTypeSnp /*tag*/)
+{
+    return store._snpData;
+}
+
+// ----------------------------------------------------------------------------
+// Function getDeltaStore()                                     [DeltaTypeDel]
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline typename Member<DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeDel>::Type &
+getDeltaStore(DeltaStore<TSnp, TDel, TIns, TSV> & store, DeltaTypeDel /*tag*/)
+{
+    return store._delData;
+}
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline typename Member<DeltaStore<TSnp, TDel, TIns, TSV> const, DeltaTypeDel>::Type &
+getDeltaStore(DeltaStore<TSnp, TDel, TIns, TSV> const & store, DeltaTypeDel /*tag*/)
+{
+    return store._delData;
+}
+
+// ----------------------------------------------------------------------------
+// Function getDeltaStore()                                     [DeltaTypeIns]
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline typename Member<DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeIns>::Type &
+getDeltaStore(DeltaStore<TSnp, TDel, TIns, TSV> & store, DeltaTypeIns /*tag*/)
+{
+    return store._insData;
+}
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline typename Member<DeltaStore<TSnp, TDel, TIns, TSV> const, DeltaTypeIns>::Type &
+getDeltaStore(DeltaStore<TSnp, TDel, TIns, TSV> const & store, DeltaTypeIns /*tag*/)
+{
+    return store._insData;
+}
+
+// ----------------------------------------------------------------------------
+// Function getDeltaStore()                                      [DeltaTypeSV]
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline typename Member<DeltaStore<TSnp, TDel, TIns, TSV>, DeltaTypeSV>::Type &
+getDeltaStore(DeltaStore<TSnp, TDel, TIns, TSV> & store, DeltaTypeSV /*tag*/)
+{
+    return store._svData;
+}
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline typename Member<DeltaStore<TSnp, TDel, TIns, TSV> const, DeltaTypeSV>::Type &
+getDeltaStore(DeltaStore<TSnp, TDel, TIns, TSV> const & store, DeltaTypeSV /*tag*/)
+{
+    return store._svData;
+}
+
+// ----------------------------------------------------------------------------
+// Function addDeltaValue()
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV, typename TTag>
+inline typename Size<DeltaStore<TSnp, TDel, TIns, TSV> >::Type
+addDeltaValue(DeltaStore<TSnp, TDel, TIns, TSV> & store,
+              typename DeltaValue<DeltaStore<TSnp, TDel, TIns, TSV>, TTag>::Type const & value,
+              TTag /*deltaType*/)
+{
+    appendValue(getDeltaStore(store, TTag()), value);
+    return length(getDeltaStore(store, TTag())) - 1;
+}
+
+// ----------------------------------------------------------------------------
+// Function eraseDeltaValue()
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV, typename TPos, typename TTag>
+inline typename Size<DeltaStore<TSnp, TDel, TIns, TSV> >::Type
+eraseDeltaValue(DeltaStore<TSnp, TDel, TIns, TSV> & store,
+                TPos recordPos,
+                TTag /*deltaType*/)
+{
+    typedef typename Size<DeltaStore<TSnp, TDel, TIns, TSV> >::Type TSize;
+    if (SEQAN_LIKELY(static_cast<TSize>(recordPos) < length(getDeltaStore(store, TTag()))))
+        erase(getDeltaStore(store, TTag()), recordPos);
+    return length(getDeltaStore(store, TTag()));
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV>
+inline void
+clear(DeltaStore<TSnp, TDel, TIns, TSV> & deltaStore)
+{
+    clear(deltaStore._delData);
+    clear(deltaStore._svData);
+    clear(deltaStore._insData);
+    clear(deltaStore._snpData);
+}
+
+// ----------------------------------------------------------------------------
+// Function deltaValue()
+// ----------------------------------------------------------------------------
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV, typename TPos, typename TTag>
+inline typename DeltaValue<DeltaStore<TSnp, TDel, TIns, TSV>, TTag>::Type &
+deltaValue(DeltaStore<TSnp, TDel, TIns, TSV> & store, TPos pos, TTag const & tag)
+{
+    typedef typename Size<DeltaStore<TSnp, TDel, TIns, TSV> >::Type TSize SEQAN_TYPEDEF_FOR_DEBUG;
+    SEQAN_ASSERT_LT(static_cast<TSize>(pos), length(getDeltaStore(store, tag)));
+
+    return value(getDeltaStore(store, tag), pos);
+}
+
+template <typename TSnp, typename TDel, typename TIns, typename TSV, typename TPos, typename TTag>
+inline typename DeltaValue<DeltaStore<TSnp, TDel, TIns, TSV> const, TTag>::Type &
+deltaValue(DeltaStore<TSnp, TDel, TIns, TSV> const & store, TPos pos, TTag const & tag)
+{
+    typedef typename Size<DeltaStore<TSnp, TDel, TIns, TSV> const>::Type TSize SEQAN_TYPEDEF_FOR_DEBUG;
+    SEQAN_ASSERT_LT(static_cast<TSize>(pos), length(getDeltaStore(store, tag)));
+
+    return value(getDeltaStore(store, tag), pos);
+}
+
+// ----------------------------------------------------------------------------
+// Function deletionSize()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaStore>
+inline typename Size<TDeltaStore>::Type
+deletionSize(typename DeltaValue<TDeltaStore, DeltaTypeSnp>::Type const & /*snp*/)
+{
+    return 1;
+}
+
+template <typename TDeltaStore>
+inline typename Size<TDeltaStore>::Type
+deletionSize(typename DeltaValue<TDeltaStore, DeltaTypeIns>::Type const & /*ins*/)
+{
+    return 0;
+}
+
+template <typename TDeltaStore>
+inline typename Size<TDeltaStore>::Type
+deletionSize(typename DeltaValue<TDeltaStore, DeltaTypeDel>::Type const & del)
+{
+    return del;
+}
+
+template <typename TDeltaStore>
+inline typename Size<TDeltaStore>::Type
+deletionSize(typename DeltaValue<TDeltaStore, DeltaTypeSV>::Type const & sv)
+{
+    return sv.i1;
+}
+
+template <typename TStore, typename TPos, typename TTag>
+inline typename Size<TStore>::Type
+deletionSize(TStore const & store, TPos const pos, TTag const & /*tag*/)
+{
+    return deletionSize<TStore>(getDeltaStore(store, TTag())[pos]);
+}
+
+// ----------------------------------------------------------------------------
+// Function insertionSize()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaStore>
+inline typename Size<TDeltaStore>::Type
+insertionSize(typename DeltaValue<TDeltaStore, DeltaTypeSnp>::Type const & /*snp*/)
+{
+    return 1;
+}
+
+template <typename TDeltaStore>
+inline typename Size<TDeltaStore>::Type
+insertionSize(typename DeltaValue<TDeltaStore, DeltaTypeIns>::Type const & ins)
+{
+    return length(ins);
+}
+
+template <typename TDeltaStore>
+inline typename Size<TDeltaStore>::Type
+insertionSize(typename DeltaValue<TDeltaStore, DeltaTypeDel>::Type const & /*del*/)
+{
+    return 0;
+}
+
+template <typename TDeltaStore>
+inline typename Size<TDeltaStore>::Type
+insertionSize(typename DeltaValue<TDeltaStore, DeltaTypeSV>::Type const & sv)
+{
+    return length(sv.i2);
+}
+
+template <typename TStore, typename TPos, typename TTag>
+inline typename Size<TStore>::Type
+insertionSize(TStore const & store, TPos const pos, TTag const & /*tag*/)
+{
+    return insertionSize<TStore>(getDeltaStore(store, TTag())[pos]);
+}
+
+// ----------------------------------------------------------------------------
+// Function netSize()
+// ----------------------------------------------------------------------------
+
+template <typename TStore, typename TPos, typename TTag>
+inline typename MakeSigned<typename Size<TStore>::Type>::Type
+netSize(TStore const & store, TPos const pos, TTag const & /*tag*/)
+{
+    typedef typename MakeSigned<typename Size<TStore>::Type>::Type TSignedSize;
+    return static_cast<TSignedSize>(insertionSize(store, pos, TTag())) -
+           static_cast<TSignedSize>(deletionSize(store, pos, TTag()));
+}
+
+}  // namespace impl
+
+}  // namespace seqan
+
+#endif // EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_DELTA_STORE_H_
diff --git a/seqan/bam_io/sam_reader.h b/seqan/journaled_string_tree/journaled_string_tree_base.h
similarity index 55%
rename from seqan/bam_io/sam_reader.h
rename to seqan/journaled_string_tree/journaled_string_tree_base.h
index 01f2b96..88de85b 100644
--- a/seqan/bam_io/sam_reader.h
+++ b/seqan/journaled_string_tree/journaled_string_tree_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,13 +29,13 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Basic defintions and forwards used globally for this module.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_SAM_READER_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_SAM_READER_H_
-
-#include <memory>
+#ifndef EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_BASE_H_
+#define EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_BASE_H_
 
 namespace seqan {
 
@@ -47,155 +47,113 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-// Implementation of reading BAM files.
-
-class SamReader_ :
-    public XamReader_
-{
-public:
-    // The size of the file in bytes.
-    __int64 _fileSize;
-
-    // Pointer to the input stream to read from.  Used such that we can also read from stdin.
-    std::ifstream _fstream;
-    // The file stream to read from if we do not read from stdout.  Pointed to by _stream.
-    std::istream * _stream;
-
-    // Record reader to use for parsing.
-    std::SEQAN_AUTO_PTR_NAME<RecordReader<std::istream, SinglePass<> > > _reader;
-
-    SamReader_() :
-        XamReader_(), _fileSize(0), _stream(0)
-    {}
-
-    SamReader_(CharString const & filename);
-
-    // XamReader_ interface.
-
-    virtual int open(CharString const & filename);
-    virtual bool isGood();
-    virtual bool atEnd();
-    virtual int readHeader(BamHeader & header, BamIOContext<StringSet<CharString> > & context);
-    virtual int readRecord(BamAlignmentRecord & record, BamIOContext<StringSet<CharString> > & context);
-    virtual int close();
+// ----------------------------------------------------------------------------
+// Tag Traversal Tags
+// ----------------------------------------------------------------------------
 
-    virtual __int64 fileSize() const;
-    virtual __int64 positionInFile() const;
-};
+struct ForwardTraversal_;
+typedef Tag<ForwardTraversal_> ForwardTraversal;
 
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
+struct BidirectionalTraversal_;
+typedef Tag<BidirectionalTraversal_> BidirectionalTraversal;
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::SamReader_()
+// Tag JSTree
 // ----------------------------------------------------------------------------
 
-inline SamReader_::SamReader_(CharString const & filename) :
-    XamReader_(filename), _stream(0), _reader()
-{
-    this->open(_filename);
-}
+template <typename TSpec = ForwardTraversal>
+struct JSTree;
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::open()
+// Tag JstBufferMember
 // ----------------------------------------------------------------------------
 
-inline int SamReader_::open(CharString const & filename)
-{
-    // Open file.
-    if (filename == "-")
-    {
-        this->_stream = &std::cin;
-    }
-    else
-    {
-        this->_stream = &this->_fstream;
-        this->_fstream.open(toCString(filename), std::ios::binary | std::ios::in);
-        if (!this->_fstream.good())
-            return 1;
-
-        // Determine file size.
-        this->_stream->seekg(0, std::ios::end);
-        this->_fileSize = this->_stream->tellg();
-        this->_stream->seekg(0, std::ios::beg);
-    }
-    this->_reader.reset(new RecordReader<std::istream, SinglePass<> >(*this->_stream));
-
-    return 0;
-}
+struct JstBufferMember_;
+typedef Tag<JstBufferMember_> JstBufferMember;
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::isGood()
+// Tag JstSourceMember
 // ----------------------------------------------------------------------------
 
-inline bool SamReader_::isGood()
-{
-    return this->_stream->good();
-}
+struct JstSourceMember_;
+typedef Tag<JstSourceMember_> JstSourceMember;
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::atEnd()
+// Tag JstDeltaMapMember
 // ----------------------------------------------------------------------------
 
-inline bool SamReader_::atEnd()
-{
-    return seqan::atEnd(*this->_reader);
-}
+struct JstDeltaMapMember_;
+typedef Tag<JstDeltaMapMember_> JstDeltaMapMember;
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::readHeader()
+// Tag PushEvent
 // ----------------------------------------------------------------------------
 
-inline int SamReader_::readHeader(BamHeader & header, BamIOContext<StringSet<CharString> > & context)
-{
-    return seqan::readRecord(header, context, *this->_reader, Sam());
-}
+struct PushEvent_;
+typedef Tag<PushEvent_> PushEvent;
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::readRecord()
+// Tag PopEvent
 // ----------------------------------------------------------------------------
 
-inline int SamReader_::readRecord(BamAlignmentRecord & record, BamIOContext<StringSet<CharString> > & context)
-{
-    return seqan::readRecord(record, context, *this->_reader, Sam());
-}
+struct PopEvent_;
+typedef Tag<PopEvent_> PopEvent;
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::readRecord()
+// Class DefaultJstConfig
 // ----------------------------------------------------------------------------
 
-inline int SamReader_::close()
+/*!
+ * @class DefaultJstConfig
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief The default Journaled-String-Tree configuration object.
+ *
+ * @signature template <typename TSequence>
+ *            class DefaultJstConfig<TDeltaStore>
+ *
+ * @tparam TSequence Type of the underlying base sequence.
+ *
+ * Defines the follwoing types used to configure the @link DeltaMap @endlink:
+ * @code{.cpp}
+ * typedef typename Size<TSequence>::Type  TDeltaPos;
+ * typedef typename Value<TSequence>::Type TSnpValue;
+ * typedef String<TSnpValue>               TInsValue;
+ * typedef typename Size<TSequence>::Type  TDelValue;
+ * typedef Pair<TDelValue, TInsValue>      TSVValue;
+ * @endcode
+ */
+template <typename TSequence>
+struct DefaultJstConfig
 {
-    if (this->_stream == &this->_fstream)
-        this->_fstream.close();
-    return 0;
-}
+    typedef typename Size<TSequence>::Type  TDeltaPos;  // Position type for delta entry.
+    typedef typename Value<TSequence>::Type TSnpValue;  // Value type of the SNPs.
+    typedef String<TSnpValue>               TInsValue;  // Value type of insertions.
+    typedef typename Size<TSequence>::Type  TDelValue;  // Value type of deletions.
+    typedef Pair<TDelValue, TInsValue>      TSVValue;   // Value type of structural variants (combination of deletion and insertion).
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::fileSize()
+// Metafunction Traverser
 // ----------------------------------------------------------------------------
 
-inline __int64 SamReader_::fileSize() const
-{
-    return this->_fileSize;
-}
+template <typename TContainer, typename TObserverList = ObserverList<> >
+struct Traverser;
 
 // ----------------------------------------------------------------------------
-// Member Function SamReader_::positionInFile()
+// Metafunction ContextIterator
 // ----------------------------------------------------------------------------
 
-// TODO(holtgrew): This does not work yet.
+template <typename TObj>
+struct ContextIterator;
 
-inline __int64 SamReader_::positionInFile() const
-{
-    return 0;
-}
+// ============================================================================
+// Functions
+// ============================================================================
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_SAM_READER_H_
+#endif  // EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_BASE_H_
diff --git a/seqan/journaled_string_tree/journaled_string_tree_impl.h b/seqan/journaled_string_tree/journaled_string_tree_impl.h
new file mode 100644
index 0000000..37b2650
--- /dev/null
+++ b/seqan/journaled_string_tree/journaled_string_tree_impl.h
@@ -0,0 +1,676 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements the default virtual string tree to traverse multiple sequences
+// in parallel. This is a facade combining the variant store with the
+// journal set.
+// ==========================================================================
+
+#ifndef EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_IMPL_H_
+#define EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_IMPL_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class JournaledStringTree                                [StringTreeDefault]
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class JournaledStringTree Journaled String Tree
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief This data structure represents a virtual set of strings using a veritcal compression scheme.
+ *
+ * @signature template <typename TSequence[, typename TConfig][, TSpec]>
+ *            class JournaledStringTree<TDeltaStore, TConfig, TSpec>;
+ *
+ * @tparam TSequence Type of underlying base sequence.
+ * @tparam TConfig   A configuration object, whose traits can be used to specialize the underlying @link DeltaMap @endlink. Defaults to @link DefaultJstConfig @endlink.
+ * @tparam TSpec     The specialization tag for the journaled string tree. Defaults to @link Default @endlink.
+ *
+ * This data structure stores a virtual set of sequences in a compressed form. The sequences are described in form of a pointer
+ * to a common reference sequence and in addition delta events, which are stored in a @link DeltaMap @endlink.
+ * The interface is a hybrid between a container interface and a associative container interface. So it uses typical 
+ * string set intrefaces to access the virtual strings. On the other hand it implements an associative container to
+ * store the delta events given their reference position as a key.
+ * This data structure can then be traversed efficiently, while exploring only those sequence contexts, that are unique
+ * to the set of sequences. This means, that redundant parts, that are shared by one or many sequences is traversed only
+ * once.
+ */
+
+
+// This data structure represents a collection of strings.
+// It facilitates an alignment representation of each sequence to a common base sequence.
+template <typename TSequence, typename TConfig = DefaultJstConfig<TSequence>, typename TSpec = Default>
+class JournaledStringTree
+{
+public:
+
+    typedef JournaledStringTree<TSequence, TConfig, Default>                        TJst;
+    typedef typename Member<TJst, JstDeltaMapMember>::Type                          TDeltaMap;
+    typedef typename Member<TJst, JstSourceMember>::Type                            TSource;
+    typedef typename Iterator<TSource, Standard>::Type                              TSrcIter;
+    typedef typename Size<TJst>::Type                                               TSize;
+
+
+    TSize       _dimension = 0;     // Number of sequences represented by the JST.
+    TSource     _source;            // A journaled String representing the baseSequence.
+    TDeltaMap   _map;
+
+    /*!
+     * @fn JournaledStringTree::JournaledStringTree
+     * @brief Constructor.
+     * @headerfile <seqan/journaled_string_tree.h>
+     *
+     * @signature JournaledStringTree();
+     * @signature JournaledStringTree(size);
+     * @signature JournaledStringTree(source, size);
+     *
+     * @param size     The number of sequences represented by the JST.
+     * @param source   The underlying base sequence to which the sequences are compressed.
+     */
+
+    // Def c'tor.
+    JournaledStringTree()
+    {}
+
+    // Custom constructor.
+    template <typename TDim>
+    JournaledStringTree(TDim const dimension) : _dimension(dimension), _source()
+    {}
+
+    // Custom constructor.
+    template <typename TSequence2, typename TDim>
+    JournaledStringTree(TSequence2 && source, TDim const dimension) : _dimension(dimension)
+    {
+        setHost(_source, std::forward<TSequence2>(source));
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Spec
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn JournaledStringTree#Spec
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns the specialization type.
+ *
+ * @signature Spec<TJst>::Type;
+ *
+ * @tparam TJst The JST type to query the specialization type for.
+ *
+ * @return TSpec The specialization type.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+struct Spec<JournaledStringTree<TSequence, TConfig, TSpec> >
+{
+    typedef TSpec Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn JournaledStringTree#Size
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief The size type.
+ *
+ * @signature Size<TJst>::Type;
+ *
+ * @tparam TJst The JST type to get the size type for.
+ *
+ * @return TSize The size type.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+struct Size<JournaledStringTree<TSequence, TConfig, TSpec> >
+{
+    typedef typename Member<JournaledStringTree<TSequence, TConfig, TSpec>, JstDeltaMapMember>::Type    TDeltaMap_;
+    typedef typename Size<TDeltaMap_>::Type                                                             TDeltaMapSize_;
+    typedef typename Member<JournaledStringTree<TSequence, TConfig, TSpec>, JstSourceMember>::Type      TSource_;
+    typedef typename Size<TSource_>::Type                                                               TSrcSize_;
+
+    typedef typename If<Eval<sizeof(TDeltaMapSize_) < sizeof(TSrcSize_)>,
+                        TSrcSize_,
+                        TDeltaMapSize_>::Type Type;  // Size type is the largest size type of delta map or source.
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn JournaledStringTree#Position
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief The position type.
+ *
+ * @signature Position<TJst>::Type;
+ *
+ * @tparam TJst The JST type to get the position type for.
+ *
+ * @return TPosition The position type.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+struct Position<JournaledStringTree<TSequence, TConfig, TSpec> >
+{
+    typedef typename Member<JournaledStringTree<TSequence, TConfig, TSpec>, JstDeltaMapMember>::Type    TDeltaMap_;
+    typedef typename Position<TDeltaMap_>::Type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Host
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn JournaledStringTree#Host
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief The host type.
+ *
+ * @signature Host<TJst>::Type;
+ *
+ * @tparam TJst The JST type to get the host type for.
+ *
+ * @return THost The type of the underlying data structure.
+ */
+template <typename TSeq, typename TConfig, typename TSpec>
+struct Host<JournaledStringTree<TSeq, TConfig, TSpec> >
+{
+    typedef TSeq Type;
+};
+
+template <typename TSeq, typename TConfig, typename TSpec>
+struct Host<JournaledStringTree<TSeq, TConfig, TSpec> const >
+{
+    typedef TSeq const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction JstSourceMember
+// ----------------------------------------------------------------------------
+
+template <typename TSeq, typename TConfig, typename TSpec>
+struct Member<JournaledStringTree<TSeq, TConfig, TSpec>, JstSourceMember>
+{
+    typedef typename Spec<TSeq>::Type                   TSpec_;
+    typedef typename Value<TSeq>::Type                  TValue_;
+    typedef String<TValue_, Journaled<TSpec_> >         Type;
+};
+
+template <typename TSeq, typename TConfig, typename TSpec>
+struct Member<JournaledStringTree<TSeq, TConfig, TSpec> const, JstSourceMember>
+{
+    typedef typename Member<JournaledStringTree<TSeq, TConfig, TSpec>, JstSourceMember>::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member<TJst, JstBufferMember>
+// ----------------------------------------------------------------------------
+
+template <typename TSeq, typename TConfig, typename TSpec>
+struct Member<JournaledStringTree<TSeq, TConfig, TSpec>, JstDeltaMapMember>
+{
+    typedef DeltaMap<TConfig> Type;
+};
+
+// TODO(rrahn): Check if there is a default const Member metafunction.
+template <typename TSeq, typename TConfig, typename TSpec>
+struct Member<JournaledStringTree<TSeq, TConfig, TSpec> const, JstDeltaMapMember>
+{
+    typedef DeltaMap<TConfig> const Type;
+};
+
+// ============================================================================
+// Private Functions
+// ============================================================================
+
+namespace impl
+{
+
+// ----------------------------------------------------------------------------
+// Function impl::member();                                   [JstSourceMember]
+// ----------------------------------------------------------------------------
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline typename Member<JournaledStringTree<TSequence, TConfig, TSpec>, JstSourceMember>::Type &
+member(JournaledStringTree<TSequence, TConfig, TSpec> & jst,
+       JstSourceMember const & /*tag*/)
+{
+    return jst._source;
+}
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline typename Member<JournaledStringTree<TSequence, TConfig, TSpec> const, JstSourceMember>::Type &
+member(JournaledStringTree<TSequence, TConfig, TSpec> const & jst,
+       JstSourceMember const & /*tag*/)
+{
+    return jst._source;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::member();                                 [JstDeltaMapMember]
+// ----------------------------------------------------------------------------
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline typename Member<JournaledStringTree<TSequence, TConfig, TSpec>, JstDeltaMapMember>::Type &
+member(JournaledStringTree<TSequence, TConfig, TSpec> & jst,
+       JstDeltaMapMember const & /*tag*/)
+{
+    return jst._map;
+}
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline typename Member<JournaledStringTree<TSequence, TConfig, TSpec> const, JstDeltaMapMember>::Type &
+member(JournaledStringTree<TSequence, TConfig, TSpec> const & jst,
+       JstDeltaMapMember const & /*tag*/)
+{
+    return jst._map;
+}
+
+//// ----------------------------------------------------------------------------
+//// Function impl::openJstFromFile();
+//// ----------------------------------------------------------------------------
+//
+//template <typename TSequence, typename TConfig, typename TSpec>
+//inline bool openJstFromFile(JournaledStringTree<TSequence, TConfig, TSpec> &, const char *,FileOpenMode const, Vcf);
+//
+//template <typename TSequence, typename TConfig, typename TSpec>
+//inline bool
+//openJstFromFile(JournaledStringTree<TSequence, TConfig, TSpec> & /*jst*/,
+//                const char * /*fileName*/,
+//                FileOpenMode const /*mode*/,
+//                TagSelector<> const & /*format*/)
+//{
+//    return false;
+//}
+//
+//template <typename TSequence, typename TConfig, typename TSpec, typename TTagList>
+//inline bool
+//openJstFromFile(JournaledStringTree<TSequence, TConfig, TSpec> & jst,
+//                const char * fileName,
+//                FileOpenMode const mode,
+//                TagSelector<TTagList> const & format)
+//{
+//    typedef typename TTagList::Type TFormat;
+//
+//    if (isEqual(format, TFormat()))
+//        return impl::openJstFromFile(jst, fileName, mode, TFormat());
+//    else
+//        return openJstFromFile(jst, fileName, mode, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+//}
+
+}
+
+// ============================================================================
+// Public Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function host()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledStringTree#host
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns the set base sequence.
+ *
+ * @signature THost host(jst);
+ *
+ * @param[in] jst The journaled string tree.
+ *
+ * @return THost A reference to the host of type @link JournaledStringTree#Host @endlink.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline typename Host<JournaledStringTree<TSequence, TConfig, TSpec> >::Type &
+host(JournaledStringTree<TSequence, TConfig, TSpec> & jst)
+{
+    return host(jst._source);
+}
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline typename Host<JournaledStringTree<TSequence, TConfig, TSpec> const>::Type &
+host(JournaledStringTree<TSequence, TConfig, TSpec> const & jst)
+{
+    return host(jst._source);
+}
+
+// ----------------------------------------------------------------------------
+// Function setHost()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledStringTree#setHost
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Sets the base sequence of the journaled string tree.
+ *
+ * @signature void setHost(jst, host);
+ *
+ * @param[in,out] jst   The journaled string tree.
+ * @param[in]     host  The new host to set.
+ *
+ * When setting a new host, the <tt>jst</tt> will be cleared all previous information are lost.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec, typename THost>
+inline void
+setHost(JournaledStringTree<TSequence, TConfig, TSpec> & jst,
+        THost && host)
+{
+    clear(jst);
+    setHost(jst._source, std::forward<THost>(host));
+}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledStringTree#length
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns the number of sequences represented by the journaled string tree.
+ *
+ * @signature TSize length(jst);
+ *
+ * @param[in] jst The journaled string tree to query the length for.
+ *
+ * @return TSize The number of sequences represented by the <tt>jst<\tt>. Of type @link JournaledStringTree#Size @endlink.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline typename Size<JournaledStringTree<TSequence, TConfig, TSpec> const>::Type
+length(JournaledStringTree<TSequence, TConfig, TSpec> const & jst)
+{
+    return jst._dimension;
+}
+
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledStringTree#resize
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Resizes the number of sequences represented by the journaled string tree.
+ *
+ * @signature void resize(jst, size);
+ *
+ * @param[in,out] jst   The journaled string tree to resize.
+ * @param[in]     size  The new size of the <tt>jst</tt>.
+ * 
+ * @see JournaledStringTree#length
+ *
+ * Note, when invoking this method all stored delta events are parsed and their coverage is resized to the given
+ * <tt>size</tt>. If <tt>size</tt> is smaller than the previous size this reduces the actual size of the stored coverages.
+ * If <tt>size</tt> is bigger than the previous size, the coverages are filled up with 0s, i.e. they represent a copy of
+ * the underlying base sequence.
+ * Hence the performance is linear in the number of stored delta events times the linear time for resizing the coverages.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec, typename TSize, typename TOverflowSpec>
+inline auto
+resize(JournaledStringTree<TSequence, TConfig, TSpec> & jst,
+       TSize const & newSize,
+       Tag<TOverflowSpec> const & /*overflow tag*/) -> decltype(jst._dimension)
+{
+    auto& deltaMap = impl::member(jst, JstDeltaMapMember());
+
+    for (auto & event : deltaMap)
+        resize(getDeltaCoverage(event), newSize, false);
+
+    jst._dimension = newSize;
+    return jst._dimension;
+}
+
+// ----------------------------------------------------------------------------
+// Function maxSize()
+// ----------------------------------------------------------------------------
+
+/*
+ * @fn JournaledStringTree#maxSize
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns the maximal number of delta events that can be stored in the journaled string tree.
+ *
+ * @signature TSize maxSize(jst);
+ *
+ * @param[in] jst The journaled string tree to query the maximal length for.
+ *
+ * @return TSize The maximal size. Of type @link JournaledStringTree#Size @endlink.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+constexpr typename Size<JournaledStringTree<TSequence, TConfig, TSpec> >::Type
+maxSize(JournaledStringTree<TSequence, TConfig, TSpec> const & /*jst*/)
+{
+    return maxSize(typename Member<JournaledStringTree<TSequence, TConfig, TSpec>, JstDeltaMapMember>::Type());
+}
+
+// ----------------------------------------------------------------------------
+// Function size()
+// ----------------------------------------------------------------------------
+
+/*
+ * @fn JournaledStringTree#size
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Returns the number of delta events stored in the journaled string tree.
+ *
+ * @signature TSize size(jst);
+ *
+ * @param[in] jst The journaled string tree to query the size for.
+ *
+ * @return TSize The current number of stored delta events. Of type @link JournaledStringTree#Size @endlink.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline typename Size<JournaledStringTree<TSequence, TConfig, TSpec> >::Type
+size(JournaledStringTree<TSequence, TConfig, TSpec> const jst)
+{
+    return size(jst._map);
+}
+
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+/*
+ * @fn JournaledStringTree#empty
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Checks whether the underlying @link DeltaMap @endlink is empty.
+ *
+ * @signature bool empty(jst);
+ *
+ * @param[in] jst The journaled string tree to check for.
+ *
+ * @return bool <tt>true</tt> if the underlying @link DeltaMap @endlink is empty, otherwise <tt>false</tt>.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline bool
+empty(JournaledStringTree<TSequence, TConfig, TSpec> const jst)
+{
+    return empty(jst._map);
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledStringTree#clear
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Clears the journaled string tree.
+ *
+ * @signature void clear(jst);
+ *
+ * @param[in,out] jst  The journaled string tree to be cleared.
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec>
+inline void
+clear(JournaledStringTree<TSequence, TConfig, TSpec> & jst)
+{
+    jst._dimension = 0;
+    reset(jst._source);
+    clear(jst._map);
+}
+
+// ----------------------------------------------------------------------------
+// Function insert();
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledStringTree#insert
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Adds a new delta ecent to the journaled string tree.
+ *
+ * @signature bool insert(jst, pos, val, ids, type);
+ *
+ * @param[in,out]   jst     The journaled string tree to be modified.
+ * @param[in]       pos     The position of the host to place the new delta event at. This position must not exceed length of the @link JournaledStringTree#host @endlink.
+ * @param[in]       val     The value of the delta event.
+ * @param[in]       ids     An object of @link ContainerConcept @endlink storing the ids of the sequences covering this delta event. The ids must be in the range [0, @link JournaledStringTree#length @endlink).
+ * @param[in]       type    A tag representing the type of the delta event. One of @link DeltaTypeTags @endlink.
+ *
+ * Note the value given by <tt>val<\tt> depends on the <tt>type<\tt>, which can be a single character, a string, 
+ * an integer or a pair of integer and string, representing a SNP, an insertion, a deletion or
+ * a structural variant respectively.
+ *
+ * When inserting a deletion of size > 1 (the same holds for the structural variant), the event is split into a left begin and a right begin and two events are inserted into the underlying @link DeltaMap @endlink.
+ * Hence the number of inserted events can differ from the actual number of calls to the insert function.
+ *
+ * @remark The insertion time depends on the implementation of the underlying @link DeltaMap @endlink. See @link DeltaMap#insert @endlink for more details.
+ *
+ * @see JournaledStringTree#erase
+ */
+
+
+template <typename TSequence, typename TConfig, typename TSpec, typename TPos, typename TValue, typename TIds,
+          typename TDeltaType>
+inline SEQAN_FUNC_ENABLE_IF(Is<ContainerConcept<TIds> >, void)
+insert(JournaledStringTree<TSequence, TConfig, TSpec> & jst,
+       TPos srcPos,
+       TValue const & deltaVal,
+       TIds const & ids,
+       TDeltaType /*deltaType*/)
+{
+    typedef JournaledStringTree<TSequence, TConfig, TSpec>  TJst;
+    typedef typename Member<TJst, JstDeltaMapMember>::Type  TDeltaMap;
+    typedef typename DeltaCoverage<TDeltaMap>::Type         TCoverage;
+    typedef typename Value<TIds>::Type                      TID;
+    typedef typename Size<TJst>::Type                       TSize   SEQAN_TYPEDEF_FOR_DEBUG;
+
+    if (IsSameType<TDeltaType, DeltaTypeIns>::VALUE)
+        SEQAN_ASSERT_LEQ(static_cast<TSize>(srcPos), length(impl::member(jst, JstSourceMember())));  // Make sure the delta position does not exceed the source.
+    else
+        SEQAN_ASSERT_LT(static_cast<TSize>(srcPos), length(impl::member(jst, JstSourceMember())));
+    // Transform the ids into coverage value.
+    TCoverage coverage;
+    resize(coverage, length(jst), false, Exact());
+
+    forEach(ids,[&jst, &coverage](TID seqId)
+    {
+        SEQAN_ASSERT_LT(static_cast<TSize>(seqId), length(jst));  // Check that id is valid.
+        coverage[seqId] = true;
+    });
+
+    insert(impl::member(jst, JstDeltaMapMember()), srcPos, deltaVal, coverage, TDeltaType());
+}
+
+// ----------------------------------------------------------------------------
+// Function erase();
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn JournaledStringTree#erase
+ * @headerfile <seqan/journaled_string_tree.h>
+ * @brief Erases a delta event in the journaled string tree.
+ *
+ * @signature bool erase(jst, pos, type);
+ *
+ * @param[in,out]   jst     The journaled string tree to be modified.
+ * @param[in]       pos     The host source position of the delta event.
+ * @param[in]       type    A tag representing the type of the delta event. One of @link DeltaTypeTags @endlink.
+ *                          Note there can be multiple nodes at the same <tt>pos<\tt> with different <tt>type<\tt>.
+ *
+ * A delta event is described by it's host position and the type. If a left end of a deletion is deleted its
+ * accompanied right end is deleted as well.
+ *
+ * @remark The deletion time is depends on the implementation of the underlying @link DeltaMap @endlink. 
+ * See @link DeltaMap#erase @endlink for detailed information.
+ * @see JournaledStringTree#insert
+ */
+
+template <typename TSequence, typename TConfig, typename TSpec, typename TPos, typename TDeltaType>
+inline auto
+erase(JournaledStringTree<TSequence, TConfig, TSpec> & jst,
+      TPos srcPos,
+      TDeltaType /*deltaType*/) -> decltype(erase(impl::member(jst, JstDeltaMapMember()), srcPos, TDeltaType()))
+{
+    return erase(impl::member(jst, JstDeltaMapMember()), srcPos, TDeltaType());
+}
+
+// TODO(rrahn): Implement emplace when needed.
+// TODO(rrahn): Implement emplace_hint when needed.
+// TODO(rrahn): Implement swap when needed.
+
+//template <typename TSequence, typename TConfig, typename TSpec>
+//inline bool
+//open(JournaledStringTree<TSequence, TConfig, TSpec> & jst,
+//     const char * fileName,
+//     FileOpenMode const mode)
+//{
+//    // Figure out the end of the file name.
+//    JstFileFormatSelector selector;
+//    guessFormatFromFilename(fileName, selector);
+//
+//    return impl::openJstFromFile(jst, fileName, mode, selector);
+//}
+
+}
+
+#endif // EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_IMPL_H_
diff --git a/seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h b/seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h
new file mode 100644
index 0000000..61b213a
--- /dev/null
+++ b/seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h
@@ -0,0 +1,561 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Jst traversal buffer used to construct sequence contents.
+// ==========================================================================
+
+#ifndef EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_SEQUENCE_BUFFER_H_
+#define EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_SEQUENCE_BUFFER_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag Member Tags
+// ----------------------------------------------------------------------------
+
+struct JstBufferSetMember_;
+typedef Tag<JstBufferSetMember_> JstBufferSetMember;
+
+struct JstBufferDeltaMapMember_;
+typedef Tag<JstBufferDeltaMapMember_> JstBufferDeltaMapMember;
+
+// ----------------------------------------------------------------------------
+// Class JstBuffer_
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledStringTree, typename TDirection = ForwardTraversal>
+class JstBuffer_
+{
+public:
+
+    // __ Types ___________________________________________________________________
+
+    typedef typename Member<JstBuffer_, JstBufferSetMember>::Type           TJournaledSet;
+    typedef typename Member<TJournaledStringTree, JstSourceMember>::Type    TSource;
+    typedef typename Iterator<TSource, Rooted>::Type                        TSourceIterator;
+
+    typedef typename Member<JstBuffer_, JstBufferDeltaMapMember>::Type      TDeltaMap;
+    typedef typename Iterator<TDeltaMap, Standard>::Type                    TDeltaIterator;
+
+    typedef typename Size<TSource>::Type                                    TSourceSize;
+    typedef String<TSourceSize>                                             TStringPositions;
+
+    // __ Members _________________________________________________________________
+
+    bool                    _isSynchronized;
+
+    TDeltaMap*              _deltaMapPtr;
+
+    TSourceIterator         _sourceBegin;       // Iterator to the clipped begin position of the source.
+    TSourceIterator         _sourceEnd;         // Iterator to the clipped end position of the source.
+
+    TDeltaIterator          _deltaRangeBegin;
+    TDeltaIterator          _deltaRangeEnd;
+
+    TStringPositions        _startPositions; // The begin positions of the strings within the chunk.
+    TJournaledSet           _journaledSet;   // The actual sequences over the current chunk.
+
+    // __ Constructor _____________________________________________________________
+
+    JstBuffer_()
+    {}
+
+    JstBuffer_(TDeltaMap & map) : _deltaMapPtr(&map)
+    {}
+
+    JstBuffer_(TDeltaMap & map, TSourceIterator const & srcBeg, TSourceIterator const & srcEnd) :
+        _deltaMapPtr(&map),
+        _sourceBegin(srcBeg),
+        _sourceEnd(srcEnd)
+    {
+        sync(*this);
+    }
+
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledStringTree, typename TSpec>
+struct Size<JstBuffer_<TJournaledStringTree, TSpec> >
+{
+    typedef typename Source<TJournaledStringTree>::Type TSource_;
+    typedef typename Size<TSource_>::Type               Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member                               [JstSeqBufferJournaledSet]
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledStringTree, typename TSpec>
+struct Member<JstBuffer_<TJournaledStringTree, TSpec>, JstBufferSetMember>
+{
+    typedef typename Member<TJournaledStringTree, JstSourceMember>::Type TSource_;
+    typedef StringSet<TSource_, Owner<JournaledSet> >   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member                                [JstBufferDeltaMapMember]
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+struct Member<JstBuffer_<TJst, TSpec>, JstBufferDeltaMapMember>
+{
+    typedef typename Member<TJst, JstDeltaMapMember>::Type Type;
+};
+
+template <typename TJst, typename TSpec>
+struct Member<JstBuffer_<TJst, TSpec> const, JstBufferDeltaMapMember>
+{
+    typedef typename Member<TJst, JstDeltaMapMember>::Type const Type;
+};
+
+// ============================================================================
+// Private Functions
+// ============================================================================
+
+namespace impl
+{
+
+// ----------------------------------------------------------------------------
+// Function impl::journalDelta()                                 [DeltaTypeSnp]
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TPos, typename TSnp>
+inline void
+journalDelta(TTarget & target,
+             TPos refPos,
+             TSnp const & snp,
+             DeltaTypeSnp const & /*tag*/)
+{
+    typedef typename JournalType<TTarget>::Type TJournalEntries;
+    typedef typename Iterator<TJournalEntries, Standard>::Type TEntriesIterator;
+    typedef typename Position<TJournalEntries>::Type TEntryPos;
+
+    TEntriesIterator entryIt = end(_journalEntries(target), Standard()) -1;
+    SEQAN_ASSERT_EQ(entryIt->segmentSource, SOURCE_ORIGINAL);
+    SEQAN_ASSERT_GEQ(refPos, entryIt->physicalOriginPosition);
+    SEQAN_ASSERT_GT(entryIt->physicalOriginPosition + entryIt->length, refPos);
+
+    TEntryPos virtPos = entryIt->virtualPosition + (refPos - entryIt->physicalOriginPosition);
+    appendValue(target._insertionBuffer, snp);
+    _doRecordInsertion(target._journalEntries, entryIt, virtPos, length(target._insertionBuffer) - 1, 1u);
+    entryIt = end(_journalEntries(target), Standard()) -1;
+    ++virtPos;
+    _doRecordErase(target._journalEntries, entryIt, virtPos, virtPos + 1);
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::journalDelta()                                 [DeltaTypeDel]
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TPos, typename TSize>
+inline void
+journalDelta(TTarget & target,
+             TPos refPos,
+             TSize const & delLength,
+             DeltaTypeDel const & /*tag*/)
+{
+    typedef typename JournalType<TTarget>::Type TJournalEntries;
+    typedef typename Iterator<TJournalEntries, Standard>::Type TEntryIterator;
+    typedef typename Position<TJournalEntries>::Type TEntryPos;
+
+    TEntryIterator entryIt = end(target._journalEntries, Standard()) - 1;
+    SEQAN_ASSERT_EQ(entryIt->segmentSource, SOURCE_ORIGINAL);
+    SEQAN_ASSERT_GEQ(refPos, entryIt->physicalOriginPosition);
+    SEQAN_ASSERT_GT(entryIt->physicalOriginPosition + entryIt->length, refPos);
+
+    target._length -= delLength;
+    TEntryPos virtPos = entryIt->virtualPosition + (refPos - entryIt->physicalOriginPosition);
+    _doRecordErase(target._journalEntries, entryIt, virtPos, virtPos + delLength);
+    if (length(target._journalEntries) == 0)
+        clear(target._insertionBuffer);
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::journalDelta()                                 [DeltaTypeIns]
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TPos, typename TInsertion>
+inline void
+journalDelta(TTarget & target,
+             TPos refPos,
+             TInsertion const & insSeq,
+             DeltaTypeIns const & /*tag*/)
+{
+    typedef typename JournalType<TTarget>::Type TJournalEntries;
+    typedef typename Iterator<TJournalEntries, Standard>::Type TEntryIterator;
+    typedef typename Position<TJournalEntries>::Type TEntryPos;
+
+    TEntryIterator entryIt = end(target._journalEntries, Standard()) - 1;
+    SEQAN_ASSERT_EQ(entryIt->segmentSource, SOURCE_ORIGINAL);
+    SEQAN_ASSERT_GEQ(refPos, entryIt->physicalOriginPosition);
+    SEQAN_ASSERT_GEQ(entryIt->physicalOriginPosition + entryIt->length, refPos);  // Special case for the insertion where it is valid to insert behind the sequence.
+
+    target._length += length(insSeq);
+    TEntryPos virtPos = entryIt->virtualPosition + (refPos - entryIt->physicalOriginPosition);
+    TEntryPos physPos = length(target._insertionBuffer);
+    append(target._insertionBuffer, insSeq);
+    _doRecordInsertion(target._journalEntries, entryIt, virtPos, physPos, length(insSeq));
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::journalDelta()                                  [DeltaTypeSV]
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TPos, typename TSV>
+inline void
+journalDelta(TTarget & target,
+             TPos refPos,
+             TSV const & sv,
+             DeltaTypeSV const & /*tag*/)
+{
+    typedef typename JournalType<TTarget>::Type TJournalEntries;
+    typedef typename Iterator<TJournalEntries, Standard>::Type TEntryIterator;
+    typedef typename Position<TJournalEntries>::Type TEntryPos;
+
+    TEntryIterator entryIt = end(target._journalEntries, Standard()) - 1;
+    SEQAN_ASSERT_EQ(entryIt->segmentSource, SOURCE_ORIGINAL);
+    SEQAN_ASSERT_GEQ(refPos, entryIt->physicalOriginPosition);
+    SEQAN_ASSERT_GT(entryIt->physicalOriginPosition + entryIt->length, refPos);
+
+    target._length -= sv.i1;
+    TEntryPos virtPos = entryIt->virtualPosition + (refPos - entryIt->physicalOriginPosition);
+    _doRecordErase(target._journalEntries, entryIt, virtPos, virtPos + sv.i1);
+    
+    entryIt = end(target._journalEntries, Standard()) - 1;
+    target._length += length(sv.i2);
+    TEntryPos physPos = length(target._insertionBuffer);
+    append(target._insertionBuffer, sv.i2);
+    _doRecordInsertion(target._journalEntries, entryIt, virtPos, physPos, length(sv.i2));
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::create()
+// ----------------------------------------------------------------------------
+
+template <typename TMapIter, typename TJSIter>
+struct JournaledStringCreateFunctor
+{
+    TMapIter mapIt;
+    TJSIter  setIt;
+
+    template <typename TTag>
+    inline void
+    operator()(TTag const & /*deltaType*/)
+    {
+        if ((*mapIt).deltaTypeEnd != DeltaEndType::IS_RIGHT)
+            impl::journalDelta(*setIt, getDeltaPosition(*mapIt), deltaValue(mapIt, TTag()), TTag());
+    }
+};
+
+template <typename TJst, typename TSpec>
+inline void
+create(JstBuffer_<TJst, TSpec> & buffer)
+{
+    typedef typename Member<JstBuffer_<TJst, TSpec>, JstBufferSetMember>::Type      TJSet;
+    typedef typename Value<TJSet>::Type                                             TJString;
+    typedef typename Iterator<TJSet, Standard>::Type                                TJSetIter;
+    typedef typename Member<JstBuffer_<TJst, TSpec>, JstBufferDeltaMapMember>::Type TDeltaMap;
+    typedef typename Iterator<TDeltaMap, Standard>::Type                            TDeltaMapIter;
+
+    SEQAN_ASSERT(!empty(buffer._startPositions));
+
+    clear(buffer._journaledSet);  // Guarentee empty set.
+
+    // Initialize the journaled set.
+    resize(buffer._journaledSet, length(buffer._startPositions), Exact());
+
+    forEach(buffer._journaledSet, [&buffer](TJString &jStr)
+    {
+        setHost(jStr, host(container(buffer._sourceBegin)));
+    }, Parallel());
+
+    // Construct the journaled string context
+
+    Splitter<TJSetIter> jSetSplitter(begin(buffer._journaledSet, Standard()), end(buffer._journaledSet, Standard()),
+                                     Parallel());
+    SEQAN_OMP_PRAGMA(parallel for)
+    for (auto jobId = 0; jobId < static_cast<int>(length(jSetSplitter)); ++jobId)
+    {
+        impl::JournaledStringCreateFunctor<TDeltaMapIter, TJSetIter> f;
+        f.mapIt = buffer._deltaRangeBegin;
+        for (; f.mapIt != buffer._deltaRangeEnd; ++f.mapIt)
+        {
+            f.setIt = jSetSplitter[jobId];
+            if (SEQAN_UNLIKELY((*f.mapIt).deltaTypeEnd == DeltaEndType::IS_RIGHT))
+                continue;
+
+            auto covIt = begin(getDeltaCoverage(*f.mapIt), Standard()) +
+                (f.setIt - begin(buffer._journaledSet, Standard()));
+            for (; f.setIt != jSetSplitter[jobId + 1]; ++f.setIt, ++covIt)
+            {
+                DeltaTypeSelector deltaSelector;
+                if (*covIt)  // If the current sequence covers the current delta.
+                    applyOnDelta(f, getDeltaType(*f.mapIt), deltaSelector);
+            }
+        }
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::synchronize()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline bool
+synchronize(JstBuffer_<TJst, TSpec> & buffer)
+{
+    typedef typename Size<JstBuffer_<TJst, TSpec> >::Type                           TSize;
+
+    SEQAN_ASSERT(buffer._sourceBegin < buffer._sourceEnd);
+
+    // TODO(rrahn): Implement block wise computation.
+    // Discover overlapping deletions at begin and end.
+    // 0123456789012345678901234...
+    // xxxxx------------xxxxxxxx...
+    //           [------xxxxxxxx...[  // Beginning of the buffer lies within a deletion of a sequence.
+    //
+    // When detecting the deletion check if end point lies behind source begin position.
+    // If false: ignore deletion.
+    // If true: Add deletion point to the mapExtension -> Maybe we can even add it as a new branching point.
+        // In this case we add a deletion right from the beginning.
+        // We just communicate through this object anyway. -> Then the algorithm does not have to change.
+    // If this is at the end: we cut the deletion -> But we have one at the same position which is just longer.
+    // But you would cut after the deletion anyway.
+    // We could only represent infixes over the journaled strings after they have been constructed?
+    // So we have a fixed end position and begin position.
+
+    buffer._deltaRangeBegin = begin(*buffer._deltaMapPtr, Standard());
+    buffer._deltaRangeEnd = end(*buffer._deltaMapPtr, Standard());
+
+// TODO(rrahn): Enable this when allowing chunking.
+//    buffer._deltaRangeBegin = std::lower_bound(begin(buffer._deltaMap, Standard()),
+//                                               end(buffer._deltaMap, Standard()),
+//                                               position(buffer._sourceBegin), DeltaExtensionCompareLessPos_());
+//    buffer._deltaRangeEnd = std::lower_bound(begin(buffer._deltaMap, Standard()), end(buffer._deltaMap, Standard()),
+//                                             position(buffer._sourceEnd), DeltaExtensionCompareLessPos_());
+
+    // Stream from the beginning to the expected range to get the begin positions of the current segment.
+    auto mapIt = begin(*buffer._deltaMapPtr, Standard());
+    resize(buffer._startPositions, length(getDeltaCoverage(*mapIt)), position(buffer._sourceBegin), Exact());
+
+    if (position(buffer._sourceBegin) == 0)  // Special case: We also set the begin position to 0 even if there is an insertion at the 0th position.
+        return true;
+
+    for (; mapIt != buffer._deltaRangeBegin; ++mapIt)
+    {
+        auto net = netSize(mapIt);
+        auto covBegin = begin(getDeltaCoverage(*mapIt), Standard());
+        for (auto covIt = covBegin; covIt != end(getDeltaCoverage(*mapIt), Standard()); ++covIt)
+        {
+            if (*covIt)
+            {
+                if (SEQAN_UNLIKELY(static_cast<TSize>(std::abs(net)) > buffer._startPositions[covIt - covBegin] &&
+                                   (net < 0)))
+                    buffer._startPositions[covIt - covBegin] = 0;  // In case the entire prefix of this sequence is deleted.
+                else
+                    buffer._startPositions[covIt - covBegin] += net;
+            }
+        }
+    }
+    buffer._isSynchronized = true;
+    return true;
+}
+
+}  // namespace impl
+
+// ============================================================================
+// Public Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function sourceBegin()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline typename JstBuffer_<TJst, TSpec>::TSourceIterator
+sourceBegin(JstBuffer_<TJst, TSpec> & buffer)
+{
+    return buffer._sourceBegin;
+}
+
+// ----------------------------------------------------------------------------
+// Function setSourceBegin()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TSourceIter>
+inline void
+setSourceBegin(JstBuffer_<TJst, TSpec> & buffer,
+               TSourceIter const & begin)
+{
+    buffer._isSynchronized = false;
+    buffer._sourceBegin = begin;
+}
+
+// ----------------------------------------------------------------------------
+// Function sourceEnd()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline typename JstBuffer_<TJst, TSpec>::TSourceIterator
+sourceEnd(JstBuffer_<TJst, TSpec> & buffer)
+{
+    return buffer._sourceEnd;
+}
+
+// ----------------------------------------------------------------------------
+// Function setSourceEnd()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TSourceIter>
+inline void
+setSourceEnd(JstBuffer_<TJst, TSpec> & buffer,
+             TSourceIter const & end)
+{
+    buffer._isSynchronized = false;
+    buffer._sourceEnd = end;
+}
+
+// ----------------------------------------------------------------------------
+// Function setDeltaMap()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline void
+setDeltaMap(JstBuffer_<TJst, TSpec> & buffer,
+            typename Member<JstBuffer_<TJst, TSpec>, JstBufferDeltaMapMember>::Type & map)
+{
+    if (buffer._deltaMapPtr != &map)
+    {
+        markModified(buffer);
+        buffer._deltaMapPtr = &map;
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function sync()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline bool
+sync(JstBuffer_<TJst, TSpec> & buffer)
+{
+    if (isSynchronized(buffer))
+        return true;
+    return impl::synchronize(buffer);
+}
+
+// ----------------------------------------------------------------------------
+// Function create()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline bool
+create(JstBuffer_<TJst, TSpec> & buffer)
+{
+    if (!isSynchronized(buffer))
+        if (!sync(buffer))
+            return false;
+    impl::create(buffer);
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function isSynchronized()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline bool
+isSynchronized(JstBuffer_<TJst, TSpec> const & buffer)
+{
+    return buffer._isSynchronized;
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline void
+clear(JstBuffer_<TJst, TSpec> & buffer)
+{
+    buffer._isSynchronized = false;
+    buffer._deltaMapPtr = nullptr;
+    clear(buffer._startPositions);
+}
+
+// ----------------------------------------------------------------------------
+// Function markModified()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec>
+inline void
+markModified(JstBuffer_<TJst, TSpec> & buffer)
+{
+    buffer._isSynchronized = false;
+}
+
+// ----------------------------------------------------------------------------
+// Function init();
+// ----------------------------------------------------------------------------
+
+// TODO(rrahn): Fix constness issue.
+template <typename TJst, typename TSpec>
+inline void
+init(JstBuffer_<TJst, TSpec> & me,
+     TJst & jst)
+{
+    setDeltaMap(me, impl::member(jst, JstDeltaMapMember()));
+    setSourceBegin(me, begin(impl::member(jst, JstSourceMember()), Standard()));
+    setSourceEnd(me, end(impl::member(jst, JstSourceMember()), Standard()));
+    sync(me);
+    create(me);
+}
+
+}  // namespace seqan
+
+#endif  // EXTRAS_INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_SEQUENCE_BUFFER_H_
diff --git a/seqan/journaled_string_tree/journaled_string_tree_traverser.h b/seqan/journaled_string_tree/journaled_string_tree_traverser.h
new file mode 100644
index 0000000..4bbac6a
--- /dev/null
+++ b/seqan/journaled_string_tree/journaled_string_tree_traverser.h
@@ -0,0 +1,432 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_H_
+#define INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TJst, typename TSpec, typename TObserverList>
+class TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserverList> : public Observable<TObserverList>
+{
+public:
+    typedef Observable<TObserverList>                                   TSuper;
+    typedef typename Member<TraverserImpl, TraverserStackMember>::Type  TStack;
+    typedef typename Value<TStack>::Type                                TNode;
+    typedef typename Size<TraverserImpl>::Type                          TSize;
+    typedef std::shared_ptr<TStack>                                     TStackPtr;
+    typedef JstBuffer_<TJst>                                            TBuffer;  // Provides a sequence context.
+    typedef std::shared_ptr<TBuffer>                                    TBufferPtr;
+
+
+
+    // __ Member Variables ____________________________________________________
+
+    TJst *      _contPtr;  // TODO(rmaerker): Should always be const.
+    TSize       _branchLength   = 1;
+    TSize       _contextSize    = 1;
+    TStackPtr   _stackPtr;
+    TBufferPtr  _bufferPtr;
+
+    // __ Constructors ________________________________________________________
+
+    // Default c'tor.
+    TraverserImpl() :
+        TSuper(),
+        _contPtr(nullptr),
+        _stackPtr(impl::createStack<TStack>()),
+        _bufferPtr(impl::createBuffer<TBuffer>())
+    {}
+
+    // C'tor with just the jst.
+    TraverserImpl(TJst & jst) :
+        TSuper(),
+        _contPtr(nullptr),
+        _stackPtr(impl::createStack<TStack>()),
+        _bufferPtr(impl::createBuffer<TBuffer>())
+    {
+        init(*this, jst);
+    }
+
+    // C'tor with the jst and the context or branch size.
+    template <typename TSize>
+    TraverserImpl(TJst & jst, TSize const contextSize) :
+    TSuper(),
+    _contPtr(nullptr),
+    _stackPtr(impl::createStack<TStack>()),
+    _bufferPtr(impl::createBuffer<TBuffer>())
+    {
+        init(*this, jst, contextSize);
+    }
+
+    // C'tor with the jst and the context or branch size.
+    template <typename TSize>
+    TraverserImpl(TJst & jst, TSize const contextSize, TSize const branchLength) :
+        TSuper(),
+        _contPtr(nullptr),
+        _stackPtr(impl::createStack<TStack>()),
+        _bufferPtr(impl::createBuffer<TBuffer>())
+    {
+        init(*this, jst, contextSize, branchLength);
+    }
+
+    // C'tor with the jst and list of observers.
+    TraverserImpl(TJst & jst, TObserverList && observers) :
+        TSuper(std::forward<TObserverList>(observers)),
+        _contPtr(nullptr),
+        _stackPtr(impl::createStack<TStack>()),
+        _bufferPtr(impl::createBuffer<TBuffer>())
+    {
+        init(*this, jst);
+    }
+
+    // C'tor with the jst and list of observers.
+    template <typename TSize>
+    TraverserImpl(TJst & jst, TSize const contextSize, TObserverList && observers) :
+        TSuper(std::forward<TObserverList>(observers)),
+        _contPtr(nullptr),
+        _stackPtr(impl::createStack<TStack>()),
+        _bufferPtr(impl::createBuffer<TBuffer>())
+    {
+        init(*this, jst, contextSize);
+    }
+
+    // C'tor with the jst and list of observers.
+    template <typename TSize>
+    TraverserImpl(TJst & jst, TSize const contextSize, TSize const branchLength, TObserverList && observers) :
+        TSuper(std::forward<TObserverList>(observers)),
+        _contPtr(nullptr),
+        _stackPtr(impl::createStack<TStack>()),
+        _bufferPtr(impl::createBuffer<TBuffer>())
+    {
+        init(*this, jst, contextSize, branchLength);
+    }
+
+    // Copy c'tor.
+    template <typename TOtherJst>
+    TraverserImpl(TraverserImpl<TOtherJst, JstTraversalSpec<TSpec>, TObserverList> const & other,
+                  SEQAN_CTOR_ENABLE_IF(IsConstructible<TJst, TOtherJst>)) :
+        _contPtr(other._contPtr),
+        _branchLength(other._historySize),
+        _contextSize(other._contextSize),
+        _stackPtr(other._stackPtr),
+        _bufferPtr(other._bufferPtr)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    // __ Member Functions ____________________________________________________
+
+    template <typename TOtherJst>
+    inline SEQAN_FUNC_ENABLE_IF(IsConstructible<TJst, TOtherJst>, TraverserImpl &)
+    operator=(TraverserImpl<TOtherJst, JstTraversalSpec<TSpec>, TObserverList> const & other)
+    {
+        if (*this != &other)
+        {
+            _contPtr = other._contPtr;
+            _branchLength =other._historySize;
+            _contextSize = other._contextSize;
+            _stackPtr = other._stackPtr;
+            _bufferPtr = other._bufferPtr;
+        }
+        return *this;
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Container
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+struct Container<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> >
+{
+    typedef TJst Type;
+};
+
+template <typename TJst, typename TSpec, typename TObserver>
+struct Container<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const>
+    : Container<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> >
+{};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+struct Size<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> >
+{
+    typedef typename Size<TJst>::Type    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction TraverserImpl
+// ----------------------------------------------------------------------------
+
+template <typename TSeq, typename TConfig, typename TSpec,
+          typename TObserver>
+struct Traverser<JournaledStringTree<TSeq, TConfig, TSpec>,
+                 TObserver>
+{
+    typedef JournaledStringTree<TSeq, TConfig, TSpec> TJst_;
+    typedef TraverserImpl<TJst_, JstTraversalSpec<void>, TObserver> Type;
+};
+
+template <typename TSeq, typename TConfig, typename TSpec,
+          typename TObserver>
+struct Traverser<JournaledStringTree<TSeq, TConfig, TSpec> const,
+                 TObserver>
+{
+    typedef JournaledStringTree<TSeq, TConfig, TSpec> const TJst_;
+    typedef TraverserImpl<TJst_, JstTraversalSpec<void>, TObserver> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction ContextIterator
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+struct ContextIterator<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> >
+{
+    typedef TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver>     TThis_;
+    typedef typename Container<TThis_>::Type                            TContainer_;
+    typedef typename Member<TContainer_, JstSourceMember>::Type         TSource_;
+
+    typedef typename Iterator<TSource_, Standard>::Type                 Type;
+};
+
+template <typename TJst, typename TSpec, typename TObserver>
+struct ContextIterator<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const>
+{
+    typedef TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> TTraverser_;
+
+    typedef typename ContextIterator<TTraverser_>::Type  const      Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Member<TraverserStackMember>
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+struct Member<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver>, TraverserStackMember>
+{
+    typedef JstTraversalNode<TJst>              TTraversalNode;
+    typedef String<TTraversalNode, Block<> >    Type;
+};
+
+// ============================================================================
+// Public Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function contextIterator();
+// ----------------------------------------------------------------------------
+
+// Returns current sequence iterator.
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename ContextIterator<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> >::Type
+contextIterator(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me)
+{
+    return impl::getContextIterator(me);
+}
+
+// ----------------------------------------------------------------------------
+// Function contextSize();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename Size<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> >::Type
+contextSize(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me)
+{
+    return me._contextSize;
+}
+
+// ----------------------------------------------------------------------------
+// Function container();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename Container<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> >::Type &
+container(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me)
+{
+    return *me._contPtr;
+}
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename Container<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const>::Type &
+container(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me)
+{
+    return *me._contPtr;
+}
+
+//// ----------------------------------------------------------------------------
+//// Function setContextSize();
+//// ----------------------------------------------------------------------------
+//
+//template <typename TJst, typename TSpec, typename TObserver, typename TSize>
+//inline void
+//setContextSize(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+//               TSize contextSize)
+//{
+//    me._contextSize = contextSize;
+//}
+//
+//// ----------------------------------------------------------------------------
+//// Function setBranchLength();
+//// ----------------------------------------------------------------------------
+//
+//template <typename TJst, typename TSpec, typename TObserver, typename TSize>
+//inline void
+//setBranchLength(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+//                TSize branchLength)
+//{
+//    me._branchLength = branchLength;
+//}
+
+// ----------------------------------------------------------------------------
+// Function goNext();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TSize>
+inline void
+goNext(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+       TSize stepSize)
+{
+    SEQAN_ASSERT(me._stackPtr != nullptr);
+
+    auto nodePtr = &back(*me._stackPtr);
+#if defined (DEBUG_JST_TRAVERSAL)
+    std::cout << "\n\nGO NEXT" << std::endl;
+    std::cout << "Node: (" << length(*me._stackPtr) << ") " << *nodePtr << std::endl;
+#endif  // DEBUG_JST_TRAVERSAL
+    stepSize = impl::moveWindow(me, nodePtr, stepSize);
+
+    if ((stepSize > 0 && nodePtr->remainingSize == 0) || atEnd(nodePtr->curDelta))
+    {
+        if (!back(*me._stackPtr).fromBase)
+        {
+            impl::popNode(me);
+            SEQAN_ASSERT(length(*me._stackPtr) > 1u);
+        }
+        else
+        {
+            eraseBack(*me._stackPtr);  // Remove the old base representing fromBase
+
+            SEQAN_ASSERT(length(*me._stackPtr) == 1u);
+            impl::moveWindow(me, &back(*me._stackPtr), stepSize + back(*me._stackPtr).remainingSize);  // Move the base to the next position coming from fromBase node.
+        }
+    }
+    else if (atEnd(nodePtr->curDelta))
+    {
+        if (!back(*me._stackPtr).fromBase)
+        {
+            impl::popNode(me);
+            SEQAN_ASSERT(length(*me._stackPtr) > 1u);
+        }
+        else
+        {
+            eraseBack(*me._stackPtr);  // Remove the old base representing fromBase
+            impl::moveWindow(me, &back(*me._stackPtr), stepSize + back(*me._stackPtr).remainingSize);  // Move the base to the next position coming from fromBase node.
+        }
+    }
+}
+
+// Special overload to move by one.
+template <typename TJst, typename TSpec, typename TObserver>
+inline void
+goNext(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & it)
+{
+    goNext(it, 1);
+}
+
+// ----------------------------------------------------------------------------
+// Function atEnd();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline bool
+atEnd(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me)
+{
+    SEQAN_ASSERT(me._stackPtr != nullptr);
+    return length(*me._stackPtr) == 1 && back(*me._stackPtr).endEdgeIt == sourceEnd(impl::buffer(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function init();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TSize>
+inline void
+init(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+     TJst & jst,
+     TSize const contextSize,
+     TSize const branchLength)
+{
+    impl::init(me, jst, contextSize, branchLength);
+}
+
+template <typename TJst, typename TSpec, typename TObserver, typename TSize>
+inline void
+init(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+     TJst & jst,
+     TSize const contextSize)
+{
+    init(me, jst, contextSize, contextSize);
+}
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline void
+init(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+     TJst & jst)
+{
+    init(me, jst, 1);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_H_
diff --git a/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h b/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h
new file mode 100644
index 0000000..51c0299
--- /dev/null
+++ b/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h
@@ -0,0 +1,124 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_NODE_H_
+#define INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_NODE_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// TODO(rrahn): Redesign interface.
+template <typename TJst>
+class JstTraversalNode
+{
+public:
+    typedef typename Member<TJst, JstSourceMember>::Type                TSequence;
+    typedef typename Iterator<TSequence, Standard>::Type                TSeqIterator;
+    typedef typename Position<TSequence>::Type                          TPosition;
+    typedef typename Member<TJst, JstDeltaMapMember>::Type              TDeltaMap;
+    typedef typename Iterator<TDeltaMap, Standard>::Type                TDeltaIterator;
+    typedef typename DeltaCoverage<TDeltaMap>::Type                     TCoverage;
+    typedef typename Size<TJst>::Type                                   TSize;
+
+    TPosition           mappedSrcEndPos;
+    TSize               remainingSize;
+    TDeltaIterator      curDelta;       // current delta iterator.
+    TDeltaIterator      nextDelta;
+    TSeqIterator        begEdgeIt;      // Current iterator of this edge.
+    TSeqIterator        curEdgeIt;      // Current iterator of this edge.
+    TSeqIterator        endEdgeIt;      // End of this edge.
+    TCoverage           coverage;       // Coverage of this node.
+    bool                isBase;
+    bool                fromBase;
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TJstLhs, typename TJstRhs>
+inline void
+swap(JstTraversalNode<TJstLhs> & lhs,
+     JstTraversalNode<TJstRhs> & rhs)
+{
+    std::swap(lhs.mappedSrcEndPos, rhs.mappedSrcEndPos);
+    std::swap(lhs.remainingSize, rhs.remainingSize);
+    std::swap(lhs.curDelta, rhs.curDelta);
+    std::swap(lhs.nextDelta, rhs.nextDelta);
+    std::swap(lhs.begEdgeIt, rhs.begEdgeIt);
+    std::swap(lhs.curEdgeIt, rhs.curEdgeIt);
+    std::swap(lhs.endEdgeIt, rhs.endEdgeIt);
+    swap(lhs.coverage, rhs.coverage);
+    std::swap(lhs.isBase, rhs.isBase);
+    std::swap(lhs.fromBase, rhs.fromBase);
+}
+
+template <typename TStream, typename TJst>
+inline TStream&
+operator<<(TStream & stream, JstTraversalNode<TJst> const & node)
+{
+    stream << "<SRC: " << node.mappedSrcEndPos;
+    stream << " REM: " << node.remainingSize;
+    stream << " CUR: (" << *node.curDelta << ")";
+    stream << " NXT: (" << *node.nextDelta << ")";
+    stream << " SEQ: " << infix(container(node.begEdgeIt), position(node.begEdgeIt), position(node.endEdgeIt));
+    stream << " PTR: " << position(node.curEdgeIt) - position(node.begEdgeIt);
+    stream << " COV: " << _printCoverage(node.coverage);
+    if (node.isBase)
+        stream << " ISB: true";
+    else
+        stream << " ISB: false";
+    if (node.fromBase)
+        stream << " FSB: true";
+    else
+        stream << " FSB: false";
+    stream << ">";
+    return stream;
+}
+
+}
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_NODE_H_
diff --git a/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h b/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h
new file mode 100644
index 0000000..2b92f0e
--- /dev/null
+++ b/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h
@@ -0,0 +1,778 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_UTIL_H_
+#define INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_UTIL_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TObject>
+struct StringContext;
+
+template <typename TContainer, typename TSpec, typename TObserverList = ObserverList<> >
+class TraverserImpl;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct TraverserStackMember_;
+typedef Tag<TraverserStackMember_> TraverserStackMember;
+
+template <typename TSpec = void>
+struct JstTraversalSpec
+{};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Member<TJst, JstBufferMember>
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+struct Member<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver>, JstBufferMember>
+{
+    typedef JstBuffer_<TJst> Type;
+};
+
+// ============================================================================
+// Private Functions
+// ============================================================================
+
+namespace impl
+{
+
+// ----------------------------------------------------------------------------
+// Function impl::createBuffer();
+// ----------------------------------------------------------------------------
+
+template <typename TBuffer>
+inline TBuffer*
+createBuffer()
+{
+    return new TBuffer;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::buffer();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename Member<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver>, JstBufferMember>::Type &
+buffer(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me)
+{
+    return *me._bufferPtr;
+}
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename Member<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const, JstBufferMember>::Type &
+buffer(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me)
+{
+    return *me._bufferPtr;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::createStack();
+// ----------------------------------------------------------------------------
+
+template <typename TStack>
+inline TStack*
+createStack()
+{
+    return new TStack;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::stack();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename Member<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver>, TraverserStackMember>::Type &
+stack(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me)
+{
+    return *me._stackPtr;
+}
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename Member<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const, TraverserStackMember>::Type &
+stack(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me)
+{
+    return *me._stackPtr;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::pushNode();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TTraversalNode>
+inline void
+pushNode(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+         TTraversalNode SEQAN_FORWARD_CARG node)
+{
+#if defined(DEBUG_JST_TRAVERSAL)
+    //    std::cout << "-----> Journal " << container(node.endEdgeIt) << std::endl;
+    std::cout << "        PUSH: (" << node << ")" << std::endl;
+#endif //defined(DEBUG_JST_TRAVERSAL)
+    appendValue(impl::stack(me), SEQAN_FORWARD(TTraversalNode, node));
+    notify(me, PushEvent());
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::popNode();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline void
+popNode(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me)
+{
+
+#if defined(DEBUG_JST_TRAVERSAL)
+    std::cout << "        POP: (" << impl::activeNode(me) << ")" << std::endl;
+#endif //defined(DEBUG_JST_TRAVERSAL)
+    eraseBack(impl::stack(me));
+    notify(me, PopEvent());
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::activeNode()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline JstTraversalNode<TJst> const &
+activeNode(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me)
+{
+    return back(impl::stack(me));
+}
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline JstTraversalNode<TJst> &
+activeNode(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me)
+{
+    return back(impl::stack(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::getContextIterator()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver>
+inline typename ContextIterator<TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const>::Type
+getContextIterator(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me)
+{
+    return impl::activeNode(me).curEdgeIt;
+}
+
+
+// ----------------------------------------------------------------------------
+// Function impl::mapSourceToVirtual()
+// ----------------------------------------------------------------------------
+
+template <typename TDeltaMapIter>
+struct MapSourceToVirtualHelper_
+{
+    typedef typename Size<TDeltaMapIter>::Type TSize;
+
+
+    TSize           virtOffset;
+    TDeltaMapIter   iter;
+
+    MapSourceToVirtualHelper_() : virtOffset(0)
+    {}
+
+    template <typename TTag>
+    inline void
+    operator()(TTag const & /*deltaType*/)
+    {
+        virtOffset += insertionSize(container(iter)._deltaStore, getStorePosition(*iter), TTag());
+    }
+
+};
+
+template <typename TIterator, typename TDeltaMap, typename TProxyId, typename THostPos>
+inline void
+mapBranchPointToVirtual(TIterator & resultIt,
+                        TDeltaMap const & variantStore,
+                        TProxyId const & proxyId,
+                        THostPos const & hostPos)
+{
+    typedef typename Container<TIterator>::Type TJournalString;
+    typedef typename JournalType<TJournalString>::Type TJournalEntries;
+    typedef typename Value<TJournalEntries>::Type TCargo;
+    typedef typename Iterator<TJournalEntries>::Type TEntriesIterator;
+    typedef typename Position<TCargo>::Type TCargoPos;
+    typedef typename Size<TCargo>::Type TCargoSize;
+    typedef typename Value<TDeltaMap>::Type TMapEntry;
+    typedef JournalEntryLtByPhysicalOriginPos<TCargoPos, TCargoSize> TComp;
+
+    typedef typename Iterator<TDeltaMap const, Standard>::Type TVarIterator;
+    typedef typename Position<TDeltaMap const>::Type TDeltaMapPos;
+
+    // We need to set the iterator to the correct position within the proxy sequence given the host pos.
+    TJournalEntries & journalEntries = _journalEntries(*resultIt._journalStringPtr);
+
+    TCargo refCargo;
+    refCargo.physicalOriginPosition = hostPos;
+    TEntriesIterator it = std::lower_bound(begin(journalEntries._journalNodes, Standard()),
+                                           end(journalEntries._journalNodes, Standard()), refCargo, TComp());
+
+    // This is now the first position whose var is equal or greater to the host pos.
+    // Since this is either a position that is deleted
+    // or a position after the insertion made -> Even for a SNP
+    // We have to go backwards.
+    if (it != begin(journalEntries, Standard()))
+        --it;
+
+    while (it != begin(journalEntries, Standard()) && it->segmentSource == SOURCE_PATCH)
+        --it;
+
+    if (it->segmentSource == SOURCE_PATCH)  // The iterator has to be at the beginning.
+    {
+        TVarIterator itVar = begin(variantStore, Standard());  // TODO(rrahn): Optimize!
+        SEQAN_ASSERT_LEQ(getDeltaPosition(*itVar), static_cast<TDeltaMapPos const>(hostPos));
+
+        TDeltaMapPos virtualOffset = 0;
+        // Now we move to the right until we find the node that we are looking for and reconstruct the offset of the virtual positions.
+        while(getDeltaPosition(*itVar) != static_cast<TDeltaMapPos const>(hostPos) && !atEnd(itVar, variantStore))
+        {
+            if (getDeltaCoverage(*itVar)[proxyId] != true)  // irrelevant variant.
+            {
+                ++itVar;
+                continue;
+            }
+
+            if (getDeltaType(*itVar) == DELTA_TYPE_INS)
+                virtualOffset += length(deltaValue(itVar, DeltaTypeIns()));
+            else if (getDeltaType(*itVar) == DELTA_TYPE_SNP)
+                ++virtualOffset;
+            else if (getDeltaType(*itVar) == DELTA_TYPE_SV)
+                virtualOffset += length(deltaValue(itVar, DeltaTypeSV()).i2);
+            ++itVar;
+        }
+        resultIt += virtualOffset;  // Set the iterator to the beginning of the variant.
+        return;
+    }
+
+    SEQAN_ASSERT_EQ(it->segmentSource, SOURCE_ORIGINAL);
+
+    // We assume that the operation begins here!
+    resultIt._journalEntriesIterator = it;
+    if (it->physicalOriginPosition + it->length > static_cast<TDeltaMapPos const>(hostPos))
+    {
+        _updateSegmentIterators(resultIt);
+        if (it->physicalOriginPosition < hostPos)
+            resultIt += hostPos - it->physicalOriginPosition;
+        return;
+    }
+
+    _updateSegmentIteratorsLeft(resultIt);  // Set the iterator to the end of the current original node.
+    if (_physicalPosition(resultIt) + 1 == static_cast<TDeltaMapPos const>(hostPos))
+    {
+        ++resultIt;
+        return;
+    }
+
+    // TODO(rmaerker): Can remove the binary Search here!
+    // Find the first node that is left or equal to the current physical position!
+    MapSourceToVirtualHelper_<TVarIterator>  f;
+    TMapEntry child;
+    child.deltaPosition = _physicalPosition(resultIt);
+    f.iter = std::upper_bound(begin(variantStore, Standard()), end(variantStore, Standard()), child,
+                              DeltaMapEntryPosLessThanComparator_());
+
+    SEQAN_ASSERT_LEQ(getDeltaPosition(*f.iter), static_cast<TDeltaMapPos const>(hostPos));
+
+//    TDeltaMapPos virtualOffset = 0;
+    // Now we move to the right until we find the node that we are looking for and reconstruct the offset of the virtual positions.
+    while (getDeltaPosition(*f.iter) != static_cast<TDeltaMapPos const>(hostPos) && !atEnd(f.iter))
+    {
+        if (getDeltaCoverage(*f.iter)[proxyId] != true || isRightEnd(*f.iter))  // irrelevant variant.
+        {
+            ++f.iter;
+            continue;
+        }
+        DeltaTypeSelector selector;
+
+        applyOnDelta(f, getDeltaType(*f.iter), selector);
+        ++f.iter;
+    }
+    resultIt += f.virtOffset + 1;  // Set the iterator to the beginning of the variant.
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::getPos()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename THostIter>
+inline typename Position<THostIter>::Type
+getPos(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me,
+       THostIter const & it)
+{
+    if (SEQAN_UNLIKELY(atEnd(it)))
+        return length(host(container(me)));
+    return getDeltaPosition(*it);
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::toNextDeltaBehindDeletion();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSize>
+inline void
+toNextDeltaBehindDeletion(JstTraversalNode<TJst> & node,
+                          TSize const delSize)
+{
+    // Move to next valid delta position. Skip all nodes that lie within the range of the deletion.
+    while (!atEnd(node.nextDelta) && (isRightEnd(*node.nextDelta) ||
+           (getDeltaPosition(*node.nextDelta)) < getDeltaPosition(*node.curDelta) + delSize))
+    {
+        ++node.nextDelta;
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::branchOut()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TTraversalNode>
+inline bool
+createBranch(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+             TTraversalNode & parent,
+             TTraversalNode & child)
+{
+    typedef typename TTraversalNode::TDeltaIterator TDeltaIt   SEQAN_TYPEDEF_FOR_DEBUG;
+    typedef typename Position<TDeltaIt>::Type       TPos       SEQAN_TYPEDEF_FOR_DEBUG;
+    // We set the coverage of the left child to be the one of the parent & coverage(curDelta);
+    transform(child.coverage, parent.coverage, getDeltaCoverage(*parent.nextDelta), FunctorBitwiseAnd());
+    transform(parent.coverage, parent.coverage, getDeltaCoverage(*parent.nextDelta),
+              FunctorNested<FunctorBitwiseAnd, FunctorIdentity, FunctorBitwiseNot>());
+
+//#if defined(DEBUG_JST_TRAVERSAL)
+//    std::cout << "Coverage Child: " << _printCoverage(child.coverage) << std::endl;
+//    std::cout << "Coverage Paren: " << _printCoverage(parent.coverage) << std::endl;
+//#endif // defined(DEBUG_JST_TRAVERSAL)
+    // Set the current delta of the child to the next delta of the parent.
+    child.curDelta = parent.nextDelta;
+
+    // A) First get the proxyId of the updated child coverage.
+    auto proxyId = bitScanForward(child.coverage);
+    if (proxyId >= length(container(me)))
+        return false;  // We can skip this child, since it has an empty coverage.
+
+    // B) Remap the sequence iterators according to the new positions.
+    if (&buffer(me)._journaledSet[proxyId] == &container(parent.endEdgeIt))
+    {
+        // remap parent node to new journal sequence.
+        proxyId = bitScanForward(parent.coverage);
+        if (proxyId < length(container(me)) && !parent.fromBase)
+        {
+            parent.endEdgeIt = begin(buffer(me)._journaledSet[proxyId], Standard());
+            impl::mapBranchPointToVirtual(parent.endEdgeIt, impl::member(container(me), JstDeltaMapMember()), proxyId,
+                                          getDeltaPosition(*parent.nextDelta));
+            // We have the sequence iterators updated and the coverage.
+            // So far the remainingLength and the curNode remain the same.
+        }
+        else  // We move to the base sequence.
+        {
+            parent.endEdgeIt = iter(impl::member((container(me)), JstSourceMember()), getDeltaPosition(*parent.nextDelta));
+        }
+    }
+    else
+    {
+        // map child node to new journal sequence.
+        // remap child node to new journal sequence.
+        child.endEdgeIt = begin(buffer(me)._journaledSet[proxyId], Standard());
+        impl::mapBranchPointToVirtual(child.endEdgeIt, impl::member(container(me), JstDeltaMapMember()), proxyId,
+                                      getDeltaPosition(*child.curDelta));
+    }
+
+    // Move to next valid delta position, note that we skip all end points and all deltas that occur at the same position.
+    while (!atEnd(child.nextDelta) && (isRightEnd(*child.nextDelta) || getPos(me, child.nextDelta) == getPos(me, child.curDelta)))
+    {
+        ++child.nextDelta;
+    }
+
+    // C) Update remaining length if we come directly from the base sequence.
+    auto iSize = insSize(child.curDelta);
+    auto dSize = delSize(child.curDelta);
+    if (parent.isBase)
+    {
+        // We should keep the mappedSrcEndPos of the base node already in sync.
+        child.mappedSrcEndPos += me._branchLength;
+        switch (getDeltaType(*child.curDelta))
+        {
+            case DELTA_TYPE_DEL:
+            {
+                if (child.remainingSize == 0)
+                    return false;
+                child.mappedSrcEndPos += dSize;
+                // We need to skip all deleted
+                impl::toNextDeltaBehindDeletion(child, dSize);
+                --child.remainingSize;
+                break;
+            }
+            case DELTA_TYPE_INS:
+            {
+                child.remainingSize += iSize;
+                break;
+            }
+            case DELTA_TYPE_SV:
+            {
+                child.mappedSrcEndPos += dSize;
+                child.remainingSize += iSize - 1;
+                impl::toNextDeltaBehindDeletion(child, dSize);
+                break;
+            }
+            default: break;
+        }
+    }
+    else
+    {
+        // Now we are down somewhere in an internal subtree.
+        switch (getDeltaType(*child.curDelta))
+        {
+            case DELTA_TYPE_DEL:
+            {
+                child.mappedSrcEndPos += dSize;
+                impl::toNextDeltaBehindDeletion(child, dSize);
+                break;
+            }
+            case DELTA_TYPE_SV:
+            {
+                child.mappedSrcEndPos += dSize;
+                impl::toNextDeltaBehindDeletion(child, dSize);
+                break;
+            }
+            default: break;
+        }
+    }
+
+    SEQAN_ASSERT(static_cast<TPos>(dSize) <= impl::getPos(me, child.nextDelta) - impl::getPos(me, child.curDelta));
+
+    child.begEdgeIt = child.endEdgeIt;
+    child.curEdgeIt = child.begEdgeIt;
+    child.endEdgeIt += (iSize + (getPos(me, child.nextDelta) - getPos(me, child.curDelta)) - dSize);
+    child.isBase = false;
+    child.fromBase = false;
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::updateOnDeletion()
+// ----------------------------------------------------------------------------
+
+template <typename TTraversalNode,
+          typename THostIter>
+inline void
+updateOnDeletion(TTraversalNode & base, THostIter const & hostIt)
+{
+    switch (getDeltaType(*hostIt))
+    {
+        case DELTA_TYPE_DEL:
+        {
+            if (deletionSize(container(hostIt)._deltaStore, getStorePosition(*hostIt), DeltaTypeDel()) > 1)
+                transform(base.coverage, base.coverage, getDeltaCoverage(*hostIt),
+                          FunctorNested<FunctorBitwiseAnd, FunctorIdentity, FunctorBitwiseNot>());
+            break;
+        }
+        case DELTA_TYPE_SV:
+        {
+            if (deletionSize(container(hostIt)._deltaStore, getStorePosition(*hostIt), DeltaTypeSV()) > 1)
+                transform(base.coverage, base.coverage, getDeltaCoverage(*hostIt),
+                          FunctorNested<FunctorBitwiseAnd, FunctorIdentity, FunctorBitwiseNot>());
+            break;
+        }
+        default: break;
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::advanceBase()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TTraversalNode>
+inline void
+advanceBase(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me,
+            TTraversalNode & base)
+{
+    SEQAN_ASSERT(base.curDelta == base.nextDelta);
+
+#if defined(DEBUG_JST_TRAVERSAL)
+    std::cout << "        BASE before --> " << base << std::endl;
+#endif // defined(DEBUG_JST_TRAVERSAL)
+
+    while (!atEnd(base.nextDelta) && impl::getPos(me, base.curDelta) == impl::getPos(me, base.nextDelta))
+    {
+        if (isRightEnd(*base.nextDelta))
+            transform(base.coverage, base.coverage, getDeltaCoverage(*base.nextDelta), FunctorBitwiseOr());
+        else
+            impl::updateOnDeletion(base, base.nextDelta);  // Update the coverage of the base node if the current delta represents a deletion.
+        ++base.nextDelta;
+    }
+    // base.nextDelta might point to an merge point.
+    base.begEdgeIt = base.endEdgeIt;
+    //getDeltaPosition(*impl::hostIter(base.curDelta)) - position(base.begEdgeIt);
+    base.curEdgeIt = base.begEdgeIt;
+    auto posN = impl::getPos(me, base.nextDelta);
+    auto posC = impl::getPos(me, base.curDelta);
+    base.endEdgeIt += posN - posC;
+    base.mappedSrcEndPos = posN;  // TODO(rrahn): Remove.
+#if defined(DEBUG_JST_TRAVERSAL)
+    std::cout << "        BASE after ---> " << base << std::endl;
+#endif // defined(DEBUG_JST_TRAVERSAL)
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::updateParent()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TTraversalNode>
+inline bool
+updateParent(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> const & me,
+             TTraversalNode & parent)
+{
+    SEQAN_ASSERT_NOT(parent.isBase);        // Should never be the base node.
+
+#if defined(DEBUG_JST_TRAVERSAL)
+    std::cout << "        EXPAND Parent before --> " << parent << std::endl;
+#endif // defined(DEBUG_JST_TRAVERSAL)
+
+//    if (testAllZeros(parent.coverage))
+//        return false;
+    // Update:
+    parent.begEdgeIt = parent.endEdgeIt;
+    parent.curEdgeIt = parent.begEdgeIt;
+
+    // Make sure that for a right subtree we don't consider merge points, because we cannot be within a branch
+    // coming from a delta while at the same time there is a deletion to be covered.
+    while(!atEnd(parent.nextDelta) && isRightEnd(*parent.nextDelta))  // Move the nextDelta iterator to the next branch point, in case the current one is an endPoint.
+    {
+        ++parent.nextDelta;
+    }
+    parent.mappedSrcEndPos += impl::getPos(me, parent.nextDelta) - impl::getPos(me, parent.curDelta);
+    auto posC = impl::getPos(me, parent.curDelta);
+    parent.endEdgeIt += impl::getPos(me, parent.nextDelta) - posC;
+
+#if defined(DEBUG_JST_TRAVERSAL)
+    std::cout << "        EXPAND Parent after ---> " << parent << std::endl;
+#endif // defined(DEBUG_JST_TRAVERSAL)
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::shiftWindowBy()
+// ----------------------------------------------------------------------------
+
+template <typename TNode, typename TSize>
+inline TSize
+shiftWindowBy(TNode & node, TSize stepSize)
+{
+    typedef typename TNode::TSeqIterator TSeqIter;
+    typedef typename Difference<TSeqIter>::Type TDiff;
+
+    SEQAN_ASSERT_GEQ(stepSize, static_cast<TSize>(0));
+
+    if (stepSize < static_cast<TSize>(node.remainingSize) || node.isBase)
+    {
+        auto minSteps = _min(static_cast<TDiff>(stepSize), node.endEdgeIt - node.curEdgeIt);
+        node.curEdgeIt += minSteps;
+        if (!node.isBase)
+            node.remainingSize -= minSteps;
+        return stepSize - minSteps;
+    }
+
+    auto minSteps = _min(static_cast<TDiff>(node.remainingSize), node.endEdgeIt - node.curEdgeIt);
+    node.curEdgeIt += minSteps;
+    if (!node.isBase)
+        node.remainingSize -= minSteps;
+    return stepSize - minSteps;
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::moveWindow();
+// ----------------------------------------------------------------------------
+
+// Forward declaration for recursive call.
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TTraversalNode,
+          typename TSize>
+inline TSize
+moveWindow(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> &, TTraversalNode*, TSize);
+
+// ----------------------------------------------------------------------------
+// Function impl::expandNode();
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TTraversalNode,
+          typename TSize>
+inline TSize
+expandNode(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & it,
+           TTraversalNode * parentPtr,
+           TSize stepSize)
+{
+
+#if defined(DEBUG_JST_TRAVERSAL)
+    std::cout << "    Expand (" << &parent << ") " << std::endl;
+#endif //defined(DEBUG_JST_TRAVERSAL)
+    parentPtr->curDelta = parentPtr->nextDelta;
+
+    if (SEQAN_UNLIKELY(atEnd(parentPtr->curDelta)))  // Reached end of tree.
+    {
+        arrayFill(begin(parentPtr->coverage), end(parentPtr->coverage), false);  // Set coverage to 0.
+        return stepSize;
+    }
+
+    if (parentPtr->isBase)  // At a branching point coming from base.
+    {
+        SEQAN_ASSERT(length(*it._stackPtr) == 1u);
+        appendValue(*it._stackPtr, *parentPtr);  // Copy the base node and mark it from base. This represents all contexts without the delta at the current position.
+        impl::advanceBase(it, *parentPtr);
+        parentPtr = &back(*it._stackPtr);
+        parentPtr->fromBase = true;
+    }
+
+    while (!atEnd(parentPtr->nextDelta) && impl::getPos(it, parentPtr->nextDelta) == impl::getPos(it, parentPtr->curDelta))
+    {
+        if (SEQAN_LIKELY(!isRightEnd(*parentPtr->nextDelta)))  // Skip points, where we merge a deletion.
+        {
+            auto child = *parentPtr;
+            if (impl::createBranch(it, *parentPtr, child) && impl::moveWindow(it, &child, stepSize) == 0 &&
+                child.remainingSize >= 0)
+            {
+                if (SEQAN_LIKELY(!atEnd(child.curDelta)))  // Skip the node in case we reached the end already.
+                    impl::pushNode(it, SEQAN_MOVE(child));
+            }
+        }
+        ++parentPtr->nextDelta;  // Move to the next branch point.
+    }
+    parentPtr->isBase = false;
+    impl::updateParent(it, *parentPtr);
+    return impl::moveWindow(it, parentPtr, stepSize);  // Recursive call to move as long as stepSize is greater 0.
+}
+
+// ----------------------------------------------------------------------------
+// Function impl::moveWindow()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TTraversalNode,
+          typename TSize>
+inline TSize
+moveWindow(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & it,
+           TTraversalNode* parentPtr,
+           TSize stepSize)
+{
+#if defined(DEBUG_JST_TRAVERSAL)
+    std::cout << "############################## BEGIN ########################################" << std::endl;
+    std::cout << "MOVE by (" << stepSize << ") -> " << parentPtr << std::endl;
+#endif //defined(DEBUG_JST_TRAVERSAL)
+    stepSize = impl::shiftWindowBy(*parentPtr, stepSize);
+    if (parentPtr->curEdgeIt == parentPtr->endEdgeIt)  // Reached branching point => expand node.
+        stepSize = impl::expandNode(it, parentPtr, stepSize);
+
+#if defined(DEBUG_JST_TRAVERSAL)
+    std::cout << "Remaining (" << stepSize << ") -> " << parentPtr << std::endl;
+    std::cout << "================================ END =========================================" << std::endl;
+#endif //defined(DEBUG_JST_TRAVERSAL)
+    return stepSize;
+}
+
+// ----------------------------------------------------------------------------
+// Function init()
+// ----------------------------------------------------------------------------
+
+template <typename TJst, typename TSpec, typename TObserver,
+          typename TSize>
+inline void
+init(TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver> & me,
+     TJst & jst,
+     TSize const contextSize,
+     TSize const branchLength)
+{
+    typedef typename TraverserImpl<TJst, JstTraversalSpec<TSpec>, TObserver>::TNode TNode;
+
+    SEQAN_ASSERT(contextSize > 0);
+    SEQAN_ASSERT(branchLength > 0);
+
+    me._contextSize = contextSize;
+    me._branchLength = _max(contextSize, branchLength);
+    me._contPtr = &jst;
+
+    SEQAN_ASSERT(me._bufferPtr);
+    SEQAN_ASSERT(me._stackPtr);
+
+    clear(buffer(me));
+    clear(stack(me));
+
+    init(buffer(me), jst);
+
+    TNode node;
+    resize(node.coverage, length(jst), true, Exact());
+
+    node.curDelta = buffer(me)._deltaRangeBegin - 1;
+    node.nextDelta = buffer(me)._deltaRangeBegin;
+
+    node.begEdgeIt = begin(impl::member(jst, JstSourceMember()), Standard());  // This points to some value already -> what could this position be?
+    node.curEdgeIt = node.begEdgeIt;
+    node.endEdgeIt = node.begEdgeIt + (getDeltaPosition(*node.nextDelta) - position(node.begEdgeIt));
+    node.mappedSrcEndPos = position(node.endEdgeIt);
+    node.remainingSize = me._branchLength - 1;
+    node.isBase = true;
+    node.fromBase = false;
+    appendValue(*me._stackPtr, SEQAN_MOVE(node));  // Push onto stack.
+
+    // After we realized this.
+    TNode* basePtr = &impl::activeNode(me);
+
+    SEQAN_ASSERT_GEQ(me._contextSize, 1u);
+    impl::moveWindow(me, basePtr, me._contextSize - 1);   // We move the traverser to the beginning of the
+}
+
+}  // namespace impl
+
+}  // namespace seqan.
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_JOURNALED_STRING_TREE_TRAVERSER_UTIL_H_
diff --git a/seqan/journaled_string_tree/observable.h b/seqan/journaled_string_tree/observable.h
new file mode 100644
index 0000000..0e65840
--- /dev/null
+++ b/seqan/journaled_string_tree/observable.h
@@ -0,0 +1,218 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_OBSERVABLE_H_
+#define INCLUDE_SEQAN_JOURNALED_STRING_TREE_OBSERVABLE_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// Type alias used to hide std::tuple in SeqAn namespace.
+template <typename... TObservers>
+using ObserverList = std::tuple<TObservers...>;
+
+// ----------------------------------------------------------------------------
+// Class Observable
+// ----------------------------------------------------------------------------
+
+template <typename TObserverList>
+class Observable;
+
+template <typename... TObservers>
+class Observable<ObserverList<TObservers...> >
+{
+public:
+    typedef ObserverList<TObservers...> TObserverList;
+    // non empty class.
+    TObserverList   observers;
+
+    // Default C'tor.
+    Observable()
+    {}
+
+    // Custom C'tor with lvalue list.
+    Observable(TObserverList const & list) : observers(list)
+    {}
+
+    // Custom C'tor with rvalue list.
+    Observable(TObserverList && list) : observers(std::forward<TObserverList>(list))
+    {}
+
+};
+
+// Special version which is the empty tuple, with no member.
+template <>
+class Observable<ObserverList<> >
+{
+    // empty class.
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction LENGTH
+// ----------------------------------------------------------------------------
+
+template <typename... TObservers>
+struct LENGTH<ObserverList<TObservers...> >
+{
+    static constexpr unsigned VALUE = sizeof...(TObservers);
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Element
+// ----------------------------------------------------------------------------
+
+template <unsigned INDEX, typename TObject>
+struct Element;
+
+template <unsigned INDEX, typename TFirst, typename... TObservers>
+struct Element<INDEX, ObserverList<TFirst, TObservers...> >
+{
+    static_assert(INDEX < LENGTH<ObserverList<TFirst, TObservers...> >::VALUE, "Trying to access element behind the end.");
+    typedef typename Element<INDEX - 1, ObserverList<TObservers...> >::Type Type;
+};
+
+template <typename TFirst, typename... TObservers>
+struct Element<0, ObserverList<TFirst, TObservers...> >
+{
+    typedef TFirst Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction NotifyObserver
+// ----------------------------------------------------------------------------
+
+template <unsigned INDEX>
+struct NotifyObserver
+{
+    template <typename TObserverList, typename TTag>
+    inline void operator()(Observable<TObserverList> & subject, TTag const & /*tag*/)
+    {
+        std::get<INDEX>(subject.observers)(TTag());
+        NotifyObserver<INDEX - 1>{}(subject, TTag());
+    }
+};
+
+template <>
+struct NotifyObserver<0>
+{
+
+    template <typename TObserverList, typename TTag>
+    inline void operator()(Observable<TObserverList> & subject, TTag const & /*tag*/)
+    {
+        std::get<0>(subject.observers)(TTag());
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+template <typename TObserverList>
+inline constexpr unsigned
+length(Observable<TObserverList> const & /*subject*/)
+{
+    return LENGTH<TObserverList>::VALUE;
+}
+
+// ----------------------------------------------------------------------------
+// Function setObserver()
+// ----------------------------------------------------------------------------
+
+template <unsigned INDEX, typename TObserver>
+inline void
+setObserver(Observable<ObserverList<> > & /*subject*/,
+            TObserver & /*observer*/)
+{
+    // no-op;
+}
+
+template <unsigned INDEX, typename TObserverList, typename TObserver>
+inline void
+setObserver(Observable<TObserverList> & subject,
+            TObserver && observer)
+{
+    static_assert(INDEX < LENGTH<TObserverList>::VALUE, "Trying to access element behind the end.");
+    std::get<INDEX>(subject.observers) = std::forward<TObserver>(observer);
+}
+
+// ----------------------------------------------------------------------------
+// Function notify()
+// ----------------------------------------------------------------------------
+
+template <typename TEventTag>
+inline void
+notify(Observable<ObserverList<> > & /*subject*/,
+       TEventTag const & /*event tag*/)
+{
+    // no-op;
+}
+
+template <typename TObserverList, typename TEventTag>
+inline void
+notify(Observable<TObserverList> & subject,
+       TEventTag const & /*event tag*/)
+{
+    NotifyObserver<LENGTH<TObserverList>::VALUE - 1>{}(subject, TEventTag());
+}
+
+// ----------------------------------------------------------------------------
+// Function makeObserverList
+// ----------------------------------------------------------------------------
+
+template <typename... TObservers>
+inline ObserverList<TObservers...>
+makeObserverList(TObservers&&... observers)
+{
+    return std::make_tuple(std::forward<TObservers>(observers)...);
+}
+
+}
+
+#endif  // #ifndef INCLUDE_SEQAN_JOURNALED_STRING_TREE_OBSERVABLE_H_
diff --git a/seqan/map.h b/seqan/map.h
index 92fc7cb..82c6638 100644
--- a/seqan/map.h
+++ b/seqan/map.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/map/INFO b/seqan/map/INFO
deleted file mode 100644
index 1b2d244..0000000
--- a/seqan/map/INFO
+++ /dev/null
@@ -1,8 +0,0 @@
-Name: seqan-map
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature, known issues
-Description: Map class and specializations.
- Contains implementations for associative arrays/mappings.
diff --git a/seqan/map/map_adapter_stl.h b/seqan/map/map_adapter_stl.h
index 0e3fa67..458d361 100644
--- a/seqan/map/map_adapter_stl.h
+++ b/seqan/map/map_adapter_stl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,13 +39,13 @@ namespace SEQAN_NAMESPACE_MAIN
 {
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-struct Value< ::std::map<TKey, TCargo, TCompare, TAlloc> > 
+struct Value< std::map<TKey, TCargo, TCompare, TAlloc> >
 {
     typedef Pair<TKey,TCargo> Type;
 };
 
 template <typename TKey, typename TCompare, typename TAlloc>
-struct Value< ::std::set<TKey, TCompare, TAlloc> > 
+struct Value< std::set<TKey, TCompare, TAlloc> >
 {
     typedef bool Type;
 };
@@ -53,13 +53,13 @@ struct Value< ::std::set<TKey, TCompare, TAlloc> >
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-struct Key< ::std::map<TKey,TCargo, TCompare, TAlloc>  >
+struct Key< std::map<TKey,TCargo, TCompare, TAlloc>  >
 {
     typedef TKey Type;
 };
 
 template <typename TKey, typename TCompare, typename TAlloc>
-struct Key< ::std::set<TKey, TCompare, TAlloc>  >
+struct Key< std::set<TKey, TCompare, TAlloc>  >
 {
     typedef TKey Type;
 };
@@ -67,7 +67,7 @@ struct Key< ::std::set<TKey, TCompare, TAlloc>  >
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-struct Cargo< ::std::map<TKey,TCargo, TCompare, TAlloc> >
+struct Cargo< std::map<TKey,TCargo, TCompare, TAlloc> >
 {
     typedef TCargo Type;
 };
@@ -75,16 +75,16 @@ struct Cargo< ::std::map<TKey,TCargo, TCompare, TAlloc> >
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TCompare, typename TAlloc>
-struct Size< ::std::set<TKey, TCompare, TAlloc> >
+struct Size< std::set<TKey, TCompare, TAlloc> >
 {
-    //typedef ::std::set<TKey>::size_type Type;
+    //typedef std::set<TKey>::size_type Type;
     typedef unsigned Type;
 };
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-struct Size< ::std::map<TKey,TCargo, TCompare, TAlloc> >
+struct Size< std::map<TKey,TCargo, TCompare, TAlloc> >
 {
-    //typedef ::std::map<TKey,TCargo>::size_type Type;
+    //typedef std::map<TKey,TCargo>::size_type Type;
     typedef unsigned Type;
 };
 
@@ -93,13 +93,13 @@ struct Size< ::std::map<TKey,TCargo, TCompare, TAlloc> >
 // traits for stl usage
 /*
 template <typename TKey, typename TCompare, typename TAlloc>
-struct AllocatorType< ::std::set<TKey, TCompare, TAlloc> >
+struct AllocatorType< std::set<TKey, TCompare, TAlloc> >
 {
     typedef TAlloc Type;
 };
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-struct AllocatorType< ::std::map<TKey, TCargo, TCompare, TAlloc> >
+struct AllocatorType< std::map<TKey, TCargo, TCompare, TAlloc> >
 {
     typedef TAlloc Type;
 };
@@ -108,13 +108,13 @@ template <typename T>
 struct StlComparator_;
 
 template <typename TKey, typename TCompare, typename TAlloc>
-struct StlComparator_< ::std::set<TKey, TCompare, TAlloc> >
+struct StlComparator_< std::set<TKey, TCompare, TAlloc> >
 {
     typedef TCompare Type;
 };
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-struct StlComparator_< ::std::map<TKey, TCargo, TCompare, TAlloc> >
+struct StlComparator_< std::map<TKey, TCargo, TCompare, TAlloc> >
 {
     typedef TCompare Type;
 };
@@ -127,35 +127,35 @@ struct StlComparator_< ::std::map<TKey, TCargo, TCompare, TAlloc> >
 template <typename T>
 struct StlIterator_
 {
-	typedef int Type;
+    typedef int Type;
 };
 
 template <typename TKey, typename TCompare, typename TAlloc>
-struct StlIterator_< ::std::set<TKey, TCompare, TAlloc> >
+struct StlIterator_< std::set<TKey, TCompare, TAlloc> >
 {
-	typedef typename ::std::set<TKey, TCompare, TAlloc>::iterator Type;
+    typedef typename std::set<TKey, TCompare, TAlloc>::iterator Type;
 };
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-struct StlIterator_< ::std::map<TKey, TCargo, TCompare, TAlloc> >
+struct StlIterator_< std::map<TKey, TCargo, TCompare, TAlloc> >
 {
-	typedef typename ::std::map<TKey, TCargo, TCompare, TAlloc>::iterator Type;
+    typedef typename std::map<TKey, TCargo, TCompare, TAlloc>::iterator Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TCompare, typename TAlloc>
 inline void
-assign(::std::set<TKey, TCompare, TAlloc> & target,
-	   ::std::set<TKey, TCompare, TAlloc> const & source)
+assign(std::set<TKey, TCompare, TAlloc> & target,
+       std::set<TKey, TCompare, TAlloc> const & source)
 {
     target = source;
 }
 
 template <typename TKey,typename TCargo, typename TCompare, typename TAlloc>
 inline void
-assign(::std::map<TKey,TCargo, TCompare, TAlloc> & target,
-	   ::std::map<TKey,TCargo, TCompare, TAlloc> const & source)
+assign(std::map<TKey,TCargo, TCompare, TAlloc> & target,
+       std::map<TKey,TCargo, TCompare, TAlloc> const & source)
 {
     target = source;
 }
@@ -164,7 +164,7 @@ assign(::std::map<TKey,TCargo, TCompare, TAlloc> & target,
 
 template <typename TValue, typename TCompare, typename TAlloc, typename TKey2>
 inline bool
-hasKey(::std::set<TValue,TCompare,TAlloc> & me, TKey2 const & _key)
+hasKey(std::set<TValue,TCompare,TAlloc> & me, TKey2 const & _key)
 {
 SEQAN_CHECKPOINT
     return (me.count(_key) != 0);
@@ -172,7 +172,7 @@ SEQAN_CHECKPOINT
 
 template <typename TValue, typename TCompare, typename TAlloc, typename TKey2>
 inline bool
-hasKey(::std::set<TValue,TCompare,TAlloc> const & me, TKey2 const & _key)
+hasKey(std::set<TValue,TCompare,TAlloc> const & me, TKey2 const & _key)
 {
 SEQAN_CHECKPOINT
     return (me.count(_key) != 0);
@@ -181,7 +181,7 @@ SEQAN_CHECKPOINT
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TKey2>
 inline bool
-hasKey(::std::map<TKey, TCargo, TCompare, TAlloc> & me, TKey2 const & _key)
+hasKey(std::map<TKey, TCargo, TCompare, TAlloc> & me, TKey2 const & _key)
 {
 SEQAN_CHECKPOINT
     return (me.count(_key) != 0);
@@ -189,7 +189,7 @@ SEQAN_CHECKPOINT
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TKey2>
 inline bool
-hasKey(::std::map<TKey, TCargo, TCompare, TAlloc> const & me, TKey2 const & _key)
+hasKey(std::map<TKey, TCargo, TCompare, TAlloc> const & me, TKey2 const & _key)
 {
 SEQAN_CHECKPOINT
     return (me.count(_key) != 0);
@@ -198,26 +198,26 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TCompare, typename TAlloc>
-inline typename Size< ::std::set<TValue, TCompare, TAlloc> >::Type
-length(::std::set<TValue, TCompare, TAlloc> const & me)
+inline typename Size< std::set<TValue, TCompare, TAlloc> >::Type
+length(std::set<TValue, TCompare, TAlloc> const & me)
 {
 SEQAN_CHECKPOINT
-	return me.size();
+    return me.size();
 }
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-inline typename Size< ::std::map<TKey,TCargo, TCompare, TAlloc> >::Type
-length(::std::map<TKey,TCargo, TCompare, TAlloc> const & me)
+inline typename Size< std::map<TKey,TCargo, TCompare, TAlloc> >::Type
+length(std::map<TKey,TCargo, TCompare, TAlloc> const & me)
 {
 SEQAN_CHECKPOINT
-	return me.size();
+    return me.size();
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TCompare, typename TAlloc, typename TValue2>
 inline void
-insert(::std::set<TValue, TCompare, TAlloc> & me,TValue2 const & _value)
+insert(std::set<TValue, TCompare, TAlloc> & me,TValue2 const & _value)
 {
 SEQAN_CHECKPOINT
     me.insert(_value);
@@ -225,28 +225,28 @@ SEQAN_CHECKPOINT
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TKey2, typename TCargo2>
 inline void
-insert(::std::map<TKey,TCargo, TCompare, TAlloc> & me, 
-	   TKey2 const & _key, 
-	   TCargo2 const & _cargo)
+insert(std::map<TKey,TCargo, TCompare, TAlloc> & me,
+       TKey2 const & _key,
+       TCargo2 const & _cargo)
 {
 SEQAN_CHECKPOINT
 
-	me[_key] = _cargo;
+    me[_key] = _cargo;
 }
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TKey2>
 inline void
-insert(::std::map<TKey,TCargo, TCompare, TAlloc> & me,TKey2 const & _key)
+insert(std::map<TKey,TCargo, TCompare, TAlloc> & me,TKey2 const & _key)
 {
 SEQAN_CHECKPOINT
 
-	insert(me, _key, TCargo());
+    insert(me, _key, TCargo());
 }
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TKey2, typename TCargo2, typename TSpec>
 inline void
-insert(::std::map<TKey,TCargo, TCompare, TAlloc> & me, Pair<TKey2,TCargo2,TSpec> const & _value)
+insert(std::map<TKey,TCargo, TCompare, TAlloc> & me, Pair<TKey2,TCargo2,TSpec> const & _value)
 {
 SEQAN_CHECKPOINT
-	insert(me, _value.i1, _value.i2);
+    insert(me, _value.i1, _value.i2);
 }
 
 
@@ -254,7 +254,7 @@ SEQAN_CHECKPOINT
 
 template <typename TValue, typename TCompare, typename TAlloc>
 inline void
-clear(::std::set<TValue, TCompare, TAlloc> & me)
+clear(std::set<TValue, TCompare, TAlloc> & me)
 {
 SEQAN_CHECKPOINT
     me.clear();
@@ -262,7 +262,7 @@ SEQAN_CHECKPOINT
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
 inline void
-clear(::std::map<TKey,TCargo, TCompare, TAlloc> & me)
+clear(std::map<TKey,TCargo, TCompare, TAlloc> & me)
 {
 SEQAN_CHECKPOINT
     me.clear();
@@ -271,22 +271,22 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////
 
 //template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TKey2>
-//inline typename Value< ::std::map<TKey,TCargo, TCompare, TAlloc> >::Type &
-//value(::std::map<TKey,TCargo, TCompare, TAlloc> & me,
-//	  TKey2 const & _key)
-//{    
+//inline typename Value< std::map<TKey,TCargo, TCompare, TAlloc> >::Type &
+//value(std::map<TKey,TCargo, TCompare, TAlloc> & me,
+//      TKey2 const & _key)
+//{
 //    return me[_key];
 //}
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TKey2>
-inline typename Cargo< ::std::map<TKey,TCargo, TCompare, TAlloc> >::Type &
-cargo(::std::map<TKey,TCargo, TCompare, TAlloc> & me,
-	  TKey2 const & _key)
+inline typename Cargo< std::map<TKey,TCargo, TCompare, TAlloc> >::Type &
+cargo(std::map<TKey,TCargo, TCompare, TAlloc> & me,
+      TKey2 const & _key)
 {
 SEQAN_CHECKPOINT
-	return me[_key];
+    return me[_key];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -299,63 +299,63 @@ struct StlMapIterator;
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TIteratorSpec>
-struct Iterator< ::std::map<TKey,TCargo, TCompare, TAlloc> , TIteratorSpec >
+struct Iterator< std::map<TKey,TCargo, TCompare, TAlloc> , TIteratorSpec >
 {
-    typedef ::std::map<TKey,TCargo, TCompare, TAlloc> TStlMap_;
-	typedef Iter<TStlMap_, StlMapIterator> Type;
+    typedef std::map<TKey,TCargo, TCompare, TAlloc> TStlMap_;
+    typedef Iter<TStlMap_, StlMapIterator> Type;
 };
 
 
 template <typename TStlMap>
 class Iter<TStlMap, StlMapIterator>
 {
-public:    
-    //typedef typename ::std::map<typename Key<TSTLMap>::Type,
+public:
+    //typedef typename std::map<typename Key<TSTLMap>::Type,
     //                            typename Cargo<TSTLMap>::Type,
     //                            typename StlComparator_<TStlMap>::Type,
     //                            typename AllocatorType<TStlMap>::Type >::iterator THostIter;
 
-	typedef typename StlIterator_<TStlMap>::Type THostIter;
-	THostIter _iter;
+    typedef typename StlIterator_<TStlMap>::Type THostIter;
+    THostIter _iter;
     Holder<TStlMap> host_map_holder;
 
-	Iter()
-	{
+    Iter()
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	Iter(Iter const & other)
-		: _iter(other._iter)
-	{
+    Iter(Iter const & other)
+        : _iter(other._iter)
+    {
 SEQAN_CHECKPOINT
         host_map_holder = other.host_map_holder;
-	}
+    }
 
-	Iter(TStlMap & map)
-		: _iter(map.begin())
+    Iter(TStlMap & map)
+        : _iter(map.begin())
     {
 SEQAN_CHECKPOINT
         setValue(host_map_holder,map);
-	}
+    }
 
-	~Iter()
-	{
+    ~Iter()
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	Iter const & 
-	operator = (Iter const & other)
-	{
+    Iter const &
+    operator = (Iter const & other)
+    {
 SEQAN_CHECKPOINT
         host_map_holder = other.host_map_holder;
         _iter = other._iter;
         return *this;
-	}
-	operator bool () const
-	{
+    }
+    operator bool () const
+    {
 SEQAN_CHECKPOINT
         return (_iter != value(host_map_holder).end());
-	}
+    }
 
 };
 
@@ -364,16 +364,16 @@ SEQAN_CHECKPOINT
 template <typename TStlMap>
 inline bool
 operator == (Iter<TStlMap, StlMapIterator> const & left,
-			 Iter<TStlMap, StlMapIterator> const & right)
+             Iter<TStlMap, StlMapIterator> const & right)
 {
 SEQAN_CHECKPOINT
-	return left._iter == right._iter;
+    return left._iter == right._iter;
 }
 
 template <typename TStlMap>
 inline bool
 operator != (Iter<TStlMap, StlMapIterator> const & left,
-			 Iter<TStlMap, StlMapIterator> const & right)
+             Iter<TStlMap, StlMapIterator> const & right)
 {
 SEQAN_CHECKPOINT
     return left._iter != right._iter;
@@ -382,19 +382,19 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TIteratorSpec>
-inline typename Iterator< ::std::map<TKey,TCargo, TCompare, TAlloc>, TIteratorSpec>::Type
-begin(::std::map<TKey,TCargo, TCompare, TAlloc> & me,
-	  TIteratorSpec)
+inline typename Iterator< std::map<TKey,TCargo, TCompare, TAlloc>, TIteratorSpec>::Type
+begin(std::map<TKey,TCargo, TCompare, TAlloc> & me,
+      TIteratorSpec)
 {
-    typedef ::std::map<TKey,TCargo, TCompare, TAlloc> TStlMap;
+    typedef std::map<TKey,TCargo, TCompare, TAlloc> TStlMap;
     typedef typename Iterator<TStlMap , TIteratorSpec>::Type TIterator;
     return TIterator(me);
 }
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-inline typename Iterator< ::std::map<TKey,TCargo, TCompare, TAlloc> >::Type
-begin(::std::map<TKey,TCargo, TCompare, TAlloc> & me)
+inline typename Iterator< std::map<TKey,TCargo, TCompare, TAlloc> >::Type
+begin(std::map<TKey,TCargo, TCompare, TAlloc> & me)
 {
-    typedef ::std::map<TKey,TCargo, TCompare, TAlloc> TStlMap;
+    typedef std::map<TKey,TCargo, TCompare, TAlloc> TStlMap;
     typedef typename Iterator<TStlMap>::Type TIterator;
     return TIterator(me);
 }
@@ -402,24 +402,24 @@ begin(::std::map<TKey,TCargo, TCompare, TAlloc> & me)
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TIteratorSpec>
-inline typename Iterator< ::std::map<TKey,TCargo, TCompare, TAlloc> >::Type
-end(::std::map<TKey,TCargo, TCompare, TAlloc> & me,
-	  TIteratorSpec)
+inline typename Iterator< std::map<TKey,TCargo, TCompare, TAlloc> >::Type
+end(std::map<TKey,TCargo, TCompare, TAlloc> & me,
+      TIteratorSpec)
 {
-    typedef ::std::map<TKey,TCargo, TCompare, TAlloc> TStlMap;
-	typedef typename Iterator<TStlMap, TIteratorSpec>::Type TIterator;
-	TIterator _iter(me);
+    typedef std::map<TKey,TCargo, TCompare, TAlloc> TStlMap;
+    typedef typename Iterator<TStlMap, TIteratorSpec>::Type TIterator;
+    TIterator _iter(me);
     _iter._iter = me.end();
     return _iter;
 }
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc>
-inline typename Iterator< ::std::map<TKey,TCargo, TCompare, TAlloc> >::Type
-end(::std::map<TKey,TCargo, TCompare, TAlloc> & me)
+inline typename Iterator< std::map<TKey,TCargo, TCompare, TAlloc> >::Type
+end(std::map<TKey,TCargo, TCompare, TAlloc> & me)
 {
-    typedef ::std::map<TKey,TCargo, TCompare, TAlloc> TStlMap;
-	typedef typename Iterator<TStlMap>::Type TIterator;
-	TIterator _iter(me);
+    typedef std::map<TKey,TCargo, TCompare, TAlloc> TStlMap;
+    typedef typename Iterator<TStlMap>::Type TIterator;
+    TIterator _iter(me);
     _iter._iter = me.end();
     return _iter;
 }
@@ -431,7 +431,7 @@ inline bool
 atEnd(Iter<TStlMap, StlMapIterator> & it)
 {
 SEQAN_CHECKPOINT
-	return (it._iter == value(it.host_map_holder).end());
+    return (it._iter == value(it.host_map_holder).end());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -441,7 +441,7 @@ inline void
 goNext(Iter<TStlMap, StlMapIterator> & it)
 {
 SEQAN_CHECKPOINT
-	it._iter++;
+    it._iter++;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -458,7 +458,7 @@ inline typename Value<TStlMap>::Type &
 value(Iter<TStlMap, StlMapIterator> const & it)
 {
 SEQAN_CHECKPOINT
-	return it._iter->second;
+    return it._iter->second;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -468,14 +468,14 @@ inline typename Key<TStlMap>::Type const &
 key(Iter<TStlMap, StlMapIterator> & it)
 {
 SEQAN_CHECKPOINT
-	return it._iter->first;
+    return it._iter->first;
 }
 template <typename TStlMap>
 inline typename Key<TStlMap>::Type const &
 key(Iter<TStlMap, StlMapIterator> const & it)
 {
 SEQAN_CHECKPOINT
-	return it._iter->first;
+    return it._iter->first;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -485,14 +485,14 @@ inline typename Cargo<TStlMap>::Type &
 cargo(Iter<TStlMap, StlMapIterator> & it)
 {
 SEQAN_CHECKPOINT
-	return it._iter->second;
+    return it._iter->second;
 }
 template <typename TStlMap>
 inline typename Cargo<TStlMap>::Type &
 cargo(Iter<TStlMap, StlMapIterator> const & it)
 {
 SEQAN_CHECKPOINT
-	return it._iter->second;
+    return it._iter->second;
 }
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -500,60 +500,60 @@ SEQAN_CHECKPOINT
 ////////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TCompare, typename TAlloc, typename TIteratorSpec>
-struct Iterator< ::std::set<TValue, TCompare, TAlloc> , TIteratorSpec >
+struct Iterator< std::set<TValue, TCompare, TAlloc> , TIteratorSpec >
 {
-    typedef ::std::set<TValue, TCompare, TAlloc> TStlSet_;
-	typedef Iter<TStlSet_, StlSetIterator> Type;
+    typedef std::set<TValue, TCompare, TAlloc> TStlSet_;
+    typedef Iter<TStlSet_, StlSetIterator> Type;
 };
 
 template <typename TStlMap>
 class Iter< TStlMap, StlSetIterator>
 {
-public:    
-    //typedef typename ::std::set<typename Key<TSTLMap>::Type,
+public:
+    //typedef typename std::set<typename Key<TSTLMap>::Type,
     //                            typename StlComparator_<TSTLMap>::Type,
     //                            typename AllocatorType<TSTLMap>::Type >::iterator THostIter;
-	typedef typename StlIterator_<TStlMap>::Type THostIter;
-	THostIter _iter;
+    typedef typename StlIterator_<TStlMap>::Type THostIter;
+    THostIter _iter;
     Holder<TStlMap> host_map_holder;
 
-	Iter()
-	{
+    Iter()
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	Iter(Iter const & other)
-		: _iter(other._iter)
-	{
+    Iter(Iter const & other)
+        : _iter(other._iter)
+    {
 SEQAN_CHECKPOINT
         host_map_holder = other.host_map_holder;
-	}
+    }
 
-	Iter(TStlMap & map)
-		: _iter(map.begin())
+    Iter(TStlMap & map)
+        : _iter(map.begin())
     {
 SEQAN_CHECKPOINT
         setValue(host_map_holder,map);
-	}
+    }
 
-	~Iter()
-	{
+    ~Iter()
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	Iter const & 
-	operator = (Iter const & other)
-	{
+    Iter const &
+    operator = (Iter const & other)
+    {
 SEQAN_CHECKPOINT
         host_map_holder = other.host_map_holder;
         _iter = other._iter;
         return *this;
-	}
-	operator bool () const
-	{
+    }
+    operator bool () const
+    {
 SEQAN_CHECKPOINT
         return (_iter != value(host_map_holder).end());
-	}
+    }
 
 };
 
@@ -562,16 +562,16 @@ SEQAN_CHECKPOINT
 template <typename TStlMap>
 inline bool
 operator == (Iter<TStlMap, StlSetIterator> const & left,
-			 Iter<TStlMap, StlSetIterator> const & right)
+             Iter<TStlMap, StlSetIterator> const & right)
 {
 SEQAN_CHECKPOINT
-	return left._iter == right._iter;
+    return left._iter == right._iter;
 }
 
 template <typename TStlMap>
 inline bool
 operator != (Iter<TStlMap, StlSetIterator> const & left,
-			 Iter<TStlMap, StlSetIterator> const & right)
+             Iter<TStlMap, StlSetIterator> const & right)
 {
 SEQAN_CHECKPOINT
     return left._iter != right._iter;
@@ -580,19 +580,19 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TCompare, typename TAlloc, typename TIteratorSpec>
-inline typename Iterator< ::std::set<TValue,TCompare,TAlloc>, TIteratorSpec>::Type
-begin(::std::set<TValue,TCompare,TAlloc> & me,
-	  TIteratorSpec)
+inline typename Iterator< std::set<TValue,TCompare,TAlloc>, TIteratorSpec>::Type
+begin(std::set<TValue,TCompare,TAlloc> & me,
+      TIteratorSpec)
 {
-    typedef ::std::set<TValue,TCompare,TAlloc> TStlMap;
+    typedef std::set<TValue,TCompare,TAlloc> TStlMap;
     typedef typename Iterator<TStlMap , TIteratorSpec>::Type TIterator;
     return TIterator(me);
 }
 template <typename TValue, typename TCompare, typename TAlloc>
-inline typename Iterator< ::std::set<TValue,TCompare,TAlloc> >::Type
-begin(::std::set<TValue,TCompare,TAlloc> & me)
+inline typename Iterator< std::set<TValue,TCompare,TAlloc> >::Type
+begin(std::set<TValue,TCompare,TAlloc> & me)
 {
-    typedef ::std::set<TValue,TCompare,TAlloc> TStlMap;
+    typedef std::set<TValue,TCompare,TAlloc> TStlMap;
     typedef typename Iterator<TStlMap>::Type TIterator;
     return TIterator(me);
 }
@@ -600,24 +600,24 @@ begin(::std::set<TValue,TCompare,TAlloc> & me)
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TCompare, typename TAlloc, typename TIteratorSpec>
-inline typename Iterator< ::std::set<TValue, TCompare, TAlloc>, TIteratorSpec>::Type
-end(::std::set<TValue, TCompare, TAlloc> & me,
-	  TIteratorSpec)
+inline typename Iterator< std::set<TValue, TCompare, TAlloc>, TIteratorSpec>::Type
+end(std::set<TValue, TCompare, TAlloc> & me,
+      TIteratorSpec)
 {
-    typedef ::std::set<TValue,TCompare,TAlloc> TStlMap;
-	typedef typename Iterator<TStlMap, TIteratorSpec>::Type TIterator;
-	TIterator _iter(me);
+    typedef std::set<TValue,TCompare,TAlloc> TStlMap;
+    typedef typename Iterator<TStlMap, TIteratorSpec>::Type TIterator;
+    TIterator _iter(me);
     _iter._iter = me.end();
     return _iter;
 }
 
 template <typename TValue, typename TCompare, typename TAlloc>
-inline typename Iterator< ::std::set<TValue,TCompare,TAlloc> >::Type
-end(::std::set<TValue,TCompare,TAlloc> & me)
+inline typename Iterator< std::set<TValue,TCompare,TAlloc> >::Type
+end(std::set<TValue,TCompare,TAlloc> & me)
 {
-    typedef ::std::set<TValue,TCompare,TAlloc> TStlMap;
-	typedef typename Iterator<TStlMap>::Type TIterator;
-	TIterator _iter(me);
+    typedef std::set<TValue,TCompare,TAlloc> TStlMap;
+    typedef typename Iterator<TStlMap>::Type TIterator;
+    TIterator _iter(me);
     _iter._iter = me.end();
     return _iter;
 }
@@ -629,7 +629,7 @@ inline bool
 atEnd(Iter<TStlMap, StlSetIterator> & it)
 {
 SEQAN_CHECKPOINT
-	return (it._iter == value(it.host_map_holder).end());
+    return (it._iter == value(it.host_map_holder).end());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -654,7 +654,7 @@ SEQAN_CHECKPOINT
 //inline typename Value<TStlMap>::Type &
 //value(Iter<TStlMap, StlSetIterator> const & it)
 //{
-//	return hasKey(*it);
+//    return hasKey(*it);
 //}
 
 //////////////////////////////////////////////////////////////////////////////
@@ -671,42 +671,42 @@ inline typename Key<TStlMap>::Type const &
 key(Iter<TStlMap, StlSetIterator> const & it)
 {
 SEQAN_CHECKPOINT
-	return (*it._iter);
+    return (*it._iter);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TCompare, typename TAlloc,typename TFind>
-inline typename Iterator< ::std::set<TValue, TCompare, TAlloc> >::Type
-find(::std::set<TValue, TCompare, TAlloc> & me,
-	 TFind const & _find)
+inline typename Iterator< std::set<TValue, TCompare, TAlloc> >::Type
+find(std::set<TValue, TCompare, TAlloc> & me,
+     TFind const & _find)
 {
 SEQAN_CHECKPOINT
-    typedef ::std::set<TValue, TCompare, TAlloc> TMap;
-    typedef typename Iterator< TMap >::Type TMapIterator;  
+    typedef std::set<TValue, TCompare, TAlloc> TMap;
+    typedef typename Iterator< TMap >::Type TMapIterator;
 
     TMapIterator _iter(me);
     _iter._iter = me.find(_find);
     if(!_iter){
-        _iter._iter = me.upper_bound(_find); 
+        _iter._iter = me.upper_bound(_find);
     }
     return _iter;
 }
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TFind>
-inline typename Iterator< ::std::map<TKey,TCargo, TCompare, TAlloc> >::Type
-find(::std::map<TKey,TCargo, TCompare, TAlloc> & me,
-	 TFind const & _find)
+inline typename Iterator< std::map<TKey,TCargo, TCompare, TAlloc> >::Type
+find(std::map<TKey,TCargo, TCompare, TAlloc> & me,
+     TFind const & _find)
 {
 SEQAN_CHECKPOINT
-    typedef ::std::map<TKey,TCargo, TCompare, TAlloc> TMap;
-    typedef typename Iterator< TMap >::Type TMapIterator;  
+    typedef std::map<TKey,TCargo, TCompare, TAlloc> TMap;
+    typedef typename Iterator< TMap >::Type TMapIterator;
 
     TMapIterator _iter(me);
     _iter._iter = me.find(_find);
     if(!_iter){
-        _iter._iter = me.upper_bound(_find); 
+        _iter._iter = me.upper_bound(_find);
     }
     return _iter;
 }
@@ -716,8 +716,8 @@ SEQAN_CHECKPOINT
 
 template <typename TValue, typename TCompare, typename TAlloc, typename TMap2>
 inline void
-erase(::std::set<TValue, TCompare, TAlloc> & me,
-	  Iter<TMap2, StlSetIterator> const & it)
+erase(std::set<TValue, TCompare, TAlloc> & me,
+      Iter<TMap2, StlSetIterator> const & it)
 {
 SEQAN_CHECKPOINT
     me.erase(it._iter);
@@ -725,8 +725,8 @@ SEQAN_CHECKPOINT
 
 template <typename TKey, typename TCargo ,typename TMap2>
 inline void
-erase(::std::map<TKey,TCargo> & me,
-	  Iter<TMap2, StlMapIterator> const & it)
+erase(std::map<TKey,TCargo> & me,
+      Iter<TMap2, StlMapIterator> const & it)
 {
 SEQAN_CHECKPOINT
     me.erase(it._iter);
@@ -737,8 +737,8 @@ SEQAN_CHECKPOINT
 
 template <typename TValue, typename TCompare, typename TAlloc, typename TToRemove>
 inline void
-erase(::std::set<TValue, TCompare, TAlloc> & me,
-	  TToRemove const & to_remove)
+erase(std::set<TValue, TCompare, TAlloc> & me,
+      TToRemove const & to_remove)
 {
 SEQAN_CHECKPOINT
     me.erase(to_remove);
@@ -746,8 +746,8 @@ SEQAN_CHECKPOINT
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TToRemove>
 inline void
-erase(::std::map<TKey,TCargo, TCompare, TAlloc> & me,
-	  TToRemove const & to_remove)
+erase(std::map<TKey,TCargo, TCompare, TAlloc> & me,
+      TToRemove const & to_remove)
 {
 SEQAN_CHECKPOINT
     me.erase(to_remove);
diff --git a/seqan/map/map_base.h b/seqan/map/map_base.h
index 6cdfed4..be3535f 100644
--- a/seqan/map/map_base.h
+++ b/seqan/map/map_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,8 +46,8 @@ namespace SEQAN_NAMESPACE_MAIN
 #if !defined(_MSC_VER) || _MSC_VER <= 1600
 
 template <typename TKey, typename TCargo, typename TCompare, typename TAlloc, typename TKey2>
-inline typename Cargo< ::std::map<TKey,TCargo, TCompare, TAlloc> >::Type &
-cargo(::std::map<TKey,TCargo, TCompare, TAlloc> & me, TKey2 const & _key);
+inline typename Cargo< std::map<TKey,TCargo, TCompare, TAlloc> >::Type &
+cargo(std::map<TKey,TCargo, TCompare, TAlloc> & me, TKey2 const & _key);
 
 #endif  // #if !defined(_MSC_VER) || _MSC_VER <= 1600
 
@@ -61,90 +61,75 @@ struct Skiplist;
  * @class Map
  * @headerfile <seqan/map.h>
  * @brief Set/dictionary container.
- * 
+ *
  * @signature template <typename TValue, typename TSpec>
  *            class Map;
- * 
+ *
  * @tparam TSpec  The specializing type. Default: @link Skiplist @endlink
  * @tparam TValue Type of values that are stored in the map. Use a Pair<Key, Cargo> to implement a dictionary
  *                mapping from <tt>Key</tt> to <tt>Cargo</tt>.
  */
 
-/**
-.Class.Map:
-..cat:Map
-..summary:Set/dictionary container.
-..signature:Map<TValue, TSpec >
-..param.TValue:Type of values that are stored in the map.
-...metafunction:Metafunction.Value
-...remarks:Use a @Class.Pair.Pair<Key, Cargo>@ to implement a dictionary mapping from $Key$ to $Cargo$.
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:@Spec.Skiplist@
-..include:seqan/map.h
-*/
 template <typename TElement, typename TSpec = Skiplist<> >
 class Map;
 
+/*!
+ * @fn Map#length
+ * @headerfile <seqan/map.h>
+ * @brief Return number of elements in map.
+ *
+ * @signature TSize length(map);
+ *
+ * @param[in] map The Map to query for its size.
+ * @return TSize The number of elements in the map.
+ */
 
 //////////////////////////////////////////////////////////////////////////////
-// In SeqAn sets and maps store elements as pairs of (key,cargo) 
+// In SeqAn sets and maps store elements as pairs of (key,cargo)
 // the elements of sets without objects are the keys.
 //////////////////////////////////////////////////////////////////////////////
 
 /*moved to basic_aggregates.h
 template <typename TKey, typename TObject, typename TSpec>
-struct Key< Pair<TKey, TObject, TSpec> > 
+struct Key< Pair<TKey, TObject, TSpec> >
 {
-	typedef TKey Type;
+    typedef TKey Type;
 };
 
 template <typename TKey, typename TCargo, typename TSpec>
-struct Cargo< Pair<TKey, TCargo, TSpec> > 
+struct Cargo< Pair<TKey, TCargo, TSpec> >
 {
-	typedef TCargo Type;
+    typedef TCargo Type;
 };
 */
 
 //////////////////////////////////////////////////////////////////////////////
-// Type for mapValue function that implements [] for map types 
+// Type for mapValue function that implements [] for map types
 
 template <typename TMap, typename TCargo>
 struct MapValueImpl_
 {
-	typedef TCargo & Type;
+    typedef TCargo & Type;
 };
 template <typename TMap>
 struct MapValueImpl_<TMap, Nothing>
 {
-	typedef bool Type;
+    typedef bool Type;
 };
 
 /*!
  * @mfn Map#MapValue
  * @brief Type of the map value type.
- * 
+ *
  * @signature MapValue<T>::Type
  * @tparam T A map type. Types: Map
- * 
+ *
  * @return Type the map value type.
  */
 
-/**
-.Metafunction.MapValue:
-..cat:Map
-..summary:Type of the map value type.
-..signature:MapValue<T>::Type
-..class:Class.Map
-..param.T:A map type.
-...type:Class.Map
-..returns.param.Type:The type of the value of T.
-..see:Metafunction.Cols
-..include:seqan/map.h
- */
 template <typename TMap>
 struct MapValue :
-	MapValueImpl_< TMap, typename Cargo<TMap>::Type >
+    MapValueImpl_< TMap, typename Cargo<TMap>::Type >
 {
 };
 
@@ -153,118 +138,91 @@ struct MapValue :
 template <typename TCargo>
 struct ImplMapValue_
 {
-	template <typename TMap, typename TKey2>
-	static inline TCargo &
-	mapValue_(TMap & me,
-		TKey2 const & _key)
-	{
-		return cargo(me, _key);
-	}
+    template <typename TMap, typename TKey2>
+    static inline TCargo &
+    mapValue_(TMap & me,
+        TKey2 const & _key)
+    {
+        return cargo(me, _key);
+    }
 };
 
 template <>
 struct ImplMapValue_<Nothing>
 {
-	template <typename TMap, typename TKey2>
-	static inline bool
-	mapValue_(TMap & me,
-		TKey2 const & _key)
-	{
-		return hasKey(me, _key);
-	}
+    template <typename TMap, typename TKey2>
+    static inline bool
+    mapValue_(TMap & me,
+        TKey2 const & _key)
+    {
+        return hasKey(me, _key);
+    }
 };
 
 /*!
  * @fn Map#mapValue
- * @brief Subscript operator <tt>[ ]</tt> of maps.
- * 
+ * @brief Subscript <tt>operator[]</tt> of maps.
+ *
  * @signature TMapValue mapValue(map, key);
- * 
- * @param map A map. Types: Map
- * @param key A key.
- * 
+ *
+ * @param[in,out] map A map. Types: Map
+ * @param[in]     key A key.
+ *
  * @return TMapValue If <tt>map</tt> is a set: The same as Map#hasKey.  If <tt>map</tt> is a dictionary: The same as
  *                   Map#value.
- * 
+ *
  * @section Remarks
- * 
+ *
  * Usually, Map#value implements the subscript operator <tt>[ ]</tt>, but for maps, this operator is implemented in
  * <tt>mapValue</tt>. The semantic of this operator depends on the kind of map: If the map has a Cargo.cargo, than
  * <tt>mapValue(map, key)</tt> returns the cargo of the (first) value in the map of the given key. If the map has no
  * Cargo.cargo, than the function returns a <tt>true</tt>, if <tt>key</tt> is in <tt>map</tt>, or <tt>false</tt>
  * otherwise.
- * 
+ *
  * @section Remarks
  *
  * There is no way to create a set of Pair, since it is always interpreted as a key/value pair.  If you need a key type
  * that holds two members, define your own key type.
- * 
+ *
  * You may overload Key and Cargo for your own value type in order to define, what part of your value type is used as
  * key and what as cargo.
  */
 
-/**
-.Function.mapValue:
-..cat:Map
-..summary:Subscript operator $[ ]$ of maps. 
-..signature:MapValue mapValue(map, key)
-..class:Class.Map
-..param.map:A map.
-...type:Class.Map
-..param.key:A key.
-...metafunction:Metafunction.Key
-..returns:If $map$ is a set: The same as @Function.Map#hasKey@.
-...text:If $map$ is a dictionary: The same as @Function.Map#value@.
-...metafunction:Metafunction.MapValue
-..remarks: Usually, @Function.Map#value@ implements the subscript operator $[ ]$, but for maps, 
-this operator is implemented in $mapValue$. 
-The semantic of this operator depends on the kind of map: If the map has a @Metafunction.Cargo.cargo@, 
-than $mapValue(map, key)$ returns the cargo of the (first) value in the map of the given key.
-If the map has no @Metafunction.Cargo.cargo@, than the function returns a $true$, if $key$ is in $map$, or $false$ otherwise.
-...note:There is no way to create a set of @Class.Pair@, since it is always interpreted as a key/value pair.
-If you need a key type that holds two members, define your own key type.
-..remarks:You may overload @Metafunction.Key@ and @Metafunction.Cargo@ for your own value type in order to define, what part of your value type is used as key and what as cargo.
-..see:Function.Map#value
-..see:Function.Map#cargo
-..see:Function.Map#hasKey
-..include:seqan/map.h
-*/
-
 template <typename TMap, typename TKey>
 inline typename MapValue<TMap>::Type
 mapValue(TMap & me,
-		 TKey const & _key)
+         TKey const & _key)
 {
-	typedef typename Cargo<TMap>::Type TCargo;
-	return ImplMapValue_<TCargo>::mapValue_(me, _key);
+    typedef typename Cargo<TMap>::Type TCargo;
+    return ImplMapValue_<TCargo>::mapValue_(me, _key);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TElement>
-inline TElement & 
-key(TElement & element) 
+inline TElement &
+key(TElement & element)
 {
-	return element;
+    return element;
 }
 template <typename TElement>
-inline TElement const & 
-key(TElement const & element) 
+inline TElement const &
+key(TElement const & element)
 {
-	return element;
+    return element;
 }
 
 template <typename TKey, typename TObject, typename TSpec>
-inline TKey & 
-key(Pair<TKey, TObject, TSpec> & element) 
+inline TKey &
+key(Pair<TKey, TObject, TSpec> & element)
 {
-	return element.i1;
+    return element.i1;
 }
 template <typename TKey, typename TObject, typename TSpec>
 inline TKey const &
-key(Pair<TKey, TObject, TSpec> const & element) 
+key(Pair<TKey, TObject, TSpec> const & element)
 {
-	return element.i1;
+    return element.i1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -272,42 +230,42 @@ key(Pair<TKey, TObject, TSpec> const & element)
 template <typename TElement, typename TSource>
 inline void
 setKey(TElement & element,
-	   TSource const & source) 
+       TSource const & source)
 {
-	element = source;
+    element = source;
 }
 template <typename TKey, typename TObject, typename TSpec, typename TSource>
-inline void 
+inline void
 setKey(Pair<TKey, TObject, TSpec> & element,
-	   TSource const & source) 
+       TSource const & source)
 {
-	element.i1 = source;
+    element.i1 = source;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 //no default cargo function
 
 template <typename TKey, typename TObject, typename TSpec>
-inline TObject & 
-cargo(Pair<TKey, TObject, TSpec> & element) 
+inline TObject &
+cargo(Pair<TKey, TObject, TSpec> & element)
 {
-	return element.i2;
+    return element.i2;
 }
 template <typename TKey, typename TObject, typename TSpec>
 inline TObject const &
-cargo(Pair<TKey, TObject, TSpec> const & element) 
+cargo(Pair<TKey, TObject, TSpec> const & element)
 {
-	return element.i2;
+    return element.i2;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TObject, typename TSpec, typename TSource>
-inline void 
+inline void
 setCargo(Pair<TKey, TObject, TSpec> & element,
-	   TSource const & source) 
+       TSource const & source)
 {
-	element.i2 = source;
+    element.i2 = source;
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/map/map_chooser.h b/seqan/map/map_chooser.h
index a7dd40b..f2a5460 100644
--- a/seqan/map/map_chooser.h
+++ b/seqan/map/map_chooser.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,18 +44,18 @@ namespace SEQAN_NAMESPACE_MAIN
 template <typename TValue, size_t SIZE>
 struct ChooseMap2_
 {
-	typedef Map<TValue, Skiplist< > > Type;
+    typedef Map<TValue, Skiplist< > > Type;
 };
 template <typename TValue>
 struct ChooseMap2_<TValue, 1>
 {
-	typedef Map<TValue, VectorSet< > > Type;
+    typedef Map<TValue, VectorSet< > > Type;
 };
 
 
 template <typename TValue>
 struct ChooseMap:
-	ChooseMap2_<TValue, sizeof(typename Key<TValue>::Type)>
+    ChooseMap2_<TValue, sizeof(typename Key<TValue>::Type)>
 {};
 
 
diff --git a/seqan/map/map_skiplist.h b/seqan/map/map_skiplist.h
index c7cc725..2f55f0c 100644
--- a/seqan/map/map_skiplist.h
+++ b/seqan/map/map_skiplist.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,34 +44,18 @@ namespace SEQAN_NAMESPACE_MAIN
  * @class Skiplist
  * @extends Map
  * @headerfile <seqan/map.h>
- * 
+ *
  * @brief General purpose map container.
- * 
+ *
  * @signature template <typename TValue, typename TSpec>
- *            class Map;
- * 
+ *            class Map<TValue, Skiplist<TSpec> >;
+ *
  * @tparam TSpec  The specializing type.
  * @tparam TValue The type of value stored in the map.
- * 
- * @section Remarks
- * 
+ *
  * The skiplist takes in average an oberhead of only two pointers per value stored in the map.
  */
 
-/**
-.Spec.Skiplist:
-..cat:Map
-..general:Class.Map
-..summary:General purpose map container.
-..signature:Map<TValue, Skiplist<TSpec> >
-..param.TValue:The type of value stored in the map.
-...metafunction:Metafunction.Value
-..param.TSpec:The specializing type.
-..remarks:The skiplist takes in average an oberhead of only two pointers per value stored in the map.
-...default:$Default$
-..include:seqan/map.h
-*/
-
 //////////////////////////////////////////////////////////////////////////////
 // Skiplist
 //////////////////////////////////////////////////////////////////////////////
@@ -103,7 +87,7 @@ struct AllocatorType;
 template <typename TValue, typename TSpec>
 struct AllocatorType<Map<TValue, Skiplist<TSpec> > >
 {
-	typedef Allocator<SimpleAlloc<> > Type;
+    typedef Allocator<SimpleAlloc<> > Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -111,7 +95,7 @@ struct AllocatorType<Map<TValue, Skiplist<TSpec> > >
 template <typename TValue, typename TSpec>
 struct Value<Map<TValue, Skiplist<TSpec> > >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -119,20 +103,20 @@ struct Value<Map<TValue, Skiplist<TSpec> > >
 template <typename T>
 struct SkiplistElement_
 {
-	typedef char Type; //dummy implementation for VC++ bug
+    typedef char Type; //dummy implementation for VC++ bug
 };
 
 template <typename TValue, typename TSpec>
 struct SkiplistElement_<Map<TValue, Skiplist<TSpec> > >
 {
-	typedef SkiplistElement<TValue, TSpec> Type;
+    typedef SkiplistElement<TValue, TSpec> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TSpec>
 struct Key<Map<TValue, Skiplist<TSpec> > >:
-	Key<typename Value< Map<TValue, Skiplist<TSpec> > >::Type>
+    Key<typename Value< Map<TValue, Skiplist<TSpec> > >::Type>
 {
 };
 
@@ -140,7 +124,7 @@ struct Key<Map<TValue, Skiplist<TSpec> > >:
 
 template <typename TValue, typename TSpec>
 struct Cargo<Map<TValue, Skiplist<TSpec> > >:
-	Cargo<typename Value< Map<TValue, Skiplist<TSpec> > >::Type>
+    Cargo<typename Value< Map<TValue, Skiplist<TSpec> > >::Type>
 {
 };
 
@@ -149,8 +133,8 @@ struct Cargo<Map<TValue, Skiplist<TSpec> > >:
 template <typename TValue, typename TSpec, typename TIteratorSpec>
 struct Iterator<Map<TValue, Skiplist<TSpec> >, TIteratorSpec >
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist_;
-	typedef Iter<TSkiplist_, SkiplistIterator> Type;
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist_;
+    typedef Iter<TSkiplist_, SkiplistIterator> Type;
 };
 
 
@@ -162,65 +146,65 @@ template <typename TValue, typename TSpec>
 class Map<TValue, Skiplist<TSpec> >
 {
 public:
-	typedef typename AllocatorType<Map>::Type TAllocator;
-	typedef SkiplistElement<TValue, TSpec> TElement;
-	typedef typename Size<Map>::Type TSize;
-
-	enum
-	{
-		MAX_HEIGHT = 28, //heights are in {0, 1, ..., MAX_HEIGHT-1}
-		BLOCK_SIZE_1_ = sizeof(TElement) * 20, //store min. 20 elements
-		BLOCK_SIZE_2_ = 0x200,	//minimal block size
-		BLOCK_SIZE = (BLOCK_SIZE_1_ > BLOCK_SIZE_2_) ? BLOCK_SIZE_1_ : BLOCK_SIZE_2_ //block size is the max out of both values
-	};
-
-	Holder<TAllocator> data_allocator;
-	TElement * data_recycle[MAX_HEIGHT];
-	unsigned char * data_mem_begin;
-	unsigned char * data_mem_end;
-
-	SkiplistElement<TValue, TSpec> data_border;
-	TSize data_length;
-	unsigned char data_height;
+    typedef typename AllocatorType<Map>::Type TAllocator;
+    typedef SkiplistElement<TValue, TSpec> TElement;
+    typedef typename Size<Map>::Type TSize;
+
+    enum
+    {
+        MAX_HEIGHT = 28, //heights are in {0, 1, ..., MAX_HEIGHT-1}
+        BLOCK_SIZE_1_ = sizeof(TElement) * 20, //store min. 20 elements
+        BLOCK_SIZE_2_ = 0x200,    //minimal block size
+        BLOCK_SIZE = (BLOCK_SIZE_1_ > BLOCK_SIZE_2_) ? BLOCK_SIZE_1_ : BLOCK_SIZE_2_ //block size is the max out of both values
+    };
+
+    Holder<TAllocator> data_allocator;
+    TElement * data_recycle[MAX_HEIGHT];
+    unsigned char * data_mem_begin;
+    unsigned char * data_mem_end;
+
+    SkiplistElement<TValue, TSpec> data_border;
+    TSize data_length;
+    unsigned char data_height;
 
     Rng<> rng;
 
-	Map()
-		: data_mem_begin(0)
-		, data_mem_end(0)
-		, data_length(0)
-		, data_height(0)
+    Map()
+        : data_mem_begin(0)
+        , data_mem_end(0)
+        , data_length(0)
+        , data_height(0)
         , rng(0)
-	{
-		for (unsigned char i = 0; i < MAX_HEIGHT; ++i)
-		{
-			data_recycle[i] = 0;
-			valueConstruct(data_border.data_next + i, NonMinimalCtor()); 
-		}
-	}
-	Map(Map const & other)
-		: data_mem_begin(0)
-		, data_mem_end(0)
-		, data_length(0)
-		, data_height(0)
+    {
+        for (unsigned char i = 0; i < MAX_HEIGHT; ++i)
+        {
+            data_recycle[i] = 0;
+            valueConstruct(data_border.data_next + i, NonMinimalCtor());
+        }
+    }
+    Map(Map const & other)
+        : data_mem_begin(0)
+        , data_mem_end(0)
+        , data_length(0)
+        , data_height(0)
         , rng(0)
-	{
-		assign(*this, other);
-	}
+    {
+        assign(*this, other);
+    }
 
-	Map &
+    Map &
     operator=(Map const & other)
-	{
-		assign(*this, other);
-		return *this;
-	}
-
-	template <typename TKey>
-	inline typename MapValue<Map>::Type
-	operator [] (TKey const & key)
-	{
-		return mapValue(*this, key);
-	}
+    {
+        assign(*this, other);
+        return *this;
+    }
+
+    template <typename TKey>
+    inline typename MapValue<Map>::Type
+    operator [] (TKey const & key)
+    {
+        return mapValue(*this, key);
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -229,19 +213,19 @@ template <typename TValue, typename TSpec>
 class SkiplistElement
 {
 public:
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
-	typedef SkiplistNext<TValue, TSpec> TNext;
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef SkiplistNext<TValue, TSpec> TNext;
 
-	enum
-	{
-		MAX_HEIGHT = TSkiplist::MAX_HEIGHT
-	};
+    enum
+    {
+        MAX_HEIGHT = TSkiplist::MAX_HEIGHT
+    };
 
-	TValue data_value;
-	TNext data_next[MAX_HEIGHT]; //note: only parts of this array available
+    TValue data_value;
+    TNext data_next[MAX_HEIGHT]; //note: only parts of this array available
 
-	//indirect constructor in _skiplistConstructElement
-	//indirect destructor in _skiplistDestructElement
+    //indirect constructor in _skiplistConstructElement
+    //indirect destructor in _skiplistDestructElement
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -252,25 +236,18 @@ template <typename TValue, typename TSpec>
 class SkiplistNext
 {
 public:
-	typedef SkiplistElement<TValue, TSpec> TElement;
-
-	TElement * data_element;
-
-	SkiplistNext()
-	{}
-	SkiplistNext(NonMinimalCtor)
-		: data_element(0)
-	{}
-	SkiplistNext(SkiplistNext const & other)
-		: data_element(other.data_element)
-	{}
-	~SkiplistNext()
-	{}
-	SkiplistNext const & operator = (SkiplistNext const & other)
-	{
-		data_element = other.data_element;
-		return *this;
-	}
+    typedef SkiplistElement<TValue, TSpec> TElement;
+
+    TElement * data_element;
+
+    SkiplistNext() : data_element(0)
+    {}
+
+    SkiplistNext(NonMinimalCtor) : data_element(0)
+    {}
+
+    SkiplistNext(SkiplistNext const & other) : data_element(other.data_element)
+    {}
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -280,15 +257,15 @@ template <typename TValue, typename TSpec>
 class SkiplistPath
 {
 public:
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
-	typedef SkiplistElement<TValue, TSpec> TElement;
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef SkiplistElement<TValue, TSpec> TElement;
 
-	enum
-	{
-		MAX_HEIGHT = TSkiplist::MAX_HEIGHT
-	};
+    enum
+    {
+        MAX_HEIGHT = TSkiplist::MAX_HEIGHT
+    };
 
-	TElement * data_elements[MAX_HEIGHT];
+    TElement * data_elements[MAX_HEIGHT];
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -296,33 +273,33 @@ class SkiplistPath
 template<typename TValue, typename TSpec>
 inline void
 assign(Map<TValue, Skiplist<TSpec> > & target,
-	   Map<TValue, Skiplist<TSpec> > const & source)
+       Map<TValue, Skiplist<TSpec> > const & source)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
-	typedef SkiplistPath<TValue, TSpec> TPath;
-	typedef SkiplistElement<TValue, TSpec> TElement;
-	typedef typename Iterator<TSkiplist>::Type TIterator;
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef SkiplistPath<TValue, TSpec> TPath;
+    typedef SkiplistElement<TValue, TSpec> TElement;
+    typedef typename Iterator<TSkiplist>::Type TIterator;
 
-	clear(target);
+    clear(target);
 
-	TPath path;
-	path.data_elements[0] = & target.data_border;
+    TPath path;
+    path.data_elements[0] = & target.data_border;
 
-	for (TIterator it(source); !atEnd(it); goNext(it))
-	{
-		unsigned char height = _skiplistCreateHeight(target, path);
-		TElement & el = _skiplistConstructElement(target, height, value(it));
+    for (TIterator it(source); !atEnd(it); goNext(it))
+    {
+        unsigned char height = _skiplistCreateHeight(target, path);
+        TElement & el = _skiplistConstructElement(target, height, value(it));
 
-		for (int i = 0; i <= height; ++i)
-		{
-			el.data_next[i].data_element = 0;
-			path.data_elements[i]->data_next[i].data_element = & el;
-			path.data_elements[i] = & el;
-		}
+        for (int i = 0; i <= height; ++i)
+        {
+            el.data_next[i].data_element = 0;
+            path.data_elements[i]->data_next[i].data_element = & el;
+            path.data_elements[i] = & el;
+        }
 
-	}
+    }
 
-	target.data_length = length(source);
+    target.data_length = length(source);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -332,41 +309,41 @@ assign(Map<TValue, Skiplist<TSpec> > & target,
 template <typename TValue, typename TSpec>
 inline SkiplistElement<TValue, TSpec> &
 _skiplistAllocateElement(Map<TValue, Skiplist<TSpec> > & me,
-						 unsigned char height)
+                         unsigned char height)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
-	typedef SkiplistElement<TValue, TSpec> TElement;
-	typedef SkiplistNext<TValue, TSpec> TNext;
-
-	TElement * ret;
-
-	if (me.data_recycle[height])
-	{//use recycled
-		ret = me.data_recycle[height];
-		me.data_recycle[height] = * reinterpret_cast<TElement **>(me.data_recycle[height]);
-	}
-	else
-	{
-		int const element_base_size = sizeof(TElement) - TSkiplist::MAX_HEIGHT * sizeof(TNext);
-		int need_size = element_base_size + (height+1) * sizeof(TNext);
-		int buf_size = me.data_mem_end - me.data_mem_begin;
-		if (buf_size < need_size)
-		{//need new memory
-			if (buf_size >= (int) (element_base_size + sizeof(TNext)))
-			{//link rest memory in recycle 
-				int rest_height = (buf_size - element_base_size) / sizeof(TNext) - 1; //must be < height, because buf_size < need_size
-				* reinterpret_cast<TElement **>(me.data_mem_begin) = me.data_recycle[rest_height];
-				me.data_recycle[rest_height] = reinterpret_cast<TElement *>(me.data_mem_begin);
-			}
-			//else: a small part of memory is wasted
-			allocate(value(me.data_allocator), me.data_mem_begin, (size_t) TSkiplist::BLOCK_SIZE, TagAllocateStorage());
-			me.data_mem_end = me.data_mem_begin + TSkiplist::BLOCK_SIZE;
-		}
-		ret = reinterpret_cast<TElement *>(me.data_mem_begin);
-		me.data_mem_begin += need_size;
-	}
-
-	return *ret;
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef SkiplistElement<TValue, TSpec> TElement;
+    typedef SkiplistNext<TValue, TSpec> TNext;
+
+    TElement * ret;
+
+    if (me.data_recycle[height])
+    {//use recycled
+        ret = me.data_recycle[height];
+        me.data_recycle[height] = * reinterpret_cast<TElement **>(me.data_recycle[height]);
+    }
+    else
+    {
+        int const element_base_size = sizeof(TElement) - TSkiplist::MAX_HEIGHT * sizeof(TNext);
+        int need_size = element_base_size + (height+1) * sizeof(TNext);
+        int buf_size = me.data_mem_end - me.data_mem_begin;
+        if (buf_size < need_size)
+        {//need new memory
+            if (buf_size >= (int) (element_base_size + sizeof(TNext)))
+            {//link rest memory in recycle
+                int rest_height = (buf_size - element_base_size) / sizeof(TNext) - 1; //must be < height, because buf_size < need_size
+                * reinterpret_cast<TElement **>(me.data_mem_begin) = me.data_recycle[rest_height];
+                me.data_recycle[rest_height] = reinterpret_cast<TElement *>(me.data_mem_begin);
+            }
+            //else: a small part of memory is wasted
+            allocate(value(me.data_allocator), me.data_mem_begin, (size_t) TSkiplist::BLOCK_SIZE, TagAllocateStorage());
+            me.data_mem_end = me.data_mem_begin + TSkiplist::BLOCK_SIZE;
+        }
+        ret = reinterpret_cast<TElement *>(me.data_mem_begin);
+        me.data_mem_begin += need_size;
+    }
+
+    return *ret;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -375,15 +352,15 @@ _skiplistAllocateElement(Map<TValue, Skiplist<TSpec> > & me,
 template <typename TValue, typename TSpec, typename TValue2>
 inline SkiplistElement<TValue, TSpec> &
 _skiplistConstructElement(Map<TValue, Skiplist<TSpec> > & me,
-						  unsigned char height,
-						  TValue2 const & _value)
+                          unsigned char height,
+                          TValue2 const & _value)
 {
-	typedef SkiplistElement<TValue, TSpec> TElement;
-	TElement & el = _skiplistAllocateElement(me, height);
-	valueConstruct(& (el.data_value), _value);
-	//no need to construct the next array
+    typedef SkiplistElement<TValue, TSpec> TElement;
+    TElement & el = _skiplistAllocateElement(me, height);
+    valueConstruct(& (el.data_value), _value);
+    //no need to construct the next array
 
-	return el;
+    return el;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -391,13 +368,13 @@ _skiplistConstructElement(Map<TValue, Skiplist<TSpec> > & me,
 template <typename TValue, typename TSpec>
 inline void
 _skiplistDeallocateElement(Map<TValue, Skiplist<TSpec> > & me,
-						   SkiplistElement<TValue, TSpec> & el,
-						   unsigned char height)
+                           SkiplistElement<TValue, TSpec> & el,
+                           unsigned char height)
 {
-	typedef SkiplistElement<TValue, TSpec> TElement;
-	* reinterpret_cast<TElement **>(& el) = me.data_recycle[height];
-	me.data_recycle[height] = reinterpret_cast<TElement *>(&el);
-	//the real deallocation is done by the allocator on destruction 
+    typedef SkiplistElement<TValue, TSpec> TElement;
+    * reinterpret_cast<TElement **>(& el) = me.data_recycle[height];
+    me.data_recycle[height] = reinterpret_cast<TElement *>(&el);
+    //the real deallocation is done by the allocator on destruction
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -406,12 +383,12 @@ _skiplistDeallocateElement(Map<TValue, Skiplist<TSpec> > & me,
 template <typename TValue, typename TSpec>
 inline void
 _skiplistDestructElement(Map<TValue, Skiplist<TSpec> > & me,
-						 SkiplistElement<TValue, TSpec> & el,
-						 unsigned char height)
+                         SkiplistElement<TValue, TSpec> & el,
+                         unsigned char height)
 {
-	valueDestruct(& (el.value) );
-	//no need to construct the next array
-	_skiplistDeallocateElement(me, el, height);
+    valueDestruct(& (el.value) );
+    //no need to construct the next array
+    _skiplistDeallocateElement(me, el, height);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -422,36 +399,36 @@ template <typename TValue, typename TSpec>
 inline unsigned char
 _skiplistCreateHeight(Map<TValue, Skiplist<TSpec> > & me)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
 
-	unsigned char height = pickRandomNumber(me.rng, Pdf<GeometricFairCoin>());
-	if (height >= TSkiplist::MAX_HEIGHT) height = TSkiplist::MAX_HEIGHT-1;
+    unsigned char height = pickRandomNumber(me.rng, Pdf<GeometricFairCoin>());
+    if (height >= TSkiplist::MAX_HEIGHT) height = TSkiplist::MAX_HEIGHT-1;
 
-	if (height > me.data_height) me.data_height = height;
+    if (height > me.data_height) me.data_height = height;
 
-	return height;
+    return height;
 }
 
 template <typename TValue, typename TSpec>
 inline unsigned char
 _skiplistCreateHeight(Map<TValue, Skiplist<TSpec> > & me,
-					  SkiplistPath<TValue, TSpec> & path) //extend path if height is increased
+                      SkiplistPath<TValue, TSpec> & path) //extend path if height is increased
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
 
-	unsigned char height = pickRandomNumber(me.rng, Pdf<GeometricFairCoin>());
-	if (height >= TSkiplist::MAX_HEIGHT) height = TSkiplist::MAX_HEIGHT-1;
+    unsigned char height = pickRandomNumber(me.rng, Pdf<GeometricFairCoin>());
+    if (height >= TSkiplist::MAX_HEIGHT) height = TSkiplist::MAX_HEIGHT-1;
 
-	if (height > me.data_height)
-	{
-		for (unsigned char i = me.data_height + 1; i <= height; ++i)
-		{
-			path.data_elements[i] = & me.data_border;
-		}
-		me.data_height = height;
-	}
+    if (height > me.data_height)
+    {
+        for (unsigned char i = me.data_height + 1; i <= height; ++i)
+        {
+            path.data_elements[i] = & me.data_border;
+        }
+        me.data_height = height;
+    }
 
-	return height;
+    return height;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -459,28 +436,28 @@ _skiplistCreateHeight(Map<TValue, Skiplist<TSpec> > & me,
 template <typename TValue, typename TSpec>
 inline unsigned char
 _skiplistGetHeight(Map<TValue, Skiplist<TSpec> > & me,
-				   SkiplistElement<TValue, TSpec> & el,
-				   SkiplistPath<TValue, TSpec> & path)
+                   SkiplistElement<TValue, TSpec> & el,
+                   SkiplistPath<TValue, TSpec> & path)
 {
-	int height = me.data_height;
-	for (; height > 0 ; --height)
-	{
-		if (path.elements[height]->data_next[height] == el) break;
-	}
-	return height;
+    int height = me.data_height;
+    for (; height > 0 ; --height)
+    {
+        if (path.elements[height]->data_next[height] == el) break;
+    }
+    return height;
 }
 
 template <typename TValue, typename TSpec>
 inline unsigned char
-_skiplistGetHeight(Map<TValue, Skiplist<TSpec> > & me, 
-				   SkiplistElement<TValue, TSpec> & el)
+_skiplistGetHeight(Map<TValue, Skiplist<TSpec> > & me,
+                   SkiplistElement<TValue, TSpec> & el)
 {
-	typedef SkiplistPath<TValue, TSpec> TPath;
+    typedef SkiplistPath<TValue, TSpec> TPath;
 
-	TPath path;
-	_skiplistFind(me, el, path);
+    TPath path;
+    _skiplistFind(me, el, path);
 
-	return _skiplistGetHeight(el, path);
+    return _skiplistGetHeight(el, path);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -501,53 +478,53 @@ _skiplistGetHeight(Map<TValue, Skiplist<TSpec> > & me,
 template <typename TValue, typename TSpec, typename TKey>
 inline bool
 _skiplistFindGoNext(SkiplistNext<TValue, TSpec> & next,
-					unsigned char,
-					TKey const & _key)
+                    unsigned char,
+                    TKey const & _key)
 {
-	return (key(next.data_element->data_value) < _key);
+    return (key(next.data_element->data_value) < _key);
 }
 
 template <typename TValue, typename TSpec>
 inline bool
 _skiplistFindGoNext(SkiplistNext<TValue, TSpec> & next,
-					unsigned char,
-					SkiplistElement<TValue, TSpec> const & el)
+                    unsigned char,
+                    SkiplistElement<TValue, TSpec> const & el)
 {
-	return (key(next.data_element->data_value) <= key(el.data_value)) && (next.data_element != & el);
+    return (key(next.data_element->data_value) <= key(el.data_value)) && (next.data_element != & el);
 }
 
 template <typename TValue, typename TSpec>
 inline bool
 _skiplistFindGoNext(SkiplistNext<TValue, TSpec> & next,
-					unsigned char /*height*/,
-					GoEnd)
+                    unsigned char /*height*/,
+                    GoEnd)
 {
-	return next.data_element;
-//	return next.data_element->data_next[height];
+    return next.data_element;
+//    return next.data_element->data_next[height];
 }
 
 
 template <typename TValue, typename TSpec, typename TFind>
 inline void
 _skiplistFind(Map<TValue, Skiplist<TSpec> > & me,
-			  TFind const & find, //can be a key or a SkiplistElement or GoEnd
-			  /*OUT*/ SkiplistPath<TValue, TSpec> & path)
+              TFind const & find, //can be a key or a SkiplistElement or GoEnd
+              /*OUT*/ SkiplistPath<TValue, TSpec> & path)
 {
-	typedef SkiplistElement<TValue, TSpec> TElement;
-	typedef SkiplistNext<TValue, TSpec> TNext;
-
-	TElement * here = & me.data_border;
-
-	for (int i = me.data_height; i >= 0; --i)
-	{
-		while (true)
-		{
-			TNext & next = here->data_next[i];
-			if (!next.data_element || !_skiplistFindGoNext(next, i, find)) break;
-			here = next.data_element;
-		}
-		path.data_elements[i] = here;
-	}
+    typedef SkiplistElement<TValue, TSpec> TElement;
+    typedef SkiplistNext<TValue, TSpec> TNext;
+
+    TElement * here = & me.data_border;
+
+    for (int i = me.data_height; i >= 0; --i)
+    {
+        while (true)
+        {
+            TNext & next = here->data_next[i];
+            if (!next.data_element || !_skiplistFindGoNext(next, i, find)) break;
+            here = next.data_element;
+        }
+        path.data_elements[i] = here;
+    }
 }
 
 
@@ -557,92 +534,75 @@ _skiplistFind(Map<TValue, Skiplist<TSpec> > & me,
  * @fn Map#find
  * @headerfile <seqan/map.h>
  * @brief Find a value in a map.
- * 
+ *
  * @signature TIterator find(map, key);
- * 
+ *
  * @param[in] map A map. Types: Map
  * @param[in] key A key.
- * 
+ *
  * @return TIterator An iterator to the first value in <tt>map</tt> of the given key, if there is any.  An iterator
  *                   to the fist value in <tt>map</tt> with key &gt; <tt>key</tt>, otherwise.
- * 
+ *
  * @see Map#value
  * @see Map#cargo
  */
 
-/**
-.Function.Map#find:
-..cat:Map
-..summary:Find a value in a map. 
-..signature:Iterator find(map, key)
-..class:Class.Map
-..param.map:A map.
-...type:Class.Map
-..param.key:A key.
-...metafunction:Metafunction.Key
-..returns:An iterator to the first value in $map$ of the given key, if there is any.
-An iterator to the fist value in $map$ with key > $key$, otherwise
-...metafunction:Metafunction.Iterator
-..see:Function.Map#value
-..include:seqan/map.h
-*/
-
 template <typename TValue, typename TSpec, typename TFind>
 inline typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type
 find(Map<TValue, Skiplist<TSpec> > & me,
-	 TFind const & _find, //can be a TKey or a SkiplistElement or GoEnd
-	 SkiplistPath<TValue, TSpec> & path) 
+     TFind const & _find, //can be a TKey or a SkiplistElement or GoEnd
+     SkiplistPath<TValue, TSpec> & path)
 {
-	typedef typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type TIterator;
+    typedef typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type TIterator;
 
-	_skiplistFind(me, _find, path);
-	return TIterator(path.data_elements[0]->data_next[0].data_element);
+    _skiplistFind(me, _find, path);
+    return TIterator(path.data_elements[0]->data_next[0].data_element);
 }
 template <typename TValue, typename TSpec, typename TFind>
 inline typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type
 find(Map<TValue, Skiplist<TSpec> > & me,
-	 TFind const & _find) //can be a TKey or a SkiplistElement or GoEnd
+     TFind const & _find) //can be a TKey or a SkiplistElement or GoEnd
 {
-	typedef SkiplistPath<TValue, TSpec> TPath;
-	TPath path;
-	return find(me, _find, path);
+    typedef SkiplistPath<TValue, TSpec> TPath;
+    TPath path;
+    return find(me, _find, path);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 //insert elements after at the position path points to
-//Requirements: 
+//Requirements:
 // - height <= height of the skiplist
 // - next must be filled at least up to height
 // - el.data_next must have space for at least height many entries
 template <typename TValue, typename TSpec>
 inline void
 _skiplistInsertElement(Map<TValue, Skiplist<TSpec> > & me,
-					   SkiplistElement<TValue, TSpec> & el,
-					   SkiplistPath<TValue, TSpec> & path,
-					   unsigned char height)
+                       SkiplistElement<TValue, TSpec> & el,
+                       SkiplistPath<TValue, TSpec> & path,
+                       unsigned char height)
 {
-	for (int i = height; i >= 0; --i)
-	{
-		el.data_next[i].data_element = path.data_elements[i]->data_next[i].data_element;
-		path.data_elements[i]->data_next[i].data_element = & el;
-	}
+    for (int i = height; i >= 0; --i)
+    {
+        el.data_next[i].data_element = path.data_elements[i]->data_next[i].data_element;
+        path.data_elements[i]->data_next[i].data_element = & el;
+    }
 
-	++me.data_length;
+    ++me.data_length;
 }
 
 template <typename TValue, typename TSpec>
 inline void
 _skiplistInsertElement(Map<TValue, Skiplist<TSpec> > & me,
-					   SkiplistElement<TValue, TSpec> & el,
-					   unsigned char height)
+                       SkiplistElement<TValue, TSpec> & el,
+                       unsigned char height)
 {
-	typedef SkiplistPath<TValue, TSpec> TPath;
+    typedef SkiplistPath<TValue, TSpec> TPath;
 
-	TPath path;
-	_skiplistFind(me, key(el.data_value), path);
+    TPath path;
+    _skiplistFind(me, key(el.data_value), path);
 
-	_skiplistInsertElement(me, el, path, height);
+    _skiplistInsertElement(me, el, path, height);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -651,66 +611,44 @@ _skiplistInsertElement(Map<TValue, Skiplist<TSpec> > & me,
 /*!
  * @fn Map#value
  * @brief Returns a value given a key.
- * 
- * @signature TReference find(map, key);
- * 
- * @param map A map.
- * @param key A key.
- * 
+ *
+ * @signature TReference value(map, key);
+ *
+ * @param[in] map A map.
+ * @param[in] key A key.
+ *
  * @return TReference The first value in <tt>map</tt> of the given key, if there is any.  Otherwise, a new value
  *                    that is inserted to <tt>map</tt>.
- * 
- * @section Remarks
- * 
- * Do not change the key of a value in the map.
+ *
+ * @note Do not change the key of a value in the map.
  */
 
-/**
-.Function.Map#value:
-..cat:Map
-..summary:Returns a value given a key. 
-..signature:Reference find(map, key)
-..class:Class.Map
-..param.map:A map.
-...type:Class.Map
-..param.key:A key.
-...metafunction:Metafunction.Key
-..returns:The first value in $map$ of the given key, if there is any.
-Otherwise, a new value that is inserted to $map$.
-...metafunction:Metafunction.Reference
-..remarks:
-...note:Do not change the key of a value in the map.
-..see:Function.Map#find
-..see:Function.Map#insert
-..include:seqan/map.h
-*/
-
 template <typename TValue, typename TSpec, typename TKey2>
 inline typename Value< Map<TValue, Skiplist<TSpec> > >::Type &
 value(Map<TValue, Skiplist<TSpec> > & me,
-	  TKey2 const & _key)
+      TKey2 const & _key)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
-	typedef SkiplistPath<TValue, TSpec> TPath;
-	typedef SkiplistElement<TValue, TSpec> TElement;
-	typedef typename Iterator<TSkiplist>::Type TIterator;
-	typedef typename Value<TSkiplist>::Type TValue2;
-
-	TPath path;
-	TIterator it = find(me, _key, path);
-	if (it && (key(it) == _key))
-	{
-		return value(it);
-	}
-	else
-	{// insert new value
-		unsigned char height = _skiplistCreateHeight(me, path);
-		TValue2 val_temp;
-		setKey(val_temp, _key);
-		TElement & el = _skiplistConstructElement(me, height, val_temp);
-		_skiplistInsertElement(me, el, path, height);
-		return el.data_value;
-	}
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef SkiplistPath<TValue, TSpec> TPath;
+    typedef SkiplistElement<TValue, TSpec> TElement;
+    typedef typename Iterator<TSkiplist>::Type TIterator;
+    typedef typename Value<TSkiplist>::Type TValue2;
+
+    TPath path;
+    TIterator it = find(me, _key, path);
+    if (it && (key(it) == _key))
+    {
+        return value(it);
+    }
+    else
+    {// insert new value
+        unsigned char height = _skiplistCreateHeight(me, path);
+        TValue2 val_temp;
+        setKey(val_temp, _key);
+        TElement & el = _skiplistConstructElement(me, height, val_temp);
+        _skiplistInsertElement(me, el, path, height);
+        return el.data_value;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -718,41 +656,22 @@ value(Map<TValue, Skiplist<TSpec> > & me,
 /*!
  * @fn Map#cargo
  * @brief Returns a cargo given a key.
- * 
+ *
  * @signature TCargo find(map, key);
- * 
- * @param map A map.
- * @param key A key.
- * 
+ *
+ * @param[in,out] map A map.
+ * @param[in]     key A key.
+ *
  * @return TReturn The cargo of the first value in <tt>map</tt> of the given key, if there is any.  Otherwise, the
  *                 cargo of a new value that is inserted to <tt>map</tt>.
  */
 
-/**
-.Function.Map#cargo:
-..cat:Map
-..summary:Returns a cargo given a key. 
-..signature:Cargo find(map, key)
-..class:Class.Map
-..param.map:A map.
-...type:Class.Map
-..param.key:A key.
-...metafunction:Metafunction.Key
-..returns:The cargo of the first value in $map$ of the given key, if there is any.
-Otherwise, the cargo of a new value that is inserted to $map$.
-...metafunction:Metafunction.Cargo
-..see:Function.Map#value
-..see:Function.Map#find
-..see:Function.Map#insert
-..include:seqan/map.h
-*/
-
 template <typename TValue, typename TSpec, typename TKey2>
 inline typename Cargo< Map<TValue, Skiplist<TSpec> > >::Type &
 cargo(Map<TValue, Skiplist<TSpec> > & me,
-	  TKey2 const & _key)
+      TKey2 const & _key)
 {
-	return cargo(value(me, _key));
+    return cargo(value(me, _key));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -760,64 +679,38 @@ cargo(Map<TValue, Skiplist<TSpec> > & me,
 /*!
  * @fn Map#insert
  * @brief Insert new value into map.
- * 
+ *
  * @signature void insert(map, value);
  * @signature void insert(map, key, cargo);
- * 
- * @param cargo A cargo.
- * @param value A value that is added to <tt>map</tt>.
- * @param key A key.
- * @param map A map.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] map   A map.
+ * @param[in]     value A value that is added to <tt>map</tt>.
+ * @param[in]     key   A key.
+ * @param[in]     cargo A cargo.
+ *
  * If <tt>key</tt> and <tt>cargo</tt> are specified, a new value of that key and value is added.  If there is already a
  * value of that key in <tt>map</tt>, the value of this element is changed to <tt>cargo</tt>.
- * 
+ *
  * If <tt>value</tt> is specified, and there is already a value in map of that key, than the cargo of this value is
  * changed to cargo.cargo(value).
- * 
+ *
  * Use Map#add instead to insert multiple values of the same key.
  */
 
-/**
-.Function.Map#insert:
-..cat:Map
-..summary:Insert new value into map. 
-..signature:insert(map, value)
-..signature:insert(map, key, cargo)
-..class:Class.Map
-..param.map:A map.
-...type:Class.Map
-..param.value:A value that is added to $map$.
-...metafunction:Metafunction.Value
-..param.key:A key.
-...metafunction:Metafunction.Key
-..param.cargo:A cargo.
-...metafunction:Metafunction.Cargo
-..remarks:If $key$ and $cargo$ are specified, a new value of that key and value is added.
-If there is already a value of that key in $map$, the value of this element is changed to $cargo$.
-...text:If $value$ is specified, and there is already a value in map of that key, than
-the cargo of this value is changed to @Function.cargo.cargo(value)@.
-...text:Use @Function.Map#add@ instead to insert multiple values of the same key
-..see:Function.Map#add
-..include:seqan/map.h
-*/
-
 template <typename TValue, typename TSpec, typename TValue2>
 inline void
 insert(Map<TValue, Skiplist<TSpec> > & me,
-	   TValue2 const & _value)
+       TValue2 const & _value)
 {
-	value(me, key(_value)) = _value;
+    value(me, key(_value)) = _value;
 }
 template <typename TValue, typename TSpec, typename TKey2, typename TCargo2>
 inline void
 insert(Map<TValue, Skiplist<TSpec> > & me,
-	   TKey2 const & _key,
-	   TCargo2 const & _cargo)
+       TKey2 const & _key,
+       TCargo2 const & _cargo)
 {
-	cargo(me, _key) = _cargo;
+    cargo(me, _key) = _cargo;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -826,61 +719,40 @@ insert(Map<TValue, Skiplist<TSpec> > & me,
 /*!
  * @fn Map#add
  * @brief Insert another value into a multi map.
- * 
+ *
  * @signature void add(map, value);
  * @signature void add(map, key, cargo);
- * 
- * @param cargo A cargo.
- * @param value A value that is added to <tt>map</tt>.
- * @param key A key.
- * @param map A map. Types: Skiplist
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] map   A map. Types: Skiplist
+ * @param[in]     value A value that is added to <tt>map</tt>.
+ * @param[in]     cargo A cargo.
+ * @param[in]     key   A key.
+ *
  * If <tt>key</tt> and <tt>cargo</tt> are specified, a new value of that key and value is added.
  */
 
-/**
-.Function.Map#add:
-..cat:Map
-..summary:Insert another value into a multi map.
-..signature:add(map, value)
-..signature:add(map, key, cargo)
-..class:Class.Map
-..param.map:A map.
-...type:Spec.Skiplist
-..param.value:A value that is added to $map$.
-...metafunction:Metafunction.Value
-..param.key:A key.
-...metafunction:Metafunction.Key
-..param.cargo:A cargo.
-...metafunction:Metafunction.Cargo
-..remarks:If $key$ and $cargo$ are specified, a new value of that key and value is added.
-..include:seqan/map.h
-*/
-
 template <typename TValue, typename TSpec, typename TValue2>
 inline void
 add(Map<TValue, Skiplist<TSpec> > & me,
-	TValue2 const & _value)
+    TValue2 const & _value)
 {
-	typedef SkiplistElement<TValue, TSpec> TElement;
+    typedef SkiplistElement<TValue, TSpec> TElement;
 
-	unsigned char height = _skiplistCreateHeight(me);
-	TElement & el = _skiplistConstructElement(me, height, _value);
-	_skiplistInsertElement(me, el, height);
+    unsigned char height = _skiplistCreateHeight(me);
+    TElement & el = _skiplistConstructElement(me, height, _value);
+    _skiplistInsertElement(me, el, height);
 }
 template <typename TValue, typename TSpec, typename TKey2, typename TCargo2>
 inline void
 add(Map<TValue, Skiplist<TSpec> > & me,
-	TKey2 const & _key,
-	TCargo2 const & _cargo)
+    TKey2 const & _key,
+    TCargo2 const & _cargo)
 {
-	TValue temp_val;
-	setKey(temp_val, _key);
-	setCargo(temp_val, _cargo);
+    TValue temp_val;
+    setKey(temp_val, _key);
+    setCargo(temp_val, _cargo);
 
-	add(me, temp_val);
+    add(me, temp_val);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -889,20 +761,20 @@ add(Map<TValue, Skiplist<TSpec> > & me,
 template <typename TValue, typename TSpec>
 inline void
 _skiplistUnlinkElement(Map<TValue, Skiplist<TSpec> > & me,
-					   SkiplistElement<TValue, TSpec> & el)
+                       SkiplistElement<TValue, TSpec> & el)
 {
-	typedef SkiplistPath<TValue, TSpec> TPath;
-
-	TPath path;
-	_skiplistFind(me, el, path);
-
-	for (int i = me.data_height; i >= 0; --i)
-	{
-		if (path.data_elements[i]->data_next[i].data_element == & el)
-		{
-			path.data_elements[i]->data_next[i].data_element = el.data_next[i].data_element;
-		}
-	}
+    typedef SkiplistPath<TValue, TSpec> TPath;
+
+    TPath path;
+    _skiplistFind(me, el, path);
+
+    for (int i = me.data_height; i >= 0; --i)
+    {
+        if (path.data_elements[i]->data_next[i].data_element == & el)
+        {
+            path.data_elements[i]->data_next[i].data_element = el.data_next[i].data_element;
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -910,62 +782,40 @@ _skiplistUnlinkElement(Map<TValue, Skiplist<TSpec> > & me,
 /*!
  * @fn Map#erase
  * @brief Removes a value from a map.
- * 
+ *
  * @signature void erase(map, key);
  * @signature void erase(map, iterator);
- * 
- * @param map      A map. Types: Map
- * @param key      The key of a value in <tt>map</tt>.
- * @param iterator An iterator to a value in <tt>map</tt>.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in] map      A map. Types: Map
+ * @param[in] key      The key of a value in <tt>map</tt>.
+ * @param[in] iterator An iterator to a value in <tt>map</tt>.
+ *
  * Removes the first value in <tt>map</tt> of the given key, if there is any.
- * 
+ *
  * Use @link Map#eraseAll @endlink to remove all values of the given key in a multi map.
  */
 
-/**
-.Function.Map#erase:
-..cat:Map
-..summary:Removes a value from a map. 
-..signature:erase(map, key)
-..signature:erase(map, iterator)
-..class:Class.Map
-..param.map:A map.
-...type:Class.Map
-..param.key:The key of a value in $map$.
-...metafunction:Metafunction.Key
-..param.iterator:An iterator to a value in $map$.
-...metafunction:Metafunction.Iterator
-..remarks:Removes the first value in $map$ of the given key, if there is any.
-...text:Use @Function.Map#eraseAll@ to remove all values of the given key in a multi map.
-..see:Function.Map#add
-..see:Function.Map#insert
-..include:seqan/map.h
-*/
-
 template <typename TValue, typename TSpec, typename TMap2>
 inline void
 erase(Map<TValue, Skiplist<TSpec> > & me,
-	  Iter<TMap2, SkiplistIterator> const & it)
+      Iter<TMap2, SkiplistIterator> const & it)
 {
-	_skiplistUnlinkElement(me, * it.data_pointer);
-	--me.data_length;
+    _skiplistUnlinkElement(me, * it.data_pointer);
+    --me.data_length;
 }
 
 template <typename TValue, typename TSpec, typename TToRemove>
 inline void
 erase(Map<TValue, Skiplist<TSpec> > & me,
-	  TToRemove const & to_remove)
+      TToRemove const & to_remove)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TMap;
-	typedef typename Iterator<TMap>::Type TIterator;
-	TIterator it = find(me, to_remove);
-	if (it && (key(it) == key(to_remove)))
-	{
-		erase(me, it);
-	}
+    typedef Map<TValue, Skiplist<TSpec> > TMap;
+    typedef typename Iterator<TMap>::Type TIterator;
+    TIterator it = find(me, to_remove);
+    if (it && (key(it) == key(to_remove)))
+    {
+        erase(me, it);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -973,48 +823,29 @@ erase(Map<TValue, Skiplist<TSpec> > & me,
 /*!
  * @fn Map#eraseAll
  * @brief Removes a value from a map.
- * 
+ *
  * @signature void eraseAll(map, key);
- * 
- * @param map A map. Types: Skiplist
- * @param key The key of a value in <tt>map</tt>.
- * 
- * @section Remarks
- * 
+ *
+ * @param[in,out] map A map. Types: Skiplist
+ * @param[in]     key The key of a value in <tt>map</tt>.
+ *
  * Removes all values in <tt>map</tt> of the given key, if there is any.
  */
 
-/**
-.Function.Map#eraseAll:
-..cat:Map
-..summary:Removes a value from a map. 
-..signature:eraseAll(map, key)
-..class:Class.Map
-..param.map:A map.
-...type:Spec.Skiplist
-..param.key:The key of a value in $map$.
-...metafunction:Metafunction.Key
-..remarks:Removes all values in $map$ of the given key, if there is any.
-..see:Function.Map#add
-..see:Function.Map#insert
-..see:Function.Map#erase
-..include:seqan/map.h
-*/
-
 template <typename TValue, typename TSpec, typename TToRemove>
 inline void
 eraseAll(Map<TValue, Skiplist<TSpec> > & me,
-		 TToRemove const & to_remove)
+         TToRemove const & to_remove)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TMap;
-	typedef typename Iterator<TMap>::Type TIterator;
-	TIterator it = find(me, to_remove);
-	while (it && (key(it) == key(to_remove)))
-	{
-		TIterator it_old = it;
-		++it;
-		erase(me, it_old);
-	}
+    typedef Map<TValue, Skiplist<TSpec> > TMap;
+    typedef typename Iterator<TMap>::Type TIterator;
+    TIterator it = find(me, to_remove);
+    while (it && (key(it) == key(to_remove)))
+    {
+        TIterator it_old = it;
+        ++it;
+        erase(me, it_old);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1023,71 +854,64 @@ template <typename TValue, typename TSpec>
 inline void
 clear(Map<TValue, Skiplist<TSpec> > & me)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
 
-	me.data_mem_begin = me.data_mem_end = 0;
-	me.data_length = 0;
-	me.data_height = 0;
+    me.data_mem_begin = me.data_mem_end = 0;
+    me.data_length = 0;
+    me.data_height = 0;
 
-	for (unsigned char i = 0; i < TSkiplist::MAX_HEIGHT; ++i)
-	{
-		me.data_recycle[i] = 0;
-		valueConstruct(me.data_border.data_next + i, NonMinimalCtor()); 
-	}
+    for (unsigned char i = 0; i < TSkiplist::MAX_HEIGHT; ++i)
+    {
+        me.data_recycle[i] = 0;
+        valueConstruct(me.data_border.data_next + i, NonMinimalCtor());
+    }
 
-	clear(value(me.data_allocator));
+    clear(value(me.data_allocator));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.length.param.object.type:Class.Map
-///.Function.length.class:Class.Map
-
 template <typename TValue, typename TSpec>
 inline typename Size< Map<TValue, Skiplist<TSpec> > >::Type
 length(Map<TValue, Skiplist<TSpec> > const & me)
 {
-	return me.data_length;
+    return me.data_length;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.begin.class:Class.Map
-
 template <typename TValue, typename TSpec, typename TIteratorSpec>
 inline typename Iterator< Map<TValue, Skiplist<TSpec> >, TIteratorSpec>::Type
 begin(Map<TValue, Skiplist<TSpec> > & me,
-	  TIteratorSpec)
+      TIteratorSpec)
 {
-	typedef typename Iterator< Map<TValue, Skiplist<TSpec> >, TIteratorSpec>::Type TIterator;
-	return TIterator(me);
+    typedef typename Iterator< Map<TValue, Skiplist<TSpec> >, TIteratorSpec>::Type TIterator;
+    return TIterator(me);
 }
 template <typename TValue, typename TSpec>
 inline typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type
 begin(Map<TValue, Skiplist<TSpec> > & me)
 {
-	typedef typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type TIterator;
-	return TIterator(me);
+    typedef typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type TIterator;
+    return TIterator(me);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.end.class:Class.Map
-
 template <typename TValue, typename TSpec, typename TIteratorSpec>
 inline typename Iterator< Map<TValue, Skiplist<TSpec> >, TIteratorSpec>::Type
 end(Map<TValue, Skiplist<TSpec> > &,
-	TIteratorSpec)
+    TIteratorSpec)
 {
-	typedef typename Iterator< Map<TValue, Skiplist<TSpec> >, TIteratorSpec>::Type TIterator;
-	return TIterator();
+    typedef typename Iterator< Map<TValue, Skiplist<TSpec> >, TIteratorSpec>::Type TIterator;
+    return TIterator();
 }
 template <typename TValue, typename TSpec>
 inline typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type
 end(Map<TValue, Skiplist<TSpec> > &)
 {
-	typedef typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type TIterator;
-	return TIterator();
+    typedef typename Iterator< Map<TValue, Skiplist<TSpec> > >::Type TIterator;
+    return TIterator();
 }
 
 
@@ -1097,35 +921,35 @@ end(Map<TValue, Skiplist<TSpec> > &)
 template <typename TCargo>
 struct SkipListMapValue_
 {
-	template <typename TValue, typename TSpec, typename TKey2>
-	static inline TCargo &
-	mapValue_(Map<TValue, Skiplist<TSpec> > & me,
-		TKey2 const & _key)
-	{
-		return cargo(me, _key);
-	}
+    template <typename TValue, typename TSpec, typename TKey2>
+    static inline TCargo &
+    mapValue_(Map<TValue, Skiplist<TSpec> > & me,
+        TKey2 const & _key)
+    {
+        return cargo(me, _key);
+    }
 };
 
 template <>
 struct SkipListMapValue_<Nothing>
 {
-	template <typename TValue, typename TSpec, typename TKey2>
-	static inline bool
-	mapValue_(Map<TValue, Skiplist<TSpec> > & me,
-		TKey2 const & _key)
-	{
-		return hasKey(me, _key);
-	}
+    template <typename TValue, typename TSpec, typename TKey2>
+    static inline bool
+    mapValue_(Map<TValue, Skiplist<TSpec> > & me,
+        TKey2 const & _key)
+    {
+        return hasKey(me, _key);
+    }
 };
 
 template <typename TValue, typename TSpec, typename TKey2>
 inline typename MapValue< Map<TValue, Skiplist<TSpec> > >::Type
 mapValue(Map<TValue, Skiplist<TSpec> > & me,
-		 TKey2 const & _key)
+         TKey2 const & _key)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
-	typedef typename Cargo<TSkiplist>::Type TCargo;
-	return SkipListMapValue_<TCargo>::mapValue_(me, _key);
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef typename Cargo<TSkiplist>::Type TCargo;
+    return SkipListMapValue_<TCargo>::mapValue_(me, _key);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1133,39 +957,25 @@ mapValue(Map<TValue, Skiplist<TSpec> > & me,
 /*!
  * @fn Map#hasKey
  * @brief Determines whether a map contains a value given key.
- * 
+ *
  * @signature bool hasKey(map, key);
- * 
- * @param map A map. Types: Map
- * @param key A key.
- * 
+ *
+ * @param[in] map A map. Types: Map
+ * @param[in] key A key.
+ *
  * @return bool <tt>true</tt>, if there is a value in <tt>map</tt> of that key, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.Map#hasKey:
-..cat:Map
-..summary:Determines whether a map contains a value given key. 
-..signature:hasKey(map, key)
-..class:Class.Map
-..param.map:A map.
-...type:Class.Map
-..param.key:A key.
-...metafunction:Metafunction.Key
-..returns:$true$, if there is a value in $map$ of that key, $false$ otherwise.
-..include:seqan/map.h
-*/
-
 template <typename TValue, typename TSpec, typename TKey2>
 inline bool
 hasKey(Map<TValue, Skiplist<TSpec> > & me,
-	   TKey2 const & _key)
+       TKey2 const & _key)
 {
-	typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
-	typedef typename Iterator<TSkiplist>::Type TIterator;
-	TIterator it = find(me, _key);
+    typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+    typedef typename Iterator<TSkiplist>::Type TIterator;
+    TIterator it = find(me, _key);
 
-	return (it && (key(it) == _key));
+    return (it && (key(it) == _key));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1176,51 +986,51 @@ template <typename TSkiplist>
 class Iter< TSkiplist, SkiplistIterator>
 {
 public:
-	typedef typename SkiplistElement_<TSkiplist>::Type TElement;
-	typedef typename Value<TSkiplist>::Type TValue;
-
-	TElement * data_pointer;
-
-	Iter()
-		: data_pointer(0)
-	{
-	}
-	Iter(Iter const & other)
-		: data_pointer(other.data_pointer)
-	{
-	}
-	Iter(TElement * ptr)
-		: data_pointer(ptr)
-	{
-	}
-	Iter(TSkiplist const & sk)
-		: data_pointer(sk.data_border.data_next[0].data_element)
-	{
-	}
-	~Iter()
-	{
-	}
-
-	Iter const & 
-	operator = (Iter const & other)
-	{
-		data_pointer = other.data_pointer;
-		return *this;
-	}
+    typedef typename SkiplistElement_<TSkiplist>::Type TElement;
+    typedef typename Value<TSkiplist>::Type TValue;
+
+    TElement * data_pointer;
+
+    Iter()
+        : data_pointer(0)
+    {
+    }
+    Iter(Iter const & other)
+        : data_pointer(other.data_pointer)
+    {
+    }
+    Iter(TElement * ptr)
+        : data_pointer(ptr)
+    {
+    }
+    Iter(TSkiplist const & sk)
+        : data_pointer(sk.data_border.data_next[0].data_element)
+    {
+    }
+    ~Iter()
+    {
+    }
+
+    Iter const &
+    operator = (Iter const & other)
+    {
+        data_pointer = other.data_pointer;
+        return *this;
+    }
 
     // TODO(holtgrew): Why conversion to boolean?
-	operator bool () const
-	{
+    operator bool () const
+    {
         // Using != 0 instead of implicit/explicit task here to suppress
         // performance warning C4800 in Visual Studio.
-		return data_pointer != 0;
-	}
+        return data_pointer != 0;
+    }
 
-	TValue *
-	operator -> () const
-	{
-		return & data_pointer->data_value;
-	}
+    TValue *
+    operator -> () const
+    {
+        return & data_pointer->data_value;
+    }
 
 };
 
@@ -1230,7 +1040,7 @@ template <typename TSkiplist>
 inline bool
 atEnd(Iter<TSkiplist, SkiplistIterator> & it)
 {
-	return (!it.data_pointer);
+    return (!it.data_pointer);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1239,7 +1049,7 @@ template <typename TSkiplist>
 inline void
 goNext(Iter<TSkiplist, SkiplistIterator> & it)
 {
-	it.data_pointer = it.data_pointer->data_next[0].data_element;
+    it.data_pointer = it.data_pointer->data_next[0].data_element;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1248,13 +1058,13 @@ template <typename TSkiplist>
 inline typename Value<TSkiplist>::Type &
 value(Iter<TSkiplist, SkiplistIterator> & it)
 {
-	return it.data_pointer->data_value;
+    return it.data_pointer->data_value;
 }
 template <typename TSkiplist>
 inline typename Value<TSkiplist>::Type &
 value(Iter<TSkiplist, SkiplistIterator> const & it)
 {
-	return it.data_pointer->data_value;
+    return it.data_pointer->data_value;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1263,13 +1073,13 @@ template <typename TSkiplist>
 inline typename Key<TSkiplist>::Type const &
 key(Iter<TSkiplist, SkiplistIterator> & it)
 {
-	return key(it.data_pointer->data_value);
+    return key(it.data_pointer->data_value);
 }
 template <typename TSkiplist>
 inline typename Key<TSkiplist>::Type const &
 key(Iter<TSkiplist, SkiplistIterator> const & it)
 {
-	return key(it.data_pointer->data_value);
+    return key(it.data_pointer->data_value);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1278,13 +1088,13 @@ template <typename TSkiplist>
 inline typename Cargo<TSkiplist>::Type &
 cargo(Iter<TSkiplist, SkiplistIterator> & it)
 {
-	return cargo(it.data_pointer->data_value);
+    return cargo(it.data_pointer->data_value);
 }
 template <typename TSkiplist>
 inline typename Cargo<TSkiplist>::Type &
 cargo(Iter<TSkiplist, SkiplistIterator> const & it)
 {
-	return cargo(it.data_pointer->data_value);
+    return cargo(it.data_pointer->data_value);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1292,17 +1102,17 @@ cargo(Iter<TSkiplist, SkiplistIterator> const & it)
 template <typename TSkiplist>
 inline bool
 operator == (Iter<TSkiplist, SkiplistIterator> const & left,
-			 Iter<TSkiplist, SkiplistIterator> const & right)
+             Iter<TSkiplist, SkiplistIterator> const & right)
 {
-	return left.data_pointer == right.data_pointer;
+    return left.data_pointer == right.data_pointer;
 }
 
 template <typename TSkiplist>
 inline bool
 operator != (Iter<TSkiplist, SkiplistIterator> const & left,
-			 Iter<TSkiplist, SkiplistIterator> const & right)
+             Iter<TSkiplist, SkiplistIterator> const & right)
 {
-	return left.data_pointer != right.data_pointer;
+    return left.data_pointer != right.data_pointer;
 }
 
 ////////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/map/map_vector.h b/seqan/map/map_vector.h
index 56f45db..28d8fc7 100644
--- a/seqan/map/map_vector.h
+++ b/seqan/map/map_vector.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,39 +43,22 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Map
  * @headerfile <seqan/map.h>
  * @brief A fast map for small key types.
- * 
+ *
  * @signature template <typename TValue[, typename TSpec]>
- *            class Map;
- * 
+ *            class Map<TValue, VectorSet<TSpec> >;
+ *
  * @tparam TValue The type of value stored in the map.
  * @tparam TSpec  The specializing type.  <tt>TSpec</tt> is used as specialization for the String type that is
  *                used to store the values, defaults to <tt>Alloc&lt;&gt;</tt>.
- * 
- * @section Remarks
- * 
+ *
  * The memory needed is linear to the number different values the Key type of <tt>TValue</tt> can
  * get.  So do not use this map for large key types.
  */
 
-/**
-.Spec.VectorSet:
-..cat:Map
-..general:Class.Map
-..summary:A fast map for small key types.
-..signature:Map<TValue, VectorSet<TSpec> >
-..param.TValue:The type of value stored in the map.
-...metafunction:Metafunction.Value
-..param.TSpec:The specializing type.
-...default:@Spec.Alloc String.Alloc@
-...remarks:$TSpec$ is used as specialization for the @Class.String@ type that is used to store the values.
-..remarks:The memory needed is linear to the number different values the @Metafunction.Key.key type@ of $TValue$ can get.
-So do not use this map for large key types.
-..include:seqan/map.h
-*/
 //////////////////////////////////////////////////////////////////////////////
-// 
-//	VectorSet
-// 
+//
+//    VectorSet
+//
 //////////////////////////////////////////////////////////////////////////////
 
 
@@ -89,13 +72,13 @@ struct VectorSet;
 template <typename TCargo>
 struct VectorSetElement_
 {
-	bool data_valid;
-	TCargo data_cargo;
+    bool data_valid;
+    TCargo data_cargo;
 };
 template <>
 struct VectorSetElement_<Nothing>
 {
-	bool data_valid;
+    bool data_valid;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -103,15 +86,15 @@ struct VectorSetElement_<Nothing>
 template <typename T>
 struct VectorSetElements_
 {
-	typedef char * Type; //dummy implementation for VC++
+    typedef char * Type; //dummy implementation for VC++
 };
 template <typename TValue, typename TSpec>
 struct VectorSetElements_<Map<TValue, VectorSet<TSpec> > >
 {
-	typedef Map<TValue, VectorSet<TSpec> > TMap_;
-	typedef typename Cargo<TMap_>::Type TCargo_;
-	typedef VectorSetElement_<TCargo_> TElement_;
-	typedef String<TElement_, TSpec> Type;
+    typedef Map<TValue, VectorSet<TSpec> > TMap_;
+    typedef typename Cargo<TMap_>::Type TCargo_;
+    typedef VectorSetElement_<TCargo_> TElement_;
+    typedef String<TElement_, TSpec> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -121,31 +104,31 @@ template <typename TValue, typename TSpec>
 class Map<TValue, VectorSet<TSpec> >
 {
 public:
-	typedef typename Key<Map>::Type TKey;
-	typedef typename Size<Map>::Type TSize;
-	typedef typename VectorSetElements_<Map>::Type TElements;
-
-	TElements	data_elements;
-	TSize		data_length;
-
-	Map()
-	{
-		resize(data_elements, (TSize) ValueSize<TKey>::VALUE); 
-		clear(*this);
-	}
-
-	Map(TSize _vectorSize)
-	{
-		resize(data_elements, (TSize) _vectorSize);
-		clear(*this);
-	}
-	
-	template <typename TKey>
-	inline typename MapValue<Map>::Type
-	operator [] (TKey const & key)
-	{
-		return mapValue(*this, key);
-	}
+    typedef typename Key<Map>::Type TKey;
+    typedef typename Size<Map>::Type TSize;
+    typedef typename VectorSetElements_<Map>::Type TElements;
+
+    TElements    data_elements;
+    TSize        data_length;
+
+    Map()
+    {
+        resize(data_elements, (TSize) ValueSize<TKey>::VALUE);
+        clear(*this);
+    }
+
+    Map(TSize _vectorSize)
+    {
+        resize(data_elements, (TSize) _vectorSize);
+        clear(*this);
+    }
+
+    template <typename TKey>
+    inline typename MapValue<Map>::Type
+    operator [] (TKey const & key)
+    {
+        return mapValue(*this, key);
+    }
 
 };
 
@@ -154,39 +137,39 @@ class Map<TValue, VectorSet<TSpec> >
 // set meta-functions
 
 template <typename TValue, typename TSpec>
-struct Value< Map<TValue, VectorSet<TSpec> > > 
+struct Value< Map<TValue, VectorSet<TSpec> > >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 template <typename TValue, typename TSpec>
-struct Reference< Map<TValue, VectorSet<TSpec> > > 
+struct Reference< Map<TValue, VectorSet<TSpec> > >
 {
-	typedef Map<TValue, VectorSet<TSpec> > TMap_;
-	typedef typename Iterator<TMap_>::Type TIterator_;
-	typedef Proxy<IteratorProxy<TIterator_> > Type;
+    typedef Map<TValue, VectorSet<TSpec> > TMap_;
+    typedef typename Iterator<TMap_>::Type TIterator_;
+    typedef Proxy<IteratorProxy<TIterator_> > Type;
 };
 
 
 template <typename TValue, typename TSpec>
 struct Size< Map<TValue, VectorSet<TSpec> > >:
-	Size<typename VectorSetElements_< Map<TValue, VectorSet<TSpec> > >::Type> {};
+    Size<typename VectorSetElements_< Map<TValue, VectorSet<TSpec> > >::Type> {};
 
 template <typename TValue, typename TSpec>
 struct Key< Map<TValue, VectorSet<TSpec> > > :
-	Key<TValue> {};
+    Key<TValue> {};
 
 template <typename TValue, typename TSpec>
 struct Cargo< Map<TValue, VectorSet<TSpec> > > :
-	Cargo<TValue> {};
+    Cargo<TValue> {};
 
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TSpec>
-inline typename Size< Map<TValue, VectorSet<TSpec> > >::Type 
-length(Map<TValue, VectorSet<TSpec>  > const &set) 
+inline typename Size< Map<TValue, VectorSet<TSpec> > >::Type
+length(Map<TValue, VectorSet<TSpec>  > const &set)
 {
-	return set.data_length;
+    return set.data_length;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -195,75 +178,75 @@ length(Map<TValue, VectorSet<TSpec>  > const &set)
 struct VectorSetIterator;
 
 template <typename TMap>
-class Iter<TMap,  VectorSetIterator> 
+class Iter<TMap,  VectorSetIterator>
 {
 public:
-	typedef typename Size<TMap>::Type TSize;
-	typedef typename VectorSetElements_<TMap>::Type TElements;
-	typedef typename Iterator<TElements, Rooted>::Type TElementsIterator;
-	typedef typename Value<TElementsIterator>::Type TValue;
-
-	TElementsIterator data_iterator;
-
-	Iter() 
-	{	}
-	Iter(TElementsIterator it) 
-		: data_iterator(it)
-	{	
-		if (!atEnd(*this) && !(*data_iterator).data_valid) 
-		{
-			goNext(*this);
-		}
-	}
-	Iter(Iter const & other)
-		: data_iterator(other.data_iterator)
-	{	}
-	~Iter()
-	{	}
-
-	Iter const & operator = (Iter const & other)
-	{
-		data_iterator = other.data_iterator;
-		return *this;
-	}
-
-	operator bool()
-	{
-		return data_iterator != 0;
-	}
-
-	TValue *
-	operator -> () const
-	{
-		return & value(data_iterator);
-	}
+    typedef typename Size<TMap>::Type TSize;
+    typedef typename VectorSetElements_<TMap>::Type TElements;
+    typedef typename Iterator<TElements, Rooted>::Type TElementsIterator;
+    typedef typename Value<TElementsIterator>::Type TValue;
+
+    TElementsIterator data_iterator;
+
+    Iter()
+    {    }
+    Iter(TElementsIterator it)
+        : data_iterator(it)
+    {
+        if (!atEnd(*this) && !(*data_iterator).data_valid)
+        {
+            goNext(*this);
+        }
+    }
+    Iter(Iter const & other)
+        : data_iterator(other.data_iterator)
+    {    }
+    ~Iter()
+    {    }
+
+    Iter const & operator = (Iter const & other)
+    {
+        data_iterator = other.data_iterator;
+        return *this;
+    }
+
+    operator bool()
+    {
+        return data_iterator != 0;
+    }
+
+    TValue *
+    operator -> () const
+    {
+        return & value(data_iterator);
+    }
 
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TObject, typename TSpec, typename TIteratorSpec>
-struct Iterator< Map<TObject, VectorSet<TSpec> >, TIteratorSpec > 
+struct Iterator< Map<TObject, VectorSet<TSpec> >, TIteratorSpec >
 {
-	typedef Map<TObject, VectorSet<TSpec> > TMap_;
-	typedef Iter<TMap_, VectorSetIterator> Type;
+    typedef Map<TObject, VectorSet<TSpec> > TMap_;
+    typedef Iter<TMap_, VectorSetIterator> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TSpec>
-inline void 
-clear(Map<TValue, VectorSet<TSpec> > & me) 
-{
-	typedef Map<TValue, VectorSet<TSpec> > TMap;
-	typedef typename VectorSetElements_<TMap>::Type TElements;
-	typedef typename Iterator<TElements>::Type TIterator;
-	TIterator it_end = end(me.data_elements);
-	for (TIterator it = begin(me.data_elements); it != it_end; ++it)
-	{
-		(*it).data_valid = false;
-	}
-	me.data_length = 0;
+inline void
+clear(Map<TValue, VectorSet<TSpec> > & me)
+{
+    typedef Map<TValue, VectorSet<TSpec> > TMap;
+    typedef typename VectorSetElements_<TMap>::Type TElements;
+    typedef typename Iterator<TElements>::Type TIterator;
+    TIterator it_end = end(me.data_elements);
+    for (TIterator it = begin(me.data_elements); it != it_end; ++it)
+    {
+        (*it).data_valid = false;
+    }
+    me.data_length = 0;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -271,178 +254,178 @@ clear(Map<TValue, VectorSet<TSpec> > & me)
 template <typename TCargo>
 struct VectorSetInsert_
 {
-	template <typename TValue, typename TSpec, typename TElement>
-	static inline void 
-	insert_(Map<TValue, VectorSet<TSpec> > & set,
-		TElement const &element) 
-	{
-		if (!set.data_elements[ordValue(key(element))].data_valid) 
-		{
-			++set.data_length;
-			set.data_elements[ordValue(key(element))].data_valid = true;
-		}
-		set.data_elements[ordValue(key(element))].data_cargo = cargo(element);
-	}
+    template <typename TValue, typename TSpec, typename TElement>
+    static inline void
+    insert_(Map<TValue, VectorSet<TSpec> > & set,
+        TElement const &element)
+    {
+        if (!set.data_elements[ordValue(key(element))].data_valid)
+        {
+            ++set.data_length;
+            set.data_elements[ordValue(key(element))].data_valid = true;
+        }
+        set.data_elements[ordValue(key(element))].data_cargo = cargo(element);
+    }
 };
 template <>
 struct VectorSetInsert_<Nothing>
 {
-	template <typename TValue, typename TSpec, typename TElement>
-	static inline void 
-	insert_(Map<TValue, VectorSet<TSpec> > & set,
-		TElement const &element) 
-	{
-		if (!set.data_elements[ordValue(key(element))].data_valid) 
-		{
-			++set.data_length;
-			set.data_elements[ordValue(key(element))].data_valid = true;
-		}
-	}
+    template <typename TValue, typename TSpec, typename TElement>
+    static inline void
+    insert_(Map<TValue, VectorSet<TSpec> > & set,
+        TElement const &element)
+    {
+        if (!set.data_elements[ordValue(key(element))].data_valid)
+        {
+            ++set.data_length;
+            set.data_elements[ordValue(key(element))].data_valid = true;
+        }
+    }
 };
 
 template <typename TValue, typename TSpec, typename TElement>
-inline void 
+inline void
 insert(Map<TValue, VectorSet<TSpec> > & set,
-	   TElement const &element) 
+       TElement const &element)
 {
-	typedef Map<TValue, VectorSet<TSpec> > TMap;
-	typedef typename Cargo<TMap>::Type TCargo;
-	VectorSetInsert_<TCargo>::insert_(set, element);
+    typedef Map<TValue, VectorSet<TSpec> > TMap;
+    typedef typename Cargo<TMap>::Type TCargo;
+    VectorSetInsert_<TCargo>::insert_(set, element);
 }
 template <typename TValue, typename TSpec, typename TKey, typename TCargo>
-inline void 
+inline void
 insert(Map<TValue, VectorSet<TSpec> > &set,
-	   TKey const & _key,
-	   TCargo const & _cargo) 
-{
-	typedef Map<TValue, VectorSet<TSpec> > TMap;
-	typedef typename Value<TMap>::Type TValue2;
-	TValue2 new_val;
-	key(new_val) = _key;
-	cargo(new_val) = _cargo;
-	VectorSetInsert_<TCargo>::insert_(set, new_val);
+       TKey const & _key,
+       TCargo const & _cargo)
+{
+    typedef Map<TValue, VectorSet<TSpec> > TMap;
+    typedef typename Value<TMap>::Type TValue2;
+    TValue2 new_val;
+    key(new_val) = _key;
+    cargo(new_val) = _cargo;
+    VectorSetInsert_<TCargo>::insert_(set, new_val);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TValue, typename TSpec, typename T>
-inline void 
-erase(Map<TValue, VectorSet<TSpec> > &set, 
-	  T const & tokill)  //can be an element, a key, or an iterator
-{
-	if (set.data_elements[ordValue(key(tokill))].data_valid) 
-	{
-		--set.data_length;
-		set.data_elements[ordValue(key(tokill))].data_valid = false;
-	}
+inline void
+erase(Map<TValue, VectorSet<TSpec> > &set,
+      T const & tokill)  //can be an element, a key, or an iterator
+{
+    if (set.data_elements[ordValue(key(tokill))].data_valid)
+    {
+        --set.data_length;
+        set.data_elements[ordValue(key(tokill))].data_valid = false;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TValue, typename TSpec>
-inline bool 
-hasKey(Map<TValue, VectorSet<TSpec> > const &set, TKey const &key) 
+inline bool
+hasKey(Map<TValue, VectorSet<TSpec> > const &set, TKey const &key)
 {
-	return set.data_elements[ordValue(key)].data_valid;
+    return set.data_elements[ordValue(key)].data_valid;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TKey2, typename TSpec>
-inline typename Iterator< Map<TKey2, VectorSet<TSpec> > >::Type 
-find(Map<TKey2, VectorSet<TSpec> > & set, 
-	 TKey const &key) 
+inline typename Iterator< Map<TKey2, VectorSet<TSpec> > >::Type
+find(Map<TKey2, VectorSet<TSpec> > & set,
+     TKey const &key)
 {
-	typedef Map<TKey2, VectorSet<TSpec> > TMap;
-	typedef typename Iterator<TMap>::Type TIterator;
-	return TIterator(begin(set.data_elements) + ordValue(key));
+    typedef Map<TKey2, VectorSet<TSpec> > TMap;
+    typedef typename Iterator<TMap>::Type TIterator;
+    return TIterator(begin(set.data_elements) + ordValue(key));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TKey, typename TSpec, typename TKey2>
 inline typename Cargo< Map<TKey, VectorSet<TSpec> > >::Type &
-cargo(Map<TKey, VectorSet<TSpec> > & set, 
-	  TKey2 const & _key) 
-{
-	if (!hasKey(set, _key))
-	{
-		typedef Map<TKey, VectorSet<TSpec> > TMap;
-		typedef typename Value<TMap>::Type TValue;
-		TValue new_value;
-		key(new_value) = _key;
-		insert(set, new_value);
-	}
-	return set.data_elements[ordValue(_key)].data_cargo;
+cargo(Map<TKey, VectorSet<TSpec> > & set,
+      TKey2 const & _key)
+{
+    if (!hasKey(set, _key))
+    {
+        typedef Map<TKey, VectorSet<TSpec> > TMap;
+        typedef typename Value<TMap>::Type TValue;
+        TValue new_value;
+        key(new_value) = _key;
+        insert(set, new_value);
+    }
+    return set.data_elements[ordValue(_key)].data_cargo;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TElement, typename TSpec>
-inline typename Iterator< Map<TElement, VectorSet<TSpec> > >::Type 
-begin(Map<TElement, VectorSet<TSpec> > & set) 
+inline typename Iterator< Map<TElement, VectorSet<TSpec> > >::Type
+begin(Map<TElement, VectorSet<TSpec> > & set)
 {
-	typedef Map<TElement, VectorSet<TSpec> > TMap;
-	typedef typename Iterator<TMap>::Type TIterator;
-	return TIterator(begin(set.data_elements));
+    typedef Map<TElement, VectorSet<TSpec> > TMap;
+    typedef typename Iterator<TMap>::Type TIterator;
+    return TIterator(begin(set.data_elements));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TElement, typename TSpec>
-inline typename Iterator< Map<TElement, VectorSet<TSpec> > >::Type 
-end(Map<TElement, VectorSet<TSpec> > &set) 
+inline typename Iterator< Map<TElement, VectorSet<TSpec> > >::Type
+end(Map<TElement, VectorSet<TSpec> > &set)
 {
-	typedef Map<TElement, VectorSet<TSpec> > TMap;
-	typedef typename Iterator<TMap>::Type TIterator;
-	return TIterator(end(set.data_elements));
+    typedef Map<TElement, VectorSet<TSpec> > TMap;
+    typedef typename Iterator<TMap>::Type TIterator;
+    return TIterator(end(set.data_elements));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSet>
-inline bool 
-operator==(Iter<TSet, VectorSetIterator> const &a, 
-		   Iter<TSet, VectorSetIterator> const &b) 
+inline bool
+operator==(Iter<TSet, VectorSetIterator> const &a,
+           Iter<TSet, VectorSetIterator> const &b)
 {
-	return a.data_iterator == b.data_iterator;
+    return a.data_iterator == b.data_iterator;
 }
 template <typename TSet>
-inline bool 
-operator!=(Iter<TSet, VectorSetIterator> const &a, 
-		   Iter<TSet, VectorSetIterator> const &b) 
+inline bool
+operator!=(Iter<TSet, VectorSetIterator> const &a,
+           Iter<TSet, VectorSetIterator> const &b)
 {
-	return a.data_iterator != b.data_iterator;
+    return a.data_iterator != b.data_iterator;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSet>
-inline bool 
-atEnd(Iter<TSet, VectorSetIterator> & a) 
+inline bool
+atEnd(Iter<TSet, VectorSetIterator> & a)
 {
-	return atEnd(a.data_iterator);
+    return atEnd(a.data_iterator);
 }
 template <typename TSet>
-inline bool 
-atEnd(Iter<TSet, VectorSetIterator> const & a) 
+inline bool
+atEnd(Iter<TSet, VectorSetIterator> const & a)
 {
-	return atEnd(a.data_iterator);
+    return atEnd(a.data_iterator);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSet>
 inline typename Key<TSet>::Type
-key(Iter<TSet, VectorSetIterator> &it) 
+key(Iter<TSet, VectorSetIterator> &it)
 {
-	return position(it.data_iterator);
+    return position(it.data_iterator);
 }
 template <typename TSet>
 inline typename Key<TSet>::Type
-key(Iter<TSet, VectorSetIterator> const &it) 
+key(Iter<TSet, VectorSetIterator> const &it)
 {
-	return position(it.data_iterator);
+    return position(it.data_iterator);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -450,29 +433,29 @@ key(Iter<TSet, VectorSetIterator> const &it)
 template <typename TSet>
 inline typename Cargo<TSet>::Type &
 cargo(Iter<TSet, VectorSetIterator> &it) {
-	return (*it.data_iterator).data_cargo;
+    return (*it.data_iterator).data_cargo;
 }
 template <typename TSet>
 inline typename Cargo<TSet>::Type &
 cargo(Iter<TSet, VectorSetIterator> const &it) {
-	return (*it.data_iterator).data_cargo;
+    return (*it.data_iterator).data_cargo;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSet>
-inline typename Reference<TSet>::Type 
-value(Iter<TSet, VectorSetIterator> &it) 
+inline typename Reference<TSet>::Type
+value(Iter<TSet, VectorSetIterator> &it)
 {
-	typedef typename Reference<TSet>::Type TReference;
-	return TReference(it);
+    typedef typename Reference<TSet>::Type TReference;
+    return TReference(it);
 }
 template <typename TSet>
-inline typename Reference<TSet>::Type 
-value(Iter<TSet, VectorSetIterator> const &it) 
+inline typename Reference<TSet>::Type
+value(Iter<TSet, VectorSetIterator> const &it)
 {
-	typedef typename Reference<TSet>::Type TReference;
-	return TReference(it);
+    typedef typename Reference<TSet>::Type TReference;
+    return TReference(it);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -480,15 +463,15 @@ value(Iter<TSet, VectorSetIterator> const &it)
 
 template <typename TSet>
 inline void
-goNext(Iter<TSet, VectorSetIterator> & it) 
-{
-	++it.data_iterator;
-	while (!atEnd(it.data_iterator))
-	{
-		if ((*it.data_iterator).data_valid) 
-			break;
-		++it.data_iterator;
-	}
+goNext(Iter<TSet, VectorSetIterator> & it)
+{
+    ++it.data_iterator;
+    while (!atEnd(it.data_iterator))
+    {
+        if ((*it.data_iterator).data_valid)
+            break;
+        ++it.data_iterator;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -496,30 +479,30 @@ goNext(Iter<TSet, VectorSetIterator> & it)
 
 template <typename TSet>
 inline typename Key<TSet>::Type
-key(Proxy<IteratorProxy<Iter<TSet, VectorSetIterator> > > & pr) 
+key(Proxy<IteratorProxy<Iter<TSet, VectorSetIterator> > > & pr)
 {
-	return key(iter(pr));
+    return key(iter(pr));
 }
 template <typename TSet>
 inline typename Key<TSet>::Type
-key(Proxy<IteratorProxy<Iter<TSet, VectorSetIterator> > > const & pr) 
+key(Proxy<IteratorProxy<Iter<TSet, VectorSetIterator> > > const & pr)
 {
-	return key(iter(pr));
+    return key(iter(pr));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSet>
 inline typename Cargo<TSet>::Type &
-cargo(Proxy<IteratorProxy<Iter<TSet, VectorSetIterator> > >& pr) 
+cargo(Proxy<IteratorProxy<Iter<TSet, VectorSetIterator> > >& pr)
 {
-	return cargo(iter(pr));
+    return cargo(iter(pr));
 }
 template <typename TSet>
 inline typename Cargo<TSet>::Type &
-cargo(Proxy<IteratorProxy<Iter<TSet, VectorSetIterator> > > const & pr) 
+cargo(Proxy<IteratorProxy<Iter<TSet, VectorSetIterator> > > const & pr)
 {
-	return cargo(iter(pr));
+    return cargo(iter(pr));
 }
 
 
diff --git a/seqan/map/sumlist.h b/seqan/map/sumlist.h
index d323896..ae5bff7 100644
--- a/seqan/map/sumlist.h
+++ b/seqan/map/sumlist.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -52,18 +52,18 @@ class SumList;
 template <typename T>
 struct DIMENSION
 {
-	enum { VALUE = 1}; //dummy implementation to make VC++ happy
+    enum { VALUE = 1}; //dummy implementation to make VC++ happy
 };
 
 template <unsigned int DIM_, typename TValue, typename TSpec>
 struct DIMENSION< SumList<DIM_, TValue, TSpec> >
 {
-	enum { VALUE = DIM_};
+    enum { VALUE = DIM_};
 };
 template <unsigned int DIM_, typename TValue, typename TSpec>
 struct DIMENSION< SumList<DIM_, TValue, TSpec> const>
 {
-	enum { VALUE = DIM_};
+    enum { VALUE = DIM_};
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -71,17 +71,17 @@ struct DIMENSION< SumList<DIM_, TValue, TSpec> const>
 template <unsigned int DIM, typename TValue, typename TSpec>
 struct Value< SumList<DIM, TValue, TSpec> >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 template <unsigned int DIM, typename TValue, typename TSpec>
 struct Value< SumList<DIM, TValue, TSpec> const >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 
 
 //////////////////////////////////////////////////////////////////////////////
-// SumListValues: 
+// SumListValues:
 // Stores one DIM tupel of Values
 //////////////////////////////////////////////////////////////////////////////
 
@@ -89,44 +89,44 @@ struct Value< SumList<DIM, TValue, TSpec> const >
 template <unsigned int DIM, typename TValue>
 struct SumListValues
 {
-	TValue values[DIM];
-
-	SumListValues(MinimalCtor)
-	{}
-	SumListValues()
-	{
-		clear(*this);
-	}
-	SumListValues(SumListValues const & other)
-	{
-		*this = other;
-	}
-	SumListValues(TValue const * arr)
-	{
-		*this = arr;
-	}
-	~SumListValues()
-	{
-	}
-	SumListValues const & operator = (SumListValues const & other)
-	{
-		arrayCopy(other.values, other.values + DIM, values);
-		return *this;
-	}
-	SumListValues const & operator = (TValue const * arr)
-	{
-		arrayCopy(arr, arr + DIM, values);
-		return *this;
-	}
-
-	TValue & operator [] (unsigned int pos)
-	{
-		return values[pos];
-	}
-	TValue const & operator [] (unsigned int pos) const
-	{
-		return values[pos];
-	}
+    TValue values[DIM];
+
+    SumListValues(MinimalCtor)
+    {}
+    SumListValues()
+    {
+        clear(*this);
+    }
+    SumListValues(SumListValues const & other)
+    {
+        *this = other;
+    }
+    SumListValues(TValue const * arr)
+    {
+        *this = arr;
+    }
+    ~SumListValues()
+    {
+    }
+    SumListValues const & operator = (SumListValues const & other)
+    {
+        arrayCopy(other.values, other.values + DIM, values);
+        return *this;
+    }
+    SumListValues const & operator = (TValue const * arr)
+    {
+        arrayCopy(arr, arr + DIM, values);
+        return *this;
+    }
+
+    TValue & operator [] (unsigned int pos)
+    {
+        return values[pos];
+    }
+    TValue const & operator [] (unsigned int pos) const
+    {
+        return values[pos];
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -137,7 +137,7 @@ struct Values;
 template <unsigned int DIM, typename TValue, typename TSpec>
 struct Values< SumList<DIM, TValue, TSpec> >
 {
-	typedef SumListValues<DIM, TValue> Type;
+    typedef SumListValues<DIM, TValue> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -145,13 +145,13 @@ struct Values< SumList<DIM, TValue, TSpec> >
 template <unsigned int DIM, typename TValue>
 inline SumListValues<DIM, TValue> const &
 operator += (SumListValues<DIM, TValue> & left,
-			 SumListValues<DIM, TValue> const & right)
+             SumListValues<DIM, TValue> const & right)
 {
-	for (unsigned int i = 0; i < DIM; ++i)
-	{
-		left.values[i] += right.values[i];
-	}
-	return left;
+    for (unsigned int i = 0; i < DIM; ++i)
+    {
+        left.values[i] += right.values[i];
+    }
+    return left;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -159,13 +159,13 @@ operator += (SumListValues<DIM, TValue> & left,
 template <unsigned int DIM, typename TValue>
 inline SumListValues<DIM, TValue> const &
 operator -= (SumListValues<DIM, TValue> & left,
-			 SumListValues<DIM, TValue> const & right)
+             SumListValues<DIM, TValue> const & right)
 {
-	for (unsigned int i = 0; i < DIM; ++i)
-	{
-		left.values[i] -= right.values[i];
-	}
-	return left;
+    for (unsigned int i = 0; i < DIM; ++i)
+    {
+        left.values[i] -= right.values[i];
+    }
+    return left;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -173,24 +173,24 @@ operator -= (SumListValues<DIM, TValue> & left,
 template <unsigned int DIM, typename TValue>
 inline bool
 operator == (SumListValues<DIM, TValue> const & left,
-			 SumListValues<DIM, TValue> const & right)
+             SumListValues<DIM, TValue> const & right)
 {
-	for (unsigned int i = 0; i < DIM; ++i)
-	{
-		if (left.values[i] != right.values[i]) return false;
-	}
-	return true;
+    for (unsigned int i = 0; i < DIM; ++i)
+    {
+        if (left.values[i] != right.values[i]) return false;
+    }
+    return true;
 }
 template <unsigned int DIM, typename TValue>
 inline bool
 operator != (SumListValues<DIM, TValue> const & left,
-			 SumListValues<DIM, TValue> const & right)
+             SumListValues<DIM, TValue> const & right)
 {
-	for (unsigned int i = 0; i < DIM; ++i)
-	{
-		if (left.values[i] != right.values[i]) return true;
-	}
-	return false;
+    for (unsigned int i = 0; i < DIM; ++i)
+    {
+        if (left.values[i] != right.values[i]) return true;
+    }
+    return false;
 }
 //////////////////////////////////////////////////////////////////////////////
 
@@ -198,7 +198,7 @@ template <unsigned int DIM, typename TValue>
 inline void
 clear(SumListValues<DIM, TValue> & me)
 {
-	arrayFill(me.values, me.values + DIM, 0);
+    arrayFill(me.values, me.values + DIM, 0);
 }
 
 
diff --git a/seqan/map/sumlist_mini.h b/seqan/map/sumlist_mini.h
index 356fb92..629463b 100644
--- a/seqan/map/sumlist_mini.h
+++ b/seqan/map/sumlist_mini.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,111 +44,111 @@ namespace SEQAN_NAMESPACE_MAIN
 template <typename TValue>
 struct MiniListEntry_
 {
-	enum
-	{
-		LIMIT_0 = 1 << 6,
-		LIMIT_1 = 1 << 14,
-		LIMIT_2 = 1 << 30
-	};
-
-	static const unsigned char SIZES [4]; 
-
-	union _union
-	{
-		struct struct_0
-		{
-			unsigned char select: 2;
-			unsigned char value_0: 6;
-		} _0;
-		struct struct_1
-		{
-			unsigned short select_1: 2;
-			unsigned short value_1: 14;
-		} _1;
-		struct struct_2
-		{
-			unsigned int select_2: 2;
-			unsigned int value_2: 30;
-		} _2;
-		unsigned char value_3[sizeof(TValue)+1];
-	} data;
-
-	MiniListEntry_() {}
-	MiniListEntry_(TValue val) { this->assignValue(val); }
-	~MiniListEntry_() {}
-
-	static inline unsigned int
-	sizeNeeded(TValue val)
-	{
-		if (val < LIMIT_1)
-		{
-			if (val < LIMIT_0)
-			{
-				return SIZES[0];
-			}
-			else
-			{
-				return SIZES[1];
-			}
-		}
-		else
-		{
-			if (val < LIMIT_2)
-			{
-				return SIZES[2];
-			}
-			else
-			{
-				return SIZES[3];
-			}
-		}
-	}
-
-	inline TValue getValue() const
-	{
-		switch(data._0.select)
-		{
-		case 0: return data._0.value_0;
-		case 1: return data._1.value_1;
-		case 2: return data._2.value_2;
-		default: return * reinterpret_cast<TValue const *>(data.value_3 + 1);
-		}
-	}
-
-	inline int size() const
-	{
-		return SIZES[data._0.select];
-	}
-
-	inline void assignValue(TValue val)
-	{
-		if (val < LIMIT_1)
-		{
-			if (val < LIMIT_0)
-			{
-				data._0.select = 0;
-				data._0.value_0 = val;
-			}
-			else
-			{
-				data._0.select = 1;
-				data._1.value_1 = val;
-			}
-		}
-		else
-		{
-			if (val < LIMIT_2)
-			{
-				data._0.select = 2;
-				data._2.value_2 = val;
-			}
-			else
-			{
-				data._0.select = 3;
-				*reinterpret_cast<TValue *>(data.value_3 + 1) = val;
-			}
-		}
-	}
+    enum
+    {
+        LIMIT_0 = 1 << 6,
+        LIMIT_1 = 1 << 14,
+        LIMIT_2 = 1 << 30
+    };
+
+    static const unsigned char SIZES [4];
+
+    union _union
+    {
+        struct struct_0
+        {
+            unsigned char select: 2;
+            unsigned char value_0: 6;
+        } _0;
+        struct struct_1
+        {
+            unsigned short select_1: 2;
+            unsigned short value_1: 14;
+        } _1;
+        struct struct_2
+        {
+            unsigned int select_2: 2;
+            unsigned int value_2: 30;
+        } _2;
+        unsigned char value_3[sizeof(TValue)+1];
+    } data;
+
+    MiniListEntry_() {}
+    MiniListEntry_(TValue val) { this->assignValue(val); }
+    ~MiniListEntry_() {}
+
+    static inline unsigned int
+    sizeNeeded(TValue val)
+    {
+        if (val < LIMIT_1)
+        {
+            if (val < LIMIT_0)
+            {
+                return SIZES[0];
+            }
+            else
+            {
+                return SIZES[1];
+            }
+        }
+        else
+        {
+            if (val < LIMIT_2)
+            {
+                return SIZES[2];
+            }
+            else
+            {
+                return SIZES[3];
+            }
+        }
+    }
+
+    inline TValue getValue() const
+    {
+        switch(data._0.select)
+        {
+        case 0: return data._0.value_0;
+        case 1: return data._1.value_1;
+        case 2: return data._2.value_2;
+        default: return * reinterpret_cast<TValue const *>(data.value_3 + 1);
+        }
+    }
+
+    inline int size() const
+    {
+        return SIZES[data._0.select];
+    }
+
+    inline void assignValue(TValue val)
+    {
+        if (val < LIMIT_1)
+        {
+            if (val < LIMIT_0)
+            {
+                data._0.select = 0;
+                data._0.value_0 = val;
+            }
+            else
+            {
+                data._0.select = 1;
+                data._1.value_1 = val;
+            }
+        }
+        else
+        {
+            if (val < LIMIT_2)
+            {
+                data._0.select = 2;
+                data._2.value_2 = val;
+            }
+            else
+            {
+                data._0.select = 3;
+                *reinterpret_cast<TValue *>(data.value_3 + 1) = val;
+            }
+        }
+    }
 };
 
 //____________________________________________________________________________
@@ -168,37 +168,37 @@ template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec
 class SumList<DIM, TValue, MiniSumList<SIZE, TSpec> >
 {
 public:
-	typedef typename Size<SumList>::Type TSize;
-	typedef SumListValues<DIM, TValue> TValues;
-
-	unsigned char data_ [SIZE];
-	TSize data_length;  //number of elements in list
-	TSize data_size;  //number of bytes used in data_
-	TValues data_sum; //sum of all list numbers
-
-	SumList()
-		: data_length(0)
-		, data_size(0)
-	{
-	}
-
-	SumList(SumList const & other)
-		: data_length(other.data_length)
-		, data_size(other.data_size)
-		, data_sum(other.data_sum)
-	{
-		arrayCopyForward(other.data_, other.data_ + SIZE, data_);
-	}
-
-	~SumList() 
-	{}
-
-	SumList const &
-	operator = (SumList const & other)
-	{
-		assign(*this, other);
-		return *this;
-	}
+    typedef typename Size<SumList>::Type TSize;
+    typedef SumListValues<DIM, TValue> TValues;
+
+    unsigned char data_ [SIZE];
+    TSize data_length;  //number of elements in list
+    TSize data_size;  //number of bytes used in data_
+    TValues data_sum; //sum of all list numbers
+
+    SumList()
+        : data_length(0)
+        , data_size(0)
+    {
+    }
+
+    SumList(SumList const & other)
+        : data_length(other.data_length)
+        , data_size(other.data_size)
+        , data_sum(other.data_sum)
+    {
+        arrayCopyForward(other.data_, other.data_ + SIZE, data_);
+    }
+
+    ~SumList()
+    {}
+
+    SumList const &
+    operator = (SumList const & other)
+    {
+        assign(*this, other);
+        return *this;
+    }
 
 
 //____________________________________________________________________________
@@ -210,7 +210,7 @@ class SumList<DIM, TValue, MiniSumList<SIZE, TSpec> >
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec>
 struct Size< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > >
 {
-	typedef unsigned short Type;
+    typedef unsigned short Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -218,7 +218,7 @@ struct Size< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > >
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec>
 struct Position< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > >
 {
-	typedef unsigned short Type;
+    typedef unsigned short Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -226,12 +226,12 @@ struct Position< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > >
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec>
 inline void
 assign(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & target,
-	   SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const & source)
+       SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const & source)
 {
-	arrayCopyForward(source.data_, source.data_ + source.data_size, target.data_);
-	target.data_length = source.data_length;
-	target.data_size = source.data_size;
-	target.data_sum = source.data_sum;
+    arrayCopyForward(source.data_, source.data_ + source.data_size, target.data_);
+    target.data_length = source.data_length;
+    target.data_size = source.data_size;
+    target.data_sum = source.data_sum;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -240,7 +240,7 @@ template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec
 inline typename Size< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > >::Type
 length(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me)
 {
-	return me.data_length;
+    return me.data_length;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -248,9 +248,9 @@ length(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me)
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec>
 inline typename Value< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > >::Type &
 getSum(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
-	   unsigned int dim)
+       unsigned int dim)
 {
-	return me.data_sum[dim];
+    return me.data_sum[dim];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -259,9 +259,9 @@ template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec
 inline void
 clear(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me)
 {
-	me.data_length = 0;
-	me.data_size = 0;
-	clear(me.data_sum);
+    me.data_length = 0;
+    me.data_size = 0;
+    clear(me.data_sum);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -270,17 +270,17 @@ template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec
 inline typename Iterator< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > >::Type
 begin(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me)
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TMe;
-	typedef typename Iterator<TMe>::Type TIterator;
-	return TIterator(me);
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TMe;
+    typedef typename Iterator<TMe>::Type TIterator;
+    return TIterator(me);
 }
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec>
 inline typename Iterator< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const>::Type
 begin(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const & me)
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const TMe;
-	typedef typename Iterator<TMe>::Type TIterator;
-	return TIterator(me);
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const TMe;
+    typedef typename Iterator<TMe>::Type TIterator;
+    return TIterator(me);
 }
 //////////////////////////////////////////////////////////////////////////////
 
@@ -288,43 +288,43 @@ template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec
 inline typename Iterator< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > >::Type
 end(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me)
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TMe;
-	typedef typename Iterator<TMe>::Type TIterator;
-	return TIterator(me, GoEnd());
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TMe;
+    typedef typename Iterator<TMe>::Type TIterator;
+    return TIterator(me, GoEnd());
 }
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec>
 inline typename Iterator< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const>::Type
 end(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const& me)
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const TMe;
-	typedef typename Iterator<TMe>::Type TIterator;
-	return TIterator(me, GoEnd());
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const TMe;
+    typedef typename Iterator<TMe>::Type TIterator;
+    return TIterator(me, GoEnd());
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 //changes the value at ptr (which is at the dim-th tuple position) to new_value
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec, typename TValue2>
-inline bool 
+inline bool
 _miniSumListAssignValue(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
-						 unsigned char * ptr,
-						 int dim,
-						 TValue2 new_value)
+                         unsigned char * ptr,
+                         int dim,
+                         TValue2 new_value)
 {
-	typedef MiniListEntry_<TValue> TEntry;
+    typedef MiniListEntry_<TValue> TEntry;
 
-	TEntry new_entr(new_value);
-	TEntry & old_entr = * reinterpret_cast<TEntry *>(ptr);
+    TEntry new_entr(new_value);
+    TEntry & old_entr = * reinterpret_cast<TEntry *>(ptr);
 
-	if (new_entr.size() != old_entr.size())
-	{
-		int new_size = me.data_size + new_entr.size() - old_entr.size();
-		if (new_size > SIZE) return false; //not enough space
-		arrayCopy(ptr + old_entr.size(), me.data_ + me.data_size, ptr + new_entr.size());
-	}
-	me.data_sum[dim] += (new_value - old_entr.getValue());
-	old_entr.assignValue(new_value);
-	return true;
+    if (new_entr.size() != old_entr.size())
+    {
+        int new_size = me.data_size + new_entr.size() - old_entr.size();
+        if (new_size > SIZE) return false; //not enough space
+        arrayCopy(ptr + old_entr.size(), me.data_ + me.data_size, ptr + new_entr.size());
+    }
+    me.data_sum[dim] += (new_value - old_entr.getValue());
+    old_entr.assignValue(new_value);
+    return true;
 }
 
 
@@ -335,12 +335,12 @@ template <unsigned int DIM, typename TValue>
 inline TValue
 _miniSumListSizeOfValues(SumListValues<DIM, TValue> const & vals)
 {
-	unsigned int sum = 0;
-	for (unsigned int i = 0; i < DIM; ++i)
-	{
-		sum += MiniListEntry_<TValue>::sizeNeeded(vals[i]);
-	}
-	return sum;
+    unsigned int sum = 0;
+    for (unsigned int i = 0; i < DIM; ++i)
+    {
+        sum += MiniListEntry_<TValue>::sizeNeeded(vals[i]);
+    }
+    return sum;
 }
 
 
@@ -348,78 +348,78 @@ _miniSumListSizeOfValues(SumListValues<DIM, TValue> const & vals)
 //inserts DIM-tupel at byte_position
 //returns false on capacity owerflow, true otherwise
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec, typename TPosition, typename TValue2>
-inline bool 
+inline bool
 _miniSumListInsertValues(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
-						  TPosition byte_pos,
-						  TValue2 const & new_values,
-						  /*OUT*/ unsigned int & new_values_size)
+                          TPosition byte_pos,
+                          TValue2 const & new_values,
+                          /*OUT*/ unsigned int & new_values_size)
 {
-	typedef MiniListEntry_<TValue> TEntry;
+    typedef MiniListEntry_<TValue> TEntry;
+
+    new_values_size = _miniSumListSizeOfValues<DIM>(new_values);
+    unsigned int new_size = me.data_size + new_values_size;
+    if (new_size > SIZE) return false; //not enough space
 
-	new_values_size = _miniSumListSizeOfValues<DIM>(new_values);
-	unsigned int new_size = me.data_size + new_values_size;
-	if (new_size > SIZE) return false; //not enough space
+    if (byte_pos < me.data_size)
+    { //make room
+        arrayCopyBackward(me.data_ + byte_pos, me.data_ + me.data_size, me.data_ + byte_pos + new_values_size);
+    }
 
-	if (byte_pos < me.data_size)
-	{ //make room
-		arrayCopyBackward(me.data_ + byte_pos, me.data_ + me.data_size, me.data_ + byte_pos + new_values_size);
-	}
+    unsigned char * ptr = me.data_ + byte_pos;
+    for (unsigned int i = 0; i < DIM; ++i)
+    {
+        TEntry & entr = * reinterpret_cast<TEntry *>(ptr);
+        entr.assignValue(new_values[i]);
+        ptr += entr.size();
+    }
 
-	unsigned char * ptr = me.data_ + byte_pos;
-	for (unsigned int i = 0; i < DIM; ++i)
-	{
-		TEntry & entr = * reinterpret_cast<TEntry *>(ptr);
-		entr.assignValue(new_values[i]);
-		ptr += entr.size();
-	}
-	
-	me.data_size = new_size;
-	me.data_sum += new_values;
-	++me.data_length;
-	return true;
+    me.data_size = new_size;
+    me.data_sum += new_values;
+    ++me.data_length;
+    return true;
 }
 
 
 template <typename TSumList, typename TValues>
-inline bool 
+inline bool
 _insertValues(TSumList & me,
-			  Iter<TSumList, MiniSumListValueIterator_> it,
-			  TValues const & new_values,
-			  /*OUT*/ unsigned int & new_values_size)
+              Iter<TSumList, MiniSumListValueIterator_> it,
+              TValues const & new_values,
+              /*OUT*/ unsigned int & new_values_size)
 {
-	return _miniSumListInsertValues(me, it.data_ptr - me.data_, new_values, new_values_size);
+    return _miniSumListInsertValues(me, it.data_ptr - me.data_, new_values, new_values_size);
 }
 template <typename TSumList, typename TValue>
-inline bool 
+inline bool
 _insertValues(TSumList & me,
-			  Iter<TSumList, MiniSumListValueIterator_> it,
-			  TValue const * new_values,
-			  /*OUT*/ unsigned int & new_values_size)
+              Iter<TSumList, MiniSumListValueIterator_> it,
+              TValue const * new_values,
+              /*OUT*/ unsigned int & new_values_size)
 {
-	SumListValues<DIMENSION<TSumList>::VALUE, typename Value<TSumList>::Type > vals(new_values);
-	return _miniSumListInsertValues(me, it.data_ptr - me.data_, vals, new_values_size);
+    SumListValues<DIMENSION<TSumList>::VALUE, typename Value<TSumList>::Type > vals(new_values);
+    return _miniSumListInsertValues(me, it.data_ptr - me.data_, vals, new_values_size);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 //appends DIM-tupel
 //returns false on capacity owerflow, true otherwise
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec, typename TValues>
-inline bool 
+inline bool
 appendValues(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
-			 TValues const & new_values)
+             TValues const & new_values)
 {
-	unsigned int dummy;
-	return _miniSumListInsertValues(me, me.data_size, new_values, dummy);
+    unsigned int dummy;
+    return _miniSumListInsertValues(me, me.data_size, new_values, dummy);
 }
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec, typename TValue2>
-inline bool 
+inline bool
 appendValues(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
-			 TValue2 const * new_values)
+             TValue2 const * new_values)
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TSumList;
-	SumListValues<DIMENSION<TSumList>::VALUE, typename Value<TSumList>::Type > vals(new_values);
-	unsigned int dummy;
-	return _miniSumListInsertValues(me, me.data_size, vals, dummy);
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TSumList;
+    SumListValues<DIMENSION<TSumList>::VALUE, typename Value<TSumList>::Type > vals(new_values);
+    unsigned int dummy;
+    return _miniSumListInsertValues(me, me.data_size, vals, dummy);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -428,46 +428,46 @@ appendValues(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec>
 inline void
 splitSumList(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
-			 SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & right)
+             SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & right)
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TSumList;
-	typedef Iter<TSumList, MiniSumListValueIterator_> TIterator;
-	typedef typename Size<TSumList>::Type TSize;
-	typedef SumListValues<DIM, TValue> TValues;
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TSumList;
+    typedef Iter<TSumList, MiniSumListValueIterator_> TIterator;
+    typedef typename Size<TSumList>::Type TSize;
+    typedef SumListValues<DIM, TValue> TValues;
 
-	clear(right);
+    clear(right);
 
-	if (me.data_size <= SIZE/2) return; //nothing to split
+    if (me.data_size <= SIZE/2) return; //nothing to split
 
-	TIterator it(me);
-	if (atEnd(it, me)) return; //nothing to split
+    TIterator it(me);
+    if (atEnd(it, me)) return; //nothing to split
 
-	TValues sum;
+    TValues sum;
 
-	TSize me_len = 0;
-	while (true)
-	{
-		if ((it.data_ptr - me.data_) >= SIZE/2) break;
+    TSize me_len = 0;
+    while (true)
+    {
+        if ((it.data_ptr - me.data_) >= SIZE/2) break;
 
-		TValues vals;
-		scanValues(it, vals);
-		sum += vals;
-		++me_len;
-	}
+        TValues vals;
+        scanValues(it, vals);
+        sum += vals;
+        ++me_len;
+    }
 
-	if (atEnd(it, me)) return; //nothing to split
+    if (atEnd(it, me)) return; //nothing to split
 
-	//split
+    //split
 
-	arrayCopyForward(it.data_ptr, me.data_ + me.data_size, right.data_);
-	right.data_length = me.data_length - me_len;
-	right.data_size = me.data_size - (it.data_ptr - me.data_);
-	right.data_sum = me.data_sum;
-	right.data_sum -= sum;
+    arrayCopyForward(it.data_ptr, me.data_ + me.data_size, right.data_);
+    right.data_length = me.data_length - me_len;
+    right.data_size = me.data_size - (it.data_ptr - me.data_);
+    right.data_sum = me.data_sum;
+    right.data_sum -= sum;
 
-	me.data_length = me_len;
-	me.data_size = it.data_ptr - me.data_;
-	me.data_sum = sum;
+    me.data_length = me_len;
+    me.data_size = it.data_ptr - me.data_;
+    me.data_sum = sum;
 }
 
 
@@ -476,27 +476,27 @@ splitSumList(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
 //template <typename TSumList, typename TValue2, typename TValues>
 //inline Iter<TSumList, MiniSumListValueIterator_>
 //_miniSumListSearchSumList(TSumList & me,
-//						   TValue2 val,
-//						   int dim,
-//						   /*OUT*/ TValues const & sums)
+//                           TValue2 val,
+//                           int dim,
+//                           /*OUT*/ TValues const & sums)
 //{
-//	typedef Iter<TSumList, MiniSumListValueIterator_> TIterator;
+//    typedef Iter<TSumList, MiniSumListValueIterator_> TIterator;
 //
-//	clear(sums);
-//	TIterator it(me);
+//    clear(sums);
+//    TIterator it(me);
 //
-//	while (true)
-//	{
-//		if (atEnd(it, me)) return it;
+//    while (true)
+//    {
+//        if (atEnd(it, me)) return it;
 //
-//		TIterator it_next = it;
-//		TValues vals;
-//		scanValues(it_next, vals);
+//        TIterator it_next = it;
+//        TValues vals;
+//        scanValues(it_next, vals);
 //
-//		if (sums[dim] + vals[dim] >= val) return it;
+//        if (sums[dim] + vals[dim] >= val) return it;
 //
-//		it = it_next;
-//	}
+//        it = it_next;
+//    }
 //}
 //
 
@@ -511,37 +511,37 @@ splitSumList(SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & me,
 //class Iter<SumList<DIM, TValue, MiniSumList<SIZE, TSpec> >, MiniSumListIteratorRooted>
 //{
 //public:
-//	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TContainer;
-//	typedef typename Size<TContainer>::Type TContainerSize;
-//	typedef typename Position<TContainer>::Type TContainerPosition;
+//    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TContainer;
+//    typedef typename Size<TContainer>::Type TContainerSize;
+//    typedef typename Position<TContainer>::Type TContainerPosition;
 //
-//	TContainer & data_container;
-//	TContainerSize data_bytepos;  //position of entry in container.data_
-//	TContainerPosition data_position;
-//	TValue data_sum[DIM];
+//    TContainer & data_container;
+//    TContainerSize data_bytepos;  //position of entry in container.data_
+//    TContainerPosition data_position;
+//    TValue data_sum[DIM];
 //
-//	Iter(TContainer & cont, TContainerSize bytepos = 0, TContainerPosition pos = 0)
-//		: data_container(cont)
-//		, data_bytepos(bytepos)
-//		, data_position(pos)
-//	{
-//	}
-//	Iter(Iter const & other)
-//		: data_container(other.data_container)
-//		, data_bytepos(other.bytepos)
-//		, data_position(other.data_position)
-//	{
-//	}
-//	~Iter()
-//	{
-//	}
-//	inline Iter const & 
-//	operator = (Iter const & other)
-//	{
-//		data_container = other.data_container;
-//		data_bytepos = other.bytepos;
-//		data_position = other.data_position;
-//	}
+//    Iter(TContainer & cont, TContainerSize bytepos = 0, TContainerPosition pos = 0)
+//        : data_container(cont)
+//        , data_bytepos(bytepos)
+//        , data_position(pos)
+//    {
+//    }
+//    Iter(Iter const & other)
+//        : data_container(other.data_container)
+//        , data_bytepos(other.bytepos)
+//        , data_position(other.data_position)
+//    {
+//    }
+//    ~Iter()
+//    {
+//    }
+//    inline Iter const &
+//    operator = (Iter const & other)
+//    {
+//        data_container = other.data_container;
+//        data_bytepos = other.bytepos;
+//        data_position = other.data_position;
+//    }
 //};
 
 //////////////////////////////////////////////////////////////////////////////
@@ -552,40 +552,40 @@ template <typename TSumList>
 class Iter<TSumList, MiniSumListValueIterator_>
 {
 public:
-	typedef typename CopyConst_<TSumList, unsigned char>::Type TUnsignedChar;
-	mutable TUnsignedChar * data_ptr;
-
-	Iter()
-		: data_ptr(0)
-	{
-	}
-	Iter(TSumList & cont)
-		: data_ptr(cont.data_)
-	{
-	}
-	Iter(Iter const & other)
-		: data_ptr(other.data_ptr)
-	{
-	}
-	Iter(TUnsignedChar * ptr)
-		: data_ptr(ptr)
-	{
-	}
-	~Iter()
-	{
-	}
-	inline Iter const & 
-	operator = (Iter const & other)
-	{
-		data_ptr = other.data_ptr;
-		return *this;
-	}
-	inline Iter const & 
-	operator = (TUnsignedChar * ptr)
-	{
-		data_ptr = ptr;
-		return *this;
-	}
+    typedef typename CopyConst_<TSumList, unsigned char>::Type TUnsignedChar;
+    mutable TUnsignedChar * data_ptr;
+
+    Iter()
+        : data_ptr(0)
+    {
+    }
+    Iter(TSumList & cont)
+        : data_ptr(cont.data_)
+    {
+    }
+    Iter(Iter const & other)
+        : data_ptr(other.data_ptr)
+    {
+    }
+    Iter(TUnsignedChar * ptr)
+        : data_ptr(ptr)
+    {
+    }
+    ~Iter()
+    {
+    }
+    inline Iter const &
+    operator = (Iter const & other)
+    {
+        data_ptr = other.data_ptr;
+        return *this;
+    }
+    inline Iter const &
+    operator = (TUnsignedChar * ptr)
+    {
+        data_ptr = ptr;
+        return *this;
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -594,10 +594,10 @@ template <typename TSumList>
 inline void
 goNext(Iter< TSumList, MiniSumListValueIterator_ > & it)
 {
-	typedef typename Value<TSumList>::Type TValue;
-	typedef MiniListEntry_<TValue> const TEntry;
-	TEntry & entr = * reinterpret_cast<TEntry *>(it.data_ptr);
-	it.data_ptr += entr.size();
+    typedef typename Value<TSumList>::Type TValue;
+    typedef MiniListEntry_<TValue> const TEntry;
+    TEntry & entr = * reinterpret_cast<TEntry *>(it.data_ptr);
+    it.data_ptr += entr.size();
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -606,10 +606,10 @@ template <typename TSumList>
 inline typename Value<TSumList>::Type
 getValue(Iter<TSumList, MiniSumListValueIterator_ > & it)
 {
-	typedef typename Value<TSumList>::Type TValue;
-	typedef MiniListEntry_<TValue> const TEntry;
-	TEntry & entr = * reinterpret_cast<TEntry *>(it.data_ptr);
-	return entr.getValue();
+    typedef typename Value<TSumList>::Type TValue;
+    typedef MiniListEntry_<TValue> const TEntry;
+    TEntry & entr = * reinterpret_cast<TEntry *>(it.data_ptr);
+    return entr.getValue();
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -617,13 +617,13 @@ getValue(Iter<TSumList, MiniSumListValueIterator_ > & it)
 template <typename TSumList, typename TValues>
 inline void
 scanValues(/*IN and OUT*/ Iter< TSumList, MiniSumListValueIterator_ > & it,
-		   /*OUT*/ TValues & values)
+           /*OUT*/ TValues & values)
 {
-	for (unsigned int i = 0; i < DIMENSION<TSumList>::VALUE; ++i)
-	{
-		values[i] = getValue(it);
-		goNext(it);
-	}
+    for (unsigned int i = 0; i < DIMENSION<TSumList>::VALUE; ++i)
+    {
+        values[i] = getValue(it);
+        goNext(it);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -631,17 +631,17 @@ scanValues(/*IN and OUT*/ Iter< TSumList, MiniSumListValueIterator_ > & it,
 template <typename TSumList, typename TSumList2>
 inline bool
 atEnd(Iter< TSumList, MiniSumListValueIterator_ > & it,
-	  TSumList2 & container)
+      TSumList2 & container)
 {
-	return (!it.data_ptr) || (it.data_ptr == container.data_ + container.data_size);
+    return (!it.data_ptr) || (it.data_ptr == container.data_ + container.data_size);
 }
 
 template <typename TSumList, typename TSumList2>
 inline bool
 atEnd(Iter< TSumList, MiniSumListValueIterator_ > & it,
-	  TSumList2 const & container)
+      TSumList2 const & container)
 {
-	return (!it.data_ptr) || (it.data_ptr == container.data_ + container.data_size);
+    return (!it.data_ptr) || (it.data_ptr == container.data_ + container.data_size);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -656,58 +656,58 @@ template <typename TSumList>
 class Iter<TSumList, MiniSumListIterator>
 {
 public:
-	typedef Iter<TSumList, MiniSumListValueIterator_> TValueIterator;
-//	typedef typename CopyConst_<TSumList, TValueIterator_>::Type TValueIterator;
-	typedef typename Value<TSumList>::Type TValue;
-	typedef SumListValues<DIMENSION<TSumList>::VALUE, TValue> TValues;
-
-	TSumList * container_;
-	mutable TValueIterator here_;
-	mutable TValueIterator next_;
-	mutable TValues values_;
-	mutable TValues sums_;
-
-	Iter()
-	{
-	}
-	Iter(TSumList & cont)
-		: container_(& cont)
-		, here_(cont.data_)
-		, next_(cont.data_)
-	{
-		if (!atEnd(next_, cont))
-		{
-			scanValues(next_, values_);
-		}
-	}
-	Iter(TSumList & cont, GoEnd)
-		: container_(& cont)
-		, here_(cont.data_ + cont.data_size)
-		, sums_(cont.data_sum)
-	{
-	}
-	Iter(Iter const & other)
-		: container_(other.container_)
-		, here_(other.here_)
-		, next_(other.next_)
-		, values_(other.values_)
-		, sums_(other.sums_)
-	{
-	}
-
-	~Iter()
-	{
-	}
-	inline Iter const & 
-	operator = (Iter const & other)
-	{
-		container_ = other.container_;
-		here_ = other.here_;
-		next_ = other.next_;
-		values_ = other.values_;
-		sums_ = other.sums_;
-		return *this;
-	}
+    typedef Iter<TSumList, MiniSumListValueIterator_> TValueIterator;
+//    typedef typename CopyConst_<TSumList, TValueIterator_>::Type TValueIterator;
+    typedef typename Value<TSumList>::Type TValue;
+    typedef SumListValues<DIMENSION<TSumList>::VALUE, TValue> TValues;
+
+    TSumList * container_;
+    mutable TValueIterator here_;
+    mutable TValueIterator next_;
+    mutable TValues values_;
+    mutable TValues sums_;
+
+    Iter()
+    {
+    }
+    Iter(TSumList & cont)
+        : container_(& cont)
+        , here_(cont.data_)
+        , next_(cont.data_)
+    {
+        if (!atEnd(next_, cont))
+        {
+            scanValues(next_, values_);
+        }
+    }
+    Iter(TSumList & cont, GoEnd)
+        : container_(& cont)
+        , here_(cont.data_ + cont.data_size)
+        , sums_(cont.data_sum)
+    {
+    }
+    Iter(Iter const & other)
+        : container_(other.container_)
+        , here_(other.here_)
+        , next_(other.next_)
+        , values_(other.values_)
+        , sums_(other.sums_)
+    {
+    }
+
+    ~Iter()
+    {
+    }
+    inline Iter const &
+    operator = (Iter const & other)
+    {
+        container_ = other.container_;
+        here_ = other.here_;
+        next_ = other.next_;
+        values_ = other.values_;
+        sums_ = other.sums_;
+        return *this;
+    }
 };
 
 
@@ -716,14 +716,14 @@ class Iter<TSumList, MiniSumListIterator>
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec, typename TIteratorSpec>
 struct Iterator< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> >, TIteratorSpec>
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TSumList_;
-	typedef Iter<TSumList_, MiniSumListIterator> Type;
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TSumList_;
+    typedef Iter<TSumList_, MiniSumListIterator> Type;
 };
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec, typename TIteratorSpec>
 struct Iterator< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const, TIteratorSpec>
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const TSumList_;
-	typedef Iter<TSumList_, MiniSumListIterator> Type;
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const TSumList_;
+    typedef Iter<TSumList_, MiniSumListIterator> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -731,8 +731,8 @@ struct Iterator< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > const, TIterato
 //template <typename TSumList>
 //struct Values< Iter<TSumList, MiniSumListIterator> >
 //{
-//	typedef typename Value<TSumList>::Type TValue;
-//	typedef SumListValues<DIMENSION<TSumList>::VALUE, TValue> Type;
+//    typedef typename Value<TSumList>::Type TValue;
+//    typedef SumListValues<DIMENSION<TSumList>::VALUE, TValue> Type;
 //};
 
 //////////////////////////////////////////////////////////////////////////////
@@ -741,10 +741,10 @@ template <typename TSumList>
 inline void
 clear(Iter<TSumList, MiniSumListIterator> & it)
 {
-	it.here_ = it.next_ = 0;
-	it.container_ = 0;
-	clear(it.values_);
-	clear(it.sums_);
+    it.here_ = it.next_ = 0;
+    it.container_ = 0;
+    clear(it.values_);
+    clear(it.sums_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -753,12 +753,12 @@ template <typename TSumList>
 inline void
 goNext(Iter<TSumList, MiniSumListIterator> & it)
 {
-	it.sums_ += it.values_;
-	it.here_ = it.next_;
-	if (!atEnd(it.next_, *it.container_))
-	{
-		scanValues(it.next_, it.values_);
-	}
+    it.sums_ += it.values_;
+    it.here_ = it.next_;
+    if (!atEnd(it.next_, *it.container_))
+    {
+        scanValues(it.next_, it.values_);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -767,9 +767,9 @@ template <typename TSumList>
 inline void
 goBegin(Iter<TSumList, MiniSumListIterator> & it)
 {
-	clear(it.sums_);
-	it.here_ = it.next_ = it.container_->data_;
-	scanValues(it.next_, it.values_);
+    clear(it.sums_);
+    it.here_ = it.next_ = it.container_->data_;
+    scanValues(it.next_, it.values_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -778,11 +778,11 @@ template <typename TSumList>
 inline void
 goBeforeEnd(Iter<TSumList, MiniSumListIterator> & it)
 {
-	goBegin(it);
-	while (!atEnd(it.next_, *it.container_))
-	{
-		goNext(it);
-	}
+    goBegin(it);
+    while (!atEnd(it.next_, *it.container_))
+    {
+        goNext(it);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -791,7 +791,7 @@ template <typename TSumList>
 inline bool
 atEnd(Iter<TSumList, MiniSumListIterator> & it)
 {
-	return atEnd(it.here_, * it.container_);
+    return atEnd(it.here_, * it.container_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -799,9 +799,9 @@ atEnd(Iter<TSumList, MiniSumListIterator> & it)
 template <typename TSumList>
 inline typename Value<TSumList>::Type
 getValue(Iter<TSumList, MiniSumListIterator > & it,
-		 int dim)
+         int dim)
 {
-	return it.values_[dim];
+    return it.values_[dim];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -809,9 +809,9 @@ getValue(Iter<TSumList, MiniSumListIterator > & it,
 template <typename TSumList>
 inline typename Value<TSumList>::Type
 getSum(Iter<TSumList, MiniSumListIterator > & it,
-		 int dim)
+         int dim)
 {
-	return it.sums_[dim];
+    return it.sums_[dim];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -819,116 +819,116 @@ getSum(Iter<TSumList, MiniSumListIterator > & it,
 template <typename TSumList, typename TValue>
 inline void
 searchSumList(Iter< TSumList, MiniSumListIterator > & it,
-			  TValue const & val,
-			  int dim)
+              TValue const & val,
+              int dim)
 {
-	goBegin(it);
-	while (!atEnd(it) && ((getSum(it, dim) + getValue(it, dim))<= val)) // SEARCH SEMANTICS
-	{
-		goNext(it);
-	}
+    goBegin(it);
+    while (!atEnd(it) && ((getSum(it, dim) + getValue(it, dim))<= val)) // SEARCH SEMANTICS
+    {
+        goNext(it);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec, typename TValue2>
-inline bool 
+inline bool
 assignValue(Iter<SumList<DIM, TValue, MiniSumList<SIZE, TSpec> >, MiniSumListIterator > & it,
-			int dim,
-			TValue2 val)
+            int dim,
+            TValue2 val)
 {
-	typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TSumList;
-	typedef Iter<TSumList, MiniSumListValueIterator_> TValueIterator;
-	typedef MiniListEntry_<TValue> TEntry;
+    typedef SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > TSumList;
+    typedef Iter<TSumList, MiniSumListValueIterator_> TValueIterator;
+    typedef MiniListEntry_<TValue> TEntry;
 
-	//find a pointer to the value
-	TValueIterator vit = it.here_;
-	for (int i = 0; i < dim; ++i)
-	{
-		goNext(vit);
-	}
+    //find a pointer to the value
+    TValueIterator vit = it.here_;
+    for (int i = 0; i < dim; ++i)
+    {
+        goNext(vit);
+    }
 
-	//save old value
-	TValue old_val = getValue(vit);
+    //save old value
+    TValue old_val = getValue(vit);
 
-	//create TEntry accessors
-	TEntry new_entr(val);
-	TEntry & old_entr = * reinterpret_cast<TEntry *>(vit.data_ptr);
+    //create TEntry accessors
+    TEntry new_entr(val);
+    TEntry & old_entr = * reinterpret_cast<TEntry *>(vit.data_ptr);
 
-	int diff = new_entr.size() -  old_entr.size();
-	if (diff)
-	{//entries take different spaces:
+    int diff = new_entr.size() -  old_entr.size();
+    if (diff)
+    {//entries take different spaces:
 
-		int new_size = it.container_->data_size + diff;
-		if (new_size > SIZE) return false; //not enough space
+        int new_size = it.container_->data_size + diff;
+        if (new_size > SIZE) return false; //not enough space
 
-		//make room!
-		arrayCopy(vit.data_ptr + old_entr.size(), it.container_->data_ + it.container_->data_size, vit.data_ptr + new_entr.size());
-		it.container_->data_size += diff;
+        //make room!
+        arrayCopy(vit.data_ptr + old_entr.size(), it.container_->data_ + it.container_->data_size, vit.data_ptr + new_entr.size());
+        it.container_->data_size += diff;
 
-		//adjust next_ pointer
-		it.next_.data_ptr += diff;
-	}
-	//adjust sum
-	it.container_->data_sum[dim] += (val - old_val);
+        //adjust next_ pointer
+        it.next_.data_ptr += diff;
+    }
+    //adjust sum
+    it.container_->data_sum[dim] += (val - old_val);
 
-	//save new value
-	old_entr.assignValue(val);
-	it.values_[dim] = val;
+    //save new value
+    old_entr.assignValue(val);
+    it.values_[dim] = val;
 
-	return true;
+    return true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSumList, typename TValues>
-inline bool 
+inline bool
 insertValues(Iter<TSumList, MiniSumListIterator > & it,
-			 TValues const & vals)
+             TValues const & vals)
 {
-	unsigned int new_values_size;
-	bool ret = _insertValues(*it.container_, it.here_, vals, new_values_size);
-	if (ret)
-	{
-		it.next_.data_ptr = it.here_.data_ptr + new_values_size;
-		it.values_ = vals;
-	}
-	return ret;
+    unsigned int new_values_size;
+    bool ret = _insertValues(*it.container_, it.here_, vals, new_values_size);
+    if (ret)
+    {
+        it.next_.data_ptr = it.here_.data_ptr + new_values_size;
+        it.values_ = vals;
+    }
+    return ret;
 }
 template <typename TSumList, typename TValue>
-inline bool 
+inline bool
 insertValues(Iter<TSumList, MiniSumListIterator > & it,
-			 TValue const * p_vals)
+             TValue const * p_vals)
 {
-	SumListValues<DIMENSION<TSumList>::VALUE, typename Value<TSumList>::Type > vals(p_vals);
-	return insertValues(it, vals);
+    SumListValues<DIMENSION<TSumList>::VALUE, typename Value<TSumList>::Type > vals(p_vals);
+    return insertValues(it, vals);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSumList>
-inline void 
+inline void
 removeValues(Iter<TSumList, MiniSumListIterator > & it)
 {
-	//adjust sums
-	for (int i = 0; i < DIMENSION<TSumList>::VALUE; ++i)
-	{
-		it.container_->data_sum[i] -= it.values_[i];
-	}
-	if (!atEnd(it.next_, * it.container_))
-	{//move the rest
-		arrayCopyForward(it.next_.data_ptr, it.container_->data_ + it.container_->data_size, it.here_.data_ptr);
-	}
-	//adjust size and length
-	it.container_->data_size -= (it.next_.data_ptr - it.here_.data_ptr);
-	--it.container_->data_length;
+    //adjust sums
+    for (int i = 0; i < DIMENSION<TSumList>::VALUE; ++i)
+    {
+        it.container_->data_sum[i] -= it.values_[i];
+    }
+    if (!atEnd(it.next_, * it.container_))
+    {//move the rest
+        arrayCopyForward(it.next_.data_ptr, it.container_->data_ + it.container_->data_size, it.here_.data_ptr);
+    }
+    //adjust size and length
+    it.container_->data_size -= (it.next_.data_ptr - it.here_.data_ptr);
+    --it.container_->data_length;
 
-	//find new next pointer
-	it.next_ = it.here_;
-	if (!atEnd(it.next_, *it.container_))
-	{
-		scanValues(it.next_, it.values_);
-	}
+    //find new next pointer
+    it.next_ = it.here_;
+    if (!atEnd(it.next_, *it.container_))
+    {
+        scanValues(it.next_, it.values_);
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -936,17 +936,17 @@ removeValues(Iter<TSumList, MiniSumListIterator > & it)
 template <typename TSumList, typename TSumList2>
 inline bool
 operator == (Iter<TSumList, MiniSumListIterator> const & left,
-			 Iter<TSumList2, MiniSumListIterator> const & right)
+             Iter<TSumList2, MiniSumListIterator> const & right)
 {
-	return left.here_.data_ptr == right.here_.data_ptr;
+    return left.here_.data_ptr == right.here_.data_ptr;
 }
 
 template <typename TSumList, typename TSumList2>
 inline bool
 operator != (Iter<TSumList, MiniSumListIterator> const & left,
-			 Iter<TSumList2, MiniSumListIterator> const & right)
+             Iter<TSumList2, MiniSumListIterator> const & right)
 {
-	return left.here_.data_ptr != right.here_.data_ptr;
+    return left.here_.data_ptr != right.here_.data_ptr;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -958,9 +958,9 @@ operator != (Iter<TSumList, MiniSumListIterator> const & left,
 //template <unsigned int DIM, typename TValue, unsigned short SIZE, typename TSpec>
 //inline bool
 //atEnd(Iter< SumList<DIM, TValue, MiniSumList<SIZE, TSpec> >, MiniSumListValueIterator_ > & it,
-//	  SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & container)
+//      SumList<DIM, TValue, MiniSumList<SIZE, TSpec> > & container)
 //{
-//	return it.data_ptr == container.data_ + container.data_size;
+//    return it.data_ptr == container.data_ + container.data_size;
 //}
 
 
diff --git a/seqan/map/sumlist_skip.h b/seqan/map/sumlist_skip.h
index d64ae46..6b3c0c6 100644
--- a/seqan/map/sumlist_skip.h
+++ b/seqan/map/sumlist_skip.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -56,12 +56,12 @@ struct Skipsumlist_;
 template <typename TValue, unsigned int DIM, typename TSpec>
 struct SkipListBlockSize_<Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > >
 {
-	typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
-	typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
-	enum
-	{
-		VALUE = sizeof(TMiniSumList) + TMap::MAX_HEIGHT * sizeof(
-	};
+    typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
+    typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
+    enum
+    {
+        VALUE = sizeof(TMiniSumList) + TMap::MAX_HEIGHT * sizeof(
+    };
 };
 */
 
@@ -71,31 +71,31 @@ template <typename TValue, unsigned int DIM, typename TSpec>
 class SkiplistNext<TValue, Skipsumlist_<DIM, TSpec> >
 {
 public:
-	typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef SumListValues<DIM, TValue> TValues;
-
-	TElement * data_element;
-	TValues values;
-
-	SkiplistNext()
-		: values(MinimalCtor())
-	{}
-	SkiplistNext(NonMinimalCtor)
-		: data_element(0)
-	{}
-	SkiplistNext(SkiplistNext const & other)
-		: data_element(other.data_element)
-		, values(other.values)
-	{}
-	~SkiplistNext()
-	{}
-	SkiplistNext const & operator = (SkiplistNext const & other)
-	{
-		data_element = other.data_element;
-		values = other.values;
-		return *this;
-	}
+    typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef SumListValues<DIM, TValue> TValues;
+
+    TElement * data_element;
+    TValues values;
+
+    SkiplistNext()
+        : values(MinimalCtor())
+    {}
+    SkiplistNext(NonMinimalCtor)
+        : data_element(0)
+    {}
+    SkiplistNext(SkiplistNext const & other)
+        : data_element(other.data_element)
+        , values(other.values)
+    {}
+    ~SkiplistNext()
+    {}
+    SkiplistNext const & operator = (SkiplistNext const & other)
+    {
+        data_element = other.data_element;
+        values = other.values;
+        return *this;
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -105,17 +105,17 @@ template <typename TValue, unsigned int DIM, typename TSpec>
 class SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> >
 {
 public:
-	typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TSkiplist;
-	typedef SkiplistNext<TValue, Skipsumlist_<DIM, TSpec> > TNext;
-	typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
+    typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TSkiplist;
+    typedef SkiplistNext<TValue, Skipsumlist_<DIM, TSpec> > TNext;
+    typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
 
-	enum
-	{
-		MAX_HEIGHT = TSkiplist::MAX_HEIGHT
-	};
+    enum
+    {
+        MAX_HEIGHT = TSkiplist::MAX_HEIGHT
+    };
 
-	TMiniSumList minilist;
-	TNext data_next[MAX_HEIGHT]; //note: only parts of this array available
+    TMiniSumList minilist;
+    TNext data_next[MAX_HEIGHT]; //note: only parts of this array available
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -124,26 +124,26 @@ template <typename TValue, unsigned int DIM, typename TSpec>
 class SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> >
 {
 public:
-	typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TSkiplist;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef SumListValues<DIM, TValue> TValues;
-
-	enum
-	{
-		MAX_HEIGHT = TSkiplist::MAX_HEIGHT
-	};
-
-	TElement * data_elements[MAX_HEIGHT];
-	TValues sums[MAX_HEIGHT];
-
-	SkiplistPath() {}
-	SkiplistPath(TSkiplist & sl)
-	{
-		for (unsigned int i = 0; i <= sl.data_height; ++i)
-		{
-			data_elements[i] = & (sl.data_border);
-		}
-	}
+    typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TSkiplist;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef SumListValues<DIM, TValue> TValues;
+
+    enum
+    {
+        MAX_HEIGHT = TSkiplist::MAX_HEIGHT
+    };
+
+    TElement * data_elements[MAX_HEIGHT];
+    TValues sums[MAX_HEIGHT];
+
+    SkiplistPath() {}
+    SkiplistPath(TSkiplist & sl)
+    {
+        for (unsigned int i = 0; i <= sl.data_height; ++i)
+        {
+            data_elements[i] = & (sl.data_border);
+        }
+    }
 };
 
 
@@ -154,25 +154,25 @@ class SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> >
 template <typename TValue, unsigned int DIM, typename TSpec>
 bool atEnd(SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > & path)
 {
-	return (!path.data_elements[0]);
+    return (!path.data_elements[0]);
 }
 
 template <typename TValue, unsigned int DIM, typename TSpec, typename TSkiplist>
 void goNext(SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > & path,
-			TSkiplist const & skiplist)
+            TSkiplist const & skiplist)
 {
-	typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-
-	TElement * next = path.data_elements[0]->data_next[0].data_element;
-	for (unsigned int i = 0; i <= skiplist.data_height; ++i)
-	{
-		if (!path.data_elements[i]) break;
-		if (path.data_elements[i]->data_next[i].data_element != next) break;
-
-		path.sums[i] += path.data_elements[i]->data_next[i].values;
-		path.data_elements[i] = next;
-	}
+    typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+
+    TElement * next = path.data_elements[0]->data_next[0].data_element;
+    for (unsigned int i = 0; i <= skiplist.data_height; ++i)
+    {
+        if (!path.data_elements[i]) break;
+        if (path.data_elements[i]->data_next[i].data_element != next) break;
+
+        path.sums[i] += path.data_elements[i]->data_next[i].values;
+        path.data_elements[i] = next;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -184,148 +184,148 @@ void goNext(SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > & path,
 template <typename TNext, typename THere, typename TValues, typename TValue>
 inline bool
 _skipsumlistFindGoNext(TNext const & _next,
-					   THere const & /*_here*/,
-					   unsigned char /*_height*/,
-					   TValues const & _sum,
-					   unsigned int _dim,
-					   TValue const & _value)
+                       THere const & /*_here*/,
+                       unsigned char /*_height*/,
+                       TValues const & _sum,
+                       unsigned int _dim,
+                       TValue const & _value)
 {
-	return (static_cast<TValue>((_sum[_dim] + _next.values[_dim])) <= _value); // SEARCH SEMANTICS
+    return (static_cast<TValue>((_sum[_dim] + _next.values[_dim])) <= _value); // SEARCH SEMANTICS
 }
 //find an element, given (sum, element_pointer)-pair
 template <typename TNext, typename THere, typename TValues, typename TValue, typename TElementPtr>
 inline bool
 _skipsumlistFindGoNext(TNext const & _next,
-					   THere const & _here,
-					   unsigned char /*_height*/,
-					   TValues const & _sum,
-					   unsigned int _dim,
-					   Pair<TValue, TElementPtr> const & pair)
+                       THere const & _here,
+                       unsigned char /*_height*/,
+                       TValues const & _sum,
+                       unsigned int _dim,
+                       Pair<TValue, TElementPtr> const & pair)
 {
-	return (_sum[_dim] + _next.values[_dim] <= pair.i1) && (pair.i2 != _here);
+    return (_sum[_dim] + _next.values[_dim] <= pair.i1) && (pair.i2 != _here);
 }
 //find the end of the skiplist
 template <typename TNext, typename THere, typename TValues>
 inline bool
 _skipsumlistFindGoNext(TNext const & _next,
-					   THere const & /*_here*/,
-					   unsigned char /*_height*/,
-					   TValues const & /*_sum*/,
-					   unsigned int /*_dim*/,
-					   GoEnd)
+                       THere const & /*_here*/,
+                       unsigned char /*_height*/,
+                       TValues const & /*_sum*/,
+                       unsigned int /*_dim*/,
+                       GoEnd)
 {
-	return _next.data_element != 0;
+    return _next.data_element != 0;
 }
 
 
 template <typename TValue, unsigned int DIM, typename TSpec, typename TFind>
 inline void
 _skipsumlistFind(Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > & me,
-				 TFind const & find,
-				 unsigned int dim,
-				 /*OUT*/ SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > & path)
+                 TFind const & find,
+                 unsigned int dim,
+                 /*OUT*/ SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > & path)
 {
-	typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef SkiplistNext<TValue, Skipsumlist_<DIM, TSpec> > TNext;
-	typedef SumListValues<DIM, TValue> TValues;
+    typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef SkiplistNext<TValue, Skipsumlist_<DIM, TSpec> > TNext;
+    typedef SumListValues<DIM, TValue> TValues;
 
-	typedef typename Size<TMap>::Type TSize;
+    typedef typename Size<TMap>::Type TSize;
 
-	TElement * here = & me.data_border;
+    TElement * here = & me.data_border;
 
-	TValues sum;
+    TValues sum;
 
-	for (int i = me.data_height; i >= 0; --i)
-	{
-		while (true)
-		{
-			TNext & next = here->data_next[i];
-			if (!next.data_element) break;
+    for (int i = me.data_height; i >= 0; --i)
+    {
+        while (true)
+        {
+            TNext & next = here->data_next[i];
+            if (!next.data_element) break;
 
-			if (!_skipsumlistFindGoNext(next, here, i, sum, dim, find)) break;
+            if (!_skipsumlistFindGoNext(next, here, i, sum, dim, find)) break;
 
-			here = next.data_element;
-			sum += next.values;
-		}
-		path.data_elements[i] = here;
-		path.sums[i] = sum;
-	}
+            here = next.data_element;
+            sum += next.values;
+        }
+        path.data_elements[i] = here;
+        path.sums[i] = sum;
+    }
 }
 template <typename TValue, unsigned int DIM, typename TSpec, typename TFind>
 inline void
 _skipsumlistFind(Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > const & me,
-				 TFind const & find,
-				 unsigned int dim,
-				 /*OUT*/ SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > & path)
+                 TFind const & find,
+                 unsigned int dim,
+                 /*OUT*/ SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > & path)
 {//destroy const
-	typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
-	_skipsumlistFind(const_cast<TMap &>(me), find, dim, path);
+    typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
+    _skipsumlistFind(const_cast<TMap &>(me), find, dim, path);
 }
 
 
 template <typename TValue, unsigned int DIM, typename TSpec>
 inline void
 assign(Map<TValue, Skiplist< Skipsumlist_<DIM, TSpec> > > & target,
-	   Map<TValue, Skiplist< Skipsumlist_<DIM, TSpec> > > const & source_)
+       Map<TValue, Skiplist< Skipsumlist_<DIM, TSpec> > > const & source_)
 {
-	typedef Map<TValue, Skiplist< Skipsumlist_<DIM, TSpec> > > TSkiplist;
-	typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	//typedef typename Iterator<TSkiplist>::Type TIterator;
-	//typedef typename Value<TSkiplist>::Type TValue2;
-
-	TSkiplist & source = const_cast<TSkiplist &>(source_); //oh, I'm so damned lazy :-P
-
-	//first clear target
-	clear(target);
-
-	//init path variable that is used as iterator-like construct to build up target
-	//and copy link values outgoing from target border
-	TPath target_path(target);
-	target.data_height = source.data_height;
-	for (unsigned int i = 0; i <= target.data_height; ++i)
-	{
-		target_path.data_elements[i] = & target.data_border;
-		target.data_border.data_next[i].values = source.data_border.data_next[i].values;
-	}
-
-	//copy the first minilist
-	target.data_border.minilist = source.data_border.minilist;
-
-	TPath source_path(source);
-	//copy rest of the values
-	while (true)
-	{
-		goNext(source_path, source);
-
-		if (atEnd(source_path)) break;
-
-		//determine height of current tower
-		unsigned char height;
-		for (height = 1; height < TSkiplist::MAX_HEIGHT; ++height)
-		{
-			if (source_path.data_elements[height] != source_path.data_elements[0]) break;
-		}
-		--height;
-
-		//create new element in target and copy minilist
-		TElement & el = _skiplistAllocateElement(target, height);
-		el.minilist = source_path.data_elements[0]->minilist;
-
-		//insert element in target
-		for (int i = 0; i <= height; ++i)
-		{
-			el.data_next[i].data_element = 0;
-			el.data_next[i].values = source_path.data_elements[i]->data_next[i].values;
-			target_path.data_elements[i]->data_next[i].data_element = & el;
-			target_path.data_elements[i] = & el;
-		}
-
-	}
-
-	//set length
-	target.data_length = length(source);
+    typedef Map<TValue, Skiplist< Skipsumlist_<DIM, TSpec> > > TSkiplist;
+    typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    //typedef typename Iterator<TSkiplist>::Type TIterator;
+    //typedef typename Value<TSkiplist>::Type TValue2;
+
+    TSkiplist & source = const_cast<TSkiplist &>(source_); //oh, I'm so damned lazy :-P
+
+    //first clear target
+    clear(target);
+
+    //init path variable that is used as iterator-like construct to build up target
+    //and copy link values outgoing from target border
+    TPath target_path(target);
+    target.data_height = source.data_height;
+    for (unsigned int i = 0; i <= target.data_height; ++i)
+    {
+        target_path.data_elements[i] = & target.data_border;
+        target.data_border.data_next[i].values = source.data_border.data_next[i].values;
+    }
+
+    //copy the first minilist
+    target.data_border.minilist = source.data_border.minilist;
+
+    TPath source_path(source);
+    //copy rest of the values
+    while (true)
+    {
+        goNext(source_path, source);
+
+        if (atEnd(source_path)) break;
+
+        //determine height of current tower
+        unsigned char height;
+        for (height = 1; height < TSkiplist::MAX_HEIGHT; ++height)
+        {
+            if (source_path.data_elements[height] != source_path.data_elements[0]) break;
+        }
+        --height;
+
+        //create new element in target and copy minilist
+        TElement & el = _skiplistAllocateElement(target, height);
+        el.minilist = source_path.data_elements[0]->minilist;
+
+        //insert element in target
+        for (int i = 0; i <= height; ++i)
+        {
+            el.data_next[i].data_element = 0;
+            el.data_next[i].values = source_path.data_elements[i]->data_next[i].values;
+            target_path.data_elements[i]->data_next[i].data_element = & el;
+            target_path.data_elements[i] = & el;
+        }
+
+    }
+
+    //set length
+    target.data_length = length(source);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -334,20 +334,20 @@ template <typename TValue, unsigned int DIM, typename TSpec>
 inline void
 clear(Map<TValue, Skiplist< Skipsumlist_<DIM, TSpec> > > & me)
 {
-	typedef Map<TValue, Skiplist< Skipsumlist_<DIM, TSpec> > > TSkiplist;
+    typedef Map<TValue, Skiplist< Skipsumlist_<DIM, TSpec> > > TSkiplist;
 
-	me.data_mem_begin = me.data_mem_end = 0;
-	me.data_length = 0;
-	me.data_height = 0;
+    me.data_mem_begin = me.data_mem_end = 0;
+    me.data_length = 0;
+    me.data_height = 0;
 
-	for (unsigned char i = 0; i < TSkiplist::MAX_HEIGHT; ++i)
-	{
-		me.data_recycle[i] = 0;
-		valueConstruct(me.data_border.data_next + i, NonMinimalCtor()); 
-	}
-	clear(me.data_border.minilist); //thats new
+    for (unsigned char i = 0; i < TSkiplist::MAX_HEIGHT; ++i)
+    {
+        me.data_recycle[i] = 0;
+        valueConstruct(me.data_border.data_next + i, NonMinimalCtor());
+    }
+    clear(me.data_border.minilist); //thats new
 
-	clear(value(me.data_allocator));
+    clear(value(me.data_allocator));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -359,29 +359,29 @@ template <unsigned int DIM, typename TValue, typename TSpec>
 class SumList<DIM, TValue, SkipSumList<TSpec> >
 {
 public:
-	typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
-	typedef typename Size<SumList>::Type TSize;
-	typedef SumListValues<DIM, TValue> TValues;
-
-	TMap map;
-	TSize length;
-	TValues sum;
-
-	SumList()
-		: length(0)
-	{}
-	SumList(SumList const & other)
-		: length(0)
-	{
-		assign(*this, other);
-	}
-	~SumList() 
-	{}
-	SumList const & operator = (SumList const & other)
-	{
-		assign(*this, other);
-		return *this;
-	}
+    typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TMap;
+    typedef typename Size<SumList>::Type TSize;
+    typedef SumListValues<DIM, TValue> TValues;
+
+    TMap map;
+    TSize length;
+    TValues sum;
+
+    SumList()
+        : length(0)
+    {}
+    SumList(SumList const & other)
+        : length(0)
+    {
+        assign(*this, other);
+    }
+    ~SumList()
+    {}
+    SumList const & operator = (SumList const & other)
+    {
+        assign(*this, other);
+        return *this;
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -390,11 +390,11 @@ class SumList<DIM, TValue, SkipSumList<TSpec> >
 template <unsigned int DIM, typename TValue, typename TSpec>
 inline void
 assign(SumList<DIM, TValue, SkipSumList<TSpec> > & target,
-	   SumList<DIM, TValue, SkipSumList<TSpec> > const & source)
+       SumList<DIM, TValue, SkipSumList<TSpec> > const & source)
 {
-	target.map = source.map;
-	target.length = source.length;
-	target.sum = source.sum;
+    target.map = source.map;
+    target.length = source.length;
+    target.sum = source.sum;
 }
 
 
@@ -404,17 +404,17 @@ template <unsigned int DIM, typename TValue, typename TSpec>
 inline typename Size< SumList<DIM, TValue, SkipSumList<TSpec> > >::Type
 length(SumList<DIM, TValue, SkipSumList<TSpec> > const & me)
 {
-	return me.length;
+    return me.length;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <unsigned int DIM, typename TValue, typename TSpec>
-inline typename Value< SumList<DIM, TValue, SkipSumList<TSpec> > >::Type 
+inline typename Value< SumList<DIM, TValue, SkipSumList<TSpec> > >::Type
 getSum(SumList<DIM, TValue, SkipSumList<TSpec> > const & me,
-	   unsigned int dim)
+       unsigned int dim)
 {
-	return me.sum[dim];
+    return me.sum[dim];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -423,9 +423,9 @@ template <unsigned int DIM, typename TValue, typename TSpec>
 inline void
 clear(SumList<DIM, TValue, SkipSumList<TSpec> > & me)
 {
-	clear(me.map);
-	me.length = 0;
-	clear(me.sum);
+    clear(me.map);
+    me.length = 0;
+    clear(me.sum);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -434,17 +434,17 @@ template <unsigned int DIM, typename TValue, typename TSpec>
 inline typename Iterator< SumList<DIM, TValue, SkipSumList<TSpec> > >::Type
 begin(SumList<DIM, TValue, SkipSumList<TSpec> > & me)
 {
-	typedef SumList<DIM, TValue, SkipSumList<TSpec> >  TMe;
-	typedef typename Iterator<TMe>::Type TIterator;
-	return TIterator(me);
+    typedef SumList<DIM, TValue, SkipSumList<TSpec> >  TMe;
+    typedef typename Iterator<TMe>::Type TIterator;
+    return TIterator(me);
 }
 template <unsigned int DIM, typename TValue, typename TSpec>
 inline typename Iterator< SumList<DIM, TValue, SkipSumList<TSpec> > const>::Type
 begin(SumList<DIM, TValue, SkipSumList<TSpec> > const & me)
 {
-	typedef SumList<DIM, TValue, SkipSumList<TSpec> > const TMe;
-	typedef typename Iterator<TMe>::Type TIterator;
-	return TIterator(me);
+    typedef SumList<DIM, TValue, SkipSumList<TSpec> > const TMe;
+    typedef typename Iterator<TMe>::Type TIterator;
+    return TIterator(me);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -453,17 +453,17 @@ template <unsigned int DIM, typename TValue, typename TSpec>
 inline typename Iterator< SumList<DIM, TValue, SkipSumList<TSpec> > >::Type
 end(SumList<DIM, TValue, SkipSumList<TSpec> > & me)
 {
-	typedef SumList<DIM, TValue, SkipSumList<TSpec> >  TMe;
-	typedef typename Iterator<TMe>::Type TIterator;
-	return TIterator(me, GoEnd());
+    typedef SumList<DIM, TValue, SkipSumList<TSpec> >  TMe;
+    typedef typename Iterator<TMe>::Type TIterator;
+    return TIterator(me, GoEnd());
 }
 template <unsigned int DIM, typename TValue, typename TSpec>
 inline typename Iterator< SumList<DIM, TValue, SkipSumList<TSpec> > const>::Type
 end(SumList<DIM, TValue, SkipSumList<TSpec> > const & me)
 {
-	typedef SumList<DIM, TValue, SkipSumList<TSpec> > const TMe;
-	typedef typename Iterator<TMe>::Type TIterator;
-	return TIterator(me, GoEnd());
+    typedef SumList<DIM, TValue, SkipSumList<TSpec> > const TMe;
+    typedef typename Iterator<TMe>::Type TIterator;
+    return TIterator(me, GoEnd());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -472,97 +472,97 @@ end(SumList<DIM, TValue, SkipSumList<TSpec> > const & me)
 template <typename TValue, unsigned int DIM, typename TSpec, typename TSpec2>
 inline unsigned char
 _skiplistCreateHeight(SumList<DIM, TValue, SkipSumList<TSpec> > & me,
-					  SkiplistPath<TValue, TSpec2 > & path) //extend path if height is increased
+                      SkiplistPath<TValue, TSpec2 > & path) //extend path if height is increased
 {
-	typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TSkiplist;
-
-	unsigned char height = geomRand<unsigned char>();
-	if (height >= TSkiplist::MAX_HEIGHT) height = TSkiplist::MAX_HEIGHT-1;
-
-	if (height > me.map.data_height)
-	{
-		for (unsigned char i = me.map.data_height + 1; i <= height; ++i)
-		{
-			path.data_elements[i] = & me.map.data_border;
-			//path.sums[i] = me.sum;
-			me.map.data_border.data_next[i].values = me.sum;
-		}
-		me.map.data_height = height;
-	}
-
-	return height;
+    typedef Map<TValue, Skiplist<Skipsumlist_<DIM, TSpec> > > TSkiplist;
+
+    unsigned char height = geomRand<unsigned char>();
+    if (height >= TSkiplist::MAX_HEIGHT) height = TSkiplist::MAX_HEIGHT-1;
+
+    if (height > me.map.data_height)
+    {
+        for (unsigned char i = me.map.data_height + 1; i <= height; ++i)
+        {
+            path.data_elements[i] = & me.map.data_border;
+            //path.sums[i] = me.sum;
+            me.map.data_border.data_next[i].values = me.sum;
+        }
+        me.map.data_height = height;
+    }
+
+    return height;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <unsigned int DIM, typename TValue, typename TSpec, typename TValues>
-inline void 
+inline void
 appendValues(SumList<DIM, TValue, SkipSumList<TSpec> > & me,
-			 TValues const & vals)
+             TValues const & vals)
 {
-	typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef Pair<TValue, TElement *> TPair;
-	typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
-
-	//find end of skip list
-	TPath path;
-	_skipsumlistFind(me.map, GoEnd(), 0, path);
-
-	if (!appendValues(path.data_elements[0]->minilist, vals))
-	{//not enough space in the current last element: append new
-		//create new element
-		unsigned char height = _skiplistCreateHeight(me, path);
-		TElement & el = _skiplistAllocateElement(me.map, height); //see map_skiplist.
-		valueConstruct(& (el.minilist));
-
-		//append value into minilist of the new element
-		appendValues(el.minilist, vals);
-
-		//link new element el into skiplist, adjust link weights
-		for (int i = height; i >= 0; --i)
-		{
-			path.data_elements[i]->data_next[i].data_element = & el;
-
-			el.data_next[i].data_element = 0;
-			el.data_next[i].values = vals;
-		}
-		for (int i = me.map.data_height; i > height ; --i)
-		{
-			path.data_elements[i]->data_next[i].values += vals;
-		}
-
-		//adjust map properties
-		++me.map.data_length;
-	}
-	else
-	{
-		//update skiplist path sums
-		for (int i = me.map.data_height; i >= 0 ; --i)
-		{
-			path.data_elements[i]->data_next[i].values += vals;
-		}
-	}
-
-	//update sumlist variables
-	me.sum += vals;
-	++me.length;
+    typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef Pair<TValue, TElement *> TPair;
+    typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
+
+    //find end of skip list
+    TPath path;
+    _skipsumlistFind(me.map, GoEnd(), 0, path);
+
+    if (!appendValues(path.data_elements[0]->minilist, vals))
+    {//not enough space in the current last element: append new
+        //create new element
+        unsigned char height = _skiplistCreateHeight(me, path);
+        TElement & el = _skiplistAllocateElement(me.map, height); //see map_skiplist.
+        valueConstruct(& (el.minilist));
+
+        //append value into minilist of the new element
+        appendValues(el.minilist, vals);
+
+        //link new element el into skiplist, adjust link weights
+        for (int i = height; i >= 0; --i)
+        {
+            path.data_elements[i]->data_next[i].data_element = & el;
+
+            el.data_next[i].data_element = 0;
+            el.data_next[i].values = vals;
+        }
+        for (int i = me.map.data_height; i > height ; --i)
+        {
+            path.data_elements[i]->data_next[i].values += vals;
+        }
+
+        //adjust map properties
+        ++me.map.data_length;
+    }
+    else
+    {
+        //update skiplist path sums
+        for (int i = me.map.data_height; i >= 0 ; --i)
+        {
+            path.data_elements[i]->data_next[i].values += vals;
+        }
+    }
+
+    //update sumlist variables
+    me.sum += vals;
+    ++me.length;
 }
 template <unsigned int DIM, typename TValue, typename TSpec>
-inline void 
+inline void
 appendValues(SumList<DIM, TValue, SkipSumList<TSpec> > & me,
-			 TValue * p_vals)
+             TValue * p_vals)
 {
-	SumListValues<DIM, TValue> vals(p_vals);
-	appendValues(me, vals);
+    SumListValues<DIM, TValue> vals(p_vals);
+    appendValues(me, vals);
 }
 template <unsigned int DIM, typename TValue, typename TSpec>
-inline void 
+inline void
 appendValues(SumList<DIM, TValue, SkipSumList<TSpec> > & me,
-			 TValue const * p_vals)
+             TValue const * p_vals)
 {
-	SumListValues<DIM, TValue> vals(p_vals);
-	appendValues(me, vals);
+    SumListValues<DIM, TValue> vals(p_vals);
+    appendValues(me, vals);
 }
 
 
@@ -575,17 +575,17 @@ appendValues(SumList<DIM, TValue, SkipSumList<TSpec> > & me,
 template <typename TSumList>
 struct SumlistSkipListElement_
 {//dummy implementation
-	typedef SkiplistElement<int, void> Type;
+    typedef SkiplistElement<int, void> Type;
 };
 template <unsigned int DIM, typename TValue, typename TSpec>
 struct SumlistSkipListElement_< SumList<DIM, TValue, SkipSumList<TSpec> > >
 {
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > Type;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > Type;
 };
 template <unsigned int DIM, typename TValue, typename TSpec>
 struct SumlistSkipListElement_< SumList<DIM, TValue, SkipSumList<TSpec> > const >
 {
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > const Type;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > const Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -594,18 +594,18 @@ struct SumlistSkipListElement_< SumList<DIM, TValue, SkipSumList<TSpec> > const
 template <typename TSumList>
 struct SumListSkiplistMinilist_
 {//dummy implementation
-	typedef SumList<1, int, MiniSumList< > > Type;
+    typedef SumList<1, int, MiniSumList< > > Type;
 };
 
 template <unsigned int DIM, typename TValue, typename TSpec>
 struct SumListSkiplistMinilist_< SumList<DIM, TValue, SkipSumList<TSpec> > >
 {
-	typedef SumList<DIM, TValue, MiniSumList< > > Type;
+    typedef SumList<DIM, TValue, MiniSumList< > > Type;
 };
 template <unsigned int DIM, typename TValue, typename TSpec>
 struct SumListSkiplistMinilist_< SumList<DIM, TValue, SkipSumList<TSpec> > const >
 {
-	typedef SumList<DIM, TValue, MiniSumList< > > const Type;
+    typedef SumList<DIM, TValue, MiniSumList< > > const Type;
 };
 */
 
@@ -617,48 +617,48 @@ template <typename TSumList>
 class Iter<TSumList, SkipSumListIterator>
 {
 public:
-	typedef typename Value<TSumList>::Type TValue;
-	typedef SumList<DIMENSION<TSumList>::VALUE, TValue, MiniSumList< > > TMiniSumList_;
-	typedef typename CopyConst_<TSumList, TMiniSumList_>::Type TMiniSumList;
-//	typedef typename SumListSkiplistMinilist_<TSumList>::Type TMiniSumList;
-	typedef typename Iterator<TMiniSumList>::Type TMiniSumListIterator;
-	typedef typename SumlistSkipListElement_<TSumList>::Type TElement;
-
-	TSumList * container;
-	mutable TMiniSumListIterator iter;
-	mutable TElement * element;
-
-	Iter()
-	{
-	}
-	Iter(TSumList & cont)
-		: container(& cont)
-	{
-		goBegin(*this);
-	}
-	Iter(TSumList & cont, GoEnd)
-		: container(& cont)
-		, element(0)
-	{
-	}
-	Iter(Iter const & other)
-		: container(other.container)
-		, iter(other.iter)
-		, element(other.element)
-	{
-	}
-
-	~Iter()
-	{
-	}
-	inline Iter const & 
-	operator = (Iter const & other)
-	{
-		container = other.container;
-		iter = other.iter;
-		element = other.element;
-		return *this;
-	}
+    typedef typename Value<TSumList>::Type TValue;
+    typedef SumList<DIMENSION<TSumList>::VALUE, TValue, MiniSumList< > > TMiniSumList_;
+    typedef typename CopyConst_<TSumList, TMiniSumList_>::Type TMiniSumList;
+//    typedef typename SumListSkiplistMinilist_<TSumList>::Type TMiniSumList;
+    typedef typename Iterator<TMiniSumList>::Type TMiniSumListIterator;
+    typedef typename SumlistSkipListElement_<TSumList>::Type TElement;
+
+    TSumList * container;
+    mutable TMiniSumListIterator iter;
+    mutable TElement * element;
+
+    Iter()
+    {
+    }
+    Iter(TSumList & cont)
+        : container(& cont)
+    {
+        goBegin(*this);
+    }
+    Iter(TSumList & cont, GoEnd)
+        : container(& cont)
+        , element(0)
+    {
+    }
+    Iter(Iter const & other)
+        : container(other.container)
+        , iter(other.iter)
+        , element(other.element)
+    {
+    }
+
+    ~Iter()
+    {
+    }
+    inline Iter const &
+    operator = (Iter const & other)
+    {
+        container = other.container;
+        iter = other.iter;
+        element = other.element;
+        return *this;
+    }
 };
 
 
@@ -667,14 +667,14 @@ class Iter<TSumList, SkipSumListIterator>
 template <unsigned int DIM, typename TValue, typename TSpec, typename TIteratorSpec>
 struct Iterator< SumList<DIM, TValue, SkipSumList<TSpec> >, TIteratorSpec>
 {
-	typedef SumList<DIM, TValue, SkipSumList<TSpec> > TSumList_;
-	typedef Iter<TSumList_, SkipSumListIterator> Type;
+    typedef SumList<DIM, TValue, SkipSumList<TSpec> > TSumList_;
+    typedef Iter<TSumList_, SkipSumListIterator> Type;
 };
 template <unsigned int DIM, typename TValue, typename TSpec, typename TIteratorSpec>
 struct Iterator< SumList<DIM, TValue, SkipSumList<TSpec> > const, TIteratorSpec>
 {
-	typedef SumList<DIM, TValue, SkipSumList<TSpec> > const TSumList_;
-	typedef Iter<TSumList_, SkipSumListIterator> Type;
+    typedef SumList<DIM, TValue, SkipSumList<TSpec> > const TSumList_;
+    typedef Iter<TSumList_, SkipSumListIterator> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -683,17 +683,17 @@ template <typename TSumList>
 inline void
 goNext(Iter<TSumList, SkipSumListIterator> & it)
 {
-	goNext(it.iter);
-	if (atEnd(it.iter))
-	{
-		it.element = it.element->data_next[0].data_element;
-		if (it.element)
-		{
-			it.iter.container_ = & it.element->minilist;
-			it.iter.next_ = it.iter.here_ = it.element->minilist.data_;
-			scanValues(it.iter.next_, it.iter.values_);
-		}
-	}
+    goNext(it.iter);
+    if (atEnd(it.iter))
+    {
+        it.element = it.element->data_next[0].data_element;
+        if (it.element)
+        {
+            it.iter.container_ = & it.element->minilist;
+            it.iter.next_ = it.iter.here_ = it.element->minilist.data_;
+            scanValues(it.iter.next_, it.iter.values_);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -703,7 +703,7 @@ template <typename TSumList>
 inline void
 goPrevious(Iter<TSumList, SkipSumListIterator> & it)
 {
-	searchSumList(it, getSum(it, 0) - 1, 0);
+    searchSumList(it, getSum(it, 0) - 1, 0);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -712,8 +712,8 @@ template <typename TSumList>
 inline void
 goBegin(Iter<TSumList, SkipSumListIterator> & it)
 {
-	it.element = & (it.container->map.data_border);
-	it.iter = begin(it.element->minilist);
+    it.element = & (it.container->map.data_border);
+    it.iter = begin(it.element->minilist);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -722,29 +722,29 @@ template <typename TSumList>
 inline void
 goEnd(Iter<TSumList, SkipSumListIterator> & it)
 {
-	it.element = 0;
-	it.iter.sums_ = it.container->sum;
+    it.element = 0;
+    it.iter.sums_ = it.container->sum;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <unsigned int DIM, typename TValue, typename TSpec>
-inline void 
+inline void
 goBeforeEnd(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it)
 {
-	typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
+    typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
 
-	//find end of skip list
-	TPath path;
-	_skipsumlistFind(it.container->map, GoEnd(), 0, path);
+    //find end of skip list
+    TPath path;
+    _skipsumlistFind(it.container->map, GoEnd(), 0, path);
 
-	it.element = path.data_elements[0];
+    it.element = path.data_elements[0];
 
-	//set minilist iterator to end of last minilist
-	it.iter.container_ = & it.element->minilist;
-	goBeforeEnd(it.iter);
+    //set minilist iterator to end of last minilist
+    it.iter.container_ = & it.element->minilist;
+    goBeforeEnd(it.iter);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -753,7 +753,7 @@ template <typename TSumList>
 inline bool
 atBegin(Iter<TSumList, SkipSumListIterator> & it)
 {
-	return (it.iter == begin(it.element->minilist));
+    return (it.iter == begin(it.element->minilist));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -762,7 +762,7 @@ template <typename TSumList>
 inline bool
 atEnd(Iter<TSumList, SkipSumListIterator> & it)
 {
-	return (!it.element);
+    return (!it.element);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -770,16 +770,16 @@ atEnd(Iter<TSumList, SkipSumListIterator> & it)
 template <typename TSumList>
 inline typename Value<TSumList>::Type
 getValue(Iter<TSumList, SkipSumListIterator > & it,
-		 int dim)
+         int dim)
 {
-	return it.iter.values_[dim];
+    return it.iter.values_[dim];
 }
 template <typename TSumList>
 inline typename Value<TSumList>::Type
 getValue(Iter<TSumList, SkipSumListIterator > const & it,
-		 int dim)
+         int dim)
 {
-	return it.iter.values_[dim];
+    return it.iter.values_[dim];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -788,13 +788,13 @@ template <typename TSumList>
 inline typename Values<TSumList>::Type
 getValues(Iter<TSumList, SkipSumListIterator > & it)
 {
-	return it.iter.values_;
+    return it.iter.values_;
 }
 template <typename TSumList>
 inline typename Values<TSumList>::Type
 getValues(Iter<TSumList, SkipSumListIterator > const & it)
 {
-	return it.iter.values_;
+    return it.iter.values_;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -802,16 +802,16 @@ getValues(Iter<TSumList, SkipSumListIterator > const & it)
 template <typename TSumList>
 inline typename Value<TSumList>::Type
 getSum(Iter<TSumList, SkipSumListIterator > & it,
-	   int dim)
+       int dim)
 {
-	return it.iter.sums_[dim];
+    return it.iter.sums_[dim];
 }
 template <typename TSumList>
 inline typename Value<TSumList>::Type
 getSum(Iter<TSumList, SkipSumListIterator > const & it,
-	   int dim)
+       int dim)
 {
-	return it.iter.sums_[dim];
+    return it.iter.sums_[dim];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -819,276 +819,276 @@ getSum(Iter<TSumList, SkipSumListIterator > const & it,
 //path must be a path to it.element
 //path and it are adjusted to the new element if necessary
 template <unsigned int DIM, typename TValue, typename TSpec, typename TPath>
-inline void 
+inline void
 _splitMiniList(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it,
-			   TPath & path)
+               TPath & path)
 {
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef SumListValues<DIM, TValue> TValues;
-
-	//height for new element, adjust path if necessary (if the height of the complete skiplist increases)
-	unsigned char height = _skiplistCreateHeight(* it.container, path);
-
-	//the current element
-	TElement & el1 = *(it.element);
-
-	//create new element
-	TElement & el2 = _skiplistAllocateElement(it.container->map, height); //see map_skiplist.h
-	valueConstruct(& (el2.minilist));
-
-	//move half of the values in el1 to el2
-	splitSumList(el1.minilist, el2.minilist);
-
-	if (!length(el2))
-	{//el1 was not full enough to create a split: remove el2 from skiplist and exit
-	 //(this should not happen, since _splitMiniList is only called it el1 is full)
-		_skiplistDeallocateElement(it.container->map, el2, height);
-		return;
-	}
-
-	//must adjust the iterator "it"?
-	int it_bytepos = it.iter.here_.data_ptr - el1.minilist.data_;
-	bool it_was_moved = (it_bytepos >= el1.minilist.data_size); //true if "it" points to el2
-
-	//insert new element el2 into skiplist
-	for (int i = height; i >= 0; --i)
-	{
-		TElement * predecessor;
-		if (path.data_elements[i] == & el1)
-		{//el2 is linked behind el1
-			predecessor = & el1;
-
-			//adjust values
-			el2.data_next[i].values = predecessor->data_next[i].values;
-			el2.data_next[i].values -= predecessor->minilist.data_sum;
-			predecessor->data_next[i].values = predecessor->minilist.data_sum;
-
-			if (it_was_moved)
-			{//adjust path
-				path.data_elements[i] = & el2;
-				path.sums[i] += predecessor->minilist.data_sum;
-			}
-		}
-		else
-		{//el2 is linked behind another element
-			predecessor = path.data_elements[i];
-
-			//adjust values
-			TValues pred_values = path.sums[0];
-			pred_values -= path.sums[i];
-			pred_values += el1.minilist.data_sum;
-
-			el2.data_next[i].values = predecessor->data_next[i].values;
-			el2.data_next[i].values -= pred_values;
-			predecessor->data_next[i].values = pred_values;
-
-			if (it_was_moved)
-			{//adjust path
-				path.data_elements[i] = & el2;
-				path.sums[i] += pred_values;
-			}
-		}
-
-		//link el2 into skiplist
-		el2.data_next[i].data_element = predecessor->data_next[i].data_element;
-		predecessor->data_next[i].data_element = & el2;
-	}
-
-	//adjust map properties
-	++it.container->map.data_length;
-
-	//adjust it.iter if it was moved
-	if (it_was_moved)
-	{
-		int here_length = it.iter.next_.data_ptr - it.iter.here_.data_ptr; //difference between next_ and here_
-		it.iter.here_.data_ptr = el2.minilist.data_ + it_bytepos - el1.minilist.data_size; //redirect here_
-		it.iter.next_.data_ptr = it.iter.here_.data_ptr + here_length; //redirect next_
-		it.element = & el2;
-		it.iter.container_ = & el2.minilist;
-	}
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef SumListValues<DIM, TValue> TValues;
+
+    //height for new element, adjust path if necessary (if the height of the complete skiplist increases)
+    unsigned char height = _skiplistCreateHeight(* it.container, path);
+
+    //the current element
+    TElement & el1 = *(it.element);
+
+    //create new element
+    TElement & el2 = _skiplistAllocateElement(it.container->map, height); //see map_skiplist.h
+    valueConstruct(& (el2.minilist));
+
+    //move half of the values in el1 to el2
+    splitSumList(el1.minilist, el2.minilist);
+
+    if (!length(el2))
+    {//el1 was not full enough to create a split: remove el2 from skiplist and exit
+     //(this should not happen, since _splitMiniList is only called it el1 is full)
+        _skiplistDeallocateElement(it.container->map, el2, height);
+        return;
+    }
+
+    //must adjust the iterator "it"?
+    int it_bytepos = it.iter.here_.data_ptr - el1.minilist.data_;
+    bool it_was_moved = (it_bytepos >= el1.minilist.data_size); //true if "it" points to el2
+
+    //insert new element el2 into skiplist
+    for (int i = height; i >= 0; --i)
+    {
+        TElement * predecessor;
+        if (path.data_elements[i] == & el1)
+        {//el2 is linked behind el1
+            predecessor = & el1;
+
+            //adjust values
+            el2.data_next[i].values = predecessor->data_next[i].values;
+            el2.data_next[i].values -= predecessor->minilist.data_sum;
+            predecessor->data_next[i].values = predecessor->minilist.data_sum;
+
+            if (it_was_moved)
+            {//adjust path
+                path.data_elements[i] = & el2;
+                path.sums[i] += predecessor->minilist.data_sum;
+            }
+        }
+        else
+        {//el2 is linked behind another element
+            predecessor = path.data_elements[i];
+
+            //adjust values
+            TValues pred_values = path.sums[0];
+            pred_values -= path.sums[i];
+            pred_values += el1.minilist.data_sum;
+
+            el2.data_next[i].values = predecessor->data_next[i].values;
+            el2.data_next[i].values -= pred_values;
+            predecessor->data_next[i].values = pred_values;
+
+            if (it_was_moved)
+            {//adjust path
+                path.data_elements[i] = & el2;
+                path.sums[i] += pred_values;
+            }
+        }
+
+        //link el2 into skiplist
+        el2.data_next[i].data_element = predecessor->data_next[i].data_element;
+        predecessor->data_next[i].data_element = & el2;
+    }
+
+    //adjust map properties
+    ++it.container->map.data_length;
+
+    //adjust it.iter if it was moved
+    if (it_was_moved)
+    {
+        int here_length = it.iter.next_.data_ptr - it.iter.here_.data_ptr; //difference between next_ and here_
+        it.iter.here_.data_ptr = el2.minilist.data_ + it_bytepos - el1.minilist.data_size; //redirect here_
+        it.iter.next_.data_ptr = it.iter.here_.data_ptr + here_length; //redirect next_
+        it.element = & el2;
+        it.iter.container_ = & el2.minilist;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <unsigned int DIM, typename TValue, typename TSpec, typename TValue2>
-inline void 
+inline void
 assignValue(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it,
-			int dim,
-			TValue2 val)
+            int dim,
+            TValue2 val)
 {
-	typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef Pair<TValue, TElement *> TPair;
-
-	TValue val_old = getValue(it, dim);
-
-	TPath path;
-	_skipsumlistFind(it.container->map, TPair(getSum(it, 0), it.element), 0, path);
-
-	if (!assignValue(it.iter, dim, val))
-	{//split
-		_splitMiniList(it, path);
-		assignValue(it.iter, dim, val);
-	}
-
-	//update skiplist path sums
-	for (int i = it.container->map.data_height; i >= 0 ; --i)
-	{
-		if (path.data_elements[i]->data_next[i].data_element == it.element)
-		{// adjust link outgoing from it.element
-			it.element->data_next[i].values[dim] += (val - val_old);
-		}
-		else
-		{// adjust link that jumps over it.element
-			path.data_elements[i]->data_next[i].values[dim] += (val - val_old);
-		}
-	}
-	it.container->sum[dim] += (val - val_old);
+    typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef Pair<TValue, TElement *> TPair;
+
+    TValue val_old = getValue(it, dim);
+
+    TPath path;
+    _skipsumlistFind(it.container->map, TPair(getSum(it, 0), it.element), 0, path);
+
+    if (!assignValue(it.iter, dim, val))
+    {//split
+        _splitMiniList(it, path);
+        assignValue(it.iter, dim, val);
+    }
+
+    //update skiplist path sums
+    for (int i = it.container->map.data_height; i >= 0 ; --i)
+    {
+        if (path.data_elements[i]->data_next[i].data_element == it.element)
+        {// adjust link outgoing from it.element
+            it.element->data_next[i].values[dim] += (val - val_old);
+        }
+        else
+        {// adjust link that jumps over it.element
+            path.data_elements[i]->data_next[i].values[dim] += (val - val_old);
+        }
+    }
+    it.container->sum[dim] += (val - val_old);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <unsigned int DIM, typename TValue, typename TSpec, typename TValues>
-inline void 
+inline void
 insertValues(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it,
-			 TValues const & vals)
+             TValues const & vals)
 {
-	typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef Pair<TValue, TElement *> TPair;
-
-	TPath path;
-	_skipsumlistFind(it.container->map, TPair(getSum(it, 0), it.element), 0, path);
-
-	if (!insertValues(it.iter, vals))
-	{//split
-		_splitMiniList(it, path);
-		insertValues(it.iter, vals);
-	}
-
-	//update skiplist path sums
-	for (int i = it.container->map.data_height; i >= 0 ; --i)
-	{
-		path.data_elements[i]->data_next[i].values += vals;
-	}
-
-	//update sumlist variables
-	it.container->sum += vals;
-	++it.container->length;
+    typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef Pair<TValue, TElement *> TPair;
+
+    TPath path;
+    _skipsumlistFind(it.container->map, TPair(getSum(it, 0), it.element), 0, path);
+
+    if (!insertValues(it.iter, vals))
+    {//split
+        _splitMiniList(it, path);
+        insertValues(it.iter, vals);
+    }
+
+    //update skiplist path sums
+    for (int i = it.container->map.data_height; i >= 0 ; --i)
+    {
+        path.data_elements[i]->data_next[i].values += vals;
+    }
+
+    //update sumlist variables
+    it.container->sum += vals;
+    ++it.container->length;
 }
 template <unsigned int DIM, typename TValue, typename TSpec>
-inline void 
+inline void
 insertValues(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it,
-			 TValue * p_vals)
+             TValue * p_vals)
 {
-	SumListValues<DIM, TValue > vals(p_vals);
-	insertValues(it, vals);
+    SumListValues<DIM, TValue > vals(p_vals);
+    insertValues(it, vals);
 }
 template <unsigned int DIM, typename TValue, typename TSpec>
-inline void 
+inline void
 insertValues(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it,
-			 TValue const * p_vals)
+             TValue const * p_vals)
 {
-	SumListValues<DIM, TValue > vals(p_vals);
-	insertValues(it, vals);
+    SumListValues<DIM, TValue > vals(p_vals);
+    insertValues(it, vals);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <unsigned int DIM, typename TValue, typename TSpec>
-inline void 
+inline void
 removeValues(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it)
 {
-	typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
-	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-	typedef Pair<TValue, TElement *> TPair;
-
-	TPath path;
-	_skipsumlistFind(it.container->map, TPair(getSum(it, 0), it.element), 0, path);
-
-	//update skiplist path sums
-	for (int i = it.container->map.data_height; i >= 0 ; --i)
-	{
-		path.data_elements[i]->data_next[i].values -= it.iter.values_;
-	}
-
-	//update sumlist variables
-	it.container->sum -= it.iter.values_;
-	--it.container->length;
-
-	//remove values
-	removeValues(it.iter);
-		
-	if (atEnd(it.iter))
-	{//move to next element
-		it.element = it.element->data_next[0].data_element;
-		if (it.element)
-		{
-			it.iter.container_ = & it.element->minilist;
-			it.iter.here_ = it.iter.next_ = it.iter.container_->data_;
-			scanValues(it.iter.next_, it.iter.values_);
-		}
-	}
+    typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
+    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+    typedef Pair<TValue, TElement *> TPair;
+
+    TPath path;
+    _skipsumlistFind(it.container->map, TPair(getSum(it, 0), it.element), 0, path);
+
+    //update skiplist path sums
+    for (int i = it.container->map.data_height; i >= 0 ; --i)
+    {
+        path.data_elements[i]->data_next[i].values -= it.iter.values_;
+    }
+
+    //update sumlist variables
+    it.container->sum -= it.iter.values_;
+    --it.container->length;
+
+    //remove values
+    removeValues(it.iter);
+
+    if (atEnd(it.iter))
+    {//move to next element
+        it.element = it.element->data_next[0].data_element;
+        if (it.element)
+        {
+            it.iter.container_ = & it.element->minilist;
+            it.iter.here_ = it.iter.next_ = it.iter.container_->data_;
+            scanValues(it.iter.next_, it.iter.values_);
+        }
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 //template <unsigned int DIM, typename TValue, typename TSpec, typename TValue2>
-//inline void 
+//inline void
 //searchSumList(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it,
-//			  TValue2 const & val,
-//			  int dim)
+//              TValue2 const & val,
+//              int dim)
 template <unsigned int DIM, typename TValue, typename TSpec, typename TSumList, typename TValue2>
-inline void 
+inline void
 _searchSumlistSkip(Iter<TSumList, SkipSumListIterator > & it,
-					TValue2 const & val,
-					int dim)
+                    TValue2 const & val,
+                    int dim)
 {
-	typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
-//	typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
-//	typedef Pair<TValue, TElement *> TPair;
-//	typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
+    typedef SkiplistPath<TValue, Skipsumlist_<DIM, TSpec> > TPath;
+//    typedef SkiplistElement<TValue, Skipsumlist_<DIM, TSpec> > TElement;
+//    typedef Pair<TValue, TElement *> TPair;
+//    typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
 
-	TPath path;
+    TPath path;
 
   // The assumpiton here is that val is signed and getSum() fits into it.
-	if (val >= static_cast<TValue2>(getSum(*it.container, dim)))
-	{
-		goEnd(it);
-		return;
-	}
-
-	_skipsumlistFind(it.container->map, val, dim, path);
-
-	it.element = path.data_elements[0];
-	it.iter.container_ = & it.element->minilist;
-	searchSumList(it.iter, val - path.sums[0][dim], dim);
-	it.iter.sums_ += path.sums[0];
+    if (val >= static_cast<TValue2>(getSum(*it.container, dim)))
+    {
+        goEnd(it);
+        return;
+    }
+
+    _skipsumlistFind(it.container->map, val, dim, path);
+
+    it.element = path.data_elements[0];
+    it.iter.container_ = & it.element->minilist;
+    searchSumList(it.iter, val - path.sums[0][dim], dim);
+    it.iter.sums_ += path.sums[0];
 }
 
 template <unsigned int DIM, typename TValue, typename TSpec, typename TValue2>
-inline void 
+inline void
 searchSumList(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >, SkipSumListIterator > & it,
-			  TValue2 const & val,
-			  int dim)
+              TValue2 const & val,
+              int dim)
 {
-	_searchSumlistSkip<DIM, TValue, TSpec>(it, val, dim);
+    _searchSumlistSkip<DIM, TValue, TSpec>(it, val, dim);
 }
 template <unsigned int DIM, typename TValue, typename TSpec, typename TValue2>
-inline void 
+inline void
 searchSumList(Iter<SumList<DIM, TValue, SkipSumList<TSpec> > const, SkipSumListIterator > & it,
-			  TValue2 const & val,
-			  int dim)
+              TValue2 const & val,
+              int dim)
 {
-	_searchSumlistSkip<DIM, TValue, TSpec>(it, val, dim);
+    _searchSumlistSkip<DIM, TValue, TSpec>(it, val, dim);
 }
 //template <unsigned int DIM, typename TValue, typename TSpec, typename TValue2>
-//inline void 
+//inline void
 //searchSumList(Iter<SumList<DIM, TValue, SkipSumList<TSpec> > const, SkipSumListIterator > & it,
-//			  TValue2 const & val,
-//			  int dim)
+//              TValue2 const & val,
+//              int dim)
 //{
-//	_searchSumlistSkip<DIM, TValue, TSpec>(it, val, dim);
+//    _searchSumlistSkip<DIM, TValue, TSpec>(it, val, dim);
 //}
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1096,17 +1096,17 @@ searchSumList(Iter<SumList<DIM, TValue, SkipSumList<TSpec> > const, SkipSumListI
 template <typename TSumList, typename TSumList2>
 inline bool
 operator == (Iter<TSumList, SkipSumListIterator> const & left,
-			 Iter<TSumList2, SkipSumListIterator> const & right)
+             Iter<TSumList2, SkipSumListIterator> const & right)
 {
-	return ((left.element == 0) && (right.element == 0)) || ((left.element == right.element) && (left.iter == right.iter));
+    return ((left.element == 0) && (right.element == 0)) || ((left.element == right.element) && (left.iter == right.iter));
 }
 
 template <typename TSumList, typename TSumList2>
 inline bool
 operator != (Iter<TSumList, SkipSumListIterator> const & left,
-			 Iter<TSumList2, SkipSumListIterator> const & right)
+             Iter<TSumList2, SkipSumListIterator> const & right)
 {
-	return !(left == right);
+    return !(left == right);
 }
 
 
diff --git a/seqan/math.h b/seqan/math.h
new file mode 100644
index 0000000..390e8a4
--- /dev/null
+++ b/seqan/math.h
@@ -0,0 +1,55 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// This is the facade header for the math module.
+// ==========================================================================
+
+#ifndef SEQAN_MATH_H_
+#define SEQAN_MATH_H_
+
+// ==========================================================================
+// Prerequisites
+// ==========================================================================
+
+#include <seqan/basic.h>
+#include <limits>
+
+// ==========================================================================
+// Math Data Structures
+// ==========================================================================
+
+#include "math/math_common_factor.h"
+#include "math/math_operators.h"
+#include "math/math_rational.h"
+
+#endif  // SEQAN_MATH_H_
diff --git a/seqan/math/math_common_factor.h b/seqan/math/math_common_factor.h
new file mode 100644
index 0000000..80243a6
--- /dev/null
+++ b/seqan/math/math_common_factor.h
@@ -0,0 +1,524 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// A data type to represent rational numbers.
+// Taken from the Rational Number Library in Boost version 1.47 adapted
+// to SeqAn's code conventions.
+// ==========================================================================
+
+#ifndef SEQAN_MATH_COMMON_FACTOR_H_
+#define SEQAN_MATH_COMMON_FACTOR_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template < typename IntegerType >
+inline IntegerType
+greatestCommonDivisor( IntegerType const &a, IntegerType const &b );
+
+template < typename IntegerType >
+inline IntegerType
+leastCommonMultiple( IntegerType const &a, IntegerType const &b );
+
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template < typename IntegerType >
+class GcdEvaluator
+{
+public:
+    // Types
+    typedef IntegerType  resultType, firstArgumentType, secondArgumentType;
+
+    // Function object interface
+    resultType  operator ()( firstArgumentType const &a,
+     secondArgumentType const &b ) const;
+
+};  // boost::math::GcdEvaluator
+
+
+//  Least common multiple evaluator class declaration  -----------------------//
+
+template < typename IntegerType >
+class LcmEvaluator
+{
+public:
+    // Types
+    typedef IntegerType  resultType, firstArgumentType, secondArgumentType;
+
+    // Function object interface
+    resultType  operator ()( firstArgumentType const &a,
+     secondArgumentType const &b ) const;
+
+};  // boost::math::LcmEvaluator
+
+//  Implementation details  --------------------------------------------------//
+
+namespace detail
+{
+    // Greatest common divisor for rings (including unsigned integers)
+    template < typename RingType >
+    RingType
+    gcdEuclidean
+    (
+        RingType a,
+        RingType b
+    )
+    {
+        // Avoid repeated construction
+        RingType const  zero = static_cast<RingType>( 0 );
+
+        // Reduce by GCD-remainder property [GCD(a,b) == GCD(b,a MOD b)]
+        while ( true )
+        {
+            if ( a == zero )
+                return b;
+            b %= a;
+
+            if ( b == zero )
+                return a;
+            a %= b;
+        }
+    }
+
+    // Greatest common divisor for (signed) integers
+    template < typename IntegerType >
+    inline
+    IntegerType
+    gcdInteger
+    (
+        IntegerType const &  a,
+        IntegerType const &  b
+    )
+    {
+        // Avoid repeated construction
+        IntegerType const  zero = static_cast<IntegerType>( 0 );
+        IntegerType const  result = gcdEuclidean( a, b );
+
+        return ( result < zero ) ? static_cast<IntegerType>(-result) : result;
+    }
+
+    // Greatest common divisor for unsigned binary integers
+    template < typename BuiltInUnsigned >
+    BuiltInUnsigned
+    gcd_binary
+    (
+        BuiltInUnsigned  u,
+        BuiltInUnsigned  v
+    )
+    {
+        if ( u && v )
+        {
+            // Shift out common factors of 2
+            unsigned  shifts = 0;
+
+            while ( !(u & 1u) && !(v & 1u) )
+            {
+                ++shifts;
+                u >>= 1;
+                v >>= 1;
+            }
+
+            // Start with the still-even one, if any
+            BuiltInUnsigned  r[] = { u, v };
+            unsigned         which = static_cast<bool>( u & 1u );
+
+            // Whittle down the values via their differences
+            do
+            {
+                // Remove factors of two from the even one
+                while ( !(r[ which ] & 1u) )
+                {
+                    r[ which ] >>= 1;
+                }
+
+                // Replace the larger of the two with their difference
+                if ( r[!which] > r[which] )
+                {
+                    which ^= 1u;
+                }
+
+                r[ which ] -= r[ !which ];
+            }
+            while ( r[which] );
+
+            // Shift-in the common factor of 2 to the residues' GCD
+            return r[ !which ] << shifts;
+        }
+        else
+        {
+            // At least one input is zero, return the other
+            // (adding since zero is the additive identity)
+            // or zero if both are zero.
+            return u + v;
+        }
+    }
+
+    // Least common multiple for rings (including unsigned integers)
+    template < typename RingType >
+    inline
+    RingType
+    lcmEuclidean
+    (
+        RingType const &  a,
+        RingType const &  b
+    )
+    {
+        RingType const  zero = static_cast<RingType>( 0 );
+        RingType const  temp = gcdEuclidean( a, b );
+
+        return ( temp != zero ) ? ( a / temp * b ) : zero;
+    }
+
+    // Least common multiple for (signed) integers
+    template < typename IntegerType >
+    inline
+    IntegerType
+    lcmInteger
+    (
+        IntegerType const &  a,
+        IntegerType const &  b
+    )
+    {
+        // Avoid repeated construction
+        IntegerType const  zero = static_cast<IntegerType>( 0 );
+        IntegerType const  result = lcmEuclidean( a, b );
+
+        return ( result < zero ) ? static_cast<IntegerType>(-result) : result;
+    }
+
+    // Function objects to find the best way of computing GCD or LCM
+#ifndef BOOST_NO_LIMITS_COMPILE_TIME_CONSTANTS
+#ifndef BOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION
+    template < typename T, bool IsSpecialized, bool IsSigned >
+    struct GcdOptimalEvaluatorHelper
+    {
+        T  operator ()( T const &a, T const &b )
+        {
+            return gcdEuclidean( a, b );
+        }
+    };
+
+    template < typename T >
+    struct GcdOptimalEvaluatorHelper< T, true, true >
+    {
+        T  operator ()( T const &a, T const &b )
+        {
+            return gcdInteger( a, b );
+        }
+    };
+#else
+    template < bool IsSpecialized, bool IsSigned >
+    struct GcdOptimalEvaluatorHelper2
+    {
+        template < typename T >
+        struct Helper
+        {
+            T  operator ()( T const &a, T const &b )
+            {
+                return gcdEuclidean( a, b );
+            }
+        };
+    };
+
+    template < >
+    struct GcdOptimalEvaluatorHelper2< true, true >
+    {
+        template < typename T >
+        struct Helper
+        {
+            T  operator ()( T const &a, T const &b )
+            {
+                return gcdInteger( a, b );
+            }
+        };
+    };
+
+    template < typename T, bool IsSpecialized, bool IsSigned >
+    struct GcdOptimalEvaluatorHelper
+        : GcdOptimalEvaluatorHelper2<IsSpecialized, IsSigned>
+           ::BOOST_NESTED_TEMPLATE helper<T>
+    {
+    };
+#endif
+
+    template < typename T >
+    struct GcdOptimalEvaluator
+    {
+        T  operator ()( T const &a, T const &b )
+        {
+            typedef std::numeric_limits<T>  limitsType;
+
+            typedef GcdOptimalEvaluatorHelper<T,
+             limitsType::is_specialized, limitsType::is_signed>  helperType;
+
+            helperType  solver;
+
+            return solver( a, b );
+        }
+    };
+#else // BOOST_NO_LIMITS_COMPILE_TIME_CONSTANTS
+    template < typename T >
+    struct GcdOptimalEvaluator
+    {
+        T  operator ()( T const &a, T const &b )
+        {
+            return gcdInteger( a, b );
+        }
+    };
+#endif
+
+    // Specialize for the built-in integers
+#define BOOST_PRIVATE_GCD_UF( Ut )                  \
+    template < >  struct GcdOptimalEvaluator<Ut>  \
+    {  Ut  operator ()( Ut a, Ut b ) const  { return gcd_binary( a, b ); }  }
+
+    BOOST_PRIVATE_GCD_UF( unsigned char );
+    BOOST_PRIVATE_GCD_UF( unsigned short );
+    BOOST_PRIVATE_GCD_UF( unsigned );
+    BOOST_PRIVATE_GCD_UF( unsigned long );
+
+#ifdef BOOST_HAS_LONG_LONG
+    BOOST_PRIVATE_GCD_UF( boost::ulong_longType );
+#elif defined(BOOST_HAS_MS_INT64)
+    BOOST_PRIVATE_GCD_UF( unsigned __int64 );
+#endif
+
+#if CHAR_MIN == 0
+    BOOST_PRIVATE_GCD_UF( char ); // char is unsigned
+#endif
+
+#undef BOOST_PRIVATE_GCD_UF
+
+#define BOOST_PRIVATE_GCD_SF( St, Ut )                            \
+    template < >  struct GcdOptimalEvaluator<St>                \
+    {  St  operator ()( St a, St b ) const  { Ut const  a_abs =   \
+    static_cast<Ut>( a < 0 ? -a : +a ), b_abs = static_cast<Ut>(  \
+    b < 0 ? -b : +b ); return static_cast<St>(                    \
+    GcdOptimalEvaluator<Ut>()(a_abs, b_abs) ); }  }
+
+    BOOST_PRIVATE_GCD_SF( signed char, unsigned char );
+    BOOST_PRIVATE_GCD_SF( short, unsigned short );
+    BOOST_PRIVATE_GCD_SF( int, unsigned );
+    BOOST_PRIVATE_GCD_SF( long, unsigned long );
+
+#if CHAR_MIN < 0
+    BOOST_PRIVATE_GCD_SF( char, unsigned char ); // char is signed
+#endif
+
+#ifdef BOOST_HAS_LONG_LONG
+    BOOST_PRIVATE_GCD_SF( boost::long_longType, boost::ulong_longType );
+#elif defined(BOOST_HAS_MS_INT64)
+    BOOST_PRIVATE_GCD_SF( __int64, unsigned __int64 );
+#endif
+
+#undef BOOST_PRIVATE_GCD_SF
+
+#ifndef BOOST_NO_LIMITS_COMPILE_TIME_CONSTANTS
+#ifndef BOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION
+    template < typename T, bool IsSpecialized, bool IsSigned >
+    struct LcmOptimalEvaluatorHelper
+    {
+        T  operator ()( T const &a, T const &b )
+        {
+            return lcmEuclidean( a, b );
+        }
+    };
+
+    template < typename T >
+    struct LcmOptimalEvaluatorHelper< T, true, true >
+    {
+        T  operator ()( T const &a, T const &b )
+        {
+            return lcmInteger( a, b );
+        }
+    };
+#else
+    template < bool IsSpecialized, bool IsSigned >
+    struct LcmOptimalEvaluatorHelper2
+    {
+        template < typename T >
+        struct Helper
+        {
+            T  operator ()( T const &a, T const &b )
+            {
+                return lcmEuclidean( a, b );
+            }
+        };
+    };
+
+    template < >
+    struct LcmOptimalEvaluatorHelper2< true, true >
+    {
+        template < typename T >
+        struct Helper
+        {
+            T  operator ()( T const &a, T const &b )
+            {
+                return lcmInteger( a, b );
+            }
+        };
+    };
+
+    template < typename T, bool IsSpecialized, bool IsSigned >
+    struct LcmOptimalEvaluatorHelper
+        : lcmOptimalEvaluatorHelper2<IsSpecialized, IsSigned>
+           ::BOOST_NESTED_TEMPLATE helper<T>
+    {
+    };
+#endif
+
+    template < typename T >
+    struct LcmOptimalEvaluator
+    {
+        T  operator ()( T const &a, T const &b )
+        {
+            typedef std::numeric_limits<T>  limitsType;
+
+            typedef LcmOptimalEvaluatorHelper<T,
+             limitsType::is_specialized, limitsType::is_signed>  helperType;
+
+            helperType  solver;
+
+            return solver( a, b );
+        }
+    };
+#else // BOOST_NO_LIMITS_COMPILE_TIME_CONSTANTS
+    template < typename T >
+    struct LcmOptimalEvaluator
+    {
+        T  operator ()( T const &a, T const &b )
+        {
+            return lcmInteger( a, b );
+        }
+    };
+#endif
+
+    // Functions to find the GCD or LCM in the best way
+    template < typename T >
+    inline
+    T
+    gcdOptimal
+    (
+        T const &  a,
+        T const &  b
+    )
+    {
+        GcdOptimalEvaluator<T>  solver;
+
+        return solver( a, b );
+    }
+
+    template < typename T >
+    inline
+    T
+    lcmOptimal
+    (
+        T const &  a,
+        T const &  b
+    )
+    {
+        LcmOptimalEvaluator<T>  solver;
+
+        return solver( a, b );
+    }
+
+}  // namespace detail
+
+
+//  Greatest common divisor evaluator member function definition  ------------//
+
+template < typename IntegerType >
+inline
+typename GcdEvaluator<IntegerType>::resultType
+GcdEvaluator<IntegerType>::operator ()
+(
+    firstArgumentType const &   a,
+    secondArgumentType const &  b
+) const
+{
+    return detail::gcdOptimal( a, b );
+}
+
+
+//  Least common multiple evaluator member function definition  --------------//
+
+template < typename IntegerType >
+inline
+typename LcmEvaluator<IntegerType>::resultType
+LcmEvaluator<IntegerType>::operator ()
+(
+    firstArgumentType const &   a,
+    secondArgumentType const &  b
+) const
+{
+    return detail::lcmOptimal( a, b );
+}
+
+
+//  Greatest common divisor and least common multiple function definitions  --//
+
+template < typename IntegerType >
+inline IntegerType
+greatestCommonDivisor
+(
+    IntegerType const &  a,
+    IntegerType const &  b
+)
+{
+    GcdEvaluator<IntegerType>  solver;
+
+    return solver( a, b );
+}
+
+template < typename IntegerType >
+inline IntegerType
+leastCommonMultiple
+(
+    IntegerType const &  a,
+    IntegerType const &  b
+)
+{
+    LcmEvaluator<IntegerType>  solver;
+
+    return solver( a, b );
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_MATH_COMMON_FACTOR_H_
diff --git a/seqan/math/math_operators.h b/seqan/math/math_operators.h
new file mode 100644
index 0000000..db57a16
--- /dev/null
+++ b/seqan/math/math_operators.h
@@ -0,0 +1,911 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Superclasses to extend a class by standard operators that make use of a
+// minimal set of basic operators.
+// Taken from the Math Library in Boost version 1.47.
+// ==========================================================================
+
+#ifndef SEQAN_MATH_OPERATORS_H_
+#define SEQAN_MATH_OPERATORS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+namespace detail
+{
+
+    template <typename T> class empty_base {};
+
+} // namespace detail
+
+// In this section we supply the xxxx1 and xxxx2 forms of the operator
+// templates, which are explicitly targeted at the 1-type-argument and
+// 2-type-argument operator forms, respectively. Some compilers get confused
+// when inline friend functions are overloaded in namespaces other than the
+// global namespace. When SEQAN_NO_OPERATORS_IN_NAMESPACE is defined, all of
+// these templates must go in the global namespace.
+
+//  Basic operator classes (contributed by Dave Abrahams) ------------------//
+
+//  Note that friend functions defined in a class are implicitly inline.
+//  See the C++ std, 11.4 [class.friend] paragraph 5
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct less_than_comparable2 : B
+{
+     friend bool operator<=(const T& x, const U& y) { return !static_cast<bool>(x > y); }
+     friend bool operator>=(const T& x, const U& y) { return !static_cast<bool>(x < y); }
+     friend bool operator>(const U& x, const T& y)  { return y < x; }
+     friend bool operator<(const U& x, const T& y)  { return y > x; }
+     friend bool operator<=(const U& x, const T& y) { return !static_cast<bool>(y < x); }
+     friend bool operator>=(const U& x, const T& y) { return !static_cast<bool>(y > x); }
+};
+
+template <class T, class B = detail::empty_base<T> >
+struct less_than_comparable1 : B
+{
+     friend bool operator>(const T& x, const T& y)  { return y < x; }
+     friend bool operator<=(const T& x, const T& y) { return !static_cast<bool>(y < x); }
+     friend bool operator>=(const T& x, const T& y) { return !static_cast<bool>(x < y); }
+};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct equality_comparable2 : B
+{
+     friend bool operator==(const U& y, const T& x) { return x == y; }
+     friend bool operator!=(const U& y, const T& x) { return !static_cast<bool>(x == y); }
+     friend bool operator!=(const T& y, const U& x) { return !static_cast<bool>(y == x); }
+};
+
+template <class T, class B = detail::empty_base<T> >
+struct equality_comparable1 : B
+{
+     friend bool operator!=(const T& x, const T& y) { return !static_cast<bool>(x == y); }
+};
+
+// A macro which produces "name_2left" from "name".
+#define SEQAN_OPERATOR2_LEFT(name) name##2##_##left
+
+//  NRVO-friendly implementation (contributed by Daniel Frey) ---------------//
+
+#if defined(SEQAN_HAS_NRVO) || defined(SEQAN_FORCE_SYMMETRIC_OPERATORS)
+
+// This is the optimal implementation for ISO/ANSI C++,
+// but it requires the compiler to implement the NRVO.
+// If the compiler has no NRVO, this is the best symmetric
+// implementation available.
+
+#define SEQAN_BINARY_OPERATOR_COMMUTATIVE( NAME, OP )                         \
+template <class T, class U, class B = detail::empty_base<T> >        \
+struct NAME##2 : B                                                            \
+{                                                                             \
+  friend T operator OP( const T& lhs, const U& rhs )                          \
+    { T nrv( lhs ); nrv OP##= rhs; return nrv; }                              \
+  friend T operator OP( const U& lhs, const T& rhs )                          \
+    { T nrv( rhs ); nrv OP##= lhs; return nrv; }                              \
+};                                                                            \
+                                                                              \
+template <class T, class B = detail::empty_base<T> >                 \
+struct NAME##1 : B                                                            \
+{                                                                             \
+  friend T operator OP( const T& lhs, const T& rhs )                          \
+    { T nrv( lhs ); nrv OP##= rhs; return nrv; }                              \
+};
+
+#define SEQAN_BINARY_OPERATOR_NON_COMMUTATIVE( NAME, OP )               \
+template <class T, class U, class B = detail::empty_base<T> >  \
+struct NAME##2 : B                                                      \
+{                                                                       \
+  friend T operator OP( const T& lhs, const U& rhs )                    \
+    { T nrv( lhs ); nrv OP##= rhs; return nrv; }                        \
+};                                                                      \
+                                                                        \
+template <class T, class U, class B = detail::empty_base<T> >  \
+struct SEQAN_OPERATOR2_LEFT(NAME) : B                                   \
+{                                                                       \
+  friend T operator OP( const U& lhs, const T& rhs )                    \
+    { T nrv( lhs ); nrv OP##= rhs; return nrv; }                        \
+};                                                                      \
+                                                                        \
+template <class T, class B = detail::empty_base<T> >           \
+struct NAME##1 : B                                                      \
+{                                                                       \
+  friend T operator OP( const T& lhs, const T& rhs )                    \
+    { T nrv( lhs ); nrv OP##= rhs; return nrv; }                        \
+};
+
+#else // defined(SEQAN_HAS_NRVO) || defined(SEQAN_FORCE_SYMMETRIC_OPERATORS)
+
+// For compilers without NRVO the following code is optimal, but not
+// symmetric!  Note that the implementation of
+// SEQAN_OPERATOR2_LEFT(NAME) only looks cool, but doesn't provide
+// optimization opportunities to the compiler :)
+
+#define SEQAN_BINARY_OPERATOR_COMMUTATIVE( NAME, OP )                   \
+template <class T, class U, class B = detail::empty_base<T> >  \
+struct NAME##2 : B                                                      \
+{                                                                       \
+  friend T operator OP( T lhs, const U& rhs ) { return lhs OP##= rhs; } \
+  friend T operator OP( const U& lhs, T rhs ) { return rhs OP##= lhs; } \
+};                                                                      \
+                                                                        \
+template <class T, class B = detail::empty_base<T> >           \
+struct NAME##1 : B                                                      \
+{                                                                       \
+  friend T operator OP( T lhs, const T& rhs ) { return lhs OP##= rhs; } \
+};
+
+#define SEQAN_BINARY_OPERATOR_NON_COMMUTATIVE( NAME, OP )               \
+template <class T, class U, class B = detail::empty_base<T> >  \
+struct NAME##2 : B                                                      \
+{                                                                       \
+  friend T operator OP( T lhs, const U& rhs ) { return lhs OP##= rhs; } \
+};                                                                      \
+                                                                        \
+template <class T, class U, class B = detail::empty_base<T> >  \
+struct SEQAN_OPERATOR2_LEFT(NAME) : B                                   \
+{                                                                       \
+  friend T operator OP( const U& lhs, const T& rhs )                    \
+    { return T( lhs ) OP##= rhs; }                                      \
+};                                                                      \
+                                                                        \
+template <class T, class B = detail::empty_base<T> >           \
+struct NAME##1 : B                                                      \
+{                                                                       \
+  friend T operator OP( T lhs, const T& rhs ) { return lhs OP##= rhs; } \
+};
+
+#endif // defined(SEQAN_HAS_NRVO) || defined(SEQAN_FORCE_SYMMETRIC_OPERATORS)
+
+SEQAN_BINARY_OPERATOR_COMMUTATIVE( multipliable, * )
+SEQAN_BINARY_OPERATOR_COMMUTATIVE( addable, + )
+SEQAN_BINARY_OPERATOR_NON_COMMUTATIVE( subtractable, - )
+SEQAN_BINARY_OPERATOR_NON_COMMUTATIVE( dividable, / )
+SEQAN_BINARY_OPERATOR_NON_COMMUTATIVE( modable, % )
+SEQAN_BINARY_OPERATOR_COMMUTATIVE( xorable, ^ )
+SEQAN_BINARY_OPERATOR_COMMUTATIVE( andable, & )
+SEQAN_BINARY_OPERATOR_COMMUTATIVE( orable, | )
+
+#undef SEQAN_BINARY_OPERATOR_COMMUTATIVE
+#undef SEQAN_BINARY_OPERATOR_NON_COMMUTATIVE
+#undef SEQAN_OPERATOR2_LEFT
+
+//  incrementable and decrementable contributed by Jeremy Siek
+
+template <class T, class B = detail::empty_base<T> >
+struct incrementable : B
+{
+  friend T operator++(T& x, int)
+  {
+    incrementable_type nrv(x);
+    ++x;
+    return nrv;
+  }
+private: // The use of this typedef works around a Borland bug
+  typedef T incrementable_type;
+};
+
+template <class T, class B = detail::empty_base<T> >
+struct decrementable : B
+{
+  friend T operator--(T& x, int)
+  {
+    decrementable_type nrv(x);
+    --x;
+    return nrv;
+  }
+private: // The use of this typedef works around a Borland bug
+  typedef T decrementable_type;
+};
+
+//  Iterator operator classes (contributed by Jeremy Siek) ------------------//
+
+template <class T, class P, class B = detail::empty_base<T> >
+struct dereferenceable : B
+{
+  P operator->() const
+  {
+    return &*static_cast<const T&>(*this);
+  }
+};
+
+template <class T, class I, class R, class B = detail::empty_base<T> >
+struct indexable : B
+{
+  R operator[](I n) const
+  {
+    return *(static_cast<const T&>(*this) + n);
+  }
+};
+
+//  More operator classes (contributed by Daryle Walker) --------------------//
+//  (NRVO-friendly implementation contributed by Daniel Frey) ---------------//
+
+#if defined(SEQAN_HAS_NRVO) || defined(SEQAN_FORCE_SYMMETRIC_OPERATORS)
+
+#define SEQAN_BINARY_OPERATOR( NAME, OP )                                     \
+template <class T, class U, class B = detail::empty_base<T> >        \
+struct NAME##2 : B                                                            \
+{                                                                             \
+  friend T operator OP( const T& lhs, const U& rhs )                          \
+    { T nrv( lhs ); nrv OP##= rhs; return nrv; }                              \
+};                                                                            \
+                                                                              \
+template <class T, class B = detail::empty_base<T> >                 \
+struct NAME##1 : B                                                            \
+{                                                                             \
+  friend T operator OP( const T& lhs, const T& rhs )                          \
+    { T nrv( lhs ); nrv OP##= rhs; return nrv; }                              \
+};
+
+#else // defined(SEQAN_HAS_NRVO) || defined(SEQAN_FORCE_SYMMETRIC_OPERATORS)
+
+#define SEQAN_BINARY_OPERATOR( NAME, OP )                                     \
+template <class T, class U, class B = detail::empty_base<T> >        \
+struct NAME##2 : B                                                            \
+{                                                                             \
+  friend T operator OP( T lhs, const U& rhs ) { return lhs OP##= rhs; }       \
+};                                                                            \
+                                                                              \
+template <class T, class B = detail::empty_base<T> >                 \
+struct NAME##1 : B                                                            \
+{                                                                             \
+  friend T operator OP( T lhs, const T& rhs ) { return lhs OP##= rhs; }       \
+};
+
+#endif // defined(SEQAN_HAS_NRVO) || defined(SEQAN_FORCE_SYMMETRIC_OPERATORS)
+
+SEQAN_BINARY_OPERATOR( left_shiftable, << )
+SEQAN_BINARY_OPERATOR( right_shiftable, >> )
+
+#undef SEQAN_BINARY_OPERATOR
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct equivalent2 : B
+{
+  friend bool operator==(const T& x, const U& y)
+  {
+    return !static_cast<bool>(x < y) && !static_cast<bool>(x > y);
+  }
+};
+
+template <class T, class B = detail::empty_base<T> >
+struct equivalent1 : B
+{
+  friend bool operator==(const T&x, const T&y)
+  {
+    return !static_cast<bool>(x < y) && !static_cast<bool>(y < x);
+  }
+};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct partially_ordered2 : B
+{
+  friend bool operator<=(const T& x, const U& y)
+    { return static_cast<bool>(x < y) || static_cast<bool>(x == y); }
+  friend bool operator>=(const T& x, const U& y)
+    { return static_cast<bool>(x > y) || static_cast<bool>(x == y); }
+  friend bool operator>(const U& x, const T& y)
+    { return y < x; }
+  friend bool operator<(const U& x, const T& y)
+    { return y > x; }
+  friend bool operator<=(const U& x, const T& y)
+    { return static_cast<bool>(y > x) || static_cast<bool>(y == x); }
+  friend bool operator>=(const U& x, const T& y)
+    { return static_cast<bool>(y < x) || static_cast<bool>(y == x); }
+};
+
+template <class T, class B = detail::empty_base<T> >
+struct partially_ordered1 : B
+{
+  friend bool operator>(const T& x, const T& y)
+    { return y < x; }
+  friend bool operator<=(const T& x, const T& y)
+    { return static_cast<bool>(x < y) || static_cast<bool>(x == y); }
+  friend bool operator>=(const T& x, const T& y)
+    { return static_cast<bool>(y < x) || static_cast<bool>(x == y); }
+};
+
+//  Combined operator classes (contributed by Daryle Walker) ----------------//
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct totally_ordered2
+    : less_than_comparable2<T, U
+    , equality_comparable2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct totally_ordered1
+    : less_than_comparable1<T
+    , equality_comparable1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct additive2
+    : addable2<T, U
+    , subtractable2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct additive1
+    : addable1<T
+    , subtractable1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct multiplicative2
+    : multipliable2<T, U
+    , dividable2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct multiplicative1
+    : multipliable1<T
+    , dividable1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct integer_multiplicative2
+    : multiplicative2<T, U
+    , modable2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct integer_multiplicative1
+    : multiplicative1<T
+    , modable1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct arithmetic2
+    : additive2<T, U
+    , multiplicative2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct arithmetic1
+    : additive1<T
+    , multiplicative1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct integer_arithmetic2
+    : additive2<T, U
+    , integer_multiplicative2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct integer_arithmetic1
+    : additive1<T
+    , integer_multiplicative1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct bitwise2
+    : xorable2<T, U
+    , andable2<T, U
+    , orable2<T, U, B
+      > > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct bitwise1
+    : xorable1<T
+    , andable1<T
+    , orable1<T, B
+      > > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct unit_steppable
+    : incrementable<T
+    , decrementable<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct shiftable2
+    : left_shiftable2<T, U
+    , right_shiftable2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct shiftable1
+    : left_shiftable1<T
+    , right_shiftable1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct ring_operators2
+    : additive2<T, U
+    , subtractable2_left<T, U
+    , multipliable2<T, U, B
+      > > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct ring_operators1
+    : additive1<T
+    , multipliable1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct ordered_ring_operators2
+    : ring_operators2<T, U
+    , totally_ordered2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct ordered_ring_operators1
+    : ring_operators1<T
+    , totally_ordered1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct field_operators2
+    : ring_operators2<T, U
+    , dividable2<T, U
+    , dividable2_left<T, U, B
+      > > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct field_operators1
+    : ring_operators1<T
+    , dividable1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct ordered_field_operators2
+    : field_operators2<T, U
+    , totally_ordered2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct ordered_field_operators1
+    : field_operators1<T
+    , totally_ordered1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct euclidian_ring_operators2
+    : ring_operators2<T, U
+    , dividable2<T, U
+    , dividable2_left<T, U
+    , modable2<T, U
+    , modable2_left<T, U, B
+      > > > > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct euclidian_ring_operators1
+    : ring_operators1<T
+    , dividable1<T
+    , modable1<T, B
+      > > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct ordered_euclidian_ring_operators2
+    : totally_ordered2<T, U
+    , euclidian_ring_operators2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct ordered_euclidian_ring_operators1
+    : totally_ordered1<T
+    , euclidian_ring_operators1<T, B
+      > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct euclidean_ring_operators2
+    : ring_operators2<T, U
+    , dividable2<T, U
+    , dividable2_left<T, U
+    , modable2<T, U
+    , modable2_left<T, U, B
+      > > > > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct euclidean_ring_operators1
+    : ring_operators1<T
+    , dividable1<T
+    , modable1<T, B
+      > > > {};
+
+template <class T, class U, class B = detail::empty_base<T> >
+struct ordered_euclidean_ring_operators2
+    : totally_ordered2<T, U
+    , euclidean_ring_operators2<T, U, B
+      > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct ordered_euclidean_ring_operators1
+    : totally_ordered1<T
+    , euclidean_ring_operators1<T, B
+      > > {};
+
+template <class T, class P, class B = detail::empty_base<T> >
+struct input_iteratable
+    : equality_comparable1<T
+    , incrementable<T
+    , dereferenceable<T, P, B
+      > > > {};
+
+template <class T, class B = detail::empty_base<T> >
+struct output_iteratable
+    : incrementable<T, B
+      > {};
+
+template <class T, class P, class B = detail::empty_base<T> >
+struct forward_iteratable
+    : input_iteratable<T, P, B
+      > {};
+
+template <class T, class P, class B = detail::empty_base<T> >
+struct bidirectional_iteratable
+    : forward_iteratable<T, P
+    , decrementable<T, B
+      > > {};
+
+//  To avoid repeated derivation from equality_comparable,
+//  which is an indirect base class of bidirectional_iterable,
+//  random_access_iteratable must not be derived from totally_ordered1
+//  but from less_than_comparable1 only. (Helmut Zeisel, 02-Dec-2001)
+template <class T, class P, class D, class R, class B = detail::empty_base<T> >
+struct random_access_iteratable
+    : bidirectional_iteratable<T, P
+    , less_than_comparable1<T
+    , additive2<T, D
+    , indexable<T, D, R, B
+      > > > > {};
+
+
+// SEQAN_IMPORT_TEMPLATE1 .. SEQAN_IMPORT_TEMPLATE4 -
+//
+// When SEQAN_NO_OPERATORS_IN_NAMESPACE is defined we need a way to import an
+// operator template into the boost namespace. SEQAN_IMPORT_TEMPLATE1 is used
+// for one-argument forms of operator templates; SEQAN_IMPORT_TEMPLATE2 for
+// two-argument forms. Note that these macros expect to be invoked from within
+// boost.
+
+#ifndef SEQAN_NO_OPERATORS_IN_NAMESPACE
+
+  // The template is already in boost so we have nothing to do.
+# define SEQAN_IMPORT_TEMPLATE4(template_name)
+# define SEQAN_IMPORT_TEMPLATE3(template_name)
+# define SEQAN_IMPORT_TEMPLATE2(template_name)
+# define SEQAN_IMPORT_TEMPLATE1(template_name)
+
+#else // SEQAN_NO_OPERATORS_IN_NAMESPACE
+
+#  ifndef SEQAN_NO_USING_TEMPLATE
+
+     // Bring the names in with a using-declaration
+     // to avoid stressing the compiler.
+#    define SEQAN_IMPORT_TEMPLATE4(template_name) using ::template_name;
+#    define SEQAN_IMPORT_TEMPLATE3(template_name) using ::template_name;
+#    define SEQAN_IMPORT_TEMPLATE2(template_name) using ::template_name;
+#    define SEQAN_IMPORT_TEMPLATE1(template_name) using ::template_name;
+
+#  else
+
+     // Otherwise, because a Borland C++ 5.5 bug prevents a using declaration
+     // from working, we are forced to use inheritance for that compiler.
+#    define SEQAN_IMPORT_TEMPLATE4(template_name)                                             \
+     template <class T, class U, class V, class W, class B = detail::empty_base<T> > \
+     struct template_name : ::template_name<T, U, V, W, B> {};
+
+#    define SEQAN_IMPORT_TEMPLATE3(template_name)                                    \
+     template <class T, class U, class V, class B = detail::empty_base<T> > \
+     struct template_name : ::template_name<T, U, V, B> {};
+
+#    define SEQAN_IMPORT_TEMPLATE2(template_name)                           \
+     template <class T, class U, class B = detail::empty_base<T> > \
+     struct template_name : ::template_name<T, U, B> {};
+
+#    define SEQAN_IMPORT_TEMPLATE1(template_name)                  \
+     template <class T, class B = detail::empty_base<T> > \
+     struct template_name : ::template_name<T, B> {};
+
+#  endif // SEQAN_NO_USING_TEMPLATE
+
+#endif // SEQAN_NO_OPERATORS_IN_NAMESPACE
+
+//
+// Here's where we put it all together, defining the xxxx forms of the templates
+// in namespace boost. We also define specializations of is_chained_base<> for
+// the xxxx, xxxx1, and xxxx2 templates, importing them into boost:: as
+// necessary.
+//
+#ifndef SEQAN_NO_TEMPLATE_PARTIAL_SPECIALIZATION
+
+// is_chained_base<> - a traits class used to distinguish whether an operator
+// template argument is being used for base class chaining, or is specifying a
+// 2nd argument type.
+
+// A type parameter is used instead of a plain bool because Borland's compiler
+// didn't cope well with the more obvious non-type template parameter.
+namespace detail {
+  struct true_t {};
+  struct false_t {};
+} // namespace detail
+
+// Unspecialized version assumes that most types are not being used for base
+// class chaining. We specialize for the operator templates defined in this
+// library.
+template<class T> struct is_chained_base {
+  typedef detail::false_t value;
+};
+
+// Import a 4-type-argument operator template into boost (if necessary) and
+// provide a specialization of 'is_chained_base<>' for it.
+# define SEQAN_OPERATOR_TEMPLATE4(template_name4)                     \
+  SEQAN_IMPORT_TEMPLATE4(template_name4)                              \
+  template<class T, class U, class V, class W, class B>               \
+  struct is_chained_base< template_name4<T, U, V, W, B> > {  \
+    typedef detail::true_t value;                            \
+  };
+
+// Import a 3-type-argument operator template into boost (if necessary) and
+// provide a specialization of 'is_chained_base<>' for it.
+# define SEQAN_OPERATOR_TEMPLATE3(template_name3)                     \
+  SEQAN_IMPORT_TEMPLATE3(template_name3)                              \
+  template<class T, class U, class V, class B>                        \
+  struct is_chained_base< template_name3<T, U, V, B> > {     \
+    typedef detail::true_t value;                            \
+  };
+
+// Import a 2-type-argument operator template into boost (if necessary) and
+// provide a specialization of 'is_chained_base<>' for it.
+# define SEQAN_OPERATOR_TEMPLATE2(template_name2)                  \
+  SEQAN_IMPORT_TEMPLATE2(template_name2)                           \
+  template<class T, class U, class B>                              \
+  struct is_chained_base< template_name2<T, U, B> > {     \
+    typedef detail::true_t value;                         \
+  };
+
+// Import a 1-type-argument operator template into boost (if necessary) and
+// provide a specialization of 'is_chained_base<>' for it.
+# define SEQAN_OPERATOR_TEMPLATE1(template_name1)                  \
+  SEQAN_IMPORT_TEMPLATE1(template_name1)                           \
+  template<class T, class B>                                       \
+  struct is_chained_base< template_name1<T, B> > {        \
+    typedef detail::true_t value;                         \
+  };
+
+// SEQAN_OPERATOR_TEMPLATE(template_name) defines template_name<> such that it
+// can be used for specifying both 1-argument and 2-argument forms. Requires the
+// existence of two previously defined class templates named '<template_name>1'
+// and '<template_name>2' which must implement the corresponding 1- and 2-
+// argument forms.
+//
+// The template type parameter O == is_chained_base<U>::value is used to
+// distinguish whether the 2nd argument to <template_name> is being used for
+// base class chaining from another boost operator template or is describing a
+// 2nd operand type. O == true_t only when U is actually an another operator
+// template from the library. Partial specialization is used to select an
+// implementation in terms of either '<template_name>1' or '<template_name>2'.
+//
+
+# define SEQAN_OPERATOR_TEMPLATE(template_name)                    \
+template <class T                                                  \
+         ,class U = T                                              \
+         ,class B = detail::empty_base<T>                 \
+         ,class O = typename is_chained_base<U>::value             \
+         >                                                         \
+struct template_name : template_name##2<T, U, B> {};               \
+                                                                   \
+template<class T, class U, class B>                                \
+struct template_name<T, U, B, detail::true_t>             \
+  : template_name##1<T, U> {};                                     \
+                                                                   \
+template <class T, class B>                                        \
+struct template_name<T, T, B, detail::false_t>            \
+  : template_name##1<T, B> {};                                     \
+                                                                   \
+template<class T, class U, class B, class O>                       \
+struct is_chained_base< template_name<T, U, B, O> > {     \
+  typedef detail::true_t value;                           \
+};                                                                 \
+                                                                   \
+SEQAN_OPERATOR_TEMPLATE2(template_name##2)                         \
+SEQAN_OPERATOR_TEMPLATE1(template_name##1)
+
+
+#else // SEQAN_NO_TEMPLATE_PARTIAL_SPECIALIZATION
+
+#  define SEQAN_OPERATOR_TEMPLATE4(template_name4) \
+        SEQAN_IMPORT_TEMPLATE4(template_name4)
+#  define SEQAN_OPERATOR_TEMPLATE3(template_name3) \
+        SEQAN_IMPORT_TEMPLATE3(template_name3)
+#  define SEQAN_OPERATOR_TEMPLATE2(template_name2) \
+        SEQAN_IMPORT_TEMPLATE2(template_name2)
+#  define SEQAN_OPERATOR_TEMPLATE1(template_name1) \
+        SEQAN_IMPORT_TEMPLATE1(template_name1)
+
+   // In this case we can only assume that template_name<> is equivalent to the
+   // more commonly needed template_name1<> form.
+#  define SEQAN_OPERATOR_TEMPLATE(template_name)                   \
+   template <class T, class B = detail::empty_base<T> >   \
+   struct template_name : template_name##1<T, B> {};
+
+#endif // SEQAN_NO_TEMPLATE_PARTIAL_SPECIALIZATION
+
+SEQAN_OPERATOR_TEMPLATE(less_than_comparable)
+SEQAN_OPERATOR_TEMPLATE(equality_comparable)
+SEQAN_OPERATOR_TEMPLATE(multipliable)
+SEQAN_OPERATOR_TEMPLATE(addable)
+SEQAN_OPERATOR_TEMPLATE(subtractable)
+SEQAN_OPERATOR_TEMPLATE2(subtractable2_left)
+SEQAN_OPERATOR_TEMPLATE(dividable)
+SEQAN_OPERATOR_TEMPLATE2(dividable2_left)
+SEQAN_OPERATOR_TEMPLATE(modable)
+SEQAN_OPERATOR_TEMPLATE2(modable2_left)
+SEQAN_OPERATOR_TEMPLATE(xorable)
+SEQAN_OPERATOR_TEMPLATE(andable)
+SEQAN_OPERATOR_TEMPLATE(orable)
+
+SEQAN_OPERATOR_TEMPLATE1(incrementable)
+SEQAN_OPERATOR_TEMPLATE1(decrementable)
+
+SEQAN_OPERATOR_TEMPLATE2(dereferenceable)
+SEQAN_OPERATOR_TEMPLATE3(indexable)
+
+SEQAN_OPERATOR_TEMPLATE(left_shiftable)
+SEQAN_OPERATOR_TEMPLATE(right_shiftable)
+SEQAN_OPERATOR_TEMPLATE(equivalent)
+SEQAN_OPERATOR_TEMPLATE(partially_ordered)
+
+SEQAN_OPERATOR_TEMPLATE(totally_ordered)
+SEQAN_OPERATOR_TEMPLATE(additive)
+SEQAN_OPERATOR_TEMPLATE(multiplicative)
+SEQAN_OPERATOR_TEMPLATE(integer_multiplicative)
+SEQAN_OPERATOR_TEMPLATE(arithmetic)
+SEQAN_OPERATOR_TEMPLATE(integer_arithmetic)
+SEQAN_OPERATOR_TEMPLATE(bitwise)
+SEQAN_OPERATOR_TEMPLATE1(unit_steppable)
+SEQAN_OPERATOR_TEMPLATE(shiftable)
+SEQAN_OPERATOR_TEMPLATE(ring_operators)
+SEQAN_OPERATOR_TEMPLATE(ordered_ring_operators)
+SEQAN_OPERATOR_TEMPLATE(field_operators)
+SEQAN_OPERATOR_TEMPLATE(ordered_field_operators)
+SEQAN_OPERATOR_TEMPLATE(euclidian_ring_operators)
+SEQAN_OPERATOR_TEMPLATE(ordered_euclidian_ring_operators)
+SEQAN_OPERATOR_TEMPLATE(euclidean_ring_operators)
+SEQAN_OPERATOR_TEMPLATE(ordered_euclidean_ring_operators)
+SEQAN_OPERATOR_TEMPLATE2(input_iteratable)
+SEQAN_OPERATOR_TEMPLATE1(output_iteratable)
+SEQAN_OPERATOR_TEMPLATE2(forward_iteratable)
+SEQAN_OPERATOR_TEMPLATE2(bidirectional_iteratable)
+SEQAN_OPERATOR_TEMPLATE4(random_access_iteratable)
+
+#undef SEQAN_OPERATOR_TEMPLATE
+#undef SEQAN_OPERATOR_TEMPLATE4
+#undef SEQAN_OPERATOR_TEMPLATE3
+#undef SEQAN_OPERATOR_TEMPLATE2
+#undef SEQAN_OPERATOR_TEMPLATE1
+#undef SEQAN_IMPORT_TEMPLATE1
+#undef SEQAN_IMPORT_TEMPLATE2
+#undef SEQAN_IMPORT_TEMPLATE3
+#undef SEQAN_IMPORT_TEMPLATE4
+
+// The following 'operators' classes can only be used portably if the derived class
+// declares ALL of the required member operators.
+template <class T, class U>
+struct operators2
+    : totally_ordered2<T,U
+    , integer_arithmetic2<T,U
+    , bitwise2<T,U
+      > > > {};
+
+#ifndef SEQAN_NO_TEMPLATE_PARTIAL_SPECIALIZATION
+template <class T, class U = T>
+struct operators : operators2<T, U> {};
+
+template <class T> struct operators<T, T>
+#else
+template <class T> struct operators
+#endif
+    : totally_ordered<T
+    , integer_arithmetic<T
+    , bitwise<T
+    , unit_steppable<T
+      > > > > {};
+
+/*
+
+//  Iterator helper classes (contributed by Jeremy Siek) -------------------//
+//  (Input and output iterator helpers contributed by Daryle Walker) -------//
+//  (Changed to use combined operator classes by Daryle Walker) ------------//
+template <class T,
+          class V,
+          class D = std::ptrdiff_t,
+          class P = V const *,
+          class R = V const &>
+struct input_iterator_helper
+  : input_iteratable<T, P
+  , boost::iterator<std::input_iterator_tag, V, D, P, R
+    > > {};
+
+template<class T>
+struct output_iterator_helper
+  : output_iteratable<T
+  , boost::iterator<std::output_iterator_tag, void, void, void, void
+  > >
+{
+  T& operator*()  { return static_cast<T&>(*this); }
+  T& operator++() { return static_cast<T&>(*this); }
+};
+
+template <class T,
+          class V,
+          class D = std::ptrdiff_t,
+          class P = V*,
+          class R = V&>
+struct forward_iterator_helper
+  : forward_iteratable<T, P
+  , boost::iterator<std::forward_iterator_tag, V, D, P, R
+    > > {};
+
+template <class T,
+          class V,
+          class D = std::ptrdiff_t,
+          class P = V*,
+          class R = V&>
+struct bidirectional_iterator_helper
+  : bidirectional_iteratable<T, P
+  , boost::iterator<std::bidirectional_iterator_tag, V, D, P, R
+    > > {};
+
+template <class T,
+          class V,
+          class D = std::ptrdiff_t,
+          class P = V*,
+          class R = V&>
+struct random_access_iterator_helper
+  : random_access_iteratable<T, P, D, R
+  , boost::iterator<std::random_access_iterator_tag, V, D, P, R
+    > >
+{
+  friend D requires_difference_operator(const T& x, const T& y) {
+    return x - y;
+  }
+}; // random_access_iterator_helper
+
+*/
+
+} // namespace seqan
+
+#endif // SEQAN_MATH_OPERATORS_H_
diff --git a/seqan/math/math_rational.h b/seqan/math/math_rational.h
new file mode 100644
index 0000000..a3b6235
--- /dev/null
+++ b/seqan/math/math_rational.h
@@ -0,0 +1,584 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// A data type to represent Rational numbers.
+// Taken from the Rational Number Library in Boost version 1.47.
+// ==========================================================================
+
+#ifndef SEQAN_MATH_RATIONAL_H_
+#define SEQAN_MATH_RATIONAL_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TInt>
+class Rational;
+
+template <typename TInt>
+Rational<TInt> abs(const Rational<TInt>& r);
+
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TInt>
+class Rational :
+    less_than_comparable < Rational<TInt>,
+    equality_comparable < Rational<TInt>,
+    less_than_comparable2 < Rational<TInt>, TInt,
+    equality_comparable2 < Rational<TInt>, TInt,
+    addable < Rational<TInt>,
+    subtractable < Rational<TInt>,
+    multipliable < Rational<TInt>,
+    dividable < Rational<TInt>,
+    addable2 < Rational<TInt>, TInt,
+    subtractable2 < Rational<TInt>, TInt,
+    subtractable2_left < Rational<TInt>, TInt,
+    multipliable2 < Rational<TInt>, TInt,
+    dividable2 < Rational<TInt>, TInt,
+    dividable2_left < Rational<TInt>, TInt,
+    incrementable < Rational<TInt>,
+    decrementable < Rational<TInt>
+    > > > > > > > > > > > > > > > >
+{
+    // Class-wide pre-conditions
+//    SEQAN_STATIC_ASSERT( std::numeric_limits<TInt>::is_specialized );
+
+    // Helper types
+//    typedef typename boost::call_traits<TInt>::param_type param_type;
+    typedef const TInt & param_type;
+
+    struct helper { TInt parts[2]; };
+    typedef TInt (helper::* bool_type)[2];
+
+public:
+    typedef TInt int_type;
+    Rational() : num(0), den(1) {}
+
+    template <typename T>
+    Rational(T const & n, SEQAN_CTOR_ENABLE_IF( IsInteger<T> ) ) : num(n), den(1) { (void)dummy; }
+    Rational(param_type n, param_type d) : num(n), den(d) { normalize(); }
+
+    // Default copy constructor and assignment are fine
+
+    // Add assignment from TInt
+    Rational& operator=(param_type n) { return assign(n, 1); }
+
+    // Assign in place
+    Rational& assign(param_type n, param_type d);
+
+    // Access to representation
+    TInt numerator() const { return num; }
+    TInt denominator() const { return den; }
+
+    // Arithmetic assignment operators
+    Rational& operator+= (const Rational& r);
+    Rational& operator-= (const Rational& r);
+    Rational& operator*= (const Rational& r);
+    Rational& operator/= (const Rational& r);
+
+    Rational& operator+= (param_type i);
+    Rational& operator-= (param_type i);
+    Rational& operator*= (param_type i);
+    Rational& operator/= (param_type i);
+
+    // Increment and decrement
+    const Rational& operator++();
+    const Rational& operator--();
+
+    // Operator not
+    bool operator!() const { return !num; }
+
+    // Boolean conversion
+
+
+    operator bool_type() const { return operator !() ? 0 : &helper::parts; }
+    operator double() const
+    {
+        SEQAN_ASSERT_NEQ (den, TInt(0));
+        return (double)num / (double)den;
+    }
+
+    // Comparison operators
+    bool operator< (const Rational& r) const;
+    bool operator== (const Rational& r) const;
+
+    bool operator< (param_type i) const;
+    bool operator> (param_type i) const;
+    bool operator== (param_type i) const;
+
+private:
+    // Implementation - numerator and denominator (normalized).
+    // Other possibilities - separate whole-part, or sign, fields?
+    TInt num;
+    TInt den;
+
+    // Representation note: Fractions are kept in normalized form at all
+    // times. normalized form is defined as gcd(num,den) == 1 and den > 0.
+    // In particular, note that the implementation of abs() below relies
+    // on den always being positive.
+    bool test_invariant() const;
+    void normalize();
+};
+
+// Assign in place
+template <typename TInt>
+inline Rational<TInt>& Rational<TInt>::assign(param_type n, param_type d)
+{
+    num = n;
+    den = d;
+    normalize();
+    return *this;
+}
+
+// Unary plus and minus
+template <typename TInt>
+inline Rational<TInt> operator+ (const Rational<TInt>& r)
+{
+    return r;
+}
+
+template <typename TInt>
+inline Rational<TInt> operator- (const Rational<TInt>& r)
+{
+    return Rational<TInt>(-r.numerator(), r.denominator());
+}
+
+// Arithmetic assignment operators
+template <typename TInt>
+Rational<TInt>& Rational<TInt>::operator+= (const Rational<TInt>& r)
+{
+    // This calculation avoids overflow, and minimises the number of expensive
+    // calculations. Thanks to Nickolay Mladenov for this algorithm.
+    //
+    // Proof:
+    // We have to compute a/b + c/d, where gcd(a,b)=1 and gcd(b,c)=1.
+    // Let g = gcd(b,d), and b = b1*g, d=d1*g. Then gcd(b1,d1)=1
+    //
+    // The result is (a*d1 + c*b1) / (b1*d1*g).
+    // Now we have to normalize this ratio.
+    // Let's assume h | gcd((a*d1 + c*b1), (b1*d1*g)), and h > 1
+    // If h | b1 then gcd(h,d1)=1 and hence h|(a*d1+c*b1) => h|a.
+    // But since gcd(a,b1)=1 we have h=1.
+    // Similarly h|d1 leads to h=1.
+    // So we have that h | gcd((a*d1 + c*b1) , (b1*d1*g)) => h|g
+    // Finally we have gcd((a*d1 + c*b1), (b1*d1*g)) = gcd((a*d1 + c*b1), g)
+    // Which proves that instead of normalizing the result, it is better to
+    // divide num and den by gcd((a*d1 + c*b1), g)
+
+    // Protect against self-modification
+    TInt r_num = r.num;
+    TInt r_den = r.den;
+
+    TInt g = greatestCommonDivisor(den, r_den);
+    den /= g;  // = b1 from the calculations above
+    num = num * (r_den / g) + r_num * den;
+    g = greatestCommonDivisor(num, g);
+    num /= g;
+    den *= r_den/g;
+
+    return *this;
+}
+
+template <typename TInt>
+Rational<TInt>& Rational<TInt>::operator-= (const Rational<TInt>& r)
+{
+    // Protect against self-modification
+    TInt r_num = r.num;
+    TInt r_den = r.den;
+
+    // This calculation avoids overflow, and minimises the number of expensive
+    // calculations. It corresponds exactly to the += case above
+    TInt g = greatestCommonDivisor(den, r_den);
+    den /= g;
+    num = num * (r_den / g) - r_num * den;
+    g = greatestCommonDivisor(num, g);
+    num /= g;
+    den *= r_den/g;
+
+    return *this;
+}
+
+template <typename TInt>
+Rational<TInt>& Rational<TInt>::operator*= (const Rational<TInt>& r)
+{
+    // Protect against self-modification
+    TInt r_num = r.num;
+    TInt r_den = r.den;
+
+    // Avoid overflow and preserve normalization
+    TInt gcd1 = greatestCommonDivisor(num, r_den);
+    TInt gcd2 = greatestCommonDivisor(r_num, den);
+    num = (num/gcd1) * (r_num/gcd2);
+    den = (den/gcd2) * (r_den/gcd1);
+    return *this;
+}
+
+template <typename TInt>
+Rational<TInt>& Rational<TInt>::operator/= (const Rational<TInt>& r)
+{
+    // Protect against self-modification
+    TInt r_num = r.num;
+    TInt r_den = r.den;
+
+    // Avoid repeated construction
+    TInt zero(0);
+
+    // Trap division by zero
+    SEQAN_ASSERT_NEQ (r_num, zero);
+
+    if (num == zero)
+        return *this;
+
+    // Avoid overflow and preserve normalization
+    TInt gcd1 = greatestCommonDivisor(num, r_num);
+    TInt gcd2 = greatestCommonDivisor(r_den, den);
+    num = (num/gcd1) * (r_den/gcd2);
+    den = (den/gcd2) * (r_num/gcd1);
+
+    if (den < zero) {
+        num = -num;
+        den = -den;
+    }
+    return *this;
+}
+
+// Mixed-mode operators
+template <typename TInt>
+inline Rational<TInt>&
+Rational<TInt>::operator+= (param_type i)
+{
+    return operator+= (Rational<TInt>(i));
+}
+
+template <typename TInt>
+inline Rational<TInt>&
+Rational<TInt>::operator-= (param_type i)
+{
+    return operator-= (Rational<TInt>(i));
+}
+
+template <typename TInt>
+inline Rational<TInt>&
+Rational<TInt>::operator*= (param_type i)
+{
+    return operator*= (Rational<TInt>(i));
+}
+
+template <typename TInt>
+inline Rational<TInt>&
+Rational<TInt>::operator/= (param_type i)
+{
+    return operator/= (Rational<TInt>(i));
+}
+
+// Increment and decrement
+template <typename TInt>
+inline const Rational<TInt>& Rational<TInt>::operator++()
+{
+    // This can never denormalise the fraction
+    num += den;
+    return *this;
+}
+
+template <typename TInt>
+inline const Rational<TInt>& Rational<TInt>::operator--()
+{
+    // This can never denormalise the fraction
+    num -= den;
+    return *this;
+}
+
+// Comparison operators
+template <typename TInt>
+bool Rational<TInt>::operator< (const Rational<TInt>& r) const
+{
+    // Avoid repeated construction
+    int_type const  zero( 0 );
+
+    // This should really be a class-wide invariant.  The reason for these
+    // checks is that for 2's complement systems, INT_MIN has no corresponding
+    // positive, so negating it during normalization keeps it INT_MIN, which
+    // is bad for later calculations that assume a positive denominator.
+    SEQAN_ASSERT_GT( this->den, zero );
+    SEQAN_ASSERT_GT( r.den, zero );
+
+    // Determine relative order by expanding each value to its simple continued
+    // fraction representation using the Euclidian GCD algorithm.
+    struct { int_type  n, d, q, r; }  ts = { this->num, this->den, this->num /
+     this->den, this->num % this->den }, rs = { r.num, r.den, r.num / r.den,
+     r.num % r.den };
+    unsigned  reverse = 0u;
+
+    // Normalize negative moduli by repeatedly adding the (positive) denominator
+    // and decrementing the quotient.  Later cycles should have all positive
+    // values, so this only has to be done for the first cycle.  (The rules of
+    // C++ require a nonnegative quotient & remainder for a nonnegative dividend
+    // & positive divisor.)
+    while ( ts.r < zero )  { ts.r += ts.d; --ts.q; }
+    while ( rs.r < zero )  { rs.r += rs.d; --rs.q; }
+
+    // Loop through and compare each variable's continued-fraction components
+    while ( true )
+    {
+        // The quotients of the current cycle are the continued-fraction
+        // components.  Comparing two c.f. is comparing their sequences,
+        // stopping at the first difference.
+        if ( ts.q != rs.q )
+        {
+            // Since reciprocation changes the relative order of two variables,
+            // and c.f. use reciprocals, the less/greater-than test reverses
+            // after each index.  (Start w/ non-reversed @ whole-number place.)
+            return reverse ? ts.q > rs.q : ts.q < rs.q;
+        }
+
+        // Prepare the next cycle
+        reverse ^= 1u;
+
+        if ( (ts.r == zero) || (rs.r == zero) )
+        {
+            // At least one variable's c.f. expansion has ended
+            break;
+        }
+
+        ts.n = ts.d;         ts.d = ts.r;
+        ts.q = ts.n / ts.d;  ts.r = ts.n % ts.d;
+        rs.n = rs.d;         rs.d = rs.r;
+        rs.q = rs.n / rs.d;  rs.r = rs.n % rs.d;
+    }
+
+    // Compare infinity-valued components for otherwise equal sequences
+    if ( ts.r == rs.r )
+    {
+        // Both remainders are zero, so the next (and subsequent) c.f.
+        // components for both sequences are infinity.  Therefore, the sequences
+        // and their corresponding values are equal.
+        return false;
+    }
+    else
+    {
+        // Exactly one of the remainders is zero, so all following c.f.
+        // components of that variable are infinity, while the other variable
+        // has a finite next c.f. component.  So that other variable has the
+        // lesser value (modulo the reversal flag!).
+        return ( ts.r != zero ) != static_cast<bool>( reverse );
+    }
+}
+
+template <typename TInt>
+bool Rational<TInt>::operator< (param_type i) const
+{
+    // Avoid repeated construction
+    int_type const  zero( 0 );
+
+    // Break value into mixed-fraction form, w/ always-nonnegative remainder
+    SEQAN_ASSERT_GT( this->den, zero );
+    int_type  q = this->num / this->den, r = this->num % this->den;
+    while ( r < zero )  { r += this->den; --q; }
+
+    // Compare with just the quotient, since the remainder always bumps the
+    // value up.  [Since q = floor(n/d), and if n/d < i then q < i, if n/d == i
+    // then q == i, if n/d == i + r/d then q == i, and if n/d >= i + 1 then
+    // q >= i + 1 > i; therefore n/d < i iff q < i.]
+    return q < i;
+}
+
+template <typename TInt>
+bool Rational<TInt>::operator> (param_type i) const
+{
+    // Trap equality first
+    if (num == i && den == TInt(1))
+        return false;
+
+    // Otherwise, we can use operator<
+    return !operator<(i);
+}
+
+template <typename TInt>
+inline bool Rational<TInt>::operator== (const Rational<TInt>& r) const
+{
+    return ((num == r.num) && (den == r.den));
+}
+
+template <typename TInt>
+inline bool Rational<TInt>::operator== (param_type i) const
+{
+    return ((den == TInt(1)) && (num == i));
+}
+
+// Invariant check
+template <typename TInt>
+inline bool Rational<TInt>::test_invariant() const
+{
+    return ( this->den > int_type(0) ) && ( greatestCommonDivisor(this->num, this->den) ==
+     int_type(1) );
+}
+
+// Normalisation
+template <typename TInt>
+void Rational<TInt>::normalize()
+{
+    // Avoid repeated construction
+    TInt zero(0);
+
+    SEQAN_ASSERT_NEQ (den, zero);
+
+    // Handle the case of zero separately, to avoid division by zero
+    if (num == zero) {
+        den = TInt(1);
+        return;
+    }
+
+    TInt g = greatestCommonDivisor(num, den);
+
+    num /= g;
+    den /= g;
+
+    // Ensure that the denominator is positive
+    if (den < zero) {
+        num = -num;
+        den = -den;
+    }
+
+    SEQAN_ASSERT( this->test_invariant() );
+}
+
+// Input and output
+template <typename TInt>
+std::istream& operator>> (std::istream& is, Rational<TInt>& r)
+{
+    TInt n = TInt(0), d = TInt(1);
+    char c = 0;
+
+    is >> n;
+    if (!is) return is;
+
+    c = is.get();
+    if (c == '/')
+    {
+        is >> std::noskipws >> d;
+    }
+    else if (c == '.')
+    {
+        bool negative = false;
+        if (n < TInt(0))
+        {
+            n = -n;
+            negative = true;
+        }
+        c = is.get();
+        // read digits as long we can store them
+        while ('0' <= c && c <= '9' &&
+                (n < (TInt)MaxValue<TInt>::VALUE / (TInt)10 - (TInt)9) &&
+                (d < (TInt)MaxValue<TInt>::VALUE / (TInt)10))
+        {
+            n = 10 * n + (c - '0');
+            d *= 10;
+            c = is.get();
+        }
+        // ignore remaining digits
+        while ('0' <= c && c <= '9')
+            is.get();
+        is.unget();
+
+        if (negative) n = -n;
+    }
+    r.assign(n, d);
+
+    return is;
+}
+
+// Add manipulators for output format?
+template <typename TInt>
+std::ostream& operator<< (std::ostream& os, const Rational<TInt>& r)
+{
+    os << r.numerator() << '/' << r.denominator();
+    return os;
+}
+
+// Type conversion
+template <typename T, typename TInt>
+inline T rational_cast(const Rational<TInt>& src)
+{
+    return static_cast<T>(src.numerator())/static_cast<T>(src.denominator());
+}
+
+// Do not use any abs() defined on TInt - it isn't worth it, given the
+// difficulties involved (Koenig lookup required, there may not *be* an abs()
+// defined, etc etc).
+template <typename TInt>
+inline Rational<TInt> abs(const Rational<TInt>& r)
+{
+    if (r.numerator() >= TInt(0))
+        return r;
+
+    return Rational<TInt>(-r.numerator(), r.denominator());
+}
+
+
+template <typename TInt>
+inline TInt floor(const Rational<TInt>& r)
+{
+    // Avoid repeated construction
+    TInt zero(0);
+
+    SEQAN_ASSERT_NEQ (r.denominator(), zero);
+
+    if (r.numerator() >= zero)
+        return r.numerator() / r.denominator();
+    else
+        return ((r.numerator() + 1) / r.denominator()) - 1;
+}
+
+template <typename TInt>
+inline TInt ceil(const Rational<TInt>& r)
+{
+    // Avoid repeated construction
+    TInt zero(0);
+
+    SEQAN_ASSERT_NEQ (r.denominator(), zero);
+
+    if (r.numerator() > zero)
+        return ((r.numerator() - 1) / r.denominator()) + 1;
+    else
+        return r.numerator() / r.denominator();
+}
+
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_MATH_RATIONAL_H_
diff --git a/seqan/misc/INFO b/seqan/misc/INFO
deleted file mode 100644
index b962f1d..0000000
--- a/seqan/misc/INFO
+++ /dev/null
@@ -1,14 +0,0 @@
-Name: seqan-misc
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Author: Tobias Rausch <rausch@embl.de>
-Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Miscellaneous helper code.
- This module contains misc helper code, such as interval trees, priority queues,
- or the old random number generator.
diff --git a/seqan/misc/misc_accumulators.h b/seqan/misc/accumulators.h
similarity index 64%
rename from seqan/misc/misc_accumulators.h
rename to seqan/misc/accumulators.h
index 261bf1e..7ef805d 100644
--- a/seqan/misc/misc_accumulators.h
+++ b/seqan/misc/accumulators.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,8 +38,8 @@
 // analysis algorithms than then Boost one.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_MISC_MISC_ACCUMULATORS_H_
-#define CORE_INCLUDE_SEQAN_MISC_MISC_ACCUMULATORS_H_
+#ifndef INCLUDE_SEQAN_MISC_ACCUMULATORS_H_
+#define INCLUDE_SEQAN_MISC_ACCUMULATORS_H_
 
 #include <seqan/sequence.h>
 
@@ -55,69 +55,53 @@ template <typename T, typename TTag> struct Result;
 // Tags, Classes, Enums
 // ============================================================================
 
-struct Average_;
-typedef Tag<Average_> Average;
+struct AccuAverage_;
+typedef Tag<AccuAverage_> AccuAverage;
 
-struct Sum_;
-typedef Tag<Sum_> Sum;
+struct AccuSum_;
+typedef Tag<AccuSum_> AccuSum;
 
-struct Count_;
-typedef Tag<Count_> Count;
+struct AccuCount_;
+typedef Tag<AccuCount_> AccuCount;
 
 /*!
  * @class Accumulator
- * @headerfile <seqan/misc/misc_accumulators.h>
+ * @headerfile <seqan/misc/accumulators.h>
  * @brief Accumulator base class.
- * 
+ *
  * @signature template <typename TValue, typename TSpec>
  *            struct Accumulator;
- * 
+ *
  * @tparam TSpec  The specialization tag.
  * @tparam TValue The type of the values to accumulate.
- * 
- * @section Remarks
- * 
+ *
  * Accumulators are for computing statistics on streams of values.
- * 
+ *
  * Currently, this is only meant for accumulating integers.
  */
 
-/**
-.Class.Accumulator
-..cat:Miscellaneous
-..summary:Accumulator base class.
-..signature:Accumulator<TValue, TSpec>
-..param.TValue:The type of the values to accumulate.
-..param.TSpec:The specialization tag.
-..remarks:Accumulators are for computing statistics on streams of values.
-..remarks:Currently, this is only meant for accumulating integers.
-..include:seqan/misc/misc_accumulators.h
-*/
-
 template <typename TValue, typename TSpec>
 struct Accumulator;
 
 /*!
  * @class AverageAccumulator
  * @extends Accumulator
- * @headerfile <seqan/misc/misc_accumulators.h>
+ * @headerfile <seqan/misc/accumulators.h>
  * @brief Accumulator for computing averages.
- * 
+ *
  * @signature template <typename TValue>
- *            struct Accumulator<TValue, Average>;
- * 
+ *            struct Accumulator<TValue, AccuAverage>;
+ *
  * @tparam TValue The type of the values to compute the average of.
- * 
- * @section Remarks
- * 
+ *
  * The average of an empty sequence is defined to be 0.
- * 
+ *
  * @section Examples
- * 
+ *
  * This program shows how to use the Average Accumulator.
- * 
+ *
  * @code{.cpp}
- * Accumulator<int, Average> acc;
+ * Accumulator<int, AccuAverage> acc;
  * push(acc, 1);
  * push(acc, 2);
  * push(acc, 3);
@@ -127,7 +111,7 @@ struct Accumulator;
  * @endcode
  *
  * The output is then:
- * 
+ *
  * @code{.console}
  * average: 2
  * sum:     6
@@ -135,38 +119,12 @@ struct Accumulator;
  * @endcode
  */
 
-/**
-.Spec.Average Accumulator
-..general:Class.Accumulator
-..cat:Miscellaneous
-..summary:Accumulator for computing averages.
-..signature:Accumulator<TValue, TSpec>
-..param.TValue:The type of the values to compute the average of.
-..param.TSpec:The specialization tag.
-..remarks:The average of an empty sequence is defined to be 0.
-..example.text:This program shows how to use the Average Accumulator.
-..example.code:
-Accumulator<int, Average> acc;
-push(acc, 1);
-push(acc, 2);
-push(acc, 3);
-std::cout << "average: " << average(acc) << "\n"
-          << "sum:     " << sum(acc) << "\n"
-          << "count:   " << count(acc) << "\n";
-..example.text:The output is then:
-..example.code:
-average: 2
-sum:     6
-count:   3
-..include:seqan/misc/misc_accumulators.h
-*/
-
 template <typename TValue>
-struct Accumulator<TValue, Average>
+struct Accumulator<TValue, AccuAverage>
 {
-    typedef typename Result<Accumulator<TValue, Average>, Sum>::Type TSum_;
+    typedef typename Result<Accumulator<TValue, AccuAverage>, AccuSum>::Type TAccuSum_;
 
-    TSum_ sum_;
+    TAccuSum_ sum_;
     unsigned count_;
 
     Accumulator() : sum_(0), count_(0) {}
@@ -191,17 +149,14 @@ struct Accumulator<TValue, Average>
  * @return Type The value type.
  */
 
-///.Metafunction.Value.param.T.type:Class.Accumulator
-///.Metafunction.Value.class:Class.Accumulator
-
 template <typename TValue>
-struct Value<Accumulator<TValue, Average> >
+struct Value<Accumulator<TValue, AccuAverage> >
 {
     typedef double Type;
 };
 
 template <typename TValue>
-struct Value<Accumulator<TValue, Average> const > : Value<Accumulator<TValue, Average> >
+struct Value<Accumulator<TValue, AccuAverage> const > : Value<Accumulator<TValue, AccuAverage> >
 {};
 
 // ----------------------------------------------------------------------------
@@ -221,17 +176,6 @@ struct Value<Accumulator<TValue, Average> const > : Value<Accumulator<TValue, Av
  * @return Type The result type.
  */
 
-/**
-.Metafunction.Result
-..cat:Miscellaneous
-..summary:Return the result of a computation.
-..signature:Result<T, TTag>::Type
-..param.T:The type to query
-..param.TTag:The type of the result to query.
-...remarks:E.g. $Average$, $Sum$, $Count$.
-..include:seqan/misc/misc_accumulators.h
- */
-
 template <typename T, typename TTag = void>
 struct Result;
 
@@ -239,30 +183,28 @@ struct Result;
 // Metafunction Result                                      Average Accumulator
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Result.param.T.type:Class.Accumulator
-
 template <typename TValue>
-struct Result<Accumulator<TValue, Average>, Average>
+struct Result<Accumulator<TValue, AccuAverage>, AccuAverage>
 {
     typedef double Type;
 };
 
 template <typename TValue>
-struct Result<Accumulator<TValue, Average> const, Average> : Result<Accumulator<TValue, Average>, Average>
+struct Result<Accumulator<TValue, AccuAverage> const, AccuAverage> : Result<Accumulator<TValue, AccuAverage>, AccuAverage>
 {};
 
 template <typename TValue>
-struct Result<Accumulator<TValue, Average>, Count>
+struct Result<Accumulator<TValue, AccuAverage>, AccuCount>
 {
     typedef unsigned Type;
 };
 
 template <typename TValue>
-struct Result<Accumulator<TValue, Average> const, Count> : Result<Accumulator<TValue, Average>, Count>
+struct Result<Accumulator<TValue, AccuAverage> const, AccuCount> : Result<Accumulator<TValue, AccuAverage>, AccuCount>
 {};
 
 template <typename TValue>
-struct Result<Accumulator<TValue, Average>, Sum>
+struct Result<Accumulator<TValue, AccuAverage>, AccuSum>
 {
     typedef typename IfC<Is<IntegerConcept<TValue> >::VALUE,
                          __int64,
@@ -270,7 +212,7 @@ struct Result<Accumulator<TValue, Average>, Sum>
 };
 
 template <typename TValue>
-struct Result<Accumulator<TValue, Average> const, Sum> : Result<Accumulator<TValue, Average>, Sum>
+struct Result<Accumulator<TValue, AccuAverage> const, AccuSum> : Result<Accumulator<TValue, AccuAverage>, AccuSum>
 {};
 
 // ============================================================================
@@ -281,8 +223,6 @@ struct Result<Accumulator<TValue, Average> const, Sum> : Result<Accumulator<TVal
 // Function clear()                                                 Accumulator
 // ----------------------------------------------------------------------------
 
-///.Function.clear.param.object.type:Class.Accumulator
-
 // ----------------------------------------------------------------------------
 // Function push()                                                  Accumulator
 // ----------------------------------------------------------------------------
@@ -294,21 +234,9 @@ struct Result<Accumulator<TValue, Average> const, Sum> : Result<Accumulator<TVal
  * @signature void push(acc, x);
  *
  * @param[in,out] acc The Accumulator to push the value to.
- * @param[in]     x   The value to include in the accumulation.
+ * @param[in]     x   The value to include in the accumulation (@link IntegerConcept @endlink).
  */
 
-/**
-.Function.Accumulator#push
-..cat:Miscellaneous
-..summary:Adds a value to an accumulator.
-..signature:push(acc, x)
-..class:Class.Accumulator
-..param.acc:The accumulator to add the value to.
-...type:Class.Accumulator
-..param.x:The value to push.
-..returns:$void$
-*/
-
 // ----------------------------------------------------------------------------
 // Function clear()                                                 Accumulator
 // ----------------------------------------------------------------------------
@@ -328,7 +256,7 @@ struct Result<Accumulator<TValue, Average> const, Sum> : Result<Accumulator<TVal
 
 template <typename TValue>
 inline void
-clear(Accumulator<TValue, Average> & accumulator)
+clear(Accumulator<TValue, AccuAverage> & accumulator)
 {
     accumulator.sum_ = 0;
     accumulator.count_ = 0;
@@ -340,10 +268,10 @@ clear(Accumulator<TValue, Average> & accumulator)
 
 template <typename TValue, typename TValue2>
 inline void
-push(Accumulator<TValue, Average> & acc, TValue2 value)
+push(Accumulator<TValue, AccuAverage> & acc, TValue2 value)
 {
-    typedef typename Result<Accumulator<TValue, Average>, Sum>::Type TSum;
-    acc.sum_ += static_cast<TSum>(value);
+    typedef typename Result<Accumulator<TValue, AccuAverage>, AccuSum>::Type TAccuSum;
+    acc.sum_ += static_cast<TAccuSum>(value);
     acc.count_ += 1;
 }
 
@@ -355,30 +283,18 @@ push(Accumulator<TValue, Average> & acc, TValue2 value)
  * @fn AverageAccumulator#average
  * @brief Return the average of the included values.
  *
- * @signtature TResult average(acc);
+ * @signature TResult average(acc);
  *
  * @param[in] acc The Accumulator to compute the average for.
  *
- * @return TResult The average of the values.
+ * @return TResult The average of the values (Metafunction: @link Accumulator#Result @endlink).
  */
 
-/**
-.Function.Accumulator#average
-..cat:Miscellaneous
-..summary:Return average from an accumulator.
-..signature:average(acc)
-..class:Spec.Average Accumulator
-..param.acc:The accumulator to return the average from.
-...type:Spec.Average Accumulator
-..returns:nolink:$double$
-..include:seqan/misc/misc_accumulators.h
-*/
-
 template <typename TValue>
-inline typename Result<Accumulator<TValue, Average>, Average>::Type
-average(Accumulator<TValue, Average> const & acc)
+inline typename Result<Accumulator<TValue, AccuAverage>, AccuAverage>::Type
+average(Accumulator<TValue, AccuAverage> const & acc)
 {
-    typedef typename Result<Accumulator<TValue, Average>, Average>::Type TResult;
+    typedef typename Result<Accumulator<TValue, AccuAverage>, AccuAverage>::Type TResult;
     if (acc.count_ == 0u)
         return 0;
     return static_cast<TResult>(acc.sum_ / static_cast<TResult>(acc.count_));
@@ -392,28 +308,16 @@ average(Accumulator<TValue, Average> const & acc)
  * @fn AverageAccumulator#sum
  * @brief Return the sum of the included values.
  *
- * @signtature TResult sum(acc);
+ * @signature TResult sum(acc);
  *
  * @param[in] acc The Accumulator to compute the sum for.
  *
- * @return TResult The sum of the values.
+ * @return TResult The sum of the values (Metafunction: @link Accumulator#Result @endlink).
  */
 
-/**
-.Function.Accumulator#sum
-..cat:Miscellaneous
-..summary:Return sum from an accumulator.
-..signature:average(acc)
-..class:Spec.Average Accumulator
-..param.acc:The accumulator to return the sum from.
-...type:Spec.Average Accumulator
-..returns:@Metafunction.Value@$<typeof(acc)>::Type$
-..include:seqan/misc/misc_accumulators.h
-*/
-
 template <typename TValue>
-inline typename Result<Accumulator<TValue, Average>, Sum>::Type
-sum(Accumulator<TValue, Average> const & acc)
+inline typename Result<Accumulator<TValue, AccuAverage>, AccuSum>::Type
+sum(Accumulator<TValue, AccuAverage> const & acc)
 {
     return acc.sum_;
 }
@@ -426,32 +330,20 @@ sum(Accumulator<TValue, Average> const & acc)
  * @fn AverageAccumulator#count
  * @brief Return the number of included values.
  *
- * @signtature TResult count(acc);
+ * @signature TResult count(acc);
  *
  * @param[in] count The number of values pushed to the accumulator.
  *
- * @return TResult The number of pushed values.
+ * @return TResult The number of pushed values (Metafunction: @link Accumulator#Result @endlink).
  */
 
-/**
-.Function.Accumulator#count
-..cat:Miscellaneous
-..summary:Return sum from an accumulator.
-..signature:average(acc)
-..class:Spec.Average Accumulator
-..param.acc:The accumulator to return the sum from.
-...type:Spec.Average Accumulator
-..returns:@Metafunction.Value@$<typeof(acc)>::Type$
-..include:seqan/misc/misc_accumulators.h
-*/
-
 template <typename TValue>
-inline typename Result<Accumulator<TValue, Average>, Count>::Type
-count(Accumulator<TValue, Average> const & acc)
+inline typename Result<Accumulator<TValue, AccuAverage>, AccuCount>::Type
+count(Accumulator<TValue, AccuAverage> const & acc)
 {
     return acc.count_;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_MISC_MISC_ACCUMULATORS_H_
+#endif  // #ifndef INCLUDE_SEQAN_MISC_ACCUMULATORS_H_
diff --git a/seqan/misc/misc_base.h b/seqan/misc/base.h
similarity index 51%
rename from seqan/misc/misc_base.h
rename to seqan/misc/base.h
index f714bd6..1c51591 100644
--- a/seqan/misc/misc_base.h
+++ b/seqan/misc/base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,73 +39,73 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-	//////////////////////////////////////////////////////////////////////////////
-	// In SeqAn sets and maps store elements as pairs of (key,object) 
-	// the elements of sets without objects are the keys.
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // In SeqAn sets and maps store elements as pairs of (key,object)
+    // the elements of sets without objects are the keys.
+    //////////////////////////////////////////////////////////////////////////////
 
-	//////////////////////////////////////////////////////////////////////////////
-	// Key/Object meta-functions
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
+    // Key/Object meta-functions
+    //////////////////////////////////////////////////////////////////////////////
 
 /* moved to basic_h, see #6
-	template <typename TElement>
-	struct Key {
-		typedef TElement Type;
-	};
+    template <typename TElement>
+    struct Key {
+        typedef TElement Type;
+    };
 */
 /* moved to basic_aggregates
-	template <typename TKey, typename TObject, typename TSpec>
-	struct Key< Pair<TKey, TObject, TSpec> > 
-	{
-		typedef TKey Type;
-	};
+    template <typename TKey, typename TObject, typename TSpec>
+    struct Key< Pair<TKey, TObject, TSpec> >
+    {
+        typedef TKey Type;
+    };
 */
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template <typename TElement>
-	struct Object {
-		typedef Nothing Type;
-	};
-
-	template <typename TKey, typename TObject, typename TSpec>
-	struct Object< Pair<TKey, TObject, TSpec> > {
-		typedef TObject Type;
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// keyOf function
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <typename TElement>
-	inline typename Key<TElement const>::Type & 
-	keyOf(TElement const & element) 
-	{
-		return element;
-	}
-
-	template <typename TKey, typename TObject, typename TSpec>
-	inline TKey const &
-	keyOf(Pair<TKey, TObject, TSpec> const &element) {
-		return element.i1;
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// objectOf
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <typename TKey, typename TObject, typename TSpec>
-	inline TObject & 
-	objectOf(Pair<TKey, TObject, TSpec> &element) {
-		return element.i2;
-	}
-	template <typename TKey, typename TObject, typename TSpec>
-	inline TObject const &
-	objectOf(Pair<TKey, TObject, TSpec> const &element) {
-		return element.i2;
-	}
+    template <typename TElement>
+    struct Object {
+        typedef Nothing Type;
+    };
+
+    template <typename TKey, typename TObject, typename TSpec>
+    struct Object< Pair<TKey, TObject, TSpec> > {
+        typedef TObject Type;
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // keyOf function
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <typename TElement>
+    inline typename Key<TElement const>::Type &
+    keyOf(TElement const & element)
+    {
+        return element;
+    }
+
+    template <typename TKey, typename TObject, typename TSpec>
+    inline TKey const &
+    keyOf(Pair<TKey, TObject, TSpec> const &element) {
+        return element.i1;
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // objectOf
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <typename TKey, typename TObject, typename TSpec>
+    inline TObject &
+    objectOf(Pair<TKey, TObject, TSpec> &element) {
+        return element.i2;
+    }
+    template <typename TKey, typename TObject, typename TSpec>
+    inline TObject const &
+    objectOf(Pair<TKey, TObject, TSpec> const &element) {
+        return element.i2;
+    }
 
 }
 
diff --git a/seqan/misc/bit_twiddling.h b/seqan/misc/bit_twiddling.h
new file mode 100644
index 0000000..a1623da
--- /dev/null
+++ b/seqan/misc/bit_twiddling.h
@@ -0,0 +1,772 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Various useful bit-twiddling routines, mostly taken from the website
+// http://www-graphics.stanford.edu/~seander/bithacks.html
+// ==========================================================================
+
+#ifndef SEQAN_MISC_BIT_TWIDDLING_H_
+#define SEQAN_MISC_BIT_TWIDDLING_H_
+
+#ifdef PLATFORM_WINDOWS_VS
+
+// Make intrinsics visible.  It appears that this is not necessary with VS 10
+// any more, for VS 9, it must be included.
+#include <intrin.h>
+
+#ifdef __SSE4_2__
+#include <nmmintrin.h>
+#endif
+
+#endif  // #ifdef PLATFORM_WINDOWS_VS
+
+// TODO(holtgrew): Test this!
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TWord>
+struct SimdVectorConcept;
+
+// ============================================================================
+// Classes, Structs, Enums, Tags
+// ============================================================================
+
+// DeBruijn sequence for 64 bit bitScanReverse.
+static const int DeBruijnMultiplyLookupBSR64[64] =
+{
+    0, 47,  1, 56, 48, 27,  2, 60,
+   57, 49, 41, 37, 28, 16,  3, 61,
+   54, 58, 35, 52, 50, 42, 21, 44,
+   38, 32, 29, 23, 17, 11,  4, 62,
+   46, 55, 26, 59, 40, 36, 15, 53,
+   34, 51, 20, 43, 31, 22, 10, 45,
+   25, 39, 14, 33, 19, 30,  9, 24,
+   13, 18,  8, 12,  7,  6,  5, 63
+};
+
+// DeBruijn sequence for 64 bit bitScanForward.
+static const int DeBruijnMultiplyLookupBSF64[64] =
+{
+    0,  1, 48,  2, 57, 49, 28,  3,
+   61, 58, 50, 42, 38, 29, 17,  4,
+   62, 55, 59, 36, 53, 51, 43, 22,
+   45, 39, 33, 30, 24, 18, 12,  5,
+   63, 47, 56, 27, 60, 41, 37, 16,
+   54, 35, 52, 21, 44, 32, 23, 11,
+   46, 26, 40, 15, 34, 20, 31, 10,
+   25, 14, 19,  9, 13,  8,  7,  6
+};
+
+// DeBruijn sequence for 32 bit bitScanForward and bitScanReverse.
+static const int DeBruijnMultiplyLookup[32] =
+{
+  0,   1, 28,  2, 29, 14, 24, 3,
+  30, 22, 20, 15, 25, 17,  4, 8,
+  31, 27, 13, 23, 21, 19, 16, 7,
+  26, 12, 18,  6, 11,  5, 10, 9
+};
+
+// ----------------------------------------------------------------------------
+// Tag WordSize_
+// ----------------------------------------------------------------------------
+// This parametrized tag is used for selecting a _popCountImpl() implementation.
+
+template <unsigned int NUM_BITS>
+struct WordSize_ {};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function setBitTo()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn setBitTo
+ * @headerfile <seqan/misc/bit_twiddling.h>
+ * @brief Set the bit with the given index to the given value.
+ *
+ * @signature void setBitTo(word, index, value);
+ *
+ * @param[in,out] word  The machine word (number) to set bits of (@link IntegerConcept @endlink).
+ * @param[in]     index The index of the bit in the word to set (@link IntegerConcept @endlink).
+ * @param[in]     value The value to set to, <tt>bool</tt>.
+ */
+
+template <typename TWord, typename TPos>
+inline void
+setBitTo(TWord & word, TPos index, bool value)
+{
+    // See http://www-graphics.stanford.edu/~seander/bithacks.html#ConditionalSetOrClearBitsWithoutBranching
+    word = (word & ~(1u << index)) | (-value & (1u << index));
+}
+
+// ----------------------------------------------------------------------------
+// Function setBit()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn setBit
+ * @headerfile <seqan/misc/bit_twiddling.h>
+ * @brief Set the bit with the given index to 1.
+ *
+ * @signature void setBit(word, index);
+ *
+ * @param[in,out] word  The word to set the bit of (@link IntegerConcept @endlink).
+ * @param[in]     index The index of the bit to set (@link IntegerConcept @endlink).
+ */
+
+template <typename TWord, typename TPos>
+inline void
+setBit(TWord & word, TPos index)
+{
+    word |= (1u << index);
+}
+
+// ----------------------------------------------------------------------------
+// Function clearBit()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn clearBit
+ * @headerfile <seqan/misc/bit_twiddling.h>
+ * @brief Set the bit with the given index to 0.
+ *
+ * @signature void clearBit(word, index);
+ *
+ * @param[in,out] word  The machine word to set the bit of (@link IntegerConcept @endlink).
+ * @param[in]     index The index of the bit to set to 0 (@link IntegerConcept @endlink).
+ */
+
+template <typename TWord, typename TPos>
+inline void
+clearBit(TWord & word, TPos index)
+{
+    word &= ~(1u << index);
+}
+
+// ----------------------------------------------------------------------------
+// Function clearAllBits()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn clearAllBits
+ * @headerfile <seqan/misc/bit_twiddling.h>
+ * @brief Set all bits to 0.
+ *
+ * @signature void clearAllBits(word);
+ *
+ * @param[in,out] word The word to clear all bits of (@link IntegerConcept @endlink).
+ */
+
+template <typename TWord>
+inline void
+clearBits(TWord & word)
+{
+    word = 0;
+}
+
+// ----------------------------------------------------------------------------
+// Function isBitSet()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn isBitSet
+ * @headerfile <seqan/misc/bit_twiddling.h>
+ * @brief Returns whether the bit with the given index is set to 1.
+ *
+ * @signature bool isBitSet(word, index);
+ *
+ * @param[in] word  The word to check (@link IntegerConcept @endlink).
+ * @param[in] index The index of the bit to check (@link IntegerConcept @endlink).
+ *
+ * @return bool Whether the bit with the given index is set in <tt>word</tt>.
+ */
+
+template <typename TWord, typename TIndex>
+inline bool
+isBitSet(TWord word, TIndex index)
+{
+    typedef typename MakeUnsigned<TWord>::Type TUnsignedWord;
+    return (word & (TUnsignedWord(1) << index)) != static_cast<TWord>(0);
+}
+
+// ----------------------------------------------------------------------------
+// Function hiBits()
+// ----------------------------------------------------------------------------
+
+template <typename TWord, typename TPos>
+SEQAN_HOST_DEVICE inline TWord
+hiBits(TWord word, TPos index)
+{
+    return word & ~((TWord(1) << (BitsPerValue<TWord>::VALUE - index)) - TWord(1));
+}
+
+// ----------------------------------------------------------------------------
+// Function popCount()
+// ----------------------------------------------------------------------------
+// The compiler-dependent implementations of _popCountImpl() follow.
+
+/*!
+ * @fn popCount
+ * @headerfile <seqan/misc/bit_twiddling.h>
+ * @brief Returns number of set bits in an integer.
+ *
+ * @signature unsigned popCount(words);
+ *
+ * @param[in] word The word to count the number of set bits of (@link IntegerConcept @endlink).
+ *
+ * @return unsigned The number of set bits in <tt>word</tt>.
+ */
+
+template <typename TWord>
+SEQAN_HOST_DEVICE
+inline unsigned
+popCount(TWord word)
+{
+    return _popCountImpl(word, WordSize_<BitsPerValue<TWord>::VALUE>());
+}
+
+// Implementing this platform-independent is tricky.  There are two points to platform independentness. First, the
+// choice of compiler and second the used CPU.  Currently, we do not perform any checks for the CPU and assume that
+// the Intel intrinsic POPCNT is available.  The function is implemented to work on the supported compilers GCC/MINGW,
+// CLANG (which has the same interface as GCC here) and Visual C++.
+//
+// GCC, MINGW and CLANG provide the intrinsics __builtin_popcount, __builtin_popcountl, and __builtin_popcountll for
+// the types unsigned, unsigned long, and unsigned long long.  Starting with version 2008, Visual C++ provides the
+// intrinsics __popcnt16, __popcnt, and __popcnt64 for 16, 32, and 64 bit words.
+//
+// The functions below are implemented as follows.  _popCountImplGeneric() is used if there are no intrinsics provided
+// by the compiler (the case for Visual C++ 2008).  Otherwise, we define different overloads of the function
+// _popCountImpl() that are given the length of the word as a template argument.  If necessary, we copy the word in a
+// variable of next largest size and call the best suited builtin on this copy.
+
+// ----------------------------------------------------------------------------
+// Function _popCountImplGeneric()
+// ----------------------------------------------------------------------------
+// Generic implementation of counting bits.  Taken from http://graphics.stanford.edu/~seander/bithacks.html
+//
+// Brian Kernighan's method goes through as many iterations as there are set bits. So if we have a 32-bit word with
+// only the high bit set, then it will only go once through the loop.
+//
+// Published in 1988, the C Programming Language 2nd Ed. (by Brian W. Kernighan and Dennis M. Ritchie) mentions this
+// in exercise 2-9. On April 19, 2006 Don Knuth pointed out to me that this method "was first published by Peter
+// Wegner in CACM 3 (1960), 322. (Also discovered independently by Derrick Lehmer and published in 1964 in a book
+// edited by Beckenbach.)"
+
+template <typename TWord>
+inline unsigned
+_popCountImplGeneric(TWord word)  // Note that word is copied!
+{
+    typename MakeUnsigned<TWord>::Type x = word;
+    unsigned int c = 0;  // c accumulates the total bits set in v
+    for (c = 0; x; c++)
+        x &= x - 1;  // clear the least significant bit set
+    return c;
+}
+
+// ----------------------------------------------------------------------------
+// Function _popCountImpl()
+// ----------------------------------------------------------------------------
+// CUDA implementations.
+
+#if defined(__CUDA_ARCH__)
+
+template <typename TWord>
+SEQAN_DEVICE
+inline unsigned _popCountImpl(TWord word, WordSize_<32> const & /*tag*/)
+{
+    return __popc(static_cast<__uint32>(word));
+}
+
+template <typename TWord>
+SEQAN_DEVICE
+inline unsigned _popCountImpl(TWord word, WordSize_<16> const & /*tag*/)
+{
+    return __popc(static_cast<__uint32>(word));
+}
+
+template <typename TWord>
+SEQAN_DEVICE
+inline unsigned _popCountImpl(TWord word, WordSize_<8> const & /*tag*/)
+{
+    return __popc(static_cast<__uint32>(word));
+}
+
+#else   // #if defined(__CUDA_ARCH__)
+
+// ----------------------------------------------------------------------------
+// Function _popCountImpl()
+// ----------------------------------------------------------------------------
+// MSVC implementations.
+
+#if defined(_MSC_VER) && (_MSC_VER <= 1400)  // MSVC <= 2005, no intrinsic.
+
+template <typename TWord, unsigned NUM_BITS>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<NUM_BITS> const & /*tag*/)
+{
+    return _popCountImplGeneric(word);
+}
+
+#endif  // #if defined(_MSC_VER) && (_MSC_VER <= 1400)  // MSVC <= 2005, no intrinsic.
+
+#if defined(_MSC_VER) && (_MSC_VER > 1400)  // MSVC >= 2008, has intrinsic
+
+#if defined(__SSE4_2__)
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<64> const & /*tag*/)
+{
+    // 64-bit Windows, 64 bit intrinsic available
+    return __popcnt64(static_cast<__uint64>(word));
+}
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<32> const & /*tag*/)
+{
+    return __popcnt(static_cast<__uint32>(word));
+}
+
+#else // #if defined(__SSE4_2__)
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<64> const & /*tag*/)
+{
+#if defined(_WIN64)
+
+#if defined(__SSE4_2__)
+    // 64-bit Windows, SSE4.2 bit intrinsic available
+    return _mm_popcnt_u64(static_cast<__uint64>(word));
+#else
+    // 64-bit Windows, 64 bit intrinsic available
+    return __popcnt64(static_cast<__uint64>(word));
+#endif
+
+#else // #if defined(_WIN64)
+
+    // 32-bit Windows, 64 bit intrinsic not available
+    return __popcnt(static_cast<__uint32>(word)) + __popcnt(static_cast<__uint32>(word >> 32));
+
+#endif // #if defined(_WIN64)
+}
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<32> const & /*tag*/)
+{
+#if defined(__SSE4_2__)
+    // SSE4.2 bit intrinsic available
+    return _mm_popcnt_u32(static_cast<__uint32>(word));
+#else
+    return __popcnt(static_cast<__uint32>(word));
+#endif
+}
+
+#endif // #if defined(__SSE4_2__)
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<16> const & /*tag*/)
+{
+    return __popcnt16(static_cast<__uint16>(word));
+}
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<8> const & /*tag*/)
+{
+    return _popCountImpl(static_cast<const __uint16>(word), WordSize_<16>());
+}
+
+#endif  // #if defined(_MSC_VER) && (_MSC_VER <= 1400)
+
+// ----------------------------------------------------------------------------
+// Function _popCountImpl()
+// ----------------------------------------------------------------------------
+// GCC or CLANG implementations.
+// SSE4.2 popcnt is emitted when compiling with -mpopcnt or -march=corei7
+
+#if !defined(_MSC_VER)  // GCC or CLANG
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<64> const & /*tag*/)
+{
+    return __builtin_popcountll(static_cast<unsigned long long>(word));
+}
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<32> const & /*tag*/)
+{
+    return __builtin_popcount(static_cast<unsigned int>(word));
+}
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<16> const & /*tag*/)
+{
+    return _popCountImpl(static_cast<__uint32>(word), WordSize_<32>());
+}
+
+template <typename TWord>
+inline unsigned
+_popCountImpl(TWord word, WordSize_<8> const & /*tag*/)
+{
+    return _popCountImpl(static_cast<__uint32>(word), WordSize_<32>());
+}
+
+#endif    // GCC or CLANG
+
+#endif    // #if !defined(__CUDA_ARCH__)
+
+// ----------------------------------------------------------------------------
+// Function printBits()
+// ----------------------------------------------------------------------------
+
+//template <typename TValue>
+//inline void printBits(TValue word)
+//{
+//    unsigned bitsPerValue = BitsPerValue<TValue>::VALUE;
+//    TValue one = 1;
+//    for (TValue i = 0; i < bitsPerValue; ++i)
+//        std::cout << ((word >> i) & one);
+//    std::cout << std::endl;
+//}
+
+//template <typename TValue, typename TSize>
+//inline std::ostream & printBits(std::ostream & stream, TValue word, TSize blockSize)
+//{
+//    unsigned bitsPerValue = BitsPerValue<TValue>::VALUE;
+//    bool temp;
+//    for (int i = bitsPerValue - 1; i >= 0; --i)
+//    {
+//        temp = (word >> i) & 1;
+//        stream << temp;
+//        if ((bitsPerValue - i) % blockSize == 0)
+//            stream << " ";
+//    }
+//    return stream;
+//}
+
+// ----------------------------------------------------------------------------
+// Function testAllZeros()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn testAllZeros
+ * @headerfile <seqan/misc.h>
+ * @brief Tests whether all bits of the given value are set to <b>0</b>.
+ *
+ * @signature bool testAllZeros(val)
+ *
+ * @param[in]  val The value to check the bits for. Must be of type @link IntegerConcept @endlink.
+ *
+ * @return bool  <tt>true</tt> if all bits are set to <b>0</b>, <tt>false</tt> otherwise.
+ *
+ * @see testAllOnes
+ */
+
+template <typename TWord>
+inline bool testAllZeros(TWord const & val)
+{
+    return val == 0;
+}
+
+// ----------------------------------------------------------------------------
+// Function testAllOnes()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn testAllOnes
+ * @headerfile <seqan/misc.h>
+ * @brief Tests whether all bits of the given value are set to <b>1</b>.
+ *
+ * @signature bool testAllOnes(val)
+ *
+ * @param[in]  val The value to check the bits for. Must be of type @link IntegerConcept @endlink.
+ *
+ * @return bool <tt>true</tt> if all bits are set to <b>1</b>, <tt>false</tt> otherwise.
+ *
+ * @see testAllZeros
+ */
+
+template <typename TWord>
+inline bool _testAllOnes(TWord const & val, False)
+{
+    return val == ~static_cast<TWord>(0);
+}
+
+template <typename TWord>
+inline bool testAllOnes(TWord const & val)
+{
+    return _testAllOnes(val, typename Is<SimdVectorConcept<TWord> >::Type());
+}
+
+// ----------------------------------------------------------------------------
+// Function _bitScanReverseGeneric()                     [Platform independent]
+// ----------------------------------------------------------------------------
+
+// bitScanReverse for 32 bit integers using DeBruijn sequence by Eric Cole, January 8, 2006.
+template <typename TWord>
+inline TWord
+_bitScanReverseGeneric(TWord word, WordSize_<32>)
+{
+    return DeBruijnMultiplyLookup[static_cast<__uint32>(word * 0x077CB531U) >> 27];
+}
+
+// bitScanReverse for 64 bit integers using DeBruijn sequence by Kim Walisch and Mark Dickinson.
+template <typename TWord>
+inline TWord
+_bitScanReverseGeneric(TWord word, WordSize_<64>)
+{
+    word |= word >> 1; word |= word >> 2; word |= word >> 4; word |= word >> 8; word |= word >> 16; word |= word >> 32;
+    return DeBruijnMultiplyLookupBSR64[static_cast<__uint64>(word * 0x03f79d71b4cb0a89ULL) >> 58];
+}
+
+// ----------------------------------------------------------------------------
+// Function _bitScanReverse()                            [Platform independent]
+// ----------------------------------------------------------------------------
+
+template <typename TWord, unsigned int NUM_BITS>
+inline TWord
+_bitScanReverse(TWord word, WordSize_<NUM_BITS>)
+{
+    return _bitScanReverseGeneric(word, WordSize_<NUM_BITS>());
+}
+
+// ----------------------------------------------------------------------------
+// Function _bitScanForwardGeneric()                     [Platform independent]
+// ----------------------------------------------------------------------------
+
+// bitScanForward implementations for 64 and 32 bit values using DeBruijn sequence by Martin LŠuter, Charles E. Leiserson,
+// Harald Prokop and Keith H. Randall; "Using de Bruijn Sequences to Index a 1 in a Computer Word"; (1997)
+
+// Note, the cast of word to a signed integer is necessary to fix compiler warning C4146 on Windows platforms.
+template <typename TWord>
+inline TWord
+_bitScanForwardGeneric(TWord word, WordSize_<32>)
+{
+    return DeBruijnMultiplyLookup[static_cast<__uint32>(((word & -static_cast<__int32>(word)) * 0x077CB531U)) >> 27];
+}
+
+template <typename TWord>
+inline TWord
+_bitScanForwardGeneric(TWord word, WordSize_<64>)
+{
+    return DeBruijnMultiplyLookupBSF64[static_cast<__uint64>((word & -static_cast<__int64>(word)) * 0x03f79d71b4cb0a89ULL) >> 58];
+}
+
+// ----------------------------------------------------------------------------
+// Function _bitScanForward()                            [Platform independent]
+// ----------------------------------------------------------------------------
+
+template <typename TWord, unsigned int NUM_BITS>
+inline TWord
+_bitScanForward(TWord word, WordSize_<NUM_BITS>)
+{
+    return _bitScanForwardGeneric(word, WordSize_<NUM_BITS>());
+}
+
+#if defined(PLATFORM_GCC) || defined(PLATFORM_WINDOWS_MINGW)
+
+template <typename TWord>
+inline TWord
+_bitScanReverse(TWord word, WordSize_<64>)
+{
+    return 63 - __builtin_clzll(static_cast<unsigned long long>(word));
+}
+
+template <typename TWord>
+inline TWord
+_bitScanReverse(TWord word, WordSize_<32>)
+{
+    return 31 - __builtin_clz(static_cast<unsigned int>(word));
+}
+
+
+template <typename TWord>
+inline TWord
+_bitScanForward(TWord word, WordSize_<64>)
+{
+    return __builtin_ctzll(static_cast<unsigned long long>(word));
+}
+
+template <typename TWord>
+inline TWord
+_bitScanForward(TWord word, WordSize_<32>)
+{
+    return __builtin_ctz(static_cast<unsigned int>(word));
+}
+#else
+#ifdef PLATFORM_WINDOWS
+#if (SEQAN_IS_64_BIT)
+
+template <typename TWord>
+inline TWord
+_bitScanReverse(TWord word, WordSize_<64>)
+{
+    unsigned long index;
+    _BitScanReverse64(&index, static_cast<unsigned __int64>(word));
+    return index;
+}
+
+template <typename TWord>
+inline TWord
+_bitScanForward(TWord word, WordSize_<64>)
+{
+    unsigned long index;
+    _BitScanForward64(&index, static_cast<unsigned __int64>(word));
+    return index;
+}
+#else
+
+template <typename TWord>
+inline TWord
+_bitScanReverse(TWord word, WordSize_<64>)
+{
+    unsigned long index;
+    unsigned long hi = word >> 32;
+    if (hi == 0u)
+    {
+        _BitScanReverse(&index, word);
+        return index;
+    }
+    _BitScanReverse(&index, hi);
+    return index + 32;
+}
+
+template <typename TWord>
+inline TWord
+_bitScanForward(TWord word, WordSize_<64>)
+{
+    unsigned long index;
+    unsigned long lo = word & ~static_cast<unsigned long>(0);
+    if (lo == 0u)
+    {
+        _BitScanForward(&index, word >> 32);
+        return index + 32;
+    }
+    _BitScanForward(&index, lo);
+    return index;
+}
+#endif  // if (SEQAN_IS_64_BIT)
+
+template <typename TWord>
+inline TWord
+_bitScanReverse(TWord word, WordSize_<32>)
+{
+    unsigned long index;
+    _BitScanReverse(&index, static_cast<unsigned long>(word));
+    return index;
+}
+
+template <typename TWord>
+inline TWord
+_bitScanForward(TWord word, WordSize_<32>)
+{
+    unsigned long index;
+    _BitScanForward(&index, static_cast<unsigned long>(word));
+    return index;
+}
+#endif  // #if defined(PLATFORM_GCC) || defined(PLATFORM_WINDOWS_MINGW)
+#endif  // #ifdef PLATFORM_GCC
+
+// ----------------------------------------------------------------------------
+// Function bitScanReverse()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn bitScanReverse
+ * @headerfile <seqan/misc.h>
+ * @brief Returns the index of the last set bit in the binary representation of the given value.
+ * @note If <tt>val</tt> is 0 the return value is undefined.
+ *
+ * @signature TWord bitScanReverse(val)
+ *
+ * @param[in]  val The value to scan. Has to be non-zero.
+ *
+ * @return TWord The index of the last set bit in <tt>val</tt>, where <tt>TWord</tt> is the value of <tt>val</tt>.
+ *
+ * @see bitScanForward
+ */
+
+template <typename TWord>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TWord> >, TWord)
+bitScanReverse(TWord word)
+{
+   SEQAN_ASSERT_NEQ(word, static_cast<TWord>(0));
+
+   return _bitScanReverse(word, WordSize_<(BitsPerValue<TWord>::VALUE <= 32) ? 32 : BitsPerValue<TWord>::VALUE>());
+}
+
+// ----------------------------------------------------------------------------
+// Function bitScanForward()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn bitScanForward
+ * @headerfile <seqan/misc.h>
+ * @brief Returns the index of the first set bit in the binary representation of the given value.
+ * @note If <tt>val</tt> is 0 the return value is undefined.
+ *
+ * @signature TWord bitScanForward(val)
+ *
+ * @param[in]  val The value to scan. Has to be non-zero.
+ *
+ * @return TWord The index of the first set bit in <tt>val</tt>, where <tt>TWord</tt> is the value of <tt>val</tt>.
+ *
+ * @see bitScanReverse
+ */
+
+template <typename TWord>
+inline SEQAN_FUNC_ENABLE_IF( Is<IntegerConcept<TWord> >, TWord)
+bitScanForward(TWord word)
+{
+   SEQAN_ASSERT_NEQ(word, static_cast<TWord>(0));
+   return _bitScanForward(word, WordSize_<(BitsPerValue<TWord>::VALUE <= 32) ? 32 : BitsPerValue<TWord>::VALUE>());
+}
+
+}  // namespace seqan
+
+#endif // #ifndef SEQAN_MISC_BIT_TWIDDLING_H_
diff --git a/seqan/bam_io/sam_writer.h b/seqan/misc/bit_twiddling_functors.h
similarity index 58%
rename from seqan/bam_io/sam_writer.h
rename to seqan/misc/bit_twiddling_functors.h
index 627d7d9..9e146e0 100644
--- a/seqan/bam_io/sam_writer.h
+++ b/seqan/misc/bit_twiddling_functors.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,13 +29,16 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements basic functors.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_SAM_WRITER_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_SAM_WRITER_H_
+#ifndef INCLUDE_SEQAN_MISC_BIT_TWIDDLING_FUNCTORS_H_
+#define INCLUDE_SEQAN_MISC_BIT_TWIDDLING_FUNCTORS_H_
 
-namespace seqan {
+namespace seqan
+{
 
 // ============================================================================
 // Forwards
@@ -45,117 +48,93 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-class SamWriter_ :
-    public XamWriter_
-{
-public:
-    // Pointer to the output stream to write to.  Used such that we can also write SAM to stdout.
-    std::ostream * _stream;
-    // The file stream to write to if we do not write to stdout.  Pointed to by _stream.
-    std::ofstream _fstream;
-
-    SamWriter_() :
-        XamWriter_(), _stream(0)
-    {}
-
-    SamWriter_(CharString const & filename);
-
-    // XamWriter_ interface.
-
-    virtual int open(CharString const & filename);
-    virtual bool isGood();
-    virtual int writeHeader(BamHeader const & header, BamIOContext<StringSet<CharString> > const & context);
-    virtual int writeRecord(BamAlignmentRecord const & record, BamIOContext<StringSet<CharString> > const & context);
-    virtual int flush();
-    virtual int close();
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
 // ----------------------------------------------------------------------------
-// Member Function SamWriter_::SamWriter_()
+// Functor FunctorIdentity
 // ----------------------------------------------------------------------------
 
-inline SamWriter_::SamWriter_(CharString const & filename) :
-    XamWriter_(filename), _stream(0)
+struct FunctorIdentity
 {
-    this->open(filename);
-}
+    template <typename TValue>
+    inline TValue const & operator()(TValue const & val) const
+    {
+        return val;
+    }
+};
 
 // ----------------------------------------------------------------------------
-// Member Function SamWriter_::open()
+// Functor FunctorBitwiseAnd
 // ----------------------------------------------------------------------------
 
-inline int SamWriter_::open(CharString const & filename)
+struct FunctorBitwiseAnd
 {
-    if (filename == "-")
-    {
-        this->_stream = &std::cout;
-    }
-    else
+    template<typename TValue>
+    inline TValue operator()(TValue const & valLhs, TValue const & valRhs) const
     {
-        this->_stream = &this->_fstream;
-        this->_fstream.open(toCString(filename), std::ios::binary | std::ios::out);
-        if (!this->_fstream.good())
-            return 1;
+        return valLhs & valRhs;
     }
-
-    return 0;
-}
+};
 
 // ----------------------------------------------------------------------------
-// Member Function SamWriter_::isGood()
+// Functor FunctorBitwiseOr
 // ----------------------------------------------------------------------------
 
-inline bool SamWriter_::isGood()
+struct FunctorBitwiseOr
 {
-    return this->_stream->good();
-}
+    template <typename TValue>
+    inline TValue operator()(TValue const & valLhs, TValue const & valRhs) const
+    {
+        return valLhs | valRhs;
+    }
+};
 
 // ----------------------------------------------------------------------------
-// Member Function SamWriter_::writeHeader()
+// Functor FunctorBitwiseXor
 // ----------------------------------------------------------------------------
 
-inline int SamWriter_::writeHeader(BamHeader const & header, BamIOContext<StringSet<CharString> > const & context)
+struct FunctorBitwiseXor
 {
-    return seqan::write2(*this->_stream, header, context, Sam());
-}
+    template <typename TValue>
+    inline TValue operator()(TValue const & valLhs, TValue const & valRhs) const
+    {
+        return valLhs ^ valRhs;
+    }
+};
 
 // ----------------------------------------------------------------------------
-// Member Function SamWriter_::writeRecord()
+// Functor FunctorBitwiseNot
 // ----------------------------------------------------------------------------
 
-inline int SamWriter_::writeRecord(BamAlignmentRecord const & record, BamIOContext<StringSet<CharString> > const & context)
+struct FunctorBitwiseNot
 {
-    return seqan::write2(*this->_stream, record, context, Sam());
-}
+    template <typename TValue>
+    inline TValue operator()(TValue const & val) const
+    {
+        return ~val;
+    }
+};
 
 // ----------------------------------------------------------------------------
-// Member Function SamWriter_::flush()
+// Functor FunctorNested
 // ----------------------------------------------------------------------------
 
-inline int SamWriter_::flush()
+template <typename TBinaryFunctor, typename TUnaryFunctor1, typename TUnaryFunctor2>
+struct FunctorNested
 {
-    return streamFlush(*this->_stream);
-}
+    template <typename TValue>
+    inline TValue operator()(TValue const & lhs, TValue const & rhs) const
+    {
+        return TBinaryFunctor()(TUnaryFunctor1()(lhs), TUnaryFunctor2()(rhs));
+    }
+};
 
-// ----------------------------------------------------------------------------
-// Member Function SamWriter_::close()
-// ----------------------------------------------------------------------------
+// ============================================================================
+// Metafunctions
+// ============================================================================
 
-inline int SamWriter_::close()
-{
-    if (this->_stream == &this->_fstream)  // not to stdout
-        this->_fstream.close();
-    return 0;
-}
+// ============================================================================
+// Functions
+// ============================================================================
 
-}  // namespace seqan
+}
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_SAM_WRITER_H_
+#endif // INCLUDE_SEQAN_MISC_BIT_TWIDDLING_FUNCTORS_H_
diff --git a/seqan/misc/cmdparser/INFO b/seqan/misc/cmdparser/INFO
deleted file mode 100644
index 9b4a35f..0000000
--- a/seqan/misc/cmdparser/INFO
+++ /dev/null
@@ -1,11 +0,0 @@
-Name: cmdparser
-Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Maintainer: Stephan Aiche <stephan.aiche@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: experimental
-Description: Commandline parser module.
- This module contains all command line parsing code.
diff --git a/seqan/misc/cmdparser/cmdoption.h b/seqan/misc/cmdparser/cmdoption.h
deleted file mode 100644
index b0051a7..0000000
--- a/seqan/misc/cmdparser/cmdoption.h
+++ /dev/null
@@ -1,664 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDOPTION_H_
-#define CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDOPTION_H_
-
-#include <seqan/sequence.h>
-
-namespace seqan {
-
-/*
- * TODO: support some more formating options
- * TODO: store/return error code (invalid argument, invalid option, etc.)
- * TODO: support named arguments (e.g. <ARG1> -> <INPUT FILE>)
- * TODO: support user defined option argument names (e.g., -q QUALITY instead of -q NUM
- * TODO: correct parameter ordering of nearly all cmdparser function to be seqan conform f(out,in)
- */
-struct OptionType
-{
-    // TODO(holtgrew): Should be all upper case!
-    enum
-    {
-        Bool = 1,                   // option needs no argument, value is true iff given on command line
-        Boolean = 1,                // option needs no argument, value is true iff given on command line
-        String = 2,                 // argument is a string
-        Int = 4,                    // ... an integer
-        Integer = 4,                // ... an integer
-        Double = 8,                 // ... a float
-        Mandatory = 16,             // option must be set
-        Label = 32,                 // automatically print a label for the argument(s) on the help screen
-        List = 64,                  // option is a list of values
-        Hidden = 128,               // hide this option from the help screen
-        INPUTFILE = 256,            // this option is an input file .. is implicitly also a string, since paths/filenames are strings
-        OUTPUTFILE = 512            // this option is an output file .. is implicitly also a string, since paths/filenames are strings
-    };
-};
-
-// ----------------------------------------------------------------------------
-// Class CommandLineOption
-// ----------------------------------------------------------------------------
-
-/*
-.Class.CommandLineOption:
-..cat:Miscellaneous
-..summary:Stores information for a specific command line option.
-..signature:CommandLineOption
-..remarks:A @Class.CommandLineOption@ object can be added to a @Class.CommandLineParser@ via @Function.addOption@.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-/*
-.Memfunc.CommandLineOption#CommandLineOption:
-..class:Class.CommandLineOption
-..summary:Constructor
-..signature:CommandLineOption ()
-..signature:CommandLineOption (shortName, longName[, argumentsPerOption], helpText, optionType[, defaultValue])
-..param.shortName:A @Shortcut.CharString@ containing the short-name option identifier (e.g. $"h"$ for the $-h/--help$ option).
-Although not suggested the short-name can contain more than 1 character.
-...remarks:Note that the leading "-" is not passed.
-..param.longName:A @Shortcut.CharString@ containing the long-name option identifier (e.g. $"help"$ for the $-h/--help$ option).
-...type:Shortcut.CharString
-...remarks:Note that the leading "--" is not passed.
-..param.argumentsPerOption:The number of required arguments per option (e.g. if set to 3 then 3 arguments must follow the option: "-foo x1 x2 x3").
-...default:0 for boolean options and 1 for the rest.
-..param.helpText:A @Shortcut.CharString@ containing the help text associated with this option.
-...type:Shortcut.CharString
-..param.optionType:Option type. This can be the sum of the some of the following values:
-...tableheader:Flag|Value|Description
-...table:$OptionType::Bool$ or $OptionType::Boolean$|1|Option needs no argument, value is true iff given on command line
-...table:$OptionType::String$|2|Argument is a string
-...table:$OptionType::Int$ or $OptionType::Integer$|4|An integer
-...table:$OptionType::Double$|8|A float
-...table:$OptionType::Mandatory$|16|Option must be set
-...table:$OptionType::Label$|32|Automatically print a label for the argument(s) on the help screen
-...table:$OptionType::List$|64|Option is a list of values
-...table:$OptionType::Hidden$|128|Hide this option from the help screen
-...table:$OptionType::INPUTFILE$|256|Argument is an input file
-...table:$OptionType::OUTPUTFILE$|512|Argument is an output file
-..param.defaultValue:The default value of this option.
-...default:No default value.
-*/
-
-class CommandLineOption
-{
-public:
-    CharString          longName;           // long option name
-    CharString          shortName;          // short option name
-    CharString          arguments;          // argument names seperated by spaces
-
-    CharString          helpText;           // option description
-    int                 optionType;         // option type
-    int                 argumentsPerOption; // number of arguments per option
-
-    // ----------------------------------------------------------------------------
-    // Members to store the values
-    // ----------------------------------------------------------------------------
-    String<CharString>  defaultValue;
-    String<CharString>  value;
-
-    // ----------------------------------------------------------------------------
-    // Members for restrictions
-    // ----------------------------------------------------------------------------
-    CharString            minValue;
-    CharString            maxValue;
-    StringSet<CharString> validValues;
-
-    // ----------------------------------------------------------------------------
-    // Constructors
-    // ----------------------------------------------------------------------------
-    CommandLineOption() {}
-
-    CommandLineOption(CharString const & _short,
-                      CharString const & _long,
-                      CharString const & _help,
-                      int _type) :
-        longName(_long),
-        shortName(_short),
-        helpText(_help),
-        optionType(_type),
-        argumentsPerOption(1),
-        minValue(""),
-        maxValue("")
-    {}
-
-    CommandLineOption(CharString const & _short,
-                      CharString const & _long,
-                      int _argumentsPerOption,
-                      CharString const & _help,
-                      int _type) :
-        longName(_long),
-        shortName(_short),
-        helpText(_help),
-        optionType(_type),
-        argumentsPerOption(_argumentsPerOption),
-        minValue(""),
-        maxValue("")
-    {}
-
-    template <typename TValue>
-    CommandLineOption(CharString const & _short,
-                      CharString const & _long,
-                      int _argumentsPerOption,
-                      CharString const & _help,
-                      int _type,
-                      TValue const & _default) :
-        longName(_long),
-        shortName(_short),
-        helpText(_help),
-        optionType(_type),
-        argumentsPerOption(_argumentsPerOption),
-        minValue(""),
-        maxValue("")
-    {
-        std::stringstream strm;
-        strm << _default;
-        appendValue(defaultValue, strm.str());
-        append(helpText, " (default: ");
-        append(helpText, strm.str());
-        appendValue(helpText, ')');
-    }
-
-    template <typename TValue>
-    CommandLineOption(CharString const & _short,
-                      CharString const & _long,
-                      CharString const & _help,
-                      int _type,
-                      TValue const & _default) :
-        longName(_long),
-        shortName(_short),
-        helpText(_help),
-        optionType(_type),
-        argumentsPerOption(1),
-        minValue(""),
-        maxValue("")
-    {
-        std::stringstream strm;
-        strm << _default;
-        appendValue(defaultValue, strm.str());
-        append(helpText, " (default: ");
-        append(helpText, strm.str());
-        appendValue(helpText, ')');
-    }
-
-};
-
-// ----------------------------------------------------------------------------
-// Function addArgumentText()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.addArgumentText:
-..summary:Return a @Class.CommandLineOption@ object extended by an argument text.
-..cat:Miscellaneous
-..signature:addArgumentText(option, text)
-..param.option:A @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..param.text:A @Shortcut.CharString@ containing the argument text.
-...type:Shortcut.CharString
-..returns:The option extended by the argument text.
-Instead of using $option$, the return value can be used as argument for @Function.addOption@.
-..remarks:The result type is a @Class.CommandLineOption@ object.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline CommandLineOption
-addArgumentText(CommandLineOption const & opt, CharString const & text)
-{
-    CommandLineOption temp = opt;
-    temp.arguments = " ";
-    append(temp.arguments, text);
-    return temp;
-}
-
-// ----------------------------------------------------------------------------
-// Function isStringOption()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isStringOption
-..summary:Returns whether option argument can be a string.
-..cat:Miscellaneous
-..signature:isStringOption(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the option argument can be a string.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isStringOption(CommandLineOption const & me)
-{
-    return (me.optionType & (OptionType::String | OptionType::INPUTFILE | OptionType::OUTPUTFILE)) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isBooleanOption()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isBooleanOption
-..summary:Returns whether option is a switch.
-..cat:Miscellaneous
-..signature:isBooleanOption(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the option is a switch.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isBooleanOption(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::Boolean) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isDoubleOption()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isDoubleOption
-..summary:Returns whether option argument can be a double.
-..cat:Miscellaneous
-..signature:isDoubleOption(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the option argument can be a double.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isDoubleOption(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::Double) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isIntOption()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isIntOption
-..summary:Returns whether option argument can be an integer.
-..cat:Miscellaneous
-..signature:isIntOption(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the option argument can be an integer.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isIntOption(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::Int) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isHiddenOption()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isHiddenOption
-..summary:Returns whether option is hidden on the help screen.
-..cat:Miscellaneous
-..signature:isHiddenOption(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the option is hidden on the help screen.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isHiddenOption(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::Hidden) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isOptionMandatory()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isOptionMandatory
-..summary:Returns whether option is mandatory.
-..cat:Miscellaneous
-..signature:isOptionMandatory(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the option is mandatory.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isOptionMandatory(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::Mandatory) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isLabelOption()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isLabelOption
-..summary:Returns whether an option label should be printed on the help screen.
-..cat:Miscellaneous
-..signature:isLabelOption(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if an option label should be printed on the help screen.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isLabelOption(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::Label) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isOptionList()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isOptionList
-..summary:Returns whether the option can be given multiple times.
-..cat:Miscellaneous
-..signature:isOptionList(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the option can be given multiple times on command line.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isOptionList(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::List) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isInputFile()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isInputFile
-..summary:Returns whether the argument of the given option is an input file.
-..cat:Miscellaneous
-..signature:isInputFile(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the argument of the option is an input file.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isInputFile(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::INPUTFILE) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isOutputFile()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isOutputFile
-..summary:Returns whether the argument of the given option is an output file.
-..cat:Miscellaneous
-..signature:isOutputFile(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:$true$ if the argument of the option is an output file.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isOutputFile(CommandLineOption const & me)
-{
-    return (me.optionType & OptionType::OUTPUTFILE) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function setOptionType()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.setOptionType:
-..summary:Set the option type.
-..cat:Miscellaneous
-..signature:setOptionType(option, newOptionType)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..param.newOptionType:Option Type.
-..see:Memfunc.CommandLineOption#CommandLineOption.param.optionType
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-setOptionType(CommandLineOption & me, const int _newOptionType)
-{
-    me.optionType = _newOptionType;
-}
-
-// ----------------------------------------------------------------------------
-// Function argumentText()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.argumentText
-..summary:Returns the argument text of a @Class.CommandLineOption@ object.
-..cat:Miscellaneous
-..signature:argumentText(option)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..returns:A text consisting of label and help text of the option.
-...type:Shortcut.CharString
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline CharString
-argumentText(CommandLineOption const & me)
-{
-    if (empty(me.arguments))
-    {
-        CharString label;
-        if (isLabelOption(me))
-        {
-            if (isStringOption(me))
-                label = " STR";
-            else if (isIntOption(me) || isDoubleOption(me))
-                label = " NUM";
-            else if (isInputFile(me) || isOutputFile(me))
-                label = " FILE";
-            /*
-            else if (isInputFileList(me) || isOutputFileList(me))
-                label = " FILES";
-            */
-            if (me.argumentsPerOption >= 2)
-            {
-                std::stringstream strm;
-                if (!empty(label))
-                    for (int i = 0; i < me.argumentsPerOption; ++i)
-                        strm << label << (i + 1);
-                return strm.str();
-            }
-        }
-        return label;
-    }
-    else
-        return me.arguments;
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _writeOptName()
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline void
-_writeOptName(TStream & target, CommandLineOption const & me)
-{
-    //IOREV _notio_ irrelevant for iorev
-    streamPut(target, empty(me.shortName) ? "" : "-");
-    streamPut(target, me.shortName);
-    streamPut(target, (empty(me.shortName) || empty(me.longName)) ? "" : ", ");
-    if (!empty(me.longName))
-    {
-        streamPut(target, "--");
-        streamPut(target, me.longName);
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function write()                                           CommandLineOption
-// ----------------------------------------------------------------------------
-
-/*
-.Function.write
-..summary:Writes the basic information about the @Class.CommandLineOption@ to the provided stream.
-..cat:Miscellaneous
-..signature:write(stream,option)
-..param.stream:The target stream.
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TStream>
-inline void
-write(TStream & target, CommandLineOption const & me)
-{
-    //IOREV _nodoc_ this specialization is not documented
-    streamPut(target, '\t');
-    _writeOptName(target, me);
-    streamPut(target, '\t');
-    streamPut(target, '\t');
-    streamPut(target, me.helpText);
-}
-
-// ----------------------------------------------------------------------------
-// operator<<()                                               CommandLineOption
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline TStream &
-operator<<(TStream & target, CommandLineOption const & source)
-{
-    //IOREV _nodoc_ this specialization is not documented
-    write(target, source);
-    return target;
-}
-
-// ----------------------------------------------------------------------------
-// Function setMinValue()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.setMinValue
-..summary:Sets the minimum value of a @Class.CommandLineOption@ object.
-..cat:Miscellaneous
-..signature:setMinValue(option,minValue)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..param.minValue:A @Shortcut.CharString@ containing a string representation of the minimum value of the @Class.CommandLineOption@.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-setMinValue(CommandLineOption & me, const CharString _minValue)
-{
-    // TODO: check if value is applicable
-    // TODO: if max exists, check if the interval is not empty
-    me.minValue = _minValue;
-}
-
-// ----------------------------------------------------------------------------
-// Function setMaxValue()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.setMaxValue
-..summary:Sets the maximum value of a @Class.CommandLineOption@ object.
-..cat:Miscellaneous
-..signature:setMaxValue(option,maxValue)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..param.maxValue:A @Shortcut.CharString@ containing a string representation of the maximum value of the @Class.CommandLineOption@.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-setMaxValue(CommandLineOption & me, const CharString _maxValue)
-{
-    // TODO: check if value is applicable
-    // TODO: if min exists, check if the interval is not empty
-    me.maxValue = _maxValue;
-}
-
-// ----------------------------------------------------------------------------
-// Function setValidValues()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.setValidValues
-..summary:Sets the set of allowed values of a @Class.CommandLineOption@ object.
-..cat:Miscellaneous
-..signature:setValidValues(option,values)
-..param.option:The @Class.CommandLineOption@ object.
-...type:Class.CommandLineOption
-..param.values:A $String<CharString>$ containing all valid entries for the option.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-setValidValues(CommandLineOption & me, StringSet<CharString> const & _values)
-{
-    // TODO: check for collision with min/max
-    // TODO: check if _values are applicable to option
-    me.validValues = _values;
-}
-
-} // namespace seqan
-
-#endif // CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDOPTION_H_
diff --git a/seqan/misc/cmdparser/cmdparser.h b/seqan/misc/cmdparser/cmdparser.h
deleted file mode 100644
index b2bd72d..0000000
--- a/seqan/misc/cmdparser/cmdparser.h
+++ /dev/null
@@ -1,1642 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_H_
-#define CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_H_
-
-#include <sstream>
-#include <seqan/map.h>
-#include <seqan/sequence.h>
-#include <seqan/file.h>
-#include <seqan/misc/cmdparser/cmdoption.h>
-#include <seqan/misc/cmdparser/cmdparser_type_support.h>
-
-#include <iostream>
-#include <fstream>
-
-namespace seqan {
-
-/*
- * TODO: arguments also need a type if they are used as input/output file
- * TODO: correct parameter ordering of nearly all cmdparser function to be seqan conform f(out,in)
- */
-
-/*
-.Class.CommandLineParser
-..cat:Miscellaneous
-..summary:Stores multiple @Class.CommandLineOption@ objects and parses the command line _arguments for these options.
-..signature:CommandLineParser
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-/*
-.Memfunc.CommandLineParser#CommandLineParser
-..class:Class.CommandLineParser
-..summary:Constructor
-..signature:CommandLineParser ()
-..signature:CommandLineParser (applicationName)
-..param.applicationName:A @Shortcut.CharString@ containing the name of the application.
-..remarks:If the name of the application is not passed to the constructor it will be extracted from the command line.
-*/
-
-class CommandLineParser
-{
-public:
-    // ----------------------------------------------------------------------------
-    // Class Typedefs
-    // ----------------------------------------------------------------------------
-    typedef String<CommandLineOption>   TOptionMap;
-    typedef Size<TOptionMap>::Type      TSize;
-
-    typedef std::map<CharString, TSize> TStringMap;
-    typedef String<CharString>          TValueMap;
-
-    // ----------------------------------------------------------------------------
-    // Mapping of option names to options
-    // ----------------------------------------------------------------------------
-    TStringMap shortNameMap;
-    TStringMap longNameMap;
-    TOptionMap optionMap;
-
-    // ----------------------------------------------------------------------------
-    // Members
-    // ----------------------------------------------------------------------------
-    unsigned           _requiredArguments;
-    String<CharString> _arguments;
-    CharString         _appName;
-    String<CharString> _titleText;
-    String<CharString> _usageText;
-    String<CharString> _versionText;
-
-    // ----------------------------------------------------------------------------
-    // Command line formating members
-    // ----------------------------------------------------------------------------
-    unsigned _lineWidth;
-    unsigned _paddingLeft;
-    unsigned _shortWidth;
-    unsigned _longWidth;
-    unsigned _fullWidth;
-
-    // ----------------------------------------------------------------------------
-    // return values for unset parameters
-    // ----------------------------------------------------------------------------
-    const CharString         _null;
-    const String<CharString> _nullSet;
-
-    // friend declaration to make addOption() available in init function
-    friend inline void addOption(CommandLineParser & me, CommandLineOption const & opt);
-
-    // ----------------------------------------------------------------------------
-    // Function init()
-    // ----------------------------------------------------------------------------
-    void init()
-    {
-        // TODO: we could try to automatically determine these settings
-        // Linux:   http://stackoverflow.com/questions/1022957/getting-terminal-width-in-c
-        // Windows: http://stackoverflow.com/questions/8627327/how-to-get-number-of-characters-in-line-in-console-that-my-process-is-bind-to
-        _lineWidth         = 32;
-        _paddingLeft       = 2;
-        _shortWidth        = 0;
-        _longWidth         = 0;
-        _fullWidth         = 0;
-        _requiredArguments = 0;
-        addOption(*this, CommandLineOption("h", "help", "displays this help message", OptionType::Boolean));
-        addOption(*this, CommandLineOption("", "write-ctd", "exports the app's interface description to a .ctd file", OptionType::OUTPUTFILE));
-    }
-
-    // ----------------------------------------------------------------------------
-    // c'tors
-    // ----------------------------------------------------------------------------
-    CommandLineParser()
-    {
-        init();
-    }
-
-    CommandLineParser(CharString _appName) :
-        _appName(_appName)
-    {
-        init();
-    }
-
-};
-
-// ----------------------------------------------------------------------------
-// Function hasOptionLong()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.hasOptionLong:
-..summary:Returns whether a certain long-name option is registered in the parser.
-..cat:Miscellaneous
-..signature:hasOptionLong(parser, optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the long-name option.
-..returns:$true$ if the option is registered.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-hasOptionLong(CommandLineParser const & me, CharString const & _long)
-{
-    return hasKey(me.longNameMap, _long);
-}
-
-// ----------------------------------------------------------------------------
-// Function hasOptionShort()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.hasOptionShort:
-..summary:Returns whether a certain short-name option is registered in the parser.
-..cat:Miscellaneous
-..signature:hasOptionShort(parser, optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the short-name option.
-..returns:$true$ if the option is registered.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-hasOptionShort(CommandLineParser const & me, CharString const & _short)
-{
-    return hasKey(me.shortNameMap, _short);
-}
-
-// ----------------------------------------------------------------------------
-// Function hasOption()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.hasOption:
-..summary:Returns whether a certain option is registered in the parser.
-..cat:Miscellaneous
-..signature:hasOption(parser, optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the option.
-..returns:$true$ if the option is registered.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-hasOption(CommandLineParser const & me, CharString const & _name)
-{
-    return hasKey(me.shortNameMap, _name) || hasKey(me.longNameMap, _name);
-}
-
-// ----------------------------------------------------------------------------
-// Function addOption()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.addOption
-..summary:Adds a @Class.CommandLineOption@ object to the @Class.CommandLineParser@.
-..cat:Miscellaneous
-..signature:addOption(parser, option)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.option:The new @Class.CommandLineOption@ object that should be added.
-...type:Class.CommandLineOption
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-addOption(CommandLineParser & me, CommandLineOption const & opt)
-{
-    // check if an option with the same identifiers was already registered
-    SEQAN_CHECK(!hasOption(me, opt.shortName), "There already is an option with the name %s", toCString(opt.shortName));
-    SEQAN_CHECK(!hasOption(me, opt.longName), "There already is an option with the name %s", toCString(opt.longName));
-
-    // finally append the option
-    appendValue(me.optionMap, opt);
-
-    if (!empty(opt.shortName))
-    {
-        insert(me.shortNameMap, opt.shortName, length(me.optionMap) - 1);
-        unsigned width = 3 + length(opt.shortName);
-        if (me._shortWidth < width)
-            me._shortWidth = width;
-        if (empty(opt.longName))
-        {
-            width += 1 + length(argumentText(opt));
-            if (me._fullWidth < width)
-                me._fullWidth = width;
-        }
-    }
-    if (!empty(opt.longName))
-    {
-        insert(me.longNameMap, opt.longName, length(me.optionMap) - 1);
-        unsigned width = 3 + length(opt.longName) + length(argumentText(opt));
-        if (me._longWidth < width)
-            me._longWidth = width;
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function addLine()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.addLine:
-..summary:Adds a line of text to the help output of the @Class.CommandLineParser@.
-..cat:Miscellaneous
-..signature:addLine(parser, text)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.text:A line of text that will be added to the help output.
-...type:Shortcut.CharString
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TString>
-inline void
-addLine(CommandLineParser & me, TString const & line)
-{
-    addOption(me, CommandLineOption("", "", line, 0));
-}
-
-// ----------------------------------------------------------------------------
-// Function addHelpLine()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.addHelpLine:
-..summary:Adds an extra line of text below the help text of an option.
-..cat:Miscellaneous
-..signature:addHelpLine(parser, text)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.text:A line of text that will be added below the help text of an option.
-...type:Shortcut.CharString
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TString>
-inline void
-addHelpLine(CommandLineParser & me, TString const & line)
-{
-    addOption(me, CommandLineOption("", "", line, 1));
-}
-
-// ----------------------------------------------------------------------------
-// Function addSection()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.addSection:
-..summary:Adds a new section the help output of the @Class.CommandLineParser@.
-..cat:Miscellaneous
-..signature:addSection(parser, text)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.text:A section header that will be added to the help output.
-...type:Shortcut.CharString
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TString>
-inline void
-addSection(CommandLineParser & me, TString const & line)
-{
-    addLine(me, "");
-    addLine(me, line);
-}
-
-// ----------------------------------------------------------------------------
-// Function addTitleLine()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.addTitleLine:
-..summary:Adds a line of text to the title output of the @Class.CommandLineParser@.
-..cat:Miscellaneous
-..signature:addTitleLine(parser, text)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.text:A text line that will be added to the title output.
-...type:Shortcut.CharString
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TString>
-inline void
-addTitleLine(CommandLineParser & me, TString const & line)
-{
-    appendValue(me._titleText, line);
-}
-
-// ----------------------------------------------------------------------------
-// Function addVersionLine()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.addVersionLine:
-..summary:Adds a line of text to the version output of the @Class.CommandLineParser@.
-..cat:Miscellaneous
-..signature:addVersionLine(parser, text)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.text:A text line that will be added to the version output.
-...type:Shortcut.CharString
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TString>
-inline void
-addVersionLine(CommandLineParser & me, TString const & line)
-{
-    if (empty(me._versionText))
-        addOption(me, CommandLineOption("V", "version", "print version information", OptionType::Boolean));
-    appendValue(me._versionText, line);
-}
-
-// ----------------------------------------------------------------------------
-// Function addUsageLine()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.addUsageLine:
-..summary:Adds a line of text to the usage output of the @Class.CommandLineParser@.
-..cat:Miscellaneous
-..signature:addUsageLine(parser, text)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.text:A text line that will be added to the usage output.
-...type:Shortcut.CharString
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-addUsageLine(CommandLineParser & me, CharString const & line)
-{
-    appendValue(me._usageText, line);
-}
-
-// ----------------------------------------------------------------------------
-// Function _getOptionIndex()
-// ----------------------------------------------------------------------------
-
-inline Size<String<CommandLineOption> >::Type
-_getOptionIndex(CommandLineParser const & me, CharString const & _name)
-{
-    typedef Size<String<CommandLineOption> >::Type TOptionPosition;
-    TOptionPosition option_index;
-    if (hasKey(me.shortNameMap, _name))
-    {
-        option_index = me.shortNameMap.find(_name)->second;
-    }
-    else
-    {
-        option_index = me.longNameMap.find(_name)->second;
-    }
-    return option_index;
-}
-
-// ----------------------------------------------------------------------------
-// Function getOption()
-// ----------------------------------------------------------------------------
-
-inline CommandLineOption &
-getOption(CommandLineParser & me, CharString const & _name)
-{
-    SEQAN_ASSERT_MSG(hasOption(me, _name), "Unknown option: %s", toCString(_name));
-    return me.optionMap[_getOptionIndex(me, _name)];
-}
-
-inline CommandLineOption const &
-getOption(CommandLineParser const & me, CharString const & _name)
-{
-    SEQAN_ASSERT_MSG(hasOption(me, _name), "Unknown option: %s", toCString(_name));
-    return me.optionMap[_getOptionIndex(me, _name)];
-}
-
-// ----------------------------------------------------------------------------
-// Function setRequiredArguments()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.setRequiredArguments
-..summary:Sets the number of _arguments (non-parameterized options) are required by the program.
-..cat:Miscellaneous
-..signature:requiredArguments(parser, count)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.count:A $unsigned int$ defining the amount of non-parameterized options requried by the program.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-setRequiredArguments(CommandLineParser & me, unsigned count)
-{
-    me._requiredArguments = count;
-}
-
-/*
-.Function.requiredArguments
-..summary:Sets the number of _arguments (non-parameterized options) are required by the program.
-..cat:Miscellaneous
-..signature:requiredArguments(parser, count)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.count:A $unsigned int$ defining the amount of non-parameterized options requried by the program.
-..status:deprecated, use $Function.setRequiredArguments$
-..see:Function.setRequiredArguments
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-requiredArguments(CommandLineParser & me, unsigned count)
-{
-    setRequiredArguments(me, count);
-}
-
-// ----------------------------------------------------------------------------
-// Function _printStringSet()
-// ----------------------------------------------------------------------------
-
-template <typename TStringSet, typename TStream>
-inline void
-_printStringSet(TStringSet const & set, TStream & target)
-{
-    for (unsigned r = 0; r < length(set); ++r)
-    {
-        streamPut(target, set[r]);
-        streamPut(target, '\n');
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function _printUsage()
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline void
-_printUsage(CommandLineParser const & me, TStream & target)
-{
-    streamPut(target, "Usage: ");
-    if (empty(me._usageText))
-    {
-        streamPut(target, me._appName);
-        streamPut(target, " [OPTION]... ");
-        for (unsigned r = 0; r < me._requiredArguments; ++r)
-        {
-            streamPut(target, "<ARG");
-            streamPut(target, r + 1);
-            streamPut(target, "> ");
-        }
-        streamPut(target, '\n');
-    }
-    else
-    {
-        for (unsigned r = 0; r < length(me._usageText); ++r)
-        {
-            if (r)
-                streamPut(target, "       ");
-            streamPut(target, me._appName);
-            streamPut(target, ' ');
-            streamPut(target, me._usageText[r]);
-            streamPut(target, '\n');
-        }
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function _printTitle()
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline void
-_printTitle(CommandLineParser const & me, TStream & target)
-{
-    _printStringSet(me._titleText, target);
-}
-
-// ----------------------------------------------------------------------------
-// Function printShortHelp()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.printShortHelp
-..summary:Prints a short help message for the parser to a stream
-..cat:Miscellaneous
-..signature:printShortHelp(parser[, stream])
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.stream:Target stream (e.g. $std::cerr$).
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TStream>
-inline void
-printShortHelp(CommandLineParser const & me, TStream & target)
-{
-    _printTitle(me, target);
-    _printUsage(me, target);
-    streamPut(target, "Try '");
-    streamPut(target, me._appName);
-    streamPut(target, " --help' for more information.\n");
-}
-
-/*
-.Function.shortHelp
-..summary:Prints a short help message for the parser to a stream
-..cat:Miscellaneous
-..signature:shortHelp(parser[, stream])
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.stream:Target stream (e.g. $std::cerr$).
-..status:deprecated, use $Function.printShortHelp$
-..see:Function.printShortHelp
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TStream>
-inline void
-shortHelp(CommandLineParser const & me, TStream & target)
-{
-    printShortHelp(me, target);
-}
-
-template <typename TStream>
-inline void
-shortHelp(CommandLineParser const & me)
-{
-    printShortHelp(me, std::cerr);
-}
-
-// ----------------------------------------------------------------------------
-// Function printHelp()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.printHelp
-..summary:Prints the complete help message for the parser to a stream.
-..cat:Miscellaneous
-..signature:printHelp(parser[, stream])
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.stream:Target stream (e.g. $std::cerr$).
-...default: $std::cerr$
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TStream>
-inline void
-printHelp(CommandLineParser const & me, TStream & target)
-{
-    _printTitle(me, target);
-    streamPut(target, '\n');
-    _printUsage(me, target);
-    streamPut(target, '\n');
-
-    for (unsigned o = 0; o < length(me.optionMap); ++o)
-    {
-        const CommandLineOption & opt = me.optionMap[o];
-        if (isHiddenOption(opt))
-            continue;                                                   // do not print hidden options
-
-        if (opt.optionType > 0)
-        {
-            unsigned s = 0;
-            for (; s < me._paddingLeft; ++s)
-                streamPut(target, ' ');
-
-            unsigned t1 = s + me._shortWidth;                           // first tab
-            unsigned t2 = _max(t1 + me._longWidth, me._fullWidth) + 1;  // second tab (one extra space looks better)
-
-            if (!empty(opt.shortName))
-            {
-                streamPut(target, '-');
-                streamPut(target, opt.shortName);
-                s += 1 + length(opt.shortName);
-                if (!empty(opt.longName))
-                {
-                    streamPut(target, ',');
-                    ++s;
-                }
-                else
-                {
-                    streamPut(target, argumentText(opt));
-                    s += length(argumentText(opt));
-                }
-            }
-
-            for (; s < t1; ++s)
-                streamPut(target, ' ');
-
-            if (!empty(opt.longName))
-            {
-                streamPut(target, "--");
-                streamPut(target, opt.longName);
-                streamPut(target, argumentText(opt));
-                s += 2 + length(opt.longName) + length(argumentText(opt));
-            }
-
-            for (; s < t2; ++s)
-                streamPut(target, ' ');
-        }
-
-        streamPut(target, opt.helpText);
-
-        if (isOptionMandatory(opt))
-            streamPut(target, "*");
-
-        streamPut(target, '\n');
-    }
-    streamPut(target, '\n');
-}
-
-/*
-.Function.help
-..summary:Prints the complete help message for the parser to a stream.
-..cat:Miscellaneous
-..signature:help(parser[, stream])
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.stream:Target stream (e.g. $std::cerr$).
-...default: $std::cerr$
-..status:deprecated, use $Function.printHelp$
-..see:Function.printHelp
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TStream>
-inline void
-help(CommandLineParser const & me, TStream & target)
-{
-    printHelp(me, target);
-}
-
-inline void
-help(CommandLineParser const & me)
-{
-    printHelp(me, std::cerr);
-}
-
-// ----------------------------------------------------------------------------
-// Function printVersion()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.printVersion
-..summary:Prints a version text to a stream.
-..cat:Miscellaneous
-..signature:version(parser[, stream])
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.stream:Target stream (e.g. $std::cerr$).
-...default: $std::cerr$
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TStream>
-inline void
-printVersion(CommandLineParser const & me, TStream & target)
-{
-    _printStringSet(me._versionText, target);
-}
-
-/*
-.Function.version
-..summary:Prints a version text to a stream.
-..cat:Miscellaneous
-..signature:version(parser[, stream])
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.stream:Target stream (e.g. $std::cerr$).
-...default: $std::cerr$
-..status:deprecated, use $Function.printVersion$
-..see:Function.printVersion
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TStream>
-inline void
-version(CommandLineParser const & me, TStream & target)
-{
-    printVersion(me, target);
-}
-
-inline void
-version(CommandLineParser const & me)
-{
-    printVersion(me, std::cerr);
-}
-
-// ----------------------------------------------------------------------------
-// Function isSet()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.isSet
-..summary:Returns whether an option was set on the parsed command line.
-..cat:Miscellaneous
-..signature:isSet(parser,optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the option (either short or long name).
-..returns:$true$ if the option was set.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isSet(CommandLineParser const & me, CharString const & name)
-{
-    SEQAN_ASSERT_MSG(hasOption(me, name), "Unknown option: %s", toCString(name));
-    return !empty(getOption(me, name).value);
-}
-
-/*
-.Function.isSetShort
-..summary:Returns whether a short-name option was set on the parsed command line.
-..cat:Miscellaneous
-..signature:isSetShort(parser,optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the short-name option.
-..returns:$true$ if the option was set.
-..status:deprecated, use $Function.isSet$
-..see:Function.isSet
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isSetShort(CommandLineParser & me, CharString const & shortName)
-{
-    return isSet(me, shortName);
-}
-
-/*
-.Function.isSetLong
-..summary:Returns whether a long-name option was set on the parsed command line.
-..cat:Miscellaneous
-..signature:isSetLong(parser, optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the long-name option.
-..returns:$true$ if the option was set.
-..status:deprecated, use $Function.isSet$
-..see:Function.isSet
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline bool
-isSetLong(CommandLineParser & me, CharString const & longName)
-{
-    return isSet(me, longName);
-}
-
-// ----------------------------------------------------------------------------
-// Function _allMandatorySet()
-// ----------------------------------------------------------------------------
-
-inline bool
-_allMandatorySet(CommandLineParser const & me)
-{
-    for (unsigned o = 0; o < length(me.optionMap); ++o)
-        if (empty(me.optionMap[o].value) && isOptionMandatory(me.optionMap[o]))
-            return false;
-
-    return true;
-}
-
-// ----------------------------------------------------------------------------
-// Function _parseAppName()
-// ----------------------------------------------------------------------------
-
-inline CharString
-_parseAppName(CharString const & candidate)
-{
-    //IOREV _notio_ irrelevant for io-revision
-    int i = length(candidate) - 1;
-
-    for (; i >= 0; --i)
-        if (candidate[i] == '\\' || candidate[i] == '/')
-            break;
-
-    return suffix(candidate, i + 1);
-}
-
-// ----------------------------------------------------------------------------
-// Function _reportInvalidType()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-inline void
-_reportInvalidType(CommandLineParser const & me, CommandLineOption const & opt,
-                   CharString const & val, TErrorStream & estream)
-{
-    streamPut(estream, me._appName);
-    streamPut(estream, ": \"");
-    streamPut(estream, val);
-    streamPut(estream, "\" is not a valid ");
-
-    // there should be no other situation then those two
-    if (isIntOption(opt))
-        streamPut(estream, "integer");
-    else if (isDoubleOption(opt))
-        streamPut(estream, "double");
-
-    streamPut(estream, " value for '");
-    _writeOptName(estream, opt);
-    streamPut(estream, "'\n");
-}
-
-// ----------------------------------------------------------------------------
-// Function _reportMissingArguments()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-inline void
-_reportMissingArgument(CommandLineParser const & me,
-                       CommandLineOption const & opt, TErrorStream & estream)
-{
-    streamPut(estream, me._appName);
-    streamPut(estream, ": \'");
-    _writeOptName(estream, opt);
-    streamPut(estream, "\' requires ");
-    streamPut(estream, opt.argumentsPerOption);
-    streamPut(estream, " value(s)\n");
-}
-
-// ----------------------------------------------------------------------------
-// Function _reportInvalidOption()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-inline void
-_reportInvalidOption(CommandLineParser const & me, CharString const & option,
-                     TErrorStream & estream)
-{
-    streamPut(estream, me._appName);
-    streamPut(estream, ": invalid option '");
-    streamPut(estream, option);
-    streamPut(estream, "\'\n");
-}
-
-// ----------------------------------------------------------------------------
-// Function _reportValueNotInRange()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-inline void
-_reportValueNotInRange(CommandLineOption const & opt, CharString const & val,
-                       TErrorStream & estream)
-{
-    _writeOptName(estream, opt);
-    streamPut(estream, ": given argument \"");
-    streamPut(estream, val);
-    streamPut(estream, "\" is not in the required range [");
-    streamPut(estream, (opt.minValue != "" ? opt.minValue : "-inf"));
-    streamPut(estream, ":");
-    streamPut(estream, (opt.maxValue != "" ? opt.maxValue : "+inf"));
-    streamPut(estream, "]\n");
-}
-
-// ----------------------------------------------------------------------------
-// Function _reportInvalidValue()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-inline void
-_reportInvalidValue(CommandLineOption const & opt, CharString const & val,
-                    TErrorStream & estream)
-{
-    typedef Iterator<StringSet<CharString> const, Rooted>::Type TStringSetIter;
-
-    _writeOptName(estream, opt);
-    streamPut(estream, ": given argument \"");
-    streamPut(estream, val);
-    streamPut(estream, "\" is not a valid value [");
-    for (TStringSetIter valid = begin(opt.validValues);; )
-    {
-        streamPut(estream, *valid);
-
-        goNext(valid);
-        if (valid == end(opt.validValues))
-            break;
-        else
-            streamPut(estream, ", ");
-    }
-    streamPut(estream, "]\n");
-}
-
-// ----------------------------------------------------------------------------
-// Function _reportInvalidFileType()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-inline void
-_reportInvalidFileType(CommandLineOption const & opt, CharString const & val,
-                       TErrorStream & estream)
-{
-    _writeOptName(estream, opt);
-    streamPut(estream, ": given argument \"");
-    streamPut(estream, val);
-    streamPut(estream, "\" is not a valid file type [");
-    for (Iterator<StringSet<CharString> const, Rooted>::Type valid = begin(opt.validValues);; )
-    {
-        streamPut(estream, *valid);
-
-        goNext(valid);
-        if (valid == end(opt.validValues))
-            break;
-        else
-            streamPut(estream, ", ");
-    }
-    streamPut(estream, "]\n");
-}
-
-// ----------------------------------------------------------------------------
-// Function _checkMinMaxValue()
-// ----------------------------------------------------------------------------
-
-template <typename TValue, typename TErrorStream>
-bool _checkMinMaxValue(CommandLineOption const & opt, CharString const & val,
-                       TErrorStream & estream)
-{
-    TValue d_value = 0;
-    if (!_convertOptionValue(opt, d_value, val))
-        SEQAN_FAIL("Conversion should work");
-
-    if (opt.minValue != "")
-    {
-        // check min and max
-        TValue minVal = 0;
-        _convertOptionValue(opt, minVal, opt.minValue);
-
-        if (d_value < minVal)
-        {
-            _reportValueNotInRange(opt, val, estream);
-            return false;
-        }
-    }
-
-    if (opt.maxValue != "")
-    {
-        TValue maxVal = 0;
-        _convertOptionValue(opt, maxVal, opt.maxValue);
-
-        if (d_value > maxVal)
-        {
-            _reportValueNotInRange(opt, val, estream);
-            return false;
-        }
-    }
-
-    return true;
-
-}
-
-// ----------------------------------------------------------------------------
-// Function _checkValidValue()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-bool _checkValidValues(CommandLineOption const & opt, CharString const & val,
-                       TErrorStream & estream)
-{
-    typedef Iterator<StringSet<CharString> const, Rooted>::Type TStringSetIter;
-
-    if (length(opt.validValues) == 0)
-        return true;                               // no restrictions
-
-    if (isInputFile(opt) || isOutputFile(opt))
-    {
-        // check if our val is in the valid strings
-        for (TStringSetIter valid = begin(opt.validValues); valid != end(opt.validValues); goNext(valid))
-        {
-            if (length(*valid) > length(val))
-                continue;
-            else if (suffix(val, length(val) - length(*valid)) == *valid)
-                return true;
-        }
-        // couldn't find our target
-        _reportInvalidFileType(opt, val, estream);
-        return false;
-    }
-    else
-    {
-        // check if our val is in the valid strings
-        for (TStringSetIter valid = begin(opt.validValues); valid != end(opt.validValues); goNext(valid))
-        {
-            if (*valid == val)
-                return true;
-        }
-        // couldn't find our target
-        _reportInvalidValue(opt, val, estream);
-        return false;
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function _checkRestrictions()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-bool _checkRestrictions(CommandLineOption const & opt, CharString const & val,
-                        TErrorStream & estream)
-{
-    // we already know that the value can be converted to double/int, so we only need to check if it is
-    // also in the required range
-    if (isDoubleOption(opt))
-    {
-        return _checkMinMaxValue<double, TErrorStream>(opt, val, estream) && _checkValidValues(opt, val, estream);
-    }
-    if (isIntOption(opt))
-    {
-        return _checkMinMaxValue<int, TErrorStream>(opt, val, estream) && _checkValidValues(opt, val, estream);
-    }
-    if (isStringOption(opt))
-    {
-        return _checkValidValues(opt, val, estream);
-    }
-
-    // no restrictions to check
-    return true;
-}
-
-// ----------------------------------------------------------------------------
-// Function _assignOptionValue()
-// ----------------------------------------------------------------------------
-
-template <typename TErrorStream>
-bool _assignOptionValue(CommandLineParser & me, CommandLineOption & opt,
-                        CharString const & val, unsigned argNo, TErrorStream & estream)
-{
-    if (isDoubleOption(opt) && !_isDouble(val))
-    {
-        _reportInvalidType(me, opt, val, estream);
-        return false;
-    }
-    else if (isIntOption(opt) && !_isInt(val))
-    {
-        _reportInvalidType(me, opt, val, estream);
-        return false;
-    }
-
-    if (!_checkRestrictions(opt, val, estream))
-        return false;
-
-    if (isOptionList(opt))
-    {
-        appendValue(opt.value, val, Generous());
-    }
-    else
-    {
-        if (argNo == 0)
-            clear(opt.value);
-        appendValue(opt.value, val, Exact());
-    }
-    return true;
-}
-
-template <typename TErrorStream>
-bool
-_assignOptionValue(CommandLineParser & me, CommandLineOption & opt,
-                   CharString const & val, TErrorStream & estream)
-{
-    return _assignOptionValue(me, opt, val, 0, estream);
-}
-
-template <typename TErrorStream>
-bool
-_assignOptionValue(CommandLineParser & me, unsigned option_index,
-                   CharString const & val, unsigned argNo, TErrorStream & estream)
-{
-    // get the option object
-    CommandLineOption & opt = me.optionMap[option_index];
-    return _assignOptionValue(me, opt, val, argNo, estream);
-}
-
-template <typename TErrorStream>
-inline bool
-_assignOptionValue(CommandLineParser & me, unsigned option_index,
-                   CharString const & val, TErrorStream & estream)
-{
-    return _assignOptionValue(me, option_index, val, 0, estream);
-}
-
-// ----------------------------------------------------------------------------
-// Function _getOptionValues()
-// ----------------------------------------------------------------------------
-
-inline String<CharString> const &
-_getOptionValues(CommandLineParser const &, CommandLineOption const & opt)
-{
-    if (empty(opt.value))
-        return opt.defaultValue;
-    else
-        return opt.value;
-}
-
-inline String<CharString> const &
-_getOptionValues(CommandLineParser const & me, unsigned option_index)
-{
-    return _getOptionValues(me, me.optionMap[option_index]);
-}
-
-// ----------------------------------------------------------------------------
-// Function _getOptionValue()
-// ----------------------------------------------------------------------------
-
-inline CharString const &
-_getOptionValue(CommandLineParser const & me,
-                CommandLineOption const & opt, unsigned argNo)
-{
-    if (argNo < length(opt.value))
-        return opt.value[argNo];
-
-    if (argNo < length(opt.defaultValue))
-        return opt.defaultValue[argNo];
-
-    return me._null;
-}
-
-inline CharString const &
-_getOptionValue(CommandLineParser const & me, CommandLineOption const & opt)
-{
-    return _getOptionValue(me, opt, 0);
-}
-
-inline CharString const &
-_getOptionValue(CommandLineParser const & me, unsigned option_index, unsigned argNo)
-{
-    CommandLineOption const & opt = me.optionMap[option_index];
-    return _getOptionValue(me, opt, argNo);
-}
-
-inline CharString const &
-_getOptionValue(CommandLineParser const & me, unsigned option_index)
-{
-    return _getOptionValue(me, option_index, 0);
-}
-
-// ----------------------------------------------------------------------------
-// Function _convertOptionValue()
-// ----------------------------------------------------------------------------
-
-inline bool
-_convertOptionValue(CommandLineOption const & opt, bool & dst, CharString const & src)
-{
-    if (!isBooleanOption(opt))
-        return false;
-
-    dst = !empty(src);
-    return true;
-}
-
-inline bool
-_convertOptionValue(CommandLineOption const & opt, int & dst, CharString const & src)
-{
-    if (!isIntOption(opt))
-        return false;
-
-    std::istringstream stream(toCString(src));
-    return !(stream >> dst).fail();
-}
-
-inline bool
-_convertOptionValue(CommandLineOption const & opt, unsigned int & dst, CharString const & src)
-{
-    if (!isIntOption(opt))
-        return false;
-
-    std::istringstream stream(toCString(src));
-    return !(stream >> dst).fail();
-}
-
-inline bool
-_convertOptionValue(CommandLineOption const & opt, __int64 & dst, CharString const & src)
-{
-    if (!isIntOption(opt))
-        return false;
-
-    std::istringstream stream(toCString(src));
-    return !(stream >> dst).fail();
-}
-
-inline bool
-_convertOptionValue(CommandLineOption const & opt, __uint64 & dst, CharString const & src)
-{
-    if (!isIntOption(opt))
-        return false;
-
-    std::istringstream stream(toCString(src));
-    return !(stream >> dst).fail();
-}
-
-inline bool
-_convertOptionValue(CommandLineOption const & opt, float & dst, CharString const & src)
-{
-    if (!isDoubleOption(opt))
-        return false;
-
-    std::istringstream stream(toCString(src));
-    return !(stream >> dst).fail();
-}
-
-inline bool
-_convertOptionValue(CommandLineOption const & opt, double & dst, CharString const & src)
-{
-    if (!isDoubleOption(opt))
-        return false;
-
-    std::istringstream stream(toCString(src));
-    return !(stream >> dst).fail();
-}
-
-template <typename TObject>
-inline bool
-_convertOptionValue(CommandLineOption const & opt, TObject & dst, CharString const & src)
-{
-    if (!isStringOption(opt))
-        return false;
-
-    assign(dst, src);
-    return true;
-}
-
-// ----------------------------------------------------------------------------
-// Function getOptionValue()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.getOptionValue:
-..summary:Retrieves the value of an option given either the short or long name.
-..cat:Miscellaneous
-..signature:getOptionValue(parser, optionIdentifier[, argNo], value)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that is either the short or long name of the option.
-..param.argNo:If the option is list, the $argNo$-th list element is returned.
-..param.value:The variable where the resulting value should be stored.
-...remarks:The type of $value$ must be compatible the option type.
-..returns: $true$ if the requested option is set and has the requested type, $false$ otherwise.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TValue>
-inline bool
-getOptionValue(CommandLineParser const & me, CharString const & name,
-               unsigned argNo, TValue & val)
-{
-    SEQAN_ASSERT_MSG(hasOption(me, name), "Unknown option: %s", toCString(name));
-    return _convertOptionValue(getOption(me, name), val, _getOptionValue(me, getOption(me, name), argNo));
-}
-
-template <typename TValue>
-inline bool
-getOptionValue(CommandLineParser const & me, CharString const & name,
-               TValue & val)
-{
-    return getOptionValue(me, name, 0, val);
-}
-
-// ----------------------------------------------------------------------------
-// Function getOptionValues()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.getOptionValues
-..summary:Returns all values of an option given on the command line.
-..cat:Miscellaneous
-..signature:getOptionValues(parser, optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that is either the short or long name of the option.
-..returns: A $String<CharString>$ of option values.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline String<CharString> const &
-getOptionValues(CommandLineParser & me, CharString const & name)
-{
-    SEQAN_ASSERT_MSG(hasOption(me, name), "Unknown option: %s", toCString(name));
-    return _getOptionValues(me, getOption(me, name));
-}
-
-// ----------------------------------------------------------------------------
-// Function getOptionValueShort()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.getOptionValueShort
-..summary:Retrieves the value of a short-name option given on the command line.
-..cat:Miscellaneous
-..signature:getOptionValueShort(parser, optionIdentifier[, argNo], value)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the short-name of the option.
-..param.argNo:If the option is list, the $argNo$-th list element is returned.
-..param.value:The variable where the resulting value should be stored.
-...remarks:The type of $value$ must be compatible the option type.
-..returns: $true$ if the requested option is set and has the requested type, $false$ otherwise.
-..status:deprecated, use $Function.getOptionValue$
-..see:Function.getOptionValue
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TValue>
-inline bool
-getOptionValueShort(CommandLineParser const & me, CharString
-                    const & shortName, unsigned argNo, TValue & val)
-{
-    return getOptionValue(me, shortName, argNo, val);
-}
-
-template <typename TValue>
-inline bool
-getOptionValueShort(CommandLineParser const & me,
-                    CharString const & shortName, TValue & val)
-{
-    return getOptionValueShort(me, shortName, 0, val);
-}
-
-// ----------------------------------------------------------------------------
-// Function getOptionValuesShort()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.getOptionValuesShort
-..summary:Returns all values of a short-name option given on the command line.
-..cat:Miscellaneous
-..signature:getOptionValuesShort(parser, optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the short-name of the option.
-..returns: A $String<CharString>$ of option values.
-..status:deprecated, use $Function.getOptionValues$
-..see:Function.getOptionValues
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline String<CharString> const &
-getOptionValuesShort(CommandLineParser & me, CharString const & shortName)
-{
-    return getOptionValues(me, shortName);
-}
-
-// ----------------------------------------------------------------------------
-// Function getOptionValueLong()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.getOptionValueLong
-..summary:Retrieves the value of a long-name option given on the command line.
-..cat:Miscellaneous
-..signature:getOptionValueLong(parser, optionIdentifier[, argNo], value)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the long-name of the option.
-..param.argNo:If the option is list, the $argNo$-th list element is returned.
-..param.value:The variable where the resulting value should be stored.
-...remarks:The type of $value$ must be compatible the option type.
-..returns: $true$ if the requested option is set and has the requested type, $false$ otherwise.
-..status:deprecated, use $Function.getOptionValue$
-..see:Function.getOptionValue
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-template <typename TValue>
-inline bool
-getOptionValueLong(CommandLineParser const & me,
-                   CharString const & longName, unsigned argNo, TValue & val)
-{
-    return getOptionValue(me, longName, argNo, val);
-}
-
-template <typename TValue>
-inline bool
-getOptionValueLong(CommandLineParser const & me,
-                   CharString const & longName, TValue & val)
-{
-    return getOptionValueLong(me, longName, 0, val);
-}
-
-// ----------------------------------------------------------------------------
-// Function getOptionValuesLong()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.getOptionValuesLong
-..summary:Returns all values of a long-name option given on the command line.
-..cat:Miscellaneous
-..signature:getOptionValuesLong(parser, optionIdentifier)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.optionIdentifier:A @Shortcut.CharString@ that identifies the long-name of the option.
-..returns: A $String<CharString>$ of option values.
-..include:seqan/misc/misc_cmdparser.h
-..status:deprecated, use $Function.getOptionValues$
-..see:Function.getOptionValues
-*/
-
-inline String<CharString> const &
-getOptionValuesLong(CommandLineParser & me, CharString const & longName)
-{
-    return getOptionValues(me, longName);
-}
-
-// ----------------------------------------------------------------------------
-// Function getArgumentValue()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.getArgumentValue
-..summary:Returns an argument set on the command line.
-..cat:Miscellaneous
-..signature:getArgumentValue(parser, position)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.position:A zero based $int$ indicating which argument you want to get.
-..returns:The command line argument or an empty string if it doesn't exist.
-...type:Shortcut.CharString
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline CharString const &
-getArgumentValue(CommandLineParser const & me, unsigned position)
-{
-    if (position < length(me._arguments))
-        return me._arguments[position];
-    else
-        return me._null;
-}
-
-// ----------------------------------------------------------------------------
-// Function getArgumentValues()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.getArgumentValues
-..summary:Returns all _arguments set on the command line.
-..cat:Miscellaneous
-..signature:getArgumentValues(parser)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..returns:All command line _arguments as a $String<CharString>$.
-..see:Function.getArgumentValue
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline String<CharString> const &
-getArgumentValues(CommandLineParser const & me)
-{
-    return me._arguments;
-}
-
-// ----------------------------------------------------------------------------
-// Function argumentCount()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.argumentCount
-..summary:Returns the count of passed _arguments.
-..cat:Miscellaneous
-..signature:argumentCount(parser)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline Size<String<CharString> >::Type
-argumentCount(CommandLineParser const & me)
-{
-    return length(me._arguments);
-}
-
-// ----------------------------------------------------------------------------
-// Function setMinValue()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.setMinValue
-..summary:Sets the minimum value of a @Class.CommandLineOption@ object identified by .
-..cat:Miscellaneous
-..signature:setMinValue(parser,optionName,minValue)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.option:The identifier of the command line option.
-...type:Shortcut.CharString
-..param.minValue:A @Shortcut.CharString@ containing a string representation of the minimum value of the @Class.CommandLineOption@.
-..include:seqan/misc/misc_cmdparser.h
-*/
-inline void
-setMinValue(CommandLineParser & me, CharString const & name, CharString const & _minValue)
-{
-    SEQAN_ASSERT_MSG(hasOption(me, name), "Unknown option: %s", toCString(name));
-    setMinValue(getOption(me, name), _minValue);
-}
-
-// ----------------------------------------------------------------------------
-// Function setMaxValue()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.setMaxValue
-..summary:Sets the maximum value of a @Class.CommandLineOption@ object.
-..cat:Miscellaneous
-..signature:setMaxValue(parser,optionName,maxValue)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.option:The identifier of the command line option.
-...type:Shortcut.CharString
-..param.maxValue:A @Shortcut.CharString@ containing a string representation of the maximum value of the @Class.CommandLineOption@.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-setMaxValue(CommandLineParser & me, CharString const & name,
-            CharString const & _maxValue)
-{
-    SEQAN_ASSERT_MSG(hasOption(me, name), "Unknown option: %s", toCString(name));
-    setMaxValue(getOption(me, name), _maxValue);
-}
-
-// ----------------------------------------------------------------------------
-// Function setValidValues()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.setValidValues
-..summary:Sets the set of allowed values of a @Class.CommandLineOption@ object.
-..cat:Miscellaneous
-..signature:setValidValues(parser,optionName,values)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..param.option:The identifier of the command line option.
-...type:Shortcut.CharString
-..param.values:A $String<CharString>$ containing all valid entries for the option.
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-setValidValues(CommandLineParser & me, CharString const & name,
-               StringSet<CharString> const & _values)
-{
-    SEQAN_ASSERT_MSG(hasOption(me, name), "Unknown option: %s", toCString(name));
-    setValidValues(getOption(me, name), _values);
-}
-
-inline void
-setValidValues(CommandLineParser & me, CharString const & name,
-               CharString const & _values)
-{
-    // convert array to String<CharString>
-    StringSet<CharString> values;
-    CharString current_argument;
-
-    for (Iterator<CharString const, Rooted>::Type ch  = begin(_values); ch != end(_values); goNext(ch))
-    {
-        if (*ch == ' ')
-        {
-            appendValue(values, current_argument);
-            current_argument = "";
-        }
-        else
-        {
-            append(current_argument, *ch);
-        }
-    }
-    if (current_argument != "")
-        appendValue(values, current_argument);
-
-    // add as restriction
-    setValidValues(me, name, values);
-}
-
-} // end seqan
-
-#endif // CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_H_
diff --git a/seqan/misc/cmdparser/cmdparser_ctd_support.h b/seqan/misc/cmdparser/cmdparser_ctd_support.h
deleted file mode 100644
index efcb56d..0000000
--- a/seqan/misc/cmdparser/cmdparser_ctd_support.h
+++ /dev/null
@@ -1,280 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Björn Kahlert <Bjoern.Kahlert@fu-berlin.de>
-// Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
-// ==========================================================================
-
-#ifndef CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_CTD_SUPPORT_H_
-#define CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_CTD_SUPPORT_H_
-
-
-namespace seqan {
-
-// ----------------------------------------------------------------------------
-// Function _join()
-// ----------------------------------------------------------------------------
-
-/*
- * joins all elements of the the passed StringSet into a single CharString
- * the provided delimiter is used to separate the single entries in the
- * resulting CharString
- */
-template <typename TValue>
-inline CharString
-_join(StringSet<TValue> const & v, CharString const & delimiter)
-{
-    typedef typename Iterator<StringSet<TValue> const, Rooted>::Type TStringSetIterator;
-
-    std::stringstream joined;
-    for (TStringSetIterator it = begin(v); it != end(v); goNext(it))
-    {
-        if (it != begin(v))
-            joined << delimiter;
-        joined << *it;
-    }
-    return CharString(joined.str());
-}
-
-// ----------------------------------------------------------------------------
-// Function _xmlEscape()
-// ----------------------------------------------------------------------------
-
-/*
- * make sure that the text we put into the XML does not break the XML
- * candidates are
- *  " -> &quot;
- *  ' -> &apos;
- *  & -> &amp;
- *  < -> &lt;
- *  > -> &gt;
- */
-template <typename TSequence>
-inline TSequence _xmlEscape(TSequence const & original)
-{
-    TSequence escaped;
-    for (typename Iterator<TSequence const, Rooted>::Type ch  = begin(original); ch != end(original); goNext(ch))
-    {
-        if (value(ch) == '"')
-            append(escaped, "&quot;");
-        else if (value(ch) == '\'')
-            append(escaped, "&apos;");
-        else if (value(ch) == '&')
-            append(escaped, "&amp;");
-        else if (value(ch) == '<')
-            append(escaped, "&lt;");
-        else if (value(ch) == '>')
-            append(escaped, "&gt;");
-        else
-            append(escaped, *ch);
-    }
-    return escaped;
-}
-
-// ----------------------------------------------------------------------------
-// Function _addMinMaxRestrictions()
-// ----------------------------------------------------------------------------
-
-inline void
-_addMinMaxRestrictions(StringSet<CharString> & restrictions, CommandLineOption const & opt)
-{
-    CharString minMaxRestriction = "";
-    if (opt.minValue != "")
-    {
-        append(minMaxRestriction, opt.minValue);
-        append(minMaxRestriction, ":");
-    }
-    if (opt.maxValue != "")
-    {
-        if (minMaxRestriction == "")
-            append(minMaxRestriction, ":");
-        append(minMaxRestriction, opt.maxValue);
-    }
-
-    if (minMaxRestriction != "")
-        appendValue(restrictions, minMaxRestriction);
-}
-
-// ----------------------------------------------------------------------------
-// Function _addValidValuesRestrictions()
-// ----------------------------------------------------------------------------
-
-inline void
-_addValidValuesRestrictions(StringSet<CharString> & restrictions, CommandLineOption const & opt)
-{
-    if (length(opt.validValues) != 0)
-    {
-        for (Iterator<StringSet<CharString> const, Rooted>::Type valid = begin(opt.validValues); valid != end(opt.validValues); goNext(valid))
-        {
-            // for files we set *.(Name of the format)
-            if (isOutputFile(opt) || isInputFile(opt))
-            {
-                CharString filetype = "*.";
-                append(filetype, *valid);
-                appendValue(restrictions, filetype);
-            }
-            else
-            {
-                appendValue(restrictions, *valid);
-            }
-        }
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function _includeInCTD()
-// ----------------------------------------------------------------------------
-
-/*
- * returns true if this option should be included in the ctd
- */
-inline bool
-_includeInCTD(CommandLineOption const & opt)
-{
-    return !(opt.shortName == "h" || opt.shortName == "V" || opt.longName == "write-ctd" || (opt.shortName == "" && opt.longName == ""));
-}
-
-// ----------------------------------------------------------------------------
-// Function writeCTD()
-// ----------------------------------------------------------------------------
-
-/*
-.Function.writeCTD
-..summary:Exports the app's interface description to a .ctd file.
-..cat:Miscellaneous
-..signature:writeCTD(parser)
-..param.parser:The @Class.CommandLineParser@ object.
-...type:Class.CommandLineParser
-..include:seqan/misc/misc_cmdparser.h
-*/
-
-inline void
-writeCTD(CommandLineParser const & me)
-{
-    typedef Iterator<CommandLineParser::TOptionMap const>::Type TOptionMapIterator;
-    TOptionMapIterator optionMapIterator;
-
-    // create file [appname].ctd in working directory
-    CharString ctdfilename;
-    getOptionValueLong(me, "write-ctd", ctdfilename);
-
-    std::ofstream ctdfile;
-    ctdfile.open(toCString(ctdfilename));
-    ctdfile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
-    ctdfile << "<tool status=\"external\">\n";
-    ctdfile << "\t<name>" << _xmlEscape(me._appName) << "</name>\n";
-    ctdfile << "\t<version>" << _xmlEscape(me._versionText) << "</version>\n";
-    ctdfile << "\t<description><![CDATA[" << _xmlEscape(me._appName) << ".]]></description>\n";
-    ctdfile << "\t<manual><![CDATA[" << _xmlEscape(me._appName) << ".]]></manual>\n"; // TODO: as soon as we have a more sophisticated documentation embedded into the CmdParser, we should at this here
-    ctdfile << "\t<docurl>Direct links in docs</docurl>\n";
-    ctdfile << "\t<category>SeqAn - Sequence Analaysis</category>\n";
-    ctdfile << "\t<mapping><![CDATA[\n";
-
-    for (optionMapIterator = begin(me.optionMap); optionMapIterator != end(me.optionMap); optionMapIterator++)
-    {
-
-        CommandLineOption const & opt = *optionMapIterator;
-        // filter help, version and ctd_export
-        if (!_includeInCTD(opt))
-            continue;
-
-        CharString optionName = (opt.shortName != "" ? opt.shortName : opt.longName);
-        CharString flagName = (opt.shortName != "" ? "-" : "--");
-        append(flagName, optionName);
-
-        ctdfile << "<mapparam CLISwitch=\"" << flagName << "\" name=\"" << _xmlEscape(me._appName) << "." << optionName << "\"/>\n";
-    }
-
-    ctdfile << "]]></mapping>\n";
-    ctdfile << "\t<PARAMETERS version=\"1.3\" xsi:noNamespaceSchemaLocation=\"http://open-ms.sourceforge.net/schemas/Param_1_3.xsd\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">" << std::endl;
-    ctdfile << "\t\t<NODE name=\"" << _xmlEscape(me._appName) << "\" description=\"???\">" << std::endl;
-
-    for (optionMapIterator = begin(me.optionMap); optionMapIterator != end(me.optionMap); optionMapIterator++)
-    {
-        CommandLineOption const & opt = *optionMapIterator;
-
-        // filter help, version and ctd_export
-        if (!_includeInCTD(opt))
-            continue;
-
-        // prefer short name for options
-        CharString optionName = (opt.shortName != "" ? opt.shortName : opt.longName);
-
-        CharString type;
-
-        if (isStringOption(opt))
-            type = "string";
-        else if (isIntOption(opt))
-            type = "int";
-        else if (isDoubleOption(opt))
-            type = "double";
-
-        // set up tags
-        StringSet<CharString> tags;
-        if (isInputFile(opt))
-        {
-            appendValue(tags, "input file");
-        }
-        if (isOutputFile(opt))
-        {
-            appendValue(tags, "output file");
-        }
-        if (isOptionMandatory(*optionMapIterator))
-        {
-            appendValue(tags, "required");
-        }
-
-        // set up restrictions
-        StringSet<CharString> restrictions;
-        _addValidValuesRestrictions(restrictions, opt);
-        _addMinMaxRestrictions(restrictions, opt);
-
-
-        ctdfile << "\t\t\t<ITEM " <<
-        "name=\"" << _xmlEscape(optionName) << "\" " <<
-        "value=\"" << _xmlEscape(opt.defaultValue) << "\" " <<
-        "type=\"" << type << "\" " <<
-        "description=\"" << _xmlEscape(opt.helpText) << "\" " <<
-        "tags=\"" << _xmlEscape(_join(tags, ",")) << "\" " <<
-        "restrictions=\"" << _xmlEscape(_join(restrictions, ",")) << "\"" <<
-        "/>" << std::endl;
-    }
-
-    ctdfile << "\t\t</NODE>" << std::endl;
-    ctdfile << "\t</PARAMETERS>" << std::endl;
-    ctdfile << "</tool>" << std::endl;
-
-    ctdfile.close();
-}
-
-} // namespace seqan
-
-#endif // CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_CTD_SUPPORT_H_
diff --git a/seqan/misc/cmdparser/cmdparser_parse.h b/seqan/misc/cmdparser/cmdparser_parse.h
deleted file mode 100644
index b875989..0000000
--- a/seqan/misc/cmdparser/cmdparser_parse.h
+++ /dev/null
@@ -1,226 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
-// ==========================================================================
-
-#ifndef CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_PARSE_H_
-#define CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_PARSE_H_
-
-#include <seqan/misc/cmdparser/cmdoption.h>
-#include <seqan/misc/cmdparser/cmdparser.h>
-#include <seqan/misc/cmdparser/cmdparser_ctd_support.h>
-
-namespace seqan {
-
-// ----------------------------------------------------------------------------
-// Function parse()
-// ----------------------------------------------------------------------------
-
-/*
- .Function.parse:
- ..summary:Parses the command line.
- ..cat:Miscellaneous
- ..signature:parse(parser, argc, argv[, errorStream])
- ..param.parser:The @Class.CommandLineParser@ object.
- ...type:Class.CommandLineParser
- ..param.argc:Count of the objects on the command line.
- ..param.argv:Array of the different command line arguments ($const char *argv[]$).
- ..param.errorStream:A stream where error messages are sent to.
- ..remarks:Must be called before retrieving options or arguments.
- ..returns:$true$ if all required arguments are set and parseable and neither the help nor version argument is set.
- ..include:seqan/misc/misc_cmdparser.h
- */
-
-template <typename TErrorStream>
-bool parse(CommandLineParser & me, int argc, const char * argv[], TErrorStream & estream)
-{
-    // if the appName wasn't set .. parse from command line
-    if (empty(me._appName))
-        me._appName = _parseAppName(argv[0]);
-
-    for (int argument_index = 1; argument_index < argc; ++argument_index)
-    {
-        if (argv[argument_index][0] == '-')  // this is possibly an option value
-        {
-            CharString inParam = argv[argument_index];
-            unsigned len = length(inParam);
-
-            if (len == 1)
-            {
-                streamPut(estream, me._appName);
-                streamPut(estream, ": invalid option '-'\n");
-                return false;
-            }
-            else if (inParam[1] != '-') // maybe a combination of multiple bool opts
-            {
-                for (unsigned s = 1; s < len; ++s)
-                {
-                    unsigned e = len;
-                    for (; s < e; --e)
-                    {
-                        if (hasOption(me, infix(inParam, s, e)))
-                        {
-                            CommandLineOption & opt = getOption(me, infix(inParam, s, e));
-                            s = --e;
-                            if (isBooleanOption(opt))
-                                _assignOptionValue(me, opt, "true", estream);
-                            else
-                            {
-                                int firstArgIndex = 0;
-
-                                if (e < len - 1)
-                                {
-                                    // Try getting the first option argument from the remaining characters
-                                    // of this program argument. Use-case: immediately adjacent option
-                                    // values without separating space, as in `-x1` instead of `-x 1`.
-                                    if (!_assignOptionValue(me, opt, suffix(inParam, e + 1), 0, estream))
-                                        return false;
-
-                                    firstArgIndex = 1;
-                                    s = len - 1;
-                                }
-
-                                if (argument_index + opt.argumentsPerOption - firstArgIndex < argc)
-                                {
-                                    for (int t = firstArgIndex; t < opt.argumentsPerOption; ++t)
-                                        if (!_assignOptionValue(me, opt, argv[++argument_index], t, estream))
-                                            return false;
-                                }
-                                else  // no value available
-                                {
-                                    _reportMissingArgument(me, opt, estream);
-                                    return false;
-                                }
-                            }
-                        }
-                    }
-                    if (s == e)
-                    {
-                        CharString invalidOpt("-");
-                        append(invalidOpt, suffix(inParam, s));
-
-                        _reportInvalidOption(me, invalidOpt, estream);
-                        return false;
-                    }
-                }
-            }
-            else if (inParam[1] == '-')  // this is a long option
-            {
-                unsigned t = 2;
-                CharString longOpt, val;
-                for (; t < len && inParam[t] != '='; ++t)
-                    appendValue(longOpt, inParam[t], Generous());
-                if (t < len) // this one is a --name=value option
-                    val = suffix(inParam, t + 1);
-
-                // We might already have a value
-                if (hasOption(me, longOpt))
-                {
-                    CommandLineOption & opt = getOption(me, longOpt);
-
-                    if (!empty(val))
-                    {
-                        if (opt.argumentsPerOption == 1)
-                        {
-                            if (!_assignOptionValue(me, opt, val, estream))
-                                return false;
-                        }
-                        else
-                        {
-                            _reportMissingArgument(me, opt, estream);
-                            return false;
-                        }
-                    }
-                    else if (isBooleanOption(opt))
-                    {
-                        _assignOptionValue(me, opt, "true", estream);
-                    }
-                    else if (argument_index + opt.argumentsPerOption < argc)
-                    {
-                        for (int t = 0; t < opt.argumentsPerOption; ++t)
-                            if (!_assignOptionValue(me, opt, argv[++argument_index], t, estream))
-                                return false;
-                    }
-                    else  // no value available
-                    {
-                        _reportMissingArgument(me, opt, estream);
-                        return false;
-                    }
-                }
-                else
-                {
-                    CharString invalidOpt("--");
-                    append(invalidOpt, longOpt);
-                    _reportInvalidOption(me, invalidOpt, estream);
-                    return false;
-                }
-            }
-        }
-        else  // this seems to be a normal argument
-        {
-            appendValue(me._arguments, argv[argument_index]);
-        }
-    }
-    if (hasOption(me, "version") && isSet(me, "version"))
-    {
-        printVersion(me, estream);
-        return false;
-    }
-    if (hasOption(me, "write-ctd") && isSet(me, "write-ctd"))
-    {
-        writeCTD(me);
-        return false;
-    }
-    if (isSet(me, "help"))
-    {
-        printHelp(me, estream);
-        return false;
-    }
-    if (argc == 1 && me._requiredArguments > 0)
-    {
-        // print short help and exit
-        printShortHelp(me, estream);
-        return false;
-    }
-
-    return _allMandatorySet(me) && (length(me._arguments) >= me._requiredArguments);
-}
-
-inline bool
-parse(CommandLineParser & me, int argc, const char * argv[])
-{
-    return parse(me, argc, argv, std::cerr);
-}
-
-} // namespace seqan
-
-#endif // CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_PARSE_H_
diff --git a/seqan/misc/cuda.h b/seqan/misc/cuda.h
new file mode 100644
index 0000000..aa70044
--- /dev/null
+++ b/seqan/misc/cuda.h
@@ -0,0 +1,296 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jacopo Pantaleoni <jpantaleoni@nvidia.com>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_MISC_CUDA_MISC_H_
+#define SEQAN_MISC_CUDA_MISC_H_
+
+//#include <cuda_runtime.h>
+//#include <thrust/version.h>
+//#if THRUST_VERSION < 100600
+//#include <thrust/detail/backend/cuda/arch.h>
+//#else
+//#include <thrust/system/cuda/detail/arch.h>
+//#endif
+
+namespace seqan {
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+/*
+struct Arch
+{
+    static const __uint32 LOG_WARP_SIZE = 5;
+    static const __uint32 WARP_SIZE     = 1u << LOG_WARP_SIZE;
+};
+*/
+
+// --------------------------------------------------------------------------
+// Type FunctionPointer
+// --------------------------------------------------------------------------
+
+typedef void (*FunctionPointer)();
+
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function nvccShowType()
+// --------------------------------------------------------------------------
+
+template <typename TObject>
+inline void
+nvccShowType(TObject object)
+{
+    ignoreUnusedVariableWarning(static_cast<Nothing>(object));
+}
+
+// --------------------------------------------------------------------------
+// Function divideRI()
+// --------------------------------------------------------------------------
+
+// Round x/y towards +infinity for integers, used to determine # of blocks/warps etc.
+template<typename L, typename R>
+inline L divideRI(const L x, const R y)
+{
+    return L((x + (y - 1)) / y);
+}
+
+// --------------------------------------------------------------------------
+// Function roundI()
+// --------------------------------------------------------------------------
+
+// Round x towards infinity to the next multiple of y.
+template<typename L, typename R>
+inline L roundI(L x, R y)
+{
+    return L(y * divideRI(x, y));
+}
+
+// --------------------------------------------------------------------------
+// Function cudaPrintFreeMemory()
+// --------------------------------------------------------------------------
+
+inline void cudaPrintFreeMemory()
+{
+    size_t free, total;
+    cudaMemGetInfo(&free, &total);
+
+    std::cout << "Free " << free / 1024 / 1024 <<  " of " << total / 1024 / 1024 << " MB\n";
+}
+
+// --------------------------------------------------------------------------
+// Function cudaOccupancy()
+// --------------------------------------------------------------------------
+
+inline SEQAN_DEVICE
+float cudaOccupancy()
+{
+    return __popc(__ballot(true)) / 32.0f;
+}
+
+// --------------------------------------------------------------------------
+// Function cudaSmemAllocationUnit()
+// --------------------------------------------------------------------------
+// Granularity of shared memory allocation.
+
+inline size_t cudaSmemAllocationUnit(cudaDeviceProp const & /* properties */)
+{
+    return 512;
+}
+
+// --------------------------------------------------------------------------
+// Function cudaRegAllocationUnit()
+// --------------------------------------------------------------------------
+// Granularity of register allocation.
+
+inline size_t cudaRegAllocationUnit(cudaDeviceProp const & properties)
+{
+    return (properties.major <= 1) ? (properties.minor <= 1 ? 256 : 512) : 64;
+}
+
+// --------------------------------------------------------------------------
+// Function cudaWarpAllocationMultiple()
+// --------------------------------------------------------------------------
+// Granularity of warp allocation.
+
+inline size_t cudaWarpAllocationMultiple(cudaDeviceProp const & /* properties */)
+{
+    return 2;
+}
+
+// --------------------------------------------------------------------------
+// Function cudaMaxBlocksPerMultiprocessor()
+// --------------------------------------------------------------------------
+
+inline size_t cudaMaxBlocksPerMultiprocessor(cudaDeviceProp const & properties)
+{
+    return properties.major <= 2 ? 8 : 16;
+}
+
+// --------------------------------------------------------------------------
+// Function cudaKernelGetAttributes()
+// --------------------------------------------------------------------------
+
+template <typename TKernel>
+inline cudaFuncAttributes cudaKernelGetAttributes(TKernel kernel)
+{
+    FunctionPointer kernelPointer = reinterpret_cast<FunctionPointer>(kernel);
+
+    cudaFuncAttributes attributes;
+    cudaFuncGetAttributes(&attributes, kernelPointer);
+
+    return attributes;
+}
+
+// --------------------------------------------------------------------------
+// Function cudaRegistersUsed()
+// --------------------------------------------------------------------------
+
+template <typename TKernel>
+inline size_t cudaRegistersUsed(TKernel kernel)
+{
+    return cudaKernelGetAttributes(kernel).numRegs;
+}
+
+// --------------------------------------------------------------------------
+// Function cudaMaxActiveBlocks()
+// --------------------------------------------------------------------------
+
+template <typename TKernel, typename TCTASize, typename TSmemSize>
+inline size_t cudaMaxActiveBlocks(TKernel kernel, TCTASize ctaSize, TSmemSize dynamicSmemBytes)
+{
+    int device;
+    cudaGetDevice(&device);
+
+    cudaDeviceProp properties;
+    cudaGetDeviceProperties(&properties, device);
+
+    return properties.multiProcessorCount * cudaMaxActiveBlocksPerSM(kernel, ctaSize, dynamicSmemBytes, properties);
+}
+
+// --------------------------------------------------------------------------
+// Function cudaMaxActiveBlocksPerSM()
+// --------------------------------------------------------------------------
+
+template <typename TKernel, typename TCTASize, typename TSmemSize>
+inline size_t cudaMaxActiveBlocksPerSM(TKernel kernel, TCTASize ctaSize, TSmemSize dynamicSmemBytes,
+                                       cudaDeviceProp & properties)
+{
+    cudaFuncAttributes attributes = cudaKernelGetAttributes(kernel);
+
+    // Determine the maximum number of CTAs that can be run simultaneously per SM.
+    // This is equivalent to the calculation done in the CUDA Occupancy Calculator spreadsheet.
+    size_t regAllocationUnit      = cudaRegAllocationUnit(properties);
+    size_t warpAllocationMultiple = cudaWarpAllocationMultiple(properties);
+    size_t smemAllocationUnit     = cudaSmemAllocationUnit(properties);
+    size_t maxThreadsPerSM        = properties.maxThreadsPerMultiProcessor;  // 768, 1024, 1536, etc.
+    size_t maxBlocksPerSM         = cudaMaxBlocksPerMultiprocessor(properties);
+
+    // Number of warps (round up to nearest whole multiple of warp size & warp allocation multiple).
+    size_t numWarps = roundI(divideRI(ctaSize, properties.warpSize), warpAllocationMultiple);
+
+    // Number of regs is regs per thread times number of warps times warp size.
+    size_t regsPerCTA = properties.major < 2 ?
+            roundI(attributes.numRegs * properties.warpSize * numWarps, regAllocationUnit) :
+            roundI(attributes.numRegs * properties.warpSize, regAllocationUnit) * numWarps;
+
+    size_t smemBytes  = attributes.sharedSizeBytes + dynamicSmemBytes;
+    size_t smemPerCTA = roundI(smemBytes, smemAllocationUnit);
+
+    size_t ctaLimitRegs    = regsPerCTA > 0 ? properties.regsPerBlock      / regsPerCTA : maxBlocksPerSM;
+    size_t ctaLimitSMem    = smemPerCTA > 0 ? properties.sharedMemPerBlock / smemPerCTA : maxBlocksPerSM;
+    size_t ctaLimitThreads =                  maxThreadsPerSM              / ctaSize;
+
+  return _min(ctaLimitRegs, _min(ctaLimitSMem, _min(ctaLimitThreads, maxBlocksPerSM)));
+}
+
+// --------------------------------------------------------------------------
+// Function checkCudaError()
+// --------------------------------------------------------------------------
+
+//inline void checkCudaError(const char *message)
+//{
+//    cudaError_t error = cudaGetLastError();
+//    if(error!=cudaSuccess) {
+//        fprintf(stderr,"%s: %s\n", message, cudaGetErrorString(error) );
+//        exit(1);
+//    }
+//}
+
+// --------------------------------------------------------------------------
+// Functions not yet used.
+// --------------------------------------------------------------------------
+
+/*
+template <typename KernelFunction>
+size_t auto_blocksize(KernelFunction kernel, size_t dynamic_smem_bytes_per_thread = 0)
+{
+#if THRUST_VERSION < 100600
+    return thrust::detail::backend::cuda::arch::max_blocksize_with_highest_occupancy(kernel, dynamic_smem_bytes_per_thread);
+#else
+    return thrust::system::cuda::detail::arch::max_blocksize_with_highest_occupancy(kernel, dynamic_smem_bytes_per_thread);
+#endif
+}
+
+inline bool is_tcc_enabled()
+{
+    int            device;
+    cudaDeviceProp device_properties;
+    cudaGetDevice(&device);
+    cudaGetDeviceProperties( &device_properties, device );
+    return device_properties.tccDriver ? true : false;
+}
+
+/// a generic syncthreads() implementation to synchronize contiguous
+/// blocks of N threads at a time
+///
+template <__uint32 N>
+SEQAN_HOST_DEVICE inline
+void syncThreads()
+{
+    #ifdef __CUDA_ARCH__
+    if ((N > cuda::Arch::WARP_SIZE) || (is_pow2<N>() == false))
+        __syncthreads();
+    #endif
+}
+*/
+
+}
+
+#endif  // SEQAN_MISC_CUDA_MISC_H_
diff --git a/seqan/misc/misc_dequeue.h b/seqan/misc/dequeue.h
similarity index 50%
rename from seqan/misc/misc_dequeue.h
rename to seqan/misc/dequeue.h
index 3a6ef1b..0014f27 100644
--- a/seqan/misc/misc_dequeue.h
+++ b/seqan/misc/dequeue.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,46 +54,34 @@ namespace SEQAN_NAMESPACE_MAIN
  * @tparam TSpec  Specialization tag for the String.  Default: <tt>Alloc&lt;&gt;</tt>.
  */
 
-/**
-.Class.Dequeue:
-..cat:Miscellaneous
-..summary:A double-ended queue implementation on top of a @Class.String@.
-..signature:Dequeue<TValue, TSpec>
-..param.TValue:Type of the ungapped sequences.
-...metafunction:Metafunction.Value
-..param.TSpec:The specializing type of the underlying @Class.String@.
-...metafunction:Metafunction.Spec
-...default:$Alloc<>$, see @Spec.Alloc String@
-..include:seqan/misc.h
-*/
 template <typename TValue, typename TSpec = Alloc<> >
 class Dequeue
 {
 public:
-	typedef String<TValue, TSpec>						TString;
-	typedef typename Iterator<TString, Standard>::Type	TIter;
+    typedef String<TValue, TSpec>                        TString;
+    typedef typename Iterator<TString, Standard>::Type    TIter;
 
-	String<TValue, TSpec> data_string;
+    String<TValue, TSpec> data_string;
 
-	TIter data_begin;	// string beginning
-	TIter data_end;		// string end
+    TIter data_begin;    // string beginning
+    TIter data_end;        // string end
 
-	TIter data_front;	// front fifo character
-	TIter data_back;	// back fifo character
-	bool data_empty;	// fifo is empty
+    TIter data_front;    // front fifo character
+    TIter data_back;    // back fifo character
+    bool data_empty;    // fifo is empty
 
 //____________________________________________________________________________
 
 public:
-	inline Dequeue()
-	{
-		clear(*this);
-	}
+    inline Dequeue()
+    {
+        clear(*this);
+    }
 
     // ----------------------------------------------------------------------
     // Subscription operators; have to be defined in class def.
     // ----------------------------------------------------------------------
-	
+
     template <typename TPos>
     inline typename Reference<Dequeue>::Type
     operator[] (TPos pos)
@@ -101,7 +89,7 @@ class Dequeue
         SEQAN_CHECKPOINT;
         return value(*this, pos);
     }
-	
+
     template <typename TPos>
     inline typename Reference<Dequeue const>::Type
     operator[] (TPos pos) const
@@ -113,19 +101,16 @@ class Dequeue
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Reference.param.T.type:Class.Segment
-///.Metafunction.Reference.class:Class.Segment
-
 template <typename TValue, typename TSpec>
 struct Reference<Dequeue<TValue, TSpec> >
 {
-	typedef typename Reference<TValue>::Type Type;
+    typedef typename Reference<TValue>::Type Type;
 };
 
 template <typename TValue, typename TSpec>
 struct Reference<Dequeue<TValue, TSpec> const >
 {
-	typedef typename Reference<TValue>::Type Type;
+    typedef typename Reference<TValue>::Type Type;
 };
 
 
@@ -133,31 +118,28 @@ struct Reference<Dequeue<TValue, TSpec> const >
 // Iterators
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Iterator.param.T.type:Class.Dequeue
-///.Metafunction.Iterator.class:Class.Dequeue
-
 template<typename TValue, typename TSpec>
-struct Iterator<Dequeue<TValue, TSpec>, Standard> 
+struct Iterator<Dequeue<TValue, TSpec>, Standard>
 {
-	typedef Iter<Dequeue<TValue, TSpec>, PositionIterator> Type;
+    typedef Iter<Dequeue<TValue, TSpec>, PositionIterator> Type;
 };
 
 template<typename TValue, typename TSpec>
-struct Iterator<Dequeue<TValue, TSpec> const, Standard> 
+struct Iterator<Dequeue<TValue, TSpec> const, Standard>
 {
-	typedef Iter<Dequeue<TValue, TSpec> const, PositionIterator> Type;
+    typedef Iter<Dequeue<TValue, TSpec> const, PositionIterator> Type;
 };
 
 template<typename TValue, typename TSpec>
-struct Iterator<Dequeue<TValue, TSpec>, Rooted> 
+struct Iterator<Dequeue<TValue, TSpec>, Rooted>
 {
-	typedef Iter<Dequeue<TValue, TSpec>, PositionIterator> Type;
+    typedef Iter<Dequeue<TValue, TSpec>, PositionIterator> Type;
 };
 
 template<typename TValue, typename TSpec>
-struct Iterator<Dequeue<TValue, TSpec> const, Rooted> 
+struct Iterator<Dequeue<TValue, TSpec> const, Rooted>
 {
-	typedef Iter<Dequeue<TValue, TSpec> const, PositionIterator> Type;
+    typedef Iter<Dequeue<TValue, TSpec> const, PositionIterator> Type;
 };
 
 
@@ -167,7 +149,7 @@ template <typename TValue, typename TSpec>
 inline bool
 empty(Dequeue<TValue, TSpec> const &me)
 {
-	return me.data_empty;
+    return me.data_empty;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -176,12 +158,12 @@ template <typename TValue, typename TSpec>
 inline void
 clear(Dequeue<TValue, TSpec> &me)
 {
-	clear(me.data_string);
-	me.data_begin = begin(me.data_string, Standard());
-	me.data_end = end(me.data_string, Standard());
+    clear(me.data_string);
+    me.data_begin = begin(me.data_string, Standard());
+    me.data_end = end(me.data_string, Standard());
 
-	me.data_front = me.data_back = me.data_begin;
-	me.data_empty = true;
+    me.data_front = me.data_back = me.data_begin;
+    me.data_empty = true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -190,26 +172,26 @@ template <typename TValue, typename TSpec, typename TPos>
 inline TValue &
 value(Dequeue<TValue, TSpec> &me, TPos pos)
 {
-	typedef typename Size<Dequeue<TValue, TSpec> >::Type TSize;
-	TSize wrap = length(me.data_string) - (me.data_front - me.data_begin);
-	
-	if ((TSize)pos < wrap)
-		return value(me.data_front + pos);
-	else
-		return value(me.data_begin + (pos - wrap));
+    typedef typename Size<Dequeue<TValue, TSpec> >::Type TSize;
+    TSize wrap = length(me.data_string) - (me.data_front - me.data_begin);
+
+    if ((TSize)pos < wrap)
+        return value(me.data_front + pos);
+    else
+        return value(me.data_begin + (pos - wrap));
 }
 
 template <typename TValue, typename TSpec, typename TPos>
 inline TValue const &
 value(Dequeue<TValue, TSpec> const &me, TPos pos)
 {
-	typedef typename Size<Dequeue<TValue, TSpec> >::Type TSize;
-	TSize wrap = length(me.data_string) - (me.data_front - me.data_begin);
-	
-	if ((TSize)pos < wrap)
-		return value(me.data_front + pos);
-	else
-		return value(me.data_begin + (pos - wrap));
+    typedef typename Size<Dequeue<TValue, TSpec> >::Type TSize;
+    TSize wrap = length(me.data_string) - (me.data_front - me.data_begin);
+
+    if ((TSize)pos < wrap)
+        return value(me.data_front + pos);
+    else
+        return value(me.data_begin + (pos - wrap));
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -218,14 +200,14 @@ template <typename TValue, typename TSpec>
 inline TValue &
 front(Dequeue<TValue, TSpec> &me)
 {
-	return *me.data_front;
+    return *me.data_front;
 }
 
 template <typename TValue, typename TSpec>
 inline TValue const &
 front(Dequeue<TValue, TSpec> const &me)
 {
-	return *me.data_front;
+    return *me.data_front;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -234,14 +216,14 @@ template <typename TValue, typename TSpec>
 inline TValue &
 back(Dequeue<TValue, TSpec> &me)
 {
-	return *me.data_back;
+    return *me.data_back;
 }
 
 template <typename TValue, typename TSpec>
 inline TValue const &
 back(Dequeue<TValue, TSpec> const &me)
 {
-	return *me.data_back;
+    return *me.data_back;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -250,35 +232,35 @@ template <typename TValue, typename TSpec>
 inline bool
 popFront(Dequeue<TValue, TSpec> &me)
 {
-	if (me.data_empty) return false;
+    if (me.data_empty) return false;
 
-	if (me.data_front == me.data_back)
-		me.data_empty = true;
-	else
-	{
-		if (++me.data_front == me.data_end)
-			me.data_front = me.data_begin;
-	}
+    if (me.data_front == me.data_back)
+        me.data_empty = true;
+    else
+    {
+        if (++me.data_front == me.data_end)
+            me.data_front = me.data_begin;
+    }
 
-	return true;
+    return true;
 }
 
 template <typename TValue, typename TSpec>
 inline bool
 popBack(Dequeue<TValue, TSpec> &me)
 {
-	if (me.data_empty) return false;
-
-	if (me.data_front == me.data_back)
-		me.data_empty = true;
-	else
-	{
-		if (me.data_back == me.data_begin)
-			me.data_back = me.data_end;
-		--me.data_back;
-	}
-
-	return true;
+    if (me.data_empty) return false;
+
+    if (me.data_front == me.data_back)
+        me.data_empty = true;
+    else
+    {
+        if (me.data_back == me.data_begin)
+            me.data_back = me.data_end;
+        --me.data_back;
+    }
+
+    return true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -287,61 +269,61 @@ template <typename TValue, typename TSpec>
 inline void
 pushFront(Dequeue<TValue, TSpec> &me, TValue const & _value)
 {
-	typedef typename Dequeue<TValue, TSpec>::TIter TIter;
-
-	if (me.data_empty) 
-	{
-		if (me.data_begin == me.data_end)
-			reserve(me, computeGenerousCapacity(me, length(me.data_string) + 1), Generous());
-		me.data_empty = false;
-	}
-	else 
-	{
-		TIter new_front = me.data_front;
-		if (new_front == me.data_begin)
-			new_front = me.data_end;
-		--new_front;
-
-		if (new_front == me.data_back)
-		{
-			reserve(me, computeGenerousCapacity(me, length(me.data_string) + 1), Generous());
-
-			if (me.data_front == me.data_begin)
-				me.data_front = me.data_end;
-			--me.data_front;
-		} else
-			me.data_front = new_front;
-	}
-	assign(*me.data_front, _value);
+    typedef typename Dequeue<TValue, TSpec>::TIter TIter;
+
+    if (me.data_empty)
+    {
+        if (me.data_begin == me.data_end)
+            reserve(me, computeGenerousCapacity(me, length(me.data_string) + 1), Generous());
+        me.data_empty = false;
+    }
+    else
+    {
+        TIter new_front = me.data_front;
+        if (new_front == me.data_begin)
+            new_front = me.data_end;
+        --new_front;
+
+        if (new_front == me.data_back)
+        {
+            reserve(me, computeGenerousCapacity(me, length(me.data_string) + 1), Generous());
+
+            if (me.data_front == me.data_begin)
+                me.data_front = me.data_end;
+            --me.data_front;
+        } else
+            me.data_front = new_front;
+    }
+    assign(*me.data_front, _value);
 }
 
 template <typename TValue, typename TSpec>
 inline void
 pushBack(Dequeue<TValue, TSpec> &me, TValue const & _value)
 {
-	typedef typename Dequeue<TValue, TSpec>::TIter TIter;
-
-	if (me.data_empty) 
-	{
-		if (me.data_begin == me.data_end)
-			reserve(me, computeGenerousCapacity(me, length(me.data_string) + 1), Generous());
-		me.data_empty = false;
-	}
-	else 
-	{
-		TIter new_back = me.data_back;
-		if (++new_back == me.data_end)
-			new_back = me.data_begin;
-
-		if (new_back == me.data_front)
-		{
-			reserve(me, computeGenerousCapacity(me, length(me.data_string) + 1), Generous());
-			// in this case reserve adds new space behind data_back
-			++me.data_back;
-		} else
-			me.data_back = new_back;
-	}
-	assign(*me.data_back, _value);
+    typedef typename Dequeue<TValue, TSpec>::TIter TIter;
+
+    if (me.data_empty)
+    {
+        if (me.data_begin == me.data_end)
+            reserve(me, computeGenerousCapacity(me, length(me.data_string) + 1), Generous());
+        me.data_empty = false;
+    }
+    else
+    {
+        TIter new_back = me.data_back;
+        if (++new_back == me.data_end)
+            new_back = me.data_begin;
+
+        if (new_back == me.data_front)
+        {
+            reserve(me, computeGenerousCapacity(me, length(me.data_string) + 1), Generous());
+            // in this case reserve adds new space behind data_back
+            ++me.data_back;
+        } else
+            me.data_back = new_back;
+    }
+    assign(*me.data_back, _value);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -350,12 +332,12 @@ template <typename TValue, typename TSpec>
 inline typename Size<Dequeue<TValue, TSpec> >::Type
 length(Dequeue<TValue, TSpec> const &me)
 {
-	if (empty(me)) return 0;
+    if (empty(me)) return 0;
 
-	if (me.data_front <= me.data_back)
-		return (me.data_back - me.data_front) + 1;
-	else
-		return (me.data_end - me.data_begin) - (me.data_front - me.data_back) + 1;
+    if (me.data_front <= me.data_back)
+        return (me.data_back - me.data_front) + 1;
+    else
+        return (me.data_end - me.data_begin) - (me.data_front - me.data_back) + 1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -364,55 +346,55 @@ template <typename TValue, typename TSpec, typename TSize_, typename TExpand>
 inline typename Size<Dequeue<TValue, TSpec> >::Type
 reserve(Dequeue<TValue, TSpec> &me, TSize_ new_capacity, Tag<TExpand> tag)
 {
-	typedef typename Size<Dequeue<TValue, TSpec> >::Type TSize;
-//	::std::cout << "resize to "<<new_capacity<<::std::endl;
-	TSize len = length(me);
-	if (len < new_capacity && length(me.data_string) != new_capacity)
-	{
-		TSize pos_front = me.data_front - me.data_begin;
-		TSize pos_back  = me.data_back  - me.data_begin;
-		TSize new_freeSpace = new_capacity - len;
-
-		if (pos_front <= pos_back)
-		{
-			// |empty|data|empty|
-			// 0
-			TSize freeSpace = length(me.data_string) - len;
-			if (new_freeSpace > freeSpace)
-				resize(me.data_string, new_capacity, tag);
-			else
-			{
-				freeSpace -= new_freeSpace;	// reduce the free space by <freeSpace>
-				if (pos_front >= freeSpace)
-				{
-					resizeSpace(me.data_string, pos_front - freeSpace, (TSize)0, pos_front, tag);
-					pos_back -= freeSpace;
-					pos_front -= freeSpace;
-				}
-				else
-				{
-					freeSpace -= pos_front;
-					resizeSpace(me.data_string, length(me.data_string) - freeSpace, pos_back + 1, length(me.data_string), tag);
-					resizeSpace(me.data_string, (TSize)0, (TSize)0, pos_front, tag);
-					pos_back -= pos_front;
-					pos_front = 0;
-				}
-			}
-		}
-		else
-		{
-			// |data|empty|data|
-			// 0
-			resizeSpace(me.data_string, new_freeSpace, pos_back + 1, pos_front, tag);
-			pos_front += new_freeSpace;
-		}
-
-		me.data_begin = begin(me.data_string, Standard());
-		me.data_end = end(me.data_string, Standard());
-		me.data_front = me.data_begin + pos_front;
-		me.data_back = me.data_begin + pos_back;
-	}
-	return length(me.data_string);
+    typedef typename Size<Dequeue<TValue, TSpec> >::Type TSize;
+//    std::cout << "resize to "<<new_capacity<<std::endl;
+    TSize len = length(me);
+    if (len < new_capacity && length(me.data_string) != new_capacity)
+    {
+        TSize pos_front = me.data_front - me.data_begin;
+        TSize pos_back  = me.data_back  - me.data_begin;
+        TSize new_freeSpace = new_capacity - len;
+
+        if (pos_front <= pos_back)
+        {
+            // |empty|data|empty|
+            // 0
+            TSize freeSpace = length(me.data_string) - len;
+            if (new_freeSpace > freeSpace)
+                resize(me.data_string, new_capacity, tag);
+            else
+            {
+                freeSpace -= new_freeSpace;    // reduce the free space by <freeSpace>
+                if (pos_front >= freeSpace)
+                {
+                    resizeSpace(me.data_string, pos_front - freeSpace, (TSize)0, pos_front, tag);
+                    pos_back -= freeSpace;
+                    pos_front -= freeSpace;
+                }
+                else
+                {
+                    freeSpace -= pos_front;
+                    resizeSpace(me.data_string, length(me.data_string) - freeSpace, pos_back + 1, length(me.data_string), tag);
+                    resizeSpace(me.data_string, (TSize)0, (TSize)0, pos_front, tag);
+                    pos_back -= pos_front;
+                    pos_front = 0;
+                }
+            }
+        }
+        else
+        {
+            // |data|empty|data|
+            // 0
+            resizeSpace(me.data_string, new_freeSpace, pos_back + 1, pos_front, tag);
+            pos_front += new_freeSpace;
+        }
+
+        me.data_begin = begin(me.data_string, Standard());
+        me.data_end = end(me.data_string, Standard());
+        me.data_front = me.data_begin + pos_front;
+        me.data_back = me.data_begin + pos_back;
+    }
+    return length(me.data_string);
 }
 
 }
diff --git a/seqan/misc/edit_environment.h b/seqan/misc/edit_environment.h
index 13e913f..5d3e293 100644
--- a/seqan/misc/edit_environment.h
+++ b/seqan/misc/edit_environment.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,8 +38,8 @@
 // TODO(holtgrew): It would be nice if the maximal distance would be given as a run time parameter.
 // TODO(holtgrew): Document iterator?
 
-#ifndef SEQAN_CORE_INCLUDE_MISC_EDIT_ENVIRONMENT_H_
-#define SEQAN_CORE_INCLUDE_MISC_EDIT_ENVIRONMENT_H_
+#ifndef SEQAN_INCLUDE_MISC_EDIT_ENVIRONMENT_H_
+#define SEQAN_INCLUDE_MISC_EDIT_ENVIRONMENT_H_
 
 namespace seqan {
 
@@ -71,7 +71,6 @@ struct EditEnvironment;
  *
  *
  * @fn StringEnumerator::StringEnumerator
- *
  * @brief Constructor
  *
  * @signature StringEnumerator::StringEnumerator(string[, minDist]);
@@ -81,20 +80,17 @@ struct EditEnvironment;
  *
  *
  * @var bool StringEnumerator::trim
- *
  * @brief Indicate whether to ignore substitutions in first or last character of string in Levenshtein mode
  *        (optimization for approximate search).
  *
- * @section Remarks
- *
  * This is useful when searching for such enumerated strings in large texts.  Patterns with substitutions in the first
  * base would also be found.
  *
- * @section Example
+ * @section Examples
  *
- * @include demos/misc/enumerate_strings.cpp
+ * @include demos/dox/misc/enumerate_strings.cpp
  *
- * @include demos/misc/enumerate_strings.cpp.stdout
+ * @include demos/dox/misc/enumerate_strings.cpp.stdout
  */
 
 /*!
@@ -109,8 +105,6 @@ struct EditEnvironment;
  * @tparam TString  Type of the string to enumerate the environment of.
  * @tparam DISTANCE The maximal distance to generate strings with.
  *
- * @section Remarks
- *
  * See @link StringEnumerator @endlink for examples.
  */
 
@@ -118,73 +112,18 @@ struct EditEnvironment;
  * @class LevenshteinStringEnumerator
  * @extends StringEnumerator
  * @headerfile <seqan/misc/edit_environment.h>
- * @brief Enumerate all strings within a given edit distance of a "center string".
- * 
+ * @brief Enumerate all strings within a given edit distance of a "center string" (of edit distance &lt; 3).
+ *
  * @signature template <typename TString, unsigned DISTANCE>
  *            class StringEnumerator<TString, EditEnvironment<LevenshteinDistance, DISTANCE> >;
- * 
+ *
  * @tparam TString  Type of the string to enumerate the environment of.
  * @tparam DISTANCE The maximal distance to generate strings with.
- * 
- * @section Remarks
- * 
+ *
  * See @link StringEnumerator @endlink for examples.
- * 
- * Note that the @link StringEnumerator#length LevenshteinStringEnumerator#length @endlink function does not work for
- * <tt>DISTANCE &gt; 2</tt>.
- */
-
-/**
-.Class.StringEnumerator
-..cat:Miscellaneous
-..summary:Class to enumerate all strings within a given edit/Hamming distance.
-..signature:StringEnumerator<TString, TSpec>
-..param.TString:Type of the string to enumerate the environment of.
-..param.TSpec:Specialization.
-..example.text:
-..include:seqan/misc/edit_environment.h
-
-.Memfunc.StringEnumerator#StringEnumerator
-..class:Class.StringEnumerator
-..summary:Constructor
-..signature:StringEnumerator(string[, minDist])
-..param.string:The string to use as the center.
-...type:nolink:$TString$
-..param.minDist:The smallest distance to generate strings with.
-...type:nolink:$unsigned$
-...default:0
-
-.Memvar.StringEnumerator#trim
-..class:Class.StringEnumerator
-..summary:Indicate whether to ignore substitutions in first or last character of string in Levenshtein mode (optimization for approximate search).
-..signature:trim
-..remarks:
-This is useful when searching for such enumerated strings in large texts.
-Patterns with substitutions in the first base would also be found
-..default:$true$
-
-.Spec.Hamming StringEnumerator
-..general:Class.StringEnumerator
-..cat:Miscellaneous
-..summary:Enumerate all strings within a given edit distance of a "center string".
-..signature:StringEnumerator<TString, EditEnvironment<HammingDistance, DISTANCE> >
-..param.TString:Type of the string to enumerate the environment of.
-..param.DISTANCE:The maximal distance to generate strings with.
-...type:nolink:$unsigned$
-..remarks:See @Class.StringEnumerator@ for examples.
-..include:seqan/misc/edit_environment.h
-
-.Spec.Levenshtein StringEnumerator
-..general:Class.StringEnumerator
-..cat:Miscellaneous
-..summary:Enumerate all strings within a given edit distance of a "center string".
-..signature:StringEnumerator<TString, EditEnvironment<LevenshteinDistance, DISTANCE> >
-..param.TString:Type of the string to enumerate the environment of.
-..param.DISTANCE:The maximal distance to generate strings with.
-...type:nolink:$unsigned$
-..remarks:See @Class.StringEnumerator@ for examples.
-..remarks:Note that the @Function.length@ function does not work for $DISTANCE > 2$.
-..include:seqan/misc/edit_environment.h
+ *
+ * @note The @link StringEnumerator#length LevenshteinStringEnumerator#length @endlink function does not work for
+ *       <tt>DISTANCE &gt; 2</tt>.
  */
 
 template <typename TObject, typename TSpec>
@@ -233,7 +172,7 @@ class Iter<StringEnumerator<TObject, EditEnvironment<HammingDistance, DISTANCE>
     typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier;
 
     TObject & orig;
-//		typename RemoveConst_<TObject>::Type	tmp;
+//        typename RemoveConst_<TObject>::Type    tmp;
     String<TValue>                          tmp;
 
     TModifier   mod[DISTANCE];
@@ -242,7 +181,8 @@ class Iter<StringEnumerator<TObject, EditEnvironment<HammingDistance, DISTANCE>
 
     Iter(TObject & _original) :
         orig(_original),
-        minDist(0)
+        minDist(0),
+        trim(true)
     {
         goBegin(*this);
     }
@@ -257,7 +197,8 @@ class Iter<StringEnumerator<TObject, EditEnvironment<HammingDistance, DISTANCE>
 
     Iter(TObject & _original, MinimalCtor) :
         orig(_original),
-        minDist(0) {}
+        minDist(0),
+        trim(true) {}
 
     Iter(TObject & _original, unsigned _minDist, bool _trim, MinimalCtor) :
         orig(_original),
@@ -295,7 +236,7 @@ class Iter<StringEnumerator<TObject, EditEnvironment<LevenshteinDistance, DISTAN
     typedef StringEnumeratorLevenshteinModifier_<TSignedSize> TModifier;
 
     TObject & orig;
-//		typename RemoveConst_<TObject>::Type	tmp;
+//        typename RemoveConst_<TObject>::Type    tmp;
     String<TValue>                          tmp;
 
     TModifier   mod[DISTANCE + 1];
@@ -306,6 +247,7 @@ class Iter<StringEnumerator<TObject, EditEnvironment<LevenshteinDistance, DISTAN
     Iter(TObject & _original) :
         orig(_original),
         minDist(0),
+        currentDistance(0),
         trim(true)
     {
         goBegin(*this);
@@ -314,6 +256,7 @@ class Iter<StringEnumerator<TObject, EditEnvironment<LevenshteinDistance, DISTAN
     Iter(TObject & _original, unsigned _minDist, bool _trim) :
         orig(_original),
         minDist(_minDist),
+        currentDistance(0),
         trim(_trim)
     {
         goBegin(*this);
@@ -321,11 +264,14 @@ class Iter<StringEnumerator<TObject, EditEnvironment<LevenshteinDistance, DISTAN
 
     Iter(TObject & _original, MinimalCtor) :
         orig(_original),
-        minDist(0) {}
+        minDist(0),
+        currentDistance(0),
+        trim(true) {}
 
     Iter(TObject & _original, unsigned _minDist, bool _trim, MinimalCtor) :
         orig(_original),
         minDist(_minDist),
+        currentDistance(0),
         trim(_trim) {}
 
     inline bool _reinit(int pos, int posOrig)
@@ -454,9 +400,6 @@ class Iter<StringEnumerator<TObject, EditEnvironment<LevenshteinDistance, DISTAN
  * @signature Value<TStringEnumerator>::Type;
  */
 
-///.Metafunction.Value.param.T.type:Class.StringEnumerator
-///.Metafunction.Value.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 struct Value<StringEnumerator<TObject, TSpec> > : Value<TObject>
 {};
@@ -472,9 +415,6 @@ struct Value<StringEnumerator<TObject, TSpec> > : Value<TObject>
  * @signature Reference<TStringEnumerator>::Type;
  */
 
-///.Metafunction.Reference.param.T.type:Class.StringEnumerator
-///.Metafunction.Reference.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 struct Reference<StringEnumerator<TObject, TSpec> >
 {
@@ -498,9 +438,6 @@ struct Reference<StringEnumerator<TObject, TSpec> const>
  * @signature Size<TStringEnumerator>::Type;
  */
 
-///.Metafunction.Size.param.T.type:Class.StringEnumerator
-///.Metafunction.Size.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 struct Size<StringEnumerator<TObject, TSpec> > : Size<TObject>
 {};
@@ -516,9 +453,6 @@ struct Size<StringEnumerator<TObject, TSpec> > : Size<TObject>
  * @signature Difference<TStringEnumerator>::Type;
  */
 
-///.Metafunction.Difference.param.T.type:Class.StringEnumerator
-///.Metafunction.Difference.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 struct Difference<StringEnumerator<TObject, TSpec> > : Difference<TObject>
 {};
@@ -534,9 +468,6 @@ struct Difference<StringEnumerator<TObject, TSpec> > : Difference<TObject>
  * @signature Position<TStringEnumerator>::Type;
  */
 
-///.Metafunction.Position.param.T.type:Class.StringEnumerator
-///.Metafunction.Position.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 struct Position<StringEnumerator<TObject, TSpec> > : Position<TObject>
 {};
@@ -552,9 +483,6 @@ struct Position<StringEnumerator<TObject, TSpec> > : Position<TObject>
  * @signature Position<TStringEnumerator, TSpec>::Type;
  */
 
-///.Metafunction.Iterator.param.T.type:Class.StringEnumerator
-///.Metafunction.Iterator.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 struct Iterator<StringEnumerator<TObject, TSpec>, Standard>
 {
@@ -578,9 +506,6 @@ struct Iterator<StringEnumerator<TObject, TSpec> const, Standard>
  * @signature Host<TStringEnumerator>::Type;
  */
 
-///.Metafunction.Host.param.T.type:Class.StringEnumerator
-///.Metafunction.Host.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 struct Host<StringEnumerator<TObject, TSpec> >
 {
@@ -624,11 +549,13 @@ _dataHost(StringEnumerator<TText, TSpec> const & enumerator)
  * @brief Return begin iterator.
  *
  * @signature TIter begin(stringEnum[, tag]);
+ *
+ * @param[in] stringEnum StringEnumerator to query.
+ * @param[in] tag        Iterator tag to use.
+ *
+ * @return TIter Iterator to the first string in the enumerator.
  */
 
-///.Function.begin.param.object.type:Class.StringEnumerator
-///.Function.begin.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 inline Iter<StringEnumerator<TObject, TSpec>, Standard>
 begin(StringEnumerator<TObject, TSpec> & enumerator, Standard)
@@ -652,11 +579,13 @@ begin(StringEnumerator<TObject, TSpec> const & enumerator, Standard)
  * @brief Return end iterator.
  *
  * @signature TIter end(stringEnum[, tag]);
+ *
+ * @param[in] stringEnum StringEnumerator to query.
+ * @param[in] tag        Iterator tag to use.
+ *
+ * @return TIter End iterator for the string enumerator.
  */
 
-///.Function.end.param.object.type:Class.StringEnumerator
-///.Function.end.class:Class.StringEnumerator
-
 template <typename TObject, typename TSpec>
 inline Iter<StringEnumerator<TObject, TSpec>, Standard>
 end(StringEnumerator<TObject, TSpec> & enumerator, Standard)
@@ -684,11 +613,12 @@ end(StringEnumerator<TObject, TSpec> const & enumerator, Standard)
  * @brief Return number of strings that will be enumerated.
  *
  * @signature TSize length(stringEnum);
+ *
+ * @param[in] stringEnum StringEnumerator to query.
+ *
+ * @return TSize The number of elements in the enumerator  (Metafunction: @link StringEnumerator#Size @endlink).
  */
 
-///.Function.length.param.object.type:Class.StringEnumerator
-///.Function.length.class:Class.StringEnumerator
-
 template <typename TObject, unsigned DISTANCE>
 inline typename Size<StringEnumerator<TObject, EditEnvironment<HammingDistance, DISTANCE> > >::Type
 length(StringEnumerator<TObject, EditEnvironment<HammingDistance, DISTANCE> > const & me)
@@ -1059,8 +989,8 @@ operator++(Iter<StringEnumerator<TObject, EditEnvironment<LevenshteinDistance, D
         if (mod->errorPos >= 0 && static_cast<unsigned>(mod->errorPos) < length(it.tmp))
             assignValue(it.tmp, mod->errorPos, it.orig[mod->errorPosOrig]);
 
-//					int iMax = (TSignedSize)(length(it.tmp) - i);
-//					if (mod->state == mod->INSERT_) ++iMax;
+//                    int iMax = (TSignedSize)(length(it.tmp) - i);
+//                    if (mod->state == mod->INSERT_) ++iMax;
 
         // next error position
         if (++(mod->errorPos) < mod->errorPosEnd)
@@ -1302,6 +1232,6 @@ operator!=(
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_MISC_EDIT_ENVIRONMENT_H_
+#endif  // #ifndef SEQAN_INCLUDE_MISC_EDIT_ENVIRONMENT_H_
 
 //  LocalWords:  StringEnumerator
diff --git a/seqan/misc/interval_tree.h b/seqan/misc/interval_tree.h
new file mode 100644
index 0000000..da2f336
--- /dev/null
+++ b/seqan/misc/interval_tree.h
@@ -0,0 +1,1930 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Anne-Katrin Emde <emde@fu-berlin.de>
+// ==========================================================================
+
+
+// TODO(holtgrew): Bring back random center computation using new random module?
+
+// (weese:) This header needs improvement
+//
+// documentation lacks:
+//   - is createIntervalTree clearing the tree first (what happens after a second call of createIntervalTree?)
+//   - where is clear(itree)?
+//   - some flags are missing in the dddoc entries, e.g. ..cat:, class:, or ..type: of arguments
+//
+// interface flaws:
+//   - there are 2 interfaces for createIntervalTree
+//      - based on IntervalTree
+//      - based on Graph and PropertyMap (should be removed)
+//   - addInterval
+
+
+#ifndef SEQAN_HEADER_MISC_INTERVAL_TREE_H
+#define SEQAN_HEADER_MISC_INTERVAL_TREE_H
+
+#include <seqan/graph_types.h>
+
+
+namespace SEQAN_NAMESPACE_MAIN {
+//////////////////////////////////////////////////////////////////////////////
+// Graph - Interval Tree Types
+//////////////////////////////////////////////////////////////////////////////
+
+///---------------------------------------------------------------///
+
+//////////////////// Interval and ID type ///////////////////
+
+// TODO(holtgrew): Are these actual the first/last or begin/end entries?
+
+/*!
+ * @class IntervalAndCargo
+ * @headerfile <seqan/misc/interval_tree.h>
+ * @brief A simple record type that stores an interval and a cargo value.
+ *
+ * @signature template <[typename TValue[, typename TCargo]]>
+ *            class IntervalAndCargo;
+ *
+ * @tparam TValue The value type.  Default: <tt>int</tt>.
+ * @tparam TCargo The cargo type.  Default: <tt>int</tt>.
+ *
+ * @fn IntervalAndCargo::IntervalAndCargo
+ * @brief Constructor
+ *
+ * @signature IntervalAndCargo::IntervalAndCargo();
+ * @signature IntervalAndCargo::IntervalAndCargo(i1, i2, cargo);
+ *
+ * @param[in] i1    The first element in the interval.
+ * @param[in] i2    The last element in the interval.
+ * @param[in] cargo The cargo to store together with the interval.
+ *
+ * @var TValue IntervalAndCargo::i1;
+ * @brief The first element in the interval.
+ *
+ * @var TValue IntervalAndCargo::i2;
+ * @brief The last element in the interval.
+ *
+ * @var TCargo IntervalAndCargo::cargo;
+ * @brief The stored cargo.
+ */
+
+template <typename TValue = int, typename TCargo = int>
+class IntervalAndCargo
+{
+public:
+    TValue i1;
+
+    TValue i2;
+
+    TCargo cargo;
+
+    IntervalAndCargo() :
+        i1(), i2(), cargo()
+    {}
+
+    IntervalAndCargo(TValue i1, TValue i2, TCargo cargo) :
+        i1(i1), i2(i2), cargo(cargo)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+};
+
+
+
+/////////////////////// Point and ID type ////////////////
+
+/*!
+ * @class PointAndCargo
+ * @headerfile <seqan/misc/interval_tree.h>
+ * @brief Simple record class storing a point (one-value) interval and cargo.
+ *
+ * @signature template <[typename TValue[, typename TCargo]]>
+ *            class PointAndCargo;
+ *
+ * @tparam TValue The value type.
+ * @tparam TCargo The cargo type.
+ *
+ * @fn PointAndCargo::PointAndCargo
+ * @brief Constructor
+ *
+ * @signature PointAndCargo::PointAndCargo();
+ * @signature PointAndCargo::PointAndCargo(point, cargo);
+ *
+ * @param[in] point The point to store.
+ * @param[in] cargo The cargo to store.
+ *
+ * @var TValue PointAndCargo::point
+ * @brief The point to store.
+ *
+ * @var TCargo PointAndCargo::cargo
+ * @brief The cargo to store.
+ */
+
+template <typename TValue = int, typename TCargo = int>
+class PointAndCargo
+{
+public:
+    TValue point;
+
+    TCargo cargo;
+
+    PointAndCargo() :
+        point(), cargo()
+    {}
+
+    PointAndCargo(TValue point, TCargo cargo) :
+        point(point), cargo(cargo)
+    {}
+};
+
+///////////////////////////////////////////////////////////////////////////
+/////////////////////////// IntervalTreeNode    ///////////////////////////
+
+/*!
+ * @defgroup IntervalTreeNodeTypeTags IntervalTree Node Types Tags
+ * @brief Tags to select the node type for @link IntervalTree @endlink.
+ *
+ * @tag IntervalTreeNodeTypeTags#StorePointsOnly
+ * @headerfile <seqan/misc/interval_tree.h>
+ * @signature struct StorePointsOnly {};
+ * @brief The tree nodes store points.
+ *
+ * @tag IntervalTreeNodeTypeTags#StoreIntervals
+ * @headerfile <seqan/misc/interval_tree.h>
+ * @signature struct StoreIntervals {};
+ * @brief The tree nodes store intervals.
+ */
+
+struct StorePointsOnly {};
+
+
+struct StoreIntervals {};
+
+/*!
+ * @class IntervalTreeNode
+ * @headerfile <seqan/misc/interval_tree.h>
+ * @brief Element of @link IntervalTree @endlink.
+ *
+ * @signature template <typename TInterval[, typename TSpec]>
+ *            class IntervalTreeNode;
+ *
+ * @tparam TInterval The type to use for intervals.
+ * @tparam TSpec     The specializing tag.  Default: @link IntervalTreeNodeTypeTags#StorePointsOnly @endlink.
+ */
+
+
+template <typename TInterval, typename TSpec = StorePointsOnly>
+class IntervalTreeNode;
+
+/*!
+ * @class StoreIntervalsIntervalTreeNode
+ * @extends IntervalTreeNode
+ * @headerfile <seqan/misc/interval_tree.h>
+ * @brief An IntervalTreeNode that stores intervals explicitely in each node.
+ *
+ * @signature template <typename TInterval>
+ *            class IntervalTreeNode<TInterval, StoreIntervals>;
+ *
+ * @tparam TInterval The Interval type to use.
+ */
+
+/*!
+ * @var TValue StoreIntervalsIntervalTreeNode::center;
+ * @brief Center of the interval tree node.
+ *
+ * @var TString StoreIntervalsIntervalTreeNode::list1;
+ * @brief @link AllocString @endlink of intervals sorted by begin point.
+ *
+ * @var TString StoreIntervalsIntervalTreeNode::list;
+ * @brief @link AllocString @endlink of intervals sorted by end point.
+ */
+
+template <typename TInterval>
+class IntervalTreeNode<TInterval, StoreIntervals>
+{
+public:
+    typedef typename Value<TInterval>::Type TValue;
+
+    TValue center;
+    String<TInterval> list1;
+    String<TInterval> list2;
+
+    IntervalTreeNode() :
+        center()
+    {}
+};
+
+/*!
+ * @class StorePointsOnlyIntervalTreeNode
+ * @extends IntervalTreeNode
+ * @headerfile <seqan/misc/interval_tree.h>
+ * @brief An IntervalTreeNode that stores only the relevant points in each node.
+ *
+ * Only the end points of the intervals in the list sorted by endpoints (list2) and only the begin point of the interval
+ * list sorted by begin points (list1) are stored.
+ *
+ * @signature template <typename TInterval>
+ *            class IntervalTreeNode<TInterval, StoreIntervals>;
+ *
+ * @tparam TInterval The Interval type to use.
+ */
+
+/*!
+ * @var TValue StorePointsOnlyIntervalTreeNode::center;
+ * @brief Center of the interval.
+ *
+ * @var TString StorePointsOnlyIntervalTreeNode::list1;
+ * @brief Points with cargo sorted by the begin points.
+ *
+ * @var TString StorePointsOnlyIntervalTreeNode::list2;
+ * @brief Points with cargo sorted by the end points.
+ */
+
+template <typename TInterval>
+class IntervalTreeNode<TInterval, StorePointsOnly>
+{
+public:
+    typedef typename Cargo<TInterval>::Type TCargo;
+    typedef typename Value<TInterval>::Type TValue;
+
+    TValue center;
+    String<PointAndCargo<TValue, TCargo> > list1;
+    String<PointAndCargo<TValue, TCargo> > list2;
+
+    IntervalTreeNode() :
+        center()
+    {
+        SEQAN_CHECKPOINT
+    }
+
+    IntervalTreeNode(IntervalTreeNode const & other) :
+        center(other.center),
+        list1(other.list1),
+        list2(other.list2)
+    {
+        SEQAN_CHECKPOINT
+    }
+
+};
+
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Graph - Interval Tree
+//////////////////////////////////////////////////////////////////////////////
+
+/*!
+ * @class IntervalTree
+ * @headerfile <seqan/misc/interval_tree.h>
+ * @brief Data structure for efficient interval storage.
+ *
+ * @signature template <[typename TValue[, typename TCargo]]>
+ *            class IntervalTree;
+ *
+ * @tparam TValue The type to use for coordinates.  Default: <tt>int</tt>.
+ * @tparam TCargo The type to use for cargo.  Default: <tt>unsigned</tt>.
+ *
+ * @section Remarks
+ *
+ * If the intervals are not associated with cargos/IDs, they will be numbered consecutively.
+ *
+ * @section Example
+ *
+ * The following example creates an integer interval tree with string keys.  This tree is quired for keys of intervals
+ * that overlap the interval <tt>[550, 990)</tt>.
+ *
+ * @include demos/dox/misc/interval_tree_example.cpp
+ *
+ * The resulting keys are:
+ *
+ * @code{.console}
+ * gene
+ * exon2
+ * coding2
+ * @endcode
+ *
+ *
+ * @fn IntervalTree::IntervalTree
+ * @brief Constructor
+ *
+ * @signature IntervalTree::IntervalTree();
+ * @signature IntervalTree::IntervalTree(intervals);
+ * @signature IntervalTree::IntervalTree(intervals[, center]);
+ * @signature IntervalTree::IntervalTree(intervals[, tag]);
+ * @signature IntervalTree::IntervalTree(intervalBegins, intervalEnds, [intervalCargos,] len);
+ *
+ * @param[in] intervals Container of intervals.  A strin gof <tt>IntervalAndCargo&lt;Value, TCargo&gt;</tt>
+ *                      objects, see @link IntervalAndCargo @endlink.
+ * @param[in] intervalBegins
+ *                      Iterator pointing to begin position of first interval.
+ * @param[in] intervalEnds
+ *                      Iterator pointing to end position of first interval.
+ * @param[in] intervalCargos
+ *                      Iterator pointing to cargo/ids for intervals.
+ * @param[in] len       Number of intervals to store in tree.
+ * @param[in] tag       Tag for tree construction method.
+ */
+
+template <typename TValue = int, typename TCargo = unsigned int>
+class IntervalTree
+{
+public:
+    typedef Graph<Directed<void, WithoutEdgeId> > TGraph;
+    typedef IntervalAndCargo<TValue, TCargo> TInterval;
+    typedef IntervalTreeNode<TInterval> TNode;
+    typedef String<TNode> TPropertyMap;
+
+    TGraph g;
+    TPropertyMap pm;
+    size_t interval_counter;
+
+    IntervalTree()
+    {
+        SEQAN_CHECKPOINT
+            interval_counter = 0;
+    }
+
+    template <typename TIterator, typename TCargoIterator>
+    IntervalTree(TIterator interval_begins,
+                 TIterator interval_ends,
+                 TCargoIterator interval_cargos,
+                 size_t len)
+    {
+        SEQAN_CHECKPOINT
+        String<TInterval> intervals;
+        resize(intervals, len);
+        size_t i = 0;
+        while (i < len)
+        {
+            intervals[i].i1 = value(interval_begins);
+            ++interval_begins;
+            intervals[i].i2 = value(interval_ends);
+            ++interval_ends;
+            intervals[i].cargo = value(interval_cargos);
+            ++interval_cargos;
+            ++i;
+        }
+        createIntervalTree(*this, intervals);
+    }
+
+    template <typename TIterator>
+    IntervalTree(TIterator interval_begins,
+                 TIterator interval_ends,
+                 size_t len)
+    {
+        SEQAN_CHECKPOINT
+        String<TInterval> intervals;
+        resize(intervals, len);
+        size_t i = 0;
+        while (i < len)
+        {
+            intervals[i].i1 = value(interval_begins);
+            ++interval_begins;
+            intervals[i].i2 = value(interval_ends);
+            ++interval_ends;
+            intervals[i].cargo = i;
+            ++i;
+        }
+        createIntervalTree(*this, intervals);
+    }
+
+    IntervalTree(String<TInterval> intervals)
+    {
+        SEQAN_CHECKPOINT
+            createIntervalTree(*this, intervals);
+    }
+
+    template <typename TTagSpec>
+    IntervalTree(String<TInterval> intervals, Tag<TTagSpec> const tag)
+    {
+        SEQAN_CHECKPOINT
+            interval_counter = length(intervals);
+        createIntervalTree(g, pm, intervals, tag);
+    }
+
+    IntervalTree(String<TInterval> intervals, TValue center)
+    {
+        SEQAN_CHECKPOINT
+            interval_counter = length(intervals);
+        createIntervalTree(g, pm, intervals, center);
+    }
+
+};
+
+
+
+///////Specs for the way interval centers are determined
+
+//template <typename TSpec = SpecPointAndCargo>
+struct TagComputeCenter_;
+typedef Tag<TagComputeCenter_> const ComputeCenter;
+
+
+///////////////////////////////////////////////////////////////////////////
+///////////////////// IntervalAndCargo functions //////////////////////////
+///////////////////////////////////////////////////////////////////////////
+
+/*!
+ * @fn IntervalAndCargo#leftBoundary
+ * @brief Access to left boundary.
+ *
+ * @signature TBoundary leftBoundary(interval);
+ *
+ * @param[in] interval The IntervalAndCargo to query for its left boundary.
+ *
+ * @return TBoundary Reference to the left boundary value.
+ */
+
+template <typename TValue, typename TCargo>
+TValue &
+leftBoundary(IntervalAndCargo<TValue, TCargo> & interval)
+{
+    return interval.i1;
+}
+
+template <typename TValue, typename TCargo>
+TValue const &
+leftBoundary(IntervalAndCargo<TValue, TCargo> const & interval)
+{
+    return interval.i1;
+}
+
+/*!
+ * @fn IntervalAndCargo#rightBoundary
+ * @brief Access to right boundary.
+ *
+ * @signature TBoundary rightBoundary(interval);
+ *
+ * @param[in] interval The IntervalAndCargo to query for its right boundary.
+ *
+ * @return TBoundary Reference to the right boundary value.
+ */
+
+template <typename TValue, typename TCargo>
+TValue &
+rightBoundary(IntervalAndCargo<TValue, TCargo> & interval)
+{
+    return interval.i2;
+}
+
+template <typename TValue, typename TCargo>
+TValue const &
+rightBoundary(IntervalAndCargo<TValue, TCargo> const & interval)
+{
+    return interval.i2;
+}
+
+/*!
+ * @fn IntervalAndCargo#getLeftBoundary
+ * @brief Access to getLeft boundary.
+ *
+ * @signature TBoundary getLeftBoundary(interval);
+ *
+ * @param[in] interval The IntervalAndCargo to query for its left boundary.
+ *
+ * @return TBoundary Copy of the left boundary value.
+ */
+
+template <typename TValue, typename TCargo>
+TValue
+getLeftBoundary(IntervalAndCargo<TValue, TCargo> const & interval)
+{
+    return interval.i1;
+}
+
+/*!
+ * @fn IntervalAndCargo#getRightBoundary
+ * @brief Access to getRight boundary.
+ *
+ * @signature TBoundary getRightBoundary(interval);
+ *
+ * @param[in] interval The IntervalAndCargo to query for its right boundary.
+ *
+ * @return TBoundary Copy of the right boundary value.
+ */
+
+template <typename TValue, typename TCargo>
+TValue
+getRightBoundary(IntervalAndCargo<TValue, TCargo> const & interval)
+{
+    return interval.i2;
+}
+
+/*!
+ * @fn IntervalAndCargo#cargo
+ * @brief Access to the cargo.
+ *
+ * @signature TCargo cargo(interval);
+ *
+ * @param[in] interval The IntervalAndCargo to query for its cargo.
+ *
+ * @return TCargo Reference to the cargo member.
+ */
+
+template <typename TValue, typename TCargo>
+TCargo const &
+cargo(IntervalAndCargo<TValue, TCargo> const & interval)
+{
+    return interval.cargo;
+}
+
+template <typename TValue, typename TCargo>
+TCargo &
+cargo(IntervalAndCargo<TValue, TCargo> & interval)
+{
+    return interval.cargo;
+}
+
+/*!
+ * @fn IntervalAndCargo#getCargo
+ * @brief Access to the cargo.
+ *
+ * @signature TCargo getCargo(interval);
+ *
+ * @param[in] interval The IntervalAndCargo to query for its cargo.
+ *
+ * @return TCargo Copy of the cargo member.
+ */
+
+template <typename TValue, typename TCargo>
+TCargo
+getCargo(IntervalAndCargo<TValue, TCargo> const & interval)
+{
+    return interval.cargo;
+}
+
+/////////////////// Metafunctions //////////////////////
+
+/*!
+ * @mfn IntervalAndCargo#Value
+ * @brief Return the value type.
+ *
+ * @signature Value<TIntervalAndCargo>::Type;
+ */
+
+template <typename TValue, typename TCargo>
+struct Value<IntervalAndCargo<TValue, TCargo> >
+{
+    typedef TValue Type;
+};
+
+/*!
+ * @mfn IntervalAndCargo#Cargo
+ * @brief Return the cargo type.
+ *
+ * @signature Cargo<TIntervalAndCargo>::Type;
+ */
+
+template <typename TValue, typename TCargo>
+struct Cargo<IntervalAndCargo<TValue, TCargo> >
+{
+    typedef TCargo Type;
+};
+
+
+///////////////////////////////////////////////////////////////////////////
+///////////////////// PointAndCargo functions /////////////////////////////
+///////////////////////////////////////////////////////////////////////////
+
+/*!
+ * @fn PointAndCargo#leftBoundary
+ * @brief Access to left boundary.
+ *
+ * @signature TBoundary leftBoundary(point);
+ *
+ * @param[in] point The PointAndCargo to query for its left boundary.
+ *
+ * @return TBoundary Reference to the left boundary value.
+ */
+
+template <typename TValue, typename TCargo>
+TValue const &
+leftBoundary(PointAndCargo<TValue, TCargo> const & point)
+{
+    return point.point;
+}
+
+template <typename TValue, typename TCargo>
+TValue &
+leftBoundary(PointAndCargo<TValue, TCargo> & point)
+{
+    return point.point;
+}
+
+/*!
+ * @fn PointAndCargo#rightBoundary
+ * @brief Access to right boundary.
+ *
+ * @signature TBoundary rightBoundary(point);
+ *
+ * @param[in] point The PointAndCargo to query for its right boundary.
+ *
+ * @return TBoundary Reference to the right boundary value.
+ */
+
+template <typename TValue, typename TCargo>
+TValue const &
+rightBoundary(PointAndCargo<TValue, TCargo> const & point)
+{
+    return point.point;
+}
+
+template <typename TValue, typename TCargo>
+TValue &
+rightBoundary(PointAndCargo<TValue, TCargo> & point)
+{
+    return point.point;
+}
+
+template <typename TValue, typename TCargo>
+TValue
+getLeftBoundary(PointAndCargo<TValue, TCargo> const & point)
+{
+    return point.point;
+}
+
+/*!
+ * @fn PointAndCargo#getLeftBoundary
+ * @brief Access to getLeft boundary.
+ *
+ * @signature TBoundary getLeftBoundary(point);
+ *
+ * @param[in] point The PointAndCargo to query for its left boundary.
+ *
+ * @return TBoundary Copy of the left boundary value.
+ */
+
+template <typename TValue, typename TCargo>
+TValue
+getRightBoundary(PointAndCargo<TValue, TCargo> const & point)
+{
+    return point.point;
+}
+
+/*!
+ * @fn PointAndCargo#cargo
+ * @brief Access to the cargo.
+ *
+ * @signature TCargo cargo(point);
+ *
+ * @param[in] point The PointAndCargo to query for its cargo.
+ *
+ * @return TCargo Reference to the cargo member.
+ */
+
+
+template <typename TValue, typename TCargo>
+TCargo const &
+cargo(PointAndCargo<TValue, TCargo> const & point)
+{
+    return point.cargo;
+}
+
+template <typename TValue, typename TCargo>
+TCargo &
+cargo(PointAndCargo<TValue, TCargo> & point)
+{
+    return point.cargo;
+}
+
+/*!
+ * @fn PointAndCargo#getCargo
+ * @brief Access to the cargo.
+ *
+ * @signature TCargo getCargo(point);
+ *
+ * @param[in] point The PointAndCargo to query for its cargo.
+ *
+ * @return TCargo Copy of the cargo member.
+ */
+
+template <typename TValue, typename TCargo>
+TCargo
+getCargo(PointAndCargo<TValue, TCargo> const & point)
+{
+    return point.cargo;
+}
+
+////////////////// Metafunctions //////////////////
+
+/*!
+ * @mfn PointAndCargo#Value
+ * @brief Return the value type.
+ *
+ * @signature Value<TPointAndCargo>::Type;
+ */
+
+template <typename TValue, typename TCargo>
+struct Value<PointAndCargo<TValue, TCargo> >
+{
+    typedef TValue Type;
+};
+
+/*!
+ * @mfn PointAndCargo#Cargo
+ * @brief Return the cargo type.
+ *
+ * @signature Cargo<TPointAndCargo>::Type;
+ */
+
+template <typename TValue, typename TCargo>
+struct Cargo<PointAndCargo<TValue, TCargo> >
+{
+    typedef TCargo Type;
+};
+
+
+//// Comparators
+template <typename TPair>
+bool _less_compI1_ITree(TPair const & p1, TPair const & p2)
+{
+    return leftBoundary(p1) < leftBoundary(p2);
+}
+
+template <typename TPair>
+bool _greater_compI2_ITree(TPair const & p1, TPair const & p2)
+{
+    return rightBoundary(p1) > rightBoundary(p2);
+}
+
+///////////////////////////////////////////////////////////////////////////
+///////////////////// IntervalTreeNode functions //////////////////////////
+///////////////////////////////////////////////////////////////////////////
+
+
+
+
+
+// internal set node functions
+template <typename TValue, typename TInterval>
+void
+_setIntervalTreeNode(IntervalTreeNode<TInterval, StoreIntervals> & knot, TValue center, TInterval const & interval)
+{
+    knot.center = center;
+    appendValue(knot.list1, interval);
+    appendValue(knot.list2, interval);
+}
+
+// append intervals to lists in node knot
+template <typename TInterval>
+void
+_appendIntervalTreeNodeLists(IntervalTreeNode<TInterval, StoreIntervals> & knot, TInterval const & interval)
+{
+    appendValue(knot.list1, interval);
+    appendValue(knot.list2, interval);
+}
+
+//internal set node functions
+template <typename TValue, typename TInterval>
+void
+_setIntervalTreeNode(IntervalTreeNode<TInterval, StorePointsOnly> & knot, TValue center, TInterval const & interval)
+{
+    knot.center = center;
+    appendValue(knot.list1, PointAndCargo<TValue, typename Cargo<TInterval>::Type>(leftBoundary(interval), cargo(interval)));
+    appendValue(knot.list2, PointAndCargo<TValue, typename Cargo<TInterval>::Type>(rightBoundary(interval), cargo(interval)));
+}
+
+template <typename TInterval>
+void
+_appendIntervalTreeNodeLists(IntervalTreeNode<TInterval, StorePointsOnly> & knot, TInterval const & interval)
+{
+    appendValue(knot.list1, PointAndCargo<typename Value<TInterval>::Type, typename Cargo<TInterval>::Type>(leftBoundary(interval), cargo(interval)));
+    appendValue(knot.list2, PointAndCargo<typename Value<TInterval>::Type, typename Cargo<TInterval>::Type>(rightBoundary(interval), cargo(interval)));
+
+
+}
+
+/////////////////// Metafunctions ///////////////////////
+
+/*!
+ * @mfn IntervalTreeNode#Value
+ * @brief Return value type.
+ *
+ * @signature Value<TNode>::Type;
+ */
+
+template <typename TInterval, typename TSpec>
+struct Value<IntervalTreeNode<TInterval, TSpec> >
+{
+    typedef typename Value<TInterval>::Type Type;
+};
+
+/*!
+ * @mfn IntervalTreeNode#Cargo
+ * @brief Return cargo type.
+ *
+ * @signature Cargo<TNode>::Type;
+ */
+
+template <typename TInterval, typename TSpec>
+struct Cargo<IntervalTreeNode<TInterval, TSpec> >
+{
+    typedef typename Cargo<TInterval>::Type Type;
+};
+
+
+/*!
+ * @mfn IntervalTreeNode#ListType
+ * @brief Type of the lists in tree nodes.
+ *
+ * @signature ListType<T>::Type;
+ */
+
+template <typename T>
+struct ListType;
+
+
+template <typename TInterval>
+struct ListType<IntervalTreeNode<TInterval, StorePointsOnly> >
+{
+    typedef String<PointAndCargo<typename Value<TInterval>::Type, typename Cargo<TInterval>::Type> > Type;
+
+};
+
+
+template <typename TInterval>
+struct ListType<IntervalTreeNode<TInterval, StoreIntervals> >
+{
+    typedef String<IntervalAndCargo<typename Value<TInterval>::Type, typename Cargo<TInterval>::Type> > Type;
+
+};
+
+
+
+///////////////////////////////////////////////////////////////////////////
+/////////////////////// IntervalTree functions ////////////////////////////
+///////////////////////////////////////////////////////////////////////////
+
+/*!
+ * @fn IntervalTree#createIntervalTree
+ * @brief Create an interval tree.
+ *
+ * @signature void createIntervalTree(intervalTree, intervals[, tag]);
+ * @signature void createIntervalTree(g, pm, intervals[, tag]);
+ * @signature void createIntervalTree(g, pm, intervals, center[, tag]]);
+ *
+ * @param[in,out] intervalTree An interval tree Types: IntervalTree
+ * @param[in,out] g            DirectedGraph to create interval tree in. Types: @link Graph @endlink.
+ * @param[in,out] pm           Property map to use for the created interval tree.
+ * @param[in]     tag          Tag for tree construction method;
+ * @param[in]     intervals    Container of intervals.  A string of <tt>IntervalAndCargo&lt;TValue, TCargo&gt;</tt>
+ *                             objects, see @link IntervalAndCargo @endlink. Types: @link AllocString @endlink.
+ */
+
+template <typename TGraph, typename TPropertyMap, typename TIntervals, typename TSpec>
+inline void
+createIntervalTree(TGraph & g,
+                   TPropertyMap & pm,
+                   TIntervals & intervals,
+                   Tag<TSpec> const tag)
+{
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Value<TIntervals>::Type TInterval;
+    typedef typename Value<TInterval>::Type TValue;
+
+    reserve(g.data_vertex, length(intervals));
+    reserve(pm, length(intervals));
+
+    TVertexDescriptor root = addVertex(g);
+    resizeVertexMap(pm, g);
+
+    if (length(intervals) > 0u)
+    {
+        TValue center = _calcIntervalTreeRootCenter(intervals);
+
+        std::sort(begin(intervals, Standard()), end(intervals, Standard()), _less_compI1_ITree<TInterval>);
+
+        String<TInterval *> interval_pointers;
+        // interval tree stores pointers to intervals, not original intervals
+        _makePointerInterval(intervals, interval_pointers);
+
+        _createIntervalTree(g, pm, interval_pointers, root, (TValue)0.0, center, length(intervals), tag);
+        reserve(pm, length(pm), Exact());
+        reserve(g.data_vertex, length(g.data_vertex), Exact());
+    }
+}
+
+template <typename TGraph, typename TPropertyMap, typename TIntervals>
+inline void
+createIntervalTree(TGraph & g,
+                   TPropertyMap & pm,
+                   TIntervals & intervals)
+{
+    createIntervalTree(g, pm, intervals, ComputeCenter());
+}
+
+template <typename TGraph, typename TPropertyMap, typename TIntervals, typename TSpec>
+inline void
+createIntervalTree(TGraph & g,
+                   TPropertyMap & pm,
+                   TIntervals & intervals,
+                   typename Value<typename Value<TIntervals>::Type>::Type center,
+                   Tag<TSpec> const tag)
+{
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Value<TIntervals>::Type TInterval;
+    typedef typename Value<typename Value<TIntervals>::Type>::Type TValue;
+
+    reserve(g.data_vertex, length(intervals));
+    reserve(pm, length(intervals));
+
+    TVertexDescriptor root = addVertex(g);
+    resizeVertexMap(pm, g);
+
+    if (length(intervals) > 0u)
+    {
+        TInterval a;
+        typename Iterator<TIntervals, Standard>::Type begin_ = begin(intervals, Standard());
+        typename Iterator<TIntervals, Standard>::Type end_ = end(intervals, Standard());
+        std::sort(begin_, end_, _less_compI1_ITree<TInterval>);
+
+        String<TInterval const *> interval_pointers;
+        _makePointerInterval(intervals, interval_pointers);
+
+        if (length(intervals) == 1) // if there is just one interval ->  center = center of this interval
+            center = (rightBoundary(intervals[0]) - leftBoundary(intervals[0])) / (TValue)2.0;
+
+        _createIntervalTree(g, pm, interval_pointers, root, (TValue)0.0, center, length(intervals), tag);
+
+        reserve(pm, length(pm), Exact());
+        reserve(g.data_vertex, length(g.data_vertex), Exact());
+    }
+}
+
+// ComputeCenter tag as default construction method
+template <typename TGraph, typename TPropertyMap, typename TIntervals>
+inline void
+createIntervalTree(TGraph & g, TPropertyMap & pm,
+                   TIntervals & intervals,
+                   typename Value<typename Value<TIntervals>::Type>::Type center)
+{
+    createIntervalTree(g, pm, intervals, center, ComputeCenter());
+}
+
+template <typename TValue, typename TCargo, typename TIntervals, typename TSpec>
+inline void
+createIntervalTree(IntervalTree<TValue, TCargo> & it,
+                   TIntervals & intervals,
+                   Tag<TSpec> const tag)
+{
+    it.interval_counter = length(intervals);
+    createIntervalTree(it.g, it.pm, intervals, tag);
+}
+
+template <typename TValue, typename TCargo, typename TIntervals>
+inline void
+createIntervalTree(IntervalTree<TValue, TCargo> & it,
+                   TIntervals & intervals)
+{
+    createIntervalTree(it, intervals, ComputeCenter());
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//remembers minimum and maximum of point values in intervals and sets the center
+//of each node to min+(max-min)/2
+template <typename TGraph, typename TPropertyMap, typename TIntervalPointer, typename TValue>
+inline void
+_createIntervalTree(TGraph & g, TPropertyMap & pm,
+                    String<TIntervalPointer *> & intervals,
+                    typename VertexDescriptor<TGraph>::Type & knot,
+                    TValue,
+                    TValue center,
+                    typename VertexDescriptor<TGraph>::Type len,
+                    Tag<TagComputeCenter_> const tag)
+{
+    //  Rekursionsanker
+    if (len == 1)
+    {
+        _setIntervalTreeNode(value(pm, knot), center, *intervals[0]);
+        return;
+    }
+
+    typedef typename Value<TPropertyMap>::Type TNode;
+    typedef typename ListType<TNode>::Type TList;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef String<TIntervalPointer *> TIntervalPointers;
+
+    // one list of interval pointers for the intervals to the left of center
+    TIntervalPointers S_left;
+    // one list of interval pointers for the intervals to the right of center
+    TIntervalPointers S_right;
+
+    TValue min1 = maxValue<TValue>();
+    TValue min2 = maxValue<TValue>();
+    TValue max1 = minValue<TValue>();
+    TValue max2 = minValue<TValue>();
+
+    value(pm, knot).center = center;
+
+
+    typedef typename Iterator<TIntervalPointers, Standard>::Type TIntervalIterator;
+    TIntervalIterator it = begin(intervals, Standard());
+    TIntervalIterator it_end = end(intervals, Standard());
+
+    // walk through intervals
+    while (it != it_end)
+    {
+        // interval belongs to the left list
+        if ((**it).i2 <= center)
+        {
+            appendValue(S_left, *it, Generous());
+            //remember right most and left most point in left list
+            if ((**it).i2 > max1)
+                max1 = (**it).i2;
+            if ((**it).i1 < min1)
+                min1 = (**it).i1;
+        }
+        else
+        {
+            // interval belongs to the right list
+            if ((**it).i1 > center)
+            {
+                appendValue(S_right, (*it), Generous());
+                //remember right most and left most point in right list
+                if ((**it).i2 > max2)
+                    max2 = (**it).i2;
+                if ((**it).i1 < min2)
+                    min2 = (**it).i1;
+            }
+            else // interval belongs to this node
+            {
+                _appendIntervalTreeNodeLists(value(pm, knot), **it);
+            }
+        }
+        ++it;
+    }
+
+//    std::sort(begin(value(pm,knot).list1),end(value(pm,knot).list1),_less_compI1_ITree<typename Value<TList>::Type>);
+    std::sort(begin(value(pm, knot).list2), end(value(pm, knot).list2), _greater_compI2_ITree<typename Value<TList>::Type>);
+
+    // build subtree to the left
+    if (!empty(S_left))
+    {
+        TVertexDescriptor vd = addVertex(g);
+        resize(pm, vd + 1);
+        addEdge(g, knot, vd);
+        _createIntervalTree(g, pm, S_left, vd, center, min1 + (max1 - min1) / 2, length(S_left), tag);
+    }
+    // build subtree to the right
+    if (!empty(S_right))
+    {
+        TVertexDescriptor vd = addVertex(g);
+        resize(pm, vd + 1);
+        addEdge(g, knot, vd);
+        _createIntervalTree(g, pm, S_right, vd, center, min2 + (max2 - min2) / 2, length(S_right), tag);
+    }
+}
+
+//////////////////////////////////////////////////////////////////////////////
+//createIntervalTree for all specs except CompCenter, the center value of each
+//node is determined by functions _calcIntervalTreeNodeCenterLeft and
+//_calcIntervalTreeNodeCenterRight
+template <typename TGraph, typename TPropertyMap, typename TSpec, typename TInterval, typename TValue>
+inline void
+_createIntervalTree(TGraph & g, TPropertyMap & pm,
+                    String<TInterval *> & intervals,
+                    typename VertexDescriptor<TGraph>::Type & knot,
+                    TValue last_center, TValue center,
+                    typename VertexDescriptor<TGraph>::Type len,
+                    Tag<TSpec> const tag)
+{
+    SEQAN_CHECKPOINT
+    // Rekursionsanker
+    if (len == 1)
+    {
+        _setIntervalTreeNode(value(pm, knot), center, *value(intervals, 0));
+        return;
+    }
+
+    typedef typename Value<TPropertyMap>::Type TNode;
+    typedef typename ListType<TNode>::Type TList;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef String<TInterval *> TIntervalPointers;
+
+    // one list of interval pointers for the intervals to the left of center
+    TIntervalPointers S_left;
+    // one list of interval pointers for the intervals to the right of center
+    TIntervalPointers S_right;
+
+    value(pm, knot).center = center;
+
+    typedef typename Iterator<TIntervalPointers, Standard>::Type TIntervalIterator;
+    TIntervalIterator it = begin(intervals, Standard());
+    TIntervalIterator it_end = end(intervals, Standard());
+
+    // walk through intervals
+    while (it != it_end)
+    {
+        // interval belongs to the left list
+        if ((**it).i2 <= center)
+        {
+            appendValue(S_left, *it, Generous());
+        }
+        else
+        {   // interval belongs to the right list
+            if ((**it).i1 > center)
+                appendValue(S_right, (*it), Generous());
+            else
+                // interval belongs to the current node
+                _appendIntervalTreeNodeLists(value(pm, knot), **it);
+        }
+        ++it;
+    }
+
+//    std::sort(begin(value(pm,knot).list1),end(value(pm,knot).list1),_less_compI1_ITree<typename Value<TList>::Type>);
+    std::sort(begin(value(pm, knot).list2), end(value(pm, knot).list2), _greater_compI2_ITree<typename Value<TList>::Type>);
+
+    // build subtree to the left
+    if (!empty(S_left))
+    {
+        TVertexDescriptor vd = addVertex(g);
+        resizeVertexMap(pm, g);
+        addEdge(g, knot, vd);
+        TValue next_center = _calcIntervalTreeNodeCenterLeft(S_left, last_center, center, tag);
+        _createIntervalTree(g, pm, S_left, vd, center, next_center, length(S_left), tag);
+    }
+    // build subtree to the right
+    if (!empty(S_right))
+    {
+        TVertexDescriptor vd = addVertex(g);
+        resizeVertexMap(pm, g);
+        addEdge(g, knot, vd);
+        TValue next_center = _calcIntervalTreeNodeCenterRight(S_right, last_center, center, tag);
+        _createIntervalTree(g, pm, S_right, vd, center, next_center, length(S_right), tag);
+    }
+}
+
+// fill the container interval_pointers with pointers to the corresponding objects in intervals.
+// this is done to avoid copying and passing the whole IntervalAndCargo objects during interval tree construction
+template <typename TIntervals, typename TIntervalPointers>
+void
+_makePointerInterval(TIntervals & intervals, TIntervalPointers & interval_pointers)
+{
+    typedef typename Iterator<TIntervals, Standard>::Type TIntervalIterator;
+    typedef typename Iterator<TIntervalPointers, Standard>::Type TIntervalPointerIterator;
+
+    resize(interval_pointers, length(intervals));
+    if (empty(intervals))
+        return;
+
+    TIntervalIterator it = begin(intervals, Standard());
+    TIntervalIterator itEnd = end(intervals, Standard());
+    TIntervalPointerIterator iit = begin(interval_pointers, Standard());
+
+    for (; it != itEnd; ++it, ++iit)
+        *iit = it;
+}
+
+// if the center of the root is not given, it is placed in the "ComputeCenter way": in the middle of minValue and maxValue
+// where minValue is the minimum left boundary and maxValue is the maximum right boundary of all intervals
+template <typename TIntervals>
+typename Value<typename Value<TIntervals>::Type>::Type
+_calcIntervalTreeRootCenter(TIntervals & intervals)
+{
+    SEQAN_CHECKPOINT;
+
+    SEQAN_ASSERT_GT(length(intervals), 0u);
+
+    typedef typename Value<typename Value<TIntervals>::Type>::Type TValue;
+    typedef typename Iterator<TIntervals, Standard>::Type TIntervalIterator;
+
+    TIntervalIterator it = begin(intervals);
+    TIntervalIterator it_end = end(intervals);
+
+    TValue min = maxValue<TValue>();
+    TValue max = minValue<TValue>();
+
+    // get min and max
+    while (it != it_end)
+    {
+        if (leftBoundary(*it) < min)
+            min = leftBoundary(*it);
+        if (rightBoundary(*it) > max)
+            max = rightBoundary(*it);
+        SEQAN_ASSERT_LEQ(min, max);
+        ++it;
+    }
+
+    SEQAN_ASSERT_LEQ(min, max);
+
+    // return middle between max and min
+    return min + (max - min) / (TValue)2.0;
+
+}
+
+/*!
+ * @fn IntervalTree#addInterval
+ *
+ * @headerfile <seqan/misc/interval_tree.h>
+ *
+ * @brief Adds an interval to an interval tree.
+ *
+ * @signature void addInterval(intervalTree, interval);
+ * @signature void addInterval(intervalTree, begin, end[, cargo]);
+ * @signature void addInterval(graph, propertyMap, interval);
+ *
+ * @param[in,out] intervalTree The interval tree to add the interval to. Types: @link IntervalTree @endlink.
+ * @param[in]     interval     The interval to be added to the interval tree.
+ * @param[in]     begin        Begin position of interval of type TValue.
+ * @param[in]     end          End position of interval of type TValue.
+ * @param[in]     cargo        Cargo to attach to the interval. Types: @link IntervalAndCargo @endlink.
+ * @param[in,out] graph        The directed graph that contains the topography of the interval tree.
+ * @param[in,out] propertyMap  The property map containing the node properties of the interval tree.
+ */
+
+
+template <typename TGraph, typename TPropertyMap, typename TInterval>
+void
+addInterval(TGraph & g, TPropertyMap & pm, TInterval interval)
+{
+    SEQAN_CHECKPOINT
+
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Value<TPropertyMap>::Type TProperty;
+    typedef typename Value<TInterval>::Type TValue;
+    typedef typename ListType<TProperty>::Type TList;
+
+
+    if (empty(pm))
+    {
+        TVertexDescriptor vd = addVertex(g);
+        resizeVertexMap(pm, g);
+        _setIntervalTreeNode(property(pm, vd), (rightBoundary(interval) + leftBoundary(interval)) / 2, interval);
+        return;
+
+    }
+    // start at root
+    TVertexDescriptor act_knot = 0;
+    TProperty act_prop = property(pm, act_knot);
+    TProperty next_prop;
+
+    // look for the right node to add interval to
+    while (true)
+    {
+        TOutEdgeIterator it(g, act_knot);
+        act_prop = property(pm, act_knot);
+        if (act_prop.center < leftBoundary(interval)) // interval to the left of current node?
+        {
+            if (atEnd(it))
+            {
+                TVertexDescriptor vd = addVertex(g);
+                resizeVertexMap(pm, g);
+                addEdge(g, act_knot, vd);
+                _setIntervalTreeNode(property(pm, vd), (rightBoundary(interval) + leftBoundary(interval)) / (TValue)2.0, interval);
+                break;
+            }
+            else
+            {
+                next_prop = property(pm, targetVertex(it));
+                if (next_prop.center <= act_prop.center)
+                {
+                    goNext(it);
+                    if (atEnd(it))
+                    {
+                        TVertexDescriptor vd = addVertex(g);
+                        resizeVertexMap(pm, g);
+                        addEdge(g, act_knot, vd);
+                        _setIntervalTreeNode(property(pm, vd), (rightBoundary(interval) + leftBoundary(interval)) / (TValue)2.0, interval);
+                        break;
+                    }
+                }
+            }
+            act_knot = targetVertex(it);
+        }
+        else
+        {
+            if (rightBoundary(interval) <= act_prop.center) // interval to the right of current node?
+            {
+                if (atEnd(it))
+                {
+                    TVertexDescriptor vd = addVertex(g);
+                    resizeVertexMap(pm, g);
+                    addEdge(g, act_knot, vd);
+                    _setIntervalTreeNode(property(pm, vd), (rightBoundary(interval) + leftBoundary(interval)) / 2, interval);
+                    break;
+                }
+                else
+                {
+                    next_prop = property(pm, targetVertex(it));
+                    if (next_prop.center >= act_prop.center)
+                    {
+                        goNext(it);
+                        if (atEnd(it))
+                        {
+                            TVertexDescriptor vd = addVertex(g);
+                            resizeVertexMap(pm, g);
+                            addEdge(g, act_knot, vd);
+                            _setIntervalTreeNode(property(pm, vd), (rightBoundary(interval) + leftBoundary(interval)) / 2, interval);
+                            break;
+                        }
+                    }
+                }
+                act_knot = targetVertex(it);
+            }
+            else  // need to create new node for interval
+            {
+                _appendIntervalTreeNodeLists(property(pm, act_knot), interval);
+                std::sort(begin(property(pm, act_knot).list1), end(property(pm, act_knot).list1), _less_compI1_ITree<typename Value<TList>::Type>);
+                std::sort(begin(property(pm, act_knot).list2), end(property(pm, act_knot).list2), _greater_compI2_ITree<typename Value<TList>::Type>);
+                break;
+            }
+        }
+    }
+
+}
+
+template <typename TValue, typename TCargo, typename TInterval>
+void
+addInterval(IntervalTree<TValue, TCargo> & itree, TInterval interval)
+{
+    SEQAN_CHECKPOINT
+
+    ++ itree.interval_counter;
+    addInterval(itree.g, itree.pm, interval);
+
+}
+
+template <typename TValue, typename TCargo>
+void
+addInterval(IntervalTree<TValue, TCargo> & itree, TValue begin, TValue end, TCargo cargo)
+{
+    SEQAN_CHECKPOINT
+
+    IntervalAndCargo<TValue, TCargo> interval;
+    interval.i1 = begin;
+    interval.i2 = end;
+    interval.cargo = cargo;
+    ++itree.interval_counter;
+    addInterval(itree.g, itree.pm, interval);
+
+}
+
+template <typename TValue, typename TCargo>
+void
+addInterval(IntervalTree<TValue, TCargo> & itree, TValue begin, TValue end)
+{
+    SEQAN_CHECKPOINT
+
+    IntervalAndCargo<TValue, TCargo> interval;
+    interval.i1 = begin;
+    interval.i2 = end;
+    interval.cargo = itree.interval_counter;
+    ++itree.interval_counter;
+    addInterval(itree.g, itree.pm, interval);
+
+}
+
+/*!
+ * @fn IntervalTree#findIntervals
+ * @brief Find all intervals that contain the query point or overlap with the query interval.
+ *
+ * @signature void findIntervals(result, intervalTree, query);
+ * @signature void findIntervals(result, intervalTree, queryBegin, queryEnd);
+ * @signature void findIntervals(result, graph, propertyMap, query);
+ *
+ * @param[out] result       A reference to the result string of <tt>TCargo</tt> objects. Types: @link String @endlink.
+ * @param[in]  intervalTree An IntervalTree.
+ * @param[in]  graph        The directed @link Graph graph @endlink that contains the topography of the interval tree.
+ * @param[in]  propertyMap  The property map containing the node properties of the interval tree.
+ * @param[in]  query        A query point.
+ * @param[in]  queryBegin   The begin position of the query interval.
+ * @param[in]  queryEnd     The end position of the query interval.
+ */
+
+template <typename TSpec, typename TPropertyMap, typename TValue, typename TCargo>
+inline void
+findIntervals(
+        String<TCargo> & result,
+        Graph<TSpec> const & g,
+        TPropertyMap const & pm,
+        TValue query)
+{
+    typedef Graph<TSpec> const TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Value<TPropertyMap>::Type TProperty;
+    typedef typename Value<TProperty>::Type TPropertyValue;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    resize(result, 0);
+    if (empty(g))
+        return;
+
+    // start at root
+    TVertexDescriptor act_knot = 0;
+    TProperty act_prop = property(pm, act_knot);
+    TProperty next_prop;
+
+    while (true)
+    {
+        typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type it7;
+        Iter<Graph<TSpec>, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > it5(g, act_knot);
+        TOutEdgeIterator it4;
+        TOutEdgeIterator it(g, act_knot);
+        act_prop = property(pm, act_knot);
+        if (act_prop.center < (TPropertyValue)query) // look in current node and right subtree
+        {
+            unsigned int i = 0;
+            while (i<length(act_prop.list2) && rightBoundary(value(act_prop.list2, i))>(TPropertyValue) query)
+            {
+                appendValue(result, cargo(value(act_prop.list2, i)), Generous());
+                ++i;
+            }
+            if (atEnd(it))
+                break;
+
+            next_prop = property(pm, targetVertex(it));
+            if (next_prop.center <= act_prop.center)
+            {
+                goNext(it);
+                if (atEnd(it))
+                    break;
+            }
+            act_knot = targetVertex(it);
+        }
+        else
+        {
+            if ((TPropertyValue)query < act_prop.center) // look in current node and left subtree
+            {
+                unsigned int i = 0;
+                while (i < length(act_prop.list1) && leftBoundary(value(act_prop.list1, i)) <= (TPropertyValue)query)
+                {
+                    appendValue(result, cargo(value(act_prop.list1, i)), Generous());
+                    ++i;
+                }
+                if (atEnd(it))
+                    break;
+
+                next_prop = property(pm, targetVertex(it));
+                if (next_prop.center >= act_prop.center)
+                {
+                    goNext(it);
+                    if (atEnd(it))
+                        break;
+                }
+                act_knot = targetVertex(it);
+            }
+            else  // look in current node only, as query is center
+            {
+                for (unsigned int i = 0; i < length(act_prop.list1); ++i)
+                    appendValue(result, cargo(value(act_prop.list1, i)), Generous());
+                break;
+            }
+        }
+    }
+
+}
+
+template <typename TValue, typename TCargo, typename TValue2>
+inline void
+findIntervals(
+        String<TCargo> & result,
+        IntervalTree<TValue, TCargo> const & it,
+        TValue2 query)
+{
+    findIntervals(result, it.g, it.pm, query);
+}
+
+template <typename TValue, typename TCargo, typename TValue2>
+inline void
+findIntervals(
+        String<TCargo> & result,
+        IntervalTree<TValue, TCargo> const & tree,
+        TValue2 query_begin,
+        TValue2 query_end)
+{
+    findIntervals(result, tree.g, tree.pm, query_begin, query_end);
+}
+
+template <typename TSpec, typename TPropertyMap, typename TValue, typename TCargo>
+inline void
+findIntervals(
+        String<TCargo> & result,
+        Graph<TSpec> const & g,
+        TPropertyMap const & pm,
+        TValue query_begin,
+        TValue query_end)
+{
+    typedef Graph<TSpec> const TGraph;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+
+    resize(result, 0);
+
+    // start at root
+    TVertexDescriptor act_knot = 0;
+    findIntervals(result, g, pm, act_knot, query_begin, query_end);
+}
+
+template <
+    typename TSpec,
+    typename TPropertyMap,
+    typename TVertexDescriptor,
+    typename TValue,
+    typename TCargo>
+inline void
+findIntervals(
+        String<TCargo> & result,
+        Graph<TSpec> const & g,
+        TPropertyMap const & pm,
+        TVertexDescriptor & act_knot,
+        TValue query_begin,
+        TValue query_end)
+{
+    typedef typename Value<TPropertyMap>::Type TProperty;
+    typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    if (empty(g))
+        return;
+
+    TProperty act_prop = property(pm, act_knot);
+    TProperty next_prop;
+
+    while (true)
+    {
+        TOutEdgeIterator it(g, act_knot);
+        act_prop = property(pm, act_knot);
+        //
+        if (act_prop.center < query_begin) // query interval is to the right of node center
+        {
+            unsigned int i = 0;
+            while (i<length(act_prop.list2) && rightBoundary(value(act_prop.list2, i))> query_begin)
+            {
+                appendValue(result, cargo(value(act_prop.list2, i)), Generous());
+                ++i;
+            }
+            if (atEnd(it))
+                break;
+
+            next_prop = property(pm, targetVertex(it));
+            if (next_prop.center <= act_prop.center)
+            {
+                goNext(it);
+                if (atEnd(it))
+                    break;
+            }
+            act_knot = targetVertex(it);
+        }
+        else
+        {
+            if (query_end <= act_prop.center) // query interval is to the left of node center
+            {
+                unsigned int i = 0;
+                while (i < length(act_prop.list1) && leftBoundary(value(act_prop.list1, i)) < query_end)
+                {
+                    appendValue(result, cargo(value(act_prop.list1, i)), Generous());
+                    ++i;
+                }
+
+                if (atEnd(it))
+                    break;
+
+                next_prop = property(pm, targetVertex(it));
+                if (next_prop.center >= act_prop.center)
+                {
+                    goNext(it);
+                    if (atEnd(it))
+                        break;
+                }
+                act_knot = targetVertex(it);
+            }
+            else
+            { //node center is contained in query interval
+                for (unsigned int i = 0; i < length(act_prop.list1); ++i)
+                    appendValue(result, cargo(value(act_prop.list1, i)), Generous());
+
+                while (!atEnd(it))
+                {
+                    TVertexDescriptor next_knot = targetVertex(it);
+                    findIntervals(result, g, pm, next_knot, query_begin, query_end);
+                    goNext(it);
+                }
+                break;
+
+                //break; //dont break! continue in both subtrees!!
+            }
+        }
+    }
+}
+
+/*!
+ * @fn IntervalTree#findIntervalsExcludeTouching
+ * @brief Find all intervals that contain the query point, exclude intervals that touch the query, i.e. where the query
+ *        point equals the start or end point.
+ *
+ * @signature void findIntervalsExcludeTouching(result, intervalTree, query);
+ * @signature void findIntervalsExcludeTouching(result, graph, propertyMap, query,);
+ *
+ * @param[out] result      The resulting string of cargos/ids of the intervals that contain the query point.  Should
+ *                         be a string of TCargo. Types: String
+ * @param[in] intervalTree An interval tree Types: IntervalTree
+ * @param[in] graph        The directed graph that contains the topography of the interval tree.
+ * @param[in] query        The TValue to query here.
+ * @param[in] propertyMap  The property map containing the node properties of the interval tree
+ */
+
+template <typename TSpec, typename TPropertyMap, typename TValue, typename TCargo>
+inline void
+findIntervalsExcludeTouching(
+        String<TCargo> & result,
+        Graph<TSpec> const & g,
+        TPropertyMap const & pm,
+        TValue query)
+{
+    typedef Graph<TSpec> const TGraph;
+    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+    typedef typename Value<TPropertyMap>::Type TProperty;
+
+    resize(result, 0);
+    if (empty(g))
+        return;
+
+    // start at root
+    TVertexDescriptor act_knot = 0;
+    TProperty act_prop = property(pm, act_knot);
+    TProperty next_prop;
+
+    while (true)
+    {
+        TOutEdgeIterator it(g, act_knot);
+        act_prop = property(pm, act_knot);
+        if ((TValue) act_prop.center < query) // look in current node and right subtree
+        {
+            int i = 0;
+            while (i < (int)length(act_prop.list2) && (TValue)rightBoundary(value(act_prop.list2, i)) > query)
+            {
+                appendValue(result, cargo(value(act_prop.list2, i)), Generous());
+                ++i;
+            }
+            if (atEnd(it))
+                break;
+
+            next_prop = property(pm, targetVertex(it));
+            if (next_prop.center <= act_prop.center)
+            {
+                goNext(it);
+                if (atEnd(it))
+                    break;
+            }
+            act_knot = targetVertex(it);
+        }
+        else
+        {
+            if (query < (TValue) act_prop.center) // look in current node and left subtree
+            {
+                int i = 0;
+                while (i < (int)length(act_prop.list1) && (TValue)leftBoundary(value(act_prop.list1, i)) < query)
+                {
+                    appendValue(result, cargo(value(act_prop.list1, i)), Generous());
+                    ++i;
+                }
+                if (atEnd(it))
+                    break;
+
+                next_prop = property(pm, targetVertex(it));
+                if (next_prop.center >= act_prop.center)
+                {
+                    goNext(it);
+                    if (atEnd(it))
+                        break;
+                }
+                act_knot = targetVertex(it);
+            }
+            else  // look in current node only
+            {
+                int i = 0;
+                while (i < (int)length(act_prop.list1) && (TValue)leftBoundary(value(act_prop.list1, i)) < query)
+                {
+                    appendValue(result, cargo(value(act_prop.list1, i)), Generous());
+                    ++i;
+                }
+                break;
+            }
+        }
+    }
+
+}
+
+template <typename TValue, typename TCargo>
+inline void
+findIntervalsExcludeTouching(
+        String<TCargo> & result,
+        IntervalTree<TValue, TCargo> const & tree,
+        TValue query)
+{
+    findIntervalsExcludeTouching(result, tree.g, tree.pm, query);
+}
+
+/*!
+ * @fn IntervalTree#removeInterval
+ * @brief Removes an interval from the interval tree.
+ *
+ * @signature bool removeInterval(intervalTree, iBegin, iEnd, iId);
+ *
+ * @param[in,out] intervalTree An interval tree Types: IntervalTree
+ * @param[in]     iBegin       The begin position of the interval to be removed.
+ * @param[in]     iEnd         The end position of the interval to be removed.
+ * @param[in]     iId          The ID of the interval to be removed.
+ *
+ * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
+ */
+
+template <
+    typename TSpec,
+    typename TPropertyMap,
+    typename TVertexDescriptor,
+    typename TValue,
+    typename TCargo>
+inline bool
+removeInterval(
+    Graph<TSpec> & g,
+    TPropertyMap & pm,
+    TVertexDescriptor & act_knot,
+    TValue i_begin,
+    TValue i_end,
+    TCargo i_id)
+{
+    SEQAN_CHECKPOINT
+
+    typedef typename Value<TPropertyMap>::Type TProperty;
+    typedef typename ListType<TProperty>::Type TList;
+    typedef typename Iterator<TList, Standard>::Type TListIterator;
+    typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
+
+    if (empty(g))
+        return false;
+
+    TProperty act_prop = property(pm, act_knot);
+    TProperty next_prop;
+
+    while (true)
+    {
+        TOutEdgeIterator it(g, act_knot);
+        act_prop = property(pm, act_knot);
+        //
+        if (act_prop.center < i_begin) // interval is to the right of node center
+        {
+            if (atEnd(it))
+                break;
+
+            next_prop = property(pm, targetVertex(it));
+            if (next_prop.center <= act_prop.center)
+            {
+                goNext(it);
+                if (atEnd(it))
+                    break;
+            }
+            act_knot = targetVertex(it);
+        }
+        else
+        {
+            if (i_end < act_prop.center) // interval is to the left of node center
+            {
+                if (atEnd(it))
+                    break;
+
+                next_prop = property(pm, targetVertex(it));
+                if (next_prop.center >= act_prop.center)
+                {
+                    goNext(it);
+                    if (atEnd(it))
+                        break;
+                }
+                act_knot = targetVertex(it);
+            }
+            else //node center is contained in interval, this is where we should find the interval to be removed
+            {   // remove from list1
+                TProperty & change_prop = property(pm, act_knot);
+                bool foundInLeft = false;
+                TListIterator list_it_keep = begin(change_prop.list1, Standard());
+                TListIterator list_it = begin(change_prop.list1, Standard());
+                while (list_it != end(change_prop.list1, Standard()))
+                {
+                    //std::cout << "Element: " << getLeftBoundary(*list_it) << ".." << getRightBoundary(*list_it) << " " << cargo(*list_it) << std::endl;
+                    if (getLeftBoundary(*list_it) == i_begin && cargo(*list_it) == i_id)
+                    {
+                        foundInLeft = true;
+                        ++list_it;
+                        continue;
+                    }
+                    *list_it_keep = *list_it;
+                    //std::cout << "Element keep: " << getLeftBoundary(*list_it_keep) << ".." << getRightBoundary(*list_it_keep) << " " << cargo(*list_it_keep) << std::endl;
+                    ++list_it; ++list_it_keep;
+                }
+
+                bool foundInRight = false;
+                list_it_keep = begin(change_prop.list2, Standard());
+                list_it = begin(change_prop.list2, Standard());
+                while (list_it != end(change_prop.list2, Standard()))
+                {
+                    //std::cout << "Element: " << getLeftBoundary(*list_it) << ".." << getRightBoundary(*list_it) << " " << cargo(*list_it) << std::endl;
+                    if (getRightBoundary(*list_it) == i_end && cargo(*list_it) == i_id)
+                    {
+                        foundInRight = true;
+                        ++list_it;
+                        continue;
+                    }
+                    *list_it_keep = *list_it;
+                    //std::cout << "Element keep: " << getLeftBoundary(*list_it_keep) << ".." << getRightBoundary(*list_it_keep) << " " << cargo(*list_it_keep) << std::endl;
+                    ++list_it; ++list_it_keep;
+
+                }
+
+
+                // TODO: if node is empty and does not have child nodes --> remove node.
+                // keeping these empty leaf nodes just takes space unnecessarily
+                if (foundInRight && foundInLeft)
+                {
+                    resize(change_prop.list2, length(change_prop.list2) - 1);
+                    resize(change_prop.list1, length(change_prop.list1) - 1);
+                    return true;
+                }
+
+            }
+        }
+    }
+    return false;
+}
+
+template <
+    typename TSpec,
+    typename TPropertyMap,
+    typename TValue,
+    typename TCargo>
+inline bool
+removeInterval(
+    Graph<TSpec> & g,
+    TPropertyMap & pm,
+    TValue i_begin,
+    TValue i_end,
+    TCargo i_id)
+{
+    typedef typename VertexDescriptor<Graph<TSpec> >::Type TVertexDescriptor;
+
+    // start looking at root
+    TVertexDescriptor act_knot = 0;
+    return removeInterval(g, pm, act_knot, i_begin, i_end, i_id);
+}
+
+template <typename TValue, typename TCargo>
+inline bool
+removeInterval(
+    IntervalTree<TValue, TCargo> & tree,
+    TValue i_begin,
+    TValue i_end,
+    TCargo i_id)
+{
+    return removeInterval(tree.g, tree.pm, i_begin, i_end, i_id);
+    // we do not decrease the interval_counter of tree, as it would mix up interval IDs
+}
+
+/////////////////// Metafunctions ///////////////////////
+
+template <typename TValue, typename TCargo>
+struct Value<IntervalTree<TValue, TCargo> >
+{
+    typedef TValue Type;
+};
+
+
+template <typename TValue, typename TCargo>
+struct Cargo<IntervalTree<TValue, TCargo> >
+{
+    typedef TCargo Type;
+};
+
+}  // namespace SEQAN_NAMESPACE_MAIN
+
+#endif  //#ifndef SEQAN_MISC_INTERVAL_TREE_H
diff --git a/seqan/misc/map.h b/seqan/misc/map.h
new file mode 100644
index 0000000..43d7f60
--- /dev/null
+++ b/seqan/misc/map.h
@@ -0,0 +1,88 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
+// ==========================================================================
+// Note that this file originally did not compile.  Me (holtgrew) change it
+// it it compiled.  However, it might not make sense to fix it so it actually
+// works.
+// ==========================================================================
+
+//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
+
+#ifndef SEQAN_HEADER_MISC_MAP_H
+#define SEQAN_HEADER_MISC_MAP_H
+
+#include <algorithm>
+#include "base.h"
+
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+    //////////////////////////////////////////////////////////////////////////////
+    //
+
+    template <typename TPair>
+    inline typename TPair::T1 & keyOf(TPair &pair) {
+        return getValueI1(pair);
+    }
+    template <typename TPair>
+    inline typename TPair::T1 const & keyOf(TPair const &pair) {
+        return getValueI1(pair);
+    }
+    template <typename TPair>
+    inline typename TPair::T2 & objectOf(TPair &pair) {
+        return getValueI2(pair);
+    }
+    template <typename TPair>
+    inline typename TPair::T2 const & objectOf(TPair const &pair) {
+        return getValueI2(pair);
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    //
+
+//    template <typename TKey>
+//    struct Map {
+//        typedef std::map<TKey> Type;
+//    };
+    template <typename TKey, typename TObject>
+    class Map< Pair<TKey, TObject> > {
+//        typedef std::set< Pair<TKey, TObject>, SetLess< Pair<TKey, TObject> > > Type;
+    };
+
+}
+
+#endif
+
diff --git a/seqan/misc/misc_memset.h b/seqan/misc/memset.h
similarity index 87%
rename from seqan/misc/misc_memset.h
rename to seqan/misc/memset.h
index 4cb8927..784405c 100644
--- a/seqan/misc/misc_memset.h
+++ b/seqan/misc/memset.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                               misc_memset.h
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_MISC_MISC_MEMSET_H_
-#define CORE_INCLUDE_SEQAN_MISC_MISC_MEMSET_H_
+#ifndef INCLUDE_SEQAN_MISC_MEMSET_H_
+#define INCLUDE_SEQAN_MISC_MEMSET_H_
 
 #include <seqan/basic/basic_metaprogramming.h>
 
@@ -61,7 +61,7 @@ namespace seqan {
 
 /*!
  * @fn memset
- * @headerfile <seqa/misc/misc_memset.h>
+ * @headerfile <seqa/misc/memset.h>
  * @brief An implementation of <tt>memset</tt> with fixed number of bytes using Metaprogramming.
  *
  * @signature template <unsigned SIZE>
@@ -73,25 +73,9 @@ namespace seqan {
  * @param[in]     c   The value to set to.
  */
 
-/**
-.Function.memset
-..cat:Memory
-..summary:An implementation of $memset$ with fixed number of bytes using Metaprogramming.
-..signature:memset<SIZE>(ptr, c)
-..signature:memset<SIZE, c>(ptr)
-..param.SIZE:The number of bytes to set.
-...type:nolink:$unsigned$
-..param.ptr:Pointer to the data to set.
-...type:nolink:$unsigned char *$
-..param.c:The character to fill the memory with.
-....type:nolink:$unsigned char$
-..remarks:These functions can be completely unrolled and inlined by the compiler.
-..include:seqan/misc/misc_memset.h
- */
-
 // TODO(holtgrew): Does memset() really belong in this header? Used in find_myers_ukknonen.h, pump_lcp_core.h, pipe_sample.h, file_async
 
-using ::std::memset;
+using std::memset;
 
 // Implementation of memset() with fill size.
 
@@ -101,7 +85,7 @@ struct MemsetWorker
     finline static
     void run(unsigned char * ptr, unsigned char c)
     {
-        ::std::memset(ptr, c, SIZE);
+        std::memset(ptr, c, SIZE);
     }
 };
 
@@ -165,7 +149,7 @@ finline void memset(void* ptr, unsigned char c)
 template <unsigned SIZE, bool direct, unsigned char c>
 struct MemsetConstValueWorker
 {
-    finline static void run(unsigned char* ptr) { ::std::memset(ptr, c, SIZE); }
+    finline static void run(unsigned char* ptr) { std::memset(ptr, c, SIZE); }
 };
 
 template <unsigned  SIZE, unsigned char c>
@@ -225,4 +209,4 @@ memset(void* ptr)
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_MISC_MISC_MEMSET_H_
+#endif  // #ifndef INCLUDE_SEQAN_MISC_MEMSET_H_
diff --git a/seqan/misc/misc_bit_twiddling.h b/seqan/misc/misc_bit_twiddling.h
deleted file mode 100644
index eadbeeb..0000000
--- a/seqan/misc/misc_bit_twiddling.h
+++ /dev/null
@@ -1,498 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// Copyright (c) 2013 NVIDIA Corporation
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Various useful bit-twiddling routines, mostly taken from the website
-// http://www-graphics.stanford.edu/~seander/bithacks.html
-// ==========================================================================
-
-#ifndef SEQAN_MISC_MISC_BIT_TWIDDLING_H_
-#define SEQAN_MISC_MISC_BIT_TWIDDLING_H_
-
-#ifdef PLATFORM_WINDOWS_VS
-// Make intrinsics visible.  It appears that this is not necessary with VS 10
-// any more, for VS 9, it must be included.
-#include <intrin.h>
-#endif  // #ifdef PLATFORM_WINDOWS_VS
-
-// TODO(holtgrew): Test this!
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Classes, Structs, Enums, Tags
-// ============================================================================
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function setBitTo()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn setBitTo
- * @headerfile <seqan/misc/misc_bit_twiddling.h>
- * @brief Set the bit with the given index to the given value.
- *
- * @signature void setBitTo(word, index, value);
- *
- * @param[in,out] word  The machine word (number) to set bits of.
- * @param[in]     index The index of the bit in the word to set, integer.
- * @param[in]     value The value to set to, <tt>bool</tt>.
- */
-
-/**
-.Function.setBitTo
-..cat:Bit Twiddling
-..summary:Set the bit with the given index to the given value.
-..signature:setBitTo(word, index, value)
-..param.word:The number.
-..param.index:The index of the bit in the word.
-...type:nolink:$unsigned$
-..param.value:The value to set the bit to.
-...type:nolink:$bool
-..returns:$void$
-..include:seqan/misc/misc_bit_twiddling.h
-..see:Function.setBit
-..see:Function.clearBit
-..see:Function.clearAllBits
-..see:Function.isBitSet
- */
-
-template <typename TWord, typename TPos>
-inline void
-setBitTo(TWord & word, TPos index, bool value)
-{
-    // See http://www-graphics.stanford.edu/~seander/bithacks.html#ConditionalSetOrClearBitsWithoutBranching
-    word = (word & ~(1u << index)) | (-value & (1u << index));
-}
-
-// ----------------------------------------------------------------------------
-// Function setBit()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn setBit
- * @headerfile <seqan/misc/misc_bit_twiddling.h>
- * @brief Set the bit with the given index to 1.
- *
- * @signature void setBit(word, index);
- *
- * @param[in,out] word  The word to set the bit of.
- * @param[in]     index The index of the bit to set.
- */
-
-/**
-.Function.setBit
-..cat:Bit Twiddling
-..summary:Set the bit with the given index to 1.
-..signature:setBit(word, index)
-..param.word:The number.
-..param.index:The index of the bit in the word.
-...type:nolink:$unsigned$
-..returns:$void$
-..include:seqan/misc/misc_bit_twiddling.h
-..see:Function.setBitTo
-..see:Function.clearBit
-..see:Function.clearAllBits
-..see:Function.isBitSet
- */
-
-template <typename TWord, typename TPos>
-inline void
-setBit(TWord & word, TPos index)
-{
-    word |= (1u << index);
-}
-
-// ----------------------------------------------------------------------------
-// Function clearBit()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn clearBit
- * @headerfile <seqan/misc/misc_bit_twiddling.h>
- * @brief Set the bit with the given index to 0.
- *
- * @signature void clearBit(word, index);
- *
- * @param[in,out] word  The machine word to set the bit of.
- * @param[in]     index The index of the bit to set to 0.
- */
-
-/**
-.Function.clearBit
-..cat:Bit Twiddling
-..summary:Set the bit with the given index to 0.
-..signature:clearBit(word, index)
-..param.word:The number.
-..param.index:The index of the bit in the word.
-...type:nolink:$unsigned$
-..returns:$void$
-..include:seqan/misc/misc_bit_twiddling.h
-..see:Function.setBitTo
-..see:Function.setBit
-..see:Function.clearAllBits
-..see:Function.isBitSet
- */
-
-template <typename TWord, typename TPos>
-inline void
-clearBit(TWord & word, TPos index)
-{
-    word &= ~(1u << index);
-}
-
-// ----------------------------------------------------------------------------
-// Function clearAllBits()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn clearAllBits
- * @headerfile <seqan/misc/misc_bit_twiddling.h>
- * @brief Set all bits to 0.
- *
- * @signature void clearAllBits(word);
- *
- * @param[in,out] word The word to clear all bits of.
- */
-
-/**
-.Function.clearAllBits
-..cat:Bit Twiddling
-..summary:Set all bits to 0.
-..signature:clearAllBits(word)
-..param.word:The number.
-..returns:$void$
-..include:seqan/misc/misc_bit_twiddling.h
-..see:Function.setBitTo
-..see:Function.setBit
-..see:Function.clearBit
-..see:Function.isBitSet
- */
-
-template <typename TWord>
-inline void
-clearBits(TWord & word)
-{
-    word = 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function isBitSet()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn isBitSet
- * @headerfile <seqan/misc/misc_bit_twiddling.h>
- * @brief Returns whether the bit with the given index is set to 1.
- *
- * @signature bool isBitSet(word, index);
- *
- * @param[in] word  The word to check.
- * @param[in] index The index of the bit to check.
- */
-
-/**
-.Function.isBitSet
-..cat:Bit Twiddling
-..summary:Returns whether the bit with the given index is set to 1.
-..signature:isBitSet(word, index)
-..param.word:The number.
-..param.index:The index.
-...type:nolink:$unsigned$
-..returns:$true$ if the bit was set and $false$ otherwise.
-...type:nolink:$bool$
-..include:seqan/misc/misc_bit_twiddling.h
-..see:Function.setBitTo
-..see:Function.setBit
-..see:Function.clearBit
-..see:Function.clearAllBits
- */
-
-template <typename TWord, typename TIndex>
-inline bool
-isBitSet(TWord word, TIndex index)
-{
-    typedef typename MakeUnsigned<TWord>::Type TUnsignedWord;
-    return (word & (TUnsignedWord(1) << index)) != static_cast<TWord>(0);
-}
-
-// ----------------------------------------------------------------------------
-// Function hiBits()
-// ----------------------------------------------------------------------------
-
-template <typename TWord, typename TPos>
-SEQAN_HOST_DEVICE inline TWord
-hiBits(TWord word, TPos index)
-{
-    return word & ~((TWord(1) << (BitsPerValue<TWord>::VALUE - index)) - TWord(1));
-}
-
-// ----------------------------------------------------------------------------
-// Function popCount()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn popCount
- * @headerfile <seqan/misc/misc_bit_twiddling.h>
- * @brief Returns number of set bits in an integer.
- *
- * @signature unsigned popCount(words);
- *
- * @param[in] word The word to count the number of set bits of.
- *
- * @return unsigned The number of set bits in <tt>word</tt>.
- */
-
-/**
-.Function.popCount
-..cat:Bit Twiddling
-..summary:Returns number of set bits in an integer.
-..signature:popCount(word)
-..param.word:The number.
-..returns:The number of set bits (1s) in an integer.
-...type:nolink:$unsigned$
-..include:seqan/misc/misc_bit_twiddling.h
- */
-
-// Implementing this platform-independent is tricky.  There are two points to platform independentness. First, the
-// choice of compiler and second the used CPU.  Currently, we do not perform any checks for the CPU and assume that
-// the Intel intrinsic POPCNT is available.  The function is implemented to work on the supported compilers GCC/MINGW,
-// CLANG (which has the same interface as GCC here) and Visual C++.
-//
-// GCC, MINGW and CLANG provide the intrinsics __builtin_popcount, __builtin_popcountl, and __builtin_popcountll for
-// the types unsigned, unsigned long, and unsigned long long.  Starting with version 2008, Visual C++ provides the
-// intrinsics __popcnt16, __popcnt, and __popcnt64 for 16, 32, and 64 bit words.
-//
-// The functions below are implemented as follows.  _popCountImplGeneric() is used if there are no intrinsics provided
-// by the compiler (the case for Visual C++ 2008).  Otherwise, we define different overloads of the function
-// _popCountImpl() that are given the length of the word as a template argument.  If necessary, we copy the word in a
-// variable of next largest size and call the best suited builtin on this copy.
-
-// Generic implementation of counting bits.  Taken from http://graphics.stanford.edu/~seander/bithacks.html
-//
-// Brian Kernighan's method goes through as many iterations as there are set bits. So if we have a 32-bit word with
-// only the high bit set, then it will only go once through the loop.
-//
-// Published in 1988, the C Programming Language 2nd Ed. (by Brian W. Kernighan and Dennis M. Ritchie) mentions this
-// in exercise 2-9. On April 19, 2006 Don Knuth pointed out to me that this method "was first published by Peter
-// Wegner in CACM 3 (1960), 322. (Also discovered independently by Derrick Lehmer and published in 1964 in a book
-// edited by Beckenbach.)"
-
-template <typename TWord>
-inline unsigned
-_popCountImplGeneric(TWord word)  // Note that word is copied!
-{
-    typename MakeUnsigned<TWord>::Type x = word;
-	unsigned int c = 0;  // c accumulates the total bits set in v
-	for (c = 0; x; c++)
-		x &= x - 1;  // clear the least significant bit set
-	return c;
-}
-
-// This parametrized tag is used for selecting a _popCountImpl() implementation.
-
-template <unsigned int NUM_BITS>
-struct WordSize_ {};
-
-// The compiler-dependent implementations of _popCountImpl() follow.
-
-#if defined(__CUDA_ARCH__)
-
-template <typename TWord>
-inline SEQAN_DEVICE
-unsigned _popCountImpl(TWord const & word, WordSize_<32> const & /*tag*/)
-{
-    return __popc(static_cast<__uint32>(word));
-}
-
-template <typename TWord>
-inline SEQAN_DEVICE
-unsigned _popCountImpl(TWord word, WordSize_<16> const & /*tag*/)
-{
-    return __popc(static_cast<__uint32>(word));
-}
-
-template <typename TWord>
-inline SEQAN_DEVICE
-unsigned _popCountImpl(TWord word, WordSize_<8> const & /*tag*/)
-{
-    return __popc(static_cast<__uint32>(word));
-}
-
-#else   // #if defined(__CUDA_ARCH__)
-
-#if defined(_MSC_VER) && (_MSC_VER <= 1400)  // MSVC <= 2005, no intrinsic.
-
-template <typename TWord, unsigned NUM_BITS>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<NUM_BITS> const & /*tag*/)
-{
-    return _popCountImplGeneric(word);
-}
-
-#endif  // #if defined(_MSC_VER) && (_MSC_VER <= 1400)  // MSVC <= 2005, no intrinsic.
-
-#if defined(_MSC_VER) && (_MSC_VER > 1400)  // MSVC >= 2008, has intrinsic
-
-#if defined(_WIN64)
-
-// 64-bit Windows, 64 bit intrinsic available
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<64> const & /*tag*/)
-{
-    return __popcnt64(static_cast<__uint64>(word));
-}
-
-#else  // #if defined(_WIN64)
-
-// 32-bit Windows, 64 bit intrinsic not available
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<64> const & /*tag*/)
-{
-	return __popcnt(static_cast<__uint32>(word)) + __popcnt(static_cast<__uint32>(word >> 32));
-}
-
-#endif  // #if defined(_WIN64)
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<32> const & /*tag*/)
-{
-    return __popcnt(static_cast<__uint32>(word));
-}
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<16> const & /*tag*/)
-{
-    return __popcnt16(static_cast<__uint16>(word));
-}
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<8> const & /*tag*/)
-{
-    return _popCountImpl(static_cast<const __uint16>(word), WordSize_<16>());
-}
-
-#endif  // #if defined(_MSC_VER) && (_MSC_VER <= 1400)
-
-#if !defined(_MSC_VER)  // GCC or CLANG
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<64> const & /*tag*/)
-{
-    return __builtin_popcountll(static_cast<unsigned long long>(word));
-}
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<32> const & /*tag*/)
-{
-    return __builtin_popcount(static_cast<unsigned int>(word));
-}
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<16> const & /*tag*/)
-{
-    return _popCountImpl(static_cast<__uint32>(word), WordSize_<32>());
-}
-
-template <typename TWord>
-inline unsigned
-_popCountImpl(TWord word, WordSize_<8> const & /*tag*/)
-{
-    return _popCountImpl(static_cast<__uint32>(word), WordSize_<32>());
-}
-
-#endif    // GCC or CLANG
-
-#endif    // #if !defined(__CUDA_ARCH__)
-
-template <typename TWord>
-SEQAN_HOST_DEVICE inline unsigned
-popCount(TWord word)
-{
-    return _popCountImpl(word, WordSize_<BitsPerValue<TWord>::VALUE>());
-}
-
-// ----------------------------------------------------------------------------
-// Function printBits()
-// ----------------------------------------------------------------------------
-
-//template <typename TValue>
-//inline void printBits(TValue word)
-//{
-//    unsigned bitsPerValue = BitsPerValue<TValue>::VALUE;
-//    TValue one = 1;
-//    for (TValue i = 0; i < bitsPerValue; ++i)
-//        std::cout << ((word >> i) & one);
-//    std::cout << std::endl;
-//}
-
-//template <typename TValue, typename TSize>
-//inline std::ostream & printBits(std::ostream & stream, TValue word, TSize blockSize)
-//{
-//    unsigned bitsPerValue = BitsPerValue<TValue>::VALUE;
-//    bool temp;
-//    for (int i = bitsPerValue - 1; i >= 0; --i)
-//    {
-//        temp = (word >> i) & 1;
-//        stream << temp;
-//        if ((bitsPerValue - i) % blockSize == 0)
-//            stream << " ";
-//    }
-//    return stream;
-//}
-
-}  // namespace seqan
-
-#endif // #ifndef SEQAN_MISC_MISC_BIT_TWIDDLING_H_
diff --git a/seqan/misc/misc_interval_tree.h b/seqan/misc/misc_interval_tree.h
deleted file mode 100644
index 09fef29..0000000
--- a/seqan/misc/misc_interval_tree.h
+++ /dev/null
@@ -1,2333 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Anne-Katrin Emde <emde@fu-berlin.de>
-// ==========================================================================
-
-
-// TODO(holtgrew): Bring back random center computation using new random module?
-
-// (weese:) This header needs improvement
-//
-// documentation lacks:
-//   - is createIntervalTree clearing the tree first (what happens after a second call of createIntervalTree?)
-//   - where is clear(itree)?
-//   - some flags are missing in the dddoc entries, e.g. ..cat:, class:, or ..type: of arguments
-//
-// interface flaws:
-//   - there are 2 interfaces for createIntervalTree
-//      - based on IntervalTree
-//      - based on Graph and PropertyMap (should be removed)
-//   - addInterval
-
-
-#ifndef SEQAN_HEADER_MISC_INTERVAL_TREE_H
-#define SEQAN_HEADER_MISC_INTERVAL_TREE_H
-
-#include <seqan/graph_types.h>
-
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
-// Graph - Interval Tree Types
-//////////////////////////////////////////////////////////////////////////////
-
-///---------------------------------------------------------------///
-
-//////////////////// Interval and ID type ///////////////////
-
-// TODO(holtgrew): Are these actual the first/last or begin/end entries?
-
-/*!
- * @class IntervalAndCargo
- * @headerfile <seqan/misc/misc_interval_tree.h>
- * @brief A simple record type that stores an interval and a cargo value.
- *
- * @signature template <[typename TValue[, typename TCargo]]>
- *            class IntervalAndCargo;
- *
- * @tparam TValue The value type.  Default: <tt>int</tt>.
- * @tparam TCargo The cargo type.  Default: <tt>int</tt>.
- *
- * @fn IntervalAndCargo::IntervalAndCargo
- * @brief Constructor
- *
- * @signature IntervalAndCargo::IntervalAndCargo();
- * @signature IntervalAndCargo::IntervalAndCargo(i1, i2, cargo);
- *
- * @param[in] i1    The first element in the interval.
- * @param[in] i2    The last element in the interval.
- * @param[in] cargo The cargo to store together with the interval.
- *
- * @var TValue IntervalAndCargo::i1;
- * @brief The first element in the interval.
- *
- * @var TValue IntervalAndCargo::i2;
- * @brief The last element in the interval.
- *
- * @var TCargo IntervalAndCargo::cargo;
- * @brief The stored cargo.
- */
-
-/**
-.Class.IntervalAndCargo:
-..cat:Miscellaneous
-..summary:A simple record type that stores an interval and a cargo value.
-..signature:IntervalAndCargo<TValue, TCargo>
-..param.TValue:The value type, that is the type of the interval borders.
-...default:int.
-...metafunction:Metafunction.Value
-..param.TCargo:The cargo type.
-...default:int.
-...metafunction:Metafunction.Cargo
-..include:seqan/misc/misc_interval_tree.h
-*/
-template<typename TValue = int, typename TCargo = int>
-class IntervalAndCargo
-{
-public:
-    /**
-.Memvar.IntervalAndCargo#i1:
-..class:Class.PointAndCargo
-..summary:The first element in the interval of type i1.
-     */
-	TValue i1;
-
-    /**
-.Memvar.IntervalAndCargo#i2:
-..class:Class.PointAndCargo
-..summary:The last element in the interval of type i2.
-     */
-	TValue i2;
-
-    /**
-.Memvar.IntervalAndCargo#cargo:
-..class:Class.PointAndCargo
-..summary:The stored cargo of type TCargo.
-     */
-	TCargo cargo;
-
-    /**
-.Memfunc.IntervalAndCargo#IntervalAndCargo:
-..signature:IntervalAndCargo()
-     */
-    IntervalAndCargo()
-    {
-SEQAN_CHECKPOINT
-    }
-
-    /**
-.Memfunc.IntervalAndCargo#IntervalAndCargo:
-..class:Class.IntervalAndCargo
-..summary:Constructor.
-..signature:IntervalAndCargo(i1, i2, cargo)
-..param.i1:The first element in the interval, of type TValue.
-..param.i2:The last element in the interval of type TValue.
-..param.cargo:The cargo value of type TCargo.
-     */
-	IntervalAndCargo(TValue i1, TValue i2, TCargo cargo):
-		i1(i1), i2(i2), cargo(cargo)
-	{
-SEQAN_CHECKPOINT
-	}
-};
-
-
-
-/////////////////////// Point and ID type ////////////////
-
-/*!
- * @class PointAndCargo
- * @headerfile <seqan/misc/misc_interval_tree.h>
- * @brief Simple record class storing a point (one-value) interval and cargo.
- *
- * @signature template <[typename TValue[, typename TCargo]]>
- *            class PointAndCargo;
- *
- * @tparam TValue The value type.
- * @tparam TCargo The cargo type.
- *
- * @fn PointAndCargo::PointAndCargo
- * @brief Constructor
- *
- * @signature PointAndCargo::PointAndCargo();
- * @signature PointAndCargo::PointAndCargo(point, cargo);
- *
- * @param[in] point The point to store.
- * @param[in] cargo The cargo to store.
- *
- * @var TValue PointAndCargo::point
- * @brief The point to store.
- *
- * @var TCargo PointAndCargo::cargo
- * @brief The cargo to store.
- */
-
-/**
-.Class.PointAndCargo:
-..cat:Miscellaneous
-..summary:Simple record class storing a point (one-value interval) and a cargo.
-..signature:PointAndCargo<TValue, TCargo>
-..param.TValue:
-...default:int.
-...metafunction:Metafunction.Value
-..param.TCargo:
-...default:int.
-...metafunction:Metafunction.Value
-..include:seqan/misc/misc_interval_tree.h
-*/
-template<typename TValue=int, typename TCargo=int>
-class PointAndCargo {
-public:
-    /**
-.Memvar.PointAndCargo#point:
-..class:Class.PointAndCargo
-..summary:The stored point of type TValue.
-     */
-	TValue point;
-
-    /**
-.Memvar.PointAndCargo#cargo:
-..class:Class.PointAndCargo
-..summary:The stored cargo of type TCargo.
-     */
-	TCargo cargo;
-
-    /**
-.Memfunc.PointAndCargo#PointAndCargo
-..class:Class.PointAndCargo
-..signature:PointAndCargo(point, cargo)
-    */
-	PointAndCargo() {
-SEQAN_CHECKPOINT
-	}
-
-    /**
-.Memfunc.PointAndCargo#PointAndCargo
-..class:Class.PointAndCargo
-..summary:Constructor.
-..signature:PointAndCargo(point, cargo)
-..param.point:
-...summary:The point to store of type TValue.
-..param.cargo:
-...summary:The cargo to store of type TCargo.
-    */
-	PointAndCargo(TValue point, TCargo cargo):
-		point(point), cargo(cargo)
-	{
-SEQAN_CHECKPOINT
-	}
-};
-
-///////////////////////////////////////////////////////////////////////////
-/////////////////////////// IntervalTreeNode	///////////////////////////
-
-/*!
- * @defgroup IntervalTreeNodeTypeTags IntervalTree Node Types Tags
- * @brief Tags to select the node type for @link IntervalTree @endlink.
- *
- * @tag IntervalTreeNodeTypeTags#StorePointsOnly
- * @headerfile <seqan/misc/misc_interval_tree.h>
- * @brief The tree nodes store points.
- *
- * @tag IntervalTreeNodeTypeTags#StoreIntervals
- * @headerfile <seqan/misc/misc_interval_tree.h>
- * @brief The tree nodes store intervals.
- */
-
-/**
-.Tag.IntervalTree Node Types
-..summary:Tags to select the node type for @Class.IntervalTree@.
-..cat:Miscellaneous
-..see:Class.IntervalTree
-
-..tag.StorePointsOnly:The tree nodes store points.
-..include:seqan/misc/misc_interval_tree.h
-*/
-struct StorePointsOnly {};
-
-
-///..tag.StoreIntervals:The tree nodes store intervals.
-struct StoreIntervals {};
-
-/*!
- * @class IntervalTreeNode
- * @headerfile <seqan/misc/misc_interval_tree.h>
- * @brief Element of @link IntervalTree @endlink.
- *
- * @signature template <typename TInterval[, typename TSpec]>
- *            class IntervalTreeNode;
- *
- * @tparam TInterval The type to use for intervals.
- * @tparam TSpec     The specializing tag.  Default: @link IntervalTreeNodeTypeTags#StorePointsOnly @endlink.
- */
-
-
-/**
-.Class.IntervalTreeNode:
-..cat:Miscellaneous
-..summary:Element of @Class.IntervalTree@.
-..signature:IntervalTreeNode<TInterval, TSpec>
-..param.TInterval:The type of interval to store.
-..param.TSpec:The type of interval to store.
-...default:StorePointsOnly.
-...metafunction:Metafunction.Spec
-..include: seqan/misc/misc_interval_tree.h
-
-.Memvar.IntervalTreeNode#center:
-..class:Class.IntervalTreeNode
-..summary:The center of the interval of type TValue.
-
-.Memvar.IntervalTreeNode#list1
-..class:Class.IntervalTreeNode
-..summary:Sorted list of pointers to intervals, sorted in ascending according to their left boundary points.
-
-.Memvar.IntervalTreeNode#list2
-..class:Class.IntervalTreeNode
-..summary:Sorted list of pointers to intervals, sorted in descending according to their right boundary points.
- */
-template<typename TInterval, typename TSpec=StorePointsOnly>
-class IntervalTreeNode;
-
-/*!
- * @class StoreIntervalsIntervalTreeNode
- * @headerfile <seqan/misc/misc_interval_tree.h>
- * @brief An IntervalTreeNode that stores intervals explicitely in each node.
- *
- * @signature template <typename TInterval>
- *            class IntervalTreeNode<TInterval, StoreIntervals>;
- *
- * @tparam TInterval The Interval type to use.
- */
-
-/**
-.Spec.Interval Tree Node
-..cat:Miscellaneous
-..general:Class.IntervalTreeNode
-..summary:An Interval Tree Node that stores intervals explicitely in each node.
-..signature:IntervalTreeNode<TInterval, StoreIntervals>
-..param.TInterval:The interval type to store in the node.
-..include:seqan/misc/misc_interval_tree.h
- */
-template<typename TInterval>
-class IntervalTreeNode<TInterval, StoreIntervals> {
-public:
-	typedef typename Value<TInterval>::Type TValue;
-
-	TValue center;
-	String<TInterval> list1;
-	String<TInterval> list2;
-
-    IntervalTreeNode() : center()
-    {}
-};
-
-/*!
- * @class StorePointsOnlyIntervalTreeNode
- * @headerfile <seqan/misc/misc_interval_tree.h>
- * @brief An IntervalTreeNode that stores only the relevant points in each node.
- *
- * Only the end points of the intervals in the list sorted by endpoints (list2) and only the begin point of the interval
- * list sorted by begin points (list1) are stored.
- *
- * @signature template <typename TInterval>
- *            class IntervalTreeNode<TInterval, StoreIntervals>;
- *
- * @tparam TInterval The Interval type to use.
- */
-
-/**
-.Spec.Points Only Tree Node
-..cat:Miscellaneous
-..general:Class.IntervalTreeNode
-..summary:Spec for IntervalTreeNode that stores only the relevant point in each node meaning the endpoint of the interval in the list sorted by endpoints (list2) and only the beginpoint of the interval in the list sorted by beginpoints (list1).
-..signature:IntervalTreeNode<TInterval, StorePointsOnly>
-..param.TInterval:The interval type to store in the node.
-..include:seqan/misc/misc_interval_tree.h
- */
-template<typename TInterval>
-class IntervalTreeNode<TInterval, StorePointsOnly> {
-public:
-	typedef typename Cargo<TInterval>::Type TCargo;
-	typedef typename Value<TInterval>::Type TValue;
-
-	TValue center;
-	String<PointAndCargo<TValue,TCargo> > list1;
-	String<PointAndCargo<TValue,TCargo> > list2;
-
-    /**
-.Memfunc.IntervalTreeNode#IntervalTreeNode:
-..class:Class.IntervalTreeNode
-..summary:Default constructor.
-..signature:IntervalTreeNode()
-     */
-    IntervalTreeNode() : center()
-    {
-SEQAN_CHECKPOINT
-    }
-
-	IntervalTreeNode(IntervalTreeNode const & other):
-		center(other.center),
-		list1(other.list1),
-		list2(other.list2)
-	{
-SEQAN_CHECKPOINT
-	}
-};
-
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Graph - Interval Tree
-//////////////////////////////////////////////////////////////////////////////
-
-/*!
- * @class IntervalTree
- * @headerfile <seqan/misc/misc_interval_tree.h>
- * @brief Data structure for efficient interval storage.
- *
- * @signature template <[typename TValue[, typename TCargo]]>
- *            class IntervalTree;
- *
- * @tparam TValue The type to use for coordinates.  Default: <tt>int</tt>.
- * @tparam TCargo The type to use for cargo.  Default: <tt>unsigned</tt>.
- *
- * @section Remarks
- *
- * If the intervals are not associated with cargos/IDs, they will be numbered consecutively.
- *
- * @section Example
- *
- * The following example creates an integer interval tree with string keys.  This tree is quired for keys of intervals
- * that overlap the interval <tt>[550, 990)</tt>.
- *
- * @include demos/misc/interval_tree_example.cpp
- *
- * The resulting keys are:
- *
- * @code{.console}
- * gene
- * exon2
- * coding2
- * @endcode
- *
- *
- * @fn IntervalTree::IntervalTree
- * @brief Constructor
- *
- * @signature IntervalTree::IntervalTree();
- * @signature IntervalTree::IntervalTree(intervals);
- * @signature IntervalTree::IntervalTree(intervals[, center]);
- * @signature IntervalTree::IntervalTree(intervals[, tag]);
- * @signature IntervalTree::IntervalTree(intervalBegins, intervalEnds, [intervalCargos,] len);
- *
- * @param[in] intervals Container of intervals.  A strin gof <tt>IntervalAndCargo&lt;Value, TCargo&gt;</tt>
- *                      objects, see @link IntervalAndCargo @endlink.
- * @param[in] intervalBegins
- *                      Iterator pointing to begin position of first interval.
- * @param[in] intervalEnds
- *                      Iterator pointing to end position of first interval.
- * @param[in] intervalCargos
- *                      Iterator pointing to cargo/ids for intervals.
- * @param[in] len       Number of intervals to store in tree.
- * @param[in] tag       Tag for tree construction method.
- */
-
-/**
-.Class.IntervalTree:
-..cat:Miscellaneous
-..summary:A datastructure that efficiently stores intervals.
-..signature:IntervalTree<TValue, TCargo>
-..param.TValue:The value type.
-...default:int
-..param.TCargo:The cargo/id type.
-...default:int
-...remarks:If the intervals are not associated with cargos/IDs, they will be numbered consecutively.
-..example:The following example creates an integer interval tree with string keys.
-This tree is queried for keys of intervals that overlap the interval [550,900).
-...file:demos/misc/interval_tree_example.cpp
-...text:The resulting keys are:
-...output:
-gene
-exon2
-coding2
-..include:seqan/misc/misc_interval_tree.h
-*/
-template <typename TValue = int, typename TCargo = unsigned int>
-class IntervalTree
-{
-public:
-	typedef Graph<Directed<void,WithoutEdgeId> > TGraph;
-	typedef IntervalAndCargo<TValue,TCargo> TInterval;
-	typedef IntervalTreeNode<TInterval> TNode;
-	typedef String<TNode> TPropertyMap;
-
-	TGraph g;
-	TPropertyMap pm;
-	size_t interval_counter;
-	
-/**
-.Memfunc.IntervalTree#IntervalTree:
-..class:Class.IntervalTree
-..summary:Constructor
-..signature:IntervalTree()
-..signature:IntervalTree(String<TInterval> intervals)
-..signature:IntervalTree(String<TInterval> intervals, TValue center)
-..signature:IntervalTree(String<TInterval> intervals, Tag<TTagSpec> const tag)
-..signature:IntervalTree(intervalBegins, intervalEnds, len)
-..signature:IntervalTree(intervalBegins, intervalEnds, intervalCargos, len)
-..param.intervals:Container of intervals.
-...type:Spec.Alloc String
-...remarks:A string of $IntervalAndCargo<TValue, TCargo>$ objects, see @Class.IntervalAndCargo@.
-..param.intervalBegins:Iterator pointing to begin position of first interval.
-..param.intervalEnds:Iterator pointing to end position of first interval.
-..param.intervalCargos:Iterator pointing to cargos/ids for intervals.
-..param.len:Number of intervals to store in tree.
-..param.tag:Tag for tree construction method; @Tag.IntervalTree Centers.tag.ComputeCenter@
-...default:@Tag.IntervalTree Centers.tag.ComputeCenter@
-..remarks:center of root node is computed by _calcIntervalTreeRootCenter
-*/
-	
-	IntervalTree()
-	{
-SEQAN_CHECKPOINT
-		interval_counter = 0;
-	}
-	
-	template<typename TIterator,typename TCargoIterator>
-	IntervalTree(TIterator interval_begins,
-				 TIterator interval_ends, 
-				 TCargoIterator interval_cargos, 
-				 size_t len)	
-	{
-SEQAN_CHECKPOINT
-		String<TInterval> intervals;
-		resize(intervals,len);
-		size_t i = 0;
-		while(i<len)
-		{
-			intervals[i].i1 = value(interval_begins);
-			++interval_begins;
-			intervals[i].i2 = value(interval_ends);
-			++interval_ends;
-			intervals[i].cargo = value(interval_cargos);
-			++interval_cargos;
-			++i;
-		}
-		createIntervalTree(*this, intervals);
-	}
-
-	template<typename TIterator>
-	IntervalTree(TIterator interval_begins,
-				 TIterator interval_ends,
-				 size_t len)
-	{
-SEQAN_CHECKPOINT
-		String<TInterval> intervals;
-		resize(intervals,len);
-		size_t i = 0;
-		while(i<len)
-		{
-			intervals[i].i1 = value(interval_begins);
-			++interval_begins;
-			intervals[i].i2 = value(interval_ends);
-			++interval_ends;
-			intervals[i].cargo = i;
-			++i;
-		}
-		createIntervalTree(*this, intervals);
-	}
-	
-	IntervalTree(String<TInterval> intervals)	
-	{
-SEQAN_CHECKPOINT
-		createIntervalTree(*this, intervals);
-	}
-
-	template <typename TTagSpec>
-	IntervalTree(String<TInterval> intervals, Tag<TTagSpec> const tag)
-	{
-SEQAN_CHECKPOINT
-		interval_counter = length(intervals);
-		createIntervalTree(g,pm,intervals,tag);
-	}
-
-	IntervalTree(String<TInterval> intervals, TValue center)	
-	{
-SEQAN_CHECKPOINT
-		interval_counter = length(intervals);
-		createIntervalTree(g,pm,intervals,center);
-	}
-};
-
-
-
-///////Specs for the way interval centers are determined
-/**
-.Tag.IntervalTree Centers
-..cat:Miscellaneous
-..summary:Tag to select a specific way to compute the center of an interval tree node.
-..see:Class.IntervalTree
-..include:seqan/misc/misc_interval_tree.h
- */
-
-
-/**
-..tag.ComputeCenter
-...summary:For intervals that are more or less uniformly distributed in the value range, using the ComputeCenter tag may result in a more balanced tree compared to using a random approach.
-...signature:ComputeCenter
-...remarks:center = minbegin + (maxend-minbegin)/2
- */
-//template <typename TSpec = SpecPointAndCargo>
-struct TagComputeCenter_;
-typedef Tag<TagComputeCenter_> const ComputeCenter;
-
-
-///////////////////////////////////////////////////////////////////////////
-///////////////////// IntervalAndCargo functions //////////////////////////
-///////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn IntervalAndCargo#leftBoundary
- * @brief Access to left boundary.
- *
- * @signature TBoundary leftBoundary(interval);
- *
- * @param[in] interval The IntervalAndCargo to query for its left boundary.
- *
- * @return TBoundary Reference to the left boundary value.
- */
-
-/**
-.Function.leftBoundary
-..cat:Miscellaneous
-..summary:Access to the left boundary.
-..signature:leftBoundary(interval)
-..class:Class.IntervalAndCargo
-..param.interval:The interval to return the left boundary for.
-...type:Class.IntervalAndCargo
-..returns:The reference to the left boundary of the interval of type TValue&.
-..see:Function.getLeftBoundary
-..see:Function.rightBoundary
-..see:Function.getRightBoundary
-*/
-
-template<typename TValue, typename TCargo>
-TValue &
-leftBoundary(IntervalAndCargo<TValue, TCargo> & interval)
-{
-	return interval.i1;
-}
-
-template<typename TValue, typename TCargo>
-TValue const &
-leftBoundary(IntervalAndCargo<TValue, TCargo> const & interval)
-{
-	return interval.i1;
-}
-
-/*!
- * @fn IntervalAndCargo#rightBoundary
- * @brief Access to right boundary.
- *
- * @signature TBoundary rightBoundary(interval);
- *
- * @param[in] interval The IntervalAndCargo to query for its right boundary.
- *
- * @return TBoundary Reference to the right boundary value.
- */
-
-/**
-.Function.rightBoundary
-..cat:Miscellaneous
-..summary:Access to the right boundary.
-..signature:leftBoundary(interval)
-..class:Class.IntervalAndCargo
-..param.interval:The interval to return the left boundary for.
-...type:Class.IntervalAndCargo
-..returns:The reference to the right boundary of the interval of type TValue&.
-..see:Function.getRightBoundary
-..see:Function.leftBoundary
-..see:Function.getLeftBoundary
-*/
-
-template<typename TValue, typename TCargo>
-TValue &
-rightBoundary(IntervalAndCargo<TValue, TCargo> & interval)
-{
-	return interval.i2;
-}
-
-template<typename TValue, typename TCargo>
-TValue const &
-rightBoundary(IntervalAndCargo<TValue, TCargo> const & interval)
-{
-	return interval.i2;
-}
-
-/*!
- * @fn IntervalAndCargo#getLeftBoundary
- * @brief Access to getLeft boundary.
- *
- * @signature TBoundary getLeftBoundary(interval);
- *
- * @param[in] interval The IntervalAndCargo to query for its left boundary.
- *
- * @return TBoundary Copy of the left boundary value.
- */
-
-/**
-.Function.getLeftBoundary
-..cat:Miscellaneous
-..summary:Get method for the left boundary.
-..signature:leftBoundary(interval)
-..class:Class.IntervalAndCargo
-..param.interval:The interval to return the left boundary for.
-...type:Class.IntervalAndCargo
-..returns:The copy of the left boundary of the interval of type TValue.
-..see:Function.leftBoundary
-..see:Function.getRightBoundary
-..see:Function.rightBoundary
-*/
-
-template<typename TValue, typename TCargo>
-TValue
-getLeftBoundary(IntervalAndCargo<TValue, TCargo> const & interval)
-{
-	return interval.i1;
-}
-
-/*!
- * @fn IntervalAndCargo#getRightBoundary
- * @brief Access to getRight boundary.
- *
- * @signature TBoundary getRightBoundary(interval);
- *
- * @param[in] interval The IntervalAndCargo to query for its right boundary.
- *
- * @return TBoundary Copy of the right boundary value.
- */
-
-/**
-.Function.getRightBoundary
-..cat:Miscellaneous
-..summary:Get method for the right boundary.
-..signature:leftBoundary(interval)
-..class:Class.IntervalAndCargo
-..param.interval:The interval to return the right boundary for.
-...type:Class.IntervalAndCargo
-..returns:The copy of the right boundary of the interval of type TValue.
-..see:Function.rightBoundary
-..see:Function.getLeftBoundary
-..see:Function.leftBoundary
-*/
-
-template<typename TValue, typename TCargo>
-TValue
-getRightBoundary(IntervalAndCargo<TValue, TCargo> const & interval)
-{
-	return interval.i2;
-}
-
-
-/*!
- * @fn IntervalAndCargo#cargo
- * @brief Access to the cargo.
- *
- * @signature TCargo cargo(interval);
- *
- * @param[in] interval The IntervalAndCargo to query for its cargo.
- * 
- * @return TCargo Reference to the cargo member.
- */
-
-/**
-.Function.cargo
-..signature:cargo(me)
-..class:Class.IntervalAndCargo
-..param.me:
-...type:Class.IntervalAndCargo
-..see:Function.getCargo
-*/
-
-template<typename TValue, typename TCargo>
-TCargo const &
-cargo(IntervalAndCargo<TValue, TCargo> const & interval)
-{
-	return interval.cargo;
-}
-
-template<typename TValue, typename TCargo>
-TCargo &
-cargo(IntervalAndCargo<TValue, TCargo> & interval)
-{
-	return interval.cargo;
-}
-
-/*!
- * @fn IntervalAndCargo#getCargo
- * @brief Access to the cargo.
- *
- * @signature TCargo getCargo(interval);
- *
- * @param[in] interval The IntervalAndCargo to query for its cargo.
- * 
- * @return TCargo Copy of the cargo member.
- */
- 
-/**
-.Function.getCargo
-..signature:getCargo(me)
-..class:Class.IntervalAndCargo
-..param.me:
-...type:Class.IntervalAndCargo
-..see:Function.cargo
-*/
-
-template<typename TValue, typename TCargo>
-TCargo
-getCargo(IntervalAndCargo<TValue,TCargo> const & interval)
-{
-	return interval.cargo;
-}
-
-
-/////////////////// Metafunctions //////////////////////
-
-/*!
- * @mfn IntervalAndCargo#Value
- * @brief Return the value type.
- *
- * @signature Value<TIntervalAndCargo>::Type;
- */
-
-///.Metafunction.Value.param.T.type:Class.IntervalAndCargo
-///.Metafunction.Value.class:Class.IntervalAndCargo
-template<typename TValue,typename TCargo>
-struct Value<IntervalAndCargo<TValue,TCargo> >
-{
-	typedef TValue Type;
-};
-
-/*!
- * @mfn IntervalAndCargo#Cargo
- * @brief Return the cargo type.
- *
- * @signature Cargo<TIntervalAndCargo>::Type;
- */
-
-///.Metafunction.Cargo.param.T.type:Class.IntervalAndCargo
-///.Metafunction.Cargo.class:Class.IntervalAndCargo
-template<typename TValue,typename TCargo>
-struct Cargo<IntervalAndCargo<TValue, TCargo> >
-{
-	typedef TCargo Type;
-};
-
-
-///////////////////////////////////////////////////////////////////////////
-///////////////////// PointAndCargo functions /////////////////////////////
-///////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn PointAndCargo#leftBoundary
- * @brief Access to left boundary.
- *
- * @signature TBoundary leftBoundary(point);
- *
- * @param[in] point The PointAndCargo to query for its left boundary.
- *
- * @return TBoundary Reference to the left boundary value.
- */
-
-/**
-.Function.leftBoundary
-..signature:leftBoundary(point)
-..class:Class.PointAndCargo
-..param.point.type:Class.PointAndCargo
- */
-
-template<typename TValue, typename TCargo>
-TValue const &
-leftBoundary(PointAndCargo<TValue, TCargo> const & point)
-{
-	return point.point;
-}
-
-template<typename TValue, typename TCargo>
-TValue &
-leftBoundary(PointAndCargo<TValue, TCargo> & point)
-{
-	return point.point;
-}
-
-/*!
- * @fn PointAndCargo#rightBoundary
- * @brief Access to right boundary.
- *
- * @signature TBoundary rightBoundary(point);
- *
- * @param[in] point The PointAndCargo to query for its right boundary.
- *
- * @return TBoundary Reference to the right boundary value.
- */
-
-/**
-.Function.rightBoundary
-..signature:rightBoundary(point)
-..class:Class.PointAndCargo
-..param.point.type:Class.PointAndCargo
- */
-
-template<typename TValue, typename TCargo>
-TValue const &
-rightBoundary(PointAndCargo<TValue, TCargo> const & point)
-{
-	return point.point;
-}
-
-template<typename TValue, typename TCargo>
-TValue &
-rightBoundary(PointAndCargo<TValue, TCargo> & point)
-{
-	return point.point;
-}
-
-
-/**
-.Function.getLeftBoundary
-..signature:getLeftBoundary(point)
-..class:Class.PointAndCargo
-..param.point.type:Class.PointAndCargo
- */
-
-template<typename TValue, typename TCargo>
-TValue
-getLeftBoundary(PointAndCargo<TValue, TCargo> const & point)
-{
-    return point.point;
-}
-
-/*!
- * @fn PointAndCargo#getLeftBoundary
- * @brief Access to getLeft boundary.
- *
- * @signature TBoundary getLeftBoundary(point);
- *
- * @param[in] point The PointAndCargo to query for its left boundary.
- *
- * @return TBoundary Copy of the left boundary value.
- */
-
-/**
-.Function.getRightBoundary
-..signature:getRightBoundary(point)
-..class:Class.PointAndCargo
-..param.point.type:Class.PointAndCargo
- */
-
-template<typename TValue, typename TCargo>
-TValue
-getRightBoundary(PointAndCargo<TValue,TCargo> const & point)
-{
-	return point.point;
-}
-
-/*!
- * @fn PointAndCargo#cargo
- * @brief Access to the cargo.
- *
- * @signature TCargo cargo(point);
- *
- * @param[in] point The PointAndCargo to query for its cargo.
- * 
- * @return TCargo Reference to the cargo member.
- */
-
-
-/**
-.Function.cargo
-..signature:cargo(point)
-..class:Class.PointAndCargo
-..param.point.type:Class.PointAndCargo
- */
-
-template<typename TValue, typename TCargo>
-TCargo const &
-cargo(PointAndCargo<TValue,TCargo> const & point)
-{
-	return point.cargo;
-}
-
-template<typename TValue, typename TCargo>
-TCargo &
-cargo(PointAndCargo<TValue,TCargo> & point)
-{
-	return point.cargo;
-}
-
-/*!
- * @fn PointAndCargo#getCargo
- * @brief Access to the cargo.
- *
- * @signature TCargo getCargo(point);
- *
- * @param[in] point The PointAndCargo to query for its cargo.
- * 
- * @return TCargo Copy of the cargo member.
- */
-
-/**
-.Function.cargo
-..signature:getCargo(point)
-..class:Class.IntervalAndCargo
-..param.point:
-...type:Class.IntervalAndCargo
-..see:Function.getCargo
-*/
-
-template<typename TValue, typename TCargo>
-TCargo
-getCargo(PointAndCargo<TValue,TCargo> const & point)
-{
-	return point.cargo;
-}
-
-////////////////// Metafunctions //////////////////
-
-/*!
- * @mfn PointAndCargo#Value
- * @brief Return the value type.
- *
- * @signature Value<TPointAndCargo>::Type;
- */
-
-///.Metafunction.Value.param.T.type:Class.PointAndCargo
-///.Metafunction.Value.class:Class.PointAndCargo
-template<typename TValue,typename TCargo>
-struct Value<PointAndCargo<TValue,TCargo> >
-{
-	typedef TValue Type;
-};
-
-/*!
- * @mfn PointAndCargo#Cargo
- * @brief Return the cargo type.
- *
- * @signature Cargo<TPointAndCargo>::Type;
- */
-
-///.Metafunction.Cargo.param.T.type:Class.PointAndCargo
-///.Metafunction.Cargo.class:Class.PointAndCargo
-template<typename TValue,typename TCargo>
-struct Cargo<PointAndCargo<TValue,TCargo> >
-{
-	typedef TCargo Type;
-};
-
-
-//// Comparators
-template <typename TPair>
-bool _less_compI1_ITree(TPair const & p1, TPair const & p2)
-{
-    return (leftBoundary(p1) < leftBoundary(p2));
-}
-
-
-template <typename TPair>
-bool _greater_compI2_ITree(TPair const & p1, TPair const & p2)
-{
-    return (rightBoundary(p1) > rightBoundary(p2));
-}
-
-
-
-///////////////////////////////////////////////////////////////////////////
-///////////////////// IntervalTreeNode functions //////////////////////////
-///////////////////////////////////////////////////////////////////////////
-
-
-
-
-
-// internal set node functions
-template<typename TValue, typename TInterval>
-void
-_setIntervalTreeNode(IntervalTreeNode<TInterval, StoreIntervals> & knot, TValue center, TInterval const & interval)
-{
-	knot.center = center;
-	appendValue(knot.list1, interval);
-	appendValue(knot.list2, interval);
-}
-
-// append intervals to lists in node knot
-template<typename TInterval>
-void
-_appendIntervalTreeNodeLists(IntervalTreeNode<TInterval, StoreIntervals> & knot,TInterval const & interval)
-{
-	appendValue(knot.list1, interval);
-	appendValue(knot.list2, interval);
-}
-
-
-//internal set node functions
-template<typename TValue, typename TInterval>
-void
-_setIntervalTreeNode(IntervalTreeNode<TInterval, StorePointsOnly> & knot, TValue center, TInterval const & interval)
-{
-	knot.center = center;
-	appendValue(knot.list1,PointAndCargo<TValue,typename Cargo<TInterval>::Type>(leftBoundary(interval),cargo(interval)));
-	appendValue(knot.list2,PointAndCargo<TValue,typename Cargo<TInterval>::Type>(rightBoundary(interval),cargo(interval)));
-}
-
-
-template<typename TInterval>
-void
-_appendIntervalTreeNodeLists(IntervalTreeNode<TInterval, StorePointsOnly> & knot, TInterval const & interval)
-{
-	appendValue(knot.list1,PointAndCargo<typename Value<TInterval>::Type,typename Cargo<TInterval>::Type>(leftBoundary(interval),cargo(interval)));
-	appendValue(knot.list2,PointAndCargo<typename Value<TInterval>::Type,typename Cargo<TInterval>::Type>(rightBoundary(interval),cargo(interval)));
-	
-
-}
-
-/////////////////// Metafunctions ///////////////////////
-
-/*!
- * @mfn IntervalTreeNode#Value
- * @brief Return value type.
- *
- * @signature Value<TNode>::Type;
- */
-
-///.Metafunction.Value.param.T.type:Class.IntervalTreeNode
-///.Metafunction.Value.class:Class.IntervalTreeNode
-template<typename TInterval, typename TSpec>
-struct Value<IntervalTreeNode<TInterval,TSpec> >
-{
-	typedef typename Value<TInterval>::Type Type;
-};
-
-/*!
- * @mfn IntervalTreeNode#Cargo
- * @brief Return cargo type.
- *
- * @signature Cargo<TNode>::Type;
- */
-
-///.Metafunction.Cargo.param.T.type:Class.IntervalTreeNode
-///.Metafunction.Cargo.class:Class.IntervalTreeNode
-template<typename TInterval, typename TSpec>
-struct Cargo<IntervalTreeNode<TInterval,TSpec> >
-{
-	typedef typename Cargo<TInterval>::Type Type;
-};
-
-
-/*!
- * @mfn IntervalTreeNode#ListType
- * @brief Type of the lists in tree nodes.
- *
- * @signature ListType<T>::Type;
- */
-
-/**
-.Metafunction.ListType:
-..cat:Miscellaneous
-..signature:ListType<T>::ListType
-..class.Class.IntervalTreeNode
-..summary:Type of lists in tree nodes.
-..param.T:The type to retrieve the list type for.
-..returns:Returns the type of the lists in @Class.IntervalTreeNode@ objects.
-..include:seqan/misc/misc_interval_tree.h
- */
-template<typename T>
-struct ListType;
-
-
-///.Metafunction.ListType.param.T.type:Class.IntervalTreeNode
-///.Metafunction.ListType.class:Class.IntervalTreeNode
-template<typename TInterval>
-struct ListType<IntervalTreeNode<TInterval,StorePointsOnly> >
-{
-	typedef String<PointAndCargo<typename Value<TInterval>::Type,typename Cargo<TInterval>::Type> > Type;
-
-};
-
-
-///.Metafunction.ListType.param.T.type:Class.IntervalTreeNode
-///.Metafunction.ListType.class:Class.IntervalTreeNode
-template<typename TInterval>
-struct ListType<IntervalTreeNode<TInterval,StoreIntervals> >
-{
-	typedef String<IntervalAndCargo<typename Value<TInterval>::Type,typename Cargo<TInterval>::Type> > Type;
-
-};
-
-
-
-///////////////////////////////////////////////////////////////////////////
-/////////////////////// IntervalTree functions ////////////////////////////
-///////////////////////////////////////////////////////////////////////////
-
-/*!
- * @fn IntervalTree#createIntervalTree
- * @brief Create an interval tree.
- * 
- * @signature void createIntervalTree(intervalTree, intervals[, tag]);
- * @signature void createIntervalTree(g, pm, intervals[, tag]);
- * @signature void createIntervalTree(g, pm, intervals, center[, tag]]);
- * 
- * @param intervalTree An interval tree Types: IntervalTree
- * @param intervals    Container of intervals.  A string of <tt>IntervalAndCargo&lt;TValue, TCargo&gt;</tt> objects, see
- *                     @link IntervalAndCargo @endlink. Types: AllocString
- * @param g            DirectedGraph to create interval tree in. Types: Graph
- * @param pm           Property map to use for the created interval tree.
- * @param tag          Tag for tree construction method;
- */
-
-/**
-.Function.createIntervalTree
-..summary:Create an interval tree.
-..cat:Miscellaneous
-..class:Class.IntervalTree
-..signature:createIntervalTree(intervalTree, intervals [, tag])
-..signature:createIntervalTree(g, pm, intervals [, tag])
-..signature:createIntervalTree(g, pm, intervals, center [, tag]])
-..param.intervalTree:An interval tree
-...type:Class.IntervalTree
-..param.g:DirectedGraph to create interval tree in.
-...type:Class.Graph
-..param.pm:Property map to use for the created interval tree.
-..param.intervals:Container of intervals.
-...type:Spec.Alloc String
-...remarks:A string of $IntervalAndCargo<TValue, TCargo>$ objects, see @Class.IntervalAndCargo@.
-..param.tag:Tag for tree construction method; @Tag.IntervalTree Centers.tag.ComputeCenter@
-...default:@Tag.IntervalTree Centers.tag.ComputeCenter@
-..remarks:center of root node is computed by _calcIntervalTreeRootCenter
-..include:seqan/misc/misc_interval_tree.h
- */
- 
-template <typename TGraph, typename TPropertyMap, typename TIntervals, typename TSpec>
-inline void 
-createIntervalTree(TGraph & g,
-				   TPropertyMap & pm, 
-				   TIntervals & intervals,
-				   Tag<TSpec> const tag)
-{
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Value<TIntervals>::Type TInterval;
-	typedef typename Value<TInterval>::Type TValue;
-
-	reserve(g.data_vertex,length(intervals));
-	reserve(pm,length(intervals));
-
-	TVertexDescriptor root = addVertex(g);
-	resizeVertexMap(g,pm);
-
-    if (length(intervals) > 0u) {
-        TValue center =	_calcIntervalTreeRootCenter(intervals);
-
-        std::sort(begin(intervals, Standard()),end(intervals, Standard()),_less_compI1_ITree<TInterval>);
-
-        String<TInterval *> interval_pointers;
-        // interval tree stores pointers to intervals, not original intervals
-        _makePointerInterval(intervals, interval_pointers);
-
-        _createIntervalTree(g,pm,interval_pointers,root,(TValue)0.0,center,length(intervals),tag);
-        reserve(pm, length(pm), Exact());
-        reserve(g.data_vertex, length(g.data_vertex), Exact());
-    }
-}
-
-template <typename TGraph, typename TPropertyMap, typename TIntervals>
-inline void 
-createIntervalTree(TGraph & g, 
-				   TPropertyMap & pm, 
-				   TIntervals & intervals)
-{
-	createIntervalTree(g, pm, intervals, ComputeCenter());
-}
-
-template <typename TGraph, typename TPropertyMap, typename TIntervals, typename TSpec>
-inline void 
-createIntervalTree(TGraph & g,
-                   TPropertyMap & pm,
-				   TIntervals & intervals,
-				   typename Value<typename Value<TIntervals>::Type>::Type center,
-				   Tag<TSpec> const tag)
-{
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Value<TIntervals>::Type TInterval;
-	typedef typename Value<typename Value<TIntervals>::Type>::Type TValue;
-	
-	reserve(g.data_vertex,length(intervals));
-	reserve(pm,length(intervals));
-	
-	TVertexDescriptor root = addVertex(g);
-	resizeVertexMap(g,pm);
-	
-    if (length(intervals) > 0u) {
-	    TInterval a;
-	    typename Iterator<TIntervals, Standard>::Type begin_ = begin(intervals, Standard());
-	    typename Iterator<TIntervals, Standard>::Type end_ = end(intervals, Standard());
-	    std::sort(begin_, end_ ,_less_compI1_ITree<TInterval>);
-
-	    String<TInterval const*> interval_pointers;
-	    _makePointerInterval(intervals,interval_pointers);
-
-	    if(length(intervals)==1) // if there is just one interval ->  center = center of this interval
-		    center = (rightBoundary(intervals[0])-leftBoundary(intervals[0]))/(TValue)2.0;
-
-	    _createIntervalTree(g, pm, interval_pointers, root, (TValue)0.0, center, length(intervals), tag);
-		
-	    reserve(pm, length(pm), Exact());
-	    reserve(g.data_vertex, length(g.data_vertex), Exact());
-    }
-}
-
-// ComputeCenter tag as default construction method
-template <typename TGraph, typename TPropertyMap, typename TIntervals>
-inline void
-createIntervalTree(TGraph & g, TPropertyMap & pm, 
-				   TIntervals & intervals, 
-				   typename Value<typename Value<TIntervals>::Type>::Type center)
-{
-	createIntervalTree(g, pm, intervals, center, ComputeCenter());
-}
-
-
-template <typename TValue,typename TCargo, typename TIntervals, typename TSpec>
-inline void
-createIntervalTree(IntervalTree<TValue,TCargo> & it,
-				   TIntervals & intervals,
-				   Tag<TSpec> const tag)
-{
-	it.interval_counter = length(intervals);
-	createIntervalTree(it.g, it.pm, intervals, tag);
-}
-
-template <typename TValue,typename TCargo, typename TIntervals>
-inline void 
-createIntervalTree(IntervalTree<TValue, TCargo> & it,
-				   TIntervals & intervals)
-{
-	createIntervalTree(it, intervals, ComputeCenter());
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-//remembers minimum and maximum of point values in intervals and sets the center
-//of each node to min+(max-min)/2
-template<typename TGraph, typename TPropertyMap, typename TIntervalPointer, typename TValue>
-inline void
-_createIntervalTree(TGraph & g, TPropertyMap & pm, 
-				   String<TIntervalPointer*> & intervals,
-				   typename VertexDescriptor<TGraph>::Type & knot, 
-				   TValue, 
-				   TValue center, 
-				   typename VertexDescriptor<TGraph>::Type len,
-				   Tag<TagComputeCenter_> const tag)
-{
-	//  Rekursionsanker
-	if (len == 1)
-    {
-		_setIntervalTreeNode(value(pm, knot), center, *intervals[0]);
-		return;
-	}
-
-	typedef typename Value<TPropertyMap>::Type TNode;
-	typedef typename ListType<TNode>::Type TList;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef String<TIntervalPointer*> TIntervalPointers;
-
-	// one list of interval pointers for the intervals to the left of center
-	TIntervalPointers S_left;
-	// one list of interval pointers for the intervals to the right of center
-	TIntervalPointers S_right;
-
-	TValue min1 = maxValue<TValue>();
-	TValue min2 = maxValue<TValue>();
-	TValue max1 = minValue<TValue>();
-	TValue max2 = minValue<TValue>();
-
-	value(pm,knot).center = center;
-	
- 
-	typedef typename Iterator<TIntervalPointers,Standard>::Type TIntervalIterator;
-	TIntervalIterator it = begin(intervals,Standard());
-	TIntervalIterator it_end = end(intervals,Standard());
-	
-	// walk through intervals
-	while(it != it_end)
-	{
-		// interval belongs to the left list
-		if((**it).i2<=center)
-		{
-			appendValue(S_left,*it, Generous());
-			 //remember right most and left most point in left list
-			if((**it).i2 > max1)
-				max1 = (**it).i2;
-			if((**it).i1 < min1)
-				min1 = (**it).i1;
-		}
-		else
-		{
-			// interval belongs to the right list
-			if((**it).i1>center)
-			{
-				appendValue(S_right,(*it), Generous());
-				 //remember right most and left most point in right list
-				if((**it).i2 > max2)
-					max2 = (**it).i2;
-				if ((**it).i1 < min2)
-					min2 = (**it).i1;
-			}
-			else // interval belongs to this node
-			{
-				_appendIntervalTreeNodeLists(value(pm,knot), **it);
-			}
-		}
-        ++it;
-	}
-
-//	std::sort(begin(value(pm,knot).list1),end(value(pm,knot).list1),_less_compI1_ITree<typename Value<TList>::Type>);
-	std::sort(begin(value(pm,knot).list2),end(value(pm,knot).list2),_greater_compI2_ITree<typename Value<TList>::Type>);
-
-	// build subtree to the left
-	if(!empty(S_left))
-	{
-		TVertexDescriptor vd = addVertex(g);
-		resize(pm, vd+1); 
-		addEdge(g,knot,vd);
-		_createIntervalTree(g,pm,S_left,vd,center,min1+(max1-min1)/2,length(S_left),tag);
-	}
-	// build subtree to the right
-	if(!empty(S_right))
-	{
-		TVertexDescriptor vd = addVertex(g);
-		resize(pm, vd+1); 
-		addEdge(g,knot,vd);
-		_createIntervalTree(g,pm,S_right,vd,center,min2+(max2-min2)/2,length(S_right),tag);
-	}
-}
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-//createIntervalTree for all specs except CompCenter, the center value of each 
-//node is determined by functions _calcIntervalTreeNodeCenterLeft and 
-//_calcIntervalTreeNodeCenterRight
-template<typename TGraph, typename TPropertyMap, typename TSpec, typename TInterval, typename TValue>
-inline void
-_createIntervalTree(TGraph & g, TPropertyMap & pm, 
-				   String<TInterval*> & intervals, 
-				   typename VertexDescriptor<TGraph>::Type & knot, 
-				   TValue last_center, TValue center, 
-				   typename VertexDescriptor<TGraph>::Type len,
-				   Tag<TSpec> const tag)
-{
-SEQAN_CHECKPOINT
-	// Rekursionsanker
-	if(len==1){
-		_setIntervalTreeNode(value(pm,knot),center,*value(intervals,0));
-		return;
-	}
-
-	typedef typename Value<TPropertyMap>::Type TNode;
-	typedef typename ListType<TNode>::Type TList;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef String<TInterval*> TIntervalPointers;
-	
-	// one list of interval pointers for the intervals to the left of center
-	TIntervalPointers S_left;
-	// one list of interval pointers for the intervals to the right of center
-	TIntervalPointers S_right;
-		
-	value(pm,knot).center = center;
-	
-	typedef typename Iterator<TIntervalPointers,Standard>::Type TIntervalIterator;
-	TIntervalIterator it = begin(intervals,Standard());
-	TIntervalIterator it_end = end(intervals,Standard());
-	
-	// walk through intervals
-	while(it != it_end)
-	{
-		// interval belongs to the left list
-		if((**it).i2<=center)
-		{
-			appendValue(S_left,*it, Generous());
-		}
-		else
-		{	// interval belongs to the right list
-			if((**it).i1>center)
-			{
-				appendValue(S_right,(*it), Generous());
-			}
-			else
-			{
-				// interval belongs to the current node
-				_appendIntervalTreeNodeLists(value(pm,knot),**it);
-			}
-		}
-        ++it;
-	}
-
-//	std::sort(begin(value(pm,knot).list1),end(value(pm,knot).list1),_less_compI1_ITree<typename Value<TList>::Type>);
-	std::sort(begin(value(pm,knot).list2),end(value(pm,knot).list2),_greater_compI2_ITree<typename Value<TList>::Type>);
-
-	// build subtree to the left
-	if(!empty(S_left))
-	{
-		TVertexDescriptor vd = addVertex(g);
-		resizeVertexMap(g,pm);
-		addEdge(g,knot,vd);
-		TValue next_center = _calcIntervalTreeNodeCenterLeft(S_left,last_center,center,tag);
-		_createIntervalTree(g,pm,S_left,vd,center,next_center,length(S_left),tag);
-	}
-	// build subtree to the right
-	if(!empty(S_right))
-	{
-		TVertexDescriptor vd = addVertex(g);
-		resizeVertexMap(g,pm);
-		addEdge(g,knot,vd);
-		TValue next_center = _calcIntervalTreeNodeCenterRight(S_right,last_center,center,tag);
-		_createIntervalTree(g,pm,S_right,vd,center,next_center,length(S_right),tag);
-	}
-}
-
-
-// fill the container interval_pointers with pointers to the corresponding objects in intervals.
-// this is done to avoid copying and passing the whole IntervalAndCargo objects during interval tree construction
-template<typename TIntervals, typename TIntervalPointers>
-void
-_makePointerInterval(TIntervals & intervals, TIntervalPointers & interval_pointers)
-{
-	typedef typename Iterator<TIntervals, Standard>::Type TIntervalIterator;
-	typedef typename Iterator<TIntervalPointers, Standard>::Type TIntervalPointerIterator;
-
-    resize(interval_pointers, length(intervals));
-	if (empty(intervals))
-        return;
-
-	TIntervalIterator it = begin(intervals, Standard());
-	TIntervalIterator itEnd = end(intervals, Standard());
-	TIntervalPointerIterator iit = begin(interval_pointers, Standard());
-
-    for (; it != itEnd; ++it, ++iit)
-        *iit = it;
-}
-
-// if the center of the root is not given, it is placed in the "ComputeCenter way": in the middle of minValue and maxValue
-// where minValue is the minimum left boundary and maxValue is the maximum right boundary of all intervals
-template<typename TIntervals>
-typename Value<typename Value<TIntervals>::Type>::Type
-_calcIntervalTreeRootCenter(TIntervals & intervals)
-{
-    SEQAN_CHECKPOINT;
-
-    SEQAN_ASSERT_GT(length(intervals), 0u);
-	
-	typedef typename Value<typename Value<TIntervals>::Type>::Type TValue;
-	typedef typename Iterator<TIntervals,Standard>::Type TIntervalIterator;
-
-	TIntervalIterator it = begin(intervals);
-	TIntervalIterator it_end = end(intervals);
-
-	TValue min = maxValue<TValue>();
-	TValue max = minValue<TValue>();
-
-    // get min and max
-	while(it != it_end)
-	{
-		if(leftBoundary(*it)<min) min = leftBoundary(*it);
-		if(rightBoundary(*it)>max) max = rightBoundary(*it);
-	  SEQAN_ASSERT_LEQ(min, max);
-		++it;
-	}
-
-	SEQAN_ASSERT_LEQ(min, max);
-	
-    // return middle between max and min
-	return (min+(max-min)/(TValue)2.0);
-
-}
-
-/*!
- * @fn IntervalTree#addInterval
- * 
- * @headerfile seqan/misc/misc_interval_tree.h
- * 
- * @brief Adds an interval to an interval tree.
- * 
- * @signature void addInterval(intervalTree, interval);
- * @signature void addInterval(intervalTree, begin, end[, cargo]);
- * @signature void addInterval(graph, propertyMap, interval);
- * 
- * @param cargo        Cargo to attach to the interval. Types: IntervalAndCargo
- * @param begin        Begin position of interval of type TValue.
- * @param end          End position of interval of type TValue.
- * @param graph        The directed graph that contains the topography of the interval tree.
- * @param interval     The interval to be added to the interval tree.
- * @param propertyMap  The property map containing the node properties of the interval tree.
- * @param intervalTree The interval tree to add the interval to. Types: IntervalTree
- */
-
-
-/**
-.Function.addInterval
-..summary:Adds an interval to an interval tree.
-..cat:Miscellaneous
-..class:Class.IntervalTree
-..signature:addInterval(intervalTree, interval)
-..signature:addInterval(intervalTree, begin, end)
-..signature:addInterval(intervalTree, begin, end, cargo)
-..signature:addInterval(graph, propertyMap, interval)
-..param.intervalTree:The interval tree to add the interval to.
-...type:Class.IntervalTree
-..param.interval:The interval to be added to the interval tree.
-..param.begin:Begin position of interval of type TValue.
-..param.end:End position of interval of type TValue.
-..param.cargo:Cargo to attach to the interval.
-...type:Class.IntervalAndCargo
-..param.graph:The directed graph that contains the topography of the interval tree.
-..param.propertyMap:The property map containing the node properties of the interval tree.
-..include:seqan/misc/misc_interval_tree.h
-*/
-
-template<typename TGraph, typename TPropertyMap, typename TInterval>
-void
-addInterval(TGraph & g, TPropertyMap & pm, TInterval interval)
-{
-SEQAN_CHECKPOINT
-
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Value<TPropertyMap>::Type TProperty;
-	typedef typename Value<TInterval>::Type TValue;
-	typedef typename ListType<TProperty>::Type TList;
-	
-
-	if(empty(pm))
-	{
-		TVertexDescriptor vd = addVertex(g);
-		resizeVertexMap(g,pm);
-		_setIntervalTreeNode(property(pm,vd),(rightBoundary(interval)+leftBoundary(interval))/2,interval);
-		return;
-		
-	}
-	// start at root
-	TVertexDescriptor act_knot = 0;
-	TProperty act_prop = property(pm,act_knot);
-	TProperty next_prop;
-	
-    // look for the right node to add interval to
-	while(true)
-	{
-		TOutEdgeIterator it(g, act_knot);
-		act_prop = property(pm,act_knot);
-		if(act_prop.center < leftBoundary(interval)) // interval to the left of current node?
-		{
-			if(atEnd(it)){
-				TVertexDescriptor vd = addVertex(g);
-				resizeVertexMap(g,pm);
-				addEdge(g,act_knot,vd);
-				_setIntervalTreeNode(property(pm,vd),(rightBoundary(interval)+leftBoundary(interval))/(TValue)2.0,interval);
-				break;
-			}
-			else{
-				next_prop = property(pm,targetVertex(it));
-				if(next_prop.center <= act_prop.center)
-				{
-					goNext(it);
-					if(atEnd(it)){
-						TVertexDescriptor vd = addVertex(g);
-						resizeVertexMap(g,pm);
-						addEdge(g,act_knot,vd);
-						_setIntervalTreeNode(property(pm,vd),(rightBoundary(interval)+leftBoundary(interval))/(TValue)2.0,interval);
-						break;
-					}
-				}
-			}
-			act_knot = targetVertex(it);
-		}
-		else{
-			if(rightBoundary(interval) <= act_prop.center) // interval to the right of current node?
-			{
-				if(atEnd(it)){
-					TVertexDescriptor vd = addVertex(g);
-					resizeVertexMap(g,pm);
-					addEdge(g,act_knot,vd);
-					_setIntervalTreeNode(property(pm,vd),(rightBoundary(interval)+leftBoundary(interval))/2,interval);
-					break;
-				}
-				else
-				{
-					next_prop = property(pm,targetVertex(it));
-					if(next_prop.center >= act_prop.center)
-					{
-						goNext(it);
-						if(atEnd(it)){
-							TVertexDescriptor vd = addVertex(g);
-							resizeVertexMap(g,pm);
-							addEdge(g,act_knot,vd);
-							_setIntervalTreeNode(property(pm,vd),(rightBoundary(interval)+leftBoundary(interval))/2,interval);
-							break;
-						}
-					}
-				}
-				act_knot = targetVertex(it);
-			}
-			else{ // need to create new node for interval
-				_appendIntervalTreeNodeLists(property(pm, act_knot),interval);
-				std::sort(begin(property(pm,act_knot).list1),end(property(pm,act_knot).list1),_less_compI1_ITree<typename Value<TList>::Type>);
-				std::sort(begin(property(pm,act_knot).list2),end(property(pm,act_knot).list2),_greater_compI2_ITree<typename Value<TList>::Type>);
-				break;
-			}
-		}
-	}
-
-}
-
-template<typename TValue, typename TCargo, typename TInterval>
-void
-addInterval(IntervalTree<TValue,TCargo> & itree, TInterval interval)
-{
-SEQAN_CHECKPOINT
-
-	++itree.interval_counter;
-	addInterval(itree.g,itree.pm,interval);
-
-}
-
-template<typename TValue, typename TCargo>
-void
-addInterval(IntervalTree<TValue,TCargo> & itree, TValue begin, TValue end, TCargo cargo)
-{
-SEQAN_CHECKPOINT
-
-	IntervalAndCargo<TValue,TCargo> interval;
-	interval.i1 = begin;
-	interval.i2 = end;
-	interval.cargo = cargo;
-	++itree.interval_counter;
-	addInterval(itree.g,itree.pm,interval);
-
-}
-
-template<typename TValue, typename TCargo>
-void
-addInterval(IntervalTree<TValue,TCargo> & itree, TValue begin, TValue end)
-{
-SEQAN_CHECKPOINT
-
-	IntervalAndCargo<TValue,TCargo> interval;
-	interval.i1 = begin;
-	interval.i2 = end;
-	interval.cargo = itree.interval_counter;
-	++itree.interval_counter;
-	addInterval(itree.g,itree.pm,interval);
-
-}
-
-/*!
- * @fn IntervalTree#findIntervals
- * @brief Find all intervals that contain the query point or overlap with the query interval.
- * 
- * @signature void findIntervals(intervalTree, query, result);
- * @signature void findIntervals(intervalTree, queryBegin, queryEnd, result);
- * @signature void findIntervals(graph, propertyMap, query, result);
- * 
- * @param intervalTree An interval tree Types: IntervalTree
- * @param query        A query point.
- * @param queryBegin   The begin position of the query interval.
- * @param queryEnd     The end position of the query interval.
- * @param result       A reference to the result string of <tt>TCargo</tt> objects. Types: String
- */
-
-/**
-.Function.findIntervals
-..summary:Find all intervals that contain the query point or overlap with the query interval.
-..cat:Miscellaneous
-..class:Class.IntervalTree
-..signature:findIntervals(intervalTree, query, result)
-..signature:findIntervals(intervalTree, query_begin, query_end, result)
-..signature:findIntervals(graph, propertyMap, query, result)
-..param.intervalTree:An interval tree
-...type:Class.IntervalTree
-..param.query:A query point.
-..param.query_begin:The begin position of the query interval.
-..param.query_end:The end position of the query interval.
-..param.result:A reference to the result string of $TCargo$ objects
-...type:Class.String
-..include:seqan/misc/misc_interval_tree.h
-*/
-template <typename TSpec, typename TPropertyMap, typename TValue, typename TCargo>
-inline void
-findIntervals(
-    Graph<TSpec> const & g,
-    TPropertyMap const & pm,
-    TValue query,
-    String<TCargo> & result)
-{
-SEQAN_CHECKPOINT
-
-    typedef Graph<TSpec> const TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Value<TPropertyMap>::Type TProperty;
-	typedef typename Value<TProperty>::Type TPropertyValue;
-	typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
-    
-    resize(result,0);
-    if (empty(g)) return;
-
-	// start at root
-	TVertexDescriptor act_knot = 0;
-	TProperty act_prop = property(pm,act_knot);
-	TProperty next_prop;
-		
-	while(true)
-	{
-        typename Iterator<Graph<TSpec> , OutEdgeIterator>::Type it7;
-        Iter<Graph<TSpec>, GraphIterator<InternalOutEdgeIterator<OutEdgeIterator> > > it5(g,act_knot);
-        TOutEdgeIterator it4;
-		TOutEdgeIterator it(g, act_knot);
-		act_prop = property(pm,act_knot);
-		if(act_prop.center < (TPropertyValue)query) // look in current node and right subtree
-		{
-			unsigned int i = 0;
-			while(i < length(act_prop.list2) && rightBoundary(value(act_prop.list2,i)) > (TPropertyValue)query)
-			{
-				appendValue(result,cargo(value(act_prop.list2,i)), Generous());
-				++i;	
-			}
-			if(atEnd(it)) break;
-			else{
-				next_prop = property(pm,targetVertex(it));
-				if(next_prop.center <= act_prop.center)
-				{
-					goNext(it);
-					if(atEnd(it)) break;
-				}
-			}
-			act_knot = targetVertex(it);
-		}
-		else{
-			if((TPropertyValue)query < act_prop.center) // look in current node and left subtree
-			{
-				unsigned int i = 0;
-				while(i < length(act_prop.list1) && leftBoundary(value(act_prop.list1,i)) <= (TPropertyValue)query)
-				{
-					appendValue(result,cargo(value(act_prop.list1,i)), Generous());
-					++i;
-				}
-				if(atEnd(it)) break;
-				else
-				{
-					next_prop = property(pm,targetVertex(it));
-					if(next_prop.center >= act_prop.center)
-					{
-						goNext(it);
-						if(atEnd(it)) break;
-					}
-				}
-				act_knot = targetVertex(it);
-			}
-			else{ // look in current node only, as query is center
-				for(unsigned int i = 0; i < length(act_prop.list1); ++i)
-                    appendValue(result, cargo(value(act_prop.list1,i)), Generous());
-				break;
-			}
-		}
-	}
-
-}
-
-template <typename TValue, typename TCargo>
-inline void
-findIntervals(
-    IntervalTree<TValue,TCargo> const & it,
-    TValue query,
-    String<TCargo> & result)
-{
-SEQAN_CHECKPOINT
-	findIntervals(it.g,it.pm,query,result);
-}
-
-template <typename TValue, typename TCargo>
-inline void
-findIntervals(
-    IntervalTree<TValue,TCargo> const & tree,
-    TValue query_begin,
-    TValue query_end,
-    String<TCargo> & result)
-{
-SEQAN_CHECKPOINT
-	findIntervals(tree.g,tree.pm,query_begin,query_end,result);
-}
-
-template <typename TSpec, typename TPropertyMap, typename TValue, typename TCargo>
-inline void
-findIntervals(
-    Graph<TSpec> const & g,
-    TPropertyMap const & pm,
-    TValue query_begin,
-    TValue query_end,
-    String<TCargo> & result)
-{
-    typedef Graph<TSpec> const TGraph;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-
-    resize(result,0);
-
-	// start at root
-	TVertexDescriptor act_knot = 0;
-	findIntervals(g, pm, act_knot, query_begin, query_end, result);
-}
-
-
-template <
-    typename TSpec,
-    typename TPropertyMap,
-    typename TVertexDescriptor,
-    typename TValue,
-    typename TCargo >
-inline void
-findIntervals(
-    Graph<TSpec> const & g,
-    TPropertyMap const & pm,
-    TVertexDescriptor & act_knot,
-    TValue query_begin, 
-    TValue query_end, 
-    String<TCargo> & result)
-{
-SEQAN_CHECKPOINT
-
-	typedef typename Value<TPropertyMap>::Type TProperty;
-	typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
-
-    if (empty(g)) return;
-
-    TProperty act_prop = property(pm,act_knot);
-	TProperty next_prop;
-		
-	while(true)
-	{
-		TOutEdgeIterator it(g, act_knot);
-		act_prop = property(pm,act_knot);
-		//
-		if(act_prop.center < query_begin) // query interval is to the right of node center
-		{
-			unsigned int i = 0;
-			while(i < length(act_prop.list2) && rightBoundary(value(act_prop.list2,i)) > query_begin)
-			{
-				appendValue(result,cargo(value(act_prop.list2,i)), Generous());
-				++i;	
-			}
-			if(atEnd(it)) break;
-			else{
-				next_prop = property(pm,targetVertex(it));
-				if(next_prop.center <= act_prop.center)
-				{
-					goNext(it);
-					if(atEnd(it)) break;
-				}
-			}
-			act_knot = targetVertex(it);
-		}
-		else{
-			if(query_end <= act_prop.center) // query interval is to the left of node center
-			{
-				unsigned int i = 0;
-				while(i < length(act_prop.list1) && leftBoundary(value(act_prop.list1,i)) < query_end)
-				{
-					appendValue(result,cargo(value(act_prop.list1,i)), Generous());
-					++i;
-				}
-				if(atEnd(it)) break;
-				else
-				{
-					next_prop = property(pm,targetVertex(it));
-					if(next_prop.center >= act_prop.center)
-					{
-						goNext(it);
-						if(atEnd(it)) break;
-					}
-				}
-				act_knot = targetVertex(it);
-			}
-			else{//node center is contained in query interval
-				for(unsigned int i = 0; i < length(act_prop.list1); ++i)
-                    appendValue(result, cargo(value(act_prop.list1,i)), Generous());
-				
-				while(!atEnd(it))
-				{
-					TVertexDescriptor next_knot = targetVertex(it);
-					findIntervals(g,pm, next_knot, query_begin, query_end, result);
-					goNext(it);
-				}
-				break;
-
-				//break; //dont break! continue in both subtrees!!
-			}
-		}
-	}
-}
-
-/*!
- * @fn IntervalTree#findIntervalsExcludeTouching
- * @brief Find all intervals that contain the query point, exclude intervals that touch the query, i.e. where the query
- *        point equals the start or end point.
- * 
- * @signature void findIntervalsExcludeTouching(intervalTree, query, result);
- * @signature void findIntervalsExcludeTouching(graph, propertyMap, query, result);
- * 
- * @param graph        The directed graph that contains the topography of the interval tree.
- * @param query        The TValue to query here.
- * @param propertyMap  The property map containing the node properties of the interval tree
- * @param result       The resulting string of cargos/ids of the intervals that contain the query point.  Should
- *                     be a string of TCargo. Types: String
- * @param intervalTree An interval tree Types: IntervalTree
- */
-
-/**
-.Function.findIntervalsExcludeTouching
-..summary:Find all intervals that contain the query point, exclude intervals that touch the query, i.e. where the query point equals the start or end point.
-..signature:findIntervalsExcludeTouching(intervalTree, query, result)
-..signature:findIntervalsExcludeTouching(graph, propertyMap, query, result)
-..cat:Miscellaneous
-..class:Class.IntervalTree
-..param.intervalTree:An interval tree
-...type:Class.IntervalTree
-..param.graph:The directed graph that contains the topography of the interval tree.
-..param.propertyMap:The property map containing the node properties of the interval tree
-..param.query:The TValue to query here.
-..param.result:The resulting string of cargos/ids of the intervals that contain the query point.
-...type:Class.String
-...remarks:Should be a string of TCargo.
-..include:seqan/misc/misc_interval_tree.h
-*/
-template <typename TSpec, typename TPropertyMap, typename TValue, typename TCargo>
-inline void
-findIntervalsExcludeTouching(
-    Graph<TSpec> const & g,
-    TPropertyMap const & pm,
-    TValue query,
-    String<TCargo> & result)
-{
-SEQAN_CHECKPOINT
-
-    typedef Graph<TSpec> const TGraph;
-	typedef typename Iterator<TGraph, OutEdgeIterator >::Type TOutEdgeIterator;
-	typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
-	typedef typename Value<TPropertyMap>::Type TProperty;
-	
-	resize(result,0);
-    if (empty(g)) return;
-
-	// start at root
-	TVertexDescriptor act_knot = 0;
-	TProperty act_prop = property(pm,act_knot);
-	TProperty next_prop;
-		
-	while(true)
-	{
-		TOutEdgeIterator it(g, act_knot);
-		act_prop = property(pm,act_knot);
-		if( (TValue) act_prop.center < query) // look in current node and right subtree
-		{
-			int i = 0;
-			while(i < (int) length(act_prop.list2) && (TValue) rightBoundary(value(act_prop.list2,i)) > query)
-			{
-				appendValue(result,cargo(value(act_prop.list2,i)), Generous());
-				++i;	
-			}
-			if(atEnd(it)) break;
-			else{
-				next_prop = property(pm,targetVertex(it));
-				if(next_prop.center <= act_prop.center)
-				{
-					goNext(it);
-					if(atEnd(it)) break;
-				}
-			}
-			act_knot = targetVertex(it);
-		}
-		else{
-			if(query < (TValue) act_prop.center) // look in current node and left subtree
-			{
-				int i = 0;
-				while(i < (int) length(act_prop.list1) && (TValue) leftBoundary(value(act_prop.list1,i)) < query)
-				{
-					appendValue(result,cargo(value(act_prop.list1,i)), Generous());
-					++i;
-				}
-				if(atEnd(it)) break;
-				else
-				{
-					next_prop = property(pm,targetVertex(it));
-					if(next_prop.center >= act_prop.center)
-					{
-						goNext(it);
-						if(atEnd(it)) break;
-					}
-				}
-				act_knot = targetVertex(it);
-			}
-			else{ // look in current node only
-				int i = 0;
-				while(i < (int) length(act_prop.list1) && (TValue) leftBoundary(value(act_prop.list1,i)) < query)
-				{
-					appendValue(result,cargo(value(act_prop.list1,i)), Generous());
-					++i;
-				}
-				break;
-			}
-		}
-	}
-
-}
-
-template <typename TValue, typename TCargo>
-inline void
-findIntervalsExcludeTouching(
-    IntervalTree<TValue,TCargo> const & tree,
-    TValue query,
-    String<TCargo> & result)
-{
-SEQAN_CHECKPOINT
-	findIntervalsExcludeTouching(tree.g,tree.pm,query,result);
-}
-
-/*!
- * @fn IntervalTree#removeInterval
- * @brief Removes an interval from the interval tree.
- * 
- * @signature bool removeInterval(intervalTree, iBegin, iEnd, iId);
- * 
- * @param intervalTree An interval tree Types: IntervalTree
- * @param iBegin       The begin position of the interval to be removed.
- * @param iEnd         The end position of the interval to be removed.
- * @param iId          The ID of the interval to be removed.
- *
- * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
- */
-
-/**
-.Function.removeInterval
-..summary:Removes an interval from the interval tree.
-..signature:removeInterval(intervalTree, i_begin, i_end, i_id)
-..cat:Miscellaneous
-..class:Class.IntervalTree
-..param.intervalTree:An interval tree
-...type:Class.IntervalTree
-..param.i_begin:The begin position of the interval to be removed.
-..param.i_end:The end position of the interval to be removed.
-..param.i_id:The ID of the interval to be removed.
-*/
-
-template <
-    typename TSpec,
-    typename TPropertyMap,
-    typename TVertexDescriptor,
-    typename TValue,
-    typename TCargo >
-inline bool
-removeInterval(
-    Graph<TSpec> & g,
-    TPropertyMap & pm, 
-    TVertexDescriptor & act_knot, 
-    TValue i_begin, 
-    TValue i_end,
-    TCargo i_id)
-{
-SEQAN_CHECKPOINT
-
-	typedef typename Value<TPropertyMap>::Type TProperty;
-	typedef typename ListType<TProperty>::Type TList;
-	typedef typename Iterator<TList, Standard>::Type TListIterator;
-	typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type TOutEdgeIterator;
-
-    if (empty(g)) return false;
-
-    TProperty act_prop = property(pm,act_knot);
-	TProperty next_prop;
-		
-	while(true)
-	{
-		TOutEdgeIterator it(g, act_knot);
-		act_prop = property(pm,act_knot);
-		//
-		if(act_prop.center < i_begin) // interval is to the right of node center
-		{
-			if(atEnd(it)) break;
-			else{
-				next_prop = property(pm,targetVertex(it));
-				if(next_prop.center <= act_prop.center)
-				{
-					goNext(it);
-					if(atEnd(it)) break;
-				}
-			}
-			act_knot = targetVertex(it);
-		}
-		else{
-			if(i_end < act_prop.center) // interval is to the left of node center
-			{
-				if(atEnd(it)) break;
-				else
-				{
-					next_prop = property(pm,targetVertex(it));
-					if(next_prop.center >= act_prop.center)
-					{
-						goNext(it);
-						if(atEnd(it)) break;
-					}
-				}
-				act_knot = targetVertex(it);
-			}
-			else{//node center is contained in interval, this is where we should find the interval to be removed
-                // remove from list1
-                TProperty& change_prop = property(pm,act_knot);
-                bool foundInLeft = false;
-                TListIterator list_it_keep = begin(change_prop.list1,Standard());
-                TListIterator list_it = begin(change_prop.list1,Standard());
-				while(list_it != end(change_prop.list1,Standard()))
-                {
-                    //std::cout << "Element: " << getLeftBoundary(*list_it) << ".." << getRightBoundary(*list_it) << " " << cargo(*list_it) << std::endl;
-                    if (getLeftBoundary(*list_it) == i_begin && cargo(*list_it) == i_id)
-                    {
-                        foundInLeft = true;
-                        ++list_it;
-                        continue;
-                    }
-                    *list_it_keep = *list_it;
-                    //std::cout << "Element keep: " << getLeftBoundary(*list_it_keep) << ".." << getRightBoundary(*list_it_keep) << " " << cargo(*list_it_keep) << std::endl;
-                    ++list_it; ++list_it_keep;
-                }
-
-	            bool foundInRight = false;
-                list_it_keep = begin(change_prop.list2,Standard());
-                list_it = begin(change_prop.list2,Standard());
-				while(list_it != end(change_prop.list2,Standard()))
-                {
-                    //std::cout << "Element: " << getLeftBoundary(*list_it) << ".." << getRightBoundary(*list_it) << " " << cargo(*list_it) << std::endl;
-                    if (getRightBoundary(*list_it) == i_end && cargo(*list_it) == i_id)
-                    {
-                        foundInRight = true;
-                        ++list_it;
-                        continue;
-                    }
-                    *list_it_keep = *list_it;
-                    //std::cout << "Element keep: " << getLeftBoundary(*list_it_keep) << ".." << getRightBoundary(*list_it_keep) << " " << cargo(*list_it_keep) << std::endl;
-                    ++list_it; ++list_it_keep;
-
-                }
-                
-
-                // TODO: if node is empty and does not have child nodes --> remove node.
-                // keeping these empty leaf nodes just takes space unnecessarily
-				if(foundInRight && foundInLeft)
-                {
-                    resize(change_prop.list2, length(change_prop.list2)-1);
-                    resize(change_prop.list1, length(change_prop.list1)-1);
-                    return true;
-                }
-
-			}
-		}
-	}
-    return false;
-}
-
-template <
-    typename TSpec,
-    typename TPropertyMap,
-    typename TValue,
-    typename TCargo >
-inline bool
-removeInterval(
-    Graph<TSpec> & g,
-    TPropertyMap & pm,
-    TValue i_begin,
-    TValue i_end,
-    TCargo i_id)
-{
-SEQAN_CHECKPOINT
-
-	typedef typename VertexDescriptor<Graph<TSpec> >::Type TVertexDescriptor;
-
-	// start looking at root
-	TVertexDescriptor act_knot = 0;
-	return removeInterval(g, pm, act_knot, i_begin, i_end, i_id);
-}
-
-template <typename TValue, typename TCargo>
-inline bool
-removeInterval(
-    IntervalTree<TValue,TCargo> & tree,
-    TValue i_begin,
-    TValue i_end,
-    TCargo i_id)
-{
-SEQAN_CHECKPOINT
-
-	return removeInterval(tree.g, tree.pm, i_begin, i_end, i_id);
-    // we do not decrease the interval_counter of tree, as it would mix up interval IDs
-}
-
-
-
-
-/////////////////// Metafunctions ///////////////////////
-
-///.Metafunction.Value.param.T.type:Class.IntervalTree
-template<typename TValue, typename TCargo>
-struct Value<IntervalTree<TValue,TCargo> >
-{
-	typedef TValue Type;
-};
-
-
-///.Metafunction.Cargo.param.T.type:Class.IntervalTree
-template<typename TValue, typename TCargo>
-struct Cargo<IntervalTree<TValue,TCargo> >
-{
-	typedef TCargo Type;
-};
-
-}  // namespace SEQAN_NAMESPACE_MAIN
-
-#endif  //#ifndef SEQAN_MISC_INTERVAL_TREE_H
diff --git a/seqan/misc/misc_map.h b/seqan/misc/misc_map.h
deleted file mode 100644
index e52268d..0000000
--- a/seqan/misc/misc_map.h
+++ /dev/null
@@ -1,218 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-// ==========================================================================
-// Note that this file originally did not compile.  Me (holtgrew) change it
-// it it compiled.  However, it might not make sense to fix it so it actually
-// works.
-// ==========================================================================
-
-//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
-
-#ifndef SEQAN_HEADER_MISC_MAP_H
-#define SEQAN_HEADER_MISC_MAP_H
-
-#include <algorithm>
-#include "misc_base.h"
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-	//////////////////////////////////////////////////////////////////////////////
-	//
-
-	template <typename TPair>
-	inline typename TPair::T1 & keyOf(TPair &pair) {
-		return getValueI1(pair);
-	}
-	template <typename TPair>
-	inline typename TPair::T1 const & keyOf(TPair const &pair) {
-		return getValueI1(pair);
-	}
-	template <typename TPair>
-	inline typename TPair::T2 & objectOf(TPair &pair) {
-		return getValueI2(pair);
-	}
-	template <typename TPair>
-	inline typename TPair::T2 const & objectOf(TPair const &pair) {
-		return getValueI2(pair);
-	}
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	//
-
-	template <typename TString, typename TLess = ::std::less<typename Value<TString>::Type::T1> >
-	struct SequenceMap;
-
-
-	template <typename TString>
-	struct Value< SequenceMap<TString> > {
-		typedef typename Value<TString>::Type Type;
-	};
-	template <typename TString>
-	struct Size< SequenceMap<TString> > {
-		typedef typename Size<TString>::Type Type;
-	};
-
-	template <typename TString>
-	inline typename Size< SequenceMap<TString> >::Type length(SequenceMap<TString> const &set) {
-		return length(set.string);
-	}
-
-
-
-	template <typename TKey, typename TObject, typename TSpec, typename TLess>
-	struct SequenceMap< String< Pair<TKey, TObject>, TSpec >, TLess > {
-		typedef Pair<TKey, TObject>						TValue;
-		typedef String< Pair<TKey, TObject>, TSpec >	TSequence;
-		typedef typename TSequence::size_type				TSize;
-
-		TKey				maxKey;
-		TLess				comp;
-		Holder<TSequence>	string;
-
-		SequenceMap():
-			maxKey(0)	{}
-
-		SequenceMap(TLess const &_comp):
-			maxKey(0),
-			comp(_comp) {}
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	//
-
-//	template <typename TKey>
-//	struct Map {
-//		typedef ::std::map<TKey> Type;
-//	};
-	template <typename TKey, typename TObject>
-	class Map< Pair<TKey, TObject> > {
-//		typedef ::std::set< Pair<TKey, TObject>, SetLess< Pair<TKey, TObject> > > Type;
-	};
-
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	//
-
-	template <typename TString, typename TLess>
-	struct Iterator< SequenceMap<TString, TLess> > {
-		typedef typename Iterator<TString>::Type	Type;
-	};
-
-	template <typename TString, typename TLess>
-	struct Iterator< SequenceMap<TString, TLess> const > {
-		typedef typename Iterator<TString const>::Type	Type;
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	//
-
-	template <typename TString, typename TLess>
-	inline void clear(SequenceMap<TString, TLess> &map) {
-		clear(map.string);
-		map.maxKey = 0;
-	}
-
-	template <typename TKey, typename TString, typename TLess>
-	inline typename Iterator< SequenceMap<TString, TLess> >::Type find(TKey const &key, SequenceMap<TString, TLess> &map) {
-
-		typedef typename Size< SequenceMap<TString, TLess> >::Type		TSize;
-		typedef typename Iterator< SequenceMap<TString, TLess> >::Type	TIter;
-		
-		// accelerate binary search
-		if (map.comp(map.maxKey, key))
-			return end(map.string);
-
-		TIter First_ = begin(map.string);
-		TSize Count_ = end(map.string) - First_;
-
-		for (; 0 < Count_; )
-		{	// divide and conquer, find half that contains answer
-			TSize Count2_ = Count_ / 2;
-			TIter Mid_ = First_ + Count2_;
-
-			if (map.comp((*Mid_).i1, key))
-				First_ = ++Mid_, Count_ -= Count2_ + 1;
-			else
-				Count_ = Count2_;
-		}
-		return (First_);
-	}
-
-	template <typename TPair, typename TString, typename TLess>
-	inline void insert(TPair &pair, SequenceMap<TString> &map)
-	{
-		typedef typename Iterator< SequenceMap<TString, TLess> >::Type	TIter;
-
-		// accelerate binary search
-		if (map.comp(map.maxKey, pair.i1)) {
-// whatever
-			map.maxKey = pair.i1;
-			return append(map.string);
-		}
-
-		TIter iter = find(pair.i1, map);
-// whatever
-		insert(pair, map);
-	}
-
-
-	template <typename TKey, typename TString>
-	inline void erase(TKey const &/*key*/, SequenceMap<TString> &/*map*/)
-	{
-            // TODO(holtgrew): Commented out the following, no idea how to make it work.
-            /* 
-		if (!max.comp(map.maxKey, key) && !max.comp(key, map.maxKey)) {
-			// delete last element
-			if (length(map.string))
-				map.maxKey = *(map.string.end() - 1).i2;
-			else
-				map.maxKey = 0;
-		}
-
-		typedef typename Iterator< SequenceMap<TString, TLess> >::Type	TIter;
-		TIter iter = find(pair.i1, map);
-		delete iter;
-            */
-	}
-}
-
-#endif
-
diff --git a/seqan/misc/misc_parsing.h b/seqan/misc/misc_parsing.h
deleted file mode 100644
index 6f2f157..0000000
--- a/seqan/misc/misc_parsing.h
+++ /dev/null
@@ -1,723 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
-
-#ifndef SEQAN_HEADER_MISC_PARSING_H
-#define SEQAN_HEADER_MISC_PARSING_H
-
-#include <cmath>
-
-/* IOREV
- *
- * _tested_
- * _nodoc_
- *
- *
- * used in different places
- * except one function non are documented
- *
- * NOTE atof is used in some functions, but according to standard this is
- * locale dependent (',' or '.' as decimal seperator). Has someone experienced
- * issues with this? we should probably replace it with a local independent
- * version to make sure
- *
- * Also in general atof should be replaced with strod, atoi with strtol etc
- *
- * it should also be noted that there are standard C functions in ctype.h
- * for the _is* cases, e.g. isspace(), isdigit() isprint(), isalnum() etc
- * why don't we use these?
- *
- * when returning a string we should remember to always use Generous() as
- * resize policy to avoid some reallocation efforts (some parsing functions
- * do this already, others don't)
- * 
- */
-
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// General parsing funtions
-//////////////////////////////////////////////////////////////////////////////
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TChar>
-inline void 
-_parseSkipLine(TFile& file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ treats \n as EOL 
-	if (c == '\n') {
-		c = _streamGet(file);
-		return;
-	}
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (c == '\n') break;
-	}
-	c = _streamGet(file);
-}
-//////////////////////////////////////////////////////////////////////////////
-
-
-template<typename TFile, typename TChar>
-inline void 
-_parseSkipWhitespace(TFile& file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ _bug_ WRONG NAME, should be parseSkipNonprintable, but even that is wrong, because printable begins at c >= 32 not c > 32, also 127 (DEL) is non-printable; name does not indicate whether multiple chars are skipped or only one
-	if ((unsigned) c > 32) return;
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if ((unsigned) c > 32) break;
-	}
-}
-
-template<typename TFile, typename TChar>
-inline void 
-_parseSkipSpace(TFile& file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ WRONG NAME: should be _parseSkipSpaceTab; name does not indicate whether multiple chars are skipped or only one
-	if (c != '\t' && c != ' ') return;
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (c != '\t' && c != ' ') break;
-	}
-}
-
-
-/**
-.Internal._parseSkipUntilChar:
-..summary:Skip to the next ocurrence of x in file.
-..cat:Miscenalleous
-..signature:_parseSkipUntilChar(file, x, c)
-..param.file:The file to read from.
-..param.x:The character to skip to.
-..param.c:Parser state character.
- */
-template<typename TFile, typename TChar>
-inline void 
-_parseSkipUntilChar(TFile& file, const TChar &x, TChar& c)
-{
-//IOREV _doc_ _hasCRef_ _duplicate_ use _parseUntil() instead
-	if (c == x) return;
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (c == x) break;
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TChar>
-inline bool
-_parseIsWhiteSpace(TChar const c)
-{
-//IOREV _nodoc_ lacks Ref, maybe rename to _is* because there is no fileparsing
-    return ((unsigned char)c <= ' ');
-}
-
-
-template<typename TChar>
-inline bool
-_parseIsDigit(TChar const c)
-{
-//IOREV _nodoc_ lacks Ref, maybe rename to _is* because there is no fileparsing
-	return (((unsigned) c >  47) && ((unsigned) c <  58));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TChar>
-inline bool
-_parseIsLetter(TChar const c)
-{
-//IOREV _nodoc_ lacks Ref, maybe rename to _is* because there is no fileparsing
-	return ( (((unsigned) c > 64) && ((unsigned) c < 91)) || (((unsigned) c > 96) && ((unsigned) c < 123)) );
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-// TODO(holtgrew): The name of this function is WRONG.
-template<typename TChar>
-inline bool
-_parseIsAlphanumericChar(TChar const c)
-{
-//IOREV _nodoc_ _bug_ lacks Ref; maybe rename to _is* because there is no fileparsing; rename to sth that describes this regex, ITS NOT alphnumeric
-	return ((_parseIsDigit(c)) || (_parseIsLetter(c)) || (c == '_') || (c == '.') || (c == '-') || (c == '|') || (c == '/') || (c == ':'));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TChar>
-inline int
-_parseReadNumber(TFile & file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ rename to something more generic, e.g. parseInt; strtol() / strtoll() is recommended over atoi in C99
-	// Read number
-	String<char> str(c);
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (!_parseIsDigit(c)) break;
-		append(str, c);
-	}
- 	return atoi(toCString(str));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TChar>
-inline double
-_parseReadDouble(TFile & file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ rename to something more generic, e.g. parseDouble; _bug_ allows multiple dots in one number; strtod is recommended over atof in C99
-	// Read number
-	String<char> str(c);
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (!_parseIsDigit(c) && (c != '.')) break;
-		append(str, c);
-	}
- 	return atof(toCString(str));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TChar>
-inline String<char>
-_parseReadIdentifier(TFile & file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ rename to something more specific (is this related to FASTA?)
-	// Read identifier
-	String<char> str(c);
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (!_parseIsAlphanumericChar(c)) break;
-		append(str, c);
-	}
-	return str;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TChar>
-inline char
-_parseReadChar(TFile & file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ what exactly is the point of this?
-    char result = c;
-    if (!_streamEOF(file))
-        c = _streamGet(file);
-    return result;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TString, typename TChar>
-inline void
-_parseReadIdentifier(TFile & file, TString& str, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ _duplicate_ or just:  str = _parseReadIdentifier(file, c) ?
-	// Read identifier
-	append(str, c, Generous());
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (!_parseIsAlphanumericChar(c)) break;
-		append(str, c, Generous());
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TString, typename TChar>
-inline void
-_parseReadAlnum(TFile & file, TString& str, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ _duplicate_ or just:  str = _parseReadIdentifier(file, c) ?
-	// Read identifier
-	appendValue(str, c, Generous());
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-        if (!isalnum(c))
-            break;
-		appendValue(str, c, Generous());
-	}
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TChar>
-inline String<char>
-_parseReadWord(TFile & file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ rename to _parseLetters()
-	// Read word
-	String<char> str(c);
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (!_parseIsLetter(c)) break;
-		append(str, c);
-	}
-	return str;
-}
-
-
-// parse word up to a maximum length
-template<typename TFile, typename TChar, typename TSize>
-inline String<char>
-_parseReadWord(TFile & file, TChar& c, TSize max_len)
-{
-//IOREV _nodoc_ _hasCRef_ rename to _parseNLetters()
-	// Read word
-	String<char> str(c);
-	--max_len;
-	TSize i = 0;
-	while (!_streamEOF(file) ) {
-		c = _streamGet(file);
-		if (!_parseIsLetter(c) || i >= max_len) break;
-		append(str, c);
-		++i;
-	}
-	return str;
-}
-
-
-
-
-//read filename (read line and trim trailing whitespaces)
-template<typename TFile, typename TChar>
-inline String<char>
-_parseReadFilepath(TFile& file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ rename to something more generic _parseLineStripTrailingWhitespace; simplify code
-	String<char> str(c);
-	if (c == '\n' || (c == '\r' && _streamPeek(file) != '\n')) {
-		c = _streamGet(file);
-		return str;
-	}
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (c == '\n' || (c == '\r' && _streamPeek(file) != '\n')) break;
-		append(str, c);
-	}
-	typename Iterator<String<char>,Rooted >::Type str_it = end(str);	
-	while(str_it != begin(str)) {
-		--str_it;
-		if(*str_it != ' ' && *str_it != '\t'){
-		++str_it;
-		break;
-		}
-	}
-	resize(str,position(str_it));
-	return str;
-}
-
-
-// read filename (read line and trim trailing whitespaces)
-// OBSOLETE
-template<typename TFile, typename TChar>
-inline String<char>
-_parseReadWordUntilWhitespace(TFile& file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ rename to _parseCharsUntilWhitespace(); simplify code and use proper whitespace definition
-	String<char> str(c);
-	if (c == '\n' || (c == '\r' && _streamPeek(file) != '\n')) {
-		c = _streamGet(file);
-		return str;
-	}
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (c== ' ' || c== '\t' || c == '\n' || (c == '\r' && _streamPeek(file) != '\n')) break;
-		append(str, c);
-	}
-	return str;
-}
-
-// better use this function instead of _parseReadWordUntilWhitespace
-template<typename TFile, typename TChar, typename TString>
-inline void
-_parseCharsUntilWhitespace(TFile & file, TChar& c, TString & str)
-{
-//IOREV _nodoc_ _hasCRef_
-    if (_parseIsWhiteSpace(c)) return;
-    appendValue(str, c);
-    while (!_streamEOF(file)) 
-    {
-        c = _streamGet(file);
-        if (_parseIsWhiteSpace(c)) return;
-        appendValue(str, c);
-    }
-}
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template<typename TFile, typename TChar, typename TString>
-inline void
-_parseReadSequenceData(TFile & file,
-						TChar & c,
-						TString& str)
-{
-//IOREV _nodoc_ _hasCRef_ _duplicate_ use _parseReadWord instead
-	SEQAN_CHECKPOINT
-
-	append(str, c);
-
-	// Read sequence
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (!_parseIsLetter(c)) break;
-		else append(str, c);
-	}
-}
-
-
-
-template<typename TFile, typename TChar>
-inline void 
-_parseSkipBlanks(TFile& file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ what is a blank? change to whitespace or define blank as (' '|'\t') 
-	if ((c != ' ') && (c != '\t')) return;
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if ((c != ' ') && (c != '\t')) break;
-	}
-}
-
-template<typename TFile, typename TChar>
-inline void 
-_parseSkipLine2(TFile& file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ _duplicate_ obviously duplicate, but different (non-expected) behaviour: will return '\n' not 'f' of string f o o \r \n b a r
-	if (c != '\n' && c != '\r')
-		while (!_streamEOF(file)) {
-			c = _streamGet(file);
-			if (c == '\n' || c == '\r') break;
-		}
-	if (!_streamEOF(file))
-		c = _streamGet(file);
-}
-
-
-
-//////////////////////////////////////////////////////////////////////////////
-template<typename TFile, typename TChar>
-inline double
-_parseReadEValue(TFile & file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ probably for blast-parsing, rename to resemble this; use strtod instead of atofs
-SEQAN_CHECKPOINT
-
-	// Read number
-	String<char> str(c);
-	bool e = false;
-	double val1 = 0;
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if(!e && c == 'e'){
-			e = true;
-			val1 = atof(toCString(str));
-			c = _streamGet(file);
-			resize(str,0);
-		}
-		if (!_parseIsDigit(c) && c != '.' && c != '-' && c != '+') break;
-		append(str, c);
-	}
-	if(e)
-	{
-		return val1 * pow((double)10.0,(double)atof(toCString(str)));
-	}	
- 	else 
-		return (double)atof(toCString(str));
-}
-
-
-
-
-
-/////////////////////////////////////////////////////////////////////////////////
-// read floating point value
-template<typename TFile, typename TChar>
-inline float
-_parseReadFloat(TFile & file, TChar& c)
-{
-//IOREV _nodoc_ _hasCRef_ _duplicate_ use _parseReadDouble() instead.   
-SEQAN_CHECKPOINT
-	// Read number
-	String<char> str(c);
-	while (!_streamEOF(file)) {
-		c = _streamGet(file);
-		if (c != '.' && c != ',' && !_parseIsDigit(c)) break;
-		append(str, c);
-	}
- 	return atof(toCString(str));
-}
-
-
-
-
-/////////////////////////////////////////////////////////////////////////////////
-//parse until line begins with character x (skip whitespaces)
-// zeigt am ende darauf!!!
-template<typename TFile, typename TChar>
-inline bool
-_parseUntilBeginLine(TFile & file, TChar& c, TChar x)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ rename to something more understandable; does a "reset", if seek fails; unify behaviour and doc with similar functions
-SEQAN_CHECKPOINT
-	_parseSkipWhitespace(file,c);
-	typename Position<TFile>::Type pos = _streamTellG(file);
-	TChar c_before = c;
-	while (!_streamEOF(file) && c != x){
-		_parseSkipLine(file, c);
-		_parseSkipWhitespace(file,c);
-	}
-	if(!_streamEOF(file)) return true;
-	_streamSeekG(file,pos);
-	c = c_before;
-	return false;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////
-//parse until line begins with word
-//zeigt am ende dahinter!
-template<typename TFile, typename TChar, typename TSize>
-inline bool
-_parseUntilBeginLine(TFile & file, TChar& c, String<TChar> & word, TSize len)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ rename to something more understandable; does a "reset", if seek fails; unify behaviour and doc with similar functions
-SEQAN_CHECKPOINT
-	_parseSkipWhitespace(file,c);
-	typename Position<TFile>::Type pos = _streamTellG(file);
-	TChar c_before = c;
-	while (!_streamEOF(file)){
-		if(c == word[0])
-			if(word == _parseReadWord(file,c,len))
-				break;
-		_parseSkipLine(file, c);
-		_parseSkipWhitespace(file,c);
-	}
-	if(!_streamEOF(file)) return true;
-	_streamSeekG(file,pos);
-	c = c_before;
-	return false;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////
-//parse until line begins with word (parse no more than num_lines lines)
-//zeigt am ende dahinter!
-template<typename TFile, typename TChar, typename TSize>
-inline bool
-_parseUntilBeginLine(TFile & file, TChar& c, String<TChar> & word, TSize len, TSize num_lines)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ rename to something more understandable; does a "reset", if seek fails; unify behaviour and doc with similar functions
-SEQAN_CHECKPOINT
-	_parseSkipWhitespace(file,c);
-	typename Position<TFile>::Type pos = _streamTellG(file);
-	TChar c_before = c;
-	TSize i = 0;
-	bool found = false;
-	while (!_streamEOF(file)){
-		if(c == word[0])
-			if(word == _parseReadWord(file,c,len))
-			{
-				found = true;
-				break;
-			}
-		if(i >= num_lines)
-			break;
-		++i;
-		_parseSkipLine(file, c);
-		_parseSkipWhitespace(file,c);
-	}
-	if(!_streamEOF(file) && found) return true;
-	_streamSeekG(file,pos);
-	c = c_before;
-	return false;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////
-//parse until line begins with one of the characters in string x (skip whitespaces)
-//zeigt am ende darauf!
-template<typename TFile, typename TChar, typename TSize>
-inline bool
-_parseUntilBeginLineOneOf(TFile & file, TChar& c, String<TChar> & x, TSize len)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ rename to something more understandable; does a "reset", if seek fails; unify behaviour and doc with similar functions
-SEQAN_CHECKPOINT
-	_parseSkipWhitespace(file,c);
-	typename Position<TFile>::Type pos = _streamTellG(file);
-	TChar c_before = c;
-	bool found = false;
-	while (!_streamEOF(file)){
-		for(int i = 0; i < len; ++i)
-			if(c == x[i]) 
-			{
-				found = true;
-				break;
-			}
-		if(found) break;
-		_parseSkipLine(file, c);
-		_parseSkipWhitespace(file,c);
-	}
-	if(!_streamEOF(file)) return true;
-	_streamSeekG(file,pos);
-	c = c_before;
-	return false;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////
-//parse until c == x
-//zeigt am ende darauf!
-template<typename TFile, typename TChar>
-inline bool
-_parseUntil(TFile & file, TChar& c, TChar x)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ does "reset" if x not found
-SEQAN_CHECKPOINT
-	typename Position<TFile>::Type pos = _streamTellG(file);
-	TChar c_before = c;
-	while (!_streamEOF(file) && c != x){
-		c = _streamGet(file);
-	}
-	if(!_streamEOF(file)) return true;
-	_streamSeekG(file,pos);
-	c = c_before;
-	return false;
-}
-
-
-
-/////////////////////////////////////////////////////////////////////////////////
-//parse until word
-//zeigt am ende dahinter!
-template<typename TFile, typename TChar, typename TSize>
-inline bool
-_parseUntil(TFile & file, TChar& c, String<TChar> & word, TSize len)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ does "reset" if word not found
-SEQAN_CHECKPOINT
-	typename Position<TFile>::Type pos = _streamTellG(file);
-	TChar c_before = c;
-	while (!_streamEOF(file)){
-		if(c == word[0])
-			if(word == _parseReadWord(file,c,len))
-				break;
-		c = _streamGet(file);
-	}
-	if(!_streamEOF(file)) return true;
-	_streamSeekG(file,pos);
-	c = c_before;
-	return false;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////
-//parse until c == x or new line
-//zeigt am ende darauf!
-template<typename TFile, typename TChar>
-inline bool
-_parseLineUntil(TFile & file, TChar& c, TChar x)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ does "reset" if x not found in line
-SEQAN_CHECKPOINT
-	typename Position<TFile>::Type pos = _streamTellG(file);
-	TChar c_before = c;
-	while (!_streamEOF(file) && c != x){
-		if (c == '\n' || c == '\r')
-		{
-			_streamSeekG(file,pos);
-			c = c_before;
-			return false;
-		}
-		c = _streamGet(file);
-	}
-	if(!_streamEOF(file)) return true;
-	_streamSeekG(file,pos);
-	c = c_before;
-	return false;
-}
-
-
-/////////////////////////////////////////////////////////////////////////////////
-//parse this line until word
-//zeigt am ende hinter wort if true, oder auf ende der zeile
-template<typename TFile, typename TChar, typename TSize>
-inline bool
-_parseLineUntil(TFile & file, TChar& c, String<TChar> & word, TSize len)
-{
-//IOREV _nodoc_ _hasCRef_ _requiresSeek_ does "reset" if word not found in line
-SEQAN_CHECKPOINT
-	typename Position<TFile>::Type pos = _streamTellG(file);
-	TChar c_before = c;
-	while (!_streamEOF(file)){
-		if(c == word[0])
-		{	if(word == _parseReadWord(file,c,len))
-				break;
-		}
-		else if (c == '\n' || c == '\r')
-			{
-				_streamSeekG(file,pos);
-				c = c_before;
-				return false;
-			}
-		c = _streamGet(file);
-	}
-	if(!_streamEOF(file)) return true;
-	_streamSeekG(file,pos);
-	c = c_before;
-	return false;
-}
-
-
-
-
-
-
-}
-
-#endif
-
diff --git a/seqan/misc/misc_set.h b/seqan/misc/misc_set.h
deleted file mode 100644
index c515463..0000000
--- a/seqan/misc/misc_set.h
+++ /dev/null
@@ -1,608 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_MISC_SET_H
-#define SEQAN_HEADER_MISC_SET_H
-
-#include <set>
-#include <seqan/misc/misc_base.h>
-
-//////////////////////////////////////////////////////////////////////////////
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-	//////////////////////////////////////////////////////////////////////////////
-	// 
-	//	VectorSet_
-	// 
-	//////////////////////////////////////////////////////////////////////////////
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// forward declaration
-
-	template <typename TElement, typename TSpec>
-	class VectorSet_;
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// internal set meta-functions
-
-	template <typename TElement>
-	struct VectorSetKeySize_ {
-		enum { VALUE = ValueSize< typename Key<TElement>::Type >::VALUE };
-	};
-
-
-	template <typename TSet>
-	struct SetSetVector_ {
-		typedef void* Type;
-	};
-	template <typename TElement, typename TSpec>
-	struct SetSetVector_< VectorSet_<TElement, TSpec> > {
-		typedef String<bool, TSpec> Type;
-	};
-	template <typename TSet>
-	struct SetSetVector_<TSet const> {
-		typedef typename SetSetVector_<TSet>::Type const Type;
-	};
-
-
-
-	template <typename TSet>
-	struct SetObjVector_ {
-		typedef void* Type;
-	};
-	template <typename TKey, typename TObject, typename TPairSpec, typename TSpec>
-	struct SetObjVector_< VectorSet_<Pair<TKey, TObject, TPairSpec>, TSpec> > {
-		typedef String<TObject, TSpec> Type;
-	};
-	template <typename TSet>
-	struct SetObjVector_<TSet const> {
-		typedef typename SetObjVector_<TSet>::Type const Type;
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// VectorSet_ class
-
-	template <
-		typename TElement = char,
-		typename TSpec = Alloc<> /*Array<VectorSetKeySize_<TKey>::VALUE>*/
-	>
-	class VectorSet_ {
-	public:
-		typedef typename SetSetVector_<VectorSet_>::Type		TSetVector;
-		typedef typename SetObjVector_<VectorSet_>::Type		TObjVector;
-		typedef typename Size<VectorSet_>::Type				TSize;
-
-		TSetVector	vector;
-		TObjVector	obj;
-		TSize		size;
-
-		VectorSet_():
-			size(0)	
-		{
-			_autoSize(*this);
-			clear(*this);
-		}
-
-		VectorSet_(TSize _vectorSize):
-			size(0)	
-		{
-			resize(vector, _vectorSize);
-			clear(*this);
-		}
-		
-		template <typename TSet_>
-		inline void _autoSize(TSet_ &) {}
-
-		template <typename TElement_>
-		inline void _autoSize(VectorSet_<TElement_, Alloc<> > &) {
-			resize(vector, (unsigned)ValueSize<TElement_>::VALUE);
-		}
-
-		template <typename TKey_, typename TObject_, typename TSpec_>
-		inline void _autoSize(VectorSet_<Pair<TKey_, TObject_, TSpec_>, Alloc<> > &) {
-			resize(vector, (unsigned)ValueSize<TKey_>::VALUE);
-			resize(obj, (unsigned)ValueSize<TKey_>::VALUE);
-		}
-	};
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// set meta-functions
-
-	template <typename TElement, typename TSpec>
-	struct Value< VectorSet_<TElement, TSpec> > {
-		typedef TElement Type;
-	};
-	template <typename TElement, typename TSpec>
-	struct Size< VectorSet_<TElement, TSpec> >:
-		Size< SetSetVector_< VectorSet_<TElement, TSpec> > > {};
-
-	template <typename TElement, typename TSpec>
-	struct Key< VectorSet_<TElement, TSpec> > :
-		Key<TElement> {};
-
-	template <typename TElement, typename TSpec>
-	struct Object< VectorSet_<TElement, TSpec> > :
-		Object<TElement> {};
-
-	template <typename TObject, typename TSpec>
-	inline typename Size< VectorSet_<TObject, TSpec> >::Type 
-	length(VectorSet_<TObject, TSpec> const &set) {
-		return set.size;
-	}
-
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	//
-
-	struct VectorSetIterator_;
-	typedef Tag<VectorSetIterator_> VectorSetIterator__;
-
-	template <typename TVectorSet>
-	class Iter< TVectorSet, VectorSetIterator__ > 
-	{
-		typedef typename SetSetVector_<TVectorSet>::Type		TSetVector;
-		typedef typename SetObjVector_<TVectorSet>::Type		TObjVector;
-
-		typedef Iter											iterator;
-		typedef typename Value<TSetVector>::Type				TValue, value;
-		typedef typename Iterator<TSetVector, Rooted>::Type		TSetIter;
-		typedef typename Iterator<TObjVector, Standard>::Type	TObjIter;
-
-	public:
-		TSetIter	ptr;
-		TObjIter	obj;
-
-		Iter():
-			obj(NULL) {}
-
-		Iter(TSetIter _ptr, TObjIter _obj):
-			ptr(_ptr), obj(_obj)
-		{
-			while (!atEnd(ptr) && !(*ptr)) {
-				++ptr;
-				++obj;
-			}
-		}
-
-//		inline TValue operator*() { return TValue(ptr - begin, *obj); }
-
-		inline iterator operator++() {
-			++ptr;
-			++obj;
-			while (!atEnd(ptr) && !(*ptr)) {
-				++ptr;
-				++obj;
-			}
-			return *this;
-		}
-	};
-
-
-	template <typename TObject, typename TSpec, typename TIteratorSpec>
-	struct Iterator< VectorSet_<TObject, TSpec>, TIteratorSpec > {
-		typedef Iter<VectorSet_<TObject, TSpec>, VectorSetIterator__> Type;
-	};
-	template <typename TObject, typename TSpec, typename TIteratorSpec>
-	struct Iterator< VectorSet_<TObject, TSpec> const, TIteratorSpec> {
-		typedef Iter<VectorSet_<TObject, TSpec> const, VectorSetIterator__> Type;
-	};
-
-	template <typename TValue, typename TSpec>
-	finline void 
-	clear(VectorSet_<TValue, TSpec> &set) {
-		arrayFill(begin(set.vector), end(set.vector), false);
-		set.size = 0;
-	}
-
-	template <typename TElement, typename TSetKey, typename TSpec>
-	finline void 
-	insert(TElement const &element, VectorSet_<TSetKey, TSpec> &set) {
-		if (!set.vector[(unsigned)(element)]) {
-			++set.size;
-			set.vector[(unsigned)(element)] = true;
-		}
-	}
-	template <
-		typename TElement,
-		typename TSetKey, 
-		typename TSetObject, 
-		typename TPairSpec, 
-		typename TSpec>
-	finline void 
-	insert(TElement const &element, VectorSet_< Pair<TSetKey, TSetObject, TPairSpec>, TSpec > &set) {
-		if (!set.vector[(unsigned)(keyOf(element))]) {
-			++set.size;
-			set.vector[(unsigned)(keyOf(element))] = true;
-		}
-		set.obj[(unsigned)(keyOf(element))] = objectOf(element);
-	}
-
-	template <typename TKey, typename TValue, typename TSpec>
-	finline void 
-	erase(TKey const &key, VectorSet_<TValue, TSpec> &set) {
-		if (set.vector[(unsigned)(key)]) {
-			--set.size;
-			set.vector[(unsigned)(key)] = false;
-		}
-	}
-
-	template <typename TKey, typename TValue, typename TSpec>
-	finline bool 
-	in(TKey const &key, VectorSet_<TValue, TSpec> const &set) {
-		return set.vector[(unsigned)(key)];
-	}
-
-	template <typename TKey, typename TKey2, typename TSpec>
-	inline typename Iterator< VectorSet_<TKey2, TSpec> >::Type 
-	find(TKey const &key, VectorSet_<TKey2, TSpec> &set) {
-		if (in(key, set))
-			return Iter<VectorSet_<TKey2, TSpec>, VectorSetIterator__>
-				(begin(set.vector, Rooted()) + (unsigned)(key),
-				 begin(set.obj, Standard()) + (unsigned)(key));
-		else
-			return end(set);
-	}
-	template <typename TKey, typename TKey2, typename TSpec>
-	inline typename Iterator< VectorSet_<TKey2, TSpec> const>::Type 
-	find(TKey const &key, VectorSet_<TKey2, TSpec> const &set) {
-		if (in(key, set))
-			return Iter<VectorSet_<TKey2, TSpec> const, VectorSetIterator__>
-				(begin(set.vector, Rooted()) + (unsigned)(key), 
-				 begin(set.obj, Standard()) + (unsigned)(key));
-		else
-			return end(set);
-	}
-
-	template <typename TElement, typename TSpec>
-	inline typename Iterator< VectorSet_<TElement, TSpec> >::Type 
-	begin(VectorSet_<TElement, TSpec> &set) {
-		return Iter<VectorSet_<TElement, TSpec>, VectorSetIterator__> 
-			(begin(set.vector, Rooted()), begin(set.obj, Standard()));
-	}
-	template <typename TElement, typename TSpec>
-	inline typename Iterator< VectorSet_<TElement, TSpec> const>::Type 
-	begin(VectorSet_<TElement, TSpec> const &set) {
-		return Iter<VectorSet_<TElement, TSpec> const, VectorSetIterator__> 
-			(begin(set.vector, Rooted()), begin(set.obj, Standard()));
-	}
-
-	template <typename TElement, typename TSpec>
-	inline typename Iterator< VectorSet_<TElement, TSpec> >::Type 
-	end(VectorSet_<TElement, TSpec> &set) {
-		return Iter<VectorSet_<TElement, TSpec>, VectorSetIterator__> 
-			(end(set.vector, Rooted()), begin(set.obj, Standard()));
-	}
-	template <typename TElement, typename TSpec>
-	inline typename Iterator< VectorSet_<TElement, TSpec> const>::Type 
-	end(VectorSet_<TElement, TSpec> const &set) {
-		return Iter<VectorSet_<TElement, TSpec> const, VectorSetIterator__> 
-			(end(set.vector, Rooted()), begin(set.obj, Standard()));
-	}
-
-	template <typename TSet>
-	inline bool 
-	operator==(Iter<TSet, VectorSetIterator__> const &a, Iter<TSet, VectorSetIterator__> const &b) {
-		return a.ptr == b.ptr;
-	}
-	template <typename TSet>
-	inline bool 
-	operator!=(Iter<TSet, VectorSetIterator__> const &a, Iter<TSet, VectorSetIterator__> const &b) {
-		return a.ptr != b.ptr;
-	}
-	template <typename TSet>
-	inline bool 
-	eof(Iter<TSet, VectorSetIterator__> const &a) {
-		return atEnd(a.ptr);
-	}
-	template <typename TSet>
-	inline bool 
-	atEnd(Iter<TSet, VectorSetIterator__> const &a) {
-		return atEnd(a.ptr);
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <typename TSet>
-	inline typename Key<TSet>::Type
-	keyOf(Iter<TSet, VectorSetIterator__> const &it) {
-		return position(it.ptr);
-	}
-
-	template <typename TSet>
-	inline typename Object<TSet>::Type &
-	objectOf(Iter<TSet, VectorSetIterator__> const &it) {
-		return *it.obj;
-	}
-	template <typename TSet>
-	inline typename Object<TSet>::Type const &
-	objectOf(Iter<TSet const, VectorSetIterator__> const &it) {
-		return *it.obj;
-	}
-
-
-
-//____________________________________________________________________________
-
-
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// 
-	//	STL set adaptation
-	// 
-	//////////////////////////////////////////////////////////////////////////////
-
-
-	template <typename TElement>
-	struct SetLess_ : public ::std::binary_function<TElement, TElement, bool>
-	{
-		// key less
-		inline bool operator() (TElement const &a, TElement const &b) {
-			return keyOf(a) < keyOf(b);
-		}
-	};
-
-/* DISABLED: this part of code interferes with map_adapter_stl.h
-
-	template <typename TElement>
-	struct Value< ::std::set<TElement> > {
-		typedef TElement Type;
-	};
-	template <typename TElement>
-	struct Size< ::std::set<TElement> > {
-		typedef typename ::std::set<TElement>::size_type Type;
-	};
-
-	template <typename TElement>
-	struct Key< ::std::set<TElement> > :
-		Key<TElement> {};
-
-	template <typename TElement>
-	struct Object< ::std::set<TElement> > :
-		Object<TElement> {};
-
-
-
-	template <typename TKey>
-	inline void 
-	clear(::std::set<TKey> &set) {
-		set.clear();
-	}
-
-	template <typename TElement, typename TSetKey>
-	inline void 
-	insert(TElement const &element, ::std::set<TSetKey> &set) {
-		set.insert(element);
-	}
-
-	template <typename TKey, typename TSetKey>
-	inline void 
-	erase(TKey const &key, ::std::set<TSetKey> &set) {
-		set.erase(key);
-	}
-	template <typename TKey, typename TSetKey, typename TSetObject, typename TPairSpec>
-	inline void 
-	erase(TKey const &key, ::std::set< Pair<TSetKey, TSetObject, TPairSpec> > &set) {
-		set.erase(Pair<TSetKey, TSetObject, TPairSpec>(key, TSetObject()));
-	}
-
-	template <typename TKey, typename TSetKey>
-	inline bool 
-	in(TKey const &key, ::std::set<TSetKey> const &set) {
-		return set.count(key) != 0;
-	}
-	template <typename TKey, typename TSetKey, typename TSetObject, typename TPairSpec>
-	inline bool 
-	in(TKey const &key, ::std::set<Pair<TSetKey, TSetObject, TPairSpec> > const &set) {
-		return set.count(Pair<TSetKey, TSetObject, TPairSpec>(key, TSetObject())) != 0;
-	}
-
-	template <typename TKey>
-	inline typename Size< ::std::set<TKey> >::Type 
-	length(::std::set<TKey> const &set) {
-		return set.size();
-	}
-
-	template <typename TKey, typename TSetKey>
-	inline typename Iterator< ::std::set<TSetKey> >::Type 
-	find(TKey const &key, ::std::set<TSetKey> &set) {
-		return set.find(key);
-	}
-	template <typename TKey, typename TSetKey>
-	inline typename Iterator< ::std::set<TSetKey> const>::Type 
-	find(TKey const &key, ::std::set<TSetKey> const &set) {
-		return set.find(key);
-	}
-	template <typename TKey, typename TSetKey, typename TSetObject, typename TPairSpec>
-	inline typename Iterator< ::std::set<Pair<TSetKey, TSetObject, TPairSpec> > >::Type 
-	find(TKey const &key, ::std::set<Pair<TSetKey, TSetObject> > &set) {
-		return set.find(Pair<TSetKey, TSetObject>(key, TSetObject()));
-	}
-	template <typename TKey, typename TSetKey, typename TSetObject>
-	inline typename Iterator< ::std::set<Pair<TSetKey, TSetObject> > const>::Type 
-	find(TKey const &key, ::std::set<Pair<TSetKey, TSetObject> > const &set) {
-		return set.find(Pair<TSetKey, TSetObject>(key, TSetObject()));
-	}
-
-
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <typename TObject>
-	struct Iterator< ::std::set<TObject> > {
-		typedef typename ::std::set<TObject>::iterator Type;
-	};
-	template <typename TObject>
-	struct Iterator< ::std::set<TObject> const > {
-		typedef typename ::std::set<TObject>::const_iterator Type;
-	};
-
-
-	template <typename TObject>
-	typename Iterator< ::std::set<TObject> >::Type begin(::std::set<TObject> &set) {
-		return set.begin();
-	}
-	template <typename TObject>
-	typename Iterator< ::std::set<TObject> const >::Type begin(::std::set<TObject> const &set) {
-		return set.begin();
-	}
-	template <typename TObject>
-	typename Iterator< ::std::set<TObject> >::Type end(::std::set<TObject> &set) {
-		return set.end();
-	}
-	template <typename TObject>
-	typename Iterator< ::std::set<TObject> const >::Type end(::std::set<TObject> const &set) {
-		return set.end();
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-
-	template <typename TElement>
-	inline typename Key< ::std::set<TElement> >::Type &
-	keyOf(typename ::std::set<TElement>::iterator &it) {
-		return keyOf(*it);
-	}
-	template <typename TElement>
-	inline typename Key< ::std::set<TElement> >::Type &
-	keyOf(typename ::std::set<TElement>::iterator const &it) {
-		return keyOf(*it);
-	}
-	template <typename TElement>
-	inline typename Key< ::std::set<TElement> >::Type const &
-	keyOf(typename ::std::set<TElement>::const_iterator &it) {
-		return keyOf(*it);
-	}
-	template <typename TElement>
-	inline typename Key< ::std::set<TElement> >::Type const &
-	keyOf(typename ::std::set<TElement>::const_iterator const &it) {
-		return keyOf(*it);
-	}
-
-	template <typename TElement>
-	inline typename Object< ::std::set<TElement> >::Type &
-	objectOf(typename ::std::set<TElement>::iterator &it) {
-		return objectOf(*it);
-	}
-	template <typename TElement>
-	inline typename Object< ::std::set<TElement> >::Type &
-	objectOf(typename ::std::set<TElement>::iterator const &it) {
-		return objectOf(*it);
-	}
-	template <typename TElement>
-	inline typename Object< ::std::set<TElement> >::Type const &
-	objectOf(typename ::std::set<TElement>::const_iterator &it) {
-		return objectOf(*it);
-	}
-	template <typename TElement>
-	inline typename Object< ::std::set<TElement> >::Type const &
-	objectOf(typename ::std::set<TElement>::const_iterator const &it) {
-		return objectOf(*it);
-	}
-
-
-*/
-
-//____________________________________________________________________________
-
-
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// 
-	//	Set chooser
-	// 
-	//////////////////////////////////////////////////////////////////////////////
-
-
-	//////////////////////////////////////////////////////////////////////////////
-	// Set meta-function to choose an efficient implementation
-
-	template <typename TKey>
-	struct Set {
-		typedef ::std::set<TKey> Type;
-	};
-	template <typename TKey, typename TObject, typename TPairSpec>
-	struct Set< Pair<TKey, TObject, TPairSpec> > {
-		typedef ::std::set< 
-			Pair<TKey, TObject, TPairSpec>, 
-			SetLess_< Pair<TKey, TObject, TPairSpec> > > Type;
-	};
-
-
-	template <typename TValue, typename TSpec>
-	struct Set< SimpleType<TValue, TSpec> > {
-		typedef VectorSet_< SimpleType<TValue, TSpec> > Type;
-	};
-	template <typename TValue, typename TSpec, typename TObject, typename TPairSpec>
-	struct Set< Pair<SimpleType<TValue, TSpec>, TObject, TPairSpec> > {
-		typedef VectorSet_< Pair<SimpleType<TValue, TSpec>, TObject, TPairSpec> > Type;
-	};
-
-
-	template <>
-	struct Set<char> {
-		typedef VectorSet_<char> Type;
-	};
-	template <typename TObject, typename TPairSpec>
-	struct Set< Pair<char, TObject, TPairSpec> > {
-		typedef VectorSet_< Pair<char, TObject, TPairSpec> > Type;
-	};
-
-
-	template <>
-	struct Set<signed char> {
-		typedef VectorSet_<signed char> Type;
-	};
-	template <typename TObject, typename TPairSpec>
-	struct Set< Pair<signed char, TObject, TPairSpec> > {
-		typedef VectorSet_< Pair<signed char, TObject, TPairSpec> > Type;
-	};
-
-	template <>
-	struct Set<unsigned char> {
-		typedef VectorSet_<unsigned char> Type;
-	};
-	template <typename TObject, typename TPairSpec>
-	struct Set< Pair<unsigned char, TObject, TPairSpec> > {
-		typedef VectorSet_< Pair<unsigned char, TObject, TPairSpec> > Type;
-	};
-
-}
-
-#endif
diff --git a/seqan/misc/misc_sse2.h b/seqan/misc/misc_sse2.h
deleted file mode 100644
index 8ea2e95..0000000
--- a/seqan/misc/misc_sse2.h
+++ /dev/null
@@ -1,508 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-// TODO(holtgrew): What's the state of this file? I remember David saying that it brought no real performance improvements.
-
-#ifndef SEQAN_HEADER_MISC_SSE2_H
-#define SEQAN_HEADER_MISC_SSE2_H
-
-//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
-
-#ifdef SEQAN_USE_SSE2_WORDS
-#ifdef __SSE2__
-
-#include <emmintrin.h>
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-    
-//  #define __int128 Sse2Int128
-    
-    #ifndef SEQAN_SSE2_INT128
-    #define SEQAN_SSE2_INT128
-    #endif
-        
-    // ATTENTION:
-    // The Sse2Int128 struct must be 16-byte aligned. Some allocators
-    // don't ensure the correct alignment, e.g. the STL allocators.
-    // Either avoid STL classes holding Sse2Int128 structs (maps in find_pex.h)
-    // or avoid the SEQAN_USE_SSE2_WORDS define above.
-
-    // may become obsolete when 128-bit integers will be introduced
-    struct Sse2Int128
-    {
-    public:
-        union {
-            __m128i  v;
-            __uint64 v64[2];
-            unsigned v32[4];
-        }                       data;
-
-//____________________________________________________________________________
-
-    public:
-        Sse2Int128();
-        Sse2Int128(Sse2Int128 const &);
-        Sse2Int128(__m128i const &);
-        Sse2Int128(__int64, __int64);
-        Sse2Int128(int, int, int, int);
-        Sse2Int128(short, short, short, short, short, short, short, short);
-
-        template <typename TValue>
-        Sse2Int128(TValue const &);
-        
-        //____________________________________________________________________________
-        
-        template <typename TValue>
-        Sse2Int128 & operator = (TValue const &);
-        
-        //____________________________________________________________________________
-
-        operator __m128i () const;
-        operator __int64 () const;
-/*      operator bool () const;
-        operator __uint64 ();
-        operator int ();
-        operator unsigned int ();
-        operator short ();
-        operator unsigned short ();
-        operator char ();
-        operator signed char ();
-        operator unsigned char ();
-*/  };
-    
-    template <> struct IsSimple_<__m128i> { typedef True Type; };
-    template <> struct IsSimple_<Sse2Int128> { typedef True Type; };
-
-//____________________________________________________________________________
-// clear
-
-inline void
-clear(Sse2Int128 &me)
-{
-    me.data.v = _mm_setzero_si128();
-}
-
-//____________________________________________________________________________
-// assign
-
-inline void
-assign(Sse2Int128 &me, Sse2Int128 const &other)
-{
-    me.data = other.data;
-}
-
-// 1x 128bit
-inline void
-assign(Sse2Int128 &me, __m128i const &other)
-{
-    me.data.v = other;
-}
-inline Sse2Int128::operator __m128i () const
-{
-    return data.v;
-}
-    
-// 64bit => 128bit
-inline void
-assign(Sse2Int128 &me, __int64 other)
-{
-    me.data.v = _mm_set_epi32(0, 0, other >> 32, other);
-}
-inline void
-assign(Sse2Int128 &me, __uint64 other)
-{
-    me.data.v = _mm_set_epi32(0, 0, other >> 32, other);
-}
-// 64bit <= 128bit
-inline Sse2Int128::operator __int64 () const
-{
-    return data.v64[0];
-}
-/*inline Sse2Int128::operator __uint64 ()
-{
-    return data.v64[0];
-}
-*/
-// 32bit => 128bit
-inline void
-assign(Sse2Int128 &me, int other)
-{
-    me.data.v = _mm_set_epi32(0, 0, 0, other);
-}
-inline void
-assign(Sse2Int128 &me, unsigned int other)
-{
-    me.data.v = _mm_set_epi32(0, 0, 0, other);
-}
-// 32bit <= 128bit
-/*inline Sse2Int128::operator int ()
-{
-    return data.v32[0];
-}
-inline Sse2Int128::operator unsigned int ()
-{
-    return data.v32[0];
-}
-*/
-// 16bit => 128bit
-inline void
-assign(Sse2Int128 &me, short other)
-{
-    me.data.v = _mm_set_epi16(0, 0, 0, 0, 0, 0, 0, other);
-}
-inline void
-assign(Sse2Int128 &me, unsigned short other)
-{
-    me.data.v = _mm_set_epi16(0, 0, 0, 0, 0, 0, 0, other);
-}
-// 16bit <= 128bit
-/*inline Sse2Int128::operator short ()
-{
-    return _mm_extract_epi16(data.v, 0);
-}
-inline Sse2Int128::operator unsigned short ()
-{
-    return _mm_extract_epi16(data.v, 0);
-}
-*/
-// 8bit => 128bit
-inline void
-assign(Sse2Int128 &me, char other)
-{
-    me.data.v = _mm_set_epi8(
-        0, 0, 0, 0, 0, 0, 0, 0,
-        0, 0, 0, 0, 0, 0, 0, other);
-}
-inline void
-assign(Sse2Int128 &me, signed char other)
-{
-    me.data.v = _mm_set_epi8(
-        0, 0, 0, 0, 0, 0, 0, 0,
-        0, 0, 0, 0, 0, 0, 0, other);
-}
-inline void
-assign(Sse2Int128 &me, unsigned char other)
-{
-    me.data.v = _mm_set_epi8(
-        0, 0, 0, 0, 0, 0, 0, 0,
-        0, 0, 0, 0, 0, 0, 0, other);
-}
-// 8bit <= 128bit
-/*inline Sse2Int128::operator char ()
-{
-    return _mm_extract_epi16(data.v, 0);
-}
-inline Sse2Int128::operator signed char ()
-{
-    return _mm_extract_epi16(data.v, 0);
-}
-inline Sse2Int128::operator unsigned char ()
-{
-    return _mm_extract_epi16(data.v, 0);
-}
-    
-inline Sse2Int128::operator bool () const
-{
-    return (__int64)(Sse2Int128)_mm_or_si128(data.v, _mm_unpackhi_epi64(data.v, data.v));
-}
-*/
-//____________________________________________________________________________
-// constructors
-
-inline Sse2Int128::Sse2Int128()
-{
-    clear(*this);
-}
-    
-inline Sse2Int128::Sse2Int128(Sse2Int128 const &other)
-{
-    assign(*this, other);
-}
-
-inline Sse2Int128::Sse2Int128(__m128i const &other)
-{
-    assign(*this, other);
-}
-
-// 2x 64bit
-inline Sse2Int128::Sse2Int128(__int64 q1, __int64 q0)
-{
-    data.v = _mm_set_epi32(q1 >> 32, q1, q0 >> 32, q0);
-}
-
-// 4x 32bit
-inline Sse2Int128::Sse2Int128(int q3, int q2, int q1, int q0)
-{
-    data.v = _mm_set_epi32(q3, q2, q1, q0);
-}
-
-// 8x 16bit
-inline Sse2Int128::Sse2Int128(
-                   short q7, short q6, short q5, short q4,
-                   short q3, short q2, short q1, short q0)
-{
-    data.v = _mm_set_epi16(q7, q6, q5, q4, q3, q2, q1, q0);
-}
-    
-template <typename TValue>
-inline Sse2Int128::Sse2Int128(TValue const &other)
-{
-    assign(*this, other);
-}
-
-//____________________________________________________________________________
-// operator =
-
-template <typename TValue>
-inline Sse2Int128 &
-Sse2Int128::operator = (TValue const &other)
-{
-    assign(*this, other);
-    return *this;
-}
-    
-//____________________________________________________________________________
-// logical operators
-
-inline Sse2Int128
-operator & (Sse2Int128 const &a, Sse2Int128 const &b)
-{
-    return _mm_and_si128((__m128i)a, (__m128i)b);
-}
-inline Sse2Int128
-operator &= (Sse2Int128 &a, Sse2Int128 const &b)
-{
-    a.data.v = _mm_and_si128((__m128i)a, (__m128i)b);
-    return a;
-}
-
-inline Sse2Int128
-operator | (Sse2Int128 const &a, Sse2Int128 const &b)
-{
-    return _mm_or_si128((__m128i)a, (__m128i)b);
-}
-inline Sse2Int128
-operator |= (Sse2Int128 &a, Sse2Int128 const &b)
-{
-    a.data.v = _mm_or_si128((__m128i)a, (__m128i)b);
-    return a;
-}
-
-inline Sse2Int128
-operator ^ (Sse2Int128 const &a, Sse2Int128 const &b)
-{
-    return _mm_xor_si128((__m128i)a, (__m128i)b);
-}
-inline Sse2Int128
-operator ^= (Sse2Int128 &a, Sse2Int128 const &b)
-{
-    a.data.v = _mm_xor_si128((__m128i)a, (__m128i)b);
-    return a;
-}
-
-inline Sse2Int128
-operator ~ (Sse2Int128 const &a)
-{
-    __m128i _a = (__m128i)a;
-    return _mm_xor_si128(_a, _mm_cmpeq_epi32(_a, _a));
-}
-
-//____________________________________________________________________________
-// shift operators
-
-inline Sse2Int128
-operator << (Sse2Int128 const &a, int n)
-{
-    return _mm_or_si128(
-        // n <= 64
-        _mm_or_si128(
-            _mm_sll_epi64((__m128i)a, (Sse2Int128)n),
-            _mm_srl_epi64(
-                _mm_unpacklo_epi64(_mm_setzero_si128(), (__m128i)a),
-                (Sse2Int128)(64-n)
-            )
-        ),
-        // n >= 64
-        _mm_sll_epi64(
-            _mm_unpacklo_epi64(_mm_setzero_si128(), (__m128i)a),
-            (Sse2Int128)(n-64)
-        )
-    );
-}
-inline Sse2Int128
-operator <<= (Sse2Int128 &a, int n)
-{
-    a.data.v = _mm_or_si128(
-        // n <= 64
-        _mm_or_si128(
-            _mm_sll_epi64((__m128i)a, (Sse2Int128)n),
-            _mm_srl_epi64(
-                _mm_unpacklo_epi64(_mm_setzero_si128(), (__m128i)a),
-                (Sse2Int128)(64-n)
-            )
-        ),
-        // n >= 64
-        _mm_sll_epi64(
-            _mm_unpacklo_epi64(_mm_setzero_si128(), (__m128i)a),
-            (Sse2Int128)(n-64)
-        )
-    );
-    return a;
-}
-inline Sse2Int128
-operator << (Sse2Int128 const &a, unsigned int n)
-{
-    return a << (int)n;
-}
-inline Sse2Int128
-operator <<= (Sse2Int128 &a, unsigned int n)
-{
-    return a <<= (int)n;
-}
-
-inline Sse2Int128
-operator >> (Sse2Int128 const &a, int n)
-{
-    return _mm_or_si128(
-        // n <= 64
-        _mm_or_si128(
-            _mm_srl_epi64((__m128i)a, (Sse2Int128)n),
-            _mm_sll_epi64(
-                _mm_unpackhi_epi64(a.data.v, _mm_setzero_si128()),
-                (Sse2Int128)(64-n)
-            )
-        ),
-        // n >= 64
-        _mm_srl_epi64(
-            _mm_unpackhi_epi64((__m128i)a, _mm_setzero_si128()),
-            (Sse2Int128)(n-64)
-        )
-    );
-}
-inline Sse2Int128
-operator >>= (Sse2Int128 &a, int n)
-{
-    a.data.v = _mm_or_si128(
-        // n <= 64
-        _mm_or_si128(
-            _mm_srl_epi64((__m128i)a, (Sse2Int128)n),
-            _mm_sll_epi64(
-                _mm_unpackhi_epi64((__m128i)a, _mm_setzero_si128()),
-                (Sse2Int128)(64-n)
-            )
-        ),
-        // n >= 64
-        _mm_srl_epi64(
-            _mm_unpackhi_epi64((__m128i)a, _mm_setzero_si128()),
-            (Sse2Int128)(n-64)
-        )
-    );
-    return a;
-}
-inline Sse2Int128
-operator >> (Sse2Int128 const &a, unsigned int n)
-{
-    return a >> (int)n;
-}
-inline Sse2Int128
-operator >>= (Sse2Int128 &a, unsigned int n)
-{
-    return a >>= (int)n;
-}
-
-//____________________________________________________________________________
-// artihmetic operators
-
-//template <typename T>
-inline Sse2Int128
-operator + (Sse2Int128 const &a, Sse2Int128 const &b)
-{
-    static const __m128i carry = Sse2Int128(0, 1, 0, 0);
-
-    union {
-        __uint64 v64[2];
-        __m128i v;
-    } _sum;
-    
-    _sum.v = _mm_add_epi64((__m128i)a, (__m128i)b);
-    if (_sum.v64[0] >= a.data.v64[0])
-        return _sum.v;
-    else
-        return _mm_add_epi64(_sum.v, carry);
-}
-
-//template <typename T>
-inline Sse2Int128
-operator - (Sse2Int128 const &a, Sse2Int128 const &b)
-{
-    static const __m128i carry = Sse2Int128(0, 1, 0, 0);
-
-    union {
-        __uint64 v64[2];
-        __m128i v;
-    } _diff;
-    
-    _diff.v = _mm_sub_epi64((__m128i)a, (__m128i)b);
-    if (_diff.v64[0] <= a.data.v64[0])
-        return _diff.v;
-    else
-        return _mm_sub_epi64(_diff.v, carry);
-}
-
-// TODO: operator *, /
-
-//____________________________________________________________________________
-// compares
-
-inline bool
-operator == (Sse2Int128 const &a, Sse2Int128 const &b)
-{
-    __m128i _e = _mm_cmpeq_epi32((__m128i)a, (__m128i)b);
-    return ((__int64)(Sse2Int128)_mm_and_si128(_e, _mm_unpackhi_epi64(_e, _e))) == ~(__int64)0;
-}
-
-inline bool
-operator != (Sse2Int128 const &a, Sse2Int128 const &b)
-{
-    __m128i _e = _mm_cmpeq_epi32((__m128i)a, (__m128i)b);
-    return ((__int64)(Sse2Int128)_mm_and_si128(_e, _mm_unpackhi_epi64(_e, _e))) != ~(__int64)0;
-}
-    
-// TODO: operator <, <=, >, >=
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifdef __SSE2__
-#endif //#ifdef SEQAN_USE_SSE2_WORDS
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/misc/misc_svg.h b/seqan/misc/misc_svg.h
deleted file mode 100644
index 555de92..0000000
--- a/seqan/misc/misc_svg.h
+++ /dev/null
@@ -1,498 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-
-#ifndef SEQAN_HEADER_MISC_SVG_H
-#define SEQAN_HEADER_MISC_SVG_H
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//////////////////////////////////////////////////////////////////////////////
-// SVG File Context
-//////////////////////////////////////////////////////////////////////////////
-
-struct SVGFile
-{
-//IOREV _nodoc_ no documentation whatsoever; uses custom IO, fully independent (maybe postpone adaption)
-	std::fstream file;
-
-	Pair<int> cursor;
-    Pair<int> size;
-	String<CharString> style;
-	
-	int dpSequence;
-	int dpMatrix;
-	int dpTrace;
-	
-	int text;
-	
-	int readForward;
-	int readReverse;
-	int readText;
-	int rulerTextTicks;
-	int rulerTextLabel;
-
-	friend inline void svgWriteHeader(SVGFile &svg);
-	friend inline void svgWriteFooter(SVGFile &svg);
-	
-	template <typename TFileName>
-	friend inline bool open(SVGFile &svg, TFileName const &fileName);
-	friend inline bool close(SVGFile &svg);
-	
-	SVGFile():
-		cursor(0,0),
-        size(0,0)
-	{
-		resetStyles();
-	}
-
-	SVGFile(char const *fileName):
-		cursor(0,0),
-        size(0,0)
-	{
-		resetStyles();
-		open(*this, fileName);
-	}
-
-	~SVGFile()
-	{
-		close(*this);
-	}
-
-private:
-
-	inline void resetStyles()
-	{
-		clear(style);
-		readText = dpSequence = length(style);
-		appendValue(style, "style=\"text-anchor:middle; font-family:Bitstream Vera Sans,Verdana,sans-serif;\" font-size=\"18px\"");
-		text = length(style);
-		appendValue(style, "style=\"text-anchor:middle; font-family:Courier New,Verdana,sans-serif; font-weight:bold;\" font-size=\"20px\"");
-		rulerTextTicks = length(style);
-		appendValue(style, "style=\"text-anchor:middle; font-family:Verdana,sans-serif;\" font-size=\"6px\"");
-		rulerTextLabel = length(style);
-		appendValue(style, "style=\"text-anchor:left; font-family:Verdana,sans-serif; font-weight:bold;\" font-size=\"8px\"");
-
-		dpMatrix = length(style);
-		appendValue(style, "style=\"stroke:lightgray;stroke-width:1;\" marker-end=\"url(#startMarkerNormal)\"");
-		dpTrace = length(style);
-		appendValue(style, "style=\"stroke:black;stroke-width:2;\" marker-end=\"url(#startMarkerBold)\"");
-
-		readForward = length(style);
-		appendValue(style, "style=\"stroke:darkblue;stroke-width:3;\"");
-		appendValue(style, "style=\"stroke:lightblue;stroke-width:1;\"");
-		appendValue(style, "style=\"stroke:darkblue;stroke-width:3;\" marker-end=\"url(#startMarkerForward)\"");
-		appendValue(style, "style=\"stroke:lightblue;stroke-width:1;\" marker-end=\"url(#startMarkerForward)\"");
-		readReverse = length(style);
-		appendValue(style, "style=\"stroke:darkred;stroke-width:3;\"");
-		appendValue(style, "style=\"stroke:salmon;stroke-width:1;\"");
-		appendValue(style, "style=\"stroke:darkred;stroke-width:3;\" marker-end=\"url(#startMarkerReverse)\"");
-		appendValue(style, "style=\"stroke:salmon;stroke-width:1;\" marker-end=\"url(#startMarkerReverse)\"");
-	}
-};
-
-inline void svgResize(SVGFile &svg, int width, int height)
-{
-    svg.size.i1 = width;
-    svg.size.i2 = height;
-}
-
-inline void svgWriteHeader(SVGFile &svg)
-{
-	svg.file << "<?xml version=\"1.0\"?>" << std::endl;
-	svg.file << "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"" << std::endl;
-	svg.file << "  \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">" << std::endl;
-	svg.file << std::endl;
-	svg.file << "<svg version=\"1.1\"" << std::endl;
-	svg.file << "    xmlns=\"http://www.w3.org/2000/svg\"" << std::endl;
-	svg.file << "    xmlns:xlink=\"http://www.w3.org/1999/xlink\"" << std::endl;
-    if (svg.size.i1 != 0)
-    {
-        svg.file << "    width=\"" << svg.size.i1 * 20 << "px\" height=\"" << svg.size.i2 * 20 << "px\"" << std::endl;
-    }
-    svg.file << ">" << std::endl;
-    svg.file << "<defs>" << std::endl;
-
-	// trace back arrow markers
-    svg.file << "	<g id=\"arrowMarker\" stroke-linecap=\"round\">" << std::endl;
-    svg.file << "		<line x1=\"-6\" y1=\"1.5\" x2=\"0\" y2=\"0\" />" << std::endl;
-    svg.file << "		<line x1=\"-6\" y1=\"-1.5\" x2=\"0\" y2=\"0\" />" << std::endl;
-    svg.file << "	</g>" << std::endl;
-    svg.file << "	<marker id=\"startMarkerNormal\" markerWidth=\"6\" markerHeight=\"3\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
-    svg.file << "		<use xlink:href=\"#arrowMarker\" stroke=\"lightgray\" />" << std::endl;
-    svg.file << "	</marker>" << std::endl;
-    svg.file << "	<marker id=\"startMarkerBold\" markerWidth=\"6\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
-    svg.file << "		<use xlink:href=\"#arrowMarker\" stroke-width=\"2\" stroke=\"black\" />" << std::endl;
-    svg.file << "	</marker>" << std::endl;
-
-	// read mapping arrow markers
-    svg.file << "	<marker id=\"startMarkerForward\" markerWidth=\"10\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
-    svg.file << "		<polyline points=\"-8,0 -9,-6 3,0 -9,6 -8,0\" fill=\"darkblue\" />" << std::endl;
-    svg.file << "	</marker>" << std::endl;
-    svg.file << "	<marker id=\"startMarkerReverse\" markerWidth=\"10\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
-    svg.file << "		<polyline points=\"-8,0 -9,-6 3,0 -9,6 -8,0\" fill=\"darkred\" />" << std::endl;
-    svg.file << "	</marker>" << std::endl;
-	
-    svg.file << " </defs>" << std::endl;
-	svg.file << std::endl;
-}
-
-inline void svgWriteFooter(SVGFile &svg)
-{
-	svg.file << std::endl;
-	svg.file << "</svg>" << std::endl;
-}
-
-
-template <typename TFileName>
-inline bool open(SVGFile &svg, TFileName const &fileName)
-{
-	svg.file.open(fileName, std::ios_base::out);
-	if (!svg.file.is_open()) return false;
-	svgWriteHeader(svg);
-	return true;
-}
-
-inline bool close(SVGFile &svg)
-{
-	if (svg.file.is_open())
-	{
-		svgWriteFooter(svg);
-		svg.file.close();
-	}
-	return true;
-}
-
-template <typename TChar>
-inline void
-streamPut(SVGFile & svg, TChar character)
-{
-//IOREV
-	if (convert<char>(character) == '\n')
-	{
-		++svg.cursor.i2;
-		svg.cursor.i1 = 0;
-	} else if (convert<char>(character) == '\t')
-	{
-		svg.cursor.i1 = (svg.cursor.i1 & ~7) + 8;
-	} else
-	{
-		if (convert<char>(character) != ' ')
-		{
-			svg.file << "<g transform=\"translate(" << svg.cursor.i1*20+10 << ',' << svg.cursor.i2*20+10 << ")\"><text y=\"0.3em\" " << svg.style[svg.text] << '>';
-			streamPut(svg.file, convert<char>(character));
-			svg.file << "</text></g>" << std::endl;
-		}
-		++svg.cursor.i1;
-	}
-}
-
-template <typename TFormatTag, typename TContigGaps, typename TContigName>
-inline void _printContig(
-	SVGFile &svg, 
-	Tag<TFormatTag> const &format,
-	AlignedReadLayout &, 
-	TContigGaps &contigGaps,
-	TContigName const &contigName)
-{
-	typedef typename Iterator<TContigGaps, Standard>::Type TContigIterator;
-
-	TContigIterator cit = begin(contigGaps, Standard());
-	TContigIterator citEnd = end(contigGaps, Standard());	
-	for (__int64 ofs = 0; cit != citEnd; ++cit, ++ofs)
-	{
-		if (!isGap(cit))
-		{
-			if (ofs == 0)
-			{
-				svg.file << "<g transform=\"translate(" << ofs*20+2 << ',' << svg.cursor.i2*20+10 << ")\"><text y=\"0.3em\" " << svg.style[svg.rulerTextLabel] << '>';
-				svg.file << contigName << "</text></g>" << std::endl;
-			}
-			
-			__int64 seqPos = cit.current.seqPos + 1;
-			if (seqPos % 5 == 0)
-			{
-				if (seqPos % 10 == 0)
-				{
-					if (ofs >= 5)
-					{
-						svg.file << "<g transform=\"translate(" << ofs*20+10 << ',' << svg.cursor.i2*20+10 << ")\"><text y=\"0.3em\" " << svg.style[svg.rulerTextTicks] << '>';
-						svg.file << seqPos << "</text></g>" << std::endl;
-					}
-					
-					svg.file << "<line x1=\"" << ofs*20+10 << "\" x2=\"" << ofs*20+10 << "\" ";
-					svg.file << "y1=\"" << svg.cursor.i2*20+12 << "\" y2=\"" << svg.cursor.i2*20+15 << "\" ";
-				} else {
-					svg.file << "<line x1=\"" << ofs*20+10 << "\" x2=\"" << ofs*20+10 << "\" ";
-					svg.file << "y1=\"" << svg.cursor.i2*20+12 << "\" y2=\"" << svg.cursor.i2*20+15 << "\" ";
-				}
-				svg.file << "stroke-width=\"1\" stroke=\"gray\" />" << std::endl;
-			}
-		}
-	}
-	streamPut(svg, '\n');
-	
-	int savedStyle = svg.text;
-	svg.text = svg.readText;
-	write(svg, contigGaps, "", format);
-	svg.text = savedStyle;
-}
-
-template <typename TFormatTag, typename TContigGaps, typename TReadGaps, typename TAlignedRead, typename TLine>
-inline void _printRead(
-	SVGFile &svg, 
-	Tag<TFormatTag> const &,
-	AlignedReadLayout &layout, 
-	TContigGaps &contigGaps,
-	TReadGaps &readGaps,
-	TAlignedRead &alignedRead,
-	TLine line)
-{
-	typedef typename Iterator<TContigGaps, Standard>::Type TContigIterator;
-	typedef typename Iterator<TReadGaps, Standard>::Type TIterator;
-
-	__int64 xEnd = svg.cursor.i1 * 20;
-	__int64 x = 0;
-
-	int style, arrow = 0;
-	const char *first;
-	const char *second;
-	__int64 ofs;
-	
-	if (alignedRead.beginPos < alignedRead.endPos)
-	{
-		ofs = alignedRead.beginPos - svg.cursor.i1 + beginPosition(readGaps);
-		first = "<line x1=\"";
-		second = "\" x2=\"";
-		style = svg.readForward;
-	} else {
-		ofs = alignedRead.endPos - svg.cursor.i1 + beginPosition(readGaps);
-		first = "<line x2=\"";
-		second = "\" x1=\"";
-		style = svg.readReverse;
-	}
-
-	if (beginPosition(readGaps) == 0)
-	{
-		if (alignedRead.beginPos < alignedRead.endPos)
-			x = xEnd + 5;
-		else {
-			x = xEnd + 10;
-			arrow = 2;
-		}
-	}
-	line = svg.cursor.i2 * 20 + 10;
-	
-	if (length(layout.mateCoords) <= alignedRead.pairMatchId)
-		resize(layout.mateCoords, alignedRead.pairMatchId + 1, Pair<int>(-1,-1));
-	else
-	{
-		if (layout.mateCoords[alignedRead.pairMatchId].i2 != -1)
-		{
-			Pair<__int64> a((alignedRead.beginPos - ofs) * 20, line);
-			Pair<__int64> b(layout.mateCoords[alignedRead.pairMatchId]);
-			if (a.i1 < b.i1)
-			{
-				Pair<__int64> tmp = a;
-				a = b;
-				b = tmp;
-			}
-			__int64 dx = (b.i1 - a.i1);
-			__int64 dy = (b.i2 - a.i2);
-			
-			svg.file << "<path d=\"M " << a.i1 << ',' << a.i2;
-			svg.file << " C " << a.i1+dy/10 << ',' << a.i2-dx/10;
-			svg.file << ' ' << b.i1+dy/10 << ',' << b.i2-dx/10;
-			svg.file << ' ' << b.i1 << ',' << b.i2;
-			svg.file << "\" stroke-width=\"2\" stroke=\"black\" stroke-opacity=\"0.2\" fill=\"none\"/>";
-		}
-		else
-			layout.mateCoords[alignedRead.pairMatchId] = Pair<int>((alignedRead.beginPos - ofs) * 20, line);
-	}
-	
-
-	TContigIterator cit = begin(contigGaps, Standard()) + (_min(alignedRead.beginPos, alignedRead.endPos) + beginPosition(readGaps));
-	TIterator it = begin(readGaps, Standard());
-	TIterator itEnd = end(readGaps, Standard());
-	int lastWasGap = -1;
-	int inGap;
-	
-	for (; it != itEnd; ++it, ++cit, xEnd += 20, ++svg.cursor.i1)
-	{
-		inGap = isGap(it);
-		if (lastWasGap != inGap || inGap != static_cast<int>(isGap(cit)) || (!inGap && convert<Dna5>(*cit) != convert<Dna5>(*it)))
-		{
-			if (x < xEnd && lastWasGap != -1)
-			{
-				svg.file << first << x << "\" y1=\"" << line << second << xEnd; 
-				svg.file << "\" y2=\"" << line << "\" " << svg.style[style + arrow + lastWasGap] << " />" << std::endl;
-				arrow = 0;
-			}
-			lastWasGap = inGap;
-			x = xEnd;
-			if (!inGap && convert<Dna5>(*cit) != convert<Dna5>(*it))
-			{
-				svg.file << "<g transform=\"translate(" << xEnd + 10 << ',' << line << ")\"><text y=\"0.3em\" " << svg.style[svg.readText] << '>';
-				streamPut(svg.file, convert<char>(*it));
-				svg.file << "</text></g>" << std::endl;
-				x += 20;
-				arrow = 0;
-			}
-		}
-	}
-	if (x < xEnd && lastWasGap != -1)
-	{
-		if (static_cast<int>(_unclippedLength(readGaps)) == static_cast<int>(endPosition(readGaps)))
-		{
-			if (alignedRead.beginPos < alignedRead.endPos)
-			{
-				arrow = 2;
-				xEnd -= 10;
-			} else
-				xEnd -= 5;
-		}
-		svg.file << first << x << "\" y1=\"" << line << second << xEnd;
-		svg.file << "\" y2=\"" << line << "\" " << svg.style[style + arrow + lastWasGap] << " />" << std::endl;
-	}
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// stream operators
-//////////////////////////////////////////////////////////////////////////////
-/*
-template <typename TSource>
-inline SVGFile &
-operator << (SVGFile & target, 
-			 TSource  source)
-{
-SEQAN_CHECKPOINT
-	write(target, source);
-	return target;
-}
-*/
-
-inline SVGFile &
-operator << (SVGFile & target, char source)
-{
-SEQAN_CHECKPOINT
-	write(target, source);
-	return target;
-}
-
-inline SVGFile &
-operator << (SVGFile & target, char const *source)
-{
-SEQAN_CHECKPOINT
-	write(target, source);
-	return target;
-}
-
-
-template <typename TStringSet, typename TTrace, typename TIndexPair>
-void
-_alignNeedlemanWunschMatrix(SVGFile& svg,
-							  TStringSet const& str,
-							  TTrace const& trace,
-							  TIndexPair const&)
-{
-SEQAN_CHECKPOINT
-	typedef typename Size<TStringSet>::Type TSize;
-	//typedef typename Value<TTrace>::Type TTraceValue;
-
-	// TraceBack values
-	const int Diagonal = 0; 
-	const int Horizontal = 1; 
-	const int Vertical = 2;
-	
-	// Initialization
-	TSize numCols = length(str[0]);
-	TSize numRows = length(str[1]);
-
-	// Print trace matrix	
-	for (TSize pos0 = 0; pos0 < numCols; ++pos0)
-	{
-		for (TSize pos1 = 0; pos1 < numRows; ++pos1)
-		{
-			int tv =(int)trace[pos0*numRows + pos1];
-				if (tv & (1 << Diagonal))
-					svg.file << "<line x2=\"" << pos0*20+10 << "\" y2=\"" << pos1*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;
-				
-				if (tv & (1 << Horizontal))
-					svg.file << "<line x2=\"" << pos0*20+10 << "\" y2=\"" << (pos1+1)*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;
-
-				if (tv & (1 << Vertical))
-					svg.file << "<line x2=\"" << (pos0+1)*20+10 << "\" y2=\"" << pos1*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;
-		}
-	}
-
-	// Print sequences
-	for (TSize pos0 = 0; pos0 < numCols; ++pos0)
-		svg.file << "<g transform=\"translate(" << pos0*20+20 << ",5)\"><text y=\"0.3em\" " << svg.style[svg.dpSequence] << '>' << str[0][pos0] << "</text></g>" << std::endl;
-
-	for (TSize pos1 = 0; pos1 < numRows; ++pos1)
-		svg.file << "<g transform=\"translate(0," << pos1*20+25 << ")\"><text y=\"0.3em\" " << svg.style[svg.dpSequence] << '>' << str[1][pos1] << "</text></g>" << std::endl;
-}
-
-template <typename TStringSet, typename TId, typename TPos, typename TTraceValue>
-inline void
-_alignTracePrint(SVGFile& svg,
-				   TStringSet const&,
-				   TId const,
-				   TPos pos1,
-				   TId const,
-				   TPos pos2,
-				   TPos const segLen,
-				   TTraceValue const tv)
-{
-	// TraceBack values
-	TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2;
-
-	svg.file << "<line x2=\"" << pos1*20+10 << "\" y2=\"" << pos2*20+10 << "\"";
-	if (tv == Diagonal) {
-		pos1 += segLen; pos2 += segLen;
-	} else if (tv == Horizontal) {
-		pos1 += segLen;
-	} else if (tv == Vertical) {
-		pos2 += segLen;
-	}
-	svg.file << " x1=\"" << pos1*20+10 << "\" y1=\"" << pos2*20+10;
-	svg.file << "\" " << svg.style[svg.dpTrace] << " />" << std::endl;
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/misc/misc_name_store_cache.h b/seqan/misc/name_store_cache.h
old mode 100755
new mode 100644
similarity index 51%
rename from seqan/misc/misc_name_store_cache.h
rename to seqan/misc/name_store_cache.h
index b500cf7..3216549
--- a/seqan/misc/misc_name_store_cache.h
+++ b/seqan/misc/name_store_cache.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -61,13 +61,13 @@ struct NameStoreLess_
 
     TNameStore *nameStore;
     TName *name;
-    
+
     NameStoreLess_() {}
 
     NameStoreLess_(TNameStore &_nameStore, TName &_name):
         nameStore(&_nameStore),
         name(&_name) {}
-    
+
     template <typename TId>
     inline bool operator() (TId a, TId b) const
     {
@@ -93,63 +93,80 @@ struct NameStoreLess_
 
 /*!
  * @class NameStoreCache
- * @headerfile <seqan/misc/misc_name_store_cache.h>
- * @brief Stores a mapping from names to ids.
+ * @headerfile <seqan/misc/name_store_cache.h>
+ * @brief Fast mapping from string names to numeric ids.
+ *
+ * NameStore objects store a binary search tree (using <tt>std::map&lt;&gt;</tt>) on a @link StringSet @endlink (the
+ * name store).  They store a pointer to this name store but not the name store itself.
+ *
+ * When adding values to the name store using @link NameStoreCache#appendName @endlink, the cache (i.e, the binary
+ * search tree) is automatically updated.  When modifying the name store when not using @link NameStoreCache#appendName
+ * @endlink, you have to use @link NameStoreCache#refresh @endlink to update the cache after modifying and before
+ * querying.
+ *
+ * The fast lookups can be performed using @link NameStoreCache#getIdByName @endlink and @link NameStoreCache#nameToId
+ * @endlink.  The query function @link NameStoreCache#nameToId @endlink, the cache can also be modified (and thus
+ * updated).
  *
  * @signature template <typename TNameStore[, typename TName]>
  *            class NameStoreCache;
  *
- * @tparam TNameStore The type to use for the name store.  Usually a @link StringSet @endlink.
- * @tparam TName      The type to use for the names.  Defaults to <tt>Value&lt;TNameStore&gt;::Type</tt>.
+ * @tparam TNameStore The type to use for the name store.  Usually a @link StringSet @endlink of
+ *                    @link CharString @endlink.
+ * @tparam TName      The type to use for the names, defaults to <tt>Value&lt;TNameStore&gt;::Type</tt>.
  *
+ * @section Example
  *
+ * The demo below shows how to initialize a NameStoreCache with an existing name store, lookup existing names, add new
+ * names, and add names during lookup.
+ *
+ * @include demos/dox/misc/name_store_cache.cpp
+ *
+ * Here is the output:
+ *
+ * @include demos/dox/misc/name_store_cache.cpp.stdout
+ */
+
+/*!
  * @fn NameStoreCache::NameStoreCache
- * @brief Constructor
+ * @brief Constructors.
+ *
+ * NameStore cache offers the default constructor, copy constructor, and construction using an existing name store.
  *
+ * @signature NameStoreCache::NameStoreCache();
+ * @signature NameStoreCache::NameStoreCache(other);
  * @signature NameStoreCache::NameStoreCache(nameStore);
  *
- * @param[in] nameStore The name store to manage the cache for.
+ * @param[in] other     The other NameStoreCache to copy from.
+ * @param[in] nameStore A NameStore for which a pointer is stored.
  */
 
-/**
-.Class.NameStoreCache
-..summary:Stores a mapping from names to ids.
-..cat:Fragment Store
-..signature:FragmentStore<>
-..signature:NameStoreCache<TNameStore[, TName]>
-..param.TNameStore:The name store to be cached.
-...see:Class.FragmentStore
-..param.TName:The name type.
-...default:$Value<TNameStore>::Type$
-...type:Shortcut.CharString
-
-.Memfunc.NameStoreCache#NameStoreCache
-..summary:Constructor
-..signature:NameStoreCache<TNameStore, TName> (nameStore)
-..param.nameStore:A name store, e.g. @Memvar.FragmentStore#readNameStore@
-...see:Class.FragmentStore
-..class:Class.NameStoreCache
-..include:seqan/store.h
-*/
-	
-template <typename TNameStore, typename TName = typename Value<TNameStore>::Type>
+template <typename TNameStore, typename TName = String<typename Value<typename Value<TNameStore>::Type>::Type> >
 class NameStoreCache
 {
 public:
     typedef typename Position<TNameStore>::Type TId;
     typedef NameStoreLess_<TNameStore, TName> TLess;
     typedef std::set<TId, TLess> TSet;
-    
+
     TSet nameSet;
-    TNameStore *nameStore;
     // TODO(holtgrew): Mutable here necessary for conceptual const-ness.  However, we would rather have a thread-safe interface!
     TName mutable name;
 
-    NameStoreCache(TNameStore &_nameStore):
-        nameSet(TLess(_nameStore, name)),
-        nameStore(&_nameStore)
+    NameStoreCache()
+    {}
+
+    NameStoreCache(TNameStore & nameStore):
+        nameSet(TLess(nameStore, name))
     {
-        for (unsigned i = 0; i < length(*nameStore); ++i)
+        for (unsigned i = 0; i < length(nameStore); ++i)
+            nameSet.insert(i);
+    }
+
+    NameStoreCache(NameStoreCache const & other):
+        nameSet(TLess(host(other), name))
+    {
+        for (unsigned i = 0; i < length(host(other)); ++i)
             nameSet.insert(i);
     }
 };
@@ -166,80 +183,157 @@ class NameStoreCache
 // refresh()
 // ----------------------------------------------------------------------------
 
+template <typename TNameStore, typename TName>
+inline TNameStore &
+host(NameStoreCache<TNameStore, TName> & cache)
+{
+    return *cache.nameSet.key_comp().nameStore;
+}
+
+template <typename TNameStore, typename TName>
+inline TNameStore &
+host(NameStoreCache<TNameStore, TName> const & cache)
+{
+    return *cache.nameSet.key_comp().nameStore;
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn NameStoreCache#clear
+ * @brief Reset the NameStoreCache (not the name store).
+ *
+ * @signature void clear(cache);
+ *
+ * @param[in,out] cache The NameStoreCache to clear.
+ */
+
+template <typename TNameStore, typename TName>
+inline void
+clear(NameStoreCache<TNameStore, TName> &cache)
+{
+    cache.nameSet.clear();
+}
+
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn NameStoreCache#empty
+ * @brief Query whether there are any entries in the cache (not the name store).
+ *
+ * @signature bool empty(cache);
+ *
+ * @param[in,out] cache The NameStoreCache to clear.
+ *
+ * @return bool <tt>true</tt> if the NameStoreCache is empty.
+ */
+
+template <typename TNameStore, typename TName>
+inline bool
+empty(NameStoreCache<TNameStore, TName> const &cache)
+{
+    return cache.nameSet.empty();
+}
+
+// ----------------------------------------------------------------------------
+// Function refresh()
+// ----------------------------------------------------------------------------
+
 /*!
  * @fn NameStoreCache#refresh
- * @brief Recreate a NameStoreCache.
+ * @brief Rebuild the name store cache.
+ *
+ * Use this after modifying the underlying NameStore before querying.
  *
  * @signature void refresh(cache);
  *
- * @param[in,out] nameStore The NameStoreCache to refresh.
+ * @param[in,out] nameStore The NameStoreCache to rebuild.
  */
 
-/**
-.Function.refresh:
-..class:Class.NameStoreCache
-..summary:Recreate a name store cache.
-..cat:Fragment Store
-..signature:refresh(cache)
-..param.cache:A @Class.NameStoreCache@ object.
-...type:Class.NameStoreCache
-..see:Function.getIdByName
-..include:seqan/store.h
-*/
-    
 template <typename TNameStore, typename TName>
 inline void
 refresh(NameStoreCache<TNameStore, TName> &cache)
 {
-    cache.nameSet.clear();
-    for (unsigned i = 0; i < length(*cache.nameStore); ++i)
+    clear(cache);
+    for (unsigned i = 0; i < length(*cache.nameSet.key_comp().nameStore); ++i)
         cache.nameSet.insert(i);
 }
 
+// ----------------------------------------------------------------------------
+// Function appendName()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn NameStoreCache#appendName
+ * @brief Append a name to a name store and register it in the cache.
+ *
+ * The NameStoreCache only registers update to the name store when performed by this function.
+ *
+ * @signature void appendName(cache, name);
+ *
+ * @param[in,out] cache     The NameStoreCache to use for faster access.
+ * @param[in]     name      The name to append to the store (@link ContainerConcept#Value @endlink of
+ *                          <tt>TNameStore</tt>).
+ */
+
+template <typename TNameStore, typename TName>
+void appendName(TNameStore & nameStore, TName const & name)
+{
+    appendValue(nameStore, name, Generous());
+}
+
+template <typename TCNameStore, typename TCName, typename TName>
+void appendName(NameStoreCache<TCNameStore, TCName> & cache, TName const & name)
+{
+    appendValue(host(cache), name, Generous());
+    cache.nameSet.insert(length(host(cache)) - 1);
+}
+
+// TODO(holtgrew): Add deprecation annotation for compiler warnings.
+
+// deprecated.
+// In the future we want to use only one argument either nameStore or nameStoreCache (has a reference to the nameStore)
+template <typename TNameStore, typename TName, typename TContext>
+void appendName(TNameStore &nameStore, TName const & name, TContext &)
+{
+    appendName(nameStore, name);
+}
+
+// deprecated.
+template <typename TNameStore, typename TName, typename TCNameStore, typename TCName>
+void appendName(TNameStore &nameStore, TName const & name, NameStoreCache<TCNameStore, TCName> &context)
+{
+    appendValue(nameStore, name, Generous());
+    context.nameSet.insert(length(nameStore) - 1);
+}
 
 // ----------------------------------------------------------------------------
-// getIdByName()
+// Function getIdByName()
 // ----------------------------------------------------------------------------
 
 /*!
  * @fn NameStoreCache#getIdByName
  * @brief Get id/index of a string in a name store using a NameStoreCache.
  *
- * @signature bool getIdByName(nameStore, name, idx[, cache]);
+ * @signature bool getIdByName(idx, cache, name);
  *
- * @param[in]     nameStore The name store to search the name in.
- * @param[in]     name      The name to search in the name store.
- * @param[out]    idx       The variable to store the id/index at.
- * @param[in,out] cache     The NameStoreCache to use for speeding up the lookup.  If omitted then a linear
- *                          search is used.
+ * @param[out]    idx       The variable to store the index in the store of (@link IntegerConcept @endlink).
+ * @param[in]     cache     The NameStoreCache to use for speeding up the lookup.
+ * @param[in]     name      The name to search in the name store (@link ContainerConcept#Value @endlink of
+ *                          <tt>TNameStore</tt>).
  *
  * @return bool <tt>true</tt> if the name could be found and <tt>false</tt> otherwise.
  */
 
-/**
-.Function.getIdByName:
-..summary:Get the id/index of a string in a name store with a cache.
-..cat:Fragment Store
-..signature:getIdByName(nameStore, name, id[, cache])
-..param.nameStore:A name store, e.g. @Memvar.FragmentStore#readNameStore@
-...see:Class.FragmentStore
-..param.name:The name to be searched.
-...type:Shortcut.CharString
-..param.id:The resulting id.
-..param.cache:A structure to efficiently retrieve the id for a given name. If ommited a brute force method is used to search.
-...default:Tag.Nothing
-...type:Class.NameStoreCache
-..returns:$true$ if the name was found and $false$ if not.
-..see:Function.getIdByName
-..include:seqan/store.h
-*/
-
-template <typename TNameStore, typename TName, typename TPos>
-inline bool 
-getIdByName(TNameStore const & nameStore, TName const & name, TPos & pos)
+template <typename TPos, typename TNameStore, typename TName>
+bool getIdByName(TPos & pos, TNameStore const & nameStore, TName const & name)
 {
     typedef typename Iterator<TNameStore const, Standard>::Type TNameStoreIter;
-    
+
     // Iterator over read names
     for (TNameStoreIter iter = begin(nameStore, Standard()); iter != end(nameStore, Standard()); ++iter)
     {
@@ -247,7 +341,7 @@ getIdByName(TNameStore const & nameStore, TName const & name, TPos & pos)
         if (name == getValue(iter))
         {
             // set the ID
-            pos = position(iter);
+            pos = iter - begin(nameStore, Standard());
             // and break the loop
             return true;
         }
@@ -255,18 +349,11 @@ getIdByName(TNameStore const & nameStore, TName const & name, TPos & pos)
     return false;
 }
 
-template <typename TNameStore, typename TName, typename TPos, typename TContext>
+template <typename TCNameStore, typename TCName, typename TName, typename TPos>
 inline bool
-getIdByName(TNameStore const & nameStore, TName const & name, TPos & pos, TContext const & /*not a cache*/)
+getIdByName(TPos & pos, NameStoreCache<TCNameStore, TCName> const & context, TName const & name)
 {
-    return getIdByName(nameStore, name, pos);
-}
-
-template<typename TNameStore, typename TName, typename TPos, typename TCNameStore, typename TCName>
-inline bool
-getIdByName(TNameStore const & /*nameStore*/, TName const & name, TPos & pos, NameStoreCache<TCNameStore, TCName> const & context)
-{
-    typedef typename Position<TNameStore const>::Type TId;
+    typedef typename Position<TCNameStore const>::Type TId;
     typedef NameStoreCache<TCNameStore, TCName> const TNameStoreCache;
     typedef typename TNameStoreCache::TSet TSet;
 
@@ -283,7 +370,7 @@ getIdByName(TNameStore const & /*nameStore*/, TName const & name, TPos & pos, Na
         context.name = name;
         it = set.find(maxValue<TId>());
     }
-    
+
     if (it != set.end())
     {
         pos = *it;
@@ -292,57 +379,57 @@ getIdByName(TNameStore const & /*nameStore*/, TName const & name, TPos & pos, Na
     return false;
 }
 
+// deprecated.
+template <typename TNameStore, typename TName, typename TPos, typename TContext>
+inline bool
+getIdByName(TNameStore const & nameStore, TName const & name, TPos & pos, TContext const & /*not a cache*/)
+{
+    return getIdByName(pos, nameStore, name);
+}
+
+// deprecated.
+template<typename TNameStore, typename TName, typename TPos, typename TCNameStore, typename TCName>
+inline bool
+getIdByName(TNameStore const & /*nameStore*/, TName const & name, TPos & pos, NameStoreCache<TCNameStore, TCName> const & context)
+{
+    return getIdByName(pos, context, name);
+}
+
 // ----------------------------------------------------------------------------
-// appendName()
+// Function nametoId()
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn NameStoreCache#appendName
- * @brief Append a name to a name store and register it in the cache.
+ * @fn NameStoreCache#nameToId
+ * @brief Translate a name to a numeric id, adding the name to the store and cache if new.
  *
- * @signature void appendName(nameStore, name, cache);
+ * @signature TPos nameToId(cache, name);
  *
- * @param[in,out] nameStore The name store to append the name to.
- * @param[in]     name      The name to append to the store.
- * @param[in,out] cache     The NameStoreCache to use for faster access.
+ * @param[in,out] cache The NameStoreCache use for translating the name to a numeric id.
+ * @param[in]     name  The name to add (@link ContainerConcept#Value @endlink of <tt>TNameStore</tt>).
+ *
+ * @return TPos The numeric id of the name in the store and cache (@link ContainerConcept#Position Position @endlink of
+ *              <tt>TNameStore</tt>).
+ *
+ * @note Since <tt>cache</tt> is modified if <tt>name</tt> is not known in cache, it is a <b>non-const</b> parameter
+ *       for this function.
+ *
+ * If <tt>name</tt> is in <tt>cache</tt> then its numeric position/index/id in the name store is returned.  If it is not
+ * in the name store then it is appended to the name store and registered with the NameStoreCache.
  */
 
-/**
-.Function.appendName:
-..summary:Appends a name to a name store.
-..cat:Fragment Store
-..signature:appendName(nameStore, name[, cache])
-..param.nameStore:A name store, e.g. @Memvar.FragmentStore#readNameStore@
-...see:Class.FragmentStore
-..param.name:The name to be appended.
-...type:Shortcut.CharString
-..param.cache:A structure to efficiently retrieve the id for a given name. See @Function.getIdByName@.
-...default:Tag.Nothing
-...type:Class.NameStoreCache
-..see:Function.getIdByName
-..include:seqan/store.h
-*/
-
-template <typename TNameStore, typename TName>
-inline void
-appendName(TNameStore &nameStore, TName const & name)
-{
-    appendValue(nameStore, name, Generous());
-}
-
-template <typename TNameStore, typename TName, typename TContext>
-inline void
-appendName(TNameStore &nameStore, TName const & name, TContext &)
+// Append contig name to name store, if not known already.
+template <typename TNameStore, typename TName, typename TName2>
+typename Position<TNameStore>::Type
+nameToId(NameStoreCache<TNameStore, TName> & cache, TName2 const & name)
 {
-    appendName(nameStore, name);
-}
-
-template <typename TNameStore, typename TName, typename TCNameStore, typename TCName>
-inline void
-appendName(TNameStore &nameStore, TName const & name, NameStoreCache<TCNameStore, TCName> &context)
-{
-    appendValue(nameStore, name, Generous());
-    context.nameSet.insert(length(nameStore) - 1);
+    typename Size<TNameStore>::Type nameId = 0;
+    if (!getIdByName(nameId, cache, name))
+    {
+        nameId = length(host(cache));
+        appendName(cache, name);
+    }
+    return nameId;
 }
 
 }  // namespace seqan
diff --git a/seqan/misc/priority_type_base.h b/seqan/misc/priority_type_base.h
index 8b4e219..513804d 100644
--- a/seqan/misc/priority_type_base.h
+++ b/seqan/misc/priority_type_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -57,20 +57,7 @@ struct PriorityHeap;
  * @tparam TSpec  The specialization.  Default: <tt>PriorityHeap</tt>.
  */
 
-/**
-.Class.PriorityType:
-..cat:Miscellaneous
-..summary:Stores items in such a way that the item with the highest priority is at the top.
-..signature:PriorityType<TValue, TLess, TSpec>
-..param.TValue:The value type that is stored.
-...default:int
-..param.TLess:The comparator type that is used for sorting the items stored.
-...default:std::less<TValue>
-..param.TSpec:The specializing type.
-...default:@Spec.PriorityHeap@
-..include:seqan/misc.h
-*/
-template <typename TValue = int, typename TLess = ::std::less<TValue>, typename TSpec = PriorityHeap>
+template <typename TValue = int, typename TLess = std::less<TValue>, typename TSpec = PriorityHeap>
 class PriorityType;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -78,13 +65,13 @@ class PriorityType;
 template <typename TValue, typename TLess, typename TSpec>
 struct Value< PriorityType<TValue, TLess, TSpec> >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 
 template <typename TValue, typename TLess, typename TSpec>
 struct Size< PriorityType<TValue, TLess, TSpec> >
 {
-	typedef typename Size<TValue>::Type Type;
+    typedef typename Size<TValue>::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/misc/priority_type_heap.h b/seqan/misc/priority_type_heap.h
index 12c218a..9f8524c 100644
--- a/seqan/misc/priority_type_heap.h
+++ b/seqan/misc/priority_type_heap.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,92 +45,108 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Stores the priority data on a heap.
  *
  * @signature template <[typename TValue[, typename TLess]]>
- *            class PriorityType;
+ *            class PriorityType<TValue, TLess, PriorityHeap>;
  *
  * @tparam TValue The value type.  Default: <tt>int</tt>.
  * @tparam TLess  The less-than comparator.  Default: <tt>std::less&lt;TValue&gt;</tt>.
  */
 
-/**
-.Spec.PriorityHeap
-..cat:Miscellaneous
-..general:Class.PriorityType
-..summary:Stores the priority data on a heap.
-..signature:PriorityType<TValue, TLess, PriorityHeap> >
-..include:seqan/misc.h
-*/
 template < typename TValue, typename TLess>
 class PriorityType<TValue,TLess,PriorityHeap>
 {
-public: 
-	typedef String<TValue> THeap;
+public:
+    typedef String<TValue> THeap;
 //____________________________________________________________________________
 
-	TLess less;
-	THeap heap;
+    TLess less;
+    THeap heap;
 //____________________________________________________________________________
 
-	inline PriorityType()
-	{
+    inline PriorityType()
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	inline explicit PriorityType(TLess const & _less):
-		less(_less)
-	{
+    inline explicit PriorityType(TLess const & _less):
+        less(_less)
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	inline PriorityType(PriorityType const & _other):
-		less(_other.less),
-		heap(_other.heap)
-	{
+    inline PriorityType(PriorityType const & _other):
+        less(_other.less),
+        heap(_other.heap)
+    {
 SEQAN_CHECKPOINT
-	}
-		
-//	inline PriorityType const &
-//	operator = (PriorityType const & other_)
-//	{
-//		less = other_.less;
-//		heap = other_.heap;
-//		return *this;
-//	}
-	
+    }
+
+//    inline PriorityType const &
+//    operator = (PriorityType const & other_)
+//    {
+//        less = other_.less;
+//        heap = other_.heap;
+//        return *this;
+//    }
+
 }; // class PriorityType
 
 
 
+/*!
+ * @fn PriorityType#clear
+ * @brief Remove all elements from the PriorityType.
+ *
+ * @signature void clear(pq);
+ *
+ * @param[in,out] pq PriorityType to clear.
+ */
 
 // Empty the priority queue
-///.Function.clear.param.object.type:Class.PriorityType
-///.Function.clear.class:Class.PriorityType
 template <typename TValue, typename TLess>
-inline void 
+inline void
 clear (PriorityType<TValue,TLess, PriorityHeap> & me)
 {
-	clear(me.heap); 
+    clear(me.heap);
 }
 
-// true if priority queue is empty 
-///.Function.empty.param.object.type:Class.PriorityType
-///.Function.empty.class:Class.PriorityType
+/*!
+ * @fn PriorityType#empty
+ * @headerfile <seqan/misc/priority_type_heap.h>
+ * @brief Query priority queue for beging empty.
+ *
+ * @signature bool empty(pq);
+ *
+ * @param[in] pq The @link PriorityType @endlink to query.
+ *
+ * @return bool <tt>true</tt> if <tt>pq</tt> queue is empty.
+ */
+
 template <typename TValue, typename TLess>
-inline bool 
-empty(PriorityType<TValue, TLess, PriorityHeap> const & me) 
+inline bool
+empty(PriorityType<TValue, TLess, PriorityHeap> const & me)
 {
 SEQAN_CHECKPOINT
-	return empty(me.heap); 
+    return empty(me.heap);
 }
 
+/*!
+ * @fn PriorityType#length
+ * @headerfile <seqan/misc/priority_type_heap.h>
+ * @brief Return number of elements in priority queue.
+ *
+ * @signature TSize length(pq);
+ *
+ * @param[in] pq The PriorityType to query.
+ * @return TSize Number of elements in priority queue.
+ */
+
 // Number of elements in the priority queue
-///.Function.length.param.object.type:Class.PriorityType
-///.Function.length.class:Class.PriorityType
 template <typename TValue, typename TLess>
 inline typename Size<PriorityType<TValue, TLess, PriorityHeap> >::Type
 length( PriorityType<TValue, TLess, PriorityHeap> const & me)
-{ 
+{
 SEQAN_CHECKPOINT
-	return length(me.heap);
+    return length(me.heap);
 }
 
 
@@ -144,86 +160,67 @@ SEQAN_CHECKPOINT
  * @fn PriorityType#top
  * @brief Reference to the item with the highest priority.
  *
- * @signature TReference top(priorityType);
+ * @signature TReference top(pq);
  *
- * @param priorityType The PriorityType to query.
+ * @param[in] pq The PriorityType to query.
  *
  * @return TReference The result, reference to Value type.
  */
 
-/**
-.Function.PriorityType#top:
-..summary:Reference to the item with the highest priority.
-..cat:Content Manipulation
-..signature:top(object)
-..class:Class.PriorityType
-..param.object:A priority queue.
-...type:Class.PriorityType
-..remarks:To delete this item and adjust the priority queue use @Function.PriorityType#pop@.
-..see:Function.PriorityType#pop
-..see:Function.PriorityType#push
-..include:seqan/misc.h
-*/
 template <typename TValue, typename TLess>
-inline TValue & 
+inline TValue &
 top(PriorityType<TValue, TLess, PriorityHeap> & me)
 {
 SEQAN_CHECKPOINT
-	return value(me.heap, beginPosition(me.heap));
+    return value(me.heap, beginPosition(me.heap));
 }
 
 template <typename TValue, typename TLess>
-inline TValue const & 
+inline TValue const &
 top(PriorityType<TValue, TLess, PriorityHeap> const & me)
 {
 SEQAN_CHECKPOINT
-	return value(me.heap, beginPosition(me.heap));
+    return value(me.heap, beginPosition(me.heap));
 }
 
 // Copy heap position i to heap position h.
 template <typename TValue, typename TLess, typename TSize>
-inline void 
+inline void
 _copyHeapElement (PriorityType<TValue, TLess, PriorityHeap> & me, TSize i, TSize & h)
 {
 SEQAN_CHECKPOINT
-	me.heap[h] = me.heap[i];
-	h = i;
+    me.heap[h] = me.heap[i];
+    h = i;
 }
 
 // Copy element to heap position h.
 template <typename TValue, typename TLess, typename TSize>
-inline void 
+inline void
 _copyHeapElement (PriorityType<TValue, TLess, PriorityHeap> & me, TValue const & element, TSize h)
 {
 SEQAN_CHECKPOINT
-	me.heap[h] = element;
+    me.heap[h] = element;
 }
 
 /////////////////////////////////////////////////////////////////////////////////
-//  lower priority of first element in queue 
+//  lower priority of first element in queue
 
 /*!
  * @fn PriorityType#adjustTop
  * @brief Adjusts the priority of the first item.
+ *
+ * @signature void adjustTop(pq);
+ *
+ * @param[in,out] pq The PriorityType to adjust.
  */
 
-/**
-.Function.adjustTop
-..cat:Miscellaneous
-..signature:adjustTop(object)
-..class:Class.PriorityType
-..summary:Adjusts the priority of the first item.
-..param.object
-...type:Class.PriorityType
-..include:seqan/misc.h
-*/
 template <typename TValue, typename TLess>
-inline void 
-adjustTop (PriorityType<TValue, TLess, PriorityHeap> & me)	// so könnte man es dann auch nennen
+inline void
+adjustTop (PriorityType<TValue, TLess, PriorityHeap> & me)    // so könnte man es dann auch nennen
 {
 SEQAN_CHECKPOINT
-	if (!empty(me.heap))
-		_adjustHeapTowardLeaves (me, me.heap[0], 0, 2);
+    if (!empty(me.heap))
+        _adjustHeapTowardLeaves (me, me.heap[0], 0, 2);
 }
 
 ////////////
@@ -237,63 +234,48 @@ SEQAN_CHECKPOINT
  * @fn PriorityType#push
  * @brief Inserts a new item and adjusts the priority queue if necessary.
  *
- * @signature void push(pt, element);
+ * @signature void push(pq, element);
  *
- * @param[in,out] pt      The PriorityType to push to.
+ * @param[in,out] pq      The PriorityType to push to.
  * @param[in]     element The element to push.
  */
 
-/**
-.Function.PriorityType#push:
-..summary:Inserts a new item and adjusts the priority queue if necessary.
-..cat:Content Manipulation
-..signature:push(object, element)
-..class:Class.PriorityType
-..param.object:A priority queue.
-...type:Class.PriorityType
-..param.element:The item to be inserted in the priority queue.
-...metafunction:Metafunction.Value
-..remarks:The result of this operation is stored in $object$.
-..see:Function.PriorityType#top
-..see:Function.PriorityType#pop
-..include:seqan/misc.h
-*/
 template <typename TValue, typename TLess>
-inline void 
+inline void
 push (PriorityType<TValue, TLess, PriorityHeap> & me, TValue const & element)
 {
 SEQAN_CHECKPOINT
-	// root index is zero
-	if (empty(me.heap)) {
-		resize(me.heap, 1, Generous());
-		_copyHeapElement (me, element, 0);
-		return;
-	}
-	typedef typename Size<PriorityType<TValue, TLess, PriorityHeap> >::Type TSize;
-	TSize h = length(me.heap); 
-	resize(me.heap, h + 1, Generous());
-	_adjustHeapTowardRoot(me, element, h); 
+    // root index is zero
+    if (empty(me.heap)) {
+        resize(me.heap, 1, Generous());
+        _copyHeapElement (me, element, 0);
+        return;
+    }
+    typedef typename Size<PriorityType<TValue, TLess, PriorityHeap> >::Type TSize;
+    TSize h = length(me.heap);
+    resize(me.heap, h + 1, Generous());
+    _adjustHeapTowardRoot(me, element, h);
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 /// Priority got better.  Perform a cyclic shift along the tree edges toward root.
 template <typename TValue, typename TLess, typename TSize>
-inline void 
+inline void
 _adjustHeapTowardRoot(
-	PriorityType<TValue, TLess, PriorityHeap> & me, 
-	TValue const & element, 
-	TSize h )
+    PriorityType<TValue, TLess, PriorityHeap> & me,
+    TValue const & element,
+    TSize h )
 {
 SEQAN_CHECKPOINT
-	// root index is zero
-	while ( h > 0) {
-		const TSize i = (h-1)/2; 
-		if ( me.less ( me.heap[i], element ) )
-			_copyHeapElement ( me, i, h );
-		else
-			break;
-	}
-	_copyHeapElement ( me, element, h );
+    // root index is zero
+    while ( h > 0) {
+        const TSize i = (h-1)/2;
+        if ( me.less ( me.heap[i], element ) )
+            _copyHeapElement ( me, i, h );
+        else
+            break;
+    }
+    _copyHeapElement ( me, element, h );
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -303,36 +285,23 @@ SEQAN_CHECKPOINT
  * @fn PriorityType#pop
  * @brief Deletes item with the highest priority and adjusts the priority queue.
  *
- * @signature void push(pt);
+ * @signature void push(pq);
  *
- * @param[in,out] pt      The PriorityType to pop from.
+ * @param[in,out] pq      The PriorityType to pop from.
  */
 
-/**
-.Function.PriorityType#pop:
-..summary:Deletes item with the highest priority and adjusts the priority queue.
-..cat:Content Manipulation
-..signature:pop(object)
-..class:Class.PriorityType
-..param.object:A priority queue.
-...type:Class.PriorityType
-..remarks:This function only deletes this item, but does not return it. To access the item use @Function.PriorityType#top@.
-..see:Function.PriorityType#top
-..see:Function.PriorityType#push
-..include:seqan/misc.h
-*/
 template <typename TValue, typename TLess>
-inline void 
+inline void
 pop (PriorityType<TValue, TLess, PriorityHeap> & me)
 {
 SEQAN_CHECKPOINT
-	// root index is zero
-	TValue element = getValue(me.heap,endPosition(me.heap)-1); 
-	typedef typename Size<PriorityType<TValue, TLess, PriorityHeap> >::Type TSize;
-	TSize heapsize = length(me.heap) - 1 ;
-	resize(me.heap, heapsize, Generous());
-	if ( heapsize > 0 ) 
-		_adjustHeapTowardLeaves(me, element, 0, 2 );
+    // root index is zero
+    TValue element = getValue(me.heap,endPosition(me.heap)-1);
+    typedef typename Size<PriorityType<TValue, TLess, PriorityHeap> >::Type TSize;
+    TSize heapsize = length(me.heap) - 1 ;
+    resize(me.heap, heapsize, Generous());
+    if ( heapsize > 0 )
+        _adjustHeapTowardLeaves(me, element, 0, 2 );
 
 }
 
@@ -340,53 +309,49 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////////
 /// Priority got worse. Perform a cyclic shift along the tree edges toward leaves.
 template <typename TValue, typename TLess, typename TSize>
-inline void 
+inline void
 _adjustHeapTowardLeaves(
-	PriorityType<TValue, TLess, PriorityHeap> & me, 
-	TValue element, 
-	TSize h, 
-	TSize i ) //für mich: h=0, i=1
+    PriorityType<TValue, TLess, PriorityHeap> & me,
+    TValue element,
+    TSize h,
+    TSize i ) //für mich: h=0, i=1
 {
 SEQAN_CHECKPOINT
-	// root index is zero
-	const TSize heapsize = length(me.heap);
-	TLess less = me.less;
-	while ( i < heapsize )
-	{
-		if ( less ( element, me.heap[i] ) )
-			if ( less ( me.heap[i-1], me.heap[i] ) )
-				_copyHeapElement ( me, i, h );
-			else
-				_copyHeapElement ( me, i-1, h );
-		else
-			if ( less ( element, me.heap[i-1] ) )
-				_copyHeapElement ( me, i-1, h );
-			else
-				break;
-		i = 2*(h+1);
-	}
-	if ( i == heapsize && less ( element, me.heap[i-1] ) )
-		_copyHeapElement ( me, i-1, h );
-	_copyHeapElement ( me, element, h );
+    // root index is zero
+    const TSize heapsize = length(me.heap);
+    TLess less = me.less;
+    while ( i < heapsize )
+    {
+        if ( less ( element, me.heap[i] ) )
+            if ( less ( me.heap[i-1], me.heap[i] ) )
+                _copyHeapElement ( me, i, h );
+            else
+                _copyHeapElement ( me, i-1, h );
+        else
+            if ( less ( element, me.heap[i-1] ) )
+                _copyHeapElement ( me, i-1, h );
+            else
+                break;
+        i = 2*(h+1);
+    }
+    if ( i == heapsize && less ( element, me.heap[i-1] ) )
+        _copyHeapElement ( me, i-1, h );
+    _copyHeapElement ( me, element, h );
 }
 
 
-	//MetaFunctions
+    //MetaFunctions
 
-///.Metafunction.Size.param.T.type:Class.PriorityType
-///.Metafunction.Size.class:Class.PriorityType
 template < typename TValue, typename TLess>
 struct Size<PriorityType<TValue, TLess, PriorityHeap> >
 {
-	typedef typename Size<typename PriorityType<TValue, TLess, PriorityHeap>::THeap>::Type Type;
+    typedef typename Size<typename PriorityType<TValue, TLess, PriorityHeap>::THeap>::Type Type;
 };
 
-///.metafunction.value.param.t.type:class.prioritytype
-///.metafunction.value.class:class.prioritytype
 template < typename TValue, typename TLess>
 struct Value<PriorityType<TValue, TLess, PriorityHeap> >
 {
-	typedef TValue Type;
+    typedef TValue Type;
 };
 
 
@@ -396,20 +361,20 @@ struct Value<PriorityType<TValue, TLess, PriorityHeap> >
 // debug
 //template <typename TValue, typename THeap, typename TLess>
 //void check(PriorityType<TValue, THeap, TLess> & me) { // debug
-//	typedef typename Size<PriorityType<TValue, THeap, TLess> >::Type TSize;
-//	bool okay = true;
-//	for ( TSize i = 1; i < length(me.heap)-1; ++i )
-//		if ( me.less ( me.heap[(i-1)/2], me.heap[i] ) ) {
-//			cout << '\n' << (i-1)/2 << " < " << i << " : "<< (me.heap[(i-1)/2]).value_ << " !< " << (me.heap[i]).value_;
-//			okay = false;
-//		}
-//	if ( okay )
-//		cout << " ... seems okay\n";
-//	else
-//		cout << "\n... there were errors!\n";
+//    typedef typename Size<PriorityType<TValue, THeap, TLess> >::Type TSize;
+//    bool okay = true;
+//    for ( TSize i = 1; i < length(me.heap)-1; ++i )
+//        if ( me.less ( me.heap[(i-1)/2], me.heap[i] ) ) {
+//            cout << '\n' << (i-1)/2 << " < " << i << " : "<< (me.heap[(i-1)/2]).value_ << " !< " << (me.heap[i]).value_;
+//            okay = false;
+//        }
+//    if ( okay )
+//        cout << " ... seems okay\n";
+//    else
+//        cout << "\n... there were errors!\n";
 //}
 
-	//////////////////////////////////////////////////
+    //////////////////////////////////////////////////
 
 
 
diff --git a/seqan/misc/set.h b/seqan/misc/set.h
new file mode 100644
index 0000000..8503c71
--- /dev/null
+++ b/seqan/misc/set.h
@@ -0,0 +1,608 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+
+#ifndef SEQAN_HEADER_MISC_SET_H
+#define SEQAN_HEADER_MISC_SET_H
+
+#include <set>
+#include <seqan/misc/base.h>
+
+//////////////////////////////////////////////////////////////////////////////
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+    //////////////////////////////////////////////////////////////////////////////
+    //
+    //    VectorSet_
+    //
+    //////////////////////////////////////////////////////////////////////////////
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // forward declaration
+
+    template <typename TElement, typename TSpec>
+    class VectorSet_;
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // internal set meta-functions
+
+    template <typename TElement>
+    struct VectorSetKeySize_ {
+        enum { VALUE = ValueSize< typename Key<TElement>::Type >::VALUE };
+    };
+
+
+    template <typename TSet>
+    struct SetSetVector_ {
+        typedef void* Type;
+    };
+    template <typename TElement, typename TSpec>
+    struct SetSetVector_< VectorSet_<TElement, TSpec> > {
+        typedef String<bool, TSpec> Type;
+    };
+    template <typename TSet>
+    struct SetSetVector_<TSet const> {
+        typedef typename SetSetVector_<TSet>::Type const Type;
+    };
+
+
+
+    template <typename TSet>
+    struct SetObjVector_ {
+        typedef void* Type;
+    };
+    template <typename TKey, typename TObject, typename TPairSpec, typename TSpec>
+    struct SetObjVector_< VectorSet_<Pair<TKey, TObject, TPairSpec>, TSpec> > {
+        typedef String<TObject, TSpec> Type;
+    };
+    template <typename TSet>
+    struct SetObjVector_<TSet const> {
+        typedef typename SetObjVector_<TSet>::Type const Type;
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // VectorSet_ class
+
+    template <
+        typename TElement = char,
+        typename TSpec = Alloc<> /*Array<VectorSetKeySize_<TKey>::VALUE>*/
+    >
+    class VectorSet_ {
+    public:
+        typedef typename SetSetVector_<VectorSet_>::Type        TSetVector;
+        typedef typename SetObjVector_<VectorSet_>::Type        TObjVector;
+        typedef typename Size<VectorSet_>::Type                TSize;
+
+        TSetVector    vector;
+        TObjVector    obj;
+        TSize        size;
+
+        VectorSet_():
+            obj(), size(0)
+        {
+            _autoSize(*this);
+            clear(*this);
+        }
+
+        VectorSet_(TSize _vectorSize):
+            obj(), size(0)
+        {
+            resize(vector, _vectorSize);
+            clear(*this);
+        }
+
+        template <typename TSet_>
+        inline void _autoSize(TSet_ &) {}
+
+        template <typename TElement_>
+        inline void _autoSize(VectorSet_<TElement_, Alloc<> > &) {
+            resize(vector, (unsigned)ValueSize<TElement_>::VALUE);
+        }
+
+        template <typename TKey_, typename TObject_, typename TSpec_>
+        inline void _autoSize(VectorSet_<Pair<TKey_, TObject_, TSpec_>, Alloc<> > &) {
+            resize(vector, (unsigned)ValueSize<TKey_>::VALUE);
+            resize(obj, (unsigned)ValueSize<TKey_>::VALUE);
+        }
+    };
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // set meta-functions
+
+    template <typename TElement, typename TSpec>
+    struct Value< VectorSet_<TElement, TSpec> > {
+        typedef TElement Type;
+    };
+    template <typename TElement, typename TSpec>
+    struct Size< VectorSet_<TElement, TSpec> >:
+        Size< SetSetVector_< VectorSet_<TElement, TSpec> > > {};
+
+    template <typename TElement, typename TSpec>
+    struct Key< VectorSet_<TElement, TSpec> > :
+        Key<TElement> {};
+
+    template <typename TElement, typename TSpec>
+    struct Object< VectorSet_<TElement, TSpec> > :
+        Object<TElement> {};
+
+    template <typename TObject, typename TSpec>
+    inline typename Size< VectorSet_<TObject, TSpec> >::Type
+    length(VectorSet_<TObject, TSpec> const &set) {
+        return set.size;
+    }
+
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    //
+
+    struct VectorSetIterator_;
+    typedef Tag<VectorSetIterator_> VectorSetIterator__;
+
+    template <typename TVectorSet>
+    class Iter< TVectorSet, VectorSetIterator__ >
+    {
+        typedef typename SetSetVector_<TVectorSet>::Type        TSetVector;
+        typedef typename SetObjVector_<TVectorSet>::Type        TObjVector;
+
+        typedef Iter                                            iterator;
+        typedef typename Value<TSetVector>::Type                TValue, value;
+        typedef typename Iterator<TSetVector, Rooted>::Type        TSetIter;
+        typedef typename Iterator<TObjVector, Standard>::Type    TObjIter;
+
+    public:
+        TSetIter    ptr;
+        TObjIter    obj;
+
+        Iter():
+            obj(NULL) {}
+
+        Iter(TSetIter _ptr, TObjIter _obj):
+            ptr(_ptr), obj(_obj)
+        {
+            while (!atEnd(ptr) && !(*ptr)) {
+                ++ptr;
+                ++obj;
+            }
+        }
+
+//        inline TValue operator*() { return TValue(ptr - begin, *obj); }
+
+        inline iterator operator++() {
+            ++ptr;
+            ++obj;
+            while (!atEnd(ptr) && !(*ptr)) {
+                ++ptr;
+                ++obj;
+            }
+            return *this;
+        }
+    };
+
+
+    template <typename TObject, typename TSpec, typename TIteratorSpec>
+    struct Iterator< VectorSet_<TObject, TSpec>, TIteratorSpec > {
+        typedef Iter<VectorSet_<TObject, TSpec>, VectorSetIterator__> Type;
+    };
+    template <typename TObject, typename TSpec, typename TIteratorSpec>
+    struct Iterator< VectorSet_<TObject, TSpec> const, TIteratorSpec> {
+        typedef Iter<VectorSet_<TObject, TSpec> const, VectorSetIterator__> Type;
+    };
+
+    template <typename TValue, typename TSpec>
+    finline void
+    clear(VectorSet_<TValue, TSpec> &set) {
+        arrayFill(begin(set.vector), end(set.vector), false);
+        set.size = 0;
+    }
+
+    template <typename TElement, typename TSetKey, typename TSpec>
+    finline void
+    insert(TElement const &element, VectorSet_<TSetKey, TSpec> &set) {
+        if (!set.vector[(unsigned)(element)]) {
+            ++set.size;
+            set.vector[(unsigned)(element)] = true;
+        }
+    }
+    template <
+        typename TElement,
+        typename TSetKey,
+        typename TSetObject,
+        typename TPairSpec,
+        typename TSpec>
+    finline void
+    insert(TElement const &element, VectorSet_< Pair<TSetKey, TSetObject, TPairSpec>, TSpec > &set) {
+        if (!set.vector[(unsigned)(keyOf(element))]) {
+            ++set.size;
+            set.vector[(unsigned)(keyOf(element))] = true;
+        }
+        set.obj[(unsigned)(keyOf(element))] = objectOf(element);
+    }
+
+    template <typename TKey, typename TValue, typename TSpec>
+    finline void
+    erase(TKey const &key, VectorSet_<TValue, TSpec> &set) {
+        if (set.vector[(unsigned)(key)]) {
+            --set.size;
+            set.vector[(unsigned)(key)] = false;
+        }
+    }
+
+    template <typename TKey, typename TValue, typename TSpec>
+    finline bool
+    in(TKey const &key, VectorSet_<TValue, TSpec> const &set) {
+        return set.vector[(unsigned)(key)];
+    }
+
+    template <typename TKey, typename TKey2, typename TSpec>
+    inline typename Iterator< VectorSet_<TKey2, TSpec> >::Type
+    find(TKey const &key, VectorSet_<TKey2, TSpec> &set) {
+        if (in(key, set))
+            return Iter<VectorSet_<TKey2, TSpec>, VectorSetIterator__>
+                (begin(set.vector, Rooted()) + (unsigned)(key),
+                 begin(set.obj, Standard()) + (unsigned)(key));
+        else
+            return end(set);
+    }
+    template <typename TKey, typename TKey2, typename TSpec>
+    inline typename Iterator< VectorSet_<TKey2, TSpec> const>::Type
+    find(TKey const &key, VectorSet_<TKey2, TSpec> const &set) {
+        if (in(key, set))
+            return Iter<VectorSet_<TKey2, TSpec> const, VectorSetIterator__>
+                (begin(set.vector, Rooted()) + (unsigned)(key),
+                 begin(set.obj, Standard()) + (unsigned)(key));
+        else
+            return end(set);
+    }
+
+    template <typename TElement, typename TSpec>
+    inline typename Iterator< VectorSet_<TElement, TSpec> >::Type
+    begin(VectorSet_<TElement, TSpec> &set) {
+        return Iter<VectorSet_<TElement, TSpec>, VectorSetIterator__>
+            (begin(set.vector, Rooted()), begin(set.obj, Standard()));
+    }
+    template <typename TElement, typename TSpec>
+    inline typename Iterator< VectorSet_<TElement, TSpec> const>::Type
+    begin(VectorSet_<TElement, TSpec> const &set) {
+        return Iter<VectorSet_<TElement, TSpec> const, VectorSetIterator__>
+            (begin(set.vector, Rooted()), begin(set.obj, Standard()));
+    }
+
+    template <typename TElement, typename TSpec>
+    inline typename Iterator< VectorSet_<TElement, TSpec> >::Type
+    end(VectorSet_<TElement, TSpec> &set) {
+        return Iter<VectorSet_<TElement, TSpec>, VectorSetIterator__>
+            (end(set.vector, Rooted()), begin(set.obj, Standard()));
+    }
+    template <typename TElement, typename TSpec>
+    inline typename Iterator< VectorSet_<TElement, TSpec> const>::Type
+    end(VectorSet_<TElement, TSpec> const &set) {
+        return Iter<VectorSet_<TElement, TSpec> const, VectorSetIterator__>
+            (end(set.vector, Rooted()), begin(set.obj, Standard()));
+    }
+
+    template <typename TSet>
+    inline bool
+    operator==(Iter<TSet, VectorSetIterator__> const &a, Iter<TSet, VectorSetIterator__> const &b) {
+        return a.ptr == b.ptr;
+    }
+    template <typename TSet>
+    inline bool
+    operator!=(Iter<TSet, VectorSetIterator__> const &a, Iter<TSet, VectorSetIterator__> const &b) {
+        return a.ptr != b.ptr;
+    }
+    template <typename TSet>
+    inline bool
+    eof(Iter<TSet, VectorSetIterator__> const &a) {
+        return atEnd(a.ptr);
+    }
+    template <typename TSet>
+    inline bool
+    atEnd(Iter<TSet, VectorSetIterator__> const &a) {
+        return atEnd(a.ptr);
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <typename TSet>
+    inline typename Key<TSet>::Type
+    keyOf(Iter<TSet, VectorSetIterator__> const &it) {
+        return position(it.ptr);
+    }
+
+    template <typename TSet>
+    inline typename Object<TSet>::Type &
+    objectOf(Iter<TSet, VectorSetIterator__> const &it) {
+        return *it.obj;
+    }
+    template <typename TSet>
+    inline typename Object<TSet>::Type const &
+    objectOf(Iter<TSet const, VectorSetIterator__> const &it) {
+        return *it.obj;
+    }
+
+
+
+//____________________________________________________________________________
+
+
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    //
+    //    STL set adaptation
+    //
+    //////////////////////////////////////////////////////////////////////////////
+
+
+    template <typename TElement>
+    struct SetLess_ : public std::binary_function<TElement, TElement, bool>
+    {
+        // key less
+        inline bool operator() (TElement const &a, TElement const &b) {
+            return keyOf(a) < keyOf(b);
+        }
+    };
+
+/* DISABLED: this part of code interferes with map_adapter_stl.h
+
+    template <typename TElement>
+    struct Value< std::set<TElement> > {
+        typedef TElement Type;
+    };
+    template <typename TElement>
+    struct Size< std::set<TElement> > {
+        typedef typename std::set<TElement>::size_type Type;
+    };
+
+    template <typename TElement>
+    struct Key< std::set<TElement> > :
+        Key<TElement> {};
+
+    template <typename TElement>
+    struct Object< std::set<TElement> > :
+        Object<TElement> {};
+
+
+
+    template <typename TKey>
+    inline void
+    clear(std::set<TKey> &set) {
+        set.clear();
+    }
+
+    template <typename TElement, typename TSetKey>
+    inline void
+    insert(TElement const &element, std::set<TSetKey> &set) {
+        set.insert(element);
+    }
+
+    template <typename TKey, typename TSetKey>
+    inline void
+    erase(TKey const &key, std::set<TSetKey> &set) {
+        set.erase(key);
+    }
+    template <typename TKey, typename TSetKey, typename TSetObject, typename TPairSpec>
+    inline void
+    erase(TKey const &key, std::set< Pair<TSetKey, TSetObject, TPairSpec> > &set) {
+        set.erase(Pair<TSetKey, TSetObject, TPairSpec>(key, TSetObject()));
+    }
+
+    template <typename TKey, typename TSetKey>
+    inline bool
+    in(TKey const &key, std::set<TSetKey> const &set) {
+        return set.count(key) != 0;
+    }
+    template <typename TKey, typename TSetKey, typename TSetObject, typename TPairSpec>
+    inline bool
+    in(TKey const &key, std::set<Pair<TSetKey, TSetObject, TPairSpec> > const &set) {
+        return set.count(Pair<TSetKey, TSetObject, TPairSpec>(key, TSetObject())) != 0;
+    }
+
+    template <typename TKey>
+    inline typename Size< std::set<TKey> >::Type
+    length(std::set<TKey> const &set) {
+        return set.size();
+    }
+
+    template <typename TKey, typename TSetKey>
+    inline typename Iterator< std::set<TSetKey> >::Type
+    find(TKey const &key, std::set<TSetKey> &set) {
+        return set.find(key);
+    }
+    template <typename TKey, typename TSetKey>
+    inline typename Iterator< std::set<TSetKey> const>::Type
+    find(TKey const &key, std::set<TSetKey> const &set) {
+        return set.find(key);
+    }
+    template <typename TKey, typename TSetKey, typename TSetObject, typename TPairSpec>
+    inline typename Iterator< std::set<Pair<TSetKey, TSetObject, TPairSpec> > >::Type
+    find(TKey const &key, std::set<Pair<TSetKey, TSetObject> > &set) {
+        return set.find(Pair<TSetKey, TSetObject>(key, TSetObject()));
+    }
+    template <typename TKey, typename TSetKey, typename TSetObject>
+    inline typename Iterator< std::set<Pair<TSetKey, TSetObject> > const>::Type
+    find(TKey const &key, std::set<Pair<TSetKey, TSetObject> > const &set) {
+        return set.find(Pair<TSetKey, TSetObject>(key, TSetObject()));
+    }
+
+
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <typename TObject>
+    struct Iterator< std::set<TObject> > {
+        typedef typename std::set<TObject>::iterator Type;
+    };
+    template <typename TObject>
+    struct Iterator< std::set<TObject> const > {
+        typedef typename std::set<TObject>::const_iterator Type;
+    };
+
+
+    template <typename TObject>
+    typename Iterator< std::set<TObject> >::Type begin(std::set<TObject> &set) {
+        return set.begin();
+    }
+    template <typename TObject>
+    typename Iterator< std::set<TObject> const >::Type begin(std::set<TObject> const &set) {
+        return set.begin();
+    }
+    template <typename TObject>
+    typename Iterator< std::set<TObject> >::Type end(std::set<TObject> &set) {
+        return set.end();
+    }
+    template <typename TObject>
+    typename Iterator< std::set<TObject> const >::Type end(std::set<TObject> const &set) {
+        return set.end();
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+
+    template <typename TElement>
+    inline typename Key< std::set<TElement> >::Type &
+    keyOf(typename std::set<TElement>::iterator &it) {
+        return keyOf(*it);
+    }
+    template <typename TElement>
+    inline typename Key< std::set<TElement> >::Type &
+    keyOf(typename std::set<TElement>::iterator const &it) {
+        return keyOf(*it);
+    }
+    template <typename TElement>
+    inline typename Key< std::set<TElement> >::Type const &
+    keyOf(typename std::set<TElement>::const_iterator &it) {
+        return keyOf(*it);
+    }
+    template <typename TElement>
+    inline typename Key< std::set<TElement> >::Type const &
+    keyOf(typename std::set<TElement>::const_iterator const &it) {
+        return keyOf(*it);
+    }
+
+    template <typename TElement>
+    inline typename Object< std::set<TElement> >::Type &
+    objectOf(typename std::set<TElement>::iterator &it) {
+        return objectOf(*it);
+    }
+    template <typename TElement>
+    inline typename Object< std::set<TElement> >::Type &
+    objectOf(typename std::set<TElement>::iterator const &it) {
+        return objectOf(*it);
+    }
+    template <typename TElement>
+    inline typename Object< std::set<TElement> >::Type const &
+    objectOf(typename std::set<TElement>::const_iterator &it) {
+        return objectOf(*it);
+    }
+    template <typename TElement>
+    inline typename Object< std::set<TElement> >::Type const &
+    objectOf(typename std::set<TElement>::const_iterator const &it) {
+        return objectOf(*it);
+    }
+
+
+*/
+
+//____________________________________________________________________________
+
+
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    //
+    //    Set chooser
+    //
+    //////////////////////////////////////////////////////////////////////////////
+
+
+    //////////////////////////////////////////////////////////////////////////////
+    // Set meta-function to choose an efficient implementation
+
+    template <typename TKey>
+    struct Set {
+        typedef std::set<TKey> Type;
+    };
+    template <typename TKey, typename TObject, typename TPairSpec>
+    struct Set< Pair<TKey, TObject, TPairSpec> > {
+        typedef std::set<
+            Pair<TKey, TObject, TPairSpec>,
+            SetLess_< Pair<TKey, TObject, TPairSpec> > > Type;
+    };
+
+
+    template <typename TValue, typename TSpec>
+    struct Set< SimpleType<TValue, TSpec> > {
+        typedef VectorSet_< SimpleType<TValue, TSpec> > Type;
+    };
+    template <typename TValue, typename TSpec, typename TObject, typename TPairSpec>
+    struct Set< Pair<SimpleType<TValue, TSpec>, TObject, TPairSpec> > {
+        typedef VectorSet_< Pair<SimpleType<TValue, TSpec>, TObject, TPairSpec> > Type;
+    };
+
+
+    template <>
+    struct Set<char> {
+        typedef VectorSet_<char> Type;
+    };
+    template <typename TObject, typename TPairSpec>
+    struct Set< Pair<char, TObject, TPairSpec> > {
+        typedef VectorSet_< Pair<char, TObject, TPairSpec> > Type;
+    };
+
+
+    template <>
+    struct Set<signed char> {
+        typedef VectorSet_<signed char> Type;
+    };
+    template <typename TObject, typename TPairSpec>
+    struct Set< Pair<signed char, TObject, TPairSpec> > {
+        typedef VectorSet_< Pair<signed char, TObject, TPairSpec> > Type;
+    };
+
+    template <>
+    struct Set<unsigned char> {
+        typedef VectorSet_<unsigned char> Type;
+    };
+    template <typename TObject, typename TPairSpec>
+    struct Set< Pair<unsigned char, TObject, TPairSpec> > {
+        typedef VectorSet_< Pair<unsigned char, TObject, TPairSpec> > Type;
+    };
+
+}
+
+#endif
diff --git a/seqan/misc/svg.h b/seqan/misc/svg.h
new file mode 100644
index 0000000..c4e88cb
--- /dev/null
+++ b/seqan/misc/svg.h
@@ -0,0 +1,513 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+
+#ifndef SEQAN_HEADER_MISC_SVG_H
+#define SEQAN_HEADER_MISC_SVG_H
+
+namespace SEQAN_NAMESPACE_MAIN
+{
+
+//////////////////////////////////////////////////////////////////////////////
+// SVG File Context
+//////////////////////////////////////////////////////////////////////////////
+
+struct SVGFile
+{
+//IOREV _nodoc_ no documentation whatsoever; uses custom IO, fully independent (maybe postpone adaption)
+    std::fstream file;
+
+    Pair<int> cursor;
+    Pair<int> size;
+    String<CharString> style;
+
+    int dpSequence;
+    int dpMatrix;
+    int dpTrace;
+
+    int text;
+
+    int readForward;
+    int readReverse;
+    int readText;
+    int rulerTextTicks;
+    int rulerTextLabel;
+
+    friend inline void svgWriteHeader(SVGFile &svg);
+    friend inline void svgWriteFooter(SVGFile &svg);
+
+    friend inline bool open(SVGFile &svg, char const * fileName);
+    friend inline bool close(SVGFile &svg);
+
+    SVGFile():
+        cursor(0,0),
+        size(0,0)
+    {
+        resetStyles();
+    }
+
+    SVGFile(char const *fileName):
+        cursor(0,0),
+        size(0,0)
+    {
+        resetStyles();
+        open(*this, fileName);
+    }
+
+    ~SVGFile()
+    {
+        close(*this);
+    }
+
+private:
+
+    inline void resetStyles()
+    {
+        clear(style);
+        readText = dpSequence = length(style);
+        appendValue(style, "style=\"text-anchor:middle; font-family:Bitstream Vera Sans,Verdana,sans-serif;\" font-size=\"18px\"");
+        text = length(style);
+        appendValue(style, "style=\"text-anchor:middle; font-family:Courier New,Verdana,sans-serif; font-weight:bold;\" font-size=\"20px\"");
+        rulerTextTicks = length(style);
+        appendValue(style, "style=\"text-anchor:middle; font-family:Verdana,sans-serif;\" font-size=\"6px\"");
+        rulerTextLabel = length(style);
+        appendValue(style, "style=\"text-anchor:left; font-family:Verdana,sans-serif; font-weight:bold;\" font-size=\"8px\"");
+
+        dpMatrix = length(style);
+        appendValue(style, "style=\"stroke:lightgray;stroke-width:1;\" marker-end=\"url(#startMarkerNormal)\"");
+        dpTrace = length(style);
+        appendValue(style, "style=\"stroke:black;stroke-width:2;\" marker-end=\"url(#startMarkerBold)\"");
+
+        readForward = length(style);
+        appendValue(style, "style=\"stroke:darkblue;stroke-width:3;\"");
+        appendValue(style, "style=\"stroke:lightblue;stroke-width:1;\"");
+        appendValue(style, "style=\"stroke:darkblue;stroke-width:3;\" marker-end=\"url(#startMarkerForward)\"");
+        appendValue(style, "style=\"stroke:lightblue;stroke-width:1;\" marker-end=\"url(#startMarkerForward)\"");
+        readReverse = length(style);
+        appendValue(style, "style=\"stroke:darkred;stroke-width:3;\"");
+        appendValue(style, "style=\"stroke:salmon;stroke-width:1;\"");
+        appendValue(style, "style=\"stroke:darkred;stroke-width:3;\" marker-end=\"url(#startMarkerReverse)\"");
+        appendValue(style, "style=\"stroke:salmon;stroke-width:1;\" marker-end=\"url(#startMarkerReverse)\"");
+    }
+};
+
+template <>
+struct DirectionIterator<SVGFile, Output>
+{
+    typedef SVGFile* Type;
+};
+
+inline void svgResize(SVGFile &svg, int width, int height)
+{
+    svg.size.i1 = width;
+    svg.size.i2 = height;
+}
+
+inline void svgWriteHeader(SVGFile &svg)
+{
+    svg.file << "<?xml version=\"1.0\"?>" << std::endl;
+    svg.file << "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"" << std::endl;
+    svg.file << "  \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">" << std::endl;
+    svg.file << std::endl;
+    svg.file << "<svg version=\"1.1\"" << std::endl;
+    svg.file << "    xmlns=\"http://www.w3.org/2000/svg\"" << std::endl;
+    svg.file << "    xmlns:xlink=\"http://www.w3.org/1999/xlink\"" << std::endl;
+    if (svg.size.i1 != 0)
+    {
+        svg.file << "    width=\"" << svg.size.i1 * 20 << "px\" height=\"" << svg.size.i2 * 20 << "px\"" << std::endl;
+    }
+    svg.file << ">" << std::endl;
+    svg.file << "<defs>" << std::endl;
+
+    // trace back arrow markers
+    svg.file << "    <g id=\"arrowMarker\" stroke-linecap=\"round\">" << std::endl;
+    svg.file << "        <line x1=\"-6\" y1=\"1.5\" x2=\"0\" y2=\"0\" />" << std::endl;
+    svg.file << "        <line x1=\"-6\" y1=\"-1.5\" x2=\"0\" y2=\"0\" />" << std::endl;
+    svg.file << "    </g>" << std::endl;
+    svg.file << "    <marker id=\"startMarkerNormal\" markerWidth=\"6\" markerHeight=\"3\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
+    svg.file << "        <use xlink:href=\"#arrowMarker\" stroke=\"lightgray\" />" << std::endl;
+    svg.file << "    </marker>" << std::endl;
+    svg.file << "    <marker id=\"startMarkerBold\" markerWidth=\"6\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
+    svg.file << "        <use xlink:href=\"#arrowMarker\" stroke-width=\"2\" stroke=\"black\" />" << std::endl;
+    svg.file << "    </marker>" << std::endl;
+
+    // read mapping arrow markers
+    svg.file << "    <marker id=\"startMarkerForward\" markerWidth=\"10\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
+    svg.file << "        <polyline points=\"-8,0 -9,-6 3,0 -9,6 -8,0\" fill=\"darkblue\" />" << std::endl;
+    svg.file << "    </marker>" << std::endl;
+    svg.file << "    <marker id=\"startMarkerReverse\" markerWidth=\"10\" markerHeight=\"4\" style=\"overflow:visible\" orient=\"auto\" markerUnits=\"userSpaceOnUse\">" << std::endl;
+    svg.file << "        <polyline points=\"-8,0 -9,-6 3,0 -9,6 -8,0\" fill=\"darkred\" />" << std::endl;
+    svg.file << "    </marker>" << std::endl;
+
+    svg.file << " </defs>" << std::endl;
+    svg.file << std::endl;
+}
+
+inline void svgWriteFooter(SVGFile &svg)
+{
+    svg.file << std::endl;
+    svg.file << "</svg>" << std::endl;
+}
+
+
+inline bool open(SVGFile &svg, char const * fileName)
+{
+    svg.file.open(fileName, std::ios_base::out);
+    if (!svg.file.is_open()) return false;
+    svgWriteHeader(svg);
+    return true;
+}
+
+inline bool close(SVGFile &svg)
+{
+    if (svg.file.is_open())
+    {
+        svgWriteFooter(svg);
+        svg.file.close();
+    }
+    return true;
+}
+
+SVGFile *
+directionIterator(SVGFile & svg, Output)
+{
+    return &svg;
+}
+
+
+template <typename TCharacter>
+inline void
+writeValue(SVGFile *svg, TCharacter character)
+{
+    char x = static_cast<char>(character);
+    if (x == '\n')
+    {
+        ++svg->cursor.i2;
+        svg->cursor.i1 = 0;
+    }
+    else if (x == '\t')
+    {
+        svg->cursor.i1 = (svg->cursor.i1 & ~7) + 8;
+    }
+    else
+    {
+        if (x != ' ')
+        {
+            svg->file << "<g transform=\"translate(" << svg->cursor.i1*20+10 << ',' << svg->cursor.i2*20+10
+                      << ")\"><text y=\"0.3em\" " << svg->style[svg->text] << '>';
+            svg->file << x;
+            svg->file << "</text></g>" << std::endl;
+        }
+        ++svg->cursor.i1;
+    }
+}
+
+template <typename TContigGaps, typename TContigName>
+inline void _printContig(
+    SVGFile &svg,
+    AlignedReadLayout &,
+    TContigGaps &contigGaps,
+    TContigName const &contigName)
+{
+    typedef typename Iterator<TContigGaps, Standard>::Type TContigIterator;
+
+    TContigIterator cit = begin(contigGaps, Standard());
+    TContigIterator citEnd = end(contigGaps, Standard());
+    for (__int64 ofs = 0; cit != citEnd; ++cit, ++ofs)
+    {
+        if (!isGap(cit))
+        {
+            if (ofs == 0)
+            {
+                svg.file << "<g transform=\"translate(" << ofs*20+2 << ',' << svg.cursor.i2*20+10 << ")\"><text y=\"0.3em\" " << svg.style[svg.rulerTextLabel] << '>';
+                svg.file << contigName << "</text></g>" << std::endl;
+            }
+
+            __int64 seqPos = cit.current.seqPos + 1;
+            if (seqPos % 5 == 0)
+            {
+                if (seqPos % 10 == 0)
+                {
+                    if (ofs >= 5)
+                    {
+                        svg.file << "<g transform=\"translate(" << ofs*20+10 << ',' << svg.cursor.i2*20+10 << ")\"><text y=\"0.3em\" " << svg.style[svg.rulerTextTicks] << '>';
+                        svg.file << seqPos << "</text></g>" << std::endl;
+                    }
+
+                    svg.file << "<line x1=\"" << ofs*20+10 << "\" x2=\"" << ofs*20+10 << "\" ";
+                    svg.file << "y1=\"" << svg.cursor.i2*20+12 << "\" y2=\"" << svg.cursor.i2*20+15 << "\" ";
+                } else {
+                    svg.file << "<line x1=\"" << ofs*20+10 << "\" x2=\"" << ofs*20+10 << "\" ";
+                    svg.file << "y1=\"" << svg.cursor.i2*20+12 << "\" y2=\"" << svg.cursor.i2*20+15 << "\" ";
+                }
+                svg.file << "stroke-width=\"1\" stroke=\"gray\" />" << std::endl;
+            }
+        }
+    }
+    writeValue(&svg, '\n');
+
+    int savedStyle = svg.text;
+    svg.text = svg.readText;
+    svg << contigGaps;
+    svg.text = savedStyle;
+}
+
+template <typename TContigGaps, typename TReadGaps, typename TAlignedRead, typename TLine>
+inline void _printRead(
+    SVGFile &svg,
+    AlignedReadLayout &layout,
+    TContigGaps &contigGaps,
+    TReadGaps &readGaps,
+    TAlignedRead &alignedRead,
+    TLine line)
+{
+    typedef typename Iterator<TContigGaps, Standard>::Type TContigIterator;
+    typedef typename Iterator<TReadGaps, Standard>::Type TIterator;
+
+    __int64 xEnd = svg.cursor.i1 * 20;
+    __int64 x = 0;
+
+    int style, arrow = 0;
+    const char *first;
+    const char *second;
+    __int64 ofs;
+
+    if (alignedRead.beginPos < alignedRead.endPos)
+    {
+        ofs = alignedRead.beginPos - svg.cursor.i1 + beginPosition(readGaps);
+        first = "<line x1=\"";
+        second = "\" x2=\"";
+        style = svg.readForward;
+    } else {
+        ofs = alignedRead.endPos - svg.cursor.i1 + beginPosition(readGaps);
+        first = "<line x2=\"";
+        second = "\" x1=\"";
+        style = svg.readReverse;
+    }
+
+    if (beginPosition(readGaps) == 0)
+    {
+        if (alignedRead.beginPos < alignedRead.endPos)
+            x = xEnd + 5;
+        else {
+            x = xEnd + 10;
+            arrow = 2;
+        }
+    }
+    line = svg.cursor.i2 * 20 + 10;
+
+    if (length(layout.mateCoords) <= alignedRead.pairMatchId)
+        resize(layout.mateCoords, alignedRead.pairMatchId + 1, Pair<int>(-1,-1));
+    else
+    {
+        if (layout.mateCoords[alignedRead.pairMatchId].i2 != -1)
+        {
+            Pair<__int64> a((alignedRead.beginPos - ofs) * 20, line);
+            Pair<__int64> b(layout.mateCoords[alignedRead.pairMatchId]);
+            if (a.i1 < b.i1)
+            {
+                Pair<__int64> tmp = a;
+                a = b;
+                b = tmp;
+            }
+            __int64 dx = (b.i1 - a.i1);
+            __int64 dy = (b.i2 - a.i2);
+
+            svg.file << "<path d=\"M " << a.i1 << ',' << a.i2;
+            svg.file << " C " << a.i1+dy/10 << ',' << a.i2-dx/10;
+            svg.file << ' ' << b.i1+dy/10 << ',' << b.i2-dx/10;
+            svg.file << ' ' << b.i1 << ',' << b.i2;
+            svg.file << "\" stroke-width=\"2\" stroke=\"black\" stroke-opacity=\"0.2\" fill=\"none\"/>";
+        }
+        else
+            layout.mateCoords[alignedRead.pairMatchId] = Pair<int>((alignedRead.beginPos - ofs) * 20, line);
+    }
+
+
+    TContigIterator cit = begin(contigGaps, Standard()) + (_min(alignedRead.beginPos, alignedRead.endPos) + beginPosition(readGaps));
+    TIterator it = begin(readGaps, Standard());
+    TIterator itEnd = end(readGaps, Standard());
+    int lastWasGap = -1;
+    int inGap;
+
+    for (; it != itEnd; ++it, ++cit, xEnd += 20, ++svg.cursor.i1)
+    {
+        inGap = isGap(it);
+        if (lastWasGap != inGap || inGap != static_cast<int>(isGap(cit)) || (!inGap && convert<Dna5>(*cit) != convert<Dna5>(*it)))
+        {
+            if (x < xEnd && lastWasGap != -1)
+            {
+                svg.file << first << x << "\" y1=\"" << line << second << xEnd;
+                svg.file << "\" y2=\"" << line << "\" " << svg.style[style + arrow + lastWasGap] << " />" << std::endl;
+                arrow = 0;
+            }
+            lastWasGap = inGap;
+            x = xEnd;
+            if (!inGap && convert<Dna5>(*cit) != convert<Dna5>(*it))
+            {
+                svg.file << "<g transform=\"translate(" << xEnd + 10 << ',' << line << ")\"><text y=\"0.3em\" " << svg.style[svg.readText] << '>';
+                writeValue(&svg, convert<char>(*it));
+                svg.file << "</text></g>" << std::endl;
+                x += 20;
+                arrow = 0;
+            }
+        }
+    }
+    if (x < xEnd && lastWasGap != -1)
+    {
+        if (static_cast<int>(_unclippedLength(readGaps)) == static_cast<int>(endPosition(readGaps)))
+        {
+            if (alignedRead.beginPos < alignedRead.endPos)
+            {
+                arrow = 2;
+                xEnd -= 10;
+            }
+            else
+            {
+                xEnd -= 5;
+            }
+        }
+        svg.file << first << x << "\" y1=\"" << line << second << xEnd;
+        svg.file << "\" y2=\"" << line << "\" " << svg.style[style + arrow + lastWasGap] << " />" << std::endl;
+    }
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// stream operators
+//////////////////////////////////////////////////////////////////////////////
+/*
+template <typename TSource>
+inline SVGFile &
+operator << (SVGFile & target,
+             TSource  source)
+{
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
+    return target;
+}
+*/
+
+//inline SVGFile &
+//operator << (SVGFile & target, char source)
+//{
+//  typename DirectionIterator<SVGFile, Output>::Type it = directionIterator(target, Output());
+//  write(it, source);
+//    return target;
+//}
+//
+//inline SVGFile &
+//operator << (SVGFile & target, char const *source)
+//{
+//  typename DirectionIterator<SVGFile, Output>::Type it = directionIterator(target, Output());
+//  write(it, source);
+//    return target;
+//}
+
+
+template <typename TStringSet, typename TTrace, typename TIndexPair>
+void
+_alignNeedlemanWunschMatrix(SVGFile& svg,
+                              TStringSet const& str,
+                              TTrace const& trace,
+                              TIndexPair const&)
+{
+SEQAN_CHECKPOINT
+    typedef typename Size<TStringSet>::Type TSize;
+    //typedef typename Value<TTrace>::Type TTraceValue;
+
+    // TraceBack values
+    const int Diagonal = 0;
+    const int Horizontal = 1;
+    const int Vertical = 2;
+
+    // Initialization
+    TSize numCols = length(str[0]);
+    TSize numRows = length(str[1]);
+
+    // Print trace matrix
+    for (TSize pos0 = 0; pos0 < numCols; ++pos0)
+    {
+        for (TSize pos1 = 0; pos1 < numRows; ++pos1)
+        {
+            int tv =(int)trace[pos0*numRows + pos1];
+                if (tv & (1 << Diagonal))
+                    svg.file << "<line x2=\"" << pos0*20+10 << "\" y2=\"" << pos1*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;
+
+                if (tv & (1 << Horizontal))
+                    svg.file << "<line x2=\"" << pos0*20+10 << "\" y2=\"" << (pos1+1)*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;
+
+                if (tv & (1 << Vertical))
+                    svg.file << "<line x2=\"" << (pos0+1)*20+10 << "\" y2=\"" << pos1*20+10 << "\"" << " x1=\"" << (pos0+1)*20+10 << "\" y1=\"" << (pos1+1)*20+10 << "\" " << svg.style[svg.dpMatrix] << " />" << std::endl;
+        }
+    }
+
+    // Print sequences
+    for (TSize pos0 = 0; pos0 < numCols; ++pos0)
+        svg.file << "<g transform=\"translate(" << pos0*20+20 << ",5)\"><text y=\"0.3em\" " << svg.style[svg.dpSequence] << '>' << str[0][pos0] << "</text></g>" << std::endl;
+
+    for (TSize pos1 = 0; pos1 < numRows; ++pos1)
+        svg.file << "<g transform=\"translate(0," << pos1*20+25 << ")\"><text y=\"0.3em\" " << svg.style[svg.dpSequence] << '>' << str[1][pos1] << "</text></g>" << std::endl;
+}
+
+template <typename TStringSet, typename TId, typename TPos, typename TTraceValue>
+inline void
+_alignTracePrint(SVGFile& svg,
+                   TStringSet const&,
+                   TId const,
+                   TPos pos1,
+                   TId const,
+                   TPos pos2,
+                   TPos const segLen,
+                   TTraceValue const tv)
+{
+    // TraceBack values
+    TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2;
+
+    svg.file << "<line x2=\"" << pos1*20+10 << "\" y2=\"" << pos2*20+10 << "\"";
+    if (tv == Diagonal) {
+        pos1 += segLen; pos2 += segLen;
+    } else if (tv == Horizontal) {
+        pos1 += segLen;
+    } else if (tv == Vertical) {
+        pos2 += segLen;
+    }
+    svg.file << " x1=\"" << pos1*20+10 << "\" y1=\"" << pos2*20+10;
+    svg.file << "\" " << svg.style[svg.dpTrace] << " />" << std::endl;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+} //namespace SEQAN_NAMESPACE_MAIN
+
+#endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/misc/misc_terminal.h b/seqan/misc/terminal.h
similarity index 77%
rename from seqan/misc/misc_terminal.h
rename to seqan/misc/terminal.h
index e7bcd15..82fba15 100644
--- a/seqan/misc/misc_terminal.h
+++ b/seqan/misc/terminal.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Terminal-related functionality.
 // ==========================================================================
 
-#ifndef SEQAN_MISC_MISC_TERMINAL_H_
-#define SEQAN_MISC_MISC_TERMINAL_H_
+#ifndef SEQAN_MISC_TERMINAL_H_
+#define SEQAN_MISC_TERMINAL_H_
 
 #include <cstdio>
 
@@ -65,23 +65,17 @@ namespace seqan {
 
 /*!
  * @fn isTerminal
- * @headerfile <seqan/misc/misc_termina.h>
+ * @headerfile <seqan/misc/terminal.h>
  * @brief Check whether we are printing to a terminal.
  *
  * @signature bool isTerminal();
  *
  * @return bool true if we are on the terminal, false otherwise.
+ *
+ * @see getTerminalSize
+ * @see isAnsiColorTerminal
  */
 
-/**
-.Function.isTerminal()
-..cat:Miscellaneous
-..summary:Check whether we are printing to a terminal.
-..signature:isTerminal()
-..returns:$true$ if we are on the terminal, false otherwise.
-..include:seqan/misc/misc_terminal.h
-*/
-
 #if defined(PLATFORM_WINDOWS)
 
 #include <io.h>
@@ -114,28 +108,21 @@ inline bool isTerminal()
 
 /*!
  * @fn isAnsiColorTerminal
- * @headerfile <seqan/misc/misc_terminal.h>
+ * @headerfile <seqan/misc/terminal.h>
  * @brief Check whether we are printing to a terminal that supports ANSI color codes.
  *
  * @signature bool isAnsiColorTerminal();
  *
- * @return bool true if we are in a terminal and the terminal interprets ANSI color code.s
+ * @return bool true if we are in a terminal and the terminal interprets ANSI color code.
  *
  * @section Remarks
  *
  * Currently, we assume that UNIX terminals support color while Windows terminals and non-terminals do not.
+ *
+ * @see isTerminal
+ * @see getTerminalSize
  */
 
-/**
-.Function.isAnsiColorTerminal
-..cat:Miscellaneous
-..summary:Check whether we are printing to a terminal.
-..signature:isTerminal()
-..returns:$true$ if we are in a terminal and the terminal knows ANSI color codes.
-..remarks:Currently, we assume that Unix terminals support color while Windows terminals and no terminals do not.
-..include:seqan/misc/misc_terminal.h
-*/
-
 #if defined(PLATFORM_WINDOWS) || defined(PLATFORM_GCC_MINGW)
 
 inline bool isAnsiColorTerminal()
@@ -158,7 +145,7 @@ inline bool isAnsiColorTerminal()
 
 /*!
  * @fn getTerminalSize
- * @headerfile <seqan/misc/misc_terminal.h>
+ * @headerfile <seqan/misc/terminal.h>
  * @brief Retrieve size of terminal.
  *
  * @signature bool getTerminalSize(cols, rows);
@@ -176,32 +163,12 @@ inline bool isAnsiColorTerminal()
  *
  * The following demonstrates the usage.
  *
- * @include demos/misc/get_terminal_size.cpp
+ * @include demos/dox/misc/get_terminal_size.cpp
+ *
+ * @see isTerminal
+ * @see isAnsiColorTerminal
  */
 
-/**
-.Function.getTerminalSize
-..cat:Miscellaneous
-..summary:Retrieve size of terminal.
-..signature:getTerminalSize(cols, rows)
-..param.cols:The column count is written here.
-...type:nolink:$unsigned$
-..param.rows:The line count is written here.
-...type:nolink:$unsigned$
-..returns:$true$ on success, $false$ otherwise.
-...type:nolink:$bool$
-..remarks:On Windows, $rows$ contains the number of rows in the terminal *buffer*, not the window.
-..include:seqan/misc/misc_terminal.h
-..example:The following demonstrates the usage.
-..example.code:
-#include <seqan/misc/misc_terminal.h>
-
-unsigned rows = 0, cols = 0;
-bool success = getTerminalSize(cols, rows);
-std::cerr << "rows == " << rows << ", cols == " << cols
-          << ", success == " << success << "\n";
-*/
-
 #if defined(PLATFORM_WINDOWS)
 
 #include <Windows.h>
@@ -245,4 +212,4 @@ inline bool getTerminalSize(unsigned & cols, unsigned & rows)
 
 }  // namespace seqan
 
-#endif // #ifndef SEQAN_MISC_MISC_TERMINAL_H_
+#endif // #ifndef SEQAN_MISC_TERMINAL_H_
diff --git a/seqan/misc/misc_union_find.h b/seqan/misc/union_find.h
similarity index 79%
rename from seqan/misc/misc_union_find.h
rename to seqan/misc/union_find.h
index 88a2c9c..544fb02 100644
--- a/seqan/misc/misc_union_find.h
+++ b/seqan/misc/union_find.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,9 +34,11 @@
 // Implementation of the Union-Find data structure.
 // ==========================================================================
 
-#ifndef SEQAN_MISC_MISC_UNION_FIND_H_
-#define SEQAN_MISC_MISC_UNION_FIND_H_
+#ifndef SEQAN_MISC_UNION_FIND_H_
+#define SEQAN_MISC_UNION_FIND_H_
 
+#include <seqan/basic.h>
+#include <seqan/sequence.h>
 // TODO(holtgrew): Comprehensive tests. Currently, there are *some* tests in the tests for graph_algorithm.
 
 namespace seqan {
@@ -45,13 +47,15 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
+template <typename TSpec> class Graph;
+
 // ============================================================================
 // Classes, Structs, Enums, Tags
 // ============================================================================
 
 /*!
  * @class UnionFind
- * @headerfile <seqan/misc/misc_union_find.h>
+ * @headerfile <seqan/misc/union_find.h>
  * @brief Union-Find data structure.
  *
  * @signature template <typename T>
@@ -59,24 +63,11 @@ namespace seqan {
  *
  * @tparam T The integer type the data structure operates on.
  *
- * @section Remarks
- *
  * The data structure uses union by rank and path compresison to achieve almost linear running time.
  *
  * Note that internally T is used as signed, so not the whole range is available if T is unsigned.
  */
 
-/**
-.Class.UnionFind
-..cat:Miscellaneous
-..summary:Union-Find data structure.
-..signature:UnionFind<T>
-..param.T:The type the data structure operates on.
-..remarks:The data structure uses union by rank and path compression to achieve almost linear running time.
-..remarks:Note that internally, T is used signed so not the whole range might be available.
-..include:seqan/misc/misc_union_find.h
- */
-
 template <typename TValue>
 class UnionFind
 {
@@ -104,9 +95,6 @@ class UnionFind
  * @tparam TUnionFind The UnionFind specialization to query for its value type.
  */
 
-///.Metafunction.Value.param.T.type:Class.UnionFind
-///.Metafunction.Value.class:Class.UnionFind
-
 template <typename TValue>
 struct Value<UnionFind<TValue> >
 {
@@ -131,14 +119,11 @@ struct Value<UnionFind<TValue> const>
  * @mfn UnionFind#GetValue
  * @brief Returns the get-value type for the given UnionFind specialization.
  *
- * @signature Value<TUnionFind>::Type
+ * @signature GetValue<TUnionFind>::Type
  *
  * @tparam TUnionFind The UnionFind specialization to query for its get-value type.
  */
 
-///.Metafunction.GetValue.param.T.type:Class.UnionFind
-///.Metafunction.GetValue.class:Class.UnionFind
-
 template <typename TValue>
 struct GetValue<UnionFind<TValue> >
 {
@@ -168,9 +153,6 @@ struct GetValue<UnionFind<TValue> const>
  * @tparam TUnionFind The UnionFind specialization to query for its size type.
  */
 
-///.Metafunction.Size.param.T.type:Class.UnionFind
-///.Metafunction.Size.class:Class.UnionFind
-
 template <typename TValue>
 struct Size<UnionFind<TValue> >
 {
@@ -204,9 +186,6 @@ struct Size<UnionFind<TValue> const>
  * @param[in,out] uf The Union-Find object to clear
  */
 
-///.Function.clear.param.object.type:Class.UnionFind
-///.Function.clear.class:Class.UnionFind
-
 template <typename TValue>
 inline
 void
@@ -227,12 +206,9 @@ clear(UnionFind<TValue> & unionFind)
  *
  * @param[in] uf The Union-Find object to query.
  *
- * @return TSize The length of the Union-Find object.  TSize is the size type of uf.
+ * @return TSize The length of the Union-Find object  (Metafunction: @link UnionFind#Size @endlink).
  */
 
-///.Function.length.param.object.type:Class.UnionFind
-///.Function.length.class:Class.UnionFind
-
 template <typename TValue>
 inline
 typename Size<UnionFind<TValue> >::Type
@@ -251,16 +227,13 @@ length(UnionFind<TValue> const & unionFind)
  * @fn UnionFind#reverse
  * @brief Reserve memory for the Union-Find object.
  *
- * @signature TSize reserve(uf, size, tag);
+ * @signature void reserve(uf, size, tag);
  *
  * @param[in,out] uf    The Union-Find object to reserve memory in.
  * @param[in]     size  The number of elements to reserve.
  * @param[in]     tag   The tag to use for reserving (defaults to <tt>Generous()</tt>).
  */
 
-///.Function.reserve.param.object.type:Class.UnionFind
-///.Function.reserve.class:Class.UnionFind
-
 template <typename TValue, typename TSize, typename TTag>
 inline
 typename Size<UnionFind<TValue> >::Type
@@ -287,12 +260,10 @@ reserve(UnionFind<TValue> & unionFind,
  * @param[in,out] uf    The Union-Find object to resize.
  * @param[in]     size  The number of elements to reserve.
  * @param[in]     tag   The tag to use for reserving (defaults to <tt>Generous()</tt>).
+ *
+ * @return TSize The new length of the Union-Find object  (Metafunction: @link UnionFind#Size @endlink).
  */
 
-///.Function.resize.param.object.type:Class.UnionFind
-///.Function.resize.class:Class.UnionFind
-///.Function.resize.remarks:If $pm$ is of the @Class.UnionFind@, $value$ will automatically be set to -1.
-
 template <typename TValue, typename TSize, typename TTag>
 inline
 typename Size<UnionFind<TValue> >::Type
@@ -313,21 +284,18 @@ resize(UnionFind<TValue> & unionFind,
  * @fn UnionFind#resizeVertexMap
  * @brief Resize Union-Find data structure to appropriate size for a vertex map.
  *
- * @signature TSize resizeVertexMap(g, uf);
+ * @signature TSize resizeVertexMap(uf, g);
  *
- * @param[in]     g  The graph to use for getting the vertex number.
  * @param[in,out] uf The Union-Find object to resize.
+ * @param[in]     g  The graph to use for getting the vertex number.
+ *
+ * @return TSize New size of the vertex map  (Metafunction: @link UnionFind#Size @endlink).
  */
 
-///.Function.resizeVertexMap.param.pm.type:Class.UnionFind
-///.Function.resizeVertexMap.class:Class.UnionFind
-///.Function.resizeVertexMap.remarks:If $pm$ is of type @Class.UnionFind@ then the $prototype$ parameter is not available.
-
 template <typename TSpec, typename TValue>
-inline
 typename Size<UnionFind<TValue> >::Type
-resizeVertexMap(Graph<TSpec> const & g,
-                UnionFind<TValue> & unionFind)
+resizeVertexMap(UnionFind<TValue> & unionFind,
+                Graph<TSpec> const & g)
 {
     clear(unionFind);
     return resize(unionFind, numVertices(g));
@@ -346,23 +314,11 @@ resizeVertexMap(Graph<TSpec> const & g,
  * @param[in] uf  The Union-Find object to query.
  * @param[in] q   The value to get the set identifier for.
  *
+ * @return TValue Identifier of the set that <tt>q</tt> is in  (Metafunction: @link UnionFind#Value @endlink).
+ *
  * @see UnionFind#joinSets
  */
 
-/**
-.Function.findSet:
-..cat:Miscellaneous
-..summary:Return set identifier, given an element identifier.
-..signature:find(unionFind, query)
-..class:Class.UnionFind
-..param.unionFind:The Union-Find data structure query.
-...type:Class.UnionFind
-..param.query:The value to query for.
-..returns:The set identifier for the given element id.
-..see:Function.joinSets
-..include:seqan/misc/misc_union_find.h
- */
-
 template <typename TValue, typename TQuery>
 inline
 TValue
@@ -375,7 +331,7 @@ findSet(UnionFind<TValue> & unionFind,
     SEQAN_ASSERT_LT(unionFind._values[j], static_cast<int>(length(unionFind._values)));
     SEQAN_ASSERT_GEQ(j, static_cast<TValue>(0));
     SEQAN_ASSERT_LT(j, static_cast<TValue>(length(unionFind._values)));
-    
+
     TValue i = query;
     while (unionFind._values[i] >= 0)
     {
@@ -383,7 +339,7 @@ findSet(UnionFind<TValue> & unionFind,
         i = unionFind._values[i];
         unionFind._values[tmp] = j;
     }
-    
+
     return j;
 }
 
@@ -401,8 +357,6 @@ findSet(UnionFind<TValue> & unionFind,
  * @param[in]     left  Representant of the left set to union.
  * @param[in]     right Representant of the right set to union.
  *
- * @section Remarks
- *
  * This function is called <tt>join</tt> and not <tt>union</tt> since <tt>union</tt> is a reserved keyword in the
  * C and C++ programming languages.
  *
@@ -412,22 +366,6 @@ findSet(UnionFind<TValue> & unionFind,
  * @see UnionFind#findSet
  */
 
-/**
-.Function.joinSets
-..cat:Miscellaneous
-..summary:UNION() operation for UF data structure.
-..signature:joinSets(unionFind, left, right)
-..class:Class.UnionFind
-..param.unionFind:The type the data structure operates on.
-...type:Class.UnionFind
-..param.left:Representant of the left set to union.
-..param.right:Representant of the right set to union.
-..remarks:This function is called $join$ and not $union$ since $union$ is a reserved keyword in the C and C++ programming languages.
-..remarks:Note that you most likely want to put return values of $findSet()$ as the values for $left$ and $right$.
-..see:Function.findSet
-..include:seqan/misc/misc_union_find.h
- */
-
 template <typename TValue, typename TLeft, typename TRight>
 inline
 void
@@ -449,4 +387,4 @@ joinSets(UnionFind<TValue> & unionFind,
 
 }  // namespace seqan
 
-#endif // #ifndef SEQAN_MISC_MISC_UNION_FIND_H_
+#endif // #ifndef SEQAN_MISC_UNION_FIND_H_
diff --git a/seqan/modifier.h b/seqan/modifier.h
index aa3cdae..187cb06 100644
--- a/seqan/modifier.h
+++ b/seqan/modifier.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Umbrella header for the modifier module.
 // ==========================================================================
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_MODIFIER_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_MODIFIER_H_
+#ifndef SEQAN_INCLUDE_SEQAN_MODIFIER_H_
+#define SEQAN_INCLUDE_SEQAN_MODIFIER_H_
 
 // --------------------------------------------------------------------------
 // Prerequisites
@@ -61,6 +61,12 @@
 #include <seqan/modifier/modifier_iterator.h>
 #include <seqan/modifier/modifier_string.h>
 
+// --------------------------------------------------------------------------
+// Auxiliary header for special modifiers
+// --------------------------------------------------------------------------
+
+#include <seqan/modifier/cyclic_shape.h>
+
 // --------------------------------------------------------------------------
 // Applications of Base Classes
 // --------------------------------------------------------------------------
@@ -69,5 +75,7 @@
 #include <seqan/modifier/modifier_view.h>
 #include <seqan/modifier/modifier_reverse.h>
 #include <seqan/modifier/modifier_shortcuts.h>
+#include <seqan/modifier/modifier_cyclic_shape.h>
+#include <seqan/modifier/modifier_position.h>
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_MODIFIER_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_MODIFIER_H_
diff --git a/seqan/modifier/INFO b/seqan/modifier/INFO
deleted file mode 100644
index 98f4164..0000000
--- a/seqan/modifier/INFO
+++ /dev/null
@@ -1,11 +0,0 @@
-Name: seqan-modifier
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Sequence and alphabet modifications.
- This module contains the implementation of the modified strings, alphabet
- expansions and in-place conversions.
diff --git a/seqan/modifier/cyclic_shape.h b/seqan/modifier/cyclic_shape.h
new file mode 100644
index 0000000..967cf76
--- /dev/null
+++ b/seqan/modifier/cyclic_shape.h
@@ -0,0 +1,622 @@
+// ========================================================================== 
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Sascha Meiers <meiers@inf.fu-berlin.de>
+// ==========================================================================
+// Definition of generic and fixed-at-compile-time CyclicShapes
+// ==========================================================================
+
+#ifndef SEQAN_HEADER_CYCLIC_SHAPE_H
+#define SEQAN_HEADER_CYCLIC_SHAPE_H
+
+#include <seqan/index/shape_base.h>
+#include <seqan/index/shape_gapped.h>
+
+namespace seqan {
+
+// ==========================================================================
+// Forwards
+// ==========================================================================
+
+// needed for GappedShape<HardwiredShape<...> >
+template<typename TSpec> struct GappedShape;
+
+// GenericShape defined in shape_gapped.h via typedef
+typedef GappedShape<Default> GenericShape;
+
+// ==========================================================================
+// Tags, Classes, Enums
+// ==========================================================================
+
+// --------------------------------------------------------------------------
+// Class CyclicShape
+// --------------------------------------------------------------------------
+
+/*!
+ * @class CyclicShape
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief A pattern of zeros and ones to mark "don't care"-positions in a text.
+ *
+ * @signature template <typename TShapeSpec>
+ *            class CyclicShape<TShapeSpec>;
+ *
+ * @tparam TShapeSpec The specializing type. Default is @link GenericCyclicShape
+ *         GenericShape @endlink, another option is @link FixedCyclicShape
+ *         FixedShape @endlink.
+ * @tparam TSize Size type of the CyclicShape
+ *
+ * CyclicShapes store a pattern like <tt>11010100110</tt> that mark
+ * care (match) positions and don't-care positions.
+ * Unlike @link Shape @endlink, the CyclicShape does not perform hashing of q-grams.
+ * It is instead useful to modify a text in such a way that zero
+ * position are ignored. The pattern is applied repeatedly on the whole
+ * text, as the example shows.
+ *
+ * Note that CyclicShapes can start and end with zero characters, which
+ * is not allowed in @link Shape @endlink.
+ *
+ * @section Examples
+ * @include demos/dox/modifier/cyclic_shape.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/modifier/cyclic_shape.cpp.stdout
+ *
+ * @see ModCyclicShapeModifiedString
+ * @see ModCyclicShapeModifiedIterator
+ */
+template<typename TCyclicSpec = GenericShape>
+class CyclicShape;                           // member: diffs, loffset, span
+
+template<unsigned L, typename THardWiredShape, unsigned R>
+struct FixedShape;
+
+// --------------------------------------------------------------------------
+// Metafunction Size
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn CyclicShape#Size
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief Size type for parameters used in CyclicShape.
+ *
+ * @signature Size<CyclicShape<TSpec> >::Type;
+ *
+ * @tparam TSpec The CyclicShape specialization.
+ *
+ * @return TReturn Currently the return type <tt>unsigned char</tt>.
+ *
+ * @section Remarks
+ */
+template<typename TSpec>
+struct Size<CyclicShape<TSpec> >
+{
+    typedef unsigned char Type;
+};
+
+// --------------------------------------------------------------------------
+// Class GenericCyclicShape
+// --------------------------------------------------------------------------
+
+/*!
+ * @class GenericCyclicShape Generic CyclicShape
+ * @extends CyclicShape
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief CyclicShape initiated at runtime.
+ *
+ * @tparam TSize Size type of the CyclicShape
+ *
+ * @signature template <>
+ *            class CyclicShape<GenericShape>;
+ *
+ * Generic Shapes can be easily created using <tt>stringToCyclicShape</tt>,
+ * but their usage comes with a significant loss in efficiency.
+ * For longer sequences, prefer the @link FixedCyclicShape @endlink.
+ *
+ * @section Examples
+ * @include demos/dox/modifier/cyclic_shape.cpp
+ *
+ * The output is as follows:
+ *
+ * @include demos/dox/modifier/cyclic_shape.cpp.stdout
+ *
+ * @see ModCyclicShapeModifiedString
+ * @see ModCyclicShapeModifiedIterator
+ */
+template<>
+class CyclicShape<GenericShape>
+{
+public:
+    /*!
+     * @var String<TSize> GenericCyclicShape::diffs;
+     * @brief Distances between care positions.
+     *
+     * <tt>diffs</tt> has <i>weight</i> many non-zero entries describing the size
+     * of the gap after a care-position. The last entry holds the cyclic distance from
+     * the last "1" to the first one.
+     */
+    String<Size<CyclicShape>::Type> diffs;
+
+    /*!
+     * @var TSize CyclicShape::span;
+     * @brief span of the CyclicShape.
+     * @var TSize CyclicShape::loffset;
+     * @brief left offset (number of leading zeros) of the CyclicShape.
+     */
+    Size<CyclicShape>::Type loffset, span;
+
+    /*!
+     * @fn GenericCyclicShape::CyclicShape
+     * @brief The constructor
+     * @signature CyclicShape();
+     * @signature CyclicShape(shape);
+     * @param[in] shape A GenericCyclicShape to be copied.
+     *
+     * The default constructor generates the pattern "1".
+     * The copy constructor copies the GenericCyclicShape shape.
+     *
+     * @snippet demos/dox/modifier/cyclic_shape_snippets.cpp Define GenericCyclicShape
+     *
+     * @Remarks
+     *
+     * If you want to generate a GenericCyclicShape from a FixedCyclicShape,
+     * use @link CyclicShape#cyclicShapeToString @endlink and @link GenericCyclicShape#stringToCyclicShape @endlink
+     */
+    CyclicShape() :
+        loffset(0), span(1)
+    {
+        // Pattern "1"
+        appendValue(diffs, 1);
+    }
+
+    CyclicShape(CyclicShape const & other) :
+        diffs(other.diffs), loffset(other.loffset), span(other.span)
+    {}
+};
+
+// --------------------------------------------------------------------------
+// Class FixedCyclicShape
+// --------------------------------------------------------------------------
+
+/*!
+ * @class FixedCyclicShape Fixed CyclicShape
+ * @extends CyclicShape
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief CyclicShape defined at compile time.
+ *
+ * @signature template <unsigned L, typename THardwiredShape, unsigned R>
+ *            class CycledShape<FixedShape<L, GappedShape<THardwiredShape>, R> >;
+ *
+ * @tparam L Left offset. Number of leading zeros of the Shape.
+ * @tparam R Right offset. Number of trailing zeros of the Shape.
+ * @tparam THardwiredShape A specialization of @link HardwiredShape @endlink
+ * @tparam TSize Size type of the CyclicShape
+ *
+ * Fixed CylcicShapes contain their information at compile time, so in
+ * most cases no object must be created.
+ * The notation is similar to the one of @link HardwiredShape @endlink: Template
+ * paramters code for the distance between ones. Additionally you have to specify
+ * the number of leading and trailing zeros.
+ *
+ * The notation is chosen in such a way that predefined Shapes like
+ * PatternHunter can be plugged into a CyclicShape. Like
+ * HardwiredShapes, Fixed CyclicShapes are limited to a weight of 21.
+ *
+ * See @link CyclicShape @endlink for an example on how to use a CyclicShape.
+ *
+ * @see ModCyclicShapeModifiedString
+ * @see ModCyclicShapeModifiedIterator
+ */
+template<unsigned LeftOffset, unsigned RightOffset,
+         int P00, int P01, int P02, int P03, int P04,
+         int P05, int P06, int P07, int P08, int P09,
+         int P10, int P11, int P12, int P13, int P14,
+         int P15, int P16, int P17, int P18, int P19>
+class CyclicShape<FixedShape<LeftOffset, GappedShape<HardwiredShape<
+        P00, P01, P02, P03, P04, P05, P06, P07, P08, P09, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19>
+        >, RightOffset> >
+{
+public:
+    typedef HardwiredShape<
+            P00, P01, P02, P03, P04, P05, P06, P07, P08, P09, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19>
+            THardWiredShape;
+
+    enum {loffset = LeftOffset};
+    enum {span = LeftOffset + LENGTH<THardWiredShape>::VALUE + RightOffset};
+
+    /*!
+     * @var TSize[] FixedCyclicShape::diffs;
+     * @brief Distances between care positions.
+     *
+     * <tt>static const TSize diffs[]</tt> has <i>weight</i> many non-zero entries
+     * in the beginning, the remaining ones are zero. An additional entry at position
+     * <i>weight1</i> holds the cyclic distance from the last "1" to the first one.
+     * During the iteration with a @link ModCyclicShapeModifiedIterator @endlink
+     * an index position keeps track of the position inside <tt>diffs</tt>.
+     */
+    static const typename Size<CyclicShape>::Type diffs[];
+
+    /*!
+     * @fn FixedCyclicShape::CyclicShape
+     * @brief The constructor
+     *
+     * @signature CyclicShape();
+     * @signature CyclicShape(shape);
+     *
+     * @param[in] shape A FixedCyclicShape of this type
+     *
+     * This constructor does not do anything, the FixedCyclicShape is defined by its type alone.
+     * See the example on how to create a CyclicShape:
+     *
+     * @snippet demos/dox/modifier/cyclic_shape_snippets.cpp Define FixedCyclicShape
+     */
+    CyclicShape()
+    {}
+
+    CyclicShape(CyclicShape const &)
+    {}
+};
+
+// --------------------------------------------------------------------------
+// static const int CyclicShape<FixedShape<L, TSpec, R> >::diffs[]
+//
+// ugly work around to derive the static const array diffs[] from
+// the static const array HardwiredShape::DIFFS. In diffs, the first
+// zero-entry of DIFFS had to be changed.
+// Note: This requires that the non-used entries of
+// HardwiredShape::DIFFS are zero.
+// --------------------------------------------------------------------------
+
+template<unsigned entry, typename TFixedS>
+struct _tmpArrEntry;
+
+// normal positions in diff[]
+template<unsigned entry, unsigned L, unsigned R,
+         int P00, int P01, int P02, int P03, int P04,
+         int P05, int P06, int P07, int P08, int P09,
+         int P10, int P11, int P12, int P13, int P14,
+         int P15, int P16, int P17, int P18, int P19>
+struct _tmpArrEntry<entry, FixedShape<L, GappedShape<HardwiredShape
+        <P00, P01, P02, P03, P04, P05, P06, P07, P08, P09, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19> >, R> >
+{
+    enum {VALUE = entry};
+};
+
+// zero positions in diff[]
+template<unsigned L, unsigned R,
+         int P00, int P01, int P02, int P03, int P04,
+         int P05, int P06, int P07, int P08, int P09,
+         int P10, int P11, int P12, int P13, int P14,
+         int P15, int P16, int P17, int P18, int P19>
+struct _tmpArrEntry<0, FixedShape<L, GappedShape<HardwiredShape
+        <P00, P01, P02, P03, P04, P05, P06, P07, P08, P09, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19> >, R> >
+{
+    enum {VALUE = L + R + 1};
+};
+
+#define ENTRY(X) \
+    _tmpArrEntry<X, FixedShape<L, GappedShape<HardwiredShape \
+    <P00, P01, P02, P03, P04, P05, P06, P07, P08, P09, \
+    P10, P11, P12, P13, P14, P15, P16, P17, P18, P19> >, R> >::VALUE
+
+template<unsigned L, unsigned R,
+        int P00, int P01, int P02, int P03, int P04,
+        int P05, int P06, int P07, int P08, int P09,
+        int P10, int P11, int P12, int P13, int P14,
+        int P15, int P16, int P17, int P18, int P19>
+const typename Size<CyclicShape<FixedShape<L, GappedShape<HardwiredShape
+        <P00, P01, P02, P03, P04, P05, P06, P07, P08, P09, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19>
+        >, R> > >::Type
+CyclicShape<FixedShape<L, GappedShape<HardwiredShape
+        <P00, P01, P02, P03, P04, P05, P06, P07, P08, P09, P10, P11, P12, P13, P14, P15, P16, P17, P18, P19>
+        >, R> >::diffs[] =
+{
+    ENTRY(P00), ENTRY(P01), ENTRY(P02), ENTRY(P03), ENTRY(P04),
+    ENTRY(P05), ENTRY(P06), ENTRY(P07), ENTRY(P08), ENTRY(P09),
+    ENTRY(P10), ENTRY(P11), ENTRY(P12), ENTRY(P13), ENTRY(P14),
+    ENTRY(P15), ENTRY(P16), ENTRY(P17), ENTRY(P18), ENTRY(P19),
+    ENTRY(0)
+};
+
+#undef ENTRY
+
+
+
+// ==========================================================================
+// Metafunctions
+// ==========================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction WEIGHT
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn FixedCyclicShape#WEIGHT
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief Weight (number of care-positions) of Fixed CyclicShapes
+ *
+ * @signature WEIGHT<CyclicShape<FixedShape<L, TInnerShape, R> > >::VALUE;
+ *
+ * @tparam L left offset
+ * @tparam R right offset
+ * @tparam TInnerShape specialization of a hardwired GappedShape
+ *
+ * @return Weight of a fixed CyclicShape (enum).
+ *
+ * @see CyclicShape#weight
+ */
+
+template<unsigned L, typename THardwiredShape, unsigned R>
+struct WEIGHT<CyclicShape<FixedShape<L, GappedShape<THardwiredShape>, R> > >
+{
+    enum {VALUE = WEIGHT<THardwiredShape>::VALUE};
+};
+
+
+// ==========================================================================
+// Functions
+// ==========================================================================
+
+// --------------------------------------------------------------------------
+// Function weight
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn CyclicShape#weight
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief Return the weight of a CyclicShape
+ *
+ * @signature TSize weight(const & cyclicShape);
+ *
+ * @tparam TSpec Specialisation of the CyclicShape.
+ * @tparam TSize Size type of CyclicShape
+ * @param[in] cyclicShape CyclicShape object
+ * @return weight of the CyclicShape (number of care positions)
+ */
+template<typename TSpec>
+inline typename Size<CyclicShape<TSpec> >::Type
+weight(CyclicShape<TSpec> const & s)
+{
+    return static_cast<Size<CyclicShape<> >::Type>(length(s.diffs));
+}
+
+template<unsigned L, typename THardwiredShape, unsigned R>
+inline typename Size<CyclicShape<FixedShape<L, GappedShape<THardwiredShape>, R> > >::Type
+weight(CyclicShape<FixedShape<L, GappedShape<THardwiredShape>, R> > const &)
+{
+    typedef CyclicShape<FixedShape<L, GappedShape<THardwiredShape>, R> > TCyclicShape;
+    return WEIGHT<TCyclicShape>::VALUE;
+}
+
+// --------------------------------------------------------------------------
+// Function stringToCyclicShape()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn GenericCyclicShape#stringToCyclicShape
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief Converts a 0/1 string to a Generic CyclicShape.
+ *
+ * @signature void stringToCyclicShape(shape, bitmap);
+ *
+ * @tparam TString A string type, e.g. CharString.
+ * @param[out] shape Generic CyclicShape
+ * @param[in] bitmap 0/1 string of type TString. CyclicShapes may start and end with zeros,
+ *            but must contain at least one 1.
+ *
+ */
+template<typename TString>
+inline bool
+stringToCyclicShape(CyclicShape<GenericShape> & shape, TString const & bitmap)
+{
+    typename Iterator<TString const>::Type it    = begin(bitmap);
+    typename Iterator<TString const>::Type itBeg = begin(bitmap);
+    typename Iterator<TString const>::Type itEnd = end(bitmap);
+
+    Size<CyclicShape<GenericShape> >::Type countOnes = 0;
+    for (; it != itEnd; ++it)
+    {
+        if (*it == '1')
+            ++countOnes;
+    }
+    SEQAN_ASSERT_GT(countOnes, 0u);
+
+    resize(shape.diffs, countOnes);
+
+    typename Iterator<String<Size<CyclicShape<GenericShape> >::Type> >::Type diffIter = begin(shape.diffs);
+
+    // go to first 1
+    for (it = itBeg; *it != '1'; ++it)
+        continue;
+    shape.loffset = (Size<CyclicShape<GenericShape> >::Type)(it - itBeg);
+
+    countOnes = 1; // now used as the distance between 1s
+    for (++it; it != itEnd; ++it)
+    {
+        if (*it == '1')
+        {
+            *diffIter = countOnes;
+            ++diffIter;
+            countOnes = 1;
+        }
+        else
+            ++countOnes;
+    }
+
+    *diffIter = countOnes + shape.loffset;
+    shape.span = (typename Size<CyclicShape<GenericShape> >::Type)(it - itBeg);
+    return true;
+}
+
+// --------------------------------------------------------------------------
+// Function cyclicShapeToString()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn CyclicShape#cyclicShapeToString
+ *
+ * @brief Print a given cyclic shape as a sequence of '1' (care position) and
+ *        '0' (don't-care position).
+ *
+ * @signature void cyclicShapeToString(bitmap, cyclicShape);
+ *
+ * @param[in] cyclicShape CyclicShape object. Types: @link CyclicShape @endlink
+ * @param[out] bitmap The resulting sequence object. Type: @link String @endlink,
+ *             e.g. CharString
+ *
+ * @see GenericCyclicShape#stringToCyclicShape
+ */
+template<typename TShapeString, typename TSpec>
+inline void
+cyclicShapeToString(
+    TShapeString & bitmap,
+    CyclicShape<TSpec> const & me)
+{
+    clear(bitmap);
+    if (weight(me) == 0)
+        return;
+
+    typename Size<CyclicShape<TSpec> >::Type i, j;
+    for (i = 0; i < me.loffset; ++i)
+        appendValue(bitmap, '0');
+    for (i = 0; i < weight(me) - 1; ++i)
+    {
+        appendValue(bitmap, '1');
+        for (j = 1; j < static_cast<typename Size<CyclicShape<TSpec> >::Type>(me.diffs[i]); ++j)
+            appendValue(bitmap, '0');
+    }
+    appendValue(bitmap, '1');
+    for (i = length(bitmap); i < me.span; ++i)
+        appendValue(bitmap, '0');
+}
+
+// --------------------------------------------------------------------------
+// Function carePositions()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn CyclicShape#carePositions
+ *
+ * @brief Determine the indices of care positions in the range <i>[0,span)</i>
+ *
+ * @signature void carePositions(positions, cyclicShape);
+ *
+ * @param[in] cyclicShape CyclicShape object.
+ * @param[out] positions The resulting @link String @endlink to store the care-positions in. Type TString.
+ *
+ * @tparam TString String or array. Value type should be an integral size type.
+ * @tparam TSpec Specialization of CyclicShape.
+ *
+ * This function can be used to convert <tt>CyclicShape.diffs</tt>, which stores
+ * the distances between care positions, to a <tt>positions</tt> string directly
+ * containing the care positions. See the example:
+ *
+ * @snippet demos/dox/modifier/cyclic_shape_snippets.cpp CyclicShape Care Positions
+ */
+
+template<typename TString, typename TSpec>
+inline void
+carePositions(TString & output, CyclicShape<TSpec> const & shape)
+{
+    typedef typename Size<CyclicShape<TSpec> >::Type TPos;
+
+    resize(output, weight(shape));
+    TPos val = shape.loffset;
+    output[0] = shape.loffset;
+
+    for (TPos i = 1; i < weight(shape); ++i)
+    {
+        val += shape.diffs[i - 1];
+        output[i] = val;
+    }
+}
+
+// --------------------------------------------------------------------------
+// Function cyclicShapeToSuffixLengths()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn CyclicShape#cyclicShapeToSuffixLengths
+ *
+ * @brief Calculates the number of characters of modified Strings
+ *        shorter than the Shape's span.
+ *
+ * @signature void cyclicShapeToSuffixLengths(TString suffLengths, cyclicShape);
+ *
+ * @param[in] cyclicShape CyclicShape object.
+ * @param[in,out] suffLengths String to be filled. Must be resized beforehands.
+ *                Fixed length arrays also work.
+ *
+ * @tparam TString String type or array with an integral value type, i.e. unsigned or int.
+ *
+ * Given a CyclicShape, this function calculates a how many characters a String of length
+ * <i>x</i> contains after the CyclicShape is applied to it. This is done for all <tt>0 <= x < span</tt>.
+ * <tt>suffLengths</tt> therefore must be resized to the shape's span beforehands.
+ * The resizing is not done in this function so that it can be applied to arrays, too.
+ */
+
+template<typename TString,
+         typename TShape>
+inline void cyclicShapeToSuffixLengths(TString & suffLengths, TShape const & shape)
+{
+    typedef typename Size<TString>::Type TSize;
+
+    TSize w = weight(shape);
+    TSize s = shape.span;
+    TSize o = shape.loffset;
+
+    SEQAN_ASSERT_GEQ(s, 1u);
+    //SEQAN_ASSERT_EQ(length(suffLengths), s); // Disabled to support arrays too.
+
+    // build cummulative some of distances first
+    String<TSize> sums;
+    resize(sums, w);
+    sums[0] = o;
+    for (unsigned i = 0; i < w - 1; ++i)
+        sums[i + 1] = sums[i] + shape.diffs[i];
+
+    // write suffixLengths
+    unsigned sumPos = 0;
+    for (unsigned i = 0; i < s; ++i)
+        suffLengths[i] = (sumPos < w && i == sums[sumPos]) ? sumPos++ : sumPos;
+}
+
+} //namespace
+
+
+#endif
diff --git a/seqan/modifier/modifier_alphabet.h b/seqan/modifier/modifier_alphabet.h
index 63e2075..ced5a71 100644
--- a/seqan/modifier/modifier_alphabet.h
+++ b/seqan/modifier/modifier_alphabet.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,6 +42,7 @@ namespace seqan
 
 /*!
  * @class ModifiedAlphabet
+ * @implements AlphabetConcept
  * @headerfile <seqan/modifier.h>
  * @brief Modifies value types.
  *
@@ -52,18 +53,6 @@ namespace seqan
  * @tparam TSpec     The modifier type.
  */
 
-/**
-.Class.ModifiedAlphabet:
-..summary:Modifies value types.
-..cat:Modifier
-..signature:ModifiedAlphabet<TAlphabet, TSpec>
-..param.TAlphabet:Original value type.
-..param.TSpec:The modifier type.
-...metafunction:Metafunction.Spec
-...remarks:There is no default specialization.
-..include:seqan/modifier.h
-*/
-
 template <typename THost, typename TSpec>
 class ModifiedAlphabet;
 
@@ -84,6 +73,18 @@ struct ValueSize<ModifiedAlphabet<THost, TSpec> >
     : ValueSize<THost>
 {};
 
+// ----------------------------------------------------------------------------
+// Concept Convertible
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TSource>
+struct Is< Convertible<ModifiedAlphabet<THost, TSpec>, TSource> > :
+    Is< Convertible<THost, TSource> > {};
+
+template <typename TTarget, typename THost, typename TSpec>
+struct Is< Convertible<TTarget, ModifiedAlphabet<THost, TSpec> > > :
+    Is< Convertible<TTarget, THost> > {};
+
 //////////////////////////////////////////////////////////////////////////////
 // conversions
 //////////////////////////////////////////////////////////////////////////////
@@ -91,19 +92,19 @@ struct ValueSize<ModifiedAlphabet<THost, TSpec> >
 template <typename TTarget, typename T, typename THost, typename TSpec>
 inline typename Convert<TTarget, THost>::Type
 convertImpl(Convert<TTarget, T> const convert_,
-			ModifiedAlphabet<THost, TSpec> const & source_)
+            ModifiedAlphabet<THost, TSpec> const & source_)
 {
     SEQAN_CHECKPOINT;
-	return convertImpl(convert_, static_cast<THost const &>(source_));
+    return convertImpl(convert_, static_cast<THost const &>(source_));
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename THost, typename TSpec>
-inline unsigned ordValue(ModifiedAlphabet<THost,TSpec> const &c) 
+inline unsigned ordValue(ModifiedAlphabet<THost,TSpec> const &c)
 {
     SEQAN_CHECKPOINT;
-	return ordValue(static_cast<THost const &>(c));
+    return ordValue(static_cast<THost const &>(c));
 }
 
 template <typename TStream, typename THost, typename TSpec>
@@ -121,7 +122,7 @@ TStream & operator<<(TStream & stream, ModifiedAlphabet<THost, TSpec> const & c)
 template <typename THost, typename TSpec, typename TRight>
 struct CompareType<ModifiedAlphabet<THost, TSpec>, TRight>
 {
-	typedef typename CompareType<THost, TRight>::Type Type;
+    typedef typename CompareType<THost, TRight>::Type Type;
 };
 
 
@@ -130,59 +131,59 @@ struct CompareType<ModifiedAlphabet<THost, TSpec>, TRight>
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator==(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator==(ModifiedAlphabet<THost, TSpec> const & left_,
            TRight const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) == convert<TCompareType>(right_);
 }
 
 template <typename TLeft, typename THost, typename TSpec>
 inline bool
-operator==(TLeft const & left_, 
+operator==(TLeft const & left_,
            ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) == convert<TCompareType>(right_);
 }
 
 template <typename TLeftHost, typename TLeftSpec, typename TRightHost, typename TRightSpec>
 inline bool
-operator==(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_, 
+operator==(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_,
            ModifiedAlphabet<TRightHost, TRightSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
-	typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
+    typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) == convert<TCompareType>(right_);
 }
 
 template <typename THost, typename TSpec>
 inline bool
-operator==(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator==(ModifiedAlphabet<THost, TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	return ordValue(left_) == ordValue(right_);
+    return ordValue(left_) == ordValue(right_);
 }
 
 //SimpleType
 
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator==(SimpleType<TValue, TSpec> const & left_, 
+operator==(SimpleType<TValue, TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef SimpleType<TValue, TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+    typedef SimpleType<TValue, TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) == convert<TCompareType>(right_);
 }
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -190,35 +191,35 @@ operator==(ModifiedAlphabet<THost, TSpec2> const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef SimpleType<TValue, TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef SimpleType<TValue, TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) == convert<TCompareType>(right_);
 }
 
 //Proxy
 
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator==(Proxy<TSpec> const & left_, 
+operator==(Proxy<TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef Proxy<TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+    typedef Proxy<TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) == convert<TCompareType>(right_);
 }
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
 operator==(ModifiedAlphabet<THost, TSpec2> const & left_,
-			 Proxy<TSpec> const & right_)
+             Proxy<TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef Proxy<TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) == convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef Proxy<TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) == convert<TCompareType>(right_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -226,59 +227,59 @@ operator==(ModifiedAlphabet<THost, TSpec2> const & left_,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator!=(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator!=(ModifiedAlphabet<THost, TSpec> const & left_,
            TRight const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) != convert<TCompareType>(right_);
 }
 
 template <typename TLeft, typename THost, typename TSpec>
 inline bool
-operator!=(TLeft const & left_, 
+operator!=(TLeft const & left_,
            ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) != convert<TCompareType>(right_);
 }
 
 template <typename TLeftHost, typename TLeftSpec, typename TRightHost, typename TRightSpec>
 inline bool
-operator!=(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_, 
-			 ModifiedAlphabet<TRightHost, TRightSpec> const & right_)
+operator!=(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_,
+             ModifiedAlphabet<TRightHost, TRightSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
-	typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
+    typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) != convert<TCompareType>(right_);
 }
 
 template <typename THost, typename TSpec>
 inline bool
-operator!=(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator!=(ModifiedAlphabet<THost, TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	return ordValue(left_) != ordValue(right_);
+    return ordValue(left_) != ordValue(right_);
 }
 
 //SimpleType
 
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator!=(SimpleType<TValue, TSpec> const & left_, 
+operator!=(SimpleType<TValue, TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef SimpleType<TValue, TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+    typedef SimpleType<TValue, TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) != convert<TCompareType>(right_);
 }
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -286,24 +287,24 @@ operator!=(ModifiedAlphabet<THost, TSpec2> const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef SimpleType<TValue, TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef SimpleType<TValue, TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) != convert<TCompareType>(right_);
 }
 
 //Proxy
 
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator!=(Proxy<TSpec> const & left_, 
+operator!=(Proxy<TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef Proxy<TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+    typedef Proxy<TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) != convert<TCompareType>(right_);
 }
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -311,10 +312,10 @@ operator!=(ModifiedAlphabet<THost, TSpec2> const & left_,
            Proxy<TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef Proxy<TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) != convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef Proxy<TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) != convert<TCompareType>(right_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -322,59 +323,59 @@ operator!=(ModifiedAlphabet<THost, TSpec2> const & left_,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator<=(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator<=(ModifiedAlphabet<THost, TSpec> const & left_,
            TRight const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
 }
 
 template <typename TLeft, typename THost, typename TSpec>
 inline bool
-operator<=(TLeft const & left_, 
+operator<=(TLeft const & left_,
            ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
 }
 
 template <typename TLeftHost, typename TLeftSpec, typename TRightHost, typename TRightSpec>
 inline bool
-operator<=(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_, 
-			 ModifiedAlphabet<TRightHost, TRightSpec> const & right_)
+operator<=(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_,
+             ModifiedAlphabet<TRightHost, TRightSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
-	typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
+    typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
 }
 
 template <typename THost, typename TSpec>
 inline bool
-operator<=(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator<=(ModifiedAlphabet<THost, TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	return ordValue(left_) <= ordValue(right_);
+    return ordValue(left_) <= ordValue(right_);
 }
 
 //SimpleType
 
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator<=(SimpleType<TValue, TSpec> const & left_, 
+operator<=(SimpleType<TValue, TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef SimpleType<TValue, TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+    typedef SimpleType<TValue, TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
 }
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -382,24 +383,24 @@ operator<=(ModifiedAlphabet<THost, TSpec2> const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef SimpleType<TValue, TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef SimpleType<TValue, TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
 }
 
 //Proxy
 
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator<=(Proxy<TSpec> const & left_, 
+operator<=(Proxy<TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef Proxy<TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+    typedef Proxy<TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
 }
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -407,10 +408,10 @@ operator<=(ModifiedAlphabet<THost, TSpec2> const & left_,
            Proxy<TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef Proxy<TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef Proxy<TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) <= convert<TCompareType>(right_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -418,59 +419,59 @@ operator<=(ModifiedAlphabet<THost, TSpec2> const & left_,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator<(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator<(ModifiedAlphabet<THost, TSpec> const & left_,
           TRight const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) < convert<TCompareType>(right_);
 }
 
 template <typename TLeft, typename THost, typename TSpec>
 inline bool
-operator<(TLeft const & left_, 
+operator<(TLeft const & left_,
           ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) < convert<TCompareType>(right_);
 }
 
 template <typename TLeftHost, typename TLeftSpec, typename TRightHost, typename TRightSpec>
 inline bool
-operator<(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_, 
+operator<(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_,
           ModifiedAlphabet<TRightHost, TRightSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
-	typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
+    typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) < convert<TCompareType>(right_);
 }
 
 template <typename THost, typename TSpec>
 inline bool
-operator<(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator<(ModifiedAlphabet<THost, TSpec> const & left_,
           ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	return ordValue(left_) < ordValue(right_);
+    return ordValue(left_) < ordValue(right_);
 }
 
 //SimpleType
 
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator<(SimpleType<TValue, TSpec> const & left_, 
+operator<(SimpleType<TValue, TSpec> const & left_,
           ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef SimpleType<TValue, TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+    typedef SimpleType<TValue, TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) < convert<TCompareType>(right_);
 }
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -478,24 +479,24 @@ operator<(ModifiedAlphabet<THost, TSpec2> const & left_,
           SimpleType<TValue, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef SimpleType<TValue, TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef SimpleType<TValue, TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) < convert<TCompareType>(right_);
 }
 
 //Proxy
 
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator<(Proxy<TSpec> const & left_, 
+operator<(Proxy<TSpec> const & left_,
           ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef Proxy<TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+    typedef Proxy<TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) < convert<TCompareType>(right_);
 }
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -503,10 +504,10 @@ operator<(ModifiedAlphabet<THost, TSpec2> const & left_,
           Proxy<TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef Proxy<TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) < convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef Proxy<TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) < convert<TCompareType>(right_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -514,59 +515,59 @@ operator<(ModifiedAlphabet<THost, TSpec2> const & left_,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator>=(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator>=(ModifiedAlphabet<THost, TSpec> const & left_,
            TRight const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
 }
 
 template <typename TLeft, typename THost, typename TSpec>
 inline bool
-operator>=(TLeft const & left_, 
+operator>=(TLeft const & left_,
            ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
 }
 
 template <typename TLeftHost, typename TLeftSpec, typename TRightHost, typename TRightSpec>
 inline bool
-operator>=(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_, 
+operator>=(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_,
            ModifiedAlphabet<TRightHost, TRightSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
-	typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
+    typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
 }
 
 template <typename THost, typename TSpec>
 inline bool
-operator>=(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator>=(ModifiedAlphabet<THost, TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	return ordValue(left_) >= ordValue(right_);
+    return ordValue(left_) >= ordValue(right_);
 }
 
 //SimpleType
 
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator>=(SimpleType<TValue, TSpec> const & left_, 
+operator>=(SimpleType<TValue, TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef SimpleType<TValue, TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+    typedef SimpleType<TValue, TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
 }
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -574,24 +575,24 @@ operator>=(ModifiedAlphabet<THost, TSpec2> const & left_,
            SimpleType<TValue, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef SimpleType<TValue, TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef SimpleType<TValue, TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
 }
 
 //Proxy
 
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator>=(Proxy<TSpec> const & left_, 
+operator>=(Proxy<TSpec> const & left_,
            ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef Proxy<TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+    typedef Proxy<TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
 }
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -599,10 +600,10 @@ operator>=(ModifiedAlphabet<THost, TSpec2> const & left_,
            Proxy<TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef Proxy<TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef Proxy<TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) >= convert<TCompareType>(right_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -610,59 +611,59 @@ operator>=(ModifiedAlphabet<THost, TSpec2> const & left_,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator>(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator>(ModifiedAlphabet<THost, TSpec> const & left_,
           TRight const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) > convert<TCompareType>(right_);
 }
 
 template <typename TLeft, typename THost, typename TSpec>
 inline bool
-operator>(TLeft const & left_, 
+operator>(TLeft const & left_,
           ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) > convert<TCompareType>(right_);
 }
 
 template <typename TLeftHost, typename TLeftSpec, typename TRightHost, typename TRightSpec>
 inline bool
-operator>(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_, 
+operator>(ModifiedAlphabet<TLeftHost, TLeftSpec> const & left_,
           ModifiedAlphabet<TRightHost, TRightSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
-	typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<TLeftHost, TLeftSpec> TLeft;
+    typedef ModifiedAlphabet<TRightHost, TRightSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) > convert<TCompareType>(right_);
 }
 
 template <typename THost, typename TSpec>
 inline bool
-operator>(ModifiedAlphabet<THost, TSpec> const & left_, 
+operator>(ModifiedAlphabet<THost, TSpec> const & left_,
           ModifiedAlphabet<THost, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	return ordValue(left_) > ordValue(right_);
+    return ordValue(left_) > ordValue(right_);
 }
 
 //SimpleType
 
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator>(SimpleType<TValue, TSpec> const & left_, 
+operator>(SimpleType<TValue, TSpec> const & left_,
           ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef SimpleType<TValue, TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+    typedef SimpleType<TValue, TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) > convert<TCompareType>(right_);
 }
 template <typename TValue, typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -670,24 +671,24 @@ operator>(ModifiedAlphabet<THost, TSpec2> const & left_,
           SimpleType<TValue, TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef SimpleType<TValue, TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef SimpleType<TValue, TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) > convert<TCompareType>(right_);
 }
 
 //Proxy
 
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
-operator>(Proxy<TSpec> const & left_, 
+operator>(Proxy<TSpec> const & left_,
           ModifiedAlphabet<THost, TSpec2> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef Proxy<TSpec> TLeft;
-	typedef ModifiedAlphabet<THost, TSpec> TRight;
-	typedef typename CompareType<TRight, TLeft>::Type TCompareType;
-	return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+    typedef Proxy<TSpec> TLeft;
+    typedef ModifiedAlphabet<THost, TSpec> TRight;
+    typedef typename CompareType<TRight, TLeft>::Type TCompareType;
+    return convert<TCompareType>(left_) > convert<TCompareType>(right_);
 }
 template <typename TSpec, typename THost, typename TSpec2>
 inline bool
@@ -695,10 +696,10 @@ operator>(ModifiedAlphabet<THost, TSpec2> const & left_,
           Proxy<TSpec> const & right_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, TSpec> TLeft;
-	typedef Proxy<TSpec> TRight;
-	typedef typename CompareType<TLeft, TRight>::Type TCompareType;
-	return convert<TCompareType>(left_) > convert<TCompareType>(right_);
+    typedef ModifiedAlphabet<THost, TSpec> TLeft;
+    typedef Proxy<TSpec> TRight;
+    typedef typename CompareType<TLeft, TRight>::Type TCompareType;
+    return convert<TCompareType>(left_) > convert<TCompareType>(right_);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -707,32 +708,32 @@ operator>(ModifiedAlphabet<THost, TSpec2> const & left_,
 template <typename TTarget, typename TSource>
 inline void
 _initializeAlphabetConversionTable(TTarget *,
-								   TSource const &)
+                                   TSource const &)
 {
     SEQAN_CHECKPOINT;
-	//default: do nothing (because this array is not used)
-	//define this function for each conversion table
+    //default: do nothing (because this array is not used)
+    //define this function for each conversion table
 }
 
 
 template <typename TTarget, typename TSource>
 struct AlphabetConversionTable_
 {
-	enum { SIZE = InternalValueSize_<TSource>::VALUE };
+    enum { SIZE = InternalValueSize_<TSource>::VALUE };
 public:
-	static TTarget * table;
-	static TTarget * initialize()
-	{
+    static TTarget * table;
+    static TTarget * initialize()
+    {
         SEQAN_CHECKPOINT;
         static TTarget table_store[SIZE];
-		static bool _is_initialized = false;
-		if (! _is_initialized)
-		{
-			_initializeAlphabetConversionTable(table_store, TSource());
-		}
-		_is_initialized = true;
-		return table_store;
-	}
+        static bool _is_initialized = false;
+        if (! _is_initialized)
+        {
+            _initializeAlphabetConversionTable(table_store, TSource());
+        }
+        _is_initialized = true;
+        return table_store;
+    }
 };
 
 template <typename TTarget, typename TSource>
@@ -744,32 +745,32 @@ TTarget * AlphabetConversionTable_<TTarget, TSource>::table = AlphabetConversion
 template <typename TTarget, typename TSource>
 inline void
 _initializeAlphabetOrdTable(TTarget *,
-							TSource const &)
+                            TSource const &)
 {
     SEQAN_CHECKPOINT;
-	//default: do nothing (because this array is not used)
-	//define this function for each conversion table
+    //default: do nothing (because this array is not used)
+    //define this function for each conversion table
 }
 
 
 template <typename TSource>
 struct AlphabetOrdTable_
 {
-	enum { SIZE = InternalValueSize_<TSource>::VALUE };
+    enum { SIZE = InternalValueSize_<TSource>::VALUE };
 public:
-	static unsigned * table;
-	static unsigned * initialize()
-	{
+    static unsigned * table;
+    static unsigned * initialize()
+    {
         SEQAN_CHECKPOINT;
         static unsigned table_store[SIZE];
-		static bool _is_initialized = false;
-		if (! _is_initialized)
-		{
-			_initializeAlphabetOrdTable(table_store, TSource());
-		}
-		_is_initialized = true;
-		return table_store;
-	}
+        static bool _is_initialized = false;
+        if (! _is_initialized)
+        {
+            _initializeAlphabetOrdTable(table_store, TSource());
+        }
+        _is_initialized = true;
+        return table_store;
+    }
 };
 
 
diff --git a/seqan/modifier/modifier_alphabet_expansion.h b/seqan/modifier/modifier_alphabet_expansion.h
index 24abdef..f21a854 100644
--- a/seqan/modifier/modifier_alphabet_expansion.h
+++ b/seqan/modifier/modifier_alphabet_expansion.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,7 +46,7 @@ namespace SEQAN_NAMESPACE_MAIN
  * @class AlphabetExpansion
  * @headerfile <seqan/modifier.h>
  * @brief Modifier that adds a character to an alphabet.
- * 
+ *
  * @signature template <typename TAlphabet, char CHAR[, typename TSpec]>
  *            class ModifiedAlphabet<TAlphabet, ModExpand<CHAR,TSpec> >;
  *
@@ -56,7 +56,7 @@ namespace SEQAN_NAMESPACE_MAIN
  *                   example, do not use <tt>'A'</tt> or <tt>'a'</tt> as <tt>CHAR</tt> when expanding Dna.
  * @tparam TSpec     Optional specialization tag.  This modifier is intended to expand SimpleType classes, default is <tt>Default</tt>.
  *
- * @section Remarks
+ * @section Special Characters
  *
  * Some values of <tt>CHAR</tt> have special meaning:
  *
@@ -69,24 +69,6 @@ namespace SEQAN_NAMESPACE_MAIN
  * </dl>
  */
 
-/**
-.Spec.Alphabet Expansion:
-..summary:Modifier that adds a character to an alphabet.
-..cat:Modifier
-..signature:ModifiedAlphabet<TAlphabet, ModExpand<CHAR [,TSpec]> >
-..param.TAlphabet:Original value type.
-..param.CHAR:$char$ character that specifies, what value should added to the alphabet.
-...remarks:$CHAR$ should not be a $char$ that already stands for a value in $TAlphabet$.
-	For example, do not use $'A'$ or $'a'$ as $CHAR$ when expanding @Spec.Dna@.
-...remarks:Some values of $CHAR$ have special meaning:
-....table:$'-'$|A gap character. The value in the expanded alphabet that corresponds to $'-'$ will be returned by the @Function.gapValue@.
-....table:$'\$'$|An end of string character.
-..param.TSpec:Optional specialization tag.
-...default:$Default$
-...remarks:This modifier is intended to expand @Class.SimpleType@ classes.
-..include:seqan/modifier.h
-*/
-
 template <char CHAR, typename TSpec = Default>
 struct ModExpand;
 
@@ -95,108 +77,106 @@ template <typename THost, char CHAR, typename TSpec>
 class ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >
 {
 public:
-	typedef typename IntegralForValue<ModifiedAlphabet>::Type TData;
-	TData data;
-
-	ModifiedAlphabet() 
-	{
-	}
-	ModifiedAlphabet(ModifiedAlphabet const & other)
-		: data(_internalOrdValue(other))
-	{
-	}
-	template <typename TOther>
-	ModifiedAlphabet(TOther const & other_data)
-		: data(_internalOrdValue(convert<ModifiedAlphabet>(other_data)))
-	{
-	}
-	~ModifiedAlphabet()
-	{
-	}
-	ModifiedAlphabet const & 
-	operator = (ModifiedAlphabet const & other)
-	{
-		data = other.data;
-		return *this;
-	}
-	template <typename TOther>
-	ModifiedAlphabet const & 
-	operator = (TOther const & other_data)
-	{
-		data = _internalOrdValue(convert<ModifiedAlphabet>(other_data));
-		return *this;
-	}
-
-/*	operator TData ()
-	{
-		return data;
-	}
-
-	operator THost()
-	{
-		return convert<THost>(data);
-	}
+    typedef typename IntegralForValue<ModifiedAlphabet>::Type TData;
+    TData data;
+
+    ModifiedAlphabet() : data()
+    {}
+
+    ModifiedAlphabet(ModifiedAlphabet const & other)
+        : data(_internalOrdValue(other))
+    {}
+
+    template <typename TOther>
+    ModifiedAlphabet(TOther const & other_data)
+        : data(_internalOrdValue(convert<ModifiedAlphabet>(other_data)))
+    {}
+
+    ModifiedAlphabet const &
+    operator = (ModifiedAlphabet const & other)
+    {
+        data = other.data;
+        return *this;
+    }
+
+    template <typename TOther>
+    ModifiedAlphabet const &
+    operator = (TOther const & other_data)
+    {
+        data = _internalOrdValue(convert<ModifiedAlphabet>(other_data));
+        return *this;
+    }
+
+/*    operator TData ()
+    {
+        return data;
+    }
+
+    operator THost()
+    {
+        return convert<THost>(data);
+    }
 */
 //____________________________________________________________________________
 
-	//TODO(weese): investigate the issue below
-	//this cannot be a template since a template would be in conflict to
-	//the template c'tor
+    //TODO(weese): investigate the issue below
+    //this cannot be a template since a template would be in conflict to
+    //the template c'tor
 
 /*
-	// weese: I tried the template below without problems in the tests
-	template <typename TValue>
-	operator TValue() const
-	{
+    // weese: I tried the template below without problems in the tests
+    template <typename TValue>
+    operator TValue() const
+    {
 SEQAN_CHECKPOINT
-		return convert<TValue>(*this);
-	}
+        return convert<TValue>(*this);
+    }
 */
-	operator long() const
-	{
+    operator long() const
+    {
 SEQAN_CHECKPOINT
-		return convert<long>(*this);
-	}
-	operator unsigned long() const
-	{
+        return convert<long>(*this);
+    }
+    operator unsigned long() const
+    {
 SEQAN_CHECKPOINT
-		return convert<unsigned long>(*this);
-	}
-	operator int() const
-	{
+        return convert<unsigned long>(*this);
+    }
+    operator int() const
+    {
 SEQAN_CHECKPOINT
-		return convert<int>(*this);
-	}
-	operator unsigned int() const
-	{
+        return convert<int>(*this);
+    }
+    operator unsigned int() const
+    {
 SEQAN_CHECKPOINT
-		return convert<unsigned int>(*this);
-	}
-	operator short() const
-	{
+        return convert<unsigned int>(*this);
+    }
+    operator short() const
+    {
 SEQAN_CHECKPOINT
-		return convert<short>(*this);
-	}
-	operator unsigned short() const
-	{
+        return convert<short>(*this);
+    }
+    operator unsigned short() const
+    {
 SEQAN_CHECKPOINT
-		return convert<unsigned short>(*this);
-	}
-	operator char() const
-	{
+        return convert<unsigned short>(*this);
+    }
+    operator char() const
+    {
 SEQAN_CHECKPOINT
-		return convert<char>(*this);
-	}
-	operator signed char() const
-	{
+        return convert<char>(*this);
+    }
+    operator signed char() const
+    {
 SEQAN_CHECKPOINT
-		return convert<signed char>(*this);
-	}
-	operator unsigned char() const
-	{
+        return convert<signed char>(*this);
+    }
+    operator unsigned char() const
+    {
 SEQAN_CHECKPOINT
-		return convert<unsigned char>(*this);
-	}
+        return convert<unsigned char>(*this);
+    }
 };
 
 
@@ -219,8 +199,8 @@ unknownValueImpl(ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > *)
 template <typename THost, char CHAR, typename TSpec>
 struct BitsPerValue<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > >
 {
-	typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TValue;
-	enum { VALUE = Log2< ValueSize<TValue>::VALUE >::VALUE };
+    typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TValue;
+    enum { VALUE = Log2< ValueSize<TValue>::VALUE >::VALUE };
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -228,13 +208,13 @@ struct BitsPerValue<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > >
 template <typename THost, char CHAR, typename TSpec>
 struct ValueSize<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > >
 {
-	enum { VALUE = ValueSize<THost>::VALUE + 1 };
+    enum { VALUE = ValueSize<THost>::VALUE + 1 };
 };
 
 template <typename THost, char CHAR, typename TSpec>
 struct InternalValueSize_<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > >
 {
-	enum { VALUE = InternalValueSize_<THost>::VALUE + 1 };
+    enum { VALUE = InternalValueSize_<THost>::VALUE + 1 };
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -245,16 +225,16 @@ template <typename TValue, typename TNum>
 inline TValue
 _internalCreateChar(TValue const &, TNum i)
 {
-	return convert<TValue>(i);
+    return convert<TValue>(i);
 }
 
 template <typename TValue, typename TSpec, typename TNum>
 inline SimpleType<TValue, TSpec>
 _internalCreateChar(SimpleType<TValue, TSpec> const &, TNum i)
 {
-	SimpleType<TValue, TSpec> s;
-	s.value = i;
-	return s;
+    SimpleType<TValue, TSpec> s;
+    s.value = i;
+    return s;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -287,79 +267,79 @@ gapValueImpl(ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > /*const*/ *)
 template <typename THost, char CHAR, typename TSpec, typename TSource>
 inline void
 _initializeAlphabetConversionTable(ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > * buf,
-								   TSource const &)
+                                   TSource const &)
 {
-	//assure that the conversion from TSource to THost is possible
-//	AlphabetConversionTable_<THost, TSource>::initialize();
-
-	//copy the conversion table for converting TSouce => THost
-	//maybe, if there is no CHAR in TSource, the entry for CHAR is overwritten now
-	for (int i = InternalValueSize_<TSource>::VALUE; i > 0; )
-	{
-		--i;
-		buf[i].data = _internalOrdValue(convert<THost>(_internalCreateChar(TSource(), i)));
-	}
-
-	//add the new character CHAR to the table
-	buf[_internalOrdValue(convert<TSource>(CHAR))].data = InternalValueSize_<THost>::VALUE;
+    //assure that the conversion from TSource to THost is possible
+//    AlphabetConversionTable_<THost, TSource>::initialize();
+
+    //copy the conversion table for converting TSouce => THost
+    //maybe, if there is no CHAR in TSource, the entry for CHAR is overwritten now
+    for (int i = InternalValueSize_<TSource>::VALUE; i > 0; )
+    {
+        --i;
+        buf[i].data = _internalOrdValue(convert<THost>(_internalCreateChar(TSource(), i)));
+    }
+
+    //add the new character CHAR to the table
+    buf[_internalOrdValue(convert<TSource>(CHAR))].data = InternalValueSize_<THost>::VALUE;
 }
 
 template <int SIZE_OF_SOURCE>
 struct ConvertImplModExpand_
 {
-	//default implementation for large source types
-	template <typename THost, char CHAR, typename TSpec, typename T, typename TSource>
-	inline
-	static typename Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, TSource>::Type
-	_convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const,
-		TSource const & source_)
-	{
-		typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
-		if (source_ == ValueSize<THost>::VALUE)
-		{// the extra character
-			TTarget tmp;
-			tmp.data = InternalValueSize_<THost>::VALUE;
-			return tmp;
-		}
-		return convert<TTarget>(convert<THost>(source_));
-	}
+    //default implementation for large source types
+    template <typename THost, char CHAR, typename TSpec, typename T, typename TSource>
+    inline
+    static typename Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, TSource>::Type
+    _convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const,
+        TSource const & source_)
+    {
+        typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
+        if (source_ == ValueSize<THost>::VALUE)
+        {// the extra character
+            TTarget tmp;
+            tmp.data = InternalValueSize_<THost>::VALUE;
+            return tmp;
+        }
+        return convert<TTarget>(convert<THost>(source_));
+    }
 };
 
 //for 1 byte source: use translation table
 template <>
 struct ConvertImplModExpand_<1>
 {
-	template <typename THost, char CHAR, typename TSpec, typename T, typename TSource>
-	inline 
-	static typename Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, TSource>::Type
-	_convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const,
-		TSource const & source_)
-	{
-		typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
-		TTarget * table = AlphabetConversionTable_<TTarget, TSource>::table;
-		return table[_internalOrdValue(source_)];
-	}
+    template <typename THost, char CHAR, typename TSpec, typename T, typename TSource>
+    inline
+    static typename Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, TSource>::Type
+    _convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const,
+        TSource const & source_)
+    {
+        typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
+        TTarget * table = AlphabetConversionTable_<TTarget, TSource>::table;
+        return table[_internalOrdValue(source_)];
+    }
 };
 
 //generic source: dispatch for size of BytesPerValue
 template <typename THost, char CHAR, typename TSpec, typename T, typename TSource>
 inline typename Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, TSource>::Type
 convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const convert_,
-			TSource const & source_)
+            TSource const & source_)
 {
-	return ConvertImplModExpand_<BytesPerValue<TSource>::VALUE>::_convertImpl(convert_, source_);
+    return ConvertImplModExpand_<BytesPerValue<TSource>::VALUE>::_convertImpl(convert_, source_);
 }
 
 //for SimpleType sources
 template <typename THost, char CHAR, typename TSpec, typename T, typename TSourceValue, typename TSourceSpec>
 inline typename Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, SimpleType<TSourceValue, TSourceSpec> >::Type
 convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const,
-			SimpleType<TSourceValue, TSourceSpec> const & source_)
+            SimpleType<TSourceValue, TSourceSpec> const & source_)
 {
 SEQAN_CHECKPOINT
-	typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
-	typedef SimpleType<TSourceValue, TSourceSpec> TSource;
-	return AlphabetConversionTable_<TTarget, TSource>::table[_internalOrdValue(source_)];
+    typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
+    typedef SimpleType<TSourceValue, TSourceSpec> TSource;
+    return AlphabetConversionTable_<TTarget, TSource>::table[_internalOrdValue(source_)];
 }
 
 
@@ -367,15 +347,15 @@ SEQAN_CHECKPOINT
 template <char CHAR, typename TSpec, typename T, typename TSourceValue, typename TSourceSpec>
 inline typename Convert<ModifiedAlphabet<SimpleType<TSourceValue, TSourceSpec>, ModExpand<CHAR, TSpec> >, SimpleType<TSourceValue, TSourceSpec> >::Type
 convertImpl(Convert<ModifiedAlphabet<SimpleType<TSourceValue, TSourceSpec>, ModExpand<CHAR, TSpec> >, T> const,
-			SimpleType<TSourceValue, TSourceSpec> const & source_)
+            SimpleType<TSourceValue, TSourceSpec> const & source_)
 {
     SEQAN_CHECKPOINT;
-	typedef SimpleType<TSourceValue, TSourceSpec> TSource;
-	typedef ModifiedAlphabet<TSource, ModExpand<CHAR, TSpec> > TTarget;
-	
-	TTarget tmp;
-	tmp.data = _internalOrdValue(source_);
-	return tmp;
+    typedef SimpleType<TSourceValue, TSourceSpec> TSource;
+    typedef ModifiedAlphabet<TSource, ModExpand<CHAR, TSpec> > TTarget;
+
+    TTarget tmp;
+    tmp.data = _internalOrdValue(source_);
+    return tmp;
 }
 
 
@@ -383,11 +363,11 @@ convertImpl(Convert<ModifiedAlphabet<SimpleType<TSourceValue, TSourceSpec>, ModE
 template <typename THost, char CHAR, typename TSpec, typename T, typename TSpec2>
 inline typename Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, Proxy<TSpec2> >::Type
 convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const,
-			Proxy<TSpec2> const & source_)
+            Proxy<TSpec2> const & source_)
 {
 SEQAN_CHECKPOINT
-	typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
-	return convert<TTarget>(getValue(source_));
+    typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
+    return convert<TTarget>(getValue(source_));
 }
 
 
@@ -396,39 +376,39 @@ SEQAN_CHECKPOINT
 template <typename TTarget, typename THost, char CHAR, typename TSpec>
 inline void
 _initializeAlphabetConversionTable(TTarget * buf,
-								   ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const &)
+                                   ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const &)
 {
-	//assure that the conversion from THost to TTarget is possible
-	AlphabetConversionTable_<TTarget, THost>::initialize();
-
-	//copy the conversion table for converting THost => TTarget
-	for (int i = InternalValueSize_<THost>::VALUE; i > 0; )
-	{
-		--i;
-		buf[i] = convert<TTarget>(_internalCreateChar(THost(), i));
-	}
-
-	//add the new character CHAR to the table
-	buf[InternalValueSize_<THost>::VALUE] = convert<TTarget, char>(CHAR);
+    //assure that the conversion from THost to TTarget is possible
+    AlphabetConversionTable_<TTarget, THost>::initialize();
+
+    //copy the conversion table for converting THost => TTarget
+    for (int i = InternalValueSize_<THost>::VALUE; i > 0; )
+    {
+        --i;
+        buf[i] = convert<TTarget>(_internalCreateChar(THost(), i));
+    }
+
+    //add the new character CHAR to the table
+    buf[InternalValueSize_<THost>::VALUE] = convert<TTarget, char>(CHAR);
 }
 
 template <typename TTarget, typename THost, char CHAR, typename TSpec>
 inline void
 _initializeAlphabetOrdTable(TTarget * buf,
-							ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const &)
+                            ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const &)
 {
-	//assure that the conversion from THost to TTarget is possible
-	AlphabetOrdTable_<THost>::initialize();
-
-	//copy the conversion table for converting THost => TTarget
-	for (int i = InternalValueSize_<THost>::VALUE; i > 0; )
-	{
-		--i;
-		buf[i] = ordValue(_internalCreateChar(THost(), i));
-	}
-
-	//add the new character CHAR to the table
-	buf[InternalValueSize_<THost>::VALUE] = ValueSize<THost>::VALUE;
+    //assure that the conversion from THost to TTarget is possible
+    AlphabetOrdTable_<THost>::initialize();
+
+    //copy the conversion table for converting THost => TTarget
+    for (int i = InternalValueSize_<THost>::VALUE; i > 0; )
+    {
+        --i;
+        buf[i] = ordValue(_internalCreateChar(THost(), i));
+    }
+
+    //add the new character CHAR to the table
+    buf[InternalValueSize_<THost>::VALUE] = ValueSize<THost>::VALUE;
 }
 
 
@@ -440,11 +420,11 @@ _initializeAlphabetOrdTable(TTarget * buf,
 template <typename TTarget, typename T, typename THost, char CHAR, typename TSpec>
 inline typename Convert<TTarget, ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > >::Type
 convertImpl(Convert<TTarget, T> const,
-			ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & source_)
+            ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & source_)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TSource;
-	return AlphabetConversionTable_<TTarget, TSource>::table[_internalOrdValue(source_)];
+    typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TSource;
+    return AlphabetConversionTable_<TTarget, TSource>::table[_internalOrdValue(source_)];
 }
 
 
@@ -452,15 +432,15 @@ convertImpl(Convert<TTarget, T> const,
 template <typename TTargetValue, typename TTargetSpec, char CHAR, typename TSpec>
 inline typename Convert<SimpleType<TTargetValue, TTargetSpec>, ModifiedAlphabet<SimpleType<TTargetValue, TTargetSpec>, ModExpand<CHAR, TSpec> > >::Type
 convertImpl(Convert<SimpleType<TTargetValue, TTargetSpec>, ModifiedAlphabet<SimpleType<TTargetValue, TTargetSpec>, ModExpand<CHAR, TSpec> > > const,
-			ModifiedAlphabet<SimpleType<TTargetValue, TTargetSpec>, ModExpand<CHAR, TSpec> > const & source_)
+            ModifiedAlphabet<SimpleType<TTargetValue, TTargetSpec>, ModExpand<CHAR, TSpec> > const & source_)
 {
     SEQAN_CHECKPOINT;
     typedef SimpleType<TTargetValue, TTargetSpec> TTarget;
     TTarget target;
-	if (source_.data == InternalValueSize_<TTarget>::VALUE)
-		assign(target, CHAR);
-	else
-		target.value = source_.data;
+    if (source_.data == InternalValueSize_<TTarget>::VALUE)
+        assign(target, CHAR);
+    else
+        target.value = source_.data;
     return target;
 }
 
@@ -469,28 +449,28 @@ convertImpl(Convert<SimpleType<TTargetValue, TTargetSpec>, ModifiedAlphabet<Simp
 
 
 /*
-template 
+template
 <
-	typename TTargetHost, char TARGET_CHAR, typename TTargetSpec, typename T, 
-	typename TSourceHost, char SOURCE_CHAR, typename TSourceSpec
+    typename TTargetHost, char TARGET_CHAR, typename TTargetSpec, typename T,
+    typename TSourceHost, char SOURCE_CHAR, typename TSourceSpec
 >
 inline typename Convert<ModifiedAlphabet<TTargetHost, ModExpand<TARGET_CHAR, TTargetSpec> > , ModifiedAlphabet<TSourceHost, ModExpand<SOURCE_CHAR, TSourceSpec> > >::Type
 convertImpl(Convert<ModifiedAlphabet<TTargetHost, ModExpand<TARGET_CHAR, TTargetSpec> >, T> const,
-			ModifiedAlphabet<TSourceHost, ModExpand<SOURCE_CHAR, TSourceSpec> > const & source_)
+            ModifiedAlphabet<TSourceHost, ModExpand<SOURCE_CHAR, TSourceSpec> > const & source_)
 {
-	ModifiedAlphabet<TTargetHost, ModExpand<TARGET_CHAR, TTargetSpec> > TTarget;
-	ModifiedAlphabet<TSourceHost, ModExpand<SOURCE_CHAR, TSourceSpec> > TSource;
-	return convert<TTarget>(convert<TTargetHost>(convert<TSourceHost>(source_)));
+    ModifiedAlphabet<TTargetHost, ModExpand<TARGET_CHAR, TTargetSpec> > TTarget;
+    ModifiedAlphabet<TSourceHost, ModExpand<SOURCE_CHAR, TSourceSpec> > TSource;
+    return convert<TTarget>(convert<TTargetHost>(convert<TSourceHost>(source_)));
 }
 */
 
-//no conversion 
+//no conversion
 template <typename THost, char CHAR, typename TSpec, typename T>
 inline ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >
 convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const,
-			ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & source_)
+            ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & source_)
 {
-	return source_;
+    return source_;
 }
 
 
@@ -498,18 +478,18 @@ convertImpl(Convert<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, T> const,
 
 template <typename THost, char CHAR, typename TSpec>
 inline unsigned
-_internalOrdValue(ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & c) 
+_internalOrdValue(ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & c)
 {
-	return c.data;
+    return c.data;
 }
 
 template <typename THost, char CHAR, typename TSpec>
 inline unsigned
-ordValue(ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & c) 
+ordValue(ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & c)
 {
     SEQAN_CHECKPOINT;
-	typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TSource;
-	return AlphabetOrdTable_<TSource>::table[_internalOrdValue(c)];
+    typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TSource;
+    return AlphabetOrdTable_<TSource>::table[_internalOrdValue(c)];
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -519,30 +499,30 @@ ordValue(ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const & c)
 template <typename TModExpand, typename THost, typename TRight, typename TCompareHostRight>
 struct CompareTypeModExpandImpl_
 {
-	typedef TCompareHostRight Type; //fallback
+    typedef TCompareHostRight Type; //fallback
 };
 template <typename TModExpand, typename THost, typename TRight>
 struct CompareTypeModExpandImpl_<TModExpand, THost, TRight, THost>
 {
-	typedef TModExpand Type;
+    typedef TModExpand Type;
 };
 template <typename TModExpand, typename THost, typename TRight>
 struct CompareTypeModExpandImpl_<TModExpand, THost, TRight, TRight>
 {
-	typedef TRight Type;
+    typedef TRight Type;
 };
 
 
 template <typename THost, char CHAR, typename TSpec, typename TRight>
 struct CompareType<ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> >, TRight>
 {
-	typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TModExpand;
-	typedef typename CompareType<THost, TRight>::Type TCompareHostRight;
-	typedef typename CompareTypeModExpandImpl_<TModExpand, THost, TRight, TCompareHostRight>::Type Type;
+    typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TModExpand;
+    typedef typename CompareType<THost, TRight>::Type TCompareHostRight;
+    typedef typename CompareTypeModExpandImpl_<TModExpand, THost, TRight, TCompareHostRight>::Type Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
-}// namespace 
+}// namespace
 
 #endif
diff --git a/seqan/modifier/modifier_cyclic_shape.h b/seqan/modifier/modifier_cyclic_shape.h
new file mode 100644
index 0000000..f77f3a0
--- /dev/null
+++ b/seqan/modifier/modifier_cyclic_shape.h
@@ -0,0 +1,759 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Sascha Meiers <meiers@inf.fu-berlin.de>
+// ==========================================================================
+// Modified Iterator and Modified String for CyclicShapes
+// ==========================================================================
+
+#ifndef SEQAN_HEADER_MODIFIER_SHAPE_H
+#define SEQAN_HEADER_MODIFIER_SHAPE_H
+
+
+namespace seqan {
+
+// NOTE(meiers): Only a few functions are documented, the rest should be derived
+
+// ==========================================================================
+// Classes, Enums, Typedefs
+// ==========================================================================
+
+// --------------------------------------------------------------------------
+// Class ModCyclicShape Iterator
+// --------------------------------------------------------------------------
+
+template<typename TSpec>
+struct ModCyclicShape
+{};
+
+/*!
+ * @class ModCyclicShapeModifiedIterator ModCyclicShape ModifiedIterator
+ * @extends ModifiedIterator
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief Iterates over a string leaving out don't-care-positions defined in
+ *      CyclicShape.
+ *
+ * @signature template <typename THost, typename TSpec>
+ *            class ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > >;
+ *
+ * @tparam THost The host iterator.
+ * @tparam TSpec The specialization of @link CyclicShape @endlink.
+ * @tparam TCargo Cargo type of ModCyclicShape
+ * @tparam TSize Size type of ModCyclicShape
+ *
+ * Using ModCyclicShape you can <i>mask</i> characters at certain positions of a text.
+ * A CylcicShape defines these positions (so called don't-care-positions) and the
+ * CyclicShape is repeated till the end of the string. The iterator behaves as if
+ * the don't-care-positions had been deleted without actually copying the string.
+ *
+ * @snippet demos/dox/modifier/cyclic_shape_snippets.cpp Define CyclicShape Modified Iterator
+ *
+ * @see ModCyclicShapeModifiedString
+ * @see CyclicShape
+ *
+ * @note ModCyclicShape Modifier should only be used to <b>view/read a sequence</b>,
+ *       never to change the underlying sequence. Some operations will work, e.g.
+ *       you can use the <tt>operator*()</tt> of the ModifiedIterator to change
+ *       a character, but other operations like <tt>replace</tt> or <tt>append</tt>
+ *       are unsafe or even conceptionally wrong.
+ */
+
+template<typename THost, typename TSpec>
+class ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > >
+{
+public:
+    typedef typename Cargo<ModifiedIterator>::Type TCargo_;
+    typedef CyclicShape<TSpec>  TCyclicShape;
+
+    THost _host;
+
+    /*!
+     * @var TCargo ModCyclicShapeModifiedIterator::_cargo;
+     * @brief Copy of a Cargo object, which is a CyclicShape.
+     *
+     * The Cargo is a CyclicShape. This can be very heavy in case of GenericCyclicShape,
+     * so prefer the lightweight FixedCyclicShape.
+     */
+    TCargo_ _cargo;
+
+    /*!
+     * @var TSize ModCyclicShapeModifiedIterator::_idx;
+     * @brief Internal position inside <tt>diffs</tt> of the CylicShape.
+     */
+    typename Size<TCyclicShape>::Type _idx;
+
+    /*!
+     * @fn ModCyclicShapeModifiedIterator::ModifiedIterator
+     * @brief The constructor.
+     *
+     * @signature ModifiedIterator::ModifiedIterator();
+     * @signature ModifiedIterator::ModifiedIterator(host);
+     * @signature ModifiedIterator::ModifiedIterator(otherModIter);
+     * @param[in] host Host iterator to set.
+     * @param[in] otherModIter ModifiedIterator which may differ in its host type.
+     *            Copy construction.
+     *
+     * The safe way to create this ModifiedIterator is to use the <tt>begin</tt> and <tt>end</tt>
+     * functions of the ModifiedString or to copy construct.
+     * When directly initialized with a host iterator,
+     * the CyclicShape is not yet taken into account and you have to set it up yourself,
+     * for example a CyclicShape starting with a 01... will have skip the first position.
+     * So you would have to reset the host iterator using <tt>++host(myCyclicShape)</tt>.
+     * Use <tt>cargo()</tt> to assign a shape to the iterator.
+     */
+    ModifiedIterator() :
+        _idx(0)
+    {}
+
+    template<typename TOtherHost>
+    ModifiedIterator(ModifiedIterator<TOtherHost, ModCyclicShape<CyclicShape<TSpec> > > const & origin) :
+        _host(origin._host), _cargo(origin._cargo), _idx(origin._idx)
+    {}
+
+    template<typename T>
+    explicit
+    ModifiedIterator(T const & host) :
+        _host(host), _idx(0)
+    {}
+};
+
+
+/*!
+ * @class ModCyclicShapeModifiedString ModCyclicShape ModifiedString
+ * @extends ModifiedString
+ * @headerfile <seqan/modifier.h>
+ *
+ * @brief A string leaving out don't-care-positions defined in CyclicShape.
+ *
+ * @signature template <typename THost, typename TSpec>
+ *            class ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > >;
+ *
+ * @tparam THost The host string.
+ * @tparam TSpec The specialization of CyclicShape.
+ *
+ * Applies a CyclicShape to a string. The resulting modified string skips don't-care positions
+ * and can thus be shorter than the original string. Of course the underlying string is not changed
+ * by the modifier.
+ *
+ * @section Examples
+ *
+ * Use case for GenericCyclicShapes:
+ *
+ * @snippet demos/dox/modifier/cyclic_shape_snippets.cpp Define GenericCyclicShape Modified String
+ *
+ * Use case for FixedCyclicShapes:
+ *
+ * @snippet demos/dox/modifier/cyclic_shape_snippets.cpp Define FixedCyclicShape Modified String
+ *
+ *
+ * @see CyclicShape
+ * @see ModCyclicShapeModifiedIterator
+ *
+ * @note ModCyclicShape Modifier should only be used to <b>view/read a sequence</b>,
+ *       never to change the underlying sequence. Some operations will work, e.g.
+ *       you can use the <tt>operator*()</tt> of the ModifiedIterator to change
+ *       a character, but other operations like <tt>replace</tt> or <tt>append</tt>
+ *       are unsafe or even conceptionally wrong.
+ */
+
+template<typename THost, typename TSpec>
+class ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > >
+{
+public:
+    typedef typename Pointer_<THost>::Type                  THostPointer_;
+    typedef typename Cargo<ModifiedString>::Type            TCargo_;
+    typedef CyclicShape<TSpec>                              TCyclicShape;
+
+    mutable THostPointer_ _host;
+    TCargo_ _cargo;
+
+    // TODO(meiers): Once the Modified String has been propperly documented, document
+    //               the special constructors for ModCyclicShape Modified Strings
+
+    // Default constructor.
+    ModifiedString()
+    {}
+
+    // Construct with the actual host.
+    explicit
+    ModifiedString(typename Parameter_<THost>::Type host) :
+        _host(_toPointer(host))
+    {}
+
+    // Construct with the actual host; variant with shape.
+    explicit
+    ModifiedString(typename Parameter_<THost>::Type host, TCyclicShape const & shape) :
+        _host(_toPointer(host)), _cargo(shape)
+    {}
+
+    // Constructor for creating a ModifiedString with const host with a non-const host.
+    template<typename THost_>
+    explicit
+    ModifiedString(THost_ & host,
+                   SEQAN_CTOR_ENABLE_IF(IsConstructible<THost, THost_>)) :
+        _host(_toPointer(host))
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    // Constructor for creating a ModifiedString with const host with a non-const host; variant with shape.
+    template<typename THost_>
+    explicit ModifiedString(THost_ & host,
+                            TCyclicShape const & shape,
+                            SEQAN_CTOR_ENABLE_IF(IsConstructible<THost, THost_>)) :
+        _host(_toPointer(host)), _cargo(shape)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+#ifdef SEQAN_CXX11_STANDARD
+
+    // Constructor for innermost type; hand down to _host which is a ModifiedString itself.  Non-const variant.
+    template<typename THost_>
+    explicit
+    ModifiedString(THost_ && host,
+                   SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<
+                                            typename RemoveReference<THost>::Type,
+                                            typename RemoveReference<THost_>::Type>)) :
+        _host(host)                     // TODO(meiers): need std::forward<THost_>(host) here?
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    // Constructor for innermost type; hand down to _host which is a ModifiedString itself.
+    // Non-const variant with shape.
+    template<typename THost_>
+    explicit
+    ModifiedString(THost_ && host,
+                   TCyclicShape const & shape,
+                   SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<
+                                            typename RemoveReference<THost>::Type,
+                                            typename RemoveReference<THost_>::Type>)) :
+        _host(host), _cargo(shape)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+#else // SEQAN_CXX11_STANDARD
+
+    // Constructor for innermost type; hand down to _host which is a ModifiedString itself.  Non-const variant.
+    template<typename THost_>
+    explicit
+    ModifiedString(THost_ & host,
+                   SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<THost, THost_>)) :
+        _host(host)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    // Constructor for innermost type; hand down to _host which is a ModifiedString itself.  Const variant.
+    template<typename THost_>
+    explicit
+    ModifiedString(THost_ const & host,
+                   SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<THost, THost_ const>)) :
+        _host(host)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    // Constructor for innermost type; hand down to _host which is a ModifiedString itself.  Non-const variant with
+    // shape.
+    template<typename THost_>
+    explicit
+    ModifiedString(THost_ & host,
+                   TCyclicShape const & shape,
+                   SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<THost, THost_>)) :
+        _host(host), _cargo(shape)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    // Constructor for innermost type; hand down to _host which is a ModifiedString itself.
+    // Const variant with shape.
+    template<typename THost_>
+    explicit
+    ModifiedString(THost_ const & host,
+                   TCyclicShape const & shape,
+                   SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<THost, THost_ const>)) :
+        _host(host), _cargo(shape)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+#endif // SEQAN_CXX11_STANDARD
+
+    template<typename TPos>
+    inline typename Reference<ModifiedString>::Type
+        operator[] (TPos pos)
+    {
+        return value(*this, pos);
+    }
+
+    template<typename TPos>
+    inline typename Reference<ModifiedString const>::Type
+        operator[] (TPos pos) const
+    {
+        return value(*this, pos);
+    }
+};
+
+// ==========================================================================
+// Metafunctions
+// ==========================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction Cargo                       [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn ModCyclicShapeModifiedIterator#Cargo
+ * @headerfile <seqan/modifier.h>
+ * @brief Cargo of ModCyclicShape ModCyclicShape Modified Iterator and ModCyclicShape Modified String.
+ * @signature Cargo<ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > >::Type;
+ * @tparam THost Host iterator of ModifiedIterator.
+ * @tparam TSpec Specialization of CyclicShape.
+ * @return Cargo type of ModCyclicShape Modified Iterator is the CyclicShape itself.
+ */
+
+template<typename THost, typename TSpec>
+struct Cargo<ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > >
+{
+    typedef CyclicShape<TSpec> Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction Cargo                         [ModCyclicShape ModifiedString]
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn ModCyclicShapeModifiedString#Cargo
+ * @headerfile <seqan/modifier.h>
+ * @brief Cargo of ModCyclicShape ModCyclicShape Modified Iterator and ModCyclicShape Modified String.
+ * @signature Cargo<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > >::Type;
+ * @tparam THost Host container of ModifiedString.
+ * @tparam TSpec Specialization of CyclicShape.
+ * @return Cargo type of ModCyclicShape Modified String is the CyclicShape itself.
+ */
+
+template<typename THost, typename TSpec>
+struct Cargo<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > >
+{
+    typedef CyclicShape<TSpec> Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction Iterator                      [ModCyclicShape ModifiedString]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+struct Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > >, Standard>
+{
+    typedef ModifiedIterator<typename Iterator<THost, Standard>::Type,
+        ModCyclicShape<CyclicShape<TSpec> > > Type;
+};
+
+// TODO(meiers): Rooted ?
+
+template<typename THost, typename TSpec>
+struct Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > const, Standard>
+{
+    typedef ModifiedIterator<typename Iterator<THost const, Standard>::Type,
+        ModCyclicShape<CyclicShape<TSpec> > > Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction DefaultIteratorSpec           [ModCyclicShape ModifiedString]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+struct DefaultIteratorSpec<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > >
+{
+    typedef Standard Type;
+};
+
+// ==========================================================================
+// Functions
+// ==========================================================================
+
+// --------------------------------------------------------------------------
+// Function begin()                           [ModCyclicShape ModifiedString]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec, typename TTagSpec>
+inline typename Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > const,
+    Tag<TTagSpec> const>::Type
+begin(ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > const & me, Tag<TTagSpec> const tag_)
+{
+    typedef typename Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > const,
+        Tag<TTagSpec> const>::Type TResult;
+    typedef typename Size<CyclicShape<TSpec> >::Type TSize;
+
+    TResult tmp(begin(host(me), tag_));
+    _copyCargo(tmp, me);
+    host(tmp) += (TSize)cargo(me).loffset;
+    return tmp;
+}
+
+template<typename THost, typename TSpec, typename TTagSpec>
+inline typename Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > >,
+    Tag<TTagSpec> const>::Type
+begin(ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > & me, Tag<TTagSpec> const tag_)
+{
+    typedef typename Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > >,
+        Tag<TTagSpec> const>::Type TResult;
+    typedef typename Size<CyclicShape<TSpec> >::Type TSize;
+
+    TResult tmp(begin(host(me), tag_));
+    _copyCargo(tmp, me);
+    host(tmp) += (TSize)cargo(me).loffset;
+    return tmp;
+}
+
+// --------------------------------------------------------------------------
+// Function end()                             [ModCyclicShape ModifiedString]
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn ModCyclicShapeModifiedString#end
+ * @headerfile <seqan/modifier.h>
+ * @brief Returns an iterator to the end of the container.
+ * @signature TIterator end(modStr[, tag]);
+ * @tparam TIterator ModCyclicShape Modified Iterator to be returned.
+ * @param[in] modStr ModCyclicShape Modified String.
+ * @param[in] An optional tag for selecting the type of the iterator.
+ *            One of Standard and Rooted. When left out,
+ *            @link ContainerConcept#DefaultGetIteratorSpec @endlink of <tt>modStr</tt> is used.
+ * @return Iterator to the end of the container, the type is selected by #Fn<>ContainerConcept#Iterator
+ *         with the given (or default) tag.
+ *
+ * The end iterator is not guaranteed to be at position <tt>length(modStr)</tt>, where
+ * a standard iterator ends. Due to the jumping-tequniche of ModCyclicShape
+ * Modified Iterator, the end iterator is set to the first care position after
+ * the end of the string. The invariant is: <tt>host(end(modStr)) >= end(host(modStr))<tt>
+ * where the the larger or equal operator refers to the position in the sequence.
+ *
+ * If for some reason you use the host iterator to check an end condition, make sure
+ * you use <tt> for(...; host(modIter) >= end(host(modStr)); ...) </tt> instead of
+ * <tt> for(...; host(modIter) != end(host(modStr)); ...) </tt>.
+ */
+
+template<typename THost, typename TSpec, typename TTagSpec>
+inline typename Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > const,
+    Tag<TTagSpec> const>::Type
+end(ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > const & me, Tag<TTagSpec> const tag_)
+{
+    typedef typename Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > const,
+        Tag<TTagSpec> const>::Type TResult;
+    TResult tmp(end(host(me), tag_));
+    _copyCargo(tmp, me);
+    goEnd(tmp, me);
+    return tmp;
+}
+
+template<typename THost, typename TSpec, typename TTagSpec>
+inline typename Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > >,
+    Tag<TTagSpec> const>::Type
+end(ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > > & me, Tag<TTagSpec> const tag_)
+{
+    typedef typename Iterator<ModifiedString<THost, ModCyclicShape<CyclicShape<TSpec> > >,
+        Tag<TTagSpec> const>::Type TResult;
+    TResult tmp(end(host(me), tag_));
+    _copyCargo(tmp, me);
+    goEnd(tmp, me);
+    return tmp;
+}
+
+// --------------------------------------------------------------------------
+// Function goNext()                        [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline void
+goNext(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me)
+{
+    host(me) += cargo(me).diffs[me._idx];
+    if (++me._idx == weight(cargo(me)))
+        me._idx = 0;
+}
+
+// --------------------------------------------------------------------------
+// Function goPrevious()                    [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline void
+goPrevious(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me)
+{
+    if (me._idx == 0)
+        me._idx = weight(cargo(me));
+    --me._idx;
+    host(me) -= cargo(me).diffs[me._idx];
+}
+
+// --------------------------------------------------------------------------
+// Function goBegin()                       [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline void
+goBegin(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me)
+{
+    goBegin(host(me));
+    me._idx = 0;
+    host(me) += cargo(me).loffset;
+}
+
+template<typename THost, typename TSpec, typename TContainer>
+inline void
+goBegin(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me, TContainer & cont)
+{
+    goBegin(host(me), host(cont));
+    me._idx = 0;
+    host(me) += cargo(me).loffset;
+}
+
+template<typename THost, typename TSpec, typename TContainer>
+inline void
+goBegin(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me, TContainer const & cont)
+{
+    goBegin(host(me), host(cont));
+    me._idx = 0;
+    host(me) += cargo(me).loffset;
+}
+
+// --------------------------------------------------------------------------
+// Function goEnd()                         [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline void
+goEnd(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me)
+{
+    goBegin(host(me));
+
+    THost _end(host(me));
+    goEnd(_end);
+
+    typedef typename Position<THost>::Type TPos;
+    TPos len = _end - host(me);
+    TPos pos = cargo(me).span * (len / cargo(me).span) + cargo(me).loffset;
+
+    for (me._idx = 0; pos < len; me._idx = (me._idx + 1) % weight(cargo(me)))
+        pos += cargo(me).diffs[me._idx];
+
+    host(me) += pos;
+}
+
+template<typename THost, typename TSpec, typename TContainer>
+inline void
+goEnd(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me, TContainer & cont)
+{
+    goBegin(host(me), host(cont));
+
+    typedef typename Position<THost>::Type TPos;
+    TPos len = length(host(cont));
+    TPos pos = cargo(me).span * (len / cargo(me).span) + cargo(me).loffset;
+
+    for (me._idx = 0; pos < len; me._idx = (me._idx + 1) % weight(cargo(me)))
+        pos += cargo(me).diffs[me._idx];
+
+    host(me) += pos;
+}
+
+template<typename THost, typename TSpec, typename TContainer>
+inline void
+goEnd(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me, TContainer const & cont)
+{
+    goBegin(host(me), host(cont));
+
+    typedef typename Position<THost>::Type TPos;
+    TPos len = length(host(cont));
+    TPos pos = cargo(me).span * (len / cargo(me).span) + cargo(me).loffset;
+
+    for (me._idx = 0; pos < len; me._idx = (me._idx + 1) % weight(cargo(me)))
+        pos += cargo(me).diffs[me._idx];
+
+    host(me) += pos;
+}
+
+// --------------------------------------------------------------------------
+// Function operator+=()                    [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec, typename TDelta>
+inline ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > &
+operator+=(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > >&me, TDelta delta)
+{
+    if (isNegative(delta))
+    {
+        me -= -(typename MakeSigned<TDelta>::Type)delta;
+    }
+    else
+    {
+        // jump full patterns
+        host(me) += (delta / weight(cargo(me))) * cargo(me).span;
+
+        // number of jumps in dist that remain
+        for (delta = delta % weight(cargo(me)); delta != 0; --delta)
+            goNext(me);
+    }
+    return me;
+}
+
+// --------------------------------------------------------------------------
+// Function operator-=()                    [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec, typename TDelta>
+inline ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > &
+operator-=(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > >&me, TDelta delta)
+{
+    if (isNegative(delta))
+    {
+        me += -(typename MakeSigned<TDelta>::Type)delta;
+    }
+    else
+    {
+        // jump full patterns
+        host(me) -= (delta / weight(cargo(me))) * cargo(me).span;
+
+        // number of jumps in dist that remain
+        for (delta = delta % weight(cargo(me)); delta != 0; --delta)
+            goPrevious(me);
+    }
+    return me;
+}
+
+// --------------------------------------------------------------------------
+// Function atBegin()                       [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline bool
+atBegin(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me)
+{
+    THost _beg(host(me));
+    goBegin(_beg);
+    _beg += cargo(me).DIFFS[0];
+    return host(me) == _beg && me._idx == 0;
+}
+
+// --------------------------------------------------------------------------
+// Function atEnd()                         [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline bool
+atEnd(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > & me)
+{
+    ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > _tmp(me);
+    goEnd(_tmp);
+    return _tmp == me;
+}
+
+// --------------------------------------------------------------------------
+// Function operator==()                        [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline bool
+    operator == (ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > const & a,
+                 ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > const & b)
+{
+    // TODO(meiers): check whether cargo is equal (but there is no operator == for CyclicShape yet)
+
+    return host(a) == host(b) && a._idx == b._idx;
+}
+
+// --------------------------------------------------------------------------
+// Function operator<()                     [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+// uses general version from modifier_iterator.h
+
+// --------------------------------------------------------------------------
+// Function operator-()                     [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline typename Difference<ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > >::Type
+operator-(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > const & a,
+                ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > const & b)
+{
+    typedef typename Difference<ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > >::Type TDiff;
+    if (host(a) == host(b))
+        return 0;
+
+    if (a > b)
+    {
+        THost _a(host(a));
+        THost _b(host(b));
+        TDiff diff = ((_a - _b) / cargo(a).span) * weight(cargo(a));
+        diff += a._idx;
+        diff -= b._idx;
+        return diff;
+    }
+    else
+    {
+        return -(b - a);
+    }
+}
+
+// --------------------------------------------------------------------------
+// Function length()                          [ModCyclicShape ModifiedString]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline typename Size<ModifiedString<THost, ModCyclicShape<TSpec> > >::Type
+length(ModifiedString<THost, ModCyclicShape<TSpec> > const & me)
+{
+    return end(me, Standard()) - begin(me, Standard());
+}
+
+// --------------------------------------------------------------------------
+// Function position()                      [ModCyclicShape ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template<typename THost, typename TSpec>
+inline typename Position<ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > const>::Type
+position(ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > const & me)
+{
+    ModifiedIterator<THost, ModCyclicShape<CyclicShape<TSpec> > > _tmp(me);
+    goEnd(_tmp);
+    return _tmp - me;
+}
+
+// TODO(meiers): What about setPosition() ??
+
+} // namespace
+
+#endif
diff --git a/seqan/modifier/modifier_functors.h b/seqan/modifier/modifier_functors.h
index fc394d7..b8e16ca 100644
--- a/seqan/modifier/modifier_functors.h
+++ b/seqan/modifier/modifier_functors.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -64,20 +64,19 @@ namespace seqan
  *
  * @tparam TInType The parameter/input type.
  * @tparam TResult The return/result type, defaults to TInType.
+ *
+ *
+ * @fn FunctorUpcase::operator()
+ * @brief Function call operator.
+ * @signature TResult FunctorUpcase::operator()(in);
+ *
+ * @param[in] in The value to convert (<tt>in</tt>).
+ *
+ * @return TResult The converted value (<tt>TResult</tt>).
  */
 
-/**
-.Class.FunctorUpcase
-..cat:Modifier
-..summary:Functor that returns the upper case character to a given character.
-..signature:FunctorUpcase<TValue>
-..param.TValue:The input value type.
-..remarks:This Functor is a derivation of the STL unary function.
-..include:seqan/modifier.h
-*/
-
 template <typename InType, typename Result = InType>
-struct FunctorUpcase : public std::unary_function<InType, Result> 
+struct FunctorUpcase : public std::unary_function<InType, Result>
 {
     inline Result operator()(InType x) const
     {
@@ -99,20 +98,19 @@ struct FunctorUpcase : public std::unary_function<InType, Result>
  *
  * @tparam TInType The parameter/input type.
  * @tparam TResult The return/result type, defaults to TInType.
+ *
+ *
+ * @fn FunctorLowcase::operator()
+ * @brief Function call operator.
+ * @signature TResult FunctorLowcase::operator()(in);
+ *
+ * @param[in] in The value to convert (<tt>in</tt>).
+ *
+ * @return TResult The converted value (<tt>TResult</tt>).
  */
 
-/**
-.Class.FunctorLowcase
-..cat:Modifier
-..summary:Functor that returns the lower case character to a given character.
-..signature:FunctorLowcase<TValue>
-..param.TValue:The input value type.
-..remarks:This Functor is a derivation of the STL unary function.
-..include:seqan/modifier.h
-*/
-
 template <typename InType, typename Result = InType>
-struct FunctorLowcase : public std::unary_function<InType, Result> 
+struct FunctorLowcase : public std::unary_function<InType, Result>
 {
     inline Result operator()(InType x) const
     {
@@ -134,25 +132,23 @@ struct FunctorLowcase : public std::unary_function<InType, Result>
  *
  * @tparam TInType  The parameter/input type.
  * @tparam TOutType The return/result type, defaults to TInType.
+ *
+ *
+ * @fn FunctorConvert::operator()
+ * @brief Function call operator.
+ * @signature TOutType FunctorLowcase::operator()(in);
+ *
+ * @param[in] in The value to convert (<tt>in</tt>).
+ *
+ * @return TOutType The converted value (<tt>TOutType</tt>).
  */
 
-/**
-.Class.FunctorConvert
-..cat:Modifier
-..summary:Functor that converts a $TInValue$ type to a $TOutValue$ type character.
-..signature:FunctorConvert<TInValue, TOutValue>
-..param.TInValue:The input value type.
-..param.TOutValue:The output value type.
-..remarks:This Functor is a derivation of the STL unary function.
-..include:seqan/modifier.h
-*/
-
 template <typename InType, typename OutType>
-struct FunctorConvert : public std::unary_function<InType,OutType> 
+struct FunctorConvert : public std::unary_function<InType,OutType>
 {
     inline OutType operator()(InType x) const
     {
-        return x; 
+        return x;
     }
 };
 
@@ -179,10 +175,18 @@ struct TranslateTableRna5ToRna5Complement_
     static char const VALUE[5];
 };
 
-
 template <typename T>
 char const TranslateTableRna5ToRna5Complement_<T>::VALUE[5] = {'U', 'G', 'C', 'A', 'N'};
 
+template <typename T = void>
+struct TranslateTableIupacToIupacComplement_
+{
+    static signed char const VALUE[16];
+};
+
+template <typename T>
+signed char const TranslateTableIupacToIupacComplement_<T>::VALUE[16] = {0, 8, 4, 12, 2, 10, 6, 14, 1, 9, 5, 13, 3, 11, 7, 15};
+
 // --------------------------------------------------------------------------
 // Class FunctorComplement
 // --------------------------------------------------------------------------
@@ -200,72 +204,64 @@ char const TranslateTableRna5ToRna5Complement_<T>::VALUE[5] = {'U', 'G', 'C', 'A
  * @section Remarks
  *
  * If TValue is char, then the characters are complemented as Dna5.
+ *
+ *
+ * @fn FunctorComplement::operator()
+ * @brief Function call operator.
+ * @signature TValue FunctorComplement::operator()(in);
+ *
+ * @param[in] in The value to convert (<tt>in</tt>).
+ *
+ * @return TValue The converted value (<tt>TValue</tt>).
  */
 
-/**
-.Class.FunctorComplement:
-..cat:Modifier
-..summary:Functor that returns the complement nucleotide to a given nucleotide.
-..signature:FunctorComplement<TValue>
-..param.TValue:The input value type.
-...type:Spec.Dna
-...type:Spec.Dna5
-...type:Spec.Rna
-...type:Spec.Rna5
-..remarks:This Functor is a derivation of the STL unary function.
-..include:seqan/modifier.h
-*/
-
 template <>
-struct FunctorComplement<char> : public std::unary_function<Dna5,Dna5> 
+struct FunctorComplement<char> : public std::unary_function<Dna5,Dna5>
 {
     inline Dna5 operator()(Dna5 x) const
     {
-        return TranslateTableDna5ToDna5Complement_<>::VALUE[x.value]; 
+        return TranslateTableDna5ToDna5Complement_<>::VALUE[x.value];
     }
 };
 
 template <>
-struct FunctorComplement<Dna> : public std::unary_function<Dna,Dna> 
+struct FunctorComplement<Dna> : public std::unary_function<Dna,Dna>
 {
     inline Dna operator()(Dna x) const
     {
-        return TranslateTableDna5ToDna5Complement_<>::VALUE[x.value]; 
+        return TranslateTableDna5ToDna5Complement_<>::VALUE[x.value];
     }
 };
 
-
 template <>
-struct FunctorComplement<Dna5> : public std::unary_function<Dna5,Dna5> 
+struct FunctorComplement<Dna5> : public std::unary_function<Dna5,Dna5>
 {
     inline Dna5 operator()(Dna5 x) const
     {
-        return TranslateTableDna5ToDna5Complement_<>::VALUE[x.value]; 
+        return TranslateTableDna5ToDna5Complement_<>::VALUE[x.value];
     }
 };
 
-
 template <>
-struct FunctorComplement<Rna> : public std::unary_function<Rna,Rna> 
+struct FunctorComplement<Rna> : public std::unary_function<Rna,Rna>
 {
     inline Rna operator()(Rna x) const
     {
-        return TranslateTableRna5ToRna5Complement_<>::VALUE[x.value]; 
+        return TranslateTableRna5ToRna5Complement_<>::VALUE[x.value];
     }
 };
 
-
 template <>
-struct FunctorComplement<Rna5> : public std::unary_function<Rna5,Rna5> 
+struct FunctorComplement<Rna5> : public std::unary_function<Rna5,Rna5>
 {
     inline Dna5 operator()(Rna5 x) const
     {
-        return TranslateTableRna5ToRna5Complement_<>::VALUE[x.value]; 
+        return TranslateTableRna5ToRna5Complement_<>::VALUE[x.value];
     }
 };
 
 template <>
-struct FunctorComplement<DnaQ> : public std::unary_function<DnaQ,DnaQ> 
+struct FunctorComplement<DnaQ> : public std::unary_function<DnaQ,DnaQ>
 {
     inline DnaQ operator()(DnaQ x) const
     {
@@ -277,7 +273,7 @@ struct FunctorComplement<DnaQ> : public std::unary_function<DnaQ,DnaQ>
 };
 
 template <>
-struct FunctorComplement<Dna5Q> : public std::unary_function<Dna5Q,Dna5Q> 
+struct FunctorComplement<Dna5Q> : public std::unary_function<Dna5Q,Dna5Q>
 {
     inline Dna5Q operator()(Dna5Q x) const {
         int qual = getQualityValue(x);
@@ -287,6 +283,16 @@ struct FunctorComplement<Dna5Q> : public std::unary_function<Dna5Q,Dna5Q>
     }
 };
 
+template <>
+struct FunctorComplement<Iupac> : public std::unary_function<Iupac,Iupac>
+{
+    inline Iupac operator()(Iupac x) const
+    {
+        return TranslateTableIupacToIupacComplement_<>::VALUE[x.value];
+    }
+};
+
+
 }  // namespace seqan
 
 #endif  // SEQAN_MODIFIER_MODIFIER_FUNCTORS_H_
diff --git a/seqan/modifier/modifier_iterator.h b/seqan/modifier/modifier_iterator.h
index 7699d6c..2b15381 100644
--- a/seqan/modifier/modifier_iterator.h
+++ b/seqan/modifier/modifier_iterator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -63,46 +63,30 @@ template <typename THost, typename TSpec> class ModifiedString;
  *            class ModifiedIterator;
  *
  * @tparam THost The host iterator type.
- * @tparam TSpec Tag used for the specialization, defaults to void.
+ * @tparam TSpec Tag used for the specialization, defaults to <tt>void</tt>.
  *
- * @section Remarks
- *
- * THost can also be a modified iterator, so you can create custom iterators by combining predefined ones.
+ * <tt>THost</tt> can also be a modified iterator, so you can create custom iterators by combining predefined ones.
  */
 
-/**
-.Class.ModifiedIterator:
-..summary:Allows to modify arbitrary iterators by specializing what differs from an origin.
-..cat:Modifier
-..signature:ModifiedIterator<THost[, TSpec]>
-..param.THost:Original iterator.
-...type:Concept.RandomAccessIteratorConcept
-..param.TSpec:The modifier type.
-...metafunction:Metafunction.Spec
-..implements:Concept.RandomAccessIteratorConcept
-..remarks:$THost$ can also be a modified iterator, so you can create custom iterators by combining predefined ones.
-..include:seqan/modifier.h
-*/
-
-template <typename THost, typename TSpec = void>
+template <typename THostIter, typename TSpec = void>
 class ModifiedIterator
 {
 public:
     typedef typename Cargo<ModifiedIterator>::Type TCargo_;
 
-    THost _host;
+    THostIter _host;
     TCargo_ _cargo;
 
     ModifiedIterator()
     {}
 
-    template <typename TOtherHost>
-    ModifiedIterator(ModifiedIterator<TOtherHost, TSpec> const & origin):
-			_host(origin._host), _cargo(origin._cargo)
+    template <typename TOtherHostIter>
+    ModifiedIterator(ModifiedIterator<TOtherHostIter, TSpec> const & origin):
+            _host(origin._host), _cargo(origin._cargo)
     {}
 
     explicit
-    ModifiedIterator(THost const & host): _host(host)
+    ModifiedIterator(THostIter const & host): _host(host)
     {}
 };
 
@@ -163,7 +147,7 @@ struct Reference<ModifiedIterator<THost, TSpec> > : Reference<THost>
 {};
 
 template <typename THost, typename TSpec>
-struct Reference<ModifiedIterator<THost, TSpec> const> : Reference< ModifiedIterator<THost, TSpec> >
+struct Reference<ModifiedIterator<THost, TSpec> const> : Reference<THost>
 {};
 
 // --------------------------------------------------------------------------
@@ -252,14 +236,14 @@ host(ModifiedIterator<THost, TSpec> const & me)
 
 // template <typename THost, typename TSpec>
 // inline THost &
-// host(ModifiedIterator<THost, TSpec> & me) 
+// host(ModifiedIterator<THost, TSpec> & me)
 // {
 //     return value(me.data_host);
 // }
 
 // template <typename THost, typename TSpec>
 // inline THost const &
-// host(ModifiedIterator<THost, TSpec> const & me) 
+// host(ModifiedIterator<THost, TSpec> const & me)
 // {
 //     return value(me._host);
 // }
@@ -270,14 +254,14 @@ host(ModifiedIterator<THost, TSpec> const & me)
 
 template <typename THost, typename TSpec>
 inline typename Reference<typename Cargo<ModifiedIterator<THost, TSpec> >::Type>::Type
-cargo(ModifiedIterator<THost, TSpec> & me) 
+cargo(ModifiedIterator<THost, TSpec> & me)
 {
     return me._cargo;
 }
 
 template <typename THost, typename TSpec>
 inline typename Reference<typename Cargo<ModifiedIterator<THost, TSpec> const>::Type>::Type
-cargo(ModifiedIterator<THost, TSpec> const & me) 
+cargo(ModifiedIterator<THost, TSpec> const & me)
 {
     return me._cargo;
 }
@@ -288,7 +272,7 @@ cargo(ModifiedIterator<THost, TSpec> const & me)
 
 template <typename THost, typename TSpec>
 inline typename Container<ModifiedIterator<THost, TSpec> >::Type //no reference
-container(ModifiedIterator<THost, TSpec> & me) 
+container(ModifiedIterator<THost, TSpec> & me)
 {
     typedef typename Container<ModifiedIterator<THost, TSpec> >::Type TContainer;
     TContainer cont(container(host(me)));
@@ -298,7 +282,7 @@ container(ModifiedIterator<THost, TSpec> & me)
 
 template <typename THost, typename TSpec>
 inline typename Container<ModifiedIterator<THost, TSpec> const>::Type //no reference
-container(ModifiedIterator<THost, TSpec> const & me) 
+container(ModifiedIterator<THost, TSpec> const & me)
 {
     typedef typename Container<ModifiedIterator<THost, TSpec> const>::Type TContainer;
     TContainer cont(container(host(me)));
@@ -313,8 +297,8 @@ container(ModifiedIterator<THost, TSpec> const & me)
 template <typename TIteratorHost, typename TSpec, typename TStringHost>
 inline void
 setContainer(
-		ModifiedIterator<TIteratorHost, TSpec> & me, 
-		ModifiedString<TStringHost, TSpec> & cont) 
+        ModifiedIterator<TIteratorHost, TSpec> & me,
+        ModifiedString<TStringHost, TSpec> & cont)
 {
     setContainer(host(me), host(cont));
     _copyCargo(me, cont);
@@ -323,8 +307,8 @@ setContainer(
 template <typename TIteratorHost, typename TSpec, typename TStringHost>
 inline void
 setContainer(
-		ModifiedIterator<TIteratorHost, TSpec> & me, 
-		ModifiedString<TStringHost, TSpec> const & cont) 
+        ModifiedIterator<TIteratorHost, TSpec> & me,
+        ModifiedString<TStringHost, TSpec> const & cont)
 {
     setContainer(host(me), host(const_cast<ModifiedString<TStringHost, TSpec> &>(cont)));
     _copyCargo(me, cont);
@@ -341,14 +325,14 @@ setContainer(
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec>
-inline typename Reference<ModifiedIterator<THost, TSpec> >::Type 
+inline typename Reference<ModifiedIterator<THost, TSpec> >::Type
 value(ModifiedIterator<THost, TSpec> & me)
 {
     return value(host(me));
 }
 
 template <typename THost, typename TSpec>
-inline typename Reference<ModifiedIterator<THost, TSpec> const>::Type 
+inline typename Reference<ModifiedIterator<THost, TSpec> const>::Type
 value(ModifiedIterator<THost, TSpec> const & me)
 {
     return value(host(me));
@@ -359,14 +343,14 @@ value(ModifiedIterator<THost, TSpec> const & me)
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec>
-inline typename Reference<ModifiedIterator<THost, TSpec> >::Type 
+inline typename Reference<ModifiedIterator<THost, TSpec> >::Type
 operator*(ModifiedIterator<THost, TSpec> & me)
 {
     return value(me);
 }
 
 template <typename THost, typename TSpec>
-inline typename Reference<ModifiedIterator<THost, TSpec> const>::Type 
+inline typename Reference<ModifiedIterator<THost, TSpec> const>::Type
 operator*(ModifiedIterator<THost, TSpec> const & me)
 {
     return value(me);
@@ -390,7 +374,7 @@ goNext(ModifiedIterator<THost, TSpec> & me)
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec>
-inline ModifiedIterator<THost, TSpec> const &
+inline ModifiedIterator<THost, TSpec> &
 operator++(ModifiedIterator<THost, TSpec> & me)
 {
     goNext(me);
@@ -422,7 +406,7 @@ goPrevious(ModifiedIterator<THost, TSpec> & me)
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec>
-inline ModifiedIterator<THost, TSpec> const &
+inline ModifiedIterator<THost, TSpec> &
 operator--(ModifiedIterator<THost, TSpec> & me)
 {
     goPrevious(me);
@@ -536,21 +520,22 @@ operator-(ModifiedIterator<THost, TSpec> const & a, ModifiedIterator<THost, TSpe
 //}
 
 // --------------------------------------------------------------------------
-// Function position()
+// Function position() (overloads for rooted iterators only)
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec>
-inline typename Position<ModifiedIterator<THost, TSpec> const>::Type 
+inline typename Position<ModifiedIterator<THost, TSpec> const>::Type
 position(ModifiedIterator<THost, TSpec> const & me)
 {
     return position(host(me));
 }
 
-template <typename THost, typename TSpec, typename TContainer>
-inline typename Position<ModifiedIterator<THost, TSpec> const>::Type 
-position(ModifiedIterator<THost, TSpec> const & me, TContainer const &cont)
+template <typename TContainer1, typename TIterator, typename TSpec1, typename TSpec2, typename TContainer2>
+inline typename Position<ModifiedIterator<Iter<TContainer1, AdaptorIterator<TIterator, TSpec1> >, TSpec2> const>::Type
+position(ModifiedIterator<Iter<TContainer1, AdaptorIterator<TIterator, TSpec1> >, TSpec2> const & me,
+        TContainer2 const &)
 {
-    return position(host(me), cont);
+    return position(me); // rooted has container
 }
 
 // --------------------------------------------------------------------------
@@ -598,32 +583,9 @@ operator>(ModifiedIterator<THost, TSpec> const & a, ModifiedIterator<THost, TSpe
 }
 
 // --------------------------------------------------------------------------
-// Function atBegin()
+// Function atBegin() (overloads for rooted iterators only)
 // --------------------------------------------------------------------------
 
-template <typename THost, typename TSpec, typename TContainer>
-inline bool
-atBegin(ModifiedIterator<THost, TSpec> & me,
-        TContainer const & container)
-{
-    return atBegin(const_cast<ModifiedIterator<THost, TSpec> const &>(me), container);
-}
-
-template <typename THost, typename TSpec, typename TContainer>
-inline bool
-atBegin(ModifiedIterator<THost, TSpec> const & me,
-        TContainer const & container)
-{
-    return atBegin(host(me), container);
-}
-
-template <typename THost, typename TSpec>
-inline bool
-atBegin(ModifiedIterator<THost, TSpec> & me)
-{
-    return atBegin(const_cast<ModifiedIterator<THost, TSpec> const &>(me));
-}
-
 template <typename THost, typename TSpec>
 inline bool
 atBegin(ModifiedIterator<THost, TSpec> const & me)
@@ -631,38 +593,33 @@ atBegin(ModifiedIterator<THost, TSpec> const & me)
     return atBegin(host(me));
 }
 
-// --------------------------------------------------------------------------
-// Function atEnd()
-// --------------------------------------------------------------------------
-
-template <typename THost, typename TSpec, typename TContainer>
+// rooted overload
+template <typename TContainer1, typename TIterator, typename TSpec1, typename TSpec2, typename TContainer2>
 inline bool
-atEnd(ModifiedIterator<THost, TSpec> & me,
-      TContainer const & container)
+atBegin(ModifiedIterator<Iter<TContainer1, AdaptorIterator<TIterator, TSpec1> >, TSpec2> const & me,
+        TContainer2 const &)
 {
-    return atEnd(const_cast<ModifiedIterator<THost, TSpec> const &>(me), container);
+    return atBegin(me);
 }
 
-template <typename THost, typename TSpec, typename TContainer>
-inline bool
-atEnd(ModifiedIterator<THost, TSpec> const & me,
-      TContainer const & container)
-{
-    return atEnd(host(me), container);
-}
+// --------------------------------------------------------------------------
+// Function atEnd() (overloads for rooted iterators only)
+// --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec>
 inline bool
-atEnd(ModifiedIterator<THost, TSpec> & me)
+atEnd(ModifiedIterator<THost, TSpec> const & me)
 {
-    return atEnd(const_cast<ModifiedIterator<THost, TSpec> const &>(me));
+    return atEnd(host(me));
 }
 
-template <typename THost, typename TSpec>
+// rooted overload
+template <typename TContainer1, typename TIterator, typename TSpec1, typename TSpec2, typename TContainer2>
 inline bool
-atEnd(ModifiedIterator<THost, TSpec> const & me)
+atEnd(ModifiedIterator<Iter<TContainer1, AdaptorIterator<TIterator, TSpec1> >, TSpec2> const & me,
+      TContainer2 const &)
 {
-    return atEnd(host(me));
+    return atEnd(me);
 }
 
 }
@@ -670,17 +627,17 @@ atEnd(ModifiedIterator<THost, TSpec> const & me)
 // Adapt SeqAn modified to std.
 namespace std
 {
-	template<typename THost, typename TSpec>
-	struct iterator_traits<seqan::ModifiedIterator<THost, TSpec> >
-	{
-		typedef ::seqan::ModifiedIterator<THost, TSpec> TIter;
-
-		typedef random_access_iterator_tag iterator_category;
-		typedef typename ::seqan::Value<TIter>::Type value_type;
-		typedef typename ::seqan::Difference<TIter>::Type difference_type;
-		typedef typename ::seqan::Value<TIter>::Type * pointer;
-		typedef typename ::seqan::Reference<TIter>::Type reference;
-	};
+    template<typename THost, typename TSpec>
+    struct iterator_traits<seqan::ModifiedIterator<THost, TSpec> >
+    {
+        typedef seqan::ModifiedIterator<THost, TSpec> TIter;
+
+        typedef random_access_iterator_tag iterator_category;
+        typedef typename seqan::Value<TIter>::Type value_type;
+        typedef typename seqan::Difference<TIter>::Type difference_type;
+        typedef typename seqan::Value<TIter>::Type * pointer;
+        typedef typename seqan::Reference<TIter>::Type reference;
+    };
 }
 
 #endif
diff --git a/seqan/modifier/modifier_position.h b/seqan/modifier/modifier_position.h
new file mode 100644
index 0000000..75ce029
--- /dev/null
+++ b/seqan/modifier/modifier_position.h
@@ -0,0 +1,451 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// A Position ModifiedString represents a permutation of the host string.
+
+#ifndef SEQAN_MODIFIER_MODIFIER_POSITION_H_
+#define SEQAN_MODIFIER_MODIFIER_POSITION_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag ModPos
+// ----------------------------------------------------------------------------
+
+template <typename TPositions>
+struct ModPos {};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction Cargo
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct Cargo<ModifiedString<THost, ModPos<TPositions> > >
+{
+    typedef typename Pointer_<TPositions>::Type  Type;
+};
+
+template <typename THost, typename TPositions>
+struct Cargo<ModifiedString<THost, ModPos<TPositions> > const>
+{
+    typedef typename Pointer_<TPositions>::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct Value<ModifiedString<THost, ModPos<TPositions> > > : Value<THost> {};
+
+template <typename THost, typename TPositions>
+struct Value<ModifiedString<THost, ModPos<TPositions> > const> : Value<THost> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction GetValue
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct GetValue<ModifiedString<THost, ModPos<TPositions> > > : GetValue<THost> {};
+
+template <typename THost, typename TPositions>
+struct GetValue<ModifiedString<THost, ModPos<TPositions> > const> : GetValue<THost> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Reference
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct Reference<ModifiedString<THost, ModPos<TPositions> > > : Reference<THost> {};
+
+template <typename THost, typename TPositions>
+struct Reference<ModifiedString<THost, ModPos<TPositions> > const> : Reference<THost> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Difference
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct Difference<ModifiedString<THost, ModPos<TPositions> > > : Difference<TPositions> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct Size<ModifiedString<THost, ModPos<TPositions> > > : Size<TPositions> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct Position<ModifiedString<THost, ModPos<TPositions> > > : Position<TPositions> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct Iterator<ModifiedString<THost, ModPos<TPositions> >, Standard>
+{
+    typedef Iter<ModifiedString<THost, ModPos<TPositions> >, PositionIterator>   Type;
+};
+
+template <typename THost, typename TPositions>
+struct Iterator<ModifiedString<THost, ModPos<TPositions> > const, Standard>
+{
+    typedef Iter<ModifiedString<THost, ModPos<TPositions> > const, PositionIterator>   Type;
+};
+
+template <typename THost, typename TPositions>
+struct Iterator<ModifiedString<THost, ModPos<TPositions> >, Rooted>
+{
+    typedef Iter<ModifiedString<THost, ModPos<TPositions> >, PositionIterator>   Type;
+};
+
+template <typename THost, typename TPositions>
+struct Iterator<ModifiedString<THost, ModPos<TPositions> > const, Rooted>
+{
+    typedef Iter<ModifiedString<THost, ModPos<TPositions> > const, PositionIterator>   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Prefix
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): not implemented.
+
+// ----------------------------------------------------------------------------
+// Metafunction Suffix
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): not implemented.
+
+// ----------------------------------------------------------------------------
+// Metafunction Infix
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct Infix<ModifiedString<THost, ModPos<TPositions> > >
+{
+    typedef ModifiedString<THost, ModPos<typename Infix<TPositions>::Type> >    Type;
+};
+
+template <typename THost, typename TPositions>
+struct Infix<ModifiedString<THost, ModPos<TPositions> > const>
+{
+    typedef ModifiedString<THost, ModPos<typename Infix<TPositions>::Type> > const   Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction AllowsFastRandomAccess
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+struct AllowsFastRandomAccess<ModifiedString<THost, ModPos<TPositions> > > :
+    And<AllowsFastRandomAccess<THost>, AllowsFastRandomAccess<TPositions> >
+{};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function cargo()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+inline typename Parameter_<TPositions>::Type
+cargo(ModifiedString<THost, ModPos<TPositions> > & me)
+{
+    return _toParameter<TPositions>(me._cargo);
+}
+
+template <typename THost, typename TPositions>
+inline typename Parameter_<TPositions>::Type
+cargo(ModifiedString<THost, ModPos<TPositions> > const & me)
+{
+    return _toParameter<TPositions>(me._cargo);
+}
+
+// --------------------------------------------------------------------------
+// Function setCargo()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+inline void
+setCargo(ModifiedString<THost, ModPos<TPositions> > & me, typename Parameter_<TPositions>::Type _cargo)
+{
+    me._cargo = _toPointer(_cargo);
+}
+
+// ----------------------------------------------------------------------------
+// Function begin()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions, typename TTagSpec>
+inline typename Iterator<ModifiedString<THost, ModPos<TPositions> >, Tag<TTagSpec> const>::Type
+begin(ModifiedString<THost, ModPos<TPositions> > & me, Tag<TTagSpec> const /* tag */)
+{
+    return typename Iterator<ModifiedString<THost, ModPos<TPositions> >, Tag<TTagSpec> const>::Type(me);
+}
+
+template <typename THost, typename TPositions, typename TTagSpec>
+inline typename Iterator<ModifiedString<THost, ModPos<TPositions> > const, Tag<TTagSpec> const>::Type
+begin(ModifiedString<THost, ModPos<TPositions> > const & me, Tag<TTagSpec> const /* tag */)
+{
+    return typename Iterator<ModifiedString<THost, ModPos<TPositions> > const, Tag<TTagSpec> const>::Type(me);
+}
+
+// ----------------------------------------------------------------------------
+// Function end()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions, typename TTagSpec>
+inline typename Iterator<ModifiedString<THost, ModPos<TPositions> >, Tag<TTagSpec> const>::Type
+end(ModifiedString<THost, ModPos<TPositions> > & me, Tag<TTagSpec> const /* tag */)
+{
+    return typename Iterator<ModifiedString<THost, ModPos<TPositions> >, Tag<TTagSpec> const>::Type(me, length(me));
+}
+
+template <typename THost, typename TPositions, typename TTagSpec>
+inline typename Iterator<ModifiedString<THost, ModPos<TPositions> > const, Tag<TTagSpec> const>::Type
+end(ModifiedString<THost, ModPos<TPositions> > const & me, Tag<TTagSpec> const /* tag */)
+{
+    return typename Iterator<ModifiedString<THost, ModPos<TPositions> > const, Tag<TTagSpec> const>::Type(me, length(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions, typename TPos>
+inline typename Reference<ModifiedString<THost, ModPos<TPositions> > >::Type
+value(ModifiedString<THost, ModPos<TPositions> > & me, TPos pos)
+{
+    return value(host(me), getValue(cargo(me), pos));
+}
+
+template <typename THost, typename TPositions, typename TPos>
+inline typename Reference<ModifiedString<THost, ModPos<TPositions> > const>::Type
+value(ModifiedString<THost, ModPos<TPositions> > const & me, TPos pos)
+{
+    return value(host(me), getValue(cargo(me), pos));
+}
+
+// ----------------------------------------------------------------------------
+// Function getValue()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions, typename TPos>
+inline typename GetValue<ModifiedString<THost, ModPos<TPositions> > >::Type
+getValue(ModifiedString<THost, ModPos<TPositions> > & me, TPos pos)
+{
+    return getValue(host(me), getValue(cargo(me), pos));
+}
+
+template <typename THost, typename TPositions, typename TPos>
+inline typename GetValue<ModifiedString<THost, ModPos<TPositions> > const>::Type
+getValue(ModifiedString<THost, ModPos<TPositions> > const & me, TPos pos)
+{
+    return getValue(host(me), getValue(cargo(me), pos));
+}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+inline typename Size<ModifiedString<THost, ModPos<TPositions> > >::Type
+length(ModifiedString<THost, ModPos<TPositions> > const & me)
+{
+    return length(cargo(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+inline bool empty(ModifiedString<THost, ModPos<TPositions> > const & me)
+{
+    return empty(cargo(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions>
+inline void clear(ModifiedString<THost, ModPos<TPositions> > & me)
+{
+    clear(cargo(me));
+}
+
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): a dummy implementation like ContainerView could be necessary.
+
+// ----------------------------------------------------------------------------
+// Function prefix()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): not implemented.
+
+// ----------------------------------------------------------------------------
+// Function suffix()
+// ----------------------------------------------------------------------------
+// NOTE(esiragusa): not implemented.
+
+// ----------------------------------------------------------------------------
+// Function infix()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions, typename TPosBegin, typename TPosEnd>
+inline typename Infix<ModifiedString<THost, ModPos<TPositions> > const>::Type
+infix(ModifiedString<THost, ModPos<TPositions> > const & me, TPosBegin pos_begin, TPosEnd pos_end)
+{
+    typename Infix<ModifiedString<THost, ModPos<TPositions> > const>::Type other;
+    setHost(other, host(me));
+    setCargo(other, infix(cargo(me), pos_begin, pos_end));
+    return other;
+}
+
+template <typename THost, typename TPositions, typename TPosBegin, typename TPosEnd>
+inline typename Infix<ModifiedString<THost, ModPos<TPositions> > >::Type
+infix(ModifiedString<THost, ModPos<TPositions> > & me, TPosBegin pos_begin, TPosEnd pos_end)
+{
+    typename Infix<ModifiedString<THost, ModPos<TPositions> > >::Type other;
+    setHost(other, host(me));
+    setCargo(other, infix(cargo(me), pos_begin, pos_end));
+    return other;
+}
+
+// ----------------------------------------------------------------------------
+// Function position()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions, typename TPos>
+inline typename Position<ModifiedString<THost, ModPos<TPositions> > const>::Type
+position(ModifiedString<THost, ModPos<TPositions> > const & me, TPos i)
+{
+    return getValue(cargo(me), i);
+}
+
+// ----------------------------------------------------------------------------
+// Function setPosition()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions, typename TPos>
+inline void setPosition(ModifiedString<THost, ModPos<TPositions> > & me, TPos i, TPos j)
+{
+    assignValue(cargo(me), i, j);
+}
+
+template <typename THost, typename TPositions, typename TPos>
+inline void setPosition(ModifiedString<THost, ModPos<TPositions> > const & me, TPos i, TPos j)
+{
+    assignValue(cargo(me), i, j);
+}
+
+// ----------------------------------------------------------------------------
+// Functor PosLess_
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPos = typename Position<THost>::Type, typename TPredicate = std::less<TPos> >
+struct PosLess_ : public std::binary_function<TPos, TPos, bool>
+{
+    THost const & _host;
+    TPredicate pred;
+
+    PosLess_(THost const & _host) :
+        _host(_host)
+    {}
+
+    PosLess_(THost const & _host, TPredicate const & pred) :
+        _host(_host),
+        pred(pred)
+    {}
+
+    bool operator()(TPos a, TPos b)
+    {   
+        return pred(getValue(_host, a), getValue(_host, b));
+    }   
+};
+
+// ----------------------------------------------------------------------------
+// Function sort()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TPositions, typename TBinaryPredicate, typename TParallelTag>
+inline void sort(ModifiedString<THost, ModPos<TPositions> > SEQAN_FORWARD_ARG me, TBinaryPredicate p, Tag<TParallelTag> const & tag)
+{
+    typedef typename Position<ModifiedString<THost, ModPos<TPositions> > >::Type TPos;
+
+    sort(cargo(me), PosLess_<THost, TPos, TBinaryPredicate>(host(me), p), tag);
+}
+
+template <typename THost, typename TPositions, typename TParallelTag>
+inline void sort(ModifiedString<THost, ModPos<TPositions> > SEQAN_FORWARD_ARG me, Tag<TParallelTag> const & tag)
+{
+    typedef typename Position<ModifiedString<THost, ModPos<TPositions> > >::Type TPos;
+
+    sort(cargo(me), PosLess_<THost, TPos>(host(me)), tag);
+}
+
+template <typename THost, typename TPositions, typename TBinaryPredicate, typename TParallelTag>
+inline void sort(ModifiedString<THost, ModPos<TPositions> > const & me, TBinaryPredicate p, Tag<TParallelTag> const & tag)
+{
+    typedef typename Position<ModifiedString<THost, ModPos<TPositions> > >::Type TPos;
+
+    sort(cargo(me), PosLess_<THost, TPos, TBinaryPredicate>(host(me), p), tag);
+}
+
+template <typename THost, typename TPositions, typename TParallelTag>
+inline void sort(ModifiedString<THost, ModPos<TPositions> > const & me, Tag<TParallelTag> const & tag)
+{
+    typedef typename Position<ModifiedString<THost, ModPos<TPositions> > >::Type TPos;
+
+    sort(cargo(me), PosLess_<THost, TPos>(host(me)), tag);
+}
+
+}  // namespace seqan
+
+#endif  // SEQAN_MODIFIER_MODIFIER_POSITION_H_
diff --git a/seqan/modifier/modifier_reverse.h b/seqan/modifier/modifier_reverse.h
index 98690ae..2a06b80 100644
--- a/seqan/modifier/modifier_reverse.h
+++ b/seqan/modifier/modifier_reverse.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -75,19 +75,6 @@ namespace seqan
  * @tparam THost original string.
  */
 
-/**
-.Spec.ModReverse:
-..summary:Mirrors the characters from begin to end.
-..cat:Modifier
-..general:Class.ModifiedIterator
-..general:Class.ModifiedString
-..signature:ModifiedIterator<THost, ModReverse>
-..signature:ModifiedString<THost, ModReverse>
-..param.THost:Original string/iterator.
-...type:Concept.RandomAccessIteratorConcept
-..include:seqan/modifier.h
-*/
-
 struct ModReverse_;
 typedef Tag<ModReverse_> ModReverse;
 
@@ -102,7 +89,7 @@ typedef Tag<ModReverse_> ModReverse;
 template <typename THost>
 struct Cargo<ModifiedIterator<THost, ModReverse> >
 {
-    typedef Cargo Type;		// to reduce namespace pollution
+    typedef Cargo Type;        // to reduce namespace pollution
     bool _atEnd;
 
     Cargo() : _atEnd(false)
@@ -116,13 +103,13 @@ struct Cargo<ModifiedIterator<THost, ModReverse> >
 template <typename THost>
 struct Iterator<ModifiedString<THost, ModReverse>, Standard>
 {
-    typedef ModifiedIterator<typename Iterator<THost const, Rooted>::Type, ModReverse> Type;
+    typedef ModifiedIterator<typename Iterator<THost, Rooted>::Type, ModReverse> Type;
 };
 
 template <typename THost>
 struct Iterator<ModifiedString<THost, ModReverse> const, Standard>
 {
-    typedef ModifiedIterator<typename Iterator<THost const, Rooted>::Type, ModReverse> Type;
+    typedef ModifiedIterator<typename Iterator<THost, Rooted>::Type, ModReverse> Type;
 };
 
 // --------------------------------------------------------------------------
@@ -225,12 +212,12 @@ goBegin(ModifiedIterator<THost, ModReverse> & me,
 
 template <typename THost, typename TDelta>
 inline ModifiedIterator<THost, ModReverse> &
-operator+=(ModifiedIterator<THost, ModReverse> & me, TDelta delta_) 
+operator+=(ModifiedIterator<THost, ModReverse> & me, TDelta delta_)
 {
     typedef ModifiedIterator<THost, ModReverse> TIterator;
     typedef typename Position<TIterator>::Type TPosition;
     TPosition delta = delta_;
-    
+
     if (delta == 0)
     {
         return me;
@@ -252,7 +239,7 @@ operator+=(ModifiedIterator<THost, ModReverse> & me, TDelta delta_)
             ++delta;
         }
         host(me) -= delta;
-    } 
+    }
     return me;
 }
 
@@ -287,6 +274,16 @@ operator-=(ModifiedIterator<THost, ModReverse> & me, TDelta delta)
     }
     return me;
 }
+// --------------------------------------------------------------------------
+// Function operator-()                         [ModReverse ModifiedIterator]
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TPos>
+inline ModifiedIterator<THost, ModReverse>
+operator-(ModifiedIterator<THost, ModReverse> me, TPos const i)
+{
+    return me -= i;
+}
 
 // --------------------------------------------------------------------------
 // Function operator-()                         [ModReverse ModifiedIterator]
@@ -310,7 +307,7 @@ operator-(ModifiedIterator<THost, ModReverse> const & a,
 // --------------------------------------------------------------------------
 
 template <typename THost>
-inline typename Position<ModifiedIterator<THost, ModReverse> const>::Type 
+inline typename Position<ModifiedIterator<THost, ModReverse> const>::Type
 position(ModifiedIterator<THost, ModReverse> const & me)
 {
     if (cargo(me)._atEnd)
@@ -319,8 +316,17 @@ position(ModifiedIterator<THost, ModReverse> const & me)
         return length(container(host(me))) - 1 - position(host(me));
 }
 
+// rooted overload
+template <typename TContainer1, typename TIterator, typename TSpec, typename TContainer2>
+inline typename Position<ModifiedIterator<Iter<TContainer1, AdaptorIterator<TIterator, TSpec> >, ModReverse> const>::Type
+position(ModifiedIterator<Iter<TContainer1, AdaptorIterator<TIterator, TSpec> >, ModReverse> const & me,
+         TContainer2 const &)
+{
+    return position(me); // rooted has container
+}
+
 template <typename THost, typename TContainer>
-inline typename Position<ModifiedIterator<THost, ModReverse> const>::Type 
+inline typename Position<ModifiedIterator<THost, ModReverse> const>::Type
 position(ModifiedIterator<THost, ModReverse> const & me, TContainer const &cont)
 {
     if (cargo(me)._atEnd)
@@ -408,14 +414,14 @@ atEnd(ModifiedIterator<THost, ModReverse> const & me)
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TPos>
-inline typename Reference<ModifiedString<THost, ModReverse> >::Type 
+inline typename Reference<ModifiedString<THost, ModReverse> >::Type
 value(ModifiedString<THost, ModReverse> & me, TPos pos)
 {
     return value(host(me), (length(host(me)) - 1) - pos);
 }
 
 template <typename THost, typename TPos>
-inline typename Reference<ModifiedString<THost, ModReverse> const>::Type 
+inline typename Reference<ModifiedString<THost, ModReverse> const>::Type
 value(ModifiedString<THost, ModReverse> const & me, TPos pos)
 {
     return value(host(me), (length(host(me)) - 1) - pos);
@@ -426,7 +432,7 @@ value(ModifiedString<THost, ModReverse> const & me, TPos pos)
 // --------------------------------------------------------------------------
 
 template < typename THost>
-inline typename Iterator< ModifiedString<THost, ModReverse> const >::Type 
+inline typename Iterator< ModifiedString<THost, ModReverse> const >::Type
 begin(ModifiedString<THost, ModReverse> const & me)
 {
     typename Iterator< ModifiedString<THost, ModReverse> const >::Type temp_(end(host(me), Rooted()));
@@ -436,7 +442,7 @@ begin(ModifiedString<THost, ModReverse> const & me)
 }
 
 template < typename THost >
-inline typename Iterator< ModifiedString<THost, ModReverse> >::Type 
+inline typename Iterator< ModifiedString<THost, ModReverse> >::Type
 begin(ModifiedString<THost, ModReverse> & me)
 {
     typename Iterator< ModifiedString<THost, ModReverse> >::Type temp_(end(host(me), Rooted()));
@@ -446,7 +452,7 @@ begin(ModifiedString<THost, ModReverse> & me)
 }
 
 template < typename THost, typename TTagSpec >
-inline typename Iterator< ModifiedString<THost, ModReverse> const, Tag<TTagSpec> const >::Type 
+inline typename Iterator< ModifiedString<THost, ModReverse> const, Tag<TTagSpec> const >::Type
 begin(ModifiedString<THost, ModReverse> const & me, Tag<TTagSpec> const)
 {
     typename Iterator< ModifiedString<THost, ModReverse> const, Tag<TTagSpec> const >::Type temp_(end(host(me), Rooted()));
@@ -456,7 +462,7 @@ begin(ModifiedString<THost, ModReverse> const & me, Tag<TTagSpec> const)
 }
 
 template < typename THost, typename TTagSpec >
-inline typename Iterator< ModifiedString<THost, ModReverse>, Tag<TTagSpec> const >::Type 
+inline typename Iterator< ModifiedString<THost, ModReverse>, Tag<TTagSpec> const >::Type
 begin(ModifiedString<THost, ModReverse> & me, Tag<TTagSpec> const)
 {
     typedef typename Iterator< ModifiedString<THost, ModReverse>, Tag<TTagSpec> const >::Type TIterator;
@@ -471,7 +477,7 @@ begin(ModifiedString<THost, ModReverse> & me, Tag<TTagSpec> const)
 // --------------------------------------------------------------------------
 
 template <typename THost >
-inline typename Iterator<ModifiedString<THost, ModReverse> const >::Type 
+inline typename Iterator<ModifiedString<THost, ModReverse> const >::Type
 end(ModifiedString<THost, ModReverse> const & me)
 {
     typename Iterator<ModifiedString<THost, ModReverse> const >::Type temp_(begin(host(me), Rooted()));
@@ -481,7 +487,7 @@ end(ModifiedString<THost, ModReverse> const & me)
 }
 
 template <typename THost >
-inline typename Iterator<ModifiedString<THost, ModReverse> >::Type 
+inline typename Iterator<ModifiedString<THost, ModReverse> >::Type
 end(ModifiedString<THost, ModReverse> & me)
 {
     typename Iterator<ModifiedString<THost, ModReverse> >::Type temp_(begin(host(me), Rooted()));
@@ -491,7 +497,7 @@ end(ModifiedString<THost, ModReverse> & me)
 }
 
 template <typename THost, typename TTagSpec >
-inline typename Iterator<ModifiedString<THost, ModReverse> const, Tag<TTagSpec> const>::Type 
+inline typename Iterator<ModifiedString<THost, ModReverse> const, Tag<TTagSpec> const>::Type
 end(ModifiedString<THost, ModReverse> const & me, Tag<TTagSpec> const)
 {
     typename Iterator<ModifiedString<THost, ModReverse> const, Tag<TTagSpec> const >::Type temp_(begin(host(me), Rooted()));
@@ -501,7 +507,7 @@ end(ModifiedString<THost, ModReverse> const & me, Tag<TTagSpec> const)
 }
 
 template <typename THost, typename TTagSpec >
-inline typename Iterator<ModifiedString<THost, ModReverse>, Tag<TTagSpec> const>::Type 
+inline typename Iterator<ModifiedString<THost, ModReverse>, Tag<TTagSpec> const>::Type
 end(ModifiedString<THost, ModReverse> & me, Tag<TTagSpec> const)
 {
     typename Iterator<ModifiedString<THost, ModReverse>, Tag<TTagSpec> const >::Type temp_(begin(host(me), Rooted()));
@@ -531,16 +537,18 @@ end(ModifiedString<THost, ModReverse> & me, Tag<TTagSpec> const)
  * remains the same.
  */
 
-/**
-.Function.reverse
-..summary:Reverse an object/container in-place.
-..cat:Modifier
-..signature:reverse(object)
-..param.object:The object/container whose elements to reverse.
-...type:Concept.ContainerConcept
-...type:Adaption.std::list
-..include:seqan/modifier.h
-*/
+template <typename TValue>
+inline bool
+_reverseDoSequential(TValue size)
+{
+    return size < (TValue)10000;
+}
+
+inline bool
+_reverseDoSequential(unsigned char)
+{
+    return true;
+}
 
 template < typename TSequence, typename TParallelTag >
 inline void
@@ -548,13 +556,14 @@ reverse(TSequence & sequence, Tag<TParallelTag> parallelTag)
 {
     typedef typename Position<TSequence>::Type              TPos;
     typedef typename Iterator<TSequence, Standard>::Type    TIter;
-    
+
     TIter itBeg = begin(sequence, Standard());
     TIter itEnd = end(sequence, Standard());
     Splitter<TPos> splitter(0, length(sequence) / 2, parallelTag);
 
     // disable multi-threading if sequence is too small
-    if (IsSameType<Tag<TParallelTag>, Parallel>::VALUE && length(sequence) < 10000)
+    // __uint64 cast is for 8bit size types for which comparison would be always true
+    if (IsSameType<Tag<TParallelTag>, Parallel>::VALUE && _reverseDoSequential(length(sequence)))
         resize(splitter, 1);
 
     // (weese:) We have to cast the result of length to int to circumvent an internal gcc compiler error
@@ -582,25 +591,18 @@ reverse(StringSet<TSequence, TSpec> & stringSet, Tag<TParallelTag>)
         reverse(stringSet[seqNo], Serial());
 }
 
-template <typename TValue>
-inline void
-reverse(std::list<TValue> & list)
-{
-    list.reverse();
-}
-
 template < typename TText >
-inline void
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<TText> >)
 reverse(TText & text)
 {
     reverse(text, Parallel());
 }
 
 // const variants for segments/modifiers
-
+//NOTE(h-2): why do we remove constnes??
 template < typename TText >
 inline void
-reverse(TText const & text) 
+reverse(TText const & text)
 {
     reverse(const_cast<TText &>(text), Parallel());
 }
@@ -612,7 +614,6 @@ reverse(TText const & text, Tag<TParallelTag> parallelTag)
     reverse(const_cast<TText &>(text), parallelTag);
 }
 
-
 // --------------------------------------------------------------------------
 // Function reverseString()
 // --------------------------------------------------------------------------
@@ -621,7 +622,7 @@ template <typename THost>
 inline ModifiedString<THost, ModReverse>
 reverseString(THost & host)
 {
-	return ModifiedString<THost, ModReverse>(host);
+    return ModifiedString<THost, ModReverse>(host);
 }
 
 }
diff --git a/seqan/modifier/modifier_shortcuts.h b/seqan/modifier/modifier_shortcuts.h
index fe10536..69a71d9 100644
--- a/seqan/modifier/modifier_shortcuts.h
+++ b/seqan/modifier/modifier_shortcuts.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,49 +42,7 @@ namespace seqan
 // Shortcuts for Modified Strings.
 // ==========================================================================
 
-/**
-.Shortcut.ModComplementDna:
-..cat:Modifier
-..summary:Modifier specialization type for the complement of @Spec.Dna@ alphabet sequences.
-..signature:DnaStringComplement
-..shortcutfor:Spec.ModView
-...signature:ModView< FunctorComplement<Dna> >
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
-/**
-.Shortcut.ModComplementDna5:
-..cat:Modifier
-..summary:Modifier specialization type for the complement of @Spec.Dna5@ alphabet sequences.
-..signature:Dna5StringComplement
-..shortcutfor:Spec.ModView
-...signature:ModView< FunctorComplement<Dna5> >
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
-/**
-.Shortcut.ModComplementRna:
-..cat:Modifier
-..summary:Modifier specialization type for the complement of @Spec.Rna@ alphabet sequences.
-..signature:RnaStringComplement
-..shortcutfor:Spec.ModView
-...signature:ModView< FunctorComplement<Rna> >
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
-/**
-.Shortcut.ModComplementRna5:
-..cat:Modifier
-..summary:Modifier specialization type for the complement of @Spec.Rna5@ alphabet sequences.
-..signature:Rna5StringComplement
-..shortcutfor:Spec.ModView
-...signature:ModView< FunctorComplement<Rna5> >
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
+
 
 /*!
  * @typedef DnaStringComplement
@@ -94,19 +52,6 @@ namespace seqan
  * @signature typedef ModifiedString<DnaString, ModView<FunctorComplementDna> > > DnaStringComplement;
  */
 
-/**
-.Shortcut.DnaStringComplement:
-..cat:Modifier
-..summary:Modifier for the complement of a @Shortcut.DnaString@.
-..signature:DnaStringComplement
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<DnaString, ModView< FunctorComplement<Dna> > >
-..see:Shortcut.DnaString
-..see:Class.ModifiedString
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
 /*!
  * @typedef Dna5StringComplement
  * @headerfile <seqan/modifier.h>
@@ -115,19 +60,6 @@ namespace seqan
  * @signature typedef ModifiedString<Dna5String, ModView<FunctorComplementDna> > > DnaStringComplement;
  */
 
-/**
-.Shortcut.Dna5StringComplement:
-..cat:Modifier
-..summary:Modifier for the complement of a @Shortcut.Dna5String@.
-..signature:Dna5StringComplement
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<Dna5String, ModView< FunctorComplement<Dna5> > >
-..see:Shortcut.Dna5String
-..see:Class.ModifiedString
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
 /*!
  * @typedef RnaStringComplement
  * @headerfile <seqan/modifier.h>
@@ -136,19 +68,6 @@ namespace seqan
  * @signature typedef ModifiedString<RnaString, ModView<FunctorComplementDna> > > DnaStringComplement;
  */
 
-/**
-.Shortcut.RnaStringComplement:
-..cat:Modifier
-..summary:Modifier for the complement of a @Shortcut.RnaString@.
-..signature:RnaStringComplement
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<RnaString, ModView< FunctorComplement<Rna> > >
-..see:Shortcut.RnaString
-..see:Class.ModifiedString
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
 /*!
  * @typedef Rna5StringComplement
  * @headerfile <seqan/modifier.h>
@@ -157,19 +76,6 @@ namespace seqan
  * @signature typedef ModifiedString<Rna5String, ModView<FunctorComplementDna> > > DnaStringComplement;
  */
 
-/**
-.Shortcut.Rna5StringComplement:
-..cat:Modifier
-..summary:Modifier for the complement of a @Shortcut.Rna5String@.
-..signature:Rna5StringComplement
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<Rna5String, ModView< FunctorComplement<Rna5> > >
-..see:Shortcut.Rna5String
-..see:Class.ModifiedString
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
 /*!
  * @typedef DnaStringReverse
  * @headerfile <seqan/modifier.h>
@@ -178,18 +84,6 @@ namespace seqan
  * @signature typedef ModifiedString<DnaString, ModReverse> DnaStringReverse;
  */
 
-/**
-.Shortcut.DnaStringReverse:
-..cat:Modifier
-..summary:Modifier for the reverse of a @Shortcut.DnaString@.
-..signature:DnaStringReverse
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<DnaString, ModReverse>
-..see:Shortcut.DnaString
-..see:Class.ModifiedString
-..see:Spec.ModReverse
-*/
-
 /*!
  * @typedef Dna5StringReverse
  * @headerfile <seqan/modifier.h>
@@ -198,18 +92,6 @@ namespace seqan
  * @signature typedef ModifiedString<Dna5String, ModReverse> DnaStringReverse;
  */
 
-/**
-.Shortcut.Dna5StringReverse:
-..cat:Modifier
-..summary:Modifier for the reverse of a @Shortcut.Dna5String@.
-..signature:Dna5StringReverse
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<Dna5String, ModReverse>
-..see:Shortcut.Dna5String
-..see:Class.ModifiedString
-..see:Spec.ModReverse
-*/
-
 /*!
  * @typedef RnaStringReverse
  * @headerfile <seqan/modifier.h>
@@ -218,18 +100,6 @@ namespace seqan
  * @signature typedef ModifiedString<RnaString, ModReverse> DnaStringReverse;
  */
 
-/**
-.Shortcut.RnaStringReverse:
-..cat:Modifier
-..summary:Modifier for the reverse of a @Shortcut.RnaString@.
-..signature:RnaStringReverse
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<RnaString, ModReverse>
-..see:Shortcut.RnaString
-..see:Class.ModifiedString
-..see:Spec.ModReverse
-*/
-
 /*!
  * @typedef Rna5StringReverse
  * @headerfile <seqan/modifier.h>
@@ -238,18 +108,6 @@ namespace seqan
  * @signature typedef ModifiedString<Rna5String, ModReverse> DnaStringReverse;
  */
 
-/**
-.Shortcut.Rna5StringReverse:
-..cat:Modifier
-..summary:Modifier for the reverse of a @Shortcut.Rna5String@.
-..signature:Rna5StringReverse
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<Rna5String, ModReverse>
-..see:Shortcut.Rna5String
-..see:Class.ModifiedString
-..see:Spec.ModReverse
-*/
-
 /*!
  * @typedef DnaStringReverseComplement
  * @headerfile <seqan/modifier.h>
@@ -258,20 +116,6 @@ namespace seqan
  * @signature typedef ModifiedString<ModifiedString<DnaString, ModView<FunctorComplement<Dna5> >, ModReverse> DnaStringReverseComplement;
  */
 
-/**
-.Shortcut.DnaStringReverseComplement:
-..cat:Modifier
-..summary:Modifier for the reverse complement of a @Shortcut.DnaString@.
-..signature:DnaStringReverseComplement
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<ModifiedString<DnaString, ModView< FunctorComplement<Dna> > >, ModReverse>
-..see:Shortcut.DnaString
-..see:Class.ModifiedString
-..see:Spec.ModReverse
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
 /*!
  * @typedef Dna5StringReverseComplement
  * @headerfile <seqan/modifier.h>
@@ -280,20 +124,6 @@ namespace seqan
  * @signature typedef ModifiedString<ModifiedString<Dna5String, ModView<FunctorComplement<Dna55> >, ModReverse> Dna5StringReverseComplement;
  */
 
-/**
-.Shortcut.Dna5StringReverseComplement:
-..cat:Modifier
-..summary:Modifier for the reverse complement of a @Shortcut.Dna5String@.
-..signature:Dna5StringReverseComplement
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<ModifiedString<Dna5String, ModView< FunctorComplement<Dna> > >, ModReverse>
-..see:Shortcut.Dna5String
-..see:Class.ModifiedString
-..see:Spec.ModReverse
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
 /*!
  * @typedef RnaStringReverseComplement
  * @headerfile <seqan/modifier.h>
@@ -302,20 +132,6 @@ namespace seqan
  * @signature typedef ModifiedString<ModifiedString<RnaString, ModView<FunctorComplement<Rna5> >, ModReverse> RnaStringReverseComplement;
  */
 
-/**
-.Shortcut.RnaStringReverseComplement:
-..cat:Modifier
-..summary:Modifier for the reverse complement of a @Shortcut.RnaString@.
-..signature:RnaStringReverseComplement
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<ModifiedString<RnaString, ModView< FunctorComplement<Rna> > >, ModReverse>
-..see:Shortcut.RnaString
-..see:Class.ModifiedString
-..see:Spec.ModReverse
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
 /*!
  * @typedef Rna5StringReverseComplement
  * @headerfile <seqan/modifier.h>
@@ -324,24 +140,10 @@ namespace seqan
  * @signature typedef ModifiedString<ModifiedString<Rna5String, ModView<FunctorComplement<Rna55> >, ModReverse> Rna5StringReverseComplement;
  */
 
-/**
-.Shortcut.Rna5StringReverseComplement:
-..cat:Modifier
-..summary:Modifier for the reverse complement of a @Shortcut.Rna5String@.
-..signature:Rna5StringReverseComplement
-..shortcutfor:Class.ModifiedString
-...signature:ModifiedString<ModifiedString<Rna5String, ModView< FunctorComplement<Rna> > >, ModReverse>
-..see:Shortcut.Rna5String
-..see:Class.ModifiedString
-..see:Spec.ModReverse
-..see:Spec.ModView
-..see:Class.FunctorComplement
-*/
-
-typedef ModView<FunctorComplement<Dna> >	ModComplementDna;
-typedef ModView<FunctorComplement<Dna5> >	ModComplementDna5;
-typedef ModView<FunctorComplement<Rna> >	ModComplementRna;
-typedef ModView<FunctorComplement<Rna5> >	ModComplementRna5;
+typedef ModView<FunctorComplement<Dna> >    ModComplementDna;
+typedef ModView<FunctorComplement<Dna5> >    ModComplementDna5;
+typedef ModView<FunctorComplement<Rna> >    ModComplementRna;
+typedef ModView<FunctorComplement<Rna5> >    ModComplementRna5;
 
 template <typename THost>
 struct ReverseString
@@ -373,10 +175,10 @@ typedef ReverseString<Dna5String>::Type             Dna5StringReverse;
 typedef ReverseString<RnaString>::Type              RnaStringReverse;
 typedef ReverseString<Rna5String>::Type             Rna5StringReverse;
 
-typedef ReverseComplementString<DnaString>::Type	DnaStringReverseComplement;
-typedef ReverseComplementString<Dna5String>::Type	Dna5StringReverseComplement;
-typedef ReverseComplementString<RnaString>::Type	RnaStringReverseComplement;
-typedef ReverseComplementString<Rna5String>::Type	Rna5StringReverseComplement;
+typedef ReverseComplementString<DnaString>::Type    DnaStringReverseComplement;
+typedef ReverseComplementString<Dna5String>::Type    Dna5StringReverseComplement;
+typedef ReverseComplementString<RnaString>::Type    RnaStringReverseComplement;
+typedef ReverseComplementString<Rna5String>::Type    Rna5StringReverseComplement;
 
 // --------------------------------------------------------------------------
 // Function complement()
@@ -386,71 +188,47 @@ typedef ReverseComplementString<Rna5String>::Type	Rna5StringReverseComplement;
  * @fn complement
  * @headerfile <seqan/modifier.h>
  * @brief Complement a sequence or a StringSet in-place.
- * 
+ *
  * @signature void complement(sequence);
  * @signature void complement(stringSet);
- * 
- * @param[in,out] stringSet The StringSet to complement.
- * @param[in,out] sequence  The SequenceConcept to complement.
  *
- * @section Remarks
+ * @param[in,out] stringSet The StringSet to complement.
+ * @param[in,out] sequence  The ContainerConcept to complement.
  *
  * Complementing only works for alphabets where a <tt>FunctorComplement&lt;T&gt;</tt> is implemented.  SeqAn comes with
  * such definitions for Dna, Dna5, Rna, Rna5.
  */
 
-/**
-.Function.complement
-..cat:Modifier
-..summary:Complement a sequence or a @Class.StringSet@ in-place.
-..signature:complement(sequence)
-..param.sequence:The sequence to complement.
-...type:Class.String
-...type:Class.Segment
-..include:seqan/modifier.h
-..see:Function.reverseComplement
-..see:Function.toLower
-..see:Function.toUpper
-*/
-
 template <typename TSequence >
-inline void complement(TSequence & sequence) 
+inline void complement(TSequence & sequence)
 {
-	convert(sequence, FunctorComplement<typename Value<TSequence>::Type>());
-} 
+    convert(sequence, FunctorComplement<typename Value<TSequence>::Type>());
+}
 
 template <typename TSequence >
-inline void complement(TSequence const & sequence) 
+inline void complement(TSequence const & sequence)
 {
-	convert(sequence, FunctorComplement<typename Value<TSequence>::Type>());
-} 
+    convert(sequence, FunctorComplement<typename Value<TSequence>::Type>());
+}
 
 // --------------------------------------------------------------------------
 // Function complement()
 // --------------------------------------------------------------------------
 
-/**
-.Function.complement
-..signature:complement(stringSet)
-..param.stringSet:The @Class.StringSet@ to complement.
-...type:Class.StringSet
-..include:seqan/modifier.h
-*/
-
 template < typename TSequence, typename TSpec >
 inline void complement(StringSet<TSequence, TSpec> & stringSet)
 {
-	unsigned seqCount = length(stringSet);
-	for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
-		complement(stringSet[seqNo]);
+    unsigned seqCount = length(stringSet);
+    for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
+        complement(stringSet[seqNo]);
 }
 
 template < typename TSequence, typename TSpec >
 inline void complement(StringSet<TSequence, TSpec> const & stringSet)
 {
-	unsigned seqCount = length(stringSet);
-	for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
-		complement(stringSet[seqNo]);
+    unsigned seqCount = length(stringSet);
+    for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
+        complement(stringSet[seqNo]);
 }
 
 // --------------------------------------------------------------------------
@@ -461,14 +239,14 @@ template <typename THost>
 inline ModifiedString<THost, ModView<FunctorComplement<typename Value<THost>::Type> > >
 complementString(THost & host)
 {
-	return ModifiedString<THost, ModView<FunctorComplement<typename Value<THost>::Type> > >(host);
+    return ModifiedString<THost, ModView<FunctorComplement<typename Value<THost>::Type> > >(host);
 }
 
 template <typename THost>
 inline ModifiedString<THost const, ModView<FunctorComplement<typename Value<THost>::Type> > >
 complementString(THost const & host)
 {
-	return ModifiedString<THost const, ModView<FunctorComplement<typename Value<THost>::Type> > >(host);
+    return ModifiedString<THost const, ModView<FunctorComplement<typename Value<THost>::Type> > >(host);
 }
 
 // --------------------------------------------------------------------------
@@ -479,14 +257,12 @@ complementString(THost const & host)
  * @fn reverseComplement
  * @headerfile <seqan/modifier.h>
  * @brief Reverse-complement a sequence or a StringSet in-place.
- * 
+ *
  * @signature void reverseComplement(sequence);
  * @signature void reverseComplement(stringSet);
- * 
- * @param[in,out] stringSet The StringSet to complement.
- * @param[in,out] sequence  The SequenceConcept to complement.
  *
- * @section Remarks
+ * @param[in,out] stringSet The StringSet to complement.
+ * @param[in,out] sequence  The ContainerConcept to complement.
  *
  * StringSet objects are reverse-complemented element-wise, i.e. the order of the sequences stays the same but the
  * sequences in the StringSet themselves are reverse-complemented.
@@ -496,49 +272,29 @@ complementString(THost const & host)
  */
 
 
-/**
-.Function.reverseComplement:
-..cat:Modifier
-..summary:Reverse and complement a sequence or a @Class.StringSet@ in-place.
-..signature:reverseComplement(sequence)
-..param.sequence:The sequence to complement.
-...type:Class.String
-...type:Class.Segment
-..include:seqan/modifier.h
-..see:Function.complement
-..see:Function.toLower
-..see:Function.toUpper
- */
 template < typename TSequence, typename TParallelTag >
 inline void reverseComplement(TSequence & sequence, Tag<TParallelTag> parallelTag)
 {
-	complement(sequence);
-	reverse(sequence, parallelTag);
-} 
+    complement(sequence);
+    reverse(sequence, parallelTag);
+}
 
 // TODO(holtgrew): How is doing anything in-place on a const value possible?
 // (weese:) it is possible for rvalue references like temporary Segments/ModifiedStrings
 template < typename TSequence, typename TParallelTag >
 inline void reverseComplement(TSequence const & sequence, Tag<TParallelTag> parallelTag)
 {
-	complement(sequence);
-	reverse(sequence, parallelTag);
-} 
-
-/**
-.Function.reverseComplement:
-..signature:reverseComplement(stringSet)
-..param.stringSet:The @Class.StringSet@ to complement.
-...type:Class.StringSet
-..include:seqan/modifier.h
- */
+    complement(sequence);
+    reverse(sequence, parallelTag);
+}
+
 template < typename TSequence, typename TSpec, typename TParallelTag >
 inline void reverseComplement(StringSet<TSequence, TSpec> & stringSet, Tag<TParallelTag>)
 {
-	int seqCount = length(stringSet);
+    int seqCount = length(stringSet);
     SEQAN_OMP_PRAGMA(parallel for if(IsSameType<Tag<TParallelTag>, Parallel>::VALUE))
-	for(int seqNo = 0; seqNo < seqCount; ++seqNo)
-		reverseComplement(stringSet[seqNo], Serial());
+    for(int seqNo = 0; seqNo < seqCount; ++seqNo)
+        reverseComplement(stringSet[seqNo], Serial());
 }
 
 // TODO(holtgrew): How is doing anything in-place on a const value possible?
@@ -546,10 +302,10 @@ inline void reverseComplement(StringSet<TSequence, TSpec> & stringSet, Tag<TPara
 template < typename TSequence, typename TSpec, typename TParallelTag >
 inline void reverseComplement(StringSet<TSequence, TSpec> const & stringSet, Tag<TParallelTag>)
 {
-	int seqCount = length(stringSet);
+    int seqCount = length(stringSet);
     SEQAN_OMP_PRAGMA(parallel for if(IsSameType<Tag<TParallelTag>, Parallel>::VALUE))
-	for(int seqNo = 0; seqNo < seqCount; ++seqNo)
-		reverseComplement(stringSet[seqNo], Serial());
+    for(int seqNo = 0; seqNo < seqCount; ++seqNo)
+        reverseComplement(stringSet[seqNo], Serial());
 }
 
 template <typename TText>
@@ -573,7 +329,7 @@ inline typename ReverseComplementString<THost>::Type
 reverseComplementString(THost & host)
 {
     typedef typename ReverseComplementString<THost>::Type TRevComp;
-	return TRevComp(host);
+    return TRevComp(host);
 }
 
 template <typename THost>
@@ -581,7 +337,7 @@ inline typename ReverseComplementString<THost const>::Type
 reverseComplementString(THost const & host)
 {
     typedef typename ReverseComplementString<THost const>::Type TRevComp;
-	return TRevComp(host);
+    return TRevComp(host);
 }
 
 // --------------------------------------------------------------------------
@@ -596,51 +352,30 @@ reverseComplementString(THost const & host)
  * @signature void toLower(sequence);
  * @signature void toLower(stringSet);
  *
- * @param[in,out] sequence  The SequenceConcept to convert to lower-case.
+ * @param[in,out] sequence  The ContainerConcept to convert to lower-case.
  * @param[in,out] stringSet The StringSet to convert to lower-case.
  */
 
-/**
-.Function.toLower:
-..cat:Modifier
-..summary:Convert characters in sequence or @Class.StringSet@ to lower case in-place.
-..signature:toLower(sequence)
-..param.sequence:The sequence to convert into lowercase.
-...type:Class.String
-...type:Class.Segment
-..include:seqan/modifier.h
-..see:Function.toUpper
-..see:Function.reverseComplement
-..see:Function.complement
- */
-
 template < typename TSequence >
-inline void toLower(TSequence & sequence) 
+inline void toLower(TSequence & sequence)
 {
-	convert(sequence, FunctorLowcase<typename Value<TSequence>::Type>());
-} 
+    convert(sequence, FunctorLowcase<typename Value<TSequence>::Type>());
+}
 
 // TODO(holtgrew): How is doing anything in-place on a const value possible?
 // (weese:) it is possible for rvalue references like temporary Segments/ModifiedStrings
 template < typename TSequence >
-inline void toLower(TSequence const & sequence) 
+inline void toLower(TSequence const & sequence)
 {
-	convert(sequence, FunctorLowcase<typename Value<TSequence>::Type>());
-} 
-
-/**
-.Function.toLower:
-..signature:toLower(stringSet)
-..param.stringSet:The @Class.StringSet@ to convert into lowercase.
-...type:Class.StringSet
-..include:seqan/modifier.h
- */	
+    convert(sequence, FunctorLowcase<typename Value<TSequence>::Type>());
+}
+
 template < typename TSequence, typename TSpec >
 inline void toLower(StringSet<TSequence, TSpec> & stringSet)
 {
-	unsigned seqCount = length(stringSet);
-	for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
-		toLower(stringSet[seqNo]);
+    unsigned seqCount = length(stringSet);
+    for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
+        toLower(stringSet[seqNo]);
 }
 
 // TODO(holtgrew): How is doing anything in-place on a const value possible?
@@ -648,9 +383,9 @@ inline void toLower(StringSet<TSequence, TSpec> & stringSet)
 template < typename TSequence, typename TSpec >
 inline void toLower(StringSet<TSequence, TSpec> const & stringSet)
 {
-	unsigned seqCount = length(stringSet);
-	for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
-		toLower(stringSet[seqNo]);
+    unsigned seqCount = length(stringSet);
+    for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
+        toLower(stringSet[seqNo]);
 }
 
 // --------------------------------------------------------------------------
@@ -665,50 +400,30 @@ inline void toLower(StringSet<TSequence, TSpec> const & stringSet)
  * @signature void toUpper(sequence);
  * @signature void toUpper(stringSet);
  *
- * @param[in,out] sequence  The SequenceConcept to convert to upper-case.
+ * @param[in,out] sequence  The ContainerConcept to convert to upper-case.
  * @param[in,out] stringSet The StringSet to convert to upper-case.
  */
 
-/**
-.Function.toUpper:
-..cat:Modifier
-..summary:Convert characters in sequence or @Class.StringSet@ to lower case in-place.
-..signature:toUpper(sequence)
-..param.sequence:The sequence to convert into uppercase.
-...type:Class.String
-...type:Class.Segment
-..include:seqan/modifier.h
-..see:Function.toLower
-..see:Function.reverseComplement
-..see:Function.complement
- */
 template < typename TSequence >
-inline void toUpper(TSequence & sequence) 
+inline void toUpper(TSequence & sequence)
 {
-	convert(sequence, FunctorUpcase<typename Value<TSequence>::Type>());
-} 
+    convert(sequence, FunctorUpcase<typename Value<TSequence>::Type>());
+}
 
 // TODO(holtgrew): How is doing anything in-place on a const value possible?
 // (weese:) it is possible for rvalue references like temporary Segments/ModifiedStrings
 template < typename TSequence >
-inline void toUpper(TSequence const & sequence) 
+inline void toUpper(TSequence const & sequence)
 {
-	convert(sequence, FunctorUpcase<typename Value<TSequence>::Type>());
-} 
-
-/**
-.Function.toUpper:
-..signature:toUpper(stringSet)
-..param.stringSet:The @Class.StringSet@ to convert into uppercase.
-...type:Class.StringSet
-..include:seqan/modifier.h
- */	
+    convert(sequence, FunctorUpcase<typename Value<TSequence>::Type>());
+}
+
 template < typename TSequence, typename TSpec >
 inline void toUpper(StringSet<TSequence, TSpec> & stringSet)
 {
-	unsigned seqCount = length(stringSet);
-	for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
-		toUpper(stringSet[seqNo]);
+    unsigned seqCount = length(stringSet);
+    for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
+        toUpper(stringSet[seqNo]);
 }
 
 // TODO(holtgrew): How is doing anything in-place on a const value possible?
@@ -717,9 +432,31 @@ template < typename TSequence, typename TSpec >
 inline void toUpper(StringSet<TSequence, TSpec> const & stringSet)
 {
 
-	unsigned seqCount = length(stringSet);
-	for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
-		toUpper(stringSet[seqNo]);
+    unsigned seqCount = length(stringSet);
+    for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo)
+        toUpper(stringSet[seqNo]);
+}
+
+// --------------------------------------------------------------------------
+// Function lowerString()
+// --------------------------------------------------------------------------
+
+template <typename THost>
+inline ModifiedString<THost const, ModView<FunctorLowcase<typename Value<THost>::Type> > >
+lowerString(THost const & host)
+{
+    return ModifiedString<THost const, ModView<FunctorLowcase<typename Value<THost>::Type> > >(host);
+}
+
+// --------------------------------------------------------------------------
+// Function upperString()
+// --------------------------------------------------------------------------
+
+template <typename THost>
+inline ModifiedString<THost const, ModView<FunctorUpcase<typename Value<THost>::Type> > >
+upperString(THost const & host)
+{
+    return ModifiedString<THost const, ModView<FunctorUpcase<typename Value<THost>::Type> > >(host);
 }
 
 }
diff --git a/seqan/modifier/modifier_string.h b/seqan/modifier/modifier_string.h
index 4fd92ed..c84f9f9 100644
--- a/seqan/modifier/modifier_string.h
+++ b/seqan/modifier/modifier_string.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -57,7 +57,7 @@ template <typename TType, typename TTestType> struct IsAnInnerHost;
 
 /*!
  * @class ModifiedString
- * @implements SequenceConcept
+ * @implements ContainerConcept
  * @headerfile <seqan/modifier.h>
  * @brief Allows you to generate modified versions of a string in a non-inplace way.
  *
@@ -67,59 +67,35 @@ template <typename TType, typename TTestType> struct IsAnInnerHost;
  * @tparam THost The host sequence.
  * @tparam TSpec The specialization tag, defaults to <tt>void</tt>.
  *
- * @section Remarks
- *
- * THost can also be a modified string, so you can create nest modified strings to create custom combinations.
+ * <tt>THost</tt> can also be a modified string, so you can create nest modified strings to create custom combinations.
  *
  * @section Examples
  *
  * @subsection Using ModReverseString
  *
- * @include demos/modifier/modified_string.cpp
+ * @include demos/dox/modifier/modified_string.cpp
  *
  * The output is als follows:
  *
- * @include demos/modifier/modified_string.cpp.stdout
+ * @include demos/dox/modifier/modified_string.cpp.stdout
  *
  * @subsection Using a custom functor for ModViewString
  *
- * @include demos/modifier/modified_string_mod_view.cpp
+ * @include demos/dox/modifier/modified_string_mod_view.cpp
  *
  * The output is as follows:
  *
- * @include demos/modifier/modified_string_mod_view.cpp.stdout
+ * @include demos/dox/modifier/modified_string_mod_view.cpp.stdout
  *
  * @subsection Using nested modified strings.
  *
- * @include demos/modifier/modified_string_nested.cpp
+ * @include demos/dox/modifier/modified_string_nested.cpp
  *
  * The output is as follows:
  *
- * @include demos/modifier/modified_string_nested.cpp.stdout
+ * @include demos/dox/modifier/modified_string_nested.cpp.stdout
  */
 
-/**
-.Class.ModifiedString:
-..summary:Allows to modify arbitrary strings by specializing what differs from an origin.
-..cat:Modifier
-..signature:ModifiedString<THost[, TSpec]>
-..param.THost:Original sequence type.
-...type:Concept.ContainerConcept
-..param.TSpec:The modifier type.
-...metafunction:Metafunction.Spec
-..implements:Concept.ContainerConcept
-..remarks:$THost$ can also be a modified string, so you can create custom strings by combining predefined ones.
-..example.file:demos/modifier/modified_string.cpp
-..example.text:The output is as follows:
-..example.output:
-TATACGCGAAAA
-AAAAGCGCATAT
-
-TATACGCGTTTT
-TTTTGCGCATAT
-..include:seqan/modifier.h
-*/
-
 template <typename THost, typename TSpec = void>
 class ModifiedString
 {
@@ -131,12 +107,16 @@ class ModifiedString
     TCargo_ _cargo;
 
     // Default constructor.
-    ModifiedString()
+    ModifiedString() :
+        _host(),
+        _cargo()
     {}
 
     // Construct with the actual host.
     explicit
-    ModifiedString(typename Parameter_<THost>::Type host) : _host(_toPointer(host))
+    ModifiedString(typename Parameter_<THost>::Type host) :
+        _host(_toPointer(host)),
+        _cargo()
     {}
 
     // Constructor for creating a ModifiedString with const host from a non-const host.
@@ -144,7 +124,8 @@ class ModifiedString
     explicit
     ModifiedString(THost_ & host,
                    SEQAN_CTOR_ENABLE_IF(IsConstructible<THost, THost_>)) :
-            _host(_toPointer(host))
+            _host(_toPointer(host)),
+            _cargo()
     {
         ignoreUnusedVariableWarning(dummy);
     }
@@ -158,7 +139,8 @@ class ModifiedString
                    SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<
                                             typename RemoveReference<THost>::Type,
                                             typename RemoveReference<THost_>::Type >)) :
-            _host(std::forward<THost_>(host))
+            _host(std::forward<THost_>(host)),
+            _cargo()
     {
         ignoreUnusedVariableWarning(dummy);
     }
@@ -170,7 +152,8 @@ class ModifiedString
     explicit
     ModifiedString(THost_ & host,
                    SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<THost, THost_>)) :
-            _host(host)
+            _host(host),
+            _cargo()
     {
         ignoreUnusedVariableWarning(dummy);
     }
@@ -179,7 +162,8 @@ class ModifiedString
     explicit
     ModifiedString(THost_ const & host,
                    SEQAN_CTOR_ENABLE_IF(IsAnInnerHost<THost, THost_ const>)) :
-            _host(host)
+            _host(host),
+            _cargo()
     {
         ignoreUnusedVariableWarning(dummy);
     }
@@ -193,11 +177,17 @@ class ModifiedString
         return value(*this, pos);
     }
 
-    template <typename TPos> 
-    inline typename Reference<ModifiedString const>::Type  
-    operator[](TPos pos) const 
-    { 
-        return value(*this, pos); 
+    template <typename TPos>
+    inline typename Reference<ModifiedString const>::Type
+    operator[](TPos pos) const
+    {
+        return value(*this, pos);
+    }
+
+    ModifiedString & operator= (THost & other)
+    {
+        assign(*this, other);
+        return *this;
     }
 };
 
@@ -319,9 +309,6 @@ struct Reference< ModifiedString<THost, TSpec> const >:
 // Metafunction Size
 // --------------------------------------------------------------------------
 
-///.Metafunction.Size.param.T.type:Class.ModifiedString
-///.Metafunction.Size.class:Class.ModifiedString
-
 template < typename THost, typename TSpec >
 struct Size< ModifiedString<THost, TSpec> >:
     Size< typename Iterator< ModifiedString<THost, TSpec>, Rooted >::Type > {};
@@ -346,52 +333,77 @@ struct Difference< ModifiedString<THost, TSpec> >:
 // Metafunction Iterator
 // --------------------------------------------------------------------------
 
-// TODO(holtgrew): Should the result of Iterator<> be a const iterator for const ModifiedString objects?
-
-///.Metafunction.Iterator.param.T.type:Class.ModifiedString
-///.Metafunction.Iterator.class:Class.ModifiedString
-
 template <typename THost, typename TSpec>
 struct Iterator<ModifiedString<THost, TSpec>, Standard>
 {
     typedef ModifiedIterator<typename Iterator<THost, Standard>::Type, TSpec> Type;
 };
-
-template <typename THost, typename TSpec >
-struct Iterator<ModifiedString<THost, TSpec> const, Standard>
-{
-    typedef ModifiedIterator<typename Iterator<THost, Standard>::Type, TSpec> Type;
-};
-
 template <typename THost, typename TSpec>
 struct Iterator<ModifiedString<THost, TSpec>, Rooted>
 {
     typedef ModifiedIterator<typename Iterator<THost, Rooted>::Type, TSpec> Type;
 };
 
+// TODO(holtgrew): Should the result of Iterator<> be a const iterator for const ModifiedString objects?
+//          weese: I chose more lenient variant (A), i.e. constness is not propagated upwards.
+
+// VARIANT A: const ModifiedString does not propagate its constness upwards
+template <typename THost, typename TSpec >
+struct Iterator<ModifiedString<THost, TSpec> const, Standard>
+{
+    typedef ModifiedIterator<typename Iterator<THost, Standard>::Type, TSpec> Type;
+};
 template <typename THost, typename TSpec >
 struct Iterator<ModifiedString<THost, TSpec> const, Rooted>
 {
     typedef ModifiedIterator<typename Iterator<THost, Rooted>::Type, TSpec> Type;
 };
 
+// VARIANT B: const ModifiedString propagates its constness upwards
+//template <typename THost, typename TSpec >
+//struct Iterator<ModifiedString<THost, TSpec> const, Standard>
+//{
+//    typedef ModifiedIterator<typename Iterator<THost const, Standard>::Type, TSpec> Type;
+//};
+//template <typename THost, typename TSpec >
+//struct Iterator<ModifiedString<THost, TSpec> const, Rooted>
+//{
+//    typedef ModifiedIterator<typename Iterator<THost const, Rooted>::Type, TSpec> Type;
+//};
+
 // --------------------------------------------------------------------------
 // Metafunction Host
 // --------------------------------------------------------------------------
 
-///.Metafunction.Host.param.T.type:Class.ModifiedString
-///.Metafunction.Host.class:Class.ModifiedString
+template <typename T>
+struct ConvertArrayToPointer
+{
+    typedef T Type;
+};
+
+template <typename T, int SIZE>
+struct ConvertArrayToPointer<T[SIZE]>
+{
+    typedef T* Type;
+};
 
 template <typename THost, typename TSpec >
 struct Host<ModifiedString<THost, TSpec> > {
-    typedef THost Type;
+    typedef typename ConvertArrayToPointer<THost>::Type Type;
 };
 
+// VARIANT A: const ModifiedString does not propagate its constness upwards
 template <typename THost, typename TSpec >
 struct Host<ModifiedString<THost, TSpec> const > {
-    typedef THost const Type;
+    typedef typename ConvertArrayToPointer<THost>::Type Type;
 };
 
+// VARIANT B: const ModifiedString propagates its constness upwards
+//template <typename THost, typename TSpec >
+//struct Host<ModifiedString<THost, TSpec> const > {
+//    typedef typename ConvertArrayToPointer<THost const>::Type Type;
+//};
+
 // --------------------------------------------------------------------------
 // Metafunction Parameter_
 // --------------------------------------------------------------------------
@@ -427,12 +439,20 @@ struct Pointer_<ModifiedString<THost, TSpec> const > : Pointer_<ModifiedString<T
 // Metafunction IsSequence
 // --------------------------------------------------------------------------
 
-///.Metafunction.IsSequence.param.T.type:Class.ModifiedString
-
 template <typename THost, typename TSpec >
 struct IsSequence<ModifiedString<THost, TSpec> > : True
 {};
 
+// ----------------------------------------------------------------------------
+// Concept ContainerConcept
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+SEQAN_CONCEPT_IMPL((ModifiedString<THost, TSpec>), (ContainerConcept));
+
+template <typename THost, typename TSpec>
+SEQAN_CONCEPT_IMPL((ModifiedString<THost, TSpec> const), (ContainerConcept));
+
 // --------------------------------------------------------------------------
 // Metafunction AllowsFastRandomAccess
 // --------------------------------------------------------------------------
@@ -463,7 +483,7 @@ template <typename TDest, typename TSource>
 inline void _copyCargo(TDest & me, TSource & _origin)
 {
     _copyCargoImpl(me, _origin, typename IsSameType<
-                   typename RemoveConst_<typename Cargo<TDest>::Type >::Type, 
+                   typename RemoveConst_<typename Cargo<TDest>::Type >::Type,
                    typename RemoveConst_<typename Cargo<TSource>::Type>::Type >::Type());
 }
 
@@ -508,17 +528,17 @@ _toParameter(ModifiedString<THost, TSpec> const & me)
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec>
-inline THost &
+inline typename Host<ModifiedString<THost, TSpec> >::Type &
 host(ModifiedString<THost, TSpec> & me)
 {
-    return _dereference<THost &>(me._host);
+    return _referenceCast<typename Host<ModifiedString<THost, TSpec> >::Type &>(me._host);
 }
 
 template <typename THost, typename TSpec>
-inline THost &
+inline typename Host<ModifiedString<THost, TSpec> const>::Type &
 host(ModifiedString<THost, TSpec> const & me)
 {
-    return _dereference<THost &>(me._host);
+    return _referenceCast<typename Host<ModifiedString<THost, TSpec> const>::Type &>(me._host);
 }
 
 // --------------------------------------------------------------------------
@@ -543,14 +563,14 @@ inline void setHost(ModifiedString<THost, TSpec> & me, THost const & host)
 
 template <typename THost, typename TSpec>
 inline typename Reference<typename Cargo<ModifiedString<THost, TSpec> >::Type >::Type
-cargo(ModifiedString<THost, TSpec> & me) 
+cargo(ModifiedString<THost, TSpec> & me)
 {
     return me._cargo;
 }
 
 template <typename THost, typename TSpec>
 inline typename Reference<typename Cargo<ModifiedString<THost, TSpec> const>::Type >::Type
-cargo(ModifiedString<THost, TSpec> const & me) 
+cargo(ModifiedString<THost, TSpec> const & me)
 {
     return me._cargo;
 }
@@ -560,14 +580,14 @@ cargo(ModifiedString<THost, TSpec> const & me)
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec, typename TPos>
-inline typename Reference<ModifiedString<THost, TSpec> >::Type 
+inline typename Reference<ModifiedString<THost, TSpec> >::Type
 value(ModifiedString<THost, TSpec> & me, TPos pos)
 {
     return value(begin(me, Standard()) + pos);
 }
 
 template <typename THost, typename TSpec, typename TPos>
-inline typename Reference<ModifiedString<THost, TSpec> const >::Type 
+inline typename Reference<ModifiedString<THost, TSpec> const>::Type
 value(ModifiedString<THost, TSpec> const & me, TPos pos)
 {
     return value(begin(me, Standard()) + pos);
@@ -578,7 +598,7 @@ value(ModifiedString<THost, TSpec> const & me, TPos pos)
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TSpec>
-inline typename Size<ModifiedString<THost, TSpec> >::Type 
+inline typename Size<ModifiedString<THost, TSpec> >::Type
 length(ModifiedString<THost, TSpec> const & me)
 {
     return length(host(me));
@@ -589,7 +609,7 @@ length(ModifiedString<THost, TSpec> const & me)
 // --------------------------------------------------------------------------
 //
 //template <typename THost, typename TSpec>
-//inline typename Iterator<ModifiedString<THost, TSpec> const>::Type 
+//inline typename Iterator<ModifiedString<THost, TSpec> const>::Type
 //begin(ModifiedString<THost, TSpec> const & me)
 //{
 //    typedef typename Iterator<ModifiedString<THost, TSpec> const>::Type TResult;
@@ -599,7 +619,7 @@ length(ModifiedString<THost, TSpec> const & me)
 //}
 //
 //template <typename THost, typename TSpec>
-//inline typename Iterator<ModifiedString<THost, TSpec> >::Type 
+//inline typename Iterator<ModifiedString<THost, TSpec> >::Type
 //begin(ModifiedString<THost, TSpec> & me)
 //{
 //    typedef typename Iterator<ModifiedString<THost, TSpec> >::Type TResult;
@@ -609,7 +629,7 @@ length(ModifiedString<THost, TSpec> const & me)
 //}
 
 template <typename THost, typename TSpec, typename TTagSpec>
-inline typename Iterator<ModifiedString<THost, TSpec> const, Tag<TTagSpec> const>::Type 
+inline typename Iterator<ModifiedString<THost, TSpec> const, Tag<TTagSpec> const>::Type
 begin(ModifiedString<THost, TSpec> const & me, Tag<TTagSpec> const tag_)
 {
     typedef typename Iterator<ModifiedString<THost, TSpec> const, Tag<TTagSpec> const>::Type TResult;
@@ -619,7 +639,7 @@ begin(ModifiedString<THost, TSpec> const & me, Tag<TTagSpec> const tag_)
 }
 
 template <typename THost, typename TSpec, typename TTagSpec>
-inline typename Iterator<ModifiedString<THost, TSpec>, Tag<TTagSpec> const>::Type 
+inline typename Iterator<ModifiedString<THost, TSpec>, Tag<TTagSpec> const>::Type
 begin(ModifiedString<THost, TSpec> & me, Tag<TTagSpec> const tag_)
 {
     typedef typename Iterator<ModifiedString<THost, TSpec>, Tag<TTagSpec> const>::Type TResult;
@@ -633,7 +653,7 @@ begin(ModifiedString<THost, TSpec> & me, Tag<TTagSpec> const tag_)
 // --------------------------------------------------------------------------
 //
 //template < typename THost, typename TSpec >
-//inline typename Iterator< ModifiedString<THost, TSpec> const >::Type 
+//inline typename Iterator< ModifiedString<THost, TSpec> const >::Type
 //end(ModifiedString<THost, TSpec> const & me)
 //{
 //    typedef typename Iterator<ModifiedString<THost, TSpec> >::Type TResult;
@@ -643,7 +663,7 @@ begin(ModifiedString<THost, TSpec> & me, Tag<TTagSpec> const tag_)
 //}
 //
 //template < typename THost, typename TSpec >
-//inline typename Iterator< ModifiedString<THost, TSpec> >::Type 
+//inline typename Iterator< ModifiedString<THost, TSpec> >::Type
 //end(ModifiedString<THost, TSpec> & me)
 //{
 //    typedef typename Iterator<ModifiedString<THost, TSpec> const>::Type TResult;
@@ -653,7 +673,7 @@ begin(ModifiedString<THost, TSpec> & me, Tag<TTagSpec> const tag_)
 //}
 
 template < typename THost, typename TSpec, typename TTagSpec >
-inline typename Iterator< ModifiedString<THost, TSpec> const, Tag<TTagSpec> const >::Type 
+inline typename Iterator< ModifiedString<THost, TSpec> const, Tag<TTagSpec> const >::Type
 end(ModifiedString<THost, TSpec> const & me, Tag<TTagSpec> const tag_)
 {
     typedef typename Iterator<ModifiedString<THost, TSpec> const, Tag<TTagSpec> const>::Type TResult;
@@ -663,7 +683,7 @@ end(ModifiedString<THost, TSpec> const & me, Tag<TTagSpec> const tag_)
 }
 
 template < typename THost, typename TSpec, typename TTagSpec >
-inline typename Iterator< ModifiedString<THost, TSpec>, Tag<TTagSpec> const >::Type 
+inline typename Iterator< ModifiedString<THost, TSpec>, Tag<TTagSpec> const >::Type
 end(ModifiedString<THost, TSpec> & me, Tag<TTagSpec> const tag_)
 {
     typedef typename Iterator<ModifiedString<THost, TSpec>, Tag<TTagSpec> const>::Type TResult;
@@ -678,10 +698,10 @@ end(ModifiedString<THost, TSpec> & me, Tag<TTagSpec> const tag_)
 
 template <typename THost, typename TSpec, typename TRight >
 inline bool
-operator==(ModifiedString<THost, TSpec> const & left, 
+operator==(ModifiedString<THost, TSpec> const & left,
            TRight const & right)
 {
-	typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
+    typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
     return isEqual(_lex);
 }
 
@@ -690,7 +710,7 @@ inline bool
 operator==(TLeftValue * left,
            ModifiedString<THost, TSpec> const & right)
 {
-	typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
+    typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
     return isEqual(_lex);
 }
 
@@ -700,10 +720,10 @@ operator==(TLeftValue * left,
 
 template <typename THost, typename TSpec, typename TRight >
 inline bool
-operator!=(ModifiedString<THost, TSpec> const & left, 
+operator!=(ModifiedString<THost, TSpec> const & left,
            TRight const & right)
 {
-	typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
+    typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
     return isNotEqual(_lex);
 }
 
@@ -712,7 +732,7 @@ inline bool
 operator!= (TLeftValue * left,
             ModifiedString<THost, TSpec> const & right)
 {
-	typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
+    typename Comparator<ModifiedString<THost, TSpec> >::Type _lex(left, right);
     return isNotEqual(_lex);
 }
 
@@ -722,10 +742,10 @@ operator!= (TLeftValue * left,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator<(ModifiedString<THost, TSpec> const & left, 
+operator<(ModifiedString<THost, TSpec> const & left,
           TRight const & right)
 {
-	return isLess(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
+    return isLess(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
 }
 
 template <typename TLeftValue, typename THost, typename TSpec >
@@ -733,7 +753,7 @@ inline bool
 operator<(TLeftValue * left,
           ModifiedString<THost, TSpec> const & right)
 {
-	return isLess(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+    return isLess(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -742,10 +762,10 @@ operator<(TLeftValue * left,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator<=(ModifiedString<THost, TSpec> const & left, 
+operator<=(ModifiedString<THost, TSpec> const & left,
            TRight const & right)
 {
-	return isLessOrEqual(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
+    return isLessOrEqual(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
 }
 
 template <typename TLeftValue, typename THost, typename TSpec >
@@ -753,7 +773,7 @@ inline bool
 operator<=(TLeftValue * left,
            ModifiedString<THost, TSpec> const & right)
 {
-	return isLessOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+    return isLessOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -762,10 +782,10 @@ operator<=(TLeftValue * left,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator>(ModifiedString<THost, TSpec> const & left, 
+operator>(ModifiedString<THost, TSpec> const & left,
           TRight const & right)
 {
-	return isGreater(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
+    return isGreater(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
 }
 
 template <typename TLeftValue, typename THost, typename TSpec >
@@ -773,7 +793,7 @@ inline bool
 operator>(TLeftValue * left,
           ModifiedString<THost, TSpec> const & right)
 {
-	return isGreater(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+    return isGreater(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -782,10 +802,10 @@ operator>(TLeftValue * left,
 
 template <typename THost, typename TSpec, typename TRight>
 inline bool
-operator>=(ModifiedString<THost, TSpec> const & left, 
+operator>=(ModifiedString<THost, TSpec> const & left,
            TRight const & right)
 {
-	return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
+    return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<ModifiedString<THost, TSpec> >::Type());
 }
 
 template <typename TLeftValue, typename THost, typename TSpec >
@@ -793,7 +813,7 @@ inline bool
 operator>=(TLeftValue * left,
            ModifiedString<THost, TSpec> const & right)
 {
-	return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
+    return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -804,7 +824,8 @@ template < typename TStream, typename THost, typename TSpec >
 inline TStream &
 operator<<(TStream & target, ModifiedString<THost, TSpec> const & source)
 {
-    write(target, source);
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
     return target;
 }
 
@@ -816,7 +837,8 @@ template < typename TStream, typename THost, typename TSpec >
 inline TStream &
 operator>>(TStream & source, ModifiedString<THost, TSpec> & target)
 {
-    read(source, target);
+    typename DirectionIterator<TStream, Input>::Type it = directionIterator(source, Input());;
+    read(it, target);
     return source;
 }
 
@@ -826,18 +848,69 @@ operator>>(TStream & source, ModifiedString<THost, TSpec> & target)
 
 template <typename THost, typename TSpec>
 inline void const *
-getObjectId(ModifiedString<THost, TSpec> & me) 
+getObjectId(ModifiedString<THost, TSpec> & me)
 {
     return getObjectId(host(me));
 }
 
 template <typename THost, typename TSpec>
 inline void const *
-getObjectId(ModifiedString<THost, TSpec> const & me) 
+getObjectId(ModifiedString<THost, TSpec> const & me)
 {
     return getObjectId(host(me));
 }
 
+// ----------------------------------------------------------------------------
+// Function assign()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TOtherHost, typename TOtherSpec>
+inline void assign(ModifiedString<THost, TSpec> & me, ModifiedString<TOtherHost, TOtherSpec> const & other)
+{
+    setHost(me, host(other));
+    assign(cargo(me), cargo(other));
+}
+
+// --------------------------------------------------------------------------
+// Function open()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec >
+inline bool
+open(ModifiedString<THost, TSpec> &, const char *, int)
+{
+    return true; // NOOP; this has to be done manually right now
+}
+
+template <typename THost, typename TSpec, typename TSpec2>
+inline bool
+open(StringSet<ModifiedString<THost, TSpec>, Owner<ConcatDirect<TSpec2> > > &,
+     const char *,
+     int)
+{
+    return true; // NOOP; this has to be done manually right now
+}
+
+// --------------------------------------------------------------------------
+// Function save()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec >
+inline bool
+save(ModifiedString<THost, TSpec> const &, const char *, int)
+{
+    return true; // NOOP; this has to be done manually right now
+}
+
+template <typename THost, typename TSpec, typename TSpec2>
+inline bool
+save(StringSet<ModifiedString<THost, TSpec>, Owner<ConcatDirect<TSpec2> > > const &,
+     const char *,
+     int)
+{
+    return true; // NOOP; this has to be done manually right now
+}
+
 }  // namespace seqan
 
 #endif  // SEQAN_MODIFIER_MODIFIER_STRING_H_
diff --git a/seqan/modifier/modifier_view.h b/seqan/modifier/modifier_view.h
index 4892b0c..96db20c 100644
--- a/seqan/modifier/modifier_view.h
+++ b/seqan/modifier/modifier_view.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -82,29 +82,16 @@ namespace seqan
  * @tparam TFunctor A unary functor type.
  */
 
-/**
-.Spec.ModView:
-..summary:Transforms the characters of the $THost$ string/iterator using a custom function.
-..cat:Modifier
-..general:Class.ModifiedIterator
-..general:Class.ModifiedString
-..signature:ModifiedIterator<THost, ModView<TFunctor> >
-..signature:ModifiedString<THost, ModView<TFunctor> >
-..param.THost:Original string/iterator.
-...type:Concept.RandomAccessIteratorConcept
-..param.TFunctor:A unary function (see STL's $unary_function$).
-...remarks:The argument type of $TFunctor$ must be $VALUE<THost>::Type$.
-..remarks:The @Metafunction.Value@ type of this modifier is the result type of $TFunctor$.
-..include:seqan/modifier.h
-*/
-
 template <typename TFunctor>
 struct ModView {};
 
 template <typename TFunctor>
 struct ModViewCargo
 {
-    TFunctor	func;
+    TFunctor    func;
+
+    ModViewCargo() : func()
+    {}
 };
 
 template <typename THost, typename TFunctor>
@@ -118,17 +105,16 @@ class ModifiedIterator<THost, ModView<TFunctor> >
 
     mutable typename Value<ModifiedIterator>::Type tmp_value;
 
-    ModifiedIterator():
-        tmp_value()
+    ModifiedIterator() : _host(), tmp_value()
     {}
 
     template <typename TOtherHost>
-    ModifiedIterator(ModifiedIterator<TOtherHost, ModView<TFunctor> > & origin):
+    ModifiedIterator(ModifiedIterator<TOtherHost, ModView<TFunctor> > & origin) :
         _host(origin._host), _cargo(origin._cargo), tmp_value()
     {}
 
     explicit
-    ModifiedIterator(THost const & host):
+    ModifiedIterator(THost const & host) :
         _host(host), tmp_value()
     {}
 
@@ -156,8 +142,7 @@ class ModifiedString<THost, ModView<TFunctor> >
     mutable typename Value<ModifiedString>::Type tmp_value;
 
     // Default constructor.
-    ModifiedString():
-        tmp_value()
+    ModifiedString() : _host(), tmp_value()
     {}
 
     // Construct with the actual host.
@@ -169,7 +154,7 @@ class ModifiedString<THost, ModView<TFunctor> >
     // Construct with the functor.
     explicit
     ModifiedString(TFunctor const & functor):
-        tmp_value()
+        _host(), tmp_value()
     {
         cargo(*this).func = functor;
     }
@@ -252,7 +237,7 @@ class ModifiedString<THost, ModView<TFunctor> >
     {
         ignoreUnusedVariableWarning(dummy);
     }
-    
+
     // Constructor for innermost type; hand down to _host which is a ModifiedString itself.  Non-const variant with
     // functor.
     template <typename THost_>
@@ -278,18 +263,18 @@ class ModifiedString<THost, ModView<TFunctor> >
         ignoreUnusedVariableWarning(dummy);
         cargo(*this).func = functor;
     }
-    
+
 #endif
 
     template <typename TPos>
-    inline typename Reference<ModifiedString>::Type 
+    inline typename Reference<ModifiedString>::Type
     operator[](TPos pos)
     {
         return value(*this, pos);
     }
 
     template <typename TPos>
-    inline typename Reference<ModifiedString const>::Type 
+    inline typename Reference<ModifiedString const>::Type
     operator[](TPos pos) const
     {
         return value(*this, pos);
@@ -307,7 +292,7 @@ class ModifiedString<THost, ModView<TFunctor> >
 template <typename THost, typename TFunctor>
 struct Cargo<ModifiedIterator<THost, ModView<TFunctor> > >
 {
-    typedef ModViewCargo<TFunctor>	Type;
+    typedef ModViewCargo<TFunctor>    Type;
 };
 
 // --------------------------------------------------------------------------
@@ -317,16 +302,27 @@ struct Cargo<ModifiedIterator<THost, ModView<TFunctor> > >
 template <typename THost, typename TFunctor>
 struct Value<ModifiedIterator<THost, ModView<TFunctor> > >
 {
-    typedef typename TFunctor::result_type			TResult_;
+    typedef typename TFunctor::result_type            TResult_;
     typedef typename RemoveConst_<TResult_>::Type   Type;
 };
 
+template <typename THost, typename TFunctor>
+struct Value<ModifiedIterator<THost, ModView<TFunctor> > const> :
+    Value<ModifiedIterator<THost, ModView<TFunctor> > >
+{};
+
 // --------------------------------------------------------------------------
 // Metafunction GetValue                                   [ModifiedIterator]
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TFunctor>
-struct GetValue<ModifiedIterator<THost, ModView<TFunctor> > > : Value<ModifiedIterator<THost, ModView<TFunctor> > >
+struct GetValue<ModifiedIterator<THost, ModView<TFunctor> > > :
+    Value<ModifiedIterator<THost, ModView<TFunctor> > >
+{};
+
+template <typename THost, typename TFunctor>
+struct GetValue<ModifiedIterator<THost, ModView<TFunctor> > const> :
+    Value<ModifiedIterator<THost, ModView<TFunctor> > >
 {};
 
 // --------------------------------------------------------------------------
@@ -334,10 +330,26 @@ struct GetValue<ModifiedIterator<THost, ModView<TFunctor> > > : Value<ModifiedIt
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TFunctor>
-struct Reference<ModifiedIterator<THost, ModView<TFunctor> > >
-{
-    typedef typename Value<ModifiedIterator<THost, ModView<TFunctor> > >::Type & Type;
-};
+struct Reference<ModifiedIterator<THost, ModView<TFunctor> > > :
+    Value<ModifiedIterator<THost, ModView<TFunctor> > >
+{};
+
+template <typename THost, typename TFunctor>
+struct Reference<ModifiedIterator<THost, ModView<TFunctor> > const> :
+    Value<ModifiedIterator<THost, ModView<TFunctor> > >
+{};
+
+// NOTE(h-2): ModView element access is always by copy never by reference
+// This is a workaround for dangling references to the stack when
+// combining infixes and modified views, more precisely:
+//  if you iterate over an infix of a modview then value() on the iterator
+//  will return reference to the tmp_value inside the moditerator
+//  which might have been destructed.
+// This is a more general problem that stems from the fact that
+// "virtual strings" of the same type (infixes, modstrings) can be
+// automatically compacted into one layer, but combinations cannot.
+// This workaround happens in ModView, because it is used less frequently
+// then Infixes.
 
 // --------------------------------------------------------------------------
 // Metafunction Cargo                                        [ModifiedString]
@@ -346,7 +358,7 @@ struct Reference<ModifiedIterator<THost, ModView<TFunctor> > >
 template <typename THost, typename TFunctor>
 struct Cargo< ModifiedString<THost, ModView<TFunctor> > >
 {
-    typedef ModViewCargo<TFunctor>	Type;
+    typedef ModViewCargo<TFunctor>    Type;
 };
 
 // ==========================================================================
@@ -354,79 +366,75 @@ struct Cargo< ModifiedString<THost, ModView<TFunctor> > >
 // ==========================================================================
 
 // --------------------------------------------------------------------------
-// Function value()                                        [ModifiedIterator]
+// Function getValue()                                     [ModifiedIterator]
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TFunctor>
-inline typename Reference<ModifiedIterator<THost, ModView<TFunctor> > >::Type 
-value(ModifiedIterator<THost, ModView<TFunctor> > & me)
+inline typename GetValue<ModifiedIterator<THost, ModView<TFunctor> > >::Type
+getValue(ModifiedIterator<THost, ModView<TFunctor> > & me)
 {
-    me.tmp_value = cargo(me).func(getValue(host(me)));
-    return me.tmp_value;
+    return cargo(me).func(getValue(host(me)));
 }
 
 template <typename THost, typename TFunctor>
-inline typename Reference<ModifiedIterator<THost, ModView<TFunctor> > const>::Type 
-value(ModifiedIterator<THost, ModView<TFunctor> > const & me)
+inline typename GetValue<ModifiedIterator<THost, ModView<TFunctor> > const>::Type
+getValue(ModifiedIterator<THost, ModView<TFunctor> > const & me)
 {
-    me.tmp_value = cargo(me).func(getValue(host(me)));
-    return me.tmp_value;
+    return cargo(me).func(getValue(host(me)));
 }
 
 // --------------------------------------------------------------------------
-// Function getValue()                                     [ModifiedIterator]
+// Function value()                                        [ModifiedIterator]
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TFunctor>
-inline typename GetValue<ModifiedIterator<THost, ModView<TFunctor> > >::Type 
-getValue(ModifiedIterator<THost, ModView<TFunctor> > & me)
+inline typename GetValue<ModifiedIterator<THost, ModView<TFunctor> > >::Type
+value(ModifiedIterator<THost, ModView<TFunctor> > & me)
 {
-    return cargo(me).func(getValue(host(me)));
+    return getValue(me);
 }
 
 template <typename THost, typename TFunctor>
-inline typename GetValue<ModifiedIterator<THost, ModView<TFunctor> > const>::Type 
-getValue(ModifiedIterator<THost, ModView<TFunctor> > const & me)
+inline typename GetValue<ModifiedIterator<THost, ModView<TFunctor> > const>::Type
+value(ModifiedIterator<THost, ModView<TFunctor> > const & me)
 {
-    return cargo(me).func(getValue(host(me)));
+    return getValue(me);
 }
 
 // --------------------------------------------------------------------------
-// Function value()                                          [ModifiedString]
+// Function getValue()                                       [ModifiedString]
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TFunctor, typename TPos>
-inline typename Reference<ModifiedString<THost, ModView<TFunctor> > >::Type 
-value(ModifiedString<THost, ModView<TFunctor> > & me, TPos pos)
+inline typename GetValue<ModifiedString<THost, ModView<TFunctor> > >::Type
+getValue(ModifiedString<THost, ModView<TFunctor> > & me, TPos pos)
 {
-    me.tmp_value = cargo(me).func(getValue(host(me), pos));
-    return me.tmp_value;
+    return cargo(me).func(getValue(host(me), pos));
 }
 
 template <typename THost, typename TFunctor, typename TPos>
-inline typename Reference<ModifiedString<THost, ModView<TFunctor> > const>::Type 
-value(ModifiedString<THost, ModView<TFunctor> > const & me, TPos pos)
+inline typename GetValue<ModifiedString<THost, ModView<TFunctor> > const>::Type
+getValue(ModifiedString<THost, ModView<TFunctor> > const & me, TPos pos)
 {
-    me.tmp_value = cargo(me).func(getValue(host(me), pos));
-    return me.tmp_value;
+    return cargo(me).func(getValue(host(me), pos));
 }
 
 // --------------------------------------------------------------------------
-// Function getValue()                                       [ModifiedString]
+// Function value()                                          [ModifiedString]
 // --------------------------------------------------------------------------
 
 template <typename THost, typename TFunctor, typename TPos>
-inline typename GetValue<ModifiedString<THost, ModView<TFunctor> > >::Type 
-getValue(ModifiedString<THost, ModView<TFunctor> > & me, TPos pos)
+inline typename GetValue<ModifiedString<THost, ModView<TFunctor> > >::Type
+value(ModifiedString<THost, ModView<TFunctor> > & me, TPos pos)
 {
-    return cargo(me).func(getValue(host(me), pos));
+    return getValue(me, pos);
 }
 
 template <typename THost, typename TFunctor, typename TPos>
-inline typename GetValue<ModifiedString<THost, ModView<TFunctor> > const>::Type 
-getValue(ModifiedString<THost, ModView<TFunctor> > const & me, TPos pos)
+inline typename GetValue<ModifiedString<THost, ModView<TFunctor> > const>::Type
+value(ModifiedString<THost, ModView<TFunctor> > const & me, TPos pos)
 {
-    return cargo(me).func(getValue(host(me), pos));
+    return getValue(me, pos);
 }
 
 // --------------------------------------------------------------------------
@@ -449,21 +457,21 @@ inline void
 convert(TSequence & sequence, TFunctor const &F)
 {
 #if defined (_OPENMP) && defined (SEQAN_PARALLEL)
-	// OpenMP does not support for loop with iterators. Therefore use index variables.
-	typedef typename Position<TSequence>::Type	TPos;
-	typedef typename MakeSigned_<TPos>::Type	TSignedPos;
-
-	#pragma omp parallel for if(length(sequence) > 1000000)
-	for(TSignedPos p = 0; p < (TSignedPos)length(sequence); ++p)
-		sequence[p] = F(sequence[p]);
-	
+    // OpenMP does not support for loop with iterators. Therefore use index variables.
+    typedef typename Position<TSequence>::Type    TPos;
+    typedef typename MakeSigned_<TPos>::Type    TSignedPos;
+
+    #pragma omp parallel for if(length(sequence) > 1000000)
+    for(TSignedPos p = 0; p < (TSignedPos)length(sequence); ++p)
+        sequence[p] = F(sequence[p]);
+
 #else
-	typedef typename Iterator<TSequence, Standard>::Type	TIter;
+    typedef typename Iterator<TSequence, Standard>::Type    TIter;
 
-	TIter it = begin(sequence, Standard());
-	TIter itEnd = end(sequence, Standard());
-	for(; it != itEnd; ++it)
-		*it = F(*it);
+    TIter it = begin(sequence, Standard());
+    TIter itEnd = end(sequence, Standard());
+    for(; it != itEnd; ++it)
+        *it = F(*it);
 #endif
 }
 
@@ -472,21 +480,21 @@ inline void
 convert(TSequence const & sequence, TFunctor const &F)
 {
 #if defined (_OPENMP) && defined (SEQAN_PARALLEL)
-	// OpenMP does not support for loop with iterators. Therefore use index variables.
-	typedef typename Position<TSequence>::Type	TPos;
-	typedef typename MakeSigned_<TPos>::Type	TSignedPos;
-
-	#pragma omp parallel for if(length(sequence) > 1000000)
-	for(TSignedPos p = 0; p < (TSignedPos)length(sequence); ++p)
-		sequence[p] = F(sequence[p]);
-	
+    // OpenMP does not support for loop with iterators. Therefore use index variables.
+    typedef typename Position<TSequence>::Type    TPos;
+    typedef typename MakeSigned_<TPos>::Type    TSignedPos;
+
+    #pragma omp parallel for if(length(sequence) > 1000000)
+    for(TSignedPos p = 0; p < (TSignedPos)length(sequence); ++p)
+        sequence[p] = F(sequence[p]);
+
 #else
-	typedef typename Iterator<TSequence const, Standard>::Type	TIter;
+    typedef typename Iterator<TSequence const, Standard>::Type    TIter;
 
-	TIter it = begin(sequence, Standard());
-	TIter itEnd = end(sequence, Standard());
-	for(; it != itEnd; ++it)
-		*it = F(*it);
+    TIter it = begin(sequence, Standard());
+    TIter itEnd = end(sequence, Standard());
+    for(; it != itEnd; ++it)
+        *it = F(*it);
 #endif
 }
 
diff --git a/seqan/parallel.h b/seqan/parallel.h
old mode 100755
new mode 100644
index 74ca5f7..882f9f4
--- a/seqan/parallel.h
+++ b/seqan/parallel.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,15 +37,45 @@
 #ifndef SEQAN_PARALLEL_H_
 #define SEQAN_PARALLEL_H_
 
-//____________________________________________________________________________
+// ============================================================================
 // Prerequisites
+// ============================================================================
 
 #include <seqan/platform.h>
 #include <seqan/basic.h>
 #include <seqan/sequence.h>
 
-//____________________________________________________________________________
+#ifdef PLATFORM_WINDOWS
+#include <windows.h>
+#else
+#include <pthread.h>
+#include <errno.h>
+#endif
+
+#include <seqan/system/system_critical_section.h>   // Suspendable Queue
+#include <seqan/system/system_condition.h>          // Suspendable Queue
+
+// ----------------------------------------------------------------------------
+// STL
+// ----------------------------------------------------------------------------
+// Use MCSTL which is part of the GCC since version 4.3
+
+#if defined(_OPENMP) && defined(PLATFORM_GCC) && __GNUC__ >= 4 && __GNUC_MINOR__ >= 3
+#include <parallel/algorithm>
+#include <parallel/numeric>
+#else
+#include <algorithm>
+#include <numeric>
+#endif // PLATFORM_GCC
+
+#ifdef SEQAN_CXX11_STL
+#include <atomic>
+#include <thread>
+#endif
+
+// ============================================================================
 // Module Headers
+// ============================================================================
 
 // Misc.
 #include <seqan/parallel/parallel_tags.h>
@@ -54,6 +84,7 @@
 // Atomic operations.
 #include <seqan/parallel/parallel_atomic_primitives.h>
 #include <seqan/parallel/parallel_atomic_misc.h>
+#include <seqan/parallel/parallel_lock.h>
 
 // Splitting.
 #include <seqan/parallel/parallel_splitting.h>
@@ -61,6 +92,11 @@
 // Parallel variants of basic algorithms
 #include <seqan/parallel/parallel_algorithms.h>
 
-//____________________________________________________________________________
+// Thread-safe / lock-free container operations.
+#include <seqan/parallel/parallel_sequence.h>
+#include <seqan/parallel/parallel_queue.h>
+#include <seqan/parallel/parallel_queue_suspendable.h>
+#include <seqan/parallel/parallel_resource_pool.h>
+#include <seqan/parallel/parallel_serializer.h>
 
 #endif  // SEQAN_PARALLEL_H_
diff --git a/seqan/parallel/INFO b/seqan/parallel/INFO
deleted file mode 100644
index 37f7d48..0000000
--- a/seqan/parallel/INFO
+++ /dev/null
@@ -1,12 +0,0 @@
-Name: seqan-parallel
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Helper code for parallel programming.
- This module contains helper code for parallel programming.
- .
- Among this are portable atomic read-and-write functions, min/max functions
- based on the RAW functions and helper code for splitter computation.
diff --git a/seqan/parallel/parallel_algorithms.h b/seqan/parallel/parallel_algorithms.h
index 02cec4b..0f12e96 100644
--- a/seqan/parallel/parallel_algorithms.h
+++ b/seqan/parallel/parallel_algorithms.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,14 +39,6 @@
 
 namespace seqan {
 
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
 // ============================================================================
 // Functions
 // ============================================================================
@@ -55,19 +47,10 @@ namespace seqan {
 // Function arrayFill
 // ----------------------------------------------------------------------------
 
-/**
-.Function.arrayFill
-..signature:arrayFill(begin, end, value, parallelTag)
-..param.parallelTag:Tag to enable/disable parallelism.
-...type:Tag.Serial
-...type:Tag.Parallel
-..include:seqan/basic.h
-*/
-
 template <typename TIterator, typename TValue, typename TParallelTag>
-inline void 
+inline void
 arrayFill(TIterator begin_,
-          TIterator end_, 
+          TIterator end_,
           TValue const & value,
           Tag<TParallelTag> parallelTag)
 {
@@ -84,9 +67,10 @@ arrayFill(TIterator begin_,
 
 /*!
  * @fn sum
+ * @headerfile <seqan/parallel.h>
  * @brief Returns the sum of all elements in a sequence.
  *
- * @signature TValue sum(seq[, parallelTag);
+ * @signature TValue sum(seq[, parallelTag]);
  *
  * @param[in] seq         The sequence to sum up, o ftype <tt>TSequence</tt>.
  * @param[in] parallelTag Tag to enable/disable parallelism, one of <tt>Serial</tt> and <tt>Parallel</tt>,
@@ -94,36 +78,18 @@ arrayFill(TIterator begin_,
  *
  * @return TValue The sum of the elements in <tt>seq</tt>, of type <tt>Value&lt;TSequence&gt;::Type</tt>.
  *
- * @section Remarks
- *
  * The sequence alphabet must support the <tt>operator+</tt> and conversion from zero.
  *
  * @see partialSum
  */
 
-/**
-.Function.sum
-..cat:Miscellaneous
-..summary:Returns the sum of all elements in a sequence.
-..signature:sum(seq[, parallelTag])
-..param.seq:A sequence of elements that should be summed.
-...remarks:The sequence alphabet must support the $operator+$ and conversion from zero.
-..param.parallelTag:Tag to enable/disable parallelism.
-...default:Tag.Serial
-...type:Tag.Serial
-...type:Tag.Parallel
-..returns:The sum of all contained elements.
-..see:Function.partialSum
-..include:seqan/parallel.h
-*/
-
 template <typename TSequence>
 inline typename Value<TSequence>::Type
 sum(TSequence const &seq, Serial)
 {
-    register typename Iterator<TSequence const>::Type it = begin(seq, Standard());
-    register typename Iterator<TSequence const>::Type itEnd = end(seq, Standard());
-    register typename Value<TSequence>::Type sum = 0;
+    typename Iterator<TSequence const>::Type it = begin(seq, Standard());
+    typename Iterator<TSequence const>::Type itEnd = end(seq, Standard());
+    typename Value<TSequence>::Type sum = 0;
     for (; it != itEnd; ++it)
         sum += *it;
     return sum;
@@ -135,7 +101,7 @@ sum(TSequence const &seq, Tag<TParallelTag> parallelTag)
 {
     Splitter<typename Size<TSequence>::Type> splitter(0, length(seq), parallelTag);
 
-    register typename Value<TSequence>::Type threadSum = 0;
+    typename Value<TSequence>::Type threadSum = 0;
     SEQAN_OMP_PRAGMA(parallel for reduction(+:threadSum))
     for (int job = 0; job < (int)length(splitter); ++job)
         threadSum += sum(infix(seq, splitter[job], splitter[job + 1]), Serial());
@@ -157,42 +123,23 @@ sum(TSequence const &seq)
  * @fn partialSum
  * @headerfile <seqan/parallel.h>
  * @brief Computes the partial sum of a sequence.
- * 
- * @signature TValue partialSum(target, source[, parallelTag])
- * 
+ *
+ * @signature TValue partialSum(target, source[, parallelTag]);
+ *
  * @param[in]  source      A sequence of elements that should be partially summed.  The sequence alphabet must support
  *                         the <tt>operator+</tt> and conversion from zero, the type is <tt>TSource</tt>.
  * @param[in]  parallelTag Tag to enable/disable parallelism, one of <tt>Serial</tt>, <tt>Parallel</tt>, default is
  *                         <tt>Serial</tt>.
- * @param[out] targ et     The resulting partial sum.  This sequence will have the same length as <tt>source</tt> and
+ * @param[out] target      The resulting partial sum.  This sequence will have the same length as <tt>source</tt> and
  *                         contains at position <tt>i</tt> the sum of elements <tt>source[0]</tt>, <tt>source[1]</tt>,
  *                         ..., <tt>source[i]</tt>.
- * 
+ *
  * @return TValue The sum of all elements in <tt>source</tt>.  The returned value equals the last value in target.
  *                <tt>TValue</tt> is <tt>Value&lt;TSource&gt;::Type</tt>.
- * 
+ *
  * @see sum
  */
 
-/**
-.Function.partialSum
-..cat:Miscellaneous
-..summary:Computes the partial sum of a sequence.
-..signature:partialSum(target, source[, parallelTag])
-..param.source:A sequence of elements that should be partially summed.
-...remarks:The sequence alphabet must support the $operator+$ and conversion from zero.
-..param.target:The resulting partial sum. This sequence will have the same length as $source$ and contains
-at position $i$ the sum of elements $source[0]$, $source[1]$, ..., $source[i]$.
-..param.parallelTag:Tag to enable/disable parallelism.
-...default:@Tag.Serial@
-...type:Tag.Serial
-...type:Tag.Parallel
-..returns:The sum of all elements in $source$.
-...remarks:The returned value equals the last value in target.
-..see:Function.sum
-..include:seqan/parallel.h
-*/
-
 template <typename TTarget, typename TSource, typename TParallelTag>
 inline typename Value<TSource>::Type
 partialSum(TTarget &target, TSource const &source, Tag<TParallelTag> parallelTag)
@@ -201,7 +148,7 @@ partialSum(TTarget &target, TSource const &source, Tag<TParallelTag> parallelTag
     typedef typename Size<TSource>::Type TSize;
     typedef typename Iterator<TSource const, Standard>::Type TConstIterator;
     typedef typename Iterator<TTarget, Standard>::Type TIterator;
-    
+
     resize(target, length(source), Exact());
     if (empty(target))
         return 0;
@@ -227,10 +174,10 @@ partialSum(TTarget &target, TSource const &source, Tag<TParallelTag> parallelTag
     SEQAN_OMP_PRAGMA(parallel for)
     for (int job = 0; job < (int)length(splitter); ++job)
     {
-        register TConstIterator it = begin(source, Standard()) + splitter[job];
-        register TConstIterator itEnd = begin(source, Standard()) + splitter[job + 1];
-        register TIterator dstIt = begin(target, Standard()) + splitter[job];
-        register TValue sum = localSums[job];
+        TConstIterator it = begin(source, Standard()) + splitter[job];
+        TConstIterator itEnd = begin(source, Standard()) + splitter[job + 1];
+        TIterator dstIt = begin(target, Standard()) + splitter[job];
+        TValue sum = localSums[job];
         for (; it != itEnd; ++it, ++dstIt)
         {
             sum += *it;
@@ -238,17 +185,658 @@ partialSum(TTarget &target, TSource const &source, Tag<TParallelTag> parallelTag
         }
         localSums[job] = sum;
     }
-    
+
     return back(localSums);
 }
 
+template <typename TTarget, typename TParallelTag>
+inline typename Value<TTarget>::Type
+partialSum(TTarget & target, Tag<TParallelTag> parallelTag)
+{
+    return partialSum(target, target, parallelTag);
+}
+
 template <typename TTarget, typename TSource>
 inline typename Value<TSource>::Type
-partialSum(TTarget &target, TSource const &source)
+partialSum(TTarget & target, TSource const & source)
 {
     return partialSum(target, source, Serial());
 }
 
+template <typename TTarget>
+inline typename Value<TTarget>::Type
+partialSum(TTarget & target)
+{
+    return partialSum(target, target);
+}
+
+// ----------------------------------------------------------------------------
+// Function iterate()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor, typename TIterTag, typename TParallelTag>
+inline void iterate(TContainer & c, TFunctor f, Tag<TIterTag> const & iterTag, Tag<TParallelTag> const & /* tag */)
+{
+    typedef Tag<TIterTag> const                                     TIterSpec;
+    typedef typename Iterator<TContainer, TIterSpec>::Type          TIter;
+
+    for (TIter it = begin(c, iterTag); !atEnd(it, c); ++it)
+        f(it);
+}
+
+// ----------------------------------------------------------------------------
+// Function iterate(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor, typename TIterTag>
+inline void iterate(TContainer & c, TFunctor f, Tag<TIterTag> const & iterTag, Parallel)
+{
+    typedef Tag<TIterTag> const                                     TIterSpec;
+    typedef typename Position<TContainer>::Type                     TPos;
+    typedef typename Iterator<TContainer, TIterSpec>::Type          TIter;
+
+    Splitter<TPos> splitter(0, length(c), Parallel());
+
+    SEQAN_OMP_PRAGMA(parallel for firstprivate(f))
+    for (TPos i = 0; i < length(splitter); ++i)
+    {
+       TIter it = begin(c, iterTag) + splitter[i];
+       TIter itEnd = begin(c, iterTag) + splitter[i + 1];
+
+       for (; it != itEnd; ++it)
+            f(it);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function iterate()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline void iterate(TContainer & c, TFunctor f)
+{
+    iterate(c, f, typename DefaultIteratorSpec<TContainer>::Type(), Serial());
+}
+
+// ============================================================================
+// STL Wrappers
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function forEach()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor, typename TParallelTag>
+inline TFunctor
+forEach(TContainer & c, TFunctor f, Tag<TParallelTag> const & /* tag */)
+{
+    return std::for_each(begin(c, Standard()), end(c, Standard()), f);
+}
+
+template <typename TContainer, typename TFunctor, typename TParallelTag>
+inline TFunctor
+forEach(TContainer const & c, TFunctor f, Tag<TParallelTag> const & /* tag */)
+{
+    return std::for_each(begin(c, Standard()), end(c, Standard()), f);
+}
+
+// ----------------------------------------------------------------------------
+// Function transform()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TSource, typename TUnaryOperator, typename TParallelTag>
+inline void transform(TTarget & target, TSource & source, TUnaryOperator o, Tag<TParallelTag> const & /* tag */)
+{
+    SEQAN_ASSERT_GEQ(length(target), length(source));
+    std::transform(begin(source, Standard()), end(source, Standard()), begin(target, Standard()), o);
+}
+
+template <typename TContainer, typename TUnaryOperator, typename TParallelTag>
+inline void transform(TContainer & c, TUnaryOperator o, Tag<TParallelTag> const & tag)
+{
+    transform(c, c, o, tag);
+}
+
+// ----------------------------------------------------------------------------
+// Function generate()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TGenerator, typename TParallelTag>
+inline void generate(TTarget & target, TGenerator g, Tag<TParallelTag> const & /* tag */)
+{
+    std::generate(begin(target, Standard()), end(target, Standard()), g);
+}
+
+// ----------------------------------------------------------------------------
+// Function iota()
+// ----------------------------------------------------------------------------
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TTarget, typename TValue, typename TParallelTag>
+inline void iota(TTarget & target, TValue val, Tag<TParallelTag> const & /* tag */)
+{
+    std::iota(begin(target, Standard()), end(target, Standard()), val);
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function count()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue, typename TParallelTag>
+inline typename Difference<TContainer>::Type
+count(TContainer const & c, TValue const & v, Tag<TParallelTag> const & /* tag */)
+{
+    return std::count(begin(c, Standard()), end(c, Standard()), v);
+}
+
+// ----------------------------------------------------------------------------
+// Function countIf()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate, typename TParallelTag>
+inline typename Difference<TContainer>::Type
+countIf(TContainer const & c, TUnaryPredicate p, Tag<TParallelTag> const & /* tag */)
+{
+    return std::count_if(begin(c, Standard()), end(c, Standard()), p);
+}
+
+// ----------------------------------------------------------------------------
+// Function removeIf()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate, typename TParallelTag>
+inline void
+removeIf(TContainer & c, TUnaryPredicate p, Tag<TParallelTag> const & /* tag */)
+{
+    typename Iterator<TContainer, Standard>::Type newEnd = std::remove_if(begin(c, Standard()), end(c, Standard()), p);
+    resize(c, position(newEnd, c), Exact());
+}
+
+// ----------------------------------------------------------------------------
+// Function accumulate()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue, typename TParallelTag>
+inline typename Value<TContainer>::Type
+accumulate(TContainer const & c, TValue const & v, Tag<TParallelTag> const & /* tag */)
+{
+    return std::accumulate(begin(c, Standard()), end(c, Standard()), v);
+}
+
+// ----------------------------------------------------------------------------
+// Function innerProduct()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue, typename TParallelTag>
+inline typename Value<TContainer>::Type
+innerProduct(TContainer const & c, TValue const & v, Tag<TParallelTag> const & /* tag */)
+{
+    return std::inner_product(begin(c, Standard()), end(c, Standard()), begin(c, Standard()), v);
+}
+
+// ----------------------------------------------------------------------------
+// Function nthElement()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TPosition, typename TParallelTag>
+inline typename Value<TContainer>::Type
+nthElement(TContainer & c, TPosition p, Tag<TParallelTag> const & /* tag */)
+{
+    std::nth_element(begin(c, Standard()), begin(c, Standard()) + p, end(c, Standard()));
+    return getValue(c, p);
+}
+
+// ----------------------------------------------------------------------------
+// Function maxElement()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate, typename TParallelTag>
+inline typename Reference<TContainer const>::Type
+maxElement(TContainer const & c, TUnaryPredicate p, Tag<TParallelTag> const & /* tag */)
+{
+    SEQAN_ASSERT_NOT(empty(c));
+    return value(std::max_element(begin(c, Standard()), end(c, Standard()), p));
+}
+
+template <typename TContainer, typename TParallelTag>
+inline typename Reference<TContainer const>::Type
+maxElement(TContainer const & c, Tag<TParallelTag> const & /* tag */)
+{
+    SEQAN_ASSERT_NOT(empty(c));
+    return value(std::max_element(begin(c, Standard()), end(c, Standard())));
+}
+
+// ----------------------------------------------------------------------------
+// Function minElement()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate, typename TParallelTag>
+inline typename Reference<TContainer const>::Type
+minElement(TContainer const & c, TUnaryPredicate p, Tag<TParallelTag> const & /* tag */)
+{
+    SEQAN_ASSERT_NOT(empty(c));
+    return value(std::min_element(begin(c, Standard()), end(c, Standard()), p));
+}
+
+template <typename TContainer, typename TParallelTag>
+inline typename Reference<TContainer const>::Type
+minElement(TContainer const & c, Tag<TParallelTag> const & /* tag */)
+{
+    SEQAN_ASSERT_NOT(empty(c));
+    return value(std::min_element(begin(c, Standard()), end(c, Standard())));
+}
+
+// ----------------------------------------------------------------------------
+// Function sort()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TBinaryPredicate, typename TParallelTag>
+inline void sort(TContainer SEQAN_FORWARD_ARG c, TBinaryPredicate p, Tag<TParallelTag> const & /* tag */)
+{
+    return std::sort(begin(c, Standard()), end(c, Standard()), p);
+}
+
+template <typename TContainer, typename TParallelTag>
+inline void sort(TContainer SEQAN_FORWARD_ARG c, Tag<TParallelTag> const & /* tag */)
+{
+    return std::sort(begin(c, Standard()), end(c, Standard()));
+}
+
+// ----------------------------------------------------------------------------
+// Function stableSort()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TBinaryPredicate, typename TParallelTag>
+inline void stableSort(TContainer SEQAN_FORWARD_ARG c, TBinaryPredicate p, Tag<TParallelTag> const & /* tag */)
+{
+    return std::stable_sort(begin(c, Standard()), end(c, Standard()), p);
+}
+
+template <typename TContainer, typename TParallelTag>
+inline void stableSort(TContainer SEQAN_FORWARD_ARG c, Tag<TParallelTag> const & /* tag */)
+{
+    return std::stable_sort(begin(c, Standard()), end(c, Standard()));
+}
+
+// ============================================================================
+// MCSTL Wrappers
+// ============================================================================
+
+// use MCSTL which is part of the GCC since version 4.3
+#if defined(_OPENMP) && defined(PLATFORM_GCC) && __GNUC__ >= 4 && __GNUC_MINOR__ >= 3
+
+// ----------------------------------------------------------------------------
+// Function forEach(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline TFunctor forEach(TContainer & c, TFunctor f, Parallel)
+{
+    return __gnu_parallel::for_each(begin(c, Standard()), end(c, Standard()), f);
+}
+
+template <typename TContainer, typename TFunctor>
+inline TFunctor forEach(TContainer const & c, TFunctor f, Parallel)
+{
+    return __gnu_parallel::for_each(begin(c, Standard()), end(c, Standard()), f);
+}
+
+// ----------------------------------------------------------------------------
+// Function transform(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TSource, typename TUnaryOperator>
+inline void transform(TTarget & target, TSource & source, TUnaryOperator o, Parallel)
+{
+    SEQAN_ASSERT_GEQ(length(target), length(source));
+    __gnu_parallel::transform(begin(source, Standard()), end(source, Standard()), begin(target, Standard()), o);
+}
+
+// ----------------------------------------------------------------------------
+// Function generate(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TGenerator>
+inline void generate(TTarget & target, TGenerator g, Parallel)
+{
+    __gnu_parallel::generate(begin(target, Standard()), end(target, Standard()), g);
+}
+
+// ----------------------------------------------------------------------------
+// Function count(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue>
+inline typename Difference<TContainer>::Type
+count(TContainer const & c, TValue const & v, Parallel)
+{
+    return __gnu_parallel::count(begin(c, Standard()), end(c, Standard()), v);
+}
+
+// ----------------------------------------------------------------------------
+// Function countIf(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate>
+inline typename Difference<TContainer>::Type
+countIf(TContainer const & c, TUnaryPredicate p, Parallel)
+{
+    return __gnu_parallel::count_if(begin(c, Standard()), end(c, Standard()), p);
+}
+
+// ----------------------------------------------------------------------------
+// Function removeIf(Parallel)
+// ----------------------------------------------------------------------------
+
+//template <typename TContainer, typename TUnaryPredicate>
+//inline void
+//removeIf(TContainer & c, TUnaryPredicate p, Parallel)
+//{
+//    typename Iterator<TContainer, Standard>::Type newEnd = __gnu_parallel::remove_if(begin(c, Standard()), end(c, Standard()), p);
+//    resize(c, position(newEnd, c), Exact());
+//}
+
+// ----------------------------------------------------------------------------
+// Function accumulate(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue>
+inline typename Value<TContainer>::Type
+accumulate(TContainer const & c, TValue const & v, Parallel)
+{
+    return __gnu_parallel::accumulate(begin(c, Standard()), end(c, Standard()), v);
+}
+
+// ----------------------------------------------------------------------------
+// Function innerProduct(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue>
+inline typename Value<TContainer>::Type
+innerProduct(TContainer const & c, TValue const & v, Parallel)
+{
+    return __gnu_parallel::inner_product(begin(c, Standard()), end(c, Standard()), begin(c, Standard()), v);
+}
+
+// ----------------------------------------------------------------------------
+// Function nthElement(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TPosition>
+inline typename Value<TContainer>::Type
+nthElement(TContainer & c, TPosition p, Parallel)
+{
+    __gnu_parallel::nth_element(begin(c, Standard()), begin(c, Standard()) + p, end(c, Standard()));
+    return getValue(c, p);
+}
+
+// ----------------------------------------------------------------------------
+// Function maxElement(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate>
+inline typename Reference<TContainer const>::Type
+maxElement(TContainer const & c, TUnaryPredicate p, Parallel)
+{
+    SEQAN_ASSERT_NOT(empty(c));
+    return value(__gnu_parallel::max_element(begin(c, Standard()), end(c, Standard()), p));
+}
+
+template <typename TContainer>
+inline typename Reference<TContainer const>::Type
+maxElement(TContainer const & c, Parallel)
+{
+    SEQAN_ASSERT_NOT(empty(c));
+    return value(__gnu_parallel::max_element(begin(c, Standard()), end(c, Standard())));
+}
+
+// ----------------------------------------------------------------------------
+// Function minElement(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate>
+inline typename Reference<TContainer const>::Type
+minElement(TContainer const & c, TUnaryPredicate p, Parallel)
+{
+    SEQAN_ASSERT_NOT(empty(c));
+    return value(__gnu_parallel::min_element(begin(c, Standard()), end(c, Standard()), p));
+}
+
+template <typename TContainer>
+inline typename Reference<TContainer const>::Type
+minElement(TContainer const & c, Parallel)
+{
+    SEQAN_ASSERT_NOT(empty(c));
+    return value(__gnu_parallel::min_element(begin(c, Standard()), end(c, Standard())));
+}
+
+// ----------------------------------------------------------------------------
+// Function sort(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TBinaryPredicate>
+inline void sort(TContainer SEQAN_FORWARD_ARG c, TBinaryPredicate p, Parallel)
+{
+    return __gnu_parallel::sort(begin(c, Standard()), end(c, Standard()), p);
+}
+
+template <typename TContainer>
+inline void sort(TContainer SEQAN_FORWARD_ARG c, Parallel)
+{
+    return __gnu_parallel::sort(begin(c, Standard()), end(c, Standard()));
+}
+
+// ----------------------------------------------------------------------------
+// Function stableSort(Parallel)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TBinaryPredicate>
+inline void stableSort(TContainer SEQAN_FORWARD_ARG c, TBinaryPredicate p, Parallel)
+{
+    return __gnu_parallel::stable_sort(begin(c, Standard()), end(c, Standard()), p);
+}
+
+template <typename TContainer>
+inline void stableSort(TContainer SEQAN_FORWARD_ARG c, Parallel)
+{
+    return __gnu_parallel::stable_sort(begin(c, Standard()), end(c, Standard()));
+}
+
+#endif  // #ifdef PLATFORM_GCC
+
+// ============================================================================
+// Shortcuts for STL Wrappers
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function forEach()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline TFunctor forEach(TContainer & c, TFunctor f)
+{
+    return forEach(c, f, Serial());
+}
+
+template <typename TContainer, typename TFunctor>
+inline TFunctor forEach(TContainer const & c, TFunctor f)
+{
+    return forEach(c, f, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function transform()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TSource, typename TUnaryOperator>
+inline void transform(TTarget & target, TSource & source, TUnaryOperator o)
+{
+    transform(target, source, o, Serial());
+}
+
+template <typename TContainer, typename TUnaryOperator>
+inline void transform(TContainer & c, TUnaryOperator o)
+{
+    transform(c, o, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function generate()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TGenerator>
+inline void generate(TTarget & target, TGenerator g)
+{
+    generate(target, g, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function iota()
+// ----------------------------------------------------------------------------
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TTarget, typename TValue>
+inline void iota(TTarget & target, TValue val)
+{
+    iota(target, val, Serial());
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function count()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue>
+inline typename Difference<TContainer>::Type
+count(TContainer const & c, TValue const & v)
+{
+    return count(c, v, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function countIf()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate>
+inline typename Difference<TContainer>::Type
+countIf(TContainer const & c, TUnaryPredicate p)
+{
+    return countIf(c, p, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function removeIf()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate>
+inline void
+removeIf(TContainer & c, TUnaryPredicate p)
+{
+    removeIf(c, p, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function accumulate()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue>
+inline typename Value<TContainer>::Type
+accumulate(TContainer const & c, TValue const & v)
+{
+    return accumulate(c, v, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function innerProduct()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TValue>
+inline typename Value<TContainer>::Type
+innerProduct(TContainer const & c, TValue const & v)
+{
+    return innerProduct(c, v, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function nthElement()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TPosition>
+inline typename Value<TContainer>::Type
+nthElement(TContainer & c, TPosition p)
+{
+    return nthElement(c, p, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function maxElement()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate>
+inline typename Reference<TContainer const>::Type
+maxElement(TContainer const & c, TUnaryPredicate p)
+{
+    return maxElement(c, p, Serial());
+}
+
+template <typename TContainer>
+inline typename Reference<TContainer const>::Type
+maxElement(TContainer const & c)
+{
+    return maxElement(c, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function minElement()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TUnaryPredicate>
+inline typename Reference<TContainer const>::Type
+minElement(TContainer const & c, TUnaryPredicate p)
+{
+    return minElement(c, p, Serial());
+}
+
+template <typename TContainer>
+inline typename Reference<TContainer const>::Type
+minElement(TContainer const & c)
+{
+    return minElement(c, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function sort()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TBinaryPredicate>
+inline void sort(TContainer SEQAN_FORWARD_ARG c, TBinaryPredicate p)
+{
+    sort(c, p, Serial());
+}
+
+template <typename TContainer>
+inline void sort(TContainer SEQAN_FORWARD_ARG c)
+{
+    sort(c, Serial());
+}
+
+// ----------------------------------------------------------------------------
+// Function stableSort()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TBinaryPredicate>
+inline void stableSort(TContainer SEQAN_FORWARD_ARG c, TBinaryPredicate p)
+{
+    stableSort(c, p, Serial());
+}
+
+template <typename TContainer>
+inline void stableSort(TContainer SEQAN_FORWARD_ARG c)
+{
+    stableSort(c, Serial());
+}
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_PARALLEL_PARALLEL_ALGORITHMS_H_
diff --git a/seqan/parallel/parallel_atomic_misc.h b/seqan/parallel/parallel_atomic_misc.h
old mode 100755
new mode 100644
index 729f33a..e6ac51e
--- a/seqan/parallel/parallel_atomic_misc.h
+++ b/seqan/parallel/parallel_atomic_misc.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -71,8 +71,6 @@ namespace seqan {
  * @param[in,out] x Integer to set to <tt>max(x, y)</tt>.
  * @param[in]     y Other integer.
  *
- * @section Remarks
- *
  * This is equivalent to
  *
  * @code{.cpp}
@@ -82,23 +80,6 @@ namespace seqan {
  * @endcode
  */
 
-/**
-.Function.atomicMax
-..summary:Lock-free implementation of $x = max(x, y)$.
-..cat:Atomic Operations
-..signature:atomicMax(x, y)
-..param.x:Integer to set to $max(x, y)$
-..param.y:Other integer.
-..remarks:This is equivalent to
-...code:
-atomic {
-    x = max(x, y);
-}
-...text:While lock-free, the function tries to update $x$ as long as $x < y$ in a loop and might run a long time if x is incremented continuously in another thread.
-..header:seqan/parallel.h
-..see:Function.atomicMin
- */
-
 template <typename T>
 inline void
 atomicMax(T volatile & x, T y)
@@ -124,8 +105,6 @@ atomicMax(T volatile & x, T y)
  * @param[in,out] x Integer to set to <tt>min(x, y)</tt>.
  * @param[in]     y Other integer.
  *
- * @section Remarks
- *
  * This is equivalent to
  *
  * @code{.cpp}
@@ -135,23 +114,6 @@ atomicMax(T volatile & x, T y)
  * @endcode
  */
 
-/**
-.Function.atomicMin
-..summary:Lock-free implementation of $x = min(x, y)$.
-..cat:Atomic Operations
-..signature:atomicMin(x, y)
-..param.x:Integer to set to min(x, y)$
-..param.y:Other integer.
-..remarks:This is equivalent to
-...code:
-atomic {
-    x = min(x, y);
-}
-...text:While lock-free, the function tries to update $x$ as long as $x > y$ in a loop and might run a long time if x is incremented continuously in another thread.
-..header:seqan/parallel.h
-..see:Function.atomicMax
- */
-
 template <typename T>
 inline void
 atomicMin(T volatile & x, T y)
diff --git a/seqan/parallel/parallel_atomic_primitives.h b/seqan/parallel/parallel_atomic_primitives.h
old mode 100755
new mode 100644
index a76c8bc..fe353a8
--- a/seqan/parallel/parallel_atomic_primitives.h
+++ b/seqan/parallel/parallel_atomic_primitives.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -56,7 +56,23 @@ namespace seqan {
 // Metafunctions
 // ============================================================================
 
-// TODO(holtgrew): One could implement an HasAtomicFunction<T, Function> Metafunction but that would probably be pretty useless.
+#ifdef SEQAN_CXX11_STL
+
+template <typename T>
+struct Atomic
+{
+    typedef std::atomic<T> Type;
+};
+
+#else
+
+template <typename T>
+struct Atomic
+{
+    typedef T Type;
+};
+
+#endif
 
 // ============================================================================
 // Functions
@@ -71,19 +87,19 @@ namespace seqan {
  * @fn AtomicPrimitives#atomicInc
  * @headerfile <seqan/parallel.h>
  * @brief Atomically increment an integer.
- * 
+ *
  * @signature TResult atomicInc(x);
- * 
+ *
  * @param[in,out] x An integer, by reference.
- * 
+ *
  * @return TResult The old value of $x$, <tt>TResult</tt> has the same type as <tt>x</tt>.
- * 
+ *
  * @section Remarks
- * 
+ *
  * This is equivalent to an atomic <tt>++x</tt>.
- * 
+ *
  * Note that atomic increments are limited to 32 bit and 64 bit with MSVC (64 bit is only available on 64 bit Windows).
- * 
+ *
  * You are responsible for correctly aligning <tt>x</tt> such that the atomic increment works on the hardware you
  * target.
  */
@@ -92,19 +108,19 @@ namespace seqan {
  * @fn AtomicPrimitives#atomicDec
  * @headerfile <seqan/parallel.h>
  * @brief Atomically decrement an integer.
- * 
+ *
  * @signature TResult atomicDec(x);
- * 
+ *
  * @param[in,out] x An integer, by reference.
- * 
+ *
  * @return TResult The old value of $x$, <tt>TResult</tt> has the same type as <tt>x</tt>.
- * 
+ *
  * @section Remarks
- * 
+ *
  * This is equivalent to an atomic <tt>--x</tt>.
- * 
+ *
  * Note that atomic decrements are limited to 32 bit and 64 bit with MSVC (64 bit is only available on 64 bit Windows).
- * 
+ *
  * You are responsible for correctly aligning <tt>x</tt> such that the atomic decrement works on the hardware you
  * target.
  */
@@ -113,21 +129,21 @@ namespace seqan {
  * @fn AtomicPrimitives#atomicAdd
  * @headerfile <seqan/parallel.h>
  * @brief Atomically add an integer to another integer.
- * 
+ *
  * @signature TResult atomicAdd(x, y)
- * 
+ *
  * @param[in,out] x Integer, by reference.
  * @param[in]     y Integer to add to <tt>x</tt>.
- * 
+ *
  * @return TResult The old value of <tt>x</tt>.
- * 
+ *
  * @section Remarks
- * 
+ *
  * This is equivalent to an atomic <tt>x += y</tt>.
- * 
+ *
  * Note that atomic fetch-and-add is limited to 32 bit and 64 bit with MSVC (64 bit is only available on 64 bit
  * Windows).
- * 
+ *
  * You are responsible for correctly aligning <tt>x</tt> such that the atomic increment works on the hardware you
  * target.
  */
@@ -136,23 +152,23 @@ namespace seqan {
  * @fn AtomicPrimitives#atomicOr
  * @headerfile <seqan/parallel.h>
  * @brief Atomically combine two integers with <tt>OR</tt> operation.
- * 
+ *
  * @signature TResult atomicOr(x, y);
- * 
+ *
  * @param[in,out] x Integer, by reference.
  * @param[in]     y Integer to combine with <tt>OR</tt> operation.
- * 
+ *
  * @return TResult The old value of <tt>x</tt>, <tt>TResult</tt> is the type of <tt>x</tt>.
- * 
+ *
  * @section Remarks
- * 
+ *
  * This is equivalent to an atomic <tt>x |= y</tt>.
- * 
+ *
  * Atomic fetch-and-or for 64 bit integers is only available on 64 bit processors when targeting Intel.
- * 
+ *
  * Atomic fetch-and-or does not work in VS8 on 64 bit Windows, you can only use <tt>atomicOr()</tt> portably on 32 and
  * 64 bit integers.
- * 
+ *
  * You are responsible for correctly aligning <tt>x</tt> such that the atomic increment works on the hardware you
  * target.
  */
@@ -161,23 +177,23 @@ namespace seqan {
  * @fn AtomicPrimitives#atomicXor
  * @headerfile <seqan/parallel.h>
  * @brief Atomically combine two integers with <tt>XOR</tt> operation.
- * 
+ *
  * @signature TResult atomicXor(x, y);
- * 
+ *
  * @param[in,out] x Integer, by reference.
  * @param[in]     y Integer to combine with <tt>XOR</tt> operation.
- * 
+ *
  * @return TResult The old value of <tt>x</tt>, <tt>TResult</tt> is the type of <tt>x</tt>.
- * 
+ *
  * @section Remarks
- * 
+ *
  * This is equivalent to an atomic <tt>x ^= y</tt>.
- * 
+ *
  * Atomic fetch-and-xor fxor 64 bit integers is only available on 64 bit processxors when targeting Intel.
- * 
+ *
  * Atomic fetch-and-xor does not wxork in VS8 on 64 bit Windows, you can only use <tt>atomicXor()</tt> pxortably on 32 and
  * 64 bit integers.
- * 
+ *
  * You are responsible fxor cxorrectly aligning <tt>x</tt> such that the atomic increment wxorks on the hardware you
  * target.
  */
@@ -186,19 +202,19 @@ namespace seqan {
  * @fn AtomicPrimitives#atomicCas
  * @headerfile <seqan/parallel.h>
  * @brief Atomic ompare-and-Swap operation.
- * 
+ *
  * @signature TResult atomicCas(x, cmp, y)
- * 
+ *
  * @param[in,out] x   Pointer to the integer to swap.
  * @param[in,out] cmp Value to compare <tt>x</tt> with.
  * @param[in]     y   Value to set <tt>x</tt> to if it is equal to <tt>cmp</tt>.
  *
  * @return TResult Returns the original value of x.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The pseudo code for this is as follows:
- * 
+ *
  * @code{.cpp}
  * atomic {
  *     T val = *(&x);
@@ -207,126 +223,18 @@ namespace seqan {
  *     return val;
  * }
  * @endcode
- * 
+ *
  * On Windows, atomic CAS is only available for 16, 32, and 64 bit integers, 64 bit is only available on 64 bit Windows.
- * 
+ *
  * You are responsible for correctly aligning <tt>x</tt> such that the atomic increment works on the hardware you
  * target.
  */
 
 // TODO(holtgrew): What about correct alignment?!
 
-/**
-.Function.atomicInc
-..summary:Atomically increment an integer.
-..cat:Atomic Operations
-..signature:atomicInc(x)
-..param.x:Integer, by reference.
-..returns:The old value of $x.
-..remarks:This is equivalent to an atomic $++x$.
-..remarks:Note that atomic increments are limited to 32 bit and 64 bit with MSVC (64 bit is only available on 64 bit Windows).
-..remarks:You are responsible for correctly aligning $x$ such that the atomic increment works on the hardware you target.
-..see:Function.atomicDec
-..see:Function.atomicAdd
-..see:Function.atomicOr
-..see:Function.atomicXor
-..see:Function.atomicCas
-..include:seqan/parallel.h
-
-.Function.atomicDec
-..summary:Atomically decrement an integer.
-..cat:Atomic Operations
-..signature:atomicDec(x)
-..param.x:Integer, by reference.
-..returns:The old value of $x$.
-..remarks:This is equivalent to an atomic $--x$.
-..remarks:Note that atomic decrements are limited to 32 bit and 64 bit with MSVC (64 bit is only available on 64 bit Windows).
-..remarks:You are responsible for correctly aligning $x$ such that the atomic increment works on the hardware you target.
-..see:Function.atomicInc
-..see:Function.atomicAdd
-..see:Function.atomicOr
-..see:Function.atomicXor
-..see:Function.atomicCas
-..include:seqan/parallel.h
-
-.Function.atomicAdd
-..summary:Atomically add an integer to another integer.
-..cat:Atomic Operations
-..signature:atomicAdd(x, y)
-..param.x:Integer, by reference.
-..param.y:Integer to add to the given value.
-..returns:The old value of $x$.
-..remarks:This is equivalent to an atomic $x += y$.
-..remarks:Note that atomic fetch-and-add is limited to 32 bit and 64 bit with MSVC (64 bit is only available on 64 bit Windows).
-..remarks:You are responsible for correctly aligning $x$ such that the atomic increment works on the hardware you target.
-..see:Function.atomicInc
-..see:Function.atomicDec
-..see:Function.atomicOr
-..see:Function.atomicXor
-..see:Function.atomicCas
-..include:seqan/parallel.h
-
-.Function.atomicOr
-..summary:Atomically combine two integers with $OR$ operation.
-..cat:Atomic Operations
-..signature:atomicOr(x, y)
-..param.x:Integer, by reference.
-..param.y:Integer to combine with $OR$ operation.
-..returns:The old value of $x$.
-..remarks:This is equivalent to an atomic $x |= y$.
-..remarks:Atomic fetch-and-or for 64 bit integers is only available on 64 bit processors when targeting Intel.
-..remarks:Atomic fetch-and-or does not work in VS8 on 64 bit Windows, you can only use $atomicOr()$ portably on 32 and 64 bit integers.
-..remarks:You are responsible for correctly aligning $x$ such that the atomic increment works on the hardware you target.
-..see:Function.atomicInc
-..see:Function.atomicDec
-..see:Function.atomicAdd
-..see:Function.atomicXor
-..see:Function.atomicCas
-..include:seqan/parallel.h
-
-.Function.atomicXor
-..summary:Atomically combine wto integers with $XOR$ operation.
-..cat:Atomic Operations
-..signature:atomicXor(x, y)
-..param.x:x, by reference.
-..param.y:Integer to combine with $XOR$ operation.
-..returns:The old value of $x$.
-..remarks:This is equivalent to an atomic $x ^= y$.
-..remarks:Atomic fetch-and-xor for 64 bit integers is only available on 64 bit processors when targeting Intel.
-..remarks:Atomic fetch-and-xor does not work in VS8 on 64 bit Windows, you can only use $atomicXor()$ portably on 32 and 64 bit integers.
-..remarks:You are responsible for correctly aligning $x$ such that the atomic increment works on the hardware you target.
-..see:Function.atomicInc
-..see:Function.atomicDec
-..see:Function.atomicAdd
-..see:Function.atomicOr
-..see:Function.atomicCas
-..include:seqan/parallel.h
-
-.Function.atomicCas
-..summary:Compare-and-Swap operation.
-..cat:Atomic Operations
-..signature:atomicCas(x, cmp, y)
-..param.x:Pointer to the integer to swap.
-..param.cmp:Value to compare $x$ with.
-..param.y:Value to set $x$ to if it is equal to $cmp$.
-..remarks:The pseudo code for this is
-..remarks:On Windows, atomic CAS is only available for 16, 32, and 64 bit integers, 64 bit is only available on 64 bit Windows.
-..remarks:You are responsible for correctly aligning $x$ such that the atomic increment works on the hardware you target.
-...code:
-atomic
-{
-    T val = *(&x);
-    if (val == cmp)
-        *(&x) = y;
-    return val;
-}
-..see:Function.atomicInc
-..see:Function.atomicDec
-..see:Function.atomicAdd
-..see:Function.atomicOr
-..see:Function.atomicXor
-..include:seqan/parallel.h
- */
+#ifndef SEQAN_CACHE_LINE_SIZE
+#define SEQAN_CACHE_LINE_SIZE 128
+#endif
 
 #if defined(PLATFORM_WINDOWS) && !defined(PLATFORM_WINDOWS_MINGW)
 
@@ -396,10 +304,12 @@ template <typename T, typename S>
 inline T atomicXor(T volatile &x, S y) { return _atomicXor(x, ConstInt<sizeof(T)>(), y); }
 template <typename T, typename S, typename U>
 inline T atomicCas(T volatile &x, S cmp, U y) { return _atomicCas(x, ConstInt<sizeof(T)>(), cmp, y); }
+template <typename T, typename S, typename U>
+inline bool atomicCasBool(T volatile &x, S cmp, U y) { return _atomicCas(x, ConstInt<sizeof(T)>(), cmp, y) == cmp; }
 
-template <typename T> 
+template <typename T>
 inline T atomicPostInc(T volatile & x) { return atomicInc(x) - 1; }
-template <typename T> 
+template <typename T>
 inline T atomicPostDec(T volatile & x) { return atomicDec(x) + 1; }
 
 
@@ -457,6 +367,12 @@ inline T atomicCas(T volatile & x, T cmp, T y)
     return __sync_val_compare_and_swap(&x, cmp, y);
 }
 
+template <typename T>
+inline bool atomicCasBool(T volatile & x, T cmp, T y)
+{
+    return __sync_bool_compare_and_swap(&x, cmp, y);
+}
+
 template <typename T>
 inline T atomicSwap(T volatile & x, T y)
 {
@@ -506,9 +422,12 @@ template <typename T>   inline T atomicInc(T          & x,             Serial)
 template <typename T>   inline T atomicPostInc(T      & x,             Serial)      { return x++;                    }
 template <typename T>   inline T atomicDec(T          & x,             Serial)      { return --x;                    }
 template <typename T>   inline T atomicPostDec(T      & x,             Serial)      { return x--;                    }
-template <typename T>   inline T atomicOr (T          & x, T y,        Serial)      { return x = x | y;              }
-template <typename T>   inline T atomicXor(T          & x, T y,        Serial)      { return x = x ^ y;              }
+template <typename T>   inline T atomicOr (T          & x, T y,        Serial)      { return x |= y;                 }
+template <typename T>   inline T atomicXor(T          & x, T y,        Serial)      { return x ^= y;                 }
+// In serial mode, there is no other thread changing cmp except us
 template <typename T>   inline T atomicCas(T          & x, T cmp, T y, Serial)      { if (x == cmp) x = y; return x; }
+//template <typename T>   inline bool atomicCasBool(T   & x, T cmp, T y, Serial)      { if (x == cmp) { x = y; return true; } return false; }
+template <typename T>   inline bool atomicCasBool(T volatile & x, T, T y, Serial)   { x = y; return true;            }
 
 template <typename T>   inline T atomicInc(T volatile & x,             Parallel)    { return atomicInc(x);           }
 template <typename T>   inline T atomicPostInc(T volatile & x,         Parallel)    { return atomicPostInc(x);       }
@@ -517,11 +436,27 @@ template <typename T>   inline T atomicPostDec(T volatile & x,         Parallel)
 template <typename T>   inline T atomicOr (T volatile & x, T y,        Parallel)    { return atomicOr(x, y);         }
 template <typename T>   inline T atomicXor(T volatile & x, T y,        Parallel)    { return atomicXor(x, y);        }
 template <typename T>   inline T atomicCas(T volatile & x, T cmp, T y, Parallel)    { return atomicCas(x, cmp, y);   }
+template <typename T>   inline bool atomicCasBool(T volatile & x, T cmp, T y, Parallel) { return atomicCasBool(x, cmp, y); }
 
 template <typename T1, typename T2>   inline T1 atomicAdd(T1          & x, T2 y, Serial)    { return x = x + y; }
 template <typename T1, typename T2>   inline T1 atomicAdd(T1 volatile & x, T2 y, Parallel)  { return atomicAdd(x, y); }
 
 
+// C++11 atomic wrappers
+
+#ifdef SEQAN_CXX11_STL
+template <typename T>   inline T atomicInc(std::atomic<T>        & x     )        { return ++x;                    }
+template <typename T>   inline T atomicPostInc(std::atomic<T>    & x     )        { return x++;                    }
+template <typename T>   inline T atomicDec(std::atomic<T>        & x     )        { return --x;                    }
+template <typename T>   inline T atomicPostDec(std::atomic<T>    & x     )        { return x--;                    }
+template <typename T>   inline T atomicOr (std::atomic<T>        & x, T y)        { return x |= y;                 }
+template <typename T>   inline T atomicXor(std::atomic<T>        & x, T y)        { return x ^= y;                 }
+template <typename T>   inline T atomicCas(std::atomic<T>        & x, T cmp, T y, Serial)   { if (x == cmp) x = y;             return x;   }
+template <typename T>   inline T atomicCas(std::atomic<T>        & x, T cmp, T y, Parallel) { x.compare_exchange_weak(cmp, y); return cmp; }
+template <typename T>   inline bool atomicCasBool(std::atomic<T> & x, T    , T y, Serial)   { x = y; return true;                          }
+template <typename T>   inline bool atomicCasBool(std::atomic<T> & x, T cmp, T y, Parallel) { return x.compare_exchange_weak(cmp, y);      }
+#endif  // #ifdef SEQAN_CXX11_STL
+
 } // namespace seqan
 
 #endif  // #if defined(PLATFORM_WINDOWS) && !defined(PLATFORM_WINDOWS_MINGW)
diff --git a/seqan/parallel/parallel_lock.h b/seqan/parallel/parallel_lock.h
new file mode 100644
index 0000000..46857a2
--- /dev/null
+++ b/seqan/parallel/parallel_lock.h
@@ -0,0 +1,341 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// 2-level spinlock and corresponding scoped locks for each level
+// ==========================================================================
+
+#ifndef SEQAN_PARALLEL_PARALLEL_LOCK_H_
+#define SEQAN_PARALLEL_PARALLEL_LOCK_H_
+
+#if defined(__SSE2__) && !defined(__CUDACC__)
+#include <xmmintrin.h>  // _mm_pause()
+#endif
+
+#ifdef PLATFORM_WINDOWS
+#include <Windows.h>
+#else
+#include <sched.h>
+#endif
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+struct Mutex;
+inline void yieldProcessor();
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+class SpinDelay
+{
+public:
+    static const unsigned LOOPS_BEFORE_YIELD = 16;
+    unsigned duration;
+
+    SpinDelay() :
+        duration(1)
+    {}
+};
+
+inline void
+clear(SpinDelay & me)
+{
+    me.duration = 1;
+}
+
+inline void
+waitFor(SpinDelay & me)
+{
+    if (me.duration <= me.LOOPS_BEFORE_YIELD)
+    {
+        for (unsigned i = me.duration; i != 0; --i)
+            yieldProcessor();
+        me.duration *= 2;
+    }
+    else
+    {
+#ifdef PLATFORM_WINDOWS
+#if _WIN32_WINNT >= 0x0400
+        SwitchToThread();
+#endif
+#else
+        sched_yield();
+#endif
+    }
+}
+
+template <typename TAtomic, typename TValue>
+inline void
+spinWhileEq(TAtomic & x, TValue cmp)
+{
+    SpinDelay spinDelay;
+    while (x == cmp)
+        waitFor(spinDelay);
+}
+
+template <typename TAtomic, typename TValue>
+inline void
+spinWhileNeq(TAtomic & x, TValue cmp)
+{
+    SpinDelay spinDelay;
+    while (x != cmp)
+        waitFor(spinDelay);
+}
+
+template <typename TAtomic, typename TValue>
+inline void
+spinCas(TAtomic & x, TValue cmp, TValue y)
+{
+    SpinDelay spinDelay;
+#ifdef SEQAN_CXX11_STL
+    TValue exp = cmp;
+    while (!x.compare_exchange_weak(exp, y))
+    {
+        exp = cmp;
+        waitFor(spinDelay);
+    }
+#else
+    while (!atomicCasBool(x, cmp, y))
+        waitFor(spinDelay);
+#endif
+}
+
+// ----------------------------------------------------------------------------
+// Class ReadWriteLock
+// ----------------------------------------------------------------------------
+// this lock augments a class by thread-safety as follows:
+//  - supports multiple concurrent readers (possibly waiting for writer to finish)
+//  - supports only a single writer at a time (possibly waiting for readers or other writers to finish)
+//  - the writer has higher priority than all readers
+
+class ReadWriteLock
+{
+public:
+    Atomic<unsigned>::Type readers;
+    Atomic<unsigned>::Type writers;
+
+    ReadWriteLock() :
+        readers(0),
+        writers(0)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class ScopedLock
+// ----------------------------------------------------------------------------
+
+template <typename TMutex = Mutex, typename TParallel = Parallel>
+struct ScopedLock
+{
+    TMutex & mutex;
+
+    explicit
+    ScopedLock(TMutex & mutex) :
+        mutex(mutex)
+    {
+        lock(mutex);
+    }
+
+    ~ScopedLock()
+    {
+        unlock(mutex);
+    }
+
+};
+
+template <typename TLock>
+struct ScopedLock<TLock, Serial>
+{
+    explicit
+    ScopedLock(TLock &)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class ScopedReadLock
+// ----------------------------------------------------------------------------
+
+template <typename TLock = ReadWriteLock, typename TParallel = Parallel>
+struct ScopedReadLock
+{
+    TLock & lock;
+
+    explicit
+    ScopedReadLock(TLock & lock) :
+        lock(lock)
+    {
+        lockReading(lock);
+    }
+
+    ~ScopedReadLock()
+    {
+        unlockReading(lock);
+    }
+
+};
+
+template <typename TLock>
+struct ScopedReadLock<TLock, Serial>
+{
+    explicit
+    ScopedReadLock(TLock &)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class ScopedWriteLock
+// ----------------------------------------------------------------------------
+
+template <typename TLock = ReadWriteLock, typename TParallel = Parallel>
+struct ScopedWriteLock
+{
+    TLock & lock;
+
+    explicit
+    ScopedWriteLock(TLock & lock) :
+        lock(lock)
+    {
+        lockWriting(lock);
+    }
+
+    ~ScopedWriteLock()
+    {
+        unlockWriting(lock);
+    }
+
+};
+
+template <typename TLock>
+struct ScopedWriteLock<TLock, Serial>
+{
+    explicit
+    ScopedWriteLock(TLock &)
+    {}
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function yieldProcessor()
+// ----------------------------------------------------------------------------
+
+inline void
+yieldProcessor()
+{
+#if defined( __CUDACC__)
+    // don't wait on the GPU
+#elif defined(PLATFORM_WINDOWS_VS)
+    YieldProcessor();
+#elif defined(__SSE2__)
+    _mm_pause();
+#else
+    __asm__ __volatile__("rep; nop" : : );
+#endif
+}
+
+// ----------------------------------------------------------------------------
+// Function lockReading()
+// ----------------------------------------------------------------------------
+
+inline void
+lockReading(ReadWriteLock & lock)
+{
+    do
+    {
+        // wait for the end of a write access
+        spinWhileNeq(lock.writers, 0u);
+
+        atomicInc(lock.readers);
+
+        if (lock.writers == 0u)
+            break;
+
+        // writer hasn't noticed us -> retry
+        atomicDec(lock.readers);
+    }
+    while (true);
+}
+
+// ----------------------------------------------------------------------------
+// Function unlockReading()
+// ----------------------------------------------------------------------------
+
+inline void
+unlockReading(ReadWriteLock & lock)
+{
+    atomicDec(lock.readers);
+}
+
+// ----------------------------------------------------------------------------
+// Function lockWriting()
+// ----------------------------------------------------------------------------
+
+inline void
+lockWriting(ReadWriteLock & lock)
+{
+    // wait until we are the only writer
+    spinCas(lock.writers, 0u, 1u);
+
+    // wait until all readers are done
+    spinWhileNeq(lock.readers, 0u);
+}
+
+// ----------------------------------------------------------------------------
+// Function unlockWriting()
+// ----------------------------------------------------------------------------
+
+inline void
+unlockWriting(ReadWriteLock & lock)
+{
+    lock.writers = 0;
+}
+
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+inline bool
+empty(ReadWriteLock & lock)
+{
+    return (lock.readers == 0u && lock.writers == 0u);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_PARALLEL_PARALLEL_LOCK_H_
diff --git a/seqan/parallel/parallel_macros.h b/seqan/parallel/parallel_macros.h
old mode 100755
new mode 100644
index d9d11ed..11f0fe7
--- a/seqan/parallel/parallel_macros.h
+++ b/seqan/parallel/parallel_macros.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,6 +40,7 @@
 
 /*!
  * @macro SEQAN_OMP_PRAGMA
+ * @headerfile <seqan/parallel.h>
  * @brief Portable conditional <tt>#pragma</tt> issuing if OpenMP is enabled.
  *
  * @signature SEQAN_OMP_PRAGMA(x)
@@ -74,44 +75,46 @@
  * @endcode
  */
 
-/**
-.Macro.SEQAN_OMP_PRAGMA
-..summary:Portable conditional $#pragma$ issuing if OpenMP is enabled.
-..cat:Parallelism
-..signature:SEQAN_OMP_PRAGMA(x)
-..param.x:The string to issue behind $#pragma omp$.
-..remarks:This macro uses portable pragma generation, dependent on the macro $_OPENMP$ being defined (as by the OpenMP standard).
-..remarks:This is useful for disabling OpenMP pragmas on compilers that do not support OpenMP to suppress warnings.
-..example.text:Parallelize loop with OpenMP if OpenMP is enabled:
-..example.code:
-SEQAN_OMP_PRAGMA(parallel for) // becomes: #pragma omp parallel for
-for (int i = 0; i < x; ++i) {
-    // Do work.
-}
-..example.text:Make an addition atomic if OpenMP is enabled:
-..example.code:
-SEQAN_OMP_PRAGMA(parallel atomic) // becomes: #pragma omp parallel atomic
-i += 1;
- */
-
 #ifdef _OPENMP
-  #include <omp.h>
-  #if defined(PLATFORM_WINDOWS_MINGW) || defined(PLATFORM_GCC)
-    // GCC _Pragma operator
-    #define SEQAN_DO_PRAGMA(x) _Pragma(#x)
-    #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x)
-  #else  // #if defined(PLATFORM_WINDOWS_MINGW) || defined(PLATFORM_GCC)
-    // MSVC __pragma-operator
-    #define SEQAN_OMP_PRAGMA(x) __pragma (omp x)
-  #endif // #if defined(PLATFORM_WINDOWS_MINGW) || defined(PLATFORM_GCC)
+
+#include <omp.h>
+
+#if defined(PLATFORM_WINDOWS_MINGW) || defined(PLATFORM_GCC)
+  // GCC _Pragma operator
+  #define SEQAN_DO_PRAGMA(x) _Pragma(# x)
+  #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x)
+#else  // #if defined(PLATFORM_WINDOWS_MINGW) || defined(PLATFORM_GCC)
+  // MSVC __pragma-operator
+  #define SEQAN_OMP_PRAGMA(x) __pragma(omp x)
+#endif // #if defined(PLATFORM_WINDOWS_MINGW) || defined(PLATFORM_GCC)
+
 #else  // #ifdef _OPENMP
-  #define SEQAN_OMP_PRAGMA(x)
 
-  // low-level OpenMP runtime compatibility
-  inline void omp_set_num_threads(int) {}
-  inline int  omp_get_num_threads()    { return 1; }
-  inline int  omp_get_max_threads()    { return 1; }
-  inline int  omp_get_thread_num()     { return 0; }
+#define SEQAN_OMP_PRAGMA(x)
+
+// low-level OpenMP runtime compatibility
+inline void omp_set_num_threads(int)
+{}
+
+inline int omp_get_num_threads()
+{
+    return 1;
+}
+
+inline int omp_get_max_threads()
+{
+    return 1;
+}
+
+inline int omp_get_thread_num()
+{
+    return 0;
+}
+
+inline double omp_get_wtime()
+{
+    return seqan::sysTime();
+}
 
 #endif  // #ifdef _OPENMP
 
@@ -121,12 +124,15 @@ i += 1;
 
 SEQAN_HOST_DEVICE inline unsigned getThreadId()
 {
-#ifdef _OPENMP
-    return omp_get_thread_num();
-#elif __CUDA_ARCH__
+#if defined(__CUDA_ARCH__)
     return blockIdx.x * blockDim.x + threadIdx.x;
+
+#elif defined(_OPENMP)
+    return omp_get_thread_num();
+
 #else
     return 0;
+
 #endif
 }
 
diff --git a/seqan/parallel/parallel_queue.h b/seqan/parallel/parallel_queue.h
new file mode 100644
index 0000000..7c88ddb
--- /dev/null
+++ b/seqan/parallel/parallel_queue.h
@@ -0,0 +1,803 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Thread-safe queue
+// ==========================================================================
+// This queue (almost) lock-free. It only uses spin-locks when the queue must
+// be resized or for blocking if the queue is full or empty.
+//
+// If the queue is often empty or full, the suspendable queue should be used.
+
+#ifndef SEQAN_PARALLEL_PARALLEL_QUEUE_H_
+#define SEQAN_PARALLEL_PARALLEL_QUEUE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class ConcurrentQueue
+// ----------------------------------------------------------------------------
+/*!
+ * @class ConcurrentQueue Concurrent Queue
+ * @headerfile <seqan/parallel.h>
+ * @brief Thread-safe queue for multiple producers and multiple consumers.
+ *
+ * @signature template <typename TValue, typename TSpec>
+ *            class ConcurrentQueue;
+ *
+ * @tparam TValue Element type of the queue.
+ * @tparam TSpec  Tag for further specializing the Concurrent Queue. Default is <tt>void</tt>.
+ *
+ * The Concurrent Queue is a thread-safe FIFO queue that supports multiple producers and multiple consumers (MPMC).
+ * Elements are enqueued via @link ConcurrentQueue#appendValue @endlink and dequeued with @link
+ * ConcurrentQueue#tryPopFront @endlink or @link ConcurrentQueue#popFront @endlink.
+ * Depending on the expansion tag of appendValue it can grow dynamically or have a fixed size.
+ *
+ * The implementation is lock-free and uses a @Class.AllocString@ as ring buffer.
+ *
+ * @section Examples
+ *
+ * Simple example for a single producer single consumer (SPSC) dynamic queue.
+ *
+ * @include demos/dox/parallel/queue_example.cpp
+ *
+ * The output is:
+ *
+ * @include demos/dox/parallel/queue_example.cpp.stdout
+ */
+
+template <typename TValue, typename TSpec = void>
+class ConcurrentQueue
+{
+public:
+    typedef typename Host<ConcurrentQueue>::Type                TString;
+    typedef typename Size<TString>::Type                        TSize;
+    typedef typename Atomic<TSize>::Type                        TAtomicSize;
+    typedef typename If<typename IsSameType<TSpec, Limit>::Type,
+                        Serial,
+                        typename DefaultParallelSpec<ConcurrentQueue>::Type
+                     >::Type                                    TLockTag;
+
+    TString                 data;
+    mutable ReadWriteLock   lock;           char pad1[SEQAN_CACHE_LINE_SIZE - sizeof(ReadWriteLock)];
+    size_t                  readerCount;
+    size_t                  writerCount;
+
+    TAtomicSize headPos;                    char pad4[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)];
+    TAtomicSize headReadPos;                char pad5[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)];
+    TAtomicSize tailPos;                    char pad6[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)];
+    TAtomicSize tailWritePos;               char pad7[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)];
+    TAtomicSize roundSize;                  char pad8[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)];
+    Atomic<bool>::Type virgin;              char pad9[SEQAN_CACHE_LINE_SIZE - sizeof(Atomic < bool > ::Type)];
+
+    ConcurrentQueue() :
+        readerCount(0),
+        writerCount(0),
+        headPos(0),
+        headReadPos(0),
+        tailPos(0),
+        tailWritePos(0),
+        roundSize(0),
+        virgin(true)
+    {}
+
+    // you can set the initial capacity here
+    explicit
+    ConcurrentQueue(TSize initCapacity) :
+        readerCount(0),
+        writerCount(0),
+        headPos(0),
+        headReadPos(0),
+        tailPos(0),
+        tailWritePos(0),
+        virgin(true)
+    {
+        reserve(data, initCapacity + 1, Exact());
+        roundSize = (TSize)1 << (log2(capacity(data) - 1) + 1);
+    }
+
+    explicit
+    ConcurrentQueue(TString & data) :
+        data(data),
+        readerCount(0),
+        writerCount(0),
+        headPos(0),
+        headReadPos(0),
+        tailPos(length(data)),
+        tailWritePos(length(data)),
+        virgin(true)
+    {
+        roundSize = (TSize)1 << (log2(capacity(data) - 1) + 1);
+    }
+
+    ~ConcurrentQueue()
+    {
+        SEQAN_ASSERT_EQ(tailPos, tailWritePos);
+        SEQAN_ASSERT_EQ(headPos, headReadPos);
+        SEQAN_ASSERT(empty(lock));
+        SEQAN_ASSERT_EQ(writerCount, 0u);
+
+        TSize mask = roundSize - 1;
+        headPos &= mask;
+        tailPos &= mask;
+
+        // wait for all pending readers to finish
+        while (readerCount != 0)
+        {}
+
+        typename Iterator<TString, Standard>::Type arrayBegin = begin(data, Standard());
+
+        if (headPos <= tailPos)
+        {
+            arrayDestruct(arrayBegin + headPos, arrayBegin + tailPos);
+        }
+        else
+        {
+            arrayDestruct(arrayBegin, arrayBegin + tailPos);
+            arrayDestruct(arrayBegin + headPos, arrayBegin + capacity(data));
+        }
+        _setLength(data, 0);
+    }
+
+private:
+    ConcurrentQueue(ConcurrentQueue const &);
+    void operator=(ConcurrentQueue const &);
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultParallelSpec
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+struct DefaultParallelSpec<ConcurrentQueue<TValue, Serial> >
+{
+    typedef Serial Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct Value<ConcurrentQueue<TValue, TSpec> >
+{
+    typedef TValue Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Host<ConcurrentQueue<TValue, TSpec> >
+{
+    typedef String<TValue> Type;
+};
+
+template <typename TValue, typename TSpec>
+struct Size<ConcurrentQueue<TValue, TSpec> >:
+    Size<Host<ConcurrentQueue<TValue, TSpec> > >
+{};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function lockReading() / unlockReading()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#lockReading
+ * @brief Register a reader.
+ *
+ * @signature void lockReading(queue);
+ *
+ * @param[in] queue The queue to register a reader at.
+ *
+ * The destructor of the queue will spinlock until all readers are deregistered.
+ */
+
+template <typename TValue, typename TSpec>
+inline void
+lockReading(ConcurrentQueue<TValue, TSpec> & me)
+{
+    atomicInc(me.readerCount);
+}
+
+/*!
+ * @fn ConcurrentQueue#unlockReading
+ * @brief Deregister a reader.
+ *
+ * @signature void unlockReading(queue);
+ *
+ * @param[in] queue The queue to deregister a reader from.
+ *
+ * The destructor of the queue will spinlock until all readers are deregistered.
+ */
+
+template <typename TValue, typename TSpec>
+inline void
+unlockReading(ConcurrentQueue<TValue, TSpec> & me)
+{
+    atomicDec(me.readerCount);
+}
+
+// ----------------------------------------------------------------------------
+// Function lockWriting() / unlockWriting()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#lockWriting
+ * @brief Register a writer.
+ *
+ * @signature void lockWriting(queue);
+ *
+ * @param[in] queue The queue to register a writer at.
+ *
+ */
+
+template <typename TValue, typename TSpec>
+inline void
+lockWriting(ConcurrentQueue<TValue, TSpec> & me)
+{
+    atomicInc(me.writerCount);
+}
+
+/*!
+ * @fn ConcurrentQueue#unlockWriting
+ * @brief Deregister a writer.
+ *
+ * @signature void unlockWriting(queue);
+ *
+ * @param[in] queue The queue to deregister a writer from.
+ *
+ */
+
+template <typename TValue, typename TSpec>
+inline void
+unlockWriting(ConcurrentQueue<TValue, TSpec> & me)
+{
+    atomicDec(me.writerCount);
+}
+
+// ----------------------------------------------------------------------------
+// Function _cyclicInc()
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+inline TValue
+_cyclicInc(TValue value, TValue modulo, TValue roundSize)
+{
+    // invariants:
+    //   - roundSize is a power of 2
+    //   - (value % roundSize) is in [0, modulo)
+    //
+    // return the next greater value that fulfills the invariants
+    if ((++value & (roundSize - 1)) >= modulo)
+        value += roundSize - modulo;
+    return value;
+}
+
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#empty
+ * @brief Returns whether a queue is empty.
+ *
+ * @signature bool empty(queue);
+ *
+ * @param[in] queue The queue to query.
+ *
+ * @return bool Whether or not the queue is empty.
+ */
+
+template <typename TValue, typename TSpec>
+inline bool
+empty(ConcurrentQueue<TValue, TSpec> const & me)
+{
+    typedef ConcurrentQueue<TValue, TSpec>  TQueue;
+    typedef typename TQueue::TLockTag       TLockTag;
+
+    ScopedWriteLock<ReadWriteLock, TLockTag> writeLock(me.lock);
+    return me.headPos == me.tailPos;
+}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#length
+ * @brief Returns the size of a queue.
+ *
+ * @signature TSize length(queue);
+ *
+ * @param[in] queue The queue to query for its size.
+ *
+ * @return TSize The number of elements in the queue.
+ */
+
+template <typename TValue, typename TSpec>
+inline typename Size<ConcurrentQueue<TValue, TSpec> >::Type
+length(ConcurrentQueue<TValue, TSpec> const & me)
+{
+    typedef ConcurrentQueue<TValue, TSpec>  TQueue;
+    typedef typename TQueue::TLockTag       TLockTag;
+    typedef typename Size<TQueue>::Type     TSize;
+
+    ScopedWriteLock<ReadWriteLock, TLockTag> writeLock(me.lock);
+    TSize mask = me.roundSize - 1;
+    if ((me.headPos & mask) <= (me.tailPos & mask))
+        return me.tailPos - me.headPos;
+    else
+        return me.tailPos - me.headPos - (me.roundSize - capacity(me.data));
+}
+
+// ----------------------------------------------------------------------------
+// Function capacity()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#capacity
+ * @brief Returns the capacity of a queue.
+ *
+ * @signature TSize capacity(queue);
+ *
+ * @param[in] queue The queue to query for its capacity.
+ *
+ * @return TSize Returns the capacity of the queue.
+ *
+ * The capacity is the number of elements that can be enqueued at the same time without reallocating memory.
+ */
+
+template <typename TValue, typename TSpec>
+inline typename Size<ConcurrentQueue<TValue, TSpec> >::Type
+capacity(ConcurrentQueue<TValue, TSpec> const & me)
+{
+    typedef ConcurrentQueue<TValue, TSpec>  TQueue;
+    typedef typename TQueue::TLockTag       TLockTag;
+
+    ScopedReadLock<ReadWriteLock, TLockTag> writeLock(me.lock);
+    return capacity(me.data) - 1;
+}
+
+// ----------------------------------------------------------------------------
+// Function tryPopFront()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#tryPopFront
+ * @headerfile <seqan/parallel.h>
+ * @brief Try to dequeue a value from a queue.
+ *
+ * @signature bool tryPopFront(result, queue[, parallelTag]);
+ *
+ *
+ * @param[in,out] queue       A queue.
+ * @param[out]    result      The dequeued value (if available).
+ * @param[in]     parallelTag The concurrency scheme. If multiple threads dequeue values concurrently this tag must be
+ *                            @link ParallelismTags#Parallel @endlink. The more efficient @link ParallelismTags#Serial
+ *                            @endlink tag can only be used if one thread calls <tt>popFront</tt> at a time.
+ *                            Default is @link ParallelismTags#Parallel @endlink.
+ * @return        bool        Returns <tt>true</tt> if a value could be dequeued and <tt>false</tt> otherwise.
+ */
+
+//
+//  [  ?  ]  [  4  ]  [  3  ]  [  8  ]  [  0  ]  [  x  ]  [  ?  ]
+//                       |                          ^
+//                       v                          |
+//             head            headRead   tail  tailWrite
+//
+// empty = (head == tail)
+// full = (tail + 1 == head)
+//
+// valid data between  [headRead, tail)
+// currently filled    [tail, tailWrite)
+// currently removed   [head, headRead)
+
+template <typename TValue2, typename TValue, typename TSpec, typename TParallel>
+inline bool
+tryPopFront(TValue2 & result, ConcurrentQueue<TValue, TSpec> & me, Tag<TParallel> parallelTag)
+{
+    typedef ConcurrentQueue<TValue, TSpec>              TQueue;
+    typedef typename TQueue::TLockTag                   TLockTag;
+    typedef typename Host<TQueue>::Type                 TString;
+    typedef typename Size<TString>::Type                TSize;
+    typedef typename Iterator<TString, Standard>::Type  TIter;
+
+    // try to extract a value
+    ScopedReadLock<ReadWriteLock, TLockTag> readLock(me.lock);
+
+    TSize cap = capacity(me.data);
+    TSize roundSize = me.roundSize;
+    TSize headReadPos;
+    TSize newHeadReadPos;
+    SpinDelay spinDelay;
+
+    // wait for queue to become filled
+    while (true)
+    {
+        headReadPos = me.headReadPos;
+        TSize tailPos = me.tailPos;
+
+        SEQAN_ASSERT_LEQ(headReadPos, tailPos);
+
+        // return if queue is empty
+        if (headReadPos == tailPos)
+            return false;
+
+        newHeadReadPos = _cyclicInc(headReadPos, cap, roundSize);
+
+        if (atomicCasBool(me.headReadPos, headReadPos, newHeadReadPos, parallelTag))
+            break;
+
+        waitFor(spinDelay);
+    }
+
+    // extract value and destruct it in the data string
+    TIter it = begin(me.data, Standard()) + (headReadPos & (roundSize - 1));
+    std::swap(result, *it);
+    valueDestruct(it);
+
+    // wait for pending previous reads and synchronize headPos to headReadPos
+    spinCas(me.headPos, headReadPos, newHeadReadPos);
+
+    return true;
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+tryPopFront(TValue & result, ConcurrentQueue<TValue, TSpec> & me)
+{
+    return tryPopFront(result, me, typename DefaultParallelSpec<ConcurrentQueue<TValue, TSpec> >::Type());
+}
+
+// ----------------------------------------------------------------------------
+// Function waitForWriters()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#waitForWriters
+ * @brief Wait for writers to register.
+ *
+ * @signature void waitForWriters(queue, writerCount);
+ *
+ * @param[in] queue       A queue.
+ * @param[in] writerCount The minimal required number of registered writers, see @link
+ *                        ConcurrentQueue#lockWriting @endlink.
+ *
+ * If the values are dequeued with @link ConcurrentQueue#popFront2 @endlink,
+ * this function is a barrier for all writers to set up completely and should be called before calling @link
+ * ConcurrentQueue#appendValue @endlink the first time.
+ */
+
+template <typename TValue, typename TSpec>
+inline void
+waitForWriters(ConcurrentQueue<TValue, TSpec> & me, unsigned writerCount)
+{
+    SpinDelay spinDelay;
+    while (me.writerCount < writerCount)
+    {
+        waitFor(spinDelay);
+    }
+    me.virgin = false;
+}
+
+/*!
+ * @fn ConcurrentQueue#waitForFirstValue
+ * @brief Wait for writers to enqueue the first value.
+ *
+ * @signature void waitForFirstValue(queue);
+ *
+ * @param[in] queue       A queue.
+ *
+ * If the values are dequeued with @link ConcurrentQueue#popFront2 @endlink,
+ * this function is a barrier for all readers to wait until all writers are set up completely and should be called
+ * before calling @link ConcurrentQueue#popFront2 @endlink the first time.
+ */
+
+template <typename TValue, typename TSpec>
+inline void
+waitForFirstValue(ConcurrentQueue<TValue, TSpec> & me)
+{
+    spinWhileEq(me.virgin, true);
+}
+
+// ----------------------------------------------------------------------------
+// Function popFront()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#popFront
+ * @headerfile <seqan/parallel.h>
+ * @brief Dequeue a value from a queue.
+ *
+ * @signature bool popFront(result, queue[, parallelTag]);
+ *
+ *
+ * @param[in,out] queue       A queue.
+ * @param[out]    result      The dequeued value. If the queue is empty but writers are available the thread spinlocks
+ *                            until a value becomes available.
+ * @param[in]     parallelTag The concurrency scheme. If multiple threads dequeue values concurrently this tag must be
+ *                            @link ParallelismTags#Parallel @endlink. The more efficient @link ParallelismTags#Serial
+ *                            @endlink tag can only be used if one thread calls <tt>popFront</tt> at a time.
+ *                            Default is @link ParallelismTags#Parallel @endlink.
+ * @return        bool        Returns <tt>true</tt> if a value could be dequeued or <tt>false</tt> if no writer is
+ *                            available, see @link ConcurrentQueue#waitForWriters @endlink.
+ */
+
+// returns if no writer is locked the queue and queue is empty
+template <typename TValue, typename TSpec, typename TParallel>
+inline bool
+popFront(TValue & result, ConcurrentQueue<TValue, TSpec> & me, Tag<TParallel> parallelTag)
+{
+    SpinDelay spinDelay;
+
+    while (me.writerCount != 0)
+    {
+        if (tryPopFront(result, me, parallelTag))
+            return true;
+        waitFor(spinDelay);
+    }
+    // we have to give it another try if the queue was empty inside the loop
+    // but after the check a writer pushes a value and zeroes the writerCount
+    return tryPopFront(result, me);
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+popFront(TValue & result, ConcurrentQueue<TValue, TSpec> & me)
+{
+    return popFront(result, me, typename DefaultParallelSpec<ConcurrentQueue<TValue, TSpec> >::Type());
+}
+
+/*!
+ * @fn ConcurrentQueue#popFront2
+ * @headerfile <seqan/parallel.h>
+ * @brief Dequeue a value from a queue.
+ *
+ * @signature TValue popFront(queue[, parallelTag]);
+ *
+ *
+ * @param[in,out] queue       A queue.
+ * @param[in]     parallelTag The concurrency scheme. If multiple threads dequeue values concurrently this tag must be
+ *                            @link ParallelismTags#Parallel @endlink. The more efficient @link ParallelismTags#Serial
+ *                            @endlink tag can only be used if one thread calls <tt>popFront</tt> at a time.
+ *                            Default is @link ParallelismTags#Parallel @endlink.
+ * @return        TValue      The dequeued value. If the queue is empty the thread spinlocks until a value becomes
+ *                            available.
+ */
+
+template <typename TValue, typename TSpec, typename TParallel>
+inline TValue SEQAN_FORWARD_RETURN
+popFront(ConcurrentQueue<TValue, TSpec> & me, Tag<TParallel> parallelTag)
+{
+    TValue result;
+    SpinDelay spinDelay;
+
+    while (!tryPopFront(result, me, parallelTag))
+    {
+        waitFor(spinDelay);
+    }
+    return SEQAN_MOVE(result);
+}
+
+template <typename TValue, typename TSpec>
+inline TValue SEQAN_FORWARD_RETURN
+popFront(ConcurrentQueue<TValue, TSpec> & me)
+{
+    return popFront(me, typename DefaultParallelSpec<ConcurrentQueue<TValue, TSpec> >::Type());
+}
+
+template <typename TValue, typename TSpec, typename TValue2>
+inline bool
+_queueOverflow(ConcurrentQueue<TValue, TSpec> & me, TValue2 SEQAN_FORWARD_CARG, Insist)
+{
+    ignoreUnusedVariableWarning(me);
+    SEQAN_ASSERT_GT(capacity(me.data), 1u);
+    return false;
+}
+
+template <typename TValue, typename TSpec, typename TValue2>
+inline bool
+_queueOverflow(ConcurrentQueue<TValue, TSpec> & me, TValue2 SEQAN_FORWARD_CARG, Limit)
+{
+    ignoreUnusedVariableWarning(me);
+    SEQAN_ASSERT_GT(capacity(me.data), 1u);
+    return false;
+}
+
+template <typename TValue, typename TSpec, typename TValue2, typename TExpand>
+inline bool
+_queueOverflow(ConcurrentQueue<TValue, TSpec> & me,
+               TValue2 SEQAN_FORWARD_CARG val,
+               Tag<TExpand> expandTag)
+{
+    typedef ConcurrentQueue<TValue, TSpec>                  TQueue;
+    typedef typename TQueue::TLockTag                       TLockTag;
+    typedef typename Host<TQueue>::Type                     TString;
+    typedef typename Size<TString>::Type                    TSize;
+    typedef typename Iterator<TString, Standard>::Type      TIter;
+
+    bool queueIsResizable = !IsSameType<TLockTag, Limit>::VALUE;
+    ignoreUnusedVariableWarning(queueIsResizable);
+    SEQAN_ASSERT(queueIsResizable);
+
+    // try to extend capacity
+
+    ScopedWriteLock<ReadWriteLock, TLockTag> writeLock(me.lock);
+    TSize cap = capacity(me.data);
+    TSize roundSize = me.roundSize;
+    TSize headPos = me.headPos;
+    TSize tailPos = me.tailPos;
+
+    SEQAN_ASSERT_EQ(tailPos, me.tailWritePos);
+    SEQAN_ASSERT_EQ(headPos, me.headReadPos);
+
+    bool valueWasAppended = false;
+
+    // did we reach the capacity limit (another thread could have done the upgrade already)?
+    if (_cyclicInc((TSize)tailPos, cap, roundSize) >= headPos + roundSize)
+    {
+        if (cap != 0)
+        {
+            TIter it = begin(me.data, Standard()) + (tailPos & (roundSize - 1));
+            valueConstruct(it, SEQAN_FORWARD(TValue2, val));
+            tailPos = headPos + roundSize;
+            valueWasAppended = true;
+        }
+
+        SEQAN_ASSERT_EQ(tailPos, headPos + roundSize);
+
+        // get positions of head/tail in current data sequence
+        TSize headIdx = headPos & (roundSize - 1);
+        TSize tailIdx = tailPos & (roundSize - 1);
+
+        // increase capacity
+        _setLength(me.data, cap);
+        reserve(me.data, cap + 1, expandTag);
+        TSize delta = capacity(me.data) - cap;
+        roundSize = (TSize)1 << (log2(capacity(me.data) - 1) + 1);
+
+        // create a gap of delta many values between tail and head
+        _clearSpace(me.data, delta, headIdx, headIdx, expandTag);
+        if (cap != 0)
+        {
+            me.headReadPos = me.headPos = headIdx + delta;
+            me.tailWritePos = me.tailPos = tailIdx + roundSize;
+        }
+        me.roundSize = roundSize;
+    }
+    return valueWasAppended;
+}
+
+// ----------------------------------------------------------------------------
+// Function appendValue()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn ConcurrentQueue#appendValue
+ * @headerfile <seqan/parallel.h>
+ * @brief Enqueue a value to a queue.
+ *
+ * @signature void appendValue(queue, val[, expandTag[, parallelTag]);
+ *
+ *
+ * @param[in,out] queue       A queue.
+ * @param[in]     val         The value to enqueue.
+ * @param[in]     expandTag   The overflow strategy. If @link OverflowStrategyTags#Generous @endlink the queue will be
+ *                            automatically resized if the capacity is exceeded, otherwise the thread spinlocks until
+ *                            the element can be enqueued.
+ *                            Default is the @link DefaultOverflowImplicit @endlink result for the <tt>queue</tt> type.
+ * @param[in]     parallelTag The concurrency scheme. If multiple threads enqueue values concurrently this tag must be
+ *                            @link ParallelismTags#Parallel @endlink. The more efficient @link ParallelismTags#Serial
+ *                            @endlink tag can only be used if one thread calls <tt>appendValue</tt> at a time.
+ *                            Default is @link ParallelismTags#Parallel @endlink.
+ */
+
+template <typename TValue, typename TSpec, typename TValue2, typename TExpand, typename TParallel>
+inline void
+appendValue(ConcurrentQueue<TValue, TSpec> & me,
+            TValue2 SEQAN_FORWARD_CARG val,
+            Tag<TExpand> expandTag,
+            Tag<TParallel> parallelTag)
+{
+    typedef ConcurrentQueue<TValue, TSpec>              TQueue;
+    typedef typename TQueue::TLockTag                   TLockTag;
+    typedef typename Host<TQueue>::Type                 TString;
+    typedef typename Size<TString>::Type                TSize;
+    typedef typename Iterator<TString, Standard>::Type  TIter;
+
+    SpinDelay spinDelay;
+
+    while (true)
+    {
+        // try to append the value
+        {
+            ScopedReadLock<ReadWriteLock, TLockTag> readLock(me.lock);
+            TSize cap = capacity(me.data);
+            TSize roundSize = me.roundSize;
+
+            while (true)
+            {
+                TSize tailWritePos = me.tailWritePos;
+                TSize newTailWritePos = _cyclicInc(tailWritePos, cap, roundSize);
+                TSize headPos = me.headPos;
+
+                SEQAN_ASSERT_LEQ(newTailWritePos, headPos + roundSize + 1);
+
+                // break if we have a wrap around, i.e. queue is full
+                if (newTailWritePos >= headPos + roundSize)
+                    break;
+
+                if (atomicCasBool(me.tailWritePos, tailWritePos, newTailWritePos, parallelTag))
+                {
+                    TIter it = begin(me.data, Standard()) + (tailWritePos & (roundSize - 1));
+                    valueConstruct(it, SEQAN_FORWARD(TValue2, val));
+
+                    // wait for pending previous writes and synchronize tailPos to tailWritePos
+                    spinCas(me.tailPos, tailWritePos, newTailWritePos);
+
+                    return;
+                }
+
+                waitFor(spinDelay);
+            }
+        }
+
+        // if possible extend capacity and return (spin loop otherwise)
+        if (_queueOverflow(me, SEQAN_FORWARD(TValue2, val), expandTag))
+            return;
+
+        waitFor(spinDelay);
+    }
+}
+
+template <typename TValue, typename TSpec, typename TValue2, typename TExpand>
+inline void
+appendValue(ConcurrentQueue<TValue, TSpec> & me,
+            TValue2 SEQAN_FORWARD_CARG val,
+            Tag<TExpand> expandTag)
+{
+    appendValue(me, SEQAN_FORWARD(TValue2, val), expandTag, typename DefaultParallelSpec<ConcurrentQueue<TValue, TSpec> >::Type());
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_PARALLEL_PARALLEL_QUEUE_H_
diff --git a/seqan/parallel/parallel_queue_suspendable.h b/seqan/parallel/parallel_queue_suspendable.h
new file mode 100644
index 0000000..cb2811e
--- /dev/null
+++ b/seqan/parallel/parallel_queue_suspendable.h
@@ -0,0 +1,458 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Thread-safe suspenable queue
+// ==========================================================================
+// This queue suspends the caller if it pops a value when the queue was empty
+// or appends a value to a full fixed-size queue.
+
+#ifndef SEQAN_PARALLEL_PARALLEL_QUEUE_SUSPENDABLE_H_
+#define SEQAN_PARALLEL_PARALLEL_QUEUE_SUSPENDABLE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+struct CriticalSection;
+struct Condition;
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class ConcurrentQueue
+// ----------------------------------------------------------------------------
+/*!
+ * @class ConcurrentSuspendableQueue Concurrent Suspendable Queue
+ * @extends ConcurrentQueue
+ * @headerfile <seqan/parallel.h>
+ * @brief Thread-safe suspendable queue for multiple producers and multiple consumers.
+ *
+ * @signature template <typename TValue, typename TSpec>
+ *            class ConcurrentQueue<TValue, Suspendable<TSpec> >;
+ *
+ * @tparam TValue Element type of the queue.
+ * @tparam TSpec  Tag for further specializing the Concurrent Queue. Default is <tt>void</tt>.
+ *
+ * In contrast to the standard @Class.ConcurrentQueue@ this queue suspends the caller
+ * if it pops a value when the queue was empty or appends a value to a full
+ * fixed-size queue.
+ *
+ * The implementation uses Mutexes and Events to optionally suspend the calling
+ * thread and uses a @Class.AllocString@ as ring buffer.
+ *
+ */
+
+template <typename TSpec = void>
+struct Suspendable;
+
+template <typename TValue, typename TSpec>
+class ConcurrentQueue<TValue, Suspendable<TSpec> >
+{
+public:
+    typedef typename Host<ConcurrentQueue>::Type    TString;
+    typedef typename Size<TString>::Type            TSize;
+
+    size_t          readerCount;
+    size_t          writerCount;
+
+    TString         data;
+    TSize           occupied;
+    TSize           back;
+    TSize           front;
+
+    CriticalSection cs;
+    Condition       more;
+
+    bool        virgin;
+
+    ConcurrentQueue():
+        readerCount(0),
+        writerCount(0),
+        occupied(0),
+        back(0),
+        front(0),
+        more(cs),
+        virgin(true)
+    {}
+
+    ~ConcurrentQueue()
+    {
+        SEQAN_ASSERT_EQ(writerCount, 0u);
+
+        // wait for all pending readers to finish
+        while (readerCount != 0u)
+        {}
+
+        typename Iterator<TString, Standard>::Type arrayBegin = begin(data, Standard());
+
+        if (occupied != 0)
+        {
+            if (front < back)
+            {
+                arrayDestruct(arrayBegin + front, arrayBegin + back);
+            }
+            else
+            {
+                arrayDestruct(arrayBegin, arrayBegin + back);
+                arrayDestruct(arrayBegin + front, arrayBegin + capacity(data));
+            }
+        }
+        _setLength(data, 0);
+    }
+};
+
+template <typename TValue>
+class ConcurrentQueue<TValue, Suspendable<Limit> >:
+    public ConcurrentQueue<TValue, Suspendable<> >
+{
+public:
+    typedef ConcurrentQueue<TValue, Suspendable<> > TBase;
+    typedef typename Host<ConcurrentQueue>::Type    TString;
+    typedef typename Size<TString>::Type            TSize;
+
+    Condition less;
+
+    ConcurrentQueue(TSize maxSize):
+        TBase(),
+        less(TBase::cs)
+    {
+        reserve(this->data, maxSize, Exact());
+        _setLength(this->data, maxSize);
+    }
+
+    ConcurrentQueue(ConcurrentQueue const & other):
+        TBase((TBase const &)other),
+        less(this->mutex)
+    {}
+};
+
+template <typename TValue>
+struct DefaultOverflowImplicit<ConcurrentQueue<TValue, Suspendable<Limit> > >
+{
+    typedef Limit Type;
+};
+
+template <typename TValue, typename TSpec>
+inline void
+lockReading(ConcurrentQueue<TValue, Suspendable<TSpec> > &)
+{}
+
+template <typename TValue, typename TSpec>
+inline void
+unlockReading(ConcurrentQueue<TValue, Suspendable<TSpec> > & me)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    if (--me.readerCount == 0u)
+        signal(me.less);
+}
+
+template <typename TValue, typename TSpec>
+inline void
+lockWriting(ConcurrentQueue<TValue, Suspendable<TSpec> > &)
+{}
+
+template <typename TValue, typename TSpec>
+inline void
+unlockWriting(ConcurrentQueue<TValue, Suspendable<TSpec> > & me)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    if (--me.writerCount == 0u)
+        signal(me.more);
+}
+
+template <typename TValue, typename TSize, typename TSpec>
+inline void
+setReaderCount(ConcurrentQueue<TValue, Suspendable<TSpec> > & me, TSize readerCount)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    me.readerCount = readerCount;
+}
+
+template <typename TValue, typename TSize, typename TSpec>
+inline void
+setWriterCount(ConcurrentQueue<TValue, Suspendable<TSpec> > & me, TSize writerCount)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    me.writerCount = writerCount;
+}
+
+template <typename TValue, typename TSize1, typename TSize2, typename TSpec>
+inline void
+setReaderWriterCount(ConcurrentQueue<TValue, Suspendable<TSpec> > & me, TSize1 readerCount, TSize2 writerCount)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    me.readerCount = readerCount;
+    me.writerCount = writerCount;
+}
+
+template <typename TValue, typename TSize, typename TSpec>
+inline bool
+waitForMinSize(ConcurrentQueue<TValue, Suspendable<TSpec> > & me,
+               TSize minSize)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    while (me.occupied < minSize && me.writerCount > 0u)
+        waitFor(me.more);
+    return me.occupied >= minSize;
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+empty(ConcurrentQueue<TValue, Suspendable<TSpec> > const & me)
+{
+    return me.occupied == 0;
+}
+
+template <typename TValue, typename TSpec>
+inline typename Size<ConcurrentQueue<TValue, Suspendable<TSpec> > >::Type
+length(ConcurrentQueue<TValue, Suspendable<TSpec> > const & me)
+{
+    return me.occupied;
+}
+
+
+template <typename TValue, typename TSpec>
+inline bool
+_popFront(TValue & result, ConcurrentQueue<TValue, Suspendable<TSpec> > & me)
+{
+    typedef ConcurrentQueue<TValue, Suspendable<TSpec> >    TQueue;
+    typedef typename Host<TQueue>::Type                     TString;
+    typedef typename Size<TString>::Type                    TSize;
+    typedef typename Iterator<TString, Standard>::Type      TIter;
+
+    TSize cap = capacity(me.data);
+
+    while (me.occupied == 0u && me.writerCount > 0u)
+        waitFor(me.more);
+
+    if (me.occupied == 0u)
+        return false;
+
+    SEQAN_ASSERT_NEQ(me.occupied, 0u);
+
+    // extract value and destruct it in the data string
+    TIter it = begin(me.data, Standard()) + me.front;
+    std::swap(result, *it);
+    valueDestruct(it);
+
+    me.front = (me.front + 1) % cap;
+    me.occupied--;
+
+    /* now: either me.occupied > 0 and me.nextout is the index
+       of the next occupied slot in the buffer, or
+       me.occupied == 0 and me.nextout is the index of the next
+       (empty) slot that will be filled by a producer (such as
+       me.nextout == me.nextin) */
+
+    return true;
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+_popBack(TValue & result, ConcurrentQueue<TValue, Suspendable<TSpec> > & me)
+{
+    typedef ConcurrentQueue<TValue, Suspendable<TSpec> >    TQueue;
+    typedef typename Host<TQueue>::Type                     TString;
+    typedef typename Size<TString>::Type                    TSize;
+    typedef typename Iterator<TString, Standard>::Type      TIter;
+
+    TSize cap = capacity(me.data);
+
+    while (me.occupied == 0u && me.writerCount > 0u)
+        waitFor(me.more);
+
+    if (me.occupied == 0u)
+        return false;
+
+    SEQAN_ASSERT_NEQ(me.occupied, 0u);
+
+    me.back = (me.back + cap - 1) % cap;
+
+    // extract value and destruct it in the data string
+    TIter it = begin(me.data, Standard()) + me.back;
+    std::swap(result, *it);
+    valueDestruct(it);
+
+    me.occupied--;
+
+    /* now: either me.occupied > 0 and me.nextout is the index
+       of the next occupied slot in the buffer, or
+       me.occupied == 0 and me.nextout is the index of the next
+       (empty) slot that will be filled by a producer (such as
+       me.nextout == me.nextin) */
+
+    return true;
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+popFront(TValue & result, ConcurrentQueue<TValue, Suspendable<TSpec> > & me)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    return _popFront(result, me);
+}
+
+template <typename TValue>
+inline bool
+popFront(TValue & result, ConcurrentQueue<TValue, Suspendable<Limit> > & me)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    if (_popFront(result, me))
+    {
+        signal(me.less);
+        return true;
+    }
+    return false;
+}
+
+template <typename TValue, typename TSpec>
+inline bool
+popBack(TValue & result, ConcurrentQueue<TValue, Suspendable<TSpec> > & me)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    return _popBack(result, me);
+}
+
+template <typename TValue>
+inline bool
+popBack(TValue & result, ConcurrentQueue<TValue, Suspendable<Limit> > & me)
+{
+    ScopedLock<CriticalSection> lock(me.cs);
+    if (_popBack(result, me))
+    {
+        signal(me.less);
+        return true;
+    }
+    return false;
+}
+
+
+template <typename TValue, typename TValue2, typename TSpec, typename TExpand>
+inline bool
+appendValue(ConcurrentQueue<TValue, Suspendable<TSpec> > & me,
+            TValue2 SEQAN_FORWARD_CARG val,
+            Tag<TExpand> expandTag)
+{
+    typedef ConcurrentQueue<TValue, Suspendable<TSpec> >    TQueue;
+    typedef typename Host<TQueue>::Type                     TString;
+    typedef typename Size<TString>::Type                    TSize;
+
+    ScopedLock<CriticalSection> lock(me.cs);
+    TSize cap = capacity(me.data);
+
+    if (me.occupied >= cap)
+    {
+        // increase capacity
+        _setLength(me.data, cap);
+        reserve(me.data, cap + 1, expandTag);
+        TSize delta = capacity(me.data) - cap;
+
+        // create a gap of delta many values between tail and head
+        _clearSpace(me.data, delta, me.back, me.back, expandTag);
+        if (me.occupied != 0 && me.back <= me.front)
+            me.front += delta;
+
+        cap += delta;
+    }
+
+    valueConstruct(begin(me.data, Standard()) + me.back, val);
+    me.back = (me.back + 1) % cap;
+
+    me.occupied++;
+
+    /* now: either me.occupied < BSIZE and me.nextin is the index
+       of the next empty slot in the buffer, or
+       me.occupied == BSIZE and me.nextin is the index of the
+       next (occupied) slot that will be emptied by a consumer
+       (such as me.nextin == me.nextout) */
+
+    signal(me.more);
+    return true;
+}
+
+template <typename TValue, typename TValue2, typename TSpec, typename TExpand>
+inline bool
+appendValue(ConcurrentQueue<TValue, Suspendable<Limit> > & me,
+            TValue2 SEQAN_FORWARD_CARG val,
+            Tag<TExpand> expandTag);
+
+template <typename TValue, typename TValue2>
+inline bool
+appendValue(ConcurrentQueue<TValue, Suspendable<Limit> > & me,
+            TValue2 SEQAN_FORWARD_CARG val,
+            Limit)
+{
+    typedef ConcurrentQueue<TValue, Suspendable<Limit> >    TQueue;
+    typedef typename Host<TQueue>::Type                     TString;
+    typedef typename Size<TString>::Type                    TSize;
+
+    ScopedLock<CriticalSection> lock(me.cs);
+    TSize cap = capacity(me.data);
+
+    while (me.occupied >= cap && me.readerCount > 0u)
+        waitFor(me.less);
+
+    if (me.occupied >= cap)
+        return false;
+
+    SEQAN_ASSERT_LT(me.occupied, cap);
+
+    valueConstruct(begin(me.data, Standard()) + me.back, val);
+    me.back = (me.back + 1) % cap;
+    me.occupied++;
+
+    /* now: either me.occupied < BSIZE and me.nextin is the index
+       of the next empty slot in the buffer, or
+       me.occupied == BSIZE and me.nextin is the index of the
+       next (occupied) slot that will be emptied by a consumer
+       (such as me.nextin == me.nextout) */
+
+    signal(me.more);
+    return true;
+}
+
+template <typename TValue, typename TValue2, typename TSpec>
+inline bool
+appendValue(ConcurrentQueue<TValue, Suspendable<TSpec> > & me,
+            TValue2 SEQAN_FORWARD_CARG val)
+{
+    return appendValue(me, val, typename DefaultOverflowImplicit<ConcurrentQueue<TValue, Suspendable<TSpec> > >::Type());
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_PARALLEL_PARALLEL_QUEUE_SUSPENDABLE_H_
diff --git a/seqan/parallel/parallel_resource_pool.h b/seqan/parallel/parallel_resource_pool.h
new file mode 100644
index 0000000..6bf03f1
--- /dev/null
+++ b/seqan/parallel/parallel_resource_pool.h
@@ -0,0 +1,114 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Pool for reusable items, e.g. buffer strings
+// ==========================================================================
+
+#ifndef SEQAN_PARALLEL_PARALLEL_RESOURCE_POOL_H_
+#define SEQAN_PARALLEL_PARALLEL_RESOURCE_POOL_H_
+
+namespace seqan {
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class ResourcePool
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+struct ResourcePool
+{
+    typedef ConcurrentQueue<TValue *, Suspendable<> >   TStack;
+    typedef typename Size<TStack>::Type                 TSize;
+
+    TStack recycled;
+
+    ResourcePool(TSize maxSize)
+    {
+        setWriterCount(recycled, 1);
+        for (; maxSize != 0; --maxSize)
+            appendValue(recycled, (TValue *)NULL);
+    }
+
+    ~ResourcePool()
+    {
+        unlockWriting(recycled);
+        TValue *ptr = NULL;
+        unsigned count = 0;
+        while (popBack(ptr, recycled))
+        {
+            if (ptr != NULL)
+                count++;
+            delete ptr;
+        }
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function aquireValue()
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+inline TValue *
+aquireValue(ResourcePool<TValue> & me)
+{
+    TValue *ptr = NULL;
+    if (!popBack(ptr, me.recycled))
+        return NULL;
+
+    if (ptr == NULL)
+        ptr = new TValue;
+
+    return ptr;
+}
+
+// ----------------------------------------------------------------------------
+// Function releaseValue()
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+inline void
+releaseValue(ResourcePool<TValue> & me, TValue *ptr)
+{
+    appendValue(me.recycled, ptr);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_PARALLEL_PARALLEL_RESOURCE_POOL_H_
diff --git a/seqan/parallel/parallel_sequence.h b/seqan/parallel/parallel_sequence.h
new file mode 100644
index 0000000..ab3d134
--- /dev/null
+++ b/seqan/parallel/parallel_sequence.h
@@ -0,0 +1,190 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Thread-safe / lock-free sequence operations.
+// ==========================================================================
+
+#ifndef SEQAN_PARALLEL_PARALLEL_SEQUENCE_H_
+#define SEQAN_PARALLEL_PARALLEL_SEQUENCE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class ConcurrentAppender
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec = void>
+struct ConcurrentAppender
+{
+    TString *       data_host;
+    ReadWriteLock   lock;
+
+    ConcurrentAppender() :
+        data_host()
+    {}
+
+    ConcurrentAppender(TString & string)
+    {
+        setHost(*this, string);
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+struct Value<ConcurrentAppender<TString, TSpec> > : Value<TString> {};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function host()
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+inline TString &
+host(ConcurrentAppender<TString, TSpec> & me)
+{
+    return *me.data_host;
+}
+
+template <typename TString, typename TSpec>
+inline TString const &
+host(ConcurrentAppender<TString, TSpec> const & me)
+{
+    return *me.data_host;
+}
+
+// ----------------------------------------------------------------------------
+// Function setHost()
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+inline void
+setHost(ConcurrentAppender<TString, TSpec> & me, TString & string)
+{
+    me.data_host = &string;
+}
+
+// ----------------------------------------------------------------------------
+// Function _incLength()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TParallel>
+inline typename Size<String<TValue, Alloc<TSpec> > >::Type
+_incLength(String<TValue, Alloc<TSpec> > & me, Tag<TParallel> const & tag)
+{
+    return atomicInc(me.data_end, tag) - begin(me, Standard());
+}
+
+// ----------------------------------------------------------------------------
+// Function _decLength()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TParallel>
+inline typename Size<String<TValue, Alloc<TSpec> > >::Type
+_decLength(String<TValue, Alloc<TSpec> > & me, Tag<TParallel> const & tag)
+{
+    return atomicDec(me.data_end, tag) - begin(me, Standard());
+}
+
+// ----------------------------------------------------------------------------
+// Function appendValue()
+// ----------------------------------------------------------------------------
+
+template <typename TTargetValue, typename TTargetSpec, typename TValue>
+inline void
+appendValue(String<TTargetValue, TTargetSpec> & me, TValue const & _value, Insist, Parallel)
+{
+    valueConstruct(begin(me, Standard()) + _incLength(me, Parallel()) - 1, _value);
+}
+
+template <typename TString, typename TSpec, typename TValue, typename TExpand, typename TParallel>
+inline void
+appendValue(ConcurrentAppender<TString, TSpec> & me,
+            TValue const & val,
+            Tag<TExpand> const & expandTag,
+            Tag<TParallel> const & parallelTag)
+{
+    appendValue(host(me), val, expandTag, parallelTag);
+}
+
+template <typename TString, typename TSpec, typename TValue, typename TExpand>
+inline void
+appendValue(ConcurrentAppender<TString, TSpec> & me,
+            TValue const & val,
+            Tag<TExpand> const & expandTag,
+            Parallel)
+{
+    typedef typename Size<TString>::Type TSize;
+
+    TString & string = host(me);
+
+    while (true)
+    {
+        // try to append the value
+        {
+            ScopedReadLock<> readLock(me.lock);
+            TSize newLen = _incLength(string, Parallel());
+            if (newLen <= capacity(string))
+            {
+                valueConstruct(begin(string, Standard()) + newLen - 1, val);
+                break;
+            }
+            _decLength(string, Parallel());
+        }
+
+        // try to extend capacity
+        {
+            ScopedWriteLock<> writeLock(me.lock);
+            TSize cap = capacity(string);
+            if (cap == length(string))
+                reserve(string, cap + 1, expandTag);
+        }
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_PARALLEL_PARALLEL_SEQUENCE_H_
diff --git a/seqan/parallel/parallel_serializer.h b/seqan/parallel/parallel_serializer.h
new file mode 100644
index 0000000..8b979d0
--- /dev/null
+++ b/seqan/parallel/parallel_serializer.h
@@ -0,0 +1,219 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Class to aquire items, process them in parallel and serialize them in the
+// order of acquirement.
+// ==========================================================================
+
+#ifndef SEQAN_PARALLEL_PARALLEL_SERIALIZER_H_
+#define SEQAN_PARALLEL_PARALLEL_SERIALIZER_H_
+
+namespace seqan {
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Struct SerializerItem
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+struct SerializerItem
+{
+    TValue          val;
+    SerializerItem  *next;
+    bool            ready;
+};
+
+// ----------------------------------------------------------------------------
+// Class Serializer
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TWorker>
+class Serializer
+{
+public:
+    typedef SerializerItem<TValue>          TItem;
+    typedef TItem *                         TItemPtr;
+    typedef ResourcePool<TItem>             TPool;
+    typedef typename Size<Serializer>::Type TSize;
+
+    CriticalSection     cs;
+    TWorker             worker;
+    TItemPtr            first;
+    TItemPtr            last;
+    TPool               pool;
+    bool                stop;
+
+    Serializer() :
+        first(NULL),
+        last(NULL),
+        stop(false)
+    {}
+
+    template <typename TArg>
+    explicit
+    Serializer(TArg &arg, TSize maxItems = 1024) :
+        worker(arg),
+        first(NULL),
+        last(NULL),
+        pool(maxItems),
+        stop(false)
+    {}
+
+    ~Serializer()
+    {
+        while (first != NULL)
+        {
+            TItemPtr item = first;
+            first = first->next;
+            delete item;
+        }
+    }
+
+    operator bool()
+    {
+        return !stop;
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TWorker>
+inline void
+clear(Serializer<TValue, TWorker> & me)
+{
+    me.stop = false;
+    while (me.first != NULL)
+    {
+        TValue *item = me.first;
+        me.first = me.first->next;
+        releaseValue(me.recycled, item);
+    }
+    me.last = NULL;
+}
+
+// ----------------------------------------------------------------------------
+// Function aquireValue()
+// ----------------------------------------------------------------------------
+
+// this function is not thread-safe as it would make
+// not much sense to order a stream by the random
+// order of executition behind a mutex
+template <typename TValue, typename TWorker>
+inline TValue *
+aquireValue(Serializer<TValue, TWorker> & me)
+{
+    typedef SerializerItem<TValue> TItem;
+
+    TItem *item = aquireValue(me.pool);
+    item->next = NULL;
+    item->ready = false;
+
+    // add item to the end of our linked list
+    {
+        ScopedLock<CriticalSection> lock(me.cs);
+        if (me.first == NULL)
+            me.first = item;
+        else
+            me.last->next = item;
+        me.last = item;
+    }
+    return &item->val;
+}
+
+// ----------------------------------------------------------------------------
+// Function releaseValue()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TWorker>
+inline bool
+releaseValue(Serializer<TValue, TWorker> & me, TValue *ptr)
+{
+    typedef SerializerItem<TValue> TItem;
+
+    TItem *item = reinterpret_cast<TItem *>(ptr);
+    SEQAN_ASSERT_NOT(item->ready);
+
+    // changing me.first or the ready flag must be done synchronized (me.mutex)
+    // the thread who changed me.first->ready to be true has to write it.
+
+    // change our ready flag and test if me.first->ready became true
+    {
+        ScopedLock<CriticalSection> lock(me.cs);
+        item->ready = true;
+        if (item != me.first)
+            return true;
+    }
+
+    // ok, if we are here it seems that we are responsible for writing the buffer
+
+    SEQAN_ASSERT(me.first != NULL);
+
+    bool success;
+    do
+    {
+        // process item
+        success = me.worker(item->val);
+
+        // remove item from linked list
+        {
+            ScopedLock<CriticalSection> lock(me.cs);
+            me.first = item->next;
+
+            // recycle released items
+            releaseValue(me.pool, item);
+
+            // can we leave?
+            item = me.first;
+            if (item == NULL || !item->ready)
+                return success;
+        }
+
+        // we continue to process the next buffer
+    }
+    while (success);
+
+    return false;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_PARALLEL_PARALLEL_SERIALIZER_H_
diff --git a/seqan/parallel/parallel_splitting.h b/seqan/parallel/parallel_splitting.h
old mode 100755
new mode 100644
index a4edb5a..65686db
--- a/seqan/parallel/parallel_splitting.h
+++ b/seqan/parallel/parallel_splitting.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,92 +47,48 @@ typedef Tag<Equidistant_> Equidistant;
  * @class Splitter
  * @headerfile <seqan/parallel.h>
  * @brief Splits an interval into subintervals.
- * 
+ *
  * @signature template <typename TValue, typename TSpec>
  *            class Splitter;
- * 
+ *
  * @tparam TValue Type of the interval boundaries.
  * @tparam TSpec  Tag to select the way the values are sampled.
- * 
+ *
  * This class divides an interval into the disjoint union of subintervals and enumerates its boundaries.  It can be used
  * to parallelize large for-loops that iterate over a contiguous range of elements.  The interval and the number of
  * subintervals can be set in the constructor @link Splitter::Splitter @endlink.  @link Splitter#length @endlink and
  * @link Splitter#resize @endlink can be used to retrieve or change the number of subintervals later.  In contrast to
  * other containers the Splitter allows to access one more element than its length would imply to allow to retrieve the
  * right boundary of each subinterval (see example code below).
- * 
+ *
  * @section Examples
- * 
+ *
  * Simple example for equidistant (default) splitting.
- * 
- * @include demos/parallel/splitter_example.cpp
+ *
+ * @include demos/dox/parallel/splitter_example.cpp
  *
  * The output is:
  *
- * @code
- * [10,14)
- * [14,17)
- * [17,20)
- * @endlink
+ * @include demos/dox/parallel/splitter_example.cpp.stdout
  */
 
 /*!
  * @fn Splitter::Splitter
  * @brief Constructor
- * 
+ *
  * @signature Splitter::Splitter(beginPos, endPos[, subintervalCount]);
  * @signature Splitter::Splitter(beginPos, endPos, parallelTag);
  *
- * @param beginPos         Left interval boundary.
- * @param endPos           Right interval boundary.
- * @param subintervalCount Number of subintervals.  @link Splitter#length @endlink and @link Splitter#resize @endlink
- *                         can be used to retrieve or change the number of subintervals later.  Default: The minimum of
- *                         interval size and the number of available threads (returned by
- *                         <tt>omp_get_max_threads()</tt>).
- * @param parallelTag      Tag to generically enable/disable parallelism.  If its type is <tt>Parallel</tt>, the
- *                         default number of subintervals is used.  If it is <tt>Serial</tt>, only one subinterval
- *                         is used.  This tag should be used to write generic parallel algorithms and to switch
- *                         between parallel and serial variants.
- */
-
-/**
-.Class.Splitter
-..cat:Parallelism
-..summary:Splits an interval into subintervals.
-..description:This class divides an interval into the disjoint union of subintervals and enumerates its boundaries.
-It can be used to parallelize large for-loops that iterate over a contiguous range of elements.
-The interval and the number of subintervals can be set in the constructor @Memfunc.Splitter#Splitter@.
-@Function.length@ and @Function.resize@ can be used to retrieve or change the number of subintervals later.
-In contrast to other containers the Splitter allows to access one more element than its length would imply to allow to retrieve the right boundary of each subinterval (see example code below).
-
-..signature:Splitter<TValue, TSpec>
-..param.TValue:Type of the interval boundaries.
-..param.TSpec:Tag to select the way the values are sampled.
-...default:Equidistant Splitter
-..example:
-...text:Simple example for equidistant (default) splitting.
-...file:demos/parallel/splitter_example.cpp
-...output:
-[10,14)
-[14,17)
-[17,20)
-..include:seqan/parallel.h
-
-.Memfunc.Splitter#Splitter
-..summary:Constructor
-..signature:Splitter(beginPos, endPos[, subintervalCount])
-..signature:Splitter(beginPos, endPos, parallelTag)
-..param.beginPos:Left interval boundary.
-..param.endPos:Right interval boundary.
-..param.subintervalCount:Number of subintervals.
-...default:The minimum of interval size and the number of available threads (returned by $omp_get_max_threads()$).
-...remarks:@Function.length@ and @Function.resize@ can be used to retrieve or change the number of subintervals later.
-..param.parallelTag:Tag to generically enable/disable parallelism. If its type is @Tag.Parallel@, the default number of subintervals is used.
-If it is @Tag.Serial@, only one subinterval is used.
-...type:Tag.Serial
-...type:Tag.Parallel
-...remarks:This tag should be used to write generic parallel algorithms and to switch between parallel and serial variants.
-..class:Class.Splitter
+ * @param[in] beginPos         Left interval boundary.
+ * @param[in] endPos           Right interval boundary.
+ * @param[in] subintervalCount Number of subintervals.  @link Splitter#length @endlink and @link Splitter#resize
+ *                             @endlink can be used to retrieve or change the number of subintervals later.
+ *                             Default: The minimum of interval size and the number of available threads (returned by
+ *                             <tt>omp_get_max_threads()</tt>).
+ * @param[in] parallelTag      Tag to generically enable/disable parallelism.  If its type is <tt>Parallel</tt>, the
+ *                             default number of subintervals is used.  If it is <tt>Serial</tt>, only one subinterval
+ *                             is used.  This tag should be used to write generic parallel algorithms and to switch
+ *                             between parallel and serial variants.
  */
 
 /*!
@@ -140,20 +96,20 @@ If it is @Tag.Serial@, only one subinterval is used.
  * @extends Splitter
  * @headerfile <seqan/parallel.h>
  * @brief Splits an interval into equal-sized subintervals.
- * 
+ *
  * @signature template <typename TValue>
  *            class Splitter<TValue, Equidistant>;
- * 
+ *
  * @tparam TValue Type of the interval boundaries.
- * 
+ *
  * This @link Splitter @endlink specialization divides an interval into subintervals of (almost) equal length, i.e. two
  * subintervals differ by at most 1 in size.
- * 
+ *
  * @section Examples
- * 
+ *
  * Simple example for equidistant splitting.
- * 
- * @include demos/parallel/splitter_example.cpp
+ *
+ * @include demos/dox/parallel/splitter_example.cpp
  *
  * Output:
  *
@@ -164,24 +120,7 @@ If it is @Tag.Serial@, only one subinterval is used.
  * @endcode
  */
 
-/**
-.Spec.Equidistant Splitter
-..cat:Parallelism
-..general:Class.Splitter
-..summary:Splits an interval into equal-sized subintervals.
-..signature:Splitter<TValue[, Equidistant]>
-..description:This @Class.Splitter@ specialization divides an interval into subintervals of (almost) equal length, i.e.
-two subintervals differ by at most 1 in size.
-..param.TValue:Type of the interval boundaries.
-..example:
-...text:Simple example for equidistant splitting.
-...file:demos/parallel/splitter_example.cpp
-...output:
-[10,14)
-[14,17)
-[17,20)
-..include:seqan/parallel.h */
- 
+
 template <typename TValue, typename TSpec = Equidistant>
 class Splitter
 {
@@ -213,7 +152,7 @@ class Splitter
         // we produce at most 1 job (or none if interval is empty)
         _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)1));
     }
-    
+
     Splitter(TValue beginPos_, TValue endPos, TSize subintervalCount):
         beginPos(beginPos_)
     {
@@ -236,7 +175,6 @@ class Splitter
  * @tparam TSplitter The Splitter to query for its size type.
  */
 
-///.Metafunction.Size.param.T.type:Class.Splitter
 template <typename TValue, typename TSpec>
 struct Size<Splitter<TValue, TSpec> >
 {
@@ -252,7 +190,6 @@ struct Size<Splitter<TValue, TSpec> >
  * @tparam TSplitter The Splitter to query for its value type.
  */
 
-///.Metafunction.Value.param.T.type:Class.Splitter
 template <typename TValue, typename TSpec>
 struct Value<Splitter<TValue, TSpec> >
 {
@@ -270,8 +207,6 @@ struct Value<Splitter<TValue, TSpec> >
  * @return TSize The number of elements in the Splitter, <tt>TSize</tt> is the size type.
  */
 
-///.Function.length.param.object.type:Class.Splitter
-///.Function.length.class:Class.Splitter
 template <typename TValue, typename TSpec>
 inline typename Size<Splitter<TValue, TSpec> >::Type
 length(Splitter<TValue, TSpec> const &splitter)
@@ -306,8 +241,6 @@ _resize(Splitter<TValue, TSpec> &splitter, TSize1 intervalLen, TSize2 newCount)
     splitter.subintervalCount = newCount;
 }
 
-///.Function.resize.param.object.type:Class.Splitter
-///.Function.resize.class:Class.Splitter
 template <typename TValue, typename TSpec, typename TSize>
 inline typename Size<Splitter<TValue, TSpec> >::Type
 resize(Splitter<TValue, TSpec> &splitter, TSize newCount)
@@ -324,23 +257,23 @@ resize(Splitter<TValue, TSpec> &splitter, TSize newCount)
  * @fn computeSplitters
  * @headerfile <seqan/parallel.h>
  * @brief Compute splitters for a sequence of objects.
- * 
+ *
  * @signature void computeSplitters(splitters, size, count);
- * 
+ *
  * @param[out] splitters Resulting splitters, will be resized to contain <tt>count + 1</tt> elements, e.g. an
  *                       @link AllocString @endlink of integers.
  * @param[in]  size     The number of objects to split.
  * @param[in]  count     The number of chunks.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The first <tt>count - 1</tt> chunks will have the size <tt>ceil(size / count)</tt>, the last chunk will contain the
  * rest.
- * 
+ *
  * @section Examples
- * 
+ *
  * Most simple case for splitting.
- * 
+ *
  * @code{.cpp}
  * String<unsigned> splitters;
  * computeSplitters(splitters, 10, 5);
@@ -348,33 +281,13 @@ resize(Splitter<TValue, TSpec> &splitter, TSize newCount)
  * @endcode
  *
  * In this case, the last chunks will stay empty.
- * 
+ *
  * @code{.cpp}
  * computeSplitters(splitters, 3, 5);
  * // splitters == {0, 1, 2, 3, 3, 3}
  * @endcode
  */
 
-/**
-.Function.computeSplitters
-..cat:Parallelism
-..summary:Compute splitters for a sequence of objects.
-..signature:computeSplitters(splitters, size, count)
-..param.splitters:Resulting splitters, will be resized to contain $count + 1$ elements.
-...type:Spec.Alloc String
-..param.size:The number of objects to split.
-..param.count:The number of chunks.
-..remarks:The first $count - 1$ chunks will have the size $ceil(size / count)$, the last chunk will contain the rest.
-..example.text:Most simple case for splitting.
-..example.code:String<unsigned> splitters;
-computeSplitters(splitters, 10, 5);
-// splitters == {0, 5, 10}
-..example.text:In this case, the last chunks will stay empty.
-..example.code:computeSplitters(splitters, 3, 5);
-// splitters == {0, 1, 2, 3, 3, 3}
-..include:seqan/parallel.h
- */
-
 template <typename TPosString, typename TSize, typename TCount>
 void computeSplitters(TPosString & splitters, TSize size, TCount count)
 {
diff --git a/seqan/parallel/parallel_tags.h b/seqan/parallel/parallel_tags.h
index 4131f54..1477520 100644
--- a/seqan/parallel/parallel_tags.h
+++ b/seqan/parallel/parallel_tags.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -64,17 +64,23 @@ namespace seqan {
  * @brief Tag to select the serial implementation of an algorithm.
  */
 
-/**
-.Tag.Parallel:
-..cat:Parallelism
-..summary:Tag to select a parallel implementation of an algorithm.
-..tag.Parallel:Select serial implementation of an algorithm.
-..include:seqan/parallel.h
-*/
-
 struct Parallel_;
 typedef Tag<Parallel_> Parallel;
 
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultParallelSpec
+// ----------------------------------------------------------------------------
+
+template <typename TObject>
+struct DefaultParallelSpec
+{
+    typedef Parallel Type;
+};
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_PARALLEL_PARALLEL_TAGS_H_
diff --git a/seqan/parse_lm.h b/seqan/parse_lm.h
new file mode 100644
index 0000000..4052ab2
--- /dev/null
+++ b/seqan/parse_lm.h
@@ -0,0 +1,60 @@
+// ==========================================================================
+//                                  parse_lm
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for module parse_lm.
+// ==========================================================================
+
+#ifndef SANDBOX_HOLTGREW_INCLUDE_SEQAN_PARSE_LM_H_
+#define SANDBOX_HOLTGREW_INCLUDE_SEQAN_PARSE_LM_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/basic.h>
+#include <seqan/file.h>
+#include <seqan/sequence.h>
+#include <seqan/store.h>
+#include <seqan/stream.h>
+
+// ===========================================================================
+// First Header Group.
+// ===========================================================================
+
+#include <seqan/parse_lm/local_match_store.h>
+
+#include <seqan/parse_lm/parse_blastn_tabular.h>
+#include <seqan/parse_lm/parse_lastz_general.h>
+#include <seqan/parse_lm/parse_stellar_gff.h>
+
+#endif  // SANDBOX_HOLTGREW_INCLUDE_SEQAN_PARSE_LM_H_
diff --git a/seqan/parse_lm/local_match_store.h b/seqan/parse_lm/local_match_store.h
new file mode 100644
index 0000000..17747cd
--- /dev/null
+++ b/seqan/parse_lm/local_match_store.h
@@ -0,0 +1,418 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+// TODO(holtgrew): Allow the storage of additional fields.
+/* This could look as follows:
+
+   The values of the additional fields are stored as strings.  Either we store name/value pairs or, more efficiently,
+   store a stringset for each match, with the same number of entries.  An additional String/Map maps from field name to
+   index in this string sets.
+ */
+
+#ifndef INCLUDE_SEQAN_PARSE_LM_LOCAL_MATCH_STORE_H_
+#define INCLUDE_SEQAN_PARSE_LM_LOCAL_MATCH_STORE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+/*!
+ * @class LocalMatch
+ * @headerfile <seqan/parse_lm.h>
+ * @brief Stores information about local matches.
+ *
+ * @signature template <typename TId, typename TPosition>
+ *            class LocalMatch;
+ *
+ * @tparam TId       Type to use for subject/query id.
+ * @tparam TPosition Type to use for storing positions.
+ *
+ * Matches on the reverse-complement are encoded by the begin position being greater than the end position.
+ *
+ * Sequence names are not stored in LocalMatch objects but in the @link LocalMatchStore @endlink they belong to.
+ *
+ * @see LocalMatchStore
+ *
+ *
+ * @var TId LocalMatch::queryId
+ * @brief The id of the query.
+ *
+ * @var TPosition LocalMatch::queryBeginPos
+ * @brief Begin position of local match in the query.
+ *
+ * @var TPosition LocalMatch::queryEndPos
+ * @brief End position of local match in the query.
+ *
+ * @var TPosition LocalMatch::subjectBeginPos
+ * @brief Begin position of local match in the subject.
+ *
+ * @var TPosition LocalMatch::subjectEndPos
+ * @brief End position of local match in the subject.
+ *
+ * @var TId LocalMatch::subjectId
+ * @brief The id of the subject.
+ */
+
+template <typename TId, typename TPosition>
+class LocalMatch
+{
+public:
+    TId id;
+    TId subjectId;
+    TPosition subjectBeginPos;
+    TPosition subjectEndPos;
+    TId queryId;
+    TPosition queryBeginPos;
+    TPosition queryEndPos;
+
+    LocalMatch() :
+            id(MaxValue<TId>::VALUE),
+            subjectId(MaxValue<TId>::VALUE),
+            subjectBeginPos(MaxValue<TPosition>::VALUE),
+            subjectEndPos(MaxValue<TPosition>::VALUE),
+            queryId(MaxValue<TId>::VALUE),
+            queryBeginPos(MaxValue<TPosition>::VALUE),
+            queryEndPos(MaxValue<TPosition>::VALUE)
+    {}
+
+    LocalMatch(TId id_,
+               TId subjectId_,
+               TPosition subjectBeginPos_,
+               TPosition subjectEndPos_,
+               TId queryId_,
+               TPosition queryBeginPos_,
+               TPosition queryEndPos_) :
+            id(id_),
+            subjectId(subjectId_),
+            subjectBeginPos(subjectBeginPos_),
+            subjectEndPos(subjectEndPos_),
+            queryId(queryId_),
+            queryBeginPos(queryBeginPos_),
+            queryEndPos(queryEndPos_)
+    {}
+
+    bool operator==(LocalMatch const & other) const
+    {
+        return id == other.id && subjectId == other.subjectId && subjectBeginPos == other.subjectBeginPos &&
+                subjectEndPos == other.subjectEndPos && queryId == other.queryId &&
+                queryBeginPos == other.queryBeginPos && queryEndPos == other.queryEndPos;
+    }
+};
+
+/*!
+ * @class LocalMatchStoreConfig
+ * @headerfile <seqan/parse_lm.h>
+ * @brief Stores information about local matches.
+ *
+ * @signature template <typename TSpec>
+ *            struct LocalMatchStoreConfig;
+ *
+ * @tparam TSpec Specializing type.
+ *
+ *
+ * @typedef LocalMatchStoreConfig::TId;
+ * @brief Type to use for ids.
+ * @signature typedef unsigned LocalMatchStoreConfig::TId;
+ *
+ * @typedef LocalMatchStoreConfig::TPosition;
+ * @brief The type to use for positions.
+ * @signature typedef (...) LocalMatchStoreConfig::TPosition;
+ */
+
+template <typename TSpec>
+struct LocalMatchStoreConfig
+{
+    typedef unsigned TId;
+    typedef typename Position<Dna5String>::Type TPosition;
+};
+
+/*!
+ * @class LocalMatchStore
+ * @headerfile <seqan/parse_lm.h>
+ * @brief Stores information about local matches.
+ *
+ * @signature template <typename TSpec = void, TConfig = LocalMatchStoreConfig<TSpec> >
+ *            struct LocalMatchStore;
+ *
+ * @tparam TSpec   Specialization tag.
+ * @tparam TConfig Configuration class.
+ *
+ * The LocalMatchStore provides information about matches.  Similar to the @link FragmentStore @endlink, the
+ * information is split into multiple sub stores.  Each sub store stores a part of the information.
+ *
+ * The LocalMatchStore#matchStore stores the information about a match.  The LocalMatchStore#sequenceNameStore stores
+ * the sequence names.  These both sub stores are "core stores", they are filled with consistent information, i.e. for
+ * each sequence id in the matchStore, there has to be a valid entry in the sequenceNameStore.
+ *
+ * The LocalMatchStore#cigarStore optionally stores CIGAR strings for the matches.  Its entries are referenced by
+ * <tt>matchStore[i].id</tt>.
+ *
+ * @section Examples
+ *
+ * Read Lastz matches from a link RecordReader and then print them to stdout.
+ *
+ * @code{.cpp}
+ * // Read local alignments from record reader.  Note that in real-world code,
+ * // you should have error handling.
+ * LocalMatchStore<> lmStore;
+ * while (!atEnd(recordReader))
+ *     readRecord(lmStore, recordReader, StellarGff());
+ *
+ * // Print local alignment information to stdout.
+ * std::cout << "# Reverse strandness is indicated by end < begin\n"
+ *           << "#db\tdb_beg\tdb_end\tquery\tq_beg\tq_end\n";
+ * for (unsigned i = 0; i < length(lmStore.matchStore); ++i)
+ *     std::cout << lmStore.sequenceNameStore[lmStore.matchStore[i].queryId] << "\t"
+ *               << lmStore.matchStore[i].queryBeginPos << "\t"
+ *               << lmStore.matchStore[i].queryEndPos << "\t"
+ *               << lmStore.sequenceNameStore[lmStore.matchStore[i].subjectId] << "\t"
+ *               << lmStore.matchStore[i].subjectBeginPos << "\t"
+ *               << lmStore.matchStore[i].subjectEndPos << "\n";
+ * @endcode
+ * @see LocalMatch
+ *
+ * @var TMatchStore LocalMatchStore::matchStore
+ * @brief String storing the LocalMatch local matches.
+ *
+ * @var TStringSet LocalMatchStore::sequenceNameStore
+ * @brief StringSet storing the sequence names.
+ *
+ * @var TCigarString LocalMatchStore::cigarStore
+ * @brief String storing the CIGAR strings.
+ */
+
+/*!
+ * @fn LocalMatchStore#readRecord
+ *
+ * @headerfile <seqan/parse_lm.h>
+ *
+ * @brief Read Lastz "general" format record.
+ *
+ * @signature int readRecord(store, reader, tag);
+ *
+ * @param[in,out] store  LocalMatchStore object to read into.
+ * @param[in,out] stream SinglePassRecordReader to read from.
+ * @param[in]     tag    The tag for selecting the format, one of BlastnTabular, LastzGeneral, and StellarGff.
+ *
+ * @return int 0 on success, non-0 on errors and EOF
+ */
+
+template <typename TSpec=void, typename TConfig=LocalMatchStoreConfig<TSpec> >
+class LocalMatchStore
+{
+public:
+    // ----------------------------------------------------------------------------
+    // Typedefs
+    // ----------------------------------------------------------------------------
+
+    typedef typename TConfig::TId TId;
+    typedef typename TConfig::TPosition TPosition;
+
+    typedef LocalMatch<TId, TPosition> TLocalMatch;
+    typedef String<TLocalMatch> TMatchStore;
+
+    typedef String<CigarElement<> > TCigarString;
+    typedef String<TCigarString> TCigarStore;
+
+    typedef StringSet<CharString> TNameStore;
+    typedef NameStoreCache<TNameStore> TNameStoreCache_;
+
+    // ----------------------------------------------------------------------------
+    // Member Variables
+    // ----------------------------------------------------------------------------
+
+    TNameStore       sequenceNameStore;
+    TNameStoreCache_ _sequenceNameStoreCache;
+
+    TMatchStore       matchStore;
+    TCigarStore       cigarStore;
+
+    LocalMatchStore() :
+            _sequenceNameStoreCache(sequenceNameStore)
+    {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function registerSequenceName
+// ----------------------------------------------------------------------------
+
+template <typename TLocalMatchStore>
+inline void
+registerSequenceName(TLocalMatchStore & store,
+                     CharString const & sequenceName)
+{
+    unsigned id = 0;
+    if (!getIdByName(store.sequenceNameStore, sequenceName, id, store._sequenceNameStoreCache))
+    {
+        id = length(store.sequenceNameStore);
+        appendName(store.sequenceNameStore, sequenceName, store._sequenceNameStoreCache);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function appendLocalMatch
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn LocalMatchStore#appendLocalMatch
+ * @brief Append a new local match to a @link LocalMatchStore @endlink
+ *
+ * @signature void appendLocalMatchStore(store, subjectId, subjectBeginPos, subjectEndPos, queryId, queryBeginPos, queryEndPos);
+ * @signature void appendLocalMatchStore(store, subjectName, subjectBeginPos, subjectEndPos, queryName, queryBeginPos, queryEndPos, cigarStringBuffer);
+ *
+ * @param[in,out] store             The LocalMatchStore to add the local match to.
+ * @param[in]     subjectId         Numeric subject sequence identifier, @link IntegerConcept @endlink.
+ * @param[in]     subjectName       The textual name of the query sequence, @link CharString @endlink.
+ * @param[in]     subjectBegin      The begin position of the match in the subject, @link IntegerConcept @endlink.
+ * @param[in]     subjectEnd        The end position of the match in the subject, @link IntegerConcept @endlink.
+ * @param[in]     queryId           Numeric query sequence identifier, @link IntegerConcept @endlink.
+ * @param[in]     queryName         The textual name of the query sequence, @link CharString @endlink.
+ * @param[in]     queryBegin        The begin position of the match in the query, @link IntegerConcept @endlink.
+ * @param[in]     queryEnd          The end position of the match in the query, @link IntegerConcept @endlink.
+ * @param[in]     cigarStringBuffer Buffer with the cigar string of the local alignment,  @link CharString @endlink.
+ *
+ * Matches on the reverse-complement are encoded by the begin position being greater than the begin position.
+ */
+
+template <typename TLocalMatchStore, typename TPosition>
+inline void
+appendLocalMatch(TLocalMatchStore & store,
+                 unsigned const & subjectId,
+                 TPosition const subjectBeginPos,
+                 TPosition const subjectEndPos,
+                 unsigned const & queryId,
+                 TPosition const queryBeginPos,
+                 TPosition const queryEndPos)
+{
+    typedef typename TLocalMatchStore::TLocalMatch TLocalMatch;
+
+    SEQAN_ASSERT_LT(subjectId, length(store.sequenceNameStore));
+    SEQAN_ASSERT_LT(queryId, length(store.sequenceNameStore));
+
+    TLocalMatch localMatch(length(store.matchStore),
+                           subjectId,
+                           subjectBeginPos,
+                           subjectEndPos,
+                           queryId,
+                           queryBeginPos,
+                           queryEndPos);
+    appendValue(store.matchStore, localMatch);
+}
+
+template <typename TLocalMatchStore, typename TPosition>
+inline void
+appendLocalMatch(TLocalMatchStore & store,
+                 CharString const & subjectName,
+                 TPosition const subjectBeginPos,
+                 TPosition const subjectEndPos,
+                 CharString const & queryName,
+                 TPosition const queryBeginPos,
+                 TPosition const queryEndPos)
+{
+    typedef typename TLocalMatchStore::TId         TId;
+
+    // Get id for subject and query sequences;  Insert sequences into name stores/caches if not already there.
+    TId subjectId = 0;
+    if (!getIdByName(store.sequenceNameStore, subjectName, subjectId, store._sequenceNameStoreCache))
+    {
+        subjectId = length(store.sequenceNameStore);
+        appendName(store.sequenceNameStore, subjectName, store._sequenceNameStoreCache);
+    }
+    TId queryId = 0;
+    if (!getIdByName(store.sequenceNameStore, queryName, queryId, store._sequenceNameStoreCache))
+    {
+        queryId = length(store.sequenceNameStore);
+        appendName(store.sequenceNameStore, queryName, store._sequenceNameStoreCache);
+    }
+
+    appendLocalMatch(store, subjectId, subjectBeginPos, subjectEndPos, queryId, queryBeginPos, queryEndPos);
+}
+
+template <typename TLocalMatchStore, typename TPosition>
+inline void
+appendLocalMatch(TLocalMatchStore & store,
+                 CharString const & subjectName,
+                 TPosition const subjectBeginPos,
+                 TPosition const subjectEndPos,
+                 CharString const & queryName,
+                 TPosition const queryBeginPos,
+                 TPosition const queryEndPos,
+                 CharString const & cigarStringBuffer)
+{
+    // Append local match.
+    appendLocalMatch(store, subjectName, subjectBeginPos, subjectEndPos, queryName, queryBeginPos, queryEndPos);
+    // Make space for CIGAR string.
+    resize(store.cigarStore, back(store.matchStore).id + 1);
+    // TODO(holtgrew): Something can go wrong when parsing CIGAR string, need return value?
+    // Parse out cigar string.
+    /*
+    typedef Stream<CharArray<char const *> > TCharArrayStream;
+    TCharArrayStream cigarStream(&cigarStringBuffer[0], &cigarStringBuffer[0] + length(cigarStringBuffer));
+    RecordReader<TCharArrayStream, SinglePass<> > recordReader(cigarStream);
+    */
+    DirectionIterator<CharString const, Input>::Type iter = begin(cigarStringBuffer);
+    CharString numBuf;
+    while (!atEnd(iter))
+    {
+        // Get number string into buffer.
+        clear(numBuf);
+        readUntil(numBuf, iter, NotFunctor<IsDigit>());
+        unsigned num = 0;
+        lexicalCast<unsigned>(num, numBuf);
+
+        // Read operation char and advance record reader.
+        char op;
+        readOne(op, iter);
+        // Append CIGAR element to CIGAR string.
+        appendValue(back(store.cigarStore), CigarElement<>(op, num));
+    }
+}
+
+}  // namespace seqan
+
+#endif  // INCLUDE_SEQAN_PARSE_LM_LOCAL_MATCH_STORE_H_
diff --git a/seqan/parse_lm/parse_blastn_tabular.h b/seqan/parse_lm/parse_blastn_tabular.h
new file mode 100644
index 0000000..45e4339
--- /dev/null
+++ b/seqan/parse_lm/parse_blastn_tabular.h
@@ -0,0 +1,184 @@
+// ==========================================================================
+//                                  parse_lm
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+// SEQAN_NO_GENERATED_FORWARDS
+
+#ifndef INCLUDE_SEQAN_PARSE_LM_PARSE_BLASTN_TABULAR_H_
+#define INCLUDE_SEQAN_PARSE_LM_PARSE_BLASTN_TABULAR_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct BlastnTabular_;
+typedef Tag<BlastnTabular_> BlastnTabular;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord()
+// ----------------------------------------------------------------------------
+
+template <typename TLocalMatchStore, typename TForwardIter>
+inline void
+readRecord(TLocalMatchStore & store,
+           TForwardIter & iter,
+           BlastnTabular const & /*tag*/)
+{
+    typedef typename TLocalMatchStore::TPosition TPosition;
+
+    if (atEnd(iter))
+    {
+        throw ParseError("Unexpected end of file!");
+        return;
+    }
+
+    // Skip any comments.
+    while (value(iter) == '#') {
+        skipLine(iter);
+        if (atEnd(iter))
+        {
+            throw ParseError("Unexpected end of file!");
+            return;
+        }
+    }
+
+    SEQAN_ASSERT_NEQ(value(iter), '#');
+
+    // Read line.
+    CharString buffer;
+
+    CharString subjectName;
+    CharString queryName;
+    TPosition subjectBeginPos = 0;
+    TPosition subjectEndPos = 0;
+    TPosition queryBeginPos = 0;
+    TPosition queryEndPos = 0;
+
+    // Field: query id
+    readUntil(queryName, iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: subject id
+    readUntil(subjectName, iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: % identity
+    skipUntil(iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: alignment length
+    skipUntil(iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: mismatches
+    skipUntil(iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: gap opens
+    skipUntil(iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: q. start
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    queryBeginPos = lexicalCast<TPosition>(buffer) - 1;
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: q. end
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    queryEndPos = lexicalCast<TPosition>(buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: s. start
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    subjectBeginPos = lexicalCast<TPosition>(buffer) - 1;
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: s. end
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    subjectEndPos = lexicalCast<TPosition>(buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: evalue
+    skipUntil(iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: bit score
+    skipUntil(iter, IsWhitespace());
+
+    // Finally, append the local match.
+    appendLocalMatch(store, subjectName, subjectBeginPos, subjectEndPos, queryName, queryBeginPos, queryEndPos);
+}
+
+}  // namespace seqan
+
+#endif  // INCLUDE_SEQAN_PARSE_LM_PARSE_BLASTN_TABULAR_H_
diff --git a/seqan/parse_lm/parse_lastz_general.h b/seqan/parse_lm/parse_lastz_general.h
new file mode 100644
index 0000000..367d5ed
--- /dev/null
+++ b/seqan/parse_lm/parse_lastz_general.h
@@ -0,0 +1,216 @@
+// ==========================================================================
+//                                  parse_lm
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Parsing for the "general" format of lastz.
+// ==========================================================================
+
+// SEQAN_NO_GENERATED_FORWARDS
+
+#ifndef INCLUDE_SEQAN_PARSE_LM_PARSE_LASTZ_GENERAL_H_
+#define INCLUDE_SEQAN_PARSE_LM_PARSE_LASTZ_GENERAL_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct LastzGeneral_;
+typedef Tag<LastzGeneral_> LastzGeneral;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord()
+// ----------------------------------------------------------------------------
+
+template <typename TLocalMatchStore, typename TForwardIter>
+inline void
+readRecord(TLocalMatchStore & store,
+           TForwardIter & iter,
+           LastzGeneral const & /*tag*/)
+{
+    typedef typename TLocalMatchStore::TPosition TPosition;
+
+    // Skip any comments.
+    while (true)
+    {
+        if (atEnd(iter))
+        {
+            throw UnexpectedEnd();
+            return;
+        }
+        if (value(iter) != '#')
+            break;
+        skipLine(iter);
+    }
+
+    SEQAN_ASSERT_NEQ(value(iter), '#');
+
+    // Read line.
+    CharString buffer;
+
+    CharString subjectName;
+    CharString queryName;
+    char subjectStrand = 'X';
+    char queryStrand = 'X';
+    TPosition subjectBeginPos = 0;
+    TPosition subjectEndPos = 0;
+    TPosition queryBeginPos = 0;
+    TPosition queryEndPos = 0;
+
+    // Field: score
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: name1
+    readUntil(subjectName, iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: strand1
+    readOne(subjectStrand, iter, OrFunctor<EqualsChar<'+'>, EqualsChar<'-'> >());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: size1
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: zstart1
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    subjectBeginPos = lexicalCast<TPosition>(buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: end1
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    subjectEndPos = lexicalCast<TPosition>(buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: name2
+    readUntil(queryName, iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: strand2
+    readOne(queryStrand, iter, OrFunctor<EqualsChar<'+'>, EqualsChar<'-'> >());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: size2
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: zstart2
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    queryBeginPos = lexicalCast<TPosition>(buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: end2
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    queryEndPos = lexicalCast<TPosition>(buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: identity
+    clear(buffer);
+    readUntil(buffer, iter, IsWhitespace());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: idPct
+    clear(buffer);
+    readUntil(buffer, iter, IsWhitespace());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: coverage
+    clear(buffer);
+    readUntil(buffer, iter, IsWhitespace());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: covPct
+    clear(buffer);
+    readUntil(buffer, iter, IsWhitespace());
+
+    // Skip to next line, ignore EOF here.
+    skipLine(iter);
+
+    // Finally, append the local match.
+    if (subjectStrand == '-')
+        std::swap(subjectBeginPos, subjectEndPos);
+    if (queryStrand == '-')
+        std::swap(queryBeginPos, queryEndPos);
+    appendLocalMatch(store, subjectName, subjectBeginPos, subjectEndPos, queryName, queryBeginPos, queryEndPos);
+}
+
+}  // namespace seqan
+
+#endif  // INCLUDE_SEQAN_PARSE_LM_PARSE_LASTZ_GENERAL_H_
diff --git a/seqan/parse_lm/parse_stellar_gff.h b/seqan/parse_lm/parse_stellar_gff.h
new file mode 100644
index 0000000..b411c6c
--- /dev/null
+++ b/seqan/parse_lm/parse_stellar_gff.h
@@ -0,0 +1,223 @@
+// ==========================================================================
+//                                  parse_lm
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+// SEQAN_NO_GENERATED_FORWARDS
+
+#ifndef INCLUDE_SEQAN_PARSE_LM_PARSE_STELLAR_GFF_H_
+#define INCLUDE_SEQAN_PARSE_LM_PARSE_STELLAR_GFF_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+struct StellarGff_;
+typedef Tag<StellarGff_> StellarGff;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord()
+// ----------------------------------------------------------------------------
+
+template <typename TLocalMatchStore, typename TForwardIter>
+inline void
+readRecord(TLocalMatchStore & store,
+           TForwardIter & iter,
+           StellarGff const & /*tag*/)
+{
+    typedef typename TLocalMatchStore::TPosition TPosition;
+
+    // Read line.
+    CharString buffer;
+    char subjectStrand = 'X';
+
+    CharString subjectName;
+    CharString queryName;
+    TPosition subjectBeginPos = 0;
+    TPosition subjectEndPos = 0;
+    TPosition queryBeginPos = 0;
+    TPosition queryEndPos = 0;
+
+    // Field: SUBJECT
+    readUntil(subjectName, iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: SOURCE
+    skipUntil(iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: TYPE
+    skipUntil(iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: START
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    subjectBeginPos = lexicalCast<TPosition>(buffer) - 1;
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: END
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    subjectEndPos = lexicalCast<TPosition>(buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: SCORE
+    skipUntil(iter, IsTab());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: STRAND
+    clear(buffer);
+    readOne(subjectStrand, iter, OrFunctor<EqualsChar<'+'>, EqualsChar<'-'> >());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Field: FRAME
+    skipOne(iter);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // The GROUP field contains the information about the query.
+    // query sequence
+    readUntil(queryName, iter, EqualsChar<';'>());
+
+    // Skip semicolon.
+    skipOne(iter, EqualsChar<';'>());
+
+    // "seq2Range="
+    clear(buffer);
+    readUntil(buffer, iter, EqualsChar<'='>());
+    if (buffer != "seq2Range")
+    {
+        throw ParseError("Format error; Expected 'seq2Range'");
+        return;  // FORMAT ERROR, should probably be a constant
+    }
+    // Skip '='
+    skipOne(iter, EqualsChar<'='>());
+
+    // query begin pos
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    queryBeginPos = lexicalCast<TPosition>(buffer) - 1;
+
+    // skip comma
+    skipOne(iter, EqualsChar<','>());
+
+    // query end pos
+    clear(buffer);
+    readUntil(buffer, iter, NotFunctor<IsDigit>());
+    queryEndPos = lexicalCast<TPosition>(buffer);
+
+    // Skip semicolon.
+    skipOne(iter, EqualsChar<';'>());
+
+    // Skip "eValue=*;"
+    clear(buffer);
+    readUntil(buffer, iter, EqualsChar<'='>());
+    if (buffer != "eValue")
+    {
+        throw ParseError("Format error; Expected 'eValue'");
+        return;  // FORMAT ERROR, should probably be a constant
+    }
+
+    // Skip '='
+    skipOne(iter, EqualsChar<'='>());
+
+    // Skip until semicolon.
+    skipUntil(iter, EqualsChar<';'>());
+
+    // And skip the semicolon.
+    skipOne(iter, EqualsChar<';'>());
+
+    // Skip "cigar".
+    clear(buffer);
+    readUntil(buffer, iter, EqualsChar<'='>());
+    if (buffer != "cigar")
+    {
+        throw ParseError("Format error; Expected 'cigar'");
+        return;  // FORMAT ERROR, should probably be a constant
+    }
+
+    // Skip '='
+    skipOne(iter, EqualsChar<'='>());
+
+    // Read cigar string.
+    clear(buffer);
+    readUntil(buffer, iter, EqualsChar<';'>());
+
+    // Skip semicolon.
+    skipOne(iter, EqualsChar<';'>());
+
+    // ignore rest of the field, skip to next line
+    skipLine(iter);
+
+    // Finally, append the local match.
+    if (subjectStrand == '-')
+        std::swap(subjectBeginPos, subjectEndPos);
+    appendLocalMatch(store, subjectName, subjectBeginPos, subjectEndPos, queryName, queryBeginPos, queryEndPos, buffer);
+}
+
+}  // namespace seqan
+
+#endif  // INCLUDE_SEQAN_PARSE_LM_PARSE_STELLAR_GFF_H_
diff --git a/seqan/pipe.h b/seqan/pipe.h
index d0987d0..e204889 100644
--- a/seqan/pipe.h
+++ b/seqan/pipe.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/pipe/INFO b/seqan/pipe/INFO
deleted file mode 100644
index abc0eb0..0000000
--- a/seqan/pipe/INFO
+++ /dev/null
@@ -1,10 +0,0 @@
-Name: seqan-pipe
-Author: David Weese <david.weese@fu-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Pipelined I/O.
- This module contains the Pipe and Pool classes as well as various
- implementations.  The code is used for the external I/O functionality of SeqAn.
- Besides other things, this class contains the external sorting algorithm.
diff --git a/seqan/pipe/pipe_base.h b/seqan/pipe/pipe_base.h
index 2584ec4..2de77f6 100644
--- a/seqan/pipe/pipe_base.h
+++ b/seqan/pipe/pipe_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,7 +37,7 @@
 
 namespace seqan {
 
-	// shortcuts to ease pipeline construction
+    // shortcuts to ease pipeline construction
     #define TypeOf_(TObject)  typename Value<TObject>::Type
     #define TSizeOf_(TObject) typename Size<TObject>::Type
 
@@ -45,101 +45,63 @@ namespace seqan {
  * @class Pipe
  * @headerfile <seqan/pipe.h>
  * @brief Pipes are pop-passive pipeline modules.
- * 
+ *
  * @signature template <typename TInput, typename TSpec>
  *            class Pipe;
- * 
+ *
  * @tparam TSpec  The specializing type.
  * @tparam TInput The type of the pipeline module this module reads from.  Use Bundle2, Bundle3, etc. to read
  *                from more than one module.
- * 
- * @section Remarks
- * 
- * Use Value to get the output type of a given Pipe (returns <tt>Value&lt;TInput&gt;::Type</tt> by
+ *
+ * Use @link Pipe#Value @endlink to get the output type of a given Pipe (returns <tt>Value&lt;TInput&gt;::Type</tt> by
  * default).
- * 
+ *
  * Use Size to get the size type of a given Pipe (returns <tt>Size&lt;TInput&gt;::Type</tt> by default).
  */
 
 /*!
  * @fn Pipe::Pipe
  * @brief Constructor
- * 
+ *
  * @signature Pipe::Pipe(in);
  *
  * @param[in] in Reference to an input pipe.
  */
 
-/**
-.Class.Pipe:
-..cat:Pipelining
-..summary:Pipes are pop-passive pipeline modules.
-..signature:Pipe<TInput, TSpec>
-..param.TInput:The type of the pipeline module this module reads from.
-...remarks:Use @Class.Bundle2@, @Class.Bundle3@, etc. to read from more than one module.
-..param.TSpec:The specializing type.
-..remarks:Use @Metafunction.Value@ to get the output type of a given Pipe (returns $Value<TInput>::Type$ by default).
-..remarks:Use @Metafunction.Size@ to get the size type of a given Pipe (returns $Size<TInput>::Type$ by default).
-.Memfunc.Pipe#Pipe:
-..class:Class.Pipe
-..summary:Constructor
-..signature:Pipe<TInput, TSpec> (in)
-..param.in:Reference to an input pipe.
-..include:seqan/pipe.h
-*/
-
     template < typename TInput, typename TSpec >
     struct Pipe {
         TInput &in;
         Pipe(TInput &_in): in(_in) {}
     };
 
-	// base class for multiple sequence algorithms
-	// to hold extra information about desired position type (TPair)
-	// and the type storing absolute sequence offsets (TLimitsString)
+    // base class for multiple sequence algorithms
+    // to hold extra information about desired position type (TPair)
+    // and the type storing absolute sequence offsets (TLimitsString)
     template <typename TSpec, typename TPair, typename TLimitsString>
-	struct Multi;
+    struct Multi;
 
 /*!
  * @class Bundle2
  * @headerfile <seqan/pipe.h>
  * @brief Stores references to two arbitrary objects.
- * 
+ *
  * @signature template <typename TInput1, typename TInput2>
  *            class Bundle2;
- * 
+ *
  * @tparam TInput1 The type of the first object.
  * @tparam TInput2 The type of the second object.
- * 
- * @section Remarks
- * 
+ *
  * Primarily used as an adaptor for pipes with two sources.
- * 
+ *
  * @see bundle2
- * 
- * @var VariableType Bundle2::in1
+ *
+ * @var TInput1 Bundle2::in1;
  * @brief TInput1 reference
- * 
- * @var TInput1 Bundle2::in2
+ *
+ * @var TInput2 Bundle2::in2;
  * @brief TInput2 reference
  */
 
-/**
-.Class.Bundle2:
-..cat:Aggregates
-..summary:Stores references to two arbitrary objects.
-..signature:Bundle2<TInput1, TInput2>
-..param.TInput1:The type of the first object.
-..param.TInput2:The type of the second object.
-..remarks:Primarily used as an adaptor for pipes with two sources.
-.Memvar.Bundle2#in1:
-..class:Class.Bundle2
-..summary:TInput1 reference
-.Memvar.Bundle2#in2:
-..class:Class.Bundle2
-..summary:TInput2 reference
-..include:seqan/pipe.h
-*/
     // pipe input adapter 2->1 pipe
     template < typename TInput1, typename TInput2 >
     struct Bundle2 {
@@ -154,81 +116,48 @@ namespace seqan {
  * @fn bundle2
  * @headerfile <seqan/pipe.h>
  * @brief Returns a bundle of two objects.
- * 
+ *
  * @signature TBundle bundle2(in1, in2);
- * 
- * @param in1 First object.
- * @param in2 Second object.
- * 
+ *
+ * @param[in] in1 First object.
+ * @param[in] in2 Second object.
+ *
  * @return TBundle A Bundle2 with references to <tt>in1</tt> and <tt>in2</tt>.
- * 
+ *
  * @see Bundle2
  */
 
-/**
-.Function.bundle2
-..class:Class.Bundle2
-..cat:Pipelining
-..summary:Returns a bundle of two objects.
-..signature:bundle2(in1, in2)
-..param.in1:First object.
-..param.in2:Second object.
-..returns:A @Class.Bundle2@ with references to $in1$ and $in2$.
-..see:Class.Bundle2
-..include:seqan/pipe.h
-*/
-	template < typename TInput1, typename TInput2 >
-	inline Bundle2< TInput1, TInput2 >
-	bundle2(TInput1 &_in1, TInput2 &_in2) {
-		return Bundle2< TInput1, TInput2 >(_in1, _in2);
-	}
+    template < typename TInput1, typename TInput2 >
+    inline Bundle2< TInput1, TInput2 >
+    bundle2(TInput1 &_in1, TInput2 &_in2) {
+        return Bundle2< TInput1, TInput2 >(_in1, _in2);
+    }
 /*!
  * @class Bundle3
- * 
+ *
  * @brief Stores references to three arbitrary objects.
- * 
- * @signature Bundle3<TInput1, TInput2, TInput3>
- * 
+ *
+ * @signature template <typename TInput1, typename TInput2, typename TInput3>
+ *            struct Bundle3;
+ *
  * @tparam TInput3 The type of the third object.
  * @tparam TInput2 The type of the second object.
  * @tparam TInput1 The type of the first object.
- * 
- * @section Remarks
- * 
+ *
  * Primarily used as an adaptor for pipes with three sources.
- * 
+ *
  * @see bundle3
- * 
- * @var TInput1 Bundle3::in1
+ *
+ * @var TInput1 Bundle3::in1;
  * @brief TInput1 reference
- * 
- * @var TInput2 Bundle3::in2
+ *
+ * @var TInput2 Bundle3::in2;
  * @brief TInput2 reference
- * 
- * @var TInput3 Bundle3::in3
+ *
+ * @var TInput3 Bundle3::in3;
  * @brief TInput3 reference
  */
 
-/**
-.Class.Bundle3:
-..cat:Aggregates
-..summary:Stores references to three arbitrary objects.
-..signature:Bundle3<TInput1, TInput2, TInput3>
-..param.TInput1:The type of the first object.
-..param.TInput2:The type of the second object.
-..param.TInput3:The type of the third object.
-..remarks:Primarily used as an adaptor for pipes with three sources.
-.Memvar.Bundle3#in1:
-..class:Class.Bundle3
-..summary:TInput1 reference
-.Memvar.Bundle3#in2:
-..class:Class.Bundle3
-..summary:TInput2 reference
-.Memvar.Bundle3#in3:
-..class:Class.Bundle3
-..summary:TInput3 reference
-..include:seqan/pipe.h
-*/
     // pipe input adapter 3->1 pipe
     template < typename TInput1, typename TInput2, typename TInput3 >
     struct Bundle3 {
@@ -245,36 +174,23 @@ namespace seqan {
  * @fn bundle3
  * @headerfile <seqan/pipe.h>
  * @brief Returns a bundle of three objects.
- * 
+ *
  * @signature TBundle bundle3(in1, in2, in3);
- * 
- * @param in1 First object.
- * @param in2 Second object.
- * @param in3 Third object.
- * 
+ *
+ * @param[in] in1 First object.
+ * @param[in] in2 Second object.
+ * @param[in] in3 Third object.
+ *
  * @return TBundle A Bundle3 with references to <tt>in1</tt>, <tt>in2</tt>, and <tt>in3</tt>.
- * 
+ *
  * @see Bundle3
  */
 
-/**
-.Function.bundle3
-..class:Class.Bundle3
-..cat:Pipelining
-..summary:Returns a bundle of three objects.
-..signature:bundle3(in1, in2, in3)
-..param.in1:First object.
-..param.in2:Second object.
-..param.in3:Third object.
-..returns:A @Class.Bundle3@ with references to $in1$, $in2$, and $in3$.
-..see:Class.Bundle3
-..include:seqan/pipe.h
-*/
-	template < typename TInput1, typename TInput2, typename TInput3 >
-	inline Bundle3< TInput1, TInput2, TInput3 >
-	bundle3(TInput1 &_in1, TInput2 &_in2, TInput3 &_in3) {
-		return Bundle3< TInput1, TInput2, TInput3 >(_in1, _in2, _in3);
-	}
+    template < typename TInput1, typename TInput2, typename TInput3 >
+    inline Bundle3< TInput1, TInput2, TInput3 >
+    bundle3(TInput1 &_in1, TInput2 &_in2, TInput3 &_in3) {
+        return Bundle3< TInput1, TInput2, TInput3 >(_in1, _in2, _in3);
+    }
 
 /*!
  * @class Bundle5
@@ -282,64 +198,34 @@ namespace seqan {
  * @brief Stores references to five arbitrary objects.
  *
  * @signature template <typename TInput1, typename TInput2, typename TInput3, typename TInput4, typename TInput5>
- *            class Bundle 5;
- * 
+ *            class Bundle5;
+ *
  * @tparam TInput1 The type of the first object.
  * @tparam TInput2 The type of the second object.
  * @tparam TInput3 The type of the third object.
  * @tparam TInput4 The type of the fourth object.
  * @tparam TInput5 The type of the fifth object.
- * 
- * @section Remarks
- * 
+ *
  * Primarily used as an adaptor for pipes with five sources.
- * 
+ *
  * @see bundle5
- * 
- * @var TInput1 Bundle5::in1
+ *
+ * @var TInput1 Bundle5::in1;
  * @brief TInput1 reference
- * 
- * @var TInput2 Bundle5::in2
+ *
+ * @var TInput2 Bundle5::in2;
  * @brief TInput2 reference
- * 
- * @var TInput3 Bundle5::in3
+ *
+ * @var TInput3 Bundle5::in3;
  * @brief TInput3 reference
- * 
- * @var TInput4 Bundle5::in4
+ *
+ * @var TInput4 Bundle5::in4;
  * @brief TInput4 reference
- * 
- * @var TInput5 Bundle5::in5
+ *
+ * @var TInput5 Bundle5::in5;
  * @brief TInput5 reference
  */
 
-/**
-.Class.Bundle5:
-..cat:Aggregates
-..summary:Stores references to five arbitrary objects.
-..signature:Bundle5<TInput1, TInput2, TInput3, TInput4, TInput5>
-..param.TInput1:The type of the first object.
-..param.TInput2:The type of the second object.
-..param.TInput3:The type of the third object.
-..param.TInput4:The type of the fourth object.
-..param.TInput5:The type of the fifth object.
-..remarks:Primarily used as an adaptor for pipes with five sources.
-.Memvar.Bundle5#in1:
-..class:Class.Bundle5
-..summary:TInput1 reference
-.Memvar.Bundle5#in2:
-..class:Class.Bundle5
-..summary:TInput2 reference
-.Memvar.Bundle5#in3:
-..class:Class.Bundle5
-..summary:TInput3 reference
-.Memvar.Bundle5#in4:
-..class:Class.Bundle5
-..summary:TInput4 reference
-.Memvar.Bundle5#in5:
-..class:Class.Bundle5
-..summary:TInput5 reference
-..include:seqan/pipe.h
-*/
     // pipe input adapter 5->1 pipe
     template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5 >
     struct Bundle5 {
@@ -357,58 +243,62 @@ namespace seqan {
  * @fn bundle5
  * @headerfile <seqan/pipe.h>
  * @brief Returns a bundle of five objects.
- * 
+ *
  * @signature TBundle bundle5(in1, in2, in3, in4, in5);
- * 
- * @param in1 First object.
- * @param in2 Second object.
- * @param in3 Third object.
- * @param in4 Fourth object.
- * @param in5 Fifth object.
- * 
+ *
+ * @param[in] in1 First object.
+ * @param[in] in2 Second object.
+ * @param[in] in3 Third object.
+ * @param[in] in4 Fourth object.
+ * @param[in] in5 Fifth object.
+ *
  * @return TBundle A Bundle5 with references to <tt>in1</tt>, <tt>in2</tt>, <tt>in3</tt>, <tt>in4</tt>,
  *                 and <tt>in5</tt>.
- * 
+ *
  * @see Bundle5
  */
 
-/**
-.Function.bundle5
-..class:Class.Bundle5
-..cat:Pipelining
-..summary:Returns a bundle of five objects.
-..signature:bundle5(in1, in2, in3, in4, in5)
-..param.in1:First object.
-..param.in2:Second object.
-..param.in3:Third object.
-..param.in4:Fourth object.
-..param.in5:Fifth object.
-..returns:A @Class.Bundle5@ with references to $in1$, $in2$, $in3$, $in4$, and $in5$.
-..see:Class.Bundle5
-..include:seqan/pipe.h
-*/
     template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5 >
-	inline Bundle5< TIn1, TIn2, TIn3, TIn4, TIn5 >
-	bundle5(TIn1 &_in1, TIn2 &_in2, TIn3 &_in3, TIn4 &_in4, TIn5 &_in5) {
-		return Bundle5< TIn1, TIn2, TIn3, TIn4, TIn5 >(_in1, _in2, _in3, _in4, _in5);
-	}
+    inline Bundle5< TIn1, TIn2, TIn3, TIn4, TIn5 >
+    bundle5(TIn1 &_in1, TIn2 &_in2, TIn3 &_in3, TIn4 &_in4, TIn5 &_in5) {
+        return Bundle5< TIn1, TIn2, TIn3, TIn4, TIn5 >(_in1, _in2, _in3, _in4, _in5);
+    }
 
     template < typename TValue, typename TSize >
     struct AbstractSource {};
 
+/*!
+ * @mfn Pipe#Value
+ * @brief Return value type of the Pipe specialization.
+ *
+ * @signature Value<TPipe>::Type;
+ *
+ * @tparam TPipe The Pipe specialization to query.
+ *
+ * @return Type The resulting value type.
+ */
+
     template < typename TValue, typename TSize >
     struct Value< Pipe<void, AbstractSource<TValue, TSize> > > {
         typedef TValue Type;
     };
 
+/*!
+ * @mfn Pipe#Size
+ * @brief Return size type of the Pipe specialization.
+ *
+ * @signature Size<TPipe>::Type;
+ *
+ * @tparam TPipe The Pipe specialization to query.
+ *
+ * @return Type The resulting size type.
+ */
+
     template < typename TValue, typename TSize >
     struct Size< Pipe<void, AbstractSource<TValue, TSize> > > {
         typedef TSize Type;
     };
 
-
-
-    
     template < typename TInput, typename TSpec >
     struct Value< Pipe<TInput, TSpec> > {
         typedef typename Value<TInput>::Type Type;
@@ -441,45 +331,53 @@ namespace seqan {
 
     template < typename TInput, typename TSpec >
     struct Difference< Pipe<TInput, TSpec> > {
-		typedef typename MakeSigned_<typename Size<Pipe<TInput, TSpec> >::Type>::Type Type;
+        typedef typename MakeSigned_<typename Size<Pipe<TInput, TSpec> >::Type>::Type Type;
     };
 /*
     template < typename TInput, typename TSpec >
-	struct Iterator< Pipe<TInput, TSpec> >;
+    struct Iterator< Pipe<TInput, TSpec> >;
 
     template < typename TInput, typename TSpec >
-	struct Iterator< Pipe<TInput, TSpec> const >:
-		Iterator< Pipe<TInput, TSpec> > {};
+    struct Iterator< Pipe<TInput, TSpec> const >:
+        Iterator< Pipe<TInput, TSpec> > {};
 */
 
-	template <typename T>
-	struct Source;
+    template <typename T>
+    struct Source;
 
-	template <typename TInput, typename TSpec>
-	struct Source<Pipe<TInput, TSpec> >
-	{
-		typedef TInput Type;
-	};
+    template <typename TInput, typename TSpec>
+    struct Source<Pipe<TInput, TSpec> >
+    {
+        typedef TInput Type;
+    };
 
-	template < typename TInput, typename TSpec >
+    template < typename TInput, typename TSpec >
     inline TInput const &
     source(Pipe<TInput, TSpec> const &me) {
 SEQAN_CHECKPOINT
         return me.in;
     }
 
-	template < typename TInput, typename TSpec >
+    template < typename TInput, typename TSpec >
     inline TInput &
     source(Pipe<TInput, TSpec> &me) {
 SEQAN_CHECKPOINT
         return me.in;
     }
 
+/*!
+ * @fn Pipe#length
+ * @headerfile <seqan/pipe.h>
+ * @brief Length of the pipe.
+ *
+ * @signature TSize length(pipe);
+ *
+ * @param[in] pipe  The Pipe to query for its size.
+ *
+ * @return    TSize The size of the pipe.
+ */
 
-///.Function.length.param.object.type:Class.Pipe
-///.Function.length.class:Class.Pipe
-
-	template < typename TInput, typename TSpec >
+    template < typename TInput, typename TSpec >
     inline typename Size< Pipe<TInput, TSpec> >::Type
     length(Pipe<TInput, TSpec> const &me) {
 SEQAN_CHECKPOINT
@@ -510,7 +408,7 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////
 
 
-	template < typename TInput, typename TSpec >
+    template < typename TInput, typename TSpec >
     inline typename Size< Pipe<TInput, TSpec> >::Type
     countSequences(Pipe<TInput, TSpec> const &me) {
 SEQAN_CHECKPOINT
@@ -542,36 +440,19 @@ SEQAN_CHECKPOINT
  * @fn Pipe#front
  * @headerfile <seqan/pipe.h>
  * @brief Gets the first element of the remaining stream.
- * 
+ *
  * @signature TValue front(object);
- * 
- * @param object A pop-passive pipeline module. Types: Pipe, Pool
- * 
+ *
+ * @param[in] object A pop-passive pipeline module.
+ *
  * @return TValue The first element of the remaining input stream.  Return type is <tt>Value&lt;TObject&gt;::Type</tt>
  *                for <tt>object</tt> type <tt>TObject</tt>.
- * 
- * @section Remarks
- * 
+ *
  * Pipe#front or Pipe#pop can only be called within a read process surrounded by beginRead and endRead.
- * 
+ *
  * @see Pipe#pop
  */
 
-/**
-.Function.Pipe#front
-..class:Class.Pipe
-..cat:Pipelining
-..summary:Gets the first element of the remaining stream.
-..signature:front(object)
-..param.object:A pop-passive pipeline module.
-...type:Class.Pipe
-..returns:The first element of the remaining input stream.
-Return type is $Value<TObject>::Type$ for $object$ type $TObject$.
-..remarks:@Function.Pipe#front@ or @Function.pop@ can only be called within a read process surrounded by @Function.beginRead@ and @Function.endRead@.
-..see:Function.pop
-..include:seqan/pipe.h
-*/
-
     template < typename TInput, typename TSpec, typename TValue >
     inline typename Value< Pipe<TInput, TSpec> >::Type const &
     front(Pipe<TInput, TSpec> &me) {
@@ -583,36 +464,18 @@ SEQAN_CHECKPOINT
  * @fn Pipe#pop
  * @headerfile <seqan/pipe.h>
  * @brief Pops the first element of the remaining stream.
- * 
- * @signature void pop(object[, ref]);
- * 
- * @param[in,out] object A pop-passive pipeline module. Types: Pipe, Pool
+ *
+ * @signature void pop(pipe[, ref]);
+ *
+ * @param[in,out] pipe A pop-passive pipeline module.
  * @param[out]    ref    Reference to the result.  Result type is <tt>Value&lt;TObject&gt;::Type</tt> for <tt>object</tt>
  *                       type <tt>TObject</tt>.  Returns the first element of the remaining input stream.
- * 
- * @section Remarks
- * 
+ *
  * In contrast to Pipe#front this function also steps one element further.
- * 
+ *
  * Pipe#front or Pipe#pop can only be called within a read process surrounded by beginRead and endRead.
  */
 
-/**
-.Function.pop:
-..class:Class.Pipe
-..cat:Pipelining
-..summary:Pops the first element of the remaining stream.
-..signature:pop(object[, ref])
-..param.object:A pop-passive pipeline module.
-...type:Class.Pipe
-..param.ref:Reference to the result. Result type is $Value<TObject>::Type$ for $object$ type $TObject$.
-...remarks:Returns the first element of the remaining input stream.
-..remarks:In contrast to @Function.Pipe#front@ this function also steps one element further.
-..remarks:@Function.Pipe#front@ or @Function.pop@ can only be called within a read process surrounded by @Function.beginRead@ and @Function.endRead@.
-..DISABLED.see:Function.top
-..include:seqan/pipe.h
-*/
-
     template < typename TInput, typename TSpec, typename TValue >
     inline void pop(Pipe<TInput, TSpec> &me, TValue &Ref_) {
 SEQAN_CHECKPOINT
@@ -626,45 +489,52 @@ SEQAN_CHECKPOINT
         ++me;
     }
 
-///.Function.atEnd.param.iterator.type:Class.Pipe
-///.Function.atEnd.class:Class.Pipe
-
+/*!
+ * @fn Pipe#atEnd
+ * @brief Check whether the @link Pipe @endlink object is at end.
+ *
+ * @signature bool atEnd(pipe);
+ *
+ * @param[in] pipe The @link Pipe @endlink object to query.
+ *
+ * @return bool true in case of the pipe being at the end, false otherwise.
+ */
 
     //////////////////////////////////////////////////////////////////////////////
     // pipe flow control
 
-	struct ControlEof_;			// end of stream
-	struct ControlEos_;			// end of sequence (for multiple sequences)
-	struct ControlClear_;		// clear previous pool
-	struct ControlBeginRead_;	// begin read process
-	struct ControlEndRead_;		// end read process
+    struct ControlEof_;            // end of stream
+    struct ControlEos_;            // end of sequence (for multiple sequences)
+    struct ControlClear_;        // clear previous pool
+    struct ControlBeginRead_;    // begin read process
+    struct ControlEndRead_;        // end read process
 
-	typedef Tag<ControlEof_>		ControlEof;
-	typedef Tag<ControlEos_>		ControlEos;
-	typedef Tag<ControlClear_>		ControlClear;
-	typedef Tag<ControlBeginRead_>	ControlBeginRead;
-	typedef Tag<ControlEndRead_>	ControlEndRead;
+    typedef Tag<ControlEof_>        ControlEof;
+    typedef Tag<ControlEos_>        ControlEos;
+    typedef Tag<ControlClear_>        ControlClear;
+    typedef Tag<ControlBeginRead_>    ControlBeginRead;
+    typedef Tag<ControlEndRead_>    ControlEndRead;
 
     template < typename TInput, typename TSpec, typename TCommand >
-	inline bool control(Pipe<TInput, TSpec> &me, TCommand const &command) {
+    inline bool control(Pipe<TInput, TSpec> &me, TCommand const &command) {
 SEQAN_CHECKPOINT
         return control(me.in, command);
     }
 
     template < typename TInput, typename TSpec >
-	inline bool eof(Pipe<TInput, TSpec> &me) {
+    inline bool eof(Pipe<TInput, TSpec> &me) {
 SEQAN_CHECKPOINT
         return control(me, ControlEof());
     }
 
     template < typename TInput, typename TSpec >
-	inline bool eos(Pipe<TInput, TSpec> &me) {
+    inline bool eos(Pipe<TInput, TSpec> &me) {
 SEQAN_CHECKPOINT
         return control(me, ControlEos());
     }
 
     template < typename TInput, typename TSpec >
-	inline bool clear(Pipe<TInput, TSpec> &me) {
+    inline bool clear(Pipe<TInput, TSpec> &me) {
 SEQAN_CHECKPOINT
         return control(me, ControlClear());
     }
@@ -673,42 +543,24 @@ SEQAN_CHECKPOINT
  * @fn Pipe#beginRead
  * @headerfile <seqan/pipe.h>
  * @brief Initiates a read process.
- * 
+ *
  * @signature bool beginRead(object);
- * 
- * @param object A pop-passive pipeline module. Types: Pipe, Pool
- * 
+ *
+ * @param[in,out] object A pop-passive pipeline module.
+ *
  * @return bool true on success, false on failure.
- * 
- * @section Remarks
- * 
+ *
  * <tt>beginRead</tt> rewinds the output stream, prepares <tt>object</tt> for succeeding reads, and typically calls
  * <tt>beginRead</tt> of the input pipeline modules.
- * 
+ *
  * A read process must be terminated with endRead. Nested read processes are not allowed.
- * 
+ *
  * @see Pipe#endRead
  */
 
-/**
-.Function.beginRead
-..class:Class.Pipe
-..class:Class.Pool
-..cat:Pipelining
-..summary:Initiates a read process.
-..signature:beginRead(object)
-..param.object:A pop-passive pipeline module.
-...type:Class.Pipe
-...type:Class.Pool
-..returns:A $bool$ which is $true$ on success.
-..remarks:$beginRead$ rewinds the output stream, prepares $object$ for succeeding reads, and typically calls $beginRead$ of the input pipeline modules.
-..remarks:A read process must be terminated with @Function.endRead@. Nested read processes are not allowed.
-..see:Function.endRead
-..include:seqan/pipe.h
-*/
-
     template < typename TInput, typename TSpec >
-	inline bool beginRead(Pipe<TInput, TSpec> &me) {
+    inline bool beginRead(Pipe<TInput, TSpec> &me)
+    {
         return control(me, ControlBeginRead());
     }
 
@@ -716,39 +568,21 @@ SEQAN_CHECKPOINT
  * @fn Pipe#endRead
  * @headerfile <seqan/pipe.h>
  * @brief Terminates a read process.
- * 
- * @signature bool beginRead(object);
- * 
- * @param object A pop-passive pipeline module. Types: Pipe, Pool
- * 
+ *
+ * @signature bool endRead(object);
+ *
+ * @param[in,out] object A pop-passive pipeline module.
+ *
  * @return bool true on success, false on failure.
- * 
- * @section Remarks
- * 
+ *
  * <tt>endRead</tt> closes the output stream, frees resources possibly allocated by beginRead, and typically calls
  * <tt>endRead</tt> of the input pipeline modules.
- * 
+ *
  * @see Pipe#beginRead
  */
 
-/**
-.Function.endRead
-..class:Class.Pipe
-..class:Class.Pool
-..cat:Pipelining
-..summary:Terminates a read process.
-..signature:beginRead(object)
-..param.object:A pop-passive pipeline module.
-...type:Class.Pipe
-...type:Class.Pool
-..returns:A $bool$ which is $true$ on success.
-..remarks:$endRead$ closes the output stream, frees resources possibly allocated by @Function.beginRead@, and typically calls $endRead$ of the input pipeline modules.
-..see:Function.beginRead
-..include:seqan/pipe.h
-*/
-
     template < typename TInput, typename TSpec >
-	inline bool endRead(Pipe<TInput, TSpec> &me) {
+    inline bool endRead(Pipe<TInput, TSpec> &me) {
         return control(me, ControlEndRead());
     }
 
@@ -757,34 +591,42 @@ SEQAN_CHECKPOINT
     // 2->1 pipe flow control
     template < typename TInput1, typename TInput2, typename TCommand >
     inline bool control(Bundle2<TInput1, TInput2> &me, TCommand const &command) {
-        return	control(me.in1, command) &&
-				control(me.in2, command);
+        return    control(me.in1, command) &&
+                control(me.in2, command);
     }
 
     //////////////////////////////////////////////////////////////////////////////
     // 3->1 pipe flow control
     template < typename TInput1, typename TInput2, typename TInput3, typename TCommand >
     inline bool control(Bundle3<TInput1, TInput2, TInput3> &me, TCommand const &command) {
-        return	control(me.in1, command) &&
-				control(me.in2, command) &&
-				control(me.in3, command);
+        return    control(me.in1, command) &&
+                control(me.in2, command) &&
+                control(me.in3, command);
     }
 
     //////////////////////////////////////////////////////////////////////////////
     // 5->1 pipe flow control
     template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5, typename TCommand >
     inline bool control(Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5 > &me, TCommand const &command) {
-        return	control(me.in1, command) &&
-				control(me.in2, command) &&
-				control(me.in3, command) &&
-				control(me.in4, command) &&
-				control(me.in5, command);
+        return    control(me.in1, command) &&
+                control(me.in2, command) &&
+                control(me.in3, command) &&
+                control(me.in4, command) &&
+                control(me.in5, command);
     }
-
-///.Function.assign.param.source.type:Class.Pipe
-///.Function.assign.class:Class.Pipe
-
-	//////////////////////////////////////////////////////////////////////////////
+/*!
+ * @fn Pipe#assign
+ * @headerfile <seqan/pipe.h>
+ * @brief Assigns one object to another object.
+ *
+ * @signature void assign(target, source);
+ *
+ * @param[out] target Reference to assign to.
+ * @param[in]  source Value to assign.
+ *
+ * Assign value of source to target.
+ */
+    //////////////////////////////////////////////////////////////////////////////
     // pipe -> string
 
     // We cannot use the most-generic TObject as first argument, as operator << specialized somewhere else in
@@ -835,19 +677,19 @@ SEQAN_CHECKPOINT
         assign(dest, src);
     }
 
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // pipe -> out_stream
     template <typename TInput, typename TSpec>
-	std::ostream& operator << (std::ostream &out, Pipe<TInput, TSpec> &src)
+    std::ostream& operator << (std::ostream &out, Pipe<TInput, TSpec> &src)
     {
         beginRead(src);
         while (!eof(src)) {
-			out << *src << ::std::endl;
+            out << *src << std::endl;
             ++src;
         }
         endRead(src);
-		return out;
-	}
+        return out;
+    }
 
 
     template < typename TObject, typename TSpec >
@@ -877,28 +719,28 @@ SEQAN_CHECKPOINT
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// generic adapter for buffered readers/writers
+    //////////////////////////////////////////////////////////////////////////////
+    // generic adapter for buffered readers/writers
 
-	template <typename TValue, typename TSpec, typename TSize >
+    template <typename TValue, typename TSpec, typename TSize >
     inline void resize(Buffer<TValue, TSpec> &me, TSize size);
 
-	struct AdapterSpec;
+    struct AdapterSpec;
 
-	template <typename TBufferHandler>
+    template <typename TBufferHandler>
     struct Handler<TBufferHandler, AdapterSpec>
     {
         typedef typename Value<TBufferHandler>::Type        TBuffer;
         typedef typename Value<TBuffer>::Type               TValue;
-		typedef typename Iterator<TBuffer, Standard>::Type  TIterator;
+        typedef typename Iterator<TBuffer, Standard>::Type  TIterator;
 
         TBufferHandler  handler;
-        TBuffer			buffer;
+        TBuffer            buffer;
         TIterator       cur;
 
         template < typename TObject >
-        Handler(TObject &_object):
-            handler(_object) {}
+        Handler(TObject &_object) :
+            handler(_object), cur() {}
 
         inline bool begin()
         {
@@ -914,11 +756,11 @@ SEQAN_CHECKPOINT
 
         inline void pop()
         {
-			if (++cur == seqan::end(buffer, Standard()))
+            if (++cur == seqan::end(buffer, Standard()))
             {
                 buffer = handler.next();
-				cur = seqan::begin(buffer, Standard());
-			}
+                cur = seqan::begin(buffer, Standard());
+            }
         }
 
         inline void pop(TValue &Ref_)
@@ -973,238 +815,240 @@ SEQAN_CHECKPOINT
     };
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// pair incrementer
-	//
-	// used by pipes processing multiples sequences 
-	// for generating pairs (seqNo, seqOffs)
+    //////////////////////////////////////////////////////////////////////////////
+    // pair incrementer
+    //
+    // used by pipes processing multiples sequences
+    // for generating pairs (seqNo, seqOffs)
 
-	template <typename TPair, typename TLimits>
-	struct PairIncrementer_
+    template <typename TPair, typename TLimits>
+    struct PairIncrementer_
     {
         typedef typename Iterator<TLimits const, Standard>::Type            TIter;
         typedef typename RemoveConst_<typename Value<TLimits>::Type>::Type  TSize;
         typedef typename Value<TPair, 2>::Type                              TOffset;
 
         TIter   it, itEnd;
-		TSize   old;
+        TSize   old;
         TOffset localEnd;
 
-		TPair pos;
-		inline operator TPair () const
+        TPair pos;
+        inline operator TPair () const
         {
-			return pos;
-		}
+            return pos;
+        }
 
-		inline TPair const & operator++ ()
+        inline TPair const & operator++ ()
         {
-			TOffset i2 = getValueI2(pos) + 1;
-			if (i2 >= localEnd)
+            TOffset i2 = getValueI2(pos) + 1;
+            if (i2 >= localEnd)
             {
-				i2 = 0;
-				localEnd = 0;
-				while (!localEnd && (it != itEnd))
-				{
+                i2 = 0;
+                localEnd = 0;
+                while (!localEnd && (it != itEnd))
+                {
                     typename Value<TPair,1>::Type i1 = getValueI1(pos);
                     assignValueI1(pos, i1 + 1);
-					localEnd = (*it - old);
+                    localEnd = (*it - old);
                     // test for overflows
                     SEQAN_ASSERT_LT_MSG(i1, getValueI1(pos), "Overflow detected. Use a bigger type for the *first* value in the SAValue pair!");
                     SEQAN_ASSERT_EQ_MSG((TSize)localEnd, (*it - old), "Overflow detected. Use a bigger type for the *second* value in the SAValue pair!");
-					old = *it;
-					++it;
-				}
-				if (!localEnd && it == itEnd)
-					assignValueI1(pos, getValueI1(pos) + 1);	// set pos behind the last sequence
-			}
-			assignValueI2(pos, i2);
-			return pos;
-		}
-	};
-
-	template <typename TPair, typename TLimits, typename TLimits2>
-	void setHost(PairIncrementer_<TPair, TLimits> &me, TLimits2 const &limits)
+                    old = *it;
+                    ++it;
+                }
+                if (!localEnd && it == itEnd)
+                    assignValueI1(pos, getValueI1(pos) + 1);    // set pos behind the last sequence
+            }
+            assignValueI2(pos, i2);
+            return pos;
+        }
+    };
+
+    template <typename TPair, typename TLimits, typename TLimits2>
+    void setHost(PairIncrementer_<TPair, TLimits> &me, TLimits2 const &limits)
     {
-		me.it = begin(limits, Standard());
-		me.itEnd = end(limits, Standard());
-		me.old = 0;
-		me.localEnd = 0;
+        me.it = begin(limits, Standard());
+        me.itEnd = end(limits, Standard());
+        me.old = 0;
+        me.localEnd = 0;
         me.pos = TPair(0, 0);
-		if (length(limits) > 1)
+        if (length(limits) > 1)
         {
-			++me.it;
-			++me;
-			assignValueI1(me.pos, getValueI1(me.pos) - 1);
-		}
-	}
-
-	template <typename TPair, typename TLimits, typename TLimits2>
-	void setHost(PairIncrementer_<TPair, TLimits> &me, TLimits2 &limits)
+            ++me.it;
+            ++me;
+            assignValueI1(me.pos, getValueI1(me.pos) - 1);
+        }
+    }
+
+    template <typename TPair, typename TLimits, typename TLimits2>
+    void setHost(PairIncrementer_<TPair, TLimits> &me, TLimits2 &limits)
     {
         setHost(me, const_cast<TLimits2 const &>(limits));
     }
 //____________________________________________________________________________
 
-	template <typename TPair, typename TLimits>
-	TPair const & value(PairIncrementer_<TPair, TLimits> const &me) {
-		return me.pos;
-	}
+    template <typename TPair, typename TLimits>
+    TPair const & value(PairIncrementer_<TPair, TLimits> const &me) {
+        return me.pos;
+    }
 
-	template <typename TPair, typename TLimits>
-	TPair & value(PairIncrementer_<TPair, TLimits> &me) {
-		return me.pos;
-	}
+    template <typename TPair, typename TLimits>
+    TPair & value(PairIncrementer_<TPair, TLimits> &me) {
+        return me.pos;
+    }
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// pair decrementer
-	//
-	// used by pipes processing multiples sequences 
-	// for generating pairs (seqNo, seqOffs)
+    //////////////////////////////////////////////////////////////////////////////
+    // pair decrementer
+    //
+    // used by pipes processing multiples sequences
+    // for generating pairs (seqNo, seqOffs)
 
-	template <typename TPair, typename TLimits, unsigned m = 0>
-	struct PairDecrementer_
+    template <typename TPair, typename TLimits, unsigned m = 0>
+    struct PairDecrementer_
     {
         typedef typename Iterator<TLimits const, Standard>::Type            TIter;
         typedef typename RemoveConst_<typename Value<TLimits>::Type>::Type  TSize;
-        
+
         TIter       it, itEnd;
-		TSize       old;
-		TPair		pos;
-		unsigned	residue;
+        TSize       old;
+        TPair        pos;
+        unsigned    residue;
 
-		PairDecrementer_() {}
-		PairDecrementer_(TLimits const &_limits) { setHost(*this, _limits); }
+        PairDecrementer_() : it(), itEnd(), old(), pos(), residue() {}
+        PairDecrementer_(TLimits const &_limits) : it(), itEnd(), old(), pos(), residue()
+        { setHost(*this, _limits); }
 
-		inline operator TPair () const {
-			return pos;
-		}
+        inline operator TPair () const
+        {
+            return pos;
+        }
 
-		inline TPair const & operator-- ()
+        inline TPair const & operator-- ()
         {
-			typename Value<TPair,2>::Type i2 = getValueI2(pos);
-			if (i2 > 1)
+            typename Value<TPair,2>::Type i2 = getValueI2(pos);
+            if (i2 > 1)
             {
-				--i2;
-				if (residue == 0) residue = m;
-				--residue;
-			}
-			else
-			{
-				i2 = 0;
-				while (!i2 && (it != itEnd))
-				{
+                --i2;
+                if (residue == 0) residue = m;
+                --residue;
+            }
+            else
+            {
+                i2 = 0;
+                while (!i2 && (it != itEnd))
+                {
                     typename Value<TPair,1>::Type i1 = getValueI1(pos);
-					assignValueI1(pos, i1 + 1);
-					i2 = (*it - old);
+                    assignValueI1(pos, i1 + 1);
+                    i2 = (*it - old);
                     // test for overflows
                     SEQAN_ASSERT_LT_MSG(i1, getValueI1(pos), "Overflow detected. Use a bigger type for the *first* value in the SAValue pair!");
                     SEQAN_ASSERT_EQ_MSG((TSize)i2, *it - old, "Overflow detected. Use a bigger type for the *second* value in the SAValue pair!");
-					old = *it;
-					++it;
-				} 
-				residue = i2 % m;
-			}
-			assignValueI2(pos, i2);
-			return pos;
-		}
-	};
-
-	template <typename TPair, typename TLimits, unsigned m, typename TLimits2>
-	void setHost(PairDecrementer_<TPair, TLimits, m> &me, TLimits2 const &limits)
+                    old = *it;
+                    ++it;
+                }
+                residue = i2 % m;
+            }
+            assignValueI2(pos, i2);
+            return pos;
+        }
+    };
+
+    template <typename TPair, typename TLimits, unsigned m, typename TLimits2>
+    void setHost(PairDecrementer_<TPair, TLimits, m> &me, TLimits2 const &limits)
     {
-		me.it = begin(limits);
-		me.itEnd = end(limits);
-		me.old = 0;
+        me.it = begin(limits);
+        me.itEnd = end(limits);
+        me.old = 0;
         me.pos = TPair(0, 0);
-		if (length(limits) > 1)
+        if (length(limits) > 1)
         {
-			++me.it;
-			--me;
-			assignValueI1(me.pos, getValueI1(me.pos) - 1);
-		} else
-			me.residue = 0;
-	}
-
-	template <typename TPair, typename TLimits, unsigned m, typename TLimits2>
-	void setHost(PairDecrementer_<TPair, TLimits, m> &me, TLimits2 &limits)
+            ++me.it;
+            --me;
+            assignValueI1(me.pos, getValueI1(me.pos) - 1);
+        } else
+            me.residue = 0;
+    }
+
+    template <typename TPair, typename TLimits, unsigned m, typename TLimits2>
+    void setHost(PairDecrementer_<TPair, TLimits, m> &me, TLimits2 &limits)
     {
         setHost(me, const_cast<TLimits const &>(limits));
     }
 //____________________________________________________________________________
 
-	template <typename TPair, typename TLimits>
-	struct PairDecrementer_<TPair, TLimits, 0>
+    template <typename TPair, typename TLimits>
+    struct PairDecrementer_<TPair, TLimits, 0>
     {
         typedef typename Iterator<TLimits const, Standard>::Type            TIter;
         typedef typename RemoveConst_<typename Value<TLimits>::Type>::Type  TSize;
 
         TIter       it, itEnd;
-		TSize       old;
-		TPair		pos;
+        TSize       old;
+        TPair        pos;
 
-		PairDecrementer_() {}
-		PairDecrementer_(TLimits const &_limits) { setHost(*this, _limits); }
+        PairDecrementer_() {}
+        PairDecrementer_(TLimits const &_limits) { setHost(*this, _limits); }
 
-		inline operator TPair () const {
-			return pos;
-		}
+        inline operator TPair () const {
+            return pos;
+        }
 
-		inline TPair const & operator-- ()
+        inline TPair const & operator-- ()
         {
-			typename Value<TPair,2>::Type i2 = getValueI2(pos);
-			if (i2 > 1)
-				--i2;
-			else
-			{
-				i2 = 0;
-				while (!i2 && (it != itEnd))
-				{
+            typename Value<TPair,2>::Type i2 = getValueI2(pos);
+            if (i2 > 1)
+                --i2;
+            else
+            {
+                i2 = 0;
+                while (!i2 && (it != itEnd))
+                {
                     typename Value<TPair,1>::Type i1 = getValueI1(pos);
-					assignValueI1(pos, i1 + 1);
-					i2 = (*it - old);
+                    assignValueI1(pos, i1 + 1);
+                    i2 = (*it - old);
                     // test for overflows
                     SEQAN_ASSERT_LT_MSG(i1, getValueI1(pos), "Overflow detected. Use a bigger type for the *first* value in the SAValue pair!");
                     SEQAN_ASSERT_EQ_MSG((TSize)i2, *it - old, "Overflow detected. Use a bigger type for the *second* value in the SAValue pair!");
-					old = *it;
-					++it;
-				} 
-			}
-			assignValueI2(pos, i2);
-			return pos;
-		}
-	};
-
-	template <typename TPair, typename TLimits, typename TLimits2>
-	void setHost(PairDecrementer_<TPair, TLimits, 0> &me, TLimits2 const &limits) {
-		me.it = begin(limits);
-		me.itEnd = end(limits);
-		me.old = 0;
-		assignValueI1(me.pos, 0);
-		assignValueI2(me.pos, 0);
-		if (length(limits) > 1) {
-			++me.it;
-			--me;
-			assignValueI1(me.pos, getValueI1(me.pos) - 1);
-		}
-	}
-
-	template <typename TPair, typename TLimits, typename TLimits2>
-	void setHost(PairDecrementer_<TPair, TLimits, 0> &me, TLimits2 &limits)
+                    old = *it;
+                    ++it;
+                }
+            }
+            assignValueI2(pos, i2);
+            return pos;
+        }
+    };
+
+    template <typename TPair, typename TLimits, typename TLimits2>
+    void setHost(PairDecrementer_<TPair, TLimits, 0> &me, TLimits2 const &limits) {
+        me.it = begin(limits);
+        me.itEnd = end(limits);
+        me.old = 0;
+        assignValueI1(me.pos, 0);
+        assignValueI2(me.pos, 0);
+        if (length(limits) > 1) {
+            ++me.it;
+            --me;
+            assignValueI1(me.pos, getValueI1(me.pos) - 1);
+        }
+    }
+
+    template <typename TPair, typename TLimits, typename TLimits2>
+    void setHost(PairDecrementer_<TPair, TLimits, 0> &me, TLimits2 &limits)
     {
         setHost(me, const_cast<TLimits const &>(limits));
     }
 //____________________________________________________________________________
 
-	template <typename TPair, typename TLimits, unsigned m>
-	TPair const & value(PairDecrementer_<TPair, TLimits, m> const &me) {
-		return me.pos;
-	}
+    template <typename TPair, typename TLimits, unsigned m>
+    TPair const & value(PairDecrementer_<TPair, TLimits, m> const &me) {
+        return me.pos;
+    }
 
-	template <typename TPair, typename TLimits, unsigned m>
-	TPair & value(PairDecrementer_<TPair, TLimits, m> &me) {
-		return me.pos;
-	}
+    template <typename TPair, typename TLimits, unsigned m>
+    TPair & value(PairDecrementer_<TPair, TLimits, m> &me) {
+        return me.pos;
+    }
 
 }
 
diff --git a/seqan/pipe/pipe_caster.h b/seqan/pipe/pipe_caster.h
index ece9557..dadf0a7 100644
--- a/seqan/pipe/pipe_caster.h
+++ b/seqan/pipe/pipe_caster.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,58 +41,43 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct CasterReinterpret;
-	struct CasterConvert;
-    
+    struct CasterReinterpret;
+    struct CasterConvert;
+
     template < typename TValue, typename TSpec = CasterReinterpret >
     struct Caster;
 
-	template < typename TInput, typename TValue, typename TSpec >
+    template < typename TInput, typename TValue, typename TSpec >
     struct Value< Pipe< TInput, Caster<TValue, TSpec> > > {
-		typedef TValue Type;
-	};
+        typedef TValue Type;
+    };
 
 /*!
  * @class Caster
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
  * @brief Casts the input type in a specific output type.
- * 
+ *
  * @signature template <typename TInput, typename TValue[, typename TSpec]>
  *            class Pipe<TInput, Caster<TValue, TSpec> >;
- * 
+ *
  * @tparam TInput The type of the pipeline module this module reads from.
  * @tparam TValue The new output type.
  * @tparam TSpec  <tt>CasterReinterpret</tt> (default) or <tt>CasterConvert</tt>.
- * 
- * @section Remarks
- * 
+ *
  * The input stream is casted using <tt>reinterpret_cast&lt;TValue&gt;</tt>.
  */
 
-/**
-.Spec.Caster:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Casts the input type in a specific output type.
-..signature:Pipe<TInput, Caster<TValue[, TSpec]> >
-..param.TInput:The type of the pipeline module this module reads from.
-..param.TValue:The new output type.
-..param.TSpec:$CasterReinterpret$ (default) or $CasterConvert$.
-..remarks: The input stream is casted using $reinterpret_cast<TValue>$.
-..include:seqan/pipe.h
-*/
-
     //////////////////////////////////////////////////////////////////////////////
     // caster pipe
     template <typename TInput, typename TValue >
     struct Pipe< TInput, Caster<TValue, CasterReinterpret> >
     {
-		TInput      &in;
-        
+        TInput      &in;
+
         Pipe(TInput& _in):
             in(_in) {}
-        
+
         inline TValue const & operator*() const {
             return reinterpret_cast<TValue const &>(*in);
         }
@@ -101,16 +86,16 @@ namespace SEQAN_NAMESPACE_MAIN
             ++in;
             return *this;
         }
-	};
-    
+    };
+
     template <typename TInput, typename TValue >
     struct Pipe< TInput, Caster<TValue, CasterConvert> >
     {
-		TInput      &in;
-        
+        TInput      &in;
+
         Pipe(TInput& _in):
             in(_in) {}
-        
+
         inline TValue operator*() const {
             return TValue(*in);
         }
@@ -119,7 +104,7 @@ namespace SEQAN_NAMESPACE_MAIN
             ++in;
             return *this;
         }
-	};
+    };
 //}
 
 }
diff --git a/seqan/pipe/pipe_counter.h b/seqan/pipe/pipe_counter.h
index 7b5d868..74140a7 100644
--- a/seqan/pipe/pipe_counter.h
+++ b/seqan/pipe/pipe_counter.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,16 +41,16 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct Counter;
+    struct Counter;
 
-	template < typename TInput >
+    template < typename TInput >
     struct Value< Pipe< TInput, Counter > > {
-		typedef Pair<
-			typename Value<TInput>::Type,
-			typename Size<TInput>::Type,
-			Pack
-		> Type;
-	};
+        typedef Pair<
+            typename Value<TInput>::Type,
+            typename Size<TInput>::Type,
+            Pack
+        > Type;
+    };
 
 /*!
  * @class Counter
@@ -59,48 +59,33 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Extends the input stream by a second field which enumerates the elements.
  *
  * @signature template <typename TInput>
- *            Pipe<TInput, Counter>;
- * 
+ *            class Pipe<TInput, Counter>;
+ *
  * @tparam TInput The type of the pipeline module this module reads from.
- * 
- * @section Remarks
- * 
+ *
  * The output type is a Pair of input type and size type (i.e.  <tt>Pair&lt;Value&lt;TInput&gt;::Type, Size&lt;TInput&gt;::Type</tt>).
- * 
+ *
  * The first output field is the original input stream.
- * 
+ *
  * The second output field begins with 0 and increases by 1 per element.
- */ 
-
-/**
-.Spec.Counter:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Extends the input stream by a second field which enumerates the elements.
-..signature:Pipe<TInput, Counter>
-..param.TInput:The type of the pipeline module this module reads from.
-..remarks:The output type is a @Class.Pair@ of input type and size type (i.e. $Pair<Value<TInput>::Type, Size<TInput>::Type>$).
-..remarks:The first output field is the original input stream.
-..remarks:The second output field begins with 0 and increases by 1 per element.
-..include:seqan/pipe.h
-*/
+ */
 
     //////////////////////////////////////////////////////////////////////////////
     // counter class
     template < typename TInput >
     struct Pipe< TInput, Counter >
     {
-		TInput                      &in;
-        typename Value<Pipe>::Type	tmp;
-        
+        TInput                      &in;
+        typename Value<Pipe>::Type    tmp;
+
         Pipe(TInput& _in):
             in(_in) {}
-        
+
         inline typename Value<Pipe>::Type const & operator*() {
             tmp.i1 = *in;
             return tmp;
         }
-        
+
         inline Pipe& operator++() {
             ++in;
             ++tmp.i2;
@@ -112,12 +97,12 @@ namespace SEQAN_NAMESPACE_MAIN
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
     template < typename TInput >
-	inline bool control(Pipe< TInput, Counter > &me, ControlBeginRead const &command) {
+    inline bool control(Pipe< TInput, Counter > &me, ControlBeginRead const &command) {
         if (!control(me.in, command)) return false;
         me.tmp.i2 = 0;
-		return true;
-	}
-    
+        return true;
+    }
+
 //}
 
 }
diff --git a/seqan/pipe/pipe_echoer.h b/seqan/pipe/pipe_echoer.h
index 826c73f..56e8983 100644
--- a/seqan/pipe/pipe_echoer.h
+++ b/seqan/pipe/pipe_echoer.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,21 +42,21 @@ namespace SEQAN_NAMESPACE_MAIN
 //{
 
     //////////////////////////////////////////////////////////////////////////////
-	// some metaprogramming to unrool fixed-size loops
+    // some metaprogramming to unrool fixed-size loops
     struct EchoerFillWorker_ {
         template <typename Arg>
         static inline void body(Arg &arg, unsigned I) {
             arg.tmp.i2[I-1] = *(arg.in); ++(arg.in);
         }
     };
-    
+
     struct EchoerClearWorker_ {
         template <typename Arg>
         static inline void body(Arg &arg, unsigned I) {
-			arg.i2[I] = typename Value< typename Value<Arg, 2>::Type >::Type ();
+            arg.i2[I] = typename Value< typename Value<Arg, 2>::Type >::Type ();
         }
     };
-    
+
     struct EchoerShiftWorker_ {
         template <typename Arg>
         static inline void body(Arg &arg, unsigned I) {
@@ -70,52 +70,33 @@ namespace SEQAN_NAMESPACE_MAIN
 
     template < typename TInput, unsigned echoRepeats, bool omitFirst >
     struct Value< Pipe< TInput, Echoer< echoRepeats, omitFirst > > > {
-        typedef Tuple<typename Value<TInput>::Type, echoRepeats>	EchoType;
-        typedef Pair<typename Size<TInput>::Type, EchoType>			Type;
+        typedef Tuple<typename Value<TInput>::Type, echoRepeats>    EchoType;
+        typedef Pair<typename Size<TInput>::Type, EchoType>            Type;
     };
 
 /*!
  * @class Echoer
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
- * 
+ *
  * @brief Outputs tuples of the <tt>echoRepeats</tt> last elements of the input stream.
- * 
+ *
  * @signature template <typename Input, unsigned ECHO_REPEATS, bool OMIT_FIRST>
  *            class Pipe;
- * 
+ *
  * @tparam TInput       The type of the pipeline module this module reads from.
  * @tparam ECHO_REPEATS The tuple length.The tuples contain elements <tt>in[i]in[i-1]...in[i-(echoRepeats-1)]</tt>.
  * @tparam OMIT_FIRST   Omit half filled tuples.  If <tt>true</tt>, the output stream is <tt>echoRepeats-1</tt>
  *                      elements shorter than the input stream.  If <tt>false</tt>, the lengths are identical and the
  *                      tuple is filled with blanks (default constructed elements) for undefined entries.
- * 
- * @section Remarks
- * 
+ *
  * The output type is a @link Tuple @endlink of input elements and length <tt>echoRepeats</tt> (i.e.
  * <tt>Tuple&lt;Value&lt;TInput&lt;::Type, echoRepeats&gt;</tt>).
- * 
+ *
  * The tuples are sequences of the form <tt>in[i]in[i-1]in[i-2]..in[i-echoRepeats+1]</tt>. For <tt>omitFirst=false</tt>
  * <tt>i</tt> begins with 0 and for <tt>omitFirst=true</tt> <tt>i</tt> begins with <tt>echoRepeats-1</tt>.
  */
 
-/**
-.Spec.Echoer:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Outputs tuples of the $echoRepeats$ last elements of the input stream.
-..signature:Pipe<TInput, Echoer<echoRepeats, omitFirst> >
-..param.TInput:The type of the pipeline module this module reads from.
-..param.echoRepeats:The tuple length.
-...remarks:The tuples contain elements $in[i]in[i-1]...in[i-(echoRepeats-1)]$.
-..param.omitFirst:Omit half filled tuples.
-..param.omitFirst:If $true$, the output stream is $echoRepeats-1$ elements shorter than the input stream.
-..param.omitFirst:If $false$, the lengths are identical and the tuple is filled with blanks (default constructed elements) for undefined entries.
-..remarks:The output type is a @Class.Tuple@ of input elements and length $echoRepeats$ (i.e. $Tuple<Value<TInput>::Type, echoRepeats>$).
-..remarks:The tuples are sequences of the form $in[i]in[i-1]in[i-2]..in[i-echoRepeats+1]$. For $omitFirst=false$ $i$ begins with 0 and for $omitFirst=true$ $i$ begins with $echoRepeats-1$.
-..include:seqan/pipe.h
-*/
-
     //////////////////////////////////////////////////////////////////////////////
     // echoer class
     template < typename TInput, unsigned echoRepeats, bool omitFirst >
@@ -123,8 +104,8 @@ namespace SEQAN_NAMESPACE_MAIN
     {
         typedef typename Value<Pipe>::Type TValue;
 
-        TInput	&in;
-        TValue	tmp;
+        TInput    &in;
+        TValue    tmp;
 
         Pipe(TInput& _in):
             in(_in),
@@ -135,10 +116,10 @@ namespace SEQAN_NAMESPACE_MAIN
         }
 
         inline Pipe& operator++() {
-			++in;
+            ++in;
             if (eof(in)) return *this;
             LoopReverse<EchoerShiftWorker_, echoRepeats - 1>::run(this->tmp);
-			++tmp.i1;
+            ++tmp.i1;
             tmp.i2[0] = *in;
             return *this;
         }
@@ -148,21 +129,21 @@ namespace SEQAN_NAMESPACE_MAIN
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
     template < typename TInput, unsigned echoRepeats, bool omitFirst >
-	inline bool control(Pipe< TInput, Echoer< echoRepeats, omitFirst > > &me, ControlBeginRead const &command) {
+    inline bool control(Pipe< TInput, Echoer< echoRepeats, omitFirst > > &me, ControlBeginRead const &command) {
         if (!control(me.in, command)) return false;
         me.tmp.i1 = 0;
         Loop<EchoerClearWorker_, echoRepeats - 1>::run(me.tmp);
         if (!eof(me.in)) me.tmp.i2[0] = *me.in;
-		return true;
-	}
-    
+        return true;
+    }
+
     template < typename TInput, unsigned echoRepeats >
     inline bool control(Pipe< TInput, Echoer< echoRepeats, true > > &me, ControlBeginRead const &command) {
-        if (!control(me.in, command) || size(me.in) < echoRepeats - 1) return false;
+        if (!control(me.in, command) || length(me.in) < echoRepeats - 1) return false;
         me.tmp.i1 = 0;
         LoopReverse<EchoerFillWorker_, echoRepeats - 1>::run(me);
         if (!eof(me.in)) me.tmp.i2[0] = *me.in;
-		return true;
+        return true;
     }
 
     template < typename TInput, unsigned echoRepeats >
diff --git a/seqan/pipe/pipe_edit_environment.h b/seqan/pipe/pipe_edit_environment.h
index 2194eed..5b35cec 100644
--- a/seqan/pipe/pipe_edit_environment.h
+++ b/seqan/pipe/pipe_edit_environment.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -49,56 +49,37 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
  * @brief Outputs tuples of the <tt>tupleLen</tt> consecutive elements of the input stream.
- * 
+ *
  * @signature template <typename TInput, unsigned TUPLE_LEN, bool OMIT_LAST>
  *            class Pipe<TInput, Tupler<TUPLE_LEN, OMIT_LAST> >;
- * 
+ *
  * @tparam OMIT_LAST Omit half filled tuples.  If <tt>true</tt>, the output stream is <tt>tupleLen-1</tt> elements
  *                   shorter than the input stream.  If <tt>false</tt>, the lengths are identical and the last
  *                   tuples are filled with blanks (default constructed elements) for undefined entries.
  * @tparam TInput    The type of the pipeline module this module reads from.
  * @tparam TUPLE_LEN The tuple length.The tuples contain elements <tt>in[i]in[i+1]...in[i+(tupleLen-1)]</tt>.
- * 
- * @section Remarks
- * 
+ *
  * The output type is a @link Tuple @endlink of input elements and length <tt>tupleLen</tt> (i.e.
  * <tt>Tuple&lt;Value&lt;TInput&gt;::Type, tupleLen&gt;</tt>).
- * 
+ *
  * The tuples are sequences of the form <tt>in[i]in[i-1]in[i-2]..in[i-tupleLen+1]</tt>. For <tt>omitLast=false</tt>
  * <tt>i</tt> begins with 0 and for <tt>omitLast=true</tt> <tt>i</tt> begins with <tt>tupleLen-1</tt>.
  */
 
-/**
-.Spec.EditEnvironment:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Outputs tuples of the $tupleLen$ consecutive elements of the input stream.
-..signature:Pipe<TInput, Tupler<tupleLen, omitLast> >
-..param.TInput:The type of the pipeline module this module reads from.
-..param.tupleLen:The tuple length.
-...remarks:The tuples contain elements $in[i]in[i+1]...in[i+(tupleLen-1)]$.
-..param.omitLast:Omit half filled tuples.
-..param.omitLast:If $true$, the output stream is $tupleLen-1$ elements shorter than the input stream.
-..param.omitLast:If $false$, the lengths are identical and the last tuples are filled with blanks (default constructed elements) for undefined entries.
-..remarks:The output type is a @Class.Tuple@ of input elements and length $tupleLen$ (i.e. $Tuple<Value<TInput>::Type, tupleLen>$).
-..remarks:The tuples are sequences of the form $in[i]in[i-1]in[i-2]..in[i-tupleLen+1]$. For $omitLast=false$ $i$ begins with 0 and for $omitLast=true$ $i$ begins with $tupleLen-1$.
-..include:seqan/pipe.h
-*/
-
     //////////////////////////////////////////////////////////////////////////////
     // pipe to enumerate the hamming 1-environment
     template < typename TInput, unsigned STEP_SIZE >
     struct Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > >
     {
-		typedef typename Value< typename Value<TInput>::Type, 2 >::Type	TTuple;
-		typedef typename Value<TTuple>::Type							TValue;
+        typedef typename Value< typename Value<TInput>::Type, 2 >::Type    TTuple;
+        typedef typename Value<TTuple>::Type                            TValue;
 
         TInput                      &in;
-        typename Value<Pipe>::Type	tmp, orig;
-		unsigned					errorPos;		// position of substitution
-		unsigned					character;		// replacement character 
-		unsigned					skipChar;		// skip the original character 
-        
+        typename Value<Pipe>::Type    tmp, orig;
+        unsigned                    errorPos;        // position of substitution
+        unsigned                    character;        // replacement character
+        unsigned                    skipChar;        // skip the original character
+
         Pipe(TInput& _in):
             in(_in) {}
 
@@ -107,35 +88,35 @@ namespace SEQAN_NAMESPACE_MAIN
         }
 
         inline Pipe& operator++() {
-			do {
-				if (++character < ValueSize<TValue>::VALUE)
-					// next replacement value
-					assignValue(tmp.i2, errorPos, (TValue) character);
-				else {
-					// next error position					
-					assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
-					character = 0;
-					if (++errorPos < length(tmp.i2)) {
-						skipChar = (unsigned) orig.i2[errorPos];
-						assignValue(tmp.i2, errorPos, (TValue) 0);
-					} else {
-						// next tuple
-						errorPos = 0;
-						++in;
-						for(unsigned i = 1; i < STEP_SIZE && !eof(in); ++i)
-							++in;
-						if (!eof(in)) {
-							tmp = orig = *in;
-							assignValue(tmp.i2, 0, (TValue) 0);
-						}
-					}
-				}
-			// output the original tuple only once
-			} while ((errorPos > 0) && (character == skipChar)); 
+            do {
+                if (++character < ValueSize<TValue>::VALUE)
+                    // next replacement value
+                    assignValue(tmp.i2, errorPos, (TValue) character);
+                else {
+                    // next error position
+                    assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
+                    character = 0;
+                    if (++errorPos < length(tmp.i2)) {
+                        skipChar = (unsigned) orig.i2[errorPos];
+                        assignValue(tmp.i2, errorPos, (TValue) 0);
+                    } else {
+                        // next tuple
+                        errorPos = 0;
+                        ++in;
+                        for(unsigned i = 1; i < STEP_SIZE && !eof(in); ++i)
+                            ++in;
+                        if (!eof(in)) {
+                            tmp = orig = *in;
+                            assignValue(tmp.i2, 0, (TValue) 0);
+                        }
+                    }
+                }
+            // output the original tuple only once
+            } while ((errorPos > 0) && (character == skipChar));
 
             return *this;
         }
-	};
+    };
 
 
     //////////////////////////////////////////////////////////////////////////////
@@ -143,227 +124,227 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TInput, unsigned STEP_SIZE >
     struct Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > >
     {
-		typedef typename Value< typename Value<TInput>::Type, 2 >::Type	TTuple;
-		typedef typename Value<TTuple>::Type							TValue;
+        typedef typename Value< typename Value<TInput>::Type, 2 >::Type    TTuple;
+        typedef typename Value<TTuple>::Type                            TValue;
 
-		enum TState { SUBST_, DELETE_, INSERT_, INSERT_LAST_, Eof_, INSERT_EOS_ };
+        enum TState { SUBST_, DELETE_, INSERT_, INSERT_LAST_, Eof_, INSERT_EOS_ };
 
         TInput                      &in;
-        typename Value<Pipe>::Type	tmp, orig, prev;
-		unsigned					errorPos;		// position of substitution
-		unsigned					character;		// replacement character 
-		unsigned					skipChar;		// skip the original character 
-		TState						state;
+        typename Value<Pipe>::Type    tmp, orig, prev;
+        unsigned                    errorPos;        // position of substitution
+        unsigned                    character;        // replacement character
+        unsigned                    skipChar;        // skip the original character
+        TState                        state;
 
         Pipe(TInput& _in):
             in(_in),
-			state(Eof_) {}
+            state(Eof_) {}
 
         inline typename Value<Pipe>::Type const & operator*() const {
             return tmp;
         }
 
         inline Pipe& operator++() {
-			switch (state) {
-			case SUBST_:
-				// before SUBST_ (tmp[1..] == orig[1..] and tmp[0] == 0) holds
-				do {
-					if (++character < ValueSize<TValue>::VALUE) {
-						// next replacement value
-						assignValue(tmp.i2, errorPos, (TValue) character);
-					} else {
-						// next substitution position
-						assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
-						character = 0;
-						if (++errorPos < length(tmp.i2)) {
-							skipChar = (unsigned) orig.i2[errorPos];
-							assignValue(tmp.i2, errorPos, (TValue) 0);
-						} else {
-							// NEXT TUPLE
-							// now (tmp == orig) holds
-							++in;
-							for(unsigned i = 1; i < STEP_SIZE && !eof(in); ++i)
-								++in;
-							if (!eos(in)) {
-								prev = orig;
-								orig = *in;
-								tmp.i2 = orig.i2;
-								assignValue(tmp.i2, 0, prev.i2[0]);
-								assignValue(tmp.i2, 1, prev.i2[1]);
-								if (length(tmp.i2) >= 4) {
-									errorPos = 2;
-									state = DELETE_;
-									//::std::cerr << ::std::endl << "_DELETIONS____" << ::std::endl;
-									return *this;
-								}
-							} else {
-								// LAST TUPLE
-								shiftLeft(orig.i2);
-								assignValue(tmp.i2, 0, orig.i2[0]);
-								assignValue(tmp.i2, 1, (TValue) 0);
-								character = 0;
-								errorPos = 1;
-								state = INSERT_LAST_;
-								//::std::cerr << ::std::endl << "_INSERTS______" << ::std::endl;
-								return *this;
-							}
-						}
-					}
-				// output the original tuple only once
-				} while ((errorPos > 0) && (character == skipChar));
-				break;
-			case DELETE_:
-				// before DELETE_ (prev=orig, ++in; tmp=orig=*in) holds
-				assignValue(tmp.i2, errorPos, prev.i2[errorPos]);
-				if (++errorPos >= length(tmp.i2) - 1) {
-					assignValue(tmp.i2, length(tmp.i2)-1, prev.i2[length(tmp.i2)-1]);
-					assignValue(tmp.i2, 0, orig.i2[0]);
-					assignValue(tmp.i2, 1, (TValue) 0);
-					character = 0;
-					errorPos = 1;
-					state = INSERT_;
-					//::std::cerr << ::std::endl << "_INSERTS______" << ::std::endl;
-				}
-				break;
-
-			case INSERT_EOS_:
-				state = INSERT_;
-			case INSERT_:
-			case INSERT_LAST_:
-				// before INSERT_ (prev=orig, ++in; tmp=prev) holds
-				if (++character < ValueSize<TValue>::VALUE)
-					// next replacement value
-					assignValue(tmp.i2, errorPos, (TValue) character);
-				else {
-					// next insert position					
-					assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
-					character = 0;
-					if (++errorPos >= length(tmp.i2) - 1 && state == INSERT_) {
-						tmp = orig;
-						state = SUBST_;
-						//::std::cerr << ::std::endl << "_REPLACEMENTS_" << ::std::endl;
-						errorPos = 0;
-						assignValue(tmp.i2, 0, (TValue) 0);
-						break;
-					}
-					if (errorPos >= length(tmp.i2)) {
-						if (eof(in))
-							state = Eof_;
-						else {
-							tmp = orig = *in;
-
-							// begin to insert the first char at position 0
-							shiftRight(tmp.i2);
-							assignValue(tmp.i2, 1, (TValue) 0);
-							errorPos = 0;
-							state = INSERT_EOS_;
-							//::std::cerr << ::std::endl << "_INSERTS______" << ::std::endl;
-						}
-						break;
-					}
-					assignValue(tmp.i2, errorPos, (TValue) 0);
-				}
-			default:;
-			}			
+            switch (state) {
+            case SUBST_:
+                // before SUBST_ (tmp[1..] == orig[1..] and tmp[0] == 0) holds
+                do {
+                    if (++character < ValueSize<TValue>::VALUE) {
+                        // next replacement value
+                        assignValue(tmp.i2, errorPos, (TValue) character);
+                    } else {
+                        // next substitution position
+                        assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
+                        character = 0;
+                        if (++errorPos < length(tmp.i2)) {
+                            skipChar = (unsigned) orig.i2[errorPos];
+                            assignValue(tmp.i2, errorPos, (TValue) 0);
+                        } else {
+                            // NEXT TUPLE
+                            // now (tmp == orig) holds
+                            ++in;
+                            for(unsigned i = 1; i < STEP_SIZE && !eof(in); ++i)
+                                ++in;
+                            if (!eos(in)) {
+                                prev = orig;
+                                orig = *in;
+                                tmp.i2 = orig.i2;
+                                assignValue(tmp.i2, 0, prev.i2[0]);
+                                assignValue(tmp.i2, 1, prev.i2[1]);
+                                if (length(tmp.i2) >= 4) {
+                                    errorPos = 2;
+                                    state = DELETE_;
+                                    //std::cerr << std::endl << "_DELETIONS____" << std::endl;
+                                    return *this;
+                                }
+                            } else {
+                                // LAST TUPLE
+                                shiftLeft(orig.i2);
+                                assignValue(tmp.i2, 0, orig.i2[0]);
+                                assignValue(tmp.i2, 1, (TValue) 0);
+                                character = 0;
+                                errorPos = 1;
+                                state = INSERT_LAST_;
+                                //std::cerr << std::endl << "_INSERTS______" << std::endl;
+                                return *this;
+                            }
+                        }
+                    }
+                // output the original tuple only once
+                } while ((errorPos > 0) && (character == skipChar));
+                break;
+            case DELETE_:
+                // before DELETE_ (prev=orig, ++in; tmp=orig=*in) holds
+                assignValue(tmp.i2, errorPos, prev.i2[errorPos]);
+                if (++errorPos >= length(tmp.i2) - 1) {
+                    assignValue(tmp.i2, length(tmp.i2)-1, prev.i2[length(tmp.i2)-1]);
+                    assignValue(tmp.i2, 0, orig.i2[0]);
+                    assignValue(tmp.i2, 1, (TValue) 0);
+                    character = 0;
+                    errorPos = 1;
+                    state = INSERT_;
+                    //std::cerr << std::endl << "_INSERTS______" << std::endl;
+                }
+                break;
+
+            case INSERT_EOS_:
+                state = INSERT_;
+            case INSERT_:
+            case INSERT_LAST_:
+                // before INSERT_ (prev=orig, ++in; tmp=prev) holds
+                if (++character < ValueSize<TValue>::VALUE)
+                    // next replacement value
+                    assignValue(tmp.i2, errorPos, (TValue) character);
+                else {
+                    // next insert position
+                    assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
+                    character = 0;
+                    if (++errorPos >= length(tmp.i2) - 1 && state == INSERT_) {
+                        tmp = orig;
+                        state = SUBST_;
+                        //std::cerr << std::endl << "_REPLACEMENTS_" << std::endl;
+                        errorPos = 0;
+                        assignValue(tmp.i2, 0, (TValue) 0);
+                        break;
+                    }
+                    if (errorPos >= length(tmp.i2)) {
+                        if (eof(in))
+                            state = Eof_;
+                        else {
+                            tmp = orig = *in;
+
+                            // begin to insert the first char at position 0
+                            shiftRight(tmp.i2);
+                            assignValue(tmp.i2, 1, (TValue) 0);
+                            errorPos = 0;
+                            state = INSERT_EOS_;
+                            //std::cerr << std::endl << "_INSERTS______" << std::endl;
+                        }
+                        break;
+                    }
+                    assignValue(tmp.i2, errorPos, (TValue) 0);
+                }
+            default:;
+            }
             return *this;
-		}
-	};
+        }
+    };
 
 
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
     template < typename TInput, unsigned STEP_SIZE >
-	inline bool 
-	control(
-		Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > &me, 
-		ControlBeginRead const &command) 
-	{
+    inline bool
+    control(
+        Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > &me,
+        ControlBeginRead const &command)
+    {
         if (!control(me.in, command)) return false;
 
-		me.tmp = me.orig = *me.in;
-		me.errorPos = 0;
-		me.character = 0;
+        me.tmp = me.orig = *me.in;
+        me.errorPos = 0;
+        me.character = 0;
+
+        return true;
+    }
 
-		return true;
-	}
-    
     template < typename TInput, unsigned STEP_SIZE >
-	inline bool 
-	control(
-		Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me, 
-		ControlBeginRead const &command) 
-	{
+    inline bool
+    control(
+        Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me,
+        ControlBeginRead const &command)
+    {
         if (!control(me.in, command)) return false;
 
-		if (eof(me.in)) {
-			me.state = me.Eof_;
-			return true;
-		}
+        if (eof(me.in)) {
+            me.state = me.Eof_;
+            return true;
+        }
+
+        typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
+        typedef typename Value<TTuple>::Type                            TValue;
 
-		typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
-		typedef typename Value<TTuple>::Type							TValue;
+        me.tmp = me.orig = *me.in;
 
-		me.tmp = me.orig = *me.in;
+        // begin to insert the first char at position 0
+        shiftRight(me.tmp.i2);
+        assignValue(me.tmp.i2, 0, (TValue) 0);
+        me.character = 0;
+        me.errorPos = 0;
+        me.state = me.INSERT_;
+        //std::cerr << std::endl << "_INSERTS______" << std::endl;
 
-		// begin to insert the first char at position 0
-		shiftRight(me.tmp.i2);
-		assignValue(me.tmp.i2, 0, (TValue) 0);
-		me.character = 0;
-		me.errorPos = 0;
-		me.state = me.INSERT_;
-		//::std::cerr << ::std::endl << "_INSERTS______" << ::std::endl;
+        return true;
+    }
 
-		return true;
-	}
-    
     template < typename TInput, unsigned STEP_SIZE >
-	inline bool 
-	control(
-		Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me, 
-		ControlEof const &) 
-	{
-		return me.state == me.Eof_;
+    inline bool
+    control(
+        Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me,
+        ControlEof const &)
+    {
+        return me.state == me.Eof_;
     }
 
     template < typename TInput, unsigned STEP_SIZE >
-	inline bool 
-	control(
-		Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me, 
-		ControlEos const &) 
-	{
-		return me.state == me.Eof_ || me.state == me.INSERT_EOS;
+    inline bool
+    control(
+        Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me,
+        ControlEos const &)
+    {
+        return me.state == me.Eof_ || me.state == me.INSERT_EOS;
     }
 
     template < typename TInput, unsigned STEP_SIZE >
     inline typename Size< Pipe< TInput, Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > > >::Type
     length(Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > const &me) {
-		typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
-		typedef typename Size< Pipe< TInput, Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > > >::Type TSize;
-
-		unsigned alphabetSize = ValueSize< typename Value<TTuple>::Type >::VALUE;
-		/*unsigned seqs = countSequences(me.in);*/
-		TSize sum = 0;
-/*		for(unsigned i = 0; i < seqs; ++i)
-			sum += (length((*me.in.in.in.in.set)[i]) / STEP_SIZE) * (1 + length(me.tmp.i2) * (alphabetSize - 1));
-		return sum;
-*/		return (length(me.in) / STEP_SIZE) * (1 + length(me.tmp.i2) * (alphabetSize - 1));
+        typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
+        typedef typename Size< Pipe< TInput, Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > > >::Type TSize;
+
+        unsigned alphabetSize = ValueSize< typename Value<TTuple>::Type >::VALUE;
+        /*unsigned seqs = countSequences(me.in);*/
+        TSize sum = 0;
+/*        for(unsigned i = 0; i < seqs; ++i)
+            sum += (length((*me.in.in.in.in.set)[i]) / STEP_SIZE) * (1 + length(me.tmp.i2) * (alphabetSize - 1));
+        return sum;
+*/        return (length(me.in) / STEP_SIZE) * (1 + length(me.tmp.i2) * (alphabetSize - 1));
     }
 
     template < typename TInput, unsigned STEP_SIZE >
     inline typename Size< Pipe< TInput, Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > > >::Type
     length(Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > const &me) {
-		typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
-		unsigned alphabetSize = ValueSize< typename Value<TTuple>::Type >::VALUE;
-		unsigned seqs = countSequences(me.in);
-		// TODO: We run into problems when one sequence contains 1 or less tuples
-		// length should be ommitted in future, but Pools or the skew algorithm needs to know the stream length
-		if (length(me.in) >= seqs)
-			return 
-				  (length(me.in) / STEP_SIZE)     * (1 + length(me.tmp.i2) * (alphabetSize - 1)) +			// substitutions and original
-				 ((length(me.in) / STEP_SIZE) - seqs) * (length(me.tmp.i2) - 3) +							// deletions
-				(((length(me.in) / STEP_SIZE) + seqs) * (length(me.tmp.i2) - 2) + 2 * seqs) * alphabetSize;	// insertions
-		else
-			return 0;
+        typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
+        unsigned alphabetSize = ValueSize< typename Value<TTuple>::Type >::VALUE;
+        unsigned seqs = countSequences(me.in);
+        // TODO: We run into problems when one sequence contains 1 or less tuples
+        // length should be ommitted in future, but Pools or the skew algorithm needs to know the stream length
+        if (length(me.in) >= seqs)
+            return
+                  (length(me.in) / STEP_SIZE)     * (1 + length(me.tmp.i2) * (alphabetSize - 1)) +            // substitutions and original
+                 ((length(me.in) / STEP_SIZE) - seqs) * (length(me.tmp.i2) - 3) +                            // deletions
+                (((length(me.in) / STEP_SIZE) + seqs) * (length(me.tmp.i2) - 2) + 2 * seqs) * alphabetSize;    // insertions
+        else
+            return 0;
     }
 //}
 
diff --git a/seqan/pipe/pipe_filter.h b/seqan/pipe/pipe_filter.h
index d0b412e..7776142 100644
--- a/seqan/pipe/pipe_filter.h
+++ b/seqan/pipe/pipe_filter.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,9 +40,9 @@ namespace SEQAN_NAMESPACE_MAIN
 
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
-    
+
     template <typename TValue, typename TResult = typename Value<TValue, 1>::Type>
-    struct filterI1 : public ::std::unary_function<TValue, TResult>
+    struct filterI1 : public std::unary_function<TValue, TResult>
     {
         inline TResult operator() (const TValue & x) const
         {
@@ -51,7 +51,7 @@ namespace SEQAN_NAMESPACE_MAIN
     };
 
     template <typename TValue, typename TResult = typename Value<TValue, 2>::Type>
-    struct filterI2 : public ::std::unary_function<TValue, TResult>
+    struct filterI2 : public std::unary_function<TValue, TResult>
     {
         inline TResult operator() (const TValue & x) const
         {
@@ -60,7 +60,7 @@ namespace SEQAN_NAMESPACE_MAIN
     };
 
     template <typename TValue, typename TResult = typename Value<TValue, 3>::Type>
-    struct filterI3 : public ::std::unary_function<TValue, TResult>
+    struct filterI3 : public std::unary_function<TValue, TResult>
     {
         inline TResult operator() (const TValue & x) const
         {
@@ -72,77 +72,53 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TFunctor >
     struct Filter;
 
-	template < typename TInput, typename TFunctor >
+    template < typename TInput, typename TFunctor >
     struct Value< Pipe< TInput, Filter<TFunctor> > >
     {
-		typedef typename TFunctor::result_type Type;
-	};
+        typedef typename TFunctor::result_type Type;
+    };
 
 /*!
  * @class Filter
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
  * @brief Applies a specific function to the input stream.
- * 
+ *
  * @signature template <typename TInput, typename TFunctor>
  *            struct Pipe<TInput, Filter<TFunctor> >;
- * 
+ *
  * @tparam TFunctor A unary function (see STL's <tt>unary_function</tt>).  The argument type of <tt>TFunctor</tt>
  *                  must be <tt>VALUE&lt;TInput&gt;::Type</tt>.
  * @tparam TInput   The type of the pipeline module this module reads from.
- * 
- * @section Remarks
- * 
+ *
  * The output type of this pipe is the result type of <tt>TFunctor</tt>.
  */
 
-/**
-.Spec.Filter:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Applies a specific function to the input stream.
-..signature:Pipe<TInput, Filter<TFunctor> >
-..param.TInput:The type of the pipeline module this module reads from.
-..param.TFunctor:A unary function (see STL's $unary_function$).
-...remarks:The argument type of $TFunctor$ must be $VALUE<TInput>::Type$.
-..remarks: The output type of this pipe is the result type of $TFunctor$.
-..include:seqan/pipe.h
-*/
-
-	//////////////////////////////////////////////////////////////////////////////
+    //////////////////////////////////////////////////////////////////////////////
     // filter class
     template <typename TInput, typename TFunctor >
     struct Pipe< TInput, Filter<TFunctor> >
     {
-		TInput      &in;
+        TInput      &in;
         TFunctor    F;
 
 /*!
  * @fn Filter::Pipe
  * @brief Constructor
- * 
+ *
  * @signature Pipe::Pipe(in[, func]);
- * 
+ *
  * @param[in] in   Reference to an input pipe.
- * @param[in] func A TFunctor object (copy constructor).
+ * @param[in] func A <tt>TFunctor</tt> object.
  */
-        
-/**
-.Memfunc.Filter#Pipe:
-..class:Spec.Filter
-..summary:Constructor
-..signature:Pipe<TInput, Filter<TFunctor> > (in)
-..signature:Pipe<TInput, Filter<TFunctor> > (in, func)
-..param.in:Reference to an input pipe.
-..param.func:A TFunctor object (copy constructor).
-*/
+
         Pipe(TInput& _in):
             in(_in) {}
-        
+
         Pipe(TInput& _in, const TFunctor& F_) :
             in(_in),
             F(F_) {}
-        
+
         inline typename Value<Pipe>::Type const operator*() const
         {
             return F(*in);
@@ -153,9 +129,9 @@ namespace SEQAN_NAMESPACE_MAIN
             ++in;
             return *this;
         }
-                
+
     };
-    
+
 //}
 
 }
diff --git a/seqan/pipe/pipe_iterator.h b/seqan/pipe/pipe_iterator.h
index 0f211a3..18c109c 100644
--- a/seqan/pipe/pipe_iterator.h
+++ b/seqan/pipe/pipe_iterator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,217 +41,217 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	//////////////////////////////////////////////////////////////////////////////
-	// input pipe iterator
-	// interface between pipe modules and algorithms working with iterators
+    //////////////////////////////////////////////////////////////////////////////
+    // input pipe iterator
+    // interface between pipe modules and algorithms working with iterators
 
     template <typename TInput>
     struct IPipeIterator
     {
-		//////////////////////////////////////////////////////////////////////////////
-		// public iterator interface
-
-		typedef IPipeIterator					iterator;
-		typedef ::std::forward_iterator_tag		iterator_category;
-		typedef typename Value<TInput>::Type	value_type;
-		typedef const value_type			    const_value_type;
-		typedef typename Size<TInput>::Type		difference_type;
-		typedef value_type*						pointer;
-		typedef value_type&						reference;
-		typedef const value_type&				const_reference;
-		
-        TInput*			in;
-		difference_type	rest;
-        
-	    IPipeIterator():
-			in(NULL),
-			rest(0) {}
-
-	    IPipeIterator(TInput &_in):
-			in(&_in),
-			rest(length(_in))
-		{
-			beginRead(*in);
-		}
-
-		IPipeIterator(const iterator &I):
-			in(I.in),
-			rest(I.rest) {}
-
-		const_value_type operator* () const {
-			return **in;
-		}
-    
-		//const_reference operator* () const {
-		//	return **in;
-		//}
-    
-		iterator& operator++ () {
-			++(*in); 
-			if (!--rest) endRead(*in);
-			return *this;
-		}
-
-		iterator operator++ (int) {
-			iterator before = *this;
-			++*this;
-			return before;
-		}
-
-		iterator operator+ (difference_type delta) {
-			for(; delta != 0; --delta)
-				++*this;
-			return *this;
-		}
-		
+        //////////////////////////////////////////////////////////////////////////////
+        // public iterator interface
+
+        typedef IPipeIterator                    iterator;
+        typedef std::forward_iterator_tag        iterator_category;
+        typedef typename Value<TInput>::Type    value_type;
+        typedef const value_type                const_value_type;
+        typedef typename Size<TInput>::Type        difference_type;
+        typedef value_type*                        pointer;
+        typedef value_type&                        reference;
+        typedef const value_type&                const_reference;
+
+        TInput*            in;
+        difference_type    rest;
+
+        IPipeIterator():
+            in(NULL),
+            rest(0) {}
+
+        IPipeIterator(TInput &_in):
+            in(&_in),
+            rest(length(_in))
+        {
+            beginRead(*in);
+        }
+
+        IPipeIterator(const iterator &I):
+            in(I.in),
+            rest(I.rest) {}
+
+        const_value_type operator* () const {
+            return **in;
+        }
+
+        //const_reference operator* () const {
+        //    return **in;
+        //}
+
+        iterator& operator++ () {
+            ++(*in);
+            if (!--rest) endRead(*in);
+            return *this;
+        }
+
+        iterator operator++ (int) {
+            iterator before = *this;
+            ++*this;
+            return before;
+        }
+
+        iterator operator+ (difference_type delta) {
+            for(; delta != 0; --delta)
+                ++*this;
+            return *this;
+        }
+
         difference_type operator- (const iterator &I) const {
-			return I.rest - rest;
-		}
-		
-		bool Equal_(const iterator &I) const {
-			return rest == I.rest;
-		}
-	};
-    
+            return I.rest - rest;
+        }
+
+        bool Equal_(const iterator &I) const {
+            return rest == I.rest;
+        }
+    };
+
     template <typename TInput>
-	bool operator==(const IPipeIterator<TInput>& _Left, const IPipeIterator<TInput>& Right_)
-	{
-		return _Left.Equal_(Right_);
-	}
+    bool operator==(const IPipeIterator<TInput>& _Left, const IPipeIterator<TInput>& Right_)
+    {
+        return _Left.Equal_(Right_);
+    }
 
     template <typename TInput>
-	bool operator!=(const IPipeIterator<TInput>& _Left, const IPipeIterator<TInput>& Right_)
-	{
-		return !(_Left == Right_);
-	}
+    bool operator!=(const IPipeIterator<TInput>& _Left, const IPipeIterator<TInput>& Right_)
+    {
+        return !(_Left == Right_);
+    }
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// output pipe iterator
-	// interface between algorithms working with iterators and pipe modules 
+    //////////////////////////////////////////////////////////////////////////////
+    // output pipe iterator
+    // interface between algorithms working with iterators and pipe modules
 
     template <typename TOutput>
     struct OPipeIterator
-    {        
-		//////////////////////////////////////////////////////////////////////////////
-		// public iterator interface
-
-		typedef OPipeIterator					iterator;
-		typedef ::std::forward_iterator_tag		iterator_category;
-		typedef typename Value<TOutput>::Type	value_type;
-		typedef typename Size<TOutput>::Type	difference_type;
-		typedef iterator*						pointer;
-		typedef iterator&						reference;
-		typedef value_type const &				const_reference;
-		
-        TOutput*		out;
-		difference_type	rest;
-        
-	    OPipeIterator():
-			out(NULL),
-			rest(0) {}
-
-	    OPipeIterator(TOutput &_out):
-			out(&_out),
-			rest(length(_out))
-		{
-			beginWrite(*out);
-		}
-
-		OPipeIterator(const iterator &I):
-			out(I.out),
-			rest(I.rest) {}
-
-		reference operator* () {
-			return *this;
-		}
-
-		iterator operator= (const_reference _v) {
-			out->push(_v);
-			return *this;
-		}
-    
-		iterator& operator++ () {
-			++(*out);
-			if (!--rest) endWrite(*out);
-			return *this;
-		}
-
-		iterator operator++ (int) {
-			iterator before = *this;
-			++*this;
-			return before;
-		}
+    {
+        //////////////////////////////////////////////////////////////////////////////
+        // public iterator interface
+
+        typedef OPipeIterator                    iterator;
+        typedef std::forward_iterator_tag        iterator_category;
+        typedef typename Value<TOutput>::Type    value_type;
+        typedef typename Size<TOutput>::Type    difference_type;
+        typedef iterator*                        pointer;
+        typedef iterator&                        reference;
+        typedef value_type const &                const_reference;
+
+        TOutput*        out;
+        difference_type    rest;
+
+        OPipeIterator():
+            out(NULL),
+            rest(0) {}
+
+        OPipeIterator(TOutput &_out):
+            out(&_out),
+            rest(length(_out))
+        {
+            beginWrite(*out);
+        }
+
+        OPipeIterator(const iterator &I):
+            out(I.out),
+            rest(I.rest) {}
+
+        reference operator* () {
+            return *this;
+        }
+
+        iterator operator= (const_reference _v) {
+            out->push(_v);
+            return *this;
+        }
+
+        iterator& operator++ () {
+            ++(*out);
+            if (!--rest) endWrite(*out);
+            return *this;
+        }
+
+        iterator operator++ (int) {
+            iterator before = *this;
+            ++*this;
+            return before;
+        }
 
         difference_type operator- (const iterator &I) const {
-			return I.rest - rest;
-		}
-		
-		bool Equal_(const iterator &I) const {
-			return rest == I.rest;
-		}
-	};
+            return I.rest - rest;
+        }
+
+        bool Equal_(const iterator &I) const {
+            return rest == I.rest;
+        }
+    };
 
     template <typename TOutput>
-	bool operator==(const OPipeIterator<TOutput>& _Left, const OPipeIterator<TOutput>& Right_)
-	{
-		return _Left.Equal_(Right_);
-	}
+    bool operator==(const OPipeIterator<TOutput>& _Left, const OPipeIterator<TOutput>& Right_)
+    {
+        return _Left.Equal_(Right_);
+    }
 
     template <typename TOutput>
-	bool operator!=(const OPipeIterator<TOutput>& _Left, const OPipeIterator<TOutput>& Right_)
-	{
-		return !(_Left == Right_);
-	}
+    bool operator!=(const OPipeIterator<TOutput>& _Left, const OPipeIterator<TOutput>& Right_)
+    {
+        return !(_Left == Right_);
+    }
 
 
     template < typename TInput, typename TSpec, typename TIteratorSpec >
-	struct Iterator< Pipe< TInput, TSpec >, TIteratorSpec> {
-		typedef IPipeIterator< Pipe< TInput, TSpec > > Type;
-	};
+    struct Iterator< Pipe< TInput, TSpec >, TIteratorSpec> {
+        typedef IPipeIterator< Pipe< TInput, TSpec > > Type;
+    };
 
-	template < typename TInput >
-	struct Value< IPipeIterator< TInput > > {
-		typedef typename Value<TInput>::Type Type;
-	};
+    template < typename TInput >
+    struct Value< IPipeIterator< TInput > > {
+        typedef typename Value<TInput>::Type Type;
+    };
 
-	template < typename TInput >
-	struct Size< IPipeIterator< TInput > > {
-		typedef typename Size<TInput>::Type Type;
-	};
+    template < typename TInput >
+    struct Size< IPipeIterator< TInput > > {
+        typedef typename Size<TInput>::Type Type;
+    };
 
-	template < typename TOutput >
-	struct Value< OPipeIterator< TOutput > > {
-		typedef typename Value<TOutput>::Type Type;
-	};
+    template < typename TOutput >
+    struct Value< OPipeIterator< TOutput > > {
+        typedef typename Value<TOutput>::Type Type;
+    };
 
-	template < typename TOutput >
-	struct Size< OPipeIterator< TOutput > > {
-		typedef typename Size<TOutput>::Type Type;
-	};
+    template < typename TOutput >
+    struct Size< OPipeIterator< TOutput > > {
+        typedef typename Size<TOutput>::Type Type;
+    };
 
 
     template < typename TInput, typename TSpec >
-	IPipeIterator< Pipe< TInput, TSpec > >
-	begin(Pipe< TInput, TSpec > &pipe) {
-		return IPipeIterator< Pipe< TInput, TSpec > >(pipe);
-	}
+    IPipeIterator< Pipe< TInput, TSpec > >
+    begin(Pipe< TInput, TSpec > &pipe) {
+        return IPipeIterator< Pipe< TInput, TSpec > >(pipe);
+    }
 
     template < typename TInput, typename TSpec >
-	IPipeIterator< Pipe< TInput, TSpec > >
-	end(Pipe< TInput, TSpec > &/*pipe*/) {
-		return IPipeIterator< Pipe< TInput, TSpec > >();
-	}
+    IPipeIterator< Pipe< TInput, TSpec > >
+    end(Pipe< TInput, TSpec > &/*pipe*/) {
+        return IPipeIterator< Pipe< TInput, TSpec > >();
+    }
 
 
-	template < typename TInput >
+    template < typename TInput >
     inline typename Difference<TInput>::Type
     difference(IPipeIterator<TInput> first, IPipeIterator<TInput> last) {
         return last - first;
     }
 
-	template < typename TOutput >
+    template < typename TOutput >
     inline typename Difference<TOutput>::Type
     difference(OPipeIterator<TOutput> first, OPipeIterator<TOutput> last) {
         return last - first;
diff --git a/seqan/pipe/pipe_joiner.h b/seqan/pipe/pipe_joiner.h
index 9e77327..b0e869f 100644
--- a/seqan/pipe/pipe_joiner.h
+++ b/seqan/pipe/pipe_joiner.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,76 +41,60 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	struct Joiner;
+    struct Joiner;
 
-	template < typename TInput1, typename TInput2 >
+    template < typename TInput1, typename TInput2 >
     struct Value< Pipe< Bundle2< TInput1, TInput2 >, Joiner > > {
-		typedef Pair<
-			typename Value<TInput1>::Type,
-			typename Value<TInput2>::Type
-		> Type;
-	};
+        typedef Pair<
+            typename Value<TInput1>::Type,
+            typename Value<TInput2>::Type
+        > Type;
+    };
 
-	template < typename TInput1, typename TInput2, typename TInput3 >
+    template < typename TInput1, typename TInput2, typename TInput3 >
     struct Value< Pipe< Bundle3< TInput1, TInput2, TInput3 >, Joiner > > {
-		typedef Triple<
-			typename Value<TInput1>::Type,
-			typename Value<TInput2>::Type,
-			typename Value<TInput3>::Type
-		> Type;
-	};
+        typedef Triple<
+            typename Value<TInput1>::Type,
+            typename Value<TInput2>::Type,
+            typename Value<TInput3>::Type
+        > Type;
+    };
 
 /*!
  * @class Joiner
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
  * @brief Joins two or three input streams.
- * 
+ *
  * @signature template <typename TInput1, typename TInput2>
- *            class Pipe<Bundle3<TInput1, TInput2>, Joiner>;
+ *            class Pipe<Bundle2<TInput1, TInput2>, Joiner>;
  * @signature template <typename TInput1, typename TInput2, typename TInput3>
  *            class Pipe<Bundle3<TInput1, TInput2, TInput3>, Joiner>;
- * 
+ *
  * @tparam TInput1 The type of the first pipeline module this module reads from.
  * @tparam TInput2 The type of the second pipeline module this module reads from.
  * @tparam TInput3 The type of the third pipeline module this module reads from.
- * 
- * @section Remarks
- * 
- * The output type is a packed Pair or Triple of the input types <tt>Value&lt;TInputX&gt;::Type</tt>.
+ *
+ * The output type is a packed @link  Pair  @endlink or @link Triple @endlink of the input types <tt>Value&lt;TInputX&gt;::Type</tt>.
  */
 
-/**
-.Spec.Joiner:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Joins two or three input streams.
-..signature:Pipe<Bundle2<TInput1, TInput2>, Joiner>
-..signature:Pipe<Bundle3<TInput1, TInput2, TInput3>, Joiner>
-..param.TInput1:The type of the first pipeline module this module reads from.
-..param.TInput2:The type of the second pipeline module this module reads from.
-..param.TInput3:The type of the third pipeline module this module reads from.
-..remarks: The output type is a packed @Class.Pair@ or @Class.Triple@ of the input types $Value<TInputX>::Type$.
-..include:seqan/pipe.h
-*/
-
     //////////////////////////////////////////////////////////////////////////////
     // joiner class
-	template < typename TInput1, typename TInput2 >
+    template < typename TInput1, typename TInput2 >
     struct Pipe< Bundle2< TInput1, TInput2 >, Joiner >
     {
-		Bundle2< TInput1, TInput2 >	in;
-        typename Value<Pipe>::Type	tmp;
-        
+        Bundle2< TInput1, TInput2 >    in;
+        typename Value<Pipe>::Type    tmp;
+
         Pipe(Bundle2< TInput1, TInput2 > _in):
             in(_in) {}
-        
+
         inline typename Value<Pipe>::Type const & operator*() {
             tmp.i1 = *in.in1;
             tmp.i2 = *in.in2;
             return tmp;
         }
-        
+
         inline Pipe& operator++() {
             ++in.in1;
             ++in.in2;
@@ -118,22 +102,22 @@ namespace SEQAN_NAMESPACE_MAIN
         }
     };
 
-	template < typename TInput1, typename TInput2, typename TInput3 >
+    template < typename TInput1, typename TInput2, typename TInput3 >
     struct Pipe< Bundle3< TInput1, TInput2, TInput3 >, Joiner >
     {
-		Bundle3< TInput1, TInput2, TInput3 >	in;
-        typename Value<Pipe>::Type				tmp;
-        
+        Bundle3< TInput1, TInput2, TInput3 >    in;
+        typename Value<Pipe>::Type                tmp;
+
         Pipe(Bundle3< TInput1, TInput2, TInput3 > _in):
             in(_in) {}
-        
+
         inline typename Value<Pipe>::Type const & operator*() {
             tmp.i1 = *in.in1;
             tmp.i2 = *in.in2;
             tmp.i3 = *in.in3;
             return tmp;
         }
-        
+
         inline Pipe& operator++() {
             ++in.in1;
             ++in.in2;
diff --git a/seqan/pipe/pipe_namer.h b/seqan/pipe/pipe_namer.h
index b5e6527..5a8ba44 100644
--- a/seqan/pipe/pipe_namer.h
+++ b/seqan/pipe/pipe_namer.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,61 +44,44 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TCompare >
     struct Namer;
 
-	template < typename TInput, typename TCompare >
+    template < typename TInput, typename TCompare >
     struct Value< Pipe< TInput, Namer<TCompare> > >
     {
         typedef Pair<
             typename Value<typename Value<TInput>::Type, 1>::Type,
-			typename Size<TInput>::Type,
-			Pack
-		> Type;
+            typename Size<TInput>::Type,
+            Pack
+        > Type;
     };
 
 /*!
  * @class Namer
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
- * 
+ *
  * @brief Extends the input stream by a second field which names the elements.
- * 
+ *
  * @signature template <typename TInput, typename TCompare>
  *            class Pipe<TInput, Namer<TCompare> >;
- * 
+ *
  * @tparam TInput   The type of the pipeline module this module reads from.
  * @tparam TCompare A binary function (see STL's <tt>binary_function</tt>) with result type <tt>int</tt>.  Should
  *                  return <tt>0</tt> if and only if two elements are equal.
- * 
- * @section Remarks
- * 
+ *
  * The output type is a Pair of input type and size type (i.e. <tt>Pair&lt;Value&lt;TInput&gt;::Type, Size&lt;TInput&gt;::Type&gt;</tt>).
- * 
+ *
  * The first output field is the original input stream.
- * 
+ *
  * The second output field is the name. This field begins with 0 and increases by 1 for every distinct element. Two
  * elements gets the same name, if and only if they are equal.
  */
 
-/**
-.Spec.Namer:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Extends the input stream by a second field which names the elements.
-..signature:Pipe<TInput, Namer<TCompare> >
-..param.TInput:The type of the pipeline module this module reads from.
-..param.TCompare:A binary function (see STL's $binary_function$) with result type $int$.
-...remarks:Should return $0$ if and only if two elements are equal.
-..remarks:The output type is a @Class.Pair@ of input type and size type (i.e. $Pair<Value<TInput>::Type, Size<TInput>::Type>$).
-..remarks:The first output field is the original input stream.
-..remarks:The second output field is the name. This field begins with 0 and increases by 1 for every distinct element. Two elements gets the same name, if and only if they are equal.
-..include:seqan/pipe.h
-*/
-
     //////////////////////////////////////////////////////////////////////////////
     // namer class
     template < typename TInput, typename TCompare >
     struct Pipe< TInput, Namer<TCompare> >
     {
-		TInput                          &in;
+        TInput                          &in;
         TCompare                        C;
         typename Value<Pipe>::Type      tmp;
         typename Value<TInput>::Type    last;
@@ -106,29 +89,20 @@ namespace SEQAN_NAMESPACE_MAIN
 /*!
  * @fn Namer::Pipe
  * @brief Constructor
- * 
+ *
  * @signature Pipe::Pipe(in[, comp]);
- * 
+ *
  * @param[in] in   Reference to an input pipe.
  * @param[in] comp A <tt>TCompare</tt> object (copied).
  */
 
-/**
-.Memfunc.Namer#Pipe:
-..class:Spec.Namer
-..summary:Constructor
-..signature:Pipe<TInput, Namer<TCompare> > (in)
-..signature:Pipe<TInput, Namer<TCompare> > (in, comp)
-..param.in:Reference to an input pipe.
-..param.comp:A $TCompare$ object (copy constructor).
-*/
         Pipe(TInput& _in):
             in(_in) {}
-        
+
         Pipe(TInput& _in, const TCompare& tmpC) :
             in(_in),
             C(tmpC) {}
-        
+
         inline typename Value<Pipe>::Type const & operator*()
         {
             tmp.i1 = getValueI1(*in);
@@ -143,7 +117,7 @@ namespace SEQAN_NAMESPACE_MAIN
                 last = *in;
                 ++tmp.i2;
             }
-			return *this;
+            return *this;
         }
 
         bool unique() const
@@ -151,12 +125,12 @@ namespace SEQAN_NAMESPACE_MAIN
             return tmp.i2 == (length(in) - 1);
         }
     };
-    
+
 
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
     template < typename TInput, typename TCompare >
-	inline bool control(Pipe< TInput, Namer<TCompare> > &me, ControlBeginRead const &command)
+    inline bool control(Pipe< TInput, Namer<TCompare> > &me, ControlBeginRead const &command)
     {
         if (!control(me.in, command)) return false;
         if (!eof(me.in))
@@ -165,9 +139,9 @@ namespace SEQAN_NAMESPACE_MAIN
             me.tmp.i1 = me.last.i1;
         }
         me.tmp.i2 = 0;
-		return true;
-	}
-    
+        return true;
+    }
+
 //}
 
 }
diff --git a/seqan/pipe/pipe_sampler.h b/seqan/pipe/pipe_sampler.h
index b06a76a..e6ce0ac 100644
--- a/seqan/pipe/pipe_sampler.h
+++ b/seqan/pipe/pipe_sampler.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -41,18 +41,18 @@ namespace SEQAN_NAMESPACE_MAIN
 //namespace SEQAN_NAMESPACE_PIPELINING
 //{
 
-	template <int I, typename T = void>
-	struct SkewDC_;
+    template <int I, typename T = void>
+    struct SkewDC_;
 
 //////////////////////////////////////////////////////////////////////////////
 
-	template < unsigned m, typename TPack = Pack >
-	struct Sampler;
+    template < unsigned m, typename TPack = Pack >
+    struct Sampler;
 
     template < typename TInput, unsigned m, typename TPack >
     struct Value< Pipe< TInput, Sampler<m, TPack> > >
     {
-        typedef Tuple<typename Value<TInput>::Type, m, TPack>	mTuple;
+        typedef Tuple<typename Value<TInput>::Type, m, TPack>    mTuple;
         typedef Pair<typename Size<TInput>::Type, mTuple, Pack> Type;
     };
 
@@ -61,7 +61,7 @@ namespace SEQAN_NAMESPACE_MAIN
     template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
     struct Value< Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > >
     {
-        typedef Tuple<typename Value<TInput>::Type, m, TPack>	mTuple;
+        typedef Tuple<typename Value<TInput>::Type, m, TPack>    mTuple;
         typedef Pair<TPair, mTuple, Pack> Type;
     };
 
@@ -74,49 +74,28 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
  * @brief Outputs m-tuples beginning at a position of difference cover DC.
- * 
+ *
  * @signature template <typename TInput, unsigned M[, typename TPack]>
  *            class Pipe<TInput, Sampler<M, TPack> >;
- * 
+ *
  * @tparam TInput The type of the pipeline module this module reads from.
  * @tparam m      The tuple size.
  * @tparam TPack  Specifies the packing method of the tuples (<tt>void</tt> = no packing), default is <tt>Pack</tt>.
- * 
- * @section Remarks
- * 
+ *
  * The output type is a Pair of size type and Tuple of input elements and length m (i.e. <tt>Pair&lt;Size&lt;TInput&gt;::Type,
  * Tuple&lt;Value&lt;TInput&gt;::Type, m, TPack&gt; &gt;</tt>).
- * 
+ *
  * The first output field contains the number of remaining pipe elements. The m-tuple in the second field contains the
  * first m elements of them. The m-tuples are substrings of the input stream beginning at positions <tt>i</tt>, with
  * <tt>(n-i) mod m</tt> is element of the set DC (n is the input stream length).
- * 
+ *
  * @section Examples
- * 
+ *
  * The set <tt>{1,2,4}</tt> is represented by <tt>int DC[] = { 3, 1, 2, 4 }</tt>.
- * 
+ *
  * @see BitPackedTuple
  */
 
-/**
-.Spec.Sampler:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Outputs m-tuples beginning at a position of difference cover DC.
-..signature:Pipe<TInput, Sampler<m, DC[, TPacked]> >
-..param.TInput:The type of the pipeline module this module reads from.
-..param.m:The tuple size.
-..param.DC:A set of non-negative integers less than $m$.
-..param.DC:$DC[0]$ contains the size of the set and $DC[1..DC[0]]$ contains the distinct and ordered elements.
-..param.TPack:Specifies the packing method of the tuples ($void$ = no packing).
-...default:@Tag.Pack@.
-..example:The set ${1,2,4}$ is represented by $int DC[] = { 3, 1, 2, 4 }$.
-..remarks:The output type is a @Class.Pair@ of size type and @Class.Tuple@ of input elements and length m (i.e. $Pair<Size<TInput>::Type, Tuple<Value<TInput>::Type, m, TPack> >$).
-..remarks:The first output field contains the number of remaining pipe elements. The m-tuple in the second field contains the first m elements of them.
-The m-tuples are substrings of the input stream beginning at positions $i$, with $(n-i) mod m$ is element of the set DC (n is the input stream length).
-..include:seqan/pipe.h
-*/
-
     //////////////////////////////////////////////////////////////////////////////
     // sampler class
     template < typename TInput, unsigned m, typename TPack >
@@ -125,24 +104,24 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
         typedef typename Value<Pipe>::Type  TOutValue;
         typedef typename Size<Pipe>::Type   TSize;
 
-		TInput		&in;
+        TInput        &in;
         bool        filter[m];
         TSize       idx, _size, _rest;
         unsigned    idxMod;
         TOutValue   tmp1, tmp2;
         TOutValue   *outRef, *tmpRef;
         bool        last;
-        
+
         Pipe(TInput& _in):
             in(_in),
             outRef(&tmp1),
             tmpRef(&tmp2) {}
-        
+
         inline void prepare()
         {
             for (unsigned i = 0; i < m; ++i)
                 filter[i] = 0;
-			for(unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
+            for(unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
                 filter[SkewDC_<m>::VALUE[i]] = true;
 
             idx = length(in);
@@ -158,7 +137,7 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
             fill();
             swap();
         }
-        
+
         inline void fill()
         {
             unsigned i;
@@ -169,7 +148,7 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
                 tmpRef->i2.i[i] = 0;
             tmpRef->i1 = idx;
         }
-        
+
         inline void rotate(unsigned r)
         {
             for(unsigned i = 0; i < m; ++i, ++r)
@@ -178,61 +157,61 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
                 tmpRef->i2.i[i] = outRef->i2.i[r];
             }
         }
-        
+
         inline void swap()
         {
             TOutValue *newOutRef = tmpRef;
             tmpRef = outRef;
             outRef = newOutRef;
         }
-        
+
         inline TOutValue const& operator*()
         {
             return *outRef;
         }
-        
+
         Pipe& operator++()
         {
             unsigned skipped = 0;
-			if (--_rest)
+            if (--_rest)
             {
-				if (!last)
+                if (!last)
                 {
-					do
+                    do
                     {
-						outRef->i2.i[skipped++] = *in;
-						++in;
-						if (idxMod == 0) idxMod = m;
-						--idxMod; --idx;
-						if (eof(in))
+                        outRef->i2.i[skipped++] = *in;
+                        ++in;
+                        if (idxMod == 0) idxMod = m;
+                        --idxMod; --idx;
+                        if (eof(in))
                         {
-							last = true;
-							while (!filter[idxMod])
+                            last = true;
+                            while (!filter[idxMod])
                             {
-								outRef->i2.i[skipped++] = 0;
-								if (idxMod == 0) idxMod = m;
-								--idxMod; --idx;
-							}
-							break;
-						}
-					} while (!filter[idxMod]);
+                                outRef->i2.i[skipped++] = 0;
+                                if (idxMod == 0) idxMod = m;
+                                --idxMod; --idx;
+                            }
+                            break;
+                        }
+                    } while (!filter[idxMod]);
                 }
-				else
+                else
                 {
-					do
+                    do
                     {
-						outRef->i2.i[skipped++] = 0;
-						if (idxMod == 0) idxMod = m;
-						--idxMod; --idx;
-					}
+                        outRef->i2.i[skipped++] = 0;
+                        if (idxMod == 0) idxMod = m;
+                        --idxMod; --idx;
+                    }
                     while (!filter[idxMod]);
                 }
-			}
+            }
             rotate(skipped);
             tmpRef->i1 = idx;
             swap();
             return *this;
-        }        
+        }
     };
 
 
@@ -245,16 +224,16 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
         typedef typename Size<Pipe>::Type           TSize;
         typedef typename Value<TOutValue, 2>::Type  TTuple;
 
-		TInput		&in;
+        TInput        &in;
         bool        filter[m];
         TSize       _size, _rest;
         unsigned    idxMod;
         TOutValue   tmp;
         bool        last;
-        
-        Pipe(TInput& _in):
-            in(_in) {}
-        
+
+        Pipe(TInput & _in) : in(_in), _size(0), _rest(0), idxMod(0), last(false)
+        {}
+
         inline void prepare()
         {
             for (unsigned i = 0; i < m; ++i)
@@ -274,7 +253,7 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
             _rest = length(*this);
             fill();
         }
-        
+
         inline void fill()
         {
             unsigned i;
@@ -287,51 +266,51 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
             last = eof(in);
             tmp.i2 <<= (m - i);
         }
-        
+
         inline TOutValue const& operator*()
         {
             return tmp;
         }
-        
+
         Pipe& operator++()
         {
-			if (--_rest)
+            if (--_rest)
             {
-				if (!last)
+                if (!last)
                 {
-					do
+                    do
                     {
-						tmp.i2 <<= 1;
-						tmp.i2 |= *in;
-						++in;
-						if (idxMod == 0) idxMod = m;
-						--idxMod; --tmp.i1;
-						if (eof(in))
+                        tmp.i2 <<= 1;
+                        tmp.i2 |= *in;
+                        ++in;
+                        if (idxMod == 0) idxMod = m;
+                        --idxMod; --tmp.i1;
+                        if (eof(in))
                         {
-							last = true;
-							while (!filter[idxMod])
+                            last = true;
+                            while (!filter[idxMod])
                             {
-								tmp.i2 <<= 1;
-								if (idxMod == 0) idxMod = m;
-								--idxMod; --tmp.i1;
-							}
-							break;
-						}
-					} while (!filter[idxMod]);
+                                tmp.i2 <<= 1;
+                                if (idxMod == 0) idxMod = m;
+                                --idxMod; --tmp.i1;
+                            }
+                            break;
+                        }
+                    } while (!filter[idxMod]);
                 }
-				else
+                else
                 {
-					do
+                    do
                     {
-						tmp.i2 <<= 1;
-						if (idxMod == 0) idxMod = m;
-						--idxMod; --tmp.i1;
-					}
+                        tmp.i2 <<= 1;
+                        if (idxMod == 0) idxMod = m;
+                        --idxMod; --tmp.i1;
+                    }
                     while (!filter[idxMod]);
                 }
-			}
+            }
             return *this;
-        }        
+        }
     };
 
 
@@ -339,22 +318,22 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
     template < typename TInput, unsigned m, typename TPack >
-	inline bool control(Pipe< TInput, Sampler<m, TPack> > &me, ControlBeginRead const &command)
+    inline bool control(Pipe< TInput, Sampler<m, TPack> > &me, ControlBeginRead const &command)
     {
         if (!control(me.in, command)) return false;
         me.prepare();
-		return true;
+        return true;
     }
 
     template < typename TInput, unsigned m, typename TPack >
-	inline bool control(Pipe< TInput, Sampler<m, TPack> > &me, ControlEof const &/*command*/)
+    inline bool control(Pipe< TInput, Sampler<m, TPack> > &me, ControlEof const &/*command*/)
     {
-		return me._rest == 0;
+        return me._rest == 0;
     }
 
     template < typename TInput, unsigned m, typename TPack >
     inline typename Size< Pipe< TInput, Sampler<m, TPack> > >::Type
-	length(Pipe< TInput, Sampler<m, TPack> > const &me)
+    length(Pipe< TInput, Sampler<m, TPack> > const &me)
     {
         typedef typename Size< Pipe< TInput, Sampler<m> > >::Type TSize;
 
@@ -389,44 +368,44 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
         typedef typename Value<Pipe>::Type  TOutValue;
         typedef typename Size<Pipe>::Type   TSize;
 
-		typedef PairDecrementer_<TPair, TLimitsString, m> Decrementer;
+        typedef PairDecrementer_<TPair, TLimitsString, m> Decrementer;
 
-		TInput		&in;
-        bool		filter[m];
-        Decrementer	localPos;
-		TSize       _size, _rest;
+        TInput        &in;
+        bool        filter[m];
+        Decrementer    localPos;
+        TSize       _size, _rest;
         TOutValue   tmp1, tmp2;
         TOutValue   *outRef, *tmpRef;
-        bool		last;
+        bool        last;
 
-		TLimitsString const &limits;
+        TLimitsString const &limits;
 
         template <typename TLimitsString_>
         Pipe(TInput& _in, TLimitsString_ &_limits):  // const &_limits is intentionally omitted to suppress implicit casts (if types mismatch) and taking refs of them
             in(_in),
             outRef(&tmp1),
             tmpRef(&tmp2),
-			limits(_limits) {}
-       
+            limits(_limits) {}
+
         inline void prepare()
         {
             for (unsigned i = 0; i < m; ++i)
                 filter[i] = 0;
-			for(unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
+            for(unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
                 filter[SkewDC_<m>::VALUE[i]] = true;
 
-			setHost(localPos, limits);
+            setHost(localPos, limits);
 
-			while (!filter[localPos.residue] && !eof(in))
+            while (!filter[localPos.residue] && !eof(in))
             {
                 ++in;
-				--localPos;
+                --localPos;
             }
             _rest = length(*this);
             fill();
             swap();
         }
-        
+
         inline void fill()
         {
             unsigned i;
@@ -437,7 +416,7 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
                 tmpRef->i2.i[i] = 0;
             tmpRef->i1 = localPos;
         }
-        
+
         inline void rotate(unsigned r)
         {
             for(unsigned i = 0; i < m; ++i, ++r)
@@ -446,87 +425,87 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
                 tmpRef->i2.i[i] = outRef->i2.i[r];
             }
         }
-        
+
         inline void swap()
         {
             TOutValue *newOutRef = tmpRef;
             tmpRef = outRef;
             outRef = newOutRef;
         }
-        
+
         inline TOutValue const& operator*()
         {
             return *outRef;
         }
-        
+
         Pipe& operator++()
         {
             unsigned skipped = 0;
-			if (--_rest)
+            if (--_rest)
             {
-				if (!last)
+                if (!last)
                 {
-					do
+                    do
                     {
-						outRef->i2.i[skipped++] = *in;
-						++in;
-						--localPos;
-						if (eof(in))
+                        outRef->i2.i[skipped++] = *in;
+                        ++in;
+                        --localPos;
+                        if (eof(in))
                         {
-							last = true;
-							while (!filter[localPos.residue])
+                            last = true;
+                            while (!filter[localPos.residue])
                             {
-								outRef->i2.i[skipped++] = 0;
-								--localPos;
-							}
-							break;
-						}
-					}
+                                outRef->i2.i[skipped++] = 0;
+                                --localPos;
+                            }
+                            break;
+                        }
+                    }
                     while (!filter[localPos.residue]);
                 }
-				else
+                else
                 {
-					do
+                    do
                     {
-						outRef->i2.i[skipped++] = 0;
-						--localPos;
-					}
+                        outRef->i2.i[skipped++] = 0;
+                        --localPos;
+                    }
                     while (!filter[localPos.residue]);
                 }
-				rotate(skipped);
-				tmpRef->i1 = localPos;
-				swap();
-			}
+                rotate(skipped);
+                tmpRef->i1 = localPos;
+                swap();
+            }
             return *this;
-        }        
+        }
     };
 
 
     //////////////////////////////////////////////////////////////////////////////
     // sampler class (uses bit-packing)
-	template < typename TInput, unsigned m, typename TPair, typename TLimitsString >
+    template < typename TInput, unsigned m, typename TPair, typename TLimitsString >
     struct Pipe< TInput, Multi<Sampler<m, BitPacked<> >, TPair, TLimitsString> >
     {
         typedef typename Value<Pipe>::Type          TOutValue;
         typedef typename Size<Pipe>::Type           TSize;
         typedef typename Value<TOutValue, 2>::Type  TTuple;
 
-		typedef PairDecrementer_<TPair, TLimitsString, m> Decrementer;
+        typedef PairDecrementer_<TPair, TLimitsString, m> Decrementer;
 
-		TInput		&in;
-        bool		filter[m];
+        TInput        &in;
+        bool        filter[m];
         TSize       _size, _rest;
         Decrementer localPos;
         TOutValue   tmp;
-        bool		last;
+        bool        last;
+
+        TLimitsString const &limits;
 
-		TLimitsString const &limits;
-        
         template <typename TLimitsString_>
         Pipe(TInput& _in, TLimitsString_ &_limits):  // const &_limits is intentionally omitted to suppress implicit casts (if types mismatch) and taking refs of them
             in(_in),
-			limits(_limits) {}
-        
+            limits(_limits) {}
+
         inline void prepare()
         {
             for (unsigned i = 0; i < m; ++i)
@@ -534,16 +513,16 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
             for(unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
                 filter[SkewDC_<m>::VALUE[i]] = true;
 
-			setHost(localPos, limits);
+            setHost(localPos, limits);
 
-			while (!filter[localPos.residue] && !eof(in)) {
+            while (!filter[localPos.residue] && !eof(in)) {
                 ++in;
-				--localPos;
+                --localPos;
             }
             _rest = length(*this);
             fill();
         }
-        
+
         inline void fill()
         {
             unsigned i;
@@ -554,110 +533,110 @@ The m-tuples are substrings of the input stream beginning at positions $i$, with
             }
             last = eof(in);
             tmp.i2 <<= (m - i);
-			tmp.i1 = localPos;
+            tmp.i1 = localPos;
         }
-        
+
         inline TOutValue const& operator*()
         {
             return tmp;
         }
-        
+
         Pipe& operator++()
         {
-			if (--_rest)
+            if (--_rest)
             {
-				if (!last)
+                if (!last)
                 {
-					do
+                    do
                     {
-						tmp.i2 <<= 1;
-						tmp.i2 |= *in;
-						++in;
-						--localPos;
-						if (eof(in))
+                        tmp.i2 <<= 1;
+                        tmp.i2 |= *in;
+                        ++in;
+                        --localPos;
+                        if (eof(in))
                         {
-							last = true;
-							while (!filter[localPos.residue])
+                            last = true;
+                            while (!filter[localPos.residue])
                             {
-								tmp.i2 <<= 1;
-								--localPos;
-							}
-							break;
-						}
-					}
+                                tmp.i2 <<= 1;
+                                --localPos;
+                            }
+                            break;
+                        }
+                    }
                     while (!filter[localPos.residue]);
                 }
-				else
+                else
                 {
-					do
+                    do
                     {
-						tmp.i2 <<= 1;
-						--localPos;
-					} while (!filter[localPos.residue]);
+                        tmp.i2 <<= 1;
+                        --localPos;
+                    } while (!filter[localPos.residue]);
                 }
-			}
+            }
             tmp.i1 = localPos;
             return *this;
-        }        
+        }
     };
 
 
 
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
-	template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
-	inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlBeginRead const &command)
+    template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
+    inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlBeginRead const &command)
     {
         if (!control(me.in, command))
             return false;
         me.prepare();
-		return true;
+        return true;
     }
 
-	template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
-	inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlEof const &/*command*/)
+    template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
+    inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlEof const &/*command*/)
     {
-		return me._rest == 0;
+        return me._rest == 0;
     }
 
-	template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
-	inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlEos const &/*command*/)
+    template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
+    inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlEos const &/*command*/)
     {
-		return control(me, ControlEof());
+        return control(me, ControlEof());
     }
 
-	template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
+    template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
     inline typename Size< Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > >::Type
-	length(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > const &me)
-	{
-		typedef typename Size< Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > >::Type TSize;
+    length(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > const &me)
+    {
+        typedef typename Size< Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > >::Type TSize;
 
-		if (empty(me.limits))
+        if (empty(me.limits))
             return 0;
 
-		TSize sum = 0;
+        TSize sum = 0;
         TLimitsString const &limits = me.limits;
         __int64 seqCountPlusOne = length(me.limits);
 
         SEQAN_OMP_PRAGMA(parallel for reduction(+:sum))
         for (__int64 i = 1; i < seqCountPlusOne; ++i)
         {
-			TSize prev = limits[i - 1];
-			TSize cur = limits[i];
+            TSize prev = limits[i - 1];
+            TSize cur = limits[i];
 
             SEQAN_ASSERT_LEQ(prev, cur);
-			register TSize size = cur - prev;
+            TSize size = cur - prev;
 
             // sum up the number of tuples in each residue class
             // for a string of length n there are 1+(n-x)/m suffixes
             // whose lengths are in residue class x
-			for (unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; ++i)
+            for (unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; ++i)
             {
                 sum += (size + m - SkewDC_<m>::VALUE[i]) / m;
                 if (SkewDC_<m>::VALUE[i] == 0)
                     --sum;  // we don't consider empty suffixes
             }
-		}
+        }
 
         return sum;
     }
diff --git a/seqan/pipe/pipe_shifter.h b/seqan/pipe/pipe_shifter.h
index 05963d7..925ecc9 100644
--- a/seqan/pipe/pipe_shifter.h
+++ b/seqan/pipe/pipe_shifter.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -48,97 +48,78 @@ namespace SEQAN_NAMESPACE_MAIN
 
 /*!
  * @class Shifter
- * 
+ *
  * @extends Pipe
- * 
- * @headerfile seqan/pipe.h
- * 
+ *
+ * @headerfile <seqan/pipe.h>
+ *
  * @brief Shifts the input stream by <tt>delta</tt> elements.
- * 
+ *
  * @signature template <typename TInput, int DELTA[, bool OMIT_BLANK]>
  *            class Pipe<TInput, Shifter<DELTA, OMIT_BLANK> >;
- * 
+ *
  * @tparam TInput     The type of the pipeline module this module reads from.
  * @tparam OMIT_BLANK Omit undefined entries.  If <tt>true</tt>, the output stream is <tt>|delta|</tt> elements shorter
  *                    than the input stream.  If <tt>false</tt>, the lengths are equal and blanks (default constructed
  *                    elements) are inserted on the cut-off-opposite side, defaults to false.
  * @tparam DELTA      The shift size. For the output stream holds <tt>out[i]=in[i+delta]</tt>.  For <tt>delta>0</tt>
  *                    the input stream is cut of at the beginning and for <tt>delta<0</tt> at the end.
- * 
- * @section Remarks
- * 
+ *
  * The output type equals the input type.
  */
 
-/**
-.Spec.Shifter:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Shifts the input stream by $delta$ elements.
-..signature:Pipe<TInput, Shifter<delta, omitBlank> >
-..param.TInput:The type of the pipeline module this module reads from.
-..param.delta:The shift size. For the output stream holds $out[i]=in[i+delta]$.
-...remarks:For $delta>0$ the input stream is cut of at the beginning and for $delta<0$ at the end.
-..param.omitBlank:Omit undefined entries.
-..param.omitBlank:If $true$, the output stream is $|delta|$ elements shorter than the input stream.
-..param.omitBlank:If $false$, the lengths are equal and blanks (default constructed elements) are inserted on the cut-off-opposite side.
-...default:$false$
-..remarks:The output type equals the input type.
-..include:seqan/pipe.h
-*/
-
     //////////////////////////////////////////////////////////////////////////////
     // echoer class
     template < typename TInput, int delta, bool omitBlank >
     struct Pipe< TInput, Shifter<delta, omitBlank, true> >
     {
         TInput                      &in;
-        typename Size<Pipe>::Type	blankCounter, charCounter;
-		typename Value<Pipe>::Type	blank;
-        
+        typename Size<Pipe>::Type    blankCounter, charCounter;
+        typename Value<Pipe>::Type    blank;
+
         Pipe(TInput& _in):
             in(_in),
-			blank()	{}
+            blank()    {}
 
         inline typename Value<Pipe>::Type const & operator*() {
-			if (blankCounter)	return blank;
-			else				return *in;
+            if (blankCounter)    return blank;
+            else                return *in;
         }
 
         inline Pipe& operator++() {
-			if (blankCounter)
-				--blankCounter;
-			else {
-				++in;
-				--charCounter;
-			}
+            if (blankCounter)
+                --blankCounter;
+            else {
+                ++in;
+                --charCounter;
+            }
             return *this;
         }
     };
 
 
-	template < typename TInput, int delta, bool omitBlank >
+    template < typename TInput, int delta, bool omitBlank >
     struct Pipe< TInput, Shifter<delta, omitBlank, false> >
     {
         TInput                      &in;
-        typename Size<Pipe>::Type	blankCounter, charCounter;
-		typename Value<Pipe>::Type	blank;
-        
+        typename Size<Pipe>::Type    blankCounter, charCounter;
+        typename Value<Pipe>::Type    blank;
+
         Pipe(TInput& _in):
             in(_in),
-			blank()	{}
+            blank()    {}
 
         inline typename Value<Pipe>::Type const & operator*() {
-			if (charCounter)	return *in;
-			else				return blank;
+            if (charCounter)    return *in;
+            else                return blank;
         }
 
         inline Pipe& operator++() {
-			if (charCounter) {
-				++in;
-				--charCounter;
-			} else
-				--blankCounter;
+            if (charCounter) {
+                ++in;
+                --charCounter;
+            } else
+                --blankCounter;
             return *this;
         }
     };
@@ -147,22 +128,22 @@ namespace SEQAN_NAMESPACE_MAIN
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
     template < typename TInput, int delta, bool omitBlank >
-	inline bool control(Pipe< TInput, Shifter< delta, omitBlank, false > > &me, ControlBeginRead const &command) {
+    inline bool control(Pipe< TInput, Shifter< delta, omitBlank, false > > &me, ControlBeginRead const &command) {
         if (!control(me.in, command)) return false;
-		for(typename Size<TInput>::Type i = 0; i < delta && !eof(me.in); ++i)
-			++me.in;
-		me.blankCounter = (omitBlank)? 0: delta;
-		me.charCounter = length(me.in) - delta;
-		return !eof(me.in);
-	}
+        for(typename Size<TInput>::Type i = 0; i < delta && !eof(me.in); ++i)
+            ++me.in;
+        me.blankCounter = (omitBlank)? 0: delta;
+        me.charCounter = length(me.in) - delta;
+        return !eof(me.in);
+    }
 
     template < typename TInput, int delta, bool omitBlank >
-	inline bool control(Pipe< TInput, Shifter< delta, omitBlank, true > > &me, ControlBeginRead const &command) {
+    inline bool control(Pipe< TInput, Shifter< delta, omitBlank, true > > &me, ControlBeginRead const &command) {
         if (!control(me.in, command)) return false;
-		me.blankCounter = (omitBlank)? 0: -delta;
-		me.charCounter = length(me.in) + delta;
-		return true;
-	}
+        me.blankCounter = (omitBlank)? 0: -delta;
+        me.charCounter = length(me.in) + delta;
+        return true;
+    }
 
 
 
@@ -174,13 +155,13 @@ namespace SEQAN_NAMESPACE_MAIN
     }
 
     template < typename TInput, int delta, bool omitBlank, bool _echoing >
-	inline bool control(Pipe< TInput, Shifter< delta, omitBlank, _echoing > > &me, ControlEof const &/*command*/) {
-		return me.charCounter == 0 && me.blankCounter == 0;
+    inline bool control(Pipe< TInput, Shifter< delta, omitBlank, _echoing > > &me, ControlEof const &/*command*/) {
+        return me.charCounter == 0 && me.blankCounter == 0;
     }
 
     template < typename TInput, int delta, bool omitBlank, bool _echoing >
-	inline bool control(Pipe< TInput, Shifter< delta, omitBlank, _echoing > > &me, ControlEos const &/*command*/) {
-		return control(me, ControlEof());
+    inline bool control(Pipe< TInput, Shifter< delta, omitBlank, _echoing > > &me, ControlEos const &/*command*/) {
+        return control(me, ControlEof());
     }
 
 //}
diff --git a/seqan/pipe/pipe_source.h b/seqan/pipe/pipe_source.h
index 93fa686..a15dd63 100644
--- a/seqan/pipe/pipe_source.h
+++ b/seqan/pipe/pipe_source.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,10 +39,10 @@ namespace SEQAN_NAMESPACE_MAIN
 {
 
 /*
-	template < typename TValue >
+    template < typename TValue >
     struct Size< Pipe< TValue*, Source<> > > {
-		typedef ptrdiff_t Type;
-	};
+        typedef ptrdiff_t Type;
+    };
 */
 
 /*!
@@ -50,166 +50,156 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
  * @brief Pipelining adaptor for arbitrary containers or iterators.
- * 
+ *
  * @signature template <typename TInput>
  *            class Pipe<TInput, Source<> >;
- * 
+ *
  * @tparam TInput The type of container or iterator this module reads from.
  */
 
-/**
-.Spec.Source:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Pipelining adaptor for arbitrary containers or iterators.
-..signature:Pipe<TInput, Source<> >
-..param.TInput:The type of container or iterator this module reads from.
-..include:seqan/pipe.h
-*/
-
 
-	//////////////////////////////////////////////////////////////////////////////
-	// source class
-	template < typename TInput, typename TSpec >
-	struct Pipe< TInput, Source<TSpec> >
+    //////////////////////////////////////////////////////////////////////////////
+    // source class
+    template < typename TInput, typename TSpec >
+    struct Pipe< TInput, Source<TSpec> >
     {
-		TInput const &in;
-		typename Iterator<TInput const, Rooted>::Type cur;
-		typename Value<TInput>::Type val;
+        TInput const &in;
+        typename Iterator<TInput const, Rooted>::Type cur;
+        typename Value<TInput>::Type val;
 
-		Pipe(typename RemoveConst_<TInput>::Type &_cont):
-			in(_cont) {}
+        Pipe(typename RemoveConst_<TInput>::Type &_cont):
+            in(_cont), cur(), val() {}
 
-		Pipe(TInput const &_cont):
-			in(_cont) {}
+        Pipe(TInput const &_cont):
+            in(_cont), cur(), val() {}
 
-        inline typename Value<TInput>::Type const & operator*() {
-            return val = getValue(cur);
-        }
-    
-        inline Pipe& operator++() {
+        inline typename Value<TInput>::Type const & operator*()
+        { return val = getValue(cur); }
+
+        inline Pipe& operator++()
+        {
             ++cur;
             return *this;
         }
     };
 
     template < typename TInput, typename TSpec, typename TIteratorSpec >
-	struct Iterator< Pipe< TInput, Source<TSpec> >, TIteratorSpec> {
-		typedef typename Iterator<TInput const, TIteratorSpec>::Type Type;
-	};
+    struct Iterator< Pipe< TInput, Source<TSpec> >, TIteratorSpec> {
+        typedef typename Iterator<TInput const, TIteratorSpec>::Type Type;
+    };
 
     template < typename TInput, typename TSpec, typename TTag >
-	inline typename Iterator< Pipe< TInput, Source<TSpec> >, Tag<TTag> const >::Type
-	begin(Pipe< TInput, Source<TSpec> > &pipe, Tag<TTag> const) {
-		return begin(pipe.in);
-	}
+    inline typename Iterator< Pipe< TInput, Source<TSpec> >, Tag<TTag> const >::Type
+    begin(Pipe< TInput, Source<TSpec> > &pipe, Tag<TTag> const) {
+        return begin(pipe.in);
+    }
 
     template < typename TInput, typename TSpec, typename TTag >
-	inline typename Iterator< Pipe< TInput, Source<TSpec> >, Tag<TTag> const >::Type
-	end(Pipe< TInput, Source<TSpec> > &pipe, Tag<TTag> const) {
-		return end(pipe.in);
-	}
+    inline typename Iterator< Pipe< TInput, Source<TSpec> >, Tag<TTag> const >::Type
+    end(Pipe< TInput, Source<TSpec> > &pipe, Tag<TTag> const) {
+        return end(pipe.in);
+    }
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// simple buffer adaption for fast random accessable containers
+    //////////////////////////////////////////////////////////////////////////////
+    // simple buffer adaption for fast random accessable containers
     template < typename TContainer >
-	struct ContainerBuffer 
-	{
-		TContainer *cont;
+    struct ContainerBuffer
+    {
+        TContainer *cont;
 
         ContainerBuffer(): cont(NULL) {}
-		ContainerBuffer(TContainer &_cont): cont(&_cont) {}
+        ContainerBuffer(TContainer &_cont): cont(&_cont) {}
 
-		template <typename TSize>
-		inline typename Reference<TContainer>::Type 
-		operator[] (TSize i) {
-			return (*cont)[i];
-		}
+        template <typename TSize>
+        inline typename Reference<TContainer>::Type
+        operator[] (TSize i) {
+            return (*cont)[i];
+        }
     };
 
     template < typename TContainer, typename TIteratorSpec >
-	struct Iterator< ContainerBuffer<TContainer>, TIteratorSpec>:
-		Iterator<TContainer, TIteratorSpec> {};
+    struct Iterator< ContainerBuffer<TContainer>, TIteratorSpec>:
+        Iterator<TContainer, TIteratorSpec> {};
 
     template < typename TContainer  >
-	struct Value< ContainerBuffer<TContainer> >:
-		Value<TContainer> {};
+    struct Value< ContainerBuffer<TContainer> >:
+        Value<TContainer> {};
 
     template < typename TContainer >
-	struct Size< ContainerBuffer<TContainer> >:
-		Size<TContainer> {};
+    struct Size< ContainerBuffer<TContainer> >:
+        Size<TContainer> {};
 
 
-	template < typename TContainer >
+    template < typename TContainer >
     inline typename Size< ContainerBuffer<TContainer> >::Type
     length(ContainerBuffer<TContainer> const &me) {
-		if (me.cont)
-			return length(*me.cont);
-		else
-			return 0;
+        if (me.cont)
+            return length(*me.cont);
+        else
+            return 0;
     }
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// simple buffer adaption for fast random accessable iterators
+    //////////////////////////////////////////////////////////////////////////////
+    // simple buffer adaption for fast random accessable iterators
     template < typename TIterator >
-	struct IteratorBuffer 
-	{
-		TIterator						begin;
-		typename Size<TIterator>::Type	size;
+    struct IteratorBuffer
+    {
+        TIterator                        begin;
+        typename Size<TIterator>::Type    size;
 
         IteratorBuffer(): begin(NULL), size(0) {}
-		template <typename TSize>
-		IteratorBuffer(TIterator &_begin, TSize _size): begin(&_begin), size(_size) {}
-
-		template <typename TSize>
-		inline typename Reference<TIterator>::Type 
-		operator[] (TSize i) {
-			return *(begin + i);
-		}
+        template <typename TSize>
+        IteratorBuffer(TIterator &_begin, TSize _size): begin(&_begin), size(_size) {}
+
+        template <typename TSize>
+        inline typename Reference<TIterator>::Type
+        operator[] (TSize i) {
+            return *(begin + i);
+        }
     };
 
     template < typename TIterator, typename TIteratorSpec >
-	struct Iterator< IteratorBuffer<TIterator>, TIteratorSpec >:
-		Iterator<TIterator, TIteratorSpec> {};
+    struct Iterator< IteratorBuffer<TIterator>, TIteratorSpec >:
+        Iterator<TIterator, TIteratorSpec> {};
 
     template < typename TIterator  >
-	struct Value< IteratorBuffer<TIterator> >:
-		Value<TIterator> {};
+    struct Value< IteratorBuffer<TIterator> >:
+        Value<TIterator> {};
 
     template < typename TIterator >
-	struct Size< IteratorBuffer<TIterator> >:
-		Size<TIterator> {};
+    struct Size< IteratorBuffer<TIterator> >:
+        Size<TIterator> {};
 
 
-	template < typename TIterator >
+    template < typename TIterator >
     inline typename Size< IteratorBuffer<TIterator> >::Type
     length(IteratorBuffer<TIterator> const &me) {
-		return me.size;
+        return me.size;
     }
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// handler that emulates a buffer by using a container buffer
+    // handler that emulates a buffer by using a container buffer
     struct SourceNonCachingSpec_;
-	typedef Tag<SourceNonCachingSpec_> SourceNonCachingSpec;
+    typedef Tag<SourceNonCachingSpec_> SourceNonCachingSpec;
 
-	template < typename TPipe >
-	struct BufferHandler< TPipe, SourceNonCachingSpec >
+    template < typename TPipe >
+    struct BufferHandler< TPipe, SourceNonCachingSpec >
     {
-        typedef typename Source<TPipe>::Type	TSource;
-        typedef ContainerBuffer<TSource const>	TBuffer;
+        typedef typename Source<TPipe>::Type    TSource;
+        typedef ContainerBuffer<TSource const>    TBuffer;
 
-		TPipe	&pipe;
+        TPipe    &pipe;
 
-		BufferHandler(TPipe &_pipe):
-			pipe(_pipe) {}
+        BufferHandler(TPipe &_pipe):
+            pipe(_pipe) {}
 
-		template <typename TSize>
-		BufferHandler(TPipe &_pipe, TSize):
-			pipe(_pipe) {}
+        template <typename TSize>
+        BufferHandler(TPipe &_pipe, TSize):
+            pipe(_pipe) {}
 
         inline TBuffer first() {
             return TBuffer(pipe.in);
@@ -224,59 +214,59 @@ namespace SEQAN_NAMESPACE_MAIN
         inline void cancel() {}
     };
 
-	template < typename TPipe >
+    template < typename TPipe >
     struct Value< BufferHandler< TPipe, SourceNonCachingSpec > > {
         typedef ContainerBuffer< typename Source<TPipe>::Type const > Type;
     };
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// caching buffer handler
+    // caching buffer handler
     struct SourceCachingSpec_;
-	typedef Tag<SourceCachingSpec_> SourceCachingSpec;
+    typedef Tag<SourceCachingSpec_> SourceCachingSpec;
 
-	template < typename TPipe >
-	struct BufferHandler< TPipe, SourceCachingSpec >
+    template < typename TPipe >
+    struct BufferHandler< TPipe, SourceCachingSpec >
     {
-        typedef typename Value<TPipe>::Type			TValue;
-        typedef typename Size<TPipe>::Type			TSize;
+        typedef typename Value<TPipe>::Type            TValue;
+        typedef typename Size<TPipe>::Type            TSize;
 
         typedef Buffer<TValue>                              TBuffer;
-		typedef IPipeIterator<TPipe>						ISource;
-		typedef typename Iterator<TBuffer, Standard>::Type	ITarget;
-
-		TPipe		&pipe;
-		size_t		bufferSize;
-        TSize		rest;
-        TBuffer		buffer;
-		ISource		source;
-
-		BufferHandler(TPipe &_pipe, size_t requestedSize):
-			pipe(_pipe),
-			bufferSize(requestedSize),
+        typedef IPipeIterator<TPipe>                        ISource;
+        typedef typename Iterator<TBuffer, Standard>::Type    ITarget;
+
+        TPipe        &pipe;
+        size_t        bufferSize;
+        TSize        rest;
+        TBuffer        buffer;
+        ISource        source;
+
+        BufferHandler(TPipe &_pipe, size_t requestedSize):
+            pipe(_pipe),
+            bufferSize(requestedSize),
             rest(0) {}
 
         inline TBuffer& first() {
             rest = length(pipe);
-			allocPage(buffer, _min(bufferSize, rest), *this);
-			source = ISource(pipe);
-			for(ITarget target = buffer.begin; target != buffer.end; ++target) {
-				*target = *source;
-				++source;
-			}
+            allocPage(buffer, _min(bufferSize, rest), *this);
+            source = ISource(pipe);
+            for(ITarget target = buffer.begin; target != buffer.end; ++target) {
+                *target = *source;
+                ++source;
+            }
             if (!(rest -= length(buffer))) source = ISource();
-			return buffer;
+            return buffer;
         }
 
         inline TBuffer& next() {
-			resize(buffer, _min(bufferSize, rest));
-			ITarget _end = buffer.begin + length(buffer);
-			for(ITarget target = buffer.begin; target != _end; ++target) {
-				*target = *source;
-				++source;
-			}
+            resize(buffer, _min(bufferSize, rest));
+            ITarget _end = buffer.begin + length(buffer);
+            for(ITarget target = buffer.begin; target != _end; ++target) {
+                *target = *source;
+                ++source;
+            }
             if (!(rest -= length(buffer))) source = ISource();
-			return buffer;
+            return buffer;
         }
 
         inline void process() {}
@@ -284,59 +274,59 @@ namespace SEQAN_NAMESPACE_MAIN
         inline void cancel() { source = ISource(); freePage(buffer, *this); }
     };
 
-	template < typename TPipe >
+    template < typename TPipe >
     struct Value< BufferHandler< TPipe, SourceCachingSpec > > {
         typedef Buffer<typename Value<TPipe>::Type> Type;
     };
 
     //////////////////////////////////////////////////////////////////////////////
-	// buffer handler optimized for external string sources
+    // buffer handler optimized for external string sources
     struct ExtStringSourceCachingSpec_;
-	typedef Tag<ExtStringSourceCachingSpec_> ExtStringSourceCachingSpec;
+    typedef Tag<ExtStringSourceCachingSpec_> ExtStringSourceCachingSpec;
 
-	template < typename TSequence, typename TSpec >
-	struct BufferHandler< Pipe<TSequence, TSpec>, ExtStringSourceCachingSpec >
+    template < typename TSequence, typename TSpec >
+    struct BufferHandler< Pipe<TSequence, TSpec>, ExtStringSourceCachingSpec >
     {
-		typedef typename Value<TSequence>::Type		TValue;
-        typedef typename Size<TSequence>::Type		TSize;
+        typedef typename Value<TSequence>::Type        TValue;
+        typedef typename Size<TSequence>::Type        TSize;
         typedef Buffer<TValue>                      TBuffer;
-        typedef Pipe<TSequence, TSpec>				TPipe;
+        typedef Pipe<TSequence, TSpec>                TPipe;
 
-		typedef typename Iterator<TSequence const, Standard>::Type	ISource;
-		typedef typename Iterator<TBuffer, Standard>::Type			ITarget;
+        typedef typename Iterator<TSequence const, Standard>::Type    ISource;
+        typedef typename Iterator<TBuffer, Standard>::Type            ITarget;
 
-		TPipe		&pipe;
-		unsigned	bufferSize;
-        TSize		rest;
-        TBuffer		buffer;
-		ISource		source;
+        TPipe        &pipe;
+        unsigned    bufferSize;
+        TSize        rest;
+        TBuffer        buffer;
+        ISource        source;
 
-		BufferHandler(TPipe &_pipe, unsigned requestedSize):
-			pipe(_pipe),
-			bufferSize(requestedSize),
+        BufferHandler(TPipe &_pipe, unsigned requestedSize):
+            pipe(_pipe),
+            bufferSize(requestedSize),
             rest(0) {}
 
         inline TBuffer& first() {
             rest = length(pipe.in);
-			allocPage(buffer, _min(bufferSize, rest), *this);
-			source = begin(pipe.in);
-			for(ITarget target = buffer.begin; target != buffer.end; ++target) {
-				*target = *source;
-				++source;
-			}
+            allocPage(buffer, _min(bufferSize, rest), *this);
+            source = begin(pipe.in);
+            for(ITarget target = buffer.begin; target != buffer.end; ++target) {
+                *target = *source;
+                ++source;
+            }
             if (!(rest -= length(buffer))) source = ISource();
-			return buffer;
+            return buffer;
         }
 
         inline TBuffer& next() {
-			resize(buffer, _min(bufferSize, rest));
-			ITarget _end = buffer.begin + length(buffer);
-			for(ITarget target = buffer.begin; target != _end; ++target) {
-				*target = *source;
-				++source;
-			}
+            resize(buffer, _min(bufferSize, rest));
+            ITarget _end = buffer.begin + length(buffer);
+            for(ITarget target = buffer.begin; target != _end; ++target) {
+                *target = *source;
+                ++source;
+            }
             if (!(rest -= length(buffer))) source = ISource();
-			return buffer;
+            return buffer;
         }
 
         inline void process() {}
@@ -344,10 +334,10 @@ namespace SEQAN_NAMESPACE_MAIN
         inline void cancel() { source = ISource(); freePage(buffer, *this); }
     };
 
-	template < typename TSequence, typename TSpec >
+    template < typename TSequence, typename TSpec >
     struct Value<BufferHandler< Pipe<TSequence, TSpec>, ExtStringSourceCachingSpec > >
     {
-		typedef Buffer<typename Value<TSequence>::Type> Type;
+        typedef Buffer<typename Value<TSequence>::Type> Type;
     };
 
     //////////////////////////////////////////////////////////////////////////////
@@ -355,64 +345,73 @@ namespace SEQAN_NAMESPACE_MAIN
 
     // choose the most efficient buffer handler
     template < typename TInput, typename TSpec >
-    struct BufReadHandler< Pipe<TInput, TSpec> > {
-		typedef			
-			typename IfC<
-				AllowsFastRandomAccess<TInput>::VALUE,
-				SourceNonCachingSpec,
-//				SourceCachingSpec>
-				ExtStringSourceCachingSpec >::Type			TTag;
-		typedef BufferHandler< Pipe<TInput, TSpec>, TTag>	Type;
+    struct BufReadHandler< Pipe<TInput, TSpec> >
+    {
+        typedef
+            typename IfC<
+                AllowsFastRandomAccess<TInput>::VALUE,
+                SourceNonCachingSpec,
+//                SourceCachingSpec>
+                ExtStringSourceCachingSpec >::Type            TTag;
+        typedef BufferHandler< Pipe<TInput, TSpec>, TTag>    Type;
     };
 
 
     template < typename TValue, typename TConfig, typename TSpec >
-    struct BufReadHandler< Pipe< String<TValue, External<TConfig> >, TSpec > > {
-		typedef BufferHandler< 
-			Pipe< String<TValue, External<TConfig> >, TSpec >, 
-			ExtStringSourceCachingSpec 
-		> Type;
+    struct BufReadHandler< Pipe< String<TValue, External<TConfig> >, TSpec > >
+    {
+        typedef BufferHandler<
+            Pipe< String<TValue, External<TConfig> >, TSpec >,
+            ExtStringSourceCachingSpec
+        > Type;
     };
 
     template < typename TValue, typename TConfig, typename TSpec >
-    struct BufReadHandler< Pipe< String<TValue, External<TConfig> > const, TSpec > > {
-		typedef BufferHandler< 
-			Pipe< String<TValue, External<TConfig> > const, TSpec >, 
-			ExtStringSourceCachingSpec 
-		> Type;
+    struct BufReadHandler< Pipe< String<TValue, External<TConfig> > const, TSpec > >
+    {
+        typedef BufferHandler<
+            Pipe< String<TValue, External<TConfig> > const, TSpec >,
+            ExtStringSourceCachingSpec
+        > Type;
     };
 
 
-	template < typename TInput, typename TSpec, typename TCommand >
-	inline bool control(Pipe< TInput, Source<TSpec> > &/*me*/, TCommand const &) {
+    template < typename TInput, typename TSpec, typename TCommand >
+    inline bool control(Pipe< TInput, Source<TSpec> > &/*me*/, TCommand const &)
+    {
+        return true;
+    }
+
+    template < typename TInput, typename TSpec >
+    inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlBeginRead const &)
+    {
+        me.cur = begin(me.in, Rooted());
         return true;
     }
 
-	template < typename TInput, typename TSpec >
-	inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlBeginRead const &) {
-		me.cur = begin(me.in, Rooted());
-		return true;
-	}
-	
-	template < typename TInput, typename TSpec >
-	inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEndRead const &) {
+    template < typename TInput, typename TSpec >
+    inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEndRead const &)
+    {
         me.cur = end(me.in, Rooted());
-		return true;
-	}
-	
-	template < typename TInput, typename TSpec >
-	inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEof const &) {
-		return atEnd(me.cur);
-	}
-
-	template < typename TInput, typename TSpec >
-	inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEos const &) {
-		return atEndOfSequence(me.cur);
-	}
+        return true;
+    }
+
+    template < typename TInput, typename TSpec >
+    inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEof const &)
+    {
+        return atEnd(me.cur);
+    }
+
+    template < typename TInput, typename TSpec >
+    inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEos const &)
+    {
+        return atEndOfSequence(me.cur);
+    }
 
     template < typename TInput, typename TSpec >
     inline typename Size< Pipe< TInput, Source<TSpec> > >::Type
-	length(Pipe< TInput, Source<TSpec> > const &me) {
+    length(Pipe< TInput, Source<TSpec> > const &me)
+    {
         return length(me.in);
     }
 
diff --git a/seqan/pipe/pipe_tupler.h b/seqan/pipe/pipe_tupler.h
index 2ae6690..e2c8471 100644
--- a/seqan/pipe/pipe_tupler.h
+++ b/seqan/pipe/pipe_tupler.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,158 +38,122 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
-//namespace SEQAN_NAMESPACE_PIPELINING
-//{
-
 //////////////////////////////////////////////////////////////////////////////
 
-    template < unsigned tupleLen, bool omitLast = false, typename TPack = void >
+    template < unsigned SIZE, bool omitLast = false, typename TPack = void >
     struct Tupler;
 
-    template < typename TInput, unsigned tupleLen, bool omitLast, typename TPack >
-    struct Value< Pipe< TInput, Tupler< tupleLen, omitLast, TPack > > >
+    template < typename TInput, unsigned SIZE, bool omitLast, typename TPack >
+    struct Value< Pipe< TInput, Tupler<SIZE, omitLast, TPack> > >
     {
-        typedef Tuple<typename Value<TInput>::Type, tupleLen, TPack>	TTuple;
-        typedef Pair<typename Size<TInput>::Type, TTuple, Pack>         Type;
+        typedef Tuple<typename Value<TInput>::Type, SIZE, TPack>    TTuple;
+        typedef Pair<typename Size<TInput>::Type, TTuple, Pack>     Type;
     };
 
 //////////////////////////////////////////////////////////////////////////////
 
-    template < 
-		typename TInput, 
-		unsigned tupleLen, 
-		bool omitLast, 
-		typename TPack,
-		typename TPair, 
-		typename TLimitsString >
-    struct Value< Pipe< TInput, Multi< Tupler< tupleLen, omitLast, TPack >, TPair, TLimitsString > > >
+    template <
+        typename TInput,
+        unsigned SIZE,
+        bool omitLast,
+        typename TPack,
+        typename TPair,
+        typename TLimitsString >
+    struct Value< Pipe< TInput, Multi< Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString > > >
     {
-        typedef Tuple<typename Value<TInput>::Type, tupleLen, TPack>	TTuple;
-        typedef Pair<TPair, TTuple, Pack>								Type;
+        typedef Tuple<typename Value<TInput>::Type, SIZE, TPack>    TTuple;
+        typedef Pair<TPair, TTuple, Pack>                           Type;
     };
 
 //////////////////////////////////////////////////////////////////////////////
 
 
-	// output only fully filled tuples
-	template < typename TTupler >
-	struct TuplerLastTuples_ {
-		enum { VALUE = 1 };
-	};
+    // output only fully filled tuples
+    template <unsigned SIZE, bool omitLast>
+    struct TuplerNumberOfLastTuples_
+    {
+        enum { VALUE = 1 };
+    };
 
-	// output tupleLen-1 half filled tuples at the end
-    template < typename TInput, unsigned tupleLen, typename TPack >
-	struct TuplerLastTuples_< Pipe< TInput, Tupler<tupleLen, false, TPack> > > {
-		enum { VALUE = tupleLen };
-	};
+    // output SIZE-1 half filled tuples at the end
+    template <unsigned SIZE>
+    struct TuplerNumberOfLastTuples_<SIZE, false>
+    {
+        enum { VALUE = SIZE };
+    };
 
     struct ShiftLeftWorker_ {
         template <typename Arg>
         static inline void body(Arg &arg, unsigned I) {
-            arg.i2[I-1] = arg.i2[I];
+            arg[I-1] = arg[I];
         }
     };
 
+
+    // shift left by 1 character
+    template <typename TValue, unsigned SIZE, typename TSpec>
+    inline void
+    _tuplerShiftLeft(Tuple<TValue, SIZE, TSpec> & tuple)
+    {
+        Loop<ShiftLeftWorker_, SIZE - 1>::run(tuple);
+    }
+    template <typename TValue, unsigned SIZE>
+    inline void
+    _tuplerShiftLeft(Tuple<TValue, SIZE, BitPacked<> > & tuple)
+    {
+        tuple <<= 1;
+    }
+
+    // assign last character
+    template <typename TValue, unsigned SIZE, typename TSpec>
+    inline void
+    _tuplerAssignLast(Tuple<TValue, SIZE, TSpec> & tuple, TValue const & val)
+    {
+        tuple[SIZE - 1] = val;
+    }
+    template <typename TValue, unsigned SIZE>
+    inline void
+    _tuplerAssignLast(Tuple<TValue, SIZE, BitPacked<> > & tuple, TValue const & val)
+    {
+        tuple |= val;
+    }
+
+
+
 /*!
  * @class Tupler
  * @extends Pipe
  * @headerfile <seqan/pipe.h>
- * 
- * @brief Outputs tuples of the <tt>tupleLen</tt> consecutive elements of the input stream.
+ *
+ * @brief Outputs tuples of the <tt>SIZE</tt> consecutive elements of the input stream.
  *
  * @signature template <typename TInput, unsigned TUPLE_LEN, bool OMIT_LAST>
  *            class Pipe<TInput, Tupler<TUPLE_LEN, OMIT_LAST> >;
- * 
+ *
  * @tparam TInput    The type of the pipeline module this module reads from.
- * @tparam TUPLE_LEN The tuple length.The tuples contain elements <tt>in[i]in[i+1]...in[i+(tupleLen-1)]</tt>.
- * @tparam OMIT_LAST Omit half filled tuples.If <tt>true</tt>, the output stream is <tt>tupleLen-1</tt> elements
+ * @tparam TUPLE_LEN The tuple length.The tuples contain elements <tt>in[i]in[i+1]...in[i+(SIZE-1)]</tt>.
+ * @tparam OMIT_LAST Omit half filled tuples.  If <tt>true</tt>, the output stream is <tt>SIZE-1</tt> elements
  *                   shorter than the input stream.  If <tt>false</tt>, the lengths are identical and the last tuples
  *                   are filled with blanks (default constructed elements) for undefined entries.
- * 
- * @section Remarks
- * 
+ *
  * The output type is a @link Tuple @endlink of input elements and length
- * <tt>tupleLen</tt> (i.e. <tt>Tuple&lt;Value&lt;TInput&gt;::Type, TUPLE_LEN&gt;</tt>).
- * 
+ * <tt>SIZE</tt> (i.e. <tt>Tuple&lt;Value&lt;TInput&gt;::Type, TUPLE_LEN&gt;</tt>).
+ *
  * The tuples are sequences of the form
- * <tt>in[i]in[i-1]in[i-2]..in[i-tupleLen+1]</tt>. For <tt>omitLast=false</tt>
+ * <tt>in[i]in[i-1]in[i-2]..in[i-SIZE+1]</tt>. For <tt>omitLast=false</tt>
  * <tt>i</tt> begins with 0 and for <tt>omitLast=true</tt> <tt>i</tt> begins
- * with <tt>tupleLen-1</tt>.
+ * with <tt>SIZE-1</tt>.
  */
 
-/**
-.Spec.Tupler:
-..cat:Pipelining
-..general:Class.Pipe
-..summary:Outputs tuples of the $tupleLen$ consecutive elements of the input stream.
-..signature:Pipe<TInput, Tupler<tupleLen, omitLast> >
-..param.TInput:The type of the pipeline module this module reads from.
-..param.tupleLen:The tuple length.
-...remarks:The tuples contain elements $in[i]in[i+1]...in[i+(tupleLen-1)]$.
-..param.omitLast:Omit half filled tuples.
-..param.omitLast:If $true$, the output stream is $tupleLen-1$ elements shorter than the input stream.
-..param.omitLast:If $false$, the lengths are identical and the last tuples are filled with blanks (default constructed elements) for undefined entries.
-..remarks:The output type is a @Class.Tuple@ of input elements and length $tupleLen$ (i.e. $Tuple<Value<TInput>::Type, tupleLen>$).
-..remarks:The tuples are sequences of the form $in[i]in[i-1]in[i-2]..in[i-tupleLen+1]$. For $omitLast=false$ $i$ begins with 0 and for $omitLast=true$ $i$ begins with $tupleLen-1$.
-..include:seqan/pipe.h
-*/
-
-    //////////////////////////////////////////////////////////////////////////////
-    // tupler class
-    template < typename TInput, unsigned tupleLen, bool omitLast, typename TPack >
-    struct Pipe< TInput, Tupler<tupleLen, omitLast, TPack> >
+    template <typename TInput, unsigned SIZE, bool omitLast, typename TPack>
+    struct Pipe<TInput, Tupler<SIZE, omitLast, TPack> >
     {
-		typedef typename Value< typename Value<Pipe>::Type, 2 >::Type	TTuple;
-		typedef typename Value<TTuple>::Type							TValue;
+        typedef typename Value<TInput>::Type TValue;
 
-		TInput                      &in;
-        typename Value<Pipe>::Type	tmp;
-		typename Size<TInput>::Type	lastTuples;
-        
-        Pipe(TInput& _in):
-            in(_in) {}
-
-        inline typename Value<Pipe>::Type const & operator*() const {
-            return tmp;
-        }
-
-        inline Pipe& operator++() {
-            if (eof(in)) --lastTuples;
-            Loop<ShiftLeftWorker_, tupleLen - 1>::run(this->tmp);
-			++tmp.i1;
-			if (lastTuples < TuplerLastTuples_<Pipe>::VALUE)
-	            tmp.i2[tupleLen - 1] = TValue();
-			else {
-				tmp.i2[tupleLen - 1] = *in;
-				++in;
-			}
-            return *this;
-        }
-
-        inline void fill() {
-            unsigned i;
-            for(i = 0; i < tupleLen && !eof(in); ++i, ++in)
-                tmp.i2.i[i] = *in;
-			if (TuplerLastTuples_<Pipe>::VALUE > tupleLen - i)
-				lastTuples = TuplerLastTuples_<Pipe>::VALUE - (tupleLen - i);
-			else
-				lastTuples = 0;
-            for(; i < tupleLen; ++i)
-                tmp.i2.i[i] = TValue();
-            tmp.i1 = 0;
-        }
-	};
-
-//____________________________________________________________________________
-
-
-	template < typename TInput, unsigned tupleLen, bool omitLast >
-    struct Pipe< TInput, Tupler<tupleLen, omitLast, BitPacked<> > >
-    {
         TInput                      &in;
-        typename Value<Pipe>::Type	tmp;
-		typename Size<TInput>::Type	lastTuples;
-        
+        typename Value<Pipe>::Type    tmp;
+        typename Size<TInput>::Type    lastTuples;
+
         Pipe(TInput& _in):
             in(_in) {}
 
@@ -201,62 +165,85 @@ namespace SEQAN_NAMESPACE_MAIN
         inline Pipe& operator++()
         {
             if (eof(in)) --lastTuples;
-			tmp.i2 <<= 1;
-			++tmp.i1;
-			if (lastTuples == TuplerLastTuples_<Pipe>::VALUE)
-            {
-				tmp.i2 |= *in;
-				++in;
-			}
+            _tuplerShiftLeft(tmp.i2);
+            ++tmp.i1;
+            if (lastTuples < TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE)
+                _tuplerAssignLast(tmp.i2, TValue());
+            else {
+                _tuplerAssignLast(tmp.i2, *in);
+                ++in;
+            }
             return *this;
         }
 
-        inline void fill()
+
+        template <typename TPack_>
+        inline unsigned _tryFill(TPack_ *)
+        {
+            unsigned i;
+            for (i = 0; i < SIZE && !eof(in); ++i, ++in)
+                tmp.i2.i[i] = *in;
+            for (unsigned j = i; j < SIZE; ++j)
+                tmp.i2.i[j] = TValue();
+            return i;
+        }
+
+        inline unsigned _tryFill(BitPacked<> *)
         {
             unsigned i;
             clear(tmp.i2);
-			for(i = 0; i < tupleLen && !eof(in); ++i, ++in)
+            for (i = 0; i < SIZE && !eof(in); ++i, ++in)
             {
                 tmp.i2 <<= 1;
                 tmp.i2 |= *in;
-			}
-			if (TuplerLastTuples_<Pipe>::VALUE > tupleLen - i)
-				lastTuples = TuplerLastTuples_<Pipe>::VALUE - (tupleLen - i);
-			else
-				lastTuples = 0;
-            tmp.i2 <<= (tupleLen - i);
+            }
+            tmp.i2 <<= (SIZE - i);
+            return i;
+        }
+
+        inline void fill()
+        {
+            unsigned charsRead = _tryFill(static_cast<TPack*>(NULL));
+            if (TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE > SIZE - charsRead)
+                lastTuples = TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE - (SIZE - charsRead);
+            else
+                lastTuples = 0;
             tmp.i1 = 0;
         }
-	};
+    };
 
+//____________________________________________________________________________
 
-    //////////////////////////////////////////////////////////////////////////////
-    // tupler class for multiple sequences
-    template < 
-		typename TInput, 
-		unsigned tupleLen, 
-		bool omitLast, 
-		typename TPack, 
-		typename TPair, 
-		typename TLimitsString >
-    struct Pipe< TInput, Multi<Tupler<tupleLen, omitLast, TPack>, TPair, TLimitsString> >
+
+    template <
+        typename TInput,
+        unsigned SIZE,
+        bool omitLast,
+        typename TPack,
+        typename TPair,
+        typename TLimitsString >
+    struct Pipe<TInput, Multi<Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString> >
     {
-		typedef typename Value< typename Value<Pipe>::Type, 2 >::Type	TTuple;
-		typedef typename Value<TTuple>::Type							TValue;
+        typedef typename Value<typename Value<Pipe>::Type, 2>::Type TTuple;
+        typedef typename Value<TTuple>::Type                        TValue;
 
-		typedef PairIncrementer_<TPair, TLimitsString>	Incrementer;
+        typedef PairIncrementer_<TPair, TLimitsString>              Incrementer;
 
-		TInput                      &in;
-        Incrementer					localPos;
-        typename Value<Pipe>::Type	tmp;
-		typename Size<TInput>::Type	seqLength, lastTuples;
+        TInput                      &in;
+        Incrementer                    localPos;
+        typename Value<Pipe>::Type    tmp;
+        typename Size<TInput>::Type    seqLength, lastTuples;
 
-		TLimitsString const &limits;
+        TLimitsString const &limits;
 
         template <typename TLimitsString_>
         Pipe(TInput& _in, TLimitsString_ &_limits):  // const &_limits is intentionally omitted to suppress implicit casts (if types mismatch) and taking refs of them
             in(_in),
-			limits(_limits) {}
+            tmp(),
+            seqLength(),
+            lastTuples(),
+            limits(_limits)
+        {}
 
         inline typename Value<Pipe>::Type const & operator*() const
         {
@@ -265,292 +252,230 @@ namespace SEQAN_NAMESPACE_MAIN
 
         inline Pipe& operator++()
         {
-			// process next sequence
-			if (eos())
-				if (--lastTuples == 0)
+            // process next sequence
+            if (eos())
+                if (--lastTuples == 0)
                 {
-					assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
-					fill();
-					return *this;
-				}
-
-			// shift left 1 character
-            Loop<ShiftLeftWorker_, tupleLen - 1>::run(this->tmp);
-			assignValueI2(tmp.i1, getValueI2(tmp.i1) + 1);
-
-			if (lastTuples < TuplerLastTuples_<Pipe>::VALUE)
+                    assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
+                    fill();
+                    return *this;
+                }
+
+            // shift left by 1 character
+            _tuplerShiftLeft(tmp.i2);
+            assignValueI2(tmp.i1, getValueI2(tmp.i1) + 1);
+            if (lastTuples < TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE)
             {
-	            tmp.i2[tupleLen - 1] = TValue();
-			} else
+                _tuplerAssignLast(tmp.i2, TValue());
+            }
+            else
             {
-				tmp.i2[tupleLen - 1] = *in;
-				++localPos;
-				++in;
-			}
+                _tuplerAssignLast(tmp.i2, *in);
+                ++in;
+                ++localPos;
+            }
             return *this;
         }
 
-        inline void fill()
-        {
-			do {
-				unsigned i = 0;
-				if (!eof(in))
-					do {
-						tmp.i2.i[i] = *in;
-						++in;
-						++i;
-						++localPos;
-					} while ((i < tupleLen) && !eos());
-				lastTuples = TuplerLastTuples_<Pipe>::VALUE;
-
-				// fill up with null chars
-				for(; i < tupleLen; ++i)
-					tmp.i2.i[i] = TValue();
-				
-				// eventually, reduce the number of half-filled tuples
-				if (lastTuples <= tupleLen - i)
-					lastTuples = 0;
-				else
-					lastTuples -= tupleLen - i;
-
-				if (lastTuples == 0)
-					assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
-
-			} while ((lastTuples == 0) && !eof(in));
-
-			assignValueI2(tmp.i1, 0);
-		}
-
-		inline bool eos()
+        template <typename TPack_>
+        inline unsigned _tryFill(TPack_ *)
         {
-			return (getValueI1(localPos) > 0) && (getValueI2(localPos) == 0);
-		}
-	};
-
-//____________________________________________________________________________
-
-
-	template < 
-		typename TInput, 
-		unsigned tupleLen, 
-		bool omitLast, 
-		typename TPair, 
-		typename TLimitsString >
-    struct Pipe< TInput, Multi<Tupler<tupleLen, omitLast, BitPacked<> >, TPair, TLimitsString> >
-    {
-		typedef typename Value< typename Value<Pipe>::Type, 2 >::Type	TTuple;
-		typedef typename Value<TTuple>::Type							TValue;
-
-		typedef PairIncrementer_<TPair, TLimitsString>	Incrementer;
-
-		TInput                      &in;
-        Incrementer					localPos;
-        typename Value<Pipe>::Type	tmp;
-		typename Size<TInput>::Type	seqLength, lastTuples;
-
-		TLimitsString const &limits;
-        
-        template <typename TLimitsString_>
-        Pipe(TInput& _in, TLimitsString_ &_limits):  // const &_limits is intentionally omitted to suppress implicit casts (if types mismatch) and taking refs of them
-            in(_in),
-			limits(_limits) {}
-
-        inline typename Value<Pipe>::Type const & operator*() const
-        {
-            return tmp;
+            unsigned i = 0;
+            if (!eof(in))
+            {
+                do {
+                    tmp.i2.i[i] = *in;
+                    ++in;
+                    ++i;
+                    ++localPos;
+                } while ((i < SIZE) && !eos());
+            }
+
+            // fill up with null chars
+            for (unsigned j = i; j < SIZE; ++j)
+                tmp.i2.i[j] = TValue();
+            return i;
         }
 
-        inline Pipe& operator++() {
-			// process next sequence
-			if (eos())
-				if (--lastTuples == 0) {
-					assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
-					fill();
-					return *this;
-				}
-
-			// shift left 1 character
-			tmp.i2 <<= 1;
-			assignValueI2(tmp.i1, getValueI2(tmp.i1) + 1);
-			if (lastTuples == TuplerLastTuples_<Pipe>::VALUE) {
-				tmp.i2 |= *in;
-				++localPos;
-				++in;
-			}
-            return *this;
+        inline unsigned _tryFill(BitPacked<> *)
+        {
+            unsigned i = 0;
+            if (!eof(in))
+            {
+                do
+                {
+                    tmp.i2 <<= 1;
+                    tmp.i2 |= *in;
+                    ++in;
+                    ++i;
+                    ++localPos;
+                } while ((i < SIZE) && !eos());
+            }
+
+            // fill up with null chars
+            tmp.i2 <<= (SIZE - i);
+            return i;
         }
 
         inline void fill()
         {
-			do
+            assignValueI2(tmp.i1, 0);
+            do
             {
-				unsigned i = 0;
-				if (!eof(in))
-					do
-                    {
-						tmp.i2 <<= 1;
-						tmp.i2 |= *in;
-						++in;
-						++i;
-						++localPos;
-					} while ((i < tupleLen) && !eos());
-				lastTuples = TuplerLastTuples_<Pipe>::VALUE;
-
-				// fill up with null chars
-	            tmp.i2 <<= (tupleLen - i);
-				
-				// eventually, reduce the number of half-filled tuples
-				if (lastTuples <= tupleLen - i)
-					lastTuples = 0;
-				else
-					lastTuples -= tupleLen - i;
-
-				if (lastTuples == 0)
-					assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
-
-			} while ((lastTuples == 0) && !eof(in));
-
-			assignValueI2(tmp.i1, 0);
+                assignValueI1(tmp.i1, getValueI1(value(localPos)));
+                unsigned charsRead = _tryFill(static_cast<TPack*>(NULL));
+                lastTuples = TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE;
+
+                // eventually, reduce the number of half-filled tuples
+                if (lastTuples <= SIZE - charsRead)
+                    lastTuples = 0;
+                else
+                    lastTuples -= SIZE - charsRead;
+
+            } while ((lastTuples == 0) && !eof(in));
         }
 
-		inline bool eos()
+        inline bool eos()
         {
-			return (getValueI1(value(localPos)) > 0) && (getValueI2(value(localPos)) == 0);
-		}
-	};
+            return (getValueI1(value(localPos)) > 0) && (getValueI2(value(localPos)) == 0);
+        }
+    };
 
 
     //////////////////////////////////////////////////////////////////////////////
     // global pipe functions
-    template < typename TInput, unsigned tupleLen, bool omitLast, typename TPack >
-	inline bool 
-	control(
-		Pipe< TInput, Tupler< tupleLen, omitLast, TPack > > &me, 
-		ControlBeginRead const &command) 
-	{
+    template < typename TInput, unsigned SIZE, bool omitLast, typename TPack >
+    inline bool
+    control(
+        Pipe< TInput, Tupler<SIZE, omitLast, TPack> > &me,
+        ControlBeginRead const &command)
+    {
         if (!control(me.in, command)) return false;
-		me.fill();
-		return true;
-	}
-    
-    template < 
-		typename TInput,
-		unsigned tupleLen,
-		bool omitLast,
-		typename TPack,
-		typename TPair, 
-		typename TLimitsString >
-	inline bool 
-	control(
-		Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TPack >, TPair, TLimitsString> > &me, 
-		ControlBeginRead const &command) 
-	{
+        me.fill();
+        return true;
+    }
+
+    template <
+        typename TInput,
+        unsigned SIZE,
+        bool omitLast,
+        typename TPack,
+        typename TPair,
+        typename TLimitsString >
+    inline bool
+    control(
+        Pipe< TInput, Multi<Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString> > &me,
+        ControlBeginRead const &command)
+    {
         if (!control(me.in, command)) return false;
-		setHost(me.localPos, me.limits);
-		assignValueI1(me.tmp.i1, 0);
-		me.fill();
-		return true;
-	}
-    
-    template < typename TInput, unsigned tupleLen, bool omitLast, typename TPack >
-	inline bool 
-	control(
-		Pipe< TInput, Tupler< tupleLen, omitLast, TPack > > &me, 
-		ControlEof const &)
-	{
-		return me.lastTuples == 0;
+        setHost(me.localPos, me.limits);
+        assignValueI1(me.tmp.i1, 0);
+        me.fill();
+        return true;
     }
 
-    template < 
-		typename TInput,
-		unsigned tupleLen,
-		bool omitLast,
-		typename TPack,
-		typename TPair, 
-		typename TLimitsString >
-	inline bool 
-	control(
-		Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TPack >, TPair, TLimitsString> > &me, 
-		ControlEof const &) 
-	{
-		return me.lastTuples == 0;
-	}
-
-    template < typename TInput, unsigned tupleLen, bool omitLast, typename TPack >
-	inline bool 
-	control(
-		Pipe< TInput, Tupler< tupleLen, omitLast, TPack > > &me, 
-		ControlEos const &) 
-	{
-		return control(me, ControlEof());
-	}
-
-    template < 
-		typename TInput,
-		unsigned tupleLen,
-		bool omitLast,
-		typename TPack,
-		typename TPair, 
-		typename TLimitsString >
-	inline bool 
-	control(
-		Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TPack >, TPair, TLimitsString> > &me, 
-		ControlEos const &) 
-	{
-		return (getValueI1(me.tmp.i1) > 0) && (getValueI2(me.tmp.i1) == 0);
-	}
-
-    template < typename TInput, unsigned tupleLen, bool omitLast, typename TPack >
-    inline typename Size< Pipe< TInput, Tupler< tupleLen, omitLast, TPack > > >::Type
-    length(Pipe< TInput, Tupler< tupleLen, omitLast, TPack > > const &me) 
-	{
-		typedef Pipe< TInput, Tupler< tupleLen, omitLast, TPack > >	TPipe;
-		if (length(me.in) >= (tupleLen - TuplerLastTuples_<TPipe>::VALUE))
-			return length(me.in) - (tupleLen - TuplerLastTuples_<TPipe>::VALUE);
-		else
-			return 0;
+    template < typename TInput, unsigned SIZE, bool omitLast, typename TPack >
+    inline bool
+    control(
+        Pipe< TInput, Tupler<SIZE, omitLast, TPack> > &me,
+        ControlEof const &)
+    {
+        return me.lastTuples == 0;
     }
 
-    template < 
-		typename TInput,
-		unsigned tupleLen,
-		bool omitLast,
-		typename TPack,
-		typename TPair, 
-		typename TLimitsString >
-    inline typename Size< Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TPack >, TPair, TLimitsString> > >::Type
-    length(Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TPack >, TPair, TLimitsString> > const &me)
-	{
-		typedef Pipe< TInput, Tupler< tupleLen, omitLast, TPack > >	TPipe;
-		unsigned seqs = countSequences(me);
-		
-		if (length(me.in) >= seqs * (tupleLen - TuplerLastTuples_<TPipe>::VALUE))
-			return length(me.in) - seqs * (tupleLen - TuplerLastTuples_<TPipe>::VALUE);
-		else
-			return 0;
+    template <
+        typename TInput,
+        unsigned SIZE,
+        bool omitLast,
+        typename TPack,
+        typename TPair,
+        typename TLimitsString >
+    inline bool
+    control(
+        Pipe< TInput, Multi<Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString> > &me,
+        ControlEof const &)
+    {
+        return me.lastTuples == 0;
     }
 
-    template < typename TInput, unsigned tupleLen, bool omitLast, typename TPack >
-    inline unsigned
-    countSequences(Pipe< TInput, Tupler< tupleLen, omitLast, TPack > > const &)
+    template < typename TInput, unsigned SIZE, bool omitLast, typename TPack >
+    inline bool
+    control(
+        Pipe< TInput, Tupler<SIZE, omitLast, TPack> > &me,
+        ControlEos const &)
+    {
+        return control(me, ControlEof());
+    }
+
+    template <
+        typename TInput,
+        unsigned SIZE,
+        bool omitLast,
+        typename TPack,
+        typename TPair,
+        typename TLimitsString >
+    inline bool
+    control(
+        Pipe< TInput, Multi<Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString> > &me,
+        ControlEos const &)
+    {
+        return (getValueI1(me.tmp.i1) > 0) && (getValueI2(me.tmp.i1) == 0);
+    }
+
+    template < typename TInput, unsigned SIZE, bool omitLast, typename TPack >
+    inline typename Size< Pipe< TInput, Tupler<SIZE, omitLast, TPack> > >::Type
+    length(Pipe< TInput, Tupler<SIZE, omitLast, TPack> > const &me)
     {
-		return 1;
-	}
-
-    template < 
-		typename TInput,
-		unsigned tupleLen,
-		bool omitLast,
-		typename TPack,
-		typename TPair, 
-		typename TLimitsString >
+        if (length(me.in) > (SIZE - TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE))
+            return length(me.in) - (SIZE - TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE);
+        else
+            return 0;
+    }
+
+    template <
+        typename TInput,
+        unsigned SIZE,
+        bool omitLast,
+        typename TPack,
+        typename TPair,
+        typename TLimitsString >
+    inline typename Size<Pipe<TInput, Multi<Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString> > >::Type
+    length(Pipe<TInput, Multi<Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString> > const &me)
+    {
+        typedef Pipe<TInput, Multi<Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString> >   TPipe;
+        typedef typename Size<TPipe>::Type                                                  TSize;
+
+        // count all overlapping q-grams
+        TSize count = 0;
+        TSize seqs = countSequences(me);
+        for (TSize i = 0; i < seqs; ++i)
+        {
+            TSize seqLength = me.limits[i + 1] - me.limits[i];
+            if (seqLength > (SIZE - TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE))
+                count += seqLength - (SIZE - TuplerNumberOfLastTuples_<SIZE, omitLast>::VALUE);
+        }
+        return count;
+    }
+
+    template < typename TInput, unsigned SIZE, bool omitLast, typename TPack >
     inline unsigned
-	countSequences(Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TPack >, TPair, TLimitsString> > const &me)
+    countSequences(Pipe< TInput, Tupler<SIZE, omitLast, TPack> > const &)
     {
-		return length(me.limits) - 1;
-	}
+        return 1;
+    }
 
-//}
+    template <
+        typename TInput,
+        unsigned SIZE,
+        bool omitLast,
+        typename TPack,
+        typename TPair,
+        typename TLimitsString >
+    inline unsigned
+    countSequences(Pipe< TInput, Multi<Tupler<SIZE, omitLast, TPack>, TPair, TLimitsString> > const &me)
+    {
+        return length(me.limits) - 1;
+    }
 
 }
 
diff --git a/seqan/pipe/pool_base.h b/seqan/pipe/pool_base.h
index e76f4ba..e8e55a9 100644
--- a/seqan/pipe/pool_base.h
+++ b/seqan/pipe/pool_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,33 +43,20 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends PoolSpec
  * @headerfile <seqan/pipe.h.
  * @brief Configuration of Pool.
- * 
+ *
  * @signature template <typename TSize[, typename TFile]>
  *            struct PoolConfigSize;
- * 
+ *
  * @tparam TSize The Pool's size type.
  * @tparam TFile The underlying File type, defaults to <tt>File&lt;&gt;</tt>.
- * 
+ *
  * @see PoolConfig
- */ 
-
-/**
-.Spec.PoolConfigSize:
-..cat:Pipelining
-..general:Spec.PoolSpec
-..summary:Configuration of Pool.
-..signature:PoolConfig<TSize, TFile>
-..param.TSize:The Pool's size type.
-..param.TFile:The underlying @Class.File@ type.
-...default:$File<>$, see @Class.File@.
-..see:Spec.PoolConfig
-..include:seqan/pipe.h
-*/
+ */
 
-	template < typename TSize,
-		       typename TFile = File<> >						// default file type
+    template < typename TSize,
+               typename TFile = File<> >                        // default file type
     struct PoolConfigSize {
-		typedef TSize SizeType;
+        typedef TSize SizeType;
         typedef TFile File;
     };
 
@@ -78,36 +65,21 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends PoolSpec
  * @headerfile <seqan/pipe.h>
  * @brief Configuration of Pool.
- * 
+ *
  * @signature template <typename TFile>
  *            struct PoolConfig;
- * 
+ *
  * @tparam TFile The underlying File type, defaults to <tt>File&lt;&gt;</tt>.
- * 
- * @section Remarks
- * 
+ *
  * Using this configuration spec., the Pool's size type is <tt>Size&lt;TFile&gt;::Type</tt>.  To use a custom size type
  * PoolConfigSize should be used.
- * 
+ *
  * @see PoolConfigSize
  */
 
-/**
-.Spec.PoolConfig:
-..cat:Pipelining
-..general:Spec.PoolSpec
-..summary:Configuration of Pool.
-..signature:PoolConfig<TFile>
-..param.TFile:The underlying @Class.File@ type.
-...default:$File<>$, see @Class.File@.
-..remarks:Using this configuration spec., the Pool's size type is $Size<TFile>::Type$. To use a custom size type @Spec.PoolConfigSize@ should be used.
-..see:Spec.PoolConfigSize
-..include:seqan/pipe.h
-*/
-
-	template < typename TFile = File<> >						// default file type
+    template < typename TFile = File<> >                        // default file type
     struct PoolConfig {
-		typedef typename Size<TFile>::Type SizeType;
+        typedef typename Size<TFile>::Type SizeType;
         typedef TFile File;
     };
 
@@ -116,33 +88,17 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pool
  * @headerfile <seqan/pipe.h>
  * @brief Stores/Retrieves all elements to/from disk.
- * 
+ *
  * @signature template <typename TValue, typename TConfig>
  *            class Pool<TValue, PoolSpec<TConfig> >;
- * 
+ *
  * @tparam TConfig Configuration Spec.  Defines destination function, size type, and file type.
  *                 Types: PoolConfig, PoolConfigSize
  * @tparam TValue  The value type, that is the type of the stream elements.
- * 
- * @section Remarks
- * 
+ *
  * The Pool's input/output type is <tt>TValue</tt> and the size type is determined by the <tt>TConfig</tt>.
  */
 
-/**
-.Spec.PoolSpec:
-..cat:Pipelining
-..general:Class.Pool
-..summary:Stores/Retrieves all elements to/from disk.
-..signature:Pool<TValue, PoolSpec<TConfig> >
-..param.TValue:The value type, that is the type of the stream elements.
-..param.TConfig:Configuration Spec. Defines destination function, size type, and file type.
-...type:Spec.PoolConfig
-...type:Spec.PoolConfigSize
-..remarks:The Pool's input/output type is $TValue$ and the size type is determined by the $TConfig$.
-..include:seqan/pipe.h
-*/
-
     template < typename TConfig = PoolConfig<> >
     struct PoolSpec {
         typedef TConfig Config;
@@ -152,33 +108,18 @@ namespace SEQAN_NAMESPACE_MAIN
  * @class Pool
  * @headerfile <seqan/pipe.h>
  * @brief Pools are push- and pop-passive pipeline modules.
- * 
+ *
  * @signature template <typename TValue[, typename TSpec]>
  *            class Pool;
- * 
+ *
  * @tparam TSpec  The specializing type. Default: PoolSpec&lt;&gt;, see PoolSpec.
  * @tparam TValue The value type, that is the type of the stream elements.
- * 
- * @section Remarks
- * 
+ *
  * Use Value to get the output type of a given Pipe (returns <tt>Value&lt;TInput&gt;::Type</tt> by default).
- * 
+ *
  * Use Size to get the size type of a given Pipe (returns <tt>Size&lt;TInput&gt;::Type</tt> by default).
  */
 
-/**
-.Class.Pool:
-..cat:Pipelining
-..summary:Pools are push- and pop-passive pipeline modules.
-..signature:Pool<TValue, TSpec>
-..param.TValue:The value type, that is the type of the stream elements.
-..param.TSpec:The specializing type.
-...default:PoolSpec<>, see @Spec.PoolSpec@.
-..remarks:Use @Metafunction.Value@ to get the output type of a given Pipe (returns $Value<TInput>::Type$ by default).
-..remarks:Use @Metafunction.Size@ to get the size type of a given Pipe (returns $Size<TInput>::Type$ by default).
-..include:seqan/pipe.h
-*/
-
     template < typename TValue,
                typename TSpec = PoolSpec<> >
     struct Pool;
@@ -217,7 +158,7 @@ namespace SEQAN_NAMESPACE_MAIN
 */
 
 /*
-        enum { DefaultMemBufferSize     = 0*8192,//64 * 1024,	// low memory config [kB]
+        enum { DefaultMemBufferSize     = 0*8192,//64 * 1024,    // low memory config [kB]
                DefaultPageSize          = 2 * 1024,             // [kB]
                DefaultBucketBufferSize  = 6 * 1024,             // [kB]
                DefaultReadAheadBuffers  = 4,
@@ -264,9 +205,9 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// handler that manages a simple memory buffer
+    // handler that manages a simple memory buffer
     struct MemorySpec_;
-	typedef Tag<MemorySpec_> MemorySpec;
+    typedef Tag<MemorySpec_> MemorySpec;
 
     template <typename TValue, typename TPoolSpec>
     struct BufferHandler<Pool<TValue, TPoolSpec>, MemorySpec>
@@ -274,14 +215,14 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef Pool<TValue, TPoolSpec> TPool;
         typedef Buffer<TValue>          TBuffer;
 
-		TPool	&pool;
-        TBuffer	empty;
+        TPool    &pool;
+        TBuffer    empty;
 
-		BufferHandler(TPool &_pool):
-			pool(_pool) {}
+        BufferHandler(TPool &_pool):
+            pool(_pool) {}
 
-		BufferHandler(TPool &_pool, size_t):
-			pool(_pool) {}
+        BufferHandler(TPool &_pool, size_t):
+            pool(_pool) {}
 
         inline TBuffer & first()
         {
@@ -304,15 +245,15 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// generic block based asynchronous read handler
+    // generic block based asynchronous read handler
     struct ReadFileSpec_;
 //IOREV _notio_ not directly relevant to iorev
-	typedef Tag<ReadFileSpec_> ReadFileSpec; //IOREV _notio_ not directly relevant to iorev
+    typedef Tag<ReadFileSpec_> ReadFileSpec; //IOREV _notio_ not directly relevant to iorev
 
     template <typename TValue, typename TSpec>
     struct BufferHandler<Pool<TValue, TSpec>, ReadFileSpec >
     {
-		typedef Pool<TValue, TSpec>                         TPool;
+        typedef Pool<TValue, TSpec>                         TPool;
         typedef typename TPool::File                        TFile;
 
         typedef Buffer<TValue>                              TBuffer;
@@ -323,31 +264,31 @@ namespace SEQAN_NAMESPACE_MAIN
         TPageChain  chain;
         size_t      pageSize;
         size_t      readPageNo, _pages;
-        TBuffer	    empty;
+        TBuffer        empty;
 
         BufferHandler(TPool &_pool):
             pool(_pool),
             chain(_min(_pool.readAheadBuffers, _pool.pages())),
-			pageSize(_pool.pageSize) {}
+            pageSize(_pool.pageSize) {}
 
         BufferHandler(TPool &_pool, size_t _requestedBufferSize, size_t _readAheadBuffers = 1):
             pool(_pool),
 //            pageSize(alignSize(_min(_pool.size(), _requestedBufferSize), _pool.pageSize)),
-            chain(_min(_readAheadBuffers, _pool.pages(pageSize = alignSize(_min(_pool.size(), _requestedBufferSize), _pool.pageSize)))) 
+            chain(_min(_readAheadBuffers, _pool.pages(pageSize = alignSize(_min(_pool.size(), _requestedBufferSize), _pool.pageSize))))
         {
-			#ifdef SEQAN_HEADER_PIPE_DEBUG
-				::std::cerr << "___BufferHandler___" << ::std::endl;
-				::std::cerr << "pagesize: " << pageSize << ::std::endl;
-				::std::cerr << "readaheadbuffers: " << chain.maxFrames << ::std::endl;
-				::std::cerr << "pages: " << pool.pages(pageSize) << ::std::endl;
-			#endif
+            #ifdef SEQAN_HEADER_PIPE_DEBUG
+                std::cerr << "___BufferHandler___" << std::endl;
+                std::cerr << "pagesize: " << pageSize << std::endl;
+                std::cerr << "readaheadbuffers: " << chain.maxFrames << std::endl;
+                std::cerr << "pages: " << pool.pages(pageSize) << std::endl;
+            #endif
         }
 
         ~BufferHandler()
         {
             end();
         }
-        
+
         inline TBuffer & first()
         {
             _pages = pool.pages(pageSize);
@@ -365,7 +306,9 @@ namespace SEQAN_NAMESPACE_MAIN
             // retrieve the very first and wait for I/O transfer to complete
             bool waitResult = waitFor(*chain.first);
             if (!waitResult)
-                SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(*chain.first), strerror(errno));
+                SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                           _pageFrameStatusString(chain.first->status),
+                           strerror(errno));
 
             return processBuffer(*chain.first, *this);
         }
@@ -378,11 +321,13 @@ namespace SEQAN_NAMESPACE_MAIN
             // read ahead
             chain.last->pageNo = readPageNo++;
             _read(*chain.last);
-            
+
             // retrieve the next buffer in order and wait for I/O transfer to complete
             bool waitResult = waitFor(*chain.first);
             if (!waitResult)
-                SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(*chain.first), strerror(errno));
+                SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                           _pageFrameStatusString(chain.first->status),
+                           strerror(errno));
 
             return processBuffer(*chain.first, *this);
         }
@@ -396,7 +341,7 @@ namespace SEQAN_NAMESPACE_MAIN
         {
             TPageFrame *p = chain.first;
             while (p) {
-				::seqan::cancel(*p, pool.file);
+                seqan::cancel(*p, pool.file);
                 freePage(*p, pool.file);
                 p = p->next;
             }
@@ -405,8 +350,8 @@ namespace SEQAN_NAMESPACE_MAIN
         inline void process() {}
 
     private:
-		bool _error() {
-//            ::std::cerr << "Error in BufWriteFileHandler::_read " << pool.file.error() << ::std::endl;
+        bool _error() {
+//            std::cerr << "Error in BufWriteFileHandler::_read " << pool.file.error() << std::endl;
             return true;
         }
 
@@ -432,16 +377,16 @@ namespace SEQAN_NAMESPACE_MAIN
     };
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// generic block based asynchronous write handler
+    //////////////////////////////////////////////////////////////////////////////
+    // generic block based asynchronous write handler
     struct WriteFileSpec_;
 //IOREV _notio_ not directly relevant to iorev
-	typedef Tag<WriteFileSpec_> WriteFileSpec; //IOREV _notio_ not directly relevant to iorev
+    typedef Tag<WriteFileSpec_> WriteFileSpec; //IOREV _notio_ not directly relevant to iorev
 
     template < typename TValue, typename TSpec >
     struct BufferHandler<Pool<TValue, TSpec>, WriteFileSpec>
     {
-		typedef Pool<TValue, TSpec>                 TPool;
+        typedef Pool<TValue, TSpec>                 TPool;
         typedef typename TPool::File                TFile;
 
         typedef Buffer<TValue>                              TBuffer;
@@ -452,22 +397,24 @@ namespace SEQAN_NAMESPACE_MAIN
         TPageChain  chain;
         size_t      pageSize;
         size_t      writePageNo, _pages;
-        TBuffer	    empty;
+        TBuffer        empty;
 
         BufferHandler(TPool &_pool):
             pool(_pool),
             chain(_min(_pool.writeBackBuffers, _pool.pages())),
-			pageSize(_pool.pageSize) {}
+            pageSize(_pool.pageSize),
+            writePageNo(0),
+            _pages(0) {}
 
         BufferHandler(TPool &_pool, size_t _requestedBufferSize, size_t _writeBackBuffers = 1):
             pool(_pool),
             chain(_min(_writeBackBuffers, _pool.pages(pageSize))),
-			pageSize(alignSize(_min(_pool.size(), _requestedBufferSize), _pool.pageSize)) {}
+            pageSize(alignSize(_min(_pool.size(), _requestedBufferSize), _pool.pageSize)) {}
 
         ~BufferHandler() {
             cancel();
         }
-        
+
     public:
 
         inline TBuffer & first()
@@ -516,19 +463,21 @@ namespace SEQAN_NAMESPACE_MAIN
                 // wait for I/O transfer to complete
                 bool waitResult = waitFor(*p);
                 if (!waitResult)
-                    SEQAN_FAIL("%s operation could not be completed: \"%s\"", _pageFrameStatusString(*p), strerror(errno));
+                    SEQAN_FAIL("%s operation could not be completed: \"%s\"",
+                               _pageFrameStatusString(p->status),
+                               strerror(errno));
 
                 freePage(*p, pool.file);
                 p = p->next;
             }
-			::seqan::flush(pool.file);
+            seqan::flush(pool.file);
         }
 
         inline void cancel()
         {
             TPageFrame *p = chain.first;
             while (p) {
-                ::seqan::cancel(*p, pool.file);
+                seqan::cancel(*p, pool.file);
                 freePage(*p, pool.file);
                 p = p->next;
             }
@@ -540,7 +489,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
         bool _error()
         {
-//            ::std::cerr << "Error in BufWriteFileHandler::_write " << pool.file.error() << ::std::endl;
+//            std::cerr << "Error in BufWriteFileHandler::_write " << pool.file.error() << std::endl;
             return true;
         }
 
@@ -557,159 +506,159 @@ namespace SEQAN_NAMESPACE_MAIN
         }
     };
 
-	//////////////////////////////////////////////////////////////////////////////
-	// generic buffered multiplex handler
+    //////////////////////////////////////////////////////////////////////////////
+    // generic buffered multiplex handler
     struct MultiplexSpec_;
-	typedef Tag<MultiplexSpec_> MultiplexSpec;
+    typedef Tag<MultiplexSpec_> MultiplexSpec;
 
-	template < typename TBufferHandler1, typename TBufferHandler2 >
+    template < typename TBufferHandler1, typename TBufferHandler2 >
     struct BufferHandler< Bundle2< TBufferHandler1, TBufferHandler2 >, MultiplexSpec >
-	{
+    {
         typedef typename Value<TBufferHandler1>::Type TBuffer;
 
-		TBufferHandler1 *handler1;
-		TBufferHandler2 *handler2;
-
-		template <typename TPool>
-		BufferHandler(TPool &_pool) {
-			if (_pool.memBuffer.begin || _pool._size == 0) {	// decision to choose handler1 or handler2
-				handler1 = new TBufferHandler1(_pool);
-				handler2 = NULL;
-			} else {
-				handler1 = NULL;
-				handler2 = new TBufferHandler2(_pool);
-			}
-		}
-
-		template <typename TPool>
-		BufferHandler(TPool &_pool, size_t _requestedBufferSize) {
-			if (_pool.memBuffer.begin || _pool._size == 0) {	// decision to choose handler1 or handler2
-				handler1 = new TBufferHandler1(_pool, _requestedBufferSize);
-				handler2 = NULL;
-			} else {
-				handler1 = NULL;
-				handler2 = new TBufferHandler2(_pool, _requestedBufferSize);
-			}
-		}
-
-		~BufferHandler() {
-			delete handler1;
-			delete handler2;
-		}
-		
+        TBufferHandler1 *handler1;
+        TBufferHandler2 *handler2;
+
+        template <typename TPool>
+        BufferHandler(TPool &_pool) {
+            if (_pool.memBuffer.begin || _pool._size == 0) {    // decision to choose handler1 or handler2
+                handler1 = new TBufferHandler1(_pool);
+                handler2 = NULL;
+            } else {
+                handler1 = NULL;
+                handler2 = new TBufferHandler2(_pool);
+            }
+        }
+
+        template <typename TPool>
+        BufferHandler(TPool &_pool, size_t _requestedBufferSize) {
+            if (_pool.memBuffer.begin || _pool._size == 0) {    // decision to choose handler1 or handler2
+                handler1 = new TBufferHandler1(_pool, _requestedBufferSize);
+                handler2 = NULL;
+            } else {
+                handler1 = NULL;
+                handler2 = new TBufferHandler2(_pool, _requestedBufferSize);
+            }
+        }
+
+        ~BufferHandler() {
+            delete handler1;
+            delete handler2;
+        }
+
         inline TBuffer first() {
-			if (handler1)	return handler1->first();
-			else			return handler2->first();
-		}
+            if (handler1)    return handler1->first();
+            else            return handler2->first();
+        }
 
-		inline TBuffer next() {
-			if (handler1)	return handler1->next();
-			else			return handler2->next();
-		}
+        inline TBuffer next() {
+            if (handler1)    return handler1->next();
+            else            return handler2->next();
+        }
 
-		inline void end() {
-			if (handler1)	handler1->end();
-			else			handler2->end();
-		}
+        inline void end() {
+            if (handler1)    handler1->end();
+            else            handler2->end();
+        }
 
-		inline void process() {
-			if (handler1)	handler1->process();
-			else			handler2->process();
-		}
+        inline void process() {
+            if (handler1)    handler1->process();
+            else            handler2->process();
+        }
 
-		inline void cancel() {
-			if (handler1)	handler1->cancel();
-			else			handler2->cancel();
-		}
-	};
+        inline void cancel() {
+            if (handler1)    handler1->cancel();
+            else            handler2->cancel();
+        }
+    };
 
 
-	template < typename THandler1, typename THandler2 >
+    template < typename THandler1, typename THandler2 >
     struct Handler< Bundle2< THandler1, THandler2 >, MultiplexSpec >
-	{
+    {
         typedef typename Value<Handler>::Type TValue;
 
         THandler1 *handler1;
-		THandler2 *handler2;
+        THandler2 *handler2;
 
-		template <typename TPool>
-		Handler(TPool &_pool)
+        template <typename TPool>
+        Handler(TPool &_pool)
         {
-			if (_pool.memBuffer.begin || _pool._size == 0) {	// decision to choose handler1 or handler2
-				handler1 = new THandler1(_pool);
-				handler2 = NULL;
-			} else {
-				handler1 = NULL;
-				handler2 = new THandler2(_pool);
-			}
-		}
-
-		~Handler() {
-			delete handler1;
-			delete handler2;
-		}
-		
+            if (_pool.memBuffer.begin || _pool._size == 0) {    // decision to choose handler1 or handler2
+                handler1 = new THandler1(_pool);
+                handler2 = NULL;
+            } else {
+                handler1 = NULL;
+                handler2 = new THandler2(_pool);
+            }
+        }
+
+        ~Handler() {
+            delete handler1;
+            delete handler2;
+        }
+
         inline bool begin() {
-			if (handler1)	return handler1->begin();
-			else			return handler2->begin();
-		}
+            if (handler1)    return handler1->begin();
+            else            return handler2->begin();
+        }
 
         inline TValue const & front() const {
-            if (handler1)	return handler1->front();
-			else			return handler2->front();
+            if (handler1)    return handler1->front();
+            else            return handler2->front();
         }
 
         inline void pop() {
-            if (handler1)	handler1->pop();
-			else			handler2->pop();
+            if (handler1)    handler1->pop();
+            else            handler2->pop();
         }
 
         inline void pop(TValue &Ref_) {
-            if (handler1)	handler1->pop(Ref_);
-			else			handler2->pop(Ref_);
+            if (handler1)    handler1->pop(Ref_);
+            else            handler2->pop(Ref_);
         }
 
         inline void push(TValue const & Val_) {
-            if (handler1)	handler1->push(Val_);
-			else			handler2->push(Val_);
+            if (handler1)    handler1->push(Val_);
+            else            handler2->push(Val_);
         }
 
         inline bool eof() const {
-            if (handler1)	return handler1->eof();
-			else			return handler2->eof();
+            if (handler1)    return handler1->eof();
+            else            return handler2->eof();
         }
 
-		inline void end() {
-			if (handler1)	handler1->end();
-			else			handler2->end();
-		}
+        inline void end() {
+            if (handler1)    handler1->end();
+            else            handler2->end();
+        }
 
-		inline void process() {
-			if (handler1)	handler1->process();
-			else			handler2->process();
-		}
-	};
+        inline void process() {
+            if (handler1)    handler1->process();
+            else            handler2->process();
+        }
+    };
 
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// character and buffer based handler definitions
+    //////////////////////////////////////////////////////////////////////////////
+    // character and buffer based handler definitions
     template < typename TValue, typename TSpec >
     struct BufReadHandler< Pool< TValue, TSpec > >
     {
         typedef BufferHandler< Bundle2<
-			BufferHandler< Pool< TValue, TSpec >, MemorySpec >, 
-			BufferHandler< Pool< TValue, TSpec >, ReadFileSpec >
-		>, MultiplexSpec > Type;
+            BufferHandler< Pool< TValue, TSpec >, MemorySpec >,
+            BufferHandler< Pool< TValue, TSpec >, ReadFileSpec >
+        >, MultiplexSpec > Type;
     };
 
     template < typename TValue, typename TSpec >
     struct BufWriteHandler< Pool< TValue, TSpec > >
     {
         typedef BufferHandler< Bundle2<
-			BufferHandler< Pool< TValue, TSpec >, MemorySpec >, 
-			BufferHandler< Pool< TValue, TSpec >, WriteFileSpec >
-		>, MultiplexSpec > Type;
+            BufferHandler< Pool< TValue, TSpec >, MemorySpec >,
+            BufferHandler< Pool< TValue, TSpec >, WriteFileSpec >
+        >, MultiplexSpec > Type;
     };
 
 
@@ -723,12 +672,12 @@ namespace SEQAN_NAMESPACE_MAIN
 
     template < typename TPool >
     struct HandlerArgs {
-		typedef Nothing Type;
-	};
+        typedef Nothing Type;
+    };
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// base class of all pool classes like Pool, Mapper, Sorter
+    // base class of all pool classes like Pool, Mapper, Sorter
 
     template < typename TValue,
                typename TSpec >
@@ -739,14 +688,14 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef typename Config::SizeType   SizeType;
         typedef Buffer<TValue>              TBuffer;
 
-		// public handlers to read simultanously buffer- or character-wise
+        // public handlers to read simultanously buffer- or character-wise
         typedef typename ReadHandler<Pool>::Type    ReadHandler;
         typedef typename WriteHandler<Pool>::Type   WriteHandler;
-		typedef typename HandlerArgs<Pool>::Type	HandlerArgs;
+        typedef typename HandlerArgs<Pool>::Type    HandlerArgs;
 
-		File				file;
+        File                file;
         bool                _temporary, _ownFile;
-		SizeType			_size;
+        SizeType            _size;
         size_t              _pages;
         size_t              pageSize;
         size_t              bucketBufferSize;
@@ -754,19 +703,19 @@ namespace SEQAN_NAMESPACE_MAIN
         size_t              writeBackBuffers;
         size_t              writeBackBuckets;
 
-        TBuffer				memBuffer;
+        TBuffer                memBuffer;
         size_t              memBufferSize;
         HandlerArgs         handlerArgs;
 
-		bool				_partiallyFilled;		// the pool is partially filled (it contains undefined values)
-		TValue				undefinedValue;			// value to represent undefined (unwritten) entries
+        bool                _partiallyFilled;        // the pool is partially filled (it contains undefined values)
+        TValue                undefinedValue;            // value to represent undefined (unwritten) entries
 
     protected:
         size_t              _lastPageNo;
         size_t              _lastPageSize;
 
         int                 listeners;
-       
+
         ReadHandler         *reader;
         WriteHandler        *writer;
 
@@ -774,114 +723,114 @@ namespace SEQAN_NAMESPACE_MAIN
     public:
 
         //////////////////////////////////////////////////////////////////////////////
-		// public iterator types
+        // public iterator types
 
-		typedef SizeType				size_type;
+        typedef SizeType                size_type;
 
-        Pool(const PoolParameters &_conf = PoolParameters()):
-            file(NULL)
+        Pool(const PoolParameters &_conf = PoolParameters()) :
+            file(NULL), undefinedValue()
         {
-			_init(_conf);
+            _init(_conf);
             _setSize(0);
         }
-        
-		Pool(HandlerArgs const &args, PoolParameters const &_conf = PoolParameters()):
-            file(NULL),
-			handlerArgs(args)
+
+        Pool(HandlerArgs const &args, PoolParameters const &_conf = PoolParameters()):
+            file(NULL), handlerArgs(args), undefinedValue()
         {
-			_init(_conf);
+            _init(_conf);
             _setSize(0);
         }
-        
+
         template < typename TInput, typename TPipeSpec >
         Pool(Pipe<TInput, TPipeSpec> &, const PoolParameters &_conf = PoolParameters()):
-            file(NULL)
+            file(NULL), undefinedValue()
         {
-			_init(_conf);
+            _init(_conf);
             _setSize(0);
         }
-        
+
         template < typename TInput, typename TPipeSpec >
-		Pool(Pipe<TInput, TPipeSpec> &, HandlerArgs const &args, PoolParameters const &_conf = PoolParameters()):
-            file(NULL),
-			handlerArgs(args)
+        Pool(Pipe<TInput, TPipeSpec> &, HandlerArgs const &args, PoolParameters const &_conf = PoolParameters()):
+            file(NULL), handlerArgs(args), undefinedValue()
         {
-			_init(_conf);
+            _init(_conf);
             _setSize(0);
         }
-        
+
         Pool(File &_file, const PoolParameters &_conf = PoolParameters()):
-            file(_file)
+            file(_file), undefinedValue()
         {
-			_init(_conf);
+            _init(_conf);
             _ownFile = false;
             _temporary = false;
             memBufferSize = 0;
-			_setSize(::seqan::size(file) / sizeof(TValue));
+            _setSize(seqan::length(file) / sizeof(TValue));
         }
-        
-        Pool(const char *fileName, const PoolParameters &_conf = PoolParameters())
+
+        Pool(const char *fileName, const PoolParameters &_conf = PoolParameters()) :
+            file(NULL), undefinedValue()
         {
-			_init(_conf);
+            _init(_conf);
             _temporary = false;
             memBufferSize = 0;
             _ownFile = open(file, fileName);
             if (_ownFile)
-                _setSize(::seqan::size(file) / sizeof(TValue));
+                _setSize(seqan::length(file) / sizeof(TValue));
             else
                 _setSize(0);
         }
-        
-        ~Pool() {
+
+        ~Pool()
+        {
             endRead();
             endWrite();
-            if (_temporary) 
+            if (_temporary)
                 clear();
             else
                 if (_ownFile) close(file);
         }
-        
+
         inline void clear() {
             resize(0);
         }
 
-		inline size_type size() const {
-			return _size;
-		}
+        inline size_type size() const {
+            return _size;
+        }
 
         // this is not a real resize
         void resize(size_type _newSize) {
-			typedef typename Size<File>::Type TFSize SEQAN_UNUSED_TYPEDEF;
+            typedef typename Size<File>::Type TFSize SEQAN_UNUSED_TYPEDEF;
             if (_newSize == _size) return;
 
-            _freeHandlers();	// if you forgot to call endRead/endWrite we have no trouble
+            _freeHandlers();    // if you forgot to call endRead/endWrite we have no trouble
 
-			if (_temporary && _ownFile) {
-				if (_size != 0) {
-					if (memBuffer.begin)
-						freePage(memBuffer, *this);
+            if (_temporary && _ownFile) {
+                if (_size != 0) {
+                    if (memBuffer.begin)
+                        freePage(memBuffer, *this);
                     else {
-						close(file);
+                        close(file);
                         SEQAN_PROSUB(SEQAN_PROIOVOLUME, (_proFloat)((TFSize)_size * (TFSize)sizeof(TValue)));
                     }
-				}
+                }
 
-				if (_newSize != 0) {
-					if (_newSize <= (size_type)memBufferSize)
-						allocPage(memBuffer, _newSize, *this);
+                if (_newSize != 0) {
+                    if (_newSize <= (size_type)memBufferSize)
+                        allocPage(memBuffer, _newSize, *this);
                     else {
-						openTemp(file);
+                        openTemp(file);
                         SEQAN_PROADD(SEQAN_PROIOVOLUME, (_proFloat)((TFSize)_newSize * (TFSize)sizeof(TValue)));
                     }
-				}
-			}
+                }
+            }
 
             _setSize(_newSize);
         }
 
 
         //////////////////////////////////////////////////////////////////////////////
-		// auto-disposal interface (deprecated)
+        // auto-disposal interface (deprecated)
 
         inline void addListener() {
             if (!listeners) return;
@@ -897,27 +846,27 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
         //////////////////////////////////////////////////////////////////////////////
-		// queue interface
+        // queue interface
 
         inline TValue const & front() const
         {
             return reader->front();
         }
 
-		inline TValue const & operator*() const
+        inline TValue const & operator*() const
         {
-			return reader->front();
-		}
+            return reader->front();
+        }
 
         inline void pop()
         {
-			reader->pop();
+            reader->pop();
         }
 
         inline Pool& operator++()
         {
-			reader->pop();
-			return *this;
+            reader->pop();
+            return *this;
         }
 
         inline void pop(TValue &Ref_)
@@ -939,20 +888,20 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
         //////////////////////////////////////////////////////////////////////////////
-		// flow control
+        // flow control
 
         bool beginWrite() {
             _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble
-			return (
-                (writer = new WriteHandler(*this)) && 
+            return (
+                (writer = new WriteHandler(*this)) &&
                 writer->begin());
         }
 
         bool endWrite() {
-			if (writer) {
-				writer->end();
-				writer->process();
-			}
+            if (writer) {
+                writer->end();
+                writer->process();
+            }
             delete writer;
             writer = NULL;
             return true;
@@ -960,7 +909,7 @@ namespace SEQAN_NAMESPACE_MAIN
 
         bool beginRead() {
             _freeHandlers(); // if you forgot to call endRead/endWrite we have no trouble
-			return (
+            return (
                 (reader = new ReadHandler(*this)) &&
                 reader->begin());
         }
@@ -1010,50 +959,51 @@ namespace SEQAN_NAMESPACE_MAIN
             _lastPageSize = _size % pageSize;
         }
 
-		void _init(PoolParameters _conf = PoolParameters()) 
-		{
+        void _init(PoolParameters _conf = PoolParameters())
+        {
             _conf.absolutize(16*1024/*sectorSize(file)*/, (TValue*)NULL);
             memBufferSize    = _conf.memBufferSize;
-            pageSize		 = _conf.pageSize;
+            pageSize         = _conf.pageSize;
             bucketBufferSize = _conf.bucketBufferSize;
             readAheadBuffers = _conf.readAheadBuffers;
             writeBackBuffers = _conf.writeBackBuffers;
             writeBackBuckets = _conf.writeBackBuffers;
+            _partiallyFilled = true;
             listeners = 0;
             reader = NULL;
             writer = NULL;
             _ownFile = true;
             _temporary = true;
-		}
+        }
 
     };
 
     template < typename TValue, typename TSpec, typename TIteratorSpec>
-	struct Iterator< Pool< TValue, TSpec > const, TIteratorSpec> {
-		typedef IPipeIterator< Pool< TValue, TSpec > > Type;
-	};
+    struct Iterator< Pool< TValue, TSpec > const, TIteratorSpec> {
+        typedef IPipeIterator< Pool< TValue, TSpec > > Type;
+    };
 
     template < typename TValue, typename TSpec, typename TIteratorSpec>
-	struct Iterator< Pool< TValue, TSpec >, TIteratorSpec> {
-		typedef OPipeIterator< Pool< TValue, TSpec > > Type;
-	};
+    struct Iterator< Pool< TValue, TSpec >, TIteratorSpec> {
+        typedef OPipeIterator< Pool< TValue, TSpec > > Type;
+    };
 
     template < typename TValue, typename TSpec >
-	OPipeIterator< Pool< TValue, TSpec > >
-	begin(Pool< TValue, TSpec > &pool) {
-		return OPipeIterator< Pool< TValue, TSpec > >(pool);
-	}
+    OPipeIterator< Pool< TValue, TSpec > >
+    begin(Pool< TValue, TSpec > &pool) {
+        return OPipeIterator< Pool< TValue, TSpec > >(pool);
+    }
 
     template < typename TValue, typename TSpec >
-	OPipeIterator< Pool< TValue, TSpec > >
-	end(Pool< TValue, TSpec > &/*pool*/) {
-		return OPipeIterator< Pool< TValue, TSpec > >();
-	}
+    OPipeIterator< Pool< TValue, TSpec > >
+    end(Pool< TValue, TSpec > &/*pool*/) {
+        return OPipeIterator< Pool< TValue, TSpec > >();
+    }
 
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// a pool is a queue-like container for a large amount of data
+    // a pool is a queue-like container for a large amount of data
     // in contrast to a queue you can read the whole content more than once
     // but can't pop directly after a push
     // instead, access to a pool looks like the following:
@@ -1073,13 +1023,13 @@ namespace SEQAN_NAMESPACE_MAIN
     //template < typename TValue, typename TFile = File<> >
     //struct Pool: public Pool< TValue, PoolSpec< PoolConfig< TFile > > >
     //{
-    //    typedef TValue	                    Type;
+    //    typedef TValue                        Type;
     //    typedef TFile                       File;
     //    typedef typename Size<TFile>::Type  SizeType;
     //};
 
 
-	// seqan namespace traits
+    // seqan namespace traits
     template < typename TValue, typename TSpec >
     struct Value< Pool< TValue, TSpec > > {
         typedef TValue Type;
@@ -1097,20 +1047,24 @@ namespace SEQAN_NAMESPACE_MAIN
 
     template < typename TValue, typename TSpec >
     struct Difference< Pool< TValue, TSpec > > {
-		typedef typename MakeSigned_<typename Size<Pool< TValue, TSpec > >::Type>::Type Type;
+        typedef typename MakeSigned_<typename Size<Pool< TValue, TSpec > >::Type>::Type Type;
     };
 
-
-///.Function.clear.param.object.type:Class.Pool
-///.Function.clear.class:Class.Pool
-
+/*!
+ * @fn Pool#clear
+ * @brief Remove all elements from the pool.
+ *
+ * @signature void clear(pool);
+ *
+ * @param[in,out] pool Pool to clear.
+ */
     template < typename TValue, typename TSpec >
     inline void clear(Pool<TValue, TSpec> &me)
     {
         return me.clear();
     }
 
-	// deprecated
+    // deprecated
     template < typename TValue, typename TSpec >
     inline typename Size< Pool<TValue, TSpec> >::Type
     size(Pool<TValue, TSpec> const &me)
@@ -1118,37 +1072,72 @@ namespace SEQAN_NAMESPACE_MAIN
         return me.size();
     }
 
-///.Function.length.param.object.type:Class.Pool
-///.Function.length.class:Class.Pool
+/*!
+ * @fn Pool#length
+ * @headerfile <seqan/pipe.h>
+ * @brief Length of the pool.
+ *
+ * @signature TSize length(pool);
+ *
+ * @param[in] pool  The Pool to query for its size.
+ *
+ * @return    TSize The number of elements in the pool.
+ */
 
-	template < typename TValue, typename TSpec >
+    template < typename TValue, typename TSpec >
     inline typename Size< Pool<TValue, TSpec> >::Type
     length(Pool<TValue, TSpec> const &me)
     {
         return me.size();
     }
 
-///.Function.resize.param.object.type:Class.Pool
-///.Function.resize.class:Class.Pool
+/*!
+ * @fn Pool#resize
+ * @brief Resize a pool.
+ *
+ * @signature void resize(pool, len);
+ *
+ * @param[in,out] pool Pool to resize.
+ * @param[in]     len  Length to resize <tt>pool</tt> to.
+ */
 
-	template < typename TValue, typename TSpec, typename TSize >
+    template < typename TValue, typename TSpec, typename TSize >
     inline TSize resize(Pool<TValue, TSpec> &me, TSize new_length)
     {
-	    me.resize(new_length);
+        me.resize(new_length);
         return me.size();
     }
 
-///.Function.Pipe#front.param.object.type:Class.Pool
-///.Function.Pipe#front.class:Class.Pool
+/*!
+ * @fn Pool#front
+ * @brief Return reference to the first element.
+ *
+ * @signature TReference front(pool);
+ *
+ * @param[in] pool The pool to get the first element of.
+ *
+ * @return TReference A reference to the first element of <tt>seq</tt>.
+ */
 
     template < typename TValue, typename TSpec >
-	inline typename Value< Pool<TValue, TSpec> >::Type const & front(Pool<TValue, TSpec> &me) {
+    inline typename Value< Pool<TValue, TSpec> >::Type const & front(Pool<TValue, TSpec> &me) {
         return me.front();
     }
-
-///.Function.pop.param.object.type:Class.Pool
-///.Function.pop.class:Class.Pool
-
+/*!
+ * @fn Pool#pop
+ * @headerfile <seqan/pipe.h>
+ * @brief Pops the first element of the remaining stream.
+ *
+ * @signature void pop(pool[, ref]);
+ *
+ * @param[in,out] pool A pop-passive pipeline module.
+ * @param[out]    ref    Reference to the result.  Result type is <tt>Value&lt;TObject&gt;::Type</tt> for <tt>object</tt>
+ *                       type <tt>TObject</tt>.  Returns the first element of the remaining input stream.
+ *
+ * In contrast to Pool#front this function also steps one element further.
+ *
+ * Pool#front or Pool#pop can only be called within a read process surrounded by beginRead and endRead.
+ */
     template < typename TValue, typename TSpec >
     inline void pop(Pool<TValue, TSpec> &me) {
         me.pop();
@@ -1162,188 +1151,174 @@ namespace SEQAN_NAMESPACE_MAIN
 /*!
  * @fn Pool#push
  * @brief Appends an item at the end of an input stream.
- * 
- * @signature void push(object, val);
- * 
- * @param[in,out] object A push-passive pipeline module.
+ *
+ * @signature void push(pool, val);
+ *
+ * @param[in,out] pool A pool module.
  * @param[in]     val    Item to be pushed.
- * 
- * @section Remarks
- * 
+ *
  * The function <tt>push</tt> can only be called within a write process surrounded by beginWrite and endWrite.
  */
 
-/**
-.Function.push:
-..class:Class.Pool
-..cat:Pipelining
-..summary:Appends an item at the end of an input stream.
-..signature:push(object, val)
-..param.object:A push-passive pipeline module.
-...type:Class.Pool
-..param.val:Item to be pushed.
-..remarks:@Function.push@ can only be called within a write process surrounded by @Function.beginWrite@ and @Function.endWrite@.
-..include:seqan/pipe.h
-*/
-
     template < typename TValue, typename TSpec >
     inline void push(Pool<TValue, TSpec> &me, TValue const &Val_) {
         me.push(Val_);
     }
 
     template < typename TValue, typename TSpec >
-    ::std::ostream& operator<<(::std::ostream &out, Pool<TValue, TSpec> &p) {
+    std::ostream& operator<<(std::ostream &out, Pool<TValue, TSpec> &p) {
         beginRead(p);
         while (!eof(p)) {
-		    out << front(p) << ::std::endl;
+            out << front(p) << std::endl;
             pop(p);
         }
         endRead(p);
-		return out;
-	}
-
-
-	// the pipe interface of pool classes
-	//namespace SEQAN_NAMESPACE_PIPELINING
-	//{
-		//template < typename TValue, typename TSpec >
-		//struct Value< Pool< TValue, TSpec > >
-		//{
-		//	typedef TValue Type;
-		//};
-
-		//template < typename TValue, typename TSpec >
-		//struct Size< Pool< TValue, TSpec > >
-		//{
-		//	typedef typename Size< TFile >::Type Type;
-		//};
-
-		template < typename TValue, typename TSpec >
-	    inline bool control(Pool< TValue, TSpec > &me, ControlEof const &) {
-		    return me.eof();
-	    }
-    	
-		template < typename TValue, typename TSpec >
-	    inline bool control(Pool< TValue, TSpec > &me, ControlEos const &) {
-		    return me.eof();
-	    }
-    	
-		template < typename TValue, typename TSpec >
-	    inline bool control(Pool< TValue, TSpec > &me, ControlClear const &) {
-		    me.clear();
-		    return true;
-	    }
-    	
-		template < typename TValue, typename TSpec >
-	    inline bool control(Pool< TValue, TSpec > &me, ControlBeginRead const &) {
-		    return me.beginRead();
-	    }
-    	
-		template < typename TValue, typename TSpec >
-	    inline bool control(Pool< TValue, TSpec > &me, ControlEndRead const &) {
-		    return me.endRead();
-	    }
+        return out;
+    }
+
+
+    // the pipe interface of pool classes
+    //namespace SEQAN_NAMESPACE_PIPELINING
+    //{
+        //template < typename TValue, typename TSpec >
+        //struct Value< Pool< TValue, TSpec > >
+        //{
+        //    typedef TValue Type;
+        //};
+
+        //template < typename TValue, typename TSpec >
+        //struct Size< Pool< TValue, TSpec > >
+        //{
+        //    typedef typename Size< TFile >::Type Type;
+        //};
+
+        template < typename TValue, typename TSpec >
+        inline bool control(Pool< TValue, TSpec > &me, ControlEof const &) {
+            return me.eof();
+        }
+
+        template < typename TValue, typename TSpec >
+        inline bool control(Pool< TValue, TSpec > &me, ControlEos const &) {
+            return me.eof();
+        }
+
+        template < typename TValue, typename TSpec >
+        inline bool control(Pool< TValue, TSpec > &me, ControlClear const &) {
+            me.clear();
+            return true;
+        }
+
+        template < typename TValue, typename TSpec >
+        inline bool control(Pool< TValue, TSpec > &me, ControlBeginRead const &) {
+            return me.beginRead();
+        }
+
+        template < typename TValue, typename TSpec >
+        inline bool control(Pool< TValue, TSpec > &me, ControlEndRead const &) {
+            return me.endRead();
+        }
 
 /*!
  * @fn Pool#beginWrite
  * @headerfile <seqan/pipe.h>
  * @brief Initiates a write process.
- * 
- * @signature bool beginWrite(object);
- * 
- * @param object A push-passive pipeline module.
- * 
+ *
+ * @signature bool beginWrite(pool);
+ *
+ * @param[in,out] pool A pool module.
+ *
  * @return bool <tt>true</tt> on success, false on failure.
- * 
- * @section Remarks
- * 
- * <tt>beginWrite</tt> prepares a Pool for succeeding writes.
- * 
+ *
+ * <tt>beginWrite</tt> prepares a pool for succeeding writes.
+ *
  * A write process must be terminated with endWrite.  Nested write processes are not allowed.
- * 
+ *
  * @see Pool#endWrite
 */
 
-/**
-.Function.beginWrite
-..class:Class.Pool
-..cat:Pipelining
-..summary:Initiates a write process.
-..signature:beginWrite(object)
-..param.object:A push-passive pipeline module.
-...type:Class.Pool
-..returns:A $bool$ which is $true$ on success.
-..remarks:$beginWrite$ prepares a @Class.Pool@ for succeeding writes.
-..remarks:A write process must be terminated with @Function.endWrite@. Nested write processes are not allowed.
-..see:Function.endWrite
-..include:seqan/pipe.h
-*/
-
-		template < typename TValue, typename TSpec >
-	    inline bool beginWrite(Pool< TValue, TSpec > &me) {
+        template < typename TValue, typename TSpec >
+        inline bool beginWrite(Pool< TValue, TSpec > &me) {
 SEQAN_CHECKPOINT
-		    return me.beginWrite();
+            return me.beginWrite();
         }
 
 /*!
  * @fn Pool#endWrite
  * @brief Terminates a write process.
- * 
+ *
  * @signature bool endWrite(pool);
- * 
- * @param pool A push-passive pipeline module.
- * 
+ *
+ * @param[in,out] pool A push-passive pipeline module.
+ *
  * @return bool true on success, false on failure.
- * 
- * @section Remarks
- * 
- * <tt>endWrite</tt> closes the input stream and frees resources possibly allocated by beginWrite 
- * 
+ *
+ * <tt>endWrite</tt> closes the input stream and frees resources possibly allocated by beginWrite
+ *
  * @see Pool#beginWrite
  */
 
-/**
-.Function.endWrite:
-..class:Class.Pool
-..cat:Pipelining
-..summary:Terminates a write process.
-..signature:endWrite(object)
-..param.object:A push-passive pipeline module.
-...type:Class.Pool
-..returns:A $bool$ which is $true$ on success.
-..remarks:$endWrite$ closes the input stream and frees resources possibly allocated by @Function.beginWrite@.
-..see:Function.beginWrite
-..include:seqan/pipe.h
-*/
-
-		template < typename TValue, typename TSpec >
-	    inline bool endWrite(Pool< TValue, TSpec > &me) {
-		    return me.endWrite();
+        template < typename TValue, typename TSpec >
+        inline bool endWrite(Pool< TValue, TSpec > &me) {
+            return me.endWrite();
         }
 
-///.Function.atEnd.param.iterator.type:Class.Pool
-///.Function.atEnd.class:Class.Pool
-// TODO(holtgrew): Documentation bug!
+/*!
+ * @fn Pool#atEnd
+ * @brief Check whether the @link Pool @endlink object is at end.
+ *
+ * @signature bool atEnd(pool);
+ *
+ * @param[in] pool The @link Pool @endlink object to query.
+ *
+ * @return bool true in case of the pool being at the end, false otherwise.
+ */
 
-		template < typename TValue, typename TSpec >
-	    inline bool eof(Pool< TValue, TSpec > &me) {
+        template < typename TValue, typename TSpec >
+        inline bool eof(Pool< TValue, TSpec > &me) {
 SEQAN_CHECKPOINT
             return control(me, ControlEof());
         }
 
-		template < typename TValue, typename TSpec >
-	    inline bool beginRead(Pool< TValue, TSpec > &me) {
+/*!
+ * @fn Pool#beginRead
+ * @headerfile <seqan/pipe.h>
+ * @brief Initiates a read process.
+ *
+ * @signature bool beginRead(pool);
+ *
+ * @param[in,out] pool A pool module.
+ *
+ * @return bool true on success, false on failure.
+ *
+ * A read process must be terminated with endRead. Nested read processes are not allowed.
+ *
+ * @see Pool#endRead
+ */
+        template < typename TValue, typename TSpec >
+        inline bool beginRead(Pool< TValue, TSpec > &me) {
 SEQAN_CHECKPOINT
             return control(me, ControlBeginRead());
         }
-
-		template < typename TValue, typename TSpec >
-	    inline bool endRead(Pool< TValue, TSpec > &me) {
+/*!
+ * @fn Pool#endRead
+ * @headerfile <seqan/pipe.h>
+ * @brief Terminates a read process.
+ *
+ * @signature bool endRead(pool);
+ *
+ * @param[in,out] pool A pool module.
+ *
+ * @return bool true on success, false on failure.
+ *
+ * @see Pool#beginRead
+ */
+        template < typename TValue, typename TSpec >
+        inline bool endRead(Pool< TValue, TSpec > &me) {
 SEQAN_CHECKPOINT
             return control(me, ControlEndRead());
         }
 
-	//}
+    //}
 
     // pipe/pool -> pool
     template < typename TValue,
@@ -1368,17 +1343,25 @@ SEQAN_CHECKPOINT
     inline bool append(Pool<TValue, TSpec> &dest, String<TValue, TStringSpec> &src) {
         typedef typename Iterator< String<TValue, TStringSpec> const, Standard >::Type TIter;
         TIter _cur = begin(src, Standard());
-		TIter _end = end(src, Standard());
+        TIter _end = end(src, Standard());
         while (_cur != _end) {
             push(dest, *_cur);
             ++_cur;
         }
         return true;
     }
-
-///.Function.assign.param.target.type:Class.Pool
-///.Function.assign.class:Class.Pool
-
+/*!
+ * @fn Pool#assign
+ * @headerfile <seqan/pipe.h>
+ * @brief Assigns one object to another object.
+ *
+ * @signature void assign(target, source);
+ *
+ * @param[out] target Reference to assign to.
+ * @param[in]  source Value to assign.
+ *
+ * Assign value of source to target.
+ */
     template < typename TValue,
                typename TSpec,
                typename TSource >
@@ -1397,21 +1380,18 @@ SEQAN_CHECKPOINT
 
 
 
-///.Function.assign.param.source.type:Class.Pool
-///.Function.assign.class:Class.Pool
-
     // pool -> string
     template < typename TValue1,
-			   typename TStringSpec,
-			   typename TValue2,
-			   typename TSpec >
+               typename TStringSpec,
+               typename TValue2,
+               typename TSpec >
     inline bool assign(String<TValue1, TStringSpec> &dest, Pool<TValue2, TSpec> &src) {
         typedef typename Iterator< String<TValue1, TStringSpec>, Standard >::Type TIter;
         typename Size< String<TValue1, TStringSpec> >::Type _size = length(src);
         resize(dest, _size);
         if (!beginRead(src)) return false;
         TIter _cur = begin(dest, Standard());
-		TIter _end = end(dest, Standard());
+        TIter _end = end(dest, Standard());
         while (_cur != _end) {
             *_cur = *src;
             ++_cur;
@@ -1422,9 +1402,9 @@ SEQAN_CHECKPOINT
     }
 
     template < typename TValue1,
-			   typename TStringSpec,
-			   typename TValue2,
-			   typename TSpec >
+               typename TStringSpec,
+               typename TValue2,
+               typename TSpec >
     inline bool operator<<(String<TValue1, TStringSpec> &dest, Pool<TValue2, TSpec> &src) {
         return assign(dest, src);
     }
diff --git a/seqan/pipe/pool_mapper.h b/seqan/pipe/pool_mapper.h
index 6eab299..a382665 100644
--- a/seqan/pipe/pool_mapper.h
+++ b/seqan/pipe/pool_mapper.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,41 +45,25 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends MapperSpec
  * @headerfile <seqan/pipe.h>
  * @brief Configuration of Mapper.
- * 
+ *
  * @signature template <typename TMap, typename TSize[, typename TFile]>
  *            struct MapperConfigSize;
- * 
+ *
  * @tparam TMap  The destination function (see STL's <tt>unary_function</tt>).  This functions maps a stream element
  *               to its destined position.  The result type of this unary function should convertible to
  *               <tt>TSize</tt>.
  * @tparam TFile The underlying File type, defaults to <tt>File&lt;&gt;</tt>.
  * @tparam TSize The Mapper's size type.
- * 
+ *
  * @see MapperConfig
  */
 
-/**
-.Spec.MapperConfigSize:
-..cat:Pipelining
-..general:Spec.MapperSpec
-..summary:Configuration of Mapper.
-..signature:MapperConfigSize<TMap, TSize, TFile>
-..param.TMap:The destination function (see STL's $unary_function$).
-...remarks:This functions maps a stream element to its destined position. The result type of this unary function should convertible to $TSize$.
-...note:The destination function must be bijective.
-..param.TSize:The Mapper's size type.
-..param.TFile:The underlying @Class.File@ type.
-...default:$File<>$, see @Class.File@.
-..see:Spec.MapperConfig
-..include:seqan/pipe.h
-*/
-
     template < typename TMap,
-		       typename TSize,
-		       typename TFile = File<> >						// default file type
+               typename TSize,
+               typename TFile = File<> >                        // default file type
     struct MapperConfigSize {
         typedef TMap        Map;
-		typedef TSize		SizeType;
+        typedef TSize        SizeType;
         typedef TFile       File;
     };
 
@@ -88,44 +72,26 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends MapperSpec
  * @headerfile <seqan/pipe.h>
  * @brief Configuration of Mapper.
- * 
+ *
  * @signature template <typename TMap[, typename TFile]>
  *            struct MapperConfig;
- * 
+ *
  * @tparam TMap  The destination function (see STL's <tt>unary_function</tt>).  This functions maps a stream element to
  *               its destined position. The result type of this unary function should convertible to <tt>TSize</tt>.
  * @tparam TFile The underlying File type, defaults to <tt>File&lg;&gt;</tt>.
- * 
- * @section Remarks
- * 
+ *
  * Using this configuration spec., the Mapper's size type is <tt>Size&lt;TFile&gt;::Type</tt>. To use a custom size type
  * MapperConfigSize should be used.
- * 
+ *
  * @see MapperConfigSize
  */
 
-/**
-.Spec.MapperConfig:
-..cat:Pipelining
-..general:Spec.MapperSpec
-..summary:Configuration of Mapper.
-..signature:MapperConfig<TMap, TFile>
-..param.TMap:The destination function (see STL's $unary_function$).
-...remarks:This functions maps a stream element to its destined position. The result type of this unary function should convertible to $TSize$.
-...note:The destination function must be bijective.
-..param.TFile:The underlying @Class.File@ type.
-...default:$File<>$, see @Class.File@.
-..remarks:Using this configuration spec., the Mapper's size type is $Size<TFile>::Type$. To use a custom size type @Spec.MapperConfigSize@ should be used.
-..see:Spec.MapperConfigSize
-..include:seqan/pipe.h
-*/
-
     template < typename TMap,
-		       typename TFile = File<> >
+               typename TFile = File<> >
     struct MapperConfig {
-        typedef TMap						Map;
-		typedef typename Size<TFile>::Type	SizeType;
-        typedef TFile						File;
+        typedef TMap                        Map;
+        typedef typename Size<TFile>::Type    SizeType;
+        typedef TFile                        File;
     };
 
 /*!
@@ -133,82 +99,66 @@ namespace SEQAN_NAMESPACE_MAIN
  * @extends Pool
  * @headerfile <seqan/pipe.h>
  * @brief Permutes all elements using a custom destination function.
- * 
+ *
  * @signature template <typename TValue, typename TConfig>
  *            class Pool<TValue, MapperSpec<TConfig> >;
- * 
+ *
  * @tparam TConfig Configuration Spec. Defines destination function, size type, and file type.
  *                 Types: MapperConfig, MapperConfigSize
  * @tparam TValue  The value type, that is the type of the stream elements.
- * 
- * @section Remarks
- * 
+ *
  * The Pool's input/output type is <tt>TValue</tt> and the size type is determined by the <tt>TConfig</tt>.
  */
 
-/**
-.Spec.MapperSpec:
-..cat:Pipelining
-..general:Class.Pool
-..summary:Permutes all elements using a custom destination function.
-..signature:Pool<TValue, MapperSpec<TConfig> >
-..param.TValue:The value type, that is the type of the stream elements.
-..param.TConfig:Configuration Spec. Defines destination function, size type, and file type.
-...type:Spec.MapperConfig
-...type:Spec.MapperConfigSize
-..remarks:The Pool's input/output type is $TValue$ and the size type is determined by the $TConfig$.
-..include:seqan/pipe.h
-*/
-
     template <typename TConfig>
     struct MapperSpec {
         typedef TConfig Config;
     };
 
     template < typename TValue,
-			   typename TConfig >
+               typename TConfig >
     struct HandlerArgs< Pool< TValue, MapperSpec<TConfig> > >
     {
         typedef typename TConfig::Map Type;
     };
 
     struct ReadMapperSpec_;
-	typedef Tag<ReadMapperSpec_> ReadMapperSpec;
+    typedef Tag<ReadMapperSpec_> ReadMapperSpec;
 
 /*
     // mapping phase 2
     template < typename TValue,
-			   typename TConfig >
+               typename TConfig >
     inline Buffer<TValue> & processBuffer(
         PageFrame< TValue, typename TConfig::File, Dynamic> &buf,
         BufferHandler<Pool< TValue, MapperSpec<TConfig> >, ReadFileSpec> &_me)
     {
-		typedef BufferHandler<Pool< TValue, MapperSpec<TConfig> >, ReadMapperSpec> Handler;
+        typedef BufferHandler<Pool< TValue, MapperSpec<TConfig> >, ReadMapperSpec> Handler;
         Handler *me = static_cast<Handler*>(&_me);
-        
+
         typename Size< Pool< TValue, MapperSpec<TConfig> > >::Type offset = buf.pageNo;
-	    offset *= (unsigned)capacity(buf);
+        offset *= (unsigned)capacity(buf);
 
-		typename TConfig::Map M = me->pool.handlerArgs;
+        typename TConfig::Map M = me->pool.handlerArgs;
         for(TValue *cur = buf.begin; cur != buf.end; ++cur) {
             #ifdef SEQAN_DEBUG
                 if (!(M(*cur) >= offset && M(*cur) < offset + capacity(buf))) {
-					::std::cerr << "Mapper assertion failed: " << ::std::hex << M(*cur);
-					::std::cerr << " not in [" << offset << "," << (offset + capacity(buf)) << ") at " << (cur - buf.begin);
-                    ::std::cerr << " element is " << ::std::dec << *cur << ::std::endl;
+                    std::cerr << "Mapper assertion failed: " << std::hex << M(*cur);
+                    std::cerr << " not in [" << offset << "," << (offset + capacity(buf)) << ") at " << (cur - buf.begin);
+                    std::cerr << " element is " << std::dec << *cur << std::endl;
                 }
             #endif
             SEQAN_ASSERT(M(*cur) >= offset && M(*cur) < offset + capacity(buf));
             me->mapBuffer[M(*cur) - offset] = *cur;
         }
-		resize(me->mapBuffer, size(buf));
+        resize(me->mapBuffer, size(buf));
         return me->mapBuffer;
     }
 */
 
     // mapping phase 2 (in-place)
     template < typename TValue,
-			   typename TConfig >
+               typename TConfig >
     inline Buffer<TValue> &
     processBuffer(
         Buffer<TValue, PageFrame<typename TConfig::File, Dynamic> > &buf,
@@ -216,81 +166,81 @@ namespace SEQAN_NAMESPACE_MAIN
     {
         typedef typename Size< Pool< TValue, MapperSpec<TConfig> > >::Type TSize;
 
-		TSize undefinedPos = 0;
-		TSize offset = buf.pageNo;
-		TSize dstPos;
-	    offset *= capacity(buf);
+        TSize undefinedPos = 0;
+        TSize offset = buf.pageNo;
+        TSize dstPos;
+        offset *= capacity(buf);
 
-		typename TConfig::Map M = me.pool.handlerArgs;
-		bool partiallyFilled = me.pool._partiallyFilled;
+        typename TConfig::Map M = me.pool.handlerArgs;
+        bool partiallyFilled = me.pool._partiallyFilled;
 
-		if (partiallyFilled)
-			undefinedPos = M(me.pool.undefinedValue);
+        if (partiallyFilled)
+            undefinedPos = M(me.pool.undefinedValue);
 
-		for(TValue *cur = buf.begin; cur != buf.end; ++cur) {
+        for(TValue *cur = buf.begin; cur != buf.end; ++cur) {
 
-			dstPos = M(*cur);
+            dstPos = M(*cur);
 
-			if (partiallyFilled && dstPos == undefinedPos) 
-				continue;							// don't move undefined values
+            if (partiallyFilled && dstPos == undefinedPos)
+                continue;                            // don't move undefined values
 
-			#ifdef SEQAN_DEBUG
+            #ifdef SEQAN_DEBUG
                 if (!(dstPos >= offset && dstPos < offset + (TSize)capacity(buf))) {
-					::std::cerr << "Mapper assertion failed: " << ::std::hex << dstPos;
-					::std::cerr << " not in [" << offset << "," << (offset + capacity(buf)) << ") at " << (cur - buf.begin);
-                    ::std::cerr << " element is " << ::std::dec << *cur << ::std::endl;
+                    std::cerr << "Mapper assertion failed: " << std::hex << dstPos;
+                    std::cerr << " not in [" << offset << "," << (offset + capacity(buf)) << ") at " << (cur - buf.begin);
+                    std::cerr << " element is " << std::dec << *cur << std::endl;
                 }
-			#endif
+            #endif
             SEQAN_ASSERT(dstPos >= offset && dstPos < offset + (TSize)capacity(buf));
 
             TValue *I = buf.begin + (dstPos - offset);
             if (I != cur) {
-				TValue tmp;
-				TValue *refPrev = cur, *refNext = &tmp;
-
-				do {
-					*refNext = *I;
-					*I = *refPrev;
-
-					dstPos = M(*refNext);
-
-					if (partiallyFilled && dstPos == undefinedPos)
-						I = cur;					// move the undefined value to an arbitrary free position (*cur)
-					else 
-					{
-						#ifdef SEQAN_DEBUG
-							if (!(dstPos >= offset && dstPos < offset + (TSize)capacity(buf))) {
-								::std::cerr << "Mapper assertion failed: " << ::std::hex << dstPos;
-								::std::cerr << " not in [" << offset << "," << (offset + capacity(buf)) << ") at " << (refNext - buf.begin);
-								::std::cerr << " element is " << ::std::dec << *refNext << ::std::endl;
-							}
-							TValue *oldI = I;
-						#endif
-						SEQAN_ASSERT(dstPos >= offset && dstPos < offset + (TSize)capacity(buf));
-
-						I = buf.begin + (dstPos - offset);
-
-						#ifdef SEQAN_DEBUG
-							if (!partiallyFilled && I < cur) {
-								::std::cerr << "Mapper assertion failed: I=" << ::std::hex << I;
-								::std::cerr << " < cur=" << cur << ::std::dec << ::std::endl;
-								break;
-							}
-							if (I == oldI) {
-								::std::cerr << "Mapper assertion failed: I=" << ::std::hex << I;
-								::std::cerr << " in endless loop" << ::std::dec << ::std::endl;
-								break;
-							}
-						#endif
-					}
-
-					TValue *_swap = refNext;
-					refNext = refPrev;
-					refPrev = _swap;
-				} while (I != cur);
-
-				if (refPrev != cur)
-					*cur = *refPrev;
+                TValue tmp;
+                TValue *refPrev = cur, *refNext = &tmp;
+
+                do {
+                    *refNext = *I;
+                    *I = *refPrev;
+
+                    dstPos = M(*refNext);
+
+                    if (partiallyFilled && dstPos == undefinedPos)
+                        I = cur;                    // move the undefined value to an arbitrary free position (*cur)
+                    else
+                    {
+                        #ifdef SEQAN_DEBUG
+                            if (!(dstPos >= offset && dstPos < offset + (TSize)capacity(buf))) {
+                                std::cerr << "Mapper assertion failed: " << std::hex << dstPos;
+                                std::cerr << " not in [" << offset << "," << (offset + capacity(buf)) << ") at " << (refNext - buf.begin);
+                                std::cerr << " element is " << std::dec << *refNext << std::endl;
+                            }
+                            TValue *oldI = I;
+                        #endif
+                        SEQAN_ASSERT(dstPos >= offset && dstPos < offset + (TSize)capacity(buf));
+
+                        I = buf.begin + (dstPos - offset);
+
+                        #ifdef SEQAN_DEBUG
+                            if (!partiallyFilled && I < cur) {
+                                std::cerr << "Mapper assertion failed: I=" << std::hex << I;
+                                std::cerr << " < cur=" << cur << std::dec << std::endl;
+                                break;
+                            }
+                            if (I == oldI) {
+                                std::cerr << "Mapper assertion failed: I=" << std::hex << I;
+                                std::cerr << " in endless loop" << std::dec << std::endl;
+                                break;
+                            }
+                        #endif
+                    }
+
+                    TValue *_swap = refNext;
+                    refNext = refPrev;
+                    refPrev = _swap;
+                } while (I != cur);
+
+                if (refPrev != cur)
+                    *cur = *refPrev;
             }
         }
         return buf;
@@ -299,13 +249,13 @@ namespace SEQAN_NAMESPACE_MAIN
 /*
     // inherits buffered file reader and uses a map buffer
     template <typename TPool>
-    struct BufferHandler<TPool, ReadMapperSpec >: public BufferHandler< TPool, ReadFileSpec> 
+    struct BufferHandler<TPool, ReadMapperSpec >: public BufferHandler< TPool, ReadFileSpec>
     {
         typedef BufferHandler<TPool, ReadFileSpec>    Base;
         typedef typename Base::Type                     Type;
-        typedef typename Base::Buffer					Buffer;
+        typedef typename Base::Buffer                    Buffer;
 
-        Buffer	mapBuffer;
+        Buffer    mapBuffer;
 
         BufferHandler(TPool &_pool):
             Base(_pool)
@@ -327,30 +277,30 @@ namespace SEQAN_NAMESPACE_MAIN
 */
 
     //////////////////////////////////////////////////////////////////////////////
-	// generic adapter for buffered memory writers
+    // generic adapter for buffered memory writers
     struct MapperMemAdapter;
 
-	template <typename TBufferHandler>
-	struct Handler<TBufferHandler, MapperMemAdapter>
+    template <typename TBufferHandler>
+    struct Handler<TBufferHandler, MapperMemAdapter>
     {
-		typedef typename TBufferHandler::TPool          TPool;
+        typedef typename TBufferHandler::TPool          TPool;
         typedef typename Value<TBufferHandler>::Type    TBuffer;
         typedef typename Value<Handler>::Type           TValue;
 
-		TPool			&pool;
+        TPool            &pool;
         TBufferHandler  handler;
-        TBuffer			buffer;
+        TBuffer            buffer;
 
         template <typename TPool>
         Handler(TPool &_pool):
-			pool(_pool),
+            pool(_pool),
             handler(_pool) { }
 
         inline void _initializeBuffer() {
             if (empty(buffer)) return;
             arrayFill(seqan::begin(buffer, Standard()), seqan::end(buffer, Standard()), pool.undefinedValue);
         }
-        
+
         inline bool begin() {
             buffer = handler.first();
             _initializeBuffer();
@@ -365,8 +315,8 @@ namespace SEQAN_NAMESPACE_MAIN
             handler.end();
         }
 
-		inline bool eof() { return false; }
-		inline void process() {}
+        inline bool eof() { return false; }
+        inline void process() {}
     };
 
     template <typename TBufferHandler>
@@ -376,16 +326,16 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// cache bucket based synchronous write handler
+    // cache bucket based synchronous write handler
     struct MapperSyncWriter;
 
-	template <typename TValue, typename TSpec>
-	struct Handler<Pool<TValue, TSpec>, MapperSyncWriter>
+    template <typename TValue, typename TSpec>
+    struct Handler<Pool<TValue, TSpec>, MapperSyncWriter>
     {
         typedef Pool<TValue, TSpec>             TPool;
         typedef Buffer<TValue>                  TBuffer;
         typedef PageBucket<TValue>              TPageBucket;
-        typedef ::std::vector<TPageBucket>      TCache;
+        typedef std::vector<TPageBucket>      TCache;
 
         TPool   &pool;
         TBuffer bucketBuffer;
@@ -397,21 +347,21 @@ namespace SEQAN_NAMESPACE_MAIN
         ~Handler() {
             cancel();
         }
-        
-		struct insertBucket : public ::std::unary_function<TPageBucket,void>
+
+        struct insertBucket : public std::unary_function<TPageBucket,void>
         {
-			Handler &me;
-			insertBucket(Handler &_me): me(_me) {}
+            Handler &me;
+            insertBucket(Handler &_me): me(_me) {}
 
-			inline void operator() (TPageBucket const &cb) const
+            inline void operator() (TPageBucket const &cb) const
             {
                 me.cache.push_back(cb);
-			}
-		};
+            }
+        };
 
         bool begin()
         {
-    		cache.reserve(pool.pages);
+            cache.reserve(pool.pages);
             return equiDistantDistribution(
                 bucketBuffer, pool.bucketBufferSize, *this,
                 pool._size, pool.pageSize,
@@ -419,76 +369,76 @@ namespace SEQAN_NAMESPACE_MAIN
         }
 
         inline void push(TValue const &item) {
-			unsigned pageNo = pool.handlerArgs(item) / pool.pageSize;
+            unsigned pageNo = pool.handlerArgs(item) / pool.pageSize;
             #ifdef SEQAN_DEBUG
                 if (!(pageNo < cache.size())) {
-					::std::cerr << "Mapper push assertion failed: " << pageNo << " >= " << cache.size();
-                    ::std::cerr << " element is " << item << ::std::endl;
+                    std::cerr << "Mapper push assertion failed: " << pageNo << " >= " << cache.size();
+                    std::cerr << " element is " << item << std::endl;
                 }
-			#endif
-    		SEQAN_ASSERT_LT(pageNo, cache.size());
-			TPageBucket &cb = cache[pageNo];
+            #endif
+            SEQAN_ASSERT_LT(pageNo, cache.size());
+            TPageBucket &cb = cache[pageNo];
 
-			*cb.cur = item;
-			if (++cb.cur == cb.end)
-				writeBucket(cb, pageNo, pool.pageSize, pool.file);
+            *cb.cur = item;
+            if (++cb.cur == cb.end)
+                writeBucket(cb, pageNo, pool.pageSize, pool.file);
         }
 
         inline void end()
         {
             // flush all cache buckets to disk and compact cache
-			pool._partiallyFilled = false;
-			unsigned pageNo = 0;
-			unsigned curOfs, endOfs;
-			for(typename TCache::iterator cb = cache.begin(); cb != cache.end(); ++cb, ++pageNo) {
-				curOfs = cb->pageOfs + (cb->cur - cb->begin);
-				endOfs = pool.dataSize(pageNo);
-				if (curOfs < endOfs) {
-					// this page is partially filled and needs to be filled up with undefined entries
-					for(unsigned i = curOfs; i < endOfs; ++i) {
-						*cb.cur = pool.undefinedValue;
-						if (++cb.cur == cb.end)
-							writeBucket(cb, pageNo, pool.pageSize, pool.file);
-					}
-					pool._partiallyFilled = true;
-				}
-				writeBucket(*cb, pageNo, pool.pageSize, pool.file);
-			}
-			flush(pool.file);
+            pool._partiallyFilled = false;
+            unsigned pageNo = 0;
+            unsigned curOfs, endOfs;
+            for(typename TCache::iterator cb = cache.begin(); cb != cache.end(); ++cb, ++pageNo) {
+                curOfs = cb->pageOfs + (cb->cur - cb->begin);
+                endOfs = pool.dataSize(pageNo);
+                if (curOfs < endOfs) {
+                    // this page is partially filled and needs to be filled up with undefined entries
+                    for(unsigned i = curOfs; i < endOfs; ++i) {
+                        *cb.cur = pool.undefinedValue;
+                        if (++cb.cur == cb.end)
+                            writeBucket(cb, pageNo, pool.pageSize, pool.file);
+                    }
+                    pool._partiallyFilled = true;
+                }
+                writeBucket(*cb, pageNo, pool.pageSize, pool.file);
+            }
+            flush(pool.file);
             cancel();
         }
 
         inline void cancel()
         {
             cache.clear();
-			cache.reserve(0);
+            cache.reserve(0);
             freePage(bucketBuffer, *this);
         }
-        
-		inline bool eof() { return false; }
+
+        inline bool eof() { return false; }
         inline void process() {}
-	};
+    };
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// cache bucket based synchronous write handler
+    // cache bucket based synchronous write handler
     struct MapperAsyncWriter;
 
-	template <typename TValue, typename TConfig>
-	struct Handler<Pool<TValue, MapperSpec<TConfig> >, MapperAsyncWriter>
+    template <typename TValue, typename TConfig>
+    struct Handler<Pool<TValue, MapperSpec<TConfig> >, MapperAsyncWriter>
     {
         typedef Pool<TValue, MapperSpec<TConfig> >          TPool;
         typedef typename TConfig::File                      TFile;
         typedef Buffer<TValue>                              TBuffer;
         typedef Buffer<TValue, PageFrame<TFile, Dynamic> >  TPageFrame;
         typedef PageBucket<TValue>                          TPageBucket;
-        typedef ::std::vector<TPageBucket>                  Cache;
+        typedef std::vector<TPageBucket>                  Cache;
         typedef PageChain<TPageFrame>                       TPageChain;
 
         TPool       &pool;
-        TBuffer		bucketBuffer;
-        TPageChain	chain;
-        TBuffer		writeCache;
+        TBuffer        bucketBuffer;
+        TPageChain    chain;
+        TBuffer        writeCache;
         Cache       cache;
         unsigned    clusterSize;
 
@@ -503,39 +453,39 @@ namespace SEQAN_NAMESPACE_MAIN
         ~Handler() {
             cancel();
         }
-        
-		struct insertBucket : public ::std::unary_function<TPageBucket,void>
+
+        struct insertBucket : public std::unary_function<TPageBucket,void>
         {
-			Handler &me;
-			insertBucket(Handler &_me): me(_me) {}
+            Handler &me;
+            insertBucket(Handler &_me): me(_me) {}
 
-			inline void operator() (TPageBucket const &cb) const {
+            inline void operator() (TPageBucket const &cb) const {
                 me.cache.push_back(cb);
-			}
-		};
+            }
+        };
 
         bool begin()
         {
-    		cache.reserve(pool.pages());
+            cache.reserve(pool.pages());
             clusterSize = equiDistantAlignedDistribution(
                 bucketBuffer, sectorSize(pool.file), pool.bucketBufferSize, pool.file,
                 pool._size, pool.pageSize,
                 insertBucket(*this));
 
-			if (clusterSize == 0) {
-				clusterSize = UINT_MAX;
-				#ifdef SEQAN_DEBUG
-					::std::cerr << "mapper switched to synchronous mode" << ::std::endl;
-				#endif
-				return equiDistantDistribution(
-					bucketBuffer, pool.bucketBufferSize, pool.file,
-					pool._size, pool.pageSize,
-					insertBucket(*this));
-			}
-
-			#ifdef SEQAN_VERBOSE
-				::std::cerr << "async mapper clustersize " << clusterSize << ::std::endl;
-			#endif
+            if (clusterSize == 0) {
+                clusterSize = UINT_MAX;
+                #ifdef SEQAN_DEBUG
+                    std::cerr << "mapper switched to synchronous mode" << std::endl;
+                #endif
+                return equiDistantDistribution(
+                    bucketBuffer, pool.bucketBufferSize, pool.file,
+                    pool._size, pool.pageSize,
+                    insertBucket(*this));
+            }
+
+            #ifdef SEQAN_VERBOSE
+                std::cerr << "async mapper clustersize " << clusterSize << std::endl;
+            #endif
             allocPage(writeCache, chain.maxFrames * clusterSize, pool.file);
 
             // distribute write back buffers
@@ -552,45 +502,45 @@ namespace SEQAN_NAMESPACE_MAIN
 
         inline void push(TValue const &item)
         {
-			unsigned pageNo = pool.handlerArgs(item) / pool.pageSize;
+            unsigned pageNo = pool.handlerArgs(item) / pool.pageSize;
             #ifdef SEQAN_DEBUG
                 if (!(pageNo < cache.size())) {
-					::std::cerr << "Mapper push assertion failed: " << pageNo << " >= " << cache.size();
-                    ::std::cerr << " element is " << item << ::std::endl;
-					::std::cerr << ::std::hex << pool.handlerArgs(item) << " / " << pool.pageSize;
-					::std::cerr << " = " << pageNo << ::std::dec << ::std::endl;
+                    std::cerr << "Mapper push assertion failed: " << pageNo << " >= " << cache.size();
+                    std::cerr << " element is " << item << std::endl;
+                    std::cerr << std::hex << pool.handlerArgs(item) << " / " << pool.pageSize;
+                    std::cerr << " = " << pageNo << std::dec << std::endl;
                 }
-			#endif
+            #endif
             SEQAN_ASSERT_LT(pageNo, cache.size());
-			TPageBucket &cb = cache[pageNo];
+            TPageBucket &cb = cache[pageNo];
 
-			*cb.cur = item;
-			if (++cb.cur == cb.end)
-				_writeBucket(cb, pageNo);
+            *cb.cur = item;
+            if (++cb.cur == cb.end)
+                _writeBucket(cb, pageNo);
         }
 
         inline void end()
         {
             // flush all cache buckets to disk and compact cache
-			pool._partiallyFilled = false;
-			unsigned pageNo = 0;
-			unsigned curOfs, endOfs;
-			for(typename Cache::iterator cb = cache.begin(); cb != cache.end(); ++cb, ++pageNo) {
-				curOfs = cb->pageOfs + (cb->cur - cb->begin);
-				endOfs = pool.dataSize(pageNo);
-				if (curOfs < endOfs) {
-					// this page is partially filled and needs to be filled up with undefined entries
-					for(unsigned i = curOfs; i < endOfs; ++i) {
-						*cb->cur = pool.undefinedValue;
-						if (++cb->cur == cb->end)
-							_writeBucket(*cb, pageNo);
-					}
-					pool._partiallyFilled = true;
-				} else
-					_writeBucket(*cb, pageNo);
-			}
+            pool._partiallyFilled = false;
+            unsigned pageNo = 0;
+            unsigned curOfs, endOfs;
+            for(typename Cache::iterator cb = cache.begin(); cb != cache.end(); ++cb, ++pageNo) {
+                curOfs = cb->pageOfs + (cb->cur - cb->begin);
+                endOfs = pool.dataSize(pageNo);
+                if (curOfs < endOfs) {
+                    // this page is partially filled and needs to be filled up with undefined entries
+                    for(unsigned i = curOfs; i < endOfs; ++i) {
+                        *cb->cur = pool.undefinedValue;
+                        if (++cb->cur == cb->end)
+                            _writeBucket(*cb, pageNo);
+                    }
+                    pool._partiallyFilled = true;
+                } else
+                    _writeBucket(*cb, pageNo);
+            }
             chain.waitForAll();
-			flush(pool.file);
+            flush(pool.file);
             cancel();
         }
 
@@ -598,12 +548,12 @@ namespace SEQAN_NAMESPACE_MAIN
         {
             chain.cancelAll(pool.file);
             cache.clear();
-			cache.reserve(0);
+            cache.reserve(0);
             freePage(writeCache, pool.file);
             freePage(bucketBuffer, pool.file);
         }
-        
-		inline bool eof() { return false; }
+
+        inline bool eof() { return false; }
         inline void process() {}
 
     protected:
@@ -629,57 +579,57 @@ namespace SEQAN_NAMESPACE_MAIN
             pf->pageNo = pageNo;
             return writeBucket(*pf, cb.pageOfs, pool.file);
         }
-	};
+    };
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// character and buffer based handler definitions
-	template < typename TValue,
-			   typename TConfig >
+    //////////////////////////////////////////////////////////////////////////////
+    // character and buffer based handler definitions
+    template < typename TValue,
+               typename TConfig >
     struct BufReadHandler<Pool< TValue, MapperSpec<TConfig> > >
     {
         typedef BufferHandler< Bundle2<
-			BufferHandler<Pool< TValue, MapperSpec<TConfig> >, MemorySpec>,
-//			BufferHandler<Pool< TValue, MapperSpec<TConfig> >, ReadMapperSpec>
-			BufferHandler<Pool< TValue, MapperSpec<TConfig> >, ReadFileSpec>
-		>, MultiplexSpec > Type;
+            BufferHandler<Pool< TValue, MapperSpec<TConfig> >, MemorySpec>,
+//            BufferHandler<Pool< TValue, MapperSpec<TConfig> >, ReadMapperSpec>
+            BufferHandler<Pool< TValue, MapperSpec<TConfig> >, ReadFileSpec>
+        >, MultiplexSpec > Type;
     };
 
     template < typename TValue,
-			   typename TConfig >
+               typename TConfig >
     struct WriteHandler<Pool< TValue, MapperSpec<TConfig> > >
     {
         typedef Handler< Bundle2<
-			Handler<BufferHandler < Pool< TValue, MapperSpec<TConfig> >, MemorySpec >, MapperMemAdapter>,
-			Handler<Pool< TValue, MapperSpec<TConfig> >, MapperSyncWriter>
-		>, MultiplexSpec > Type;
-	};
+            Handler<BufferHandler < Pool< TValue, MapperSpec<TConfig> >, MemorySpec >, MapperMemAdapter>,
+            Handler<Pool< TValue, MapperSpec<TConfig> >, MapperSyncWriter>
+        >, MultiplexSpec > Type;
+    };
 
 
-	// use async MapperHandler for all async files classes
+    // use async MapperHandler for all async files classes
 
     template < typename TValue,
-   	           typename TMap,
-		       typename TSize,
-			   typename TSpec >
+                  typename TMap,
+               typename TSize,
+               typename TSpec >
     struct WriteHandler<Pool< TValue, MapperSpec< MapperConfigSize< TMap, TSize, File<Async<TSpec> > > > > >
     {
         typedef Handler< Bundle2<
-			Handler<BufferHandler	< Pool< TValue, MapperSpec<MapperConfigSize< TMap, TSize, File<Async<TSpec> > > > >, MemorySpec >, MapperMemAdapter>,
-			Handler<Pool< TValue, MapperSpec<MapperConfigSize< TMap, TSize, File<Async<TSpec> > > > >, MapperAsyncWriter>
-		>, MultiplexSpec > Type;
-	};
+            Handler<BufferHandler    < Pool< TValue, MapperSpec<MapperConfigSize< TMap, TSize, File<Async<TSpec> > > > >, MemorySpec >, MapperMemAdapter>,
+            Handler<Pool< TValue, MapperSpec<MapperConfigSize< TMap, TSize, File<Async<TSpec> > > > >, MapperAsyncWriter>
+        >, MultiplexSpec > Type;
+    };
 
     template < typename TValue,
-   	           typename TMap,
-			   typename TSpec >
+                  typename TMap,
+               typename TSpec >
     struct WriteHandler<Pool< TValue, MapperSpec< MapperConfig< TMap, File<Async<TSpec> > > > > >
     {
         typedef Handler< Bundle2<
-			Handler<BufferHandler < Pool< TValue, MapperSpec<MapperConfig< TMap, File<Async<TSpec> > > > >, MemorySpec >, MapperMemAdapter>,
-			Handler<Pool< TValue, MapperSpec<MapperConfig< TMap, File<Async<TSpec> > > > >, MapperAsyncWriter>
-		>, MultiplexSpec > Type;
-	};
+            Handler<BufferHandler < Pool< TValue, MapperSpec<MapperConfig< TMap, File<Async<TSpec> > > > >, MemorySpec >, MapperMemAdapter>,
+            Handler<Pool< TValue, MapperSpec<MapperConfig< TMap, File<Async<TSpec> > > > >, MapperAsyncWriter>
+        >, MultiplexSpec > Type;
+    };
 
 }
 
diff --git a/seqan/pipe/pool_sorter.h b/seqan/pipe/pool_sorter.h
index b70ff4e..69a5469 100644
--- a/seqan/pipe/pool_sorter.h
+++ b/seqan/pipe/pool_sorter.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -39,32 +39,32 @@ namespace SEQAN_NAMESPACE_MAIN
 {
 
     template < typename TValue, typename Compare >
-    struct MergeStreamComparer : public ::std::binary_function < PageBucket<TValue>,
-														       PageBucket<TValue>,
-														       bool>
+    struct MergeStreamComparer : public std::binary_function < PageBucket<TValue>,
+                                                               PageBucket<TValue>,
+                                                               bool>
     {
         Compare C;
         MergeStreamComparer(Compare &tmpC): C(tmpC) { }
         inline bool operator()(const PageBucket<TValue> &a,
-			                   const PageBucket<TValue> &b) const {
+                               const PageBucket<TValue> &b) const {
             return C(static_cast<const TValue&>(*(a.cur)),
                      static_cast<const TValue&>(*(b.cur))) > 0;
         }
     };
 
     template < typename TCompare >
-	struct AdaptorCompare2Less : 
-		public ::std::binary_function <
-			typename TCompare::first_argument_type, 
-			typename TCompare::second_argument_type, 
-			bool >
+    struct AdaptorCompare2Less :
+        public std::binary_function <
+            typename TCompare::first_argument_type,
+            typename TCompare::second_argument_type,
+            bool >
     {
         TCompare const & C;
         AdaptorCompare2Less(TCompare const & tmpC): C(tmpC) { }
         inline bool operator() (
-			typename TCompare::first_argument_type const &a, 
-			typename TCompare::second_argument_type const &b) const 
-		{
+            typename TCompare::first_argument_type const &a,
+            typename TCompare::second_argument_type const &b) const
+        {
             return C(a, b) < 0;
         }
     };
@@ -73,17 +73,15 @@ namespace SEQAN_NAMESPACE_MAIN
  * @class SorterConfigSize
  * @extends SorterSpec
  * @headerfile <seqan/pipe.h>
- * 
+ *
  * @brief Configuration of Sorter.
- * 
+ *
  * @signature template <typename TCompare, typename TSize[, typename TFile>
  *            struct SorterConfigSize;
- * 
+ *
  * @tparam TCompare The compare function (see STL's <tt>binary_function</tt>).
  * @tparam TSize    The Sorter's size type.
  * @tparam TFile    The underlying File type.  <tt>File&lt;&gt;</tt>
- * 
- * @section Remarks
  *
  * The requirement on TCompare are as follows: let <tt>comp</tt> be an object of type <tt>TCompare</tt>.  <tt>comp(a,
  * b)</tt> should return a value less, equal, or greater than 0 if <tt>a &lt; b</tt>, <tt>a == b</tt>, or <tt>a &gt;
@@ -92,28 +90,13 @@ namespace SEQAN_NAMESPACE_MAIN
  * @see SorterConfig
  */
 
-/**
-.Spec.SorterConfigSize:
-..cat:Pipelining
-..general:Spec.SorterSpec
-..summary:Configuration of Sorter.
-..signature:SorterConfigSize<TCompare, TSize, TFile>
-..param.TCompare:The compare function (see STL's $binary_function$).
-...remarks:Let $comp$ be an object of type $TCompare$. $comp(a,b)$ should return a value less, equal, or greater than $0$ if $a<b$, $a==b$, or $a>b$.
-..param.TSize:The Sorter's size type.
-..param.TFile:The underlying @Class.File@ type.
-...default:$File<>$, see @Class.File@.
-..see:Spec.SorterConfig
-..include:seqan/pipe.h
-*/
-
-	template < typename TCompare,
-		       typename TSize,
-			   typename TFile = File<> >
+    template < typename TCompare,
+               typename TSize,
+               typename TFile = File<> >
     struct SorterConfigSize {
-        typedef TCompare	Compare;
-		typedef TSize		SizeType;
-        typedef TFile		File;
+        typedef TCompare    Compare;
+        typedef TSize        SizeType;
+        typedef TFile        File;
     };
 
 /*!
@@ -124,42 +107,25 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * @signature template <typename TCompare[, typename TFile]>
  *            struct SorterConfig;
- * 
+ *
  * @tparam TCompare The compare function (see STL's <tt>binary_function</tt>).
  * @tparam TFile The underlying File type, defaults to <tt>File&lt;&gt;</tt>.
- * 
- * @section Remarks
- * 
+ *
  * The requirement on TCompare are as follows: let <tt>comp</tt> be an object of type <tt>TCompare</tt>.  <tt>comp(a,
  * b)</tt> should return a value less, equal, or greater than 0 if <tt>a &lt; b</tt>, <tt>a == b</tt>, or <tt>a &gt;
  * b</tt>.
  *
  * Using this configuration spec., the Sorter's size type is <tt>Size&lt;TFile&gt;::Type</tt>.  To use a custom size
  * type @link SorterConfigSize @endlink should be used.
- * 
+ *
  * @see SorterConfigSize
  */
 
-/**
-.Spec.SorterConfig:
-..cat:Pipelining
-..general:Spec.SorterSpec
-..summary:Configuration of Sorter.
-..signature:SorterConfig<TCompare, TFile>
-..param.TCompare:The compare function (see STL's $binary_function$).
-...remarks:Let $comp$ be an object of type $TCompare$. $comp(a,b)$ should return a value less, equal, or greater than $0$ if $a<b$, $a==b$, or $a>b$.
-..param.TFile:The underlying @Class.File@ type.
-...default:$File<>$, see @Class.File@.
-..remarks:Using this configuration spec., the Sorter's size type is $Size<TFile>::Type$. To use a custom size type @Spec.SorterConfigSize@ should be used.
-..see:Spec.SorterConfigSize
-..include:seqan/pipe.h
-*/
-
     template < typename TCompare, typename TFile = File<> >
     struct SorterConfig {
-        typedef TCompare					Compare;
-		typedef typename Size<TFile>::Type	SizeType;
-        typedef TFile						File;
+        typedef TCompare                    Compare;
+        typedef typename Size<TFile>::Type    SizeType;
+        typedef TFile                        File;
     };
 
 /*!
@@ -169,21 +135,19 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Sorts all elements using a custom compare function.
  *
  * @signature template <typename TValue, typename TConfig>
- *            struct Pool<TVAlue, SorterSpec<TConfig > >;
- * 
+ *            struct Pool<TValue, SorterSpec<TConfig > >;
+ *
  * @tparam TConfig Configuration Spec.  Defines compare function, size type, and file type.
  * @tparam TValue  The value type, that is the type of the stream elements.
- * 
- * @section Remarks
- * 
+ *
  * The Pool's input/output type is <tt>TValue</tt> and the size type is determined by the <tt>TConfig</tt>.
- * 
+ *
  * If there exists an explicit function mapping input elements to their destined positions in the output
  * stream, @link MapperSpec @endlink should be preferred.
  *
  * @section Example
  *
- * @include demos/pipe/pool_sorter.cpp
+ * @include demos/dox/pipe/pool_sorter.cpp
  *
  * @code{.console}
  * Sorted elements:
@@ -193,28 +157,13 @@ namespace SEQAN_NAMESPACE_MAIN
  * @endcode
  */
 
-/**
-.Spec.SorterSpec:
-..cat:Pipelining
-..general:Class.Pool
-..summary:Sorts all elements using a custom compare function.
-..signature:Pool<TValue, SorterSpec<TConfig> >
-..param.TValue:The value type, that is the type of the stream elements.
-..param.TConfig:Configuration Spec. Defines compare function, size type, and file type.
-...type:Spec.SorterConfig
-...type:Spec.SorterConfigSize
-..remarks:The Pool's input/output type is $TValue$ and the size type is determined by the $TConfig$.
-...note:If there exists an explicit function mapping input elements to their destined positions in the output stream, @Spec.MapperSpec@ should be preferred.
-..include:seqan/pipe.h
-*/
-
     template < typename TConfig >
     struct SorterSpec {
         typedef TConfig Config;
     };
 
     template < typename TValue,
-			   typename TConfig >
+               typename TConfig >
     struct HandlerArgs< Pool< TValue, SorterSpec<TConfig> > >
     {
         typedef typename TConfig::Compare Type;
@@ -222,27 +171,27 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
     //////////////////////////////////////////////////////////////////////////////
-	// cache bucket based synchronous multiway merge
+    // cache bucket based synchronous multiway merge
     struct ReadSorterSpec_;
-	typedef Tag<ReadSorterSpec_> ReadSorterSpec;
+    typedef Tag<ReadSorterSpec_> ReadSorterSpec;
 
     template <typename TValue, typename TPoolSpec>
     struct Handler<Pool<TValue, TPoolSpec>, ReadSorterSpec>
     {
         typedef Pool<TValue, TPoolSpec>                 TPool;
-        typedef typename TPool::TBuffer					TBuffer;
+        typedef typename TPool::TBuffer                    TBuffer;
         typedef typename TPoolSpec::Config::Compare     TCompare;
         typedef PageBucketExtended<TValue>              TPageBucket;
 
         typedef MergeStreamComparer<TValue, TCompare>   TStreamComparer;
-/*        typedef ::std::priority_queue <
+/*        typedef std::priority_queue <
             TPageBucket,
-            ::std::vector<TPageBucket>,
-            MergeStreamComparer<Type, Compare> >	    PQueue;
+            std::vector<TPageBucket>,
+            MergeStreamComparer<Type, Compare> >        PQueue;
 */
         typedef PriorityType<TPageBucket, TStreamComparer> TPrioQueue;
 
-		TPool       &pool;
+        TPool       &pool;
         TBuffer     bucketBuffer;
         TPrioQueue  pqueue;
 
@@ -254,23 +203,23 @@ namespace SEQAN_NAMESPACE_MAIN
             cancel();
         }
 
-		struct insertBucket : public ::std::unary_function<TPageBucket,void>
+        struct insertBucket : public std::unary_function<TPageBucket,void>
         {
-			Handler &me;
-			insertBucket(Handler &_me): me(_me) {}
+            Handler &me;
+            insertBucket(Handler &_me): me(_me) {}
 
-			inline void operator() (TPageBucket &pb) const
+            inline void operator() (TPageBucket &pb) const
             {
                 pb.pageNo = length(me.pqueue);
                 readBucket(pb, pb.pageNo, me.pool.pageSize, me.pool.dataSize(pb.pageNo), me.pool.file);
                 push(me.pqueue, pb);
-			}
-		};
+            }
+        };
 
         bool begin()
         {
             // 1. initially fill priority queue
-//    		pqueue.reserve(pool.pages);
+//            pqueue.reserve(pool.pages);
             equiDistantDistribution(
                 bucketBuffer, pool.bucketBufferSize, *this,
                 pool._size, pool.pageSize,
@@ -280,50 +229,50 @@ namespace SEQAN_NAMESPACE_MAIN
 
         inline TValue const & front() const
         {
-			return *(top(pqueue).cur);
+            return *(top(pqueue).cur);
         }
 
-        inline void pop(TValue &Ref_) 
-		{
+        inline void pop(TValue &Ref_)
+        {
             TPageBucket &pb = top(pqueue);
-			SEQAN_ASSERT_LEQ(pb.cur, pb.end);
+            SEQAN_ASSERT_LEQ(pb.cur, pb.end);
 
             Ref_ = *pb.cur;
             if (++pb.cur == pb.end)
-			{
+            {
                 // bucket is empty, we have to fetch the next bucket
-				if (!readBucket(pb, pb.pageNo, pool.pageSize, pool.dataSize(pb.pageNo), pool.file)) {
-					::seqan::pop(pqueue);
-					return;
-				}
-			}
-			adjustTop(pqueue);
+                if (!readBucket(pb, pb.pageNo, pool.pageSize, pool.dataSize(pb.pageNo), pool.file)) {
+                    seqan::pop(pqueue);
+                    return;
+                }
+            }
+            adjustTop(pqueue);
         }
 
         inline void pop()
         {
             TPageBucket &pb = top(pqueue);
-			SEQAN_ASSERT_LEQ(pb.cur, pb.end);
+            SEQAN_ASSERT_LEQ(pb.cur, pb.end);
 
             if (++pb.cur == pb.end)
                 // bucket is empty, we have to fetch the next bucket
-				if (!readBucket(pb, pb.pageNo, pool.pageSize, pool.dataSize(pb.pageNo), pool.file)) {
-					::seqan::pop(pqueue);
-					return;
-				}
-			adjustTop(pqueue);
+                if (!readBucket(pb, pb.pageNo, pool.pageSize, pool.dataSize(pb.pageNo), pool.file)) {
+                    seqan::pop(pqueue);
+                    return;
+                }
+            adjustTop(pqueue);
         }
 
-		inline bool eof() const
+        inline bool eof() const
         {
-			return empty(pqueue);
-		}
+            return empty(pqueue);
+        }
 
         inline void end()
         {
             cancel();
         }
-        
+
         void cancel()
         {
             clear(pqueue);
@@ -342,12 +291,12 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef typename TPool::Buffer                  TBuffer;
         typedef typename TPool::Spec::Compare           TCompare;
 
-		typedef PageBucketExtended<TValue>              TPageBucket;
+        typedef PageBucketExtended<TValue>              TPageBucket;
 
         typedef MergeStreamComparer<TValue, TCompare>   StreamComparer;
-        typedef ::std::priority_queue <
+        typedef std::priority_queue <
             TPageBucket,
-            ::std::vector<TPageBucket>,
+            std::vector<TPageBucket>,
             MergeStreamComparer<TValue, TCompare> >     TPrioQueue;
 
         TPool       &pool;
@@ -364,46 +313,46 @@ namespace SEQAN_NAMESPACE_MAIN
             pool(_pool),
             mergeBufferSize(_min(_pool.size(), _requestedBufferSize)),
             pqueue(StreamComparer(_pool.handlerData.compare)) { }
-        
+
         ~BufferHandler() {
             cancel();
         }
 
-		struct insertBucket : public ::std::unary_function<TPageBucket, void> {
-			BufferHandler &me;
-			insertBucket(BufferHandler &_me): me(_me) {}
+        struct insertBucket : public std::unary_function<TPageBucket, void> {
+            BufferHandler &me;
+            insertBucket(BufferHandler &_me): me(_me) {}
 
-			inline void operator() (TPageBucket &pb) const
+            inline void operator() (TPageBucket &pb) const
             {
                 pb.pageNo = length(pqueue);
                 readBucket(pb, pb.pageNo, me.pool.pageSize, me.pool.dataSize(pb.pageNo), pool.file);
                 push(pqueue, pb);
-			}
-		};
+            }
+        };
 
         inline TBuffer & first() {
             // 1. initially fill priority queue
-//    		pqueue.reserve(pool.pages);
+//            pqueue.reserve(pool.pages);
             equiDistantDistribution(
                 bucketBuffer, pool.bucketBufferSize, *this,
                 pool._size, pool.pageSize,
                 insertBucket(*this));
-			allocPage(mergeBuffer, mergeBufferSize, *this);
-			return merge();
+            allocPage(mergeBuffer, mergeBufferSize, *this);
+            return merge();
         }
 
-		inline TBuffer & next() {
-			return merge();
-		}
+        inline TBuffer & next() {
+            return merge();
+        }
 
         inline void end() {
             cancel();
         }
-        
+
         void cancel()
         {
             clear(pqueue);
-			freePage(mergeBuffer, *this);
+            freePage(mergeBuffer, *this);
             freePage(bucketBuffer, *this);
         }
 
@@ -414,76 +363,76 @@ namespace SEQAN_NAMESPACE_MAIN
         TBuffer & merge()
         {
             // 2. merge streams into mergeBuffer
-            
-			typename TPrioQueue::size_type pqsize = length(pqueue);
-			if (!pqsize) {
-				resize(tmpBuffer, 0);
-				return tmpBuffer;
-			}
+
+            typename TPrioQueue::size_type pqsize = length(pqueue);
+            if (!pqsize) {
+                resize(tmpBuffer, 0);
+                return tmpBuffer;
+            }
 
             if (pqsize == 1)
-			{
+            {
                 // only one stream left => retrieve what's left in stream es
                 TPageBucket &pb = pqueue.top();
 
                 // flush stream
-				if (pb.cur != pb.end) {
-					tmpBuffer.begin = pb.cur;
-					tmpBuffer.end = pb.end;
-					pb.cur = pb.end;
-					if (pb.pageOfs == pool.dataSize(pb.pageNo))
-						pop(pqueue);
-					return tmpBuffer;
-				}
+                if (pb.cur != pb.end) {
+                    tmpBuffer.begin = pb.cur;
+                    tmpBuffer.end = pb.end;
+                    pb.cur = pb.end;
+                    if (pb.pageOfs == pool.dataSize(pb.pageNo))
+                        pop(pqueue);
+                    return tmpBuffer;
+                }
 
                 // read directly from disk
-				pb.begin = mergeBuffer.begin;
-				pb.end = pb.cur = pb.begin + pageSize(mergeBuffer);
+                pb.begin = mergeBuffer.begin;
+                pb.end = pb.cur = pb.begin + pageSize(mergeBuffer);
 
-				resize(mergeBuffer, readBucket(pb, pb.pageNo, pool.pageSize, pool.dataSize(pb.pageNo)));
-				if (pb.pageOfs == pool.dataSize(pb.pageNo))
-					pop(pqueue);
-			}
+                resize(mergeBuffer, readBucket(pb, pb.pageNo, pool.pageSize, pool.dataSize(pb.pageNo)));
+                if (pb.pageOfs == pool.dataSize(pb.pageNo))
+                    pop(pqueue);
+            }
             else
             {
                 for(TValue *cur = mergeBuffer.begin; cur != mergeBuffer.end; ++cur) {
                     TPageBucket &pb = pqueue.top();
                     *cur = *pb.cur;
-					if (++pb.cur == pb.end) {
-						// bucket is empty, we have to fetch the next bucket
-						if (!readBucket(pb, pb.pageNo, pool.pageSize, pool.dataSize(pb.pageNo), pool.file)) {
-							pop(pqueue);
-							// queue contains only one stream
-							// => we return what we have merged
-							if (--pqsize == 1) {
-								resize(cur - mergeBuffer.begin + 1);
-								return mergeBuffer;
-							}
-						}
-					}
-					adjustTop(pqueue);
+                    if (++pb.cur == pb.end) {
+                        // bucket is empty, we have to fetch the next bucket
+                        if (!readBucket(pb, pb.pageNo, pool.pageSize, pool.dataSize(pb.pageNo), pool.file)) {
+                            pop(pqueue);
+                            // queue contains only one stream
+                            // => we return what we have merged
+                            if (--pqsize == 1) {
+                                resize(cur - mergeBuffer.begin + 1);
+                                return mergeBuffer;
+                            }
+                        }
+                    }
+                    adjustTop(pqueue);
                 }
-				resize(mergeBuffer, pageSize(mergeBuffer));
+                resize(mergeBuffer, pageSize(mergeBuffer));
             }
-            
+
             return mergeBuffer;
         }
-	};
+    };
 
-	template < typename TValue,
-			   typename TConfig >
+    template < typename TValue,
+               typename TConfig >
     inline Buffer<TValue, PageFrame<typename TConfig::File, Dynamic> > & processBuffer(
         Buffer<TValue, PageFrame<typename TConfig::File, Dynamic> > &buf,
         BufferHandler< Pool< TValue, SorterSpec<TConfig> >, WriteFileSpec > &me)
     {
         AdaptorCompare2Less<typename TConfig::Compare> cmp(me.pool.handlerArgs);
         std::sort(buf.begin, buf.end, cmp);
-		return buf;
+        return buf;
     }
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// character and buffer based handler definitions
+    //////////////////////////////////////////////////////////////////////////////
+    // character and buffer based handler definitions
     template < typename TValue,
                typename TConfig >
     inline Buffer<TValue> & processBuffer(
@@ -492,27 +441,27 @@ namespace SEQAN_NAMESPACE_MAIN
     {
         AdaptorCompare2Less<typename TConfig::Compare> cmp(me.pool.handlerArgs);
         std::sort(buf.begin, buf.end, cmp);
-		return buf;
+        return buf;
     }
 
     template < typename TValue,
-			   typename TConfig >
+               typename TConfig >
     struct BufReadHandler< Pool< TValue, SorterSpec<TConfig> > >
     {
         typedef BufferHandler< Bundle2<
-			BufferHandler< Pool< TValue, SorterSpec<TConfig> >, MemorySpec >,
-			BufferHandler< Pool< TValue, SorterSpec<TConfig> >, ReadSorterSpec >
-		>, MultiplexSpec > Type;
+            BufferHandler< Pool< TValue, SorterSpec<TConfig> >, MemorySpec >,
+            BufferHandler< Pool< TValue, SorterSpec<TConfig> >, ReadSorterSpec >
+        >, MultiplexSpec > Type;
     };
 
     template < typename TValue,
-			   typename TConfig >
+               typename TConfig >
     struct ReadHandler< Pool< TValue, SorterSpec<TConfig> > >
     {
         typedef Handler< Bundle2<
-			Handler< BufferHandler < Pool< TValue, SorterSpec<TConfig> >, MemorySpec >, AdapterSpec >,
-			Handler<				 Pool< TValue, SorterSpec<TConfig> >, ReadSorterSpec >
-		>, MultiplexSpec > Type;
+            Handler< BufferHandler < Pool< TValue, SorterSpec<TConfig> >, MemorySpec >, AdapterSpec >,
+            Handler<                 Pool< TValue, SorterSpec<TConfig> >, ReadSorterSpec >
+        >, MultiplexSpec > Type;
     };
 
 }
diff --git a/seqan/platform.h b/seqan/platform.h
old mode 100755
new mode 100644
index 576e326..12c5f72
--- a/seqan/platform.h
+++ b/seqan/platform.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -35,27 +35,75 @@
 #define SEQAN_PLATFORM_H
 
 #ifdef __MINGW32__
-	#include "platform/platform_mingw.h"
+    #include "platform/platform_mingw.h"
 #elif _MSC_VER
-	#include "platform/platform_windows.h"
+    #include "platform/platform_windows.h"
 #elif __SUNPRO_C
-	#include "platform/platform_solaris.h"
+    #include "platform/platform_solaris.h"
 #elif __ICC
-	#include "platform/platform_icc.h"
+    #include "platform/platform_icc.h"
 #elif __PGI
-	#include "platform/platform_pgi.h"
+    #include "platform/platform_pgi.h"
 #else
-	#include "platform/platform_gcc.h"
+    #include "platform/platform_gcc.h"
 #endif
 
 // NOTE(esiragusa): nvcc header must be included even if __CUDACC__ is not defined.
 #include "platform/platform_nvcc.h"
 
-// This macro defines an alias for the auto_ptr class template deprecated in C++11.
+// SEQAN_AUTO_PTR_NAME .... alias for the auto_ptr class template deprecated in C++11.
+// SEQAN_FORWARD_ARG,
+// SEQAN_FORWARD_CARG ..... macros to insert between argument type and name ...
+// SEQAN_FORWARD_RETURN ... or return type and function name to declare forwarding of variables
+// SEQAN_FORWARD .......... pass a variable as (of type T) as it was given to a function
+// SEQAN_MOVE ............. pass a variable to a function and never use it again
+
 #ifdef SEQAN_CXX11_STANDARD
-    #define SEQAN_AUTO_PTR_NAME unique_ptr
+
+    #define SEQAN_AUTO_PTR_NAME     unique_ptr
+    #define SEQAN_FORWARD_ARG       &&
+    #define SEQAN_FORWARD_CARG      &&
+    #define SEQAN_FORWARD_RETURN    &&
+    #define SEQAN_FORWARD(T, x)     std::forward<T>(x)
+    #define SEQAN_MOVE(x)           std::move(x)
+
 #else  // #ifdef SEQAN_CXX11_STANDARD
-    #define SEQAN_AUTO_PTR_NAME auto_ptr
+
+    #define SEQAN_AUTO_PTR_NAME     auto_ptr
+    #define SEQAN_FORWARD_ARG       &
+    #define SEQAN_FORWARD_CARG      const &
+    #define SEQAN_FORWARD_RETURN
+    #define SEQAN_FORWARD(T, x)     x
+    #define SEQAN_MOVE(x)           x
+
 #endif  // #ifdef SEQAN_CXX11_STANDARD
 
+// Is the C++11 STL (thread, atomic, chrono) available?
+#if defined(SEQAN_CXX11_STANDARD) && (!defined(_MSC_VER) || _MSC_VER >= 1700) && !defined(PLATFORM_WINDOWS_MINGW)
+#define SEQAN_CXX11_STL
+#endif
+
+// C++ restrict keyword, see e.g. platform_gcc.h
+#ifndef SEQAN_RESTRICT
+#define SEQAN_RESTRICT
+#endif
+
+// C++ branch hints
+#ifndef SEQAN_LIKELY
+#define SEQAN_LIKELY(x) (x)
+#endif
+
+#ifndef SEQAN_UNLIKELY
+#define SEQAN_UNLIKELY(x) (x)
+#endif
+
+// A macro to eliminate warnings on GCC and Clang
+#if (defined(__GNUC__) && ((__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)))) || defined(__clang__)
+#  define SEQAN_UNUSED __attribute__((unused))
+#else
+#  define SEQAN_UNUSED
+#endif
+// backwards compatibility
+#define SEQAN_UNUSED_TYPEDEF SEQAN_UNUSED
+
 #endif
diff --git a/seqan/platform/INFO b/seqan/platform/INFO
deleted file mode 100644
index 62f7a7f..0000000
--- a/seqan/platform/INFO
+++ /dev/null
@@ -1,11 +0,0 @@
-Name: seqan-platform
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: stable
-Description: Helper code for differentiating between compilers.
- The code in this module helps in differentiating between different compilers,
- redefining symbols so POSIX functions are available by their original names in
- Visual Studio, for example.
diff --git a/seqan/platform/platform_gcc.h b/seqan/platform/platform_gcc.h
index add0506..05180df 100644
--- a/seqan/platform/platform_gcc.h
+++ b/seqan/platform/platform_gcc.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -62,7 +62,7 @@
  * @headerfile <seqan/platform.h>
  * @brief Defined when compiling in 32 bit mode.
  *
- * @signature @define SEQAN_IS_32_BIT
+ * @signature #define SEQAN_IS_32_BIT
  */
 
 // The symbols SEQAN_IS_64_BIT and SEQAN_IS_32_BIT can be used to check
@@ -158,9 +158,7 @@ typedef uint8_t __uint8;   // nolint
  *
  * @signature #define SEQAN_CXX_STANDARD
  *
- * @section Remarks
- *
- * Note that this auto-detection is not perfect and support differs.
+ * @note This this auto-detection is not perfect and support differs.
  */
 
 // detect gcc C++11 support
@@ -175,4 +173,20 @@ typedef uint8_t __uint8;   // nolint
 #  endif
 #endif
 
+// full C++11 support in GCC >= 4.9 and Clang >= 3.4 (unless linked against old glibcxx)
+#if defined(SEQAN_CXX11_STANDARD)
+#   if !defined(__clang__) && (__GNUC__ * 100 + __GNUC_MINOR__ >= 409)
+#       define SEQAN_CXX11_COMPLETE
+#   elif defined(__clang__) && (__clang_major__ * 100 + __clang_minor__ >= 304)
+#       if __has_include(<regex>) && !__has_include(<bits/regex_grep_matcher.h>)
+#           define SEQAN_CXX11_COMPLETE
+#       endif
+#   endif
+#endif
+
+#define SEQAN_LIKELY(expr)    __builtin_expect(!!(expr), 1)
+#define SEQAN_UNLIKELY(expr)  __builtin_expect(!!(expr), 0)
+
+#define SEQAN_RESTRICT  __restrict__
+
 #endif  // #ifndef PLATFORM_GCC
diff --git a/seqan/platform/platform_icc.h b/seqan/platform/platform_icc.h
index fa2c972..9cdb3d8 100644
--- a/seqan/platform/platform_icc.h
+++ b/seqan/platform/platform_icc.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
diff --git a/seqan/platform/platform_mingw.h b/seqan/platform/platform_mingw.h
index 9874cb4..e94c6ea 100644
--- a/seqan/platform/platform_mingw.h
+++ b/seqan/platform/platform_mingw.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
diff --git a/seqan/platform/platform_nvcc.h b/seqan/platform/platform_nvcc.h
index 62b5281..4d4845f 100644
--- a/seqan/platform/platform_nvcc.h
+++ b/seqan/platform/platform_nvcc.h
@@ -100,7 +100,7 @@
  *
  * @section Remarks
  *
- * Note that a device function containing CUDA intrinsics will not compile on non CUDA-capable compilers. Therefore, to 
+ * Note that a device function containing CUDA intrinsics will not compile on non CUDA-capable compilers. Therefore, to
  * insure graceful compilation, it is still necessary to wrap CUDA-intrinsic code inside __CUDA_ARCH__ defines.
  */
 
@@ -132,6 +132,11 @@
 #define SEQAN_DEVICE __device__
 #define SEQAN_GLOBAL __global__
 
+// NOTE(esiragusa): this solves a problem with nvcc using gcc4.x on MacOS X
+#if defined(PLATFORM_GCC) && defined (__APPLE__)
+#undef _GLIBCXX_USE_INT128
+#endif
+
 #else
 
 #define SEQAN_FUNC inline
diff --git a/seqan/platform/platform_pgi.h b/seqan/platform/platform_pgi.h
index 03533d8..8bac835 100644
--- a/seqan/platform/platform_pgi.h
+++ b/seqan/platform/platform_pgi.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
diff --git a/seqan/platform/platform_solaris.h b/seqan/platform/platform_solaris.h
index a7c84e9..2b944be 100644
--- a/seqan/platform/platform_solaris.h
+++ b/seqan/platform/platform_solaris.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
diff --git a/seqan/platform/platform_windows.h b/seqan/platform/platform_windows.h
index 20e2e11..3058b1f 100644
--- a/seqan/platform/platform_windows.h
+++ b/seqan/platform/platform_windows.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -71,6 +71,11 @@
 #pragma warning( disable : 4345 )
 #pragma warning( disable : 4351 )
 
+// Disable warning for "this" used in derived c'tor
+// Documentation of C4355 from Microsoft:
+//   https://msdn.microsoft.com/en-us/library/3c594ae3(v=vs.100).aspx
+#pragma warning( disable : 4355 )
+
 // ==========================================================================
 // Define Integers
 // ==========================================================================
@@ -113,7 +118,12 @@ typedef unsigned __int8 __uint8;
 
 // C++11 is supported by Visual C++ >=v10
 #if _MSC_VER >= 1600
-#  define SEQAN_CXX11_STANDARD
+#define SEQAN_CXX11_STANDARD
+#endif
+
+// full C++11 support in Visual C++ >= 2015
+#if _MSC_VER >= 1900
+#define SEQAN_CXX11_COMPLETE
 #endif
 
 // ==========================================================================
@@ -124,17 +134,22 @@ typedef unsigned __int8 __uint8;
 template <typename T>
 inline T round(T const & x)
 {
-	return static_cast<T>(floor(x + 0.5));
+    return static_cast<T>(floor(x + 0.5));
 }
 
 // Rename some underscore-functions in Windows.
+#if _MSC_VER < 1900
 #ifndef snprintf
 #define snprintf _snprintf
 #endif  // #ifndef snprintf
+#endif
 
 // Define ftello
 #ifndef ftello
 #define ftello(fp) ftell(fp)
 #endif  // #ifndef ftello
 
+//#define SEQAN_RESTRICT  __restrict
+//#define SEQAN_RESTRICT  __declspec(restrict)
+
 #endif  // #ifndef PLATFORM_WINDOWS
diff --git a/seqan/platform/windows_stdint.h b/seqan/platform/windows_stdint.h
index 5ec9b67..caea990 100644
--- a/seqan/platform/windows_stdint.h
+++ b/seqan/platform/windows_stdint.h
@@ -1,32 +1,32 @@
 // ISO C9x  compliant stdint.h for Microsoft Visual Studio
-// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124 
-// 
+// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124
+//
 //  Copyright (c) 2006-2008 Alexander Chemeris
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are met:
-// 
+//
 //   1. Redistributions of source code must retain the above copyright notice,
 //      this list of conditions and the following disclaimer.
-// 
+//
 //   2. Redistributions in binary form must reproduce the above copyright
 //      notice, this list of conditions and the following disclaimer in the
 //      documentation and/or other materials provided with the distribution.
-// 
+//
 //   3. The name of the author may be used to endorse or promote products
 //      derived from this software without specific prior written permission.
-// 
+//
 // THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
 // WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 // MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
 // EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-// 
+//
 ///////////////////////////////////////////////////////////////////////////////
 
 #ifndef SEQAN_PLATFORM_WINDOWS_STDINT_H_
diff --git a/seqan/random.h b/seqan/random.h
index d74dade..c6f137d 100644
--- a/seqan/random.h
+++ b/seqan/random.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/random/INFO b/seqan/random/INFO
deleted file mode 100644
index 1e5630d..0000000
--- a/seqan/random/INFO
+++ /dev/null
@@ -1,8 +0,0 @@
-Name: seqan-random
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Pseudo random number generation.
- This module contains code for the generation of pseudo random numbers.
diff --git a/seqan/random/ext_MersenneTwister.h b/seqan/random/ext_MersenneTwister.h
old mode 100755
new mode 100644
index cea1d74..0b991ad
--- a/seqan/random/ext_MersenneTwister.h
+++ b/seqan/random/ext_MersenneTwister.h
@@ -19,11 +19,11 @@
 // Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
 // Copyright (C) 2000 - 2009, Richard J. Wagner
 // All rights reserved.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions
 // are met:
-// 
+//
 //   1. Redistributions of source code must retain the above copyright
 //      notice, this list of conditions and the following disclaimer.
 //
@@ -31,10 +31,10 @@
 //      notice, this list of conditions and the following disclaimer in the
 //      documentation and/or other materials provided with the distribution.
 //
-//   3. The names of its contributors may not be used to endorse or promote 
-//      products derived from this software without specific prior written 
+//   3. The names of its contributors may not be used to endorse or promote
+//      products derived from this software without specific prior written
 //      permission.
-// 
+//
 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS And CONTRIBUTORS "AS IS"
 // And ANY EXPRESS Or IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 // IMPLIED WARRANTIES OF MERCHANTABILITY And FITNESS FOR A PARTICULAR PURPOSE
@@ -48,10 +48,10 @@
 // POSSIBILITY OF SUCH DAMAGE.
 
 // The original code included the following notice:
-// 
+//
 //     When you use this, send an email to: m-mat@math.sci.hiroshima-u.ac.jp
 //     with an appropriate reference to your work.
-// 
+//
 // It would be nice to CC: wagnerr@umich.edu and Cokus@math.washington.edu
 // when you write.
 
@@ -61,9 +61,9 @@
 namespace seqan {
 namespace ext {
 
-#define SEQAN_MERSENNE_MT_LEN			624
-#define SEQAN_MERSENNE_MT_IA			397
-#define SEQAN_MERSENNE_MT_IB			(SEQAN_MERSENNE_MT_LEN - SEQAN_MERSENNE_MT_IA)
+#define SEQAN_MERSENNE_MT_LEN            624
+#define SEQAN_MERSENNE_MT_IA            397
+#define SEQAN_MERSENNE_MT_IB            (SEQAN_MERSENNE_MT_LEN - SEQAN_MERSENNE_MT_IA)
 #define SEQAN_MERSENNE_UPPER_MASK      0x80000000
 #define SEQAN_MERSENNE_LOWER_MASK      0x7FFFFFFF
 #define SEQAN_MERSENNE_MATRIX_A        0x9908B0DF
@@ -82,344 +82,344 @@ namespace ext {
 class MTRand {
 // Data
 public:
-	typedef unsigned long uint32;  // unsigned integer type, at least 32 bits
-	
-	enum { N = 624 };       // length of state vector
-	enum { SAVE = N + 1 };  // length of array for save()
+    typedef unsigned long uint32;  // unsigned integer type, at least 32 bits
+
+    enum { N = 624 };       // length of state vector
+    enum { SAVE = N + 1 };  // length of array for save()
 
 protected:
-	enum { M = 397 };  // period parameter
-	
-	uint32 state[N];   // internal state
-	uint32 *pNext;     // next value to get from state
-	int left;          // number of values left before reload needed
+    enum { M = 397 };  // period parameter
+
+    uint32 state[N];   // internal state
+    uint32 *pNext;     // next value to get from state
+    int left;          // number of values left before reload needed
 
 // Methods
 public:
-	MTRand( const uint32 oneSeed );  // initialize with a simple uint32
-	MTRand( uint32 *const bigSeed, uint32 const seedLength = N );  // or array
-	MTRand();  // auto-initialize with /dev/urandom or time() and clock()
-	MTRand( const MTRand& o );  // copy
-	
-	// Do NOT use for CRYPTOGRAPHY without securely hashing several returned
-	// values together, otherwise the generator state can be learned after
-	// reading 624 consecutive values.
-	
-	// Access to 32-bit random numbers
-	uint32 randInt();                     // integer in [0,2^32-1]
-	uint32 randInt( const uint32 n );     // integer in [0,n] for n < 2^32
-	double rand();                        // real number in [0,1]
-	double rand( const double n );        // real number in [0,n]
-	double randExc();                     // real number in [0,1)
-	double randExc( const double n );     // real number in [0,n)
-	double randDblExc();                  // real number in (0,1)
-	double randDblExc( const double n );  // real number in (0,n)
-	double operator()();                  // same as rand()
-	
-	// Access to 53-bit random numbers (capacity of IEEE double precision)
-	double rand53();  // real number in [0,1)
-	
-	// Access to nonuniform random number distributions
-	double randNorm( const double mean = 0.0, const double stddev = 1.0 );
-	
-	// Re-seeding functions with same behavior as initializers
-	void seed( const uint32 oneSeed );
-	void seed( uint32 *const bigSeed, const uint32 seedLength = N );
-	void seed();
-	
-	// Saving and loading generator state
-	void save( uint32* saveArray ) const;  // to array of size SAVE
-	void load( uint32 *const loadArray );  // from such array
-	friend std::ostream& operator<<( std::ostream& os, const MTRand& mtrand );
-	friend std::istream& operator>>( std::istream& is, MTRand& mtrand );
-	MTRand& operator=( const MTRand& o );
+    MTRand( const uint32 oneSeed );  // initialize with a simple uint32
+    MTRand( uint32 *const bigSeed, uint32 const seedLength = N );  // or array
+    MTRand();  // auto-initialize with /dev/urandom or time() and clock()
+    MTRand( const MTRand& o );  // copy
+
+    // Do NOT use for CRYPTOGRAPHY without securely hashing several returned
+    // values together, otherwise the generator state can be learned after
+    // reading 624 consecutive values.
+
+    // Access to 32-bit random numbers
+    uint32 randInt();                     // integer in [0,2^32-1]
+    uint32 randInt( const uint32 n );     // integer in [0,n] for n < 2^32
+    double rand();                        // real number in [0,1]
+    double rand( const double n );        // real number in [0,n]
+    double randExc();                     // real number in [0,1)
+    double randExc( const double n );     // real number in [0,n)
+    double randDblExc();                  // real number in (0,1)
+    double randDblExc( const double n );  // real number in (0,n)
+    double operator()();                  // same as rand()
+
+    // Access to 53-bit random numbers (capacity of IEEE double precision)
+    double rand53();  // real number in [0,1)
+
+    // Access to nonuniform random number distributions
+    double randNorm( const double mean = 0.0, const double stddev = 1.0 );
+
+    // Re-seeding functions with same behavior as initializers
+    void seed( const uint32 oneSeed );
+    void seed( uint32 *const bigSeed, const uint32 seedLength = N );
+    void seed();
+
+    // Saving and loading generator state
+    void save( uint32* saveArray ) const;  // to array of size SAVE
+    void load( uint32 *const loadArray );  // from such array
+    friend std::ostream& operator<<( std::ostream& os, const MTRand& mtrand );
+    friend std::istream& operator>>( std::istream& is, MTRand& mtrand );
+    MTRand& operator=( const MTRand& o );
 
 protected:
-	void initialize( const uint32 oneSeed );
-	void reload();
-	uint32 hiBit( const uint32 u ) const { return u & 0x80000000UL; }
-	uint32 loBit( const uint32 u ) const { return u & 0x00000001UL; }
-	uint32 loBits( const uint32 u ) const { return u & 0x7fffffffUL; }
-	uint32 mixBits( const uint32 u, const uint32 v ) const
-		{ return hiBit(u) | loBits(v); }
-	uint32 magic( const uint32 u ) const
-		{ return loBit(u) ? 0x9908b0dfUL : 0x0UL; }
-	uint32 twist( const uint32 m, const uint32 s0, const uint32 s1 ) const
-		{ return m ^ (mixBits(s0,s1)>>1) ^ magic(s1); }
-	static uint32 hash( time_t t, clock_t c );
+    void initialize( const uint32 oneSeed );
+    void reload();
+    uint32 hiBit( const uint32 u ) const { return u & 0x80000000UL; }
+    uint32 loBit( const uint32 u ) const { return u & 0x00000001UL; }
+    uint32 loBits( const uint32 u ) const { return u & 0x7fffffffUL; }
+    uint32 mixBits( const uint32 u, const uint32 v ) const
+        { return hiBit(u) | loBits(v); }
+    uint32 magic( const uint32 u ) const
+        { return loBit(u) ? 0x9908b0dfUL : 0x0UL; }
+    uint32 twist( const uint32 m, const uint32 s0, const uint32 s1 ) const
+        { return m ^ (mixBits(s0,s1)>>1) ^ magic(s1); }
+    static uint32 hash( time_t t, clock_t c );
 };
 
 // Functions are defined in order of usage to assist inlining
 
 inline MTRand::uint32 MTRand::hash( time_t t, clock_t c )
 {
-	// Get a uint32 from t and c
-	// Better than uint32(x) in case x is floating point in [0,1]
-	// Based on code by Lawrence Kirby (fred@genesis.demon.co.uk)
-	
-	static uint32 differ = 0;  // guarantee time-based seeds will change
-	
-	uint32 h1 = 0;
-	unsigned char *p = (unsigned char *) &t;
-	for( size_t i = 0; i < sizeof(t); ++i )
-	{
-		h1 *= UCHAR_MAX + 2U;
-		h1 += p[i];
-	}
-	uint32 h2 = 0;
-	p = (unsigned char *) &c;
-	for( size_t j = 0; j < sizeof(c); ++j )
-	{
-		h2 *= UCHAR_MAX + 2U;
-		h2 += p[j];
-	}
-	return ( h1 + differ++ ) ^ h2;
+    // Get a uint32 from t and c
+    // Better than uint32(x) in case x is floating point in [0,1]
+    // Based on code by Lawrence Kirby (fred@genesis.demon.co.uk)
+
+    static uint32 differ = 0;  // guarantee time-based seeds will change
+
+    uint32 h1 = 0;
+    unsigned char *p = (unsigned char *) &t;
+    for( size_t i = 0; i < sizeof(t); ++i )
+    {
+        h1 *= UCHAR_MAX + 2U;
+        h1 += p[i];
+    }
+    uint32 h2 = 0;
+    p = (unsigned char *) &c;
+    for( size_t j = 0; j < sizeof(c); ++j )
+    {
+        h2 *= UCHAR_MAX + 2U;
+        h2 += p[j];
+    }
+    return ( h1 + differ++ ) ^ h2;
 }
 
 inline void MTRand::initialize( const uint32 seed )
 {
-	// Initialize generator state with seed
-	// See Knuth TAOCP Vol 2, 3rd Ed, p.106 for multiplier.
-	// In previous versions, most significant bits (MSBs) of the seed affect
-	// only MSBs of the state array.  Modified 9 Jan 2002 by Makoto Matsumoto.
-	register uint32 *s = state;
-	register uint32 *r = state;
-	register int i = 1;
-	*s++ = seed & 0xffffffffUL;
-	for( ; i < N; ++i )
-	{
-		*s++ = ( 1812433253UL * ( *r ^ (*r >> 30) ) + i ) & 0xffffffffUL;
-		r++;
-	}
+    // Initialize generator state with seed
+    // See Knuth TAOCP Vol 2, 3rd Ed, p.106 for multiplier.
+    // In previous versions, most significant bits (MSBs) of the seed affect
+    // only MSBs of the state array.  Modified 9 Jan 2002 by Makoto Matsumoto.
+    uint32 *s = state;
+    uint32 *r = state;
+    int i = 1;
+    *s++ = seed & 0xffffffffUL;
+    for( ; i < N; ++i )
+    {
+        *s++ = ( 1812433253UL * ( *r ^ (*r >> 30) ) + i ) & 0xffffffffUL;
+        r++;
+    }
 }
 
 inline void MTRand::reload()
 {
-	// Generate N new values in state
-	// Made clearer and faster by Matthew Bellew (matthew.bellew@home.com)
-	static const int MmN = int(M) - int(N);  // in case enums are unsigned
-	register uint32 *p = state;
-	register int i;
-	for( i = N - M; i--; ++p )
-		*p = twist( p[M], p[0], p[1] );
-	for( i = M; --i; ++p )
-		*p = twist( p[MmN], p[0], p[1] );
-	*p = twist( p[MmN], p[0], state[0] );
-	
-	left = N, pNext = state;
+    // Generate N new values in state
+    // Made clearer and faster by Matthew Bellew (matthew.bellew@home.com)
+    static const int MmN = int(M) - int(N);  // in case enums are unsigned
+    uint32 *p = state;
+    int i;
+    for( i = N - M; i--; ++p )
+        *p = twist( p[M], p[0], p[1] );
+    for( i = M; --i; ++p )
+        *p = twist( p[MmN], p[0], p[1] );
+    *p = twist( p[MmN], p[0], state[0] );
+
+    left = N, pNext = state;
 }
 
 inline void MTRand::seed( const uint32 oneSeed )
 {
-	// Seed the generator with a simple uint32
-	initialize(oneSeed);
-	reload();
+    // Seed the generator with a simple uint32
+    initialize(oneSeed);
+    reload();
 }
 
 inline void MTRand::seed( uint32 *const bigSeed, const uint32 seedLength )
 {
-	// Seed the generator with an array of uint32's
-	// There are 2^19937-1 possible initial states.  This function allows
-	// all of those to be accessed by providing at least 19937 bits (with a
-	// default seed length of N = 624 uint32's).  Any bits above the lower 32
-	// in each element are discarded.
-	// Just call seed() if you want to get array from /dev/urandom
-	initialize(19650218UL);
-	register int i = 1;
-	register uint32 j = 0;
-	register int k = ( static_cast<uint32>(N) > seedLength ? static_cast<uint32>(N) : seedLength );
-	for( ; k; --k )
-	{
-		state[i] =
-		state[i] ^ ( (state[i-1] ^ (state[i-1] >> 30)) * 1664525UL );
-		state[i] += ( bigSeed[j] & 0xffffffffUL ) + j;
-		state[i] &= 0xffffffffUL;
-		++i;  ++j;
-		if( i >= N ) { state[0] = state[N-1];  i = 1; }
-		if( j >= seedLength ) j = 0;
-	}
-	for( k = N - 1; k; --k )
-	{
-		state[i] =
-		state[i] ^ ( (state[i-1] ^ (state[i-1] >> 30)) * 1566083941UL );
-		state[i] -= i;
-		state[i] &= 0xffffffffUL;
-		++i;
-		if( i >= N ) { state[0] = state[N-1];  i = 1; }
-	}
-	state[0] = 0x80000000UL;  // MSB is 1, assuring non-zero initial array
-	reload();
+    // Seed the generator with an array of uint32's
+    // There are 2^19937-1 possible initial states.  This function allows
+    // all of those to be accessed by providing at least 19937 bits (with a
+    // default seed length of N = 624 uint32's).  Any bits above the lower 32
+    // in each element are discarded.
+    // Just call seed() if you want to get array from /dev/urandom
+    initialize(19650218UL);
+    int i = 1;
+    uint32 j = 0;
+    int k = ( static_cast<uint32>(N) > seedLength ? static_cast<uint32>(N) : seedLength );
+    for( ; k; --k )
+    {
+        state[i] =
+        state[i] ^ ( (state[i-1] ^ (state[i-1] >> 30)) * 1664525UL );
+        state[i] += ( bigSeed[j] & 0xffffffffUL ) + j;
+        state[i] &= 0xffffffffUL;
+        ++i;  ++j;
+        if( i >= N ) { state[0] = state[N-1];  i = 1; }
+        if( j >= seedLength ) j = 0;
+    }
+    for( k = N - 1; k; --k )
+    {
+        state[i] =
+        state[i] ^ ( (state[i-1] ^ (state[i-1] >> 30)) * 1566083941UL );
+        state[i] -= i;
+        state[i] &= 0xffffffffUL;
+        ++i;
+        if( i >= N ) { state[0] = state[N-1];  i = 1; }
+    }
+    state[0] = 0x80000000UL;  // MSB is 1, assuring non-zero initial array
+    reload();
 }
 
 inline void MTRand::seed()
 {
-	// Seed the generator with an array from /dev/urandom if available
-	// Otherwise use a hash of time() and clock() values
-	
-	// First try getting an array from /dev/urandom
-	FILE* urandom = fopen( "/dev/urandom", "rb" );
-	if( urandom )
-	{
-		uint32 bigSeed[N];
-		register uint32 *s = bigSeed;
-		register int i = N;
-		register bool success = true;
-		while( success && i-- )
-			success = fread( s++, sizeof(uint32), 1, urandom ) != 0;
-		fclose(urandom);
-		if( success ) { seed( bigSeed, N );  return; }
-	}
-	
-	// Was not successful, so use time() and clock() instead
-	seed( hash( time(NULL), clock() ) );
+    // Seed the generator with an array from /dev/urandom if available
+    // Otherwise use a hash of time() and clock() values
+
+    // First try getting an array from /dev/urandom
+    FILE* urandom = fopen( "/dev/urandom", "rb" );
+    if( urandom )
+    {
+        uint32 bigSeed[N];
+        uint32 *s = bigSeed;
+        int i = N;
+        bool success = true;
+        while( success && i-- )
+            success = fread( s++, sizeof(uint32), 1, urandom ) != 0;
+        fclose(urandom);
+        if( success ) { seed( bigSeed, N );  return; }
+    }
+
+    // Was not successful, so use time() and clock() instead
+    seed( hash( time(NULL), clock() ) );
 }
 
 inline MTRand::MTRand( const uint32 oneSeed )
-	{ seed(oneSeed); }
+    { seed(oneSeed); }
 
 inline MTRand::MTRand( uint32 *const bigSeed, const uint32 seedLength )
-	{ seed(bigSeed,seedLength); }
+    { seed(bigSeed,seedLength); }
 
 inline MTRand::MTRand()
-	{ seed(); }
+    { seed(); }
 
 inline MTRand::MTRand( const MTRand& o )
 {
-	register const uint32 *t = o.state;
-	register uint32 *s = state;
-	register int i = N;
-	for( ; i--; *s++ = *t++ ) {}
-	left = o.left;
-	pNext = &state[N-left];
+    const uint32 *t = o.state;
+    uint32 *s = state;
+    int i = N;
+    for( ; i--; *s++ = *t++ ) {}
+    left = o.left;
+    pNext = &state[N-left];
 }
 
 inline MTRand::uint32 MTRand::randInt()
 {
-	// Pull a 32-bit integer from the generator state
-	// Every other access function simply transforms the numbers extracted here
-	
-	if( left == 0 ) reload();
-	--left;
-	
-	register uint32 s1;
-	s1 = *pNext++;
-	s1 ^= (s1 >> 11);
-	s1 ^= (s1 <<  7) & 0x9d2c5680UL;
-	s1 ^= (s1 << 15) & 0xefc60000UL;
-	return ( s1 ^ (s1 >> 18) );
+    // Pull a 32-bit integer from the generator state
+    // Every other access function simply transforms the numbers extracted here
+
+    if( left == 0 ) reload();
+    --left;
+
+    uint32 s1;
+    s1 = *pNext++;
+    s1 ^= (s1 >> 11);
+    s1 ^= (s1 <<  7) & 0x9d2c5680UL;
+    s1 ^= (s1 << 15) & 0xefc60000UL;
+    return ( s1 ^ (s1 >> 18) );
 }
 
 inline MTRand::uint32 MTRand::randInt( const uint32 n )
 {
-	// Find which bits are used in n
-	// Optimized by Magnus Jonsson (magnus@smartelectronix.com)
-	uint32 used = n;
-	used |= used >> 1;
-	used |= used >> 2;
-	used |= used >> 4;
-	used |= used >> 8;
-	used |= used >> 16;
-	
-	// Draw numbers until one is found in [0,n]
-	uint32 i;
-	do
-		i = randInt() & used;  // toss unused bits to shorten search
-	while( i > n );
-	return i;
+    // Find which bits are used in n
+    // Optimized by Magnus Jonsson (magnus@smartelectronix.com)
+    uint32 used = n;
+    used |= used >> 1;
+    used |= used >> 2;
+    used |= used >> 4;
+    used |= used >> 8;
+    used |= used >> 16;
+
+    // Draw numbers until one is found in [0,n]
+    uint32 i;
+    do
+        i = randInt() & used;  // toss unused bits to shorten search
+    while( i > n );
+    return i;
 }
 
 inline double MTRand::rand()
-	{ return double(randInt()) * (1.0/4294967295.0); }
+    { return double(randInt()) * (1.0/4294967295.0); }
 
 inline double MTRand::rand( const double n )
-	{ return rand() * n; }
+    { return rand() * n; }
 
 inline double MTRand::randExc()
-	{ return double(randInt()) * (1.0/4294967296.0); }
+    { return double(randInt()) * (1.0/4294967296.0); }
 
 inline double MTRand::randExc( const double n )
-	{ return randExc() * n; }
+    { return randExc() * n; }
 
 inline double MTRand::randDblExc()
-	{ return ( double(randInt()) + 0.5 ) * (1.0/4294967296.0); }
+    { return ( double(randInt()) + 0.5 ) * (1.0/4294967296.0); }
 
 inline double MTRand::randDblExc( const double n )
-	{ return randDblExc() * n; }
+    { return randDblExc() * n; }
 
 inline double MTRand::rand53()
 {
-	uint32 a = randInt() >> 5, b = randInt() >> 6;
-	return ( a * 67108864.0 + b ) * (1.0/9007199254740992.0);  // by Isaku Wada
+    uint32 a = randInt() >> 5, b = randInt() >> 6;
+    return ( a * 67108864.0 + b ) * (1.0/9007199254740992.0);  // by Isaku Wada
 }
 
 inline double MTRand::randNorm( const double mean, const double stddev )
 {
-	// Return a real number from a normal (Gaussian) distribution with given
-	// mean and standard deviation by polar form of Box-Muller transformation
-	double x, y, r;
-	do
-	{
-		x = 2.0 * rand() - 1.0;
-		y = 2.0 * rand() - 1.0;
-		r = x * x + y * y;
-	}
-	while ( r >= 1.0 || r == 0.0 );
-	double s = sqrt( -2.0 * log(r) / r );
-	return mean + x * s * stddev;
+    // Return a real number from a normal (Gaussian) distribution with given
+    // mean and standard deviation by polar form of Box-Muller transformation
+    double x, y, r;
+    do
+    {
+        x = 2.0 * rand() - 1.0;
+        y = 2.0 * rand() - 1.0;
+        r = x * x + y * y;
+    }
+    while ( r >= 1.0 || r == 0.0 );
+    double s = sqrt( -2.0 * log(r) / r );
+    return mean + x * s * stddev;
 }
 
 inline double MTRand::operator()()
 {
-	return rand();
+    return rand();
 }
 
 inline void MTRand::save( uint32* saveArray ) const
 {
-	register const uint32 *s = state;
-	register uint32 *sa = saveArray;
-	register int i = N;
-	for( ; i--; *sa++ = *s++ ) {}
-	*sa = left;
+    const uint32 *s = state;
+    uint32 *sa = saveArray;
+    int i = N;
+    for( ; i--; *sa++ = *s++ ) {}
+    *sa = left;
 }
 
 inline void MTRand::load( uint32 *const loadArray )
 {
-	register uint32 *s = state;
-	register uint32 *la = loadArray;
-	register int i = N;
-	for( ; i--; *s++ = *la++ ) {}
-	left = *la;
-	pNext = &state[N-left];
+    uint32 *s = state;
+    uint32 *la = loadArray;
+    int i = N;
+    for( ; i--; *s++ = *la++ ) {}
+    left = *la;
+    pNext = &state[N-left];
 }
 
 inline std::ostream& operator<<( std::ostream& os, const MTRand& mtrand )
 {
-	register const MTRand::uint32 *s = mtrand.state;
-	register int i = mtrand.N;
-	for( ; i--; os << *s++ << "\t" ) {}
-	return os << mtrand.left;
+    const MTRand::uint32 *s = mtrand.state;
+    int i = mtrand.N;
+    for( ; i--; os << *s++ << "\t" ) {}
+    return os << mtrand.left;
 }
 
 inline std::istream& operator>>( std::istream& is, MTRand& mtrand )
 {
-	register MTRand::uint32 *s = mtrand.state;
-	register int i = mtrand.N;
-	for( ; i--; is >> *s++ ) {}
-	is >> mtrand.left;
-	mtrand.pNext = &mtrand.state[mtrand.N-mtrand.left];
-	return is;
+    MTRand::uint32 *s = mtrand.state;
+    int i = mtrand.N;
+    for( ; i--; is >> *s++ ) {}
+    is >> mtrand.left;
+    mtrand.pNext = &mtrand.state[mtrand.N-mtrand.left];
+    return is;
 }
 
 inline MTRand& MTRand::operator=( const MTRand& o )
 {
-	if( this == &o ) return (*this);
-	register const uint32 *t = o.state;
-	register uint32 *s = state;
-	register int i = N;
-	for( ; i--; *s++ = *t++ ) {}
-	left = o.left;
-	pNext = &state[N-left];
-	return (*this);
+    if( this == &o ) return (*this);
+    const uint32 *t = o.state;
+    uint32 *s = state;
+    int i = N;
+    for( ; i--; *s++ = *t++ ) {}
+    left = o.left;
+    pNext = &state[N-left];
+    return (*this);
 }
 
 #undef SEQAN_MERSENNE_MT_LEN
diff --git a/seqan/random/random_base.h b/seqan/random/random_base.h
index 156d195..19e8d79 100644
--- a/seqan/random/random_base.h
+++ b/seqan/random/random_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,13 +54,13 @@ struct MersenneTwister;
  * @signature template <[typename TSpec]>
  *                     class Rng;
  *
- * @tparam TSpec Tag for selecting the specialization.  Defaults to MersenneTwister.
+ * @tparam TSpec Tag for selecting the specialization.  Defaults to @link MersenneTwisterRng @endlink.
  *
  * @section Examples
  *
  * The following code shows how to generate random numbers and shuffle a text.
  *
- * @include demos/random/random.cpp
+ * @include demos/dox/random/random.cpp
  *
  * @code{.console}
  * pickRandomNumber(rng) == 1608637542
@@ -73,36 +73,26 @@ struct MersenneTwister;
  * shuffle("Hello World!") ==  o!reWlloHld
  * @endcode
  *
- * @see http://trac.seqan.de/wiki/Tutorial/Randomness
+ * @see http://seqan.readthedocs.org/en/develop/Tutorial/Randomness.html
  */
 
-/**
-.Class.Rng:
-..summary:Random Number Generator
-..signature:Rng<>
-..signature:Rng<TSpec>
-..cat:Random
-..param.TSpec:Random Number Generator specialization.
-...default:@Spec.Mersenne Twister Rng@
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-..example
-...text:The following code shows how to generate random numbers and shuffle a text.
-...file:demos/random/random.cpp
-...output:
-pickRandomNumber(rng) == 1608637542
-pickRandomNumber(rng, uniformDouble) == 0.950714
-pickRandomNumber(rng, uniformInt) == 27
-pickRandomNumber(rng, normal) == 0.419823
-pickRandomNumber(rng, logNormal) == 1.22431
-pickRandomNumber(rng, logNormal2) == 2.78004
-pickRandomNumber(rng, logNormal3) == 0.00155248
-shuffle("Hello World!") ==  o!reWlloHld
-*/
-
 template <typename TSpec = MersenneTwister>
 class Rng;
 
+
+// ===========================================================================
+// Classes
+// ===========================================================================
+
+/*!
+ * @fn Rng::operator()
+ * @brief Function all operator.
+ *
+ * @signature TValue Rng::operator();
+ *
+ * @return TValue Random number, TValue can be retrieved with Rng#Value.
+ */
+
 /*!
  * @class Pdf
  * @headerfile <seqan/random.h>
@@ -113,41 +103,14 @@ class Rng;
  *
  * @tparam TSpec Tag for selecting the specialization.
  *
- * Also see the <a href="http://trac.seqan.de/wiki/Tutorial/Randomness">SeqAn Randomness Tutorial</a>.
+ * This class is used together with @link Rng @endlink in the function @link Rng#pickRandomNumber @endlink. See the
+ * <a href="http://seqan.readthedocs.org/en/develop/Tutorial/Randomness.html">SeqAn Randomness Tutorial</a> for more
+ * details.
  */
 
-/**
-.Class.Pdf:
-..summary:ProbabilityDensityFunction
-..signature:Pdf<TSpec>
-..cat:Random
-..param.TSpec:Specialization.
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-*/
-
 template <typename TSpec>
 class Pdf;
 
-// ===========================================================================
-// Classes
-// ===========================================================================
-
-/*!
- * @fn Rng::operator()
- * @brief Function all operator.
- *
- * @signature TValue Rng::operator()();
- *
- * @return TValue Random number, TValue can be retrieved with Rng#Value.
- */
-
-/**
-.Memfunc.Rng#operator()
-..class:Class.Rng
-..summary:Function call operator.
-..signature:operator()
-*/
 
 // ===========================================================================
 // Metafunctions
@@ -160,12 +123,10 @@ class Pdf;
  * @signature Value<TPdf>::Type
  *
  * @tparam TPdf The Pdf for the value type.
- * 
+ *
  * @return Type The value type of the Pdf.
  */
 
-///.Metafunction.Value.param.T.type:Class.Pdf
-///.Metafunction.Value.class:Class.Pdf
 // specification only
 
 /*!
@@ -173,7 +134,7 @@ class Pdf;
  * @brief Value type of a Rng.
  *
  * @signature Value<TRng>::Type
- * 
+ *
  * @tparam TRng the Rng to get the value type for.
  *
  * @return Type the value type for the Rng.
@@ -201,13 +162,6 @@ class Pdf;
  * @return VALUE The largest value a Rng can return.
  */
 
-///.Metafunction.Value.param.T.type:Class.Rng
-///.Metafunction.Value.class:Class.Rng
-///.Metafunction.MinValue.param.T.type:Class.Rng
-///.Metafunction.MinValue.class:Class.Rng
-///.Metafunction.MaxValue.param.T.type:Class.Rng
-///.Metafunction.MaxValue.class:Class.Rng
-
 template <typename TSpec>
 struct MaxValue<Rng<TSpec> >
 {
@@ -221,8 +175,8 @@ const typename Value<Rng<TSpec> >::Type MaxValue<Rng<TSpec> >::VALUE = MaxValue<
 template <typename TSpec>
 struct MaxValue<Rng<TSpec> const>
 {
-	typedef typename Value<Rng<TSpec> const>::Type TValue_;
-	static const TValue_ VALUE;
+    typedef typename Value<Rng<TSpec> const>::Type TValue_;
+    static const TValue_ VALUE;
 };
 
 template <typename TSpec>
@@ -231,8 +185,8 @@ const typename Value<Rng<TSpec> const>::Type MaxValue<Rng<TSpec> const>::VALUE =
 template <typename TSpec>
 struct MinValue<Rng<TSpec> >
 {
-	typedef typename Value<Rng<TSpec> >::Type TValue_;
-	static const TValue_ VALUE;
+    typedef typename Value<Rng<TSpec> >::Type TValue_;
+    static const TValue_ VALUE;
 };
 
 template <typename TSpec>
@@ -241,8 +195,8 @@ const typename Value<Rng<TSpec> >::Type MinValue<Rng<TSpec> >::VALUE = MinValue<
 template <typename TSpec>
 struct MinValue<Rng<TSpec> const>
 {
-	typedef typename Value<Rng<TSpec> const>::Type TValue_;
-	static const TValue_ VALUE;
+    typedef typename Value<Rng<TSpec> const>::Type TValue_;
+    static const TValue_ VALUE;
 };
 
 template <typename TSpec>
@@ -262,16 +216,6 @@ const typename Value<Rng<TSpec> const>::Type MinValue<Rng<TSpec> const>::VALUE =
  * @see defaultRng
  */
 
-/**
-.Metafunction.GetDefaultRng
-..cat:Random
-..summary:Return the default @Class.Rng|Random Number Generator@ to use in a given class, spezialiation or algorithm.
-..signature:GetDefaultRng<T>::Type
-..param.T:The class or algorithm tag to get the default @Class.Rng@ for.
-..returns:The type of Rng specialization to use.
-..remarks:Currently, the default value is @Spec.Mersenne Twister Rng@.
-..see:Function.defaultRng
- */
 template <typename T>
 struct GetDefaultRng
 {
@@ -296,24 +240,10 @@ struct GetDefaultRng
  *
  * @section Remarks
  *
- * For more details see the <a href="http://trac.seqan.de/wiki/Tutorial/Randomness">SeqAn Tutorial on Randomness</a>.
+ * For more details see the <a href="http://seqan.readthedocs.org/en/develop/Tutorial/Randomness.html">SeqAn
+ * Tutorial on Randomness</a>.
  */
 
-/**
-.Function.pickRandomNumber
-..class:Class.Rng
-..class:Class.Pdf
-..summary:Pick a random number using a random number generator object, possibly following the given distribution.
-..cat:Random
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-..signature:pickRandomNumber(rng[, pdf])
-..param.rng:Random number generator to use.
-...type:Class.Rng
-..param.pdf:Probability density function to use, if any.
-...type:Class.Pdf
-..returns:Random number as specified in pdf, if any, or rng. For more details refer to the SeqAn Tutorial.
- */
 // specification only
 
 /*!
@@ -338,20 +268,6 @@ struct GetDefaultRng
  * @see GetDefaultRng
  */
 
-/**
-.Function.defaultRng
-..summary:Default default random number generator object of a given type.
-..cat:Random
-..signature:defaultRng<TRng>()
-..param.TRng:Type of the @Class.Rng@ to return the global default object of.
-...default:$MersenneTwister$
-...type:nolink:$MersenneTwister$
-..returns:Default random number generator object of the type given by $tag$.
-..remarks:The random number generator will be default constructed, i.e. with the default seed.
-..remarks:This function is NOT thread-safe! Also, data structures using such global state are not thread-safe! Data structures using global random number generator state should use pointers or @Class.Holder|Holder instances@. This way, the random number generator state to be used can be set to be thread-local.
-..see:Metafunction.GetDefaultRng
- */
-
 template <typename TRng>
 inline TRng &
 defaultRng()
diff --git a/seqan/random/random_beta.h b/seqan/random/random_beta.h
index e244d60..6394b48 100644
--- a/seqan/random/random_beta.h
+++ b/seqan/random/random_beta.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -85,15 +85,6 @@ typedef Tag<MeanStdDev_> MeanStdDev;
  * @param[in] sigma Standard deviation value for the beta distribution, <tt>double</tt>.
  */
 
-/**
-.Spec.Beta Pdf
-..signature:Pdf<Beta>
-..general:Class.Pdf
-..summary:Beta probability density function.
-..cat:Random
-..include:seqan/random.h
-*/
-
 template <>
 class Pdf<Beta>
 {
@@ -101,18 +92,6 @@ class Pdf<Beta>
     double _alpha;
     double _beta;
 
-/**
-.Memfunc.Beta Pdf#Pdf
-..class:Spec.Beta Pdf
-..summary:Constructor for beta Pdf.
-..description:Use the tags $AlphaBeta$ and $MeanStdDev$ to select the meaning of the two parameters.
-..signature:Pdf::Pdf(mu, sigma[, AlphaBeta()])
-..signature:Pdf::Pdf(mu, sigma, MeanStdDev())
-..param.mu:Mean of the beta distribution.
-...type:nolink:double
-..param.sigma:Standard deviation of the beta distribution.
-...type:nolink:double
-*/
     Pdf(double mu, double sigma, MeanStdDev const & /*tag*/)
             : _alpha(((1 - mu) / sigma / sigma - 1 / mu) * mu * mu),
               _beta(_alpha * (1 / mu - 1))
diff --git a/seqan/random/random_beta_kfunc.h b/seqan/random/random_beta_kfunc.h
index 4ad4c2f..f3fdbe9 100644
--- a/seqan/random/random_beta_kfunc.h
+++ b/seqan/random/random_beta_kfunc.h
@@ -25,8 +25,8 @@
 
 // Taken from bcftool's kfunc.c
 
-#ifndef SEQAN_CORE_INCLUDE_SEQAN_RANDOM_RANDOM_BETA_KFUNC_H_
-#define SEQAN_CORE_INCLUDE_SEQAN_RANDOM_RANDOM_BETA_KFUNC_H_
+#ifndef SEQAN_INCLUDE_SEQAN_RANDOM_RANDOM_BETA_KFUNC_H_
+#define SEQAN_INCLUDE_SEQAN_RANDOM_RANDOM_BETA_KFUNC_H_
 
 #include <cmath>
 #define SEQAN_M_SQRT2 1.41421356237309504880
@@ -39,17 +39,17 @@ namespace seqan {
  */
 inline double kf_lgamma(double z)
 {
-	double x = 0;
-	x += 0.1659470187408462e-06 / (z+7);
-	x += 0.9934937113930748e-05 / (z+6);
-	x -= 0.1385710331296526     / (z+5);
-	x += 12.50734324009056      / (z+4);
-	x -= 176.6150291498386      / (z+3);
-	x += 771.3234287757674      / (z+2);
-	x -= 1259.139216722289      / (z+1);
-	x += 676.5203681218835      / z;
-	x += 0.9999999999995183;
-	return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);
+    double x = 0;
+    x += 0.1659470187408462e-06 / (z+7);
+    x += 0.9934937113930748e-05 / (z+6);
+    x -= 0.1385710331296526     / (z+5);
+    x += 12.50734324009056      / (z+4);
+    x -= 176.6150291498386      / (z+3);
+    x += 771.3234287757674      / (z+2);
+    x -= 1259.139216722289      / (z+1);
+    x += 676.5203681218835      / z;
+    x += 0.9999999999995183;
+    return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);
 }
 
 /* complementary error function
@@ -58,30 +58,30 @@ inline double kf_lgamma(double z)
  */
 inline double kf_erfc(double x)
 {
-	const double p0 = 220.2068679123761;
-	const double p1 = 221.2135961699311;
-	const double p2 = 112.0792914978709;
-	const double p3 = 33.912866078383;
-	const double p4 = 6.37396220353165;
-	const double p5 = .7003830644436881;
-	const double p6 = .03526249659989109;
-	const double q0 = 440.4137358247522;
-	const double q1 = 793.8265125199484;
-	const double q2 = 637.3336333788311;
-	const double q3 = 296.5642487796737;
-	const double q4 = 86.78073220294608;
-	const double q5 = 16.06417757920695;
-	const double q6 = 1.755667163182642;
-	const double q7 = .08838834764831844;
-	double expntl, z, p;
-	z = fabs(x) * SEQAN_M_SQRT2;
-	if (z > 37.) return x > 0.? 0. : 2.;
-	expntl = exp(z * z * - .5);
-	if (z < 10. / SEQAN_M_SQRT2) // for small z
-	    p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0)
-			/ (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0);
-	else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65)))));
-	return x > 0.? 2. * p : 2. * (1. - p);
+    const double p0 = 220.2068679123761;
+    const double p1 = 221.2135961699311;
+    const double p2 = 112.0792914978709;
+    const double p3 = 33.912866078383;
+    const double p4 = 6.37396220353165;
+    const double p5 = .7003830644436881;
+    const double p6 = .03526249659989109;
+    const double q0 = 440.4137358247522;
+    const double q1 = 793.8265125199484;
+    const double q2 = 637.3336333788311;
+    const double q3 = 296.5642487796737;
+    const double q4 = 86.78073220294608;
+    const double q5 = 16.06417757920695;
+    const double q6 = 1.755667163182642;
+    const double q7 = .08838834764831844;
+    double expntl, z, p;
+    z = fabs(x) * SEQAN_M_SQRT2;
+    if (z > 37.) return x > 0.? 0. : 2.;
+    expntl = exp(z * z * - .5);
+    if (z < 10. / SEQAN_M_SQRT2) // for small z
+        p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0)
+            / (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0);
+    else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65)))));
+    return x > 0.? 2. * p : 2. * (1. - p);
 }
 
 /* The following computes regularized incomplete gamma functions.
@@ -103,44 +103,44 @@ inline double kf_erfc(double x)
 // regularized lower incomplete gamma function, by series expansion
 inline double _kf_gammap(double s, double z)
 {
-	double sum, x;
-	int k;
-	for (k = 1, sum = x = 1.; k < 100; ++k) {
-		sum += (x *= z / (s + k));
-		if (x / sum < KF_GAMMA_EPS) break;
-	}
-	return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum));
+    double sum, x;
+    int k;
+    for (k = 1, sum = x = 1.; k < 100; ++k) {
+        sum += (x *= z / (s + k));
+        if (x / sum < KF_GAMMA_EPS) break;
+    }
+    return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum));
 }
 // regularized upper incomplete gamma function, by continued fraction
 inline double _kf_gammaq(double s, double z)
 {
-	int j;
-	double C, D, f;
-	f = 1. + z - s; C = f; D = 0.;
-	// Modified Lentz's algorithm for computing continued fraction
-	// See Numerical Recipes in C, 2nd edition, section 5.2
-	for (j = 1; j < 100; ++j) {
-		double a = j * (s - j), b = (j<<1) + 1 + z - s, d;
-		D = b + a * D;
-		if (D < KF_TINY) D = KF_TINY;
-		C = b + a / C;
-		if (C < KF_TINY) C = KF_TINY;
-		D = 1. / D;
-		d = C * D;
-		f *= d;
-		if (fabs(d - 1.) < KF_GAMMA_EPS) break;
-	}
-	return exp(s * log(z) - z - kf_lgamma(s) - log(f));
+    int j;
+    double C, D, f;
+    f = 1. + z - s; C = f; D = 0.;
+    // Modified Lentz's algorithm for computing continued fraction
+    // See Numerical Recipes in C, 2nd edition, section 5.2
+    for (j = 1; j < 100; ++j) {
+        double a = j * (s - j), b = (j<<1) + 1 + z - s, d;
+        D = b + a * D;
+        if (D < KF_TINY) D = KF_TINY;
+        C = b + a / C;
+        if (C < KF_TINY) C = KF_TINY;
+        D = 1. / D;
+        d = C * D;
+        f *= d;
+        if (fabs(d - 1.) < KF_GAMMA_EPS) break;
+    }
+    return exp(s * log(z) - z - kf_lgamma(s) - log(f));
 }
 
 inline double kf_gammap(double s, double z)
 {
-	return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z);
+    return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z);
 }
 
 inline double kf_gammaq(double s, double z)
 {
-	return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z);
+    return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z);
 }
 
 /* Regularized incomplete beta function. The method is taken from
@@ -152,31 +152,31 @@ inline double kf_gammaq(double s, double z)
  */
 inline double kf_betai_aux(double a, double b, double x)
 {
-	double C, D, f;
-	int j;
-	if (x == 0.) return 0.;
-	if (x == 1.) return 1.;
-	f = 1.; C = f; D = 0.;
-	// Modified Lentz's algorithm for computing continued fraction
-	for (j = 1; j < 200; ++j) {
-		double aa, d;
-		int m = j>>1;
-		aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1))
-			: m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m));
-		D = 1. + aa * D;
-		if (D < KF_TINY) D = KF_TINY;
-		C = 1. + aa / C;
-		if (C < KF_TINY) C = KF_TINY;
-		D = 1. / D;
-		d = C * D;
-		f *= d;
-		if (fabs(d - 1.) < KF_GAMMA_EPS) break;
-	}
-	return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f;
+    double C, D, f;
+    int j;
+    if (x == 0.) return 0.;
+    if (x == 1.) return 1.;
+    f = 1.; C = f; D = 0.;
+    // Modified Lentz's algorithm for computing continued fraction
+    for (j = 1; j < 200; ++j) {
+        double aa, d;
+        int m = j>>1;
+        aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1))
+            : m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m));
+        D = 1. + aa * D;
+        if (D < KF_TINY) D = KF_TINY;
+        C = 1. + aa / C;
+        if (C < KF_TINY) C = KF_TINY;
+        D = 1. / D;
+        d = C * D;
+        f *= d;
+        if (fabs(d - 1.) < KF_GAMMA_EPS) break;
+    }
+    return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f;
 }
 inline double kf_betai(double a, double b, double x)
 {
-	return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x);
+    return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x);
 }
 
 #undef KF_TINY
@@ -184,4 +184,4 @@ inline double kf_betai(double a, double b, double x)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_RANDOM_RANDOM_BETA_KFUNC_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_RANDOM_RANDOM_BETA_KFUNC_H_
diff --git a/seqan/random/random_geometric.h b/seqan/random/random_geometric.h
index 7db1811..54b2e25 100644
--- a/seqan/random/random_geometric.h
+++ b/seqan/random/random_geometric.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,6 +54,8 @@ struct GeometricFairCoin {};
  * @class GeometricPdf
  * @headerfile <seqan/random.h>
  * @extends Pdf
+ * @signature template <>
+ *            class Pdf<Geometric>;
  * @brief Geometric probability density function with <i>p = 0.5</i>.
  *
  * The PDF is implemented efficiently without using any floating point arithmetics, just some bit operations.
@@ -64,30 +66,11 @@ struct GeometricFairCoin {};
  * @signature Pdf::Pdf();
  */
 
-/**
-.Spec.Geometric Pdf
-..signature:Pdf<GeometricFairCoin>
-..general:Class.Pdf
-..summary:Geometric probability density function with $p=0.5$.
-
-This can be implemented efficiently not using any floating point arithmetics.
-Just bit operations are needed.
-..cat:Random
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-*/
-
 template <>
 class Pdf<GeometricFairCoin>
 {
 public:
 
-/**
-.Memfunc.Geometric Pdf#Pdf
-..class:Spec.Geometric Pdf
-..summary:Constructor for geometric Pdf.
-..signature:Pdf<GeometricFairCoin>()
-*/
     Pdf() { SEQAN_CHECKPOINT; }
 };
 
@@ -108,9 +91,6 @@ struct Value<const Pdf<GeometricFairCoin> > : Value<Pdf<GeometricFairCoin> > {};
 // Functions
 // ===========================================================================
 
-/*
-..summary:Pick a geometricly distributed random number.
-*/
 template <typename TRNG>
 inline
 typename Value<Pdf<GeometricFairCoin> >::Type
@@ -123,7 +103,7 @@ pickRandomNumber(TRNG & rng, Pdf<GeometricFairCoin> const & /*pdf*/)
     const int RG_IB5 = 16;
     const int RG_IB18 = 131072;
     const int RG_MASK = RG_IB1 + RG_IB2 + RG_IB5;
-    
+
     typename Value<TRNG>::Type seed = pickRandomNumber(rng);
     typename Value<Pdf<GeometricFairCoin> >::Type value = 0;
 
diff --git a/seqan/random/random_lognormal.h b/seqan/random/random_lognormal.h
index dc2618e..2cb2883 100644
--- a/seqan/random/random_lognormal.h
+++ b/seqan/random/random_lognormal.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -66,19 +66,6 @@ typedef Tag<LogNormal_> LogNormal;
  *        for lognormal distributions.
  */
 
-/**
-.Tag.Lognormal Construction:
-..summary:Specify parameters for lognormal distribution construction.
-..cat:Random
-..include:seqan/random.h
-..tag.MuSigma:
-...summary:Tag to specify that the given parameters are mu and sigma of the underlying normal distribution for lognormal distributions.
-..tag.MeanStdDev:
-...summary:Tag to specify that the given parameters are mean an standard deviation of the lognormal distribution.
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-..see:Spec.Log-Normal Pdf
-*/
-
 struct MuSigma_;
 typedef Tag<MuSigma_> MuSigma;
 struct MeanStdDev_;
@@ -102,53 +89,25 @@ typedef Tag<MeanStdDev_> MeanStdDev;
  * Note that you can construct this either with mu/sigma of the underlying normal distribution (default) or with the
  * mean and standard deviation of the log-normal distribution.
  *
- * 
+ *
  * @fn LogNormalPdf::Pdf
  * @brief Constructor for log-normal Pdf.
  *
  * @signature Pdf::Pdf(mu,   sigma[, MuSigma()]);
  * @signature Pdf::Pdf(mean, stdDev, MeanStdDev());
  *
- * @param mu     Mean of the underlying normal distribution, double.
- * @param sigma  Standard deviation of the underlying normal distribution, double.
- * @param mean   Mean of the log-normal distribution, double.
- * @param stdDev Standard deviation of the log-normal distribution, double.
+ * @param[in] mu     Mean of the underlying normal distribution, double.
+ * @param[in] sigma  Standard deviation of the underlying normal distribution, double.
+ * @param[in] mean   Mean of the log-normal distribution, double.
+ * @param[in] stdDev Standard deviation of the log-normal distribution, double.
  */
 
-/**
-.Spec.Log-Normal Pdf
-..general:Class.Pdf
-..summary:Log-normal probability density function.
-..remark:Note that you can construct this either with mu/sigma of the underlying normal distribution (default) or with the mean and standard deviation of the log-normal distribution.
-..cat:Random
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-*/
-
 template <>
 class Pdf<LogNormal>
 {
 public:
     Pdf<Normal> _normalDist;
 
-/**
-.Memfunc.Log-Normal Pdf#Pdf
-..class:Spec.Log-Normal Pdf
-..summary:Constructor for log-normal Pdf.
-Log-normal PDFs can either be initialized by the mean and standard deviation of the underlying normal distribution or directly of the log-normal distribution.
-..signature:Pdf<LogNormal>(mu, sigma[, MuSigma()])
-..signature:Pdf<LogNormal>(mean, stdDev, MeanStdDev())
-..param.mu:Mean of the underlying normal distribution.
-...type:nolink:double
-..param.sigma:Standard deviation of the underlying normal distribution.
-...type:nolink:double
-..param.mean:Mean of the log-normal distribution.
-...type:nolink:double
-..param.stdDev:Standard deviation of the log-normal distribution.
-...type:nolink:double
-..see:Tag.Lognormal Construction.tag.MuSigma
-..see:Tag.Lognormal Construction.tag.MeanStdDev
-*/
     Pdf(double mu, double sigma, MuSigma const &)
             : _normalDist(mu, sigma)
     {
@@ -156,8 +115,8 @@ Log-normal PDFs can either be initialized by the mean and standard deviation of
     }
 
     Pdf(double mean, double stddev, MeanStdDev const &)
-            : _normalDist(::std::log(mean) - 0.5 * ::std::log(1.0 + stddev * stddev / mean / mean),
-                          ::std::sqrt(::std::log(1.0 + stddev * stddev / mean / mean)))
+            : _normalDist(std::log(mean) - 0.5 * std::log(1.0 + stddev * stddev / mean / mean),
+                          std::sqrt(std::log(1.0 + stddev * stddev / mean / mean)))
     {
         SEQAN_CHECKPOINT;
     }
diff --git a/seqan/random/random_mt19937.h b/seqan/random/random_mt19937.h
index af21d0b..cd9ee38 100644
--- a/seqan/random/random_mt19937.h
+++ b/seqan/random/random_mt19937.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -62,15 +62,6 @@ struct MersenneTwister {};
  *            class Rng<MersenneTwister>;
  */
 
-/**
-.Spec.Mersenne Twister Rng
-..general:Class.Rng
-..signature:Rng<MersenneTwister>
-..summary:Mersenne Twister 19937 Random Number Generator
-..cat:Random
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-*/
 template <>
 class Rng<MersenneTwister>
 {
@@ -83,23 +74,15 @@ class Rng<MersenneTwister>
  *
  * @signature Rng::Rng([seed]);
  *
- * @param seed The <tt>unsigned</tt> value to use for seeding, defaults to 0.
+ * @param[in] seed The <tt>unsigned</tt> value to use for seeding, defaults to 0.
  */
 
-/**
-.Memfunc.Mersenne Twister Rng#Rng
-..class:Spec.Mersenne Twister Rng
-..summary:Constructor Mersenne Twister Rng.
-..signature:Rng<MersenneTwister>([seed])
-..param.seed:Seed for the initialization of the Mersenne Twister, defaults to 0.
-...type:nolink:double.
-*/
     Rng() : _mtRand(0lu)
     { SEQAN_CHECKPOINT; }
 
     Rng(unsigned seed) : _mtRand(seed)
     { SEQAN_CHECKPOINT; }
-    
+
     inline
     unsigned
     operator()()
@@ -121,7 +104,7 @@ struct Value<Rng<MersenneTwister> >
 
 template <>
 struct Value<const Rng<MersenneTwister> > : Value<Rng<MersenneTwister> > {};
-	
+
 // ===========================================================================
 // Functions
 // ===========================================================================
@@ -138,27 +121,12 @@ pickRandomNumber(Rng<MersenneTwister> & mt)
  * @fn MersenneTwisterRng#reSeed
  * @brief Reset and re-seed Mersenne Twister Rng.
  *
- * @signature reSeed(mt[, seed]);
+ * @signature void reSeed(mt[, seed]);
  *
  * @param[in,out] mt   The MersenneTwisterRng to re-seed.
  * @param[in]     seed The <tt>unsigned</tt> to use for re-seeding, defaults to 0.
  */
 
-/**
-.Function.reSeed
-..class:Spec.Mersenne Twister Rng
-..summary:Reset and re-seed MersenneTwister
-..cat:Random
-..signature:reSeed(mt[, seed])
-..param.mt:The @Spec.Mersenne Twister Rng@ to reset.
-...type:Spec.Mersenne Twister Rng
-..param.seed:Optional seed to initialize the RNG with.
-...default:0
-...type:nolink:$__uint32$
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-*/
-
 inline void
 reSeed(Rng<MersenneTwister> & mt, __uint32 const seed = 0)
 {
diff --git a/seqan/random/random_normal.h b/seqan/random/random_normal.h
index 92ae51d..94f1042 100644
--- a/seqan/random/random_normal.h
+++ b/seqan/random/random_normal.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -53,6 +53,7 @@ typedef Tag<Normal_> Normal;
 
 /*!
  * @class NormalPdf Normal Pdf
+ * @brief Probability density function for normal distribution.
  * @extends Pdf
  * @headerfile <seqan/random.h>
  *
@@ -60,16 +61,6 @@ typedef Tag<Normal_> Normal;
  *            class Pdf<Normal>;
  */
 
-/**
-.Spec.Normal Pdf
-..signature:Pdf<Normal>
-..general:Class.Pdf
-..summary:Normal probability density function.
-..cat:Random
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-*/
-
 template <>
 class Pdf<Normal>
 {
@@ -87,16 +78,6 @@ class Pdf<Normal>
  * @param[in] sigma Standard deviation of the normal distribution, double.
  */
 
-/**
-.Memfunc.Normal Pdf#Pdf
-..class:Spec.Normal Pdf
-..summary:Constructor for normal Pdf.
-..signature:Pdf<Normal>(mu, sigma)
-..param.mu:Mean of the normal distribution.
-...type:nolink:double
-..param.sigma:Standard deviation of the normal distribution.
-...type:nolink:double
-*/
     Pdf(double mu, double sigma)
             : _mu(mu), _sigma(sigma)
     {
@@ -123,9 +104,6 @@ struct Value<const Pdf<Normal> > : Value<Pdf<Normal> > {};
 
 static const double SEQAN_NV_MAGICCONST = 1.7155277699214135;  // == 4 * exp(-0.5)/sqrt(2.0)
 
-/*
-..summary:Pick a normally distributed random number.
-*/
 template <typename TRNG>
 inline
 typename Value<Pdf<Normal> >::Type
@@ -147,7 +125,7 @@ pickRandomNumber(TRNG & rng, Pdf<Normal> const & pdf)
         double u2 = 1 - pickRandomNumber(rng, pdfUniform);
         z = SEQAN_NV_MAGICCONST * (u1 - 0.5) / u2;
         double zz = z * z / 4.0;
-        if (zz < -::std::log10(u2))
+        if (zz < -std::log10(u2))
             break;
     }
     return pdf._mu + z * pdf._sigma;
diff --git a/seqan/random/random_rng_functor.h b/seqan/random/random_rng_functor.h
index a9dfae5..dca6e02 100644
--- a/seqan/random/random_rng_functor.h
+++ b/seqan/random/random_rng_functor.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -46,7 +46,7 @@ namespace seqan {
 // Tag for selecting the Rng functor specialization.
 template <typename TRng, typename TPdf>
 struct RngFunctor {};
-    
+
 // ===========================================================================
 // Classes
 // ===========================================================================
@@ -64,16 +64,6 @@ struct RngFunctor {};
  * @tparam TPdf The probability density function type to use.
  */
 
-/**
-.Spec.Rng Functor
-..general:Class.Rng
-..signature:Rng<RngFunctor<TRng, TPdf> >
-..summary:Functor wrapper for random number generation.
-..cat:Random
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-*/
-
 template <typename TRng, typename TPdf>
 class Rng<RngFunctor<TRng, TPdf> >
 {
@@ -92,18 +82,10 @@ class Rng<RngFunctor<TRng, TPdf> >
  * @param[in] pdf A reference to the underlying Pdf to use.
  */
 
-/**
-.Memfunc.Rng Functor#Rng
-..class:Spec.Rng Functor
-..summary:Constructor Functor Rng.
-..signature:Rng<RngFunctor<TRng, TPdf> >(rng, pdf)
-..param.rng:@Class.Rng@ object to use.
-..param.pdf:@Class.Pdf@ object to use.
-*/
     Rng(TRng & rng, TPdf & pdf)
-	    : _rng(rng), _pdf(pdf)
+        : _rng(rng), _pdf(pdf)
     {}
-    
+
     inline
     typename Value<TPdf>::Type
     operator()()
@@ -134,7 +116,7 @@ struct MinValue<RngFunctor<TRng, TPdf> > : MinValue<TPdf> {};
 
 template <typename TRng, typename TPdf>
 struct MinValue<RngFunctor<TRng, TPdf> const> : MinValue<TPdf> {};
-    
+
 // ===========================================================================
 // Functions
 // ===========================================================================
@@ -144,7 +126,7 @@ inline unsigned
 pickRandomNumber(Rng<RngFunctor<TRng, TPdf> > & rng)
 {
     SEQAN_CHECKPOINT;
-    
+
     return pickRandomNumber(rng._rng, rng._pdf);
 }
 
diff --git a/seqan/random/random_shuffle.h b/seqan/random/random_shuffle.h
index d0e38f8..af6b3a8 100644
--- a/seqan/random/random_shuffle.h
+++ b/seqan/random/random_shuffle.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -57,6 +57,7 @@ namespace seqan {
 
 /*!
  * @fn shuffle
+ * @headerfile <seqan/random.h>
  * @brief Shuffle the given container.
  *
  * @signature void shuffle(container, rng);
@@ -65,18 +66,6 @@ namespace seqan {
  * @param[in,out] rng       The random number generator to use.
  */
 
-/**
-.Function.shuffle
-..summary:Shuffle the given container.
-..cat:Random
-..include:seqan/random.h
-..signature:shuffle(container, rng)
-..param.container:Container to shuffle elements of.
-..param.rng:Random number generator to use.
-...type:Class.Rng
-..wiki:Tutorial/Randomness#Shuffling|Tutorial: Randomness
-*/
-
 template <typename TContainer, typename TRNG>
 void shuffle(TContainer & container, TRNG & rng)
 {
diff --git a/seqan/random/random_uniform.h b/seqan/random/random_uniform.h
index 472dfe4..7b8fb07 100644
--- a/seqan/random/random_uniform.h
+++ b/seqan/random/random_uniform.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -63,17 +63,6 @@ struct Uniform;
  * @tparam T The number type to use (integer or floating point).
  */
 
-/**
-.Spec.Uniform Pdf
-..signature:Pdf<Uniform<T> >
-..general:Class.Pdf
-..summary:Uniform distribution probability density function over a closed interval [min, max].
-..param.T:Type of the values the Pdf is defined on.
-..cat:Random
-..include:seqan/random.h
-..wiki:Tutorial/Randomness|Tutorial: Randomness
-*/
-
 template <typename T>
 class Pdf<Uniform<T> >
 {
@@ -91,16 +80,6 @@ class Pdf<Uniform<T> >
  * @param[in] max The largest value of the interval, of the Value type of the Pdf.
  */
 
-/**
-.Memfunc.Uniform Pdf#Pdf
-..class:Spec.Uniform Pdf
-..summary:Constructor for uniform Pdf.
-..signature:Pdf<Uniform<T> >(min, max)
-..param.min:Smallest value of interval.
-...type:nolink:T
-..param.max:Largest value of interval.
-...type:nolink:T
-*/
     Pdf(T min, T max)
             : _min(min), _max(max)
     {
@@ -114,9 +93,9 @@ template <>
 class Pdf<Uniform<bool> >
 {
 public:
-	Pdf() {}
+    Pdf() {}
 };
-	
+
 // ===========================================================================
 // Metafunctions
 // ===========================================================================
@@ -180,8 +159,8 @@ typename Value<Pdf<Uniform<bool> > >::Type
 pickRandomNumber(TRNG & rng, Pdf<Uniform<bool> > const &)
 {
     SEQAN_CHECKPOINT;
-	typename Value<TRNG>::Type x = pickRandomNumber(rng);
-	return x % 2;
+    typename Value<TRNG>::Type x = pickRandomNumber(rng);
+    return x % 2;
 }
 
 }  // namespace seqan
diff --git a/seqan/realign.h b/seqan/realign.h
new file mode 100644
index 0000000..b027516
--- /dev/null
+++ b/seqan/realign.h
@@ -0,0 +1,57 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for module realign.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_REALIGN_H_
+#define INCLUDE_SEQAN_REALIGN_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/basic.h>
+#include <seqan/file.h>
+#include <seqan/sequence.h>
+#include <seqan/store.h>
+#include <seqan/consensus.h>
+
+// ===========================================================================
+// Realignment Code
+// ===========================================================================
+
+#include <seqan/realign/realign_helper_functions.h>
+#include <seqan/realign/realign_base.h>
+
+#endif  // INCLUDE_SEQAN_REALIGN_H_
diff --git a/seqan/realign/realign_base.h b/seqan/realign/realign_base.h
new file mode 100644
index 0000000..61e649b
--- /dev/null
+++ b/seqan/realign/realign_base.h
@@ -0,0 +1,1823 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+// TODO(holtgrew): After this has been thoroughly tested, debug output should be removed.
+// TODO(holtgrew): With gaps instead of align we can now create "real" profile-sequence alignments.
+// TODO(holtgrew): For windows, we only need to create the profile of the window, this should save time for string resizing on replace().
+// TODO(holtgrew): Need to resort after display, changes order and might break realignment!
+
+#include <seqan/align_profile/score_profile_seq.h>
+
+#ifndef INCLUDE_SEQAN_REALIGN_REALIGN_BASE_H_
+#define INCLUDE_SEQAN_REALIGN_REALIGN_BASE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class RealignmentOptions_
+// ----------------------------------------------------------------------------
+
+// Class used for holding the realignment options.
+
+struct RealignmentOptions_
+{
+    // Enum for selecting a realignment method.
+    enum RealignmentMethod
+    {
+        ANSON_MYERS_NW,    // Anson-Myers with Needleman-Wunsch alignment.
+        ANSON_MYERS_GOTOH  // Anson-Mysers with Gotoh alignment.
+    };
+
+    // The realignment method to use.
+    RealignmentMethod method;
+    // The number of bases in the environment to use left and right of the current alignment.
+    unsigned environment;
+    // The bandwidth to use for realignment for lower and higher band.
+    unsigned bandwidth;
+    // Whether or not to include the reference as a read on the contig.  This is useful for disconnected read alignment
+    // groups and gap-rich alignments (454 data).
+    bool includeReference;
+    // Whether or not to print timing information.
+    bool printTiming;
+    // Whether or not to print debugging information.
+    bool debug;
+
+    RealignmentOptions_() :
+            method(ANSON_MYERS_NW), environment(0), bandwidth(0), includeReference(false), printTiming(false),
+            debug(false)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class ContigAlignmentsInfo_
+// ----------------------------------------------------------------------------
+
+// Helper class that bundles the information for the alignments on a contig.
+
+template <typename TFragmentStore>
+struct ContigAlignmentsInfo_
+{
+    typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignedReadIter;
+    typedef typename TFragmentStore::TReadPos TReadPos;
+
+    TReadPos minPos, maxPos;
+    TAlignedReadIter alignedItBegin, alignedItEnd;
+
+    ContigAlignmentsInfo_() : minPos(0), maxPos(0), alignedItBegin(), alignedItEnd()
+    {
+        reset();
+    }
+
+    // Reset everything.
+    void reset()
+    {
+        minPos = maxValue<TReadPos>();
+        maxPos = minValue<TReadPos>();
+        alignedItBegin = TAlignedReadIter();
+        alignedItEnd = TAlignedReadIter();
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Helper class for storing timing information.
+// ----------------------------------------------------------------------------
+
+struct AnsonMyersTimes_
+{
+    // Time for preparation step in realigner run() function.
+    double mainBeginContig;
+    // Time for writing back information in realigner run() function.
+    double mainEndContig;
+    // Total time spent in main.
+    double mainTotal;
+
+    // Time for extracting information from the store into the profile.
+    double realignExtractProfile;
+    // Time for realignment.
+    double realignAlign;
+    // Time for integration of information.
+    double realignIntegration;
+    // Time for total realignment rounds.
+    double realignTotal;
+
+    // The times for each realignment round.
+    std::vector<double> roundTimes;
+
+    AnsonMyersTimes_() :
+            mainBeginContig(0), mainEndContig(0), mainTotal(0), realignExtractProfile(0),
+            realignAlign(0), realignIntegration(0), realignTotal(0)
+    {}
+};
+
+
+// ----------------------------------------------------------------------------
+// Class ExtractProfileInfo_
+// ----------------------------------------------------------------------------
+
+// Struct for storing positions to extract from profile.
+
+struct ExtractProfileInfo_
+{
+    // Begin and end positions in the profile to extract.
+    unsigned profBeginPos, profEndPos;
+    // Begin and end positions of the alignment within the profile.
+    unsigned aliBeginPos, aliEndPos;
+
+    ExtractProfileInfo_() : profBeginPos(0), profEndPos(0), aliBeginPos(0), aliEndPos(0)
+    {}
+};
+
+
+// ----------------------------------------------------------------------------
+// Class WindowClippingInfo_
+// ----------------------------------------------------------------------------
+
+// Information that stores flags for whether the window clips into the read from the left or right.
+
+struct WindowClippingInfo_
+{
+    // Flag clipLeft is true if left window border clips into the read alignment.
+    bool clipLeft;
+    // Flag clipRight is true if right window border clips into the read alignment.
+    bool clipRight;
+
+    // Begin and end position in the read sequence for clipping.
+    unsigned readBeginPos, readEndPos;
+    // Begin and end position in the read alignment.
+    unsigned readAliBeginPos, readAliEndPos;
+
+    WindowClippingInfo_() : clipLeft(false), clipRight(false), readBeginPos(0), readEndPos(0),
+                            readAliBeginPos(0), readAliEndPos(0)
+    {}
+
+    // Return true if window clipped into both borders.
+    bool clipBoth() const
+    {
+        return clipLeft && clipRight;
+    }
+};
+
+
+// ----------------------------------------------------------------------------
+// Class AnsonMyersRealignmentRound_
+// ----------------------------------------------------------------------------
+
+// One iteration of the realignment.
+
+template <typename TFragmentStore>
+class AnsonMyersRealignmentRound_
+{
+public:
+    typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore;
+    typedef typename Value<TAlignedReadStore>::Type TAlignedReadElement;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignedReadIter;
+
+    typedef typename TFragmentStore::TReadSeqStore      TReadSeqStore;
+    typedef typename Value<TReadSeqStore>::Type         TReadSeq;
+    typedef typename Value<TReadSeq>::Type              TStoreAlphabet;
+    typedef typename BaseAlphabet<TStoreAlphabet>::Type TAlphabet;  // TODO(holtgrew): Rename?
+    typedef ProfileChar<TAlphabet> TProfileChar;
+    typedef String<TProfileChar>   TProfileString;
+    typedef typename Iterator<TProfileString>::Type TProfileIter;
+
+    // The FragmentStore for the sequences.
+    TFragmentStore & store;
+    // The contig's profile sequence.
+    TProfileString & contigProfile;
+    // The aligned reads for this contig.
+    TAlignedReadStore & contigAlignedReads;
+    // The timing helper struct.
+    AnsonMyersTimes_ & times;
+    // The options.
+    RealignmentOptions_ const & options;
+
+    // -----------------------------------------------------------------------
+    // Public Interface
+    // -----------------------------------------------------------------------
+
+    AnsonMyersRealignmentRound_(TFragmentStore & store,
+                                TProfileString & contigProfile,
+                                TAlignedReadStore & contigAlignedReads,
+                                AnsonMyersTimes_ & times,
+                                RealignmentOptions_ const & options) :
+            store(store), contigProfile(contigProfile), contigAlignedReads(contigAlignedReads), times(times),
+            options(options)
+    {}
+
+    // Run one round of realignment.
+    void run(unsigned windowBegin, unsigned & windowEnd);
+
+    // Helper that returns whether the given profile character is for an all-gaps column.
+    bool _allGaps(TProfileChar const & c)
+    {
+        return (c.count[0] + c.count[1] + c.count[2] + c.count[3] + c.count[4] == 0u);
+    }
+
+    bool _empty(TProfileChar const & c)
+    {
+        return (c.count[0] + c.count[1] + c.count[2] + c.count[3] + c.count[4] + c.count[5] == 0u);
+    }
+
+    // -----------------------------------------------------------------------
+    // Implementation Functions
+    // -----------------------------------------------------------------------
+
+    inline bool _overlap(unsigned begin1, unsigned end1, unsigned begin2, unsigned end2)
+    {
+        return (begin1 < end2) && (begin2 < end1);
+    }
+
+    void _getReadAsProfile(TProfileString & profileStr,
+                           TAlignedReadElement /*const*/ & el)
+    {
+        clear(profileStr);
+        resize(profileStr, length(store.readSeqStore[el.readId]), TProfileChar());
+
+        TProfileIter itP = begin(profileStr);
+
+        typedef typename Iterator<TReadSeq, Standard>::Type TReadSeqIter;
+        for (TReadSeqIter it = begin(store.readSeqStore[el.readId]),
+                     itEnd = end(store.readSeqStore[el.readId]); it != itEnd; ++it, ++itP)
+            itP->count[ordValue(*it)] = 1;
+    }
+
+    // Returns the information about the infix from the profile to extract.
+    ExtractProfileInfo_ _getExtractPositions(TAlignedReadElement const & el)
+    {
+        ExtractProfileInfo_ result;
+        if ((unsigned)el.beginPos < options.environment)
+        {
+            result.profBeginPos = 0;
+            result.aliBeginPos = el.beginPos;
+        }
+        else
+        {
+            result.profBeginPos = el.beginPos - options.environment;
+            result.aliBeginPos = options.environment;
+        }
+
+        if ((int)(el.endPos + options.environment) > (int)length(contigProfile))
+            result.profEndPos = length(contigProfile);
+        else
+            result.profEndPos = el.endPos + options.environment;
+        result.aliEndPos = result.aliBeginPos + (el.endPos - el.beginPos);
+
+        // Sanity check on the result.
+        SEQAN_ASSERT_LEQ(result.aliEndPos, result.profEndPos - result.profBeginPos);
+        SEQAN_ASSERT_EQ((unsigned)(el.endPos - el.beginPos), result.aliEndPos - result.aliBeginPos);
+        SEQAN_ASSERT_GEQ(result.profEndPos - result.profBeginPos, (unsigned)(el.endPos - el.beginPos));
+        SEQAN_ASSERT_LEQ(result.profEndPos - result.profBeginPos,
+                         (unsigned)(el.endPos - el.beginPos + 2 * options.environment));
+
+        return result;
+    }
+
+    // Adjusts the ExtractProfileInfo_ object for the given window.
+    void _updateExtractPositions(ExtractProfileInfo_ & info,
+                                 unsigned windowBegin, unsigned windowEnd)
+    {
+        if (windowBegin == windowEnd)
+            return;  // No update if window is disabled.
+
+        // Get positions of read alignment from ExtractProfileInfo_.
+        unsigned globalAliBeginPos = info.profBeginPos + info.aliBeginPos;
+        unsigned globalAliEndPos = info.profBeginPos + info.aliEndPos;
+
+        // Adjust begin positions in ExtractProfileInfo_.
+        if (info.profBeginPos < windowBegin)
+            info.profBeginPos = windowBegin;
+        info.aliBeginPos = (globalAliBeginPos > info.profBeginPos) ? (globalAliBeginPos - info.profBeginPos) : 0;
+
+        // Adjust end positions in ExtractProfileInfo_.
+        if (info.profEndPos > windowEnd)
+            info.profEndPos = windowEnd;
+        if (globalAliEndPos > info.profEndPos)
+            info.aliEndPos = info.profEndPos - info.profBeginPos;
+        else
+            info.aliEndPos = (info.profEndPos - info.profBeginPos) - (info.profEndPos - globalAliEndPos);
+    }
+
+    // Compute the WindowClippingInfo_.
+    void _computeReadClippingInfo(WindowClippingInfo_ & windowInfo, TAlignedReadElement const & el,
+                                  unsigned windowBegin, unsigned windowEnd)
+    {
+        if (windowBegin == windowEnd)  // no window
+        {
+            windowInfo.clipLeft = false;
+            windowInfo.clipRight = false;
+            windowInfo.readAliBeginPos = 0;
+            windowInfo.readAliEndPos = el.endPos - el.beginPos;
+            windowInfo.readBeginPos = 0;
+            windowInfo.readEndPos = length(store.readSeqStore[el.readId]);
+            return;
+        }
+
+        // Compute clipping flags.
+        windowInfo.clipLeft = ((unsigned)el.beginPos < windowBegin);
+        windowInfo.clipRight = ((unsigned)el.endPos > windowEnd);
+
+        // Compute read alignment begin and end position.
+        typedef Gaps<TReadSeq, AnchorGaps<String<typename TFragmentStore::TReadGapAnchor> > > TReadGaps;
+        TReadGaps readGaps(store.readSeqStore[el.readId], el.gaps);
+        if (options.debug)
+            std::cerr << "READ GAPS\t" << readGaps << "\n";
+        if (windowBegin < (unsigned)el.beginPos)
+            windowInfo.readAliBeginPos = 0;
+        else
+            windowInfo.readAliBeginPos = windowBegin - el.beginPos;
+        if (windowEnd > (unsigned)el.endPos)
+            windowInfo.readAliEndPos = length(readGaps);
+        else
+            windowInfo.readAliEndPos = length(readGaps) - (el.endPos - windowEnd);
+
+        // Compute source begin and end position.
+        windowInfo.readBeginPos = toSourcePosition(readGaps, windowInfo.readAliBeginPos);
+        windowInfo.readEndPos = toSourcePosition(readGaps, windowInfo.readAliEndPos);
+    }
+
+    // TODO(holtgrew): Build profile here to circumvent profileStr2 and the swap().
+    // Subtract the counts for the alignment from the profile part.
+    //
+    // The aligned read element is given by copy since the original one can be altered through the removeGaps() call.
+    void _subtractReadAlignment(unsigned windowBegin,
+                                unsigned & windowEnd,
+                                TProfileString & profileStr,
+                                ExtractProfileInfo_ & info,
+                                TAlignedReadElement el,
+                                int elPos /*pos of el in aligned reads*/,
+                                WindowClippingInfo_ const & windowInfo)
+    {
+        typedef typename Iterator<TProfileString, Standard>::Type TProfileIt;
+        typedef Gaps<TReadSeq, AnchorGaps<String<typename TFragmentStore::TReadGapAnchor> > > TReadGaps;
+        typedef typename Iterator<TReadGaps, Standard>::Type TReadGapsIter;
+
+        TReadGaps readGaps(store.readSeqStore[el.readId], el.gaps);
+        TReadGapsIter itR = iter(readGaps, windowInfo.readAliBeginPos, Standard());
+        TReadGapsIter itREnd = iter(readGaps, windowInfo.readAliEndPos, Standard());
+        TProfileIt itP = iter(profileStr, info.aliBeginPos, Standard());
+        TProfileIt itPEnd = iter(profileStr, info.aliEndPos, Standard());
+        (void)itPEnd;  // TODO(holtgrew): Still required?
+
+        if (options.debug)
+        {
+            std::cerr << "READ GAPS\t";
+            for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2)
+                if (isGap(itR2))
+                    std::cerr << "-";
+                else
+                    std::cerr << convert<char>(*itR2);
+            std::cerr << "\n";
+
+            std::cerr << "  ==> el.beginPos == " << el.beginPos << "\n";
+        }
+
+        // We will build a profileStr2 that has fewer gaps.
+        TProfileString profileStr2;
+        reserve(profileStr2, length(profileStr));
+        // Append profile charactes without alignment by read.
+        append(profileStr2, prefix(profileStr, info.aliBeginPos));
+
+        // Subtract read alignment from profile, yielding profileStr2.
+        int removeLeft = 0, removeRight = 0;  // number of bases removed left and right of read
+        unsigned pos = info.aliBeginPos;   // position in profileStr
+        unsigned posA = el.beginPos + windowInfo.readAliBeginPos;  // position in current multi-read aligment, including
+                                                                   // removeGap()s.
+        int gapsRemoved = 0;
+        unsigned dbgCounter = 0;
+        (void)dbgCounter;
+        for (; itR != itREnd; ++itR, ++itP, ++pos)
+        {
+            SEQAN_ASSERT_MSG(itP != end(profileStr, Standard()),
+                             "Profile part includes read alignment (debug counter = %u).", dbgCounter);
+
+            unsigned idx = isGap(itR) ? valueSize<TAlphabet>() : ordValue(*itR);
+#if SEQAN_ENABLE_DEBUG
+            int posP = itP - begin(profileStr, Standard());
+            int posR = itR - begin(readGaps, Standard());
+#endif  // #if SEQAN_ENABLE_DEBUG
+            // std::cerr << "idx == " << idx << "\tpos == " << pos << "\tidx == " << idx << "\tposP == " << posP
+            //           << "\tposR == " << posR << "\t" << "posA == " << posA << "\t"
+            //           << "itP->count[0] == " << itP->count[0] << "\t" << "itP->count[1] == " << itP->count[1] << "\t"
+            //           << "itP->count[2] == " << itP->count[2] << "\t" << "itP->count[3] == " << itP->count[3] << "\t"
+            //           << "itP->count[4] == " << itP->count[4] << "\t" << "itP->count[5] == " << itP->count[5] << "\t"
+            //           << "*itR == " << (isGap(itR) ? '-' : convert<char>(TAlphabet(*itR))) << "\n";
+            SEQAN_ASSERT_GT_MSG(itP->count[idx], 0u,
+                                "Must have count for alignment char (pos = %u, idx = %u, posP = %d, posR = %d).",
+                                pos, idx, posP, posR);
+            itP->count[idx] -= 1;
+
+            // Append to profile2 unless there is an all-gaps column and there is a gap in the read gaps.
+            if ((!_allGaps(*itP) || isGap(itR)) && !_empty(*itP))
+            {
+                appendValue(profileStr2, *itP);
+                ++posA;
+            }
+            else
+            {
+                if (options.debug)
+                {
+                    swap(store.alignedReadStore, contigAlignedReads);
+                    std::cerr << "ALIGNMENT is (current == " << store.readSeqStore[el.readId] << ")\n";
+                    seqan::AlignedReadLayout layout;
+                    layoutAlignment(layout, store);
+                    std::stringstream ss;
+                    printAlignment(std::cerr, layout, store, front(store.alignedReadStore).contigId,
+                                   0, 1000, 0, 100);
+                    swap(store.alignedReadStore, contigAlignedReads);
+
+                    std::cerr << " => removeGap(contigAlignedReads, " << posA << ", " << elPos << ")\n"
+                              << "       pos == " << pos << "\n";
+                    // std::cerr << "    itP:";
+                    // for (unsigned i = 0; i < 6u; ++i)
+                    //     std::cerr << "\titP->count[" << i << "] == " << itP->count[i];
+                    // std::cerr << "\n";
+                }
+                _removeGap(contigAlignedReads, posA, iter(contigAlignedReads, elPos, Standard()));
+                gapsRemoved += 1;  // WAS: (removeGap(contigAlignedReads, posA, iter(contigAlignedReads, elPos,
+                                   //                 Standard())) > 0);
+                if (pos < info.aliBeginPos)
+                    removeLeft += 1;  // TODO(holtgrew): cannot be reached!
+                if (pos >= info.aliEndPos)
+                    removeRight += 1;  // TODO(holtgrew): can also not be reached!
+            }
+        }
+
+        if (options.debug)
+            std::cerr << "gapsRemoved == " << gapsRemoved << "\n"
+                      << "adjusting window from " << windowBegin << " " << windowEnd << "\n";
+        if (windowBegin != windowEnd)
+            windowEnd -= gapsRemoved;
+        if (options.debug)
+            std::cerr << "adjusting window to " << windowBegin << " " << windowEnd << "\n";
+
+        // Add remaining profile characters.
+        append(profileStr2, suffix(profileStr, pos));
+
+        SEQAN_ASSERT_LEQ(removeLeft, (int)info.aliBeginPos);
+        SEQAN_ASSERT_LEQ(removeRight, (int)(length(profileStr) - info.aliEndPos));
+        info.aliBeginPos -= removeLeft;
+        info.aliEndPos -= removeRight;
+
+        // Write out other profile string.
+        swap(profileStr, profileStr2);
+    }
+
+    // Use the alignment result in matches to update contigProfile and insert/remove gaps from the fragment store.
+    //
+    // matches     -- alignment result
+    // profilePart -- the part of the profile that was extracted
+    // info        -- extraction information about profilePart
+    // el          -- aligned read store element
+    void _updateAlignments(
+            unsigned windowBegin,
+            unsigned & windowEnd,  // only updated
+            TProfileString & profilePart,
+            // Align<TProfileString> /*const*/ & align,
+            Gaps<TProfileString> /*const*/ & profileGaps,
+            Gaps<TReadSeq> /*const*/ & readGaps,
+            ExtractProfileInfo_ & info,
+            WindowClippingInfo_ const & windowInfo,
+            TAlignedReadIter const & it);
+};
+
+// ----------------------------------------------------------------------------
+// Class AnsonMyersRealigner_
+// ----------------------------------------------------------------------------
+
+// Implementation of the Anson-Myers algorithm for realigning the fragments in a FragmentStore.
+//
+// This class is used for holding references to the input data structures and the helper data structures.
+
+template <typename TFragmentStore>
+class AnsonMyersRealigner_
+{
+public:
+    typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignedReadIter;
+
+    typedef typename TFragmentStore::TReadSeq           TReadSeq;
+    typedef typename Value<TReadSeq>::Type              TStoreAlphabet;
+    typedef typename BaseAlphabet<TStoreAlphabet>::Type TAlphabet;  // TODO(holtgrew): Rename?
+    typedef ProfileChar<TAlphabet> TProfileChar;
+    typedef String<TProfileChar>   TProfileString;
+    typedef typename Iterator<TProfileString, Standard>::Type TProfileIter;
+
+    // The FragmentStore object with the reads.
+    TFragmentStore & store;
+    // The configuration to use for the realignment.
+    RealignmentOptions_ options;
+
+    // A copy of the aligned reads for the current contig.
+    TAlignedReadStore contigAlignedReads;
+    // Information on the alignments of the current contig.
+    ContigAlignmentsInfo_<TFragmentStore> contigAlignmentInfos;
+
+    // The contig's profile sequence.
+    TProfileString contigProfile;
+
+    // Timing information.
+    AnsonMyersTimes_ times;
+
+    // -----------------------------------------------------------------------
+    // Public Interface
+    // -----------------------------------------------------------------------
+
+    // Construct
+    AnsonMyersRealigner_(TFragmentStore & store, RealignmentOptions_ const & options) :
+            store(store), options(options)
+    {}
+
+    // Run the realignment on the given contig.  If windowBegin != windowEnd then only the given window is realigned.
+    // The value of windowEnd is adjusted in case columns are added to or removed from the window.
+    void run(unsigned contigID, unsigned windowBegin, unsigned &windowEnd);
+
+    // Run on the whole contig without a window.
+    void run(unsigned contigID)
+    {
+        unsigned windowBegin = 0;
+        unsigned windowEnd = 0;
+        run(contigID, windowBegin, windowEnd);
+    }
+
+    // -----------------------------------------------------------------------
+    // Implementation Functions
+    // -----------------------------------------------------------------------
+
+    // Check read alignments for consistency.
+    void _checkReadAlignments(TAlignedReadStore & alignedReadStore)
+    {
+        if (options.debug)
+            std::cerr << "begin/end positions of alignments (central check)\n";
+        TAlignedReadIter itEnd = end(alignedReadStore, Standard());
+        for (TAlignedReadIter it2 = begin(alignedReadStore, Standard()); it2 != itEnd; ++it2)
+        {
+            typedef Gaps<TReadSeq, AnchorGaps<String<typename TFragmentStore::TReadGapAnchor> > > TReadGaps;
+            TReadGaps readGaps(static_cast<TReadSeq>(store.readSeqStore[it2->readId]), it2->gaps);
+            // if (options.debug)
+            //     std::cerr << "it2->beginPos == " << it2->beginPos << ", it2->endPos == " << it2->endPos << "\n";
+            if ((unsigned)abs((int)(it2->endPos - it2->beginPos)) != length(readGaps))
+            {
+                std::cerr << "READ GAPS\t>>>" << readGaps << "<<<\n";
+                SEQAN_FAIL("Inconsistent begin/endPos");
+            }
+        }
+    }
+
+    void _checkReadAlignments()
+    {
+        _checkReadAlignments(store.alignedReadStore);
+        _checkReadAlignments(contigAlignedReads);
+    }
+
+    // Sort aligned reads, fill contigAlignedReads and fill contigAlignmentInfos, add reference sequence as read if
+    // configured to do so.
+    void _beginContig(unsigned contigID);
+
+    // Write back the updated information from contigAlignedReads to store, add reference sequence alignment if
+    // configured to do so.
+    void _endContig(unsigned contigID);
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function AnsonMyersRealigner_::run()
+// ----------------------------------------------------------------------------
+
+template <typename TProfileGaps, typename TReadGaps, typename TConsensusScore, typename TAlignConfig,
+          typename TAlgoTag>
+void _readToProfileAlignment(TProfileGaps & profileGaps, TReadGaps & readGaps, TConsensusScore const & consScore,
+                             TAlignConfig const & alignConfig, int & lowerBand, int & upperBand, TAlgoTag const & tag)
+{
+    _fixBandSize(lowerBand, upperBand, source(profileGaps), source(readGaps), alignConfig, tag);
+    globalAlignment(profileGaps, readGaps, consScore, alignConfig, /*lowerBand, upperBand, */tag);
+}
+
+template <typename TProfileGaps, typename TReadGaps, typename TConsensusScore, typename TAlignConfig>
+void _readToProfileAlignment(TProfileGaps & profileGaps, TReadGaps & readGaps, TConsensusScore const & consScore,
+                             TAlignConfig const & alignConfig, int & lowerBand, int & upperBand, bool linear)
+{
+    // Handle the case where the read was the only one aligning at this position.  It would be impossible to compute a
+    // pairwise alignment below.
+    if (empty(source(profileGaps)))
+    {
+        clearGaps(readGaps);
+        clearGaps(profileGaps);
+        insertGaps(profileGaps, 0, length(readGaps));
+    }
+    else
+    {
+        if (linear)
+            _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand,
+                                    NeedlemanWunsch());
+        else
+            _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand,
+                                    Gotoh());
+    }
+}
+
+template <typename TFragmentStore>
+void AnsonMyersRealigner_<TFragmentStore>::run(unsigned contigID, unsigned windowBegin, unsigned & windowEnd)
+{
+    _checkReadAlignments();
+
+    // Fill contigAlignedReads, contigAlignmentInfos, contigProfile.
+    _beginContig(contigID);
+
+    _checkReadAlignments();
+
+    // Perform realignment round until the score does not decrease any more.
+    int score = maxValue<int>();
+    int oldScore = maxValue<int>();
+    for (unsigned roundNo = 0; score == maxValue<int>() || score < oldScore; ++roundNo)
+    {
+        if (options.debug)
+            std::cerr << "Realignment round " << roundNo << "\n";
+        oldScore = score;
+        AnsonMyersRealignmentRound_<TFragmentStore> round(store, contigProfile, contigAlignedReads, times, options);
+        _checkReadAlignments();
+        round.run(windowBegin, windowEnd);
+        _checkReadAlignments();
+        // TODO(holtgrew): This is not a similarity score but more of a distance score.
+        score = scoreConsensus(contigProfile);
+        if (options.debug)
+            std::cerr << "Old score = " << oldScore << ", score == " << score << "\n";
+    }
+
+    _checkReadAlignments();
+
+    // Write back the realigned read alignments into store and set contig to the consensus in case that the original
+    // reference was included as a pseudo-read.
+    _endContig(contigID);
+
+    _checkReadAlignments();
+}
+
+// ----------------------------------------------------------------------------
+// Function AnsonMyersRealigner_::_beginContig()
+// ----------------------------------------------------------------------------
+
+// TODO(holtgrew): Completely restore RC state of sequence and begin/end position again.
+// TODO(holtgrew): Split into smaller functions.
+
+template <typename TFragmentStore>
+void AnsonMyersRealigner_<TFragmentStore>::_beginContig(unsigned contigID)
+{
+    double startTime = sysTime();
+    contigAlignmentInfos.reset();  // reset/clear
+
+    // ------------------------------------------------------------------------
+    // Read Sorting
+    // ------------------------------------------------------------------------
+
+    // Sort aligned reads by contig id and get iterators to begin/end of the alignments on the contig.
+    sortAlignedReads(store.alignedReadStore, SortContigId());
+    contigAlignmentInfos.alignedItBegin = lowerBoundAlignedReads(store.alignedReadStore, contigID, SortContigId());
+    contigAlignmentInfos.alignedItEnd = upperBoundAlignedReads(store.alignedReadStore, contigID, SortContigId());
+
+    // Sort the reads on the current contig according to their begin posiiton.
+    sortAlignedReads(infix(store.alignedReadStore,
+                           contigAlignmentInfos.alignedItBegin - begin(store.alignedReadStore, Standard()),
+                           contigAlignmentInfos.alignedItEnd - begin(store.alignedReadStore, Standard())),
+                     SortBeginPos());
+
+    // ------------------------------------------------------------------------
+    // Extract Alignment; Reverse-Complement Fragment Sequence
+    // ------------------------------------------------------------------------
+
+    // Copy out the read alignments belonging to the contig and reverse-complement the read sequence if necessary.
+    //
+    // We will later work on the copy of the read alignments and at the end we will write it back to store.  The
+    // reverse-complements are also used in the alignments.  In _endContig(), we will restore the original sequence
+    // again.
+    //
+    // TODO(holtgrew): We could also work on an infix of the read alignments. Advantages/Disadvantages?
+    clear(contigAlignedReads);
+    typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore;
+    typedef typename Value<TAlignedReadStore>::Type TAlignedElement;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignedReadIter;
+    for (TAlignedReadIter it = contigAlignmentInfos.alignedItBegin; it != contigAlignmentInfos.alignedItEnd; ++it)
+    {
+        TAlignedElement el = *it;
+        if (it->beginPos > it->endPos)  // reverse-complemented
+        {
+            reverseComplement(store.readSeqStore[it->readId]);
+            std::swap(el.beginPos, el.endPos);
+        }
+        contigAlignmentInfos.minPos = std::min(contigAlignmentInfos.minPos, el.beginPos);
+        contigAlignmentInfos.maxPos = std::max(contigAlignmentInfos.maxPos, el.endPos);
+        appendValue(contigAlignedReads, el);
+    }
+
+    // ------------------------------------------------------------------------
+    // Include Reference Sequence
+    // ------------------------------------------------------------------------
+
+    if (options.includeReference)
+    {
+        // Compute read and match ID.
+        unsigned readID = length(store.readSeqStore);
+        unsigned matchID = length(store.alignedReadStore);
+
+        // Append sequence and name of pseudo-read.
+        appendRead(store, store.contigStore[contigID].seq);
+        appendValue(store.readNameStore, store.contigNameStore[contigID]);
+        store.contigNameStore[contigID] += "Consensus_";  // TODO(holtgrew): Prepend?
+
+        // Create alignment for pseudo-read.
+        typedef typename TFragmentStore::TReadPos       TReadPos;
+        typedef typename TFragmentStore::TContigStore   TContigStore;
+        typedef typename Value<TContigStore>::Type      TContig;
+        // typedef typename TFragmentStore::TContigPos     TContigPos;
+        typedef typename TFragmentStore::TContigSeq     TContigSeq;
+        typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
+        // Construct aligned read element.
+        TAlignedElement el;
+        el.id = matchID;
+        el.readId = readID;
+        el.contigId = contigID;
+        contigAlignmentInfos.minPos = el.beginPos = 0;
+        el.gaps = store.contigStore[contigID].gaps;
+        // Compute begin/end positions and append element to the contig's read alignments.
+        TContigGaps contigGaps(store.contigStore[contigID].seq, store.contigStore[contigID].gaps);
+        TReadPos contigLength = length(store.contigStore[contigID].seq);
+        TReadPos contigEndGapPos = positionSeqToGap(contigGaps, contigLength - 1) + 1;
+        contigAlignmentInfos.maxPos = el.endPos = std::max(contigAlignmentInfos.maxPos,
+                                                           std::max(contigEndGapPos, contigLength));
+        appendValue(contigAlignedReads, el);
+    }
+
+    // ------------------------------------------------------------------------
+    // Create Profile Sequence
+    // ------------------------------------------------------------------------
+
+    clear(contigProfile);
+    resize(contigProfile, contigAlignmentInfos.maxPos - contigAlignmentInfos.minPos, TProfileChar());
+
+    // Iterate over the pairwise alignments of the reads against the contig that are stored in the fragment store.
+    for (TAlignedReadIter it = begin(contigAlignedReads, Standard());
+         it != end(contigAlignedReads, Standard()); ++it)
+    {
+        // Shift the aligned reads from the contig to the left by contigAlignmentInfos.minPos;
+        it->beginPos -= contigAlignmentInfos.minPos;
+        it->endPos -= contigAlignmentInfos.minPos;
+
+        typedef Gaps<TReadSeq, AnchorGaps<String<typename TFragmentStore::TReadGapAnchor> > > TReadGaps;
+        typedef typename Iterator<TReadGaps, Standard>::Type TReadGapsIter;
+
+        // We create Gaps for the read we are iterating over.
+        // TODO(holtgrew): Is clipping stored in the read gaps? It appears so in Tobias' original code.
+        TReadGaps readGaps(static_cast<TReadSeq>(store.readSeqStore[it->readId]), it->gaps);
+
+        // Get iterators to beginning of read gaps and the corresponding positions in the contig gaps and the profile
+        // string.
+        TProfileIter itP = iter(contigProfile, it->beginPos, Standard());
+        TReadGapsIter itR = begin(readGaps, Standard());
+        TReadGapsIter itREnd = end(readGaps, Standard());
+
+        // TODO(holtgrew): This could become easier if there was a countTrailingGaps() function.
+        // Skip over leading gaps, advance iterator into profile.
+        itP += countGaps(itR);
+        itR += countGaps(itR);
+        // Skip over trailing gaps.
+        if (itR != itREnd)
+        {
+            --itREnd;
+            while (itREnd != itR && isGap(itREnd))
+                --itREnd;
+            if (!isGap(itREnd))
+                ++itREnd;
+        }
+
+        // Copy over characters/gaps into profile.
+        for (; itR != itREnd; ++itR, ++itP)
+            ++itP->count[isGap(itR) ? valueSize<TAlphabet>() : ordValue(*itR)];
+    }
+
+    if (options.debug)
+    {
+        std::cerr << "INITIAL PROFILE\n";
+        _printProfile(std::cerr, contigProfile);
+    }
+
+    // Update times used for processing beginning of contig.
+    times.mainBeginContig += sysTime() - startTime;
+}
+
+// ----------------------------------------------------------------------------
+// Function AnsonMyersRealigner_::_endContig()
+// ----------------------------------------------------------------------------
+
+template <typename TFragmentStore>
+void AnsonMyersRealigner_<TFragmentStore>::_endContig(unsigned contigID)
+{
+    // -----------------------------------------------------------------------
+    // Update Read Alignments
+    // -----------------------------------------------------------------------
+
+    TAlignedReadIter it = contigAlignmentInfos.alignedItBegin;
+    TAlignedReadIter itEnd = contigAlignmentInfos.alignedItEnd;
+    TAlignedReadIter itNew = begin(contigAlignedReads, Standard());
+
+    for (unsigned idx = 0; it != itEnd; ++idx, ++it, ++itNew)
+    {
+        it->beginPos = itNew->beginPos;
+        it->endPos = itNew->endPos;
+        it->gaps = itNew->gaps;  // TODO(holtgrew): Old code removed empty anchors -- required?
+        if (it->endPos < it->beginPos)
+            reverseComplement(store.readSeqStore[it->readId]);
+    }
+
+    // -----------------------------------------------------------------------
+    // Update Contig
+    // -----------------------------------------------------------------------
+
+    // The contig will be replaced by the consensus sequence.
+
+    typedef typename TFragmentStore::TContigStore   TContigStore;
+    typedef typename Value<TContigStore>::Type      TContig;
+    typedef typename TContig::TContigSeq            TContigSeq;
+    typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
+    typedef typename Position<TContigSeq>::Type     TContigPos;
+
+    // typedef typename Iterator<TContigGaps, Standard>::Type TContigGapsIter;
+
+    // Get shortcut to contig sequence and clear for rebuilding.
+    TContigSeq & contigSeq = store.contigStore[contigID].seq;
+    clear(contigSeq);
+
+    // Iterate over the profile and build up the contig sequence and store gap positions.
+    unsigned gapLen = 0;  // length of current gap
+    TContigPos contigPos = 0;  // with gaps
+    String<Pair<unsigned, unsigned> > gaps;  // Gap positions and lengths.
+    for (TProfileIter it = begin(contigProfile, Standard()), itEnd = end(contigProfile, Standard());
+         it != itEnd; ++it, ++contigPos)
+    {
+        if (static_cast<char>(*it) == gapValue<char>())
+        {
+            ++gapLen;
+            continue;
+        }
+
+        // Record gaps position.
+        if (gapLen)
+            appendValue(gaps, Pair<unsigned, unsigned>(contigPos - gapLen, gapLen));
+        gapLen = 0;
+
+        // Append to contig sequence.
+        //
+        // TODO(weese): Here we convert from ProfileChar<Dna5>->Dna5->Dna5Q
+        // instead diverting through Dna5 we could think of directly converting
+        // a profile to a quality value, e.g. like the base caller Phred does.
+        // Therefore the conversion ProfileChar<Dna5> <-> Dna5Q needs to be
+        // defined.
+        appendValue(contigSeq, static_cast<TAlphabet>(*it));
+    }
+
+    // Rebuild contig gaps.
+    TContigGaps contigGaps(store.contigStore[contigID].seq, store.contigStore[contigID].gaps);
+    clearGaps(contigGaps);
+    for (unsigned i = 0; i < length(gaps); ++i)
+    {
+        if (options.debug)
+            std::cerr << "insertGaps(contigGaps, " << gaps[i].i1 << ", " << gaps[i].i2 << ")\n";
+        insertGaps(contigGaps, gaps[i].i1, gaps[i].i2);
+    }
+
+    if (options.debug)
+    {
+        std::cerr << "Resulting contig gaps\n"
+                  << contigGaps << "\n";
+    }
+
+    // -----------------------------------------------------------------------
+    // Include Reference
+    // -----------------------------------------------------------------------
+
+    if (options.includeReference)
+        appendValue(store.alignedReadStore, back(contigAlignedReads));
+}
+
+
+// ----------------------------------------------------------------------------
+// Function _fixBandSize()
+// ----------------------------------------------------------------------------
+
+/*
+ * @fn _fixBandSize
+ * @headerfile <seqan/align.h>
+ * @brief Fix a band for alignment given sequences (for their lengths) and an @link AlignConfig @endlink.
+ *
+ * @signature void _fixBandSize(lowerDiag, upperDiag, seqH, seqV, alignConfig);
+ *
+ * @param[in,out] lowerDiag   The lower band position (<tt>int</tt>) to adjust.
+ * @param[in,out] upperDiag   The upper band position (<tt>int</tt>) to adjust.
+ * @param[in]     seqH        The @link ContainerConcept container @endlink to use in horizontal direction of alignment
+ *                            matrix.
+ * @param[in]     seqV        The @link ContainerConcept container @endlink to use in vertical direction of alignment
+ *                            matrix.
+ * @param[in]     alignConfig The @link AlignConfig @endlink to use for the alignment configuration.
+ */
+
+template <typename TSequenceH, typename TSequenceV, typename TAlignConfig, typename TAlgoTag>
+void _fixBandSize(int & lDiag,
+                  int & uDiag,
+                  TSequenceH const & seqH,
+                  TSequenceV const & seqV,
+                  TAlignConfig const & /*alignConfig*/,
+                  TAlgoTag const & /*algoTag*/)
+{
+    typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
+    typedef typename If<typename IsSameType<TAlgoTag, Gotoh>::Type, AffineGaps, LinearGaps>::Type TGapsType;
+    typedef typename SetupAlignmentProfile_<DPGlobal, TFreeEndGaps, TGapsType,
+                                            TracebackOn<TracebackConfig_<SingleTrace, GapsLeft> > >::Type TDPProfile;
+
+    if (uDiag < -(int)length(seqV))
+        uDiag = -(int)length(seqV);
+    if (lDiag > (int)length(seqH))
+        lDiag = length(seqV);
+
+    if (uDiag < 0 && !IsFreeEndGap_<TDPProfile, DPFirstColumn>::VALUE)
+        uDiag = 0;
+
+    if (lDiag > 0 && !IsFreeEndGap_<TDPProfile, DPFirstRow>::VALUE)
+        lDiag = 0;
+
+    if (uDiag + (int)length(seqV) < (int)length(seqH) && !IsFreeEndGap_<TDPProfile, DPLastRow>::VALUE)
+        uDiag = (int)length(seqH) - (int)length(seqV);
+
+    if (lDiag + (int)length(seqV) > (int)length(seqH) && !IsFreeEndGap_<TDPProfile, DPLastColumn>::VALUE)
+        lDiag = (int)length(seqH) - (int)length(seqV);
+}
+
+// ----------------------------------------------------------------------------
+// Function AnsonMyersRealignmentRound_::run()
+// ----------------------------------------------------------------------------
+
+template <typename TFragmentStore>
+void AnsonMyersRealignmentRound_<TFragmentStore>::run(unsigned windowBegin, unsigned & windowEnd)
+{
+    if (empty(contigAlignedReads))
+        return;
+    // If there is only one read on this contig and no window is set or the window spans the whole alignment then remove
+    // all gaps from this one read and exit.
+    if (length(contigAlignedReads) == 1u)  // only one alignment
+    {
+        if (((windowBegin == 0u) && (windowBegin == windowEnd)) ||  // no window
+            (windowBegin <= (unsigned)contigAlignedReads[0].beginPos &&
+             windowEnd >= (unsigned)contigAlignedReads[0].endPos))  // spans only
+                                                                                                           // alignment
+        {
+            contigAlignedReads[0].beginPos = 0;
+            contigAlignedReads[0].endPos = length(store.readSeqStore[contigAlignedReads[0].readId]);
+            clear(contigAlignedReads[0].gaps);
+            _getReadAsProfile(contigProfile, contigAlignedReads[0]);
+            return;
+        }
+    }
+
+    double roundStartTime = sysTime();  // round start time
+    if (options.debug)
+        std::cerr << "STARTING ROUND WITH windowBegin == " << windowBegin << ", windowEnd == " << windowEnd << "\n";
+    SEQAN_ASSERT_LEQ(windowBegin, windowEnd);
+    if (windowBegin == windowEnd && windowBegin != 0u)
+    {
+        if (options.debug)
+            std::cerr << "Window is empty.\n";
+        return;
+    }
+
+    // The currently extracted part from the sequence and the read as profile (ord values stored in read[i].count[0].
+    TProfileString profilePart;
+
+    // Remove each read from the profile, realign it to the profile, and update the profile.
+    TAlignedReadIter itEnd = end(contigAlignedReads, Standard());
+    for (TAlignedReadIter it = begin(contigAlignedReads, Standard()); it != itEnd; ++it)
+    {
+        if (options.includeReference && it->readId + 1 == length(store.readSeqStore))
+            continue;  // do not subtract reference pseudo-read
+        // Ignore reads that do not overlap with the window.
+        if (windowBegin != windowEnd && !_overlap(windowBegin, windowEnd, it->beginPos, it->endPos))
+            continue;
+
+        // Extract the profile around the alignment.
+        double beginExtractProfile = sysTime();
+        // Get positions in the alignment to extrad and positions in the alignment in this part.
+        ExtractProfileInfo_ info = _getExtractPositions(*it);
+        SEQAN_ASSERT_EQ(info.profBeginPos + info.aliBeginPos, (unsigned)it->beginPos);
+        SEQAN_ASSERT_EQ(info.profBeginPos + info.aliEndPos, (unsigned)it->endPos);
+        if (options.debug)
+            std::cerr << "WINDOW                       [" << windowBegin << ", " << windowEnd << ")\n"
+                      << "UNADJUSTED\n"
+                      << "Extracting profile begin/end " << info.profBeginPos << "/" << info.profEndPos << "\n"
+                      << "Aligned read begin/end       " << it->beginPos << "/" << it->endPos << "\n"
+                      << "Alignment begin/end          " << info.aliBeginPos << "/" << info.aliEndPos << "\n"
+                      << "Read sequence                " << store.readSeqStore[it->readId] << "\n"
+                      << "it->beginPos == " << it->beginPos << ", it->endPos == " << it->endPos << "\n";
+        // Update these extraction positions for the given window.
+        _updateExtractPositions(info, windowBegin, windowEnd);
+        // Compute read window clipping info.
+        WindowClippingInfo_ windowInfo;
+        _computeReadClippingInfo(windowInfo, *it, windowBegin, windowEnd);
+        if (options.debug)
+            std::cerr << "ADJUSTED\n"
+                      << "Extracting profile begin/end " << info.profBeginPos << "/" << info.profEndPos << "\n"
+                      << "Aligned read begin/end       " << it->beginPos << "/" << it->endPos << "\n"
+                      << "Alignment begin/end          " << info.aliBeginPos << "/" << info.aliEndPos << "\n"
+                      << "Read sequence                " << store.readSeqStore[it->readId] << "\n"
+                      << "window clips left?  " << windowInfo.clipLeft << "\n"
+                      << "window clips right? " << windowInfo.clipRight << "\n"
+                      << "read begin pos      " << windowInfo.readBeginPos << "\n"
+                      << "read end pos        " << windowInfo.readEndPos << "\n"
+                      << "read ali begin pos  " << windowInfo.readAliBeginPos << "\n"
+                      << "read ali end pos    " << windowInfo.readAliEndPos << "\n";
+        if (windowInfo.readBeginPos == windowInfo.readEndPos)
+            continue;  // Skip if we only cut out gap characters.
+        SEQAN_ASSERT_EQ(windowInfo.readAliEndPos - windowInfo.readAliBeginPos,
+                        info.aliEndPos - info.aliBeginPos);
+        // Extract part of the profile with buffer bases left and right.
+        profilePart = infix(contigProfile, info.profBeginPos, info.profEndPos);
+        if (options.debug)
+        {
+            typedef typename TFragmentStore::TContigStore   TContigStore;
+            typedef typename Value<TContigStore>::Type      TContig;
+            typedef typename TContig::TContigSeq            TContigSeq;
+            typedef typename Position<TContigSeq>::Type TContigPos;
+            TContigSeq contigSeq;
+
+            unsigned gapLen = 0;  // length of current gap
+            TContigPos contigPos = 0;  // with gaps
+            String<Pair<unsigned, unsigned> > gaps;  // Gap positions and lengths.
+            for (TProfileIter it2 = begin(contigProfile, Standard()), itEnd = end(contigProfile, Standard());
+                 it2 != itEnd; ++it2, ++contigPos)
+            {
+                if (static_cast<char>(*it2) == gapValue<char>())
+                {
+                    ++gapLen;
+                    continue;
+                }
+
+                // Record gaps position.
+                if (gapLen)
+                    appendValue(gaps, Pair<unsigned, unsigned>(contigPos - gapLen, gapLen));
+                gapLen = 0;
+
+                // Append to contig sequence.
+                //
+                // TODO(weese): Here we convert from ProfileChar<Dna5>->Dna5->Dna5Q
+                // instead diverting through Dna5 we could think of directly converting
+                // a profile to a quality value, e.g. like the base caller Phred does.
+                // Therefore the conversion ProfileChar<Dna5> <-> Dna5Q needs to be
+                // defined.
+                appendValue(contigSeq, static_cast<TAlphabet>(*it2));
+            }
+            std::cerr << "Consensus                    " << contigSeq << "\n";
+
+            swap(store.alignedReadStore, contigAlignedReads);
+            std::cerr << "ALIGNMENT is\n";
+            seqan::AlignedReadLayout layout;
+            layoutAlignment(layout, store);
+            std::stringstream ss;
+            printAlignment(std::cerr, layout, store, front(store.alignedReadStore).contigId,
+                           0, 1000, 0, 100);
+            swap(store.alignedReadStore, contigAlignedReads);
+
+            std::cerr << "PROFILE\n";
+            _printProfile(std::cerr, contigProfile);
+            std::cerr << "PROFILE PART BEFORE SUBTRACTION\n";
+            _printProfile(std::cerr, profilePart);
+        }
+
+        // Subtract the read alignment from the profile.
+        _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads,
+                                                                                          Standard()),
+                               windowInfo);
+        SEQAN_ASSERT_LEQ(windowBegin, windowEnd);
+        times.realignExtractProfile += sysTime() - beginExtractProfile;
+
+        if (options.debug)
+        {
+            std::cerr << "PROFILE PART AFTER SUBTRACTION\n";
+            _printProfile(std::cerr, profilePart);
+
+            swap(store.alignedReadStore, contigAlignedReads);
+            std::cerr << "AFTER SUBTRACTION of " << store.readSeqStore[it->readId] << " id= " << it->readId << "\n";
+            seqan::AlignedReadLayout layout;
+            layoutAlignment(layout, store);
+            std::stringstream ss;
+            printAlignment(std::cerr, layout, store, front(store.alignedReadStore).contigId,
+                           0, 1000, 0, 100);
+            swap(store.alignedReadStore, contigAlignedReads);
+        }
+
+        // Realign the read against the profile.
+        double beginAlign = sysTime();
+        Gaps<TProfileString> profileGaps(profilePart);
+        Gaps<TReadSeq> readGaps;
+        assignSource(readGaps, infix(store.readSeqStore[it->readId], windowInfo.readBeginPos, windowInfo.readEndPos));
+        if (options.debug)
+        {
+            std::cerr << "READ PART; SOURCE OF READ GAPS (seq = " << store.readSeqStore[it->readId] << ")\n";
+            std::cerr << source(readGaps) << "\n";
+        }
+
+        // Setup the score (same as in Anson-Myers paper), requires knowledge about the profile that is to be aligned
+        // against.
+        Score<int, WeightedConsensusScore<Score<int, ProfileSeqFracScore>,
+                                          Score<int, ProfileSeqScore> > > consScore;
+        assignProfile(consScore, profilePart);
+
+        // Compute the flag isSingleLeft that indicates whether the current read is the first read and the coverage at
+        // the first position is 1 (i.e. only this reads aligns there).  In this case, we have to use an overlap
+        // alignment here instead of a semiglobal alignment and also adjust the band for the alignment.
+        bool isSingleLeft = (it->beginPos == 0u) &&
+                (it == begin(contigAlignedReads, Standard())) &&
+                (it - begin(contigAlignedReads, Standard()) + 1 < (int)length(contigAlignedReads)) &&
+                (((it + 1)->beginPos - it->beginPos) > 0);
+        if (windowBegin != windowEnd && windowBegin > 0)
+            isSingleLeft = false;  // Cannot be case of single left if window does not start at begin.
+        int bandDelta = isSingleLeft ? ((it + 1)->beginPos - it->beginPos) : 0;
+        // Compute the upper and lower band for the alignment of the read to the profile.  The band will be fixed
+        // further using _fixBandSize() below.
+        int upperBand = std::max((int)info.aliBeginPos + (int)options.bandwidth + bandDelta,
+                                 (int)length(profilePart) - (int)length(readGaps) + (int)options.bandwidth + bandDelta);
+        int lowerBand = std::min(-(int)options.bandwidth - bandDelta,
+                                 (int)length(profilePart) - (int)length(readGaps) - (int)options.bandwidth - bandDelta);
+
+        if (options.debug)
+            std::cerr << "BEFORE ALIGNMENT\n"
+                      << "length of align row 0\t" << length(profileGaps) << "\n"
+                      << "length of align row 1\t" << length(readGaps) << "\n"
+                      << "\n"
+                      << "PROFILE\t" << profileGaps << "\n"
+                      << "READ   \t" << readGaps << "\n";
+
+        // TODO(holtgrew): Adjust begin/end gap scoring.
+        bool linear = (options.method == RealignmentOptions_::ANSON_MYERS_NW);
+        if (isSingleLeft)
+        {
+            if (options.debug)
+                std::cerr << "CASE OF LEFT (lowerBand == " << lowerBand << ", upperBand == " << upperBand
+                          << ", bandDelta == " << bandDelta << ")\n";
+            AlignConfig<false, true, false, true> alignConfig;
+            _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, linear);
+        }
+        else
+        {
+            if (windowInfo.clipLeft)
+            {
+                if (options.debug)
+                    std::cerr << "Clipped left. (lowerBand == " << lowerBand << ", upperBand == " << upperBand << ")\n";
+                AlignConfig<false, false, false, true> alignConfig;
+                _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, linear);
+            }
+            else if (windowInfo.clipRight)
+            {
+                if (options.debug)
+                    std::cerr << "Clipped right. (lowerBand == " << lowerBand << ", upperBand == "
+                              << upperBand << ")\n";
+                AlignConfig<true, false, false, false> alignConfig;
+                _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, linear);
+            }
+            else if (windowInfo.clipBoth())
+            {
+                if (options.debug)
+                    std::cerr << "Clipped both. (lowerBand == " << lowerBand << ", upperBand == "
+                              << upperBand << ")\n";
+                AlignConfig<false, false, false, false> alignConfig;
+                _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, linear);
+            }
+            else // clipNone
+            {
+                if (options.debug)
+                    std::cerr << "NOT case of left (lowerBand == " << lowerBand << ", upperBand == "
+                              << upperBand << ")\n";
+                AlignConfig<true, false, false, true> alignConfig;
+                _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, linear);
+            }
+        }
+#if 0
+        if (isSingleLeft)
+        {
+            AlignConfig<false, true, false, true> alignConfig;
+            if (options.debug)
+                std::cerr << "CASE OF LEFT (lowerBand == " << lowerBand << ", upperBand == " << upperBand
+                          << ", bandDelta == " << bandDelta << ")\n";
+            if (options.method == RealignmentOptions_::ANSON_MYERS_NW)
+            {
+                _fixBandSize(lowerBand, upperBand, profilePart, source(readGaps), alignConfig, NeedlemanWunsch());
+                globalAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand,
+                                NeedlemanWunsch());
+            }
+            else
+            {
+                _fixBandSize(lowerBand, upperBand, profilePart, source(readGaps), alignConfig, Gotoh());
+                globalAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, Gotoh());
+            }
+        }
+        else
+        {
+            AlignConfig<true, false, false, true> alignConfig;
+            if (options.debug)
+                std::cerr << "NOT case of left (lowerBand == " << lowerBand << ", upperBand == "
+                          << upperBand << ")\n";
+            if (options.method == RealignmentOptions_::ANSON_MYERS_NW)
+            {
+                _fixBandSize(lowerBand, upperBand, profilePart, source(readGaps), alignConfig, NeedlemanWunsch());
+                globalAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand,
+                                NeedlemanWunsch());
+            }
+            else
+            {
+                _fixBandSize(lowerBand, upperBand, profilePart, source(readGaps), alignConfig, Gotoh());
+                globalAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, Gotoh());
+            }
+        }
+#endif  // #if 0
+        times.realignAlign = sysTime() - beginAlign;
+
+        if (options.debug)
+            std::cerr << "AFTER ALIGNMENT\n"
+                      << "length of align row 0\t" << length(profileGaps) << "\n"
+                      << "length of align row 1\t" << length(readGaps) << "\n"
+                      << "\n"
+                      << "ALIGNMENT\n"
+                      << _profileGapsStructureStr(begin(profileGaps, Standard()), end(profileGaps, Standard())) << "\n"
+                      << readGaps << "\n";
+
+        if (options.debug)
+        {
+            swap(store.alignedReadStore, contigAlignedReads);
+            std::cerr << "BEFORE INTEGRATION of " << store.readSeqStore[it->readId] << "\n";
+            seqan::AlignedReadLayout layout;
+            layoutAlignment(layout, store);
+            std::stringstream ss;
+            printAlignment(std::cerr, layout, store, front(store.alignedReadStore).contigId,
+                           0, 1000, 0, 100);
+            swap(store.alignedReadStore, contigAlignedReads);
+
+            std::cerr << "begin/end positions of alignments after update\n";
+            for (TAlignedReadIter it2 = begin(contigAlignedReads, Standard()); it2 != itEnd; ++it2)
+            {
+                typedef Gaps<TReadSeq, AnchorGaps<String<typename TFragmentStore::TReadGapAnchor> > > TReadGaps;
+                TReadGaps readGaps(store.readSeqStore[it2->readId], it2->gaps);
+                std::cerr << "it2->beginPos == " << it2->beginPos << ", it2->endPos == " << it2->endPos << "\n";
+                std::cerr << "    " << source(readGaps) << "\n";
+                if (windowBegin == windowEnd)
+                    SEQAN_ASSERT_EQ((int)(it2->endPos - it2->beginPos), (int)length(readGaps));
+            }
+        }
+
+        // Integrate back the profile and the new alignment.
+        double beginIntegration = sysTime();
+        if (options.debug)
+            std::cerr << "WINDOW BEFORE UPDATE ALIGNMENTS [" << windowBegin << ", " << windowEnd << ")\n";
+        _updateAlignments(windowBegin, windowEnd, profilePart, profileGaps, readGaps, info, windowInfo, it);
+        SEQAN_ASSERT_LEQ(windowBegin, windowEnd);
+        if (options.debug)
+            std::cerr << "WINDOW AFTER UPDATE ALIGNMENTS [" << windowBegin << ", " << windowEnd << ")\n";
+        times.realignIntegration = sysTime() - beginIntegration;
+
+        if (options.debug)
+        {
+            std::cerr << "PROFILE PART AFTER ALIGNMENT UPDATE\n";
+            _printProfile(std::cerr, profilePart);
+        }
+
+        replace(contigProfile, info.profBeginPos, info.profEndPos, profilePart);
+
+        if (options.debug)
+        {
+            std::cerr << "PROFILE AFTER INTEGRATION PROFILE\n";
+            _printProfile(std::cerr, contigProfile);
+
+            swap(store.alignedReadStore, contigAlignedReads);
+            std::cerr << "AFTER REALIGNMENT STEP of " << store.readSeqStore[it->readId] << "\n";
+            seqan::AlignedReadLayout layout;
+            layoutAlignment(layout, store);
+            std::stringstream ss;
+            printAlignment(std::cerr, layout, store, front(store.alignedReadStore).contigId,
+                           0, 1000, 0, 100);
+            swap(store.alignedReadStore, contigAlignedReads);
+
+            std::cerr << "begin/end positions of alignments after update\n";
+            for (TAlignedReadIter it2 = begin(contigAlignedReads, Standard()); it2 != itEnd; ++it2)
+            {
+                typedef Gaps<TReadSeq, AnchorGaps<String<typename TFragmentStore::TReadGapAnchor> > > TReadGaps;
+                TReadGaps readGaps(store.readSeqStore[it2->readId], it2->gaps);
+                std::cerr << "it2->beginPos == " << it2->beginPos << ", it2->endPos == " << it2->endPos << "\n";
+                std::cerr << "    " << source(readGaps) << "\n";
+                if (windowBegin == windowEnd)
+                    SEQAN_ASSERT_EQ((int)(it2->endPos - it2->beginPos), (int)length(readGaps));
+            }
+        }
+        SEQAN_ASSERT_LEQ(windowBegin, windowEnd);
+    }
+
+    // Register round's times.
+    double t = sysTime() - roundStartTime;
+    times.realignTotal += t;
+    times.roundTimes.push_back(t);
+
+    // Print times if configured to do so.
+    if (options.printTiming)
+    {
+        std::cerr << "ANSON-MYERS REALIGNMENT TIMES (s)\n"
+                  << "  main begin contig " << times.mainBeginContig << "\n"
+                  << "  main end contig " << times.mainEndContig << "\n"
+                  << "  main total " << times.mainTotal << "\n"
+                  << "\n"
+                  << "  realign extract profile " << times.realignExtractProfile << "\n"
+                  << "  realign align profile " << times.realignAlign << "\n"
+                  << "  realign integration profile " << times.realignIntegration << "\n"
+                  << "  realign total " << times.realignTotal << "\n"
+                  << "\n"
+                  << "round times";
+        for (unsigned i = 0; i < length(times.roundTimes); ++i)
+            std::cerr << " " << times.roundTimes[i];
+        std::cerr << "\n";
+    }
+
+    if (options.debug)
+        std::cerr << "DONE ROUND WITH windowBegin == " << windowBegin << ", windowEnd == " << windowEnd << "\n";
+}
+
+// ----------------------------------------------------------------------------
+// Function AnsonMyersRealignmentRound_::_updateAlignments()
+// ----------------------------------------------------------------------------
+
+// Return gaps/non-gaps string with c as the non-gaps character.
+template <typename TGapsIter>
+std::string _gapsStructureStr(TGapsIter begin, TGapsIter end)
+{
+    std::stringstream ss;
+    for (; begin != end; ++begin)
+        if (isGap(begin))
+            ss << '-';
+        else
+            ss << *begin;
+    return ss.str();
+}
+
+// Return gaps/non-gaps string with c as the non-gaps character.
+template <typename TGapsIter>
+std::string _profileGapsStructureStr(TGapsIter begin, TGapsIter end)
+{
+    // TGapsIter it = begin;
+    std::stringstream ss;
+    for (; begin != end; ++begin)
+        if (isGap(begin))
+        {
+            ss << '-';
+        }
+        else
+        {
+            ProfileChar<Dna5> y = *begin;
+            unsigned x = getMaxIndex(y);
+            if (x == 5)
+                ss << '=';
+            else
+                ss << Dna5(x);
+        }
+
+    // unsigned i = 0;
+    // for (; it != end; ++it, ++i)
+    // {
+    //     for (unsigned x = 0; x < 5; ++x)
+    //     {
+    //         ProfileChar<Dna5> y = *it;
+    //         // if (y.count[x])
+    //         //     std::cout << "profile[" << i << "].count[ordValue(Dna5('" << Dna5(x) << "'))] = "
+    //         //               << y.count[x] << ";\n";
+    //         // if (y.count[5])
+    //         //     std::cout << "profile[" << i << "].count[valueSize<Dna5>()] = " << y.count[5] << ";\n";
+    //     }
+    // }
+
+    return ss.str();
+}
+
+template <typename TFragmentStore>
+void AnsonMyersRealignmentRound_<TFragmentStore>::_updateAlignments(
+        unsigned windowBegin,
+        unsigned & windowEnd,  // only updated
+        TProfileString & profilePart,
+        // Align<TProfileString> /*const*/ & align,
+        Gaps<TProfileString> /*const*/ & profileGaps,
+        Gaps<TReadSeq> /*const*/ & readGaps,
+        ExtractProfileInfo_ & info,
+        WindowClippingInfo_ const & _windowInfo,
+        TAlignedReadIter const & it)
+{
+    WindowClippingInfo_ windowInfo = _windowInfo;
+
+    // typedef Align<TProfileString> TAlign;
+    // typedef typename Row<TAlign>::Type TGaps;
+    // typedef typename Iterator<TGaps, Standard>::Type TGapsIter;
+    typedef Gaps<TProfileString> TProfileGaps;
+    typedef typename Iterator<TProfileGaps>::Type TProfileGapsIter;
+    typedef Gaps<TReadSeq> TReadGaps;
+    typedef typename Iterator<TReadGaps>::Type TReadGapsIter;
+
+    // Get copy of aligned read element.
+    TAlignedReadElement el = *it, el2 = *it;
+
+    // We build a new profile part.
+    TProfileString newProfilePart;
+    // reserve(newProfilePart, length(source(row(align, 0))));
+    reserve(newProfilePart, length(source(profileGaps)));
+
+    // Get iterators of alignment for profile (horizontal) and read (vertical).
+    TProfileGapsIter itP = begin(profileGaps, Standard());
+    TProfileGapsIter itPEnd = end(profileGaps, Standard());
+    TReadGapsIter itR = begin(readGaps, Standard());
+    TReadGapsIter itREnd = end(readGaps, Standard());
+    // TGapsIter itP = begin(row(align, 0), Standard());
+    // TGapsIter itPEnd = end(row(align, 0), Standard());
+    // TGapsIter itR = begin(row(align, 1), Standard());
+    // TGapsIter itREnd = end(row(align, 1), Standard());
+
+    if (options.debug)
+    {
+        std::string str = _profileGapsStructureStr(itP, itPEnd);
+        std::cerr << "PROFILE GAPS\t" << str << "\n"
+                  << "READ GAPS   \t" << _gapsStructureStr(itR, itREnd) << "\n";
+    }
+
+    // Flags whether we are (possibly) in the initial or the trailing gap in the read/profile.
+    bool inLeadingGapR = true, inLeadingGapP = true;
+    if (windowInfo.clipLeft)
+        inLeadingGapR = false;  // at least one base precedes current
+    bool inTrailingGapR = false, inTrailingGapP = false;
+    // Number of remaining alignment columns.
+    // unsigned remainingCols = length(row(align, 0));
+    unsigned remainingCols = length(profileGaps);
+
+    // Reset begin/end position of alignment in profile
+    info.aliBeginPos = info.aliEndPos = 0;
+
+    // Construct read gaps, clear gaps from current alignment clipping (we get this through windowInfo) and keep a
+    // counter for the position in the read gaps.  This is done by using a second copy since iterating and removing is
+    // broken somehow.
+    //
+    // TODO(holtgrew): Iteration really broken after removal?
+    typedef Gaps<TReadSeq, AnchorGaps<String<typename TFragmentStore::TReadGapAnchor> > > TAnchorReadGaps;
+    TAnchorReadGaps anchorReadGaps(store.readSeqStore[el.readId], el.gaps);
+    {
+        TAnchorReadGaps anchorReadGaps2(store.readSeqStore[el2.readId], el2.gaps);
+        if (options.debug)
+            std::cerr << "removing gaps from " << windowInfo.readAliBeginPos << " to " << windowInfo.readAliEndPos
+                      << "\n"
+                      << "    from " << anchorReadGaps << "\n";
+        clearGaps(anchorReadGaps);
+        setClippedBeginPosition(anchorReadGaps, windowInfo.readEndPos);
+        setClippedBeginPosition(anchorReadGaps2, windowInfo.readAliEndPos);
+        if (options.debug)
+            std::cerr << "copying gaps from >>" << anchorReadGaps2 << "<< to >>" << anchorReadGaps << "<<\n";
+        copyGaps(anchorReadGaps, anchorReadGaps2);
+        clearClipping(anchorReadGaps);
+        clearClipping(anchorReadGaps2);
+
+        setClippedEndPosition(anchorReadGaps, windowInfo.readBeginPos);
+        setClippedEndPosition(anchorReadGaps2, windowInfo.readAliBeginPos);
+        if (options.debug)
+            std::cerr << "copying gaps from >>" << anchorReadGaps2 << "<< to >>" << anchorReadGaps << "<<\n";
+        copyGaps(anchorReadGaps, anchorReadGaps2);
+        clearClipping(anchorReadGaps);
+        clearClipping(anchorReadGaps2);
+        windowInfo.readAliEndPos -= (length(anchorReadGaps2) - length(anchorReadGaps));
+        if (options.debug)
+            std::cerr << "resulted in window on read " << windowInfo.readAliBeginPos << " to "
+                      << windowInfo.readAliEndPos << "\n"
+                      << "    for  " << anchorReadGaps << "\n";
+    }
+    int readGapsPos = windowInfo.readAliBeginPos;
+
+    // Position in contig's multi-read alignment.
+    unsigned pos = info.profBeginPos;
+
+    // Iterate over both profile and read gaps and add the read bases back to the profile.  In case of new gaps, we have
+    // to add a gap to the read alignments and also to the profile (as a new profile char).
+    //
+    // We record the positions of all-gaps columns and remove them later.  We also insert all-gaps columns into *it and
+    // remove it together with the rest of the alignment.
+    seqan::String<unsigned> gapPositions;
+    for (; itP != itPEnd;)
+    {
+        SEQAN_ASSERT_NOT_MSG(isGap(itP) && isGap(itR), "No all-gaps columns in pairwise alignment.");
+
+        // Without a countTrailingGaps() function, this is the best way to check whether we are in the trailing gap.
+        inTrailingGapR = (inTrailingGapR || countGaps(itR) >= remainingCols);
+        if (windowInfo.clipRight)
+            inTrailingGapR = false;  // at least one base follows
+        inTrailingGapP = (inTrailingGapP || countGaps(itP) >= remainingCols);
+
+        if (isGap(itP))
+        {
+            // Case 1: gap in profile.
+            //
+            // Determine number of gaps in the profile/characters in the read and advance that far in profile and
+            // multi-read alignment.  Extend the profile, adding the characters from the read alignment.  We need to
+            // insert a gap in the whole multi-read alignment.
+            unsigned numChars = std::min(countGaps(itP), countCharacters(itR));
+            for (unsigned i = 0; i < numChars; ++i, ++itR, ++pos)
+            {
+                appendValue(newProfilePart, TProfileChar());  // new empty profile character
+                TAlphabet x = *itR;
+                back(newProfilePart).count[ordValue(x)] += 1;
+                int numGaps = _insertGap(contigAlignedReads, pos, it);
+                if (options.debug)
+                    std::cerr << "inTrailingGapP == " << inTrailingGapP << "\n"
+                              << "insertGap(contigAlignedRead, " << pos << ") == " << numGaps << "\n";
+                if (windowBegin != windowEnd && !inTrailingGapP)
+                    windowEnd += 1;  // gap inserted into profile/msa, increase window size
+                back(newProfilePart).count[valueSize<TAlphabet>()] += numGaps;
+                ++readGapsPos;
+            }
+            // Batch-update the profile gaps iterator and remaining column count.
+            itP += numChars;
+            remainingCols -= numChars;
+            // We cannot be in the leading profile gap any more.
+            inLeadingGapR = false;
+            // Extend read alignment position.
+            info.aliEndPos += numChars;
+            if (options.debug)
+                std::cerr << "info.aliEndPos += " << numChars << " == " << info.aliEndPos << "\n";
+        }
+        else if (isGap(itR))
+        {
+            // Case 2: gap in read (but not in profile, see assertion above).
+            //
+            // Determine number of gaps in the read/characters in the profile and advance that far in profile and
+            // multi-read alignment.  Extend the profile, adding the gap from the read if we are neither in the leading
+            // nore in the trailing part of the read's alignment row.
+            unsigned numChars = std::min(countCharacters(itP), countGaps(itR));
+            for (unsigned i = 0; i < numChars; ++i, ++itP, ++pos)
+            {
+                TProfileChar p = *itP;  // TODO(holtgrew): Copy because of proxy issues.
+                appendValue(newProfilePart, p);
+                if (!inLeadingGapR && !inTrailingGapR)
+                {
+                    back(newProfilePart).count[valueSize<TAlphabet>()] += 1;
+                    if (options.debug)
+                        std::cerr << "insertGap(anchorReadGaps, " << readGapsPos << ")\n";
+                    insertGap(anchorReadGaps, readGapsPos++);
+                    if (!inTrailingGapR)
+                    {
+                        info.aliEndPos += 1;
+                        if (options.debug)
+                            std::cerr << "info.aliEndPos += 1 == " << info.aliEndPos << "\n";
+                    }
+                }
+                if (empty(p))
+                    appendValue(gapPositions, pos);
+            }
+            // Batch-update the read gaps iterator and remaining column count.
+            itR += numChars;
+            remainingCols -= numChars;
+            // We cannot be in the leading gap of the profile any more.
+            inLeadingGapP = false;
+            // If we are in the leading gap of the read, it begins (and ends) yet some character further to the right.
+            if (inLeadingGapR)
+            {
+                info.aliBeginPos += numChars;
+                info.aliEndPos += numChars;
+                if (options.debug)
+                    std::cerr << "info.aliBeginPos += " << numChars << " == " << info.aliBeginPos << "\n"
+                              << "info.aliEndPos += " << numChars << " == " << info.aliEndPos << "\n";
+            }
+        }
+        else
+        {
+            // Case 3: characters in both read and profile.
+            //
+            // Append the new character to the profile we create and update the counts.
+            TProfileChar p = *itP;  // TODO(holtgrew): copy because of proxy issues
+            appendValue(newProfilePart, p);
+            TAlphabet x = *itR;
+            back(newProfilePart).count[ordValue(x)] += 1;
+            // Advance in profile and read row of alignment.
+            ++itP;
+            ++itR;
+            // Advance in the read gaps and the position in the multi-read alignment.
+            ++readGapsPos;
+            ++pos;
+            // One more character in read alignment and one fewer column to go.
+            ++info.aliEndPos;
+            --remainingCols;
+            // Cannot be in leadin gaps any more.
+            inLeadingGapR = inLeadingGapP = false;
+        }
+    }
+
+    // Must be both at the end of the read and the profile alignment.
+    SEQAN_ASSERT(itR == itREnd);
+    SEQAN_ASSERT(itP == itPEnd);
+    if (options.debug)
+        std::cerr << "windowEnd == " << windowEnd << "\n";
+
+    // -----------------------------------------------------------------------
+    // Update the read alignment, write out new profile.
+    // -----------------------------------------------------------------------
+
+    // The read alignment in *it might have been updated in the process.  We update the position from info and the gaps
+    // from el and info and windowInfo.
+
+    if (options.debug)
+        std::cerr << "REPLACING\tit->beginPos == " << it->beginPos << ", it->endPos == " << it->endPos << "\n";
+    it->beginPos = info.profBeginPos + info.aliBeginPos - windowInfo.readAliBeginPos;
+    it->endPos = it->beginPos + length(anchorReadGaps);
+    swap(it->gaps, el.gaps);
+
+    if (options.debug)
+        std::cerr << "it->profBeginPos == " << info.profBeginPos << ", info.aliBeginPos == "
+                  << info.aliBeginPos << "\n"
+                  << "it->profEndPos == " << info.profEndPos << ", info.aliEndPos == " << info.aliEndPos << "\n"
+                  << "windowInfo.readAliBeginPos == " << windowInfo.readAliBeginPos
+                  << ", windowInfo.readAliEndPos == " << windowInfo.readAliEndPos << "\n"
+                  << "it->beginPos == " << it->beginPos << ", it->endPos == " << it->endPos << "\n";
+    int newContigProfileLength = length(contigProfile) + length(newProfilePart) - length(profilePart);
+    (void)newContigProfileLength;  // only used for assertion
+    SEQAN_ASSERT_LEQ(it->beginPos, newContigProfileLength);
+    SEQAN_ASSERT_LEQ(it->endPos, newContigProfileLength);
+    // SEQAN_ASSERT_EQ(it->endPos - it->beginPos, length(row(align, 0))); // TODO(holtgrew): Remove!
+
+    // Write out the new profile.
+    swap(newProfilePart, profilePart);
+
+    // -----------------------------------------------------------------------
+    // Remove all-gaps columns.
+    // -----------------------------------------------------------------------
+
+    if (options.debug && !empty(gapPositions))
+        std::cerr << "removing all-gaps columns\n";
+    for (unsigned i = 0; i < length(gapPositions); ++i)
+    {
+        if (options.debug)
+            std::cerr << "removeGaps(contigAlignedReads, " << (gapPositions[i] - i)
+                      << ") (info.profBeginPos == " << info.profBeginPos << ")\n";
+        removeGap(contigAlignedReads, gapPositions[i] - i);
+        SEQAN_ASSERT(empty(profilePart[gapPositions[i] - i - info.profBeginPos]));
+        erase(profilePart, gapPositions[i] - i - info.profBeginPos);
+        if (windowBegin != windowEnd)
+            windowEnd -= 1;  // gap removed from profile/MSA, decrease window size
+    }
+
+#if SEQAN_ENABLE_TESTING
+    {
+        TAnchorReadGaps anchorReadGaps2(store.readSeqStore[it->readId], it->gaps);
+        if (options.debug)
+            std::cerr << "anchorReadGaps == " << anchorReadGaps2 << "\n";
+        SEQAN_ASSERT_EQ(it->endPos - it->beginPos, (int)length(anchorReadGaps2));
+    }
+#endif  // #if SEQAN_ENABLE_TESTING
+}
+
+// ----------------------------------------------------------------------------
+// Function reAlignment()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn reAlignment
+ * @headerfile <seqan/realign.h>
+ * @brief Perform realignment on a @link FragmentStore @endlink object.
+ *
+ * @signature void reAlignment(store, contigID, realignmentMethod, bandwidth, includeReference[,
+ *                             windowBegin, windowEnd][, debug][, printTiming]);
+ *
+ * @param[in,out] store             The @link FragmentStore @endlink to perform realignment for.
+ * @param[in]     realignmentMethod The realignment algorithm to use, <tt>1</tt> for affine gap costs, <tt>0</tt>
+ *                                  for linear gap costs, affine gap costs are recommended, <tt>unsigned</tt>.
+ * @param[in]     contigID          Identifier of the contig to realign, <tt>unsigned</tt>
+ * @param[in]     bandwidth         Bandwidth to use in the pairwise DP alignment algorithms <tt>unsigned</tt>.
+ * @param[in]     includeReference  A <tt>bool</tt>, if <tt>true</tt> then the reference will be included as a
+ *                                  pseudo-read to increase stability in case of indels.  See section "Including
+ *                                  the Reference" for details.
+ * @param[in]     windowBegin       Optional <tt>unsigned</tt> window begin for windowed alignment,
+ *                                  default: <tt>0</tt>, i.e. no windowing.  Also see section "Windowed
+ *                                  Realignment" below.
+ * @param[in]     windowEnd         Optional <tt>unsigned</tt> window end for windowed alignment, default: <tt>0</tt>,
+ *                                  i.e. no windowing.  Also see section "Windowed Realignment" below.
+ * @param[in]     debug             Optional <tt>bool</tt> to enable verbose logging, default: <tt>false</tt>.
+ * @param[in]     printTiming       Optional <tt>bool</tt> to enable printing of times, default: <tt>false</tt>.
+ *
+ * This function implements a variant of the Anson-Myers algorithm to refine the multi-read alignments.  The algorithm
+ * works in a round-robin fashion:
+ *
+ * First, the profile sequence is created for the multi-read alignment.  The algorithm then works in round.
+ *
+ * In each round, each read alignment is selected, removed from the profile and then aligned against the profile using
+ * a DP algorithm.  For this alignment, a region of <tt>bandwidth / 2</tt> positions around the previous alignment
+ * locus is chosen and aligned using a bandwidth of <tt>bandwidth</tt> in the DP alignment algorithm.  The profile is
+ * then updated with the resulting pairwise alignment.  This is iterated until the global alignment score does not
+ * improve.
+ *
+ * In the end, the reference sequence of the given contig is replaced by the consensus of the multi-read alignment.
+ *
+ * @section Including the Reference
+ *
+ * You can choose to include the reference sequence of the selected contig as a pseudo-read.  In this case, the
+ * reference sequence of the selected contig will be added as an additional read and also a read alignment will be
+ * created for it.  The appended pseudo-read will have the highest read ID in the store.
+ *
+ * @section Windowed Realignment
+ *
+ * Sometimes, it is useful to just realign a part of the fragment store.  This can be done by using the parameters
+ * <tt>windowBegin</tt> and <tt>windowEnd</tt>.  This refers to view positions in the current multi-read alignment.
+ * Set both to <tt>0</tt> (also the default) to disalbe windowed realignment.
+ *
+ * @section References
+ *
+ * <ul><li>Anson, Eric L., and Eugene W. Myers. "ReAligner: a program for refining DNA sequence multi-alignments."
+ *         Journal of Computational Biology 4.3 (1997): 369-383.</li></ul>
+ */
+
+template <typename TSpec, typename TConfig>
+void reAlignment(FragmentStore<TSpec, TConfig> & store,
+                 unsigned contigID,
+                 unsigned realignmentMethod,
+                 unsigned bandwidth,
+                 bool includeReference,
+                 unsigned windowBegin = 0,
+                 unsigned windowEnd = 0,
+                 bool debug = false,
+                 bool printTiming = false)
+{
+    RealignmentOptions_ options;
+    options.method = realignmentMethod ? RealignmentOptions_::ANSON_MYERS_GOTOH : RealignmentOptions_::ANSON_MYERS_NW;
+    options.bandwidth = bandwidth;
+    options.environment = bandwidth / 2;
+    options.includeReference = includeReference;
+    options.debug = debug;
+    options.printTiming = printTiming;
+
+    AnsonMyersRealigner_<FragmentStore<TSpec, TConfig> > realigner(store, options);
+    realigner.run(contigID, windowBegin, windowEnd);
+}
+
+template <typename TSpec, typename TConfig, typename TScore>
+void reAlignment(FragmentStore<TSpec, TConfig> & store,
+                 TScore & score,
+                 unsigned contigID,
+                 unsigned realignmentMethod,
+                 unsigned bandwidth,
+                 bool includeReference,
+                 unsigned windowBegin = 0,
+                 unsigned windowEnd = 0,
+                 bool debug = false,
+                 bool printTiming = false)
+{
+    (void)score;
+    reAlignment(store, contigID, realignmentMethod, bandwidth, includeReference, windowBegin, windowEnd, debug,
+                printTiming);
+}
+
+}  // namespace seqan
+
+#endif  // INCLUDE_SEQAN_REALIGN_REALIGN_BASE_H_
diff --git a/seqan/realign/realign_helper_functions.h b/seqan/realign/realign_helper_functions.h
new file mode 100644
index 0000000..fb4cbbe
--- /dev/null
+++ b/seqan/realign/realign_helper_functions.h
@@ -0,0 +1,205 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_REALIGN_REALIGN_HELPER_FUNCTIONS_H_
+#define INCLUDE_SEQAN_REALIGN_REALIGN_HELPER_FUNCTIONS_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+template <typename TPos, typename TGapAnchor, typename TSpec, typename TGapPos>
+inline bool  // true if removed gap that is not leading/trailing gap
+_removeGap2(AlignedReadStoreElement<TPos, TGapAnchor, TSpec> & alignedRead,
+            TGapPos const gapPos)
+{
+    typedef String<TGapAnchor> TGaps;
+    typedef typename Iterator<TGaps, Standard>::Type TGapIter;
+    if (gapPos < (TGapPos) alignedRead.beginPos)
+    {
+        --alignedRead.beginPos; --alignedRead.endPos;
+    }
+    else if (gapPos < (TGapPos) alignedRead.endPos)
+    {
+        --alignedRead.endPos;
+        TGapIter gapIt = upperBoundGapAnchor(alignedRead.gaps, gapPos - alignedRead.beginPos, SortGapPos());
+        TGapIter gapItEnd = end(alignedRead.gaps, Standard());
+        // Note: We might create empty gaps here
+        for(; gapIt != gapItEnd; ++gapIt)
+            --(gapIt->gapPos);
+        return true;
+    }
+    return false;
+}
+
+// Returns number of returned gaps.
+template <typename TAlignedReads, typename TSpec, typename TGapPos, typename TAlignedReadIt>
+inline int
+_removeGap(String<TAlignedReads, TSpec>& alignedReadStore,
+           TGapPos const gapPos,
+           TAlignedReadIt const & skipIt)
+{
+    typedef String<TAlignedReads, TSpec> TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
+    int result = 0;
+
+    TAlignIter alignIt = begin(alignedReadStore, Standard());
+    TAlignIter alignItEnd = end(alignedReadStore, Standard());
+    for(;alignIt != alignItEnd; ++alignIt)
+        if (alignIt != skipIt)
+            result += _removeGap2(*alignIt, gapPos);
+    return result;
+}
+
+template <typename TAlignedReads, typename TSpec, typename TGapPos, typename TAlignedReadIt>
+inline int
+_insertGap(String<TAlignedReads, TSpec>& alignedReadStore,
+           TGapPos const gapPos,
+           TAlignedReadIt const & skipIt)
+{
+    typedef String<TAlignedReads, TSpec> TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
+
+    int numGaps = 0;
+    TAlignIter alignIt = begin(alignedReadStore, Standard());
+    TAlignIter alignItEnd = end(alignedReadStore, Standard());
+    for(;alignIt != alignItEnd; ++alignIt)
+        if (alignIt != skipIt)
+            numGaps += insertGap(*alignIt, gapPos);
+    return numGaps;
+}
+
+// ----------------------------------------------------------------------------
+// Helper Function _printProfile()
+// ----------------------------------------------------------------------------
+
+// 0   - space
+// 1-9 - 1..9
+// >10 - '!' + ceil(log(count))
+inline char _countToLogChar(int count)
+{
+    if (count <= 0)
+        return ' ';
+    else if (count <= 9)
+        return '0' + count;
+    else
+        return '!' + int(ceil(log10(1.0 * count)));
+}
+
+template <typename TStream, typename TAlphabet, typename TSpec>
+void _printProfile(TStream & stream,
+                   String<ProfileChar<TAlphabet>, TSpec> const & profile)
+{
+    stream << "PROFILE (0 - space, 1..9 - 1..9, >10 - ! + int(ceil(log10(count)))\n"
+           << "------------------------------------------------------------------\n";
+
+    stream << "   ";
+    for (unsigned i = 0 ; i < length(profile); ++i)
+    {
+        if (i % 10 == 0)
+            stream << (i / 100) % 10;
+        else if (i % 5 == 0)
+            stream << (i / 100) % 10;
+        else
+            stream << ' ';
+    }
+    stream << "\n";
+
+    stream << "   ";
+    for (unsigned i = 0 ; i < length(profile); ++i)
+    {
+        if (i % 10 == 0)
+            stream << (i / 10) % 10;
+        else if (i % 5 == 0)
+            stream << (i / 10) % 10;
+        else
+            stream << ' ';
+    }
+    stream << "\n";
+
+    stream << "   ";
+    for (unsigned i = 0 ; i < length(profile); ++i)
+    {
+        if (i % 10 == 0)
+            stream << '0';
+        else if (i % 5 == 0)
+            stream << '5';
+        else
+            stream << ' ';
+    }
+    stream << "\n";
+
+    stream << "   ";
+    for (unsigned i = 0 ; i < length(profile); ++i)
+    {
+        if (i % 10 == 0)
+            stream << ':';
+        else if (i % 5 == 0)
+            stream << '.';
+        else
+            stream << ' ';
+    }
+    stream << "\n";
+
+    for (unsigned i = 0; i <= valueSize<TAlphabet>(); ++i)
+    {
+        if (i == valueSize<TAlphabet>())
+            stream << "-: ";
+        else
+            stream << TAlphabet(i) << ": ";
+
+        for (unsigned j = 0; j < length(profile); ++j)
+            stream << _countToLogChar(profile[j].count[i]);
+
+        stream << "\n";
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_REALIGN_REALIGN_HELPER_FUNCTIONS_H_
diff --git a/seqan/reduced_aminoacid.h b/seqan/reduced_aminoacid.h
new file mode 100644
index 0000000..ece4bf1
--- /dev/null
+++ b/seqan/reduced_aminoacid.h
@@ -0,0 +1,55 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Module with reduced versions of alphabets
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_H_
+#define SEQAN_REDUCED_AMINOACID_H_
+
+#include <seqan/basic.h>
+#include <seqan/score.h>
+
+#include <seqan/reduced_aminoacid/reduced_aminoacid_base.h>
+
+#include <seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h>
+#include <seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h>
+
+// #include <seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h>
+// #include <seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h>
+// #include <seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h>
+// #include <seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h>
+
+#include <seqan/reduced_aminoacid/reduced_aminoacid_base_late.h>
+
+#endif // def SEQAN_REDUCED_AMINOACID_H_
diff --git a/seqan/reduced_aminoacid/reduced_aminoacid_base.h b/seqan/reduced_aminoacid/reduced_aminoacid_base.h
new file mode 100644
index 0000000..a53f1e9
--- /dev/null
+++ b/seqan/reduced_aminoacid/reduced_aminoacid_base.h
@@ -0,0 +1,134 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Reduced Versions of the 24-letter amino acid alphabet
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_BASE_H_
+#define SEQAN_REDUCED_AMINOACID_BASE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Tag ReducedAminoAcid
+// -----------------------------------------------------------------------
+
+/*!
+ * @class ReducedAminoAcid
+ * @extends SimpleType
+ * @brief Reduced versions of the amino acid alphabet.
+ * @headerfile seqan/reduced_aminoacid.h
+ *
+ * @signature template <typename TReductionSpec>
+ * using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TReductionSpec> >;
+ *
+ * @tparam TReductionSpec Currently only @link Murphy10 @endlink available
+ *
+ * @section Remarks
+ *
+ * The alias template is only available when SEQAN_CXX11_STANDARD is defined
+ * and your compiler supports alias templates (Visual Studio >= 2006-2014, any fairly
+ * recent Clang, GCC). Otherwise you have to use the underscored type and
+ * the full definition, i.e.
+ * <tt>SimpleType&lt;unsigned char, ReducedAminoAcid_&lt;TReductionSpec&gt; &gt;</tt>.
+ *
+ * @see Murphy10
+ */
+
+template <typename TRedSpec>
+struct ReducedAminoAcid_ {};
+
+#if defined (SEQAN_CXX11_STANDARD) && ( !defined (_MSC_VER) || _MSC_VER >= 1800 )
+template <typename TRedSpec>
+using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >;
+#endif
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Metafunction CompareType
+// -----------------------------------------------------------------------
+
+template <typename TRedSpec>
+struct CompareType<SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >,
+                   __uint8>
+{
+    typedef SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> > Type;
+};
+
+template <typename TRedSpec>
+struct CompareType<SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >,
+                   char>
+{
+    typedef SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> > Type;
+};
+
+template <typename TRedSpec>
+struct CompareType<SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >,
+                   AminoAcid>
+{
+    typedef SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> > Type;
+};
+
+// -----------------------------------------------------------------------
+// Translation Tables (implementations see extra files)
+// -----------------------------------------------------------------------
+
+template <typename TRedSpec, typename TSpec = void>
+struct TranslateTableCharToRedAA_;
+
+template <typename TRedSpec, typename TSpec = void>
+struct TranslateTableAAToRedAA_;
+
+template <typename TRedSpec, typename TSpec = void>
+struct TranslateTableByteToRedAA_;
+
+template <typename TRedSpec, typename TSpec = void>
+struct TranslateTableRedAAToChar_;
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}
+#endif // def SEQAN_REDUCED_AMINOACID_BASE_H_
diff --git a/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h b/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h
new file mode 100644
index 0000000..9d51b07
--- /dev/null
+++ b/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h
@@ -0,0 +1,107 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Reduced Versions of the 24-letter amino acid alphabet
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_BASE_LATE_H_
+#define SEQAN_REDUCED_AMINOACID_BASE_LATE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Function unknownValueImpl()
+// -----------------------------------------------------------------------
+
+template <typename TRedSpec>
+inline SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >
+unknownValueImpl(SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> > *)
+{
+    static const SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >
+      _result = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >('X');
+    return _result;
+}
+
+// -----------------------------------------------------------------------
+// Function assign()
+// -----------------------------------------------------------------------
+
+template <typename TRedSpec>
+inline void assign(char & c_target, SimpleType<unsigned char,
+                   ReducedAminoAcid_<TRedSpec> > const & source)
+{
+    c_target = TranslateTableRedAAToChar_<TRedSpec>::VALUE[source.value];
+}
+
+template <typename TRedSpec>
+inline void assign(SimpleType<unsigned char,
+                   ReducedAminoAcid_<TRedSpec> > & target,
+                   __uint8 c_source)
+{
+    target.value = TranslateTableByteToRedAA_<TRedSpec>::VALUE[c_source];
+}
+
+template <typename TRedSpec>
+inline void assign(SimpleType<unsigned char,
+                   ReducedAminoAcid_<TRedSpec> > & target,
+                   char c_source)
+{
+    target.value = TranslateTableCharToRedAA_<TRedSpec>::VALUE[(unsigned char) c_source];
+}
+
+template <typename TRedSpec>
+inline void assign(SimpleType<unsigned char,
+                   ReducedAminoAcid_<TRedSpec> > & target,
+                   AminoAcid c_source)
+{
+    target.value = TranslateTableAAToRedAA_<TRedSpec>::VALUE[c_source.value];
+}
+
+}
+#endif // def SEQAN_REDUCED_AMINOACID_BASE_LATE_H_
diff --git a/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h b/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h
new file mode 100644
index 0000000..a07d62b
--- /dev/null
+++ b/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h
@@ -0,0 +1,135 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Reduced Versions of the 24-letter amino acid alphabet
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_CLUSTER_RED_BASE_H_
+#define SEQAN_REDUCED_AMINOACID_CLUSTER_RED_BASE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Tag ClusterReduction
+// -----------------------------------------------------------------------
+
+/*
+ * @class ClusterReduction
+ * @brief Specialization for @link ReducedAminoAcid @endlink
+ * @headerfile seqan/reduced_aminoacid.h
+ *
+ * @signature template <unsigned char n, unsigned char m = 24, typename TMatrix = Blosum62>
+ * struct ClusterReduction;
+ *
+ * @tparam n the size of the reduced alphabet (between 2 and m-1)
+ * @tparam m size to truncate alphabet to, <b>before</b> clustering
+ * (one of 20, 22, 24; default 24)
+ * @tparam TMatrix Matrix used for clustering (default @link Blosum62 @endlink,
+ * none other supported right now)
+ *
+ * @section WhenToUse
+ *
+ * Use m = 24 when you expect 'X' and '*' in the dataset you reduce
+ * from. This is especially the case on translated genomic reads.
+ *
+ * If you have validated protein sequences, you can use can use m = 20 or
+ * m = 22, which will not include special characters (see
+ * @link AminoAcid @endlink for details).
+ *
+ * @section Background
+ *
+ * The method employed for reducing the alphabet is similar to Murphy et al,
+ * 2000, <a href="http://www.ncbi.nlm.nih.gov/pubmed/10775656">http://www.ncbi.nlm.nih.gov/pubmed/10775656</a>
+ *
+ * Correlation coefficients for the Blosum62 scores of all pairs of amino
+ * acids in the alphabet were computed and clustered with WPGMA (using
+ * UPGMA as second criterium when WPGMA yields the same
+ * distance between two clusters).
+ *
+ * <img src="ClusterReduction.png">
+ *
+ * The exact clustering for m = 24.
+ *
+ */
+
+template <unsigned char n, unsigned char m = 24, typename TMatrix = Blosum62>
+struct ClusterReduction;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Metafunction ValueSize
+// -----------------------------------------------------------------------
+
+template <unsigned char n, unsigned char m, typename TMatrix>
+struct ValueSize<
+        SimpleType<unsigned char,
+                   ReducedAminoAcid_<ClusterReduction<n, m, TMatrix> > > >
+{
+    typedef uint8_t Type;
+    static const Type VALUE = n;
+};
+
+// -----------------------------------------------------------------------
+// Metafunction BitPerValue
+// -----------------------------------------------------------------------
+
+template <unsigned char n, unsigned char m, typename TMatrix>
+struct BitsPerValue<
+         SimpleType<unsigned char,
+                    ReducedAminoAcid_<ClusterReduction<n, m, TMatrix> > > >
+{
+    typedef uint8_t Type;
+    static const Type VALUE = Log2<n>::VALUE;
+};
+
+// -----------------------------------------------------------------------
+// Translation Tables (implementations see extra files)
+// -----------------------------------------------------------------------
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}
+#endif // def SEQAN_REDUCED_AMINOACID_CLUSTER_RED_BASE_H_
diff --git a/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h b/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h
new file mode 100644
index 0000000..27153f4
--- /dev/null
+++ b/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h
@@ -0,0 +1,1853 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Reduced Versions of the 22-letter amino acid alphabet
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_20_to_n_B62_H_
+#define SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_20_to_n_B62_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ========================== DECLARATIONS FIRST ===========================
+
+// ---------------------------------- N = 19 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<19, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<19, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<19, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<19, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<19, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 18 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<18, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<18, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<18, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<18, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<18, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 17 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<17, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<17, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<17, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<17, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<17, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 16 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<16, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<16, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<16, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<16, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<16, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 15 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<15, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<15, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<15, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<15, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<15, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 14 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<14, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<14, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<14, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<14, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<14, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 13 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<13, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<13, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<13, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<13, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<13, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 12 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<12, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<12, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<12, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<12, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<12, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 11 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<11, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<11, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<11, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<11, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<11, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 10 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<10, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<10, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<10, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<10, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<10, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 9 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<9, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<9, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<9, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<9, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<9, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 8 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<8, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<8, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<8, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<8, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<8, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 7 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<7, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<7, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<7, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<7, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<7, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 6 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<6, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<6, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<6, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<6, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<6, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 5 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<5, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<5, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<5, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<5, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<5, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 4 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<4, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<4, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<4, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<4, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<4, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 3 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<3, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<3, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<3, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<3, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<3, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 2 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<2, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<2, 20, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<2, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<2, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<2, 20, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 19 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<19, 20, Blosum62>, TVoidSpec>::VALUE[19] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D
+    'C', // C
+    'Q', // Q
+    'E', // E
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y'  // Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<19, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  4,  3,  6, 13,  7,  8,  9,  0,
+    11, 10, 12,  2,  0, 14,  5,  1, 15, 16,  0,  9, 17,  0, 18,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  3,  6, 13,  7,  8,
+     9,  0, 11, 10, 12,  2,  0, 14,  5,  1, 15, 16,  0,  9, 17,
+     0, 18,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<19, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,
+    12, 13, 14, 15, 16, 17, 18,  9,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<19, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 18 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<18, 20, Blosum62>, TVoidSpec>::VALUE[18] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D
+    'C', // C
+    'Q', // Q
+    'E', // E
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L M
+    'K', // K
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y'  // Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<18, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  4,  3,  6, 12,  7,  8,  9,  0,
+    11, 10, 10,  2,  0, 13,  5,  1, 14, 15,  0,  9, 16,  0, 17,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  3,  6, 12,  7,  8,
+     9,  0, 11, 10, 10,  2,  0, 13,  5,  1, 14, 15,  0,  9, 16,
+     0, 17,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<18, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,
+    10, 12, 13, 14, 15, 16, 17,  9,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<18, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 17 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<17, 20, Blosum62>, TVoidSpec>::VALUE[17] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N
+    'D', // D
+    'C', // C
+    'Q', // Q
+    'E', // E
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y'  // Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<17, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  4,  3,  6, 11,  7,  8,  9,  0,
+     1, 10, 10,  2,  0, 12,  5,  1, 13, 14,  0,  9, 15,  0, 16,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  3,  6, 11,  7,  8,
+     9,  0,  1, 10, 10,  2,  0, 12,  5,  1, 13, 14,  0,  9, 15,
+     0, 16,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<17, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10,  1,
+    10, 11, 12, 13, 14, 15, 16,  9,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<17, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 16 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<16, 20, Blosum62>, TVoidSpec>::VALUE[16] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N
+    'D', // D
+    'C', // C
+    'Q', // Q E
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y'  // Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<16, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  4,  3,  5, 10,  6,  7,  8,  0,
+     1,  9,  9,  2,  0, 11,  5,  1, 12, 13,  0,  8, 14,  0, 15,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  3,  5, 10,  6,  7,
+     8,  0,  1,  9,  9,  2,  0, 11,  5,  1, 12, 13,  0,  8, 14,
+     0, 15,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<16, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  9,  1,
+     9, 10, 11, 12, 13, 14, 15,  8,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<16, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 15 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<15, 20, Blosum62>, TVoidSpec>::VALUE[15] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N
+    'D', // D
+    'C', // C
+    'Q', // Q E
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L M
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W'  // W
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<15, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  4,  3,  5, 10,  6,  7,  8,  0,
+     1,  9,  9,  2,  0, 11,  5,  1, 12, 13,  0,  8, 14,  0, 10,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  3,  5, 10,  6,  7,
+     8,  0,  1,  9,  9,  2,  0, 11,  5,  1, 12, 13,  0,  8, 14,
+     0, 10,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<15, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  9,  1,
+     9, 10, 11, 12, 13, 14, 10,  8,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<15, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 14 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<14, 20, Blosum62>, TVoidSpec>::VALUE[14] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N
+    'D', // D
+    'C', // C
+    'Q', // Q E
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W'  // W
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<14, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  4,  3,  5,  9,  6,  7,  8,  0,
+     1,  8,  8,  2,  0, 10,  5,  1, 11, 12,  0,  8, 13,  0,  9,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  3,  5,  9,  6,  7,
+     8,  0,  1,  8,  8,  2,  0, 10,  5,  1, 11, 12,  0,  8, 13,
+     0,  9,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<14, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  8,  1,
+     8,  9, 10, 11, 12, 13,  9,  8,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<14, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 13 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<13, 20, Blosum62>, TVoidSpec>::VALUE[13] =
+{
+    'A', // A
+    'R', // R Q E K
+    'N', // N
+    'D', // D
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W'  // W
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<13, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  4,  3,  1,  8,  5,  6,  7,  0,
+     1,  7,  7,  2,  0,  9,  1,  1, 10, 11,  0,  7, 12,  0,  8,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  3,  1,  8,  5,  6,
+     7,  0,  1,  7,  7,  2,  0,  9,  1,  1, 10, 11,  0,  7, 12,
+     0,  8,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<13, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  1,  1,  5,  6,  7,  7,  1,
+     7,  8,  9, 10, 11, 12,  8,  7,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<13, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 12 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<12, 20, Blosum62>, TVoidSpec>::VALUE[12] =
+{
+    'A', // A
+    'R', // R Q E K
+    'N', // N D
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W'  // W
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<12, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  3,  2,  1,  7,  4,  5,  6,  0,
+     1,  6,  6,  2,  0,  8,  1,  1,  9, 10,  0,  6, 11,  0,  7,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  3,  2,  1,  7,  4,  5,
+     6,  0,  1,  6,  6,  2,  0,  8,  1,  1,  9, 10,  0,  6, 11,
+     0,  7,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<12, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  9, 10, 11,  7,  6,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<12, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 11 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<11, 20, Blosum62>, TVoidSpec>::VALUE[11] =
+{
+    'A', // A
+    'R', // R Q E K
+    'N', // N D
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    'S', // S
+    'T'  // T
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<11, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  3,  2,  1,  7,  4,  5,  6,  0,
+     1,  6,  6,  2,  0,  8,  1,  1,  9, 10,  0,  6,  7,  0,  7,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  3,  2,  1,  7,  4,  5,
+     6,  0,  1,  6,  6,  2,  0,  8,  1,  1,  9, 10,  0,  6,  7,
+     0,  7,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<11, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  9, 10,  7,  7,  6,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<11, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 10 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<10, 20, Blosum62>, TVoidSpec>::VALUE[10] =
+{
+    'A', // A
+    'R', // R Q E K
+    'N', // N D S
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    'T'  // T
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<10, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  3,  2,  1,  7,  4,  5,  6,  0,
+     1,  6,  6,  2,  0,  8,  1,  1,  2,  9,  0,  6,  7,  0,  7,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  3,  2,  1,  7,  4,  5,
+     6,  0,  1,  6,  6,  2,  0,  8,  1,  1,  2,  9,  0,  6,  7,
+     0,  7,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<10, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  2,  9,  7,  7,  6,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<10, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 9 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<9, 20, Blosum62>, TVoidSpec>::VALUE[9] =
+{
+    'A', // A
+    'R', // R N D Q E K S
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    'T'  // T
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<9, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  6,  3,  4,  5,  0,
+     1,  5,  5,  1,  0,  7,  1,  1,  1,  8,  0,  5,  6,  0,  6,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  6,  3,  4,
+     5,  0,  1,  5,  5,  1,  0,  7,  1,  1,  1,  8,  0,  5,  6,
+     0,  6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<9, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  4,  5,  5,  1,
+     5,  6,  7,  1,  8,  6,  6,  5,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<9, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 8 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<8, 20, Blosum62>, TVoidSpec>::VALUE[8] =
+{
+    'A', // A T
+    'R', // R N D Q E K S
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P'  // P
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<8, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  6,  3,  4,  5,  0,
+     1,  5,  5,  1,  0,  7,  1,  1,  1,  0,  0,  5,  6,  0,  6,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  6,  3,  4,
+     5,  0,  1,  5,  5,  1,  0,  7,  1,  1,  1,  0,  0,  5,  6,
+     0,  6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<8, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  4,  5,  5,  1,
+     5,  6,  7,  1,  0,  6,  6,  5,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<8, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 7 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<7, 20, Blosum62>, TVoidSpec>::VALUE[7] =
+{
+    'A', // A T
+    'R', // R N D Q E H K S
+    'C', // C
+    'G', // G
+    'I', // I L M V
+    'F', // F W Y
+    'P'  // P
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<7, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  5,  3,  1,  4,  0,
+     1,  4,  4,  1,  0,  6,  1,  1,  1,  0,  0,  4,  5,  0,  5,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  5,  3,  1,
+     4,  0,  1,  4,  4,  1,  0,  6,  1,  1,  1,  0,  0,  4,  5,
+     0,  5,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<7, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  1,  4,  4,  1,
+     4,  5,  6,  1,  0,  5,  5,  4,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<7, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 6 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<6, 20, Blosum62>, TVoidSpec>::VALUE[6] =
+{
+    'A', // A T
+    'R', // R N D Q E H K S
+    'C', // C I L M V
+    'G', // G
+    'F', // F W Y
+    'P'  // P
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<6, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  4,  3,  1,  2,  0,
+     1,  2,  2,  1,  0,  5,  1,  1,  1,  0,  0,  2,  4,  0,  4,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  4,  3,  1,
+     2,  0,  1,  2,  2,  1,  0,  5,  1,  1,  1,  0,  0,  2,  4,
+     0,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<6, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  1,  2,  2,  1,
+     2,  4,  5,  1,  0,  4,  4,  2,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<6, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 5 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<5, 20, Blosum62>, TVoidSpec>::VALUE[5] =
+{
+    'A', // A T
+    'R', // R N D Q E G H K S
+    'C', // C I L M V
+    'F', // F W Y
+    'P'  // P
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<5, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  3,  1,  1,  2,  0,
+     1,  2,  2,  1,  0,  4,  1,  1,  1,  0,  0,  2,  3,  0,  3,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  3,  1,  1,
+     2,  0,  1,  2,  2,  1,  0,  4,  1,  1,  1,  0,  0,  2,  3,
+     0,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<5, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  1,  1,  2,  2,  1,
+     2,  3,  4,  1,  0,  3,  3,  2,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<5, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 4 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<4, 20, Blosum62>, TVoidSpec>::VALUE[4] =
+{
+    'A', // A T
+    'R', // R N D Q E G H K P S
+    'C', // C I L M V
+    'F'  // F W Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<4, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  3,  1,  1,  2,  0,
+     1,  2,  2,  1,  0,  1,  1,  1,  1,  0,  0,  2,  3,  0,  3,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  1,  1,  3,  1,  1,
+     2,  0,  1,  2,  2,  1,  0,  1,  1,  1,  1,  0,  0,  2,  3,
+     0,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<4, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  1,  1,  2,  2,  1,
+     2,  3,  1,  1,  0,  3,  3,  2,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<4, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 3 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<3, 20, Blosum62>, TVoidSpec>::VALUE[3] =
+{
+    'A', // A C I L M T V
+    'R', // R N D Q E G H K P S
+    'F'  // F W Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<3, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  2,  1,  1,  0,  0,
+     1,  0,  0,  1,  0,  1,  1,  1,  1,  0,  0,  0,  2,  0,  2,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  2,  1,  1,
+     0,  0,  1,  0,  0,  1,  0,  1,  1,  1,  1,  0,  0,  0,  2,
+     0,  2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<3, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  0,  1,  1,  1,  1,  0,  0,  1,
+     0,  2,  1,  1,  0,  2,  2,  0,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<3, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 2 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<2, 20, Blosum62>, TVoidSpec>::VALUE[2] =
+{
+    'A', // A C I L M F T W Y V
+    'R'  // R N D Q E G H K P S
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<2, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  0,  1,  1,  0,  0,
+     1,  0,  0,  1,  0,  1,  1,  1,  1,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  0,  1,  1,
+     0,  0,  1,  0,  0,  1,  0,  1,  1,  1,  1,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<2, 20, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  0,  1,  1,  1,  1,  0,  0,  1,
+     0,  0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<2, 20, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+} // namespace
+
+#endif // SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_20_to_n_B62_H_
diff --git a/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h b/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h
new file mode 100644
index 0000000..ae1f2ea
--- /dev/null
+++ b/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h
@@ -0,0 +1,2074 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Reduced Versions of the 22-letter amino acid alphabet
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_22_to_n_B62_H_
+#define SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_22_to_n_B62_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ========================== DECLARATIONS FIRST ===========================
+
+// ---------------------------------- N = 21 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<21, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<21, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<21, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<21, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<21, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 20 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<20, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<20, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<20, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<20, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<20, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 19 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<19, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<19, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<19, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<19, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<19, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 18 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<18, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<18, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<18, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<18, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<18, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 17 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<17, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<17, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<17, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<17, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<17, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 16 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<16, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<16, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<16, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<16, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<16, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 15 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<15, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<15, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<15, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<15, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<15, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 14 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<14, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<14, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<14, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<14, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<14, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 13 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<13, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<13, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<13, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<13, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<13, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 12 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<12, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<12, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<12, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<12, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<12, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 11 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<11, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<11, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<11, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<11, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<11, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 10 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<10, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<10, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<10, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<10, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<10, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 9 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<9, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<9, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<9, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<9, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<9, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 8 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<8, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<8, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<8, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<8, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<8, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 7 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<7, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<7, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<7, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<7, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<7, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 6 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<6, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<6, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<6, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<6, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<6, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 5 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<5, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<5, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<5, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<5, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<5, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 4 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<4, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<4, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<4, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<4, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<4, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 3 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<3, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<3, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<3, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<3, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<3, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 2 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<2, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<2, 22, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<2, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<2, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<2, 22, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ========================== DEFINITIONS SECOND ===========================
+
+// ---------------------------------- N = 21 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<21, 22, Blosum62>, TVoidSpec>::VALUE[21] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D
+    'C', // C
+    'Q', // Q
+    'E', // E Z
+    'G', // G
+    'H', // H
+    'I', // I
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y', // Y
+    'V', // V
+    'B'  // B
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<21, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0, 20,  4,  3,  6, 13,  7,  8,  9,  0,
+    11, 10, 12,  2,  0, 14,  5,  1, 15, 16,  0, 19, 17,  0, 18,
+     6,  0,  0,  0,  0,  0,  0,  0, 20,  4,  3,  6, 13,  7,  8,
+     9,  0, 11, 10, 12,  2,  0, 14,  5,  1, 15, 16,  0, 19, 17,
+     0, 18,  6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<21, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,
+    12, 13, 14, 15, 16, 17, 18, 19, 20,  6,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<21, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18, 19, 20,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 20 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<20, 22, Blosum62>, TVoidSpec>::VALUE[20] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q
+    'E', // E Z
+    'G', // G
+    'H', // H
+    'I', // I
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y', // Y
+    'V'  // V
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<20, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  3,  4,  3,  6, 13,  7,  8,  9,  0,
+    11, 10, 12,  2,  0, 14,  5,  1, 15, 16,  0, 19, 17,  0, 18,
+     6,  0,  0,  0,  0,  0,  0,  0,  3,  4,  3,  6, 13,  7,  8,
+     9,  0, 11, 10, 12,  2,  0, 14,  5,  1, 15, 16,  0, 19, 17,
+     0, 18,  6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<20, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,
+    12, 13, 14, 15, 16, 17, 18, 19,  3,  6,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<20, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18, 19,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 19 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<19, 22, Blosum62>, TVoidSpec>::VALUE[19] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q
+    'E', // E Z
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y'  // Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<19, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  3,  4,  3,  6, 13,  7,  8,  9,  0,
+    11, 10, 12,  2,  0, 14,  5,  1, 15, 16,  0,  9, 17,  0, 18,
+     6,  0,  0,  0,  0,  0,  0,  0,  3,  4,  3,  6, 13,  7,  8,
+     9,  0, 11, 10, 12,  2,  0, 14,  5,  1, 15, 16,  0,  9, 17,
+     0, 18,  6,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<19, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,
+    12, 13, 14, 15, 16, 17, 18,  9,  3,  6,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<19, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 18 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<18, 22, Blosum62>, TVoidSpec>::VALUE[18] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y'  // Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<18, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  3,  4,  3,  5, 12,  6,  7,  8,  0,
+    10,  9, 11,  2,  0, 13,  5,  1, 14, 15,  0,  8, 16,  0, 17,
+     5,  0,  0,  0,  0,  0,  0,  0,  3,  4,  3,  5, 12,  6,  7,
+     8,  0, 10,  9, 11,  2,  0, 13,  5,  1, 14, 15,  0,  8, 16,
+     0, 17,  5,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<18, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  9, 10,
+    11, 12, 13, 14, 15, 16, 17,  8,  3,  5,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<18, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 17 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<17, 22, Blosum62>, TVoidSpec>::VALUE[17] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L M
+    'K', // K
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y'  // Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<17, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  3,  4,  3,  5, 11,  6,  7,  8,  0,
+    10,  9,  9,  2,  0, 12,  5,  1, 13, 14,  0,  8, 15,  0, 16,
+     5,  0,  0,  0,  0,  0,  0,  0,  3,  4,  3,  5, 11,  6,  7,
+     8,  0, 10,  9,  9,  2,  0, 12,  5,  1, 13, 14,  0,  8, 15,
+     0, 16,  5,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<17, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  9, 10,
+     9, 11, 12, 13, 14, 15, 16,  8,  3,  5,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<17, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 16 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<16, 22, Blosum62>, TVoidSpec>::VALUE[16] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y'  // Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<16, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  3,  4,  3,  5, 10,  6,  7,  8,  0,
+     1,  9,  9,  2,  0, 11,  5,  1, 12, 13,  0,  8, 14,  0, 15,
+     5,  0,  0,  0,  0,  0,  0,  0,  3,  4,  3,  5, 10,  6,  7,
+     8,  0,  1,  9,  9,  2,  0, 11,  5,  1, 12, 13,  0,  8, 14,
+     0, 15,  5,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<16, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  9,  1,
+     9, 10, 11, 12, 13, 14, 15,  8,  3,  5,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<16, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 15 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<15, 22, Blosum62>, TVoidSpec>::VALUE[15] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L M
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W'  // W
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<15, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  3,  4,  3,  5, 10,  6,  7,  8,  0,
+     1,  9,  9,  2,  0, 11,  5,  1, 12, 13,  0,  8, 14,  0, 10,
+     5,  0,  0,  0,  0,  0,  0,  0,  3,  4,  3,  5, 10,  6,  7,
+     8,  0,  1,  9,  9,  2,  0, 11,  5,  1, 12, 13,  0,  8, 14,
+     0, 10,  5,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<15, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  9,  1,
+     9, 10, 11, 12, 13, 14, 10,  8,  3,  5,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<15, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 14 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<14, 22, Blosum62>, TVoidSpec>::VALUE[14] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L M
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W'  // W
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<14, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  2,  3,  2,  4,  9,  5,  6,  7,  0,
+     1,  8,  8,  2,  0, 10,  4,  1, 11, 12,  0,  7, 13,  0,  9,
+     4,  0,  0,  0,  0,  0,  0,  0,  2,  3,  2,  4,  9,  5,  6,
+     7,  0,  1,  8,  8,  2,  0, 10,  4,  1, 11, 12,  0,  7, 13,
+     0,  9,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<14, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  4,  4,  5,  6,  7,  8,  1,
+     8,  9, 10, 11, 12, 13,  9,  7,  2,  4,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<14, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 13 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<13, 22, Blosum62>, TVoidSpec>::VALUE[13] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W'  // W
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<13, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  2,  3,  2,  4,  8,  5,  6,  7,  0,
+     1,  7,  7,  2,  0,  9,  4,  1, 10, 11,  0,  7, 12,  0,  8,
+     4,  0,  0,  0,  0,  0,  0,  0,  2,  3,  2,  4,  8,  5,  6,
+     7,  0,  1,  7,  7,  2,  0,  9,  4,  1, 10, 11,  0,  7, 12,
+     0,  8,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<13, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  4,  4,  5,  6,  7,  7,  1,
+     7,  8,  9, 10, 11, 12,  8,  7,  2,  4,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<13, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 12 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<12, 22, Blosum62>, TVoidSpec>::VALUE[12] =
+{
+    'A', // A
+    'R', // R Q E K Z
+    'N', // N D B
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W'  // W
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<12, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  2,  3,  2,  1,  7,  4,  5,  6,  0,
+     1,  6,  6,  2,  0,  8,  1,  1,  9, 10,  0,  6, 11,  0,  7,
+     1,  0,  0,  0,  0,  0,  0,  0,  2,  3,  2,  1,  7,  4,  5,
+     6,  0,  1,  6,  6,  2,  0,  8,  1,  1,  9, 10,  0,  6, 11,
+     0,  7,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<12, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  9, 10, 11,  7,  6,  2,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<12, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 11 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<11, 22, Blosum62>, TVoidSpec>::VALUE[11] =
+{
+    'A', // A
+    'R', // R Q E K Z
+    'N', // N D B
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    'S', // S
+    'T'  // T
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<11, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  2,  3,  2,  1,  7,  4,  5,  6,  0,
+     1,  6,  6,  2,  0,  8,  1,  1,  9, 10,  0,  6,  7,  0,  7,
+     1,  0,  0,  0,  0,  0,  0,  0,  2,  3,  2,  1,  7,  4,  5,
+     6,  0,  1,  6,  6,  2,  0,  8,  1,  1,  9, 10,  0,  6,  7,
+     0,  7,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<11, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  9, 10,  7,  7,  6,  2,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<11, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 10 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<10, 22, Blosum62>, TVoidSpec>::VALUE[10] =
+{
+    'A', // A
+    'R', // R Q E K Z
+    'N', // N D S B
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    'T'  // T
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<10, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  2,  3,  2,  1,  7,  4,  5,  6,  0,
+     1,  6,  6,  2,  0,  8,  1,  1,  2,  9,  0,  6,  7,  0,  7,
+     1,  0,  0,  0,  0,  0,  0,  0,  2,  3,  2,  1,  7,  4,  5,
+     6,  0,  1,  6,  6,  2,  0,  8,  1,  1,  2,  9,  0,  6,  7,
+     0,  7,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<10, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  2,  9,  7,  7,  6,  2,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<10, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 9 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<9, 22, Blosum62>, TVoidSpec>::VALUE[9] =
+{
+    'A', // A
+    'R', // R N D Q E K S B Z
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    'T'  // T
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<9, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  6,  3,  4,  5,  0,
+     1,  5,  5,  1,  0,  7,  1,  1,  1,  8,  0,  5,  6,  0,  6,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  6,  3,  4,
+     5,  0,  1,  5,  5,  1,  0,  7,  1,  1,  1,  8,  0,  5,  6,
+     0,  6,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<9, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  4,  5,  5,  1,
+     5,  6,  7,  1,  8,  6,  6,  5,  1,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<9, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 8 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<8, 22, Blosum62>, TVoidSpec>::VALUE[8] =
+{
+    'A', // A T
+    'R', // R N D Q E K S B Z
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P'  // P
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<8, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  6,  3,  4,  5,  0,
+     1,  5,  5,  1,  0,  7,  1,  1,  1,  0,  0,  5,  6,  0,  6,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  6,  3,  4,
+     5,  0,  1,  5,  5,  1,  0,  7,  1,  1,  1,  0,  0,  5,  6,
+     0,  6,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<8, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  4,  5,  5,  1,
+     5,  6,  7,  1,  0,  6,  6,  5,  1,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<8, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 7 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<7, 22, Blosum62>, TVoidSpec>::VALUE[7] =
+{
+    'A', // A T
+    'R', // R N D Q E H K S B Z
+    'C', // C
+    'G', // G
+    'I', // I L M V
+    'F', // F W Y
+    'P'  // P
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<7, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  5,  3,  1,  4,  0,
+     1,  4,  4,  1,  0,  6,  1,  1,  1,  0,  0,  4,  5,  0,  5,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  5,  3,  1,
+     4,  0,  1,  4,  4,  1,  0,  6,  1,  1,  1,  0,  0,  4,  5,
+     0,  5,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<7, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  1,  4,  4,  1,
+     4,  5,  6,  1,  0,  5,  5,  4,  1,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<7, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 6 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<6, 22, Blosum62>, TVoidSpec>::VALUE[6] =
+{
+    'A', // A T
+    'R', // R N D Q E H K S B Z
+    'C', // C I L M V
+    'G', // G
+    'F', // F W Y
+    'P'  // P
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<6, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  4,  3,  1,  2,  0,
+     1,  2,  2,  1,  0,  5,  1,  1,  1,  0,  0,  2,  4,  0,  4,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  4,  3,  1,
+     2,  0,  1,  2,  2,  1,  0,  5,  1,  1,  1,  0,  0,  2,  4,
+     0,  4,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<6, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  1,  2,  2,  1,
+     2,  4,  5,  1,  0,  4,  4,  2,  1,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<6, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 5 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<5, 22, Blosum62>, TVoidSpec>::VALUE[5] =
+{
+    'A', // A T
+    'R', // R N D Q E G H K S B Z
+    'C', // C I L M V
+    'F', // F W Y
+    'P'  // P
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<5, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  3,  1,  1,  2,  0,
+     1,  2,  2,  1,  0,  4,  1,  1,  1,  0,  0,  2,  3,  0,  3,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  3,  1,  1,
+     2,  0,  1,  2,  2,  1,  0,  4,  1,  1,  1,  0,  0,  2,  3,
+     0,  3,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<5, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  1,  1,  2,  2,  1,
+     2,  3,  4,  1,  0,  3,  3,  2,  1,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<5, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 4 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<4, 22, Blosum62>, TVoidSpec>::VALUE[4] =
+{
+    'A', // A T
+    'R', // R N D Q E G H K P S B Z
+    'C', // C I L M V
+    'F'  // F W Y
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<4, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  3,  1,  1,  2,  0,
+     1,  2,  2,  1,  0,  1,  1,  1,  1,  0,  0,  2,  3,  0,  3,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  3,  1,  1,
+     2,  0,  1,  2,  2,  1,  0,  1,  1,  1,  1,  0,  0,  2,  3,
+     0,  3,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<4, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  1,  1,  2,  2,  1,
+     2,  3,  1,  1,  0,  3,  3,  2,  1,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<4, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 3 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<3, 22, Blosum62>, TVoidSpec>::VALUE[3] =
+{
+    'A', // A T
+    'R', // R N D Q E G H K P S B Z
+    'C'  // C I L M F W Y V
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<3, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  2,  1,  1,  2,  0,
+     1,  2,  2,  1,  0,  1,  1,  1,  1,  0,  0,  2,  2,  0,  2,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  2,  1,  1,
+     2,  0,  1,  2,  2,  1,  0,  1,  1,  1,  1,  0,  0,  2,  2,
+     0,  2,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<3, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  1,  1,  2,  2,  1,
+     2,  2,  1,  1,  0,  2,  2,  2,  1,  1,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<3, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 2 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<2, 22, Blosum62>, TVoidSpec>::VALUE[2] =
+{
+    'A', // A R N D Q E G H K P S T B Z
+    'C'  // C I L M F W Y V
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<2, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  1,  0,  0,  1,  0,
+     0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  0,  1,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  1,  0,  0,
+     1,  0,  0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,
+     0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<2, 22, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  0,  0,  0,  1,  0,  0,  0,  0,  1,  1,  0,
+     1,  1,  0,  0,  0,  1,  1,  1,  0,  0,  0,  0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<2, 22, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+} // namespace
+
+#endif // SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_22_to_n_B62_H_
diff --git a/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h b/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h
new file mode 100644
index 0000000..d744156
--- /dev/null
+++ b/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h
@@ -0,0 +1,2296 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Reduced Versions of the 24-letter amino acid alphabet
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_24_to_n_B62_H_
+#define SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_24_to_n_B62_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ========================== DECLARATIONS FIRST ===========================
+
+// ---------------------------------- N = 23 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<23, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<23, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<23, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<23, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<23, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 22 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<22, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<22, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<22, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<22, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<22, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 21 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<21, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<21, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<21, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<21, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<21, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 20 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<20, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<20, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<20, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<20, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<20, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 19 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<19, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<19, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<19, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<19, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<19, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 18 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<18, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<18, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<18, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<18, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<18, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 17 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<17, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<17, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<17, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<17, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<17, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 16 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<16, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<16, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<16, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<16, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<16, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 15 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<15, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<15, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<15, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<15, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<15, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 14 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<14, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<14, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<14, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<14, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<14, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 13 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<13, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<13, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<13, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<13, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<13, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 12 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<12, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<12, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<12, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<12, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<12, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 11 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<11, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<11, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<11, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<11, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<11, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 10 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<10, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<10, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<10, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<10, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<10, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 9 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<9, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<9, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<9, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<9, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<9, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 8 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<8, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<8, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<8, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<8, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<8, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 7 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<7, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<7, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<7, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<7, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<7, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 6 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<6, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<6, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<6, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<6, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<6, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 5 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<5, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<5, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<5, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<5, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<5, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 4 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<4, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<4, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<4, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<4, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<4, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 3 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<3, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<3, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<3, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<3, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<3, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 2 ------------------------------
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<ClusterReduction<2, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<2, 24, Blosum62> > > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<ClusterReduction<2, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<ClusterReduction<2, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[24];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<ClusterReduction<2, 24, Blosum62>, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ========================== DEFINITIONS SECOND ===========================
+
+// ---------------------------------- N = 23 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<23, 24, Blosum62>, TVoidSpec>::VALUE[23] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D
+    'C', // C
+    'Q', // Q
+    'E', // E Z
+    'G', // G
+    'H', // H
+    'I', // I
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y', // Y
+    'V', // V
+    'B', // B
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<23, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21,  0, 20,  4,  3,  6, 13,  7,  8,  9, 21,
+    11, 10, 12,  2, 21, 14,  5,  1, 15, 16, 21, 19, 17, 21, 18,
+     6, 21, 21, 21, 21, 21, 21,  0, 20,  4,  3,  6, 13,  7,  8,
+     9, 21, 11, 10, 12,  2, 21, 14,  5,  1, 15, 16, 21, 19, 17,
+    21, 18,  6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<23, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,
+    12, 13, 14, 15, 16, 17, 18, 19, 20,  6, 21, 22
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<23, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18, 19, 20, 21, 22, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+    21
+};
+
+// ---------------------------------- N = 22 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<22, 24, Blosum62>, TVoidSpec>::VALUE[22] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q
+    'E', // E Z
+    'G', // G
+    'H', // H
+    'I', // I
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y', // Y
+    'V', // V
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<22, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20,  0,  3,  4,  3,  6, 13,  7,  8,  9, 20,
+    11, 10, 12,  2, 20, 14,  5,  1, 15, 16, 20, 19, 17, 20, 18,
+     6, 20, 20, 20, 20, 20, 20,  0,  3,  4,  3,  6, 13,  7,  8,
+     9, 20, 11, 10, 12,  2, 20, 14,  5,  1, 15, 16, 20, 19, 17,
+    20, 18,  6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<22, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,
+    12, 13, 14, 15, 16, 17, 18, 19,  3,  6, 20, 21
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<22, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18, 19, 20, 21, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+    20
+};
+
+// ---------------------------------- N = 21 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<21, 24, Blosum62>, TVoidSpec>::VALUE[21] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q
+    'E', // E Z
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y', // Y
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<21, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19,  0,  3,  4,  3,  6, 13,  7,  8,  9, 19,
+    11, 10, 12,  2, 19, 14,  5,  1, 15, 16, 19,  9, 17, 19, 18,
+     6, 19, 19, 19, 19, 19, 19,  0,  3,  4,  3,  6, 13,  7,  8,
+     9, 19, 11, 10, 12,  2, 19, 14,  5,  1, 15, 16, 19,  9, 17,
+    19, 18,  6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<21, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,
+    12, 13, 14, 15, 16, 17, 18,  9,  3,  6, 19, 20
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<21, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18, 19, 20, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
+    19
+};
+
+// ---------------------------------- N = 20 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<20, 24, Blosum62>, TVoidSpec>::VALUE[20] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I V
+    'L', // L
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y', // Y
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<20, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 19, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18,  0,  3,  4,  3,  5, 12,  6,  7,  8, 18,
+    10,  9, 11,  2, 18, 13,  5,  1, 14, 15, 18,  8, 16, 18, 17,
+     5, 18, 18, 18, 18, 18, 18,  0,  3,  4,  3,  5, 12,  6,  7,
+     8, 18, 10,  9, 11,  2, 18, 13,  5,  1, 14, 15, 18,  8, 16,
+    18, 17,  5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<20, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  9, 10,
+    11, 12, 13, 14, 15, 16, 17,  8,  3,  5, 18, 19
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<20, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
+    18
+};
+
+// ---------------------------------- N = 19 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<19, 24, Blosum62>, TVoidSpec>::VALUE[19] =
+{
+    'A', // A
+    'R', // R
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I L V
+    'K', // K
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y', // Y
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<19, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 18, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17,  0,  3,  4,  3,  5, 11,  6,  7,  8, 17,
+     9,  8, 10,  2, 17, 12,  5,  1, 13, 14, 17,  8, 15, 17, 16,
+     5, 17, 17, 17, 17, 17, 17,  0,  3,  4,  3,  5, 11,  6,  7,
+     8, 17,  9,  8, 10,  2, 17, 12,  5,  1, 13, 14, 17,  8, 15,
+    17, 16,  5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<19, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  8,  9,
+    10, 11, 12, 13, 14, 15, 16,  8,  3,  5, 17, 18
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<19, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 18, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
+    17
+};
+
+// ---------------------------------- N = 18 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<18, 24, Blosum62>, TVoidSpec>::VALUE[18] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I L V
+    'M', // M
+    'F', // F
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'Y', // Y
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<18, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16,  0,  3,  4,  3,  5, 10,  6,  7,  8, 16,
+     1,  8,  9,  2, 16, 11,  5,  1, 12, 13, 16,  8, 14, 16, 15,
+     5, 16, 16, 16, 16, 16, 16,  0,  3,  4,  3,  5, 10,  6,  7,
+     8, 16,  1,  8,  9,  2, 16, 11,  5,  1, 12, 13, 16,  8, 14,
+    16, 15,  5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<18, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  8,  1,
+     9, 10, 11, 12, 13, 14, 15,  8,  3,  5, 16, 17
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<18, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+    16
+};
+
+// ---------------------------------- N = 17 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<17, 24, Blosum62>, TVoidSpec>::VALUE[17] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N
+    'D', // D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I L V
+    'M', // M
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<17, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15,  0,  3,  4,  3,  5, 10,  6,  7,  8, 15,
+     1,  8,  9,  2, 15, 11,  5,  1, 12, 13, 15,  8, 14, 15, 10,
+     5, 15, 15, 15, 15, 15, 15,  0,  3,  4,  3,  5, 10,  6,  7,
+     8, 15,  1,  8,  9,  2, 15, 11,  5,  1, 12, 13, 15,  8, 14,
+    15, 10,  5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<17, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  3,  4,  5,  5,  6,  7,  8,  8,  1,
+     9, 10, 11, 12, 13, 14, 10,  8,  3,  5, 15, 16
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<17, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 16, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+    15
+};
+
+// ---------------------------------- N = 16 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<16, 24, Blosum62>, TVoidSpec>::VALUE[16] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I L V
+    'M', // M
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<16, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14,  0,  2,  3,  2,  4,  9,  5,  6,  7, 14,
+     1,  7,  8,  2, 14, 10,  4,  1, 11, 12, 14,  7, 13, 14,  9,
+     4, 14, 14, 14, 14, 14, 14,  0,  2,  3,  2,  4,  9,  5,  6,
+     7, 14,  1,  7,  8,  2, 14, 10,  4,  1, 11, 12, 14,  7, 13,
+    14,  9,  4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<16, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  4,  4,  5,  6,  7,  7,  1,
+     8,  9, 10, 11, 12, 13,  9,  7,  2,  4, 14, 15
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<16, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    15, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+    14
+};
+
+// ---------------------------------- N = 15 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<15, 24, Blosum62>, TVoidSpec>::VALUE[15] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S
+    'T', // T
+    'W', // W
+    'X', // X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<15, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13,  0,  2,  3,  2,  4,  8,  5,  6,  7, 13,
+     1,  7,  7,  2, 13,  9,  4,  1, 10, 11, 13,  7, 12, 13,  8,
+     4, 13, 13, 13, 13, 13, 13,  0,  2,  3,  2,  4,  8,  5,  6,
+     7, 13,  1,  7,  7,  2, 13,  9,  4,  1, 10, 11, 13,  7, 12,
+    13,  8,  4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<15, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  4,  4,  5,  6,  7,  7,  1,
+     7,  8,  9, 10, 11, 12,  8,  7,  2,  4, 13, 14
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<15, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+    13
+};
+
+// ---------------------------------- N = 14 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<14, 24, Blosum62>, TVoidSpec>::VALUE[14] =
+{
+    'A', // A
+    'R', // R K
+    'N', // N D B
+    'C', // C
+    'Q', // Q E Z
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S X
+    'T', // T
+    'W', // W
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<14, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10,  0,  2,  3,  2,  4,  8,  5,  6,  7, 10,
+     1,  7,  7,  2, 10,  9,  4,  1, 10, 11, 10,  7, 12, 10,  8,
+     4, 10, 10, 10, 10, 10, 10,  0,  2,  3,  2,  4,  8,  5,  6,
+     7, 10,  1,  7,  7,  2, 10,  9,  4,  1, 10, 11, 10,  7, 12,
+    10,  8,  4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<14, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  4,  4,  5,  6,  7,  7,  1,
+     7,  8,  9, 10, 11, 12,  8,  7,  2,  4, 10, 13
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<14, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
+    10
+};
+
+// ---------------------------------- N = 13 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<13, 24, Blosum62>, TVoidSpec>::VALUE[13] =
+{
+    'A', // A
+    'R', // R Q E K Z
+    'N', // N D B
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S X
+    'T', // T
+    'W', // W
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<13, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9, 12,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  0,  2,  3,  2,  1,  7,  4,  5,  6,  9,
+     1,  6,  6,  2,  9,  8,  1,  1,  9, 10,  9,  6, 11,  9,  7,
+     1,  9,  9,  9,  9,  9,  9,  0,  2,  3,  2,  1,  7,  4,  5,
+     6,  9,  1,  6,  6,  2,  9,  8,  1,  1,  9, 10,  9,  6, 11,
+     9,  7,  1,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<13, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  9, 10, 11,  7,  6,  2,  1,  9, 12
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<13, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9
+};
+
+// ---------------------------------- N = 12 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<12, 24, Blosum62>, TVoidSpec>::VALUE[12] =
+{
+    'A', // A
+    'R', // R Q E K Z
+    'N', // N D B
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F Y
+    'P', // P
+    'S', // S T X
+    'W', // W
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<12, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9, 11,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  0,  2,  3,  2,  1,  7,  4,  5,  6,  9,
+     1,  6,  6,  2,  9,  8,  1,  1,  9,  9,  9,  6, 10,  9,  7,
+     1,  9,  9,  9,  9,  9,  9,  0,  2,  3,  2,  1,  7,  4,  5,
+     6,  9,  1,  6,  6,  2,  9,  8,  1,  1,  9,  9,  9,  6, 10,
+     9,  7,  1,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<12, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  9,  9, 10,  7,  6,  2,  1,  9, 11
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<12, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9
+};
+
+// ---------------------------------- N = 11 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<11, 24, Blosum62>, TVoidSpec>::VALUE[11] =
+{
+    'A', // A
+    'R', // R Q E K Z
+    'N', // N D B
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    'S', // S T X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<11, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9, 10,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  0,  2,  3,  2,  1,  7,  4,  5,  6,  9,
+     1,  6,  6,  2,  9,  8,  1,  1,  9,  9,  9,  6,  7,  9,  7,
+     1,  9,  9,  9,  9,  9,  9,  0,  2,  3,  2,  1,  7,  4,  5,
+     6,  9,  1,  6,  6,  2,  9,  8,  1,  1,  9,  9,  9,  6,  7,
+     9,  7,  1,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<11, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  9,  9,  7,  7,  6,  2,  1,  9, 10
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<11, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
+     9
+};
+
+// ---------------------------------- N = 10 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<10, 24, Blosum62>, TVoidSpec>::VALUE[10] =
+{
+    'A', // A S T X
+    'R', // R Q E K Z
+    'N', // N D B
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<10, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  9,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  2,  3,  2,  1,  7,  4,  5,  6,  0,
+     1,  6,  6,  2,  0,  8,  1,  1,  0,  0,  0,  6,  7,  0,  7,
+     1,  0,  0,  0,  0,  0,  0,  0,  2,  3,  2,  1,  7,  4,  5,
+     6,  0,  1,  6,  6,  2,  0,  8,  1,  1,  0,  0,  0,  6,  7,
+     0,  7,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<10, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  2,  2,  3,  1,  1,  4,  5,  6,  6,  1,
+     6,  7,  8,  0,  0,  7,  7,  6,  2,  1,  0,  9
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<10, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 9 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<9, 24, Blosum62>, TVoidSpec>::VALUE[9] =
+{
+    'A', // A S T X
+    'R', // R N D Q E K B Z
+    'C', // C
+    'G', // G
+    'H', // H
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<9, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  8,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  6,  3,  4,  5,  0,
+     1,  5,  5,  1,  0,  7,  1,  1,  0,  0,  0,  5,  6,  0,  6,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  6,  3,  4,
+     5,  0,  1,  5,  5,  1,  0,  7,  1,  1,  0,  0,  0,  5,  6,
+     0,  6,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<9, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  4,  5,  5,  1,
+     5,  6,  7,  0,  0,  6,  6,  5,  1,  1,  0,  8
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<9, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 8 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<8, 24, Blosum62>, TVoidSpec>::VALUE[8] =
+{
+    'A', // A S T X
+    'R', // R N D Q E H K B Z
+    'C', // C
+    'G', // G
+    'I', // I L M V
+    'F', // F W Y
+    'P', // P
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<8, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  7,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  5,  3,  1,  4,  0,
+     1,  4,  4,  1,  0,  6,  1,  1,  0,  0,  0,  4,  5,  0,  5,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  5,  3,  1,
+     4,  0,  1,  4,  4,  1,  0,  6,  1,  1,  0,  0,  0,  4,  5,
+     0,  5,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<8, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  1,  4,  4,  1,
+     4,  5,  6,  0,  0,  5,  5,  4,  1,  1,  0,  7
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<8, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 7 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<7, 24, Blosum62>, TVoidSpec>::VALUE[7] =
+{
+    'A', // A S T X
+    'R', // R N D Q E H K B Z
+    'C', // C I L M V
+    'G', // G
+    'F', // F W Y
+    'P', // P
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<7, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  6,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  4,  3,  1,  2,  0,
+     1,  2,  2,  1,  0,  5,  1,  1,  0,  0,  0,  2,  4,  0,  4,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  4,  3,  1,
+     2,  0,  1,  2,  2,  1,  0,  5,  1,  1,  0,  0,  0,  2,  4,
+     0,  4,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<7, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  3,  1,  2,  2,  1,
+     2,  4,  5,  0,  0,  4,  4,  2,  1,  1,  0,  6
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<7, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 6 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<6, 24, Blosum62>, TVoidSpec>::VALUE[6] =
+{
+    'A', // A G S T X
+    'R', // R N D Q E H K B Z
+    'C', // C I L M V
+    'F', // F W Y
+    'P', // P
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<6, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  5,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  3,  0,  1,  2,  0,
+     1,  2,  2,  1,  0,  4,  1,  1,  0,  0,  0,  2,  3,  0,  3,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  3,  0,  1,
+     2,  0,  1,  2,  2,  1,  0,  4,  1,  1,  0,  0,  0,  2,  3,
+     0,  3,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<6, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  1,  1,  1,  2,  1,  1,  0,  1,  2,  2,  1,
+     2,  3,  4,  0,  0,  3,  3,  2,  1,  1,  0,  5
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<6, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 5 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<5, 24, Blosum62>, TVoidSpec>::VALUE[5] =
+{
+    'A', // A R N D Q E G H K S T B Z X
+    'C', // C I L M V
+    'F', // F W Y
+    'P', // P
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<5, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  4,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  2,  0,  0,  1,  0,
+     0,  1,  1,  0,  0,  3,  0,  0,  0,  0,  0,  1,  2,  0,  2,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  2,  0,  0,
+     1,  0,  0,  1,  1,  0,  0,  3,  0,  0,  0,  0,  0,  1,  2,
+     0,  2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<5, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  0,  0,  0,  1,  0,  0,  0,  0,  1,  1,  0,
+     1,  2,  3,  0,  0,  2,  2,  1,  0,  0,  0,  4
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<5, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 4 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<4, 24, Blosum62>, TVoidSpec>::VALUE[4] =
+{
+    'A', // A R N D Q E G H K P S T B Z X
+    'C', // C I L M V
+    'F', // F W Y
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<4, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  3,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  2,  0,  0,  1,  0,
+     0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0,  1,  2,  0,  2,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  2,  0,  0,
+     1,  0,  0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0,  1,  2,
+     0,  2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<4, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  0,  0,  0,  1,  0,  0,  0,  0,  1,  1,  0,
+     1,  2,  0,  0,  0,  2,  2,  1,  0,  0,  0,  3
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<4, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 3 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<3, 24, Blosum62>, TVoidSpec>::VALUE[3] =
+{
+    'A', // A R N D Q E G H K P S T B Z X
+    'C', // C I L M F W Y V
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<3, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  1,  0,  0,  1,  0,
+     0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  0,  1,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  1,  0,  0,
+     1,  0,  0,  1,  1,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,
+     0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<3, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  0,  0,  0,  1,  0,  0,  0,  0,  1,  1,  0,
+     1,  1,  0,  0,  0,  1,  1,  1,  0,  0,  0,  2
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<3, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ---------------------------------- N = 2 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<
+                ClusterReduction<2, 24, Blosum62>, TVoidSpec>::VALUE[2] =
+{
+    'A', // A R N D C Q E G H I L K M F P S T W Y V B Z X
+    '*'  // *
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<
+                ClusterReduction<2, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<
+                ClusterReduction<2, 24, Blosum62>, TVoidSpec>::VALUE[24] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<
+                ClusterReduction<2, 24, Blosum62>, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+// ============================================================================
+// Functions
+// ============================================================================
+
+}
+
+#endif // def SEQAN_REDUCED_AMINOACID_CLUSTER_RED_TABLES_24_to_n_B62_H_
diff --git a/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h b/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h
new file mode 100644
index 0000000..387d13e
--- /dev/null
+++ b/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h
@@ -0,0 +1,122 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Murphy10 reduction of AminoAcid alphabet
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_MURPHY10_BASE_H_
+#define SEQAN_REDUCED_AMINOACID_MURPHY10_BASE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Tag Murphy10
+// -----------------------------------------------------------------------
+
+/*!
+ * @tag Murphy10
+ * @brief Specialization for @link ReducedAminoAcid @endlink#
+ * @headerfile seqan/reduced_aminoacid.h
+ *
+ * @signature typedef Murphy10 Tag<Murphy10_>;
+ *
+ * This is the 10-character reduction defined by Murphy et al,
+ * 2000, <a href="http://www.ncbi.nlm.nih.gov/pubmed/10775656">http://www.ncbi.nlm.nih.gov/pubmed/10775656</a>
+ *
+ * This alphabet is used by many tools, e.g. Rapsearch2, Lambda, UBlast.
+ *
+ * Since it was created from the 20-letter alphabet the clusters in SeqAn are
+ * not identical (they contain more symbols). This is the clustering:
+ * @code{.txt}
+ *   'A', // A O U X
+ *   'B', // B D E N Q Z
+ *   'C', // C
+ *   'F', // F W Y *
+ *   'G', // G
+ *   'H', // H
+ *   'I', // I J L M V
+ *   'K', // K R
+ *   'P', // P
+ *   'S'  // S T
+ * @endcode
+ *
+ */
+
+struct Murphy10_ {};
+
+typedef Tag<Murphy10_> Murphy10;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Metafunction ValueSize
+// -----------------------------------------------------------------------
+
+template <>
+struct ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Murphy10> > >
+{
+    typedef uint8_t Type;
+    static const Type VALUE = 10;
+};
+
+// -----------------------------------------------------------------------
+// Metafunction BitPerValue
+// -----------------------------------------------------------------------
+
+template <>
+struct BitsPerValue<SimpleType<unsigned char, ReducedAminoAcid_<Murphy10> > >
+{
+    typedef uint8_t Type;
+    static const Type VALUE = 4;
+};
+
+// -----------------------------------------------------------------------
+// Translation Tables (implementations see extra files)
+// -----------------------------------------------------------------------
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+}
+#endif // def SEQAN_REDUCED_AMINOACID_MURPHY10_BASE_H_
diff --git a/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h b/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h
new file mode 100644
index 0000000..c2e8083
--- /dev/null
+++ b/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h
@@ -0,0 +1,154 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Murphy10 reduction tables
+// ==========================================================================
+
+#ifndef SEQAN_REDUCED_AMINOACID_MURPHY10_TABLES_H_
+#define SEQAN_REDUCED_AMINOACID_MURPHY10_TABLES_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+template <typename TSpec>
+struct TranslateTableRedAAToChar_<Murphy10, TSpec>
+{
+    static const char VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Murphy10> > >::VALUE];
+};
+
+template <typename TSpec>
+struct TranslateTableCharToRedAA_<Murphy10, TSpec>
+{
+    static const char VALUE[256];
+};
+
+template <typename TSpec>
+struct TranslateTableAAToRedAA_<Murphy10, TSpec>
+{
+    static const char VALUE[27];
+};
+
+template <typename TSpec>
+struct TranslateTableByteToRedAA_<Murphy10, TSpec>
+{
+    static const char VALUE[256];
+};
+
+// ---------------------------------- N = 10 ------------------------------
+
+template <typename TVoidSpec>
+char const TranslateTableRedAAToChar_<Murphy10, TVoidSpec>::VALUE[10] =
+{
+    'A', // A O U X
+    'B', // B D E N Q Z
+    'C', // C
+    'F', // F W Y *
+    'G', // G
+    'H', // H
+    'I', // I J L M V
+    'K', // K R
+    'P', // P
+    'S'  // S T
+};
+
+template <typename TVoidSpec>
+char const TranslateTableCharToRedAA_<Murphy10, TVoidSpec>::VALUE[256] =
+{
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  3,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  3,  4,  5,  6,  6,
+     7,  6,  6,  1,  0,  8,  1,  7,  9,  9,  0,  6,  3,  0,  3,
+     1,  0,  0,  0,  0,  0,  0,  0,  1,  2,  1,  1,  3,  4,  5,
+     6,  6,  7,  6,  6,  1,  0,  8,  1,  7,  9,  9,  0,  6,  3,
+     0,  3,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+template <typename TVoidSpec>
+char const TranslateTableAAToRedAA_<Murphy10, TVoidSpec>::VALUE[27] =
+{
+     0,  1,  2,  1,  1,  3,  4,  5,  6,  6,  7,  6,  6,
+     1,  0,  8,  1,  7,  9,  9,  0,  6,  3,  3,  1,  0,  3
+};
+
+template <typename TVoidSpec>
+char const TranslateTableByteToRedAA_<Murphy10, TVoidSpec>::VALUE[256] =
+{
+     0,  1,  2,  3,  4,  5,  6,  7,  8,  9,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+     0
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+} // namespace
+
+#endif // SEQAN_REDUCED_AMINOACID_MURPHY10_TABLES_H_
diff --git a/seqan/roi_io.h b/seqan/roi_io.h
new file mode 100644
index 0000000..3c8ac6a
--- /dev/null
+++ b/seqan/roi_io.h
@@ -0,0 +1,59 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for module roi_io.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ROI_IO_H_
+#define INCLUDE_SEQAN_ROI_IO_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/basic.h>
+#include <seqan/file.h>
+#include <seqan/sequence.h>
+
+// ===========================================================================
+// Module Contents
+// ===========================================================================
+
+#include <seqan/roi_io/roi_record.h>
+
+#include <seqan/roi_io/roi_io_context.h>
+#include <seqan/roi_io/read_roi.h>
+#include <seqan/roi_io/write_roi.h>
+#include <seqan/roi_io/roi_file.h>
+
+#endif  // INCLUDE_SEQAN_ROI_IO_H_
diff --git a/seqan/roi_io/read_roi.h b/seqan/roi_io/read_roi.h
new file mode 100644
index 0000000..5b59fec
--- /dev/null
+++ b/seqan/roi_io/read_roi.h
@@ -0,0 +1,252 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ROI_IO_READ_ROI_H_
+#define INCLUDE_SEQAN_ROI_IO_READ_ROI_H_
+
+#include <seqan/stream.h>
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+struct Roi_;
+typedef Tag<Roi_> Roi;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class MagicHeader
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<Roi, T> :
+    public MagicHeader<Nothing, T> {};
+
+// ----------------------------------------------------------------------------
+// Class FileExtensions
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<Roi, T>
+{
+    static char const * VALUE[1];    // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<Roi, T>::VALUE[1] =
+{
+    ".roi"     // default output extension
+};
+
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord()                                            [RoiHeader]
+// ----------------------------------------------------------------------------
+
+template <typename TForwardIter>
+void readHeader(RoiHeader & header, RoiIOContext &, TForwardIter & iter, Roi const & /*tag*/)
+{
+    typedef OrFunctor<IsTab, IsNewline> TNextEntry;
+
+    // skip first hash
+    skipOne(iter, EqualsChar<'#'>());
+    if (!atEnd(iter) && *iter != '#')
+        skipLine(iter);  // skip ROI line if any.
+
+    // check if column header present
+    if (!atEnd(iter) && *iter != '#')
+        return;  // no header
+    // skip run of hashes
+    skipUntil(iter, NotFunctor<EqualsChar<'#'> >());
+
+    // skip REF\t
+    skipUntil(iter, TNextEntry());
+    skipOne(iter, EqualsChar<'\t'>());
+
+    // skip START\t
+    skipUntil(iter, TNextEntry());
+    skipOne(iter, EqualsChar<'\t'>());
+
+    // skip END\t
+    skipUntil(iter, TNextEntry());
+    skipOne(iter, EqualsChar<'\t'>());
+
+    // skip NAME\t
+    skipUntil(iter, TNextEntry());
+    skipOne(iter, EqualsChar<'\t'>());
+
+    // skip LENGTH\t
+    skipUntil(iter, TNextEntry());
+    skipOne(iter, EqualsChar<'\t'>());
+
+    // skip STRAND\t
+    skipUntil(iter, TNextEntry());
+    skipOne(iter, EqualsChar<'\t'>());
+
+    // skip MAX_COUNT
+    skipUntil(iter, TNextEntry());
+
+    do
+    {
+        resize(header.extraColumns, length(header.extraColumns) + 1);
+        skipOne(iter, EqualsChar<'\t'>());
+        readUntil(header.extraColumns[length(header.extraColumns) - 1], iter, TNextEntry());
+    }
+    while (!atEnd(iter) && !IsNewline()(*iter));
+
+    resize(header.extraColumns, length(header.extraColumns) - 1);
+    skipLine(iter);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord()                                            [RoiRecord]
+// ----------------------------------------------------------------------------
+
+template <typename TForwardIter>
+void readRecord(RoiRecord & record, RoiIOContext & context, TForwardIter & iter, Roi const & /*tag*/)
+{
+    typedef OrFunctor<IsTab, IsNewline> TNextEntry;
+
+    // Read reference name.
+    clear(record.ref);
+    readUntil(record.ref, iter, TNextEntry());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Read and parse start position.
+    clear(context.buffer);
+    readUntil(context.buffer, iter, TNextEntry());
+    if (!lexicalCast(record.beginPos, context.buffer))
+        throw BadLexicalCast(record.beginPos, context.buffer);
+    record.beginPos -= 1;  // transform to 0-based
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Read and parse end position.
+    clear(context.buffer);
+    readUntil(context.buffer, iter, TNextEntry());
+    if (!lexicalCast(record.endPos, context.buffer))
+        throw BadLexicalCast(record.endPos, context.buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Read and parse region name.
+    clear(record.name);
+    readUntil(record.name, iter, TNextEntry());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Read and parse region length.
+    clear(context.buffer);
+    readUntil(context.buffer, iter, TNextEntry());
+    if (!lexicalCast(record.len, context.buffer))
+        throw BadLexicalCast(record.len, context.buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Read strand.
+    readOne(record.strand, iter, OrFunctor<OrFunctor<EqualsChar<'.'>, EqualsChar<'+'> >, EqualsChar<'-'> >());
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Read max count.
+    clear(context.buffer);
+    readUntil(context.buffer, iter, TNextEntry());
+    if (!lexicalCast(record.countMax, context.buffer))
+        throw BadLexicalCast(record.countMax, context.buffer);
+
+    // Skip TAB.
+    skipOne(iter, IsTab());
+
+    // Read data field.
+    do
+    {
+        clear(context.buffer);
+        readUntil(context.buffer, iter, TNextEntry());
+        if (!atEnd(iter))
+        {
+            if (!IsNewline()(value(iter)))
+                appendValue(record.data, context.buffer);
+            else
+                break;
+
+            skipOne(iter);
+        }
+    }
+    while (true);
+    skipLine(iter);
+
+    // Individual counts.
+    clear(record.count);
+    DirectionIterator<String<char>, Input>::Type castIter = begin(context.buffer);
+
+    while (!atEnd(castIter))
+    {
+        clear(context.castBuffer);
+        readUntil(context.castBuffer, castIter, OrFunctor<EqualsChar<','>, IsNewline>());
+        if (!empty(context.castBuffer))
+        {
+            unsigned count = 0;
+            if (!lexicalCast(count, context.castBuffer))
+                throw BadLexicalCast(count, context.castBuffer);
+            appendValue(record.count, count);
+            record.countMax = std::max(record.countMax, back(record.count));
+        }
+        if (!atEnd(castIter))
+            skipOne(castIter);
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_ROI_IO_READ_ROI_H_
diff --git a/seqan/roi_io/roi_file.h b/seqan/roi_io/roi_file.h
new file mode 100644
index 0000000..5697a47
--- /dev/null
+++ b/seqan/roi_io/roi_file.h
@@ -0,0 +1,147 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Class for reading/writing files in ROI format.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_ROI_IO_ROI_STREAM_H_
+#define SEQAN_INCLUDE_SEQAN_ROI_IO_ROI_STREAM_H_
+
+namespace seqan {
+
+// ============================================================================
+// Typedefs
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Type RoiFileIn
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class RoiFileIn
+ * @signature typedef FormattedFile<Roi, Input> RoiFileIn;
+ * @extends FormattedFileIn
+ * @headerfile <seqan/roi_io.h>
+ * @brief Class for reading ROI files.
+ */
+
+typedef FormattedFile<Roi, Input>   RoiFileIn;
+
+// ----------------------------------------------------------------------------
+// Type RoiFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class RoiFileOut
+ * @signature typedef FormattedFile<Roi, Output> RoiFileOut;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/roi_io.h>
+ * @brief Class for writing ROI files.
+ */
+
+typedef FormattedFile<Roi, Output>  RoiFileOut;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<Roi, TDirection, TSpec>, TStorageSpec>
+{
+    typedef RoiIOContext Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec>
+struct FileFormat<FormattedFile<Roi, TDirection, TSpec> >
+{
+    typedef Roi Type;
+};
+
+// ----------------------------------------------------------------------------
+// Function readHeader(); RoiHeader
+// ----------------------------------------------------------------------------
+
+// convient RoiFile variant
+template <typename TSpec>
+inline void
+readHeader(RoiHeader & header, FormattedFile<Roi, Input, TSpec> & file)
+{
+    readHeader(header, context(file), file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(); RoiRecord
+// ----------------------------------------------------------------------------
+
+// convient RoiFile variant
+template <typename TSpec>
+inline void
+readRecord(RoiRecord & record, FormattedFile<Roi, Input, TSpec> & file)
+{
+    readRecord(record, context(file), file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeHeader(); RoiHeader
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+inline void
+writeHeader(FormattedFile<Roi, Output, TSpec> & file, RoiHeader const & header)
+{
+    writeHeader(file.iter, header, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(); RoiRecord
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+inline void
+writeRecord(FormattedFile<Roi, Output, TSpec> & file, RoiRecord const & record)
+{
+    writeRecord(file.iter, record, file.format);
+}
+
+}  // namespace seqan
+
+#endif // SEQAN_INCLUDE_SEQAN_ROI_IO_ROI_STREAM_H_
+
diff --git a/seqan/bam_io/xam_writer.h b/seqan/roi_io/roi_io_context.h
similarity index 68%
rename from seqan/bam_io/xam_writer.h
rename to seqan/roi_io/roi_io_context.h
index 9961f68..c1e5376 100644
--- a/seqan/bam_io/xam_writer.h
+++ b/seqan/roi_io/roi_io_context.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -31,9 +31,13 @@
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
+// Class RoiIOContext, accessor functions.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ROI_IO_ROI_IO_CONTEXT_H_
+#define INCLUDE_SEQAN_ROI_IO_ROI_IO_CONTEXT_H_
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_XAM_WRITER_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_XAM_WRITER_H_
+#include <seqan/store.h>
 
 namespace seqan {
 
@@ -45,44 +49,12 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-// Base class for writing SAM and BAM.
-
-class XamWriter_
+class RoiIOContext
 {
 public:
-    CharString _filename;
-
-    XamWriter_()
-    {}
-
-    XamWriter_(CharString const & filename) :
-        _filename(filename)
-    {}
-
-    virtual ~XamWriter_()
-    {}
-
-    // Those of the following functions that return integers return status codes.  As usual, a status code of 0 means
-    // "OK", one != 0 means that there was an error.
-
-    // Open file with given name.
-    virtual int open(CharString const & filename) = 0;
-
-    // Return true if there is no error, false otherwise.
-    virtual bool isGood() = 0;
-
-    // Write the BAM header to the wrapped file.
-    virtual int writeHeader(BamHeader const & header, BamIOContext<StringSet<CharString> > const & bamIOContext) = 0;
-
-    // Write the BAM record to the wrapped file.
-    virtual int writeRecord(BamAlignmentRecord const & record,
-                            BamIOContext<StringSet<CharString> > const & bamIOContext) = 0;
-
-    // Flush all buffers.
-    virtual int flush() = 0;
-
-    // Close the file again.
-    virtual int close() = 0;
+    // Just two buffers needed for reading.
+    CharString buffer;
+    CharString castBuffer;
 };
 
 // ============================================================================
@@ -95,4 +67,5 @@ class XamWriter_
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_XAM_WRITER_H_
+#endif  // #ifndef INCLUDE_SEQAN_ROI_IO_ROI_IO_CONTEXT_H_
+
diff --git a/seqan/bam_io/bam_index_base.h b/seqan/roi_io/roi_record.h
similarity index 54%
rename from seqan/bam_io/bam_index_base.h
rename to seqan/roi_io/roi_record.h
index 35e3ad4..3498bc2 100644
--- a/seqan/bam_io/bam_index_base.h
+++ b/seqan/roi_io/roi_record.h
@@ -1,7 +1,7 @@
 // ==========================================================================
-//                              bam_index_base.h
+//                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BASE_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BASE_H_
+#ifndef INCLUDE_SEQAN_ROI_IO_ROI_RECORD_H_
+#define INCLUDE_SEQAN_ROI_IO_ROI_RECORD_H_
 
 namespace seqan {
 
@@ -45,32 +45,55 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-/*!
- * @class BamIndex
- * @headerfile <seqan/bam_io.h>
- *
- * @brief Access to BAM indices.
- *
- * @signature template <typename TSpec>
- *            class BamIndex;
- *
- * @section Remarks
- *
- * This is an abstract class, don't use it itself but its specializations.
- */
-
-/**
-.Class.BamIndex
-..cat:BAM I/O
-..summary:Access to BAM Indices.
-..signature:BamIndex<TSpec>
-..param.TSpec:Tag to specialize index.
-..remarks:This is an abstract class, don't use it itself but its specializations.
-..include:seqan/bam_io.h
-*/
-
-template <typename TSpec>
-class BamIndex;
+// ----------------------------------------------------------------------------
+// Class RoiHeader
+// ----------------------------------------------------------------------------
+
+class RoiHeader
+{
+public:
+    seqan::StringSet<seqan::CharString> extraColumns;
+};
+
+// ----------------------------------------------------------------------------
+// Class RoiRecord
+// ----------------------------------------------------------------------------
+
+// One entry in a ROI file.
+
+class RoiRecord
+{
+public:
+    static const int INVALID_POS = -1;
+
+    // Chromosome that this region is on.
+    CharString ref;
+
+    // Begin and end position.
+    int beginPos;
+    int endPos;
+
+    // The strand of this region.
+    char strand;  // TODO(holtgrew): Rename to strand and make char?
+
+    // The name of the region.
+    CharString name;
+
+    // The coverage over the length of the region.
+    String<unsigned> count;  // TODO(holtgrew): Rename to coverages/counts?
+
+    // The length of the region.
+    unsigned len;
+
+    // The largest count.
+    unsigned countMax;  // TODO(holtgrew): Rename to maxCount/maxCoverages?
+
+    // Additional data as string.
+    seqan::StringSet<seqan::CharString> data;
+
+    RoiRecord() : beginPos(INVALID_POS), endPos(INVALID_POS), strand('.'), len(0), countMax(0)
+    {}
+};
 
 // ============================================================================
 // Metafunctions
@@ -81,50 +104,16 @@ class BamIndex;
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function BamIndex#jumpToRegion
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BamIndex#jumpToRegion
- * @brief Seek in BAM BGZF stream using an index.
- *
- * You provide a region <tt>[pos, posEnd)</tt> on the reference <tt>refID</tt> that you want to jump to and the function
- * jumps to the first alignment in this region, if any.
- *
- * @signature bool jumpToRegion(stream, hasAlignments, bamIOContext, refID, pos, posEnd, index);
- *
- * @param[in,out] stream        The @link BgzfStream @endlink to jump with.
- * @param[out]    hasAlignments A <tt>bool</tt> that is set true if the region <tt>[pos, posEnd)</tt> has any
- *                              alignments.
- * @param[in,out] bamIOContext  The @link BamIOContext @endlink to use for jumping.
- * @param[in]     refID         The reference id to jump to (<tt>__int32</tt>).
- * @param[in]     pos           The begin of the region to jump to.
- * @param[in]     posEnd        The end of the region to jump to.
- * @param[in]     index         The @link BamIndex @endlink to use for the jumping.
- *
- * @return bool true if seeking was successful, false if not.
- *
- * @section Remarks
- *
- * This function fails if <tt>refID</tt>/<tt>pos</tt> are invalid.
- */
-
-// ----------------------------------------------------------------------------
-// Function jumpToOrphans
+// Function clear()
 // ----------------------------------------------------------------------------
 
-/*!
- * @fn BamIndex#jumpToOrphans
- * @brief Seek to orphans block in BAM BGZF stream using an index.
- *
- * @signature bool jumpToOrphans(stream, hasAlignments, bamIOContext, index);
- *
- * @param[in,out] stream         The @link BgzfStream @endlink object to jump with.
- * @param[out]    hasAlignments  A <tt>bool</tt> that is set to true if there are any orphans.
- * @param[in,out] bamIOContext   The @link BamIOContext @endlink to use for the state.
- * @param[in]     index          The index to use for jumping.
- */
+inline void clear(RoiRecord & record)
+{
+    clear(record.ref);
+    clear(record.count);
+    clear(record.data);
+}
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BASE_H_
+#endif  // #ifndef INCLUDE_SEQAN_ROI_IO_ROI_RECORD_H_
diff --git a/seqan/roi_io/write_roi.h b/seqan/roi_io/write_roi.h
new file mode 100644
index 0000000..ca4393f
--- /dev/null
+++ b/seqan/roi_io/write_roi.h
@@ -0,0 +1,122 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_ROI_IO_WRITE_ROI_H_
+#define INCLUDE_SEQAN_ROI_IO_WRITE_ROI_H_
+
+#include <seqan/stream.h>
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+struct Roi_;
+typedef Tag<Roi_> Roi;
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()                                           [RoiHeader]
+// ----------------------------------------------------------------------------
+
+template <typename TTarget>
+void writeHeader(TTarget & target, RoiHeader const & header, Roi const & /*tag*/)
+{
+    write(target, "#ROI 0.3\n"
+                  "##ref\t"
+                  "begin_pos\t"
+                  "end_pos\t"
+                  "region_name\t"
+                  "length\t"
+                  "strand\t"
+                  "max_count\t");
+    for (unsigned i = 0; i < length(header.extraColumns); ++i)
+    {
+        write(target, header.extraColumns[i]);
+        write(target, "\t");
+    }
+    write(target, "counts\n");
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()                                           [RoiRecord]
+// ----------------------------------------------------------------------------
+
+template <typename TTarget>
+void writeRecord(TTarget & target, RoiRecord const & record, Roi const & /*tag*/)
+{
+    write(target, record.ref);
+    writeValue(target, '\t');
+    appendNumber(target, record.beginPos + 1);  // 0-based to 1-based
+    writeValue(target, '\t');
+    appendNumber(target, record.endPos);
+    writeValue(target, '\t');
+    write(target, record.name);
+    writeValue(target, '\t');
+    appendNumber(target, record.len);
+    writeValue(target, '\t');
+    writeValue(target, record.strand);
+    writeValue(target, '\t');
+    appendNumber(target, record.countMax);
+    writeValue(target, '\t');
+    for (unsigned i = 0; i < length(record.data); ++i)
+    {
+        write(target, record.data[i]);
+        writeValue(target, '\t');
+    }
+
+    for (unsigned i = 0; i < length(record.count); ++i)
+    {
+        if (i > 0)
+            writeValue(target, ',');
+        appendNumber(target, record.count[i]);
+    }
+    writeValue(target, '\n');
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_ROI_IO_WRITE_ROI_H_
diff --git a/seqan/score.h b/seqan/score.h
index 906d718..821db1c 100644
--- a/seqan/score.h
+++ b/seqan/score.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // This is the facade header for the score module.
 // ==========================================================================
 
-#ifndef SEQAN_SCORE_H_
-#define SEQAN_SCORE_H_
+#ifndef SEQAN_SH_
+#define SEQAN_SH_
 
 #include <seqan/basic.h>
 
@@ -48,4 +48,4 @@
 #include <seqan/score/score_matrix_data.h>
 #include <seqan/score/score_simple.h>
 
-#endif  // SEQAN_SCORE_H_
+#endif  // SEQAN_SH_
diff --git a/seqan/score/INFO b/seqan/score/INFO
deleted file mode 100644
index b1bd7d8..0000000
--- a/seqan/score/INFO
+++ /dev/null
@@ -1,11 +0,0 @@
-Name: seqan-score
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Alignment score related code.
- This module contains the Score class and specializations for edit distance
- scores.  Furthermore, it contains predefined values for matrices such as
- BLOSUM, PAM and VTML200.
diff --git a/seqan/score/score_base.h b/seqan/score/score_base.h
index e8c323c..4346d61 100644
--- a/seqan/score/score_base.h
+++ b/seqan/score/score_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 
 // TODO(holtgrew): Should the public interface for the class Score not be defined here?
 
-#ifndef SEQAN_SCORE_SCORE_BASE_H_
-#define SEQAN_SCORE_SCORE_BASE_H_
+#ifndef SEQAN_SSCORE_BASE_H_
+#define SEQAN_SSCORE_BASE_H_
 
 namespace seqan {
 
@@ -57,33 +57,13 @@ namespace seqan {
  *
  * @section Examples
  *
- * @include demos/score/score.cpp
+ * @include demos/dox/score/score.cpp
  *
  * The output is as follows:
  *
- * @include demos/score/score.cpp.stdout
+ * @include demos/dox/score/score.cpp.stdout
  */
 
-/**
-.Class.Score:
-..cat:Miscellaneous
-..summary:A scoring scheme.
-..signature:Score<TValue, TSpec>
-..param.TValue:The value type.
-...default:int
-..param.TSpec:The specializing type.
-...default:$Tag.Simple$
-..example.snippet:demos/score/score.cpp|UsingScore
-..example.text:The output is as follows:
-..example.output:
-Score = 66
-Alignment:
-0     .    :    .    :    .
-  ACGTG--GATCGGTGACTTACGGACTG
-  |||||  ||   |||| ||||||||||
-  ACGTGTTGA---GTGA-TTACGGACTG
-..include:seqan/score.h
-*/
 template <typename TValue = int, typename TSpec = Simple>
 class Score;
 
@@ -98,7 +78,6 @@ class Score;
  * @return Type The score value type of the scoring scheme.
  */
 
-///.Metafunction.Value.param.T.type:Class.Score
 template <typename TValue, typename TSpec>
 struct Value<Score<TValue, TSpec> > {
     typedef TValue Type;
@@ -111,39 +90,23 @@ struct Value<Score<TValue, TSpec> > {
 /*!
  * @mfn Score#SequenceEntryForScore
  * @headerfile <seqan/score.h>
+ *
+ * @note This is used for unified interfaces for position dependent and independent scores.
  * @brief Returns representation type for a character of a position in a sequence.
- * 
- * @signature SequenceEntryForScore<TScore, TSequence>::Type
- * 
+ *
+ * @signature SequenceEntryForScore<TScore, TSequence>::Type;
+ *
  * @tparam TScore    The score type to use. Types: Score
- * @tparam TSequence The underlying sequence of the alignments or gaps. Types: SequenceConcept
- * 
+ * @tparam TSequence The underlying sequence of the alignments or gaps. Types: ContainerConcept
+ *
  * @return Type The type to use for representing a character in a sequence over its position.
- * 
- * This is used for unified interfaces for position dependent and independent scores.
- * 
+ *
+ *
  * @see Score#SequenceEntryForScore
  * @see Score#sequenceEntryForScore
  * @see ConsensusScoreSequenceEntry
  */
 
-/**
-.Metafunction.Score#SequenceEntryForScore
-..cat:Alignments
-..class:Class.Score
-..signature:SequenceEntryForScore<TScore, TSequence>::Type
-..summary:Returns representation type for a character of a position in a sequence.
-..description:This is used for unified interfaces for position dependent and independent scores.
-..param.TScore:The score type to use.
-...type:Class.Score
-..param.TSequence:The underlying sequence of the alignments or gaps.
-...type:Concept.SequenceConcept
-..return:The type to use for the representation of sequence entries.
-..see:Metafunction.Score#SequenceEntryForScore
-..see:Function.Score#sequenceEntryForScore
-..include:seqan/score.h
-*/
-
 template <typename TScore, typename TSequence>
 struct SequenceEntryForScore
 {
@@ -157,31 +120,16 @@ struct SequenceEntryForScore
 /*!
  * @fn Score#sequenceEntryForScore
  * @brief Helper function for element access, depending on score type.
- * 
+ *
  * @signature TAlphabet sequenceEntryForScore(scoringScheme, seq, pos);
- * 
+ *
  * @param[in] scoringScheme The Score to get the representation for.
  * @param[in] pos           The position of the character.
  * @param[in] seq           The sequence to get the representation for.
- * 
+ *
  * @return TAlphabet The value of <tt>seq</tt> at <tt>pos</tt>.
  */
 
-/**
-.Function.Score#sequenceEntryForScore
-..summary:Helper function for element access, depending on score type.
-..cat:Alignments
-..signature:sequenceEntryForScore(scoringScheme, seq, pos)
-..param.scoringScheme:The scoring scheme to get the representation for.
-...type:Class.Score
-..param.seq:The sequence to get the representation for.
-...type:Concept.SequenceConcept
-..param.pos:The position of the character.
-..return:
-Representation of the character $seq[pos]$ to be used for the given scoring scheme.
-The resulting type is $SequenceEntryForScore<TScore, TSequence>::Type$.
-*/
-
 // TODO(rmaerker): Check if using iterator instead would be more efficient than subscript operator.
 template <typename TScore, typename TSequence, typename TPosition>
 inline typename Value<TSequence>::Type
@@ -193,37 +141,20 @@ sequenceEntryForScore(TScore const & /*scoringScheme*/, TSequence const & seq, T
 /*!
  * @fn Score#scoreGapOpenHorizontal
  * @brief Returns the score for opening a gap in horizontal direction.
- * 
+ *
  * @signature TValue scoreGapOpenHorizontal(score, entryH, entryV);
- * 
+ *
  * @param[in] score  The Score to query.
  * @param[in] entryH Entry in sequence one (horizontal), type from Score#SequenceEntryForScore.
  * @param[in] entryV Entry in sequence two (vertical), type from Score#SequenceEntryForScore.
  *
  * @return TValue The score open cost for gaps at the given position/entry.  TValue is the value type of score.
- * 
+ *
  * @section Remarks
- * 
+ *
  * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
  */
 
-/**
-.Function.scoreGapOpenHorizontal
-..class:Class.Score
-..cat:Scoring
-..signature:scoreGapOpenHorizontal(score, entryH, entryV)
-..param.score:The scoring scheme to use.
-...type:Class.Score
-..param.entryH:Entry in sequence one (horizontal).
-...type:Metafunction.Score#SequenceEntryForScore
-..param.entryV:Entry in sequence two (vertical).
-...type:Metafunction.Score#SequenceEntryForScore
-..summary:Returns the score for opening a gap in horizontal direction.
-..remarks:Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
-..see:Function.Score#sequenceEntryForScore
-..see:Class.ConsensusScoreSequenceEntry
-..include:seqan/score.h
- */
 template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
 inline TValue
 scoreGapOpenHorizontal(
@@ -238,37 +169,20 @@ scoreGapOpenHorizontal(
 /*!
  * @fn Score#scoreGapOpenVertical
  * @brief Returns the score for opening a gap in vertical direction.
- * 
+ *
  * @signature TValue scoreGapOpenVertical(score, entryH, entryV);
- * 
+ *
  * @param[in] score  The Score to query.
  * @param[in] entryH Entry in sequence one (horizontal), type from Score#SequenceEntryForScore.
  * @param[in] entryV Entry in sequence two (vertical), type from Score#SequenceEntryForScore.
  *
  * @return TValue The score open cost for gaps at the given position/entry.  TValue is the value type of score.
- * 
+ *
  * @section Remarks
- * 
+ *
  * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
  */
 
-/**
-.Function.scoreGapOpenVertical
-..class:Class.Score
-..cat:Scoring
-..signature:scoreGapOpenVertical(score, entryH, entryV)
-..param.score:The scoring scheme to use.
-...type:Class.Score
-..param.entryH:Entry in sequence one (horizontal).
-...type:Metafunction.Score#SequenceEntryForScore
-..param.entryV:Entry in sequence two (vertical).
-...type:Metafunction.Score#SequenceEntryForScore
-..summary:Returns the score for opening a gap in vertical direction.
-..remarks:Corresponds to a deletion event in sequence one and an insertion event in sequence two, respectively.
-..see:Function.Score#sequenceEntryForScore
-..see:Class.ConsensusScoreSequenceEntry
-..include:seqan/score.h
- */
 template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
 inline TValue
 scoreGapOpenVertical(
@@ -282,7 +196,7 @@ scoreGapOpenVertical(
 
 /*!
  * @fn Score#scoreGapExtendHorizontal
- * @brief The score for extending a gap in the horizontal direction at the given position.
+ * @brief Returns the score for extending a gap in horizontal direction.
  *
  * @signature TValue scoreGapExtendHorizontal(score, entryH, entryV);
  *
@@ -293,26 +207,10 @@ scoreGapOpenVertical(
  * @return TValue The score extension cost for gaps at the given position/entry.  TValue is the value type of score.
  *
  * @section Remarks
- * 
+ *
  * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
  */
 
-/**
-.Function.scoreGapExtendHorizontal
-..cat:Scoring
-..signature:scoreGapExtendHorizontal(score, entryH, entryV)
-..param.score:The scoring scheme to use.
-...type:Class.Score
-..param.entryH:Entry in sequence one (horizontal).
-...type:Metafunction.Score#SequenceEntryForScore
-..param.entryV:Entry in sequence two (vertical).
-...type:Metafunction.Score#SequenceEntryForScore
-..summary:Returns the score for extending a gap in horizontal direction.
-..remarks:Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
-..see:Function.Score#sequenceEntryForScore
-..see:Class.ConsensusScoreSequenceEntry
-..include:seqan/score.h
- */
 template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
 inline TValue
 scoreGapExtendHorizontal(
@@ -326,7 +224,7 @@ scoreGapExtendHorizontal(
 
 /*!
  * @fn Score#scoreGapExtendVertical
- * @brief The score for extending a gap in the vertical direction at the given position.
+ * @brief Returns the score for extending a gap in vertical direction.
  *
  * @signature TValue scoreGapExtendVertical(score, entryH, entryV);
  *
@@ -337,26 +235,10 @@ scoreGapExtendHorizontal(
  * @return TValue The score extension cost for gaps at the given position/entry.  TValue is the value type of score.
  *
  * @section Remarks
- * 
+ *
  * Corresponds to a deletion event in sequence one and an insertion event in sequence two, respectively.
  */
 
-/**
-.Function.scoreGapExtendVertical
-..cat:Scoring
-..signature:scoreGapExtendVertical(score, entryH, entryV)
-..param.score:The scoring scheme to use.
-...type:Class.Score
-..param.entryH:Entry in sequence one (horizontal).
-...type:Metafunction.Score#SequenceEntryForScore
-..param.entryV:Entry in sequence two (vertical).
-...type:Metafunction.Score#SequenceEntryForScore
-..summary:Returns the score for extending a gap in vertical direction.
-..remarks:Corresponds to a deletion event in sequence one and an insertion event in sequence two, respectively.
-..see:Function.Score#sequenceEntryForScore
-..see:Class.ConsensusScoreSequenceEntry
-..include:seqan/score.h
- */
 template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
 inline TValue
 scoreGapExtendVertical(
@@ -370,7 +252,7 @@ scoreGapExtendVertical(
 
 /*!
  * @fn Score#scoreGapHorizontal
- * @brief Return the score value for one gap in the horizontal position.
+ * @brief Returns the score for a gap in horizontal direction.
  *
  * @signature TValue scoreGapHorizontal(score, entryH, entryV);
  *
@@ -385,22 +267,6 @@ scoreGapExtendVertical(
  * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
  */
 
-/**
-.Function.scoreGapHorizontal
-..cat:Scoring
-..signature:scoreGapHorizontal(score, entryH, entryV)
-..param.score:The scoring scheme to use.
-...type:Class.Score
-..param.entryH:Entry in sequence one (horizontal).
-...type:Metafunction.Score#SequenceEntryForScore
-..param.entryV:Entry in sequence two (vertical).
-...type:Metafunction.Score#SequenceEntryForScore
-..summary:Returns the score for a gap in horizontal direction.
-..remarks:Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
-..see:Function.Score#sequenceEntryForScore
-..see:Class.ConsensusScoreSequenceEntry
-..include:seqan/score.h
- */
 template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
 inline TValue
 scoreGapHorizontal(
@@ -414,7 +280,7 @@ scoreGapHorizontal(
 
 /*!
  * @fn Score#scoreGapVertical
- * @brief Return the score value for one gap in the vertical position.
+ * @brief Returns the score for a gap in vertical direction.
  *
  * @signature TValue scoreGapVertical(score, entryH, entryV);
  *
@@ -429,22 +295,6 @@ scoreGapHorizontal(
  * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
  */
 
-/**
-.Function.scoreGapVertical
-..cat:Scoring
-..signature:scoreGapVertical(score, entryH, entryV)
-..param.score:The scoring scheme to use.
-...type:Class.Score
-..param.entryH:Entry in sequence one (horizontal).
-...type:Metafunction.Score#SequenceEntryForScore
-..param.entryV:Entry in sequence two (vertical).
-...type:Metafunction.Score#SequenceEntryForScore
-..summary:Returns the score for a gap in vertical direction.
-..remarks:Corresponds to a deletion event in sequence one and an insertion event in sequence two, respectively.
-..see:Function.Score#sequenceEntryForScore
-..see:Class.ConsensusScoreSequenceEntry
-..include:seqan/score.h
- */
 template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
 inline TValue
 scoreGapVertical(
@@ -458,7 +308,7 @@ scoreGapVertical(
 
 /*!
  * @fn Score#score
- * @brief Return similarity score of two sequence entries.
+ * @brief Returns similarity score for two sequence entries.
  *
  * @signature TValue score(score, entryH, entryV);
  *
@@ -470,21 +320,6 @@ scoreGapVertical(
  *                score.
  */
 
-/**
-.Function.score
-..cat:Scoring
-..signature:score(score, entryH, entryV)
-..param.score:The scoring scheme to use.
-...type:Class.Score
-..param.entryH:Entry in sequence one.
-...type:Metafunction.Score#SequenceEntryForScore
-..param.entryV:Entry in sequence two.
-...type:Metafunction.Score#SequenceEntryForScore
-..summary:Returns the score for aligning the entries $entryH$ and $entryV$.
-..see:Function.Score#sequenceEntryForScore
-..see:Class.ConsensusScoreSequenceEntry
-..include:seqan/score.h
- */
 template <typename TValue, typename TSpec, typename TSeqHVal, typename TSeqVVal>
 inline TValue
 score(Score<TValue, TSpec> const & me, TSeqHVal valH, TSeqVVal valV) {
@@ -497,4 +332,4 @@ score(Score<TValue, TSpec> const & me, TSeqHVal valH, TSeqVVal valV) {
 
 }  // namespace SEQAN_NAMESPACE_MAIN
 
-#endif  // SEQAN_SCORE_SCORE_BASE_H_
+#endif  // SEQAN_SSCORE_BASE_H_
diff --git a/seqan/score/score_edit.h b/seqan/score/score_edit.h
index e59b551..2a60eab 100644
--- a/seqan/score/score_edit.h
+++ b/seqan/score/score_edit.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Edit distance score class and supporting code.
 // ==========================================================================
 
-#ifndef SEQAN_SCORE_SCORE_EDIT_H_
-#define SEQAN_SCORE_SCORE_EDIT_H_
+#ifndef SEQAN_SSCORE_EDIT_H_
+#define SEQAN_SSCORE_EDIT_H_
 
 namespace seqan {
 
@@ -53,19 +53,6 @@ namespace seqan {
  * @tparam TValue The score value type to use.
  */
 
-/**
-.Spec.EditDistance
-..cat:Scoring
-..summary:Edit distance scoring scheme.
-..signature:Score<TValue, EditDistance>
-..param.TValue:The value type.
-...default:int
-..general:Class.Score
-..remarks:Semantically equivalent to a default contructed @Spec.Simple Score.Score<int, Simple>@.
-..remarks:$EditDistance$ is a synonym for @Tag.LevenshteinDistance@.
-..include:seqan/score.h
-*/
-
 // TODO(holtgrew): Should EditDistance better live here instead of basic_tag.h?
 // EditDistance is defined in basic_tag.h
 template <typename TValue>
@@ -77,24 +64,13 @@ class Score<TValue, EditDistance> {
 // TODO(holtgrew): Remove this?
 
 /*!
- * @typedef EditDistanceScoreShortcut EditDistance
+ * @typedef EditDistanceScoreTypedef EditDistance
  * @headerfile <seqan/score.h>
  * @brief Edit distance scoring scheme shortcut.
  *
  * @signature typedef Score<int, EditDistance> EditDistanceScore;
  */
 
-/**
-.Shortcut.EditDistanceScore:
-..cat:Scoring
-..summary:Edit distance scoring scheme.
-..signature:EditDistanceScore
-..shortcutfor:Spec.EditDistance
-...signature:Score<int, EditDistance>
-..see:Spec.EditDistance
-..include:seqan/score.h
-*/
-
 typedef Score<int, EditDistance> EditDistanceScore;
 
 template <typename TValue>
@@ -162,4 +138,4 @@ scoreGapOpen(Score<TValue, EditDistance> const &) {
 
 }  // namespace SEQAN_NAMESPACE_MAIN
 
-#endif  // SEQAN_SCORE_SCORE_EDIT_H_
+#endif  // SEQAN_SSCORE_EDIT_H_
diff --git a/seqan/score/score_matrix.h b/seqan/score/score_matrix.h
index 7057ab5..e60c5ce 100644
--- a/seqan/score/score_matrix.h
+++ b/seqan/score/score_matrix.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Code for score matrices with data from files or built-in data.
 // ==========================================================================
 
-#ifndef SEQAN_SCORE_SCORE_MATRIX_H_
-#define SEQAN_SCORE_SCORE_MATRIX_H_
+#ifndef SEQAN_SSCORE_MATRIX_H_
+#define SEQAN_SSCORE_MATRIX_H_
 
 // TODO(holtgrew): If the complex type conversions are necessary, a static_cast<> is more C++ and explicit.
 
@@ -61,6 +61,19 @@ struct ScoreMatrix;
  * @tparam TSeqValue The alphabet type, defaults to AminoAcid.
  * @tparam TSpec     Further specialization, defaults to Default.
  *
+ * The TSpec argument can be used to obtain a predefined matrix.
+ * Specify one of the following tags:
+ *
+ * ScoreSpecBlosum30, ScoreSpecBlosum45, ScoreSpecBlosum62, ScoreSpecBlosum80,
+ * ScoreSpecPam40, ScoreSpecPam120, ScoreSpecPam200, ScoreSpecPam250, ScoreSpecVtml200.
+ *
+ * This will internally call @link MatrixScore#setDefaultScoreMatrix setDefaultScoreMatrix@endlink.
+ *
+ * In order to provide a more user-friendly access to the predefined scoring matrixes, typedefs exist:
+ * @link Blosum30 @endlink, @link Blosum45 @endlink,  @link Blosum62 @endlink,
+ * @link Blosum80 @endlink, @link Pam40 @endlink,     @link Pam120 @endlink,
+ * @link Pam200 @endlink,   @link Pam250 @endlink and @link Vtml200 @endlink.
+ *
  * @fn MatrixScore::Score
  * @brief Constructor
  *
@@ -72,18 +85,6 @@ struct ScoreMatrix;
  * @param[in] gapOpen   Gap open score, defaults to gapExtend, type is TValue.
  */
 
-/**
-.Spec.Score Matrix:
-..cat:Scoring
-..summary:A general scoring matrix.
-..general:Class.Score
-..signature:Score<TValue, ScoreMatrix<TSequenceValue, TSpec> >
-..param.TValue:Type of the score values.
-...default:$int$
-..param.TSequenceValue:Type of alphabet underlying the matrix.
-...default:$AminoAcid$
-..include:seqan/score.h
- */
 template <typename TValue, typename TSequenceValue, typename TSpec>
 class Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > {
 public:
@@ -102,15 +103,6 @@ class Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > {
     // The gap open score.
     TValue data_gap_open;
 
-    /**
-.Memfunc.Score Matrix#Score
-..cat:Scoring
-..summary:Constructor.
-..class:Spec.Score Matrix
-..signature:Score(gapExtend)
-..param.gapExtend:The gap extension penalty.
-...remark:TValue
-     */
     explicit Score(TValue _gap_extend = -1)
         : data_gap_extend(_gap_extend),
           data_gap_open(_gap_extend) {
@@ -118,38 +110,19 @@ class Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > {
         setDefaultScoreMatrix(*this, TSpec());
     }
 
-    /**
-.Memfunc.Score Matrix#Score
-..signature:Score(gapExtend, gapOpen)
-..param.gapOpen:The gap open penalty.
-...remark:TValue
-     */
     Score(TValue _gap_extend, TValue _gap_open)
         : data_gap_extend(_gap_extend), data_gap_open(_gap_open) {
         SEQAN_CHECKPOINT;
         setDefaultScoreMatrix(*this, TSpec());
     }
 
-    /**
-.Memfunc.Score Matrix#Score
-..signature:Score(filename, gapExtend)
-..param.filename:The path to the file to load.
-...type:Class.String
-..see:Function.loadScoreMatrix
-     */
-    template <typename TString>
-    Score(TString const & filename, TValue _gap_extend = -1)
+    explicit Score(char const * filename, TValue _gap_extend = -1)
         : data_gap_extend(_gap_extend), data_gap_open(_gap_extend) {
         SEQAN_CHECKPOINT;
         loadScoreMatrix(*this, filename);
     }
 
-    /**
-.Memfunc.Score Matrix#Score
-..signature:Score(filename, gapExtend, gapOpen)
-     */
-    template <typename TString>
-    Score(TString const & filename, TValue _gap_extend, TValue _gap_open)
+    Score(char const * filename, TValue _gap_extend, TValue _gap_open)
         : data_gap_extend(_gap_extend), data_gap_open(_gap_open) {
         SEQAN_CHECKPOINT;
         loadScoreMatrix(*this, filename);
@@ -182,19 +155,6 @@ score(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > const & sc, TVal1 val1,
  * @param[in]     v     The score value to set.
  */
 
-/**
-.Function.setScore:
-..class:Spec.Score Matrix
-..cat:Scoring
-..summary:Set the substitution score between two values.
-..signature:setScore(scoreMatrix, val1, val2, score)
-..param.scoreMatrix:
-...type:Spec.Score Matrix
-..param.val1:First value.
-..param.val2:Second value.
-..param.score:The value to set the score to.
-..include:seqan/score.h
- */
 template <typename TValue, typename TSequenceValue, typename TSpec, typename TVal1, typename TVal2, typename T>
 inline void
 setScore(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, TVal1 val1, TVal2 val2, T score) {
@@ -210,29 +170,20 @@ setScore(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, TVal1 val1, TV
  * @fn MatrixScore#setDefaultScoreMatrix
  * @brief Set the score matrix of a Score to one of the default matrixes.
  *
- * @signature void setScore(score, tag);
+ * @signature void setDefaultScoreMatrix(score, tag);
  *
  * @param[in,out] score The MatrixScore to update.
- * @param[in]     tag   The tag to select the default matrix from, one of Default, Blosum30, Blosum62, and Blosum80.
+ * @param[in]     tag   The tag to select the default matrix, see description below.
  *
  * @section Remarks
  *
+ * The tag must be one of the following:
+ * Default, ScoreSpecBlosum30, ScoreSpecBlosum45, ScoreSpecBlosum62, ScoreSpecBlosum80,
+ * ScoreSpecPam40, ScoreSpecPam120, ScoreSpecPam200, ScoreSpecPam250, ScoreSpecVtml200.
+ *
  * If Default is used for tag then the matrix will be filled with default-constructed TValue values.
  */
 
-/**
-.Function.setDefaultScoreMatrix:
-..cat:Scoring
-..summary:Set the value of the given matrix to the default value.
-..signature:setDefaultScoreMatrix(scoreMatrix, tag)
-..param.scoreMatrix:The @Spec.Score Matrix@ to set.
-...type:Spec.Score Matrix
-..param.tag:The tag to specify the matrix.
-...type:Shortcut.Blosum30
-...type:Shortcut.Blosum62
-...type:Shortcut.Blosum80
-..include:seqan/score.h
- */
 template <typename TValue, typename TSequenceValue, typename TSpec, typename TTag>
 inline void
 setDefaultScoreMatrix(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, TTag) {
@@ -243,13 +194,6 @@ setDefaultScoreMatrix(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, T
 }
 
 
-/**
-.Function.setDefaultScoreMatrix
-..param.tag:
-...type:Tag.Default
-...remark:If @Tag.Default@, then the matrix will be filled with default constructed $TValue$ values.
-..include:seqan/score.h
- */
 template <typename TValue, typename TSequenceValue, typename TSpec>
 inline void
 setDefaultScoreMatrix(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, Default) {
@@ -260,4 +204,4 @@ setDefaultScoreMatrix(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, D
 
 }  // namespace SEQAN_NAMESPACE_MAIN
 
-#endif  // SEQAN_SCORE_SCORE_MATRIX_H_
+#endif  // SEQAN_SSCORE_MATRIX_H_
diff --git a/seqan/score/score_matrix_data.h b/seqan/score/score_matrix_data.h
index 6ab04a8..0ae9c17 100644
--- a/seqan/score/score_matrix_data.h
+++ b/seqan/score/score_matrix_data.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -51,41 +51,76 @@
 
 // TODO(holtgrew): Maybe also set gap penalties when setting matrices?
 
-#ifndef SEQAN_SCORE_SCORE_MATRIX_DATA_H_
-#define SEQAN_SCORE_SCORE_MATRIX_DATA_H_
+/* GNU Octave code to produce our format of matrix from matblas output:
+ * [strip matrix file of all data except the matrix itself (also labels)
+M = dlmread("matrixfile.txt");
+## rearrange
+M2 = M([1 21 5 4 7 14 8 9 10 12 11 13 3 15 6 2 16 17 20 18 19 22 23 24],:);
+M3 = M2(:,[1 21 5 4 7 14 8 9 10 12 11 13 3 15 6 2 16 17 20 18 19 22 23 24]);
+## add J column
+M4 = [M3(1:9,:); round((M3(9,:) + M3(11,:)) /2); M3(10:end,:)];
+M4 = [M4(:,1:9), round((M4(:,9) + M4(:,11)) /2), M4(:,10:end)];
+## add O column
+M5 = [M4(:,1:14), M4(:,24), M4(:,15:25)];
+M5 = [M5(1:14,:); M5(24,:); M5(15:25,:)];
+## add U column
+M6 = [M5(:,1:20), M5(:,25), M5(:,21:26)];
+M6 = [M6(1:20,:); M6(25,:); M6(21:26,:)];
+ */
+
+#ifndef SEQAN_SSCORE_MATRIX_DATA_H_
+#define SEQAN_SSCORE_MATRIX_DATA_H_
 
 namespace seqan {
 
-/*
-.Tag.Blosum30_:
-..cat:Scoring
-..summary:Tag for Retrieving a BLOSUM30 matrix.
-..include:seqan/score.h
- */
 struct Blosum30_ {};
+typedef Blosum30_ ScoreSpecBlosum30;
 
 /*!
  * @typedef Blosum30
  * @headerfile <seqan/score.h>
  * @brief BLOSUM30 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Blosum30_> > Blosum30;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecBlosum30> > Blosum30;
+ *
+ * @code{.txt}
+ * A   4
+ * B   0  5
+ * C  -3 -2 17
+ * D   0  5 -3  9
+ * E   0  0  1  1  6
+ * F  -2 -3 -3 -5 -4 10
+ * G   0  0 -4 -1 -2 -3  8
+ * H  -2 -2 -5 -2  0 -3 -3 14
+ * I   0 -2 -2 -4 -3  0 -1 -2  6
+ * J  -1 -2 -1 -3 -2  1 -2 -2  4  4
+ * K   0  0 -3  0  2 -1 -1 -2 -2 -2  4
+ * L  -1 -1  0 -1 -1  2 -2 -1  2  3 -2  4
+ * M   1 -2 -2 -3 -1 -2 -2  2  1  2  2  2  6
+ * N   0  4 -1  1 -1 -1  0 -1  0 -1  0 -2  0  8
+ * X   0 -1 -2 -1 -1 -1 -1 -1  0  0  0  0  0  0 -1
+ * P  -1 -2 -3 -1  1 -4 -1  1 -3 -3  1 -3 -4 -3 -1 11
+ * Q   1 -1 -2 -1  2 -3 -2  0 -2 -2  0 -2 -1 -1  0  0  8
+ * R  -1 -2 -2 -1 -1 -1 -2 -1 -3 -3  1 -2  0 -2 -1 -1  3  8
+ * S   1  0 -2  0  0 -1  0 -1 -1 -2  0 -2 -2  0  0 -1 -1 -1  4
+ * T   1  0 -2 -1 -2 -2 -2 -2  0  0 -1  0  0  1  0  0  0 -3  2  5
+ * U   0 -1 -2 -1 -1 -1 -1 -1  0  0  0  0  0  0 -1 -1  0 -1  0  0 -1
+ * V   1 -2 -2 -2 -3  1 -3 -3  4  3 -2  1  0 -2  0 -4 -3 -1 -1  1  0  5
+ * W  -5 -5 -2 -4 -1  1  1 -5 -3 -3 -2 -2 -3 -7 -2 -3 -1  0 -3 -5 -2 -3 20
+ * Y  -4 -3 -6 -1 -2  3 -3  0 -1  1 -1  3 -1 -4 -1 -2 -1  0 -2 -1 -1  1  5  9
+ * Z   0  0  0  0  5 -4 -2  0 -3 -2  1 -1 -1 -1  0  0  4  0 -1 -1  0 -3 -1 -2  4
+ * X   0 -1 -2 -1 -1 -1 -1 -1  0  0  0  0  0  0 -1 -1  0 -1  0  0 -1  0 -2 -1  0 -1
+ * *  -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7  1
+ *
+ *     A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  Y  Z  X  *
+ * @endcode
  */
 
-/**
-.Shortcut.Blosum30:
-..cat:Scoring
-..summary:Blosum30 scoring matrix.
-..signature:Blosum30
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Blosum30_> >
-..include:seqan/score.h
-*/
-typedef Score<int, ScoreMatrix<AminoAcid, Blosum30_> > Blosum30;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecBlosum30> > Blosum30;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Blosum30_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecBlosum30> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -93,7 +128,7 @@ struct ScoringMatrixData_<int, AminoAcid, Blosum30_> {
 
     static inline int const * getData() {
         SEQAN_CHECKPOINT;
-        // The matrix data, ordered by amino acid alphabet.
+        // The matrix data, ordered by letter.
         // Matrix made by matblas from blosum30.iij
         // * column uses minimum score
         // BLOSUM Clustered Scoring Matrix in 1/5 Bit Units
@@ -101,66 +136,87 @@ struct ScoringMatrixData_<int, AminoAcid, Blosum30_> {
         // Cluster Percentage: >= 30
         // Entropy =   0.1424, Expected =  -0.1074
         static int const _data[TAB_SIZE] = {
-             4, -1,  0,  0, -3,  1,  0,  0, -2,  0, -1,  0,  1, -2, -1,  1,  1, -5, -4,  1,  0,  0,  0, -7,
-            -1,  8, -2, -1, -2,  3, -1, -2, -1, -3, -2,  1,  0, -1, -1, -1, -3,  0,  0, -1, -2,  0, -1, -7,
-             0, -2,  8,  1, -1, -1, -1,  0, -1,  0, -2,  0,  0, -1, -3,  0,  1, -7, -4, -2,  4, -1,  0, -7,
-             0, -1,  1,  9, -3, -1,  1, -1, -2, -4, -1,  0, -3, -5, -1,  0, -1, -4, -1, -2,  5,  0, -1, -7,
-            -3, -2, -1, -3, 17, -2,  1, -4, -5, -2,  0, -3, -2, -3, -3, -2, -2, -2, -6, -2, -2,  0, -2, -7,
-             1,  3, -1, -1, -2,  8,  2, -2,  0, -2, -2,  0, -1, -3,  0, -1,  0, -1, -1, -3, -1,  4,  0, -7,
-             0, -1, -1,  1,  1,  2,  6, -2,  0, -3, -1,  2, -1, -4,  1,  0, -2, -1, -2, -3,  0,  5, -1, -7,
-             0, -2,  0, -1, -4, -2, -2,  8, -3, -1, -2, -1, -2, -3, -1,  0, -2,  1, -3, -3,  0, -2, -1, -7,
-            -2, -1, -1, -2, -5,  0,  0, -3, 14, -2, -1, -2,  2, -3,  1, -1, -2, -5,  0, -3, -2,  0, -1, -7,
-             0, -3,  0, -4, -2, -2, -3, -1, -2,  6,  2, -2,  1,  0, -3, -1,  0, -3, -1,  4, -2, -3,  0, -7,
-            -1, -2, -2, -1,  0, -2, -1, -2, -1,  2,  4, -2,  2,  2, -3, -2,  0, -2,  3,  1, -1, -1,  0, -7,
-             0,  1,  0,  0, -3,  0,  2, -1, -2, -2, -2,  4,  2, -1,  1,  0, -1, -2, -1, -2,  0,  1,  0, -7,
-             1,  0,  0, -3, -2, -1, -1, -2,  2,  1,  2,  2,  6, -2, -4, -2,  0, -3, -1,  0, -2, -1,  0, -7,
-            -2, -1, -1, -5, -3, -3, -4, -3, -3,  0,  2, -1, -2, 10, -4, -1, -2,  1,  3,  1, -3, -4, -1, -7,
-            -1, -1, -3, -1, -3,  0,  1, -1,  1, -3, -3,  1, -4, -4, 11, -1,  0, -3, -2, -4, -2,  0, -1, -7,
-             1, -1,  0,  0, -2, -1,  0,  0, -1, -1, -2,  0, -2, -1, -1,  4,  2, -3, -2, -1,  0, -1,  0, -7,
-             1, -3,  1, -1, -2,  0, -2, -2, -2,  0,  0, -1,  0, -2,  0,  2,  5, -5, -1,  1,  0, -1,  0, -7,
-            -5,  0, -7, -4, -2, -1, -1,  1, -5, -3, -2, -2, -3,  1, -3, -3, -5, 20,  5, -3, -5, -1, -2, -7,
-            -4,  0, -4, -1, -6, -1, -2, -3,  0, -1,  3, -1, -1,  3, -2, -2, -1,  5,  9,  1, -3, -2, -1, -7,
-             1, -1, -2, -2, -2, -3, -3, -3, -3,  4,  1, -2,  0,  1, -4, -1,  1, -3,  1,  5, -2, -3,  0, -7,
-             0, -2,  4,  5, -2, -1,  0,  0, -2, -2, -1,  0, -2, -3, -2,  0,  0, -5, -3, -2,  5,  0, -1, -7,
-             0,  0, -1,  0,  0,  4,  5, -2,  0, -3, -1,  1, -1, -4,  0, -1, -1, -1, -2, -3,  0,  4,  0, -7,
-             0, -1,  0, -1, -2,  0, -1, -1, -1,  0,  0,  0,  0, -1, -1,  0,  0, -2, -1,  0, -1,  0, -1, -7,
-            -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7,  1,
+             4,  0, -3,  0,  0, -2,  0, -2,  0, -1,  0, -1,  1,  0,  0, -1,  1, -1,  1,  1,  0,  1, -5, -4,  0,  0, -7,
+             0,  5, -2,  5,  0, -3,  0, -2, -2, -2,  0, -1, -2,  4, -1, -2, -1, -2,  0,  0, -1, -2, -5, -3,  0, -1, -7,
+            -3, -2, 17, -3,  1, -3, -4, -5, -2, -1, -3,  0, -2, -1, -2, -3, -2, -2, -2, -2, -2, -2, -2, -6,  0, -2, -7,
+             0,  5, -3,  9,  1, -5, -1, -2, -4, -3,  0, -1, -3,  1, -1, -1, -1, -1,  0, -1, -1, -2, -4, -1,  0, -1, -7,
+             0,  0,  1,  1,  6, -4, -2,  0, -3, -2,  2, -1, -1, -1, -1,  1,  2, -1,  0, -2, -1, -3, -1, -2,  5, -1, -7,
+            -2, -3, -3, -5, -4, 10, -3, -3,  0,  1, -1,  2, -2, -1, -1, -4, -3, -1, -1, -2, -1,  1,  1,  3, -4, -1, -7,
+             0,  0, -4, -1, -2, -3,  8, -3, -1, -2, -1, -2, -2,  0, -1, -1, -2, -2,  0, -2, -1, -3,  1, -3, -2, -1, -7,
+            -2, -2, -5, -2,  0, -3, -3, 14, -2, -2, -2, -1,  2, -1, -1,  1,  0, -1, -1, -2, -1, -3, -5,  0,  0, -1, -7,
+             0, -2, -2, -4, -3,  0, -1, -2,  6,  4, -2,  2,  1,  0,  0, -3, -2, -3, -1,  0,  0,  4, -3, -1, -3,  0, -7,
+            -1, -2, -1, -3, -2,  1, -2, -2,  4,  4, -2,  3,  2, -1,  0, -3, -2, -3, -2,  0,  0,  3, -3,  1, -2,  0, -7,
+             0,  0, -3,  0,  2, -1, -1, -2, -2, -2,  4, -2,  2,  0,  0,  1,  0,  1,  0, -1,  0, -2, -2, -1,  1,  0, -7,
+            -1, -1,  0, -1, -1,  2, -2, -1,  2,  3, -2,  4,  2, -2,  0, -3, -2, -2, -2,  0,  0,  1, -2,  3, -1,  0, -7,
+             1, -2, -2, -3, -1, -2, -2,  2,  1,  2,  2,  2,  6,  0,  0, -4, -1,  0, -2,  0,  0,  0, -3, -1, -1,  0, -7,
+             0,  4, -1,  1, -1, -1,  0, -1,  0, -1,  0, -2,  0,  8,  0, -3, -1, -2,  0,  1,  0, -2, -7, -4, -1,  0, -7,
+             0, -1, -2, -1, -1, -1, -1, -1,  0,  0,  0,  0,  0,  0, -1, -1,  0, -1,  0,  0, -1,  0, -2, -1,  0, -1, -7,
+            -1, -2, -3, -1,  1, -4, -1,  1, -3, -3,  1, -3, -4, -3, -1, 11,  0, -1, -1,  0, -1, -4, -3, -2,  0, -1, -7,
+             1, -1, -2, -1,  2, -3, -2,  0, -2, -2,  0, -2, -1, -1,  0,  0,  8,  3, -1,  0,  0, -3, -1, -1,  4,  0, -7,
+            -1, -2, -2, -1, -1, -1, -2, -1, -3, -3,  1, -2,  0, -2, -1, -1,  3,  8, -1, -3, -1, -1,  0,  0,  0, -1, -7,
+             1,  0, -2,  0,  0, -1,  0, -1, -1, -2,  0, -2, -2,  0,  0, -1, -1, -1,  4,  2,  0, -1, -3, -2, -1,  0, -7,
+             1,  0, -2, -1, -2, -2, -2, -2,  0,  0, -1,  0,  0,  1,  0,  0,  0, -3,  2,  5,  0,  1, -5, -1, -1,  0, -7,
+             0, -1, -2, -1, -1, -1, -1, -1,  0,  0,  0,  0,  0,  0, -1, -1,  0, -1,  0,  0, -1,  0, -2, -1,  0, -1, -7,
+             1, -2, -2, -2, -3,  1, -3, -3,  4,  3, -2,  1,  0, -2,  0, -4, -3, -1, -1,  1,  0,  5, -3,  1, -3,  0, -7,
+            -5, -5, -2, -4, -1,  1,  1, -5, -3, -3, -2, -2, -3, -7, -2, -3, -1,  0, -3, -5, -2, -3, 20,  5, -1, -2, -7,
+            -4, -3, -6, -1, -2,  3, -3,  0, -1,  1, -1,  3, -1, -4, -1, -2, -1,  0, -2, -1, -1,  1,  5,  9, -2, -1, -7,
+             0,  0,  0,  0,  5, -4, -2,  0, -3, -2,  1, -1, -1, -1,  0,  0,  4,  0, -1, -1,  0, -3, -1, -2,  4,  0, -7,
+             0, -1, -2, -1, -1, -1, -1, -1,  0,  0,  0,  0,  0,  0, -1, -1,  0, -1,  0,  0, -1,  0, -2, -1,  0, -1, -7,
+            -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7,  1
         };
         return _data;
     }
 };
 
-
-/*
-.Tag.Blosum45_:
-..cat:Scoring
-..summary:Tag for Retrieving a BLOSUM45 matrix.
-..include:seqan/score.h
- */
 struct Blosum45_ {};
+typedef Blosum45_ ScoreSpecBlosum45;
 
 /*!
  * @typedef Blosum45
  * @headerfile <seqan/score.h>
  * @brief BLOSUM45 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Blosum45_> > Blosum45;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecBlosum45> > Blosum45;
+ *
+ * @code{.txt}
+ * A   5
+ * B  -1  4
+ * C  -1 -2 12
+ * D  -2  5 -3  7
+ * E  -1  1 -3  2  6
+ * F  -2 -3 -2 -4 -3  8
+ * G   0 -1 -3 -1 -2 -3  7
+ * H  -2  0 -3  0  0 -2 -2 10
+ * I  -1 -3 -3 -4 -3  0 -4 -3  5
+ * J  -1 -3 -3 -4 -3  1 -4 -3  4  4
+ * K  -1  0 -3  0  1 -3 -2 -1 -3 -3  5
+ * L  -1 -3 -2 -3 -2  1 -3 -2  2  4 -3  5
+ * M  -1 -2 -2 -3 -2  0 -2  0  2  2 -1  2  6
+ * N  -1  4 -2  2  0 -2  0  1 -2 -3  0 -3 -2  6
+ * O   0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+ * P  -1 -2 -4 -1  0 -3 -2 -2 -2 -3 -1 -3 -2 -2 -1  9
+ * Q  -1  0 -3  0  2 -4 -2  1 -2 -2  1 -2  0  0 -1 -1  6
+ * R  -2 -1 -3 -1  0 -2 -2  0 -3 -3  3 -2 -1  0 -1 -2  1  7
+ * S   1  0 -1  0  0 -2  0 -1 -2 -3 -1 -3 -2  1  0 -1  0 -1  4
+ * T   0  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1  0  0 -1 -1 -1  2  5
+ * U   0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1  0  0 -1
+ * V   0 -3 -1 -3 -3  0 -3 -3  3  2 -2  1  1 -3 -1 -3 -3 -2 -1  0 -1  5
+ * W  -2 -4 -5 -4 -3  1 -2 -3 -2 -2 -2 -2 -2 -4 -2 -3 -2 -2 -4 -3 -2 -3 15
+ * Y  -2 -2 -3 -2 -2  3 -3  2  0  0 -1  0  0 -2 -1 -3 -1 -1 -2 -1 -1 -1  3  8
+ * Z  -1  2 -3  1  4 -3 -2  0 -3 -3  1 -2 -1  0 -1 -1  4  0  0 -1 -1 -3 -2 -2  4
+ * X   0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1  0  0 -1 -1 -2 -1 -1 -1
+ * *  -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1
+ *
+ *     A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  Y  Z  X  *
+ *
+ * @endcode
  */
 
-/**
-.Shortcut.Blosum45:
-..cat:Scoring
-..summary:Blosum45 scoring matrix.
-..signature:Blosum45
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Blosum45_> >
-..include:seqan/score.h
-*/
-typedef Score<int, ScoreMatrix<AminoAcid, Blosum45_> > Blosum45;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecBlosum45> > Blosum45;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Blosum45_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecBlosum45> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -175,66 +231,86 @@ struct ScoringMatrixData_<int, AminoAcid, Blosum45_> {
         // Cluster Percentage: >= 45
         // Entropy =   0.3795, Expected =  -0.2789
         static int const _data[TAB_SIZE] = {
-             5, -2, -1, -2, -1, -1, -1,  0, -2, -1, -1, -1, -1, -2, -1,  1,  0, -2, -2,  0, -1, -1,  0, -5,
-            -2,  7,  0, -1, -3,  1,  0, -2,  0, -3, -2,  3, -1, -2, -2, -1, -1, -2, -1, -2, -1,  0, -1, -5,
-            -1,  0,  6,  2, -2,  0,  0,  0,  1, -2, -3,  0, -2, -2, -2,  1,  0, -4, -2, -3,  4,  0, -1, -5,
-            -2, -1,  2,  7, -3,  0,  2, -1,  0, -4, -3,  0, -3, -4, -1,  0, -1, -4, -2, -3,  5,  1, -1, -5,
-            -1, -3, -2, -3, 12, -3, -3, -3, -3, -3, -2, -3, -2, -2, -4, -1, -1, -5, -3, -1, -2, -3, -2, -5,
-            -1,  1,  0,  0, -3,  6,  2, -2,  1, -2, -2,  1,  0, -4, -1,  0, -1, -2, -1, -3,  0,  4, -1, -5,
-            -1,  0,  0,  2, -3,  2,  6, -2,  0, -3, -2,  1, -2, -3,  0,  0, -1, -3, -2, -3,  1,  4, -1, -5,
-             0, -2,  0, -1, -3, -2, -2,  7, -2, -4, -3, -2, -2, -3, -2,  0, -2, -2, -3, -3, -1, -2, -1, -5,
-            -2,  0,  1,  0, -3,  1,  0, -2, 10, -3, -2, -1,  0, -2, -2, -1, -2, -3,  2, -3,  0,  0, -1, -5,
-            -1, -3, -2, -4, -3, -2, -3, -4, -3,  5,  2, -3,  2,  0, -2, -2, -1, -2,  0,  3, -3, -3, -1, -5,
-            -1, -2, -3, -3, -2, -2, -2, -3, -2,  2,  5, -3,  2,  1, -3, -3, -1, -2,  0,  1, -3, -2, -1, -5,
-            -1,  3,  0,  0, -3,  1,  1, -2, -1, -3, -3,  5, -1, -3, -1, -1, -1, -2, -1, -2,  0,  1, -1, -5,
-            -1, -1, -2, -3, -2,  0, -2, -2,  0,  2,  2, -1,  6,  0, -2, -2, -1, -2,  0,  1, -2, -1, -1, -5,
-            -2, -2, -2, -4, -2, -4, -3, -3, -2,  0,  1, -3,  0,  8, -3, -2, -1,  1,  3,  0, -3, -3, -1, -5,
-            -1, -2, -2, -1, -4, -1,  0, -2, -2, -2, -3, -1, -2, -3,  9, -1, -1, -3, -3, -3, -2, -1, -1, -5,
-             1, -1,  1,  0, -1,  0,  0,  0, -1, -2, -3, -1, -2, -2, -1,  4,  2, -4, -2, -1,  0,  0,  0, -5,
-             0, -1,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1,  2,  5, -3, -1,  0,  0, -1,  0, -5,
-            -2, -2, -4, -4, -5, -2, -3, -2, -3, -2, -2, -2, -2,  1, -3, -4, -3, 15,  3, -3, -4, -2, -2, -5,
-            -2, -1, -2, -2, -3, -1, -2, -3,  2,  0,  0, -1,  0,  3, -3, -2, -1,  3,  8, -1, -2, -2, -1, -5,
-             0, -2, -3, -3, -1, -3, -3, -3, -3,  3,  1, -2,  1,  0, -3, -1,  0, -3, -1,  5, -3, -3, -1, -5,
-            -1, -1,  4,  5, -2,  0,  1, -1,  0, -3, -3,  0, -2, -3, -2,  0,  0, -4, -2, -3,  4,  2, -1, -5,
-            -1,  0,  0,  1, -3,  4,  4, -2,  0, -3, -2,  1, -1, -3, -1,  0, -1, -2, -2, -3,  2,  4, -1, -5,
-             0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  0,  0, -2, -1, -1, -1, -1, -1, -5,
-            -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5,  1,
+             5, -1, -1, -2, -1, -2,  0, -2, -1, -1, -1, -1, -1, -1,  0, -1, -1, -2,  1,  0,  0,  0, -2, -2, -1,  0, -5,
+            -1,  4, -2,  5,  1, -3, -1,  0, -3, -3,  0, -3, -2,  4, -1, -2,  0, -1,  0,  0, -1, -3, -4, -2,  2, -1, -5,
+            -1, -2, 12, -3, -3, -2, -3, -3, -3, -3, -3, -2, -2, -2, -2, -4, -3, -3, -1, -1, -2, -1, -5, -3, -3, -2, -5,
+            -2,  5, -3,  7,  2, -4, -1,  0, -4, -4,  0, -3, -3,  2, -1, -1,  0, -1,  0, -1, -1, -3, -4, -2,  1, -1, -5,
+            -1,  1, -3,  2,  6, -3, -2,  0, -3, -3,  1, -2, -2,  0, -1,  0,  2,  0,  0, -1, -1, -3, -3, -2,  4, -1, -5,
+            -2, -3, -2, -4, -3,  8, -3, -2,  0,  1, -3,  1,  0, -2, -1, -3, -4, -2, -2, -1, -1,  0,  1,  3, -3, -1, -5,
+             0, -1, -3, -1, -2, -3,  7, -2, -4, -4, -2, -3, -2,  0, -1, -2, -2, -2,  0, -2, -1, -3, -2, -3, -2, -1, -5,
+            -2,  0, -3,  0,  0, -2, -2, 10, -3, -3, -1, -2,  0,  1, -1, -2,  1,  0, -1, -2, -1, -3, -3,  2,  0, -1, -5,
+            -1, -3, -3, -4, -3,  0, -4, -3,  5,  4, -3,  2,  2, -2, -1, -2, -2, -3, -2, -1, -1,  3, -2,  0, -3, -1, -5,
+            -1, -3, -3, -4, -3,  1, -4, -3,  4,  4, -3,  4,  2, -3, -1, -3, -2, -3, -3, -1, -1,  2, -2,  0, -3, -1, -5,
+            -1,  0, -3,  0,  1, -3, -2, -1, -3, -3,  5, -3, -1,  0, -1, -1,  1,  3, -1, -1, -1, -2, -2, -1,  1, -1, -5,
+            -1, -3, -2, -3, -2,  1, -3, -2,  2,  4, -3,  5,  2, -3, -1, -3, -2, -2, -3, -1, -1,  1, -2,  0, -2, -1, -5,
+            -1, -2, -2, -3, -2,  0, -2,  0,  2,  2, -1,  2,  6, -2, -1, -2,  0, -1, -2, -1, -1,  1, -2,  0, -1, -1, -5,
+            -1,  4, -2,  2,  0, -2,  0,  1, -2, -3,  0, -3, -2,  6, -1, -2,  0,  0,  1,  0, -1, -3, -4, -2,  0, -1, -5,
+             0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  0,  0, -1, -1, -2, -1, -1, -1, -5,
+            -1, -2, -4, -1,  0, -3, -2, -2, -2, -3, -1, -3, -2, -2, -1,  9, -1, -2, -1, -1, -1, -3, -3, -3, -1, -1, -5,
+            -1,  0, -3,  0,  2, -4, -2,  1, -2, -2,  1, -2,  0,  0, -1, -1,  6,  1,  0, -1, -1, -3, -2, -1,  4, -1, -5,
+            -2, -1, -3, -1,  0, -2, -2,  0, -3, -3,  3, -2, -1,  0, -1, -2,  1,  7, -1, -1, -1, -2, -2, -1,  0, -1, -5,
+             1,  0, -1,  0,  0, -2,  0, -1, -2, -3, -1, -3, -2,  1,  0, -1,  0, -1,  4,  2,  0, -1, -4, -2,  0,  0, -5,
+             0,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -1,  0,  0, -1, -1, -1,  2,  5,  0,  0, -3, -1, -1,  0, -5,
+             0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  0,  0, -1, -1, -2, -1, -1, -1, -5,
+             0, -3, -1, -3, -3,  0, -3, -3,  3,  2, -2,  1,  1, -3, -1, -3, -3, -2, -1,  0, -1,  5, -3, -1, -3, -1, -5,
+            -2, -4, -5, -4, -3,  1, -2, -3, -2, -2, -2, -2, -2, -4, -2, -3, -2, -2, -4, -3, -2, -3, 15,  3, -2, -2, -5,
+            -2, -2, -3, -2, -2,  3, -3,  2,  0,  0, -1,  0,  0, -2, -1, -3, -1, -1, -2, -1, -1, -1,  3,  8, -2, -1, -5,
+            -1,  2, -3,  1,  4, -3, -2,  0, -3, -3,  1, -2, -1,  0, -1, -1,  4,  0,  0, -1, -1, -3, -2, -2,  4, -1, -5,
+             0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  0,  0, -1, -1, -2, -1, -1, -1, -5,
+            -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5,  1
         };
         return _data;
     }
 };
 
-
-/*
-.Tag.Blosum62_:
-..cat:Scoring
-..summary:Tag for Retrieving a BLOSUM62 matrix.
-..include:seqan/score.h
- */
 struct Blosum62_ {};
+typedef Blosum62_ ScoreSpecBlosum62;
 
 /*!
  * @typedef Blosum62
  * @headerfile <seqan/score.h>
  * @brief BLOSUM62 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Blosum62_> > Blosum62;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecBlosum62> > Blosum62;
+ *
+ * @code{.txt}
+ * A   4
+ * B  -2  4
+ * C   0 -3  9
+ * D  -2  4 -3  6
+ * E  -1  1 -4  2  5
+ * F  -2 -3 -2 -3 -3  6
+ * G   0 -1 -3 -1 -2 -3  6
+ * H  -2  0 -3 -1  0 -1 -2  8
+ * I  -1 -3 -1 -3 -3  0 -4 -3  4
+ * J  -1 -4 -1 -4 -3  0 -4 -3  3  3
+ * K  -1  0 -3 -1  1 -3 -2 -1 -3 -3  5
+ * L  -1 -4 -1 -4 -3  0 -4 -3  2  3 -2  4
+ * M  -1 -3 -1 -3 -2  0 -3 -2  1  2 -1  2  5
+ * N  -2  3 -3  1  0 -3  0  1 -3 -3  0 -3 -2  6
+ * X   0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
+ * P  -1 -2 -3 -1 -1 -4 -2 -2 -3 -3 -1 -3 -2 -2 -2  7
+ * Q  -1  0 -3  0  2 -3 -2  0 -3 -3  1 -2  0  0 -1 -1  5
+ * R  -1 -1 -3 -2  0 -3 -2  0 -3 -3  2 -2 -1  0 -1 -2  1  5
+ * S   1  0 -1  0  0 -2  0 -1 -2 -2  0 -2 -1  1  0 -1  0 -1  4
+ * T   0 -1 -1 -1 -1 -2 -2 -2 -1 -1 -1 -1 -1  0  0 -1 -1 -1  1  5
+ * U   0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1  0  0 -1
+ * V   0 -3 -1 -3 -2 -1 -3 -3  3  2 -2  1  1 -3 -1 -2 -2 -3 -2  0 -1  4
+ * W  -3 -4 -2 -4 -3  1 -2 -2 -3 -3 -3 -2 -1 -4 -2 -4 -2 -3 -3 -2 -2 -3 11
+ * Y  -2 -3 -2 -3 -2  3 -3  2 -1 -1 -2 -1 -1 -2 -1 -3 -1 -2 -2 -2 -1 -1  2  7
+ * Z  -1  1 -3  1  4 -3 -2  0 -3 -3  1 -3 -1  0 -1 -1  3  0  0 -1 -1 -2 -3 -2  4
+ * X   0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1  0  0 -1 -1 -2 -1 -1 -1
+ * *  -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1
+ *
+ *     A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  Y  Z  X  *
+ * @endcode
  */
 
-/**
-.Shortcut.Blosum62:
-..cat:Scoring
-..summary:Blosum62 scoring matrix.
-..signature:Blosum62
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Blosum62_> >
-..include:seqan/score.h
- */
-typedef Score<int, ScoreMatrix<AminoAcid, Blosum62_> > Blosum62;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecBlosum62> > Blosum62;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Blosum62_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecBlosum62> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -249,66 +325,86 @@ struct ScoringMatrixData_<int, AminoAcid, Blosum62_> {
         // Cluster Percentage: >= 62
         // Entropy =   0.6979, Expected =  -0.5209
         static int const _data[TAB_SIZE] = {
-             4, -1, -2, -2,  0, -1, -1,  0, -2, -1, -1, -1, -1, -2, -1,  1,  0, -3, -2,  0, -2, -1,  0, -4,
-            -1,  5,  0, -2, -3,  1,  0, -2,  0, -3, -2,  2, -1, -3, -2, -1, -1, -3, -2, -3, -1,  0, -1, -4,
-            -2,  0,  6,  1, -3,  0,  0,  0,  1, -3, -3,  0, -2, -3, -2,  1,  0, -4, -2, -3,  3,  0, -1, -4,
-            -2, -2,  1,  6, -3,  0,  2, -1, -1, -3, -4, -1, -3, -3, -1,  0, -1, -4, -3, -3,  4,  1, -1, -4,
-             0, -3, -3, -3,  9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4,
-            -1,  1,  0,  0, -3,  5,  2, -2,  0, -3, -2,  1,  0, -3, -1,  0, -1, -2, -1, -2,  0,  3, -1, -4,
-            -1,  0,  0,  2, -4,  2,  5, -2,  0, -3, -3,  1, -2, -3, -1,  0, -1, -3, -2, -2,  1,  4, -1, -4,
-             0, -2,  0, -1, -3, -2, -2,  6, -2, -4, -4, -2, -3, -3, -2,  0, -2, -2, -3, -3, -1, -2, -1, -4,
-            -2,  0,  1, -1, -3,  0,  0, -2,  8, -3, -3, -1, -2, -1, -2, -1, -2, -2,  2, -3,  0,  0, -1, -4,
-            -1, -3, -3, -3, -1, -3, -3, -4, -3,  4,  2, -3,  1,  0, -3, -2, -1, -3, -1,  3, -3, -3, -1, -4,
-            -1, -2, -3, -4, -1, -2, -3, -4, -3,  2,  4, -2,  2,  0, -3, -2, -1, -2, -1,  1, -4, -3, -1, -4,
-            -1,  2,  0, -1, -3,  1,  1, -2, -1, -3, -2,  5, -1, -3, -1,  0, -1, -3, -2, -2,  0,  1, -1, -4,
-            -1, -1, -2, -3, -1,  0, -2, -3, -2,  1,  2, -1,  5,  0, -2, -1, -1, -1, -1,  1, -3, -1, -1, -4,
-            -2, -3, -3, -3, -2, -3, -3, -3, -1,  0,  0, -3,  0,  6, -4, -2, -2,  1,  3, -1, -3, -3, -1, -4,
-            -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4,  7, -1, -1, -4, -3, -2, -2, -1, -2, -4,
-             1, -1,  1,  0, -1,  0,  0,  0, -1, -2, -2,  0, -1, -2, -1,  4,  1, -3, -2, -2,  0,  0,  0, -4,
-             0, -1,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1,  1,  5, -2, -2,  0, -1, -1,  0, -4,
-            -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1,  1, -4, -3, -2, 11,  2, -3, -4, -3, -2, -4,
-            -2, -2, -2, -3, -2, -1, -2, -3,  2, -1, -1, -2, -1,  3, -3, -2, -2,  2,  7, -1, -3, -2, -1, -4,
-             0, -3, -3, -3, -1, -2, -2, -3, -3,  3,  1, -2,  1, -1, -2, -2,  0, -3, -1,  4, -3, -2, -1, -4,
-            -2, -1,  3,  4, -3,  0,  1, -1,  0, -3, -4,  0, -3, -3, -2,  0, -1, -4, -3, -3,  4,  1, -1, -4,
-            -1,  0,  0,  1, -3,  3,  4, -2,  0, -3, -3,  1, -1, -3, -1,  0, -1, -3, -2, -2,  1,  4, -1, -4,
-             0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2,  0,  0, -2, -1, -1, -1, -1, -1, -4,
-            -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,  1,
+             4, -2,  0, -2, -1, -2,  0, -2, -1, -1, -1, -1, -1, -2,  0, -1, -1, -1,  1,  0,  0,  0, -3, -2, -1,  0, -4,
+            -2,  4, -3,  4,  1, -3, -1,  0, -3, -4,  0, -4, -3,  3, -1, -2,  0, -1,  0, -1, -1, -3, -4, -3,  1, -1, -4,
+             0, -3,  9, -3, -4, -2, -3, -3, -1, -1, -3, -1, -1, -3, -2, -3, -3, -3, -1, -1, -2, -1, -2, -2, -3, -2, -4,
+            -2,  4, -3,  6,  2, -3, -1, -1, -3, -4, -1, -4, -3,  1, -1, -1,  0, -2,  0, -1, -1, -3, -4, -3,  1, -1, -4,
+            -1,  1, -4,  2,  5, -3, -2,  0, -3, -3,  1, -3, -2,  0, -1, -1,  2,  0,  0, -1, -1, -2, -3, -2,  4, -1, -4,
+            -2, -3, -2, -3, -3,  6, -3, -1,  0,  0, -3,  0,  0, -3, -1, -4, -3, -3, -2, -2, -1, -1,  1,  3, -3, -1, -4,
+             0, -1, -3, -1, -2, -3,  6, -2, -4, -4, -2, -4, -3,  0, -1, -2, -2, -2,  0, -2, -1, -3, -2, -3, -2, -1, -4,
+            -2,  0, -3, -1,  0, -1, -2,  8, -3, -3, -1, -3, -2,  1, -1, -2,  0,  0, -1, -2, -1, -3, -2,  2,  0, -1, -4,
+            -1, -3, -1, -3, -3,  0, -4, -3,  4,  3, -3,  2,  1, -3, -1, -3, -3, -3, -2, -1, -1,  3, -3, -1, -3, -1, -4,
+            -1, -4, -1, -4, -3,  0, -4, -3,  3,  3, -3,  3,  2, -3, -1, -3, -3, -3, -2, -1, -1,  2, -3, -1, -3, -1, -4,
+            -1,  0, -3, -1,  1, -3, -2, -1, -3, -3,  5, -2, -1,  0, -1, -1,  1,  2,  0, -1, -1, -2, -3, -2,  1, -1, -4,
+            -1, -4, -1, -4, -3,  0, -4, -3,  2,  3, -2,  4,  2, -3, -1, -3, -2, -2, -2, -1, -1,  1, -2, -1, -3, -1, -4,
+            -1, -3, -1, -3, -2,  0, -3, -2,  1,  2, -1,  2,  5, -2, -1, -2,  0, -1, -1, -1, -1,  1, -1, -1, -1, -1, -4,
+            -2,  3, -3,  1,  0, -3,  0,  1, -3, -3,  0, -3, -2,  6, -1, -2,  0,  0,  1,  0, -1, -3, -4, -2,  0, -1, -4,
+             0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1,  0,  0, -1, -1, -2, -1, -1, -1, -4,
+            -1, -2, -3, -1, -1, -4, -2, -2, -3, -3, -1, -3, -2, -2, -2,  7, -1, -2, -1, -1, -2, -2, -4, -3, -1, -2, -4,
+            -1,  0, -3,  0,  2, -3, -2,  0, -3, -3,  1, -2,  0,  0, -1, -1,  5,  1,  0, -1, -1, -2, -2, -1,  3, -1, -4,
+            -1, -1, -3, -2,  0, -3, -2,  0, -3, -3,  2, -2, -1,  0, -1, -2,  1,  5, -1, -1, -1, -3, -3, -2,  0, -1, -4,
+             1,  0, -1,  0,  0, -2,  0, -1, -2, -2,  0, -2, -1,  1,  0, -1,  0, -1,  4,  1,  0, -2, -3, -2,  0,  0, -4,
+             0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, -1,  0,  0, -1, -1, -1,  1,  5,  0,  0, -2, -2, -1,  0, -4,
+             0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1,  0,  0, -1, -1, -2, -1, -1, -1, -4,
+             0, -3, -1, -3, -2, -1, -3, -3,  3,  2, -2,  1,  1, -3, -1, -2, -2, -3, -2,  0, -1,  4, -3, -1, -2, -1, -4,
+            -3, -4, -2, -4, -3,  1, -2, -2, -3, -3, -3, -2, -1, -4, -2, -4, -2, -3, -3, -2, -2, -3, 11,  2, -3, -2, -4,
+            -2, -3, -2, -3, -2,  3, -3,  2, -1, -1, -2, -1, -1, -2, -1, -3, -1, -2, -2, -2, -1, -1,  2,  7, -2, -1, -4,
+            -1,  1, -3,  1,  4, -3, -2,  0, -3, -3,  1, -3, -1,  0, -1, -1,  3,  0,  0, -1, -1, -2, -3, -2,  4, -1, -4,
+             0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1,  0,  0, -1, -1, -2, -1, -1, -1, -4,
+            -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,  1
         };
         return _data;
     }
 };
 
-
-/*
-.Tag.Blosum80_:
-..cat:Scoring
-..summary:Tag for Retrieving a BLOSUM80 matrix.
-..include:seqan/score.h
- */
 struct Blosum80_ {};
+typedef Blosum80_ ScoreSpecBlosum80;
 
 /*!
  * @typedef Blosum80
  * @headerfile <seqan/score.h>
  * @brief BLOSUM80 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Blosum80_> > Blosum80;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecBlosum80> > Blosum80;
+ *
+ * @code{.txt}
+ * A   7
+ * B  -3  6
+ * C  -1 -6 13
+ * D  -3  6 -7 10
+ * E  -2  1 -7  2  8
+ * F  -4 -6 -4 -6 -6 10
+ * G   0 -2 -6 -3 -4 -6  9
+ * H  -3 -1 -7 -2  0 -2 -4 12
+ * I  -3 -6 -2 -7 -6 -1 -7 -6  7
+ * J  -3 -7 -3 -7 -6 -1 -7 -6  5  5
+ * K  -1 -1 -6 -2  1 -5 -3 -1 -5 -5  8
+ * L  -3 -7 -3 -7 -6  0 -7 -5  2  4 -4  6
+ * M  -2 -5 -3 -6 -4  0 -5 -4  2  3 -3  3  9
+ * N  -3  5 -5  2 -1 -6 -1  1 -6 -6  0 -6 -4  9
+ * O  -1 -3 -4 -3 -2 -3 -3 -2 -2 -2 -2 -2 -2 -2 -2
+ * P  -1 -4 -6 -3 -2 -6 -5 -4 -5 -5 -2 -5 -4 -4 -3 12
+ * Q  -2 -1 -5 -1  3 -5 -4  1 -5 -5  2 -4 -1  0 -2 -3  9
+ * R  -3 -2 -6 -3 -1 -5 -4  0 -5 -5  3 -4 -3 -1 -2 -3  1  9
+ * S   2  0 -2 -1 -1 -4 -1 -2 -4 -4 -1 -4 -3  1 -1 -2 -1 -2  7
+ * T   0 -1 -2 -2 -2 -4 -3 -3 -2 -3 -1 -3 -1  0 -1 -3 -1 -2  2  8
+ * U  -1 -3 -4 -3 -2 -3 -3 -2 -2 -2 -2 -2 -2 -2 -2 -3 -2 -2 -1 -1 -2
+ * V  -1 -6 -2 -6 -4 -2 -6 -5  4  3 -4  1  1 -5 -2 -4 -4 -4 -3  0 -2  7
+ * W  -5 -8 -5 -8 -6  0 -6 -4 -5 -5 -6 -4 -3 -7 -5 -7 -4 -5 -6 -5 -5 -5 16
+ * Y  -4 -5 -5 -6 -5  4 -6  3 -3 -3 -4 -2 -3 -4 -3 -6 -3 -4 -3 -3 -3 -3  3 11
+ * Z  -2  0 -7  1  6 -6 -4  0 -6 -6  1 -5 -3 -1 -1 -2  5  0 -1 -2 -1 -4 -5 -4  6
+ * X  -1 -3 -4 -3 -2 -3 -3 -2 -2 -2 -2 -2 -2 -2 -2 -3 -2 -2 -1 -1 -2 -2 -5 -3 -1 -2
+ * *  -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8  1
+ *
+ *     A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  Y  Z  X  *
+ * @endcode
  */
 
-/**
-.Shortcut.Blosum80:
-..cat:Scoring
-..summary:Blosum80 scoring matrix.
-..signature:Blosum80
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Blosum80_> >
-..include:seqan/score.h
-*/
-typedef Score<int, ScoreMatrix<AminoAcid, Blosum80_> > Blosum80;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecBlosum80> > Blosum80;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Blosum80_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecBlosum80> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -323,66 +419,86 @@ struct ScoringMatrixData_<int, AminoAcid, Blosum80_> {
         // Cluster Percentage: >= 80
         // Entropy =   0.9868, Expected =  -0.7442
         static int const _data[TAB_SIZE] = {
-             7, -3, -3, -3, -1, -2, -2,  0, -3, -3, -3, -1, -2, -4, -1,  2,  0, -5, -4, -1, -3, -2, -1, -8,
-            -3,  9, -1, -3, -6,  1, -1, -4,  0, -5, -4,  3, -3, -5, -3, -2, -2, -5, -4, -4, -2,  0, -2, -8,
-            -3, -1,  9,  2, -5,  0, -1, -1,  1, -6, -6,  0, -4, -6, -4,  1,  0, -7, -4, -5,  5, -1, -2, -8,
-            -3, -3,  2, 10, -7, -1,  2, -3, -2, -7, -7, -2, -6, -6, -3, -1, -2, -8, -6, -6,  6,  1, -3, -8,
-            -1, -6, -5, -7, 13, -5, -7, -6, -7, -2, -3, -6, -3, -4, -6, -2, -2, -5, -5, -2, -6, -7, -4, -8,
-            -2,  1,  0, -1, -5,  9,  3, -4,  1, -5, -4,  2, -1, -5, -3, -1, -1, -4, -3, -4, -1,  5, -2, -8,
-            -2, -1, -1,  2, -7,  3,  8, -4,  0, -6, -6,  1, -4, -6, -2, -1, -2, -6, -5, -4,  1,  6, -2, -8,
-             0, -4, -1, -3, -6, -4, -4,  9, -4, -7, -7, -3, -5, -6, -5, -1, -3, -6, -6, -6, -2, -4, -3, -8,
-            -3,  0,  1, -2, -7,  1,  0, -4, 12, -6, -5, -1, -4, -2, -4, -2, -3, -4,  3, -5, -1,  0, -2, -8,
-            -3, -5, -6, -7, -2, -5, -6, -7, -6,  7,  2, -5,  2, -1, -5, -4, -2, -5, -3,  4, -6, -6, -2, -8,
-            -3, -4, -6, -7, -3, -4, -6, -7, -5,  2,  6, -4,  3,  0, -5, -4, -3, -4, -2,  1, -7, -5, -2, -8,
-            -1,  3,  0, -2, -6,  2,  1, -3, -1, -5, -4,  8, -3, -5, -2, -1, -1, -6, -4, -4, -1,  1, -2, -8,
-            -2, -3, -4, -6, -3, -1, -4, -5, -4,  2,  3, -3,  9,  0, -4, -3, -1, -3, -3,  1, -5, -3, -2, -8,
-            -4, -5, -6, -6, -4, -5, -6, -6, -2, -1,  0, -5,  0, 10, -6, -4, -4,  0,  4, -2, -6, -6, -3, -8,
-            -1, -3, -4, -3, -6, -3, -2, -5, -4, -5, -5, -2, -4, -6, 12, -2, -3, -7, -6, -4, -4, -2, -3, -8,
-             2, -2,  1, -1, -2, -1, -1, -1, -2, -4, -4, -1, -3, -4, -2,  7,  2, -6, -3, -3,  0, -1, -1, -8,
-             0, -2,  0, -2, -2, -1, -2, -3, -3, -2, -3, -1, -1, -4, -3,  2,  8, -5, -3,  0, -1, -2, -1, -8,
-            -5, -5, -7, -8, -5, -4, -6, -6, -4, -5, -4, -6, -3,  0, -7, -6, -5, 16,  3, -5, -8, -5, -5, -8,
-            -4, -4, -4, -6, -5, -3, -5, -6,  3, -3, -2, -4, -3,  4, -6, -3, -3,  3, 11, -3, -5, -4, -3, -8,
-            -1, -4, -5, -6, -2, -4, -4, -6, -5,  4,  1, -4,  1, -2, -4, -3,  0, -5, -3,  7, -6, -4, -2, -8,
-            -3, -2,  5,  6, -6, -1,  1, -2, -1, -6, -7, -1, -5, -6, -4,  0, -1, -8, -5, -6,  6,  0, -3, -8,
-            -2,  0, -1,  1, -7,  5,  6, -4,  0, -6, -5,  1, -3, -6, -2, -1, -2, -5, -4, -4,  0,  6, -1, -8,
-            -1, -2, -2, -3, -4, -2, -2, -3, -2, -2, -2, -2, -2, -3, -3, -1, -1, -5, -3, -2, -3, -1, -2, -8,
-            -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,  1,
+             7,  -3,  -1,  -3,  -2,  -4,   0,  -3,  -3,  -3,  -1,  -3,  -2,  -3,  -1,  -1,  -2,  -3,   2,   0,  -1,  -1,  -5,  -4,  -2,  -1,  -8,
+            -3,   6,  -6,   6,   1,  -6,  -2,  -1,  -6,  -7,  -1,  -7,  -5,   5,  -3,  -4,  -1,  -2,   0,  -1,  -3,  -6,  -8,  -5,   0,  -3,  -8,
+            -1,  -6,  13,  -7,  -7,  -4,  -6,  -7,  -2,  -3,  -6,  -3,  -3,  -5,  -4,  -6,  -5,  -6,  -2,  -2,  -4,  -2,  -5,  -5,  -7,  -4,  -8,
+            -3,   6,  -7,  10,   2,  -6,  -3,  -2,  -7,  -7,  -2,  -7,  -6,   2,  -3,  -3,  -1,  -3,  -1,  -2,  -3,  -6,  -8,  -6,   1,  -3,  -8,
+            -2,   1,  -7,   2,   8,  -6,  -4,   0,  -6,  -6,   1,  -6,  -4,  -1,  -2,  -2,   3,  -1,  -1,  -2,  -2,  -4,  -6,  -5,   6,  -2,  -8,
+            -4,  -6,  -4,  -6,  -6,  10,  -6,  -2,  -1,  -1,  -5,   0,   0,  -6,  -3,  -6,  -5,  -5,  -4,  -4,  -3,  -2,   0,   4,  -6,  -3,  -8,
+             0,  -2,  -6,  -3,  -4,  -6,   9,  -4,  -7,  -7,  -3,  -7,  -5,  -1,  -3,  -5,  -4,  -4,  -1,  -3,  -3,  -6,  -6,  -6,  -4,  -3,  -8,
+            -3,  -1,  -7,  -2,   0,  -2,  -4,  12,  -6,  -6,  -1,  -5,  -4,   1,  -2,  -4,   1,   0,  -2,  -3,  -2,  -5,  -4,   3,   0,  -2,  -8,
+            -3,  -6,  -2,  -7,  -6,  -1,  -7,  -6,   7,   5,  -5,   2,   2,  -6,  -2,  -5,  -5,  -5,  -4,  -2,  -2,   4,  -5,  -3,  -6,  -2,  -8,
+            -3,  -7,  -3,  -7,  -6,  -1,  -7,  -6,   5,   5,  -5,   4,   3,  -6,  -2,  -5,  -5,  -5,  -4,  -3,  -2,   3,  -5,  -3,  -6,  -2,  -8,
+            -1,  -1,  -6,  -2,   1,  -5,  -3,  -1,  -5,  -5,   8,  -4,  -3,   0,  -2,  -2,   2,   3,  -1,  -1,  -2,  -4,  -6,  -4,   1,  -2,  -8,
+            -3,  -7,  -3,  -7,  -6,   0,  -7,  -5,   2,   4,  -4,   6,   3,  -6,  -2,  -5,  -4,  -4,  -4,  -3,  -2,   1,  -4,  -2,  -5,  -2,  -8,
+            -2,  -5,  -3,  -6,  -4,   0,  -5,  -4,   2,   3,  -3,   3,   9,  -4,  -2,  -4,  -1,  -3,  -3,  -1,  -2,   1,  -3,  -3,  -3,  -2,  -8,
+            -3,   5,  -5,   2,  -1,  -6,  -1,   1,  -6,  -6,   0,  -6,  -4,   9,  -2,  -4,   0,  -1,   1,   0,  -2,  -5,  -7,  -4,  -1,  -2,  -8,
+            -1,  -3,  -4,  -3,  -2,  -3,  -3,  -2,  -2,  -2,  -2,  -2,  -2,  -2,  -2,  -3,  -2,  -2,  -1,  -1,  -2,  -2,  -5,  -3,  -1,  -2,  -8,
+            -1,  -4,  -6,  -3,  -2,  -6,  -5,  -4,  -5,  -5,  -2,  -5,  -4,  -4,  -3,  12,  -3,  -3,  -2,  -3,  -3,  -4,  -7,  -6,  -2,  -3,  -8,
+            -2,  -1,  -5,  -1,   3,  -5,  -4,   1,  -5,  -5,   2,  -4,  -1,   0,  -2,  -3,   9,   1,  -1,  -1,  -2,  -4,  -4,  -3,   5,  -2,  -8,
+            -3,  -2,  -6,  -3,  -1,  -5,  -4,   0,  -5,  -5,   3,  -4,  -3,  -1,  -2,  -3,   1,   9,  -2,  -2,  -2,  -4,  -5,  -4,   0,  -2,  -8,
+             2,   0,  -2,  -1,  -1,  -4,  -1,  -2,  -4,  -4,  -1,  -4,  -3,   1,  -1,  -2,  -1,  -2,   7,   2,  -1,  -3,  -6,  -3,  -1,  -1,  -8,
+             0,  -1,  -2,  -2,  -2,  -4,  -3,  -3,  -2,  -3,  -1,  -3,  -1,   0,  -1,  -3,  -1,  -2,   2,   8,  -1,   0,  -5,  -3,  -2,  -1,  -8,
+            -1,  -3,  -4,  -3,  -2,  -3,  -3,  -2,  -2,  -2,  -2,  -2,  -2,  -2,  -2,  -3,  -2,  -2,  -1,  -1,  -2,  -2,  -5,  -3,  -1,  -2,  -8,
+            -1,  -6,  -2,  -6,  -4,  -2,  -6,  -5,   4,   3,  -4,   1,   1,  -5,  -2,  -4,  -4,  -4,  -3,   0,  -2,   7,  -5,  -3,  -4,  -2,  -8,
+            -5,  -8,  -5,  -8,  -6,   0,  -6,  -4,  -5,  -5,  -6,  -4,  -3,  -7,  -5,  -7,  -4,  -5,  -6,  -5,  -5,  -5,  16,   3,  -5,  -5,  -8,
+            -4,  -5,  -5,  -6,  -5,   4,  -6,   3,  -3,  -3,  -4,  -2,  -3,  -4,  -3,  -6,  -3,  -4,  -3,  -3,  -3,  -3,   3,  11,  -4,  -3,  -8,
+            -2,   0,  -7,   1,   6,  -6,  -4,   0,  -6,  -6,   1,  -5,  -3,  -1,  -1,  -2,   5,   0,  -1,  -2,  -1,  -4,  -5,  -4,   6,  -1,  -8,
+            -1,  -3,  -4,  -3,  -2,  -3,  -3,  -2,  -2,  -2,  -2,  -2,  -2,  -2,  -2,  -3,  -2,  -2,  -1,  -1,  -2,  -2,  -5,  -3,  -1,  -2,  -8,
+            -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,   1
         };
         return _data;
     }
 };
 
-
-/*
-.Tag.Pam40_:
-..cat:Scoring
-..summary:Tag for Retrieving a PAM40 matrix.
-..include:seqan/score.h
- */
 struct Pam40_ {};
+typedef Pam40_ ScoreSpecPam40;
 
 /*!
  * @typedef Pam40
  * @headerfile <seqan/score.h>
  * @brief PAM40 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Pam40_> > Pam40;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecPam40> > Pam40;
+ *
+ * @code{.txt}
+ * A     6
+ * B    -3   6
+ * C    -6 -11   9
+ * D    -3   6 -12   7
+ * E    -2   2 -12   3   7
+ * F    -7  -9 -11 -13 -12   9
+ * G    -1  -2  -8  -3  -3  -8   6
+ * H    -6  -1  -7  -3  -4  -5  -8   9
+ * I    -4  -5  -5  -6  -5  -2  -9  -8   8
+ * J    -5  -7  -9  -9  -7  -2  -9  -7   4   4
+ * K    -6  -2 -12  -4  -4 -12  -6  -5  -5  -6   6
+ * L    -5  -8 -13 -11  -8  -2  -9  -5  -1   3  -7   7
+ * M    -4  -8 -12  -9  -6  -3  -7  -9   0   1  -1   1  11
+ * N    -3   6  -9   2  -1  -8  -2   1  -4  -5   0  -6  -7   7
+ * O    -3  -4  -8  -5  -4  -7  -4  -4  -4  -5  -4  -5  -4  -3  -4
+ * P    -1  -6  -7  -7  -5  -9  -5  -3  -7  -7  -6  -6  -7  -5  -4   8
+ * Q    -3  -2 -12  -2   2 -11  -6   1  -7  -6  -2  -4  -3  -3  -4  -2   8
+ * R    -6  -6  -7  -9  -8  -8  -8  -1  -5  -7   1  -8  -3  -5  -5  -3  -1   8
+ * S     0  -1  -2  -3  -4  -6  -1  -5  -6  -7  -3  -7  -5   0  -2  -1  -4  -2   6
+ * T     0  -2  -7  -4  -5  -8  -5  -6  -2  -4  -2  -6  -3  -1  -3  -3  -5  -5   1   7
+ * U    -3  -4  -8  -5  -4  -7  -4  -4  -4  -5  -4  -5  -4  -3  -4  -4  -4  -5  -2  -3  -4
+ * V    -2  -7  -5  -7  -6  -7  -5  -6   2   0  -8  -2  -1  -7  -4  -5  -6  -7  -5  -2  -4   7
+ * W   -12  -9 -14 -13 -15  -4 -13  -6 -12  -9 -10  -5 -11  -7  -9 -12 -11  -1  -4 -11  -9 -14  13
+ * Y    -7  -6  -3 -10  -8   2 -12  -3  -5  -6  -8  -6 -10  -4  -7 -12 -10  -9  -6  -6  -7  -6  -4  10
+ * Z    -2   1 -12   2   6 -12  -4   0  -5  -6  -3  -6  -4  -2  -4  -3   6  -3  -4  -5  -4  -6 -13  -8   6
+ * X    -3  -4  -8  -5  -4  -7  -4  -4  -4  -5  -4  -5  -4  -3  -4  -4  -4  -5  -2  -3  -4  -4  -9  -7  -4  -4
+ * *   -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15   1
+ *
+ *       A   B   C   D   E   F   G   H   I   J   K   L   M   N   O   P   Q   R   S   T   U   V   W   Y   Z   X   *
+ * @endcode
  */
 
-/**
-.Shortcut.Pam40:
-..cat:Scoring
-..summary:Pam40 scoring matrix.
-..signature:Pam40
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Pam40_> >
-..include:seqan/score.h
-*/
-typedef Score<int, ScoreMatrix<AminoAcid, Pam40_> > Pam40;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecPam40> > Pam40;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Pam40_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecPam40> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -390,76 +506,96 @@ struct ScoringMatrixData_<int, AminoAcid, Pam40_> {
 
     static inline int const * getData() {
         SEQAN_CHECKPOINT;
-        // 
+        //
         // This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-        // 
+        //
         // PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574
-        // 
+        //
         // Expected score = -4.27, Entropy = 2.26 bits
-        // 
+        //
         // Lowest score = -15, Highest score = 13
-        // 
+        //
         static int const _data[TAB_SIZE] = {
-              6,  -6,  -3,  -3,  -6,  -3,  -2,  -1,  -6,  -4,  -5,  -6,  -4,  -7,  -1,   0,   0, -12,  -7,  -2,  -3,  -2,  -3, -15,
-             -6,   8,  -5,  -9,  -7,  -1,  -8,  -8,  -1,  -5,  -8,   1,  -3,  -8,  -3,  -2,  -5,  -1,  -9,  -7,  -6,  -3,  -5, -15,
-             -3,  -5,   7,   2,  -9,  -3,  -1,  -2,   1,  -4,  -6,   0,  -7,  -8,  -5,   0,  -1,  -7,  -4,  -7,   6,  -2,  -3, -15,
-             -3,  -9,   2,   7, -12,  -2,   3,  -3,  -3,  -6, -11,  -4,  -9, -13,  -7,  -3,  -4, -13, -10,  -7,   6,   2,  -5, -15,
-             -6,  -7,  -9, -12,   9, -12, -12,  -8,  -7,  -5, -13, -12, -12, -11,  -7,  -2,  -7, -14,  -3,  -5, -11, -12,  -8, -15,
-             -3,  -1,  -3,  -2, -12,   8,   2,  -6,   1,  -7,  -4,  -2,  -3, -11,  -2,  -4,  -5, -11, -10,  -6,  -2,   6,  -4, -15,
-             -2,  -8,  -1,   3, -12,   2,   7,  -3,  -4,  -5,  -8,  -4,  -6, -12,  -5,  -4,  -5, -15,  -8,  -6,   2,   6,  -4, -15,
-             -1,  -8,  -2,  -3,  -8,  -6,  -3,   6,  -8,  -9,  -9,  -6,  -7,  -8,  -5,  -1,  -5, -13, -12,  -5,  -2,  -4,  -4, -15,
-             -6,  -1,   1,  -3,  -7,   1,  -4,  -8,   9,  -8,  -5,  -5,  -9,  -5,  -3,  -5,  -6,  -6,  -3,  -6,  -1,   0,  -4, -15,
-             -4,  -5,  -4,  -6,  -5,  -7,  -5,  -9,  -8,   8,  -1,  -5,   0,  -2,  -7,  -6,  -2, -12,  -5,   2,  -5,  -5,  -4, -15,
-             -5,  -8,  -6, -11, -13,  -4,  -8,  -9,  -5,  -1,   7,  -7,   1,  -2,  -6,  -7,  -6,  -5,  -6,  -2,  -8,  -6,  -5, -15,
-             -6,   1,   0,  -4, -12,  -2,  -4,  -6,  -5,  -5,  -7,   6,  -1, -12,  -6,  -3,  -2, -10,  -8,  -8,  -2,  -3,  -4, -15,
-             -4,  -3,  -7,  -9, -12,  -3,  -6,  -7,  -9,   0,   1,  -1,  11,  -3,  -7,  -5,  -3, -11, -10,  -1,  -8,  -4,  -4, -15,
-             -7,  -8,  -8, -13, -11, -11, -12,  -8,  -5,  -2,  -2, -12,  -3,   9,  -9,  -6,  -8,  -4,   2,  -7,  -9, -12,  -7, -15,
-             -1,  -3,  -5,  -7,  -7,  -2,  -5,  -5,  -3,  -7,  -6,  -6,  -7,  -9,   8,  -1,  -3, -12, -12,  -5,  -6,  -3,  -4, -15,
-              0,  -2,   0,  -3,  -2,  -4,  -4,  -1,  -5,  -6,  -7,  -3,  -5,  -6,  -1,   6,   1,  -4,  -6,  -5,  -1,  -4,  -2, -15,
-              0,  -5,  -1,  -4,  -7,  -5,  -5,  -5,  -6,  -2,  -6,  -2,  -3,  -8,  -3,   1,   7, -11,  -6,  -2,  -2,  -5,  -3, -15,
-            -12,  -1,  -7, -13, -14, -11, -15, -13,  -6, -12,  -5, -10, -11,  -4, -12,  -4, -11,  13,  -4, -14,  -9, -13,  -9, -15,
-             -7,  -9,  -4, -10,  -3, -10,  -8, -12,  -3,  -5,  -6,  -8, -10,   2, -12,  -6,  -6,  -4,  10,  -6,  -6,  -8,  -7, -15,
-             -2,  -7,  -7,  -7,  -5,  -6,  -6,  -5,  -6,   2,  -2,  -8,  -1,  -7,  -5,  -5,  -2, -14,  -6,   7,  -7,  -6,  -4, -15,
-             -3,  -6,   6,   6, -11,  -2,   2,  -2,  -1,  -5,  -8,  -2,  -8,  -9,  -6,  -1,  -2,  -9,  -6,  -7,   6,   1,  -4, -15,
-             -2,  -3,  -2,   2, -12,   6,   6,  -4,   0,  -5,  -6,  -3,  -4, -12,  -3,  -4,  -5, -13,  -8,  -6,   1,   6,  -4, -15,
-             -3,  -5,  -3,  -5,  -8,  -4,  -4,  -4,  -4,  -4,  -5,  -4,  -4,  -7,  -4,  -2,  -3,  -9,  -7,  -4,  -4,  -4,  -4, -15,
-            -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15,   1,
+             6,  -3,  -6,  -3,  -2,  -7,  -1,  -6,  -4,  -5,  -6,  -5,  -4,  -3,  -3,  -1,  -3,  -6,   0,   0,  -3,  -2, -12,  -7,  -2,  -3, -15,
+            -3,   6, -11,   6,   2,  -9,  -2,  -1,  -5,  -7,  -2,  -8,  -8,   6,  -4,  -6,  -2,  -6,  -1,  -2,  -4,  -7,  -9,  -6,   1,  -4, -15,
+            -6, -11,   9, -12, -12, -11,  -8,  -7,  -5,  -9, -12, -13, -12,  -9,  -8,  -7, -12,  -7,  -2,  -7,  -8,  -5, -14,  -3, -12,  -8, -15,
+            -3,   6, -12,   7,   3, -13,  -3,  -3,  -6,  -9,  -4, -11,  -9,   2,  -5,  -7,  -2,  -9,  -3,  -4,  -5,  -7, -13, -10,   2,  -5, -15,
+            -2,   2, -12,   3,   7, -12,  -3,  -4,  -5,  -7,  -4,  -8,  -6,  -1,  -4,  -5,   2,  -8,  -4,  -5,  -4,  -6, -15,  -8,   6,  -4, -15,
+            -7,  -9, -11, -13, -12,   9,  -8,  -5,  -2,  -2, -12,  -2,  -3,  -8,  -7,  -9, -11,  -8,  -6,  -8,  -7,  -7,  -4,   2, -12,  -7, -15,
+            -1,  -2,  -8,  -3,  -3,  -8,   6,  -8,  -9,  -9,  -6,  -9,  -7,  -2,  -4,  -5,  -6,  -8,  -1,  -5,  -4,  -5, -13, -12,  -4,  -4, -15,
+            -6,  -1,  -7,  -3,  -4,  -5,  -8,   9,  -8,  -7,  -5,  -5,  -9,   1,  -4,  -3,   1,  -1,  -5,  -6,  -4,  -6,  -6,  -3,   0,  -4, -15,
+            -4,  -5,  -5,  -6,  -5,  -2,  -9,  -8,   8,   4,  -5,  -1,   0,  -4,  -4,  -7,  -7,  -5,  -6,  -2,  -4,   2, -12,  -5,  -5,  -4, -15,
+            -5,  -7,  -9,  -9,  -7,  -2,  -9,  -7,   4,   4,  -6,   3,   1,  -5,  -5,  -7,  -6,  -7,  -7,  -4,  -5,   0,  -9,  -6,  -6,  -5, -15,
+            -6,  -2, -12,  -4,  -4, -12,  -6,  -5,  -5,  -6,   6,  -7,  -1,   0,  -4,  -6,  -2,   1,  -3,  -2,  -4,  -8, -10,  -8,  -3,  -4, -15,
+            -5,  -8, -13, -11,  -8,  -2,  -9,  -5,  -1,   3,  -7,   7,   1,  -6,  -5,  -6,  -4,  -8,  -7,  -6,  -5,  -2,  -5,  -6,  -6,  -5, -15,
+            -4,  -8, -12,  -9,  -6,  -3,  -7,  -9,   0,   1,  -1,   1,  11,  -7,  -4,  -7,  -3,  -3,  -5,  -3,  -4,  -1, -11, -10,  -4,  -4, -15,
+            -3,   6,  -9,   2,  -1,  -8,  -2,   1,  -4,  -5,   0,  -6,  -7,   7,  -3,  -5,  -3,  -5,   0,  -1,  -3,  -7,  -7,  -4,  -2,  -3, -15,
+            -3,  -4,  -8,  -5,  -4,  -7,  -4,  -4,  -4,  -5,  -4,  -5,  -4,  -3,  -4,  -4,  -4,  -5,  -2,  -3,  -4,  -4,  -9,  -7,  -4,  -4, -15,
+            -1,  -6,  -7,  -7,  -5,  -9,  -5,  -3,  -7,  -7,  -6,  -6,  -7,  -5,  -4,   8,  -2,  -3,  -1,  -3,  -4,  -5, -12, -12,  -3,  -4, -15,
+            -3,  -2, -12,  -2,   2, -11,  -6,   1,  -7,  -6,  -2,  -4,  -3,  -3,  -4,  -2,   8,  -1,  -4,  -5,  -4,  -6, -11, -10,   6,  -4, -15,
+            -6,  -6,  -7,  -9,  -8,  -8,  -8,  -1,  -5,  -7,   1,  -8,  -3,  -5,  -5,  -3,  -1,   8,  -2,  -5,  -5,  -7,  -1,  -9,  -3,  -5, -15,
+             0,  -1,  -2,  -3,  -4,  -6,  -1,  -5,  -6,  -7,  -3,  -7,  -5,   0,  -2,  -1,  -4,  -2,   6,   1,  -2,  -5,  -4,  -6,  -4,  -2, -15,
+             0,  -2,  -7,  -4,  -5,  -8,  -5,  -6,  -2,  -4,  -2,  -6,  -3,  -1,  -3,  -3,  -5,  -5,   1,   7,  -3,  -2, -11,  -6,  -5,  -3, -15,
+            -3,  -4,  -8,  -5,  -4,  -7,  -4,  -4,  -4,  -5,  -4,  -5,  -4,  -3,  -4,  -4,  -4,  -5,  -2,  -3,  -4,  -4,  -9,  -7,  -4,  -4, -15,
+            -2,  -7,  -5,  -7,  -6,  -7,  -5,  -6,   2,   0,  -8,  -2,  -1,  -7,  -4,  -5,  -6,  -7,  -5,  -2,  -4,   7, -14,  -6,  -6,  -4, -15,
+           -12,  -9, -14, -13, -15,  -4, -13,  -6, -12,  -9, -10,  -5, -11,  -7,  -9, -12, -11,  -1,  -4, -11,  -9, -14,  13,  -4, -13,  -9, -15,
+            -7,  -6,  -3, -10,  -8,   2, -12,  -3,  -5,  -6,  -8,  -6, -10,  -4,  -7, -12, -10,  -9,  -6,  -6,  -7,  -6,  -4,  10,  -8,  -7, -15,
+            -2,   1, -12,   2,   6, -12,  -4,   0,  -5,  -6,  -3,  -6,  -4,  -2,  -4,  -3,   6,  -3,  -4,  -5,  -4,  -6, -13,  -8,   6,  -4, -15,
+            -3,  -4,  -8,  -5,  -4,  -7,  -4,  -4,  -4,  -5,  -4,  -5,  -4,  -3,  -4,  -4,  -4,  -5,  -2,  -3,  -4,  -4,  -9,  -7,  -4,  -4, -15,
+           -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15, -15,   1
         };
         return _data;
     }
 };
 
-
-/*
-.Tag.Pam120_:
-..cat:Scoring
-..summary:Tag for Retrieving a PAM120 matrix.
-..include:seqan/score.h
- */
 struct Pam120_ {};
+typedef Pam120_ ScoreSpecPam120;
 
 /*!
  * @typedef Pam120
  * @headerfile <seqan/score.h>
  * @brief PAM120 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Pam120_> > Pam120;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecPam120> > Pam120;
+ *
+ * @code{.txt}
+ * A   3
+ * B   0  4
+ * C  -3 -6  9
+ * D   0  4 -7  5
+ * E   0  3 -7  3  5
+ * F  -4 -5 -6 -7 -7  8
+ * G   1  0 -4  0 -1 -5  5
+ * H  -3  1 -4  0 -1 -3 -4  7
+ * I  -1 -3 -3 -3 -3  0 -4 -4  6
+ * J  -2 -4 -5 -4 -4  0 -5 -4  4  4
+ * K  -2  0 -7 -1 -1 -7 -3 -2 -3 -4  5
+ * L  -3 -4 -7 -5 -4  0 -5 -3  1  3 -4  5
+ * M  -2 -4 -6 -4 -3 -1 -4 -4  1  2  0  3  8
+ * N  -1  3 -5  2  1 -4  0  2 -2 -3  1 -4 -3  4
+ * O  -1 -1 -4 -2 -1 -3 -2 -2 -1 -2 -2 -2 -2 -1 -1
+ * P   1 -2 -4 -3 -2 -5 -2 -1 -3 -3 -2 -3 -3 -2 -2  6
+ * Q  -1  0 -7  1  2 -6 -3  3 -3 -3  0 -2 -1  0 -1  0  6
+ * R  -3 -2 -4 -3 -3 -5 -4  1 -2 -3  2 -4 -1 -1 -2 -1  1  6
+ * S   1  0  0  0 -1 -3  1 -2 -2 -3 -1 -4 -2  1 -1  1 -2 -1  3
+ * T   1  0 -3 -1 -2 -4 -1 -3  0 -2 -1 -3 -1  0 -1 -1 -2 -2  2  4
+ * U  -1 -1 -4 -2 -1 -3 -2 -2 -1 -2 -2 -2 -2 -1 -2 -2 -1 -2 -1 -1 -2
+ * V   0 -3 -3 -3 -3 -3 -2 -3  3  2 -4  1  1 -3 -1 -2 -3 -3 -2  0 -1  5
+ * W  -7 -6 -8 -8 -8 -1 -8 -3 -6 -5 -5 -3 -6 -4 -5 -7 -6  1 -2 -6 -5 -8 12
+ * Y  -4 -3 -1 -5 -5  4 -6 -1 -2 -2 -5 -2 -4 -2 -3 -6 -5 -5 -3 -3 -3 -3 -2  8
+ * Z  -1  2 -7  3  4 -6 -2  1 -3 -3 -1 -3 -2  0 -1 -1  4 -1 -1 -2 -1 -3 -7 -5  4
+ * X  -1 -1 -4 -2 -1 -3 -2 -2 -1 -2 -2 -2 -2 -1 -2 -2 -1 -2 -1 -1 -2 -1 -5 -3 -1 -2
+ * *  -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8  1
+ *
+ *     A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  Y  Z  X  *
+ * @endcode
  */
 
-/**
-.Shortcut.Pam120:
-..cat:Scoring
-..summary:Pam120 scoring matrix.
-..signature:Pam120
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Pam120_> >
-..include:seqan/score.h
-*/
-typedef Score<int, ScoreMatrix<AminoAcid, Pam120_> > Pam120;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecPam120> > Pam120;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Pam120_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecPam120> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -468,74 +604,94 @@ struct ScoringMatrixData_<int, AminoAcid, Pam120_> {
     static inline int const * getData() {
         SEQAN_CHECKPOINT;
         // This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-        // 
+        //
         // PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574
-        // 
+        //
         // Expected score = -1.64, Entropy = 0.979 bits
-        // 
+        //
         // Lowest score = -8, Highest score = 12
-        // 
+        //
         static int const _data[TAB_SIZE] = {
-              3,  -3,  -1,   0,  -3,  -1,   0,   1,  -3,  -1,  -3,  -2,  -2,  -4,   1,   1,   1,  -7,  -4,   0,   0,  -1,  -1,  -8,
-             -3,   6,  -1,  -3,  -4,   1,  -3,  -4,   1,  -2,  -4,   2,  -1,  -5,  -1,  -1,  -2,   1,  -5,  -3,  -2,  -1,  -2,  -8,
-             -1,  -1,   4,   2,  -5,   0,   1,   0,   2,  -2,  -4,   1,  -3,  -4,  -2,   1,   0,  -4,  -2,  -3,   3,   0,  -1,  -8,
-              0,  -3,   2,   5,  -7,   1,   3,   0,   0,  -3,  -5,  -1,  -4,  -7,  -3,   0,  -1,  -8,  -5,  -3,   4,   3,  -2,  -8,
-             -3,  -4,  -5,  -7,   9,  -7,  -7,  -4,  -4,  -3,  -7,  -7,  -6,  -6,  -4,   0,  -3,  -8,  -1,  -3,  -6,  -7,  -4,  -8,
-             -1,   1,   0,   1,  -7,   6,   2,  -3,   3,  -3,  -2,   0,  -1,  -6,   0,  -2,  -2,  -6,  -5,  -3,   0,   4,  -1,  -8,
-              0,  -3,   1,   3,  -7,   2,   5,  -1,  -1,  -3,  -4,  -1,  -3,  -7,  -2,  -1,  -2,  -8,  -5,  -3,   3,   4,  -1,  -8,
-              1,  -4,   0,   0,  -4,  -3,  -1,   5,  -4,  -4,  -5,  -3,  -4,  -5,  -2,   1,  -1,  -8,  -6,  -2,   0,  -2,  -2,  -8,
-             -3,   1,   2,   0,  -4,   3,  -1,  -4,   7,  -4,  -3,  -2,  -4,  -3,  -1,  -2,  -3,  -3,  -1,  -3,   1,   1,  -2,  -8,
-             -1,  -2,  -2,  -3,  -3,  -3,  -3,  -4,  -4,   6,   1,  -3,   1,   0,  -3,  -2,   0,  -6,  -2,   3,  -3,  -3,  -1,  -8,
-             -3,  -4,  -4,  -5,  -7,  -2,  -4,  -5,  -3,   1,   5,  -4,   3,   0,  -3,  -4,  -3,  -3,  -2,   1,  -4,  -3,  -2,  -8,
-             -2,   2,   1,  -1,  -7,   0,  -1,  -3,  -2,  -3,  -4,   5,   0,  -7,  -2,  -1,  -1,  -5,  -5,  -4,   0,  -1,  -2,  -8,
-             -2,  -1,  -3,  -4,  -6,  -1,  -3,  -4,  -4,   1,   3,   0,   8,  -1,  -3,  -2,  -1,  -6,  -4,   1,  -4,  -2,  -2,  -8,
-             -4,  -5,  -4,  -7,  -6,  -6,  -7,  -5,  -3,   0,   0,  -7,  -1,   8,  -5,  -3,  -4,  -1,   4,  -3,  -5,  -6,  -3,  -8,
-              1,  -1,  -2,  -3,  -4,   0,  -2,  -2,  -1,  -3,  -3,  -2,  -3,  -5,   6,   1,  -1,  -7,  -6,  -2,  -2,  -1,  -2,  -8,
-              1,  -1,   1,   0,   0,  -2,  -1,   1,  -2,  -2,  -4,  -1,  -2,  -3,   1,   3,   2,  -2,  -3,  -2,   0,  -1,  -1,  -8,
-              1,  -2,   0,  -1,  -3,  -2,  -2,  -1,  -3,   0,  -3,  -1,  -1,  -4,  -1,   2,   4,  -6,  -3,   0,   0,  -2,  -1,  -8,
-             -7,   1,  -4,  -8,  -8,  -6,  -8,  -8,  -3,  -6,  -3,  -5,  -6,  -1,  -7,  -2,  -6,  12,  -2,  -8,  -6,  -7,  -5,  -8,
-             -4,  -5,  -2,  -5,  -1,  -5,  -5,  -6,  -1,  -2,  -2,  -5,  -4,   4,  -6,  -3,  -3,  -2,   8,  -3,  -3,  -5,  -3,  -8,
-              0,  -3,  -3,  -3,  -3,  -3,  -3,  -2,  -3,   3,   1,  -4,   1,  -3,  -2,  -2,   0,  -8,  -3,   5,  -3,  -3,  -1,  -8,
-              0,  -2,   3,   4,  -6,   0,   3,   0,   1,  -3,  -4,   0,  -4,  -5,  -2,   0,   0,  -6,  -3,  -3,   4,   2,  -1,  -8,
-             -1,  -1,   0,   3,  -7,   4,   4,  -2,   1,  -3,  -3,  -1,  -2,  -6,  -1,  -1,  -2,  -7,  -5,  -3,   2,   4,  -1,  -8,
-             -1,  -2,  -1,  -2,  -4,  -1,  -1,  -2,  -2,  -1,  -2,  -2,  -2,  -3,  -2,  -1,  -1,  -5,  -3,  -1,  -1,  -1,  -2,  -8,
-             -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,   1,
+             3,  0, -3,  0,  0, -4,  1, -3, -1, -2, -2, -3, -2, -1, -1,  1, -1, -3,  1,  1, -1,  0, -7, -4, -1, -1, -8,
+             0,  4, -6,  4,  3, -5,  0,  1, -3, -4,  0, -4, -4,  3, -1, -2,  0, -2,  0,  0, -1, -3, -6, -3,  2, -1, -8,
+            -3, -6,  9, -7, -7, -6, -4, -4, -3, -5, -7, -7, -6, -5, -4, -4, -7, -4,  0, -3, -4, -3, -8, -1, -7, -4, -8,
+             0,  4, -7,  5,  3, -7,  0,  0, -3, -4, -1, -5, -4,  2, -2, -3,  1, -3,  0, -1, -2, -3, -8, -5,  3, -2, -8,
+             0,  3, -7,  3,  5, -7, -1, -1, -3, -4, -1, -4, -3,  1, -1, -2,  2, -3, -1, -2, -1, -3, -8, -5,  4, -1, -8,
+            -4, -5, -6, -7, -7,  8, -5, -3,  0,  0, -7,  0, -1, -4, -3, -5, -6, -5, -3, -4, -3, -3, -1,  4, -6, -3, -8,
+             1,  0, -4,  0, -1, -5,  5, -4, -4, -5, -3, -5, -4,  0, -2, -2, -3, -4,  1, -1, -2, -2, -8, -6, -2, -2, -8,
+            -3,  1, -4,  0, -1, -3, -4,  7, -4, -4, -2, -3, -4,  2, -2, -1,  3,  1, -2, -3, -2, -3, -3, -1,  1, -2, -8,
+            -1, -3, -3, -3, -3,  0, -4, -4,  6,  4, -3,  1,  1, -2, -1, -3, -3, -2, -2,  0, -1,  3, -6, -2, -3, -1, -8,
+            -2, -4, -5, -4, -4,  0, -5, -4,  4,  4, -4,  3,  2, -3, -2, -3, -3, -3, -3, -2, -2,  2, -5, -2, -3, -2, -8,
+            -2,  0, -7, -1, -1, -7, -3, -2, -3, -4,  5, -4,  0,  1, -2, -2,  0,  2, -1, -1, -2, -4, -5, -5, -1, -2, -8,
+            -3, -4, -7, -5, -4,  0, -5, -3,  1,  3, -4,  5,  3, -4, -2, -3, -2, -4, -4, -3, -2,  1, -3, -2, -3, -2, -8,
+            -2, -4, -6, -4, -3, -1, -4, -4,  1,  2,  0,  3,  8, -3, -2, -3, -1, -1, -2, -1, -2,  1, -6, -4, -2, -2, -8,
+            -1,  3, -5,  2,  1, -4,  0,  2, -2, -3,  1, -4, -3,  4, -1, -2,  0, -1,  1,  0, -1, -3, -4, -2,  0, -1, -8,
+            -1, -1, -4, -2, -1, -3, -2, -2, -1, -2, -2, -2, -2, -1, -2, -2, -1, -2, -1, -1, -2, -1, -5, -3, -1, -2, -8,
+             1, -2, -4, -3, -2, -5, -2, -1, -3, -3, -2, -3, -3, -2, -2,  6,  0, -1,  1, -1, -2, -2, -7, -6, -1, -2, -8,
+            -1,  0, -7,  1,  2, -6, -3,  3, -3, -3,  0, -2, -1,  0, -1,  0,  6,  1, -2, -2, -1, -3, -6, -5,  4, -1, -8,
+            -3, -2, -4, -3, -3, -5, -4,  1, -2, -3,  2, -4, -1, -1, -2, -1,  1,  6, -1, -2, -2, -3,  1, -5, -1, -2, -8,
+             1,  0,  0,  0, -1, -3,  1, -2, -2, -3, -1, -4, -2,  1, -1,  1, -2, -1,  3,  2, -1, -2, -2, -3, -1, -1, -8,
+             1,  0, -3, -1, -2, -4, -1, -3,  0, -2, -1, -3, -1,  0, -1, -1, -2, -2,  2,  4, -1,  0, -6, -3, -2, -1, -8,
+            -1, -1, -4, -2, -1, -3, -2, -2, -1, -2, -2, -2, -2, -1, -2, -2, -1, -2, -1, -1, -2, -1, -5, -3, -1, -2, -8,
+             0, -3, -3, -3, -3, -3, -2, -3,  3,  2, -4,  1,  1, -3, -1, -2, -3, -3, -2,  0, -1,  5, -8, -3, -3, -1, -8,
+            -7, -6, -8, -8, -8, -1, -8, -3, -6, -5, -5, -3, -6, -4, -5, -7, -6,  1, -2, -6, -5, -8, 12, -2, -7, -5, -8,
+            -4, -3, -1, -5, -5,  4, -6, -1, -2, -2, -5, -2, -4, -2, -3, -6, -5, -5, -3, -3, -3, -3, -2,  8, -5, -3, -8,
+            -1,  2, -7,  3,  4, -6, -2,  1, -3, -3, -1, -3, -2,  0, -1, -1,  4, -1, -1, -2, -1, -3, -7, -5,  4, -1, -8,
+            -1, -1, -4, -2, -1, -3, -2, -2, -1, -2, -2, -2, -2, -1, -2, -2, -1, -2, -1, -1, -2, -1, -5, -3, -1, -2, -8,
+            -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,  1
         };
         return _data;
     }
 };
 
-
-/*
-.Tag.Pam200_:
-..cat:Scoring
-..summary:Tag for Retrieving a PAM200 matrix.
-..include:seqan/score.h
- */
 struct Pam200_ {};
+typedef Pam200_ ScoreSpecPam200;
 
 /*!
  * @typedef Pam200
  * @headerfile <seqan/score.h>
  * @brief PAM200 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Pam200_> > Pam200;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecPam200> > Pam200;
+ *
+ * @code{.txt}
+ * A   3
+ * B   0  3
+ * C  -3 -5 12
+ * D   0  4 -6  5
+ * E   0  3 -7  4  5
+ * F  -4 -6 -6 -7 -7 10
+ * G   1  0 -4  0  0 -6  6
+ * H  -2  1 -4  0  0 -2 -3  8
+ * I  -1 -3 -3 -3 -3  1 -3 -3  6
+ * J  -2 -4 -5 -4 -4  2 -4 -3  4  5
+ * K  -2  0 -7  0  0 -7 -2 -1 -2 -3  6
+ * L  -2 -4 -7 -5 -4  2 -5 -3  2  5 -4  7
+ * M  -2 -3 -6 -4 -3  0 -4 -3  2  3  1  4  8
+ * N   0  3 -5  3  2 -4  0  2 -2 -3  1 -4 -2  3
+ * O   0 -1 -4 -1 -1 -3 -1 -1 -1 -2 -1 -2 -1  0 -1
+ * P   1 -1 -4 -2 -1 -6 -1 -1 -3 -3 -2 -3 -3 -1 -1  7
+ * Q  -1  1 -7  2  3 -6 -2  3 -3 -3  1 -2 -1  1 -1  0  5
+ * R  -2 -1 -4 -2 -2 -5 -4  2 -2 -3  4 -4 -1  0 -1  0  1  7
+ * S   1  1  0  0  0 -4  1 -1 -2 -3  0 -4 -2  1  0  1 -1 -1  2
+ * T   1  0 -3  0 -1 -4  0 -2  0 -1  0 -2 -1  0  0  0 -1 -1  2  4
+ * U   0 -1 -4 -1 -1 -3 -1 -1 -1 -2 -1 -2 -1  0 -1 -1 -1 -1  0  0 -1
+ * V   0 -3 -2 -3 -2 -2 -2 -3  4  3 -3  2  2 -2 -1 -2 -3 -3 -1  0 -1  5
+ * W  -7 -6 -9 -8 -9  0 -8 -3 -6 -4 -4 -2 -5 -5 -5 -7 -6  2 -3 -6 -5 -8 18
+ * Y  -4 -4  0 -5 -5  7 -6  0 -2 -2 -5 -2 -3 -2 -3 -6 -5 -5 -3 -3 -3 -3 -1 11
+ * Z   0  2 -7  3  4 -6 -1  2 -3 -3  0 -3 -2  1 -1 -1  4  0 -1 -1 -1 -2 -7 -5  4
+ * X   0 -1 -4 -1 -1 -3 -1 -1 -1 -2 -1 -2 -1  0 -1 -1 -1 -1  0  0 -1 -1 -5 -3 -1 -1
+ * *  -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9  1
+ *
+ *     A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  Y  Z  X  *
+ * @endcode
  */
 
-/**
-.Shortcut.Pam200:
-..cat:Scoring
-..summary:Pam200 scoring matrix.
-..signature:Pam200
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Pam200_> >
-..include:seqan/score.h
-*/
-typedef Score<int, ScoreMatrix<AminoAcid, Pam200_> > Pam200;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecPam200> > Pam200;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Pam200_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecPam200> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -544,74 +700,94 @@ struct ScoringMatrixData_<int, AminoAcid, Pam200_> {
     static inline int const * getData() {
         SEQAN_CHECKPOINT;
         // This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-        // 
+        //
         // PAM 200 substitution matrix, scale = ln(2)/3 = 0.231049
-        // 
+        //
         // Expected score = -1.23, Entropy = 0.507 bits
-        // 
+        //
         // Lowest score = -9, Highest score = 18
-        // 
+        //
         static int const _data[TAB_SIZE] = {
-              3,  -2,   0,   0,  -3,  -1,   0,   1,  -2,  -1,  -2,  -2,  -2,  -4,   1,   1,   1,  -7,  -4,   0,   0,   0,   0,  -9,
-             -2,   7,   0,  -2,  -4,   1,  -2,  -4,   2,  -2,  -4,   4,  -1,  -5,   0,  -1,  -1,   2,  -5,  -3,  -1,   0,  -1,  -9,
-              0,   0,   3,   3,  -5,   1,   2,   0,   2,  -2,  -4,   1,  -2,  -4,  -1,   1,   0,  -5,  -2,  -2,   3,   1,   0,  -9,
-              0,  -2,   3,   5,  -6,   2,   4,   0,   0,  -3,  -5,   0,  -4,  -7,  -2,   0,   0,  -8,  -5,  -3,   4,   3,  -1,  -9,
-             -3,  -4,  -5,  -6,  12,  -7,  -7,  -4,  -4,  -3,  -7,  -7,  -6,  -6,  -4,   0,  -3,  -9,   0,  -2,  -5,  -7,  -4,  -9,
-             -1,   1,   1,   2,  -7,   5,   3,  -2,   3,  -3,  -2,   1,  -1,  -6,   0,  -1,  -1,  -6,  -5,  -3,   1,   4,  -1,  -9,
-              0,  -2,   2,   4,  -7,   3,   5,   0,   0,  -3,  -4,   0,  -3,  -7,  -1,   0,  -1,  -9,  -5,  -2,   3,   4,  -1,  -9,
-              1,  -4,   0,   0,  -4,  -2,   0,   6,  -3,  -3,  -5,  -2,  -4,  -6,  -1,   1,   0,  -8,  -6,  -2,   0,  -1,  -1,  -9,
-             -2,   2,   2,   0,  -4,   3,   0,  -3,   8,  -3,  -3,  -1,  -3,  -2,  -1,  -1,  -2,  -3,   0,  -3,   1,   2,  -1,  -9,
-             -1,  -2,  -2,  -3,  -3,  -3,  -3,  -3,  -3,   6,   2,  -2,   2,   1,  -3,  -2,   0,  -6,  -2,   4,  -3,  -3,  -1,  -9,
-             -2,  -4,  -4,  -5,  -7,  -2,  -4,  -5,  -3,   2,   7,  -4,   4,   2,  -3,  -4,  -2,  -2,  -2,   2,  -4,  -3,  -2,  -9,
-             -2,   4,   1,   0,  -7,   1,   0,  -2,  -1,  -2,  -4,   6,   1,  -7,  -2,   0,   0,  -4,  -5,  -3,   0,   0,  -1,  -9,
-             -2,  -1,  -2,  -4,  -6,  -1,  -3,  -4,  -3,   2,   4,   1,   8,   0,  -3,  -2,  -1,  -5,  -3,   2,  -3,  -2,  -1,  -9,
-             -4,  -5,  -4,  -7,  -6,  -6,  -7,  -6,  -2,   1,   2,  -7,   0,  10,  -6,  -4,  -4,   0,   7,  -2,  -6,  -6,  -3,  -9,
-              1,   0,  -1,  -2,  -4,   0,  -1,  -1,  -1,  -3,  -3,  -2,  -3,  -6,   7,   1,   0,  -7,  -6,  -2,  -1,  -1,  -1,  -9,
-              1,  -1,   1,   0,   0,  -1,   0,   1,  -1,  -2,  -4,   0,  -2,  -4,   1,   2,   2,  -3,  -3,  -1,   1,  -1,   0,  -9,
-              1,  -1,   0,   0,  -3,  -1,  -1,   0,  -2,   0,  -2,   0,  -1,  -4,   0,   2,   4,  -6,  -3,   0,   0,  -1,   0,  -9,
-             -7,   2,  -5,  -8,  -9,  -6,  -9,  -8,  -3,  -6,  -2,  -4,  -5,   0,  -7,  -3,  -6,  18,  -1,  -8,  -6,  -7,  -5,  -9,
-             -4,  -5,  -2,  -5,   0,  -5,  -5,  -6,   0,  -2,  -2,  -5,  -3,   7,  -6,  -3,  -3,  -1,  11,  -3,  -4,  -5,  -3,  -9,
-              0,  -3,  -2,  -3,  -2,  -3,  -2,  -2,  -3,   4,   2,  -3,   2,  -2,  -2,  -1,   0,  -8,  -3,   5,  -3,  -2,  -1,  -9,
-              0,  -1,   3,   4,  -5,   1,   3,   0,   1,  -3,  -4,   0,  -3,  -6,  -1,   1,   0,  -6,  -4,  -3,   3,   2,  -1,  -9,
-              0,   0,   1,   3,  -7,   4,   4,  -1,   2,  -3,  -3,   0,  -2,  -6,  -1,  -1,  -1,  -7,  -5,  -2,   2,   4,  -1,  -9,
-              0,  -1,   0,  -1,  -4,  -1,  -1,  -1,  -1,  -1,  -2,  -1,  -1,  -3,  -1,   0,   0,  -5,  -3,  -1,  -1,  -1,  -1,  -9,
-             -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,  -9,   1,
+             3,  0, -3,  0,  0, -4,  1, -2, -1, -2, -2, -2, -2,  0,  0,  1, -1, -2,  1,  1,  0,  0, -7, -4,  0,  0, -9,
+             0,  3, -5,  4,  3, -6,  0,  1, -3, -4,  0, -4, -3,  3, -1, -1,  1, -1,  1,  0, -1, -3, -6, -4,  2, -1, -9,
+            -3, -5, 12, -6, -7, -6, -4, -4, -3, -5, -7, -7, -6, -5, -4, -4, -7, -4,  0, -3, -4, -2, -9,  0, -7, -4, -9,
+             0,  4, -6,  5,  4, -7,  0,  0, -3, -4,  0, -5, -4,  3, -1, -2,  2, -2,  0,  0, -1, -3, -8, -5,  3, -1, -9,
+             0,  3, -7,  4,  5, -7,  0,  0, -3, -4,  0, -4, -3,  2, -1, -1,  3, -2,  0, -1, -1, -2, -9, -5,  4, -1, -9,
+            -4, -6, -6, -7, -7, 10, -6, -2,  1,  2, -7,  2,  0, -4, -3, -6, -6, -5, -4, -4, -3, -2,  0,  7, -6, -3, -9,
+             1,  0, -4,  0,  0, -6,  6, -3, -3, -4, -2, -5, -4,  0, -1, -1, -2, -4,  1,  0, -1, -2, -8, -6, -1, -1, -9,
+            -2,  1, -4,  0,  0, -2, -3,  8, -3, -3, -1, -3, -3,  2, -1, -1,  3,  2, -1, -2, -1, -3, -3,  0,  2, -1, -9,
+            -1, -3, -3, -3, -3,  1, -3, -3,  6,  4, -2,  2,  2, -2, -1, -3, -3, -2, -2,  0, -1,  4, -6, -2, -3, -1, -9,
+            -2, -4, -5, -4, -4,  2, -4, -3,  4,  5, -3,  5,  3, -3, -2, -3, -3, -3, -3, -1, -2,  3, -4, -2, -3, -2, -9,
+            -2,  0, -7,  0,  0, -7, -2, -1, -2, -3,  6, -4,  1,  1, -1, -2,  1,  4,  0,  0, -1, -3, -4, -5,  0, -1, -9,
+            -2, -4, -7, -5, -4,  2, -5, -3,  2,  5, -4,  7,  4, -4, -2, -3, -2, -4, -4, -2, -2,  2, -2, -2, -3, -2, -9,
+            -2, -3, -6, -4, -3,  0, -4, -3,  2,  3,  1,  4,  8, -2, -1, -3, -1, -1, -2, -1, -1,  2, -5, -3, -2, -1, -9,
+             0,  3, -5,  3,  2, -4,  0,  2, -2, -3,  1, -4, -2,  3,  0, -1,  1,  0,  1,  0,  0, -2, -5, -2,  1,  0, -9,
+             0, -1, -4, -1, -1, -3, -1, -1, -1, -2, -1, -2, -1,  0, -1, -1, -1, -1,  0,  0, -1, -1, -5, -3, -1, -1, -9,
+             1, -1, -4, -2, -1, -6, -1, -1, -3, -3, -2, -3, -3, -1, -1,  7,  0,  0,  1,  0, -1, -2, -7, -6, -1, -1, -9,
+            -1,  1, -7,  2,  3, -6, -2,  3, -3, -3,  1, -2, -1,  1, -1,  0,  5,  1, -1, -1, -1, -3, -6, -5,  4, -1, -9,
+            -2, -1, -4, -2, -2, -5, -4,  2, -2, -3,  4, -4, -1,  0, -1,  0,  1,  7, -1, -1, -1, -3,  2, -5,  0, -1, -9,
+             1,  1,  0,  0,  0, -4,  1, -1, -2, -3,  0, -4, -2,  1,  0,  1, -1, -1,  2,  2,  0, -1, -3, -3, -1,  0, -9,
+             1,  0, -3,  0, -1, -4,  0, -2,  0, -1,  0, -2, -1,  0,  0,  0, -1, -1,  2,  4,  0,  0, -6, -3, -1,  0, -9,
+             0, -1, -4, -1, -1, -3, -1, -1, -1, -2, -1, -2, -1,  0, -1, -1, -1, -1,  0,  0, -1, -1, -5, -3, -1, -1, -9,
+             0, -3, -2, -3, -2, -2, -2, -3,  4,  3, -3,  2,  2, -2, -1, -2, -3, -3, -1,  0, -1,  5, -8, -3, -2, -1, -9,
+            -7, -6, -9, -8, -9,  0, -8, -3, -6, -4, -4, -2, -5, -5, -5, -7, -6,  2, -3, -6, -5, -8, 18, -1, -7, -5, -9,
+            -4, -4,  0, -5, -5,  7, -6,  0, -2, -2, -5, -2, -3, -2, -3, -6, -5, -5, -3, -3, -3, -3, -1, 11, -5, -3, -9,
+             0,  2, -7,  3,  4, -6, -1,  2, -3, -3,  0, -3, -2,  1, -1, -1,  4,  0, -1, -1, -1, -2, -7, -5,  4, -1, -9,
+             0, -1, -4, -1, -1, -3, -1, -1, -1, -2, -1, -2, -1,  0, -1, -1, -1, -1,  0,  0, -1, -1, -5, -3, -1, -1, -9,
+            -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9, -9,  1
         };
         return _data;
     }
 };
 
-
-/*
-.Tag.Pam250_:
-..cat:Scoring
-..summary:Tag for Retrieving a PAM250 matrix.
-..include:seqan/score.h
- */
 struct Pam250_ {};
+typedef Pam250_ ScoreSpecPam250;
 
 /*!
  * @typedef Pam250
  * @headerfile <seqan/score.h>
  * @brief PAM250 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Pam250_> > Pam250;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecPam250> > Pam250;
+ *
+ * @code{.txt}
+ * A   2
+ * B   0  3
+ * C  -2 -4 12
+ * D   0  3 -5  4
+ * E   0  3 -5  3  4
+ * F  -3 -4 -4 -6 -5  9
+ * G   1  0 -3  1  0 -5  5
+ * H  -1  1 -3  1  1 -2 -2  6
+ * I  -1 -2 -2 -2 -2  1 -3 -2  5
+ * J  -2 -3 -4 -3 -3  2 -4 -2  4  4
+ * K  -1  1 -5  0  0 -5 -2  0 -2 -3  5
+ * L  -2 -3 -6 -4 -3  2 -4 -2  2  4 -3  6
+ * M  -1 -2 -5 -3 -2  0 -3 -2  2  3  0  4  6
+ * N   0  2 -4  2  1 -3  0  2 -2 -3  1 -3 -2  2
+ * O   0 -1 -3 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1  0 -1
+ * P   1 -1 -3 -1 -1 -5  0  0 -2 -3 -1 -3 -2  0 -1  6
+ * Q   0  1 -5  2  2 -5 -1  3 -2 -2  1 -2 -1  1 -1  0  4
+ * R  -2 -1 -4 -1 -1 -4 -3  2 -2 -3  3 -3  0  0 -1  0  1  6
+ * S   1  0  0  0  0 -3  1 -1 -1 -2  0 -3 -2  1  0  1 -1  0  2
+ * T   1  0 -2  0  0 -3  0 -1  0 -1  0 -2 -1  0  0  0 -1 -1  1  3
+ * U   0 -1 -3 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1  0 -1 -1 -1 -1  0  0 -1
+ * V   0 -2 -2 -2 -2 -1 -1 -2  4  3 -2  2  2 -2 -1 -1 -2 -2 -1  0 -1  4
+ * W  -6 -5 -8 -7 -7  0 -7 -3 -5 -4 -3 -2 -4 -4 -4 -6 -5  2 -2 -5 -4 -6 17
+ * Y  -3 -3  0 -4 -4  7 -5  0 -1 -1 -4 -1 -2 -2 -2 -5 -4 -4 -3 -3 -2 -2  0 10
+ * Z   0  2 -5  3  3 -5  0  2 -2 -3  0 -3 -2  1 -1  0  3  0  0 -1 -1 -2 -6 -4  3
+ * X   0 -1 -3 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1  0 -1 -1 -1 -1  0  0 -1 -1 -4 -2 -1 -1
+ * *  -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8  1
+ *
+ *     A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  Y  Z  X  *
+ * @endcode
  */
 
-/**
-.Shortcut.Pam250:
-..cat:Scoring
-..summary:Pam250 scoring matrix.
-..signature:Pam250
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Pam250_> >
-..include:seqan/score.h
-*/
-typedef Score<int, ScoreMatrix<AminoAcid, Pam250_> > Pam250;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecPam250> > Pam250;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Pam250_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecPam250> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -620,74 +796,94 @@ struct ScoringMatrixData_<int, AminoAcid, Pam250_> {
     static inline int const * getData() {
         SEQAN_CHECKPOINT;
         // This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-        // 
+        //
         // PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
-        // 
+        //
         // Expected score = -0.844, Entropy = 0.354 bits
-        // 
+        //
         // Lowest score = -8, Highest score = 17
-        // 
+        //
         static int const _data[TAB_SIZE] = {
-              2,  -2,   0,   0,  -2,   0,   0,   1,  -1,  -1,  -2,  -1,  -1,  -3,   1,   1,   1,  -6,  -3,   0,   0,   0,   0,  -8,
-             -2,   6,   0,  -1,  -4,   1,  -1,  -3,   2,  -2,  -3,   3,   0,  -4,   0,   0,  -1,   2,  -4,  -2,  -1,   0,  -1,  -8,
-              0,   0,   2,   2,  -4,   1,   1,   0,   2,  -2,  -3,   1,  -2,  -3,   0,   1,   0,  -4,  -2,  -2,   2,   1,   0,  -8,
-              0,  -1,   2,   4,  -5,   2,   3,   1,   1,  -2,  -4,   0,  -3,  -6,  -1,   0,   0,  -7,  -4,  -2,   3,   3,  -1,  -8,
-             -2,  -4,  -4,  -5,  12,  -5,  -5,  -3,  -3,  -2,  -6,  -5,  -5,  -4,  -3,   0,  -2,  -8,   0,  -2,  -4,  -5,  -3,  -8,
-              0,   1,   1,   2,  -5,   4,   2,  -1,   3,  -2,  -2,   1,  -1,  -5,   0,  -1,  -1,  -5,  -4,  -2,   1,   3,  -1,  -8,
-              0,  -1,   1,   3,  -5,   2,   4,   0,   1,  -2,  -3,   0,  -2,  -5,  -1,   0,   0,  -7,  -4,  -2,   3,   3,  -1,  -8,
-              1,  -3,   0,   1,  -3,  -1,   0,   5,  -2,  -3,  -4,  -2,  -3,  -5,   0,   1,   0,  -7,  -5,  -1,   0,   0,  -1,  -8,
-             -1,   2,   2,   1,  -3,   3,   1,  -2,   6,  -2,  -2,   0,  -2,  -2,   0,  -1,  -1,  -3,   0,  -2,   1,   2,  -1,  -8,
-             -1,  -2,  -2,  -2,  -2,  -2,  -2,  -3,  -2,   5,   2,  -2,   2,   1,  -2,  -1,   0,  -5,  -1,   4,  -2,  -2,  -1,  -8,
-             -2,  -3,  -3,  -4,  -6,  -2,  -3,  -4,  -2,   2,   6,  -3,   4,   2,  -3,  -3,  -2,  -2,  -1,   2,  -3,  -3,  -1,  -8,
-             -1,   3,   1,   0,  -5,   1,   0,  -2,   0,  -2,  -3,   5,   0,  -5,  -1,   0,   0,  -3,  -4,  -2,   1,   0,  -1,  -8,
-             -1,   0,  -2,  -3,  -5,  -1,  -2,  -3,  -2,   2,   4,   0,   6,   0,  -2,  -2,  -1,  -4,  -2,   2,  -2,  -2,  -1,  -8,
-             -3,  -4,  -3,  -6,  -4,  -5,  -5,  -5,  -2,   1,   2,  -5,   0,   9,  -5,  -3,  -3,   0,   7,  -1,  -4,  -5,  -2,  -8,
-              1,   0,   0,  -1,  -3,   0,  -1,   0,   0,  -2,  -3,  -1,  -2,  -5,   6,   1,   0,  -6,  -5,  -1,  -1,   0,  -1,  -8,
-              1,   0,   1,   0,   0,  -1,   0,   1,  -1,  -1,  -3,   0,  -2,  -3,   1,   2,   1,  -2,  -3,  -1,   0,   0,   0,  -8,
-              1,  -1,   0,   0,  -2,  -1,   0,   0,  -1,   0,  -2,   0,  -1,  -3,   0,   1,   3,  -5,  -3,   0,   0,  -1,   0,  -8,
-             -6,   2,  -4,  -7,  -8,  -5,  -7,  -7,  -3,  -5,  -2,  -3,  -4,   0,  -6,  -2,  -5,  17,   0,  -6,  -5,  -6,  -4,  -8,
-             -3,  -4,  -2,  -4,   0,  -4,  -4,  -5,   0,  -1,  -1,  -4,  -2,   7,  -5,  -3,  -3,   0,  10,  -2,  -3,  -4,  -2,  -8,
-              0,  -2,  -2,  -2,  -2,  -2,  -2,  -1,  -2,   4,   2,  -2,   2,  -1,  -1,  -1,   0,  -6,  -2,   4,  -2,  -2,  -1,  -8,
-              0,  -1,   2,   3,  -4,   1,   3,   0,   1,  -2,  -3,   1,  -2,  -4,  -1,   0,   0,  -5,  -3,  -2,   3,   2,  -1,  -8,
-              0,   0,   1,   3,  -5,   3,   3,   0,   2,  -2,  -3,   0,  -2,  -5,   0,   0,  -1,  -6,  -4,  -2,   2,   3,  -1,  -8,
-              0,  -1,   0,  -1,  -3,  -1,  -1,  -1,  -1,  -1,  -1,  -1,  -1,  -2,  -1,   0,   0,  -4,  -2,  -1,  -1,  -1,  -1,  -8,
-             -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,  -8,   1,
+             2,  0, -2,  0,  0, -3,  1, -1, -1, -2, -1, -2, -1,  0,  0,  1,  0, -2,  1,  1,  0,  0, -6, -3,  0,  0, -8,
+             0,  3, -4,  3,  3, -4,  0,  1, -2, -3,  1, -3, -2,  2, -1, -1,  1, -1,  0,  0, -1, -2, -5, -3,  2, -1, -8,
+            -2, -4, 12, -5, -5, -4, -3, -3, -2, -4, -5, -6, -5, -4, -3, -3, -5, -4,  0, -2, -3, -2, -8,  0, -5, -3, -8,
+             0,  3, -5,  4,  3, -6,  1,  1, -2, -3,  0, -4, -3,  2, -1, -1,  2, -1,  0,  0, -1, -2, -7, -4,  3, -1, -8,
+             0,  3, -5,  3,  4, -5,  0,  1, -2, -3,  0, -3, -2,  1, -1, -1,  2, -1,  0,  0, -1, -2, -7, -4,  3, -1, -8,
+            -3, -4, -4, -6, -5,  9, -5, -2,  1,  2, -5,  2,  0, -3, -2, -5, -5, -4, -3, -3, -2, -1,  0,  7, -5, -2, -8,
+             1,  0, -3,  1,  0, -5,  5, -2, -3, -4, -2, -4, -3,  0, -1,  0, -1, -3,  1,  0, -1, -1, -7, -5,  0, -1, -8,
+            -1,  1, -3,  1,  1, -2, -2,  6, -2, -2,  0, -2, -2,  2, -1,  0,  3,  2, -1, -1, -1, -2, -3,  0,  2, -1, -8,
+            -1, -2, -2, -2, -2,  1, -3, -2,  5,  4, -2,  2,  2, -2, -1, -2, -2, -2, -1,  0, -1,  4, -5, -1, -2, -1, -8,
+            -2, -3, -4, -3, -3,  2, -4, -2,  4,  4, -3,  4,  3, -3, -1, -3, -2, -3, -2, -1, -1,  3, -4, -1, -3, -1, -8,
+            -1,  1, -5,  0,  0, -5, -2,  0, -2, -3,  5, -3,  0,  1, -1, -1,  1,  3,  0,  0, -1, -2, -3, -4,  0, -1, -8,
+            -2, -3, -6, -4, -3,  2, -4, -2,  2,  4, -3,  6,  4, -3, -1, -3, -2, -3, -3, -2, -1,  2, -2, -1, -3, -1, -8,
+            -1, -2, -5, -3, -2,  0, -3, -2,  2,  3,  0,  4,  6, -2, -1, -2, -1,  0, -2, -1, -1,  2, -4, -2, -2, -1, -8,
+             0,  2, -4,  2,  1, -3,  0,  2, -2, -3,  1, -3, -2,  2,  0,  0,  1,  0,  1,  0,  0, -2, -4, -2,  1,  0, -8,
+             0, -1, -3, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1, -1,  0,  0, -1, -1, -4, -2, -1, -1, -8,
+             1, -1, -3, -1, -1, -5,  0,  0, -2, -3, -1, -3, -2,  0, -1,  6,  0,  0,  1,  0, -1, -1, -6, -5,  0, -1, -8,
+             0,  1, -5,  2,  2, -5, -1,  3, -2, -2,  1, -2, -1,  1, -1,  0,  4,  1, -1, -1, -1, -2, -5, -4,  3, -1, -8,
+            -2, -1, -4, -1, -1, -4, -3,  2, -2, -3,  3, -3,  0,  0, -1,  0,  1,  6,  0, -1, -1, -2,  2, -4,  0, -1, -8,
+             1,  0,  0,  0,  0, -3,  1, -1, -1, -2,  0, -3, -2,  1,  0,  1, -1,  0,  2,  1,  0, -1, -2, -3,  0,  0, -8,
+             1,  0, -2,  0,  0, -3,  0, -1,  0, -1,  0, -2, -1,  0,  0,  0, -1, -1,  1,  3,  0,  0, -5, -3, -1,  0, -8,
+             0, -1, -3, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1, -1,  0,  0, -1, -1, -4, -2, -1, -1, -8,
+             0, -2, -2, -2, -2, -1, -1, -2,  4,  3, -2,  2,  2, -2, -1, -1, -2, -2, -1,  0, -1,  4, -6, -2, -2, -1, -8,
+            -6, -5, -8, -7, -7,  0, -7, -3, -5, -4, -3, -2, -4, -4, -4, -6, -5,  2, -2, -5, -4, -6, 17,  0, -6, -4, -8,
+            -3, -3,  0, -4, -4,  7, -5,  0, -1, -1, -4, -1, -2, -2, -2, -5, -4, -4, -3, -3, -2, -2,  0, 10, -4, -2, -8,
+             0,  2, -5,  3,  3, -5,  0,  2, -2, -3,  0, -3, -2,  1, -1,  0,  3,  0,  0, -1, -1, -2, -6, -4,  3, -1, -8,
+             0, -1, -3, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1, -1,  0,  0, -1, -1, -4, -2, -1, -1, -8,
+            -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,  1,
         };
         return _data;
     }
 };
 
-
-/*
-.Tag.Vtml200_:
-..cat:Scoring
-..summary:Tag for Retrieving a PAM200 matrix.
-..include:seqan/score.h
- */
 struct Vtml200_ {};
+typedef Vtml200_ ScoreSpecVtml200;
 
 /*!
  * @typedef Vtml200
  * @headerfile <seqan/score.h>
  * @brief VTML200 scoring matrix.
  *
- * @signature typedef Score<int, ScoreMatrix<AminoAcid, Vtml200_> > Vtml200;
+ * @signature typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecVtml200> > Vtml200;
+ *
+ * @code{.txt}
+ * A   4
+ * B  -1  4
+ * C   1 -3 12
+ * D  -1  5 -4  6
+ * E  -1  2 -4  3  5
+ * F  -3 -5 -3 -6 -5  8
+ * G   0  0 -2 -1 -1 -5  8
+ * H  -2  1 -2  0  0  0 -2  8
+ * I  -1 -4  0 -5 -4  0 -6 -3  5
+ * J  -2 -5 -2 -5 -4  1 -6 -3  4  4
+ * K  -1  0 -4  0  1 -5 -2  0 -3 -3  5
+ * L  -2 -5 -3 -5 -4  2 -5 -2  3  4 -3  5
+ * M  -1 -3 -1 -4 -3  1 -4 -3  2  3 -2  3  6
+ * N  -1  4 -2  3  1 -4  0  1 -4 -4  1 -4 -3  6
+ * X  -1 -1 -1 -2 -1 -1 -2  0 -1 -1 -1 -1 -1 -1 -1
+ * P   0 -1 -3 -1 -1 -4 -2 -2 -4 -4 -1 -3 -3 -2 -2  9
+ * Q  -1  1 -3  1  2 -3 -2  2 -3 -3  2 -2 -1  1 -1 -1  5
+ * R  -2 -1 -3 -2 -1 -4 -2  1 -3 -3  4 -3 -2  0 -1 -1  2  7
+ * S   1  1  1  0  0 -3  0  0 -3 -3  0 -3 -2  1 -1  0  0 -1  4
+ * T   1  0  0 -1 -1 -3 -2 -1 -1 -2  0 -2 -1  0 -1 -1  0 -1  2  4
+ * U  -1 -1 -1 -2 -1 -1 -2  0 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1
+ * V   0 -3  1 -4 -3 -1 -4 -3  4  3 -3  2  2 -3 -1 -3 -2 -3 -2  0 -1  4
+ * W  -4 -5 -6 -6 -6  3 -5 -1 -2 -2 -4 -1 -3 -5 -2 -4 -6 -3 -4 -5 -2 -4 15
+ * Y  -3 -3  0 -4 -3  5 -5  3 -2 -2 -3 -1 -2 -2 -1 -5 -3 -2 -2 -3 -1 -2  4  9
+ * Z  -1  1 -4  2  4 -4 -2  1 -3 -3  2 -3 -2  1 -1 -1  4  0  0 -1 -1 -3 -6 -3  4
+ * X  -1 -1 -1 -2 -1 -1 -2  0 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1
+ * *  -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6  1
+ *
+ *     A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  Y  Z  X  *
+ * @endcode
  */
 
-/**
-.Shortcut.Vtml200:
-..cat:Scoring
-..summary:Vtml200 scoring matrix.
-..signature:Vtml200
-..shortcutfor:Spec.Score Matrix
-...signature:Score<int, ScoreMatrix<AminoAcid, Vtml200_> >
-..include:seqan/score.h
-*/
-typedef Score<int, ScoreMatrix<AminoAcid, Vtml200_> > Vtml200;
+typedef Score<int, ScoreMatrix<AminoAcid, ScoreSpecVtml200> > Vtml200;
 
 
 template <>
-struct ScoringMatrixData_<int, AminoAcid, Vtml200_> {
+struct ScoringMatrixData_<int, AminoAcid, ScoreSpecVtml200> {
     enum {
         VALUE_SIZE = ValueSize<AminoAcid>::VALUE,
         TAB_SIZE = VALUE_SIZE * VALUE_SIZE
@@ -696,55 +892,58 @@ struct ScoringMatrixData_<int, AminoAcid, Vtml200_> {
     static inline int const * getData() {
         SEQAN_CHECKPOINT;
         // VTML200
-        // 
+        //
         // This matrix was produced by scripts written by
         // Kai Kneutgen and Tobias Mueller [Mai-2002]
-        // 
+        //
         // VTML200  substitution matrix, Units = Third-Bits
-        // 
+        //
         // Expected Score = -1.038 Third-Bits
         // Lowest Score   = -6.432
         // Highest Score  = 15.127
         // Entropy H      = 0.420 Bits
-        // 
-        // 
+        //
+        //
         // For further information on the VTML substitution model, see
-        // 
+        //
         // Estimating Amino Acid Substitution Models:
         // A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method.
         // T. Mueller, R. Spang and M. Vingron
         // Mol Biol Evol 19(1): 8-13. 2002.
-        // 
+        //
         // or mail to
         // Tobias.Mueller@molgen.mpg.de
-        // 
+        //
         // The latest version of this perl script can be downloaded at
         // http://www.molgen.mpg.de/~muelle_t
         static int const _data[TAB_SIZE] = {
-              4,  -2,  -1,  -1,   1,  -1,  -1,   0,  -2,  -1,  -2,  -1,  -1,  -3,   0,   1,   1,  -4,  -3,   0,  -1,  -1,  -1,  -6,
-             -2,   7,   0,  -2,  -3,   2,  -1,  -2,   1,  -3,  -3,   4,  -2,  -4,  -1,  -1,  -1,  -3,  -2,  -3,  -1,   0,  -1,  -6,
-             -1,   0,   6,   3,  -2,   1,   1,   0,   1,  -4,  -4,   1,  -3,  -4,  -2,   1,   0,  -5,  -2,  -3,   4,   1,  -1,  -6,
-             -1,  -2,   3,   6,  -4,   1,   3,  -1,   0,  -5,  -5,   0,  -4,  -6,  -1,   0,  -1,  -6,  -4,  -4,   5,   2,  -2,  -6,
-              1,  -3,  -2,  -4,  12,  -3,  -4,  -2,  -2,   0,  -3,  -4,  -1,  -3,  -3,   1,   0,  -6,   0,   1,  -3,  -4,  -1,  -6,
-             -1,   2,   1,   1,  -3,   5,   2,  -2,   2,  -3,  -2,   2,  -1,  -3,  -1,   0,   0,  -6,  -3,  -2,   1,   4,  -1,  -6,
-             -1,  -1,   1,   3,  -4,   2,   5,  -1,   0,  -4,  -4,   1,  -3,  -5,  -1,   0,  -1,  -6,  -3,  -3,   2,   4,  -1,  -6,
-              0,  -2,   0,  -1,  -2,  -2,  -1,   8,  -2,  -6,  -5,  -2,  -4,  -5,  -2,   0,  -2,  -5,  -5,  -4,   0,  -2,  -2,  -6,
-             -2,   1,   1,   0,  -2,   2,   0,  -2,   8,  -3,  -2,   0,  -3,   0,  -2,   0,  -1,  -1,   3,  -3,   1,   1,   0,  -6,
-             -1,  -3,  -4,  -5,   0,  -3,  -4,  -6,  -3,   5,   3,  -3,   2,   0,  -4,  -3,  -1,  -2,  -2,   4,  -4,  -3,  -1,  -6,
-             -2,  -3,  -4,  -5,  -3,  -2,  -4,  -5,  -2,   3,   5,  -3,   3,   2,  -3,  -3,  -2,  -1,  -1,   2,  -5,  -3,  -1,  -6,
-             -1,   4,   1,   0,  -4,   2,   1,  -2,   0,  -3,  -3,   5,  -2,  -5,  -1,   0,   0,  -4,  -3,  -3,   0,   2,  -1,  -6,
-             -1,  -2,  -3,  -4,  -1,  -1,  -3,  -4,  -3,   2,   3,  -2,   6,   1,  -3,  -2,  -1,  -3,  -2,   2,  -3,  -2,  -1,  -6,
-             -3,  -4,  -4,  -6,  -3,  -3,  -5,  -5,   0,   0,   2,  -5,   1,   8,  -4,  -3,  -3,   3,   5,  -1,  -5,  -4,  -1,  -6,
-              0,  -1,  -2,  -1,  -3,  -1,  -1,  -2,  -2,  -4,  -3,  -1,  -3,  -4,   9,   0,  -1,  -4,  -5,  -3,  -1,  -1,  -2,  -6,
-              1,  -1,   1,   0,   1,   0,   0,   0,   0,  -3,  -3,   0,  -2,  -3,   0,   4,   2,  -4,  -2,  -2,   1,   0,  -1,  -6,
-              1,  -1,   0,  -1,   0,   0,  -1,  -2,  -1,  -1,  -2,   0,  -1,  -3,  -1,   2,   4,  -5,  -3,   0,   0,  -1,  -1,  -6,
-             -4,  -3,  -5,  -6,  -6,  -6,  -6,  -5,  -1,  -2,  -1,  -4,  -3,   3,  -4,  -4,  -5,  15,   4,  -4,  -5,  -6,  -2,  -6,
-             -3,  -2,  -2,  -4,   0,  -3,  -3,  -5,   3,  -2,  -1,  -3,  -2,   5,  -5,  -2,  -3,   4,   9,  -2,  -3,  -3,  -1,  -6,
-              0,  -3,  -3,  -4,   1,  -2,  -3,  -4,  -3,   4,   2,  -3,   2,  -1,  -3,  -2,   0,  -4,  -2,   4,  -3,  -3,  -1,  -6,
-             -1,  -1,   4,   5,  -3,   1,   2,   0,   1,  -4,  -5,   0,  -3,  -5,  -1,   1,   0,  -5,  -3,  -3,   4,   1,  -1,  -6,
-             -1,   0,   1,   2,  -4,   4,   4,  -2,   1,  -3,  -3,   2,  -2,  -4,  -1,   0,  -1,  -6,  -3,  -3,   1,   4,  -1,  -6,
-             -1,  -1,  -1,  -2,  -1,  -1,  -1,  -2,   0,  -1,  -1,  -1,  -1,  -1,  -2,  -1,  -1,  -2,  -1,  -1,  -1,  -1,  -1,  -6,
-             -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,  -6,   1,
+             4, -1,  1, -1, -1, -3,  0, -2, -1, -2, -1, -2, -1, -1, -1,  0, -1, -2,  1,  1, -1,  0, -4, -3, -1, -1, -6,
+            -1,  4, -3,  5,  2, -5,  0,  1, -4, -5,  0, -5, -3,  4, -1, -1,  1, -1,  1,  0, -1, -3, -5, -3,  1, -1, -6,
+             1, -3, 12, -4, -4, -3, -2, -2,  0, -2, -4, -3, -1, -2, -1, -3, -3, -3,  1,  0, -1,  1, -6,  0, -4, -1, -6,
+            -1,  5, -4,  6,  3, -6, -1,  0, -5, -5,  0, -5, -4,  3, -2, -1,  1, -2,  0, -1, -2, -4, -6, -4,  2, -2, -6,
+            -1,  2, -4,  3,  5, -5, -1,  0, -4, -4,  1, -4, -3,  1, -1, -1,  2, -1,  0, -1, -1, -3, -6, -3,  4, -1, -6,
+            -3, -5, -3, -6, -5,  8, -5,  0,  0,  1, -5,  2,  1, -4, -1, -4, -3, -4, -3, -3, -1, -1,  3,  5, -4, -1, -6,
+             0,  0, -2, -1, -1, -5,  8, -2, -6, -6, -2, -5, -4,  0, -2, -2, -2, -2,  0, -2, -2, -4, -5, -5, -2, -2, -6,
+            -2,  1, -2,  0,  0,  0, -2,  8, -3, -3,  0, -2, -3,  1,  0, -2,  2,  1,  0, -1,  0, -3, -1,  3,  1,  0, -6,
+            -1, -4,  0, -5, -4,  0, -6, -3,  5,  4, -3,  3,  2, -4, -1, -4, -3, -3, -3, -1, -1,  4, -2, -2, -3, -1, -6,
+            -2, -5, -2, -5, -4,  1, -6, -3,  4,  4, -3,  4,  3, -4, -1, -4, -3, -3, -3, -2, -1,  3, -2, -2, -3, -1, -6,
+            -1,  0, -4,  0,  1, -5, -2,  0, -3, -3,  5, -3, -2,  1, -1, -1,  2,  4,  0,  0, -1, -3, -4, -3,  2, -1, -6,
+            -2, -5, -3, -5, -4,  2, -5, -2,  3,  4, -3,  5,  3, -4, -1, -3, -2, -3, -3, -2, -1,  2, -1, -1, -3, -1, -6,
+            -1, -3, -1, -4, -3,  1, -4, -3,  2,  3, -2,  3,  6, -3, -1, -3, -1, -2, -2, -1, -1,  2, -3, -2, -2, -1, -6,
+            -1,  4, -2,  3,  1, -4,  0,  1, -4, -4,  1, -4, -3,  6, -1, -2,  1,  0,  1,  0, -1, -3, -5, -2,  1, -1, -6,
+            -1, -1, -1, -2, -1, -1, -2,  0, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -6,
+             0, -1, -3, -1, -1, -4, -2, -2, -4, -4, -1, -3, -3, -2, -2,  9, -1, -1,  0, -1, -2, -3, -4, -5, -1, -2, -6,
+            -1,  1, -3,  1,  2, -3, -2,  2, -3, -3,  2, -2, -1,  1, -1, -1,  5,  2,  0,  0, -1, -2, -6, -3,  4, -1, -6,
+            -2, -1, -3, -2, -1, -4, -2,  1, -3, -3,  4, -3, -2,  0, -1, -1,  2,  7, -1, -1, -1, -3, -3, -2,  0, -1, -6,
+             1,  1,  1,  0,  0, -3,  0,  0, -3, -3,  0, -3, -2,  1, -1,  0,  0, -1,  4,  2, -1, -2, -4, -2,  0, -1, -6,
+             1,  0,  0, -1, -1, -3, -2, -1, -1, -2,  0, -2, -1,  0, -1, -1,  0, -1,  2,  4, -1,  0, -5, -3, -1, -1, -6,
+            -1, -1, -1, -2, -1, -1, -2,  0, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -6,
+             0, -3,  1, -4, -3, -1, -4, -3,  4,  3, -3,  2,  2, -3, -1, -3, -2, -3, -2,  0, -1,  4, -4, -2, -3, -1, -6,
+            -4, -5, -6, -6, -6,  3, -5, -1, -2, -2, -4, -1, -3, -5, -2, -4, -6, -3, -4, -5, -2, -4, 15,  4, -6, -2, -6,
+            -3, -3,  0, -4, -3,  5, -5,  3, -2, -2, -3, -1, -2, -2, -1, -5, -3, -2, -2, -3, -1, -2,  4,  9, -3, -1, -6,
+            -1,  1, -4,  2,  4, -4, -2,  1, -3, -3,  2, -3, -2,  1, -1, -1,  4,  0,  0, -1, -1, -3, -6, -3,  4, -1, -6,
+            -1, -1, -1, -2, -1, -1, -2,  0, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -6,
+            -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6,  1
         };
         return _data;
     }
@@ -752,4 +951,4 @@ struct ScoringMatrixData_<int, AminoAcid, Vtml200_> {
 
 }  // namespace SEQAN_NAMESPACE_MAIN
 
-#endif  // SEQAN_SCORE_SCORE_MATRIX_DATA_H_
+#endif  // SEQAN_SSCORE_MATRIX_DATA_H_
diff --git a/seqan/score/score_matrix_io.h b/seqan/score/score_matrix_io.h
index cb51f67..b3b2ae8 100644
--- a/seqan/score/score_matrix_io.h
+++ b/seqan/score/score_matrix_io.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 
 // TODO(holtgrew): We need to adapt this to the new I/O scheme.
 
-#ifndef CORE_INCLUDE_SEQAN_SCORE_SCORE_MATRIX_IO_H_
-#define CORE_INCLUDE_SEQAN_SCORE_SCORE_MATRIX_IO_H_
+#ifndef INCLUDE_SEQAN_SCORE_SCORE_MATRIX_IO_H_
+#define INCLUDE_SEQAN_SCORE_SCORE_MATRIX_IO_H_
 
 #include <seqan/stream.h>
 
@@ -57,11 +57,6 @@ namespace seqan {
 
 // TODO(holtgrew): What format is this actually?
 
-/**
-.Tag.File Format.tag.ScoreMatrixFile:Score matrix file.
-..include:seqan/score.h
-*/
-
 struct TagScoreMatrixFile_;
 typedef Tag<TagScoreMatrixFile_> ScoreMatrixFile;
 
@@ -73,128 +68,42 @@ typedef Tag<TagScoreMatrixFile_> ScoreMatrixFile;
 // Functions
 // ============================================================================
 
-// ----------------------------------------------------------------------------
-// Helper Function _sscanfValue()                                 [DEPRECATED!]
-// ----------------------------------------------------------------------------
-
-/*
-.Function._sscanfValue:
-..cat:Input/Output
-..summary:Use sscanf to parse a value from a $char *$ buffer.
-..signature:_sscanfValue(buffer, value)
-..param.buffer:Buffer to parse into.
-...type:const char *
-..param.value:Variable to parse the value from $buffer$ to.
-...type:unsigned int
-..include:seqan/score.h
- */
-
-inline void
-SEQAN_DEPRECATED_PRE("Use new RecordReader-based parsing functionality instead")
-_sscanfValue(const char * buf, unsigned int & val)
-SEQAN_DEPRECATED_POST("Use new RecordReader-based parsing functionality instead");
-
-inline void
-_sscanfValue(const char * buf, unsigned int & val)
-{
-    SEQAN_CHECKPOINT;
-    std::sscanf(buf, "%u", & val);
-}
-
-/*
-.Function._sscanfValue.param.value.type:int
-..include:seqan/score.h
- */
-
-inline void
-SEQAN_DEPRECATED_PRE("Use new RecordReader-based parsing functionality instead")
-_sscanfValue(const char * buf, int & val)
-SEQAN_DEPRECATED_POST("Use new RecordReader-based parsing functionality instead");
-
-inline void
-_sscanfValue(const char * buf, int & val)
-{
-    SEQAN_CHECKPOINT;
-    std::sscanf(buf, "%i", & val);
-}
-
-/*
-.Function._sscanfValue.param.value.type:float
-..include:seqan/score.h
- */
-
-inline void
-SEQAN_DEPRECATED_PRE("Use new RecordReader-based parsing functionality instead")
-_sscanfValue(const char * buf, float & val)
-SEQAN_DEPRECATED_POST("Use new RecordReader-based parsing functionality instead");
-
-inline void
-_sscanfValue(const char * buf, float & val)
-{
-    SEQAN_CHECKPOINT;
-    std::sscanf(buf, "%f", & val);
-}
-
-/*
-.Function._sscanfValue.param.value.type:double
-..include:seqan/score.h
- */
-
-inline void
-SEQAN_DEPRECATED_PRE("Use new RecordReader-based parsing functionality instead")
-_sscanfValue(const char * buf, double & val)
-SEQAN_DEPRECATED_POST("Use new RecordReader-based parsing functionality instead");
-
-inline void
-_sscanfValue(const char * buf, double & val)
-{
-    SEQAN_CHECKPOINT;
-    std::sscanf(buf, "%lf", & val);
-}
-
 // ----------------------------------------------------------------------------
 // Function readMeta()                                        [ScoreMatrixFile]
 // ----------------------------------------------------------------------------
 
-// TODO(holtgrew): Fix parameter order, adjust to new style I/O system.
-
-template <typename TStream, typename TMeta>
-int
-readMeta(RecordReader<TStream, SinglePass<> > & reader,
-         TMeta & meta,
+template <typename TMeta, typename TSourceIter>
+inline void
+readMeta(TMeta & meta,
+         TSourceIter & reader,
          ScoreMatrixFile const & /*tag*/)
 {
     clear(meta);
     while (!atEnd(reader) && value(reader) == '#')
     {
-        goNext(reader);
-        int res = readLine(meta, reader);
-        if (res != 0 && res != EOF_BEFORE_SUCCESS)
-            return 1;
+        skipOne(reader);
+        readLine(meta, reader);
     }
-
-    return 0;
 }
 
 // ----------------------------------------------------------------------------
 // Function read()                                            [ScoreMatrixFile]
 // ----------------------------------------------------------------------------
 
-template <typename TStream, typename TValue, typename TSequenceValue, typename TSpec>
-int
-read(RecordReader<TStream, SinglePass<> > & reader,
-     Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc,
+template <typename TValue, typename TSequenceValue, typename TSpec, typename TSourceIter>
+inline void
+read(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc,
+     TSourceIter & reader,
      ScoreMatrixFile const & /*tag*/)
 {
     typedef Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > TScore;
 
     // Clear the matrix.
-    std::fill(sc.data_tab, sc.data_tab + TScore::TAB_SIZE, TValue());
+    arrayFill(sc.data_tab, sc.data_tab + TScore::TAB_SIZE, TValue());
 
     // Skip header.
     while (!atEnd(reader) && value(reader) == '#')
-        if (skipLine(reader) != 0)
-            return 1;  // Also at EOF!
+        skipLine(reader);
 
     // -----------------------------------------------------------------------
     // Read alphabet line.
@@ -202,77 +111,48 @@ read(RecordReader<TStream, SinglePass<> > & reader,
     // The first non-header line is the alphabet line.  Read in the characters and build a map from column to character.
     // Such a line could read " A R N D C Q E G H I L K M F P S T W Y V B Z X *".
     String<TSequenceValue> mapping;
-    // Skip blanks (TAB and SPACE).
-    while (!atEnd(reader) && isblank(value(reader)))
-        goNext(reader);
-    while (!atEnd(reader) && value(reader) != '\n' && value(reader) != '\r')
-    {
-        appendValue(mapping, value(reader));  // Conversion char => TSequenceValue
-        goNext(reader);
-        // Skip blanks (TAB and SPACE).
-        while (!atEnd(reader) && isblank(value(reader)))
-            goNext(reader);
-    }
-    if (skipLine(reader) != 0)  // Go to next line.
-        return 1;
+
+    skipUntil(reader, NotFunctor<IsWhitespace>());
+    readUntil(mapping, reader, IsNewline(), IsWhitespace());    // Conversion char => TSequenceValue, Skip blanks
+    skipLine(reader);
 
     // -----------------------------------------------------------------------
     // Read the matrix.
     // -----------------------------------------------------------------------
     // The matrix is read line-wise, we read the score for a (source, dest) replacement.
+
+    CharString buffer;
     for (unsigned row = 0; !atEnd(reader); ++row)
     {
-        while (!atEnd(reader) && isblank(value(reader)))  // Skip blanks (TAB and SPACE).
-            goNext(reader);
-        if (atEnd(reader))
-            return 1;  // No label.
+        skipUntil(reader, NotFunctor<IsBlank>());
 
         // Read label.
-        TSequenceValue source = value(reader);
-        unsigned const OFFSET = ordValue(source) * TScore::VALUE_SIZE;
-        goNext(reader);
-        while (!atEnd(reader) && isblank(value(reader)))  // Skip blanks (TAB and SPACE).
-            goNext(reader);
-        if (atEnd(reader))
-            return 1;  // No entries.
+        TSequenceValue source;
+        readOne(source, reader);
+        unsigned const offset = ordValue(source) * TScore::VALUE_SIZE;
+
+        skipUntil(reader, NotFunctor<IsBlank>());
 
         // Read numbers.
-        CharString buffer;
-        for (unsigned col = 0; !atEnd(reader) && value(reader) != '\r' && value(reader) != '\n'; ++col)
+        for (unsigned col = 0; !atEnd(reader) && !IsNewline()(value(reader)); ++col)
         {
-            if (atEnd(reader))
-                return 1;  // No number.
-
+            readUntil(buffer, reader, IsWhitespace());
+            sc.data_tab[offset + ordValue(mapping[col])] = lexicalCast<TValue>(buffer);
             clear(buffer);
-            int res = readUntilWhitespace(buffer, reader);
-            if (res != 0 && res != EOF_BEFORE_SUCCESS)
-                return 1;  // Error reading.
-            TValue val = 0;
-            if (!lexicalCast2(val, buffer))
-                return 1;  // Invalid number.
-
-            TSequenceValue destChar = mapping[col];
-            sc.data_tab[OFFSET + ordValue(destChar)] = val;
-
-            while (!atEnd(reader) && isblank(value(reader)))  // Skip blanks (TAB and SPACE).
-                goNext(reader);
+            skipUntil(reader, NotFunctor<IsBlank>());
         }
 
-        int res = skipLine(reader);  // Go to next line.
-        if (res != 0)
-            return 1;
+        skipLine(reader);  // Go to next line.
     }
-
-    return 0;
 }
 
 
-template <typename TStream, typename TValue, typename TSequenceValue, typename TSpec>
+template <typename TValue, typename TSequenceValue, typename TSpec, typename TSourceIter>
 inline void
-read(RecordReader<TStream, SinglePass<> > & fl,
-     Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc)
+read(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc,
+     TSourceIter & iter)
 {
-    read(fl, sc, ScoreMatrixFile());
+    read(sc, iter, ScoreMatrixFile());
 }
 
 // ----------------------------------------------------------------------------
@@ -290,103 +170,34 @@ read(RecordReader<TStream, SinglePass<> > & fl,
  * @param[out]    meta     Meta information is stored here, CharString.
  */
 
-/**
-.Function.loadScoreMatrix
-..cat:Input/Output
-..summary:Load a score matrix from a file.
-..signature:loadScoreMatrix(score, filename)
-..param.score:Score matrix object to load into.
-...type:Spec.Score Matrix
-..param.filename:Path to the file to load.
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSequenceValue, typename TSpec>
-inline void
+inline bool
 loadScoreMatrix(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc,
-                CharString const & filename)
-{
-    std::fstream fin(toCString(filename), std::ios::binary | std::ios::in);
-    RecordReader<std::fstream, SinglePass<> > reader(fin);
-    read(reader, sc);
-}
-
-// TODO(holtgrew): Change parameter order?
-
-/**
-.Function.loadScoreMatrix
-..signature:loadScoreMatrix(score, filename, meta)
-..param.meta:Meta information read from the file.
-..status:The order of the parameters filename and meta will switch.
-..include:seqan/score.h
-*/
-template <typename TValue, typename TSequenceValue, typename TSpec, typename TMeta>
-inline void
-loadScoreMatrix(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, CharString const & filename, TMeta & meta)
-{
-    std::fstream fin(toCString(filename), std::ios::binary | std::ios::in);
-    RecordReader<std::fstream, SinglePass<> > reader(fin);
-    readMeta(reader, meta, ScoreMatrixFile());
-    read(reader, sc, ScoreMatrixFile());
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _sprintfValue()
-// ----------------------------------------------------------------------------
-
-// TODO(holtgrew): Can we solve this more eleganly using std::stringstream's?
-
-/*
-.Function._sprintfValue
-..cat:Input/Output
-..summary:Use sprintf to print a value into a $const char *$ buffer.
-..signature:_sprintf(buffer, value)
-..param.buffer:Buffer to write to.
-...type:char *
-...remark:Must be of sufficient size.
-..param.value:Variable for which to write the string value to $buffer$.
-...type:unsigned int
-...type:int
-...type:float
-...type:double
-..includes:seqan/score.h
-..include:seqan/score.h
- */
-
-inline void
-_sprintfValue(char * buf, unsigned val)
+                const char * filename)
 {
-    std::sprintf(buf, "%u", val);
-}
+    VirtualStream<char, Input> fin;
+    if (!open(fin, toCString(filename)))
+        return false;
 
-/*
-.Function._sprintfValue.param.value.type:int
-..include:seqan/score.h
- */
-inline void
-_sprintfValue(char * buf, int val)
-{
-    std::sprintf(buf, "%d", val);
+    typename DirectionIterator<VirtualStream<char, Input>, Input>::Type reader = directionIterator(fin, Input());
+    read(sc, reader);
+    return true;
 }
 
-/*
-.Function._sprintfValue.param.value.type:float
-..include:seqan/score.h
- */
-inline void
-_sprintfValue(char * buf, float val)
-{
-    double d = val;
-    std::sprintf(buf, "%G", d);
-}
-
-/*
-.Function._sprintfValue.param.value.type:float
-..include:seqan/score.h
- */
-inline void
-_sprintfValue(char * buf, double val)
+template <typename TMeta, typename TValue, typename TSequenceValue, typename TSpec>
+inline bool
+loadScoreMatrix(TMeta & meta,
+                Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc,
+                const char * filename)
 {
-    std::sprintf(buf, "%G", val);
+    VirtualStream<char, Input> fin;
+    if (!open(fin, toCString(filename)))
+        return false;
+
+    typename DirectionIterator<VirtualStream<char, Input>, Input>::Type reader = directionIterator(fin, Input());
+    readMeta(meta, reader, ScoreMatrixFile());
+    read(sc, reader, ScoreMatrixFile());
+    return true;
 }
 
 // ----------------------------------------------------------------------------
@@ -406,24 +217,9 @@ _sprintfValue(char * buf, double val)
  * @return int Status code, 0 on success, a different value on errors.
  */
 
-/**
-.Function.Score Matrix#write
-..summary:Write a score matrix to a stream.
-..cat:Input/Output
-..class:Spec.Score Matrix
-..signature:write(stream, scoreMatrix[, meta])
-..param.stream:A @Concept.StreamConcept@ to write to.
-...type:Concept.StreamConcept
-..param.scoreMatrix:The matrix to write out.
-...type:Spec.Score Matrix
-..param.meta:Optional description.
-...type:Shortcut.CharString
-..include:seqan/score.h
- */
-
-template <typename TStream, typename TValue, typename TSequenceValue, typename TSpec>
-inline int
-write(TStream & stream,
+template <typename TTarget, typename TValue, typename TSequenceValue, typename TSpec>
+inline void
+write(TTarget & target,
       Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > const & sc,
       CharString const & meta)
 {
@@ -436,52 +232,52 @@ write(TStream & stream,
     // -----------------------------------------------------------------------
     // Write meta data.
     // -----------------------------------------------------------------------
-    if (!empty(meta)) {
+    if (!empty(meta))
+    {
         bool lineBegin = true;
         for (unsigned int i = 0; i < length(meta); ++i) {
             if (lineBegin)
             {
                 // Escape each line with a starting '#'.
-                streamPut(stream, '#');
+                writeValue(target, '#');
                 lineBegin = false;
             }
             if (meta[i] == '\r')
                 continue;
             if (meta[i] == '\n')
                 lineBegin = true;
-            streamPut(stream, meta[i]);
+            writeValue(target, meta[i]);
         }
         if (!lineBegin)
-            streamPut(stream, '\n');
+            writeValue(target, '\n');
     }
 
     // -----------------------------------------------------------------------
     // Determine maximal column width.
     // -----------------------------------------------------------------------
-    unsigned colWidth = 1;
-    char buf[100];  // 100 is enough for printing int, unsigned, dobule
+    size_t colWidth = 1;
+    String<char, Array<100> > buf;  // 100 is enough for printing int, unsigned, dobule
     for (unsigned i = 0; i < TAB_SIZE; ++i)
     {
-        _sprintfValue(buf, tab[i]);
-        unsigned cellWidth = std::strlen(buf);
-        if (cellWidth > colWidth)
-            colWidth = cellWidth;  // Compute maximum.
+        clear(buf);
+        appendNumber(buf, tab[i]);
+        colWidth = std::max(colWidth, (size_t)length(buf));
     }
-    colWidth += 1;  // Increase colWidth for an additional blank.
+    colWidth++;     // Increase colWidth for an additional blank.
 
     // -----------------------------------------------------------------------
     // Write alphabet line.
     // -----------------------------------------------------------------------
-    streamPut(stream, ' ');  // A blank for alphabet column.
+    writeValue(target, ' ');  // A blank for alphabet column.
     for (unsigned j = 0; j < VALUE_SIZE; ++j)
     {
         char val = static_cast<TSequenceValue>(j);  // Conversion integral => TSequenceValue => char.
         // Leading blanks for column j.
         for (unsigned k = 1; k < colWidth; ++k)
-            streamPut(stream, ' ');
-        streamPut(stream, val);
+            writeValue(target, ' ');
+        writeValue(target, val);
     }
-    streamPut(stream, '\n');
+    writeValue(target, '\n');
 
     // -----------------------------------------------------------------------
     // Write rest of matrix.
@@ -490,36 +286,44 @@ write(TStream & stream,
     {
         // Write alphabet column cell.
         char val = static_cast<TSequenceValue>(i);  // Conversion integral => TSequenceValue => char.
-        streamPut(stream, val);
+        writeValue(target, val);
 
         // Write rest of line i.
         unsigned offset = i * VALUE_SIZE;
         for (unsigned j = 0; j < VALUE_SIZE; ++j)
         {
-            _sprintfValue(buf, tab[offset + j]);
-            unsigned len = strlen(buf);
+            clear(buf);
+            appendNumber(buf, tab[offset + j]);
 
             // Leading blanks.
-            for (unsigned k = 0; k < colWidth - len; ++k)
-                streamPut(stream, ' ');
+            for (unsigned k = length(buf); k < colWidth; ++k)
+                writeValue(target, ' ');
 
             // Write cell.
-            streamPut(stream, buf);
+            write(target, buf);
         }
-        streamPut(stream, '\n');
+        writeValue(target, '\n');
     }
+}
 
-    return 0;
+template <typename TTarget, typename TValue, typename TSequenceValue, typename TSpec>
+inline void
+write(TTarget & target,
+      Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > const & sc)
+{
+    write(target, sc, "");
 }
 
 template <typename TStream, typename TValue, typename TSequenceValue, typename TSpec>
-inline int
-write(TStream & stream,
-      Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > const & sc)
+inline TStream &
+operator<<(TStream & target,
+           Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > const & sc)
 {
-    return write(stream, sc, "");
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, sc);
+    return target;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SCORE_SCORE_MATRIX_IO_H_
+#endif  // #ifndef INCLUDE_SEQAN_SCORE_SCORE_MATRIX_IO_H_
diff --git a/seqan/score/score_simple.h b/seqan/score/score_simple.h
index 5b969dd..d3cc49b 100644
--- a/seqan/score/score_simple.h
+++ b/seqan/score/score_simple.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Code for the Simple Scoring Schema.
 // ==========================================================================
 
-#ifndef SEQAN_SCORE_SCORE_SIMPLE_H_
-#define SEQAN_SCORE_SCORE_SIMPLE_H_
+#ifndef SEQAN_SSCORE_SIMPLE_H_
+#define SEQAN_SSCORE_SIMPLE_H_
 
 namespace seqan {
 
@@ -51,16 +51,6 @@ namespace seqan {
  * @tparam TValue The score value to use.
  */
 
-/**
-.Spec.Simple Score
-..cat:Scoring
-..signature:Score<TValue, Simple>
-..param.TValue:The value type.
-...default:int
-..general:Class.Score
-..summary:Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
-..include:seqan/score.h
-*/
 template <typename TValue>
 class Score<TValue, Simple> {
 public:
@@ -103,28 +93,6 @@ class Score<TValue, Simple> {
  * @param[in] gapOpen Gap open value (defaults to gap), type TValue.
  */
 
-/**
-.Memfunc.Score#Score:
-..class:Class.Score
-..summary:Constructor
-..signature:Score<TValue, Simple>()
-..signature:Score<TValue, Simple>(score)
-..signature:Score<TValue, Simple>(match, mismatch, gap [, gap_open])
-..param.score:Other Score object. (copy constructor)
-..param.match:TValue object.
-...default:0
-..param.mismatch:TValue object.
-...default:-1
-..param.gap:TValue object.
-...remarks:The score for a single blank in a gap (linear gap costs).
-...default:-1
-..param.gap_open:TValue object.
-...remarks:The score for the first blank in a gap (affine gap costs).
-...default:$gap$
-..remarks:
-...text:If both gap and gap_open are specified, the total score of a length $n$ gap is $gap_open (n-1)*gap$.
-...note:Usually $mismatch$, $gap$, and $gap_open$ are negative values.
- */
     Score(TValue _match, TValue _mismatch, TValue _gap_extend, TValue _gap_open)
         : data_match(_match), data_mismatch(_mismatch),
           data_gap_extend(_gap_extend), data_gap_open(_gap_open) {
@@ -133,22 +101,13 @@ class Score<TValue, Simple> {
 };
 
 /*!
- * @typedef SimpleScoreShortcut
+ * @typedef SimpleScoreTypedef SimpleScore
  * @headerfile <seqan/score.h>
  * @brief Simple scoring scheme.
  *
  * @signature typedef Score<int, Simple> SimpleScore;
  */
 
-/**
-.Shortcut.SimpleScore:
-..cat:Scoring
-..summary:Simple scoring scheme.
-..signature:SimpleScore
-..shortcutfor:Spec.Simple Score
-...signature:Score<int, Simple>
-..see:Spec.Simple Score
-*/
 typedef Score<int, Simple> SimpleScore;
 
 /*!
@@ -158,23 +117,10 @@ typedef Score<int, Simple> SimpleScore;
  * @signature TValue scoreMatch(score);
  *
  * @param[in] score The SimpleScore scoring scheme.
- * 
+ *
  * @return TValue The match score.
  */
 
-/**
-.Function.scoreMatch:
-..class:Class.Score
-..cat:Alignments
-..summary:Match score.
-..signature:scoreMatch(object)
-..param.object.type:Class.Score
-..returns:Match score.
-..see:Function.scoreMismatch
-..see:Function.scoreGapExtend
-..see:Function.scoreGapOpen
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline TValue
 scoreMatch(Score<TValue, TSpec> const & me) {
@@ -192,19 +138,6 @@ scoreMatch(Score<TValue, TSpec> const & me) {
  * @param[in]     value The value to set the match score to.
  */
 
-/**
-.Function.setScoreMatch:
-..class:Class.Score
-..cat:Alignments
-..summary:Set match score.
-..signature:setScoreMatch(object, value)
-..param.object.type:Class.Score
-..param.value.type:nolink:TValue
-..see:Function.scoreMismatch
-..see:Function.scoreGapExtend
-..see:Function.scoreGapOpen
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline void
 setScoreMatch(Score<TValue, TSpec> & me, TValue const & value) {
@@ -219,24 +152,10 @@ setScoreMatch(Score<TValue, TSpec> & me, TValue const & value) {
  * @signature TValue scoreMismatch(score);
  *
  * @param[in] score The SimpleScore to query for its mismatch score.
- * 
+ *
  * @return TValue The mismatch score.
  */
 
-/**
-.Function.scoreMismatch:
-..class:Class.Score
-..cat:Alignments
-..summary:Mismatch score.
-..signature:scoreMismatch(object)
-..param.object.type:Class.Score
-..returns:Mismatch score.
-...note:Usually, mismatches have negative scores.
-..see:Function.scoreMatch
-..see:Function.scoreGapExtend
-..see:Function.scoreGapOpen
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline TValue
 scoreMismatch(Score<TValue, TSpec> const & me) {
@@ -254,19 +173,6 @@ scoreMismatch(Score<TValue, TSpec> const & me) {
  * @param[in]     value The value to set the mismatch score to.
  */
 
-/**
-.Function.setScoreMismatch:
-..class:Class.Score
-..cat:Alignments
-..summary:Set mismatch score.
-..signature:setScoreMismatch(object, value)
-..param.object.type:Class.Score
-..param.value.type:nolink:TValue
-..see:Function.scoreMismatch
-..see:Function.scoreGapExtend
-..see:Function.scoreGapOpen
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline void
 setScoreMismatch(Score<TValue, TSpec> & me, TValue const & value) {
@@ -281,24 +187,10 @@ setScoreMismatch(Score<TValue, TSpec> & me, TValue const & value) {
  * @signature TValue scoreGapExtend(score);
  *
  * @param[in] score The SimpleScore to query for its gap extension score.
- * 
+ *
  * @return TValue The gap extension score.
  */
 
-/**
-.Function.scoreGapExtend:
-..class:Class.Score
-..cat:Alignments
-..summary:Score for extending gaps.
-..signature:scoreGapExtend(object)
-..param.object.type:Class.Score
-..returns:Score for extending gaps.
-...note:Usually, gaps have negative scores.
-..see:Function.scoreMismatch
-..see:Function.scoreMatch
-..see:Function.scoreGapOpen
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline TValue
 scoreGapExtend(Score<TValue, TSpec> const & me) {
@@ -306,20 +198,16 @@ scoreGapExtend(Score<TValue, TSpec> const & me) {
     return me.data_gap_extend;
 }
 
+/*!
+ * @fn SimpleScore#setScoreGapExtend
+ * @brief Set gap extend score.
+ *
+ * @signature void setScoreGapExtend(score, value);
+ *
+ * @param[in,out] score The SimpleScore scoring scheme to set the gap extend value for.
+ * @param[in]     value The value to set the gap open score to.
+ */
 
-/**
-.Function.setScoreGapExtend:
-..class:Class.Score
-..cat:Alignments
-..summary:Set gap extension score.
-..signature:setScoreGapExtend(object, value)
-..param.object.type:Class.Score
-..param.value.type:nolink:TValue
-..see:Function.scoreMismatch
-..see:Function.scoreGapExtend
-..see:Function.scoreGapOpen
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline void
 setScoreGapExtend(Score<TValue, TSpec> & me, TValue const & value) {
@@ -334,24 +222,10 @@ setScoreGapExtend(Score<TValue, TSpec> & me, TValue const & value) {
  * @signature TValue scoreGapOpen(score);
  *
  * @param[in] score The SimpleScore to query for its gap open score.
- * 
+ *
  * @return TValue The gap open score.
  */
 
-/**
-.Function.scoreGapOpen:
-..class:Class.Score
-..cat:Alignments
-..summary:Score for opening a gap.
-..signature:scoreGapOpen(object)
-..param.object.type:Class.Score
-..returns:Score for opening a gap.
-...note:Usually, gaps have negative scores.
-..see:Function.scoreMismatch
-..see:Function.scoreGapExtend
-..see:Function.scoreMatch
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline TValue
 scoreGapOpen(Score<TValue, TSpec> const & me) {
@@ -370,19 +244,6 @@ scoreGapOpen(Score<TValue, TSpec> const & me) {
  * @param[in]     value The value to set the gap open score to.
  */
 
-/**
-.Function.setScoreGapOpen:
-..class:Class.Score
-..cat:Alignments
-..summary:Set gap opening score.
-..signature:setScoreGapOpen(object, value)
-..param.object.type:Class.Score
-..param.value.type:nolink:TValue
-..see:Function.scoreMismatch
-..see:Function.scoreGapExtend
-..see:Function.scoreGapOpen
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline void
 setScoreGapOpen(Score<TValue, TSpec> & me, TValue const & value) {
@@ -397,27 +258,11 @@ setScoreGapOpen(Score<TValue, TSpec> & me, TValue const & value) {
  * @signature TValue scoreGap(score);
  *
  * @param[in] score The SimpleScore to query for its gap score.
- * 
+ *
  * @return TValue The gap score.
  */
 
 
-/**
-.Function.scoreGap:
-..class:Class.Score
-..cat:Alignments
-..summary:Score for gaps.
-..signature:scoreGapExtend(object)
-..param.object.type:Class.Score
-..returns:Score for extending gaps.
-...note:Usually, gaps have negative scores.
-..remarks:This score is used for linear gap costs. For affine gap costs use @Function.scoreGapExtend@ and @Function.scoreGapOpen@ instead.
-..see:Function.scoreMismatch
-..see:Function.scoreMatch
-..see:Function.scoreGapOpen
-..see:Function.scoreGapExtend
-..include:seqan/score.h
-*/
 // TODO(holtgrew): This shortcut/forward should live in score_base.h.
 template <typename TValue, typename TSpec>
 inline TValue
@@ -436,19 +281,6 @@ scoreGap(Score<TValue, TSpec> const & me) {
  * @param[in]     value The value to set the gap score to.
  */
 
-/**
-.Function.setScoreGap:
-..class:Class.Score
-..cat:Alignments
-..summary:Set gap opening and extension score.
-..signature:setScoreGap(object, value)
-..param.object.type:Class.Score
-..param.value.type:nolink:TValue
-..see:Function.scoreMismatch
-..see:Function.scoreGapExtend
-..see:Function.scoreGapOpen
-..include:seqan/score.h
-*/
 template <typename TValue, typename TSpec>
 inline void
 setScoreGap(Score<TValue, TSpec> & me, TValue const & value) {
@@ -459,20 +291,6 @@ setScoreGap(Score<TValue, TSpec> & me, TValue const & value) {
 
 
 // TODO(rmaerker): Remove this here!
-/**
-.Function.score:
-..cat:Scoring
-..class:Class.Score
-..signature:score(score, value1, value2) [deprecated]
-..param.score:A scoring scheme.
-...type:Class.Score
-..param.value1:Aligned character in the first sequence.
-..param.value2:Aligned character in the second sequence.
-..status:The version that explicitely requires two characters is deprecated. For using (or defining) custom scoring schemes better use the functions
-@Function.score@, @Function.scoreGapOpenVertical@, @Function.scoreGapExtendVertical@, @Function.scoreGapOpenHorizontal@ and @Function.scoreGapExtendHorizontal@ 
-as they require character positions and sequences and allow for position-dependent scoring schemes.
-..include:seqan/score.h
-*/
 //template <typename TValue, typename TSpec, typename TVal1, typename TVal2>
 //inline TValue
 //score(Score<TValue, TSpec> const & me, TVal1 left, TVal2 right) {
@@ -485,4 +303,4 @@ as they require character positions and sequences and allow for position-depende
 
 }  // namespace SEQAN_NAMESPACE_MAIN
 
-#endif  // SEQAN_SCORE_SCORE_SIMPLE_H_
+#endif  // SEQAN_SSCORE_SIMPLE_H_
diff --git a/seqan/seeds.h b/seqan/seeds.h
index ea70cef..ecf3985 100644
--- a/seqan/seeds.h
+++ b/seqan/seeds.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/seeds/INFO b/seqan/seeds/INFO
deleted file mode 100644
index 1aa3834..0000000
--- a/seqan/seeds/INFO
+++ /dev/null
@@ -1,18 +0,0 @@
-Name: seqan-seeds
-Author: Birte Kehr <birte.kehr@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Author: Rene Rahn <rene.rahn@fu-berlin.de>
-Maintainer: Rene Rahn <rene.rahn@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Everything seeds: Local/global chaining, seed extension, ...
- .
- This module contains seed-related code.  The seed set class allows the
- efficient management of seeds and local chaining.  Furthermore, the module
- contains code for global, 2-dimensional chaining and gapped as well as ungapped
- X-drop seed extension. Recently, a new banded chain alignment algorithm was
- added to the module, such that a global alignment can be computed between large
- genomic sequences given a monotonic non-decreasing chain of seeds.
- .
- This module will eventually be renamed to seeds and replace the old module.
diff --git a/seqan/seeds/banded_chain_alignment.h b/seqan/seeds/banded_chain_alignment.h
index 4cb0be8..58231cc 100644
--- a/seqan/seeds/banded_chain_alignment.h
+++ b/seqan/seeds/banded_chain_alignment.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // algorithm.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_H_
-#define CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_H_
+#ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_H_
+#define INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_H_
 
 namespace seqan {
 
@@ -60,48 +60,46 @@ namespace seqan {
  * @fn bandedChainAlignment
  * @headerfile <seqan/seeds.h>
  * @brief Computes the best global pairwise alignment between two sequences given a non-empty seed chain.
- * 
+ *
  * @signature TValue bandedChainAlignment(align,          seedChain, scoringScheme1[, scoringScheme2] [, alignConfig] [, k]);
  * @signature TValue bandedChainAlignment(gapsH, gapsV,   seedChain, scoringScheme1[, scoringScheme2] [, alignConfig] [, k]);
  * @signature TValue bandedChainAlignment(frags, strings, seedChain, scoringScheme1[, scoringScheme2] [, alignConfig] [, k]);
  * @signature TValue bandedChainAlignment(alignmentGraph, seedChain, scoringScheme1[, scoringScheme2] [, alignConfig] [, k]);
- * 
- * @param align[in,out]  An @link Align @endlink object that stores the alignment. The number of rows must be 2 and the
- *                       sequences must have already been set.  <tt>row(align, 0)</tt> is the horizontal sequence in the
- *                       alignment matrix, <tt>row(align, 1)</tt> is the vertical sequence.
- * @param gapsH[in,out]  Horizontal gapped sequence in alignment matrix. Type: @link Gaps @endlink.
- * @param gapsV[in,out]  Vertical gapped sequence in alignment matrix. Type: @link Gaps @endlink.
- * @param frags[out]     String of @link Fragment @endlink objects.  The sequence with id <tt>0</tt> is the horizontal
- *                       one, the sequence with id <tt>1</tt> is the vertical one.
- * @param strings[in]    A @link StringSet @endlink containing two sequences.
- * @param alignmentGraph[in,out]
+ *
+ * @param[in,out] align   An @link Align @endlink object that stores the alignment. The number of rows must be 2 and the
+ *                        sequences must have already been set.  <tt>row(align, 0)</tt> is the horizontal sequence in the
+ *                        alignment matrix, <tt>row(align, 1)</tt> is the vertical sequence.
+ * @param[in,out] gapsH   Horizontal gapped sequence in alignment matrix. Type: @link Gaps @endlink.
+ * @param[in,out] gapsV   Vertical gapped sequence in alignment matrix. Type: @link Gaps @endlink.
+ * @param[out]    frags   @link String @endlink of @link Fragment @endlink objects.  The sequence with id <tt>0</tt>
+ *                        is the horizontal one, the sequence with id <tt>1</tt> is the vertical one.
+ * @param[in]     strings A @link StringSet @endlink containing two sequences.
+ * @param[in,out] alignmentGraph
  *                       @link AlignmentGraph @endlink object to store the alignment in.  The underlying @link
  *                       StringSet @endlink must be an @link DependentStringSet @endlink. Types: AlignmentGraph.
- * @param seedChain[in]  The container holding the @link Seed seeds @endlink.  Note that the @link Seed seeds @endlink
+ * @param[in] seedChain  The container holding the @link Seed seeds @endlink.  Note that the @link Seed seeds @endlink
  *                       have to be in montonic non-decreasing order and the container has to implement a forward-iterator.
  *                       Type: @link SeedSet @endlink.
- * @param scoringScheme1[in]
+ * @param[in] scoringScheme1
  *                       The scoring scheme used for the alignment. If <tt>scoringScheme2</tt> is specified, then
  *                       <tt>scoringScheme1</tt> is used for the regions around the seeds and <tt>scoringScheme2</tt>
  *                       for the gap regions between two consecutive seeds.  Types: Score
- * @param scoringScheme2[in]
+ * @param[in] scoringScheme2
  *                       The optional scoring scheme for the gap regions between two anchors. Types: Score
- * @param k[in]          Optional extension of the band around the seeds.  At the moment only band extensions greater
+ * @param[in] k          Optional extension of the band around the seeds.  At the moment only band extensions greater
  *                       or equal <tt>1</tt> are allowed. Type: nolink:<tt>int</tt>. Default: 15.
- * @param alignConfig[in]
+ * @param[in] alignConfig
  *                       The @link AlignConfig @endlink to use for the alignment.
- * 
+ *
  * @return TValue An integer with the alignment score, as given by the @link Score#Value @endlink metafunction of the
  *                @link Score @endlink type.  If the seed chain is empty then the @link OrderedAlphabetConcept#MinValue
  *                smallest value of the score type @endlink is used to return the minimal value of the selected score
  *                type and no alignment is computed.
- * 
- * @section Remarks
- * 
+ *
  * There exist multiple overloads for this function with four configuration dimensions.
- * 
+ *
  * First, you can select whether begin and end gaps are free in either sequence using <tt>alignConfig</tt>.
- * 
+ *
  * Second, you can select the type of the target storing the alignment. This can be either an @link Align @endlink
  * object, two @link Gaps @endlink objects, a @link AlignmentGraph @endlink, or a string of @link Fragment @endlink
  * objects. @link Align @endlink objects provide an interface to tabular alignments with the restriction of all rows
@@ -110,67 +108,67 @@ namespace seqan {
  * Graphs @endlink provide a graph-based representation of segment-based colinear alignments. Using @link Fragment
  * @endlink strings is useful for collecting many pairwise alignments, for example in the construction of @link
  * AlignmentGraph Alignment Graphs @endlink for multiple-sequence alignments (MSA).
- * 
+ *
  * Third, you can optionally give a second scoring scheme to fill the gaps between two consecutive seeds. Note that
  * based on the specified scores either an affine or linear gap cost function is used. This only depends on whether for
  * one of the scoring schemes the scores for gap opening and gap extension differ or not. If only one scoring scheme is
  * defined the complete region is computed with the same scoring scheme.
- * 
+ *
  * Fourth, you can optinally select a proper band extension for the bands around the seeds.  At the moment only band
  * extensions of at least <tt>1</tt> are allowed.  The default value is <tt>15</tt> and is based on the default values
  * for the LAGAN-algorithm described by Brudno et al., 2003.
- * 
+ *
  * The examples below show some common use cases.
- * 
+ *
  * @section Examples
- * 
+ *
  * Banded chain alignment of two sequences using an @link Align @endlink object and using only one scoring scheme and no
  * free end-gaps.
- * 
+ *
  * @code{.cpp}
  * Dna5String seqH = "CGAATCCATCCCACACA";
  * Dna5String seqV = "GGCGATNNNCATGGCACA";
- *  
+ *
  * String<Seed<Simple> > seedChain;
  * appendValue(seedChain, Seed<Simple>(2, 0, 6, 5));
  * appendValue(seedChain, Seed<Simple>(9, 6, 12, 9));
  * appendValue(seedChain, Seed<Simple>(14, 11, 16, 17));
- *  
+ *
  * Align<Dna5String, ArrayGaps> alignment;
  * resize(rows(alignment), 2);
  * assignSource(row(alignment, 0), seqH);
  * assignSource(row(alignment, 1), seqV);
- *  
+ *
  * Score<int, Simple> scoringScheme(2, -1, -2);
- *  
+ *
  * int result = bandedChainAlignment(alignment, seedChain, scoringScheme, 2);
  * @endcode
  *
  * Banded chain alignment of two sequences using two @link Gaps @endlink objects, an unordered seed set to hold the
  * seeds, two different scoring schemes for the gaps between the seeds and the seeds and free end-gaps.
- * 
+ *
  * @code{.cpp}
  * DnaString seqH = "CGAATCCATCCCACACA";
  * Dna5String seqV = "GGCGATNNNCATGGCACA";
- *  
+ *
  * SeedSet<Simple, Unordered> seedChain;
  * addSeed(seedChain, Seed<Simple>(2, 0, 6, 5), Single());
  * addSeed(seedChain, Seed<Simple>(9, 6, 12, 9), Single());
  * addSeed(seedChain, Seed<Simple>(14, 11, 16, 17), Single());
- *  
+ *
  * Gaps<DnaString, ArrayGaps> gapsH(seqH);
  * Gaps<Dna5String, AnchorGaps<> > gapsV(seqV);
- *  
+ *
  * Score<int, Simple> scoringSchemeSeed(2, -1, -2);
  * Score<int, Simple> scoringSchemeGap(5, -3, -1, -5);
  * AlignConfig<true, true, true, true> alignConfig;
- *  
+ *
  * int result = globalAlignment(gapsH, gapsV, scoringSchemeSeed, scoringSchemeGap, alignConfig, 2);
  * @endcode
  *
  * @section Tutorial
  *
- * Also see the <a href="http://trac.seqan.de/wiki/Tutorial/Seed-and-Extend">Seed-and-Extend Tutorial</a>
+ * Also see the <a href="http://seqan.readthedocs.org/en/develop/Tutorial/SeedAndExtend.html">Seed-and-Extend Tutorial</a>
  *
  * @section Reference
  *
@@ -180,114 +178,6 @@ namespace seqan {
  * </ul>
  */
 
-/**
-.Function.bandedChainAlignment
-..summary:Computes the best global pairwise alignment between two sequences given a non-empty seed chain.
-..cat:Alignments
-..signature:bandedChainAlignment(align,          seedChain, scoringScheme1 [, scoringScheme2] [, alignConfig] [, k])
-..signature:bandedChainAlignment(gapsH, gapsV,   seedChain, scoringScheme1 [, scoringScheme2] [, alignConfig] [, k])
-..signature:bandedChainAlignment(frags, strings, seedChain, scoringScheme1 [, scoringScheme2] [, alignConfig] [, k])
-..signature:bandedChainAlignment(alignmentGraph, seedChain, scoringScheme1 [, scoringScheme2] [, alignConfig] [, k])
-..param.align:
-An @Class.Align@ object that stores the alignment.
-The number of rows must be 2 and the sequences must have already been set.
-$row(align, 0)$ is the horizontal sequence in the alignment matrix, $row(align, 1)$ is the vertical sequence.
-...type:Class.Align
-..param.gapsH:Horizontal gapped sequence in alignment matrix.
-...type:Class.Gaps
-..param.gapsV:Vertical gapped sequence in alignment matrix.
-...type:Class.Gaps
-..param.frags:
-String of @Class.Fragment@ objects.
-The sequence with id $0$ is the horizontal one, the sequence with id $1$ is the vertical one.
-..param.alignmentGraph:
-@Spec.Alignment Graph@ object to store the alignment in.
-...type:Spec.Alignment Graph
-...remarks:The underlying @Class.StringSet@ must be an @Spec.Dependent|Dependent StringSet@.
-..param.strings:A @Class.StringSet@ containing two sequences.
-...type:Class.StringSet
-..param.seedChain:
-The container holding the @Class.Seed|seeds@. Note that the @Class.Seed|seeds@ have to be in montonic non-decreasing order
-and the container has to implement a forward-iterator.
-...see:Class.SeedSet
-..param.scoringScheme1:The scoring scheme used for the alignment.
-...remarks:If $scoringScheme2$ is specified, then $scoringScheme1$ is used for the regions around the seeds
-and $scoringScheme2$ for the gap regions between two consecutive seeds.
-...type:Class.Score
-..param.scoringScheme2:The optional scoring scheme for the gap regions between two anchors.
-...type:Class.Score
-..param.alignConfig:The @Class.AlignConfig@ to use for the alignment.
-...type:Class.AlignConfig
-..param.k:Optional extension of the band around the seeds.
-...type:nolink:$int$
-...default:15
-...remarks:At the moment only band extensions greater or equal $1$ are allowed.
-..returns:An integer with the alignment score, as given by the @Metafunction.Value@ metafunction of the @Class.Score@ type.
-If the seed chain is empty the metafunction @Metafunction.MinValue@ is used to return the minimal value of the selected score type and no alignment is computed.
-..remarks:
-There exist multiple overloads for this function with four configuration dimensions.
-..remarks:
-First, you can select whether begin and end gaps are free in either sequence using $alignConfig$.
-..remarks:
-Second, you can select the type of the target storing the alignment.
-This can be either an @Class.Align@ object, two @Class.Gaps@ objects, a @Spec.Alignment Graph@, or a string of @Class.Fragment@ objects.
-@Class.Align@ objects provide an interface to tabular alignments with the restriction of all rows having the same type.
-Using two @Class.Gaps@ objects has the advantage that you can align sequences with different types, for example @Shortcut.DnaString@ and @Shortcut.Dna5String@.
-@Spec.Alignment Graph|Alignment Graphs@ provide a graph-based representation of segment-based colinear alignments.
-Using @Class.Fragment@ strings is useful for collecting many pairwise alignments, for example in the construction of @Spec.Alignment Graph|Alignment Graphs@ for multiple-sequence alignments (MSA).
-..remarks:
-Third, you can optionally give a second scoring scheme to fill the gaps between two consecutive seeds. Note that based on the specified scores
-either an affine or linear gap cost function is used. This only depends on whether for one of the scoring schemes the scores for gap opening and gap extension differ or not.
-If only one scoring scheme is defined the complete region is computed with the same scoring scheme.
-..remarks:
-Fourth, you can optinally select a proper band extension for the bands around the seeds. At the moment only band extensions of at least $1$ are allowed.
-The default value is $15$ and is based on the default values for the LAGAN-algorithm described by Brudno et al., Genome Research, 2003.
-..remarks:
-The examples below show some common use cases.
-..example.text:Banded chain alignment of two sequences using an @Class.Align@ object and using only one scoring scheme and no free end-gaps.
-..example.code:
-Dna5String seqH = "CGAATCCATCCCACACA";
-Dna5String seqV = "GGCGATNNNCATGGCACA";
-
-String<Seed<Simple> > seedChain;
-appendValue(seedChain, Seed<Simple>(2, 0, 6, 5));
-appendValue(seedChain, Seed<Simple>(9, 6, 12, 9));
-appendValue(seedChain, Seed<Simple>(14, 11, 16, 17));
-
-Align<Dna5String, ArrayGaps> alignment;
-resize(rows(alignment), 2);
-assignSource(row(alignment, 0), seqH);
-assignSource(row(alignment, 1), seqV);
-
-Score<int, Simple> scoringScheme(2, -1, -2);
-
-int result = bandedChainAlignment(alignment, seedChain, scoringScheme, 2);
-
-..example.text:Banded chain alignment of two sequences using two @Class.Gaps@ objects, an unordered seed set to hold the seeds,
-two different scoring schemes for the gaps between the seeds and the seeds and free end-gaps.
-..example.code:
-DnaString seqH = "CGAATCCATCCCACACA";
-Dna5String seqV = "GGCGATNNNCATGGCACA";
-
-SeedSet<Simple, Unordered> seedChain;
-addSeed(seedChain, Seed<Simple>(2, 0, 6, 5), Single());
-addSeed(seedChain, Seed<Simple>(9, 6, 12, 9), Single());
-addSeed(seedChain, Seed<Simple>(14, 11, 16, 17), Single());
-
-Gaps<DnaString, ArrayGaps> gapsH(seqH);
-Gaps<Dna5String, AnchorGaps<> > gapsV(seqV);
-
-Score<int, Simple> scoringSchemeSeed(2, -1, -2);
-Score<int, Simple> scoringSchemeGap(5, -3, -1, -5);
-AlignConfig<true, true, true, true> alignConfig;
-
-int result = globalAlignment(gapsH, gapsV, scoringSchemeSeed, scoringSchemeGap, alignConfig, 2);
-..include:seqan/seeds.h
-..wiki:Tutorial/Seed-and-Extend
-..cite:Brudno M, Do CB, Cooper GM, et al.: LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA. Genome Research 2003, 13: 721-731.
-.
-*/
-
 // ----------------------------------------------------------------------------
 // Function bandedChainAlignment()                                      [Align]
 // ----------------------------------------------------------------------------
@@ -581,4 +471,4 @@ bandedChainAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragm
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_H_
diff --git a/seqan/seeds/banded_chain_alignment_impl.h b/seqan/seeds/banded_chain_alignment_impl.h
index c8532fa..f9eabbb 100644
--- a/seqan/seeds/banded_chain_alignment_impl.h
+++ b/seqan/seeds/banded_chain_alignment_impl.h
@@ -1,7 +1,7 @@
-    // ==========================================================================
+// ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,8 +38,8 @@
 // Genome Res. 2003, 13: 721-731, doi:10.1101/gr.926603
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_IMPL_H_
-#define CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_IMPL_H_
+#ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_IMPL_H_
+#define INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_IMPL_H_
 
 namespace seqan
 {
@@ -86,11 +86,11 @@ struct BandedChainTracking
 
 template <typename TSeedSet>
 inline bool
-_isLastSeed(typename Iterator<TSeedSet const>::Type iter,
+_isLastSeed(typename Iterator<TSeedSet const, Standard>::Type iter,
             TSeedSet const & seedSet)
 {
     typedef typename Iterator<TSeedSet const>::Type TSeedIterator;
-    TSeedIterator itEnd = end(seedSet);
+    TSeedIterator itEnd = end(seedSet, Standard());
     return iter == --itEnd;
 }
 
@@ -379,7 +379,8 @@ _applyBandedChainTracking(TDPScout & scout,
 {
     unsigned result = BandedChainTracking::OPTION_INIT;
     _determineTrackingOptions(result, scout, traceMatrixNavigator, TColumnDescriptor(), TCellDescriptor(), TDPProfile());
-    _scoutBestScore(scout, activeCell, traceMatrixNavigator, (result & BandedChainTracking::OPTION_IS_LAST_COLUMN),
+    _scoutBestScore(scout, activeCell, traceMatrixNavigator,
+                    (result & BandedChainTracking::OPTION_IS_LAST_COLUMN),
                     (result & BandedChainTracking::OPTION_IS_LAST_ROW),
                     (result & BandedChainTracking::OPTION_STORE_INIT_COLUMN),
                     (result & BandedChainTracking::OPTION_STORE_INIT_ROW));
@@ -523,7 +524,7 @@ _computeCell(TDPScout & scout,
 }
 
 // ----------------------------------------------------------------------------
-// Function _computeCell()		  [BandedChainAlignment, FullColumn, FirstCell]
+// Function _computeCell()          [BandedChainAlignment, FullColumn, FirstCell]
 // ----------------------------------------------------------------------------
 
 // For DPInnerColumn.
@@ -587,8 +588,8 @@ _findFirstAnchor(TSeedSet const & seedSet, int bandExtension)
 
     SEQAN_ASSERT_GT_MSG(length(seedSet), 0u, "SeedSet is empty!");
 
-    TIterator it = begin(seedSet);
-    TIterator itEnd = end(seedSet);
+    TIterator it = begin(seedSet, Standard());
+    TIterator itEnd = end(seedSet, Standard());
     --itEnd;
 
     while (it != itEnd)
@@ -600,7 +601,7 @@ _findFirstAnchor(TSeedSet const & seedSet, int bandExtension)
             continue;
         else
         { // found seed which is not crossing the begin.
-            SEQAN_ASSERT(it != static_cast<TIterator>(begin(seedSet)));
+            SEQAN_ASSERT(it != static_cast<TIterator>(begin(seedSet, Standard())));
             return --it;
         }
     }
@@ -623,7 +624,7 @@ _findLastAnchor(typename Iterator<TSeedSet const, Standard>::Type & iterBegin,
 
     SEQAN_ASSERT_GT_MSG(length(seedSet), 0u, "SeedSet is empty!");
 
-    TIterator it = end(seedSet);
+    TIterator it = end(seedSet, Standard());
     --it;
 
     while (it != iterBegin)
@@ -749,7 +750,7 @@ _initializeBandedChain(TTraceSet & globalTraceSet,
     TSeedSize verticalNextGridOrigin = _max(0, static_cast<TSignedPosition>(beginPositionV(seed)) + 1 -
                                             static_cast<TSignedPosition>(bandExtension));
 
-    DPBand_<BandOn> band;
+    DPBandConfig<BandOn> band;
     // Determine coordinates of lower right corner of gap-area.
     setUpperDiagonal(band, static_cast<TSignedPosition>(_min(static_cast<TSignedSize>(length(seqH)),
         static_cast<TSignedPosition>(horizontalNextGridOrigin +  (bandExtension << 1) + horizontalBandShift +
@@ -782,7 +783,7 @@ _initializeBandedChain(TTraceSet & globalTraceSet,
                           1 - lowerDiagonal(band) - verticalNextGridOrigin);
 
         // Call the basic alignment function.
-        score = _computeAlignment(globalTraceSet, scoutState, infixH, infixV, scoreSchemeGap, DPBand_<BandOff>(),
+        score = _computeAlignment(globalTraceSet, scoutState, infixH, infixV, scoreSchemeGap, DPBandConfig<BandOff>(),
                                   DPProfile_<BandedChainAlignment_<TFreeEndGaps, BandedChainInitialDPMatrix>, TGaps,
                                              TracebackOn<TTracebackConfig> >());
     }
@@ -836,7 +837,8 @@ _initializeBandedChain(TTraceSet & globalTraceSet,
         if (gridEnd.i1 == length(seqH) && gridEnd.i2 == length(seqV))   // Standard global alignment problem.
         {
             resize(localTraceSet, 1);
-            score = _computeAlignment(localTraceSet[0], infixH, infixV, scoreSchemeGap, band,
+            DPScoutState_<Default> noScout;
+            score = _computeAlignment(localTraceSet[0], noScout, infixH, infixV, scoreSchemeGap, band,
                       DPProfile_<GlobalAlignment_<TFreeEndGaps>, TGaps, TracebackOn<TTracebackConfig> >());
         }
         else
@@ -891,7 +893,7 @@ _computeGapArea(TTraceSet & globalTraceSet,
     typedef typename Position<TSeqH>::Type TPosH;
     typedef typename Position<TSeqV>::Type TPosV;
     typedef typename Position<TSeed const>::Type TPosition;
-    typedef DPBand_<BandOff> TBand;
+    typedef DPBandConfig<BandOff> TBand;
     typedef typename Value<TScoreScheme>::Type TScoreValue;
     typedef Pair<TPosition, TPosition> TGridPoint;
 
@@ -923,7 +925,7 @@ _computeGapArea(TTraceSet & globalTraceSet,
     _adaptLocalTracesToGlobalGrid(localTraceSet, gridBegin);
     if (!empty(localTraceSet))
         _glueTracebacks(globalTraceSet, localTraceSet);
-    
+
     scoutState._horizontalNextGridOrigin += gridBegin.i1;
     scoutState._verticalNextGridOrigin += gridBegin.i2;
     return score;
@@ -951,7 +953,7 @@ _computeAnchorArea(TTraceSet & globalTraceSet,
     typedef typename MakeSigned<TSize>::Type TSignedSize;
     typedef typename Position<TSeed const>::Type TPosition;
     typedef typename MakeSigned<TPosition>::Type TSignedPosition;
-    //typedef DPBand_<BandOn> TBand;
+    //typedef DPBandConfig<BandOn> TBand;
     typedef typename Value<TScoreScheme>::Type TScore;
     typedef Pair<TPosition, TPosition> TGridPoint;
 
@@ -973,7 +975,7 @@ _computeAnchorArea(TTraceSet & globalTraceSet,
     // Computing the start position of the band according to the start point.
     // TODO(rmaerker): Rename the function _verticalBandShift to _verticalBandShiftBeginPoint()
     // TODO(rmaerker): Rename the function _horiontalBandShift to _horizontalBandShiftBeginPoint()
-    DPBand_<BandOn> band(-static_cast<TSignedPosition>((bandExtension << 1)) -static_cast<TSignedPosition>(verticalBandShift),
+    DPBandConfig<BandOn> band(-static_cast<TSignedPosition>((bandExtension << 1)) -static_cast<TSignedPosition>(verticalBandShift),
                          static_cast<TSignedPosition>((bandExtension << 1) + horizontalBandShift));
 
     TPosition relativeVerticalNextGridOrigin = verticalNextGridOrigin;
@@ -1057,7 +1059,7 @@ _finishBandedChain(TTraceSet & globalTraceSet,
 
     // Compute the alignment.
     TTraceSet localTraceSet;
-    _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeGap, DPBand_<BandOff>(), dpProfile);
+    _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeGap, DPBandConfig<BandOff>(), dpProfile);
 
     // Adapt the local traces to match the positions of the  global grid.
     _adaptLocalTracesToGlobalGrid(localTraceSet, gridBegin);
@@ -1080,21 +1082,22 @@ _finishBandedChain(TTraceSet & globalTraceSet,
     // The last anchor is crossing the end of the global matrix in both directions.
     if(gridEnd.i1 == length(seqH) && gridEnd.i2 == length(seqV))
     {
-        DPBand_<BandOn> band(-static_cast<TSignedPosition>(gridEnd.i2 - gridBegin.i2), static_cast<TSignedPosition>(gridEnd.i1 - gridBegin.i1));
+        DPBandConfig<BandOn> band(-static_cast<TSignedPosition>(gridEnd.i2 - gridBegin.i2), static_cast<TSignedPosition>(gridEnd.i1 - gridBegin.i1));
         _reinitScoutState(dpScoutState, 0, 0, upperDiagonal(band)+ 1, 1 - lowerDiagonal(band),
                           upperDiagonal(band)+ 1, 1 - lowerDiagonal(band));
             // TODO(rmaerker): Should we not set the nextGridOrigin to 0 as it is the case for the last rectangle? We want to compute the last full path.
             // Compute the last anchor which crosses the end of the global grid.
+        clear(localTraceSet);
         TScoreValue score = _computeAlignment(localTraceSet, dpScoutState, infixH, infixV, scoreSchemeAnchor, band,
                                   DPProfile_<BandedChainAlignment_<TFreeEndGaps, BandedChainFinalDPMatrix>, TGaps, TracebackOn<TTracebackConfig> >());
 
         _adaptLocalTracesToGlobalGrid(localTraceSet, gridBegin);
         if (!empty(localTraceSet))
             _glueTracebacks(globalTraceSet, localTraceSet);
-        return score;   
+        return score;
     }
 
-    DPBand_<BandOn> band(-static_cast<TSignedPosition>((bandExtension << 1)) -static_cast<TSignedPosition>(verticalBandShift),
+    DPBandConfig<BandOn> band(-static_cast<TSignedPosition>((bandExtension << 1)) -static_cast<TSignedPosition>(verticalBandShift),
                          static_cast<TSignedPosition>((bandExtension << 1) + horizontalBandShift));
 
     // Compute the last anchor and the rectangle to fill the gap between the end of the global matrix and the last anchor.
@@ -1136,7 +1139,7 @@ _finishBandedChain(TTraceSet & globalTraceSet,
     // Compute the alignment.
     clear(localTraceSet);
     score = _computeAlignment(localTraceSet, dpScoutState, suffix(seqH, gridBegin.i1), suffix(seqV,gridBegin.i2),
-                              scoreSchemeGap, DPBand_<BandOff>(), DPProfile_<BandedChainAlignment_<TFreeEndGaps,
+                              scoreSchemeGap, DPBandConfig<BandOff>(), DPProfile_<BandedChainAlignment_<TFreeEndGaps,
                               BandedChainFinalDPMatrix>, TGaps, TracebackOn<TTracebackConfig> >());
 
     _adaptLocalTracesToGlobalGrid(localTraceSet, gridBegin);
@@ -1145,6 +1148,27 @@ _finishBandedChain(TTraceSet & globalTraceSet,
     return score;
 }
 
+// ----------------------------------------------------------------------------
+// Function _computeAlignment()                                    [DP-Wrapper]
+// ----------------------------------------------------------------------------
+
+template <typename TGapScheme, typename TTraceTarget, typename TScoutState, typename TSequenceH, typename TSequenceV,
+          typename TScoreScheme, typename TBandSwitch, typename TAlignmentAlgorithm, typename TTraceFlag>
+inline typename Value<TScoreScheme>::Type
+_computeAlignment(TTraceTarget & traceSegments,
+                  TScoutState & scoutState,
+                  TSequenceH const & seqH,
+                  TSequenceV const & seqV,
+                  TScoreScheme const & scoreScheme,
+                  DPBandConfig<TBandSwitch> const & band,
+                  DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag> const & dpProfile)
+{
+    typedef typename Value<TScoreScheme>::Type TScoreValue;
+    typedef DPContext<TScoreValue, TGapScheme> TDPContext;
+    TDPContext dpContext;
+    return _computeAlignment(dpContext, traceSegments, scoutState, seqH, seqV, scoreScheme, band, dpProfile);
+}
+
 // ----------------------------------------------------------------------------
 // Function _computeAlignment()                          [BandedChainAlignment]
 // ----------------------------------------------------------------------------
@@ -1170,7 +1194,7 @@ _computeAlignment(TTraceSet & globalTraceSet,
 
     typedef typename Position<TSequenceH>::Type TPosH;
     typedef typename Position<TSequenceV>::Type TPosV;
-    typedef typename Iterator<TSeedSet const>::Type TSeedSetIterator;
+    typedef typename Iterator<TSeedSet const, Standard>::Type TSeedSetIterator;
 
     typedef DPCell_<TScoreValue, TGapSpec> TDPCell;
     typedef DPScoutState_<BandedChainAlignmentScoutState<TDPCell> > TScoutState;
@@ -1192,7 +1216,7 @@ _computeAlignment(TTraceSet & globalTraceSet,
     // Find the last anchor that is not covered by the region between the previous anchor and the end of the matrix.
     TSeedSetIterator itEnd = _findLastAnchor(it, seedSet, seqH, seqV, bandExtension);
 
-    SEQAN_ASSERT(itEnd != static_cast<TSeedSetIterator>(end(seedSet)));
+    SEQAN_ASSERT(itEnd != static_cast<TSeedSetIterator>(end(seedSet, Standard())));
     // The scout state stores the current state of the dp scout and is used to store the
     // initialization values for the next intersecting grid.
     TScoutState scoutState;
@@ -1217,7 +1241,7 @@ _computeAlignment(TTraceSet & globalTraceSet,
             // compute the alignment
             TTraceSet localTraceSet;
             score = _computeAlignment(localTraceSet, scoutState, suffix(seqH, gridBeginH), suffix(seqV, gridBeginV),
-                              scoreSchemeGap, DPBand_<BandOff>(), DPProfile_<BandedChainAlignment_<TFreeEndGaps,
+                              scoreSchemeGap, DPBandConfig<BandOff>(), DPProfile_<BandedChainAlignment_<TFreeEndGaps,
                               BandedChainFinalDPMatrix>, TGapSpec, TracebackOn<TTracebackConfig> >());
             _adaptLocalTracesToGlobalGrid(localTraceSet, Pair<TPosH, TPosV>(gridBeginH, gridBeginV));
             _glueTracebacks(globalTraceSet, localTraceSet);
@@ -1244,4 +1268,4 @@ _computeAlignment(TTraceSet & globalTraceSet,
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_IMPL_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_IMPL_H_
diff --git a/seqan/seeds/banded_chain_alignment_profile.h b/seqan/seeds/banded_chain_alignment_profile.h
index 60fdb17..860cb08 100644
--- a/seqan/seeds/banded_chain_alignment_profile.h
+++ b/seqan/seeds/banded_chain_alignment_profile.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,8 @@
 // alignment.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_META_INFO_H_
-#define CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_META_INFO_H_
+#ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_META_INFO_H_
+#define INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_META_INFO_H_
 
 namespace seqan {
 
@@ -87,7 +87,7 @@ struct BandedChainAlignment_{};
 
 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTraceback, typename TColumnType>
 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTraceback>,
-					MetaColumnDescriptor<TColumnType, FullColumn> >
+                    MetaColumnDescriptor<TColumnType, FullColumn> >
 {
     // If InitialColumn -> replaced, replaced, replaced
     // If InnerColumn -> replaced, All, All
@@ -108,13 +108,13 @@ struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLoc
 
 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTraceback, typename TColumnType>
 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTraceback>,
-					MetaColumnDescriptor<TColumnType, PartialColumnTop> >
+                    MetaColumnDescriptor<TColumnType, PartialColumnTop> >
 {
     // If InitialColumn -> replaced, replaced, replaced
     // If InnerColumn -> replaced, All, LowerBand
     // If FinalColumn -> replaced, All, LowerBand
 
-	typedef RecursionDirectionZero  TRecursionTypeFirstCell_;
+    typedef RecursionDirectionZero  TRecursionTypeFirstCell_;
     typedef RecursionDirectionAll TRecursionTypeInnerCell_;
     typedef RecursionDirectionLowerDiagonal TRecursionTypeLastCell_;
 
@@ -124,12 +124,12 @@ struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLoc
 };
 
 // ----------------------------------------------------------------------------
-// Class DPMetaColumn									  [PartialColumnMiddle]
+// Class DPMetaColumn                                      [PartialColumnMiddle]
 // ----------------------------------------------------------------------------
 
 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTraceback, typename TColumnType>
 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTraceback>,
-					MetaColumnDescriptor<TColumnType, PartialColumnMiddle> >
+                    MetaColumnDescriptor<TColumnType, PartialColumnMiddle> >
 {
     // If InitialColumn -> replaced, replaced, replaced
     // If InnerColumn -> UpperDiagonal, All, LowerDiagonal
@@ -145,12 +145,12 @@ struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLoc
 };
 
 // ----------------------------------------------------------------------------
-// Class DPMetaColumn									  [PartialColumnBottom]
+// Class DPMetaColumn                                      [PartialColumnBottom]
 // ----------------------------------------------------------------------------
 
 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTraceback, typename TColumnType>
 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTraceback>,
-					MetaColumnDescriptor<TColumnType, PartialColumnBottom> >
+                    MetaColumnDescriptor<TColumnType, PartialColumnBottom> >
 {
     // If InitialColumn -> replaced, replaced, replaced
     // If InnerColumn -> UpperDiagonal, All, All
@@ -264,4 +264,4 @@ _setupAndRunBandedChainAlignment(StringSet<String<TTraceSegment>, TStringSetSpec
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_META_INFO_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_META_INFO_H_
diff --git a/seqan/seeds/banded_chain_alignment_scout.h b/seqan/seeds/banded_chain_alignment_scout.h
index e25ce9e..f566037 100644
--- a/seqan/seeds/banded_chain_alignment_scout.h
+++ b/seqan/seeds/banded_chain_alignment_scout.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,8 +36,8 @@
 // the next matrix.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_SCOUT_H_
-#define CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_SCOUT_H_
+#ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_SCOUT_H_
+#define INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_SCOUT_H_
 
 namespace seqan {
 
@@ -283,6 +283,18 @@ _scoutBestScore(DPScout_<TDPCell, BandedChainAlignmentScout> &,
     //no-op
 }
 
+// Delegate.
+template <typename TDPCell, typename TTraceMatrixNavigator, typename TIsLastColumn, typename TIsLastRow>
+inline void
+_scoutBestScore(DPScout_<TDPCell, BandedChainAlignmentScout> & dpScout,
+                TDPCell const & activeCell,
+                TTraceMatrixNavigator const & navigator,
+                TIsLastColumn const & /**/,
+                TIsLastRow const & /**/)
+{
+    _scoutBestScore(dpScout, activeCell, navigator, TIsLastColumn::VALUE, TIsLastRow::VALUE);
+}
+
 // ----------------------------------------------------------------------------
 // Function maxScore()
 // ----------------------------------------------------------------------------
@@ -291,14 +303,14 @@ template <typename TDPCell>
 inline typename Value<TDPCell>::Type &
 maxScore(DPScout_<TDPCell, BandedChainAlignmentScout> & scout)
 {
-	return _scoreOfCell(scout._maxScore);
+    return _scoreOfCell(scout._maxScore);
 }
 
 template <typename TDPCell>
 inline typename Value<TDPCell>::Type const &
 maxScore(DPScout_<TDPCell, BandedChainAlignmentScout> const & scout)
 {
-	return _scoreOfCell(scout._maxScore);
+    return _scoreOfCell(scout._maxScore);
 }
 
 // ----------------------------------------------------------------------------
@@ -309,7 +321,7 @@ template <typename TDPCell>
 inline typename DPScout_<TDPCell, BandedChainAlignmentScout>::TMaxHostPositionString const &
 maxHostPositions(DPScout_<TDPCell, BandedChainAlignmentScout> const & scout)
 {
-	return scout._maxHostPositions;
+    return scout._maxHostPositions;
 }
 
 template <typename TDPCell>
@@ -327,7 +339,7 @@ template <typename TDPCell>
 inline unsigned int
 maxHostPosition(DPScout_<TDPCell, BandedChainAlignmentScout> const & scout)
 {
-	return scout._maxHostPositions[0];
+    return scout._maxHostPositions[0];
 }
 
 // ----------------------------------------------------------------------------
@@ -338,7 +350,7 @@ template <typename TDPCell>
 inline unsigned int
 _nextMatrixBeginH(DPScout_<TDPCell, BandedChainAlignmentScout> const & scout)
 {
-	return scout._posH;
+    return scout._posH;
 }
 
 // ----------------------------------------------------------------------------
@@ -349,9 +361,9 @@ template <typename TDPCell>
 inline unsigned int
 _nextMatrixBeginV(DPScout_<TDPCell, BandedChainAlignmentScout> const & scout)
 {
-	return scout._posV;
+    return scout._posV;
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_SCOUT_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_SCOUT_H_
diff --git a/seqan/seeds/banded_chain_alignment_traceback.h b/seqan/seeds/banded_chain_alignment_traceback.h
index a8add41..7266d54 100644
--- a/seqan/seeds/banded_chain_alignment_traceback.h
+++ b/seqan/seeds/banded_chain_alignment_traceback.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,8 +38,8 @@
 // fir the current dp matrix.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_TRACEBACK_H_
-#define CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_TRACEBACK_H_
+#ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_TRACEBACK_H_
+#define INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_TRACEBACK_H_
 
 namespace seqan {
 
@@ -125,6 +125,12 @@ inline void _glueTracebacks(TTraceSet & globalTraces, TTraceSet & localTraces)
 
     bool isGlued = false;
 
+    if (empty(globalTraces))
+    {
+        globalTraces = localTraces;
+        return;
+    }
+
     TSize lengthGlobalTraces = length(globalTraces);
     TSize oldNumOfGlobalTraces = lengthGlobalTraces;
     String<unsigned> elementsToErase;
@@ -193,6 +199,7 @@ inline void _glueTracebacks(TTraceSet & globalTraces, TTraceSet & localTraces)
         erase(globalTraces, elementsToErase[i-1]); // erase from behind to avoid accessing an element beyond the scope
     }
     SEQAN_ASSERT_EQ_MSG(isGlued, true, "Fatal error while trying to connect trace backs: No glue point available!");
+    ignoreUnusedVariableWarning(isGlued);
 }
 
 // ----------------------------------------------------------------------------
@@ -203,23 +210,23 @@ template <typename TScoreValue, typename TTraceValue>
 inline void
 _correctDPCellForAffineGaps(DPCell_<TScoreValue, LinearGaps> const &, TTraceValue /*lastTraceValue*/)
 {
-	//no-op
+    //no-op
 }
 
 template <typename TScoreValue, typename TTraceValue>
 inline void
 _correctDPCellForAffineGaps(DPCell_<TScoreValue, AffineGaps> & dpCell, TTraceValue lastTraceValue)
 {
-	typedef DPCell_<TScoreValue, AffineGaps> TDPCell;
-	if (lastTraceValue & TraceBitMap_::DIAGONAL)
-	{
-		dpCell._verticalScore = DPCellDefaultInfinity<TDPCell>::VALUE;
-		dpCell._horizontalScore = DPCellDefaultInfinity<TDPCell>::VALUE;
-	}
-	else if (lastTraceValue & TraceBitMap_::VERTICAL)
-		dpCell._horizontalScore = DPCellDefaultInfinity<TDPCell>::VALUE;
-	else
-		dpCell._verticalScore = DPCellDefaultInfinity<TDPCell>::VALUE;
+    typedef DPCell_<TScoreValue, AffineGaps> TDPCell;
+    if (lastTraceValue & TraceBitMap_::DIAGONAL)
+    {
+        dpCell._verticalScore = DPCellDefaultInfinity<TDPCell>::VALUE;
+        dpCell._horizontalScore = DPCellDefaultInfinity<TDPCell>::VALUE;
+    }
+    else if (lastTraceValue & TraceBitMap_::VERTICAL)
+        dpCell._horizontalScore = DPCellDefaultInfinity<TDPCell>::VALUE;
+    else
+        dpCell._verticalScore = DPCellDefaultInfinity<TDPCell>::VALUE;
 }
 
 // ----------------------------------------------------------------------------
@@ -227,7 +234,7 @@ _correctDPCellForAffineGaps(DPCell_<TScoreValue, AffineGaps> & dpCell, TTraceVal
 // ----------------------------------------------------------------------------
 
 template<typename TTarget, typename TDPTraceMatrixNavigator, typename TDPCell, typename TScoutSpec,
-		 typename TSequenceH, typename TSequenceV, typename TBandFlag, typename TFreeEndGaps, typename TDPMatrixLocation,
+         typename TSequenceH, typename TSequenceV, typename TBandFlag, typename TFreeEndGaps, typename TDPMatrixLocation,
          typename TGapCosts, typename TTracebackSpec>
 void _computeTraceback(TTarget & target,
                        TDPTraceMatrixNavigator & matrixNavigator,
@@ -235,33 +242,33 @@ void _computeTraceback(TTarget & target,
                        DPScout_<TDPCell, TScoutSpec> & dpScout,
                        TSequenceH const & seqH,
                        TSequenceV const & seqV,
-                       DPBand_<TBandFlag> const & band,
+                       DPBandConfig<TBandFlag> const & band,
                        DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTracebackSpec> const & dpProfile)
 {
     typedef DPScout_<TDPCell, TScoutSpec> TDPScout_;
     typedef typename TDPScout_::TScoutState TScoutState_;
     typedef typename TScoutState_::TInitCell TInitCell;
-	typedef typename Container<TDPTraceMatrixNavigator>::Type TContainer;
-	typedef typename Size<TContainer>::Type TSize;
-	//typedef typename MakeSigned<TSize>::Type TSignedSize;
-	typedef typename Position<TContainer>::Type TPosition;
-	typedef typename MakeSigned<TPosition>::Type TSignedPosition;
+    typedef typename Container<TDPTraceMatrixNavigator>::Type TContainer;
+    typedef typename Size<TContainer>::Type TSize;
+    //typedef typename MakeSigned<TSize>::Type TSignedSize;
+    typedef typename Position<TContainer>::Type TPosition;
+    typedef typename MakeSigned<TPosition>::Type TSignedPosition;
     typedef typename Size<TSequenceH>::Type TSizeSeqH;
     typedef typename Size<TSequenceV>::Type TSizeSeqV;
-	typedef typename TraceBitMap_::TTraceValue TTraceValue;
+    typedef typename TraceBitMap_::TTraceValue TTraceValue;
 
-	if (IsSameType<TTracebackSpec, TracebackOff>::VALUE)
-		return;
+    if (IsSameType<TTracebackSpec, TracebackOff>::VALUE)
+        return;
 
-	TSizeSeqH seqHSize = length(seqH);
-	TSizeSeqV seqVSize = length(seqV);
+    TSizeSeqH seqHSize = length(seqH);
+    TSizeSeqV seqVSize = length(seqV);
 
     // Determine whether or not we place gaps to the left.
-    typedef typename IsGapsLeft_<TTracebackSpec>::Type TIsGapsLeft; 
+    typedef typename IsGapsLeft_<TTracebackSpec>::Type TIsGapsLeft;
 
     // TODO(rmaerker): Define separate function for this.
     // Set to the correct position within the trace matrix.
-	_setToPosition(matrixNavigator, maxHostPosition);
+    _setToPosition(matrixNavigator, maxHostPosition);
 
     SEQAN_ASSERT_LEQ(coordinate(matrixNavigator, +DPMatrixDimension_::HORIZONTAL), seqHSize);
     SEQAN_ASSERT_LEQ(coordinate(matrixNavigator, +DPMatrixDimension_::VERTICAL), seqVSize);
@@ -355,7 +362,7 @@ void _computeTraceback(StringSet<TTarget> & targetSet,
                        TDPScout & dpScout,
                        TSequenceH const & seqH,
                        TSequenceV const & seqV,
-                       DPBand_<TBandFlag> const & band,
+                       DPBandConfig<TBandFlag> const & band,
                        DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTracebackSpec> const & dpProfile)
 {
     typedef typename TDPScout::TMaxHostPositionString TMaxHostPositions;
@@ -378,4 +385,4 @@ void _computeTraceback(StringSet<TTarget> & targetSet,
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_TRACEBACK_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEEDS_BANDED_CHAIN_ALIGNMENT_TRACEBACK_H_
diff --git a/seqan/seeds/basic_iter_indirect.h b/seqan/seeds/basic_iter_indirect.h
index 3606ec6..d8f4083 100644
--- a/seqan/seeds/basic_iter_indirect.h
+++ b/seqan/seeds/basic_iter_indirect.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -55,7 +55,7 @@ class Iter<TContainer, Indirect<TWrappedIter> >
 {
 public:
     TWrappedIter _wrappedIter;
-    
+
     Iter() : _wrappedIter(0)
     {}
 
diff --git a/seqan/seeds/seeds_base.h b/seqan/seeds/seeds_base.h
index a26e614..7e9f302 100644
--- a/seqan/seeds/seeds_base.h
+++ b/seqan/seeds/seeds_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/seeds/seeds_combination.h b/seqan/seeds/seeds_combination.h
index 8de9f3c..dad14be 100644
--- a/seqan/seeds/seeds_combination.h
+++ b/seqan/seeds/seeds_combination.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -53,40 +53,28 @@ namespace seqan {
  * @headerfile <seqan/seeds.h>
  * @brief Try to merge with existing seed.
  *
- * @typedef Tag<Merge_> Merge;
+ * @signature typedef Tag<Merge_> Merge;
  *
  * @tag LocalChainingTags#Chaos
  * @headerfile <seqan/seeds.h>
  * @brief Chain to other seed using CHAOS chaining condition.
  *
- * @typedef Tag<Chaos_> Chaos;
+ * @signature typedef Tag<Chaos_> Chaos;
  *
  * @tag LocalChainingTags#SimpleChain
  * @headerfile <seqan/seeds.h>
  * @brief Chain to other seed by simple chaining.
  *
- * @typedef Tag<SimpleChain_> SimpleChain;
+ * @signature typedef Tag<SimpleChain_> SimpleChain;
  *
  * @tag LocalChainingTags#Single
  * @headerfile <seqan/seeds.h>
  * @brief Force adding without chaining.
  *
- * @typedef Tag<Single_> Single;
+ * @signature typedef Tag<Single_> Single;
  */
 
 // TODO(holtgrew): Stream-line tags to Merge, ChaosChain, SimpleChain?
-/**
-.Tag.Local Chaining
-..cat:Seed Handling
-..summary:The local chaining algorithms to use when adding a seed to a @Class.SeedSet@.
-..see:Class.SeedSet
-..see:Function.SeedSet#addSeed
-..tag.Merge:Merge with existing seed.
-..tag.Chaos:CHAOS chaining.
-..tag.SimpleChain:Simple chaining.
-..tag.Single:Add single seed without merging and chaining.
-..include:seqan/seeds.h
-*/
 struct Merge_;
 typedef Tag<Merge_> Merge;
 
@@ -323,7 +311,7 @@ _combineSeeds(Seed<ChainedSeed, TSeedConfig> & seed,
     // std::cout << "Merging chained seeds " << seed << " and " << other << std::endl;
     SEQAN_ASSERT_LEQ_MSG(beginPositionH(seed), beginPositionH(other), "Monotony in both dimensions required for merging.");
     SEQAN_ASSERT_LEQ_MSG(beginPositionV(seed), beginPositionV(other), "Monotony in both dimensions required for merging.");
-    
+
     _updateSeedsScoreMerge(seed, other);
 
     // Remove diagonals.
diff --git a/seqan/seeds/seeds_extension.h b/seqan/seeds/seeds_extension.h
index 1edc9d9..049bdb5 100644
--- a/seqan/seeds/seeds_extension.h
+++ b/seqan/seeds/seeds_extension.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -62,6 +62,8 @@ namespace seqan {
  * @defgroup SeedExtensionTags
  * @brief Tags for selecting seed extension algorithm.
  *
+ * @see Seed#extendSeed
+ *
  * @tag SeedExtensionTags#MatchExtend
  * @headerfile <seqan/seeds.h>
  * @brief Extends a seed until a mismatch occurs.
@@ -81,16 +83,6 @@ namespace seqan {
  * @signature typedef Tag<GappedXDrop_> const GappedXDrop;
  */
 
-/**
-.Tag.Seed Extension
-..cat:Seed Handling
-..summary:The algorithms used to extend a seed.
-..see:Function.extendSeed
-..tag.MatchExtend:Extends a seed until a mismatch occurs.
-..tag.UngappedXDrop:Ungapped extension of a seed until score drops below a Value.
-..tag.GappedXDrop:Gapped extension of a seed until score drops below a Value. Only @Spec.Simple Seed@s.
-..include:seqan/seeds.h
-*/
 struct MatchExtend_;
 typedef Tag<MatchExtend_> const MatchExtend;
 
@@ -113,31 +105,21 @@ typedef Tag<GappedXDrop_> const GappedXDrop;
  *
  * @signature enum ExtensionDirection;
  *
- * @var ExtensionDirection EXTEND_NONE = 0;
+ * @see Seed#extendSeed
+ *
+ * @val ExtensionDirection EXTEND_NONE = 0;
  * @brief Perform no extension.
  *
- * @var ExtensionDirection EXTEND_LEFT = 0;
+ * @val ExtensionDirection EXTEND_LEFT = 1;
  * @brief Perform extension towards the left.
  *
- * @var ExtensionDirection EXTEND_RIGHT = 0;
+ * @val ExtensionDirection EXTEND_RIGHT = 2;
  * @brief Perform extension towards the right.
  *
- * @var ExtensionDirection EXTEND_BOTH = 0;
+ * @val ExtensionDirection EXTEND_BOTH = 3;
  * @brief Perform extension to both directions.
  */
 
-/**
-.Enum.Extension Direction
-..cat:Seed Handling
-..summary:The direction in which a seed should be extended.
-..value.EXTEND_NONE:Perform no extension.
-..value.EXTEND_LEFT:Extend the seed to the left.
-..value.EXTEND_RIGHT:Extend the seed to the right.
-..value.EXTEND_BOTH:Extend the seed in both directions.
-..see:Function.extendSeed
-..include:seqan/seeds.h
-*/
-
 enum ExtensionDirection
 {
     EXTEND_NONE  = 0,
@@ -162,118 +144,90 @@ enum ExtensionDirection
  * @fn Seed#extendSeed
  * @headerfile <seqan/seeds.h>
  * @brief Extends a seed.
- * 
+ *
  * @signature void extendSeed(seed, database, query, direction, MatchExtend);
  * @signature void extendSeed(seed, database, query, direction, scoringScheme, scoreDropOff, xDropTag);
  *
- * @param seed[in,out]      The seed to extend.
- * @param database[in]      The database (horizontal) sequence.
- * @param query[in]         The query (vertical) sequence.
- * @param direction[in]     The extension direction.  Type: @link ExtensionDirection @endlink.
- * @param scoringScheme[in] The @link Score @endlink object to use for scoring alignments and gaps.
- * @param scoreDropOff[in]  The score drop after which the extension should stop.  The extension stops if this value is
- *                          exceeded.  Only given for when using an x-drop algorithm.
- * @param xDropTag[in]      Tag for selecting x-drop method, one of <tt>UnGappedXDrop</tt> and <tt>GappedXDrop</tt>.
- * 
- * @section Remarks
- * 
+ * @param[in,out] seed          The Seed to extend.
+ * @param[in]     database      The database (horizontal) @link ContainerConcept sequence @endlink.
+ * @param[in]     query         The query (vertical) @link ContainerConcept sequence @endlink.
+ * @param[in]     direction     The extension direction.  Type: @link ExtensionDirection @endlink.
+ * @param[in]     scoringScheme The @link Score @endlink object to use for scoring alignments and gaps.
+ * @param[in]     scoreDropOff  The score drop after which the extension should stop.  The extension stops if this
+ *                              value is exceeded.  Only given for when using an x-drop algorithm.
+ * @param[in]     xDropTag      Tag for selecting x-drop method, one of <tt>UnGappedXDrop</tt> and
+ *                              <tt>GappedXDrop</tt>.
+ *
  * You can use the tags, <tt>MatchExtend</tt>, <tt>UnGappedXDrop</tt>, and <tt>GappedXDrop</tt>.
- * 
+ *
  * Note that the diagonals updated in <tt>seed</tt> do not necessarily reflect the diagonals for the optimal extension
  * but the diagonals used in all traces of the extension.  However, they are guaranteed to include the optimal
  * extension's trace.
- * 
+ *
  * @section Examples
- * 
+ *
  * The documentation of the class @link Seed @endlink contains an example for
  * seed extension.
- * 
+ *
  * @see ExtensionDirection
  * @see SeedExtensionTags
  */
 
-/**
-.Function.extendSeed
-..summary:Extends a seed.
-..cat:Seed Handling
-..signature:void extendSeed(seed, database, query, direction, MatchExtend);
-..signature:void extendSeed(seed, database, query, direction, scoreMatrix, scoreDropOff, {UngappedXDrop, GappedXDrop});
-..class:Class.Seed
-..param.seed: The seed to extend.
-...type:Class.Seed
-..param.query: The query sequence (vertical).
-...type:Class.String
-..param.database: The database sequence (horizontal).
-...type:Class.String
-..param.direction: Defines the direction in which the seed should be extended.
-...type:Enum.Extension Direction
-..param.scoreDropOff: The score drop after which the extension should stop. The extension stops if this value is exceeded.
-...remarks:Only used for the algorithms @Tag.Seed Extension.UngappedXDrop@ and @Tag.Seed Extension.GappedXDrop@
-..param.scoreMatrix: The scoring scheme.
-...type:Spec.Simple Score
-...remarks:Only used for the algorithms @Tag.Seed Extension.UngappedXDrop@ and @Tag.Seed Extension.GappedXDrop@
-..remarks:You can use the tags, @Tag.Seed Extension.MatchExtend@, @Tag.Seed Extension.UngappedXDrop@, and @Tag.Seed Extension.GappedXDrop@.
-..remarks:Note that the diagonals updated in $seed$ do not necessarily reflect the diagonals for the optimal extension but the diagonals used in all traces of the extension.
-However, they are guaranteed to include the optimal extension's trace.
-..example.text:The documentation of the class @Class.Seed@ contains an example for seed extension.
-..include:seqan/seeds.h
-*/
-
 // We need one specialization for each combination of the extension variants and seeds.  It is not worth to extract the
 // common parts for simple and chained seeds.
 
 template <typename TConfig, typename TDatabase, typename TQuery>
-inline void 
-extendSeed(Seed<Simple, TConfig> & seed, 
-		   TDatabase const & database,
-		   TQuery const & query,
-		   ExtensionDirection direction,
-		   MatchExtend const &)
+inline void
+extendSeed(Seed<Simple, TConfig> & seed,
+           TDatabase const & database,
+           TQuery const & query,
+           ExtensionDirection direction,
+           MatchExtend const &)
 {
     // For match extension of Simple Seeds, we can simply update the begin and end values in each dimension.
     typedef Seed<Simple, TConfig> TSeed;
     typedef typename Position<TSeed>::Type TPosition;
     typedef typename Size<TSeed>::Type TSize;
-    
-	// Extension to the left
-	if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
+
+    // Extension to the left
+    if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
     {
-		TPosition posH = beginPositionH(seed);
-		TPosition posV = beginPositionV(seed);
-		while (posH >= 1 && posV >= 1 && database[posH - 1] == query[posV - 1])
+        TPosition posH = beginPositionH(seed);
+        TPosition posV = beginPositionV(seed);
+        while (posH >= 1 && posV >= 1 && database[posH - 1] == query[posV - 1])
         {
-			--posH;
-			--posV;
-		}
-		setBeginPositionH(seed, posH);
-		setBeginPositionV(seed, posV);
-	}
-
-	// Extension to the right
-	if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
+            --posH;
+            --posV;
+        }
+        setBeginPositionH(seed, posH);
+        setBeginPositionV(seed, posV);
+    }
+
+    // Extension to the right
+    if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
     {
-		TSize lengthH = length(database);
-		TSize lengthV = length(query);
-		TPosition posH = endPositionH(seed);
-		TPosition posV = endPositionV(seed);
-		while (posH < lengthH && posV < lengthV && database[posH] == query[posV])
+        TSize lengthH = length(database);
+        TSize lengthV = length(query);
+        TPosition posH = endPositionH(seed);
+        TPosition posV = endPositionV(seed);
+        while (posH < lengthH && posV < lengthV && database[posH] == query[posV])
         {
-			++posH;
-			++posV;
-		}
+            ++posH;
+            ++posV;
+        }
         setEndPositionH(seed, posH);
         setEndPositionV(seed, posV);
-	}
+    }
 }
 
 
 template <typename TConfig, typename TDatabase, typename TQuery>
-inline void 
-extendSeed(Seed<ChainedSeed, TConfig> & seed, 
-		   TDatabase const & database,
-		   TQuery const & query,
-		   ExtensionDirection direction,
-		   MatchExtend const &)
+inline void
+extendSeed(Seed<ChainedSeed, TConfig> & seed,
+           TDatabase const & database,
+           TQuery const & query,
+           ExtensionDirection direction,
+           MatchExtend const &)
 {
     // For match extension of Chained Seeds, we extend the first and the last Seed Diagonal.
     SEQAN_ASSERT_GT(length(seed), 0u);
@@ -282,42 +236,42 @@ extendSeed(Seed<ChainedSeed, TConfig> & seed,
     typedef typename Value<TSeed>::Type TSeedDiagonal;
     typedef typename Position<TSeedDiagonal>::Type TPosition;
     typedef typename Size<TSeedDiagonal>::Type TSize;
-    
-	// Extension to the left
-	if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
+
+    // Extension to the left
+    if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
     {
         TSeedDiagonal & diag = front(seed);
-		TPosition posH = diag.beginPositionH;
-		TPosition posV = diag.beginPositionV;
+        TPosition posH = diag.beginPositionH;
+        TPosition posV = diag.beginPositionV;
         TSize diagonalLength = diag.length;
-		while (posH >= 1 && posV >= 1 && database[posH - 1] == query[posV - 1])
+        while (posH >= 1 && posV >= 1 && database[posH - 1] == query[posV - 1])
         {
-			--posH;
-			--posV;
+            --posH;
+            --posV;
             ++diagonalLength;
-		}
+        }
         diag.beginPositionH = posH;
         diag.beginPositionV = posV;
         diag.length = diagonalLength;
-	}
+    }
 
-	// Extension to the right
-	if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
+    // Extension to the right
+    if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
     {
-		TSize lengthH = length(database);
-		TSize lengthV = length(query);
+        TSize lengthH = length(database);
+        TSize lengthV = length(query);
         TSeedDiagonal & diag = back(seed);
-		TPosition posH = diag.beginPositionH + diag.length;
-		TPosition posV = diag.beginPositionV + diag.length;
+        TPosition posH = diag.beginPositionH + diag.length;
+        TPosition posV = diag.beginPositionV + diag.length;
         TSize diagonalLength = diag.length;
-		while (posH < lengthH && posV < lengthV && database[posH] == query[posV])
+        while (posH < lengthH && posV < lengthV && database[posH] == query[posV])
         {
-			++posH;
-			++posV;
+            ++posH;
+            ++posV;
             ++diagonalLength;
-		}
+        }
         diag.length = diagonalLength;
-	}
+    }
 }
 
 // ---------------------------------------------------------------------------
@@ -325,7 +279,7 @@ extendSeed(Seed<ChainedSeed, TConfig> & seed,
 // ---------------------------------------------------------------------------
 
 template <typename TConfig, typename TDatabase, typename TQuery, typename TScoreValue, typename TScoreSpec>
-inline void 
+inline void
 extendSeed(Seed<Simple, TConfig> & seed,
            TDatabase const & database,
            TQuery const & query,
@@ -341,15 +295,15 @@ extendSeed(Seed<Simple, TConfig> & seed,
     typedef Seed<ChainedSeed, TConfig> TSeed;
     typedef typename Position<TSeed>::Type TPosition;
     typedef typename Size<TSeed>::Type TSize;
-    
-	// Extension to the left
-	if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
+
+    // Extension to the left
+    if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
     {
         TScoreValue tmpScore = 0;
-		TPosition posH = beginPositionH(seed);
-		TPosition posV = beginPositionV(seed);
+        TPosition posH = beginPositionH(seed);
+        TPosition posV = beginPositionV(seed);
         TPosition mismatchingSuffixLength = 0;
-		while (posH >= 1 && posV >= 1 && tmpScore > scoreDropOff)
+        while (posH >= 1 && posV >= 1 && tmpScore > scoreDropOff)
         {
             tmpScore += score(scoringScheme, sequenceEntryForScore(scoringScheme, database, posH),
                               sequenceEntryForScore(scoringScheme, query, posV));
@@ -363,23 +317,23 @@ extendSeed(Seed<Simple, TConfig> & seed,
             {
                 mismatchingSuffixLength += 1;
             }
-			--posH;
-			--posV;
-		}
-		setBeginPositionH(seed, posH + mismatchingSuffixLength);
-		setBeginPositionV(seed, posV + mismatchingSuffixLength);
-	}
-
-	// Extension to the right
-	if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
+            --posH;
+            --posV;
+        }
+        setBeginPositionH(seed, posH + mismatchingSuffixLength);
+        setBeginPositionV(seed, posV + mismatchingSuffixLength);
+    }
+
+    // Extension to the right
+    if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
     {
         TScoreValue tmpScore = 0;
-		TSize lengthH = length(database);
-		TSize lengthV = length(query);
-		TPosition posH = endPositionH(seed);
-		TPosition posV = endPositionV(seed);
+        TSize lengthH = length(database);
+        TSize lengthV = length(query);
+        TPosition posH = endPositionH(seed);
+        TPosition posV = endPositionV(seed);
         TPosition mismatchingSuffixLength = 0;
-		while (posH < lengthH && posV < lengthV && tmpScore > scoreDropOff)
+        while (posH < lengthH && posV < lengthV && tmpScore > scoreDropOff)
         {
             tmpScore += score(scoringScheme, sequenceEntryForScore(scoringScheme, database, posH),
                               sequenceEntryForScore(scoringScheme, query, posV));
@@ -395,9 +349,9 @@ extendSeed(Seed<Simple, TConfig> & seed,
             }
             ++posH;
             ++posV;
-		}
-		setEndPositionH(seed, posH - mismatchingSuffixLength);
-		setEndPositionV(seed, posV - mismatchingSuffixLength);
+        }
+        setEndPositionH(seed, posH - mismatchingSuffixLength);
+        setEndPositionV(seed, posV - mismatchingSuffixLength);
     }
 
     // TODO(holtgrew): Update score?!
@@ -405,14 +359,14 @@ extendSeed(Seed<Simple, TConfig> & seed,
 
 
 template <typename TConfig, typename TDatabase, typename TQuery, typename TScoreValue, typename TScoreSpec>
-inline void 
-extendSeed(Seed<ChainedSeed, TConfig> & seed, 
-		   TDatabase const & database,
-		   TQuery const & query,
-		   ExtensionDirection direction,
+inline void
+extendSeed(Seed<ChainedSeed, TConfig> & seed,
+           TDatabase const & database,
+           TQuery const & query,
+           ExtensionDirection direction,
            Score<TScoreValue, TScoreSpec> const & scoringScheme,
            TScoreValue scoreDropOff,
-		   UnGappedXDrop const &)
+           UnGappedXDrop const &)
 {
     // For ungapped X-drop extension of Chained Seeds, we extend the
     // first and the last Seed Diagonal.
@@ -422,17 +376,17 @@ extendSeed(Seed<ChainedSeed, TConfig> & seed,
     typedef typename Value<TSeed>::Type TSeedDiagonal;
     typedef typename Position<TSeedDiagonal>::Type TPosition;
     typedef typename Size<TSeedDiagonal>::Type TSize;
-    
-	// Extension to the left
-	if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
+
+    // Extension to the left
+    if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
     {
         TScoreValue tmpScore = 0;
         TPosition mismatchingSuffixLength = 0;
         TSeedDiagonal & diag = front(seed);
-		TPosition posH = beginPositionH(seed);
-		TPosition posV = beginPositionV(seed);
+        TPosition posH = beginPositionH(seed);
+        TPosition posV = beginPositionV(seed);
         TSize diagonalLength = diag.length;
-		while (posH >= 1 && posV >= 1 && tmpScore > scoreDropOff)
+        while (posH >= 1 && posV >= 1 && tmpScore > scoreDropOff)
         {
             tmpScore += score(scoringScheme, sequenceEntryForScore(scoringScheme, database, posH),
                               sequenceEntryForScore(scoringScheme, query, posV));
@@ -446,27 +400,27 @@ extendSeed(Seed<ChainedSeed, TConfig> & seed,
             {
                 mismatchingSuffixLength += 1;
             }
-			--posH;
-			--posV;
+            --posH;
+            --posV;
             ++diagonalLength;
-		}
+        }
         diag.beginPositionH = posH + mismatchingSuffixLength;
         diag.beginPositionV = posV + mismatchingSuffixLength;
         diag.length = diagonalLength - mismatchingSuffixLength;
-	}
+    }
 
-	// Extension to the right
-	if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
+    // Extension to the right
+    if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
     {
         TScoreValue tmpScore = 0;
         TPosition mismatchingSuffixLength = 0;
-		TSize lengthH = length(query);
-		TSize lengthV = length(database);
+        TSize lengthH = length(query);
+        TSize lengthV = length(database);
         TSeedDiagonal & diag = back(seed);
-		TPosition posH = diag.beginPositionH + diag.length;
-		TPosition posV = diag.beginPositionV + diag.length;
+        TPosition posH = diag.beginPositionH + diag.length;
+        TPosition posV = diag.beginPositionV + diag.length;
         TSize diagonalLength = diag.length;
-		while (posH < lengthH && posV < lengthV && tmpScore > scoreDropOff)
+        while (posH < lengthH && posV < lengthV && tmpScore > scoreDropOff)
         {
             tmpScore += score(scoringScheme, sequenceEntryForScore(scoringScheme, database, posH),
                               sequenceEntryForScore(scoringScheme, query, posV));
@@ -483,9 +437,9 @@ extendSeed(Seed<ChainedSeed, TConfig> & seed,
             ++posH;
             ++posV;
             ++diagonalLength;
-		}
+        }
         diag.length = diagonalLength - mismatchingSuffixLength;
-	}
+    }
 
     // TODO(holtgrew): Update score?!
 }
@@ -503,8 +457,8 @@ _initAntiDiags(TAntiDiag & ,
                TScoreValue gapCost,
                TScoreValue undefined)
 {
-	// antiDiagonals will be swaped in while loop BEFORE computation of antiDiag3 entries
-	//  -> no initialization of antiDiag1 necessary
+    // antiDiagonals will be swaped in while loop BEFORE computation of antiDiag3 entries
+    //  -> no initialization of antiDiag1 necessary
 
     resize(antiDiag2, 1);
     antiDiag2[0] = 0;
@@ -526,7 +480,7 @@ template<typename TAntiDiag>
 inline void
 _swapAntiDiags(TAntiDiag & antiDiag1,
                TAntiDiag & antiDiag2,
-			   TAntiDiag & antiDiag3)
+               TAntiDiag & antiDiag3)
 {
     TAntiDiag temp;
     move(temp, antiDiag1);
@@ -538,83 +492,83 @@ _swapAntiDiags(TAntiDiag & antiDiag1,
 template<typename TAntiDiag, typename TSize, typename TScoreValue>
 inline TSize
 _initAntiDiag3(TAntiDiag & antiDiag3,
-			   TSize offset,
-			   TSize maxCol,
-			   TSize antiDiagNo,
-			   TScoreValue minScore,
+               TSize offset,
+               TSize maxCol,
+               TSize antiDiagNo,
+               TScoreValue minScore,
                TScoreValue gapCost,
                TScoreValue undefined)
 {
-	resize(antiDiag3, maxCol + 1 - offset);
+    resize(antiDiag3, maxCol + 1 - offset);
 
     antiDiag3[0] = undefined;
-	antiDiag3[maxCol - offset] = undefined;
+    antiDiag3[maxCol - offset] = undefined;
 
-	if ((int)antiDiagNo * gapCost > minScore)
+    if ((int)antiDiagNo * gapCost > minScore)
     {
-		if (offset == 0) // init first column
-			antiDiag3[0] = antiDiagNo * gapCost;
-		if (antiDiagNo - maxCol == 0) // init first row
-			antiDiag3[maxCol - offset] = antiDiagNo * gapCost;
-	}
-	return offset;
+        if (offset == 0) // init first column
+            antiDiag3[0] = antiDiagNo * gapCost;
+        if (antiDiagNo - maxCol == 0) // init first row
+            antiDiag3[maxCol - offset] = antiDiagNo * gapCost;
+    }
+    return offset;
 }
 
 template<typename TDiagonal, typename TSize>
 inline void
 _calcExtendedLowerDiag(TDiagonal & lowerDiag,
-					   TSize minCol,
-					   TSize antiDiagNo)
+                       TSize minCol,
+                       TSize antiDiagNo)
 {
-	TSize minRow = antiDiagNo - minCol;
-	if ((TDiagonal)minCol - (TDiagonal)minRow < lowerDiag)
-		lowerDiag = (TDiagonal)minCol - (TDiagonal)minRow;
+    TSize minRow = antiDiagNo - minCol;
+    if ((TDiagonal)minCol - (TDiagonal)minRow < lowerDiag)
+        lowerDiag = (TDiagonal)minCol - (TDiagonal)minRow;
 }
 
 template<typename TDiagonal, typename TSize>
 inline void
 _calcExtendedUpperDiag(TDiagonal & upperDiag,
-					   TSize maxCol,
-					   TSize antiDiagNo)
+                       TSize maxCol,
+                       TSize antiDiagNo)
 {
-	TSize maxRow = antiDiagNo + 1 - maxCol;
-	if ((TDiagonal)maxCol - 1 - (TDiagonal)maxRow > upperDiag)
-		upperDiag = maxCol - 1 - maxRow;
+    TSize maxRow = antiDiagNo + 1 - maxCol;
+    if ((TDiagonal)maxCol - 1 - (TDiagonal)maxRow > upperDiag)
+        upperDiag = maxCol - 1 - maxRow;
 }
 
 template<typename TSeed, typename TSize, typename TDiagonal>
 inline void
 _updateExtendedSeed(TSeed & seed,
-					ExtensionDirection direction,
-					TSize cols,
-					TSize rows,
-					TDiagonal lowerDiag,
-					TDiagonal upperDiag)
+                    ExtensionDirection direction,
+                    TSize cols,
+                    TSize rows,
+                    TDiagonal lowerDiag,
+                    TDiagonal upperDiag)
 {
-	if (direction == EXTEND_LEFT)
+    if (direction == EXTEND_LEFT)
     {
-		// Set lower and upper diagonals.
-		TDiagonal beginDiag = beginDiagonal(seed);
-		if (lowerDiagonal(seed) > beginDiag + lowerDiag)
-			setLowerDiagonal(seed, beginDiag + lowerDiag);
-		if (upperDiagonal(seed) < beginDiag + upperDiag)
-			setUpperDiagonal(seed, beginDiag + upperDiag);
-
-		// Set new start position of seed.
-		setBeginPositionH(seed, beginPositionH(seed) - rows);
-		setBeginPositionV(seed, beginPositionV(seed) - cols);
-	} else {  // direction == EXTEND_RIGHT
-		// Set new lower and upper diagonals.
-		TDiagonal endDiag = endDiagonal(seed);
-		if (upperDiagonal(seed) < endDiag - lowerDiag)
-			setUpperDiagonal(seed, endDiag - lowerDiag);
-		if (lowerDiagonal(seed) > endDiag - upperDiag)
-			setLowerDiagonal(seed, endDiag - upperDiag);
-
-		// Set new end position of seed.
+        // Set lower and upper diagonals.
+        TDiagonal beginDiag = beginDiagonal(seed);
+        if (lowerDiagonal(seed) > beginDiag + lowerDiag)
+            setLowerDiagonal(seed, beginDiag + lowerDiag);
+        if (upperDiagonal(seed) < beginDiag + upperDiag)
+            setUpperDiagonal(seed, beginDiag + upperDiag);
+
+        // Set new start position of seed.
+        setBeginPositionH(seed, beginPositionH(seed) - rows);
+        setBeginPositionV(seed, beginPositionV(seed) - cols);
+    } else {  // direction == EXTEND_RIGHT
+        // Set new lower and upper diagonals.
+        TDiagonal endDiag = endDiagonal(seed);
+        if (upperDiagonal(seed) < endDiag - lowerDiag)
+            setUpperDiagonal(seed, endDiag - lowerDiag);
+        if (lowerDiagonal(seed) > endDiag - upperDiag)
+            setLowerDiagonal(seed, endDiag - upperDiag);
+
+        // Set new end position of seed.
         setEndPositionH(seed, endPositionH(seed) + rows);
         setEndPositionV(seed, endPositionV(seed) + cols);
-	}
+    }
     SEQAN_ASSERT_GEQ(upperDiagonal(seed), lowerDiagonal(seed));
     SEQAN_ASSERT_GEQ(upperDiagonal(seed), beginDiagonal(seed));
     SEQAN_ASSERT_GEQ(upperDiagonal(seed), endDiagonal(seed));
@@ -662,14 +616,14 @@ _extendSeedGappedXDropOneDirection(
         TDatabaseSegment const & databaseSeg,
         ExtensionDirection direction,
         Score<TScoreValue, TScoreSpec> scoringScheme,
-		TScoreValue scoreDropOff)
+        TScoreValue scoreDropOff)
 {
     typedef typename Size<TQuerySegment>::Type TSize;
-	typedef typename Seed<Simple,TConfig>::TDiagonal TDiagonal;
+    typedef typename Seed<Simple,TConfig>::TDiagonal TDiagonal;
 
     TSize cols = length(querySeg)+1;
     TSize rows = length(databaseSeg)+1;
-	if (rows == 1 || cols == 1)
+    if (rows == 1 || cols == 1)
         return 0;
 
     TScoreValue len = 2 * _max(cols, rows); // number of antidiagonals
@@ -683,153 +637,153 @@ _extendSeedGappedXDropOneDirection(
     TScoreValue undefined = minValue<TScoreValue>() - gapCost;
 
     // DP matrix is calculated by anti-diagonals
-    String<TScoreValue> antiDiag1;	//smallest anti-diagonal
-	String<TScoreValue> antiDiag2;
-	String<TScoreValue> antiDiag3;	//current anti-diagonal
+    String<TScoreValue> antiDiag1;    //smallest anti-diagonal
+    String<TScoreValue> antiDiag2;
+    String<TScoreValue> antiDiag3;    //current anti-diagonal
 
-	// Indices on anti-diagonals include gap column/gap row:
-	//   - decrease indices by 1 for position in query/database segment
-	//   - first calculated entry is on anti-diagonal n° 2
+    // Indices on anti-diagonals include gap column/gap row:
+    //   - decrease indices by 1 for position in query/database segment
+    //   - first calculated entry is on anti-diagonal n\B0 2
 
     TSize minCol = 1;
     TSize maxCol = 2;
 
-	TSize offset1 = 0; // number of leading columns that need not be calculated in antiDiag1
-	TSize offset2 = 0; //                                                       in antiDiag2
-	TSize offset3 = 0; //                                                       in antiDiag3
+    TSize offset1 = 0; // number of leading columns that need not be calculated in antiDiag1
+    TSize offset2 = 0; //                                                       in antiDiag2
+    TSize offset3 = 0; //                                                       in antiDiag3
 
     _initAntiDiags(antiDiag1, antiDiag2, antiDiag3, scoreDropOff, gapCost, undefined);
     TSize antiDiagNo = 1; // the currently calculated anti-diagonal
 
-	TScoreValue best = 0; // maximal score value in the DP matrix (for drop-off calculation)
+    TScoreValue best = 0; // maximal score value in the DP matrix (for drop-off calculation)
 
-	TDiagonal lowerDiag = 0;
-	TDiagonal upperDiag = 0;
+    TDiagonal lowerDiag = 0;
+    TDiagonal upperDiag = 0;
 
     while (minCol < maxCol)
     {
         ++antiDiagNo;
-		_swapAntiDiags(antiDiag1, antiDiag2, antiDiag3);
-		offset1 = offset2;
-		offset2 = offset3;
-		offset3 = minCol-1;
-		_initAntiDiag3(antiDiag3, offset3, maxCol, antiDiagNo, best - scoreDropOff, gapCost, undefined);
+        _swapAntiDiags(antiDiag1, antiDiag2, antiDiag3);
+        offset1 = offset2;
+        offset2 = offset3;
+        offset3 = minCol-1;
+        _initAntiDiag3(antiDiag3, offset3, maxCol, antiDiagNo, best - scoreDropOff, gapCost, undefined);
 
-		TScoreValue antiDiagBest = antiDiagNo * gapCost;
+        TScoreValue antiDiagBest = antiDiagNo * gapCost;
         for (TSize col = minCol; col < maxCol; ++col) {
-			// indices on anti-diagonals
-			TSize i3 = col - offset3;
-			TSize i2 = col - offset2;
-			TSize i1 = col - offset1;
-
-			// indices in query and database segments
-			TSize queryPos, dbPos;
-			if (direction == EXTEND_RIGHT)
+            // indices on anti-diagonals
+            TSize i3 = col - offset3;
+            TSize i2 = col - offset2;
+            TSize i1 = col - offset1;
+
+            // indices in query and database segments
+            TSize queryPos, dbPos;
+            if (direction == EXTEND_RIGHT)
             {
-				queryPos = col - 1;
-				dbPos = antiDiagNo - col - 1;
-			}
+                queryPos = col - 1;
+                dbPos = antiDiagNo - col - 1;
+            }
             else // direction == EXTEND_LEFT
             {
-				queryPos = cols - 1 - col;
-				dbPos = rows - 1 + col - antiDiagNo;
-			}
-
-			// Calculate matrix entry (-> antiDiag3[col])
-			TScoreValue tmp = _max(antiDiag2[i2-1], antiDiag2[i2]) + gapCost;
-			tmp = _max(tmp, antiDiag1[i1 - 1] + score(scoringScheme, sequenceEntryForScore(scoringScheme, querySeg, queryPos),
-			                                          sequenceEntryForScore(scoringScheme, databaseSeg, dbPos)));
-			if (tmp < best - scoreDropOff)
+                queryPos = cols - 1 - col;
+                dbPos = rows - 1 + col - antiDiagNo;
+            }
+
+            // Calculate matrix entry (-> antiDiag3[col])
+            TScoreValue tmp = _max(antiDiag2[i2-1], antiDiag2[i2]) + gapCost;
+            tmp = _max(tmp, antiDiag1[i1 - 1] + score(scoringScheme, sequenceEntryForScore(scoringScheme, querySeg, queryPos),
+                                                      sequenceEntryForScore(scoringScheme, databaseSeg, dbPos)));
+            if (tmp < best - scoreDropOff)
             {
-				antiDiag3[i3] = undefined;
-			}
+                antiDiag3[i3] = undefined;
+            }
             else
             {
-				antiDiag3[i3] = tmp;
-				antiDiagBest = _max(antiDiagBest, tmp);
-			}
+                antiDiag3[i3] = tmp;
+                antiDiagBest = _max(antiDiagBest, tmp);
+            }
         }
-		best = _max(best, antiDiagBest);
+        best = _max(best, antiDiagBest);
 
-		// Calculate new minCol and minCol
-		while (minCol - offset3 < length(antiDiag3) && antiDiag3[minCol - offset3] == undefined &&
-			   minCol - offset2 - 1 < length(antiDiag2) && antiDiag2[minCol - offset2 - 1] == undefined)
+        // Calculate new minCol and minCol
+        while (minCol - offset3 < length(antiDiag3) && antiDiag3[minCol - offset3] == undefined &&
+               minCol - offset2 - 1 < length(antiDiag2) && antiDiag2[minCol - offset2 - 1] == undefined)
         {
-			++minCol;
-		}
+            ++minCol;
+        }
 
-		// Calculate new maxCol
-		while (maxCol - offset3 > 0 && (antiDiag3[maxCol - offset3 - 1] == undefined) &&
-			                           (antiDiag2[maxCol - offset2 - 1] == undefined))
+        // Calculate new maxCol
+        while (maxCol - offset3 > 0 && (antiDiag3[maxCol - offset3 - 1] == undefined) &&
+                                       (antiDiag2[maxCol - offset2 - 1] == undefined))
         {
-			--maxCol;
-		}
-		++maxCol;
+            --maxCol;
+        }
+        ++maxCol;
 
         // Calculate new lowerDiag and upperDiag of extended seed
-		_calcExtendedLowerDiag(lowerDiag, minCol, antiDiagNo);
-		_calcExtendedUpperDiag(upperDiag, maxCol - 1, antiDiagNo);
+        _calcExtendedLowerDiag(lowerDiag, minCol, antiDiagNo);
+        _calcExtendedUpperDiag(upperDiag, maxCol - 1, antiDiagNo);
 
-		// end of databaseSeg reached?
-		minCol = _max((int)minCol, (int)antiDiagNo + 2 - (int)rows);
-		// end of querySeg reached?
-		maxCol = _min(maxCol, cols);
+        // end of databaseSeg reached?
+        minCol = _max((int)minCol, (int)antiDiagNo + 2 - (int)rows);
+        // end of querySeg reached?
+        maxCol = _min(maxCol, cols);
     }
 
-	// find positions of longest extension
+    // find positions of longest extension
 
-	// reached ends of both segments
-	TSize longestExtensionCol = length(antiDiag3) + offset3 - 2;
-	TSize longestExtensionRow = antiDiagNo - longestExtensionCol;
-	TScoreValue longestExtensionScore = antiDiag3[longestExtensionCol - offset3];
+    // reached ends of both segments
+    TSize longestExtensionCol = length(antiDiag3) + offset3 - 2;
+    TSize longestExtensionRow = antiDiagNo - longestExtensionCol;
+    TScoreValue longestExtensionScore = antiDiag3[longestExtensionCol - offset3];
 
-	if (longestExtensionScore == undefined)
+    if (longestExtensionScore == undefined)
     {
-		if (antiDiag2[length(antiDiag2)-2] != undefined)
+        if (antiDiag2[length(antiDiag2)-2] != undefined)
         {
-			// reached end of query segment
-			longestExtensionCol = length(antiDiag2) + offset2 - 2;
-			longestExtensionRow = antiDiagNo - 1 - longestExtensionCol;
-			longestExtensionScore = antiDiag2[longestExtensionCol - offset2];
-		}
-		else if (length(antiDiag2) > 2 && antiDiag2[length(antiDiag2)-3] != undefined)
+            // reached end of query segment
+            longestExtensionCol = length(antiDiag2) + offset2 - 2;
+            longestExtensionRow = antiDiagNo - 1 - longestExtensionCol;
+            longestExtensionScore = antiDiag2[longestExtensionCol - offset2];
+        }
+        else if (length(antiDiag2) > 2 && antiDiag2[length(antiDiag2)-3] != undefined)
         {
-			// reached end of database segment
-			longestExtensionCol = length(antiDiag2) + offset2 - 3;
-			longestExtensionRow = antiDiagNo - 1 - longestExtensionCol;
-			longestExtensionScore = antiDiag2[longestExtensionCol - offset2];
-		}
-	}
-
-	if (longestExtensionScore == undefined)
+            // reached end of database segment
+            longestExtensionCol = length(antiDiag2) + offset2 - 3;
+            longestExtensionRow = antiDiagNo - 1 - longestExtensionCol;
+            longestExtensionScore = antiDiag2[longestExtensionCol - offset2];
+        }
+    }
+
+    if (longestExtensionScore == undefined)
     {
-		// general case
-		for (TSize i = 0; i < length(antiDiag1); ++i)
+        // general case
+        for (TSize i = 0; i < length(antiDiag1); ++i)
         {
-			if (antiDiag1[i] > longestExtensionScore)
+            if (antiDiag1[i] > longestExtensionScore)
             {
-				longestExtensionScore = antiDiag1[i];
-				longestExtensionCol = i + offset1;
-				longestExtensionRow = antiDiagNo - 2 - longestExtensionCol;
-			}
-		}
-	}
-
-	// update seed
+                longestExtensionScore = antiDiag1[i];
+                longestExtensionCol = i + offset1;
+                longestExtensionRow = antiDiagNo - 2 - longestExtensionCol;
+            }
+        }
+    }
+
+    // update seed
     if (longestExtensionScore != undefined)
-		_updateExtendedSeed(seed, direction, longestExtensionCol, longestExtensionRow, lowerDiag, upperDiag);
-	return longestExtensionScore;
+        _updateExtendedSeed(seed, direction, longestExtensionCol, longestExtensionRow, lowerDiag, upperDiag);
+    return longestExtensionScore;
 }
 
 template <typename TConfig, typename TDatabase, typename TQuery, typename TScoreValue, typename TScoreSpec>
-inline void 
-extendSeed(Seed<Simple, TConfig> & seed, 
-		   TDatabase const & database,
-		   TQuery const & query,
-		   ExtensionDirection direction,
+inline void
+extendSeed(Seed<Simple, TConfig> & seed,
+           TDatabase const & database,
+           TQuery const & query,
+           ExtensionDirection direction,
            Score<TScoreValue, TScoreSpec> const & scoringScheme,
            TScoreValue scoreDropOff,
-		   GappedXDrop const &)
+           GappedXDrop const &)
 {
     // For gapped X-drop extension of Simple Seeds, we can simply
     // update the begin and end values in each dimension as well as the diagonals.
@@ -844,7 +798,7 @@ extendSeed(Seed<Simple, TConfig> & seed,
     SEQAN_ASSERT_LT(scoreGapExtend(scoringScheme), 0);
     SEQAN_ASSERT_EQ(scoreGapExtend(scoringScheme), scoreGapOpen(scoringScheme));
 
-	if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
+    if (direction == EXTEND_LEFT || direction == EXTEND_BOTH)
     {
         // Do not extend to the left if we are already at the beginning of an
         // infix or the sequence itself.
@@ -858,20 +812,20 @@ extendSeed(Seed<Simple, TConfig> & seed,
         _extendSeedGappedXDropOneDirection(seed, queryPrefix, databasePrefix, EXTEND_LEFT, scoringScheme, scoreDropOff);
     }
 
-	if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
+    if (direction == EXTEND_RIGHT || direction == EXTEND_BOTH)
     {
         // Do not extend to the right if we are already at the beginning of an
         // infix or the sequence itself.
 
         typedef typename Suffix<TDatabase const>::Type TDatabaseSuffix;
         typedef typename Suffix<TQuery const>::Type TQuerySuffix;
-        
+
         TDatabaseSuffix databaseSuffix = suffix(database, endPositionH(seed));
         TQuerySuffix querySuffix = suffix(query, endPositionV(seed));
-		// std::cout << "database = " << database << std::endl;
-		// std::cout << "database Suffix = " << databaseSuffix << std::endl;
-		// std::cout << "query = " << query << std::endl;
-		// std::cout << "query Suffix = " << querySuffix << std::endl;
+        // std::cout << "database = " << database << std::endl;
+        // std::cout << "database Suffix = " << databaseSuffix << std::endl;
+        // std::cout << "query = " << query << std::endl;
+        // std::cout << "query Suffix = " << querySuffix << std::endl;
         // TODO(holtgrew): Update _extendSeedGappedXDropOneDirection and switch query/database order.
         _extendSeedGappedXDropOneDirection(seed, querySuffix, databaseSuffix, EXTEND_RIGHT, scoringScheme, scoreDropOff);
     }
@@ -881,19 +835,19 @@ extendSeed(Seed<Simple, TConfig> & seed,
 
 
 template <typename TConfig, typename TDatabase, typename TQuery, typename TScoreValue, typename TScoreSpec>
-inline void 
+inline void
 extendSeed(Seed<ChainedSeed, TConfig> & /*seed*/,
-		   TDatabase const & /*database*/,
-		   TQuery const & /*query*/,
-		   ExtensionDirection /*direction*/,
+           TDatabase const & /*database*/,
+           TQuery const & /*query*/,
+           ExtensionDirection /*direction*/,
            Score<TScoreValue, TScoreSpec> const & /*scoringScheme*/,
            TScoreValue /*scoreDropOff*/,
-		   GappedXDrop const &)
+           GappedXDrop const &)
 {
     // For ungapped X-drop extension of Chained Seeds, we have to append
     // diagonals to the front and end of the list of seed diagonals and modify
     // the first and last one of the current set of seed diagonals.
-	SEQAN_CHECKPOINT;
+    SEQAN_CHECKPOINT;
 
     SEQAN_ASSERT_FAIL("Write me! Look into the function where this assertion fails for instructions on how to do this.");
     // TODO(holtgrew): Implement gapped X-drop extension with Chained seeds. As follows:
diff --git a/seqan/seeds/seeds_global_chaining.h b/seqan/seeds/seeds_global_chaining.h
index d79fbcc..68cce42 100644
--- a/seqan/seeds/seeds_global_chaining.h
+++ b/seqan/seeds/seeds_global_chaining.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,15 +43,14 @@ namespace seqan {
 // Enums, Tags, Classes, Specializations
 // ===========================================================================
 
-/**
-.Tag.Global Chaining
-..summary:Tags for selecting the global chaining algorithm.
-..cat:Seed Handling
-..see:Function.chainSeedsGlobally
-..tag:SparseChaining:
-    Chaining as described in (Gusfield, 1997) section 13.3.
-..include:seqan/seeds.h
+/*!
+ * @defgroup GlobalChainingTags Global Chaining Tags
+ * @brief Tags for specifying global chaining method.
+ *
+ * @tag GlobalChainingTags#SparseChaining
+ * @brief Tag for global sparse chaining.
  */
+
 struct SparseChaining_;
 typedef Tag<SparseChaining_> SparseChaining;
 
@@ -71,26 +70,40 @@ typedef Tag<SparseChaining_> SparseChaining;
  * @signature void chainSeedsGlobally(target, seedSet, tag);
  *
  * @param[out] target  A @link ContainerConcept container @endlink to append the seeds to.
- * @param[in]  seedSet The SeedSet object to get the seeds from.
- * @param[in]  tag     The tag to select the algorithm with (currently only <tt>SparseChaining</tt> is supported).
+ * @param[in]  seedSet The @link SeedSet @endlink object to get the seeds from.
+ * @param[in]  tag     The tag to select the algorithm with (currently only @link GlobalChainingTags#SparseChaining
+ *                     SparseChaining @endlink is supported).
+ *
+ * Chaining of seeds between two sequences can be performed using sparse chaining as defined in (Gusfield, 1997).
+ *
+ * @section Example
+ *
+ * The following example demonstrates how to use the <tt>chainSeedsGlobally()</tt> function.  First, a @link SeedSet
+ * @endlink is built and filled with @link SimpleSeed @endlink object.  Then, a @link String @endlink of @link
+ * SimpleSeed @endlink objects is defined and filled using the <tt>chainSeedsGlobally()</tt> function.
+ *
+ * @include demos/dox/seeds/seeds_chaining.cpp
+ *
+ * The output is as follows.  Only the first and last seeds are written to <tt>std::cout</tt>.
+ *
+ * @include demos/dox/seeds/seeds_chaining.cpp.stdout
+ *
+ * @section References
+ *
+ * <ul>
+ * <li>Dan Gusfield. Algorithms on Strings, Trees, and Sequences:  Computer Science and Computational Biology.
+ *     Cambridge University Press, January 1997.</li>
+ * </ul>
  */
 
 // TODO(holtgrew): Implement scored!
-/**
-.Function.chainSeedsGlobally
-..summary:Global chaining of seeds.
-..signature:chainSeedsGlobally(target, seedSet, tag)
-..include:seqan/seeds.h
-*/
-template <typename TTargetContainer, typename TSeedSpec, typename TSeedSetSpec>
+template <typename TTargetContainer, typename TSeed, typename TSeedSetSpec>
 void
 chainSeedsGlobally(
         TTargetContainer & target,
-        SeedSet<TSeedSpec, TSeedSetSpec> const & seedSet,
+        SeedSet<TSeed, TSeedSetSpec> const & seedSet,
         SparseChaining const &)
 {
-    typedef SeedSet<TSeedSpec, TSeedSetSpec> TSeedSet;
-    typedef typename Value<TSeedSet>::Type TSeed;
     typedef typename Position<TSeed>::Type TPosition;
     typedef typename Size<TSeed>::Type TSize;
 
@@ -164,7 +177,7 @@ chainSeedsGlobally(
             // *first* one that compares greater than the reference
             // one.  Searching for the this one and decrementing the
             // result iterator gives the desired result.
-            TIntermediateSolution referenceSolution(beginPositionV(seedK), 0, maxValue<unsigned>());
+            TIntermediateSolution referenceSolution(beginPositionV(seedK), maxValue<TSize>(), maxValue<unsigned>());
             // std::cout << "    intermediateSolutions.upper_bound(" << beginPositionV(seedK) << ")" << std::endl;
             TIntermediateSolutionsIterator itJ = intermediateSolutions.upper_bound(referenceSolution);
             if (itJ == intermediateSolutions.begin()) {
@@ -220,7 +233,7 @@ chainSeedsGlobally(
                     intermediateSolutions.insert(sol);
                 }
             }
-            
+
             // Delete all intermediate solutions where end1 >= end1 of k and have a lower quality than k.
             TIntermediateSolutionsIterator itDel = intermediateSolutions.upper_bound(referenceSolution);
             TIntermediateSolutionsIterator itDelEnd = intermediateSolutions.end();
diff --git a/seqan/seeds/seeds_global_chaining_base.h b/seqan/seeds/seeds_global_chaining_base.h
index 0d47a77..a91c889 100644
--- a/seqan/seeds/seeds_global_chaining_base.h
+++ b/seqan/seeds/seeds_global_chaining_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/seeds/seeds_global_chaining_gusfield.h b/seqan/seeds/seeds_global_chaining_gusfield.h
index 95b265c..9fba71e 100644
--- a/seqan/seeds/seeds_global_chaining_gusfield.h
+++ b/seqan/seeds/seeds_global_chaining_gusfield.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/seeds/seeds_seed_base.h b/seqan/seeds/seeds_seed_base.h
index 87ac51c..267316b 100644
--- a/seqan/seeds/seeds_seed_base.h
+++ b/seqan/seeds/seeds_seed_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,8 +54,6 @@ namespace seqan {
  *
  * @signature struct DefaultSeedConfig.
  *
- * @section Remarks
- *
  * The default definition is as follows.  You use this as a blueprint for your own TConfig struct for a Seed or SeedSet
  * class.
  *
@@ -68,6 +66,24 @@ namespace seqan {
  *     typedef int TScoreValue;
  * };
  * @endcode
+ *
+ * @see Seed
+ *
+ * @typedef DefaultSeedConfig::TPosition
+ * @brief Position type to use in the seed.
+ * @signature size_t DefaultSeedConfig::TPosition;
+ *
+ * @typedef DefaultSeedConfig::TSize
+ * @brief Size type to use in the seed.
+ * @signature size_t DefaultSeedConfig::TSize;
+ *
+ * @typedef DefaultSeedConfig::TDiagonal
+ * @brief Type to use for diagonals (signed version of TSize).
+ * @signature (...) DefaultSeedConfig::TDiagonal;
+ *
+ * @typedef DefaultSeedConfig::TScoreValue
+ * @brief Type to use for storing score values.
+ * @signature int DefaultSeedConfig::TScoreValue;
  */
 
 // Default configuration for seeds without score.
@@ -88,51 +104,28 @@ struct DefaultSeedConfig
  * @headerfile <seqan/seeds.h>
  * @brief Stores the start and end positions in the horizonal and vertical dimension.
  *
- * @signature template <typename TSpec, typename TConfig>
+ * @signature template <typename TSpec[, typename TConfig]>
  *            class Seed;
  *
  * @tparam TSpec   The seed specialization type.
- * @tparam TConfig The configuration object to use for this seed.
+ * @tparam TConfig The configuration object to use for this seed, defaults to @link DefaultSeedConfig @endlink.
  *
  * @section Examples
  *
  * The following example shows the usage of three seed extension algorithms using the tags <tt>MaxExtend</tt>,
  * <tt>UnGappedXDrop</tt>, and <tt>GappedXDrop</tt>.
  *
- * @include demos/seeds/seeds_extension.cpp
+ * @include demos/dox/seeds/seeds_extension.cpp
  *
  * The output is as follows:
  *
- * @include demos/seeds/seeds_extension.cpp.stdout
+ * @include demos/dox/seeds/seeds_extension.cpp.stdout
  *
  * Here is an example for global seed chaining:
  *
- * @include demos/seeds/seeds_chaining.cpp
+ * @include demos/dox/seeds/seeds_chaining.cpp
  */
 
-/**
-.Class.Seed:
-..summary:A seed in a dotplot.
-..description:Stores the start and end positions in the horizonal and vertical dimension.
-..cat:Seed Handling
-..signature:Seed<TSpec, TConfig>
-..param.TSpec:The seed specialization type.
-..param.TConfig:The configuration object to use for this seed.
-..include:seqan/seeds.h
-..example:
-...text:The following example shows the usage of three seed extension algorithms the tags @Tag.Seed Extension.MatchExtend@, @Tag.Seed Extension.UngappedXDrop@, and @Tag.Seed Extension.GappedXDrop@:
-...file:demos/seeds/seeds_extension.cpp
-...text:The output is as follows:
-...output:endPositionH(seed1) = 6
-endPositionV(seed1) = 6
-endPositionH(seed2) = 9
-endPositionV(seed2) = 9
-endPositionH(seed3) = 14
-endPositionV(seed3) = 13
-...text:This is an example for global seed chaining:
-...file:demos/seeds/seeds_chaining.cpp
-*/
-
 template <typename TSpec, typename TConfig = DefaultSeedConfig>
 class Seed;
 
@@ -155,17 +148,6 @@ class Seed;
  * @return Type The position type of <tt>TSeed</tt>.
  */
 
-/**
-.Metafunction.Seed#Position
-..cat:Seed Handling
-..class:Class.Seed
-..summary:The position type of a @Class.Seed@.
-..signature:Position<TSeed>::Type
-..param.TSeed:The seed to query for its position type.
-...type:Class.Seed
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig>
 struct Position<Seed<TSpec, TConfig> >
 {
@@ -191,18 +173,6 @@ struct Position<Seed<TSpec, TConfig> const> : Position<Seed<TSpec, TConfig> >
  * @return Type The size type of <tt>TSeed</tt>.
  */
 
-/**
-.Metafunction.Seed#Size
-..cat:Seed Handling
-..class:Class.Seed
-..summary:The size type of a @Class.Seed@.
-..description:This is used for the size value/score of a seed.
-..signature:Size<TSeed>::Type
-..param.TSeed:The seed to query for its size type.
-...type:Class.Seed
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig>
 struct Size<Seed<TSpec, TConfig> >
 {
@@ -228,17 +198,6 @@ struct Size<Seed<TSpec, TConfig> const> : Size<Seed<TSpec, TConfig> >
  * @return Type The diagonal type of <tt>TSeed</tt>.
  */
 
-/**
-.Metafunction.Seed#Diagonal
-..cat:Seed Handling
-..class:Class.Seed
-..summary:Returns type of the value for the diagonal of a seed.
-..signature:Diagonal<TSeed>::Type
-..param.TSeed:Type of the seed to query for its diagonal type.
-...type:Class.Seed
-..include:seqan/seeds.h
- */
-
 template <typename T>
 struct Diagonal;
 
@@ -264,18 +223,7 @@ struct Diagonal<Seed<TSpec, TConfig> const>
  *
  * @tparam TSeed The Seed to query for its seed score type.
  *
- * @return Type The seed score type of <tt>TSeed</tt>.
- */
-
-/**
-.Metafunction.Seed#SeedScore
-..cat:Seed Handling
-..class:Class.Seed
-..summary:Returns type of the value for the score of a seed.
-..signature:SeedScore<TSeed>::Type
-..param.TSeed:Type of the seed to retrieve the score for.
-...type:Class.Seed
-..include:seqan/seeds.h
+ * @return Type The score type of <tt>TSeed</tt>.
  */
 
 template <typename T>
@@ -297,73 +245,37 @@ struct SeedScore<Seed<TSpec, TConfig> const> : SeedScore<Seed<TSpec, TConfig> >
 
 // TODO(holtgrew): COULD introduce {get,set}{Begin,End}(dim, value), but probably only necessary to make consistent with multi dimensional chaining interface.
 
-/**
-.Function.assign.param.source.type:Class.Seed
-.Function.assign.class:Class.Seed
-.Function.assign.param.target.type:Class.Seed
-.Function.assign.class:Class.Seed
-.Function.move.param.source.type:Class.Seed
-.Function.move.class:Class.Seed
-.Function.move.param.target.type:Class.Seed
-.Function.move.class:Class.Seed
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function beginPositionH()
 // ---------------------------------------------------------------------------
 
 /*!
  * @fn Seed#beginPositionH
- * @brief Return the begin position of the seed in the database (horizontal direction).
+ * @brief Returns the begin position of the seed in the database (horizontal direction).
  *
  * @signature TPosition beginPositionH(seed);
  *
  * @param[in] seed The seed to query.
  *
- * @return TPosition The begin position.  <tt>TPosition</tt> is the position type of <tt>seed</tt>.
+ * @return TPosition The horizontal begin position of type @link Seed#Position @endlink.
  */
 
-/**
-.Function.Seed#beginPositionH
-..summary: Returns the begin position of the seed in the database.
-..cat:Seed Handling
-..signature:beginPositionH(seed)
-..class:Class.Seed
-..param.seed:The seed whose database position should be returned.
-...type:Class.Seed
-..returns:Begin position of the seed in the database.
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function endPositionH()
 // ---------------------------------------------------------------------------
 
 /*!
  * @fn Seed#endPositionH
- * @brief Return the end position of the seed in the database (horizontal direction).
+ * @brief Returns the end position of the seed in the database (horizontal direction).
  *
  * @signature TPosition endPositionH(seed);
  *
  * @param[in] seed The seed to query.
  *
- * @return TPosition The end position.  <tt>TPosition</tt> is the position type of <tt>seed</tt>.
+ * @return TPosition The horizontal end position of type @link Seed#Position @endlink.
  */
 
 
-/**
-.Function.Seed#endPositionH
-..summary: Returns the end position of the seed in the database.
-..cat:Seed Handling
-..signature:endPositionH(seed)
-..class:Class.Seed
-..param.seed:The seed whose end position in the database position should be returned.
-...type:Class.Seed
-..returns:End of the seed in the database.
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function setBeginPositionH()
 // ---------------------------------------------------------------------------
@@ -378,17 +290,6 @@ struct SeedScore<Seed<TSpec, TConfig> const> : SeedScore<Seed<TSpec, TConfig> >
  * @param[in]     pos  The value to set for the horizontal begin position.
  */
 
-/**
-.Function.Seed#setBeginPositionH
-..summary: Sets the begin position of the seed in the database.
-..cat:Seed Handling
-..signature:setBeginPositionH(seed)
-..class:Class.Seed
-..param.seed:The seed for which to set the begin position in the database sequence.
-...type:Class.Seed
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function setEndPositionH()
 // ---------------------------------------------------------------------------
@@ -403,72 +304,36 @@ struct SeedScore<Seed<TSpec, TConfig> const> : SeedScore<Seed<TSpec, TConfig> >
  * @param[in]     pos  The value to set for the horizontal end position.
  */
 
-/**
-.Function.Seed#setEndPositionH
-..summary: Sets the end position of the seed in the database.
-..cat:Seed Handling
-..signature:setEndPositionH(seed)
-..class:Class.Seed
-..param.seed:The seed for which to set the end position in the database sequence.
-...type:Class.Seed
-..returns:End of the seed in the database.
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function beginPositionV()
 // ---------------------------------------------------------------------------
 
 /*!
  * @fn Seed#beginPositionV
- * @brief Return the begin position of the seed in the query (vertical direction).
+ * @brief Returns the begin position of the seed in the query (vertical direction).
  *
  * @signature TPosition beginPositionV(seed);
  *
  * @param[in] seed The seed to query.
  *
- * @return TPosition The begin position.  <tt>TPosition</tt> is the position type of <tt>seed</tt>.
+ * @return TPosition The vertical begin position of type @link Seed#Position @endlink.
  */
 
-/**
-.Function.Seed#beginPositionV
-..summary: Returns the begin position of the seed in the query.
-..cat:Seed Handling
-..signature:beginPositionV(seed)
-..class:Class.Seed
-..param.seed:The seed whose query position should be returned.
-...type:Class.Seed
-..returns: Begin of the seed.
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function endPositionV()
 // ---------------------------------------------------------------------------
 
 /*!
  * @fn Seed#endPositionV
- * @brief Return the end position of the seed in the query (vertical direction).
+ * @brief Returns the end position of the seed in the query (vertical direction).
  *
  * @signature TPosition endPositionV(seed);
  *
  * @param[in] seed The seed to query.
  *
- * @return TPosition The end position.  <tt>TPosition</tt> is the position type of <tt>seed</tt>.
+ * @return TPosition The vertical end position of type @link Seed#Position @endlink.
  */
 
-/**
-.Function.Seed#endPositionV
-..summary: Returns the end position of the seed in the query.
-..cat:Seed Handling
-..signature:endPositionV(seed)
-..class:Class.Seed
-..param.seed:The seed whose end in the query position should be returned.
-...type:Class.Seed
-..returns: End of the seed.
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function setBeginPositionV()
 // ---------------------------------------------------------------------------
@@ -483,18 +348,6 @@ struct SeedScore<Seed<TSpec, TConfig> const> : SeedScore<Seed<TSpec, TConfig> >
  * @param[in]     pos  The value to set for the vertical begin position.
  */
 
-/**
-.Function.Seed#setBeginPositionV
-..summary: Sets the begin position of the seed in the query.
-..cat:Seed Handling
-..signature:setBeginPositionV(seed)
-..class:Class.Seed
-..param.seed:The seed for which to set the begin position in the query sequence.
-...type:Class.Seed
-..returns: Begin of the seed.
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function setEndPositionV()
 // ---------------------------------------------------------------------------
@@ -509,45 +362,21 @@ struct SeedScore<Seed<TSpec, TConfig> const> : SeedScore<Seed<TSpec, TConfig> >
  * @param[in]     pos  The value to set for the vertical end position.
  */
 
-/**
-.Function.Seed#setEndPositionV
-..summary: Returns the end position of the seed in the query.
-..cat:Seed Handling
-..signature:setEndPositionV(seed)
-..class:Class.Seed
-..param.seed:The seed for which to set the end position in the query sequence.
-...type:Class.Seed
-..returns: End of the seed.
-..include:seqan/seeds.h
-*/
-
 // ---------------------------------------------------------------------------
 // Function lowerDiagonal()
 // ---------------------------------------------------------------------------
 
 /*!
  * @fn Seed#lowerDiagonal
- * @brief Return the leftmost diagonal of the seed (minimum diagonal value).
+ * @brief Returns the leftmost diagonal of the seed (minimum diagonal value).
  *
  * @signature TDiagonal lowerDiagonal(seed);
  *
  * @param[in] seed The seed to query for its lower diagonal.
  *
- * @return TDiagonal The lower diagonal value.  TDiagonal is the diagonal type of <tt>seed</tt>.
+ * @return TDiagonal The lower diagonal value of type @link Seed#Diagonal @endlink.
  */
 
-/**
-.Function.Seed#lowerDiagonal
-..summary:Returns the leftmost diagonal of the seed (minimum diagonal value).
-..cat:Seed Handling
-..signature:lowerDiagonal(seed)
-..class:Class.Seed
-..param.seed:The seed whose database position should be returned.
-...type:Class.Seed
-..returns:The most left diagonal.
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig>
 inline typename Diagonal<Seed<TSpec, TConfig> >::Type
 lowerDiagonal(Seed<TSpec, TConfig> const & seed)
@@ -561,31 +390,19 @@ lowerDiagonal(Seed<TSpec, TConfig> const & seed)
 
 /*!
  * @fn Seed#setLowerDiagonal
- * @brief Set a new value for the leftmost diagonal of a seed.
+ * @brief Sets a new value for the leftmost diagonal of a seed.
  *
  * @signature void setLowerDigonal(seed, diag);
  *
- * @param seed[in,out] The Seed to set the diagonal value for.
- * @param diag[in]     The value to set for the diagonal.
+ * @param[in,out] seed The Seed to set the diagonal value for.
+ * @param[in]     diag The value to set for the diagonal.
  */
 
-/**
-.Function.Seed#setLowerDiagonal
-..summary: Sets a new value for the leftmost diagonal.
-..cat:Seed Handling
-..signature:setLowerDiagonal(seed, diag)
-..class:Class.Seed
-..param.seed:The seed whose left diagonal value should be updated.
-...type:Class.Seed
-..param.diag:The new value for the leftmost diagonal.
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig, typename TDiagonal>
-inline void 
+inline void
 setLowerDiagonal(Seed<TSpec, TConfig> & seed, TDiagonal newDiag)
 {
-	seed._lowerDiagonal = newDiag;
+    seed._lowerDiagonal = newDiag;
 }
 
 // ---------------------------------------------------------------------------
@@ -594,27 +411,15 @@ setLowerDiagonal(Seed<TSpec, TConfig> & seed, TDiagonal newDiag)
 
 /*!
  * @fn Seed#upperDiagonal
- * @brief Return the rightmost diagonal of the seed (maximum diagonal value).
+ * @brief Returns the rightmost diagonal of the seed (maximum diagonal value).
  *
  * @signature TDiagonal upperDiagonal(seed);
  *
  * @param[in] seed The seed to query for its upper diagonal.
  *
- * @return TDiagonal The upper diagonal value.  TDiagonal is the diagonal type of <tt>seed</tt>.
+ * @return TDiagonal The upper diagonal value of type @link Seed#Diagonal @endlink.
  */
 
-/**
-.Function.Seed#upperDiagonal
-..summary:Returns the rightmost diagonal of the seed (maximum diagonal value).
-..cat:Seed Handling
-..signature:upperDiagonal(seed)
-..class:Class.Seed
-..param.seed:The seed whose upper right diagonal value should be returned.
-...type:Class.Seed
-..returns:The right diagonal.
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig>
 inline typename Diagonal<Seed<TSpec, TConfig> >::Type
 upperDiagonal(Seed<TSpec, TConfig> const & seed)
@@ -628,32 +433,20 @@ upperDiagonal(Seed<TSpec, TConfig> const & seed)
 
 /*!
  * @fn Seed#setUpperDiagonal
- * @brief Set a new value for the rightmost diagonal of a seed.
+ * @brief Sets a new value for the rightmost diagonal of a seed.
  *
  * @signature void setUpperDigonal(seed, diag);
  *
- * @param seed[in,out] The Seed to set the diagonal value for.
- * @param diag[in]     The value to set for the diagonal.
+ * @param[in,out] seed The Seed to set the diagonal value for.
+ * @param[in]     diag The value to set for the diagonal.
  */
 
-/**
-.Function.Seed#setUpperDiagonal
-..summary: Sets a new value for the rightmost diagonal.
-..cat:Seed Handling
-..signature:setUpperDiagonal(seed, diag)
-..class:Class.Seed
-..param.seed:The seed whose right diagonal value should be updated.
-...type:Class.Seed
-..param.diag:The new value for the most right diagonal.
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig, typename TPosition>
-inline void 
-setUpperDiagonal(Seed<TSpec, TConfig> & seed, 
-				 TPosition newDiag)
+inline void
+setUpperDiagonal(Seed<TSpec, TConfig> & seed,
+                 TPosition newDiag)
 {
-	seed._upperDiagonal = newDiag;
+    seed._upperDiagonal = newDiag;
 }
 
 // ---------------------------------------------------------------------------
@@ -669,18 +462,9 @@ setUpperDiagonal(Seed<TSpec, TConfig> & seed,
  *
  * @param[in] seed The Seed to query for its size.
  *
- * @return TSize The size of the type.  TSize is the size type of <tt>seed</tt>.
+ * @return TSize The size of the type @link Seed#Size @endlink.
  */
 
-/**
-.Function.Seed#seedSize
-..summary:Returns the number of matches and mismatches of the seed.  This is the longest true diagonal fitting into its dimensions.
-..signature:seedSize(seed)
-..class:Class.Seed
-..remark:"Seed size" is mostly called "seed length" in the literature.  However, in SeqAn the term "length" is reserved to be the size of a container.
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig>
 inline typename Size<Seed<TSpec, TConfig> >::Type
 seedSize(Seed<TSpec, TConfig> & seed)
@@ -703,28 +487,16 @@ seedSize(Seed<TSpec, TConfig> const & seed)
 
 /*!
  * @fn Seed#beginDiagonal
- * @brief Return the begin diagonal of a Seed.
+ * @brief Returns the begin diagonal of a Seed.
  *
  * @signature TDiagonal beginDiagonal(seed);
  *
  * @param[in] seed The Seed to query for its begin diagonal.
  *
- * @return TDiagonal The diagonal of the Seed's begin position.  TDiagonal is the diagonal type of <tt>seed</tt>.
+ * @return TDiagonal The diagonal of the Seed's begin position of type @link Seed#Diagonal @endlink.
  */
 
 // TODO(holtgrew): Rename to getBeginDiagonal.
-/**
-.Function.Seed#beginDiagonal
-..summary:Returns the diagonal of the start point.
-..cat:Seed Handling
-..signature:beginDiagonal(seed)
-..class:Class.Seed
-..param.seed:The seed whose start diagonal should be returned.
-...type:Class.Seed
-..returns:The diagonal of the start point.
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig>
 inline typename Diagonal<Seed<TSpec, TConfig> >::Type
 beginDiagonal(Seed<TSpec, TConfig> const & seed)
@@ -738,27 +510,15 @@ beginDiagonal(Seed<TSpec, TConfig> const & seed)
 
 /*!
  * @fn Seed#endDiagonal
- * @brief Return the end diagonal of a Seed.
+ * @brief Returns the end diagonal of a Seed.
  *
  * @signature TDiagonal endDiagonal(seed);
  *
  * @param[in] seed The Seed to query for its end diagonal.
  *
- * @return TDiagonal The diagonal of the Seed's end position.  TDiagonal is the diagonal type of <tt>seed</tt>.
+ * @return TDiagonal The diagonal of the Seed's end position of type @link Seed#Diagonal @endlink.
  */
 
-/**
-.Function.Seed#endDiagonal
-..summary:Returns the diagonal of the end point.
-..cat:Seed Handling
-..signature:endDiagonal(seed)
-..class:Class.Seed
-..param.seed:The seed whose end diagonal should be returned.
-...type:Class.Seed
-..returns:The diagonal of the end point.
-..include:seqan/seeds.h
-*/
-
 template <typename TSpec, typename TConfig>
 inline typename Diagonal<Seed<TSpec, TConfig> >::Type
 endDiagonal(Seed<TSpec, TConfig> const & seed)
@@ -772,28 +532,15 @@ endDiagonal(Seed<TSpec, TConfig> const & seed)
 
 /*!
  * @fn Seed#score
- * @brief Return the score of a Seed.
+ * @brief Returns the score of a Seed.
  *
  * @signature TSeedScore score(seed);
  *
  * @param[in] seed The Seed to query for its score.
  *
- * @return TSeedScore The score value of the seed.  TSeedScore can be queried from the type of <tt>seed</tt> using
- *                    @link Seed#SeedScore @endlink.
+ * @return TSeedScore The score value of the seed of type @link Seed#SeedScore @endlink.
  */
 
-/**
-.Function.Seed#score
-..summary:Returns the score of the seed.
-..cat:Seed Handling
-..signature:score(seed)
-..class:Class.Seed
-..param.seed:The seed to query for the score.
-...type:Class.Seed
-..returns:The seed's score.
-..include:seqan/seeds.h
-*/
-
 template <typename TSeed>
 inline typename SeedScore<TSeed>::Type
 score(TSeed const & seed)
@@ -807,7 +554,7 @@ score(TSeed const & seed)
 
 /*!
  * @fn Seed#setScore
- * @brief Set the Seed score value.
+ * @brief Sets the Seed score value.
  *
  * @signature void setScore(seed, scoreVal);
  *
@@ -816,19 +563,6 @@ score(TSeed const & seed)
  *                         @link Seed#SeedScore @endlink.
  */
 
-/**
-.Function.Seed#setScore
-..summary:Set the score value of a seed.
-..cat:Seed Handling
-..signature:setScore(seed, val)
-..class:Class.Seed
-..param.seed:The seed to set the score value of.
-...type:Class.Seed
-..param.val:The score value to set.
-..returns:The seed's score.
-..include:seqan/seeds.h
-*/
-
 template <typename TSeed, typename TScore>
 inline void
 setScore(TSeed & seed, TScore const & score)
@@ -884,7 +618,7 @@ _updateSeedsScoreMerge(Seed<TSpec, TConfig> & seed, Seed<TSpec, TConfig> const &
     double fracSeed = static_cast<double>(seedSize(seed) - 0.5 * overlap) / static_cast<double>(total);
     double fracOther = static_cast<double>(seedSize(other) - 0.5 * overlap) / static_cast<double>(total);
     typedef typename SeedScore<TSeed>::Type TScoreValue;
-	TScoreValue newScore = static_cast<TScoreValue>(round(fracSeed * score(seed) + fracOther * score(other)));
+    TScoreValue newScore = static_cast<TScoreValue>(round(fracSeed * score(seed) + fracOther * score(other)));
     setScore(seed, newScore);
 }
 
diff --git a/seqan/seeds/seeds_seed_chained.h b/seqan/seeds/seeds_seed_chained.h
index 5edca3a..179d0d4 100644
--- a/seqan/seeds/seeds_seed_chained.h
+++ b/seqan/seeds/seeds_seed_chained.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -61,7 +61,10 @@ typedef Tag<Chained_> ChainedSeed;  // TODO(holtgrew): Chained already taken as
  * @signature template <[typename TConfig]>
  *            class Seed<ChainedSeed, TConfig>;
  *
- * @tparam TConfig The configuration to use for the chained seed specialization.
+ * @tparam TConfig The configuration to use for the chained seed specialization.  Defaults to
+ *                 @link DefaultSeedConfig @endlink.
+ *
+ * Diagonals are stored as @link SeedDiagonal @endlink objects.
  *
  *
  * @fn ChainedSeed::Seed
@@ -75,27 +78,6 @@ typedef Tag<Chained_> ChainedSeed;  // TODO(holtgrew): Chained already taken as
  * @param[in] length    The length of the seed.
  */
 
-/**
-.Spec.Chained Seed
-..cat:Seed Handling
-..summary:
-..description:Additionaly diagonal segments between start and end position2 are stored.
-..general:Class.Seed
-..signature:Seed<ChainedSeed, TConfig>
-..param.TConfig:The configuration object used for the seed.
-...default:DefaultSeedConfig.
-
-.Memfunc.Chained Seed#Seed
-..class:Spec.Chained Seed
-..summary:Constructor
-..signature: Seed<ChainedSeed, TConfig> ()
-..signature: Seed<ChainedSeed, TConfig> (beginPosH, beginPosV, length)
-..param.beginPosH: Begin position in database (horizontal).
-..param.beginPosV: Begin position in query (vertical).
-..param.length: Length of the seed.
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 class Seed<ChainedSeed, TConfig>
 {
@@ -142,17 +124,6 @@ class Seed<ChainedSeed, TConfig>
  * @return Type The resulting diagonal seed.
  */
 
-/**
-.Metafunction.Chained Seed#Value
-..cat:Seed Handling
-..class:Spec.Chained Seed
-..summary:The seed diagonal type.
-..signature:Value<TSeed>::Type
-..param.TSeed:The seed to query for its diagonal object type.
-...type:Spec.Chained Seed
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 struct Value<Seed<ChainedSeed, TConfig> >
 {
@@ -188,17 +159,6 @@ struct Value<Seed<ChainedSeed, TConfig> const>
  * @return Type Reference to the contained seeds.
  */
 
-/**
-.Metafunction.Chained Seed#Reference
-..cat:Seed Handling
-..class:Spec.Chained Seed
-..summary:The seed diagonal reference type.
-..signature:Reference<TSeed>::Type
-..param.TSeed:The seed to query for its seed diagonal reference type.
-...type:Spec.Chained Seed
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 struct Reference<Seed<ChainedSeed, TConfig> >
 {
@@ -231,24 +191,12 @@ struct Reference<Seed<ChainedSeed, TConfig> const>
  * @return Type Reference to the contained seeds.
  */
 
-/**
-.Metafunction.Chained Seed#Iterator
-..cat:Seed Handling
-..class:Spec.Chained Seed
-..summary:The seed diagonal iterator type.
-..signature:Iterator<TSeed, Tag>::Type
-..param.TSeed:The seed to query for its seed diagonal iterator type.
-...type:Spec.Chained Seed
-..param.Tag:The tag to select the iterator type with.
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 struct Iterator<Seed<ChainedSeed, TConfig>, Standard>
 {
     typedef Seed<ChainedSeed, TConfig> TSeed_;
     typedef typename Value<TSeed_>::Type TSeedDiagonal_;
-    typedef typename ::std::list<TSeedDiagonal_>::iterator Type;
+    typedef typename std::list<TSeedDiagonal_>::iterator Type;
 };
 
 template <typename TConfig>
@@ -256,7 +204,7 @@ struct Iterator<Seed<ChainedSeed, TConfig> const, Standard>
 {
     typedef Seed<ChainedSeed, TConfig> TSeed_;
     typedef typename Value<TSeed_>::Type TSeedDiagonal_;
-    typedef typename ::std::list<TSeedDiagonal_>::const_iterator Type;
+    typedef typename std::list<TSeedDiagonal_>::const_iterator Type;
 };
 
 // ===========================================================================
@@ -307,7 +255,7 @@ template <typename TConfig>
 inline typename Position<Seed<ChainedSeed, TConfig> >::Type
 beginPositionH(Seed<ChainedSeed, TConfig> const & seed)
 {
-	return front(seed._seedDiagonals).beginPositionH;
+    return front(seed._seedDiagonals).beginPositionH;
 }
 
 // ---------------------------------------------------------------------------
@@ -318,7 +266,7 @@ template <typename TConfig>
 inline typename Position<Seed<ChainedSeed, TConfig> >::Type
 endPositionH(Seed<ChainedSeed, TConfig> const & seed)
 {
-	return back(seed._seedDiagonals).beginPositionH + back(seed._seedDiagonals).length;
+    return back(seed._seedDiagonals).beginPositionH + back(seed._seedDiagonals).length;
 }
 
 // ---------------------------------------------------------------------------
@@ -329,7 +277,7 @@ template <typename TConfig>
 inline typename Position<Seed<ChainedSeed, TConfig> >::Type
 beginPositionV(Seed<ChainedSeed, TConfig> const & seed)
 {
-	return front(seed._seedDiagonals).beginPositionV;
+    return front(seed._seedDiagonals).beginPositionV;
 }
 
 // ---------------------------------------------------------------------------
@@ -340,7 +288,7 @@ template <typename TConfig>
 inline typename Position<Seed<ChainedSeed, TConfig> >::Type
 endPositionV(Seed<ChainedSeed, TConfig> const & seed)
 {
-	return back(seed._seedDiagonals).beginPositionV + back(seed._seedDiagonals).length;
+    return back(seed._seedDiagonals).beginPositionV + back(seed._seedDiagonals).length;
 }
 
 // ---------------------------------------------------------------------------
@@ -359,17 +307,6 @@ endPositionV(Seed<ChainedSeed, TConfig> const & seed)
  *               <tt>seed</tt>
  */
 
-/**
-.Function.Chained Seed#length
-..summary:Returns the number of diagonals in the chained seed.
-..signature:TSize length(seed)
-..class:Spec.Chained Seed
-..param.seed:The seed to query.
-...type:Spec.Chained Seed
-..returns:The number of diagonals in the chained seed.
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 inline typename Size<Seed<ChainedSeed, TConfig> >::Type
 length(Seed<ChainedSeed, TConfig> const & seed)
@@ -391,20 +328,6 @@ length(Seed<ChainedSeed, TConfig> const & seed)
  * @param[in]     diagonal The SeedDiagional to add to <tt>seed</tt>.
  */
 
-/**
-.Function.appendDiagonal
-..summary: Adds diagonal to the Chained Seed.
-..cat:Seed Handling
-..signature:appendDiag(seed, diagonal)
-..class:Spec.Chained Seed
-..param.seed: The seed to which the diagonal should be added.
-...type:Spec.Chained Seed
-..param.diag: The diagonal to add.
-...type:Class.SeedDiagonal
-...remarks: A diagonal consists of three values: 1: start in 1. sequence, 2: start in 2. sequence, 3: length of match
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 inline void
 appendDiagonal(Seed<ChainedSeed, TConfig> & seed,
@@ -434,18 +357,6 @@ appendDiagonal(Seed<ChainedSeed, TConfig> & seed,
  * @param[in]     first An iterator into the ChainedSeed, as returned by @link ChainedSeed#Iterator @endlink.
  */
 
-/**
-.Function.truncateDiagonals
-..summary:Removes diagonals from the given first one to the end of the seed's diagonals.
-..cat:Seed Handling
-..signature:truncateDiagonals(seed, first)
-..class:Spec.Chained Seed
-..param.seed: The seed to which the diagonal should be added.
-...type:Spec.Chained Seed
-..param.first: Iterator the first diagonal to remove.
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 inline void
 truncateDiagonals(Seed<ChainedSeed, TConfig> & seed,
@@ -469,14 +380,6 @@ truncateDiagonals(Seed<ChainedSeed, TConfig> & seed,
  * @param[in] tag  A tag for selecting the type of the iterator, one of <tt>Standard</tt> and <tt>Rooted</tt>.
  */
 
-/**
-.Function.Chained Seed#begin
-..summary:Returns an iterator to the beginning of the seed digonals.
-..class:Spec.Chained Seed
-..signature:TIterator begin(seed, tag)
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 inline typename Iterator<Seed<ChainedSeed, TConfig> >::Type
 begin(Seed<ChainedSeed, TConfig> & seed, Standard const &)
@@ -505,14 +408,6 @@ begin(Seed<ChainedSeed, TConfig> const & seed, Standard const &)
  * @param[in] tag  A tag for selecting the type of the iterator, one of <tt>Standard</tt> and <tt>Rooted</tt>.
  */
 
-/**
-.Function.Chained Seed#end
-..summary:Returns an iterator to the end of the seed diagonals.
-..class:Spec.Chained Seed
-..signature:TIterator end(seed, tag)
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 inline typename Iterator<Seed<ChainedSeed, TConfig> >::Type
 end(Seed<ChainedSeed, TConfig> & seed, Standard const &)
@@ -542,14 +437,6 @@ end(Seed<ChainedSeed, TConfig> const & seed, Standard const &)
  * @return TReference Reference to first ChainedSeed diagonal.  TReference is the reference type of <tt>seed</tt>.
  */
 
-/**
-.Function.Chained Seed#front
-..summary:Returns a reference to the first seed diagonal.
-..class:Spec.Chained Seed
-..signature:TReference front(seed)
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 inline typename Reference<Seed<ChainedSeed, TConfig> >::Type
 front(Seed<ChainedSeed, TConfig> & seed)
@@ -579,14 +466,6 @@ front(Seed<ChainedSeed, TConfig> const & seed)
  * @return TReference Reference to the last ChainedSeed diagonal.  TReference is the reference type of <tt>seed</tt>.
  */
 
-/**
-.Function.Chained Seed#back
-..summary:Returns a reference to the last seed diagonal.
-..class:Spec.Chained Seed
-..signature:TReference back(seed)
-..include:seqan/seeds.h
-*/
-
 template <typename TConfig>
 inline typename Reference<Seed<ChainedSeed, TConfig> >::Type
 back(Seed<ChainedSeed, TConfig> & seed)
diff --git a/seqan/seeds/seeds_seed_diagonal.h b/seqan/seeds/seeds_seed_diagonal.h
index ac50cc9..89bc347 100644
--- a/seqan/seeds/seeds_seed_diagonal.h
+++ b/seqan/seeds/seeds_seed_diagonal.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -52,18 +52,30 @@ namespace seqan {
  * @class SeedDiagonal
  * @headerfile <seqan/seeds.h>
  * @brief Store the information about a seed segment.
- * 
+ *
  * @signature template <typename TPosition, typename TSize>
  *            class SeedDiagonal;
- * 
+ *
  * @tparam TSize The type to use for the seed length.
  * @tparam TPosition The type to use for positions.
  */
 
-/*
+/*!
+ * @fn SeedDiagonal::SeedDiagonal
+ * @brief Constructor
+ *
+ * @signature SeedDiagonal::SeedDiagonal();
+ * @signature SeedDiagonal::SeedDiagonal(beginPosH, beginPosV, length);
+ *
+ * @param[in] beginPosH The begin position in the horizontal orientation.
+ * @param[in] beginPosV The begin position in the vertical orientation.
+ * @param[in] length    The length of the seed diagonal.
+ */
+
+/*!
  * @var TPosition SeedDiagonal::beginPositionH
  * @brief The position in the database sequence (horizontal).
- * 
+ *
  * @var TPosition SeedDiagonal::beginPositionV
  * @brief The position in the query sequence (vertical).
  *
@@ -71,27 +83,6 @@ namespace seqan {
  * @brief The length of the diagonal.
  */
 
-/**
-.Class.SeedDiagonal
-..summary:Store the information about a seed segment.
-..signature:SeedDiagonal<TPosition, TSize>
-..cat:Seed Handling
-..param.TPosition:The type to use for positions.
-..param.TSize:The type to use for the seed length.
-..include:seqan/seeds.h
-
-.Memvar.SeedDiagonal#beginPositionH
-..summary:The position in the database sequence (horizontal).
-..class:Class.SeedDiagonal
-
-.Memvar.SeedDiagonal#beginPositionV:
-..summary:The position in the query sequence (vertical).
-..class:Class.SeedDiagonal
-
-.Memvar.SeedDiagonal#length:
-..summary:The length of the diagonal.
-..class:Class.SeedDiagonal
-*/
 template <typename TPosition, typename TSize>
 class SeedDiagonal
 {
@@ -99,7 +90,7 @@ class SeedDiagonal
     TPosition beginPositionH;
     TPosition beginPositionV;
     TSize length;
-    
+
     SeedDiagonal() : beginPositionH(0), beginPositionV(0), length(0)
     {}
 
@@ -111,7 +102,7 @@ class SeedDiagonal
 // ===========================================================================
 // Metafunctions
 // ===========================================================================
-  
+
 // ---------------------------------------------------------------------------
 // Metafunction Position
 // ---------------------------------------------------------------------------
@@ -119,25 +110,14 @@ class SeedDiagonal
 /*!
  * @mfn SeedDiagonal#Position
  * @brief The position type of a @link SeedDiagonal @endlink.
- * 
- * @signature Position<TSeed>::Type;
- * 
- * @tparam TSeed The seed diagonal to query for its position type. Types: Seed
  *
- * @return Type The position type of <tt>TSeed</tt>.
+ * @signature Position<TDiagonal>::Type;
+ *
+ * @tparam TDiagonal A @link SeedDiagonal @endlink.
+ *
+ * @return Type The position type of <tt>TDiagonal</tt>.
  */
 
-/**
-.Metafunction.SeedDiagonal#Position
-..cat:Seed Handling
-..class:Class.SeedDiagonal
-..summary:The position type of a @Class.SeedDiagonal@.
-..signature:Position<TSeed>::Type
-..param.TSeed:The seed diagonal to query for its position type.
-...type:Class.Seed
-..include:seqan/seeds.h
-*/
-
 template <typename TPosition, typename TSize>
 struct Position<SeedDiagonal<TPosition, TSize> >
 {
@@ -147,33 +127,22 @@ struct Position<SeedDiagonal<TPosition, TSize> >
 template <typename TPosition, typename TSize>
 struct Position<SeedDiagonal<TPosition, TSize> const> : Position<SeedDiagonal<TPosition, TSize> >
 {};
-  
+
 // ---------------------------------------------------------------------------
 // Metafunction Size
 // ---------------------------------------------------------------------------
 
 /*!
  * @mfn SeedDiagonal#Size
- * @brief The position type of a @link SeedDiagonal @endlink.
- * 
- * @signature Size<TSeed>::Type
- * 
- * @tparam TSeed The seed diagonal to query for its position type. Types: Seed
- * 
- * @return Type The size type of <tt>TSeed</tt>.
+ * @brief The size type of a @link SeedDiagonal @endlink.
+ *
+ * @signature Size<TDiagonal>::Type;
+ *
+ * @tparam TDiagonal A @link SeedDiagonal @endlink.
+ *
+ * @return Type The size type of <tt>TDiagonal</tt>.
  */
 
-/**
-.Metafunction.SeedDiagonal#Size
-..cat:Seed Handling
-..class:Class.SeedDiagonal
-..summary:The position type of a @Class.SeedDiagonal@.
-..signature:Size<TSeed>::Type
-..param.TSeed:The seed diagonal to query for its position type.
-...type:Class.Seed
-..include:seqan/seeds.h
-*/
-
 template <typename TPosition, typename TSize>
 struct Size<SeedDiagonal<TPosition, TSize> >
 {
@@ -183,7 +152,7 @@ struct Size<SeedDiagonal<TPosition, TSize> >
 template <typename TPosition, typename TSize>
 struct Size<SeedDiagonal<TPosition, TSize> const> : Size<SeedDiagonal<TPosition, TSize> >
 {};
-  
+
 // ===========================================================================
 // Functions
 // ===========================================================================
diff --git a/seqan/seeds/seeds_seed_set_base.h b/seqan/seeds/seeds_seed_set_base.h
index d3443b5..2f3d4b8 100644
--- a/seqan/seeds/seeds_seed_set_base.h
+++ b/seqan/seeds/seeds_seed_set_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -62,83 +62,49 @@ typedef Tag<Unordered_> Unordered;
  * @headerfile <seqan/seeds.h>
  * @implements ContainerConcept
  * @brief Handles a set of seeds with local chaining on adding seeds.
+ * @note At the moment only <tt>Unordered SeedSets</tt> are supported.
  *
- * @signature template <typename TSeedSpec[, typename TSpec]>
+ * @signature template <typename TSeed[, typename TSpec]>
  *            class SeedSet;
  *
- * @tparam TSeedSpec Tag for specialization of contained Seed objects.
- * @tparam TSpec     Optional tag for seed set specialization.  Defaults to <tt>Unordered</tt>.
+ * @tparam TSeed     Type of the @link Seed @endlink objects stored in the seed set.
+ * @tparam TSpec     Optional tag for seed set specialization. Defaults to <tt>Unordered</tt>.
  */
 
-/**
-.Class.SeedSet:
-..summary:Handles a set of seeds with local chaining on adding seeds.
-..cat:Seed Handling
-..signature:SeedSet<TSeedSpec>
-..param.TSeedSpec:Specialization of the underlying seed to use.
-..include:seqan/seeds.h
-*/
-
 // ..param.TScored:Either UnScored or a seed set scoring scheme specification.
 // ..param.TSpec:Specialization of the seed set.
 // ..param.TSeedConfig:Configuration for the seeds.  Sensible defaults are chosen based on the other template parameters.
 
-template <typename TSeedSpec, typename TSpec = Unordered>
+template <typename TSeed, typename TSpec = Unordered>
 class SeedSet;
 
 // ===========================================================================
 // Metafunctions
 // ===========================================================================
 
-///.Metafunction.Position.param.T.type:Class.SeedSet
-///.Metafunction.Position.class:Class.SeedSet
-///.Metafunction.Size.param.T.type:Class.SeedSet
-///.Metafunction.Size.class:Class.SeedSet
-///.Metafunction.Value.param.T.type:Class.SeedSet
-///.Metafunction.Value.class:Class.SeedSet
-///.Metafunction.GetValue.param.T.type:Class.SeedSet
-///.Metafunction.GetValue.class:Class.SeedSet
-///.Metafunction.Reference.param.T.type:Class.SeedSet
-///.Metafunction.Reference.class:Class.SeedSet
-///.Metafunction.Iterator.param.T.type:Class.SeedSet
-///.Metafunction.Iterator.class:Class.SeedSet
-
-
 // ===========================================================================
 // Functions
 // ===========================================================================
 
 // Basic Container Functions
 
-/**
-.Function.begin.param.object.type:Class.SeedSet
-..class:Class.SeedSet
-.Function.end.param.object.type:Class.SeedSet
-..class:Class.SeedSet
-.Function.length.param.object.type:Class.SeedSet
-..class:Class.SeedSet
-.Function.front.param.container.type:Class.SeedSet
-..class:Class.SeedSet
-.Function.back.param.container.type:Class.SeedSet
-..class:Class.SeedSet
-*/
 // TODO(holtgrew): dddoc {begin,end,length,front,back}All(T)
 
 // SeedSet Functions
 
 /*!
  * @fn SeedSet#addSeed
- * 
- * @headerfile seqan/seeds.h
- * 
+ *
+ * @headerfile <seqan/seeds.h>
+ *
  * @brief Adds a seed to an existing @link SeedSet @endlink using different
  *        algorithms for local chaining.
- * 
+ *
  * @signature bool addSeed(seedSet, seed, distance, bandwidth, score, seqH, seqV, tag);
  * @signature bool addSeed(seedSet, seed, distance, score, SimpleChain);
  * @signature bool addSeed(seedSet, seed, distance, Merge);
  * @signature bool addSeed(seedSet, seed, Single);
- * 
+ *
  * @param[in,out] seedSet   The SeedSet to add the seed to.
  * @param[in]     seed      The seed to be added.
  * @param[in]     distance  The maximal distance between the end point of the upper left and the begin point of the
@@ -148,19 +114,19 @@ class SeedSet;
  *                          requires the bandwidth information.
  * @param[in]     score     The scoring scheme.Note, only Chaos and SimpleChain require the score.
  *                          Type: @link SimpleScore @endlink.
- * @param[in]     seqH      Database sequence (horizontal).  Only required for Chaos Chaining.  Types: SequenceConcept.
- * @param[in]     seqV      Query sequence (vertical).  Only required for Chaos Chaining.  Types: SequenceConcept.
+ * @param[in]     seqH      Database sequence (horizontal).  Only required for Chaos Chaining.  Types: ContainerConcept.
+ * @param[in]     seqV      Query sequence (vertical).  Only required for Chaos Chaining.  Types: ContainerConcept.
  * @param[in]     tag       Select the algorithm that is used to add the new seed.  Note that not every algorithm can
  *                          be used with each type of @link Seed @endlink.  See special signatures above.  The seed is
  *                          copied and then added.
- * 
+ *
  * @return bool <tt>true</tt> if successful.  Adding can fail if no appropriate seed is there for chaining or merging.
  *              Adding using <tt>Single</tt> ever fails.
- * 
+ *
  * @section Examples
- * 
- * @include demos/seeds/seeds_add_seed.cpp
- * 
+ *
+ * @include demos/dox/seeds/seeds_add_seed.cpp
+ *
  * The output is as follows:
  *
  * @code{.console}
@@ -169,14 +135,14 @@ class SeedSet;
  * Seed: Seed<Simple, TConfig>(10, 10, 15, 15, lower diag = 0, upper diag = 0)
  * Seed: Seed<Simple, TConfig>(14, 14, 18, 18, lower diag = 0, upper diag = 0)
  * Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
- *  
- *  
+ *
+ *
  * Merge Method:
  * Seed: Seed<Simple, TConfig>(4, 5, 8, 9, lower diag = -1, upper diag = -1)
  * Seed: Seed<Simple, TConfig>(10, 10, 18, 18, lower diag = 0, upper diag = 0)
  * Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
- *  
- *  
+ *
+ *
  * Chaos Method:
  * Seed: Seed<Simple, TConfig>(4, 5, 15, 15, lower diag = -1, upper diag = 0)
  * Seed: Seed<Simple, TConfig>(14, 14, 18, 18, lower diag = 0, upper diag = 0)
@@ -184,81 +150,6 @@ class SeedSet;
  * @endcode
  */
 
-/**
-.Function.SeedSet#addSeed:
-..summary:Adds a seed to an existing @Class.SeedSet@ using different algorithms for local chaining.
-..cat:Seed Handling
-..signature:addSeed(set, seed, distance, bandwidth, score, seqH, seqV, tag)
-..signature:addSeed(set, seed, distance, score, SimpleChain())
-..signature:addSeed(set, seed, distance, Merge())
-..signature:addSeed(set, seed, Single())
-..class:Class.SeedSet
-..param.set:The set to add the seed to.
-...type:Class.SeedSet
-..param.seed:The seed to be added.
-...type:Class.Seed
-..param.seqH: Database sequence (horizontal).
-...type:Concept.SequenceConcept
-...remarks:Only required for @Tag.Local Chaining|Chaos Chaining@.
-..param.seqV: Query sequence (vertical).
-...type:Concept.SequenceConcept
-...remarks:Only required for @Tag.Local Chaining|Chaos Chaining@.
-..param.score:The scoring scheme.
-...type:Spec.Simple Score
-...remarks:Note, only @Tag.Local Chaining|Chaos and SimpleChain@ require the score.
-..param.distance:The maximal distance between the end point of the upper left and the begin point of the lower right @Class.Seed@ allowed for local chaining.
-...type:Concept.IntegerConcept
-...remarks: Note, only @Tag.Local Chaining| Chaos, SimpleChain and Merge@ require the distance information.
-..param.bandwidth: The window size to search for a chainable @Class.Seed@.
-...type:Concept.IntegerConcept
-...remarks: Note, only @Tag.Local Chaining|Chaos@ requires the bandwidth information.
-..param.tag: The algorithm that is used to add the new seed.
-...type:Tag.Local Chaining
-...remarks: Note that not every algorithm can be used with each type of @Class.Seed@. See special signatures above.
-...remarks: The seed is copied and then added.
-..returns:Boolean if successfully added.
-...remarks:Always true for Tag Single.
-..example.file:demos/seeds/seeds_add_seed.cpp
-..example.text:The output is as follows:
-..example.output:
-Single Method:
-Seed: Seed<Simple, TConfig>(4, 5, 8, 9, lower diag = -1, upper diag = -1)
-Seed: Seed<Simple, TConfig>(10, 10, 15, 15, lower diag = 0, upper diag = 0)
-Seed: Seed<Simple, TConfig>(14, 14, 18, 18, lower diag = 0, upper diag = 0)
-Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
-
-
-Merge Method:
-Seed: Seed<Simple, TConfig>(4, 5, 8, 9, lower diag = -1, upper diag = -1)
-Seed: Seed<Simple, TConfig>(10, 10, 18, 18, lower diag = 0, upper diag = 0)
-Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
-
-
-Chaos Method:
-Seed: Seed<Simple, TConfig>(4, 5, 15, 15, lower diag = -1, upper diag = 0)
-Seed: Seed<Simple, TConfig>(14, 14, 18, 18, lower diag = 0, upper diag = 0)
-Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
-..include:seqan/seeds.h
-*/
-
-/**
-.Intenral.Function.SeedSet#addSeeds:
-..summary:Adds several seeds to an existing set. If a merging or chaining algorithm is used seeds are added if the merging or chaining fails.
-..cat:Seed Handling
-..signature:addSeed(set, container, tag)
-..signature:addSeed(set, begin, end, tag)
-..class:Class.SeedSet
-..param.set:The set to which the new seed sould be added.
-...type:Class.SeedSet
-..param.container: Content is copied to set.
-...type:Concept.ContainerConcept
-..param.begin: Iterator pointing to the first value to add.
-..param.end: Iterator pointing just behind the last value to add.
-..param.tag: The algorithm that should be used to add the new @Class.Seed@.
-...type:Tag.Local Chaining
-...remarks: Note that not every algorithm can be used with each specialization of @Class.Seed@.
-..include:seqan/seeds.h
-*/
 
 // ---------------------------------------------------------------------------
 // Function minScore()
@@ -268,35 +159,21 @@ Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
  * @fn SeedSet#minScore
  * @headerfile <seqan/seeds.h>
  * @brief Returns the threshold to distinguish between high-scoring and low-scoring seeds.
- * 
+ *
  * @signature TSeedScore minScore(seedSet);
- * 
+ *
  * @param[in] seedSet The SeedSet for which the threshold is set.  If the score of a seed is higher than the given
  *                    threshold, then it is virtually put into a container storing the high-scoring seeds which can
  *                    be iterated separately.
  *
  * @return TSeedScore The score threshold.  TSeedScore is the @link Seed#SeedScore @endlink of the contained seeds.
- * 
+ *
  * @see SeedSet#setMinScore
  */
 
-/**
-.Function.SeedSet#minScore:
-..summary:Returns the threshold to distinguish between high-scoring and low-scoring seeds.
-..cat:Seed Handling
-..signature:minScore(set)
-..class:Class.SeedSet
-..param.set:The set for which the threshold is set.
-...type:Class.SeedSet
-...remarks: If the score of a seed is higher than the given threshold, then it is virtually put
-into a container storing the high-scoring seeds which can be iterated separately.
-..see:Function.SeedSet#setMinScore
-..include:seqan/seeds.h
-*/
-
-template <typename TSeedSpec, typename TSeedSetSpec>
-typename SeedScore<typename Value<SeedSet<TSeedSpec, TSeedSetSpec> >::Type >::Type
-minScore(SeedSet<TSeedSpec, TSeedSetSpec> const & seedSet)
+template <typename TSeed, typename TSeedSetSpec>
+typename SeedScore<typename Value<SeedSet<TSeed, TSeedSetSpec> >::Type >::Type
+minScore(SeedSet<TSeed, TSeedSetSpec> const & seedSet)
 {
     return seedSet._minScore;
 }
@@ -309,34 +186,19 @@ minScore(SeedSet<TSeedSpec, TSeedSetSpec> const & seedSet)
  * @fn SeedSet#setMinScore
  * @headerfile <seqan/seeds.h>
  * @brief Sets the threshold at which seeds are considered high-scoring.
- * 
+ *
  * @signature void setMinScore(seedSet, scoreValue);
- * 
+ *
  * @param[in,out] seedSet    The SeedSet for which the threshold is to be set.
  * @param[in]     scoreValue The new threshold to set.  If the score of a seed is higher than the given threshold, then
  *                           it is virtually put into a container storing the high-scoring seeds which can be iterated
- *                           separately.
- * 
+ *                           separately  (@link IntegerConcept @endlink).
+ *
  * @see SeedSet#minScore
  */
 
-/**
-.Function.SeedSet#setMinScore:
-..summary:Sets the threshold at which seeds are considered high-scoring.
-..cat:Seed Handling
-..signature:setMinScore(set, score)
-..class:Class.SeedSet
-..param.set:The seed set for which the threshold is to be set.
-...type:Class.SeedSet
-..param.score:The new threshold to set.
-...remarks: If the score of a seed is higher than the given threshold, then it is virtually put
-into a container storing the high-scoring seeds which can be iterated separately.
-..see:Function.SeedSet#minScore
-..include:seqan/seeds.h
-*/
-
-template <typename TSeedSpec, typename TSeedSetSpec, typename TScoreValue>
-void setMinScore(SeedSet<TSeedSpec, TSeedSetSpec> & seedSet, TScoreValue val)
+template <typename TSeed, typename TSeedSetSpec, typename TScoreValue>
+void setMinScore(SeedSet<TSeed, TSeedSetSpec> & seedSet, TScoreValue val)
 {
     seedSet._minScore = val;
 }
@@ -345,9 +207,9 @@ void setMinScore(SeedSet<TSeedSpec, TSeedSetSpec> & seedSet, TScoreValue val)
 // Function minSeedSize()
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec, typename TSeedSetSpec>
-typename Size<typename Value<SeedSet<TSeedSpec, TSeedSetSpec> >::Type >::Type
-minSeedSize(SeedSet<TSeedSpec, TSeedSetSpec> const & seedSet)
+template <typename TSeed, typename TSeedSetSpec>
+typename Size<typename Value<SeedSet<TSeed, TSeedSetSpec> >::Type >::Type
+minSeedSize(SeedSet<TSeed, TSeedSetSpec> const & seedSet)
 {
     return seedSet._minSeedSize;
 }
@@ -356,8 +218,8 @@ minSeedSize(SeedSet<TSeedSpec, TSeedSetSpec> const & seedSet)
 // Function setMinSeedSize()
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec, typename TSeedSetSpec, typename TSize>
-void setMinSeedSize(SeedSet<TSeedSpec, TSeedSetSpec> & seedSet, TSize siz)
+template <typename TSeed, typename TSeedSetSpec, typename TSize>
+void setMinSeedSize(SeedSet<TSeed, TSeedSetSpec> & seedSet, TSize siz)
 {
     seedSet._minSeedSize = siz;
 }
@@ -366,10 +228,12 @@ void setMinSeedSize(SeedSet<TSeedSpec, TSeedSetSpec> & seedSet, TSize siz)
 // Helper Function _qualityReached()
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec, typename TSeedSetSpec, typename TSeedConfig>
-inline bool _qualityReached(SeedSet<TSeedSpec, TSeedSetSpec> const & seedSet,
+// TODO(rmaerker): Is this function used anywhere?
+template <typename TSeed, typename TSeedSetSpec, typename TSeedSpec, typename TSeedConfig>
+inline bool _qualityReached(SeedSet<TSeed, TSeedSetSpec> const & seedSet,
                             Seed<TSeedSpec, TSeedConfig> const & seed)
 {
+    // TODO(rmaerker): If different seed configs are supported we must make sure, that the scoreValues are comparable to avoid compiler warnings.
     return score(seed) >= minScore(seedSet) && seedSize(seed) >= minSeedSize(seedSet);
 }
 
@@ -377,9 +241,18 @@ inline bool _qualityReached(SeedSet<TSeedSpec, TSeedSetSpec> const & seedSet,
 // Function clear()
 // ---------------------------------------------------------------------------
 
-///.Function.clear.param.object.type:Class.SeedSet
-template <typename TSeedSpec, typename TSeedSetSpec>
-inline void clear(SeedSet<TSeedSpec, TSeedSetSpec> & seedSet)
+/*!
+ * @fn SeedSet#clear
+ * @headerfile <seqan/sequence.h>
+ * @brief Clear the SeedSet.
+ *
+ * @signature void clear(seedSet);
+ *
+ * @param[in,out] seedSet The SeedSet to clear.
+ */
+
+template <typename TSeed, typename TSeedSetSpec>
+inline void clear(SeedSet<TSeed, TSeedSetSpec> & seedSet)
 {
     seedSet._seeds.clear();
     seedSet._minScore = 0;
@@ -389,16 +262,16 @@ inline void clear(SeedSet<TSeedSpec, TSeedSetSpec> & seedSet)
 
 // Debugging / TikZ Output
 
-template <typename TStream, typename TQuerySequence, typename TDatabaseSequence, typename TSeedSetSpec, typename TSeedSpec>
+template <typename TStream, typename TQuerySequence, typename TDatabaseSequence, typename TSeedSetSpec, typename TSeed>
 inline void
 __write(TStream & stream,
        TQuerySequence & sequence0,
        TDatabaseSequence & sequence1,
-       SeedSet<TSeedSpec, TSeedSetSpec> const & seedSet,
+       SeedSet<TSeed, TSeedSetSpec> const & seedSet,
        Tikz_ const &)
 {
 //IOREV _nodoc_ specialization not documented
-    typedef SeedSet<TSeedSpec, TSeedSetSpec> TSeedSet;
+    typedef SeedSet<TSeed, TSeedSetSpec> TSeedSet;
 
     stream << "\\begin{tikzpicture}[" << std::endl
            << "    seed/.style={very thick}," << std::endl
diff --git a/seqan/seeds/seeds_seed_set_non_scored.h b/seqan/seeds/seeds_seed_set_non_scored.h
index 9ecd0b3..527d684 100644
--- a/seqan/seeds/seeds_seed_set_non_scored.h
+++ b/seqan/seeds/seeds_seed_set_non_scored.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,19 +43,6 @@ namespace seqan {
 // Enums, Tags, Classes, Specializations
 // ===========================================================================
 
-/**
-.Internal.Spec.Non-Scored SeedSet
-..summary:SeedSet that uses non-scored Seeds.
-..cat:Seed Handling
-..general:Class.SeedSet
-..signature:SeedSet<TPosition, TSeedSpec, TScoringScheme>
-..param.TPosition: Type that saves the positions and upper/lower bounds.
-...remarks: Positive and negative values are needed.
-..param.TSeedSpec:The @Class.Seed@ specialization.
-..param.TScoringScheme:The scoring sheme to use.
-..include:seqan/seeds.h
-*/
-
 // ===========================================================================
 // Metafunctions
 // ===========================================================================
diff --git a/seqan/seeds/seeds_seed_set_scored.h b/seqan/seeds/seeds_seed_set_scored.h
index d652022..0cf72e9 100644
--- a/seqan/seeds/seeds_seed_set_scored.h
+++ b/seqan/seeds/seeds_seed_set_scored.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,19 +43,6 @@ namespace seqan {
 // Enums, Tags, Classes, Specializations
 // ===========================================================================
 
-/**
-.Internal.Spec.Scored SeedSet
-..summary:SeedSet that uses scored Seeds.
-..cat:Seed Handling
-..general:Class.SeedSet
-..signature:SeedSet<TPosition, TSeedSpec, TScoringScheme>
-..param.TPosition: Type that saves the positions and upper/lower bounds.
-...remarks: Positive and negative values are needed.
-..param.TSeedSpec:The @Class.Seed@ specialization.
-..param.TScoringScheme:The scoring sheme to use.
-..include:seqan/seeds.h
-*/
-
 // ===========================================================================
 // Metafunctions
 // ===========================================================================
diff --git a/seqan/seeds/seeds_seed_set_unordered.h b/seqan/seeds/seeds_seed_set_unordered.h
index dae59e7..2c23ce2 100644
--- a/seqan/seeds/seeds_seed_set_unordered.h
+++ b/seqan/seeds/seeds_seed_set_unordered.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -55,15 +55,14 @@ typedef Tag<Unordered_> Unordered;
 
 // TODO(holtgrew): Maybe allow iterating over seeds that have reached a certain quality (length/score).
 
-template <typename TSeedSpec>
-class SeedSet<TSeedSpec, Unordered>
+template <typename TSeed>
+class SeedSet<TSeed, Unordered>
 {
 public:
-    typedef Seed<TSeedSpec> TSeed_;
-    typedef typename SeedScore<TSeed_>::Type TScoreValue_;
-    typedef typename Size<TSeed_>::Type TSize_;
-    typedef LessBeginDiagonal<TSeed_> TSeedCmp_;
-    typedef std::multiset<TSeed_, TSeedCmp_> TSet_;
+    typedef typename SeedScore<TSeed>::Type TScoreValue_;
+    typedef typename Size<TSeed>::Type TSize_;
+    typedef LessBeginDiagonal<TSeed> TSeedCmp_;
+    typedef std::multiset<TSeed, TSeedCmp_> TSet_;
 
     TSet_ _seeds;
 
@@ -82,82 +81,77 @@ class SeedSet<TSeedSpec, Unordered>
 // Metafunction Position
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-struct Position<SeedSet<TSeedSpec, Unordered> >
+template <typename TSeed>
+struct Position<SeedSet<TSeed, Unordered> >
 {
-    typedef SeedSet<TSeedSpec, Unordered> TSeedSet_;
+    typedef SeedSet<TSeed, Unordered> TSeedSet_;
     typedef String<typename TSeedSet_::TSeed> TSeedString_;
     typedef typename Position<TSeedString_>::Type Type;
 };
 
-template <typename TSeedSpec>
-struct Position<SeedSet<TSeedSpec, Unordered> const> : Position<SeedSet<TSeedSpec, Unordered> >
+template <typename TSeed>
+struct Position<SeedSet<TSeed, Unordered> const> : Position<SeedSet<TSeed, Unordered> >
 {};
 
 // ---------------------------------------------------------------------------
 // Metafunction Size
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-struct Size<SeedSet<TSeedSpec, Unordered> >
+template <typename TSeed>
+struct Size<SeedSet<TSeed, Unordered> >
 {
-    typedef SeedSet<TSeedSpec, Unordered> TSeedSet_;
-    typedef String<typename TSeedSet_::TSeed_> TSeedString_;
+    typedef SeedSet<TSeed, Unordered> TSeedSet_;
+    typedef String<TSeed> TSeedString_;
     typedef typename Size<TSeedString_>::Type Type;
 };
 
-template <typename TSeedSpec>
-struct Size<SeedSet<TSeedSpec, Unordered> const> : Size<SeedSet<TSeedSpec, Unordered> >
+template <typename TSeed>
+struct Size<SeedSet<TSeed, Unordered> const> : Size<SeedSet<TSeed, Unordered> >
 {};
 
 // ---------------------------------------------------------------------------
 // Metafunction Value
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-struct Value<SeedSet<TSeedSpec, Unordered> >
+template <typename TSeed>
+struct Value<SeedSet<TSeed, Unordered> >
 {
-    typedef SeedSet<TSeedSpec, Unordered> TSeedSet;
-    typedef typename TSeedSet::TSeed_ Type;
+    typedef TSeed Type;
 };
 
-template <typename TSeedSpec>
-struct Value<SeedSet<TSeedSpec, Unordered> const> : Value<SeedSet<TSeedSpec, Unordered> >
-{};
+template <typename TSeed>
+struct Value<SeedSet<TSeed, Unordered> const>
+{
+    typedef typename Value<SeedSet<TSeed, Unordered> >::Type const Type;
+};
 
 // ---------------------------------------------------------------------------
 // Metafunction Reference
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-struct Reference<SeedSet<TSeedSpec, Unordered> >
-{
-    typedef typename Value<SeedSet<TSeedSpec, Unordered> >::Type & Type;
-};
-
-template <typename TSeedSpec>
-struct Reference<SeedSet<TSeedSpec, Unordered> const>
+template <typename TSeed>
+struct Reference<SeedSet<TSeed, Unordered> >
 {
-    typedef typename Value<SeedSet<TSeedSpec, Unordered> >::Type const & Type;
+    typedef typename Value<SeedSet<TSeed, Unordered> >::Type & Type;
 };
 
 // ---------------------------------------------------------------------------
 // Metafunction Iterator
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-struct Iterator<SeedSet<TSeedSpec, Unordered>, Standard>
+template <typename TSeed>
+struct Iterator<SeedSet<TSeed, Unordered>, Standard>
 {
-    typedef SeedSet<TSeedSpec, Unordered> TSeedSet_;
-	typedef typename TSeedSet_::TSet_ TMultiSet_;
+    typedef SeedSet<TSeed, Unordered> TSeedSet_;
+    typedef typename TSeedSet_::TSet_ TMultiSet_;
     typedef Iter<TMultiSet_, StdIteratorAdaptor> Type;
 };
 
-template <typename TSeedSpec>
-struct Iterator<SeedSet<TSeedSpec, Unordered> const, Standard>
+template <typename TSeed>
+struct Iterator<SeedSet<TSeed, Unordered> const, Standard>
 {
-    typedef SeedSet<TSeedSpec, Unordered> const TSeedSet_;
-	typedef typename TSeedSet_::TSet_ const TMultiSet_;
+    typedef SeedSet<TSeed, Unordered> const TSeedSet_;
+    typedef typename TSeedSet_::TSet_ const TMultiSet_;
     typedef Iter<TMultiSet_, StdIteratorAdaptor> Type;
 };
 
@@ -171,16 +165,16 @@ struct Iterator<SeedSet<TSeedSpec, Unordered> const, Standard>
 
 // Standard Container Functions
 
-template <typename TSeedSpec>
-inline typename Size<SeedSet<TSeedSpec, Unordered> >::Type
-length(SeedSet<TSeedSpec, Unordered> & seedSet)
+template <typename TSeed>
+inline typename Size<SeedSet<TSeed, Unordered> >::Type
+length(SeedSet<TSeed, Unordered> & seedSet)
 {
     return seedSet._seeds.size();
 }
 
-template <typename TSeedSpec>
-inline typename Size<SeedSet<TSeedSpec, Unordered> const>::Type
-length(SeedSet<TSeedSpec, Unordered> const & seedSet)
+template <typename TSeed>
+inline typename Size<SeedSet<TSeed, Unordered> const>::Type
+length(SeedSet<TSeed, Unordered> const & seedSet)
 {
     return seedSet._seeds.size();
 }
@@ -189,16 +183,16 @@ length(SeedSet<TSeedSpec, Unordered> const & seedSet)
 // Function begin()
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-inline typename Iterator<SeedSet<TSeedSpec, Unordered> >::Type
-begin(SeedSet<TSeedSpec, Unordered> & seedSet, Standard const &)
+template <typename TSeed>
+inline typename Iterator<SeedSet<TSeed, Unordered> >::Type
+begin(SeedSet<TSeed, Unordered> & seedSet, Standard const &)
 {
-	return seedSet._seeds.begin();
+    return seedSet._seeds.begin();
 }
 
-template <typename TSeedSpec>
-inline typename Iterator<SeedSet<TSeedSpec, Unordered> const>::Type
-begin(SeedSet<TSeedSpec, Unordered> const & seedSet, Standard const &)
+template <typename TSeed>
+inline typename Iterator<SeedSet<TSeed, Unordered> const>::Type
+begin(SeedSet<TSeed, Unordered> const & seedSet, Standard const &)
 {
     return seedSet._seeds.begin();
 }
@@ -207,16 +201,16 @@ begin(SeedSet<TSeedSpec, Unordered> const & seedSet, Standard const &)
 // Function end()
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-inline typename Iterator<SeedSet<TSeedSpec, Unordered> >::Type
-end(SeedSet<TSeedSpec, Unordered> & seedSet, Standard const &)
+template <typename TSeed>
+inline typename Iterator<SeedSet<TSeed, Unordered> >::Type
+end(SeedSet<TSeed, Unordered> & seedSet, Standard const &)
 {
     return seedSet._seeds.end();
 }
 
-template <typename TSeedSpec>
-inline typename Iterator<SeedSet<TSeedSpec, Unordered> const>::Type
-end(SeedSet<TSeedSpec, Unordered> const & seedSet, Standard const &)
+template <typename TSeed>
+inline typename Iterator<SeedSet<TSeed, Unordered> const>::Type
+end(SeedSet<TSeed, Unordered> const & seedSet, Standard const &)
 {
     return seedSet._seeds.end();
 }
@@ -225,16 +219,16 @@ end(SeedSet<TSeedSpec, Unordered> const & seedSet, Standard const &)
 // Function front()
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-inline typename Reference<typename Iterator<SeedSet<TSeedSpec, Unordered>, Standard>::Type >::Type
-front(SeedSet<TSeedSpec, Unordered> & seedSet)
+template <typename TSeed>
+inline typename Reference<typename Iterator<SeedSet<TSeed, Unordered>, Standard>::Type >::Type
+front(SeedSet<TSeed, Unordered> & seedSet)
 {
     return *seedSet._seeds.begin();
 }
 
-template <typename TSeedSpec>
-inline typename Reference<typename Iterator<SeedSet<TSeedSpec, Unordered> const, Standard>::Type >::Type
-front(SeedSet<TSeedSpec, Unordered> const & seedSet)
+template <typename TSeed>
+inline typename Reference<typename Iterator<SeedSet<TSeed, Unordered> const, Standard>::Type >::Type
+front(SeedSet<TSeed, Unordered> const & seedSet)
 {
     return *seedSet._seeds.begin();
 }
@@ -243,16 +237,16 @@ front(SeedSet<TSeedSpec, Unordered> const & seedSet)
 // Function back()
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec>
-inline typename Reference<typename Iterator<SeedSet<TSeedSpec, Unordered> , Standard>::Type >::Type
-back(SeedSet<TSeedSpec, Unordered> & seedSet)
+template <typename TSeed>
+inline typename Reference<typename Iterator<SeedSet<TSeed, Unordered> , Standard>::Type >::Type
+back(SeedSet<TSeed, Unordered> & seedSet)
 {
     return *seedSet._seeds.rbegin();
 }
 
-template <typename TSeedSpec>
-inline typename Reference<typename Iterator<SeedSet<TSeedSpec, Unordered> const, Standard>::Type >::Type
-back(SeedSet<TSeedSpec, Unordered> const & seedSet)
+template <typename TSeed>
+inline typename Reference<typename Iterator<SeedSet<TSeed, Unordered> const, Standard>::Type >::Type
+back(SeedSet<TSeed, Unordered> const & seedSet)
 {
     return *seedSet._seeds.rbegin();
 }
@@ -265,13 +259,13 @@ back(SeedSet<TSeedSpec, Unordered> const & seedSet)
 
 // TODO(holtgrew): Add bulk-addSeeds functions.
 
-template <typename TSeedIter, typename TSeedSpec, typename TDistanceThreshold, typename TBandwidth, typename TCombination>
+template <typename TSeedIter, typename TSeed, typename TDistanceThreshold, typename TBandwidth, typename TCombination>
 bool
 _findSeedForCombination(
         TSeedIter & mergePartner,
         bool & seedIsOnTheLeft,
-        SeedSet<TSeedSpec, Unordered> & seedSet,
-        typename Value<SeedSet<TSeedSpec, Unordered> >::Type const & seed,
+        SeedSet<TSeed, Unordered> & seedSet,
+        typename Value<SeedSet<TSeed, Unordered> >::Type const & seed,
         TDistanceThreshold const & maxDistance,
         TBandwidth const & bandwidth,
         TCombination const & tag)
@@ -286,7 +280,7 @@ _findSeedForCombination(
     {
         if (_seedsCombineable(*it, seed, maxDistance, bandwidth, tag))
         {
-//			std::cout << "Combineable: " << (*value(it)) << " and " << seed << std::endl;
+//            std::cout << "Combineable: " << (*value(it)) << " and " << seed << std::endl;
             // seed is to be merged into *it.
             mergePartner = it;
             seedIsOnTheLeft = false;
@@ -294,7 +288,7 @@ _findSeedForCombination(
         }
         else if (_seedsCombineable(seed, *it, maxDistance, bandwidth, tag))
         {
-//			std::cout << "Combineable: " << seed << " and " << (*value(it)) << std::endl;
+//            std::cout << "Combineable: " << seed << " and " << (*value(it)) << std::endl;
             // *it is to be merged into seed.
             mergePartner = it;
             seedIsOnTheLeft = true;
@@ -310,10 +304,10 @@ _findSeedForCombination(
 // Function addSeed()
 // ---------------------------------------------------------------------------
 
-template <typename TSeedSpec, typename TDistanceThreshold, typename TBandwidth, typename TScoreValue, typename TSequence0, typename TSequence1, typename TCombination>
+template <typename TSeed, typename TDistanceThreshold, typename TBandwidth, typename TScoreValue, typename TSequence0, typename TSequence1, typename TCombination>
 inline bool
-addSeed(SeedSet<TSeedSpec, Unordered> & seedSet,
-        typename Value<SeedSet<TSeedSpec, Unordered> >::Type const & seed,
+addSeed(SeedSet<TSeed, Unordered> & seedSet,
+        TSeed const & seed,
         TDistanceThreshold const & maxDiagDist,
         TBandwidth const & bandwidth,
         Score<TScoreValue, Simple> const & scoringScheme,
@@ -323,10 +317,9 @@ addSeed(SeedSet<TSeedSpec, Unordered> & seedSet,
 {
     SEQAN_CHECKPOINT;
 
-    typedef SeedSet<TSeedSpec, Unordered> TSeedSet;
+    typedef SeedSet<TSeed, Unordered> TSeedSet;
     typedef typename TSeedSet::TSet_ TSet;
     typedef typename TSet::iterator TSeedIterator;
-    typedef typename Value<TSeedSet>::Type TSeed;
 
     // Try to find a seed for recombination.
     TSeedIterator it;
@@ -356,20 +349,20 @@ addSeed(SeedSet<TSeedSpec, Unordered> & seedSet,
 }
 
 // TODO(holtgrew): Score not needed for Merge!
-template <typename TSeedSpec, typename TDistanceThreshold>
+template <typename TSeed, typename TDistanceThreshold>
 inline bool
-addSeed(SeedSet<TSeedSpec, Unordered> & seedSet,
-        typename Value<SeedSet<TSeedSpec, Unordered> >::Type const & seed,
+addSeed(SeedSet<TSeed, Unordered> & seedSet,
+        TSeed const & seed,
         TDistanceThreshold const & maxDiagDist,
         Merge const &)
 {
     return addSeed(seedSet, seed, maxDiagDist, 0, Score<int, Simple>(), Nothing(), Nothing(), Merge());
 }
 
-template <typename TSeedSpec, typename TDistanceThreshold, typename TScoreValue>
+template <typename TSeed, typename TDistanceThreshold, typename TScoreValue>
 inline bool
-addSeed(SeedSet<TSeedSpec, Unordered> & seedSet,
-        typename Value<SeedSet<TSeedSpec, Unordered> >::Type const & seed,
+addSeed(SeedSet<TSeed, Unordered> & seedSet,
+        TSeed const & seed,
         TDistanceThreshold const & maxDiagDist,
         Score<TScoreValue, Simple> const & scoringScheme,
         SimpleChain const &)
@@ -377,9 +370,9 @@ addSeed(SeedSet<TSeedSpec, Unordered> & seedSet,
     return addSeed(seedSet, seed, maxDiagDist, 0, scoringScheme, Nothing(), Nothing(), SimpleChain());
 }
 
-template <typename TSeedSpec, typename TSeed>
+template <typename TSeed>
 inline bool
-addSeed(SeedSet<TSeedSpec, Unordered> & seedSet,
+addSeed(SeedSet<TSeed, Unordered> & seedSet,
         TSeed const & seed,
         Single const &)
 {
diff --git a/seqan/seeds/seeds_seed_simple.h b/seqan/seeds/seeds_seed_simple.h
index 65a5bc3..43365e6 100644
--- a/seqan/seeds/seeds_seed_simple.h
+++ b/seqan/seeds/seeds_seed_simple.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -50,12 +50,13 @@ namespace seqan {
 /*!
  * @class SimpleSeed
  * @headerfile <seqan/seeds.h>
+ * @extends Seed
  * @brief Describes a seed with start and end position and diagonal upper and lower bounds.
  *
  * @signature template <[typename TConfig]>
  *            class Seed<Simple, TConfig>;
  *
- * @tparam TConfig The configuration to use.  Defaults to DefaultSeedConfig.
+ * @tparam TConfig The configuration to use.  Defaults to @link DefaultSeedConfig @endlink.
  */
 
 /*!
@@ -66,36 +67,13 @@ namespace seqan {
  * @signature Seed::Seed(beginPosH, beginPosV, length);
  * @signature Seed::Seed(beginPosH, beginPosV, endPosH, endPosV);
  *
- * @param beginPosH[in] The begin position in the horizontal position.
- * @param beginPosV[in] The begin position in the vertical position.
- * @param length[in]    The length of the seed (in both directions).
- * @param endPosH[in]   The end position in the horizontal position.
- * @param endPosV[in]   The end position in the vertical position.
+ * @param[in] beginPosH The begin position in the horizontal position.
+ * @param[in] beginPosV The begin position in the vertical position.
+ * @param[in] length    The length of the seed (in both directions).
+ * @param[in] endPosH   The end position in the horizontal position.
+ * @param[in] endPosV   The end position in the vertical position.
  */
 
-/**
-.Spec.Simple Seed
-..summary:Describes a seed with start and end position and diagonal upper and lower bounds.
-..cat:Seed Handling
-..general:Class.Seed
-..signature:Seed<Simple, TConfig>
-..param.TConfig:The configuration object used for the seed.
-...default:DefaultSeedConfig.
-
-.Memfunc.Simple Seed#Seed
-..class:Spec.Simple Seed
-..summary:Constructor
-..signature: Seed<Simple, TConfig> ()
-..signature: Seed<Simple, TConfig> (beginPosH, beginPosV, length)
-..signature: Seed<Simple, TConfig> (beginPosH, beginPosV, endPosH, endPosV)
-..param.beginPosH: Begin position in database (horizontal).
-..param.beginPosV: Begin position in query (vertical).
-..param.endPosH: End position in database (horizontal).
-..param.endPosV: End position in query (vertical).
-..param.length: Length of the seed.
-..include:seqan/seeds.h
-*/
-
 template <typename TConfiguration>
 class Seed<Simple, TConfiguration>
 {
@@ -146,7 +124,8 @@ class Seed<Simple, TConfiguration>
               _endPositionH(endPositionH(other)),
               _endPositionV(endPositionV(other)),
               _lowerDiagonal(lowerDiagonal(other)),
-              _upperDiagonal(upperDiagonal(other))
+              _upperDiagonal(upperDiagonal(other)),
+              _score(0)
     {
         SEQAN_ASSERT_GEQ(_upperDiagonal, _lowerDiagonal);
     }
@@ -200,7 +179,7 @@ template <typename TConfig>
 inline typename Position<Seed<Simple, TConfig> >::Type
 beginPositionH(Seed<Simple, TConfig> const & seed)
 {
-	return seed._beginPositionH;
+    return seed._beginPositionH;
 }
 
 // ---------------------------------------------------------------------------
@@ -208,10 +187,10 @@ beginPositionH(Seed<Simple, TConfig> const & seed)
 // ---------------------------------------------------------------------------
 
 template <typename TConfig, typename TPosition>
-inline void 
+inline void
 setBeginPositionH(Seed<Simple, TConfig> & seed, TPosition pos)
 {
-	seed._beginPositionH = pos;
+    seed._beginPositionH = pos;
 }
 
 // ---------------------------------------------------------------------------
@@ -222,7 +201,7 @@ template <typename TConfig>
 inline typename Position<Seed<Simple, TConfig> >::Type
 endPositionH(Seed<Simple, TConfig> const & seed)
 {
-	return seed._endPositionH;
+    return seed._endPositionH;
 }
 
 // ---------------------------------------------------------------------------
@@ -230,10 +209,10 @@ endPositionH(Seed<Simple, TConfig> const & seed)
 // ---------------------------------------------------------------------------
 
 template <typename TConfig, typename TPosition>
-inline void 
+inline void
 setEndPositionH(Seed<Simple, TConfig> & seed, TPosition pos)
 {
-	seed._endPositionH = pos;
+    seed._endPositionH = pos;
 }
 
 // ---------------------------------------------------------------------------
@@ -244,7 +223,7 @@ template <typename TConfig>
 inline typename Position<Seed<Simple, TConfig> >::Type
 beginPositionV(Seed<Simple, TConfig> const & seed)
 {
-	return seed._beginPositionV;
+    return seed._beginPositionV;
 }
 
 // ---------------------------------------------------------------------------
@@ -252,10 +231,10 @@ beginPositionV(Seed<Simple, TConfig> const & seed)
 // ---------------------------------------------------------------------------
 
 template <typename TConfig, typename TPosition>
-inline void 
+inline void
 setBeginPositionV(Seed<Simple, TConfig> & seed, TPosition pos)
 {
-	seed._beginPositionV = pos;
+    seed._beginPositionV = pos;
 }
 
 // ---------------------------------------------------------------------------
@@ -266,7 +245,7 @@ template <typename TConfig>
 inline typename Position<Seed<Simple, TConfig> >::Type
 endPositionV(Seed<Simple, TConfig> const & seed)
 {
-	return seed._endPositionV;
+    return seed._endPositionV;
 }
 
 // ---------------------------------------------------------------------------
@@ -274,10 +253,10 @@ endPositionV(Seed<Simple, TConfig> const & seed)
 // ---------------------------------------------------------------------------
 
 template <typename TConfig, typename TPosition>
-inline void 
+inline void
 setEndPositionV(Seed<Simple, TConfig> & seed, TPosition pos)
 {
-	seed._endPositionV = pos;
+    seed._endPositionV = pos;
 }
 
 // ---------------------------------------------------------------------------
diff --git a/seqan/seq_io.h b/seqan/seq_io.h
index 7c9f0ec..19cd9ca 100644
--- a/seqan/seq_io.h
+++ b/seqan/seq_io.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Facade header for module seq_io.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEQ_IO_H_
-#define CORE_INCLUDE_SEQAN_SEQ_IO_H_
+#ifndef INCLUDE_SEQAN_SEQ_IO_H_
+#define INCLUDE_SEQAN_SEQ_IO_H_
 
 // ===========================================================================
 // Prerequisites.
@@ -43,32 +43,21 @@
 
 #include <seqan/basic.h>
 #include <seqan/stream.h>
+#include <seqan/misc/name_store_cache.h>
 
 // ===========================================================================
-// Lower-Level I/O Interface for Sequences
+// Sequence File Formats
 // ===========================================================================
 
-// File Format Guessing
-#include <seqan/seq_io/guess_stream_format.h>
-
-#include <seqan/seq_io/read_fasta_fastq.h>
+#include <seqan/seq_io/fasta_fastq.h>
 #include <seqan/seq_io/read_embl.h>
 #include <seqan/seq_io/read_genbank.h>
 
-#include <seqan/seq_io/write_fasta_fastq.h>
-
-// ===========================================================================
-// SequenceStream
-// ===========================================================================
-
-#include <seqan/seq_io/sequence_stream_impl.h>
-#include <seqan/seq_io/sequence_stream.h>
-
 // ===========================================================================
-// Reading FASTA for Demos
+// Sequence File
 // ===========================================================================
 
-#include <seqan/seq_io/simple_read_fasta.h>
+#include <seqan/seq_io/sequence_file.h>
 
 // ===========================================================================
 // Genomic Region
@@ -82,4 +71,4 @@
 
 #include <seqan/seq_io/fai_index.h>
 
-#endif  // CORE_INCLUDE_SEQAN_SEQ_IO_H_
+#endif  // INCLUDE_SEQAN_SEQ_IO_H_
diff --git a/seqan/seq_io/INFO b/seqan/seq_io/INFO
deleted file mode 100644
index 5567121..0000000
--- a/seqan/seq_io/INFO
+++ /dev/null
@@ -1,12 +0,0 @@
-Name: seq_io
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: new
-Description: Sequence I/O Interface
- This module contains I/O code for accessing sequence files such as FASTA
- and FASTQ.
- .
- Simple sequential access is provided by the class EasySeqIO while indexed
- access to FASTA file is provided by the class FaiIndex.
diff --git a/seqan/seq_io/fai_index.h b/seqan/seq_io/fai_index.h
index e800d05..aabef85 100644
--- a/seqan/seq_io/fai_index.h
+++ b/seqan/seq_io/fai_index.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,6 +30,7 @@
 //
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 // Code for loading and writing FAI FASTA index files.
 // ==========================================================================
@@ -41,8 +42,8 @@
 #include <seqan/file.h>
 #include <seqan/stream.h>
 
-#ifndef SEQAN_CORE_APPS_RABEMA_FAI_INDEX_H_
-#define SEQAN_CORE_APPS_RABEMA_FAI_INDEX_H_
+#ifndef SEQAN_APPS_RABEMA_FAI_INDEX_H_
+#define SEQAN_APPS_RABEMA_FAI_INDEX_H_
 
 namespace seqan {
 
@@ -63,15 +64,15 @@ namespace seqan {
 class FaiIndexEntry_
 {
 public:
-    // Name of reference sequence.
+    // Name of the sequences.
     CharString name;
-    // Number of nucleotides in sequence.
+    // Length of the sequence.
     __uint64 sequenceLength;
     // Offset in the file.
     __uint64 offset;
     // Number of sequence characters per line.
     unsigned lineLength;
-    // Number of overall characters per line, including newline character(s).
+    // Number of bytes per line, including newline character(s).
     unsigned overallLineLength;
 
     FaiIndexEntry_() :
@@ -79,6 +80,16 @@ class FaiIndexEntry_
     {}
 };
 
+inline void
+clear(FaiIndexEntry_ &entry)
+{
+    clear(entry.name);
+    entry.sequenceLength = 0;
+    entry.offset = 0;
+    entry.lineLength = 0;
+    entry.overallLineLength = 0;
+}
+
 // ----------------------------------------------------------------------------
 // Class FaiIndex
 // ----------------------------------------------------------------------------
@@ -93,17 +104,18 @@ class FaiIndexEntry_
  * FAI indices allow the rast random access to sequences or parts of sequences in a FASTA file.  Originally, they were
  * introduced in the <a href="http://samtools.sourceforge.net/samtools.shtml">samtools</a> program.
  *
- * Also see the <a href="http://trac.seqan.de/wiki/Tutorial/IndexedFastaIO">Indexed FASTA I/O Tutorial</a>.
+ * Also see the <a href="http://seqan.readthedocs.org/en/develop/Tutorial/IndexedFastaIO.html">Indexed FASTA I/O
+ * Tutorial</a>.
  *
  * @section Example
  *
  * The following example demonstrates the usage of the FaiIndex class.
  *
- * @include demos/seq_io/fai_index_example.cpp
+ * @include demos/dox/seq_io/fai_index_example.cpp
  *
  * The output is as follows:
  *
- * @include demos/seq_io/fai_index_example.cpp.stdout
+ * @include demos/dox/seq_io/fai_index_example.cpp.stdout
  *
  * @fn FaiIndex::FaiIndex
  * @brief Constructor.
@@ -111,27 +123,9 @@ class FaiIndexEntry_
  * @signature FaiIndex::FaiIndex();
  */
 
-/**
-.Class.FaiIndex
-..cat:Input/Output
-..signature:FaiIndex
-..summary:Data type for storing FAI indices.
-..wiki:Tutorial/IndexedFastaIO|Tutorial: Indexed FASTA I/O
-..example.text:The following example demonstrate the usage of the FAIIndex class.
-..example.file:demos/seq_io/fai_index_example.cpp
-..include:seqan/seq_io.h
-
-.Memvar.FaiIndex#FaiIndex
-..class:Class.FaiIndex
-..signature:FaiIndex()
-..summary:The @Class.FaiIndex@ class only provides the default constructor.
-*/
-
 class FaiIndex
 {
 public:
-    // TODO(holtgrew): The members are not publically documented for now. Keep it this way?
-
     // The name of the FASTA file.
     CharString fastaFilename;
     // The name of the FAI file.
@@ -139,17 +133,15 @@ class FaiIndex
 
     // The index entries.
     String<FaiIndexEntry_> indexEntryStore;
-    // A store for the reference names.
-    StringSet<CharString> refNameStore;
-    // A cache for fast access to the reference name store.
-    NameStoreCache<StringSet<CharString> > refNameStoreCache;
+    // A store for the sequence names.
+    StringSet<CharString> seqNameStore;
+    // A cache for fast access to the sequence name store.
+    NameStoreCache<StringSet<CharString> > seqNameStoreCache;
 
-    // We use this memory mapped string (opened read-only) to read from the file.
-    String<char, MMap<> > mmapString;
-    bool mmapStringOpen;
+    mutable std::ifstream file;
 
     FaiIndex() :
-        refNameStoreCache(refNameStore), mmapStringOpen(false)
+        seqNameStoreCache(seqNameStore)
     {}
 };
 
@@ -174,73 +166,56 @@ class FaiIndex
  * @param[in,out] faiIndex The FaiIndex to clear.
  */
 
-/**
-.Function.FaiIndex#clear
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:clear(faiIndex)
-..param.faiIndex:The @Class.FaiIndex@ to reset.
-...type:Class.FaiIndex
-..summary:Reset a @Class.FaiIndex@ object to the state after default construction.
-..include:seqan/seq_io.h
-*/
-
 inline void clear(FaiIndex & index)
 {
     clear(index.fastaFilename);
     clear(index.faiFilename);
     clear(index.indexEntryStore);
-    clear(index.refNameStore);
-    refresh(index.refNameStoreCache);
+    clear(index.seqNameStore);
+    clear(index.seqNameStoreCache);
 }
 
 // ----------------------------------------------------------------------------
-// Function getIdByName()
+// Function empty()
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn FaiIndex#getIdByName
- * @brief Return id (numeric index in the file) of a sequence in a FAI file.
+ * @fn FaiIndex#empty
+ * @brief Returns whether the FaiIndex is empty.
  *
- * @signature bool getIdByName(faiIndex, name, id);
+ * @signature void empty(faiIndex);
  *
- * @param[in]  faiIndex The FaiIndex to query.
- * @param[in]  name     The name of the sequence to look the id up for.  Type: @link SequenceConcept @endlink.
- * @param[out] id       The id of the sequence is written here.
+ * @param[in] faiIndex The FaiIndex to check.
  *
- * @return bool true if a reference with the given name is known in the index.
+ * @return bool <tt>true</tt> if the index is empty and needs to be built via @link FaiIndex#build @endlink.
  */
 
-/**
-.Function.FaiIndex#getIdByName
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:getIdByName(faiIndex, name, refId)
-..summary:Return id (numeric index in the file) of a sequence in a FAI file.
-..param.faiIndex:The @Class.FaiIndex@ to query.
-...type:Class.FaiIndex
-..param.name:The name of the sequence to get the id for.
-...type:Shortcut.CharString
-..param.refId:The id of the sequence is written here.
-...type:nolink:$unsigned$
-..return:$bool$ indicating whether a reference with this name is known in the index.
-..include:seqan/seq_io.h
-*/
-
-// TODO(holtgrew): Fix parameter order when getIdByName() has good parameter order.
-
-// TODO(holtgrew): Using templates here because of ambiguities hit otherwise.
-
-template <typename TName, typename TId>
-inline bool getIdByName(FaiIndex & index, TName const & name, TId & id)
+inline bool empty(FaiIndex & index)
 {
-    return getIdByName(index.refNameStore, name, id, index.refNameStoreCache);
+    return empty(index.indexEntryStore);
 }
 
+// ----------------------------------------------------------------------------
+// Function getIdByName()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FaiIndex#getIdByName
+ * @brief Return reference ID (numeric index in the file) of a sequence in a FAI file.
+ *
+ * @signature bool getIdByName(rID, faiIndex, name);
+ *
+ * @param[in]  faiIndex The FaiIndex to query.
+ * @param[in]  name     The name of the sequence to look the id up for.  Type: @link ContainerConcept @endlink.
+ * @param[out] rID      The id of the sequence is written here.
+ *
+ * @return bool <tt>true</tt> if a sequence with the given name is known in the index, <tt>false</tt> otherwise.
+ */
+
 template <typename TName, typename TId>
-inline bool getIdByName(FaiIndex const & index, TName const & name, TId & id)
+inline bool getIdByName(TId & rID, FaiIndex const & index, TName const & name)
 {
-    return getIdByName(index.refNameStore, name, id, index.refNameStoreCache);
+    return getIdByName(rID, index.seqNameStoreCache, name);
 }
 
 // ----------------------------------------------------------------------------
@@ -251,40 +226,26 @@ inline bool getIdByName(FaiIndex const & index, TName const & name, TId & id)
  * @fn FaiIndex#sequenceLength
  * @brief Return length of the sequence with the given id in the FaiIndex.
  *
- * @signature __uint64 sequenceLength(faiIndex, refId);
+ * @signature __uint64 sequenceLength(faiIndex, rID);
  *
  * @param[in] faiIndex The FaiIndex to query.
- * @param[in] refId    The id of the sequence to get the length of.
+ * @param[in] rID    The id of the sequence to get the length of.
  *
- * @return __uint64 The length of the sequence with index refId in faiIndex.
+ * @return __uint64 The length of the sequence with index rID in faiIndex.
  */
 
-/**
-.Function.FaiIndex#sequenceLength
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:__uint64 sequenceLength(faiIndex, refId)
-..summary:Return length of the sequence with the given id in the @Class.FaiIndex@.
-..param.faiIndex:The @Class.FaiIndex@ to query.
-...type:Class.FaiIndex
-..param.refId:The id of the sequence to get the length of.
-...type:nolink:$unsigned$
-..return:$__uint64$ with the length of the sequence.
-..include:seqan/seq_io.h
-*/
-
-template <typename TRefId>
-inline __uint64 sequenceLength(FaiIndex const & index, TRefId refId)
+template <typename TSeqId>
+inline __uint64 sequenceLength(FaiIndex const & index, TSeqId rID)
 {
-    return index.indexEntryStore[refId].sequenceLength;
+    return index.indexEntryStore[rID].sequenceLength;
 }
 
 // TODO(holtgrew): Wrapper and template only here because sequenceLength in string_set_base.h is weird.
 
-template <typename TRefId>
-inline __uint64 sequenceLength(FaiIndex & index, TRefId refId)
+template <typename TSeqId>
+inline __uint64 sequenceLength(FaiIndex & index, TSeqId rID)
 {
-    return index.indexEntryStore[refId].sequenceLength;
+    return index.indexEntryStore[rID].sequenceLength;
 }
 
 // ----------------------------------------------------------------------------
@@ -293,33 +254,19 @@ inline __uint64 sequenceLength(FaiIndex & index, TRefId refId)
 
 /*!
  * @fn FaiIndex#sequenceName
- * @brief Return the name of the sequence with th egiven id in the FaiIndex.
+ * @brief Return the name of the sequence with the given id in the FaiIndex.
  *
- * @signature CharString sequenceName(faiIndex, refId);
+ * @signature CharString sequenceName(faiIndex, rID);
  *
  * @param[in] faiIndex The FaiIndex to query.
- * @param[in] refId    The index of the sequence.
+ * @param[in] rID    The index of the sequence.
  *
  * @return CharString The name of the sequence with the given id.
  */
 
-/**
-.Function.FaiIndex#sequenceName
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:CharString sequenceName(faiIndex, refId)
-..summary:Return the name of the sequence with the given id in the @Class.FaiIndex@.
-..param.faiIndex:The @Class.FaiIndex@ to query.
-...type:Class.FaiIndex
-..param.refId:The id of the sequence to get the name of.
-...type:Shortcut.CharString
-..return:@Shortcut.CharString@ with the name of the sequence.
-..include:seqan/seq_io.h
-*/
-
-inline CharString sequenceName(FaiIndex const & index, unsigned refId)
+inline CharString const & sequenceName(FaiIndex const & index, unsigned rID)
 {
-    return index.indexEntryStore[refId].name;
+    return index.indexEntryStore[rID].name;
 }
 
 // ----------------------------------------------------------------------------
@@ -337,18 +284,6 @@ inline CharString sequenceName(FaiIndex const & index, unsigned refId)
  * @return __uint64 The number of sequences in the index.
  */
 
-/**
-.Function.FaiIndex#numSeqs
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:numSeqs(faiIndex)
-..summary:Return number of sequences known to an @Class.FaiIndex@.
-..param.faiIndex:The @Class.FaiIndex@ to query.
-...type:Class.FaiIndex
-..return:$__uint64$ with the number of sequences.
-..include:seqan/seq_io.h
-*/
-
 inline __uint64 numSeqs(FaiIndex const & index)
 {
     return length(index.indexEntryStore);
@@ -359,108 +294,104 @@ inline __uint64 numSeqs(FaiIndex const & index)
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn FaiIndex#readRegion.
+ * @fn FaiIndex#readRegion
+ * @brief Read a region through an FaiIndex.
  *
- * @signature int readRegion(str, faiIndex, refId, beginPos, endPos);
- * @signature int readRegion(str, faiIndex, region);
+ * @signature void readRegion(str, faiIndex, rID, beginPos, endPos);
+ * @signature void readRegion(str, faiIndex, region);
  *
  * @param[out] str      The @link String @endlink to read the sequence into.
  * @param[in]  faiIndex The FaiIndex to read from.
- * @param[in]  refId    The id of the reference to read.  Type: unsigned.
- * @param[in]  beginPos The begin position of the region to read.  Type: unsigned.
- * @param[in]  endPos   The end position of the region to read.  Type: unsigned.
+ * @param[in]  rID    The id of the sequence to read (Type: <tt>unsigned).
+ * @param[in]  beginPos The begin position of the region to read (Type: <tt>unsigned).
+ * @param[in]  endPos   The end position of the region to read  (Type: <tt>unsigned).
  * @param[in]  region   The @link GenomicRegion @endlink to read.
  */
 
-/**
-.Function.FaiIndex#readRegion
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:readRegion(str, faiIndex, refId, beginPos, endPos)
-..signature:readRegion(str, faiIndex, region);
-..summary:Load the infix of a sequence from a @Class.FaiIndex@.
-..description:The given region is loaded from the indexed FASTA file.
-..param.str:The sequence infix is written into this string.
-...type:Class.String
-..param.faiIndex:The @Class.FaiIndex@ to query.
-...type:Class.FaiIndex
-..param.refId:The index of the reference in the file.
-...type:nolink:$unsigned$
-..param.beginPos:The begin position of the infix to write to $str$.
-...type:nolink:$unsigned$
-..param.endPos:The end position of the infix to write to $str$.
-...type:nolink:$unsigned$
-..param.region:The @Class.GenomicRegion@ to read.
-...type:Class.GenomicRegion
-..return:Status code $int$, $0$ indicating success and $1$ an error.
-..include:seqan/seq_io.h
-*/
-
-template <typename TValue, typename TSpec>
-inline int readRegion(String<TValue, TSpec> & str,
-                      FaiIndex const & index,
-                      unsigned refId,
-                      unsigned beginPos,
-                      unsigned endPos)
+template <typename TValue, typename TSpec, typename TSeqId, typename TBeginPos, typename TEndPos>
+inline void readRegion(String<TValue, TSpec> & str,
+                       FaiIndex const & index,
+                       TSeqId rID,
+                       TBeginPos beginPos,
+                       TEndPos endPos)
 {
-    // Limit region to the infix, make sure that beginPos < endPos, compute character to read.
-    unsigned seqLen = index.indexEntryStore[refId].sequenceLength;;
-    beginPos = std::min(beginPos, seqLen);
-    endPos = std::min(std::max(beginPos, endPos), seqLen);
-    unsigned toRead = endPos - beginPos;
-
-    typedef typename Iterator<String<char, MMap<> > const, Standard>::Type TSourceIter;
-    typedef typename Iterator<String<TValue, TSpec>, Standard>::Type TTargetIter;
-    TSourceIter itSource = begin(index.mmapString, Standard());
-    __uint64 offset = index.indexEntryStore[refId].offset;
-    // First, compute offset of the completely filled lines.
-    unsigned numLines = beginPos / index.indexEntryStore[refId].lineLength;
-    unsigned numBytes = numLines * index.indexEntryStore[refId].overallLineLength;
-    // Then, compute overall offset by adding remaining bytes, too.
-    numBytes += beginPos % index.indexEntryStore[refId].lineLength;
-    offset += numBytes;
-    // Advance iterator in MMap file.
-    itSource += offset;
-
-    // Copy out the characters from FASTA file and convert via iterator assignment to target string's type.
-    resize(str, toRead, TValue());
-    TTargetIter itTarget = begin(str, Standard());
-    for (unsigned i = 0; i < toRead; )
-    {
-        if (isspace(*itSource))
-        {
-            ++itSource;
-            continue;  // Skip spaces.
-        }
-        *itTarget = *itSource;
-        ++itTarget;
-        ++itSource;
-        ++i;
-    }
+    FaiIndexEntry_ const & entry = index.indexEntryStore[rID];
 
-    return 0;
+    // Limit region to the infix, make sure that beginPos < endPos, compute character to read.
+    TEndPos seqLen = entry.sequenceLength;;
+    beginPos = std::min((TEndPos)beginPos, seqLen);
+    endPos = std::min(std::max((TEndPos)beginPos, endPos), seqLen);
+    TEndPos toRead = endPos - beginPos;
+    
+    clear(str);
+    if (toRead == 0)
+        return;
+
+    // seek to start position
+    DirectionIterator<std::ifstream, Input>::Type reader = directionIterator(index.file, Input());
+    setPosition(
+        reader,
+        index.indexEntryStore[rID].offset +
+        (beginPos / entry.lineLength) * entry.overallLineLength);
+
+    // set up countdowns
+    CountDownFunctor<NotFunctor<IsWhitespace> > countDownIgnore(beginPos % entry.lineLength);
+    CountDownFunctor<NotFunctor<IsWhitespace> > countDownData(toRead);
+    IsWhitespace ignWhiteSpace;
+
+    // read characters
+    skipUntil(reader, countDownIgnore);
+    readUntil(str, reader, countDownData, ignWhiteSpace);
+    if (!countDownData)
+        SEQAN_THROW(UnexpectedEnd());
+//
+//
+//    typedef typename Iterator<String<char, MMap<> > const, Standard>::Type TSourceIter;
+//    typedef typename Iterator<String<TValue, TSpec>, Standard>::Type TTargetIter;
+//    TSourceIter itSource = begin(index.mmapString, Standard());
+//    __uint64 offset = index.indexEntryStore[rID].offset;
+//    // First, compute offset of the completely filled lines.
+//    unsigned numLines = beginPos / index.indexEntryStore[rID].lineLength;
+//    unsigned numBytes = numLines * index.indexEntryStore[rID].overallLineLength;
+//    // Then, compute overall offset by adding remaining bytes, too.
+//    numBytes += beginPos % index.indexEntryStore[rID].lineLength;
+//    offset += numBytes;
+//    // Advance iterator in MMap file.
+//    itSource += offset;
+//
+//    // Copy out the characters from FASTA file and convert via iterator assignment to target string's type.
+//    resize(str, toRead, TValue());
+//    TTargetIter itTarget = begin(str, Standard());
+//    for (TEndPos i = 0; i < toRead; )
+//    {
+//        if (isspace(*itSource))
+//        {
+//            ++itSource;
+//            continue;  // Skip spaces.
+//        }
+//        *itTarget = *itSource;
+//        ++itTarget;
+//        ++itSource;
+//        ++i;
+//    }
+//
+//    return true;
 }
 
 template <typename TValue, typename TSpec>
-inline int readRegion(String<TValue, TSpec> & str,
-                      FaiIndex const & index,
-                      GenomicRegion const & region)
+inline bool readRegion(String<TValue, TSpec> & str,
+                       FaiIndex const & index,
+                       GenomicRegion const & region)
 {
-    int seqId = region.seqId;
-    if (seqId == -1)
-    {
-        unsigned x = 0;
-        if (!getIdByName(index, region.seqName, x))
-            return 1;  // Sequence with this name could not be found.
-        seqId = x;
-    }
-    int beginPos = region.beginPos;
-    if (beginPos == -1)
-        beginPos = 0;
-    int endPos = region.endPos;
-    if (endPos == -1)
-        endPos = sequenceLength(index, seqId);
-    return readRegion(str, index, seqId, beginPos, endPos);
+    int rID = region.rID;
+    if (rID == GenomicRegion::INVALID_ID)
+        if (!getIdByName(rID, index, region.seqName))
+            return false;  // Sequence with this name could not be found.
+
+    int beginPos = (region.beginPos != GenomicRegion::INVALID_POS)? region.beginPos : 0;
+    int endPos = (region.endPos != GenomicRegion::INVALID_POS)? region.endPos : sequenceLength(index, rID);
+    readRegion(str, index, rID, beginPos, endPos);
+    return true;
 }
 
 // ----------------------------------------------------------------------------
@@ -471,218 +402,139 @@ inline int readRegion(String<TValue, TSpec> & str,
  * @fn FaiIndex#readSequence
  * @brief Load a whole sequence from a FaiIndex.
  *
- * @signature int readSequence(str, faiIndex, refId);
+ * @signature void readSequence(str, faiIndex, rID);
  *
  * @param[out] str      The @link String @endlink to read into.
  * @param[in]  faiIndex The FaiIndex to read from.
- * @param[in]  refID    The index of the sequence in the file.
- *
- * @return int 0 on success, non-0 on errors.
+ * @param[in]  seqID    The index of the sequence in the file.
  */
 
-/**
-.Function.FaiIndex#readSequence
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:readSequence(str, faiIndex, refId)
-..summary:Load a whole sequence from an @Class.FaiIndex@.
-..param.str:The sequence is written into this string.
-...type:Class.String
-..param.faiIndex:The @Class.FaiIndex@ to use.
-...type:Class.FaiIndex
-..param.refId:The index of the reference in the file.
-...type:nolink:$unsigned$
-..return:Status code $int$, $0$ indicating success and $1$ an error.
-..include:seqan/seq_io.h
-*/
-
 template <typename TValue, typename TSpec>
-inline int readSequence(String<TValue, TSpec> & str, FaiIndex const & index, unsigned refId)
+inline void readSequence(String<TValue, TSpec> & str, FaiIndex const & index, unsigned rID)
 {
-    if (refId > numSeqs(index))
-        return 1;  // Out of bounds.
-
-    return readRegion(str, index, refId, 0, sequenceLength(index, refId));
+    readRegion(str, index, rID, 0u, sequenceLength(index, rID));
 }
 
 // ----------------------------------------------------------------------------
-// Function read()
+// Function readRecord()
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn FaiIndex#read
- * @summary Read a FAI index from file.
+ * @fn FaiIndex#readRecord
+ * @brief Read a FAI index from file.
  *
- * @signature int read(faiIndex, fastaFileName[, faiFileName]);
+ * @signature void readRecord(faiIndex, fastaFileName[, faiFileName]);
  *
  * @param[out] faiIndex      The FaiIndex to read into.
  * @param[in]  fastaFileName Path to the FASTA file to read.  Type: <tt>char const *</tt>.
  * @param[in]  faiFileName   Path to the FAI file to read.  Type: <tt>char const *</tt>.  Defaults to
  *                           <tt>"${fastaFileName}.fai"</tt>.
- *
- * @return int 0 on success, non-0 on errors.
  */
 
-/**
-.Function.FaiIndex#read
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:read(faiIndex, fastaFileName[, faiFileName])
-..summary:Read a FAI index.
-..param.faiIndex:The @Class.FaiIndex@ object to read the file into.
-...type:Class.FaiIndex
-..param.fastaFileName:The name of the FASTA file to read.
-...type:nolink:$char const *$
-..param.faiFileName:The name of the FAI file to read.
-...default:$fastaFileName + ".fai"$.
-...type:nolink:$char const *$
-..return:Status code $int$, $0$ indicating success and $1$ an error.
-..include:seqan/seq_io.h
-*/
-
-inline int read(FaiIndex & index, char const * fastaFilename, char const * faiFilename)
+template <typename TFwdIterator>
+inline void
+readRecord(FaiIndexEntry_ & entry, TFwdIterator & reader, CharString & buffer)
 {
-    clear(index);  // Also clears filename, thus backup above and restore below.
-    index.fastaFilename = fastaFilename;
-    index.faiFilename = faiFilename;
-
-    if (index.mmapStringOpen)
-        close(index.mmapString);
-    if (!open(index.mmapString, toCString(fastaFilename), OPEN_RDONLY))
-        return 1;  // Could not open file.
-    index.mmapStringOpen = true;
+    clear(entry);
 
-    // Open file.
-    std::ifstream faiStream(toCString(index.faiFilename), std::ios::binary | std::ios::in);
-    if (!faiStream.good())
-        return 1;
+    // Read REF_NAME.
+    readUntil(entry.name, reader, IsTab());
 
-    // Read FAI file.
-    RecordReader<std::ifstream, SinglePass<> > reader(faiStream);
-    CharString buffer;
-    while (!atEnd(reader))
-    {
-        FaiIndexEntry_ entry;
+    skipOne(reader, IsTab());   // Must have been on tab
 
-        // Read REF_NAME.
-        if (readUntilTabOrLineBreak(entry.name, reader) != 0)
-            return 1;
+    // Read SEQ_LENGTH.
+    clear(buffer);
+    readUntil(buffer, reader, IsTab());
+    lexicalCast(entry.sequenceLength, buffer);
 
-        appendValue(index.refNameStore, entry.name);
-        if (atEnd(reader) || value(reader) != '\t')
-            return 1;  // Must be on tab.
+    skipOne(reader, IsTab());   // Must have been on tab
 
-        skipChar(reader, '\t');  // Must have been on tab, no checking.
+    // Read OFFSET.
+    clear(buffer);
+    readUntil(buffer, reader, IsTab());
+    lexicalCast(entry.offset, buffer);
 
-        // Read SEQ_LENGTH.
-        clear(buffer);
-        if (readUntilTabOrLineBreak(buffer, reader) != 0)
-            return 1;
+    skipOne(reader, IsTab());   // Must have been on tab
 
-        if (!lexicalCast2(entry.sequenceLength, buffer))
-            return 1;  // Could not cast to integer.
+    // Read LINE_LENGTH.
+    clear(buffer);
+    readUntil(buffer, reader, IsTab());
+    lexicalCast(entry.lineLength, buffer);
 
-        if (atEnd(reader) || value(reader) != '\t')
-            return 1;  // Must be on tab.
+    skipOne(reader, IsTab());   // Must have been on tab
 
-        skipChar(reader, '\t');  // Must have been on tab, no checking.
+    // Read OVERALL_LINE_LENGTH.
+    clear(buffer);
+    readUntil(buffer, reader, OrFunctor<IsTab, IsNewline>());
+    lexicalCast(entry.overallLineLength, buffer);
 
-        // Read OFFSET.
-        clear(buffer);
-        if (readUntilTabOrLineBreak(buffer, reader) != 0)
-            return 1;
-
-        if (!lexicalCast2(entry.offset, buffer))
-            return 1;  // Could not cast to integer.
-
-        if (atEnd(reader) || value(reader) != '\t')
-            return 1;  // Must be on tab.
-
-        skipChar(reader, '\t');  // Must have been on tab, no checking.
-
-        // Read LINE_LENGTH.
-        clear(buffer);
-        if (readUntilTabOrLineBreak(buffer, reader) != 0)
-            return 1;
-
-        if (!lexicalCast2(entry.lineLength, buffer))
-            return 1;  // Could not cast to integer.
-
-        if (atEnd(reader) || value(reader) != '\t')
-            return 1;  // Must be on tab.
+    skipLine(reader);           // Skip over line ending.
+}
 
-        skipChar(reader, '\t');  // Must have been on tab, no checking.
+// ---------------------------------------------------------------------------
+// Function open()
+// ---------------------------------------------------------------------------
 
-        // Read OVERALL_LINE_LENGTH.
-        clear(buffer);
-        if (readUntilTabOrLineBreak(buffer, reader) != 0)
-            return 1;
+/*!
+ * @fn FaiIndex#open
+ * @brief Open a FaiIndex object.
+ *
+ * @signature bool open(faiIndex, fastaFilename [, faiFileName]);
+ *
+ * @param[in] faiIndex      The FaiIndex to write out.
+ * @param[in] fastaFilename Path to the FASTA file to build an index for.  Type: <tt>char const *</tt>.
+ * @param[in] faiFileName   The name of the FAI file to open.  This parameter is optional.  By default, the FAI
+ *                          file name is derived from the FASTA file name.  Type: <tt>char const *</tt>.
+ *
+ * @return bool <tt>true</tt> on success, <tt>false</tt> otherwise.
+ */
 
-        if (!lexicalCast2(entry.overallLineLength, buffer))
-            return 1;  // Could not cast to integer.
+inline bool open(FaiIndex & index, char const * fastaFilename, char const * faiFilename)
+{
+    clear(index);  // Also clears filename, thus backup above and restore below.
+    index.fastaFilename = fastaFilename;
+    index.faiFilename = faiFilename;
 
-        if (!atEnd(reader) && value(reader) != '\r' && value(reader) != '\n')
-            return 1;  // Must be on end of line or file.
+    if (!open(index.file, toCString(fastaFilename), OPEN_RDONLY))
+        return false;  // Could not open file.
 
-        if (!atEnd(reader))
-            skipLine(reader);  // Skip over line ending.
+    // Open file.
+    std::ifstream faiStream(toCString(index.faiFilename));
+    if (!faiStream.good())
+        return false;  // problem opening
+    DirectionIterator<std::ifstream, Input>::Type reader = directionIterator(faiStream, Input());
 
+    // Read FAI file.
+    CharString buffer;
+    FaiIndexEntry_ entry;
+    while (!atEnd(reader))
+    {
+        readRecord(entry, reader, buffer);
+        appendValue(index.seqNameStore, entry.name);
         appendValue(index.indexEntryStore, entry);
     }
 
-    // Refresh name store cache.
-    refresh(index.refNameStoreCache);
-
-    return 0;
-}
-
-// TODO(holtgrew): The wrappers can go when the clash from read() from the file module is gone.
-
-inline int read(FaiIndex & index, char * fastaFilename, char const * faiFilename)
-{
-    return read(index, static_cast<char const *>(fastaFilename), faiFilename);
-}
-
-inline int read(FaiIndex & index, char const * fastaFilename, char * faiFilename)
-{
-    return read(index, fastaFilename, static_cast<char const *>(faiFilename));
-}
-
-inline int read(FaiIndex & index, char * fastaFilename, char * faiFilename)
-{
-    return read(index, static_cast<char const *>(fastaFilename), static_cast<char const *>(faiFilename));
+    // Recreate name store cache.
+    refresh(index.seqNameStoreCache);
+    return true;
 }
 
-inline int read(FaiIndex & index, char const * fastaFilename)
+inline bool open(FaiIndex & index, char const * fastaFilename)
 {
-    char buffer[1000];
-    snprintf(buffer, 999, "%s.fai", toCString(fastaFilename));
-    return read(index, fastaFilename, &buffer[0]);
-}
-
-inline int read(FaiIndex & index, char * fastaFilename)
-{
-    return read(index, static_cast<char const *>(fastaFilename));
-}
-
-inline int read(FaiIndex & index)
-{
-    // Cannot read if FAI filename is empty.
-    if (empty(index.faiFilename))
-        return 1;
-
-    return read(index, toCString(index.fastaFilename), toCString(index.faiFilename));
+    std::string faiFilename = fastaFilename;
+    faiFilename += ".fai";
+    return open(index, fastaFilename, toCString(faiFilename));
 }
 
 // ---------------------------------------------------------------------------
-// Function write()
+// Function save()
 // ---------------------------------------------------------------------------
 
 /*!
- * @fn FaiIndex#write
- * @brief Write out an FaiIndex object.
+ * @fn FaiIndex#save
+ * @brief Save a FaiIndex object.
  *
- * @signature int write(faiIndex[, faiFileName]);
+ * @signature bool save(faiIndex[, faiFileName]);
  *
  * @param[in] faiIndex    The FaiIndex to write out.
  * @param[in] faiFileName The name of the FAI file to write to.  This parameter is optional only if the FAI index knows
@@ -690,67 +542,95 @@ inline int read(FaiIndex & index)
  *                        file name from the previous call to @link FaiIndex#build @endlink is used.  Type: <tt>char
  *                        const *</tt>.
  *
- * @return int 0 on success, 1 on errors.
+ * @return bool <tt>true</tt> on success, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.FaiIndex#write
-..cat:Input/Output
-..class:Class.FaiIndex
-..signature:write(faiIndex[, faiFileName])
-..summary:Write out an @Class.FaiIndex@ object.
-..param.faiIndex:The @Class.FaiIndex@ object to write out.
-...type:Class.FaiIndex
-..param.faiFileName:The name of the FAI file to write to.
-...remarks:This is optional only if the FAI index knows the FAI file name from a previous @Function.FaiIndex#build@ call.
-...default:The FAI file name from the previous call to @Function.FaiIndex#build@, if any.
-...type:nolink:$char const *$
-..return:Status code $int$, $0$ indicating success and $1$ an error.
-..include:seqan/seq_io.h
-*/
-
-// TODO(holtgrew): The wrappers can go when the clash from read() from the file module is gone.
-
-inline int write(FaiIndex const & index, char const * faiFilename)
+inline bool save(FaiIndex const & index, char const * faiFilename)
 {
     // Open index files.
-    std::ofstream indexOut(faiFilename, std::ios::binary | std::ios::out);
+    std::ofstream file(faiFilename);
+    if (!file.good())
+        return false;
 
+    file.exceptions(std::ios_base::badbit);
     for (unsigned i = 0; i < length(index.indexEntryStore); ++i)
     {
         FaiIndexEntry_ const & entry = index.indexEntryStore[i];
-        indexOut << entry.name << '\t' << entry.sequenceLength << '\t' << entry.offset << '\t'
-                 << entry.lineLength << '\t' << entry.overallLineLength << '\n';
+        file << entry.name << '\t' << entry.sequenceLength << '\t' << entry.offset << '\t'
+             << entry.lineLength << '\t' << entry.overallLineLength << '\n';
     }
-
-    return !indexOut.good();  // 1 on errors, 0 on success.
+    return true;
 }
 
-inline int write(FaiIndex const & index, char * faiFilename)
+inline bool save(FaiIndex const & index)
 {
-    return write(index, static_cast<char const *>(faiFilename));
+    if (empty(index.faiFilename))
+        return false;  // Cannot write out if faiFilename member is empty.
+    return save(index, toCString(index.faiFilename));
 }
 
-inline int write(FaiIndex & index, char const * faiFilename)
-{
-    return write(static_cast<FaiIndex const &>(index), faiFilename);
-}
+// ----------------------------------------------------------------------------
+// Function getRecordInfo(Fastq);
+// ----------------------------------------------------------------------------
 
-inline int write(FaiIndex & index, char * faiFilename)
+template <typename TFwdIterator>
+inline void getRecordInfo(FaiIndexEntry_ & entry, TFwdIterator & iter, Fasta)
 {
-    return write(static_cast<FaiIndex const &>(index), static_cast<char const *>(faiFilename));
-}
+    typedef EqualsChar<'>'> TFastaBegin;
 
-inline int write(FaiIndex const & index)
-{
-    if (empty(index.faiFilename))
-        return 1;  // Cannot write out if faiFilename member is empty.
-    return write(index, toCString(index.faiFilename));
-}
+    clear(entry);
 
-inline int write(FaiIndex & index)
-{
-    return write(static_cast<FaiIndex const &>(index));
+    skipUntil(iter, TFastaBegin());     // forward to the next '>'
+    skipOne(iter);                      // skip '>'
+
+    readUntil(entry.name, iter, IsWhitespace());    // read Fasta id (up to first whitespace)
+    skipLine(iter);
+    entry.offset = position(iter);      // store offset
+
+    FaiIndexEntry_ temp;
+    FaiIndexEntry_ *entryPtr = &entry;
+    FaiIndexEntry_ *cmpPtr = &entry;
+
+    OrFunctor<IsNewline, OrFunctor<
+                            CountFunctor<True>,                             // 1st count functor counts bytes
+                            CountFunctor<NotFunctor<IsWhitespace> >         // 2nd count functor counts non-whitespaces
+                         > > countCharsPerLine;
+    
+    while (!atEnd(iter) && !TFastaBegin()(value(iter)))
+    {
+        // check for consistency
+        if (cmpPtr->lineLength != entry.lineLength ||
+            cmpPtr->overallLineLength != entry.overallLineLength)
+        {
+            SEQAN_THROW(ParseError("FastaIndex: Record has inconsistent line lengths or line endings"));
+        }
+
+        clear(countCharsPerLine.func2.func1);
+        clear(countCharsPerLine.func2.func2);
+
+        // skip to the end of line and count non-whitespace characters
+        skipUntil(iter, countCharsPerLine);
+        entry.sequenceLength += value(countCharsPerLine.func2.func2);
+
+        // determine line length in bases and bytes
+        entryPtr->lineLength = value(countCharsPerLine.func2.func2);
+        entryPtr->overallLineLength = value(countCharsPerLine.func2.func1);
+
+        // skip linebreak and count consumed bytes
+        if (!atEnd(iter) && *iter == '\r')
+        {
+            ++iter;
+            entryPtr->overallLineLength++;
+        }
+        if (!atEnd(iter) && *iter == '\n')
+        {
+            ++iter;
+            entryPtr->overallLineLength++;
+        }
+
+        cmpPtr = entryPtr;
+        entryPtr = &temp;
+    }
 }
 
 // ---------------------------------------------------------------------------
@@ -761,117 +641,47 @@ inline int write(FaiIndex & index)
  * @fn FaiIndex#build
  * @brief Create a FaiIndex from FASTA file.
  *
- * @signature int build(faiIndex, seqFileName[, faiFileName]);
+ * @signature bool build(faiIndex, fastaFilename[, faiFileName]);
  *
- * @param[out] faiIndex    The FaiIndex to build into.
- * @param[in]  seqFileName Path to the FASTA file to build an index for.  Type: <tt>char const *</tt>.
- * @param[in]  faiFileName Path to the FAI file to use as the index file.  Type: <tt>char const *</tt>.
- *                         Default: <tt>"${seqFileName}.fai"</tt>.
+ * @param[out] faiIndex      The FaiIndex to build into.
+ * @param[in]  fastaFilename Path to the FASTA file to build an index for.  Type: <tt>char const *</tt>.
+ * @param[in]  faiFileName   Path to the FAI file to use as the index file.  Type: <tt>char const *</tt>.
+ *                           Default: <tt>"${fastaFilename}.fai"</tt>.
  *
- * @return 0 on success, non-0 on errors.
+ * @return bool <tt>true</tt> on success, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.FaiIndex#build
-..class:Class.FaiIndex
-..summary:Create @Class.FaiIndex@ from FASTA file.
-..signature:build(faiIndex, fastaFilename[, faiFilename])
-..description:The index can later be written out with @Function.FaiIndex#write@ and be loaded again using @Function.FaiIndex#read@.
-..param.faiIndex:@Class.FaiIndex@ to write index to.
-...type:Class.FaiIndex
-..param.fastaFilename:Name of FASTA file to build an index for.
-...type:Shortcut.CharString
-..param.faiFilename:Name of FAI index file, stored in $faiIndex$. Optional.
-...default:$fastaFilename + ".fai"$
-...type:nolink:$char const *$
-..returns:$int$, equal to 0 on success, != 0 otherwise.
-..include:seqan/stream.h
- */
-
-inline int build(FaiIndex & index, char const * seqFilename, char const * faiFilename)
+inline bool build(FaiIndex & index, char const * fastaFilename, char const * faiFilename)
 {
-    index.fastaFilename = seqFilename;
+    index.fastaFilename = fastaFilename;
     index.faiFilename = faiFilename;
-    
-    if (index.mmapStringOpen)
-        close(index.mmapString);
-    if (!open(index.mmapString, toCString(seqFilename), OPEN_RDONLY))
-        return 1;  // Could not open file.
-    index.mmapStringOpen = true;
-
-    typedef String<char, MMap<> > TMMapString;
-    RecordReader<TMMapString, SinglePass<StringReader> > reader(index.mmapString);
-    // Get file format, must be FASTA for FAI.
-    AutoSeqStreamFormat tagSelector;
-    if (!guessStreamFormat(reader, tagSelector))
-        return 1;  // Invalid format.
-
-    if (!isEqual(tagSelector, seqan::Fasta()))
-        return 1;  // Invalid format, not FASTA.
-
-    // Re-using the FASTA/FASTQ parsing code from read_fasta_fastq is not really feasible here.  We roll our own
-    // mini-parser from scratch.
-    CharString line;
-    CharString seqName;
-    __uint32 seqLength = 0;
-    __uint64 seqOffset = 0;
-    __uint32 lineLength = 0;
-    __uint32 lineSize = 0;
-    while (!atEnd(reader))
-    {
-        clear(line);
-        clear(seqName);
-
-        if (value(reader) != '>')
-            return 1;  // Must be >.
 
-        goNext(reader);
+    if (!open(index.file, toCString(fastaFilename), OPEN_RDONLY))
+        return false;  // Could not open file.
 
-        int res = readUntilWhitespace(seqName, reader);
-        if (res != 0)
-            return res;  // Error reading.
+    DirectionIterator<std::ifstream, Input>::Type iter = directionIterator(index.file, Input());
 
-        res = skipLine(reader);
-        if (res != 0)
-            return res;  // Error reading.
-
-        seqOffset = reader._current - begin(reader._string, Standard());
-
-        res = readLine(line, reader);
-        if (res != 0 && res != EOF_BEFORE_SUCCESS)
-            return res;  // Error reading.
-
-        lineSize = reader._current - begin(reader._string, Standard()) - seqOffset;
-        lineLength = length(line);
-        seqLength = lineLength;
-
-        while (!atEnd(reader))
-        {
-            char c = value(reader);
-            if (c == '>')
-                break;
-            if (!isspace(c))
-                seqLength += 1;
-            goNext(reader);
-        }
+    // Clear everything.
+    clear(index.seqNameStore);
+    clear(index.seqNameStoreCache);
+    clear(index.indexEntryStore);
 
-        FaiIndexEntry_ entry;
-        entry.name = seqName;
-        entry.sequenceLength = seqLength;
-        entry.offset = seqOffset;
-        entry.lineLength = lineLength;
-        entry.overallLineLength = lineSize;
+    // Create FastaIndex
+    FaiIndexEntry_ entry;
+    while (!atEnd(iter))
+    {
+        getRecordInfo(entry, iter, Fasta());
+        appendValue(index.seqNameStore, entry.name);
         appendValue(index.indexEntryStore, entry);
-        appendValue(index.refNameStore, entry.name);
     }
 
-    // Refresh name store cache.
-    refresh(index.refNameStoreCache);
+    // Recreate name store cache.
+    refresh(index.seqNameStoreCache);
 
-    return 0;
+    return true;
 }
 
-inline int build(FaiIndex & index, char const * seqFilename)
+inline bool build(FaiIndex & index, char const * seqFilename)
 {
     CharString faiFilename(seqFilename);
     append(faiFilename, ".fai");
@@ -880,4 +690,4 @@ inline int build(FaiIndex & index, char const * seqFilename)
 
 }  // namespace seqan
 
-#endif  // #ifndef SEQAN_CORE_APPS_RABEMA_FAI_INDEX_H_
+#endif  // #ifndef SEQAN_APPS_RABEMA_FAI_INDEX_H_
diff --git a/seqan/seq_io/fasta_fastq.h b/seqan/seq_io/fasta_fastq.h
new file mode 100644
index 0000000..47f4432
--- /dev/null
+++ b/seqan/seq_io/fasta_fastq.h
@@ -0,0 +1,572 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Input/Output on FASTA and FASTQ files.
+// ==========================================================================
+
+#ifndef SEQAN_SEQ_IO_FASTA_FASTQ_H_
+#define SEQAN_SEQ_IO_FASTA_FASTQ_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Tag Fasta
+// --------------------------------------------------------------------------
+
+struct TagFasta_;
+typedef Tag<TagFasta_> Fasta;
+
+// --------------------------------------------------------------------------
+// Tag Fastq
+// --------------------------------------------------------------------------
+
+struct TagFastq_;
+typedef Tag<TagFastq_> Fastq;
+
+// --------------------------------------------------------------------------
+// Tag Raw
+// --------------------------------------------------------------------------
+
+struct Raw_;
+typedef Tag<Raw_> Raw;
+
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction MagicHeader
+// --------------------------------------------------------------------------
+
+// TODO(weese:) The following defines makes the old guessFormat functions in file_format_mmap.h obsolete. Disable them!
+template <typename T>
+struct MagicHeader<Fasta, T>
+{
+    static char const VALUE[1];
+};
+template <typename T>
+char const MagicHeader<Fasta, T>::VALUE[1] = { '>' };  // Fasta's first character
+
+
+template <typename T>
+struct MagicHeader<Fastq, T>
+{
+    static char const VALUE[1];
+};
+template <typename T>
+char const MagicHeader<Fastq, T>::VALUE[1] = { '@' };  // Fastq's first character
+
+
+template <typename T>
+struct MagicHeader<Raw, T> :
+    MagicHeader<Nothing, T> {};
+
+// --------------------------------------------------------------------------
+// Metafunction FileExtensions
+// --------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<Fasta, T>
+{
+    static char const * VALUE[6];
+};
+template <typename T>
+char const * FileExtensions<Fasta, T>::VALUE[6] =
+{
+    ".fa",      // default output extension
+    ".fasta",
+    ".faa",     // FASTA Amino Acid file
+    ".ffn",     // FASTA nucleotide coding regions file
+    ".fna",     // FASTA Nucleic Acid file
+    ".frn"
+};
+
+
+template <typename T>
+struct FileExtensions<Fastq, T>
+{
+    static char const * VALUE[2];
+};
+template <typename T>
+char const * FileExtensions<Fastq, T>::VALUE[2] =
+{
+    ".fq",      // default output extension
+    ".fastq"
+};
+
+
+template <typename T>
+struct FileExtensions<Raw, T>
+{
+    static char const * VALUE[1];
+};
+template <typename T>
+char const * FileExtensions<Raw, T>::VALUE[1] =
+{
+    ".raw"      // default output extension
+};
+
+// ----------------------------------------------------------------------------
+// Class FastaIgnoreFunctor_
+// ----------------------------------------------------------------------------
+
+template <typename TAlphabet>
+struct FastaIgnoreFunctor_
+{
+    typedef typename If< Or< IsSameType<TAlphabet, char>,
+                         Or< IsSameType<TAlphabet, signed char>,
+                             IsSameType<TAlphabet, unsigned char> > >,
+                         IsNewline,                     // ignore only newline if the target alphabet is a char
+                         IsWhitespace                   // ignore whitespace as well for all other alphabets
+                     >::Type Type;
+};
+
+template <typename TAlphabet>
+struct FastaIgnoreOrAssertFunctor_
+{
+    typedef typename FastaIgnoreFunctor_<TAlphabet>::Type               TIgnore;
+    typedef AssertFunctor<IsInAlphabet<TAlphabet>, ParseError, Fasta>   TAsserter;
+
+    typedef typename If< Or< IsSameType<TAlphabet, char>,
+                         Or< IsSameType<TAlphabet, signed char>,
+                             IsSameType<TAlphabet, unsigned char> > >,
+                         TIgnore,                       // don't assert in case of char alphabets
+                         OrFunctor<TIgnore, TAsserter>  // assert being part of the alphabet for other alphabets
+                     >::Type Type;
+};
+
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class SequenceOutputOptions
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class SequenceOutputOptions
+ * @headerfile <seqan/seq_io.h>
+ * @signature struct SequenceOutputOptions
+ * @brief Configuration for writing sequence (FASTA/FASTQ) files.
+ *
+ * This struct is used for the configuration of writing out FASTA and FASTQ files.
+ *
+ * @var int SequenceOutputOptions::lineLength;
+ * @brief Length of the lines when writing out.
+ *
+ * Set to <tt>-1</tt> for default behaviour (no line break for FASTQ, line length of 70 for FASTA) and <tt>0</tt> for
+ * disabling line breaks.
+ *
+ * @var bool SequenceOutputOptions::qualMeta;
+ * @brief Whether or not to write the meta information into the <tt>"+"</tt> line before the qualities (interpreted for
+ *        FASTQ only). Default is <tt>false</tt>.
+ */
+
+// TODO(holtgrew): Would it be worth having two/three shortcuts for "short reads" and "genomic sequence" and faster or can the compiler optimize the creation away?
+
+struct SequenceOutputOptions
+{
+    int lineLength;
+    bool qualMeta;
+
+    explicit
+    SequenceOutputOptions(int lineLength = -1, bool qualMeta = false) :
+        lineLength(lineLength),
+        qualMeta(qualMeta)
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class QualityExtractor
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+struct QualityExtractor : public std::unary_function<TValue, char>
+{
+    inline char operator()(TValue const & x) const
+    {
+        return '!' + static_cast<char>(getQualityValue(x));
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord(TagSelector); Qualities inside seq
+// ----------------------------------------------------------------------------
+
+template <typename TIdString, typename TSeqString, typename TFwdIterator>
+inline void
+readRecord(TIdString & /* meta */, TSeqString & /* seq */, TFwdIterator & /* iter */,
+           TagSelector<> const & /* format */)
+{}
+
+template <typename TIdString, typename TSeqString, typename TFwdIterator, typename TTagList>
+inline void
+readRecord(TIdString & meta, TSeqString & seq, TFwdIterator & iter, TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        readRecord(meta, seq, iter, TFormat());
+    else
+        readRecord(meta, seq, iter, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(TagSelector); Qualities inside qual
+// ----------------------------------------------------------------------------
+
+template <typename TIdString, typename TSeqString, typename TQualString, typename TFwdIterator>
+inline void
+readRecord(TIdString & /* meta */, TSeqString & /* seq */, TQualString & /* qual */, TFwdIterator & /* iter */,
+           TagSelector<> const & /* format */)
+{}
+
+template <typename TIdString, typename TSeqString, typename TQualString, typename TFwdIterator, typename TTagList>
+inline void
+readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TFwdIterator & iter, TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        readRecord(meta, seq, qual, iter, TFormat());
+    else
+        readRecord(meta, seq, qual, iter, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(Raw);
+// ----------------------------------------------------------------------------
+
+template <typename TIdString, typename TSeqString, typename TFwdIterator>
+inline void readRecord(TIdString & meta, TSeqString & seq, TFwdIterator & iter, Raw)
+{
+    typedef typename Value<TSeqString>::Type                        TAlphabet;
+    typedef typename FastaIgnoreOrAssertFunctor_<TAlphabet>::Type   TIgnoreOrAssert;
+
+    clear(meta);
+    clear(seq);
+    readUntil(seq, iter, IsNewline(), TIgnoreOrAssert());
+    skipLine(iter);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(Raw);
+// ----------------------------------------------------------------------------
+
+template <typename TIdString, typename TSeqString, typename TQualString, typename TFwdIterator>
+inline void readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TFwdIterator & iter, Raw const & raw)
+{
+    clear(qual);
+    readRecord(meta, seq, iter, raw);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(Fasta); Qualities inside seq
+// ----------------------------------------------------------------------------
+
+template <typename TIdString, typename TSeqString, typename TFwdIterator>
+inline void readRecord(TIdString & meta, TSeqString & seq, TFwdIterator & iter, Fasta)
+{
+    typedef typename Value<TSeqString>::Type                        TAlphabet;
+    typedef typename FastaIgnoreOrAssertFunctor_<TAlphabet>::Type   TIgnoreOrAssert;
+    typedef EqualsChar<'>'>                                         TFastaBegin;
+
+    clear(meta);
+    clear(seq);
+
+    skipUntil(iter, TFastaBegin());     // forward to the next '>'
+    skipOne(iter);                      // assert and skip '>'
+
+    readLine(meta, iter);               // read Fasta id
+    readUntil(seq, iter, TFastaBegin(), TIgnoreOrAssert()); // read Fasta sequence
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(Fasta); Qualities inside qual
+// ----------------------------------------------------------------------------
+
+template <typename TIdString, typename TSeqString, typename TQualString, typename TFwdIterator>
+inline void readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TFwdIterator & iter, Fasta)
+{
+    clear(qual);
+    readRecord(meta, seq, iter, Fasta());
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(Fastq); Qualities inside seq
+// ----------------------------------------------------------------------------
+
+template <typename TIdString, typename TSeqString, typename TFwdIterator>
+inline void readRecord(TIdString & meta, TSeqString & seq, TFwdIterator & iter, Fastq)
+{
+    typedef typename Value<TSeqString>::Type                                TAlphabet;
+    typedef typename FastaIgnoreFunctor_<TAlphabet>::Type                   TIgnore;
+    typedef typename FastaIgnoreOrAssertFunctor_<TAlphabet>::Type           TIgnoreOrAssert;
+    typedef EqualsChar<'@'>                                                 TFastqBegin;
+    typedef EqualsChar<'+'>                                                 TQualsBegin;
+
+    clear(meta);
+    clear(seq);
+
+    skipUntil(iter, TFastqBegin());     // forward to the next '@'
+    skipOne(iter);                      // skip '@'
+
+    readLine(meta, iter);               // read Fastq id
+
+    readUntil(seq, iter, TQualsBegin(), TIgnoreOrAssert());     // read Fastq sequence
+    skipOne(iter, TQualsBegin());       // assert and skip '+'
+    skipLine(iter);                     // skip optional 2nd Fastq id
+
+    // as '@' could be either part of the base-call qualities or mark the
+    // beginning of the next record, we count the number of consumed quality
+    // values instead of (1) reading only 1 line or (2) until the next '@'
+    CountDownFunctor<NotFunctor<TIgnore> > qualCountDown(length(seq));
+
+    if (HasQualities<TAlphabet>::VALUE)
+    {
+        // TODO: Replace this temporary by Modifier
+        CharString qual;
+        TIgnore qualIgnore;
+        readUntil(qual, iter, qualCountDown, qualIgnore);  // read Fastq qualities
+        assignQualities(seq, qual);
+    }
+    else
+    {
+        skipUntil(iter, qualCountDown);                     // skip Fastq qualities
+    }
+    skipUntil(iter, TFastqBegin());                         // forward to the next '@'
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(Fastq); Qualities inside qual
+// ----------------------------------------------------------------------------
+
+template <typename TIdString, typename TSeqString, typename TQualString, typename TFwdIterator>
+inline void readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TFwdIterator & iter, Fastq)
+{
+    typedef typename Value<TSeqString>::Type                                TSeqAlphabet;
+    typedef typename Value<TQualString>::Type                               TQualAlphabet;
+    typedef typename FastaIgnoreOrAssertFunctor_<TSeqAlphabet>::Type        TSeqIgnoreOrAssert;
+    typedef typename FastaIgnoreFunctor_<TQualAlphabet>::Type               TQualIgnore;
+    typedef typename FastaIgnoreOrAssertFunctor_<TQualAlphabet>::Type       TQualIgnoreOrAssert;
+    typedef EqualsChar<'@'>                                                 TFastqBegin;
+    typedef EqualsChar<'+'>                                                 TQualsBegin;
+
+    clear(meta);
+    clear(seq);
+    clear(qual);
+
+    skipUntil(iter, TFastqBegin());     // forward to the next '@'
+    skipOne(iter);                      // skip '@'
+
+    readLine(meta, iter);               // read Fastq id
+
+    readUntil(seq, iter, TQualsBegin(), TSeqIgnoreOrAssert());  // read Fastq sequence
+    skipOne(iter, TQualsBegin());       // assert and skip '+'
+    skipLine(iter);                     // skip optional 2nd Fastq id
+
+    // as '@' could be either part of the base-call qualities or mark the
+    // beginning of the next record, we count the number of consumed quality
+    // values instead of (1) reading only 1 line or (2) until the next '@'
+    CountDownFunctor<NotFunctor<TQualIgnore> > qualCountDown(length(seq));
+    TQualIgnoreOrAssert qualIgnore;
+
+    readUntil(qual, iter, qualCountDown, qualIgnore);  // read Fastq qualities
+    skipUntil(iter, TFastqBegin());     // forward to the next '@'
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(Raw); Qualities inside seq
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator, typename TIdString, typename TSeqString>
+inline void
+writeRecord(TFwdIterator & iter, TIdString const & /* meta */, TSeqString const & seq, Raw const &,
+            SequenceOutputOptions const & = SequenceOutputOptions())
+{
+    write(iter, seq);
+    writeValue(iter, '\n');
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(Raw); Qualities inside qual
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator, typename TIdString, typename TSeqString, typename TQualString>
+inline void
+writeRecord(TFwdIterator & iter, TIdString const & /* meta */, TSeqString const & seq, TQualString const & /* qual */, Raw const &,
+            SequenceOutputOptions const & = SequenceOutputOptions())
+{
+    write(iter, seq);
+    writeValue(iter, '\n');
+}
+
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(Fasta);
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TIdString, typename TSeqString>
+inline void
+writeRecord(TTarget & target,
+            TIdString const & meta,
+            TSeqString const & seq,
+            Fasta const & /*tag*/,
+            SequenceOutputOptions const & options = SequenceOutputOptions())
+{
+    writeValue(target, '>');
+    write(target, meta);
+    writeValue(target, '\n');
+
+    writeWrappedString(target, seq, (options.lineLength < 0)? 70 : options.lineLength); // 70bp wrapping, by default
+}
+
+template <typename TTarget, typename TIdString, typename TSeqString, typename TQualString>
+inline void
+writeRecord(TTarget & target,
+            TIdString const & meta,
+            TSeqString const & seq,
+            TQualString const & /*tag*/,
+            Fasta const & fasta,
+            SequenceOutputOptions const & options = SequenceOutputOptions())
+{
+    writeRecord(target, meta, seq, fasta, options);
+}
+
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(Fastq); Qualities inside qual
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TIdString, typename TSeqString, typename TQualString>
+inline void
+writeRecord(TTarget & target,
+            TIdString const & meta,
+            TSeqString const & seq,
+            TQualString const & qual,
+            Fastq const & /*tag*/,
+            SequenceOutputOptions const & options = SequenceOutputOptions())
+{
+    writeValue(target, '@');
+    write(target, meta);
+    writeValue(target, '\n');
+
+    int lineLength = (options.lineLength < 0)? 0 : options.lineLength;  // no wrapping, by default
+    writeWrappedString(target, seq, lineLength);
+
+    writeValue(target, '+');
+    if (options.qualMeta)
+        write(target, meta);
+    writeValue(target, '\n');
+
+    writeWrappedString(target, qual, lineLength);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(Fastq); Qualities inside seq
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TIdString, typename TSeqString>
+inline void
+writeRecord(TTarget & target,
+            TIdString const & meta,
+            TSeqString const & seq,
+            Fastq const & tag,
+            SequenceOutputOptions const & options = SequenceOutputOptions())
+{
+    typedef QualityExtractor<typename Value<TSeqString>::Type> TQualityExtractor;
+    ModifiedString<TSeqString const, ModView<TQualityExtractor> > quals(seq);
+    writeRecord(target, meta, seq, quals, tag, options);
+}
+
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(TagSelector); Qualities inside seq
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator, typename TIdString, typename TSeqString>
+inline void
+writeRecord(TFwdIterator & /* iter */, TIdString const & /* meta */, TSeqString const & /* seq */,
+            TagSelector<> const & /* format */, SequenceOutputOptions const & /* options */)
+{}
+
+template <typename TFwdIterator, typename TIdString, typename TSeqString, typename TTagList>
+inline void
+writeRecord(TFwdIterator & iter, TIdString const & meta, TSeqString const & seq,
+            TagSelector<TTagList> const & format, SequenceOutputOptions const & options = SequenceOutputOptions())
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        writeRecord(iter, meta, seq, TFormat(), options);
+    else
+        writeRecord(iter, meta, seq, static_cast<typename TagSelector<TTagList>::Base const &>(format), options);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(TagSelector); Qualities inside qual
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator, typename TIdString, typename TSeqString, typename TQualString>
+inline void
+writeRecord(TFwdIterator & /* iter */, TIdString const & /* meta */, TSeqString const & /* seq */, TQualString const & /* qual */,
+            TagSelector<> const & /* format */, SequenceOutputOptions const & /* options */)
+{}
+
+template <typename TFwdIterator, typename TIdString, typename TSeqString, typename TQualString, typename TTagList>
+inline void
+writeRecord(TFwdIterator & iter, TIdString const & meta, TSeqString const & seq, TQualString const & qual,
+            TagSelector<TTagList> const & format, SequenceOutputOptions const & options = SequenceOutputOptions())
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        writeRecord(iter, meta, seq, qual, TFormat(), options);
+    else
+        writeRecord(iter, meta, seq, qual, static_cast<typename TagSelector<TTagList>::Base const &>(format), options);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_SEQ_IO_FASTA_FASTQ_H_
diff --git a/seqan/seq_io/genomic_region.h b/seqan/seq_io/genomic_region.h
index 6dbbbf2..3d02b5b 100644
--- a/seqan/seq_io/genomic_region.h
+++ b/seqan/seq_io/genomic_region.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,13 +30,17 @@
 //
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 // The GenomicRegion class represents a region on one chromosome/contig in a
 // genome, e.g. chr1, chr1:15,000, chr1:100,000-200,000.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEQ_IO_GENOMIC_REGION_H_
-#define CORE_INCLUDE_SEQAN_SEQ_IO_GENOMIC_REGION_H_
+#ifndef INCLUDE_SEQAN_SEQ_IO_GENOMIC_REGION_H_
+#define INCLUDE_SEQAN_SEQ_IO_GENOMIC_REGION_H_
+
+#include <seqan/sequence.h>
+#include <seqan/stream.h>  // for tokenization
 
 namespace seqan {
 
@@ -44,8 +48,8 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
-class GenomicRegion;
-inline bool parse(GenomicRegion & region, CharString const & regionString);
+struct GenomicRegion;
+inline void parse(GenomicRegion & region, CharString const & regionString);
 
 // ============================================================================
 // Tags, Classes, Enums
@@ -59,162 +63,130 @@ inline bool parse(GenomicRegion & region, CharString const & regionString);
  * @class GenomicRegion
  * @headerfile <seqan/seq_io.h>
  * @brief Store information about a genomic region.
- * 
+ *
  * @signature class GenomicRegion;
- * 
+ *
  * A genomic region is a range on a chromosome.  The chromosome is identified by its name (as text in @link
- * GenomicRegion::seqName @endlink, optionally also as an <tt>integer</tt> in @link GenomicRegion::seqId @endlink).  The
+ * GenomicRegion::seqName @endlink, optionally also as an <tt>integer</tt> in @link GenomicRegion::rID @endlink).  The
  * range is stored as a half-open interval [@link GenomicRegion::beginPos @endlink, @link GenomicRegion::endPos @endlink).
  * If @link GenomicRegion::beginPos @endlink is set to <tt>-1</tt> then the range spans the whole chromosome.  If @link
  * GenomicRegion::beginPos @endlink is set to a value <tt>&gt;= 0</tt> and @link GenomicRegion::endPos @endlink is set ot
  * <tt>-1</tt>, then the chromosome is selected from @link GenomicRegion::beginPos @endlink to the end.
- * 
+ *
  * Examples for genomic regions are <tt>chr1</tt>, <tt>chr1:1,000</tt>, <tt>chr1:1,000-2,000</tt>.
- * 
+ *
  * The textual description of a genomic region has one of the formats <tt>NAME</tt>, <tt>NAME:START</tt>,
  * <tt>NAME:START-END</tt>.  The positions in the textual representation <tt>START</tt> and <tt>END</tt> are one-based.
  * However, the representation in the members of @link GenomicRegion @endlink is zero-based.
- * 
+ *
  * @section Examples
- * 
+ *
  * Construct a @link GenomicRegion @endlink object and fill it from different region strings.
- * 
+ *
  * @code{.cpp}
  * seqan::GenomicRegion genomicRegion;
- *  
+ *
  * parse(genomicRegion, "chr1");
  * // genomicRegion.seqName == "chr1"
- * // genomicRegion.seqId == -1, genomicRegion.beginPos == -1, genomicRegion.beginPos == -1
- *  
+ * // genomicRegion.rID == -1, genomicRegion.beginPos == -1, genomicRegion.beginPos == -1
+ *
  * parse(genomicRegion, "chr1:1000");
  * // genomicRegion.seqName == "chr1"
  * // genomicRegion.beginPos == 999
- * // genomicRegion.seqId == -1, genomicRegion.beginPos == -1
- *  
+ * // genomicRegion.rID == -1, genomicRegion.beginPos == -1
+ *
  * parse(genomicRegion, "chr1:1000-2000");
  * // genomicRegion.seqName == "chr1"
  * // genomicRegion.beginPos == 999
  * // genomicRegion.beginPos == 2000
- * // genomicRegion.seqId == -1
+ * // genomicRegion.rID == -1
  * @endcode
  *
- *
- * @fn GenomicRegion::GenomicRegion
- * @brief Constructor.
- * 
- * @signature GenomicRegion::GenomicRegion();
- * @signature GenomicRegion::GenomicRegion(str);
- * 
- * @param[in] str The string to parse region from. Types: CharString
- * 
- * The default constructor sets all integer members to <tt>-1</tt>, the <tt>seqName</tt> member is left empty.
  */
 
-/*!
- * @var CharString GenomicRegion::seqName;
- * @brief Name of the sequence the region lies on, default is the empty string.
- * 
- * @var __int32 GenomicRegion::seqId;
- * @brief An optional field storing an integer.  Default is <tt>-1</tt>.
- * 
- * @var __int32 GenomicRegion::beginPos;
- * @brief Begin position of the range on the chromosome.  Default is <tt>-1</tt>.
- * 
- * @var __int32 GenomicRegion::endPos;
- * @brief End position of the range on the chromosome.  Default is <tt>-1</tt>.
- */
-
-/**
-.Class.GenomicRegion
-..cat:Input/Output
-..signature:GenomicRegion
-..summary:Store information about a genomic region.
-..description.text:
-A genomic region is a range on a chromosome.
-The chromosome is identified by its name (as text in @Memvar.GenomicRegion#seqName@, optionally also as an $integer$ in @Memvar.GenomicRegion#seqId@).
-The range is stored as a half-open interval [@Memvar.GenomicRegion#beginPos@, @Memvar.GenomicRegion#endPos@).
-If @Memvar.GenomicRegion#beginPos@ is set to $-1$ then the range spans the whole chromosome.
-If @Memvar.GenomicRegion#beginPos@ is set to a value $>= 0$ and @Memvar.GenomicRegion#endPos@ is set ot $-1$, then the chromosome is selected from @Memvar.GenomicRegion#beginPos@ to the end.
-..description.text:
-Examples for genomic regions are $chr1$, $chr1:1,000$, $chr1:1,000-2,000$.
-..description.text:
-The textual description of a genomic region has one of the formats $NAME$, $NAME:START$, $NAME:START-END$.
-The positions in the textual representation $START$ and $END$ are one-based.
-However, the representation in the members of @Class.GenomicRegion@ is zero-based.
-..example.text:Construct a @Class.GenomicRegion@ object and fill it from different region strings.
-..example.code:
-seqan::GenomicRegion genomicRegion;
-
-parse(genomicRegion, "chr1");
-// genomicRegion.seqName == "chr1"
-// genomicRegion.seqId == -1, genomicRegion.beginPos == -1, genomicRegion.beginPos == -1
-
-parse(genomicRegion, "chr1:1000");
-// genomicRegion.seqName == "chr1"
-// genomicRegion.beginPos == 999
-// genomicRegion.seqId == -1, genomicRegion.beginPos == -1
-
-parse(genomicRegion, "chr1:1000-2000");
-// genomicRegion.seqName == "chr1"
-// genomicRegion.beginPos == 999
-// genomicRegion.beginPos == 2000
-// genomicRegion.seqId == -1
-
-
-..include:seqan/seq_io.h
-
-.Memfunc.GenomicRegion#GenomicRegion
-..class:Class.GenomicRegion
-..summary:Constructor.
-..description:
-The default constructor sets all integer members to $-1$, the $seqName$ member is left empty.
-..signature:GenomicRegion()
-..signature:GenomicRegion(str)
-..param.str:The string to parse region from.
-...type:Shortcut.CharString
-
-.Memvar.GenomicRegion#seqName
-..class:Class.GenomicRegion
-..summary:Name of the sequence the region lies on, default is the empty string.
-..type:Shortcut.CharString
-
-.Memvar.GenomicRegion#seqId
-..class:Class.GenomicRegion
-..summary:An optional field storing an integer. Default is $-1$.
-..type:nolink:$__int32$
-
-.Memvar.GenomicRegion#beginPos
-..class:Class.GenomicRegion
-..summary:Begin position of the range on the chromosome. Default is $-1$.
-..type:nolink:$__int32$
-
-.Memvar.GenomicRegion#endPos
-..class:Class.GenomicRegion
-..summary:End position of the range on the chromosome. Default is $-1$.
-..type:nolink:$__int32$
-*/
-
-class GenomicRegion
+struct GenomicRegion
 {
-public:
-    // Name of sequence.
+    /*!
+     * @var __int32 GenomicRegion::INVALID_POS;
+     * @brief Constant for marking a position as invalid (static-const member).
+     */
+    static __int32 const INVALID_POS = -1;
+
+    /*!
+     * @var __int32 GenomicRegion::INVALID_ID;
+     * @brief Constant for marking a position as invalid (static-const member).
+     */
+    static __int32 const INVALID_ID = -1;
+
+    /*!
+     * @var CharString GenomicRegion::seqName;
+     * @brief Name of the sequence the region lies on, default is the empty string.
+     */
     CharString seqName;
-    // Index of sequence in FASTA file.  -1 if not set.
-    __int32 seqId;
-    // 0-based begin position.  -1 if not set.
+
+    /*!
+     * @var __int32 GenomicRegion::rID;
+     * @brief An optional field storing an integer.  Default is <tt>-1</tt>.
+     */
+    __int32 rID;
+
+    /*!
+     * @var __int32 GenomicRegion::beginPos;
+     * @brief Begin position of the range on the chromosome.  Default is <tt>-1</tt>.
+     */
     __int32 beginPos;
-    // 0-based, C-style end position.  -1 if not set.
+
+    /*!
+     * @var __int32 GenomicRegion::endPos;
+     * @brief End position of the range on the chromosome.  Default is <tt>-1</tt>.
+     */
     __int32 endPos;
 
-    GenomicRegion(CharString const & str) :
-            seqId(-1), beginPos(-1), endPos(-1)
+    /*!
+     * @fn GenomicRegion::GenomicRegion
+     * @brief Constructor.
+     *
+     * @signature GenomicRegion::GenomicRegion();
+     * @signature GenomicRegion::GenomicRegion(str);
+     *
+     * @param[in] str The string to parse region from. Types: CharString
+     *
+     * The default constructor sets all integer members to <tt>INVALID_POS</tt>, the <tt>seqName</tt> member is left empty.
+     */
+
+    GenomicRegion() : rID(INVALID_ID), beginPos(INVALID_POS), endPos(INVALID_POS)
+    {}
+
+    GenomicRegion(CharString const & str) : rID(INVALID_ID), beginPos(INVALID_POS), endPos(INVALID_POS)
     {
         parse(*this, str);
     }
 
-    GenomicRegion() :
-        seqId(-1), beginPos(-1), endPos(-1)
-    {}
+    /*!
+     * @fn GenomicRegion::toString
+     * @brief Write string representation of interval to out.
+     *
+     * @signature void GenomicRegion::toString(out);
+     *
+     * @param[in,out] out Target to write textual interval description to.
+     */
+    template <typename TString>
+    void toString(TString & out) const
+    {
+        clear(out);
+        append(out, seqName);
+        appendValue(out, ':');
+        if (beginPos + 1 == endPos)
+        {
+            appendNumber(out, beginPos + 1);
+        }
+        else
+        {
+            appendNumber(out, beginPos + 1);
+            appendValue(out, '-');
+            appendNumber(out, endPos);
+        }
+    }
 };
 
 // ============================================================================
@@ -232,30 +204,19 @@ class GenomicRegion
 /*!
  * @fn GenomicRegion#clear
  * @brief Reset a GenomicRegion object to the same state after default construction.
- * 
+ *
  * @signature void clear(genomicRegion);
- * 
+ *
  * @param[in,out] genomicRegion The @link GenomicRegion @endlink object to reset.  Types: GenomicRegion
  */
 
-/**
-.Function.GenomicRegion#clear
-..cat:Input/Output
-..class:Class.GenomicRegion
-..summary:Reset a @Class.GenomicRegion@ object to the same state after default construction.
-..signature:reset(genomicRegion)
-..param.genomicRegion:The @Class.GenomicRegion@ object to reset.
-...type:Class.GenomicRegion
-..returns:$void$, where $true$ indicates sucess
-..include:seqan/seq_io.h
-*/
-
-inline void clear(GenomicRegion & region)
+inline void
+clear(GenomicRegion & region)
 {
     clear(region.seqName);
-    region.seqId = -1;
-    region.beginPos = -1;
-    region.endPos = -1;
+    region.rID = region.INVALID_ID;
+    region.beginPos = region.INVALID_POS;
+    region.endPos = region.INVALID_POS;
 }
 
 // ---------------------------------------------------------------------------
@@ -265,101 +226,58 @@ inline void clear(GenomicRegion & region)
 /*!
  * @fn GenomicRegion#parse
  * @brief Parse genomic region string store results in @link GenomicRegion @endlink.
- * 
+ *
  * @signature bool parse(genomicRegion, regionString);
- * 
- * @param regionString The region string to prse. Types: CharString
- * @param genomicRegion The @link GenomicRegion @endlink object to write the
- *                      results to. Types: GenomicRegion
- * 
+ *
+ * @param[in]  regionString  The region string to prse.  Types: @link CharString @endlink.
+ * @param[out] genomicRegion The @link GenomicRegion @endlink object to write the results to.
+ *                           Types: GenomicRegion
+ *
  * @return bool true indicates successful parsing.
  */
 
-/**
-.Function.GenomicRegion#parse
-..cat:Input/Output
-..class:Class.GenomicRegion
-..summary:Parse genomic region string store results in @Class.GenomicRegion@.
-..signature:parse(genomicRegion, regionString)
-..param.genomicRegion:The @Class.GenomicRegion@ object to write the results to.
-...type:Class.GenomicRegion
-..param.regionString:The region string to prse.
-...type:Shortcut.CharString
-..returns:$bool$, where $true$ indicates sucess
-..example.text:See the example for parsing in the @Class.GenomicRegion@.
-..include:seqan/seq_io.h
-*/
-
-// Parse regionString and write to region.  region.seqId will not be set but
+// Parse regionString and write to region.  region.rID will not be set but
 // region.seqName will be.  Return true on success.
 
-inline bool parse(GenomicRegion & region, CharString const & regionString)
+inline void
+parse(GenomicRegion & region, CharString const & regionString)
 {
-    Stream<CharArray<char const *> > stream(begin(regionString, Standard()),
-                                            end(regionString, Standard()));
-    RecordReader<Stream<CharArray<char const *> >, SinglePass<> > reader(stream);
+    DirectionIterator<CharString const, Input>::Type reader = directionIterator(regionString, Input());
 
     // Parse out sequence name.
-    CharString buffer;
-    int res = readUntilChar(buffer, reader, ':');
-    if (res != 0 && res != EOF_BEFORE_SUCCESS)
-        return 1;  // Parse error.
-
-    region.seqName = buffer;
+    clear(region.seqName);
+    readUntil(region.seqName, reader, EqualsChar<':'>());
     if (atEnd(reader))
-        return true;  // Done after parsing the sequence name.
+        return;
 
-    goNext(reader);  // Skip ':'.
+    skipOne(reader, EqualsChar<':'>());     // Skip ':'.
 
     // Parse out begin position.
-    clear(buffer);
-    while (!atEnd(reader) && value(reader) != '-')
-    {
-        if (!isdigit(value(reader)) && value(reader) != ',')
-            return false;  // Error parsing.
-
-        if (isdigit(value(reader)))
-            appendValue(buffer, value(reader));
-        goNext(reader);
-    }
-    if (empty(buffer))
-        return false;
-
-    if (!lexicalCast2(region.beginPos, buffer))
-        return false;
-
-    if (region.beginPos <= 0)
-        return false;
-
-    region.beginPos -= 1;  // Adjust to 0-based.
-    if (atEnd(reader))
-        return true;
+    CharString buffer;
+    readUntil(buffer, reader, EqualsChar<'-'>(), EqualsChar<','>());
+    lexicalCastWithException(region.beginPos, buffer);
 
-    goNext(reader);  // Skip '-'.
+    if (region.beginPos < 1)
+        SEQAN_THROW(ParseError("GenomicRegion: Begin postition less than 1"));
 
-    // Parse out end position.
-    clear(buffer);
-    while (!atEnd(reader))
+    region.beginPos--;                      // Adjust to 0-based.
+    if (atEnd(reader))  // just one position
     {
-        if (!isdigit(value(reader)) && value(reader) != ',')
-            return false;  // Error parsing.
-
-        if (isdigit(value(reader)))
-            appendValue(buffer, value(reader));
-        goNext(reader);
+        region.endPos = region.INVALID_POS;
+        return;
     }
-    if (empty(buffer))
-        return false;
 
-    if (!lexicalCast2(region.endPos, buffer))
-        return false;
+    skipOne(reader, EqualsChar<'-'>());     // Skip '-'.
 
-    if (region.endPos <= 0)
-        return false;
+    // Parse out end position.
+    clear(buffer);
+    readUntil(buffer, reader, False(), EqualsChar<','>());
+    lexicalCastWithException(region.endPos, buffer);
 
-    return atEnd(reader);
+    if (region.endPos < 1)
+        SEQAN_THROW(ParseError("GenomicRegion: End postition less than 1"));
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEQ_IO_GENOMIC_REGION_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEQ_IO_GENOMIC_REGION_H_
diff --git a/seqan/seq_io/guess_stream_format.h b/seqan/seq_io/guess_stream_format.h
deleted file mode 100644
index def0035..0000000
--- a/seqan/seq_io/guess_stream_format.h
+++ /dev/null
@@ -1,477 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
-// Author: David Weese <david.weese@fu-berlin.de>
-// ==========================================================================
-// File Format detection with Stream Class.
-// ==========================================================================
-
-#ifndef SEQAN_SEQ_IO_GUESSSEQ_IOFORMAT_H_
-#define SEQAN_SEQ_IO_GUESSSEQ_IOFORMAT_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// NOTE: Must be kept in sync with Function.getAutoSeqStreamFormatName().
-
-/*!
- * @typedef SeqStreamFormats
- * @headerfile <seqan/seq_io.h>
- * @brief A Tag list of the currently implemented sequence formats (in RecordReader/Stream-IO)
- * 
- * @signature typedef TagList<...> SeqStreamFormats;
- * 
- * @see AutoSeqStreamFormat
- */
-
-/**
-.Shortcut.SeqStreamFormats
-..cat:Input/Output
-..summary:A Tag list of the currently implemented Sequence-Formats (in RecordReader/Stream-IO)
-..signature:SeqStreamFormats
-..shortcutfor:Tag.TagList
-...signature:TagList<Fastq, TagList<Fasta > >
-..include:seqan/stream.h
-*/
-
-// TODO(weese): File formats should be independent of the I/O interface?
-// Why adding SeqStreamFormats and AutoSeqStreamFormat instead of using
-// the existing AutoSeqFormat and SeqFormats?
-typedef TagList<Fastq, TagList<Fasta> > SeqStreamFormats;
-
-/*!
- * @typedef AutoSeqStreamFormat
- * @headerfile <seqan/seq_io.h>
- * @brief A TagSelector for @link SeqStreamFormats @endlink, the list of the currently implemented Sequence-Formats (in
- *        RecordReader/Stream-IO)
- * 
- * @signature typedef TagSelector<SeqStreamFormats> AutoSeqStreamFormat;
- * 
- * @section Remarks
- * 
- * Variables of this type an be passed to @link guessStreamFormat @endlink and will offer the index of the detected
- * FileFormat in its member <tt>tagId</tt>.  The values of its member <tt>tagId</tt> can be as follows:
- *
- * <table>
- *   <tr>
- *     <th>value</th>
- *     <th>meaning</th>
- *   </tr>
- *   <tr>
- *     <td>0</td>
- *     <td>unknown file format</td>
- *   </tr>
- *   <tr>
- *     <td>1</td>
- *     <td>FASTA</td>
- *   </tr>
- *   <tr>
- *     <td>2</td>
- *     <td>FASTQ</td>
- *   </tr>
- *
- * @see SeqStreamFormats
- * @see guessStreamFormat
- * @see getAutoSeqStreamFormatName
- */
-
-/**
-.Shortcut.AutoSeqStreamFormat
-..cat:Input/Output
-..summary:A TagSelector for @Shortcut.SeqStreamFormats@, the list of the currently implemented Sequence-Formats (in RecordReader/Stream-IO)
-..signature:AutoSeqStreamFormat
-..shortcutfor:Class.TagSelector
-..shortcutfor:Tag.TagList
-..remarks:This shortcut is a typedef of $TagSelector<TagList<Fastq, TagList<Fasta > > >$.
-..remarks:Variables of this type an be passed to @Function.guessStreamFormat@ and will offer the index of the detected FileFormat in its member $tagId$.
-The values of its member $tagId$ can be as follows:
-..remarks.tableheader:value|meaning
-..remarks.table:0|Unknown file format.
-..remarks.table:1|FASTA
-..remarks.table:2|FASTQ
-..see:Shortcut.SeqStreamFormats
-..see:Function.guessStreamFormat
-..include:seqan/stream.h
-*/
-
-typedef TagSelector<SeqStreamFormats> AutoSeqStreamFormat;
-
-/*!
- * @class LimitRecordReaderInScope
- * @headerfile <seqan/seq_io.h>
- * @brief Manipulates a @link RecordReader @endlink -Object so that it operates only on the first buffer
- * 
- * @signature template <typename TStream, typename TSpec>
- *            class LimitRecordReaderInScope;
- * 
- * @tparam TSpec   The specialization of the @link RecordReader @endlink. Types: RecordReader
- * @tparam TStream The @link StreamConcept @endlink of the @link RecordReader @endlink. Types: StreamConcept
- * 
- * @section Remarks
- * 
- * This class is intended for situations, where you do not wish the RecordReader to rebuffer and where you wish to
- * return to the original reading position after reading, e.g. when detecting the file format of the stream.
- * 
- * It is used by passing the RecordReader-object on construction (this already does the necessary changes in the
- * RecordReader).  Upon deconstruction of this object, the RecordReader is reset to its original state, including all
- * iterators.
- * 
- * This works on all RecordReader-objects, independent of the underlying stream- object.  It also works if the
- * underlying stream does not support seeking.
- * 
- * @see RecordReader
- * @see guessStreamFormat
- */
-
-/**
-.Class.LimitRecordReaderInScope
-..cat:Input/Output
-..summary:manipulates a @Class.RecordReader@ -Object so that it operates only on one buffer
-..signature:LimitRecordReaderInScope<TStream, TSpec>
-..param.TStream:The @Concept.StreamConcept@ of the @Class.RecordReader@.
-...type:Concept.StreamConcept
-..param.TSpec:The specialization of the @Class.RecordReader@.
-...type:Class.RecordReader
-..see:Class.RecordReader
-..see:Function.guessStreamFormat
-..include:seqan/stream.h
-..remarks:This class is intended for situations, where you do not wish the RecordReader to rebuffer and where you wish to return to the original reading position after reading, e.g. when detecting the file format of the stream.
-..remarks:It is used by passing the RecordReader-object on construction (this already does the necessary changes in the RecordReader). Upon deconstruction of this object, the RecordReader is reset to its original state, including all iterators.
-..remarks:This works on all RecordReader-objects, independent of the underlying stream-object. It also works, if the underlying stream does not support seeking.
-..include:seqan/stream.h
-*/
-
-// TODO(holtgrew): Rename to LimitRecordReaderRIIA?
-
-template <typename TStream, typename TPass>
-class LimitRecordReaderInScope
-{
-public:
-    RecordReader<TStream, TPass> & _recordreader;
-    typename RecordReader<TStream, TPass>::TIter _currentBeforeSuspend;
-    // the following is only needed for MMapStrings
-    typename RecordReader<TStream, TPass>::TIter _endBeforeSuspend;
-
-    LimitRecordReaderInScope(RecordReader<TStream, TPass> & reader)
-            : _recordreader(reader),
-              _currentBeforeSuspend(reader._current),
-              _endBeforeSuspend(reader._end)
-    {
-        _suspendRefill(TPass());
-    }
-
-    ~LimitRecordReaderInScope()
-    {
-        _resumeRefillAndReset(TPass());
-    }
-private:
-    inline void
-    _suspendRefill(SinglePass<void> const & /* tag */)
-    {
-        _recordreader._stayInOneBuffer = true;
-    }
-
-    inline void
-    _suspendRefill(SinglePass<StringReader> const & /* tag */)
-    {
-        if (_recordreader._end - _recordreader._current > BUFSIZ)
-            _recordreader._end = _recordreader._current + BUFSIZ;
-    }
-
-    template <typename TSpec>
-    inline void
-    _suspendRefill(DoublePass<TSpec> const & /* tag */)
-    {
-        _suspendRefill(SinglePass<TSpec>());
-    }
-
-
-    inline void
-    _resumeRefillAndReset(SinglePass<void> const & /* tag */)
-    {
-        _recordreader._stayInOneBuffer = false;
-        if (_currentBeforeSuspend == 0) // there had been no Buffer at start
-            _recordreader._current = begin(_recordreader._buffer, Standard());
-        else
-            _recordreader._current = _currentBeforeSuspend;
-    }
-
-    inline void
-    _resumeRefillAndReset(DoublePass<void> const & /* tag */)
-    {
-        _recordreader._stayInOneBuffer = false;
-        if (_currentBeforeSuspend == 0) // there had been no Buffer at start
-            _recordreader._current = begin(*_recordreader._currentBuffer,
-                                           Standard());
-        else
-            _recordreader._current = _currentBeforeSuspend;
-    }
-
-    inline void
-    _resumeRefillAndReset(SinglePass<StringReader> const & /* tag */)
-    {
-        _recordreader._end = _endBeforeSuspend;
-        _recordreader._current = _currentBeforeSuspend;
-    }
-
-    template <typename TSpec>
-    inline void
-    _resumeRefillAndReset(DoublePass<TSpec> const & /* tag */)
-    {
-        _resumeRefillAndReset(SinglePass<TSpec>());
-    }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function autoSeqStreamFormatName()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn getAutoSeqStreamFormatName
- * @headerfile <seqan/seq_io.h>
- * @brief Returns the name of a stream file format.
- * 
- * @signature TCString getAutoSeqStreamFormatName(autoSeqStreamFormat);
- * 
- * @param[in] autoSeqStreamFormat The @link AutoSeqStreamFormat @endlink object to get the format name from. Types:
- *                                AutoSeqStreamFormat
- * 
- * @return TCString <tt>char const *</tt> with the format name.
- * 
- * @section Examples
- * 
- * @code{.cpp}
- * // (Create RecordReader object recordReader with sequence file here).
- * AutoSeqStreamFormat formatTag;
- * if (checkFormat(recordReader, formatTag))
- *     std::cout << "File format is " << getAutoSeqStreamFormatName(formatTag) << '\n';
- * @endcode
- *
- * @see guessStreamFormat
- * @see AutoSeqStreamFormat
- */
-
-/**
-.Function.getAutoSeqStreamFormatName
-..summary:Returns
-..signature:getAutoSeqStreamFormatName(autoSeqStreamFormat)
-..param.autoSeqStreamFormat:The @Shortcut.AutoSeqStreamFormat@ object to get the format name from.
-...type:Shortcut.AutoSeqStreamFormat
-..returns:$char const *$ with the format name.
-..include:seqan/stream.h
-..see:Function.guessStreamFormat
-..see:Shortcut.AutoSeqStreamFormat
-..example.code:
-// (Create RecordReader object recordReader with sequence file here).
-AutoSeqStreamFormat formatTag;
-if (checkFormat(recordReader, formatTag))
-    std::cout << "File format is " << getAutoSeqStreamFormatName(formatTag) << '\n';
-*/
-
-// NOTE: Must be kept in sync with the typedef SeqStreamFormats.
-
-inline char const *
-getAutoSeqStreamFormatName(AutoSeqStreamFormat const & format)
-{
-    switch (format.tagId)
-    {
-        case Find<SeqStreamFormats, Fasta>::VALUE: return "FASTA";
-        case Find<SeqStreamFormats, Fastq>::VALUE: return "FASTQ";
-    }
-
-    return "INVALID FORMAT";
-}
-
-// ----------------------------------------------------------------------------
-// Function guessStreamFormat()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn guessStreamFormat
- * @headerfile <seqan/seq_io.h>
- * @brief Check whether the data provided by reader is (one of) the specified format(s).
- * 
- * @signature bool guessStreamFormat(reader, tag);
- * @signature bool guessStreamFormat(reader, tagSelector);
- *
- * @param[in,out] reader      The @link RecordReader @endlink to from.
- * @param[in]     tag         A file format tag.
- * @param[in]     tagSelector The TagSelector to use.
- *
- * @return true <tt>true</tt> if (one of) the specified Tag(s) tested positive and <tt>False</tt> otherwise
- * 
- * @section Remarks
- * 
- * With the help of @link LimitRecordReaderInScope @endlink these functions do not (permanently) alter the position in
- * the stream.
- * 
- * The tagId-member of the TagSelector holds the index in inside-to-outside order and begins counting at one.  E.g. The
- * Index of FASTQ in <tt>TagList&lt;Fastq, TagList&lt;Fasta&gt; &gt; is be 2.
- * 
- * @section Examples
- * 
- * The following example guesses the sequence file format of the already open fstream <tt>in</tt>.  After the call to
- * <tt>guessStreamFormat()</tt>, the <tt>tagSelector.tagId</tt> contains the 1-based index of the matching tag.  Here,
- * we use the @link AutoSeqStreamFormat @endlink tag selector.
- * 
- * @code{.cpp}
- * RecordReader<std::fstream, SinglePass<> > reader(in);
- * AutoSeqStreamFormat tagSelector;
- * bool b = guessStreamFormat(reader, tagSelector);
- * // b is true if any format was detected successfully.
- * if (tagSelector.tagId == 1)
- *     std::cerr << "Detected FASTA." << std::endl;
- * else if (tagSelector.tagId == 2)
- *     std::cerr << "Detected FASTQ." << std::endl;
- * else
- *     std::cerr << "Unknown file format!" << std::endl;
- * @endcode
- *
- * Alternatively, we can define your own tag selector.  Note that we reverse the order of FASTA and FASTQ in respect to
- * @link AutoSeqStreamFormat @endlink
- * 
- * @code{.cpp}
- * typedef TagSelector<TagList<Fasta, TagList<Fastq> > > MyTagSelector;
- *  
- * RecordReader<std::fstream, SinglePass<> > reader(in);
- * AutoSeqStreamFormat tagSelector;
- * MyTagSelector tagSelector;
- * bool b = guessStreamFormat(reader, tagSelector);
- * // b is true if any format was detected successfully.
- * if (tagSelector.tagId == 1)
- *     std::cerr << "Detected FASTQ." << std::endl;
- * else if (tagSelector.tagId == 2)
- *     std::cerr << "Detected FASTA." << std::endl;
- * else
- *     std::cerr << "Unknown file format!" << std::endl;
- * @endcode
- *
- * @see AutoSeqStreamFormat
- * @see getAutoSeqStreamFormatName
- * @see LimitRecordReaderInScope
- */
-
-/**
-.Function.guessStreamFormat
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:check whether the data provided by reader is (one of) the specified format(s).
-..signature:guessStreamFormat(TRecordReader & reader, TTag const &)
-..param.reader:The @Class.RecordReader@ to read from
-..param.TTag:The tag to check against.
-..signature:guessStreamFormat(TRecordReader & reader, TagSelector<TTagList> & formats)
-..param.formats:A @Class.TagSelector@ object that contains the list of tags to check and provides a tagId member with index of the detected tag.
-..returns: $true$ if (one of) the specified Tag(s) tested positive and $False$ otherwise
-...type:nolink:$bool$
-..remarks:With the help of @Class.LimitRecordReaderInScope@ these functions do not (permanently) alter the position in the stream.
-..remarks:The tagId-member of the TagSelector holds the index in inside-to-outside order and begins counting at one. E.g. The Index of FASTQ in TagList<Fastq, TagList<Fasta > > would be 2.
-..include:seqan/stream.h
-..example.text:
-The following example guesses the sequence file format of the already open fstream $in$.
-After the call to $guessStreamFormat()$, the $tagSelector.tagId$ contains the 1-based index of the matching tag.
-Here, we use the @Shortcut.AutoSeqStreamFormat@ tag selector.
-..example.code:
-RecordReader<std::fstream, SinglePass<> > reader(in);
-AutoSeqStreamFormat tagSelector;
-bool b = guessStreamFormat(reader, tagSelector);
-// b is true if any format was detected successfully.
-if (tagSelector.tagId == 1)
-    std::cerr << "Detected FASTA." << std::endl;
-else if (tagSelector.tagId == 2)
-    std::cerr << "Detected FASTQ." << std::endl;
-else
-    std::cerr << "Unknown file format!" << std::endl;
-..example.text:
-Alternatively, we can define your own tag selector.
-Note that we reverse the order of FASTA and FASTQ in respect to @Shortcut.AutoSeqStreamFormat@
-..example.code:
-typedef TagSelector<TagList<Fasta, TagList<Fastq> > > MyTagSelector;
-
-RecordReader<std::fstream, SinglePass<> > reader(in);
-AutoSeqStreamFormat tagSelector;
-MyTagSelector tagSelector;
-bool b = guessStreamFormat(reader, tagSelector);
-// b is true if any format was detected successfully.
-if (tagSelector.tagId == 1)
-    std::cerr << "Detected FASTQ." << std::endl;
-else if (tagSelector.tagId == 2)
-    std::cerr << "Detected FASTA." << std::endl;
-else
-    std::cerr << "Unknown file format!" << std::endl;
-
-*/
-
-template < typename TRecordReader >
-inline bool
-guessStreamFormat(TRecordReader &, TagSelector<> &)
-{
-    // we get here if the file format could not be determined
-    return false;
-}
-
-template <typename TRecordReader, typename TTagList >
-inline bool
-guessStreamFormat(TRecordReader & reader, TagSelector<TTagList> & format)
-{
-    // (weese:) compare with guessFormat in file_format_mmap.h
-    typedef typename TTagList::Type TFormatTag;
-
-    if (value(format) == -1 || value(format) == Find<TTagList, TFormatTag>::VALUE)
-    {
-        // if tagId is set to -1 (auto-detect) or the current format (TFormatTag) then test for TFormatTag format
-        if (guessStreamFormat(reader, TFormatTag()))
-        {
-            value(format) = Find<TTagList, TFormatTag>::VALUE;
-            return true;
-        }
-    }
-    return guessStreamFormat(reader, static_cast<typename TagSelector<TTagList>::Base &>(format));
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_SEQ_IO_ADAPT_FSEQ_IO_H_
diff --git a/seqan/seq_io/read_embl.h b/seqan/seq_io/read_embl.h
index f81322a..67c36b9 100644
--- a/seqan/seq_io/read_embl.h
+++ b/seqan/seq_io/read_embl.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Read support for the EMBL file format.
 // ==========================================================================
 
-#ifndef EXTRAS_INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
-#define EXTRAS_INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
+#ifndef INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
+#define INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
 
 namespace seqan {
 
@@ -47,10 +47,8 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-/*
 struct Embl_;
 typedef Tag<Embl_> Embl;
-*/
 
 struct EmblHeader_;
 typedef Tag<EmblHeader_> EmblHeader;
@@ -58,15 +56,37 @@ typedef Tag<EmblHeader_> EmblHeader;
 struct EmblSequence_;
 typedef Tag<EmblSequence_> EmblSequence;
 
-enum EmblErrorCodes_
-{
-    IOERR_EMBL_WRONG_RECORD = 2048
-};
-
 // ============================================================================
 // Metafunctions
 // ============================================================================
 
+// --------------------------------------------------------------------------
+// Metafunction MagicHeader
+// --------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<Embl, T>
+{
+    static char const VALUE[3];
+};
+template <typename T>
+char const MagicHeader<Embl, T>::VALUE[3] = { 'I','D',' ' };  // typical Embl header
+
+// --------------------------------------------------------------------------
+// Metafunction FileExtensions
+// --------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<Embl, T>
+{
+    static char const * VALUE[1];
+};
+template <typename T>
+char const * FileExtensions<Embl, T>::VALUE[1] =
+{
+    ".embl",     // default output extension
+};
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -76,55 +96,32 @@ enum EmblErrorCodes_
 // ----------------------------------------------------------------------------
 
 /*!
- * @fn splitEmblHeader
- * @header <seqan/seq_io.h>
+ * @fn readEmblHeader
+ * @headerfile <seqan/seq_io.h>
  * @brief Split an EMBL header line.
  *
- * @signature void splitEmblHeader(key, value, line);
+ * @signature void readEmblHeader(key, value, iter);
  *
- * @param[out] key   A @link SequenceConcept @endlink object to write the key to.
- * @param[out] value A @link SequenceConcept @endlink object to write the value to.
- * @param[in]  line  A @link SequenceConcept @endlink object with the line.
+ * @param[out] key   A @link ContainerConcept @endlink object to write the key to.
+ * @param[out] value A @link ContainerConcept @endlink object to write the value to.
+ * @param[in]  iter  Input iterator.
  */
 
-/**
-.Function.splitEmblHeader
-..cat:Input/Output
-..signature:startsWith(key, value, line)
-..summary:Split an EMBL header line.
-..param.key:The 2-character header type.
-..param.value:The line's value.
-..param.line:The header line to split.
-..returns:$void$
-..include:seqan/stream.h
-*/
-
-template <typename TKey, typename TValue, typename TLine>
+template <typename TKey, typename TValue, typename TFwdIterator>
 inline void
-splitEmblHeader(TKey & key, TValue & value, TLine const & line)
+readRecord(TKey & key, TValue & val, TFwdIterator & iter, EmblHeader)
 {
     clear(key);
+    clear(val);
 
-    enum State { IN_KEY, IN_SPACE, IN_VALUE };
-    State state = IN_KEY;
-
-    typedef typename Iterator<TLine const, Rooted>::Type TIterator;
-    TIterator it = begin(line, Rooted());
-    for (; !atEnd(it); goNext(it))
+    skipUntil(iter, NotFunctor<IsWhitespace>());
+    readUntil(key, iter, IsWhitespace(), AssertFunctor<NotFunctor<CountDownFunctor<True, 2> >, ParseError>());
+    if (!atEnd(iter) && IsBlank()(value(iter)))
     {
-        if (state == IN_KEY)
-        {
-            appendValue(key, *it);
-            if (length(key) == 2u)
-                state = IN_SPACE;
-        }
-        else if (state == IN_SPACE && !isblank(*it))
-        {
-            break;
-        }
+        skipUntil(iter, NotFunctor<IsBlank>());
+        readUntil(val, iter, IsNewline());
     }
-
-    value = suffix(line, position(it));
+    skipLine(iter);
 }
 
 // ----------------------------------------------------------------------------
@@ -133,135 +130,94 @@ splitEmblHeader(TKey & key, TValue & value, TLine const & line)
 
 // nextIs() for EMBL header records.
 
-template <typename TStream, typename TSpec>
+template <typename TFwdIterator>
 inline bool
-nextIs(RecordReader<TStream, TSpec> & reader, EmblHeader const & /*tag*/)
+nextIs(TFwdIterator & iter, EmblHeader)
 {
-    return !atEnd(reader) && !isblank(value(reader));
+    return !atEnd(iter) && !IsWhitespace()(value(iter));
 }
 
 // nextIs() for EMBL sequence records.
 
-template <typename TStream, typename TSpec>
+template <typename TFwdIterator>
 inline bool
-nextIs(RecordReader<TStream, TSpec> & reader, EmblSequence const & /*tag*/)
+nextIs(TFwdIterator & iter, EmblSequence)
 {
-    return !atEnd(reader) && isblank(value(reader));
+    return !atEnd(iter) && IsWhitespace()(value(iter));
 }
 
+
 // ----------------------------------------------------------------------------
 // Function readRecord()
 // ----------------------------------------------------------------------------
 
-// readRecord() for EMBL header records.
-
-template <typename TTarget, typename TStream, typename TSpec>
-inline int
-readRecord(TTarget & buffer, RecordReader<TStream, SinglePass<TSpec> > & reader,
-           EmblHeader const & tag)
-{
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (!nextIs(reader, tag))
-        return IOERR_EMBL_WRONG_RECORD;
-    clear(buffer);
-
-    return readLine(buffer, reader);
-}
-
 // readRecord() for EMBL sequences records.
 
 // Read all sequence, eat/ignore '//' line.
 
-template <typename TTarget, typename TStream, typename TSpec>
-inline int
-readRecord(TTarget & buffer, RecordReader<TStream, SinglePass<TSpec> > & reader,
-           EmblSequence const & tag)
+template <typename TSeqString, typename TFwdIterator>
+inline void
+readRecord(TSeqString & seq, TFwdIterator & iter, EmblSequence)
 {
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (!nextIs(reader, tag))
-        return IOERR_EMBL_WRONG_RECORD;
-    clear(buffer);
+    typedef typename Value<TSeqString>::Type TSeqAlphabet;
+    typedef OrFunctor<OrFunctor<IsBlank, IsDigit>,
+                      AssertFunctor<IsInAlphabet<TSeqAlphabet>, ParseError, Embl> > TSeqAsserter;
+
+    IsNewline isNewline;
+    TSeqAsserter asserter;
 
-    for (; !atEnd(reader); goNext(reader))
+    if (!atEnd(iter) && value(iter) == 'I')
+        skipLine(iter);
+
+    clear(seq);
+    for (; !atEnd(iter); skipLine(iter))
     {
-        if (isspace(value(reader)) || isdigit(value(reader)))
-            continue;  // Skip blanks.
-        // If we found a slash, look for the next one.
-        if (value(reader) == '/')
+        if (value(iter) == '/')
         {
-            if (goNext(reader))  // Returns true if at end.
-                break;
-            if (value(reader) == '/')
-            {
-                skipLine(reader);
-                return 0;  // OK, found complete terminator.
-            }
+            skipLine(iter);
+            break;
         }
 
-        // Otherwise, append the just found character to buffer.
-        appendValue(buffer, value(reader));
+        readUntil(seq, iter, isNewline, asserter);
     }
-
-    return EOF_BEFORE_SUCCESS;
 }
 
 // readRecord() for EMBL id/seq pairs.
 
-template <typename TId, typename TSequence, typename TStream, typename TSpec>
-inline int
-readRecord(TId & id,
-           TSequence & sequence,
-           RecordReader<TStream, SinglePass<TSpec> > & reader,
-           Embl const & /*tag*/)
+template <typename TIdString, typename TSeqString, typename TFwdIterator>
+inline void
+readRecord(TIdString & meta, TSeqString & seq, TFwdIterator & iter, Embl)
 {
-    CharString buffer;
-    while (nextIs(reader, EmblHeader()))
+    IsBlank isBlank;
+    IsWhitespace isWhite;
+    String<char, Array<2> > key;
+
+    // extract meta from "ID" line
+    clear(meta);
+    for (; !atEnd(iter) && !isBlank(value(iter)); skipLine(iter))
     {
-        int res = readRecord(buffer, reader, EmblHeader());
-        if (res != 0)
-            return res;
-        if (startsWith(buffer, "ID"))
+        AssertFunctor<NotFunctor<CountDownFunctor<True, 2> >, ParseError, Embl> asserter;
+
+        clear(key);
+        readUntil(key, iter, isWhite, asserter);
+        if (!atEnd(iter) && isBlank(value(iter)) && key == "ID")
         {
-            CharString k, v;
-            splitEmblHeader(k, id, buffer);
+            skipUntil(iter, NotFunctor<IsBlank>());
+            readUntil(meta, iter, IsNewline());
         }
     }
-    clear(sequence);
-    int res = readRecord(sequence, reader, EmblSequence());
-    if (res != 0)
-        return res;
-    
-    return 0;
-}
 
-// ----------------------------------------------------------------------------
-// Function read2()
-// ----------------------------------------------------------------------------
+    readRecord(seq, iter, EmblSequence());
+}
 
-template <typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec,
-          typename TStream, typename TSpec>
-int read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-          StringSet<TSeqString, TSeqSpec> & sequences,
-          RecordReader<TStream, SinglePass<TSpec> > & reader,
-          Embl const & tag)
+template <typename TIdString, typename TSeqString, typename TQualString, typename TFwdIterator>
+inline void
+readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TFwdIterator & iter, Embl)
 {
-    TIdString id;
-    TSeqString seq;
-
-    while (!atEnd(reader))
-    {
-        int res = readRecord(id, seq, reader, tag);
-        if (res != 0)
-            return res;
-        appendValue(sequenceIds, id);
-        appendValue(sequences, seq);
-    }
-
-    return 0;
+    clear(qual);
+    readRecord(meta, seq, iter, Embl());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef EXTRAS_INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEQ_IO_READ_EMBL_H_
diff --git a/seqan/seq_io/read_fasta_fastq.h b/seqan/seq_io/read_fasta_fastq.h
deleted file mode 100644
index 5567533..0000000
--- a/seqan/seq_io/read_fasta_fastq.h
+++ /dev/null
@@ -1,1131 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
-// ==========================================================================
-// Record and Document Reading for FASTA and FASTQ files.
-// ==========================================================================
-
-//TODO(h4nn3s): double-check if we really want to allow EOF inside meta-line
-// and also if a fastq file is legal if a record contains no qualities
-
-#ifndef SEQAN_SEQ_IO_READ_FASTA_FASTQ_H_
-#define SEQAN_SEQ_IO_READ_FASTA_FASTQ_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/**
-.Tag.File Format.tag.Fasta:
-    FASTA file format for sequences.
-..include:seqan/file.h
-*/
-struct TagFasta_;
-typedef Tag<TagFasta_> Fasta;
-
-/**
-.Tag.File Format.tag.Fastq:
-    FASTQ file format for sequences.
-..include:seqan/file.h
-*/
-struct TagFastq_;
-typedef Tag<TagFastq_> Fastq;
-
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// Returns character starting a meta field.
-
-template <typename TTag>
-struct MetaFirstChar_;
-
-template <>
-struct MetaFirstChar_<Tag<TagFasta_> >
-{
-    static const char VALUE = '>';
-};
-
-template <>
-struct MetaFirstChar_<Tag<TagFastq_> >
-{
-    static const char VALUE = '@';
-};
-
-// Returns character starting a field after the sequence field.  In the case of FASTA, this is '>' since a new meta
-// field will be created.  In the case of FASTQ, this is '+'.
-
-template <typename TTag>
-struct AfterSeqFirstChar_;
-
-template <>
-struct AfterSeqFirstChar_<Tag<TagFasta_> >
-{
-    static const char VALUE = '>';
-};
-
-template <>
-struct AfterSeqFirstChar_<Tag<TagFastq_> >
-{
-    static const char VALUE = '+';
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function _clearAndReserveMemory() and helpers
-// ----------------------------------------------------------------------------
-
-// When not reading char values, we can simply use _countHelper() since the separators '>' and '+' are not part of the
-// sequence alphabet.
-
-template <typename TFormatTag, typename TAlph, typename TRecordReader>
-inline int
-_countSequenceFastAQ(unsigned int & count,
-                     TRecordReader & reader,
-                     TFormatTag const & /* formatTag */,
-                     TAlph const & /* Alphabet type */)
-{
-//     return _countHelper(count, reader, Tag<TAlph>(), Whitespace_(), false);
-    return _countHelper(count, reader, AlphaNum_(), Whitespace_(), false);
-}
-
-// When reading char values, we have to use a more complicated algorithm:  Read until the separator char '>'/'+' begins
-// a line.  Note that when reading text including these characters then there is ambiguity.  When we find such a
-// character then we greedily decide that this does not belong to the sequence.
-
-// template <typename TFormatTag, typename TRecordReader>
-// inline int
-// _countSequenceFastAQ(unsigned int & count,
-//                      TRecordReader & reader,
-//                      TFormatTag const & /* formatTag */,
-//                      char const & /* Alphabet type */)
-// {
-//     // The variable afterEol is true if we are after an EOL char and we are not at the beginning of the sequence
-//     // record.  Empty sequence lines are fine, non-existent ones are not.
-//     bool afterEol = false;
-// 
-//     while (!atEnd(reader))
-//     {
-//         char c = value(reader);
-//         if (c == '\r' || c == '\n')
-//         {
-//             afterEol = true;
-//             goNext(reader);
-//             if (resultCode(reader) != 0)
-//                 return resultCode(reader);
-//             continue;
-//         }
-// 
-//         if (afterEol && c == AfterSeqFirstChar_<TFormatTag>::VALUE)
-//         {
-//             return 0;  // Done, at stop char.
-//         }
-// 
-//         if (!isspace(c))
-//             count += 1;
-//         afterEol = false;
-//         goNext(reader);
-//         if (resultCode(reader) != 0)
-//             return resultCode(reader);
-//     }
-// 
-//     return EOF_BEFORE_SUCCESS;
-// }
-
-template <typename TSeqAlph,
-          typename TFile,
-          typename TSpec,
-          typename TTag>
-inline int
-_countMetaAndSequence(unsigned int & metaLength,
-                      unsigned int & seqLength,
-                      RecordReader<TFile, DoublePass<TSpec> > & reader,
-                      TTag const & formatTag,
-                      TSeqAlph const & /* tag*/)
-{
-    metaLength=0;
-    seqLength=0;
-
-    // COUNT META
-    if (atEnd(reader) || value(reader) != MetaFirstChar_<TTag>::VALUE)
-        return RecordReader<TFile, DoublePass<TSpec> >::INVALID_FORMAT;
-    goNext(reader);
-    if (resultCode(reader))
-        return resultCode(reader);
-    if (atEnd(reader)) // empty ID, no sequence, this is legal TODO?
-        return 0;
-
-    int res = countLine(metaLength, reader);
-    if (res == EOF_BEFORE_SUCCESS)  // EOF half way in ID is legal
-        return 0;
-    else if (res)
-        return res;
-
-    if (atEnd(reader)) // no sequence
-        return 0;
-
-    // COUNT SEQUENCE
-    res = _countSequenceFastAQ(seqLength, reader, formatTag, TSeqAlph());
-    if (res == EOF_BEFORE_SUCCESS)  // EOF half way in sequence is legal
-        return 0;
-    else if (res)
-        return res;
-
-    return 0;
-}
-
-// SINGLE-Pass
-template <typename TIdString,
-          typename TSeqString,
-          typename TFile,
-          typename TSpec,
-          typename TTag>
-inline int
-_clearAndReserveMemory(TIdString & meta, TSeqString & seq,
-                       RecordReader<TFile, SinglePass<TSpec> > & /**/,
-                       TTag const & /*tag*/)
-{
-    clear(meta);
-    clear(seq);
-    return 0;
-}
-
-// DOUBLE-Pass
-template <typename TIdString,
-          typename TSeqString,
-          typename TFile,
-          typename TSpec,
-          typename TTag>
-inline int
-_clearAndReserveMemory(TIdString & meta, TSeqString & seq,
-                       RecordReader<TFile, DoublePass<TSpec> > & reader,
-                       TTag const & /*tag*/)
-{
-    clear(meta);
-    clear(seq);
-    startFirstPass(reader);
-
-    unsigned int metaLength=0;
-    unsigned int seqLength=0;
-    // COUNT
-    int res = _countMetaAndSequence(metaLength,
-                                    seqLength,
-                                    reader,
-                                    TTag(),
-                                    typename Value<TSeqString>::Type());
-    if ((res != 0) && (res != EOF_BEFORE_SUCCESS))
-        return res;
-
-    // RESERVE FOR META
-    reserve(meta, metaLength, Exact());
-
-    // RESERVE FOR SEQUENCE
-    reserve(seq, seqLength, Exact());
-
-    startSecondPass(reader);
-    return 0;
-}
-
-template <typename TIdString,
-          typename TSeqString,
-          typename TQualString,
-          typename TFile,
-          typename TSpec,
-          typename TTag>
-inline int
-_clearAndReserveMemory(TIdString & meta, TSeqString & seq, TQualString & qual,
-                       RecordReader<TFile, TSpec> & reader,
-                       TTag const & tag)
-{
-    int res = _clearAndReserveMemory(meta, seq, reader, tag);
-    clear(qual);
-    reserve(qual, capacity(seq), Exact());
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function _readMetaAndSequence() and helpers
-// ----------------------------------------------------------------------------
-
-// This overload of _readSequenceFastAQ() assumes that the separator characters, such as '>'/'+' are not part of
-// the alphabet.  This way, we can use _readHelper() and do not have to fall back to the more complicated way
-// used in the case of char.
-
-template <typename TAlph, typename TSpec, typename TRecordReader, typename TFormatTag>
-inline int
-_readSequenceFastAQ(String<TAlph, TSpec> & string,
-                    TRecordReader & reader,
-                    TFormatTag const & /*formatTag*/)
-{
-//     return _readHelper(string, reader, Tag<TAlph>(), Whitespace_(), false);
-    return _readHelper(string, reader, AlphaNum_(), Whitespace_(), false);
-}
-
-// If we want to read char values from a FASTA or FASTQ file then we have to fall back to a more complicated
-// algorithm, this is similar to the corresponding variant of _countSequenceFastAQ().
-//
-// TODO(holtgrew): Very similar to the _countSequenceFastAQ() function, can we make improve this using functors?
-
-template <typename TString, typename TRecordReader, typename TFormatTag>
-inline int
-_readSequenceFastAQCharImpl(TString & string,
-                            TRecordReader & reader,
-                            TFormatTag const & /*formatTag*/)
-{
-    // The variable afterEol is true if we are after an EOL char and we are not at the beginning of the sequence
-    // record.  Empty sequence lines are fine, non-existent ones are not.
-    bool afterEol = false;
-
-    while (!atEnd(reader))
-    {
-        char c = value(reader);
-        if (c == '\r' || c == '\n')
-        {
-            afterEol = true;
-            goNext(reader);
-            if (resultCode(reader) != 0)
-                return resultCode(reader);
-            continue;
-        }
-
-        if (afterEol && c == AfterSeqFirstChar_<TFormatTag>::VALUE)
-        {
-            return 0;  // Done, at stop char.
-        }
-
-        if (!isspace(c))
-            appendValue(string, c);
-        afterEol = false;
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-
-    return EOF_BEFORE_SUCCESS;
-}
-
-template <typename TSpec, typename TRecordReader, typename TFormatTag>
-inline int
-_readSequenceFastAQ(String<char, TSpec> & string,
-                    TRecordReader & reader,
-                    TFormatTag const & formatTag)
-{
-    return _readSequenceFastAQCharImpl(string, reader, formatTag);
-}
-
-template <typename TString, typename TRecordReader, typename TFormatTag>
-inline int
-_readSequenceFastAQ(TString & string,
-                    TRecordReader & reader,
-                    TFormatTag const & formatTag)
-{
-    return _readSequenceFastAQCharImpl(string, reader, formatTag);
-}
-
-// This reads Meta and Sequence
-template <typename TIdString,
-          typename TSeqString,
-          typename TFile,
-          typename TPass,
-          typename TTag>
-inline int
-_readMetaAndSequence(TIdString & meta, TSeqString & seq,
-                     RecordReader<TFile, TPass > & reader,
-                     TTag const & formatTag)
-{
-    // READ META
-    if (atEnd(reader) || value(reader) != MetaFirstChar_<TTag>::VALUE)
-        return RecordReader<TFile, TPass>::INVALID_FORMAT;
-    goNext(reader);
-    if (resultCode(reader))
-        return resultCode(reader);
-    if (atEnd(reader)) // empty ID, no sequence, this is legal
-        return 0;
-
-    int res = readLine(meta, reader);
-    if (res == EOF_BEFORE_SUCCESS)
-        return EOF_BEFORE_SUCCESS;
-    else if (res)
-        return res;
-
-    if (atEnd(reader)) // no sequence
-        return 0;
-
-    // READ SEQUENCE
-    res = _readSequenceFastAQ(seq, reader, formatTag);
-    if (res && res != EOF_BEFORE_SUCCESS)
-        return res;
-
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function _skipQualityBlock() and _readQualityBlock()
-// ----------------------------------------------------------------------------
-
-template <typename TFile, typename TPass>
-inline int
-_skipQualityBlock(RecordReader<TFile, TPass > & /**/,
-                  unsigned const /**/,
-                  Fasta const & /*tag*/)
-{
-    // NOOP for Fasta
-    return 0;
-}
-
-template <typename TFile, typename TPass>
-inline int
-_skipQualityBlock(RecordReader<TFile, TPass > & reader,
-                  unsigned const seqLength,
-                  Fastq const & /*tag*/)
-{
-    int res = 0;
-    // SKIP QUALITIES' META
-    skipLine(reader);
-    if (res == EOF_BEFORE_SUCCESS)  // EOF half way in ID is legal
-        return 0;
-    else if (res)
-        return res;
-
-    // SKIP QUALITIES
-    res = skipNCharsIgnoringWhitespace(reader, seqLength); // there have to be n qualities
-    if (res && res == EOF_BEFORE_SUCCESS)
-        return EOF_BEFORE_SUCCESS;
-    else if (res)
-        return RecordReader<TFile, TPass >::INVALID_FORMAT;
-    skipLine(reader); // goto to next line if it exists, result is unimportant
-
-    return 0;
-}
-
-// Reading of the quality block.
-template <typename TSeqString, typename TFile, typename TPass>
-inline int _readQualityBlockHelper(TSeqString & seq,
-                                   RecordReader<TFile, TPass > & reader,
-                                   unsigned const seqLength,
-                                   True const & /*assign qualities to seq*/)
-{
-    // Copy of readNCharsIgnoringWhitespace but we assign to seq instead of appending
-    // to a string.
-    typedef typename Iterator<TSeqString, Rooted>::Type TSeqIter;
-    TSeqIter it = begin(seq, Rooted());
-    
-    for (unsigned i = 0; i < seqLength; ++i)
-    {
-        if (atEnd(reader))
-            return EOF_BEFORE_SUCCESS;
-
-        if (_charCompare(value(reader), Whitespace_()))
-        {
-            --i;
-        }
-        else
-        {
-            SEQAN_ASSERT(!atEnd(it));
-            assignQualityValue(*it, value(reader));
-            goNext(it);
-        }
-
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return 0;
-}
-
-template <typename TQualString, typename TFile, typename TPass>
-inline int _readQualityBlockHelper(TQualString & qual,
-                                   RecordReader<TFile, TPass > & reader,
-                                   unsigned const seqLength,
-                                   False const & /*qual is character sequence*/)
-{
-    reserve(qual, seqLength, Exact());
-    return readNCharsIgnoringWhitespace(qual, reader, seqLength);
-}
-
-template <typename TIdString,
-          typename TQualString,
-          typename TFile,
-          typename TPass>
-inline int
-_readQualityBlock(TQualString & qual,
-                  RecordReader<TFile, TPass > & reader,
-                  unsigned const seqLength,
-                  TIdString const & meta,
-                  Fastq const & /*tag*/)
-{
-    // READ AND CHECK QUALITIES' META
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (value(reader) != '+')
-        return RecordReader<TFile, TPass >::INVALID_FORMAT;
-    goNext(reader);
-    if (resultCode(reader))
-        return resultCode(reader);
-    if (atEnd(reader)) // empty ID, no sequence, this is legal? TODO
-        return 0;
-
-    CharString qualmeta_buffer;
-    int res = readLine(qualmeta_buffer, reader);
-    if (res && res == EOF_BEFORE_SUCCESS)
-        return EOF_BEFORE_SUCCESS;
-    else if (res)
-        return RecordReader<TFile, TPass >::INVALID_FORMAT;
-
-    // meta string has to be empty or identical to sequence's meta
-    if ((qualmeta_buffer != "") && (qualmeta_buffer != meta))
-        return RecordReader<TFile, TPass >::INVALID_FORMAT;
-
-    if (atEnd(reader)) // empty qualities, is this legal?
-        return 0;
-
-    // READ QUALITIES
-    res = _readQualityBlockHelper(qual, reader, seqLength, typename HasQualities<typename Value<TQualString>::Type>::Type());
-    // there have to be n qualities
-    if (res && res == EOF_BEFORE_SUCCESS)
-        return EOF_BEFORE_SUCCESS;
-    else if (res)
-        return RecordReader<TFile, TPass >::INVALID_FORMAT;
-    skipLine(reader); // goto to next line if it exists, result is unimportant
-
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function readRecord()                               [Single and double pass]
-// ----------------------------------------------------------------------------
-/**
-.Function.readRecord
-..signature:readRecord(TIdString & meta, TSeqString & seq, TRecordReader & reader, Fasta const &)
-..remarks:For FASTA-Files a double-Pass implementation of RecordReader is implemented, which offers better performance. Just pass a Double-Pass reader object (only works with seekable Streams).
-*/
-
-/**
-.Function.readRecord
-..signature:readRecord(TIdString & meta, TSeqString & seq, TRecordReader & reader, Fastq const &)
-*/
-
-template <typename TIdString,
-          typename TSeqString,
-          typename TFile,
-          typename TPass>
-inline int
-readRecord(TIdString & meta,
-           TSeqString & seq,
-           RecordReader<TFile, TPass > & reader,
-           Fasta const & /*tag*/)
-{
-    int res = _clearAndReserveMemory(meta, seq, reader, Fasta());
-    if (res)
-        return res;
-
-    res = _readMetaAndSequence(meta, seq, reader, Fasta());
-    if (res)
-        return res;
-
-    return _skipQualityBlock(reader, length(seq), Fasta());
-}
-
-template <typename TIdString,
-          typename TSeqString,
-          typename TQualString,
-          typename TFile,
-          typename TPass>
-inline int
-readRecord(TIdString & meta,
-           TSeqString & seq,
-           TQualString & quals,
-           RecordReader<TFile, TPass > & reader,
-           Fasta const & /*tag*/)
-{
-    int res = _clearAndReserveMemory(meta, seq, reader, Fasta());
-    if (res)
-        return res;
-
-    clear(quals);
-
-    res = _readMetaAndSequence(meta, seq, reader, Fasta());
-    if (res)
-        return res;
-
-    return _skipQualityBlock(reader, length(seq), Fasta());
-}
-
-template <typename TIdString,
-          typename TSeqString,
-          typename TFile,
-          typename TPass>
-inline int
-readRecord(TIdString & meta,
-           TSeqString & seq,
-           RecordReader<TFile, TPass > & reader,
-           Fastq const & /*tag*/)
-{
-    int res = _clearAndReserveMemory(meta, seq, reader, Fastq());
-    if (res)
-        return res;
-
-    res = _readMetaAndSequence(meta, seq, reader, Fastq());
-    if (res)
-        return res;
-
-    if (HasQualities<typename Value<TSeqString>::Type>::VALUE)
-        return _readQualityBlock(seq, reader, length(seq), meta, Fastq());
-    else
-        return _skipQualityBlock(reader, length(seq), Fastq());
-}
-
-/*!
- * @fn FastaFastqIO#readRecord
- * @headerfile <seqan/seq_io.h>
- * @brief Read one FASTA or FASTQ record.
- * 
- * @signature int readRecord(id, seq, stream, tag);
- * @signature int readRecord(id, seq, quals, stream, tag);
- * 
- * @param[in,out] stream  The @link StreamConcept @endlink to read from.
- * @param[in]     id      @link SequenceConcept @endlink to read identifier into.
- * @param[in]     seq     @link SequenceConcept @endlink to read sequence into.
- * @param[in]     quals   @link SequenceConcept @endlink to read qualities into.
- * @param[in]     tag     The format selector. Types: nolink:<tt>Fasta</tt>, <tt>Fastq</tt>
- *
- * @return int 0 on success, non-0 value on errors.
- */
-
-/**
-.Function.readRecord
-..signature:readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TRecordReader & reader, Fastq const &)
-..remarks:For FASTQ-Files a double-Pass implementation of RecordReader is implemented, which offers better performance. Just pass a Double-Pass reader object (only works with seekable Streams).
-*/
-
-// FASTQ and we want explicit qualities
-template <typename TIdString,
-          typename TSeqString,
-          typename TQualString,
-          typename TFile,
-          typename TPass>
-inline int
-readRecord(TIdString & meta,
-           TSeqString & seq,
-           TQualString & qual,
-           RecordReader<TFile, TPass > & reader,
-           Fastq const & /*tag*/)
-{
-    int res = _clearAndReserveMemory(meta, seq, qual, reader, Fastq());
-    if (res)
-        return res;
-
-    res = _readMetaAndSequence(meta, seq, reader, Fastq());
-    if (res)
-        return res;
-
-    res = _readQualityBlock(qual, reader, length(seq), meta, Fastq());
-    if (res == 0 || res == EOF_BEFORE_SUCCESS)
-        return 0;
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function read();  Double-Pass.
-// ----------------------------------------------------------------------------
-
-// Reads a whole FASTA/FASTQ file into string sets, optimizing memory usage.
-// optimized for ConcatDirect StringSets
-
-template <typename TIdString, typename TSeqString, typename TQualString, typename TRecordReader>
-inline int
-_readFastAQQualityReadDispatcher(StringSet<TIdString, Owner<ConcatDirect<> > > & sequenceIds,
-                                 StringSet<TSeqString, Owner<ConcatDirect<> > > & sequences,
-                                 StringSet<TQualString, Owner<ConcatDirect<> > > & /*qualities*/,
-                                 TRecordReader & reader,
-                                 unsigned i,
-                                 True const & /*seq has qualities*/)
-{
-    typedef StringSet<TSeqString, Owner<ConcatDirect<> > > TSequenceSet;
-    typedef typename Concatenator<TSequenceSet>::Type TConcat;
-    typedef typename Suffix<TConcat>::Type TSuffix;
-    TSuffix s(concat(sequences), sequences.limits[i]);
-    return _readQualityBlock(s, reader, length(sequences[i]), sequenceIds[i], Fastq());
-}
-
-template <typename TIdString, typename TSeqString, typename TQualString, typename TRecordReader>
-inline int
-_readFastAQQualityReadDispatcher(StringSet<TIdString, Owner<ConcatDirect<> > > & sequenceIds,
-                                 StringSet<TSeqString, Owner<ConcatDirect<> > > & sequences,
-                                 StringSet<TQualString, Owner<ConcatDirect<> > > & qualities,
-                                 TRecordReader & reader,
-                                 unsigned i,
-                                 False const & /*qualities are explicit*/)
-{
-    return _readQualityBlock(qualities.concat, reader, length(sequences[i]), sequenceIds[i], Fastq());
-}
-
-template <typename TIdString,
-          typename TSeqString,
-          typename TQualString,
-          typename TFile,
-          typename TSpec,
-          typename TTag>
-int _readFastAQ(StringSet<TIdString, Owner<ConcatDirect<> > > & sequenceIds,
-                StringSet<TSeqString, Owner<ConcatDirect<> > > & sequences,
-                StringSet<TQualString, Owner<ConcatDirect<> > > & qualities,
-                RecordReader<TFile, DoublePass<TSpec> > & reader,
-                bool const withQual,
-                TTag const & /*tag*/)
-{
-    int res = 0;
-    String<unsigned> metaLengths;
-    String<unsigned> seqLengths;
-
-    // ------------------------------------------------------------------------
-    // First Pass: Compute meta and sequence lengths.
-    // ------------------------------------------------------------------------
-    startFirstPass(reader);
-    size_t sequenceCount = 0;
-    while (!atEnd(reader))
-    {
-        sequenceCount += 1;
-        unsigned metaLength = 0;
-        unsigned seqLength = 0;
-        res = _countMetaAndSequence(metaLength,
-                                    seqLength,
-                                    reader,
-                                    TTag(),
-                                    typename Value<TSeqString>::Type());
-        if (res)
-            return res;
-
-        appendValue(metaLengths, metaLength, Generous());
-        appendValue(seqLengths, seqLength, Generous());
-
-        res = _skipQualityBlock(reader, seqLength, TTag());
-        if (res)
-            return res;
-    }
-
-    // ------------------------------------------------------------------------
-    // Allocate memory.
-    // ------------------------------------------------------------------------
-    clear(sequenceIds);
-    clear(sequences);
-    if (withQual && !HasQualities<typename Value<TSeqString>::Type>::VALUE)
-        clear(qualities);
-
-    resize(sequenceIds.limits, sequenceCount + 1, Exact());
-    resize(sequences.limits, sequenceCount + 1, Exact());
-    sequenceIds.limits[0] = 0;
-    sequences.limits[0] = 0;
-
-    unsigned long metaLengthsSum = 0;
-    unsigned long seqLengthsSum = 0;
-
-    for (unsigned int i = 0; i < sequenceCount; ++i)
-    {
-        metaLengthsSum += metaLengths[i];
-        sequenceIds.limits[i+1] = metaLengthsSum;
-        seqLengthsSum += seqLengths[i];
-        sequences.limits[i+1] = seqLengthsSum;
-    }
-
-    reserve(sequenceIds.concat, metaLengthsSum + 1, Exact());
-    reserve(sequences.concat, seqLengthsSum + 1, Exact());
-    if (withQual && !HasQualities<typename Value<TSeqString>::Type>::VALUE)
-    {
-        assign(qualities.limits, sequences.limits);
-        reserve(qualities.concat, seqLengthsSum + 1, Exact());
-    }
-
-    // ------------------------------------------------------------------------
-    // Second Pass: Actually read data.
-    // ------------------------------------------------------------------------
-    startSecondPass(reader);
-    for (unsigned int i = 0; i < sequenceCount; ++i)
-    {
-        res = _readMetaAndSequence(sequenceIds.concat,
-                                   sequences.concat,
-                                   reader,
-                                   TTag());
-        switch(res)
-        {
-            case 0:
-                break;
-            case EOF_BEFORE_SUCCESS:        // file may end without newline
-                if (i >= sequenceCount -1)
-                    break;
-            default:
-                return res;
-        }
-        if (withQual)
-        {
-            _readFastAQQualityReadDispatcher(sequenceIds, sequences, qualities, reader, i, typename HasQualities<typename Value<TSeqString>::Type>::Type());
-        }
-        else
-        {
-            res = _skipQualityBlock(reader, length(sequences[i]), TTag());
-        }
-        if (res)
-            return res;
-    }
-
-    return 0;
-}
-
-// Reads a whole FASTA/FASTQ file into string sets, optimizing memory usage.
-// Generic, non-concat version
-template <typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec,
-          typename TQualString, typename TQualSpec,
-          typename TFile,
-          typename TSpec,
-          typename TTag>
-int _readFastAQ(StringSet<TIdString, TIdSpec> & sequenceIds,
-                StringSet<TSeqString, TSeqSpec> & sequences,
-                StringSet<TQualString, TQualSpec> & qualities,
-                RecordReader<TFile, DoublePass<TSpec> > & reader,
-                bool const withQual,
-                TTag const & /*tag*/)
-{
-    int res = 0;
-    String<unsigned> metaLengths;
-    String<unsigned> seqLengths;
-
-    // ------------------------------------------------------------------------
-    // First Pass: Compute meta and sequence lengths.
-    // ------------------------------------------------------------------------
-    startFirstPass(reader);
-    size_t sequenceCount = 0;
-    while (!atEnd(reader))
-    {
-        sequenceCount += 1;
-        unsigned metaLength = 0;
-        unsigned seqLength = 0;
-        res = _countMetaAndSequence(metaLength,
-                                    seqLength,
-                                    reader,
-                                    TTag(),
-                                    typename Value<TSeqString>::Type());
-        if (res)
-            return res;
-
-        appendValue(metaLengths, metaLength, Generous());
-        appendValue(seqLengths, seqLength, Generous());
-
-        res = _skipQualityBlock(reader, seqLength, TTag());
-        if (res)
-            return res;
-    }
-
-    // ------------------------------------------------------------------------
-    // Allocate memory.
-    // ------------------------------------------------------------------------
-    clear(sequenceIds);
-    clear(sequences);
-    if (withQual && !HasQualities<typename Value<TSeqString>::Type>::VALUE)
-        clear(qualities);
-
-    resize(sequenceIds, sequenceCount, Exact());
-    resize(sequences, sequenceCount, Exact());
-    if (withQual && !HasQualities<typename Value<TSeqString>::Type>::VALUE)
-        resize(qualities, sequenceCount, Exact());
-
-    for (unsigned int i = 0; i < sequenceCount; ++i)
-    {
-        reserve(sequenceIds[i], metaLengths[i], Exact());
-        reserve(sequences[i], seqLengths[i], Exact());
-        if (withQual && !HasQualities<typename Value<TSeqString>::Type>::VALUE)
-            reserve(qualities[i], seqLengths[i], Exact());
-    }
-
-    // ------------------------------------------------------------------------
-    // Second Pass: Actually read data.
-    // ------------------------------------------------------------------------
-    startSecondPass(reader);
-    for (unsigned int i = 0; i < sequenceCount; ++i)
-    {
-        res = _readMetaAndSequence(sequenceIds[i],
-                                   sequences[i],
-                                   reader,
-                                   TTag());
-        switch(res)
-        {
-            case 0:
-                break;
-            case EOF_BEFORE_SUCCESS:        // file may end without newline
-                if (i >= sequenceCount -1)
-                    break;
-            default:
-                return res;
-        }
-        if (withQual)
-        {
-            if (HasQualities<typename Value<TSeqString>::Type>::VALUE)
-                res = _readQualityBlock(sequences[i], reader, length(sequences[i]), sequenceIds[i], Fastq());
-            else
-                res = _readQualityBlock(qualities[i], reader, length(sequences[i]), sequenceIds[i], Fastq());
-        }
-        else
-        {
-            res = _skipQualityBlock(reader, length(sequences[i]), TTag());
-        }
-        if (res)
-            return res;
-    }
-    return 0;
-}
-
-/*!
- * @fn FastaFastqIO#read2
- * @headerfile <seqan/seq_io.h>
- * @brief Read a whole FASTA or FASTQ file into StringSet objects.
- * 
- * @signature int read2(ids, seqs, reader, tag);
- * @signature int read2(ids, seqs, qualss, reader, tag);
- * 
- * @param[in,out] stream  The @link StreamConcept @endlink to read from.
- * @param[in]     ids     The @link StringSet @endlink to read the ids into.
- * @param[in]     seqs    The @link StringSet @endlink to read the sequences into.
- * @param[in]     quals   The @link StringSet @endlink to read the ASCII qualities into.
- * @param[in]     tags    The format selector. Types: nolink:<tt>Fasta</tt>, <tt>Fastq</tt>
- *
- * @return int 0 on success, non-0 value on errors.
- */
-
-/**
-.Function.read2
-..signature:read2(StringSet<TIdString, TIdSpec> & sequenceIds, StringSet<TSeqString, TSeqSpec> & sequences, RecordReader<TFile, DoublePass<TSpec> > & reader, Fasta const &)
-*/
-
-// FASTA
-template <typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec,
-          typename TFile,
-          typename TSpec>
-int read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> & sequences,
-         RecordReader<TFile, DoublePass<TSpec> > & reader,
-         Fasta const & /*tag*/)
-{
-    StringSet<CharString, TSeqSpec> qualities;
-    return _readFastAQ(sequenceIds, sequences, qualities, reader, false, Fasta());
-}
-
-template <typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec,
-          typename TQualString, typename TQualSpec,
-          typename TFile,
-          typename TSpec>
-int read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> & sequences,
-         StringSet<TQualString, TQualSpec> & qualities,
-         RecordReader<TFile, DoublePass<TSpec> > & reader,
-         Fasta const & /*tag*/)
-{
-    int res = _readFastAQ(sequenceIds, sequences, qualities, reader, false, Fasta());
-    clear(qualities);
-    resize(qualities, length(sequences));
-    return res;
-}
-
-/**
-.Function.read2
-..signature:read2(StringSet<TIdString, TIdSpec> & sequenceIds, StringSet<TSeqString, TSeqSpec> & sequences, RecordReader<TFile, DoublePass<TSpec> > & reader, Fastq const &)
-*/
-
-// FASTQ, if we don't have explicit qualities.
-template <typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec,
-          typename TFile,
-          typename TSpec>
-int read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> & sequences,
-         RecordReader<TFile, DoublePass<TSpec> > & reader,
-         Fastq const & /*tag*/)
-{
-    typedef typename Value<TSeqString>::Type TChar;
-    StringSet<CharString, TSeqSpec> qualities;
-    return _readFastAQ(sequenceIds, sequences, qualities, reader, HasQualities<TChar>::VALUE, Fastq());
-}
-
-/**
-.Function.read2
-..signature:read2(StringSet<TIdString, TIdSpec> & sequenceIds, StringSet<TSeqString, TSeqSpec> & sequences, StringSet<TQualString, TQualSpec> & qualities, RecordReader<TFile, DoublePass<TSpec> > & reader, Fastq const &)
-*/
-
-// FASTQ and we want Qualities
-template <typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec,
-          typename TQualString, typename TQualSpec,
-          typename TFile,
-          typename TSpec>
-int read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> & sequences,
-         StringSet<TQualString, TQualSpec> & qualities,
-         RecordReader<TFile, DoublePass<TSpec> > & reader,
-         Fastq const & /*tag*/)
-{
-    return _readFastAQ(sequenceIds, sequences, qualities, reader, true, Fastq());
-}
-
-// ----------------------------------------------------------------------------
-// Function read();  Single-Pass
-// ----------------------------------------------------------------------------
-
-template <typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec,
-          typename TFile,
-          typename TSpec, typename TTag>
-typename EnableIf<typename Or<typename IsSameType<typename RemoveConst_<TTag>::Type, typename RemoveConst_<Fasta>::Type >::Type,
-                              typename IsSameType<typename RemoveConst_<TTag>::Type, typename RemoveConst_<Fastq>::Type >::Type>::Type,
-                   int>::Type
-read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-      StringSet<TSeqString, TSeqSpec> & sequences,
-      RecordReader<TFile, SinglePass<TSpec> > & reader,
-      TTag const & tag)
-{
-    TIdString id;
-    TSeqString seq;
-    while (!atEnd(reader))
-    {
-        int res = readRecord(id, seq, reader, tag);
-        if (res != 0)
-            return res;
-        appendValue(sequenceIds, id);
-        appendValue(sequences, seq);
-    }
-    return 0;
-}
-
-template <typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec,
-          typename TQualString, typename TQualSpec,
-          typename TFile,
-          typename TSpec, typename TTag>
-int read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-          StringSet<TSeqString, TSeqSpec> & sequences,
-          StringSet<TQualString, TQualSpec> & qualities,
-          RecordReader<TFile, SinglePass<TSpec> > & reader,
-          TTag const & tag)
-{
-    clear(qualities);
-    return read2(sequenceIds, sequences, reader, tag);
-}
-
-template <typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec,
-          typename TQualString, typename TQualSpec,
-          typename TFile,
-          typename TSpec>
-int read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> & sequences,
-         StringSet<TQualString, TQualSpec> & qualities,
-         RecordReader<TFile, SinglePass<TSpec> > & reader,
-         Fastq const & tag)
-{
-    TIdString id;
-    TSeqString seq;
-    TQualString qual;
-    while (!atEnd(reader))
-    {
-        int res = readRecord(id, seq, qual, reader, tag);
-        if (res != 0)
-            return res;
-        appendValue(sequenceIds, id);
-        appendValue(sequences, seq);
-        appendValue(qualities, qual);
-    }
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function guessStreamFormat()
-// ----------------------------------------------------------------------------
-
-/**
-.Function.guessStreamFormat
-..signature:guessStreamFormat(reader, tag)
-..returns:$bool$, indicating whether the file of $reader$ is of the given format.
-..param.reader:RecordReader to query.
-...type:Class.RecordReader
-..param.tag:Format indicator
-...type:Tag.File Format
-...type:nolink:$Fasta$
-...type:nolink:$Fastq$
-..include:seqan/stream.h
-*/
-
-template <typename TStream, typename TPass>
-inline bool
-guessStreamFormat(RecordReader<TStream, TPass> & reader, Fasta const & /*tag*/)
-{
-    LimitRecordReaderInScope<TStream, TPass> limiter(reader);
-    while (!atEnd(reader))
-    {
-        CharString meta;
-        CharString seq;
-        int r = readRecord(meta, seq, reader, Fasta());
-//         std::cout << "Meta: " << toCString(meta) << "\nSeq: " << toCString(seq) << "\n";
-        if (r == RecordReader<TStream, TPass>::INVALID_FORMAT)
-            return false;
-    }
-    return true;
-}
-
-template <typename TStream, typename TPass>
-inline bool
-guessStreamFormat(RecordReader<TStream, TPass> & reader, Fastq const & /*tag*/)
-{
-    LimitRecordReaderInScope<TStream, TPass> limiter(reader);
-    while (!atEnd(reader))
-    {
-        CharString meta;
-        CharString seq;
-        CharString qual;
-        int r = readRecord(meta, seq, qual, reader, Fastq());
-        if (r == RecordReader<TStream, TPass>::INVALID_FORMAT)
-            return false;
-    }
-    return true;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_SEQ_IO_READ_FASTA_FASTQ_H_
diff --git a/seqan/seq_io/read_genbank.h b/seqan/seq_io/read_genbank.h
index 8d6d1ed..54d41e9 100644
--- a/seqan/seq_io/read_genbank.h
+++ b/seqan/seq_io/read_genbank.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -42,8 +42,8 @@
 // ==========================================================================
 
 
-#ifndef EXTRAS_INCLUDE_SEQAN_SEQ_IO_READ_GENBANK_H_
-#define EXTRAS_INCLUDE_SEQAN_SEQ_IO_READ_GENBANK_H_
+#ifndef INCLUDE_SEQAN_SEQ_IO_READ_GENBANK_H_
+#define INCLUDE_SEQAN_SEQ_IO_READ_GENBANK_H_
 
 namespace seqan {
 
@@ -64,15 +64,38 @@ typedef Tag<GenBankHeader_> GenBankHeader;
 struct GenBankSequence_;
 typedef Tag<GenBankSequence_> GenBankSequence;
 
-enum GenBankErrorCodes_
-{
-    IOERR_GENBANK_WRONG_RECORD = 2048
-};
 
 // ============================================================================
 // Metafunctions
 // ============================================================================
 
+// --------------------------------------------------------------------------
+// Metafunction MagicHeader
+// --------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<GenBank, T>
+{
+    static char const VALUE[6];
+};
+template <typename T>
+char const MagicHeader<GenBank, T>::VALUE[6] = { 'L','O','C','U','S',' ' };  // typical GenBank header
+
+// --------------------------------------------------------------------------
+// Metafunction FileExtensions
+// --------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<GenBank, T>
+{
+    static char const * VALUE[1];
+};
+template <typename T>
+char const * FileExtensions<GenBank, T>::VALUE[1] =
+{
+    ".gbk",     // default output extension
+};
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -86,55 +109,35 @@ enum GenBankErrorCodes_
  * @headerfile <seqan/seq_io.h>
  * @brief Split a GenBank header field/value.
  *
- * @void splitGenkBankHeader(key, value, lines);
+ * @signature void readGenBankHeader(key, value, iter);
  *
- * @param[out] key   The 2-character header type.
- * @param[out] value The line's value.
- * @param[out] lines The lines with the header field to split.
+ * @param[out] key   A @link ContainerConcept @endlink object to write the key to.
+ * @param[out] value A @link ContainerConcept @endlink object to write the value to.
+ * @param[in]  iter  Input iterator.
  */
 
-/**
-.Function.splitGenBankHeader
-..cat:Input/Output
-..signature:splitGenBankHeader(key, value, lines)
-..summary:Split an GenBank header field/value.
-..remarks:You can only call this on a whole top-level field such as $SOURCE$, possibly including the following subfields! You cannot split out subfield values.
-..param.key:The 2-character header type.
-..param.value:The line's value.
-..param.line:The lines with the header field to split.
-..returns:$void$
-..include:seqan/stream.h
-..see:Function.splitEmblHeader
-*/
-
-template <typename TKey, typename TValue, typename TLine>
+// readGenBankHeader() for GenBank header records.
+
+template <typename TKey, typename TValue, typename TFwdIterator>
 inline void
-splitGenBankHeader(TKey & key, TValue & value, TLine const & lines)
+readRecord(TKey & key, TValue & val, TFwdIterator & iter, GenBankHeader)
 {
-    splitEmblHeader(key, value, lines);
     clear(key);
+    clear(val);
 
-    enum State { IN_KEY, IN_SPACE, IN_VALUE };
-    State state = IN_KEY;
+    readUntil(key, iter, IsWhitespace());
 
-    typedef typename Iterator<TLine const, Rooted>::Type TIterator;
-    TIterator it = begin(lines, Rooted());
-    for (; !atEnd(it); goNext(it))
+    if (IsBlank()(value(iter)))
     {
-        if (state == IN_KEY)
-        {
-            if (isblank(*it))
-                state = IN_SPACE;
-            else
-                appendValue(key, *it);
-        }
-        else if (state == IN_SPACE && !isblank(*it))
-        {
-            break;
-        }
+        skipUntil(iter, NotFunctor<IsBlank>());
+        readLine(val, iter);
     }
 
-    value = suffix(lines, position(it));
+    while (IsBlank()(value(iter)))
+    {
+        appendValue(val, '\n');
+        readLine(val, iter);
+    }
 }
 
 // ----------------------------------------------------------------------------
@@ -143,157 +146,102 @@ splitGenBankHeader(TKey & key, TValue & value, TLine const & lines)
 
 // nextIs() for GenBank header records.
 
-template <typename TStream, typename TSpec>
+template <typename TFwdIterator>
 inline bool
-nextIs(RecordReader<TStream, TSpec> & reader, GenBankHeader const & /*tag*/)
+nextIs(TFwdIterator & iter, GenBankHeader)
 {
-    return !atEnd(reader) && value(reader) != 'O' && !isblank(value(reader));
+    return !atEnd(iter) && value(iter) != 'O' && !IsWhitespace()(value(iter));
 }
 
 // nextIs() for GenBank sequence records.
 
-template <typename TStream, typename TSpec>
+template <typename TFwdIterator>
 inline bool
-nextIs(RecordReader<TStream, TSpec> & reader, GenBankSequence const & /*tag*/)
+nextIs(TFwdIterator & iter, GenBankSequence)
 {
-    return !atEnd(reader) && value(reader) == 'O';
+    return !atEnd(iter) && value(iter) == 'O';
 }
 
 // ----------------------------------------------------------------------------
 // Function readRecord()
 // ----------------------------------------------------------------------------
 
-// readRecord() for GenBank header records.
+// readRecord() for GenBank sequences records.
 
-// Normalize in-field line endings to '\n'.
+// Read all sequence, eat/ignore '//' line.
 
-template <typename TTarget, typename TStream, typename TSpec>
-inline int
-readRecord(TTarget & result, RecordReader<TStream, SinglePass<TSpec> > & reader,
-           GenBankHeader const & tag)
+template <typename TSeqString, typename TFwdIterator>
+inline void
+readRecord(TSeqString & seq, TFwdIterator & iter, GenBankSequence)
 {
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (!nextIs(reader, tag))
-        return IOERR_GENBANK_WRONG_RECORD;
-    clear(result);
-
-    int res = readLine(result, reader);
-    if (res != 0)
-        return res;
-    while (!atEnd(reader) && isblank(value(reader)))
-    {
-        appendValue(result, '\n');
-        res = readLine(result, reader);
-        if (res != 0)
-            return res;
-    }
+    typedef typename Value<TSeqString>::Type TSeqAlphabet;
+    typedef OrFunctor<OrFunctor<IsBlank, IsDigit>,
+                      AssertFunctor<IsInAlphabet<TSeqAlphabet>, ParseError, Embl> > TSeqAsserter;
 
-    return 0;
-}
-
-// readRecord() for GenBank sequences records.
+    IsNewline isNewline;
+    TSeqAsserter asserter;
 
-// Read all sequence, eat/ignore '//' line.
+    if (!atEnd(iter) && value(iter) == 'O')
+        skipLine(iter);
 
-template <typename TTarget, typename TStream, typename TSpec>
-inline int
-readRecord(TTarget & result, RecordReader<TStream, SinglePass<TSpec> > & reader,
-           GenBankSequence const & tag)
-{
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (!nextIs(reader, tag))
-        return IOERR_GENBANK_WRONG_RECORD;
-    clear(result);
-
-    // Skip 'ORIGIN' line.
-    CharString buffer;
-    int res = readLine(buffer, reader);
-    if (res != 0)
-        return res;
-    if (!startsWith(buffer, "ORIGIN"))
-        return IOERR_GENBANK_WRONG_RECORD;
-
-    // Read sequence.
-    for (; !atEnd(reader); goNext(reader))
+    clear(seq);
+    for (; !atEnd(iter); skipLine(iter))
     {
-        if (isspace(value(reader)) || isdigit(value(reader)))
-            continue;  // Skip blanks.
-        // If we found a slash, look for the next one.
-        if (value(reader) == '/')
+        if (value(iter) == '/')
         {
-            if (goNext(reader))  // Returns true if at end.
-                break;
-            if (value(reader) == '/')
-            {
-                skipLine(reader);
-                return 0;  // OK, found complete terminator.
-            }
+            skipLine(iter);
+            break;
         }
 
-        // Otherwise, append the just found character to buffer.
-        appendValue(result, value(reader));
+        readUntil(seq, iter, isNewline, asserter);
     }
-
-    return EOF_BEFORE_SUCCESS;
 }
 
 // readRecord() for GenBank id/seq pairs.
 
-template <typename TId, typename TSequence, typename TStream, typename TSpec>
-inline int
-readRecord(TId & id,
-           TSequence & sequence,
-           RecordReader<TStream, SinglePass<TSpec> > & reader,
-           GenBank const & /*tag*/)
+template <typename TIdString, typename TSeqString, typename TFwdIterator>
+inline void
+readRecord(TIdString & meta, TSeqString & seq, TFwdIterator & iter, GenBank)
 {
-    CharString buffer;
-    while (nextIs(reader, GenBankHeader()))
+    IsWhitespace isWhite;
+    IsBlank isBlank;
+    String<char, Array<20> > key;
+
+    // extract meta from "ID" line
+    clear(meta);
+    for (; !atEnd(iter); skipLine(iter))
     {
-        int res = readRecord(buffer, reader, GenBankHeader());
-        if (res != 0)
-            return res;
-        if (startsWith(buffer, "VERSION"))
+        if (isBlank(value(iter)))
+            continue;
+
+        AssertFunctor<NotFunctor<CountDownFunctor<True, 20> >, ParseError, Embl> asserter;
+
+        clear(key);
+        readUntil(key, iter, isWhite, asserter);
+
+        if (key == "VERSION")
         {
-            CharString k;
-            splitGenBankHeader(k, id, buffer);
+            skipUntil(iter, NotFunctor<IsBlank>());
+            readUntil(meta, iter, IsNewline());
+        }
+        else if (key == "ORIGIN")
+        {
+            skipLine(iter);
+            break;
         }
     }
-    clear(sequence);
-    int res = readRecord(sequence, reader, GenBankSequence());
-    if (res != 0)
-        return res;
-    
-    return 0;
-}
 
-// ----------------------------------------------------------------------------
-// Function read2()
-// ----------------------------------------------------------------------------
+    readRecord(seq, iter, GenBankSequence());
+}
 
-template <typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec,
-          typename TStream, typename TSpec>
-int read2(StringSet<TIdString, TIdSpec> & sequenceIds,
-          StringSet<TSeqString, TSeqSpec> & sequences,
-          RecordReader<TStream, SinglePass<TSpec> > & reader,
-          GenBank const & tag)
+template <typename TIdString, typename TSeqString, typename TQualString, typename TFwdIterator>
+inline void
+readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TFwdIterator & iter, GenBank)
 {
-    TIdString id;
-    TSeqString seq;
-
-    while (!atEnd(reader))
-    {
-        int res = readRecord(id, seq, reader, tag);
-        if (res != 0)
-            return res;
-        appendValue(sequenceIds, id);
-        appendValue(sequences, seq);
-    }
-
-    return 0;
+    clear(qual);
+    readRecord(meta, seq, iter, GenBank());
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef EXTRAS_INCLUDE_SEQAN_SEQ_IO_READ_GENBANK_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEQ_IO_READ_GENBANK_H_
diff --git a/seqan/seq_io/sequence_file.h b/seqan/seq_io/sequence_file.h
new file mode 100644
index 0000000..7c717fe
--- /dev/null
+++ b/seqan/seq_io/sequence_file.h
@@ -0,0 +1,417 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+//         David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Class for reading/writing files in Fasta or Fastq format.
+// ==========================================================================
+
+#ifndef SEQAN_SEQ_IO_SEQUENCE_FILE_H_
+#define SEQAN_SEQ_IO_SEQUENCE_FILE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ============================================================================
+// Typedefs
+// ============================================================================
+
+/*!
+ * @class SeqFileIn
+ * @signature typedef FormattedFile<Fastq, Input> SeqFileIn;
+ * @extends FormattedFileIn
+ * @headerfile <seqan/seq_io.h>
+ * @brief Class for reading RAW, FASTA, FASTQ, EMBL and GENBANK files containing unaligned sequences.
+ */
+
+typedef FormattedFile<Fastq, Input>     SeqFileIn;
+
+/*!
+ * @class SeqFileOut
+ * @signature typedef FormattedFile<Fastq, Output> SeqFileOut;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/seq_io.h>
+ * @brief Class for writing RAW, FASTA, FASTQ, EMBL and GENBANK files containing unaligned sequences.
+ */
+
+typedef FormattedFile<Fastq, Output>    SeqFileOut;
+
+// --------------------------------------------------------------------------
+// Tag AutoSeqFormat
+// --------------------------------------------------------------------------
+// if TagSelector is set to -1, the file format is auto-detected
+
+/*!
+ * @class AutoSeqFormat
+ * @extends TagSelector
+ * @headerfile <seqan/file.h>
+ * @brief Auto-detects and stores a file format.
+ *
+ * @signature typedef TagList<Fastq, TagList<Fasta, TagList<Raw> > > SeqFormats;
+ * @signature typedef TagSelector<SeqFormat> AutoSeqFormat;
+ */
+
+typedef
+    TagList<Fastq,
+    TagList<Fasta,
+    TagList<Embl,
+    TagList<GenBank,
+    TagList<Raw
+    > > > > >
+    SeqInFormats;
+
+typedef
+    TagList<Fastq,
+    TagList<Fasta,
+    TagList<Raw
+    > > >
+    SeqOutFormats;
+
+typedef TagSelector<SeqInFormats>   SeqInFormat;
+typedef TagSelector<SeqOutFormats>  SeqOutFormat;
+
+// deprecated
+typedef SeqInFormat AutoSeqFormat;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction SeqFileBuffer_
+// ----------------------------------------------------------------------------
+
+template <typename TSeqStringSet, typename TSpec>
+struct SeqFileBuffer_
+{
+    typedef typename Value<TSeqStringSet>::Type     TSeqString;
+    typedef typename Value<TSeqString>::Type        TSeqAlphabet;
+
+    typedef String<TSeqAlphabet>                    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction SeqFileContext_
+// ----------------------------------------------------------------------------
+
+template <typename TDirection>
+struct SeqFileContext_;
+
+template <>
+struct SeqFileContext_<Input>
+{
+    Tuple<CharString, 3>    buffer;
+    Dna5QString             hybrid;
+};
+
+template <>
+struct SeqFileContext_<Output>
+{
+    SequenceOutputOptions   options;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TDirection, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<Fastq, TDirection, TSpec>, TStorageSpec>
+{
+    typedef SeqFileContext_<TDirection> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TSpec>
+struct FileFormat<FormattedFile<Fastq, Input, TSpec> >
+{
+    typedef TagSelector<SeqInFormats> Type;
+};
+
+template <typename TSpec>
+struct FileFormat<FormattedFile<Fastq, Output, TSpec> >
+{
+    typedef TagSelector<SeqOutFormats> Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord(); Qualities in seq string
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn SeqFileIn#readRecord
+ * @brief Read one @link FormattedFileRecordConcept @endlink from a @link SeqFileIn @endlink object.
+ *
+ * @signature void readRecord(meta, seq, qual, fileIn);
+ *
+ * @param[out] meta         The @link StringConcept @endlink object where to read the meta information into.
+ * @param[out] seq          The @link StringConcept @endlink object where to read the sequence information into.
+ * @param[out] qual         The @link StringConcept @endlink object where to read the quality information into.
+ * @param[in,out] fileIn    The @link SeqFileIn @endlink object to read from.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+template <typename TSpec, typename TIdString, typename TSeqString>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<InputStreamConcept<typename FormattedFile<Fastq, Input, TSpec>::TStream> >,
+                                Not<HasQualities<typename Value<TSeqString>::Type> > >, void)
+readRecord(TIdString & meta, TSeqString & seq, FormattedFile<Fastq, Input, TSpec> & file)
+{
+    readRecord(meta, seq, file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(); No qualities in seq string
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIdString, typename TSeqString>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<InputStreamConcept<typename FormattedFile<Fastq, Input, TSpec>::TStream> >,
+                                HasQualities<typename Value<TSeqString>::Type> >, void)
+readRecord(TIdString & meta, TSeqString & seq, FormattedFile<Fastq, Input, TSpec> & file)
+{
+    readRecord(meta, seq, context(file).buffer[2], file.iter, file.format);
+    assignQualities(seq, context(file).buffer[2]);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord(); With separate qualities
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIdString, typename TSeqString, typename TQualString>
+inline SEQAN_FUNC_ENABLE_IF(Is<InputStreamConcept<typename FormattedFile<Fastq, Input, TSpec>::TStream> >, void)
+readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, FormattedFile<Fastq, Input, TSpec> & file)
+{
+    readRecord(meta, seq, qual, file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecords()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn SeqFileIn#readRecords
+ * @brief Read many @link FormattedFileRecordConcept @endlink from a @link SeqFileIn @endlink object.
+ * @signature void readRecords(metas, seqs, quals, fileIn, numRecord);
+ * @see SeqFileIn#readRecord
+ */
+
+template <typename TPtrA, typename TPtrB>
+inline void
+swapPtr(TPtrA &a, TPtrB &b)
+{
+    union {
+        TPtrA a;
+        TPtrB b;
+    } tmp1, tmp2;
+    tmp1.a = a;
+    tmp2.b = b;
+    b = tmp1.b;
+    a = tmp2.a;
+}
+
+template <typename TIdStringSet, typename TSeqStringSet, typename TSpec, typename TSize>
+inline void readRecords(TIdStringSet & meta,
+                        TSeqStringSet & seq,
+                        FormattedFile<Fastq, Input, TSpec> & file,
+                        TSize maxRecords)
+{
+    typedef typename SeqFileBuffer_<TSeqStringSet, TSpec>::Type TSeqBuffer;
+
+    TSeqBuffer seqBuffer;
+
+    // reuse the memory of context(file).buffer for seqBuffer (which has a different type but same sizeof(Alphabet))
+    swapPtr(seqBuffer.data_begin, context(file).buffer[1].data_begin);
+    swapPtr(seqBuffer.data_end, context(file).buffer[1].data_end);
+    seqBuffer.data_capacity = context(file).buffer[1].data_capacity;
+
+    for (; !atEnd(file) && maxRecords > 0; --maxRecords)
+    {
+        readRecord(context(file).buffer[0], seqBuffer, file);
+        appendValue(meta, context(file).buffer[0]);
+        appendValue(seq, seqBuffer);
+    }
+
+    swapPtr(seqBuffer.data_begin, context(file).buffer[1].data_begin);
+    swapPtr(seqBuffer.data_end, context(file).buffer[1].data_end);
+    context(file).buffer[1].data_capacity = seqBuffer.data_capacity;
+    seqBuffer.data_capacity = 0;
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecords(); Without max records
+// ----------------------------------------------------------------------------
+
+template <typename TIdStringSet, typename TSeqStringSet, typename TSpec>
+inline void readRecords(TIdStringSet & meta,
+                        TSeqStringSet & seq,
+                        FormattedFile<Fastq, Input, TSpec> & file)
+{
+    readRecords(meta, seq, file, MaxValue<__uint64>::VALUE);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecords(); With separate qualities
+// ----------------------------------------------------------------------------
+
+template <typename TIdStringSet, typename TSeqStringSet, typename TQualStringSet, typename TSpec, typename TSize>
+inline void readRecords(TIdStringSet & meta,
+                        TSeqStringSet & seq,
+                        TQualStringSet & qual,
+                        FormattedFile<Fastq, Input, TSpec> & file,
+                        TSize maxRecords)
+{
+    typedef typename SeqFileBuffer_<TSeqStringSet, TSpec>::Type TSeqBuffer;
+
+    TSeqBuffer seqBuffer;
+
+    // reuse the memory of context(file).buffer for seqBuffer (which has a different type but same sizeof(Alphabet))
+    std::swap(reinterpret_cast<char* &>(seqBuffer.data_begin), context(file).buffer[1].data_begin);
+    std::swap(reinterpret_cast<char* &>(seqBuffer.data_end), context(file).buffer[1].data_end);
+    std::swap(seqBuffer.data_capacity, context(file).buffer[1].data_capacity);
+
+    for (; !atEnd(file) && maxRecords > 0; --maxRecords)
+    {
+        readRecord(context(file).buffer[0], seqBuffer, context(file).buffer[2], file);
+        appendValue(meta, context(file).buffer[0]);
+        appendValue(seq, seqBuffer);
+        appendValue(qual, context(file).buffer[2]);
+    }
+
+    std::swap(reinterpret_cast<char* &>(seqBuffer.data_begin), context(file).buffer[1].data_begin);
+    std::swap(reinterpret_cast<char* &>(seqBuffer.data_end), context(file).buffer[1].data_end);
+    std::swap(seqBuffer.data_capacity, context(file).buffer[1].data_capacity);
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecords(); With separate qualities; Without max records
+// ----------------------------------------------------------------------------
+
+template <typename TIdStringSet, typename TSeqStringSet, typename TQualStringSet, typename TSpec>
+inline void readRecords(TIdStringSet & meta,
+                        TSeqStringSet & seq,
+                        TQualStringSet & qual,
+                        FormattedFile<Fastq, Input, TSpec> & file)
+{
+    readRecords(meta, seq, qual, file, MaxValue<__uint64>::VALUE);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn SeqFileOut#writeRecord
+ * @brief Write one @link FormattedFileRecordConcept @endlink into a @link SeqFileOut @endlink object.
+ *
+ * @signature void writeRecord(fileOut, meta, seq, qual);
+ *
+ * @param[in,out] fileOut   The @link SeqFileOut @endlink object to write into.
+ * @param[in] meta          The @link StringConcept @endlink object where to read the meta information from.
+ * @param[in] seq           The @link StringConcept @endlink object where to read the sequence information from.
+ * @param[in] qual          The @link StringConcept @endlink object where to read the quality information from.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+template <typename TSpec, typename TIdString, typename TSeqString>
+inline SEQAN_FUNC_ENABLE_IF(Is<OutputStreamConcept<typename FormattedFile<Fastq, Output, TSpec>::TStream> >, void)
+writeRecord(FormattedFile<Fastq, Output, TSpec> & file,
+            TIdString const & meta,
+            TSeqString const & seq)
+{
+    writeRecord(file.iter, meta, seq, file.format, context(file).options);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(); With separate qualities
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIdString, typename TSeqString, typename TQualString>
+inline SEQAN_FUNC_ENABLE_IF(Is<OutputStreamConcept<typename FormattedFile<Fastq, Output, TSpec>::TStream> >, void)
+writeRecord(FormattedFile<Fastq, Output, TSpec> & file,
+            TIdString const & meta,
+            TSeqString const & seq,
+            TQualString const & qual)
+{
+    writeRecord(file.iter, meta, seq, qual, file.format, context(file).options);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecords()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn SeqFileOut#writeRecords
+ * @brief Write many @link FormattedFileRecordConcept @endlink into a @link SeqFileOut @endlink object.
+ * @signature void writeRecords(fileOut, metas, seqs, quals);
+ * @see SeqFileOut#writeRecord
+ */
+
+template <typename TSpec, typename TIdStringSet, typename TSeqStringSet>
+inline void
+writeRecords(FormattedFile<Fastq, Output, TSpec> & file,
+             TIdStringSet const & meta,
+             TSeqStringSet const & seq)
+{
+    for (typename Size<TIdStringSet>::Type i = 0; i != length(seq); ++i)
+        writeRecord(file, meta[i], seq[i]);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecords(); With separate qualities
+// ----------------------------------------------------------------------------
+
+template <typename TSpec, typename TIdStringSet, typename TSeqStringSet, typename TQualStringSet>
+inline void
+writeRecords(FormattedFile<Fastq, Output, TSpec> & file,
+             TIdStringSet const & meta,
+             TSeqStringSet const & seq,
+             TQualStringSet const & qual)
+{
+    for (typename Size<TIdStringSet>::Type i = 0; i != length(seq); ++i)
+        writeRecord(file, meta[i], seq[i], qual[i]);
+}
+
+}  // namespace seqan
+
+#endif // SEQAN_SEQ_IO_SEQUENCE_FILE_H_
diff --git a/seqan/seq_io/sequence_stream.h b/seqan/seq_io/sequence_stream.h
deleted file mode 100644
index 9484ec2..0000000
--- a/seqan/seq_io/sequence_stream.h
+++ /dev/null
@@ -1,1265 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-
-// TODO(holtgrew): Add EMBL support.
-// TODO(holtgrew): Add function readFasta(SEQ, FILENAME).
-
-#ifndef CORE_INCLUDE_SEQAN_SEQ_IO_SEQUENCE_SEQ_IO_H_
-#define CORE_INCLUDE_SEQAN_SEQ_IO_SEQUENCE_SEQ_IO_H_
-
-#include <memory>
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// ---------------------------------------------------------------------------
-// Class SequenceStream
-// ---------------------------------------------------------------------------
-/*!
- * @class SequenceStream
- * @headerfile <seqan/seq_io.h>
- *
- * @signature class SequenceStream;
- * 
- * @brief High-level reading and writing of sequences.
- * 
- * Building upon the more low-level sequence I/O functionality of SeqAn, this class provides easier to use I/O
- * facilities.  Especially, the underlying @link Stream stream layer @endlink and using @link RecordReader @endlinks is
- * hidden from the user. This is achieved by using dynamic polymorphism which comes at some performance cost.
- * 
- * Also see the <a href="http://trac.seqan.de/wiki/Tutorial/SimpleSeqIO">Simple Sequence I/O Tutorial</a>.
- *
- * @section Remarks
- * 
- * @subsection Operation Mode
- * 
- * When reading, there are two operation modes: Normal reading and reading of "persistent" records.  When reading in
- * "persistent" mode, @link SequenceStream @endlink will scan over each record twice: once for determining its size and
- * once for actually reading the sequences.  After the first pass, we can allocate a buffer of the exact size we need.
- * This can save memory up to a factor of two, at the cost of scanning each record twice.  Note that this is only
- * possible for reading uncompressed files.
- * 
- * @subsection File Format and File Type
- * 
- * The file type determines whether a file is stored as raw text or whether it is compressed.  Examples for file types
- * are text files or <tt>gzip</tt> compressed files (<tt>FILE.gz</tt>).  The file format considers the contents of the
- * raw/decompressed file.  Examples for file formats are FASTA, FASTQ, or EMBL.
- * 
- * When reading, the file type and format are guessed from the file itself.  You do not have to specify any but you can
- * force the @link SequenceStream @endlink to use the ones you provide.  When writing, you should specify a file type
- * and format when constructing the @link SequenceStream @endlink object.  Otherwise, it will default to writing out
- * raw-text FASTA files.
- * 
- * @section Examples
- * 
- * Read a sequence file <tt>"example.fa"</tt> record by record.  See the documentation of @link
- * SequenceStream#readRecord @endlink, @link SequenceStream#readBatch @endlink, and @link SequenceStream#readAll
- * @endlink for more examples, including record-wise reading, reading in batches, and reading all records in a file.
- *
- * @subsection Reading from SequenceStream
- *
- * @include demos/seq_io/sequence_stream_read.cpp
- *
- * The output is as follows:
- *
- * @include demos/seq_io/sequence_stream_read.cpp.stdout
- *
- * @subsection Writing to SequenceStream
- *
- * @include demos/seq_io/sequence_stream_write.cpp
- *
- * @fn SequenceStream::SequenceStream
- * @brief Constructor
- * 
- * @signature SequenceStream::SequenceStream();
- * @signature SequenceStream::SequenceStream(fileName[, operationMode[, format[, fileType]]]);
- * 
- * @param[in] fileName      Path to the file to open.  Type: <tt>char const *</tt>
- * @param[in] operationMode Mode to open the file in.  Optional.  Type: SequenceStream::OperationMode.
- *                          Default: <tt>READ</tt>
- * @param[in] format        Mode to open the file in.  Optional.  Type: SequenceStream::FileFormat.
- *                          Default: <tt>AUTO_FORMAT</tt>.
- * @param[in] fileType      Mode to open the file in.  Optional.  Type: SequenceStream::FileType.
- *                          Default: <tt>AUTO_TYPE</tt>.
- */
-
-/*!
- * @enum SequenceStream::OperationMode
- * @headerfile <seqan/seq_io.h>
- * @brief Select the operation mode of a @link SequenceStream @endlink.
- *
- * @signature enum OperationMode;
- * 
- * @var SequenceStream::OperationMode SequenceStream::READ;
- * @brief Open stream for reading.
- * 
- * @var SequenceStream::OperationMode SequenceStream::WRITE;
- * @brief Open stream for writing.
- * 
- * @var SequenceStream::OperationMode SequenceStream::READ_PERSISTENT;
- * @brief Open stream for reading, mark as "persisent reading".  See @link SequenceStream @endlink for more information
- *        on the difference between normal and persistent reading.
- */
-
-/*!
- * @enum SequenceStream::FileType
- * @headerfile <seqan/seq_io.h>
- * @brief Select the file type to read/write.
- * 
- * @signature enum FileType;
- * 
- * The file type is the type of the file itself, i.e. plain text or compressed.
- * 
- * @var SequenceStream::FileType SequenceStream::AUTO_TYPE;
- * 
- * @brief Auto-detect format from file content on reading and from the file name on writing.  If Auto-detection fails,
- *        <tt>PLAIN_TEXT</tt> is used.
- * 
- * @var SequenceStream::FileType SequenceStream::PLAIN_TEXT;
- * @brief Force reading/writing of plain text.
- * 
- * @var SequenceStream::FileType SequenceStream::BZ2;
- * @brief Force reading/writing with bzip compression.
- * 
- * @var SequenceStream::FileType SequenceStream::GZ;
- * @brief Force reading/writing with gzip compression.
- */
-
-/*!
- * @enum SequenceStream::FileFormat
- * @headerfile <seqan/seq_io.h>
- * @brief Select the file format to read/write.
- *
- * @signature enum FileFormat;
- * 
- * The file format is the format of the possibly compressed content.
- * 
- * @var SequenceStream::FileFormat SequenceStream::AUTO_FORMAT;
- * @brief Auto-detect format from file content on reading and from the file name on writing.  If Auto-detection fails,
- *        FASTA is used.
- * 
- * @var SequenceStream::FileFormat SequenceStream::FASTA;
- * @brief Force reading/writing of FASTA.
- * 
- * @var SequenceStream::FileFormat SequenceStream::FASTQ;
- * @brief Force reading/writing of FASTQ.
- */
-
-/**
-.Class.SequenceStream
-..cat:Input/Output
-..summary:High-level reading and writing of sequences.
-..description:
-Building upon the more low-level sequence I/O functionality of SeqAn, this class provides easier to use I/O facilities.
-Especially, the underlying @Class.Stream|stream layer@ and using @Class.RecordReader@s is hidden from the user.
-This is achieved by using dynamic polymorphism which comes at some performance cost.
-..remarks:Operation Mode
-..remarks.text:
-When reading, there are two operation modes:
-Normal reading and reading of "persistent" records.
-When reading in "persistent" mode, @Class.SequenceStream@ will scan over each record twice:
-Once for determining its size and once for actually reading the sequences.
-After the first pass, we can allocate a buffer of the exact size we need.
-This can save memory up to a factor of two, at the cost of scanning each record twice.
-Note that this is only possible for reading uncompressed files.
-..remarks:File Format and File Type
-..remarks.text:
-The file type determines whether a file is stored as raw text or whether it is compressed.
-Examples for file types are text files or $gzip$ compressed files ($FILE.gz$).
-The file format considers the contents of the raw/decompressed file.
-Examples for file formats are FASTA, FASTQ, or EMBL.
-..remarks.text:
-When reading, the file type and format are guessed from the file itself.
-You do not have to specify any but you can force the @Class.SequenceStream@ to use the ones you provide.
-When writing, you should specify a file type and format when constructing the @Class.SequenceStream@ object.
-Otherwise, it will default to writing out raw-text FASTA files.
-..example.text:
-Read the sequence file (FASTA or FASTQ) from $argv[1]$ record by record.
-The identifiers and sequences of the stream are printed to stdout.
-See the documentation of @Function.SequenceStream#readRecord@, @Function.SequenceStream#readBatch@, and @Function.SequenceStream#readAll@ for more examples, including record-wise reading, reading in batches, and reading all records in a file.
-..example.file:demos/seq_io/sequence_stream_read.cpp
-..example.text:
-Open a SequenceStream for writing and write two sequences to it.
-..example.file:demos/seq_io/sequence_stream_write.cpp
-..wiki:Tutorial/SimpleSeqIO|Simple Sequence I/O
-..include:seqan/seq_io.h
-
-.Memfunc.SequenceStream#SequenceStream
-..summary:Constructor
-..description:See documentation of @Class.SequenceStream@ for more information.
-..class:Class.SequenceStream
-..signature:SequenceStream()
-..signature:SequenceStream(fileName[, operationMode[, format[, fileType]]])
-..param.fileName:Path to the file to open.
-...type:nolink:$char const *$
-..param.operationMode:Mode to open the file in. Optional.
-...default:@Enum.SequenceStream\colon\colonOperationMode.value.READ@
-...type:Enum.SequenceStream\colon\colonOperationMode
-..param.format:Mode to open the file in. Optional.
-...type:Enum.SequenceStream\colon\colonFileFormat
-...default:@Enum.SequenceStream\colon\colonFileFormat.value.AUTO_FORMAT@
-..param.fileType:Mode to open the file in. Optional.
-...type:Enum.SequenceStream\colon\colonFileType
-...default:@Enum.SequenceStream\colon\colonFileType.value.AUTO_TYPE@
-
-.Enum.SequenceStream\colon\colonOperationMode
-..cat:Input/Output
-..summary:Select the operation mode of a @Class.SequenceStream@.
-..value.READ:Open stream for reading.
-..value.READ_PERSISTENT:Open stream for reading, mark as "persisent reading". See @Class.SequenceStream@ for more information on the difference between normal and persistent reading.
-..value.WRITE:Open stream for writing.
-..include:seqan/seq_io.h
-
-.Enum.SequenceStream\colon\colonFileFormat
-..cat:Input/Output
-..summary:Select the file format to read/write.
-..description:The file format is the format of the possibly compressed content.
-..value.AUTO_FORMAT:Auto-detect format from file content on reading and from the file name on writing. If Auto-detection fails, FASTA is used.
-..value.FASTA:Force reading/writing of FASTA.
-..value.FASTQ:Force reading/writing of FASTQ.
-..include:seqan/seq_io.h
-
-.Enum.SequenceStream\colon\colonFileType
-..cat:Input/Output
-..summary:Select the file type to read/write.
-..description:The file type is the type of the file itself, i.e. plain text or compressed.
-..value.AUTO_TYPE:Auto-detect format from file content on reading and from the file name on writing. If Auto-detection fails, $PLAIN_TEXT$ is used.
-..value.PLAIN_TEXT:Force reading/writing of plain text.
-..value.GZ:Force reading/writing with gzip compression.
-..value.BZ2:Force reading/writing with bzip compression.
-..include:seqan/seq_io.h
-*/
-
-class SequenceStream
-{
-public:
-    // -----------------------------------------------------------------------
-    // Operation Mode
-    // -----------------------------------------------------------------------
-
-    // This enum is used to select the operation mode.
-    enum OperationMode
-    {
-        READ,
-        READ_PERSISTENT,
-        WRITE
-    };
-
-    // This enum is used to select the file format.
-    enum FileFormat
-    {
-        FASTA,
-        FASTQ,
-        AUTO_FORMAT
-    };
-
-    // This enum is used to select the file type, compression if any.
-    enum FileType
-    {
-        AUTO_TYPE,
-        PLAIN_TEXT
-#if SEQAN_HAS_ZLIB
-        ,
-        GZ
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        ,
-        BZ2
-#endif  // #if SEQAN_HAS_BZIP2
-    };
-
-    // -----------------------------------------------------------------------
-    // Member Variables
-    // -----------------------------------------------------------------------
-
-    // The configuration for the output format options.
-    SequenceOutputOptions outputOptions;
-
-    CharString filename;
-    OperationMode operationMode;
-    bool _atEnd;
-    bool _isGood;
-
-    std::SEQAN_AUTO_PTR_NAME<SequenceStreamImpl_> _impl;
-
-    SeqIOFileType_::Type _fileType;
-    SeqIOFileFormat_::Type _fileFormat;
-
-    // -----------------------------------------------------------------------
-    // Constructor
-    // -----------------------------------------------------------------------
-
-    SequenceStream() : _atEnd(false), _isGood(false), _fileType(SeqIOFileType_::FILE_TYPE_TEXT),
-        _fileFormat(SeqIOFileFormat_::FILE_FORMAT_FASTA)
-    {}
-
-    SequenceStream(char const * filename,
-                   OperationMode operationMode = READ,
-                   FileFormat format = AUTO_FORMAT,
-                   FileType fileType = AUTO_TYPE) :
-        filename(filename), operationMode(operationMode), _atEnd(false), _isGood(true), _fileType(SeqIOFileType_::FILE_TYPE_TEXT),
-        _fileFormat(SeqIOFileFormat_::FILE_FORMAT_FASTA)
-    {
-        _init(operationMode, format, fileType);
-    }
-
-    void _init(OperationMode operationMode, FileFormat format, FileType fileType)
-    {
-        // Translate from FileFormat to SeqIOFileFormat_::Type.
-        switch (format)
-        {
-            case FASTQ:
-                _fileFormat = SeqIOFileFormat_::FILE_FORMAT_FASTQ;
-                break;
-            case FASTA:
-                _fileFormat = SeqIOFileFormat_::FILE_FORMAT_FASTA;
-                break;
-            case AUTO_FORMAT:
-                _fileFormat = SeqIOFileFormat_::FILE_FORMAT_AUTO;
-                break;
-        }
-        // Translate from FileFormat to SeqIOFileFormat_::Type.
-        switch (fileType)
-        {
-            case AUTO_TYPE:
-                _fileType = SeqIOFileType_::FILE_TYPE_AUTO;
-                break;
-            case PLAIN_TEXT:
-                _fileType = SeqIOFileType_::FILE_TYPE_TEXT;
-                break;
-#if SEQAN_HAS_ZLIB
-            case GZ:
-                _fileType = SeqIOFileType_::FILE_TYPE_GZ;
-                break;
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-            case BZ2:
-                _fileType = SeqIOFileType_::FILE_TYPE_BZ2;
-                break;
-#endif  // #if SEQAN_HAS_BZIP2
-        }
-
-        bool isRead = (operationMode != WRITE);
-        bool hintDoublePass = (operationMode == READ_PERSISTENT);
-        _impl.reset(new SequenceStreamImpl_(filename, _fileFormat, _fileType, isRead, hintDoublePass));
-        // Copy out, possibly detected/adjusted file type and format.
-        _fileType = _impl->_fileType;
-        _fileFormat = _impl->_fileFormat;
-        _isGood = _impl->_isGood && (_fileType != SeqIOFileType_::FILE_TYPE_ERROR) &&
-                (_fileFormat != SeqIOFileFormat_::FILE_FORMAT_ERROR);
-        _atEnd = _impl->_atEnd;
-    }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function open()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#open
- * @brief Open or re-open a file using a SequenceStream.
- * 
- * @signature void open(seqStream, fileName[, operationMode[, format[, fileType]]]);
- * 
- * @param[in,out] seqStream     The SequenceStream object to open. Types: SequenceStream.
- * @param[in]     fileType      Mode to open the file in. Optional. Types: SequenceStream::FileType  Default:
- *                              AUTO_TYPE.
- * @param[in]     format        Mode to open the file in. Optional.  Types: SequenceStream::FileFormat.
- *                              Default: AUTO_FORMAT.
- * @param[in]     operationMode Mode to open the file in.  Optional. Types: SequenceStream::OperationMode.
- *                              Default: READ.
- * @param[in]     fileName      Path to the file to open. Types: <tt>char const *</tt>
- */
-
-/**
-.Function.SequenceStream#open
-..summary:Open or re-open a file using a SequenceStream.
-..class:Class.SequenceStream
-..signature:void open(seqStream, fileName[, operationMode[, format[, fileType]]])
-..param.seqStream:The SequenceStream object to open.
-...type:Class.SequenceStream
-..param.fileName:Path to the file to open.
-...type:nolink:$char const *$
-..param.operationMode:Mode to open the file in. Optional.
-...default:@Enum.SequenceStream\colon\colonOperationMode.value.READ@
-...type:Enum.SequenceStream\colon\colonOperationMode
-..param.format:Mode to open the file in. Optional.
-...type:Enum.SequenceStream\colon\colonFileFormat
-...default:@Enum.SequenceStream\colon\colonFileFormat.value.AUTO_FORMAT@
-..param.fileType:Mode to open the file in. Optional.
-...type:Enum.SequenceStream\colon\colonFileType
-...default:@Enum.SequenceStream\colon\colonFileType.value.AUTO_TYPE@
-*/
-
-inline void open(SequenceStream & seqIO,
-                 char const * filename,
-                 SequenceStream::OperationMode operationMode = SequenceStream::READ,
-                 SequenceStream::FileFormat format = SequenceStream::AUTO_FORMAT,
-                 SequenceStream::FileType fileType = SequenceStream::AUTO_TYPE)
-{
-    seqIO.filename = filename;
-    seqIO.operationMode = operationMode;
-    seqIO._atEnd = false;
-    seqIO._isGood = true;
-    seqIO._fileType = SeqIOFileType_::FILE_TYPE_TEXT;
-    seqIO._fileFormat = SeqIOFileFormat_::FILE_FORMAT_FASTA;
-
-    seqIO._init(operationMode, format, fileType);
-}
-
-// ----------------------------------------------------------------------------
-// Function close()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#close
- * @brief Close a SequenceStream.
- *
- * @signature close(seqStream);
- *
- * @param[in,out] seqStream The SequenceStream to close.
- */
-
-/**
-.Function.SequenceStream#close
-..class:Class.SequenceStream
-..summary:Close the @Class.SequenceStream@.
-..signature:void close(seqIO)
-..param.seqIO:The @Class.SequenceStream@ object to close.
-...type:Class.SequenceStream
-..include:seqan/seq_io.h
-*/
-
-inline void close(SequenceStream & seqIO)
-{
-    seqIO._impl->close();
-}
-
-// ----------------------------------------------------------------------------
-// Function flush()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#flush
- * @brief Write all remaining data from a SequenceStream to disk.
- *
- * @signature flush(seqStream);
- *
- * @param[in,out] seqStream The SequenceStream to flush.
- */
-
-/**
-.Function.SequenceStream#flush
-..class:Class.SequenceStream
-..summary:Write all data from SequenceStream to disk.
-..signature:void close(seqIO)
-..param.seqIO:The @Class.SequenceStream@ object to flush.
-...type:Class.SequenceStream
-..include:seqan/seq_io.h
-*/
-
-inline void flush(SequenceStream & seqIO)
-{
-    seqIO._impl->flush();
-}
-
-// ----------------------------------------------------------------------------
-// Function atEnd()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#atEnd
- * @brief Check whether a SequenceStream is at the end of the file.
- * 
- * @signature bool isGood(seqStream);
- * 
- * @param seqStream The SequenceStream object to read from. Type: SequenceStream
- * 
- * @return bool true if the SequenceStream is at the end of the file and false otherwise.
- * 
- * @see SequenceStream#isGood
- */
-
-/**
-.Function.SequenceStream#atEnd
-..class:Class.SequenceStream
-..summary:Check whether a @Class.SequenceStream@ is at the end of the file.
-..signature:bool isGood(seqIO)
-..param.seqIO:The @Class.SequenceStream@ object to read from.
-...type:Class.SequenceStream
-..returns:A $bool$, $true$ indicating that the $seqIO$ is at the end of the file, $false$ indicating otherwise.
-..see:Function.SequenceStream#isGood
-..include:seqan/seq_io.h
-*/
-
-inline bool atEnd(SequenceStream const & seqIO)
-{
-    return seqIO._atEnd;
-}
-
-// TODO(holtgrew): We'd rather only have the const variant.
-inline bool atEnd(SequenceStream & seqIO)
-{
-    return seqIO._atEnd;
-}
-
-// ----------------------------------------------------------------------------
-// Function isGood()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#isGood
- * @brief Check whether a SequenceStream is ready for reading or writing.
- *
- * @signature bool isGood(seqStream);
- *
- * @param[in] seqStream The SequenceStream to query.
- *
- * @return bool true if the stream is ready and false otherwise.
- */
-
-/**
-.Function.SequenceStream#isGood
-..class:Class.SequenceStream
-..summary:Check whether a @Class.SequenceStream@ object is ready for reading.
-..signature:bool isGood(seqIO)
-..param.seqIO:The @Class.SequenceStream@ object to read from.
-...type:Class.SequenceStream
-..returns:A $bool$, $true$ indicating that the $seqIO$ is ready for reading, $false$ that there was an error or it is at the end of the file.
-..see:Function.SequenceStream#atEnd
-..include:seqan/seq_io.h
-*/
-
-inline bool isGood(SequenceStream const & seqIO)
-{
-    return seqIO._isGood;
-}
-
-// ----------------------------------------------------------------------------
-// Function readRecord()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#readRecord
- * @brief Read the next sequence record from @link SequenceStream @endlink.
- * 
- * @signature int readRecord(id, seq, seqStream);
- * @signature int readRecord(id, seq, quals, seqStream);
- * 
- * @param[out]    id    The identifier of the sequence is written here.  Types: CharString
- * @param[out]    seq   The sequence of the record is written here. Types: String
- * @param[out]    quals The qualities of the sequence is written here.  Optional.  If the sequence has no qualities,
- *                      @link SequenceConcept#clear @endlink is called on <tt>quals</tt> to indicate this.  Type:
- *                      CharString
- * @param[in,out] seqIO The @link SequenceStream @endlink object to read from. Type: SequenceStream
- * 
- * @return int 0 on success, non-0 on error.
- * 
- * @section Examples
- * 
- * Read the first sequence of a FASTA file.
- * 
- * @code{.cpp}
- * int main()
- * {
- *     seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::READ_SINGLE);
- *     seqan::CharString id;
- *     seqan::Dna5String seq;
- *  
- *     if (atEnd(seqIO))
- *     {
- *         std::cerr << "ERROR: File does not contain any sequences!\n";
- *         return 1;
- *     }
- *     int res = readRecord(id, seq, seqIO);
- *     if (res != 0)
- *     {
- *         std::cerr << "ERROR: Could not read first record!\n";
- *         return 1;
- *     }
- *  
- *     return 0;
- * }
- * @endcode
- */
-
-/**
-.Function.SequenceStream#readRecord
-..class:Class.SequenceStream
-..summary:Read the next sequence record from @Class.SequenceStream@.
-..signature:int readRecord(id, seq, seqIO)
-..signature:int readRecord(id, seq, quals, seqIO)
-..param.id:The identifier of the sequence is written here.
-...type:Shortcut.CharString
-..param.seq:The sequence of the record is written here.
-...type:Class.String
-..param.quals:The qualities of the sequence is written here. Optional.
-...type:Shortcut.CharString
-...remarks:If the sequence has no qualities, @Function.clear@ is called on $quals$ to indicate this.
-..param.seqIO:The @Class.SequenceStream@ object to read from.
-...type:Class.SequenceStream
-..returns:An integer, $0$ on success, $1$ on errors.
-...type:nolink:$int$
-..example:Read the first sequence of a FASTA file.
-..example.code:
-int main()
-{
-    seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::READ_SINGLE);
-    seqan::CharString id;
-    seqan::Dna5String seq;
-
-    if (atEnd(seqIO))
-    {
-        std::cerr << "ERROR: File does not contain any sequences!\n";
-        return 1;
-    }
-    int res = readRecord(id, seq, seqIO);
-    if (res != 0)
-    {
-        std::cerr << "ERROR: Could not read first record!\n";
-        return 1;
-    }
-
-    return 0;
-}
-..include:seqan/seq_io.h
-*/
-
-template <typename TId, typename TSequence, typename TQualities>
-int readRecord(TId & id, TSequence & seq, TQualities & qual, SequenceStream & seqIO)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->readRecord(id, seq, qual, Fasta());
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->readRecord(id, seq, qual, Fastq());
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    seqIO._atEnd = seqIO._impl->_atEnd;
-    return res;
-}
-
-template <typename TId, typename TSequence>
-int readRecord(TId & id, TSequence & seq, SequenceStream & seqIO)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->readRecord(id, seq, Fasta());
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->readRecord(id, seq, Fastq());
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    seqIO._atEnd = seqIO._impl->_atEnd;
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function readBatch()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#readBatch
- * @brief Read a given number of sequence records from SequenceStream.
- * 
- * @signature int readBatch(ids, seqs, seqStream, num);
- * @signature int readBatch(ids, seqs, quals, seqStream, num);
- * 
- * @param[out]    ids   The identifiers of the sequence are written here.  Type: @link StringSet @endlink of @link
- *                      CharString @endlink.
- * @param[out]    seqs  The sequence of the record is written here.  Type: @link StringSet @endlink.
- * @param[out]    quals The qualities of the sequence is written here.  Optional.  If the sequences have no qualities,
- *                      as in FASTA files, the @link StringSet @endlink will contain empty strings.  Type: @link
- *                      StringSet @endlink of @link CharString @endlink
- * @param[in,out] seqIO The SequenceStream object to read from.
- * 
- * @return int 0 on success, non-0 value on errors.
- * 
- * @section Examples
- * 
- * Read the first sequences of a FASTA file, up to ten.
- * 
- * @code{.cpp}
- * int main()
- * {
- *     seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::READ_BATCH);
- *     seqan::StringSet<seqan::CharString> ids;
- *     seqan::StringSet<seqan::Dna5String> seqs;
- *  
- *     int res = readBatch(ids, seqs, seqIO, 10);
- *     if (res != 0)
- *     {
- *         std::cerr << "ERROR: Could not read records!\n";
- *         return 1;
- *     }
- *  
- *     return 0;
- * }
- * @endcode
- */
-
-/**
-.Function.SequenceStream#readBatch
-..class:Class.SequenceStream
-..summary:Read a given number of sequence records from @Class.SequenceStream@.
-..signature:int readBatch(ids, seqs, seqIO, num)
-..signature:int readBatch(ids, seqs, quals, seqIO, num)
-..param.ids:The identifiers of the sequence are written here.
-...type:nolink:@Class.StringSet@ of @Shortcut.CharString@.
-..param.seq:The sequence of the record is written here.
-...type:Class.StringSet
-..param.quals:The qualities of the sequence is written here. Optional.
-...type:nolink:@Class.StringSet@ of @Shortcut.CharString@.
-...remarks:If the sequences have no qualities, as in FASTA files, the @Class.StringSet@ will contain empty strings.
-..param.seqIO:The @Class.SequenceStream@ object to read from.
-..returns:An integer, $0$ on success, $1$ on errors.
-...type:nolink:$int$
-..example:Read the first sequences of a FASTA file, up to ten.
-..example.code:
-int main()
-{
-    seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::READ_BATCH);
-    seqan::StringSet<seqan::CharString> ids;
-    seqan::StringSet<seqan::Dna5String> seqs;
-
-    int res = readBatch(ids, seqs, seqIO, 10);
-    if (res != 0)
-    {
-        std::cerr << "ERROR: Could not read records!\n";
-        return 1;
-    }
-
-    return 0;
-}
-..include:seqan/seq_io.h
-*/
-
-template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TQualities,
-          typename TQualSpec>
-int readBatch(StringSet<TId, TIdSpec> & ids,
-              StringSet<TSequence, TSeqSpec> & seqs,
-              StringSet<TQualities, TQualSpec> & quals,
-              SequenceStream & seqIO,
-              unsigned num)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->readBatch(ids, seqs, quals, num, Fasta());
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->readBatch(ids, seqs, quals, num, Fastq());
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    seqIO._atEnd = seqIO._impl->_atEnd;
-    return res;
-}
-
-template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec>
-int readBatch(StringSet<TId, TIdSpec> & ids,
-              StringSet<TSequence, TSeqSpec> & seqs,
-              SequenceStream & seqIO,
-              unsigned num)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->readBatch(ids, seqs, num, Fasta());
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->readBatch(ids, seqs, num, Fastq());
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    seqIO._atEnd = seqIO._impl->_atEnd;
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function readAll()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#readAll
- * @brief Read all sequence records from a @link SequenceStream @endlink object.
- * 
- * @signature int readAll(ids, seqs, seqStream);
- * @signature int readAll(ids, seqs, quals, seqStream);
- * 
- * @param[out] ids       The identifiers of the sequence are written here. Types: @link StringSet @endlink of @link
- *                       CharString @endlink.
- * @param[out] seqs      The sequence of the record is written here. Types: StringSet
- * @param[out] quals     The qualities of the sequence is written here.  Optional.  If the sequences have no
- *                       qualities, as in FASTA files, the @link StringSet @endlink will contain empty strings.
- *                       Type: @link StringSet @endlink of @link CharString @endlink
- * @param[out] seqStream The @link SequenceStream @endlink object to read from.  Type: SequenceStream
- * 
- * @return int 0 on success, non-0 value on success.
- * 
- * @section Examples
- * 
- * Read the sequences of a FASTA file.
- * 
- * @code{.cpp}
- * int main()
- * {
- *     seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::READ_ALL);
- *     seqan::StringSet<seqan::CharString> ids;
- *     seqan::StringSet<seqan::Dna5String> seqs;
- *  
- *     int res = readAll(ids, seqs, seqIO);
- *     if (res != 0)
- *     {
- *         std::cerr << "ERROR: Could not read records!\n";
- *         return 1;
- *     }
- *  
- *     return 0;
- * }
- * @endcode
- */
-
-/**
-.Function.SequenceStream#readAll
-..class:Class.SequenceStream
-..summary:Read all sequence records from a @Class.SequenceStream@ object.
-..signature:int readAll(ids, seqs, seqIO)
-..signature:int readAll(ids, seqs, quals, seqIO)
-..param.ids:The identifiers of the sequence are written here.
-...type:nolink:@Class.StringSet@ of @Shortcut.CharString@.
-..param.seq:The sequence of the record is written here.
-...type:Class.StringSet
-..param.quals:The qualities of the sequence is written here. Optional.
-...type:nolink:@Class.StringSet@ of @Shortcut.CharString@.
-...remarks:If the sequences have no qualities, as in FASTA files, the @Class.StringSet@ will contain empty strings.
-..param.seqIO:The @Class.SequenceStream@ object to read from.
-...type:Class.SequenceStream
-..returns:An integer, $0$ on success, $1$ on errors.
-...type:nolink:$int$
-..example:Read the sequences of a FASTA file.
-..example.code:
-int main()
-{
-    seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::READ_ALL);
-    seqan::StringSet<seqan::CharString> ids;
-    seqan::StringSet<seqan::Dna5String> seqs;
-
-    int res = readAll(ids, seqs, seqIO);
-    if (res != 0)
-    {
-        std::cerr << "ERROR: Could not read records!\n";
-        return 1;
-    }
-
-    return 0;
-}
-..include:seqan/seq_io.h
-*/
-
-template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TQualities,
-          typename TQualSpec>
-int readAll(StringSet<TId, TIdSpec> & ids,
-            StringSet<TSequence, TSeqSpec> & seqs,
-            StringSet<TQualities, TQualSpec> & quals,
-            SequenceStream & seqIO)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->readAll(ids, seqs, quals, Fasta());
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->readAll(ids, seqs, quals, Fastq());
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    seqIO._atEnd = seqIO._impl->_atEnd;
-    return res;
-}
-
-template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec>
-int readAll(StringSet<TId, TIdSpec> & ids,
-            StringSet<TSequence, TSeqSpec> & seqs,
-            SequenceStream & seqIO)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->readAll(ids, seqs, Fasta());
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->readAll(ids, seqs, Fastq());
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    seqIO._atEnd = seqIO._impl->_atEnd;
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function writeRecord()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#writeRecord
- * @brief Write one sequence record from to a @link SequenceStream @endlink object.
- * 
- * @signature int writeRecord(seqStream, id, seq[, options]);
- * @signature int writeRecord(seqStream id, seq, quals[, options]);
- * 
- * @param[in,out] seqStream The @link SequenceStream @endlink object to write to.  Type: SequenceStream
- * @param[in] quals         The qualities to write out.
- * @param[in] id            The identifier to write.  Type: CharString
- * @param[in] seq           The sequence to write.  Type: String
- * @param[in] options       The configuration for writing FASTA and FASTQ files.  Type: SequenceOutputOptions
- * 
- * @return int 0 on success, non-0 value on errors.
- * 
- * The record is appended to the file if you have written out any previously.  When writing out @link Dna5 @endlink,
- * qualities are automatically taken from the sequence characters.
- * 
- * @section Examples
- * 
- * Write out two sequences to a FASTQ file.
- * 
- * @code{.cpp}
- * int main()
- * {
- *     seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::WRITE);
- *     seqan::StringSet<seqan::CharString> ids;
- *     appendValue(ids, "seq1");
- *     appendValue(ids, "seq2");
- *     seqan::StringSet<seqan::Dna5String> seqs;
- *     appendValue(seqs, "CGAT");
- *     appendValue(seqs, "TTTT");
- *  
- *     for (unsigned i = 0; i < length(ids); ++i)
- *     {
- *         int res = writeRecord(seqIO, ids[0], seqs[0]);
- *         if (res != 0)
- *         {
- *             std::cerr << "ERROR: Could not write records!\n";
- *             return 1;
- *         }
- *     }
- *  
- *     return 0;
- * }
- * @endcode
- */
-
-/**
-.Function.SequenceStream#writeRecord
-..class:Class.SequenceStream
-..summary:Write one sequence record from to a @Class.SequenceStream@ object.
-..description:
-The record is appended to the file if you have written out any previously.
-When writing out @Spec.Dna5@, qualities are automatically taken from the sequence characters.
-..signature:int writeRecord(seqIO, id, seq, [options])
-..signature:int writeRecord(seqIO, id, seq, quals, [options])
-..param.seqIO:The @Class.SequenceStream@ object to write to.
-...type:Class.SequenceStream
-..param.id:The identifier to write.
-...type:Shortcut.CharString
-..param.seq:The sequence to write.
-...type:Class.String
-..param.quals:The qualities to write out.
-...type:Shortcut.CharString
-...remarks:If the sequence has no qualities, @Function.clear@ is called on $quals$ to indicate this.
-..param.options:The configuration for writing FASTA and FASTQ files.
-...type:Class.SequenceOutputOptions
-..returns:An integer, $0$ on success, $1$ on errors.
-...type:nolink:$int$
-..example:Write out two sequences to a FASTQ file.
-..example.code:
-int main()
-{
-    seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::WRITE);
-    seqan::StringSet<seqan::CharString> ids;
-    appendValue(ids, "seq1");
-    appendValue(ids, "seq2");
-    seqan::StringSet<seqan::Dna5String> seqs;
-    appendValue(seqs, "CGAT");
-    appendValue(seqs, "TTTT");
-
-    for (unsigned i = 0; i < length(ids); ++i)
-    {
-        int res = writeRecord(seqIO, ids[0], seqs[0]);
-        if (res != 0)
-        {
-            std::cerr << "ERROR: Could not write records!\n";
-            return 1;
-        }
-    }
-
-    return 0;
-}
-..include:seqan/seq_io.h
-*/
-
-template <typename TId, typename TSequence, typename TQualities>
-int writeRecord(SequenceStream & seqIO,
-                TId const & id,
-                TSequence const & seq,
-                TQualities const & qual,
-                SequenceOutputOptions const & options)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->writeRecord(id, seq, Fasta(), options);
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->writeRecord(id, seq, qual, Fastq(), options);
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    return res;
-}
-
-template <typename TId, typename TSequence, typename TQualities>
-int writeRecord(SequenceStream & seqIO,
-                TId const & id,
-                TSequence const & seq,
-                TQualities const & qual)
-{
-    return writeRecord(seqIO, id, seq, qual, seqIO.outputOptions);
-}
-
-template <typename TId, typename TSequence>
-int writeRecord(SequenceStream & seqIO,
-                TId const & id,
-                TSequence const & seq,
-                SequenceOutputOptions const & options)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->writeRecord(id, seq, Fasta(), options);
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->writeRecord(id, seq, Fastq(), options);
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    return res;
-}
-
-template <typename TId, typename TSequence>
-int writeRecord(SequenceStream & seqIO,
-                TId const & id,
-                TSequence const & seq)
-{
-    return writeRecord(seqIO, id, seq, seqIO.outputOptions);
-}
-
-// ----------------------------------------------------------------------------
-// Function writeAll()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn SequenceStream#writeAll
- * @brief Write sequence records from to a SequenceStream object.
- * 
- * @signature int writeAll(seqStream, ids, seqs[, options]);
- * @signature int writeAll(seqStream, ids, seqs, quals[, options]);
- * 
- * @param[in,out] seqStream The @link SequenceStream @endlink object to write to.  Types: SequenceStream
- * @param[in]     ids       Identifiers to write out. Type: @link StringSet @endlink of @link CharString @endlink.
- * @param[in]     seqs      Sequences to write out.  Type: StringSet.
- * @param[in]     quals     Qualities to write out.  Optional.  Qualities are ignored if the file format
- *                          does not support them.  If none are given for FASTQ, score 40 is written out
- *                          for all.  Typex: @link StringSet @endlink of @link CharString @endlink.
- * @param[in]     options   The configuration for writing FASTA and FASTQ files.  Type: SequenceOutputOptions
- * 
- * @return int 0 on success, non-0 value on errors.
- * 
- * The records are appended to the file if you have written out any previously.  When writing out @link Dna5Q @endlink,
- * qualities are automatically taken from the sequence characters.
- * 
- * @section Examples
- * 
- * Write out all sequences.
- * 
- * @code{.cpp}
- * int main()
- * {
- *     seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::WRITE);
- *     seqan::StringSet<seqan::CharString> ids;
- *     appendValue(ids, "seq1");
- *     appendValue(ids, "seq2");
- *     seqan::StringSet<seqan::Dna5String> seqs;
- *     appendValue(seqs, "CGAT");
- *     appendValue(seqs, "TTTT");
- *  
- *     int res = writeAll(seqIO, ids, seqs);
- *     if (res != 0)
- *     {
- *         std::cerr << "ERROR: Could not write records!\n";
- *         return 1;
- *     }
- *  
- *     return 0;
- * }
- * @endcode
- */  
-
-/**
-.Function.SequenceStream#writeAll
-..class:Class.SequenceStream
-..summary:Write sequence records from to a @Class.SequenceStream@ object.
-..description:
-The records are appended to the file if you have written out any previously.
-When writing out @Spec.Dna5@, qualities are automatically taken from the sequence characters.
-..signature:int writeAll(seqIO, ids, seqs[, options])
-..signature:int writeAll(seqIO, ids, seqs, quals, [options])
-..param.seqIO:The @Class.SequenceStream@ object to write to.
-...type:Class.SequenceStream
-..param.ids:Identifiers to write out.
-...type:nolink:@Class.StringSet@ of @Shortcut.CharString@.
-..param.seq:Sequences to write out.
-...type:Class.StringSet
-..param.quals:Qualities to write out. Optional.
-...type:nolink:@Class.StringSet@ of @Shortcut.CharString@.
-...remarks:Qualities are ignored if the file format does not suppor them.  If none are given for FASTQ, score 40 is written out for all.
-..param.options:The configuration for writing FASTA and FASTQ files.
-...type:Class.SequenceOutputOptions
-..returns:An integer, $0$ on success, $1$ on errors.
-...type:nolink:$int$
-..example:Write out all sequences.
-..example.code:
-int main()
-{
-    seqan::SequenceStream seqIO("in.fasta", seqan::SequenceStream::WRITE);
-    seqan::StringSet<seqan::CharString> ids;
-    appendValue(ids, "seq1");
-    appendValue(ids, "seq2");
-    seqan::StringSet<seqan::Dna5String> seqs;
-    appendValue(seqs, "CGAT");
-    appendValue(seqs, "TTTT");
-
-    int res = writeAll(seqIO, ids, seqs);
-    if (res != 0)
-    {
-        std::cerr << "ERROR: Could not write records!\n";
-        return 1;
-    }
-
-    return 0;
-}
-..include:seqan/seq_io.h
-*/
-
-template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TQualities,
-          typename TQualSpec>
-int writeAll(SequenceStream & seqIO,
-             StringSet<TId, TIdSpec> const & ids,
-             StringSet<TSequence, TSeqSpec> const & seqs,
-             StringSet<TQualities, TQualSpec> const & quals,
-             SequenceOutputOptions const & options)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->writeAll(ids, seqs, Fasta(), options);
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->writeAll(ids, seqs, quals, Fastq(), options);
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    return res;
-}
-
-template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TQualities,
-          typename TQualSpec>
-int writeAll(SequenceStream & seqIO,
-             StringSet<TId, TIdSpec> const & ids,
-             StringSet<TSequence, TSeqSpec> const & seqs,
-             StringSet<TQualities, TQualSpec> const & quals)
-{
-    return writeAll(seqIO, ids, seqs, quals, seqIO.outputOptions);
-}
-
-template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec>
-int writeAll(SequenceStream & seqIO,
-             StringSet<TId, TIdSpec> const & ids,
-             StringSet<TSequence, TSeqSpec> const & seqs,
-             SequenceOutputOptions const & options)
-{
-    int res = 0;
-
-    if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTA)
-        res = seqIO._impl->writeAll(ids, seqs, Fasta(), options);
-    else if (seqIO._fileFormat == SeqIOFileFormat_::FILE_FORMAT_FASTQ)
-        res = seqIO._impl->writeAll(ids, seqs, Fastq(), options);
-    else
-        res = 1;
-
-    seqIO._isGood = seqIO._impl->_isGood;
-    return res;
-}
-
-template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec>
-int writeAll(SequenceStream & seqIO,
-             StringSet<TId, TIdSpec> const & ids,
-             StringSet<TSequence, TSeqSpec> const & seqs)
-{
-    return writeAll(seqIO, ids, seqs, seqIO.outputOptions);
-}
-
-}  // namespace seqan
-
-#endif  // CORE_INCLUDE_SEQAN_SEQ_IO_SEQUENCE_SEQ_IO_H_
diff --git a/seqan/seq_io/sequence_stream_impl.h b/seqan/seq_io/sequence_stream_impl.h
deleted file mode 100644
index 7b4bf0e..0000000
--- a/seqan/seq_io/sequence_stream_impl.h
+++ /dev/null
@@ -1,1091 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-
-// TODO(holtgrew): Add #if guards for bz2 and zlib.
-
-#ifndef CORE_INCLUDE_SEQAN_SEQ_IO_SEQ_IO_IMPL_H_
-#define CORE_INCLUDE_SEQAN_SEQ_IO_SEQ_IO_IMPL_H_
-
-#include <memory>
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// ---------------------------------------------------------------------------
-// Class SeqIOFileType_
-// ---------------------------------------------------------------------------
-
-struct SeqIOFileType_
-{
-    // Used for storing the file type guess.
-    enum Type
-    {
-        FILE_TYPE_AUTO,
-        FILE_TYPE_ERROR,
-        FILE_TYPE_TEXT_STD,  // text stdin, stdout
-        FILE_TYPE_TEXT
-#if SEQAN_HAS_ZLIB
-        ,
-        FILE_TYPE_GZ,
-        FILE_TYPE_GZ_DIRECT  // gzfile stream but uncompressed/direct (stdin)
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        ,
-        FILE_TYPE_BZ2
-#endif  // #if SEQAN_HAS_BZIP2
-    };
-};
-
-// ---------------------------------------------------------------------------
-// Class SeqIOFileFormat_
-// ---------------------------------------------------------------------------
-
-struct SeqIOFileFormat_
-{
-    enum Type
-    {
-        FILE_FORMAT_AUTO,
-        FILE_FORMAT_ERROR,
-        FILE_FORMAT_FASTA,
-        FILE_FORMAT_FASTQ,
-        FILE_FORMAT_EMBL
-    };
-};
-
-// ----------------------------------------------------------------------------
-// Class SequenceStreamImpl_
-// ----------------------------------------------------------------------------
-
-// Implementation of EasySeqIO class.
-//
-// This class does the multiplexing from settings known at runtime (file format) to types at compile-time.
-
-class SequenceStreamImpl_
-{
-public:
-
-#if SEQAN_HAS_ZLIB
-    std::SEQAN_AUTO_PTR_NAME<Stream<GZFile> > _gzStream;
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-    std::SEQAN_AUTO_PTR_NAME<Stream<BZ2File> > _bz2Stream;
-#endif  // #if SEQAN_HAS_BZIP2
-    std::SEQAN_AUTO_PTR_NAME<String<char, MMap<> > > _mmapString;
-
-    // TODO(holtgrew): We could get rid of some of these with type erasure on streams and record readers. Would this be enough?
-
-#if SEQAN_HAS_ZLIB
-    std::SEQAN_AUTO_PTR_NAME<RecordReader<Stream<GZFile>, SinglePass<> > > _gzReader;
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-    std::SEQAN_AUTO_PTR_NAME<RecordReader<Stream<BZ2File>, SinglePass<> > > _bz2Reader;
-#endif  // #if SEQAN_HAS_BZIP2
-    std::SEQAN_AUTO_PTR_NAME<RecordReader<String<char, MMap<> >, SinglePass<StringReader> > > _mmapReaderSinglePass;
-    std::SEQAN_AUTO_PTR_NAME<RecordReader<String<char, MMap<> >, DoublePass<StringReader> > > _mmapReaderDoublePass;
-    std::SEQAN_AUTO_PTR_NAME<RecordReader<std::istream, SinglePass<> > > _istreamReader;
-
-    CharString _filename;
-    SeqIOFileFormat_::Type _fileFormat;
-    SeqIOFileType_::Type _fileType;
-
-    // Whether or not we are at the end of the underlying file.
-    bool _atEnd;
-    // Whether or not there was no error.
-    bool _isGood;
-    // Whether or not we open the file for reading only.
-    bool _isRead;
-    // Whether or not to use double pass record reader.
-    bool _hintDoublePass;
-
-    SequenceStreamImpl_(CharString const & filename,
-                        SeqIOFileFormat_::Type fileFormat,
-                        SeqIOFileType_::Type fileType,
-                        bool isRead,
-                        bool hintDoublePass = false) :
-            _filename(filename), _fileFormat(fileFormat), _fileType(fileType), _atEnd(false), _isGood(true),
-            _isRead(isRead), _hintDoublePass(hintDoublePass)
-    {
-        // Guess file types.
-        if (_isRead)
-        {
-            this->_guessFileTypeAndFormatForReadingAndInitialize();
-        }
-        else
-        {
-            this->_guessFileTypeAndFormatForWriting();
-            this->_initializeStreamsForWriting();
-        }
-    }
-
-    // -----------------------------------------------------------------------
-    // Flag Query Functions.
-    // -----------------------------------------------------------------------
-
-    bool atEnd()
-    {
-        return _atEnd;
-    }
-
-    bool isGood()
-    {
-        return _isGood;
-    }
-
-    // -----------------------------------------------------------------------
-    // File and Format Guessing Functions.
-    // -----------------------------------------------------------------------
-
-    // Guess file type and format for reading.  This will also create the required record reader objects etc.  The
-    // reason for interweaving this so strongly here is that we have to reuse the record reader in the case of stdin for
-    // reading.
-    void _guessFileTypeAndFormatForReadingAndInitialize()
-    {
-        // When reading from STDIN, we use a GZFile stream if possible.  This will automatically decompress .gz files
-        // and just pass through plain text files.  Otherwise, we would have to use buffer ourselves and use zlib/bzlib
-        // directly.
-        //
-        // TODO(holtgrew): Re-implement manual decompression/compression using the zlib and bzlib consistently using one interface?
-        if (_filename == "-")
-        {
-#if SEQAN_HAS_ZLIB
-            _fileType = SeqIOFileType_::FILE_TYPE_GZ;
-#else  // #if SEQAN_HAS_ZLIB
-            _fileType = SeqIOFileType_::FILE_TYPE_TEXT_STD;
-#endif  // #if SEQAN_HAS_ZLIB
-        }
-        else
-        {
-            // Read magic numbers.
-            std::fstream testStream(toCString(_filename), std::ios::binary | std::ios::in);
-            if (!testStream.good())
-            {
-                _fileType = SeqIOFileType_::FILE_TYPE_ERROR;
-                return;
-            }
-
-            char buffer[4] = { '\0', '\0', '\0', '\0' };
-            testStream.get(&buffer[0], 4);
-            if (testStream.eof())
-            {
-                _atEnd = true;
-                return;
-            }
-            if (!testStream.good())
-            {
-                _fileType = SeqIOFileType_::FILE_TYPE_ERROR;
-                return;
-            }
-
-            if (buffer[0] == '\x1F' && buffer[1] == '\x8B' && buffer[2] == '\x08')
-            {
-#if SEQAN_HAS_ZLIB
-                _fileType = SeqIOFileType_::FILE_TYPE_GZ;
-#else // #if SEQAN_HAS_ZLIB
-                std::cerr << "ERROR: File looks like .gz but zlib not available!\n";
-                _fileType = SeqIOFileType_::FILE_TYPE_ERROR;
-                return;
-#endif  // #if SEQAN_HAS_ZLIB
-            }
-            else if (buffer[0] == 'B' && buffer[1] == 'Z' && buffer[2] == 'h')
-            {
-#if SEQAN_HAS_BZIP2
-                _fileType = SeqIOFileType_::FILE_TYPE_BZ2;
-#else // #if SEQAN_HAS_BZ2
-                std::cerr << "ERROR: File looks like .bz2 but libbz2 not available!\n";
-                _fileType = SeqIOFileType_::FILE_TYPE_ERROR;
-                return;
-#endif  // #if SEQAN_HAS_BZ2
-            }
-            else
-            {
-                // Fall-back is raw text.
-                _fileType = SeqIOFileType_::FILE_TYPE_TEXT;
-            }
-        }
-
-        // Open stream or memory mapped file and create MMap reader.
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-        {
-            _mmapString.reset(new String<char, MMap<> >());
-            if (!open(*_mmapString, toCString(_filename), OPEN_RDONLY))
-            {
-                _isGood = false;
-            }
-            else
-            {
-                if (!_hintDoublePass)
-                {
-                    _mmapReaderSinglePass.reset(new RecordReader<String<char, MMap<> >, SinglePass<StringReader> >(*_mmapString));
-                    _fileFormat = this->_checkFormat(*_mmapReaderSinglePass);
-                }
-                else
-                {
-                    _mmapReaderDoublePass.reset(new RecordReader<String<char, MMap<> >, DoublePass<StringReader> >(*_mmapString));
-                    _fileFormat = this->_checkFormat(*_mmapReaderDoublePass);
-                }
-            }
-        }
-        break;
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-        {
-            _gzStream.reset(new Stream<GZFile>());
-            if (!open(*_gzStream, toCString(_filename), "r"))
-            {
-                _isGood = false;
-            }
-            else
-            {
-                _gzReader.reset(new RecordReader<Stream<GZFile>, SinglePass<> >(*_gzStream));
-                _fileFormat = this->_checkFormat(*_gzReader);
-                if (_filename == "-" && isDirect(*_gzStream))
-                    _fileType = SeqIOFileType_::FILE_TYPE_GZ_DIRECT;
-            }
-        }
-        break;
-
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-        {
-            _bz2Stream.reset(new Stream<BZ2File>());
-            if (!open(*_bz2Stream, toCString(_filename), "r"))
-            {
-                _isGood = false;
-            }
-            else
-            {
-                _bz2Reader.reset(new RecordReader<Stream<BZ2File>, SinglePass<> >(*_bz2Stream));
-                _fileFormat = this->_checkFormat(*_bz2Reader);
-            }
-        }
-        break;
-
-#endif  // #if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_TEXT_STD:
-        {
-            _istreamReader.reset(new RecordReader<std::istream, SinglePass<> >(std::cin));
-            _fileFormat = this->_checkFormat(*_istreamReader);
-        }
-
-        case SeqIOFileType_::FILE_TYPE_AUTO:
-        case SeqIOFileType_::FILE_TYPE_ERROR:
-            _fileType = SeqIOFileType_::FILE_TYPE_ERROR;
-            _fileFormat = SeqIOFileFormat_::FILE_FORMAT_ERROR;
-            break;
-        }
-
-        // Update _isGood flag from format detection errors.
-        if (_fileFormat == SeqIOFileFormat_::FILE_FORMAT_ERROR)
-            _isGood = false;
-    }
-
-    // Method used in _guessFileTypeAndFormatForReadingAndInitialize() for guessing file format from record reader.
-    template <typename TStream, typename TSpec>
-    SeqIOFileFormat_::Type _checkFormat(RecordReader<TStream, TSpec> & recordReader)
-    {
-        AutoSeqStreamFormat formatTag;
-        if (!guessStreamFormat(recordReader, formatTag))
-            return SeqIOFileFormat_::FILE_FORMAT_ERROR;
-
-        switch (formatTag.tagId)
-        {
-        case Find<AutoSeqStreamFormat, Fasta>::VALUE:
-            return SeqIOFileFormat_::FILE_FORMAT_FASTA;
-
-        case Find<AutoSeqStreamFormat, Fastq>::VALUE:
-            return SeqIOFileFormat_::FILE_FORMAT_FASTQ;
-
-        default:
-            return SeqIOFileFormat_::FILE_FORMAT_ERROR;
-        }
-    }
-
-    // Guess file type and format for writing.
-    void _guessFileTypeAndFormatForWriting()
-    {
-        CharString tmp = _filename;  // copy, we'll trim .gz/.bz2 suffix.
-
-        // Guess file type from file name if requested.
-        if (_fileType == SeqIOFileType_::FILE_TYPE_AUTO)
-        {
-#if SEQAN_HAS_ZLIB
-            if (endsWith(tmp, ".gz"))
-            {
-                _fileType = SeqIOFileType_::FILE_TYPE_GZ;
-                tmp = prefix(tmp, length(tmp) - 3);
-            }
-            else
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-            if (endsWith(tmp, ".bz2"))
-            {
-                _fileType = SeqIOFileType_::FILE_TYPE_BZ2;
-                tmp = prefix(tmp, length(tmp) - 4);
-            }
-            else
-#endif  // #if SEQAN_HAS_BZIP2
-            if (tmp == "-")
-            {
-                _fileType = SeqIOFileType_::FILE_TYPE_TEXT_STD;
-            }
-            else
-            {
-                _fileType = SeqIOFileType_::FILE_TYPE_TEXT;
-            }
-        }
-
-        // Guess file format from file name if requested.
-        if (_fileFormat == SeqIOFileFormat_::FILE_FORMAT_AUTO)
-        {
-            if (endsWith(tmp, ".fastq") || endsWith(tmp, ".fq"))
-                _fileFormat = SeqIOFileFormat_::FILE_FORMAT_FASTQ;
-            else  // must be FASTA.
-                _fileFormat = SeqIOFileFormat_::FILE_FORMAT_FASTA;
-        }
-    }
-
-    // Open the stream members for writing.
-    void _initializeStreamsForWriting()
-    {
-        // Open for writing.
-        //
-        // Note that BZ2 Stream and GZFile Stream already interpret the filename "-" correctly.
-        switch (_fileType)
-        {
-#if SEQAN_HAS_ZLIB
-            case SeqIOFileType_::FILE_TYPE_GZ:
-                {
-                    _gzStream.reset(new Stream<GZFile>());
-                    if (!open(*_gzStream, toCString(_filename), "w"))
-                        _isGood = false;
-                }
-                break;
-
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-            case SeqIOFileType_::FILE_TYPE_BZ2:
-                {
-                    _bz2Stream.reset(new Stream<BZ2File>());
-                    if (!open(*_bz2Stream, toCString(_filename), "w"))
-                        _isGood = false;
-                }
-                break;
-
-#endif  // #if SEQAN_HAS_BZIP2
-            case SeqIOFileType_::FILE_TYPE_TEXT:
-                {
-                    _mmapString.reset(new String<char, MMap<> >());
-                    if (!open(*_mmapString, toCString(_filename), OPEN_CREATE | OPEN_RDWR))
-                        _isGood = false;
-                }
-                break;
-
-            case SeqIOFileType_::FILE_TYPE_TEXT_STD:
-                {
-                    _isGood = std::cout.good();
-                }
-                break;
-
-            default:  // No error possible here.
-                break;
-        }
-    }
-
-    // -----------------------------------------------------------------------
-    // Function readRecord()
-    // -----------------------------------------------------------------------
-
-    // These two template functions implement the record-wise reading of sequence files.
-
-    template <typename TId, typename TSequence, typename TQualities, typename TFormatTag>
-    int readRecord(TId & id, TSequence & seq, TQualities & qual, TFormatTag const & tag)
-    {
-        int res = 0;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            if (!_hintDoublePass)
-            {
-                res = seqan::readRecord(id, seq, qual, *_mmapReaderSinglePass, tag);
-                _atEnd = seqan::atEnd(*_mmapReaderSinglePass);
-            }
-            else
-            {
-                res = seqan::readRecord(id, seq, qual, *_mmapReaderDoublePass, tag);
-                _atEnd = seqan::atEnd(*_mmapReaderDoublePass);
-            }
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-            res = seqan::readRecord(id, seq, qual, *_gzReader, tag);
-            _atEnd = seqan::atEnd(*_gzReader);
-            break;      // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-            res = seqan::readRecord(id, seq, qual, *_bz2Reader, tag);
-            _atEnd = seqan::atEnd(*_bz2Reader);
-            break;      // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    template <typename TId, typename TSequence, typename TFormatTag>
-    int readRecord(TId & id, TSequence & seq, TFormatTag const & tag)
-    {
-        int res = 0;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            if (!_hintDoublePass)
-            {
-                res = seqan::readRecord(id, seq, *_mmapReaderSinglePass, tag);
-                _atEnd = seqan::atEnd(*_mmapReaderSinglePass);
-            }
-            else
-            {
-                res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag);
-                _atEnd = seqan::atEnd(*_mmapReaderDoublePass);
-            }
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-            res = seqan::readRecord(id, seq, *_gzReader, tag);
-            _atEnd = seqan::atEnd(*_gzReader);
-            break;      // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-            res = seqan::readRecord(id, seq, *_bz2Reader, tag);
-            _atEnd = seqan::atEnd(*_bz2Reader);
-            break;      // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    // -----------------------------------------------------------------------
-    // Function readBatch()
-    // -----------------------------------------------------------------------
-
-    // These two template functions implement the batch-wise reading of sequence files.
-
-    template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TQualities,
-              typename TQualSpec, typename TFormatTag>
-    int readBatch(StringSet<TId, TIdSpec> & ids,
-                  StringSet<TSequence, TSeqSpec> & seqs,
-                  StringSet<TQualities, TQualSpec> & quals,
-                  unsigned num,
-                  TFormatTag const & tag)
-    {
-        clear(ids);
-        clear(seqs);
-        clear(quals);
-
-        int res = 0;
-        TId id;
-        TSequence seq;
-        TQualities qual;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            if (!_hintDoublePass)
-            {
-                for (unsigned i = 0; (res == 0) && (i < num) && !seqan::atEnd(*_mmapReaderSinglePass); ++i)
-                {
-                    if ((res = seqan::readRecord(id, seq, qual, *_mmapReaderSinglePass, tag)) != 0)
-                        continue;
-                    appendValue(ids, id);
-                    appendValue(seqs, seq);
-                    appendValue(quals, qual);
-                }
-                _atEnd = seqan::atEnd(*_mmapReaderSinglePass);
-            }
-            else
-            {
-                for (unsigned i = 0; (res == 0) && (i < num) && !seqan::atEnd(*_mmapReaderDoublePass); ++i)
-                {
-                    if ((res = seqan::readRecord(id, seq, qual, *_mmapReaderDoublePass, tag)) != 0)
-                        continue;
-                    appendValue(ids, id);
-                    appendValue(seqs, seq);
-                    appendValue(quals, qual);
-                }
-                _atEnd = seqan::atEnd(*_mmapReaderDoublePass);
-            }
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-        {
-            for (unsigned i = 0; (res == 0) && (i < num) && !seqan::atEnd(*_gzReader); ++i)
-            {
-                if ((res = seqan::readRecord(id, seq, qual, *_gzReader, tag)) != 0)
-                    continue;
-                appendValue(ids, id);
-                appendValue(seqs, seq);
-                appendValue(quals, qual);
-            }
-            _atEnd = seqan::atEnd(*_gzReader);
-        }
-        break;          // end of case
-
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-        {
-            for (unsigned i = 0; (res == 0) && (i < num) && !seqan::atEnd(*_bz2Reader); ++i)
-            {
-                if ((res = seqan::readRecord(id, seq, qual, *_bz2Reader, tag)) != 0)
-                    continue;
-                appendValue(ids, id);
-                appendValue(seqs, seq);
-                appendValue(quals, qual);
-            }
-            _atEnd = seqan::atEnd(*_bz2Reader);
-        }
-        break;          // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TFormatTag>
-    int readBatch(StringSet<TId, TIdSpec> & ids,
-                  StringSet<TSequence, TSeqSpec> & seqs,
-                  unsigned num,
-                  TFormatTag const & tag)
-    {
-        clear(ids);
-        clear(seqs);
-
-        int res = 0;
-        TId id;
-        TSequence seq;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            if (!_hintDoublePass)
-            {
-                for (unsigned i = 0; (res == 0) && (i < num) && !seqan::atEnd(*_mmapReaderSinglePass); ++i)
-                {
-                    if ((res = seqan::readRecord(id, seq, *_mmapReaderSinglePass, tag)) != 0)
-                        continue;
-                    appendValue(ids, id);
-                    appendValue(seqs, seq);
-                }
-                _atEnd = seqan::atEnd(*_mmapReaderSinglePass);
-            }
-            else
-            {
-                for (unsigned i = 0; (res == 0) && (i < num) && !seqan::atEnd(*_mmapReaderDoublePass); ++i)
-                {
-                    if ((res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag)) != 0)
-                        continue;
-                    appendValue(ids, id);
-                    appendValue(seqs, seq);
-                }
-                _atEnd = seqan::atEnd(*_mmapReaderDoublePass);
-            }
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-        {
-            for (unsigned i = 0; (res == 0) && (i < num) && !seqan::atEnd(*_gzReader); ++i)
-            {
-                if ((res = seqan::readRecord(id, seq, *_gzReader, tag)) != 0)
-                    continue;
-                appendValue(ids, id);
-                appendValue(seqs, seq);
-            }
-            _atEnd = seqan::atEnd(*_gzReader);
-        }
-        break;          // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-        {
-            for (unsigned i = 0; (res == 0) && (i < num) && !seqan::atEnd(*_bz2Reader); ++i)
-            {
-                if ((res = seqan::readRecord(id, seq, *_bz2Reader, tag)) != 0)
-                    continue;
-                appendValue(ids, id);
-                appendValue(seqs, seq);
-            }
-            _atEnd = seqan::atEnd(*_bz2Reader);
-        }
-        break;          // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    // -----------------------------------------------------------------------
-    // Function readAll()
-    // -----------------------------------------------------------------------
-
-    // These two template functions implement the reading of whole sequence files.
-
-    template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TQualities,
-              typename TQualSpec, typename TFormatTag>
-    int readAll(StringSet<TId, TIdSpec> & ids,
-                StringSet<TSequence, TSeqSpec> & seqs,
-                StringSet<TQualities, TQualSpec> & quals,
-                TFormatTag const & tag)
-    {
-        clear(ids);
-        clear(seqs);
-        clear(quals);
-
-        int res = 0;
-        TId id;
-        TSequence seq;
-        TQualities qual;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            if (!_hintDoublePass)
-            {
-                while (!seqan::atEnd(*_mmapReaderSinglePass) && res == 0)
-                {
-                    if ((res = seqan::readRecord(id, seq, qual, *_mmapReaderSinglePass, tag)) != 0)
-                        continue;
-                    appendValue(ids, id);
-                    appendValue(seqs, seq);
-                    appendValue(quals, qual);
-                }
-                _atEnd = seqan::atEnd(*_mmapReaderSinglePass);
-            }
-            else
-            {
-                while (!seqan::atEnd(*_mmapReaderDoublePass) && res == 0)
-                {
-                    if ((res = seqan::readRecord(id, seq, qual, *_mmapReaderDoublePass, tag)) != 0)
-                        continue;
-                    appendValue(ids, id);
-                    appendValue(seqs, seq);
-                    appendValue(quals, qual);
-                }
-                _atEnd = seqan::atEnd(*_mmapReaderDoublePass);
-            }
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-        {
-            while (!seqan::atEnd(*_gzReader) && res == 0)
-            {
-                if ((res = seqan::readRecord(id, seq, qual, *_gzReader, tag)) != 0)
-                    continue;
-                appendValue(ids, id);
-                appendValue(seqs, seq);
-                appendValue(quals, qual);
-            }
-            _atEnd = seqan::atEnd(*_gzReader);
-        }
-        break;          // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-        {
-            while (!seqan::atEnd(*_bz2Reader) && res == 0)
-            {
-                if ((res = seqan::readRecord(id, seq, qual, *_bz2Reader, tag)) != 0)
-                    continue;
-                appendValue(ids, id);
-                appendValue(seqs, seq);
-                appendValue(quals, qual);
-            }
-            _atEnd = seqan::atEnd(*_bz2Reader);
-        }
-        break;          // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TFormatTag>
-    int readAll(StringSet<TId, TIdSpec> & ids,
-                StringSet<TSequence, TSeqSpec> & seqs,
-                TFormatTag const & tag)
-    {
-        clear(ids);
-        clear(seqs);
-
-        int res = 0;
-        TId id;
-        TSequence seq;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            if (!_hintDoublePass)
-            {
-                while (!seqan::atEnd(*_mmapReaderSinglePass) && res == 0)
-                {
-                    if ((res = seqan::readRecord(id, seq, *_mmapReaderSinglePass, tag)) != 0)
-                        continue;
-                    appendValue(ids, id);
-                    appendValue(seqs, seq);
-                }
-                _atEnd = seqan::atEnd(*_mmapReaderSinglePass);
-            }
-            else
-            {
-                while (!seqan::atEnd(*_mmapReaderDoublePass) && res == 0)
-                {
-                    if ((res = seqan::readRecord(id, seq, *_mmapReaderDoublePass, tag)) != 0)
-                        continue;
-                    appendValue(ids, id);
-                    appendValue(seqs, seq);
-                }
-                _atEnd = seqan::atEnd(*_mmapReaderDoublePass);
-            }
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-        {
-            while (!seqan::atEnd(*_gzReader) && res == 0)
-            {
-                if ((res = seqan::readRecord(id, seq, *_gzReader, tag)) != 0)
-                    continue;
-
-                appendValue(ids, id);
-                appendValue(seqs, seq);
-            }
-            _atEnd = seqan::atEnd(*_gzReader);
-        }
-        break;          // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-        {
-            while (!seqan::atEnd(*_bz2Reader) && res == 0)
-            {
-                if ((res = seqan::readRecord(id, seq, *_bz2Reader, tag)) != 0)
-                    continue;
-                appendValue(ids, id);
-                appendValue(seqs, seq);
-            }
-            _atEnd = seqan::atEnd(*_bz2Reader);
-        }
-        break;          // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    // -----------------------------------------------------------------------
-    // Function writeRecord()
-    // -----------------------------------------------------------------------
-
-    // These two template functions implement the writing of one record-by-record writing.
-
-    template <typename TId, typename TSequence, typename TQualities, typename TFormatTag>
-    int writeRecord(TId const & id, TSequence const & seq, TQualities const & qual, TFormatTag const & tag,
-                    SequenceOutputOptions const & options)
-    {
-        int res = 0;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            res = seqan::writeRecord(*_mmapString, id, seq, qual, tag, options);
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-            res = seqan::writeRecord(*_gzStream, id, seq, qual, tag, options);
-            break;      // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-            res = seqan::writeRecord(*_bz2Stream, id, seq, qual, tag, options);
-            break;      // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    template <typename TId, typename TSequence, typename TFormatTag>
-    int writeRecord(TId const & id, TSequence const & seq, TFormatTag const & tag,
-                    SequenceOutputOptions const & options)
-    {
-        int res = 0;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            res = seqan::writeRecord(*_mmapString, id, seq, tag, options);
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-            res = seqan::writeRecord(*_gzStream, id, seq, tag, options);
-            break;      // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-            res = seqan::writeRecord(*_bz2Stream, id, seq, tag, options);
-            break;      // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    // -----------------------------------------------------------------------
-    // Function writeAll()
-    // -----------------------------------------------------------------------
-
-    // These two template functions implement the writing of multiple strings to a sequence file.
-
-    template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TQualities,
-              typename TQualSpec, typename TFormatTag>
-    int writeAll(StringSet<TId, TIdSpec> const & ids,
-                 StringSet<TSequence, TSeqSpec> const & seqs,
-                 StringSet<TQualities, TQualSpec> const & quals,
-                 TFormatTag const & tag,
-                 SequenceOutputOptions const & options)
-    {
-        int res = 0;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            res = seqan::write2(*_mmapString, ids, seqs, quals, tag, options);
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-            res = seqan::write2(*_gzStream, ids, seqs, quals, tag, options);
-            break;      // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-            res = seqan::write2(*_bz2Stream, ids, seqs, quals, tag, options);
-            break;      // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    template <typename TId, typename TIdSpec, typename TSequence, typename TSeqSpec, typename TFormatTag>
-    int writeAll(StringSet<TId, TIdSpec> const & ids,
-                 StringSet<TSequence, TSeqSpec> const & seqs,
-                 TFormatTag const & tag,
-                 SequenceOutputOptions const & options)
-    {
-        int res = 0;
-        TId id;
-        TSequence seq;
-
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            res = seqan::write2(*_mmapString, ids, seqs, tag, options);
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-            res = seqan::write2(*_gzStream, ids, seqs, tag, options);
-            break;      // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-            res = seqan::write2(*_bz2Stream, ids, seqs, tag, options);
-            break;      // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            return 1;
-        }
-
-        _isGood = _isGood && (res == 0);
-        return res;
-    }
-
-    // -----------------------------------------------------------------------
-    // Functions for closing/flushing.
-    // -----------------------------------------------------------------------
-
-    void flush()
-    {
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            seqan::flush(*_mmapString);
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-            seqan::streamFlush(*_gzStream);
-            break;      // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-            seqan::streamFlush(*_bz2Stream);
-            break;      // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            break;
-        }
-    }
-
-    void close()
-    {
-        switch (_fileType)
-        {
-        case SeqIOFileType_::FILE_TYPE_TEXT:
-            seqan::close(*_mmapString);
-            break;      // end of case
-
-#if SEQAN_HAS_ZLIB
-        case SeqIOFileType_::FILE_TYPE_GZ:
-        case SeqIOFileType_::FILE_TYPE_GZ_DIRECT:
-            seqan::close(*_gzStream);
-            break;      // end of case
-
-#endif // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2
-        case SeqIOFileType_::FILE_TYPE_BZ2:
-            seqan::close(*_bz2Stream);
-            break;      // end of case
-
-#endif  // #if SEQAN_HAS_BZIP2
-        default:
-            break;
-        }
-    }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-}  // namespace seqan
-
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEQ_IO_SEQ_IO_IMPL_H_
diff --git a/seqan/seq_io/write_fasta_fastq.h b/seqan/seq_io/write_fasta_fastq.h
deleted file mode 100644
index 12c337e..0000000
--- a/seqan/seq_io/write_fasta_fastq.h
+++ /dev/null
@@ -1,605 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
-// ==========================================================================
-// Code for writing FASTA and FASTQ files
-// ==========================================================================
-
-#ifndef SEQAN_SEQ_IO_WRITE_H_
-#define SEQAN_SEQ_IO_WRITE_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Class SequenceOutputOptions
-// ----------------------------------------------------------------------------
-
-/*!
- * @class SequenceOutputOptions
- * @headerfile <seqan/seq_io.h>
- * @brief Configuration for writing sequence (FASTA/FASTQ) files.
- * 
- * This struct is used for the configuration of writing out FASTA and FASTQ files.
- * 
- * @var int SequenceOutputOptions::lineLength;
- * @brief Length of the lines when writing out.
- * 
- * Set to <tt>-1</tt> for default behaviour (no line break for FASTQ, line length of 70 for FASTA) and <tt>0</tt> for
- * disabling line breaks.
- * 
- * @var bool SequenceOutputOptions::qualMeta;
- * @brief Whether or not to write the meta information into the <tt>"+"</tt> line before the qualities (interpreted for
- *        FASTQ only). Default is <tt>false</tt>.
- */
-
-/**
-.Class.SequenceOutputOptions
-..cat:Input/Output
-..summary:Configuration for writing sequence (FASTA/FASTQ) files.
-..description:
-This $struct$ is used for the configuration of writing out FASTA and FASTQ files.
-..include:seqan/seq_io.h
-
-.Memvar.SequenceOutputOptions#lineLength
-..class:Class.SequenceOutputOptions
-..type:nolink:$int$
-..summary:Length of the lines when writing out.
-..description:Set to $-1$ for default behaviour (no line break for FASTQ, line length of 70 for FASTA) and $0$ for disabling line breaks.
-
-.Memvar.SequenceOutputOptions#qualMeta
-..class:Class.SequenceOutputOptions
-..type:nolink:$bool$
-..summary:Whether or not to write the meta information into the $"+"$ line before the qualities (interpreted for FASTQ only). Default is $false$.
-*/
-
-// TODO(holtgrew): Would it be worth having two/three shortcuts for "short reads" and "genomic sequence" and faster or can the compiler optimize the creation away?
-
-struct SequenceOutputOptions
-{
-public:
-    int lineLength;
-    bool qualMeta;
-
-    explicit
-    SequenceOutputOptions(int lineLength = -1, bool qualMeta = false) : lineLength(lineLength), qualMeta(qualMeta)
-    {}    
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-/*!
- * @defgroup FastaFastqIO FASTA/FASTQ I/O
- * @brief Functions for FASTA and FASTQ I/O.
- *
- * These functions are very low-level.  Consider using @link SequenceStream @endlink for an easier to use API.
- */
-
-// ----------------------------------------------------------------------------
-// Function writeRecord()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn FastaFastqIO#writeRecord
- * @headerfile <seqan/seq_io.h>
- * @brief Write one FASTA or FASTQ record.
- * 
- * @signature int writeRecord(stream, id, seq, tag[, options]);
- * @signature int writeRecord(stream, id, seq, quals, tag[, options]);
- * 
- * @param[in,out] stream  The stream to write to.  Type: StreamConcept
- * @param[in]     id      ID/Meta information line to write out. Types: SequenceConcept
- * @param[in]     seq     Sequence to write out.  Type: SequenceConcept
- * @param[in]     quals   ASCII quality characters to write out.  Types: SequenceConcept
- * @param[in]     tag     The format selector. Types: nolink:<tt>Fasta</tt>, <tt>Fastq</tt>
- * @param[in]     options if not supplied, defaults are chosen.  Types: SequenceOutputOptions
- *
- * @return int 0 on success, non-0 value on errors.
- */
-
-/**
-.Function.FASTA/FASTQ I/O#writeRecord
-..summary:Write one FASTA or FASTQ record.
-..signature:int writeRecord(stream, id, seq, tag[, options])
-..signature:int writeRecord(stream, id, seq, quals, tag[, options])
-..param.stream:The stream to write to.
-...type:Concept.StreamConcept
-..param.id:ID/Meta information line to write out.
-...type:Concept.SequenceConcept
-..param.seq:Sequence to write out.
-...type:Concept.SequenceConcept
-..param.quals:ASCII quality characters to write out.
-...type:Concept.SequenceConcept
-..param.tag:The format selector.
-...type:nolink:$Fasta$, $Fastq$
-..param.options:if not supplied defaults are chosen.
-...type:Class.SequenceOutputOptions
-..include:seqan/seq_io.h
-*/
-
-template <typename TStream, typename TIdString, typename TSeqString>
-inline int
-writeRecord(TStream & stream,
-            TIdString const & meta,
-            TSeqString const & seq,
-            Fasta const & /*tag*/,
-            SequenceOutputOptions const & options)
-{
-    int res = streamWriteChar(stream, '>');
-    if (res)
-        return res;
-
-    if (streamWriteBlock(stream, &*begin(meta, Standard()), length(meta)) != length(meta))
-        return 1;
-
-    res = streamWriteChar(stream, '\n');
-    if (res)
-        return res;
-
-    int lineLength = (options.lineLength >= 0) ? options.lineLength : 70;
-
-    if (lineLength > 0)
-    {
-        // write stream character by character
-        typename Iterator<TSeqString const, Standard>::Type it = begin(seq);
-        typename Iterator<TSeqString const, Standard>::Type it_end = end(seq);
-        for (int l = 0; it < it_end; ++it)
-        {
-            res = streamWriteChar(stream, (char)*it);
-            if (res)
-                return res;
-            if (++l == lineLength && (it + 1 != it_end))
-            {
-                res = streamWriteChar(stream, '\n');
-                l = 0;
-                if (res)
-                    return res;
-            }
-        }
-        if (res)
-            return res;
-    }
-    else
-    {
-        for (typename Iterator<TSeqString const, Rooted>::Type it = begin(seq, Rooted()); !atEnd(it); ++it)
-            res = streamWriteChar(stream, (char)*it);
-        if (res)
-            return res;
-    }
-
-    res = streamWriteChar(stream, '\n');
-    return res;
-}
-
-// FASTA
-template <typename TStream, typename TIdString, typename TSeqString>
-inline int
-writeRecord(TStream & stream,
-            TIdString const & meta,
-            TSeqString const & seq,
-            Fasta const & /*tag*/)
-{
-    return writeRecord(stream, meta, seq, Fasta(), SequenceOutputOptions());
-}
-
-
-template <typename TStream, typename TSequence, typename TQualString>
-inline int _writeRecordFastq(TStream & stream, TSequence const & seq, TQualString const &, SequenceOutputOptions const & options, True const & /*HasQualities<Value<TSequence>::Type>::VALUE*/)
-{
-    int res = 0;
-
-    if (options.lineLength > 0)
-    {
-        // write stream character by character
-        typename Iterator<TSequence const>::Type it = begin(seq);
-        typename Iterator<TSequence const>::Type it_end = end(seq);
-        for (int l = 0; it < it_end; ++it)
-        {
-            res = streamWriteChar(stream, static_cast<char>('!' + getQualityValue(*it)));
-            if (res)
-                return res;
-            if (++l == options.lineLength)
-            {
-                res = streamWriteChar(stream, '\n');
-                l = 0;
-                if (res)
-                    return res;
-            }
-        }
-        if (res)
-            return res;
-    }
-    else
-    {
-        typename Iterator<TSequence const>::Type it = begin(seq);
-        typename Iterator<TSequence const>::Type it_end = end(seq);
-        for (; it < it_end; ++it)
-        {
-            res = streamWriteChar(stream, static_cast<char>('!' + getQualityValue(*it)));
-            if (res)
-                return res;
-        }
-    }
-
-    return 0;
-}
-
-
-template <typename TStream, typename TSequence, typename TQualString>
-inline int _writeRecordFastq(TStream & stream, TSequence const & seq, TQualString const & qual, SequenceOutputOptions const & options, False const & /*HasQualities<Value<TSequence>::Type>::VALUE*/)
-{
-    int res = 0;
-
-    if (empty(qual)) // we don't actually have qualities
-    {
-        if (options.lineLength > 0)
-        {
-            for (int i = 0, l = 0; i < (int)length(seq); ++i)
-            {
-                res = streamWriteChar(stream, char(126));
-                if (res)
-                    return res;
-                if (++l == options.lineLength)
-                {
-                    res = streamWriteChar(stream, '\n');
-                    l = 0;
-                    if (res)
-                        return res;
-                }
-            }
-        } else
-        {
-            for (int i = 0; i < (int)length(seq); ++i)
-            {
-                res = streamWriteChar(stream, char(33 + 40));
-                if (res)
-                    return res;
-            }
-        }
-    } else
-    {
-        if (options.lineLength > 0)
-        {
-            // write stream character by character
-            typename Iterator<TQualString const>::Type it = begin(qual);
-            typename Iterator<TQualString const>::Type it_end = end(qual);
-            for (int l = 0; it < it_end; ++it)
-            {
-                res = streamWriteChar(stream, (char)*it);
-                if (res)
-                    return res;
-                if (++l == options.lineLength)
-                {
-                    res = streamWriteChar(stream, '\n');
-                    l = 0;
-                    if (res)
-                        return res;
-                }
-            }
-            if (res)
-                return res;
-        } else
-        {
-            if (streamWriteBlock(stream, &*begin(qual, Standard()), length(qual)) != length(qual))
-                return 1;
-        }
-    }
-    return 0;
-}
-
-// FASTQ
-template <typename TStream,
-          typename TIdString,
-          typename TQualString,
-          typename TSeqString>
-inline int
-writeRecord(TStream & stream,
-            TIdString const & meta,
-            TSeqString const & seq,
-            TQualString const & qual,
-            Fastq const & /*tag*/,
-            SequenceOutputOptions const & options)
-{
-    int res = streamWriteChar(stream, '@');
-    if (res)
-        return res;
-
-    if (streamWriteBlock(stream, &*begin(meta, Standard()), length(meta)) != length(meta))
-        return 1;
-
-    res = streamWriteChar(stream, '\n');
-    if (res)
-        return res;
-
-    if (options.lineLength > 0)
-    {
-        // write stream character by character
-        typename Iterator<TSeqString const>::Type it = begin(seq);
-        typename Iterator<TSeqString const>::Type it_end = end(seq);
-        for (int l = 0; it < it_end; ++it)
-        {
-            res = streamWriteChar(stream, (char)*it);
-            if (res)
-                return res;
-            if (++l == options.lineLength)
-            {
-                res = streamWriteChar(stream, '\n');
-                l = 0;
-                if (res)
-                    return res;
-            }
-        }
-        if (res)
-            return res;
-    } else
-    {
-        for (typename Iterator<TSeqString const, Rooted>::Type it = begin(seq, Rooted()); !atEnd(it); ++it)
-            res = streamWriteChar(stream, (char)*it);
-        if (res)
-            return res;
-    }
-
-    if (streamWriteBlock(stream, "\n+", 2) != 2)
-        return 1;
-
-    if (options.qualMeta)
-    {
-        if (streamWriteBlock(stream, &*begin(meta, Standard()), length(meta)) != length(meta))
-            return res;
-    }
-
-    res = streamWriteChar(stream, '\n');
-    if (res)
-        return res;
-
-    res = _writeRecordFastq(stream, seq, qual, options, typename HasQualities<typename Value<TSeqString>::Type>::Type());
-    if (res)
-        return res;
-    res = streamWriteChar(stream, '\n');
-    return res;
-}
-
-// FASTQ and we have no qualities
-template <typename TStream, typename TIdString, typename TQualString, typename TSeqString>
-inline int
-writeRecord(TStream & stream,
-            TIdString const & meta,
-            TSeqString const & seq,
-            TQualString const & qual,
-            Fastq const & /*tag*/)
-{
-    return writeRecord(stream, meta, seq, qual, Fastq(), SequenceOutputOptions());
-}
-
-// FASTQ and we don't have the qualities
-template <typename TStream, typename TIdString, typename TSeqString>
-inline int
-writeRecord(TStream & stream,
-            TIdString const & meta,
-            TSeqString const & seq,
-            Fastq const & /*tag*/,
-            SequenceOutputOptions const & options)
-{
-    return writeRecord(stream, meta, seq, CharString(), Fastq(), options);
-}
-// FASTQ and we don't have the qualities
-template <typename TStream,
-          typename TIdString,
-          typename TSeqString>
-inline int
-writeRecord(TStream & stream,
-            TIdString const & meta,
-            TSeqString const & seq,
-            Fastq const & /*tag*/)
-{
-    return writeRecord(stream, meta, seq, CharString(), Fastq(), SequenceOutputOptions());
-}
-
-
-
-// ----------------------------------------------------------------------------
-// Function write2()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn FastaFastqIO#write2
- * @headerfile <seqan/seq_io.h>
- * @brief Write FASTA or FASTQ records.
- * 
- * @signature int write2(stream, ids, seqs, tag[, options]);
- * @signature int write2(stream, ids, seqs, quals, tag[, options]);
- * 
- * @param[in,out] stream  The stream to write to. Types: StreamConcept
- * @param[in]     ids     IDs/Metainformation strings to write out.  Type: StringSet
- * @param[in]     seqs    Sequences to write out.  Type: StringSet
- * @param[in]     quals   ASCII quality characters to write out.  Type: StringSet
- * @param[in]     tag     The format selector.  Types: <tt>Fasta</tt>, <tt>Fastq</tt>
- * @param[in]     options if not supplied defaults are chosen.  Type: SequenceOutputOptions
- *
- * @return int 0 on success, non-0 value on errors.
- */
-
-/**
-.Function.FASTA/FASTQ I/O#write2
-..summary:Write FASTA or FASTQ records.
-..signature:int write2(stream, ids, seqs, tag[, options])
-..signature:int write2(stream, ids, seqs, quals, tag[, options])
-..param.stream:The stream to write to.
-...type:Concept.StreamConcept
-..param.ids:IDs/Metainformation strings to write out.
-...type:Class.StringSet
-..param.seqs:Sequences to write out.
-...type:Class.StringSet
-..param.quals:ASCII quality characters to write out.
-...type:Class.StringSet
-..param.tag:The format selector.
-...type:nolink:$Fasta$, $Fastq$
-..param.options:if not supplied defaults are chosen.
-...type:Class.SequenceOutputOptions
-..include:seqan/seq_io.h
-*/
-
-// FASTA
-template <typename TStream, typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec>
-int write2(TStream & stream,
-         StringSet<TIdString, TIdSpec> const & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> const & sequences,
-         Fasta const & /*tag*/,
-         SequenceOutputOptions const & options)
-{
-    if (length(sequenceIds) != length(sequences))
-        return -1;
-
-    typedef StringSet<TIdString, TIdSpec> const TIdSet;
-    typedef StringSet<TSeqString, TSeqSpec> const TSeqSet;
-
-    typename Iterator<TIdSet>::Type  itMeta     = begin(sequenceIds);
-    typename Iterator<TIdSet>::Type  itMeta_end = end(sequenceIds);
-    typename Iterator<TSeqSet>::Type itSeq      = begin(sequences);
-//    typename Iterator<TSeqSet>::Type itSeq_end  = end(sequences);
-
-    for (; itMeta != itMeta_end; ++itMeta, ++itSeq)
-    {
-        int res = writeRecord(stream, *itMeta, *itSeq, Fasta(), options);
-        if (res)
-            return res;
-    }
-    return 0;
-}
-
-template <typename TStream,
-          typename TIdString, typename TIdSpec,
-          typename TSeqString, typename TSeqSpec>
-int write2(TStream & stream,
-         StringSet<TIdString, TIdSpec> const & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> const & sequences,
-         Fasta const & /*tag*/)
-{
-    return write2(stream, sequenceIds, sequences, Fasta(), SequenceOutputOptions());
-
-}
-
-// FASTQ
-template <typename TStream, typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec,
-          typename TQualString, typename TQualSpec>
-int write2(TStream & stream,
-         StringSet<TIdString, TIdSpec> const & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> const & sequences,
-         StringSet<TQualString, TQualSpec> const & qualities,
-         Fastq const & /*tag*/,
-         SequenceOutputOptions const & options)
-{
-    if (length(sequenceIds) != length(sequences) ||
-        length(qualities) != length(sequences))
-        return -1;
-
-    typedef StringSet<TIdString, TIdSpec> const TIdSet;
-    typedef StringSet<TSeqString, TSeqSpec> const TSeqSet;
-    typedef StringSet<TQualString, TSeqSpec> const TQualSet;
-
-    typename Iterator<TIdSet>::Type   itMeta      = begin(sequenceIds);
-    typename Iterator<TIdSet>::Type   itMeta_end  = end(sequenceIds);
-    typename Iterator<TSeqSet>::Type  itSeq       = begin(sequences);
-//    typename Iterator<TSeqSet>::Type  itSeq_end   = end(sequences);
-    typename Iterator<TQualSet>::Type itQual      = begin(qualities);
-    // typename Iterator<TQualSet>::Type itQual_end  = end(qualities);
-
-    for (; itMeta != itMeta_end; ++itMeta, ++itSeq, ++itQual)
-    {
-        int res = writeRecord(stream,*itMeta, *itSeq, *itQual, Fastq(), options);
-        if (res)
-            return res;
-    }
-    return 0;
-}
-
-template <typename TStream, typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec,
-          typename TQualString, typename TQualSpec>
-int write2(TStream & stream,
-         StringSet<TIdString, TIdSpec> const & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> const & sequences,
-         StringSet<TQualString, TQualSpec> const & qualities,
-         Fastq const & /*tag*/)
-{
-    return write2(stream, sequenceIds, sequences, qualities, Fastq(), SequenceOutputOptions());
-}
-
-template <typename TStream, typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec>
-int write2(TStream & stream,
-         StringSet<TIdString, TIdSpec> const & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> const & sequences,
-         Fastq const & /*tag*/,
-         SequenceOutputOptions const & options)
-{
-    typedef StringSet<TIdString, TIdSpec> const TIdSet;
-    typedef StringSet<TSeqString, TSeqSpec> const TSeqSet;
-
-    typename Iterator<TIdSet>::Type   itMeta      = begin(sequenceIds);
-    typename Iterator<TIdSet>::Type   itMeta_end  = end(sequenceIds);
-    typename Iterator<TSeqSet>::Type  itSeq       = begin(sequences);
-//    typename Iterator<TSeqSet>::Type  itSeq_end   = end(sequences);
-
-    for (; itMeta != itMeta_end; ++itMeta, ++itSeq)
-    {
-        int res = writeRecord(stream, *itMeta, *itSeq, Fastq(), options);
-        if (res)
-            return res;
-    }
-    return 0;
-}
-
-template <typename TStream, typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec>
-int write2(TStream & stream,
-         StringSet<TIdString, TIdSpec> const & sequenceIds,
-         StringSet<TSeqString, TSeqSpec> const & sequences,
-         Fastq const & /*tag*/)
-{
-    return write2(stream, sequenceIds, sequences, Fastq(), SequenceOutputOptions());
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_SEQ_IO_WRITE_H_
diff --git a/seqan/sequence.h b/seqan/sequence.h
index baf626f..65ecd98 100644
--- a/seqan/sequence.h
+++ b/seqan/sequence.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -48,8 +48,6 @@
 // Prerequisites.
 // ===========================================================================
 
-#include <seqan/basic.h>
-
 // ----------------------------------------------------------------------------
 // STL prerequisites.
 // ----------------------------------------------------------------------------
@@ -61,7 +59,23 @@
 #include <string>
 #include <list>
 #include <vector>
+#include <deque>
 #include <algorithm>
+#include <numeric>
+
+#include <seqan/platform.h>
+#ifdef SEQAN_CXX11_STANDARD
+#include <forward_list>
+#include <array>
+#endif
+
+// ----------------------------------------------------------------------------
+// Basic
+// ----------------------------------------------------------------------------
+
+#include <seqan/basic.h>
+#include <seqan/misc/bit_twiddling_functors.h>
+#include <seqan/misc/bit_twiddling.h>
 
 // ----------------------------------------------------------------------------
 // Thrust prerequisites.
@@ -93,6 +107,7 @@
 #include <seqan/sequence/segment_infix.h>
 #include <seqan/sequence/segment_suffix.h>
 #include <seqan/sequence/segment_prefix.h>
+#include <seqan/sequence/segment_utils.h>
 
 // ===========================================================================
 // Strings.
@@ -108,30 +123,36 @@
 #include <seqan/sequence/sequence_shortcuts.h>
 
 // ===========================================================================
-// StringSets.
+// Lightweight Containers.
 // ===========================================================================
 
-#include <seqan/sequence/iter_concat_virtual.h>
-#include <seqan/sequence/sequence_concatenator.h>
-#include <seqan/sequence/string_set_base.h>
-#include <seqan/sequence/string_set_concat_direct.h>
-#include <seqan/sequence/string_set_dependent_tight.h>
-#include <seqan/sequence/string_set_dependent_generous.h>
-#include <seqan/sequence/string_set_owner.h>
+#include <seqan/sequence/container_view.h>
 
 // ===========================================================================
 // Adaptions.
 // ===========================================================================
 
-#include <seqan/sequence/adapt_std_list.h>
-#include <seqan/sequence/adapt_std_string.h>
-#include <seqan/sequence/adapt_std_vector.h>
+#include <seqan/sequence/adapt_stl_container.h>
 #include <seqan/sequence/adapt_array_pointer.h>
+#ifdef PLATFORM_CUDA
+#include <seqan/sequence/adapt_thrust_vector.h>
+#endif
 
 // ===========================================================================
-// Utilities.
+// StringSets.
 // ===========================================================================
 
-#include <seqan/sequence/segment_utils.h>
+#include <seqan/sequence/iter_concat_virtual.h>
+#include <seqan/sequence/sequence_concatenator.h>
+#include <seqan/sequence/string_set_base.h>
+#include <seqan/sequence/string_set_view.h>
+#ifdef PLATFORM_CUDA
+#include <seqan/sequence/string_set_device.h>
+#endif
+#include <seqan/sequence/string_set_concat_direct.h>
+#include <seqan/sequence/string_set_dependent_tight.h>
+#include <seqan/sequence/string_set_dependent_generous.h>
+#include <seqan/sequence/string_set_owner.h>
+#include <seqan/sequence/string_set_segment.h>
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/sequence/INFO b/seqan/sequence/INFO
deleted file mode 100644
index 1661d65..0000000
--- a/seqan/sequence/INFO
+++ /dev/null
@@ -1,15 +0,0 @@
-Name: seqan-sequence
-Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-Author: Tobias Rausch <rausch@embl.de>
-Author: David Weese <david.weese@fu-berlin.de>
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Jochen Singer <jochen.singer@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: SeqAn core module with string and string set containers.
- The sequence module contains the implementations of the String class, basic
- implementations of the string class, adaptions from arrays and STL strings to
- the String class, the StringSet class and basic implementations for this class
- as well.
diff --git a/seqan/sequence/adapt_array_pointer.h b/seqan/sequence/adapt_array_pointer.h
index af19c37..8e43419 100644
--- a/seqan/sequence/adapt_array_pointer.h
+++ b/seqan/sequence/adapt_array_pointer.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,17 +45,6 @@ namespace seqan {
 // Enums, Tags, Classes, Specializations
 // ===========================================================================
 
-/**
-.Adaption.char array:
-..summary:Zero terminated $char[]$ or $wchar_t[]$.
-..remarks:Char arrays only support the Insist @Tag.Overflow Strategy.overflow strategy@.
-*/
-
-/**
-.Adaption.char array.remarks:The default overflow strategy
-(both @Metafunction.DefaultOverflowImplicit@ and @Metafunction.DefaultOverflowExplicit@)
-for all operations on char arrays is @Tag.Overflow Strategy.insist@.
-*/
 
 // ===========================================================================
 // Metafunctions
@@ -112,62 +101,45 @@ struct DefaultOverflowExplicit< TValue const [SIZE] >
     typedef Insist Type;
 };
 
-///.Metafunction.IsContiguous.param.T.type:Adaption.char array
-///.Metafunction.IsContiguous.class:Adaption.char array
-
 template <typename TValue>
-struct IsContiguous;
+struct IsContiguous< TValue * > : public True {};
+
+template <typename TValue, size_t SIZE>
+struct IsContiguous< TValue [SIZE] > : public True {};
+
+template <typename TValue, size_t SIZE>
+struct IsContiguous< TValue const [SIZE] > : public True {};
 
 template <typename TValue>
-struct IsContiguous< TValue * >
-{
-    typedef True Type;
-    enum { VALUE = true };
-};
+struct IsSequence< TValue * > : public True {};
 
 template <typename TValue, size_t SIZE>
-struct IsContiguous< TValue [SIZE] >
-{
-    typedef True Type;
-    enum { VALUE = true };
-};
+struct IsSequence< TValue [SIZE] > : public True {};
 
 template <typename TValue, size_t SIZE>
-struct IsContiguous< TValue const [SIZE] >
-{
-    typedef True Type;
-    enum { VALUE = true };
-};
+struct IsSequence< TValue const [SIZE] > : public True {};
+
+// ----------------------------------------------------------------------------
+// Concept Sequence
+// ----------------------------------------------------------------------------
 
-///.Metafunction.IsSequence.param.T.type:Adaption.char array
-///.Metafunction.IsSequence.class:Adaption.char array
+// NOTE(h-2): removed because we really don't want this
+// template <typename TValue>
+// SEQAN_CONCEPT_IMPL((TValue *), (ContainerConcept));
+//
+// template <typename TValue>
+// SEQAN_CONCEPT_IMPL((TValue * const), (ContainerConcept));
 
-template <typename TValue>
-struct IsSequence< TValue * >
-{
-    typedef True Type;
-    enum { VALUE = true };
-};
 template <typename TValue, size_t SIZE>
-struct IsSequence< TValue [SIZE] >
-{
-    typedef True Type;
-    enum { VALUE = true };
-};
+SEQAN_CONCEPT_IMPL((TValue [SIZE]), (ContainerConcept));
+
 template <typename TValue, size_t SIZE>
-struct IsSequence< TValue const [SIZE] >
-{
-    typedef True Type;
-    enum { VALUE = true };
-};
+SEQAN_CONCEPT_IMPL((TValue const [SIZE]), (ContainerConcept));
 
 // ----------------------------------------------------------------------------
 // Metafunction Iterator
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Iterator.param.T.type:Adaption.char array
-///.Metafunction.Iterator.class:Adaption.char array
-
 template <typename TValue>
 struct Iterator<TValue *, Standard>
 {
@@ -216,9 +188,6 @@ SEQAN_CHECKPOINT
     return begin(me, typename DefaultGetIteratorSpec<T>::Type()) ;
 }
 
-///.Function.begin.param.object.type:Adaption.char array
-///.Function.begin.class:Adaption.char array
-
 template <typename TValue>
 inline typename Iterator<TValue *, Standard>::Type
 begin(TValue * me,
@@ -259,9 +228,6 @@ SEQAN_CHECKPOINT
     return TIterator(me, begin(me, Standard()));
 }
 
-///.Function.end.param.object.type:Adaption.char array
-///.Function.end.class:Adaption.char array
-
 template <typename TValue>
 inline typename Iterator<TValue *, Standard>::Type
 end(TValue * me,
@@ -299,9 +265,6 @@ SEQAN_CHECKPOINT
     return begin(me, tag_) + length(me);
 }
 
-///.Function.value.param.container.type:Adaption.char array
-///.Function.value.class:Adaption.char array
-
 template <typename TValue, typename TPos>
 inline TValue &
 value(TValue * me,
@@ -320,9 +283,6 @@ SEQAN_CHECKPOINT
     return me[pos];
 }
 
-///.Function.assignValue.param.container.type:Adaption.char array
-///.Function.assignValue.class:Adaption.char array
-
 template <typename TValue, typename TPos>
 inline void
 assignValue(TValue * me,
@@ -333,9 +293,6 @@ SEQAN_CHECKPOINT
     assign(value(me, pos), _value);
 }
 
-///.Function.moveValue.param.container.type:Adaption.char array
-///.Function.moveValue.class:Adaption.char array
-
 template <typename TValue, typename TPos>
 inline void
 moveValue(TValue * me,
@@ -365,9 +322,6 @@ SEQAN_CHECKPOINT
     return *pos == 0;
 }
 
-///.Function.length.param.object.type:Adaption.char array
-///.Function.length.class:Adaption.char array
-
 template <typename TValue>
 inline size_t
 length(TValue * me)
@@ -396,14 +350,14 @@ inline size_t
 length(char * me)
 {
 SEQAN_CHECKPOINT
-    return ::std::strlen(me);
+    return std::strlen(me);
 }
 
 inline size_t
 length(char const * me)
 {
 SEQAN_CHECKPOINT
-    return ::std::strlen(me);
+    return std::strlen(me);
 }
 
 template <typename TValue>
@@ -415,8 +369,6 @@ SEQAN_CHECKPOINT
     me[new_length] = 0;
 }
 
-///.Function.clear.param.object.type:Adaption.char array
-
 template <typename TValue>
 inline void
 clear(TValue * me)
@@ -427,8 +379,6 @@ SEQAN_CHECKPOINT
     _setLength(me, 0);
 }
 
-///.Function.empty.param.object.type:Adaption.char array
-
 template <typename TValue>
 inline bool
 empty(TValue * me)
@@ -483,10 +433,6 @@ SEQAN_CHECKPOINT
     return ClearSpaceStringBase_<Tag<TExpand> >::_clearSpace_(me, size, pos_begin, pos_end, limit);
 }
 
-///.Function.assign.param.target.type:.Adaption.char array
-///.Function.assign.param.source.type:.Adaption.char array
-///.Function.assign.class:Adaption.char array
-
 //overload of binary version for strings:
 
 template<typename TTargetValue, typename TSource>
@@ -553,9 +499,6 @@ SEQAN_CHECKPOINT
     AssignString_<Tag<TExpand> >::assign_(target, source, limit);
 }
 
-///.Function.move.param.target.type:Adaption.char array
-///.Function.move.class:Adaption.char array
-
 //overload of binary version for strings:
 
 template<typename TTargetValue, typename TSource>
@@ -580,10 +523,6 @@ SEQAN_CHECKPOINT
 // append
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.append.param.target.type:.Adaption.char array
-///.Function.append.param.source.type:.Adaption.char array
-///.Function.append.class:Adaption.char array
-
 template<typename TTargetValue, typename TSource, typename TExpand>
 inline void
 append(TTargetValue * target,
@@ -633,9 +572,6 @@ SEQAN_CHECKPOINT
 // replace
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.replace.param.target.type:.Adaption.char array
-///.Function.replace.param.source.type:.Adaption.char array
-
 template<typename TTargetValue, typename TSource, typename TExpand>
 inline void
 replace(TTargetValue * target,
@@ -714,8 +650,6 @@ replace(TTargetValue * target,
 }
 */
 //////////////////////////////////////////////////////////////////////////////
-///.Function.resize.param.object.type:Adaption.char array
-
 template <typename TValue, typename TSize, typename TExpand>
 inline size_t
 resize(
@@ -724,7 +658,9 @@ resize(
     Tag<TExpand>)
 {
 SEQAN_CHECKPOINT
-    return _Resize_String<Tag<TExpand> >::resize_(me, new_length);
+    if (static_cast<TSize>(std::strlen(me)) > new_length)
+        me[new_length] = 0;
+    return std::strlen(me);
 }
 
 template <typename TValue, typename TSize, typename TExpand>
@@ -736,7 +672,11 @@ resize(
     Tag<TExpand>)
 {
 SEQAN_CHECKPOINT
-    return _Resize_String<Tag<TExpand> >::resize_(me, new_length, val);
+    TSize old_length = std::strlen(me);
+    if (old_length < new_length)
+        std::memset(me + old_length, int(val), new_length - old_length);
+    me[new_length] = 0;
+    return std::strlen(me);
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/sequence/adapt_std_list.h b/seqan/sequence/adapt_std_list.h
deleted file mode 100644
index 0c27987..0000000
--- a/seqan/sequence/adapt_std_list.h
+++ /dev/null
@@ -1,362 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Adaptions for STL vectors to SeqAn sequences.
-// ==========================================================================
-
-// SEQAN_NO_GENERATED_FORWARDS: No forwards are generated for this file.
-
-#ifndef SEQAN_SEQUENCE_ADAPT_STD_LIST_H_
-#define SEQAN_SEQUENCE_ADAPT_STD_LIST_H_
-
-namespace seqan {
-
-// ===========================================================================
-// Enums, Tags, Classes, Specializations
-// ===========================================================================
-
-/**
-.Adaption."std::list"
-..summary:Adaption for STL list objects.
- */
-
-// ===========================================================================
-// Metafunctions
-// ===========================================================================
-
-///.Metafunction.IsContiguous.param.T.type:Adaption.std::list
-///.Metafunction.IsContiguous.class:Adaption.std::list
-
-template <typename TValue, typename TAlloc>
-struct IsContiguous< std::list<TValue, TAlloc> >
-{
-    enum { VALUE = false };
-};
-
-template <typename  TValue, typename TAlloc>
-struct IsContiguous< std::list<TValue, TAlloc> const>
-        : IsContiguous< std::list<TValue, TAlloc> > {};
-
-///.Metafunction.Value.param.T.type:Adaption.std::list
-///.Metafunction.Value.class:Adaption.std::list
-
-template <typename TValue, typename TAlloc>
-struct Value< std::list<TValue, TAlloc> >
-{
-    typedef typename std::list<TValue, TAlloc>::value_type Type;
-};
-
-template <typename TValue, typename TAlloc>
-struct Value< std::list<TValue, TAlloc> const>
-        : Value< std::list<TValue, TAlloc> > {};
-
-///.Metafunction.GetValue.param.T.type:Adaption.std::list
-// TODO(holtgrew): GetValue is a reference?! I thought the reverse was true in respect to Value<>.
-///.Metafunction.GetValue.class:Adaption.std::list
-
-template <typename TValue, typename TAlloc>
-struct GetValue< std::list<TValue, TAlloc> >
-{
-    typedef typename std::list<TValue, TAlloc>::reference Type;
-};
-
-template <typename TValue, typename TAlloc>
-struct GetValue< std::list<TValue, TAlloc> const>
-{
-    typedef typename std::list<TValue, TAlloc>::const_reference Type;
-};
-
-///.Metafunction.Reference.param.T.type:Adaption.std::vector
-///.Metafunction.Reference.class:Adaption.std::vector
-
-template <typename TValue, typename TAlloc>
-struct Reference< std::list<TValue, TAlloc> >
-{
-    typedef typename std::list<TValue, TAlloc>::reference Type;
-};
-
-template <typename TValue,  typename TAlloc>
-struct Reference< std::list<TValue, TAlloc> const>
-{
-    typedef typename std::list<TValue,  TAlloc>::const_reference Type;
-};
-
-///.Metafunction.Iterator.param.T.type:Adaption.std::list
-///.Metafunction.Iterator.class:Adaption.std::list
-
-template <typename TValue, typename TAlloc>
-struct Iterator< std::list<TValue, TAlloc>, Rooted>
-{
-    typedef std::list<TValue, TAlloc> TString_;
-    typedef Iter<TString_, StdIteratorAdaptor> TIterator_;
-    typedef Iter<TString_, AdaptorIterator<TIterator_> > Type;
-};
-
-template <typename TValue, typename TAlloc>
-struct Iterator< std::list<TValue, TAlloc> const, Rooted>
-{
-    typedef std::list<TValue, TAlloc> const TString_;
-    typedef Iter<TString_, StdIteratorAdaptor> TIterator_;
-    typedef Iter<TString_, AdaptorIterator<TIterator_> > Type;
-};
-
-template <typename TValue, typename TAlloc>
-struct Iterator< std::list<TValue, TAlloc>, Standard>
-{
-    typedef Iter< std::list<TValue, TAlloc>, StdIteratorAdaptor> Type;
-};
-
-template <typename TValue, typename TAlloc>
-struct Iterator< std::list<TValue, TAlloc> const, Standard>
-{
-    typedef Iter< std::list<TValue, TAlloc> const, StdIteratorAdaptor> Type;
-};
-
-///.Metafunction.Position.param.T.type:Adaption.std::list
-///.Metafunction.Position.class:Adaption.std::list
-
-template <typename TValue, typename TAlloc>
-struct Position< std::list<TValue, TAlloc> >
-{
-    typedef typename std::list<TValue, TAlloc>::size_type Type;
-};
-
-template <typename TValue, typename TAlloc>
-struct Position< std::list<TValue, TAlloc> const>
-        : Position< std::list<TValue, TAlloc> > {};
-
-///.Metafunction.Size.param.T.type:Adaption.std::list
-///.Metafunction.Size.class:Adaption.std::list
-
-template <typename TValue, typename TAlloc>
-struct Size< std::list<TValue, TAlloc> >
-{
-    typedef typename std::list<TValue, TAlloc>::size_type Type;
-};
-
-template <typename TValue, typename TAlloc>
-struct Size< std::list<TValue, TAlloc> const>
-        : Size< std::list<TValue, TAlloc> > {};
-
-///.Metafunction.StdContainerIterator.param.T.type:Adaption.std::list
-///.Metafunction.StdContainerIterator.class:Adaption.std::list
-
-template <typename TValue, typename TAlloc>
-struct StdContainerIterator< std::list<TValue, TAlloc> >
-{
-    typedef std::list<TValue, TAlloc> TContainer_;
-    typedef typename TContainer_::iterator Type;
-};
-
-template <typename TValue, typename TAlloc>
-struct StdContainerIterator< std::list<TValue, TAlloc> const>
-{
-    typedef std::list<TValue, TAlloc> TContainer_;
-    typedef typename TContainer_::const_iterator Type;
-};
-
-// ===========================================================================
-// Functions
-// ===========================================================================
-
-///.Function.begin.param.object.type:Adaption.std::list
-///.Function.begin.class:Adaption.std::list
-
-template<typename TValue>
-inline
-typename Iterator<std::list<TValue>, Standard>::Type
-begin(std::list<TValue> & list,
-      Standard const &)
-{
-    SEQAN_CHECKPOINT;
-    return list.begin();
-}
-
-template <typename TValue>
-inline
-typename Iterator<std::list<TValue> const, Standard>::Type
-begin(std::list<TValue> const & list,
-      Standard const &)
-{
-    SEQAN_CHECKPOINT;
-    return list.begin();
-}
-
-///.Function.end.param.object.type:Adaption.std::list
-///.Function.end.class:Adaption.std::list
-
-template<typename TValue>
-inline
-typename Iterator<std::list<TValue>, Standard>::Type
-end(std::list<TValue> & list,
-      Standard const &)
-{
-    SEQAN_CHECKPOINT;
-    return list.end();
-}
-
-template <typename TValue>
-inline
-typename Iterator<std::list<TValue> const, Standard>::Type
-end(std::list<TValue> const & list,
-      Standard const &)
-{
-    SEQAN_CHECKPOINT;
-    return list.end();
-}
-
-///.Function.front.param.container.type:Adaption.std::list
-///.Function.front.class:Adaption.std::list
-
-template <typename TValue>
-inline typename Reference<std::list<TValue> >::Type
-front(std::list<TValue> & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.front();
-}
-
-template <typename TValue>
-inline typename Reference<std::list<TValue> const>::Type
-front(std::list<TValue> const & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.front();
-}
-
-///.Function.back.param.container.type:Adaption.std::list
-///.Function.back.class:Adaption.std::list
-
-template <typename TValue>
-inline typename Reference<std::list<TValue> >::Type
-back(std::list<TValue> & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.back();
-}
-
-template <typename TValue>
-inline typename Reference<std::list<TValue> const>::Type
-back(std::list<TValue> const & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.back();
-}
-
-///.Function.length.param.object.type:Adaption.std::list
-///.Function.length.class:Adaption.std::list
-
-template <typename TValue>
-inline typename Size<std::list<TValue> >::Type
-length(std::list<TValue> & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.size();
-}
-
-template <typename TValue>
-inline typename Size<std::list<TValue> const>::Type
-length(std::list<TValue> const & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.size();
-}
-
-/**
-.Function.prependValue:
-..cat:Sequences
-..summary:Prepend a value to a container.
-..signature:prependValue(container, value)
-..param.container:The container to prepend to.
-...type:Adaption.std::list
-..param.value:The value to prepend to the container.
-..include:seqan/sequence.h
-*/
-///.Function.prependValue.class:Adaption.std::list
-
-template <typename T, typename T2>
-inline void
-prependValue(std::list<T> & list,
-             T2 value)
-{
-    SEQAN_CHECKPOINT;
-    list.push_front(value);
-}
-
-///.Function.appendValue.param.target.type:Adaption.std::list
-///.Function.appendValue.class:Adaption.std::list
-
-template <typename T, typename T2>
-inline void
-appendValue(std::list<T> & list,
-            T2 value)
-{
-    SEQAN_CHECKPOINT;
-    list.push_back(value);
-}
-
-///.Function.clear.param.object.type:Adaption.std::list
-///.Function.clear.class:Adaption.std::list
-
-template <typename T>
-inline void
-clear(std::list<T> & list)
-{
-    SEQAN_CHECKPOINT;
-    list.clear();
-}
-
-///.Function.reserve.param.object.type:Adaption.std::list
-///.Function.reserve.class:Adaption.std::list
-
-template <typename T, typename TTag>
-inline void
-reserve(std::list<T> & /*list*/, TTag const & /*tag*/)
-{
-    SEQAN_CHECKPOINT;
-}
-
-///.Function.capacity.param.object.type:Adaption.std::list
-///.Function.capacity.class:Adaption.std::list
-
-template <typename T>
-inline typename Size<std::list<T> >::Type
-capacity(std::list<T> const & list)
-{
-    SEQAN_CHECKPOINT;
-    return length(list);
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_SEQUENCE_ADAPT_STD_LIST_H_
diff --git a/seqan/sequence/adapt_std_string.h b/seqan/sequence/adapt_std_string.h
deleted file mode 100644
index 2de4964..0000000
--- a/seqan/sequence/adapt_std_string.h
+++ /dev/null
@@ -1,761 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
-// Author: David Weese <david.weese@fu-berlin.de>
-// ==========================================================================
-// Adaptions for STL strings to SeqAn strings.
-// ==========================================================================
-
-#ifndef SEQAN_SEQUENCE_ADAPT_STD_STRING_H_
-#define SEQAN_SEQUENCE_ADAPT_STD_STRING_H_
-
-namespace seqan {
-
-// ===========================================================================
-// Enums, Tags, Classes, Specializations
-// ===========================================================================
-
-/**
-.Adaption."std::basic_string"
-..summary:Adaption for STL strings.
- */
-
-// ===========================================================================
-// Metafunctions
-// ===========================================================================
-
-///.Metafunction.StdContainerIterator.param.T.type:Adaption."std::basic_string"
-///.Metafunction.StdContainerIterator.class:Adaption."std::basic_string"
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct StdContainerIterator< std::basic_string<TChar, TCharTraits, TAlloc> >
-{
-    typedef std::basic_string<TChar, TCharTraits, TAlloc> TContainer;
-    typedef typename TContainer::iterator Type;
-};
-    
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct StdContainerIterator< std::basic_string<TChar, TCharTraits, TAlloc> const>
-{
-    typedef std::basic_string<TChar, TCharTraits, TAlloc> TContainer;
-    typedef typename TContainer::const_iterator Type;
-};
-
-///.Metafunction.IsContiguous.param.T.type:Adaption.std::basic_string
-///.Metafunction.IsContiguous.class:Adaption."std::basic_string"
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct IsContiguous< std::basic_string<TChar, TCharTraits, TAlloc> >
-{
-    enum { VALUE = false };
-};
-
-template <typename  TChar, typename TCharTraits, typename TAlloc>
-struct IsContiguous< std::basic_string<TChar, TCharTraits, TAlloc> const>
-        : IsContiguous< std::basic_string<TChar, TCharTraits, TAlloc> > {};
-
-///.Metafunction.Value.param.T.type:Adaption.std::basic_string
-///.Metafunction.Value.class:Adaption."std::basic_string"
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Value< std::basic_string<TChar, TCharTraits, TAlloc> >
-{
-    typedef typename std::basic_string<TChar, TCharTraits, TAlloc>::value_type Type;
-};
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Value< std::basic_string<TChar, TCharTraits, TAlloc> const>
-        : Value< std::basic_string<TChar, TCharTraits, TAlloc> > {};
-
-///.Metafunction.GetValue.param.T.type:Adaption.std::basic_string
-///.Metafunction.GetValue.class:Adaption."std::basic_string"
-// TODO(holtgrew): GetValue is a reference?! I thought the reverse was true in respect to Value<>.
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct GetValue< std::basic_string<TChar, TCharTraits, TAlloc> >
-{
-    typedef typename std::basic_string<TChar, TCharTraits, TAlloc>::reference Type;
-};
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct GetValue< std::basic_string<TChar, TCharTraits, TAlloc> const>
-{
-    typedef typename std::basic_string<TChar, TCharTraits, TAlloc>::const_reference Type;
-};
-
-///.Metafunction.Reference.param.T.type:Adaption.std::basic_string
-///.Metafunction.Reference.class:Adaption."std::basic_string"
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Reference< std::basic_string<TChar, TCharTraits, TAlloc> >
-{
-    typedef typename std::basic_string<TChar, TCharTraits, TAlloc>::reference Type;
-};
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Reference< std::basic_string<TChar, TCharTraits, TAlloc> const>
-{
-    typedef typename std::basic_string<TChar, TCharTraits, TAlloc>::const_reference Type;
-};
-
-///.Metafunction.Iterator.param.T.type:Adaption.std::basic_string
-///.Metafunction.Iterator.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>
-{
-    typedef std::basic_string<TChar, TCharTraits, TAlloc> TString_;
-    typedef Iter<TString_, StdIteratorAdaptor> TIterator_;
-    typedef Iter<TString_, AdaptorIterator<TIterator_> > Type;
-};
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Iterator< std::basic_string<TChar, TCharTraits, TAlloc> const, Rooted>
-{
-    typedef std::basic_string<TChar, TCharTraits, TAlloc> const TString_;
-    typedef Iter<TString_, StdIteratorAdaptor> TIterator_;
-    typedef Iter<TString_, AdaptorIterator<TIterator_> > Type;
-};
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Standard >
-{
-    typedef Iter< std::basic_string<TChar, TCharTraits, TAlloc>, StdIteratorAdaptor > Type;
-};
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Iterator< std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>
-{
-    typedef Iter< std::basic_string<TChar, TCharTraits, TAlloc> const, StdIteratorAdaptor > Type;
-};
-
-///.Metafunction.Position.param.T.type:Adaption.std::basic_string
-///.Metafunction.Position.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Position< std::basic_string<TChar, TCharTraits, TAlloc> >
-{
-    typedef typename std::basic_string<TChar, TCharTraits, TAlloc>::size_type Type;
-};
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Position< std::basic_string<TChar, TCharTraits, TAlloc> const>
-        : Position< std::basic_string<TChar, TCharTraits, TAlloc> > {};
-
-///.Metafunction.Size.param.T.type:Adaption.std::basic_string
-///.Metafunction.Size.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Size< std::basic_string<TChar, TCharTraits, TAlloc> >
-{
-    typedef typename std::basic_string<TChar, TCharTraits, TAlloc>::size_type Type;
-};
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct Size< std::basic_string<TChar, TCharTraits, TAlloc> const>
-        : Size< std::basic_string<TChar, TCharTraits, TAlloc> > {};
-
-///.Metafunction.Size.param.T.type:Adaption.std::basic_string
-///.Metafunction.Size.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct DefaultOverflowImplicit< std::basic_string<TChar, TCharTraits, TAlloc> >
-{
-    typedef Generous Type;
-};
-
-///.Metafunction.IsSequence.param.T.type:Adaption.std::basic_string
-///.Metafunction.IsSequence.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-struct IsSequence<std::basic_string<TChar, TCharTraits, TAlloc> > : True {};
-
-// ===========================================================================
-// Functions
-// ===========================================================================
-
-///.Function.getObjectId.param.object.type:Adaption.std::basic_string
-///.Function.getObjectId.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline void const *
-getObjectId(std::basic_string<TChar, TCharTraits, TAlloc> const & me)
-{
-    SEQAN_CHECKPOINT;
-    if (me.empty())
-        return NULL;
-    else
-        return (& *(me.end() - 1)) + 1;
-}
-
-///.Function.begin.param.object.type:Adaption.std::basic_string
-///.Function.begin.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type
-begin(std::basic_string<TChar, TCharTraits, TAlloc> & me,
-      Standard)
-{
-    SEQAN_CHECKPOINT;
-    return typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type(me.begin());
-}
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type
-begin(std::basic_string<TChar, TCharTraits, TAlloc> const & me,
-      Standard)
-{
-    SEQAN_CHECKPOINT;
-    return typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type(me.begin());
-}
-
-///.Function.end.param.object.type:Adaption.std::basic_string
-///.Function.end.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type
-end(std::basic_string<TChar, TCharTraits, TAlloc> & me,
-    Standard)
-{
-    SEQAN_CHECKPOINT;
-    return typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type(me.end());
-}
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type
-end(std::basic_string<TChar, TCharTraits, TAlloc> const & me,
-    Standard)
-{
-    SEQAN_CHECKPOINT;
-    return typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type(me.end());
-}
-
-///.Function.value.param.container.type:Adaption.std::basic_string
-///.Function.value.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos>
-inline typename GetValue< std::basic_string<TChar, TCharTraits, TAlloc> >::Type
-value(std::basic_string<TChar, TCharTraits, TAlloc> & me,
-      TPos pos)
-{
-    SEQAN_CHECKPOINT;
-    return me[pos];
-}
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos>
-inline typename GetValue< std::basic_string<TChar, TCharTraits, TAlloc> const>::Type
-value(std::basic_string<TChar, TCharTraits, TAlloc> const & me,
-      TPos pos)
-{
-    SEQAN_CHECKPOINT;
-    return me[pos];
-}
-
-///.Function.length.param.object.type:Adaption.std::basic_string
-///.Function.length.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type
-length(std::basic_string<TChar, TCharTraits, TAlloc> const & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.length();
-}
-
-///.Function.capacity.param.object.type:Adaption.std::basic_string
-///.Function.capacity.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type
-capacity(std::basic_string<TChar, TCharTraits, TAlloc> const & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.capacity();
-}
-
-///.Function.empty.param.object.type:Adaption.std::basic_string
-///.Function.empty.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline bool
-empty(std::basic_string<TChar, TCharTraits, TAlloc> const & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.empty();
-}
-
-///.Function.clear.param.object.type:Adaption.std::basic_string
-///.Function.clear.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc>
-inline void
-clear(std::basic_string<TChar, TCharTraits, TAlloc> & me)
-{
-    SEQAN_CHECKPOINT;
-    me.clear();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//assign to std::basic_string
-
-///.Function.assign.param.target.type:Adaption.std::basic_string
-///.Function.assign.param.source.type:Adaption.std::basic_string
-///.Function.assign.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource & source)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, Generous());
-}
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, Generous());
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TSize>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource & source,
-       TSize limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, limit, Generous());
-}
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TSize>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       TSize limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, limit, Generous());
-}
-
-//____________________________________________________________________________
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource & source,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    target.assign(begin(source, Standard()), end(source, Standard()));
-}
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    target.assign(begin(source, Standard()), end(source, Standard()));
-}
-
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign_std_string_Generous_impl(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-                                TSource & source,
-                                typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit)
-{
-    SEQAN_CHECKPOINT;
-    typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
-    typename Size<TSource const>::Type source_length = length(source);
-    if (source_length > limit)
-    {
-        source_length = limit;
-    }
-    target.assign(source_begin, source_begin + source_length);
-}
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource & source,
-       typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    assign_std_string_Generous_impl(target, source, limit);
-}
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    assign_std_string_Generous_impl(target, source, limit);
-}
-
-//____________________________________________________________________________
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource & source,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, target.capacity(), Generous());
-}
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, target.capacity(), Generous());
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource & source,
-       typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (limit > target.capacity())
-    {
-        limit = target.capacity();
-    }
-
-    assign(target, source, limit, Generous());
-}
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-assign(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (limit > target.capacity())
-    {
-        limit = target.capacity();
-    }
-
-    assign(target, source, limit, Generous());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//append to std::basic_string
-
-///.Function.append.param.target.type:Adaption.std::basic_string
-///.Function.append.param.source.type:Adaption.std::basic_string
-///.Function.append.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-append(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    target.append(begin(source, Standard()), end(source, Standard()));
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-append(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type target_length = target.length();
-    if (target_length > limit)
-    {
-        target.resize(limit);
-    }
-    else
-    {
-        limit -= target_length;
-        typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
-        typename Size<TSource const>::Type source_length = length(source);
-        if (source_length > limit)
-        {
-            source_length = limit;
-        }
-        target.append(source_begin, source_begin + source_length);
-    }
-}
-
-//____________________________________________________________________________
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-append(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    append(target, source, target.capacity(), Generous());
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-append(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-       TSource const & source,
-       typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (limit > target.capacity())
-    {
-        limit = target.capacity();
-    }
-
-    append(target, source, limit, Generous());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-///.Function.appendValue.param.target.type:Adaption.std::basic_string
-///.Function.appendValue.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TValue, typename TTag>
-inline void
-appendValue(std::basic_string<TChar, TCharTraits, TAlloc> & me,
-            TValue const & _value,
-            TTag)
-{
-    SEQAN_CHECKPOINT;
-    me.push_back(_value);
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TValue>
-inline void
-appendValue(std::basic_string<TChar, TCharTraits, TAlloc> & me,
-            TValue const & _value,
-            Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (capacity(me) > length(me)) me.push_back(_value);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//replace to std::basic_string
-
-///.Function.replace.param.target.type:Adaption.std::basic_string
-///.Function.replace.param.source.type:Adaption.std::basic_string
-///.Function.replace.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-replace(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-        typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin,
-        typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end,
-        TSource const & source,
-        Generous)
-{
-    SEQAN_CHECKPOINT;
-    target.replace(target.begin() + pos_begin, target.begin() + pos_end, begin(source, Standard()), end(source, Standard()));
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-replace(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-        typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin,
-        typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end,
-        TSource const & source,
-        typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-        Generous)
-{
-    SEQAN_CHECKPOINT;
-    if (pos_begin >= limit)
-    {
-        target.resize(limit);
-    }
-    else
-    {
-        typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
-        typename Size<TSource const>::Type source_length = length(source);
-        typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_mid = pos_begin + source_length;
-        if (pos_mid > limit)
-        {
-            target.replace(target.begin() + pos_begin, target.begin() + limit, source_begin, source_begin + limit - pos_begin);
-            target.resize(limit);
-        }
-        else
-        {
-            target.replace(target.begin() + pos_begin, target.begin() + pos_end, source_begin, end(source, Standard()));
-            if (target.length() > limit)
-            {
-                target.resize(limit);
-            }
-        }
-    }
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-replace(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-        typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin,
-        typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end,
-        TSource const & source,
-        Limit)
-{
-    SEQAN_CHECKPOINT;
-    replace(target, pos_begin, pos_end, source, target.capacity(), Generous());
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource>
-inline void
-replace(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-        typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin,
-        typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end,
-        TSource const & source,
-        typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-        Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (limit > target.capacity())
-    {
-        limit = target.capacity();
-    }
-
-    replace(target, pos_begin, pos_end, source, limit, Generous());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// handling of iterators as begin and end
-
-/*
-template<typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TExpand>
-inline void
-replace(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-        typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>::Type pos_begin,
-        typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>::Type pos_end,
-        TSource & source,
-        Tag<TExpand> tag)
-{
-    replace(target, position(pos_begin), position(pos_end), source, tag);
-}
-
-template<typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TExpand>
-inline void
-replace(std::basic_string<TChar, TCharTraits, TAlloc> & target,
-        typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>::Type pos_begin,
-        typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Rooted>::Type pos_end,
-        TSource & source,
-        typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit,
-        Tag<TExpand> tag)
-{
-    replace(target,  position(pos_begin),  position(pos_end), source, tag);
-}
-*/
-
-///.Function.reserve.param.object.type:Adaption.std::basic_string
-///.Function.reserve.remarks:For @Adaption.std::basic_string|STL Adaptions@, $reserve$ is only guaranteed to have the specified behaviour with $Insist$ and $Generous$.
-///.Function.reserve.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand>
-inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type
-reserve(
-    std::basic_string<TChar, TCharTraits, TAlloc> & seq,
-    TSize new_capacity,
-    Tag<TExpand> tag)
-{
-    SEQAN_CHECKPOINT;
-    seq.reserve(new_capacity);
-    return _capacityReturned(seq, new_capacity, tag);
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize>
-inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type
-reserve(
-    std::basic_string<TChar, TCharTraits, TAlloc> & seq,
-    TSize new_capacity,
-    Insist const &)
-{
-    SEQAN_CHECKPOINT;
-    // do nothing
-    return _capacityReturned(seq, new_capacity, Insist());
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize>
-inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type
-reserve(
-    std::basic_string<TChar, TCharTraits, TAlloc> & seq,
-    TSize new_capacity,
-    Limit const &)
-{
-    SEQAN_CHECKPOINT;
-    // do nothing
-    return _capacityReturned(seq, new_capacity, Limit());
-}
-
-///.Function.resize.param.object.type:Adaption.std::basic_string
-///.Function.resize.class:Adaption.std::basic_string
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand>
-inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type
-resize(
-    std::basic_string<TChar, TCharTraits, TAlloc> & me,
-    TSize new_length,
-    Tag<TExpand>)
-{
-    SEQAN_CHECKPOINT;
-    me.resize(new_length);
-    return me.length();
-}
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand>
-inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type
-resize(
-    std::basic_string<TChar, TCharTraits, TAlloc> & me,
-    TSize new_length,
-    TChar const & val,
-    Tag<TExpand>)
-{
-    SEQAN_CHECKPOINT;
-    me.resize(new_length, val);
-    return me.length();
-}
-
-inline char const *
-toCString(std::string const & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.c_str();
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_SEQUENCE_ADAPT_STD_STRING_H_
diff --git a/seqan/sequence/adapt_std_vector.h b/seqan/sequence/adapt_std_vector.h
deleted file mode 100644
index 2f8b73a..0000000
--- a/seqan/sequence/adapt_std_vector.h
+++ /dev/null
@@ -1,806 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Knut Reinert <knut.reinert@fu-berlin.de>
-// ==========================================================================
-// Adaptions for STL vectors to SeqAn strings.
-// ==========================================================================
-
-// SEQAN_NO_GENERATED_FORWARDS: No forwards are generated for this file.
-
-#ifndef SEQAN_SEQUENCE_ADAPT_STD_VECTOR_H_
-#define SEQAN_SEQUENCE_ADAPT_STD_VECTOR_H_
-
-namespace seqan {
-
-// ===========================================================================
-// Enums, Tags, Classes, Specializations
-// ===========================================================================
-
-/**
-.Adaption."std::vector"
-..summary:Adaption for STL vector class.
- */
-
-// ===========================================================================
-// Metafunctions
-// ===========================================================================
-
-///.Metafunction.IsContiguous.param.T.type:Adaption.std::vector
-///.Metafunction.IsContiguous.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-struct IsContiguous< std::vector<TChar, TAlloc> >
-{
-    enum { VALUE = true };
-};
-
-template <typename  TChar, typename TAlloc>
-struct IsContiguous< std::vector<TChar, TAlloc> const>
-        : IsContiguous< std::vector<TChar, TAlloc> > {};
-
-///.Metafunction.Value.param.T.type:Adaption.std::vector
-///.Metafunction.Value.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-struct Value< std::vector<TChar, TAlloc> >
-{
-    typedef typename std::vector<TChar, TAlloc>::value_type Type;
-};
-
-template <typename TChar, typename TAlloc>
-struct Value< std::vector<TChar, TAlloc> const>
-        : Value< std::vector<TChar, TAlloc> > {};
-
-///.Metafunction.GetValue.param.T.type:Adaption.std::vector
-// TODO(holtgrew): GetValue is a reference?! I thought the reverse was true in respect to Value<>.
-///.Metafunction.GetValue.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-struct GetValue< std::vector<TChar, TAlloc> >
-{
-    typedef typename std::vector<TChar, TAlloc>::reference Type;
-};
-
-template <typename TChar, typename TAlloc>
-struct GetValue< std::vector<TChar,  TAlloc> const>
-{
-    typedef typename std::vector<TChar, TAlloc>::const_reference Type;
-};
-
-///.Metafunction.Reference.param.T.type:Adaption.std::vector
-///.Metafunction.Reference.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-struct Reference< std::vector<TChar, TAlloc> >
-{
-    typedef typename std::vector<TChar, TAlloc>::reference Type;
-};
-
-template <typename TChar,  typename TAlloc>
-struct Reference< std::vector<TChar, TAlloc> const>
-{
-    typedef typename std::vector<TChar,  TAlloc>::const_reference Type;
-};
-
-///.Metafunction.Iterator.param.T.type:Adaption.std::vector
-///.Metafunction.Iterator.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-struct Iterator< std::vector<TChar, TAlloc>, Rooted>
-{
-    typedef std::vector<TChar, TAlloc> TVector_;
-    typedef Iter<TVector_, StdIteratorAdaptor> TIterator_;
-    typedef Iter<TVector_, AdaptorIterator<TIterator_> > Type;
-};
-
-template <typename TChar, typename TAlloc>
-struct Iterator< std::vector<TChar, TAlloc> const, Rooted>
-{
-    typedef std::vector<TChar, TAlloc> const TVector_;
-    typedef Iter<TVector_, StdIteratorAdaptor> TIterator_;
-    typedef Iter<TVector_, AdaptorIterator<TIterator_> > Type;
-};
-
-template <typename TChar,  typename TAlloc>
-struct Iterator< std::vector<TChar, TAlloc>, Standard >
-{
-    typedef Iter< std::vector<TChar,  TAlloc>, StdIteratorAdaptor > Type;
-};
-
-template <typename TChar,  typename TAlloc>
-struct Iterator< std::vector<TChar,  TAlloc> const, Standard>
-{
-    typedef Iter< std::vector<TChar, TAlloc> const, StdIteratorAdaptor > Type;
-};
-
-///.Metafunction.Position.param.T.type:Adaption.std::vector
-///.Metafunction.Position.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc>
-struct Position< std::vector<TChar, TAlloc> >
-{
-    typedef typename std::vector<TChar,  TAlloc>::size_type Type;
-};
-
-template <typename TChar,  typename TAlloc>
-struct Position< std::vector<TChar,  TAlloc> const>
-        : Position< std::vector<TChar,  TAlloc> > {};
-
-///.Metafunction.Position.param.T.type:Adaption.std::vector
-///.Metafunction.Position.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc>
-struct Size< std::vector<TChar, TAlloc> >
-{
-    typedef typename std::vector<TChar, TAlloc>::size_type Type;
-};
-
-template <typename TChar, typename TAlloc>
-struct Size< std::vector<TChar, TAlloc> const>
-        : Size< std::vector<TChar, TAlloc> > {};
-
-///.Metafunction.Size.param.T.type:Adaption.std::vector
-///.Metafunction.Size.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-struct DefaultOverflowImplicit< std::vector<TChar, TAlloc> >
-{
-    typedef Generous Type;
-};
-
-///.Metafunction.StdContainerIterator.param.T.type:Adaption.std::vector
-///.Metafunction.StdContainerIterator.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-struct StdContainerIterator< std::vector<TChar, TAlloc> >
-{
-    typedef std::vector<TChar, TAlloc> TContainer_;
-    typedef typename TContainer_::iterator Type;
-};
-
-template <typename TChar, typename TAlloc>
-struct StdContainerIterator< std::vector<TChar, TAlloc> const>
-{
-    typedef std::vector<TChar, TAlloc> TContainer_;
-    typedef typename TContainer_::const_iterator Type;
-};
-
-///.Metafunction.IsSequence.param.T.type:Adaption.std::vector
-///.Metafunction.IsSequence.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-struct IsSequence<std::vector<TChar, TAlloc> > : True {};
-
-// ===========================================================================
-// Functions
-// ===========================================================================
-
-///.Function.getObjectId.param.object.type:Adaption.std::vector
-///.Function.getObjectId.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc>
-inline void const *
-getObjectId(std::vector<TChar, TAlloc> const & me)
-{
-    SEQAN_CHECKPOINT;
-    if (me.empty())
-        return NULL;
-    else
-        return (& *(me.end() - 1)) + 1;
-}
-
-///.Function.begin.param.object.type:Adaption.std::vector
-///.Function.begin.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc>
-inline typename Iterator< std::vector<TChar,  TAlloc>, Standard>::Type
-begin(std::vector<TChar,  TAlloc> & me,
-      Standard)
-{
-    SEQAN_CHECKPOINT;
-    return typename Iterator< std::vector<TChar,  TAlloc>, Standard>::Type(me.begin());
-}
-template <typename TChar,  typename TAlloc>
-inline typename Iterator< std::vector<TChar,  TAlloc> const, Standard>::Type
-begin(std::vector<TChar, TAlloc> const & me,
-      Standard)
-{
-    SEQAN_CHECKPOINT;
-    return typename Iterator< std::vector<TChar,  TAlloc> const, Standard>::Type(me.begin());
-}
-
-///.Function.end.param.object.type:Adaption.std::vector
-///.Function.end.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-inline typename Iterator< std::vector<TChar, TAlloc>, Standard>::Type
-end(std::vector<TChar,  TAlloc> & me,
-    Standard)
-{
-    SEQAN_CHECKPOINT;
-    return typename Iterator< std::vector<TChar, TAlloc>, Standard>::Type(me.end());
-}
-template <typename TChar,  typename TAlloc>
-inline typename Iterator< std::vector<TChar,  TAlloc> const, Standard>::Type
-end(std::vector<TChar,  TAlloc> const & me,
-    Standard)
-{
-    SEQAN_CHECKPOINT;
-    return typename Iterator< std::vector<TChar,  TAlloc> const, Standard>::Type(me.end());
-}
-
-///.Function.value.param.container.type:Adaption.std::vector
-///.Function.value.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc, typename TPos>
-inline typename GetValue< std::vector<TChar, TAlloc> >::Type
-value(std::vector<TChar,  TAlloc> & me,
-      TPos pos)
-{
-    SEQAN_CHECKPOINT;
-    return me[pos];
-}
-template <typename TChar,  typename TAlloc, typename TPos>
-inline typename GetValue< std::vector<TChar,  TAlloc> const>::Type
-value(std::vector<TChar, TAlloc> const & me,
-      TPos pos)
-{
-    SEQAN_CHECKPOINT;
-    return me[pos];
-}
-
-///.Function.value.param.container.type:Adaption.std::vector
-///.Function.value.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-inline typename Size< std::vector<TChar, TAlloc> >::Type
-length(std::vector<TChar, TAlloc> const & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.size();
-}
-
-///.Function.capacity.param.object.type:Adaption.std::vector
-///.Function.capacity.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-inline typename Size< std::vector<TChar, TAlloc> >::Type
-capacity(std::vector<TChar, TAlloc> const & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.capacity();
-}
-
-///.Function.empty.param.object.type:Adaption.std::vector
-///.Function.empty.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc>
-inline bool
-empty(std::vector<TChar, TAlloc> const & me)
-{
-    SEQAN_CHECKPOINT;
-    return me.empty();
-}
-
-///.Function.clear.param.object.type:Adaption.std::vector
-///.Function.clear.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc>
-inline void
-clear(std::vector<TChar, TAlloc> & me)
-{
-    SEQAN_CHECKPOINT;
-    me.clear();
-}
-
-///.Function.front.param.container.type:Adaption.std::vector
-///.Function.front.class:Adaption.std::vector
-
-template <typename TChar>
-inline typename Reference<std::vector<TChar> >::Type
-front(std::vector<TChar> & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.front();
-}
-
-template <typename TChar>
-inline typename Reference<std::vector<TChar> const>::Type
-front(std::vector<TChar> const & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.front();
-}
-
-///.Function.back.param.container.type:Adaption.std::vector
-///.Function.back.class:Adaption.std::vector
-
-template <typename TChar>
-inline typename Reference<std::vector<TChar> >::Type
-back(std::vector<TChar> & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.back();
-}
-
-template <typename TChar>
-inline typename Reference<std::vector<TChar> const>::Type
-back(std::vector<TChar> const & list)
-{
-    SEQAN_CHECKPOINT;
-    return list.back();
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//assign to std::vector
-
-///.Function.assign.param.target.type:Adaption.std::vector
-///.Function.assign.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar,  TAlloc> & target,
-       TSource & source)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, Generous());
-}
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar,  TAlloc> & target,
-       TSource const & source)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, Generous());
-}
-
-template <typename TChar,  typename TAlloc, typename TSource, typename TSize>
-inline void
-assign(std::vector<TChar,  TAlloc> & target,
-       TSource & source,
-       TSize limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, limit, Generous());
-}
-template <typename TChar,  typename TAlloc, typename TSource, typename TSize>
-inline void
-assign(std::vector<TChar,  TAlloc> & target,
-       TSource const & source,
-       TSize limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, limit, Generous());
-}
-
-//____________________________________________________________________________
-
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar, TAlloc> & target,
-       TSource & source,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    target.assign(begin(source, Standard()), end(source, Standard()));
-}
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar, TAlloc> & target,
-       TSource const & source,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    target.assign(begin(source, Standard()), end(source, Standard()));
-}
-
-
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-assign_std_vector_Generous_impl(std::vector<TChar,  TAlloc> & target,
-                                TSource & source,
-                                typename Size< std::vector<TChar,  TAlloc> >::Type limit)
-{
-    SEQAN_CHECKPOINT;
-    typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
-    typename Size<TSource const>::Type source_length = length(source);
-    if (source_length > limit)
-    {
-        source_length = limit;
-    }
-    target.assign(source_begin, source_begin + source_length);
-}
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar,  TAlloc> & target,
-       TSource & source,
-       typename Size< std::vector<TChar, TAlloc> >::Type limit,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    assign_std_vector_Generous_impl(target, source, limit);
-}
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar, TAlloc> & target,
-       TSource const & source,
-       typename Size< std::vector<TChar, TAlloc> >::Type limit,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    assign_std_vector_Generous_impl(target, source, limit);
-}
-
-//____________________________________________________________________________
-
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar,  TAlloc> & target,
-       TSource & source,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, target.capacity(), Generous());
-}
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar,  TAlloc> & target,
-       TSource const & source,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, target.capacity(), Generous());
-}
-
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar, TAlloc> & target,
-       TSource & source,
-       typename Size< std::vector<TChar, TAlloc> >::Type limit,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (limit > target.capacity())
-    {
-        limit = target.capacity();
-    }
-
-    assign(target, source, limit, Generous());
-}
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-assign(std::vector<TChar,  TAlloc> & target,
-       TSource const & source,
-       typename Size< std::vector<TChar,  TAlloc> >::Type limit,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (limit > target.capacity())
-    {
-        limit = target.capacity();
-    }
-
-    assign(target, source, limit, Generous());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//append to std::vector
-
-///.Function.append.param.target.type:Adaption.std::vector
-///.Function.append.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-append(std::vector<TChar,  TAlloc> & target,
-       TSource const & source,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    target.insert(target.end(), begin(source, Standard()), end(source, Standard()));
-}
-
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-append(std::vector<TChar, TAlloc> & target,
-       TSource const & source,
-       typename Size< std::vector<TChar, TAlloc> >::Type limit,
-       Generous)
-{
-    SEQAN_CHECKPOINT;
-    typename Size< std::vector<TChar, TAlloc> >::Type target_length = target.length();
-    if (target_length > limit)
-    {
-        target.resize(limit);
-    }
-    else
-    {
-        limit -= target_length;
-        typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
-        typename Size<TSource const>::Type source_length = length(source);
-        if (source_length > limit)
-        {
-            source_length = limit;
-        }
-
-        target.insert(target.end(), source_begin, source_begin + source_length);
-    }
-}
-
-//____________________________________________________________________________
-
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-append(std::vector<TChar,  TAlloc> & target,
-       TSource const & source,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    append(target, source, target.capacity(), Generous());
-}
-
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-append(std::vector<TChar, TAlloc> & target,
-       TSource const & source,
-       typename Size< std::vector<TChar, TAlloc> >::Type limit,
-       Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (limit > target.capacity())
-    {
-        limit = target.capacity();
-    }
-
-    append(target, source, limit, Generous());
-}
-
-//////////////////////////////////////////////////////////////////////////////
-///.Function.appendValue.param.target.type:Adaption.std::vector
-///.Function.appendValue.class:Adaption.std::vector
-
-template <typename TChar, typename TAlloc, typename TValue, typename TTag>
-inline void
-appendValue(std::vector<TChar, TAlloc> & me,
-            TValue const & _value,
-            TTag)
-{
-    SEQAN_CHECKPOINT;
-    me.push_back(_value);
-}
-
-template <typename TChar, typename TAlloc, typename TValue>
-inline void
-appendValue(std::vector<TChar,  TAlloc> & me,
-            TValue const & _value,
-            Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (capacity(me) > length(me)) me.push_back(_value);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-//replace to std::vector
-
-///.Function.replace.param.target.type:Adaption.std::vector
-///.Function.replace.param.source.type:Adaption.std::vector
-///.Function.replace.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-replace(std::vector<TChar, TAlloc> & target,
-        typename Position< std::vector<TChar, TAlloc> >::Type pos_begin,
-        typename Position< std::vector<TChar, TAlloc> >::Type pos_end,
-        TSource const & source,
-        Generous)
-{
-    SEQAN_CHECKPOINT;
-    typename Size< std::vector<TChar, TAlloc> >::Type target_size = pos_end-pos_begin;
-    typename Size< std::vector<TChar, TAlloc> >::Type source_size =length(source);
-
-    if(target_size >= source_size)
-        {
-            copy(source.begin(),source.end(), target.begin()+pos_begin);
-            if( target_size > source_size )
-                target.erase(target.begin()+pos_begin+source_size,target.begin()+pos_end);
-        }
-    else
-        {
-            copy(source.begin(),source.begin()+target_size,target.begin()+pos_begin);
-            target.insert(target.begin()+pos_end,source.begin()+target_size,source.end());
-        }
-}
-
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-replace(std::vector<TChar, TAlloc> & target,
-        typename Position< std::vector<TChar, TAlloc> >::Type pos_begin,
-        typename Position< std::vector<TChar, TAlloc> >::Type pos_end,
-        TSource const & source,
-        typename Size< std::vector<TChar, TAlloc> >::Type limit,
-        Generous)
-{
-    SEQAN_CHECKPOINT;
-    if (pos_begin >= limit)
-    {
-        target.resize(limit);
-    }
-    else
-    {
-        typename Size<TSource const>::Type source_length = length(source);
-        typename Size< std::vector<TChar, TAlloc> >::Type pos_mid = pos_begin + source_length;
-        typename Size< std::vector<TChar, TAlloc> >::Type pos_limit(limit);
-        if (pos_mid > limit)
-        {
-            target.resize(limit);
-            replace(target,pos_begin,pos_limit,source);
-            target.resize(limit);
-        }
-        else
-        {
-            replace(target,pos_begin,pos_end,source);
-            if (target.size() > limit)
-            {
-                target.resize(limit);
-            }
-        }
-    }
-
-}
-
-template <typename TChar,  typename TAlloc, typename TSource>
-inline void
-replace(std::vector<TChar,  TAlloc> & target,
-        typename Position< std::vector<TChar, TAlloc> >::Type pos_begin,
-        typename Position< std::vector<TChar, TAlloc> >::Type pos_end,
-        TSource const & source,
-        Limit)
-{
-    SEQAN_CHECKPOINT;
-    replace(target, pos_begin, pos_end, source, target.capacity(), Generous());
-}
-
-template <typename TChar, typename TAlloc, typename TSource>
-inline void
-replace(std::vector<TChar, TAlloc> & target,
-        typename Position< std::vector<TChar,  TAlloc> >::Type pos_begin,
-        typename Position< std::vector<TChar,  TAlloc> >::Type pos_end,
-        TSource const & source,
-        typename Size< std::vector<TChar, TAlloc> >::Type limit,
-        Limit)
-{
-    SEQAN_CHECKPOINT;
-    if (limit > target.capacity())
-    {
-        limit = target.capacity();
-    }
-    replace(target, pos_begin, pos_end, source, limit, Generous());
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-// handling of iterators as begin and end
-
-template<typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TExpand>
-inline void
-replace(std::vector<TChar, TAlloc> & target,
-        typename Iterator< std::vector<TChar, TAlloc>, Rooted>::Type pos_begin,
-        typename Iterator< std::vector<TChar, TAlloc>, Rooted>::Type pos_end,
-        TSource & source,
-        Tag<TExpand> tag)
-{
-    replace(target, position(pos_begin), position(pos_end), source, tag);
-}
-
-/*
-template<typename TChar, typename TAlloc, typename TSource, typename TExpand>
-inline void
-replace(std::vector<TChar, TAlloc> & target,
-        typename Iterator< std::vector<TChar, TAlloc>, Rooted>::Type pos_begin,
-        typename Iterator< std::vector<TChar, TAlloc>, Rooted>::Type pos_end,
-        TSource & source,
-        typename Size< std::vector<TChar, TAlloc> >::Type limit,
-        Tag<TExpand> tag)
-{
-    replace(target,  position(pos_begin),  position(pos_end), source, tag);
-}
-*/
-
-
-///.Function.reserve.param.object.type:Adaption.std::vector
-///.Function.reserve.remarks:For @Adaption.std::vector|STL Adaptions@, $reserve$ is only guaranteed to have the specified behaviour with $Insist$ and $Generous$.
-///.Function.reserve.class:Adaption.std::vector
-
-template <typename TChar,  typename TAlloc, typename TSize, typename TExpand>
-inline typename Size< std::vector<TChar, TAlloc> >::Type
-reserve(
-    std::vector<TChar, TAlloc> & seq,
-    TSize new_capacity,
-    Tag<TExpand> tag)
-{
-    SEQAN_CHECKPOINT;
-    seq.reserve(new_capacity);
-    return _capacityReturned(seq, new_capacity, tag);
-}
-
-template <typename TChar, typename TAlloc, typename TSize>
-inline typename Size< std::vector<TChar, TAlloc> >::Type
-reserve(
-    std::vector<TChar, TAlloc> & seq,
-    TSize new_capacity,
-    Insist const &)
-{
-    SEQAN_CHECKPOINT;
-    // do nothing
-    return _capacityReturned(seq, new_capacity, Insist());
-}
-
-template <typename TChar,  typename TAlloc, typename TSize>
-inline typename Size< std::vector<TChar, TAlloc> >::Type
-reserve(
-    std::vector<TChar,  TAlloc> & seq,
-    TSize new_capacity,
-    Limit const &)
-{
-    SEQAN_CHECKPOINT;
-    // do nothing
-    return _capacityReturned(seq, new_capacity, Limit());
-}
-
-///.Function.resize.param.object.type:Adaption.std::vector
-template <typename TChar,  typename TAlloc, typename TSize, typename TExpand>
-inline typename Size< std::vector<TChar,  TAlloc> >::Type
-resize(
-    std::vector<TChar, TAlloc> & me,
-    TSize new_length,
-    Tag<TExpand>)
-{
-    SEQAN_CHECKPOINT;
-    me.resize(new_length);
-    return me.size();
-}
-
-template <typename TChar, typename TAlloc, typename TSize, typename TExpand>
-inline typename Size< std::vector<TChar,  TAlloc> >::Type
-fill(
-    std::vector<TChar, TAlloc> & me,
-    TSize new_length,
-    TChar const & val,
-    Tag<TExpand>)
-{
-    SEQAN_CHECKPOINT;
-    me.resize(new_length, val);
-    return me.length();
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_SEQUENCE_ADAPT_STD_VECTOR_H_
diff --git a/seqan/sequence/adapt_stl_container.h b/seqan/sequence/adapt_stl_container.h
new file mode 100644
index 0000000..42e8e23
--- /dev/null
+++ b/seqan/sequence/adapt_stl_container.h
@@ -0,0 +1,1424 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
+// ==========================================================================
+// Adaptions for STL containers to SeqAn sequences.
+// ==========================================================================
+
+#ifndef SEQAN_SEQUENCE_ADAPT_STL_CONTAINER_H_
+#define SEQAN_SEQUENCE_ADAPT_STL_CONTAINER_H_
+
+namespace seqan {
+
+// ===========================================================================
+// Enums, Tags, Classes, Specializations
+// ===========================================================================
+
+// ===========================================================================
+// Concepts
+// ===========================================================================
+
+template <typename TChar, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::vector<TChar, TAlloc>), (StlContainerConcept));
+
+template <typename TChar, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::vector<TChar, TAlloc> const), (StlContainerConcept));
+
+template <typename TChar, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::deque<TChar, TAlloc>), (StlContainerConcept));
+
+template <typename TChar, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::deque<TChar, TAlloc> const), (StlContainerConcept));
+
+template <typename TChar, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::list<TChar, TAlloc>), (StlContainerConcept));
+
+template <typename TChar, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::list<TChar, TAlloc> const), (StlContainerConcept));
+
+template<typename TChar, typename TTraits, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::basic_string<TChar, TTraits, TAlloc>), (StlContainerConcept));
+
+template<typename TChar, typename TTraits, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::basic_string<TChar, TTraits, TAlloc> const), (StlContainerConcept));
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::forward_list<TChar, TAlloc>), (StlContainerConcept));
+
+template <typename TChar, typename TAlloc>
+SEQAN_CONCEPT_IMPL((std::forward_list<TChar, TAlloc> const), (StlContainerConcept));
+
+template <typename TChar, std::size_t N>
+SEQAN_CONCEPT_IMPL((std::array<TChar, N>), (StlContainerConcept));
+
+template <typename TChar, std::size_t N>
+SEQAN_CONCEPT_IMPL((std::array<TChar, N> const), (StlContainerConcept));
+#endif
+
+/* NOTE(h-2) on ConceptChecking and universal references
+ *
+ * When type deduction takes place before && then && can act as both && or &
+ * [https://isocpp.org/blog/2012/11/universal-references-in-c11-scott-meyers]
+ *
+ * This has the effect that in
+ *      foobar(T &&)
+ * T actually can be "int &". Consequently the above becomes "int & &&" which
+ * collapses to "int &". The important thing is that in
+ *      template<typename EnableIf<Is<SuperConcept<T> >
+ * this will result in the ConceptCheck always failing (because the Concept is
+ * not defined for reference types).
+ *
+ * So in the following you will see a RemoveReference< > around the type
+ * whenever the function takes a && argument or SEQAN_FORWARD_ARG argument AND
+ * it shall act as univeral reference (e.g. length()). But in some cases it
+ * shall not (because there is a different overload for the l-value-reference
+ * arg) and it is  intentionally omitted, e.g. value().
+ */
+
+// ===========================================================================
+// Metafunctions
+// ===========================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunctions that are the same for all STL containers
+// ----------------------------------------------------------------------------
+
+#define COMMA ,
+
+#define SUPERMACRO__(CONT, TMPL) \
+template <TMPL> \
+struct Value<CONT> \
+{ \
+    typedef typename CONT::value_type Type; \
+};\
+template <TMPL> \
+struct Value<CONT const> \
+{ \
+    typedef typename CONT::value_type Type; \
+};\
+template <TMPL> \
+struct Reference<CONT> \
+{ \
+    typedef typename CONT::reference Type; \
+};\
+template <TMPL> \
+struct Reference<CONT const> \
+{ \
+    typedef typename CONT::const_reference Type; \
+};\
+template <TMPL> \
+struct GetValue<CONT> \
+{ \
+    typedef typename CONT::const_reference Type; \
+};\
+template <TMPL> \
+struct GetValue<CONT const> \
+{ \
+    typedef typename CONT::const_reference Type; \
+};\
+template <TMPL> \
+struct Position<CONT> \
+{ \
+    typedef typename CONT::size_type Type; \
+};\
+template <TMPL> \
+struct Position<CONT const> \
+{ \
+    typedef typename CONT::size_type Type; \
+};\
+template <TMPL> \
+struct Size<CONT> \
+{ \
+    typedef typename CONT::size_type Type; \
+};\
+template <TMPL> \
+struct Size<CONT const> \
+{ \
+    typedef typename CONT::size_type Type; \
+};\
+template <TMPL> \
+struct Iterator<CONT, Standard> \
+{ \
+    typedef Iter<CONT, StdIteratorAdaptor> Type;\
+};\
+template <TMPL> \
+struct Iterator<CONT const, Standard> \
+{ \
+    typedef Iter<CONT const, StdIteratorAdaptor> Type;\
+};\
+template <TMPL> \
+struct Iterator<CONT, Rooted> \
+{ \
+    typedef Iter<CONT, AdaptorIterator<Iter<CONT, StdIteratorAdaptor> > > Type;\
+}; \
+template <TMPL> \
+struct Iterator<CONT const, Rooted> \
+{ \
+    typedef Iter<CONT const, AdaptorIterator<Iter<CONT const, StdIteratorAdaptor> > > Type;\
+};
+
+SUPERMACRO__(std::vector<TChar COMMA TAlloc>,      typename TChar COMMA typename TAlloc)
+SUPERMACRO__(std::deque<TChar COMMA TAlloc>,       typename TChar COMMA typename TAlloc)
+SUPERMACRO__(std::list<TChar COMMA TAlloc>,        typename TChar COMMA typename TAlloc)
+#ifdef SEQAN_CXX11_STANDARD
+SUPERMACRO__(std::forward_list<TChar COMMA TAlloc>,typename TChar COMMA typename TAlloc)
+SUPERMACRO__(std::array<TChar COMMA N>,            typename TChar COMMA std::size_t N)
+#endif
+SUPERMACRO__(std::basic_string<TChar COMMA TTraits COMMA TAlloc>, typename TChar COMMA typename TTraits COMMA typename TAlloc)
+
+// ----------------------------------------------------------------------------
+// Mfn IsContiguous (default is False)
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct IsContiguous<std::vector<TChar, TAlloc> > :
+    public True
+{};
+
+template <typename TChar, typename TAlloc>
+struct IsContiguous<std::vector<TChar, TAlloc> const> :
+    public True
+{};
+
+template <typename TChar, typename TTraits, typename TAlloc>
+struct IsContiguous<std::basic_string<TChar, TTraits, TAlloc> > :
+    public True
+{};
+
+template <typename TChar, typename TTraits, typename TAlloc>
+struct IsContiguous<std::basic_string<TChar, TTraits, TAlloc> const> :
+    public True
+{};
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, size_t N>
+struct IsContiguous<std::array<TChar, N> > :
+    public True
+{};
+
+template <typename TChar, size_t N>
+struct IsContiguous<std::array<TChar, N> const> :
+    public True
+{};
+#endif
+
+// ----------------------------------------------------------------------------
+// Mfn HasSubscriptOperator (different for e.g. std::deque)
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct HasSubscriptOperator<std::deque<TChar, TAlloc> > :
+    public True
+{};
+
+template <typename TChar, typename TAlloc>
+struct HasSubscriptOperator<std::deque<TChar, TAlloc> const> :
+    public True
+{};
+
+// ----------------------------------------------------------------------------
+// Mfn IsSequence
+// ----------------------------------------------------------------------------
+
+//NOTE(h-2): shouldnt we be using Is<StringConcept> or IsContiguous<> or ...?
+
+template <typename TChar, typename TAlloc>
+struct IsSequence<std::vector<TChar, TAlloc> > : True {};
+
+template <typename TChar, typename TAlloc>
+struct IsSequence<std::deque<TChar, TAlloc> > : True {};
+
+template <typename TChar, typename TAlloc>
+struct IsSequence<std::list<TChar, TAlloc> > : True {};
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc>
+struct IsSequence<std::forward_list<TChar, TAlloc> > : True {};
+
+//NOTE(h-2): array isn't by SeqAn definition, right?
+#endif
+
+template <typename TChar, typename TCharTraits, typename TAlloc>
+struct IsSequence<std::basic_string<TChar, TCharTraits, TAlloc> > : True {};
+
+// ----------------------------------------------------------------------------
+// Mfn FixedSize_ (private)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+struct FixedSize_ : public False {};
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, size_t N>
+struct FixedSize_<std::array<TChar, N> > : public True {};
+#endif
+
+// ===========================================================================
+// Functions
+// ===========================================================================
+
+// ----------------------------------------------------------------------------
+// Function getObjectId
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >, void const *)
+getObjectId(TContainer SEQAN_FORWARD_CARG me)
+{
+    if (me.empty())
+        return NULL;
+    else
+        return (& *(me.end() - 1)) + 1;
+}
+
+// ----------------------------------------------------------------------------
+// Function begin (standard)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Iterator<TContainer, Standard>::Type)
+begin(TContainer & me, Standard const &)
+{
+    return me.begin();
+}
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Iterator<TContainer const, Standard>::Type)
+begin(TContainer const & me, Standard const &)
+{
+    return me.begin();
+}
+
+// ----------------------------------------------------------------------------
+// Function begin (rooted)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Iterator<TContainer, Rooted>::Type)
+begin(TContainer & me, Rooted const &)
+{
+    return _beginDefault(me, Rooted());
+}
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Iterator<TContainer const, Rooted>::Type)
+begin(TContainer const & me, Rooted const &)
+{
+    return _beginDefault(me, Rooted());
+}
+
+// ----------------------------------------------------------------------------
+// Function end (standard)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Iterator<TContainer, Standard>::Type)
+end(TContainer & me, Standard const &)
+{
+    return me.end();
+}
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Iterator<TContainer const, Standard>::Type)
+end(TContainer const & me, Standard const &)
+{
+    return me.end();
+}
+
+// ----------------------------------------------------------------------------
+// Function end (rooted)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Iterator<TContainer, Rooted>::Type)
+end(TContainer & me, Rooted const &)
+{
+    return _endDefault(me, Rooted());
+}
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Iterator<TContainer const, Rooted>::Type)
+end(TContainer const & me, Rooted const &)
+{
+    return _endDefault(me, Rooted());
+}
+
+// ----------------------------------------------------------------------------
+// Function _iterStl (like seqan's iter() but for stl-iterators)
+// ----------------------------------------------------------------------------
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TContainer,
+          typename TPos>
+inline typename TContainer::iterator
+_iterStl(TContainer & me,
+         TPos const pos)
+{
+    SEQAN_ASSERT_LEQ_MSG(pos,
+                         static_cast<TPos>(length(me)),
+                         "Trying to get an iterator behind a container through _iterStl().");
+    return std::next(me.begin(), pos);
+}
+
+template <typename TContainer,
+          typename TPos>
+inline typename TContainer::const_iterator
+_iterStl(TContainer const & me,
+         TPos const pos)
+{
+    SEQAN_ASSERT_LEQ_MSG(pos,
+                         static_cast<TPos>(length(me)),
+                         "Trying to get an iterator behind a container through _iterStl().");
+    return std::next(me.begin(), pos);
+}
+#else
+template <typename TContainer,
+          typename TPos>
+inline typename TContainer::iterator
+_iterStl(TContainer & me,
+         TPos const pos)
+{
+    SEQAN_ASSERT_LEQ_MSG(pos,
+                         static_cast<TPos>(length(me)),
+                         "Trying to get an iterator behind a container through _iterStl().");
+    typename TContainer::iterator it = me.begin();
+    std::advance(it, pos);
+    return it;
+}
+
+template <typename TContainer,
+          typename TPos>
+inline typename TContainer::const_iterator
+_iterStl(TContainer const & me,
+         TPos const pos)
+{
+    SEQAN_ASSERT_LEQ_MSG(pos,
+                         static_cast<TPos>(length(me)),
+                         "Trying to get an iterator behind a container through _iterStl().");
+    typename TContainer::const_iterator it = me.begin();
+    std::advance(it, pos);
+    return it;
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function iter (Standard) (only overloaded for non-contiguous)
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc, typename TPos>
+inline typename Iterator<std::list<TChar, TAlloc>, Standard>::Type
+iter(std::list<TChar, TAlloc> & me,
+     TPos const pos,
+     Standard const &)
+{
+    return _iterStl(me, pos);
+}
+
+template <typename TChar, typename TAlloc, typename TPos>
+inline typename Iterator<std::list<TChar, TAlloc> const, Standard>::Type
+iter(std::list<TChar, TAlloc> const & me,
+     TPos const pos,
+     Standard const &)
+{
+    return _iterStl(me, pos);
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc, typename TPos>
+inline typename Iterator<std::forward_list<TChar, TAlloc>, Standard const>::Type
+iter(std::forward_list<TChar, TAlloc> & me,
+     TPos const pos,
+     Standard const &)
+{
+    return _iterStl(me, pos);
+}
+
+template <typename TChar, typename TAlloc, typename TPos>
+inline typename Iterator<std::forward_list<TChar, TAlloc> const, Standard>::Type
+iter(std::forward_list<TChar, TAlloc> const & me,
+     TPos const pos,
+     Standard const &)
+{
+    return _iterStl(me, pos);
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function iter (Rooted) (only overloaded for non-contiguous)
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc, typename TPos>
+inline typename Iterator<std::list<TChar, TAlloc>, Rooted>::Type
+iter(std::list<TChar, TAlloc> & me,
+     TPos const pos,
+     Rooted const &)
+{
+    typedef typename Iterator<std::list<TChar, TAlloc>, Rooted>::Type TIterator;
+    return TIterator(me, iter(me, pos, Standard()));
+}
+
+template <typename TChar, typename TAlloc, typename TPos>
+inline typename Iterator<std::list<TChar, TAlloc> const, Rooted>::Type
+iter(std::list<TChar, TAlloc> const & me,
+     TPos const pos,
+     Rooted const &)
+{
+    typedef typename Iterator<std::list<TChar, TAlloc> const, Rooted>::Type TIterator;
+    return TIterator(me, iter(me, pos, Standard()));
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc, typename TPos>
+inline typename Iterator<std::forward_list<TChar, TAlloc>, Rooted>::Type
+iter(std::forward_list<TChar, TAlloc> & me,
+     TPos const pos,
+     Rooted const &)
+{
+    typedef typename Iterator<std::forward_list<TChar, TAlloc>, Rooted>::Type TIterator;
+    return TIterator(me, iter(me, pos, Standard()));
+}
+
+template <typename TChar, typename TAlloc, typename TPos>
+inline typename Iterator<std::forward_list<TChar, TAlloc> const, Rooted>::Type
+iter(std::forward_list<TChar, TAlloc> const & me,
+     TPos const pos,
+     Rooted const &)
+{
+    typedef typename Iterator<std::forward_list<TChar, TAlloc> const, Rooted>::Type TIterator;
+    return TIterator(me, iter(me, pos, Standard()));
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function length
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Size<TContainer>::Type)
+length(TContainer const & me)
+{
+    return me.size();
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc>
+inline typename Size<std::forward_list<TChar, TAlloc> >::Type
+length(std::forward_list<TChar, TAlloc> const & me)
+{
+    typename Size<std::forward_list<TChar, TAlloc> >::Type l = 0;
+
+    for (auto it = me.begin(), itEnd = me.end(); it != itEnd; ++it, ++l);
+
+    return l;
+}
+#endif
+
+#ifdef SEQAN_CXX11_COMPLETE
+template <typename TChar, std::size_t N>
+constexpr std::size_t
+length(std::array<TChar, N> const & me)
+{
+    return me.size();
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function capacity
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+inline typename Size<std::vector<TChar, TAlloc> >::Type
+capacity(std::vector<TChar, TAlloc> const & me)
+{
+    return me.capacity();
+}
+
+template <typename TChar, typename TTraits, typename TAlloc>
+inline typename Size<std::basic_string<TChar, TTraits, TAlloc> >::Type
+capacity(std::basic_string<TChar, TTraits, TAlloc> const & me)
+{
+    return me.capacity();
+}
+
+#ifdef SEQAN_CXX11_COMPLETE
+template <typename TChar, std::size_t N>
+constexpr std::size_t
+capacity(std::array<TChar, N> const & me)
+{
+    return me.size();
+}
+#endif
+
+// for other types the default overload to length holds
+
+// ----------------------------------------------------------------------------
+// Function empty
+// ----------------------------------------------------------------------------
+
+// VC2015 implements some C++17 functions which would collide for 
+// applications that do using namespace std
+// http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2014/n4280.pdf
+#if _MSC_VER < 1900
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, bool)
+empty(TContainer const & me)
+{
+    return me.empty();
+}
+
+#ifdef SEQAN_CXX11_COMPLETE
+template <typename TChar, std::size_t N>
+constexpr bool
+empty(std::array<TChar, N> const & me)
+{
+    return me.empty();
+}
+#endif
+#endif
+
+// ----------------------------------------------------------------------------
+// Function reserve
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc, typename TSize, typename TExpand>
+inline typename Size<std::vector<TChar, TAlloc> >::Type
+reserve(std::vector<TChar, TAlloc> & me,
+        TSize const s,
+        Tag<TExpand> const &)
+{
+    me.reserve(s);
+    return capacity(me);
+}
+
+template <typename TChar, typename TTraits, typename TAlloc, typename TSize, typename TExpand>
+inline typename Size<std::basic_string<TChar, TTraits, TAlloc> >::Type
+reserve(std::basic_string<TChar, TTraits, TAlloc> & me,
+        TSize const s,
+        Tag<TExpand> const &)
+{
+    me.reserve(s);
+    return capacity(me);
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc, typename TSize, typename TExpand>
+inline typename Size<std::vector<TChar, TAlloc> >::Type
+reserve(std::vector<TChar, TAlloc> && me,
+        TSize const s,
+        Tag<TExpand> const &)
+{
+    me.reserve(s);
+    return capacity(me);
+}
+
+template <typename TChar, typename TTraits, typename TAlloc, typename TSize, typename TExpand>
+inline typename Size<std::basic_string<TChar, TTraits, TAlloc> >::Type
+reserve(std::basic_string<TChar, TTraits, TAlloc> && me,
+        TSize const s,
+        Tag<TExpand> const &)
+{
+    me.reserve(s);
+    return capacity(me);
+}
+#endif
+
+// for other types the default overload holds
+
+// ----------------------------------------------------------------------------
+// Function resize
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TSize,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >,
+                            typename Size<typename RemoveReference<TContainer>::Type>::Type)
+resize(TContainer SEQAN_FORWARD_ARG me,
+       TSize const s,
+       Tag<TExpand> const &)
+{
+    me.resize(s);
+    return length(me);
+}
+
+template <typename TContainer,
+          typename TSize,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >,
+                            typename Size<typename RemoveReference<TContainer>::Type>::Type)
+resize(TContainer SEQAN_FORWARD_ARG me,
+       TSize const s,
+       typename Value<typename RemoveReference<TContainer>::Type>::Type const & val,
+       Tag<TExpand> const &)
+{
+    me.resize(s, val);
+    return length(me);
+}
+
+// ----------------------------------------------------------------------------
+// Function clear
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+clear(TContainer SEQAN_FORWARD_ARG me)
+{
+    me.clear();
+}
+
+// ----------------------------------------------------------------------------
+// Function value
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                HasSubscriptOperator<TContainer> >, typename Reference<TContainer>::Type)
+value(TContainer & me, TPos const pos)
+{
+    return me[pos];
+}
+
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                HasSubscriptOperator<TContainer> >, typename Reference<TContainer const>::Type)
+value(TContainer const & me, TPos const pos)
+{
+    return me[pos];
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                HasSubscriptOperator<TContainer> >, typename Value<TContainer>::Type)
+value(TContainer && me, TPos const pos)
+{
+    return me[pos];
+}
+#endif
+
+// linear complexity for list and fwd list
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                Not<HasSubscriptOperator<TContainer> > >, typename Reference<TContainer>::Type)
+value(TContainer & me, TPos const pos)
+{
+    return *(_iterStl(me, pos));
+}
+
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                Not<HasSubscriptOperator<TContainer> > >, typename Reference<TContainer const>::Type)
+value(TContainer const & me, TPos const pos)
+{
+    return *(_iterStl(me, pos));
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                Not<HasSubscriptOperator<TContainer> > >, typename Value<TContainer>::Type)
+value(TContainer && me, TPos const pos)
+{
+    return *(_iterStl(me, pos));
+}
+#endif
+
+// --------------------------------------------------------------------------
+// Function getValue
+// --------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                HasSubscriptOperator<TContainer> >, typename Reference<TContainer const>::Type)
+getValue(TContainer const & me, TPos const pos)
+{
+    return me[pos];
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                HasSubscriptOperator<TContainer> >, typename Value<TContainer>::Type)
+getValue(TContainer && me, TPos const pos)
+{
+    return me[pos];
+}
+#endif
+
+// linear complexity for list and fwd list
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                Not<HasSubscriptOperator<TContainer> > >, typename Reference<TContainer const>::Type)
+getValue(TContainer const & me, TPos const pos)
+{
+    return *(_iterStl(me, pos));
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TContainer,
+          typename TPos>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >,
+                                Not<HasSubscriptOperator<TContainer> > >, typename Value<TContainer>::Type)
+getValue(TContainer && me, TPos const pos)
+{
+    return *(_iterStl(me, pos));
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function front
+// ----------------------------------------------------------------------------
+
+// default implementation used
+
+// ----------------------------------------------------------------------------
+// Function back
+// ----------------------------------------------------------------------------
+
+// default implementation used
+
+#ifdef SEQAN_CXX11_STANDARD
+// forward_list doesnt have back, we achieve it in linear time
+template <typename TChar, typename TAlloc>
+inline TChar &
+back(std::forward_list<TChar, TAlloc> & me)
+{
+    return *(std::next(me.before_begin(), length(me)));
+}
+
+template <typename TChar, typename TAlloc>
+inline TChar const &
+back(std::forward_list<TChar, TAlloc> const & me)
+{
+    return *(std::next(me.before_begin(), length(me)));
+}
+
+template <typename TChar, typename TAlloc>
+inline TChar
+back(std::forward_list<TChar, TAlloc> && me)
+{
+    return *(std::next(me.before_begin(), length(me)));
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function assign
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >, void)
+assign(TContainer SEQAN_FORWARD_ARG me,
+       typename RemoveReference<TContainer>::Type source)
+{
+    std::swap(me, source);
+}
+
+template <typename TContainer,
+          typename TSource>
+inline SEQAN_FUNC_ENABLE_IF(And<Not<IsSameType<typename RemoveReference<TContainer>::Type, TSource> >,
+                                Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> > >, void)
+assign(TContainer SEQAN_FORWARD_ARG me,
+       TSource const & source)
+{
+    me.assign(begin(source, Standard()), end(source, Standard()));
+}
+
+template <typename TContainer,
+          typename TSource>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >, void)
+assign(TContainer SEQAN_FORWARD_ARG me,
+       TSource const & source,
+       typename Size<TSource>::Type limit)
+{
+    me.assign(begin(source, Standard()),
+              iter(source, std::min(length(source), limit), Standard()));
+}
+
+// ----------------------------------------------------------------------------
+// Function insert
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+insert(TContainer SEQAN_FORWARD_ARG me,
+       typename Size<typename RemoveReference<TContainer>::Type>::Type const pos,
+       TSource const & source,
+       Tag<TExpand> const &)
+{
+    me.insert(_iterStl(SEQAN_FORWARD(TContainer, me), pos),
+              begin(source, Standard()),
+              end(source, Standard()));
+}
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+insert(TContainer SEQAN_FORWARD_ARG me,
+       typename Size<typename RemoveReference<TContainer>::Type>::Type const pos,
+       TSource const & source,
+       typename Size<TSource>::Type const limit,
+       Tag<TExpand> const &)
+{
+    me.insert(_iterStl(SEQAN_FORWARD(TContainer, me), pos),
+              begin(source, Standard()),
+              iter(source, std::min(length(source), limit), Standard()));
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+// forward_list doesnt have insert, we achieve it slower
+template <typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+insert(std::forward_list<TChar, TAlloc> & me,
+       typename Size<std::forward_list<TChar, TAlloc> >::Type const pos,
+       TSource const & source,
+       Tag<TExpand> const &)
+{
+    me.insert_after(std::next(me.before_begin(), pos), begin(source, Standard()), end(source, Standard()));
+}
+
+template <typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+insert(std::forward_list<TChar, TAlloc> && me,
+       typename Size<std::forward_list<TChar, TAlloc> >::Type const pos,
+       TSource const & source,
+       Tag<TExpand> const &)
+{
+    insert(me, pos, source);
+}
+
+template <typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+insert(std::forward_list<TChar, TAlloc> & me,
+       typename Size<std::forward_list<TChar, TAlloc> >::Type const pos,
+       TSource const & source,
+       typename Size<std::forward_list<TChar, TAlloc> >::Type const limit,
+       Tag<TExpand> const &)
+{
+    me.insert_after(std::next(me.before_begin(), pos),
+                    begin(source, Standard()),
+                    iter(source, std::min(length(source), limit), Standard()));
+}
+
+template <typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+insert(std::forward_list<TChar, TAlloc> && me,
+       typename Size<std::forward_list<TChar, TAlloc> >::Type const pos,
+       TSource const & source,
+       typename Size<std::forward_list<TChar, TAlloc> >::Type const limit,
+       Tag<TExpand> const &)
+{
+    insert(me, pos, source, limit);
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function append
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+append(TContainer SEQAN_FORWARD_ARG me,
+       TSource const & source,
+       Tag<TExpand> const &)
+{
+    insert(SEQAN_FORWARD(TContainer, me), length(me), source);
+}
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+append(TContainer SEQAN_FORWARD_ARG me,
+       TSource const & source,
+       typename Size<typename RemoveReference<TContainer>::Type>::Type const limit,
+       Tag<TExpand> const &)
+{
+    insert(SEQAN_FORWARD(TContainer, me), length(me), source, limit);
+}
+
+// forward list is handled downstream in insert
+
+// ----------------------------------------------------------------------------
+// Function prepend
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TSource>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+prepend(TContainer SEQAN_FORWARD_ARG me,
+        TSource const & source)
+{
+    insert(SEQAN_FORWARD(TContainer, me), 0, source);
+}
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+prepend(TContainer SEQAN_FORWARD_ARG me,
+        TSource const & source,
+        Tag<TExpand> const &)
+{
+    insert(SEQAN_FORWARD(TContainer, me), 0, source);
+}
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+prepend(TContainer SEQAN_FORWARD_ARG me,
+        TSource const & source,
+        typename Size<typename RemoveReference<TContainer>::Type>::Type const limit)
+{
+    insert(SEQAN_FORWARD(TContainer, me), 0, source, limit);
+}
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+prepend(TContainer SEQAN_FORWARD_ARG me,
+        TSource const & source,
+        typename Size<typename RemoveReference<TContainer>::Type>::Type const limit,
+        Tag<TExpand> const &)
+{
+    insert(SEQAN_FORWARD(TContainer, me), 0, source, limit);
+}
+
+// forward list is handled downstream in insert
+
+// ----------------------------------------------------------------------------
+// Function insertValue
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+insertValue(TContainer SEQAN_FORWARD_ARG me,
+            typename Size<typename RemoveReference<TContainer>::Type>::Type const pos,
+            TSource SEQAN_FORWARD_CARG source,
+            Tag<TExpand> const &)
+{
+    me.insert(_iterStl(SEQAN_FORWARD(TContainer, me), pos), SEQAN_FORWARD(TSource, source));
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+insertValue(std::forward_list<TChar, TAlloc> & me,
+            typename Size<std::forward_list<TChar, TAlloc> >::Type const pos,
+            TSource && source,
+            Tag<TExpand> const &)
+{
+    me.insert_after(std::next(me.before_begin(), pos), std::forward<TSource>(source));
+}
+
+template <typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+insertValue(std::forward_list<TChar, TAlloc> && me,
+            typename Size<std::forward_list<TChar, TAlloc> >::Type const pos,
+            TSource && source,
+            Tag<TExpand> const &)
+{
+    insertValue(me, pos, source);
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function appendValue
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+appendValue(TContainer SEQAN_FORWARD_ARG me,
+            TSource SEQAN_FORWARD_CARG source,
+            Tag<TExpand> const &)
+{
+    me.push_back(SEQAN_FORWARD(TSource, source));
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+appendValue(std::forward_list<TChar, TAlloc> & me,
+            TSource && source,
+            Tag<TExpand> const &)
+{
+    insertValue(me, length(me), std::forward<TSource>(source));
+}
+
+template <typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+appendValue(std::forward_list<TChar, TAlloc> && me,
+            TSource && source,
+            Tag<TExpand> const &)
+{
+    appendValue(me, source);
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function prependValue
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TSource>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+prependValue(TContainer SEQAN_FORWARD_ARG me,
+             TSource SEQAN_FORWARD_CARG source)
+{
+    me.push_front(SEQAN_FORWARD(TSource, source));
+}
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+prependValue(TContainer SEQAN_FORWARD_ARG me,
+             TSource SEQAN_FORWARD_CARG source,
+             Tag<TExpand> const &)
+{
+    prependValue(SEQAN_FORWARD(TContainer, me), SEQAN_FORWARD(TSource, source));
+}
+
+// vector and string dont have push_front, we achieve it in linear time
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+prependValue(std::vector<TChar, TAlloc> & me,
+             TSource SEQAN_FORWARD_CARG source)
+{
+    insertValue(me, 0, SEQAN_FORWARD(TSource, source));
+}
+
+template <typename TChar, typename TTraits, typename TAlloc, typename TSource>
+inline void
+prependValue(std::basic_string<TChar, TTraits, TAlloc> & me,
+             TSource SEQAN_FORWARD_CARG source)
+{
+    insertValue(me, 0, SEQAN_FORWARD(TSource, source));
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+// && to &
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+prependValue(std::vector<TChar, TAlloc> && me,
+             TSource && source)
+{
+    prependValue(me, std::forward<TSource>(source));
+}
+
+template <typename TChar, typename TTraits, typename TAlloc, typename TSource>
+inline void
+prependValue(std::basic_string<TChar, TTraits, TAlloc> && me,
+             TSource && source)
+{
+    prependValue(me, std::forward<TSource>(source));
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function erase
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+erase(TContainer SEQAN_FORWARD_ARG me,
+      typename Size<typename RemoveReference<TContainer>::Type>::Type const pos,
+      typename Size<typename RemoveReference<TContainer>::Type>::Type const posEnd)
+{
+    me.erase(_iterStl(me, pos), _iterStl(me, posEnd));
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc>
+inline void
+erase(std::forward_list<TChar, TAlloc> & me,
+      typename Size<std::forward_list<TChar, TAlloc> >::Type const pos,
+      typename Size<std::forward_list<TChar, TAlloc> >::Type const posEnd)
+{
+    me.erase_after(std::next(me.before_begin(), pos), std::next(me.begin(), posEnd));
+}
+
+template <typename TChar, typename TAlloc>
+inline void
+erase(std::forward_list<TChar, TAlloc> && me,
+      typename Size<std::forward_list<TChar, TAlloc> >::Type const pos,
+      typename Size<std::forward_list<TChar, TAlloc> >::Type const posEnd)
+{
+    erase(me, pos, posEnd);
+}
+#endif
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+erase(TContainer SEQAN_FORWARD_ARG me,
+      typename Size<typename RemoveReference<TContainer>::Type>::Type const pos)
+{
+    erase(SEQAN_FORWARD(TContainer, me), pos, pos + 1);
+}
+
+// ----------------------------------------------------------------------------
+// Function eraseFront
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+eraseFront(TContainer SEQAN_FORWARD_ARG me)
+{
+    me.pop_front();
+}
+
+template <typename TChar, typename TAlloc>
+inline void
+eraseFront(std::vector<TChar, TAlloc> & me)
+{
+    me.erase(me.begin());
+}
+
+template <typename TChar, typename TTraits, typename TAlloc>
+inline void
+eraseFront(std::basic_string<TChar, TTraits, TAlloc> & me)
+{
+    me.erase(me.begin());
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc>
+inline void
+eraseFront(std::vector<TChar, TAlloc> && me)
+{
+    me.erase(me.begin());
+}
+
+template <typename TChar, typename TTraits, typename TAlloc>
+inline void
+eraseFront(std::basic_string<TChar, TTraits, TAlloc> && me)
+{
+    me.erase(me.begin());
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function eraseBack
+// ----------------------------------------------------------------------------
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+eraseBack(TContainer SEQAN_FORWARD_ARG me)
+{
+    me.pop_back();
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc>
+inline void
+eraseBack(std::forward_list<TChar, TAlloc> & me)
+{
+    if (!empty(me))
+    {
+        auto it = me.before_begin(), itN = std::next(me.begin()), itEnd = me.end();
+        while (itN != itEnd)
+        {
+            ++it;
+            ++itN;
+        }
+        me.erase_after(it);
+    }
+}
+
+template <typename TChar, typename TAlloc>
+inline void
+eraseBack(std::forward_list<TChar, TAlloc> && me)
+{
+    eraseBack(me);
+}
+#endif
+
+#ifndef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TTraits, typename TAlloc>
+inline void
+eraseBack(std::basic_string<TChar, TTraits, TAlloc> & me)
+{
+    if (length(me) > 0)
+        me.erase(me.end() - 1);
+}
+#endif
+
+// ----------------------------------------------------------------------------
+// Function replace
+// ----------------------------------------------------------------------------
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+replace(TContainer SEQAN_FORWARD_ARG me,
+        typename Size<typename RemoveReference<TContainer>::Type>::Type const pos,
+        typename Size<typename RemoveReference<TContainer>::Type>::Type const posEnd,
+        TSource const & source,
+        typename Size<TSource>::Type const limit,
+        Tag<TExpand> const &)
+{
+    erase(me, pos, posEnd);
+    insert(me, pos, source, limit);
+}
+
+template <typename TContainer,
+          typename TSource,
+          typename TExpand>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >,
+                                Not<FixedSize_<typename RemoveReference<TContainer>::Type> > >, void)
+replace(TContainer SEQAN_FORWARD_ARG me,
+        typename Size<typename RemoveReference<TContainer>::Type>::Type const pos,
+        typename Size<typename RemoveReference<TContainer>::Type>::Type const posEnd,
+        TSource const & source,
+        Tag<TExpand> const &)
+{
+    erase(me, pos, posEnd);
+    insert(me, pos, source, length(source));
+}
+
+// ----------------------------------------------------------------------------
+// Function reverse
+// ----------------------------------------------------------------------------
+
+// NOTE(h-2): seqan's reverse doesn't work for some stl containers
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >, HasSubscriptOperator<TContainer> >)
+reverse(TContainer SEQAN_FORWARD_ARG me)
+{
+    std::reverse(me.begin(), me.end());
+}
+
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >, Not<HasSubscriptOperator<TContainer> > >)
+reverse(TContainer SEQAN_FORWARD_ARG me)
+{
+    me.reverse();
+}
+
+// ----------------------------------------------------------------------------
+// Function toCString
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TTraits, typename TAlloc>
+inline const TChar*
+toCString(std::basic_string<TChar, TTraits, TAlloc> const & me)
+{
+    return me.c_str();
+}
+
+// ----------------------------------------------------------------------------
+// Function assign (from CString)
+// ----------------------------------------------------------------------------
+
+// NOTE(h-2): is this optimal if container is not Contiguous?
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, void)
+assign(TContainer & me,
+       char const * source)
+{
+    resize(me, length(source));
+    std::copy(source, source + std::strlen(source), me.begin());
+}
+
+template <typename TTraits, typename TAlloc>
+inline void
+assign(std::basic_string<char, TTraits, TAlloc> & me,
+       char const * source)
+{
+    me = source;
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TContainer>
+inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, void)
+assign(TContainer && me,
+       char const * source)
+{
+    assign(me, source);
+}
+
+template <typename TTraits, typename TAlloc>
+inline void
+assign(std::basic_string<char, TTraits, TAlloc> && me,
+       char const * source)
+{
+    me = source;
+}
+#endif
+
+}
+
+#undef SUPERMACRO__
+#undef COMMA
+
+#endif
diff --git a/seqan/sequence/adapt_thrust_vector.h b/seqan/sequence/adapt_thrust_vector.h
new file mode 100644
index 0000000..efc75ad
--- /dev/null
+++ b/seqan/sequence/adapt_thrust_vector.h
@@ -0,0 +1,800 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Adaptions for Thrust device_vectors to SeqAn strings.
+// ==========================================================================
+// NOTE(esiragusa): This adaption is not tested. Anything beside assign might
+// not work as expected.
+
+#ifndef SEQAN_SEQUENCE_ADAPT_THRUST_VECTOR_H_
+#define SEQAN_SEQUENCE_ADAPT_THRUST_VECTOR_H_
+
+namespace seqan {
+
+// ===========================================================================
+// Enums, Tags, Classes, Specializations
+// ===========================================================================
+
+// ===========================================================================
+// Metafunctions
+// ===========================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction IsSequence
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct IsSequence<thrust::device_vector<TChar, TAlloc> >
+{
+    typedef True Type;
+    enum { VALUE = true };
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsContiguous
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct IsContiguous<thrust::device_vector<TChar, TAlloc> >
+{
+    enum { VALUE = true };
+};
+
+template <typename  TChar, typename TAlloc>
+struct IsContiguous<thrust::device_vector<TChar, TAlloc> const>
+        : IsContiguous<thrust::device_vector<TChar, TAlloc> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct Value<thrust::device_vector<TChar, TAlloc> >
+{
+    typedef typename thrust::device_vector<TChar, TAlloc>::value_type Type;
+};
+
+template <typename TChar, typename TAlloc>
+struct Value<thrust::device_vector<TChar, TAlloc> const>
+        : Value<thrust::device_vector<TChar, TAlloc> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Reference
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct Reference<thrust::device_vector<TChar, TAlloc> >
+{
+    typedef typename thrust::device_vector<TChar, TAlloc>::reference Type;
+};
+
+template <typename TChar,  typename TAlloc>
+struct Reference<thrust::device_vector<TChar, TAlloc> const>
+{
+    typedef typename thrust::device_vector<TChar, TAlloc>::const_reference Type;
+};
+
+template <typename TValue>
+struct Reference<thrust::detail::normal_iterator<thrust::device_ptr<TValue> > >
+{
+    typedef thrust::device_reference<TValue> Type;
+};
+
+template <typename TValue>
+struct Reference<thrust::detail::normal_iterator<thrust::device_ptr<TValue> > const>
+{
+    typedef thrust::device_reference<TValue> const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction GetValue
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct GetValue<thrust::device_vector<TChar, TAlloc> > : Reference<thrust::device_vector<TChar, TAlloc> const> {};
+
+template <typename TChar, typename TAlloc>
+struct GetValue<thrust::device_vector<TChar, TAlloc> const> : Reference<thrust::device_vector<TChar, TAlloc> const> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct Iterator<thrust::device_vector<TChar, TAlloc>, Rooted>
+{
+    typedef thrust::device_vector<TChar, TAlloc> TVector_;
+    typedef Iter<TVector_, StdIteratorAdaptor> TIterator_;
+    typedef Iter<TVector_, AdaptorIterator<TIterator_> > Type;
+};
+
+template <typename TChar, typename TAlloc>
+struct Iterator<thrust::device_vector<TChar, TAlloc> const, Rooted>
+{
+    typedef thrust::device_vector<TChar, TAlloc> const TVector_;
+    typedef Iter<TVector_, StdIteratorAdaptor> TIterator_;
+    typedef Iter<TVector_, AdaptorIterator<TIterator_> > Type;
+};
+
+template <typename TChar,  typename TAlloc>
+struct Iterator<thrust::device_vector<TChar, TAlloc>, Standard>
+{
+    typedef typename thrust::device_vector<TChar, TAlloc>::iterator Type;
+};
+
+template <typename TChar,  typename TAlloc>
+struct Iterator<thrust::device_vector<TChar, TAlloc> const, Standard>
+{
+    typedef typename thrust::device_vector<TChar, TAlloc>::const_iterator Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc>
+struct Position<thrust::device_vector<TChar, TAlloc> >
+{
+    typedef typename thrust::device_vector<TChar, TAlloc>::size_type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc>
+struct Size<thrust::device_vector<TChar, TAlloc> >
+{
+    typedef typename thrust::device_vector<TChar, TAlloc>::size_type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Difference
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct Difference<thrust::device_vector<TChar, TAlloc> >
+{
+    typedef typename thrust::device_vector<TChar, TAlloc>::difference_type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultOverflowImplicit
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct DefaultOverflowImplicit<thrust::device_vector<TChar, TAlloc> >
+{
+    typedef Generous Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction StdContainerIterator
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+struct StdContainerIterator<thrust::device_vector<TChar, TAlloc> >
+{
+    typedef thrust::device_vector<TChar, TAlloc> TContainer_;
+    typedef typename TContainer_::iterator Type;
+};
+
+template <typename TChar, typename TAlloc>
+struct StdContainerIterator<thrust::device_vector<TChar, TAlloc> const>
+{
+    typedef thrust::device_vector<TChar, TAlloc> TContainer_;
+    typedef typename TContainer_::const_iterator Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction View
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc>
+struct View<thrust::device_vector<TValue, TAlloc> >
+{
+    typedef ContainerView<thrust::device_vector<TValue, TAlloc> >   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsDevice
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc>
+struct IsDevice<thrust::device_vector<TValue, TAlloc> > : public True {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Device
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc>
+struct Device<String<TValue, TAlloc> >
+{
+    typedef thrust::device_vector<TValue>   Type;
+};
+
+template <typename TValue>
+struct Device<std::vector<TValue> >
+{
+    typedef thrust::device_vector<TValue>   Type;
+};
+
+template <>
+struct Device<std::string>
+{
+    typedef thrust::device_vector<char>     Type;
+};
+
+// ===========================================================================
+// Functions
+// ===========================================================================
+
+// ----------------------------------------------------------------------------
+// Function getObjectId()
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc>
+inline void const *
+getObjectId(thrust::device_vector<TChar, TAlloc> const & me)
+{
+    if (me.empty())
+        return NULL;
+    else
+        return (& *(me.end() - 1)) + 1;
+}
+
+// ----------------------------------------------------------------------------
+// Function begin()
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc>
+inline typename Iterator<thrust::device_vector<TChar, TAlloc>, Standard>::Type
+begin(thrust::device_vector<TChar, TAlloc> & me, Standard)
+{
+    return typename Iterator<thrust::device_vector<TChar, TAlloc>, Standard>::Type(me.begin());
+}
+
+template <typename TChar,  typename TAlloc>
+inline typename Iterator<thrust::device_vector<TChar, TAlloc> const, Standard>::Type
+begin(thrust::device_vector<TChar, TAlloc> const & me, Standard)
+{
+    return typename Iterator<thrust::device_vector<TChar, TAlloc> const, Standard>::Type(me.begin());
+}
+
+// ----------------------------------------------------------------------------
+// Function end()
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+inline typename Iterator<thrust::device_vector<TChar, TAlloc>, Standard>::Type
+end(thrust::device_vector<TChar, TAlloc> & me, Standard)
+{
+    return typename Iterator<thrust::device_vector<TChar, TAlloc>, Standard>::Type(me.end());
+}
+
+template <typename TChar,  typename TAlloc>
+inline typename Iterator<thrust::device_vector<TChar, TAlloc> const, Standard>::Type
+end(thrust::device_vector<TChar, TAlloc> const & me, Standard)
+{
+    return typename Iterator<thrust::device_vector<TChar, TAlloc> const, Standard>::Type(me.end());
+}
+
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc, typename TPos>
+inline typename Reference<thrust::device_vector<TChar, TAlloc> >::Type
+value(thrust::device_vector<TChar, TAlloc> & me, TPos pos)
+{
+    return me[pos];
+}
+
+template <typename TChar,  typename TAlloc, typename TPos>
+inline typename Reference<thrust::device_vector<TChar, TAlloc> const>::Type
+value(thrust::device_vector<TChar, TAlloc> const & me, TPos pos)
+{
+    return me[pos];
+}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+inline typename Size<thrust::device_vector<TChar, TAlloc> >::Type
+length(thrust::device_vector<TChar, TAlloc> const & me)
+{
+    return me.size();
+}
+
+// ----------------------------------------------------------------------------
+// Function capacity()
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+inline typename Size<thrust::device_vector<TChar, TAlloc> >::Type
+capacity(thrust::device_vector<TChar, TAlloc> const & me)
+{
+    return me.capacity();
+}
+
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+inline bool
+empty(thrust::device_vector<TChar, TAlloc> const & me)
+{
+    return me.empty();
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc>
+inline void
+clear(thrust::device_vector<TChar, TAlloc> & me)
+{
+    me.clear();
+}
+
+// ----------------------------------------------------------------------------
+// Function front()
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+inline typename Reference<thrust::device_vector<TChar, TAlloc> >::Type
+front(thrust::device_vector<TChar, TAlloc> & list)
+{
+    return list.front();
+}
+
+template <typename TChar, typename TAlloc>
+inline typename Reference<thrust::device_vector<TChar, TAlloc> const>::Type
+front(thrust::device_vector<TChar, TAlloc> const & list)
+{
+    return list.front();
+}
+
+// ----------------------------------------------------------------------------
+// Function back()
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc>
+inline typename Reference<thrust::device_vector<TChar, TAlloc> >::Type
+back(thrust::device_vector<TChar, TAlloc> & list)
+{
+    return list.back();
+}
+
+template <typename TChar, typename TAlloc>
+inline typename Reference<thrust::device_vector<TChar, TAlloc> const>::Type
+back(thrust::device_vector<TChar, TAlloc> const & list)
+{
+    return list.back();
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target, TSource const & source)
+{
+    assign(target, source, Generous());
+}
+
+template <typename TChar,  typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target, TSource & source)
+{
+    assign(target, reinterpret_cast<TSource const &>(source), Generous());
+}
+
+template <typename TChar,  typename TAlloc, typename TSource, typename TSize>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target, TSource const & source, TSize limit)
+{
+    assign(target, source, limit, Generous());
+}
+
+template <typename TChar,  typename TAlloc, typename TSource, typename TSize>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target, TSource & source, TSize limit)
+{
+    assign(target, reinterpret_cast<TSource const &>(source), limit, Generous());
+}
+
+// ----------------------------------------------------------------------------
+// Function assign(); Generous
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target, TSource const & source, Generous)
+{
+    target.assign(begin(source, Standard()), end(source, Standard()));
+}
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target, TSource & source, Generous)
+{
+    assign(target, reinterpret_cast<TSource const &>(source), Generous());
+}
+
+template <typename TChar,  typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target,
+       TSource const & source,
+       typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+       Generous)
+{
+    typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
+    typename Size<TSource const>::Type source_length = length(source);
+    if (source_length > limit)
+    {
+        source_length = limit;
+    }
+    target.assign(source_begin, source_begin + source_length);
+}
+
+template <typename TChar,  typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target,
+       TSource & source,
+       typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+       Generous)
+{
+    assign(target, reinterpret_cast<TSource const &>(source), limit, Generous());
+}
+
+// ----------------------------------------------------------------------------
+// Function assign(); Limit
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target, TSource const & source, Limit)
+{
+    assign(target, source, target.capacity(), Generous());
+}
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target, TSource & source, Limit)
+{
+    assign(target, reinterpret_cast<TSource const &>(source), Generous());
+}
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target,
+       TSource const & source,
+       typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+       Limit)
+{
+    if (limit > target.capacity())
+    {
+        limit = target.capacity();
+    }
+
+    assign(target, source, limit, Generous());
+}
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+assign(thrust::device_vector<TChar, TAlloc> & target,
+       TSource & source,
+       typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+       Limit)
+{
+    assign(target, reinterpret_cast<TSource const &>(source), limit, Generous());
+}
+
+// ----------------------------------------------------------------------------
+// Function append(); Generous
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+append(thrust::device_vector<TChar, TAlloc> & target, TSource const & source, Generous)
+{
+    target.insert(target.end(), begin(source, Standard()), end(source, Standard()));
+}
+
+template <typename TChar,  typename TAlloc, typename TSource>
+inline void
+append(thrust::device_vector<TChar, TAlloc> & target,
+       TSource const & source,
+       typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+       Generous)
+{
+    typename Size<thrust::device_vector<TChar, TAlloc> >::Type target_length = target.length();
+    if (target_length > limit)
+    {
+        target.resize(limit);
+    }
+    else
+    {
+        limit -= target_length;
+        typename Iterator<TSource const, Standard>::Type source_begin = begin(source, Standard());
+        typename Size<TSource const>::Type source_length = length(source);
+        if (source_length > limit)
+        {
+            source_length = limit;
+        }
+
+        target.insert(target.end(), source_begin, source_begin + source_length);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function append(); Limit
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+append(thrust::device_vector<TChar, TAlloc> & target, TSource const & source, Limit)
+{
+    append(target, source, target.capacity(), Generous());
+}
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+append(thrust::device_vector<TChar, TAlloc> & target,
+       TSource const & source,
+       typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+       Limit)
+{
+    if (limit > target.capacity())
+    {
+        limit = target.capacity();
+    }
+
+    append(target, source, limit, Generous());
+}
+
+// ----------------------------------------------------------------------------
+// Function appendValue()
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc, typename TValue, typename TTag>
+inline void
+appendValue(thrust::device_vector<TChar, TAlloc> & me, TValue const & _value, TTag)
+{
+    me.push_back(_value);
+}
+
+template <typename TChar, typename TAlloc, typename TValue>
+inline void
+appendValue(thrust::device_vector<TChar, TAlloc> & me, TValue const & _value, Limit)
+{
+    if (capacity(me) > length(me)) me.push_back(_value);
+}
+
+// ----------------------------------------------------------------------------
+// Function replace()
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc, typename TSource>
+inline void
+replace(thrust::device_vector<TChar, TAlloc> & target,
+        typename Position<thrust::device_vector<TChar, TAlloc> >::Type pos_begin,
+        typename Position<thrust::device_vector<TChar, TAlloc> >::Type pos_end,
+        TSource const & source,
+        Generous)
+{
+    typename Size<thrust::device_vector<TChar, TAlloc> >::Type target_size = pos_end-pos_begin;
+    typename Size<thrust::device_vector<TChar, TAlloc> >::Type source_size =length(source);
+
+    if (target_size >= source_size)
+    {
+        copy(source.begin(),source.end(), target.begin()+pos_begin);
+        if (target_size > source_size)
+            target.erase(target.begin()+pos_begin+source_size,target.begin()+pos_end);
+    }
+    else
+    {
+        copy(source.begin(),source.begin()+target_size,target.begin()+pos_begin);
+        target.insert(target.begin()+pos_end,source.begin()+target_size,source.end());
+    }
+}
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+replace(thrust::device_vector<TChar, TAlloc> & target,
+        typename Position<thrust::device_vector<TChar, TAlloc> >::Type pos_begin,
+        typename Position<thrust::device_vector<TChar, TAlloc> >::Type pos_end,
+        TSource const & source,
+        typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+        Generous)
+{
+    if (pos_begin >= limit)
+    {
+        target.resize(limit);
+    }
+    else
+    {
+        typename Size<TSource const>::Type source_length = length(source);
+        typename Size<thrust::device_vector<TChar, TAlloc> >::Type pos_mid = pos_begin + source_length;
+        typename Size<thrust::device_vector<TChar, TAlloc> >::Type pos_limit(limit);
+        if (pos_mid > limit)
+        {
+            target.resize(limit);
+            replace(target,pos_begin,pos_limit,source);
+            target.resize(limit);
+        }
+        else
+        {
+            replace(target,pos_begin,pos_end,source);
+            if (target.size() > limit)
+            {
+                target.resize(limit);
+            }
+        }
+    }
+
+}
+
+template <typename TChar,  typename TAlloc, typename TSource>
+inline void
+replace(thrust::device_vector<TChar, TAlloc> & target,
+        typename Position<thrust::device_vector<TChar, TAlloc> >::Type pos_begin,
+        typename Position<thrust::device_vector<TChar, TAlloc> >::Type pos_end,
+        TSource const & source,
+        Limit)
+{
+    replace(target, pos_begin, pos_end, source, target.capacity(), Generous());
+}
+
+template <typename TChar, typename TAlloc, typename TSource>
+inline void
+replace(thrust::device_vector<TChar, TAlloc> & target,
+        typename Position<thrust::device_vector<TChar, TAlloc> >::Type pos_begin,
+        typename Position<thrust::device_vector<TChar, TAlloc> >::Type pos_end,
+        TSource const & source,
+        typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+        Limit)
+{
+    if (limit > target.capacity())
+    {
+        limit = target.capacity();
+    }
+    replace(target, pos_begin, pos_end, source, limit, Generous());
+}
+
+
+// Handling of iterators as begin and end.
+
+template<typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TExpand>
+inline void
+replace(thrust::device_vector<TChar, TAlloc> & target,
+        typename Iterator<thrust::device_vector<TChar, TAlloc>, Rooted>::Type pos_begin,
+        typename Iterator<thrust::device_vector<TChar, TAlloc>, Rooted>::Type pos_end,
+        TSource & source,
+        Tag<TExpand> const tag)
+{
+    replace(target, position(pos_begin), position(pos_end), source, tag);
+}
+
+/*
+template<typename TChar, typename TAlloc, typename TSource, typename TExpand>
+inline void
+replace(thrust::device_vector<TChar, TAlloc> & target,
+        typename Iterator<thrust::device_vector<TChar, TAlloc>, Rooted>::Type pos_begin,
+        typename Iterator<thrust::device_vector<TChar, TAlloc>, Rooted>::Type pos_end,
+        TSource & source,
+        typename Size<thrust::device_vector<TChar, TAlloc> >::Type limit,
+        Tag<TExpand> const tag)
+{
+    replace(target,  position(pos_begin),  position(pos_end), source, tag);
+}
+*/
+
+// ----------------------------------------------------------------------------
+// Function reserve()
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc, typename TSize, typename TExpand>
+inline typename Size<thrust::device_vector<TChar, TAlloc> >::Type
+reserve(thrust::device_vector<TChar, TAlloc> & seq, TSize new_capacity, Tag<TExpand> const & tag)
+{
+    seq.reserve(new_capacity);
+    return _capacityReturned(seq, new_capacity, tag);
+}
+
+template <typename TChar, typename TAlloc, typename TSize>
+inline typename Size<thrust::device_vector<TChar, TAlloc> >::Type
+reserve(thrust::device_vector<TChar, TAlloc> & seq, TSize new_capacity, Insist const &)
+{
+    // do nothing
+    return _capacityReturned(seq, new_capacity, Insist());
+}
+
+template <typename TChar,  typename TAlloc, typename TSize>
+inline typename Size<thrust::device_vector<TChar, TAlloc> >::Type
+reserve(thrust::device_vector<TChar, TAlloc> & seq, TSize new_capacity, Limit const &)
+{
+    // do nothing
+    return _capacityReturned(seq, new_capacity, Limit());
+}
+
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+
+template <typename TChar,  typename TAlloc, typename TSize, typename TExpand>
+inline typename Size<thrust::device_vector<TChar, TAlloc> >::Type
+resize(thrust::device_vector<TChar, TAlloc> & me, TSize new_length, Tag<TExpand> const &)
+{
+    me.resize(new_length);
+    return me.size();
+}
+
+// ----------------------------------------------------------------------------
+// Function fill()
+// ----------------------------------------------------------------------------
+
+template <typename TChar, typename TAlloc, typename TSize, typename TExpand>
+inline typename Size<thrust::device_vector<TChar, TAlloc> >::Type
+fill(thrust::device_vector<TChar, TAlloc> & me, TSize new_length, TChar const & val, Tag<TExpand> const &)
+{
+    me.resize(new_length, val);
+    return me.length();
+}
+
+// ----------------------------------------------------------------------------
+// Function view()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TAlloc>
+inline typename View<thrust::device_vector<TContainer, TAlloc> >::Type
+view(thrust::device_vector<TContainer, TAlloc> & container)
+{
+    typedef typename View<thrust::device_vector<TContainer, TAlloc> >::Type TView;
+
+    if (empty(container)) return TView();
+
+    return TView(thrust::raw_pointer_cast(&container.front()),
+                 thrust::raw_pointer_cast(&container.front()) + container.size());
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_SEQUENCE_ADAPT_THRUST_VECTOR_H_
diff --git a/seqan/sequence/container_view.h b/seqan/sequence/container_view.h
new file mode 100644
index 0000000..bf68add
--- /dev/null
+++ b/seqan/sequence/container_view.h
@@ -0,0 +1,692 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_SEQUENCE_CONTAINER_VIEW_H
+#define SEQAN_SEQUENCE_CONTAINER_VIEW_H
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag Resizable
+// ----------------------------------------------------------------------------
+
+template <typename TSpec = void>
+struct Resizable;
+
+// ----------------------------------------------------------------------------
+// Class ContainerView
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec = void>
+class ContainerView
+{
+public:
+    typedef typename Iterator<ContainerView, Standard>::Type        TIterator;
+
+    TIterator _begin;
+    TIterator _end;
+
+    // ------------------------------------------------------------------------
+    // ContainerView Constructors
+    // ------------------------------------------------------------------------
+
+    SEQAN_HOST_DEVICE inline
+    ContainerView() :
+        _begin(),
+        _end()
+    {}
+
+    template <typename TOtherContainer>
+    SEQAN_HOST_DEVICE inline
+    ContainerView(TOtherContainer & cont):
+        _begin(begin(cont, Standard())),
+        _end(end(cont, Standard()))
+    {}
+
+    template <typename TOtherContainer>
+    SEQAN_HOST_DEVICE inline
+    ContainerView(TOtherContainer const & cont):
+        _begin(begin(cont, Standard())),
+        _end(end(cont, Standard()))
+    {}
+
+    SEQAN_HOST_DEVICE inline
+    ContainerView(TIterator const & begin, TIterator const & end):
+        _begin(begin),
+        _end(end)
+    {}
+
+    // ------------------------------------------------------------------------
+    // Operator =
+    // ------------------------------------------------------------------------
+
+    template <typename TOtherContainer>
+    SEQAN_HOST_DEVICE inline
+    ContainerView &
+    operator= (TOtherContainer & other)
+    {
+        assign(*this, other);
+        return *this;
+    }
+
+    // ------------------------------------------------------------------------
+    // Operator []
+    // ------------------------------------------------------------------------
+
+    template <typename TPos>
+    SEQAN_HOST_DEVICE inline
+    typename Reference<ContainerView>::Type
+    operator[] (TPos pos)
+    {
+        return value(*this, pos);
+    }
+
+    template <typename TPos>
+    SEQAN_HOST_DEVICE inline
+    typename GetValue<ContainerView>::Type
+    operator[] (TPos pos) const
+    {
+        return getValue(*this, pos);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class Resizable ContainerView
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+class ContainerView<TContainer, Resizable<TSpec> > :
+    public ContainerView<TContainer, TSpec>
+{
+public:
+    typedef ContainerView<TContainer, TSpec>    TBase;
+    typedef typename TBase::TIterator           TIterator;
+    typedef typename Size<TContainer>::Type     TSize;
+
+    TSize _capacity;
+
+    // ------------------------------------------------------------------------
+    // ContainerView Constructors
+    // ------------------------------------------------------------------------
+
+    SEQAN_HOST_DEVICE inline
+    ContainerView() :
+        TBase(),
+        _capacity(0)
+    {}
+
+    template <typename TOtherContainer>
+    SEQAN_HOST_DEVICE inline
+    ContainerView(TOtherContainer & cont) :
+        TBase(cont),
+        _capacity(capacity(cont))
+    {}
+
+    template <typename TOtherContainer>
+    SEQAN_HOST_DEVICE inline
+    ContainerView(TOtherContainer const & cont) :
+        TBase(cont),
+        _capacity(capacity(cont))
+    {}
+
+    SEQAN_HOST_DEVICE inline
+    ContainerView(TIterator const & begin, TIterator const & end) :
+        TBase(begin, end),
+        _capacity(end - begin)
+    {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Concept ContainerConcept
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+SEQAN_CONCEPT_IMPL((ContainerView<TContainer, TSpec>), (ContainerConcept));
+
+template <typename TContainer, typename TSpec>
+SEQAN_CONCEPT_IMPL((ContainerView<TContainer, TSpec> const), (ContainerConcept));
+
+// ----------------------------------------------------------------------------
+// Metafunction View
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc>
+struct View<String<TValue, TAlloc> >
+{
+    typedef ContainerView<String<TValue, TAlloc> >  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RemoveView
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct RemoveView<ContainerView<TContainer, TSpec> >
+{
+    typedef TContainer  Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct IsView<ContainerView<TContainer, TSpec> > : True {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct Value<ContainerView<TContainer, TSpec> >
+{
+    typedef typename Value<TContainer>::Type Type;
+};
+
+template <typename TContainer, typename TSpec>
+struct Value<ContainerView<TContainer, TSpec> const> :
+    public Value<ContainerView<TContainer const, TSpec> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction GetValue
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct GetValue<ContainerView<TContainer, TSpec> >
+{
+    typedef ContainerView<TContainer, TSpec>                        TContainerView_;
+    typedef typename Iterator<TContainerView_, Standard>::Type      TIterator_;
+    typedef typename GetValue<TIterator_>::Type                     Type;
+};
+
+template <typename TContainer, typename TSpec>
+struct GetValue<ContainerView<TContainer, TSpec> const>
+{
+    typedef ContainerView<TContainer, TSpec> const                  TContainerView_;
+    typedef typename Iterator<TContainerView_, Standard>::Type      TIterator_;
+    typedef typename GetValue<TIterator_>::Type                     Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct Iterator<ContainerView<TContainer, TSpec>, Standard>:
+    public Iterator<TContainer, Standard> {};
+
+template <typename TContainer, typename TSpec>
+struct Iterator<ContainerView<TContainer, TSpec> const, Standard>:
+    public Iterator<TContainer const, Standard> {};
+
+#ifdef PLATFORM_CUDA
+template <typename TContainer, typename TAlloc, typename TSpec>
+struct Iterator<ContainerView<thrust::device_vector<TContainer, TAlloc>, TSpec>, Standard>
+{
+    typedef typename thrust::device_vector<TContainer, TAlloc>::pointer         TIterator_;
+    typedef typename thrust::detail::pointer_traits<TIterator_>::raw_pointer    Type;
+};
+
+template <typename TContainer, typename TAlloc, typename TSpec>
+struct Iterator<ContainerView<thrust::device_vector<TContainer, TAlloc>, TSpec> const, Standard>
+{
+    typedef typename thrust::device_vector<TContainer const, TAlloc>::pointer   TIterator_;
+    typedef typename thrust::detail::pointer_traits<TIterator_>::raw_pointer    Type;
+};
+#endif
+
+// ----------------------------------------------------------------------------
+// Metafunction Difference
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct Difference<ContainerView<TContainer, TSpec> >
+{
+    typedef typename Difference<TContainer>::Type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct Size<ContainerView<TContainer, TSpec> >
+{
+    typedef typename Size<TContainer>::Type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct Position<ContainerView<TContainer, TSpec> >
+{
+    typedef typename Position<TContainer>::Type Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsSequence
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct IsSequence<ContainerView<TContainer, TSpec> >:
+    public IsSequence<TContainer> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Prefix
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct Prefix<ContainerView<TContainer, TSpec> >
+{
+    typedef ContainerView<TContainer, TSpec>    Type;
+};
+
+template <typename TContainer, typename TSpec>
+struct Prefix<ContainerView<TContainer, TSpec> const> :
+    Prefix<ContainerView<TContainer, TSpec> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Suffix
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct Suffix<ContainerView<TContainer, TSpec> >
+{
+    typedef ContainerView<TContainer, TSpec>    Type;
+};
+
+template <typename TContainer, typename TSpec>
+struct Suffix<ContainerView<TContainer, TSpec> const> :
+    Suffix<ContainerView<TContainer, TSpec> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Infix
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+struct Infix<ContainerView<TContainer, TSpec> >
+{
+    typedef ContainerView<TContainer, TSpec>    Type;
+};
+
+template <typename TContainer, typename TSpec>
+struct Infix<ContainerView<TContainer, TSpec> const> :
+    Infix<ContainerView<TContainer, TSpec> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction View
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+struct View<Segment<THost, TSpec> >
+{
+    typedef typename View<THost>::Type  Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function begin()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename Iterator<ContainerView<TContainer, TSpec>, Standard>::Type
+begin(ContainerView<TContainer, TSpec> & view, Standard)
+{
+    return view._begin;
+}
+
+template <typename TContainer, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename Iterator<ContainerView<TContainer, TSpec> const, Standard>::Type
+begin(ContainerView<TContainer, TSpec> const & view, Standard)
+{
+    return view._begin;
+}
+
+// ----------------------------------------------------------------------------
+// Function end()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename Iterator<ContainerView<TContainer, TSpec>, Standard>::Type
+end(ContainerView<TContainer, TSpec> & view, Standard)
+{
+    return view._end;
+}
+
+template <typename TContainer, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename Iterator<ContainerView<TContainer, TSpec> const, Standard>::Type
+end(ContainerView<TContainer, TSpec> const & view, Standard)
+{
+    return view._end;
+}
+
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline
+typename Reference<ContainerView<TContainer, TSpec> >::Type
+value(ContainerView<TContainer, TSpec> & view, TPos pos)
+{
+    SEQAN_ASSERT_LT_MSG(pos, static_cast<TPos>(length(view)), "Trying to acces an element behind the last one!");
+    return *(view._begin + pos);
+}
+
+template <typename TContainer, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline
+typename Reference<ContainerView<TContainer, TSpec> const>::Type
+value(ContainerView<TContainer, TSpec> const & view, TPos pos)
+{
+    SEQAN_ASSERT_LT_MSG(pos, static_cast<TPos>(length(view)), "Trying to acces an element behind the last one!");
+    return *(view._begin + pos);
+}
+
+// ----------------------------------------------------------------------------
+// Function getValue()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline
+typename GetValue<ContainerView<TContainer, TSpec> >::Type
+getValue(ContainerView<TContainer, TSpec> & view, TPos pos)
+{
+    SEQAN_ASSERT_LT_MSG(pos, static_cast<TPos>(length(view)), "Trying to acces an element behind the last one!");
+    return getValue(view._begin + pos);
+}
+
+template <typename TContainer, typename TSpec, typename TPos>
+SEQAN_HOST_DEVICE inline
+typename GetValue<ContainerView<TContainer, TSpec> const>::Type
+getValue(ContainerView<TContainer, TSpec> const & view, TPos pos)
+{
+    SEQAN_ASSERT_LT_MSG(pos, static_cast<TPos>(length(view)), "Trying to acces an element behind the last one!");
+    return getValue(view._begin + pos);
+}
+
+// ----------------------------------------------------------------------------
+// Function length()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+SEQAN_HOST_DEVICE inline
+typename Size<ContainerView<TContainer, TSpec> >::Type
+length(ContainerView<TContainer, TSpec> const & view)
+{
+    return view._end - view._begin;
+}
+
+// ----------------------------------------------------------------------------
+// Function resize()
+// ----------------------------------------------------------------------------
+
+// this function doesn't do anything as we are not allowed to change the host (only its elements)
+// it is, however, implemented for algorithms that get a sequence to work on
+// and need to make sure that it has a certain length
+
+template <typename TContainer, typename TSpec, typename TSize, typename TValue, typename TExpand>
+SEQAN_HOST_DEVICE inline typename Size< ContainerView<TContainer, TSpec> >::Type
+resize(ContainerView<TContainer, TSpec> & me, TSize new_length, TValue /* val */, Tag<TExpand>)
+{
+    ignoreUnusedVariableWarning(new_length);
+
+    SEQAN_ASSERT_EQ(new_length, (TSize)length(me));
+    return length(me);
+}
+
+template <typename TContainer, typename TSpec, typename TSize, typename TExpand>
+SEQAN_HOST_DEVICE inline typename Size< ContainerView<TContainer, TSpec> >::Type
+resize(ContainerView<TContainer, TSpec> & me, TSize new_length, Tag<TExpand> tag)
+{
+    return resize(me, new_length, Nothing(), tag);
+}
+
+// ----------------------------------------------------------------------------
+// Function resize(); Resizable ContainerView
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TSize, typename TValue, typename TExpand>
+SEQAN_HOST_DEVICE inline typename Size< ContainerView<TContainer, Resizable<TSpec> > >::Type
+resize(ContainerView<TContainer, Resizable<TSpec> > & me, TSize new_length, TValue /* val */, Tag<TExpand>)
+{
+    SEQAN_ASSERT_LEQ(new_length, (TSize)capacity(me));
+
+    me._end = me._begin + new_length;
+
+    return length(me);
+}
+
+template <typename TContainer, typename TSpec, typename TSize, typename TExpand>
+SEQAN_HOST_DEVICE inline typename Size< ContainerView<TContainer, Resizable<TSpec> > >::Type
+resize(ContainerView<TContainer, Resizable<TSpec> > & me, TSize new_length, Tag<TExpand> tag)
+{
+    return resize(me, new_length, Nothing(), tag);
+}
+
+// NOTE(esiragusa): It is not necessary to overload it, but otherwise I had to qualify the generic one :(
+template <typename TContainer, typename TSpec, typename TSize>
+SEQAN_HOST_DEVICE inline typename Size< ContainerView<TContainer, Resizable<TSpec> > >::Type
+resize(ContainerView<TContainer, Resizable<TSpec> > & me, TSize new_length)
+{
+    typedef ContainerView<TContainer, Resizable<TSpec> >    TView;
+
+    return resize(me, new_length, Nothing(), typename DefaultOverflowImplicit<TView>::Type());
+}
+
+// ----------------------------------------------------------------------------
+// Function prefix()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TPosEnd>
+SEQAN_HOST_DEVICE inline typename Prefix<ContainerView<TContainer, TSpec> const>::Type
+prefix(ContainerView<TContainer, TSpec> const & view, TPosEnd pos_end)
+{
+    return typename Prefix<ContainerView<TContainer, TSpec> const>::Type(view._begin, view._begin + pos_end);
+}
+
+template <typename TContainer, typename TSpec, typename TPosEnd>
+SEQAN_HOST_DEVICE inline typename Prefix<ContainerView<TContainer, TSpec> >::Type
+prefix(ContainerView<TContainer, TSpec> & view, TPosEnd pos_end)
+{
+    return prefix(reinterpret_cast<ContainerView<TContainer, TSpec> const &>(view), pos_end);
+}
+
+// ----------------------------------------------------------------------------
+// Function suffix()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TPosBegin>
+SEQAN_HOST_DEVICE inline typename Suffix<ContainerView<TContainer, TSpec> const>::Type
+suffix(ContainerView<TContainer, TSpec> const & view, TPosBegin pos_begin)
+{
+    return typename Suffix<ContainerView<TContainer, TSpec> const>::Type(view._begin + pos_begin, view._end);
+}
+
+template <typename TContainer, typename TSpec, typename TPosBegin>
+SEQAN_HOST_DEVICE inline typename Suffix<ContainerView<TContainer, TSpec> >::Type
+suffix(ContainerView<TContainer, TSpec> & view, TPosBegin pos_begin)
+{
+    return suffix(reinterpret_cast<ContainerView<TContainer, TSpec> const &>(view), pos_begin);
+}
+
+// ----------------------------------------------------------------------------
+// Function infix()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TPosBegin, typename TPosEnd>
+SEQAN_HOST_DEVICE inline typename Infix<ContainerView<TContainer, TSpec> const>::Type
+infix(ContainerView<TContainer, TSpec> const & view, TPosBegin pos_begin, TPosEnd pos_end)
+{
+    return typename Infix<ContainerView<TContainer, TSpec> >::Type(view._begin + pos_begin, view._begin + pos_end);
+}
+
+template <typename TContainer, typename TSpec, typename TPosBegin, typename TPosEnd>
+SEQAN_HOST_DEVICE inline typename Infix<ContainerView<TContainer, TSpec> >::Type
+infix(ContainerView<TContainer, TSpec> & view, TPosBegin pos_begin, TPosEnd pos_end)
+{
+    return infix(reinterpret_cast<ContainerView<TContainer, TSpec> const &>(view), pos_begin, pos_end);
+}
+
+// TODO(esiragusa): infix of view pointer?
+//template <typename T, typename TPosBegin, typename TPosEnd>
+//inline typename Infix<T *>::Type
+//infix(T * t, TPosBegin pos_begin, TPosEnd pos_end)
+//{
+//    return typename Infix<T *>::Type (t, pos_begin, pos_end);
+//}
+
+// ----------------------------------------------------------------------------
+// Function assign()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TOtherContainer>
+inline void assign(ContainerView<TContainer, TSpec> & view, TOtherContainer const & cont)
+{
+    view._begin = begin(cont, Standard());
+    view._end = end(cont, Standard());
+}
+
+template <typename TContainer, typename TSpec, typename TOtherContainer>
+inline void assign(ContainerView<TContainer, Resizable<TSpec> > & view, TOtherContainer const & cont)
+{
+    view._begin = begin(cont, Standard());
+    view._end = end(cont, Standard());
+    view._capacity = capacity(cont, Standard());
+}
+
+// ----------------------------------------------------------------------------
+// Function capacity()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Size<ContainerView<TContainer, Resizable<TSpec> > >::Type
+capacity(ContainerView<TContainer, Resizable<TSpec> > const & view)
+{
+    return view._capacity;
+}
+
+// ----------------------------------------------------------------------------
+// Function appendValue()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec, typename TValue, typename TExpand>
+SEQAN_HOST_DEVICE inline void
+appendValue(ContainerView<TContainer, Resizable<TSpec> > & view, TValue const & _value, Tag<TExpand> tag)
+{
+    resize(view, length(view) + 1, tag);
+    value(view, length(view) - 1) = _value;
+}
+
+// NOTE(esiragusa): It is not necessary to overload it, but otherwise I had to qualify the generic one :(
+template <typename TContainer, typename TSpec, typename TValue>
+SEQAN_HOST_DEVICE inline void
+appendValue(ContainerView<TContainer, Resizable<TSpec> > & view, TValue const & _value)
+{
+    typedef ContainerView<TContainer, Resizable<TSpec> >    TView;
+
+    appendValue(view, _value, typename DefaultOverflowImplicit<TView>::Type());
+}
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TSpec>
+SEQAN_HOST_DEVICE inline void
+clear(ContainerView<TContainer, Resizable<TSpec> > & view)
+{
+    resize(view, 0, Exact());
+}
+
+// ----------------------------------------------------------------------------
+// Operator<<
+// ----------------------------------------------------------------------------
+
+template <typename TStream, typename TContainer, typename TSpec>
+inline TStream &
+operator<<(TStream & target, ContainerView<TContainer, TSpec> const & source)
+{
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
+    return target;
+}
+
+// ----------------------------------------------------------------------------
+// Pipe interface
+// ----------------------------------------------------------------------------
+
+//template < typename TContainer,
+//           typename TSpec,
+//           typename TInput,
+//           typename TPipeSpec >
+//inline void assign(ContainerView<TContainer, TSpec> &dest, Pipe<TInput, TPipeSpec> &src)
+//{
+//    typedef typename Iterator<ContainerView<TContainer, TSpec>, Standard>::Type TDestIter;
+//    resize(dest, length(src));
+//    beginRead(src);
+//    for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src)
+//        *_cur = *src;
+//    endRead(src);
+//}
+//
+//template < typename TContainer,
+//           typename TSpec,
+//           typename TInput,
+//           typename TPipeSpec >
+//inline void operator << (ContainerView<TContainer, TSpec> &dest, Pipe<TInput, TPipeSpec> &src)
+//{
+//    assign(dest, src);
+//}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_SEQUENCE_CONTAINER_VIEW_H
diff --git a/seqan/sequence/iter_concat_virtual.h b/seqan/sequence/iter_concat_virtual.h
index 4ea7a91..4d54adc 100644
--- a/seqan/sequence/iter_concat_virtual.h
+++ b/seqan/sequence/iter_concat_virtual.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -83,26 +83,6 @@ struct ConcatVirtual;
  * If <tt>objNo</tt> and <tt>offset</tt> are not given then the iterator will point to the first element with offset 0.
  */
 
-/**
-.Spec.ConcatVirtual Iterator
-..cat:Sequences
-..general:Class.Iter
-..summary:Iterator that sequentially iterates through the elements of a @Class.StringSet@ as if they were directly concatenated, cmp. @Spec.ConcatDirect@.
-..signature:Iter<TStringSet, ConcatVirtual<TSpec> >
-..param.TStringSet:Type of the @Class.StringSet@.
-..param.TSpec:The delimiter to use.
-..include:seqan/sequence.h
-
-.Memfunc.ConcatVirtual Iterator#Iter:
-..class:Spec.ConcatVirtual Iterator
-..summary:Constructor
-..signature:Iter(host)
-..signature:Iter(host, objNo, offset)
-..param.host:Container to iterate.
-..param.objNo:Sequence number to set the iterator to.
-..param.offset:Offset in the object (specified by objNo) to point to.
-..remarks:If $objNo$ and $offset$ are not given, the iterator will point to the first element with offset 0.
- */
 template <typename TStringSet, typename TSpec >
 class Iter<TStringSet, ConcatVirtual<TSpec> >
 {
@@ -118,7 +98,7 @@ class Iter<TStringSet, ConcatVirtual<TSpec> >
     // ----------------------------------------------------------------------
     // STL compatible public iterator interface
     typedef Iter                                iterator;
-    typedef ::std::bidirectional_iterator_tag   iterator_category;
+    typedef std::bidirectional_iterator_tag   iterator_category;
     typedef TValue                              value_type;
     typedef TValue &                            reference;
     typedef TValue const &                      const_reference;
@@ -180,9 +160,9 @@ class Iter<TStringSet, ConcatVirtual<TSpec> >
     {
         if (objNo >= length(*host))
         {
-            SEQAN_ASSERT_EQ(_begin, obj_iterator());
-            SEQAN_ASSERT_EQ(_cur, obj_iterator());
-            SEQAN_ASSERT_EQ(_end, obj_iterator());
+            SEQAN_ASSERT(_begin == obj_iterator());
+            SEQAN_ASSERT(_cur == obj_iterator());
+            SEQAN_ASSERT(_end == obj_iterator());
             return;
         }
 
@@ -557,19 +537,6 @@ atEnd(Iter<TSSet, ConcatVirtual<TSpec> > const & me)
 
 // TODO(holtgrew): Specifying a catch-all implementation appears a bit too generous, what about concept checking?
 
-/**
-.Function.atEndOfSequence
-..class:Spec.ConcatVirtual Iterator
-..summary:Returns true if the iterator is at the end of a sequence.
-..cat:Sequences
-..signature:atEndOfSequence(iter)
-..param.iter:Iterator to test.
-...type:Spec.ConcatVirtual Iterator
-...type:Class.Iter
-..returns:$true$ if the iterator is at the end of a sequence.
-...type:nolink:$bool$
-..include:seqan/sequence.h
- */
 template <typename TIterator>
 inline bool
 atEndOfSequence(TIterator const & me)
diff --git a/seqan/sequence/segment_base.h b/seqan/sequence/segment_base.h
index 7397fc4..3cf74ac 100644
--- a/seqan/sequence/segment_base.h
+++ b/seqan/sequence/segment_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -44,8 +44,9 @@ namespace SEQAN_NAMESPACE_MAIN
 
 /*!
  * @concept SegmentableConcept
+ * @extends ContainerConcept
  * @headerfile <seqan/sequence.h>
- * @brief A concept for sequences that can be used as the host of a @link Segment segment @endlink.
+ * @brief A concept for containers that can be used as the host of a @link Segment segment @endlink.
  *
  * @signature concept Segmentable;
  * @brief Returns prefix type in a infix fashion.
@@ -69,8 +70,8 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * @signature TPrefix prefix(s, endPos);
  *
- * @param s      Segmentable sequence to return the prefix for (type <tt>TSeq</tt>).
- * @param endPos End position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
+ * @param[in] s      Segmentable sequence to return the prefix for (type <tt>TSeq</tt>).
+ * @param[in] endPos End position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
  *
  * @return TPrefix The prefix of length <tt>endPos</tt>.  Type as returned by @link SegmentableConcept#Prefix @endlink
  *                 for TSeq.
@@ -94,9 +95,9 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * @signature TInfix infixWithLength(s, beginPos, len);
  *
- * @param s        Segmentable sequence to return the infix for (type <tt>TSeq</tt>).
- * @param beginPos Begin position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
- * @param len      Length of the prefix, must be convertible to <tt>Size&lt;TSeq&gt;::Type</tt>.
+ * @param[in] s        Segmentable sequence to return the infix for (type <tt>TSeq</tt>).
+ * @param[in] beginPos Begin position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
+ * @param[in] len      Length of the prefix, must be convertible to <tt>Size&lt;TSeq&gt;::Type</tt>.
  *
  * Equivalent to <tt>infix(s, beginPos, beginPos + len)</tt>.
  *
@@ -109,9 +110,9 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * @signature TInfix infix(s, beginPos, endPos);
  *
- * @param s        Segmentable sequence to return the infix for (type <tt>TSeq</tt>).
- * @param beginPos Begin position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
- * @param endPos   End position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
+ * @param[in] s        Segmentable sequence to return the infix for (type <tt>TSeq</tt>).
+ * @param[in] beginPos Begin position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
+ * @param[in] endPos   End position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
  *
  * @aka substr
  */
@@ -124,7 +125,7 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * @tparam TSeq The segmentable sequence type to get suffix type for.
  * @return Type The suffix type.
- * 
+ *
  * The suffix type of a suffix is a suffix, the suffix of any other segment type is an infix.
  */
 
@@ -134,8 +135,8 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * @signature TSuffix suffix(s, beginPos);
  *
- * @param s        The segmentable type to get the suffix of.
- * @param beginPos Begin position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
+ * @param[in] s        The segmentable type to get the suffix of.
+ * @param[in] beginPos Begin position must be convertible to <tt>Position&lt;TSeq&gt;::Type</tt>.
  *
  * @return TSuffix The suffix type as returned by @link SegmentableConcept#Suffix @endlink.
  */
@@ -156,7 +157,7 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature template <typename THost, typename TSpec>
  *            class Segment;
  *
- * @tparam THost The underlying @link SequenceConcept sequence @endlink type.
+ * @tparam THost The underlying @link ContainerConcept sequence @endlink type.
  * @tparam TSpec The tag to use for selecting the Segment specialization.
  *
  * Segments are lightweight representations of an underlying sequence (host).  Only a pointer to the host and begin
@@ -164,10 +165,10 @@ namespace SEQAN_NAMESPACE_MAIN
  *
  * Segments support element access (reading and writing) as well as random access iteration.
  *
- * @snippet demos/sequence/segment.cpp basic operations
+ * @snippet demos/dox/sequence/segment.cpp basic operations
  *
- * You can get the type of the infix/prefix/suffix of a sequence using @link SequenceConcept#Infix @endlink,
- * @link SequenceConcept#Prefix @endlink, and @link SequenceConcept#Suffix @endlink.  These metafunctions will
+ * You can get the type of the infix/prefix/suffix of a sequence using @link SegmentableConcept#Infix @endlink,
+ * @link SegmentableConcept#Prefix @endlink, and @link SegmentableConcept#Suffix @endlink.  These metafunctions will
  * "flatten" the type such that using these metafunctions, the infix of an infix is an infix and not
  * an Infix Segment with an Infix Segment as its host.  Instead, it will again be an Infix Segment
  * of the host of the inner type.
@@ -175,33 +176,41 @@ namespace SEQAN_NAMESPACE_MAIN
  * A suffix of a suffix remains a suffix, a prefix of a prefix remains a prefix.  Any other combination leads to
  * the resulting type being a infix segment.
  *
- * @snippet demos/sequence/segment.cpp metafunction examples
+ * @snippet demos/dox/sequence/segment.cpp metafunction examples
  *
  * If you explicitely need a segment and keep the underlying sequence as it is, explicitely use the <tt>Segment</tt>
  * template class.
  *
- * @snippet demos/sequence/segment.cpp explicit segment
+ * @snippet demos/dox/sequence/segment.cpp explicit segment
  *
  * @aka substring
  */
 
-/**
-.Class.Segment:
-..cat:Sequences
-..summary:A contiguous part of a sequence.
-..signature:Segment<THost, TSpec>
-..param.THost:Type of the whole sequence.
-...metafunction:Metafunction.Host
-...text:Instances of $Segment<THost, TSpec>$ are subsequences of $THost$ objects.
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:@Spec.InfixSegment@.
-..example.file:demos/sequence/infix.cpp
-..example.text:The output is as follows:
-..example.output:
-Infix: CGCG
-..include:seqan/sequence.h
-*/
+/*!
+ * @fn Segment#beginPosition
+ * @headerfile <seqan/sequence.h>
+ * @brief Return segment's begin position.
+ *
+ * @signature TPos beginPosition(seg);
+ *
+ * @param[in] seg The Segment to query for its begin position.
+ *
+ * @return TPos The begin position of the segment.  TPos is the position type of the Segment as returned by
+ *              @link ContainerConcept#Position Position @endlink.
+ */
+
+/*!
+ * @fn Segment#endPosition
+ * @headerfile <seqan/sequence.h>
+ * @brief Return segment's end position.
+ *
+ * @signature TPos endPosition(seg);
+ *
+ * @param[in] seg The Segment to query for its end position.
+ *
+ * @return TPos The end position of the segment.  TPos is the position type of the Segment as returned by
+ *              @link ContainerConcept#Position Position @endlink.
+ */
 
 struct InfixSegment {};
 
@@ -212,9 +221,6 @@ class Segment
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Host.param.T.type:Class.Segment
-///.Metafunction.Host.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct Host<Segment<THost, TSpec> >
 {
@@ -257,24 +263,29 @@ struct Parameter_<Segment<THost, TSpec> const >
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Spec.param.T.type:Class.Segment
-///.Metafunction.Spec.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct Spec<Segment<THost, TSpec> >
 {
     typedef TSpec Type;
 };
+
 template <typename THost, typename TSpec>
 struct Spec<Segment<THost, TSpec> const>
 {
     typedef TSpec Type;
 };
 
-//////////////////////////////////////////////////////////////////////////////
+// ----------------------------------------------------------------------------
+// Metafunction StringSpec
+// ----------------------------------------------------------------------------
 
-///.Metafunction.Value.param.T.type:Class.Segment
-///.Metafunction.Value.class:Class.Segment
+template <typename T>
+struct StringSpec;
+
+template <typename THost, typename TSpec>
+struct StringSpec<Segment<THost, TSpec> > : StringSpec<THost> {};
+
+//////////////////////////////////////////////////////////////////////////////
 
 template <typename THost, typename TSpec>
 struct Value<Segment<THost, TSpec> > :
@@ -286,9 +297,6 @@ struct Value<Segment<THost, TSpec> const > :
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.GetValue.param.T.type:Class.Segment
-///.Metafunction.GetValue.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct GetValue<Segment<THost, TSpec> > :
     GetValue<THost> {};
@@ -299,9 +307,6 @@ struct GetValue<Segment<THost, TSpec> const > :
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Reference.param.T.type:Class.Segment
-///.Metafunction.Reference.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct Reference<Segment<THost, TSpec> > :
     Reference<THost> {};
@@ -322,9 +327,6 @@ struct Reference<Segment<THost, TSpec> const > :
 
 // TODO(holtgrew): Should the iterators of const segments be iterators with the constness of the host.
 
-///.Metafunction.Iterator.param.T.type:Class.Segment
-///.Metafunction.Iterator.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct Iterator<Segment<THost, TSpec>, Rooted>
 {
@@ -352,9 +354,6 @@ struct Iterator<Segment<THost, TSpec> const, Standard>:
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.Size.param.T.type:Class.Segment
-///.Metafunction.Size.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct Size<Segment<THost, TSpec> > :
     Size<THost> {};
@@ -373,9 +372,6 @@ struct Position<Segment<THost, TSpec> const > :
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.DefaultOverflowImplicit.param.T.type:Class.Segment
-///.Metafunction.DefaultOverflowImplicit.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct DefaultOverflowImplicit<Segment<THost, TSpec > > :
     DefaultOverflowImplicit<THost> {};
@@ -386,9 +382,6 @@ struct DefaultOverflowImplicit<Segment<THost, TSpec > const > :
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.DefaultOverflowExplicit.param.T.type:Class.Segment
-///.Metafunction.DefaultOverflowExplicit.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct DefaultOverflowExplicit<Segment<THost, TSpec > > :
     DefaultOverflowExplicit<THost> {};
@@ -399,25 +392,27 @@ struct DefaultOverflowExplicit<Segment<THost, TSpec > const > :
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.IsContiguous.param.T.type:Class.Segment
-///.Metafunction.IsContiguous.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct IsContiguous< Segment<THost, TSpec> > :
     IsContiguous<THost> {};
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Metafunction.IsSequence.param.T.type:Class.Segment
-///.Metafunction.IsSequence.class:Class.Segment
-
 template <typename THost, typename TSpec>
 struct IsSequence< Segment<THost, TSpec> > :
     True {};
 
-//////////////////////////////////////////////////////////////////////////////
+// ----------------------------------------------------------------------------
+// Concept ContainerConcept
+// ----------------------------------------------------------------------------
 
-///.Metafunction.IsLightWeight.param.T.type:Class.Segment
+template <typename THost, typename TSpec>
+SEQAN_CONCEPT_IMPL((Segment<THost, TSpec>), (ContainerConcept));
+
+template <typename THost, typename TSpec>
+SEQAN_CONCEPT_IMPL((Segment<THost, TSpec> const), (ContainerConcept));
+
+//////////////////////////////////////////////////////////////////////////////
 
 template <typename THost, typename TSpec>
 struct IsLightWeight< Segment<THost, TSpec> > :
@@ -426,31 +421,10 @@ struct IsLightWeight< Segment<THost, TSpec> > :
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.atBegin.param.iterator.type:Class.Segment
-///.Function.atBegin.class:Class.Segment
-///.Function.atEnd.param.iterator.type:Class.Segment
-///.Function.atEnd.class:Class.Segment
-///.Function.goBegin.param.iterator.type:Class.Segment
-///.Function.goBegin.class:Class.Segment
-///.Function.goEnd.param.iterator.type:Class.Segment
-///.Function.goEnd.class:Class.Segment
-///.Function.goNext.param.iterator.type:Class.Segment
-///.Function.goNext.class:Class.Segment
-///.Function.goPrevious.param.iterator.type:Class.Segment
-///.Function.goPrevious.class:Class.Segment
-///.Function.value.param.container.type:Class.Segment
-///.Function.value.class:Class.Segment
-
-///.Function.shareResources.param.sequence1, sequence2.type:Class.Segment
-///.Function.shareResources.class:Class.Segment
-
 //////////////////////////////////////////////////////////////////////////////
 // functions for all Segment classes
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.getObjectId.param.object.type:Class.Segment
-///.Function.getObjectId.class:Class.Segment
-
 template <typename THost, typename TSpec>
 inline void const *
 getObjectId(Segment<THost, TSpec> const & me)
@@ -496,8 +470,6 @@ Segment<THost, TSpec> _fromPointer(Segment<THost, TSpec> const & me)
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.empty.param.object.type:Class.Segment
-
 template <typename THost, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
 empty(Segment<THost, TSpec> const & me)
@@ -508,9 +480,6 @@ empty(Segment<THost, TSpec> const & me)
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.length.param.object.type:Class.Segment
-///.Function.length.class:Class.Segment
-
 template <typename THost, typename TSpec>
 SEQAN_HOST_DEVICE inline typename Size<Segment<THost, TSpec> const>::Type
 length(Segment<THost, TSpec> const & me)
@@ -521,9 +490,6 @@ SEQAN_CHECKPOINT
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.capacity.param.object.type:Class.Segment
-///.Function.capacity.class:Class.Segment
-
 template <typename THost, typename TSpec>
 inline typename Size< Segment<THost, TSpec> const>::Type
 capacity(Segment<THost, TSpec> const & me)
@@ -590,15 +556,6 @@ struct SegmentSetImpl_<False, True>
 // assign
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.assign:
-..class:Class.Segment
-..remarks:If $target$ is a @Class.Segment@ object, then
-$limit$ denotes the maximal length of @Function.host.$host(target)$@ after the operation.
-..param.target.type:Class.Segment
-..param.source.type:Class.Segment
-*/
-
 // TODO(holtgrew): We'd rather only have one version.
 
 template<typename THost, typename TSpec>
@@ -846,8 +803,8 @@ inline TStream &
 operator << (TStream & target,
              Segment<THost, TSpec> const & source)
 {
-SEQAN_CHECKPOINT
-    write(target, source);
+    typename DirectionIterator<TStream, Output>::Type it(target);
+    write(it, source);
     return target;
 }
 
@@ -858,8 +815,8 @@ inline TStream &
 operator >> (TStream & source,
              Segment<THost, TSpec> & target)
 {
-SEQAN_CHECKPOINT
-    read(source, target);
+    typename DirectionIterator<TStream, Input>::Type it(source);
+    read(it, target);
     return source;
 }
 template <typename TStream, typename THost, typename TSpec>
@@ -867,8 +824,8 @@ inline TStream &
 operator >> (TStream & source,
              Segment<THost, TSpec> const & target)
 {
-SEQAN_CHECKPOINT
-    read(source, target);
+    typename DirectionIterator<TStream, Input>::Type it(source);
+    read(it, target);
     return source;
 }
 
diff --git a/seqan/sequence/segment_infix.h b/seqan/sequence/segment_infix.h
index 876f5d4..414ccd2 100644
--- a/seqan/sequence/segment_infix.h
+++ b/seqan/sequence/segment_infix.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -53,33 +53,13 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature template <typename THost>
  *            class Segment<THost, InfixSegment>;
  *
- * @tparam THost The underlying @link SequenceConcept sequence @endlink type.
+ * @tparam THost The underlying @link ContainerConcept sequence @endlink type.
  *
  * @see SuffixSegment
  * @see PrefixSegment
  * @aka substring
  */
 
-/**
-.Spec.InfixSegment:
-..cat:Segments
-..summary:An arbitrary segment.
-..general:Class.Segment
-..signature:Segment<THost, InfixSegment>
-..param.THost:Type of the whole sequence.
-...text:Instances of $Segment<THost, InfixSegment>$ are infixes of $THost$ objects.
-...remarks:Use @Metafunction.Host@ to get the host type for a given class.
-..remarks.note:Since the appropriate segment type depends on the host sequence type,
-    it is recommended to use the metafunction @Metafunction.Infix@ instead of explicitely
-    choose a specialization of @Class.Segment@.
-..see:Metafunction.Infix
-..example.file:demos/sequence/infix.cpp
-..example.text:The output is as follows:
-..example.output:
-Infix: CGCG
-..include:seqan/sequence.h
-*/
-
 template <typename THost_>
 class Segment<THost_, InfixSegment>
 {
@@ -100,33 +80,6 @@ class Segment<THost_, InfixSegment>
         SEQAN_ASSERT_LEQ(data_begin_position, data_end_position);
     }
 
-/**
-.Memfunc.InfixSegment#Segment:
-..class:Spec.InfixSegment
-..summary:Constructor
-..signature:Segment<THost, InfixSegment> ()
-..signature:Segment<THost, InfixSegment> (infix)
-..signature:Segment<THost, InfixSegment> (host [, begin, end])
-..param.infix:Other infix object. (copy constructor)
-..param.host:The whole sequence.
-..param.begin:Position/iterator in $host$ of the first item in segment.
-...type:Metafunction.Position.$Position<THost>::Type$
-...type:Metafunction.Iterator.$Iterator<THost>::Type$
-..param.end:Position/iterator behind the end of the segment.
-...type:Metafunction.Position.$Position<THost>::Type$
-...type:Metafunction.Iterator.$Iterator<THost>::Type$
-..remarks:
-...text:A Segment object cannot work without a host. If the object is default constructed,
-the host must be set by @Function.setHost@ before the segment can be used.
-...text:If a segment object is constructed by the copy constructor, the
-members of the new constructed object are set to the same values as the members in the
-source object; the host object is not modified.
-Note that this is a special case, since all other copy operations result in changes
-of the host object.
-...text:$begin$ and $end$ must be valid positions/iterators in $host$.
-...text:The predicate $begin <= end$ must be true.
-*/
-
     SEQAN_HOST_DEVICE
     Segment():
         data_host(),
@@ -199,6 +152,14 @@ SEQAN_CHECKPOINT
         assign(*this, source);
         return *this;
     }
+#if defined(SEQAN_CXX11_STANDARD) && (!defined(_MSC_VER) || _MSC_VER >= 1800)
+    template<typename T> explicit operator T () const
+    {
+        T temp_copy;
+        assign(temp_copy, *this);
+        return temp_copy;
+    }
+#endif
 //____________________________________________________________________________
 
 public:
@@ -255,9 +216,6 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-///.Function.begin.param.object.type:Class.Segment
-///.Function.begin.class:Class.Segment
-
 template <typename THost_>
 SEQAN_HOST_DEVICE inline typename Iterator<Segment<THost_, InfixSegment>, Standard>::Type
 begin(Segment<THost_, InfixSegment> & me,
@@ -277,9 +235,6 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-///.Function.beginPosition.param.object.type:Class.Segment
-///.Function.beginPosition.class:Class.Segment
-
 template <typename THost_>
 SEQAN_HOST_DEVICE inline typename Position<Segment<THost_, InfixSegment> >::Type
 beginPosition(Segment<THost_, InfixSegment> & me)
@@ -297,21 +252,6 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-/**
-.Function.setBegin:
-..class:Class.Segment
-..summary:Sets begin of object in host.
-..cat:Dependent Objects
-..signature:setBegin(object, new_begin)
-..param.object:An object.
-...type:Spec.InfixSegment
-...type:Spec.SuffixSegment
-..param.new_begin:iterator to the new first item in $host(object)$ that belongs of $object$.
-...type:Metafunction.Iterator
-..see:Function.begin
-..see:Function.beginPosition
-..include:seqan/sequence.h
-*/
 template <typename THost_, typename TIterator>
 inline void
 setBegin(Segment<THost_, InfixSegment> & me, TIterator new_begin)
@@ -323,23 +263,6 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-/**
-.Function.setBeginPosition:
-..class:Class.Segment
-..summary:Sets begin position of object in host.
-..cat:Dependent Objects
-..signature:setBeginPosition(object, new_begin)
-..param.object:An object.
-...type:Spec.InfixSegment
-...type:Spec.SuffixSegment
-..param.new_begin:position of the new first item in $host(object)$ that belongs of $object$.
-...type:Metafunction.Position
-..see:Function.begin
-..see:Function.beginPosition
-..see:Function.setBegin
-..include:seqan/sequence.h
-*/
-
 template <typename THost_, typename TPosition>
 inline void
 setBeginPosition(Segment<THost_, InfixSegment> & me, TPosition new_begin)
@@ -350,9 +273,6 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-///.Function.begin.param.object.type:Class.Segment
-///.Function.begin.class:Class.Segment
-
 template <typename THost_>
 SEQAN_HOST_DEVICE inline typename Iterator<Segment<THost_, InfixSegment>, Standard>::Type
 end(Segment<THost_, InfixSegment> & me,
@@ -372,9 +292,6 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-///.Function.endPosition.param.object.type:Class.Segment
-///.Function.endPosition.class:Class.Segment
-
 template <typename THost_>
 SEQAN_HOST_DEVICE inline typename Position<Segment<THost_, InfixSegment> >::Type
 endPosition(Segment<THost_, InfixSegment> & me)
@@ -392,23 +309,6 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-/**
-.Function.setEnd:
-..class:Class.Segment
-..summary:Sets end of object in host.
-..cat:Dependent Objects
-..signature:setEnd(object, new_end)
-..param.object:An object.
-...type:Spec.InfixSegment
-...type:Spec.PrefixSegment
-..param.new_end:Iterator behind the last item in $host(object)$ belongs of $object$.
-...type:Metafunction.Iterator
-..see:Function.end
-..see:Function.endPosition
-..see:Function.setBegin
-..include:seqan/sequence.h
-*/
-
 template <typename THost_, typename TIterator>
 inline void
 setEnd(Segment<THost_, InfixSegment> & me, TIterator new_end)
@@ -421,24 +321,6 @@ setEnd(Segment<THost_, InfixSegment> & me, TIterator new_end)
 //____________________________________________________________________________
 
 
-/**
-.Function.setEndPosition:
-..class:Class.Segment
-..summary:Sets begin position of object in host.
-..cat:Dependent Objects
-..signature:setEndPosition(object, new_end)
-..param.object:An object.
-...type:Spec.InfixSegment
-...type:Spec.PrefixSegment
-..param.new_end:position behind the last item in $host(object)$ that belongs of $object$.
-...type:Metafunction.Position
-..see:Function.end
-..see:Function.endPosition
-..see:Function.setBeginPosition
-..see:Function.setEnd
-..include:seqan/sequence.h
-*/
-
 template <typename THost_, typename TPosition>
 inline void
 setEndPosition(Segment<THost_, InfixSegment> & me, TPosition new_end)
@@ -462,22 +344,6 @@ SEQAN_CHECKPOINT
 
 //____________________________________________________________________________
 
-/**
-.Function.setHost:
-..class:Class.Segment
-..summary:Sets the host of an object.
-..cat:Dependent Objects
-..signature:setHost(object, host)
-..param.object:The object that will get a new host.
-...type:Class.Segment
-..param.host:The new host.
-..remarks:After this operation, $object$ depends on $host$.
-...text:Note that setting the host can invalidate $object$.
-For example, if one changes the host of a @Class.Segment@ object, it is possible
-that begin- and end-position of the segment does not fit into the new host sequence.
-..see:Function.host
-..include:seqan/sequence.h
-*/
 template <typename THost_>
 inline void
 setHost(Segment<THost_, InfixSegment> & me, typename Parameter_<THost_>::Type _host)
@@ -496,20 +362,6 @@ SEQAN_CHECKPOINT
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Metafunction.Infix:
-..cat:Segments
-..class:Class.String
-..summary:Infix sequence type.
-..signature:Infix<T>::Type
-..remarks:Note that an infix of a @Class.Segment@ object is an @Spec.InfixSegment@ object having the same host type.
-..param.T:A sequence type.
-...type:Class.String
-..returns.param.Type:The infix type.
-..see:Spec.InfixSegment
-..include:seqan/sequence.h
-*/
-
 template <typename THost>
 struct Infix
 {
@@ -762,29 +614,6 @@ value(Segment<THost, TSpec> const & me,
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.infix:
-..cat:Containers
-..class:Class.String
-..class:Adaption.char array
-..summary:Creates infix object.
-..signature:infix(host, begin, end)
-..param.host:The complete sequence.
-...type:Class.String
-...type:Adaption.char array
-..param.begin:Position or iterator of the first element of the segment.
-...type:Metafunction.Position
-...type:Metafunction.Iterator
-..param.end:Position or iterator behind the last element of the segment.
-...remarks:$end$ must have the same type as $begin$.
-..returns:The infix of $host$ between $begin$ and $end-1$.
-...remarks:The type of the infix is given by @Metafunction.Infix@.
-..remarks:Notational sugar.
-..see:Spec.InfixSegment
-..see.Metafunction.Infix
-..include:seqan/sequence.h
-*/
-
 template <typename T, typename TPosBegin, typename TPosEnd>
 SEQAN_HOST_DEVICE inline typename Infix<T>::Type
 infix(T & t, TPosBegin pos_begin, TPosEnd pos_end)
@@ -853,33 +682,12 @@ SEQAN_CHECKPOINT
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.infixWithLength:
-..cat:Containers
-..class:Class.String
-..class:Adaption.char array
-..summary:Creates infix object.
-..signature:infixWithLength(host, begin, length)
-..param.host:The complete sequence.
-...type:Class.String
-...type:Adaption.char array
-..param.begin:Position or iterator of the first element of the segment.
-...type:Metafunction.Position
-...type:Metafunction.Iterator
-..param.length:Length of the returned infix.
-..returns:The infix of $host$ between $begin$ and $begin+length-1$.
-...remarks:The type of the infix is given by @Metafunction.Infix@.
-..remarks:Notational sugar.
-..see:Spec.InfixSegment
-..include:seqan/sequence.h
-*/
-
 template <typename T, typename TPosBegin, typename TSize>
 SEQAN_HOST_DEVICE inline typename Infix<T>::Type
-infixWithLength(T & t, TPosBegin pos_begin, TSize length)
+infixWithLength(T SEQAN_FORWARD_ARG t, TPosBegin pos_begin, TSize length)
 {
 SEQAN_CHECKPOINT
-    return typename Infix<T>::Type(t, pos_begin, pos_begin + length);
+    return infix(t, pos_begin, pos_begin + length);
 }
 
 template <typename T, typename TPosBegin, typename TSize>
@@ -887,7 +695,7 @@ SEQAN_HOST_DEVICE inline typename Infix<T *>::Type
 infixWithLength(T * t, TPosBegin pos_begin, TSize length)
 {
 SEQAN_CHECKPOINT
-    return typename Infix<T *>::Type (t, pos_begin, pos_begin + length);
+    return infix(*t, pos_begin, pos_begin + length);
 }
 
 template <typename T, typename TSpec, typename TPosBegin, typename TSize>
@@ -895,10 +703,7 @@ SEQAN_HOST_DEVICE inline typename Infix<Segment<T, TSpec> >::Type
 infixWithLength(Segment<T, TSpec> & t, TPosBegin pos_begin, TSize length)
 {
 SEQAN_CHECKPOINT
-    return typename Infix<Segment<T, TSpec> >::Type (
-        host(t),
-        beginPosition(t) + pos_begin,
-        beginPosition(t) + pos_begin + length);
+    return infix(host(t), beginPosition(t) + pos_begin, beginPosition(t) + pos_begin + length);
 }
 
 template <typename T, typename TSpec, typename TPosBegin, typename TSize>
@@ -906,10 +711,7 @@ SEQAN_HOST_DEVICE inline typename Infix<Segment<T, TSpec> const>::Type
 infixWithLength(Segment<T, TSpec> const & t, TPosBegin pos_begin, TSize length)
 {
 SEQAN_CHECKPOINT
-    return typename Infix<Segment<T, TSpec> const>::Type (
-        host(t),
-        beginPosition(t) + pos_begin,
-        beginPosition(t) + pos_begin + length);
+    return infix(host(t), beginPosition(t) + pos_begin, beginPosition(t) + pos_begin + length);
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/sequence/segment_prefix.h b/seqan/sequence/segment_prefix.h
index b52e6e3..e0f32c1 100644
--- a/seqan/sequence/segment_prefix.h
+++ b/seqan/sequence/segment_prefix.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,35 +54,13 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature template <typename THost>
  *            class Segment<THost, PrefixSegment>;
  *
- * @tparam THost The underlying @link SequenceConcept sequence @endlink type.
+ * @tparam THost The underlying @link ContainerConcept sequence @endlink type.
  *
  * @see InfixSegment
  * @see SuffixSegment
  * @aka substring
  */
 
-/**
-.Spec.PrefixSegment:
-..cat:Segments
-..summary:First part of a sequence.
-..general:Class.Segment
-..signature:Segment<THost, PrefixSegment>
-..param.THost:Type of the whole sequence.
-...text:Instances of $Segment<THost, PrefixSegment>$ are prefixes of $THost$ objects.
-...remarks:Use @Metafunction.Host@ to get the host type for a given class.
-..remarks.note:Since the appropriate segment type depends on the host sequence type,
-    it is recommended to use the metafunction @Metafunction.Prefix@ instead of explicitely
-    choose a specialization of @Class.Segment@.
-..see:Spec.InfixSegment
-..see:Spec.SuffixSegment
-..see:Metafunction.Prefix
-..example.file:demos/sequence/prefix.cpp
-..example.text:The output is as follows:
-..example.output:
-Prefix: TATA
-..include:seqan/sequence.h
-*/
-
 struct PrefixSegment {};
 
 template <typename THost_>
@@ -98,32 +76,6 @@ class Segment<THost_, PrefixSegment>
 
 public:
 
-/**
-.Memfunc.PrefixSegment#Segment:
-..class:Spec.PrefixSegment
-..summary:Constructor
-..signature:Segment<THost, PrefixSegment> ()
-..signature:Segment<THost, PrefixSegment> (prefix)
-..signature:Segment<THost, PrefixSegment> (host [, end])
-..param.prefix:Other prefix object. (copy constructor)
-..param.host:The whole sequence.
-..param.end:Position in $host$ behind the last item in segment. (optional)
-...default:$length(host)$
-...type:Metafunction.Position.$Position<THost>::Type$
-...type:Metafunction.Iterator.$Iterator<THost>::Type$
-..remarks:
-...text:A Segment object cannot work without a host. If the object is default constructed,
-the host must be set by @Function.setHost@ before the segment can be used.
-...text:If a segment object is constructed by the copy constructor, the
-members of the new constructed object are set to the same values as the members in the
-source object; the host object is not modified.
-Note that this is a special case, since all other copy operations result in changes
-of the host object.
-...text:$begin$ must be a valid position/iterator in $host$.
-If $begin$ is omitted, the prefix segment corresponding to
-the whole sequence $host$ is constructed.
-This is the same segment that is returned by @Function.goBegin@.
-*/
     Segment():
         data_host(),
         data_end_position(0)
@@ -167,6 +119,15 @@ This is the same segment that is returned by @Function.goBegin@.
         assign(*this, source);
         return *this;
     }
+
+#if defined(SEQAN_CXX11_STANDARD) && (!defined(_MSC_VER) || _MSC_VER >= 1800)
+    template<typename T> explicit operator T () const
+    {
+        T temp_copy;
+        assign(temp_copy, *this);
+        return temp_copy;
+    }
+#endif
 //____________________________________________________________________________
 
 public:
@@ -354,20 +315,6 @@ SEQAN_CHECKPOINT
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Metafunction.Prefix:
-..cat:Segments
-..class:Class.String
-..summary:Prefix sequence type.
-..signature:Prefix<T>::Type
-..param.T:A sequence type.
-...type:Class.String
-..returns.param.Type:The prefix type.
-..see:Spec.PrefixSegment
-..see:Metafunction.Infix
-..include:seqan/sequence.h
-*/
-
 struct InfixSegment;
 struct SuffixSegment;
 
@@ -525,35 +472,6 @@ operator --(Segment<THost, PrefixSegment> & segment)
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.prefix:
-..cat:Containers
-..class:Class.String
-..class:Adaption.char array
-..summary:Creates prefix object.
-..signature:prefix(host, end)
-..remarks:Note that a prefix of a @Class.Segment@ object is an @Spec.SuffixSegment@ object having the same host type.
-..param.host:The complete sequence.
-...type:Class.String
-...type:Adaption.char array
-..param.end:Position or iterator behind the last element of the segment.
-...type:Metafunction.Position
-...type:Metafunction.Iterator
-..returns:The prefix of $host that ends at $end$.
-...remarks:The type of the prefix is given by @Metafunction.Prefix@.
-..remarks:Notational sugar.
-..see:Spec.PrefixSegment
-..see:Function.suffix
-..see:Function.infix
-..see:Function.suffix
-..include:seqan/sequence.h
-..example.code:
-CharString str = "ABCDEF";
-Prefix<CharString >::Type myPrefix = prefix(str, 3);
-
-std::cout << myPrefix << std::endl;
-*/
-
 template <typename T, typename TPosEnd>
 inline typename Prefix<T>::Type
 prefix(T & t, TPosEnd pos_end)
diff --git a/seqan/sequence/segment_suffix.h b/seqan/sequence/segment_suffix.h
index 6ee55a7..2d2c9e4 100644
--- a/seqan/sequence/segment_suffix.h
+++ b/seqan/sequence/segment_suffix.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,34 +54,13 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature template <typename THost>
  *            class Segment<THost, SuffixSegment>;
  *
- * @tparam THost The underlying @link SequenceConcept sequence @endlink type.
+ * @tparam THost The underlying @link ContainerConcept sequence @endlink type.
  *
  * @see InfixSegment
  * @see PrefixSegment
  * @aka substring
  */
 
-/**
-.Spec.SuffixSegment:
-..cat:Segments
-..summary:End part segment of a sequence.
-..general:Class.Segment
-..signature:Segment<THost, SuffixSegment>
-..param.THost:Type of the whole sequence.
-...text:Instances of $Segment<THost, SuffixSegment>$ are suffixes of $THost$ objects.
-...remarks:Use @Metafunction.Host@ to get the host type for a given class.
-..remarks.note:Since the appropriate segment type depends on the host sequence type,
-    it is recommended to use the metafunction @Metafunction.Suffix@ instead of explicitely
-    choose a specialization of @Class.Segment@.
-..see:Spec.InfixSegment
-..see:Metafunction.Suffix
-..example.file:demos/sequence/suffix.cpp
-..example.text:The output is as follows:
-..example.output:
-Suffix: AAAA
-..include:seqan/sequence.h
-*/
-
 struct SuffixSegment {};
 
 template <typename THost_>
@@ -97,32 +76,6 @@ class Segment<THost_, SuffixSegment>
 
 public:
 
-/**
-.Memfunc.SuffixSegment#Segment:
-..class:Spec.SuffixSegment
-..summary:Constructor
-..signature:Segment<THost, SuffixSegment> ()
-..signature:Segment<THost, SuffixSegment> (suffix)
-..signature:Segment<THost, SuffixSegment> (host [, begin])
-..param.suffix:Other suffix object. (copy constructor)
-..param.host:The whole sequence.
-..param.begin:Position in $host$ of the first item in segment. (optional)
-...default:$0$
-...type:Metafunction.Position.$Position<THost>::Type$
-...type:Metafunction.Iterator.$Iterator<THost>::Type$
-..remarks:
-...text:A Segment object cannot work without a host. If the object is default constructed,
-the host must be set by @Function.setHost@ before the segment can be used.
-...text:If a segment object is constructed by the copy constructor, the
-members of the new constructed object are set to the same values as the members in the
-source object; the host object is not modified.
-Note that this is a special case, since all other copy operations result in changes
-of the host object.
-...text:$begin$ must be a valid position/iterator in $host$.
-If $begin$ is omitted, the suffix segment corresponding to
-the whole sequence $host$ is constructed.
-This is the same segment that is returned by @Function.goBegin@.
-*/
     SEQAN_HOST_DEVICE
     Segment():
         data_host(),
@@ -186,6 +139,14 @@ SEQAN_CHECKPOINT
         assign(*this, source);
         return *this;
     }
+#if defined(SEQAN_CXX11_STANDARD) && (!defined(_MSC_VER) || _MSC_VER >= 1800)
+    template<typename T> explicit operator T () const
+    {
+        T temp_copy;
+        assign(temp_copy, *this);
+        return temp_copy;
+    }
+#endif
 //____________________________________________________________________________
 
 public:
@@ -372,21 +333,6 @@ _setLength(Segment<THost_, SuffixSegment> &, TSize)
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Metafunction.Suffix:
-..cat:Segments
-..class:Class.String
-..summary:Suffix sequence type.
-..signature:Suffix<T>::Type
-..param.T:A sequence type.
-...type:Class.String
-..returns.param.Type:The suffix type.
-..see:Spec.SuffixSegment
-..see:Metafunction.Infix
-..see:Metafunction.Prefix
-..include:seqan/sequence.h
-*/
-
 struct PrefixSegment;
 struct InfixSegment;
 
@@ -544,29 +490,6 @@ operator --(Segment<THost, SuffixSegment> & segment)
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.suffix:
-..cat:Containers
-..class:Class.String
-..class:Adaption.char array
-..summary:Creates suffix object.
-..signature:suffix(host, begin)
-..remarks:Note that a suffix of a @Class.Segment@ object is an @Spec.SuffixSegment@ object having the same host type.
-..param.host:The complete sequence.
-...type:Class.String
-...type:Adaption.char array
-..param.begin:Position or iterator of the first element of the segment.
-...type:Metafunction.Position
-...type:Metafunction.Iterator
-..returns:The suffix of $host that begins at $begin$.
-...remarks:The type of the suffix is given by @Metafunction.Suffix@.
-..remarks:Notational sugar.
-..see:Spec.SuffixSegment
-..see:Function.infix
-..see.Metafunction.Suffix
-..include:seqan/sequence.h
-*/
-
 template <typename T, typename TPosBegin>
 inline typename Suffix<T>::Type
 suffix(T & t, TPosBegin pos_begin)
diff --git a/seqan/sequence/segment_utils.h b/seqan/sequence/segment_utils.h
index e7736b5..7f5ef20 100644
--- a/seqan/sequence/segment_utils.h
+++ b/seqan/sequence/segment_utils.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -34,8 +34,8 @@
 // Utility Functions for Sequences.
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_SEQUENCE_SEQ_UTILS_H_
-#define CORE_INCLUDE_SEQAN_SEQUENCE_SEQ_UTILS_H_
+#ifndef INCLUDE_SEQAN_SEQUENCE_SEQ_UTILS_H_
+#define INCLUDE_SEQAN_SEQUENCE_SEQ_UTILS_H_
 
 namespace seqan {
 
@@ -47,6 +47,20 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
+// --------------------------------------------------------------------------
+// Functor LengthLess
+// --------------------------------------------------------------------------
+// Compare two elements (usually segments) by their length.
+
+template <typename T1, typename T2 = T1>
+struct LengthLess
+{
+    bool operator() (T1 const & a, T2 const & b)
+    {
+        return length(a) < length(b);
+    }
+};
+
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -61,28 +75,17 @@ namespace seqan {
 
 /*!
  * @fn endsWith
+ * @brief Check whether a string is a suffix of another string.
  * @headerfile <seqan/sequence.h>
  *
  * @signature bool endsWith(str, suffix);
  *
- * @param[in] str    The string to check.
- * @param[in] suffix The suffix to check for.
+ * @param[in] str    The string to check (A @link SegmentableConcept @endlink).
+ * @param[in] suffix The suffix to check for (A @link ContainerConcept @endlink).
  *
  * @return bool <tt>true</tt> if <tt>suffix</tt> is a suffix of <tt>str</tt>.
  */
 
-/**
-.Function.endsWith
-..concept:Class.String
-..cat:Input/Output
-..signature:endsWith(str, suffix)
-..summary:Check whether a sequence ends with a given suffix.
-..param.str:The string to check.
-..param.suffix:The suffix to check for.
-..returns:$bool$
-..include:seqan/stream.h
-*/
-
 template <typename TLhs, typename TRhs>
 inline bool endsWith(TLhs const & lhs, TRhs const & rhs)
 {
@@ -100,28 +103,17 @@ inline bool endsWith(TLhs const & lhs, TRhs const & rhs)
 
 /*!
  * @fn startsWith
+ * @brief Check whether a string is a prefix of another string.
  * @headerfile <seqan/sequence.h>
  *
  * @signature bool startsWith(str, prefix);
  *
- * @param[in] str    The string to check.
- * @param[in] prefix The prefix to check for.
+ * @param[in] str    The string to check (A @link SegmentableConcept @endlink).
+ * @param[in] prefix The prefix to check for (A @link ContainerConcept @endlink).
  *
  * @return bool <tt>true</tt> if <tt>prefix</tt> is a prefix of <tt>str</tt>.
  */
 
-/**
-.Function.startsWith
-..concept:Class.String
-..cat:Input/Output
-..signature:startsWith(str, prefix)
-..summary:Check whether a sequence starts with a given prefix.
-..param.str:The string to check.
-..param.prefix:The prefix to check for.
-..returns:$bool$
-..include:seqan/stream.h
-*/
-
 // TODO(weese:) this function is doing the same as isPrefix() one should be removed
 template <typename TLhs, typename TRhs>
 inline bool startsWith(TLhs const & lhs, TRhs const & rhs)
@@ -135,4 +127,4 @@ inline bool startsWith(TLhs const & lhs, TRhs const & rhs)
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_SEQUENCE_SEQ_UTILS_H_
+#endif  // #ifndef INCLUDE_SEQAN_SEQUENCE_SEQ_UTILS_H_
diff --git a/seqan/sequence/sequence_concatenator.h b/seqan/sequence/sequence_concatenator.h
index 286ef70..7e1b3e5 100644
--- a/seqan/sequence/sequence_concatenator.h
+++ b/seqan/sequence/sequence_concatenator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -60,54 +60,35 @@ struct StringSetLimits;
  * @class ConcatenatorManyToOne
  * @headerfile <seqan/sequence.h>
  * @brief A sequence class that virtually concatenates all sequences in a @link StringSet @endlink.
- * 
+ *
  * @signature template <typename TStringSet>
  *            class ConcatenatorManyToOne;
- * 
+ *
  * @tparam TStringSet The @link StringSet @endlink type.
- * 
- * @section Remarks
- * 
+ *
  * This container can be iterated like the concatenation string of all sequences in a @link StringSet @endlink.
- * 
+ *
  * This container only is a lightweight hull around a @link StringSet @endlink.  The iteration is handled by @link
  * ConcatVirtualIterator @endlink.
- * 
+ *
  * Note that accessing an element by index through <tt>operator[]</tt> conducts a binary search and should be avoided.
  * Use the @link ConcatDirectStringSet @endlink specialization of @link StringSet @endlink for random access or only use
  * sequential access through iterators.
- * 
+ *
  * @fn ConcatenatorManyToOne::ConcatenatorManyToOne
  * @brief Constructor
- * 
+ *
  * @signature ConcatenatorManyToOne::ConcatenatorManyToOne(stringSet);
- * 
+ *
  * @param[in] stringSet The @link StringSet @endlink object to be concatenated.
  */
 
-/**
-.Class.ConcatenatorManyToOne:
-..summary:A sequence class that virtually concatenates all sequences in a @Class.StringSet@.
-..cat:Sequences
-..signature:ConcatenatorManyToOne<TStringSet>
-..param.TStringSet:The @Class.StringSet@ type.
-...type:Class.StringSet
-..remarks:This container can be iterated like the concatenation string of all sequences in a @Class.StringSet@.
-..remarks:This container only is a lightweight hull around a @Class.StringSet@. The iteration is handled by @Spec.ConcatVirtual Iterator@.
-..remarks:Note that accessing an element by index through $operator[]$ conducts a binary search and should be avoided. Use the @Spec.ConcatDirect@ specialization of @Class.StringSet@ for random access or only use sequential access through iterators.
-..include:seqan/sequence.h
-.Memfunc.ConcatenatorManyToOne#ConcatenatorManyToOne
-..summary:Constructor
-..signature:ConcatenatorManyToOne<TStringSet> (stringSet)
-..param.stringSet:The @Class.StringSet@ object to be concatenated.
-..class:Class.ConcatenatorManyToOne
- */
 template <typename TStringSet>
 class ConcatenatorManyToOne
 {
 public:
     TStringSet * set;
-    ConcatenatorManyToOne() {}
+    ConcatenatorManyToOne() : set(NULL) {}
     ConcatenatorManyToOne(TStringSet & _set) : set(&_set) {}
 
     template <typename TPos>
diff --git a/seqan/sequence/sequence_forwards.h b/seqan/sequence/sequence_forwards.h
index 5155e89..115bce2 100644
--- a/seqan/sequence/sequence_forwards.h
+++ b/seqan/sequence/sequence_forwards.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -50,32 +50,19 @@ namespace SEQAN_NAMESPACE_MAIN
 // TODO(holtgrew): Still required since we dropped support for VS2003?
 // Workaround (copied from generated forwards) for VS 2003.
 #if defined(_MSC_VER) && (_MSC_VER < 1400)
-template <unsigned int SPACE > struct Block;        // "core/include/seqan/sequence\string_stack.h"(48)
-template <typename THostspec > struct Packed;           // "core/include/seqan/sequence\string_packed.h"(33)
-template <typename TValue, typename TSpec > class String;           // "core/include/seqan/sequence\string_base.h"(54)
-template <typename TString, typename TSpec > class StringSet;           // "core/include/seqan/sequence\sequence_multiple.h"(98)
+template <unsigned int SPACE > struct Block;        // "include/seqan/sequence\string_stack.h"(48)
+template <typename THostspec > struct Packed;           // "include/seqan/sequence\string_packed.h"(33)
+template <typename TValue, typename TSpec > class String;           // "include/seqan/sequence\string_base.h"(54)
+template <typename TString, typename TSpec > class StringSet;           // "include/seqan/sequence\sequence_multiple.h"(98)
 
-template <typename TValue, typename THostspec, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type end(String<TValue, Packed<THostspec> > & me, Tag<TTag> const tag_);           // "core/include/seqan/sequence\string_packed.h"(470)
-template <typename TValue, typename THostspec, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type end(String<TValue, Packed<THostspec> > const & me, Tag<TTag> const tag_);           // "core/include/seqan/sequence\string_packed.h"(478)
-template <typename TValue, unsigned int SPACE, typename TSpec> inline typename Iterator<String<TValue, Block<SPACE> >, Tag<TSpec> const >::Type end(String<TValue, Block<SPACE> > & me, Tag<TSpec> const);           // "core/include/seqan/sequence\string_stack.h"(209)
-template <typename TValue, unsigned int SPACE, typename TSpec> inline typename Iterator<String<TValue, Block<SPACE> > const, Tag<TSpec> const>::Type end(String<TValue, Block<SPACE> > const & me, Tag<TSpec> const);        // "core/include/seqan/sequence\string_stack.h"(217)
-template <typename TString, typename TSpec, typename TTag> inline typename Iterator< StringSet< TString, TSpec >, Tag<TTag> const>::Type end(StringSet< TString, TSpec > & me, Tag<TTag> const tag);        // "core/include/seqan/sequence\sequence_multiple.h"(1398)
-template <typename TString, typename TSpec, typename TTag> inline typename Iterator< StringSet< TString, TSpec > const, Tag<TTag> const>::Type end(StringSet< TString, TSpec > const & me, Tag<TTag> const tag);        // "core/include/seqan/sequence\sequence_multiple.h"(1405)
+template <typename TValue, typename THostspec, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type end(String<TValue, Packed<THostspec> > & me, Tag<TTag> const tag_);           // "include/seqan/sequence\string_packed.h"(470)
+template <typename TValue, typename THostspec, typename TTag> inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type end(String<TValue, Packed<THostspec> > const & me, Tag<TTag> const tag_);           // "include/seqan/sequence\string_packed.h"(478)
+template <typename TValue, unsigned int SPACE, typename TSpec> inline typename Iterator<String<TValue, Block<SPACE> >, Tag<TSpec> const >::Type end(String<TValue, Block<SPACE> > & me, Tag<TSpec> const);           // "include/seqan/sequence\string_stack.h"(209)
+template <typename TValue, unsigned int SPACE, typename TSpec> inline typename Iterator<String<TValue, Block<SPACE> > const, Tag<TSpec> const>::Type end(String<TValue, Block<SPACE> > const & me, Tag<TSpec> const);        // "include/seqan/sequence\string_stack.h"(217)
+template <typename TString, typename TSpec, typename TTag> inline typename Iterator< StringSet< TString, TSpec >, Tag<TTag> const>::Type end(StringSet< TString, TSpec > & me, Tag<TTag> const tag);        // "include/seqan/sequence\sequence_multiple.h"(1398)
+template <typename TString, typename TSpec, typename TTag> inline typename Iterator< StringSet< TString, TSpec > const, Tag<TTag> const>::Type end(StringSet< TString, TSpec > const & me, Tag<TTag> const tag);        // "include/seqan/sequence\sequence_multiple.h"(1405)
 #endif  // defined(_MSC_VER) && (_MSC_VER < 1400)
 
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TData>
-void read(TFile & file, TData & data);          // "core/include/seqan/file/file_format_raw.h"(307)
-
-//////////////////////////////////////////////////////////////////////////////
-
-template <typename TFile, typename TData>
-void write(TFile & file, TData & data);         // "core/include/seqan/file/file_format_raw.h"(327)
-
-template <typename TFile, typename TData>
-void write(TFile & file, TData const & data);   // "core/include/seqan/file/file_format_raw.h"(335)
-
 // ==========================================================================
 // Adaption Forwards
 // ==========================================================================
@@ -104,7 +91,7 @@ void write(TFile & file, TData const & data);   // "core/include/seqan/file/file
 template <typename T> struct AllowsFastRandomAccess;
 template <typename T> struct DefaultOverflowExplicit;
 template <typename T> struct DefaultOverflowImplicit;
-template <typename T> struct IsContiguous;
+// template <typename T, class Enable = void> struct IsContiguous;
 template <typename T> struct IsSequence;
 struct TagExact_;
 struct TagGenerous_;
@@ -119,175 +106,59 @@ template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T, Standard>::T
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T const, Standard>::Type _beginDefault(T const & me, Standard);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T, Rooted>::Type _beginDefault(T & me, Rooted);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T const, Rooted>::Type _beginDefault(T const & me, Rooted);
-template <typename T, typename TSize, typename TExpand> inline typename Size<T>::Type _capacityReturned(T & me, TSize, Tag<TExpand>);
-template <typename T, typename TSize> inline typename Size<T>::Type _capacityReturned(T &, TSize new_capacity, Insist const & );
 template <typename T, typename TSize> inline TSize _computeSizeForCapacity(T const & , TSize capacity);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T, Standard>::Type _endDefault(T & me, Standard);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T const, Standard>::Type _endDefault(T const & me, Standard);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T, Rooted>::Type _endDefault(T & me, Rooted);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T const, Rooted>::Type _endDefault(T const & me, Rooted);
-template <typename TTarget, typename TSource> inline void append(TTarget & target, TSource & source);
-template <typename TTarget, typename TSource> inline void append(TTarget const & target, TSource & source);
-template <typename TTarget, typename TSource> inline void append(TTarget & target, TSource const & source);
-template <typename TTarget, typename TSource> inline void append(TTarget const & target, TSource const & source);
-template <typename TTarget, typename TSource> inline void append(TTarget & target, TSource & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TSource> inline void append(TTarget const & target, TSource & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TSource> inline void append(TTarget & target, TSource const & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TSource> inline void append(TTarget const & target, TSource const & source, typename Size<TTarget>::Type limit);
-template <typename T, typename TValue> inline void appendValue(T & me, TValue const & _value);
-template <typename T, typename TValue> inline void appendValue(T const & me, TValue const & _value);
-template <typename TTarget, typename TSource> inline void assign(TTarget & target, TSource & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TSource> inline void assign(TTarget const & target, TSource & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TSource> inline void assign(TTarget & target, TSource const & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TSource> inline void assign(TTarget const & target, TSource const & source, typename Size<TTarget>::Type limit);
-template <typename T, typename TValue, typename TPos> inline void assignValue(T & me, TPos pos, TValue const & _value);
-template <typename T> SEQAN_HOST_DEVICE inline typename Reference<T const>::Type back(T const & me);
-template <typename T> SEQAN_HOST_DEVICE inline typename Reference<T>::Type back(T & me);
+template <typename TContainer> inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >, void) assign(TContainer SEQAN_FORWARD_ARG me, typename RemoveReference<TContainer>::Type source);
+template <typename TContainer, typename TSource> inline SEQAN_FUNC_ENABLE_IF(And<Not<IsSameType<typename RemoveReference<TContainer>::Type, TSource> >, Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> > >, void) assign(TContainer SEQAN_FORWARD_ARG me, TSource const & source);
+template <typename TContainer, typename TSource> inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >, void) assign(TContainer SEQAN_FORWARD_ARG me, TSource const & source, typename Size<TSource>::Type limit);
+template<typename TTarget, typename TSource> inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<TTarget>::Type> >, void) assign(TTarget SEQAN_FORWARD_ARG target, TSource SEQAN_FORWARD_CARG source, typename Size<TTarget>::Type const limit);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type begin(T & me);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type begin(T const & me);
-template <typename T, typename TSpec> SEQAN_HOST_DEVICE inline typename Iterator<T, Tag<TSpec> const>::Type begin(T & me, Tag<TSpec> const tag_);
-template <typename T, typename TSpec> SEQAN_HOST_DEVICE inline typename Iterator<T const, Tag<TSpec> const>::Type begin(T const & me, Tag<TSpec> const tag_);
+template <typename T, typename TSpec> inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Iterator<T, Tag<TSpec> const>::Type) begin(T & me, Tag<TSpec> const tag_);
+template <typename T, typename TSpec> inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Iterator<T const, Tag<TSpec> const>::Type) begin(T const & me, Tag<TSpec> const tag_);
 template <typename T> inline typename Position<T>::Type beginPosition(T &);
 template <typename T> inline typename Position<T>::Type beginPosition(T const &);
-template <typename T> SEQAN_HOST_DEVICE inline typename Size<T const>::Type capacity(T const & me);
 template <typename T, typename TSize> inline TSize computeGenerousCapacity(T const & , TSize capacity);
-template <typename T> SEQAN_HOST_DEVICE inline bool empty(T const & me);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type end(T & me);
 template <typename T> SEQAN_HOST_DEVICE inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type end(T const & me);
 template <typename T, typename TSpec> SEQAN_HOST_DEVICE inline typename Iterator<T, Tag<TSpec> const>::Type end(T & me, Tag<TSpec> const tag_);
 template <typename T, typename TSpec> SEQAN_HOST_DEVICE inline typename Iterator<T const, Tag<TSpec> const>::Type end(T const & me, Tag<TSpec> const tag_);
 template <typename T> inline typename Position<T>::Type endPosition(T & me);
 template <typename T> inline typename Position<T>::Type endPosition(T const & me);
-template <typename T, typename TBeginPosition, typename TEndPosition> inline void erase(T & me, TBeginPosition pos, TEndPosition pos_end);
-template <typename T, typename TPosition> inline void erase(T & me, TPosition pos);
-template <typename T, typename TBeginPosition, typename TEndPosition> inline void erase(T const & me, TBeginPosition pos, TEndPosition pos_end);
-template <typename T, typename TPosition> inline void erase(T const & me, TPosition pos);
-template <typename T> inline void eraseBack(T & me);
-template <typename T> inline typename Reference<T>::Type front(T & me);
-template <typename T> inline typename Reference<T const>::Type front(T const & me);
-template <typename T> inline void const * getObjectId(T const & me);
-template <typename T, typename TPos> inline typename GetValue<T>::Type getValue(T & me, TPos pos);
-template <typename T, typename TPos> inline typename GetValue<T const>::Type getValue(T const & me, TPos pos);
-template <typename T, typename TPosition, typename TSeq, typename TExpand> inline void insert(T & me, TPosition pos, TSeq const & insertSeq, Tag<TExpand>);
-template <typename T, typename TPosition, typename TSeq, typename TExpand> inline void insert(T const & me, TPosition pos, TSeq const & insertSeq, Tag<TExpand>);
-template <typename T, typename TPosition, typename TSeq> inline void insert(T & me, TPosition pos, TSeq const & insertSeq);
-template <typename T, typename TPosition, typename TSeq> inline void insert(T const & me, TPosition pos, TSeq const & insertSeq);
-template <typename T, typename TPosition, typename TValue> inline void insertValue(T & me, TPosition pos, TValue const & _value);
-template <typename T, typename TPosition, typename TValue> inline void insertValue(T const & me, TPosition pos, TValue const & _value);
-template <typename T, typename TPos> inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type iter(T & me, TPos pos);
-template <typename T, typename TPos> inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type iter(T const & me, TPos pos);
-template <typename T, typename TPos, typename TTag> inline typename Iterator<T, Tag<TTag> const>::Type iter(T & me, TPos pos, Tag<TTag> const tag_);
-template <typename T, typename TPos, typename TTag> inline typename Iterator<T const, Tag<TTag> const>::Type iter(T const & me, TPos pos, Tag<TTag> const tag_);
-template <typename T> inline typename Size<T>::Type length(T const & );
+template <typename T> inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, void const *) getObjectId(T const & me);
+template <typename TContainer> inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<typename RemoveReference<TContainer>::Type> >, void const *) getObjectId(TContainer SEQAN_FORWARD_CARG me);
+template <typename T, typename TPos> inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type iter(T & me, TPos const pos);
+template <typename T, typename TPos> inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type iter(T const & me, TPos const pos);
+template <typename T, typename TPos, typename TTag> inline typename Iterator<T, Tag<TTag> const>::Type iter(T & me, TPos const pos, Tag<TTag> const &);
+template <typename T, typename TPos, typename TTag> inline typename Iterator<T const, Tag<TTag> const>::Type iter(T const & me, TPos const pos, Tag<TTag> const &);
+template <typename T> inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Size<T>::Type) length(T const & /*me*/);
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TChar, typename TAlloc> inline typename Size<std::forward_list<TChar, TAlloc> >::Type length(std::forward_list<TChar, TAlloc> const & me);
+#endif
 template <typename T, typename TValue, typename TPos> inline void moveValue(T & me, TPos pos, TValue const & _value);
 template <typename T, typename TValue, typename TPos> inline void moveValue(T const & me, TPos pos, TValue const & _value);
-template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource & source);
-template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget const & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource & source);
-template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource const & source);
-template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget const & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource const & source);
-template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget const & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource const & source, typename Size<TTarget>::Type limit);
-template <typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource> inline void replace(TTarget const & target, TPositionBegin pos_begin, TPositionEnd pos_end, TSource const & source, typename Size<TTarget>::Type limit);
-template <typename T, typename TSize, typename TExpand> inline typename Size<T>::Type reserve(T & me, TSize const & new_capacity, Tag<TExpand> tag);
-template <typename T, typename TSize> inline typename Size<T>::Type reserve(T & me, TSize const & new_capacity);
-template <typename T, typename TSize> inline typename Size<T>::Type resize(T & me, TSize new_length);
-template <typename T, typename TSize, typename TValue> inline typename Size<T>::Type resize(T & me, TSize new_length, TValue const & val);
+template <typename TContainer> inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, typename Size<TContainer>::Type) length(TContainer const & me);
 template <typename T, typename TSize, typename TBeginPosition, typename TEndPosition> inline TSize resizeSpace(T & me, TSize size, TBeginPosition pos_begin, TEndPosition pos_end);
 template <typename T, typename TSize, typename TBeginPosition, typename TEndPosition, typename TLimit> inline TSize resizeSpace(T & me, TSize size, TBeginPosition pos_begin, TEndPosition pos_end, TLimit limit);
 template <typename T1, typename T2> inline bool shareResources(T1 const & obj1, T2 const & obj2);
 template <typename T> inline void shrinkToFit(T & me);
-template <typename T, typename TPos> SEQAN_HOST_DEVICE inline typename Reference<T>::Type value(T & me, TPos );
-template <typename T, typename TPos> SEQAN_HOST_DEVICE inline typename Reference<T const>::Type value(T const & me, TPos );
-
-// --------------------------------------------------------------------------
-// Forwards For std::vector
-// --------------------------------------------------------------------------
-
-template <typename TChar, typename TAlloc, typename TSource> inline void append(std::vector<TChar, TAlloc> & target, TSource const & source, Generous);
-template <typename TChar, typename TAlloc, typename TSource> inline void append(std::vector<TChar, TAlloc> & target, TSource const & source, typename Size< std::vector<TChar, TAlloc> >::Type limit, Generous);
-template <typename TChar, typename TAlloc, typename TSource> inline void append(std::vector<TChar, TAlloc> & target, TSource const & source, Limit);
-template <typename TChar, typename TAlloc, typename TSource> inline void append(std::vector<TChar, TAlloc> & target, TSource const & source, typename Size< std::vector<TChar, TAlloc> >::Type limit, Limit);
-template <typename TChar, typename TAlloc, typename TValue, typename TTag> inline void appendValue(std::vector<TChar, TAlloc> & me, TValue const & _value, TTag);
-template <typename TChar, typename TAlloc, typename TValue> inline void appendValue(std::vector<TChar, TAlloc> & me, TValue const & _value, Limit);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource & source);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource const & source);
-template <typename TChar, typename TAlloc, typename TSource, typename TSize> inline void assign(std::vector<TChar, TAlloc> & target, TSource & source, TSize limit);
-template <typename TChar, typename TAlloc, typename TSource, typename TSize> inline void assign(std::vector<TChar, TAlloc> & target, TSource const & source, TSize limit);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource & source, Generous);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource const & source, Generous);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource & source, typename Size< std::vector<TChar, TAlloc> >::Type limit, Generous);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource const & source, typename Size< std::vector<TChar, TAlloc> >::Type limit, Generous);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource & source, Limit);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource const & source, Limit);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource & source, typename Size< std::vector<TChar, TAlloc> >::Type limit, Limit);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign(std::vector<TChar, TAlloc> & target, TSource const & source, typename Size< std::vector<TChar, TAlloc> >::Type limit, Limit);
-template <typename TChar, typename TAlloc, typename TSource> inline void assign_std_vector_Generous_impl(std::vector<TChar, TAlloc> & target, TSource & source, typename Size< std::vector<TChar, TAlloc> >::Type limit);
-template <typename TChar, typename TAlloc> inline typename Iterator< std::vector<TChar, TAlloc>, Standard>::Type begin(std::vector<TChar, TAlloc> & me, Standard);
-template <typename TChar, typename TAlloc> inline typename Iterator< std::vector<TChar, TAlloc> const, Standard>::Type begin(std::vector<TChar, TAlloc> const & me, Standard);
-template <typename TChar, typename TAlloc> inline typename Size< std::vector<TChar, TAlloc> >::Type capacity(std::vector<TChar, TAlloc> const & me);
-template <typename TChar, typename TAlloc> inline void clear(std::vector<TChar, TAlloc> & me);
-template <typename TChar, typename TAlloc> inline bool empty(std::vector<TChar, TAlloc> const & me);
-template <typename TChar, typename TAlloc> inline typename Iterator< std::vector<TChar, TAlloc>, Standard>::Type end(std::vector<TChar, TAlloc> & me, Standard);
-template <typename TChar, typename TAlloc> inline typename Iterator< std::vector<TChar, TAlloc> const, Standard>::Type end(std::vector<TChar, TAlloc> const & me, Standard);
-template <typename TChar, typename TAlloc, typename TSize, typename TExpand> inline typename Size< std::vector<TChar, TAlloc> >::Type fill( std::vector<TChar, TAlloc> & me, TSize new_length, TChar const & val, Tag<TExpand>);
-template <typename TChar, typename TAlloc> inline void const * getObjectId(std::vector<TChar, TAlloc> const & me);
-template <typename TChar, typename TAlloc> inline typename Size< std::vector<TChar, TAlloc> >::Type length(std::vector<TChar, TAlloc> const & me);
-template <typename TChar, typename TAlloc, typename TSource> inline void replace(std::vector<TChar, TAlloc> & target, typename Position< std::vector<TChar, TAlloc> >::Type pos_begin, typename Position< std::vector<TChar, TAlloc> >::Type pos_end, TSource const & source, Generous);
-template <typename TChar, typename TAlloc, typename TSource> inline void replace(std::vector<TChar, TAlloc> & target, typename Position< std::vector<TChar, TAlloc> >::Type pos_begin, typename Position< std::vector<TChar, TAlloc> >::Type pos_end, TSource const & source, typename Size< std::vector<TChar, TAlloc> >::Type limit, Generous);
-template <typename TChar, typename TAlloc, typename TSource> inline void replace(std::vector<TChar, TAlloc> & target, typename Position< std::vector<TChar, TAlloc> >::Type pos_begin, typename Position< std::vector<TChar, TAlloc> >::Type pos_end, TSource const & source, Limit);
-template <typename TChar, typename TAlloc, typename TSource> inline void replace(std::vector<TChar, TAlloc> & target, typename Position< std::vector<TChar, TAlloc> >::Type pos_begin, typename Position< std::vector<TChar, TAlloc> >::Type pos_end, TSource const & source, typename Size< std::vector<TChar, TAlloc> >::Type limit, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TExpand> inline void replace(std::vector<TChar, TAlloc> & target, typename Iterator< std::vector<TChar, TAlloc>, Rooted>::Type pos_begin, typename Iterator< std::vector<TChar, TAlloc>, Rooted>::Type pos_end, TSource & source, Tag<TExpand> tag);
-template <typename TChar, typename TAlloc, typename TSize, typename TExpand> inline typename Size< std::vector<TChar, TAlloc> >::Type reserve( std::vector<TChar, TAlloc> & seq, TSize new_capacity, Tag<TExpand> tag);
-template <typename TChar, typename TAlloc, typename TSize> inline typename Size< std::vector<TChar, TAlloc> >::Type reserve( std::vector<TChar, TAlloc> & seq, TSize new_capacity, Insist const &);
-template <typename TChar, typename TAlloc, typename TSize> inline typename Size< std::vector<TChar, TAlloc> >::Type reserve( std::vector<TChar, TAlloc> & seq, TSize new_capacity, Limit const &);
-template <typename TChar, typename TAlloc, typename TSize, typename TExpand> inline typename Size< std::vector<TChar, TAlloc> >::Type resize( std::vector<TChar, TAlloc> & me, TSize new_length, Tag<TExpand>);
-template <typename TChar, typename TAlloc, typename TPos> inline typename GetValue< std::vector<TChar, TAlloc> >::Type value(std::vector<TChar, TAlloc> & me, TPos pos);
-template <typename TChar, typename TAlloc, typename TPos> inline typename GetValue< std::vector<TChar, TAlloc> const>::Type value(std::vector<TChar, TAlloc> const & me, TPos pos);
-
-// --------------------------------------------------------------------------
-// Forwards For std::string
-// --------------------------------------------------------------------------
-
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void append(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, Generous);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void append(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Generous);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void append(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void append(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TValue, typename TTag> inline void appendValue(std::basic_string<TChar, TCharTraits, TAlloc> & me, TValue const & _value, TTag);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TValue> inline void appendValue(std::basic_string<TChar, TCharTraits, TAlloc> & me, TValue const & _value, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TSize> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, TSize limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource, typename TSize> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, TSize limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, Generous);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, Generous);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Generous);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Generous);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource const & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void assign_std_string_Generous_impl(std::basic_string<TChar, TCharTraits, TAlloc> & target, TSource & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type begin(std::basic_string<TChar, TCharTraits, TAlloc> & me, Standard);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type begin(std::basic_string<TChar, TCharTraits, TAlloc> const & me, Standard);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type capacity(std::basic_string<TChar, TCharTraits, TAlloc> const & me);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline void clear(std::basic_string<TChar, TCharTraits, TAlloc> & me);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline bool empty(std::basic_string<TChar, TCharTraits, TAlloc> const & me);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc>, Standard>::Type end(std::basic_string<TChar, TCharTraits, TAlloc> & me, Standard);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Iterator< std::basic_string<TChar, TCharTraits, TAlloc> const, Standard>::Type end(std::basic_string<TChar, TCharTraits, TAlloc> const & me, Standard);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline void const * getObjectId(std::basic_string<TChar, TCharTraits, TAlloc> const & me);
-template <typename TChar, typename TCharTraits, typename TAlloc> inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type length(std::basic_string<TChar, TCharTraits, TAlloc> const & me);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void replace(std::basic_string<TChar, TCharTraits, TAlloc> & target, typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin, typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end, TSource const & source, Generous);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void replace(std::basic_string<TChar, TCharTraits, TAlloc> & target, typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin, typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end, TSource const & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Generous);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void replace(std::basic_string<TChar, TCharTraits, TAlloc> & target, typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin, typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end, TSource const & source, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSource> inline void replace(std::basic_string<TChar, TCharTraits, TAlloc> & target, typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_begin, typename Position< std::basic_string<TChar, TCharTraits, TAlloc> >::Type pos_end, TSource const & source, typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type limit, Limit);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand> inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type reserve( std::basic_string<TChar, TCharTraits, TAlloc> & seq, TSize new_capacity, Tag<TExpand> tag);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize> inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type reserve( std::basic_string<TChar, TCharTraits, TAlloc> & seq, TSize new_capacity, Insist const &);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize> inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type reserve( std::basic_string<TChar, TCharTraits, TAlloc> & seq, TSize new_capacity, Limit const &);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand> inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type resize( std::basic_string<TChar, TCharTraits, TAlloc> & me, TSize new_length, Tag<TExpand>);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TSize, typename TExpand> inline typename Size< std::basic_string<TChar, TCharTraits, TAlloc> >::Type resize( std::basic_string<TChar, TCharTraits, TAlloc> & me, TSize new_length, TChar const & val, Tag<TExpand>);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos> inline typename GetValue< std::basic_string<TChar, TCharTraits, TAlloc> >::Type value(std::basic_string<TChar, TCharTraits, TAlloc> & me, TPos pos);
-template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos> inline typename GetValue< std::basic_string<TChar, TCharTraits, TAlloc> const>::Type value(std::basic_string<TChar, TCharTraits, TAlloc> const & me, TPos pos);
+template <typename T, typename TPos> inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Reference<T>::Type) value(T & me, TPos /*pos*/);
+template <typename T, typename TPos> inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Reference<T const>::Type) value(T const & me, TPos /*pos*/);
+template <typename TContainer, typename TPos> inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >, HasSubscriptOperator<TContainer> >, typename Reference<TContainer>::Type) value(TContainer & me, TPos const pos);
+template <typename TContainer, typename TPos> inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >, HasSubscriptOperator<TContainer> >, typename Reference<TContainer const>::Type) value(TContainer const & me, TPos const pos);
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TContainer, typename TPos> inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >, HasSubscriptOperator<TContainer> >, typename Value<TContainer>::Type) value(TContainer && me, TPos const pos);
+#endif
+template <typename TContainer, typename TPos> inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >, Not<HasSubscriptOperator<TContainer> > >, typename Reference<TContainer>::Type) value(TContainer & me, TPos const pos);
+template <typename TContainer, typename TPos> inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >, Not<HasSubscriptOperator<TContainer> > >, typename Reference<TContainer const>::Type) value(TContainer const & me, TPos const pos);
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TContainer, typename TPos> inline SEQAN_FUNC_ENABLE_IF(And<Is<StlContainerConcept<TContainer> >, Not<HasSubscriptOperator<TContainer> > >, typename Value<TContainer>::Type) value(TContainer && me, TPos const pos);
+#endif
+template <typename TContainer> inline SEQAN_FUNC_ENABLE_IF(Is<StlContainerConcept<TContainer> >, bool) empty(TContainer const & me);
+template <typename T> inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, bool) empty(T const & me);
 
 // --------------------------------------------------------------------------
 // Forwards For arrays and pointers.
@@ -295,7 +166,6 @@ template <typename TChar, typename TCharTraits, typename TAlloc, typename TPos>
 
 template <typename TValue> struct DefaultOverflowExplicit;
 template <typename TValue> struct DefaultOverflowImplicit;
-template <typename TValue> struct IsContiguous;
 template <typename TValue, typename TExpand> inline size_t _clearSpace(TValue * me, size_t size, Tag<TExpand>);
 template <typename TValue, typename TExpand> inline size_t _clearSpace(TValue * me, size_t size, size_t limit, Tag<TExpand>);
 template <typename TValue, typename TPosition, typename TExpand> inline size_t _clearSpace(TValue * me, size_t size, TPosition pos_begin, TPosition pos_end, Tag<TExpand>);
@@ -338,10 +208,6 @@ inline size_t length(char const * me);
 template <typename TTargetValue, typename TSource> inline void move(TTargetValue * & target, TSource & source);
 template <typename TTargetValue, typename TSource> inline void move(TTargetValue * & target, TSource const & source);
 template <typename TValue, typename TPos> inline void moveValue(TValue * me, TPos pos, TValue const & _value);
-template <typename TTargetValue, typename TSource, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, TSource const & source, Tag<TExpand>);
-template <typename TTargetValue, typename TSource, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, TSource const & source, size_t limit, Tag<TExpand>);
-template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, TSourceValue const * source, Tag<TExpand>);
-template <typename TTargetValue, typename TSourceValue, typename TExpand> inline void replace(TTargetValue * target, size_t pos_begin, size_t pos_end, TSourceValue const * source, size_t limit, Tag<TExpand>);
 template <typename TValue, typename TSize, typename TExpand> inline size_t resize( TValue * me, TSize new_length, Tag<TExpand>);
 template <typename TValue, typename TSize, typename TExpand> inline size_t resize( TValue * me, TSize new_length, TValue const & val, Tag<TExpand>);
 template <typename TValue, typename TPos> inline TValue & value(TValue * me, TPos pos);
diff --git a/seqan/sequence/sequence_interface.h b/seqan/sequence/sequence_interface.h
index 137acac..8630dab 100644
--- a/seqan/sequence/sequence_interface.h
+++ b/seqan/sequence/sequence_interface.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,10 +32,8 @@
 // Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
 // ==========================================================================
 // Default implementations for sequences.
-//
+
 // TODO(holtgrew): There appears to be some overlap with string_base.h. Maybe it is a good idea to move everything related to strings to string_base.h and remove all default-container behaviour.
-// TODO(holtgrew): Each value is a container by itself. This is highly undesirable since it introduces the set-of-sets problem and when users confuse atomic values with containers, bugs are hard to find. This feature should be removed.
-// ==========================================================================
 
 // TODO(holtgrew): These functions have (documentation wise) mostly gone into Container, Sequence Concepts and String class.  This is where they belong.
 
@@ -53,98 +51,61 @@ namespace seqan {
 // ============================================================================
 
 /*!
- * @defgroup OverflowStrategyTags
+ * @defgroup OverflowStrategyTags Overflow Strategy Tags
  * @brief The strategy for resizing containers.
- * 
- * @section Remarks
- * 
+ *
  * Changing the capacity of a container can invalidate the iterators of this container.
- * 
+ *
  * If no overflow tag is specified, most operations use the default overflow strategy given by @link
  * DefaultOverflowImplicit @endlink or @link DefaultOverflowExplicit @endlink, depending on the kind of operation.
- * 
- * @see computeGenerousCapacity
+ *
+ * @see StringConcept#computeGenerousCapacity
  * @see DefaultOverflowImplicit
  * @see DefaultOverflowExplicit
- * 
+ *
  * @tag OverflowStrategyTags#Limit
- * @headerfile <seqan/sequence.h> 
+ * @headerfile <seqan/sequence.h>
  * @brief Limit the contents to current capacity.
- * 
- * @typedef Tag<TagLimit_> Limit;
  *
- * @section Remarks
- * 
+ * @signature typedef Tag<TagLimit_> Limit;
+ *
  * All entries that exceed the capacity are lost.
- * @headerfile <seqan/sequence.h> 
+ *
  * @tag OverflowStrategyTags#Generous
- * 
+ * @headerfile <seqan/sequence.h>
  * @brief Expand if needed, get precautionary extra space.
- * 
- * @typedef Tag<TagGenerous_> Generous;
  *
- * @section Remarks
- * 
+ * @signature typedef Tag<TagGenerous_> Generous;
+ *
  * Whenever the capacity has to be increased, the new capacity is choosen somewhat large than actually needed.  This
  * strategy limits the number of capacity changes, so that resizing takes armotized constant time.  Use this strategy if
  * the total amount of storage is unkown at first.
- * 
- * The new capacity is computed by @link computeGenerousCapacity @endlink. By default, it is guaranteed not to exceed
- * about  tree halfs of the space that is used to store the data.  The user can overload @link computeGenerousCapacity
- * @endlink in order to change this behavior.
- * 
+ *
+ * The new capacity is computed by @link StringConcept#computeGenerousCapacity @endlink. By default, it is
+ * guaranteed not to exceed about three halfs of the space that is used to store the data.  The user can overload
+ * @link StringConcept#computeGenerousCapacity @endlink in order to change this behavior.
+ *
  * @tag OverflowStrategyTags#Exact
- * @headerfile <seqan/sequence.h> 
+ * @headerfile <seqan/sequence.h>
  * @brief Expand as far as needed.
- * 
- * @typedef Tag<TagExact_> Exact;
  *
- * @section Remarks
- * 
+ * @signature typedef Tag<TagExact_> Exact;
+ *
  * The capacity is only changed if the current capacity is not large enough.  If the capacity can only be expanded up to
  * a certain ammount, it will be increased as far as possible  and the contents are limited to the new capacity.
- * 
+ *
  * Note that the capacity will never be shrinked.  Use @link ContainerConcept#shrinkToFit @endlink to resize the
  * capacity down to the current length.
- * 
+ *
  * @tag OverflowStrategyTags#Insist
- * @headerfile <seqan/sequence.h> 
+ * @headerfile <seqan/sequence.h>
  * @brief No capacity check.
  *
- * @typedef Tag<TagInsist_> Insist;
- * 
- * @section Remarks
- * 
- * The user has to ensure that the container's capacity is large enough.
+ * @signature typedef Tag<TagInsist_> Insist;
+ *
+ * @note The user has to ensure that the container's capacity is large enough.
  */
 
-/**
-.Tag.Overflow Strategy:
-..cat:Sequences
-..summary:The strategy for resizing containers.
-..tag.Insist:No capacity check.
-...remarks:The user has to ensure that the container's capacity is large enough.
-..tag.Limit:Limit the contents to current capacity.
-...remarks: All entries that exceed the capacity are lost.
-..tag.Exact:Expand as far as needed.
-...remarks: The capacity is only changed if the current capacity is not large enough.
- If the capacity can only be expanded up to a certain ammount, it will be increased as far as possible
- and the contents are limited to the new capacity.
-...remarks:Note that the capacity will never be shrinked.
- Use @Function.shrinkToFit@ to resize the capacity down to the current length.
-..tag.Generous:Expand if needed, get precautionary extra space.
-...remarks:Whenever the capacity has to be increased, the new capacity is choosen somewhat large than actually needed.
- This strategy limits the number of capacity changes, so that resizing takes armotized constant time.
- Use this strategy if the total amount of storage is unkown at first.
-...remarks:The new capacity is computed by @Function.computeGenerousCapacity@.
-By default, it is guaranteed not to exceed about
- tree halfs of the space that is used to store the data.
- The user can overload @Function.computeGenerousCapacity@ in order to change this behavior.
-..remarks:Changing the capacity of a container can invalidate the iterators of this container.
-..remarks:If no overflow tag is specified, most operations use the default overflow strategy given by @Metafunction.DefaultOverflowImplicit@
-or @Metafunction.DefaultOverflowExplicit@, depending on the kind of operation.
-..include:seqan/sequence.h
-*/
 struct TagInsist_;
 typedef Tag<TagInsist_> Insist;
 typedef Tag<TagInsist_> Tight;  // TODO(holtgrew): Necessary?
@@ -177,26 +138,11 @@ typedef Tag<TagExact_> Exact;
  *
  * @return Type The default overflow tag.  The default implementation returns <tt>Generous</tt>.
  *
- * @section Remarks
- *
- * This function is used for functions that cause an implicit change of a container's size, like e.g. assign, append,
- * and replace.
+ * This function is used for functions that cause an implicit change of a container's size, like e.g. through
+ * @link AssignableConcept#assign @endlink, @link ContainerConcept#append @endlink and
+ * @link StringConcept#replace @endlink.
  */
 
-/**
-.Metafunction.DefaultOverflowImplicit:
-..hidefromindex
-..class:Class.String
-..summary:The default overflow strategy for implicit resize.
-..signature:DefaultOverflowImplicit<T>::Type
-..param.T:Type for which the overflow strategy is determined.
-...type:Class.String
-..returns.param.Type:Expansion tag for type of $T$.
-..remarks:This function is used for functions that cause an implicit change of a container's size, like
-e.g. @Function.assign@, @Function.append@, and @Function.replace@.
-..see:Tag.Overflow Strategy
-..include:seqan/sequence.h
-*/
 template <typename T>
 struct DefaultOverflowImplicit
 {
@@ -218,87 +164,21 @@ struct DefaultOverflowImplicit
  *
  * @return Type The resulting expantion tag for <tt>T</tt>.
  *
- * @section Remarks
- *
- * This function is used for functions that change a container's size explicit, like e.g. resize.
+ * This function is used for functions that change a container's size explicitly, like e.g.
+ * @link StringConcept#resize @endlink.
  */
 
-/**
-.Metafunction.DefaultOverflowExplicit:
-..hidefromindex
-..class:Class.String
-..summary:The default overflow strategy for explicit resize.
-..signature:DefaultOverflowExplicit<T>::Type
-..param.T:Type for which the overflow strategy is determined.
-...type:Class.String
-..returns.param.Type:Expansion tag for type of $T$.
-..remarks:This function is used for functions that change a container's size explicit, like e.g. @Function.resize@.
-..see:Tag.Overflow Strategy
-..see:Metafunction.DefaultOverflowImplicit
-..include:seqan/sequence.h
-*/
 template <typename T>
 struct DefaultOverflowExplicit
 {
     typedef Generous Type;
 };
 
-// --------------------------------------------------------------------------
-// Metafunction IsContiguous
-// --------------------------------------------------------------------------
-
-/*!
- * @mfn IsContiguous
- * @headerfile <seqan/sequence.h>
- * @brief Determines whether a container stores its elements contiguously in memory.
- *
- * @signature IsContiguous<T>::Type;
- * @signature IsContiguous<T>::VALUE;
- *
- * @tparam T The type that is tested for being a string.
- *
- * @return Type  Either <tt>True</tt> or <tt>False</tt>, depending on whether <tt>T</tt> is stored contiguously.
- * @return VALUE Either <tt>true</tt> or <tt>false</tt>, depending on whether <tt>T</tt> is stored contiguously.
- *
- * @section Remarks
- *
- * A sequence container is "contiguous", if its elements are stored in a single contiguous array.  Examples for
- * contiguous sequences are AllocString or char arrays.
- *
- * If an object <tt>obj</tt> is a contiguous sequence, then <tt>begin(obj)</tt> can be converted to a pointer to the
- * first element of the content array.
- */
-
-/**
-.Metafunction.IsContiguous:
-..cat:Sequences
-..summary:Determines whether a container stores its elements in a contiguous array.
-..signature:IsContiguous<T>::VALUE
-..param.T:Type that is tested for being a string.
-..returns.param.VALUE:$true$ if $T$ is a string, $false$ otherwise.
-..remarks:Definition: A sequence container is "contiguous", if its elements
-    are stored in a single contiguous array.
-    Examples for contiguous sequences are @Spec.Alloc String@ or @Adaption.char array@.
-..remarks:If an object $obj$ is a contiguous sequence, then $begin(obj)$ can be
-    converted to a pointer to the first element of the content array.
-..include:seqan/sequence.h
-*/
-template <typename T>
-struct IsContiguous
-{
-    typedef False Type;
-    enum { VALUE = false };
-};
-
-template <typename T>
-struct IsContiguous<T const>
-    : public IsContiguous<T> {};
-
 // --------------------------------------------------------------------------
 // Metafunction IsSequence
 // --------------------------------------------------------------------------
 
-// TODO(holtgrew): Deprecate in favour of Is<SequenceConcept>?
+// TODO(holtgrew): Deprecate in favour of Is<StringConcept>?
 
 /*!
  * @mfn IsSequence
@@ -313,21 +193,9 @@ struct IsContiguous<T const>
  * @return Type  <tt>True</tt> if <tt>T</tt> is a sequence and <tt>False</tt> otherwise.
  * @return VALUE <tt>true</tt> if <tt>T</tt> is a sequence and <tt>false</tt> otherwise.
  *
- * @section Remarks
- *
  * For example, String and Segment as <tt>T</tt> return true.
  */
 
-/**
-.Metafunction.IsSequence:
-..cat:Sequences
-..summary:Determines whether a container stores its elements in sequential order.
-..signature:IsSequence<T>::VALUE
-..param.T:Type that is tested for being a sequence.
-..returns.param.VALUE:$true$ if $T$ is a sequence, $false$ otherwise.
-..remarks:For example @Class.String@ and @Class.Segment@ return $true$.
-..include:seqan/sequence.h
-*/
 template <typename T>
 struct IsSequence
 {
@@ -336,8 +204,7 @@ struct IsSequence
 };
 
 template <typename T>
-struct IsSequence<T const>
-    : public IsSequence<T> {};
+struct IsSequence<T const> : IsSequence<T> {};
 
 // --------------------------------------------------------------------------
 // Metafunction AllowsFastRandomAccess
@@ -356,21 +223,9 @@ struct IsSequence<T const>
  * @return Type  <tt>True</tt> if <tt>T</tt> allows for fast random access and <tt>False</tt> otherwise.
  * @return VALUE <tt>true</tt> if <tt>T</tt> allows for fast random access and <tt>false</tt> otherwise.
  *
- * @section Remarks
- *
  * For example, String and std::vector allow for fast random access, while std::list does not.
  */
 
-/**
-.Metafunction.AllowsFastRandomAccess:
-..cat:Sequences
-..summary:Determines whether a sequence efficiently supports random access.
-..signature:AllowsFastRandomAccess<T>::VALUE
-..param.T:Type that is tested for fast random access.
-..returns.param.VALUE:$true$ if $T$ supports fast random access, $false$ otherwise.
-..remarks:For example @Spec.Alloc String@, @Class.Segment@, and @Spec.Block String@ return $true$.
-..include:seqan/sequence.h
-*/
 template <typename T>
 struct AllowsFastRandomAccess
 {
@@ -391,18 +246,16 @@ struct AllowsFastRandomAccess<T const>
 // --------------------------------------------------------------------------
 
 /*!
- * @fn getObjectId
- * @header <seqan/sequence.h>
+ * @fn ContainerConcept#getObjectId
+ * @headerfile <seqan/sequence.h>
  * @brief A value that identifies the underlying sequence.
  *
- * @signature TVoidPtr getObjectId(object);
+ * @signature TVoidPtr getObjectId(cont);
  *
- * @param object The object for which to determine the id.
+ * @param[in] cont The object for which to determine the id.
  *
  * @return TVoidPtr a <tt>void const *</tt> value identying the object.
  *
- * @section Remarks
- *
  * Two sequences should have the same id, if they share the same resource, e.g. the same memory buffer.
  *
  * The exact semantic of the returned id can vary for different classes.  Typically, the id of a string is a <tt>void
@@ -426,36 +279,12 @@ struct AllowsFastRandomAccess<T const>
  * compile time.
  */
 
-/**
-.Function.getObjectId:
-..cat:Miscellaneous
-..class:Class.String
-..summary:A value that identifies the underlying sequence.
-..signature:void const * getObjectId(object)
-..param.object:The object for which the id will be determined.
-..returns:The id of $sequence$.
-..remarks.text:Two sequences should have the same id, if they share the same resource, e.g. the same memory buffer.
-..remarks.text:The exact semantic of the returned id can vary for different classes.
-Typically, the id of a string is a $void const *$ to the end of the string.
-..remarks.note:The id of a single character need not to be the id of its container.
-..example.code:String<char> str = "hallo seqan";
-bool b1 = (getObjectId(str) == getObjectId(infix(str, 3, 7));   //true
-bool b2 = (getObjectId(str) == getObjectId(String<char>(str))); //false
-bool b3 = (getObjectId(str) == getObjectId(toCString(str)));
-..example.text:In this example, $b1$ is $true$, since the segment object returned by $infix()$
-is just a filter and uses the buffer of it's host object $str$.
-..example.text:$String<char>(str)$ constructs a temporary copy of $str$, so these two
-strings have different id values.
-..example.text:The result of the last comparison depends on the implementation of $toCString$
-and cannot be predicted at compile time.
-..include:seqan/sequence.h
-*/
 template <typename T>
-inline void const *
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, void const *)
 getObjectId(T const & me)
 {
     SEQAN_CHECKPOINT;
-    return end(me, Standard());
+    return &*end(me, Standard());
 }
 
 // --------------------------------------------------------------------------
@@ -466,7 +295,7 @@ getObjectId(T const & me)
  * @fn shareResources
  * @headerfile <seqan/sequence.h>
  * @brief Determines whether two sequences share the same resource.
- * 
+ *
  * @signature bool shareResources(s1, s2);
  *
  * @param[in] s1 First sequence.
@@ -475,19 +304,6 @@ getObjectId(T const & me)
  * @return bool <tt>true</tt> if the two sequences share resources and <tt>false</tt> if not.
  */
 
-/**
-.Function.shareResources:
-..cat:Miscellaneous
-..class:Class.String
-..summary:Determines whether two sequences share the same resource.
-..signature:bool shareResources(sequence1, sequence2)
-..param.sequence1, sequence2:Two sequences.
-..returns:$false$ if it can be guaranteed that $sequence1$ and $sequence2$ can be modified without changing each other, $true$ otherwise.
-..remarks:Non-sequences are interpreted as sequences of size 1.
-..remarks:Note that this function may not work properly for argument types that are not listed here.
-..include:seqan/sequence.h
-*/
-
 template <typename T1, typename T2>
 inline bool
 shareResources(T1 const & obj1,
@@ -545,45 +361,6 @@ _beginDefault(T const & me,
 // Function begin()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn begin
- * @headerfile <seqan/sequences.h>
- * @brief Returns the begin iterator of a container.
- *
- * @signature TIterator begin(object[, tag]);
- *
- * @param[in] object The container to get the begin iterator for.
- * @param[in] tag    The tag to use for picking the resulting type.
- *
- * @return TIterator An iterator to the first item in <tt>object</tt>. The type is the result of
- *                   <tt>Iterator<TContainer, TTag>::Type</tt> where <tt>TContainer</tt> is the type of
- *                   <tt>object</tt> and <tt>TTag</tt> is the type of <tt>tag</tt>.
- *
- * @section Remarks
- *
- * If the container is empty, the resulting iterator does not point to a valid element in the container.
- */
-
-/**
-.Function.begin:
-..cat:Iteration
-..cat:Containers
-..class:Class.String
-..class:Concept.ContainerConcept
-..summary:The begin of a container.
-..signature:Iterator begin(object [, tag])
-..param.object:A container.
-...type:Class.String
-...concept:Concept.ContainerConcept
-..param.tag:An @Tag.Iterator Spec.iterator spec@ tag that specifies the kind of the iterator returned. (optional)
-...default:Given by @Metafunction.DefaultGetIteratorSpec@.
-..returns:An iterator to the first item in $object$. The type is the result of $Iterator<TContainer, TTag>::Type$ where $TContainer$ is the type of $object$ and $TTag$ is the type of $tag$.
-...metafunction:Metafunction.Iterator
-..remarks.text:If the container does not contain any items at all, the function may return 0.
-..see:Function.end
-..see:Metafunction.Iterator
-..include:seqan/sequence.h
-*/
 template <typename T>
 SEQAN_HOST_DEVICE inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type
 begin(T & me)
@@ -602,13 +379,14 @@ begin(T const & me)
 
 //folgende forward Deklaration wurde wegen Phaenomene bei VC++ 2003 hinzugenommen
 //implemented in string_pointer.h
-template <typename TValue>
-SEQAN_HOST_DEVICE inline typename Iterator<TValue const *, Standard>::Type
-begin(TValue const * me,
-      Standard);
+// template <typename TValue,
+//           typename DisableIf<Is<StlContainerConcept<typename RemoveReference<T>::Type> >, int>::Type>
+// SEQAN_HOST_DEVICE inline typename Iterator<TValue const *, Standard>::Type
+// begin(TValue const * me,
+//       Standard);
 
 template <typename T, typename TSpec>
-SEQAN_HOST_DEVICE inline typename Iterator<T, Tag<TSpec> const>::Type
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Iterator<T, Tag<TSpec> const>::Type)
 begin(T & me,
       Tag<TSpec> const tag_)
 {
@@ -616,7 +394,7 @@ begin(T & me,
     return _beginDefault(me, tag_);
 }
 template <typename T, typename TSpec>
-SEQAN_HOST_DEVICE inline typename Iterator<T const, Tag<TSpec> const>::Type
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Iterator<T const, Tag<TSpec> const>::Type)
 begin(T const & me,
       Tag<TSpec> const tag_)
 {
@@ -670,55 +448,6 @@ begin(TValue const * me,
 // Function beginPosition()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn beginPosition
- * @headerfile <seqan/sequence.h>
- * @brief Begin position of an object in a host.
- *
- * @signature TPosition beginPosition(object);
- *
- * @param[in] object An object.
- *
- * @return TPosition The position of the first item in <tt>host(object)</tt> that belongs to <tt>object</tt>.
- *                   The type TPosition is the position type of <tt>object</tt>.
- *
- * @section Remarks
- *
- * For most classes, this function returns 0.  Exceptions are Segments.
- *
- * @section Examples
- * CharString str = "ABCDEF";
- * std::cout &lt;&lt; beginPosition(str) &lt;&lt; std::endl;
- * 
- * Infix&lt;CharString&gt;::Type myInfix = infix(str, 1, 5);
- * std::cout &lt;&lt; beginPosition(myInfix) &lt;&lt; std::endl;
- * @code{.cpp}
- * @endcode
- */
-
-/**
-.Function.beginPosition:
-..cat:Containers
-..summary:Begin position of object in host.
-..signature:Position beginPosition(object)
-..class:Class.String
-..class:Concept.ContainerConcept
-..param.object:An object.
-...type:Class.String
-...concept:Concept.ContainerConcept
-..returns:The position of the first item in $host(object)$ that belongs of $object$.
-...metafunction:Metafunction.Position
-..remarks
-...text:For most classes $beginPosition$ always returns 0. Exceptions are e.g. @Spec.InfixSegment@ and @Spec.SuffixSegment@.
-..see:Function.begin
-..include:seqan/sequence.h
-..example.code:
-CharString str = "ABCDEF";
-std::cout << beginPosition(str) << std::endl;
-
-Infix<CharString >::Type myInfix = infix(str, 1, 5);
-std::cout << beginPosition(myInfix) << std::endl;
-*/
 template <typename T>
 inline typename Position<T>::Type
 beginPosition(T &)
@@ -781,41 +510,6 @@ _endDefault(T const & me,
 // Function end()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn end
- * @headerfile <seqan/sequence.h>
- * @brief Return iterator to the end of a container.
- *
- * @signature TIterator end(object[, tag]);
- *
- * @param[in] object The container to get the end iterator for.
- * @param[in] tag    The tag to use for picking the resulting type.
- *
- * @return TIterator An iterator to the first item in <tt>object</tt>. The type is the result of
- *                   <tt>Iterator<TContainer, TTag>::Type</tt> where <tt>TContainer</tt> is the type of
- *                   <tt>object</tt> and <tt>TTag</tt> is the type of <tt>tag</tt>.
- */
-
-/**
-.Function.end:
-..cat:Iteration
-..cat:Containers
-..class:Class.String
-..concept:Concept.ContainerConcept
-..summary:The end of a container.
-..signature:Iterator end(object [, tag])
-..param.object:A container.
-...type:Class.String
-...concept:Concept.ContainerConcept
-..param.tag:An @Tag.Iterator Spec.iterator spec@ tag that specifies the kind of the iterator returned. (optional)
-...default:Given by @Metafunction.DefaultGetIteratorSpec@.
-..returns:An iterator that points behind the last item in $object$. The type is the result of $Iterator<TContainer, TTag>::Type$ where $TContainer$ is the type of $object$ and $TTag$ is the type of $tag$.
-...metafunction:Metafunction.Iterator
-..remarks.text:If the container does not contain any items at all, the function may return 0.
-..see:Function.begin
-..see:Metafunction.Iterator
-..include:seqan/sequence.h
-*/
 template <typename T>
 SEQAN_HOST_DEVICE inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type
 end(T & me)
@@ -854,34 +548,6 @@ end(T const & me,
 // Function endPosition()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn endPosition
- * @headerfile <seqan/sequence.h>
- * @brief End position of an object in its host.
- *
- * @signature TPosition endPosition(object);
- *
- * @param[in] object The object to query for its end position.
- *
- * @return TPosition The position behind the last item in <tt>host(object)</tt> that belongs to <tt>object</tt>.
- */
-
-/**
-.Function.endPosition:
-..cat:Containers
-..class:Class.String
-..concept:Concept.ContainerConcept
-..summary:End position of object in host.
-..signature:Position endPosition(object)
-..param.object:An object.
-...concept:Concept.ContainerConcept
-...type:Class.String
-..returns:The position behind the last item in $host(object)$ that belongs of $object$.
-...metafunction:Metafunction.Position
-..see:Function.end
-..see:Function.beginPosition
-..include:seqan/sequence.h
-*/
 template <typename T>
 inline typename Position<T>::Type
 endPosition(T & me)
@@ -902,35 +568,10 @@ endPosition(T const & me)
 // Function value()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn value
- * @headerfile <seqan/sequence.h>
- * @brief Reference to the value.
- *
- * @signature TReference value(container, position);
- *
- * @param[in] container A container of values.
- * @param[in] position  The position to query the value for.
- *
- * @return TReference A reference or proxy to the value.
- */
-
-/**
-.Function.value:
-..cat:Iteration
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:Reference to the value.
-..signature:Reference value(container, position)
-..param.container:A container of values.
-..param.position:A position in $container$ on which the value should be accessed.
-..returns:A reference or proxy to the value.
-...metafunction:Metafunction.Reference
-..include:seqan/sequence.h
-*/
 //* ???Anti Default Sequences
-template <typename T, typename TPos>
-SEQAN_HOST_DEVICE inline typename Reference<T>::Type
+template <typename T,
+          typename TPos>
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Reference<T>::Type)
 value(T & me,
       TPos /*pos*/)
 {
@@ -938,8 +579,9 @@ value(T & me,
     return me;
 }
 
-template <typename T, typename TPos>
-SEQAN_HOST_DEVICE inline typename Reference<T const>::Type
+template <typename T,
+          typename TPos>
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Reference<T const>::Type)
 value(T const & me,
       TPos /*pos*/)
 {
@@ -952,58 +594,19 @@ value(T const & me,
 // Function getValue()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn getValue
- * @headerfile <seqan/sequence.h>
- * @brief Access a value.
- *
- * @signature TGetValue getValue(container, pos);
- *
- * @param[in] container The container to query for a value.
- * @param[in] pos       The position to query the value at.
- *
- * @return TGetValue The get-value in <tt>container</tt> at position <tt>pos</tt>.
- *
- * @section Remarks
- *
- * The get value is always convertible into the Value type of the container.  It can either be a temporary copy of the
- * given item or a const reference into the container.
- *
- * If <tt>pos</tt> is outside of <tt>container</tt> then the behaviour of the function is undefined.
- */
-
-/**
-.Function.getValue:
-..summary:Access to the value.
-..cat:Containers
-..cat:Content Manipulation
-..concept:Concept.ContainerConcept
-..signature:GetValue getValue(container, pos)
-..param.container:A container.
-...concept:Concept.ContainerConcept
-..param.pos:The position of an item in $object$.
-...remarks:$pos$ should be convertible to $Position<T>::Type$ for $container$-type $T$.
-..returns:The item at position $pos$ in $container$.
-This can either be a reference to the item or a temporary copy of the item.
-...metafunction:Metafunction.GetValue
-..remarks:
-...text:If $pos$ is out of range, then the behavior of the function is undefined.
-..see:Metafunction.GetValue
-..see:Metafunction.Position
-..see:Function.value
-..include:seqan/sequence.h
-*/
-template <typename T, typename TPos>
-inline typename GetValue<T>::Type
+template <typename T,
+          typename TPos>
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename GetValue<T>::Type)
 getValue(T & me,
          TPos pos)
 {
     SEQAN_CHECKPOINT;
-    return (typename GetValue<T>::Type) value(me, pos);
+    return /*(typename GetValue<T>::Type)*/ value(me, pos);
 }
 
-template <typename T, typename TPos>
-inline typename GetValue<T const>::Type
+template <typename T,
+          typename TPos>
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename GetValue<T const>::Type)
 getValue(T const & me,
          TPos pos)
 {
@@ -1015,155 +618,87 @@ getValue(T const & me,
 // Function front()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn front
- * @headerfile <seqan/sequence.h>
- * @brief Return the first item of a container.
- *
- * @signature TReference front(container);
- *
- * @param[in] container The container to query.
- *
- * @return TReference Reference to the first item in <tt>container</tt>.
- * 
- * @section Remarks
- *
- * This function is equivaeltn to <tt>value(container, 0)</tt>.
- */
-
-/**
-.Function.front:
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:The first item in container.
-..signature:Iterator front(container)
-..param.container:A container.
-...concept:Concept.ContainerConcept
-..returns:A @Metafunction.Reference.reference@ of the first item in $container$.
-...metafunction:Metafunction.Reference
-..remarks:This function is equivalent to $value(me, 0)$.
-..see:Function.value
-..see:Function.begin
-..include:seqan/sequence.h
-*/
-
 template <typename T>
 inline typename Reference<T>::Type
 front(T & me)
 {
     SEQAN_CHECKPOINT;
-    return value(me, 0);
+    return *begin(me, Standard());
 }
+
 template <typename T>
 inline typename Reference<T const>::Type
 front(T const & me)
 {
     SEQAN_CHECKPOINT;
-    return value(me, 0);
+    return *begin(me, Standard());
 }
 
+#ifdef SEQAN_CXX11_STANDARD
+template <typename T>
+inline SEQAN_FUNC_DISABLE_IF(IsSameType<T, T &>, typename Value<T>::Type)
+front(T && me)
+{
+    SEQAN_CHECKPOINT;
+    return *begin(me, Standard());
+}
+
+#endif
+
 // --------------------------------------------------------------------------
 // Function back()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn back
- * @headerfile <seqan/sequence.h>
- * @brief Return the last item of a container.
- *
- * @signature TReference back(container);
- *
- * @param[in] container The container to query.
- *
- * @return TReference Reference to the last item in <tt>container</tt>.
- * 
- * @section Remarks
- *
- * This function is equivaeltn to <tt>value(container, length(container) - 1)</tt>.
- */
-
-/**
-.Function.back:
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:The last item in container.
-..signature:Iterator back(container)
-..param.container:A container.
-...concept:Concept.ContainerConcept
-..returns:A @Metafunction.Reference.reference@ of the last item in $container$.
-...metafunction:Metafunction.Reference
-..remarks:This function is equivalent to $value(me, length(me) - 1)$.
-..see:Function.value
-..see:Function.end
-..see:Function.front
-..include:seqan/sequence.h
-*/
-
 template <typename T>
-SEQAN_HOST_DEVICE inline typename Reference<T const>::Type
+inline typename Reference<T const>::Type
 back(T const & me)
 {
     SEQAN_CHECKPOINT;
-    return value(me, length(me) - 1);
+    return *(end(me, Standard()) - 1);
 }
 
 template <typename T>
-SEQAN_HOST_DEVICE inline typename Reference<T>::Type
+inline typename Reference<T>::Type
 back(T & me)
 {
     SEQAN_CHECKPOINT;
-    return value(me, length(me) - 1);
+    return *(end(me, Standard()) - 1);
+}
+
+#ifdef SEQAN_CXX11_STANDARD
+template <typename T>
+inline SEQAN_FUNC_DISABLE_IF(IsSameType<T, T &>, typename Value<T>::Type)
+back(T && me)
+{
+    SEQAN_CHECKPOINT;
+    return *(end(me, Standard()) - 1);
+}
+
+#endif
+
+//NOTE(h-2): why do we have this?
+template <typename T>
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Reference<T const>::Type)
+backPrev(T const & me)
+{
+    return value(me, length(me) - 2);
+}
+
+template <typename T>
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Reference<T>::Type)
+backPrev(T & me)
+{
+    return value(me, length(me) - 2);
 }
 
 // --------------------------------------------------------------------------
 // Function iter()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn iter
- * @headerfile <seqan/sequence.h>
- * @brief Iterator to the item at the given position in a container.
- *
- * @signature TIterator iter(object, pos[, tag]);
- *
- * @param[in] object The container to get the iterator for.
- * @param[in] pos    The position to get the iterator for.
- * @param[in] tag    The tag to pick the type of the iterator.
- *
- * @return TIterator The resulting iterator.  If <tt>TTag</tt> is the type of <tt>tag</tt> and <tt>TContainer</tt> the
- *                   type of <tt>object</tt> then TIterator is of the type <tt>Iterator&lt;TContainer,
- *                   TTag&gt;::Type</tt>.
- *
- * @section Remarks
- *
- * If <tt>pos</tt> is out of range then the iterator is invalid.
- */
-
-/**
-.Function.iter:
-..cat:Containers
-..class:Class.String
-..summary:Iterator to item at given position.
-..signature:Iterator iter(object, pos [, tag])
-..param.object:A container.
-...type:Class.String
-..param.pos:The position of an item in $object$.
-...metafunction:Metafunction.Position
-..param.tag:An @Tag.Iterator Spec.iterator spec@ tag that specifies the kind of the iterator returned. (optional)
-...default:Given by @Metafunction.DefaultGetIteratorSpec@.
-..returns:An iterator to the item at position $pos$ in $object$. The type is the result of $Iterator<TContainer, TTag>::Type$ where $TContainer$ is the type of $object$ and $TTag$ is the type of $tag$.
-...metafunction:Metafunction.Iterator
-..remarks:
-...text:If $pos$ is out of range, then the behavior of the function is undefined.
-..see:Function.value
-..see:Metafunction.Iterator
-..see:Metafunction.Position
-..include:seqan/sequence.h
- */
 template <typename T, typename TPos>
 inline typename Iterator<T, typename DefaultGetIteratorSpec<T>::Type>::Type
 iter(T & me,
-     TPos pos)
+     TPos const pos)
 {
     SEQAN_CHECKPOINT;
     return iter(me, pos, typename DefaultGetIteratorSpec<T>::Type());
@@ -1172,7 +707,7 @@ iter(T & me,
 template <typename T, typename TPos>
 inline typename Iterator<T const, typename DefaultGetIteratorSpec<T>::Type>::Type
 iter(T const & me,
-     TPos pos)
+     TPos const pos)
 {
     SEQAN_CHECKPOINT;
     return iter(me, pos, typename DefaultGetIteratorSpec<T>::Type());
@@ -1181,57 +716,29 @@ iter(T const & me,
 template <typename T, typename TPos, typename TTag>
 inline typename Iterator<T, Tag<TTag> const>::Type
 iter(T & me,
-     TPos pos,
-     Tag<TTag> const tag_)
+     TPos const pos,
+     Tag<TTag> const &)
 {
     SEQAN_CHECKPOINT;
     SEQAN_ASSERT_LEQ_MSG(pos, static_cast<TPos>(length(me)), "Trying to get an iterator behind a container through iter().");
-    return begin(me, tag_) + pos;
+    return begin(me, Tag<TTag>()) + pos;
 }
 
 template <typename T, typename TPos, typename TTag>
 inline typename Iterator<T const, Tag<TTag> const>::Type
 iter(T const & me,
-     TPos pos,
-     Tag<TTag> const tag_)
+     TPos const pos,
+     Tag<TTag> const &)
 {
     SEQAN_CHECKPOINT;
     SEQAN_ASSERT_LEQ_MSG(pos, static_cast<TPos>(length(me)), "Trying to get an iterator behind a container through iter().");
-    return begin(me, tag_) + pos;
+    return begin(me, Tag<TTag>()) + pos;
 }
 
 // --------------------------------------------------------------------------
 // Function assignValue()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn assignValue
- * @headerfile <seqan/sequence.h>
- * @brief Assign a value of a container at a given position.
- *
- * @signature void assignValue(container, pos, value);
- *
- * @param[in,out] container The container to manipulate.
- * @param[in]     pos       The position of the item in the container to manipulate.
- * @param[in]     value     The value to assign to <tt>container[pos]</tt>.
- */
-
-/**
-.Function.assignValue:
-..cat:Content Manipulation
-..concept:Concept.ContainerConcept
-..signature:assignValue(container, pos, value)
-..param.container:A container.
-...concept:Concept.ContainerConcept
-..param.pos:Position of the item in $container$ to that $value$ is assigned.
-..remarks:If $object$ is a container (that is $pos$ is not specified),
-    the whole content of $object$ is replaced by $value$.
-..remarks.text:
-    If $value$ is not used again after calling this function,
-    then consider to use @Function.moveValue@ that could be faster in some cases instead.
-..include:seqan/sequence.h
-*/
-
 template <typename T, typename TValue, typename TPos>
 inline void
 assignValue(T & me,
@@ -1247,35 +754,17 @@ assignValue(T & me,
 // --------------------------------------------------------------------------
 
 /*!
- * @fn moveValue
+ * @fn ContainerConcept#moveValue
  * @headerfile <seqan/sequence.h>
- * @brief Move a value of a container to a given position.
+ * @brief Move a value into a container at a given position.
  *
- * @signature void assignValue(container, pos, value);
+ * @signature void moveValue(container, pos, value);
  *
  * @param[in,out] container The container to manipulate.
  * @param[in]     pos       The position of the item in the container to manipulate.
  * @param[in,out] value     The value to move to <tt>container[pos]</tt>.
  */
 
-/**
-.Function.moveValue:
-..cat:Content Manipulation
-..concept:Concept.ContainerConcept
-..signature:moveValue(container, pos, value)
-..param.object:
-...concept:Concept.ContainerConcept
-..param.container:A container.
-...concept:Concept.ContainerConcept
-..param.pos:Position of the item in $container$ to that $value$ is moved to.
-..remarks:If $object$ is a container (that is $pos$ is not specified),
-the whole content of $object$ is replaced by $value$.
-..remarks.text:
-    This function possibly clears $value$.
-    If $value$ should be used further, consider to use @Function.assignValue@ instead.
-..include:seqan/sequence.h
-*/
-
 template <typename T, typename TValue, typename TPos>
 inline void
 moveValue(T & me,
@@ -1300,42 +789,9 @@ moveValue(T const & me,
 // Function length()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn length
- * @headerfile <seqan/sequence.h>
- * @brief Return the number of items in a container.
- *
- * @signature TSize length(object);
- *
- * @param[in] object The container to query.
- *
- * @return TSize The resulting size of the container.
- *
- * @section Remarks
- *
- * The length of a sequence can never exceed its capacity.
- *
- * @see capacity
- */
-
-/**
-.Function.length:
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:The number of items/characters.
-..signature:Size length(object)
-..param.object:A container.
-...concept:Concept.ContainerConcept
-..returns:The number of items/characters in $object$.
-...metafunction:Metafunction.Size
-..remarks.text:The length of a sequence can never exceed it's capacity.
-..see:Function.capacity
-..include:seqan/sequence.h
-*/
-
 //* ???Anti Default Sequences
 template <typename T>
-inline typename Size<T>::Type
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, typename Size<T>::Type)
 length(T const & /*me*/)
 {
     SEQAN_CHECKPOINT;
@@ -1348,39 +804,22 @@ length(T const & /*me*/)
 // --------------------------------------------------------------------------
 
 /*!
- * @fn capacity
+ * @fn StringConcept#capacity
  * @headerfile <seqan/sequence.h>
- * @brief Return the capacity of a container.
+ * @brief Returns the capacity of a sequence.
  *
- * @signature TSize capacity(object);
+ * @signature TSize capacity(seq);
  *
- * @param[in] object The container to query for its capacity.
+ * @param[in] seq The sequence to query for its capacity.
  *
- * @return TSize Returns the size of the container.
- *
- * @section Remarks
+ * @return TSize Returns the capacity of the sequence.  <tt>TSize</tt> is the result of
+ *               <tt>Size&lt;TSequence&gt;::type</tt> where <tt>TSequence</tt> is the type of <tt>seq</tt>.
  *
  * The size of a sequence can never exceed its capacity but some container support resizing of the capacity.  Some
  * functions do that implicitely if they are called with a suitable @link OverflowStrategyTags tag @endlink.  The
  * function reserve can be used to change the capacity explicitely.
  */
 
-/**
-.Function.capacity:
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:The maximal length.
-..signature:Size capacity(object)
-..param.object:A container.
-...remarks: If $object$ cannot be converted to one of these types, the function returns 1.
-..returns:The maximal number of items/characters that can be stored in $object$.
-...metafunction:Metafunction.Size
-..remarks.text:The size of a sequence can never exceed it's capacity, but some containers support
-resizing of the capacity.
-Some functions do that implicitely if they are called with a suitable @Tag.Overflow Strategy.overflow strategy@.
-The function @Function.reserve@ can be used to change the capacity explicitely.
-..include:seqan/sequence.h
-*/
 template <typename T>
 inline SEQAN_HOST_DEVICE typename Size<T const>::Type
 capacity(T const & me)
@@ -1393,33 +832,8 @@ capacity(T const & me)
 // Function empty()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn empty
- * @headerfile <seqan/sequence.h>
- * @brief Test a container for being empty.
- *
- * @signature bool empty(object);
- *
- * @param[in] object The container to query for being empty.
- *
- * @return bool <tt>true</tt> or <tt>false</tt>, depending on whether <tt>object</tt> is empty or not.
- */
-
-/**
-.Function.empty:
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:Test a container for being empty.
-..signature:bool empty(object)
-..param.object:A container.
-..returns:$true$ if $object$ contains no elements, otherwise $false$.
-..remarks.text:$empty(x)$ is guaranteed to be at least as fast as $length(me) == 0$,
-but can be significantly faster in some cases.
-..see:Function.length
-..include:seqan/sequence.h
-*/
 template <typename T>
-SEQAN_HOST_DEVICE inline bool
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, bool)
 empty(T const & me)
 {
     SEQAN_CHECKPOINT;
@@ -1454,35 +868,19 @@ _computeSizeForCapacity(T const & /*me*/,
 // --------------------------------------------------------------------------
 
 /*!
- * @fn computeGenerousCapacity
+ * @fn StringConcept#computeGenerousCapacity
  * @headerfile <seqan/sequence.h>
  * @brief Capacity for generous expansion.
  *
- * @signature TSize computeGenerousCapacity(container, capacity);
+ * @signature TSize computeGenerousCapacity(seq, capacity);
  *
- * @param[in,out] container The container to compute the generous capacity for.
- * @param[in      capacity  The minimal required capacity.
+ * @param[in,out] seq       The sequence to compute the generous capacity for.
+ * @param[in]     capacity  The minimal required capacity.
  *
  * @return TSize A value larger than <tt>capacity</tt> that should be used as the new capacity for <tt>container</tt>
  *               when it is expanded using the <tt>Generous</tt> overflow strategy.
  */
 
-// TODO(holtgrew): This is a helper and should conceptually not be in the "interface" header.
-/**
-.Function.computeGenerousCapacity:
-..hidefromindex
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:Capacity for generous expansion.
-..signature:Size computeGenerousCapacity(container, capacity)
-..param.container:A container that should be expanded.
-..param.capacity:Minimal capacity needed.
-..returns:A value larger than $capacity$ that should be used as new capacity for $container$
-when it is expanded using the @Tag.Overflow Strategy."Generous" overflow strategy@.
-...metafunction:Metafunction.Size
-..see:Tag.Overflow Strategy
-..include:seqan/sequence.h
-*/
 template <typename T, typename TSize>
 inline TSize
 computeGenerousCapacity(T const & /*me*/,
@@ -1525,43 +923,16 @@ _storageUpdated(T const & me)
 // --------------------------------------------------------------------------
 
 template<typename TTarget, typename TSource>
-inline void
-assign(TTarget & target,
-       TSource & source,
-       typename Size<TTarget>::Type limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
-}
-
-template<typename TTarget, typename TSource>
-inline void
-assign(TTarget const & target,
-       TSource & source,
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<TTarget>::Type> >, void)
+assign(TTarget SEQAN_FORWARD_ARG target,
+       TSource SEQAN_FORWARD_CARG source,
        typename Size<TTarget>::Type limit)
 {
     SEQAN_CHECKPOINT;
-    assign(target, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
-}
-
-template<typename TTarget, typename TSource>
-inline void
-assign(TTarget & target,
-       TSource const & source,
-       typename Size<TTarget>::Type limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
-}
-
-template<typename TTarget, typename TSource>
-inline void
-assign(TTarget const & target,
-       TSource const & source,
-       typename Size<TTarget>::Type limit)
-{
-    SEQAN_CHECKPOINT;
-    assign(target, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
+    assign(SEQAN_FORWARD(TTarget, target),
+           SEQAN_FORWARD(TSource, source),
+           limit,
+           typename DefaultOverflowImplicit<TTarget>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -1569,57 +940,19 @@ assign(TTarget const & target,
 // --------------------------------------------------------------------------
 
 /*!
- * @fn append
+ * @fn ContainerConcept#append
  * @headerfile <seqan/sequence.h>
  * @brief Concatenate a container to another.
  *
  * @signature void append(target, source);
  *
- * @param[in,out] target The container to append <tt>source</tt> to.
- * @param[in]     source This container will be appended to <tt>source</tt>.
+ * @param[in,out] target The @link ContainerConcept container @endlink to append <tt>source</tt> to.
+ * @param[in]     source This @link ContainerConcept container @endlink will be appended to <tt>source</tt>.
  */
 
-/**
-.Function.append
-..summary:Concatenate two containers.
-..description:This function allows to append the contents of one container to another.
-...notes:Appending a value/entry to a container can be done using @Function.appendValue@.
-..cat:Content Manipulation
-..concept:Concept.ContainerConcept
-..signature:append(target, source [, limit] [,resize_tag])
-..param.target: A container $source$ is append to.
-..param.source: A container that is append to $target$.
-...remarks:The function does not modify this container.
-..param.limit: The maximal length of $target$ after the operation. (optional)
-..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
-..remarks:The result of this operation is stored in $target$.
-..see:Function.assign
-..include:seqan/sequence.h
-*/
-
-template<typename TTarget, typename TSource>
-inline void
-append(TTarget & target,
-       TSource & source)
-{
-    SEQAN_CHECKPOINT;
-    append(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
-}
-
-template<typename TTarget, typename TSource>
-inline void
-append(TTarget const & target,
-       TSource & source)
-{
-    SEQAN_CHECKPOINT;
-    append(target, source, typename DefaultOverflowImplicit<TTarget const>::Type());
-}
-
 template<typename TTarget, typename TSource>
 inline void
-append(TTarget & target,
+append(TTarget SEQAN_FORWARD_ARG target,
        TSource const & source)
 {
     SEQAN_CHECKPOINT;
@@ -1628,59 +961,20 @@ append(TTarget & target,
 
 template<typename TTarget, typename TSource>
 inline void
-append(TTarget const & target,
-       TSource const & source)
-{
-    SEQAN_CHECKPOINT;
-    append(target, source, typename DefaultOverflowImplicit<TTarget const>::Type());
-}
-
-template<typename TTarget, typename TSource>
-inline void
-append(TTarget & target,
-       TSource & source,
-       typename Size<TTarget>::Type limit)
-{
-    SEQAN_CHECKPOINT;
-    append(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
-}
-
-template<typename TTarget, typename TSource>
-inline void
-append(TTarget const & target,
-       TSource & source,
-       typename Size<TTarget>::Type limit)
-{
-    SEQAN_CHECKPOINT;
-    append(target, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
-}
-
-template<typename TTarget, typename TSource>
-inline void
-append(TTarget & target,
+append(TTarget SEQAN_FORWARD_ARG target,
        TSource const & source,
-       typename Size<TTarget>::Type limit)
+       typename Size<TTarget>::Type const limit)
 {
     SEQAN_CHECKPOINT;
     append(target, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
 }
 
-template<typename TTarget, typename TSource>
-inline void
-append(TTarget const & target,
-       TSource const & source,
-       typename Size<TTarget>::Type limit)
-{
-    SEQAN_CHECKPOINT;
-    append(target, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
-}
-
 // --------------------------------------------------------------------------
 // Function appendValue()
 // --------------------------------------------------------------------------
 
 /*!
- * @fn appendValue
+ * @fn ContainerConcept#appendValue
  * @headerfile <seqan/sequence.h>
  * @brief Append a value to a container.
  *
@@ -1692,39 +986,12 @@ append(TTarget const & target,
  *                       <tt>target</tt>.
  */
 
-/**
-.Function.appendValue:
-..signature:appendValue(target, value [, resize_tag])
-..description:This function allows to append an element/value to a container.
-...notes:Appending the elements of a container to another container can be done using @Function.append@.
-..cat:Content Manipulation
-..concept:Concept.ContainerConcept
-..summary:Appends a value to a container.
-..param.target:A container.
-..param.value:Value that is appended to $target$.
-..param.resize_tag:
-..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
-..include:seqan/sequence.h
-*/
-
-template <typename T, typename TValue>
-inline void
-appendValue(T & me,
-            TValue const & _value)
-{
-    SEQAN_CHECKPOINT;
-    appendValue(me, _value, typename DefaultOverflowImplicit<T>::Type());
-}
-
 template <typename T, typename TValue>
 inline void
-appendValue(T const & me,
-            TValue const & _value)
+appendValue(T SEQAN_FORWARD_ARG me,
+            TValue SEQAN_FORWARD_CARG _value)
 {
-    SEQAN_CHECKPOINT;
-    appendValue(me, _value, typename DefaultOverflowImplicit<T const>::Type());
+    appendValue(SEQAN_FORWARD(T, me), SEQAN_FORWARD(TValue, _value), typename DefaultOverflowImplicit<T>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -1732,74 +999,48 @@ appendValue(T const & me,
 // --------------------------------------------------------------------------
 
 /*!
- * @fn insert
+ * @fn StringConcept#insert
  * @headerfile <seqan/sequence.h>
- * @brief Inserts a sequence into a container.
+ * @brief Inserts a sequence into another sequence.
  *
- * @signature void insert(target, pos, insertSeq[, tag]);
+ * @signature void insert(seq, pos, src[, tag]);
  *
- * @param[in,out] target    The container to insert elements into.
- * @param[in]     pos       The position to start inserting at.
- * @param[in]     insertSeq The sequence to insert at start.
- * @param[[in]    tag       The resize tag, defaults to what <tt>OverflowStrategyImplicit</tt> returns.
+ * @param[in,out] seq The sequence to insert element sinto.
+ * @param[in]     pos The position to start inserting at.
+ * @param[in]     src The sequence to insert at pos.
+ * @param[in]     tag The resize tag, defaults to what <tt>OverflowStrategyImplicit</tt> returns.
  */
 
-/**
-.Function.insert:
-..cat:Content Manipulation
-..summary:Inserts a sequence into a container.
-..signature:insert(target, pos, insertSeq [, resize_tag])
-..concept:Concept.ContainerConcept
-..param.target:The container
-..param.pos:Position within $target$ at which $insertSeq$ is to be inserted.
-..param.insertSeq:Sequence that will be inserted into $target$.
-..param.resize_tag:Strategy that is applied if $target$ has not enough capacity to store the complete content.
-...type:Tag.Overflow Strategy
-..see:Function.insertValue
-..see:Function.append
-..include:seqan/sequence.h
-*/
-
-template <typename T, typename TPosition, typename TSeq, typename TExpand>
-inline void
-insert(T & me,
-       TPosition pos,
-       TSeq const & insertSeq,
-       Tag<TExpand>)
-{
-    SEQAN_CHECKPOINT;
-    replace(me, pos, pos, insertSeq, Tag<TExpand>());
-}
-
 template <typename T, typename TPosition, typename TSeq, typename TExpand>
-inline void
-insert(T const & me,
-       TPosition pos,
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, void)
+insert(T SEQAN_FORWARD_ARG me,
+       TPosition const pos,
        TSeq const & insertSeq,
-       Tag<TExpand>)
+       Tag<TExpand> const &)
 {
     SEQAN_CHECKPOINT;
-    replace(me, pos, pos, insertSeq, Tag<TExpand>());
+    replace(SEQAN_FORWARD(T, me), pos, pos, insertSeq, Tag<TExpand>());
 }
 
 template <typename T, typename TPosition, typename TSeq>
 inline void
-insert(T & me,
-       TPosition pos,
+insert(T SEQAN_FORWARD_ARG me,
+       TPosition const pos,
        TSeq const & insertSeq)
 {
     SEQAN_CHECKPOINT;
-    replace(me, pos, pos, insertSeq, typename DefaultOverflowImplicit<T>::Type());
+    insert(SEQAN_FORWARD(T, me), pos, insertSeq, typename DefaultOverflowImplicit<T>::Type());
 }
 
-template <typename T, typename TPosition, typename TSeq>
+template <typename T,
+          typename TSource>
 inline void
-insert(T const & me,
-       TPosition pos,
-       TSeq const & insertSeq)
+insert(T SEQAN_FORWARD_ARG me,
+       typename Size<typename RemoveReference<T>::Type>::Type const pos,
+       TSource const & source,
+       typename Size<TSource>::Type const limit)
 {
-    SEQAN_CHECKPOINT;
-    replace(me, pos, pos, insertSeq, typename DefaultOverflowImplicit<T const>::Type());
+    insert(me, pos, source, limit, typename DefaultOverflowImplicit<T const>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -1807,52 +1048,26 @@ insert(T const & me,
 // --------------------------------------------------------------------------
 
 /*!
- * @fn insertValue
+ * @fn StringConcept#insertValue
  * @headerfile <seqan/sequence.h>
- * @brief Inserts an element into a container.
+ * @brief Inserts an element into a sequence.
  *
- * @signature void insertValue(target, pos, val[, tag]);
+ * @signature void insertValue(seq, pos, val[, tag]);
  *
- * @param[in,out] target    The container to insert element into.
- * @param[in]     pos       The position to insert at.
- * @param[in]     val       The value to insert at start.
- * @param[[in]    tag       The resize tag, defaults to what <tt>OverflowStrategyImplicit</tt> returns.
+ * @param[in,out] seq  The @link StringConcept sequence @endlink to insert element into.
+ * @param[in]     pos  The position to insert at.
+ * @param[in]     val  The value to insert at <tt>pos</tt> into <tt>seq<tt/>.
+ * @param[in]     tag  The resize tag, defaults to what <tt>OverflowStrategyImplicit</tt> returns.
  */
 
-/**
-.Function.insertValue:
-..cat:Content Manipulation
-..summary:Inserts a single value into a container.
-..signature:insertValue(target, pos, value [, resize_tag])
-..concept:Concept.ContainerConcept
-..param.target:The container
-..param.pos:Position within $target$ at which $value$ is to be inserted.
-..param.value:Value that will be inserted into $target$.
-..param.resize_tag:Strategy that is applied if $target$ has not enough capacity to store the complete content.
-...type:Tag.Overflow Strategy
-..see:Function.insert
-..see:Function.appendValue
-..include:seqan/sequence.h
-*/
-
 template <typename T, typename TPosition, typename TValue>
 inline void
-insertValue(T & me,
-            TPosition pos,
-            TValue const & _value)
+insertValue(T SEQAN_FORWARD_ARG me,
+            TPosition const pos,
+            TValue SEQAN_FORWARD_CARG _value)
 {
     SEQAN_CHECKPOINT;
-    insertValue(me, pos, _value, typename DefaultOverflowImplicit<T>::Type());
-}
-
-template <typename T, typename TPosition, typename TValue>
-inline void
-insertValue(T const & me,
-            TPosition pos,
-            TValue const & _value)
-{
-    SEQAN_CHECKPOINT;
-    insertValue(me, pos, _value, typename DefaultOverflowImplicit<T const>::Type());
+    insertValue(SEQAN_FORWARD(T, me), pos, SEQAN_FORWARD(TValue, _value), typename DefaultOverflowImplicit<T>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -1860,13 +1075,13 @@ insertValue(T const & me,
 // --------------------------------------------------------------------------
 
 /*!
- * @fn replace
+ * @fn StringConcept#replace
  * @headerfile <seqan/sequence.h>
- * @brief Replaces a part of a container with another container.
+ * @brief Replaces a part of a sequence with another sequence.
  *
  * @signature void replace(target, posBegin, posEnd, source[, limit][, resizeTag]);
  *
- * @param[in,out] target    The container to modify.
+ * @param[in,out] target    The sequence to modify.
  * @param[in]     posBegin  The begin position of the range to replace.
  * @param[in]     posEnd    The end position of the range to replace.
  * @param[in]     source    The source sequence to replace <tt>[posBegin, posEnd)</tt> with.
@@ -1875,112 +1090,34 @@ insertValue(T const & me,
  *                          returns.
  */
 
-/**
-.Function.replace:
-..summary:Replaces a part of a container with another container.
-..cat:Content Manipulation
-..concept:Concept.ContainerConcept
-..signature:replace(target, pos_begin, pos_end, source [, limit] [,resize_tag])
-..param.target: A container that is modified.
-..param.pos_begin: Begin of replaced area.
-...text:The first position in $target$ of the area that is replaced by $source$.
-..param.pos_end: End of replaced area.
-...text:The position behind the last position in $target$ of the area that is replaced by $source$.
-..param.source: A container that is inserted into $target$.
-...remarks:The function does not modify this container.
-..param.limit: The maximal length of $target$ after the operation. (optional)
-..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
-..see:Function.assign
-..see:Function.append
-..remarks.text:Some compilers have difficulties if $pos_begin$ and $pos_end$ are both 0, since 0 can be
-both a position or an iterator. The workaround is to convert at least one of these arguments
-explicite to the position or to the interator type.
-..include:seqan/sequence.h
-*/
 template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
 inline void
-replace(TTarget & target,
-        TPositionBegin pos_begin,
-        TPositionEnd pos_end,
-        TSource & source)
-{
-    replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit<TTarget>::Type());
-}
-
-template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
-inline void
-replace(TTarget const & target,
-        TPositionBegin pos_begin,
-        TPositionEnd pos_end,
-        TSource & source)
-{
-    replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit<TTarget const>::Type());
-}
-
-template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
-inline void
-replace(TTarget & target,
-        TPositionBegin pos_begin,
-        TPositionEnd pos_end,
+replace(TTarget SEQAN_FORWARD_ARG target,
+        TPositionBegin const pos_begin,
+        TPositionEnd const pos_end,
         TSource const & source)
 {
-    replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit<TTarget>::Type());
-}
-
-template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
-inline void
-replace(TTarget const & target,
-        TPositionBegin pos_begin,
-        TPositionEnd pos_end,
-        TSource const & source)
-{
-    replace(target, pos_begin, pos_end, source, typename DefaultOverflowImplicit<TTarget const>::Type());
-}
-
-template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
-inline void
-replace(TTarget & target,
-        TPositionBegin pos_begin,
-        TPositionEnd pos_end,
-        TSource & source,
-        typename Size<TTarget>::Type limit)
-{
-    replace(target, pos_begin, pos_end, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
+    replace(SEQAN_FORWARD(TTarget, target),
+            pos_begin,
+            pos_end,
+            source,
+            typename DefaultOverflowImplicit<TTarget>::Type());
 }
 
 template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
 inline void
-replace(TTarget const & target,
-        TPositionBegin pos_begin,
-        TPositionEnd pos_end,
-        TSource & source,
-        typename Size<TTarget>::Type limit)
-{
-    replace(target, pos_begin, pos_end, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
-}
-
-template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
-inline void
-replace(TTarget & target,
-        TPositionBegin pos_begin,
-        TPositionEnd pos_end,
+replace(TTarget SEQAN_FORWARD_ARG target,
+        TPositionBegin const pos_begin,
+        TPositionEnd const pos_end,
         TSource const & source,
-        typename Size<TTarget>::Type limit)
+        typename Size<TTarget>::Type const limit)
 {
-    replace(target, pos_begin, pos_end, source, limit, typename DefaultOverflowImplicit<TTarget>::Type());
-}
-
-template<typename TTarget, typename TPositionBegin, typename TPositionEnd, typename TSource>
-inline void
-replace(TTarget const & target,
-        TPositionBegin pos_begin,
-        TPositionEnd pos_end,
-        TSource const & source,
-        typename Size<TTarget>::Type limit)
-{
-    replace(target, pos_begin, pos_end, source, limit, typename DefaultOverflowImplicit<TTarget const>::Type());
+    replace(SEQAN_FORWARD(TTarget, target),
+            pos_begin,
+            pos_end,
+            source,
+            limit,
+            typename DefaultOverflowImplicit<TTarget>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -1991,17 +1128,17 @@ replace(TTarget const & target,
 
 template <typename T, typename TSize, typename TExpand>
 inline typename Size<T>::Type
-_capacityReturned(T & me,
-                  TSize,
-                  Tag<TExpand>)
+_capacityReturned(T const & me,
+                  TSize const,
+                  Tag<TExpand> const &)
 {
     return capacity(me);
 }
 
 template <typename T, typename TSize>
 inline typename Size<T>::Type
-_capacityReturned(T &,
-                  TSize new_capacity,
+_capacityReturned(T const &,
+                  TSize const new_capacity,
                   Insist const & )
 {
     return new_capacity;
@@ -2012,145 +1149,79 @@ _capacityReturned(T &,
 // --------------------------------------------------------------------------
 
 /*!
- * @fn reserve
- * @headerfile <seqan/sequence.h>
  * @fn String#reserve
  * @brief Increases the capacity.
- * 
- * @signature TSize reserve(object, new_capacity[, tag]);
- * 
- * @param[in,out] object      A container.
- * @param[in]     newCapacity The new capacity <tt>object</tt> will get.
+ *
+ * @signature TSize reserve(str, new_capacity[, tag]);
+ *
+ * @param[in,out] str         The String to reserve space in.
+ * @param[in]     newCapacity The new capacity <tt>str</tt> will get.
  * @param[in]     tag         Specifies the strategy that is applied for changing the capacity.
- * 
+ *
  * @return TSize The amount of the requested capacity that was available.  That is the function returns the minimum of
  *               <tt>newCapacity</tt> and <tt>capacity(me)</tt>.
- * 
+ *
  * This function allows to increase the capacity but not the length of a container.
- * 
- * Use @link resize @endlink if you want to change the size of a container.
- * 
+ *
+ * Use @link StringConcept#resize @endlink if you want to change the size of a container.
+ *
  * @section Remarks
- * 
- * For std::basic_string STL Adaptions, <tt>reserve</tt> is only guaranteed to have the specified behaviour with
- * <tt>Insist</tt> and <tt>Generous</tt>.
- * 
- * For std::vector STL Adaptions, <tt>reserve</tt> is only guaranteed to have the specified behaviour with
- * <tt>Insist</tt> and <tt>Generous</tt>.
- * 
+ *
  * At the end of the operation, <tt>capacity(me)</tt> can be larger than <tt>new_capacity</tt>.  If
  * <tt>new_capacity</tt> is smaller than <tt>capacity(me)</tt> at the beginning of the operation, the operation need not
  * to change the capacity at all.
- * 
+ *
  * This operation does not changes the content of <tt>object</tt>.
- * 
+ *
  * This operation may invalidate iterators of <tt>object</tt>.
  */
 
-/**
-.Function.reserve:
-..cat:Containers
-..summary:Increases the capacity.
-..description:This function allows to increase the capacity but not the length of a container.
-...note:Use @Function.resize@ if you want to change the size of a container.
-..concept:Concept.ContainerConcept
-..signature:Size reserve(object, new_capacity [, resize_tag])
-..param.object: A container.
-..param.new_capacity: The new capacity $object$ will get.
-..param.resize_tag: Specifies the strategy that is applied for changing the capacity. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowExplicit@.
-..returns:The amount of the requested capacity that was available.
-That is the function returns the minimum of $new_capacity$ and $capacity(me)$.
-...metafunction:Metafunction.Size
-..remarks:At the end of the operation, $capacity(me)$ can be larger than $new_capacity$.
-If $new_capacity$ is smaller than $capacity(me)$ at the beginning of the operation,
-the operation need not to change the capacity at all.
-..remarks:This operation does not changes the content of $object$.
-...note:This operation may invalidate iterators of $object$.
-..see:Function.capacity
-..include:seqan/sequence.h
-*/
-
-template <typename T, typename TSize, typename TExpand>
+template <typename T,
+          typename TSize,
+          typename TExpand>
 inline typename Size<T>::Type
-reserve(T & me,
-        TSize const & new_capacity,
-        Tag<TExpand> tag)
+reserve(T SEQAN_FORWARD_ARG me,
+        TSize const new_capacity,
+        Tag<TExpand> const &)
 {
     SEQAN_CHECKPOINT;
-    return _capacityReturned(me, new_capacity, tag);
+    return _capacityReturned(SEQAN_FORWARD(T, me), new_capacity, Tag<TExpand>());
 }
 
-template <typename T, typename TSize>
+template <typename T,
+          typename TSize>
 inline typename Size<T>::Type
-reserve(T & me,
-        TSize const & new_capacity)
+reserve(T SEQAN_FORWARD_ARG me,
+        TSize const new_capacity)
 {
     SEQAN_CHECKPOINT;
-    return reserve(me, new_capacity, typename DefaultOverflowExplicit<T>::Type());
+    return reserve(SEQAN_FORWARD(T, me), new_capacity, typename DefaultOverflowExplicit<T>::Type());
 }
 
 // --------------------------------------------------------------------------
 // Function resize()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn resize
- * @headerfile <seqan/sequence.h>
- * @brief Resizes a container.
- *
- * If the new length exceeds the old length then the new elements are filled with copies of <tt>x</tt>.
- *
- * @signature TSize resize(object, newLength[, x[, tag]]);
- *
- * @param[in,out] object  The container to resize.
- * @param[in]     newSize The new container size.
- * @param[in]     x       The value to use as the prototype when increasing the size.
- * @param[in]     tag     The strategy to apply if the capacity of <tt>object</tt> is less than <tt>newLength</tt..
- *
- * @return TSize The new length <tt>length(object)</tt>.
- */
-
-/**
-.Function.resize:
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:Resizes a container. If the new length exceeds the old length the new elements are filled with copies of $value$.
-..signature:Size resize(object, newLength [,value [,resizeTag]])
-..param.object: A container.
-...type:Class.String
-..param.newLength: The new length $object$ will get.
-..param.value: Value that is copied if new items are created in $object$.
-...remarks:If the $value$ argument is omitted, the items are not initialized if @Metafunction.IsSimple@ returns `False`.
-..param.resizeTag: Specifies the strategy that is applied if the capacity of $object$ is less than $newLength$. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowExplicit@.
-..returns:The new length $length(object)$.
-...metafunction:Metafunction.Size
-..remarks:This function can be used both for expanding and for shrinking $object$.
-..see:Function.length
-..see:Function.reserve
-..include:seqan/sequence.h
-*/
-
-template <typename T, typename TSize>
+template <typename T,
+          typename TSize>
 inline typename Size<T>::Type
-resize(T & me,
-       TSize new_length)
+resize(T SEQAN_FORWARD_ARG me,
+       TSize const new_length)
 {
     SEQAN_CHECKPOINT;
-    return resize(me, new_length, typename DefaultOverflowExplicit<T>::Type());
+    return resize(SEQAN_FORWARD(T, me), new_length, typename DefaultOverflowExplicit<T>::Type());
 }
 
-template <typename T, typename TSize, typename TValue>
+template <typename T,
+          typename TSize,
+          typename TValue>
 inline typename Size<T>::Type
-resize(T & me,
-       TSize new_length,
+resize(T SEQAN_FORWARD_ARG me,
+       TSize const new_length,
        TValue const & val)
 {
     SEQAN_CHECKPOINT;
-    return resize(me, new_length, val, typename DefaultOverflowExplicit<T>::Type());
+    return resize(SEQAN_FORWARD(T, me), new_length, val, typename DefaultOverflowExplicit<T>::Type());
 }
 
 // --------------------------------------------------------------------------
@@ -2163,10 +1234,10 @@ resize(T & me,
  * @fn String#resizeSpace
  * @headerfile <seqan/sequence.h>
  * @brief Makes free space in container
- * 
- * @signature TSize resizeSpace(object, size, posBegin, posEnd [, limit][, resizeTag]);
- * 
- * @param[in,out] object    The container. Types: String
+ *
+ * @signature TSize resizeSpace(str, size, posBegin, posEnd [, limit][, resizeTag]);
+ *
+ * @param[in,out] str       The String to modify.
  * @param[in]     size      Number of characters that should be freed.
  * @param[in]     posEnd    Position behind the last item in <tt>object</tt> that is to be destroyed.  If
  *                          <tt>posEnd == posBegin</tt>, no item in <tt>object</tt> will be destroyed.
@@ -2174,33 +1245,11 @@ resize(T & me,
  * @param[in]     limit     Maximal length <tt>object</tt> can get after this operation. (optional)
  * @param[in]     resizeTag Strategy that is applied if <tt>object</tt> has not enough capacity to store the
  *                          complete content. (optional)
- * 
+ *
  * @return TSize The number of free characters.Depeding on resizeTag, this could be <tt>size</tt> or less than
  *               <tt>size</tt> if <tt>object</tt> has not enough <tt>capacity</tt>.
  */
 
-/**
-.Function.resizeSpace:
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:Makes free space in container
-..signature:Size resizeSpace(object, size, pos_begin, pos_end [, limit] [, resize_tag])
-..param.object:The container.
-...type:Class.String
-..param.size:Number of characters that should be freed.
-..param.pos_begin:Position of the first item in $object$ that is to be destroyed.
-..param.pos_end:Position behind the last item in $object$ that is to be destroyed.
-...remarks:If $pos_end == pos_begin$, no item in $object$ will be destroyed.
-..param.limit:Maximal length $object$ can get after this operation. (optional)
-..param.resize_tag:Strategy that is applied if $object$ has not enough capacity to store the complete content. (optional)
-...metafunction:Metafunction.DefaultOverflowExplicit
-..returns:The number of free characters.
-...metafunction:Metafunction.Size
-...remarks:Depeding on the @Tag.Overflow Strategy.overflow strategy@ specified by $resize_tag$,
-this could be $size$ or less than $size$ if $object$ has not enough @Function.capacity@.
-..include:seqan/sequence.h
-*/
-
 template<typename T, typename TSize, typename TBeginPosition, typename TEndPosition>
 inline TSize
 resizeSpace(T & me,
@@ -2228,37 +1277,8 @@ resizeSpace(T & me,
 // Function erase()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn erase
- * @headerfile <seqan/sequence.h>
- * @brief Erases a part of a container.
- *
- * @signature void erase(object, pos[, posEnd]);
- *
- * @param[in,out] object The container to erase elements of.
- * @param[in]     pos    The first position to erase.
- * @param[in]     posEnd The last position to erase, defaults to <tt>pos + 1</tt>.
- */
-
-/**
-.Function.erase:
-..summary:Erases a part of a container
-..cat:Containers
-..concept:Concept.ContainerConcept
-..signature:erase(object, pos [, pos_end])
-..param.object:The container.
-...type:Class.String
-..param.pos:Position of the first item in $object$ that is to be destroyed.
-..param.pos_end:Position behind the last item in $object$ that is to be destroyed. (optional)
-...default:$pos + 1$
-...remarks:If $pos_end$ is omitted, only one element in $object$ at position $pos$ is destroyed.
-..remarks:$erase(object, pos, pos_end)$ is semantically the same as @Function.resizeSpace.resizeSpace(object, 0, pos, pos_end)@.
-..see:Function.eraseBack
-..include:seqan/sequence.h
-*/
-
 template<typename T, typename TBeginPosition, typename TEndPosition>
-inline void
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, void)
 erase(T & me,
       TBeginPosition pos,
       TEndPosition pos_end)
@@ -2268,7 +1288,7 @@ erase(T & me,
 }
 
 template<typename T, typename TPosition>
-inline void
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, void)
 erase(T & me,
       TPosition pos)
 {
@@ -2279,7 +1299,7 @@ erase(T & me,
 // For segments, we also have to define the version for const-containers.
 
 template<typename T, typename TBeginPosition, typename TEndPosition>
-inline void
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, void)
 erase(T const & me,
       TBeginPosition pos,
       TEndPosition pos_end)
@@ -2289,7 +1309,7 @@ erase(T const & me,
 }
 
 template<typename T, typename TPosition>
-inline void
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, void)
 erase(T const & me,
       TPosition pos)
 {
@@ -2301,40 +1321,13 @@ erase(T const & me,
 // Function eraseBack()
 // --------------------------------------------------------------------------
 
-/*!
- * @fn eraseBack
- * @headerfile <seqan/sequence.h>
- * @brief Deletes the last item of a container and reduces its size by 1.  The container must have a size greater than
- *        or equal to 1.
- *
- * @signature void eraseBack(object);
- *
- * @param[in,out] object The container to modify.
- *
- * @section Remarks
- *
- * This is equivalent to <tt>erase(object, length(object) - 1)</tt>.
- */
-
-/**
-.Function.eraseBack:
-..summary:Deletes the last item of a container and reduces its size by 1.  The container must have a size greater than or equal to 1.
-..cat:Containers
-..concept:Concept.ContainerConcept
-..signature:eraseBack(object)
-..param.object:The container.
-...type:Class.String
-..remarks:$erase(object)$ is semantically the same as @Function.erase.erase(me, length(me) - 1)@.
-..see:Function.erase
-..include:seqan/sequence.h
-*/
-
 template <typename T>
-inline void eraseBack(T & me)
+inline SEQAN_FUNC_DISABLE_IF(Is<StlContainerConcept<typename RemoveReference<T>::Type> >, void)
+eraseBack(T & me)
 {
     SEQAN_CHECKPOINT;
     SEQAN_ASSERT_GT_MSG(length(me), 0u, "String must have more than 0 characters in eraseBack()!");
-	resize(me, length(me) - 1);
+    resize(me, length(me) - 1);
 }
 
 // --------------------------------------------------------------------------
@@ -2351,22 +1344,6 @@ inline void eraseBack(T & me)
  * @param[in] cont The container to shrink.
  */
 
-/**
-.Function.shrinkToFit:
-..cat:Containers
-..concept:Concept.ContainerConcept
-..summary:Resizes container to minimum capacity
-..signature:shrinkToFit(object)
-..param.object: A container.
-...type:Concept.ContainerConcept
-..remarks
-...text:$shrinkToFit(object)$ is equivalent to $reserve(object, length(object), Exact())$.
-..see:Function.capacity
-..see:Function.length
-..see:Function.reserve
-..include:seqan/sequence.h
-*/
-
 template <typename T>
 inline void
 shrinkToFit(T & me)
diff --git a/seqan/sequence/sequence_lexical.h b/seqan/sequence/sequence_lexical.h
index b3387d2..da42566 100644
--- a/seqan/sequence/sequence_lexical.h
+++ b/seqan/sequence/sequence_lexical.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -63,17 +63,6 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature typedef Tag<TagPrefixGreater_> const TagPrefixGreater;
  */
 
-/**
-.Tag.Prefix Order:
-..cat:Sequences
-..summary:Specify whether less-than or greather-than comparison is meant.
-..tag.TagPrefixLess:A prefix is smaller.
-...text:For example: $"abc" < "abcde"$.
-..tag.TagPrefixGreater:A prefix is greater.
-...text:For example: $"abc" > "abcde"$.
-..remarks:The default for all comparison functions is $TagPrefixLess$.
-..include:seqan/sequence.h
-*/
 struct TagPrefixLess_ {};
 typedef Tag<TagPrefixLess_> const TagPrefixLess;
 
@@ -93,20 +82,10 @@ typedef Tag<TagPrefixGreater_> const TagPrefixGreater;
  * @return Type The prefix order tag type of T, see @link PrefixOrderTags @endlink.
  */
 
-/**
-.Metafunction.DefaultPrefixOrder:
-..hidefromindex
-..summary:The default prefix order.
-..signature:DefaultPrefixOrder<T>::Type
-..param.T:Type for which the prefix order is determined.
-..returns.param.Type:Prefix order tag for type of $T$.
-..see:Tag.Prefix Order
-..include:seqan/sequence.h
-*/
 template <typename T>
 struct DefaultPrefixOrder
 {
-	typedef TagPrefixLess Type;
+    typedef TagPrefixLess Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -123,154 +102,102 @@ struct DefaultPrefixOrder
  *
  * @tparam TSpec The specializing size type, defaults to <tt>size_t</tt>.
  *
- * @section Remarks
- * 
  * This class implement comparator objects that perform (lexical) comparisons between two sequences.  The result of the
  * comparison is stored in the data members of the instance and can be accessed by some functions, for example @link
  * Lexical#isLess @endlink or @link Lexical#isEqual @endlink.
- * 
+ *
  * In most cases, there is no need for an explicite use of comparators, but sometimes this concept provide the
  * opportunity to speed up the code.
- * 
+ *
  * @section Examples
- * 
+ *
  * This program compares the strings <tt>str1</tt> and <tt>str2</tt>:
- * 
+ *
  * @code{.cpp}
  * if (isLess(str1, str2)) //first comparison
  * {
- * 	//str1 < str2
+ *     //str1 < str2
  * }
  * else if (isGreater(str1, str2)) //second comparison
  * {
- * 	//str1 > str2
+ *     //str1 > str2
  * }
  * else
  * {
- * 	//str == str2
+ *     //str == str2
  * }
  * @endcode
  *
  * Using a comparator, the same program only needs one comparison instead of two:
- * 
+ *
  * @code{.cpp}
  * Lexical <> comparator(str1, str2); //comparison is executed here
  * if (isLess(comparator))
  * {
- * 	//str1 < str2
+ *     //str1 < str2
  * }
  * else if (lexGreater(comparator))
  * {
- * 	//str1 > str2
+ *     //str1 > str2
  * }
  * else
  * {
- * 	//str == str2
+ *     //str == str2
  * }
  * @endcode
  *
  * The state of a default constructed <tt>Lexical</tt> instance is undefined until it is set by a call of @link
  * Lexical#compare @endlink.
- * 
+ *
  * @see Comparator
  */
 
-/**
-.Class.Lexical:
-..cat:Basic
-..summary:Comparator for lexical comparison.
-..signature:Lexical<TSpec>
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...text:This type can be used for specializations of $Lexical$.
-...remarks:$TSpec$ is by default interpreted as size-type.
-...default:$size_t$
-..remarks:
-...text:This class implement comparator objects that perform (lexical) comparisons between two sequences.
-The result of the comparison is stored in the data members of the instance and can be
-accessed by some functions, for example @Function.isLess@ or @Function.isEqual@.
-...text:In most cases, there is no need for an explicite use of comparators,
-but sometimes this concept provide the opportunity to speed up the code.
-..example:
-...text:This program compares the strings $str1$ and $str2$:
-...code:if (isLess(str1, str2)) //first comparison
-{
-	//str1 < str2
-}
-else if (isGreater(str1, str2)) //second comparison
-{
-	//str1 > str2
-}
-else
-{
-	//str == str2
-}
-...text:Using a comparator, the same program only needs one comparison instead of two:
-...code:Lexical <> comparator(str1, str2); //comparison is executed here
-if (isLess(comparator))
-{
-	//str1 < str2
-}
-else if (lexGreater(comparator))
-{
-	//str1 > str2
-}
-else
-{
-	//str == str2
-}
-...text:The state of a default constructed $Lexical$ instance is undefined until
-it is set by a call of @Function.compare@.
-..see:Metafunction.Comparator
-..include:seqan/sequence.h
-*/
-
 template <typename TSpec = size_t>
 struct Lexical
 {
 public:
-	typename Size<Lexical>::Type data_lcp;
-	char data_compare;
+    typename Size<Lexical>::Type data_lcp;
+    char data_compare;
 
 public:
-	Lexical()
-	{
+    Lexical()
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	template <typename TLeft, typename TRight>
-	Lexical(TLeft const & left, TRight const & right)
-	{
+    template <typename TLeft, typename TRight>
+    Lexical(TLeft const & left, TRight const & right)
+    {
 SEQAN_CHECKPOINT
-		compare(*this, left, right);
-	}
+        compare(*this, left, right);
+    }
 
-	Lexical(Lexical const & other):
-		data_lcp(other.data_lcp),
-		data_compare(other.data_compare)
-	{
+    Lexical(Lexical const & other):
+        data_lcp(other.data_lcp),
+        data_compare(other.data_compare)
+    {
 SEQAN_CHECKPOINT
-	}
+    }
 
-	Lexical & operator=(Lexical const & other)
-	{
+    Lexical & operator=(Lexical const & other)
+    {
 SEQAN_CHECKPOINT
-		data_compare = other.data_compare;
-		data_lcp = other.data_lcp;
-		return *this;
-	}
+        data_compare = other.data_compare;
+        data_lcp = other.data_lcp;
+        return *this;
+    }
 
-	~Lexical() {}
+    ~Lexical() {}
 //____________________________________________________________________________
 
-	enum
-	{
-		EQUAL = 1,
-		LESS = 2,
-		GREATER = 4,
-		LEFT_IS_PREFIX = 8,
-		RIGHT_IS_PREFIX = 16
-	};
+    enum
+    {
+        EQUAL = 1,
+        LESS = 2,
+        GREATER = 4,
+        LEFT_IS_PREFIX = 8,
+        RIGHT_IS_PREFIX = 16
+    };
 };
 
 
@@ -279,39 +206,26 @@ SEQAN_CHECKPOINT
 //////////////////////////////////////////////////////////////////////////////
 // Comparator: returns object that can compare objects of type T
 
-// TODO(holtgrew): Does this belong to the SequenceConcept?
+// TODO(holtgrew): Does this belong to the StringConcept?
 
 /*!
  * @mfn Comparator
  * @headerfile <seqan/sequence.h>
  * @brief Type of comparator object
- * 
+ *
  * @signature Comparator<T>::Type;
- * 
+ *
  * @tparam T Type for which the comparator type is to be determined.
- * 
+ *
  * @return Type the comparator type.
- * 
- * @section Remarks
- * 
+ *
  * Comparators are objects that can be used to compare other objects and store the result of comparisons.
  */
 
-/**
-.Metafunction.Comparator:
-..cat:Basic
-..summary:Type of comparator object
-..signature:Comparator<T>::Type
-..param.T:Type for which the comparator type is to be determined.
-..returns.param.Type:Comparator type
-..remarks:Comparators are objects that can be used to compare other objects and store the
-result of comparisons.
-..include:seqan/sequence.h
-*/
 template <typename T>
 struct Comparator
 {
-	typedef Lexical<typename Size<T>::Type> Type;
+    typedef Lexical<typename Size<T>::Type> Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -320,13 +234,13 @@ struct Comparator
 template <typename TSpec>
 struct Size<Lexical<TSpec> >
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 template <typename TSpec>
 struct Size<Lexical<TSpec> const>
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -335,13 +249,13 @@ struct Size<Lexical<TSpec> const>
 template <typename TSpec>
 struct Spec<Lexical<TSpec> >
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 template <typename TSpec>
 struct Spec<Lexical<TSpec> const>
 {
-	typedef TSpec Type;
+    typedef TSpec Type;
 };
 
 
@@ -356,74 +270,61 @@ struct Spec<Lexical<TSpec> const>
  * @fn Lexical#compare
  * @headerfile <seqan/sequence.h>
  * @brief Compares two objects.
- * 
+ *
  * @signature void compare(comparator, left, right);
- * 
+ *
  * @param[out] comparator Object that stores the results. Types: Lexical
  * @param[in]  left       The first objects.
  * @param[in]  right      The second objects that is compared to <tt>left</tt>.
- * 
+ *
  * @see Comparator
  */
 
-/**
-.Function.compare:
-..cat:Comparisons
-..summary:Compares two objects.
-..signature:compare(comparator, left, right)
-..param.left:The first objects.
-..param.right:The second objects that is compared to $left$.
-..param.comparator:Object that stores the results.
-...type:Class.Lexical
-..see:Metafunction.Comparator
-..include:seqan/sequence.h
-*/
-
 template <typename TSpec, typename TLeft, typename TRight>
 inline void
 compare_(Lexical<TSpec> & lexical,
-		 TLeft & left,
-		 TRight & right)
-{
-	typename Iterator<TLeft, Standard>::Type left_it = begin(left, Standard());
-	typename Size<TLeft>::Type left_length = length(left);
-	typename Iterator<TRight, Standard>::Type right_it = begin(right, Standard());
-	typename Size<TRight>::Type right_length = length(right);
-
-	if (left_length == right_length) lexical.data_compare = Lexical<TSpec>::EQUAL;
-	else if (left_length < right_length) lexical.data_compare = Lexical<TSpec>::LEFT_IS_PREFIX;
-	else
-	{
-		lexical.data_compare = Lexical<TSpec>::RIGHT_IS_PREFIX;
-		left_length = right_length;
-	}
-
-	lexical.data_lcp = 0;
-	for (lexical.data_lcp = 0; lexical.data_lcp < left_length; ++lexical.data_lcp)
-	{
-		if (*left_it < *right_it)
-		{
-			lexical.data_compare = Lexical<TSpec>::LESS;
-			break;
-		}
-		if (*left_it > *right_it)
-		{
-			lexical.data_compare = Lexical<TSpec>::GREATER;
-			break;
-		}
-		++left_it;
-		++right_it;
-	}
+         TLeft & left,
+         TRight & right)
+{
+    typename Iterator<TLeft, Standard>::Type left_it = begin(left, Standard());
+    typename Size<TLeft>::Type left_length = length(left);
+    typename Iterator<TRight, Standard>::Type right_it = begin(right, Standard());
+    typename Size<TRight>::Type right_length = length(right);
+
+    if (left_length == right_length) lexical.data_compare = Lexical<TSpec>::EQUAL;
+    else if (left_length < right_length) lexical.data_compare = Lexical<TSpec>::LEFT_IS_PREFIX;
+    else
+    {
+        lexical.data_compare = Lexical<TSpec>::RIGHT_IS_PREFIX;
+        left_length = right_length;
+    }
+
+    lexical.data_lcp = 0;
+    for (lexical.data_lcp = 0; lexical.data_lcp < left_length; ++lexical.data_lcp)
+    {
+        if (*left_it < *right_it)
+        {
+            lexical.data_compare = Lexical<TSpec>::LESS;
+            break;
+        }
+        if (*left_it > *right_it)
+        {
+            lexical.data_compare = Lexical<TSpec>::GREATER;
+            break;
+        }
+        ++left_it;
+        ++right_it;
+    }
 }
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSpec, typename TLeft, typename TRight>
 inline void
 compare(Lexical<TSpec> & lexical,
-		TLeft const & left,
-		TRight const & right)
+        TLeft const & left,
+        TRight const & right)
 {
-	compare_(lexical, left, right);
+    compare_(lexical, left, right);
 }
 
 // TODO(holtgrew): Are these bugs present in currently supported VC++ versions or is this only a legacy issue?
@@ -431,26 +332,26 @@ compare(Lexical<TSpec> & lexical,
 template <typename TSpec, typename TLeftValue, typename TRight>
 inline void
 compare(Lexical<TSpec> & lexical,
-		TLeftValue const * left,
-		TRight const & right)
+        TLeftValue const * left,
+        TRight const & right)
 {
-	compare_(lexical, left, right);
+    compare_(lexical, left, right);
 }
 template <typename TSpec, typename TLeftValue, typename TRightValue>
 inline void
 compare(Lexical<TSpec> & lexical,
-		TLeftValue const * left,
-		TRightValue const * right)
+        TLeftValue const * left,
+        TRightValue const * right)
 {
-	compare_(lexical, left, right);
+    compare_(lexical, left, right);
 }
 template <typename TSpec, typename TLeft, typename TRightValue>
 inline void
 compare(Lexical<TSpec> & lexical,
-		TLeft const & left,
-		TRightValue const * right)
+        TLeft const & left,
+        TRightValue const * right)
 {
-	compare_(lexical, left, right);
+    compare_(lexical, left, right);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -463,39 +364,24 @@ compare(Lexical<TSpec> & lexical,
  * @fn Lexical#isEqual
  * @headerfile <seqan/sequence.h>
  * @brief Operator "==".
- * 
+ *
  * @signature bool isEqual(left, right);
  * @signature bool isEqual(comparator);
- * 
+ *
  * @param[in] left The first parameter.
  * @param[in] right The second parameter that is compared to <tt>left</tt>.
  * @param[in] comparator A comparator. Types: Lexical
- * 
+ *
  * @return bool <tt>true</tt> if <tt>left</tt> equals <tt>right</tt>, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isEqual:
-..cat:Comparisons
-..class:Class.Lexical
-..summary:Operator "==".
-..signature:isEqual(left, right)
-..signature:isEqual(comparator)
-..param.left:The first parameter.
-..param.right:The second parameter that is compared to $left$.
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:$true$ if $left$ equals $right$, $false$ otherwise.
-..see:Metafunction.Comparator
-..include:seqan/sequence.h
-*/
 template <typename TLeft, typename TRight >
 inline bool
 isEqual(TLeft const & left,
-		TRight const & right)
+        TRight const & right)
 {
 SEQAN_CHECKPOINT
-	return left == right;
+    return left == right;
 }
 
 template <typename TSpec>
@@ -503,7 +389,7 @@ inline bool
 isEqual(Lexical<TSpec> const & _lex)
 {
 SEQAN_CHECKPOINT
-	return (_lex.data_compare & Lexical<TSpec>::EQUAL);
+    return (_lex.data_compare & Lexical<TSpec>::EQUAL);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -514,39 +400,24 @@ SEQAN_CHECKPOINT
  * @fn Lexical#isNotEqual
  * @headerfile <seqan/sequence.h>
  * @brief Operator "!=".
- * 
+ *
  * @signature bool isNotEqual(left, right);
  * @signature bool isNotEqual(comparator);
- * 
+ *
  * @param[in] left The first parameter.
  * @param[in] right The second parameter that is compared to <tt>left</tt>.
  * @param[in] comparator A comparator. Types: Lexical
- * 
+ *
  * @return bool <tt>true</tt> if <tt>left</tt> does not equal <tt>right</tt>, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isNotEqual:
-..cat:Comparisons
-..class:Class.Lexical
-..summary:Operator "!=".
-..signature:isNotEqual(left, right)
-..signature:isNotEqual(comparator)
-..param.left:The first parameter.
-..param.right:The second parameter that is compared to $left$.
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:$true$ if $left$ is not equal to $right$, $false$ otherwise.
-..see:Metafunction.Comparator
-..include:seqan/sequence.h
-*/
 template <typename TLeft, typename TRight >
 inline bool
 isNotEqual(TLeft const & left,
-		 TRight const & right)
+         TRight const & right)
 {
 SEQAN_CHECKPOINT
-	return left != right;
+    return left != right;
 }
 
 template <typename TSpec>
@@ -554,7 +425,7 @@ inline bool
 isNotEqual(Lexical<TSpec> const & _lex)
 {
 SEQAN_CHECKPOINT
-	return !(_lex.data_compare & Lexical<TSpec>::EQUAL);
+    return !(_lex.data_compare & Lexical<TSpec>::EQUAL);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -565,62 +436,40 @@ SEQAN_CHECKPOINT
  * @fn Lexical#isLess
  * @headerfile <seqan/sequence.h>
  * @brief Operator "&lt;".
- * 
+ *
  * @signature bool isLess(left, right);
  * @signature bool isLess(comparator);
- * 
+ *
  * @param[in] left The first parameter.
  * @param[in] right The second parameter that is compared to <tt>left</tt>.
  * @param[in] comparator A comparator. Types: Lexical
- * 
+ *
  * @return bool <tt>true</tt> if <tt>left</tt> is less than <tt>right</tt>, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isLess:
-..cat:Comparisons
-..class:Class.Lexical
-..summary:Operator "<".
-..signature:isLess(left, right [, prefix_order_tag])
-..signature:isLess(comparator)
-..param.left:The first parameter.
-..param.right:The second parameter that is compared to $left$.
-..param.prefix_order_tag:Tag that specify whether prefixes are less or greater. (optional)
-...text:If omitted, the default tag is determined by @Metafunction.DefaultPrefixOrder@ for the type of $left$.
-...see:Tag.Prefix Order
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:$true$ if $left$ is less than $right$, $false$ otherwise.
-..see:Metafunction.Comparator
-..remarks:
-...text:Sequences are compared in lexicographical order.
-..see:Tag.Prefix Order
-..see:Metafunction.DefaultPrefixOrder
-..include:seqan/sequence.h
-*/
 template <typename TLeft, typename TRight, typename TPrefixOrder >
 inline bool
 isLess(TLeft const & left,
-	   TRight const & right,
-	   Tag<TPrefixOrder> const tag)
+       TRight const & right,
+       Tag<TPrefixOrder> const tag)
 {
 SEQAN_CHECKPOINT
-	typename Comparator<TLeft>::Type _lex(left, right);
+    typename Comparator<TLeft>::Type _lex(left, right);
     return isLess(_lex, tag);
 }
 template <typename TLeft, typename TRight>
 inline bool
 isLess(TLeft const & left,
-	   TRight const & right)
+       TRight const & right)
 {
 SEQAN_CHECKPOINT
-	return left < right;
+    return left < right;
 }
 
 template <typename TSpec>
 inline bool
 isLess(Lexical<TSpec> const & _lex,
-	   TagPrefixLess)
+       TagPrefixLess)
 {
 SEQAN_CHECKPOINT
    return (_lex.data_compare & (Lexical<TSpec>::LESS | Lexical<TSpec>::LEFT_IS_PREFIX)) != 0;
@@ -628,7 +477,7 @@ SEQAN_CHECKPOINT
 template <typename TSpec>
 inline bool
 isLess(Lexical<TSpec> const & _lex,
-	   TagPrefixGreater)
+       TagPrefixGreater)
 {
 SEQAN_CHECKPOINT
    return (_lex.data_compare & (Lexical<TSpec>::LESS | Lexical<TSpec>::RIGHT_IS_PREFIX)) != 0;
@@ -638,7 +487,7 @@ inline bool
 isLess(Lexical<TSpec> const & _lex)
 {
 SEQAN_CHECKPOINT
-	return isLess(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
+    return isLess(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -649,63 +498,40 @@ SEQAN_CHECKPOINT
  * @fn Lexical#isLessOrEqual
  * @headerfile <seqan/sequence.h>
  * @brief Operator "&lt;=".
- * 
+ *
  * @signature bool isLessOrEqual(left, right);
  * @signature bool isLessOrEqual(comparator);
- * 
+ *
  * @param[in] left The first parameter.
  * @param[in] right The second parameter that is compared to <tt>left</tt>.
  * @param[in] comparator A comparator. Types: Lexical
- * 
+ *
  * @return bool <tt>true</tt> if <tt>left</tt> is less than or equal to <tt>right</tt>, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isLessOrEqual:
-..cat:Comparisons
-..class:Class.Lexical
-..summary:Operator "<=".
-..signature:isLessOrEqual(left, right [, prefix_order_tag])
-..signature:isLessOrEqual(comparator)
-..param.left:The first parameter.
-..param.right:The second parameter that is compared to $left$.
-..param.prefix_order_tag:Tag that specify whether prefixes are less or greater. (optional)
-...text:If omitted, the default tag is determined by @Metafunction.DefaultPrefixOrder@ for the type of $left$.
-...see:Tag.Prefix Order
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:$true$ if $left$ is less than or equal to $right$, $false$ otherwise.
-..see:Metafunction.Comparator
-..remarks:
-...text:Sequences are compared in lexicographical order.
-..see:Tag.Prefix Order
-..see:Metafunction.DefaultPrefixOrder
-..include:seqan/sequence.h
-*/
-
 template <typename TLeft, typename TRight, typename TPrefixOrder >
 inline bool
 isLessOrEqual(TLeft const & left,
-		TRight const & right,
-		Tag<TPrefixOrder> const tag)
+        TRight const & right,
+        Tag<TPrefixOrder> const tag)
 {
 SEQAN_CHECKPOINT
-	typename Comparator<TLeft>::Type _lex(left, right);
+    typename Comparator<TLeft>::Type _lex(left, right);
     return isLessOrEqual(_lex, tag);
 }
 template <typename TLeft, typename TRight>
 inline bool
 isLessOrEqual(TLeft const & left,
-		TRight const & right)
+        TRight const & right)
 {
 SEQAN_CHECKPOINT
-	return left <= right;
+    return left <= right;
 }
 
 template <typename TSpec>
 inline bool
 isLessOrEqual(Lexical<TSpec> const & _lex,
-		TagPrefixLess)
+        TagPrefixLess)
 {
 SEQAN_CHECKPOINT
    return (_lex.data_compare & (Lexical<TSpec>::LESS | Lexical<TSpec>::EQUAL | Lexical<TSpec>::LEFT_IS_PREFIX)) != 0;
@@ -713,7 +539,7 @@ SEQAN_CHECKPOINT
 template <typename TSpec>
 inline bool
 isLessOrEqual(Lexical<TSpec> const & _lex,
-		TagPrefixGreater)
+        TagPrefixGreater)
 {
 SEQAN_CHECKPOINT
    return (_lex.data_compare & (Lexical<TSpec>::LESS | Lexical<TSpec>::EQUAL | Lexical<TSpec>::RIGHT_IS_PREFIX)) != 0;
@@ -723,7 +549,7 @@ inline bool
 isLessOrEqual(Lexical<TSpec> const & _lex)
 {
 SEQAN_CHECKPOINT
-	return isLessOrEqual(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
+    return isLessOrEqual(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -734,62 +560,40 @@ SEQAN_CHECKPOINT
  * @fn Lexical#isGreater
  * @headerfile <seqan/sequence.h>
  * @brief Operator "&gt;".
- * 
+ *
  * @signature bool isGreater(left, right);
  * @signature bool isGreater(comparator);
- * 
+ *
  * @param[in] left The first parameter.
  * @param[in] right The second parameter that is compared to <tt>left</tt>.
  * @param[in] comparator A comparator. Types: Lexical
- * 
+ *
  * @return bool <tt>true</tt> if <tt>left</tt> is greater than <tt>right</tt>, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isGreater:
-..cat:Comparisons
-..class:Class.Lexical
-..summary:Operator ">".
-..signature:isGreater(left, right [, prefix_order_tag])
-..signature:isGreater(comparator)
-..param.left:The first parameter.
-..param.right:The second parameter that is compared to $left$.
-..param.prefix_order_tag:Tag that specify whether prefixes are less or greater. (optional)
-...text:If omitted, the default tag is determined by @Metafunction.DefaultPrefixOrder@ for the type of $left$.
-...see:Tag.Prefix Order
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:$true$ if $left$ is greater than $right$, $false$ otherwise.
-..see:Metafunction.Comparator
-..remarks:
-...text:Sequences are compared in lexicographical order.
-..see:Tag.Prefix Order
-..see:Metafunction.DefaultPrefixOrder
-..include:seqan/sequence.h
-*/
 template <typename TLeft, typename TRight, typename TPrefixOrder >
 inline bool
 isGreater(TLeft const & left,
-		TRight const & right,
-		Tag<TPrefixOrder> const tag)
+        TRight const & right,
+        Tag<TPrefixOrder> const tag)
 {
 SEQAN_CHECKPOINT
-	typename Comparator<TLeft>::Type _lex(left, right);
+    typename Comparator<TLeft>::Type _lex(left, right);
     return isGreater(_lex, tag);
 }
 template <typename TLeft, typename TRight>
 inline bool
 isGreater(TLeft const & left,
-		TRight const & right)
+        TRight const & right)
 {
 SEQAN_CHECKPOINT
-	return left > right;
+    return left > right;
 }
 
 template <typename TSpec>
 inline bool
 isGreater(Lexical<TSpec> const & _lex,
-		TagPrefixLess)
+        TagPrefixLess)
 {
 SEQAN_CHECKPOINT
    return (_lex.data_compare & (Lexical<TSpec>::GREATER | Lexical<TSpec>::RIGHT_IS_PREFIX)) != 0;
@@ -797,7 +601,7 @@ SEQAN_CHECKPOINT
 template <typename TSpec>
 inline bool
 isGreater(Lexical<TSpec> const & _lex,
-		TagPrefixGreater)
+        TagPrefixGreater)
 {
 SEQAN_CHECKPOINT
    return (_lex.data_compare & (Lexical<TSpec>::GREATER | Lexical<TSpec>::LEFT_IS_PREFIX)) != 0;
@@ -807,7 +611,7 @@ inline bool
 isGreater(Lexical<TSpec> const & _lex)
 {
 SEQAN_CHECKPOINT
-	return isGreater(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
+    return isGreater(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -818,63 +622,40 @@ SEQAN_CHECKPOINT
  * @fn Lexical#isGreaterOrEqual
  * @headerfile <seqan/sequence.h>
  * @brief Operator "&gt;=".
- * 
+ *
  * @signature bool isGreaterOrEqual(left, right);
  * @signature bool isGreaterOrEqual(comparator);
- * 
+ *
  * @param[in] left The first parameter.
  * @param[in] right The second parameter that is compared to <tt>left</tt>.
  * @param[in] comparator A comparator. Types: Lexical
- * 
+ *
  * @return bool <tt>true</tt> if <tt>left</tt> is greater than or equal to <tt>right</tt>, <tt>false</tt> otherwise.
  */
 
-/**
-.Function.isGreaterOrEqual:
-..cat:Comparisons
-..class:Class.Lexical
-..summary:Operator ">=".
-..signature:isGreaterOrEqual(left, right [, prefix_order_tag])
-..signature:isGreaterOrEqual(comparator)
-..param.left:The first parameter.
-..param.right:The second parameter that is compared to $left$.
-..param.prefix_order_tag:Tag that specify whether prefixes are less or greater. (optional)
-...text:If omitted, the default tag is determined by @Metafunction.DefaultPrefixOrder@ for the type of $left$.
-...see:Tag.Prefix Order
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:$true$ if $left$ is greater than or equal to $right$, $false$ otherwise.
-..see:Metafunction.Comparator
-..remarks:
-...text:Sequences are compared in lexicographical order.
-..see:Tag.Prefix Order
-..see:Metafunction.DefaultPrefixOrder
-..include:seqan/sequence.h
-*/
-
 template <typename TLeft, typename TRight, typename TPrefixOrder >
 inline bool
 isGreaterOrEqual(TLeft const & left,
-		TRight const & right,
-		Tag<TPrefixOrder> const tag)
+        TRight const & right,
+        Tag<TPrefixOrder> const tag)
 {
 SEQAN_CHECKPOINT
-	typename Comparator<TLeft>::Type _lex(left, right);
+    typename Comparator<TLeft>::Type _lex(left, right);
     return isGreaterOrEqual(_lex, tag);
 }
 template <typename TLeft, typename TRight>
 inline bool
 isGreaterOrEqual(TLeft const & left,
-		TRight const & right)
+        TRight const & right)
 {
 SEQAN_CHECKPOINT
-	return left >= right;
+    return left >= right;
 }
 
 template <typename TSpec>
 inline bool
 isGreaterOrEqual(Lexical<TSpec> const & _lex,
-		TagPrefixLess)
+        TagPrefixLess)
 {
 SEQAN_CHECKPOINT
    return (_lex.data_compare & (Lexical<TSpec>::GREATER | Lexical<TSpec>::EQUAL | Lexical<TSpec>::RIGHT_IS_PREFIX)) != 0;
@@ -882,7 +663,7 @@ SEQAN_CHECKPOINT
 template <typename TSpec>
 inline bool
 isGreaterOrEqual(Lexical<TSpec> const & _lex,
-		TagPrefixGreater)
+        TagPrefixGreater)
 {
 SEQAN_CHECKPOINT
    return (_lex.data_compare & (Lexical<TSpec>::GREATER | Lexical<TSpec>::EQUAL | Lexical<TSpec>::LEFT_IS_PREFIX)) != 0;
@@ -892,7 +673,7 @@ inline bool
 isGreaterOrEqual(Lexical<TSpec> const & _lex)
 {
 SEQAN_CHECKPOINT
-	return isGreaterOrEqual(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
+    return isGreaterOrEqual(_lex, typename DefaultPrefixOrder< Lexical<TSpec> >::Type());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -903,45 +684,26 @@ SEQAN_CHECKPOINT
  * @fn Lexical#isPrefix
  * @headerfile <seqan/sequence.h>
  * @brief Test whether a sequence is the prefix of another sequence.
- * 
+ *
  * @signature bool isPrefix(left, right);
  * @signature bool isPrefix(comparator);
- * 
+ *
  * @param[in] left       The putative prefix.
  * @param[in] right      The second sequence.
  * @param[in] comparator A comparator. Types: Lexical
- * 
- * @return bool <tt>true</tt> if <tt>left</tt> is a prefix of<tt>right</tt>, <tt>false</tt> otherwise.
  *
- * @section Remarks
+ * @return bool <tt>true</tt> if <tt>left</tt> is a prefix of<tt>right</tt>, <tt>false</tt> otherwise.
  *
  * By definition, a sequence is a prefix of itself: <tt>isPrefix("abc", "abc")</tt> is <tt>true</tt>.
  */
 
-/**
-.Function.isPrefix:
-..cat:Comparisons
-..class:Class.Lexical
-..summary:Test whether a sequence is prefix of another sequence.
-..signature:isPrefix(left, right)
-..signature:isPrefix(comparator)
-..param.left:The first sequence, the putative prefix.
-..param.right:The second sequence.
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:$true$ if $left$ is a prefix of $right$, $false$ otherwise.
-..see:Metafunction.Comparator
-..remarks:By definition, the whole sequence is a prefix of itself too: $isPrefix("abc", "abc") == true$.
-..include:seqan/sequence.h
-*/
-
 template <typename TLeft, typename TRight >
 inline bool
 isPrefix(TLeft const & left,
-		TRight const & right)
+        TRight const & right)
 {
 SEQAN_CHECKPOINT
-	typename Comparator<TLeft>::Type _lex(left, right);
+    typename Comparator<TLeft>::Type _lex(left, right);
     return isPrefix(_lex);
 }
 template <typename TSpec>
@@ -961,46 +723,26 @@ SEQAN_CHECKPOINT
  * @fn Lexical#hasPrefix
  * @headerfile <seqan/sequence.h>
  * @brief Test whether a sequence is the prefix of another sequence.
- * 
+ *
  * @signature bool isPrefix(left, right);
  * @signature bool isPrefix(comparator);
- * 
+ *
  * @param[in] left       The first sequence.
  * @param[in] right      The putative prefix.
  * @param[in] comparator A comparator. Types: Lexical
- * 
- * @return bool <tt>true</tt> if <tt>left</tt> is a prefix of<tt>right</tt>, <tt>false</tt> otherwise.
  *
- * @section Remarks
+ * @return bool <tt>true</tt> if <tt>left</tt> is a prefix of<tt>right</tt>, <tt>false</tt> otherwise.
  *
  * By definition, a sequence is a prefix of itself: <tt>hasPrefix("abc", "abc")</tt> is <tt>true</tt>.
  */
 
-/**
-.Function.hasPrefix:
-..cat:Comparisons
-..class:Class.Lexical
-..summary:Test whether a sequence is prefix of another sequence.
-..signature:hasPrefix(left, right)
-..signature:hasPrefix(comparator)
-..param.left:The first sequence.
-..param.right:The second sequence, the putative prefix.
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:$true$ if $right$ is a prefix of $left$, $false$ otherwise.
-..see:Metafunction.Comparator
-..see:Function.isPrefix
-..remarks:By definition, the whole sequence is a prefix of itself too: $hasPrefix("abc", "abc") == true$.
-..include:seqan/sequence.h
-*/
-
 template <typename TLeft, typename TRight >
 inline bool
 hasPrefix(TLeft const & left,
-		TRight const & right)
+        TRight const & right)
 {
 SEQAN_CHECKPOINT
-	typename Comparator<TLeft>::Type _lex(left, right);
+    typename Comparator<TLeft>::Type _lex(left, right);
     return hasPrefix(_lex);
 }
 template <typename TSpec>
@@ -1019,43 +761,26 @@ SEQAN_CHECKPOINT
  * @fn Lexical#lcpLength
  * @headerfile <seqan/sequence.h>
  * @brief Length of the longest common prefix.
- * 
+ *
  * @signature TSize lcpLength(left, right);
  * @signature TSize lcpLength(comparator);
- * 
+ *
  * @param[in] left       The first sequence.
  * @param[in] right      The second sequence.
  * @param[in] comparator A comparator. Types: Lexical
- * 
+ *
  * @return TSize The length of the longest common prefix of <tt>left</tt> and <tt>right</tt>.  TSize is the Size type of
  *               the left size type.
  *
- * @section Remarks
- *
  * By definition, a sequence is a prefix of itself: <tt>hasPrefix("abc", "abc")</tt> is <tt>true</tt>.
  */
 
-/**
-.Function.lcpLength:
-..summary:Length of longest common prefix.
-..cat:Comparisons
-..class:Class.Lexical
-..signature:lcpLength(left, right)
-..signature:lcpLength(comparator)
-..param.left:The first sequence.
-..param.right:The second sequence that is compared to $left$.
-..param.comparator:A comparator.
-...type:Class.Lexical
-..returns:The length of the longest common prefix of $left$ and $right$.
-..see:Metafunction.Comparator
-..include:seqan/sequence.h
-*/
 template <typename TLeft, typename TRight >
 inline typename Size<TLeft>::Type
 lcpLength(TLeft const & left, TRight const & right)
 {
 SEQAN_CHECKPOINT
-	typename Comparator<TLeft>::Type _lex(left, right);
+    typename Comparator<TLeft>::Type _lex(left, right);
     return lcpLength(_lex);
 }
 
diff --git a/seqan/sequence/sequence_shortcuts.h b/seqan/sequence/sequence_shortcuts.h
index c59fd06..8d8b6c3 100644
--- a/seqan/sequence/sequence_shortcuts.h
+++ b/seqan/sequence/sequence_shortcuts.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -52,18 +52,6 @@ namespace SEQAN_NAMESPACE_MAIN
  * @signature typedef String<char> CharString;
  */
 
-/**
-.Shortcut.CharString:
-..cat:Strings
-..summary:A string of $char$.
-..signature:CharString
-..description:
-This is a useful replacement of $std::string$.
-If you want a C-style $char *$ string, use @Function.toCString@.
-..shortcutfor:Spec.Alloc String
-...signature:String<char, Alloc<> >
-*/
-
 typedef String<char, Alloc<void> > CharString;
 
 //____________________________________________________________________________
@@ -71,21 +59,11 @@ typedef String<char, Alloc<void> > CharString;
 /*!
  * @typedef CharIterator
  * @headerfile <seqan/sequence.h>
- * @brief An iterator intoa @link CharString @endlink.
+ * @brief An iterator overa a @link CharString @endlink.
  *
  * @signature typedef Iterator<CharString, Rooted>::Type CharIterator;
  */
 
-/**
-.Shortcut.CharIterator:
-..cat:Iterators
-..summary:Iterator for @Shortcut.CharString@.
-..signature:CharIterator
-..shortcutfor:Concept.RootedIteratorConcept
-...signature:Iterator<CharString, Rooted>::Type
-..see:Shortcut.CharString
-*/
-
 typedef Iterator<CharString, Rooted>::Type CharIterator;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -98,29 +76,10 @@ typedef Iterator<CharString, Rooted>::Type CharIterator;
  * @signature typedef String<wchar_t> CharString;
  */
 
-/**
-.Shortcut.UnicodeString:
-..cat:Strings
-..summary:A string of $wchar_t$.
-..signature:UnicodeString
-..shortcutfor:Spec.Alloc String
-...signature:String<wchar_t, Alloc<> >
-*/
-
 typedef String<wchar_t, Alloc<void> > UnicodeString;
 
 //____________________________________________________________________________
 
-/**
-.Shortcut.UnicodeIterator:
-..cat:Iterators
-..summary:Iterator for @Shortcut.UnicodeString@.
-..signature:UnicodeIterator
-..shortcutfor:Concept.RootedIteratorConcept
-...signature:Iterator<UnicodeString, Rooted>::Type
-..see:Shortcut.UnicodeString
-*/
-
 typedef Iterator<UnicodeString, Rooted>::Type UnicodeIterator;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -133,16 +92,6 @@ typedef Iterator<UnicodeString, Rooted>::Type UnicodeIterator;
  * @signature typedef String<Dna> CharString;
  */
 
-/**
-.Shortcut.DnaString:
-..cat:Strings
-..summary:A string of @Spec.Dna@.
-..signature:DnaString
-..shortcutfor:Spec.Alloc String
-...signature:String<Dna, Alloc<> >
-..see:Spec.Dna
-*/
-
 typedef String<Dna, Alloc<void> > DnaString;
 
 //____________________________________________________________________________
@@ -155,17 +104,6 @@ typedef String<Dna, Alloc<void> > DnaString;
  * @signature typedef Iterator<DnaString, Rooted>::Type DnaIterator;
  */
 
-/**
-.Shortcut.DnaIterator:
-..cat:Iterators
-..summary:Iterator for @Shortcut.DnaString@.
-..signature:DnaIterator
-..shortcutfor:Concept.RootedIteratorConcept
-...signature:Iterator<DnaString, Rooted>::Type
-..see:Spec.Dna
-..see:Shortcut.DnaString
-*/
-
 typedef Iterator<DnaString, Rooted>::Type DnaIterator;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -178,19 +116,32 @@ typedef Iterator<DnaString, Rooted>::Type DnaIterator;
  * @signature typedef String<Dna5> CharString;
  */
 
-/**
-.Shortcut.Dna5String:
-..cat:Strings
-..summary:A string of @Spec.Dna5@.
-..signature:Dna5String
-..shortcutfor:Spec.Alloc String
-...signature:String<Dna5, Alloc<> >
-..see:Spec.Dna5
-..see:Shortcut.DnaString
-*/
-
 typedef String<Dna5, Alloc<void> > Dna5String;
 
+//////////////////////////////////////////////////////////////////////////////
+
+/*!
+ * @typedef DnaQString
+ * @headerfile <seqan/sequence.h>
+ * @brief An AllocString with DnaQ alphabet.
+ *
+ * @signature typedef String<DnaQ> CharString;
+ */
+
+typedef String<DnaQ, Alloc<void> > DnaQString;
+
+//////////////////////////////////////////////////////////////////////////////
+
+/*!
+ * @typedef Dna5QString
+ * @headerfile <seqan/sequence.h>
+ * @brief An AllocString with Dna5Q alphabet.
+ *
+ * @signature typedef String<Dna5Q> CharString;
+ */
+
+typedef String<Dna5Q, Alloc<void> > Dna5QString;
+
 //____________________________________________________________________________
 
 /*!
@@ -201,18 +152,6 @@ typedef String<Dna5, Alloc<void> > Dna5String;
  * @signature typedef Iterator<Dna5String, Rooted>::Type Dna5Iterator;
  */
 
-/**
-.Shortcut.Dna5Iterator:
-..cat:Iterators
-..summary:Iterator for @Shortcut.Dna5String@.
-..signature:Dna5Iterator
-..shortcutfor:Concept.RootedIteratorConcept
-...signature:Iterator<Dna5String, Rooted>::Type
-..see:Spec.Dna5
-..see:Shortcut.Dna5String
-..see:Shortcut.DnaIterator
-*/
-
 typedef Iterator<Dna5String, Rooted>::Type Dna5Iterator;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -225,16 +164,6 @@ typedef Iterator<Dna5String, Rooted>::Type Dna5Iterator;
  * @signature typedef String<Rna> CharString;
  */
 
-/**
-.Shortcut.RnaString:
-..cat:Strings
-..summary:A string of @Spec.Rna@.
-..signature:RnaString
-..shortcutfor:Spec.Alloc String
-...signature:String<Rna, Alloc<> >
-..see:Spec.Rna
-*/
-
 typedef String<Rna, Alloc<void> > RnaString;
 
 //____________________________________________________________________________
@@ -247,17 +176,6 @@ typedef String<Rna, Alloc<void> > RnaString;
  * @signature typedef Iterator<RnaString, Rooted>::Type RnaIterator;
  */
 
-/**
-.Shortcut.RnaIterator:
-..cat:Iterators
-..summary:Iterator for @Shortcut.RnaString@.
-..signature:RnaIterator
-..shortcutfor:Concept.RootedIteratorConcept
-...signature:Iterator<RnaString, Rooted>::Type
-..see:Spec.Rna
-..see:Shortcut.RnaString
-*/
-
 typedef Iterator<RnaString, Rooted>::Type RnaIterator;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -270,17 +188,6 @@ typedef Iterator<RnaString, Rooted>::Type RnaIterator;
  * @signature typedef String<Rna5> CharString;
  */
 
-/**
-.Shortcut.Rna5String:
-..cat:Strings
-..summary:A string of @Spec.Rna5@.
-..signature:Rna5String
-..shortcutfor:Spec.Alloc String
-...signature:String<Rna5, Alloc<> >
-..see:Spec.Rna5
-..see:Shortcut.RnaString
-*/
-
 typedef String<Rna5, Alloc<void> > Rna5String;
 
 //____________________________________________________________________________
@@ -293,18 +200,6 @@ typedef String<Rna5, Alloc<void> > Rna5String;
  * @signature typedef Iterator<Rna5String, Rooted>::Type Rna5Iterator;
  */
 
-/**
-.Shortcut.Rna5Iterator:
-..cat:Iterators
-..summary:Iterator for @Shortcut.Rna5String@.
-..signature:Rna5Iterator
-..shortcutfor:Concept.RootedIteratorConcept
-...signature:Iterator<Rna5String, Rooted>::Type
-..see:Spec.Rna5
-..see:Shortcut.Rna5String
-..see:Shortcut.RnaIterator
-*/
-
 typedef Iterator<Rna5String, Rooted>::Type Rna5Iterator;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -317,16 +212,6 @@ typedef Iterator<Rna5String, Rooted>::Type Rna5Iterator;
  * @signature typedef String<Iupac> CharString;
  */
 
-/**
-.Shortcut.IupacString:
-..cat:Strings
-..summary:A string of @Spec.Iupac@.
-..signature:IupacString
-..shortcutfor:Spec.Alloc String
-...signature:String<Iupac, Alloc<> >
-..see:Spec.Iupac
-*/
-
 typedef String<Iupac, Alloc<void> > IupacString;
 
 //____________________________________________________________________________
@@ -339,17 +224,6 @@ typedef String<Iupac, Alloc<void> > IupacString;
  * @signature typedef Iterator<IupacString, Rooted>::Type IupacIterator;
  */
 
-/**
-.Shortcut.IupacIterator:
-..cat:Iterators
-..summary:Iterator for @Shortcut.IupacString@.
-..signature:IupacIterator
-..shortcutfor:Concept.RootedIteratorConcept
-...signature:Iterator<IupacString, Rooted>::Type
-..see:Spec.Iupac
-..see:Shortcut.IupacString
-*/
-
 typedef Iterator<IupacString, Rooted>::Type IupacIterator;
 
 //////////////////////////////////////////////////////////////////////////////
@@ -362,16 +236,6 @@ typedef Iterator<IupacString, Rooted>::Type IupacIterator;
  * @signature typedef String<AminoAcid> Peptide;
  */
 
-/**
-.Shortcut.Peptide:
-..cat:Strings
-..summary:A string of @Spec.AminoAcid@.
-..signature:Peptide
-..shortcutfor:Spec.Alloc String
-...signature:String<AminoAcid, Alloc<> >
-..see:Spec.AminoAcid
-*/
-
 typedef String<AminoAcid, Alloc<void> > Peptide;
 
 //____________________________________________________________________________
@@ -384,17 +248,6 @@ typedef String<AminoAcid, Alloc<void> > Peptide;
  * @signature typedef Iterator<Peptide, Rooted>::Type PeptideIterator;
  */
 
-/**
-.Shortcut.PeptideIterator:
-..cat:Iterators
-..summary:Iterator for @Shortcut.Peptide@.
-..signature:PeptideIterator
-..shortcutfor:Concept.RootedIteratorConcept
-...signature:Iterator<Peptide, Rooted>::Type
-..see:Spec.AminoAcid
-..see:Shortcut.Peptide
-*/
-
 typedef Iterator<Peptide, Rooted>::Type PeptideIterator;
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/sequence/string_alloc.h b/seqan/sequence/string_alloc.h
index 5f9b96c..4c9bbb0 100644
--- a/seqan/sequence/string_alloc.h
+++ b/seqan/sequence/string_alloc.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -62,18 +62,6 @@ namespace seqan {
 
 // TODO(holtgrew): Where is Alloc<> defined? In module base?
 
-/**
-.Spec.Alloc String:
-..cat:Strings
-..general:Class.String
-..summary:Expandable string that is stored on heap.
-..signature:String<TValue, Alloc<TSpec> >
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..param.TSpec:The specializing type.
-...default:$void$
-..include:seqan/sequence.h
-*/
 template <typename TValue, typename TSpec>
 class String<TValue, Alloc<TSpec> >
 {
@@ -100,7 +88,7 @@ class String<TValue, Alloc<TSpec> >
             assign(*this, source);
         SEQAN_ASSERT_LEQ_MSG(data_begin, data_end, "String end is before begin!");
     }
-    
+
     template <typename TSource>
     String(TSource const & source)
         : data_begin(0),
@@ -111,7 +99,7 @@ class String<TValue, Alloc<TSpec> >
             assign(*this, source);
         SEQAN_ASSERT_LEQ_MSG(data_begin, data_end, "String end is before begin!");
     }
-    
+
     String(String & source)
         : data_begin(0),
           data_end(0),
@@ -133,7 +121,7 @@ class String<TValue, Alloc<TSpec> >
             assign(*this, source);
         SEQAN_ASSERT_LEQ_MSG(data_begin, data_end, "String end is before begin!");
     }
-    
+
     String(String & source, Move const &)
         : data_begin(0),
           data_end(0),
@@ -142,7 +130,18 @@ class String<TValue, Alloc<TSpec> >
         move(*this, source);
         SEQAN_ASSERT_LEQ_MSG(data_begin, data_end, "String end is before begin!");
     }
-    
+
+#ifdef SEQAN_CXX11_STANDARD
+    String(String && source, Move const &)
+        : data_begin(0),
+          data_end(0),
+          data_capacity(0)
+    {
+        move(*this, source);
+        SEQAN_ASSERT_LEQ_MSG(data_begin, data_end, "String end is before begin!");
+    }
+#endif
+
     template <typename TSource, typename TSize>
     String(TSource & source, TSize limit)
             : data_begin(0),
@@ -153,7 +152,7 @@ class String<TValue, Alloc<TSpec> >
             assign(*this, source, limit);
         SEQAN_ASSERT_LEQ_MSG(data_begin, data_end, "String end is before begin!");
     }
-    
+
     template <typename TSource, typename TSize>
     String(TSource const & source, TSize limit)
             : data_begin(0),
@@ -236,6 +235,14 @@ template <typename TValue, typename TSpec>
 struct IsContiguous<String<TValue, Alloc<TSpec> > > :
     True {};
 
+// ----------------------------------------------------------------------------
+// Metafunction HasMoveConstructor
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct HasMoveConstructor<String<TValue, Alloc<TSpec> > > :
+    True {};
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -307,10 +314,6 @@ capacity(String<TValue, Alloc<TSpec> > const & me)
 // Internal Function _setBegin()
 // ----------------------------------------------------------------------------
 
-/**
-.Internal._setBegin:
-..remarks:Called by Function.move in string_base.h
-*/
 template <typename TValue, typename TSpec, typename TPtr>
 inline void
 _setBegin(String<TValue, Alloc<TSpec> > & me,
@@ -320,19 +323,9 @@ _setBegin(String<TValue, Alloc<TSpec> > & me,
 }
 
 // ----------------------------------------------------------------------------
-// Internal Function _setBegin()
+// Internal Function _setLength()
 // ----------------------------------------------------------------------------
 
-/**
-.Internal._setLength:
-..remarks:Called in string_base.h
-..cat:Functions
-..summary:Set the length of container.
-..signature:_setLength(object, new_length)
-..param.object:A container.
-..param.object.type:Spec.Alloc String
-..param.new_length:The new length.
-*/
 template <typename TValue, typename TSpec, typename TSize>
 inline void
 _setLength(String<TValue, Alloc<TSpec> > & me,
@@ -345,10 +338,6 @@ _setLength(String<TValue, Alloc<TSpec> > & me,
 // Internal Function _setCapacity()
 // ----------------------------------------------------------------------------
 
-/**
-.Internal._setCapacity:
-..remarks:Called in string_base.h
-*/
 template <typename TValue, typename TSpec, typename TSize>
 inline void
 _setCapacity(String<TValue, Alloc<TSpec> > & me,
@@ -361,20 +350,6 @@ _setCapacity(String<TValue, Alloc<TSpec> > & me,
 // Internal Function _allocateStorage()
 // ----------------------------------------------------------------------------
 
-/**
-.Internal._allocateStorage:
-..cat:Functions
-..remarks:Called in string_base.h
-..summary:Allocates a new buffer for a container.
-..signature:_allocateStorage(object, new_capacity)
-..param.object:A container.
-..param.object.type:Spec.Alloc String
-..param.new_capacity:The capacity of the new allocated buffer.
-..returns:The old butter $object$, that is replaced by the new allocated buffer.
-..remarks:The returned buffer must be deallocated by @Internal._deallocateStorage@.
-..remarks:This function does not construct objects in the allocated buffer.
-..see:Internal._reallocateStorage
-*/
 template <typename TValue, typename TSpec, typename TSize>
 inline typename Value<String<TValue, Alloc<TSpec> > >::Type *
 _allocateStorage(String<TValue, Alloc<TSpec> > & me,
@@ -391,19 +366,6 @@ _allocateStorage(String<TValue, Alloc<TSpec> > & me,
 // Internal Function _deallocateStorage()
 // ----------------------------------------------------------------------------
 
-/**
-.Internal._deallocateStorage:
-..cat:Functions
-..summary:Deallocates a buffer of a container.
-..signature:_deallocateStorage(object, buffer, capacity)
-..param.object:A container.
-..param.object.type:Spec.Alloc String
-..param.buffer:The buffer that will be deallocated.
-..param.capacity:The capacity of $buffer$.
-..remarks:All objects in the buffer must be destroyed before calling $_deallocateStorage$.
-..see:Internal._allocateStorage
-..see:Internal._reallocateStorage
-*/
 template <typename TValue, typename TSpec, typename TPtr, typename TSize>
 inline void
 _deallocateStorage(String<TValue, Alloc<TSpec> > & me,
diff --git a/seqan/sequence/string_array.h b/seqan/sequence/string_array.h
index 889a2df..a6adb5e 100644
--- a/seqan/sequence/string_array.h
+++ b/seqan/sequence/string_array.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -53,34 +53,20 @@ namespace seqan {
  * @extends String
  * @headerfile <seqan/sequence.h>
  * @brief Fast, static-size string.
- * 
+ *
  * @signature template <typename TValue, size_t CAPACITY>
  *            class String<TValue, Array<CAPACITY> >;
- * 
+ *
  * @tparam TValue The value type, that is the type of the items/characters
  *                stored in the string.Use @link Value @endlink to get the value
  *                type for a given class.
  * @tparam CAPACITY A positive integer that specifies the capacity of the
  *                string.Note that the capacity of an Array String is fixed at
  *                compile-time.
- * 
+ *
  * Having static-sized strings is useful as members of structs for external memory algorithms, for example.
  */
 
-/**
-.Spec.Array String:
-..cat:Strings
-..general:Class.String
-..summary:Fast, static-size string.
-..remarks:This is useful as members of structs for external memory algorithms, for example.
-..signature:String<TValue, Array<CAPACITY> >
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..param.CAPACITY:A positive integer that specifies the capacity of the string.
-...remarks:Note that the capacity of an Array String is fixed at compile-time.
-..include:seqan/sequence.h
-*/
-
 template <size_t CAPACITY>
 struct Array;
 
@@ -258,14 +244,27 @@ reserve(String<TValue, Array<CAPACITY> > & me,
     return capacity(me);
 }
 
+// ----------------------------------------------------------------------------
+// Function -*allocateStorage()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, size_t CAPACITY, typename TSize>
+inline TValue *
+_allocateStorage(String<TValue, Array<CAPACITY> > & me, TSize /*capacity*/)
+{
+    return me.data_begin;
+}
+
+template <typename TValue, size_t CAPACITY, typename TSize>
+inline void
+_deallocateStorage(String<TValue, Array<CAPACITY> > & /*me*/, TValue * /*ptr*/, TSize /*capacity*/)
+{
+}
 
 // ----------------------------------------------------------------------------
 // Function _setLength()
 // ----------------------------------------------------------------------------
 
-/**
-.Internal._setLength.param.object.type:Spec.Array String
-*/
 template <typename TValue, size_t CAPACITY, typename TSize>
 inline void
 _setLength(String<TValue, Array<CAPACITY> > & me,
diff --git a/seqan/sequence/string_base.h b/seqan/sequence/string_base.h
index a2ae665..d2e2289 100644
--- a/seqan/sequence/string_base.h
+++ b/seqan/sequence/string_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -86,28 +86,28 @@ struct Alloc {};
  * @mfn TextConcept#SAValue
  * @brief The default alphabet type of a suffix array, i.e. the type to store a
  *        position of a string or string set.
- * 
+ *
  * @signature SAValue<TText>::Type
- * 
+ *
  * @tparam TText The text type to query.
- * 
+ *
  * @return TReturn A type to store a position in a <tt>TText</tt>.  This could be an integer for strings or a
  *                 pair of integers for string sets.
- * 
+ *
  * @section Usage
- * 
+ *
  * This type should be removed for functions returning positions in texts such as online or index-based search.
  * Thus, always use this metafunction for declaring position variables.
  *
  * Use the functions @link TextConcept#posLocalize @endlink, @link TextConcept#posGlobalize @endlink, @link
  * TextConcept#getSeqNo @endlink, and @link TextConcept#getSeqOffset @endlink for conversion between local
  * and global positions in texts.
- * 
+ *
  * @section Examples
  *
  * The following shows the original definition of the SAValue metafunction in SeqAn.
  *
- * @code{.cpp} 
+ * @code{.cpp}
  * template <typename TString, typename TSpec>
  * struct SAValue<StringSet<TString, TSpec> >
  * {
@@ -118,7 +118,7 @@ struct Alloc {};
  *         > Type;
  * };
  * @endcode
- */ 
+ */
 
 /*!
  * @fn TextConcept#stringSetLimits
@@ -126,7 +126,7 @@ struct Alloc {};
  *
  * @signature TStringSetLimits stringSetLimits(text);
  *
- * @param text The text to query for its string set limits.
+ * @param[in] text The text to query for its string set limits.
  *
  * @return TStringSetLimits The string set limits (of type @link TextConcept#StringSetLimits @endlink).
  */
@@ -137,18 +137,18 @@ struct Alloc {};
  *
  * @signature void posLocalToX(dst, localPos, limits);
  *
- * @param dst      The local or global position (pair or integer value) is written here.
- * @param localPos The local position.
- * @param limits   The string limits as returned by @link TextConcept#stringSetLimits @endlink.
+ * @param[in] dst      The local or global position (pair or integer value) is written here.
+ * @param[in] localPos The local position.
+ * @param[in] limits   The string limits as returned by @link TextConcept#stringSetLimits @endlink.
  */
 
 /*!
  * @class String
- * @implements SequenceConcept
+ * @implements StringConcept
  * @implements TextConcept
  * @implements SegmentableConcept
  * @headerfile <seqan/sequence.h>
- * @brief @link SequenceConcept Sequence @endlink container class.
+ * @brief @link StringConcept Sequence @endlink container class.
  *
  * @signature template <typename TValue, typename TSpec>
  *            class String<TValue, TSpec>;
@@ -157,14 +157,14 @@ struct Alloc {};
  * @tparam TSpec  The tag for selecting the string specialization.
  *
  * The String class is for storing sequences and thus at the core of the sequence analysis library SeqAn.  They
- * are models for the @link SequenceConcept sequence concept @endlink but extend the sequence concept by allowing
+ * are models for the @link StringConcept sequence concept @endlink but extend the sequence concept by allowing
  * implicit conversion of other sequence into strings as long as the element conversion works:
  *
- * @snippet demos/sequence/string.cpp initializing strings
+ * @snippet demos/dox/sequence/string.cpp initializing strings
  *
  * Aside from that, the usual operations (appending, insertion, removing, element access) are available as well.
  *
- * @snippet demos/sequence/string.cpp usual operations
+ * @snippet demos/dox/sequence/string.cpp usual operations
  *
  * Strings have a size (the actual number of elements) and a capacity (the number of elements that memory has been
  * allocated for).  Note that clearing a string does not free the memory (as the STL, SeqAn assumes that strings will
@@ -172,7 +172,7 @@ struct Alloc {};
  * force a re-allocation of the memory such that the string afterward uses the minimal amount of memory to accomodate
  * all of its objects.
  *
- * @snippet demos/sequence/string.cpp clear and resize
+ * @snippet demos/dox/sequence/string.cpp clear and resize
  *
  * @section Examples
  *
@@ -181,11 +181,11 @@ struct Alloc {};
  * String container with other than simple type values.  See class @link Index @endlink example for efficiently finding
  * the same pattern matches using an index.
  *
- * @include demos/sequence/string2.cpp
+ * @include demos/dox/sequence/string2.cpp
  *
  * The output is as follows:
  *
- * @include demos/sequence/string2.cpp.stdout
+ * @include demos/dox/sequence/string2.cpp.stdout
  *
  * @see StringSet
  */
@@ -197,8 +197,8 @@ struct Alloc {};
  * @signature String::String()
  * @signature String::String(other)
  *
- * @param other The source for the copy constructor.  Can be of any @link SequenceConcept sequence @endlink type
- *              as long as <tt>other</tt>'s elements are convertible to the value type of this string.
+ * @param[in] other The source for the copy constructor.  Can be of any @link StringConcept sequence @endlink type
+ *                  as long as <tt>other</tt>'s elements are convertible to the value type of this string.
  *
  * Default and copy constructor are implemented.
  */
@@ -209,9 +209,9 @@ struct Alloc {};
  *
  * @signature TString String::operator=(other)
  *
- * @param other The other string.  Must be a sequence whose elements are convertible into this String's type.
+ * @param[in] other The other string.  Must be a sequence whose elements are convertible into this String's type.
  *
- * @returns TString Reference to the String objecta after assignment.
+ * @return TString Reference to the String objecta after assignment.
  */
 
 // TODO(holtgrew): The conversion functions rather belong into their own group than to the concept. The original documentation was a bit misleading and needs to be updated.
@@ -220,25 +220,25 @@ struct Alloc {};
  * @fn TextConcept#posLocalize
  * @brief Converts a local/global to a local position.
  * @headerfile <seqan/sequence.h>
- * 
+ *
  * @signature void posLocalize(result, pos, limits)
- * 
- * @param pos    A local or global position (pair or integer value).
- * @param limits The limits string returned by @link TextConcept#stringSetLimits @endlink.
- * @param result Reference to the resulting corresponding local position of
- *               <tt>pos</tt>.
+ *
+ * @param[in] pos    A local or global position (pair or integer value).
+ * @param[in] limits The limits string returned by @link TextConcept#stringSetLimits @endlink.
+ * @param[in] result Reference to the resulting corresponding local position of
+ *                   <tt>pos</tt>.
  */
 
 /*!
  * @fn TextConcept#posGlobalize
  * @brief Converts a local/global to a global position.
  * @headerfile <seqan/sequence.h>
- * 
+ *
  * @signature TPos posGlobalize(pos, limits)
- * 
- * @param pos A local or global position (pair or integer value). Types: Pair
- * @param limits The limits string returned by @link TextConcept#stringSetLimits @endlink.
- * 
+ *
+ * @param[in] pos A local or global position (pair or integer value). Types: Pair
+ * @param[in] limits The limits string returned by @link TextConcept#stringSetLimits @endlink.
+ *
  * @return TPos The corresponding global position of <tt>pos</tt>. If
  *                 <tt>pos</tt> is an integral type <tt>pos</tt> is returned. If
  *                 not, <tt>limits[getSeqNo(pos, limits)] + getSeqOffset(pos,
@@ -249,12 +249,12 @@ struct Alloc {};
  * @fn TextConcept#getSeqNo
  * @brief Returns the sequence number of a position.
  * @headerfile <seqan/sequence.h>
- * 
+ *
  * @signature TSeqNo getSeqNo(pos[, limits]);
- * 
- * @param pos A position. Types: Pair
- * @param limits The limits string returned by @link TextConcept#stringSetLimits @endlink.
- * 
+ *
+ * @param[in] pos A position. Types: Pair
+ * @param[in] limits The limits string returned by @link TextConcept#stringSetLimits @endlink.
+ *
  * @return TSeqNo A single integer value that identifies the string within the stringset <tt>pos</tt> points at. If
  *                <tt>limits</tt> is omitted or @link Nothing @endlink <tt>getSeqNo</tt> returns 0.If <tt>pos</tt> is a
  *                local position (of class @link Pair @endlink) then <tt>i1</tt> is returned.If <tt>pos</tt> is a global
@@ -266,12 +266,12 @@ struct Alloc {};
  * @fn TextConcept#getSeqOffset
  * @brief Returns the local sequence offset of a position.
  * @headerfile <seqan/sequence.h>
- * 
+ *
  * @signature TOffset getSeqOffset(pos[, limits]);
- * 
- * @param pos A position. Types: Pair
- * @param limits The limits string returned by @link TextConcept#stringSetLimits @endlink.
- * 
+ *
+ * @param[in] pos A position. Types: Pair
+ * @param[in] limits The limits string returned by @link TextConcept#stringSetLimits @endlink.
+ *
  * @return TOffset A single integer value that identifies the position within the string <tt>pos</tt> points at.If
  *                 <tt>limits</tt> is omitted or @link Nothing @endlink <tt>getSeqNo</tt> returns <tt>pos</tt>.  If
  *                 <tt>pos</tt> is a local position (of class @link Pair @endlink) then <tt>i2</tt> is returned.If
@@ -279,51 +279,6 @@ struct Alloc {};
  *                 <tt>pos</tt> is converted to a local position and <tt>i2</tt> is returned.
  */
 
-/**
-.Class.String
-..cat:Sequences
-..summary:A sequence container with generic alphabet and many specializations.
-..description:
-String is at the heart of the SeqAn library (SeqAn is for SEQuence ANalaysis after all).
-There are various specializations with @Spec.Alloc String@ being the default and most widely used one.
-Strings can be used to store arbitrary values and can be used for large biologicaly sequences as well as a generic, dynamic array and replace $std::vector<>$.
-..signature:String<TValue, TSpec>
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...metafunction:Metafunction.Value
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-...default:$Alloc<>$, see @Spec.Alloc String@.
-..implements:Concept.ContainerConcept
-..include:seqan/sequence.h
-..example
-...text:This example shows a brute force pattern matching scheme for two character Strings. Creation of String "text" shows the usage of some available String operating functions. See class @Class.StringSet@ for an example of a String container with other than simple type values. See class @Class.Index@ example for efficiently finding the same pattern matches using an index. 
-...file:demos/sequence/string2.cpp
-...text:The output of this demo is:
-...output:to be
-Last sign is whitespace? 1
-tobeornottobe
-hit at 2 11
-
-.Memfunc.String#String
-..class:Class.String
-..signature:String::String()
-..signature:String::String(other)
-..signature:String::String(seq)
-..summary:Constructor
-..description:
-The $String$ class provides the default constructor and copy constructor.
-Additionally, you can construct a string from any sequence.
-..param.other:Another $String$ object of the same type.
-..param.seq:A sequence to copy into the $String$.
-...type:Concept.SequenceConcept
-..remarks:
-The third variant (construction from sequence) first reserves the necessary space and then copies over the characters from $seq$.
-During this copying, the source characters are implicitely casted/converted into the alphabet of the String.
-For example, @Spec.Dna@ characters can be converted to @Spec.Dna5@ characters and vice versa.
-The conversion can be lossy, e.g. when converting from @Spec.Dna5@ to @Spec.Dna@, all $N$ characters are replaced by $A$ characters.
-Similarly, when converting from $char$ to @Spec.Dna5@, all characters except ${A, a, C, c, G, g, T, t}$ are converted to $N$.
-*/
-
 template <typename TValue, typename TSpec = Alloc<> >
 class String;
 
@@ -335,9 +290,6 @@ class String;
 // Metafunction Value
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Value.param.T.type:Class.String
-///.Metafunction.Value.class:Class.String
-
 template <typename TValue, typename TSpec>
 struct Value<String<TValue, TSpec> >
 {
@@ -353,9 +305,6 @@ struct Value<String<TValue, TSpec> const >
 // Metafunction Spec
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Spec.param.T.type:Class.String
-///.Metafunction.Spec.class:Class.String
-
 template <typename TValue, typename TSpec>
 struct Spec<String<TValue, TSpec> >
 {
@@ -368,30 +317,52 @@ struct Spec<String<TValue, TSpec> const>:
 };
 
 // ----------------------------------------------------------------------------
-// Metafunction IsSequence
+// Metafunction StringSpec
 // ----------------------------------------------------------------------------
 
-///.Metafunction.IsSequence.param.T.type:Class.String
-///.Metafunction.IsSequence.class:Class.String
+template <typename T>
+struct StringSpec
+{
+    typedef Alloc<> Type;
+};
+
+template <typename T>
+struct StringSpec<T const> : StringSpec<T> {};
 
 template <typename TValue, typename TSpec>
-struct IsSequence<String<TValue, TSpec> > {
-    typedef True Type;
-    enum { VALUE = true };
+struct StringSpec<String<TValue, TSpec> >
+{
+    typedef TSpec   Type;
 };
 
+// ----------------------------------------------------------------------------
+// Metafunction Chunk
+// ----------------------------------------------------------------------------
+
 template <typename TValue, typename TSpec>
-struct IsSequence<String<TValue, TSpec> const> : IsSequence<String<TValue, TSpec> > {};
+struct Chunk<String<TValue, TSpec> >:
+    Chunk<typename Iterator<String<TValue, TSpec>, Rooted>::Type> {};
 
 // ----------------------------------------------------------------------------
-// Internal Metafunction TempCopy_
+// Metafunction IsSequence
 // ----------------------------------------------------------------------------
 
-/**
-.Internal.TempCopy_
-..cat:Metafunctions
-..summary:Returns a Class that can be used to store a temporary copy of a String
- */
+template <typename TValue, typename TSpec>
+struct IsSequence<String<TValue, TSpec> > : True {};
+
+// ----------------------------------------------------------------------------
+// Concept StringConcept
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+SEQAN_CONCEPT_IMPL((String<TValue, TSpec>), (StringConcept));         // resizable container
+
+template <typename TValue, typename TSpec>
+SEQAN_CONCEPT_IMPL((String<TValue, TSpec> const), (ContainerConcept));  // read-only container
+
+// ----------------------------------------------------------------------------
+// Internal Metafunction TempCopy_
+// ----------------------------------------------------------------------------
 
 template <typename T>
 struct TempCopy_
@@ -407,43 +378,15 @@ struct TempCopy_
 
 // TODO(holtgrew): Where to move this documentation/specification-only stuff?
 
-///.Function.getObjectId.param.object.type:Class.String
-///.Function.getObjectId.class:Class.String
-///.Function.empty.param.object.type:Class.String
-///.Function.empty.class:Class.String
-///.Function.capacity.param.object.type:Class.String
-///.Function.capacity.class:Class.String
-
 // ----------------------------------------------------------------------------
 // Function swap()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.swap:
-..summary:Swaps the contents of two values.
-..class:Class.String
-..cat:Content Manipulation
-..signature:swap(left, right)
-..param.left:The first value.
-...type:Class.String
-..param.right:The second value.
-...type:Class.String
-..remarks:The function swaps the values of variables left and right.
-This is equivalent to using move three times with a temporary variable.
-
-Note that this function has the same name as the STL function $std::swap$ but is in a different namespace.
-Argument Dependent Lookup (ADL, aka Koenig lookup) will take care that the right $swap$ function is called from STL $sort$, for example.
-We only specialize it for Class.String and Class.StringSet.
-..see:Function.move
-..include:seqan/sequence.h
-*/
-
 template <typename TAlphabet, typename TSpec>
 inline void
 swap(String<TAlphabet, TSpec> & left,
      String<TAlphabet, TSpec> & right)
 {
-    SEQAN_CHECKPOINT;
 
     typedef String<TAlphabet, TSpec> TString;
 
@@ -456,14 +399,11 @@ swap(String<TAlphabet, TSpec> & left,
 // Function shareResources()
 // ----------------------------------------------------------------------------
 
-///.Function.shareResources.param.sequence1, sequence2.type:Class.String
-
 template <typename TValue, typename TSpec>
 inline bool
 shareResources(String<TValue, TSpec> const & obj1,
                TValue const & obj2)
 {
-    SEQAN_CHECKPOINT;
     return (begin(obj1) >= &obj2) && (end(obj1) <= &obj2);
 }
 
@@ -472,29 +412,22 @@ inline bool
 shareResources(TValue const & obj1,
                String<TValue, TSpec> const & obj2)
 {
-    SEQAN_CHECKPOINT;
     return (begin(obj2) >= &obj1) && (end(obj2) <= &obj1);
 }
 
 // TODO(holtgrew): Where to move this documentation/specification-only stuff?
-///.Function.begin.param.object.type:Class.String
-///.Function.begin.class:Class.String
-///.Function.end.param.object.type:Class.String
-///.Function.end.class:Class.String
-
 // ----------------------------------------------------------------------------
 // Function value()
 // ----------------------------------------------------------------------------
 
-///.Function.value.param.container.type:Class.String
-
 template <typename TValue, typename TSpec, typename TPos>
 SEQAN_HOST_DEVICE inline typename Reference< String<TValue, TSpec> >::Type
 value(String<TValue, TSpec> & me,
       TPos const & pos)
 {
-    SEQAN_CHECKPOINT;
+#if SEQAN_ENABLE_DEBUG
     typedef typename Position< String<TValue, TSpec> >::Type TStringPos SEQAN_TYPEDEF_FOR_DEBUG;
+#endif
     SEQAN_ASSERT_LT_MSG(static_cast<TStringPos>(pos), static_cast<TStringPos>(length(me)), "Trying to access an element behind the last one!");
     return *(begin(me, Standard()) + pos);
 }
@@ -504,8 +437,9 @@ SEQAN_HOST_DEVICE inline typename Reference< String<TValue, TSpec> const >::Type
 value(String<TValue, TSpec> const & me,
       TPos const & pos)
 {
-    SEQAN_CHECKPOINT;
+#if SEQAN_ENABLE_DEBUG
     typedef typename Position< String<TValue, TSpec> const >::Type TStringPos SEQAN_TYPEDEF_FOR_DEBUG;
+#endif
     SEQAN_ASSERT_LT_MSG(static_cast<TStringPos>(pos), static_cast<TStringPos>(length(me)), "Trying to access an element behind the last one!");
     return *(begin(me, Standard()) + pos);
 }
@@ -514,14 +448,10 @@ value(String<TValue, TSpec> const & me,
 // Function length()
 // ----------------------------------------------------------------------------
 
-///.Function.length.param.object.type:Class.String
-///.Function.length.class:Class.String
-
 template <typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline typename Size< String<TValue, TSpec> const>::Type
 length(String<TValue, TSpec> const & me)
 {
-    SEQAN_CHECKPOINT;
     return end(me, Standard()) - begin(me, Standard());
 }
 
@@ -529,14 +459,10 @@ length(String<TValue, TSpec> const & me)
 // Function empty()
 // ----------------------------------------------------------------------------
 
-///.Function.empty.param.object.type:Class.String
-///.Function.empty.class:Class.String
-
 template <typename TValue, typename TSpec>
 SEQAN_HOST_DEVICE inline bool
 empty(String<TValue, TSpec> const & me)
 {
-    SEQAN_CHECKPOINT;
     return end(me, Standard()) == begin(me, Standard());
 }
 
@@ -544,28 +470,10 @@ empty(String<TValue, TSpec> const & me)
 // Function clear()
 // ----------------------------------------------------------------------------
 
-/**
-.Function.clear:
-..cat:Containers
-..class:Class.String
-..summary:Resets an object.
-..signature:clear(object)
-..param.object:The object that will be resetted.
-...type:Class.String
-..remarks:$object$ is set to a state that is equivalent to a default constructed object of the same type.
-..remarks:If $object$ is a container, then all elements are removed from this container.
-The length is set to 0.
-The capacity can be changed, depending on the implementation.
-..see:Function.resize
-..see:Function.length
-..include:seqan/sequence.h
-*/
-
 template <typename TValue, typename TSpec>
 inline void
 clear(String<TValue, TSpec> & me)
 {
-    SEQAN_CHECKPOINT;
     arrayDestruct(begin(me, Standard()), end(me, Standard()));
     _setLength(me, 0);
 }
@@ -592,7 +500,6 @@ struct ClearSpaceStringBase_<Insist>
         T & seq,
         typename Size<T>::Type size)
     {
-        SEQAN_CHECKPOINT;
         arrayDestruct(begin(seq, Standard()), end(seq, Standard()));
         _setLength(seq, size);
         return size;
@@ -608,7 +515,6 @@ struct ClearSpaceStringBase_<Insist>
         arrayDestruct(begin(seq, Standard()), end(seq, Standard()));
         if (limit < size)
         {
-            SEQAN_CHECKPOINT;
             size = limit;
         }
         _setLength(seq, size);
@@ -623,7 +529,6 @@ struct ClearSpaceStringBase_<Insist>
         typename Size<T>::Type start,
         typename Size<T>::Type end)
     {
-        SEQAN_CHECKPOINT;
         typename Size<T>::Type new_length = length(seq) + size - (end - start);
         arrayClearSpace(begin(seq, Standard()) + start, length(seq) - start, end - start, size);
         _setLength(seq, new_length);
@@ -644,12 +549,10 @@ struct ClearSpaceStringBase_<Insist>
 
         if (limit > start + size)
         {
-            SEQAN_CHECKPOINT;
             typename Size<T>::Type removed_size = end - start;
             typename Size<T>::Type new_length = seq_length - removed_size + size;
             if (limit < new_length)
             {
-                SEQAN_CHECKPOINT;
                 arrayDestruct(seq_buffer + limit, seq_buffer + new_length);
                 seq_length -= new_length - limit;
             }
@@ -659,7 +562,6 @@ struct ClearSpaceStringBase_<Insist>
         }
         else
         {
-            SEQAN_CHECKPOINT;
             arrayDestruct(seq_buffer + start, seq_buffer + seq_length);
             _setLength(seq, limit);
             if (limit > start) return limit - start;
@@ -705,7 +607,6 @@ struct ClearSpaceStringBase_<Limit>
         T & seq,
         typename Size<T>::Type size)
     {
-        SEQAN_CHECKPOINT;
         return _clearSpace(seq, size, capacity(seq), Insist());
     }
 
@@ -719,7 +620,6 @@ struct ClearSpaceStringBase_<Limit>
         typename Size<T>::Type seq_capacity = capacity(seq);
         if (limit > seq_capacity)
         {
-            SEQAN_CHECKPOINT;
             limit = seq_capacity;
         }
         return _clearSpace(seq, size, limit, Insist());
@@ -733,7 +633,6 @@ struct ClearSpaceStringBase_<Limit>
         typename Size<T>::Type start,
         typename Size<T>::Type end)
     {
-        SEQAN_CHECKPOINT;
         return _clearSpace(seq, size, start, end, capacity(seq), Insist());
     }
 
@@ -749,7 +648,6 @@ struct ClearSpaceStringBase_<Limit>
         typename Size<T>::Type seq_capacity = capacity(seq);
         if (limit > seq_capacity)
         {
-            SEQAN_CHECKPOINT;
             limit = seq_capacity;
         }
         return _clearSpace(seq, size, start, end, limit, Insist());
@@ -797,7 +695,6 @@ struct ClearSpaceExpandStringBase_
         typename Value<T>::Type * old_array = _reallocateStorage(seq, size, TExpand());
         if (old_array)
         {
-            SEQAN_CHECKPOINT;
             _deallocateStorage(seq, old_array, old_capacity);
         }
         _setLength(seq, size);
@@ -814,7 +711,6 @@ struct ClearSpaceExpandStringBase_
         arrayDestruct(begin(seq, Standard()), end(seq, Standard()));
         if (limit < size)
         {
-            SEQAN_CHECKPOINT;
             size = limit;
         }
         typename Size<T>::Type old_capacity = capacity(seq);
@@ -839,20 +735,22 @@ struct ClearSpaceExpandStringBase_
         typename Size<T>::Type removed_size = end - start;
         typename Size<T>::Type new_length = old_length - removed_size + size;
 
+        SEQAN_ASSERT_LEQ(start, end);
+        SEQAN_ASSERT_LEQ(start, old_length);
+
         typename Size<T>::Type old_capacity = capacity(seq);
         typename Value<T>::Type * old_array = _reallocateStorage(seq, new_length, TExpand());
         typename Value<T>::Type * seq_array = begin(seq);
 
         if (old_array)
         {
-            SEQAN_CHECKPOINT;
             arrayConstructMove(old_array, old_array + start, seq_array);
             arrayConstructMove(old_array + end, old_array + old_length, seq_array + start + size);
             _deallocateStorage(seq, old_array, old_capacity);
+            // TODO(weese:) Did we miss to destruct the old_array here, e.g. with arrayDestruct
         }
         else
         {
-            SEQAN_CHECKPOINT;
             arrayClearSpace(seq_array + start, old_length - start, removed_size, size);
         }
 
@@ -874,11 +772,13 @@ struct ClearSpaceExpandStringBase_
         typename Size<T>::Type removed_size = end - start;
         typename Size<T>::Type need_length = old_length - removed_size + size;
 
+        SEQAN_ASSERT_LEQ(start, end);
+        SEQAN_ASSERT_LEQ(start, old_length);
+
         typename Size<T>::Type new_length = need_length;
         typename Size<T>::Type length_to_copy = old_length;
         if (limit < need_length)
         {
-            SEQAN_CHECKPOINT;
             new_length = limit;
             length_to_copy = new_length - size + removed_size;
         }
@@ -962,32 +862,12 @@ struct ClearSpaceStringBase_<Generous>:
 {
 };
 
-/**
-.Internal._clearSpace:
-..cat:Functions
-..summary:Makes space in container
-..signature:_clearSpace(object, size [, pos_begin, pos_end] [, limit], resize_tag)
-..param.object:The container.
-..param.size:Length of the freed space.
-..param.pos_begin:Position of the first item in $object$ that is to be destroyed. (optional)
-..param.pos_end:Position behind the last item in $object$ that is to be destroyed. (optional)
-...remarks:If $pos_end == pos_begin$, no item in $object$ will be destroyed.
-..param.limit:Maximal length $object$ can get after this operation. (optional)
-..param.resize_tag:Strategy that is applied if $object$ has not enough capacity to store the complete content.
-..returns:The number of free characters.
-...remarks:Depeding on the @Tag.Overflow Strategy.overflow strategy@ specified by $resize_tag$,
-this could be $size$ or less than $size$ if $object$ has not enough @Function.capacity@.
-..remarks:This function is similar to @Function.resizeSpace@ and @Function.fillSpace@.
-The main difference is that $_clearSpace$ does not construct objects in the new created space.
-*/
-
 template<typename TValue, typename TSpec, typename TSize, typename TExpand>
 inline typename Size< String<TValue, TSpec> >::Type
 _clearSpace(String<TValue, TSpec> & me,
         TSize size,
         Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
     return ClearSpaceStringBase_<Tag<TExpand> >::_clearSpace_(me, size);
 }
 
@@ -998,7 +878,6 @@ _clearSpace(String<TValue, TSpec> & me,
         TCapacity limit,
         Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
     return ClearSpaceStringBase_<Tag<TExpand> >::_clearSpace_(me, size, limit);
 }
 
@@ -1010,7 +889,6 @@ _clearSpace(String<TValue, TSpec> & me,
             TPosition pos_end,
             Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
     return ClearSpaceStringBase_<Tag<TExpand> >::_clearSpace_(me, size, pos_begin, pos_end);
 }
 
@@ -1023,7 +901,6 @@ _clearSpace(String<TValue, TSpec> & me,
             TCapacity limit,
             Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
     return ClearSpaceStringBase_<Tag<TExpand> >::_clearSpace_(me, size, pos_begin, pos_end, limit);
 }
 
@@ -1031,9 +908,6 @@ _clearSpace(String<TValue, TSpec> & me,
 // Function resizeSpace()
 // ----------------------------------------------------------------------------
 
-///.Function.resizeSpace.param.object.type:Class.String
-///.Function.resizeSpace.class:Class.String
-
 template<typename TValue, typename TSpec, typename TSize, typename TBeginPosition, typename TEndPosition, typename TExpand>
 inline typename Size< String<TValue, TSpec> >::Type
 resizeSpace(String<TValue, TSpec> & me,
@@ -1042,7 +916,6 @@ resizeSpace(String<TValue, TSpec> & me,
             TEndPosition pos_end,
             Tag<TExpand> tag)
 {
-    SEQAN_CHECKPOINT;
     typedef typename Size< String<TValue, TSpec> >::Type TSize_;
     typedef typename Position<String<TValue, TSpec> >::Type TPos_;
     TSize_ ret_ = _clearSpace(
@@ -1064,7 +937,6 @@ resizeSpace(String<TValue, TSpec> & me,
             TCapacity limit,
             Tag<TExpand> tag)
 {
-    SEQAN_CHECKPOINT;
     typedef typename Size< String<TValue, TSpec> >::Type TSize_;
     typedef typename Position<String<TValue, TSpec> >::Type TPos_;
     TSize_ ret_ = _clearSpace(
@@ -1082,11 +954,6 @@ resizeSpace(String<TValue, TSpec> & me,
 // Function assign()
 // ----------------------------------------------------------------------------
 
-///.Function.assign.param.target.type:Class.String
-///.Function.assign.class:Class.String
-///.Function.assign.param.source.type:Class.String
-///.Function.assign.class:Class.String
-
 // Facade version without overflow tag.  Forwards to version with overflow
 // tag, using Metafunction.DefaultOverflowImplicity.
 
@@ -1123,13 +990,11 @@ struct AssignString_
             return;  // Do nothing if both source and target are empty.
         if (!getObjectId(source) || !shareResources(target, source))
         {
-            SEQAN_CHECKPOINT;
             typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), TExpand());
             arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
         }
         else
         {
-            SEQAN_CHECKPOINT;
             if ((void *) &target == (void *) &source) return;
 
             typename TempCopy_<TSource>::Type temp(source, length(source));
@@ -1146,13 +1011,11 @@ struct AssignString_
     {
         if (!getObjectId(source) || !shareResources(target, source))
         {
-            SEQAN_CHECKPOINT;
             typename Size<TTarget>::Type part_length = _clearSpace(target, typename Size<TTarget>::Type(length(source)), limit, TExpand());
             arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()));
         }
         else
         {
-            SEQAN_CHECKPOINT;
             if ((void *) &target == (void *) &source) return;
 
             typename Size<TTarget>::Type source_length = length(source);
@@ -1185,26 +1048,26 @@ assign(String<TTargetValue, TTargetSpec> & target,
     AssignString_<Tag<TExpand> >::assign_(target, source, limit);
 }
 
-// TODO(holtgrew): Still required with dropped VC++ 2003 support?
-//this variant is a workaround for the "const array"-bug of VC++
-
-template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
-inline void
-assign(String<TTargetValue, TTargetSpec> & target,
-       TSourceValue const * source,
-       Tag<TExpand>)
-{
-    AssignString_<Tag<TExpand> >::assign_(target, source);
-}
-template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSize, typename TExpand>
-inline void
-assign(String<TTargetValue, TTargetSpec> & target,
-       TSourceValue const * source,
-       TSize limit,
-       Tag<TExpand>)
-{
-    AssignString_<Tag<TExpand> >::assign_(target, source, limit);
-}
+//// TODO(holtgrew): Still required with dropped VC++ 2003 support?
+////this variant is a workaround for the "const array"-bug of VC++
+//
+//template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
+//inline void
+//assign(String<TTargetValue, TTargetSpec> & target,
+//       TSourceValue const * source,
+//       Tag<TExpand>)
+//{
+//    AssignString_<Tag<TExpand> >::assign_(target, source);
+//}
+//template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TSize, typename TExpand>
+//inline void
+//assign(String<TTargetValue, TTargetSpec> & target,
+//       TSourceValue const * source,
+//       TSize limit,
+//       Tag<TExpand>)
+//{
+//    AssignString_<Tag<TExpand> >::assign_(target, source, limit);
+//}
 
 // ----------------------------------------------------------------------------
 // Function move()
@@ -1231,7 +1094,6 @@ _moveContiguous(TTarget & target,
     typename Size<TTarget>::Type size = sizeof(TSourceValue) * capacity(source);
     if (size >= sizeof(TTargetValue))
     {
-        SEQAN_CHECKPOINT;
         if (sizeof(TSourceValue) <= 2) ++size; //regard the "end of string termination" case
         typename Size<TTarget>::Type target_capacity = size / sizeof(TTargetValue);
         if (sizeof(TTargetValue) <= 2) --target_capacity; //regard the "end of string termination" case
@@ -1271,7 +1133,6 @@ inline void
 move(String<TTargetValue, TTargetSpec> & target,
      TSource & source)
 {
-    SEQAN_CHECKPOINT;
     typedef String<TTargetValue, TTargetSpec> TTarget;
     move(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
 }
@@ -1281,7 +1142,6 @@ inline void
 move(String<TTargetValue, TTargetSpec> & target,
      TSource const & source)
 {
-    SEQAN_CHECKPOINT;
     typedef String<TTargetValue, TTargetSpec> TTarget;
     move(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
 }
@@ -1292,7 +1152,6 @@ move(String<TTargetValue, TTargetSpec> & target,
      TSource & source,
      Tag<TTag> const & tag)
 {
-    SEQAN_CHECKPOINT;
     assign(target, source, tag);
 }
 
@@ -1302,7 +1161,6 @@ move(String<TTargetValue, TTargetSpec> & target,
      TSource const & source,
      Tag<TTag> const & tag)
 {
-    SEQAN_CHECKPOINT;
     assign(target, source, tag);
 }
 
@@ -1347,10 +1205,6 @@ _stringCheckForPossibleOverlap(TIter const &it1, TIter const &it2, TSize length)
 // Function append()
 // ----------------------------------------------------------------------------
 
-///.Function.append.param.target.type:Class.String
-///.Function.append.param.source.type:Class.String
-///.Function.append.class:Class.String
-
 template <typename TExpand>
 struct AppendString_
 {
@@ -1362,14 +1216,12 @@ struct AppendString_
         if (!getObjectId(source) || !shareResources(target, source) ||
             !_stringCheckForPossibleOverlap(begin(source, Standard()), end(target, Standard()), length(source)))
         {
-            SEQAN_CHECKPOINT;
             typename Size<TTarget>::Type target_length = length(target);
             typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), target_length, target_length, TExpand());
             arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + target_length);
         }
         else
         {
-            SEQAN_CHECKPOINT;
             typename TempCopy_<TSource>::Type temp(source, length(source));
             append(target, temp, TExpand());
         }
@@ -1384,7 +1236,6 @@ struct AppendString_
         typename Iterator<TTarget, Standard>::Type target_begin = begin(target, Standard());
         if (!getObjectId(source) || !shareResources(target, source))
         {
-SEQAN_CHECKPOINT
             typename Size<TTarget>::Type target_length = length(target);
             typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), target_length, target_length, limit, TExpand());
             arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + target_length);
@@ -1394,13 +1245,11 @@ SEQAN_CHECKPOINT
             typename Size<TTarget>::Type target_length = length(target);
             if (target_length >= limit)
             {
-                SEQAN_CHECKPOINT;
                 arrayDestruct(target_begin + limit, target_begin + target_length);
                 _setLength(target, limit);
             }
             else
             {
-                SEQAN_CHECKPOINT;
                 limit -= target_length;
                 typename Size<TTarget>::Type source_length = length(source) ;
                 if (source_length > limit) source_length = limit;
@@ -1428,63 +1277,64 @@ append(String<TTargetValue, TTargetSpec> & target,
        typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
        Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
     AppendString_<Tag<TExpand> >::append_(target, source, limit);
 }
 
 // TODO(holtgrew): Still required with dropped VC++ 2003 support?
 //this variant is a workaround for the "const array"-bug of VC++
 
-template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
-inline void
-append(String<TTargetValue, TTargetSpec> & target,
-       TSourceValue * source,
-       Tag<TExpand>)
-{
-    SEQAN_CHECKPOINT;
-    AppendString_<Tag<TExpand> >::append_(target, source);
-}
-
-template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
-inline void
-append(String<TTargetValue, TTargetSpec> & target,
-       TSourceValue * source,
-       typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
-       Tag<TExpand>)
-{
-    SEQAN_CHECKPOINT;
-    AppendString_<Tag<TExpand> >::append_(target, source, limit);
-}
+// template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
+// inline void
+// append(String<TTargetValue, TTargetSpec> & target,
+//        TSourceValue * source,
+//        Tag<TExpand>)
+// {
+//     AppendString_<Tag<TExpand> >::append_(target, source);
+// }
+//
+// template<typename TTargetValue, typename TTargetSpec, typename TSourceValue, typename TExpand>
+// inline void
+// append(String<TTargetValue, TTargetSpec> & target,
+//        TSourceValue * source,
+//        typename Size< String<TTargetValue, TTargetSpec> >::Type limit,
+//        Tag<TExpand>)
+// {
+//     AppendString_<Tag<TExpand> >::append_(target, source, limit);
+// }
 
 // ----------------------------------------------------------------------------
 // Function appendValue()
 // ----------------------------------------------------------------------------
 
+//TODO(h4nn3): why do we have these weird extra class? the function inside
+// is only ever used in the function below and could reside directly there
 template <typename TExpand>
 struct AppendValueToString_
 {
     template <typename T, typename TValue>
     static inline void
     appendValue_(T & me,
-                TValue & _value)
+                 TValue SEQAN_FORWARD_CARG _value)
     {
-        SEQAN_CHECKPOINT;
-        typename Position<T>::Type me_length = length(me);
+        typedef typename Value<T>::Type TTargetValue;
+        typedef typename Size<T>::Type TSize;
+
+        TSize me_length = length(me);
         if (capacity(me) <= me_length)
         {
-            typename Value<T>::Type temp_copy(_value); //temp copy because resize could invalidate _value
+            TTargetValue temp_copy(SEQAN_FORWARD(TValue, _value)); //temp copy because resize could invalidate _value
             // TODO(holtgrew): The resize() function will default construct the last element. This is slow. Get rid of this.
-            typename Size<T>::Type new_length = reserve(me, me_length + 1, TExpand());
+            TSize new_length = reserve(me, me_length + 1, TExpand());
             if (me_length < new_length)
             {
                 // *(begin(me) + me_length) = temp_copy;
-                valueConstruct(begin(me, Standard()) + me_length, temp_copy); //??? this should be valueMoveConstruct
+                valueConstruct(begin(me, Standard()) + me_length, SEQAN_FORWARD(TTargetValue, temp_copy)); //??? this should be valueMoveConstruct
                 _setLength(me, me_length + 1);
             }
         }
         else
         {
-            valueConstruct(begin(me, Standard()) + me_length, _value);
+            valueConstruct(begin(me, Standard()) + me_length, SEQAN_FORWARD(TValue, _value));
             _setLength(me, me_length + 1);
         }
     }
@@ -1493,23 +1343,30 @@ struct AppendValueToString_
 template <typename TTargetValue, typename TTargetSpec, typename TValue, typename TExpand>
 inline void
 appendValue(String<TTargetValue, TTargetSpec> & me,
-            TValue const & _value,
+            TValue SEQAN_FORWARD_CARG _value,
             Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
-    AppendValueToString_<Tag<TExpand> >::appendValue_(me, _value);
+    AppendValueToString_<Tag<TExpand> >::appendValue_(me, SEQAN_FORWARD(TValue, _value));
+}
+
+// ----------------------------------------------------------------------------
+// Function appendValue(Serial)
+// ----------------------------------------------------------------------------
+
+template <typename TTargetValue, typename TTargetSpec, typename TValue, typename TExpand>
+inline void
+appendValue(String<TTargetValue, TTargetSpec> & me,
+            TValue SEQAN_FORWARD_CARG _value,
+            Tag<TExpand> const & expandTag,
+            Serial)
+{
+    appendValue(me, SEQAN_FORWARD(TValue, _value), expandTag);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 // insertValue
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Function.insertValue:
-..class:Class.String
-..include:seqan/sequence.h
-*/
-
 template <typename TExpand>
 struct InsertValueToString_
 {
@@ -1519,7 +1376,6 @@ struct InsertValueToString_
                 TPosition pos,
                 TValue & _value)
     {
-        SEQAN_CHECKPOINT;
         typename Value<T>::Type temp_copy = _value; //temp copy because resizeSpace could invalidate _value
         resizeSpace(me, 1, pos, pos, TExpand());
         if ((typename Size<T>::Type) pos < length(me))
@@ -1534,7 +1390,6 @@ insertValue(String<TTargetValue, TTargetSpec> & me,
             TValue const & _value,
             Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
     InsertValueToString_<Tag<TExpand> >::insertValue_(me, pos, _value);
 }
 
@@ -1542,10 +1397,6 @@ insertValue(String<TTargetValue, TTargetSpec> & me,
 // Function replace()
 // ----------------------------------------------------------------------------
 
-///.Function.replace.param.target.type:Class.String
-///.Function.replace.param.source.type:Class.String
-///.Function.replace.class:Class.String
-
 template <typename TExpand>
 struct ReplaceString_
 {
@@ -1558,13 +1409,11 @@ struct ReplaceString_
     {
         if (!getObjectId(source) || !shareResources(target, source))
         {
-            SEQAN_CHECKPOINT;
             typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, TExpand());
             arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + pos_begin);
         }
         else
         {
-            SEQAN_CHECKPOINT;
             typename TempCopy_<TSource>::Type temp(source, length(source));
             replace(target, pos_begin, pos_end, temp, TExpand());
         }
@@ -1580,7 +1429,6 @@ struct ReplaceString_
     {
         if (!getObjectId(source) || !shareResources(target, source))
         {
-            SEQAN_CHECKPOINT;
             typename Size<TTarget>::Type part_length = _clearSpace(target, length(source), pos_begin, pos_end, limit, TExpand());
             arrayConstructCopy(begin(source, Standard()), begin(source, Standard()) + part_length, begin(target, Standard()) + pos_begin);
         }
@@ -1588,13 +1436,11 @@ struct ReplaceString_
         {
             if (pos_begin >= limit)
             {
-                SEQAN_CHECKPOINT;
                 arrayDestruct(begin(target) + limit, end(target));
                 _setLength(target, limit);
             }
             else
             {
-                SEQAN_CHECKPOINT;
                 limit -= pos_begin;
                 typename Size<TTarget>::Type source_length = length(source) ;
                 if (source_length > limit) source_length = limit;
@@ -1660,22 +1506,6 @@ replace(String<TTargetValue, TTargetSpec> & target,
 // Internal Function _reallocateStorage()
 // ----------------------------------------------------------------------------
 
-/**
-.Internal._reallocateStorage:
-..cat:Functions
-..summary:Allocates a new buffer if needed.
-..signature:_reallocateStorage(object, new_capacity, resize_tag)
-..param.object:A container for which the buffer is reallocated.
-...type:Class.String
-..param.new_capacity:The capacity $object$ will get after reallocating the buffer.
-..param.resize_tag:Strategy that is used for changing the capacity.
-..returns:Returns the old buffer, if a new buffer has been allocated, $0$ otherwise.
-..remarks:This function only allocates a new buffer if the current capacity is less then $new_capacity$.
-A new buffer is not filled with any content, all copy operations must be done by the caller.
-..remarks:If $object$ never had a buffer, or the buffer is not changed by the function,
-the returned pointer is 0.
-*/
-
 template <typename TValue, typename TSpec, typename TSize>
 inline typename Value<String<TValue, TSpec> >::Type *
 _reallocateStorage(
@@ -1793,9 +1623,6 @@ _reallocateStorage(
 // Function reserve()
 // ----------------------------------------------------------------------------
 
-///.Function.reserve.param.object.type:Class.String
-///.Function.reserve.class:Class.String
-
 template <typename TValue, typename TSpec, typename TSize_>
 inline void
 _reserveStorage(
@@ -1835,9 +1662,8 @@ _reserveStorage(
     typename Value< String<TValue, TSpec> >::Type * old_array = _reallocateStorage(seq, new_capacity, tag);
     if (old_array)
     {//buffer was replaced, destruct old buffer
-//      arrayConstruct(begin(seq, Standard()), begin(seq, Standard()) + seq_length);
-//      arrayMoveForward(old_array, old_array + seq_length, begin(seq, Standard()));
-        arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
+//        arrayConstructCopy(old_array, old_array + seq_length, begin(seq, Standard()));
+        arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard()));
         arrayDestruct(old_array, old_array + seq_length);
         _deallocateStorage(seq, old_array, old_capacity);
     }
@@ -1851,7 +1677,6 @@ reserve(
     TSize_ new_capacity,
     Tag<TExpand> tag)
 {
-SEQAN_CHECKPOINT
     _reserveStorage(seq, new_capacity, tag);
     return _capacityReturned(seq, new_capacity, tag);
 }
@@ -1860,8 +1685,6 @@ SEQAN_CHECKPOINT
 // Function resize()
 // ----------------------------------------------------------------------------
 
-///.Function.resize.param.object.type:Class.String
-
 template <typename TExpand>
 struct _Resize_String
 {
@@ -1875,7 +1698,6 @@ struct _Resize_String
         TSize me_length = length(me);
         if (new_length < me_length)
         {
-            SEQAN_CHECKPOINT;
             arrayDestruct(begin(me, Standard()) + new_length, begin(me, Standard()) + me_length);
         }
         else
@@ -1883,7 +1705,6 @@ struct _Resize_String
             typename Size<T>::Type me_capacity = capacity(me);
             if (new_length > me_capacity)
             {
-                SEQAN_CHECKPOINT;
                 TSize new_capacity = reserve(me, new_length, TExpand());
                 if (new_capacity < new_length)
                 {
@@ -1892,7 +1713,6 @@ struct _Resize_String
             }
             if (new_length > me_length)
             {
-                SEQAN_CHECKPOINT;
                 arrayConstruct(begin(me, Standard()) + me_length, begin(me, Standard()) + new_length);
             }
         }
@@ -1912,7 +1732,6 @@ struct _Resize_String
         TSize me_length = length(me);
         if (new_length < me_length)
         {
-            SEQAN_CHECKPOINT;
             arrayDestruct(begin(me, Standard()) + new_length, begin(me, Standard()) + me_length);
         }
         else
@@ -1920,7 +1739,6 @@ struct _Resize_String
             TSize me_capacity = capacity(me);
             if (new_length > me_capacity)
             {
-                SEQAN_CHECKPOINT;
                 TValue tempCopy = val;  // reserve could invalidate val
                 TSize new_capacity = reserve(me, new_length, TExpand());
                 if (new_capacity < new_length)
@@ -1931,7 +1749,6 @@ struct _Resize_String
             } else
                 if (new_length > me_length)
                 {
-                    SEQAN_CHECKPOINT;
                     arrayConstruct(begin(me, Standard()) + me_length, begin(me, Standard()) + new_length, val);
                 }
         }
@@ -1948,7 +1765,6 @@ resize(
     TSize new_length,
     Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
     return _Resize_String<Tag<TExpand> >::resize_(me, new_length);
 }
 
@@ -1960,7 +1776,6 @@ resize(
     TValue2 const & val,
     Tag<TExpand>)
 {
-    SEQAN_CHECKPOINT;
     return _Resize_String<Tag<TExpand> >::resize_(me, new_length, val);
 }
 
@@ -1976,7 +1791,6 @@ String<TLeftValue, TLeftSpec> &
 operator+=(String<TLeftValue, TLeftSpec> & left,
            TRight const & right)
 {
-    SEQAN_CHECKPOINT;
     append(left, right);
     return left;
 }
@@ -1992,7 +1806,6 @@ inline bool
 operator==(String<TLeftValue, TLeftSpec> const & left,
            TRight const & right)
 {
-    SEQAN_CHECKPOINT;
     typename Comparator<String<TLeftValue, TLeftSpec> >::Type _lex(left, right);
     return isEqual(_lex);
 }
@@ -2002,7 +1815,6 @@ inline bool
 operator==(TLeftValue * left,
            String<TRightValue, TRightSpec> const & right)
 {
-    SEQAN_CHECKPOINT;
     typename Comparator<String<TRightValue, TRightSpec> >::Type _lex(left, right);
     return isEqual(_lex);
 }
@@ -2016,7 +1828,6 @@ inline bool
 operator!=(String<TLeftValue, TLeftSpec> const & left,
            TRight const & right)
 {
-    SEQAN_CHECKPOINT;
     typename Comparator<String<TLeftValue, TLeftSpec> >::Type _lex(left, right);
     return isNotEqual(_lex);
 }
@@ -2026,7 +1837,6 @@ inline bool
 operator!=(TLeftValue * left,
            String<TRightValue, TRightSpec> const & right)
 {
-    SEQAN_CHECKPOINT;
     typename Comparator<String<TRightValue, TRightSpec> >::Type _lex(left, right);
     return isNotEqual(_lex);
 }
@@ -2040,7 +1850,6 @@ inline bool
 operator<(String<TLeftValue, TLeftSpec> const & left,
           TRight const & right)
 {
-    SEQAN_CHECKPOINT;
     return isLess(left, right, typename DefaultPrefixOrder<String<TLeftValue, TLeftSpec> >::Type());
 }
 
@@ -2049,7 +1858,6 @@ inline bool
 operator<(TLeftValue * left,
           String<TRightValue, TRightSpec> const & right)
 {
-    SEQAN_CHECKPOINT;
     return isLess(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
 }
 
@@ -2062,7 +1870,6 @@ inline bool
 operator<=(String<TLeftValue, TLeftSpec> const & left,
            TRight const & right)
 {
-    SEQAN_CHECKPOINT;
     return isLessOrEqual(left, right, typename DefaultPrefixOrder<String<TLeftValue, TLeftSpec> >::Type());
 }
 
@@ -2071,7 +1878,6 @@ inline bool
 operator<=(TLeftValue * left,
            String<TRightValue, TRightSpec> const & right)
 {
-SEQAN_CHECKPOINT
     return isLessOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
 }
 
@@ -2084,7 +1890,6 @@ inline bool
 operator>(String<TLeftValue, TLeftSpec> const & left,
           TRight const & right)
 {
-    SEQAN_CHECKPOINT;
     return isGreater(left, right, typename DefaultPrefixOrder<String<TLeftValue, TLeftSpec> >::Type());
 }
 template <typename TLeftValue, typename TRightValue, typename TRightSpec >
@@ -2092,7 +1897,6 @@ inline bool
 operator>(TLeftValue * left,
           String<TRightValue, TRightSpec> const & right)
 {
-    SEQAN_CHECKPOINT;
     return isGreater(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
 }
 
@@ -2105,7 +1909,6 @@ inline bool
 operator>=(String<TLeftValue, TLeftSpec> const & left,
            TRight const & right)
 {
-    SEQAN_CHECKPOINT;
     return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<String<TLeftValue, TLeftSpec> >::Type());
 }
 template <typename TLeftValue, typename TRightValue, typename TRightSpec>
@@ -2113,10 +1916,93 @@ inline bool
 operator>=(TLeftValue * left,
              String<TRightValue, TRightSpec> const & right)
 {
-    SEQAN_CHECKPOINT;
     return isGreaterOrEqual(left, right, typename DefaultPrefixOrder<TLeftValue *>::Type());
 }
 
+// ----------------------------------------------------------------------------
+// Function beginPosition()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn String#beginPosition
+ * @headerfile <seqan/sequence.h>
+ * @brief Return 0 for compatibility with @link Segment @endlink.
+ *
+ * @signature TPos beginPosition(str);
+ *
+ * @param[in] seg The String to use.
+ *
+ * @return TPos Always 0.
+ */
+
+
+// ----------------------------------------------------------------------------
+// Function endPosition()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn String#endPosition
+ * @headerfile <seqan/sequence.h>
+ * @brief Return length of string for compatibility with @link Segment @endlink.
+ *
+ * @signature TPos endPosition(str);
+ *
+ * @param[in] seg The string to use.
+ *
+ * @return TPos Length of the string.
+ */
+
+// ----------------------------------------------------------------------------
+// Function reserveChunk()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec, typename TSize>
+inline void reserveChunk(String<TValue, TSpec> &str, TSize size, Output)
+{
+    reserve(str, length(str) + size);
+}
+
+template <typename TValue, typename TSpec, typename TSize>
+inline void reserveChunk(String<TValue, TSpec> const &, TSize, Input)
+{}
+
+// ----------------------------------------------------------------------------
+// Function getChunk()
+// ----------------------------------------------------------------------------
+
+template <typename TChunk, typename TValue, typename TSpec>
+inline void
+getChunk(TChunk &result, String<TValue, TSpec> &cont, Output)
+{
+    return assignRange(result, end(cont, Standard()), begin(cont, Standard()) + capacity(cont));
+}
+
+// ----------------------------------------------------------------------------
+// Function advanceChunk()
+// ----------------------------------------------------------------------------
+
+// extend target string size
+template <typename TValue, typename TSpec, typename TSize>
+inline void advanceChunk(String<TValue, TSpec> &str, TSize size)
+{
+    _setLength(str, length(str) + size);
+}
+
+template <typename TValue, typename TStringSpec, typename TSpec, typename TSize>
+inline void advanceChunk(Iter<String<TValue, TStringSpec>, TSpec> &iter, TSize size)
+{
+    typedef String<TValue, TStringSpec> TContainer;
+    typedef Iter<TContainer, TSpec> TIter;
+
+    iter += size;
+
+    TContainer &cont = container(iter);
+    typename Position<TIter>::Type pos = position(iter);
+
+    if (pos > length(cont))
+        _setLength(cont, pos);
+}
+
 // ----------------------------------------------------------------------------
 // Function operator<<() for streams.
 // ----------------------------------------------------------------------------
@@ -2126,8 +2012,8 @@ inline TStream &
 operator<<(TStream & target,
            String<TValue, TSpec> const & source)
 {
-SEQAN_CHECKPOINT
-    write(target, source);
+    typename DirectionIterator<TStream, Output>::Type it = directionIterator(target, Output());
+    write(it, source);
     return target;
 }
 
@@ -2140,11 +2026,41 @@ inline TStream &
 operator>>(TStream & source,
            String<TValue, TSpec> & target)
 {
-    SEQAN_CHECKPOINT;
-    read(source, target);
+    typename DirectionIterator<TStream, Input>::Type it = directionIterator(source, Input());;
+    read(it, target);
     return source;
 }
 
+// ----------------------------------------------------------------------------
+// Function assignValueById
+// ----------------------------------------------------------------------------
+
+template<typename TValue, typename TSpec, typename TId, typename TValue2>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TId> >, void)
+assignValueById(String<TValue, TSpec> & me,
+                TId id,
+                TValue2 const & obj)
+{
+    if (length(me) <= id)
+        resize(me, id + 1, TValue());
+    assignValue(me, id, obj);
+}
+
+// ----------------------------------------------------------------------------
+// Function getValueById
+// ----------------------------------------------------------------------------
+
+template<typename TValue, typename TSpec, typename TId>
+inline SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TId> >, TValue)
+getValueById(String<TValue, TSpec> & me,
+             TId id)
+{
+    if (id < length(me))
+        return getValue(me, id);
+    else
+        return TValue();
+}
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_SEQUENCE_STRING_ARRAY_BASE_H_
diff --git a/seqan/sequence/string_block.h b/seqan/sequence/string_block.h
index ab3facf..9f41a4e 100644
--- a/seqan/sequence/string_block.h
+++ b/seqan/sequence/string_block.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -53,34 +53,22 @@ namespace seqan {
  * @class BlockString Block String
  * @extends String
  * @headerfile <seqan/sequence.h>
- * @brief String optimized for push_back, top, and pop (Stack behaviour).
- * 
+ * @brief String optimized for appendValue, back, and eraseBack (Stack behaviour).
+ *
  * @signature template <typename TValue, unsigned SPACE = 4096>
  *            class String<TValue, Block<SIZE> >;
- * 
+ *
  * @tparam TValue The value type, that is the type of the items/characters stored in the string.  Use
- *                @link String#Value @endlink to get the value type for a given class.
+ *                @link ContainerConcept#Value @endlink to get the value type for a given class.
  * @tparam SIZE A positive integer that specifies the number of values in each
  *              allocated block.  Size should be a power of 2, e.g., 1024.
- * 
+ *
  */
 
-template<unsigned int SPACE = 4096>
+template<size_t SPACE = 4096>
 struct Block;
 
-/**
-.Spec.Block String:
-..cat:Strings
-..general:Class.String
-..summary:String optimized for push_back, top, and pop (Stack behaviour).
-..signature:String<TValue, Block<size> >
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..param.size:A positive integer that specifies the number of values in each allocated block.
-...remarks: Size should be a power of 2, e.g., 1024.
-..include:seqan/sequence.h
-*/
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 class String<TValue, Block<SPACE> >
 {
     typedef String<TValue, Array<SPACE> >               TBlock;
@@ -93,7 +81,7 @@ class String<TValue, Block<SPACE> >
 
     TBlockTable     blocks;
     TBlockIter      blockFirst, blockLast;  // current block boundaries
-    TBlockIter      lastValue;              // pointer to top value
+    TBlockIter      lastValue;              // pointer to back value
     TAllocator      alloc;
 
     String():
@@ -147,7 +135,7 @@ class String<TValue, Block<SPACE> >
 
     template<typename TPos>
     inline typename Reference<String>::Type
-        operator[] (TPos pos)
+    operator[] (TPos pos)
     {
     SEQAN_CHECKPOINT
         return value(*this, pos);
@@ -155,7 +143,7 @@ class String<TValue, Block<SPACE> >
 
     template<typename TPos>
     inline typename Reference<String const>::Type
-        operator[] (TPos pos) const
+    operator[] (TPos pos) const
     {
     SEQAN_CHECKPOINT
         return value(*this, pos);
@@ -170,7 +158,7 @@ class String<TValue, Block<SPACE> >
 // Metafunction DefaultOverflowImplicit
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 struct DefaultOverflowImplicit< String<TValue, Block<SPACE> > >
 {
     typedef Generous Type;
@@ -180,28 +168,25 @@ struct DefaultOverflowImplicit< String<TValue, Block<SPACE> > >
 // Metafunction Iterator
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Iterator.param.T.type:Spec.Block String
-///.Metafunction.Iterator.class:Spec.Block String
-
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 struct Iterator<String<TValue, Block<SPACE> >, Standard>
 {
     typedef Iter<String<TValue, Block<SPACE> >, PositionIterator> Type;
 };
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 struct Iterator<String<TValue, Block<SPACE> > const, Standard>
 {
     typedef Iter<String<TValue, Block<SPACE> > const, PositionIterator> Type;
 };
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 struct Iterator<String<TValue, Block<SPACE> >, Rooted>
 {
     typedef Iter<String<TValue, Block<SPACE> >, PositionIterator> Type;
 };
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 struct Iterator<String<TValue, Block<SPACE> > const, Rooted>
 {
     typedef Iter<String<TValue, Block<SPACE> > const, PositionIterator> Type;
@@ -215,7 +200,7 @@ struct Iterator<String<TValue, Block<SPACE> > const, Rooted>
 // Function begin()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE, typename TSpec>
+template<typename TValue, size_t SPACE, typename TSpec>
 inline typename Iterator<String<TValue, Block<SPACE> >, Tag<TSpec> const >::Type
 begin(String<TValue, Block<SPACE> > & me, Tag<TSpec> const)
 {
@@ -223,7 +208,7 @@ begin(String<TValue, Block<SPACE> > & me, Tag<TSpec> const)
     return Iter<String<TValue, Block<SPACE> >, PositionIterator>(me, 0);
 }
 
-template<typename TValue, unsigned int SPACE, typename TSpec>
+template<typename TValue, size_t SPACE, typename TSpec>
 inline typename Iterator<String<TValue, Block<SPACE> > const, Tag<TSpec> const>::Type
 begin(String<TValue, Block<SPACE> > const & me, Tag<TSpec> const)
 {
@@ -235,7 +220,7 @@ begin(String<TValue, Block<SPACE> > const & me, Tag<TSpec> const)
 // Function end()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE, typename TSpec>
+template<typename TValue, size_t SPACE, typename TSpec>
 inline typename Iterator<String<TValue, Block<SPACE> >, Tag<TSpec> const >::Type
 end(String<TValue, Block<SPACE> > & me, Tag<TSpec> const)
 {
@@ -243,7 +228,7 @@ end(String<TValue, Block<SPACE> > & me, Tag<TSpec> const)
     return Iter<String<TValue, Block<SPACE> >, PositionIterator>(me, length(me));
 }
 
-template<typename TValue, unsigned int SPACE, typename TSpec>
+template<typename TValue, size_t SPACE, typename TSpec>
 inline typename Iterator<String<TValue, Block<SPACE> > const, Tag<TSpec> const>::Type
 end(String<TValue, Block<SPACE> > const & me, Tag<TSpec> const)
 {
@@ -255,38 +240,39 @@ end(String<TValue, Block<SPACE> > const & me, Tag<TSpec> const)
 // Function assign()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE, typename TSource>
+template<typename TValue, size_t SPACE, typename TSource>
 inline void
-assign(
-    String<TValue, Block<SPACE> >& target,
-    TSource const& source)
+assign(String<TValue, Block<SPACE> >& target, TSource const& source)
 {
     SEQAN_CHECKPOINT;
     clear(target);
     typedef typename Iterator<TSource const, Standard>::Type TIter;
     for(TIter it = begin(source, Standard()); !atEnd(it, source); goNext(it))
-        push(target, *it);
+        appendValue(target, *it);
+}
+
+template<typename TValue, size_t SPACE, typename TSource, typename TExpand>
+inline void
+assign(String<TValue, Block<SPACE> >& target, TSource const& source, Tag<TExpand> const &)
+{
+    assign(target, source);
 }
 
 // ----------------------------------------------------------------------------
 // Function value()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE, typename TPos>
+template<typename TValue, size_t SPACE, typename TPos>
 inline typename Reference<String<TValue, Block<SPACE> > >::Type
-value(
-    String<TValue, Block<SPACE> >& stack,
-    TPos const pos)
+value(String<TValue, Block<SPACE> >& stack, TPos const pos)
 {
     SEQAN_CHECKPOINT;
     return value(*(stack.blocks[pos / SPACE]), pos % SPACE);
 }
 
-template<typename TValue, unsigned int SPACE, typename TPos>
+template<typename TValue, size_t SPACE, typename TPos>
 inline typename Reference<String<TValue, Block<SPACE> > >::Type
-value(
-    String<TValue, Block<SPACE> > const& stack,
-    TPos const pos)
+value(String<TValue, Block<SPACE> > const& stack, TPos const pos)
 {
     SEQAN_CHECKPOINT;
     return value(*(stack.blocks[pos / SPACE]), pos % SPACE);
@@ -297,11 +283,9 @@ value(
 // ----------------------------------------------------------------------------
 
 // TODO(holtgrew): Probably wrong place?
-template<typename TValue, unsigned int SPACE, typename TIteratorSpec>
+template<typename TValue, size_t SPACE, typename TIteratorSpec>
 inline bool
-atEnd(
-    Iter<String<TValue, Block<SPACE> >, TIteratorSpec>& it,
-    String<TValue, Block<SPACE> >& container)
+atEnd(Iter<String<TValue, Block<SPACE> >, TIteratorSpec>& it, String<TValue, Block<SPACE> >& container)
 {
     SEQAN_CHECKPOINT;
     typedef typename Iterator<String<TValue, Block<SPACE> >, Standard>::Type TIter;
@@ -313,7 +297,7 @@ atEnd(
 // Function clear()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline void
 clear(String<TValue, Block<SPACE> >& me)
 {
@@ -336,11 +320,9 @@ clear(String<TValue, Block<SPACE> >& me)
 // Function resize()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE, typename TSize2, typename TExpand>
+template<typename TValue, size_t SPACE, typename TSize2, typename TExpand>
 inline typename Size< String<TValue, Block<SPACE> > >::Type
-resize(String<TValue, Block<SPACE> > & me,
-    TSize2 new_length,
-    Tag<TExpand>)
+resize(String<TValue, Block<SPACE> > & me, TSize2 new_length, Tag<TExpand>)
 {
     SEQAN_CHECKPOINT;
     typedef String<TValue, Block<SPACE> >           TBlockString;
@@ -349,20 +331,18 @@ resize(String<TValue, Block<SPACE> > & me,
 
     if ((TSize)new_length > len)
     {
-        for (; len < (TSize)new_length; ++len) push(me);
+        for (; len < (TSize)new_length; ++len) appendValue(me, TValue());
     }
     else if ((TSize)new_length < len)
     {
-        for (; len > (TSize)new_length; --len) pop(me);
+        for (; len > (TSize)new_length; --len) eraseBack(me);
     }
     return new_length;
 }
 
-template<typename TValue, unsigned int SPACE, typename TSize2>
+template<typename TValue, size_t SPACE, typename TSize2>
 inline typename Size< String<TValue, Block<SPACE> > >::Type
-resize(String<TValue, Block<SPACE> > & me,
-    TSize2 new_length,
-    Limit)
+resize(String<TValue, Block<SPACE> > & me, TSize2 new_length, Limit)
 {
     SEQAN_CHECKPOINT;
     typedef String<TValue, Block<SPACE> >           TBlockString;
@@ -378,7 +358,7 @@ resize(String<TValue, Block<SPACE> > & me,
     }
     else if (new_length < len)
     {
-        for (; len > new_length; --len) pop(me);
+        for (; len > new_length; --len) eraseBack(me);
     }
     return new_length;
 }
@@ -388,10 +368,8 @@ resize(String<TValue, Block<SPACE> > & me,
 // ----------------------------------------------------------------------------
 
 // TODO(holtgrew): Why is this only a dummy implementation?
-///.Function.reserve.param.object.type:Spec.Block String
-///.Function.reserve.class:Spec.Block String
 /*
-template <typename TValue, unsigned int SPACE, typename TSize, typename TExpand>
+template <typename TValue, size_t SPACE, typename TSize, typename TExpand>
 inline typename Size< String<TValue, Block<SPACE> > >::Type
 reserve(
     String<TValue, Block<SPACE> >& me,
@@ -405,136 +383,63 @@ SEQAN_CHECKPOINT
 */
 
 // dummy implementation
-template<typename TValue, unsigned int SPACE, typename TSize, typename TExpand>
+template<typename TValue, size_t SPACE, typename TSize, typename TExpand>
 inline typename Size< String<TValue, Block<SPACE> > >::Type
-reserve(String<TValue, Block<SPACE> > & /*me*/,
-    TSize new_capacity,
-    Tag<TExpand>)
+reserve(String<TValue, Block<SPACE> > & /*me*/, TSize new_capacity, Tag<TExpand>)
 {
     SEQAN_CHECKPOINT;
     return new_capacity;
 }
 
-// ----------------------------------------------------------------------------
-// Function append()
-// ----------------------------------------------------------------------------
-
-template<typename TValue, unsigned int SPACE, typename TSource, typename TExpand>
-inline void
-append(
-    String<TValue, Block<SPACE> >& me,
-    TSource const& source,
-    Tag<TExpand> /*tag*/)
-{
-    SEQAN_CHECKPOINT;
-    typedef typename Iterator<TSource const, Standard>::Type TIter;
-    for(TIter it = begin(source, Standard()); !atEnd(it, source); goNext(it))
-        appendValue(me, *it);
-}
-
 // ----------------------------------------------------------------------------
 // Function appendValue()
 // ----------------------------------------------------------------------------
 
-///.Function.appendValue.param.target.type:Spec.Block String
-
-template<typename TValue, unsigned int SPACE, typename TVal, typename TExpand>
+template<typename TTargetValue, size_t SPACE, typename TValue, typename TExpand>
 inline void
-appendValue(
-    String<TValue, Block<SPACE> >& me,
-    TVal const& source,
-    Tag<TExpand> tag)
+appendValue(String<TTargetValue, Block<SPACE> > & me, TValue SEQAN_FORWARD_CARG value, Tag<TExpand> tag)
 {
     // TODO(holtgrew): Why does this operate on raw memory instead of using appendValue(me.blocks[last], X)?
-    SEQAN_CHECKPOINT;
-    if (me.lastValue == me.blockLast) {
-        typename Size< String<TValue, Block<SPACE> > >::Type last = length(me.blocks);
+    typedef String<TTargetValue, Block<SPACE> > TString;
+    typedef typename Size<TString>::Type        TSize;
 
+    if (me.lastValue == me.blockLast)
+    {
+        TSize last = length(me.blocks);
         resize(me.blocks, last + 1, tag);
         allocate(me.alloc, me.blocks[last], 1);
         valueConstruct(me.blocks[last]);
         me.lastValue = me.blockFirst = begin(*me.blocks[last]);
         me.blockLast = (me.blockFirst + (SPACE - 1));
         back(me.blocks)->data_length += 1;
-    } else {
-        ++me.lastValue;
-        back(me.blocks)->data_length += 1;
     }
-    valueConstruct(me.lastValue, source);
-}
-
-// ----------------------------------------------------------------------------
-// Function push()
-// ----------------------------------------------------------------------------
-
-template<typename TValue, unsigned int SPACE, typename TVal>
-inline void
-push(
-    String<TValue, Block<SPACE> >& me,
-    TVal const& source)
-{
-    appendValue(me, source);
-}
-
-template<typename TValue, unsigned int SPACE>
-inline void
-push(String<TValue, Block<SPACE> >& me)
-{
-    SEQAN_CHECKPOINT;
-    if (me.lastValue == me.blockLast) {
-        typename Size< String<TValue, Block<SPACE> > >::Type last = length(me.blocks);
-
-        resize(me.blocks, last + 1, typename DefaultOverflowImplicit<String<TValue, Block<SPACE> > >::Type());
-        allocate(me.alloc, me.blocks[last], 1);
-        me.lastValue = me.blockFirst = begin(*me.blocks[last]);
-        me.blockLast = (me.blockFirst + (SPACE - 1));
-        back(me.blocks)->data_length += 1;
-    } else {
+    else
+    {
         ++me.lastValue;
         back(me.blocks)->data_length += 1;
     }
-    valueConstruct(me.lastValue);
+    valueConstruct(me.lastValue, SEQAN_FORWARD(TValue, value));
 }
 
 // ----------------------------------------------------------------------------
-// Function push_back()
+// Function append()
 // ----------------------------------------------------------------------------
 
-// TODO(holtgrew): Breaks naming-conventions.
-template<typename TValue, unsigned int SPACE, typename TVal>
+template<typename TValue, size_t SPACE, typename TSource, typename TExpand>
 inline void
-push_back(
-    String<TValue, Block<SPACE> >& me,
-    TVal const& source)
+append(String<TValue, Block<SPACE> >& me, TSource const& source, Tag<TExpand> /*tag*/)
 {
-    appendValue(me, source);
+    SEQAN_CHECKPOINT;
+    typedef typename Iterator<TSource const, Standard>::Type TIter;
+    for(TIter it = begin(source, Standard()); !atEnd(it, source); goNext(it))
+        appendValue(me, *it);
 }
 
 // ----------------------------------------------------------------------------
-// Function top()
+// Function back()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE>
-inline TValue &
-top(String<TValue, Block<SPACE> > & me)
-{
-    SEQAN_CHECKPOINT;
-    SEQAN_ASSERT_NOT_MSG(empty(me), "top() called on an empty string.");
-
-    return *me.lastValue;
-}
-
-template<typename TValue, unsigned int SPACE>
-inline TValue const &
-top(String<TValue, Block<SPACE> > const & me)
-{
-    SEQAN_CHECKPOINT;
-    SEQAN_ASSERT_NOT_MSG(empty(me), "top() called on an empty string.");
-
-    return *me.lastValue;
-}
-
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline TValue &
 back(String<TValue, Block<SPACE> > & me)
 {
@@ -544,7 +449,7 @@ back(String<TValue, Block<SPACE> > & me)
     return *me.lastValue;
 }
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline TValue const &
 back(String<TValue, Block<SPACE> > const & me)
 {
@@ -555,15 +460,15 @@ back(String<TValue, Block<SPACE> > const & me)
 }
 
 // ----------------------------------------------------------------------------
-// Function topPrev()
+// Function backPrev()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline TValue &
-topPrev(String<TValue, Block<SPACE> > & me)
+backPrev(String<TValue, Block<SPACE> > & me)
 {
     SEQAN_CHECKPOINT;
-    SEQAN_ASSERT_GEQ_MSG(length(me), 2u, "topPrev() called on a string with less than 2 elements.");
+    SEQAN_ASSERT_GEQ_MSG(length(me), 2u, "backPrev() called on a string with less than 2 elements.");
 
     if (me.lastValue != me.blockFirst)
         return *(me.lastValue - 1);
@@ -571,12 +476,12 @@ topPrev(String<TValue, Block<SPACE> > & me)
         return *(begin(*me.blocks[length(me.blocks) - 1]) + (SPACE - 1));
 }
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline TValue const &
-topPrev(String<TValue, Block<SPACE> > const& me)
+backPrev(String<TValue, Block<SPACE> > const& me)
 {
     SEQAN_CHECKPOINT;
-    SEQAN_ASSERT_GEQ_MSG(length(me), 2u, "topPrev() called on a string with less than 2 elements.");
+    SEQAN_ASSERT_GEQ_MSG(length(me), 2u, "backPrev() called on a string with less than 2 elements.");
 
    if (me.lastValue != me.blockFirst)
         return *(me.lastValue - 1);
@@ -585,28 +490,18 @@ topPrev(String<TValue, Block<SPACE> > const& me)
 }
 
 // ----------------------------------------------------------------------------
-// Function pop()
+// Function eraseBack()
 // ----------------------------------------------------------------------------
 
-template <typename T>
-SEQAN_HOST_DEVICE inline void
-pop(T & me)
-{
-    SEQAN_CHECKPOINT;
-    SEQAN_ASSERT_NOT_MSG(empty(me), "pop() called on an empty string.");
-
-    resize(me, length(me) - 1);
-}
-
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline void
-pop(String<TValue, Block<SPACE> >& me)
+eraseBack(String<TValue, Block<SPACE> >& me)
 {
     typedef typename String<TValue, Block<SPACE> >::TBlockIter TBlockIter;
-    
+
     SEQAN_CHECKPOINT;
-    SEQAN_ASSERT_NOT_MSG(empty(me), "pop() called on an empty string.");
-    
+    SEQAN_ASSERT_NOT_MSG(empty(me), "eraseBack() called on an empty string.");
+
     if (me.lastValue == me.blockFirst) {
         typename Size< String<TValue, Block<SPACE> > >::Type last = length(me.blocks);
 
@@ -631,24 +526,11 @@ pop(String<TValue, Block<SPACE> >& me)
     }
 }
 
-// ----------------------------------------------------------------------------
-// Function pop_back()
-// ----------------------------------------------------------------------------
-
-// TODO(holtgrew): Breaks naming-conventions.
-template<typename TValue, unsigned int SPACE>
-inline void
-pop_back(String<TValue, Block<SPACE> >& me)
-{
-    SEQAN_CHECKPOINT;
-    pop(me);
-}
-
 // ----------------------------------------------------------------------------
 // Function empty()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline bool
 empty(String<TValue, Block<SPACE> > const& me)
 {
@@ -660,7 +542,7 @@ empty(String<TValue, Block<SPACE> > const& me)
 // Function length()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline typename Size<String<TValue, Block<SPACE> > >::Type
 length(String<TValue, Block<SPACE> > const & me)
 {
@@ -675,7 +557,7 @@ length(String<TValue, Block<SPACE> > const & me)
 // Function capacity()
 // ----------------------------------------------------------------------------
 
-template<typename TValue, unsigned int SPACE>
+template<typename TValue, size_t SPACE>
 inline typename Size<String<TValue, Block<SPACE> > >::Type
 capacity(String<TValue, Block<SPACE> > const & me)
 {
diff --git a/seqan/sequence/string_cstyle.h b/seqan/sequence/string_cstyle.h
index e3bd5db..0bcc729 100644
--- a/seqan/sequence/string_cstyle.h
+++ b/seqan/sequence/string_cstyle.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -61,92 +61,53 @@ clear(String<TValue, CStyle> & me);
 /*!
  * @class CStyleString CStyle String
  * @extends String
- * @headerfile seqan/sequence.h
+ * @headerfile <seqan/sequence.h>
  * @brief Allows adaption of strings to C-style strings.
- * 
+ *
  * @signature template <typename TValue, typename TCStyle>
  *            class String<TValue, CStyle>;
- * 
+ *
  * @tparam TValue The value type, that is the type of the items/characters stored in the string.Use @link Value @endlink
  *                to get the value type for a given class.
- * 
+ *
  * Assigning a string <tt>TValue *</tt> to a CStyle String will not create a
  * copy of the string but just copy pointers.
- * 
+ *
  * @section Remarks
- * 
+ *
  * The purpose of this class is to access to the content of a sequence in a "zero terminated string" style.  This can be
  * useful if SeqAn classes has to be integrated in programs that use <tt>char</tt> arrays to store strings.  Instances
  * of <tt>String<TValue, CStyle></tt> can implicitely converted to a <tt>TValue *</tt> that points to a zero terminated
  * CStyle of <tt>TValue</tt>.
- * 
+ *
  * The stored c-style string object can be set by constructors or assignment.  The content of a c-style string can
  * eighter be stored in a separate buffer, that is the source string is copied.  Or the buffer of the source string
  * itself is used instead, in this case the c-style string depends on the source string and gets invalid as soon as the
  * buffer of the source string is destroyed.
- * 
+ *
  * Hence, this class is a kind of adaptor from an arbitrary SeqAn string to char arrays. Of course, the opposite way is
  * possible too.
- * 
+ *
  * @section Examples
- * 
+ *
  * @code{.cpp}
  * // Create a string str:
  * String<char> str = "this is a test string";
- *  
+ *
  * // Create a c-style string object for str:
  * String<char, CStyle> cStyle = str;
- *  
+ *
  * // Now use cStyle as char array:
  * strcmp(cStyle, "compare it to this string");
  * @endcode
  * If the c-style string is needed only temporarily, the function
  * <tt>toCString</tt> can be used:
- * 
+ *
  * @code{.cpp}
  * String<char> str = "this is a test string";
  * strcmp(toCString(str), "compare it to this string");
  * @endcode
  */
- 
-/**
-.Spec.CStyle String:
-..cat:Strings
-..general:Class.String
-..summary:Allows adaption of strings to C-style strings.
-..signature:String<TValue, CStyle>
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..remarks:
-..text:Assigning a string $TValue *$ to a CStyle String will not create a copy of the string but just copy pointers.
-..remarks:
-...text:The purpose of this class is to access to the content of a sequence
-in a "zero terminated string" style.
-This can be useful if SeqAn classes has to be integrated in programs that use $char$ arrays
-to store strings.
-Instances of $String<TValue, CStyle>$ can implicitely converted to a $TValue *$ that
-points to a zero terminated CStyle of $TValue$.
-...text:The stored c-style string object can be set by constructors or assignment.
-The content of a c-style string can eighter be stored in a separate buffer, that is the source string
-is copied. Or the buffer of the source string itself is used instead, in this case the c-style string
-depends on the source string and gets invalid as soon as the buffer of the source string is destroyed.
-...text:Hence, this class is a kind of adaptor from an arbitrary SeqAn string to char arrays.
-Of course, the opposite way is possible too:
-Read @Adaption.char array.here@ about adapting char arrays to SeqAn strings.
-..example:
-...code:// Create a string str:
-String<char> str = "this is a test string";
-
-// Create a c-style string object for str:
-String<char, CStyle> cStyle = str;
-
-// Now use cStyle as char array:
-strcmp(cStyle, "compare it to this string");
-...text:If the c-style string is needed only temporarily, the function $toCString$ can be used:
-...code:String<char> str = "this is a test string";
-strcmp(toCString(str), "compare it to this string");
-..include:seqan/sequence.h
-*/
 
 struct CStyle_;
 typedef Tag<CStyle_> CStyle;
@@ -423,8 +384,6 @@ capacity(String <TValue, CStyle > const & me)
 // Internal Function _reallocateStorage()
 // --------------------------------------------------------------------------
 
-///.Internal._reallocateStorage.param.object.type:Spec.CStyle String
-///.Internal._reallocateStorage.param.resize_tag.remarks:@Spec.CStyle String@ only supports @Tag.Overflow Strategy.exact@.
 //this function works also for dependent buffers
 template <typename TValue>
 inline TValue *
@@ -453,8 +412,6 @@ _reallocateStorage(
 // Internal Function _deallocateStorage()
 // --------------------------------------------------------------------------
 
-///.Internal._deallocateStorage.param.object.type:Spec.CStyle String
-
 template <typename TValue>
 inline void
 _deallocateStorage(
@@ -471,19 +428,6 @@ _deallocateStorage(
 // Function dependent()
 // --------------------------------------------------------------------------
 
-/**
-.Function.dependent:
-..summary:Test whether object depends on other objects.
-..class:Spec.CStyle String
-..cat:Dependent Objects
-..signature:bool dependent(object)
-..param.object:An object.
-...type:Spec.CStyle String
-..returns:$true$ if $object$ depends one some other object, $false$ otherwise.
-..remarks:An object "$a$" depends on another object "$b$", if changing "$b$" can invalidate "$a$";
-especially the destruction of "$b$" invalidates "$a$".
-..include:seqan/sequence.h
-*/
 template <typename TValue>
 inline bool
 dependent(String <TValue, CStyle > & me)
@@ -669,23 +613,6 @@ clear(String<TValue, CStyle> & me)
 // --------------------------------------------------------------------------
 
 //see basic_holder
-/**
-.Function.create:
-..cat:Containers
-..class:Spec.CStyle String
-..signature:create(target, source [, limit] [,resize_tag])
-..param.target: Gets a copy of the content of $source$.
-...type:Spec.CStyle String
-..param.source: Is copied to $target$.
-..param.limit: The maximal length of $target$ after the operation. (optional)
-..param.resize_tag: Specifies the strategy that is applied if $target$ has not enough capacity to store the complete content. (optional)
-...type:Tag.Overflow Strategy
-...default:Specified by @Metafunction.DefaultOverflowImplicit@ of the $target$ type.
-..remarks.text:It is guaranteed, that after calling this function $source$ and $target$ can be used independently.
-..see:Spec.CStyle String
-..include:seqan/sequence.h
-*/
-
 template <typename TExpand>
 struct CreateArrayStringExpand_
 {
@@ -908,24 +835,22 @@ create(String<TTargetValue, CStyle> & target,
 // Function toCString()
 // --------------------------------------------------------------------------
 
-/**
-.Function.toCString:
-..cat:Containers
-..class:Spec.CStyle String
-..class:Adaption.char array
-..summary:Access sequence as c-style string.
-..signature:toCString(object)
-..param.object:A string.
-...type:Class.String
-...type:Adaption.char array
-..returns:For strings that store their elements in a contiguous block (see @Metafunction.IsContiguous@)
-a pointer to first element of $object$ is returned.
-The last element is followed by a default constructed element.
-..remarks:If the alphabet of $object$ is $char$ or $wchar_t$ the return value is a c-style string representing the contents of $object$.
-Calling this function for non-contiguous containers will raise a compilation error.
-To create c-style strings for non-contiguous strings or strings with different alphabets, use a @Spec.CStyle String@ as an intermediate.
-..include:seqan/sequence.h
-*/
+/*!
+ * @fn String#toCString
+ * @brief Access sequence as c-style string.
+ * @signature TValue* toCString(seq)
+ * @param seq The sequence to be accessed. Type: @link String @endlink
+ * @return TValue* For strings that store their elements in a contiguous block (see @link IsContiguous @endlink)
+                   a pointer to first element of $object$ is returned.
+ * @section Remarks
+ *
+ * If the alphabet of $object$ is $char$ or $wchar_t$ the return value is a c-style string representing the
+ * contents of <tt>object<tt/>.
+ *
+ * Calling this function for non-contiguous containers will raise a compilation error.  To create
+ * c-style strings for non-contiguous strings or strings with different alphabets, use a @link CStyleString @endlink as an
+ * intermediate.
+ */
 
 template <typename TValue>
 inline TValue *
diff --git a/seqan/sequence/string_packed.h b/seqan/sequence/string_packed.h
index aec5f1d..74b7dcc 100644
--- a/seqan/sequence/string_packed.h
+++ b/seqan/sequence/string_packed.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -62,10 +62,10 @@ struct HostIterator;
  * @extends String
  * @headerfile <seqan/sequence.h>
  * @brief A string that stores as many values in one machine word as possible.
- * 
+ *
  * @signature template <typename TValue, typename THostSpec>
  *            class String<TValue, Packed<THostSpec> >;
- * 
+ *
  * @tparam TValue The value type, that is the type of the items/characters
  *                stored in the string.Use @link Value @endlink to get the value
  *                type for a given class.
@@ -122,20 +122,6 @@ struct PackedTraits_
     }
 };
 
-/**
-.Spec.Packed String:
-..cat:Strings
-..general:Class.String
-..summary:A string that stores as many values in one machine word as possible.
-..signature:String<TValue, Packed<THostspec> >
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..param.THostspec:The specializing type.
-...remarks:This is the specialization of the host string that is used for storing the packed values.
-...default:@Spec.Alloc String.Alloc<>@
-..include:seqan/sequence.h
-*/
-
 /*???TODO Optimierungsm�glichkeiten:
 - _clearSpace kopiert Zeichenweise im Packed-String, und nicht im Host-String
 - _clearSpace verwendet resize, um den Host zu vergr��ern, d.h. der Inhalt wird eventuell doppelt kopiert.
@@ -193,13 +179,85 @@ class String<TValue, Packed<THostspec> >
     }
 
     template <typename TPos>
-    inline typename Reference<String const>::Type 
+    inline typename Reference<String const>::Type
     operator[](TPos pos) const
     {
         return data_host[1 + pos / TTraits::VALUES_PER_HOST_VALUE][pos % TTraits::VALUES_PER_HOST_VALUE];
     }
 };
 
+// ----------------------------------------------------------------------------
+// Functor FunctorTestAllZeros
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FunctorTestAllZeros
+{};
+
+template <typename THostSpec>
+struct FunctorTestAllZeros<String<bool, Packed<THostSpec> > >
+{
+    typedef String<bool, Packed<THostSpec> > TPackedString;
+    typedef typename Host<TPackedString>::Type TPackedHost;
+    typedef typename Value<TPackedHost>::Type TPackedHostValue;
+    typedef typename Size<TPackedHostValue>::Type TSize;
+
+    TSize _wastedBits;
+
+    template <typename TShift>
+    FunctorTestAllZeros(TShift const & shift) : _wastedBits(shift)
+    {}
+
+    template <typename TValue>
+    inline bool operator()(TValue const & val, False const & /*tag*/) const
+    {
+        return testAllZeros(val);
+    }
+
+    template <typename TValue>
+    inline bool operator()(TValue const & val, True const & /*tag*/) const
+    {
+        return testAllZeros(val >> _wastedBits);
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Functor FunctorTestAllOnes
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FunctorTestAllOnes
+{};
+
+template <typename THostSpec>
+struct FunctorTestAllOnes<String<bool, Packed<THostSpec> > >
+{
+    typedef String<bool, Packed<THostSpec> > TPackedString;
+    typedef typename Host<TPackedString>::Type TPackedHost;
+    typedef typename Value<TPackedHost>::Type TPackedHostValue;
+    typedef typename TPackedHostValue::TBitVector TBitVector;
+    typedef typename Size<TPackedHostValue>::Type TSize;
+
+    TSize _wastedBits;
+
+    template <typename TShift>
+    FunctorTestAllOnes(TShift const & shift) : _wastedBits(shift)
+    {}
+
+    template <typename TValue>
+    inline bool operator()(TValue const & val, False const & /*tag*/) const
+    {
+        return testAllOnes(val);
+    }
+
+    template <typename TValue>
+    inline bool operator()(TValue const & val, True const & /*tag*/) const
+    {
+        TBitVector maskWastedBits = (1 << _wastedBits) - 1;  // We only need the mask if we are in the last value.
+        return testAllOnes(val | maskWastedBits);
+    }
+};
+
 // --------------------------------------------------------------------------
 // Specialization Packed String Iter
 // --------------------------------------------------------------------------
@@ -244,7 +302,7 @@ class Iter<TPackedString, Packed<THostspec> >
     }
 
 //    inline
-//    Iter const & 
+//    Iter const &
 //    operator=(Iter const & other_)
 //    {
 //        data_iterator = other_.data_iterator;
@@ -257,6 +315,13 @@ class Iter<TPackedString, Packed<THostspec> >
 // Metafunctions
 // ============================================================================
 
+// --------------------------------------------------------------------------
+// Metafunction StringSpec
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TSpec>
+struct StringSpec<String<TValue, Packed<TSpec> > > : StringSpec<String<TValue, TSpec> > {};
+
 // --------------------------------------------------------------------------
 // Metafunction DefaultOverflowImplicit
 // --------------------------------------------------------------------------
@@ -311,7 +376,6 @@ struct PackedHostValue_
 // Metafunction Host
 // --------------------------------------------------------------------------
 
-///.Metafunction.Host.param.T.type:Spec.Packed String
 template <typename TValue, typename THostspec>
 struct Host<String<TValue, Packed<THostspec> > >
 {
@@ -389,14 +453,14 @@ struct Size<String<TValue, Packed<THostspec> > const>
 // Metafunction Iterator
 // --------------------------------------------------------------------------
 
-template <typename TValue, typename THostspec, typename TSpec>
-struct Iterator<String<TValue, Packed<THostspec> >, TSpec>
+template <typename TValue, typename THostspec>
+struct Iterator<String<TValue, Packed<THostspec> >, Standard>
 {
     typedef Iter<String<TValue, Packed<THostspec> >, Packed<THostspec> > Type;
 };
 
-template <typename TValue, typename THostspec, typename TSpec>
-struct Iterator<String<TValue, Packed<THostspec> > const, TSpec>
+template <typename TValue, typename THostspec>
+struct Iterator<String<TValue, Packed<THostspec> > const, Standard>
 {
     typedef Iter<String<TValue, Packed<THostspec> > const, Packed<THostspec> > Type;
 };
@@ -451,9 +515,6 @@ swap(String<TValue, Packed<THostspec> > & a,
 // Function host
 // --------------------------------------------------------------------------
 
-///.Function.host.param.object.type:Spec.Packed String
-///.Function.host.class:Spec.Packed String
-
 template <typename TValue, typename THostspec>
 inline typename Host<String<TValue, Packed<THostspec> > >::Type &
 host(String<TValue, Packed<THostspec> > & me)
@@ -474,7 +535,7 @@ host(String<TValue, Packed<THostspec> > const & me)
 
 template <typename TValue, typename THostspec>
 inline typename Size<String<TValue, Packed<THostspec> > const>::Type
-length(String<TValue, Packed<THostspec> > const & me) 
+length(String<TValue, Packed<THostspec> > const & me)
 {
     if (empty(host(me)))
         return 0;
@@ -533,7 +594,7 @@ resize(
 // optimized variant for copy assignment. The host sequence is copied instead of
 // copying the packed string value by value.
 template <typename TTarget, typename TSource, typename TTag>
-inline void 
+inline void
 _assignCopyPackedString(TTarget & target,
                         TSource & source,
                         Tag<TTag> const & tag)
@@ -548,7 +609,7 @@ _assignCopyPackedString(TTarget & target,
 }
 
 template <typename TTarget, typename TSource, typename TSize, typename TTag>
-inline void 
+inline void
 _assignCopyPackedString(TTarget & target,
                         TSource & source,
                         TSize limit,
@@ -565,7 +626,7 @@ _assignCopyPackedString(TTarget & target,
 }
 
 template <typename TValue, typename THostspec, typename TTag>
-inline void 
+inline void
 assign(String<TValue, Packed<THostspec> > & target,
        String<TValue, Packed<THostspec> > & source,
        Tag<TTag> const & tag)
@@ -574,7 +635,7 @@ assign(String<TValue, Packed<THostspec> > & target,
 }
 
 template <typename TValue, typename THostspec, typename TTag>
-inline void 
+inline void
 assign(String<TValue, Packed<THostspec> > & target,
        String<TValue, Packed<THostspec> > const & source,
        Tag<TTag> const & tag)
@@ -604,7 +665,7 @@ void assign(String<TValue, Packed<THostspec> > & target,
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec>
-inline void const * 
+inline void const *
 getObjectId(String<TValue, Packed<THostspec> > const & me)
 {
     return getObjectId(host(me));
@@ -614,23 +675,23 @@ getObjectId(String<TValue, Packed<THostspec> > const & me)
 // Function iter()
 // --------------------------------------------------------------------------
 
-template <typename TValue, typename THostspec, typename TPos, typename TTag>
-inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type 
+template <typename TValue, typename THostspec, typename TPos>
+inline typename Iterator<String<TValue, Packed<THostspec> >, Standard>::Type
 iter(String<TValue, Packed<THostspec> > & me,
-     TPos pos,
-     Tag<TTag> const &)
+     TPos const pos,
+     Standard const &)
 {
-    typedef typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type TIterator;
+    typedef typename Iterator<String<TValue, Packed<THostspec> >, Standard>::Type TIterator;
     return TIterator(me, pos);
 }
 
-template <typename TValue, typename THostspec, typename TPos, typename TTag>
-inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type 
+template <typename TValue, typename THostspec, typename TPos>
+inline typename Iterator<String<TValue, Packed<THostspec> > const, Standard>::Type
 iter(String<TValue, Packed<THostspec> > const & me,
-     TPos pos,
-     Tag<TTag> const &)
+     TPos const pos,
+     Standard const &)
 {
-    typedef typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type TIterator;
+    typedef typename Iterator<String<TValue, Packed<THostspec> > const, Standard>::Type TIterator;
     return TIterator(me, pos);
 }
 
@@ -638,21 +699,21 @@ iter(String<TValue, Packed<THostspec> > const & me,
 // Function begin()
 // --------------------------------------------------------------------------
 
-template <typename TValue, typename THostspec, typename TTag>
-inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type 
+template <typename TValue, typename THostspec>
+inline typename Iterator<String<TValue, Packed<THostspec> >, Standard>::Type
 begin(String<TValue, Packed<THostspec> > & me,
-      Tag<TTag> const &)
+     Standard const &)
 {
-    typedef typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type TIterator;
+    typedef typename Iterator<String<TValue, Packed<THostspec> >, Standard>::Type TIterator;
     return TIterator(me);
 }
 
-template <typename TValue, typename THostspec, typename TTag>
-inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type 
+template <typename TValue, typename THostspec>
+inline typename Iterator<String<TValue, Packed<THostspec> > const, Standard>::Type
 begin(String<TValue, Packed<THostspec> > const & me,
-      Tag<TTag> const &)
+     Standard const &)
 {
-    typedef typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type TIterator;
+    typedef typename Iterator<String<TValue, Packed<THostspec> > const, Standard>::Type TIterator;
     return TIterator(me);
 }
 
@@ -660,20 +721,20 @@ begin(String<TValue, Packed<THostspec> > const & me,
 // Function end()
 // --------------------------------------------------------------------------
 
-template <typename TValue, typename THostspec, typename TTag>
-inline typename Iterator<String<TValue, Packed<THostspec> >, Tag<TTag> const>::Type
+template <typename TValue, typename THostspec>
+inline typename Iterator<String<TValue, Packed<THostspec> >, Standard>::Type
 end(String<TValue, Packed<THostspec> > & me,
-    Tag<TTag> const & tag_)
+     Standard const &)
 {
-    return iter(me, length(me), tag_);
+    return iter(me, length(me), Standard());
 }
 
-template <typename TValue, typename THostspec, typename TTag>
-inline typename Iterator<String<TValue, Packed<THostspec> > const, Tag<TTag> const>::Type 
+template <typename TValue, typename THostspec>
+inline typename Iterator<String<TValue, Packed<THostspec> > const, Standard>::Type
 end(String<TValue, Packed<THostspec> > const & me,
-    Tag<TTag> const & tag_)
+     Standard const &)
 {
-    return iter(me, length(me), tag_);
+    return iter(me, length(me), Standard());
 }
 
 // --------------------------------------------------------------------------
@@ -682,21 +743,21 @@ end(String<TValue, Packed<THostspec> > const & me,
 
 template <typename TValue, typename THostspec, typename TPos>
 inline typename Reference<String<TValue, Packed<THostspec> > >::Type
-value(String<TValue, Packed<THostspec> > & me, 
-      TPos const & pos)
+value(String<TValue, Packed<THostspec> > & me,
+      TPos const pos)
 {
     return *iter(me, pos, Standard());
-} 
+}
 
 template <typename TValue, typename THostspec, typename TPos>
 inline typename Reference<String<TValue, Packed<THostspec> > const>::Type
-value(String<TValue, Packed<THostspec> > const & me, 
-      TPos const & pos)
+value(String<TValue, Packed<THostspec> > const & me,
+      TPos const pos)
 {
     typedef String<TValue, Packed<THostspec> > TPackedString;
     typedef PackedTraits_<TPackedString> TTraits;
     return me.data_host[1 + pos / TTraits::VALUES_PER_HOST_VALUE][pos % TTraits::VALUES_PER_HOST_VALUE];
-} 
+}
 
 // --------------------------------------------------------------------------
 // Function capacity()
@@ -719,7 +780,7 @@ capacity(String<TValue, Packed<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec>
-inline void 
+inline void
 clear(String<TValue, Packed<THostspec> > & me)
 {
     clear(host(me));
@@ -730,18 +791,55 @@ clear(String<TValue, Packed<THostspec> > & me)
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec>
-inline void 
+inline void
 shrinkToFit(String<TValue, Packed<THostspec> > & me)
 {
     shrinkToFit(host(me));
 }
 
+// --------------------------------------------------------------------------
+// Function _clearUnusedBits()
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename THostspec>
+inline void
+_clearUnusedBits(String<TValue, Packed<THostspec> > & me)
+{
+    typedef String<TValue, Packed<THostspec> > TPackedString;
+    typedef PackedTraits_<TPackedString> TTraits;
+
+    typedef typename Host<TPackedString>::Type THost;
+    typedef typename Iterator<THost, Standard>::Type THostIterator;
+
+    typedef typename TTraits::THostValue THostValue;
+    typedef typename THostValue::TBitVector TBitVector;
+    typedef typename Size<TPackedString>::Type TSize;
+
+    static const TBitVector ALL_ONE = ~(TBitVector)0 >> TTraits::WASTED_BITS;
+
+    THostIterator it = begin(host(me), Standard());
+    THostIterator itEnd = end(host(me), Standard());
+
+    if (it == itEnd)
+        return;
+
+    // zero all wasted bits
+    if (TTraits::WASTED_BITS != 0)
+        for (++it; it != itEnd; ++it)
+            it->i &= ALL_ONE;
+
+    // zero the last half-filled tuple
+    TSize lastValues = length(me) % TTraits::VALUES_PER_HOST_VALUE;
+    if (lastValues != 0)
+        back(host(me)).i &= ALL_ONE & ~(ALL_ONE >> (lastValues * TTraits::BITS_PER_VALUE));
+}
+
 /*
 
 template<typename TTarget, typename TSource1, typename TSource2>
 inline void
-_arrayConstructCopyDefault(TSource1 source_begin, 
-                           TSource2 source_end, 
+_arrayConstructCopyDefault(TSource1 source_begin,
+                           TSource2 source_end,
                            TTarget target_begin)
 {
     SEQAN_CHECKPOINT;
@@ -772,7 +870,7 @@ _arrayConstructCopyDefault(TSource1 source_begin,
 // ------------------------------------
 
 template < typename TPackedString, typename TSpec >
-inline void 
+inline void
 arrayCopyForward(Iter<TPackedString, Packed<TSpec> > source_begin,
                  Iter<TPackedString, Packed<TSpec> > source_end,
                  Iter<TPackedString, Packed<TSpec> > target_begin)
@@ -781,7 +879,7 @@ arrayCopyForward(Iter<TPackedString, Packed<TSpec> > source_begin,
     typedef typename TTraits::THostValue THostValue;
     typedef typename Size<TPackedString>::Type TSize;
     typedef typename Host<Iter<TPackedString, Packed<TSpec> > >::Type THostIter;
-    
+
     TSize size = source_end - source_begin;
 
     // will we touch more than one word in the target string?
@@ -801,22 +899,22 @@ arrayCopyForward(Iter<TPackedString, Packed<TSpec> > source_begin,
         }
 
         // now copy whole words
-        register int leftShift = source_begin.localPos;
+        int leftShift = source_begin.localPos;
         if (leftShift != 0)
         {
             THostIter source_lastWord = hostIterator(source_end);
             if (source_end.localPos < source_begin.localPos)
                 --source_lastWord;
 
-            register typename THostValue::TBitVector prevWord = hostIterator(source_begin)->i;
-            register int rightShift = TTraits::VALUES_PER_HOST_VALUE - leftShift;
+            typename THostValue::TBitVector prevWord = hostIterator(source_begin)->i;
+            int rightShift = TTraits::VALUES_PER_HOST_VALUE - leftShift;
             leftShift *= TTraits::BITS_PER_VALUE;
             rightShift *= TTraits::BITS_PER_VALUE;
             for (; hostIterator(source_begin) != source_lastWord; ++hostIterator(target_begin))
             {
                 // words must be shifted and or'ed (BB|CCCC in the figure)
                 ++hostIterator(source_begin);
-                register typename THostValue::TBitVector curWord = hostIterator(source_begin)->i;
+                typename THostValue::TBitVector curWord = hostIterator(source_begin)->i;
                 hostIterator(target_begin)->i = (prevWord << leftShift) | (curWord >> rightShift);
                 prevWord = curWord;
             }
@@ -853,7 +951,7 @@ arrayCopyForward(Iter<TPackedString, Packed<TSpec> > source_begin,
 // ------------------------------------
 
 template < typename TPackedString, typename TSpec >
-inline void 
+inline void
 arrayCopyBackward(Iter<TPackedString, Packed<TSpec> > source_begin,
                   Iter<TPackedString, Packed<TSpec> > source_end,
                   Iter<TPackedString, Packed<TSpec> > target_begin)
@@ -883,11 +981,11 @@ arrayCopyBackward(Iter<TPackedString, Packed<TSpec> > source_begin,
         }
 
         // now copy whole words
-        register int leftShift = source_end.localPos;
+        int leftShift = source_end.localPos;
         if (leftShift != 0)
         {
-            register typename THostValue::TBitVector prevWord = hostIterator(source_end)->i;
-            register int rightShift = TTraits::VALUES_PER_HOST_VALUE - leftShift;
+            typename THostValue::TBitVector prevWord = hostIterator(source_end)->i;
+            int rightShift = TTraits::VALUES_PER_HOST_VALUE - leftShift;
             leftShift *= TTraits::BITS_PER_VALUE;
             rightShift *= TTraits::BITS_PER_VALUE;
             while (hostIterator(target_begin) != target_firstWord)
@@ -896,7 +994,7 @@ arrayCopyBackward(Iter<TPackedString, Packed<TSpec> > source_begin,
                 --hostIterator(target_begin);
 
                 // words must be shifted and or'ed (BB|CCCC in the figure)
-                register typename THostValue::TBitVector curWord = hostIterator(source_end)->i;
+                typename THostValue::TBitVector curWord = hostIterator(source_end)->i;
                 hostIterator(target_begin)->i = (curWord << leftShift) | (prevWord >> rightShift);
                 prevWord = curWord;
             }
@@ -928,7 +1026,7 @@ arrayCopyBackward(Iter<TPackedString, Packed<TSpec> > source_begin,
 }
 
 template<typename TPackedString, typename TSpec, typename TValue2>
-inline void 
+inline void
 arrayFill(Iter<TPackedString, Packed<TSpec> > begin_,
           Iter<TPackedString, Packed<TSpec> > end_,
           TValue2 const & value)
@@ -976,7 +1074,7 @@ arrayFill(Iter<TPackedString, Packed<TSpec> > begin_,
 
 // TODO(weese): There should be default wrappers using arrayCopyForward (so that these overloads are not necessary)
 template < typename TPackedString, typename TSpec >
-inline void 
+inline void
 arrayMoveForward(Iter<TPackedString, Packed<TSpec> > source_begin,
                  Iter<TPackedString, Packed<TSpec> > source_end,
                  Iter<TPackedString, Packed<TSpec> > target_begin)
@@ -1057,7 +1155,7 @@ struct ClearSpaceStringPacked_
     template <typename T>
     static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
+        T & seq,
         typename Size<T>::Type size)
     {
         typedef typename Size<T>::Type TSize;
@@ -1072,9 +1170,9 @@ struct ClearSpaceStringPacked_
     }
 
     template <typename T>
-    static inline typename Size<T>::Type 
+    static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
+        T & seq,
         typename Size<T>::Type size,
         typename Size<T>::Type limit)
     {
@@ -1084,26 +1182,26 @@ struct ClearSpaceStringPacked_
     }
 
     template <typename T>
-    static inline typename Size<T>::Type 
+    static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
-        typename Size<T>::Type size, 
-        typename Size<T>::Type start, 
+        T & seq,
+        typename Size<T>::Type size,
+        typename Size<T>::Type start,
         typename Size<T>::Type end)
     {
         return _clearSpace_(seq, size, start, end, maxValue<typename Size<T>::Type >());
     }
 
     template <typename T>
-    static typename Size<T>::Type 
+    static typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
-        typename Size<T>::Type size, 
-        typename Size<T>::Type start, 
-        typename Size<T>::Type end, 
+        T & seq,
+        typename Size<T>::Type size,
+        typename Size<T>::Type start,
+        typename Size<T>::Type end,
         typename Size<T>::Type limit)
     {
-//??? TODO: This function can be accelerated this way: 
+//??? TODO: This function can be accelerated this way:
 //              - move values in host
 //              - avoid double moving of the rest-part if "resize" allocates a new block
 
@@ -1135,11 +1233,11 @@ struct ClearSpaceStringPacked_
     }
 /*
     template <typename T>
-    static inline typename Size<T>::Type 
+    static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
-        typename Size<T>::Type size, 
-        typename Iterator<T>::Type start, 
+        T & seq,
+        typename Size<T>::Type size,
+        typename Iterator<T>::Type start,
         typename Iterator<T>::Type end)
     {
         typename Iterator<T>::Type seq_begin = begin(seq);
@@ -1147,13 +1245,13 @@ struct ClearSpaceStringPacked_
     }
 
     template <typename T>
-    static inline typename Size<T>::Type 
+    static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
-        typename Size<T>::Type size,  
+        T & seq,
+        typename Size<T>::Type size,
         typename Iterator<T>::Type start,
         typename Iterator<T>::Type end,
-        typename Size<T>::Type limit) 
+        typename Size<T>::Type limit)
     {
         typename Iterator<T>::Type seq_begin = begin(seq);
         return _clearSpace(seq, size, start - seq_begin, end - seq_begin, limit, Insist());
@@ -1161,43 +1259,43 @@ struct ClearSpaceStringPacked_
 */
 };
 
-template<typename TValue, typename THostspec, typename TExpand>
-inline typename Size< String<TValue, Packed<THostspec> > >::Type 
-_clearSpace(String<TValue, Packed<THostspec> > & me, 
-        typename Size< String<TValue, Packed<THostspec> > >::Type size, 
-        Tag<TExpand>)
+template<typename TValue, typename THostspec, typename TSize, typename TExpand>
+inline typename Size< String<TValue, Packed<THostspec> > >::Type
+_clearSpace(String<TValue, Packed<THostspec> > & me,
+            TSize size,
+            Tag<TExpand>)
 {
     return ClearSpaceStringPacked_<Tag<TExpand> >::_clearSpace_(me, size);
 }
 
-template<typename TValue, typename THostspec, typename TExpand>
-inline typename Size< String<TValue, Packed<THostspec> > >::Type 
-_clearSpace(String<TValue, Packed<THostspec> > & me, 
-        typename Size< String<TValue, Packed<THostspec> > >::Type size, 
-        typename Size< String<TValue, Packed<THostspec> > >::Type limit, 
-        Tag<TExpand>)
+template<typename TValue, typename THostspec, typename TSize, typename TCapacity, typename TExpand>
+inline typename Size< String<TValue, Packed<THostspec> > >::Type
+_clearSpace(String<TValue, Packed<THostspec> > & me,
+            TSize size,
+            TCapacity limit,
+            Tag<TExpand>)
 {
     return ClearSpaceStringPacked_<Tag<TExpand> >::_clearSpace_(me, size, limit);
 }
 
-template<typename TValue, typename THostspec, typename TPosition, typename TExpand>
-inline typename Size< String<TValue, Packed<THostspec> > >::Type 
-_clearSpace(String<TValue, Packed<THostspec> > & me, 
-            typename Size< String<TValue, Packed<THostspec> > >::Type size, 
-            TPosition pos_begin, 
-            TPosition pos_end, 
+template<typename TValue, typename THostspec, typename TSize, typename TPosition, typename TExpand>
+inline typename Size< String<TValue, Packed<THostspec> > >::Type
+_clearSpace(String<TValue, Packed<THostspec> > & me,
+            TSize size,
+            TPosition pos_begin,
+            TPosition pos_end,
             Tag<TExpand>)
 {
     return ClearSpaceStringPacked_<Tag<TExpand> >::_clearSpace_(me, size, pos_begin, pos_end);
 }
 
-template<typename TValue, typename THostspec, typename TPosition, typename TExpand>
-inline typename Size< String<TValue, Packed<THostspec> > >::Type 
-_clearSpace(String<TValue, Packed<THostspec> > & me, 
-            typename Size< String<TValue, Packed<THostspec> > >::Type size, 
-            TPosition pos_begin, 
-            TPosition pos_end, 
-            typename Size< String<TValue, Packed<THostspec> > >::Type limit, 
+template<typename TValue, typename THostspec, typename TSize, typename TPosition, typename TCapacity, typename TExpand>
+inline typename Size< String<TValue, Packed<THostspec> > >::Type
+_clearSpace(String<TValue, Packed<THostspec> > & me,
+            TSize size,
+            TPosition pos_begin,
+            TPosition pos_end,
+            TCapacity limit,
             Tag<TExpand>)
 {
     return ClearSpaceStringPacked_<Tag<TExpand> >::_clearSpace_(me, size, pos_begin, pos_end, limit);
@@ -1207,12 +1305,10 @@ _clearSpace(String<TValue, Packed<THostspec> > & me,
 // Function reserve()
 // --------------------------------------------------------------------------
 
-///.Function.reserve.param.object.type:Spec.Packed String
-
 template <typename TValue, typename TSpec, typename TSize_, typename TExpand>
 inline typename Size< String<TValue, Packed<TSpec> > >::Type
 reserve(
-    String<TValue, Packed<TSpec> > & seq, 
+    String<TValue, Packed<TSpec> > & seq,
     TSize_ new_capacity,
     Tag<TExpand> tag)
 {
@@ -1248,14 +1344,14 @@ hostIterator(Iter<TPackedString, Packed<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline typename Reference<Iter<TPackedString, Packed<THostspec> > >::Type 
+inline typename Reference<Iter<TPackedString, Packed<THostspec> > >::Type
 value(Iter<TPackedString, Packed<THostspec> > & me)
 {
     return typename Reference<Iter<TPackedString, Packed<THostspec> > >::Type(me);
 }
 
 template <typename TPackedString, typename THostspec>
-inline typename Reference<Iter<TPackedString, Packed<THostspec> > const>::Type 
+inline typename Reference<Iter<TPackedString, Packed<THostspec> > const>::Type
 value(Iter<TPackedString, Packed<THostspec> > const & me)
 {
     return typename Reference<Iter<TPackedString, Packed<THostspec> > const>::Type(me);
@@ -1280,14 +1376,14 @@ value(Iter<TPackedString const, Packed<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline typename GetValue<Iter<TPackedString, Packed<THostspec> > >::Type 
+inline typename GetValue<Iter<TPackedString, Packed<THostspec> > >::Type
 getValue(Iter<TPackedString, Packed<THostspec> > & me)
 {
     return getValue(hostIterator(me))[me.localPos];
 }
 
 template <typename TPackedString, typename THostspec>
-inline typename GetValue<Iter<TPackedString, Packed<THostspec> > const>::Type 
+inline typename GetValue<Iter<TPackedString, Packed<THostspec> > const>::Type
 getValue(Iter<TPackedString, Packed<THostspec> > const & me)
 {
     return getValue(hostIterator(me))[me.localPos];
@@ -1339,7 +1435,7 @@ moveValue(Iter<TPackedString, Packed<THostspec> > const & me,
 // Function valueConstruct()
 // --------------------------------------------------------------------------
 
-//emulate construction and destruction 
+//emulate construction and destruction
 
 template <typename TPackedString, typename THostspec>
 inline void
@@ -1351,11 +1447,12 @@ valueConstruct(Iter<TPackedString, Packed<THostspec> > const & /*it*/)
 template <typename TPackedString, typename THostspec, typename TParam>
 inline void
 valueConstruct(Iter<TPackedString, Packed<THostspec> > const & it,
-               TParam const & param_)
+               TParam SEQAN_FORWARD_CARG param_)
 {
-    assignValue(it, param_);
+    assignValue(it, SEQAN_FORWARD(TParam, param_));
 }
 
+#ifndef SEQAN_CXX11_STANDARD
 template <typename TPackedString, typename THostspec, typename TParam>
 inline void
 valueConstruct(Iter<TPackedString, Packed<THostspec> > const & it,
@@ -1364,6 +1461,7 @@ valueConstruct(Iter<TPackedString, Packed<THostspec> > const & it,
 {
     moveValue(it, param_);
 }
+#endif
 
 // --------------------------------------------------------------------------
 // Function valueDestruct()
@@ -1382,7 +1480,7 @@ valueDestruct(Iter<TPackedString, Packed<THostspec> > const & /*it*/)
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline bool 
+inline bool
 operator==(Iter<TPackedString, Packed<THostspec> > const & left,
            Iter<TPackedString, Packed<THostspec> > const & right)
 {
@@ -1394,7 +1492,7 @@ operator==(Iter<TPackedString, Packed<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline bool 
+inline bool
 operator!=(Iter<TPackedString, Packed<THostspec> > const & left,
            Iter<TPackedString, Packed<THostspec> > const & right)
 {
@@ -1406,7 +1504,7 @@ operator!=(Iter<TPackedString, Packed<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline bool 
+inline bool
 operator>(Iter<TPackedString, Packed<THostspec> > const & left,
           Iter<TPackedString, Packed<THostspec> > const & right)
 {
@@ -1418,7 +1516,7 @@ operator>(Iter<TPackedString, Packed<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline bool 
+inline bool
 operator>=(Iter<TPackedString, Packed<THostspec> > const & left,
            Iter<TPackedString, Packed<THostspec> > const & right)
 {
@@ -1430,7 +1528,7 @@ operator>=(Iter<TPackedString, Packed<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline bool 
+inline bool
 operator<(Iter<TPackedString, Packed<THostspec> > const & left,
           Iter<TPackedString, Packed<THostspec> > const & right)
 {
@@ -1442,7 +1540,7 @@ operator<(Iter<TPackedString, Packed<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline bool 
+inline bool
 operator <= (Iter<TPackedString, Packed<THostspec> > const & left,
              Iter<TPackedString, Packed<THostspec> > const & right)
 {
@@ -1481,44 +1579,18 @@ operator--(Iter<TPackedString, Packed<THostspec> > & me)
     return me;
 }
 
-// ----------------------------------------------------------------------------
-// Helper Function _helperIsNegative()
-// ----------------------------------------------------------------------------
-
-// to remove '... < 0 is always false' warning
-template <typename T>
-inline bool
-_isNegative(T, False)
-{
-    return false;
-}
-
-template <typename T>
-inline bool
-_isNegative(T t, True)
-{
-    return t < 0;
-}
-
-template <typename T>
-inline bool
-_isNegative(T t)
-{
-    return _isNegative(t, typename IsSameType<T, typename MakeSigned_<T>::Type>::Type());
-}
-
 // --------------------------------------------------------------------------
 // Function operator+() for (iter, integral)
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec, typename TIntegral>
-inline Iter<TPackedString, Packed<THostspec> >  
+inline Iter<TPackedString, Packed<THostspec> >
 operator+(Iter<TPackedString, Packed<THostspec> > const & iter,
           TIntegral const & delta)
 {
     typedef PackedTraits_<TPackedString> TTraits;
 
-    if (_isNegative(delta))
+    if (isNegative(delta))
         return iter - (-(typename MakeSigned<TIntegral>::Type)delta);
 
     TIntegral ofs = (TIntegral)iter.localPos + delta;
@@ -1528,13 +1600,13 @@ operator+(Iter<TPackedString, Packed<THostspec> > const & iter,
 }
 
 template <typename TPackedString, typename THostspec, typename TIntegral>
-inline Iter<TPackedString, Packed<THostspec> >  
+inline Iter<TPackedString, Packed<THostspec> >
 operator+(TIntegral const & delta,
           Iter<TPackedString, Packed<THostspec> > const & iter)
 {
     typedef PackedTraits_<TPackedString> TTraits;
 
-    if (_isNegative(delta))
+    if (isNegative(delta))
         return iter - (-(typename MakeSigned<TIntegral>::Type)delta);
 
     TIntegral ofs = (TIntegral)iter.localPos + delta;
@@ -1554,7 +1626,7 @@ operator+=(Iter<TPackedString, Packed<THostspec> > & iter,
 {
     typedef PackedTraits_<TPackedString> TTraits;
 
-    if (_isNegative(delta))
+    if (isNegative(delta))
         return iter -= -(typename MakeSigned<TIntegral>::Type)delta;
 
     TIntegral ofs = (TIntegral)iter.localPos + delta;
@@ -1568,13 +1640,13 @@ operator+=(Iter<TPackedString, Packed<THostspec> > & iter,
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec, typename TIntegral>
-inline Iter<TPackedString, Packed<THostspec> >  
+inline Iter<TPackedString, Packed<THostspec> >
 operator-(Iter<TPackedString, Packed<THostspec> > const & iter,
           TIntegral const & delta)
 {
     typedef PackedTraits_<TPackedString> TTraits;
 
-    if (_isNegative(delta))
+    if (isNegative(delta))
         return iter + (-(typename MakeSigned<TIntegral>::Type)delta);
 
     TIntegral ofs = delta + (TIntegral)(TTraits::VALUES_PER_HOST_VALUE - 1) - (TIntegral)iter.localPos;
@@ -1594,7 +1666,7 @@ operator-=(Iter<TPackedString, Packed<THostspec> > & iter,
 {
     typedef PackedTraits_<TPackedString> TTraits;
 
-    if (_isNegative(delta))
+    if (isNegative(delta))
         return iter += -(typename MakeSigned<TIntegral>::Type)delta;
 
     TIntegral ofs = delta + (TIntegral)(TTraits::VALUES_PER_HOST_VALUE - 1) - (TIntegral)iter.localPos;
@@ -1608,7 +1680,7 @@ operator-=(Iter<TPackedString, Packed<THostspec> > & iter,
 // --------------------------------------------------------------------------
 
 template <typename TPackedString, typename THostspec>
-inline typename Difference<Iter<TPackedString, Packed<THostspec> > >::Type  
+inline typename Difference<Iter<TPackedString, Packed<THostspec> > >::Type
 operator-(Iter<TPackedString, Packed<THostspec> > const & iterLeft,
           Iter<TPackedString, Packed<THostspec> > const & iterRight)
 {
@@ -1618,6 +1690,304 @@ operator-(Iter<TPackedString, Packed<THostspec> > const & iterLeft,
            (TDiff)iterLeft.localPos - (TDiff)iterRight.localPos;
 }
 
+// ----------------------------------------------------------------------------
+// Function bitScanReverse()
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline typename Position<String<bool, Packed<THostSpec> > >::Type
+bitScanReverse(String<bool, Packed<THostSpec> > const & obj)
+{
+    typedef String<bool, Packed<THostSpec> > TPackedString;
+    typedef typename Position<TPackedString>::Type TPosition;
+    typedef typename Host<TPackedString>::Type TPackedHost;
+    typedef typename Iterator<TPackedHost const, Standard>::Type TConstPackedHostIterator;
+    typedef PackedTraits_<TPackedString> TTraits;
+    typedef typename TTraits::THostValue THostValue;  // Is a tuple.
+    typedef typename THostValue::TBitVector TBitVector;
+
+    if (empty(host(obj)))
+        return MaxValue<TPosition>::VALUE;
+
+    TConstPackedHostIterator it = end(host(obj), Standard()) - 1;
+    TConstPackedHostIterator itBegin = begin(host(obj), Standard());
+
+    // We need to treat the last value differently, because it's possible not all bits are in use.
+    TBitVector lastVal = it->i & (~static_cast<TBitVector>(0) <<
+                                  (BitsPerValue<TBitVector>::VALUE - (length(obj) % BitsPerValue<TBitVector>::VALUE)));
+
+    if (!testAllZeros(lastVal))
+        return (((it - itBegin) - 1) * BitsPerValue<TBitVector>::VALUE) +
+               (BitsPerValue<TBitVector>::VALUE - 1) - bitScanForward(lastVal);
+    --it;
+    for(;it != itBegin && testAllZeros(*it); --it)
+    {}
+
+    if (it != itBegin)
+        return (((it - itBegin) - 1) * BitsPerValue<TBitVector>::VALUE) +
+               (BitsPerValue<TBitVector>::VALUE - 1) - bitScanForward(it->i);
+    return length(obj);
+}
+
+// ----------------------------------------------------------------------------
+// Function bitScanForward()
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline typename Position<String<bool, Packed<THostSpec> > >::Type
+bitScanForward(String<bool, Packed<THostSpec> > const & obj)
+{
+    typedef String<bool, Packed<THostSpec> > TPackedString;
+    typedef typename Position<TPackedString>::Type TPosition;
+    typedef typename Host<TPackedString>::Type TPackedHost;
+    typedef typename Iterator<TPackedHost const, Standard>::Type TConstPackedHostIterator;
+    typedef PackedTraits_<TPackedString> TTraits;
+    typedef typename TTraits::THostValue THostValue;
+    typedef typename THostValue::TBitVector TBitVector;
+
+    if (empty(host(obj)))
+        return MaxValue<TPosition>::VALUE;
+
+    TConstPackedHostIterator itBegin = begin(host(obj), Standard()) + 1;
+    TConstPackedHostIterator it = itBegin;
+    TConstPackedHostIterator itEnd = end(host(obj), Standard()) - 1;
+
+    for (; it != itEnd && testAllZeros(*it); ++it)
+    {}
+
+    // If last element is not 0, we return the last position. Note, that we do not check for the returned index to be
+    // bigger than the length of the string. The caller has to do this.
+    TBitVector lastVal = (it != itEnd) ? it->i :
+             it->i & (~static_cast<TBitVector>(0) << (BitsPerValue<TBitVector>::VALUE -
+                                                      (length(obj) % BitsPerValue<TBitVector>::VALUE)));
+    if (testAllZeros(lastVal))
+        return length(obj);
+    return ((it - itBegin) * BitsPerValue<TBitVector>::VALUE) + (BitsPerValue<TBitVector>::VALUE - 1) - bitScanReverse(lastVal);
+}
+
+// ----------------------------------------------------------------------------
+// Function transform()
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec, typename TBinaryFunctor>
+inline void transform(String<bool, Packed<THostSpec> > & target,
+                      String<bool, Packed<THostSpec> > const & lhs,
+                      String<bool, Packed<THostSpec> > const & rhs,
+                      TBinaryFunctor const & binaryFunctor)
+{
+    typedef String<bool, Packed<THostSpec> > TBitVector;
+    typedef typename Host<TBitVector>::Type THost;
+    typedef typename Iterator<THost const, Standard>::Type TConstIterator;
+    typedef typename Iterator<THost, Standard>::Type TIterator;
+
+    if (empty(host(lhs)) || empty(host(rhs)))
+        return;
+
+    SEQAN_ASSERT_EQ(length(lhs), length(rhs));
+
+    resize(target, length(lhs), Exact());
+
+    TConstIterator itLhsBegin = begin(host(lhs), Standard()) + 1;
+    TConstIterator itLhsEnd = end(host(lhs), Standard());
+    TConstIterator itRhsBegin = begin(host(rhs), Standard()) + 1;
+    TIterator itTarget = begin(host(target), Standard()) + 1;
+
+    std::transform(itLhsBegin, itLhsEnd, itRhsBegin, itTarget, binaryFunctor);
+}
+
+// ----------------------------------------------------------------------------
+// Function transform()
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec, typename TUnaryFunctor>
+inline void transform(String<bool, Packed<THostSpec> > & target,
+                      String<bool, Packed<THostSpec> > const & src,
+                      TUnaryFunctor const & unaryFunctor)
+{
+    typedef String<bool, Packed<THostSpec> > TBitVector;
+    typedef typename Host<TBitVector>::Type THost;
+    typedef typename Iterator<THost const, Standard>::Type TConstIterator;
+    typedef typename Iterator<THost, Standard>::Type TIterator;
+
+    if (empty(host(src)))
+        return;
+
+    resize(target, length(src), Exact());
+
+    TConstIterator itSrcBegin = begin(host(src), Standard()) + 1;
+    TConstIterator itSrcEnd = end(host(src), Standard());
+    TIterator itTarget = begin(host(target), Standard()) + 1;
+
+    std::transform(itSrcBegin, itSrcEnd, itTarget, unaryFunctor);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator|
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline String<bool, Packed<THostSpec> >
+operator|(String<bool, Packed<THostSpec> > const & lhs, String<bool, Packed<THostSpec> > const & rhs)
+{
+    String<bool, Packed<THostSpec> > tmp;
+    transform(tmp, lhs, rhs, FunctorBitwiseOr());
+    return tmp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator|=
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline String<bool, Packed<THostSpec> > &
+operator|=(String<bool, Packed<THostSpec> > & lhs, String<bool, Packed<THostSpec> > const & rhs)
+{
+    transform(lhs, lhs, rhs, FunctorBitwiseOr());
+    return lhs;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator&
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline String<bool, Packed<THostSpec> >
+operator&(String<bool, Packed<THostSpec> > const & lhs, String<bool, Packed<THostSpec> > const & rhs)
+{
+    String<bool, Packed<THostSpec> > tmp;
+    transform(tmp, lhs, rhs, FunctorBitwiseAnd());
+    return tmp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator&=
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline String<bool, Packed<THostSpec> > &
+operator&=(String<bool, Packed<THostSpec> > & lhs, String<bool, Packed<THostSpec> > const & rhs)
+{
+    transform(lhs, lhs, rhs, FunctorBitwiseAnd());
+    return lhs;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator~
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline String<bool, Packed<THostSpec> >
+operator~(String<bool, Packed<THostSpec> > const & vec)
+{
+    String<bool, Packed<THostSpec> > tmp;
+    transform(tmp, vec, FunctorBitwiseNot());
+    return tmp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator^
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline String<bool, Packed<THostSpec> >
+operator^(String<bool, Packed<THostSpec> > const & lhs, String<bool, Packed<THostSpec> > const & rhs)
+{
+    String<bool, Packed<THostSpec> > tmp;
+    transform(tmp, lhs, rhs, FunctorBitwiseXor());
+    return tmp;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator^=
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline String<bool, Packed<THostSpec> > &
+operator^=(String<bool, Packed<THostSpec> > & lhs, String<bool, Packed<THostSpec> > const & rhs)
+{
+    transform(lhs, lhs, rhs, FunctorBitwiseXor());
+    return lhs;
+}
+
+// ----------------------------------------------------------------------------
+// Function _packedStringTestAll()
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec, typename TTester>
+inline bool
+_packedStringTestAll(String<bool, Packed<THostSpec> > const & obj, TTester const & tester)
+{
+    typedef String<bool, Packed<THostSpec> > TPackedString;
+    typedef typename Host<TPackedString>::Type TPackedHost;
+    typedef typename Iterator<TPackedHost const>::Type TConstIterator;
+
+    if (empty(host(obj)))
+        return false;
+
+    TConstIterator itFirst = begin(host(obj), Standard()) + 1;
+    TConstIterator itLast = end(host(obj), Standard()) - 1;
+
+    while (itFirst != itLast && tester(*itFirst, False()))
+        ++itFirst;
+
+    if (itFirst != itLast)
+        return false;
+
+    return tester(*(itFirst), True());  // Test last case.
+}
+
+// ----------------------------------------------------------------------------
+// Function testAllZeros()
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline bool
+testAllZeros(String<bool, Packed<THostSpec> > const & obj)
+{
+    typedef String<bool, Packed<THostSpec> > TPackedString;
+    typedef PackedTraits_<TPackedString> TTraits;
+
+    return _packedStringTestAll(obj, FunctorTestAllZeros<TPackedString>((TTraits::VALUES_PER_HOST_VALUE -
+                                     (length(obj) % TTraits::VALUES_PER_HOST_VALUE))));
+}
+
+// ----------------------------------------------------------------------------
+// Function testAllOnes()
+// ----------------------------------------------------------------------------
+
+template <typename THostSpec>
+inline bool
+testAllOnes(String<bool, Packed<THostSpec> > const & obj)
+{
+    typedef String<bool, Packed<THostSpec> > TPackedString;
+    typedef PackedTraits_<TPackedString> TTraits;
+
+    return _packedStringTestAll(obj, FunctorTestAllOnes<TPackedString>((TTraits::VALUES_PER_HOST_VALUE -
+                                     (length(obj) % TTraits::VALUES_PER_HOST_VALUE))));
+}
+
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostspec>
+inline bool open(String<TValue, Packed<THostspec> > & me, const char *fileName, int openMode)
+{
+    return open(host(me), fileName, openMode);
+}
+
+// ----------------------------------------------------------------------------
+// Function save()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostspec>
+inline bool save(String<TValue, Packed<THostspec> > const & me, const char *fileName, int openMode)
+{
+    // the visible part of the string is kept untouched and the function is thread-safe
+    _clearUnusedBits(const_cast<String<TValue, Packed<THostspec> > &>(me));
+    return save(host(me), fileName, openMode);
+}
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_SEQUENCE_STRING_PACKED_H_
diff --git a/seqan/sequence/string_packed_old.h b/seqan/sequence/string_packed_old.h
index 36a3c1d..2fa4d91 100644
--- a/seqan/sequence/string_packed_old.h
+++ b/seqan/sequence/string_packed_old.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -59,10 +59,10 @@ struct HostIterator;
  * @extends String
  * @headerfile <seqan/sequence.h>
  * @brief A string that stores as many values in one machine word as possible.
- * 
+ *
  * @signature template <typename TValue, typename THostSpec>
  *            class String<TValue, Packed2<THostSpec> >;
- * 
+ *
  * @tparam TValue The value type, that is the type of the items/characters
  *                stored in the string.Use @link Value @endlink to get the value
  *                type for a given class.
@@ -77,20 +77,6 @@ struct Packed2;
 template <typename TPackedContainer>
 struct PackedConsts_;
 
-/**
-.Spec.Packed String:
-..cat:Strings
-..general:Class.String
-..summary:A string that stores as many values in one machine word as possible.
-..signature:String<TValue, Packed2<THostspec> >
-..param.TValue:The value type, that is the type of the items/characters stored in the string.
-...remarks:Use @Metafunction.Value@ to get the value type for a given class.
-..param.THostspec:The specializing type.
-...remarks:This is the specialization of the host string that is used for storing the packed values.
-...default:@Spec.Alloc String.Alloc<>@
-..include:seqan/sequence.h
-*/
-
 /*???TODO Optimierungsm�glichkeiten:
 - _clearSpace kopiert Zeichenweise im Packed-String, und nicht im Host-String
 - _clearSpace verwendet resize, um den Host zu vergr��ern, d.h. der Inhalt wird eventuell doppelt kopiert.
@@ -160,7 +146,7 @@ class String<TValue, Packed2<THostspec> >
     }
 
     template <typename TPos>
-    inline typename Reference<String const>::Type 
+    inline typename Reference<String const>::Type
     operator[](TPos pos) const
     {
         SEQAN_CHECKPOINT;
@@ -217,7 +203,7 @@ class Iter<TContainer, Packed2<THostspec> >
     }
 
     inline
-    Iter const & 
+    Iter const &
     operator=(Iter const & other_)
     {
         SEQAN_CHECKPOINT;
@@ -275,7 +261,6 @@ struct IsContiguous<String<TValue, Packed2<THostspec> > >
 // Metafunction Host
 // --------------------------------------------------------------------------
 
-///.Metafunction.Host.param.T.type:Spec.Packed String
 template <typename TValue, typename THostspec>
 struct Host<String<TValue, Packed2<THostspec> > >
 {
@@ -425,9 +410,6 @@ struct TempCopy_<String<TValue, Packed2<THostspec> > >
 // Function host
 // --------------------------------------------------------------------------
 
-///.Function.host.param.object.type:Spec.Packed String
-///.Function.host.class:Spec.Packed String
-
 template <typename TValue, typename THostspec>
 inline typename Host<String<TValue, Packed2<THostspec> > >::Type &
 host(String<TValue, Packed2<THostspec> > & me)
@@ -450,7 +432,7 @@ host(String<TValue, Packed2<THostspec> > const & me)
 
 template <typename TValue, typename THostspec>
 inline typename Size<String<TValue, Packed2<THostspec> > >::Type
-length(String<TValue, Packed2<THostspec> > & me) 
+length(String<TValue, Packed2<THostspec> > & me)
 {
     SEQAN_CHECKPOINT;
     return me.data_length;
@@ -458,7 +440,7 @@ length(String<TValue, Packed2<THostspec> > & me)
 
 template <typename TValue, typename THostspec>
 inline typename Size<String<TValue, Packed2<THostspec> > const>::Type
-length(String<TValue, Packed2<THostspec> > const & me) 
+length(String<TValue, Packed2<THostspec> > const & me)
 {
     SEQAN_CHECKPOINT;
     return me.data_length;
@@ -469,9 +451,9 @@ length(String<TValue, Packed2<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec, typename TSize>
-inline void 
+inline void
 _setLength(
-    String<TValue, Packed2<THostspec> > & me, 
+    String<TValue, Packed2<THostspec> > & me,
     TSize new_length)
 {
     SEQAN_CHECKPOINT;
@@ -489,7 +471,7 @@ _setLength(
 // optimized variant for copy assignment. The host sequence is copied instead of
 // copying the packed string value by value.
 template <typename TTarget, typename TSource, typename TTag>
-inline void 
+inline void
 _assignCopyPackedString(TTarget & target,
                            TSource & source,
                            Tag<TTag> const & tag)
@@ -507,7 +489,7 @@ _assignCopyPackedString(TTarget & target,
 }
 
 template <typename TTarget, typename TSource, typename TSize, typename TTag>
-inline void 
+inline void
 _assignCopyPackedString(TTarget & target,
                         TSource & source,
                         TSize limit,
@@ -531,7 +513,7 @@ _assignCopyPackedString(TTarget & target,
 }
 
 template <typename TValue, typename THostspec, typename TTag>
-inline void 
+inline void
 assign(String<TValue, Packed2<THostspec> > & target,
        String<TValue, Packed2<THostspec> > & source,
        Tag<TTag> const & tag)
@@ -540,7 +522,7 @@ assign(String<TValue, Packed2<THostspec> > & target,
 }
 
 template <typename TValue, typename THostspec, typename TTag>
-inline void 
+inline void
 assign(String<TValue, Packed2<THostspec> > & target,
        String<TValue, Packed2<THostspec> > const & source,
        Tag<TTag> const & tag)
@@ -570,7 +552,7 @@ void assign(String<TValue, Packed2<THostspec> > & target,
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec>
-inline void const * 
+inline void const *
 getObjectId(String<TValue, Packed2<THostspec> > const & me)
 {
     SEQAN_CHECKPOINT;
@@ -582,7 +564,7 @@ getObjectId(String<TValue, Packed2<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec, typename TPos, typename TTag>
-inline typename Iterator<String<TValue, Packed2<THostspec> >, Tag<TTag> const>::Type 
+inline typename Iterator<String<TValue, Packed2<THostspec> >, Tag<TTag> const>::Type
 iter(String<TValue, Packed2<THostspec> > & me,
      TPos pos_,
      Tag<TTag> const &)
@@ -593,7 +575,7 @@ iter(String<TValue, Packed2<THostspec> > & me,
 }
 
 template <typename TValue, typename THostspec, typename TPos, typename TTag>
-inline typename Iterator<String<TValue, Packed2<THostspec> > const, Tag<TTag> const>::Type 
+inline typename Iterator<String<TValue, Packed2<THostspec> > const, Tag<TTag> const>::Type
 iter(String<TValue, Packed2<THostspec> > const & me,
      TPos pos_,
      Tag<TTag> const &)
@@ -608,7 +590,7 @@ iter(String<TValue, Packed2<THostspec> > const & me,
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec, typename TTag>
-inline typename Iterator<String<TValue, Packed2<THostspec> >, Tag<TTag> const>::Type 
+inline typename Iterator<String<TValue, Packed2<THostspec> >, Tag<TTag> const>::Type
 begin(String<TValue, Packed2<THostspec> > & me,
       Tag<TTag> const & tag_)
 {
@@ -617,7 +599,7 @@ begin(String<TValue, Packed2<THostspec> > & me,
 }
 
 template <typename TValue, typename THostspec, typename TTag>
-inline typename Iterator<String<TValue, Packed2<THostspec> > const, Tag<TTag> const>::Type 
+inline typename Iterator<String<TValue, Packed2<THostspec> > const, Tag<TTag> const>::Type
 begin(String<TValue, Packed2<THostspec> > const & me,
       Tag<TTag> const & tag_)
 {
@@ -630,7 +612,7 @@ begin(String<TValue, Packed2<THostspec> > const & me,
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec, typename TTag>
-inline typename Iterator<String<TValue, Packed2<THostspec> >, Tag<TTag> const>::Type 
+inline typename Iterator<String<TValue, Packed2<THostspec> >, Tag<TTag> const>::Type
 end(String<TValue, Packed2<THostspec> > & me,
     Tag<TTag> const & tag_)
 {
@@ -639,7 +621,7 @@ end(String<TValue, Packed2<THostspec> > & me,
 }
 
 template <typename TValue, typename THostspec, typename TTag>
-inline typename Iterator<String<TValue, Packed2<THostspec> > const, Tag<TTag> const>::Type 
+inline typename Iterator<String<TValue, Packed2<THostspec> > const, Tag<TTag> const>::Type
 end(String<TValue, Packed2<THostspec> > const & me,
     Tag<TTag> const & tag_)
 {
@@ -653,23 +635,23 @@ end(String<TValue, Packed2<THostspec> > const & me,
 
 template <typename TValue, typename THostspec, typename TPos>
 inline typename Reference<String<TValue, Packed2<THostspec> > >::Type
-value(String<TValue, Packed2<THostspec> > & me, 
+value(String<TValue, Packed2<THostspec> > & me,
       TPos pos)
 {
     SEQAN_CHECKPOINT;
-    
+
     return *iter(me, pos, Standard());
-} 
+}
 
 template <typename TValue, typename THostspec, typename TPos>
 inline typename Reference<String<TValue, Packed2<THostspec> > const>::Type
-value(String<TValue, Packed2<THostspec> > const & me, 
+value(String<TValue, Packed2<THostspec> > const & me,
       TPos pos)
 {
     SEQAN_CHECKPOINT;
-    
+
     return *iter(me, pos, Standard());
-} 
+}
 
 // --------------------------------------------------------------------------
 // Function capacity()
@@ -691,7 +673,7 @@ capacity(String<TValue, Packed2<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TValue, typename THostspec>
-inline void 
+inline void
 clear(String<TValue, Packed2<THostspec> > & me)
 {
     SEQAN_CHECKPOINT;
@@ -712,7 +694,7 @@ struct ClearSpaceStringPacked2_
     template <typename T>
     static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
+        T & seq,
         typename Size<T>::Type size)
     {
     SEQAN_CHECKPOINT;
@@ -728,9 +710,9 @@ struct ClearSpaceStringPacked2_
     }
 
     template <typename T>
-    static inline typename Size<T>::Type 
+    static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
+        T & seq,
         typename Size<T>::Type size,
         typename Size<T>::Type limit)
     {
@@ -743,11 +725,11 @@ struct ClearSpaceStringPacked2_
     }
 
     template <typename T>
-    static inline typename Size<T>::Type 
+    static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
-        typename Size<T>::Type size, 
-        typename Size<T>::Type start, 
+        T & seq,
+        typename Size<T>::Type size,
+        typename Size<T>::Type start,
         typename Size<T>::Type end)
     {
     SEQAN_CHECKPOINT;
@@ -755,16 +737,16 @@ struct ClearSpaceStringPacked2_
     }
 
     template <typename T>
-    static typename Size<T>::Type 
+    static typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
-        typename Size<T>::Type size, 
-        typename Size<T>::Type start, 
-        typename Size<T>::Type end, 
+        T & seq,
+        typename Size<T>::Type size,
+        typename Size<T>::Type start,
+        typename Size<T>::Type end,
         typename Size<T>::Type limit)
     {
     SEQAN_CHECKPOINT;
-//??? TODO: This function can be accelerated this way: 
+//??? TODO: This function can be accelerated this way:
 //              - move values in host
 //              - avoid double moving of the rest-part if "resize" allocates a new block
 
@@ -800,11 +782,11 @@ struct ClearSpaceStringPacked2_
         //move [end:right_end] to [start + size:..]
         if (old_size > size)
         {//move rest to left
-            ::std::copy(iter(seq, end, Standard()), iter(seq, old_length, Standard()), iter(seq, end + size - old_size, Standard()));
+            std::copy(iter(seq, end, Standard()), iter(seq, old_length, Standard()), iter(seq, end + size - old_size, Standard()));
         }
         else
         {//move rest to right
-            ::std::copy_backward(iter(seq, end, Standard()), iter(seq, old_length, Standard()), iter(seq,  new_length, Standard()));
+            std::copy_backward(iter(seq, end, Standard()), iter(seq, old_length, Standard()), iter(seq,  new_length, Standard()));
         }
 */
         if (old_size > size)
@@ -821,11 +803,11 @@ struct ClearSpaceStringPacked2_
     }
 /*
     template <typename T>
-    static inline typename Size<T>::Type 
+    static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
-        typename Size<T>::Type size, 
-        typename Iterator<T>::Type start, 
+        T & seq,
+        typename Size<T>::Type size,
+        typename Iterator<T>::Type start,
         typename Iterator<T>::Type end)
     {
     SEQAN_CHECKPOINT;
@@ -834,13 +816,13 @@ struct ClearSpaceStringPacked2_
     }
 
     template <typename T>
-    static inline typename Size<T>::Type 
+    static inline typename Size<T>::Type
     _clearSpace_(
-        T & seq, 
-        typename Size<T>::Type size,  
+        T & seq,
+        typename Size<T>::Type size,
         typename Iterator<T>::Type start,
         typename Iterator<T>::Type end,
-        typename Size<T>::Type limit) 
+        typename Size<T>::Type limit)
     {
     SEQAN_CHECKPOINT;
         typename Iterator<T>::Type seq_begin = begin(seq);
@@ -850,9 +832,9 @@ struct ClearSpaceStringPacked2_
 };
 
 template<typename TValue, typename THostspec, typename TExpand>
-inline typename Size< String<TValue, Packed2<THostspec> > >::Type 
-_clearSpace(String<TValue, Packed2<THostspec> > & me, 
-        typename Size< String<TValue, Packed2<THostspec> > >::Type size, 
+inline typename Size< String<TValue, Packed2<THostspec> > >::Type
+_clearSpace(String<TValue, Packed2<THostspec> > & me,
+        typename Size< String<TValue, Packed2<THostspec> > >::Type size,
         Tag<TExpand>)
 {
     SEQAN_CHECKPOINT;
@@ -860,10 +842,10 @@ _clearSpace(String<TValue, Packed2<THostspec> > & me,
 }
 
 template<typename TValue, typename THostspec, typename TExpand>
-inline typename Size< String<TValue, Packed2<THostspec> > >::Type 
-_clearSpace(String<TValue, Packed2<THostspec> > & me, 
-        typename Size< String<TValue, Packed2<THostspec> > >::Type size, 
-        typename Size< String<TValue, Packed2<THostspec> > >::Type limit, 
+inline typename Size< String<TValue, Packed2<THostspec> > >::Type
+_clearSpace(String<TValue, Packed2<THostspec> > & me,
+        typename Size< String<TValue, Packed2<THostspec> > >::Type size,
+        typename Size< String<TValue, Packed2<THostspec> > >::Type limit,
         Tag<TExpand>)
 {
     SEQAN_CHECKPOINT;
@@ -871,11 +853,11 @@ _clearSpace(String<TValue, Packed2<THostspec> > & me,
 }
 
 template<typename TValue, typename THostspec, typename TPosition, typename TExpand>
-inline typename Size< String<TValue, Packed2<THostspec> > >::Type 
-_clearSpace(String<TValue, Packed2<THostspec> > & me, 
-            typename Size< String<TValue, Packed2<THostspec> > >::Type size, 
-            TPosition pos_begin, 
-            TPosition pos_end, 
+inline typename Size< String<TValue, Packed2<THostspec> > >::Type
+_clearSpace(String<TValue, Packed2<THostspec> > & me,
+            typename Size< String<TValue, Packed2<THostspec> > >::Type size,
+            TPosition pos_begin,
+            TPosition pos_end,
             Tag<TExpand>)
 {
     SEQAN_CHECKPOINT;
@@ -883,12 +865,12 @@ _clearSpace(String<TValue, Packed2<THostspec> > & me,
 }
 
 template<typename TValue, typename THostspec, typename TPosition, typename TExpand>
-inline typename Size< String<TValue, Packed2<THostspec> > >::Type 
-_clearSpace(String<TValue, Packed2<THostspec> > & me, 
-            typename Size< String<TValue, Packed2<THostspec> > >::Type size, 
-            TPosition pos_begin, 
-            TPosition pos_end, 
-            typename Size< String<TValue, Packed2<THostspec> > >::Type limit, 
+inline typename Size< String<TValue, Packed2<THostspec> > >::Type
+_clearSpace(String<TValue, Packed2<THostspec> > & me,
+            typename Size< String<TValue, Packed2<THostspec> > >::Type size,
+            TPosition pos_begin,
+            TPosition pos_end,
+            typename Size< String<TValue, Packed2<THostspec> > >::Type limit,
             Tag<TExpand>)
 {
     SEQAN_CHECKPOINT;
@@ -899,12 +881,10 @@ _clearSpace(String<TValue, Packed2<THostspec> > & me,
 // Function reserve()
 // --------------------------------------------------------------------------
 
-///.Function.reserve.param.object.type:Spec.Packed String
-
 template <typename TValue, typename TSpec, typename TSize_, typename TExpand>
 inline typename Size< String<TValue, Packed2<TSpec> > >::Type
 reserve(
-    String<TValue, Packed2<TSpec> > & seq, 
+    String<TValue, Packed2<TSpec> > & seq,
     TSize_ new_capacity,
     Tag<TExpand> tag)
 {
@@ -925,7 +905,7 @@ reserve(
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline typename Parameter_<TContainer>::Type 
+inline typename Parameter_<TContainer>::Type
 container(Iter<TContainer, Packed2<THostspec> > & me)
 {
     SEQAN_CHECKPOINT;
@@ -933,7 +913,7 @@ container(Iter<TContainer, Packed2<THostspec> > & me)
 }
 
 template <typename TContainer, typename THostspec>
-inline typename Parameter_<TContainer>::Type 
+inline typename Parameter_<TContainer>::Type
 container(Iter<TContainer, Packed2<THostspec> > const & me)
 {
     SEQAN_CHECKPOINT;
@@ -1000,7 +980,7 @@ _bitpos(Iter<TContainer, Packed2<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline typename Position<Iter<TContainer, Packed2<THostspec> > const>::Type 
+inline typename Position<Iter<TContainer, Packed2<THostspec> > const>::Type
 position(Iter<TContainer, Packed2<THostspec> > const & me)
 {
     SEQAN_CHECKPOINT;
@@ -1014,7 +994,7 @@ position(Iter<TContainer, Packed2<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec, typename TPosition>
-inline void 
+inline void
 setPosition(Iter<TContainer, Packed2<THostspec> > & me,
             TPosition pos_)
 {
@@ -1028,7 +1008,7 @@ setPosition(Iter<TContainer, Packed2<THostspec> > & me,
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline typename Reference<Iter<TContainer, Packed2<THostspec> > >::Type 
+inline typename Reference<Iter<TContainer, Packed2<THostspec> > >::Type
 value(Iter<TContainer, Packed2<THostspec> > & me)
 {
     SEQAN_CHECKPOINT;
@@ -1036,7 +1016,7 @@ value(Iter<TContainer, Packed2<THostspec> > & me)
 }
 
 template <typename TContainer, typename THostspec>
-inline typename Reference<Iter<TContainer, Packed2<THostspec> > const>::Type 
+inline typename Reference<Iter<TContainer, Packed2<THostspec> > const>::Type
 value(Iter<TContainer, Packed2<THostspec> > const & me)
 {
     SEQAN_CHECKPOINT;
@@ -1048,7 +1028,7 @@ value(Iter<TContainer, Packed2<THostspec> > const & me)
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline typename GetValue<Iter<TContainer, Packed2<THostspec> > >::Type 
+inline typename GetValue<Iter<TContainer, Packed2<THostspec> > >::Type
 getValue(Iter<TContainer, Packed2<THostspec> > & me)
 {
     SEQAN_CHECKPOINT;
@@ -1056,7 +1036,7 @@ getValue(Iter<TContainer, Packed2<THostspec> > & me)
 }
 
 template <typename TContainer, typename THostspec>
-inline typename GetValue<Iter<TContainer, Packed2<THostspec> > const>::Type 
+inline typename GetValue<Iter<TContainer, Packed2<THostspec> > const>::Type
 getValue(Iter<TContainer, Packed2<THostspec> > const & me)
 {
     SEQAN_CHECKPOINT;
@@ -1130,7 +1110,7 @@ moveValue(Iter<TContainer, Packed2<THostspec> > const & me,
 // Function valueConstruct()
 // --------------------------------------------------------------------------
 
-//emulate construction and destruction 
+//emulate construction and destruction
 
 template <typename TContainer, typename THostspec>
 inline void
@@ -1173,7 +1153,7 @@ valueDestruct(Iter<TContainer, Packed2<THostspec> > const & /*it*/)
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline bool 
+inline bool
 operator==(Iter<TContainer, Packed2<THostspec> > const & left,
            Iter<TContainer, Packed2<THostspec> > const & right)
 {
@@ -1186,7 +1166,7 @@ operator==(Iter<TContainer, Packed2<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline bool 
+inline bool
 operator!=(Iter<TContainer, Packed2<THostspec> > const & left,
            Iter<TContainer, Packed2<THostspec> > const & right)
 {
@@ -1199,7 +1179,7 @@ operator!=(Iter<TContainer, Packed2<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline bool 
+inline bool
 operator>(Iter<TContainer, Packed2<THostspec> > const & left,
           Iter<TContainer, Packed2<THostspec> > const & right)
 {
@@ -1212,7 +1192,7 @@ operator>(Iter<TContainer, Packed2<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline bool 
+inline bool
 operator>=(Iter<TContainer, Packed2<THostspec> > const & left,
            Iter<TContainer, Packed2<THostspec> > const & right)
 {
@@ -1225,7 +1205,7 @@ operator>=(Iter<TContainer, Packed2<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline bool 
+inline bool
 operator<(Iter<TContainer, Packed2<THostspec> > const & left,
           Iter<TContainer, Packed2<THostspec> > const & right)
 {
@@ -1238,7 +1218,7 @@ operator<(Iter<TContainer, Packed2<THostspec> > const & left,
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline bool 
+inline bool
 operator <= (Iter<TContainer, Packed2<THostspec> > const & left,
              Iter<TContainer, Packed2<THostspec> > const & right)
 {
@@ -1293,7 +1273,7 @@ goPrevious(Iter<TContainer, Packed2<THostspec> > & me)
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec, typename TIntegral>
-inline Iter<TContainer, Packed2<THostspec> >  
+inline Iter<TContainer, Packed2<THostspec> >
 operator+(Iter<TContainer, Packed2<THostspec> > const & left,
           TIntegral const & right)
 {
@@ -1302,7 +1282,7 @@ operator+(Iter<TContainer, Packed2<THostspec> > const & left,
 }
 
 template <typename TContainer, typename THostspec, typename TIntegral>
-inline Iter<TContainer, Packed2<THostspec> >  
+inline Iter<TContainer, Packed2<THostspec> >
 operator+(TIntegral const & left,
           Iter<TContainer, Packed2<THostspec> > const & right)
 {
@@ -1329,7 +1309,7 @@ operator+=(Iter<TContainer, Packed2<THostspec> > & left,
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec, typename TIntegral>
-inline Iter<TContainer, Packed2<THostspec> >  
+inline Iter<TContainer, Packed2<THostspec> >
 operator-(Iter<TContainer, Packed2<THostspec> > const & left,
           TIntegral const & right)
 {
@@ -1356,7 +1336,7 @@ operator-=(Iter<TContainer, Packed2<THostspec> > & left,
 // --------------------------------------------------------------------------
 
 template <typename TContainer, typename THostspec>
-inline typename Difference<Iter<TContainer, Packed2<THostspec> > >::Type  
+inline typename Difference<Iter<TContainer, Packed2<THostspec> > >::Type
 operator-(Iter<TContainer, Packed2<THostspec> > const & left,
           Iter<TContainer, Packed2<THostspec> > const & right)
 {
diff --git a/seqan/sequence/string_set_base.h b/seqan/sequence/string_set_base.h
index 65ef98a..0ba3ade 100644
--- a/seqan/sequence/string_set_base.h
+++ b/seqan/sequence/string_set_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -51,7 +51,7 @@ struct Owner {};
 
 /*!
  * @class StringSet
- * @implements SequenceConcept
+ * @implements StringConcept
  * @implements TextConcept
  * @implements SegmentableConcept
  * @headerfile <seqan/sequence.h>
@@ -74,34 +74,13 @@ struct Owner {};
  *
  * @section Examples
  *
- * @include demos/sequence/stringset.cpp
+ * @include demos/dox/sequence/stringset.cpp
  *
  * The output is as follows:
  *
- * @include demos/sequence/stringset.cpp.stdout
+ * @include demos/dox/sequence/stringset.cpp.stdout
  */
 
-/**
-.Class.StringSet:
-..cat:Sequences
-..summary:A container class for a set of strings.
-..signature:StringSet<TString, TSpec>
-..param.TString:The string type.
-...type:Class.String
-..param.TSpec:The specializing type for the StringSet.
-...metafunction:Metafunction.Spec
-...default:$Owner<Generous>$.
-..example.file:demos/sequence/stringset.cpp
-..example.text:The output is as follows:
-..example.output:
-Number of elements: 1
-Number of elements: 3
-Element 0: Hello World!
-Element 1: To be or not to be!
-Element 2: A man, a plan, a canal - Panama!
-Number of elements: 0
-..include:sequence.h
- */
 template <typename TString, typename TSpec = Owner<> >
 class StringSet;
 
@@ -109,6 +88,13 @@ class StringSet;
 // Metafunctions
 // ============================================================================
 
+// --------------------------------------------------------------------------
+// Metafunction StringSpec
+// --------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+struct StringSpec<StringSet<TString, TSpec> > : StringSpec<TString> {};
+
 // --------------------------------------------------------------------------
 // Metafunction Concatenator
 // --------------------------------------------------------------------------
@@ -124,18 +110,6 @@ class StringSet;
  * @return Type The resulting concatenator type.
  */
 
-/**
-.Metafunction.Concatenator:
-..class:Class.StringSet
-..summary:Returns the type of the concatenation sequence of all sequences in a @Class.StringSet@.
-..cat:Sequences
-..signature:Concatenator<TStringSet>::Type
-..param.TStringSet:The @Class.StringSet@ type.
-...type:Class.StringSet
-..returns:The type of a container that can be iterated like the concatenation string of all sequences in a @Class.StringSet@.
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Why is this specialized for all types?
 template <typename TObject>
 struct Concatenator
@@ -155,6 +129,38 @@ struct Concatenator<StringSet<TString, TSpec> >
     typedef ConcatenatorManyToOne<StringSet<TString, TSpec> > Type;
 };
 
+// --------------------------------------------------------------------------
+// Metafunction LengthSum
+// --------------------------------------------------------------------------
+
+/*!
+ * @mfn StringSet#LengthSum
+ * @brief Length sum type type in string set.
+ *
+ * @signature LengthSum<TStringSet>::Type
+ *
+ * @tparam TStringSet The @link StringSet @endlink to query for its length sum type.
+ *
+ * @return Type The resulting length sum type.
+ */
+
+// TODO(holtgrew): Complete documentation, part of TextConcept?
+
+template <typename TString>
+struct LengthSum
+{
+    typedef typename Size<TString>::Type Type;
+};
+
+template <typename TString, typename TSpec>
+struct LengthSum<StringSet<TString, TSpec> >
+{
+    typedef typename Size<TString>::Type Type;
+};
+
+template <typename T>
+struct LengthSum<T const> : LengthSum<T> {};
+
 // --------------------------------------------------------------------------
 // Metafunction StringSetLimits
 // --------------------------------------------------------------------------
@@ -176,8 +182,11 @@ struct StringSetLimits<TString const>
 template <typename TString, typename TSpec>
 struct StringSetLimits<StringSet<TString, TSpec> >
 {
-    typedef typename Size<TString>::Type TSize_;
-    typedef String<TSize_> Type;
+    typedef StringSet<TString, TSpec>               TStringSet_;
+    typedef typename LengthSum<TStringSet_>::Type   Value_;
+    typedef typename StringSpec<TStringSet_>::Type  TSpec_;
+
+    typedef String<Value_, TSpec_>                  Type;
 };
 
 // --------------------------------------------------------------------------
@@ -188,15 +197,14 @@ struct StringSetLimits<StringSet<TString, TSpec> >
  * @mfn StringSet#StringSetPosition
  * @brief Returns position type in string set.
  *
- * @signature StringSetPosition<T>::Type
+ * @signature StringSetPosition<TStringSet>::Type
  *
- * @tparam T
+ * @tparam TStringSet The @link StringSet @endlink to query for its position type.
  *
- * @return Type
- *
- * TODO(holtgrew): Complete documentation, part of TextConcept?
+ * @return Type The position type of TStringSet.
  */
 
+// TODO(holtgrew): Complete documentation, part of TextConcept?
 // TODO(holtgrew): Default specializations necessary?
 template <typename TString>
 struct StringSetPosition
@@ -204,48 +212,17 @@ struct StringSetPosition
     typedef typename Size<TString>::Type Type;
 };
 
-template <typename TString, typename TSpec>
-struct StringSetPosition<StringSet<TString, TSpec> >
-{
-    typedef typename Size<TString>::Type TSize_;
-    typedef Pair<TSize_> Type;
-};
-
-// --------------------------------------------------------------------------
-// Metafunction LengthSum
-// --------------------------------------------------------------------------
-
-/*!
- * @mfn StringSet#LengthSum
- * @brief Length sum type type in string set.
- *
- * @signature LengthSum<T>::Type
- *
- * @tparam T
- *
- * @return Type
- *
- * TODO(holtgrew): Complete documentation, part of TextConcept?
- */
-
 template <typename TString>
-struct LengthSum
-{
-    typedef typename Size<TString>::Type Type;
-};
+struct StringSetPosition<TString const> : StringSetPosition<TString> {};
 
 template <typename TString, typename TSpec>
-struct LengthSum<StringSet<TString, TSpec> >
+struct StringSetPosition<StringSet<TString, TSpec> >
 {
-    typedef StringSet<TString, TSpec>                   TStringSet;
-    typedef typename StringSetLimits<TStringSet>::Type  TLimits;
-    typedef typename Value<TLimits>::Type               Type;
+    typedef Pair<typename Size<StringSet<TString, TSpec> >::Type,
+                 typename Size<TString>::Type,
+                 Pack> Type;
 };
 
-template <typename T>
-struct LengthSum<T const> :
-    public LengthSum<T> {};
-
 // --------------------------------------------------------------------------
 // Metafunction GetSequenceNo
 // --------------------------------------------------------------------------
@@ -254,15 +231,14 @@ struct LengthSum<T const> :
  * @mfn StringSet#GetSequenceByNo
  * @brief Type for getting sequence by number.
  *
- * @signature GetSequenceByNo<T>::Type
+ * @signature GetSequenceByNo<TStringSet>::Type
  *
- * @tparam T
+ * @tparam TStringSet The StringSet to query for its sequence-by-number type.
  *
- * @return Type
- *
- * TODO(holtgrew): Complete documentation, part of TextConcept?
+ * @return Type The given sequence-by-number type.
  */
 
+// TODO(holtgrew): Complete documentation, part of TextConcept?
 // TODO(holtgrew): Default specializations necessary?
 template <typename TString>
 struct GetSequenceByNo
@@ -386,6 +362,16 @@ struct DefaultOverflowImplicit<StringSet< TString, TSpec> const>
     typedef Generous Type;
 };
 
+// ----------------------------------------------------------------------------
+// Concept StringConcept
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+SEQAN_CONCEPT_IMPL((StringSet<TString, TSpec>), (StringConcept));           // resizable container
+
+template <typename TString, typename TSpec>
+SEQAN_CONCEPT_IMPL((StringSet<TString, TSpec> const), (ContainerConcept));  // read-only container
+
 // ============================================================================
 // Functions
 // ============================================================================
@@ -395,22 +381,6 @@ struct DefaultOverflowImplicit<StringSet< TString, TSpec> const>
 // Function stringSetLimits()
 // --------------------------------------------------------------------------
 
-/**
-.Function.stringSetLimits:
-..cat:Sequences
-..class:Class.String
-..class:Class.StringSet
-..summary:Retrieves a string of delimiter positions of a @Class.StringSet@ which is needed for local<->global position conversions.
-..signature:stringSetLimits(me)
-..param.me:A string or string set.
-...type:Class.String
-...type:Class.StringSet
-..returns:A reference to a string.
-...remarks:If $me$ is a @Class.StringSet@ then the returned string is of size $length(me)+1$ and contains the ascending (virtual) delimiter positions of the concatenation of all strings in the string set.
-...remarks:If $me$ is a @Class.String@, @Tag.Nothing@ is returned.
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Default implementation necessary?!
 template <typename TStringSet>
 inline typename StringSetLimits<TStringSet>::Type
@@ -441,21 +411,6 @@ stringSetLimits(StringSet<TString, TSpec> const & stringSet)
 // Function getSeqNo()
 // --------------------------------------------------------------------------
 
-/**
-.Function.getSeqNo:
-..cat:Sequences
-..summary:Returns the sequence number of a position.
-..signature:getSeqNo(pos[, limits])
-..param.pos:A position.
-...type:Class.Pair
-..param.limits:The limits string returned by @Function.stringSetLimits@.
-..returns:A single integer value that identifies the string within the stringset $pos$ points at.
-...remarks:If $limits$ is omitted or @Tag.Nothing@ $getSeqNo$ returns 0.
-...remarks:If $pos$ is a local position (of class @Class.Pair@) then $i1$ is returned.
-...remarks:If $pos$ is a global position (integer type and $limits$ is a @Class.String@) then $pos$ is converted to a local position and $i1$ is returned.
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Auto-sequences should go away!
 template <typename TPosition>
 SEQAN_HOST_DEVICE inline TPosition
@@ -493,7 +448,7 @@ inline TPos getSeqNo(TPos const & pos, TLimitsString const & limits)
     typedef typename Iterator<TLimitsString const, Standard>::Type TIter;
     typedef typename Value<TLimitsString>::Type TSize;
     TIter _begin = begin(limits, Standard());
-    TIter _upper = ::std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
+    TIter _upper = std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
     return difference(_begin, _upper);
 }
 
@@ -501,21 +456,6 @@ inline TPos getSeqNo(TPos const & pos, TLimitsString const & limits)
 // Function getSeqOffset()
 // --------------------------------------------------------------------------
 
-/**
-.Function.getSeqOffset:
-..cat:Sequences
-..summary:Returns the local sequence offset of a position.
-..signature:getSeqOffset(pos[, limits])
-..param.pos:A position.
-...type:Class.Pair
-..param.limits:The limits string returned by @Function.stringSetLimits@.
-..returns:A single integer value that identifies the position within the string $pos$ points at.
-...remarks:If $limits$ is omitted or @Tag.Nothing@ $getSeqNo$ returns $pos$.
-...remarks:If $pos$ is a local position (of class @Class.Pair@) then $i2$ is returned.
-...remarks:If $pos$ is a global position (integer type and $limits$ is a @Class.String@) then $pos$ is converted to a local position and $i2$ is returned.
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Auto-sequences should go away!
 template <typename TPosition>
 SEQAN_HOST_DEVICE inline TPosition
@@ -550,7 +490,7 @@ inline TPos getSeqOffset(TPos const & pos, TLimitsString const & limits) {
     typedef typename Iterator<TLimitsString const, Standard>::Type TIter;
     typedef typename Value<TLimitsString>::Type TSize;
     TIter _begin = begin(limits, Standard());
-    TIter _upper = ::std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
+    TIter _upper = std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
     return pos - *_upper;
 }
 
@@ -578,20 +518,6 @@ setSeqOffset(Pair<T1, T2, TPack> & pos, TSeqOffset seqOffset)
 // Function posGlobalize()
 // --------------------------------------------------------------------------
 
-/**
-.Function.posGlobalize:
-..cat:Sequences
-..summary:Converts a local/global to a global position.
-..signature:posGlobalize(pos, limits)
-..param.pos:A local or global position (pair or integer value).
-...type:Class.Pair
-..param.limits:The limits string returned by @Function.stringSetLimits@.
-..returns:The corresponding global position of $pos$.
-...remarks:If $pos$ is an integral type $pos$ is returned.
-...remarks:If not, $limits[getSeqNo(pos, limits)] + getSeqOffset(pos, limits)$ is returned.
-..include:seqan/sequence.h
-*/
-
 // any_position and no limits_string -> any_position
 template <typename TPosition>
 inline TPosition posGlobalize(TPosition const & pos, Nothing const &)
@@ -625,19 +551,6 @@ posGlobalize(Pair<T1, T2, TPack> const & pos, TLimitsString const & limits)
 // Function posLocalToX()
 // --------------------------------------------------------------------------
 
-/**
-.Function.posLocalToX:
-..cat:Sequences
-..summary:Converts a local to a local/global position.
-..signature:posLocalToX(dst, localPos, limits)
-..param.dst:Destination value. A local or global position (pair or integer value).
-...type:Class.Pair
-..param.localPos:A local position (pair).
-...type:Class.Pair
-..param.limits:The limits string returned by @Function.stringSetLimits@.
-..include:seqan/sequence.h
-*/
-
 template <typename TDest, typename TLimitsString, typename T1, typename T2, typename TPack>
 inline void
 posLocalToX(TDest & dst, Pair<T1, T2, TPack> const & localPos, TLimitsString const & limits)
@@ -656,21 +569,6 @@ posLocalToX(Pair<TD1, TD2, TDPack> & dst, Pair<T1, T2, TPack> const & localPos,
 // Function posLocalize()
 // --------------------------------------------------------------------------
 
-/**
-.Function.posLocalize:
-..cat:Sequences
-..summary:Converts a local/global to a local position.
-..signature:posLocalize(result, pos, limits)
-..param.pos:A local or global position (pair or integer value).
-...type:Class.Pair
-..param.limits:The limits string returned by @Function.stringSetLimits@.
-..param.result:Reference to the resulting corresponding local position of $pos$.
-...remarks:If $pos$ is an integral type and $limits$ is omitted or @Tag.Nothing@, $pos$ is returned.
-...remarks:If $pos$ is a local position (of class @Class.Pair@) then $pos$ is returned.
-...remarks:If $pos$ is a global position (integer type and $limits$ is a @Class.String@) then $pos$ is converted to a local position.
-..include:seqan/sequence.h
-*/
-
 // any_position and no limits_string -> any_position
 template <typename TResult, typename TPosition>
 inline void posLocalize(TResult & result, TPosition const & pos, Nothing const &) {
@@ -688,7 +586,7 @@ template <typename TResult, typename TSize, typename TSpec, typename TPosition>
 inline void posLocalize(TResult & result, TPosition const & pos, String<TSize, TSpec> const & limits) {
     typedef typename Iterator<String<TSize, TSpec> const, Standard>::Type TIter;
     TIter _begin = begin(limits, Standard());
-    TIter _upper = ::std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
+    TIter _upper = std::upper_bound(_begin, end(limits, Standard()), (TSize)pos) - 1;
     result.i1 = difference(_begin, _upper);
     result.i2 = pos - *_upper;
 }
@@ -703,9 +601,6 @@ inline void posLocalize(TResult & result, Pair<T1, T2, TPack> const & pos, Strin
 // Function prefix()
 // --------------------------------------------------------------------------
 
-///.Function.prefix.param.host.type:Class.StringSet
-///.Function.prefix.class:Class.StringSet
-
 template < typename TString, typename TSpec, typename TPosition >
 inline typename Prefix<TString>::Type
 prefix(StringSet< TString, TSpec > & me, TPosition const & pos)
@@ -738,9 +633,6 @@ prefix(StringSet< TString, TSpec > const & me, TPosition const & pos)
 // Function suffix()
 // --------------------------------------------------------------------------
 
-///.Function.suffix.param.host.type:Class.StringSet
-///.Function.suffix.class:Class.StringSet
-
 template < typename TString, typename TSpec, typename TPosition >
 inline typename Suffix<TString>::Type
 suffix(StringSet< TString, TSpec > & me, TPosition const & pos)
@@ -773,9 +665,6 @@ suffix(StringSet< TString, TSpec > const & me, TPosition const & pos)
 // Function infixWithLength()
 // --------------------------------------------------------------------------
 
-///.Function.infixWithLength.param.host.type:Class.StringSet
-///.Function.infixWithLength.class:Class.StringSet
-
 template < typename TString, typename TSpec, typename TPosition, typename TSize >
 inline typename Infix<TString>::Type
 infixWithLength(StringSet< TString, TSpec > & me, TPosition const & pos, TSize length)
@@ -808,9 +697,6 @@ infixWithLength(StringSet< TString, TSpec > const & me, TPosition const & pos, T
 // Function infix()
 // --------------------------------------------------------------------------
 
-///.Function.infix.param.host.type:Class.StringSet
-///.Function.infix.class:Class.StringSet
-
 template < typename TString, typename TSpec, typename TPosBegin, typename TPosEnd >
 inline typename Infix<TString>::Type
 infix(StringSet< TString, TSpec > & me, TPosBegin const & posBegin, TPosEnd const & posEnd)
@@ -876,7 +762,12 @@ inline bool posAtEnd(TPos pos, TSequence const & seq) {
 // --------------------------------------------------------------------------
 
 /*!
- * @fn posPrev
+ * @defgroup PositionCalculation Position Calculation
+ * @brief Position calculation functions.
+ */
+
+/*!
+ * @fn PositionCalculation#posPrev
  * @headerfile <seqan/sequence.h>
  * @brief Returns a position where the local offset is decreased by one.
  *
@@ -886,24 +777,11 @@ inline bool posAtEnd(TPos pos, TSequence const & seq) {
  *
  * @return TPos The predecessor.  TPos is the type of <tt>pos</tt>.
  *
- * @see posNext
- * @see posInc
- * @see posAdd
+ * @see PositionCalculation#posNext
+ * @see PositionCalculation#posInc
+ * @see PositionCalculation#posAdd
  */
 
-/**
-.Function.posPrev
-..cat:Sequences
-..summary:Returns a position where the local offset is decreased by one.
-..signature:posPrev(pos)
-..param.pos:A position type. Could either be an integer $seqOfs$ or a pair $(seqNo, seqOfs)$.
-..returns:Returns a value of the same type as $pos$ where $seqOfs$ is decreased by one.
-..see:Function.posNext
-..see:Function.posInc
-..see:Function.posAdd
-..include:seqan/sequence.h
-*/
-
 template <typename TPos>
 inline TPos posPrev(TPos pos) {
     return pos - 1;
@@ -919,7 +797,7 @@ inline Pair<T1, T2, TPack> posPrev(Pair<T1, T2, TPack> const & pos) {
 // --------------------------------------------------------------------------
 
 /*!
- * @fn posInc
+ * @fn PositionCalculation#posInc
  * @headerfile <seqan/sequence.h>
  * @brief Increments the local offset of a position type.
  *
@@ -928,22 +806,11 @@ inline Pair<T1, T2, TPack> posPrev(Pair<T1, T2, TPack> const & pos) {
  * @param[in,out] pos A position type, an integer with <tt>seqOfs</tt> or a pair <tt>(seqNo, seqOfs)</tt>.  In both
  *                    cases, <tt>seqOfs</tt> will be incremented by one.
  *
- * @see posNext
- * @see posPrev
- * @see posAdd
+ * @see PositionCalculation#posNext
+ * @see PositionCalculation#posPrev
+ * @see PositionCalculation#posAdd
  */
 
-/**
-.Function.posInc
-..cat:Sequences
-..summary:Increments the local offset of a position type.
-..signature:posInc(pos)
-..param.pos:A position type. Could either be an integer $seqOfs$ or a pair $(seqNo, seqOfs)$. In both cases $seqOfs$ will be incremented by one.
-..see:Function.posNext
-..see:Function.posAdd
-..include:seqan/sequence.h
-*/
-
 template <typename TPos>
 inline void posInc(TPos &pos) {
     ++pos;
@@ -969,7 +836,7 @@ inline void posInc(Pair<T1, T2, TPack> & pos, TDelta delta) {
 // --------------------------------------------------------------------------
 
 /*!
- * @fn posNext
+ * @fn PositionCalculation#posNext
  * @headerfile <seqan/sequence.h>
  * @brief Returns a position where the local offset is increased by one.
  *
@@ -979,24 +846,11 @@ inline void posInc(Pair<T1, T2, TPack> & pos, TDelta delta) {
  *
  * @return TPos Returns a value of the same type as <tt>pos</tt> where <tt>seqOfs</tt> is increased by one.
  *
- * @see posInc
- * @see posPrev
- * @see posAdd
+ * @see PositionCalculation#posInc
+ * @see PositionCalculation#posPrev
+ * @see PositionCalculation#posAdd
  */
 
-/**
-.Function.posNext
-..cat:Sequences
-..summary:Returns a position where the local offset is increased by one.
-..signature:posNext(pos)
-..param.pos:A position type. Could either be an integer $seqOfs$ or a pair $(seqNo, seqOfs)$.
-..returns:Returns a value of the same type as $pos$ where $seqOfs$ is increased by one.
-..see:Function.posPrev
-..see:Function.posInc
-..see:Function.posAdd
-..include:seqan/sequence.h
-*/
-
 template <typename TPos>
 inline TPos posNext(TPos pos) {
     return pos + 1;
@@ -1013,7 +867,8 @@ posNext(Pair<T1, T2, TPack> const & pos) {
 // --------------------------------------------------------------------------
 
 /*!
- * @fn posAdd
+ * @fn PositionCalculation#posAdd
+ * @headerfile <seqan/sequence.h>
  * @brief Returns a position where the local offset is increased by a value <tt>delta</tt>.
  *
  * @signature TPos posAdd(pos, delta);
@@ -1023,25 +878,11 @@ posNext(Pair<T1, T2, TPack> const & pos) {
  *
  * @return TPos Returns a value of the same type as <tt>pos</tt> where <tt>seqOfs</tt> is increased by <tt>delta</tt>.
  *
- * @see posInc
- * @see posPrev
- * @see posNext
+ * @see PositionCalculation#posInc
+ * @see PositionCalculation#posPrev
+ * @see PositionCalculation#posNext
  */
 
-/**
-.Function.posAdd
-..cat:Sequences
-..summary:Returns a position where the local offset is increased by a value $delta$.
-..signature:posAdd(pos, delta)
-..param.pos:A position type. Could either be an integer $seqOfs$ or a pair $(seqNo, seqOfs)$.
-..param.delta:Increase the local offset of $pos$ by this value.
-..returns:Returns a value of the same type as $pos$ where $seqOfs$ is increased by $delta$.
-..see:Function.posAddAndCheck
-..see:Function.posInc
-..see:Function.posNext
-..include:seqan/sequence.h
-*/
-
 template <typename TPos, typename TDelta>
 SEQAN_HOST_DEVICE inline TPos posAdd(TPos pos, TDelta delta) {
     return pos + delta;
@@ -1059,7 +900,7 @@ posAdd(Pair<T1, T2, TPack> const & pos, TDelta delta) {
 // --------------------------------------------------------------------------
 
 /*!
- * @fn posAddAndCheck
+ * @fn PositionCalculation#posAddAndCheck
  * @headerfile <seqan/sequence.h>
  * @brief Increases the local offset of a position by a value <tt>delta</tt> and check for overflow.
  *
@@ -1069,25 +910,10 @@ posAdd(Pair<T1, T2, TPack> const & pos, TDelta delta) {
  * @param[in]     delta Increase the local offset of <tt>pos</tt> by this value.
  * @param[in]     text  The @link TextConcept text @endlink to use for checking.
  *
- * @see posAdd
- * @see posInc
+ * @see PositionCalculation#posAdd
+ * @see PositionCalculation#posInc
  */
 
-/**
-.Function.posAddAndCheck
-..cat:Sequences
-..summary:Increases the local offset of a position by a value $delta$ and check for overflow.
-..signature:posAddAndCheck(pos, delta, text)
-..param.pos:A position type. Could either be an integer $seqOfs$ or a pair $(seqNo, seqOfs)$.
-..param.delta:Increase the local offset of $pos$ by this value.
-..param.text:Single sequence or @Class.StringSet@.
-..returns:Returns a $bool$ which is $true$ if the position is still valid, i.e. 
-if it doesn't exceed the end of the referred sequence in the text.
-..see:Function.posAdd
-..see:Function.posInc
-..include:seqan/sequence.h
-*/
-
 template <typename TPos, typename TDelta, typename TSequence>
 inline bool posAddAndCheck(TPos & pos, TDelta delta, TSequence const & sequence) {
     return (pos += delta) < length(sequence);
@@ -1103,7 +929,7 @@ inline bool posAddAndCheck(TPos & pos, TDelta delta, StringSet<TSequence, TSpec>
 
     TLimits & limits = stringSetLimits(stringSet);
     TIter _end = end(limits, Standard());
-    TIter _endMark = ::std::upper_bound(begin(limits, Standard()), _end, (TSize)pos);
+    TIter _endMark = std::upper_bound(begin(limits, Standard()), _end, (TSize)pos);
     pos += delta;
     if (_endMark < _end)
         return pos < *_endMark;
@@ -1122,7 +948,7 @@ posAddAndCheck(Pair<T1, T2, TPack> & pos, TDelta delta, StringSet<TSequence, TSp
 // --------------------------------------------------------------------------
 
 /*!
- * @fn posSub
+ * @fn PositionCalculation#posSub
  * @headerfile <seqan/sequence.h>
  * @brief Returns a position where the local offset is decreased by a value <tt>delta</tt>.
  *
@@ -1133,25 +959,11 @@ posAddAndCheck(Pair<T1, T2, TPack> & pos, TDelta delta, StringSet<TSequence, TSp
  *
  * @return TPos Returns a value of the same type as <tt>pos</tt> where <tt>seqOfs</tt> is decreased by <tt>delta</tt>.
  *
- * @see posAdd
- * @see posInc
- * @see posNext
+ * @see PositionCalculation#posAdd
+ * @see PositionCalculation#posInc
+ * @see PositionCalculation#posNext
  */
 
-/**
-.Function.posSub
-..cat:Sequences
-..summary:Returns a position where the local offset is decreased by a value $delta$.
-..signature:posSub(pos, delta)
-..param.pos:A position type. Could either be an integer $seqOfs$ or a pair $(seqNo, seqOfs)$.
-..param.delta:Decrease the local offset of $pos$ by this value.
-..returns:Returns a value of the same type as $pos$ where $seqOfs$ is decreased by $delta$.
-..see:Function.posAdd
-..see:Function.posInc
-..see:Function.posNext
-..include:seqan/sequence.h
-*/
-
 template <typename TA, typename TB>
 inline TA posSub(TA a, TB b) {
     return a - b;
@@ -1353,6 +1165,50 @@ _countNonZeroValues(String<TValue, TSpec> const & me, TPos i)
     return counter;
 }
 
+// --------------------------------------------------------------------------
+// Function maxLength()
+// --------------------------------------------------------------------------
+// Returns the length of the longest string in the set.
+
+template <typename TString, typename TSpec, typename TParallel>
+inline typename Size<TString>::Type
+maxLength(StringSet<TString, TSpec> const & me, Tag<TParallel> const & tag)
+{
+    typedef StringSet<TString, TSpec>               TStringSet;
+    typedef typename Value<TStringSet const>::Type  TValue;
+
+    return empty(me) ? 0 : length(maxElement(me, LengthLess<TValue>(), tag));
+}
+
+template <typename TString, typename TSpec>
+inline typename Size<TString>::Type
+maxLength(StringSet<TString, TSpec> const & me)
+{
+    return maxLength(me, Serial());
+}
+
+// --------------------------------------------------------------------------
+// Function minLength()
+// --------------------------------------------------------------------------
+// Returns the length of the shortest string in the set.
+
+template <typename TString, typename TSpec, typename TParallel>
+inline typename Size<StringSet<TString, TSpec> const>::Type
+minLength(StringSet<TString, TSpec> const & me, Tag<TParallel> const & tag)
+{
+    typedef StringSet<TString, TSpec>               TStringSet;
+    typedef typename Value<TStringSet const>::Type  TValue;
+
+    return empty(me) ? 0 : length(minElement(me, LengthLess<TValue>(), tag));
+}
+
+template <typename TString, typename TSpec>
+inline typename Size<StringSet<TString, TSpec> const>::Type
+minLength(StringSet<TString, TSpec> const & me)
+{
+    return minLength(me, Serial());
+}
+
 // --------------------------------------------------------------------------
 // Function lengthSum()
 // --------------------------------------------------------------------------
@@ -1363,13 +1219,13 @@ _countNonZeroValues(String<TValue, TSpec> const & me, TPos i)
  *
  * @signature TSize lengthSum(s);
  *
- * @param s The string set to get length sum of.
+ * @param[in] s The string set to get length sum of.
  *
  * @return TSize The sum of the lengths of all strings in the string set.
  */
 
 template <typename TString>
-inline typename LengthSum<TString>::Type 
+inline typename LengthSum<TString>::Type
 lengthSum(TString const & me)
 {
     return length(me);
@@ -1393,19 +1249,24 @@ lengthSum(StringSet<TString, TSpec> const & me)
     return back(stringSetLimits(me));
 }
 
+// --------------------------------------------------------------------------
+// Function clear()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn StringSet#clear
+ * @headerfile <seqan/sequence.h>
+ * @brief Clear the StringSet.
+ *
+ * @signature void clear(stringSet);
+ *
+ * @param[in,out] seedSet The StringSet to clear.
+ */
 
 // --------------------------------------------------------------------------
 // Function length()
 // --------------------------------------------------------------------------
 
-///.Function.appendValue.param.target.type:Class.StringSet
-///.Function.appendValue.class:Class.StringSet
-///.Function.clear.param.object.type:Class.StringSet
-///.Function.clear.class:Class.StringSet
-///.Function.resize.param.object.type:Class.StringSet
-///.Function.resize.class:Class.StringSet
-///.Function.length.param.object.type:Class.StringSet
-///.Function.length.class:Class.StringSet
 
 template <typename TString, typename TSpec >
 inline typename Size<StringSet<TString, TSpec > >::Type
@@ -1418,7 +1279,6 @@ length(StringSet<TString, TSpec > const & me)
 // Function resize()
 // --------------------------------------------------------------------------
 
-// TODO(rmaerker): This belongs to string_set_base.h. Move it!
 template <typename TString, typename TSpec, typename TSize, typename TExpand >
 inline typename Size<StringSet<TString, TSpec > >::Type
 resize(StringSet<TString, TSpec > & me, TSize new_size, Tag<TExpand> tag)
@@ -1431,7 +1291,7 @@ resize(StringSet<TString, TSpec > & me, TSize new_size, Tag<TExpand> tag)
     //
     //        if (_validStringSetLimits(me))
     //            resize(me.limits, new_size + 1, back(me.limits), tag);
-    
+
     return resize(me.strings, new_size, tag);
 }
 
@@ -1443,11 +1303,11 @@ resize(StringSet<TString, TSpec > & me, TSize new_size, Tag<TExpand> tag)
  * @fn StringSet#reserve
  * @brief Reserve memory for string set.
  *
- * @signature TSize reserver(s, newCapacity, tag);
+ * @signature TSize reserve(s, newCapacity, tag);
  *
- * @param s           The string set to reserve memory for.
- * @param newCapacity The target capacity.
- * @param tag         A tag to select the reservation strategy.
+ * @param[in,out] s           The string set to reserve memory for.
+ * @param[in]     newCapacity The target capacity.
+ * @param[in]     tag         A tag to select the reservation strategy.
  */
 
 template <typename TString, typename TSpec, typename TSize, typename TExpand>
@@ -1460,11 +1320,41 @@ reserve(StringSet<TString, TSpec > & me,
     return reserve(me.strings, new_capacity, tag);
 }
 
+// --------------------------------------------------------------------------
+// Function assign()
+// --------------------------------------------------------------------------
+
+template <typename TString, typename TSpec, typename TSource, typename TExpand>
+inline void
+assign(StringSet<TString, TSpec> & target,
+       TSource const & source,
+       Tag<TExpand> tag)
+{
+    typedef typename Iterator<TSource const, Standard>::Type TSourceIterator;
+
+    clear(target);
+    reserve(target, length(source), tag);
+
+    // we append each source string for target being a ConcatDirect StringSet
+    TSourceIterator it = begin(source, Standard());
+    TSourceIterator itEnd = end(source, Standard());
+    for (; it != itEnd; ++it)
+        appendValue(target, getValue(it), tag);
+}
+
+template <typename TString, typename TSpec, typename TSource>
+inline void
+assign(StringSet<TString, TSpec> & target,
+       TSource const & source)
+{
+    typedef StringSet<TString, TSpec> TTarget;
+    assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
+}
+
 // --------------------------------------------------------------------------
 // Function iter()
 // --------------------------------------------------------------------------
 
-///.Function.iter.param.object.type:Class.StringSet
 template <typename TString, typename TSpec, typename TPos, typename TTag>
 inline typename Iterator<StringSet<TString, TSpec >, Tag<TTag> const>::Type
 iter(StringSet<TString, TSpec > & me,
@@ -1493,9 +1383,6 @@ iter(StringSet<TString, TSpec > const & me,
 // Function begin()
 // --------------------------------------------------------------------------
 
-///.Function.begin.param.object.type:Class.StringSet
-///.Function.begin.class:Class.StringSet
-
 template <typename TString, typename TSpec, typename TTag>
 inline typename Iterator<StringSet<TString, TSpec >, Tag<TTag> const>::Type
 begin(StringSet<TString, TSpec > & me,
@@ -1516,9 +1403,6 @@ begin(StringSet<TString, TSpec > const & me,
 // Function end()
 // --------------------------------------------------------------------------
 
-///.Function.end.param.object.type:Class.StringSet
-///.Function.end.class:Class.StringSet
-
 template <typename TString, typename TSpec, typename TTag>
 inline typename Iterator<StringSet<TString, TSpec >, Tag<TTag> const>::Type
 end(StringSet<TString, TSpec > & me,
@@ -1539,9 +1423,6 @@ return iter(me, length(me), tag);
 // Function value()
 // --------------------------------------------------------------------------
 
-///.Function.value.param.object.type:Class.StringSet
-///.Function.value.class:Class.StringSet
-
 // --------------------------------------------------------------------------
 // Function getValueById()
 // --------------------------------------------------------------------------
@@ -1563,28 +1444,12 @@ return iter(me, length(me), tag);
  *
  * @signature TString getValueById(s, id);
  *
- * @param s  The string set to get string from.
- * @param id The id of the string to get.
+ * @param[in] s  The string set to get string from.
+ * @param[in] id The id of the string to get.
  *
  * @return TString Reference to the string with the given id.
  */
 
-/**
-.Function.getValueById:
-..cat:Sequences
-..class:Class.StringSet
-..summary:Retrieves a string from the StringSet given an id.
-..signature:getValueById(me, id)
-..param.me:A StringSet.
-...type:Class.StringSet
-..param.id:An id.
-...type:Metafunction.Id
-..returns:A reference to a string.
-..see:Function.assignValueById
-..see:Function.valueById
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Why is there no generic implementation for StringSets??
 
 // --------------------------------------------------------------------------
@@ -1597,28 +1462,12 @@ return iter(me, length(me), tag);
  *
  * @signature TString valueById(s, id);
  *
- * @param s  The string set to get string from.
- * @param id The id of the string to get.
+ * @param[in] s  The string set to get string from.
+ * @param[in] id The id of the string to get.
  *
  * @return TString Reference to the string with the given id.
  */
 
-/**
-.Function.valueById:
-..cat:Sequences
-..class:Class.StringSet
-..summary:Retrieves a string from the StringSet given an id.
-..signature:valueById(me, id)
-..param.me:A StringSet.
-...type:Class.StringSet
-..param.id:An id.
-...type:Metafunction.Id
-..returns:A reference to a string.
-..see:Function.assignValueById
-..see:Function.getValueById
-..include:seqan/sequence.h
-*/
-
 template<typename TString, typename TSpec, typename TId>
 inline typename Reference<StringSet<TString, TSpec> >::Type
 valueById(StringSet<TString, TSpec> & me,
@@ -1638,35 +1487,13 @@ valueById(StringSet<TString, TSpec> & me,
  *
  * @signature TId getValueById(set, s[, id]);
  *
- * @param set The string to assign value in.
- * @param s   The string set to assign.
- * @param id  The id of the string to set.  If omitted, <tt>s</tt> will be appended to <tt>set</tt>.
+ * @param[in] set The string to assign value in.
+ * @param[in] s   The string set to assign.
+ * @param[in] id  The id of the string to set.  If omitted, <tt>s</tt> will be appended to <tt>set</tt>.
  *
  * @return TId The id of the new string in the string set.
  */
 
-/**
-.Function.assignValueById:
-..cat:Sequences
-..class:Class.StringSet
-..summary:Adds a new string to the StringSet and returns an id.
-..signature:assignValueById(dest, str, [id])
-..signature:assignValueById(dest, source, id)
-..param.dest:A StringSet.
-...type:Class.StringSet
-..param.source:A StringSet.
-...type:Class.StringSet
-..param.str:A new string.
-...type:Metafunction.Value
-..param.id:An associated id.
-...type:Metafunction.Id
-..returns:A new id
-...type:Metafunction.Id
-..see:Function.getValueById
-..see:Function.valueById
-..include:seqan/sequence.h
-*/
-
 template<typename TString, typename TSpec, typename TString2>
 inline typename Id<StringSet<TString, TSpec> >::Type
 assignValueById(StringSet<TString, TSpec>& me,
@@ -1698,25 +1525,10 @@ assignValueById(StringSet<TString, TSpec1>& dest,
  *
  * @signature void removeValueById(set, id);
  *
- * @param set The string to remove value in.
- * @param id  The id of the string to remove.
+ * @param[in,out] set The string to remove value in.
+ * @param[in]     id  The id of the string to remove.
  */
 
-/**
-.Function.removeValueById:
-..cat:Sequences
-..class:Class.StringSet
-..summary:Removes a string from the StringSet given an id.
-..signature:removeValueById(me, id)
-..param.me:A StringSet.
-...type:Class.StringSet
-..param.id:An id.
-...type:Metafunction.Id
-..returns:void
-..see:Function.assignValueById
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Why is there no generic implementation for StringSets??
 
 // --------------------------------------------------------------------------
@@ -1729,27 +1541,12 @@ assignValueById(StringSet<TString, TSpec1>& dest,
  *
  * @signature Id positionToId(set, pos);
  *
- * @param set The string to convert positions for.
- * @param pos The position to convert.
+ * @param[in] set The string to convert positions for.
+ * @param[in] pos The position to convert.
  *
  * @return TId The resulting id.
  */
 
-/**
-.Function.positionToId:
-..cat:Sequences
-..class:Class.StringSet
-..summary:Retrieves the id of a string in the StringSet given a position.
-..signature:positionToId(string_set, pos)
-..param.string_set:A StringSet.
-...type:Class.StringSet
-..param.pos:A position that is transfored into an id.
-..returns:An id that corresponds to $pos$ within $string_set$
-..see:Function.assignValueById
-..see:Function.valueById
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Why is there no generic implementation for StringSets??
 
 // --------------------------------------------------------------------------
@@ -1762,26 +1559,11 @@ assignValueById(StringSet<TString, TSpec1>& dest,
  *
  * @signature TConcat concat(set);
  *
- * @param set The string set to get the concatenation sequence for.
+ * @param[in] set The string set to get the concatenation sequence for.
  *
  * @return TConcat The concatenation sequence.
  */
 
-/**
-.Function.concat:
-..summary:Returns the concatenation sequence of all sequences in a @Class.StringSet@.
-..cat:Sequences
-..class:Class.StringSet
-..signature:concat(stringSet)
-..param.stringSet:A @Class.StringSet@ object.
-...type:Class.StringSet
-..returns:A container that can be iterated like the concatenation string of all sequences in a @Class.StringSet@.
-..remarks:If $stringSet$ is a @Spec.ConcatDirect@ StringSet a reference to $stringSet.concat$ is returned.
-For all other StringSets a @Class.ConcatenatorManyToOne@ object is returned.
-...type:Metafunction.Concatenator
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Why default concat() for any class?
 template <typename TString>
 SEQAN_HOST_DEVICE inline typename Concatenator<TString>::Type &
@@ -1815,108 +1597,58 @@ concat(StringSet<TString, TSpec> const & constMe)
     return me.concat;
 }
 
-// --------------------------------------------------------------------------
-// Function strSplit()
-// --------------------------------------------------------------------------
+// this function is deprecated and the return value is very ungeneric, e.g. doesn't work if strings are std::string
+template <typename TStrings, typename TDelim>
+inline String<typename Value<typename Value<TStrings>::Type>::Type>
+concat(TStrings const & strings, TDelim const & delimiter, bool ignoreEmptyStrings = false)
+{
+    String<typename Value<typename Value<TStrings>::Type>::Type> tmp;
 
-/*!
- * @fn StringSet#strSplit
- * @brief Append a list of the words in the string, using sep as the delimiter string @link StringSet @endlink.
- *
- * @signature void strSplit(result, sequence[, sep[, allowEmptyStrings[, maxSplit]]]);
- *
- * @param result           The resulting string set.
- * @param sequence         The sequence to split.
- * @param sep              The splitter to use (default <tt>' '</tt>).
- * @param allowEmptyString Whether or not to allow empty strings (<tt>bool</tt>, defaults to <tt>true</tt> iff
- *                         <tt>sep</tt> is given).
- * @param maxSplit         The maximal number of split operations to do if given.
- *
- * @return TConcat The concatenation sequence.
- */
+    if (empty(strings))
+        return tmp;
 
-/**
-.Function.stringSplit:
-..summary:Append a list of the words in the string, using sep as the delimiter string @Class.StringSet@.
-..cat:Sequences
-..class:Class.StringSet
-..signature:strSplit(stringSet, sequence)
-..signature:strSplit(stringSet, sequence, sep)
-..signature:strSplit(stringSet, sequence, sep, allowEmptyStrings)
-..signature:strSplit(stringSet, sequence, sep, allowEmptyStrings, maxSplit)
-..param.stringSet:The @Class.StringSet@ object the words are appended to.
-...type:Class.StringSet
-..param.sequence:A sequence of words.
-..param.sep:Word separator (default: ' ').
-..param.allowEmptyStrings:Boolean to specify whether empty words should be considered (default: true, iff sep is given).
-..param.maxSplit:If maxsplit is given, at most maxsplit splits are done.
-..include:seqan/sequence.h
-*/
-
-template <typename TString, typename TSpec, typename TSequence, typename TSeparator, typename TSize>
-inline void
-strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence, TSeparator sep, bool allowEmptyStrings, TSize maxSplit)
-{
-    typedef typename Iterator<TSequence const, Standard>::Type TIter;
-    
-    TIter itBeg = begin(sequence, Standard());
-    TIter itEnd = end(sequence, Standard());
-    TIter itFrom = itBeg;
-    
-    if (maxSplit == 0)
+    if (ignoreEmptyStrings)
     {
-        appendValue(result, sequence);
-        return;
+        for (size_t i = 0; i < length(strings); ++i)
+        {
+            if (empty(strings[i]))
+                continue;
+            if (!empty(tmp))
+                append(tmp, delimiter);
+            append(tmp, strings[i]);
+        }
     }
-    
-    for (TIter it = itBeg; it != itEnd; ++it)
-        if (*it == sep)
+    else
+    {
+        tmp = front(strings);
+        for (size_t i = 1; i < length(strings); ++i)
         {
-            if (allowEmptyStrings || itFrom != it)
-            {
-                appendValue(result, infix(sequence, itFrom - itBeg, it - itBeg));
-                if (--maxSplit == 0)
-                {
-                    if (!allowEmptyStrings)
-                    {
-                        while (it != itEnd && *it == sep)
-                            ++it;
-                    }
-                    else
-                        ++it;
-                    
-                    if (it != itEnd)
-                        appendValue(result, infix(sequence, it - itBeg, itEnd - itBeg));
-                    
-                    return;
-                }
-            }
-            itFrom = it + 1;
+            append(tmp, delimiter);
+            append(tmp, strings[i]);
         }
-    
-    if (allowEmptyStrings || itFrom != itEnd)
-        appendValue(result, infix(sequence, itFrom - itBeg, itEnd - itBeg));
+    }
+    return tmp;
 }
 
-template <typename TString, typename TSpec, typename TSequence, typename TSeparator>
-inline void
-strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence, TSeparator sep, bool allowEmptyStrings)
-{
-    strSplit(result, sequence, sep, allowEmptyStrings, maxValue<typename Size<TSequence>::Type>());
-}
+// ----------------------------------------------------------------------------
+// Function prefixSums<TValue>()
+// ----------------------------------------------------------------------------
 
-template <typename TString, typename TSpec, typename TSequence, typename TSeparator>
-inline void
-strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence, TSeparator sep)
+template <typename TValue, typename TPrefixSums, typename TText>
+inline void prefixSums(TPrefixSums & sums, TText const & text)
 {
-    strSplit(result, sequence, sep, true);
-}
+    typedef typename Concatenator<TText const>::Type        TConcat;
+    typedef typename Iterator<TConcat, Standard>::Type      TIter;
 
-template <typename TString, typename TSpec, typename TSequence>
-inline void
-strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence)
-{
-    strSplit(result, sequence, ' ', false);
+    resize(sums, ValueSize<TValue>::VALUE + 1, 0, Exact());
+
+    // Compute symbol frequencies.
+    TIter itEnd = end(concat(text), Standard());
+    for (TIter it = begin(concat(text), Standard()); it != itEnd; goNext(it))
+        sums[ordValue(static_cast<TValue>(value(it))) + 1]++;
+
+    // Cumulate symbol frequencies.
+    partialSum(sums);
 }
 
 // --------------------------------------------------------------------------
@@ -1929,28 +1661,12 @@ strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence)
  *
  * @signature TPos idToPosition(set, id);
  *
- * @param set The string to convert positions for.
- * @param id  The id to convert.
+ * @param[in] set The string to convert positions for.
+ * @param[in] id  The id to convert.
  *
- * @return The resulting position.
+ * @return TPos The resulting position.
  */
 
-/**
-.Function.idToPosition:
-..cat:Sequences
-..class:Class.StringSet
-..summary:Retrieves the position of a string in the StringSet given an id.
-..signature:idToPosition(me, id)
-..param.me:A StringSet.
-...type:Class.StringSet
-..param.id:An id.
-...type:Metafunction.Id
-..returns:A reference to a string.
-..see:Function.assignValueById
-..see:Function.valueById
-..include:seqan/sequence.h
-*/
-
 // TODO(holtgrew): Why is there no generic implementation for StringSets??
 
 
@@ -2032,6 +1748,80 @@ strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence)
 //    subset(source, dest, ids, length(ids));
 //}
 
+// ----------------------------------------------------------------------------
+// Function operator==()
+// ----------------------------------------------------------------------------
+
+template <typename TLeftString, typename TLeftSpec, typename TRight >
+inline bool
+operator==(StringSet<TLeftString, TLeftSpec> const & left,
+           TRight const & right)
+{
+    typename Comparator<StringSet<TLeftString, TLeftSpec> >::Type _lex(left, right);
+    return isEqual(_lex);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator!=()
+// ----------------------------------------------------------------------------
+
+template <typename TLeftString, typename TLeftSpec, typename TRight >
+inline bool
+operator!=(StringSet<TLeftString, TLeftSpec> const & left,
+           TRight const & right)
+{
+    typename Comparator<StringSet<TLeftString, TLeftSpec> >::Type _lex(left, right);
+    return isNotEqual(_lex);
+}
+
+// ----------------------------------------------------------------------------
+// Function write() (works on any container of container)
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TSequences, typename TDelim>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TSequences> >,
+                                Is<ContainerConcept<typename Value<TSequences>::Type > > >, void)
+write(TTarget & target, TSequences const & seqs, TDelim const & delimiter)
+{
+    typedef typename Iterator<TSequences const>::Type TSourceIt;
+
+    if (SEQAN_UNLIKELY(empty(seqs)))
+        return;
+    for (TSourceIt it = begin(seqs, Standard()), itBack = (end(seqs, Standard()) - 1); it != itBack; ++it)
+    {
+        write(target, *it);
+        write(target, delimiter);
+    }
+    write(target, back(seqs)); // no delimiter after last
+}
+
+template <typename TTarget, typename TSequences>
+inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TSequences> >,
+                                Is<ContainerConcept<typename Value<TSequences>::Type > > >, void)
+write(TTarget & target, TSequences const & seqs)
+{
+    write(target, seqs, '\n');
+}
+
+// ----------------------------------------------------------------------------
+// Function append() (works on any container of container)
+// ----------------------------------------------------------------------------
+
+template <typename TSequences1, typename TSequences2, typename TExpand >
+inline SEQAN_FUNC_ENABLE_IF(And<And<Is<ContainerConcept<TSequences1> >,
+                                    Is<ContainerConcept<typename Value<TSequences1>::Type > > >,
+                                And<Is<ContainerConcept<TSequences2> >,
+                                    Is<ContainerConcept<typename Value<TSequences2>::Type > > > >, void)
+append(TSequences1 & me, TSequences2 const & obj, Tag<TExpand>)
+{
+    typedef typename Iterator<TSequences2 const>::Type TSourceIt;
+
+    typename Size<typename Value<TSequences1>::Type>::Type oldLength = length(me);
+    resize(me, oldLength + length(obj), Tag<TExpand>());
+    for (TSourceIt it = begin(obj, Standard()), itEnd = end(obj, Standard()); it != itEnd; ++it)
+        assignValue(me, oldLength++, *it);
+}
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_SEQUENCE_STRING_SET_BASE_H_
diff --git a/seqan/sequence/string_set_concat_direct.h b/seqan/sequence/string_set_concat_direct.h
index c36b116..acdbc76 100644
--- a/seqan/sequence/string_set_concat_direct.h
+++ b/seqan/sequence/string_set_concat_direct.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // Copyright (c) 2013 NVIDIA Corporation
 // All rights reserved.
 //
@@ -40,6 +40,8 @@
 #ifndef SEQAN_SEQUENCE_STRING_SET_CONCAT_DIRECT_H_
 #define SEQAN_SEQUENCE_STRING_SET_CONCAT_DIRECT_H_
 
+#include <algorithm>
+
 namespace seqan {
 
 // ============================================================================
@@ -50,7 +52,7 @@ namespace seqan {
 // Tags, Classes, Enums
 // ============================================================================
 
-template <typename TDelimiter = void>
+template <typename TSpec = void>
 struct ConcatDirect;                    // contains 1 string (the concatenation of n strings)
 
 // TODO(holtgrew): Change name of specialization to ConcatDirect Owner StringSet?
@@ -75,24 +77,8 @@ struct ConcatDirect;                    // contains 1 string (the concatenation
  * @brief The concatenation string.  Concatenates all sequences of the StringSet without gaps.
  */
 
-/**
-.Spec.ConcatDirect:
-..summary:A string set storing the concatenation of all strings within one string.
-..cat:Sequences
-..general:Spec.Owner
-..signature:StringSet<TString, Owner<ConcatDirect<> > >
-..param.TString:The string type.
-...type:Class.String
-..remarks:The strings are internally stored in a $TString$ object and the character position type is a
-a single integer value between 0 and the sum of string lengths minus 1.
-..remarks:The position type can be returned or modified by the meta-function @Metafunction.SAValue@ called with the @Class.StringSet@ type.
-..include:seqan/sequence.h
-.Memvar.ConcatDirect#concat:
-..class:Spec.ConcatDirect
-..summary:The concatenation string. Concatenates all sequences of the StringSet without gaps.
-*/
-template <typename TString, typename TDelimiter>
-class StringSet<TString, Owner<ConcatDirect<TDelimiter> > >
+template <typename TString, typename TSpec>
+class StringSet<TString, Owner<ConcatDirect<TSpec> > >
 {
 public:
     typedef typename StringSetLimits<StringSet>::Type   TLimits;
@@ -106,6 +92,37 @@ class StringSet<TString, Owner<ConcatDirect<TDelimiter> > >
         _initStringSetLimits(*this);
     }
 
+    template <typename TOtherString, typename TOtherSpec>
+    StringSet(StringSet<TOtherString, Owner<ConcatDirect<TOtherSpec> > > & other) :
+        limits(other.limits), concat(other.concat)
+    {}
+
+    template <typename TOtherString, typename TOtherSpec>
+    StringSet(StringSet<TOtherString, Owner<ConcatDirect<TOtherSpec> > > const & other) :
+        limits(other.limits), concat(other.concat)
+    {}
+
+    template <typename TOtherString, typename TOtherSpec>
+    StringSet(StringSet<TOtherString, TOtherSpec> &other)
+    {
+        _initStringSetLimits(*this);
+        assign(*this, other);
+    }
+
+    template <typename TOtherString, typename TOtherSpec>
+    StringSet(StringSet<TOtherString, TOtherSpec> const &other)
+    {
+        _initStringSetLimits(*this);
+        assign(*this, other);
+    }
+
+    template <typename TOtherSpec>
+    StringSet(String<TString, TOtherSpec> const &other)
+    {
+        _initStringSetLimits(*this);
+        assign(*this, other);
+    }
+
     // ----------------------------------------------------------------------
     // Subscription operators; have to be defined in class def.
     // ----------------------------------------------------------------------
@@ -125,6 +142,13 @@ class StringSet<TString, Owner<ConcatDirect<TDelimiter> > >
         SEQAN_CHECKPOINT;
         return value(*this, pos);
     }
+
+    template <typename TStringSet>
+    StringSet & operator= (TStringSet const &other)
+    {
+        assign(*this, other);
+        return *this;
+    }
 };
 
 // ============================================================================
@@ -146,91 +170,107 @@ struct Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >
 // --------------------------------------------------------------------------
 
 template <typename TString, typename TSpec>
-struct Value<StringSet< TString, Owner<ConcatDirect<TSpec> > > >
-    : Infix<TString> {};
+struct Value<StringSet<TString, Owner<ConcatDirect<TSpec> > > >
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type> {};
 
 template <typename TString, typename TSpec>
-struct Value<StringSet< TString, Owner<ConcatDirect<TSpec> > > const>
-    : Infix<TString const> {};
-    
+struct Value<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type const> {};
+
 // --------------------------------------------------------------------------
 // Metafunction GetValue
 // --------------------------------------------------------------------------
 
 /* // we had a problem with constructing a Finder<GetValue<TConcatStringSet>::Type>
-template < typename TString, typename TSpec >
-struct GetValue< StringSet< TString, Owner<ConcatDirect<TSpec> > > >:
+template <typename TString, typename TSpec >
+struct GetValue<StringSet<TString, Owner<ConcatDirect<TSpec> > > >:
     Infix<TString> {};
 
-template < typename TString, typename TSpec >
-struct GetValue< StringSet< TString, Owner<ConcatDirect<TSpec> > > const >:
+template <typename TString, typename TSpec >
+struct GetValue<StringSet<TString, Owner<ConcatDirect<TSpec> > > const >:
     Infix<TString const> {};
 */
 
-template < typename TString, typename TSpec >
-struct GetValue< StringSet< TString, Owner<ConcatDirect<TSpec> > > >
+template <typename TString, typename TSpec >
+struct GetValue<StringSet<TString, Owner<ConcatDirect<TSpec> > > >
 {
-    typedef typename Infix<TString>::Type const Type;
+    typedef typename Infix<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type const Type;
 };
 
-template < typename TString, typename TSpec >
-struct GetValue< StringSet< TString, Owner<ConcatDirect<TSpec> > > const>
+template <typename TString, typename TSpec >
+struct GetValue<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>
 {
-    typedef typename Infix<TString const>::Type const Type;
+    typedef typename Infix<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>::Type const Type;
 };
 
 // --------------------------------------------------------------------------
 // Metafunction Reference
 // --------------------------------------------------------------------------
 
-template < typename TString, typename TSpec >
-struct Reference< StringSet< TString, Owner<ConcatDirect<TSpec> > > >
-    : Infix<TString> {};
+template <typename TString, typename TSpec >
+struct Reference<StringSet<TString, Owner<ConcatDirect<TSpec> > > >
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type> {};
 
-template < typename TString, typename TSpec >
-struct Reference< StringSet< TString, Owner<ConcatDirect<TSpec> > > const>
-    : Infix<TString const> {};
+template <typename TString, typename TSpec >
+struct Reference<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type const> {};
 
 // --------------------------------------------------------------------------
 // Metafunction Prefix
 // --------------------------------------------------------------------------
 
-template < typename TString, typename TSpec >
-struct Prefix<StringSet< TString, Owner<ConcatDirect<TSpec> > > >
-    : Infix<TString> {};
+template <typename TString, typename TSpec >
+struct Prefix<StringSet<TString, Owner<ConcatDirect<TSpec> > > >
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type> {};
 
-template < typename TString, typename TSpec >
+template <typename TString, typename TSpec >
 struct Prefix<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>
-    : Infix<TString const> {};
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type const> {};
 
 // --------------------------------------------------------------------------
 // Metafunction Suffix
 // --------------------------------------------------------------------------
 
 template <typename TString, typename TSpec>
-struct Suffix< StringSet< TString, Owner<ConcatDirect<TSpec> > > >
-    : Infix<TString> {};
+struct Suffix<StringSet<TString, Owner<ConcatDirect<TSpec> > > >
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type> {};
 
 template <typename TString, typename TSpec>
-struct Suffix< StringSet< TString, Owner<ConcatDirect<TSpec> > > const>
-    : Infix<TString const> {};
+struct Suffix<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type const> {};
 
 // --------------------------------------------------------------------------
 // Metafunction Infix
 // --------------------------------------------------------------------------
 
-template < typename TString, typename TSpec >
-struct Infix< StringSet< TString, Owner<ConcatDirect<TSpec> > > >
-    : Infix< TString > {};
+template <typename TString, typename TSpec >
+struct Infix<StringSet<TString, Owner<ConcatDirect<TSpec> > > >
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type> {};
 
-template < typename TString, typename TSpec >
-struct Infix< StringSet< TString, Owner<ConcatDirect<TSpec> > > const >
-    : Infix< TString const > {};
+template <typename TString, typename TSpec >
+struct Infix<StringSet<TString, Owner<ConcatDirect<TSpec> > > const >
+    : Infix<typename Concatenator<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type const> {};
 
 // ============================================================================
 // Functions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Function view()
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+typename View<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type
+view(StringSet<TString, Owner<ConcatDirect<TSpec> > > & stringSet)
+{
+    typename View<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type stringSetView;
+
+    concat(stringSetView) = view(concat(stringSet));
+    stringSetLimits(stringSetView) = view(stringSetLimits(stringSet));
+
+    return stringSetView;
+}
+
 // ----------------------------------------------------------------------------
 // Function assign()
 // ----------------------------------------------------------------------------
@@ -247,7 +287,8 @@ template <typename TString, typename TSpec, typename TString2, typename TSpec2>
 void assign(StringSet<TString, Owner<ConcatDirect<TSpec> > > & stringSet,
             StringSet<TString2, Owner<ConcatDirect<TSpec2> > > & other)
 {
-    assign(stringSet, reinterpret_cast<StringSet<TString2, Owner<ConcatDirect<TSpec2> > > const &> (other));
+    assign(concat(stringSet), concat(other));
+    assign(stringSetLimits(stringSet), stringSetLimits(other));
 }
 
 // --------------------------------------------------------------------------
@@ -282,7 +323,7 @@ inline void assignValue(
 // --------------------------------------------------------------------------
 
 template <typename TString, typename TSpec>
-inline void _initStringSetLimits(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me)
+inline void _initStringSetLimits(StringSet<TString, TSpec> & me)
 {
     appendValue(me.limits, 0);
 }
@@ -305,43 +346,76 @@ template <typename TString, typename TSpec >
 inline void _refreshStringSetLimits(StringSet<TString, Owner<ConcatDirect<TSpec> > > &) {}
 
 // --------------------------------------------------------------------------
-// Function appendValue()
+// Function append()
 // --------------------------------------------------------------------------
 
-template <typename TString, typename TString2, typename TExpand >
-inline void appendValue(
-    StringSet<TString, Owner<ConcatDirect<void> > > & me,
-    TString2 const & obj,
-    Tag<TExpand> tag)
+// more efficient overload for concat direct stringsets
+template <typename TString, typename TSpec, typename TStrings2, typename TExpand >
+inline SEQAN_FUNC_ENABLE_IF(And<Is<ContainerConcept<TStrings2> >,
+                                Is<ContainerConcept<typename Value<TStrings2>::Type > > >, void)
+append(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me,
+       TStrings2 const & obj,
+       Tag<TExpand>)
 {
-    appendValue(me.limits, lengthSum(me) + length(obj), tag);
-    append(me.concat, obj, tag);
+    typedef typename Iterator<TStrings2 const>::Type TIt;
+
+    reserve(me.concat, lengthSum(me) + lengthSum(obj), Tag<TExpand>());
+    reserve(me.limits, length(me.limits) + length(obj), Tag<TExpand>());
+
+    for (TIt it = begin(obj), itEnd = end(obj); it != itEnd; ++it)
+        appendValue(me, *it, Tag<TExpand>());
+}
+
+// even more efficient if both stringsets are concatdirect
+template <typename TString1, typename TString2, typename TSpec1, typename TSpec2, typename TExpand>
+inline void
+append(StringSet<TString1, Owner<ConcatDirect<TSpec1> > > & me,
+       StringSet<TString2, Owner<ConcatDirect<TSpec2> > > const & obj,
+       Tag<TExpand>)
+{
+    typedef typename Size<TString1>::Type TSize;
+    typedef StringSet<TString1, Owner<ConcatDirect<TSpec1> > > TMe;
+    typedef typename Iterator<typename StringSetLimits<TMe>::Type>::Type TIt;
+
+    if (SEQAN_UNLIKELY(empty(obj)))
+        return;
+
+    TSize const oldLimLength = length(me.limits);
+    TSize const oldLength = back(me.limits);
+
+    append(me.concat, obj.concat, Tag<TExpand>());
+    append(me.limits, suffix(obj.limits, 1), Tag<TExpand>());
+
+    for (TIt it = begin(me.limits, Standard()) + oldLimLength, itEnd = end(me.limits, Standard()); it != itEnd; ++it)
+        *it += oldLength;
 }
 
-template <typename TString, typename TDelimiter, typename TString2, typename TExpand >
+// --------------------------------------------------------------------------
+// Function appendValue()
+// --------------------------------------------------------------------------
+
+template <typename TString, typename TString2, typename TSpec, typename TExpand>
 inline void appendValue(
-    StringSet<TString, Owner<ConcatDirect<TDelimiter> > > & me,
+    StringSet<TString, Owner<ConcatDirect<TSpec> > > & me,
     TString2 const & obj,
-    Tag<TExpand> tag)
+    Tag<TExpand>)
 {
-    appendValue(me.limits, lengthSum(me) + length(obj) + 1, tag);
-    append(me.concat, obj, tag);
-    appendValue(me.concat, TDelimiter(), tag);
+    appendValue(me.limits, lengthSum(me) + length(obj), Tag<TExpand>());
+    append(me.concat, obj, Tag<TExpand>());
 }
 
-
 // --------------------------------------------------------------------------
 // Function insertValue()
 // --------------------------------------------------------------------------
 
-template <typename TString, typename TDelimiter, typename TPos, typename TSequence, typename TExpand >
+template <typename TString, typename TSpec, typename TPos, typename TSequence, typename TExpand >
 inline void insertValue(
-    StringSet<TString, Owner<ConcatDirect<TDelimiter> > > & me,
+    StringSet<TString, Owner<ConcatDirect<TSpec> > > & me,
     TPos pos,
     TSequence const & seq,
     Tag<TExpand> tag)
 {
-    typedef StringSet<TString, Owner<ConcatDirect<TDelimiter> > > TStringSet;
+    typedef StringSet<TString, Owner<ConcatDirect<TSpec> > > TStringSet;
     typedef typename Size<TStringSet>::Type TSize;
     typedef typename StringSetLimits<TStringSet>::Type TLimits;
     typedef typename Value<TLimits>::Type TLimitValue;
@@ -358,13 +432,13 @@ inline void insertValue(
 // Function erase()
 // --------------------------------------------------------------------------
 
-template <typename TString, typename TDelimiter, typename TPos >
+template <typename TString, typename TSpec, typename TPos >
 inline void erase(
-    StringSet<TString, Owner<ConcatDirect<TDelimiter> > > & me,
+    StringSet<TString, Owner<ConcatDirect<TSpec> > > & me,
     TPos pos,
     TPos pos_end)
 {
-    typedef StringSet<TString, Owner<ConcatDirect<TDelimiter> > > TStringSet;
+    typedef StringSet<TString, Owner<ConcatDirect<TSpec> > > TStringSet;
     typedef typename Size<TStringSet>::Type TSize;
     typedef typename StringSetLimits<TStringSet>::Type TLimits;
     typedef typename Value<TLimits>::Type TLimitValue;
@@ -372,7 +446,7 @@ inline void erase(
     erase(me.concat, me.limits[pos], me.limits[pos_end]);
 
     TLimitValue lengthSum = 0;
-    for (TSize i = pos; i <pos_end; ++i)
+    for (TSize i = pos; i < pos_end; ++i)
         lengthSum += me.limits[i];
 
     erase(me.limits, pos, pos_end);
@@ -386,10 +460,9 @@ inline void erase(
 // Function clear()
 // --------------------------------------------------------------------------
 
-template <typename TString, typename TDelimiter >
-inline void clear(StringSet<TString, Owner<ConcatDirect<TDelimiter> > > & me)
+template <typename TString, typename TSpec >
+inline void clear(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me)
 {
-    SEQAN_CHECKPOINT;
     clear(me.concat);
     resize(me.limits, 1, Exact());
 }
@@ -398,9 +471,9 @@ inline void clear(StringSet<TString, Owner<ConcatDirect<TDelimiter> > > & me)
 // Function length()
 // --------------------------------------------------------------------------
 
-template <typename TString, typename TDelimiter>
-SEQAN_HOST_DEVICE inline typename Size<StringSet<TString, Owner<ConcatDirect<TDelimiter> > > >::Type
-length(StringSet<TString, Owner<ConcatDirect<TDelimiter> > > const & me)
+template <typename TString, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Size<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type
+length(StringSet<TString, Owner<ConcatDirect<TSpec> > > const & me)
 {
     return length(me.limits) - 1;
 }
@@ -413,7 +486,8 @@ template <typename TString, typename TSpec, typename TSize, typename TExpand >
 inline typename Size<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type
 resize(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me, TSize new_size, Tag<TExpand> tag)
 {
-    if (new_size < length(me.limits))
+    typedef typename Size<typename StringSetLimits<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type>::Type TS;
+    if (static_cast<TS>(new_size) < length(me.limits))
     {
         resize(me.concat, me.limits[new_size]);
         return resize(me.limits, new_size + 1, tag) - 1;
@@ -421,7 +495,6 @@ resize(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me, TSize new_size, Ta
         return resize(me.limits, new_size + 1, back(me.limits), tag) - 1;
 }
 
-
 // --------------------------------------------------------------------------
 // Function reserve()
 // --------------------------------------------------------------------------
@@ -439,16 +512,16 @@ reserve(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me,
 // Function prefix()
 // --------------------------------------------------------------------------
 
-template < typename TString, typename TDelimiter, typename TPosition >
-inline typename Infix<TString>::Type
-prefix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > & me, TPosition pos)
+template <typename TString, typename TSpec, typename TPosition >
+inline typename Prefix<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type
+prefix(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me, TPosition pos)
 {
     return infix(me.concat, stringSetLimits(me)[getSeqNo(pos, stringSetLimits(me))], posGlobalize(pos, stringSetLimits(me)));
 }
 
-template < typename TString, typename TDelimiter, typename TPosition >
-inline typename Infix<TString const>::Type
-prefix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const & me, TPosition pos)
+template <typename TString, typename TSpec, typename TPosition >
+inline typename Prefix<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>::Type
+prefix(StringSet<TString, Owner<ConcatDirect<TSpec> > > const & me, TPosition pos)
 {
     return infix(me.concat, stringSetLimits(me)[getSeqNo(pos, stringSetLimits(me))], posGlobalize(pos, stringSetLimits(me)));
 }
@@ -457,16 +530,16 @@ prefix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const & me, TPosit
 // Function suffix()
 // --------------------------------------------------------------------------
 
-template < typename TString, typename TDelimiter, typename TPosition >
-inline typename Infix<TString>::Type
-suffix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > & me, TPosition pos)
+template <typename TString, typename TSpec, typename TPosition >
+inline typename Suffix<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type
+suffix(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me, TPosition pos)
 {
     return infix(me.concat, posGlobalize(pos, stringSetLimits(me)), stringSetLimits(me)[getSeqNo(pos, stringSetLimits(me)) + 1]);
 }
 
-template < typename TString, typename TDelimiter, typename TPosition >
-inline typename Infix<TString const>::Type
-suffix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const & me, TPosition pos)
+template <typename TString, typename TSpec, typename TPosition >
+inline typename Suffix<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>::Type
+suffix(StringSet<TString, Owner<ConcatDirect<TSpec> > > const & me, TPosition pos)
 {
     return infix(me.concat, posGlobalize(pos, stringSetLimits(me)), stringSetLimits(me)[getSeqNo(pos, stringSetLimits(me)) + 1]);
 }
@@ -475,16 +548,16 @@ suffix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const & me, TPosit
 // Function infix()
 // --------------------------------------------------------------------------
 
-template < typename TString, typename TDelimiter, typename TPosBegin, typename TPosEnd >
-inline typename Infix<TString>::Type
-infix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > & me, TPosBegin posBegin, TPosEnd posEnd)
+template <typename TString, typename TSpec, typename TPosBegin, typename TPosEnd >
+inline typename Infix<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type
+infix(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me, TPosBegin posBegin, TPosEnd posEnd)
 {
     return infix(me.concat, posGlobalize(posBegin, stringSetLimits(me)), posGlobalize(posEnd, stringSetLimits(me)));
 }
 
-template < typename TString, typename TDelimiter, typename TPosBegin, typename TPosEnd >
-inline typename Infix<TString const>::Type
-infix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const & me, TPosBegin posBegin, TPosEnd posEnd)
+template <typename TString, typename TSpec, typename TPosBegin, typename TPosEnd >
+inline typename Infix<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>::Type
+infix(StringSet<TString, Owner<ConcatDirect<TSpec> > > const & me, TPosBegin posBegin, TPosEnd posEnd)
 {
     return infix(me.concat, posGlobalize(posBegin, stringSetLimits(me)), posGlobalize(posEnd, stringSetLimits(me)));
 }
@@ -493,16 +566,16 @@ infix(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const & me, TPosBeg
 // Function infixWithLength()
 // --------------------------------------------------------------------------
 
-template < typename TString, typename TDelimiter, typename TPosition, typename TSize >
-inline typename Infix<TString>::Type
-infixWithLength(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > & me, TPosition pos, TSize length)
+template <typename TString, typename TSpec, typename TPosition, typename TSize >
+inline typename Infix<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type
+infixWithLength(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me, TPosition pos, TSize length)
 {
     return infixWithLength(me.concat, posGlobalize(pos, stringSetLimits(me)), length);
 }
 
-template < typename TString, typename TDelimiter, typename TPosition, typename TSize >
-inline typename Infix<TString const>::Type
-infixWithLength(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const & me, TPosition pos, TSize length)
+template <typename TString, typename TSpec, typename TPosition, typename TSize >
+inline typename Infix<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>::Type
+infixWithLength(StringSet<TString, Owner<ConcatDirect<TSpec> > > const & me, TPosition pos, TSize length)
 {
     return infixWithLength(me.concat, posGlobalize(pos, stringSetLimits(me)), length);
 }
@@ -512,14 +585,14 @@ infixWithLength(StringSet< TString, Owner<ConcatDirect<TDelimiter> > > const & m
 // --------------------------------------------------------------------------
 
 template <typename TString, typename TSpec, typename TPos >
-SEQAN_HOST_DEVICE inline typename Infix<TString>::Type
+SEQAN_HOST_DEVICE inline typename Value<StringSet<TString, Owner<ConcatDirect<TSpec> > > >::Type
 value(StringSet<TString, Owner<ConcatDirect<TSpec> > > & me, TPos pos)
 {
     return infix(me.concat, me.limits[pos], me.limits[pos + 1]);
 }
 
 template <typename TString, typename TSpec, typename TPos >
-SEQAN_HOST_DEVICE inline typename Infix<TString const>::Type
+SEQAN_HOST_DEVICE inline typename Value<StringSet<TString, Owner<ConcatDirect<TSpec> > > const>::Type
 value(StringSet<TString, Owner<ConcatDirect<TSpec> > > const & me, TPos pos)
 {
     return infix(me.concat, me.limits[pos], me.limits[pos + 1]);
@@ -555,6 +628,62 @@ void swap(StringSet<TString, Owner<ConcatDirect<TSpec> > > & lhs,
     swap(lhs.concat, rhs.concat);
 }
 
+// ============================================================================
+// Device Functions
+// ============================================================================
+// NOTE(esiragusa): All functions are equivalent to the originals - overloaded to remove SEQAN_HOST_DEVICE :(
+
+#ifdef PLATFORM_CUDA
+
+// --------------------------------------------------------------------------
+// Function value()
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec, typename TPos >
+inline typename Value<StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > >::Type
+value(StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > & me, TPos pos)
+{
+    return infix(me.concat, me.limits[pos], me.limits[pos + 1]);
+}
+
+template <typename TValue, typename TAlloc, typename TSpec, typename TPos >
+inline typename Value<StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > const>::Type
+value(StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > const & me, TPos pos)
+{
+    return infix(me.concat, me.limits[pos], me.limits[pos + 1]);
+}
+
+// --------------------------------------------------------------------------
+// Function length()
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+inline typename Size<StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > >::Type
+length(StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > const & me)
+{
+    return length(me.limits) - 1;
+}
+
+// --------------------------------------------------------------------------
+// Function back()
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+inline typename Reference<StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > const>::Type
+back(StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > const & me)
+{
+    return value(me, length(me) - 1);
+}
+
+template <typename TValue, typename TAlloc, typename TSpec>
+inline typename Reference<StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > >::Type
+back(StringSet<thrust::device_vector<TValue, TAlloc>, Owner<ConcatDirect<TSpec> > > & me)
+{
+    return value(me, length(me) - 1);
+}
+
+#endif // PLATFORM_CUDA
+
 }  // namespace seqan
 
 #endif  // #ifndef SEQAN_SEQUENCE_STRING_SET_CONCAT_DIRECT_H_
diff --git a/seqan/sequence/string_set_dependent_generous.h b/seqan/sequence/string_set_dependent_generous.h
index 868fc4a..62659dc 100644
--- a/seqan/sequence/string_set_dependent_generous.h
+++ b/seqan/sequence/string_set_dependent_generous.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -81,19 +81,17 @@ class StringSet<TString, Dependent<Generous> >
     bool            limitsValid;        // is true if limits contains the cumulative sum of the sequence lengths
     TConcatenator   concat;
 
-    StringSet()
-        : limitsValid(true)
+    StringSet() :
+        limitsValid(true)
     {
-        SEQAN_CHECKPOINT;
-        appendValue(limits, 0);
+        _initStringSetLimits(*this);
     }
 
     template <typename TDefault>
-    StringSet(StringSet<TString, Owner<TDefault> > const& _other)
-        : limitsValid(true)
+    StringSet(StringSet<TString, Owner<TDefault> > const& _other) :
+        limitsValid(true)
     {
-        SEQAN_CHECKPOINT;
-        appendValue(limits, 0);
+        _initStringSetLimits(*this);
         for (unsigned int i = 0; i < length(_other); ++i)
             appendValue(*this, _other[i]);
     }
diff --git a/seqan/sequence/string_set_dependent_tight.h b/seqan/sequence/string_set_dependent_tight.h
index 2c6c434..0e2b0ea 100644
--- a/seqan/sequence/string_set_dependent_tight.h
+++ b/seqan/sequence/string_set_dependent_tight.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -82,20 +82,6 @@ namespace seqan {
  * efficient access to strings in the container via ids at the cost of higher memory usage.
  */
 
-/**
-.Spec.Dependent:
-..summary:A string set storing references of the strings.
-..cat:Sequences
-..general:Class.StringSet
-..signature:StringSet<TString, Dependent<TSpec> >
-..param.TString:The string type.
-...type:Class.String
-..param.TSpec:The specializing type for the dependent string set.
-...default:$Tight$
-...remarks:Possible values are $Tight$ or $Generous$
-...remarks:$Tight$ is very space efficient whereas $Generous$ provides fast access to the strings in the container via ids.
-..include:seqan/sequence.h
- */
 // Default id holder string set
 template <typename TSpec = Tight>
 struct Dependent;
@@ -121,19 +107,19 @@ class StringSet<TString, Dependent<Tight> >
     bool            limitsValid;        // is true if limits contains the cumulative sum of the sequence lengths
     TConcatenator   concat;
 
-    StringSet()
-        : lastId(0), limitsValid(true)
+    StringSet() :
+        lastId(0),
+        limitsValid(true)
     {
-        SEQAN_CHECKPOINT;
-        appendValue(limits, 0);
+        _initStringSetLimits(*this);
     }
 
     template <typename TDefault>
-    StringSet(StringSet<TString, Owner<TDefault> > const & _other)
-        : lastId(0), limitsValid(true)
+    StringSet(StringSet<TString, Owner<TDefault> > const & _other) :
+        lastId(0),
+        limitsValid(true)
     {
-        SEQAN_CHECKPOINT;
-        appendValue(limits, 0);
+        _initStringSetLimits(*this);
         for (unsigned int i = 0; i < length(_other); ++i)
             appendValue(*this, _other[i]);
     }
diff --git a/seqan/sequence/string_set_device.h b/seqan/sequence/string_set_device.h
new file mode 100644
index 0000000..1a02615
--- /dev/null
+++ b/seqan/sequence/string_set_device.h
@@ -0,0 +1,76 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_STRING_SET_DEVICE_H
+#define SEQAN_STRING_SET_DEVICE_H
+
+namespace seqan {
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Device                                              [StringSet]
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+struct Device<StringSet<TString, TSpec> >
+{
+    typedef StringSet<typename Device<TString>::Type, TSpec>    Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsDevice                                     [Device StringSet]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+struct IsDevice<StringSet<thrust::device_vector<TValue, TAlloc>, TSpec> > : public True {};
+
+// ----------------------------------------------------------------------------
+// Metafunction StringSetLimits                              [Device StringSet]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TAlloc, typename TSpec>
+struct StringSetLimits<StringSet<thrust::device_vector<TValue, TAlloc>, TSpec> >
+{
+    typedef thrust::device_vector<TValue, TAlloc>   TString_;
+    typedef typename Size<TString_>::Type           TSize_;
+    typedef thrust::device_vector<TSize_>           Type;
+};
+
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_STRING_SET_DEVICE_H
diff --git a/seqan/sequence/string_set_owner.h b/seqan/sequence/string_set_owner.h
index af2c0a6..e810dd0 100644
--- a/seqan/sequence/string_set_owner.h
+++ b/seqan/sequence/string_set_owner.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -70,20 +70,6 @@ namespace seqan {
 
 // TODO(holtgrew): Change name of specialization to Owner StringSet.
 
-/**
-.Spec.Owner:
-..summary:A string set storing the strings as members.
-..cat:Sequences
-..general:Class.StringSet
-..signature:StringSet<TString, Owner<> >
-..signature:StringSet<TString, Owner<Default> >
-..param.TString:The string type.
-...type:Class.String
-..remarks:The strings are internally stored in a $String<TString>$ object and the character position type is a
-@Class.Pair@ $(seqNo,seqOfs)$ where seqNo identifies the string within the stringset and seqOfs identifies the position within this string.
-..remarks:The position type can be returned or modified by the meta-function @Metafunction.SAValue@ called with the @Class.StringSet@ type.
-..include:seqan/sequence.h
- */
 template <typename TString>
 class StringSet<TString, Owner<Default> >
 {
@@ -98,10 +84,26 @@ class StringSet<TString, Owner<Default> >
     bool            limitsValid;        // is true if limits contains the cumulative sum of the sequence lengths
     TConcatenator   concat;
 
-    StringSet()
-        : limitsValid(true)
+    StringSet() :
+        limitsValid(true)
+    {
+        _initStringSetLimits(*this);
+    }
+
+    template <typename TOtherString, typename TOtherSpec>
+    StringSet(StringSet<TOtherString, TOtherSpec> const &other) :
+        limitsValid(true)
     {
-        appendValue(limits, 0);
+        _initStringSetLimits(*this);
+        assign(*this, other);
+    }
+
+    template <typename TOtherSpec>
+    StringSet(String<TString, TOtherSpec> const &other) :
+        limitsValid(true)
+    {
+        _initStringSetLimits(*this);
+        assign(*this, other);
     }
 
     // ----------------------------------------------------------------------
@@ -121,6 +123,13 @@ class StringSet<TString, Owner<Default> >
     {
         return value(*this, pos);
     }
+
+    template <typename TStringSet>
+    StringSet & operator= (TStringSet const &other)
+    {
+        assign(*this, other);
+        return *this;
+    }
 };
 
 // ============================================================================
@@ -131,6 +140,21 @@ class StringSet<TString, Owner<Default> >
 // Functions
 // ============================================================================
 
+// --------------------------------------------------------------------------
+// Function append()
+// --------------------------------------------------------------------------
+
+// better solution if both stringsets are Owner<Default>
+template <typename TString, typename TString2, typename TExpand >
+inline void append(StringSet<TString, Owner<Default> > & me,
+                   StringSet<TString2, Owner<Default> > const & obj,
+                   Tag<TExpand>)
+{
+    // we rather invalidate limits here to allow to do modify appended strings:
+    me.limitsValid = false;
+    append(me.strings, obj.strings, Tag<TExpand>());
+}
+
 // --------------------------------------------------------------------------
 // Function appendValue()
 // --------------------------------------------------------------------------
@@ -141,8 +165,12 @@ inline void appendValue(
     TString2 const & obj,
     Tag<TExpand> tag)
 {
-    if (_validStringSetLimits(me))
-        appendValue(me.limits, lengthSum(me) + length(obj), tag);
+    // we rather invalidate limits here to allow to do modify appended strings:
+    // appendValue(back(stringSet), 'A');
+
+//    if (_validStringSetLimits(me))
+//        appendValue(me.limits, lengthSum(me) + length(obj), tag);
+    me.limitsValid = false;
     appendValue(me.strings, obj, tag);
 }
 
@@ -208,8 +236,6 @@ value(StringSet<TString, Owner<Default> > const & me, TPos pos)
 // Function erase()
 // --------------------------------------------------------------------------
 
-///.Function.erase.param.object.type:Spec.Owner
-
 template <typename TString, typename TPos>
 inline typename Size<StringSet<TString, Owner<Default> > >::Type
 erase(StringSet<TString, Owner<Default> > & me, TPos pos)
@@ -239,7 +265,17 @@ getValueById(StringSet<TString, Owner<TSpec> >& me,
 {
     SEQAN_CHECKPOINT;
     if (id < (TId) length(me)) return value(me, id);
-    static TString tmp = "";
+    static TString tmp = TString();
+    return tmp;
+}
+
+template <typename TString, typename TSpec, typename TId>
+inline typename Reference<StringSet<TString, Owner<TSpec> > const>::Type
+getValueById(StringSet<TString, Owner<TSpec> > const & me,
+            TId const id)
+{
+    if (id < (TId) length(me)) return value(me, id);
+    static TString tmp = TString();
     return tmp;
 }
 
diff --git a/seqan/sequence/string_set_segment.h b/seqan/sequence/string_set_segment.h
new file mode 100644
index 0000000..25f5ad4
--- /dev/null
+++ b/seqan/sequence/string_set_segment.h
@@ -0,0 +1,513 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Implementation of Segment StringSet, a string set storing segments of
+// another container.
+// ==========================================================================
+
+#ifndef SEQAN_SEQUENCE_STRING_SET_SEGMENT_H_
+#define SEQAN_SEQUENCE_STRING_SET_SEGMENT_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename THost>
+struct StringSetPositions;
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Class StringSet<Segment>
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+class StringSet<THost, Segment<TSpec> >
+{
+public:
+    typedef typename Pointer_<THost>::Type                  THostPointer;
+    typedef typename StringSetPositions<THost>::Type        TPositions;
+    typedef typename StringSetLimits<StringSet>::Type       TLimits;
+    typedef typename Concatenator<StringSet>::Type          TConcatenator;
+
+
+    THostPointer    data_host;
+    TPositions      positions;
+    TLimits         limits;
+    bool            limitsValid;
+    TConcatenator   concat;
+
+    StringSet() :
+        data_host(),
+        limitsValid(true)
+    {
+        _initStringSetLimits(*this);
+    }
+
+    StringSet(THost & _host) :
+        data_host(_toPointer(_host)),
+        limitsValid(true)
+    {
+        _initStringSetLimits(*this);
+    }
+
+    // ----------------------------------------------------------------------
+    // Subscription operators; have to be defined in class def.
+    // ----------------------------------------------------------------------
+
+    template <typename TPos>
+    SEQAN_HOST_DEVICE inline typename Reference<StringSet>::Type
+    operator[](TPos pos)
+    {
+        SEQAN_CHECKPOINT;
+        return value(*this, pos);
+    }
+
+    template <typename TPos>
+    SEQAN_HOST_DEVICE inline typename Reference<StringSet const>::Type
+    operator[](TPos pos) const
+    {
+        SEQAN_CHECKPOINT;
+        return value(*this, pos);
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Metafunction StringSetPositions
+// --------------------------------------------------------------------------
+
+template <typename THost>
+struct StringSetPositions
+{
+    typedef typename Position<THost>::Type                  TPos_;
+    typedef typename StringSpec<THost>::Type                TSpec_;
+
+    typedef String<TPos_, TSpec_>                           Type;
+};
+
+template <typename THost>
+struct StringSetPositions<THost const>
+{
+    typedef typename StringSetPositions<THost>::Type const  Type;
+};
+
+template <typename THost, typename TSpec>
+struct StringSetPositions<StringSet<THost, TSpec> >
+{
+    typedef StringSet<THost, TSpec>                         TStringSet_;
+    typedef typename StringSetPosition<TStringSet_>::Type   TPos_;
+    typedef typename StringSpec<TStringSet_>::Type          TSpec_;
+
+    typedef String<TPos_, TSpec_>                           Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction Value
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+struct Host<StringSet<THost, Segment<TSpec> > >
+{
+    typedef THost Type;
+};
+
+template <typename THost, typename TSpec>
+struct Host<StringSet<THost, Segment<TSpec> > const> :
+    Host<StringSet<THost, Segment<TSpec> > > {};
+
+// --------------------------------------------------------------------------
+// Metafunction Value
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+struct Value<StringSet<THost, Segment<TSpec> > >
+    : Infix<THost> {};
+
+template <typename THost, typename TSpec>
+struct Value<StringSet<THost, Segment<TSpec> > const>
+    : Infix<THost const> {};
+
+// --------------------------------------------------------------------------
+// Metafunction GetValue
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+struct GetValue<StringSet<THost, Segment<TSpec> > >
+{
+    typedef typename Infix<THost>::Type const Type;
+};
+
+template <typename THost, typename TSpec>
+struct GetValue<StringSet<THost, Segment<TSpec> > const>
+{
+    typedef typename Infix<THost const>::Type const Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction Reference
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+struct Reference<StringSet<THost, Segment<TSpec> > >
+    : Infix<THost> {};
+
+template <typename THost, typename TSpec>
+struct Reference<StringSet<THost, Segment<TSpec> > const>
+    : Infix<THost const> {};
+
+// --------------------------------------------------------------------------
+// Metafunction Prefix
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+struct Prefix<StringSet<THost, Segment<TSpec> > >
+    : Infix<THost> {};
+
+template <typename THost, typename TSpec>
+struct Prefix<StringSet<THost, Segment<TSpec> > const>
+    : Infix<THost const> {};
+
+// --------------------------------------------------------------------------
+// Metafunction Suffix
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+struct Suffix<StringSet<THost, Segment<TSpec> > >
+    : Infix<THost> {};
+
+template <typename THost, typename TSpec>
+struct Suffix<StringSet<THost, Segment<TSpec> > const>
+    : Infix<THost const> {};
+
+// --------------------------------------------------------------------------
+// Metafunction Infix
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+struct Infix<StringSet<THost, Segment<TSpec> > >
+    : Infix<THost> {};
+
+template <typename THost, typename TSpec>
+struct Infix<StringSet<THost, Segment<TSpec> > const >
+    : Infix<THost const> {};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _refreshStringSetLimits()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TThreading>
+SEQAN_HOST_DEVICE void
+_refreshStringSetLimits(StringSet<THost, Segment<TSpec> > & me, Tag<TThreading> const & tag)
+{
+    partialSum(me.limits, tag);
+    me.limitsValid = true;
+}
+
+template <typename THost, typename TSpec>
+SEQAN_HOST_DEVICE void
+_refreshStringSetLimits(StringSet<THost, Segment<TSpec> > & me)
+{
+    _refreshStringSetLimits(me, Serial());
+}
+
+// --------------------------------------------------------------------------
+// Function stringSetPositions()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+inline typename StringSetPositions<THost>::Type &
+stringSetPositions(StringSet<THost, Segment<TSpec> > & me)
+{
+    return me.positions;
+}
+
+template <typename THost, typename TSpec>
+inline typename StringSetPositions<THost const>::Type &
+stringSetPositions(StringSet<THost, Segment<TSpec> > const & me)
+{
+    return me.positions;
+}
+
+// ----------------------------------------------------------------------------
+// Function host()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Parameter_<THost>::Type
+host(StringSet<THost, Segment<TSpec> > & me)
+{
+    return _toParameter<THost>(me.data_host);
+}
+
+template <typename THost, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Parameter_<THost>::Type
+host(StringSet<THost, Segment<TSpec> > const & me)
+{
+    return _toParameter<THost>(me.data_host);
+}
+
+// ----------------------------------------------------------------------------
+// Function setHost()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+inline void setHost(StringSet<THost, Segment<TSpec> > & me, typename Parameter_<THost>::Type host)
+{
+    me.data_host = _toPointer(host);
+}
+
+// ----------------------------------------------------------------------------
+// Function view()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+typename View<StringSet<THost, Segment<TSpec> > >::Type
+view(StringSet<THost, Segment<TSpec> > & me)
+{
+    typename View<StringSet<THost, Segment<TSpec> > >::Type stringSetView;
+
+    stringSetView.data_host = view(host(me));
+    stringSetView.positions = view(me.positions);
+    stringSetLimits(stringSetView) = view(stringSetLimits(me));
+    stringSetView.limitsValid = me.limitsValid;
+
+    // TODO(esiragusa): define view of concat.
+//    concat(stringSetView) = view(concat(me));
+
+    return stringSetView;
+}
+
+// ----------------------------------------------------------------------------
+// Function assign()
+// ----------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TString2, typename TSpec2>
+void assign(StringSet<THost, Segment<TSpec> > & me,
+            StringSet<TString2, Segment<TSpec2> > const & other)
+{
+    setHost(me, host(other));
+    assign(stringSetPositions(me), stringSetPositions(other));
+    assign(stringSetLimits(me), stringSetLimits(other));
+    assign(me.limitsValid, other.limitsValid);
+    assign(concat(me), concat(other));
+}
+
+template <typename THost, typename TSpec, typename TString2, typename TSpec2>
+void assign(StringSet<THost, Segment<TSpec> > & me,
+            StringSet<TString2, Segment<TSpec2> > & other)
+{
+    setHost(me, host(other));
+    assign(stringSetPositions(me), stringSetPositions(other));
+    assign(stringSetLimits(me), stringSetLimits(other));
+    assign(me.limitsValid, other.limitsValid);
+    assign(concat(me), concat(other));
+}
+
+// --------------------------------------------------------------------------
+// Function assignValue()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TPos, typename TSegment>
+inline void assignValue(StringSet<THost, Segment<TSpec> > & /* me */,
+                        TPos /* pos */,
+                        TSegment const & /* seq */)
+{
+    // NOTE(esiragusa): The host global position would be lost in the Segment.
+    SEQAN_FAIL("Not implemented");
+}
+
+// --------------------------------------------------------------------------
+// Function appendValue()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TSegment, typename TExpand>
+inline void appendValue(StringSet<THost, Segment<TSpec> > & /* me */,
+                        TSegment const & /* obj */,
+                        Tag<TExpand> /* tag */)
+{
+    // NOTE(esiragusa): The host global position would be lost in the Segment.
+    SEQAN_FAIL("Not implemented");
+}
+
+// --------------------------------------------------------------------------
+// Function assignInfixWithLength()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TPos, typename TInfixPos, typename TSize>
+SEQAN_HOST_DEVICE inline void
+assignInfixWithLength(StringSet<THost, Segment<TSpec> > & me,
+                      TPos pos, TInfixPos infixPos, TSize len)
+{
+    SEQAN_ASSERT_LT(pos, length(me));
+    assignValue(me.positions, pos, infixPos);
+    me.limitsValid = false;
+    // NOTE(esiragusa): this breaks the invariant on limits.
+    assignValue(me.limits, pos + 1, len);
+//    assignValue(me.limits, pos + 1, me.limits[pos] + len);
+}
+
+// --------------------------------------------------------------------------
+// Function appendInfixWithLength()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TPos, typename TSize, typename TExpand>
+SEQAN_HOST_DEVICE inline void
+appendInfixWithLength(StringSet<THost, Segment<TSpec> > & me,
+                      TPos pos, TSize length, Tag<TExpand> tag)
+{
+    appendValue(me.positions, pos, tag);
+    appendValue(me.limits, lengthSum(me) + length, tag);
+}
+
+// --------------------------------------------------------------------------
+// Function appendInfix()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TPos, typename TExpand>
+SEQAN_HOST_DEVICE inline void
+appendInfix(StringSet<THost, Segment<TSpec> > & me,
+            TPos posBegin, TPos posEnd, Tag<TExpand> tag)
+{
+    SEQAN_ASSERT_EQ(getSeqNo(posBegin), getSeqNo(posEnd));
+    SEQAN_ASSERT_LEQ(getSeqOffset(posBegin), getSeqOffset(posEnd));
+
+    appendValue(me.positions, posBegin, tag);
+    appendValue(me.limits, lengthSum(me) + getSeqOffset(posEnd) - getSeqOffset(posBegin), tag);
+}
+
+// --------------------------------------------------------------------------
+// Function clear()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+inline void clear(StringSet<THost, Segment<TSpec> > & me)
+{
+//    me.data_host = NULL;
+    resize(me.positions, 0, Exact());
+    resize(me.limits, 1, Exact());
+    me.limitsValid = true;
+}
+
+// --------------------------------------------------------------------------
+// Function length()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+SEQAN_HOST_DEVICE inline typename Size<StringSet<THost, Segment<TSpec> > >::Type
+length(StringSet<THost, Segment<TSpec> > const & me)
+{
+    return length(me.limits) - 1;
+}
+
+// --------------------------------------------------------------------------
+// Function resize()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TSize, typename TExpand>
+inline typename Size<StringSet<THost, Segment<TSpec> > >::Type
+resize(StringSet<THost, Segment<TSpec> > & me, TSize new_size, Tag<TExpand> tag)
+{
+    resize(me.positions, new_size, tag);
+
+    if (new_size < length(me.limits))
+        return resize(me.limits, new_size + 1, tag) - 1;
+    else
+        return resize(me.limits, new_size + 1, back(me.limits), tag) - 1;
+}
+
+// --------------------------------------------------------------------------
+// Function reserve()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TSize, typename TExpand>
+inline typename Size<StringSet<THost, Segment<TSpec> > >::Type
+reserve(StringSet<THost, Segment<TSpec> > & me,
+        TSize const & new_capacity,
+        Tag<TExpand> tag)
+{
+    reserve(me.positions, new_capacity, tag);
+    return reserve(me.limits, new_capacity + 1, tag) - 1;
+}
+
+// --------------------------------------------------------------------------
+// Function value()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec, typename TPos >
+SEQAN_HOST_DEVICE inline typename Infix<THost>::Type
+value(StringSet<THost, Segment<TSpec> > & me, TPos pos)
+{
+    SEQAN_ASSERT_NOT(empty(me));
+    return infixWithLength(host(me), me.positions[pos], me.limits[pos + 1] - me.limits[pos]);
+}
+
+template <typename THost, typename TSpec, typename TPos >
+SEQAN_HOST_DEVICE inline typename Infix<THost const>::Type
+value(StringSet<THost, Segment<TSpec> > const & me, TPos pos)
+{
+    SEQAN_ASSERT_NOT(empty(me));
+    return infixWithLength(host(me), me.positions[pos], me.limits[pos + 1] - me.limits[pos]);
+}
+
+// --------------------------------------------------------------------------
+// Function swap()
+// --------------------------------------------------------------------------
+
+template <typename THost, typename TSpec>
+void swap(StringSet<THost, Segment<TSpec> > & lhs,
+          StringSet<THost, Segment<TSpec> > & rhs)
+{
+    using std::swap;
+
+    swap(lhs.data_host, rhs.data_host);
+    swap(lhs.positions, rhs.positions);
+    swap(lhs.limits, rhs.limits);
+    swap(lhs.limitsValid, rhs.limitsValid);
+    swap(lhs.concat, rhs.concat);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_SEQUENCE_STRING_SET_SEGMENT_H_
diff --git a/seqan/sequence/string_set_view.h b/seqan/sequence/string_set_view.h
new file mode 100644
index 0000000..a72d082
--- /dev/null
+++ b/seqan/sequence/string_set_view.h
@@ -0,0 +1,96 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2013 NVIDIA Corporation
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of NVIDIA Corporation nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_STRING_SET_VIEW_H
+#define SEQAN_STRING_SET_VIEW_H
+
+namespace seqan {
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction View
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TSpec>
+struct View<StringSet<TString, TSpec> >
+{
+    typedef StringSet<typename View<TString>::Type, TSpec>      Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction RemoveView
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TViewSpec, typename TSpec>
+struct RemoveView<StringSet<ContainerView<TString, TViewSpec>, TSpec> >
+{
+    typedef StringSet<TString, TSpec>   Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction IsView
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TViewSpec, typename TSpec>
+struct IsView<StringSet<ContainerView<TString, TViewSpec>, TSpec> > : public True {};
+
+// ----------------------------------------------------------------------------
+// Metafunction StringSetLimits
+// ----------------------------------------------------------------------------
+
+template <typename TString, typename TViewSpec, typename TSpec>
+struct StringSetLimits<StringSet<ContainerView<TString, TViewSpec>, TSpec> >
+{
+    typedef typename View<typename StringSetLimits<StringSet<TString, TSpec> >::Type>::Type     Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function _initStringSetLimits()
+// --------------------------------------------------------------------------
+
+template <typename TString, typename TViewSpec, typename TSpec>
+inline void
+_initStringSetLimits(StringSet<ContainerView<TString, TViewSpec>, TSpec> & /* me */) {}
+
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_STRING_SET_VIEW_H
diff --git a/seqan/sequence_journaled.h b/seqan/sequence_journaled.h
index d1cc1b6..d45376a 100644
--- a/seqan/sequence_journaled.h
+++ b/seqan/sequence_journaled.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -55,17 +55,9 @@
 // ============================================================================
 
 #include <seqan/sequence_journaled/journal_entry.h>
-#include <seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h>
-#include <seqan/sequence_journaled/journal_entries_unbalanced_tree.h>
-#include <seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h>
 #include <seqan/sequence_journaled/journal_entries_sorted_array.h>
 #include <seqan/sequence_journaled/sequence_journaled.h>
 #include <seqan/sequence_journaled/sequence_journaled_iterator.h>
-
-// ============================================================================
-// Incremental Indices.
-// ============================================================================
-
-// TODO(holtgrew): Port back the incremental index stuff to the new code.
+#include <seqan/sequence_journaled/sequence_journaled_iterator_fast.h>
 
 #endif  // SEQAN_HEADER_SEQUENCE_JOURNALED_H
diff --git a/seqan/sequence_journaled/INFO b/seqan/sequence_journaled/INFO
deleted file mode 100644
index f5757b2..0000000
--- a/seqan/sequence_journaled/INFO
+++ /dev/null
@@ -1,11 +0,0 @@
-Name: seqan-sequence_journaled
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Maintainer: Rene Rahn <rene.rahn@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: new
-Description: Implementation of journaled sequence.
- This module contains the implementation of a journaled String class.  Changes
- are not applied directly but instead organized in a journal tree.  This allows
- cheap update operations at the cost of increased time usage for read access.
diff --git a/seqan/sequence_journaled/journal_entries_sorted_array.h b/seqan/sequence_journaled/journal_entries_sorted_array.h
index 0e52c9b..3448899 100644
--- a/seqan/sequence_journaled/journal_entries_sorted_array.h
+++ b/seqan/sequence_journaled/journal_entries_sorted_array.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -166,8 +166,8 @@ bool _checkSortedArrayTree(JournalEntries<TCargo, SortedArray> const & tree)
 
     for (TIterator it = begin(tree._journalNodes, Standard()) + 1, itend = end(tree._journalNodes, Standard()); it != itend; ++it)
     {
-		if (it->length == 0)
-			return false;
+        if (it->length == 0)
+            return false;
         if ((it - 1)->virtualPosition >= it->virtualPosition)
             return false;
         if ((it - 1)->virtualPosition + (it - 1)->length != it->virtualPosition)
@@ -184,7 +184,7 @@ bool _checkSortedArrayTree(JournalEntries<TCargo, SortedArray> const & tree)
                 return false;
         }
     }
-	return true;
+    return true;
 }
 
 template <typename TCargo>
@@ -306,18 +306,21 @@ findJournalEntry(JournalEntries<TCargo, SortedArray> & journalEntries,
     return *findInJournalEntries(journalEntries, pos);
 }
 
+// ----------------------------------------------------------------------------
+// Function _doRecordInsertion()
+// ----------------------------------------------------------------------------
 
-template <typename TCargo>
+template <typename TCargo, typename TIterator>
 inline
-void recordInsertion(JournalEntries<TCargo, SortedArray> & tree,
-                     typename Position<TCargo>::Type virtualPosition,
-                     typename Position<TCargo>::Type physicalBeginPos,
-                     typename Size<TCargo>::Type len)
+void _doRecordInsertion(JournalEntries<TCargo, SortedArray> & tree,
+                        TIterator iter,
+                        typename Position<TCargo>::Type virtualPosition,
+                        typename Position<TCargo>::Type physicalBeginPos,
+                        typename Size<TCargo>::Type len)
 {
     typedef typename Position<TCargo>::Type TPos;
-    typedef typename Iterator<String<TCargo>, Standard>::Type TIterator;
 
-	//std::cerr << __FILE__ << ":" << __LINE__ << " -- INSERT(" << virtualPosition << ", " << physicalBeginPos << ", " << len << ")" << std::endl;
+    //std::cerr << __FILE__ << ":" << __LINE__ << " -- INSERT(" << virtualPosition << ", " << physicalBeginPos << ", " << len << ")" << std::endl;
     //std::cerr << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
 
     // Handle special case that the entry list is empty.
@@ -331,14 +334,14 @@ void recordInsertion(JournalEntries<TCargo, SortedArray> & tree,
     }
 
     // Find position in sorted array of nodes to insert in.
-    TIterator iter = findInJournalEntries(tree, virtualPosition);
+    iter = findInJournalEntries(tree, virtualPosition);
     // TODO(holtgrew): Maybe move and update entries right of pos at the same time?
 
     // Create new journal entries.
-	if (iter->virtualPosition + iter->length > virtualPosition)
+    if (iter->virtualPosition + iter->length > virtualPosition)
     {
-		TPos pos = iter - begin(tree._journalNodes, Standard());
-		TPos shiftRightOf = pos;
+        TPos pos = iter - begin(tree._journalNodes, Standard());
+        TPos shiftRightOf = pos;
         // Found node that contains virtualPos.
         SEQAN_ASSERT_LEQ(iter->virtualPosition, virtualPosition);
         if (iter->virtualPosition == virtualPosition)
@@ -348,7 +351,7 @@ void recordInsertion(JournalEntries<TCargo, SortedArray> & tree,
             if (iter != begin(tree._journalNodes, Standard()))
                 physicalOriginPosition = (iter - 1)->physicalOriginPosition;
             insertValue(tree._journalNodes, pos, TCargo(SOURCE_PATCH, physicalBeginPos, virtualPosition, physicalOriginPosition, len));
-			shiftRightOf += 1;
+            shiftRightOf += 1;
         }
         else
         {
@@ -364,7 +367,7 @@ void recordInsertion(JournalEntries<TCargo, SortedArray> & tree,
             buffer[2] = TCargo(iter->segmentSource, iter->physicalPosition + offset, virtualPosition + len, physicalOriginPos1, iter->length - offset);
             // Insert new journal entries.
             replace(tree._journalNodes, pos, pos + 1, buffer);
-			shiftRightOf += 3;
+            shiftRightOf += 3;
         }
         // Update journal entries right of pos.
         for (TIterator it = begin(tree._journalNodes, Standard()) + shiftRightOf, itend = end(tree._journalNodes, Standard()); it != itend; ++it)
@@ -377,7 +380,7 @@ void recordInsertion(JournalEntries<TCargo, SortedArray> & tree,
     else
     {
         // Insert at end.
-		SEQAN_ASSERT_EQ(virtualPosition, iter->virtualPosition + iter->length);
+        SEQAN_ASSERT_EQ(virtualPosition, iter->virtualPosition + iter->length);
         TPos physicalOriginPosition = back(tree._journalNodes).physicalOriginPosition;
         appendValue(tree._journalNodes, TCargo(SOURCE_PATCH, physicalBeginPos, virtualPosition, physicalOriginPosition, len));
     }
@@ -386,16 +389,52 @@ void recordInsertion(JournalEntries<TCargo, SortedArray> & tree,
     SEQAN_ASSERT(_checkSortedArrayTree(tree));
 }
 
+// ----------------------------------------------------------------------------
+// Function recordInsertion()
+// ----------------------------------------------------------------------------
+
 template <typename TCargo>
 inline
-void recordErase(JournalEntries<TCargo, SortedArray> & tree,
-                 typename Position<TCargo>::Type pos,
-                 typename Position<TCargo>::Type posEnd)
+void recordInsertion(JournalEntries<TCargo, SortedArray> & tree,
+                     typename Position<TCargo>::Type virtualPosition,
+                     typename Position<TCargo>::Type physicalBeginPos,
+                     typename Size<TCargo>::Type len)
+{
+    typedef typename Position<TCargo>::Type TPos SEQAN_TYPEDEF_FOR_DEBUG;
+    typedef typename Iterator<String<TCargo>, Standard>::Type TIterator;
+
+    //std::cerr << __FILE__ << ":" << __LINE__ << " -- INSERT(" << virtualPosition << ", " << physicalBeginPos << ", " << len << ")" << std::endl;
+    //std::cerr << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
+
+    // Handle special case that the entry list is empty.
+    if (empty(tree._journalNodes))
+    {
+        SEQAN_ASSERT_EQ(virtualPosition, static_cast<TPos>(0));
+        if (len == 0)
+            return;
+        appendValue(tree._journalNodes, TCargo(SOURCE_PATCH, physicalBeginPos, virtualPosition, 0, len));
+        return;
+    }
+
+    // Find position in sorted array of nodes to insert in.
+    TIterator iter = findInJournalEntries(tree, virtualPosition);
+    _doRecordInsertion(tree, iter, virtualPosition, physicalBeginPos, len);
+}
+
+// ----------------------------------------------------------------------------
+// Function _doRecordErase()
+// ----------------------------------------------------------------------------
+
+template <typename TCargo, typename TIter>
+inline
+void _doRecordErase(JournalEntries<TCargo, SortedArray> & tree,
+                    TIter it,
+                    typename Position<TCargo>::Type pos,
+                    typename Position<TCargo>::Type posEnd)
 {
     typedef typename Size<TCargo>::Type TSize;
     typedef typename Position<TCargo>::Type TPos;
-    typedef typename Iterator<String<TCargo>, Standard>::Type TIter;
-//	std::cerr << __FILE__ << ":" << __LINE__ << " -- ERASE(" << pos << ", " << posEnd << ")" << std::endl;
+//    std::cerr << __FILE__ << ":" << __LINE__ << " -- ERASE(" << pos << ", " << posEnd << ")" << std::endl;
 //    std::cerr << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
 
     // Handle special case of removing all of the singleton existing entry.
@@ -413,107 +452,107 @@ void recordErase(JournalEntries<TCargo, SortedArray> & tree,
     }
 
     // Find node.
-    TIter it = findInJournalEntries(tree, pos);
+    it = findInJournalEntries(tree, pos);
 
     // We will shift the virtual positions of all entries right of and
     // including beginShiftPos by delta positions to the left.
     TPos delta = 0;
     TPos beginShiftPos = 0;
 
-	TPos itPos = it - begin(tree._journalNodes, Standard());
-	if (it->virtualPosition == pos && (TPos)it->length == posEnd - pos)
+    TPos itPos = it - begin(tree._journalNodes, Standard());
+    if (it->virtualPosition == pos && (TPos)it->length == posEnd - pos)
     {
-		// Remove the whole entry.
-		erase(tree._journalNodes, itPos);
-		delta = posEnd - pos;
-		beginShiftPos = itPos;
-	}
+        // Remove the whole entry.
+        erase(tree._journalNodes, itPos);
+        delta = posEnd - pos;
+        beginShiftPos = itPos;
+    }
     else if (it->virtualPosition == pos && (TPos)it->length > posEnd - pos)
     {
-		// Remove a prefix of the entry.
-		SEQAN_ASSERT_LT(pos, it->virtualPosition + it->length);
-		delta = posEnd - pos;
-		it->physicalPosition += delta;
+        // Remove a prefix of the entry.
+        SEQAN_ASSERT_LT(pos, it->virtualPosition + it->length);
+        delta = posEnd - pos;
+        it->physicalPosition += delta;
         if (it->segmentSource == SOURCE_ORIGINAL)
             it->physicalOriginPosition += delta;
-		it->length -= delta;
-		beginShiftPos = itPos + 1;
-	}
+        it->length -= delta;
+        beginShiftPos = itPos + 1;
+    }
     else if (it->virtualPosition < pos && it->virtualPosition + it->length == posEnd)
     {
-		// Remove a suffix of the entry.
-		SEQAN_ASSERT_GT(pos, it->virtualPosition);
-		delta = posEnd - pos;
-		it->length -= delta;
-		beginShiftPos = itPos + 1;
-	}
+        // Remove a suffix of the entry.
+        SEQAN_ASSERT_GT(pos, it->virtualPosition);
+        delta = posEnd - pos;
+        it->length -= delta;
+        beginShiftPos = itPos + 1;
+    }
     else if (it->virtualPosition < pos && it->virtualPosition + it->length > posEnd)
     {
-		// Remove a true infix of the entry.
-		TSize prefixLength = pos - it->virtualPosition;
-		TSize suffixLength = it->length - prefixLength - (posEnd - pos);
-		TSize removedInfixLength = posEnd - pos;
-		// Update the left part, this must be done before the iterator is possibly invalidate because of copied memory.
-		it->length -= removedInfixLength + suffixLength;
-		// Insert a new entry for the right part.
+        // Remove a true infix of the entry.
+        TSize prefixLength = pos - it->virtualPosition;
+        TSize suffixLength = it->length - prefixLength - (posEnd - pos);
+        TSize removedInfixLength = posEnd - pos;
+        // Update the left part, this must be done before the iterator is possibly invalidate because of copied memory.
+        it->length -= removedInfixLength + suffixLength;
+        // Insert a new entry for the right part.
         TPos physicalHostPos = it->physicalPosition;
         if (it->segmentSource == SOURCE_ORIGINAL)
             physicalHostPos += prefixLength + removedInfixLength;
-		TCargo tmpEntry(it->segmentSource, it->physicalPosition + prefixLength + removedInfixLength, it->virtualPosition + prefixLength, physicalHostPos, suffixLength);
-		insertValue(tree._journalNodes, itPos + 1, tmpEntry);
-		// Set shift position and delta.
-		delta = removedInfixLength;
-		beginShiftPos = itPos + 2;
-	}
+        TCargo tmpEntry(it->segmentSource, it->physicalPosition + prefixLength + removedInfixLength, it->virtualPosition + prefixLength, physicalHostPos, suffixLength);
+        insertValue(tree._journalNodes, itPos + 1, tmpEntry);
+        // Set shift position and delta.
+        delta = removedInfixLength;
+        beginShiftPos = itPos + 2;
+    }
     else
     {
-		// Remove more than one entry.
-		TPos rmBeginPos = itPos;
-		TPos rmEndPos = itPos;
-		if (it->virtualPosition != pos)
+        // Remove more than one entry.
+        TPos rmBeginPos = itPos;
+        TPos rmEndPos = itPos;
+        if (it->virtualPosition != pos)
         {
-			// Do not remove all of first.
-			delta += it->length - (pos - it->virtualPosition);
-			rmBeginPos += 1;
-			rmEndPos += 1;
-			it->length = (pos - it->virtualPosition);
-		}
+            // Do not remove all of first.
+            delta += it->length - (pos - it->virtualPosition);
+            rmBeginPos += 1;
+            rmEndPos += 1;
+            it->length = (pos - it->virtualPosition);
+        }
         else
         {
-			// Remove all of first.
-			delta = it->length;
-			rmEndPos += 1;
-		}
-		it += 1;
-		while (posEnd > it->virtualPosition + it->length)
+            // Remove all of first.
+            delta = it->length;
+            rmEndPos += 1;
+        }
+        it += 1;
+        while (posEnd > it->virtualPosition + it->length)
         {
-			rmEndPos += 1;
-			delta += it->length;
-			it += 1;
-		}
-		if (it->virtualPosition + it->length == posEnd)
+            rmEndPos += 1;
+            delta += it->length;
+            it += 1;
+        }
+        if (it->virtualPosition + it->length == posEnd)
         {
-			// Remove all of last.
-			rmEndPos += 1;
-			delta += it->length;
-			beginShiftPos = rmBeginPos;
-		}
+            // Remove all of last.
+            rmEndPos += 1;
+            delta += it->length;
+            beginShiftPos = rmBeginPos;
+        }
         else
         {
-			// Do not remove all of last.
-			SEQAN_ASSERT_GT(it->virtualPosition + it->length, posEnd);
-			TSize tmpDelta = delta;
-			delta += posEnd - it->virtualPosition;
-			it->physicalPosition += posEnd - it->virtualPosition;
+            // Do not remove all of last.
+            SEQAN_ASSERT_GT(it->virtualPosition + it->length, posEnd);
+            TSize tmpDelta = delta;
+            delta += posEnd - it->virtualPosition;
+            it->physicalPosition += posEnd - it->virtualPosition;
             if (it->segmentSource == SOURCE_ORIGINAL)
                 it->physicalOriginPosition = it->physicalPosition;
-			it->length -= posEnd - it->virtualPosition;
-			// We update this entry manually.
-			it->virtualPosition -= tmpDelta;
-			beginShiftPos = rmBeginPos + 1;
-		}
-		erase(tree._journalNodes, rmBeginPos, rmEndPos);
-	}
+            it->length -= posEnd - it->virtualPosition;
+            // We update this entry manually.
+            it->virtualPosition -= tmpDelta;
+            beginShiftPos = rmBeginPos + 1;
+        }
+        erase(tree._journalNodes, rmBeginPos, rmEndPos);
+    }
 
     // Perform left-shift of the virtual positions.
     for (TIter it = begin(tree._journalNodes, Standard()) + beginShiftPos; it != end(tree._journalNodes, Standard()); ++it) {
@@ -529,11 +568,48 @@ void recordErase(JournalEntries<TCargo, SortedArray> & tree,
         if (it != begin(tree._journalNodes, Standard()) && it->segmentSource == SOURCE_PATCH)
             it->physicalOriginPosition = (it - 1)->physicalOriginPosition;
     }
-//	std::cerr << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
+//    std::cerr << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
 
     SEQAN_ASSERT(_checkSortedArrayTree(tree));
 }
 
+// ----------------------------------------------------------------------------
+// Function recordErase()
+// ----------------------------------------------------------------------------
+
+template <typename TCargo>
+inline
+void recordErase(JournalEntries<TCargo, SortedArray> & tree,
+                 typename Position<TCargo>::Type pos,
+                 typename Position<TCargo>::Type posEnd)
+{
+    typedef typename Position<TCargo>::Type TPos;
+    typedef typename Iterator<String<TCargo>, Standard>::Type TIter;
+    //  std::cerr << __FILE__ << ":" << __LINE__ << " -- ERASE(" << pos << ", " << posEnd << ")" << std::endl;
+    //    std::cerr << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
+
+    // Handle special case of removing all of the singleton existing entry.
+    if (length(tree._journalNodes) == 1 && pos == 0 && (TPos)front(tree._journalNodes).length == posEnd)
+    {
+        clear(tree._journalNodes);
+        return;
+    }
+    // Handle case of an empty journal.
+    if (empty(tree._journalNodes))
+    {
+        SEQAN_ASSERT_EQ(pos, static_cast<TPos>(0));
+        SEQAN_ASSERT_EQ(posEnd, static_cast<TPos>(0));
+        return;
+    }
+
+    // Find node.
+    TIter it = findInJournalEntries(tree, pos);
+    _doRecordErase(tree, it, pos, posEnd);
+}
+
+// ----------------------------------------------------------------------------
+// Function virtualToHostPosition()
+// ----------------------------------------------------------------------------
 
 template <typename TNode, typename TJournalSpec, typename TPos>
 inline
@@ -561,7 +637,7 @@ virtualToHostPosition(JournalEntries<TNode, TJournalSpec> const & journalEntries
         if (value(it).segmentSource == SOURCE_ORIGINAL)
             return value(it).physicalPosition;
     }
-	it = it2;
+    it = it2;
     // Search left;
     while (true) {
         if (value(it).segmentSource == SOURCE_ORIGINAL)
@@ -663,6 +739,16 @@ clear(JournalEntries<TNode, SortedArray> & journalEntries)
     journalEntries._originalStringLength = 0u;
 }
 
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+template <typename TNode>
+inline bool
+empty(JournalEntries<TNode, SortedArray> const & journalEntries)
+{
+    return empty(journalEntries._journalNodes);
+}
 
 }  // namespace seqan
 
diff --git a/seqan/sequence_journaled/journal_entries_unbalanced_tree.h b/seqan/sequence_journaled/journal_entries_unbalanced_tree.h
deleted file mode 100644
index 76ab00e..0000000
--- a/seqan/sequence_journaled/journal_entries_unbalanced_tree.h
+++ /dev/null
@@ -1,779 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Journal entries implementation using an unbalanced binary search tree.
-// ==========================================================================
-
-#ifndef SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_H_
-#define SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_H_
-
-namespace seqan {
-
-// ============================================================================
-// Tags, Classes
-// ============================================================================
-
-// For iterator, needs to be declared here.
-enum IterationDirection {
-    DIRECTION_NULL,
-    DIRECTION_DOWN_LEFT,
-    DIRECTION_DOWN_RIGHT,
-    DIRECTION_UP_LEFT,
-    DIRECTION_UP_RIGHT
-};
-
-
-// Tag: Unbalanced tree.
-struct UnbalancedTree {};
-
-
-template <typename TNode, typename TTreeSpec>
-class JournalEntries;
-
-
-template <typename TCargo_>
-class JournalEntries<TCargo_, UnbalancedTree>
-{
-  public:
-    typedef TCargo_ TCargo;
-    typedef JournalEntriesUnorderedTreeNode<TCargo> TNode;
-    typedef JournalEntries<TCargo, UnbalancedTree> TJournalEntries;
-    typedef typename Position<TNode>::Type TPos;
-    typedef typename Size<TNode>::Type TSize;
-    typedef UnbalancedTree TSpec;
-
-    // Allocator for the nodes.
-    Allocator<SinglePool<sizeof(TNode)> > _nodeAllocator;
-    // Length of the underlying string.
-    TSize _originalStringLength;
-    // The root node.
-    TNode * _root;
-
-    JournalEntries()
-            : _root(0)
-    {
-        SEQAN_CHECKPOINT;
-    }
-
-    JournalEntries(JournalEntries const & other)
-            : _originalStringLength(other._originalStringLength)
-    {
-        _copyJournalEntriesNodes(_root, _nodeAllocator, other._root);
-    }
-
-    JournalEntries &
-    operator=(JournalEntries const & other)
-
-    {
-        if (this != &other)
-        {
-            _originalStringLength = other._originalStringLength;
-            _copyJournalEntriesNodes(_root, _nodeAllocator, other._root);
-        }
-        return *this;
-
-    }
-
-    JournalEntries &
-    operator=(JournalEntries const & other) const
-
-    {
-        if (this != &other)
-        {
-            _originalStringLength = other._originalStringLength;
-            _copyJournalEntriesNodes(_root, _nodeAllocator, other._root);
-        }
-        return *this;
-
-    }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-template <typename TCargo>
-struct Reference<JournalEntries<TCargo, UnbalancedTree> >
-{
-    typedef TCargo & Type;
-};
-
-template <typename TCargo>
-struct Reference<JournalEntries<TCargo, UnbalancedTree> const>
-{
-    typedef TCargo const & Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-template <typename TNode, typename TAllocator>
-void
-_copyJournalEntriesNodes(TNode * & target,
-                      TAllocator & allocator,
-                      TNode * const & source)
-{
-    SEQAN_CHECKPOINT;
-    allocate(allocator, target, 1);
-    target = new (target) TNode(*source);
-
-    if (source->left != 0) {
-        _copyJournalEntriesNodes(target->left, allocator, source->left);
-        target->left->parent = target;
-    }
-    if (source->right != 0) {
-        _copyJournalEntriesNodes(target->right, allocator, source->right);
-        target->right->parent = target;
-    }
-}
-
-
-template <typename TNode>
-inline
-bool checkVirtualPositionsRec(TNode * const & node, unsigned & virtualPosition)
-{
-    SEQAN_CHECKPOINT;
-    if (node == 0)
-        return true;
-    bool res = true;
-    if (node->left)
-        res = res && checkVirtualPositionsRec(node->left, virtualPosition);
-    if (cargo(*node).virtualPosition != virtualPosition)
-        res = false;
-    virtualPosition += cargo(*node).length;
-    if (node->right)
-        res = res && checkVirtualPositionsRec(node->right, virtualPosition);
-    return res;
-}
-
-template <typename TNode>
-inline
-bool checkVirtualPositions(TNode * const & node)
-{
-    SEQAN_CHECKPOINT;
-    unsigned virtualPosition = 0;
-    return checkVirtualPositionsRec(node, virtualPosition);
-}
-
-template <typename TNode>
-inline
-bool checkOrderRec(TNode * const & node)
-{
-    SEQAN_CHECKPOINT;
-    bool result = true;
-    if (node->left != 0) {
-        result = result && (cargo(*node).virtualPosition > cargo(*node->left).virtualPosition);
-        result = result && checkOrderRec(node->left);
-    }
-    if (node->right != 0) {
-        result = result && (cargo(*node).virtualPosition < cargo(*node->right).virtualPosition);
-        result = result && checkOrderRec(node->right);
-    }
-    return result;
-}
-
-template <typename TNode>
-inline
-bool checkOrder(TNode * const & node)
-{
-    SEQAN_CHECKPOINT;
-    if (node == 0)
-        return true;
-    return checkOrderRec(node);
-}
-
-template <typename TNode>
-inline
-bool checkStructureRec(TNode * const & node)
-{
-    SEQAN_CHECKPOINT;
-    bool result = true;
-    if (node->left != 0) {
-        result = result && (node->left->parent == node);
-        result = result && checkStructureRec(node->left);
-    }
-    if (node->right != 0) {
-        result = result && (node->right->parent == node);
-        result = result && checkStructureRec(node->right);
-    }
-    return result;
-}
-
-template <typename TNode>
-inline
-bool checkStructure(TNode * const & node)
-{
-    if (node == 0)
-        return true;
-    if (node->parent == 0)
-        return checkStructureRec(node);
-    if (node->parent->left != 0 && node->parent->right != 0) {
-        if (!((node->parent->left == node) ^ (node->parent->right == node)))
-            return false;
-    } else if (node->parent->left == 0 && node->parent->right != 0) {
-        if (node->parent->right != node)
-            return false;
-    } else if (node->parent->left != 0 && node->parent->right == 0) {
-        if (node->parent->left != node)
-            return false;
-    } else {  // both == 0
-        return false;
-    }
-    return checkStructureRec(node);
-}
-
-template <typename TStream, typename TNode>
-inline
-TStream &
-operator<<(TStream & stream, JournalEntries<TNode, UnbalancedTree> const & tree)
-{
-    if (tree._root != 0)
-        return stream << "JournalEntries(" << *tree._root << ")";
-    else
-        return stream << "JournalEntries()";
-}
-
-template <typename TCargo>
-inline
-void reinit(JournalEntries<TCargo, UnbalancedTree> & tree,
-            typename Size<typename JournalEntries<TCargo, UnbalancedTree>::TNode>::Type originalStringLength)
-{
-    SEQAN_CHECKPOINT;
-    typedef typename JournalEntries<TCargo, UnbalancedTree>::TNode TNode;
-    clear(tree._nodeAllocator);
-    tree._originalStringLength = originalStringLength;
-    TNode *tmp;
-    allocate(tree._nodeAllocator, tmp, 1);
-    tree._root = new (tmp) TNode(TCargo(SOURCE_ORIGINAL, 0, 0, 0, originalStringLength));
-}
-
-
-// Subtract delta from all nodes with virtual positions right of,
-// respectively >= pos.  Note that this must not make the tree invalid.
-template <typename TNode>
-inline
-void
-_subtractFromVirtualPositionsRightOf(TNode * node,
-                                     typename Position<TNode>::Type const & pos,
-                                     typename Position<TNode>::Type const & delta)
-{
-    SEQAN_CHECKPOINT;
-
-    if (cargo(*node).virtualPosition >= pos) {
-        cargo(*node).virtualPosition -= delta;
-        if (node->left != 0)
-            _subtractFromVirtualPositionsRightOf(node->left, pos, delta);
-        if (node->right != 0)
-            _subtractFromVirtualPositionsRightOf(node->right, pos, delta);
-    } else {  // node->virtualPosition < pos
-        if (node->right != 0)
-            _subtractFromVirtualPositionsRightOf(node->right, pos, delta);
-    }
-}
-
-
-// Add delta to all nodes with virtual positions right of,
-// respectively >= pos.  Note that this must not make the tree invalid.
-template <typename TNode>
-inline
-void
-_addToVirtualPositionsRightOf(TNode * node,
-                              typename Position<TNode>::Type const & pos,
-                              typename Position<TNode>::Type const & delta)
-{
-    SEQAN_CHECKPOINT;
-
-    if (cargo(*node).virtualPosition >= pos) {
-        cargo(*node).virtualPosition += delta;
-        if (node->left != 0)
-            _addToVirtualPositionsRightOf(node->left, pos, delta);
-        if (node->right != 0)
-            _addToVirtualPositionsRightOf(node->right, pos, delta);
-    } else {  // node->virtualPosition < pos
-        if (node->right != 0)
-            _addToVirtualPositionsRightOf(node->right, pos, delta);
-    }
-}
-
-
-template <typename TCargo>
-inline
-typename Iterator<JournalEntries<TCargo, UnbalancedTree> const, Standard>::Type
-findInJournalEntries(JournalEntries<TCargo, UnbalancedTree> const & journalEntries,
-                     typename Position<TCargo>::Type const & pos) {
-    SEQAN_CHECKPOINT;
-    typedef JournalEntries<TCargo, UnbalancedTree> TJournalEntries;
-    typedef typename TJournalEntries::TNode TNode SEQAN_TYPEDEF_FOR_DEBUG;
-    typedef typename Iterator<TJournalEntries, Standard>::Type TIterator;
-
-    TIterator result;
-    result._currentNode = journalEntries._root;
-    result._iterationDirection = DIRECTION_DOWN_LEFT;
-
-    while (true) {
-        SEQAN_ASSERT_NEQ(result._currentNode, static_cast<TNode *>(0));
-
-        if ((value(result).virtualPosition <= pos) && (value(result).virtualPosition + value(result).length > pos)) {
-            break;
-        } else if (value(result).virtualPosition + value(result).length <= pos) {
-            if (!goRight(result))
-                break;
-        } else {  // pos < node->virtualPosition
-            if (!goLeft(result))
-                break;
-        }
-    }
-
-    return result;
-}
-
-
-template <typename TCargo>
-inline
-TCargo const &
-findJournalEntry(JournalEntries<TCargo, UnbalancedTree> const & journalEntries,
-                 typename Position<TCargo>::Type const & pos) {
-    SEQAN_CHECKPOINT;
-    return *findInJournalEntries(journalEntries, pos);
-}
-
-
-template <typename TCargo>
-inline
-void recordErase(JournalEntries<TCargo, UnbalancedTree> & tree,
-                 typename Position<typename JournalEntries<TCargo, UnbalancedTree>::TNode>::Type const & pos,
-                 typename Position<typename JournalEntries<TCargo, UnbalancedTree>::TNode>::Type const & posEnd)
-{
-    SEQAN_CHECKPOINT;
-    typedef JournalEntries<TCargo, UnbalancedTree> TJournalEntries;
-    typedef typename Iterator<TJournalEntries>::Type TIterator;
-    typedef typename TJournalEntries::TNode TNode;
-    typedef typename Position<TNode>::Type TPos;
-    typedef typename Size<TNode>::Type TSize;
-
-    SEQAN_ASSERT(checkStructure(tree._root));
-    SEQAN_ASSERT(checkOrder(tree._root));
-    SEQAN_ASSERT(checkVirtualPositions(tree._root));
-
-//     std::cout << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
-
-    // Handle case of an empty journal tree.
-    if (tree._root == 0) {
-        SEQAN_ASSERT_EQ(pos, 0u);
-        SEQAN_ASSERT_EQ(posEnd, 0u);
-        return;
-    }
-    // Handle special case of removing all of the root node.
-    if (tree._root->left == 0 && tree._root->right == 0 && pos == 0 && posEnd == cargo(*tree._root).length) {
-        tree._root = 0;
-        clear(tree._nodeAllocator);
-        return;
-    }
-
-    // Find node with virtual position pos.
-    TNode * node = 0;
-    TNode * parent = 0;
-    TIterator iter = findInJournalEntries(tree, pos);
-    node = iter._currentNode;
-    parent = node->parent;
-
-    // The position to subtract values from right of.
-    TPos subtractRightOf = pos;
-    // Virtual begin and end position of the node.
-    TPos nodeBegin = cargo(*node).virtualPosition;
-    TPos nodeEnd = cargo(*node).virtualPosition + cargo(*node).length;
-
-    // The simple cases are: A prefix or suffix but not all of the node are erased.
-    // Otherwise, we have to delete or split the existing node.
-    if (nodeBegin == pos && nodeEnd == posEnd) {
-//         std::cout << "whole node" << std::endl;
-        // The whole node is removed.  If there is <= one child, things are
-        // simple, otherwise, we replace node with its right child and perform
-        // a left-right traversal to find the leaf for which node's left child
-        // can become the left child of.
-        TNode * left = node->left;
-        TNode * right = node->right;
-        if (left == 0) {
-            // Replace parent's pointer.
-            if (parent == 0) {
-                // Node was root.
-                tree._root = node->right;
-                tree._root->parent = 0;
-            } else {
-                // Node was not root.
-                if (parent->left == node) {
-                    parent->left = node->right;
-                } else {
-                    SEQAN_ASSERT_EQ(parent->right, node);
-                    parent->right = node->right;
-                }
-                if (node->right != 0)
-                    node->right->parent = parent;
-            }
-        } else {
-            if (right == 0) { // left != 0 && right == 0
-                if (parent == 0) {
-                    // Node was root.
-                    node->left->parent = 0;
-                    tree._root = node->left;
-                } else {
-                    // Node was not root.
-                    if (parent->left == node) {
-                        node->left->parent = parent;
-                        parent->left = node->left;
-                    } else {
-                        node->left->parent = parent;
-                        parent->right = node->left;
-                    }
-                }
-            } else {
-                // left != 0 && right != 0
-                if (parent == 0) {
-                    // node is root
-                    node->right->parent = 0;
-                    tree._root = node->right;
-                } else {
-                    if (parent->left == node) {
-                        node->right->parent = parent;
-                        parent->left = node->right;
-                    } else {
-                        node->right->parent = parent;
-                        parent->right = node->right;
-                    }
-                }
-                TNode * tmp = node->right->left;
-                node->right->left = node->left;
-                node->left->parent = node->right;
-                // Left-right traversal from node on.
-                TNode * current = node->left;
-                SEQAN_ASSERT_NEQ(current, static_cast<TNode *>(0));
-                while (current->right != 0)
-                    current = current->right;
-                current->right = tmp;
-                if (tmp != 0)
-                    tmp->parent = current;
-            }
-        }
-        // Actually deallocate node.
-        deallocate(tree._nodeAllocator, node, 1);
-        // Adjust virtual positions.
-        _subtractFromVirtualPositionsRightOf(tree._root, subtractRightOf, posEnd - pos);
-    } else if (nodeBegin == pos && nodeEnd > posEnd) {
-//         std::cout << "true prefix" << std::endl;
-        // A true prefix is removed, not the whole node.
-        cargo(*node).length -= posEnd - pos;
-        cargo(*node).physicalPosition += posEnd - pos;
-        subtractRightOf = posEnd;  // No need to update this node!
-        // Adjust virtual positions.
-        _subtractFromVirtualPositionsRightOf(tree._root, subtractRightOf, posEnd - pos);
-    } else if (nodeBegin < pos && nodeEnd == posEnd) {
-//         std::cout << "true suffix" << std::endl;
-        // A true suffix is removed, not the whole node.
-        cargo(*node).length -= posEnd - pos;
-        subtractRightOf = posEnd;  // No need to update this node!
-        // Adjust virtual positions.
-        _subtractFromVirtualPositionsRightOf(tree._root, subtractRightOf, posEnd - pos);
-    } else if (nodeBegin < pos && nodeEnd > posEnd) {
-//         std::cout << "true infix" << std::endl;
-        // A true infix of the node is removed.  This node stores the prefix
-        // and we do a right-left traversal to place the newly created node.
-        TNode * tmp;
-        allocate(tree._nodeAllocator, tmp, 1);
-        // Perform index calculations for prefix and suffix node.
-        TSize prefixLength = pos - cargo(*node).virtualPosition;
-        TSize deletedInfixLength = posEnd - pos;
-        TSize suffixLength = cargo(*node).length - prefixLength - deletedInfixLength;
-        // Update prefix node.
-        cargo(*node).length = prefixLength;
-        // Construct suffix node.
-        TNode * suffixNode = new (tmp) TNode(TCargo(cargo(*node).segmentSource,
-                                                    cargo(*node).physicalPosition + prefixLength + deletedInfixLength,
-                                                    cargo(*node).virtualPosition + prefixLength,
-                                                    0,
-                                                    suffixLength));
-        // Insert node for suffix.
-        if (node->right == 0) {
-            node->right = suffixNode;
-            suffixNode->parent = node;
-        } else {
-            TNode * current = node->right;
-            while (current->left != 0) {
-                current = current->left;
-            }
-            current->left = suffixNode;
-            suffixNode->parent = current;
-        }
-        subtractRightOf = cargo(*node).virtualPosition + prefixLength + deletedInfixLength + 1;
-        // Adjust virtual positions.
-        _subtractFromVirtualPositionsRightOf(tree._root, subtractRightOf, posEnd - pos);
-    } else {
-//         std::cout << "spans more than one" << std::endl;
-        // The deletion range spans more than this node.  We solve this by
-        // calling this function recursively.  First, we delete a suffix of
-        // this node (possibly all of it) and then we recursively remove the
-        // remaining suffix of [pos, posEnd).
-        TSize len = cargo(*node).length - (pos - cargo(*node).virtualPosition);
-        recordErase(tree, pos, pos + len);
-        recordErase(tree, pos, posEnd - len);
-    }
-//     unsigned nextId = mtRand();
-//     journalTreeToDot(std::cerr, nextId, tree);
-//     std::cout << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
-    SEQAN_ASSERT(checkStructure(tree._root));
-    SEQAN_ASSERT(checkOrder(tree._root));
-    SEQAN_ASSERT(checkVirtualPositions(tree._root));
-}
-
-
-template <typename TCargo>
-inline
-void recordInsertion(JournalEntries<TCargo, UnbalancedTree> & tree,
-                     typename Position<typename JournalEntries<TCargo, UnbalancedTree>::TNode>::Type const & virtualPos,
-                     typename Position<typename JournalEntries<TCargo, UnbalancedTree>::TNode>::Type const & physicalBeginPos,
-                     typename Size<typename JournalEntries<TCargo, UnbalancedTree>::TNode>::Type const & length)
-{
-    SEQAN_CHECKPOINT;
-    typedef JournalEntries<TCargo, UnbalancedTree> TJournalEntries;
-    typedef typename Iterator<TJournalEntries>::Type TIterator;
-    typedef typename TJournalEntries::TNode TNode;
-    typedef typename Position<TNode>::Type TPos;
-
-    SEQAN_ASSERT(checkStructure(tree._root));
-    SEQAN_ASSERT(checkOrder(tree._root));
-    SEQAN_ASSERT(checkVirtualPositions(tree._root));
-
-    // Handle special case of empty tree.
-    if (tree._root == 0) {
-        SEQAN_ASSERT_EQ(virtualPos, 0u);
-        if (length == 0)
-            return;
-        TNode * tmp;
-        allocate(tree._nodeAllocator, tmp, 1);
-        tree._root = new (tmp) TNode(TCargo(SOURCE_PATCH, physicalBeginPos, virtualPos, 0, length));
-        return;
-    }
-
-    TNode * node;
-    TNode * parent;
-    TIterator iter = findInJournalEntries(tree, virtualPos);
-    node = iter._currentNode;
-    parent = node->parent;
-    SEQAN_ASSERT_LEQ(cargo(*node).virtualPosition, virtualPos);
-
-    if (cargo(*node).virtualPosition + cargo(*node).length > virtualPos) {
-        // Found node that contains virtualPos.
-        SEQAN_ASSERT_LEQ(cargo(*node).virtualPosition, virtualPos);
-        if (cargo(*node).virtualPosition == virtualPos) {
-            // Simple case: Insert left of current.
-            TNode * tmp;
-            allocate(tree._nodeAllocator, tmp, 1);
-            TNode * insertNode = new (tmp) TNode(TCargo(SOURCE_PATCH, physicalBeginPos, virtualPos, 0, length));
-            _addToVirtualPositionsRightOf(tree._root, virtualPos, length);
-            insertNode->left = node->left;
-            if (insertNode->left != 0)
-                insertNode->left->parent = insertNode;
-            node->left = insertNode;
-            insertNode->parent = node;
-        } else {
-            // Harder case: Split current and insert new node.
-            _addToVirtualPositionsRightOf(tree._root, cargo(*node).virtualPosition + cargo(*node).length, length);
-            TPos offset = virtualPos - cargo(*node).virtualPosition;
-            // Create right part of the node.
-            TNode * tmp;
-            allocate(tree._nodeAllocator, tmp, 1);
-            TNode * splitNode = new (tmp) TNode(TCargo(cargo(*node).segmentSource, cargo(*node).physicalPosition + offset, cargo(*node).virtualPosition + offset + length, 0, cargo(*node).length - offset));
-            // Current node becomes left part of current node.
-            cargo(*node).length = offset;
-            // Create insertion node.
-            allocate(tree._nodeAllocator, tmp, 1);
-            TNode * insertNode = new (tmp) TNode(TCargo(SOURCE_PATCH, physicalBeginPos, virtualPos, 0, length));
-            // Insert into tree...
-            insertNode->left = node;
-            node->parent = insertNode;
-            insertNode->right = splitNode;
-            splitNode->parent = insertNode;
-            splitNode->right = node->right;
-            if (node->right != 0)
-                node->right->parent = splitNode;
-            node->right = 0;
-            if (parent == 0) {
-                // current is the root node.
-                tree._root = insertNode;
-                insertNode->parent = 0;
-            } else {
-                if (parent->left == node)
-                    parent->left = insertNode;
-                else
-                    parent->right = insertNode;
-                insertNode->parent = parent;
-            }
-        }
-    } else {
-        // Returned node with highest virtualPosition but we need to insert
-        // right of it.
-        SEQAN_ASSERT_EQ(node->right, static_cast<TNode *>(0));
-        SEQAN_ASSERT_EQ(cargo(*node).virtualPosition + cargo(*node).length, virtualPos);
-        TNode * tmp;
-        allocate(tree._nodeAllocator, tmp, 1);
-        TNode * insertNode = new (tmp) TNode(TCargo(SOURCE_PATCH, physicalBeginPos, virtualPos, 0, length));
-        node->right = insertNode;
-        insertNode->parent = node;
-    }
-//     unsigned nextId = mtRand();
-//     journalTreeToDot(std::cerr, nextId, tree);
-//     std::cout << tree << std::endl;
-//     std::cout << __FILE__ << ":" << __LINE__ << " -- " << tree << std::endl;
-    SEQAN_ASSERT(checkStructure(tree._root));
-    SEQAN_ASSERT(checkOrder(tree._root));
-    SEQAN_ASSERT(checkVirtualPositions(tree._root));
-}
-
-
-// TODO(holtgrew): Remove?
-/*
-template <typename TNode>
-inline
-TNode const *
-back(JournalEntries<TNode, UnbalancedTree> const & tree)
-{
-    SEQAN_XXXCHECKPOINT;
-    TNode * current = tree._root;
-    while (current->right != 0)
-        current = current->right;
-    return current;
-}
-
-
-template <typename TNode>
-inline
-TNode const *
-front(JournalEntries<TNode, UnbalancedTree> const & tree)
-{
-    SEQAN_XXXCHECKPOINT;
-    TNode * current = tree._root;
-    while (current->left != 0)
-        current = current->left;
-    return current;
-}
-*/
-
-//---------------------------------------------------
-// function hostToVirtualPosition()
-//---------------------------------------------------
-
-template <typename TCargo, typename TPos>
-inline
-typename Position<TCargo>::Type
-hostToVirtualPosition(JournalEntries<TCargo, UnbalancedTree> const & journalEntries,
-                      TPos const & hostPos)
-{
-    typedef JournalEntries<TCargo, UnbalancedTree> TJournalEntries;
-    typedef typename Iterator<TJournalEntries>::Type TIterator;
-
-    TIterator it = begin(journalEntries, Standard());
-    SEQAN_ASSERT(it != end(journalEntries, Standard()));
-    // TCargo tmp;
-    while (it != end(journalEntries, Standard()))
-    {
-        // host position can only appear in orginal node
-        if (value(it).segmentSource == SOURCE_ORIGINAL)
-        {
-            // found a potential hit - investigate!
-            if (hostPos >= (TPos) value(it).physicalPosition)
-            {
-                // Case#1: Found searched position - report mapping to virtual position
-                if (hostPos < (TPos) value(it).physicalPosition + (TPos) value(it).length)
-                {
-                    return value(it).virtualPosition + (hostPos - value(it).physicalPosition);
-                }
-                // Case#2a: Searched position appears either in next node (see Case#1) or
-                // lies within a deletion (see Case#2b)
-                // tmp = value(it);
-            }
-            else
-            {   // Case#2b: Searched position lies within deletion - report virtual position of this node.
-                return value(it).virtualPosition;
-            }
-        }
-        ++it;
-    }
-    SEQAN_ASSERT_FAIL("Should never reach here!");
-    return 0;
-}
-
-
-
-template <typename TStream, typename TNode>
-void journalTreeToDotRec(TStream & stream, unsigned & nextId, TNode const & node)
-{
-    unsigned currentId = nextId;
-    nextId += 1;
-    stream << "  node_" << currentId << "[label=\"source=" << node.segmentSource << ", vpos=" << node.virtualPosition << ", phpos=" << node.physicalPosition << ", len=" << node.length << "\"]" << std::endl;
-    if (node.left != 0) {
-        stream << "  node_" << currentId << " -> node_" << nextId << "[label=\"L\"]" << std::endl;
-        journalTreeToDotRec(stream, nextId, *(node.left));
-        nextId += 1;
-    }
-    if (node.right != 0) {
-        stream << "  node_" << currentId << " -> node_" << nextId << "[label=\"R\"]" << std::endl;
-        journalTreeToDotRec(stream, nextId, *(node.right));
-        nextId += 1;
-    }
-}
-
-
-template <typename TStream, typename TNode>
-void journalTreeToDot(TStream & stream, unsigned & nextId, JournalEntries<TNode, UnbalancedTree> const & journalTree)
-{
-    stream << "ROOTPTR" << nextId << " -> node_" << nextId << std::endl;
-    journalTreeToDotRec(stream, nextId, *journalTree._root);
-}
-
-// ----------------------------------------------------------------------------
-// Function clear
-// ----------------------------------------------------------------------------
-
-template <typename TNode>
-inline void
-clear(JournalEntries<TNode, UnbalancedTree> & journalEntries)
-{
-    clear(journalEntries._nodeAllocator);
-    journalEntries._originalStringLength = 0u;
-    journalEntries._root = 0;
-}
-
-
-}  // namespace seqan
-
-#endif  // SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_H_
diff --git a/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h b/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h
deleted file mode 100644
index 3a05485..0000000
--- a/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h
+++ /dev/null
@@ -1,519 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Code for a SearchEntries<UnorderedTree> iterator.
-// ==========================================================================
-
-#ifndef SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_ITERATOR_H_
-#define SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_ITERATOR_H_
-
-namespace seqan {
-
-// ============================================================================
-// Tags, Classes
-// ============================================================================
-
-template <typename TJournalEntriesSpec>
-struct JournalEntriesIterSpec;
-
-
-template <typename TJournalEntries>
-class Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> >
-{
-public:
-    typedef Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > TIter;
-    typedef typename TJournalEntries::TNode TNode;
-
-    // The current node.
-    TNode * _currentNode;
-    // The direction we arrived from at this node.  The end node is
-    // encoded as the root and _iterationDirection == DIRECTION_UP_RIGHT.
-    IterationDirection _iterationDirection;
-
-    Iter() : _currentNode(0), _iterationDirection(DIRECTION_NULL) {}
-
-    Iter(TIter const & other)
-            : _currentNode(other._currentNode),
-              _iterationDirection(other._iterationDirection)
-    { SEQAN_CHECKPOINT; }
-
-    Iter(typename IterComplementConst<TIter>::Type const & other)
-            : _currentNode(other._currentNode),
-              _iterationDirection(other._iterationDirection)
-    { SEQAN_CHECKPOINT; }
-
-    explicit
-    Iter(TJournalEntries & tree)
-    {
-        SEQAN_CHECKPOINT;
-        _initJournalEntriesIterator(*this, tree);
-    }
-};
-
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-template <typename TCargo>
-struct Iterator<JournalEntries<TCargo, UnbalancedTree>, Standard>
-{
-    typedef Iter<JournalEntries<TCargo, UnbalancedTree>, JournalEntriesIterSpec<UnbalancedTree> > Type;
-};
-
-template <typename TCargo>
-struct Iterator<JournalEntries<TCargo, UnbalancedTree> const, Standard>
-{
-    typedef Iter<JournalEntries<TCargo, UnbalancedTree> const, JournalEntriesIterSpec<UnbalancedTree> > Type;
-};
-
-template <typename TJournalEntries>
-struct Value<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >
-{
-    typedef typename TJournalEntries::TCargo & Type;
-};
-
-template <typename TJournalEntries>
-struct Value<Iter<TJournalEntries const, JournalEntriesIterSpec<UnbalancedTree> > >
-{
-    typedef typename TJournalEntries::TCargo const & Type;
-};
-
-template <typename TJournalEntries>
-struct GetValue<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >
-{
-    typedef typename TJournalEntries::TCargo Type;
-};
-
-template <typename TJournalEntries>
-struct GetValue<Iter<TJournalEntries const, JournalEntriesIterSpec<UnbalancedTree> > >
-{
-    typedef typename TJournalEntries::TCargo Type;
-};
-
-template <typename TJournalEntries>
-struct Reference<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >
-{
-    typedef typename TJournalEntries::TCargo & Type;
-};
-
-template <typename TJournalEntries>
-struct Reference<Iter<TJournalEntries const, JournalEntriesIterSpec<UnbalancedTree> > >
-{
-    typedef typename TJournalEntries::TCargo const & Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// For JournalEntries<TNode, UnbalancedTree>
-
-template <typename TNode>
-inline
-typename Iterator<JournalEntries<TNode, UnbalancedTree> const, Standard>::Type
-begin(JournalEntries<TNode, UnbalancedTree> const & journalTree, Standard const &)
-{
-    SEQAN_CHECKPOINT;
-    return Iter<JournalEntries<TNode, UnbalancedTree> const, JournalEntriesIterSpec<UnbalancedTree> >(journalTree);
-}
-
-template <typename TNode>
-inline
-typename Iterator<JournalEntries<TNode, UnbalancedTree>, Standard>::Type
-begin(JournalEntries<TNode, UnbalancedTree> & journalTree, Standard const &)
-{
-    SEQAN_CHECKPOINT;
-    return Iter<JournalEntries<TNode, UnbalancedTree>, JournalEntriesIterSpec<UnbalancedTree> >(journalTree);
-}
-
-template <typename TNode>
-inline
-typename Iterator<JournalEntries<TNode, UnbalancedTree> const, Standard>::Type
-end(JournalEntries<TNode, UnbalancedTree> const & journalTree, Standard const &)
-{
-    SEQAN_CHECKPOINT;
-    typedef typename Iterator<JournalEntries<TNode, UnbalancedTree> const, Standard>::Type TIterator;
-    TIterator result;
-    result._currentNode = journalTree._root;
-    result._iterationDirection = DIRECTION_UP_RIGHT;
-    return result;
-}
-
-template <typename TNode>
-inline
-typename Iterator<JournalEntries<TNode, UnbalancedTree>, Standard>::Type
-end(JournalEntries<TNode, UnbalancedTree> & journalTree, Standard const &)
-{
-    SEQAN_CHECKPOINT;
-    typedef Iter<JournalEntries<TNode, UnbalancedTree>, JournalEntriesIterSpec<UnbalancedTree> > TIterator;
-    TIterator result;
-    result._currentNode = journalTree._root;
-    result._iterationDirection = DIRECTION_UP_RIGHT;
-    return result;
-}
-
-// For JournalEntriesIterator<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> >
-
-template <typename TJournalEntries>
-inline
-void
-_initJournalEntriesIterator(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator,
-                         TJournalEntries & tree)
-{
-    SEQAN_CHECKPOINT;
-    iterator._currentNode = tree._root;
-    if (tree._root == 0) {
-        iterator._iterationDirection = DIRECTION_UP_RIGHT;
-    } else {
-        iterator._iterationDirection = DIRECTION_DOWN_LEFT;
-        while (goLeft(iterator))
-            continue;  // Left-only traversal.
-    }
-}
-
-// Initialize journal tree iterator to end, i.e. root & direction is up right.
-template <typename TJournalEntries>
-inline
-void
-_initJournalEntriesIteratorEnd(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator,
-                            TJournalEntries & tree)
-{
-    SEQAN_CHECKPOINT;
-    iterator._currentNode = tree._root;
-    iterator._iterationDirection = DIRECTION_UP_RIGHT;
-}
-
-// TODO(holtgrew): Unused, remove?
-/*
-template <typename TJournalEntries>
-inline
-void
-setValue(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator,
-         typename Value<TJournalEntries>::Type const & value)
-{
-    SEQAN_XXXCHECKPOINT;
-    setValue(*iterator._currentNode, value);
-}
-*/
-
-template <typename TJournalEntries>
-inline
-typename Value<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >::Type
-value(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    SEQAN_CHECKPOINT;
-    return cargo(*iterator._currentNode);
-}
-
-template <typename TJournalEntries>
-inline
-typename Value<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >::Type
-value(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & iterator)
-{
-    SEQAN_CHECKPOINT;
-    return cargo(*iterator._currentNode);
-}
-
-// TODO(holtgrew): Unused, remove?
-/*
-template <typename TJournalEntries>
-inline
-typename Value<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >::Type
-operator*(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    SEQAN_XXXCHECKPOINT;
-    return value(iterator);
-}
-*/
-
-// TODO(holtgrew): Unused, remove?
-/*
-template <typename TJournalEntries>
-inline
-typename Value<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >::Type
-operator*(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & iterator)
-{
-    SEQAN_XXXCHECKPOINT;
-    return value(iterator);
-}
-*/
-
-template <typename TJournalEntries>
-inline
-bool
-hasLeftChild(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    SEQAN_CHECKPOINT;
-    return iterator._currentNode->left != 0;
-}
-
-template <typename TJournalEntries>
-inline
-bool
-goLeft(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    SEQAN_CHECKPOINT;
-    if (!hasLeftChild(iterator))
-        return false;
-    iterator._iterationDirection = DIRECTION_DOWN_LEFT;
-    iterator._currentNode = iterator._currentNode->left;
-    return true;
-}
-
-template <typename TJournalEntries>
-inline
-bool
-hasRightChild(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    SEQAN_CHECKPOINT;
-    return iterator._currentNode->right != 0;
-}
-
-template <typename TJournalEntries>
-inline
-bool
-goRight(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    SEQAN_CHECKPOINT;
-    if (!hasRightChild(iterator))
-        return false;
-    iterator._iterationDirection = DIRECTION_DOWN_RIGHT;
-    iterator._currentNode = iterator._currentNode->right;
-    return true;
-}
-
-template <typename TJournalEntries>
-inline
-bool
-hasParent(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & iterator)
-{
-    SEQAN_CHECKPOINT;
-    return iterator._currentNode->parent != 0;
-}
-    
-template <typename TJournalEntries>
-inline
-bool
-goUp(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    if (!hasParent(iterator)) {
-        // Up from the root means we go to end, set direction to up-right.
-        iterator._iterationDirection = DIRECTION_UP_RIGHT;
-        return false;
-    }
-    if (iterator._currentNode->parent->left == iterator._currentNode)
-        iterator._iterationDirection = DIRECTION_UP_LEFT;
-    else
-        iterator._iterationDirection = DIRECTION_UP_RIGHT;
-    iterator._currentNode = iterator._currentNode->parent;
-    return true;
-}
-
-template <typename TJournalEntries>
-inline
-bool
-atEnd(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & iterator)
-{
-    SEQAN_CHECKPOINT;
-    return (iterator._currentNode == 0) || (!hasParent(iterator) && (iterator._iterationDirection == DIRECTION_UP_RIGHT));
-}
-
-template <typename TJournalEntries>
-inline
-bool
-atEnd(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    return (iterator._currentNode == 0) || (!hasParent(iterator) && (iterator._iterationDirection == DIRECTION_UP_RIGHT));
-}
-
-template <typename TJournalEntries>
-inline
-Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > &
-operator++(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    SEQAN_CHECKPOINT;
-    switch (iterator._iterationDirection) {
-        case DIRECTION_DOWN_LEFT:
-        case DIRECTION_DOWN_RIGHT:
-            // Arrived here by going down (either right or left).  Next is
-            // either right-left traversal (if node has a child to the right)
-            // or going up if we do not have a child on the right.
-            if (goRight(iterator)) {
-                while (goLeft(iterator))
-                    continue;
-            } else {
-                while (goUp(iterator) && iterator._iterationDirection == DIRECTION_UP_RIGHT)
-                    continue;
-            }
-            break;
-        case DIRECTION_UP_LEFT:
-            // We came up from our left child.  Next is either right-left
-            // traversal (if node has a child to the right) or going up if
-            // we do not have a child on the left.
-            if (goRight(iterator)) {
-                while (goLeft(iterator))
-                    continue;
-            } else {
-                while (goUp(iterator) && iterator._iterationDirection == DIRECTION_UP_RIGHT)
-                    continue;
-            }
-            break;
-        case DIRECTION_UP_RIGHT:
-            // We came here from our right child.  Next is up until we got
-            // to the current node from it's left child.
-            while (goUp(iterator) && iterator._iterationDirection == DIRECTION_UP_RIGHT)
-                continue;
-            break;
-        default:
-            SEQAN_ASSERT_FAIL("Invalid iteration direction.");
-    }
-        
-    return iterator;    
-}
-
-template <typename TJournalEntries>
-inline
-Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> >
-operator++(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator,
-           int /*postfix*/)
-{
-    SEQAN_CHECKPOINT;
-    Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > temp(iterator);
-    ++iterator;
-    return temp;
-}
-
-template <typename TJournalEntries>
-inline
-Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > &
-operator--(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator)
-{
-    SEQAN_CHECKPOINT;
-    
-    // If we are at the end, go to the last vertex.
-    if (atEnd(iterator)) {
-        while (goRight(iterator))
-            continue;
-        return iterator;
-    }
-    // Otherwise, simply go one step left.
-    
-    // The following comments are from the point of perspective of having
-    // performed an increment in the previous step.
-    switch (iterator._iterationDirection) {
-        case DIRECTION_DOWN_RIGHT:
-        case DIRECTION_DOWN_LEFT:
-        case DIRECTION_UP_RIGHT:
-            // If we have a left child, we first go into the left child and then to the right
-            // until we are in the right most leaf of the left child.
-            if (goLeft(iterator))
-            {
-                while(goRight(iterator))
-                    continue;
-            }
-            else
-            {  // Otherwise we go up the tree until we used the direction up left.
-                while (goUp(iterator) && iterator._iterationDirection == DIRECTION_UP_LEFT)
-                    continue;
-                if (iterator._currentNode->parent == 0)
-                    iterator._iterationDirection = DIRECTION_DOWN_LEFT;
-            }
-            break;
-        case DIRECTION_UP_LEFT:
-            // We came up from our left child.  Next in going to predecessor
-            // is going back to the left child.
-            goLeft(iterator);
-            break;
-        default:
-            SEQAN_ASSERT_FAIL("Invalid iteration direction.");
-    }
-        
-    return iterator;    
-}
-
-template <typename TJournalEntries>
-inline
-Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> >
-operator--(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > & iterator,
-           int /*postfix*/)
-{
-    SEQAN_CHECKPOINT;
-    Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > temp(iterator);
-    --iterator;
-    return temp;
-}
-
-template <typename TJournalEntries>
-inline
-bool
-operator==(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & a,
-           Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & b)
-{
-    SEQAN_CHECKPOINT;
-    return (a._currentNode == b._currentNode) && (a._iterationDirection == b._iterationDirection);
-}
-
-template <typename TJournalEntries>
-inline
-bool
-operator==(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & a,
-           typename IterComplementConst<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >::Type const & b)
-{
-    SEQAN_CHECKPOINT;
-    return (a._currentNode == b._currentNode) && (a._iterationDirection == b._iterationDirection);
-}
-
-template <typename TJournalEntries>
-inline
-bool
-operator!=(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & a,
-           Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & b)
-{
-    SEQAN_CHECKPOINT;
-    return (a._currentNode != b._currentNode) || (a._iterationDirection != b._iterationDirection);
-}
-
-template <typename TJournalEntries>
-inline
-bool
-operator!=(Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > const & a,
-           typename IterComplementConst<Iter<TJournalEntries, JournalEntriesIterSpec<UnbalancedTree> > >::Type const & b)
-{
-    SEQAN_CHECKPOINT;
-    return (a._currentNode != b._currentNode) || (a._iterationDirection != b._iterationDirection);
-}
-
-}  // namespace seqan
-
-#endif  // SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_ITERATOR_H_
diff --git a/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h b/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h
deleted file mode 100644
index 9965f70..0000000
--- a/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h
+++ /dev/null
@@ -1,145 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Code for the node of JournalEntries<UnorderedTree>, i.e. a node of an
-// unbalanced binary search tree.  This could easily be extended to a Red Black
-// Tree with a flag (which could actually be stored in the lowest bits of one
-// of the pointers).  However, since std::set already implements balanced
-// trees, it should be sufficient to use a STL implementation of std::set for
-// balanced binary search trees.
-// ==========================================================================
-
-#ifndef SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_NODE_H_
-#define SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_NODE_H_
-
-namespace seqan {
-
-// ============================================================================
-// Classes
-// ============================================================================
-
-template <typename TCargo>
-struct JournalEntriesUnorderedTreeNode
-{
-    // Left child.
-    JournalEntriesUnorderedTreeNode * left;
-    // Right child.
-    JournalEntriesUnorderedTreeNode * right;
-    // Parent, 0 for root.
-    JournalEntriesUnorderedTreeNode * parent;
-    // The actual payload:  The journal entry.
-    TCargo cargo;
-    
-    JournalEntriesUnorderedTreeNode() : left(0), right(0), parent(0) {}
-
-    JournalEntriesUnorderedTreeNode(TCargo const & _cargo)
-            : left(0),
-              right(0),
-              parent(0),
-              cargo(_cargo) {}
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// TODO(holtgrew): Rename value to cargo?
-
-template <typename T>
-struct Cargo;
-
-template <typename TCargo>
-struct Cargo<JournalEntriesUnorderedTreeNode<TCargo> >
-{
-    typedef TCargo Type;
-};
-
-template <typename TCargo>
-struct Cargo<JournalEntriesUnorderedTreeNode<TCargo> const>
-{
-    typedef TCargo const Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-template <typename TStream, typename TCargo>
-TStream & operator<<(TStream & stream, JournalEntriesUnorderedTreeNode<TCargo> const & node)
-{
-    stream << "JournalEntriesUnorderedTreeNode(add=" << &node
-           << ", cargo=" << node.cargo
-           << ", parent=" << node.parent
-           << ", left=";
-    if (node.left)
-        stream << *node.left;
-    else
-        stream << "NULL";
-    stream << ", right=";
-    if (node.right)
-        stream << *node.right;
-    else
-        stream << "NULL";
-    return stream << ")";
-}
-
-template <typename TCargo>
-typename Cargo<JournalEntriesUnorderedTreeNode<TCargo> >::Type &
-cargo(JournalEntriesUnorderedTreeNode<TCargo> & node)
-{
-    SEQAN_CHECKPOINT;
-    return node.cargo;
-}
-
-// TODO(holtgrew): Unused, remove?
-/*
-template <typename TCargo>
-typename Cargo<JournalEntriesUnorderedTreeNode<TCargo> const>::Type &
-cargo(JournalEntriesUnorderedTreeNode<TCargo> const & node)
-{
-    SEQAN_XXXCHECKPOINT;
-    return node.cargo;
-}
-
-template <typename TCargo>
-typename Cargo<JournalEntriesUnorderedTreeNode<TCargo> const>::Type
-getCargo(JournalEntriesUnorderedTreeNode<TCargo> const & node)
-{
-    SEQAN_XXXCHECKPOINT;
-    return node.cargo;
-}
-*/
-
-}  // namespace seqan
-
-#endif  // SEQAN_SEQUENCE_JOURNALED_JOURNAL_ENTRIES_UNBALANCED_TREE_NODE_H_
diff --git a/seqan/sequence_journaled/journal_entry.h b/seqan/sequence_journaled/journal_entry.h
index 5d46fc4..83409e6 100644
--- a/seqan/sequence_journaled/journal_entry.h
+++ b/seqan/sequence_journaled/journal_entry.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/sequence_journaled/sequence_journaled.h b/seqan/sequence_journaled/sequence_journaled.h
index 472400e..6b89544 100644
--- a/seqan/sequence_journaled/sequence_journaled.h
+++ b/seqan/sequence_journaled/sequence_journaled.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -59,23 +59,15 @@ namespace seqan {
  * @headerfile <seqan/sequence_journaled.h>
  * @brief Journaled versions of arbitrary underlying strings.
  *
- * @signature <typename THostSpec[, typename TJournalSpec[, typename TBufferSpec]]>
- *            class String<Journaled<THostSpec, TJournalSpec, TBufferSpec> >;
+ * @signature template <typename TValue, typename THostSpec[, typename TJournalSpec[, typename TBufferSpec]]>
+ *            class String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >;
  *
+ * @tparam TValue       The element type of the string.
  * @tparam THostSpec    Specialization type for the host string.
  * @tparam TJournalSpec Specialization type for the journal.  Default: <tt>SortedArray</tt>.
  * @tparam TBufferSpec  Specialization type for the buffer string.  Default: <tt>Alloc&lt;&gt;</tt>.
  */
 
-/**
-.Spec.Journaled String
-..cat:Sequences
-..general:Class.String
-..summary:Journaled versions of arbitrary underlying string.
-..signature:String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >
-..include:seqan/sequence_journaled.h
- */
-
 template <typename THostSpec, typename TJournalSpec = SortedArray, typename TBufferSpec = Alloc<void> >
 struct Journaled {};
 
@@ -84,13 +76,13 @@ class String<TValue_, Journaled<THostSpec_, TJournalSpec_, TBufferSpec_> >
 {
 public:
     typedef String<TValue_, Journaled<THostSpec_, TJournalSpec_, TBufferSpec_> > TThis_;
-    
+
     typedef TValue_ TValue;
     typedef THostSpec_ THostSpec;
     typedef TJournalSpec_ TJournalSpec;
     typedef TBufferSpec_ TBufferSpec;
 
-    typedef String<TValue, THostSpec> THost;
+    typedef typename Host<TThis_>::Type THost;
     typedef typename Size<THost>::Type TSize;
     typedef typename Position<THost>::Type TPosition;
     typedef String<TValue, TBufferSpec> TInsertionBuffer;
@@ -108,34 +100,31 @@ class String<TValue_, Journaled<THostSpec_, TJournalSpec_, TBufferSpec_> >
     // The journaled string's size.
     TSize _length;
 
-    String() {
-        SEQAN_CHECKPOINT;
-    }
+    String() : _length(0)
+    {}
 
     // Note: Defining both, constructors from same type and other for clarity.
-    
-    String(THost & host)
+
+    String(THost & host) : _length(0)
     {
         SEQAN_CHECKPOINT;
         setHost(*this, host);
     }
 
-    String(String const & other)
+    String(String const & other) : _length(0)
     {
         SEQAN_CHECKPOINT;
         set(*this, other);
     }
 
     template <typename TString>
-	String(TString const & other)
+    String(TString const & other) : _length(0)
     {
         SEQAN_CHECKPOINT;
         assign(*this, other);
     }
 
-    inline
-    String &
-    operator=(String const & other)
+    String & operator=(String const & other)
     {
         if (this != &other)
             set(*this, other);
@@ -143,16 +132,13 @@ class String<TValue_, Journaled<THostSpec_, TJournalSpec_, TBufferSpec_> >
     }
 
     template <typename TString>
-    inline
-    String &
-    operator=(TString const & other)
+    String & operator=(TString const & other)
     {
         SEQAN_CHECKPOINT;
         assign(*this, other);
         return *this;
     }
 
-    inline
     typename Reference<String>::Type
     operator[](TPosition pos)
     {
@@ -160,7 +146,6 @@ class String<TValue_, Journaled<THostSpec_, TJournalSpec_, TBufferSpec_> >
         return value(*this, pos);
     }
 
-    inline
     typename Reference<String const>::Type
     operator[](TPosition pos) const
     {
@@ -173,6 +158,26 @@ class String<TValue_, Journaled<THostSpec_, TJournalSpec_, TBufferSpec_> >
 // Metafunctions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Metafunction StringSpec
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
+struct Spec<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >
+{
+    typedef TJournalSpec Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction StringSpec
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
+struct StringSpec<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >
+{
+    typedef TBufferSpec Type;
+};
+
 // ----------------------------------------------------------------------------
 // Metafunction Host
 // ----------------------------------------------------------------------------
@@ -188,12 +193,6 @@ class String<TValue_, Journaled<THostSpec_, TJournalSpec_, TBufferSpec_> >
  * @return Type The host type.
  */
 
-/**
-.Metafunction.Host
-..param.T.type:Spec.Journaled String
-..class:Spec.Journaled String
-*/
-
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 struct Host<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >
 {
@@ -221,16 +220,6 @@ struct Host<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > con
  * @return Type The insertion buffer type.
  */
 
-/**
-.Metafunction.InsertionBuffer
-..cat:Sequences
-..summary:Return type of insertion buffer string for a journaled string.
-..class:Spec.Journaled String
-..signature:InsertionBuffer<T>::Type
-..param.T:The journaled string to get the insertion buffer type for.
-...type:Spec.Journaled String
-..include:sequan/sequence_journal.h
-*/
 template <typename T>
 struct InsertionBuffer;
 
@@ -250,8 +239,6 @@ struct InsertionBuffer<String<TValue, Journaled<THostSpec, TJournalSpec, TBuffer
 // Metafunction Size
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Size.param.T.type:Spec.Journaled String
-///.Metafunction.Size.class:Spec.Journaled String
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 struct Size<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >
 {
@@ -266,8 +253,6 @@ struct Size<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > con
 // Metafunction Position
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Position.param.T.type:Spec.Journaled String
-///.Metafunction.Position.class:Spec.Journaled String
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 struct Position<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >
 {
@@ -282,8 +267,6 @@ struct Position<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >
 // Metafunction Reference
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Reference.param.T.type:Spec.Journaled String
-///.Metafunction.Reference.class:Spec.Journaled String
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 struct Reference<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >
 {
@@ -306,8 +289,6 @@ struct Reference<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec>
 // Metafunction GetValue
 // ----------------------------------------------------------------------------
 
-///.Metafunction.GetValue.param.T.type:Spec.Journaled String
-///.Metafunction.GetValue.class:Spec.Journaled String
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 struct GetValue<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >
 {
@@ -325,8 +306,6 @@ struct GetValue<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >
 // ----------------------------------------------------------------------------
 
 // TODO(holtgrew): Does Value have to be overwritten? Is not for packed strings!
-///.Metafunction.Value.param.T.type:Spec.Journaled String
-///.Metafunction.Value.class:Spec.Journaled String
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 struct Value<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >
 {
@@ -354,16 +333,6 @@ struct Value<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > co
  * @return Type the journal type.
  */
 
-/**
-.Metafunction.JournalType
-..cat:Sequences
-..summary:Metafunction for returning the type of the journal of a Journaled String.
-..signature:JournalType<T>::Type
-..class:Spec.Journaled String
-..param.T:The journaled string to get the journal type for.
-...type:Spec.Journaled String
-..include:seqan/string_journaled.h
- */
 template <typename T>
 struct JournalType;
 
@@ -387,6 +356,20 @@ struct JournalType<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec
 // Functions
 // ============================================================================
 
+// ----------------------------------------------------------------------------
+// Function empty()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
+inline bool
+empty(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const & target)
+{
+    if (empty(target._holder) || empty(target._journalEntries))
+        return true;
+
+    return begin(target, Standard()) == end(target, Standard());
+}
+
 // ----------------------------------------------------------------------------
 // Function operator<<
 // ----------------------------------------------------------------------------
@@ -400,7 +383,7 @@ operator<<(TStream & stream, String<TValue, Journaled<THostSpec, TJournalSpec, T
     typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > TString;
     typedef typename TString::TJournalEntries TJournalEntries;
     typedef typename Iterator<TJournalEntries const, Standard>::Type TIterator;
-    
+
     for (TIterator it = begin(s._journalEntries), itend = end(s._journalEntries); it != itend; ++it) {
         if (value(it).segmentSource == SOURCE_ORIGINAL) {
             stream << infix(value(s._holder), value(it).physicalPosition, value(it).physicalPosition + value(it).length);
@@ -434,7 +417,7 @@ assign(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & target
        String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const & source)
 {
     typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > TTarget;
-    assign(target, source, DefaultOverflowImplicit<TTarget>::Type());
+    assign(target, source, typename DefaultOverflowImplicit<TTarget>::Type());
 }
 
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec,
@@ -528,17 +511,22 @@ set(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & target,
  *
  * @signature void setHost(js, str);
  *
- * @param js  The JournaledString to set the host for.
- * @param str The string to set as the host.
+ * @param[in,out] js  The JournaledString to set the host for.
+ * @param[in]     str The string to set as the host.
  */
 
-/**
-.Function.setHost:
-..class:Spec.Journaled String
-..param.object.type:Spec.Journaled String
-..param.host.type:Class.String
-..include:seqan/sequence_journaled.h
-*/
+#ifdef SEQAN_CXX11_STANDARD
+template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec, typename TSequence2>
+inline
+void
+setHost(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & journaledString,
+        TSequence2 && str)
+{
+    setValue(journaledString._holder, str);
+    journaledString._length = length(str);
+    reinit(journaledString._journalEntries, length(str));
+}
+#else
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec, typename TSequence2>
 inline
 void
@@ -549,6 +537,7 @@ setHost(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & journ
     journaledString._length = length(str);
     reinit(journaledString._journalEntries, length(str));
 }
+#endif  // SEQAN_CXX11_STANDARD
 
 // ----------------------------------------------------------------------------
 // Function host
@@ -565,12 +554,6 @@ setHost(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & journ
  * @return THost Reference to the host of <tt>js</tt>.
  */
 
-/**
-.Function.host:
-..class:Spec.Journaled String
-..param.object.type:Spec.Journaled String
-..include:seqan/sequence_journaled.h
-*/
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 inline
 typename Host<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >::Type &
@@ -602,12 +585,6 @@ host(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const & jo
  * @param[in,out] js The JournaledString to clear.
  */
 
-/**
-.Function.clear:
-..class:Spec.Journaled String
-..param.object.type:Spec.Journaled String
-..include:seqan/sequence_journaled.h
- */
 // TODO(holtgrew): Behaviour is to clear the journal, not the string!
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 inline void
@@ -644,20 +621,9 @@ reset(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & journal
  * @signature void flatten(js);
  *
  * @param[in,out] js The JournaledString to flatten.
- */ 
-
-/**
-.Function.flatten:
-..class:Spec.Journaled String  
-..cat:Sequences
-..summary:Apply the journal to the underlying string, destructively on the underlying string.
-..signature:flatten(journaledString)
-..param.journaledString:The journaled string to flatten.
-...type:Spec.Journaled String
-..include:seqan/sequence_journaled.h
  */
+
 // TODO(holtgrew): What about non-destructive version that creates a new copy and sets holder to it?
-// TODO(rmaerker): Only supported by SortedArray, since there is a bug in the UnbalancedTree iterator. Is not fixed since UT is deprecated.
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 inline void
 flatten(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & journaledString)
@@ -710,8 +676,8 @@ erase(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & journal
       TEndPos posEnd)
 {
     SEQAN_CHECKPOINT;
-	SEQAN_ASSERT_GEQ(static_cast<TBeginPos>(journaledString._length), pos);
-	SEQAN_ASSERT_GEQ(static_cast<TEndPos>(journaledString._length), posEnd);
+    SEQAN_ASSERT_GEQ(static_cast<TBeginPos>(journaledString._length), pos);
+    SEQAN_ASSERT_GEQ(static_cast<TEndPos>(journaledString._length), posEnd);
     SEQAN_ASSERT_GEQ(static_cast<TBeginPos>(journaledString._length), static_cast<TBeginPos>(posEnd - pos));
     journaledString._length -= posEnd - pos;
     recordErase(journaledString._journalEntries, pos, posEnd);
@@ -870,24 +836,24 @@ length(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const &
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec, typename TPos>
 inline
 typename Reference<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >::Type
-value(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & me, 
+value(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & me,
       TPos pos)
 {
     SEQAN_CHECKPOINT;
-    
+
     return *iter(me, pos, Standard());
-} 
+}
 
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec, typename TPos>
 inline
 typename Reference<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const>::Type
-value(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const & me, 
+value(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const & me,
       TPos pos)
 {
     SEQAN_CHECKPOINT;
-    
+
     return *iter(me, pos, Standard());
-} 
+}
 
 
 // TODO(holtgrew): Maybe better use template parameter TPos?
@@ -934,24 +900,12 @@ getValue(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const
  *
  * @signature TPos virtualToHostPosition(js, pos);
  *
- * @param js  The JournaledString to translate the position for.
- * @param pos The virtual position to translate.
+ * @param[in] js  The JournaledString to translate the position for.
+ * @param[in] pos The virtual position to translate.
  *
  * @return TPos Position in the host.
  */
 
-/**
-.Function.Journaled String#virtualToHostPosition
-..class:Spec.Journaled String
-..summary:Translates virtual (view) position to position in host.
-..signature:virtualToHostPosition(journaledString, pos)
-..param.journaledString:The journaled string to translate for.
-...type:Spec.Journaled String
-..param.pos:The position to translate.
-..returns:Corresponding host position.
-...type:Metafunction.Position
-*/
-
 // Note that if pos is in a gap, we return the position of the entry
 // after the gap in the host.
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec, typename TPos>
@@ -973,34 +927,24 @@ virtualToHostPosition(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferS
  * @fn JournaledString#hostToVirtualPosition
  * @brief Translates host position to virtual position.
  *
- * @signature TPos virtualToHostPosition(js, pos);
+ * @signature TPos hostToVirtualPosition(js, pos);
  *
- * @param js  The JournaledString to translate the position for.
- * @param pos The host position to translate.
+ * @param[in] js  The JournaledString to translate the position for.
+ * @param[in] pos The host position to translate.
  *
- * @return TPos The virtual view position.
+ * @return TPos The virtual view position. Note the returned position equates to length of the journaled string
+ * if <tt>pos</tt> is greater or equal the length of the underlying host.
  */
 
-/**
-.Function.Journaled String#hostToVirtualPosition
-..class:Spec.Journaled String
-..summary:Translates position in host to virtual (view) position.
-..signature:hostToVirtualPosition(journaledString, pos)
-..param.journaledString:The journaled string to translate for.
-...type:Spec.Journaled String
-..param.pos:The position to translate.
-..returns:Corresponding virtual (view) position.
-...type:Metafunction.Position
-*/
-
 template<typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec, typename TPos>
 inline
 typename Position<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > >::Type
 hostToVirtualPosition(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const & journalString,
                       TPos const & pos)
 {
-    SEQAN_ASSERT_LEQ(pos, (TPos) length(host(journalString)));
-    return hostToVirtualPosition(journalString._journalEntries, pos);
+    if (pos < (TPos) length(host(journalString)))
+        return hostToVirtualPosition(journalString._journalEntries, pos);
+    return length(journalString);
 }
 
 // --------------------------------------------------------------------------
@@ -1146,64 +1090,63 @@ getObjectId(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > con
 // Function isFlat()
 // --------------------------------------------------------------------------
 
-/**
-.Function.Journaled String#isFlat
-..class:Spec.Journaled String
-..cat:Sequences
-..summary:Returns whether journaled string has modifications.
-..signature:isFlat(journaledString)
-..param.journaledString:The journaled string to query.
-...type:Spec.Journaled String
-..returns:$bool$ indicating whether the string has been modfieid.
-*/
+/*!
+ * @fn JournaledString#isFlat
+ * @brief Returns whether a JournaledString has modifications.
+ * @signature bool isFlat(js);
+ *
+ * @param[in] js The JournaledString to query.
+ *
+ * @return bool Indicates whether the string has been modified.
+ */
 
 // TODO(holtgrew): Is the non-const version necessary?
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
 inline bool
 isFlat(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & journaledString)
 {
-	SEQAN_CHECKPOINT;
-	typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;
-	typedef typename JournalType<TJournalString>::Type TJournalEntries;
-	typedef typename Iterator<TJournalEntries const, Standard>::Type TIteraror;
-
-	TIteraror it = begin(journaledString._journalEntries);
-	if ((*it).segmentSource == SOURCE_ORIGINAL)
-	{
-		if (((*it).physicalPosition == (*it).virtualPosition) && ((*it).length == length(host(journaledString))))
-		{
-			return true;
-		}
-	}
-	return false;
+    SEQAN_CHECKPOINT;
+    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;
+    typedef typename JournalType<TJournalString>::Type TJournalEntries;
+    typedef typename Iterator<TJournalEntries const, Standard>::Type TIteraror;
+
+    TIteraror it = begin(journaledString._journalEntries);
+    if ((*it).segmentSource == SOURCE_ORIGINAL)
+    {
+        if (((*it).physicalPosition == (*it).virtualPosition) && ((*it).length == length(host(journaledString))))
+        {
+            return true;
+        }
+    }
+    return false;
 }
 
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
 inline bool
 isFlat(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > const & journaledString)
 {
-	SEQAN_CHECKPOINT;
-	typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;
-	typedef typename JournalType<TJournalString>::Type TJournalEntries;
-	typedef typename Iterator<TJournalEntries const, Standard>::Type TIteraror;
-
-	TIteraror it = begin(journaledString._journalEntries);
-	if ((*it).segmentSource == SOURCE_ORIGINAL)
-	{
-		if (((*it).physicalPosition == (*it).virtualPosition) && ((*it).length == length(host(journaledString))))
-		{
-			return true;
-		}
-	}
-	return false;
+    SEQAN_CHECKPOINT;
+    typedef String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > TJournalString;
+    typedef typename JournalType<TJournalString>::Type TJournalEntries;
+    typedef typename Iterator<TJournalEntries const, Standard>::Type TIteraror;
+
+    TIteraror it = begin(journaledString._journalEntries);
+    if ((*it).segmentSource == SOURCE_ORIGINAL)
+    {
+        if (((*it).physicalPosition == (*it).virtualPosition) && ((*it).length == length(host(journaledString))))
+        {
+            return true;
+        }
+    }
+    return false;
 }
 
 // template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBuffSpec>
 // void
 // _deallocateStorage(String<TValue, Journaled<THostSpec, TJournalSpec, TBuffSpec> > & string,
-//				   size_t const & newCapacity)
+//                   size_t const & newCapacity)
 // {
-//	std::cout << "Now he is here but does not actually delete the contents." << std::endl;
+//    std::cout << "Now he is here but does not actually delete the contents." << std::endl;
 // }
 
 }  // namespace seqan
diff --git a/seqan/sequence_journaled/sequence_journaled_iterator.h b/seqan/sequence_journaled/sequence_journaled_iterator.h
index dcb4534..570f223 100644
--- a/seqan/sequence_journaled/sequence_journaled_iterator.h
+++ b/seqan/sequence_journaled/sequence_journaled_iterator.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -43,6 +43,9 @@ namespace seqan {
 // Tags, Classes
 // ============================================================================
 
+struct CommonSegmentIterator_;
+typedef Tag<CommonSegmentIterator_> CommonSegmentIterator;
+
 template <typename TJournaledStringSpec>
 struct JournaledStringIterSpec;
 
@@ -51,7 +54,6 @@ class Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> >
 {
 public:
     typedef Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > TIterator;
-    typedef typename TJournaledString::TValue TValue;
     typedef typename JournalType<TJournaledString>::Type TJournalEntries;
     // We need a rooted iterator for iterating the journal tree since we need atEnd().
     typedef typename Iterator<TJournalEntries, Standard>::Type TJournalEntriesIterator;
@@ -148,6 +150,13 @@ class Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> >
     }
 };
 
+// Implement concept
+template <typename TJournaledString, typename TJournalSpec>
+SEQAN_CONCEPT_IMPL((Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const), (RootedRandomAccessIteratorConcept));
+
+template <typename TJournaledString, typename TJournalSpec>
+SEQAN_CONCEPT_IMPL((Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> >), (MutableRootedRandomAccessIteratorConcept));
+
 // ============================================================================
 // Metafunctions
 // ============================================================================
@@ -158,7 +167,6 @@ class Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> >
 // Metafunction Iterator                                             [Standard]
 // ----------------------------------------------------------------------------
 
-///.Metafunction.Iterator.param.T:Spec.Journal String
 template <typename TValue, typename THostSpec, typename TJournalSpec, typename TBufferSpec>
 struct Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >, Standard>
 {
@@ -171,6 +179,22 @@ struct Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >
     typedef Iter<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const, JournaledStringIterSpec<TJournalSpec> > Type;
 };
 
+// ----------------------------------------------------------------------------
+// Metafunction Iterator                      [Standard, CommonSegmentIterator]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec>
+struct Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, THostSpec> >, Standard>
+{
+    typedef Iter<String<TValue, Journaled<THostSpec, TJournalSpec, THostSpec> >, JournaledStringIterSpec<CommonSegmentIterator> > Type;
+};
+
+template <typename TValue, typename THostSpec, typename TJournalSpec>
+struct Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, THostSpec> > const, Standard>
+{
+    typedef Iter<String<TValue, Journaled<THostSpec, TJournalSpec, THostSpec> > const, JournaledStringIterSpec<CommonSegmentIterator> > Type;
+};
+
 // ----------------------------------------------------------------------------
 // Metafunction Iterator                                               [Rooted]
 // ----------------------------------------------------------------------------
@@ -187,6 +211,22 @@ struct Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >
     typedef Iter<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const, JournaledStringIterSpec<TJournalSpec> > Type;
 };
 
+// ----------------------------------------------------------------------------
+// Metafunction Iterator                        [Rooted, CommonSegmentIterator]
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename THostSpec, typename TJournalSpec>
+struct Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, THostSpec> >, Rooted>
+{
+    typedef Iter<String<TValue, Journaled<THostSpec, TJournalSpec, THostSpec> >, JournaledStringIterSpec<CommonSegmentIterator> > Type;
+};
+
+template <typename TValue, typename THostSpec, typename TJournalSpec>
+struct Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, THostSpec> > const, Rooted>
+{
+    typedef Iter<String<TValue, Journaled<THostSpec, TJournalSpec, THostSpec> > const, JournaledStringIterSpec<CommonSegmentIterator> > Type;
+};
+
 // ----------------------------------------------------------------------------
 // Metafunction Value
 // ----------------------------------------------------------------------------
@@ -320,7 +360,8 @@ end(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const & jou
 {
     typedef typename Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const, Standard>::Type TResult;
     TResult result;
-    _initJournaledStringIteratorEnd(result, journalString);
+    result._journalStringPtr = &journalString;
+    _initJournaledStringIteratorEnd(result);
     return result;
 }
 
@@ -331,7 +372,8 @@ end(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & journalSt
 {
     typedef typename Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >, Standard>::Type TResult;
     TResult result;
-    _initJournaledStringIteratorEnd(result, journalString);
+    result._journalStringPtr = &journalString;
+    _initJournaledStringIteratorEnd(result);
     return result;
 }
 
@@ -346,7 +388,8 @@ end(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const & jou
 {
     typedef typename Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > const, Rooted>::Type TResult;
     TResult result;
-    _initJournaledStringIteratorEnd(result, journalString);
+    result._journalStringPtr = &journalString;
+    _initJournaledStringIteratorEnd(result);
     return result;
 }
 
@@ -357,10 +400,14 @@ end(String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> > & journalSt
 {
     typedef typename Iterator<String<TValue, Journaled<THostSpec, TJournalSpec, TBufferSpec> >, Rooted>::Type TResult;
     TResult result;
-    _initJournaledStringIteratorEnd(result, journalString);
+    result._journalStringPtr = &journalString;
+    _initJournaledStringIteratorEnd(result);
     return result;
 }
 
+// ----------------------------------------------------------------------------
+// Function _initJournaledStringIterator()
+// ----------------------------------------------------------------------------
 
 // For Iter<TJournaledString, JournaledStringIterSpec>
 
@@ -377,15 +424,22 @@ _initJournaledStringIterator(Iter<TJournaledString, JournaledStringIterSpec<TJou
     _updateSegmentIterators(iterator);
 }
 
+// ----------------------------------------------------------------------------
+// Function _initJournaledStringIteratorEnd()
+// ----------------------------------------------------------------------------
+
 template <typename TJournaledString, typename TJournalSpec>
 inline
 void
-_initJournaledStringIteratorEnd(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > & iterator,
-                              TJournaledString & journalString)
+_initJournaledStringIteratorEnd(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > & iterator)
 {
     SEQAN_CHECKPOINT;
-    iterator._journalStringPtr = &journalString;
-    iterator._journalEntriesIterator = end(journalString._journalEntries);
+    iterator._journalEntriesIterator = end(iterator._journalStringPtr->_journalEntries, Standard()) - 1;
+    _updateSegmentIteratorsLeft(iterator);
+    if (value(iterator._journalEntriesIterator).segmentSource == SOURCE_PATCH)
+        ++iterator._currentInsertionBufferIt;
+    else
+        ++iterator._currentHostIt;
 }
 
 // TODO(rmaerker): Rename to _updateSegmentIteratorsRight().
@@ -396,7 +450,10 @@ _updateSegmentIterators(Iter<TJournaledString, JournaledStringIterSpec<TJournalS
 {
     SEQAN_CHECKPOINT;
     if (atEnd(iterator._journalEntriesIterator, _journalEntries(container(iterator))))
+    {
+        _initJournaledStringIteratorEnd(iterator);
         return;
+    }
     switch (value(iterator._journalEntriesIterator).segmentSource) {
         case SOURCE_ORIGINAL:
             iterator._hostSegmentBegin = begin(host(*iterator._journalStringPtr), Standard()) + value(iterator._journalEntriesIterator).physicalPosition;
@@ -439,6 +496,10 @@ _updateSegmentIteratorsLeft(Iter<TJournaledString, JournaledStringIterSpec<TJour
     }
 }
 
+// ----------------------------------------------------------------------------
+// Function value()
+// ----------------------------------------------------------------------------
+
 template <typename TJournaledString, typename TJournalSpec>
 inline typename Reference<Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > >::Type
 value(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > & me)
@@ -588,19 +649,16 @@ valueDestruct(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > con
 }
 
 // ----------------------------------------------------------------------------
-// Function entryPosition
+// Function _localEntryPosition
 // ----------------------------------------------------------------------------
 
 // TODO(rmaerker): Write documentation!
 template <typename TJournaledString, typename TJournalSpec>
 inline typename Position<Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const>::Type
-entryPosition(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & iterator)
+_localEntryPosition(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & iterator)
 {
-    if (atEnd(iterator._journalEntriesIterator)) {
-        return length(*iterator._journalStringPtr);
-    }
-
-    switch (value(iterator._journalEntriesIterator).segmentSource) {
+    switch (value(iterator._journalEntriesIterator).segmentSource)
+    {
         case SOURCE_ORIGINAL:
             return iterator._currentHostIt - iterator._hostSegmentBegin;
             break;
@@ -614,28 +672,68 @@ entryPosition(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > con
 }
 
 // ----------------------------------------------------------------------------
-// Function position()
+// Function _physicalPosition()
 // ----------------------------------------------------------------------------
 
-// TODO(rmaerker): Write documentation!
 template <typename TJournaledString, typename TJournalSpec>
 inline typename Position<Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const>::Type
-position(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & iterator)
+_physicalPosition(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & iterator)
 {
-    if (atEnd(iterator._journalEntriesIterator, _journalEntries(container(iterator))))
-        return length(*iterator._journalStringPtr);
+    return value(iterator._journalEntriesIterator).physicalPosition + _localEntryPosition(iterator);
+}
 
-    switch (value(iterator._journalEntriesIterator).segmentSource) {
-        case SOURCE_ORIGINAL:
-            return value(iterator._journalEntriesIterator).virtualPosition + iterator._currentHostIt - iterator._hostSegmentBegin;
-            break;
-        case SOURCE_PATCH:
-            return value(iterator._journalEntriesIterator).virtualPosition + iterator._currentInsertionBufferIt - iterator._insertionBufferSegmentBegin;
+// ----------------------------------------------------------------------------
+// Function _physicalOriginPosition()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString, typename TJournalSpec>
+inline typename Position<Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const>::Type
+_physicalOriginPosition(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & iterator)
+{
+    typedef Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const TJournalIter;
+    typedef typename TJournalIter::TJournalEntriesIterator TEntriesIt;
+
+    if (value(iterator._journalEntriesIterator).segmentSource == SOURCE_ORIGINAL)
+        return value(iterator._journalEntriesIterator).physicalOriginPosition + _localEntryPosition(iterator);
+
+    SEQAN_ASSERT_EQ(value(iterator._journalEntriesIterator).segmentSource, SOURCE_PATCH);
+
+    TEntriesIt tmp = iterator._journalEntriesIterator;
+    while (value(tmp).segmentSource == SOURCE_PATCH)
+    {
+        if (tmp == begin(_journalEntries(*iterator._journalStringPtr), Standard()))
+        {
+            if (value(tmp).segmentSource == SOURCE_PATCH)
+                return 0;
             break;
-        default:
-            SEQAN_ASSERT_FAIL("Invalid segment source!");
-            return 0;
+        }
+        --tmp;
     }
+    SEQAN_ASSERT_EQ(tmp->segmentSource, SOURCE_ORIGINAL);
+    return value(tmp).physicalOriginPosition + value(tmp).length;
+
+}
+
+// ----------------------------------------------------------------------------
+// Function _virtualPosition()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString, typename TJournalSpec>
+inline typename Position<Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const>::Type
+_virtualPosition(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & iterator)
+{
+    return value(iterator._journalEntriesIterator).virtualPosition + _localEntryPosition(iterator);
+}
+
+// ----------------------------------------------------------------------------
+// Function position()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString, typename TJournalSpec>
+inline typename Position<Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const>::Type
+position(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & iterator)
+{
+    return _virtualPosition(iterator);
 }
 
 // ----------------------------------------------------------------------------
@@ -783,13 +881,6 @@ inline
 Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > &
 operator--(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > & iterator)
 {
-    if (atEnd(iterator._journalEntriesIterator, _journalEntries(container(iterator))))
-    {
-        --iterator._journalEntriesIterator;
-        _updateSegmentIteratorsLeft(iterator);
-    }
-    else
-    {
         switch (value(iterator._journalEntriesIterator).segmentSource) {
             case SOURCE_ORIGINAL:
                 if (iterator._currentHostIt == iterator._hostSegmentBegin) {
@@ -812,7 +903,6 @@ operator--(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > & iter
                 SEQAN_ASSERT_FAIL("Invalid segment source!");
             }
         }
-    }
     return iterator;
 }
 
@@ -857,49 +947,32 @@ operator+=(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > & iter
 {
     SEQAN_CHECKPOINT;
 
-    typedef Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > TIterator;
-
-    // TODO(holtgrew): Handle case where len_ < 0?!
     SEQAN_ASSERT_GEQ(len_, static_cast<TLen>(0));
-    size_t len = len_;
-
-    // Handle bad case of len_ pointing at/behind end.
-    if (position(iterator) + len_ >= length(*iterator._journalStringPtr)) {
-        iterator = TIterator(end(*iterator._journalStringPtr));
-        return iterator;
-    }
 
-    // Handle other case.
-    typedef typename Size<TJournaledString>::Type TSize;
-    while (len > 0) {
-        TSize remaining;
-        switch (value(iterator._journalEntriesIterator).segmentSource) {
-            case SOURCE_ORIGINAL:
+    TLen remaining;
+    if (value(iterator._journalEntriesIterator).segmentSource == SOURCE_ORIGINAL)
+        remaining = iterator._hostSegmentEnd - iterator._currentHostIt;
+    else
+        remaining = iterator._insertionBufferSegmentEnd - iterator._currentInsertionBufferIt;
+    while (len_ > 0 && remaining != 0)
+    {
+        SEQAN_ASSERT_GT(remaining, static_cast<TLen>(0));
+        if (len_ >= remaining) {
+            len_ -= remaining;
+            ++iterator._journalEntriesIterator;
+            _updateSegmentIterators(iterator);
+            if (value(iterator._journalEntriesIterator).segmentSource == SOURCE_ORIGINAL)
                 remaining = iterator._hostSegmentEnd - iterator._currentHostIt;
-                SEQAN_ASSERT_GT(remaining, 0u);
-                if (len >= remaining) {
-                    len -= remaining;
-                    ++iterator._journalEntriesIterator;
-                    _updateSegmentIterators(iterator);
-                } else {
-                    iterator._currentHostIt += len;
-                    len = 0;
-                }
-                break;
-            case SOURCE_PATCH:
+            else
                 remaining = iterator._insertionBufferSegmentEnd - iterator._currentInsertionBufferIt;
-                SEQAN_ASSERT_GT(remaining, 0u);
-                if (len >= remaining) {
-                    len -= remaining;
-                    ++iterator._journalEntriesIterator;
-                    _updateSegmentIterators(iterator);
-                } else {
-                    iterator._currentInsertionBufferIt += len;
-                    len = 0;
-                }
-                break;
-            default:
-                SEQAN_ASSERT_FAIL("Invalid segment source!");
+        }
+        else
+        {
+            if (value(iterator._journalEntriesIterator).segmentSource == SOURCE_ORIGINAL)
+                iterator._currentHostIt += len_;
+            else
+                iterator._currentInsertionBufferIt += len_;
+            len_ = 0;
         }
     }
     return iterator;
@@ -940,14 +1013,6 @@ operator-=(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > & iter
         return iterator;
     }
 
-    // Handle case when iterator is at positon at end
-    if (atEnd(iterator._journalEntriesIterator, _journalEntries(container(iterator))))
-    {
-        --iterator._journalEntriesIterator;
-        _updateSegmentIteratorsLeft(iterator);
-        --len;
-    }
-
     // Handle other case.
     typedef typename Size<TJournaledString>::Type TSize;
     while (len > 0) {
@@ -1079,9 +1144,6 @@ bool
 operator==(Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & a,
            Iter<TJournaledString, JournaledStringIterSpec<TJournalSpec> > const & b)
 {
-    SEQAN_CHECKPOINT;
-    if (atEnd(a._journalEntriesIterator, _journalEntries(container(a))) && atEnd(b._journalEntriesIterator, _journalEntries(container(b))))
-        return true;
     if (a._journalEntriesIterator != b._journalEntriesIterator)
         return false;
     if (value(a._journalEntriesIterator).segmentSource == SOURCE_ORIGINAL) {
diff --git a/seqan/sequence_journaled/sequence_journaled_iterator_fast.h b/seqan/sequence_journaled/sequence_journaled_iterator_fast.h
new file mode 100644
index 0000000..280018a
--- /dev/null
+++ b/seqan/sequence_journaled/sequence_journaled_iterator_fast.h
@@ -0,0 +1,384 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Rene Rahn <rene.rahn@fu-berlin.de>
+// ==========================================================================
+// Implements a fast version of the iterator over journal strings.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_SEQUENCE_JOURNALED_SEQUENCE_JOURNALED_ITERATOR_FAST_H_
+#define INCLUDE_SEQAN_SEQUENCE_JOURNALED_SEQUENCE_JOURNALED_ITERATOR_FAST_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+template <typename TJournaledString>
+class Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> >
+{
+public:
+    typedef Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > TIterator;
+    typedef typename JournalType<TJournaledString>::Type TJournalEntries;
+    // We need a rooted iterator for iterating the journal tree since we need atEnd().
+    typedef typename Iterator<TJournalEntries, Standard>::Type TJournalEntriesIterator;
+    typedef typename Host<TJournaledString>::Type THost;
+    typedef typename Iterator<THost, Standard>::Type TSegmentIterator;
+
+    // The journal string we iterate over.
+    TJournaledString * _journalStringPtr;
+    // Iterator over the segments in the journal tree.
+    TJournalEntriesIterator _journalEntriesIterator;
+    // Begin and end iterator in the host string of the journal string.
+    TSegmentIterator _segmentBegin;
+    TSegmentIterator _segmentEnd;
+    // Current iterator in the host segment.
+    TSegmentIterator _currentSegmentIt;
+
+    Iter() :
+        _journalStringPtr(), _journalEntriesIterator(), _segmentBegin(), _segmentEnd(),
+        _currentSegmentIt()
+    {}
+
+    template <typename TStringOther>
+    Iter(Iter<TStringOther, JournaledStringIterSpec<CommonSegmentIterator> > const & other,
+         SEQAN_CTOR_ENABLE_IF(IsConstructible<TJournaledString, TStringOther>))
+            : _journalStringPtr(other._journalStringPtr),
+              _journalEntriesIterator(other._journalEntriesIterator),
+              _segmentBegin(other._segmentBegin),
+              _segmentEnd(other._segmentEnd),
+              _currentSegmentIt(other._currentSegmentIt)
+    {
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+
+    template <typename TStringOther>
+    SEQAN_FUNC_ENABLE_IF(IsConstructible<TJournaledString, TStringOther>, TIterator &)
+    operator=(Iter<TStringOther, JournaledStringIterSpec<CommonSegmentIterator> > const & other)
+    {
+        _journalStringPtr = other._journalStringPtr;
+        _journalEntriesIterator = other._journalEntriesIterator;
+        _segmentBegin = other._segmentBegin;
+        _segmentEnd = other._segmentEnd;
+        _currentSegmentIt = other._currentSegmentIt;
+        return *this;
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _initJournaledStringIteratorEnd()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString>
+inline
+void
+_initJournaledStringIteratorEnd(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & iterator)
+{
+    iterator._journalEntriesIterator = end(iterator._journalStringPtr->_journalEntries, Standard()) - 1;
+    _updateSegmentIteratorsLeft(iterator);
+    ++iterator._currentSegmentIt;
+}
+
+// ----------------------------------------------------------------------------
+// Function _updateSegmentIterators()
+// ----------------------------------------------------------------------------
+
+// TODO(rmaerker): Rename to _updateSegmentIteratorsRight().
+template <typename TJournaledString>
+inline
+void
+_updateSegmentIterators(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & iterator)
+{
+    if (atEnd(iterator._journalEntriesIterator, _journalEntries(container(iterator))))
+    {
+        _initJournaledStringIteratorEnd(iterator);
+        return;
+    }
+
+    if (value(iterator._journalEntriesIterator).segmentSource == SOURCE_ORIGINAL)
+        iterator._segmentBegin = begin(host(*iterator._journalStringPtr), Standard()) + value(iterator._journalEntriesIterator).physicalPosition;
+    else
+        iterator._segmentBegin = begin(iterator._journalStringPtr->_insertionBuffer, Standard()) + value(iterator._journalEntriesIterator).physicalPosition;
+
+    iterator._segmentEnd = iterator._segmentBegin + value(iterator._journalEntriesIterator).length;
+    iterator._currentSegmentIt = iterator._segmentBegin;
+}
+
+// ----------------------------------------------------------------------------
+// Function _updateSegmentIteratorsLeft()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString>
+inline
+void
+_updateSegmentIteratorsLeft(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & iterator)
+{
+    if (iterator._journalEntriesIterator + 1 == begin(_journalEntries(container(iterator)), Standard()))
+    {
+        goBegin(iterator);
+        return;
+    }
+
+    if (value(iterator._journalEntriesIterator).segmentSource == SOURCE_ORIGINAL)
+        iterator._segmentBegin = begin(host(*iterator._journalStringPtr), Standard()) + value(iterator._journalEntriesIterator).physicalPosition;
+    else
+        iterator._segmentBegin = begin(iterator._journalStringPtr->_insertionBuffer, Standard()) + value(iterator._journalEntriesIterator).physicalPosition;
+    iterator._segmentEnd = iterator._segmentBegin + value(iterator._journalEntriesIterator).length;
+    iterator._currentSegmentIt = iterator._segmentEnd - 1;
+}
+
+// ----------------------------------------------------------------------------
+// Function _localEntryPosition
+// ----------------------------------------------------------------------------
+
+// TODO(rmaerker): Write documentation!
+template <typename TJournaledString>
+inline typename Position<Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > const>::Type
+_localEntryPosition(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > const & iterator)
+{
+    return iterator._currentSegmentIt - iterator._segmentBegin;
+}
+
+// ----------------------------------------------------------------------------
+// Function setPosition
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString, typename TPosition>
+inline void
+setPosition(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & me,
+            TPosition pos)
+{
+    SEQAN_ASSERT_GEQ(pos, static_cast<TPosition>(0));
+
+    // Handle case where pos points behind the container.
+    if (pos >= static_cast<TPosition>(length(container(me))))
+        goEnd(me);
+
+    // Use binary search to find corresponding node.
+    me._journalEntriesIterator = findInJournalEntries(container(me)._journalEntries, pos);
+
+    int offset = pos - value(me._journalEntriesIterator).virtualPosition;  // The offset within the current node.
+    _updateSegmentIterators(me);
+    me._currentSegmentIt += offset;
+}
+
+// ----------------------------------------------------------------------------
+// Function getValue()
+// ----------------------------------------------------------------------------
+
+// getValue
+template <typename TJournaledString>
+inline
+typename GetValue<Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > >::Type
+getValue(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > const & iterator)
+{
+    return getValue(iterator._currentSegmentIt);
+}
+
+template <typename TJournaledString>
+inline
+typename GetValue<Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > >::Type
+getValue(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & iterator)
+{
+    return getValue(iterator._currentSegmentIt);
+}
+
+// ----------------------------------------------------------------------------
+// Function operator++()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString>
+inline
+Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > &
+operator++(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & iterator)
+{
+    ++iterator._currentSegmentIt;
+    if (iterator._currentSegmentIt == iterator._segmentEnd)
+    {
+        ++iterator._journalEntriesIterator;
+        _updateSegmentIterators(iterator);
+    }
+    return iterator;
+}
+
+// ----------------------------------------------------------------------------
+// Function opertor+=()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString, typename TLen>
+inline
+Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > &
+operator+=(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & iterator,
+           TLen len_)
+{
+    SEQAN_ASSERT_GEQ(len_, static_cast<TLen>(0));
+
+    TLen remaining = iterator._segmentEnd - iterator._currentSegmentIt;
+    while (len_ > 0  && remaining != 0)
+    {
+        SEQAN_ASSERT_GT(remaining, static_cast<TLen>(0));
+        if (len_ >= remaining)
+        {
+            len_ -= remaining;
+            ++iterator._journalEntriesIterator;
+            _updateSegmentIterators(iterator);
+            remaining = iterator._segmentEnd - iterator._currentSegmentIt;
+        }
+        else
+        {
+            iterator._currentSegmentIt += len_;
+            len_ = 0;
+        }
+    }
+    return iterator;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator--()                                               [prefix]
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString>
+inline
+Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > &
+operator--(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & iterator)
+{
+    if (iterator._currentSegmentIt == iterator._segmentBegin)
+    {
+        --iterator._journalEntriesIterator;
+        _updateSegmentIteratorsLeft(iterator);
+        return iterator;
+    }
+
+    --iterator._currentSegmentIt;
+    return iterator;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator-=()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString, typename TLen>
+inline
+Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > &
+operator-=(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > & iterator,
+            TLen len_)
+{
+    typedef Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > TIterator;
+    typedef typename Size<TIterator>::Type TSize;
+
+    SEQAN_ASSERT_GEQ(len_, static_cast<TLen>(0));
+    TSize len = len_;
+
+    while (len > 0 )
+    {
+        TSize relNodePos = _localEntryPosition(iterator);
+        if (len > relNodePos)
+        {
+            len -= (relNodePos + 1);
+            --iterator._journalEntriesIterator;
+            _updateSegmentIteratorsLeft(iterator);
+        }
+        else
+        {
+            iterator._currentSegmentIt -= len;
+            len = 0;
+        }
+    }
+    return iterator;
+}
+
+// ----------------------------------------------------------------------------
+// Function operator-()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString>
+inline
+typename Difference<TJournaledString>::Type
+operator-(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > const & it1,
+          Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > const & it2)
+{
+    // First, handle the cases where it1 or it2 are at the end.
+    bool it1AtEnd = atEnd(it1._journalEntriesIterator, _journalEntries(container(it1)));
+    bool it2AtEnd = atEnd(it2._journalEntriesIterator, _journalEntries(container(it2)));
+    if (it1AtEnd && it2AtEnd)
+    {
+        return 0;
+    }
+    else if (it1AtEnd)
+    {
+        SEQAN_ASSERT_LT(value(it2._journalEntriesIterator).virtualPosition + _localEntryPosition(it2), length(*it1._journalStringPtr));
+        return length(*it1._journalStringPtr) - (value(it2._journalEntriesIterator).virtualPosition + _localEntryPosition(it2));
+    }
+    else if (it2AtEnd)
+    {
+        SEQAN_ASSERT_LT((value(it1._journalEntriesIterator).virtualPosition + _localEntryPosition(it1)), length(*it1._journalStringPtr));
+        return (value(it1._journalEntriesIterator).virtualPosition + _localEntryPosition(it1)) - length(*it1._journalStringPtr);
+    }
+    // Otherwise, we can simply subtract the virtual positions.
+    return (value(it1._journalEntriesIterator).virtualPosition + _localEntryPosition(it1)) - (value(it2._journalEntriesIterator).virtualPosition + _localEntryPosition(it2));
+}
+
+// ----------------------------------------------------------------------------
+// Function operator==()
+// ----------------------------------------------------------------------------
+
+template <typename TJournaledString>
+inline
+bool
+operator==(Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > const & a,
+           Iter<TJournaledString, JournaledStringIterSpec<CommonSegmentIterator> > const & b)
+{
+    SEQAN_CHECKPOINT;
+    if (a._journalEntriesIterator != b._journalEntriesIterator)
+        return false;
+    if (a._currentSegmentIt != b._currentSegmentIt)
+        return false;
+    return true;
+}
+
+}
+
+#endif // INCLUDE_SEQAN_SEQUENCE_JOURNALED_SEQUENCE_JOURNALED_ITERATOR_FAST_H_
diff --git a/seqan/simple_intervals_io.h b/seqan/simple_intervals_io.h
new file mode 100644
index 0000000..38762bf
--- /dev/null
+++ b/seqan/simple_intervals_io.h
@@ -0,0 +1,54 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for the intervals_io module.
+// ==========================================================================
+
+#ifndef SEQAN_SIMPLE_INTERVALS_IO_H_
+#define SEQAN_SIMPLE_INTERVALS_IO_H_
+
+// ===========================================================================
+// Prerequisites
+// ===========================================================================
+
+#include <seqan/stream.h>
+#include <seqan/seq_io/genomic_region.h>
+
+// ===========================================================================
+// Module Contents
+// ===========================================================================
+
+#include <seqan/simple_intervals_io/simple_intervals_io.h>    // read/write record functions, tags
+#include <seqan/simple_intervals_io/simple_intervals_file.h>  // FormattedFile
+
+#endif  // SEQAN_SIMPLE_INTERVALS_IO_H_
diff --git a/seqan/simple_intervals_io/simple_intervals_file.h b/seqan/simple_intervals_io/simple_intervals_file.h
new file mode 100644
index 0000000..9f5c3c9
--- /dev/null
+++ b/seqan/simple_intervals_io/simple_intervals_file.h
@@ -0,0 +1,176 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// FormattedFile for .intervals format
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_SIMPLE_INTERVALS_IO_SIMPLE_INTERVALS_FILE_H_
+#define INCLUDE_SEQAN_SIMPLE_INTERVALS_IO_SIMPLE_INTERVALS_FILE_H_
+
+#include <seqan/simple_intervals_io/simple_intervals_io.h>
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Typedef SimpleIntervalsFileIn
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class SimpleIntervalsFileIn
+ * @extends FormattedFileIn
+ * @headerfile <seqan/ucsc_io.h>
+ * @brief @link FormattedFile @endlink for reading .intervals files.
+ *
+ * @signature typedef FormattedFile<SimpleIntervals, Input> SimpleIntervalsFileIn;
+ */
+typedef FormattedFile<SimpleIntervals, Input>   SimpleIntervalsFileIn;
+
+// ----------------------------------------------------------------------------
+// Typedef SimpleIntervalsFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class SimpleIntervalsFileInOut
+ * @extends FormattedFileOut
+ * @headerfile <seqan/ucsc_io.h>
+ * @brief @link FormattedFile @endlink for reading .intervals files.
+ *
+ * @signature typedef FormattedFile<SimpleIntervals, Output> SimpleIntervalsFileOut;
+ */
+typedef FormattedFile<SimpleIntervals, Output> SimpleIntervalsFileOut;
+
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction MagicHeader
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<SimpleIntervals, T> : public MagicHeader<Nothing, T> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileExtensions
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<SimpleIntervals, T>
+{
+    static char const * VALUE[1];  // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<SimpleIntervals, T>::VALUE[1] =
+{
+    ".intervals"      // default output extension
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<SimpleIntervals, TDirection, TSpec>, TStorageSpec>
+{
+    typedef SimpleIntervalsIOContext Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec>
+struct FileFormat<FormattedFile<SimpleIntervals, TDirection, TSpec> >
+{
+    typedef SimpleIntervals Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn SimpleIntervalsFileIn#readRecord
+ * @brief Reading records from a SimpleIntervalsFileIn.
+ *
+ * @signature void readRecord(record, file);
+ *
+ * @param[out] record The resulting @link GenomicRegion @endlink.
+ * @param[out] file   The SimpleIntervalsFileIn to read from.
+ *
+ * @throw IOError in case of problems.
+ */
+template <typename TSpec>
+void readRecord(GenomicRegion & record, FormattedFile<SimpleIntervals, Input, TSpec> & file)
+{
+    readRecord(record, context(file), file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function write()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn SimpleIntervalsFileIn#writeRecord
+ * @brief Writing records to a SimpleIntervalsFileIn.
+ *
+ * @signature void readRecord(record, file);
+ *
+ * @param[out] file   The SimpleIntervalsFileIn to write to.
+ * @param[out] record The @link GenomicRegion @endlink to write out.
+ *
+ * @throw IOError in case of problems.
+ */
+template <typename TSpec>
+void writeRecord(FormattedFile<SimpleIntervals, Output, TSpec> & file, GenomicRegion & record)
+{
+    writeRecord(file.iter, context(file), record, file.format);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_SIMPLE_INTERVALS_IO_SIMPLE_INTERVALS_FILE_H_
diff --git a/seqan/simple_intervals_io/simple_intervals_io.h b/seqan/simple_intervals_io/simple_intervals_io.h
new file mode 100644
index 0000000..9640abe
--- /dev/null
+++ b/seqan/simple_intervals_io/simple_intervals_io.h
@@ -0,0 +1,161 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Reading and writing of .intervals file record plus tags.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_SIMPLE_INTERVALS_IO_SIMPLE_INTERVALS_IO_H_
+#define INCLUDE_SEQAN_SIMPLE_INTERVALS_IO_SIMPLE_INTERVALS_IO_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class SimpleIntervalsIOContext
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class SimpleIntervalsIOContext
+ * @implements DefaultConstructibleConcept
+ * @implements AssignableConcept
+ * @headerfile <seqan/simple_intervals_io.h>
+ * @brief I/O context for .intervals file.
+ *
+ * @signature class SimpleIntervalsIOContext;
+ */
+
+struct SimpleIntervalsIOContext
+{
+    CharString buffer;
+};
+
+// ----------------------------------------------------------------------------
+// Tag SimpleIntervals
+// ----------------------------------------------------------------------------
+
+/*!
+ * @tag FileFormats#SimpleIntervals
+ * @headerfile <seqan/simple_intervals_io.h>
+ * @brief Tag for the simple .intervals file format.
+ * The file contains format in the format <tt>CHR:POS</tt> or <tt>CHR:BEGIN-END</tt> in 1-based coordinates.
+ */
+
+struct SimpleIntervals_;
+typedef Tag<SimpleIntervals_> SimpleIntervals;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord()
+// ----------------------------------------------------------------------------
+
+// NOTE(esiragusa): dox disabled.
+/*
+ * @fn SimpleIntervalsFileIO#readRecord
+ * @headerfile <seqan/simple_intervals_io.h>
+ * @brief Read an intervals record.
+ *
+ * @signature void readRecord(region, buffer, iter, tag);
+ *
+ * @param[out]    region  The @link GenomicRegion @endlink to write interval to.
+ * @param[in,out] context A @link SimpleIntervalsIOContext @endlink with buffers.
+ * @param[in,out] iter    A @link ForwardIteratorConcept forward iterator @endlink to read from.
+ * @param[in]     tag     The tag @link SimpleIntervalsFileIO#SimpleIntervals SimpleIntervals @endlink for the format.
+ *
+ * @throw IOError in case of problems.
+ */
+
+template <typename TForwardIter>
+void readRecord(GenomicRegion & record,
+                SimpleIntervalsIOContext & context,
+                TForwardIter & iter,
+                SimpleIntervals const & /*tag*/)
+{
+    clear(context.buffer);
+    // Read next line until the first whitespace (could be '\r' or '\n').
+    readUntil(context.buffer, iter, IsWhitespace());
+    // Parse context.buffer into GenomicRegion.
+    parse(record, context.buffer);
+    if (record.endPos == record.INVALID_POS)  // only one position
+        record.endPos = record.beginPos + 1;
+    // Skip remaining line.
+    skipLine(iter);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()
+// ----------------------------------------------------------------------------
+
+// NOTE(esiragusa): dox disabled.
+/*
+ * @fn SimpleIntervalsFileIO#writeRecord
+ * @headerfile <seqan/simple_intervals_io.h>
+ * @brief Write out a @link GenomicRegion @endlink to an intervals file.
+ *
+ * @signature void writeRecord(target, context, region, tag);
+ *
+ * @param[in,out] target  An @link OutputIteratorConcept output iterator @endlink to write to.
+ * @param[in,out] context A @link SimpleIntervalsIOContext @endlink with buffers.
+ * @param[in]     region  The @link GenomicRegion @endlink to write out.
+ * @param[in]     tag     The tag @link SimpleIntervalsFileIO#SimpleIntervals SimpleIntervals @endlink for the format.
+ *
+ * @throw IOError in case of problems.
+ */
+
+template <typename TTarget>
+void writeRecord(TTarget & target,
+                 SimpleIntervalsIOContext & context,
+                 GenomicRegion const & region,
+                 SimpleIntervals const & /*tag*/)
+{
+    region.toString(context.buffer);
+    write(target, context.buffer);
+    write(target, "\n");
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_SIMPLE_INTERVALS_IO_SIMPLE_INTERVALS_IO_H_
diff --git a/seqan/file/meta.h b/seqan/statistics.h
similarity index 77%
rename from seqan/file/meta.h
rename to seqan/statistics.h
index 78840f0..c497821 100644
--- a/seqan/file/meta.h
+++ b/seqan/statistics.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,21 +30,20 @@
 //
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_FILE_META_H
-#define SEQAN_HEADER_FILE_META_H
+#ifndef SEQAN_HEADER_STATISTICS_H
+#define SEQAN_HEADER_STATISTICS_H
 
-/* IOREV
- * Whats this good for?
- */
+//____________________________________________________________________________
+// prerequisites
 
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
+#include <cmath>
+#include <seqan/align.h>
+#include <seqan/index.h>
+//____________________________________________________________________________
 
+#include <seqan/statistics/statistics_markov_model.h>
+#include <seqan/statistics/statistics_base.h>
 
-
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
+//____________________________________________________________________________
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/statistics/.statistics_markov_model.h.swp b/seqan/statistics/.statistics_markov_model.h.swp
new file mode 100644
index 0000000..8bfd539
Binary files /dev/null and b/seqan/statistics/.statistics_markov_model.h.swp differ
diff --git a/seqan/statistics/statistics_base.h b/seqan/statistics/statistics_base.h
new file mode 100644
index 0000000..39e7572
--- /dev/null
+++ b/seqan/statistics/statistics_base.h
@@ -0,0 +1,490 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+
+#ifndef SEQAN_STATISTICS_STATISTICS_BASE_H_
+#define SEQAN_STATISTICS_STATISTICS_BASE_H_
+
+namespace seqan
+{
+
+template <typename TAlgorithm, typename TFloat, typename TAlphabet>
+void _numOccurrences(TFloat &nW, String<TAlphabet>& haystack, StringSet<String<TAlphabet> >& needle, TAlgorithm const &);
+
+/*
+ * @fn _zscore
+ * @headerfile <seqan/statistics.h>
+ * @brief Auxiliary function to compure the z-score index for a set of patterns w.r.t. a set of text strings and a
+ *        MarkovMovel.
+ *
+ * @signature TFloat _zscore(W, X, M, tag);
+ *
+ * @param[in] W   The StringSet to use as the words.
+ * @param[in] X   The StringSet to use as the text.
+ * @param[in] M   The MarkovModel to use.
+ * @param[in] tag The tag to select the algorithm.
+ *
+ * @return TFloat The z-score, TFloat is the TFloat from the MarkovModel M.
+ */
+
+template <typename TAlgorithm, typename TFloat,  typename TStringSet, typename TAlphabet, typename TSpec>
+TFloat _zscore(TStringSet W,  TStringSet& X, MarkovModel<TAlphabet, TFloat, TSpec> & M, TAlgorithm const &)
+{
+
+
+    TFloat z_score=0;
+    TFloat nW=0;
+    //compute occurrances
+    for(unsigned int i=0; i< length(X); i++)
+    {
+        String<TAlphabet> temp = getValueById(X, i);
+        _numOccurrences(nW, temp, W, TAlgorithm());
+    }
+
+    //compute expectation
+    TFloat E = expectation(W, X, M);
+//std::cout<<"\nE:"<<E;
+    //compute variance
+    TFloat V = _computeVariance(W, X, M, E);
+//std::cout<<"\nV:"<<V;
+    //compute z-score
+    z_score=(nW-E)/sqrt(V);
+
+    return z_score;
+
+}
+
+/*
+ * @fn _numOccurences
+ * @headerfile <seqan/statistics.h>
+ * @brief Auxiliary function to compute the number of occurences of a set of patterns in a set of text strings.
+ *
+ * @signature void _numOccurences(W, haystack, needle, algoTag);
+ *
+ * @param[in,out] W        A counter, incremented by the number of occurences.
+ * @param[in]     haystack The text strings.
+ * @param[in]     needle   The set of patterns.
+ * @param[in]     algoTag  The tag to select the online text search algorithm with.
+ */
+
+//Fixed to  AhoCorasick in original code, reason???
+template <typename TAlgorithm, typename TFloat, typename TAlphabet>
+void _numOccurrences(TFloat &nW, String<TAlphabet> &haystack, StringSet<String<TAlphabet> > &needle, TAlgorithm const &)
+{
+    SEQAN_CHECKPOINT;
+    Finder<String<TAlphabet> > finder(haystack);
+    Pattern<StringSet<String<TAlphabet> >, TAlgorithm> pattern(needle);
+    while (find(finder, pattern))
+    {
+        nW++;
+    }
+}
+
+/*
+ * @fn _computeExpecttation
+ * @brief Auxiliary function to compute the expectation for a set of patterns w.r.t. a text string  and a MarkovModel.
+ *
+ * @signature TFloat _computeExpectation(mm, W, n);
+ *
+ * @param[in] mm The MarkovModel.
+ * @param[in] W  The set of patterns, StringSet.
+ * @param[in] n  The length of the string, unsigned.
+ *
+ * @return TFloat the expectation valuefor W w.r.t. a string and M.
+ */
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+TFloat _computeExpectation(MarkovModel<TAlphabet, TFloat, TSpec> &mm,
+                     StringSet<String<TAlphabet> > &W, unsigned int n)
+{
+    TFloat E=0;
+    for (unsigned int i=0; i<length(W); i++){
+        String<TAlphabet> temp = getValueById(W, i);
+        E += (n - length(temp) + 1)*mm.emittedProbability(temp);
+    }
+    return E;
+}
+
+
+/*
+ * @fn _computeVariance
+ * @headerfile <seqan/statistics.h>
+ * @brief Auxiliary function to compute the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel.
+ *
+ * @signature TFloat _computeVariance(W, X, M);
+ *
+ * @param[in] W The set of words.
+ * @param[in] X The text set.
+ * @param[in] M The MarkovModel to use.
+ * @param[in] E
+ *
+ * @return TFloat The variance for W w.r.t. X and M.
+ *
+ * @section Remarks
+ *
+ * If the alphabet is Dna, then the suitable correction factors are computed.
+ */
+
+// TODO(holtgrew): W could become const-ref.
+
+template <typename TFloat, typename TAlphabet, typename TSpec>
+TFloat _computeVariance( StringSet<String<TAlphabet> > W,  StringSet<String<TAlphabet> > &X, MarkovModel<TAlphabet, TFloat, TSpec> &M, TFloat &E)
+{
+    //V=B+2C-E^2
+    TFloat V = E;
+
+    //C=D+A
+
+    //compute A and D
+
+    TFloat A = 0;
+    TFloat D = 0;
+    TFloat tmpA, eQPPPe, eQPPQPPe;
+    unsigned int sizeW=length(W);
+    unsigned int n;
+
+    String <TFloat> pStar;
+    resize(pStar, sizeW, 0);
+
+    Shape<TAlphabet, SimpleShape> orderShape;
+    resize(orderShape, M.order);
+
+    for(unsigned int j=0; j<sizeW; j++){
+        String<TAlphabet> string =getValueById(W, j);
+
+        int row = hash(orderShape,begin(string));
+        TFloat p = 1;
+        for(unsigned int i=1; i<length(string)-M.order+1; i++)
+        {
+            int column=hash(orderShape,begin(string)+i);
+            p*=value(M.transition,row,column);
+            row = column;
+        }
+        value(pStar, j) = p;
+    }
+
+
+
+    for(unsigned int z=0; z<length(X); z++){
+
+      for(unsigned int i=0; i<length(X); i++){
+
+         n = length(getValueById(X, i));
+
+         for(unsigned int j=0; j<sizeW; j++){
+
+            String<TAlphabet> Wj =getValueById(W, j);
+
+            TFloat q = (TFloat) (n-(2*length(Wj))+2);
+
+            for(unsigned int k=0; k<sizeW; k++){
+
+                tmpA=value(pStar,j)*value(pStar,k);
+
+                unsigned int jfirst, jlast, kfirst;
+
+                jfirst = hash(orderShape,begin(Wj));
+
+                jlast = hash(orderShape,end(Wj)-M.order);
+
+                kfirst = hash(orderShape,begin(getValueById(W, k)));
+
+                eQPPPe = value(M._qppp, jlast,kfirst);
+
+                eQPPQPPe = value(M._qppqpp, jlast,kfirst);
+
+                tmpA  *= value(M.stationaryDistribution, jfirst) * ((q*(q+1)/2)* value(M.stationaryDistribution, kfirst) - (q-1)*eQPPPe - eQPPQPPe);
+
+                A += tmpA;
+            }
+         }
+      }
+
+      // Compute D
+      D+= _overlapExpectation(W,M,length(getValueById(X, z)));
+    }
+
+
+
+
+    //Compute Variance
+    V += (2*A) + (2*D) -  std::pow((double) E, (int) 2);
+
+    //return V;
+    return V;
+}
+
+/*
+ * @fn _overlapExpectation
+ * @headerfile <seqan/statistics.h>
+ * @brief Auxiliary function necessary when correction factors have to be computed.
+ *
+ * @signature TFloat _overlapExpectation(W, M, n);
+ *
+ * @param[in] W The set of words.
+ * @param[in] M The MarkovModel to use for the computation.
+ * @param[in] n The length of the text.
+ *
+ * @return TFloat The expectation value for overlapping, TFloat is the TFloat from the type of M.
+ */
+
+template <typename TFloat, typename TAlphabet, typename TSpec>
+TFloat _overlapExpectation(StringSet<String<TAlphabet> > W, MarkovModel<TAlphabet, TFloat, TSpec> &M, unsigned int n)
+{
+    TFloat E_overlap = 0;
+    unsigned int sizeW = length(W);
+    for(unsigned int i=0; i<sizeW; i++)
+    {
+        String<TAlphabet> patt1 = getValueById(W, i);
+        unsigned int size1 = length(patt1);
+        for(unsigned int j=0; j<sizeW; j++)
+        {
+            String<TAlphabet> patt2 = getValueById(W, j);
+            unsigned int k=1;
+            unsigned int size2 = length(patt2);
+            if(size1>size2)
+            {
+                k = size1 - size2 + 1;
+            }
+            for(; k<size1; k++)
+            {
+                if(isEqual(infix(patt1,begin(patt1)+k,end(patt1)),infix(patt2,begin(patt2),begin(patt2)+k-1)))
+                {
+                    String<TAlphabet> temp = infix(patt1, begin(patt1),begin(patt1)+k-1);
+                    append(temp,infix(patt2,begin(patt2),end(patt2)));
+                    E_overlap += (n - size1 + 1)*M.emittedProbability(temp);
+                }
+            }
+        }
+    }
+    return E_overlap;
+}
+
+/*
+ * @fn _addReverseComplemenents
+ * @headerfile <seqan/statistics.h>
+ * @brief Computes the reverse complemenets of a set of strings in the input.
+ *
+ * @signature void _addReverseComplements(ss);
+ *
+ * @param[in,out] ss A String set to expand.
+ */
+
+template <typename TAlphabet>
+void _addReveseComplements(StringSet<String<TAlphabet> > &stringSet)
+{
+    unsigned int num= length(stringSet);
+
+    for(unsigned int i=0; i< num; i++){
+           DnaStringReverseComplement mycom(getValueById(stringSet, i));
+         appendValue(stringSet, mycom);
+    }
+}
+
+
+///////////////////////////////////////////////////////////////////////
+// Extern functions to be provided by SeqAn
+///////////////////////////////////////////////////////////////////////
+
+typedef Dna TDnaAlphabet;
+typedef String<TDnaAlphabet> TDnaSequence;
+
+/*!
+ * @fn zscore
+ * @headerfile <seqan/statistics.h>
+ * @brief Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel.
+ *
+ * @signature TFloat zscore(W, X, M, algoTag);
+ *
+ * @param[in] W       The StringSet of pattern strings.
+ * @param[in] X       The StringSet of text strings.
+ * @param[in] M       The MarkovModel object.
+ * @param[in] algoTag The algorithm to exploit to compute the number of occurrences of patterns in the text strings
+ *                    (see @link AhoCorasickPattern @endlink etc.).
+ *
+ * @return TFloat The z-score for W w.r.t. X and M, TFloat is the TFloat from the type of M.
+ */
+
+template <typename TAlgorithm, typename TFloat, typename TSpec, typename TStringSet, typename TAlphabet>
+TFloat zscore(TStringSet W,  TStringSet &X, MarkovModel<TAlphabet, TFloat, TSpec> &M, TAlgorithm const & algorithmTag)
+{
+    ensureAuxMatrices(M);
+       return _zscore(W,X,M, algorithmTag);
+}
+
+template <typename TAlgorithm, typename TFloat, typename TSpec, typename TDnaSequence>
+TFloat zscore(StringSet<TDnaSequence> W,  StringSet<TDnaSequence> &X, MarkovModel<Dna, TFloat, TSpec> &M, TAlgorithm const &)
+{
+   //add-reverse complements
+   _addReveseComplements(W);
+
+    ensureAuxMatrices(M);
+
+   TFloat z_score=0;
+   TFloat nW=0;
+   //compute occurrences
+   for(unsigned int i=0; i < length(X); i++)
+   {
+         String<Dna> temp = getValueById(X, i);
+        _numOccurrences(nW, temp, W, TAlgorithm());
+    }
+
+    //compute expectation
+    TFloat E = expectation(W, X, M);
+    //std::cout<<"\nE: "<<E<<"\n";
+    //compute variance
+    TFloat V = _computeVariance(W, X, M, E);
+    //std::cout<<"\nV: "<<V<<"\n";
+    //compute correction factor
+    TFloat correction = 0;
+
+    unsigned int n;
+    unsigned int sizeW= length(W);
+
+    for(unsigned int j=0; j<length(X); j++){
+
+         n = length(getValueById(X, j));
+
+        for(unsigned int i=0; i<sizeW; i++)
+        {
+            String<Dna> patt = getValueById(W, i);
+            DnaStringReverseComplement revpatt(patt);
+            String<Dna> revc= revpatt;
+            if (isEqual(patt,revc))
+            {
+                correction += (n-length(patt)+1)*M.emittedProbability(revc);
+            }
+        }
+    }
+
+    V+= correction;
+
+    //compute z-score
+    z_score=(nW-E)/sqrt(V);
+    //std::cout<<"\nnW: "<<nW<<"\n";
+    //std::cout<<"\nZ: "<<z_score<<"\n";
+    return z_score;
+}
+
+/*!
+ * @fn variance
+ * @headerfile <seqan/statistics.h>
+ * @brief Computes the variance for a set of patterns w.r.t a set of text strings and a MarkovModel.
+ *
+ * @signature TFloat variance(W, X, M);
+ *
+ * @param[in] W The StringSet of word strings.
+ * @param[in] X The StringSet of text strings.
+ * @param[in] M The MarkovModel to use.
+ *
+ * @return TFloat The variance for W w.r.t. X and M, TFloat is the TFloat from the type of M.
+ */
+
+template <typename TFloat, typename TAlphabet, typename TSpec>
+TFloat variance(StringSet<String<TAlphabet> > &W, StringSet<String<TAlphabet> >& X, MarkovModel<TAlphabet, TFloat, TSpec> & M)
+{
+   TFloat E = expectation(W, X, M);
+
+   return _computeVariance(W,X,M,E);
+}
+
+//Special case for DNA sequences, reverse complement sequences are added
+template <typename TFloat, typename TSpec>
+TFloat variance(StringSet<String<Dna> > W, StringSet<String<Dna> > &X, MarkovModel<Dna, TFloat, TSpec> & M)
+{
+
+   //add-reverse complements
+    _addReveseComplements(W);
+
+    TFloat E = expectation(W, X, M);
+
+    TFloat var =  _computeVariance(W,X,M,E);
+
+    //compute correction factor
+    TFloat correction = 0;
+
+    unsigned int n;
+    unsigned int sizeW= length(W);
+
+
+   for(unsigned int j=0; j<length(X); j++){
+
+         n = length(getValueById(X, j));
+
+        for(unsigned int i=0; i<sizeW; i++)
+        {
+            String<Dna> patt = getValueById(W, i);
+            DnaStringReverseComplement revpatt(patt);
+            String<Dna> revc= revpatt;
+            if (isEqual(patt,revc))
+            {
+                correction += (n-length(patt)+1)*M.emittedProbability(revc);
+            }
+        }
+    }
+    var+=correction;
+
+  return var;
+}
+
+/*!
+ * @fn expectation
+ * @headerfile <seqan/statistics.h>
+ * @brief Computes the expectation for a set of patterns w.r.t a set of text strings and a MarkovModel.
+ *
+ * @signature TFloat expectation(W, X, M);
+ *
+ * @param[in] W The StringSet of word strings.
+ * @param[in] X The StringSet of text strings.
+ * @param[in] M The MarkovModel to use.
+ *
+ * @return TFloat The expectation for W w.r.t. X and M, TFloat is the TFloat from the type of M.
+ */
+
+// TODO(holtgrew): Add const?
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+TFloat expectation(StringSet<String<TAlphabet> > & W, StringSet<String<TAlphabet> > &X, MarkovModel<TAlphabet, TFloat, TSpec> &M)
+{
+    unsigned int n;
+    TFloat E = 0;
+
+    for(unsigned int i=0; i<length(X); i++){
+         n = length(getValueById(X, i));
+        E += _computeExpectation(M, W, n);
+    }
+
+    return E;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_STATISTICS_STATISTICS_BASE_H_
diff --git a/seqan/statistics/statistics_markov_model.h b/seqan/statistics/statistics_markov_model.h
new file mode 100644
index 0000000..90e5585
--- /dev/null
+++ b/seqan/statistics/statistics_markov_model.h
@@ -0,0 +1,879 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Author: utro@math.unipa.it
+// Author: srombo@deis.unical.it
+// Author: Jonathan Göke
+// ==========================================================================
+
+//////////////////////////////////////////////////////////////////////////////
+
+#ifndef SEQAN_STATISTICS_STATISTICS_MARKOV_MODEL_H_
+#define SEQAN_STATISTICS_STATISTICS_MARKOV_MODEL_H_
+
+#include <seqan/align.h>
+#include <seqan/index.h>
+
+namespace seqan {
+
+/*!
+ * @class MarkovModel
+ * @headerfile <seqan/statistics.h>
+ * @brief Gives a suitable representation of a Marcov Chain.
+ *
+ * @signature template <typename TAlphabet[, typename TFloat[, typename TSpec]]>
+ *            class MarkovModel;
+ *
+ *
+ * @tparam TAlphabet The type of the underlying alphabet.
+ * @tparam TFloat    The type for storing counts, default is <tt>double</tt>.
+ * @tparam TSpec     Tag for specialization.
+ *
+ * @section Examples
+ *
+ * @subsection Build a MarkovModel from Background
+ *
+ * @include demos/dox/statistics/build_markov_model.cpp
+ *
+ * The following example shows how to build a MarkovModel over a Dna alphabet from a set of background sequence.  After
+ * build the model, we compute the zscore.
+ *
+ * @code{.console}
+ * zscore: 11.8323
+ * @endcode
+ *
+ * @subsection Load a MarkovModel from File
+ *
+ * We can also load the MarkovModel from a file (previously saved using @link MarkovModel::write @endlink).  Since we do
+ * not have the background word set here but only the model, we compute the variance of a word using the function
+ * calculateVariance from the alignment_free module.
+ *
+ * @include demos/dox/statistics/load_markov_model.cpp
+ *
+ * @code{.console}
+ * variance: 0.267919
+ * @endcode
+ *
+ * @var unsigned MarkovModel::order;
+ * @brief The order of the MarkovModel.
+ *
+ * @var TMatrix MarkovModel::transition;
+ * @brief The transition matirx.
+ *
+ * @var TVector MarkovModel::stationaryDistribution;
+ * @brief The vector of characgter distribution (String of TFloat).
+ *
+ *
+ * @fn MarkovModel::MarkovModel
+ * @brief Constructor
+ *
+ * @signature MarkovModel::MarkovModel(order);
+ *
+ * @param[in] order The order of the model (<tt>unsigned</tt>).
+ *
+ *
+ * @fn MarkovModel::build
+ * @brief Compute the transition matrix from a training set.
+ *
+ * The character statitionary distribution and the auxiliary information that give raise to an instance of a
+ * Markov Model are also computed.
+ *
+ * @signature void MarkovModel::build(stringSet);
+ *
+ * @param[in] stringSet The StringSet to build the model for.
+ *
+ *
+ * @fn MarkovModel::set
+ * @brief Set transition matrix.
+ *
+ * Given e transition matrix, sets it as transition matrix of the MarkovModel and computes (if it is not available) the
+ * vector of character distributions and the auxiliary information.
+ *
+ * @signature void MarkovModel(transition[, stationaryDistribution]);
+ *
+ * @param[in,out] transition             The transition matrix.
+ * @param[in]     stationaryDistribution The vector of character distributions.
+ *
+ *
+ * @fn MarkovModel::emittedProbability
+ * @brief Computes the probability that a string or a set of strings is emitted by the MarkovModel.
+ *
+ * @signature TFloat MarkovModel::emittedProbability(s);
+ * @signature TFloat MarkovModel::emittedProbability(ss);
+ *
+ * @param[in] s  The String to compute the emission probability for.
+ * @param[in] ss The StringSet to compute the emission probability for.
+ *
+ * @return TFloat The emission probability, TFloat is the TFloat from the MarkovModel.
+ *
+ *
+ * @fn MarkovModel::write
+ * @brief Stores an instance of a markovModel in a file.
+ *
+ * @signature void MarkovModel::write(file);
+ *
+ * @param[in,out] file The file to write the model to (type <tt>FILE *</tt>).
+ *
+ *
+ * @fn MarkovModel::read
+ * @brief Load an instance of MarkovModel from a file.
+ *
+ * @signature void MarkovModel::read(file);
+ *
+ * @param[in,out] file The file to read the model from (type <tt>FILE *</tt>).
+ */
+
+/*
+with matrix calss matrices
+*/
+template <typename TAlphabet, typename TFloat = double, typename TSpec = Default>
+class MarkovModel
+{
+
+public:
+
+    //Definition of matrix types, could be set to two dimensional as soon as implemented
+    typedef Matrix<TFloat, 2> TMatrix;
+    //typedef String<TFloat> TMatrix;
+    typedef String<TFloat> TVector;
+
+    unsigned int order;
+    TMatrix transition;
+    TVector stationaryDistribution;
+    //The following matrices are only for internal use of the class
+    TMatrix _q;            //QPP^(morder-1)
+    TMatrix _qppp;        //QPP^(morder-1)
+    TMatrix _qppqpp;    //QPPQP^(morder-1)
+
+
+    MarkovModel(unsigned int order_):
+    order(order_)
+    {
+
+        unsigned int const alphabet_size = ValueSize<TAlphabet>::VALUE;
+        //unsigned int const column_size = (unsigned int) std::pow((double) alphabet_size, (int) order);
+        unsigned int column_size = (unsigned int) std::pow((double) alphabet_size, (int) order);
+
+        //Special case of order 0 marko model:
+        //A Bernoulli scheme is a special case of a Markov chain where the transition probability matrix has identical rows, which means that the next state is even independent of the current state (in addition to being independent of the past states).
+        if(order==0)
+        {
+            column_size=alphabet_size;
+
+        }
+        //resize the matrix
+        setLength(transition, 0, column_size);
+        setLength(transition, 1, column_size);
+
+        resize(transition,(TFloat) 0);
+
+        clear(stationaryDistribution);
+        resize(stationaryDistribution, column_size);
+    }
+
+
+    ///////////////////////////////////////////////////////////////
+    ///// BUILD THE MODEL
+    ///////////////////////////////////////////////////////////////
+    typedef String<Dna> TText;
+    typedef Size<TText>::Type TSize;
+    typedef StringSet<TText > TStringSet;
+
+    //template <typename TAlphabet>
+    void build(StringSet<String<TAlphabet> > const &strings)
+    {
+
+        typedef String<TAlphabet> TText;
+        //typedef Size<TText>::Type TSize;
+        typedef StringSet<TText > TStringSet;
+
+        typedef Index<TStringSet, IndexQGram<SimpleShape> > TIndex;
+        typedef typename Fibre<TIndex, QGramDir>::Type TDir;
+        typedef typename Iterator<TDir, Standard>::Type TIter;
+        unsigned int const alphabet_size = ValueSize<TAlphabet>::VALUE;
+        //unsigned int const column_size = (unsigned int) std::pow((double) alphabet_size, (int) order);
+        unsigned int column_size = (unsigned int) std::pow((double) alphabet_size, (int) order);
+
+        //Special case of order 0 marko model:
+        //A Bernoulli scheme is a special case of a Markov chain where the transition probability matrix has identical rows, which means that the next state is even independent of the current state (in addition to being independent of the past states).
+        if(order==0)
+        {
+            column_size=alphabet_size;
+
+        }
+
+        TIndex ind(strings);
+        resize(indexShape(ind), order + 1);
+        indexRequire(ind, QGramSADir());
+
+        TIter itBegin = begin(indexDir(ind), Standard());
+        TIter itEnd = end(indexDir(ind), Standard()) - 1;
+
+        //Frequency of all q-grams for a markov model of order q-1 to calculate transition probabilitiesof (q-1) gram to next (q-1)gram
+        String<TAlphabet> qgram;
+        Shape<TAlphabet, SimpleShape> orderShape;
+        resize(orderShape, order);
+        if(order==0)
+        {
+            resize(orderShape, order+1);
+        }
+
+        //count transition of sequences according to model order
+        for(TIter itA = itBegin; itA != itEnd; ++itA)
+        {
+            unhash(qgram, itA - itBegin, weight(indexShape(ind)));
+            //std::cout<<"\n"<<qgram<<"\n"<<(*(itA+1) - *itA)<<"\n"<<hash(orderShape, begin(qgram));
+            //old for the array: value(transition, hash(orderShape, begin(qgram)) * column_size + hash(orderShape, begin(qgram) + 1)) = *(itA+1) - *itA;
+
+            if(order==0)
+            {
+                for(unsigned int row=0;row<column_size;++row)
+                {
+                    value(transition, row,hash(orderShape, begin(qgram))) = static_cast<TFloat>(*(itA+1) - *itA);
+                }
+            }
+            else
+            {
+                //new for the matrix
+                value(transition, hash(orderShape, begin(qgram)),hash(orderShape, begin(qgram) + 1)) = static_cast<TFloat>(*(itA+1) - *itA);
+            }
+        }
+        //std::cout<<"\n"<<transition<<"\n\n";
+
+        //normalization, rows have to sum up to 1
+        for(unsigned int row = 0; row < column_size;++row)
+        {
+            TFloat sum = 0;
+            for(unsigned int col = 0; col < column_size;++col)
+            {
+                sum += value(transition, row,col);    //sum of the rows
+            }
+            if (sum != 0)
+            {
+                for(unsigned int col = 0; col < column_size;++col)
+                {
+                    value(transition, row, col) /= sum;    //normalize by dividing by sum of rows
+                }
+            }
+        }
+//std::cout<<transition<<"\n\n";
+        //Special case of order 0 marko model:
+        //A Bernoulli scheme is a special case of a Markov chain where the transition probability matrix has identical rows, which means that the next state is even independent of the current state (in addition to being independent of the past states).
+        if(order==0)
+        {
+            order=1;
+        }
+        //----Calculation of stationary Distribution-----
+        TMatrix temp = transition;
+        //initialise a variable t representing a good threshold to estimate the vector
+        //after multiplying t times the transition matrix with itself
+        unsigned int t=6;
+        for (unsigned int i=0; i<t; i++)
+        {
+            temp=temp*temp;
+        }
+
+        for (unsigned int i=0; i<column_size; i++){
+            value(stationaryDistribution,i)=value(temp, 0,i);
+
+        }
+        //std::cout<<temp<<"\n\n";
+
+        //for(unsigned int i=0;i<length(stationaryDistribution);++i){std::cout<<stationaryDistribution[i]<<"\t";}
+        //!is commented since I dont use it and it makes everything very slow for k>3 or 4
+        //!call ensureAuxMatrices(markovModel);
+        //_computeAuxiliaryMatrices();
+
+
+    }
+
+
+    ///////////////////////////////////////////////////////////////
+    ///// EMITTEDPROBABILITY
+    ///////////////////////////////////////////////////////////////
+
+
+    template <typename TString, typename TSetSpec>
+    TFloat emittedProbability(StringSet<TString, TSetSpec > const &stringSet)
+    {
+        TFloat p = 0;
+
+        for(unsigned int i=0; i<length(stringSet); i++)
+        {
+            p+= emittedProbability(stringSet[i]);
+        }
+
+        return p;
+    }
+
+    template <typename TString>
+    TFloat emittedProbability(TString const &string)
+    {
+        Shape<TAlphabet, SimpleShape> orderShape;
+        resize(orderShape, order);
+
+        int row = hash(orderShape,begin(string));
+        TFloat p = value(stationaryDistribution,row);
+
+        for(unsigned int i=1; i<(length(string)-order+1); i++)
+        {
+            int column=hash(orderShape,begin(string)+i);
+            p*=value(transition,row,column);
+
+            row = column;
+        }
+
+        return p;
+    }
+
+
+    ///////////////////////////////////////////////////////////////
+    ///// SET THE MODEL
+    ///////////////////////////////////////////////////////////////
+
+
+    void set(Matrix<TFloat,2> &iTransition)
+    {
+        unsigned int const alphabet_size = ValueSize<TAlphabet>::VALUE;
+        unsigned int const column_size = (unsigned int) std::pow((double) alphabet_size, (int) order);
+
+        transition = iTransition;
+
+        Matrix<TFloat,2> temp = transition;
+        //initialise a variable t representing a good threshold to estimate the vector
+        //after multiplying e times the transition matrix with itself
+        unsigned int t=6;
+        for (unsigned int i=0; i<t; i++){
+            temp=temp*temp;
+        }
+
+        for (unsigned int i=0; i<column_size; i++){
+            value(stationaryDistribution,i)=value(temp, 0,i);    //Set stationary distribution to row of transition^6
+        }
+
+        //_computeAuxiliaryMatrices();
+    }
+
+
+
+    void set(Matrix<TFloat,2> &iTransition, String<TFloat> &iStationaryDistribution)
+    {
+        transition = iTransition;
+
+        stationaryDistribution = iStationaryDistribution;
+
+        //_computeAuxiliaryMatrices();
+    }
+
+
+    ///////////////////////////////////////////////////////////////
+    ///// WRITE
+    ///////////////////////////////////////////////////////////////
+
+
+    void write(FILE *file)
+    {
+        ensureAuxMatrices(*this);
+        unsigned int const alphabet_size = ValueSize<TAlphabet>::VALUE;
+        unsigned int const column_size = (unsigned int) std::pow((double) alphabet_size, (int) order);
+
+        //write the transition matrix
+        for(unsigned int row=0; row<column_size; row++){
+            for(unsigned int col=0; col<column_size; col++){
+              fprintf(file,"%f ",value(transition, row,col));
+            }
+            fprintf(file,"\n");
+        }
+        //write the stationary distribution vector
+        for(unsigned int row=0; row<column_size; row++){
+              fprintf(file,"%f ",value(stationaryDistribution, row));
+            }
+        fprintf(file,"\n");
+
+        if(length(_q)){
+            //write the auxiliary matrix
+            for(unsigned int row=0; row<column_size; row++){
+                for(unsigned int col=0; col<column_size; col++){
+                    fprintf(file,"%f ",value(_q, row,col));
+                }
+                fprintf(file,"\n");
+            }
+
+            for(unsigned int row=0; row<column_size; row++){
+                for(unsigned int col=0; col<column_size; col++){
+                  fprintf(file,"%f ",value(_qppp,row,col));
+                }
+                fprintf(file,"\n");
+            }
+
+            for(unsigned int row=0; row<column_size; row++){
+                for(unsigned int col=0; col<column_size; col++){
+                fprintf(file,"%f ",value(_qppqpp, row,col));
+                }
+                fprintf(file,"\n");
+            }
+        }
+    }
+
+
+    ///////////////////////////////////////////////////////////////
+    ///// READ
+    ///////////////////////////////////////////////////////////////
+
+    void read(FILE *file)
+    {
+        unsigned int const alphabet_size = ValueSize<TAlphabet>::VALUE;
+        unsigned int const column_size = (unsigned int) std::pow((double) alphabet_size, (int) order);
+
+        //read the transition matrix
+        for(unsigned int row=0; row<column_size; row++)
+        {
+            for(unsigned int col=0; col<column_size; col++)
+            {
+              int unused = fscanf(file,"%lf ", & value(transition, row,col));
+              (void)unused;
+            }
+            int unused = fscanf(file,"\n");
+            (void)unused;
+        }
+        //read the stationary distribution vector
+        for(unsigned int row=0; row<column_size; row++)
+        {
+            int unused = fscanf(file,"%lf ",&value(stationaryDistribution, row));
+        (void)unused;
+        }
+        int unused = fscanf(file,"\n");
+        (void)unused;
+
+        if (!feof(file))
+        {
+            setLength(_q, 0, column_size);
+            setLength(_q, 1, column_size);
+            resize(_q);
+
+            //read the auxiliary matrix
+            for(unsigned int row=0; row<column_size; row++)
+            {
+                for(unsigned int col=0; col<column_size; col++)
+                {
+                    int unused = fscanf(file,"%lf ",&value(_q, row,col));
+                    (void)unused;
+                }
+                int unused = fscanf(file,"\n");
+                (void)unused;
+            }
+            setLength(_qppp, 0, column_size);
+            setLength(_qppp, 1, column_size);
+            resize(_qppp);
+            for(unsigned int row=0; row<column_size; row++){
+                for(unsigned int col=0; col<column_size; col++){
+                  int unused = fscanf(file,"%lf ",&value(_qppp, row,col));
+                  (void)unused;
+                }
+                int unused = fscanf(file,"\n");
+                (void)unused;
+            }
+            setLength(_qppqpp, 0, column_size);
+            setLength(_qppqpp, 1, column_size);
+            resize(_qppqpp);
+            for(unsigned int row=0; row<column_size; row++){
+                for(unsigned int col=0; col<column_size; col++){
+                    int unused = fscanf(file,"%lf ",&value(_qppqpp, row,col));
+                    (void)unused;
+                }
+                int unused = fscanf(file,"\n");
+                (void)unused;
+            }
+        }
+    }
+
+
+    /////////////////////////////////////////////////////////////////////////////
+    ///// COMPUTE THE AUXILIARY MATRICES FOR THE VARIANCE And Z-SCORE COMPUTATION
+    /////////////////////////////////////////////////////////////////////////////
+
+
+
+    void _computeAuxiliaryMatrices()
+    {
+    //std::cout<<"auxMat\n";
+        //clear(_q);
+        //clear(_qppp);
+        //clear(_qppqpp);
+
+        unsigned int const alphabet_size = ValueSize<TAlphabet>::VALUE;
+        unsigned int const column_size = (unsigned int) std::pow((double) alphabet_size, (int) order);
+        TMatrix I;
+        TMatrix Ip;
+
+        //resize the matrices
+        setLength(I, 0, column_size);
+        setLength(I, 1, column_size);
+        resize(I, 0.0);
+
+        setLength(Ip, 0, column_size);
+        setLength(Ip, 1, column_size);
+        resize(Ip, 0.0);
+
+        for(unsigned int i=0; i<column_size; i++){
+            value(I,i,i)=1.0;
+             for (unsigned int j=0; j<column_size; j++)
+                value(Ip,i,j)=value(stationaryDistribution,j);
+        }
+
+
+        _q=transition-I;
+        _q=_q+Ip;
+        _q=_computeInverseMatrix(_q);//works for simple non singular matrices, others not checked
+        //original code: _q=_computeInverseMatrix(_matricialSum(_matricialDifference(transition, I), Ip));
+
+        _qppp=_q*transition;
+        _qppqpp = _qppp*transition;
+        _qppqpp = _qppqpp*_q;
+        for(unsigned int i=1; i<order; i++)
+        {
+            _qppp=_qppp*transition;
+            _qppqpp=_qppqpp*transition;
+        }
+    }
+
+
+};
+
+//////////////////////////////////////////////////////////////////////////////
+// _computeInverseMatrix
+//////////////////////////////////////////////////////////////////////////////
+
+/*
+ * @fn _computeInverseMatrix
+ * @brief Computes the inverse matrix of a given matrix.
+ *
+ * @signature TMatrix _computeInverseMatrix(matrix);
+ *
+ * @param[in] matrix The matrix in the input (2-dimensional Matrix).
+ *
+ * @return TMatrix The inverse matrix, the same type as matrix.
+ */
+
+template <typename TValue>
+Matrix<TValue,2> _computeInverseMatrix(Matrix<TValue,2> &matrix)
+{
+    typedef Matrix<TValue,2> TMatrix;
+    unsigned int n = length(matrix,0);
+    TMatrix result;
+    //resize the matrix
+    setLength(result, 0, n);
+    setLength(result, 1, n);
+    resize(result, 0.0);
+
+    //copy the matrix in result, since the procedure is in-place
+    TMatrix tmp = matrix;
+
+    //lu decomposition of a in-place
+    String<TValue> indx=_ludcmp(tmp);
+
+    String<TValue> col;
+
+    unsigned int i;
+
+    // inverse by columns
+    for (unsigned int j=0; j<n; j++)
+    {
+        resize(col,n,0);
+        if(j>0)
+        {
+            for(i=0; i<n; i++)
+            {
+                value(col,i)=0;
+            }
+        }
+        value(col,j) = 1;
+
+        _lubksb(tmp,indx,col);
+
+        for (i=0; i<n; i++)
+        {
+            value(result, i,j)= value(col,i);
+        }
+
+    }
+
+    return result;
+}
+
+/*
+ *
+ * LU decomposition
+ *
+ */
+
+template <typename TValue>
+String<TValue> _ludcmp(Matrix<TValue,2> &result)
+{
+    double const TINY = 1.0e-20;
+    int n = length(result,0);
+    int i, imax, j, k,d;
+    imax = MinValue<int>::VALUE;
+    double big,dum,sum,temp;
+    String<TValue> vv;
+    resize(vv, n, 1.0);
+
+
+    d = 1;
+    for (i=1; i<=n; i++)
+    {
+        big = 0.0;
+        for (j=1; j<=n; j++)
+        {
+            if ((temp=fabs(value(result, i-1,j-1)))>big)
+            {
+                big = temp;
+            }
+        }
+        if (big==0.0)
+        {
+            std::cout<<"Singular matrix in routine ludcmp" << std::endl;
+            exit(1);
+        }
+
+        value(vv,i-1) = 1.0/big;
+    }
+    String<TValue> indx;
+    resize(indx,n);
+
+    for (j=1; j<=n; j++)
+    {
+        for (i=1; i<j; i++)
+        {
+            sum = value(result,i-1,j-1);
+            for (k=1; k<i; k++)
+            {
+                sum -= value(result, i-1,k-1)*value(result, k-1,j-1);
+            }
+            value(result, i-1,j-1) = sum;
+        }
+        big = 0.0;
+        for (i=j; i<=n; i++)
+        {
+            sum = value(result,i-1,j-1);
+            for (k=1; k<j; k++)
+            {
+                sum -= value(result, i-1,k-1)*value(result, k-1,j-1);
+            }
+            value(result, i-1,j-1) = sum;
+            if ((dum = value(vv, i-1)*fabs(sum))>=big)
+            {
+                big = dum;
+                imax = i;
+            }
+        }
+        if (j != imax)
+        {
+            for (k=1; k<=n; k++)
+            {
+                dum = value(result,imax-1,k-1);
+                value(result, imax-1,k-1) = value(result, j-1,k-1);
+                value(result,j-1,k-1) = dum;
+            }
+            d = -(d);
+            value(vv, imax-1)=value(vv,j-1);
+        }
+
+        value(indx, j-1) = imax;
+
+        if (value(result, j-1,j-1) == 0.0)
+        {
+            value(result, j-1,j-1) = TINY;
+        }
+        if (j!=n)
+        {
+            dum = 1.0/(value(result,j-1,j-1));
+            for (i=j+1; i<=n; i++)
+            {
+                value(result, i-1,j-1) *= dum;
+            }
+        }
+  }
+
+ return indx;
+
+}
+
+
+template <typename TValue>
+void _lubksb(Matrix<TValue,2> &a, String<TValue> &indx, String<TValue>  &b)
+{
+    int n =length(a,0);    //Number of columns in matrix a
+    int i, ii=0,ip,j;
+    double sum;
+
+    for (i=1; i<=n; i++)
+    {
+        ip = static_cast<int>(value(indx,i-1));
+        sum = value(b,ip-1);
+        value(b,ip-1) = value(b,i-1);
+        if (ii)
+        {
+            for (j=ii;j<=i-1;j++)
+            {
+                sum -=value(a,i-1,j-1)*value(b,j-1);
+            }
+        }
+        else
+        if (sum)
+        {
+            ii=i;
+        }
+        value(b,i-1) = sum;
+    }
+    for (i=n; i>=1; i--)
+    {
+        sum = value(b,i-1);
+        for (j=i+1; j<=n; j++)
+        {
+            sum -= value(a,i-1,j-1)*value(b,j-1);
+        }
+        value(b,i-1) = sum/value(a,i-1,i-1);
+    }
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Interface
+//////////////////////////////////////////////////////////////////////////////
+
+
+///////////////////////////////////////////////////////////////
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+void buildMarkovModel(MarkovModel<TAlphabet, TFloat, TSpec> &mm,
+        StringSet<String<TAlphabet > > &stringSet)
+{
+
+    mm.build(stringSet);
+
+}
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+void buildMarkovModel(MarkovModel<TAlphabet, TFloat, TSpec> &mm,
+        StringSet<String<TAlphabet > > const &stringSet)
+{
+
+    mm.build(stringSet);
+
+}
+
+
+///////////////////////////////////////////////////////////////
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+void setMarkovModel(MarkovModel<TAlphabet, TFloat, TSpec> & mm,
+                    Matrix<TFloat,2> &iTransition)
+{
+    mm.set(iTransition);
+}
+
+
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+void setMarkovModel(MarkovModel<TAlphabet, TFloat, TSpec> & mm,
+                    Matrix<TFloat,2> &iTransition,
+                    String<TFloat> &iStationaryDistribution)
+{
+    mm.set(iTransition, iStationaryDistribution);
+}
+
+///////////////////////////////////////////////////////////////
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+TFloat emittedProbability(MarkovModel<TAlphabet, TFloat, TSpec> & mm,
+        StringSet<String<TAlphabet > > & stringSet)
+{
+    return mm.emittedProbability(stringSet);
+}
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+TFloat emittedProbability(MarkovModel<TAlphabet, TFloat, TSpec> & mm,
+                          String<TAlphabet> &string)
+{
+    return mm.emittedProbability(string);
+}
+
+//const
+template <typename TAlphabet, typename TFloat, typename TSpec, typename TString, typename TSetSpec>
+TFloat emittedProbability(MarkovModel<TAlphabet, TFloat, TSpec> & mm,
+        StringSet<TString, TSetSpec> const &stringSet)
+{
+    return mm.emittedProbability(stringSet);
+}
+
+template <typename TAlphabet, typename TFloat, typename TSpec, typename TString>
+TFloat emittedProbability(MarkovModel<TAlphabet, TFloat, TSpec> & mm,
+                          TString const &string)
+{
+    return mm.emittedProbability(string);
+}
+
+///////////////////////////////////////////////////////////////
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+void write(FILE *file,
+           MarkovModel<TAlphabet, TFloat, TSpec> & mm )
+{
+//IOREV only defined for FILE* not for File(), uses custom io with fprintf
+    mm.write(file);
+}
+
+///////////////////////////////////////////////////////////////
+
+template <typename TAlphabet, typename TFloat, typename TSpec>
+void read(FILE *file,
+          MarkovModel<TAlphabet, TFloat, TSpec> & mm )
+{
+//IOREV only defined for FILE* not for File(), uses custom io with fscanf
+    mm.read(file);
+}
+//////////////////////////////////////////////////////////////////////////////
+template <typename TAlphabet, typename TFloat, typename TSpec>
+void ensureAuxMatrices(MarkovModel<TAlphabet, TFloat, TSpec> & mm )
+{
+
+    if(empty(mm._q)){
+        mm._computeAuxiliaryMatrices();
+    }
+}
+
+
+}
+
+#endif  // #ifndef SEQAN_STATISTICS_STATISTICS_MARKOV_MODEL_H_
diff --git a/seqan/store.h b/seqan/store.h
index 78e2af4..6ab5f94 100644
--- a/seqan/store.h
+++ b/seqan/store.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -36,18 +36,18 @@
 #include <seqan/basic.h>
 #include <seqan/sequence.h>
 #include <seqan/align.h>
-#include <seqan/file.h>
+#include <seqan/stream.h>
 #include <seqan/parallel.h>
+#include <seqan/seq_io.h>
 #include <seqan/bam_io.h>
-#include <seqan/misc/misc_name_store_cache.h>
+#include <seqan/gff_io.h>
+#include <seqan/ucsc_io.h>
+#include <seqan/misc/name_store_cache.h>
 
 #include <sstream>
 #include <algorithm>
 #include <set>
 
-#include <seqan/gff_io.h>
-#include <seqan/stream.h>
-
 //////////////////////////////////////////////////////////////////////////////
 // FRAGMENT STORE SUB-CONTAINERS
 //////////////////////////////////////////////////////////////////////////////
@@ -64,9 +64,9 @@
 #include <seqan/store/store_align_intervals.h>
 #include <seqan/store/store_intervaltree.h>
 
-#include <seqan/store/store_io.h>
-#include <seqan/store/store_io_sam.h>
-#include <seqan/store/store_io_gff.h>
-#include <seqan/store/store_io_ucsc.h>
+// #include <seqan/store/store_io.h>
+// #include <seqan/store/store_io_sam.h>
+// #include <seqan/store/store_io_gff.h>
+// #include <seqan/store/store_io_ucsc.h>
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/store/INFO b/seqan/store/INFO
deleted file mode 100644
index cd16c9e..0000000
--- a/seqan/store/INFO
+++ /dev/null
@@ -1,12 +0,0 @@
-Name: seqan-store
-Author: David Weese <david.weese@fu-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Contains the fragment store for NGS or assembly data.
- The store module contains the FragmentStore class and related code for storing
- NGS and assembly data.  The fragment store provides data structures for the
- efficient in-memory handling of multi-read alignments.
- .
- SAM files can be read into and written out from fragment store objects
diff --git a/seqan/store/store_align.h b/seqan/store/store_align.h
index 5ed9d33..2f83eb9 100644
--- a/seqan/store/store_align.h
+++ b/seqan/store/store_align.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -80,18 +80,22 @@ namespace SEQAN_NAMESPACE_MAIN
 
  /*!
  * @typedef AlignedReadStoreElement::TId
+ * @signature typedef (..) TAlignedReadStoreElement::TId;
  * @brief Type of all store ids.
  *
  * <tt>TId</tt> is the result of <tt>Id&lg;AlignedReadStoreElement&lgt;&gt; &gt;::Type</tt>, see @link Id @endlink.
  *
  * @typedef AlignedReadStoreElement::TPos
+ * @signature typedef (..) TAlignedReadStoreElement::TPos;
  * @brief Type of the @link AlignedReadStoreElement::beginPos @endlink and @link AlignedReadStoreElement::endPos
  *        @endlink.
  *
  * @typedef AlignedReadStoreElement::TGapAnchors
+ * @signature typedef (..) TAlignedReadStoreElement::TGapAnchors;
  * @brief Type of the @link AlignedReadStoreElement::gaps @endlink member.
  *
  * @typedef AlignedReadStoreElement::TSpec
+ * @signature typedef (..) TAlignedReadStoreElement::TSpec;
  * @brief The specializing type.
  */
 
@@ -130,123 +134,43 @@ namespace SEQAN_NAMESPACE_MAIN
  *        alignment row.
  */
 
-/**
-.Class.AlignedReadStoreElement
-..summary:Represents an alignment between read and contig.
-..cat:Fragment Store
-..signature:AlignedReadStoreElement<>
-..signature:AlignedReadStoreElement<TPos[, TGapAnchor[, TSpec]]>
-..param.TPos:Type to store (gap-space) positions.
-..param.TGapAnchor:Type of a read gap anchor.
-...type:Class.GapAnchor
-..param.TSpec:The specialization type.
-...default:$void$
-..remarks:Value type of the @Memvar.FragmentStore#alignedReadStore@ string.
-In contrast to all other @Class.FragmentStore@ stores, the @Memvar.AlignedReadStoreElement#id@ of an aligned read is explicitly stored
-as a member to allow for random reordering of the @Memvar.FragmentStore#alignedReadStore@, e.g. sorting by genomic position via @Function.sortAlignedReads@.
-..include:seqan/store.h
-
-.Typedef.AlignedReadStoreElement#TId
-..summary:Type of all stored ids.
-..remarks:$TId$ equals the result of $Id<AlignedReadStoreElement<> >::Type$, see @Metafunction.Id@.
-..class:Class.AlignedReadStoreElement
-.Typedef.AlignedReadStoreElement#TPos
-..summary:Type of the @Memvar.AlignedReadStoreElement#beginPos@ and @Memvar.AlignedReadStoreElement#endPos@ members.
-..class:Class.AlignedReadStoreElement
-.Typedef.AlignedReadStoreElement#TGapAnchors
-..summary:Type of the @Memvar.AlignedReadStoreElement#gaps@ member.
-..class:Class.AlignedReadStoreElement
-.Typedef.AlignedReadStoreElement#TSpec
-..summary:The specialization type.
-..class:Class.AlignedReadStoreElement
-
-.Memfunc.AlignedReadStoreElement#AlignedReadStoreElement
-..summary:Constructor
-..signature:AlignedReadStoreElement()
-..signature:AlignedReadStoreElement(id, readId, contigId, beginPos, endPos[, gaps])
-..param.id:The alignment id refers to associated alignment information in @Memvar.FragmentStore#alignQualityStore@ or @Memvar.FragmentStore#alignedReadTagStore@.
-..param.readId:Refers to the aligned read in the @Memvar.FragmentStore#readStore@.
-..param.contigId:Refers to the contig in the @Memvar.FragmentStore#contigStore@ the read is aligned with.
-..param.beginPos:Begin position of the alignment in gap-space.
-..param.endPos:End position of the alignment in gap-space.
-..param.gaps:Read gap anchors.
-..remarks:The default constructor sets all ids to @Memvar.AlignedReadStoreElement#INVALID_ID@ and
-@Memvar.AlignedReadStoreElement#beginPos@ and @Memvar.AlignedReadStoreElement#endPos@ to $0$.
-..class:Class.AlignedReadStoreElement
-
-.Memvar.AlignedReadStoreElement#id
-..summary:The alignment id refers to associated alignment information in @Memvar.FragmentStore#alignQualityStore@ or @Memvar.FragmentStore#alignedReadTagStore@.
-..type:Metafunction.Id
-..class:Class.AlignedReadStoreElement
-.Memvar.AlignedReadStoreElement#readId
-..summary:Refers to the aligned read in the @Memvar.FragmentStore#readStore@.
-..type:Metafunction.Id
-..class:Class.AlignedReadStoreElement
-.Memvar.AlignedReadStoreElement#contigId
-..summary:Refers to the contig in the @Memvar.FragmentStore#contigStore@ the read is aligned with.
-..type:Metafunction.Id
-..class:Class.AlignedReadStoreElement
-.Memvar.AlignedReadStoreElement#pairMatchId
-..summary:Two read alignments having the same @Memvar.AlignedReadStoreElement#pairMatchId@ form a valid pair match.
-If it equals @Memvar.AlignedReadStoreElement#INVALID_ID@, the read is either not paired or could not be aligned as part of a pair match.
-..type:Metafunction.Id
-..class:Class.AlignedReadStoreElement
-.Memvar.AlignedReadStoreElement#beginPos
-..summary:Begin position of the alignment in gap-space.
-..type:Typedef.AlignedReadStoreElement#TPos
-..class:Class.AlignedReadStoreElement
-.Memvar.AlignedReadStoreElement#endPos
-..summary:End position of the alignment in gap-space. If @Memvar.AlignedReadStoreElement#endPos@ < @Memvar.AlignedReadStoreElement#beginPos@, the read is aligned to the reverse strand, 
-where @Memvar.AlignedReadStoreElement#beginPos@ and @Memvar.AlignedReadStoreElement#endPos@ are the corresponding positions on the forward strand.
-..type:Typedef.AlignedReadStoreElement#TPos
-..class:Class.AlignedReadStoreElement
-.Memvar.AlignedReadStoreElement#gaps
-..summary:String of read gap anchors. Can be used to create a @Spec.AnchorGaps@ alignment row.
-..type:Typedef.AlignedReadStoreElement#TGapAnchors
-..class:Class.AlignedReadStoreElement
-.Memvar.AlignedReadStoreElement#INVALID_ID
-..summary:Constant to represent an invalid id.
-..type:Metafunction.Id
-..class:Class.AlignedReadStoreElement
-*/
-
 template <typename TPos_, typename TGapAnchor_, typename TSpec_ = void>
 struct AlignedReadStoreElement
 {
-	typedef typename Id<AlignedReadStoreElement>::Type	TId;
-	typedef TPos_										TPos;
-	typedef TGapAnchor_									TGapAnchor;
-	typedef TSpec_										TSpec;
-	typedef String<TGapAnchor>							TGapAnchors;
-
-	static const TId INVALID_ID;
-	
-	TId			id;
-	TId			readId;
-	TId			contigId;
-	TId			pairMatchId;	// unique id. for multiple mate-pair matches (not matePairId)
-	TPos		beginPos;		// begin position of the gapped sequence in gapped contig sequence
-	TPos		endPos;			// end position of ..., for reverse aligned reads holds end < begin
-	TGapAnchors	gaps;
-
-	AlignedReadStoreElement() : id(INVALID_ID), readId(INVALID_ID), contigId(INVALID_ID), pairMatchId(INVALID_ID), beginPos(0), endPos(0) {}
-
-	AlignedReadStoreElement(TId _id, TId _readId, TId _contigId, TPos _beginPos, TPos _endPos) :
-		id(_id), 
-		readId(_readId), 
-		contigId(_contigId), 
-		pairMatchId(INVALID_ID), 
-		beginPos(_beginPos), 
-		endPos(_endPos) {}
-
-	AlignedReadStoreElement(TId _id, TId _readId, TId _contigId, TPos _beginPos, TPos _endPos, TGapAnchors const &_gaps) :
-		id(_id), 
-		readId(_readId), 
-		contigId(_contigId), 
-		pairMatchId(INVALID_ID), 
-		beginPos(_beginPos), 
-		endPos(_endPos),
-		gaps(_gaps) {}
+    typedef typename Id<AlignedReadStoreElement>::Type    TId;
+    typedef TPos_                                        TPos;
+    typedef TGapAnchor_                                    TGapAnchor;
+    typedef TSpec_                                        TSpec;
+    typedef String<TGapAnchor>                            TGapAnchors;
+
+    static const TId INVALID_ID;
+
+    TId            id;
+    TId            readId;
+    TId            contigId;
+    TId            pairMatchId;    // unique id. for multiple mate-pair matches (not matePairId)
+    TPos        beginPos;        // begin position of the gapped sequence in gapped contig sequence
+    TPos        endPos;            // end position of ..., for reverse aligned reads holds end < begin
+    TGapAnchors    gaps;
+
+    AlignedReadStoreElement() : id(INVALID_ID), readId(INVALID_ID), contigId(INVALID_ID), pairMatchId(INVALID_ID), beginPos(0), endPos(0) {}
+
+    AlignedReadStoreElement(TId _id, TId _readId, TId _contigId, TPos _beginPos, TPos _endPos) :
+        id(_id),
+        readId(_readId),
+        contigId(_contigId),
+        pairMatchId(INVALID_ID),
+        beginPos(_beginPos),
+        endPos(_endPos) {}
+
+    AlignedReadStoreElement(TId _id, TId _readId, TId _contigId, TPos _beginPos, TPos _endPos, TGapAnchors const &_gaps) :
+        id(_id),
+        readId(_readId),
+        contigId(_contigId),
+        pairMatchId(INVALID_ID),
+        beginPos(_beginPos),
+        endPos(_endPos),
+        gaps(_gaps) {}
 
     inline bool operator==(AlignedReadStoreElement const & other) const
     {
@@ -270,9 +194,9 @@ TStream & operator<<(TStream & stream, AlignedReadStoreElement<TPos, TGapAnchor,
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TPos, typename TGapAnchor, typename TSpec> 
-const typename Id<AlignedReadStoreElement<TPos, TGapAnchor, TSpec> >::Type 
-AlignedReadStoreElement<TPos, TGapAnchor, TSpec>::INVALID_ID = MaxValue<typename Id<AlignedReadStoreElement<TPos, TGapAnchor, TSpec> >::Type>::VALUE; 
+template <typename TPos, typename TGapAnchor, typename TSpec>
+const typename Id<AlignedReadStoreElement<TPos, TGapAnchor, TSpec> >::Type
+AlignedReadStoreElement<TPos, TGapAnchor, TSpec>::INVALID_ID = MaxValue<typename Id<AlignedReadStoreElement<TPos, TGapAnchor, TSpec> >::Type>::VALUE;
 
 //////////////////////////////////////////////////////////////////////////////
 
@@ -294,7 +218,7 @@ AlignedReadStoreElement<TPos, TGapAnchor, TSpec>::INVALID_ID = MaxValue<typename
  * @brief Constructor, sets all members to 0.
  *
  * @signature AlignQualityStoreElement::AlignQualityStoreElement();
- * 
+ *
  *
  * @var TScore AlignQualityStoreElement::pairScore;
  * @brief Combined score of both alignmetns and pair match.
@@ -306,51 +230,22 @@ AlignedReadStoreElement<TPos, TGapAnchor, TSpec>::INVALID_ID = MaxValue<typename
  * @brief Absolute number of errors in the alignment (<tt>unsigned char</tt>).
  */
 
-/**
-.Class.AlignQualityStoreElement
-..summary:Stores alignment qualities.
-..cat:Fragment Store
-..signature:AlignQualityStoreElement<TScore[, TSpec]>
-..param.TScore:Type to store align and pair score values.
-..param.TSpec:The specialization type.
-...default:$void$
-..remarks:Value type of the @Memvar.FragmentStore#alignQualityStore@ string.
-
-.Memfunc.AlignQualityStoreElement#AlignQualityStoreElement
-..summary:Constructor
-..signature:AlignQualityStoreElement<TScore[, TSpec]> ()
-..remarks:Sets all members to $0$.
-
-..class:Class.AlignQualityStoreElement
-.Memvar.AlignQualityStoreElement#pairScore
-..summary:Combined score of both alignments of a pair match.
-..class:Class.AlignQualityStoreElement
-.Memvar.AlignQualityStoreElement#score
-..summary:Score of the alignment.
-..class:Class.AlignQualityStoreElement
-.Memvar.AlignQualityStoreElement#errors
-..summary:Absolute number of errors in the alignment.
-..type:nolink:unsigned char
-..class:Class.AlignQualityStoreElement
-..include:seqan/store.h
-*/
-
 template <typename TScore, typename TSpec = void>
 struct AlignQualityStoreElement
 {
-	TScore				pairScore;		// score of the mate-pair alignment (this read is part of)
-	TScore				score;			// score of the single read alignment
-	unsigned char		errors;			// absolute number of errors (Hamming or edit distance)
-	
-	AlignQualityStoreElement():
-		pairScore(0),
-		score(0),
-		errors(0) {}
-
-	AlignQualityStoreElement(TScore _pairScore, TScore _score, unsigned char _errors):
-		pairScore(_pairScore),
-		score(_score),
-		errors(_errors) {}
+    TScore                pairScore;        // score of the mate-pair alignment (this read is part of)
+    TScore                score;            // score of the single read alignment
+    unsigned char        errors;            // absolute number of errors (Hamming or edit distance)
+
+    AlignQualityStoreElement():
+        pairScore(0),
+        score(0),
+        errors(MaxValue<unsigned char>::VALUE) {}
+
+    AlignQualityStoreElement(TScore _pairScore, TScore _score, unsigned char _errors):
+        pairScore(_pairScore),
+        score(_score),
+        errors(_errors) {}
 
     inline bool operator==(AlignQualityStoreElement const & other)
     {
@@ -410,34 +305,6 @@ struct AlignQualityStoreElement
  * @signature typedef Tag<SortReadId_> const SortReadId;
  */
 
-/**
-.Tag.sortAlignedRead Tags
-..summary:Tag to select a specific field to stably sort the @Memvar.FragmentStore#alignedReadStore@ by.
-..cat:Fragment Store
-..see:Function.sortAlignedReads
-..see:Function.lowerBoundAlignedReads
-..see:Function.upperBoundAlignedReads
-..tag.SortContigId:
-...summary:Sort alignedReads by @Memvar.AlignedReadStoreElement#contigId@.
-...signature:SortContigId
-..tag.SortId:
-...summary:Sort alignedReads by @Memvar.AlignedReadStoreElement#id@.
-...signature:SortId
-..tag.SortBeginPos:
-...summary:Sort alignedReads by @Memvar.AlignedReadStoreElement#beginPos@.
-...signature:SortBeginPos
-..tag.SortEndPos:
-...summary:Sort alignedReads by @Memvar.AlignedReadStoreElement#endPos@.
-...signature:SortEndPos
-..tag.SortPairMatchId:
-...summary:Sort alignedReads by @Memvar.AlignedReadStoreElement#pairMatchId@.
-...signature:SortPairMatchId
-..tag.SortReadId:
-...summary:Sort alignedReads by @Memvar.AlignedReadStoreElement#readId@.
-...signature:SortReadId
-..include:seqan/store.h
-*/
-
 struct SortContigId_;
 typedef Tag<SortContigId_> const SortContigId;
 
@@ -482,62 +349,62 @@ struct _LessAlignedRead;
 
 template <typename TAlignedRead>
 struct _LessAlignedRead<TAlignedRead, SortId> :
-	public ::std::binary_function<TAlignedRead, TAlignedRead, bool>
+    public std::binary_function<TAlignedRead, TAlignedRead, bool>
 {
-	inline bool 
-	operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
-		return (a1.id) < (a2.id);
-	}
+    inline bool
+    operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
+        return (a1.id) < (a2.id);
+    }
 };
 
 template <typename TAlignedRead>
 struct _LessAlignedRead<TAlignedRead, SortContigId> :
-	public ::std::binary_function<TAlignedRead, TAlignedRead, bool>
+    public std::binary_function<TAlignedRead, TAlignedRead, bool>
 {
-	inline bool 
-	operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
-		return a1.contigId < a2.contigId;
-	}
+    inline bool
+    operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
+        return a1.contigId < a2.contigId;
+    }
 };
 
 template <typename TAlignedRead>
 struct _LessAlignedRead<TAlignedRead, SortBeginPos> :
-	public ::std::binary_function<TAlignedRead, TAlignedRead, bool>
+    public std::binary_function<TAlignedRead, TAlignedRead, bool>
 {
-	inline bool 
-	operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
-		return _min(a1.beginPos, a1.endPos) < _min(a2.beginPos, a2.endPos);
-	}
+    inline bool
+    operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
+        return _min(a1.beginPos, a1.endPos) < _min(a2.beginPos, a2.endPos);
+    }
 };
 
 template <typename TAlignedRead>
 struct _LessAlignedRead<TAlignedRead, SortEndPos> :
-	public ::std::binary_function<TAlignedRead, TAlignedRead, bool>
+    public std::binary_function<TAlignedRead, TAlignedRead, bool>
 {
-	inline bool 
-	operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
-		return _max(a1.beginPos, a1.endPos) < _max(a2.beginPos, a2.endPos);
-	}
+    inline bool
+    operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
+        return _max(a1.beginPos, a1.endPos) < _max(a2.beginPos, a2.endPos);
+    }
 };
 
 template <typename TAlignedRead>
 struct _LessAlignedRead<TAlignedRead, SortPairMatchId> :
-	public ::std::binary_function<TAlignedRead, TAlignedRead, bool>
+    public std::binary_function<TAlignedRead, TAlignedRead, bool>
 {
-	inline bool 
-	operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
-		return a1.pairMatchId < a2.pairMatchId;
-	}
+    inline bool
+    operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
+        return a1.pairMatchId < a2.pairMatchId;
+    }
 };
 
 template <typename TAlignedRead>
 struct _LessAlignedRead<TAlignedRead, SortReadId> :
-	public ::std::binary_function<TAlignedRead, TAlignedRead, bool>
+    public std::binary_function<TAlignedRead, TAlignedRead, bool>
 {
-	inline bool 
-	operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
-		return a1.readId < a2.readId;
-	}
+    inline bool
+    operator() (TAlignedRead const& a1, TAlignedRead const& a2) const {
+        return a1.readId < a2.readId;
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -556,7 +423,7 @@ struct _LessAlignedRead<TAlignedRead, SortReadId> :
  * @signature void sortAlignedReads(alignStore, sortTag);
  * @signature void sortAlignedReads(alignStore, lessFunctor);
  *
- * @param[in,out] alignStore  The @link SequenceConcept sequence @endlink of @link AlignedReadStoreElement @endlink
+ * @param[in,out] alignStore  The @link ContainerConcept sequence @endlink of @link AlignedReadStoreElement @endlink
  *                            to be sorted, e.g. @link FragmentStore::alignedReadStore @endlink.
  * @param[in]     sortTag     Tag for selecting the member to sort by.  See @link SortAlignedReadTags @endlink.
  * @param[in]     lessFunctor A functor to pass to <tt>std::stable_sort</tt> for sorting the sequence.
@@ -574,7 +441,7 @@ struct _LessAlignedRead<TAlignedRead, SortReadId> :
  * @signature TIter1 lowerBoundAlignedReads(alignStore, value, sortTag);
  * @signature TIter2 lowerBoundAlignedReads(itBegin, itEnd, value, sortTag);
  *
- * @param[in,out] alignStore  The @link SequenceConcept sequence @endlink of @link AlignedReadStoreElement @endlink
+ * @param[in,out] alignStore  The @link ContainerConcept sequence @endlink of @link AlignedReadStoreElement @endlink
  *                            to be searched, e.g. @link FragmentStore::alignedReadStore @endlink.
  * @param[in]     itBegin     Iterator to the begin of the sequence to search.
  * @param[in]     itEnd       Iterator to the end of the sequence to search.
@@ -598,7 +465,7 @@ struct _LessAlignedRead<TAlignedRead, SortReadId> :
  * @signature TIter1 upperBoundAlignedReads(alignStore, value, sortTag);
  * @signature TIter2 upperBoundAlignedReads(itBegin, itEnd, value, sortTag);
  *
- * @param[in,out] alignStore  The @link SequenceConcept sequence @endlink of @link AlignedReadStoreElement @endlink
+ * @param[in,out] alignStore  The @link ContainerConcept sequence @endlink of @link AlignedReadStoreElement @endlink
  *                            to be searched, e.g. @link FragmentStore::alignedReadStore @endlink.
  * @param[in]     itBegin     Iterator to the begin of the sequence to search.
  * @param[in]     itEnd       Iterator to the end of the sequence to search.
@@ -614,510 +481,462 @@ struct _LessAlignedRead<TAlignedRead, SortReadId> :
  * @see lowerBoundAlignedReads
  */
 
-/**
-.Function.sortAlignedReads
-..summary:Stably sort aligned reads.
-..cat:Fragment Store
-..signature:sortAlignedReads(alignStore, sortTag)
-..signature:sortAlignedReads(alignStore, lessFunctor)
-..param.alignStore:A sequence of @Class.AlignedReadStoreElement@ to be sorted, e.g. @Memvar.FragmentStore#alignedReadStore@.
-..param.sortTag:Selects the field to sort by.
-...type:Tag.sortAlignedRead Tags
-..param.lessFunctor:STL-less functor to compare two @Class.AlignedReadStoreElement.AlignedReadStoreElements@.
-..remarks:This function calls $std::stable_sort$ to sort the @Memvar.FragmentStore#alignedReadStore@.
-..include:seqan/store.h
-..see:Function.lowerBoundAlignedReads
-..see:Function.upperBoundAlignedReads
-
-.Function.lowerBoundAlignedReads
-..summary:Performs a binary lower bound search on the aligned reads.
-..cat:Fragment Store
-..signature:lowerBoundAlignedReads(alignStore, value, sortTag)
-..signature:lowerBoundAlignedReads(itBegin, itEnd, value, sortTag)
-..param.alignStore:A sequence of @Class.AlignedReadStoreElement@ to be searched through, e.g. @Memvar.FragmentStore#alignedReadStore@.
-..param.itBegin:An iterator to the first element of the sequence of @Class.AlignedReadStoreElement@ to be searched through.
-..param.itEnd:An iterator behind the last element of the sequence of @Class.AlignedReadStoreElement@ to be searched through.
-..param.value:The value to use for the comparison.
-..param.sortTag:Selects the field for the comparison in the binary search.
-...type:Tag.sortAlignedRead Tags
-..remarks:This is equivalent to calling $std::lower_bound$ on @Memvar.FragmentStore#alignedReadStore@ with according parameters.
-..include:seqan/store.h
-..see:Function.sortAlignedReads
-..see:Function.upperBoundAlignedReads
-
-.Function.upperBoundAlignedReads
-..summary:Performs a binary upper bound search on the aligned reads.
-..cat:Fragment Store
-..signature:upperBoundAlignedReads(alignStore, value, sortTag)
-..signature:upperBoundAlignedReads(itBegin, itEnd, value, sortTag)
-..param.alignStore:A sequence of @Class.AlignedReadStoreElement@ to be searched through, e.g. @Memvar.FragmentStore#alignedReadStore@.
-..param.itBegin:An iterator to the first element of the sequence of @Class.AlignedReadStoreElement@ to be searched through.
-..param.itEnd:An iterator behind the last element of the sequence of @Class.AlignedReadStoreElement@ to be searched through.
-..param.value:The value to use for the comparison.
-..param.sortTag:Selects the field for the comparison in the binary search.
-...type:Tag.sortAlignedRead Tags
-..remarks:This is equivalent to calling $std::upper_bound$ on @Memvar.FragmentStore#alignedReadStore@ with according parameters.
-..include:seqan/store.h
-..see:Function.sortAlignedReads
-..see:Function.lowerBoundAlignedReads
-*/
-
 template <typename TAlign, typename TSortSpec>
 inline void
-sortAlignedReads(TAlign& alignStore, Tag<TSortSpec> const &) 
+sortAlignedReads(TAlign& alignStore, Tag<TSortSpec> const &)
 {
-	std::stable_sort(
-		begin(alignStore, Standard() ), 
-		end(alignStore, Standard() ), 
-		_LessAlignedRead<typename Value<TAlign>::Type, Tag<TSortSpec> const>() );
+    std::stable_sort(
+        begin(alignStore, Standard() ),
+        end(alignStore, Standard() ),
+        _LessAlignedRead<typename Value<TAlign>::Type, Tag<TSortSpec> const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSortSpec>
 inline void
-sortAlignedReads(TAlign const & alignStore, Tag<TSortSpec> const &) 
+sortAlignedReads(TAlign const & alignStore, Tag<TSortSpec> const &)
 {
-	std::stable_sort(
-		begin(const_cast<TAlign&>(alignStore), Standard() ), 
-		end(const_cast<TAlign&>(alignStore), Standard() ), 
-		_LessAlignedRead<typename Value<TAlign>::Type, Tag<TSortSpec> const>() );
+    std::stable_sort(
+        begin(const_cast<TAlign&>(alignStore), Standard() ),
+        end(const_cast<TAlign&>(alignStore), Standard() ),
+        _LessAlignedRead<typename Value<TAlign>::Type, Tag<TSortSpec> const>() );
 }
 
 template <typename TAlign, typename TFunctorLess>
 inline void
-sortAlignedReads(TAlign & alignStore, TFunctorLess const &less) 
+sortAlignedReads(TAlign & alignStore, TFunctorLess const &less)
 {
-	std::stable_sort(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		less);
+    std::stable_sort(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        less);
 }
 
 template <typename TAlign, typename TFunctorLess>
 inline void
-sortAlignedReads(TAlign const & alignStore, TFunctorLess const &less) 
+sortAlignedReads(TAlign const & alignStore, TFunctorLess const &less)
 {
-	std::stable_sort(
-		begin(const_cast<TAlign&>(alignStore), Standard()), 
-		end(const_cast<TAlign&>(alignStore), Standard()), 
-		less);
+    std::stable_sort(
+        begin(const_cast<TAlign&>(alignStore), Standard()),
+        end(const_cast<TAlign&>(alignStore), Standard()),
+        less);
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-lowerBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortId) 
+lowerBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.id = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.id = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortId const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-lowerBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortId) 
+lowerBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.id = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.id = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-upperBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortId) 
+upperBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.id = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.id = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortId const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-upperBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortId) 
+upperBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.id = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.id = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-lowerBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortContigId) 
+lowerBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortContigId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.contigId = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortContigId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.contigId = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortContigId const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-lowerBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortContigId) 
+lowerBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortContigId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.contigId = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortContigId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.contigId = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortContigId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-upperBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortContigId) 
+upperBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortContigId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.contigId = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortContigId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.contigId = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortContigId const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-upperBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortContigId) 
+upperBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortContigId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.contigId = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortContigId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.contigId = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortContigId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-lowerBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortBeginPos) 
+lowerBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortBeginPos)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortBeginPos const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortBeginPos const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-lowerBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortBeginPos) 
+lowerBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortBeginPos)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortBeginPos const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortBeginPos const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-upperBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortBeginPos) 
+upperBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortBeginPos)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortBeginPos const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortBeginPos const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-upperBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortBeginPos) 
+upperBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortBeginPos)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortBeginPos const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortBeginPos const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-lowerBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortEndPos) 
+lowerBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortEndPos)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortEndPos const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortEndPos const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-lowerBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortEndPos) 
+lowerBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortEndPos)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortEndPos const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortEndPos const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-upperBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortEndPos) 
+upperBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortEndPos)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortEndPos const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortEndPos const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-upperBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortEndPos) 
+upperBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortEndPos)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortEndPos const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortEndPos const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-lowerBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortPairMatchId) 
+lowerBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortPairMatchId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.pairMatchId = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortPairMatchId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.pairMatchId = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortPairMatchId const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-lowerBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortPairMatchId) 
+lowerBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortPairMatchId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.pairMatchId = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortPairMatchId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.pairMatchId = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortPairMatchId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-upperBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortPairMatchId) 
+upperBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortPairMatchId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.pairMatchId = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortPairMatchId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.pairMatchId = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortPairMatchId const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-upperBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortPairMatchId) 
+upperBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortPairMatchId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.pairMatchId = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortPairMatchId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.pairMatchId = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortPairMatchId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-lowerBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortReadId) 
+lowerBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortReadId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.readId = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortReadId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.readId = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortReadId const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-lowerBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortReadId) 
+lowerBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortReadId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.readId = val;
-	return ::std::lower_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortReadId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.readId = val;
+    return std::lower_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortReadId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign const, Standard>::Type
-upperBoundAlignedReads(TAlign const & alignStore, 
-					   TSearchValue const val,
-					   SortReadId) 
+upperBoundAlignedReads(TAlign const & alignStore,
+                       TSearchValue const val,
+                       SortReadId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.readId = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortReadId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.readId = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortReadId const>() );
 }
 
 template <typename TAlign, typename TSearchValue>
 inline typename Iterator<TAlign, Standard>::Type
-upperBoundAlignedReads(TAlign & alignStore, 
-					   TSearchValue const val,
-					   SortReadId) 
+upperBoundAlignedReads(TAlign & alignStore,
+                       TSearchValue const val,
+                       SortReadId)
 {
-	typedef typename Value<TAlign>::Type TAlignElement;
-	TAlignElement el;
-	el.readId = val;
-	return ::std::upper_bound(
-		begin(alignStore, Standard()), 
-		end(alignStore, Standard()), 
-		el,
-		_LessAlignedRead<typename Value<TAlign>::Type, SortReadId const>() );
+    typedef typename Value<TAlign>::Type TAlignElement;
+    TAlignElement el;
+    el.readId = val;
+    return std::upper_bound(
+        begin(alignStore, Standard()),
+        end(alignStore, Standard()),
+        el,
+        _LessAlignedRead<typename Value<TAlign>::Type, SortReadId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1126,17 +945,17 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 lowerBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortId) 
+                       TSearchValue const val,
+                       SortId)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.id = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortId const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.id = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortId const>() );
 }
 
 
@@ -1146,17 +965,17 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 upperBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortId) 
+                       TSearchValue const val,
+                       SortId)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.id = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortId const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.id = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1165,17 +984,17 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 lowerBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortContigId) 
+                       TSearchValue const val,
+                       SortContigId)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.contigId = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortContigId const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.contigId = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortContigId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1184,17 +1003,17 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 upperBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortContigId) 
+                       TSearchValue const val,
+                       SortContigId)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.contigId = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortContigId const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.contigId = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortContigId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1203,18 +1022,18 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 lowerBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortBeginPos) 
+                       TSearchValue const val,
+                       SortBeginPos)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortBeginPos const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortBeginPos const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1223,18 +1042,18 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 upperBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortBeginPos) 
+                       TSearchValue const val,
+                       SortBeginPos)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortBeginPos const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortBeginPos const>() );
 }
 
 
@@ -1244,18 +1063,18 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 lowerBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortEndPos) 
+                       TSearchValue const val,
+                       SortEndPos)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortEndPos const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortEndPos const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1264,18 +1083,18 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 upperBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortEndPos) 
+                       TSearchValue const val,
+                       SortEndPos)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortEndPos const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortEndPos const>() );
 }
 
 
@@ -1285,17 +1104,17 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 lowerBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortPairMatchId) 
+                       TSearchValue const val,
+                       SortPairMatchId)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.pairMatchId = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortPairMatchId const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.pairMatchId = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortPairMatchId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1304,17 +1123,17 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 upperBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortPairMatchId) 
+                       TSearchValue const val,
+                       SortPairMatchId)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.pairMatchId = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortPairMatchId const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.pairMatchId = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortPairMatchId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1323,17 +1142,17 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 lowerBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortReadId) 
+                       TSearchValue const val,
+                       SortReadId)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.readId = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortReadId const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.readId = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortReadId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1342,17 +1161,17 @@ template <typename T, typename TSpec, typename TSearchValue>
 inline Iter<T, TSpec>
 upperBoundAlignedReads(Iter<T, TSpec> const & alignedReadsItBegin,
                        Iter<T, TSpec> const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortReadId) 
+                       TSearchValue const val,
+                       SortReadId)
 {
-	typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
-	TAlignElement el;
-	el.readId = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortReadId const>() );
+    typedef typename Value<Iter<T, TSpec> >::Type TAlignElement;
+    TAlignElement el;
+    el.readId = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<Iter<T, TSpec> >::Type, SortReadId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1361,17 +1180,17 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 lowerBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortId) 
+                       TSearchValue const val,
+                       SortId)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.id = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortId const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.id = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1380,17 +1199,17 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 upperBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortId) 
+                       TSearchValue const val,
+                       SortId)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.id = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortId const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.id = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1399,17 +1218,17 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 lowerBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortContigId) 
+                       TSearchValue const val,
+                       SortContigId)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.contigId = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortContigId const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.contigId = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortContigId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1418,17 +1237,17 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 upperBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortContigId) 
+                       TSearchValue const val,
+                       SortContigId)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.contigId = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortContigId const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.contigId = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortContigId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1437,18 +1256,18 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 lowerBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortBeginPos) 
+                       TSearchValue const val,
+                       SortBeginPos)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortBeginPos const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortBeginPos const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1457,18 +1276,18 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 upperBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortBeginPos) 
+                       TSearchValue const val,
+                       SortBeginPos)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortBeginPos const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortBeginPos const>() );
 }
 
 
@@ -1478,18 +1297,18 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 lowerBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortEndPos) 
+                       TSearchValue const val,
+                       SortEndPos)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortEndPos const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortEndPos const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1498,18 +1317,18 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 upperBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortEndPos) 
+                       TSearchValue const val,
+                       SortEndPos)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.beginPos = val;
-	el.endPos = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortEndPos const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.beginPos = val;
+    el.endPos = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortEndPos const>() );
 }
 
 
@@ -1519,17 +1338,17 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 lowerBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortPairMatchId) 
+                       TSearchValue const val,
+                       SortPairMatchId)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.pairMatchId = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortPairMatchId const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.pairMatchId = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortPairMatchId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1538,17 +1357,17 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 upperBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortPairMatchId) 
+                       TSearchValue const val,
+                       SortPairMatchId)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.pairMatchId = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortPairMatchId const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.pairMatchId = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortPairMatchId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1557,17 +1376,17 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 lowerBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortReadId) 
+                       TSearchValue const val,
+                       SortReadId)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.readId = val;
-	return ::std::lower_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortReadId const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.readId = val;
+    return std::lower_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortReadId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////////
@@ -1576,17 +1395,17 @@ template <typename TReadAlignElement, typename TSearchValue>
 inline TReadAlignElement *
 upperBoundAlignedReads(TReadAlignElement * const & alignedReadsItBegin,
                        TReadAlignElement * const & alignedReadsItEnd,
-					   TSearchValue const val,
-					   SortReadId) 
+                       TSearchValue const val,
+                       SortReadId)
 {
-	typedef typename Value<TReadAlignElement *>::Type TAlignElement;
-	TAlignElement el;
-	el.readId = val;
-	return ::std::upper_bound(
-		alignedReadsItBegin, 
-		alignedReadsItEnd, 
-		el,
-		_LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortReadId const>() );
+    typedef typename Value<TReadAlignElement *>::Type TAlignElement;
+    TAlignElement el;
+    el.readId = val;
+    return std::upper_bound(
+        alignedReadsItBegin,
+        alignedReadsItEnd,
+        el,
+        _LessAlignedRead<typename Value<TReadAlignElement *>::Type, SortReadId const>() );
 }
 
 //////////////////////////////////////////////////////////////////////////////
diff --git a/seqan/store/store_align_intervals.h b/seqan/store/store_align_intervals.h
index 5c9db95..adce732 100644
--- a/seqan/store/store_align_intervals.h
+++ b/seqan/store/store_align_intervals.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -45,17 +45,17 @@ namespace SEQAN_NAMESPACE_MAIN
 template<typename TValue = int >
 struct Interval
 {
-	TValue i1;
-	TValue i2;
-	
-	Interval() : i1(0), i2(0) {}
+    TValue i1;
+    TValue i2;
+
+    Interval() : i1(0), i2(0) {}
 };
 
 template<typename TValue>
 inline bool
 operator == (Interval<TValue> const & interval1, Interval<TValue> const & interval2)
 {
-	return (interval1.i1 == interval2.i1 && interval1.i2 == interval2.i2);
+    return (interval1.i1 == interval2.i1 && interval1.i2 == interval2.i2);
 }
 
 template<typename TValue>
@@ -70,12 +70,12 @@ operator < (Interval<TValue> const & interval1, Interval<TValue> const & interva
 
 //////////////////////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////////////////////
-template <typename TInterval = Interval<unsigned>, typename TSpec = void>         
+template <typename TInterval = Interval<unsigned>, typename TSpec = void>
 struct AlignIntervalsStoreElement
 {
-	typedef  String<TInterval> 	TIntervals;
-	
-	TIntervals intervals; 
+    typedef  String<TInterval>     TIntervals;
+
+    TIntervals intervals;
 };
 
 
@@ -86,26 +86,26 @@ inline void
 buildAlignIntervalsStore(TAlignIntervalsStore & alignIntervalsStore,
                          FragmentStore<TSpec, TConfig> & me, const unsigned & thresholdGaps)
 {
-	typedef typename FragmentStore<TSpec, TConfig>::TAlignedReadStore 	TAlignedReadStore;
+    typedef typename FragmentStore<TSpec, TConfig>::TAlignedReadStore     TAlignedReadStore;
 
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type 		TAlignIter;
-	typedef typename Iterator<TAlignIntervalsStore>::Type 			TAlignIntervalsStoreIter;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type         TAlignIter;
+    typedef typename Iterator<TAlignIntervalsStore>::Type             TAlignIntervalsStoreIter;
 
-	if (!empty(me.alignedReadStore))
-	{
-		resize(alignIntervalsStore, length(me.alignedReadStore));
+    if (!empty(me.alignedReadStore))
+    {
+        resize(alignIntervalsStore, length(me.alignedReadStore));
 
-		TAlignIntervalsStoreIter it = begin(alignIntervalsStore);
+        TAlignIntervalsStoreIter it = begin(alignIntervalsStore);
 
-		TAlignIter itAlign = begin(me.alignedReadStore);
-		TAlignIter itAlignEnd = end(me.alignedReadStore);
+        TAlignIter itAlign = begin(me.alignedReadStore);
+        TAlignIter itAlignEnd = end(me.alignedReadStore);
 
-		// get matched intervals for each aligned read
-		for ( ; itAlign != itAlignEnd; goNext(itAlign), goNext(it))
-		{
-			extractAlignIntervals(value(it).intervals, getValue(itAlign), me, thresholdGaps);
-		}
-	}
+        // get matched intervals for each aligned read
+        for ( ; itAlign != itAlignEnd; goNext(itAlign), goNext(it))
+        {
+            extractAlignIntervals(value(it).intervals, getValue(itAlign), me, thresholdGaps);
+        }
+    }
 }
 
 
@@ -114,235 +114,241 @@ buildAlignIntervalsStore(TAlignIntervalsStore & alignIntervalsStore,
 ////////////////////////////////////////////////////////////////////////////////////////////////////////
 
 template<typename TIntervals, typename TAlignedReadStoreElement, typename TSpec, typename TConfig>
-inline void 
+inline void
 extractAlignIntervals(TIntervals & contigIntervals, TAlignedReadStoreElement & align, FragmentStore<TSpec, TConfig> & me, const unsigned & thresholdGaps)
 {
 
-	////////////////////////////////////////////////////////////////////////////////////////////////////////
-	///////// get read intervals in gapped contig sequence:		
-	
-	typedef typename FragmentStore<TSpec, TConfig>::TContigPos 		TContigPos;
-	typedef typename FragmentStore<TSpec, TConfig>::TReadGapAnchor 		TReadGapAnchor;
-	typedef 	 String<TReadGapAnchor> 				TReadGaps;
-	typedef typename Position<TReadGaps >::Type 				TGapPos;
-	typedef typename Value<TIntervals>::Type 				TInterval;
-	typedef typename Iterator<TReadGaps>::Type 				TReadGapsIter;
-	
-	clear(contigIntervals);
-	
-	TIntervals readIntervals;
-	
-	TContigPos beginPos = align.beginPos;
-	TContigPos endPos = align.endPos;
-	if (beginPos > endPos)
-	{
-		TContigPos help = beginPos;
-		beginPos = endPos;
-		endPos = help;
-	}
-	TInterval interval;
-	if (length(align.gaps) == 0)
-	{
-		resize(readIntervals, 1, Generous());
-		interval.i1 = beginPos;
-		interval.i2 = endPos -1;
-		assignValue(readIntervals, 0, interval);
-	}
-	else 
-	{
-		TReadGapsIter itGap = begin(align.gaps);
-		TReadGapsIter itGapEnd = end(align.gaps);
-	
-		TContigPos firstSeqPos = getValue(itGap).seqPos + beginPos;   // seqPos from Read projected to pos in ungapped contig sequence
-		TContigPos firstGapPos = getValue(itGap).gapPos + beginPos;   // gapPos from Read projected to pos in ungapped contig sequence
-		TGapPos i = 0;
-		// without gaps at the beginnig
-		if (beginPos < firstGapPos) 		// end != 0 ??
-		{
-			resize(readIntervals, length(align.gaps), Generous());
-			interval.i1 = beginPos; 
-			interval.i2 = firstSeqPos - 1;
-			assignValue(readIntervals, i, interval);
-			++i;
-		}
-		// with gaps at the beginning
-		else resize(readIntervals, length(align.gaps) -1, Generous());
-		
-		TContigPos seqPos1 = 0;
-		TContigPos gapPos1 = 0;
-		TContigPos seqPos2 = firstSeqPos;
-		TContigPos gapPos2 = firstGapPos;
-		goNext(itGap);
-		// calculate interval between 2 gaps:
-		for (; itGap != itGapEnd; goNext(itGap), ++i)
-		{
-			seqPos1 = seqPos2;
-			gapPos1 = gapPos2;
-			seqPos2 = getValue(itGap).seqPos + beginPos;
-			gapPos2 = getValue(itGap).gapPos + beginPos;
-			interval.i1 = gapPos1;					// ==  gapPos of Gap-Anchor1  + beginPos 
-			interval.i2 = seqPos2 + gapPos1 - seqPos1 - 1;   	// ==  gapPos2 - ((gapPos2-seqPos2) - (gapPos1-seqPos1)) - 1
-			assignValue(readIntervals, i, interval);
-		}
-		
-		// without gaps at the end
-		if (endPos != gapPos2)
-		{
-			interval.i1 = gapPos2;
-			interval.i2 = endPos - 1;
-			appendValue(readIntervals, interval, Generous());
-		}
-		
-		// with gaps at the end
-		else if (endPos == gapPos2)
-		{
-			interval.i1 = gapPos1;
-			interval.i2 = endPos - 1;
-			assignValue(readIntervals, i - 1, interval);
-		}
-	}
-	
-	////////////////////////////////////////////////////////////////////////////////////////////////////////
-	///////// get contig intervals in ungapped sequence:
-	
-	typedef typename TAlignedReadStoreElement::TId 				TId;
-	typedef typename FragmentStore<TSpec, TConfig>::TContigGapAnchor 	TContigGapAnchor;
-	typedef		 String<TContigGapAnchor> 				TContigGaps;
-	typedef typename Iterator<TContigGaps const>::Type 			TContigGapsIter;
-	typedef typename Iterator<TIntervals>::Type 				TReadIntervalIter;
-	
-	
-	TId contigId = align.contigId;
-	
-	if (empty(getValue(me.contigStore, contigId).gaps))
-	{
-		contigIntervals = readIntervals;
-	}
-	else
-	{
-		if (front(getValue(me.contigStore, contigId).gaps).seqPos != 0) 
-		{
-			TContigGapAnchor pseudoGapAnchor;
-			pseudoGapAnchor.seqPos = 0;
-			pseudoGapAnchor.gapPos = 0;
-			insertValue(value(me.contigStore, contigId).gaps, 0, pseudoGapAnchor, Generous());
-		}
-		
-		TReadIntervalIter itI = begin(readIntervals);
-		TReadIntervalIter itIEnd = end(readIntervals);
-		
-		TContigGapsIter it1Gap = begin(getValue(me.contigStore, contigId).gaps);
-		TContigGapsIter it2Gap = begin(getValue(me.contigStore, contigId).gaps);
-		TContigGapsIter it2GapEnd = end(getValue(me.contigStore, contigId).gaps);
-		goNext(it2Gap);
-		TInterval contigInterval;
-		TInterval readInterval;
-		TContigPos lastGapPosBeforeGap1;
-		TContigPos lastGapPosBeforeGap2;
-		for ( ; itI != itIEnd; goNext(itI))
-		{
-			readInterval = getValue(itI);
-
-			if (static_cast<TContigPos>(readInterval.i2) < getValue(it1Gap).gapPos) continue;    		// interval-positions are smaller than first-position of contig: read-interval mappt in contig gaps
-		
-			// interval i1:
-			while ( (it2Gap != it2GapEnd) && (static_cast<TContigPos>(readInterval.i1) >= getValue(it2Gap).gapPos) )   // iterate over 2 contig gap-anchors, until gapPos2 is behind start of read-interval
-			{
-				goNext(it1Gap);
-				goNext(it2Gap);
-			}
-		
-			if (it2Gap != it2GapEnd)
-			{
-				lastGapPosBeforeGap1 = getValue(it2Gap).seqPos + getValue(it1Gap).gapPos - getValue(it1Gap).seqPos -1;  // last position in gapped sequence before gap 
-			
-				if (static_cast<TContigPos>(readInterval.i1) < getValue(it1Gap).gapPos)  				// occurs, if interval.i1 position is smaller than start-postion of contig
-				{
-					contigInterval.i1 = getValue(it1Gap).gapPos;
-				}
-				else if (static_cast<TContigPos>(readInterval.i1) <= lastGapPosBeforeGap1)				// read-interval starts in contig-interval between the 2 gaps		
-				{
-					contigInterval.i1 = readInterval.i1 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos);  // project position onto ungapped sequence
-				}
-				else if (static_cast<TContigPos>(readInterval.i2) < getValue(it2Gap).gapPos)				// whole read-interval lies in gaps of contig
-				{
-					continue;
-				}
-				else 										// read-interval starts in contig gap -> alignment-interval starts in seqPos2
-				{
-					contigInterval.i1 = getValue(it2Gap).seqPos;
-				}
-			}
-			else		// read-interval lies behind last gap-anchor
-			{
-				goPrevious(it1Gap);
-				goPrevious(it2Gap);
-				contigInterval.i1 = readInterval.i1 - (getValue(it2Gap).gapPos - getValue(it2Gap).seqPos); // not goPrev -> it1Gap
-			}
-		
-			// interval i2:	
-			while ( (it2Gap != it2GapEnd) && (static_cast<TContigPos>(readInterval.i2) >= getValue(it2Gap).gapPos) )		// iterate over 2 contig gap-anchors, until gapPos2 is behind end of read-interval
-			{
-				goNext(it1Gap);
-				goNext(it2Gap);
-			}
-	
-			if (it2Gap != it2GapEnd)
-			{
-				lastGapPosBeforeGap2 = getValue(it2Gap).seqPos + getValue(it1Gap).gapPos - getValue(it1Gap).seqPos -1;  // last position in gapped sequence before gap 
-				
-				if (static_cast<TContigPos>(readInterval.i2) <= lastGapPosBeforeGap2)					// read-interval ends in contig-interval between the 2 gaps	
-				{
-					contigInterval.i2 = readInterval.i2 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos);    // project position onto ungapped sequence
-				}
-				else 										// read-interval ends in gap -> end of alignment-interval is last position before gap
-				{
-					contigInterval.i2 = lastGapPosBeforeGap2 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos);
-				}
-			}
-			else if (it2Gap == it2GapEnd)				// read-intervall ends behind the last gap-anchor
-			{
-				goPrevious(it1Gap);
-				goPrevious(it2Gap);
-				contigInterval.i2 = readInterval.i2 - (getValue(it2Gap).gapPos - getValue(it2Gap).seqPos);
-			}	
-		
-			appendValue(contigIntervals, contigInterval, Generous());
-		}
-	}
-	mergeIntervals(contigIntervals, thresholdGaps);
-	
+    ////////////////////////////////////////////////////////////////////////////////////////////////////////
+    ///////// get read intervals in gapped contig sequence:
+
+    typedef typename FragmentStore<TSpec, TConfig>::TContigPos         TContigPos;
+    typedef typename FragmentStore<TSpec, TConfig>::TReadGapAnchor         TReadGapAnchor;
+    typedef      String<TReadGapAnchor>                 TReadGaps;
+    typedef typename Position<TReadGaps >::Type                 TGapPos;
+    typedef typename Value<TIntervals>::Type                 TInterval;
+    typedef typename Iterator<TReadGaps>::Type                 TReadGapsIter;
+
+    clear(contigIntervals);
+
+    TIntervals readIntervals;
+
+    TContigPos beginPos = align.beginPos;
+    TContigPos endPos = align.endPos;
+    if (beginPos > endPos)
+    {
+        TContigPos help = beginPos;
+        beginPos = endPos;
+        endPos = help;
+    }
+    TInterval interval;
+    if (length(align.gaps) == 0)
+    {
+        resize(readIntervals, 1, Generous());
+        interval.i1 = beginPos;
+        interval.i2 = endPos -1;
+        assignValue(readIntervals, 0, interval);
+    }
+    else
+    {
+        TReadGapsIter itGap = begin(align.gaps);
+        TReadGapsIter itGapEnd = end(align.gaps);
+
+        TContigPos firstSeqPos = getValue(itGap).seqPos + beginPos;   // seqPos from Read projected to pos in ungapped contig sequence
+        TContigPos firstGapPos = getValue(itGap).gapPos + beginPos;   // gapPos from Read projected to pos in ungapped contig sequence
+        TGapPos i = 0;
+        // without gaps at the beginnig
+        if (beginPos < firstGapPos)         // end != 0 ??
+        {
+            resize(readIntervals, length(align.gaps), Generous());
+            interval.i1 = beginPos;
+            interval.i2 = firstSeqPos - 1;
+            assignValue(readIntervals, i, interval);
+            ++i;
+        }
+        // with gaps at the beginning
+        else resize(readIntervals, length(align.gaps) -1, Generous());
+
+        TContigPos seqPos1 = 0;
+        TContigPos gapPos1 = 0;
+        TContigPos seqPos2 = firstSeqPos;
+        TContigPos gapPos2 = firstGapPos;
+        goNext(itGap);
+        // calculate interval between 2 gaps:
+        for (; itGap != itGapEnd; goNext(itGap), ++i)
+        {
+            seqPos1 = seqPos2;
+            gapPos1 = gapPos2;
+            seqPos2 = getValue(itGap).seqPos + beginPos;
+            gapPos2 = getValue(itGap).gapPos + beginPos;
+            interval.i1 = gapPos1;                    // ==  gapPos of Gap-Anchor1  + beginPos
+            interval.i2 = seqPos2 + gapPos1 - seqPos1 - 1;       // ==  gapPos2 - ((gapPos2-seqPos2) - (gapPos1-seqPos1)) - 1
+            assignValue(readIntervals, i, interval);
+        }
+
+        // without gaps at the end
+        if (endPos != gapPos2)
+        {
+            interval.i1 = gapPos2;
+            interval.i2 = endPos - 1;
+            appendValue(readIntervals, interval, Generous());
+        }
+
+        // with gaps at the end
+        else if (endPos == gapPos2)
+        {
+            interval.i1 = gapPos1;
+            interval.i2 = endPos - 1;
+            assignValue(readIntervals, i - 1, interval);
+        }
+    }
+
+    ////////////////////////////////////////////////////////////////////////////////////////////////////////
+    ///////// get contig intervals in ungapped sequence:
+
+    typedef typename TAlignedReadStoreElement::TId                 TId;
+    typedef typename FragmentStore<TSpec, TConfig>::TContigGapAnchor     TContigGapAnchor;
+    typedef         String<TContigGapAnchor>                 TContigGaps;
+    typedef typename Iterator<TContigGaps const>::Type             TContigGapsIter;
+    typedef typename Iterator<TIntervals>::Type                 TReadIntervalIter;
+
+
+    TId contigId = align.contigId;
+
+    if (empty(getValue(me.contigStore, contigId).gaps))
+    {
+        contigIntervals = readIntervals;
+    }
+    else
+    {
+        if (front(getValue(me.contigStore, contigId).gaps).seqPos != 0)
+        {
+            TContigGapAnchor pseudoGapAnchor;
+            pseudoGapAnchor.seqPos = 0;
+            pseudoGapAnchor.gapPos = 0;
+            insertValue(value(me.contigStore, contigId).gaps, 0, pseudoGapAnchor, Generous());
+        }
+
+        TReadIntervalIter itI = begin(readIntervals);
+        TReadIntervalIter itIEnd = end(readIntervals);
+
+        TContigGapsIter it1Gap = begin(getValue(me.contigStore, contigId).gaps);
+        TContigGapsIter it2Gap = begin(getValue(me.contigStore, contigId).gaps);
+        TContigGapsIter it2GapEnd = end(getValue(me.contigStore, contigId).gaps);
+        goNext(it2Gap);
+        TInterval contigInterval;
+        TInterval readInterval;
+        TContigPos lastGapPosBeforeGap1;
+        TContigPos lastGapPosBeforeGap2;
+        for ( ; itI != itIEnd; goNext(itI))
+        {
+            readInterval = getValue(itI);
+
+            if (static_cast<TContigPos>(readInterval.i2) < getValue(it1Gap).gapPos) continue;            // interval-positions are smaller than first-position of contig: read-interval mappt in contig gaps
+
+            // interval i1:
+            while ( (it2Gap != it2GapEnd) && (static_cast<TContigPos>(readInterval.i1) >= getValue(it2Gap).gapPos) )   // iterate over 2 contig gap-anchors, until gapPos2 is behind start of read-interval
+            {
+                goNext(it1Gap);
+                goNext(it2Gap);
+            }
+
+            if (it2Gap != it2GapEnd)
+            {
+                lastGapPosBeforeGap1 = getValue(it2Gap).seqPos + getValue(it1Gap).gapPos - getValue(it1Gap).seqPos -1;  // last position in gapped sequence before gap
+
+                if (static_cast<TContigPos>(readInterval.i1) < getValue(it1Gap).gapPos)                  // occurs, if interval.i1 position is smaller than start-postion of contig
+                {
+                    contigInterval.i1 = getValue(it1Gap).gapPos;
+                }
+                else if (static_cast<TContigPos>(readInterval.i1) <= lastGapPosBeforeGap1)                // read-interval starts in contig-interval between the 2 gaps
+                {
+                    contigInterval.i1 = readInterval.i1 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos);  // project position onto ungapped sequence
+                }
+                else if (static_cast<TContigPos>(readInterval.i2) < getValue(it2Gap).gapPos)                // whole read-interval lies in gaps of contig
+                {
+                    continue;
+                }
+                else                                         // read-interval starts in contig gap -> alignment-interval starts in seqPos2
+                {
+                    contigInterval.i1 = getValue(it2Gap).seqPos;
+                }
+            }
+            else        // read-interval lies behind last gap-anchor
+            {
+                goPrevious(it1Gap);
+                goPrevious(it2Gap);
+                contigInterval.i1 = readInterval.i1 - (getValue(it2Gap).gapPos - getValue(it2Gap).seqPos); // not goPrev -> it1Gap
+            }
+
+            // interval i2:
+            while ( (it2Gap != it2GapEnd) && (static_cast<TContigPos>(readInterval.i2) >= getValue(it2Gap).gapPos) )        // iterate over 2 contig gap-anchors, until gapPos2 is behind end of read-interval
+            {
+                goNext(it1Gap);
+                goNext(it2Gap);
+            }
+
+            if (it2Gap != it2GapEnd)
+            {
+                lastGapPosBeforeGap2 = getValue(it2Gap).seqPos + getValue(it1Gap).gapPos - getValue(it1Gap).seqPos -1;  // last position in gapped sequence before gap
+
+                if (static_cast<TContigPos>(readInterval.i2) <= lastGapPosBeforeGap2)                    // read-interval ends in contig-interval between the 2 gaps
+                {
+                    contigInterval.i2 = readInterval.i2 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos);    // project position onto ungapped sequence
+                }
+                else                                         // read-interval ends in gap -> end of alignment-interval is last position before gap
+                {
+                    contigInterval.i2 = lastGapPosBeforeGap2 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos);
+                }
+            }
+            else if (it2Gap == it2GapEnd)                // read-intervall ends behind the last gap-anchor
+            {
+                goPrevious(it1Gap);
+                goPrevious(it2Gap);
+                contigInterval.i2 = readInterval.i2 - (getValue(it2Gap).gapPos - getValue(it2Gap).seqPos);
+            }
+
+            appendValue(contigIntervals, contigInterval, Generous());
+        }
+    }
+    mergeIntervals(contigIntervals, thresholdGaps);
+
 }
 
 
 ////////////////////////////////////////////////////////////////////////////////////////////////////////
 //// merge intervals (for sortet intervals; i1 <= i2 <= (i+1)1 <= (i+1)2 )
 ////////////////////////////////////////////////////////////////////////////////////////////////////////
+
 template<typename TIntervals>
 inline void
 mergeIntervals(TIntervals & intervals, const unsigned & thresholdGaps)
 {
-	typedef typename Position<TIntervals>::Type 	TPos;
-	typedef typename Value<TIntervals>::Type 	TInterval;
-	
-	TPos j;
-	TInterval newInterval;
-	for (TPos i = 0; i < length(intervals) - 1; ++i)
-	{
-		j = i;
-		while ( (j < length(intervals) - 1) && (getValue(intervals, j).i2 + thresholdGaps >= getValue(intervals, j + 1).i1 - 1) )		// merges intervals, if the no. of gaps inbetween is smaller than threshold 
-		{
-			++j;
-		}
-		
-		if ( j != i)
-		{
-			newInterval.i1 = getValue(intervals, i).i1;
-			newInterval.i2 = getValue(intervals, j).i2;
-			replace(intervals, i, j + 1, newInterval);       
-		}
-		
-	}
+    typedef typename Position<TIntervals>::Type  TPos;
+    typedef typename Value<TIntervals>::Type     TInterval;
+
+    TPos j;
+    TInterval newInterval;
+    for (TPos i = 0; i < length(intervals) - 1; ++i)
+    {
+        j = i;
+
+        // merge intervals, if the no. of gaps inbetween is smaller than threshold
+        while ((j < length(intervals) - 1) &&
+               (getValue(intervals, j).i2 + thresholdGaps >= getValue(intervals, j + 1).i1 - 1))
+        {
+            ++j;
+        }
+
+        if (j != i)  // means j > i
+        {
+            newInterval.i1 = getValue(intervals, i).i1;
+            newInterval.i2 = getValue(intervals, j).i2;
+
+            // replace [i, j+1) in intervals by newInterval
+            erase(intervals, i + 1, j + 1);
+            intervals[i] = newInterval;
+        }
+    }
 }
 
 
diff --git a/seqan/store/store_all.h b/seqan/store/store_all.h
index c9698e0..71055e9 100644
--- a/seqan/store/store_all.h
+++ b/seqan/store/store_all.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -47,27 +47,27 @@ namespace SEQAN_NAMESPACE_MAIN
 // TODO(holtgrew): Document.
 
 template <typename TSpec = void>
-struct FragmentStoreConfig 
+struct FragmentStoreConfig
 {
-	typedef String<Dna5Q>	TReadSeq;
-	typedef String<Dna5Q>	TContigSeq;
-	
-	typedef double			TMean;
-	typedef double			TStd;
-	typedef signed char		TMappingQuality;
-		
-	typedef void					TReadStoreElementSpec;
-	typedef Owner<ConcatDirect<> >	TReadSeqStoreSpec;
-	typedef void					TMatePairStoreElementSpec;
-	typedef void					TLibraryStoreElementSpec;
-	typedef void					TContigStoreElementSpec;
-	typedef void					TContigFileSpec;
-	typedef void					TAlignedReadStoreElementSpec;
-	typedef Owner<ConcatDirect<> >	TAlignedReadTagStoreSpec;
-	typedef void					TAnnotationStoreElementSpec;
-    
-    typedef Alloc<>					TReadNameSpec;
-	typedef Owner<ConcatDirect<> >	TReadNameStoreSpec;
+    typedef String<Dna5Q>    TReadSeq;
+    typedef String<Dna5Q>    TContigSeq;
+
+    typedef double            TMean;
+    typedef double            TStd;
+    typedef signed char        TMappingQuality;
+
+    typedef void                    TReadStoreElementSpec;
+    typedef Owner<ConcatDirect<> >    TReadSeqStoreSpec;
+    typedef void                    TMatePairStoreElementSpec;
+    typedef void                    TLibraryStoreElementSpec;
+    typedef void                    TContigStoreElementSpec;
+    typedef void                    TContigFileSpec;
+    typedef void                    TAlignedReadStoreElementSpec;
+    typedef Owner<ConcatDirect<> >    TAlignedReadTagStoreSpec;
+    typedef void                    TAnnotationStoreElementSpec;
+
+    typedef Alloc<>                    TReadNameSpec;
+    typedef Owner<ConcatDirect<> >    TReadNameStoreSpec;
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -94,7 +94,7 @@ struct FragmentStoreConfig
  * of the reference genome can be annotated with features like 'gene', 'mRNA', 'exon', 'intro' or custom features.  The
  * FragmentStore supports I/O functions to read/write a read alignment in Sam or Amos format and to read/write
  * annotations in Gff/Gtf format.
- * 
+ *
  * The FragmentStore can be compared with a database where each table (called "store") is implemented as a String member
  * of the FragmentStore class.  The rows of each table (implemented as structs) are referred by their ids which are
  * their positions in the string and not stored explicitly.  The only exception is the alignedReadStore whose elements
@@ -108,7 +108,7 @@ struct FragmentStoreConfig
  *
  * Load read alignments and a reference genome and display the multiple alignment in a genomic range:
  *
- * @include demos/store/store_example.cpp
+ * @include demos/dox/store/store_example.cpp
  *
  * @code{.console}
  * ATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAA
@@ -365,467 +365,172 @@ struct FragmentStoreConfig
 
 /*!
  * @enum FragmentStore::PredefinedAnnotationTypes
+ * @headerfile <seqan/store.h>
  * @brief The @link FragmentStore @endlink predefines some commonly used @link AnnotationStoreElement::typeId @endlink
- *        values.  They can be used to compare or set the @link AnnotationStoreElement::typeId @endlink directly as a
- *        fast alternative to @link AnnotationTreeIterator#getType @endlink and @link AnnotationTreeIterator#setType
- *        @endlink.
+ *        values.
+ *
+ * These types can be used to compare or set the @link AnnotationStoreElement::typeId @endlink directly as a
+ * fast alternative to @link AnnotationTreeIterator#getType @endlink and @link AnnotationTreeIterator#setType
+ * @endlink.
  *
- * @var FragmentStore::PredefinedAnnotationTypes ANNO_ROOT;
+ * @signature enum FragmentStore::PredefinedAnnotationTypes;
+ *
+ * @val FragmentStore::PredefinedAnnotationTypes FragmentStore::ANNO_ROOT;
  * @brief The root node ("&lt;node&gt;").
  *
- * @var FragmentStore::PredefinedAnnotationTypes ANNO_GENE;
+ * @val FragmentStore::PredefinedAnnotationTypes FragmentStore::ANNO_GENE;
  * @brief A gene ("gene").
  *
- * @var FragmentStore::PredefinedAnnotationTypes ANNO_MRNA;
+ * @val FragmentStore::PredefinedAnnotationTypes FragmentStore::ANNO_MRNA;
  * @brief An mRNA sequence, aka transcript ("mRNA").
  *
- * @var FragmentStore::PredefinedAnnotationTypes ANNO_CDS;
+ * @val FragmentStore::PredefinedAnnotationTypes FragmentStore::ANNO_CDS;
  * @brief A coding region ("CDS");
  *
- * @var FragmentStore::PredefinedAnnotationTypes ANNO_EXON;
+ * @val FragmentStore::PredefinedAnnotationTypes FragmentStore::ANNO_EXON;
  * @brief An exon ("exon").
  *
- * @var FragmentStore::PredefinedAnnotationTypes ANNO_FIVE_PRIME_UTR;
+ * @val FragmentStore::PredefinedAnnotationTypes FragmentStore::ANNO_FIVE_PRIME_UTR;
  * @brief A 5' untranslated region ("five_prime_UTR").
  *
- * @var FragmentStore::PredefinedAnnotationTypes ANNO_INTRON;
+ * @val FragmentStore::PredefinedAnnotationTypes FragmentStore::ANNO_INTRON;
  * @brief An intron ("intron").
  *
- * @var FragmentStore::PredefinedAnnotationTypes ANNO_THREE_PRIME_UTR;
+ * @val FragmentStore::PredefinedAnnotationTypes FragmentStore::ANNO_THREE_PRIME_UTR;
  * @brief A 3' untranslated region ("three_prime_UTR").
  */
 
-/**
-.Class.FragmentStore
-..cat:Fragment Store
-..summary:Multi container to store contigs, reads, multiple read alignments and genome annotations.
-..signature:FragmentStore<>
-..signature:FragmentStore<TSpec[, TConfig]>
-..param.TSpec:The specializing type.
-...default:$void$
-..param.TConfig:The configuration struct.
-...default:$FragmentStoreConfig<TSpec>$
-..description:
-The FragmentStore is a data structure specifically designed for read mapping,
-genome assembly or gene annotation. These tasks typically require lots of data structures that
-are related to each other like: reads, mate-pairs, reference genome; pairwise alignments; genome annotation.
-..description:
-The FragmentStore subsumes all these data structures in an easy to use interface.
-It represents a multiple alignment of millions of reads or mate-pairs against a reference genome consisting 
-of multiple contigs. Additionally, regions of the reference genome can be annotated with features like 'gene', 
-'mRNA', 'exon', 'intro' or custom features. The FragmentStore supports I/O functions to read/write a read
-alignment in @Tag.File Format.tag.Sam@ or @Tag.File Format.tag.Amos@ format and to read/write annotations in @Tag.File Format.tag.Gff@/@Tag.File Format.tag.Gtf@ format.
-..description:
-The FragmentStore can be compared with a database where each table (called "store") is implemented as a
-@Class.String@ member of the FragmentStore class. The rows of each table (implemented as structs) are 
-referred by their ids which are their positions in the string and not stored explicitly. 
-The only exception is the @Memvar.FragmentStore#alignedReadStore@ whose elements of type @Class.AlignedReadStoreElement@
-contain an id-member as they may be rearranged in arbitrary order, e.g. by increasing genomic positions or by readId. 
-Many stores have an associated name store to store element names. Each name store is a @Class.StringSet@ that stores the
-element name at the position of its id. All stores are present in the FragmentStore and empty if unused. The concrete types,
-e.g. the position types or read/contig alphabet, can be easily changed by defining a custom config struct which is a template
-parameter of the FragmentStore class.
-
-..example:Load read alignments and a reference genome and display the multiple alignment in a genomic range:
-...file:demos/store/store_example.cpp
-...text:The staircase alignment looks as follows:
-...output:
-ATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAA
-ATTTAA  AATTACAAAATATAGTTGAAAGCTCTAACAATAGA   AACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGA  AGTCTCTTATGAATTAA
-ATTTA GAAATTACAAAATATAGTTGAAAGCTCTAACAATA ACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTG AGACAAGTCTCTTATGAATTAA
-attta GAAATTACAAAATATAGTTGAAAGCTCTAACAATAG    AACCAAGCAGAAGAAAGAGGCTCAGAACTTGAAGA  AGTCTCTTATGAATTAA
-ATTTAA   ATTACAAAATATAGTTGAAAGATCTAACAATAGAC    CCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAA     TTATGAATTAA
-ATTTAAGAA TTACAAAATATAGTTGAAAGCTCTAACAATAGACT     AAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAG     TATGAATTAA
-ATTTAAGAAA  ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA     GCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTC    ATGAATTAA
-ATTTAAGAAA  ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA      CAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCT    TGAATTAA
-ATTTAAGAAA  ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA      CAGAAGAAAGAGGTTCANANNNTGANGACAAGTCT    TGAATTAA
-ATTTAAGAAATT CAAAATATAGTTGAAAGCTCTAACAATAGACTAAA       GAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT   GAATTAA
-ATTTAAGAAAT   AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC       AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCGT  GAATTAA
-ATTTAAGAAAT   AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC       AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTT   AATTAA
-ATTTAAGAAAT    AAATATAGTTGAAAGCTCTAACAATAGACTAAACC        GAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATG
-ATTTAAGAAATT   AAATATAGTTGAAAGCTCTAACAATAGACTAAACC          AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA
-ATTTAAGAAATT    AATATAGTTGAAAGCTCTAACAATAGACTAAACCAA        AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA
-ATTTAAGAAATTACA  ATATAGTTGAAAGCTCTAACAATAGACTAAACCAA          GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT
-ATTTAAGAAATTACAA   ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC        GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT
-ATTTAAGAAATTACAAAATA AGTTGAAAGCTCTAACAATAGACTAAACCAAGCAG       AGGTTCAGAACTTGAAGACAAGTCTCTTATGAATT
-ATTTAAGAAATTACAAAATAT  TTGAAAGCTCTAACAATAGACTAAACCAAGCAGAA      GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
-ATTTAAGAAATTACAAAATATA   GAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAG TTCAGAACTTGAAGACAAGTCTCTTATGAATTAA
-ATTTAAGAAATTACAAAATATAGTTGAA    CTAACAATAGACTAAACCAAGCAGAAGAAAGAGTT      CTTGAAGACAAGTCTCTTATGAATTAA
-ATTTAAGAAATTACAAAATATAGTTGAAA   CTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT      TTGAAGACAAGTCTCTTATGAATTAA
-ATTTAAGAAATTACAAAATATAGTTGAAAG   TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT       TGAAGACAAGTCTCTTATGAATTAA
-ATTTAAGAAATTACAAAATATAGTTGAAAGCTCT ACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCA     TGAAGACAAGTCTCTTATGAATTAA
-  TTAAGAAATTACAAAATATAGTTGAAAGCTCTAAC    GACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTT AAGACAAGTCTCTTATGAATTAA
-   TAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGA                     GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
-          TTACAAAATATAGTTGAAAGCTCTAACAATAGACT                   GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
-                   ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC           GTTCAGAACTTGAAGACAAGTCTCTTATGAATTAA
-                          AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA      TCAGAACTTGAAGACAAGTCTCTTATGAATTAA
-                          AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA               NAAGACAAGTCTCTTATGAATTAA
-                           AAGCTCTAACAATAGACTAAACCAAGCAGAAGAAA              GAAGACAAGTCTCTTATGAATTAA
-                                 TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT               AGTCTCTTATGAATTAA
-                                 TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT                GTCTCTTATGAATTAA
-                                  AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC
-                                  AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC
-                                     AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA
-                                     AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA
-
-..example:
-...text:The following figures visualize the relations between the different stores:
-...image:FragmentStore|Stores that are involved in the representation of a multiple read alignment.
-...image:AnnotationStore|Stores that are involved in the representation of a genome alignment.
-..include:seqan/store.h
-
-
-.Typedef.FragmentStore#TReadStore
-..summary:Type of the @Memvar.FragmentStore#readStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TReadSeqStore
-..summary:Type of the @Memvar.FragmentStore#readSeqStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TMatePairStore
-..summary:Type of the @Memvar.FragmentStore#matePairStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TLibraryStore
-..summary:Type of the @Memvar.FragmentStore#libraryStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TContigFileStore
-..summary:Type of the @Memvar.FragmentStore#contigFileStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TContigStore
-..summary:Type of the @Memvar.FragmentStore#contigStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TAlignedReadStore
-..summary:Type of the @Memvar.FragmentStore#alignedReadStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TAnnotationStore
-..summary:Type of the @Memvar.FragmentStore#annotationStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TAlignQualityStore
-..summary:Type of the @Memvar.FragmentStore#alignQualityStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TAlignedReadTagStore
-..summary:Type of the @Memvar.FragmentStore#alignedReadTagStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TReadNameStore
-..summary:Type of the @Memvar.FragmentStore#readNameStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TMatePairNameStore
-..summary:Type of the @Memvar.FragmentStore#matePairNameStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TLibraryNameStore
-..summary:Type of the @Memvar.FragmentStore#libraryNameStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TContigNameStore
-..summary:Type of the @Memvar.FragmentStore#contigNameStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TAnnotationNameStore
-..summary:Type of the @Memvar.FragmentStore#annotationNameStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TAnnotationTypeStore
-..summary:Type of the @Memvar.FragmentStore#annotationTypeStore@ member.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Typedef.FragmentStore#TAnnotationKeyStore
-..summary:Type of the @Memvar.FragmentStore#annotationKeyStore@ member.
-..class:Class.FragmentStore
-
-.Memvar.FragmentStore#readStore
-..summary:@Class.String@ that maps from $readId$ to $<matePairId>$.
-..remarks:Value type is @Class.ReadStoreElement@.
-..type:Typedef.FragmentStore#TReadStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#readSeqStore
-..summary:@Class.StringSet@ that maps from $readId$ to $readSeq$.
-..type:Typedef.FragmentStore#TReadSeqStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#matePairStore
-..summary:@Class.String@ that maps from $matePairId$ to $<readId[2], libId>$.
-..type:Typedef.FragmentStore#TMatePairStore
-..remarks:Value type is @Class.MatePairStoreElement@.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#libraryStore
-..summary:@Class.String@ that maps from $libId$ to $<mean, std>$.
-..type:Typedef.FragmentStore#TLibraryStore
-..remarks:Value type is @Class.LibraryStoreElement@.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#contigFileStore
-..summary:@Class.String@ that maps from $contigFileId$ to $<fileName, firstContigId>$.
-..type:Typedef.FragmentStore#TContigFileStore
-..remarks:Value type is @Class.ContigFile@.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#contigStore
-..summary:@Class.String@ that maps from $contigId$ to $<contigSeq, contigGaps, contigFileId>$.
-..type:Typedef.FragmentStore#TContigStore
-..remarks:Value type is @Class.ContigStoreElement@.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#alignedReadStore
-..summary:@Class.String@ that stores $<alignId, readId, contigId, pairMatchId, beginPos, endPos, gaps>$.
-..remarks:
-You can sort the $alignedReadStore$ using @Function.sortAlignedReads@.
-After sorting, you can use the functions @Function.lowerBoundAlignedReads@ and @Function.upperBoundAlignedReads@ to perform a binary search, e.g. for accessing only a subrange.
-..type:Typedef.FragmentStore#TAlignedReadStore
-..remarks:Value type is @Class.AlignedReadStoreElement@.
-..class:Class.FragmentStore
-..see:Function.lowerBoundAlignedReads
-..see:Function.upperBoundAlignedReads
-..see:Function.sortAlignedReads
-..include:seqan/store.h
-
-.Memvar.FragmentStore#annotationStore
-..summary:@Class.String@ that maps from $annoId$ to $<contigId, typeId, beginPos, endPos, parentId, lastChildId, nextSiblingId, values>$.
-..type:Typedef.FragmentStore#TAnnotationStore
-..remarks:Value type is @Class.AnnotationStoreElement@.
-..remarks:Instead of accesing this store directly, consider to use a high-level interface like the @Spec.AnnotationTree Iterator@.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#alignQualityStore
-..summary:@Class.String@ that maps from $alignId$ to $<pairScore, score, errors>$.
-..type:Typedef.FragmentStore#TAlignQualityStore
-..remarks:Value type is @Class.AlignQualityStoreElement@.
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#alignedReadTagStore
-..summary:@Class.StringSet@ that maps from $alignId$ to $alignTag$.
-..type:Typedef.FragmentStore#TAlignedReadTagStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#readNameStore
-..summary:@Class.StringSet@ that maps from $readId$ to $readName$.
-..type:Typedef.FragmentStore#TReadNameStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#matePairNameStore
-..summary:@Class.StringSet@ that maps from $contigId$ to $contigName$.
-..type:Typedef.FragmentStore#TMatePairNameStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#libraryNameStore
-..summary:@Class.StringSet@ that maps from $libId$ to $libName$.
-..type:Typedef.FragmentStore#TLibraryNameStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#contigNameStore
-..summary:@Class.StringSet@ that maps from $contigId$ to $contigName$.
-..type:Typedef.FragmentStore#TContigNameStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#annotationNameStore
-..summary:@Class.StringSet@ that maps from $annoId$ to $annoName$.
-..type:Typedef.FragmentStore#TAnnotationNameStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Memvar.FragmentStore#annotationTypeStore
-..summary:@Class.StringSet@ that maps from $typeId$ to the type name of an annotation, e.g. "gene" or "exon". $typeId$ is a member of the @Class.AnnotationStoreElement@.
-..type:Typedef.FragmentStore#TAnnotationTypeStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-..remarks:There are @Enum.Predefined Annotation Types|predefined type ids@ for commonly used types, e.g. $ANNO_GENE$ or $ANNO_EXON$,
-which can be used to set the @Memvar.AnnotationStoreElement#typeId@ directly as a fast alternative to @Function.getType@ and @Function.setType@.
-.Memvar.FragmentStore#annotationKeyStore
-..summary:@Class.StringSet@ that maps from $keyId$ to the name of a key. The $keyId$ is used to address @Memvar.AnnotationStoreElement#values@ of an annotation.
-..type:Typedef.FragmentStore#TAnnotationKeyStore
-..class:Class.FragmentStore
-..include:seqan/store.h
-
-.Enum.Predefined Annotation Types
-..class:Class.FragmentStore
-..cat:Fragment Store
-..summary:Predefined annotation type ids.
-..remarks:The @Class.FragmentStore@ predefines some commonly used @Memvar.AnnotationStoreElement#typeId@ values.
-They can be used to compare or set the @Memvar.AnnotationStoreElement#typeId@ directly as a fast alternative to @Function.getType@ and @Function.setType@.
-..value.ANNO_ROOT:The root node ("<root>").
-..value.ANNO_GENE:A gene ("gene").
-..value.ANNO_MRNA:An mRNA sequence, aka transcript ("mRNA").
-..value.ANNO_CDS:A coding region ("CDS").
-..value.ANNO_EXON:An exon ("exon").
-..value.ANNO_FIVE_PRIME_UTR:A 5' untranslated region ("five_prime_UTR").
-..value.ANNO_INTRON:An intron ("intron").
-..value.ANNO_THREE_PRIME_UTR:A 3' untranslated region ("three_prime_UTR").
-..include:seqan/store.h
-*/
-
 
 template <typename TSpec = void, typename TConfig = FragmentStoreConfig<TSpec> >
 class FragmentStore
 {
 private:
-	typedef typename TConfig::TReadStoreElementSpec			TReadStoreElementSpec;
-	typedef typename TConfig::TReadSeqStoreSpec				TReadSeqStoreSpec;
-    typedef typename TConfig::TReadNameSpec					TReadNameSpec;
-	typedef typename TConfig::TReadNameStoreSpec			TReadNameStoreSpec;
-	typedef typename TConfig::TMatePairStoreElementSpec		TMatePairStoreElementSpec;
-	typedef typename TConfig::TLibraryStoreElementSpec		TLibraryStoreElementSpec;
-	typedef typename TConfig::TContigStoreElementSpec		TContigStoreElementSpec;
-	typedef typename TConfig::TContigFileSpec				TContigFileSpec;
-	typedef typename TConfig::TAlignedReadStoreElementSpec	TAlignedReadStoreElementSpec;
-	typedef typename TConfig::TAlignedReadTagStoreSpec		TAlignedReadTagStoreSpec;
-	typedef typename TConfig::TAnnotationStoreElementSpec	TAnnotationStoreElementSpec;
+    typedef typename TConfig::TReadStoreElementSpec            TReadStoreElementSpec;
+    typedef typename TConfig::TReadSeqStoreSpec                TReadSeqStoreSpec;
+    typedef typename TConfig::TReadNameSpec                    TReadNameSpec;
+    typedef typename TConfig::TReadNameStoreSpec            TReadNameStoreSpec;
+    typedef typename TConfig::TMatePairStoreElementSpec        TMatePairStoreElementSpec;
+    typedef typename TConfig::TLibraryStoreElementSpec        TLibraryStoreElementSpec;
+    typedef typename TConfig::TContigStoreElementSpec        TContigStoreElementSpec;
+    typedef typename TConfig::TContigFileSpec                TContigFileSpec;
+    typedef typename TConfig::TAlignedReadStoreElementSpec    TAlignedReadStoreElementSpec;
+    typedef typename TConfig::TAlignedReadTagStoreSpec        TAlignedReadTagStoreSpec;
+    typedef typename TConfig::TAnnotationStoreElementSpec    TAnnotationStoreElementSpec;
 
 public:
-	typedef typename TConfig::TMean					TMean;
-	typedef typename TConfig::TStd					TStd;
-	typedef typename TConfig::TMappingQuality		TMappingQuality;
-	
-	typedef typename TConfig::TReadSeq				TReadSeq;
-	typedef typename TConfig::TContigSeq			TContigSeq;
-
-	typedef typename Position<TReadSeq>::Type		TRSeqPos_;
-	typedef typename Position<TContigSeq>::Type     TCSeqPos_;
-	typedef typename MakeSigned_<TRSeqPos_>::Type	TReadPos;
-	typedef typename MakeSigned_<TCSeqPos_>::Type	TContigPos;
-	
-	typedef GapAnchor<TReadPos>						TReadGapAnchor;
-	typedef GapAnchor<TContigPos>					TContigGapAnchor;
-	
-	typedef StringSet<CharString>					TNameStore;
-
-	typedef AnnotationStoreElement< TContigPos, TAnnotationStoreElementSpec >	TAnnotationStoreElement;
-	typedef typename TAnnotationStoreElement::TId								TAnnotationStoreElementId;
-
-	typedef String< ReadStoreElement< TReadStoreElementSpec > >												TReadStore;
-	typedef String< MatePairStoreElement< TMatePairStoreElementSpec > >										TMatePairStore;
-	typedef String< LibraryStoreElement< TMean, TStd, TLibraryStoreElementSpec > >							TLibraryStore;
-	typedef String< ContigStoreElement< TContigSeq, TContigGapAnchor, TContigStoreElementSpec > >			TContigStore;
-	typedef String< ContigFile< TContigFileSpec > >															TContigFileStore;
-	typedef String< AlignedReadStoreElement< TContigPos, TReadGapAnchor, TAlignedReadStoreElementSpec > >	TAlignedReadStore;
-	typedef String< AlignQualityStoreElement< TMappingQuality >	>											TAlignQualityStore;
-	typedef StringSet<CharString, TAlignedReadTagStoreSpec>													TAlignedReadTagStore;
-	typedef String< TAnnotationStoreElement >																TAnnotationStore;
-	typedef String< IntervalTree< TContigPos, TAnnotationStoreElementId > >									TIntervalTreeStore;
-	typedef StringSet<TReadSeq, TReadSeqStoreSpec>															TReadSeqStore;
-	
-	typedef StringSet< String<char, TReadNameSpec>, TReadNameStoreSpec>										TReadNameStore;
-	typedef TNameStore																						TMatePairNameStore;
-	typedef TNameStore																						TLibraryNameStore;
-	typedef TNameStore																						TContigNameStore;
-	typedef TNameStore																						TAnnotationNameStore;
-	typedef TNameStore																						TAnnotationTypeStore;
-	typedef TNameStore																						TAnnotationKeyStore;
-	
-	// main containers
-	TReadStore			readStore;              // readId       -> matePairId
-	TMatePairStore		matePairStore;          // matePairId   -> readId0, readId1, libraryId
-	TLibraryStore		libraryStore;           // libraryId    -> libSizeMean, libSizeStd
-	TContigStore		contigStore;            // contigId     -> contigSeq, contigGaps, contigFileId
-	TContigFileStore	contigFileStore;        // contigFileId -> fileName, firstContigId
-	TAlignedReadStore	alignedReadStore;       //              -> id, readId, contigId, pairMatchId (not matePairId!), beginPos, endPos, gaps
-	TAnnotationStore	annotationStore;        // annoId       -> parentId, contigId, beginPos, endPos
-	TIntervalTreeStore	intervalTreeStore_F;	// treeId (same as contigId)	-> intervalTree (F: forward strand)
-	TIntervalTreeStore	intervalTreeStore_R;	// 						(R: reverse complement strand)
-
-											// REMARKS: 
-											// 1)
-											//    beginPos <= endPos     forward strand
-											//    beginPos >  endPos     backward strand (reverse complement)
-											// 2) 
-											//    The alignedReadStore can arbitrarily be resorted. The unique identifier id should
-											//    be used to address additional information for each alignedRead in additional tables.
-
-	// we store the read sequences in a seperate stringset to reduce the memory overhead 
-	TReadSeqStore		readSeqStore;
-
-	// extra Sam fields
-	TAlignQualityStore		alignQualityStore;
-	TAlignedReadTagStore	alignedReadTagStore;
-
-	// retrieve the names of reads, mate-pairs, libraries, contigs, annotations by their ids
-	TReadNameStore			readNameStore;
-	TMatePairNameStore		matePairNameStore;
-	TLibraryNameStore		libraryNameStore;
-	TContigNameStore		contigNameStore;
-	TAnnotationNameStore	annotationNameStore;
-	TAnnotationTypeStore	annotationTypeStore;
-	TAnnotationKeyStore		annotationKeyStore;
-	
-	NameStoreCache<TReadNameStore, CharString>			readNameStoreCache;
-	NameStoreCache<TContigNameStore, CharString>		contigNameStoreCache;
-	NameStoreCache<TAnnotationNameStore, CharString>	annotationNameStoreCache;
-	NameStoreCache<TAnnotationTypeStore, CharString>	annotationTypeStoreCache;
-	NameStoreCache<TAnnotationKeyStore, CharString>		annotationKeyStoreCache;
-
-	enum {
-		ANNO_ROOT,
-		ANNO_DELETED,
-		ANNO_GENE,
-		ANNO_MRNA,
-		ANNO_CDS,
-		ANNO_EXON,
-		ANNO_FIVE_PRIME_UTR,
-		ANNO_INTRON,
-		ANNO_THREE_PRIME_UTR,
-		ANNO_PREDEFINED
-	};
-    
-	FragmentStore():
-		readNameStoreCache(readNameStore),
-		contigNameStoreCache(contigNameStore),
-		annotationNameStoreCache(annotationNameStore),
-		annotationTypeStoreCache(annotationTypeStore),
-		annotationKeyStoreCache(annotationKeyStore)
-	{
-		// ATTENTION: The order of these keywords must correspond to the order of the enums above.
-		appendName(annotationTypeStore, "<root>", annotationTypeStoreCache);
-		appendName(annotationTypeStore, "<deleted>", annotationTypeStoreCache);
-		appendName(annotationTypeStore, "gene", annotationTypeStoreCache);
-		appendName(annotationTypeStore, "mRNA", annotationTypeStoreCache);
-		appendName(annotationTypeStore, "CDS", annotationTypeStoreCache);
-		appendName(annotationTypeStore, "exon", annotationTypeStoreCache);
-		appendName(annotationTypeStore, "five_prime_UTR", annotationTypeStoreCache);
-		appendName(annotationTypeStore, "intron", annotationTypeStoreCache);
-		appendName(annotationTypeStore, "three_prime_UTR", annotationTypeStoreCache);
-		_storeClearAnnotations(*this);
-	}
+    typedef typename TConfig::TMean                    TMean;
+    typedef typename TConfig::TStd                    TStd;
+    typedef typename TConfig::TMappingQuality        TMappingQuality;
+
+    typedef typename TConfig::TReadSeq                TReadSeq;
+    typedef typename TConfig::TContigSeq            TContigSeq;
+
+    typedef typename Position<TReadSeq>::Type        TRSeqPos_;
+    typedef typename Position<TContigSeq>::Type     TCSeqPos_;
+    typedef typename MakeSigned_<TRSeqPos_>::Type    TReadPos;
+    typedef typename MakeSigned_<TCSeqPos_>::Type    TContigPos;
+
+    typedef GapAnchor<TReadPos>                        TReadGapAnchor;
+    typedef GapAnchor<TContigPos>                    TContigGapAnchor;
+
+    typedef StringSet<CharString>                    TNameStore;
+
+    typedef AnnotationStoreElement< TContigPos, TAnnotationStoreElementSpec >    TAnnotationStoreElement;
+    typedef typename TAnnotationStoreElement::TId                                TAnnotationStoreElementId;
+
+    typedef String< ReadStoreElement< TReadStoreElementSpec > >                                                TReadStore;
+    typedef String< MatePairStoreElement< TMatePairStoreElementSpec > >                                        TMatePairStore;
+    typedef String< LibraryStoreElement< TMean, TStd, TLibraryStoreElementSpec > >                            TLibraryStore;
+    typedef String< ContigStoreElement< TContigSeq, TContigGapAnchor, TContigStoreElementSpec > >            TContigStore;
+    typedef String< ContigFile< TContigFileSpec > >                                                            TContigFileStore;
+    typedef String< AlignedReadStoreElement< TContigPos, TReadGapAnchor, TAlignedReadStoreElementSpec > >    TAlignedReadStore;
+    typedef String< AlignQualityStoreElement< TMappingQuality >    >                                            TAlignQualityStore;
+    typedef StringSet<CharString, TAlignedReadTagStoreSpec>                                                    TAlignedReadTagStore;
+    typedef String< TAnnotationStoreElement >                                                                TAnnotationStore;
+    typedef String< IntervalTree< TContigPos, TAnnotationStoreElementId > >                                    TIntervalTreeStore;
+    typedef StringSet<TReadSeq, TReadSeqStoreSpec>                                                            TReadSeqStore;
+
+    typedef StringSet< String<char, TReadNameSpec>, TReadNameStoreSpec>                                        TReadNameStore;
+    typedef TNameStore                                                                                        TMatePairNameStore;
+    typedef TNameStore                                                                                        TLibraryNameStore;
+    typedef TNameStore                                                                                        TContigNameStore;
+    typedef TNameStore                                                                                        TAnnotationNameStore;
+    typedef TNameStore                                                                                        TAnnotationTypeStore;
+    typedef TNameStore                                                                                        TAnnotationKeyStore;
+
+    // main containers
+    TReadStore            readStore;              // readId       -> matePairId
+    TMatePairStore        matePairStore;          // matePairId   -> readId0, readId1, libraryId
+    TLibraryStore        libraryStore;           // libraryId    -> libSizeMean, libSizeStd
+    TContigStore        contigStore;            // contigId     -> contigSeq, contigGaps, contigFileId
+    TContigFileStore    contigFileStore;        // contigFileId -> fileName, firstContigId
+    TAlignedReadStore    alignedReadStore;       //              -> id, readId, contigId, pairMatchId (not matePairId!), beginPos, endPos, gaps
+    TAnnotationStore    annotationStore;        // annoId       -> parentId, contigId, beginPos, endPos
+    TIntervalTreeStore    intervalTreeStore_F;    // treeId (same as contigId)    -> intervalTree (F: forward strand)
+    TIntervalTreeStore    intervalTreeStore_R;    //                         (R: reverse complement strand)
+
+                                            // REMARKS:
+                                            // 1)
+                                            //    beginPos <= endPos     forward strand
+                                            //    beginPos >  endPos     backward strand (reverse complement)
+                                            // 2)
+                                            //    The alignedReadStore can arbitrarily be resorted. The unique identifier id should
+                                            //    be used to address additional information for each alignedRead in additional tables.
+
+    // we store the read sequences in a seperate stringset to reduce the memory overhead
+    TReadSeqStore        readSeqStore;
+
+    // extra Sam fields
+    TAlignQualityStore        alignQualityStore;
+    TAlignedReadTagStore    alignedReadTagStore;
+
+    // retrieve the names of reads, mate-pairs, libraries, contigs, annotations by their ids
+    TReadNameStore            readNameStore;
+    TMatePairNameStore        matePairNameStore;
+    TLibraryNameStore        libraryNameStore;
+    TContigNameStore        contigNameStore;
+    TAnnotationNameStore    annotationNameStore;
+    TAnnotationTypeStore    annotationTypeStore;
+    TAnnotationKeyStore        annotationKeyStore;
+
+    NameStoreCache<TReadNameStore, CharString>            readNameStoreCache;
+    NameStoreCache<TContigNameStore, CharString>        contigNameStoreCache;
+    NameStoreCache<TAnnotationNameStore, CharString>    annotationNameStoreCache;
+    NameStoreCache<TAnnotationTypeStore, CharString>    annotationTypeStoreCache;
+    NameStoreCache<TAnnotationKeyStore, CharString>        annotationKeyStoreCache;
+
+    enum {
+        ANNO_ROOT,
+        ANNO_DELETED,
+        ANNO_GENE,
+        ANNO_MRNA,
+        ANNO_CDS,
+        ANNO_EXON,
+        ANNO_FIVE_PRIME_UTR,
+        ANNO_INTRON,
+        ANNO_THREE_PRIME_UTR,
+        ANNO_PREDEFINED
+    };
+
+    FragmentStore():
+        readNameStoreCache(readNameStore),
+        contigNameStoreCache(contigNameStore),
+        annotationNameStoreCache(annotationNameStore),
+        annotationTypeStoreCache(annotationTypeStore),
+        annotationKeyStoreCache(annotationKeyStore)
+    {
+        // ATTENTION: The order of these keywords must correspond to the order of the enums above.
+        appendName(annotationTypeStore, "<root>", annotationTypeStoreCache);
+        appendName(annotationTypeStore, "<deleted>", annotationTypeStoreCache);
+        appendName(annotationTypeStore, "gene", annotationTypeStoreCache);
+        appendName(annotationTypeStore, "mRNA", annotationTypeStoreCache);
+        appendName(annotationTypeStore, "CDS", annotationTypeStoreCache);
+        appendName(annotationTypeStore, "exon", annotationTypeStoreCache);
+        appendName(annotationTypeStore, "five_prime_UTR", annotationTypeStoreCache);
+        appendName(annotationTypeStore, "intron", annotationTypeStoreCache);
+        appendName(annotationTypeStore, "three_prime_UTR", annotationTypeStoreCache);
+        _storeClearAnnotations(*this);
+    }
 
     void swap(FragmentStore & other)
     {
@@ -870,44 +575,42 @@ inline void swap(FragmentStore<TSpec, TConfig> & lhs, FragmentStore<TSpec, TConf
 }
 
 //////////////////////////////////////////////////////////////////////////////
-    
+
 template < typename TSpec, typename TConfig >
-struct VertexDescriptor< FragmentStore<TSpec, TConfig> > 
+struct VertexDescriptor< FragmentStore<TSpec, TConfig> >
 {
-	typedef FragmentStore<TSpec, TConfig>		TFragmentStore_;
-	typedef typename Id<TFragmentStore_>::Type	Type;
+    typedef FragmentStore<TSpec, TConfig>        TFragmentStore_;
+    typedef typename Id<TFragmentStore_>::Type    Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.begin.param.object.type:Class.FragmentStore
 template < typename TConfig, typename TSpec, typename TIterSpec >
 inline typename Iterator<FragmentStore<TSpec, TConfig>, TIterSpec >::Type
-begin(FragmentStore<TSpec, TConfig> &store, TIterSpec const) 
+begin(FragmentStore<TSpec, TConfig> &store, TIterSpec const)
 {
-	return Iter<FragmentStore<TSpec, TConfig>, TIterSpec>(store);
+    return Iter<FragmentStore<TSpec, TConfig>, TIterSpec>(store);
 }
 
 template < typename TConfig, typename TSpec, typename TIterSpec >
 inline typename Iterator<FragmentStore<TSpec, TConfig> const, TIterSpec >::Type
-begin(FragmentStore<TSpec, TConfig> const &store, TIterSpec const) 
+begin(FragmentStore<TSpec, TConfig> const &store, TIterSpec const)
 {
-	return Iter<FragmentStore<TSpec, TConfig> const, TIterSpec>(store);
+    return Iter<FragmentStore<TSpec, TConfig> const, TIterSpec>(store);
 }
 
 //////////////////////////////////////////////////////////////////////////////
-///.Function.end.param.object.type:Class.FragmentStore
 template < typename TConfig, typename TSpec, typename TIterSpec >
 inline typename Iterator<FragmentStore<TSpec, TConfig>, TIterSpec >::Type
-end(FragmentStore<TSpec, TConfig> &store, TIterSpec const) 
+end(FragmentStore<TSpec, TConfig> &store, TIterSpec const)
 {
-	return Iter<FragmentStore<TSpec, TConfig>, TIterSpec>(store, MinimalCtor());
+    return Iter<FragmentStore<TSpec, TConfig>, TIterSpec>(store, MinimalCtor());
 }
 
 template < typename TConfig, typename TSpec, typename TIterSpec >
 inline typename Iterator<FragmentStore<TSpec, TConfig> const, TIterSpec >::Type
-end(FragmentStore<TSpec, TConfig> const &store, TIterSpec const) 
+end(FragmentStore<TSpec, TConfig> const &store, TIterSpec const)
 {
-	return Iter<FragmentStore<TSpec, TConfig> const, TIterSpec>(store, MinimalCtor());
+    return Iter<FragmentStore<TSpec, TConfig> const, TIterSpec>(store, MinimalCtor());
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -916,47 +619,47 @@ template < typename TConfig, typename TSpec >
 inline void
 _storeClearAnnotations(FragmentStore<TSpec, TConfig> & me)
 {
-	typedef FragmentStore<TSpec, TConfig>				TFragmentStore;
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	
-	resize(me.annotationStore, 1);
-	resize(me.annotationNameStore, 1);
-	resize(me.annotationTypeStore, (unsigned)TFragmentStore::ANNO_PREDEFINED);
-	
-	TAnnotation root;
-	root.typeId = 0;
-	me.annotationStore[0] = root;
-	me.annotationNameStore[0] = "<root>";
+    typedef FragmentStore<TSpec, TConfig>                TFragmentStore;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+
+    resize(me.annotationStore, 1);
+    resize(me.annotationNameStore, 1);
+    resize(me.annotationTypeStore, (unsigned)TFragmentStore::ANNO_PREDEFINED);
+
+    TAnnotation root;
+    root.typeId = 0;
+    me.annotationStore[0] = root;
+    me.annotationNameStore[0] = "<root>";
 }
 
 template < typename TConfig, typename TSpec >
 inline void
 _storeRemoveTempAnnoNames(FragmentStore<TSpec, TConfig> & me)
 {
-	typedef FragmentStore<TSpec, TConfig>						TFragmentStore;
-	typedef typename TFragmentStore::TAnnotationStore			TAnnotationStore;
-	typedef typename TFragmentStore::TAnnotationNameStore		TAnnotationNameStore;
-	typedef typename TFragmentStore::TAnnotationTypeStore		TAnnotationTypeStore;
-
-	typedef typename GetValue<TAnnotationNameStore>::Type		TName;
-	typedef typename GetValue<TAnnotationTypeStore>::Type		TType;
-	typedef typename Iterator<TAnnotationStore, Standard>::Type	TAnnoIter;
-	typedef typename Position<TAnnotationStore>::Type			TPosition;
-	
-	TAnnoIter it = end(me.annotationStore, Standard()) - 1;
-	TAnnoIter itBegin = begin(me.annotationStore, Standard());
-	TPosition pos = it - itBegin;
-	for (; itBegin <= it; --it, --pos)
-	{
-		if ((*it).typeId >= length(me.annotationTypeStore))
-			continue;
-		TName name = me.annotationNameStore[pos];
-		TType type = me.annotationTypeStore[(*it).typeId];
-		if (length(name) > length(type) + 3)
-			if (prefix(name, 2) == "__" && infix(name, 2, 2 + length(type)) == type && name[2 + length(type)] == '_')
-				assignValue(me.annotationNameStore, pos, "");
-	}
+    typedef FragmentStore<TSpec, TConfig>                        TFragmentStore;
+    typedef typename TFragmentStore::TAnnotationStore            TAnnotationStore;
+    typedef typename TFragmentStore::TAnnotationNameStore        TAnnotationNameStore;
+    typedef typename TFragmentStore::TAnnotationTypeStore        TAnnotationTypeStore;
+
+    typedef typename GetValue<TAnnotationNameStore>::Type        TName;
+    typedef typename GetValue<TAnnotationTypeStore>::Type        TType;
+    typedef typename Iterator<TAnnotationStore, Standard>::Type    TAnnoIter;
+    typedef typename Position<TAnnotationStore>::Type            TPosition;
+
+    TAnnoIter it = end(me.annotationStore, Standard()) - 1;
+    TAnnoIter itBegin = begin(me.annotationStore, Standard());
+    TPosition pos = it - itBegin;
+    for (; itBegin <= it; --it, --pos)
+    {
+        if ((*it).typeId >= length(me.annotationTypeStore))
+            continue;
+        TName name = me.annotationNameStore[pos];
+        TType type = me.annotationTypeStore[(*it).typeId];
+        if (length(name) > length(type) + 3)
+            if (prefix(name, 2) == "__" && infix(name, 2, 2 + length(type)) == type && name[2 + length(type)] == '_')
+                assignValue(me.annotationNameStore, pos, "");
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -965,26 +668,26 @@ template <typename TSpec, typename TConfig, typename TId>
 inline typename GetValue<typename FragmentStore<TSpec, TConfig>::TAnnotationNameStore>::Type
 getAnnoName(FragmentStore<TSpec, TConfig> const & store, TId id)
 {
-	return store.annotationNameStore[id];
+    return store.annotationNameStore[id];
 }
 
 template <typename TSpec, typename TConfig, typename TId>
 inline typename GetValue<typename FragmentStore<TSpec, TConfig>::TAnnotationTypeStore>::Type
 getAnnoType(FragmentStore<TSpec, TConfig> const & store, TId id)
 {
-	return store.annotationTypeStore[id];
+    return store.annotationTypeStore[id];
 }
 
 template <typename TSpec, typename TConfig, typename TId>
 inline CharString
 getAnnoUniqueName(FragmentStore<TSpec, TConfig> const & store, TId id)
 {
-	if (id < length(store.annotationNameStore) && !empty(getAnnoName(store, id)))
-		return getAnnoName(store, id);
-	
-	std::stringstream tmp;
-	tmp << "__" << getAnnoType(store, store.annotationStore[id].typeId) << '_' << id;
-	return tmp.str();
+    if (id < length(store.annotationNameStore) && !empty(getAnnoName(store, id)))
+        return getAnnoName(store, id);
+
+    std::stringstream tmp;
+    tmp << "__" << getAnnoType(store, store.annotationStore[id].typeId) << '_' << id;
+    return tmp.str();
 }
 
 
@@ -994,28 +697,28 @@ getAnnoUniqueName(FragmentStore<TSpec, TConfig> const & store, TId id)
 
 //////////////////////////////////////////////////////////////////////////////
 // _storeAppendRead
-// 
-// adds a new entry to the read store if neccessary. Otherwise it writes the 
+//
+// adds a new entry to the read store if neccessary. Otherwise it writes the
 // correct Id in the variable using to qname to identify it
 // If needed a mate pair entry is created.
 // Returns true, if the read hasn't been in the read store before and was appended.
-    
+
 template <typename TSpec, typename TConfig, typename TId, typename TName, typename TString, typename TFlag, typename TContext>
-inline bool 
+inline bool
 _storeAppendRead (
-	FragmentStore<TSpec, TConfig> & fragStore, 
-	TId & readId, 
-	TName const & qname,
-	TString const & readSeq,
-	TFlag const flag,
-	TContext &)
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TId & readId,
+    TName const & qname,
+    TString const & readSeq,
+    TFlag const flag,
+    TContext &)
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Value<typename TFragmentStore::TMatePairStore>::Type TMatePairElement;
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Value<typename TFragmentStore::TMatePairStore>::Type TMatePairElement;
+
+    // search for readId by name (could be me or my mate)
+    bool found = getIdByName(fragStore.readNameStore, qname, readId, fragStore.readNameStoreCache);
 
-	// search for readId by name (could be me or my mate)
-	bool found = getIdByName(fragStore.readNameStore, qname, readId, fragStore.readNameStoreCache);
-    
     // if naming scheme is xx/1, xx/2 or xx/L, xx/R try to look up my mate
     if (!found && (flag & 1) == 1 && length(qname) >= 2 && qname[length(qname) - 2] == '/')
     {
@@ -1026,7 +729,7 @@ _storeAppendRead (
         {
             mate = qname;
             back(mate) = (tag == '1')? '2': '1';
-        } 
+        }
         else if (tag == 'L' || tag == 'R')
         {
             mate = qname;
@@ -1034,107 +737,107 @@ _storeAppendRead (
         }
         found = getIdByName(fragStore.readNameStore, mate, readId, fragStore.readNameStoreCache);
     }
-    
-	if (found)
+
+    if (found)
     {
-		if ((flag & 1) == 1)
-		{
-			// if the read is in the store and paired
-			// check the mate pair store if it is the same mate of the pair
-			// assuming that only one flag 0x040 or 0x0080 is 1
-			int inPair = 1 - ((flag & 0x40) >> 6);	// bit 7 is set => inPair = 0
-													// else inPair = 1 (even if bits 6 and 7 are not set)
-			
-			TId matePairId = fragStore.readStore[readId].matePairId;
-			if (matePairId != TMatePairElement::INVALID_ID)
-			{
-				readId = fragStore.matePairStore[matePairId].readId[inPair];
-				if (readId == TMatePairElement::INVALID_ID)
-				{
-					// create new entry in read and read name store
-					// set sequence and mate pair ID in new read store element
-					readId = appendRead(fragStore, readSeq, matePairId);
-					// add the identifier to the read name store
-					appendName(fragStore.readNameStore, qname, fragStore.readNameStoreCache);
-					// set the ID in the mate pair store
-					fragStore.matePairStore[matePairId].readId[inPair] = readId;
+        if ((flag & 1) == 1)
+        {
+            // if the read is in the store and paired
+            // check the mate pair store if it is the same mate of the pair
+            // assuming that only one flag 0x040 or 0x0080 is 1
+            int inPair = 1 - ((flag & 0x40) >> 6);    // bit 7 is set => inPair = 0
+                                                    // else inPair = 1 (even if bits 6 and 7 are not set)
+
+            TId matePairId = fragStore.readStore[readId].matePairId;
+            if (matePairId != TMatePairElement::INVALID_ID)
+            {
+                readId = fragStore.matePairStore[matePairId].readId[inPair];
+                if (readId == TMatePairElement::INVALID_ID)
+                {
+                    // create new entry in read and read name store
+                    // set sequence and mate pair ID in new read store element
+                    readId = appendRead(fragStore, readSeq, matePairId);
+                    // add the identifier to the read name store
+                    appendName(fragStore.readNameStore, qname, fragStore.readNameStoreCache);
+                    // set the ID in the mate pair store
+                    fragStore.matePairStore[matePairId].readId[inPair] = readId;
                     return true;
-				} 
+                }
                 // else == I am already in the store
-			}
+            }
             // else == my mate said he has no mate (do nothing)
-		}
+        }
         return false;
-	}
-
-	// if the read name is not in the store
-	// create new entry in read and read name store
-	readId = length(fragStore.readStore);
-
-	// if the read is paired
-	if ((flag & 1) == 1)
-	{
-		TMatePairElement mateElem;
-		// set the first or second read ID in the mate pair element
-		TId matePairId = length(fragStore.matePairStore);
-		mateElem.readId[(flag & 0x80) >> 7] = readId;
-		// get a new mate pair ID and add the new mate pair element
-		appendValue(fragStore.matePairStore, mateElem);
-		// set the new mate pair ID in the read element
-		appendRead(fragStore, readSeq, matePairId);
-	} 
-	// if read is not paired
-	else
-		appendRead(fragStore, readSeq);
-	
-	appendName(fragStore.readNameStore, qname, fragStore.readNameStoreCache);
+    }
+
+    // if the read name is not in the store
+    // create new entry in read and read name store
+    readId = length(fragStore.readStore);
+
+    // if the read is paired
+    if ((flag & 1) == 1)
+    {
+        TMatePairElement mateElem;
+        // set the first or second read ID in the mate pair element
+        TId matePairId = length(fragStore.matePairStore);
+        mateElem.readId[(flag & 0x80) >> 7] = readId;
+        // get a new mate pair ID and add the new mate pair element
+        appendValue(fragStore.matePairStore, mateElem);
+        // set the new mate pair ID in the read element
+        appendRead(fragStore, readSeq, matePairId);
+    }
+    // if read is not paired
+    else
+        appendRead(fragStore, readSeq);
+
+    appendName(fragStore.readNameStore, qname, fragStore.readNameStoreCache);
     return true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 // _storeAppendContig
-// 
+//
 // adds a new entry to the contig store if neccessary. Otherwise it writes the
 // correct Id in the variable using to qname to identify it
-    
+
 template <typename TSpec, typename TConfig, typename TId, typename TName>
-inline void 
+inline void
 _storeAppendContig (
-	FragmentStore<TSpec, TConfig> & fragStore, 
-	TId & contigId, 
-	TName & rName)
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TId & contigId,
+    TName & rName)
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigElement;
-	
-	if (!getIdByName(fragStore.contigNameStore, rName, contigId, fragStore.contigNameStoreCache))
-	{
-		// if the contig is not in the store yet
-		// set the ID on the last entry after appending
-		contigId = length(fragStore.contigStore);
-		// append contig store
-		appendName(fragStore.contigNameStore, rName, fragStore.contigNameStoreCache);
-		appendValue(fragStore.contigStore, TContigElement());
-//		std::cout << "added contig:" << rName << std::endl;	
-	}
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigElement;
+
+    if (!getIdByName(fragStore.contigNameStore, rName, contigId, fragStore.contigNameStoreCache))
+    {
+        // if the contig is not in the store yet
+        // set the ID on the last entry after appending
+        contigId = length(fragStore.contigStore);
+        // append contig store
+        appendName(fragStore.contigNameStore, rName, fragStore.contigNameStoreCache);
+        appendValue(fragStore.contigStore, TContigElement());
+//        std::cout << "added contig:" << rName << std::endl;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 // _annotationAppendAnnotation
-// 
-// adds a new entry to the read store if neccessary. Otherwise it writes the 
+//
+// adds a new entry to the read store if neccessary. Otherwise it writes the
 // correct Id in the variable using to qname to identify it
 
 template <typename TSpec, typename TConfig, typename TId, typename TName, typename TTypeId>
 inline void
 _storeAppendAnnotationName (
-	FragmentStore<TSpec, TConfig> & fragStore,
-	TId & annotationId,
-	TName & annotationName,
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TId & annotationId,
+    TName & annotationName,
     TTypeId typeId)
 {
     SEQAN_ASSERT_EQ(length(fragStore.annotationStore), length(fragStore.annotationNameStore));
-	if (!empty(annotationName) && getIdByName(fragStore.annotationNameStore, annotationName, annotationId, fragStore.annotationNameStoreCache))
+    if (!empty(annotationName) && getIdByName(fragStore.annotationNameStore, annotationName, annotationId, fragStore.annotationNameStoreCache))
     {
         do
         {
@@ -1144,124 +847,126 @@ _storeAppendAnnotationName (
             ++annotationId;
         } while (annotationId < length(fragStore.annotationNameStore) && fragStore.annotationNameStore[annotationId] == annotationName);
     }
-	// if the annotation is not in the store yet
-	// set the ID on the last entry after appending
-	annotationId = length(fragStore.annotationNameStore);
-	// append to annotationName store
-	appendName(fragStore.annotationNameStore, annotationName, fragStore.annotationNameStoreCache);
+    // if the annotation is not in the store yet
+    // set the ID on the last entry after appending
+    annotationId = length(fragStore.annotationNameStore);
+    // append to annotationName store
+    appendName(fragStore.annotationNameStore, annotationName, fragStore.annotationNameStoreCache);
     // we also need to append an annotation to store the typeId in case of duplicate annotation names
     resize(fragStore.annotationStore, length(fragStore.annotationStore) + 1);
     back(fragStore.annotationStore).typeId = typeId;
 }
 
 template <typename TSpec, typename TConfig, typename TId, typename TName>
-inline void 
+inline void
 _storeAppendAnnotationName (
-	FragmentStore<TSpec, TConfig> & fragStore, 
-	TId & annotationId,
-	TName & annotationName)
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TId & annotationId,
+    TName & annotationName)
 {
     _storeAppendAnnotationName(fragStore, annotationId, annotationName, maxValue<TId>());
 }
 
 template <typename TSpec, typename TConfig, typename TId, typename TName>
-inline void 
+inline void
 _storeAppendType (
-	FragmentStore<TSpec, TConfig> & fragStore, 
-	TId & typeId, 
-	TName & annotationType)
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TId & typeId,
+    TName & annotationType)
 {
-	if (!getIdByName(fragStore.annotationTypeStore, annotationType, typeId, fragStore.annotationTypeStoreCache))
-	{
-		// if the annotation type name is not in the store yet
-		// set the ID on the last entry after appending
-		typeId = length(fragStore.annotationTypeStore);
-		// append to annotationType store
-		if (!empty(annotationType))
-			appendName(fragStore.annotationTypeStore, annotationType, fragStore.annotationTypeStoreCache);
-//		std::cout << "added type:" << annotationType << std::endl;	
-	}
+    if (!getIdByName(fragStore.annotationTypeStore, annotationType, typeId, fragStore.annotationTypeStoreCache))
+    {
+        // if the annotation type name is not in the store yet
+        // set the ID on the last entry after appending
+        typeId = length(fragStore.annotationTypeStore);
+        // append to annotationType store
+        if (!empty(annotationType))
+            appendName(fragStore.annotationTypeStore, annotationType, fragStore.annotationTypeStoreCache);
+//        std::cout << "added type:" << annotationType << std::endl;
+    }
 }
 
 template <typename TSpec, typename TConfig, typename TId, typename TName>
-inline void 
+inline void
 _storeAppendKey (
-	FragmentStore<TSpec, TConfig> & fragStore, 
-	TId & keyId,
-	TName & annotationKey)
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TId & keyId,
+    TName & annotationKey)
 {
-	if (!getIdByName(fragStore.annotationKeyStore, annotationKey, keyId, fragStore.annotationKeyStoreCache))
-	{
-		// if the key name is not in the store yet
-		// set the ID on the last entry after appending
-		keyId = length(fragStore.annotationKeyStore);
-		// append to annotationKey store
-		if (!empty(annotationKey))
-			appendName(fragStore.annotationKeyStore, annotationKey, fragStore.annotationKeyStoreCache);
-//		std::cout << "added key:" << annotationKey << std::endl;	
-	}
+    if (!getIdByName(fragStore.annotationKeyStore, annotationKey, keyId, fragStore.annotationKeyStoreCache))
+    {
+        // if the key name is not in the store yet
+        // set the ID on the last entry after appending
+        keyId = length(fragStore.annotationKeyStore);
+        // append to annotationKey store
+        if (!empty(annotationKey))
+            appendName(fragStore.annotationKeyStore, annotationKey, fragStore.annotationKeyStoreCache);
+//        std::cout << "added key:" << annotationKey << std::endl;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TSpec, typename TConfig, typename TAnnotation, typename TKey, typename TValue>
-inline void 
+inline void
 annotationAssignValueByKey (
-	FragmentStore<TSpec, TConfig> & fragStore, 
-	TAnnotation & annotation,
-	TKey const & key,
-	TValue const & value)
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TAnnotation & annotation,
+    TKey const & key,
+    TValue const & value)
 {
-	typedef typename TAnnotation::TValues	TValues;
-	typedef typename Size<TValues>::Type	TKeyId;
-	
-	TKeyId keyId = 0;	
-	_storeAppendKey(fragStore, keyId, key);
-	if (length(annotation.values) <= keyId)
-		resize(annotation.values, keyId + 1);
-	assignValue(annotation.values, keyId, value);
+    typedef typename TAnnotation::TValues    TValues;
+    typedef typename Size<TValues>::Type    TKeyId;
+
+    TKeyId keyId = 0;
+    _storeAppendKey(fragStore, keyId, key);
+    if (length(annotation.values) <= keyId)
+        resize(annotation.values, keyId + 1);
+    assignValue(annotation.values, keyId, value);
 }
 
 template <typename TSpec, typename TConfig, typename TAnnotation, typename TKey, typename TValue>
-inline bool 
+inline bool
 annotationGetValueByKey (
-	FragmentStore<TSpec, TConfig> & fragStore, 
-	TAnnotation const & annotation,
-	TKey const & key,
-	TValue & value)
+    TValue & value,
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TAnnotation const & annotation,
+    TKey const & key)
 {
-	typedef typename TAnnotation::TValues	TValues;
-	typedef typename Size<TValues>::Type	TKeyId;
-	
-	TKeyId keyId = 0;	
-	if (!getIdByName(fragStore.annotationKeyStore, key, keyId, fragStore.annotationKeyStoreCache))
-		return false;
-	
-	if (keyId >= length(annotation.values))
-		return false;
-
-	if (empty(annotation.values[keyId]))
-		return false;
-	
-	assign(value, annotation.values[keyId]);
+    typedef typename TAnnotation::TValues    TValues;
+    typedef typename Size<TValues>::Type    TKeyId;
+
+    TKeyId keyId = 0;
+    if (!getIdByName(fragStore.annotationKeyStore, key, keyId, fragStore.annotationKeyStoreCache))
+        return false;
+
+    if (keyId >= length(annotation.values))
+        return false;
+
+    if (empty(annotation.values[keyId]))
+        return false;
+
+    assign(value, annotation.values[keyId]);
     return true;
 }
 
 template <typename TSpec, typename TConfig, typename TAnnotation, typename TKey>
-inline CharString 
-annotationGetValueByKey (
-	FragmentStore<TSpec, TConfig> & fragStore, 
-	TAnnotation const & annotation,
-	TKey const & key)
+inline typename Id<TAnnotation>::Type
+annotationGetValueIdByKey (
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TAnnotation const & annotation,
+    TKey const & key)
 {
-	typedef typename TAnnotation::TValues	TValues;
-	typedef typename Size<TValues>::Type	TKeyId;
-	
-	TKeyId keyId = 0;
-	if (getIdByName(fragStore.annotationKeyStore, key, keyId, fragStore.annotationKeyStoreCache))
-		return annotation.values[keyId];
-	else
-		return "";
+    typedef typename TAnnotation::TValues           TValues;
+    typedef typename Size<TValues>::Type            TKeyId;
+
+    static const typename Value<typename TAnnotation::TValues const>::Type emptyString;
+
+    TKeyId keyId = 0;
+    if (getIdByName(fragStore.annotationKeyStore, key, keyId, fragStore.annotationKeyStoreCache))
+        if (keyId < length(annotation.values) && !empty(annotation.values[keyId]))
+            return keyId;
+    return TAnnotation::INVALID_ID;
 }
 
 /*!
@@ -1275,25 +980,13 @@ annotationGetValueByKey (
  * This function clears the @link FragmentStore::contigStore @endlink and @link FragmentStore::contigNameStore @endlink.
  */
 
-/**
-.Function.clearContigs
-..class:Class.FragmentStore
-..summary:Removes all contigs from a fragment store.
-..cat:Fragment Store
-..signature:clearContigs(store)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..remarks:This function clears the @Memvar.FragmentStore#contigStore@ and @Memvar.FragmentStore#contigNameStore@.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig>
 inline void
 clearContigs(FragmentStore<TSpec, TConfig> &me)
 {
-	clear(me.contigStore);
-	clear(me.contigNameStore);
-	refresh(me.contigNameStoreCache);
+    clear(me.contigStore);
+    clear(me.contigNameStore);
+    refresh(me.contigNameStoreCache);
 }
 
 
@@ -1313,25 +1006,13 @@ clearContigs(FragmentStore<TSpec, TConfig> &me)
  * FragmentStore::readNameStore @endlink.
  */
 
-/**
-.Function.clearReads
-..class:Class.FragmentStore
-..summary:Removes all reads from a fragment store.
-..cat:Fragment Store
-..signature:clearReads(store)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..remarks:This function clears the @Memvar.FragmentStore#readStore@, @Memvar.FragmentStore#readSeqStore@ and @Memvar.FragmentStore#readNameStore@.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig>
 inline void
 clearReads(FragmentStore<TSpec, TConfig> &me)
 {
-	clear(me.readStore);
-	clear(me.readSeqStore);
-	clear(me.readNameStore);
+    clear(me.readStore);
+    clear(me.readSeqStore);
+    clear(me.readNameStore);
     refresh(me.readNameStoreCache);
 }
 
@@ -1343,7 +1024,7 @@ clearReads(FragmentStore<TSpec, TConfig> &me)
  * @signature TSize appendRead(store, read, name[, matePairId]);
  *
  * @param[in,out] store      The FragmentStore to append the read to.
- * @param[in]     read       The read sequence.  Type: @link SequenceConcept @endlink.
+ * @param[in]     read       The read sequence.  Type: @link ContainerConcept @endlink.
  * @param[in]     name       The name of the read.  Type: @link CharString @endlink.
  * @param[in]     matePairId ID of the mate-pair that this read is part of.  Default:
  *                           <tt>FragmentStore::INVALID_ID</tt> which corresponds to an unmated read.
@@ -1356,90 +1037,69 @@ clearReads(FragmentStore<TSpec, TConfig> &me)
  *
  * @see FragmentStore#getRead
  */
- 
-
-/**
-.Function.appendRead:
-..class:Class.FragmentStore
-..summary:Appends a read to a fragment store.
-..cat:Fragment Store
-..signature:appendRead(store, read[, matePairId])
-..signature:appendRead(store, read, name[, matePairId])
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.read:The read sequence.
-..param.name:The read name.
-...type:Shortcut.CharString
-..param.matePairId:Id of mate-pair this read is part of.
-...default:$INVALID_ID$, which corresponds to an unmated read.
-..returns:The $readId$ of the newly appended read.
-..remarks:This function appends a single read to the @Memvar.FragmentStore#readStore@ and @Memvar.FragmentStore#readSeqStore@.
-If name is given, it is appended to the @Memvar.FragmentStore#readNameStore@.
-..see:Function.getRead
-..include:seqan/store.h
-*/
+
 
 template <typename TSpec, typename TConfig, typename TRead, typename TId>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TReadStore>::Type
 appendRead(
-	FragmentStore<TSpec, TConfig> &me, 
-	TRead const &read, 
-	TId matePairId)
+    FragmentStore<TSpec, TConfig> &me,
+    TRead const &read,
+    TId matePairId)
 {
-	SEQAN_ASSERT_EQ(length(me.readStore), length(me.readSeqStore));
+    SEQAN_ASSERT_EQ(length(me.readStore), length(me.readSeqStore));
 
-	typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
-	typename Value<TReadStore>::Type r;
-	r.matePairId = matePairId;
+    typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
+    typename Value<TReadStore>::Type r;
+    r.matePairId = matePairId;
 
-	appendValue(me.readStore, r, Generous());
-	appendValue(me.readSeqStore, read, Generous());
-	return length(me.readStore) - 1;
+    appendValue(me.readStore, r, Generous());
+    appendValue(me.readSeqStore, read, Generous());
+    return length(me.readStore) - 1;
 }
 
 template <typename TSpec, typename TConfig, typename TRead, typename TId>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TReadStore>::Type
 appendRead(
-	FragmentStore<TSpec, TConfig> &me, 
-	TRead const &read, 
-	CharString const &name,
-	TId matePairId)
+    FragmentStore<TSpec, TConfig> &me,
+    TRead const &read,
+    CharString const &name,
+    TId matePairId)
 {
-	SEQAN_ASSERT_EQ(length(me.readStore), length(me.readSeqStore));
+    SEQAN_ASSERT_EQ(length(me.readStore), length(me.readSeqStore));
 
-	typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
-	typename Value<TReadStore>::Type r;
-	r.matePairId = matePairId;
+    typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
+    typename Value<TReadStore>::Type r;
+    r.matePairId = matePairId;
 
-	appendValue(me.readStore, r, Generous());
-	appendValue(me.readSeqStore, read, Generous());
-	appendValue(me.readNameStore, name, Generous());
-	return length(me.readStore) - 1;
+    appendValue(me.readStore, r, Generous());
+    appendValue(me.readSeqStore, read, Generous());
+    appendValue(me.readNameStore, name, Generous());
+    return length(me.readStore) - 1;
 }
 
 template <typename TSpec, typename TConfig, typename TRead>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TReadStore>::Type
 appendRead(
-	FragmentStore<TSpec, TConfig> &me, 
-	TRead const &read)
+    FragmentStore<TSpec, TConfig> &me,
+    TRead const &read)
 {
-	typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
+    typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
     typedef typename Value<TReadStore>::Type TReadStoreElement;
-    
-	return appendRead(me, read, TReadStoreElement::INVALID_ID);
+
+    return appendRead(me, read, TReadStoreElement::INVALID_ID);
 }
 
 template <typename TSpec, typename TConfig, typename TRead>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TReadStore>::Type
 appendRead(
-	FragmentStore<TSpec, TConfig> &me, 
-	TRead const &read,
-	CharString const &name)
+    FragmentStore<TSpec, TConfig> &me,
+    TRead const &read,
+    CharString const &name)
 {
-	typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
+    typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
     typedef typename Value<TReadStore>::Type TReadStoreElement;
-    
-	return appendRead(me, read, name, TReadStoreElement::INVALID_ID);
+
+    return appendRead(me, read, name, TReadStoreElement::INVALID_ID);
 }
 
 /*!
@@ -1455,25 +1115,13 @@ appendRead(
  *               FragmentStore::readStore @endlink.
  */
 
-/**
-.Function.getRead
-..summary:Returns the read with the given $readId$.
-..cat:Fragment Store
-..signature:getRead(store, readId)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.readId:The read id.
-..returns:The sequence of the read with id $readId$ from the @Memvar.FragmentStore#readSeqStore@.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TId>
 inline typename Value<typename FragmentStore<TSpec, TConfig>::TReadSeqStore>::Type
 getRead(
-	FragmentStore<TSpec, TConfig> &me, 
-	TId id)
+    FragmentStore<TSpec, TConfig> &me,
+    TId id)
 {
-	return value(me.readSeqStore, id);
+    return value(me.readSeqStore, id);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1489,7 +1137,7 @@ getRead(
  * @param[in]     contigId    The id of the contig of the alignment.
  * @param[in]     beginPos    The begin position of the alignment.
  * @param[in]     endPos      The end position of the alignment.
- * @param[in]     pairMatchId The id of the alignedRead pair.  Default: 
+ * @param[in]     pairMatchId The id of the alignedRead pair.  Default:
  *                            <tt>FragmentStore::INVALID_ID</tt> which corresponds to an unmated read.
  *
  * @return TSize The alignedReadId of the alignment.
@@ -1503,27 +1151,6 @@ getRead(
  * @see FragmentStore#appendRead
  */
 
-/**
-.Function.appendAlignedRead:
-..class:Class.FragmentStore
-..summary:Appends an aligned read entry to a fragment store.
-..cat:Fragment Store
-..signature:appendAlignedRead(store, readId, contigId, beginPos, endPos[, pairMatchId])
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.readId:The id of the read.
-..param.contigId:The id of the contig.
-..param.beginPos:The begin position of the alignment.
-..param.endPos:The end position of the alignment.
-..param.pairMatchId:Id of alignedRead pair.
-...default:$INVALID_ID$, which corresponds to an unmated read.
-..returns:The $alignedReadId$ of the aligned read.
-..remarks:This function appends a single aligned read to the @Memvar.FragmentStore#alignedReadStore@.
-Note that this really only adds a match.
-To generate a global alignment out of all of these matches, use @Function.convertMatchesToGlobalAlignment@.
-..see:Function.appendRead
-..include:seqan/store.h
-*/
 template <typename TSpec, typename TConfig, typename TReadId, typename TContigId, typename TPos, typename TPairMatchId>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TAlignedReadStore>::Type
 appendAlignedRead(
@@ -1535,7 +1162,7 @@ appendAlignedRead(
         TPairMatchId const & pairMatchId)
 {
     SEQAN_CHECKPOINT;
-	typedef typename FragmentStore<TSpec, TConfig>::TAlignedReadStore TAlignedReadStore;
+    typedef typename FragmentStore<TSpec, TConfig>::TAlignedReadStore TAlignedReadStore;
     typedef typename Value<TAlignedReadStore>::Type TAlignedReadStoreElement;
 
     TAlignedReadStoreElement element(length(store.alignedReadStore), readId, contigId, beginPos, endPos);
@@ -1555,7 +1182,7 @@ appendAlignedRead(
         TPos const & endPos)
 {
     SEQAN_CHECKPOINT;
-	typedef typename FragmentStore<TSpec, TConfig>::TAlignedReadStore TAlignedReadStore;
+    typedef typename FragmentStore<TSpec, TConfig>::TAlignedReadStore TAlignedReadStore;
     typedef typename Value<TAlignedReadStore>::Type TAlignedReadStoreElement;
     return appendAlignedRead(store, readId, contigId, beginPos, endPos, TAlignedReadStoreElement::INVALID_ID);
 }
@@ -1584,87 +1211,66 @@ appendAlignedRead(
  * they are appended to @link FragmentStore::readNameStore @endlink.
  */
 
-/**
-.Function.appendMatePair
-..class:Class.FragmentStore
-..summary:Appends two paired-end reads to a fragment store.
-..cat:Fragment Store
-..signature:appendMatePair(store, readSeq1, readSeq2)
-..signature:appendMatePair(store, readSeq1, readSeq2, name1, name2)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.readSeq1:The read sequence of the first read.
-..param.readSeq2:The read sequence of the second read.
-..param.name1:The read name of the first read.
-..param.name2:The read name of the second read.
-..returns:The $matePairId$ of the newly appended mate-pair.
-..remarks:This function appends two reads to the @Memvar.FragmentStore#readStore@ and @Memvar.FragmentStore#readSeqStore@ 
-and a mate-pair entry between both of them to the @Memvar.FragmentStore#matePairStore@.
-If names are given, they are appended to the @Memvar.FragmentStore#readNameStore@.
-..see:Function.appendRead
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TRead>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TMatePairStore>::Type
 appendMatePair(
-	FragmentStore<TSpec, TConfig> &me, 
-	TRead const &read1, 
-	TRead const &read2)
+    FragmentStore<TSpec, TConfig> &me,
+    TRead const &read1,
+    TRead const &read2)
 {
-	typedef FragmentStore<TSpec, TConfig>			TFragmentStore;
-	typedef typename TFragmentStore::TReadStore		TReadStore;
-	typedef typename TFragmentStore::TMatePairStore	TMatePairStore;
-
-	typename Value<TReadStore>::Type r;
-	typename Value<TMatePairStore>::Type mp;
-	r.matePairId = length(me.matePairStore);
-	mp.readId[0] = length(me.readStore);
-	mp.readId[1] = length(me.readStore) + 1;
-
-	appendValue(me.readStore, r, Generous());
-	appendValue(me.readStore, r, Generous());
-	appendValue(me.matePairStore, mp, Generous());
-	appendValue(me.readSeqStore, read1, Generous());
-	appendValue(me.readSeqStore, read2, Generous());
-	return length(me.matePairStore) - 1;
+    typedef FragmentStore<TSpec, TConfig>            TFragmentStore;
+    typedef typename TFragmentStore::TReadStore        TReadStore;
+    typedef typename TFragmentStore::TMatePairStore    TMatePairStore;
+
+    typename Value<TReadStore>::Type r;
+    typename Value<TMatePairStore>::Type mp;
+    r.matePairId = length(me.matePairStore);
+    mp.readId[0] = length(me.readStore);
+    mp.readId[1] = length(me.readStore) + 1;
+
+    appendValue(me.readStore, r, Generous());
+    appendValue(me.readStore, r, Generous());
+    appendValue(me.matePairStore, mp, Generous());
+    appendValue(me.readSeqStore, read1, Generous());
+    appendValue(me.readSeqStore, read2, Generous());
+    return length(me.matePairStore) - 1;
 }
 
 template <typename TSpec, typename TConfig, typename TRead>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TMatePairStore>::Type
 appendMatePair(
-	FragmentStore<TSpec, TConfig> &me, 
-	TRead const &read1, 
-	TRead const &read2, 
-	CharString const &name1,
-	CharString const &name2)
+    FragmentStore<TSpec, TConfig> &me,
+    TRead const &read1,
+    TRead const &read2,
+    CharString const &name1,
+    CharString const &name2)
 {
-	SEQAN_ASSERT_EQ(length(me.readStore), length(me.readSeqStore));
-
-	typedef FragmentStore<TSpec, TConfig>			TFragmentStore;
-	typedef typename TFragmentStore::TReadStore		TReadStore;
-	typedef typename TFragmentStore::TMatePairStore	TMatePairStore;
-
-	typename Value<TReadStore>::Type r;
-	typename Value<TMatePairStore>::Type mp;
-	r.matePairId = length(me.matePairStore);
-	mp.readId[0] = length(me.readStore);
-	mp.readId[1] = length(me.readStore) + 1;
-
-	appendValue(me.readStore, r, Generous());
-	appendValue(me.readStore, r, Generous());
-	appendValue(me.matePairStore, mp, Generous());
-	appendValue(me.readSeqStore, read1, Generous());
-	appendValue(me.readSeqStore, read2, Generous());
-	appendValue(me.readNameStore, name1, Generous());
-	appendValue(me.readNameStore, name2, Generous());
-	return length(me.matePairStore) - 1;
+    SEQAN_ASSERT_EQ(length(me.readStore), length(me.readSeqStore));
+
+    typedef FragmentStore<TSpec, TConfig>            TFragmentStore;
+    typedef typename TFragmentStore::TReadStore        TReadStore;
+    typedef typename TFragmentStore::TMatePairStore    TMatePairStore;
+
+    typename Value<TReadStore>::Type r;
+    typename Value<TMatePairStore>::Type mp;
+    r.matePairId = length(me.matePairStore);
+    mp.readId[0] = length(me.readStore);
+    mp.readId[1] = length(me.readStore) + 1;
+
+    appendValue(me.readStore, r, Generous());
+    appendValue(me.readStore, r, Generous());
+    appendValue(me.matePairStore, mp, Generous());
+    appendValue(me.readSeqStore, read1, Generous());
+    appendValue(me.readSeqStore, read2, Generous());
+    appendValue(me.readNameStore, name1, Generous());
+    appendValue(me.readNameStore, name2, Generous());
+    return length(me.matePairStore) - 1;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
- * @fn FragmentStore#compactAlignedRead
+ * @fn FragmentStore#compactAlignedReads
  * @brief Remove invalid aligned reads and rename the alignId's sequentially beginning with 0.
  *
  * @signature TSize compactAlignedReads(store);
@@ -1682,62 +1288,46 @@ appendMatePair(
  * by previously setting their id to INVALID_ID.
  */
 
-/**
-.Function.compactAlignedReads
-..class:Class.FragmentStore
-..summary:Removes invalid aligned reads and rename $alignId$ sequentially beginning with 0.
-..cat:Fragment Store
-..signature:compactAlignedReads(store)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..returns:The new size of the @Memvar.FragmentStore#alignedReadStore@.
-..remarks:This function removes all entries from @Memvar.FragmentStore#alignedReadStore@ whose $alignId$ equals to $INVALID_ID$ as well as orphan entries
-in @Memvar.FragmentStore#alignQualityStore@.
-Afterwards the alignIds are renamed sequentially beginning with 0.
-This function can be used to remove alignments which are selected by previously setting their id to $INVALID_ID$.
-..include:seqan/store.h
-*/
-
 // 1. remove aligned reads with invalid ids
 // 2. rename ids beginning with 0
 template <typename TSpec, typename TConfig>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TAlignedReadStore>::Type
 compactAlignedReads(FragmentStore<TSpec, TConfig> &me)
 {
-	typedef FragmentStore<TSpec, TConfig>							TFragmentStore;
-	typedef typename TFragmentStore::TAlignedReadStore				TAlignedReadStore;
-	typedef typename TFragmentStore::TAlignQualityStore				TAlignQualityStore;
-
-	typedef typename Value<TAlignedReadStore>::Type					TAlignedRead;
-	typedef typename Id<TAlignedRead>::Type							TId;
-	typedef typename Size<TAlignQualityStore>::Type					TAQSize;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type	TAlignedReadIter;
-	typedef typename Iterator<TAlignQualityStore, Standard>::Type	TAlignQualityIter;
-	
-	sortAlignedReads(me.alignedReadStore, SortId());
-	
-	TAlignedReadIter itAR = begin(me.alignedReadStore, Standard());
-	TAlignedReadIter itARend = end(me.alignedReadStore, Standard());
-	TAlignQualityIter itAQ = begin(me.alignQualityStore, Standard());
-	TAlignQualityIter itAQbegin = itAQ;
-	TAQSize aqSize = length(me.alignQualityStore);
-	TId newId = 0;
-	
-	for (; itAR != itARend; ++itAR, ++newId)
-	{
-		TId id = (*itAR).id;
-		if (id == TAlignedRead::INVALID_ID) break;	// we assume that invalid ids are at the end of the AlignedReadStore
-		if (id < aqSize)
-		{
-			*itAQ = *(itAQbegin + id);
-			++itAQ;
-		}
-		(*itAR).id = newId;
-	}
-	
-	resize(me.alignedReadStore, newId, Exact());
-	resize(me.alignQualityStore, itAQ - itAQbegin, Exact());
-	return newId;
+    typedef FragmentStore<TSpec, TConfig>                            TFragmentStore;
+    typedef typename TFragmentStore::TAlignedReadStore                TAlignedReadStore;
+    typedef typename TFragmentStore::TAlignQualityStore                TAlignQualityStore;
+
+    typedef typename Value<TAlignedReadStore>::Type                    TAlignedRead;
+    typedef typename Id<TAlignedRead>::Type                            TId;
+    typedef typename Size<TAlignQualityStore>::Type                    TAQSize;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignedReadIter;
+    typedef typename Iterator<TAlignQualityStore, Standard>::Type    TAlignQualityIter;
+
+    sortAlignedReads(me.alignedReadStore, SortId());
+
+    TAlignedReadIter itAR = begin(me.alignedReadStore, Standard());
+    TAlignedReadIter itARend = end(me.alignedReadStore, Standard());
+    TAlignQualityIter itAQ = begin(me.alignQualityStore, Standard());
+    TAlignQualityIter itAQbegin = itAQ;
+    TAQSize aqSize = length(me.alignQualityStore);
+    TId newId = 0;
+
+    for (; itAR != itARend; ++itAR, ++newId)
+    {
+        TId id = (*itAR).id;
+        if (id == TAlignedRead::INVALID_ID) break;    // we assume that invalid ids are at the end of the AlignedReadStore
+        if (id < aqSize)
+        {
+            *itAQ = *(itAQbegin + id);
+            ++itAQ;
+        }
+        (*itAR).id = newId;
+    }
+
+    resize(me.alignedReadStore, newId, Exact());
+    resize(me.alignQualityStore, itAQ - itAQbegin, Exact());
+    return newId;
 }
 
 /*!
@@ -1758,54 +1348,38 @@ compactAlignedReads(FragmentStore<TSpec, TConfig> &me)
  * orientation or a wrong insert size.
  */
 
-/**
-.Function.compactPairMatchIds
-..class:Class.FragmentStore
-..summary:Renames $pairMatchId$ sequentially beginning with 0.
-..cat:Fragment Store
-..signature:compactPairMatchIds(store)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..returns:The number of pair matches.
-..remarks:This function renames the $pairMatchId$ in the @Memvar.FragmentStore#alignedReadStore@ sequentially beginning with 0.
-Two read alignments can be identified to be a pair match if they have the same $pairMatchId$.
-Please note that paired reads not necessarily have to mapped as a pair match, 
-e.g. if they are on different contigs or have the same orientation or a wrong insert size.
-..include:seqan/store.h
-*/
-
 // rename pair match ids beginning with 0, returns the number of pair matches
 template <typename TSpec, typename TConfig>
 inline typename Size<typename FragmentStore<TSpec, TConfig>::TAlignedReadStore>::Type
 compactPairMatchIds(FragmentStore<TSpec, TConfig> &me)
 {
-	typedef FragmentStore<TSpec, TConfig>							TFragmentStore;
-	typedef typename TFragmentStore::TAlignedReadStore				TAlignedReadStore;
-
-	typedef typename Value<TAlignedReadStore>::Type					TAlignedRead;
-	typedef typename Id<TAlignedRead>::Type							TId;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type	TAlignedReadIter;
-	
-	sortAlignedReads(me.alignedReadStore, SortPairMatchId());
-	
-	TAlignedReadIter itAR = begin(me.alignedReadStore, Standard());
-	TAlignedReadIter itARend = end(me.alignedReadStore, Standard());
-	if (itAR == itARend) return 0;
-	
-	TId lastId = (*itAR).pairMatchId;
-	TId newId = 0;
-	for (; itAR != itARend; ++itAR)
-	{
-		TId id = (*itAR).pairMatchId;
-		if (id == TAlignedRead::INVALID_ID) break;	// we assume that invalid ids are at the end of the AlignedReadStore
-		if (lastId < id)
-		{
-			lastId = id;
-			++newId;
-		}
-		(*itAR).pairMatchId = newId;
-	}
-	return newId + 1;
+    typedef FragmentStore<TSpec, TConfig>                            TFragmentStore;
+    typedef typename TFragmentStore::TAlignedReadStore                TAlignedReadStore;
+
+    typedef typename Value<TAlignedReadStore>::Type                    TAlignedRead;
+    typedef typename Id<TAlignedRead>::Type                            TId;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignedReadIter;
+
+    sortAlignedReads(me.alignedReadStore, SortPairMatchId());
+
+    TAlignedReadIter itAR = begin(me.alignedReadStore, Standard());
+    TAlignedReadIter itARend = end(me.alignedReadStore, Standard());
+    if (itAR == itARend) return 0;
+
+    TId lastId = (*itAR).pairMatchId;
+    TId newId = 0;
+    for (; itAR != itARend; ++itAR)
+    {
+        TId id = (*itAR).pairMatchId;
+        if (id == TAlignedRead::INVALID_ID) break;    // we assume that invalid ids are at the end of the AlignedReadStore
+        if (lastId < id)
+        {
+            lastId = id;
+            ++newId;
+        }
+        (*itAR).pairMatchId = newId;
+    }
+    return newId + 1;
 }
 
 /*!
@@ -1824,52 +1398,38 @@ compactPairMatchIds(FragmentStore<TSpec, TConfig> &me)
  * pair match.  The insert size of a pair match is the outer distance between the two matches.
  */
 
-/**
-.Function.calculateInsertSizes
-..summary:Calculates a string with insert sizes for each pair match.
-..cat:Fragment Store
-..signature:compactPairMatchIds(insertSizes, store)
-..param.insertSizes:The resulting string of insert sizes.
-...remarks:This string is accordingly resized and can be addressed by the $pairMatchId$.
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..remarks:This function calls @Function.compactPairMatchIds@ first and calculate the insert size for every pair match.
-The insert size of a pair match is the outer distance between the two matches.
-..include:seqan/store.h
-*/
-
 template <typename TLibSizeString, typename TSpec, typename TConfig>
 inline void
 calculateInsertSizes(TLibSizeString &insertSizes, FragmentStore<TSpec, TConfig> &me)
 {
-	typedef FragmentStore<TSpec, TConfig>							TFragmentStore;
-	typedef typename TFragmentStore::TAlignedReadStore				TAlignedReadStore;
-	
-	typedef typename Value<TAlignedReadStore>::Type					TAlignedRead;
-	typedef typename Id<TAlignedRead>::Type							TId;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type	TAlignedReadIter;
-	typedef typename TFragmentStore::TContigPos						TGPos;
-
-	TAlignedReadIter it = begin(me.alignedReadStore, Standard());
-	TAlignedReadIter itEnd = end(me.alignedReadStore, Standard());
-
-	resize(insertSizes, compactPairMatchIds(me), Exact());
-	TId lastId = TAlignedRead::INVALID_ID;
-	TGPos leftMatePos = 0;
-	for (; it != itEnd; ++it)
-	{
-		TId id = (*it).pairMatchId;
-		if (id == TAlignedRead::INVALID_ID) break;	// we assume that invalid ids are at the end of the AlignedReadStore
-		if (id != lastId) {
-			leftMatePos = (*it).beginPos;
-			lastId = id;
-		} else {
+    typedef FragmentStore<TSpec, TConfig>                            TFragmentStore;
+    typedef typename TFragmentStore::TAlignedReadStore                TAlignedReadStore;
+
+    typedef typename Value<TAlignedReadStore>::Type                    TAlignedRead;
+    typedef typename Id<TAlignedRead>::Type                            TId;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignedReadIter;
+    typedef typename TFragmentStore::TContigPos                        TGPos;
+
+    TAlignedReadIter it = begin(me.alignedReadStore, Standard());
+    TAlignedReadIter itEnd = end(me.alignedReadStore, Standard());
+
+    resize(insertSizes, compactPairMatchIds(me), Exact());
+    TId lastId = TAlignedRead::INVALID_ID;
+    TGPos leftMatePos = 0;
+    for (; it != itEnd; ++it)
+    {
+        TId id = (*it).pairMatchId;
+        if (id == TAlignedRead::INVALID_ID) break;    // we assume that invalid ids are at the end of the AlignedReadStore
+        if (id != lastId) {
+            leftMatePos = (*it).beginPos;
+            lastId = id;
+        } else {
             if ((*it).beginPos < leftMatePos)
                 insertSizes[id] = leftMatePos - (*it).beginPos;
             else
                 insertSizes[id] = (*it).beginPos - leftMatePos;
         }
-	}
+    }
 }
 
 /*!
@@ -1885,45 +1445,33 @@ calculateInsertSizes(TLibSizeString &insertSizes, FragmentStore<TSpec, TConfig>
  *             read is not paired.
  */
 
-/**
-.Function.getMateNo
-..summary:Returns the mate number of read for a given $readId$.
-..cat:Fragment Store
-..signature:getMateNo(store, readId)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.readId:The read id.
-..returns:The mate number (0..first mate, 1..second mate) of the read in its mate-pair or -1 if the read is not paired.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TId>
 inline int
-getMateNo(FragmentStore<TSpec, TConfig> const &me, TId readId)
+getMateNo(FragmentStore<TSpec, TConfig> const & me, TId readId)
 {
-	typedef FragmentStore<TSpec, TConfig>			TFragmentStore;
-	typedef typename TFragmentStore::TReadStore		TReadStore;
-	typedef typename TFragmentStore::TMatePairStore	TMatePairStore;
-
-	typedef typename Value<TReadStore>::Type		TRead;
-	typedef typename Value<TMatePairStore>::Type	TMatePair;
-	
-	if (readId != TRead::INVALID_ID)
-	{
-		TRead const &r = me.readStore[readId];
-		if (r.matePairId != TRead::INVALID_ID)
-		{
-			TMatePair const &mp = me.matePairStore[r.matePairId];
-			if (mp.readId[0] == readId) return 0;
-			if (mp.readId[1] == readId) return 1;
-		}
-	}
-	return -1;
+    typedef FragmentStore<TSpec, TConfig>            TFragmentStore;
+    typedef typename TFragmentStore::TReadStore        TReadStore;
+    typedef typename TFragmentStore::TMatePairStore    TMatePairStore;
+
+    typedef typename Value<TReadStore>::Type        TRead;
+    typedef typename Value<TMatePairStore>::Type    TMatePair;
+
+    if (readId != TRead::INVALID_ID)
+    {
+        TRead const &r = me.readStore[readId];
+        if (r.matePairId != TRead::INVALID_ID)
+        {
+            TMatePair const &mp = me.matePairStore[r.matePairId];
+            if (mp.readId[0] == readId) return 0;
+            if (mp.readId[1] == readId) return 1;
+        }
+    }
+    return -1;
 }
 
 /*!
  * @fn FragmentStore#calculateMateIndices
- * @brief Calculates a string that maps the readId of a read to the readId of its mate.
+ * @brief Calculates a string that maps the readId of a read to the index of its mate in the alignedReadStore.
  *
  * @signature void calculateMateIndices(mateIndices, store);
  *
@@ -1934,56 +1482,42 @@ getMateNo(FragmentStore<TSpec, TConfig> const &me, TId readId)
  * Entries of reads without a mate contain <tt>INVALID_ID</tt>.
  */
 
-/**
-.Function.calculateMateIndices
-..summary:Calculates a string that maps the $readId$ of a read to the $readId$ of its mate.
-..cat:Fragment Store
-..signature:calculateMateIndices(mateIndices, store)
-..param.mateIndices:The resulting string of mate indices.
-...remarks:This string is accordingly resized and can be addressed by the $readId$.
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..remarks:Entries of reads without a mate contain $INVALID_ID$.
-..include:seqan/store.h
-*/
-
 // calculate index of the other mate for each pair match
 template <typename TMateIndexString, typename TSpec, typename TConfig>
 inline void
-calculateMateIndices(TMateIndexString &mateIndices, FragmentStore<TSpec, TConfig> &me)
+calculateMateIndices(TMateIndexString & mateIndices, FragmentStore<TSpec, TConfig> const & me)
 {
-	typedef FragmentStore<TSpec, TConfig>							TFragmentStore;
-	typedef typename TFragmentStore::TAlignedReadStore				TAlignedReadStore;
-	
-	typedef typename Value<TAlignedReadStore>::Type					TAlignedRead;
-	typedef typename Id<TAlignedRead>::Type							TId;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type	TAlignedReadIter;
-
-	TAlignedReadIter it = begin(me.alignedReadStore, Standard());
-	TAlignedReadIter itEnd = end(me.alignedReadStore, Standard());
-
-	for (TId idx = 0; it != itEnd; ++it, ++idx)
-	{
-		TId id = (*it).pairMatchId;
-		if (id == TAlignedRead::INVALID_ID) continue;
-		if (length(mateIndices) < 2*id + 2)
-			resize(mateIndices, 2*id + 2, TAlignedRead::INVALID_ID, Generous());
-		SEQAN_ASSERT_NEQ(getMateNo(me, (*it).readId), -1);
-		mateIndices[2*id + 1 - getMateNo(me, (*it).readId)] = idx;
-	}
+    typedef FragmentStore<TSpec, TConfig> const                     TFragmentStore;
+    typedef typename TFragmentStore::TAlignedReadStore const        TAlignedReadStore;
+
+    typedef typename Value<TAlignedReadStore>::Type                 TAlignedRead;
+    typedef typename Id<TAlignedRead>::Type                         TId;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignedReadIter;
+
+    TAlignedReadIter it = begin(me.alignedReadStore, Standard());
+    TAlignedReadIter itEnd = end(me.alignedReadStore, Standard());
+
+    for (TId idx = 0; it != itEnd; ++it, ++idx)
+    {
+        TId id = (*it).pairMatchId;
+        if (id == TAlignedRead::INVALID_ID) continue;
+        if (length(mateIndices) < 2*id + 2)
+            resize(mateIndices, 2*id + 2, TAlignedRead::INVALID_ID, Generous());
+        SEQAN_ASSERT_NEQ(getMateNo(me, (*it).readId), -1);
+        mateIndices[2*id + 1 - getMateNo(me, (*it).readId)] = idx;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
  * @class AlignedReadLayout
- * @headerfile <seqan/store>
+ * @headerfile <seqan/store.h>
  * @brief Stores a two dimensional visible layout of a multi-read alignment.
  *
- * @signature struct AlignedReadLayout.
- *
+ * @signature struct AlignedReadLayout;
  *
- * @var TContigRows AlignedReadLayout#contigRows;
+ * @var TContigRows AlignedReadLayout::contigRows;
  * @brief 2D multi-read layout.
  *
  * Stores for a contig and row the ids of aligned reads from left to right.  <tt>contigRows[contigId][row]</tt> stores
@@ -1991,28 +1525,15 @@ calculateMateIndices(TMateIndexString &mateIndices, FragmentStore<TSpec, TConfig
  * alignment in the multiple sequence alignment and contigId the id of the reference contig.
  */
 
-/**
-.Class.AlignedReadLayout
-..summary:Stores a 2-dimensional visible layout of a multi-read alignment.
-..cat:Fragment Store
-..signature:AlignedReadLayout
-.Memvar.AlignedReadLayout#contigRows
-..class:Class.AlignedReadLayout
-..summary:2-D multi-read layout
-..remarks:Stores for a contig and a row the ids of aligned reads from left to right.
-$contigRows[contigId][row]$ stores the $alignId$ of all aligned reads from left to right assigned to the same row
-$row$ is the row of the alignment in the multiple sequence alignment and $contigId$ the id of the reference contig.
-..include:seqan/store.h
-*/
-	
+
 struct AlignedReadLayout
 {
-	typedef String<unsigned>	TRow;
-	typedef String<TRow>		TRows;
-	typedef String<TRows>		TContigRows;
-	
-	TContigRows contigRows;			// rows string, each row is a string of ids of alignedReads from left to right
-	String<Pair<int> > mateCoords;	// coords of mate pair
+    typedef String<unsigned>    TRow;
+    typedef String<TRow>        TRows;
+    typedef String<TRows>        TContigRows;
+
+    TContigRows contigRows;            // rows string, each row is a string of ids of alignedReads from left to right
+    String<Pair<int> > mateCoords;    // coords of mate pair
 };
 
 /*!
@@ -2029,106 +1550,107 @@ struct AlignedReadLayout
  * @see AlignedReadLayout#printAlignment
  */
 
-/**
-.Function.layoutAlignment
-..class:Class.AlignedReadLayout
-..summary:Calculates a visible layout of aligned reads.
-..cat:Fragment Store
-..signature:layoutAlignment(layout, store)
-..param.layout:The resulting layout structure.
-...type:Class.AlignedReadLayout
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..remarks:For each contig this function layouts all reads in rows from up to down reusing empty row spaces.
-..see:Function.printAlignment
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig>
 void layoutAlignment(AlignedReadLayout &layout, FragmentStore<TSpec, TConfig> &store)
 {
-	typedef FragmentStore<TSpec, TConfig>							TFragmentStore;
-
-	typedef typename TFragmentStore::TAlignedReadStore				TAlignedReadStore;
-	typedef typename Value<TAlignedReadStore>::Type					TAlignedRead;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type	TAlignedReadIter;
-
-	typedef typename Id<TAlignedRead>::Type							TId;
-	typedef typename TFragmentStore::TContigPos						TContigPos;
-	
-	typedef typename AlignedReadLayout::TRows						TRows;
-	typedef typename AlignedReadLayout::TRow						TRow;
-	typedef typename Iterator<TRows>::Type							TRowsIter;
-	
-	// sort matches by increasing begin positions
-	sortAlignedReads(store.alignedReadStore, SortBeginPos());
-	sortAlignedReads(store.alignedReadStore, SortContigId());
-
-	clear(layout.contigRows);
-	TAlignedReadIter it = begin(store.alignedReadStore, Standard());
-	TAlignedReadIter itEnd = end(store.alignedReadStore, Standard());
-
-	for (TId id = 0; it != itEnd; ++it, ++id)
-	{
-		if ((*it).contigId == TAlignedRead::INVALID_ID) continue;
-		if (length(layout.contigRows) <= (*it).contigId)
-			resize(layout.contigRows, (*it).contigId + 1);
-		
-		TRowsIter lit = begin(layout.contigRows[(*it).contigId], Standard());
-		TRowsIter litEnd = end(layout.contigRows[(*it).contigId], Standard());
-		
-		TContigPos beginPos = _min((*it).beginPos, (*it).endPos);
-		
-		for (; lit != litEnd; ++lit)
-		{
-			if (empty(*lit)) break;
-			TAlignedRead &align = store.alignedReadStore[back(*lit)];
-			if (_max(align.beginPos, align.endPos) < beginPos)			// maybe <= would be better
-				break;													// but harder to differ between reads borders
-		}
-			
-		if (lit == litEnd)
-		{
-			TRow s;
-			appendValue(s, id);
-			appendValue(layout.contigRows[(*it).contigId], s);
-		} else
-			appendValue(*lit, id);
-	}
+    typedef FragmentStore<TSpec, TConfig>                            TFragmentStore;
+
+    typedef typename TFragmentStore::TAlignedReadStore                TAlignedReadStore;
+    typedef typename Value<TAlignedReadStore>::Type                    TAlignedRead;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignedReadIter;
+
+    typedef typename Id<TAlignedRead>::Type                            TId;
+    typedef typename TFragmentStore::TContigPos                        TContigPos;
+
+    typedef typename AlignedReadLayout::TRows                        TRows;
+    typedef typename AlignedReadLayout::TRow                        TRow;
+    typedef typename Iterator<TRows>::Type                            TRowsIter;
+
+    // sort matches by increasing begin positions
+    sortAlignedReads(store.alignedReadStore, SortBeginPos());
+    sortAlignedReads(store.alignedReadStore, SortContigId());
+
+    clear(layout.contigRows);
+    TAlignedReadIter it = begin(store.alignedReadStore, Standard());
+    TAlignedReadIter itEnd = end(store.alignedReadStore, Standard());
+
+    for (TId id = 0; it != itEnd; ++it, ++id)
+    {
+        if ((*it).contigId == TAlignedRead::INVALID_ID) continue;
+        if (length(layout.contigRows) <= (*it).contigId)
+            resize(layout.contigRows, (*it).contigId + 1);
+
+        TRowsIter lit = begin(layout.contigRows[(*it).contigId], Standard());
+        TRowsIter litEnd = end(layout.contigRows[(*it).contigId], Standard());
+
+        TContigPos beginPos = _min((*it).beginPos, (*it).endPos);
+
+        for (; lit != litEnd; ++lit)
+        {
+            if (empty(*lit)) break;
+            TAlignedRead &align = store.alignedReadStore[back(*lit)];
+            if (_max(align.beginPos, align.endPos) < beginPos)            // maybe <= would be better
+                break;                                                    // but harder to differ between reads borders
+        }
+
+        if (lit == litEnd)
+        {
+            TRow s;
+            appendValue(s, id);
+            appendValue(layout.contigRows[(*it).contigId], s);
+        } else
+            appendValue(*lit, id);
+    }
 }
 
-template <typename TStream, typename TFormatTag, typename TContigGaps, typename TReadGaps, typename TAlignedRead, typename TLine>
+template <typename TStream, typename TContigGaps, typename TReadGaps, typename TAlignedRead, typename TLine>
 inline void _printRead(
-	TStream &stream, 
-	Tag<TFormatTag> const &format,
-	AlignedReadLayout &, 
-	TContigGaps &,
-	TReadGaps &readGaps,
-	TAlignedRead &,
-	TLine)
+    TStream &stream,
+    AlignedReadLayout &,
+    TContigGaps &contigGaps,
+    TReadGaps &readGaps,
+    TAlignedRead &alignedRead,
+    TLine)
 {
-	write(stream, readGaps, "", format);
+//    stream << readGaps;
+
+    typedef typename Iterator<TContigGaps, Standard>::Type TContigIterator;
+    typedef typename Iterator<TReadGaps, Standard>::Type TIterator;
+
+    TContigIterator cit = begin(contigGaps, Standard()) + (_min(alignedRead.beginPos, alignedRead.endPos) + beginPosition(readGaps));
+    TIterator it = begin(readGaps, Standard());
+    TIterator itEnd = end(readGaps, Standard());
+
+    char identityChar = (alignedRead.beginPos < alignedRead.endPos)? '.' : ',';
+
+    for (; it != itEnd; ++it, ++cit)
+    {
+        if (isGap(it))
+            stream << '*';
+        else if (convert<Dna5>(*cit) == convert<Dna5>(*it))
+            stream << identityChar;
+        else
+            stream << convert<Dna5>(*it);
+    }
 }
 
-template <typename TStream, typename TFormatTag, typename TContigGaps, typename TContigName>
+template <typename TStream, typename TContigGaps, typename TContigName>
 inline void _printContig(
-	TStream &stream,
-	Tag<TFormatTag> const &format,
-	AlignedReadLayout &, 
-	TContigGaps &contigGaps,
-	TContigName const &)
+    TStream &stream,
+    AlignedReadLayout &,
+    TContigGaps &contigGaps,
+    TContigName const &)
 {
-	write(stream, contigGaps, "", format);
+    stream << contigGaps;
 }
 
 /*!
  * @fn AlignedReadLayout#printAlignment
  * @brief Prints a window of the visible layout of reads into a std::outstream.
  *
- * @signature void printAlignment(stream, format, layout, store, contigID, posBegin, posEnd, lineBegin, lineEnd);
+ * @signature void printAlignment(stream, layout, store, contigID, posBegin, posEnd, lineBegin, lineEnd);
  *
  * @param[in,out] stream    The std::ostream to print to.
- * @param[in]     format    The output format, e.g. <tt>Raw</tt>.
  * @param[in]     layout    The @link AlignedReadLayout @endlink computed earlier in @link
  *                          AlignedReadLayout#layoutAlignment @endlink.
  * @param[in]     store     The FragmentStore that this layout belongs to.
@@ -2142,277 +1664,242 @@ inline void _printContig(
  * spaces.
  */
 
-/**
-.Function.printAlignment
-..class:Class.AlignedReadLayout
-..summary:Prints a window of the visible layout of reads into a outstream.
-..cat:Fragment Store
-..signature:printAlignment(stream, format, layout, store, contigId, posBegin, posEnd, lineBegin, lineEnd)
-..param.stream:A C++ outstream, e.g. std::cout.
-..param.layout:A layout structure created by a previous call of @Function.layoutAlignment@.
-...type:Class.AlignedReadLayout
-..param.format:Output format.
-...type:Tag.File Format.tag.Raw
-...remarks: This tag is used for subsequent calls of @Function.write@ for contig and read gaps data structures.
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.contigId:The $contigId$ of the affected contig.
-..param.posBegin:Window begin position in gap-space.
-..param.posEnd:Window end position in gap-space.
-..param.lineBegin:Begin line of the window.
-..param.lineEnd:End line of the window.
-..remarks:The window coordinates ($beginPos$, ...) may be chosen bigger than the layout.
-The empty space is then filled with whitespaces.
-..see:Function.layoutAlignment
-..include:seqan/store.h
-*/
-
-template <typename TStream, typename TFormatTag, typename TSpec, typename TConfig, typename TContigId, typename TPos, typename TNum>
+template <typename TStream, typename TSpec, typename TConfig, typename TContigId, typename TPos, typename TNum>
 void printAlignment(
-	TStream &stream, 
-	Tag<TFormatTag> const &format,
-	AlignedReadLayout &layout, 
-	FragmentStore<TSpec, TConfig> &store, 
-	TContigId contigId,
-	TPos posBegin, TPos posEnd,
-	TNum lineBegin, TNum lineEnd)
+    TStream &stream,
+    AlignedReadLayout &layout,
+    FragmentStore<TSpec, TConfig> &store,
+    TContigId contigId,
+    TPos posBegin, TPos posEnd,
+    TNum lineBegin, TNum lineEnd)
 {
-	typedef FragmentStore<TSpec, TConfig>							TFragmentStore;
-
-	typedef typename TFragmentStore::TAlignedReadStore				TAlignedReadStore;
-	typedef typename TFragmentStore::TContigStore					TContigStore;
-
-	typedef typename Value<TContigStore>::Type						TContig;
-	typedef typename Value<TAlignedReadStore>::Type					TAlignedRead;
-	typedef typename TFragmentStore::TReadSeq						TReadSeq;
-	typedef typename Id<TAlignedRead>::Type							TId;
-	typedef typename TFragmentStore::TContigPos						TContigPos;
-	typedef typename TContig::TContigSeq							TContigSeq;
-
-	typedef AlignedReadLayout::TRows								TRows;
-	typedef typename Value<TRows>::Type								TRow;
-	typedef typename Size<TRows>::Type								TRowsSize;
-	typedef typename Iterator<TRows>::Type							TRowsIter;
-	typedef typename Iterator<TRow>::Type							TRowIter;
-
-	typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> >	TContigGaps;
-	typedef Gaps<CharString, AnchorGaps<typename TAlignedRead::TGapAnchors> >	TReadGaps;
-	
-	TContigGaps	contigGaps;
-	if ((TId)contigId < length(store.contigStore))
-	{
-		set(contigGaps.data_source, store.contigStore[contigId].seq);
-		set(contigGaps.data_gaps, store.contigStore[contigId].gaps);
-//		TContigGaps	contigGaps(store.contigStore[contigId].seq, store.contigStore[contigId].gaps);
-		setClippedBeginPosition(contigGaps, posBegin);
-		setClippedEndPosition(contigGaps, posEnd);
-		_printContig(stream, format, layout, contigGaps, store.contigNameStore[contigId]);
-		stream << '\n';
-	} else
-		stream << '\n';
-	
-	if ((TId)contigId >= length(layout.contigRows))
-		return;
-	
-	if ((TRowsSize)lineEnd > length(layout.contigRows[contigId])) lineEnd = length(layout.contigRows[contigId]);
-	if ((TRowsSize)lineBegin >= (TRowsSize)lineEnd) return;
-
-	TRowsIter lit = begin(layout.contigRows[contigId], Standard()) + lineBegin;
-	TRowsIter litEnd = begin(layout.contigRows[contigId], Standard()) + lineEnd;
-	TReadSeq readSeq;
-	CharString readSeqString;
+    typedef FragmentStore<TSpec, TConfig>                            TFragmentStore;
+
+    typedef typename TFragmentStore::TAlignedReadStore                TAlignedReadStore;
+    typedef typename TFragmentStore::TContigStore                    TContigStore;
+
+    typedef typename Value<TContigStore>::Type                        TContig;
+    typedef typename Value<TAlignedReadStore>::Type                    TAlignedRead;
+    typedef typename TFragmentStore::TReadSeq                        TReadSeq;
+    typedef typename Id<TAlignedRead>::Type                            TId;
+    typedef typename TFragmentStore::TContigPos                        TContigPos;
+    typedef typename TContig::TContigSeq                            TContigSeq;
+
+    typedef AlignedReadLayout::TRows                                TRows;
+    typedef typename Value<TRows>::Type                                TRow;
+    typedef typename Size<TRows>::Type                                TRowsSize;
+    typedef typename Iterator<TRows>::Type                            TRowsIter;
+    typedef typename Iterator<TRow>::Type                            TRowIter;
+
+    typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> >    TContigGaps;
+    typedef Gaps<CharString, AnchorGaps<typename TAlignedRead::TGapAnchors> >    TReadGaps;
+
+    typedef typename DirectionIterator<TStream, Output>::Type       TOutIter;
+
+    TContigGaps    contigGaps;
+    if ((TId)contigId < length(store.contigStore))
+    {
+        set(contigGaps.data_source, store.contigStore[contigId].seq);
+        set(contigGaps.data_gaps, store.contigStore[contigId].gaps);
+//        TContigGaps    contigGaps(store.contigStore[contigId].seq, store.contigStore[contigId].gaps);
+        setClippedBeginPosition(contigGaps, posBegin);
+        setClippedEndPosition(contigGaps, posEnd);
+        _printContig(stream, layout, contigGaps, store.contigNameStore[contigId]);
+    };
+    TOutIter iter = directionIterator(stream, Output());
+    writeValue(iter, '\n');
+
+    if ((TId)contigId >= length(layout.contigRows))
+        return;
+
+    if ((TRowsSize)lineEnd > length(layout.contigRows[contigId])) lineEnd = length(layout.contigRows[contigId]);
+    if ((TRowsSize)lineBegin >= (TRowsSize)lineEnd) return;
+
+    TRowsIter lit = begin(layout.contigRows[contigId], Standard()) + lineBegin;
+    TRowsIter litEnd = begin(layout.contigRows[contigId], Standard()) + lineEnd;
+    TReadSeq readSeq;
+    CharString readSeqString;
     clearClipping(contigGaps);
 
-	for (TNum line = 1; lit < litEnd; ++lit, ++line)
-	{
-		TRowIter itEnd = end(*lit, Standard());
-		TRowIter left = begin(*lit, Standard());
-		TRowIter right = itEnd;
-		TRowIter mid = itEnd;
-
-		while (left < right)
-		{
-			mid = left + (right - left) / 2;
-			TAlignedRead &align = store.alignedReadStore[*mid];
-
-			if (align.contigId < (TId)contigId || (align.contigId == (TId)contigId && (TPos)_max(align.beginPos, align.endPos) <= posBegin))
-				left = mid + 1;	// what we search is in the right part
-			else
-				right = mid;	//            ...           left part
-		}
-		
-		TPos cursor = posBegin;
-		for (; mid < itEnd; ++mid)
-		{
-//			if (*mid >= lastRead) continue;
-			TAlignedRead &align = store.alignedReadStore[*mid];
-			if (align.contigId != (TId)contigId) break;
-
-			TReadGaps readGaps(readSeqString, align.gaps);
-			TContigPos	left = align.beginPos;
-			TContigPos	right = align.endPos;
-			TContigPos	cBegin = _min(left, right);
-			TContigPos	cEnd = _max(left, right);
-			
-			if ((TPos)cEnd <= posBegin) continue; // shouldn't occur
-			if (posEnd <= (TPos)cBegin) break;
-			
-			readSeq = store.readSeqStore[align.readId];
-			if (left > right)
-			{
-				reverseComplement(readSeq);
-				readSeqString = readSeq;
-				toLower(readSeqString);
-			} else
-				readSeqString = readSeq;
-			
-			if ((TPos)cBegin < posBegin)
-				setClippedBeginPosition(readGaps, posBegin - (TPos)cBegin);
-			else
-				for (; cursor < (TPos)cBegin; ++cursor)
-					stream << ' ';
-			
-			if (posEnd < (TPos)cEnd)
-				setClippedEndPosition(readGaps, posEnd - (TPos)cBegin);
-			
-			_printRead(stream, format, layout, contigGaps, readGaps, align, line);
-			cursor = cEnd;
-		}
-		stream << '\n';
-	}
+    for (TNum line = 1; lit < litEnd; ++lit, ++line)
+    {
+        TRowIter itEnd = end(*lit, Standard());
+        TRowIter left = begin(*lit, Standard());
+        TRowIter right = itEnd;
+        TRowIter mid = itEnd;
+
+        while (left < right)
+        {
+            mid = left + (right - left) / 2;
+            TAlignedRead &align = store.alignedReadStore[*mid];
+
+            if (align.contigId < (TId)contigId || (align.contigId == (TId)contigId && (TPos)_max(align.beginPos, align.endPos) <= posBegin))
+                left = mid + 1;    // what we search is in the right part
+            else
+                right = mid;    //            ...           left part
+        }
+
+        TPos cursor = posBegin;
+        for (; mid < itEnd; ++mid)
+        {
+//            if (*mid >= lastRead) continue;
+            TAlignedRead &align = store.alignedReadStore[*mid];
+            if (align.contigId != (TId)contigId) break;
+
+            TReadGaps   readGaps(readSeqString, align.gaps);
+            TContigPos  left = align.beginPos;
+            TContigPos    right = align.endPos;
+            TContigPos    cBegin = _min(left, right);
+            TContigPos    cEnd = _max(left, right);
+
+            if ((TPos)cEnd <= posBegin) continue; // shouldn't occur
+            if (posEnd <= (TPos)cBegin) break;
+
+            readSeq = store.readSeqStore[align.readId];
+            if (left > right)
+            {
+                reverseComplement(readSeq);
+                readSeqString = readSeq;
+                toLower(readSeqString);
+            } else
+                readSeqString = readSeq;
+
+            if ((TPos)cBegin < posBegin)
+                setClippedBeginPosition(readGaps, posBegin - (TPos)cBegin);
+            else
+            {
+                TOutIter iter = directionIterator(stream, Output());
+                for (; cursor < (TPos)cBegin; ++cursor)
+                    writeValue(iter, ' ');
+            }
+
+            if (posEnd < (TPos)cEnd)
+                setClippedEndPosition(readGaps, posEnd - (TPos)cBegin);
+
+            _printRead(stream, layout, contigGaps, readGaps, align, line);
+            cursor = cEnd;
+        }
+        TOutIter iter = directionIterator(stream, Output());
+        writeValue(iter, '\n');
+    }
 }
 
 /*!
  * @fn FragmentStore#convertMatchesToGlobalAlignment
  * @brief Converts all matches to a multiple global alignment in gap-space.
- * 
- * @signature void convertMatchesToGlobalAlignment(store, score);
- * 
+ *
+ * @signature void convertMatchesToGlobalAlignment(store, score, shrinkMatches);
+ *
  * @param[in,out] store The fragment store. Types: FragmentStore
  * @param[in]     score A score object used by @link globalAlignment @endlink in this function.
- * 
+ * @param[in]     shrinkMatches States whether the matches should be shrinked. Types: True, False
+ *
  * @section Remarks
- * 
+ *
  * Before calling this function all <tt>gaps</tt> structures in @link FragmentStore::alignedReadStore @endlink and @link
  * FragmentStore::contigStore @endlink must be empty, i.e. there are no gaps in the alignments.  This function iterates
  * over entries in the @link FragmentStore::alignedReadStore @endlink and semi-global aligns each read to its contig
  * segments given by begin and end position.  Gaps introduced by these pair-wise alignments are then inserted to the
  * affected contig and reads correspondingly.
- * 
+ *
  * The invariant that positions in the @link FragmentStore::alignedReadStore @endlink are in gap-space holds before
  * (there were no gaps in alignments) and after calling this functions.
- * 
+ *
  * If the @link FragmentStore::alignQualityStore @endlink of the @link FragmentStore @endlink is empty when
  * <tt>convertMatchesToGlobalAlignment()</tt> is called then the @link FragmentStore::alignQualityStore @endlink is
  * filled with the edit distance scores.
  */
 
-/**
-.Function.convertMatchesToGlobalAlignment
-..summary:Converts all matches to a multiple global alignment in gap-space.
-..cat:Fragment Store
-..signature:convertMatchesToGlobalAlignment(store, score)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.score:A score object used by @Function.globalAlignment@ in this function.
-..remarks:Before calling this function all $gaps$ structures in @Memvar.FragmentStore#alignedReadStore@ and @Memvar.FragmentStore#contigStore@ must be empty, i.e. there are no gaps in the alignments.
-This function iterates over entries in the @Memvar.FragmentStore#alignedReadStore@ and semi-global aligns each read to its contig segments given by begin and end position.
-Gaps introduced by these pair-wise alignments are then inserted to the affected contig and reads correspondingly.
-..remarks:The invariant that positions in the @Memvar.FragmentStore#alignedReadStore@ are in gap-space holds before (there were no gaps in alignments) and after calling this functions.
-..remarks:If the @Memvar.FragmentStore#alignQualityStore@ of the @Class.FragmentStore@ is empty when $convertMatchesToGlobalAlignment()$ is called then the @Memvar.FragmentStore#alignQualityStore@ is filled with the edit distance scores.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TScore, typename TShrinkMatches>
 void convertMatchesToGlobalAlignment(FragmentStore<TSpec, TConfig> &store, TScore const & score, TShrinkMatches const &)
 {
-	typedef FragmentStore<TSpec, TConfig>							TFragmentStore;
+    typedef FragmentStore<TSpec, TConfig>                            TFragmentStore;
 
-	//typedef typename TFragmentStore::TReadStore						TReadStore;
-	//typedef typename TFragmentStore::TReadSeqStore					TReadSeqStore;
-	typedef typename TFragmentStore::TAlignedReadStore				TAlignedReadStore;
-	typedef typename TFragmentStore::TContigStore					TContigStore;
+    //typedef typename TFragmentStore::TReadStore                        TReadStore;
+    //typedef typename TFragmentStore::TReadSeqStore                    TReadSeqStore;
+    typedef typename TFragmentStore::TAlignedReadStore                TAlignedReadStore;
+    typedef typename TFragmentStore::TContigStore                    TContigStore;
 
-	//typedef typename Value<TReadStore>::Type						TRead;
-	typedef typename Value<TContigStore>::Type						TContig;
-	typedef typename Value<TAlignedReadStore>::Type					TAlignedRead;
+    //typedef typename Value<TReadStore>::Type                        TRead;
+    typedef typename Value<TContigStore>::Type                        TContig;
+    typedef typename Value<TAlignedReadStore>::Type                    TAlignedRead;
 
-	typedef typename TFragmentStore::TReadSeq						TReadSeq;
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type	TAlignedReadIter;
-	typedef typename Id<TAlignedRead>::Type							TId;
-	typedef typename TFragmentStore::TContigPos						TContigPos;
+    typedef typename TFragmentStore::TReadSeq                        TReadSeq;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignedReadIter;
+    typedef typename Id<TAlignedRead>::Type                            TId;
+    typedef typename TFragmentStore::TContigPos                        TContigPos;
 
-	typedef typename TContig::TContigSeq							TContigSeq;
-	typedef Align<TReadSeq, ArrayGaps>								TAlign;
-	typedef Gaps<TReadSeq, ArrayGaps>								TGaps;
+    typedef typename TContig::TContigSeq                            TContigSeq;
+    typedef Align<TReadSeq, ArrayGaps>                                TAlign;
+    typedef Gaps<TReadSeq, ArrayGaps>                                TGaps;
 
-	typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> >	TContigGaps;
-	typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> >	TReadGaps;
-	typedef typename Iterator<TContigGaps>::Type							TContigIter;
-	typedef typename Iterator<TReadGaps>::Type								TReadIter;
+    typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> >    TContigGaps;
+    typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> >    TReadGaps;
+    typedef typename Iterator<TContigGaps>::Type                            TContigIter;
+    typedef typename Iterator<TReadGaps>::Type                                TReadIter;
 
     // Number of alignments with a quality score (edit distance) before computing global alignment.  We will fill the
     // store for all alignments if there are no scores yet.
     unsigned alignQualityStoreLengthPre = length(store.alignQualityStore);
     if (alignQualityStoreLengthPre == 0u)
         resize(store.alignQualityStore, length(store.alignedReadStore));
-	
-	// sort matches by increasing begin positions
-	sortAlignedReads(store.alignedReadStore, SortBeginPos());
-	sortAlignedReads(store.alignedReadStore, SortContigId());
 
-	TReadSeq readSeq;
-	TId lastContigId = TAlignedRead::INVALID_ID;
-	TAlignedReadIter it = begin(store.alignedReadStore, Standard());
-	TAlignedReadIter itEnd = end(store.alignedReadStore, Standard());
-	TAlignedReadIter firstOverlap = begin(store.alignedReadStore, Standard());
+    // sort matches by increasing begin positions
+    sortAlignedReads(store.alignedReadStore, SortBeginPos());
+    sortAlignedReads(store.alignedReadStore, SortContigId());
+
+    TReadSeq readSeq;
+    TId lastContigId = TAlignedRead::INVALID_ID;
+    TAlignedReadIter it = begin(store.alignedReadStore, Standard());
+    TAlignedReadIter itEnd = end(store.alignedReadStore, Standard());
+    TAlignedReadIter firstOverlap = begin(store.alignedReadStore, Standard());
 
 //    TAlignedReadIter theIt = it;
-//	for (; theIt != itEnd; ++theIt)
-//	{
+//    for (; theIt != itEnd; ++theIt)
+//    {
 //        if (theIt->id == 29971)
 //            break;
 //    }
-//	TReadSeq theReadSeq = store.readSeqStore[theIt->readId];
+//    TReadSeq theReadSeq = store.readSeqStore[theIt->readId];
 //    if (theIt->beginPos > theIt->endPos)
 //        reverseComplement(theReadSeq);
-    
-//    TContigPos	cBeginPrev = 0;
-	for (; it != itEnd;)
-	{
-		TContigPos	left = (*it).beginPos;
-		TContigPos	right = (*it).endPos;
-		TContigPos	cBegin = _min(left, right);
+
+//    TContigPos    cBeginPrev = 0;
+    for (; it != itEnd;)
+    {
+        TContigPos    left = (*it).beginPos;
+        TContigPos    right = (*it).endPos;
+        TContigPos    cBegin = _min(left, right);
 //    if (cBegin<cBeginPrev)
 //    {
 //        std::cout<<"SORTING ERROR"<<std::endl;
 //    }
 //    cBeginPrev=cBegin;
-		TContigPos	cEnd = _max(left, right);
-		TContigGaps	contigGaps(store.contigStore[(*it).contigId].seq, store.contigStore[(*it).contigId].gaps);
-		TReadGaps	readGaps(readSeq, (*it).gaps);
-		
-		readSeq = store.readSeqStore[(*it).readId];
-		if (left > right)
-			reverseComplement(readSeq);
-				
-		// 1. Calculate pairwise alignment
-		TAlign align;
-		resize(rows(align), 2);
-		assignSource(row(align, 0), infix(store.contigStore[it->contigId].seq, cBegin, cEnd));
-		assignSource(row(align, 1), readSeq);
+        TContigPos    cEnd = _max(left, right);
+        TContigGaps    contigGaps(store.contigStore[(*it).contigId].seq, store.contigStore[(*it).contigId].gaps);
+        TReadGaps    readGaps(readSeq, (*it).gaps);
+
+        readSeq = store.readSeqStore[(*it).readId];
+        if (left > right)
+            reverseComplement(readSeq);
+
+        // 1. Calculate pairwise alignment
+        TAlign align;
+        resize(rows(align), 2);
+        assignSource(row(align, 0), infix(store.contigStore[it->contigId].seq, cBegin, cEnd));
+        assignSource(row(align, 1), readSeq);
 //        int ud = store.alignQualityStore[it->id].errors;
 //        int ld = -ud;
-//		if (IsSameType<TShrinkMatches, True>::VALUE)
-//		    globalAlignment(align, score, AlignConfig<true, false, false, true>(), ld, ud, Gotoh());
+//        if (IsSameType<TShrinkMatches, True>::VALUE)
+//            globalAlignment(align, score, AlignConfig<true, false, false, true>(), ld, ud, Gotoh());
 //        else
-//		    globalAlignment(align, score, ld, ud);
+//            globalAlignment(align, score, ld, ud);
 
         int qualValue = 0;
-		if (IsSameType<TShrinkMatches, True>::VALUE)
-		    qualValue = globalAlignment(align, score, AlignConfig<true, false, false, true>(), Gotoh());
+        if (IsSameType<TShrinkMatches, True>::VALUE)
+            qualValue = globalAlignment(align, score, AlignConfig<true, false, false, true>(), Gotoh());
         else
-		    qualValue = globalAlignment(align, score);
+            qualValue = globalAlignment(align, score);
         // Update quality score entry if there were no scores before convertMatchesToGlobal() call.
         if (alignQualityStoreLengthPre > 0u && it->id >= alignQualityStoreLengthPre)
         {
@@ -2432,8 +1919,8 @@ void convertMatchesToGlobalAlignment(FragmentStore<TSpec, TConfig> &store, TScor
 //        }
 //
 //        TReadGaps readGaps(theReadSeq, theIt->gaps);
-//        TContigGaps	contigGaps(store.contigStore[theIt->contigId].seq, store.contigStore[theIt->contigId].gaps);
-//        if ((*theIt).beginPos <= (*theIt).endPos) 
+//        TContigGaps    contigGaps(store.contigStore[theIt->contigId].seq, store.contigStore[theIt->contigId].gaps);
+//        if ((*theIt).beginPos <= (*theIt).endPos)
 //        {
 //            setBeginPosition(contigGaps, (*theIt).beginPos);
 //            setEndPosition(contigGaps, (*theIt).endPos);
@@ -2497,50 +1984,50 @@ void convertMatchesToGlobalAlignment(FragmentStore<TSpec, TConfig> &store, TScor
         }
         SEQAN_ASSERT_EQ(toViewPosition(row(align, 1), 0), 0u);
 
-		// 2. Skip non-overlapping matches
-		cBegin = positionSeqToGap(contigGaps, cBegin);
-		if (lastContigId != (*it).contigId)
-		{
-			firstOverlap = it;
-			lastContigId = (*it).contigId;
-		} else
-			while (firstOverlap != it && _max((*firstOverlap).beginPos, (*firstOverlap).endPos) <= cBegin)
-				++firstOverlap;
-
-		// 3. Iterate over alignment
-		setClippedBeginPosition(contigGaps, cBegin);
-		
-		TContigIter cIt = begin(contigGaps);
-		TReadIter rIt = begin(readGaps);
-		typename Iterator<TGaps>::Type it1 = begin(row(align, 0));
-		typename Iterator<TGaps>::Type it2 = begin(row(align, 1));
+        // 2. Skip non-overlapping matches
+        cBegin = positionSeqToGap(contigGaps, cBegin);
+        if (lastContigId != (*it).contigId)
+        {
+            firstOverlap = it;
+            lastContigId = (*it).contigId;
+        } else
+            while (firstOverlap != it && _max((*firstOverlap).beginPos, (*firstOverlap).endPos) <= cBegin)
+                ++firstOverlap;
+
+        // 3. Iterate over alignment
+        setClippedBeginPosition(contigGaps, cBegin);
+
+        TContigIter cIt = begin(contigGaps);
+        TReadIter rIt = begin(readGaps);
+        typename Iterator<TGaps>::Type it1 = begin(row(align, 0));
+        typename Iterator<TGaps>::Type it2 = begin(row(align, 1));
 
         unsigned beginLocalContigGaps = toViewPosition(row(align, 0), 0);
         //std::cerr << "CONTIG\t" << contigGaps << "\n";
-		// Heuristic (hack) for gaps in the beginning, so the following 
-		// does not happen:
-		//
-		// contig: XXXX------AAA
-		//             CCC---AAA
-		//                CCCAAA
-		//
-		// But instead, the C's are all aligned.
-		if (beginLocalContigGaps > 0u) {
-			unsigned i = beginLocalContigGaps;
-			do {
-				goPrevious(cIt);
-				i -= 1;
-				cBegin -= 1;
-			} while (isGap(cIt) && i > 0u);
-			if (!isGap(cIt)) {
-				goNext(cIt);
-				cBegin += 1;
-			}
-		}
-		
-		// We will clip off trailing gaps in the read row.
-		unsigned charsEndPos = toViewPosition(row(align, 1), length(source(row(align, 1))));
-		setClippedEndPosition(row(align, 0), charsEndPos);
+        // Heuristic (hack) for gaps in the beginning, so the following
+        // does not happen:
+        //
+        // contig: XXXX------AAA
+        //             CCC---AAA
+        //                CCCAAA
+        //
+        // But instead, the C's are all aligned.
+        if (beginLocalContigGaps > 0u) {
+            unsigned i = beginLocalContigGaps;
+            do {
+                goPrevious(cIt);
+                i -= 1;
+                cBegin -= 1;
+            } while (isGap(cIt) && i > 0u);
+            if (!isGap(cIt)) {
+                goNext(cIt);
+                cBegin += 1;
+            }
+        }
+
+        // We will clip off trailing gaps in the read row.
+        unsigned charsEndPos = toViewPosition(row(align, 1), length(source(row(align, 1))));
+        setClippedEndPosition(row(align, 0), charsEndPos);
 
 //        std::cerr << "firstOverlap - theIt == " << firstOverlap - theIt << std::endl;
 //        if (firstOverlap - theIt > 0)
@@ -2548,95 +2035,95 @@ void convertMatchesToGlobalAlignment(FragmentStore<TSpec, TConfig> &store, TScor
 //            if (_min(firstOverlap->beginPos, firstOverlap->endPos) < _max(theIt->beginPos, theIt->endPos))
 //                std::cerr << "INVARIANT DOES NOT HOLD" << std::endl;
 //        }
-       
-		for (; !atEnd(cIt) && !atEnd(it1); goNext(cIt), goNext(rIt))
-		{
-			bool isGapContig = isGap(cIt);
-			if (isGapContig != isGap(it1))
-			{
-				if (isGapContig)
-				{
-					// *** gap in contig of the global alignment ***
-					// copy exisiting contig gap
-					insertGaps(rIt, 1);
-					continue;
-				} else
-				{
-					// *** gap in contig of the pairwise alignment ***
-					// insert padding gaps in contig and reads
-					TContigPos insPos = cIt.current.gapPos;
-					insertGaps(cIt, 1);
-					for (TAlignedReadIter j = firstOverlap; j != it; ++j)
-					{
-						TContigPos rBegin = _min((*j).beginPos, (*j).endPos);
-						TContigPos rEnd = _max((*j).beginPos, (*j).endPos);
-						if (rBegin < insPos && insPos < rEnd)
-						{
+
+        for (; !atEnd(cIt) && !atEnd(it1); goNext(cIt), goNext(rIt))
+        {
+            bool isGapContig = isGap(cIt);
+            if (isGapContig != isGap(it1))
+            {
+                if (isGapContig)
+                {
+                    // *** gap in contig of the global alignment ***
+                    // copy exisiting contig gap
+                    insertGaps(rIt, 1);
+                    continue;
+                } else
+                {
+                    // *** gap in contig of the pairwise alignment ***
+                    // insert padding gaps in contig and reads
+                    TContigPos insPos = cIt.current.gapPos;
+                    insertGaps(cIt, 1);
+                    for (TAlignedReadIter j = firstOverlap; j != it; ++j)
+                    {
+                        TContigPos rBegin = _min(j->beginPos, j->endPos);
+                        TContigPos rEnd = _max(j->beginPos, j->endPos);
+                        if (rBegin < insPos && insPos < rEnd)
+                        {
 //                    if (j->id == 29971)
 //                    {
 //                        std::cerr << "OK computer" << std::endl;
 //                    }
-							if (rBegin < insPos)
-							{
-								TReadGaps gaps(store.readSeqStore[(*j).readId], (*j).gaps);
-								insertGap(gaps, insPos - rBegin);
-							} else
-							{
-								// shift beginPos if insertion was at the front of the read
-								if ((*j).beginPos < (*j).endPos)
-									++(*j).beginPos;
-								else
-									++(*j).endPos;
-							}
-							// shift endPos as the alignment was elongated or shifted
-							if ((*j).beginPos < (*j).endPos)
-								++(*j).endPos;
-							else
-								++(*j).beginPos;
-						} else if (insPos <= rBegin) {
-                            ++(*j).endPos;
-                            ++(*j).beginPos;
+                            if (rBegin < insPos)
+                            {
+                                TReadGaps gaps(static_cast<TReadSeq>(store.readSeqStore[j->readId]), j->gaps);
+                                insertGap(gaps, insPos - rBegin);
+                            } else
+                            {
+                                // shift beginPos if insertion was at the front of the read
+                                if (j->beginPos < j->endPos)
+                                    ++j->beginPos;
+                                else
+                                    ++j->endPos;
+                            }
+                            // shift endPos as the alignment was elongated or shifted
+                            if (j->beginPos < j->endPos)
+                                ++j->endPos;
+                            else
+                                ++j->beginPos;
+                        } else if (insPos <= rBegin) {
+                            ++j->endPos;
+                            ++j->beginPos;
                         }
-					}
-				}
-			}
-			if (isGap(it2))
-			{
-				// *** gap in read of pairwise alignment ***
-				// copy gaps from alignment
-				insertGaps(rIt, 1);
-			}
+                    }
+                }
+            }
+            if (isGap(it2))
+            {
+                // *** gap in read of pairwise alignment ***
+                // copy gaps from alignment
+                insertGaps(rIt, 1);
+            }
             goNext(it1);
-			goNext(it2);
-		}
-
-		// store new gap-space alignment borders
-		cEnd = cBegin + length(readGaps);
-		if (left < right)
-		{
-			(*it).beginPos = cBegin;
-			(*it).endPos = cEnd;
-		} else
-		{
-			(*it).beginPos = cEnd;
-			(*it).endPos = cBegin;
-		}
-        
+            goNext(it2);
+        }
+
+        // store new gap-space alignment borders
+        cEnd = cBegin + length(readGaps);
+        if (left < right)
+        {
+            (*it).beginPos = cBegin;
+            (*it).endPos = cEnd;
+        } else
+        {
+            (*it).beginPos = cEnd;
+            (*it).endPos = cBegin;
+        }
+
         ++it;  // Go to next alignment.
-/*		
-//		if (interesting)
-		{
-			String<String<unsigned> > layout;
-			layoutAlignment(layout, store, (*it).contigId);
-			std::cout << store.readNameStore[(*it).readId] << std::endl;
-			std::cout << readGaps << '\t' << cBegin << '\t' << cEnd << std::endl << std::endl;
-			printAlignment(std::cout, layout, store, (*it).contigId, (int)cBegin-20, (int)cEnd+20, 0, 40, 1 + (it - begin(store.alignedReadStore, Standard())));
-//			getc(stdin);
-		}
+/*
+//        if (interesting)
+        {
+            String<String<unsigned> > layout;
+            layoutAlignment(layout, store, (*it).contigId);
+            std::cout << store.readNameStore[(*it).readId] << std::endl;
+            std::cout << readGaps << '\t' << cBegin << '\t' << cEnd << std::endl << std::endl;
+            printAlignment(std::cout, layout, store, (*it).contigId, (int)cBegin-20, (int)cEnd+20, 0, 40, 1 + (it - begin(store.alignedReadStore, Standard())));
+//            getc(stdin);
+        }
 */
-//		if (store.readNameStore[(*it).readId] == "read3305")
-//			return;
-	}
+//        if (store.readNameStore[(*it).readId] == "read3305")
+//            return;
+    }
 
     // AlignedReadLayout layout;
     // layoutAlignment(layout, store);
@@ -2647,193 +2134,326 @@ void convertMatchesToGlobalAlignment(FragmentStore<TSpec, TConfig> &store, TScor
 /*!
  * @fn FragmentStore#convertPairWiseToGlobalAlignment
  * @brief Converts pairwise alignments to a multiple global alignment.
- * 
+ *
  * @signature void convertPairWiseToGlobalAlignment(store, pairwiseContigGaps);
- * 
+ *
  * @param[in,out] store The fragment store. Types: FragmentStore
  * @param[in,out] pairwiseContigGaps
  *                      A @link String @endlink of anchored contig gaps for every pairwise alignment.
- * 
+ *
  * @section Remarks
- * 
+ *
  * Before calling this function the <tt>gaps</tt> structures in the @link FragmentStore::contigStore @endlink must be
  * empty, i.e. there are no gaps in the contig. The pairwise alignment gaps of the reads are stored in the <tt>gaps</tt>
  * structure in the @link FragmentStore::alignedReadStore @endlink, whereas the pairwise alignment gaps of the contig
  * are stored in the <tt>pairwiseContigGaps</tt> string.
- * 
+ *
  * After calling this functions all positions in the @link FragmentStore::alignedReadStore @endlink are in gap-space.
  */
 
-/**
-.Function.convertPairWiseToGlobalAlignment
-..summary:Converts pair-wise alignments to a multiple global alignment.
-..cat:Fragment Store
-..signature:convertPairWiseToGlobalAlignment(store, pairwiseContigGaps)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.pairwiseContigGaps:A string of anchored contig gaps for every pairwise alignment.
-..remarks:Before calling this function the $gaps$ structures in the @Memvar.FragmentStore#contigStore@ must be empty, i.e. there are no gaps in the contig.
-The pairwise alignment gaps of the reads are stored in the $gaps$ structure in the @Memvar.FragmentStore#alignedReadStore@, whereas the pairwise alignment gaps of the contig are stored in the $pairwiseContigGaps$ string.
-..remarks:After calling this functions all positions in the @Memvar.FragmentStore#alignedReadStore@ are in gap-space.
-..include:seqan/store.h
-*/
+
+template <typename TFragmentStore>
+struct LessConvertPairWiseToGlobalAlignment:
+    public std::binary_function<
+        typename Value<typename TFragmentStore::TAlignedReadStore>::Type,
+        typename Value<typename TFragmentStore::TAlignedReadStore>::Type,
+        bool>
+{
+    typedef typename TFragmentStore::TAlignedReadStore      TAlignedReadStore;
+    typedef typename Value<TAlignedReadStore>::Type         TAlignedRead;
+    typedef typename Size<TAlignedReadStore>::Type          TSize;
+
+    typedef typename TFragmentStore::TContigStore           TContigStore;
+    typedef typename Value<TContigStore>::Type              TContig;
+    typedef typename TFragmentStore::TContigPos             TContigPos;
+    typedef typename TContig::TContigSeq                    TContigSeq;
+    typedef typename TContig::TGapAnchors                   TContigAnchors;
+    typedef Gaps<TContigSeq, AnchorGaps<TContigAnchors> >   TContigGaps;
+
+    TFragmentStore &store;
+    TSize offset;
+
+    LessConvertPairWiseToGlobalAlignment(TFragmentStore &store_, TSize offset_):
+        store(store_),
+        offset(offset_) {}
+
+    inline bool
+    operator() (TAlignedRead const& a1, TAlignedRead const& a2) const
+    {
+//        if (a1.contigId < a2.contigId) return true;
+//        if (a1.contigId > a2.contigId) return false;
+//
+//        TContigPos pos1 = _min(a1.beginPos, a1.endPos);
+//        TContigPos pos2 = _min(a2.beginPos, a2.endPos);
+//        TContig & contig = store.contigStore[a1.contigId];
+//
+//        if (a1.id < offset)
+//        {
+//            TContigGaps    contigGaps(contig.seq, contig.gaps);
+//            pos1 = positionGapToSeq(contigGaps, pos1);
+//        }
+//
+//        if (a2.id < offset)
+//        {
+//            TContigGaps    contigGaps(contig.seq, contig.gaps);
+//            pos2 = positionGapToSeq(contigGaps, pos2);
+//        }
+//
+        if (a1.id <  offset && a2.id >= offset) return true;
+        if (a1.id >= offset && a2.id <  offset) return false;
+
+        if (a1.contigId < a2.contigId) return true;
+        if (a1.contigId > a2.contigId) return false;
+
+        TContigPos pos1 = _min(a1.beginPos, a1.endPos);
+        TContigPos pos2 = _min(a2.beginPos, a2.endPos);
+        return pos1 < pos2;
+    }
+};
+
+
+template <typename TAlignedReadIter, typename TPos, typename TSize, typename TReadSeqStore>
+void _alignedReadsInsertGaps(
+    TAlignedReadIter alignedReadsBegin,
+    TAlignedReadIter alignedReadsEnd,
+    TPos insPos,
+    TSize blkLen,
+    TReadSeqStore &readSeqStore)
+{
+    typedef typename Value<TReadSeqStore>::Type                             TReadSeq;
+    typedef typename Value<TAlignedReadIter>::Type                          TAlignedRead;
+    typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> > TReadGaps;
+    typedef __int64                                                         TContigPos;
+
+    for (TAlignedReadIter j = alignedReadsBegin; j != alignedReadsEnd; ++j)
+    {
+
+        TContigPos rBegin = _min(j->beginPos, j->endPos);
+        TContigPos rEnd = _max(j->beginPos, j->endPos);
+        if (rBegin < insPos && insPos < rEnd)
+        {
+            if (rBegin < insPos)
+            {
+                TReadGaps gaps(readSeqStore[j->readId], j->gaps);
+                insertGaps(gaps, insPos - rBegin, blkLen);
+            }
+            else
+            {
+                // shift beginPos if insertion was at the front of the read
+                if (j->beginPos < j->endPos)
+                    j->beginPos += blkLen;
+                else
+                    j->endPos += blkLen;
+            }
+            // shift endPos as the alignment was elongated or shifted
+            if (j->beginPos < j->endPos)
+                j->endPos += blkLen;
+            else
+                j->beginPos += blkLen;
+        }
+    }
+}
+
+// The following function merges a pairwise alignment (contigGapsPW, readGaps) into the multiple alignment of
+// (contigGapsGlobal, firstOverlappingAlignedRead, firstOverlappingAlignedRead+1, ... , currentAlignedRead - 1)
+// It distinguishes two cases:
+//
+// 1. Contig gaps that are in the global but not in the pairwise alignment:
+//    Insert these gaps into the read of the pairwise alignment
+//
+// 2. Contig gaps that are in the pairwise but not in the multiple alignment:
+//    Insert these gaps into the global contig and all not yet considered overlapping reads
+//    (firstOverlappingAlignedRead ... currentAlignedRead - 1)
+//
+template <typename TContigGapsGlobal, typename TContigGapsPW, typename TReadGaps, typename TAlignedReadIter, typename TReadSeqStore>
+void _twoWayMergeAlignments(
+    TContigGapsGlobal &contigGapsGlobal,
+    TContigGapsPW &contigGapsPW,
+    TReadGaps &readGaps,
+    TAlignedReadIter overlappingAlignedReadsBegin1,
+    TAlignedReadIter overlappingAlignedReadsEnd1,
+    TAlignedReadIter overlappingAlignedReadsBegin2,
+    TAlignedReadIter overlappingAlignedReadsEnd2,
+    TReadSeqStore &readSeqStore)
+{
+    // gap iterators
+    typedef typename Iterator<TContigGapsGlobal>::Type  TContigGlobalIter;
+    typedef typename Iterator<TContigGapsPW>::Type      TContigPWIter;
+    typedef typename Iterator<TReadGaps>::Type          TReadIter;
+    typedef __int64                                     TContigPos;
+
+    TContigGlobalIter cIt = begin(contigGapsGlobal);
+    TContigPWIter pIt = begin(contigGapsPW);
+    TReadIter rIt = begin(readGaps);
+
+    /*
+    std::cout << "contigGlobal\t" << contigGapsGlobal << std::endl;
+    std::cout << "contigPW    \t" << contigGapsPW << std::endl;
+    std::cout << "readPW      \t" << readGaps << std::endl;
+    */
+
+    __int64 blkLen = 0;
+    for (; !atEnd(rIt); goFurther(rIt, blkLen), goFurther(cIt, blkLen))
+    {
+        bool isGapContig = isGap(cIt);
+        bool isGapLocalContig = isGap(pIt);
+        blkLen = _min(blockLength(cIt), blockLength(pIt));
+        SEQAN_ASSERT_GT(blkLen, 0u);
+//          SEQAN_ASSERT_LT(blkLen, length(contigGapsGlobal));
+
+        if (isGapContig != isGapLocalContig)
+        {
+            if (isGapContig)
+            {
+                // CASE 1.
+                //
+                // *** gap in contig of the global alignment ***
+                // copy exisiting contig gap
+                insertGaps(rIt, blkLen);
+                continue;
+            }
+            else
+            {
+                // CASE 2.
+                //
+                // *** gap in contig of the pairwise alignment ***
+                // insert padding gaps in contig and reads
+                TContigPos insPos = cIt.current.gapPos;
+                insertGaps(cIt, blkLen);
+                _alignedReadsInsertGaps(overlappingAlignedReadsBegin1, overlappingAlignedReadsEnd1, insPos, blkLen, readSeqStore);
+                _alignedReadsInsertGaps(overlappingAlignedReadsBegin2, overlappingAlignedReadsEnd2, insPos, blkLen, readSeqStore);
+            }
+        }
+
+        // fast forward the whole block
+        goFurther(pIt, blkLen);
+    }
+}
 
 template <typename TSpec, typename TConfig, typename TContigGapsString>
 void convertPairWiseToGlobalAlignment(FragmentStore<TSpec, TConfig> &store, TContigGapsString &gaps)
 {
-	typedef FragmentStore<TSpec, TConfig>							TFragmentStore;
-
-	// stores
-	//typedef typename TFragmentStore::TReadStore						TReadStore;
-	typedef typename TFragmentStore::TReadSeqStore					TReadSeqStore;
-	typedef typename TFragmentStore::TAlignedReadStore				TAlignedReadStore;
-	typedef typename TFragmentStore::TContigStore					TContigStore;
-	//typedef typename TFragmentStore::TContigSeq  					TContigSeq;
-
-	// store elements
-	//typedef typename Value<TReadStore>::Type						TRead;
-	typedef typename Value<TReadSeqStore>::Type						TReadSeq;
-	typedef typename Value<TContigStore>::Type						TContig;
-	typedef typename Value<TAlignedReadStore>::Type					TAlignedRead;
-
-	typedef typename Iterator<TAlignedReadStore, Standard>::Type	TAlignedReadIter;
-	typedef typename Id<TAlignedRead>::Type							TId;
-	typedef typename TFragmentStore::TContigPos						TContigPos;
-
-	// gap structures
-	//typedef Gaps<TContigSeq/*Nothing*/, AnchorGaps<typename TContig::TGapAnchors> >			TContigGapsGlobal;
-	//typedef Gaps<TContigSeq/*Nothing*/, AnchorGaps<typename Value<TContigGapsString>::Type> >	TContigGapsPW;
-	typedef Gaps</*TContigSeq*/Nothing, AnchorGaps<typename TContig::TGapAnchors> >			TContigGapsGlobal;
-	typedef Gaps</*TContigSeq*/Nothing, AnchorGaps<typename Value<TContigGapsString>::Type> >	TContigGapsPW;
-	typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> >			TReadGaps;
-
-	// gap iterators
-	typedef typename Iterator<TContigGapsGlobal>::Type								TContigGlobalIter;	
-	typedef typename Iterator<TContigGapsPW>::Type									TContigPWIter;
-	typedef typename Iterator<TReadGaps>::Type										TReadIter;
-
-	// sort matches by increasing begin positions
-	sortAlignedReads(store.alignedReadStore, SortBeginPos());
-	sortAlignedReads(store.alignedReadStore, SortContigId());
-
-	TReadSeq readSeq;
-	TId lastContigId = TAlignedRead::INVALID_ID;
-	TAlignedReadIter it = begin(store.alignedReadStore, Standard());
-	TAlignedReadIter itEnd = end(store.alignedReadStore, Standard());
-	TAlignedReadIter firstOverlap = begin(store.alignedReadStore, Standard());
-	for (; it != itEnd; ++it)
-	{
-		TContigPos	left = (*it).beginPos;
-		TContigPos	right = (*it).endPos;
-		TContigPos	cBegin = _min(left, right);
-		TContigPos	cEnd = _max(left, right);
-		
-		// 1. Initialize gap structures
-		TContigGapsGlobal	contigGapsGlobal(/*store.contigStore[(*it).contigId].seq, */store.contigStore[(*it).contigId].gaps);
-		/*
-		TContigSeq contigInfix = infix(store.contigStore[(*it).contigId].seq, cBegin, cEnd);
-		if (left > right)
-		    reverseComplement(contigInfix);
-		*/
-		TContigGapsPW		contigGapsPW(/*contigInfix, */gaps[(*it).id]);
-		TReadGaps			readGaps(store.readSeqStore[(*it).readId], (*it).gaps);
-		
+    typedef FragmentStore<TSpec, TConfig>                            TFragmentStore;
+
+    // stores
+    //typedef typename TFragmentStore::TReadStore                        TReadStore;
+    typedef typename TFragmentStore::TReadSeqStore                    TReadSeqStore;
+    typedef typename TFragmentStore::TAlignedReadStore                TAlignedReadStore;
+    typedef typename TFragmentStore::TContigStore                    TContigStore;
+    //typedef typename TFragmentStore::TContigSeq                      TContigSeq;
+
+    // store elements
+    //typedef typename Value<TReadStore>::Type                        TRead;
+    typedef typename Value<TReadSeqStore>::Type                        TReadSeq;
+    typedef typename Value<TContigStore>::Type                        TContig;
+    typedef typename Value<TAlignedReadStore>::Type                    TAlignedRead;
+
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignedReadIter;
+    typedef typename Id<TAlignedRead>::Type                            TId;
+    typedef typename TFragmentStore::TContigPos                        TContigPos;
+
+    // gap structures
+    //typedef Gaps<TContigSeq/*Nothing*/, AnchorGaps<typename TContig::TGapAnchors> >            TContigGapsGlobal;
+    //typedef Gaps<TContigSeq/*Nothing*/, AnchorGaps<typename Value<TContigGapsString>::Type> >    TContigGapsPW;
+    typedef Gaps</*TContigSeq*/Nothing, AnchorGaps<typename TContig::TGapAnchors> >             TContigGapsGlobal;
+    typedef Gaps</*TContigSeq*/Nothing, AnchorGaps<typename Value<TContigGapsString>::Type> >    TContigGapsPW;
+    typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> >                     TReadGaps;
+
+    typename Size<TAlignedReadStore>::Type offsetRecord = length(store.alignedReadStore) - length(gaps);
+
+    // sort matches by increasing begin positions
+    LessConvertPairWiseToGlobalAlignment<TFragmentStore> lessFunctor(store, offsetRecord);
+    sortAlignedReads(store.alignedReadStore, lessFunctor);
+
+    TReadSeq readSeq;
+    TId lastContigId = TAlignedRead::INVALID_ID;
+    TAlignedReadIter it = begin(store.alignedReadStore, Standard());
+    TAlignedReadIter itEnd = end(store.alignedReadStore, Standard());
+
+    TAlignedReadIter firstOverlapOld = begin(store.alignedReadStore, Standard());
+    TAlignedReadIter lastOverlapOld = firstOverlapOld;
+    TAlignedReadIter firstNew = begin(store.alignedReadStore, Standard()) + offsetRecord;
+    TAlignedReadIter firstOverlapNew = firstNew;
+
+    for (; it != itEnd; ++it)
+    {
+        if ((*it).id < offsetRecord)
+            continue;
+
+        TContigPos    left = it->beginPos;
+        TContigPos    right = it->endPos;
+        TContigPos    cBegin = _min(left, right);
+        TContigPos    cEnd = _max(left, right);
+
+        // 1. Initialize gap structures
+        TContigGapsGlobal   contigGapsGlobal(/*store.contigStore[it->contigId].seq, */store.contigStore[it->contigId].gaps);
+        /*
+        TContigSeq contigInfix = infix(store.contigStore[it->contigId].seq, cBegin, cEnd);
+        if (left > right)
+            reverseComplement(contigInfix);
+        */
+        TContigGapsPW       contigGapsPW(/*contigInfix, */gaps[it->id - offsetRecord]);
+        TReadGaps           readGaps(store.readSeqStore[it->readId], it->gaps);
+
         SEQAN_ASSERT(dependent(contigGapsGlobal.data_gaps));
         SEQAN_ASSERT(dependent(readGaps.data_gaps));
 
-		// 2. Skip non-overlapping matches
-		cBegin = positionSeqToGap(contigGapsGlobal, cBegin);
-		if (lastContigId != (*it).contigId)
-		{
-			firstOverlap = it;
-			lastContigId = (*it).contigId;
-		} else
-			while (firstOverlap != it && _max((*firstOverlap).beginPos, (*firstOverlap).endPos) <= cBegin)
-				++firstOverlap;
-
-		// 3. Iterate over alignment
-		setClippedBeginPosition(contigGapsGlobal, cBegin);
-
-		TContigGlobalIter cIt = begin(contigGapsGlobal);
-		TContigPWIter pIt = begin(contigGapsPW);
-		TReadIter rIt = begin(readGaps);
-		
-		/*
-		std::cout << "contigGlobal\t" << contigGapsGlobal << std::endl;
-		std::cout << "contigPW    \t" << contigGapsPW << std::endl;
-		std::cout << "readPW      \t" << readGaps << std::endl;
-		*/
-		
-		typename Size<TContig>::Type blkLen = 0;
-		for (; !atEnd(rIt); goFurther(rIt, blkLen), goFurther(cIt, blkLen))
-		{
-			bool isGapContig = isGap(cIt);
-			bool isGapLocalContig = isGap(pIt);
-            blkLen = _min(blockLength(cIt), blockLength(pIt));
-            SEQAN_ASSERT_GT(blkLen, 0u);
-//          SEQAN_ASSERT_LT(blkLen, length(contigGapsGlobal));
 
-			if (isGapContig != isGapLocalContig)
-			{
-				if (isGapContig)
-				{
-					// *** gap in contig of the global alignment ***
-					// copy exisiting contig gap
-					insertGaps(rIt, blkLen);
-					continue;
-				}
-                else
-				{
-					// *** gap in contig of the pairwise alignment ***
-					// insert padding gaps in contig and reads
-					TContigPos insPos = cIt.current.gapPos;
-					insertGaps(cIt, blkLen);
-					for (TAlignedReadIter j = firstOverlap; j != it; ++j)
-					{
-                        
-						TContigPos rBegin = _min(j->beginPos, j->endPos);
-						TContigPos rEnd = _max(j->beginPos, j->endPos);
-						if (rBegin < insPos && insPos < rEnd)
-						{
-							if (rBegin < insPos)
-							{
-								TReadGaps gaps(store.readSeqStore[j->readId], j->gaps);
-								insertGaps(gaps, insPos - rBegin, blkLen);
-							}
-                            else
-							{
-								// shift beginPos if insertion was at the front of the read
-								if (j->beginPos < j->endPos)
-									j->beginPos += blkLen;
-								else
-									j->endPos += blkLen;
-							}
-							// shift endPos as the alignment was elongated or shifted
-							if (j->beginPos < j->endPos)
-								j->endPos += blkLen;
-							else
-								j->beginPos += blkLen;
-						}
-					}
-				}
-			}
-
-            // fast forward the whole block
-            goFurther(pIt, blkLen);
-		}
-
-		// store new gap-space alignment borders
-		cEnd = cBegin + length(readGaps);
-		if (left < right)
-		{
-			(*it).beginPos = cBegin;
-			(*it).endPos = cEnd;
-		} else
-		{
-			(*it).beginPos = cEnd;
-			(*it).endPos = cBegin;
-		}
-	}
+        // 1111111111111
+        // 22222222
+        //   33333
+        //     44444444444
+        //       555555
+        //  |cBegin---cEnd)
+
+        TId contigId = it->contigId;
+        cBegin = positionSeqToGap(contigGapsGlobal, cBegin);
+
+        // 2a. Skip non-overlapping old alignments
+        while (firstOverlapOld != firstNew &&
+               (firstOverlapOld->contigId < contigId || _max(firstOverlapOld->beginPos, firstOverlapOld->endPos) <= cBegin))
+            ++firstOverlapOld;
+
+        if (lastOverlapOld < firstOverlapOld)
+            lastOverlapOld = firstOverlapOld;
+
+        while (lastOverlapOld != firstNew &&
+               (lastOverlapOld->contigId < contigId || _min(lastOverlapOld->beginPos, lastOverlapOld->endPos) < cEnd))
+            ++lastOverlapOld;
+
+        // 2b. Skip non-overlapping new matches
+        if (lastContigId != contigId)
+        {
+            firstOverlapNew = it;
+            lastContigId = contigId;
+        }
+        else
+        {
+            while (firstOverlapNew != it && _max(firstOverlapNew->beginPos, firstOverlapNew->endPos) <= cBegin)
+                ++firstOverlapNew;
+        }
+
+        // 3. Iterate over alignment
+        setClippedBeginPosition(contigGapsGlobal, cBegin);
+
+        _twoWayMergeAlignments(
+                contigGapsGlobal, contigGapsPW, readGaps,
+                firstOverlapOld, lastOverlapOld, firstOverlapNew, it,
+                store.readSeqStore);
+
+        // store new gap-space alignment borders
+        cEnd = cBegin + length(readGaps);
+        if (left < right)
+        {
+            (*it).beginPos = cBegin;
+            (*it).endPos = cEnd;
+        }
+        else
+        {
+            (*it).beginPos = cEnd;
+            (*it).endPos = cBegin;
+        }
+    }
 }
 
 }// namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/store/store_annotation.h b/seqan/store/store_annotation.h
index 1e7944f..77308ee 100644
--- a/seqan/store/store_annotation.h
+++ b/seqan/store/store_annotation.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -131,135 +131,33 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief The id of the parent annotation.
  */
 
-/**
-.Class.AnnotationStoreElement
-..summary:Represents an annotation of a contig feature.
-..cat:Fragment Store
-..signature:AnnotationStoreElement<>
-..signature:AnnotationStoreElement<TPos[, TSpec]>
-..param.TPos:Type to store (gap-space) positions.
-..param.TSpec:The specialization type.
-...default:$void$
-..remarks:Value type of the @Memvar.FragmentStore#annotationStore@ string.
-The id of an annotation (aka annotationId) is not stored explicitly, as it is implicitly given by the position in the @Memvar.FragmentStore#annotationStore@.
-..include:seqan/store.h
-
-.Typedef.AnnotationStoreElement#TId
-..summary:Type of annotationId and @Memvar.AnnotationStoreElement#contigId@.
-..remarks:$TId$ equals the result of $Id<AnnotationStoreElement<> >::Type$, see @Metafunction.Id@.
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Typedef.AnnotationStoreElement#TPos
-..summary:Type of the @Memvar.AnnotationStoreElement#beginPos@ and @Memvar.AnnotationStoreElement#endPos@ members.
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Typedef.AnnotationStoreElement#TValues
-..summary:@Class.StringSet@ type of the @Memvar.AnnotationStoreElement#values@ member.
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-
-.Memfunc.AnnotationStoreElement#AnnotationStoreElement
-..summary:Constructor
-..signature:AnnotationStoreElement()
-..remarks:The default constructor sets all members to @Memvar.AnnotationStoreElement#INVALID_ID@ and 
-@Memvar.AnnotationStoreElement#beginPos@ and @Memvar.AnnotationStoreElement#endPos@ to @Memvar.AnnotationStoreElement#INVALID_POS@.
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#contigId
-..summary:Refers to the contig in the @Memvar.FragmentStore#contigStore@ the annotation is part of.
-..type:Metafunction.Id
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#typeId
-..summary:Refers to an entry in the @Memvar.FragmentStore#annotationTypeStore@. 
-There are some type ids predefined for commonly used types, e.g. $ANNO_GENE$. See @Enum.Predefined Annotation Types@.
-..type:Metafunction.Id
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#beginPos
-..summary:Begin position of the annotation in gap-space.
-..type:Typedef.AnnotationStoreElement#TPos
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#endPos
-..summary:End position of the annotation in gap-space. If @Memvar.AnnotationStoreElement#endPos@ < @Memvar.AnnotationStoreElement#beginPos@, 
-the annotated feature is located on the reverse strand, where @Memvar.AnnotationStoreElement#beginPos@ and @Memvar.AnnotationStoreElement#endPos@
-are the corresponding positions on the forward strand.
-..type:Typedef.AnnotationStoreElement#TPos
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#values
-..summary:@Class.StringSet@ that stores additional annotation values addressed by $keyId$. The GFF/GTF file format allows to define user-specific key-value pairs. The set of all keys addressed by $keyId$ are stored in the @Memvar.FragmentStore#annotationKeyStore@.
-..type:Typedef.AnnotationStoreElement#TValues
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#parentId
-..summary:The id of the parent annotation.
-..type:Metafunction.Id
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#nextSiblingId
-..summary:The id of the right sibling annotation.
-..type:Metafunction.Id
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#lastChildId
-..summary:The id of the rightmost child annotation.
-..type:Metafunction.Id
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#INVALID_ID
-..summary:Constant to represent an invalid id.
-..type:Metafunction.Id
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-
-.Memvar.AnnotationStoreElement#INVALID_POS
-..summary:Constant to represent an invalid position.
-..type:Typedef.AnnotationStoreElement#TPos
-..class:Class.AnnotationStoreElement
-..include:seqan/store.h
-*/
-
 template <typename TPos_, typename TSpec = void>
 struct AnnotationStoreElement
 {
-	typedef typename Id<AnnotationStoreElement>::Type		TId;
-	typedef TPos_											TPos;
-	typedef StringSet<CharString, Owner< ConcatDirect<> > >	TValues;
-
-	static const TId  INVALID_ID;
-	static const TPos INVALID_POS;
-	
-	TId					parentId;
-	TId					contigId;
-	TId					countId;
-	TId					typeId;			// gene, intron, ...
-
-	TPos				beginPos;		// begin position of the annotation in the gapped contig sequence (i.e. in gap-space)
-	TPos				endPos;			// end position of ..., for annotations on the reverse strand holds end < begin
-	
-	TId					lastChildId;	// generated back links to child
-	TId					nextSiblingId;	// and sibling
-	
-	TValues				values;			// stores values for each keyId of (key,value) pairs
-
-	AnnotationStoreElement() : 
-		parentId(INVALID_ID), contigId(INVALID_ID), countId(INVALID_ID), typeId(INVALID_ID), 
-		beginPos(INVALID_POS), endPos(INVALID_POS),
-		lastChildId(INVALID_ID), nextSiblingId(INVALID_ID) {}
+    typedef typename Id<AnnotationStoreElement>::Type        TId;
+    typedef TPos_                                            TPos;
+    typedef StringSet<CharString, Owner< ConcatDirect<> > >    TValues;
+
+    static const TId  INVALID_ID;
+    static const TPos INVALID_POS;
+
+    TId                    parentId;
+    TId                    contigId;
+    TId                    countId;
+    TId                    typeId;            // gene, intron, ...
+
+    TPos                beginPos;        // begin position of the annotation in the gapped contig sequence (i.e. in gap-space)
+    TPos                endPos;            // end position of ..., for annotations on the reverse strand holds end < begin
+
+    TId                    lastChildId;    // generated back links to child
+    TId                    nextSiblingId;    // and sibling
+
+    TValues                values;            // stores values for each keyId of (key,value) pairs
+
+    AnnotationStoreElement() :
+        parentId(INVALID_ID), contigId(INVALID_ID), countId(INVALID_ID), typeId(INVALID_ID),
+        beginPos(INVALID_POS), endPos(INVALID_POS),
+        lastChildId(INVALID_ID), nextSiblingId(INVALID_ID) {}
 };
 
 //////////////////////////////////////////////////////////////////////////////
@@ -343,130 +241,89 @@ struct AnnotationTree {};
  * @endcode
  */
 
-/**
-.Spec.AnnotationTree Iterator:
-..cat:FragmentStore
-..summary:Iterator of the annotation tree represented by a @Class.FragmentStore@.
-..remarks:This iterator can move @Function.AnnotationTree Iterator#goDown|down@, @Function.AnnotationTree Iterator#goRight|right@, and @Function.AnnotationTree Iterator#goUp|up@ in the tree and supports a preorder dfs traversal via the functions @Function.goBegin@, @Function.goNext@, and @Function.atEnd@.
-Preorder means that the iterator visits a node before its children.
-..remarks:To access the annotation, the iterator points to, use @Function.getAnnotation@. The annotation id is returned by @Function.value@.
-..signature:Iter<TFragmentStore, AnnotationTree<> >
-..signature:Iterator<TFragmentStore, AnnotationTree<> >::Type
-..general:Class.Iter
-..implements:Concept.RootedIteratorConcept
-..param.TFragmentStore:A FragmentStore class.
-...type:Class.FragmentStore
-..include:seqan/store.h
-..example:
-...image:AnnotationTree|Typical annotation tree hierarchy.
-..example:
-...text:A new annotation tree iterator can be instantiated as follows:
-...code:
-Iterator<FragmentStore<>, AnnotationTree<> >::Type it;
-it = begin(store, AnnotationTree<>());
-...text:Or shorter (see @Memfunc.AnnotationTree Iterator#AnnotationTree Iterator|AnnotationTree Iterator constructor@):
-...code:
-Iterator<FragmentStore<>, AnnotationTree<> >::Type it(store);
-
-.Memfunc.AnnotationTree Iterator#AnnotationTree Iterator
-..summary:Constructor
-..signature:Iter()
-..signature:Iter(store [, startInNode])
-..class:Spec.AnnotationTree Iterator
-..param.store:A @Class.FragmentStore@ object.
-...type:Class.FragmentStore
-..param.startInNode:Annotation id of the node the iterator should start at.
-...default:$0$, the id of the root node.
-..include:seqan/store.h
-..remarks:The @Function.begin@ function can also be used to create a tree iterator that starts in the root node:
-...code:
-Iterator<FragmentStore<>, AnnotationTree<> >::Type it;
-it = begin(store, AnnotationTree<>());
-*/
-
 template <typename TFragmentStore, typename TSpec>
 class Iter<TFragmentStore, AnnotationTree<TSpec> >
 {
 public:
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
-
-	TFragmentStore *store;
-	TId _id;
-	
-	Iter():
-		store(NULL),
-		_id(TAnnotation::INVALID_ID) {}
-
-	Iter(TFragmentStore &_store):
-		store(&_store),
-		_id(0) {}
-
-	Iter(TFragmentStore &_store, TId startInNode):
-		store(&_store),
-		_id(startInNode) {}
-
-	Iter(TFragmentStore &_store, MinimalCtor):
-		store(&_store),
-		_id(TAnnotation::INVALID_ID) {}
-
-	inline Iter const &
-	operator = (Iter const &_origin)
-	{
-		store = &container(_origin);
-		_id = _origin._id;
-		return *this;
-	}
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
+
+    TFragmentStore *store;
+    TId _id;
+
+    Iter():
+        store(NULL),
+        _id(TAnnotation::INVALID_ID) {}
+
+    Iter(TFragmentStore &_store):
+        store(&_store),
+        _id(0) {}
+
+    Iter(TFragmentStore &_store, TId startInNode):
+        store(&_store),
+        _id(startInNode) {}
+
+    Iter(TFragmentStore &_store, MinimalCtor):
+        store(&_store),
+        _id(TAnnotation::INVALID_ID) {}
+
+    inline Iter const &
+    operator = (Iter const &_origin)
+    {
+        store = &container(_origin);
+        _id = _origin._id;
+        return *this;
+    }
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TFragmentStore, typename TSpec>
 struct Iterator< TFragmentStore, AnnotationTree<TSpec> > {
-	typedef Iter< TFragmentStore, AnnotationTree<TSpec> > Type;
+    typedef Iter< TFragmentStore, AnnotationTree<TSpec> > Type;
 };
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TFragmentStore, typename TSpec>
 struct Value< Iter< TFragmentStore, AnnotationTree<TSpec> > >:
-	VertexDescriptor<TFragmentStore> {};
+    VertexDescriptor<TFragmentStore> {};
 
 template <typename TFragmentStore, typename TSpec>
 struct Size< Iter< TFragmentStore, AnnotationTree<TSpec> > > :
-	Size<TFragmentStore> {};
+    Size<TFragmentStore> {};
 
 template <typename TFragmentStore, typename TSpec>
 struct Position< Iter< TFragmentStore, AnnotationTree<TSpec> > > :
-	Position<TFragmentStore> {};
+    Position<TFragmentStore> {};
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TFragmentStore, typename TSpec>
-inline typename VertexDescriptor<TFragmentStore>::Type & 
-value(Iter< TFragmentStore, AnnotationTree<TSpec> > &it) { 
-	return it._id;
+inline typename VertexDescriptor<TFragmentStore>::Type &
+value(Iter< TFragmentStore, AnnotationTree<TSpec> > &it) {
+    return it._id;
 }
 
 template <typename TFragmentStore, typename TSpec>
-inline typename VertexDescriptor<TFragmentStore>::Type const & 
-value(Iter< TFragmentStore, AnnotationTree<TSpec> > const &it) { 
-	return it._id;
+inline typename VertexDescriptor<TFragmentStore>::Type const &
+value(Iter< TFragmentStore, AnnotationTree<TSpec> > const &it) {
+    return it._id;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
 template <typename TFragmentStore, typename TSpec>
-inline TFragmentStore & 
-container(Iter< TFragmentStore, AnnotationTree<TSpec> > &it) { 
-	return *it.store;
+inline TFragmentStore &
+container(Iter< TFragmentStore, AnnotationTree<TSpec> > &it) {
+    return *it.store;
 }
 
 template <typename TFragmentStore, typename TSpec>
-inline TFragmentStore & 
-container(Iter< TFragmentStore, AnnotationTree<TSpec> > const &it) { 
-	return *it.store;
+inline TFragmentStore &
+container(Iter< TFragmentStore, AnnotationTree<TSpec> > const &it) {
+    return *it.store;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -482,32 +339,20 @@ container(Iter< TFragmentStore, AnnotationTree<TSpec> > const &it) {
  * @return TAnnotation A reference to the AnnotationStoreElement the iterator points to.
  */
 
-/**
-.Function.getAnnotation
-..class:Spec.AnnotationTree Iterator
-..summary:Returns the current annotation.
-..cat:Fragment Store
-..signature:getAnnotation(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns:A reference to the @Class.AnnotationStoreElement@ the iterator points at.
-..include:seqan/store.h
-*/
-
 // TODO(holtgrew): Better use Reference in both cases?
 
 template <typename TFragmentStore, typename TSpec>
 inline typename GetValue<typename TFragmentStore::TAnnotationStore>::Type
 getAnnotation(Iter<TFragmentStore const, AnnotationTree<TSpec> > const & it)
 {
-	return getValue(it.store->annotationStore, it._id);
+    return getValue(it.store->annotationStore, it._id);
 }
 
 template <typename TFragmentStore, typename TSpec>
 inline typename Reference<typename TFragmentStore::TAnnotationStore>::Type
 getAnnotation(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	return value(it.store->annotationStore, it._id);
+    return value(it.store->annotationStore, it._id);
 }
 
 /*!
@@ -524,26 +369,11 @@ getAnnotation(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
  * @see AnnotationTreeIterator#setName
  */
 
-/**
-.Function.AnnotationTree Iterator#getName
-..class:Spec.AnnotationTree Iterator
-..summary:Returns the identifier of the current annotation.
-..cat:Fragment Store
-..signature:getName(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns:The name of the current annotation.
-...remarks:This a reference to the corresponding position in the @Memvar.FragmentStore#annotationNameStore@.
-...type:Concept.SequenceConcept
-..see:Function.AnnotationTree Iterator#setName
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline typename GetValue<typename TFragmentStore::TAnnotationNameStore>::Type
 getName(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	return getAnnoName(*it.store, it._id);
+    return getAnnoName(*it.store, it._id);
 }
 
 /*!
@@ -558,27 +388,13 @@ getName(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
  * @see AnnotationTreeIterator#getName
  */
 
-/**
-.Function.AnnotationTree Iterator#setName
-..class:Spec.AnnotationTree Iterator
-..summary:Sets the identifier of the current annotation.
-..cat:Fragment Store
-..signature:setName(iter, name)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..param.name:The new identifier of the current annotation element.
-...type:Concept.SequenceConcept
-..see:Function.AnnotationTree Iterator#getName
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec, typename TName>
 inline void
 setName(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it, TName const & name)
 {
-	if (length(it.store->annotationNameStore) <= it._id)
-		resize(it.store->annotationNameStore, it._id + 1);
-	it.store->annotationNameStore[it._id] = name;
+    if (length(it.store->annotationNameStore) <= it._id)
+        resize(it.store->annotationNameStore, it._id + 1);
+    it.store->annotationNameStore[it._id] = name;
 }
 
 /*!
@@ -593,32 +409,17 @@ setName(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it, TName const & n
  *               @link FragmentStore::annotationNameStore @endlink.
  */
 
-/**
-.Function.getParentName
-..class:Spec.AnnotationTree Iterator
-..summary:Returns the identifier of the parent node in the annotation tree of the current annotation.
-..cat:Fragment Store
-..signature:getParentName(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns:The name of the parent of the current annotation.
-...remarks:This a reference to the corresponding position in the @Memvar.FragmentStore#annotationNameStore@.
-...type:Concept.SequenceConcept
-..see:Function.AnnotationTree Iterator#getName
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline typename GetValue<typename TFragmentStore::TAnnotationNameStore>::Type
 getParentName(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
 
-	TId parentId = it.store->annotationStore[it._id].parentId;
-	if (parentId == TAnnotation::INVALID_ID) parentId = it._id;
-	return getAnnoName(*it.store, parentId);
+    TId parentId = it.store->annotationStore[it._id].parentId;
+    if (parentId == TAnnotation::INVALID_ID) parentId = it._id;
+    return getAnnoName(*it.store, parentId);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -637,26 +438,11 @@ getParentName(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @see AnnotationTreeIterator#setType
  */
 
-/**
-.Function.getType
-..class:Spec.AnnotationTree Iterator
-..summary:Returns the type name of the current annotation.
-..cat:Fragment Store
-..signature:getType(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns:The type name of the current annotation, e.g. "exon" or "mRNA".
-...remarks:This a reference to an entry in the @Memvar.FragmentStore#annotationTypeStore@.
-...type:Concept.SequenceConcept
-..see:Function.setType
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline typename GetValue<typename TFragmentStore::TAnnotationTypeStore>::Type
 getType(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	return getAnnoType(*it.store, getAnnotation(it).typeId);
+    return getAnnoType(*it.store, getAnnotation(it).typeId);
 }
 
 /*!
@@ -666,30 +452,16 @@ getType(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
  * @signature void setType(it, typeName);
  *
  * @param[in,out] it       The iterator to the annotation to set the type name for.
- * @param[in]     typeName The name of the type (e.g. "exon" or "mRNA").  Type: @link SequenceConcept @endlink.
+ * @param[in]     typeName The name of the type (e.g. "exon" or "mRNA").  Type: @link ContainerConcept @endlink.
  *
  * @see AnnotationTreeIterator#getType
  */
 
-/**
-.Function.setType
-..class:Spec.AnnotationTree Iterator
-..summary:Sets the type name of the current annotation.
-..cat:Fragment Store
-..signature:setType(iter, typeName)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..param.typeName:The new type name, e.g. "exon" or "mRNA".
-...type:Concept.SequenceConcept
-..see:Function.getType
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec, typename TTypeName>
 inline void
 setType(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it, TTypeName & typeName)
 {
-	_storeAppendType(*it.store, getAnnotation(it).typeId, typeName);
+    _storeAppendType(*it.store, getAnnotation(it).typeId, typeName);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -710,27 +482,11 @@ setType(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it, TTypeName & typ
  * @see AnnotationTreeIterator#getName
  */
 
-/**
-.Function.getUniqueName
-..class:Spec.AnnotationTree Iterator
-..summary:Returns a unique name of the current annotation.
-..cat:Fragment Store
-..signature:getUniqueName(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns:A unique name of the current annotation.
-...type:Shortcut.CharString
-..remarks:Some annotation file formats doesn't require that every annotation has a non-empty name.
-This function returns the name if non-empty and otherwise generates one using the type and id.
-..see:Function.AnnotationTree Iterator#getName
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline CharString
 getUniqueName(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	return getAnnoUniqueName(*it.store, it._id);
+    return getAnnoUniqueName(*it.store, it._id);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -747,24 +503,11 @@ getUniqueName(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
  * @see AnnotationTreeIterator#getValueByKey
  */
 
-/**
-.Function.clearValues
-..class:Spec.AnnotationTree Iterator
-..summary:Clear all key-value pairs of the current annotation.
-..cat:Fragment Store
-..signature:clearValues(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..see:Function.assignValueByKey
-..see:Function.getValueByKey
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
-inline void 
+inline void
 clearValues(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	clear(getAnnotation(it).values);
+    clear(getAnnotation(it).values);
 }
 
 /*!
@@ -774,45 +517,29 @@ clearValues(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @signature void assignValueByKey(it, key, value);
  *
  * @param[in,out] it    The AnnotationTreeIterator to
- * @param[in]     key   The key whose value should be changed.  Type: @link SequenceConcept @endlink.
- * @param[in]     value The value that should be assigned.  Type: @link SequenceConcept @endlink.
+ * @param[in]     key   The key whose value should be changed.  Type: @link ContainerConcept @endlink.
+ * @param[in]     value The value that should be assigned.  Type: @link ContainerConcept @endlink.
  *
  * @see AnnotationTreeIterator#clearValues
  * @see AnnotationTreeIterator#getValueByKey
  */
 
-/**
-.Function.assignValueByKey
-..class:Spec.AnnotationTree Iterator
-..summary:Add or update a key-value pair of the current annotation.
-..cat:Fragment Store
-..signature:assignValueByKey(iter, key, value)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..param.key:The key whose value should be changed.
-...type:Concept.SequenceConcept
-..param.value:The new value of the key.
-...type:Concept.SequenceConcept
-..see:Function.clearValues
-..see:Function.getValueByKey
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec, typename TKey, typename TValue>
-inline void 
+inline void
 assignValueByKey(
-	Iter<TFragmentStore, AnnotationTree<TSpec> > & it,
-	TKey const & key,
-	TValue const & value)
+    Iter<TFragmentStore, AnnotationTree<TSpec> > & it,
+    TKey const & key,
+    TValue const & value)
 {
-	annotationAssignValueByKey(*it.store, getAnnotation(it), key, value);
+    annotationAssignValueByKey(*it.store, getAnnotation(it), key, value);
 }
 
 /*!
  * @fn AnnotationTreeIterator#getValueByKey
  * @brief Retrieve a key's value in the current annotation.
  *
- * @signature bool getValueByKey(it, key, value);
+ * @signature bool getValueByKey(it, key);
+ * @signature bool getValueByKey(value, it, key);
  *
  * @param[in]  it    The AnnotationTreeIterator for which to retrieve the key.
  * @param[in]  key   The key to get the value for.
@@ -822,66 +549,42 @@ assignValueByKey(
  * @see AnnotationTreeIterator#assignValueByKey
  */
 
-/**
-.Function.getValueByKey
-..class:Spec.AnnotationTree Iterator
-..summary:Given a key, retrieve its value of the current annotation.
-..cat:Fragment Store
-..signature:getValueByKey(iter, key)
-..signature:getValueByKey(iter, key, value)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..param.key:The key to retrieve the value from.
-...type:Concept.SequenceConcept
-..param.value:The sequence where the return value should be wrote to.
-...type:Concept.SequenceConcept
-..returns:The three-parameter function returns a boolean indicating whether a non-empty value was returned.
-..returns:The two-parameter function returns the value for the given key.
-...type:nolink:bool
-...type:Shortcut.CharString
-..see:Function.clearValues
-..see:Function.assignValueByKey
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec, typename TKey, typename TValue>
-inline bool 
+inline bool
 getValueByKey(
-	Iter<TFragmentStore, AnnotationTree<TSpec> > const & it,
-	TKey const & key,
-	TValue & value)
+    TValue & value,
+    Iter<TFragmentStore, AnnotationTree<TSpec> > const & it,
+    TKey const & key)
 {
-	return annotationGetValueByKey(*it.store, getAnnotation(it), key, value);
+    return annotationGetValueByKey(*it.store, getAnnotation(it), key, value);
 }
 
 template <typename TFragmentStore, typename TSpec, typename TKey>
 inline CharString
 getValueByKey(
-	Iter<TFragmentStore, AnnotationTree<TSpec> > const & it,
-	TKey const & key)
+    Iter<TFragmentStore, AnnotationTree<TSpec> > const & it,
+    TKey const & key)
 {
-	return annotationGetValueByKey(*it.store, getAnnotation(it), key);
+    return annotationGetValueByKey(*it.store, getAnnotation(it), key);
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.goBegin.param.iterator.type:Spec.AnnotationTree Iterator
 template <typename TFragmentStore, typename TSpec>
 inline void
 goBegin(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	it._id = 0;
+    it._id = 0;
 }
 
-///.Function.goEnd.param.iterator.type:Spec.AnnotationTree Iterator
 template <typename TFragmentStore, typename TSpec>
 inline void
 goEnd(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
 
-	it._id = TAnnotation::INVALID_ID;
+    it._id = TAnnotation::INVALID_ID;
 }
 
 /*!
@@ -894,72 +597,55 @@ goEnd(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @param[in]     annoId The id of the annotation to move to.
  */
 
-/**
-.Function.goTo
-..class:Spec.AnnotationTree Iterator
-..summary:Moves the iterator to an arbitrary node given its annotationId.
-..cat:Fragment Store
-..signature:goTo(iter, annotationId)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..param.annotationId:The id of the new annotation.
-..returns: Iterator to the new node.
-...type:Spec.AnnotationTree Iterator
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec, typename TId>
 inline void
 goTo(Iter<TFragmentStore, AnnotationTree<TSpec> > & it, TId _id)
 {
-	it._id = _id;
+    it._id = _id;
 }
 
 template <typename TFragmentStore, typename TSpec>
 inline void
 clear(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
 
-	it._id = TAnnotation::INVALID_ID;
+    it._id = TAnnotation::INVALID_ID;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.atBegin.param.iterator.type:Spec.AnnotationTree Iterator
 template <typename TFragmentStore, typename TSpec>
 inline bool
 atBegin(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	return it._id == 0;
+    return it._id == 0;
 }
 
-///.Function.atEnd.param.iterator.type:Spec.AnnotationTree Iterator
 template <typename TFragmentStore, typename TSpec>
 inline bool
 atEnd(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
 
-	return it._id == TAnnotation::INVALID_ID;
+    return it._id == TAnnotation::INVALID_ID;
 }
 
 //////////////////////////////////////////////////////////////////////////////
 
-///.Function.goNext.param.iterator.type:Spec.AnnotationTree Iterator
 template <typename TFragmentStore, typename TSpec>
 inline void
 goNext(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	// preorder dfs
-	if (!goDown(it) && !goRight(it))
-		while (goUp(it) && !goRight(it)) ;
-	if (isRoot(it)) {
-		clear(it);
-		return;
-	}
+    // preorder dfs
+    if (!goDown(it) && !goRight(it))
+        while (goUp(it) && !goRight(it)) ;
+    if (isRoot(it)) {
+        clear(it);
+        return;
+    }
 }
 
 /*!
@@ -971,30 +657,17 @@ goNext(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @param[in,out] it The AnnotationTreeIterator to
  */
 
-/**
-.Function.AnnotationTree Iterator#goNextRight
-..class:Spec.AnnotationTree Iterator
-..summary:Go to the next node in preorder DFS skipping the current node's subtree.
-..cat:Fragment Store
-..signature:goNextRight(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..see:Function.goNext
-..see:Function.AnnotationTree Iterator#goNextUp
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline void
 goNextRight(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	// preorder dfs
-	if (!goRight(it))
-		while (goUp(it) && !goRight(it)) ;
-	if (isRoot(it)) {
-		clear(it);
-		return;
-	}
+    // preorder dfs
+    if (!goRight(it))
+        while (goUp(it) && !goRight(it)) ;
+    if (isRoot(it)) {
+        clear(it);
+        return;
+    }
 }
 
 /*!
@@ -1006,29 +679,16 @@ goNextRight(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @param[in,out] it The AnnotationTreeIterator to
  */
 
-/**
-.Function.AnnotationTree Iterator#goNextUp
-..class:Spec.AnnotationTree Iterator
-..summary:Go to the next node in preorder DFS skipping the subtrees of the current node and of all its siblings.
-..cat:Fragment Store
-..signature:goNextUp(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..see:Function.goNext
-..see:Function.AnnotationTree Iterator#goNextRight
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline void
 goNextUp(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	// preorder DFS
-	while (goUp(it) && !goRight(it)) ;
-	if (isRoot(it)) {
-		clear(it);
-		return;
-	}
+    // preorder DFS
+    while (goUp(it) && !goRight(it)) ;
+    if (isRoot(it)) {
+        clear(it);
+        return;
+    }
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1042,24 +702,11 @@ goNextUp(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @param[in,out] it The AnnotationTreeIterator to move.
  */
 
-/**
-.Function.AnnotationTree Iterator#goRoot
-..class:Spec.AnnotationTree Iterator
-..summary:Go to the root node in the annotation tree.
-..cat:Fragment Store
-..signature:goRoot(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..see:Function.goNext
-..see:Function.AnnotationTree Iterator#goNextRight
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline void
 goRoot(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	it._id = 0;
+    it._id = 0;
 }
 
 /*!
@@ -1076,36 +723,21 @@ goRoot(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @see AnnotationTreeIterator#goRight
  */
 
-/**
-.Function.AnnotationTree Iterator#goUp
-..class:Spec.AnnotationTree Iterator
-..summary:Move the iterator up in the annotation tree.
-..cat:Fragment Store
-..signature:goUp(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns:$true$ if the iterator could be moved, otherwise $false$.
-...type:nolink:bool
-..see:Function.AnnotationTree Iterator#goDown
-..see:Function.AnnotationTree Iterator#goRight
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline bool
 goUp(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
-	
-	TId parentId = getAnnotation(it).parentId;
-	if (parentId != TAnnotation::INVALID_ID)
-	{
-		it._id = parentId;
-		return true;
-	}
-	return false;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
+
+    TId parentId = getAnnotation(it).parentId;
+    if (parentId != TAnnotation::INVALID_ID)
+    {
+        it._id = parentId;
+        return true;
+    }
+    return false;
 }
 
 /*!
@@ -1122,36 +754,21 @@ goUp(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @see AnnotationTreeIterator#goRight
  */
 
-/**
-.Function.AnnotationTree Iterator#goDown
-..class:Spec.AnnotationTree Iterator
-..summary:Move the iterator down to the left-most child in the annotation tree.
-..cat:Fragment Store
-..signature:goDown(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns:$true$ if the iterator could be moved, otherwise $false$.
-...type:nolink:bool
-..see:Function.AnnotationTree Iterator#goUp
-..see:Function.AnnotationTree Iterator#goRight
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline bool
 goDown(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
-	
-	TId lastChildId = getAnnotation(it).lastChildId;
-	if (lastChildId != TAnnotation::INVALID_ID)
-	{
-		it._id = it.store->annotationStore[lastChildId].nextSiblingId;
-		return true;
-	}
-	return false;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
+
+    TId lastChildId = getAnnotation(it).lastChildId;
+    if (lastChildId != TAnnotation::INVALID_ID)
+    {
+        it._id = it.store->annotationStore[lastChildId].nextSiblingId;
+        return true;
+    }
+    return false;
 }
 
 /*!
@@ -1168,41 +785,26 @@ goDown(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @see AnnotationTreeIterator#goDown
  */
 
-/**
-.Function.AnnotationTree Iterator#goRight
-..class:Spec.AnnotationTree Iterator
-..summary:Move the iterator right to the next sibling in the annotation tree.
-..cat:Fragment Store
-..signature:goRight(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns:$true$ if the iterator could be moved, otherwise $false$.
-...type:nolink:bool
-..see:Function.AnnotationTree Iterator#goUp
-..see:Function.AnnotationTree Iterator#goDown
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline bool
 goRight(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
-	
-	TAnnotation const &anno = getAnnotation(it);
-	TId nextSiblingId = anno.nextSiblingId;
-	if (nextSiblingId != TAnnotation::INVALID_ID)
-	{
-		TId lastChildId = it.store->annotationStore[anno.parentId].lastChildId;
-		if (it._id != lastChildId)
-		{
-			it._id = nextSiblingId;
-			return true;
-		}
-	}
-	return false;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
+
+    TAnnotation const &anno = getAnnotation(it);
+    TId nextSiblingId = anno.nextSiblingId;
+    if (nextSiblingId != TAnnotation::INVALID_ID)
+    {
+        TId lastChildId = it.store->annotationStore[anno.parentId].lastChildId;
+        if (it._id != lastChildId)
+        {
+            it._id = nextSiblingId;
+            return true;
+        }
+    }
+    return false;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1221,28 +823,13 @@ goRight(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @see AnnotationTreeIterator#nodeRight
  */
 
-/**
-.Function.AnnotationTree Iterator#nodeUp
-..class:Spec.AnnotationTree Iterator
-..summary:Returns a new iterator to the parent node of the current annotation in the annotation tree.  
-..cat:Fragment Store
-..signature:nodeUp(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns: A new iterator to the parent node.
-....type:Spec.AnnotationTree Iterator
-..see:Function.AnnotationTree Iterator#nodeDown
-..see:Function.AnnotationTree Iterator#nodeRight
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline Iter<TFragmentStore, AnnotationTree<TSpec> >
 nodeUp(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	Iter<TFragmentStore, AnnotationTree<TSpec> > tmp(it);
-	goUp(tmp);
-	return tmp;
+    Iter<TFragmentStore, AnnotationTree<TSpec> > tmp(it);
+    goUp(tmp);
+    return tmp;
 }
 
 /*!
@@ -1259,28 +846,13 @@ nodeUp(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
  * @see AnnotationTreeIterator#nodeRight
  */
 
-/**
-.Function.AnnotationTree Iterator#nodeDown
-..class:Spec.AnnotationTree Iterator
-..summary:Returns a new iterator to the first child node of the current annotation in the annotation tree.  
-..cat:Fragment Store
-..signature:nodeDown(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns: A new iterator to the parent node.
-....type:Spec.AnnotationTree Iterator
-..see:Function.AnnotationTree Iterator#nodeUp
-..see:Function.AnnotationTree Iterator#nodeRight
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline Iter<TFragmentStore, AnnotationTree<TSpec> >
 nodeDown(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	Iter<TFragmentStore, AnnotationTree<TSpec> > tmp(it);
-	goDown(tmp);
-	return tmp;
+    Iter<TFragmentStore, AnnotationTree<TSpec> > tmp(it);
+    goDown(tmp);
+    return tmp;
 }
 
 /*!
@@ -1297,28 +869,13 @@ nodeDown(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
  * @see AnnotationTreeIterator#nodeDown
  */
 
-/**
-.Function.AnnotationTree Iterator#nodeRight
-..class:Spec.AnnotationTree Iterator
-..summary:Returns a new iterator to the right sibling of the current annotation in the annotation tree.  
-..cat:Fragment Store
-..signature:nodeRight(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns: A new iterator to the right sibling.
-....type:Spec.AnnotationTree Iterator
-..see:Function.AnnotationTree Iterator#nodeUp
-..see:Function.AnnotationTree Iterator#nodeDown
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline Iter<TFragmentStore, AnnotationTree<TSpec> >
 nodeRight(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	Iter<TFragmentStore, AnnotationTree<TSpec> > tmp(it);
-	goRight(tmp);
-	return tmp;
+    Iter<TFragmentStore, AnnotationTree<TSpec> > tmp(it);
+    goRight(tmp);
+    return tmp;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1328,27 +885,27 @@ template <typename TAnnotationStore, typename TId>
 inline TId
 _cyclicListFrontInsert(TAnnotationStore & annotationStore, TId newId, TId lastChildId)
 {
-	typedef typename Value<TAnnotationStore>::Type TAnnotation;
-
-	TId nextId, newLastId;
-	if (lastChildId != TAnnotation::INVALID_ID)
-	{
-		// get last node in the cycle
-		TAnnotation &lastChild = annotationStore[lastChildId];
-		// last child points to first child
-		nextId = lastChild.nextSiblingId;
-		// insert new node between last and first
-		lastChild.nextSiblingId = newId;
-		// last child remains the same
-		newLastId = lastChildId;
-	} else
-		// cyclic list was empty
-		newLastId = nextId = newId;
-	
-	// link new node to former first node
-	annotationStore[newId].nextSiblingId = nextId;
-	
-	return newLastId;
+    typedef typename Value<TAnnotationStore>::Type TAnnotation;
+
+    TId nextId, newLastId;
+    if (lastChildId != TAnnotation::INVALID_ID)
+    {
+        // get last node in the cycle
+        TAnnotation &lastChild = annotationStore[lastChildId];
+        // last child points to first child
+        nextId = lastChild.nextSiblingId;
+        // insert new node between last and first
+        lastChild.nextSiblingId = newId;
+        // last child remains the same
+        newLastId = lastChildId;
+    } else
+        // cyclic list was empty
+        newLastId = nextId = newId;
+
+    // link new node to former first node
+    annotationStore[newId].nextSiblingId = nextId;
+
+    return newLastId;
 }
 
 // delete an _id from a cyclic list and returns new last child _id
@@ -1356,22 +913,22 @@ template <typename TAnnotationStore, typename TId>
 inline TId
 _cyclicListSearchPrev(TAnnotationStore & annotationStore, TId _id, TId lastChildId)
 {
-	typedef typename Value<TAnnotationStore>::Type TAnnotation;
-
-	if (lastChildId == TAnnotation::INVALID_ID)
-		return TAnnotation::INVALID_ID;
-	
-	TId prevId, i = lastChildId;
-	do {
-		prevId = i;
-		i = annotationStore[i].nextSiblingId;
-		if (i == _id) break;
-	} while (i != lastChildId);
-
-	if (i == _id)
-		return prevId;
-	else
-		return TAnnotation::INVALID_ID;
+    typedef typename Value<TAnnotationStore>::Type TAnnotation;
+
+    if (lastChildId == TAnnotation::INVALID_ID)
+        return TAnnotation::INVALID_ID;
+
+    TId prevId, i = lastChildId;
+    do {
+        prevId = i;
+        i = annotationStore[i].nextSiblingId;
+        if (i == _id) break;
+    } while (i != lastChildId);
+
+    if (i == _id)
+        return prevId;
+    else
+        return TAnnotation::INVALID_ID;
 }
 
 // delete an _id from a cyclic list and returns new last child _id
@@ -1379,24 +936,24 @@ template <typename TAnnotationStore, typename TId>
 inline TId
 _cyclicListRemove(TAnnotationStore & annotationStore, TId _id, TId lastChildId)
 {
-	typedef typename Value<TAnnotationStore>::Type TAnnotation;
-
-	TId prevId = _cyclicListSearchPrev(annotationStore, _id, lastChildId);
-	
-	if (prevId != TAnnotation::INVALID_ID)
-	{
-		annotationStore[prevId].nextSiblingId = annotationStore[_id].nextSiblingId;
-		
-		if (_id == lastChildId)
-		{
-			if (prevId != _id)
-				return prevId;
-			else
-				return TAnnotation::INVALID_ID;
-		} else
-			return lastChildId;
-	}
-	return lastChildId;
+    typedef typename Value<TAnnotationStore>::Type TAnnotation;
+
+    TId prevId = _cyclicListSearchPrev(annotationStore, _id, lastChildId);
+
+    if (prevId != TAnnotation::INVALID_ID)
+    {
+        annotationStore[prevId].nextSiblingId = annotationStore[_id].nextSiblingId;
+
+        if (_id == lastChildId)
+        {
+            if (prevId != _id)
+                return prevId;
+            else
+                return TAnnotation::INVALID_ID;
+        } else
+            return lastChildId;
+    }
+    return lastChildId;
 }
 
 /*!
@@ -1413,42 +970,27 @@ _cyclicListRemove(TAnnotationStore & annotationStore, TId _id, TId lastChildId)
  * @see AnnotationTreeIterator#createSibling
  */
 
-/**
-.Function.createLeftChild
-..class:Spec.AnnotationTree Iterator
-..summary:Creates a new left-most child of the current node and returns an iterator to it.
-..cat:Fragment Store
-..signature:createLeftChild(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns: Iterator to the new left-most child.
-....type:Spec.AnnotationTree Iterator
-..see:Function.createRightChild
-..see:Function.createSibling
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline Iter<TFragmentStore, AnnotationTree<TSpec> >
 createLeftChild(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
-	
-	appendValue(it.store->annotationStore, getAnnotation(it));
-	TAnnotation &parentAnno = getAnnotation(it);
-
-	TId childId = length(it.store->annotationStore) - 1;
-	TAnnotation &childAnno = it.store->annotationStore[childId];
-	
-	parentAnno.lastChildId = _cyclicListFrontInsert(it.store->annotationStore, childId, parentAnno.lastChildId);
-	childAnno.parentId = it._id;
-	childAnno.lastChildId = TAnnotation::INVALID_ID;
-	
-	Iter<TFragmentStore, AnnotationTree<TSpec> > childIter(it);
-	childIter._id = childId;
-	return childIter;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
+
+    appendValue(it.store->annotationStore, getAnnotation(it));
+    TAnnotation &parentAnno = getAnnotation(it);
+
+    TId childId = length(it.store->annotationStore) - 1;
+    TAnnotation &childAnno = it.store->annotationStore[childId];
+
+    parentAnno.lastChildId = _cyclicListFrontInsert(it.store->annotationStore, childId, parentAnno.lastChildId);
+    childAnno.parentId = it._id;
+    childAnno.lastChildId = TAnnotation::INVALID_ID;
+
+    Iter<TFragmentStore, AnnotationTree<TSpec> > childIter(it);
+    childIter._id = childId;
+    return childIter;
 }
 
 /*!
@@ -1465,43 +1007,28 @@ createLeftChild(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @see AnnotationTreeIterator#createSibling
  */
 
-/**
-.Function.createRightChild
-..class:Spec.AnnotationTree Iterator
-..summary:Creates a new right-most child of the current node and returns an iterator to it.
-..cat:Fragment Store
-..signature:createRightChild(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns: Iterator to the new right-most child.
-....type:Spec.AnnotationTree Iterator
-..see:Function.createLeftChild
-..see:Function.createSibling
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline Iter<TFragmentStore, AnnotationTree<TSpec> >
 createRightChild(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
-	
-	appendValue(it.store->annotationStore, getAnnotation(it));
-	TAnnotation &parentAnno = getAnnotation(it);
-
-	TId childId = length(it.store->annotationStore) - 1;
-	TAnnotation &childAnno = it.store->annotationStore[childId];
-	
-	_cyclicListFrontInsert(it.store->annotationStore, childId, parentAnno.lastChildId);
-	parentAnno.lastChildId = childId;
-	childAnno.parentId = it._id;
-	childAnno.lastChildId = TAnnotation::INVALID_ID;
-	
-	Iter<TFragmentStore, AnnotationTree<TSpec> > childIter(it);
-	childIter._id = childId;
-	return childIter;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
+
+    appendValue(it.store->annotationStore, getAnnotation(it));
+    TAnnotation &parentAnno = getAnnotation(it);
+
+    TId childId = length(it.store->annotationStore) - 1;
+    TAnnotation &childAnno = it.store->annotationStore[childId];
+
+    _cyclicListFrontInsert(it.store->annotationStore, childId, parentAnno.lastChildId);
+    parentAnno.lastChildId = childId;
+    childAnno.parentId = it._id;
+    childAnno.lastChildId = TAnnotation::INVALID_ID;
+
+    Iter<TFragmentStore, AnnotationTree<TSpec> > childIter(it);
+    childIter._id = childId;
+    return childIter;
 }
 
 /*!
@@ -1518,47 +1045,32 @@ createRightChild(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @see AnnotationTreeIterator#createRightChild
  */
 
-/**
-.Function.createSibling
-..class:Spec.AnnotationTree Iterator
-..summary:Creates a new right sibling of the current node and returns an iterator to it.
-..cat:Fragment Store
-..signature:createSibling(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns: Iterator to the new right sibling.
-....type:Spec.AnnotationTree Iterator
-..see:Function.createLeftChild
-..see:Function.createRightChild
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline Iter<TFragmentStore, AnnotationTree<TSpec> >
 createSibling(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
-
-	appendValue(it.store->annotationStore, getAnnotation(it));
-	TAnnotation &anno = getAnnotation(it);
-
-	TId siblingId = length(it.store->annotationStore) - 1;
-
-	TAnnotation &parentAnno = it.store->annotationStore[anno.parentId];
-	if (parentAnno.lastChildId == it._id)
-		parentAnno.lastChildId = siblingId;
-
-	TAnnotation &siblingAnno = it.store->annotationStore[siblingId];
-	siblingAnno.nextSiblingId = anno.nextSiblingId;
-	siblingAnno.parentId = anno.parentId;
-	siblingAnno.lastChildId = TAnnotation::INVALID_ID;
-	anno.nextSiblingId = siblingId;
-	
-	Iter<TFragmentStore, AnnotationTree<TSpec> > siblingIter(it);
-	siblingIter._id = siblingId;
-	return siblingIter;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
+
+    appendValue(it.store->annotationStore, getAnnotation(it));
+    TAnnotation &anno = getAnnotation(it);
+
+    TId siblingId = length(it.store->annotationStore) - 1;
+
+    TAnnotation &parentAnno = it.store->annotationStore[anno.parentId];
+    if (parentAnno.lastChildId == it._id)
+        parentAnno.lastChildId = siblingId;
+
+    TAnnotation &siblingAnno = it.store->annotationStore[siblingId];
+    siblingAnno.nextSiblingId = anno.nextSiblingId;
+    siblingAnno.parentId = anno.parentId;
+    siblingAnno.lastChildId = TAnnotation::INVALID_ID;
+    anno.nextSiblingId = siblingId;
+
+    Iter<TFragmentStore, AnnotationTree<TSpec> > siblingIter(it);
+    siblingIter._id = siblingId;
+    return siblingIter;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1572,21 +1084,15 @@ createSibling(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
  * @param[in] it The AnnotationTreeIterator to query.
  */
 
-/**
-.Function.isRoot:
-..class:Spec.AnnotationTree Iterator
-..param.iterator.type:Spec.AnnotationTree Iterator
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline bool
 isRoot(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
 
-//	if (it._id >= length(it.store->annotationStore)) return false;
-	return it.store->annotationStore[it._id].parentId == TAnnotation::INVALID_ID;
+//    if (it._id >= length(it.store->annotationStore)) return false;
+    return it.store->annotationStore[it._id].parentId == TAnnotation::INVALID_ID;
 }
 
 /*!
@@ -1598,21 +1104,15 @@ isRoot(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
  * @param[in] it The AnnotationTreeIterator to query.
  */
 
-/**
-.Function.isLeaf:
-..class:Spec.AnnotationTree Iterator
-..param.iterator.type:Spec.AnnotationTree Iterator
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline bool
 isLeaf(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
 
-//	if (it._id >= length(it.store->annotationStore)) return false;
-	return it.store->annotationStore[it._id].lastChildId == TAnnotation::INVALID_ID;
+//    if (it._id >= length(it.store->annotationStore)) return false;
+    return it.store->annotationStore[it._id].lastChildId == TAnnotation::INVALID_ID;
 }
 
 /*!
@@ -1624,35 +1124,22 @@ isLeaf(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
  * @param[in] it The AnnotationTreeIterator to query.
  */
 
-/**
-.Function.isLastChild
-..class:Spec.AnnotationTree Iterator
-..summary:Returns a boolean value that indicates whether the current node is the last child.
-..cat:Fragment Store
-..signature:isLastChild(iter)
-..param.iter:An annotation tree iterator.
-...type:Spec.AnnotationTree Iterator
-..returns: $true$ if the iterator is the last child, otherwise $false$.
-...type:nolink:bool
-..include:seqan/store.h
-*/
-
 template <typename TFragmentStore, typename TSpec>
 inline bool
 isLastChild(Iter<TFragmentStore, AnnotationTree<TSpec> > const & it)
 {
-	typedef typename TFragmentStore::TAnnotationStore	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type		TAnnotation;
-	typedef typename TAnnotation::TId					TId;
-
-	TAnnotation const &anno = getAnnotation(it);
-	TId nextSiblingId = anno.nextSiblingId;
-	if (nextSiblingId != TAnnotation::INVALID_ID)
-	{
-		TId lastChildId = it.store->annotationStore[anno.parentId].lastChildId;
-		return it._id == lastChildId;
-	}
-	return true;
+    typedef typename TFragmentStore::TAnnotationStore    TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type        TAnnotation;
+    typedef typename TAnnotation::TId                    TId;
+
+    TAnnotation const &anno = getAnnotation(it);
+    TId nextSiblingId = anno.nextSiblingId;
+    if (nextSiblingId != TAnnotation::INVALID_ID)
+    {
+        TId lastChildId = it.store->annotationStore[anno.parentId].lastChildId;
+        return it._id == lastChildId;
+    }
+    return true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1661,53 +1148,53 @@ template <typename TAnnotationStore>
 inline void
 _storeClearAnnoBackLinks(TAnnotationStore & me)
 {
-	typedef typename Value<TAnnotationStore>::Type				TAnnotation;
-	typedef typename Iterator<TAnnotationStore, Standard>::Type TAnnoIter;
-
-	TAnnoIter it = begin(me, Standard());
-	TAnnoIter itEnd = end(me, Standard());
-	
-	for (; it != itEnd; ++it)
-	{
-		(*it).lastChildId = TAnnotation::INVALID_ID;
-		(*it).nextSiblingId = TAnnotation::INVALID_ID;
-	}
+    typedef typename Value<TAnnotationStore>::Type                TAnnotation;
+    typedef typename Iterator<TAnnotationStore, Standard>::Type TAnnoIter;
+
+    TAnnoIter it = begin(me, Standard());
+    TAnnoIter itEnd = end(me, Standard());
+
+    for (; it != itEnd; ++it)
+    {
+        (*it).lastChildId = TAnnotation::INVALID_ID;
+        (*it).nextSiblingId = TAnnotation::INVALID_ID;
+    }
 }
 
 template <typename TAnnotationStore>
 inline void
 _storeCreateAnnoBackLinks(TAnnotationStore & me)
 {
-	typedef typename Value<TAnnotationStore>::Type				TAnnotation;
-	typedef typename TAnnotation::TId							TId;
-	typedef typename Iterator<TAnnotationStore, Standard>::Type TAnnoIter;
-	
-	TAnnoIter itBegin = begin(me, Standard());
-	TAnnoIter itEnd = end(me, Standard());
-	TId _id = (itEnd - itBegin) - 1;
-	TAnnoIter it = itBegin + _id;
-	
-	for (; itBegin <= it; --it, --_id)
-	{
-		if ((*it).parentId != TAnnotation::INVALID_ID)
-		{
-			TAnnoIter parent = itBegin + (*it).parentId;
-			if ((*parent).lastChildId == TAnnotation::INVALID_ID)
-			{
-				(*parent).lastChildId = _id;
-				(*it).nextSiblingId = _id;
-			}
-
-			if ((*it).nextSiblingId == TAnnotation::INVALID_ID)
-			{
-				TAnnoIter lastChild = itBegin + (*parent).lastChildId;
-				(*it).nextSiblingId = (*lastChild).nextSiblingId;
-				(*lastChild).nextSiblingId = _id;
-			}
-		}
-		else 
-			(*it).nextSiblingId = TAnnotation::INVALID_ID;
-	}
+    typedef typename Value<TAnnotationStore>::Type                TAnnotation;
+    typedef typename TAnnotation::TId                            TId;
+    typedef typename Iterator<TAnnotationStore, Standard>::Type TAnnoIter;
+
+    TAnnoIter itBegin = begin(me, Standard());
+    TAnnoIter itEnd = end(me, Standard());
+    TId _id = (itEnd - itBegin) - 1;
+    TAnnoIter it = itBegin + _id;
+
+    for (; itBegin <= it; --it, --_id)
+    {
+        if ((*it).parentId != TAnnotation::INVALID_ID)
+        {
+            TAnnoIter parent = itBegin + (*it).parentId;
+            if ((*parent).lastChildId == TAnnotation::INVALID_ID)
+            {
+                (*parent).lastChildId = _id;
+                (*it).nextSiblingId = _id;
+            }
+
+            if ((*it).nextSiblingId == TAnnotation::INVALID_ID)
+            {
+                TAnnoIter lastChild = itBegin + (*parent).lastChildId;
+                (*it).nextSiblingId = (*lastChild).nextSiblingId;
+                (*lastChild).nextSiblingId = _id;
+            }
+        }
+        else
+            (*it).nextSiblingId = TAnnotation::INVALID_ID;
+    }
 }
 
 template <typename TPos, typename TSpec>
@@ -1722,7 +1209,7 @@ operator << (std::ostream & out, AnnotationStoreElement<TPos, TSpec> const & ann
     out << "endPos:       \t" << anno.endPos << std::endl;
     out << "lastChildId:  \t" << anno.lastChildId << std::endl;
     out << "nextSiblingId:\t" << anno.nextSiblingId << std::endl;
-    
+
     return out;
 }
 
diff --git a/seqan/store/store_base.h b/seqan/store/store_base.h
index ab6dcf0..f04d529 100644
--- a/seqan/store/store_base.h
+++ b/seqan/store/store_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/store/store_contig.h b/seqan/store/store_contig.h
index 2437151..15dc3e5 100644
--- a/seqan/store/store_contig.h
+++ b/seqan/store/store_contig.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -116,92 +116,29 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Constant to represent an invalid.
  */
 
-/**
-.Class.ContigStoreElement
-..summary:Represents a single contig.
-..cat:Fragment Store
-..signature:ContigStoreElement<>
-..signature:ContigStoreElement<TContigSeq[, TGapAnchor[, TSpec]]>
-..param.TContigSeq:Type to store the contig sequence.
-..param.TGapAnchor:Type of a contig gap anchor.
-...type:Class.GapAnchor
-..param.TSpec:The specialization type.
-...default:$void$
-..remarks:Value type of the @Memvar.FragmentStore#contigStore@ string.
-
-.Typedef.ContigStoreElement#TContigSeq
-..summary:Type of the $seq$ member.
-..class:Class.ContigStoreElement
-.Typedef.ContigStoreElement#TGapAnchors
-..summary:Type of the $gaps$ member.
-..class:Class.ContigStoreElement
-.Typedef.ContigStoreElement#TPos
-..summary:Type of the $fileBeginPos$ and $fileEndPos$ members.
-..class:Class.ContigStoreElement
-.Typedef.ContigStoreElement#TSpec
-..summary:The specialization type.
-..class:Class.ContigStoreElement
-
-
-.Memfunc.ContigStoreElement#ContigStoreElement
-..summary:Constructor
-..signature:ContigStoreElement<> ()
-..signature:ContigStoreElement<TContigSeq[, TGapAnchor[, TSpec]]> ()
-..remarks:Sets $fileId$ to $INVALID_ID$ and $usage$, $fileBeginPos$ and $fileEndPos$ to $0$.
-..class:Class.ContigStoreElement
-.Memvar.ContigStoreElement#seq
-..summary:Contig sequence.
-..type:Typedef.ContigStoreElement#TContigSeq
-..class:Class.ContigStoreElement
-.Memvar.ContigStoreElement#gaps
-..summary:String of contig gap anchors. Can be used to create a $Spec.AnchorGaps$ alignment row.
-..type:Typedef.ContigStoreElement#TGapAnchors
-..class:Class.ContigStoreElement
-.Memvar.ContigStoreElement#usage
-..summary:Counts the number of locks, see @Function.lockContigs@.
-..class:Class.ContigStoreElement
-.Memvar.ContigStoreElement#fileId
-..summary:Refers to a file in the @Memvar.FragmentStore#contigFileStore@ or is $INVALID_ID$ if the contig has no file association.
-..type:Metafunction.Id
-..class:Class.ContigStoreElement
-.Memvar.ContigStoreElement#fileBeginPos
-..summary:Begin position of the contig sequence fragment in the file.
-..type:Typedef.ContigStoreElement#TPos
-..class:Class.ContigStoreElement
-.Memvar.ContigStoreElement#fileEndPos
-..summary:End position of the contig sequence fragment in the file.
-..type:Typedef.ContigStoreElement#TPos
-..class:Class.ContigStoreElement
-.Memvar.ContigStoreElement#INVALID_ID
-..summary:Constant to represent an invalid id.
-..type:Metafunction.Id
-..class:Class.ContigStoreElement
-..include:seqan/store.h
-*/
-
 template <typename TContigSeq_, typename TGapAnchor_, typename TSpec_ = void>
 struct ContigStoreElement
 {
-	typedef typename Id<ContigStoreElement>::Type	TId;
-	
-	typedef TContigSeq_			TContigSeq;
-	typedef TGapAnchor_			TGapAnchor;
-	typedef TSpec_				TSpec;
-	typedef __int64				TPos;
-	typedef String<TGapAnchor>	TGapAnchors;
+    typedef typename Id<ContigStoreElement>::Type    TId;
+
+    typedef TContigSeq_            TContigSeq;
+    typedef TGapAnchor_            TGapAnchor;
+    typedef TSpec_                TSpec;
+    typedef __int64                TPos;
+    typedef String<TGapAnchor>    TGapAnchors;
 
-	static const TId INVALID_ID;
+    static const TId INVALID_ID;
+
+    TContigSeq    seq;
+    TGapAnchors    gaps;
 
-	TContigSeq	seq;
-	TGapAnchors	gaps;
-	
 // dynamic loading and disposing of contigs
-	unsigned	usage;			// number of threads,... using this contig
-	TId			fileId;
-	TPos		fileBeginPos;
-	TPos		fileEndPos;
+    unsigned    usage;            // number of threads,... using this contig
+    TId            fileId;
+    TPos        fileBeginPos;
+    TPos        fileEndPos;
 
-	ContigStoreElement() : usage(0), fileId(INVALID_ID), fileBeginPos(0), fileEndPos(0) {}
+    ContigStoreElement() : usage(0), fileId(INVALID_ID), fileBeginPos(0), fileEndPos(0) {}
 
     inline bool operator==(ContigStoreElement const & other) const
     {
@@ -216,9 +153,9 @@ struct ContigStoreElement
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TContigSeq_, typename TGapAnchor_, typename TSpec_> 
-const typename Id<ContigStoreElement<TContigSeq_, TGapAnchor_, TSpec_> >::Type 
-ContigStoreElement<TContigSeq_, TGapAnchor_, TSpec_>::INVALID_ID = MaxValue<typename Id<ContigStoreElement<TContigSeq_, TGapAnchor_, TSpec_> >::Type>::VALUE; 
+template <typename TContigSeq_, typename TGapAnchor_, typename TSpec_>
+const typename Id<ContigStoreElement<TContigSeq_, TGapAnchor_, TSpec_> >::Type
+ContigStoreElement<TContigSeq_, TGapAnchor_, TSpec_>::INVALID_ID = MaxValue<typename Id<ContigStoreElement<TContigSeq_, TGapAnchor_, TSpec_> >::Type>::VALUE;
 
 //////////////////////////////////////////////////////////////////////////////
 
@@ -232,8 +169,6 @@ ContigStoreElement<TContigSeq_, TGapAnchor_, TSpec_>::INVALID_ID = MaxValue<type
  *
  * @tparam TSpec The specializing type.  Default: <tt>void</tt>.
  *
- * @section Remarks
- *
  * Value type of @link FragmentStore::contigFileStore @endlink string.
  */
 
@@ -248,42 +183,17 @@ ContigStoreElement<TContigSeq_, TGapAnchor_, TSpec_>::INVALID_ID = MaxValue<type
  * @brief The contigId of the first sequence in the file.  Subsequent contig sequences have an increasing contigId.
  */
 
-/**
-.Class.ContigFile
-..summary:Represents a file containing contigs.
-..cat:Fragment Store
-..signature:ContigFile<>
-..signature:ContigFile<TSpec>
-..param.TSpec:The specialization type.
-...default:$void$
-..remarks:Value type of the @Memvar.FragmentStore#contigFileStore@ string.
-
-.Memvar.ContigFile#fileName
-..summary:Contig file name.
-..type:Shortcut.CharString
-..class:Class.ContigFile
-.Memvar.ContigFile#format
-..summary:Stores the contig file format, auto-detected in $Function.loadContigs$.
-..type:Class.AutoSeqFormat
-..class:Class.ContigFile
-.Memvar.ContigFile#firstContigId
-..summary:The $contigId$ of the first sequence in the file. Subsequent contig sequences have an increasing $contigId$.
-..type:Metafunction.Id
-..class:Class.ContigFile
-..include:seqan/store.h
-*/
-
 template <typename TSpec_ = void>
 struct ContigFile
 {
 //IOREV instead of storing filename and format store TFile ?
-	typedef typename Id<ContigFile>::Type	TId;
+    typedef typename Id<ContigFile>::Type    TId;
 
-	static const TId INVALID_ID;
+    static const TId INVALID_ID;
 
-	CharString		fileName;
-	AutoSeqFormat	format;
-	TId				firstContigId;	// first sequence of the file corresponds to this contigId
+    CharString        fileName;
+    AutoSeqFormat    format;
+    TId                firstContigId;    // first sequence of the file corresponds to this contigId
 
     inline bool operator==(ContigFile const & other) const
     {
@@ -295,9 +205,9 @@ struct ContigFile
 
 //////////////////////////////////////////////////////////////////////////////
 
-template <typename TSpec_> 
-const typename Id<ContigFile<TSpec_> >::Type 
-ContigFile<TSpec_>::INVALID_ID = MaxValue<typename Id<ContigFile<TSpec_> >::Type>::VALUE; 
+template <typename TSpec_>
+const typename Id<ContigFile<TSpec_> >::Type
+ContigFile<TSpec_>::INVALID_ID = MaxValue<typename Id<ContigFile<TSpec_> >::Type>::VALUE;
 
 //////////////////////////////////////////////////////////////////////////////
 
diff --git a/seqan/store/store_intervaltree.h b/seqan/store/store_intervaltree.h
index 1e7df7a..085e4ab 100644
--- a/seqan/store/store_intervaltree.h
+++ b/seqan/store/store_intervaltree.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -48,119 +48,119 @@ template<typename TSpec, typename TConfig>
 inline void
 createIntervalTreeStore(FragmentStore<TSpec, TConfig> & me, const bool &unknownO)
 {
-	typedef typename FragmentStore<TSpec, TConfig>::TAnnotationStore 	TAnnotationStore;
-	typedef typename Value<TAnnotationStore>::Type 				TAnnotationStoreElement;
-	typedef typename TAnnotationStoreElement::TId 				TId;
-	typedef typename Iterator<TAnnotationStore>::Type 			TAnnotationIterator;
-	
-	typedef	typename FragmentStore<TSpec, TConfig>::TIntervalTreeStore 	TIntervalTreeStore;
-	typedef typename Value<TIntervalTreeStore>::Type 			TIntervalTree;
-	typedef typename TIntervalTree::TInterval 				TInterval;
-	typedef 	 String<TInterval>					TIntervals;
-	typedef typename Iterator<String<TIntervals> >::Type			TCIter;
-	
-	static const TId INVALID_ID = TAnnotationStoreElement::INVALID_ID;
-	
-	// get intervals for each contig (R- and F-strand):
-	if (!empty(me.annotationStore) && !unknownO)
-	{
-		resize(me.intervalTreeStore_F, length(me.contigStore) );
-		resize(me.intervalTreeStore_R, length(me.contigStore) );
-
-		String<TIntervals> contigIntervals_F;
-		String<TIntervals> contigIntervals_R;
-		resize(contigIntervals_F, length(me.contigStore));
-		resize(contigIntervals_R, length(me.contigStore));
-		
-		TAnnotationIterator itAnno = begin(me.annotationStore);
-		TAnnotationIterator itAnnoEnd = end(me.annotationStore);
-		TId beginPos;
-		TId endPos;
-		TInterval interval;
-		for ( ; itAnno != itAnnoEnd; goNext(itAnno))
-		{
-			if (getValue(itAnno).contigId != INVALID_ID)
-			{
-				beginPos = getValue(itAnno).beginPos;
-				endPos = getValue(itAnno).endPos;
-				if (beginPos != INVALID_ID && beginPos <= endPos)
-				{
-					interval.i1 = beginPos;
-					interval.i2 = endPos;
-					interval.cargo = position(itAnno, me.annotationStore);
-					appendValue(value(contigIntervals_F,  getValue(itAnno).contigId), interval, Generous());		
-				}
-				else if (beginPos != INVALID_ID  && beginPos > endPos)
-				{
-					interval.i1 = endPos;					
-					interval.i2 = beginPos;
-					interval.cargo = position(itAnno, me.annotationStore);
-					appendValue(value(contigIntervals_R, getValue(itAnno).contigId), interval, Generous() );
-				}
-			}
-		}
-	
-		// build trees for each contig and each strand:
-		TCIter itF = begin(contigIntervals_F);
-		TCIter itFEnd = end(contigIntervals_F);
-		TCIter itR = begin(contigIntervals_R);
-		for ( ; itF != itFEnd; goNext(itF), goNext(itR))
-		{
-			TIntervalTree intervalTree_F(getValue(itF), ComputeCenter());
-			TIntervalTree intervalTree_R(getValue(itR), ComputeCenter());
-				
-			assignValue(me.intervalTreeStore_F, position(itF, contigIntervals_F), intervalTree_F);  
-			assignValue(me.intervalTreeStore_R, position(itR, contigIntervals_R), intervalTree_R);
-		}
-	}
-	
-	// if read orientation is not known:
-	// get intervals for each contig:
-	if (!empty(me.annotationStore) && unknownO)
-	{
-		resize(me.intervalTreeStore_F, length(me.contigStore) );
-		clear(me.intervalTreeStore_R);
-
-		String<TIntervals> contigIntervals;
-		resize(contigIntervals, length(me.contigStore));
-		TAnnotationIterator itAnno = begin(me.annotationStore);
-		TAnnotationIterator itAnnoEnd = end(me.annotationStore);
-		TId beginPos;
-		TId endPos;
-		TInterval interval;
-		for ( ; itAnno != itAnnoEnd; goNext(itAnno))
-		{
-			if (getValue(itAnno).contigId != INVALID_ID)
-			{
-				beginPos = getValue(itAnno).beginPos;
-				endPos = getValue(itAnno).endPos;
-				if (beginPos != INVALID_ID)
-				{
-					if (beginPos <= endPos)
-					{
-						interval.i1 = beginPos;
-						interval.i2 = endPos;
-					}
-					else
-					{
-						interval.i1 = endPos;
-						interval.i2 = beginPos;
-					}
-					interval.cargo = position(itAnno, me.annotationStore);
-					appendValue(value(contigIntervals,  getValue(itAnno).contigId), interval, Generous());		
-				}
-			}
-		}
-		// build trees for each contig:
-		TCIter itC = begin(contigIntervals);
-		TCIter itCEnd = end(contigIntervals);
-		for ( ; itC != itCEnd; goNext(itC))
-		{
-			TIntervalTree intervalTree(getValue(itC), ComputeCenter());
-				
-			assignValue(me.intervalTreeStore_F, position(itC, contigIntervals), intervalTree); 
-		}
-	}
+    typedef typename FragmentStore<TSpec, TConfig>::TAnnotationStore     TAnnotationStore;
+    typedef typename Value<TAnnotationStore>::Type                 TAnnotationStoreElement;
+    typedef typename TAnnotationStoreElement::TId                 TId;
+    typedef typename Iterator<TAnnotationStore>::Type             TAnnotationIterator;
+
+    typedef    typename FragmentStore<TSpec, TConfig>::TIntervalTreeStore     TIntervalTreeStore;
+    typedef typename Value<TIntervalTreeStore>::Type             TIntervalTree;
+    typedef typename TIntervalTree::TInterval                 TInterval;
+    typedef      String<TInterval>                    TIntervals;
+    typedef typename Iterator<String<TIntervals> >::Type            TCIter;
+
+    static const TId INVALID_ID = TAnnotationStoreElement::INVALID_ID;
+
+    // get intervals for each contig (R- and F-strand):
+    if (!empty(me.annotationStore) && !unknownO)
+    {
+        resize(me.intervalTreeStore_F, length(me.contigStore) );
+        resize(me.intervalTreeStore_R, length(me.contigStore) );
+
+        String<TIntervals> contigIntervals_F;
+        String<TIntervals> contigIntervals_R;
+        resize(contigIntervals_F, length(me.contigStore));
+        resize(contigIntervals_R, length(me.contigStore));
+
+        TAnnotationIterator itAnno = begin(me.annotationStore);
+        TAnnotationIterator itAnnoEnd = end(me.annotationStore);
+        TId beginPos;
+        TId endPos;
+        TInterval interval;
+        for ( ; itAnno != itAnnoEnd; goNext(itAnno))
+        {
+            if (getValue(itAnno).contigId != INVALID_ID)
+            {
+                beginPos = getValue(itAnno).beginPos;
+                endPos = getValue(itAnno).endPos;
+                if (beginPos != INVALID_ID && beginPos <= endPos)
+                {
+                    interval.i1 = beginPos;
+                    interval.i2 = endPos;
+                    interval.cargo = position(itAnno, me.annotationStore);
+                    appendValue(value(contigIntervals_F,  getValue(itAnno).contigId), interval, Generous());
+                }
+                else if (beginPos != INVALID_ID  && beginPos > endPos)
+                {
+                    interval.i1 = endPos;
+                    interval.i2 = beginPos;
+                    interval.cargo = position(itAnno, me.annotationStore);
+                    appendValue(value(contigIntervals_R, getValue(itAnno).contigId), interval, Generous() );
+                }
+            }
+        }
+
+        // build trees for each contig and each strand:
+        TCIter itF = begin(contigIntervals_F);
+        TCIter itFEnd = end(contigIntervals_F);
+        TCIter itR = begin(contigIntervals_R);
+        for ( ; itF != itFEnd; goNext(itF), goNext(itR))
+        {
+            TIntervalTree intervalTree_F(getValue(itF), ComputeCenter());
+            TIntervalTree intervalTree_R(getValue(itR), ComputeCenter());
+
+            assignValue(me.intervalTreeStore_F, position(itF, contigIntervals_F), intervalTree_F);
+            assignValue(me.intervalTreeStore_R, position(itR, contigIntervals_R), intervalTree_R);
+        }
+    }
+
+    // if read orientation is not known:
+    // get intervals for each contig:
+    if (!empty(me.annotationStore) && unknownO)
+    {
+        resize(me.intervalTreeStore_F, length(me.contigStore) );
+        clear(me.intervalTreeStore_R);
+
+        String<TIntervals> contigIntervals;
+        resize(contigIntervals, length(me.contigStore));
+        TAnnotationIterator itAnno = begin(me.annotationStore);
+        TAnnotationIterator itAnnoEnd = end(me.annotationStore);
+        TId beginPos;
+        TId endPos;
+        TInterval interval;
+        for ( ; itAnno != itAnnoEnd; goNext(itAnno))
+        {
+            if (getValue(itAnno).contigId != INVALID_ID)
+            {
+                beginPos = getValue(itAnno).beginPos;
+                endPos = getValue(itAnno).endPos;
+                if (beginPos != INVALID_ID)
+                {
+                    if (beginPos <= endPos)
+                    {
+                        interval.i1 = beginPos;
+                        interval.i2 = endPos;
+                    }
+                    else
+                    {
+                        interval.i1 = endPos;
+                        interval.i2 = beginPos;
+                    }
+                    interval.cargo = position(itAnno, me.annotationStore);
+                    appendValue(value(contigIntervals,  getValue(itAnno).contigId), interval, Generous());
+                }
+            }
+        }
+        // build trees for each contig:
+        TCIter itC = begin(contigIntervals);
+        TCIter itCEnd = end(contigIntervals);
+        for ( ; itC != itCEnd; goNext(itC))
+        {
+            TIntervalTree intervalTree(getValue(itC), ComputeCenter());
+
+            assignValue(me.intervalTreeStore_F, position(itC, contigIntervals), intervalTree);
+        }
+    }
 }
 
 
@@ -174,16 +174,16 @@ createIntervalTreeStore(FragmentStore<TSpec, TConfig> & me, const bool &unknownO
 
 template<typename TIntervalTree, typename TInterval, typename TCargo>
 inline void
-findIntervalsForInterval(String<TCargo> & result, TIntervalTree & intervalTree, TInterval & interval, const unsigned & offsetInterval)
+findIntervalsForInterval(String<TCargo> & result, TIntervalTree & intervalTree, TInterval & interval, unsigned offsetInterval)
 {
-	String<TCargo> result1;
-	String<TCargo> result2;
-	
-	findIntervals(intervalTree.g, intervalTree.pm, interval.i1 + offsetInterval, result1);
-	findIntervals(intervalTree.g, intervalTree.pm, interval.i2 - offsetInterval, result2);
-	
-	interSec(result, result1, result2); 
-	
+    String<TCargo> result1;
+    String<TCargo> result2;
+
+    findIntervals(result1, intervalTree.g, intervalTree.pm, interval.i1 + offsetInterval);
+    findIntervals(result2, intervalTree.g, intervalTree.pm, interval.i2 - offsetInterval);
+
+    interSec(result, result1, result2);
+
 }
 
 
diff --git a/seqan/store/store_io.h b/seqan/store/store_io.h
index 66f54cc..c8c0098 100644
--- a/seqan/store/store_io.h
+++ b/seqan/store/store_io.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -35,8 +35,6 @@
 #ifndef SEQAN_HEADER_STORE_IO_H
 #define SEQAN_HEADER_STORE_IO_H
 
-#include <seqan/misc/misc_parsing.h>
-
 /* IOREV
  *
  * _doc_
@@ -60,11 +58,6 @@ namespace SEQAN_NAMESPACE_MAIN
 
 //////////////////////////////////////////////////////////////////////////////
 
-/**
-.Tag.File Format.tag.Amos message file:
-	Amos message file.
-..include:seqan/store.h
-*/
 struct TagAmos_;
 typedef Tag<TagAmos_> const Amos;
 
@@ -90,59 +83,44 @@ typedef Tag<TagAmos_> const Amos;
  */
 
 
-/**
-.Function.getClrRange
-..cat:Fragment Store
-..summary:Get the "clear" range of a read alignment.
-..remarks:The clear range of a read alignment is the range of the part of the alignment that is not clipped.
-..signature:getClrRange(fragStore, alignEl, begClr, endClr)
-..param.fragStore:Fragment Store to work on.
-...type:Class.FragmentStore
-..param.alignEl:Read alignment element.
-...type:Class.AlignedReadStoreElement
-..param.begClr:Start of the clear range.
-..param.endClr:End of the clear range.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TPos, typename TGapAnchor, typename TSpecAlign, typename TBeginClr, typename TEndClr>
 inline void
 getClrRange(FragmentStore<TSpec, TConfig> const& fragStore,
-			AlignedReadStoreElement<TPos, TGapAnchor, TSpecAlign> const& alignEl,
-			TBeginClr& begClr,		// Out-parameter: left / begin position of the clear range
-			TEndClr& endClr)		// Out-parameter: right / end position of the clear range
+            AlignedReadStoreElement<TPos, TGapAnchor, TSpecAlign> const& alignEl,
+            TBeginClr& begClr,        // Out-parameter: left / begin position of the clear range
+            TEndClr& endClr)        // Out-parameter: right / end position of the clear range
 {
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	typedef typename Iterator<String<TGapAnchor> const, Standard>::Type TGapIter;
-	
-	TSize lenRead = length(fragStore.readSeqStore[alignEl.readId]);
-	TGapIter itGap = begin(alignEl.gaps, Standard());
-	TGapIter itGapEnd = end(alignEl.gaps, Standard());
-	
-	// Any gaps or clipped characters?
-	if (itGap == itGapEnd) {
-		begClr = 0;
-		endClr = lenRead;
-	} else {
-		// Begin clear range
-		begClr = (itGap->gapPos == 0) ? itGap->seqPos : 0;
-		// End clear range
-		--itGapEnd;
-		if (static_cast<TSize>(itGapEnd->seqPos) != lenRead) endClr = lenRead;
-		else {
-			int diff = (itGap != itGapEnd) ? (*(itGapEnd - 1)).gapPos - (*(itGapEnd-1)).seqPos : 0;
-			int newDiff = itGapEnd->gapPos - itGapEnd->seqPos;
-			endClr = (newDiff < diff) ? lenRead - (diff - newDiff) : lenRead;	
-		}
-	}
-
-	// For reverse reads adapt clear ranges
-	if (alignEl.beginPos > alignEl.endPos) {
-		TBeginClr tmp = begClr;
-		begClr = lenRead - endClr;
-		endClr = lenRead - tmp;
-	}
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    typedef typename Iterator<String<TGapAnchor> const, Standard>::Type TGapIter;
+
+    TSize lenRead = length(fragStore.readSeqStore[alignEl.readId]);
+    TGapIter itGap = begin(alignEl.gaps, Standard());
+    TGapIter itGapEnd = end(alignEl.gaps, Standard());
+
+    // Any gaps or clipped characters?
+    if (itGap == itGapEnd) {
+        begClr = 0;
+        endClr = lenRead;
+    } else {
+        // Begin clear range
+        begClr = (itGap->gapPos == 0) ? itGap->seqPos : 0;
+        // End clear range
+        --itGapEnd;
+        if (static_cast<TSize>(itGapEnd->seqPos) != lenRead) endClr = lenRead;
+        else {
+            int diff = (itGap != itGapEnd) ? (*(itGapEnd - 1)).gapPos - (*(itGapEnd-1)).seqPos : 0;
+            int newDiff = itGapEnd->gapPos - itGapEnd->seqPos;
+            endClr = (newDiff < diff) ? lenRead - (diff - newDiff) : lenRead;
+        }
+    }
+
+    // For reverse reads adapt clear ranges
+    if (alignEl.beginPos > alignEl.endPos) {
+        TBeginClr tmp = begClr;
+        begClr = lenRead - endClr;
+        endClr = lenRead - tmp;
+    }
 }
 
 
@@ -167,624 +145,467 @@ getClrRange(FragmentStore<TSpec, TConfig> const& fragStore,
  * @return int 0 in the case of success, non-0 value in case of errors.
  */
 
-/**
-.Function.read
-..cat:Fragment Store
-..signature:read(file, fragStore, tag)
-..param.fragStore:A fragment store. Currently @Tag.File Format.tag.Amos message file@ and @Tag.File Format.tag.Sam@ formats are supported.
-...type:Class.FragmentStore
-..param.tag.type:Tag.File Format.tag.Amos message file
-..returns:An $int$ value with a status code. $0$ on success, a non-$0$ value on failure.
-..include:seqan/store.h
-*/
+template <typename TKey, typename TValue, typename TIter>
+void readAmosKeyValue(TKey &key, TValue &value, TIter &reader)
+{
+    clear(key);
+    clear(value);
+
+    // read "KEY:VALUE" pair
+    readUntil(key, reader, EqualsChar<':'>());
+    skipOne(reader, EqualsChar<':'>());
+    readUntil(value, reader, IsWhitespace());
+}
 
 template<typename TFile, typename TSpec, typename TConfig>
 inline int
-read(TFile & file,
-	 FragmentStore<TSpec, TConfig>& fragStore,
-	 Amos)
+read(FragmentStore<TSpec, TConfig>& fragStore,
+     TFile & file,
+     Amos)
 {
-	// Basic types
-	typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-	typedef typename Id<TFragmentStore>::Type TId;
-	typedef typename Size<TFragmentStore>::Type TSize;
-	//typedef typename Value<TFile>::Type TValue;
-	typedef typename TFragmentStore::TReadSeq TReadSeq;
-
-	// All fragment store element types
-	typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigElement;
-	typedef typename Value<typename TFragmentStore::TLibraryStore>::Type TLibraryStoreElement;
-	typedef typename Value<typename TFragmentStore::TMatePairStore>::Type TMatePairElement;
-	typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement;
-	typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
-
-	// All maps to mirror file ids to our ids
-	typedef std::map<TId, TSize> TIdMap;
-	// The following maps the library/fragment/read id from AMOS into the fragment store's ids.
-	TIdMap libIdMap;
-	TIdMap frgIdMap;
-	TIdMap readIdMap;
-	// For all paired reads (inferred from FRG), a mapping from the AMOS read id to the paired match id of the one
-	// alignment read from the AMOS file.  Note that this has the assumption that there is only one alignment per read
-	// in the AMOS file.
-	TIdMap readToPairMatchId;
-	// The id of the next pair match.
-	unsigned nextPairMatchId = 0;
-
-    RecordReader<TFile, SinglePass<> > reader(file);
-
-	// Parse the file and convert the internal ids
+    // Basic types
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Id<TFragmentStore>::Type TId;
+    typedef typename Size<TFragmentStore>::Type TSize;
+    //typedef typename Value<TFile>::Type TValue;
+
+    // All fragment store element types
+    typedef typename Value<typename TFragmentStore::TContigStore>::Type TContigElement;
+    typedef typename Value<typename TFragmentStore::TLibraryStore>::Type TLibraryStoreElement;
+    typedef typename Value<typename TFragmentStore::TMatePairStore>::Type TMatePairElement;
+    typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement;
+    typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
+    typedef typename TFragmentStore::TReadSeq TReadSeq;
+    typedef typename TFragmentStore::TContigSeq TContigSeq;
+
+    // All maps to mirror file ids to our ids
+    typedef std::map<TId, TSize> TIdMap;
+    // The following maps the library/fragment/read id from AMOS into the fragment store's ids.
+    TIdMap libIdMap;
+    TIdMap frgIdMap;
+    TIdMap readIdMap;
+    // For all paired reads (inferred from FRG), a mapping from the AMOS read id to the paired match id of the one
+    // alignment read from the AMOS file.  Note that this has the assumption that there is only one alignment per read
+    // in the AMOS file.
+    TIdMap readToPairMatchId;
+    // The id of the next pair match.
+    unsigned nextPairMatchId = 0;
+
+    typename DirectionIterator<TFile, Input>::Type reader(file);
+
+    // Parse the file and convert the internal ids
     if (atEnd(reader))
         return 1;
 
+    CharString  blockIdentifier, fieldIdentifier, eid, buffer;
+    TReadSeq    readSeq;
+    CharString  contigSeq;
+    CharString  qual;
+    TId _id;
+
     while (!atEnd(reader))
     {
-		// New block?
-		if (value(reader) == '{')
+        // New block?
+        if (value(reader) == '{')
         {
-            goNext(reader);
-			String<char> blockIdentifier;
-            if (readAlphaNums(blockIdentifier, reader) != 0)
-                return 1;
-            if (skipLine(reader) != 0)
-                return 1;
-
-			// Library block
-			if (blockIdentifier == "LIB")
+            skipOne(reader, EqualsChar<'{'>());
+
+            clear(blockIdentifier);
+            readUntil(blockIdentifier, reader, NotFunctor<IsAlpha>());
+            skipLine(reader);
+
+            // reset id and eid
+            _id = TReadStoreElement::INVALID_ID;
+            clear(eid);
+
+            // Library block
+            if (blockIdentifier == "LIB")
             {
                 // The LIB block contains the mean template length/insert size and standard deviation thereof.  Besides
                 // the numeric id and (iid) a (external) name of the library (eid).
-				TLibraryStoreElement libEl;
-				TId _id = 0;
-				String<char> fieldIdentifier;
-				String<char> eid;
-				while (!atEnd(reader) && value(reader) != '}')
+                TLibraryStoreElement libEl;
+                while (!atEnd(reader) && value(reader) != '}')
                 {
-					clear(fieldIdentifier);
-                    if (readAlphaNums(fieldIdentifier, reader) != 0)
-                        return 1;
-					if (fieldIdentifier == "iid")
-                    {
-                        goNext(reader);
-                        CharString buffer;
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(_id, buffer))
-                            return 1;
-					}
+                    // read "KEY:VALUE" pair
+                    readAmosKeyValue(fieldIdentifier, buffer, reader);
+
+                    if (fieldIdentifier == "iid")
+                        _id = lexicalCast<TId>(buffer);
                     else if (fieldIdentifier == "eid")
-                    {
-                        goNext(reader);
-                        if (readUntilOneOf(eid, reader, '\n', '\r') != 0)
-                            return 1;
-					}
-                    else if (fieldIdentifier == "mea" || fieldIdentifier == "std")
-                    {
-                        goNext(reader);
-                        CharString buffer;
-                        if (readFloat(buffer, reader) != 0)
-                            return 1;
-                        if (fieldIdentifier == "mea" && !lexicalCast2(libEl.mean, buffer))
-                            return 1;
-                        if (fieldIdentifier == "std" && !lexicalCast2(libEl.std, buffer))
-                            return 1;
-					}
-                    // Always skip over the remainder of the line.
-                    if (skipLine(reader) != 0)
-                        return 1;
-				}
+                        eid = buffer;
+                    else if (fieldIdentifier == "mea")
+                        libEl.mean = lexicalCast<double>(buffer);
+                    else if (fieldIdentifier == "std")
+                        libEl.std = lexicalCast<double>(buffer);
 
-                // Skip '}'.
-                if (!atEnd(reader))
-                {
-                    SEQAN_ASSERT_EQ(value(reader), '}');
-                    goNext(reader);
+                    // Always skip over the remainder of the line.
+                    skipUntil(reader, NotFunctor<IsWhitespace>());
                 }
+                skipOne(reader, EqualsChar<'}'>());
 
                 // Insert library information into the fragmentstore.
-				libIdMap.insert(std::make_pair(_id, length(fragStore.libraryStore)));
-				appendValue(fragStore.libraryStore, libEl, Generous() );
-				appendValue(fragStore.libraryNameStore, eid, Generous() );
-			}
+                libIdMap.insert(std::make_pair(_id, length(fragStore.libraryStore)));
+                appendValue(fragStore.libraryStore, libEl, Generous());
+                appendValue(fragStore.libraryNameStore, eid, Generous());
+            }
+            // Fragment block
             else if (blockIdentifier == "FRG")
             {
                 // The FRG block contains the parent library (lib), links to the paired sequencing reads (rds), internal
                 // id (iid) and external id (eid).
-				TMatePairElement matePairEl;
-				TId _id = 0;
-				String<char> fieldIdentifier;
-				String<char> eid;
-                CharString buffer;
-				bool foundRds = false;
-				while (!atEnd(reader) && value(reader) != '}')
+                bool foundRds = false;
+                TMatePairElement matePairEl;
+                while (!atEnd(reader) && value(reader) != '}')
                 {
-					clear(fieldIdentifier);
-                    if (readAlphaNums(fieldIdentifier, reader) != 0)
-                        return 1;
-					if (fieldIdentifier == "iid")
-                    {
-                        goNext(reader);
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(_id, buffer))
-                            return 1;
-					}
+                    // read "KEY:VALUE" pair
+                    readAmosKeyValue(fieldIdentifier, buffer, reader);
+
+                    if (fieldIdentifier == "iid")
+                        _id = lexicalCast<TId>(buffer);
                     else if (fieldIdentifier == "eid")
-                    {
-                        goNext(reader);
-                        if (readUntilOneOf(eid, reader, '\n', '\r') != 0)
-                            return 1;
-					}
+                        eid = buffer;
                     else if (fieldIdentifier == "lib")
-                    {
-                        goNext(reader);
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(matePairEl.libId, buffer))
-                            return 1;
-					}
+                        matePairEl.libId = lexicalCast<TId>(buffer);
                     else if (fieldIdentifier == "rds")
                     {
-                        goNext(reader);
-						foundRds = true;
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(matePairEl.readId[0], buffer))
-                            return 1;
-                        goNext(reader);
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(matePairEl.readId[1], buffer))
-                            return 1;
-
-						// Store mapping to pair match id.
-						readToPairMatchId[matePairEl.readId[0]] = nextPairMatchId;
-						readToPairMatchId[matePairEl.readId[1]] = nextPairMatchId;
-						nextPairMatchId += 1;
+                        foundRds = true;
+                        size_t comma = findFirst(buffer, EqualsChar<','>());
+                        matePairEl.readId[0] = lexicalCast<TId>(prefix(buffer, comma));
+                        matePairEl.readId[1] = lexicalCast<TId>(suffix(buffer, comma + 1));
+
+                        // Store mapping to pair match id.
+                        readToPairMatchId[matePairEl.readId[0]] = nextPairMatchId;
+                        readToPairMatchId[matePairEl.readId[1]] = nextPairMatchId;
+                        nextPairMatchId++;
                     }
                     // Always skip over the remainder of the line.
-                    if (skipLine(reader) != 0)
-                        return 1;
-				}
+                    skipUntil(reader, NotFunctor<IsWhitespace>());
+                }
+                skipOne(reader, EqualsChar<'}'>());
 
-                // Skip '}'.
-                if (!atEnd(reader))
+                // Only insert valid mate pairs
+                if (foundRds)
                 {
-                    SEQAN_ASSERT_EQ(value(reader), '}');
-                    goNext(reader);
+                    frgIdMap.insert(std::make_pair(_id, length(fragStore.matePairStore)));
+                    appendValue(fragStore.matePairStore, matePairEl, Generous());
+                    appendValue(fragStore.matePairNameStore, eid, Generous());
                 }
-
-				// Only insert valid mate pairs
-				if (foundRds) {
-					frgIdMap.insert(std::make_pair(_id, length(fragStore.matePairStore)));
-					appendValue(fragStore.matePairStore, matePairEl, Generous() );
-					appendValue(fragStore.matePairNameStore, eid, Generous() );
-				}
-			}
-            else if (blockIdentifier == "RED")  // Read block.
+            }
+            // Read block
+            else if (blockIdentifier == "RED")
             {
-				TId _id = 0;
-				String<char> fieldIdentifier;
-				String<char> eid;
-				String<char> qual;
-                CharString buffer;
-				// If matePairId is not updated, this yields to a singleton read below.
-				TId matePairId = TReadStoreElement::INVALID_ID;
-				TReadSeq seq;
+                // If matePairId is not updated, this yields to a singleton read below.
+                clear(readSeq);
+                clear(qual);
+                TId matePairId = TReadStoreElement::INVALID_ID;
                 while (!atEnd(reader) && value(reader) != '}')
                 {
-					clear(fieldIdentifier);
-                    if (readAlphaNums(fieldIdentifier, reader) != 0)
-                        return 1;
-					if (fieldIdentifier == "iid")
-                    {
-                        goNext(reader);
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(_id, buffer))
-                            return 1;
-					}
+                    // read "KEY:VALUE" pair
+                    readAmosKeyValue(fieldIdentifier, buffer, reader);
+
+                    if (fieldIdentifier == "iid")
+                        _id = lexicalCast<TId>(buffer);
                     else if (fieldIdentifier == "eid")
-                    {
-                        goNext(reader);
-                        if (readUntilOneOf(eid, reader, '\n', '\r') != 0)
-                            return 1;
-					}
+                        eid = buffer;
                     else if (fieldIdentifier == "frg")
-                    {
-                        goNext(reader);
-                        clear(buffer);
-                        if (readDigits(buffer, reader) != 0)
-                            return 1;
-                        if (!lexicalCast2(matePairId, buffer))
-                            return 1;
-                    }
+                        matePairId = lexicalCast<TId>(buffer);
                     else if (fieldIdentifier == "seq")
                     {
-                        goNext(reader);
-                        clear(seq);
-                        if (skipWhitespaces(reader) != 0)
-                            return 1;
-                        while (!atEnd(reader) && value(reader) != '.')
-                        {
-                            if (readLetters(seq, reader) != 0)
-                                return 1;
-                            if (skipWhitespaces(reader) != 0)
-                                return 1;
-                        }
-                        // Skip '.'.
-                        if (!atEnd(reader))
-                        {
-                            SEQAN_ASSERT_EQ(value(reader), '.');
-                            goNext(reader);
-                        }
+                        readUntil(readSeq, reader, EqualsChar<'.'>(), IsWhitespace());
+                        skipOne(reader, EqualsChar<'.'>());
                     }
                     else if (fieldIdentifier == "qlt")
                     {
                         // TODO(holtgrew): Problematic if . part of qualities, need to count chars.
-                        goNext(reader);
-                        clear(qual);
-                        for (; !atEnd(reader) && value(reader) != '.'; goNext(reader))
-                            if (isgraph(value(reader)))
-                                appendValue(qual, value(reader));
+                        readUntil(qual, reader, EqualsChar<'.'>(), IsWhitespace());
+                        skipOne(reader, EqualsChar<'.'>());
                     }
                     // Always skip over the remainder of the line.
-                    if (skipLine(reader) != 0)
-                        return 1;
-				}
-				// Set quality
-				assignQualities(seq, qual);
-
-                // Skip '}'.
-                if (!atEnd(reader))
-                {
-                    SEQAN_ASSERT_EQ(value(reader), '}');
-                    goNext(reader);
+                    skipUntil(reader, NotFunctor<IsWhitespace>());
                 }
-
-				// Insert the read
-				readIdMap.insert(std::make_pair(_id, length(fragStore.readStore)));
-				appendRead(fragStore, seq, matePairId);
-				appendValue(fragStore.readNameStore, eid, Generous() );
-			}
-            else if (blockIdentifier == "CTG")  // Contig block
+                // Set quality
+                assignQualities(readSeq, qual);
+                skipOne(reader, EqualsChar<'}'>());
+
+                // Insert the read
+                readIdMap.insert(std::make_pair(_id, length(fragStore.readStore)));
+                appendRead(fragStore, readSeq, matePairId);
+                appendValue(fragStore.readNameStore, eid, Generous());
+            }
+            // Contig block
+            else if (blockIdentifier == "CTG")
             {
-				TContigElement contigEl;
-				TSize fromAligned = length(fragStore.alignedReadStore);
-				// TId _id = 0;
-				String<char> fieldIdentifier;
-				String<char> eid;
-				String<char> contigSeq;
-				String<char> contigQual;
-                String<char> buffer;
-				while (!atEnd(reader) && value(reader) != '}')
+                clear(contigSeq);
+                clear(qual);
+                TContigElement contigEl;
+                TSize fromAligned = length(fragStore.alignedReadStore);
+                while (!atEnd(reader) && value(reader) != '}')
                 {
-					// Are we entering a TLE block
-					if (value(reader) == '{')
+                    // Are we entering a TLE block
+                    if (value(reader) == '{')
                     {
-                        goNext(reader);
-						TAlignedElement alignEl;
-						String<char> fdIdentifier;
-						typedef typename TFragmentStore::TContigPos TContigPos;
-						TContigPos offsetPos = 0;
-						TContigPos clr1 = 0;
-						TContigPos clr2 = 0;
-						String<TContigPos> gaps;
-						while (!atEnd(reader) && value(reader) != '}')
+                        // skip "{TLE\n"
+                        skipOne(reader, EqualsChar<'{'>());
+                        skipOne(reader, EqualsChar<'T'>());
+                        skipOne(reader, EqualsChar<'L'>());
+                        skipOne(reader, EqualsChar<'E'>());
+                        skipUntil(reader, NotFunctor<IsWhitespace>());
+
+                        TAlignedElement alignEl;
+                        typedef typename TFragmentStore::TContigPos TContigPos;
+                        TContigPos offsetPos = 0;
+                        TContigPos clr1 = 0;
+                        TContigPos clr2 = 0;
+                        String<TContigPos> gaps;
+                        while (!atEnd(reader) && value(reader) != '}')
                         {
-							clear(fdIdentifier);
-                            if (readAlphaNums(fdIdentifier, reader) != 0)
-                                return 1;
-							if (fdIdentifier == "src")
+                            // read "KEY:VALUE" pair
+                            readAmosKeyValue(fieldIdentifier, buffer, reader);
+
+                            if (fieldIdentifier == "src")
+                                alignEl.readId = lexicalCast<TId>(buffer);
+                            else if (fieldIdentifier == "off")
                             {
-                                goNext(reader);
-                                clear(buffer);
-                                if (readDigits(buffer, reader) != 0)
-                                    return 1;
-                                if (!lexicalCast2(alignEl.readId, buffer))
-                                    return 1;
-							} else if (fdIdentifier == "off") {
-                                goNext(reader);
-                                if (atEnd(reader))
-                                    return 1;
-                                if (value(reader) == '-')
-                                {
-                                    offsetPos = 0;
-                                }
+                                if (buffer != "-")
+                                    offsetPos = lexicalCast<TContigPos>(buffer);
                                 else
-                                {
-                                    clear(buffer);
-                                    if (readDigits(buffer, reader) != 0)
-                                        return 1;
-                                    if (!lexicalCast2(offsetPos, buffer))
-                                        return 1;
-                                }
-							}
-                            else if (fdIdentifier == "clr")
+                                    offsetPos = 0;
+                            }
+                            else if (fieldIdentifier == "clr")
                             {
-                                goNext(reader);
-                                clear(buffer);
-                                if (readDigits(buffer, reader) != 0)
-                                    return 1;
-                                if (!lexicalCast2(clr1, buffer))
-                                    return 1;
-                                goNext(reader);
-                                clear(buffer);
-                                if (readDigits(buffer, reader) != 0)
-                                    return 1;
-                                if (!lexicalCast2(clr2, buffer))
-                                    return 1;
-							}
-                            else if (fdIdentifier == "gap")
+                                size_t comma = findFirst(buffer, EqualsChar<','>());
+                                clr1 = lexicalCast<TContigPos>(prefix(buffer, comma));
+                                clr2 = lexicalCast<TContigPos>(suffix(buffer, comma + 1));
+                            }
+                            else if (fieldIdentifier == "gap")
                             {
-                                goNext(reader);
-                                if (skipWhitespaces(reader) != 0)
-                                    return 1;
-                                for (; !atEnd(reader) && value(reader) != '.'; goNext(reader))
+                                skipUntil(reader, NotFunctor<IsWhitespace>());
+                                while (!atEnd(reader) && value(reader) != '.')
                                 {
-                                    if (!isspace(value(reader)))
-                                    {
-                                        clear(buffer);
-                                        if (readDigits(buffer, reader) != 0)
-                                            return 1;
-                                        TSize nextGap;
-                                        if (!lexicalCast2(nextGap, buffer))
-                                            return 1;
-										appendValue(gaps, nextGap);
-                                    }
-                                }
-
-                                // Skip '.'.
-                                if (!atEnd(reader))
-                                {
-                                    SEQAN_ASSERT_EQ(value(reader), '.');
-                                    goNext(reader);
+                                    clear(buffer);
+                                    readUntil(buffer, reader, IsWhitespace());
+                                    appendValue(gaps, lexicalCast<TContigPos>(buffer));
+                                    skipUntil(reader, NotFunctor<IsWhitespace>());
                                 }
-							}
+                                skipOne(reader, EqualsChar<'.'>());
+                            }
                             // Always skip over the remainder of the line.
-                            if (skipLine(reader) != 0)
-                                return 1;
-						}
-                        if (!atEnd(reader) && skipLine(reader) != 0)
-                            return 1;
-
-						// Get the length of the read
-						TId readId = (readIdMap.find(alignEl.readId))->second;
-						TSize lenRead = length(value(fragStore.readSeqStore, readId));
-
-						// Create the gap anchors
-						typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
-						int offset = 0;
-						if ((clr1 < clr2) && (clr1>0)) offset = clr1;
-						else if ((clr1 > clr2) && (clr1 < static_cast<TContigPos>(lenRead))) offset = lenRead - clr1;
-						int diff = -1 * (int) (offset);
-						// Clipped begin
-						if (offset != 0) appendValue(alignEl.gaps, TContigGapAnchor(offset, 0), Generous() );
-						// Internal gaps
-						typedef typename Iterator<String<TContigPos>, Standard>::Type TPosIter;
-						TPosIter posIt = begin(gaps, Standard());
-						TPosIter posItEnd = end(gaps, Standard());
-						TContigPos lastGap = 0;
-						TSize gapLen = 0;
-						TSize totalGapLen = 0;
-						for(;posIt!=posItEnd; goNext(posIt)) {
-							if (gapLen == 0) {
-								++gapLen; ++totalGapLen;
-								++diff;
-								lastGap = value(posIt);
-							}
-							else if (lastGap == value(posIt)) {
-								++gapLen; ++totalGapLen;
-								++diff;
-							}
-							else {
-								appendValue(alignEl.gaps, TContigGapAnchor(offset + lastGap, offset + lastGap + diff), Generous() );
-								gapLen = 1; ++totalGapLen;
-								lastGap = value(posIt);
-								++diff;
-							}
-						}
-						if (gapLen > 0) appendValue(alignEl.gaps, TContigGapAnchor(offset + lastGap, offset + lastGap + diff), Generous() );
-						// Clipped end
-						if ((clr1 < clr2) && (clr2 < static_cast<TContigPos>(lenRead))) {
-							diff -= (lenRead - clr2);
-							appendValue(alignEl.gaps, TContigGapAnchor(lenRead, lenRead + diff), Generous() );
-						} else if ((clr1 > clr2) && (clr2 > 0)) {
-							diff -= clr2;
-							appendValue(alignEl.gaps, TContigGapAnchor(lenRead, lenRead + diff), Generous() );
-						}
-
-						// Set begin and end position
-						if (clr1 < clr2) {
-							alignEl.beginPos = offsetPos;
-							alignEl.endPos = offsetPos + totalGapLen + (clr2 - clr1);
-						} else {
-							alignEl.beginPos = offsetPos + totalGapLen + (clr1 - clr2);
-							alignEl.endPos = offsetPos;
-						}
-
-						// Append new align fragment, note: contigId must still be set
-						alignEl.id = length(fragStore.alignedReadStore);
-						appendValue(fragStore.alignedReadStore, alignEl, Generous() );
-					}
+                            skipUntil(reader, NotFunctor<IsWhitespace>());
+                        }
+                        skipOne(reader, EqualsChar<'}'>());
+                        skipUntil(reader, NotFunctor<IsWhitespace>());
+
+                        // Get the length of the read
+                        TId readId = (readIdMap.find(alignEl.readId))->second;
+                        TSize lenRead = length(value(fragStore.readSeqStore, readId));
+
+                        // Create the gap anchors
+                        typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
+                        int offset = 0;
+                        if ((clr1 < clr2) && (clr1>0)) offset = clr1;
+                        else if ((clr1 > clr2) && (clr1 < static_cast<TContigPos>(lenRead))) offset = lenRead - clr1;
+                        int diff = -1 * (int) (offset);
+                        // Clipped begin
+                        if (offset != 0) appendValue(alignEl.gaps, TContigGapAnchor(offset, 0), Generous());
+                        // Internal gaps
+                        typedef typename Iterator<String<TContigPos>, Standard>::Type TPosIter;
+                        TPosIter posIt = begin(gaps, Standard());
+                        TPosIter posItEnd = end(gaps, Standard());
+                        TContigPos lastGap = 0;
+                        TSize gapLen = 0;
+                        TSize totalGapLen = 0;
+                        for(;posIt!=posItEnd; goNext(posIt)) {
+                            if (gapLen == 0) {
+                                ++gapLen; ++totalGapLen;
+                                ++diff;
+                                lastGap = value(posIt);
+                            }
+                            else if (lastGap == value(posIt)) {
+                                ++gapLen; ++totalGapLen;
+                                ++diff;
+                            }
+                            else {
+                                appendValue(alignEl.gaps, TContigGapAnchor(offset + lastGap, offset + lastGap + diff), Generous());
+                                gapLen = 1; ++totalGapLen;
+                                lastGap = value(posIt);
+                                ++diff;
+                            }
+                        }
+                        if (gapLen > 0) appendValue(alignEl.gaps, TContigGapAnchor(offset + lastGap, offset + lastGap + diff), Generous());
+                        // Clipped end
+                        if ((clr1 < clr2) && (clr2 < static_cast<TContigPos>(lenRead))) {
+                            diff -= (lenRead - clr2);
+                            appendValue(alignEl.gaps, TContigGapAnchor(lenRead, lenRead + diff), Generous());
+                        } else if ((clr1 > clr2) && (clr2 > 0)) {
+                            diff -= clr2;
+                            appendValue(alignEl.gaps, TContigGapAnchor(lenRead, lenRead + diff), Generous());
+                        }
+
+                        // Set begin and end position
+                        if (clr1 < clr2) {
+                            alignEl.beginPos = offsetPos;
+                            alignEl.endPos = offsetPos + totalGapLen + (clr2 - clr1);
+                        } else {
+                            alignEl.beginPos = offsetPos + totalGapLen + (clr1 - clr2);
+                            alignEl.endPos = offsetPos;
+                        }
+
+                        // Append new align fragment, note: contigId must still be set
+                        alignEl.id = length(fragStore.alignedReadStore);
+                        appendValue(fragStore.alignedReadStore, alignEl, Generous());
+                    }
                     else
                     {
-                        // String<char> buffer;
-						clear(fieldIdentifier);
-                        if (readAlphaNums(fieldIdentifier, reader) != 0)
-                            return 1;
-						if (fieldIdentifier == "iid")
-                        {
-                            // goNext(reader);
-                            // clear(buffer);
-                            // if (readDigits(buffer, reader) != 0)
-                            //     return 1;
-                            // if (!lexicalCast2(_id, buffer))
-                            //     return 1;
-						}
+                        // read "KEY:VALUE" pair
+                        readAmosKeyValue(fieldIdentifier, buffer, reader);
+
+                        if (fieldIdentifier == "iid")
+                            _id = lexicalCast<TId>(buffer);
                         else if (fieldIdentifier == "eid")
-                        {
-                            goNext(reader);
-                            if (readUntilOneOf(eid, reader, '\n', '\r') != 0)
-                                return 1;
-						}
+                            eid = buffer;
                         else if (fieldIdentifier == "seq")
                         {
-                            goNext(reader);
-                            if (skipWhitespaces(reader) != 0)
-                                return 1;
-                            while (!atEnd(reader) && value(reader) != '.')
-                            {
-                                if (readLetters(contigSeq, reader) != 0)
-                                    return 1;
-                                if (skipWhitespaces(reader) != 0)
-                                    return 1;
-                            }
-                            // Skip '.'.
-                            if (!atEnd(reader))
-                            {
-                                SEQAN_ASSERT_EQ(value(reader), '.');
-                                goNext(reader);
-                            }
-						}
+                            readUntil(contigSeq, reader, EqualsChar<'.'>(), IsWhitespace());
+                            skipOne(reader, EqualsChar<'.'>());
+                        }
                         else if (fieldIdentifier == "qlt")
                         {
-                            goNext(reader);
                             // TODO(holtgrew): Problematic if . part of qualities, need to count chars.
-                            clear(contigQual);
-                            for (; !atEnd(reader) && value(reader) != '.'; goNext(reader))
-                                if (isgraph(value(reader)))
-                                    appendValue(contigQual, value(reader));
-						}
+                            readUntil(qual, reader, EqualsChar<'.'>(), IsWhitespace());
+                            skipOne(reader, EqualsChar<'.'>());
+                        }
                         // Always skip over the remainder of the line.
-                        if (skipLine(reader) != 0)
-                            return 1;
-					}
-				}
-
-				// Create the gap anchors
-				char gapChar = gapValue<char>();
-				typedef typename Iterator<String<char> >::Type TStringIter;
-				TStringIter seqIt = begin(contigSeq);
-				TStringIter seqItEnd = end(contigSeq);
-				TStringIter qualIt = begin(contigQual);
-				typedef typename TFragmentStore::TReadPos TPos;
-				typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
-				TPos ungappedPos = 0;
-				TPos gappedPos = 0;
-				bool gapOpen = false;
-				for(;seqIt != seqItEnd; goNext(seqIt), goNext(qualIt), ++gappedPos) {
-					if (value(seqIt) == gapChar)
+                        skipUntil(reader, NotFunctor<IsWhitespace>());
+                    }
+                }
+                // Set quality
+                skipOne(reader, EqualsChar<'}'>());
+
+                // Create the gap anchors
+                char gapChar = gapValue<char>();
+                typedef typename Iterator<CharString, Standard>::Type TStringIter;
+                TStringIter seqIt = begin(contigSeq, Standard());
+                TStringIter seqItEnd = end(contigSeq, Standard());
+                TStringIter qualIt = begin(qual, Standard());
+                typedef typename TFragmentStore::TReadPos TPos;
+                typedef typename TFragmentStore::TContigGapAnchor TContigGapAnchor;
+                TPos ungappedPos = 0;
+                TPos gappedPos = 0;
+                bool gapOpen = false;
+                for (; seqIt != seqItEnd; goNext(seqIt), goNext(qualIt), ++gappedPos)
+                {
+                    if (value(seqIt) == gapChar)
+                    {
+                        gapOpen = true;
+                    }
+                    else
                     {
-					    gapOpen = true;
+                        if (gapOpen)
+                        {
+                            appendValue(contigEl.gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
+                            gapOpen = false;
+                        }
+                        typename Value<TContigSeq>::Type letter = getValue(seqIt);
+                        assignQualityValue(letter, getValue(qualIt));
+                        appendValue(contigEl.seq, letter, Generous());
+                        ++ungappedPos;
                     }
-					else
-					{
-						if (gapOpen)
-						{
-							appendValue(contigEl.gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous() );
-							gapOpen = false;
-						}
-						Dna5Q letter = value(seqIt);
-						assignQualityValue(letter, value(qualIt));
-						appendValue(contigEl.seq, letter, Generous() );
-						++ungappedPos;
-					}
-				}
-				if (gapOpen)
-				    appendValue(contigEl.gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous() );
-
-				// Set the contigId in all aligned reads
-				TSize toAligned = length(fragStore.alignedReadStore);
-				TId newContigId = length(fragStore.contigStore);
-				for (; fromAligned < toAligned; ++fromAligned)
-					fragStore.alignedReadStore[fromAligned].contigId = newContigId;
-
-				// Insert the contig
-				appendValue(fragStore.contigStore, contigEl, Generous() );
-				appendValue(fragStore.contigNameStore, eid, Generous() );
-			} else {
-                if (skipLine(reader) != 0)
-                    return 1;
-			}
-		} else {
-            if (skipLine(reader) != 0)
-                return 1;
-		}
-	}
-
-	// Renumber all ids
-	typedef typename TIdMap::const_iterator TIdMapIter;
-	typedef typename Iterator<typename TFragmentStore::TMatePairStore>::Type TMateIter;
-	TMateIter mateIt = begin(fragStore.matePairStore);
-	TMateIter mateItEnd = end(fragStore.matePairStore);
-	for(;mateIt != mateItEnd; goNext(mateIt)) {
-		if (mateIt->libId != TMatePairElement::INVALID_ID) {
-			TIdMapIter libIdPos = libIdMap.find(mateIt->libId);
-			if (libIdPos != libIdMap.end())
-			    mateIt->libId = libIdPos->second;
-			else
-			    mateIt->libId = TMatePairElement::INVALID_ID;
-		}
-		if (mateIt->readId[0] != TMatePairElement::INVALID_ID) {
-			TIdMapIter readIdPos = readIdMap.find(mateIt->readId[0]);
-			if (readIdPos != readIdMap.end())
-			    mateIt->readId[0] = readIdPos->second;
-			else
-			    mateIt->readId[0] = TMatePairElement::INVALID_ID;
-		}
-		if (mateIt->readId[1]!= TMatePairElement::INVALID_ID) {
-			TIdMapIter readIdPos = readIdMap.find(mateIt->readId[1]);
-			if (readIdPos != readIdMap.end())
-			    mateIt->readId[1] = readIdPos->second;
-			else
-			    mateIt->readId[0] = TMatePairElement::INVALID_ID;
-		}
-	}
-
-	// Copy data from frgIdMap into the matePairId members of the readStore.
-	typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter;
-	TReadIter readIt = begin(fragStore.readStore);
-	TReadIter readItEnd = end(fragStore.readStore);
-	for (;readIt != readItEnd; goNext(readIt))
-	{
-		if (readIt->matePairId != TReadStoreElement::INVALID_ID)
-		{
-			TIdMapIter mateIdPos = frgIdMap.find(readIt->matePairId);
-			if (mateIdPos != frgIdMap.end())
-			    readIt->matePairId = mateIdPos->second;
-			else
-			    readIt->matePairId = TReadStoreElement::INVALID_ID;
-		}
-	}
-
-	// Copy data from readIdMap into the pairMatchId entries of the alignedReadStore.
-	typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
-	TAlignIter alignIt = begin(fragStore.alignedReadStore);
-	TAlignIter alignItEnd = end(fragStore.alignedReadStore);
-	for (;alignIt != alignItEnd; goNext(alignIt))
-	{
-		if (alignIt->readId != TAlignedElement::INVALID_ID)
-		{
-			TIdMapIter readIdPos = readIdMap.find(alignIt->readId);
-			if (readIdPos != readIdMap.end())
+                }
+                if (gapOpen)
+                    appendValue(contigEl.gaps, TContigGapAnchor(ungappedPos, gappedPos), Generous());
+
+                // Set the contigId in all aligned reads
+                TSize toAligned = length(fragStore.alignedReadStore);
+                TId newContigId = length(fragStore.contigStore);
+                for (; fromAligned < toAligned; ++fromAligned)
+                    fragStore.alignedReadStore[fromAligned].contigId = newContigId;
+
+                // Insert the contig
+                appendValue(fragStore.contigStore, contigEl, Generous());
+                appendValue(fragStore.contigNameStore, eid, Generous());
+            }
+            // Unknown block identifier
+            else
+            {
+                // skip until closing bracket
+                while (!atEnd(reader) && value(reader) != '}')
+                    skipLine(reader);
+            }
+        }
+        else
+        {
+            // not a block - skip line
+            skipLine(reader);
+        }
+    }
+
+    // Renumber all ids
+    typedef typename TIdMap::const_iterator TIdMapIter;
+    typedef typename Iterator<typename TFragmentStore::TMatePairStore>::Type TMateIter;
+    TMateIter mateIt = begin(fragStore.matePairStore);
+    TMateIter mateItEnd = end(fragStore.matePairStore);
+    for(;mateIt != mateItEnd; goNext(mateIt)) {
+        if (mateIt->libId != TMatePairElement::INVALID_ID) {
+            TIdMapIter libIdPos = libIdMap.find(mateIt->libId);
+            if (libIdPos != libIdMap.end())
+                mateIt->libId = libIdPos->second;
+            else
+                mateIt->libId = TMatePairElement::INVALID_ID;
+        }
+        if (mateIt->readId[0] != TMatePairElement::INVALID_ID) {
+            TIdMapIter readIdPos = readIdMap.find(mateIt->readId[0]);
+            if (readIdPos != readIdMap.end())
+                mateIt->readId[0] = readIdPos->second;
+            else
+                mateIt->readId[0] = TMatePairElement::INVALID_ID;
+        }
+        if (mateIt->readId[1]!= TMatePairElement::INVALID_ID) {
+            TIdMapIter readIdPos = readIdMap.find(mateIt->readId[1]);
+            if (readIdPos != readIdMap.end())
+                mateIt->readId[1] = readIdPos->second;
+            else
+                mateIt->readId[0] = TMatePairElement::INVALID_ID;
+        }
+    }
+
+    // Copy data from frgIdMap into the matePairId members of the readStore.
+    typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter;
+    TReadIter readIt = begin(fragStore.readStore);
+    TReadIter readItEnd = end(fragStore.readStore);
+    for (;readIt != readItEnd; goNext(readIt))
+    {
+        if (readIt->matePairId != TReadStoreElement::INVALID_ID)
+        {
+            TIdMapIter mateIdPos = frgIdMap.find(readIt->matePairId);
+            if (mateIdPos != frgIdMap.end())
+                readIt->matePairId = mateIdPos->second;
+            else
+                readIt->matePairId = TReadStoreElement::INVALID_ID;
+        }
+    }
+
+    // Copy data from readIdMap into the pairMatchId entries of the alignedReadStore.
+    typedef typename Iterator<typename TFragmentStore::TAlignedReadStore>::Type TAlignIter;
+    TAlignIter alignIt = begin(fragStore.alignedReadStore);
+    TAlignIter alignItEnd = end(fragStore.alignedReadStore);
+    for (;alignIt != alignItEnd; goNext(alignIt))
+    {
+        if (alignIt->readId != TAlignedElement::INVALID_ID)
+        {
+            TIdMapIter readIdPos = readIdMap.find(alignIt->readId);
+            if (readIdPos != readIdMap.end())
             {
                 //SEQAN_ASSERT(readToPairMatchId.find(alignIt->readId) != readToPairMatchId.end());
                 if (readToPairMatchId.find(alignIt->readId) != readToPairMatchId.end())
                     alignIt->pairMatchId = readToPairMatchId[alignIt->readId];
-			    alignIt->readId = readIdPos->second;
+                alignIt->readId = readIdPos->second;
             }
-			else
+            else
             {
-			    alignIt->readId = TAlignedElement::INVALID_ID;
+                alignIt->readId = TAlignedElement::INVALID_ID;
             }
-		}
-	}
+        }
+    }
 
     return 0;
 }
@@ -805,22 +626,11 @@ read(TFile & file,
  * @return int 0 in case of success, 1 in case of errors.
  */
 
-/**
-.Function.write
-..cat:Fragment Store
-..signature:int write(file, fragStore, tag)
-..param.fragStore:A fragment store.
-...type:Class.FragmentStore
-..param.tag.type:Tag.File Format.tag.Amos message file
-..returns:An $int$ with the status code. $0$ on success, non-$0$ on errors.
-..include:seqan/store.h
-*/
-
-template<typename TFile, typename TSpec, typename TConfig>
-inline int
-write(TFile & target,
-	  FragmentStore<TSpec, TConfig>& fragStore,
-	  Amos)
+template <typename TTarget, typename TSpec, typename TConfig>
+inline void
+write(TTarget & target,
+      FragmentStore<TSpec, TConfig> & fragStore,
+      Amos)
 {
     // Basic types
     typedef FragmentStore<TSpec, TConfig> TFragmentStore;
@@ -835,95 +645,62 @@ write(TFile & target,
     typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement;
     //typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
 
+    typename DirectionIterator<TTarget, Output>::Type iter = directionIterator(target, Output());
+
     // Write Header
-    String<char> temp = "{UNV\niid:1\neid:seqan\ncom:\nafg file created with SeqAn\n.\n}\n";
-    if (streamWriteBlock(target, &temp[0], length(temp)) != length(temp))
-        return 1;
+    write(iter, "{UNV\niid:1\neid:seqan\ncom:\nafg file created with SeqAn\n.\n}\n");
 
     // Write Libraries
     typedef typename Iterator<typename TFragmentStore::TLibraryStore, Standard>::Type TLibIter;
     TLibIter libIt = begin(fragStore.libraryStore, Standard() );
     TLibIter libItEnd = end(fragStore.libraryStore, Standard() );
-    bool noNamesPresent = (length(fragStore.libraryNameStore) == 0);
-    for(TSize idCount = 0;libIt != libItEnd; goNext(libIt), ++idCount) {
-        if (streamWriteBlock(target,"{LIB\n", 5) != 5)
-            return 1;
-        if (streamWriteBlock(target,"iid:", 4) != 4)
-            return 1;
-        if (streamPut(target, idCount + 1))
-            return 1;
-        if (streamWriteChar(target, '\n'))
-            return 1;
-        if (!noNamesPresent) {
-            if (streamWriteBlock(target,"eid:", 4) != 4)
-                return 1;
-            if (streamWriteBlock(target, &value(fragStore.libraryNameStore, idCount)[0], length(value(fragStore.libraryNameStore, idCount))) != length(value(fragStore.libraryNameStore, idCount)))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
+    for(TSize idCount = 0;libIt != libItEnd; goNext(libIt), ++idCount)
+    {
+        write(iter, "{LIB\niid:");
+        appendNumber(iter, idCount + 1);
+        writeValue(iter, '\n');
+        if (!empty(fragStore.libraryNameStore) && !empty(fragStore.libraryNameStore[idCount]))
+        {
+            write(iter, "eid:");
+            write(iter, fragStore.libraryNameStore[idCount]);
+            writeValue(iter, '\n');
         }
-        if (streamWriteBlock(target,"{DST\n", 5u) != 5u)
-            return 1;
-        if (streamWriteBlock(target,"mea:", 4u) != 4u)
-            return 1;
-        if (streamPut(target, libIt->mean))
-            return 1;
-        if (streamWriteChar(target, '\n'))
-            return 1;
-        if (streamWriteBlock(target,"std:", 4u) != 4u)
-            return 1;
-        if (streamPut(target, libIt->std))
-            return 1;
-        if (streamWriteChar(target, '\n'))
-            return 1;
-        if (streamWriteBlock(target,"}\n", 2u) != 2u)
-            return 1;
-        if (streamWriteBlock(target,"}\n", 2u) != 2u)
-            return 1;
+        write(iter, "{DST\nmea:");
+        appendNumber(iter, libIt->mean);
+        writeValue(iter, '\n');
+        write(iter, "std:");
+        appendNumber(iter, libIt->std);
+        writeValue(iter, '\n');
+        write(iter, "}\n}\n");
     }
 
     // Write Fragments / mate pairs
     typedef typename Iterator<typename TFragmentStore::TMatePairStore, Standard>::Type TMateIter;
     TMateIter mateIt = begin(fragStore.matePairStore, Standard() );
     TMateIter mateItEnd = end(fragStore.matePairStore, Standard() );
-    noNamesPresent = (length(fragStore.matePairNameStore) == 0);
-    for(TSize idCount = 0;mateIt != mateItEnd; goNext(mateIt), ++idCount) {
-        if (streamWriteBlock(target,"{FRG\n", 5u) != 5u)
-            return 1;
-        if (streamWriteBlock(target,"iid:", 4u) != 4u)
-            return 1;
-        if (streamPut(target, idCount + 1))
-            return 1;
-        if (streamWriteChar(target, '\n'))
-            return 1;
-        if (!noNamesPresent) {
-            if (streamWriteBlock(target,"eid:", 4u) != 4u)
-                return 1;
-            if (streamWriteBlock(target, &value(fragStore.matePairNameStore, idCount)[0], length(value(fragStore.matePairNameStore, idCount))) != length(value(fragStore.matePairNameStore, idCount)))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
+    for(TSize idCount = 0;mateIt != mateItEnd; goNext(mateIt), ++idCount)
+    {
+        write(iter, "{FRG\niid:");
+        appendNumber(iter, idCount + 1);
+        writeValue(iter, '\n');
+        if (!empty(fragStore.matePairNameStore) && !empty(fragStore.matePairNameStore[idCount]))
+        {
+            write(iter, "eid:");
+            write(iter, fragStore.matePairNameStore[idCount]);
+            writeValue(iter, '\n');
         }
-        if (streamWriteBlock(target,"lib:", 4u) != 4u)
-            return 1;
-        if (streamPut(target, mateIt->libId + 1))
-            return 1;
-        if (streamWriteChar(target, '\n'))
-            return 1;
-        if ((mateIt->readId[0] != TMatePairElement::INVALID_ID) && (mateIt->readId[1] != TMatePairElement::INVALID_ID)) {
-            if (streamWriteBlock(target,"rds:", 4u) != 4u)
-                return 1;
-            if (streamPut(target, mateIt->readId[0] + 1))
-                return 1;
-            if (streamWriteChar(target, ','))
-                return 1;
-            if (streamPut(target, mateIt->readId[1] + 1))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
+        write(iter, "lib:");
+        appendNumber(iter, mateIt->libId + 1);
+        writeValue(iter, '\n');
+        if (mateIt->readId[0] != TMatePairElement::INVALID_ID && mateIt->readId[1] != TMatePairElement::INVALID_ID)
+        {
+            write(iter, "rds:");
+            appendNumber(iter, mateIt->readId[0] + 1);
+            writeValue(iter, ',');
+            appendNumber(iter, mateIt->readId[1] + 1);
+            writeValue(iter, '\n');
         }
-        if (streamWriteBlock(target,"}\n", 2u) != 2u)
-            return 1;
+        write(iter, "}\n");
     }
 
     // Get clear ranges
@@ -933,87 +710,56 @@ write(TFile & target,
     typedef typename Iterator<typename TFragmentStore::TAlignedReadStore, Standard>::Type TAlignIter;
     TAlignIter alignIt = begin(fragStore.alignedReadStore, Standard() );
     TAlignIter alignItEnd = end(fragStore.alignedReadStore, Standard() );
-    for(;alignIt != alignItEnd; goNext(alignIt)) {
+    for(;alignIt != alignItEnd; goNext(alignIt))
+    {
         typename TFragmentStore::TReadPos begClr = 0;
         typename TFragmentStore::TReadPos endClr = 0;
         getClrRange(fragStore, value(alignIt), begClr, endClr);
-        value(clrRange, alignIt->readId) = TClrRange(begClr, endClr);
+        clrRange[alignIt->readId] = TClrRange(begClr, endClr);
     }
 
     // Write reads
     typedef typename Iterator<typename TFragmentStore::TReadStore, Standard>::Type TReadIter;
     TReadIter readIt = begin(fragStore.readStore, Standard() );
     TReadIter readItEnd = end(fragStore.readStore, Standard() );
-    noNamesPresent = (length(fragStore.readNameStore) == 0);
-    for(TSize idCount = 0;readIt != readItEnd; ++readIt, ++idCount) {
+    for(TSize idCount = 0;readIt != readItEnd; ++readIt, ++idCount)
+    {
         // Skip reads without a name.
         if (length(value(fragStore.readNameStore, idCount)) == 0u)
             continue;
-        if (streamWriteBlock(target,"{RED\n", 5u) != 5u)
-            return 1;
-        if (streamWriteBlock(target,"iid:", 4u) != 4u)
-            return 1;
-        if (streamPut(target, idCount + 1))
-            return 1;
-        if (streamWriteChar(target, '\n'))
-            return 1;
-        if (!noNamesPresent) {
-            if (streamWriteBlock(target,"eid:", 4u) != 4u)
-                return 1;
-            if (streamWriteBlock(target, &value(fragStore.readNameStore, idCount)[0], length(value(fragStore.readNameStore, idCount))) != length(value(fragStore.readNameStore, idCount)))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
-        }
-        if (streamWriteBlock(target,"seq:\n", 5u) != 5u)
-            return 1;
-        typedef typename Iterator<typename TFragmentStore::TReadSeq const>::Type TSeqIter;
-        TSeqIter seqIt = begin(value(fragStore.readSeqStore, idCount));
-        TSeqIter seqItEnd = end(value(fragStore.readSeqStore, idCount));
-        for(TSize k = 0;seqIt!=seqItEnd;goNext(seqIt), ++k) {
-            if ((k % 60 == 0) && (k != 0))
-                if (streamWriteChar(target, '\n'))
-                    return 1;
-            if (streamWriteChar(target, getValue(seqIt)))
-                    return 1;
-        }
-        if (streamWriteBlock(target, "\n.\n", 3u) != 3u)
-            return 1;
-        if (streamWriteBlock(target,"qlt:\n", 5u) != 5u)
-            return 1;
-        seqIt = begin(value(fragStore.readSeqStore, idCount));
-        for(TSize k = 0;seqIt!=seqItEnd;goNext(seqIt), ++k) {
-            if ((k % 60 == 0) && (k != 0))
-                streamWriteChar(target, '\n');
-            Ascii c = ' ';
-            convertQuality(c, getQualityValue(value(seqIt)));
-            if (streamPut(target, c))
-                return 1;
+        write(iter, "{RED\niid:");
+        appendNumber(iter, idCount + 1);
+        writeValue(iter, '\n');
+        if (!empty(fragStore.readNameStore) && !empty(fragStore.readNameStore[idCount]))
+        {
+            write(iter, "eid:");
+            write(iter, fragStore.readNameStore[idCount]);
+            writeValue(iter, '\n');
         }
-        if (streamWriteBlock(target, "\n.\n", 3u) != 3u)
-            return 1;
-        if (readIt->matePairId != TReadStoreElement::INVALID_ID) {
-            if (streamWriteBlock(target,"frg:", 4u) != 4u)
-                return 1;
-            if (streamPut(target, readIt->matePairId + 1))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
+        write(iter, "seq:\n");
+        writeWrappedString(iter, fragStore.readSeqStore[idCount], 60);
+        write(iter, ".\nqlt:\n");
+
+        typedef typename Value<typename TFragmentStore::TReadSeqStore>::Type TReadSeq;
+        typedef QualityExtractor<typename Value<TReadSeq>::Type> TQualityExtractor;
+        ModifiedString<TReadSeq const, ModView<TQualityExtractor> > quals(fragStore.readSeqStore[idCount]);
+        writeWrappedString(iter, quals, 60);
+        write(iter,  ".\n");
+        if (readIt->matePairId != TReadStoreElement::INVALID_ID)
+        {
+            write(iter, "frg:");
+            appendNumber(iter, readIt->matePairId + 1);
+            writeValue(iter, '\n');
         }
-        if ((value(clrRange, idCount)).i1 != (value(clrRange, idCount)).i2) {
-            if (streamWriteBlock(target,"clr:", 4u) != 4u)
-                return 1;
-            if (streamPut(target, (value(clrRange, idCount)).i1))
-                return 1;
-            if (streamWriteChar(target, ','))
-                return 1;
-            if (streamPut(target, (value(clrRange, idCount)).i2))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
+        if (clrRange[idCount].i1 != clrRange[idCount].i2)
+        {
+            write(iter, "clr:");
+            appendNumber(iter, clrRange[idCount].i1);
+            writeValue(iter, ',');
+            appendNumber(iter, clrRange[idCount].i2);
+            writeValue(iter, '\n');
         }
-        if (streamWriteBlock(target,"}\n", 2u) != 2u)
-            return 1;
+        write(iter, "}\n");
     }
 
     // Sort aligned reads according to contigId
@@ -1025,27 +771,19 @@ write(TFile & target,
     TContigIter contigItEnd = end(fragStore.contigStore, Standard() );
     alignIt = begin(fragStore.alignedReadStore);
     alignItEnd = end(fragStore.alignedReadStore);
-    noNamesPresent = (length(fragStore.contigNameStore) == 0);
-    for(TSize idCount = 0;contigIt != contigItEnd; goNext(contigIt), ++idCount) {
-        if (streamWriteBlock(target,"{CTG\n", 5u ) != 5u)
-            return 1;
-        if (streamWriteBlock(target,"iid:", 4u) != 4u)
-            return 1;
-        if (streamPut(target, idCount + 1))
-            return 1;
-        if (streamWriteChar(target, '\n'))
-            return 1;
-        if (!noNamesPresent) {
-            if (streamWriteBlock(target,"eid:", 4u) != 4u)
-                return 1;
-            if (streamWriteBlock(target, &value(fragStore.contigNameStore, idCount)[0], length(value(fragStore.contigNameStore, idCount))) != length(value(fragStore.contigNameStore, idCount)))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
+    for(TSize idCount = 0;contigIt != contigItEnd; goNext(contigIt), ++idCount)
+    {
+        write(iter, "{CTG\niid:");
+        appendNumber(iter, idCount + 1);
+        writeValue(iter, '\n');
+        if (!empty(fragStore.contigNameStore) && !empty(fragStore.contigNameStore[idCount]))
+        {
+            write(iter, "eid:");
+            write(iter, fragStore.contigNameStore[idCount]);
+            writeValue(iter, '\n');
         }
         String<char> qlt;
-        if (streamWriteBlock(target,"seq:\n", 5u) != 5u)
-            return 1;
+        write(iter, "seq:\n");
         typedef typename Iterator<typename TFragmentStore::TContigSeq>::Type TContigIter;
         TContigIter seqContigIt = begin(contigIt->seq);
         TContigIter seqContigItEnd = end(contigIt->seq);
@@ -1056,65 +794,52 @@ write(TFile & target,
         char gapChar = gapValue<char>();
         typename TFragmentStore::TContigPos mySeqPos = 0;
         TSize k = 0;
-        for(;itGaps != itGapsEnd; goNext(itGaps)) {
-            while (mySeqPos < itGaps->seqPos) {
+        for(;itGaps != itGapsEnd; goNext(itGaps))
+        {
+            while (mySeqPos < itGaps->seqPos)
+            {
+
                 if ((k % 60 == 0) && (k != 0))
-                    if (streamWriteChar(target, '\n'))
-                        return 1;
+                    writeValue(iter, '\n');
                 ++k;
-                if (streamWriteChar(target, value(seqContigIt)))
-                    return 1;
-                Ascii c = ' ';
+                writeValue(iter, value(seqContigIt));
+                char c = ' ';
                 convertQuality(c, getQualityValue(value(seqContigIt)));
-                appendValue(qlt, c, Generous() );
+                appendValue(qlt, c, Generous());
                 goNext(seqContigIt);++mySeqPos;
             }
-            for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i) {
+            for(int i = 0; i < ((int) itGaps->gapPos - (int) itGaps->seqPos) - diff; ++i)
+            {
                 if ((k % 60 == 0) && (k != 0))
-                    streamWriteChar(target, '\n');
+                    writeValue(iter, '\n');
                 ++k;
-                if (streamWriteChar(target, gapChar))
-                    return 1;
-                appendValue(qlt, '0', Generous() );
+                writeValue(iter, gapChar);
+                appendValue(qlt, '0', Generous());
             }
             diff = (itGaps->gapPos - itGaps->seqPos);
         }
-        for(;seqContigIt != seqContigItEnd; goNext(seqContigIt)) {
+        for(;seqContigIt != seqContigItEnd; goNext(seqContigIt))
+        {
             if ((k % 60 == 0) && (k != 0))
-                streamWriteChar(target, '\n');
+                writeValue(iter, '\n');
             ++k;
-            if (streamWriteChar(target, value(seqContigIt)))
-                return 1;
-            Ascii c = ' ';
+            writeValue(iter, value(seqContigIt));
+            char c = ' ';
             convertQuality(c, getQualityValue(value(seqContigIt)));
-            appendValue(qlt, c, Generous() );
+            appendValue(qlt, c, Generous());
         }
-        if (streamWriteBlock(target, "\n.\n", 3u ) != 3u)
-            return 1;
-        if (streamWriteBlock(target,"qlt:\n", 5u) != 5u)
-            return 1;
-        for(TSize k = 0;k<length(qlt); k+=60) {
-            TSize endK = k + 60;
-            if (endK > length(qlt))
-                endK = length(qlt);
-            if (streamWriteBlock(target, &infix(qlt, k, endK)[0], length(infix(qlt, k, endK))) != length(infix(qlt, k, endK)))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
-        }
-        if (streamWriteBlock(target, ".\n", 2u) != 2u)
-            return 1;
-
-        while ((alignIt != alignItEnd) && (idCount < alignIt->contigId)) goNext(alignIt);
-        for(;(alignIt != alignItEnd) && (idCount == alignIt->contigId); goNext(alignIt)) {
-            if (streamWriteBlock(target,"{TLE\n", 5u) != 5u)
-                return 1;
-            if (streamWriteBlock(target,"src:", 4u) != 4u)
-                return 1;
-            if (streamPut(target, alignIt->readId + 1))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
+        write(iter, "\n.\nqlt:\n");
+        writeWrappedString(iter, qlt, 60);
+        write(iter, ".\n");
+
+        while (alignIt != alignItEnd && idCount < alignIt->contigId)
+            goNext(alignIt);
+
+        for (; alignIt != alignItEnd && idCount == alignIt->contigId; goNext(alignIt))
+        {
+            write(iter, "{TLE\nsrc:");
+            appendNumber(iter, alignIt->readId + 1);
+            writeValue(iter, '\n');
             typedef typename Iterator<String<typename TFragmentStore::TReadGapAnchor> >::Type TReadGapsIter;
             TReadGapsIter itGaps = begin(alignIt->gaps);
             TReadGapsIter itGapsEnd = end(alignIt->gaps);
@@ -1124,67 +849,68 @@ write(TFile & target,
             TSize clr1 = 0;
             TSize clr2 = lenRead;
             // Create first clear range
-            if ((itGaps != itGapsEnd) && (itGaps->gapPos == 0)) clr1 = itGaps->seqPos;
+            if (itGaps != itGapsEnd && itGaps->gapPos == 0)
+                clr1 = itGaps->seqPos;
             int diff = clr1;
             String<unsigned int> gaps;
-            for(;itGaps != itGapsEnd; goNext(itGaps)) {
-                for(int i = 0; i< diff - ((int) itGaps->seqPos - (int) itGaps->gapPos); ++i) {
-                    appendValue(gaps, itGaps->seqPos - clr1, Generous() );
-                }
+            for (; itGaps != itGapsEnd; goNext(itGaps))
+            {
+                for (int i = 0; i + itGaps->seqPos < diff + itGaps->gapPos; ++i)
+                    appendValue(gaps, itGaps->seqPos - clr1, Generous());
                 // Clipped sequence
-                if (diff - ((int) itGaps->seqPos - (int) itGaps->gapPos) < 0) {
-                    clr2 = lenRead + diff - ((int) itGaps->seqPos - (int) itGaps->gapPos);
-                }
-                diff = ((int) itGaps->seqPos - (int) itGaps->gapPos);
+                if (diff + itGaps->gapPos < itGaps->seqPos)
+                    clr2 = lenRead + diff + itGaps->gapPos - itGaps->seqPos;
+                diff = (int)itGaps->seqPos - (int)itGaps->gapPos;
             }
-            if (alignIt->beginPos > alignIt->endPos) {
+            if (alignIt->beginPos > alignIt->endPos)
+            {
                 clr1 = lenRead - clr1;
                 clr2 = lenRead - clr2;
             }
-            if (streamWriteBlock(target,"off:", 4u) != 4u)
-                return 1;
-            if (alignIt->beginPos < alignIt->endPos)
+            write(iter, "off:");
+            appendNumber(iter, std::min(alignIt->beginPos, alignIt->endPos));
+            write(iter, "\nclr:");
+            appendNumber(iter, clr1);
+            writeValue(iter, ',');
+            appendNumber(iter, clr2);
+            writeValue(iter, '\n');
+            if (!empty(gaps))
             {
-                if (streamPut(target, alignIt->beginPos))
-                    return 1;
-            }
-            else
-            {
-                streamPut(target, alignIt->endPos);
-            }
-            if (streamWriteChar(target, '\n'))
-                return 1;
-            if (streamWriteBlock(target,"clr:", 4u) != 4u)
-                return 1;
-            if (streamPut(target, clr1))
-                return 1;
-            if (streamWriteChar(target, ','))
-                return 1;
-            if (streamPut(target, clr2))
-                return 1;
-            if (streamWriteChar(target, '\n'))
-                return 1;
-            if (length(gaps)) {
-                if (streamWriteBlock(target,"gap:\n", 5u) != 5u)
-                    return 1;
-                for(TSize z = 0;z<length(gaps); ++z) {
-                    if (streamPut(target, value(gaps, z)))
-                        return 1;
-                    if (streamWriteChar(target, '\n'))
-                        return 1;
+                write(iter, "gap:\n");
+                for (TSize z = 0; z < length(gaps); ++z)
+                {
+                    appendNumber(iter, gaps[z]);
+                    writeValue(iter, '\n');
                 }
-                if (streamWriteBlock(target, ".\n", 2u) != 2u)
-                    return 1;
+                write(iter, ".\n");
             }
-            if (streamWriteBlock(target,"}\n", 2u) != 2u)
-                return 1;
+            write(iter, "}\n");
         }
-        if (streamWriteBlock(target,"}\n", 2u) != 2u)
-            return 1;
+        write(iter, "}\n");
     }
-    return 0;
 }
 
+// ----------------------------------------------------------------------------
+// Function writeRecords()
+// ----------------------------------------------------------------------------
+
+
+/*!
+ * @fn FragmentStore#writeRecords
+ * @brief Write all records to a file.
+ *
+ * @signature void writeRecords(bamFileOut, store);
+ * @signature void writeRecords(gffFileOut, store);
+ * @signature void writeRecords(ucscFileIn, store);
+ *
+ * @param[in,out] bamFileOut  The @link BamFileOut @endlink object to write into.
+ * @param[in,out] gffFileOut  The @link GffFileOut @endlink object to write into.
+ * @param[in,out] ucscFileOut The @link UcscFileOut @endlink object to write into.
+ * @param[in]     store       The @link FragmentStore @endlink object.
+ *
+ * @throw IOError On low-level I/O errors.
+ */
+
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
@@ -1198,30 +924,39 @@ write(TFile & target,
  * @param[in]     tag   A tag for the sequence format.
  *
  * @return bool true on success, false on errors.
- */ 
-
-/**
-.Function.writeContigs
-..class:Class.FragmentStore
-..summary:Write contigs from fragment store into file.
-..cat:Fragment Store
-..signature:writeContigs(file, store, tag)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.file:A file/stream.
-..param.tag:Specify format to write, e.g. Fasta.
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/store.h
-*/
-template <typename TStream, typename TFSSpec, typename TFSConfig, typename TFormat>
-bool writeContigs(TStream & file, FragmentStore<TFSSpec, TFSConfig> & store, TFormat const &)
+ */
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig>
+bool writeContigs(FormattedFile<Fastq, Output, TSpec> & file, FragmentStore<TFSSpec, TFSConfig> & store)
 {
 //IOREV _doc_
-	for (unsigned i = 0; i < length(store.contigNameStore); ++i)
-		write(file, store.contigStore[i].seq, store.contigNameStore[i], TFormat());
-	return true;
+    for (unsigned i = 0; i < length(store.contigNameStore); ++i)
+        writeRecord(file, store.contigNameStore[i], store.contigStore[i].seq);
+    return true;
 }
 
+// ----------------------------------------------------------------------------
+// Function readRecords()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FragmentStore#readRecords
+ * @brief Read all records from a file.
+ *
+ * @signature void readRecords(store, bamFileIn[, importFlags]);
+ * @signature void readRecords(store, gffFileIn);
+ * @signature void readRecords(store, ucscFileIn);
+ *
+ * @param[in,out] store       The @link FragmentStore @endlink object to store the records into.
+ * @param[in,out] bamFileIn   The @link BamFileIn @endlink object to read from.
+ * @param[in,out] gffFileIn   The @link GffFileIn @endlink object to read from.
+ * @param[in,out] ucscFileIn  The @link UcscFileIn @endlink object to read from.
+ * @param[in]     importFlags The import flags.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
 //////////////////////////////////////////////////////////////////////////////
 
 /*!
@@ -1243,74 +978,51 @@ bool writeContigs(TStream & file, FragmentStore<TFSSpec, TFSConfig> & store, TFo
  * @return bool true in case of success and false in case of error.
  */
 
-/**
-.Function.loadContigs
-..class:Class.FragmentStore
-..summary:Loads contigs into fragment store.
-..cat:Fragment Store
-..signature:loadContigs(store, fileName[, loadSeqs])
-..signature:loadContigs(store, fileNameList[, loadSeqs])
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.fileName:A sequence file name.
-...type:Shortcut.CharString
-..param.fileNameList:A @Class.StringSet@ of sequence file names.
-...type:Class.StringSet
-..param.loadSeqs:If $true$, sequences are loaded immediately. 
-If $false$, an empty contig with a reference to the file is created. Its sequence can be loaded on-demand by @Function.lockContig@ or @Function.loadContig@.
-...default:$true$
-...type:nolink:bool
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/store.h
-*/
-
 template <typename TFSSpec, typename TFSConfig>
 bool loadContigs(FragmentStore<TFSSpec, TFSConfig> &store, StringSet<CharString> const &fileNameList, bool loadSeqs)
 {
 //IOREV _nodoc_ although there is dddoc, there is no entry in html-doc
-	typedef FragmentStore<TFSSpec, TFSConfig>			TFragmentStore;
-	typedef typename TFragmentStore::TContigStore		TContigStore;
-	typedef typename TFragmentStore::TContigFileStore	TContigFileStore;
-	typedef typename Value<TContigStore>::Type			TContig;
-	typedef typename Value<TContigFileStore>::Type		TContigFile;
-	
-	unsigned seqOfs = length(store.contigStore);
-	for (unsigned filecount = 0; filecount < length(fileNameList); ++filecount)
-	{
-		MultiSeqFile multiSeqFile;
-		if (!open(multiSeqFile.concat, toCString(fileNameList[filecount]), OPEN_RDONLY))
-			return false;
-
-		TContigFile contigFile;
-		guessFormat(multiSeqFile.concat, contigFile.format);		// guess file format
-		split(multiSeqFile, contigFile.format);						// divide into single sequences
-
-		contigFile.fileName = fileNameList[filecount];
-		contigFile.firstContigId = seqOfs;
-		appendValue(store.contigFileStore, contigFile, Generous());
-
-		unsigned seqCount = length(multiSeqFile);
-		resize(store.contigStore, seqOfs + seqCount, Generous());
-		resize(store.contigNameStore, seqOfs + seqCount, Generous());
-		for (unsigned i = 0; i < seqCount; ++i)
-		{
-			store.contigStore[seqOfs + i].usage = 0;
-			store.contigStore[seqOfs + i].fileBeginPos = beginPosition(multiSeqFile[i]);
-			store.contigStore[seqOfs + i].fileEndPos = endPosition(multiSeqFile[i]);
-			store.contigStore[seqOfs + i].fileId = length(store.contigFileStore) - 1;
-			if (loadSeqs)
-				assignSeq(store.contigStore[seqOfs + i].seq, multiSeqFile[i], contigFile.format);	// read Genome sequence
-			else
-            {
-                typename TContig::TContigSeq emptySeq;
-                swap(store.contigStore[seqOfs + i].seq, emptySeq);
-            }
-			assignCroppedSeqId(store.contigNameStore[seqOfs + i], multiSeqFile[i], contigFile.format);
-		}
-		seqOfs += seqCount;
-	}
-	reserve(store.contigStore, seqOfs, Exact());
-	return seqOfs > 0;
+    typedef FragmentStore<TFSSpec, TFSConfig>            TFragmentStore;
+    typedef typename TFragmentStore::TContigStore        TContigStore;
+    typedef typename TFragmentStore::TContigFileStore    TContigFileStore;
+    typedef typename Value<TContigStore>::Type            TContig;
+    typedef typename Value<TContigFileStore>::Type        TContigFile;
+
+    SeqFileIn seqFile;
+    CharString meta, seq;
+
+    for (unsigned f = 0; f < length(fileNameList); ++f)
+    {
+        if (!open(seqFile, toCString(fileNameList[f])))
+            return false;
+
+        TContigFile contigFile;
+        contigFile.fileName = fileNameList[f];
+        contigFile.firstContigId = length(store.contigStore);
+        appendValue(store.contigFileStore, contigFile, Generous());
+
+        while (!atEnd(seqFile))
+        {
+            resize(store.contigStore, length(store.contigStore) + 1, Generous());
+
+            TContig & contig = back(store.contigStore);
+            contig.usage = 0;
+            contig.fileId = length(store.contigFileStore) - 1;
+            contig.fileBeginPos = position(seqFile);
+
+            if (loadSeqs)
+                readRecord(meta, contig.seq, seqFile);
+            else
+                readRecord(meta, seq, seqFile);
+
+            contig.fileEndPos = position(seqFile);
+
+            cropAfterFirst(meta, IsWhitespace());
+            appendValue(store.contigNameStore, meta, Generous());
+        }
+        close(seqFile);
+    }
+    return true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1318,9 +1030,9 @@ bool loadContigs(FragmentStore<TFSSpec, TFSConfig> &store, StringSet<CharString>
 template <typename TFSSpec, typename TFSConfig>
 bool loadContigs(FragmentStore<TFSSpec, TFSConfig> &store, CharString const &fileName, bool loadSeqs)
 {
-	StringSet<CharString> fileNames;
-	appendValue(fileNames, fileName);
-	return loadContigs(store, fileNames, loadSeqs);
+    StringSet<CharString> fileNames;
+    appendValue(fileNames, fileName);
+    return loadContigs(store, fileNames, loadSeqs);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1328,7 +1040,7 @@ bool loadContigs(FragmentStore<TFSSpec, TFSConfig> &store, CharString const &fil
 template <typename TFSSpec, typename TFSConfig, typename TFileNames>
 bool loadContigs(FragmentStore<TFSSpec, TFSConfig> &store, TFileNames const &fileNames)
 {
-	return loadContigs(store, fileNames, true);
+    return loadContigs(store, fileNames, true);
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1345,38 +1057,28 @@ bool loadContigs(FragmentStore<TFSSpec, TFSConfig> &store, TFileNames const &fil
  * @return bool true on success, false on failure.
  */
 
-/**
-.Function.loadContig
-..class:Class.FragmentStore
-..summary:Manually loads a contig sequence.
-..cat:Fragment Store
-..signature:loadContig(store, contigId)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.contigId:Id of the contig which was created earlier by @Function.loadContigs@.
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TId>
 bool loadContig(FragmentStore<TSpec, TConfig> &store, TId _id)
 {
-	typedef FragmentStore<TSpec, TConfig>				TFragmentStore;
-	typedef typename TFragmentStore::TContigStore		TContigStore;
-	typedef typename TFragmentStore::TContigFileStore	TContigFileStore;
-	typedef typename Value<TContigStore>::Type			TContig;
-	typedef typename Value<TContigFileStore>::Type		TContigFile;
-
-	if ((TId)length(store.contigStore) <= _id) return false;
-	TContig &contig = store.contigStore[_id];
-
-	if (contig.fileId >= length(store.contigFileStore)) return false;
-	
-	TContigFile &contigFile = store.contigFileStore[contig.fileId];
-	String<char, MMap<> > fileString(toCString(contigFile.fileName), OPEN_RDONLY);
-	assignSeq(contig.seq, infix(fileString, contig.fileBeginPos, contig.fileEndPos), contigFile.format);			// read Read sequence
-
-	return true;
+    typedef FragmentStore<TSpec, TConfig>                TFragmentStore;
+    typedef typename TFragmentStore::TContigStore        TContigStore;
+    typedef typename TFragmentStore::TContigFileStore    TContigFileStore;
+    typedef typename Value<TContigStore>::Type            TContig;
+    typedef typename Value<TContigFileStore>::Type        TContigFile;
+
+    if ((TId)length(store.contigStore) <= _id) return false;
+    TContig &contig = store.contigStore[_id];
+
+    if (contig.fileId >= length(store.contigFileStore)) return false;
+
+    TContigFile &contigFile = store.contigFileStore[contig.fileId];
+    CharString meta;                                // dummy (seq name is already in the name store)
+
+    SeqFileIn seqFile(toCString(contigFile.fileName));
+    setPosition(seqFile, contig.fileBeginPos);
+    readRecord(meta, contig.seq, seqFile);            // read contig sequence
+
+    return true;
 }
 
 //////////////////////////////////////////////////////////////////////////////
@@ -1395,31 +1097,18 @@ bool loadContig(FragmentStore<TSpec, TConfig> &store, TId _id)
  * @return bool true on success, false on failure.
  */
 
-/**
-.Function.lockContig
-..summary:Locks a contig sequence from being removed.
-..cat:Fragment Store
-..signature:lockContig(store, contigId)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.contigId:Id of the contig which was created earlier by @Function.loadContigs@.
-..returns:A $bool$ which is $true$ on success.
-..remarks:This function increases the contig usage counter by 1 and ensures that the contig sequence is loaded.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TId>
 bool lockContig(FragmentStore<TSpec, TConfig> &store, TId _id)
 {
-	typedef FragmentStore<TSpec, TConfig>				TFragmentStore;
-	typedef typename TFragmentStore::TContigStore		TContigStore;
-	typedef typename Value<TContigStore>::Type			TContig;
+    typedef FragmentStore<TSpec, TConfig>                TFragmentStore;
+    typedef typename TFragmentStore::TContigStore        TContigStore;
+    typedef typename Value<TContigStore>::Type            TContig;
 
-	if ((TId)length(store.contigStore) <= _id) return false;
-	TContig &contig = store.contigStore[_id];
+    if ((TId)length(store.contigStore) <= _id) return false;
+    TContig &contig = store.contigStore[_id];
 
-	if (contig.usage++ > 0 || !empty(contig.seq)) return true;
-	return loadContig(store, _id);
+    if (contig.usage++ > 0 || !empty(contig.seq)) return true;
+    return loadContig(store, _id);
 }
 
 /*!
@@ -1436,25 +1125,12 @@ bool lockContig(FragmentStore<TSpec, TConfig> &store, TId _id)
  * @return bool true on success, false on failure.
  */
 
-/**
-.Function.unlockContig
-..summary:Removes a previous contig lock.
-..cat:Fragment Store
-..signature:unlockContig(store, contigId)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.contigId:Id of the contig which was created earlier by @Function.loadContigs@.
-..returns:A $bool$ which is $true$ on success.
-..remarks:This function decreases the contig usage counter by 1.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TId>
 bool unlockContig(FragmentStore<TSpec, TConfig> &store, TId _id)
 {
-	if ((TId)length(store.contigStore) <= _id) return false;
-	--store.contigStore[_id].usage;
-	return true;
+    if ((TId)length(store.contigStore) <= _id) return false;
+    --store.contigStore[_id].usage;
+    return true;
 }
 
 /*!
@@ -1471,36 +1147,23 @@ bool unlockContig(FragmentStore<TSpec, TConfig> &store, TId _id)
  * @return bool true on success, false on failure.
  */
 
-/**
-.Function.unlockAndFreeContig
-..summary:Removes a previous contig lock and clears sequence no further lock exist.
-..cat:Fragment Store
-..signature:unlockAndFreeContig(store, contigId)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.contigId:Id of the contig which was created earlier by @Function.loadContigs@.
-..returns:A $bool$ which is $true$ on success.
-..remarks:This function decreases contig usage counter by 1 and clears contig sequence if counter is 0.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig, typename TId>
 bool unlockAndFreeContig(FragmentStore<TSpec, TConfig> &store, TId _id)
 {
-	typedef FragmentStore<TSpec, TConfig>				TFragmentStore;
-	typedef typename TFragmentStore::TContigStore		TContigStore;
-	typedef typename Value<TContigStore>::Type			TContig;
+    typedef FragmentStore<TSpec, TConfig>                TFragmentStore;
+    typedef typename TFragmentStore::TContigStore        TContigStore;
+    typedef typename Value<TContigStore>::Type            TContig;
 
-	if ((TId)length(store.contigStore) <= _id) return false;
-	TContig &contig = store.contigStore[_id];
+    if ((TId)length(store.contigStore) <= _id) return false;
+    TContig &contig = store.contigStore[_id];
 
-	if (--contig.usage == 0 && contig.fileId < length(store.contigFileStore))
-	{
+    if (--contig.usage == 0 && contig.fileId < length(store.contigFileStore))
+    {
         typename TContig::TContigSeq emptySeq;
         swap(contig.seq, emptySeq);
-		return true;
-	}
-	return false;
+        return true;
+    }
+    return false;
 }
 
 /*!
@@ -1514,25 +1177,13 @@ bool unlockAndFreeContig(FragmentStore<TSpec, TConfig> &store, TId _id)
  * @return bool true in case of success, false in case of errors.
  */
 
-/**
-.Function.lockContigs
-..summary:Locks all contig sequences from being removed. 
-..cat:Fragment Store
-..signature:lockContigs(store)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..returns:A $bool$ which is $true$ on success.
-..remarks:Calls @Function.lockContig@ for all contigs.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig>
 bool lockContigs(FragmentStore<TSpec, TConfig> &store)
 {
-	bool result = true;
-	for (unsigned _id = 0; _id < length(store.contigStore); ++_id)
-		result &= lockContig(store, _id);
-	return result;
+    bool result = true;
+    for (unsigned _id = 0; _id < length(store.contigStore); ++_id)
+        result &= lockContig(store, _id);
+    return result;
 }
 
 /*!
@@ -1546,25 +1197,13 @@ bool lockContigs(FragmentStore<TSpec, TConfig> &store)
  * @return bool true in case of success, false in case of errors.
  */
 
-/**
-.Function.unlockContigs
-..summary:Removes a previous lock for all contigs.
-..cat:Fragment Store
-..signature:unlockContigs(store)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..returns:A $bool$ which is $true$ on success.
-..remarks:Calls @Function.unlockContig@ for all contigs.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig>
 bool unlockContigs(FragmentStore<TSpec, TConfig> &store)
 {
-	bool result = true;
-	for (unsigned _id = 0; _id < length(store.contigStore); ++_id)
-		result &= unlockContig(store, _id);
-	return result;
+    bool result = true;
+    for (unsigned _id = 0; _id < length(store.contigStore); ++_id)
+        result &= unlockContig(store, _id);
+    return result;
 }
 
 /*!
@@ -1578,25 +1217,13 @@ bool unlockContigs(FragmentStore<TSpec, TConfig> &store)
  * @return bool true in case of success, false in case of errors.
  */
 
-/**
-.Function.unlockAndFreeContigs
-..summary:Removes a previous lock for all contigs and clears sequences without lock.
-..cat:Fragment Store
-..signature:unlockAndFreeContigs(store)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..returns:A $bool$ which is $true$ on success.
-..remarks:Calls @Function.unlockAndFreeContigs@ for all contigs.
-..include:seqan/store.h
-*/
-
 template <typename TSpec, typename TConfig>
 bool unlockAndFreeContigs(FragmentStore<TSpec, TConfig> &store)
 {
-	bool result = true;
-	for (unsigned _id = 0; _id < length(store.contigStore); ++_id)
-		result &= unlockAndFreeContig(store, _id);
-	return result;
+    bool result = true;
+    for (unsigned _id = 0; _id < length(store.contigStore); ++_id)
+        result &= unlockAndFreeContig(store, _id);
+    return result;
 }
 
 
@@ -1621,112 +1248,48 @@ bool unlockAndFreeContigs(FragmentStore<TSpec, TConfig> &store)
  * @return bool true in case of success, false in case of errors.
  */
 
-/**
-.Function.loadReads
-..class:Class.FragmentStore
-..summary:Loads reads into fragment store.
-..remarks:When two file names are given, the files are expected to contain the same number of reads and reads with the same index are assumed to be mate pairs.
-Mate pairs are stored internally in an "interleaved" mode, i.e. a read is read from each file before reading the next one.
-..cat:Fragment Store
-..signature:loadReads(store, fileName)
-..signature:loadReads(store, fileNameL, fileNameR)
-..param.store:The fragment store.
-...type:Class.FragmentStore
-..param.fileName:A sequence file name.
-...type:Shortcut.CharString
-..returns:A $bool$ which is $true$ on success.
-..include:seqan/store.h
-*/
-
-template <typename TFSSpec, typename TFSConfig, typename TFileName>
-bool loadReads(FragmentStore<TFSSpec, TFSConfig> &store, TFileName &fileName)
+template <typename TSpec, typename TConfig, typename TFileName>
+bool loadReads(FragmentStore<TSpec, TConfig> &store, TFileName &fileName)
 {
-	MultiSeqFile multiSeqFile;
-	if (!open(multiSeqFile.concat, toCString(fileName), OPEN_RDONLY))
-		return false;
-
-	// guess file format and split into sequence fractions
-	AutoSeqFormat format;
-	guessFormat(multiSeqFile.concat, format);
-	split(multiSeqFile, format);
-
-	// reserve space in fragment store
-	unsigned seqOfs = length(store.readStore);
-	unsigned seqCount = length(multiSeqFile);
-	reserve(store.readStore, seqOfs + seqCount);
-	reserve(store.readSeqStore, seqOfs + seqCount);
-	reserve(store.readNameStore, seqOfs + seqCount);
-
-	// read sequences
-	String<Dna5Q> seq;
-	CharString qual;
-	CharString _id;
-
-	for (unsigned i = 0; i < seqCount; ++i)
-	{
-		assignSeq(seq, multiSeqFile[i], format);    // read sequence
-		assignQual(qual, multiSeqFile[i], format);  // read ascii quality values
-		assignSeqId(_id, multiSeqFile[i], format);  // read sequence id
-
-		// convert ascii to values from 0..62
-		// store dna and quality together in Dna5Q
-		// TODO: support different ASCII represenations of quality values
-		assignQualities(seq, qual);
-		appendRead(store, seq, _id);
-	}
+    SEQAN_ASSERT_EQ(length(store.readStore), length(store.readSeqStore));
+    SEQAN_ASSERT_EQ(length(store.readStore), length(store.readNameStore));
+
+    typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
+    typedef typename Value<TReadStore>::Type TReadStoreElement;
+
+    SeqFileIn seqFile;
+    if (!open(seqFile, toCString(fileName)))
+        return false;
+
+    readRecords(store.readNameStore, store.readSeqStore, seqFile);
+    resize(store.readStore, length(store.readSeqStore), TReadStoreElement());
     return true;
 }
 
 
-template <typename TFSSpec, typename TFSConfig, typename TFileName>
-bool loadReads(FragmentStore<TFSSpec, TFSConfig> & store, TFileName & fileNameL, TFileName & fileNameR)
+template <typename TSpec, typename TConfig, typename TFileName>
+bool loadReads(FragmentStore<TSpec, TConfig> & store, TFileName & fileNameL, TFileName & fileNameR)
 {
-	MultiSeqFile multiSeqFileL, multiSeqFileR;
-	if (!open(multiSeqFileL.concat, toCString(fileNameL), OPEN_RDONLY))
-		return false;
-	if (!open(multiSeqFileR.concat, toCString(fileNameR), OPEN_RDONLY))
-		return false;
-
-	// Guess file format and split into sequence fractions
-	AutoSeqFormat formatL, formatR;
-	guessFormat(multiSeqFileL.concat, formatL);
-	split(multiSeqFileL, formatL);
-	guessFormat(multiSeqFileR.concat, formatR);
-	split(multiSeqFileR, formatR);
-
-    // Check that both files have the same number of reads
-	SEQAN_ASSERT_EQ(length(multiSeqFileL), length(multiSeqFileR));
-
-	// Reserve space in fragment store
-	unsigned seqOfs = length(store.readStore);
-	unsigned seqCountL = length(multiSeqFileL);
-	unsigned seqCountR = length(multiSeqFileR);
-	reserve(store.readStore, seqOfs + seqCountL + seqCountR);
-	reserve(store.readSeqStore, seqOfs + seqCountL + seqCountR);
-	reserve(store.readNameStore, seqOfs + seqCountL + seqCountR);
-
-	// Read in sequences
-	String<Dna5Q> seq[2];
-	CharString qual[2];
-	CharString _id[2];
-
-	for (unsigned i = 0; i < seqCountL; ++i) {
-		assignSeq(seq[0], multiSeqFileL[i], formatL);    // read sequence
-		assignQual(qual[0], multiSeqFileL[i], formatL);  // read ascii quality values
-		assignSeqId(_id[0], multiSeqFileL[i], formatL);  // read sequence id
-		assignSeq(seq[1], multiSeqFileR[i], formatR);    // read sequence
-		assignQual(qual[1], multiSeqFileR[i], formatR);  // read ascii quality values
-		assignSeqId(_id[1], multiSeqFileR[i], formatR);  // read sequence id
-
-		// convert ascii to values from 0..62
-		// store dna and quality together in Dna5Q
-		// TODO: support different ASCII represenations of quality values
-		for (int j = 0; j < 2; ++j)
-			assignQualities(seq[j], qual[j]);
-		
-		appendMatePair(store, seq[0], seq[1], _id[0], _id[1]);
-	}
-	return true;
+    SEQAN_ASSERT_EQ(length(store.readStore), length(store.readSeqStore));
+    SEQAN_ASSERT_EQ(length(store.readStore), length(store.readNameStore));
+
+    typedef typename FragmentStore<TSpec, TConfig>::TReadSeq TReadSeq;
+
+    SeqFileIn seqFileL, seqFileR;
+    if (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR, toCString(fileNameR)))
+        return false;
+
+    // Read in sequences
+    TReadSeq seq[2];
+    CharString meta[2];
+
+    while (!atEnd(seqFileL) && !atEnd(seqFileR))
+    {
+        readRecord(meta[0], seq[0], seqFileL);
+        readRecord(meta[1], seq[1], seqFileR);
+        appendMatePair(store, seq[0], seq[1], meta[0], meta[1]);
+    }
+    return true;
 }
 
 }  // namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/store/store_io_gff.h b/seqan/store/store_io_gff.h
old mode 100755
new mode 100644
index 5b87e9e..0472b22
--- a/seqan/store/store_io_gff.h
+++ b/seqan/store/store_io_gff.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -61,7 +61,8 @@ struct IOContextGff_
 
     CharString gtfGeneId;
     CharString gtfGeneName;
-    CharString gtfTranscriptName;       // transcipt_id is stored in parentName
+    CharString gffTranscriptId;     // For Gtf transcipt_id is stored in parentName
+    CharString gtfTranscriptName;
 
     TId annotationId;
     TAnnotation annotation;
@@ -94,11 +95,12 @@ inline void clear(IOContextGff_<TFragmentStore, TSpec> & ctx)
 //
 // reads in one annotation line from a Gff file
 
-template <typename TFragmentStore, typename TSpec>
+template <typename TFragmentStore, typename TSpec, typename TTagList>
 inline void
 _readOneAnnotation(
     IOContextGff_<TFragmentStore, TSpec> & ctx,
-    GffRecord const & record)
+    GffRecord const & record,
+    TagSelector<TTagList> const & format)
 {
 //IOREV _nodoc_ _hasCRef_
     typedef typename TFragmentStore::TContigPos         TContigPos;
@@ -127,10 +129,10 @@ _readOneAnnotation(
 
     // skip column 8
     // read column 9: name
-    for (unsigned i = 0; i < length(record.tagName); ++i)
+    for (unsigned i = 0; i < length(record.tagNames); ++i)
     {
-        ctx._key = record.tagName[i];
-        ctx._value = record.tagValue[i];
+        ctx._key = record.tagNames[i];
+        ctx._value = record.tagValues[i];
         if (ctx._key == "ID")
         {
             ctx.annotationName = ctx._value;
@@ -141,11 +143,25 @@ _readOneAnnotation(
             appendValue(ctx.values, ctx._value);
         }
 
-        if (ctx._key == "Parent" || ctx._key == "ParentID" || ctx._key == "transcript_id")
+        if (ctx._key == "Parent" || ctx._key == "ParentID")
         {
             ctx.parentKey = ctx._key;
             ctx.parentName = ctx._value;
         }
+        else if (ctx._key == "transcript_id")
+        {
+            if (isEqual(format, Gtf()))
+            {
+                ctx.parentKey = ctx._key;
+                ctx.parentName = ctx._value;
+            }
+            else
+            {
+                // According to the Gff3 specifications, transcript_id should NOT hold any special meaning,
+                // only Id should be used in determining parent/child relations.
+                ctx.gffTranscriptId = ctx._value;
+            }
+        }
         else if (ctx._key == "transcript_name")
         {
             ctx.gtfTranscriptName = ctx._value;
@@ -298,54 +314,41 @@ _storeOneAnnotation(
         _adjustParent(parent, ctx.annotation);
         if (!empty(ctx.gtfTranscriptName))
             annotationAssignValueByKey(fragStore, parent, "transcript_name", ctx.gtfTranscriptName);
+
+        // Gff only.
+        if (!empty(ctx.gffTranscriptId))
+            annotationAssignValueByKey(fragStore, parent, "transcript_id", ctx.gffTranscriptId);
     }
 }
 
-///.Function.read.param.tag.type:Tag.File Format.tag.Gff
-///.Function.read.param.tag.type:Tag.File Format.tag.Gtf
-template <typename TFile, typename TSpec, typename TConfig>
+template <typename TSpec, typename TConfig>
 inline void
-read(
-    TFile & file,
-    FragmentStore<TSpec, TConfig> & fragStore,
-    Gff)
+readRecords(FragmentStore<TSpec, TConfig> & fragStore,
+            GffFileIn & gffFile)
 {
     typedef FragmentStore<TSpec, TConfig> TFragmentStore;
 
-    if (streamEof(file))
+    if (atEnd(gffFile))
         return;
 
-    IOContextGff_<TFragmentStore> ctx;
-
     refresh(fragStore.contigNameStoreCache);
     refresh(fragStore.annotationNameStoreCache);
     refresh(fragStore.annotationTypeStoreCache);
 
-    RecordReader<TFile, SinglePass<> > reader(file);
     GffRecord record;
-    while (!atEnd(reader))
+    IOContextGff_<TFragmentStore> ctx;
+
+    while (!atEnd(gffFile))
     {
-        if (!readRecord(record, reader, Gff()))
-        {
-            _readOneAnnotation(ctx, record);
-            _storeOneAnnotation(fragStore, ctx);
-        }
+        readRecord(record, gffFile);
+        _readOneAnnotation(ctx, record, format(gffFile));
+        _storeOneAnnotation(fragStore, ctx);
     }
     _storeClearAnnoBackLinks(fragStore.annotationStore);
     _storeCreateAnnoBackLinks(fragStore.annotationStore);
     _storeRemoveTempAnnoNames(fragStore);
 }
 
-template <typename TFile, typename TSpec, typename TConfig>
-inline void
-read(
-    TFile & file,
-    FragmentStore<TSpec, TConfig> & fragStore,
-    Gtf)
-{
-    read(file, fragStore, Gff());
-}
-
 //////////////////////////////////////////////////////////////////////////////
 // Write Gff
 //////////////////////////////////////////////////////////////////////////////
@@ -359,31 +362,23 @@ _writeCommonGffGtfInfo(
     TAnnotation & annotation,
     TId /*id*/)
 {
-
     typedef FragmentStore<TSpec, TConfig>       TFragmentStore;
     typedef typename TFragmentStore::TContigPos TContigPos;
 
+    clear(record);
+
     // write column 1: contig name
     if (annotation.contigId < length(store.contigNameStore))
-    {
         if (length(store.contigNameStore[annotation.contigId]) > 0u)
-        {
             record.ref = store.contigNameStore[annotation.contigId];
-        }
-    }
 
     // skip column 2: source
     record.source = ".";
 
     // write column 3: type
     if (annotation.typeId < length(store.annotationTypeStore))
-    {
         if (length(store.annotationTypeStore[annotation.typeId]) > 0u)
-        {
             record.type = store.annotationTypeStore[annotation.typeId];
-        }
-
-    }
 
     TContigPos beginPos = annotation.beginPos;
     TContigPos endPos = annotation.endPos;
@@ -398,15 +393,11 @@ _writeCommonGffGtfInfo(
 
     // write column 4: begin position
     if (beginPos != TAnnotation::INVALID_POS)
-    {
         record.beginPos = beginPos;
-    }
 
     // write column 5: end position
     if (endPos != TAnnotation::INVALID_POS)
-    {
         record.endPos = endPos;
-    }
 
     // skip column 6: score
 
@@ -414,71 +405,65 @@ _writeCommonGffGtfInfo(
     record.strand = orientation;
 }
 
-template <typename TTargetStream, typename TSpec, typename TConfig, typename TAnnotation, typename TId>
+template <typename TRecord, typename TSpec, typename TConfig, typename TAnnotation, typename TId>
 inline bool
-_writeOneAnnotation(
-    TTargetStream & target,
+_fillAnnotationRecord(
+    TRecord & record,
     FragmentStore<TSpec, TConfig> & store,
     TAnnotation & annotation,
     TId id,
     Gff)
 {
-
     if (id == 0)
         return false;
 
-    GffRecord record;
-
     _writeCommonGffGtfInfo(record, store, annotation, id);
 
     // write column 9: group
     // write column 9.1: annotation id
-    String<char> temp;
     if (id < length(store.annotationNameStore) && !empty(getAnnoName(store, id)))
     {
-        appendValue(record.tagName, "ID");
-        appendValue(record.tagValue, getAnnoName(store, id));
+        appendValue(record.tagNames, "ID");
+        appendValue(record.tagValues, getAnnoName(store, id));
     }
     else if (annotation.lastChildId != TAnnotation::INVALID_ID)
     {
-        appendValue(record.tagName, "ID");
-        appendValue(record.tagValue, getAnnoUniqueName(store, id));
+        appendValue(record.tagNames, "ID");
+        appendValue(record.tagValues, getAnnoUniqueName(store, id));
     }
 
     // write column 9.2: parent id
     if (store.annotationStore[annotation.parentId].typeId > 1)  // ignore root/deleted nodes
     {
-        appendValue(record.tagName, "Parent");
-        appendValue(record.tagValue, getAnnoUniqueName(store, annotation.parentId));
+        appendValue(record.tagNames, "Parent");
+        appendValue(record.tagValues, getAnnoUniqueName(store, annotation.parentId));
     }
 
     // write column 9.3-...: key, value pairs
     for (unsigned keyId = 0; keyId < length(annotation.values); ++keyId)
         if (!empty(annotation.values[keyId]))
         {
-            appendValue(record.tagName, store.annotationKeyStore[keyId]);
-            appendValue(record.tagValue, annotation.values[keyId]);
+            appendValue(record.tagNames, store.annotationKeyStore[keyId]);
+            appendValue(record.tagValues, annotation.values[keyId]);
         }
 
-    return writeRecord(target, record, Gff());
+    return true;
 }
 
-template <typename TTargetStream, typename TSpec, typename TConfig, typename TAnnotation, typename TId>
+template <typename TRecord, typename TSpec, typename TConfig, typename TAnnotation, typename TId>
 inline bool
-_writeOneAnnotation(
-    TTargetStream & target,
+_fillAnnotationRecord(
+    TRecord & record,
     FragmentStore<TSpec, TConfig> & store,
     TAnnotation & annotation,
     TId id,
     Gtf)
 {
-    typedef FragmentStore<TSpec, TConfig>               TFragmentStore;
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
 
     if (annotation.typeId <= TFragmentStore::ANNO_MRNA)
         return false;
 
-    GffRecord record;
-
     _writeCommonGffGtfInfo(record, store, annotation, id);
 
     // write column 9: group
@@ -493,30 +478,32 @@ _writeOneAnnotation(
     while (geneId < length(store.annotationStore) && store.annotationStore[geneId].typeId != TFragmentStore::ANNO_GENE)
         geneId = store.annotationStore[geneId].parentId;
 
-    CharString tmpStr;
-    if (geneId < length(store.annotationStore) && annotationGetValueByKey(store, store.annotationStore[geneId], "gene_name", tmpStr))
+    typename Id<TAnnotation>::Type valueId;
+    if (geneId < length(store.annotationStore) &&
+        (valueId = annotationGetValueIdByKey(store, store.annotationStore[geneId], "gene_name")) != TAnnotation::INVALID_ID)
     {
-        appendValue(record.tagName, "gene_name");
-        appendValue(record.tagValue, tmpStr);
+        appendValue(record.tagNames, "gene_name");
+        appendValue(record.tagValues, store.annotationStore[geneId].values[valueId]);
     }
-    if (transcriptId < length(store.annotationStore) && annotationGetValueByKey(store, store.annotationStore[transcriptId], "transcript_name", tmpStr))
+    if (transcriptId < length(store.annotationStore) &&
+        (valueId = annotationGetValueIdByKey(store, store.annotationStore[transcriptId], "transcript_name")) != TAnnotation::INVALID_ID)
     {
-        appendValue(record.tagName, "transcript_name");
-        appendValue(record.tagValue, tmpStr);
+        appendValue(record.tagNames, "transcript_name");
+        appendValue(record.tagValues, store.annotationStore[transcriptId].values[valueId]);
     }
 
     if (id < length(store.annotationNameStore) && !empty(getAnnoName(store, id)))
     {
-        appendValue(record.tagName, "ID");
-        appendValue(record.tagValue, getAnnoName(store, id));
+        appendValue(record.tagNames, "ID");
+        appendValue(record.tagValues, getAnnoName(store, id));
     }
 
     // write key, value pairs
     for (unsigned keyId = 0; keyId < length(annotation.values); ++keyId)
         if (!empty(annotation.values[keyId]))
         {
-            appendValue(record.tagName, store.annotationKeyStore[keyId]);
-            appendValue(record.tagValue, annotation.values[keyId]);
+            appendValue(record.tagNames, store.annotationKeyStore[keyId]);
+            appendValue(record.tagValues, annotation.values[keyId]);
         }
 
     // The GTF format version 2.2 requires the keys gene_id and transcript_id to be the last keys of line
@@ -524,25 +511,56 @@ _writeOneAnnotation(
 
     if (geneId < length(store.annotationStore))
     {
-        appendValue(record.tagName, "gene_id");
-        appendValue(record.tagValue, getAnnoUniqueName(store, geneId));
+        appendValue(record.tagNames, "gene_id");
+        appendValue(record.tagValues, getAnnoUniqueName(store, geneId));
     }
 
     if (transcriptId < length(store.annotationStore))
     {
-        appendValue(record.tagName, "transcript_id");
-        appendValue(record.tagValue, getAnnoUniqueName(store, transcriptId));
+        appendValue(record.tagNames, "transcript_id");
+        appendValue(record.tagValues, getAnnoUniqueName(store, transcriptId));
     }
+    return true;
+}
+
+// support for dynamically chosen file formats
+template <typename TRecord, typename TSpec, typename TConfig, typename TAnnotation, typename TId>
+inline bool
+_fillAnnotationRecord(
+    TRecord & /*record*/,
+    FragmentStore<TSpec, TConfig> & /*store*/,
+    TAnnotation & /*annotation*/,
+    TId /*id*/,
+    TagSelector<> const & /*format*/)
+{
+    SEQAN_FAIL("AnnotationStore: File format not specified.");
+    return false;
+}
+
+template <typename TRecord, typename TSpec, typename TConfig, typename TAnnotation, typename TId, typename TTagList>
+inline bool
+_fillAnnotationRecord(
+    TRecord & record,
+    FragmentStore<TSpec, TConfig> & store,
+    TAnnotation & annotation,
+    TId id,
+    TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
 
-    return writeRecord(target, record, Gtf());
+    if (isEqual(format, TFormat()))
+        return _fillAnnotationRecord(record, store, annotation, id, TFormat());
+    else
+        return _fillAnnotationRecord(record, store, annotation, id, static_cast<typename TagSelector<TTagList>::Base const &>(format));
 }
 
+
 template <typename TTargetStream, typename TSpec, typename TConfig, typename TFormat>
 inline void
 _writeGffGtf(
     TTargetStream & target,
     FragmentStore<TSpec, TConfig> & store,
-    TFormat format)
+    TFormat const &format)
 {
     typedef FragmentStore<TSpec, TConfig>                           TFragmentStore;
     typedef typename TFragmentStore::TAnnotationStore               TAnnotationStore;
@@ -553,28 +571,22 @@ _writeGffGtf(
     TAnnoIter it = begin(store.annotationStore, Standard());
     TAnnoIter itEnd = end(store.annotationStore, Standard());
 
-    for (TId id = 0; it != itEnd; ++it, ++id)
-        _writeOneAnnotation(target, store, *it, id, format);
-}
+    GffRecord record;
+    typename DirectionIterator<TTargetStream, Output>::Type iter = directionIterator(target, Output());
 
-template <typename TTargetStream, typename TSpec, typename TConfig>
-inline void
-write(
-    TTargetStream & target,
-    FragmentStore<TSpec, TConfig> & store,
-    Gff format)
-{
-    _writeGffGtf(target, store, format);
+    for (TId id = 0; it != itEnd; ++it, ++id)
+    {
+        if (_fillAnnotationRecord(record, store, *it, id, format))
+            writeRecord(iter, record, format);
+    }
 }
 
-template <typename TTargetStream, typename TSpec, typename TConfig>
+template <typename TSpec, typename TFSSpec, typename TFSConfig>
 inline void
-write(
-    TTargetStream & target,
-    FragmentStore<TSpec, TConfig> & store,
-    Gtf format)
+writeRecords(FormattedFile<Gff, Output, TSpec> & gffFile,
+             FragmentStore<TFSSpec, TFSConfig> & store)
 {
-    _writeGffGtf(target, store, format);
+    _writeGffGtf(gffFile, store, format(gffFile));
 }
 
 } // namespace SEQAN_NAMESPACE_MAIN
diff --git a/seqan/store/store_io_sam.h b/seqan/store/store_io_sam.h
index 25ce60d..f57e483 100644
--- a/seqan/store/store_io_sam.h
+++ b/seqan/store/store_io_sam.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -40,829 +40,666 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
+// ============================================================================
+// Forwards
+// ============================================================================
 
-//////////////////////////////////////////////////////////////////////////////
-// Parsing functions
-//////////////////////////////////////////////////////////////////////////////
+template <typename TSpec, typename TConfig>
+class FragmentStore;
 
+// ============================================================================
+// Classes
+// ============================================================================
 
-//////////////////////////////////////////////////////////////////////////////
-// _parseReadCigar
-    
-    template <typename TFile, typename TCigarString, typename TChar>
-    inline void
-    _parseReadCigar(TFile & file, TCigarString & cigar, TChar & c)
-    {
-//IOREV _nodoc_ _hasCRef_ could be simplified by using other _is or _parse calls
-        typedef typename Value<TCigarString>::Type  TCigarElement;
-        typedef typename TCigarElement::TCount      TCount;
-
-        clear(cigar);
-        
-        // if the CIGAR is not set and '*'
-        if (c == '*')
-        {
-            c = _streamGet(file);
-            return;
-        }
-        
-        while (!_streamEOF(file)) 
-        {
-            TCount count = _parseReadNumber(file, c);
-            if (c >= 'a' && c <= 'z')
-                c = c + 'A' - 'a';
-            appendValue(cigar, TCigarElement(c, count));
-            
-            c = _streamGet(file);
-            if (c == ' ' || c == '\t' || c == '\n') break;
-        }
-    }
-    
-//////////////////////////////////////////////////////////////////////////////
-// _parseReadSamIdentifier
-    
-    template<typename TFile, typename TString, typename TChar>
-    inline void
-    _parseReadSamIdentifier(TFile & file, TString & str, TChar& c)
-    {
-//IOREV _nodoc_ _hasCRef_ _duplicate_ same as generic _parseUntilWhitespace?
-        if (c == ' ' || c == '\t' || c == '\n') return;
-        appendValue(str, c);
-        while (!_streamEOF(file)) 
-        {
-            c = _streamGet(file);
-            if (c == ' ' || c == '\t' || c == '\n') return;
-            appendValue(str, c);
-        }
-    }
-    
-//////////////////////////////////////////////////////////////////////////////
-// _parseIsDna
-    
-    template<typename TChar>
-    inline bool
-    _parseIsDna(TChar const & c)
-    {
-//IOREV _bug_ according to Dna5 doc c is already uppercase, so it should be (c == x) || (c - 'A' + 'a' == x) OR JUST: return tolower(c) == tolower(x);
-        char x = TChar(Dna5(c));
-        return (c == x) || (c + 'A' - 'a' == x);
-    }
-    
-//////////////////////////////////////////////////////////////////////////////
-//_parseReadDnaSeq
-    
-    template<typename TFile, typename TString, typename TChar>
-    inline void
-    _parseReadDnaSeq(TFile & file, TString & str, TChar & c)
-    {
-//IOREV _nodoc_ _hasCRef_ _duplicate_ same as generic _parseUntilWhitespace?
-        TChar first = c;
-        if (!_streamEOF(file)) 
-            c = _streamGet(file);
-
-        if (!_parseIsDna(first))
-            return;
-        appendValue(str, first, Generous());
-        
-        for (; !_streamEOF(file) && _parseIsDna(c); c = _streamGet(file))
-            appendValue(str, c, Generous());
-    }
-        
-//////////////////////////////////////////////////////////////////////////////
-// _parseIsPhredQual
-    
-    template <typename TChar>
-    inline bool
-    _parseIsPhredQual(TChar c)
-    {
-//IOREV _nodoc_ what does the title mean? same as return isprint(c) && c != ' '
-        return c >= '!' && c <= '~';
-    }
-    
-//////////////////////////////////////////////////////////////////////////////
-// _parseReadSeqQual
-//
-    
-    template<typename TFile, typename TQualString, typename TChar>
-    inline void
-    _parseReadSeqQual(TFile & file, TQualString & str, TChar & c)
-    {
-//IOREV _nodoc_ unclearn what this actually does
-        typedef typename Size<TQualString>::Type                TSize;
-        typedef typename Iterator<TQualString, Standard>::Type  TIter;
-        
-        if (!_parseIsPhredQual(c)) return;
-
-        TIter itBegin = begin(str, Standard());
-        TIter it = itBegin; 
-        TSize rest = length(str);
-        
-        do {
-            int q = c - '!';
-            if (!_streamEOF(file)) 
-                c = _streamGet(file);
-            else
-                if (rest > 1)
-                    rest = 1;
-            
-            if (q == '*' - '!' && !_parseIsPhredQual(c) && it == itBegin)
-                return;
-            
-            if (rest != 0)
-            {
-                assignQualityValue(*it, q);
-                ++it;
-                --rest;
-            }
-        } while (_parseIsPhredQual(c) && !_streamEOF(file));
-    }
-    
-//////////////////////////////////////////////////////////////////////////////
-// _parseReadCharsUntilEndOfLine
-//
-// Reads all symbols till the next '\n' and writes them in the CharString str
-// the c is the first character after the '\n'.
-    
-    template<typename TFile, typename TChar>
-    inline void
-    _parseReadCharsUntilEndOfLine(TFile & file, String<char> & str, TChar& c)
-    {
-//IOREV replace with generic _parseLine() function that ignores '\r' (this calls adds a lonely '\r' to the end of str if file is windows-formatted)
-        // read all chars till '\n'
-        while (c != '\n')
-        {
-            appendValue(str, c, Generous());
-            if (_streamEOF(file)) return;
-            c = _streamGet(file);
-        }
-        
-        // read the first char after the '\n'
-        if (!_streamEOF(file))
-            c = _streamGet(file);
-    }
+struct FragStoreImportFlags
+{
+    bool importRead:1;
+    bool importReadSeq:1;
+    bool importReadName:1;
+    bool importReadAlignment:1;
+    bool importReadAlignmentQuality:1;
+    bool importReadAlignmentTags:1;
+
+    FragStoreImportFlags():
+        importRead(true),
+        importReadSeq(true),
+        importReadName(true),
+        importReadAlignment(true),
+        importReadAlignmentQuality(true),
+        importReadAlignmentTags(true)
+    {}
+};
+
+template <typename TFragmentStore>
+struct FragStoreSAMContext
+{
+    typedef typename Id<TFragmentStore>::Type                                   TId;
+    typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type    TAlignedElement;
+    typedef typename TAlignedElement::TGapAnchors                               TReadGapAnchors;
+    typedef String<typename TFragmentStore::TContigGapAnchor>                   TContigAnchorGaps;
+    typedef typename TFragmentStore::TReadSeq                                   TReadSeq;
 
-//////////////////////////////////////////////////////////////////////////////
-// appendAlignment
-    
-    template<typename TSpec, typename TConfig, typename TId, typename TPos, typename TGaps>
-    inline typename Size<typename FragmentStore<TSpec, TConfig>::TAlignedReadStore>::Type
-    appendAlignment(
-        FragmentStore<TSpec, TConfig> & fragStore, 
-        TId readId, 
-        TId contigId, 
-        TPos beginPos, 
-        TPos endPos, 
-        TGaps const & gaps)
-    {
-        typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-        typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
-        
-        TId id = length(fragStore.alignedReadStore);
-        TAlignedElement alignedElem = TAlignedElement(id, readId, contigId, beginPos, endPos, gaps);
-        appendValue(fragStore.alignedReadStore, alignedElem);
-        
-        return id;
-    }
-    
+    TId                 readId;
+    TReadGapAnchors     readGapAnchors;
+    TContigAnchorGaps   contigGapAnchors;
 
+    // Buffer for the read sequence.
+    TReadSeq readSeq;
 
-//////////////////////////////////////////////////////////////////////////////
-// read functions for Sam
-//////////////////////////////////////////////////////////////////////////////
+    // Buffer for the current BamAlignmentRecord.
+    BamAlignmentRecord bamRecord;
+};
 
-    
-//////////////////////////////////////////////////////////////////////////////
-// _generatePairMatchIds
-//
-    template <typename TPos, typename TId>
-    struct MatchMateInfo_
-    {
-        TId     readId;
-        TId     contigId;
-        TId     pairMatchId;
-        TId     matePairId;//:(sizeof(TId)*8-1);
-        bool    reversed;
-        TPos    beginPos;
-    };
-    
-    template <typename TFragStore>
-    struct AlignedMateLess_
-    {
-        TFragStore &fragStore;
-        
-        AlignedMateLess_(TFragStore &fragStore_) :
-            fragStore(fragStore_) {}
-
-        template <typename TAlignedRead>
-        inline bool 
-        operator() (TAlignedRead const& a, TAlignedRead const& b) const 
-        {
-            if (a.contigId < b.contigId) return true;
-            if (a.contigId > b.contigId) return false;
-
-            typename TFragStore::TContigPos posA = _min(a.beginPos, a.endPos);
-            typename TFragStore::TContigPos posB = _min(b.beginPos, b.endPos);            
-            if (posA < posB) return true;
-            if (posA > posB) return false;
-            
-            bool reversedA = (a.beginPos > a.endPos);
-            bool reversedB = (b.beginPos > b.endPos);
-            if (reversedA != reversedB) return reversedB;
-
-            typedef typename TFragStore::TMatePairStore     TMatePairStore;
-            typedef typename Value<TMatePairStore>::Type    TMatePair;
-            typename TMatePair::TId matePairIdB = TMatePair::INVALID_ID;
-
-            if (a.readId >= length(fragStore.readStore))
-                return false;
-                
-            if (b.readId < length(fragStore.readStore))
-                matePairIdB = fragStore.readStore[b.readId].matePairId;
-
-            return (fragStore.readStore[a.readId].matePairId < matePairIdB);
-        }
-    };
+template <typename TId>
+struct MatchMateInfo_
+{
+    TId     readId;
+    __int32 contigId;
+    TId     pairMatchId;
+    TId     matePairId;//:(sizeof(TId)*8-1);
+    __int32 beginPos;
+    bool    reversed;
+};
+
+// ============================================================================
+// Functors
+// ============================================================================
+
+template <typename TFragStore>
+struct AlignedMateLess_
+{
+    TFragStore &fragStore;
 
-    struct MatchMateInfoLess_
-    {
-        template <typename TMInfo>
-        inline bool 
-        operator() (TMInfo const &a, TMInfo const &b) const 
-        {
-            if (a.contigId < b.contigId) return true;
-            if (a.contigId > b.contigId) return false;
-            if (a.beginPos < b.beginPos) return true;
-            if (a.beginPos > b.beginPos) return false;
-            if (a.reversed != b.reversed) return b.reversed;
-            return (a.matePairId < b.matePairId);
-        }
-    };
-    
-    template <typename TAlignedRead, typename TMInfo, typename TFragStore>
-    inline int 
-    _compareAlignedReadAndMateInfo(TAlignedRead const &a, TMInfo const &b, TFragStore const &fragStore)
+    AlignedMateLess_(TFragStore &fragStore_) :
+        fragStore(fragStore_) {}
+
+    template <typename TAlignedRead>
+    inline bool
+    operator() (TAlignedRead const& a, TAlignedRead const& b) const
     {
-        if (a.contigId < b.contigId) return -1;
-        if (a.contigId > b.contigId) return 1;
+        if (a.contigId < b.contigId) return true;
+        if (a.contigId > b.contigId) return false;
 
         typename TFragStore::TContigPos posA = _min(a.beginPos, a.endPos);
-        if (posA < b.beginPos) return -1;
-        if (posA > b.beginPos) return 1;
-        
-        bool reversedA = (a.beginPos > a.endPos);
-        if (!reversedA && b.reversed) return -1;
-        if (reversedA && !b.reversed) return 1;
+        typename TFragStore::TContigPos posB = _min(b.beginPos, b.endPos);
+        if (posA < posB) return true;
+        if (posA > posB) return false;
+
+        bool reversedA = (a.endPos < a.beginPos);
+        bool reversedB = (b.endPos < b.beginPos);
+        if (reversedA != reversedB) return reversedB;
 
         typedef typename TFragStore::TMatePairStore     TMatePairStore;
         typedef typename Value<TMatePairStore>::Type    TMatePair;
-        typename TMatePair::TId matePairIdA = TMatePair::INVALID_ID;
-
-        if (a.readId < length(fragStore.readStore))
-            matePairIdA = fragStore.readStore[a.readId].matePairId;
-            
-        if (matePairIdA < b.matePairId) return -1;
-        if (matePairIdA > b.matePairId) return 1;
-        return 0;
+        typename TMatePair::TId matePairIdB = TMatePair::INVALID_ID;
+
+        if (a.readId >= length(fragStore.readStore))
+            return false;
+
+        if (b.readId < length(fragStore.readStore))
+            matePairIdB = fragStore.readStore[b.readId].matePairId;
+
+        return (fragStore.readStore[a.readId].matePairId < matePairIdB);
     }
+};
 
-    template<typename TSpec, typename TConfig, typename TMatchMateInfos>
-    inline void 
-    _generatePairMatchIds (
-        FragmentStore<TSpec, TConfig> & fragStore,
-        TMatchMateInfos & matchMateInfos)
+struct MatchMateInfoLess_
+{
+    template <typename TMInfo>
+    inline bool
+    operator() (TMInfo const &a, TMInfo const &b) const
     {
-        typedef FragmentStore<TSpec, TConfig>                           TFragmentStore;        
-        typedef typename TFragmentStore::TAlignedReadStore              TAlignedReadStore;
-        typedef typename Value<TAlignedReadStore>::Type                 TAlignedRead;
-        typedef typename Iterator<TAlignedReadStore, Standard>::Type    TIter;    
-        typedef typename Iterator<TMatchMateInfos, Standard>::Type      TMIter;    
-                
-        TIter it = begin(fragStore.alignedReadStore, Standard());
-        TIter itEnd = end(fragStore.alignedReadStore, Standard());
-        TMIter mit = begin(matchMateInfos, Standard());
-        TMIter mitEnd = end(matchMateInfos, Standard());
-
-        if (it == itEnd || mit == mitEnd) return;
-
-        // sort the aligned read store by: begin position, contig name
-        std::sort(it,  itEnd,  AlignedMateLess_<TFragmentStore>(fragStore));
-        std::sort(mit, mitEnd, MatchMateInfoLess_());
-
-        while (true)
-        {
-            // skip already aligned reads
-            while (it->pairMatchId != TAlignedRead::INVALID_ID)
-                if (++it == itEnd) return;
+        if (a.contigId < b.contigId) return true;
+        if (a.contigId > b.contigId) return false;
+        if (a.beginPos < b.beginPos) return true;
+        if (a.beginPos > b.beginPos) return false;
+        if (a.reversed != b.reversed) return b.reversed;
+        if (a.matePairId < b.matePairId) return true;
+        if (a.matePairId > b.matePairId) return false;
+        return (a.pairMatchId < b.pairMatchId);
+    }
+};
 
-            int cmp = _compareAlignedReadAndMateInfo(*it, *mit, fragStore);
+// ============================================================================
+// Metafunctions
+// ============================================================================
 
-            if (cmp == 0)   // both are equal -> link them
-                (*it).pairMatchId = (*mit).pairMatchId;
+template <typename TDirection, typename TSpec, typename TConfig, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<Bam, TDirection, FragmentStore<TSpec, TConfig> >, TStorageSpec>
+{
+    typedef FragmentStore<TSpec, TConfig>                           TFragmentStore;
+    typedef typename TFragmentStore::TContigNameStore               TNameStore;
+    typedef NameStoreCache<TNameStore, CharString>                  TNameStoreCache;
+    typedef BamIOContext<TNameStore, TNameStoreCache, Dependent<> > Type;
+};
 
-            if (cmp >= 0)   // MateInfo is less or equal
-            {
-                if (++mit == mitEnd) return;
-//                if (cmp>0)
-//                    std::cout << "mateInfo:   contigId="<<mit->contigId<<"  beginPos="<<mit->beginPos<<"  reversed="<<mit->reversed<<"  matePairId="<<mit->matePairId<<std::endl;
-            }
+// ============================================================================
+// Read Functions
+// ============================================================================
 
-            if (cmp <= 0)   // AlignedRead is less or equal
-            {
-                if (++it == itEnd) return;
-//                if (cmp<0)
-//                    std::cout << "alignedR:   contigId="<<it->contigId<<"  beginPos="<<_min(it->beginPos,it->endPos)<<"  reversed="<<(it->beginPos > it->endPos)<<"  matePairId="<<fragStore.readStore[it->readId].matePairId<<std::endl;
-            }
-        }
-    }    
+// --------------------------------------------------------------------------
+// Function clear()
+// --------------------------------------------------------------------------
 
-//////////////////////////////////////////////////////////////////////////////
-// read
+inline void
+clear(FragStoreImportFlags & flags)
+{
+    flags.importRead = false;
+    flags.importReadSeq = false;
+    flags.importReadName = false;
+    flags.importReadAlignment = false;
+    flags.importReadAlignmentQuality = false;
+    flags.importReadAlignmentTags = false;
+}
 
-///.Function.read.param.tag.type:Tag.File Format.tag.Sam
-    
-    struct FragStoreImportFlags
-    {
-        bool importRead:1;
-        bool importReadSeq:1;
-        bool importReadName:1;
-        bool importReadAlignment:1;
-        bool importReadAlignmentQuality:1;
-        bool importReadAlignmentTags:1;
-
-        FragStoreImportFlags():
-            importRead(true),
-            importReadSeq(true),
-            importReadName(true),
-            importReadAlignment(true),
-            importReadAlignmentQuality(true),
-            importReadAlignmentTags(true)
-        {}
-    };
-
-    inline void
-    clear(FragStoreImportFlags & flags)
-    {
-        flags.importRead = false;
-        flags.importReadSeq = false;
-        flags.importReadName = false;
-        flags.importReadAlignment = false;
-        flags.importReadAlignmentQuality = false;
-        flags.importReadAlignmentTags = false;
-    }
+// --------------------------------------------------------------------------
+// Function appendAlignment()
+// --------------------------------------------------------------------------
 
-    template<typename TStreamOrReader, typename TSpec, typename TConfig, typename TTag>
-    inline void 
-    _readImpl(TStreamOrReader & streamOrReader,
-              FragmentStore<TSpec, TConfig> & fragStore,
-              TTag const & tag,
-              FragStoreImportFlags const & importFlags)
-    {
-        typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-        typedef typename TFragmentStore::TContigPos TContigPos;
-        typedef typename Id<TFragmentStore>::Type TId;
-        
-        // data structure to temporarily store the gaps that need to be inserted in the contig sequences
-        typedef MatchMateInfo_<TContigPos, TId> TMatchMateInfo;
-        typedef String<TMatchMateInfo> TMatchMateInfos;
-        typedef StringSet<String<typename TFragmentStore::TContigGapAnchor>, Owner<ConcatDirect<> > > TContigAnchorGaps;
-
-        // data structure to temporarily store information about match mates
-        TMatchMateInfos matchMateInfos;
-        TContigAnchorGaps contigAnchorGaps;
-
-        refresh(fragStore.contigNameStoreCache);
-
-        // Setup a BamIOContext for I/O.
-        typedef BamIOContext<typename TFragmentStore::TContigNameStore> TBamIOContext;
-        TBamIOContext bamIOContext(fragStore.contigNameStore, fragStore.contigNameStoreCache);
-
-        // Read in the header.  We will subsequently ignore it and use the information indirectly just using the
-        // sequence names if any.
-        BamHeader bamHeader;
-        if (readRecord(bamHeader, bamIOContext, streamOrReader, tag) != 0)
-        {
-            std::cerr << "ERROR: Problem reading header from SAM file.\n";
-            return;
-        }
+template<typename TSpec, typename TConfig, typename TContigId, typename TId, typename TPos, typename TGaps>
+inline typename Size<typename FragmentStore<TSpec, TConfig>::TAlignedReadStore>::Type
+appendAlignment(
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TId readId,
+    TContigId contigId,
+    TPos beginPos,
+    TPos endPos,
+    TGaps const & gaps)
+{
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
 
-        // fill up contig entries for each contig name that appears in the header
-        resize(fragStore.contigStore, length(fragStore.contigNameStore));
+    TId id = length(fragStore.alignedReadStore);
+    TAlignedElement alignedElem = TAlignedElement(id, readId, contigId, beginPos, endPos, gaps);
+    appendValue(fragStore.alignedReadStore, alignedElem);
 
-        // Read in alignments section
-        _readAlignments(streamOrReader, bamIOContext, fragStore, contigAnchorGaps, matchMateInfos, tag, importFlags);
-        
-        if (importFlags.importReadAlignment)
-        {
-            // set the match mate IDs using the information stored in matchMateInfos
-            _generatePairMatchIds(fragStore, matchMateInfos);
+    return id;
+}
 
-            convertPairWiseToGlobalAlignment(fragStore, contigAnchorGaps);
-        }
-    }
+// --------------------------------------------------------------------------
+// Function _compareAlignedReadAndMateInfo()
+// --------------------------------------------------------------------------
 
-    template <typename TFile, typename TSpec, typename TConfig>
-    inline void
-    read(TFile & file,
-         FragmentStore<TSpec, TConfig> & fragStore,
-         Sam,
-         FragStoreImportFlags const & importFlags)
-    {
-        // Construct a RecordReader from the input file.
-        RecordReader<TFile, SinglePass<> > reader(file);
-        if (atEnd(reader))
-            return;  // Done, file is empty.
-        _readImpl(reader, fragStore, Sam(), importFlags);
-    }
+template <typename TAlignedRead, typename TMInfo, typename TFragStore>
+inline int
+_compareAlignedReadAndMateInfo(TAlignedRead const &a, TMInfo const &b, TFragStore const &fragStore)
+{
+    typedef typename TAlignedRead::TId  TId;
+    typedef typename TAlignedRead::TPos TPos;
 
-#if SEQAN_HAS_ZLIB
-    template <typename TFile, typename TSpec, typename TConfig>
-    inline void
-    read(TFile & file,
-         FragmentStore<TSpec, TConfig> & fragStore,
-         Bam,
-         FragStoreImportFlags const & importFlags)
-    {
-        _readImpl(file, fragStore, Bam(), importFlags);
-    }
-#endif  // #if SEQAN_HAS_ZLIB
-
-    template <typename TFile, typename TSpec, typename TConfig>
-    inline void
-    read(
-        TFile & file,
-        FragmentStore<TSpec, TConfig> & fragStore,
-        Sam)
+    if (a.contigId < (TId)b.contigId) return -1;
+    if (a.contigId > (TId)b.contigId) return 1;
+
+    TPos posA = _min(a.beginPos, a.endPos);
+    if (posA < (TPos)b.beginPos) return -1;
+    if (posA > (TPos)b.beginPos) return 1;
+
+    bool reversedA = (a.endPos < a.beginPos);
+    if (!reversedA &&  b.reversed) return -1;
+    if ( reversedA && !b.reversed) return 1;
+
+    typedef typename TFragStore::TMatePairStore     TMatePairStore;
+    typedef typename Value<TMatePairStore>::Type    TMatePair;
+    typename TMatePair::TId matePairIdA = TMatePair::INVALID_ID;
+
+    if (a.readId < length(fragStore.readStore))
+        matePairIdA = fragStore.readStore[a.readId].matePairId;
+
+    if (matePairIdA < b.matePairId) return -1;
+    if (matePairIdA > b.matePairId) return 1;
+    return 0;
+}
+
+// --------------------------------------------------------------------------
+// Function _generatePairMatchIds()
+// --------------------------------------------------------------------------
+
+template<typename TSpec, typename TConfig, typename TMatchMateInfos>
+inline void
+_generatePairMatchIds (
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TMatchMateInfos & matchMateInfos)
+{
+    typedef FragmentStore<TSpec, TConfig>                           TFragmentStore;
+    typedef typename TFragmentStore::TAlignedReadStore              TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TIter;
+    typedef typename Iterator<TMatchMateInfos, Standard>::Type      TMIter;
+
+    TIter it = begin(fragStore.alignedReadStore, Standard());
+    TIter itEnd = end(fragStore.alignedReadStore, Standard());
+    TMIter mit = begin(matchMateInfos, Standard());
+    TMIter mitEnd = end(matchMateInfos, Standard());
+
+    if (it == itEnd || mit == mitEnd) return;
+
+    // sort the aligned read store by: begin position, contig name
+    std::sort(it,  itEnd,  AlignedMateLess_<TFragmentStore>(fragStore));
+    std::sort(mit, mitEnd, MatchMateInfoLess_());
+
+    while (true)
     {
-        read(file, fragStore, Sam(), FragStoreImportFlags());
+        int cmp = _compareAlignedReadAndMateInfo(*it, *mit, fragStore);
+
+        if (cmp == 0)   // both are equal -> link them
+            if (it->pairMatchId > mit->pairMatchId)     // avoid id swap and instead decide for
+                it->pairMatchId = mit->pairMatchId;     // the smaller of both ids
+
+        if (cmp >= 0)   // MateInfo is less or equal
+            if (++mit == mitEnd)
+                return;
+
+        if (cmp <= 0)   // AlignedRead is less or equal
+            if (++it == itEnd)
+                return;
     }
+}
+
+// --------------------------------------------------------------------------
+// Function readRecords()
+// --------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TNameStore, typename TNameStoreCache,
+          typename TStorageSpec, typename TForwardIter, typename TFormat>
+inline void
+readRecords(FragmentStore<TSpec, TConfig> & store,
+            BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & ctx,
+            TForwardIter & iter,
+            TFormat const & format,
+            FragStoreImportFlags const & importFlags)
+{
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename Id<TFragmentStore>::Type TId;
+
+    // data structure to temporarily store the gaps that need to be inserted in the contig sequences
+    typedef MatchMateInfo_<TId> TMatchMateInfo;
+    typedef String<TMatchMateInfo> TMatchMateInfos;
+    typedef StringSet<String<typename TFragmentStore::TContigGapAnchor>, Owner<ConcatDirect<> > > TContigAnchorGaps;
+
+    // data structure to temporarily store information about match mates
+    TMatchMateInfos matchMateInfos;
+    TContigAnchorGaps contigAnchorGaps;
+
+    // Read in the header.  We will subsequently ignore it and use the information indirectly just using the
+    // sequence names if any.
+    BamHeader bamHeader;
+    readHeader(bamHeader, ctx, iter, format);
+
+    // fill up contig entries for each contig name that appears in the header
+    resize(store.contigStore, length(store.contigNameStore));
+
+    // Read in alignments section
+    _readAlignments(store, contigAnchorGaps, matchMateInfos, ctx, iter, format, importFlags);
 
-#if SEQAN_HAS_ZLIB
-    template <typename TFile, typename TSpec, typename TConfig>
-    inline void
-    read(
-        TFile & file,
-        FragmentStore<TSpec, TConfig> & fragStore,
-        Bam)
+    if (importFlags.importReadAlignment)
     {
-        read(file, fragStore, Bam(), FragStoreImportFlags());
+        // set the match mate IDs using the information stored in matchMateInfos
+        _generatePairMatchIds(store, matchMateInfos);
+        convertPairWiseToGlobalAlignment(store, contigAnchorGaps);
     }
-#endif  // #if SEQAN_HAS_ZLIB
+}
 
-//////////////////////////////////////////////////////////////////////////////
-// _readAlignments
-//
-// reads in alignement sections from a Sam file
+template <typename TFSSpec, typename TConfig, typename TDirection, typename TSpec>
+inline void
+readRecords(FragmentStore<TFSSpec, TConfig> & store,
+            FormattedFile<Bam, TDirection, TSpec> & bamFile,
+            FragStoreImportFlags const & importFlags)
+{
+    typedef FragmentStore<TFSSpec, TConfig>                 TFragmentStore;
+    typedef typename TFragmentStore::TContigNameStore       TContigNameStore;
+    typedef NameStoreCache<TContigNameStore, CharString>    TContigNameStoreCache;
+
+    BamIOContext<TContigNameStore, TContigNameStoreCache, Dependent<> > ctx;
+
+    // Make sure that the BAM I/O context refers to the name cache of the FragmentStore
+    setContigNames(ctx, store.contigNameStore);
+    setContigNamesCache(ctx, store.contigNameStoreCache);
+    setContigLengths(ctx, contigLengths(context(bamFile)));
+    std::swap(ctx.buffer, context(bamFile).buffer);
+    std::swap(ctx.translateFile2GlobalRefId, context(bamFile).translateFile2GlobalRefId);
+
+    refresh(contigNamesCache(ctx));
+    readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags);
+//for(size_t i=0;i<length(contigNames(ctx));++i)
+//std::cout<<contigNames(ctx)[i]<<std::endl;
+    std::swap(ctx.buffer, context(bamFile).buffer);
+    std::swap(ctx.translateFile2GlobalRefId, context(bamFile).translateFile2GlobalRefId);
+}
 
-    template <typename TFragmentStore>
-    struct FragStoreSAMContext
-    {
-        typedef typename Id<TFragmentStore>::Type                                   TId;
-        typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type    TAlignedElement;
-        typedef typename TAlignedElement::TGapAnchors                               TReadGapAnchors;
-        typedef String<typename TFragmentStore::TContigGapAnchor>                   TContigAnchorGaps;
-        typedef typename TFragmentStore::TReadSeq                                   TReadSeq;
-
-        TId                 readId;
-        TId                 contigId;
-        TReadGapAnchors     readGapAnchors;
-        TContigAnchorGaps   contigGapAnchors;
-
-        // Buffer for SAM tags.
-        CharString tags;
-        // Buffer for the read sequence.
-        TReadSeq readSeq;
-
-        // Buffer for the current BamAlignmentRecord.
-        BamAlignmentRecord bamRecord;
-    };
-
-
-    template <typename TStreamOrReader, typename TNameStore, typename TNameStoreCache, typename TSpec, typename TConfig, typename TContigAnchorGaps, typename TMatchMateInfos, typename TTag>
-    inline void 
-    _readAlignments(
-        TStreamOrReader & streamOrReader,
-        BamIOContext<TNameStore, TNameStoreCache> & bamIOContext,
-        FragmentStore<TSpec, TConfig> & fragStore,
-        TContigAnchorGaps & contigAnchorGaps,   
-        TMatchMateInfos & matchMateInfos,
-        TTag const & tag,
-        FragStoreImportFlags const & importFlags)
-    {
+template <typename TFSSpec, typename TConfig, typename TDirection, typename TSpec>
+inline void
+readRecords(FragmentStore<TFSSpec, TConfig> & store,
+            FormattedFile<Bam, TDirection, TSpec> & bamFile)
+{
+    readRecords(store, bamFile, FragStoreImportFlags());
+}
+
+//template <typename TSpec, typename TConfig>
+//inline void
+//readRecords(FragmentStore<TSpec, TConfig> & store,
+//            FormattedFile<Bam, Input, FragmentStore<TSpec, TConfig> > & bamFile)
+//{
+//    readRecord(record, context(file), file.iter, file.format);
+//}
+//readRecord(BamAlignmentRecord & record,
+//           BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+//           TForwardIter & iter,
+//           TagSelector<TTagList> const & format)
+
+
+// --------------------------------------------------------------------------
+// Function _readAlignments()
+// --------------------------------------------------------------------------
+// reads all alignements from a SAM/BAM file into FragmentStore
+
+template <typename TSpec, typename TConfig, typename TContigAnchorGaps, typename TMatchMateInfos,
+          typename TNameStore, typename TNameStoreCache,
+          typename TStorageSpec, typename TForwardIter, typename TFormat>
+inline void
+_readAlignments(
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TContigAnchorGaps & contigAnchorGaps,
+    TMatchMateInfos & matchMateInfos,
+    BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & ctx,
+    TForwardIter & iter,
+    TFormat const & format,
+    FragStoreImportFlags const & importFlags)
+{
 //IOREV _nodoc_ docusmentation in code, but unclear
-        // create dummy entries in Sam specific aligned read quality store and aligned read tag store
-        // is needed so the ID in the aligned store can be use to access the other stores
-        // even if there exists previous entries without
-        typedef FragmentStore<TSpec, TConfig> TFragmentStore;
-        typedef typename TFragmentStore::TAlignQualityStore TAlignQualityStore;
-        typedef typename TFragmentStore::TReadSeqStore TReadSeqStore;
-        typedef typename Size<TReadSeqStore>::Type TReadSeqStoreSize;
-        typedef typename Value<TAlignQualityStore>::Type TAlignQuality;
-        
-        TAlignQuality q;
-        q.score = maxValue(q.score);
-        int diff = length(fragStore.alignedReadStore) - length(fragStore.alignQualityStore);
-        for(int i = 0; i < diff; ++i)
-            appendValue(fragStore.alignQualityStore, q, Generous());
-        
-        diff = length(fragStore.alignedReadStore) - length(fragStore.alignedReadTagStore);
-        for(int i = 0; i < diff; ++i)
-            appendValue(fragStore.alignedReadTagStore, "", Generous());
-        
-        // read in alignments
-        FragStoreSAMContext<TFragmentStore> contextSAM;
+    // create dummy entries in Sam specific aligned read quality store and aligned read tag store
+    // is needed so the ID in the aligned store can be use to access the other stores
+    // even if there exists previous entries without
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef typename TFragmentStore::TAlignQualityStore TAlignQualityStore;
+    typedef typename TFragmentStore::TReadSeqStore TReadSeqStore;
+    typedef typename Size<TReadSeqStore>::Type TReadSeqStoreSize;
+    typedef typename Value<TAlignQualityStore>::Type TAlignQuality;
+
+    // sync sizes of alignQualityStore and alignedReadTagStore with alignedReadStore
+    TAlignQuality q;
+    q.score = maxValue(q.score);
+    resize(fragStore.alignQualityStore, length(fragStore.alignedReadStore), q);
+    resize(fragStore.alignedReadTagStore, length(fragStore.alignedReadStore));
+
+    // read in alignments
+    FragStoreSAMContext<TFragmentStore> contextSAM;
 //        refresh(fragStore.contigNameStoreCache);  // was done for the BamIOContext already
-        refresh(fragStore.readNameStoreCache);
+    refresh(fragStore.readNameStoreCache);
 
-        while (!atEnd(streamOrReader))
-            _readOneAlignment(streamOrReader, bamIOContext, fragStore, contigAnchorGaps, matchMateInfos, contextSAM,
-                              importFlags, tag);
-
-        if (importFlags.importReadSeq)
+    __uint64 recNo = 0;
+    while (!atEnd(iter))
+    {
+        try
+        {
+            ++recNo;
+            _readOneAlignment(fragStore, contigAnchorGaps, matchMateInfos, ctx, iter, format, contextSAM, importFlags);
+        }
+        catch (IOError &e)
         {
-            TReadSeqStoreSize emptyReads = 0;
-            for(TReadSeqStoreSize i = 0; i < length(fragStore.alignedReadStore); ++i)
-                if (empty(fragStore.readSeqStore[fragStore.alignedReadStore[i].readId]))
-                {
-                    ++emptyReads;
-    //                std::cerr << "Read sequence empty for " << fragStore.readNameStore[fragStore.alignedReadStore[i].readId] << std::endl;
-                }
-            if (emptyReads != 0)
-                std::cerr << "Warning: " << emptyReads << " read sequences are empty." << std::endl;
+            std::stringstream sstr;
+            sstr << "Error in SAM/BAM record #" << recNo << ": " << e.what();
+            SEQAN_THROW(IOError(sstr.str()));
         }
     }
-    
-        
-    template <typename TReadSeq, typename TCigar, typename TPos, typename TId, typename TFragmentStore>
-    inline void
-    _samAppendAlignment(
-        TFragmentStore &fragStore,
-        TReadSeq const &readSeq,
-        TCigar &cigar,
-        TPos &beginPos, TPos &endPos,
-        TId &pairMatchId,
-        FragStoreSAMContext<TFragmentStore> & contextSAM)
+
+    if (importFlags.importReadSeq)
     {
-        typedef typename TFragmentStore::TAlignedReadStore                      TAlignedReadStore;
-        typedef typename Value<TAlignedReadStore>::Type                         TAlignedRead;
-        typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> > TReadGaps;
-
-        // insert alignment gaps
-        clear(contextSAM.readGapAnchors);
-        TReadGaps readGaps(readSeq, contextSAM.readGapAnchors);
-        unsigned beginGaps = cigarToGapAnchorRead(cigar, readGaps);
-
-        // adapt start or end (on reverse strand) position if alignment begins with gaps
-        if (beginPos > endPos)
-            endPos += beginGaps;
-        else
-            beginPos += beginGaps;
+        TReadSeqStoreSize emptyReads = 0;
+        for(TReadSeqStoreSize i = 0; i < length(fragStore.alignedReadStore); ++i)
+            if (empty(fragStore.readSeqStore[fragStore.alignedReadStore[i].readId]))
+            {
+                ++emptyReads;
+//                std::cerr << "Read sequence empty for " << fragStore.readNameStore[fragStore.alignedReadStore[i].readId] << std::endl;
+            }
+        if (emptyReads != 0)
+            std::cerr << "Warning: " << emptyReads << " read sequences are empty." << std::endl;
+    }
+}
+
+// --------------------------------------------------------------------------
+// Function _bamAppendAlignment()
+// --------------------------------------------------------------------------
+
+template <typename TReadSeq, typename TCigar, typename TPos, typename TContigId, typename TId, typename TFragmentStore>
+inline void
+_bamAppendAlignment(
+    TFragmentStore &fragStore,
+    TReadSeq const &readSeq,
+    TCigar &cigar,
+    TPos &beginPos, TPos &endPos,
+    TContigId contigId,
+    TId &pairMatchId,
+    FragStoreSAMContext<TFragmentStore> & contextSAM)
+{
+    typedef typename TFragmentStore::TAlignedReadStore                      TAlignedReadStore;
+    typedef typename Value<TAlignedReadStore>::Type                         TAlignedRead;
+    typedef Gaps<TReadSeq, AnchorGaps<typename TAlignedRead::TGapAnchors> > TReadGaps;
+
+    // insert alignment gaps
+    clear(contextSAM.readGapAnchors);
+    TReadGaps readGaps(readSeq, contextSAM.readGapAnchors);
+    unsigned beginGaps = cigarToGapAnchorRead(readGaps, cigar);
+
+    // adapt start or end (on reverse strand) position if alignment begins with gaps
+    if (beginPos > endPos)
+        endPos += beginGaps;
+    else
+        beginPos += beginGaps;
+
+    // create a new entry in the aligned read store
+    pairMatchId = appendAlignment(fragStore, contextSAM.readId, contigId, beginPos, endPos, contextSAM.readGapAnchors);
+}
+
+// --------------------------------------------------------------------------
+// Function _bamAppendAlignmentWithoutSeq()
+// --------------------------------------------------------------------------
 
-        // create a new entry in the aligned read store
-        pairMatchId = appendAlignment(fragStore, contextSAM.readId, contextSAM.contigId, beginPos, endPos, contextSAM.readGapAnchors);
+template <typename TCigar, typename TPos, typename TContigId, typename TId, typename TFragmentStore>
+inline void
+_bamAppendAlignmentWithoutSeq(
+    TFragmentStore &fragStore,
+    TCigar &cigar,
+    TPos &beginPos, TPos &endPos,
+    TContigId contigId,
+    TId &pairMatchId,
+    FragStoreSAMContext<TFragmentStore> & contextSAM)
+{
+    typedef typename TFragmentStore::TAlignedReadStore                      TAlignedReadStore;
+    typedef typename Value<TAlignedReadStore>::Type                         TAlignedRead;
+    typedef Gaps<Nothing, AnchorGaps<typename TAlignedRead::TGapAnchors> >  TReadGaps;
+    Nothing nothing;
+
+    // insert alignment gaps
+    clear(contextSAM.readGapAnchors);
+    TReadGaps readGaps(nothing, contextSAM.readGapAnchors);
+    unsigned beginGaps = cigarToGapAnchorRead(readGaps, cigar);
+
+    // adapt start or end (on reverse strand) position if alignment begins with gaps
+    if (beginPos > endPos)
+        endPos += beginGaps;
+    else
+        beginPos += beginGaps;
+
+    // create a new entry in the aligned read store
+    pairMatchId = appendAlignment(fragStore, contextSAM.readId, contigId, beginPos, endPos, contextSAM.readGapAnchors);
+}
+
+// --------------------------------------------------------------------------
+// Function _readAlignments()
+// --------------------------------------------------------------------------
+// read one alignment record from SAM/BAM file into FragmentStore
+
+template <
+    typename TSpec,
+    typename TConfig,
+    typename TContigAnchorGaps,
+    typename TMatchMateInfos,
+    typename TNameStore, typename TNameStoreCache,
+    typename TStorageSpec, typename TForwardIter, typename TFormat>
+inline void
+_readOneAlignment(
+    FragmentStore<TSpec, TConfig> & fragStore,
+    TContigAnchorGaps & contigAnchorGaps,
+    TMatchMateInfos & matchMateInfos,
+    BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & ctx,
+    TForwardIter & iter,
+    TFormat const & format,
+    FragStoreSAMContext<FragmentStore<TSpec, TConfig> > & contextSAM,
+    FragStoreImportFlags const & importFlags)
+{
+    // Basic types
+    typedef FragmentStore<TSpec, TConfig>                                       TFragmentStore;
+    typedef FragStoreSAMContext<TFragmentStore>                                 TSAMContext;
+    typedef typename Id<TFragmentStore>::Type                                   TId;
+    //typedef typename Size<TFragmentStore>::Type                                 TSize;
+
+    // All fragment store element types
+    //typedef typename Value<typename TFragmentStore::TContigStore>::Type         TContigElement;
+    //typedef typename Value<typename TFragmentStore::TLibraryStore>::Type        TLibraryStoreElement;
+    //typedef typename Value<typename TFragmentStore::TReadStore>::Type           TReadStoreElement;
+    typedef typename Value<typename TFragmentStore::TAlignQualityStore>::Type   TAlignQualityElement;
+
+    // Type for sequence in readstore
+    typedef typename TFragmentStore::TReadSeq                                   TReadSeq;
+
+    // Type for gap anchor
+    typedef typename TFragmentStore::TContigPos                                 TContigPos;
+    typedef Gaps<Nothing, AnchorGaps<typename TSAMContext::TContigAnchorGaps> > TContigGapsPW;
+
+    // Type to temporarily store information about match mates
+    typedef typename Value<TMatchMateInfos>::Type                               TMatchMateInfo;
+
+    // Read next BamAlignmentRecord and get shortcut.
+    BamAlignmentRecord & record = contextSAM.bamRecord;
+    readRecord(record, ctx, iter, format);
+
+    // Get element of align quality store.
+    TAlignQualityElement mapQ;
+    mapQ.score = record.mapQ;
+
+    // Get begin and end position.
+    TContigPos beginPos = record.beginPos;
+    TContigPos endPos = 0;
+    _getLengthInRef(endPos, record.cigar);
+    endPos = beginPos + endPos;
+    if (hasFlagRC(record))
+        std::swap(beginPos, endPos);
+
+    // Put read sequence and qualities into readSeq and reverseComplement if necessary.
+    TReadSeq & readSeq = contextSAM.readSeq;
+    readSeq = record.seq;
+    assignQualities(readSeq, record.qual);
+    if (hasFlagRC(record))
+        reverseComplement(readSeq);
+
+    // Check if read sequence is already in the store.  If so get the ID, otherwise create new entries in the read
+    // then read name and mate pair store.
+    contextSAM.readId = -1;
+    if (importFlags.importRead)
+    {
+        if (!importFlags.importReadName)
+            clear(record.qName);
+
+        bool newRead = _storeAppendRead(fragStore, contextSAM.readId, record.qName, readSeq, record.flag,
+                                        contextSAM);
+        (void)newRead;
+        SEQAN_ASSERT_NOT(newRead && empty(readSeq));
     }
 
-    template <typename TCigar, typename TPos, typename TId, typename TFragmentStore>
-    inline void
-    _samAppendAlignmentWithoutSeq(
-        TFragmentStore &fragStore,
-        TCigar &cigar,
-        TPos &beginPos, TPos &endPos,
-        TId &pairMatchId,
-        FragStoreSAMContext<TFragmentStore> & contextSAM)
+    // Stop here if read is unaligned.
+    if (record.rID == BamAlignmentRecord::INVALID_REFID || record.beginPos == BamAlignmentRecord::INVALID_POS)
+        return;
+
+    // Sync contigStore with size of contigNameStore (if a new contig was added)
+    resize(fragStore.contigStore, length(fragStore.contigNameStore));
+
+    // Stop if no alignment in CIGAR string.
+    if (empty(record.cigar))
+        return;
+
+    // Handle read alignment import.
+    TId pairMatchId = 0;
+    if (importFlags.importReadAlignment)
     {
-        typedef typename TFragmentStore::TAlignedReadStore                      TAlignedReadStore;
-        typedef typename Value<TAlignedReadStore>::Type                         TAlignedRead;
-        typedef Gaps<Nothing, AnchorGaps<typename TAlignedRead::TGapAnchors> >  TReadGaps;
-        Nothing nothing;
-
-        // insert alignment gaps
-        clear(contextSAM.readGapAnchors);
-        TReadGaps readGaps(nothing, contextSAM.readGapAnchors);
-        unsigned beginGaps = cigarToGapAnchorRead(cigar, readGaps);
-
-        // adapt start or end (on reverse strand) position if alignment begins with gaps
-        if (beginPos > endPos)
-            endPos += beginGaps;
+        // generate gap anchor string for the read
+        if (importFlags.importReadSeq)
+            _bamAppendAlignment(fragStore, fragStore.readSeqStore[contextSAM.readId], record.cigar, beginPos, endPos,
+                                record.rID, pairMatchId, contextSAM);
         else
-            beginPos += beginGaps;
+            _bamAppendAlignmentWithoutSeq(fragStore, record.cigar, beginPos, endPos, record.rID, pairMatchId,
+                                          contextSAM);
 
-        // create a new entry in the aligned read store
-        pairMatchId = appendAlignment(fragStore, contextSAM.readId, contextSAM.contigId, beginPos, endPos, contextSAM.readGapAnchors);
+        clear(contextSAM.contigGapAnchors);
+        TContigGapsPW contigGaps(contextSAM.contigGapAnchors);
+        cigarToGapAnchorContig(contigGaps, record.cigar);
+        appendValue(contigAnchorGaps, contextSAM.contigGapAnchors);
     }
 
-//////////////////////////////////////////////////////////////////////////////
-// _readOneAlignment
-//
-// reads in one alignement section from a Sam file
-    
-    template <
-        typename TStreamOrReader,
-        typename TNameStore,
-        typename TNameStoreCache,
-        typename TSpec,
-        typename TConfig,
-        typename TContigAnchorGaps,
-        typename TMatchMateInfos,
-        typename TFragStore,
-        typename TTag>
-    inline void
-    _readOneAlignment(
-        TStreamOrReader & streamOrReader,
-        BamIOContext<TNameStore, TNameStoreCache> & bamIOContext,
-        FragmentStore<TSpec, TConfig> & fragStore,
-        TContigAnchorGaps & contigAnchorGaps,
-        TMatchMateInfos & matchMateInfos,
-        FragStoreSAMContext<TFragStore> & contextSAM,
-        FragStoreImportFlags const & importFlags,
-        TTag const & tag)
+    // Import tags and remove some tags.
+    if (importFlags.importReadAlignmentTags || importFlags.importReadAlignmentQuality)
     {
-        // Basic types
-        typedef FragmentStore<TSpec, TConfig>                                       TFragmentStore;
-        typedef FragStoreSAMContext<TFragStore>                                     TSAMContext;
-        typedef typename Id<TFragmentStore>::Type                                   TId;
-        //typedef typename Size<TFragmentStore>::Type                                 TSize;
-
-        // All fragment store element types
-        //typedef typename Value<typename TFragmentStore::TContigStore>::Type         TContigElement;
-        //typedef typename Value<typename TFragmentStore::TLibraryStore>::Type        TLibraryStoreElement;
-        typedef typename Value<typename TFragmentStore::TMatePairStore>::Type       TMatePairElement;
-        //typedef typename Value<typename TFragmentStore::TReadStore>::Type           TReadStoreElement;
-        typedef typename Value<typename TFragmentStore::TAlignQualityStore>::Type   TAlignQualityElement;
-
-        // Type for sequence in readstore
-        typedef typename TFragmentStore::TReadSeq                                   TReadSeq;
-
-        // Type for gap anchor
-        typedef typename TFragmentStore::TContigPos                                 TContigPos;
-        typedef Gaps<Nothing, AnchorGaps<typename TSAMContext::TContigAnchorGaps> > TContigGapsPW;
-
-        // Type to temporarily store information about match mates
-        typedef typename Value<TMatchMateInfos>::Type                               TMatchMateInfo;
-
-        // Read next BamAlignmentRecord and get shortcut.
-        if (readRecord(contextSAM.bamRecord, bamIOContext, streamOrReader, tag) != 0)
-        {
-            std::cerr << "ERROR: Problem reading SAM/BAM record.\n";
-            return;
-        }
-        BamAlignmentRecord & record = contextSAM.bamRecord;
-
-        // Get element of align quality store.
-        TAlignQualityElement mapQ;
-        mapQ.score = record.mapQ;
-
-        // Get begin and end position.
-        TContigPos beginPos = record.beginPos;
-        TContigPos endPos = 0;
-        _getLengthInRef(record.cigar, endPos);
-        endPos = beginPos + endPos;
-        if (hasFlagRC(record))
-            std::swap(beginPos, endPos);
-
-        // Put read sequence and qualities into readSeq and reverseComplement if necessary.
-        TReadSeq & readSeq = contextSAM.readSeq;
-        readSeq = record.seq;
-        assignQualities(readSeq, record.qual);
-        if (hasFlagRC(record))
-            reverseComplement(readSeq);
-
-        // Get tags in SAM format.
-        assignTagsBamToSam(contextSAM.tags, record.tags);
-
-        // Check if read sequence is already in the store.  If so get the ID, otherwise create new entries in the read
-        // then read name and mate pair store.
-        contextSAM.readId = 0;
-        if (importFlags.importRead)
-        {
-            if (!importFlags.importReadName)
-                clear(record.qName);
-
-            bool newRead = _storeAppendRead(fragStore, contextSAM.readId, record.qName, readSeq, record.flag,
-                                            contextSAM);
-            (void)newRead;
-            SEQAN_ASSERT_NOT(newRead && empty(readSeq));
-        }
-        
-        // Stop if read is not aligned.
-        if (record.rID == BamAlignmentRecord::INVALID_REFID || record.beginPos == BamAlignmentRecord::INVALID_POS)
-            return;
-
-        // Check if the contig is already in the store.  Get its ID or create a new one otherwise.
-        contextSAM.contigId = 0;
-        _storeAppendContig(fragStore, contextSAM.contigId, nameStore(bamIOContext)[record.rID]);
-        resize(fragStore.contigStore, length(fragStore.contigNameStore));
-
-        // Stop if no alignment in CIGAR string.
-        if (empty(record.cigar))
-            return;
-
-        // Handle read alignment import.
-        TId pairMatchId = 0;
-        if (importFlags.importReadAlignment)
+        // extract and delete some tags
+        if (!empty(record.tags))
         {
-            // generate gap anchor string for the read
-            if (importFlags.importReadSeq)
-                _samAppendAlignment(fragStore, fragStore.readSeqStore[contextSAM.readId], record.cigar, beginPos, endPos,
-                                    pairMatchId, contextSAM);
-            else
-                _samAppendAlignmentWithoutSeq(fragStore, record.cigar, beginPos, endPos, pairMatchId, contextSAM);
-
-            clear(contextSAM.contigGapAnchors);
-            TContigGapsPW contigGaps(contextSAM.contigGapAnchors);
-            cigarToGapAnchorContig(record.cigar, contigGaps);
-            appendValue(contigAnchorGaps, contextSAM.contigGapAnchors);
+            BamTagsDict tags(record.tags);
+            int tagId = -1;
+            if (findTagKey(tagId, tags, "MD"))
+                eraseTag(tags, tagId);
+            if (findTagKey(tagId, tags, "NM") && extractTagValue(mapQ.errors, tags, tagId))
+                eraseTag(tags, tagId);
         }
+    }
 
-        // Import tags and remove some tags.
-        if (importFlags.importReadAlignmentTags || importFlags.importReadAlignmentQuality)
-        {
-            // extract and delete some tags
-            if (!empty(contextSAM.tags))
-                for (unsigned pos = length(contextSAM.tags), right = length(contextSAM.tags); pos != 0; )
-                {
-                    --pos;
-                    if (pos == 0 || contextSAM.tags[pos] == '\t')
-                    {
-                        unsigned left = pos;
-                        if (contextSAM.tags[left] == '\t') ++left;                    
-
-                        bool remove = false;
-                        if (infix(contextSAM.tags, left, left + 2) == "MD")
-                            remove = true;
-                        
-                        if (infix(contextSAM.tags, left, left + 2) == "NM")
-                        {
-                            int errors = lexicalCast<int>(infix(contextSAM.tags, left + 5, right));  // NM:i:x
-                            mapQ.errors = errors;
-                            remove = true;
-                        }
-                        
-                        if (remove)
-                            erase(contextSAM.tags, left, _min(right + 1, length(contextSAM.tags)));
-
-                        right = pos;
-                    }
-                }
-        }
+    // Create entries in Sam specific stores.
+    if (importFlags.importReadAlignmentQuality)
+        appendValue(fragStore.alignQualityStore, mapQ, Generous());
 
-        // Create entries in Sam specific stores.
-        if (importFlags.importReadAlignmentQuality)
-            appendValue(fragStore.alignQualityStore, mapQ, Generous());
-        
-        if (importFlags.importReadAlignmentTags)
-            appendValue(fragStore.alignedReadTagStore, contextSAM.tags, Generous());
+    if (importFlags.importReadAlignmentTags)
+        appendValue(fragStore.alignedReadTagStore, record.tags, Generous());
 
-        // Store additional data about match mate temporarily.
-        // used in the end of the read function to generate match mate IDs.
-        if (importFlags.importRead && importFlags.importReadAlignment && record.rNextId != BamAlignmentRecord::INVALID_REFID)
+    // Store additional data about match mate temporarily.
+    // used in the end of the read function to generate match mate IDs.
+    if (importFlags.importRead && importFlags.importReadAlignment && record.rNextId != BamAlignmentRecord::INVALID_REFID)
+    {
+        if (contextSAM.readId < length(fragStore.readStore))
         {
-            TId mcontigId = contextSAM.contigId;
-            if (record.rID != record.rNextId)
+            // insert match mate info for the mate record
+            TMatchMateInfo matchMateInfo =
             {
-                _storeAppendContig(fragStore, mcontigId, nameStore(bamIOContext)[record.rNextId]);
-                resize(fragStore.contigStore, length(fragStore.contigNameStore));
-            }
-
-            if (getMateNo(fragStore, contextSAM.readId) == 0)  // store mate info only for one mate
-            {
-                typename TMatePairElement::TId matePairId = TMatePairElement::INVALID_ID;
-                if (contextSAM.readId < length(fragStore.readStore))
-                    matePairId = fragStore.readStore[contextSAM.readId].matePairId;
-                
-                TMatchMateInfo matchMateInfo = {contextSAM.readId, mcontigId, pairMatchId, matePairId,
-                                                hasFlagNextRC(record), record.pNext};
-                appendValue(matchMateInfos, matchMateInfo);
-                back(fragStore.alignedReadStore).pairMatchId = pairMatchId;
-            }
+                /* .readId      = */  contextSAM.readId,
+                /* .contigId    = */  record.rNextId,
+                /* .pairMatchId = */  pairMatchId,
+                /* .matePairId  = */  fragStore.readStore[contextSAM.readId].matePairId,
+                /* .beginPos    = */  record.pNext,
+                /* .reversed    = */  hasFlagNextRC(record)
+            };
+            appendValue(matchMateInfos, matchMateInfo);
+            back(fragStore.alignedReadStore).pairMatchId = pairMatchId;
         }
     }
+}
 
-
-//////////////////////////////////////////////////////////////////////////////
-// write functions for Sam
-//////////////////////////////////////////////////////////////////////////////
+// ============================================================================
+// Write Functions
+// ============================================================================
 
 // --------------------------------------------------------------------------
 // Function _fillHeader()
 // --------------------------------------------------------------------------
 
-template <typename TSpec, typename TConfig>
+template <typename TSpec, typename TConfig, typename TBamIOFunctor>
 inline void
 _fillHeader(BamHeader & header,
-            FragmentStore<TSpec, TConfig> & store)
+            FragmentStore<TSpec, TConfig> & store,
+            TBamIOFunctor & /* functor */)
 {
     typedef FragmentStore<TSpec, TConfig>                       TFragmentStore;
     typedef typename TFragmentStore::TLibraryStore              TLibraryStore;
     typedef typename TFragmentStore::TContigStore               TContigStore;
-    typedef typename TFragmentStore::TNameStore                 TNameStore;
 
     typedef typename Value<TContigStore>::Type                  TContig;
     typedef typename Iterator<TLibraryStore, Standard>::Type    TLibraryIter;
-    typedef typename Iterator<TContigStore, Standard>::Type     TContigIter;
-    typedef typename Iterator<TNameStore, Standard>::Type       TContigNameIter;
     typedef typename Id<TContig>::Type                          TId;
 
-    typedef BamHeader::TSequenceInfo                            TSequenceInfo;
     typedef BamHeaderRecord::TTag                               TTag;
 
     // Fill first header line.
@@ -870,22 +707,13 @@ _fillHeader(BamHeader & header,
     firstRecord.type = BAM_HEADER_FIRST;
     appendValue(firstRecord.tags, TTag("VN", "1.4"));
     appendValue(firstRecord.tags, TTag("SO", "unsorted"));
-    appendValue(header.records, firstRecord);
-
-    // Fill sequence info header line.
-    TContigIter it          = begin(store.contigStore, Standard());
-    TContigIter itEnd       = end(store.contigStore, Standard());
-    TContigNameIter nit     = begin(store.contigNameStore, Standard());
-    TContigNameIter nitEnd  = end(store.contigNameStore, Standard());
-
-    for (; it != itEnd && nit != nitEnd; ++it, ++nit)
-        appendValue(header.sequenceInfos, TSequenceInfo(*nit, length((*it).seq)));
+    appendValue(header, firstRecord);
 
     // Fill program header line.
     BamHeaderRecord pgRecord;
     pgRecord.type = BAM_HEADER_PROGRAM;
     appendValue(pgRecord.tags, TTag("ID", "SeqAn"));
-    appendValue(header.records, pgRecord);
+    appendValue(header, pgRecord);
 
     // Fill library info header line.
     BamHeaderRecord rgRecord;
@@ -896,349 +724,400 @@ _fillHeader(BamHeader & header,
 
     for (TId id = 0; lit != litEnd; ++lit, ++id)
     {
-        appendValue(pgRecord.tags, TTag("ID", id + 1));
+        CharString buffer;
+        appendNumber(buffer, id + 1);
+        appendValue(pgRecord.tags, TTag("ID", buffer));
         appendValue(pgRecord.tags, TTag("LB", store.libraryNameStore[id]));
-        appendValue(pgRecord.tags, TTag("PI", (int)store.libraryStore[id].mean));
+        clear(buffer);
+        appendNumber(buffer, (int)store.libraryStore[id].mean);
+        appendValue(pgRecord.tags, TTag("PI", buffer));
         // Sample name needs to be included into fragment store.
         appendValue(pgRecord.tags, TTag("SM", "none"));
     }
+}
 
+// --------------------------------------------------------------------------
+// Function fillHeader()
+// --------------------------------------------------------------------------
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig, typename TBamIOFunctor>
+inline void
+fillHeader(BamHeader & header,
+           FormattedFile<Bam, Output, TSpec> & bamFile,
+           FragmentStore<TFSSpec, TFSConfig> & store,
+           TBamIOFunctor & functor)
+{
+    // Make sure that the BAM I/O context refers to the name cache of the FragmentStore
+    setContigNames(context(bamFile), store.contigNameStore);
+    setContigNamesCache(context(bamFile), store.contigNameStoreCache);
+
+    // Fill header with information from fragment store.
+    _fillHeader(header, store, functor);
+
+    // Fill sequence lengths.
+    resize(contigLengths(context(bamFile)), length(store.contigStore));
+    for (size_t i = 0; i != length(store.contigStore); ++i)
+        contigLengths(context(bamFile))[i] = length(store.contigStore[i].seq);
+}
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig>
+inline void
+fillHeader(BamHeader & header,
+           FormattedFile<Bam, Output, TSpec> & bamFile,
+           FragmentStore<TFSSpec, TFSConfig> & store)
+{
+    Nothing nothing;
+    fillHeader(header, bamFile, store, nothing);
+}
+
+// --------------------------------------------------------------------------
+// Function writeHeader()
+// --------------------------------------------------------------------------
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig, typename TBamIOFunctor>
+inline void writeHeader(FormattedFile<Bam, Output, TSpec> & bamFile,
+                        FragmentStore<TFSSpec, TFSConfig> & store,
+                        TBamIOFunctor & functor)
+{
+    BamHeader header;
+
+    // Fill header with information from fragment store.
+    fillHeader(header, bamFile, store, functor);
+
+    // Write header to target.
+    writeHeader(bamFile, header);
 }
-    
-//////////////////////////////////////////////////////////////////////////////
-// _writeAlignments
-
-    template<typename TFile, typename TSpec, typename TConfig, typename TAlignFunctor>
-    inline void _writeAlignments(TFile & target,
-                                 FragmentStore<TSpec, TConfig> & store,
-                                 Sam,
-                                 TAlignFunctor const & alignFunctor)
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig>
+inline void writeHeader(FormattedFile<Bam, Output, TSpec> & bamFile,
+                        FragmentStore<TFSSpec, TFSConfig> & store)
+{
+    Nothing nothing;
+    writeHeader(bamFile, store, nothing);
+}
+
+// --------------------------------------------------------------------------
+// Function _fillBamSeqAndQual()
+// --------------------------------------------------------------------------
+
+template <typename TSeq, typename TQual, typename TRead>
+inline void
+_fillBamSeqAndQual(TSeq &bamSeq, TQual &bamQual, TRead const &read)
+{
+    bamSeq = read;
+
+    resize(bamQual, length(read));
+    typename Iterator<TQual, Standard>::Type       tIt    = begin(bamQual, Standard());
+    typename Iterator<TRead const, Standard>::Type sIt    = begin(read, Standard());
+    typename Iterator<TRead const, Standard>::Type sItEnd = end(read, Standard());
+
+    for (; sIt != sItEnd; ++sIt, ++tIt)
+        *tIt = (char)(getQualityValue(*sIt) + '!');
+}
+
+// --------------------------------------------------------------------------
+// Function setPrimaryMatch()
+// --------------------------------------------------------------------------
+
+template <typename TSpec, typename TConfig, typename TAlignedRead, typename TAlignQuality, typename TBamIOFunctor>
+inline void
+setPrimaryMatch(BamAlignmentRecord & record,
+                FragmentStore<TSpec, TConfig> & store,
+                TAlignedRead const & alignedRead,       // read alignment to transform into a BamAlignmentRecord
+                TAlignQuality const & alignQuality,     // read alignment quality
+                TBamIOFunctor & functor,                // functor that extracts/computes alignment for cigar/md strings
+                bool secondaryAlignment)                // is this a secondary alignment?
+{
+    typedef FragmentStore<TSpec, TConfig>                           TFragmentStore;
+
+    typedef typename TFragmentStore::TContigStore                   TContigStore;
+    typedef typename Value<TContigStore>::Type                      TContig;
+    typedef typename TContig::TGapAnchors                           TContigGapAnchors;
+
+    typedef Iterator<CharString, Standard>::Type                    TCharStringIterator;
+
+    typedef Gaps<Nothing, AnchorGaps<TContigGapAnchors> >           TContigGaps;
+
+    // Fill QNAME with read name.
+    clear(record.qName);
+    TCharStringIterator it = begin(store.readNameStore[alignedRead.readId], Standard());
+    TCharStringIterator itEnd = end(store.readNameStore[alignedRead.readId], Standard());
+    for (; it != itEnd && *it != ' ' && *it != '\t'; ++it)
+        appendValue(record.qName, *it);
+
+    // Fill FLAG.
+    unsigned short flag = 0;
+
+    if (alignedRead.beginPos > alignedRead.endPos)
+        flag |= BAM_FLAG_RC;
+    if (secondaryAlignment)
+        flag |= BAM_FLAG_SECONDARY;     // we've already output an alignment for this read (this one is secondary)
+
+    signed char mateNo = getMateNo(store, alignedRead.readId);
+    if (mateNo == 0)
+        flag |= BAM_FLAG_FIRST;        // this read is the first in the pair
+    else if (mateNo == 1)
+        flag |= BAM_FLAG_LAST;         // this read is the second in the pair
+
+    // Set flags regarding mate alignment.
+
+    // We disinguish 3 cases:
+    //  1) We have no mate (single-end read)
+    //  2) We might have a mate, but it wasn't aligned properly
+    //  3) We have a mate which was aligned properly
+    //
+    // wich are encoded as follows:
+    //  1) alignedRead and alignedMate have the same address in _fillRecord
+    //  2) alignedMate has an invalid contigId (== INVALID_ID)
+    //  3) alignedRead and alignedMate have valid readIds
+
+    if (mateNo >= 0)
+        flag |=   BAM_FLAG_MULTIPLE | BAM_FLAG_NEXT_UNMAPPED;   // there is a mate
+    else
+        flag &= ~(BAM_FLAG_MULTIPLE | BAM_FLAG_NEXT_UNMAPPED);  // there is no mate
+
+    record.flag = flag;
+
+    // Fill RNAME by providing contig id.
+    record.rID = alignedRead.contigId;
+
+    // Fill POS with start position.
+    TContigGaps contigGaps(/*store.contigStore[alignedRead.contigId].seq, */store.contigStore[alignedRead.contigId].gaps);
+    record.beginPos = positionGapToSeq(contigGaps, std::min(alignedRead.beginPos, alignedRead.endPos));
+
+    // Fill MAPQ with mapping quality.
+//    if (alignQuality.score != TAlignedReadQualityElement::INVALID_SCORE)
+    if (alignQuality.score > 0)
+        record.mapQ = alignQuality.score;
+    else
+        record.mapQ = 255;
+
+//    // Fill CIGAR using aligned read.
+//    if (!IsSameType<TAlignFunctor, Nothing>::VALUE)
+//        getCigarString(record.cigar, row(align, 0), row(align, 1));
+
+    // Retrieve number of errors from quality store.
+    int errors = -1;
+    if (alignQuality.errors != MaxValue<unsigned char>::VALUE)
+        errors = alignQuality.errors;
+
+    // Use record.qual as a temporary for the md string.
+    alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId],
+            store.readSeqStore[alignedRead.readId], alignedRead, errors, functor);
+
+    if (alignQuality.errors != MaxValue<unsigned char>::VALUE)
     {
-//IOREV
-        typedef FragmentStore<TSpec, TConfig>                           TFragmentStore;
-
-        typedef typename TFragmentStore::TReadStore                     TReadStore;
-        typedef typename TFragmentStore::TReadNameStore                 TReadNameStore;
-        typedef typename TFragmentStore::TAlignedReadStore              TAlignedReadStore;
-        typedef typename TFragmentStore::TContigStore                   TContigStore;
-        typedef typename TFragmentStore::TReadSeq                       TReadSeq;
-
-        typedef typename Value<TReadStore>::Type                        TRead;
-        //typedef typename Size<TReadStore>::Type                         TSize;
-        typedef typename Value<TContigStore>::Type                      TContig;
-        typedef typename Value<TAlignedReadStore>::Type                 TAlignedRead;
-
-        typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignIter;
-        typedef typename Iterator<TReadSeq, Standard>::Type             TReadSeqIter;
-        typedef typename Id<TAlignedRead>::Type                         TId;
-
-        typedef Gaps<Nothing, AnchorGaps<typename TContig::TGapAnchors> >   TContigGaps;
-
-        String<int> mateIndex;  // store outer library size for each pair match (indexed by pairMatchId)
-        calculateMateIndices(mateIndex, store);
-        
-        TAlignIter it = begin(store.alignedReadStore, Standard());
-        TAlignIter itEnd = end(store.alignedReadStore, Standard());
-        TAlignIter mit = it;
-        CharString cigar, md;
-        TReadSeq readSeq;
-        
-        typedef unsigned long TWord;
-        const unsigned wordLen = BitsPerValue<TWord>::VALUE;
-        String<TWord> readAligned;  // bitset to signal wether a read was aligned at least once
-        resize(readAligned, (length(store.readStore) + wordLen - 1) / wordLen, (TWord)0);
-
-        for(; it != itEnd; ++it)
-        {
-            TId alignedId = (*it).id;
-            TId readId = (*it).readId;
-            TId mateIdx = TRead::INVALID_ID;
+//        if (errors > (int)alignQuality.errors)
+//            std::cerr << "WARNING: More errors in the alignment (" << errors << ") than given in NM tag / alignQuality ("
+//                      << (int)alignQuality.errors << ") for read " << record.qName << std::endl;
+
+        // To output the same NM value if a SAM file is loaded and saved, we overwrite error with the original value
+        // TODO(weese): This can be changed if desired (uncomment the following line) but now even the ex1.sam example
+        //              of the SAMtools have NM values that are inconsistent to their CIGAR/MD strings
+        errors = alignQuality.errors;
+    }
 
-            if ((*it).pairMatchId != TRead::INVALID_ID)
-                mateIdx = mateIndex[2*(*it).pairMatchId + getMateNo(store, (*it).readId)];
+    // Fill tags here to release record.qual
+    if (errors != -1)
+        appendTagValue(record.tags, "NM", errors);
+    if (!empty(record.tags))
+        appendTagValue(record.tags, "MD", record.qual, 'Z');
 
-            TContigGaps contigGaps(/*store.contigStore[(*it).contigId].seq, */store.contigStore[(*it).contigId].gaps);
-            __int64 pos = positionGapToSeq(contigGaps, _min((*it).beginPos, (*it).endPos)) + 1;
-            __int64 mpos = 0;
-            int isize = 0;
-            unsigned short flag = 0;
+    record.rNextId = BamAlignmentRecord::INVALID_REFID;
+    record.pNext = BamAlignmentRecord::INVALID_POS;
+    record.tLen = BamAlignmentRecord::INVALID_LEN;
 
-            if ((*it).beginPos > (*it).endPos)
-                flag |= 0x0010;         
+    if (!secondaryAlignment)
+    {
+        // Fill SEQ and QUAL with read sequence and quality values.
+        if (alignedRead.beginPos <= alignedRead.endPos)
+            _fillBamSeqAndQual(record.seq, record.qual, store.readSeqStore[alignedRead.readId]);
+        else
+            _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId]));
+    }
+    else
+    {
+        clear(record.seq);
+        clear(record.qual);
+    }
+}
 
-            // calculate flags, mpos, isize
-            if (mateIdx < length(store.alignedReadStore))
-            {
-                mit = begin(store.alignedReadStore, Standard()) + mateIdx;
-                if ((*it).contigId == (*mit).contigId)
-                {
-                    mpos = positionGapToSeq(contigGaps, _min((*mit).beginPos, (*mit).endPos)) + 1;
-                    if ((*it).beginPos < (*mit).beginPos)
-                        isize = positionGapToSeq(contigGaps, _max((*mit).beginPos, (*mit).endPos) - 1) + 2 - pos;
-                    else
-                        isize = mpos - positionGapToSeq(contigGaps, _max((*it).beginPos, (*it).endPos) - 1) - 2;
-                }
-                flag |= 0x0002;
-                if ((*mit).beginPos > (*mit).endPos)
-                    flag |= 0x0020;             
-            }
-            
-            signed char mateNo = getMateNo(store, readId);
-            if (mateNo == 0) flag |= 0x0040;    // this read is the first in the pair
-            if (mateNo == 1) flag |= 0x0080;    // this read is the second in the pair
-            
-            // test for secondary alignment
-            TWord mask = (TWord)1 << (readId % wordLen);
-            bool secondary = (readAligned[readId / wordLen] & mask) != 0;
-            readAligned[readId / wordLen] |= mask;
-            if (secondary) flag |= 0x0100;      // we've already output an alignment for this read (this one is secondary)
-
-            if (readId < length(store.readStore))
-            {
-                TRead &read = store.readStore[readId];
-                if (read.matePairId != TRead::INVALID_ID)
-                {
-                    flag |= 0x0001;
-                    if (mateIdx >= length(store.alignedReadStore))
-                        flag |= 0x0008;         // mate is unmapped (actually we should check if the mate has no match at all)
-                }
-            }
-            
-            // <qname>
-            if (readId < length(store.readNameStore))
-            {
-                typedef typename Iterator<typename Value<TReadNameStore>::Type const>::Type TReadNameIterator;
-                if (empty(store.readNameStore[readId]))
-                    continue;
-                for (TReadNameIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) {
-                    if (*it == ' ' || *it == '\t' || *it == '\n' || *it == '\r')
-                        break;
-                    _streamPut(target, *it);
-                }
-            } else
-                continue;
-            _streamPut(target, '\t');
-            
-            // <flag>
-            _streamPutInt(target, flag);
-            _streamPut(target, '\t');
-            
-            // <rname>
-            if ((*it).contigId < length(store.contigNameStore))
-                _streamWrite(target, store.contigNameStore[(*it).contigId]);
-            else
-                _streamWrite(target, '.');  // No reference name given.  Standard says field must not be empty but gives no "NULL" value.
-            _streamPut(target, '\t');
-            
-            // <pos>
-            _streamPutInt(target, pos);
-            _streamPut(target, '\t');
-            
-            // <mapq>
-            if (alignedId < length(store.alignQualityStore) && store.alignQualityStore[alignedId].score > 0) // a value <= 0 equals -errors (forbidden in SAM)
-                _streamPutInt(target, store.alignQualityStore[alignedId].score);
-            else
-                _streamPutInt(target, 255);
-            _streamPut(target, '\t');
-            
-            // get read sequence
-            if (readId < length(store.readSeqStore))
-            {
-                readSeq = store.readSeqStore[readId];
-                if ((*it).beginPos > (*it).endPos) 
-                    reverseComplement(readSeq);
-            } else
-                clear(readSeq);
-            
-            // <cigar>
-            int errors = -1;
-            if (alignedId < length(store.alignQualityStore))
-                errors = store.alignQualityStore[alignedId].errors;
-            // std::cout << store.readNameStore[readId] << "\n";
-            alignAndGetCigarString(cigar, md, store.contigStore[(*it).contigId], readSeq, *it, errors, alignFunctor);
-            _streamWrite(target, cigar);
-			// _streamWrite(std::cout, cigar);
-            // std::cout << "\n";
-            _streamPut(target, '\t');
-            
-            // <mrnm>
-            if ((mateIdx < length(store.alignedReadStore)))
-            {
-                if ((*it).contigId == (*mit).contigId)
-                    _streamWrite(target, '=');
-                else
-                    if ((*mit).contigId < length(store.contigNameStore))
-                        _streamWrite(target, store.contigNameStore[(*mit).contigId]);
-            } else
-                _streamWrite(target, '*');
-                
-            _streamPut(target, '\t');
-            
-            // <mpos>
-            _streamPutInt(target, (int)mpos);
-            _streamPut(target, '\t');
-            
-            // <isize>
-            _streamPutInt(target, isize);
-            _streamPut(target, '\t');
-
-            // <seq>
-            if (!secondary)
-                _streamWrite(target, readSeq);
-            else
-                _streamPut(target, '*');
-            _streamPut(target, '\t');
-            
-            // <qual>
-            if (!secondary)
-            {
-                TReadSeqIter it = begin(readSeq, Standard());
-                TReadSeqIter itEnd = end(readSeq, Standard());
-                for (; it != itEnd; ++it)
-                    _streamPut(target, (char)(getQualityValue(*it) + 33));
-            }
-            else
-                _streamPut(target, '*');
-            
-            // <tags>
-            
-            if (errors != -1)
-            {
-                _streamWrite(target, "\tNM:i:");
-                _streamPutInt(target, errors);
-            }
+// --------------------------------------------------------------------------
+// Function setMateMatch()
+// --------------------------------------------------------------------------
 
-            if (!empty(md))
-            {
-                _streamWrite(target, "\tMD:Z:");
-                _streamWrite(target, md);
-            }
+template <typename TSpec, typename TConfig, typename TAlignedRead>
+inline void
+setMateMatch(BamAlignmentRecord & record,
+             FragmentStore<TSpec, TConfig> & store,
+             TAlignedRead const & alignedRead,       // read alignment to transform into a BamAlignmentRecord
+             TAlignedRead const & alignedMate)       // alignment of the mate
+{
+    typedef FragmentStore<TSpec, TConfig>                           TFragmentStore;
 
-            if (alignedId < length(store.alignedReadTagStore) && !empty(store.alignedReadTagStore[alignedId]))
-            {
-                _streamPut(target, '\t');
-                _streamWrite(target, store.alignedReadTagStore[alignedId]);
-            }
-            
-            _streamPut(target, '\n');
-        }
+    typedef typename TFragmentStore::TContigStore                   TContigStore;
+    typedef typename Value<TContigStore>::Type                      TContig;
+    typedef typename TContig::TGapAnchors                           TContigGapAnchors;
+
+    typedef typename TFragmentStore::TReadStore                     TReadStore;
+    typedef typename Value<TReadStore>::Type                        TReadStoreElement;
+
+    typedef Gaps<Nothing, AnchorGaps<TContigGapAnchors> >           TContigGaps;
 
-#if 0  // DISABLE FOR NOW
-        // Write out records for unaligned reads.
-        TSize readCount = length(store.readSeqStore);
-        for (unsigned readId = 0; readId < readCount; ++readId)
+
+    record.flag &= ~(BAM_FLAG_ALL_PROPER | BAM_FLAG_NEXT_RC | BAM_FLAG_NEXT_UNMAPPED);
+    if (alignedMate.contigId != TReadStoreElement::INVALID_ID)
+    {
+        record.flag |= BAM_FLAG_ALL_PROPER;    // mate is mapped properly
+
+        if (alignedMate.beginPos > alignedMate.endPos)
+            record.flag |= BAM_FLAG_NEXT_RC;   // mate is mapped on reverse strand
+    }
+    else
+    {
+        record.flag |= BAM_FLAG_NEXT_UNMAPPED; // mate is unmapped
+    }
+
+    record.rNextId = (alignedMate.contigId != TContig::INVALID_ID)? alignedMate.contigId : BamAlignmentRecord::INVALID_REFID;
+
+    // Fill PNEXT with mate start position
+    // Fill TLEN with outer distance of the read alignments
+    if (alignedMate.contigId < length(store.contigStore))
+    {
+        TContigGaps contigGaps(store.contigStore[alignedMate.contigId].gaps);
+        record.pNext = positionGapToSeq(contigGaps, std::min(alignedMate.beginPos, alignedMate.endPos));
+
+        if (alignedMate.contigId == alignedRead.contigId)
+        {
+            if (alignedRead.beginPos < alignedMate.beginPos)
+                record.tLen = positionGapToSeq(contigGaps, std::max(alignedMate.beginPos, alignedMate.endPos) - 1) - record.beginPos + 1;
+            else
+                record.tLen = record.pNext - positionGapToSeq(contigGaps, std::max(alignedRead.beginPos, alignedRead.endPos) - 1) - 1;
+        }
+        else
         {
-            TWord mask = (TWord)1 << (readId % wordLen);
-            if ((readAligned[readId / wordLen] & mask) != 0)
-                continue;
-            
-            // <qname>
-            if (readId < length(store.readNameStore)) {
-                typedef typename Iterator<CharString, Standard>::Type TCharStringIterator;
-                if (empty(store.readNameStore[readId]))
-                    continue;
-                for (TCharStringIterator it = begin(store.readNameStore[readId]); it != end(store.readNameStore[readId]); ++it) {
-                    if (*it == ' ' || *it == '\t' || *it == '\n' || *it == '\r')
-                        break;
-                    _streamPut(target, *it);
-                }
-            } else
-                continue;
-            _streamPut(target, '\t');
-            
-            // <flag>
-            unsigned short flag = 0x04;         // read is unaligned
-            int mateNo = getMateNo(store, readId);
-            if (mateNo == 0) flag |= 0x0041;    // this read is the first in the pair
-            if (mateNo == 1) flag |= 0x0081;    // this read is the second in the pair
-
-            _streamPutInt(target, flag);
-            _streamPut(target, '\t');
-            
-            // <rname>
-            _streamWrite(target, '*');
-            _streamPut(target, '\t');
-            
-            // <pos>
-            _streamWrite(target, '0');
-            _streamPut(target, '\t');
-            
-            // <mapq>
-            _streamWrite(target, '0');
-            _streamPut(target, '\t');
-            
-            // <cigar>
-            _streamWrite(target, '*');
-            _streamPut(target, '\t');
-            
-            // <mrnm>
-            _streamWrite(target, '*');
-            _streamPut(target, '\t');
-            
-            // <mpos>
-            _streamWrite(target, '0');
-            _streamPut(target, '\t');
-            
-            // <isize>
-            _streamWrite(target, '0');
-            _streamPut(target, '\t');
-
-            // <seq>
-            readSeq = store.readSeqStore[readId];
-            _streamWrite(target, readSeq);
-            _streamPut(target, '\t');
-            
-            // <qual>
-            TReadSeqIter it = begin(readSeq, Standard());
-            TReadSeqIter itEnd = end(readSeq, Standard());
-            for (; it != itEnd; ++it)
-                _streamPut(target, (char)(getQualityValue(*it) + 33));
-
-            // <tags>
-            _streamWrite(target, "\tNH:i:0");
-            
-            _streamPut(target, '\n');
+            record.tLen = BamAlignmentRecord::INVALID_LEN;
         }
-#endif  // #if 0
     }
-    
-    template<typename TFile, typename TSpec, typename TConfig>
-    inline void _writeAlignments(TFile & target,
-                                 FragmentStore<TSpec, TConfig> & store,
-                                 Sam)
+    else
     {
-        _writeAlignments(target, store, Sam(), Nothing());
+        record.pNext = BamAlignmentRecord::INVALID_POS;
+        record.tLen = BamAlignmentRecord::INVALID_LEN;
     }
+}
+
+// --------------------------------------------------------------------------
+// Function writeAlignments()
+// --------------------------------------------------------------------------
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig, typename TBamIOFunctor>
+inline void
+writeAlignments(FormattedFile<Bam, Output, TSpec> & bamFile,
+                FragmentStore<TFSSpec, TFSConfig> & store,
+                TBamIOFunctor & functor)
+{
+    typedef FragmentStore<TFSSpec, TFSConfig>                       TFragmentStore;
 
-//////////////////////////////////////////////////////////////////////////////
-// write
+    typedef typename TFragmentStore::TReadStore                     TReadStore;
+    typedef typename Value<TReadStore>::Type                        TReadStoreElement;
 
-///.Function.write.param.tag.type:Tag.File Format.tag.Sam
-    
-    template<typename TFile, typename TSpec, typename TConfig>
-    inline void write(TFile & target,
-                      FragmentStore<TSpec, TConfig> & store,
-                      Sam)
+    typedef typename TFragmentStore::TAlignedReadStore              TAlignedReadStore;
+    typedef typename Iterator<TAlignedReadStore, Standard>::Type    TAlignedReadStoreIterator;
+    typedef typename Value<TAlignedReadStore>::Type                 TAlignedReadStoreElement;
+    typedef typename Id<TAlignedReadStoreElement>::Type             TAlignedReadStoreElementId;
+
+    typedef typename TFragmentStore::TAlignQualityStore             TAlignQualityStore;
+    typedef typename Value<TAlignQualityStore>::Type                TAlignQualityStoreElement;
+
+    typedef TAlignQualityStoreElement *                             TAlignQualityStoreElementPtr;
+
+    // Store outer library size for each pair match (indexed by pairMatchId)
+    String<TAlignedReadStoreElementId> mateIndices;
+    calculateMateIndices(mateIndices, store);
+
+    // Bitset to signal wether a read was aligned at least once.
+    String<bool, Packed<> > readAligned;
+    resize(readAligned, length(store.readStore), false);
+
+    // Dummy store elements to cope with missing information.
+    TAlignQualityStoreElement       noAlignQuality;
+    TAlignQualityStoreElementPtr    alignQualityPtr;
+
+    TAlignedReadStoreIterator it    = begin(store.alignedReadStore, Standard());
+    TAlignedReadStoreIterator itEnd = end(store.alignedReadStore, Standard());
+
+    BamAlignmentRecord record;
+
+    for (; it != itEnd; ++it)
     {
-        typedef FragmentStore<TSpec, TConfig>               TFragmentStore;
-        typedef typename TFragmentStore::TContigNameStore   TContigNameStore;
-        typedef BamIOContext<TContigNameStore>              TBamIOContext;
+        TAlignedReadStoreElement &alignedRead = *it;
+
+        // Try to get quality.
+        if (alignedRead.id < length(store.alignQualityStore))
+            alignQualityPtr = &store.alignQualityStore[alignedRead.id];
+        else
+            alignQualityPtr = &noAlignQuality;
 
-        TBamIOContext context(store.contigNameStore, store.contigNameStoreCache);
+        // Try to get a mate.
 
-        // 1. write header
-        BamHeader header;
+        // We disinguish 3 cases:
+        //  1) We have no mate (single-end read)
+        //  2) We might have a mate, but it wasn't aligned properly
+        //  3) We have a mate which was aligned properly
 
-        // fill header with information from fragment store.
-        _fillHeader(header, store);
+        // Test for secondary alignment and mark read as seen.
+        bool secondary = getValue(readAligned, alignedRead.readId);
+        assignValue(readAligned, alignedRead.readId, true);
 
-        // write header to target.
-        write2(target, header, context, Sam());
+        // Fill record.
+        clear(record);
 
-        // 2. write aligments
-        _writeAlignments(target, store, Sam());
+        // case 1 or 2 is handled here
+        setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary);
+
+        if (alignedRead.pairMatchId != TReadStoreElement::INVALID_ID)
+        {
+            // case 3
+            TAlignedReadStoreElementId mateIndex = mateIndices[2 * alignedRead.pairMatchId + getMateNo(store, alignedRead.readId)];
+            if (mateIndex < length(store.alignedReadStore))
+                setMateMatch(record, store, alignedRead, store.alignedReadStore[mateIndex]);
+        }
+
+        // Append additional tags.
+        if (alignedRead.id < length(store.alignedReadTagStore))
+            append(record.tags, store.alignedReadTagStore[alignedRead.id]);
+
+        // Write record to target.
+        writeRecord(bamFile, record);
     }
-    
+}
+
+// --------------------------------------------------------------------------
+// Function writeRecords()
+// --------------------------------------------------------------------------
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig, typename TBamIOFunctor>
+inline void
+writeRecords(FormattedFile<Bam, Output, TSpec> & bamFile,
+             FragmentStore<TFSSpec, TFSConfig> & store,
+             TBamIOFunctor & functor)
+{
+    // 1. write header
+    writeHeader(bamFile, store, functor);
+
+    // 2. write aligments
+    writeAlignments(bamFile, store, functor);
+}
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig>
+inline void
+writeRecords(FormattedFile<Bam, Output, TSpec> & bamFile,
+             FragmentStore<TFSSpec, TFSConfig> & store)
+{
+    BamAlignFunctorDefault functor;
+    writeRecords(bamFile, store, functor);
+}
+
 }// namespace SEQAN_NAMESPACE_MAIN
 
 #endif //#ifndef SEQAN_HEADER_...
diff --git a/seqan/store/store_io_ucsc.h b/seqan/store/store_io_ucsc.h
old mode 100755
new mode 100644
index 43e1c67..57f8b4a
--- a/seqan/store/store_io_ucsc.h
+++ b/seqan/store/store_io_ucsc.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,318 +32,22 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_STORE_IO_UCSC_H
-#define SEQAN_HEADER_STORE_IO_UCSC_H
-
-/* IOREV
- *
- * _doc_
- *
- *
- * maybe move this to file/ because its a file format
- *
- */
-
+#ifndef SEQAN_INCLUDE_STORE_STORE_IO_UCSC_H
+#define SEQAN_INCLUDE_STORE_STORE_IO_UCSC_H
 
 namespace SEQAN_NAMESPACE_MAIN {
 
-template <typename TSpec>
-struct Ucsc_;
-
-/*!
- * @tag Ucsc
- * @headerfile <seqan/store.h>
- * @brief UCSC Genome browser annotation file (aka knownGene format).
- *
- * @signature typedef Tag<Ucsc<UcscKnownGene_> > const Ucsc;
- */
-
-/**
-.Tag.File Format.tag.Ucsc:
-    Ucsc Genome Browser annotation file (a.k.a. knownGene format).
-..include:seqan/store.h
-*/
-
-struct UcscKnownGene_;
-typedef Tag<Ucsc_<UcscKnownGene_> > const Ucsc;
-
-/*!
- * @tag UcscIsoforms
- * @headerfile <seqan/store.h>
- * @brief UCSC Genome browser annotation file (aka knownIsoforms format).
- *
- * @signature typedef Tag<Ucsc<UcscKnownIsoforms_> > const UcscIsoforms;
- */
-
-/**
-.Tag.File Format.tag.UcscIsoforms:
-    Ucsc Genome Browser isoforms file (a.k.a. knownIsoforms format).
-..include:seqan/store.h
-*/
-struct UcscKnownIsoforms_;
-typedef Tag<Ucsc_<UcscKnownIsoforms_> > const UcscIsoforms;
-
-//////////////////////////////////////////////////////////////////////////////
-// Read Ucsc
 //////////////////////////////////////////////////////////////////////////////
+// add a UCSC record to FragmentStore
 
-template <typename TFragmentStore, typename TSpec = void>
-struct IOContextUcsc_
-{
-    typedef typename TFragmentStore::TAnnotationStore   TAnnotationStore;
-    typedef typename Value<TAnnotationStore>::Type      TAnnotation;
-    typedef typename TAnnotation::TId                   TId;
-
-    CharString      transName;
-    CharString      contigName;
-    __int64         cdsBegin;
-    __int64         cdsEnd;
-    String<__int64> exonBegin;
-    String<__int64> exonEnd;
-    CharString      proteinName;
-
-    enum {KNOWN_GENE, KNOWN_ISOFORMS} format;
-    TAnnotation annotation;
-};
-
-template <typename TFragmentStore, typename TSpec>
-inline void clear(IOContextUcsc_<TFragmentStore, TSpec> & ctx)
-{
-    clear(ctx.transName);
-    clear(ctx.contigName);
-    clear(ctx.exonBegin);
-    clear(ctx.exonEnd);
-    clear(ctx.proteinName);
-    clear(ctx.annotation.values);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-// _readOneAnnotation
-//
-// reads in one annotation line from a Gff file
-
-// TODO(singer): return int instead of bool
-template <typename TRecordReader, typename TFragmentStore, typename TSpec>
-inline bool
-_readOneAnnotation(
-    TRecordReader & reader,
-    IOContextUcsc_<TFragmentStore, TSpec> & ctx)
-{
-    typedef typename TFragmentStore::TContigPos         TContigPos;
-    typedef typename TFragmentStore::TAnnotationStore   TAnnotationStore;
-    typedef typename Value<TAnnotationStore>::Type      TAnnotation;
-
-    clear(ctx);
-
-    // read column 1: transcript name
-    // The letters until the first whitespace will be read.
-    // Then, we skip until we hit the first tab character.
-    if (readUntilWhitespace(ctx.transName, reader))
-        return false;
-
-    if (!empty(ctx.transName) && ctx.transName[0] == '#')
-    {
-        if (skipLine(reader))
-            return false;
-
-        return false;
-    }
-    if (skipWhitespaces(reader))
-        return false;
-
-    // read column 2: contig name
-    if (readUntilWhitespace(ctx.contigName, reader))
-        return false;
-
-    if (skipBlanks(reader))
-        return false;
-
-    // read column 3: orientation
-    String<char> temp;
-    if (readUntilWhitespace(temp, reader))
-        return false;
-
-    if (empty(temp))
-    {
-        ctx.format = ctx.KNOWN_ISOFORMS;
-        insert(ctx.transName, 0, "GENE");
-        if (skipLine(reader))
-            return false;
-
-        return true;
-    }
-    ctx.format = ctx.KNOWN_GENE;
-    char orientation = temp[0];
-    if (skipBlanks(reader))
-        return false;
-
-
-    // read column 4: transcript begin position
-    clear(temp);
-    if (readDigits(temp, reader))
-        return false;
-
-    if (length(temp) > 0u)
-    {
-        if (!lexicalCast2(ctx.annotation.beginPos, temp))
-            return false;
-    }
-    else
-    {
-        ctx.annotation.beginPos = TAnnotation::INVALID_POS;
-        if (skipUntilWhitespace(reader))
-            return false;
-    }
-    if (skipBlanks(reader))
-        return false;
-
-    // read column 5: transcript end position
-    clear(temp);
-    if (readDigits(temp, reader))
-        return false;
-
-    if (length(temp) > 0u)
-    {
-        if (!lexicalCast2(ctx.annotation.endPos, temp))
-            return false;
-    }
-    else
-    {
-        ctx.annotation.endPos = TAnnotation::INVALID_POS;
-        if (skipUntilWhitespace(reader))
-            return false;
-    }
-    if (skipBlanks(reader))
-        return false;
-
-    // read column 6: CDS begin position
-    clear(temp);
-    if (readDigits(temp, reader))
-        return false;
-
-    if (length(temp) > 0u)
-    {
-        if (!lexicalCast2(ctx.cdsBegin, temp))
-            return false;
-    }
-    else
-    {
-        ctx.cdsBegin = TAnnotation::INVALID_POS;
-        if (skipUntilWhitespace(reader))
-            return false;
-    }
-    if (skipBlanks(reader))
-        return false;
-
-    // read column 7: CDS end position
-    clear(temp);
-    if (readDigits(temp, reader))
-        return false;
-
-    if (length(temp) > 0u)
-    {
-        if (!lexicalCast2(ctx.cdsEnd, temp))
-            return false;
-    }
-    else
-    {
-        ctx.cdsEnd = TAnnotation::INVALID_POS;
-        if (skipUntilWhitespace(reader))
-            return false;
-    }
-    if (skipBlanks(reader))
-        return false;
-
-    // read column 8: exon count
-    int exons = -1;
-    clear(temp);
-    if (readDigits(temp, reader))
-        return false;
-
-    if (length(temp) > 0u)
-        if (!lexicalCast2(exons, temp))
-            return false;
-
-    if (skipBlanks(reader))
-        return false;
-
-    // read column 9: exon begin positions
-    for (int i = 0; i < exons; ++i)
-    {
-        clear(temp);
-        if (readDigits(temp, reader))
-            return false;
-
-        unsigned long long tempBegin;
-        if (!lexicalCast2(tempBegin, temp))
-            return false;
-
-        appendValue(ctx.exonBegin, tempBegin, Generous());
-        if (skipNCharsIgnoringWhitespace(reader, 1u))
-            return false;
-
-    }
-    skipBlanks(reader);
-
-    // read column 10: exon end positions
-    for (int i = 0; i < exons; ++i)
-    {
-        clear(temp);
-        if (readDigits(temp, reader))
-            return false;
-
-        unsigned long long tempEnd;
-        if (!lexicalCast2(tempEnd, temp))
-            return false;
-
-        appendValue(ctx.exonEnd, tempEnd, Generous());
-        if (skipNCharsIgnoringWhitespace(reader, 1u))
-            return false;
-    }
-    if (skipUntilChar(reader, '\t'))
-        return false;
-
-    if (skipNChars(reader, 1u))
-        return false;
-
-
-    // read column 11: protein name
-    if (readUntilWhitespace(ctx.proteinName, reader))
-        return false;
-
-    if (skipBlanks(reader))
-        return false;
-
-    // skip column 12
-    if (skipLine(reader))
-        return false;
-
-    // adapt positions
-    if (orientation == '-')
-    {
-        TContigPos tmp = ctx.annotation.beginPos;
-        ctx.annotation.beginPos = ctx.annotation.endPos;
-        ctx.annotation.endPos = tmp;
-        tmp = ctx.cdsBegin;
-        ctx.cdsBegin = ctx.cdsEnd;
-        ctx.cdsEnd = tmp;
-        for (int i = 0; i < exons; ++i)
-        {
-            tmp = ctx.exonBegin[i];
-            ctx.exonBegin[i] = ctx.exonEnd[i];
-            ctx.exonEnd[i] = tmp;
-        }
-    }
-
-    return true;
-}
-
-template <typename TFragmentStore, typename TSpec>
+template <typename TSpec, typename TConfig>
 inline void
-_storeOneAnnotationKnownGene(
-    TFragmentStore & fragStore,
-    IOContextUcsc_<TFragmentStore, TSpec> & ctx)
+_storeAnnotationRecord(
+    FragmentStore<TSpec, TConfig> & fragStore,
+    UcscRecord const & record,
+    UcscKnownGene)
 {
+    typedef FragmentStore<TSpec, TConfig>               TFragmentStore;
     typedef typename TFragmentStore::TAnnotationStore   TAnnotationStore;
     typedef typename Value<TAnnotationStore>::Type      TAnnotation;
     typedef typename TAnnotation::TId                   TId;
@@ -352,52 +56,58 @@ _storeOneAnnotationKnownGene(
 
     // add transcript and CDS
     TId transId = TAnnotation::INVALID_ID;
-    _storeAppendAnnotationName(fragStore, transId, ctx.transName, (TId) TFragmentStore::ANNO_MRNA);
+    _storeAppendAnnotationName(fragStore, transId, record.transName, (TId) TFragmentStore::ANNO_MRNA);
     TId cdsId = length(fragStore.annotationStore);
-    appendName(fragStore.annotationNameStore, ctx.proteinName, fragStore.annotationNameStoreCache);
+    appendName(fragStore.annotationNameStore, record.proteinName, fragStore.annotationNameStoreCache);
 
-    resize(fragStore.annotationStore, cdsId + 1 + length(ctx.exonBegin), Generous());
-    resize(fragStore.annotationNameStore, cdsId + 1 + length(ctx.exonBegin), Generous());
+    resize(fragStore.annotationStore, cdsId + 1 + length(record.exonBegin), Generous());
+    resize(fragStore.annotationNameStore, cdsId + 1 + length(record.exonBegin), Generous());
 
     // add contig name
-    _storeAppendContig(fragStore, ctx.annotation.contigId, ctx.contigName);
+    TId contigId = TAnnotation::INVALID_ID;
+    _storeAppendContig(fragStore, contigId, record.contigName);
 
+    // update transcript data
     TAnnotation & transcript = fragStore.annotationStore[transId];
     TId geneId = transcript.parentId;
     if (geneId == TAnnotation::INVALID_ID)
         geneId = 0;
-    transcript = ctx.annotation;
     transcript.parentId = geneId;
+    transcript.contigId = contigId;
     transcript.typeId = TFragmentStore::ANNO_MRNA;
 
+    // add CDS entry
     TAnnotation & cds = fragStore.annotationStore[cdsId];
-    cds = ctx.annotation;
     cds.parentId = transId;
+    cds.contigId = contigId;
     cds.typeId = TFragmentStore::ANNO_CDS;
-    cds.beginPos = ctx.cdsBegin;
-    cds.endPos = ctx.cdsEnd;
+    cds.beginPos = record.cdsBegin;
+    cds.endPos = record.cdsEnd;
     _adjustParent(transcript, cds);
 
-    // insert exons
-    ctx.annotation.parentId = transId;
-    ctx.annotation.typeId = TFragmentStore::ANNO_EXON;
-    for (unsigned i = 0; i < length(ctx.exonBegin); ++i)
+    // add exons
+    for (unsigned i = 0; i < length(record.exonBegin); ++i)
     {
-        ctx.annotation.beginPos = ctx.exonBegin[i];
-        ctx.annotation.endPos = ctx.exonEnd[i];
-        fragStore.annotationStore[cdsId + 1 + i] = ctx.annotation;
-        _adjustParent(transcript, ctx.annotation);
+        TAnnotation & exon = fragStore.annotationStore[cdsId + 1 + i];
+        exon.parentId = transId;
+        exon.contigId = contigId;
+        exon.typeId = TFragmentStore::ANNO_EXON;
+        exon.beginPos = record.exonBegin[i];
+        exon.endPos = record.exonEnds[i];
+        _adjustParent(transcript, exon);
     }
     if (geneId != 0)
         _adjustParent(fragStore.annotationStore[geneId], transcript);
 }
 
-template <typename TFragmentStore, typename TSpec>
+template <typename TSpec, typename TConfig>
 inline void
-_storeOneAnnotationKnownIsoforms(
-    TFragmentStore & fragStore,
-    IOContextUcsc_<TFragmentStore, TSpec> & ctx)
+_storeAnnotationRecord(
+    FragmentStore<TSpec, TConfig> & fragStore,
+    UcscRecord const & record,
+    UcscKnownIsoforms const &)
 {
+    typedef FragmentStore<TSpec, TConfig>               TFragmentStore;
     typedef typename TFragmentStore::TAnnotationStore   TAnnotationStore;
     typedef typename Value<TAnnotationStore>::Type      TAnnotation;
     typedef typename TAnnotation::TId                   TId;
@@ -408,8 +118,8 @@ _storeOneAnnotationKnownIsoforms(
     TId transId = TAnnotation::INVALID_ID;
 
     // add transcript and CDS
-    _storeAppendAnnotationName(fragStore, geneId, ctx.transName, (TId) TFragmentStore::ANNO_GENE);
-    _storeAppendAnnotationName(fragStore, transId, ctx.contigName, (TId) TFragmentStore::ANNO_MRNA);
+    _storeAppendAnnotationName(fragStore, geneId, record.transName, (TId) TFragmentStore::ANNO_GENE);
+    _storeAppendAnnotationName(fragStore, transId, record.contigName, (TId) TFragmentStore::ANNO_MRNA);
 
     // set parent link locus->root
     TAnnotation & locus = fragStore.annotationStore[geneId];
@@ -424,46 +134,60 @@ _storeOneAnnotationKnownIsoforms(
     _adjustParent(locus, transcript);
 }
 
-template <typename TFragmentStore, typename TSpec>
+// support for dynamically chosen file formats
+template <typename TSpec, typename TConfig>
 inline void
-_storeOneAnnotation(
-    TFragmentStore & fragStore,
-    IOContextUcsc_<TFragmentStore, TSpec> & ctx)
+_storeAnnotationRecord(
+    FragmentStore<TSpec, TConfig> & /*store*/,
+    UcscRecord const & /*record*/,
+    TagSelector<> const & /*format*/)
+{
+    SEQAN_FAIL("AnnotationStore: File format not specified.");
+}
+
+template <typename TSpec, typename TConfig, typename TTagList>
+inline void
+_storeAnnotationRecord(
+    FragmentStore<TSpec, TConfig> & store,
+    UcscRecord const & record,
+    TagSelector<TTagList> const & format)
 {
-    if (ctx.format == ctx.KNOWN_GENE)
-        _storeOneAnnotationKnownGene(fragStore, ctx);
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        _storeAnnotationRecord(store, record, TFormat());
     else
-        _storeOneAnnotationKnownIsoforms(fragStore, ctx);
+        _storeAnnotationRecord(store, record, static_cast<typename TagSelector<TTagList>::Base const &>(format));
 }
 
-// TODO(holtgrew): Change interface such that file is after store.
-// TODO(singer): all the other read functions get a RecordReader not a file.
-template <typename TFile, typename TSpec, typename TConfig, typename TFormatSpec>
+
+
+//////////////////////////////////////////////////////////////////////////////
+// read a whole UCSC stream into FragmentStore
+
+template <typename TFSSpec, typename TConfig, typename TSpec>
 inline void
-read(
-    TFile & file,
-    FragmentStore<TSpec, TConfig> & fragStore,
-    Tag<Ucsc_<TFormatSpec> > const)
+readRecords(FragmentStore<TFSSpec, TConfig> & fragStore,
+            FormattedFile<Ucsc, Input, TSpec> & file)
 {
-//IOREV _nodoc_
-    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+    typedef FormattedFile<Ucsc, Input, TSpec> TFile;
+    typename DirectionIterator<TFile, Input>::Type iter = directionIterator(file, Input());
 
-    if (streamEof(file))
+    if (atEnd(iter))
         return;
 
     // get first character from the stream
-    IOContextUcsc_<TFragmentStore> ctx;
+    UcscRecord record;
+    UcscIOContext ctx;
 
     refresh(fragStore.contigNameStoreCache);
     refresh(fragStore.annotationNameStoreCache);
     refresh(fragStore.annotationTypeStoreCache);
 
-    RecordReader<TFile, SinglePass<> > reader(file);
-
-    while (!atEnd(reader))
+    while (!atEnd(iter))
     {
-        if (_readOneAnnotation(reader, ctx))
-            _storeOneAnnotation(fragStore, ctx);
+        readRecord(record, ctx, iter, format(file));
+        _storeAnnotationRecord(fragStore, record, format(file));
     }
     _storeClearAnnoBackLinks(fragStore.annotationStore);
     _storeCreateAnnoBackLinks(fragStore.annotationStore);
@@ -471,32 +195,34 @@ read(
 }
 
 //////////////////////////////////////////////////////////////////////////////
-// Write Ucsc
-//////////////////////////////////////////////////////////////////////////////
+// extract FragmentStore annotation into a UCSC record
 
-template <typename TFragmentStore, typename TSpec, typename TAnnotation, typename TId>
+template <typename TRecord, typename TSpec, typename TConfig, typename TAnnotation, typename TId>
 inline bool
-_retrieveOneAnnotation(
-    TFragmentStore & fragStore,
-    IOContextUcsc_<TFragmentStore, TSpec> & ctx,
+_fillAnnotationRecord(
+    TRecord & record,
+    FragmentStore<TSpec, TConfig> & fragStore,
     TAnnotation & annotation,
     TId id,
-    Ucsc)
+    UcscKnownGene)
 {
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+
     if (annotation.typeId != TFragmentStore::ANNO_MRNA)
         return false;
 
-    ctx.format = ctx.KNOWN_GENE;
-    ctx.transName = getAnnoUniqueName(fragStore, id);
+    record.transName = getAnnoUniqueName(fragStore, id);
     if (annotation.contigId < length(fragStore.contigNameStore))
-        ctx.contigName = fragStore.contigNameStore[annotation.contigId];
+        record.contigName = fragStore.contigNameStore[annotation.contigId];
     else
-        clear(ctx.contigName);
+        clear(record.contigName);
+
+    clear(record.proteinName);
+    clear(record.exonBegin);
+    clear(record.exonEnds);
 
-    ctx.annotation = annotation;
-    clear(ctx.proteinName);
-    clear(ctx.exonBegin);
-    clear(ctx.exonEnd);
+    record.annotationBeginPos = annotation.beginPos;
+    record.annotationEndPos = annotation.endPos;
 
     TId lastChildId = annotation.lastChildId;
     TId i = lastChildId;
@@ -507,216 +233,76 @@ _retrieveOneAnnotation(
         if (anno.typeId == TFragmentStore::ANNO_CDS)
         {
             if (i < length(fragStore.annotationNameStore))
-                ctx.proteinName = fragStore.annotationNameStore[i];
-            ctx.cdsBegin = anno.beginPos;
-            ctx.cdsEnd = anno.endPos;
+                record.proteinName = fragStore.annotationNameStore[i];
+            record.cdsBegin = anno.beginPos;
+            record.cdsEnd = anno.endPos;
         }
         if (anno.typeId == TFragmentStore::ANNO_EXON)
         {
-            appendValue(ctx.exonBegin, anno.beginPos, Generous());
-            appendValue(ctx.exonEnd, anno.endPos, Generous());
+            appendValue(record.exonBegin, anno.beginPos, Generous());
+            appendValue(record.exonEnds, anno.endPos, Generous());
         }
     }
     while (i != lastChildId);
     return true;
 }
 
-template <typename TFragmentStore, typename TSpec, typename TAnnotation, typename TId>
+template <typename TRecord, typename TSpec, typename TConfig, typename TAnnotation, typename TId>
 inline bool
-_retrieveOneAnnotation(
-    TFragmentStore & fragStore,
-    IOContextUcsc_<TFragmentStore, TSpec> & ctx,
+_fillAnnotationRecord(
+    TRecord & record,
+    FragmentStore<TSpec, TConfig> & fragStore,
     TAnnotation & annotation,
     TId id,
-    UcscIsoforms)
+    UcscKnownIsoforms)
 {
+    typedef FragmentStore<TSpec, TConfig> TFragmentStore;
+
     if (annotation.typeId != TFragmentStore::ANNO_MRNA)
         return false;
 
     if (annotation.parentId == TAnnotation::INVALID_ID || annotation.parentId == 0)
         return false;
 
-    ctx.format = ctx.KNOWN_ISOFORMS;
-    ctx.transName = getAnnoUniqueName(fragStore, annotation.parentId);
-    ctx.contigName = getAnnoUniqueName(fragStore, id);
+    record.transName = getAnnoUniqueName(fragStore, annotation.parentId);
+    record.contigName = getAnnoUniqueName(fragStore, id);
     return true;
 }
 
-template <typename TTargetStream, typename TFragmentStore, typename TSpec>
-inline bool
-_writeOneAnnotation(
-    TTargetStream & file,
-    IOContextUcsc_<TFragmentStore, TSpec> & ctx)
-{
-    typedef typename TFragmentStore::TContigPos         TContigPos;
-
-    unsigned suf = 0;
-    if (ctx.format == ctx.KNOWN_ISOFORMS && length(ctx.transName) >= 4 && prefix(ctx.transName, 4) == "GENE")
-        suf = 4;
-
-    // read column 1: transcript name
-    // The letters until the first whitespace will be read.
-    // Then, we skip until we hit the first tab character.
-    if (length(suffix(ctx.transName, suf)) > 0u)
-    {
-        if (streamWriteBlock(file, &(suffix(ctx.transName, suf))[0], length(suffix(ctx.transName, suf))) < length(suffix(ctx.transName, suf)))
-            return false;
-    }
-
-    if (streamPut(file, '\t'))
-        return false;
-
-    // read column 2: contig name
-    if (length(ctx.contigName) > 0u)
-    {
-        if (streamWriteBlock(file, &ctx.contigName[0], length(ctx.contigName)) < length(ctx.contigName))
-            return false;
-    }
-
-    if (ctx.format == ctx.KNOWN_ISOFORMS)
-    {
-        if (streamWriteChar(file, '\n'))
-            return false;
-
-        return true;
-    }
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 3: orientation
-    TContigPos transBeginPos, transEndPos;
-    TContigPos cdsBeginPos, cdsEndPos;
-    if (ctx.annotation.beginPos < ctx.annotation.endPos)
-    {
-        if (streamWriteChar(file, '+'))
-            return false;
-
-        transBeginPos = ctx.annotation.beginPos;
-        transEndPos = ctx.annotation.endPos;
-        cdsBeginPos = ctx.cdsBegin;
-        cdsEndPos = ctx.cdsEnd;
-    }
-    else
-    {
-        if (streamWriteChar(file, '-'))
-            return false;
-
-        transEndPos = ctx.annotation.beginPos;
-        transBeginPos = ctx.annotation.endPos;
-        cdsEndPos = ctx.cdsBegin;
-        cdsBeginPos = ctx.cdsEnd;
-    }
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 4: transcript begin position
-    if (streamPut(file, transBeginPos))
-        return false;
-
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 5: transcript end position
-    if (streamPut(file, transEndPos))
-        return false;
-
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 6: CDS begin position
-    if (streamPut(file, cdsBeginPos))
-        return false;
-
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 7: CDS end position
-    if (streamPut(file, cdsEndPos))
-        return false;
-
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 8: exon count
-    if (streamPut(file, length(ctx.exonBegin)))
-        return false;
-
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 9: exon begin positions
-    for (unsigned i = 0; i < length(ctx.exonBegin); ++i)
-    {
-        if (streamPut(file, _min(ctx.exonBegin[i], ctx.exonEnd[i])))
-            return false;
-
-        if (streamWriteChar(file, ','))
-            return false;
-    }
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 10: exon end positions
-    for (unsigned i = 0; i < length(ctx.exonBegin); ++i)
-    {
-        if (streamPut(file, _max(ctx.exonBegin[i], ctx.exonEnd[i])))
-            return false;
-
-        if (streamWriteChar(file, ','))
-            return false;
-    }
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // read column 10: protein name
-    if (length(ctx.proteinName) > 0u)
-    {
-        if (streamWriteBlock(file, &ctx.proteinName[0], length(ctx.proteinName)) < length(ctx.proteinName))
-            return false;
-    }
-
-    if (streamWriteChar(file, '\t'))
-        return false;
-
-    // skip column 11
-    if (length(ctx.transName) > 0u)
-    {
-        if (streamWriteBlock(file, &ctx.transName[0], length(ctx.transName)) < length(ctx.transName))
-            return false;
-    }
-
-    if (streamWriteChar(file, '\n'))
-        return false;
-
-    return true;
-}
+//////////////////////////////////////////////////////////////////////////////
+// write FragmentStore to a stream in UCSC format
 
-template <typename TTargetStream, typename TSpec, typename TConfig, typename TFormatSpec>
+template <typename TSpec, typename TFSSpec, typename TFSConfig, typename TFormat>
 inline void
-write(
-    TTargetStream & target,
-    FragmentStore<TSpec, TConfig> & store,
-    Tag<Ucsc_<TFormatSpec> > const format)
+writeRecords(FormattedFile<Ucsc, Output, TSpec> & ucscFile,
+             FragmentStore<TFSSpec, TFSConfig> & store,
+             TFormat const & format)
 {
-//IOREV _nodoc_
-    typedef FragmentStore<TSpec, TConfig>                           TFragmentStore;
+    typedef FragmentStore<TFSSpec, TFSConfig>                       TFragmentStore;
     typedef typename TFragmentStore::TAnnotationStore               TAnnotationStore;
     typedef typename Value<TAnnotationStore>::Type                  TAnnotation;
     typedef typename Iterator<TAnnotationStore, Standard>::Type     TAnnoIter;
     typedef typename Id<TAnnotation>::Type                          TId;
 
-    IOContextUcsc_<TFragmentStore> ctx;
+    typename DirectionIterator<FormattedFile<Ucsc, Output, TSpec>, Output>::Type iter = directionIterator(ucscFile, Output());
+    UcscRecord record;
 
     TAnnoIter it = begin(store.annotationStore, Standard());
     TAnnoIter itEnd = end(store.annotationStore, Standard());
 
     for (TId id = 0; it != itEnd; ++it, ++id)
-    {
-        if (_retrieveOneAnnotation(store, ctx, *it, id, format))
-            _writeOneAnnotation(target, ctx);
-    }
+        if (_fillAnnotationRecord(record, store, *it, id, format))
+            writeRecord(iter, record, format);
+}
+
+template <typename TSpec, typename TFSSpec, typename TFSConfig>
+inline void
+writeRecords(FormattedFile<Ucsc, Output, TSpec> & ucscFile,
+             FragmentStore<TFSSpec, TFSConfig> & store)
+{
+    writeRecords(ucscFile, store, format(ucscFile));
 }
 
 } // namespace SEQAN_NAMESPACE_MAIN
 
-#endif //#ifndef SEQAN_HEADER_...
+#endif //#ifndef SEQAN_INCLUDE_STORE_STORE_IO_UCSC_H
diff --git a/seqan/store/store_library.h b/seqan/store/store_library.h
index 81d8d86..d8658cd 100644
--- a/seqan/store/store_library.h
+++ b/seqan/store/store_library.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -54,9 +54,9 @@ namespace SEQAN_NAMESPACE_MAIN
  * @tparam TStd  The type to use for storing library size standard deviations.  Default: <tt>double</tt>.
  * @tparam TSpec The specializing type.  Default: <tt>void</tt>.
  *
- * Valkue type of the @link FragmentStore::libraryStore @endlink string.
+ * Value type of the @link FragmentStore::libraryStore @endlink string.
  *
- * A fragment library is a set of mate pairs having a certain distribution of interst sizes.
+ * A fragment library is a set of mate pairs having a certain distribution of insert sizes.
  *
  *
  * @fn LibraryStoreElement::LibraryStoreElement
@@ -71,47 +71,17 @@ namespace SEQAN_NAMESPACE_MAIN
  * @var TMean LibraryStoreElement::mean;
  * @brief The library size mean.
  *
- * @var TStd LibraryStoreElement::std;
+ * @var TStd LibraryStoreElementstd;
  * @brief The library size standard deviation.
- */ 
-
-/**
-.Class.LibraryStoreElement
-..summary:Represents a fragment library.
-..cat:Fragment Store
-..signature:LibraryStoreElement<>
-..signature:LibraryStoreElement<TMean[, TStd[, TSpec]]>
-..param.TMean:The type to represent the library size mean.
-...default:$double$
-..param.TStd:The type to represent the library size standard deviation.
-...default:$double$
-..param.TSpec:The specialization type.
-...default:$void$
-..remarks:A fragment library is a set of mate-pairs having a certain distribution of insert sizes.
-..remarks:Value type of the @Memvar.FragmentStore#libraryStore@ string.
-
-.Memfunc.LibraryStoreElement#LibraryStoreElement
-..summary:Constructor
-..signature:LibraryStoreElement<>()
-..signature:LibraryStoreElement<TMean[, TStd[, TSpec]]> ()
-..remarks:Sets $mean$ and $std$ to $0$.
-..class:Class.LibraryStoreElement
-.Memvar.LibraryStoreElement#mean
-..summary:The library size mean.
-..class:Class.LibraryStoreElement
-.Memvar.LibraryStoreElement#std
-..summary:The library size standard deviation.
-..class:Class.LibraryStoreElement
-..include:seqan/store.h
-*/
+ */
 
 template <typename TMean = double, typename TStd = double, typename TSpec = void>
 struct LibraryStoreElement
 {
-	TMean		mean;		// mean library size in bps
-	TStd		std;	// library size variance
+    TMean        mean;        // mean library size in bps
+    TStd        std;    // library size variance
 
-	LibraryStoreElement() : mean(0), std(0) {}
+    LibraryStoreElement() : mean(0), std(0) {}
 
     inline bool operator==(LibraryStoreElement const & other) const
     {
diff --git a/seqan/store/store_matepair.h b/seqan/store/store_matepair.h
index 43996a5..1a19fda 100644
--- a/seqan/store/store_matepair.h
+++ b/seqan/store/store_matepair.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -75,54 +75,21 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Refers to two paried reads in @link FragmentStore::readStore @endlink or is INVALID_ID values.
  */
 
-/**
-.Class.MatePairStoreElement
-..summary:Represents a mate-pair.
-..cat:Fragment Store
-..signature:MatePairStoreElement<>
-..signature:MatePairStoreElement<TSpec>
-..param.TSpec:The specialization type.
-...default:$void$
-..remarks:A mate-pair consists of two reads sequenced from opposite ends and strands of the same fragment.
-The insert size of a mate-pair is the size of the fragment.
-..remarks:Value type of the @Memvar.FragmentStore#matePairStore@ string.
-
-.Memfunc.MatePairStoreElement#MatePairStoreElement
-..summary:Constructor
-..signature:MatePairStoreElement<> ()
-..signature:MatePairStoreElement<TSpec> ()
-..remarks:Sets $readId[0]$, $readId[1]$ and $libId$ to $INVALID_ID$.
-..class:Class.MatePairStoreElement
-.Memvar.MatePairStoreElement#readId[2]
-..summary:Refers to two paired reads in the @Memvar.FragmentStore#readStore@ or contains $INVALID_ID$ values.
-..type:Metafunction.Id
-..class:Class.MatePairStoreElement
-.Memvar.MatePairStoreElement#libId
-..summary:Refers to a library in the @Memvar.FragmentStore#libraryStore@ or is $INVALID_ID$ if the mate-pair has no library.
-..type:Metafunction.Id
-..class:Class.MatePairStoreElement
-.Memvar.MatePairStoreElement#INVALID_ID
-..summary:Constant to represent an invalid id.
-..type:Metafunction.Id
-..class:Class.MatePairStoreElement
-..include:seqan/store.h
-*/
-
 template <typename TSpec = void>
 struct MatePairStoreElement
 {
-	typedef typename Id<MatePairStoreElement>::Type TId;
+    typedef typename Id<MatePairStoreElement>::Type TId;
 
-	static const TId INVALID_ID;
-	
-	TId		readId[2];	// refers to the two reads of a mate-pair, INVALID_ID if this is a singleton fragment (e.g. in afg: reads refer to fragments (mate pairs) and these refer to libraries, singletons refer to an empty fragment)
-	TId		libId;
+    static const TId INVALID_ID;
 
-	MatePairStoreElement() : libId(INVALID_ID) 
-	{
-		readId[0] = INVALID_ID;
-		readId[1] = INVALID_ID;
-	}
+    TId        readId[2];    // refers to the two reads of a mate-pair, INVALID_ID if this is a singleton fragment (e.g. in afg: reads refer to fragments (mate pairs) and these refer to libraries, singletons refer to an empty fragment)
+    TId        libId;
+
+    MatePairStoreElement() : libId(INVALID_ID)
+    {
+        readId[0] = INVALID_ID;
+        readId[1] = INVALID_ID;
+    }
 
     inline bool operator==(MatePairStoreElement const & other) const
     {
@@ -134,6 +101,18 @@ struct MatePairStoreElement
 
 //////////////////////////////////////////////////////////////////////////////
 
+/*!
+ * @mfn MatePairStoreElement#Id
+ * @headerfile <seqan/store.h>
+ * @brief Returns the id type to use for <tt>MatePairStoreElement</tt>.
+ *
+ * @signature Id<TMatePairStoreElement>::Type;
+ *
+ * @tparam TMatePairStoreElement The MatePairStoreElement specialization to get the id type for.
+ *
+ * @return Type The resulting id type.
+ */
+
 template <typename TSpec>
 const typename Id<MatePairStoreElement<TSpec> >::Type
 MatePairStoreElement<TSpec>::INVALID_ID = MaxValue<typename Id<MatePairStoreElement<TSpec> >::Type>::VALUE;
diff --git a/seqan/store/store_read.h b/seqan/store/store_read.h
index 5e0f02d..b948c0c 100644
--- a/seqan/store/store_read.h
+++ b/seqan/store/store_read.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -53,7 +53,8 @@ namespace SEQAN_NAMESPACE_MAIN
  * @tparam TSpec The specializing type.  Default: <tt>void</tt>.
  *
  *
- * @fn ReadStoreElement::ReadStoreElement();
+ * @fn ReadStoreElement::ReadStoreElement
+ * @signature ReadStoreElement::ReadStoreElement();
  * @brief Constructor.
  *
  * Sets ReadStoreElement::matePairId to ReadStoreElement::INVALID_ID.
@@ -68,43 +69,16 @@ namespace SEQAN_NAMESPACE_MAIN
  * @brief Constant to represetn an invalid id.
  */
 
-/**
-.Class.ReadStoreElement
-..summary:Represents a single read (without sequence).
-..cat:Fragment Store
-..signature:ReadStoreElement<>
-..signature:ReadStoreElement<TSpec>
-..param.TSpec:The specialization type.
-...default:$void$
-..remarks:Value type of the @Memvar.FragmentStore#readStore@ string.
-
-.Memfunc.ReadStoreElement#ReadStoreElement
-..summary:Constructor
-..signature:ReadStoreElement<>()
-..signature:ReadStoreElement<TSpec> ()
-..remarks:Sets $matePairId$ to $INVALID_ID$.
-..class:Class.ReadStoreElement
-.Memvar.ReadStoreElement#matePairId
-..summary:Refers to a mate-pair in the @Memvar.FragmentStore#matePairStore@ or is $INVALID_ID$ if the read is not paired.
-..type:Metafunction.Id
-..class:Class.ReadStoreElement
-.Memvar.ReadStoreElement#INVALID_ID
-..summary:Constant to represent an invalid id.
-..type:Metafunction.Id
-..class:Class.ReadStoreElement
-..include:seqan/store.h
-*/
-
 template <typename TSpec = void>
 struct ReadStoreElement
 {
-	typedef typename Id<ReadStoreElement>::Type TId;
-	
-	static const TId INVALID_ID;
+    typedef typename Id<ReadStoreElement>::Type TId;
+
+    static const TId INVALID_ID;
 
-	TId matePairId;				// refers to the mate-pair, INVALID_ID if not part of a mate-pair
+    TId matePairId;                // refers to the mate-pair, INVALID_ID if not part of a mate-pair
 
-	ReadStoreElement() : matePairId(INVALID_ID) {}
+    ReadStoreElement() : matePairId(INVALID_ID) {}
 
     inline
     bool
diff --git a/seqan/stream.h b/seqan/stream.h
index c30389a..2a199e9 100644
--- a/seqan/stream.h
+++ b/seqan/stream.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -30,108 +30,86 @@
 //
 // ==========================================================================
 // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 // Facade header for the stream module.
 // ==========================================================================
 
-// TODO(holtgrew): Adaption for istream (and tests).
-// TODO(holtgrew): Adaption for ostream (and tests).
-// TODO(holtgrew): Adaption for stringstream (and tests).
-// TODO(holtgrew): Adaption for istringstream (and tests).
-// TODO(holtgrew): Adaption for ostringstream (and tests).
-
-// TODO(holtgrew): Adaption for external string?
-// TODO(holtgrew): Andreas' adapted the basic_* variants, why? Also, he included <iosfwd> and not <iostream> etc.
-
 #ifndef SEQAN_STREAM_H_
 #define SEQAN_STREAM_H_
 
-/*!
- * @macro SEQAN_HAS_ZLIB
- * @headerfile <seqan/stream.h>
- * @brief Defined as 0 or 1, depending on zlib being available.
- *
- * @signature #define SEQAN_HAS_ZLIB 0  // or 1
- */
-
-/*!
- * @macro SEQAN_HAS_BZIP2
- * @headerfile <seqan/stream.h>
- * @brief Defined as 0 or 1, depending on bzlib being available.
- *
- * @signature #define SEQAN_HAS_BZIP 0  // or 1
- */
-
-/**
-.Macro.SEQAN_HAS_ZLIB
-..cat:Input/Output
-..cat:From Outside
-..signature:SEQAN_HAS_ZLIB
-..summary:If set to 1 then zlib is available, i.e. including $<zlib.h>$ and linking against libz works.
-..remarks:This flag is normally set from the outside by your build system using compiler flags.
-
-.Macro.SEQAN_HAS_BZIP2
-..cat:Input/Output
-..cat:From Outside
-..signature:SEQAN_HAS_BZLIB
-..summary:If set to 1 then bzlib2 is available, i.e. including $<bzlib.h>$ and linking against libbzip2 works.
-..remarks:This flag is normally set from the outside by your build system using compiler flags.
- */
-
 // ===========================================================================
 // Prerequisites.
 // ===========================================================================
 
+#include <iostream>
+#include <fstream>
+#include <sstream>
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#ifdef _WIN32
+#ifndef ZLIB_WINAPI
+//#define ZLIB_WINAPI
+#endif
+#else
+#include <unistd.h>
+#endif
+
 #include <seqan/basic.h>
 #include <seqan/file.h>
 #include <seqan/sequence.h>
 
 // ===========================================================================
-// Stream Concept, Adaptions, Stream Class and Specializations.
+// Basic Definitions.
 // ===========================================================================
 
-#include <seqan/stream/concept_stream.h>
-
-#include <seqan/stream/adapt_cstdio.h>
-#include <seqan/stream/adapt_fstream.h>
-#include <seqan/stream/adapt_iostream.h>
-#include <seqan/stream/adapt_sstream.h>
-
 #include <seqan/stream/stream_base.h>
-#include <seqan/stream/stream_put.h>
-#include <seqan/stream/stream_char_array.h>
 
-#include <seqan/stream/adapt_mmap.h> // TODO(h4nn3s): only streamPut() right now
+// ===========================================================================
+// File Format and Type Guessing.
+// ===========================================================================
 
-#if SEQAN_HAS_ZLIB
-// Enable Stream<GZFile> and Stream<Bgzf> if available.
-#include <seqan/stream/stream_gz_file.h>
-#include <seqan/stream/stream_bgzf.h>
-#endif  // #if SEQAN_HAS_ZLIB
-#if SEQAN_HAS_BZIP2  // Enable Stream<BZ2File> if available.
-#include <seqan/stream/stream_bz2_file.h>
-#endif  // #if SEQAN_HAS_BZIP2
+#include <seqan/stream/guess_format.h>
 
-#include <seqan/stream/file_stream.h>
+// ===========================================================================
+// Stream Iterators.
+// ===========================================================================
+
+#include <seqan/stream/iter_stream.h>
 
 // ===========================================================================
-// Record Reader Class and Specializations.
+// Stream Implementations and Adaptions.
 // ===========================================================================
 
-#include <seqan/stream/record_reader_base.h>
-#include <seqan/stream/record_reader_single.h>
-#include <seqan/stream/record_reader_single_mmap.h>
-#include <seqan/stream/record_reader_double.h>
-#include <seqan/stream/record_reader_double_mmap.h>
+#include <seqan/stream/adapt_ios.h>
+#include <seqan/stream/file_stream.h>
+#include <seqan/stream/stream_compressor.h>
+#include <seqan/stream/buffered_stream.h>
+
+#if SEQAN_HAS_ZLIB
+#include <zlib.h>
+#include <seqan/stream/iostream_zutil.h>
+#include <seqan/stream/iostream_zip.h>
+#include <seqan/stream/iostream_zip_impl.h>
+#include <seqan/stream/iostream_bgzf.h>
+#endif
+
+#if SEQAN_HAS_BZIP2
+#include <seqan/stream/iostream_bzip2.h>
+#endif
 
-#include <seqan/stream/read_auto_format.h>
+#include <seqan/stream/virtual_stream.h>
+#include <seqan/stream/formatted_file.h>
 
 // ===========================================================================
-// Tokenizing and *is
+// Tokenization and Lexical Cast.
 // ===========================================================================
+// TODO(esiragusa): move these files into basic - they are not unique to streams.
 
-#include <seqan/stream/is.h> // currently empty
-#include <seqan/stream/tokenize.h>
+#include <seqan/stream/tokenization.h>
 #include <seqan/stream/lexical_cast.h>
 
 #endif  // SEQAN_STREAM_H_
diff --git a/seqan/stream/INFO b/seqan/stream/INFO
deleted file mode 100644
index 2adb91b..0000000
--- a/seqan/stream/INFO
+++ /dev/null
@@ -1,32 +0,0 @@
-Name: seqan-stream
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
-Maintainer: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-License: 3-clause BSD
-Copyright: 2011-1013, FU Berlin
-Homepage: http://www.seqan.de/
-Version: 0.1
-Status: under development
-Depends: seqan-basic
-Depends: seqan-sequence
-Depends: seqan-file
-Recommends: zlib
-Recommends: bzlib
-Description: Input / Output abstraction module.
- The stream module has two main aspects: (1) The Stream concept for abstracting
- I/O and (2) The record and document I/O concept.
- .
- It contains implementations for both concepts: Adaptions from the <cstdio>
- FILE* stream and streams from the IOstreams library to the Stream concept and
- wrapper classes for reading and writing .gz and .bz2 files (if available).
- Implementations of the record reader class are available for Streams and memory
- mapped strings.
- .
- Furthermore, it provides record and documentation reading functionality for
- FASTA and FASTQ files.
- .
- Demos:
- .
- benchmark_stream  FASTA input/output using all stream implementations and
- also demonstrates how to use the SEQAN_HAS* macros defined in this module to
- conditionally enable .gz and .bz2 support.
diff --git a/seqan/stream/adapt_fstream.h b/seqan/stream/adapt_fstream.h
deleted file mode 100644
index 3933dba..0000000
--- a/seqan/stream/adapt_fstream.h
+++ /dev/null
@@ -1,720 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Adaptions for the <fstream> streams: std::ifstream, std::fstream,
-// std::ofstream.
-// ==========================================================================
-
-#include <fstream>
-#include <sstream>
-#include <string>
-
-#ifndef SEQAN_STREAM_ADAPT_FSTREAM_H_
-#define SEQAN_STREAM_ADAPT_FSTREAM_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/**
-.Adaption.File stream
-..cat:Input/Output
-..summary:Adaption from $fstream$, $ifstream$ and $ofstream$ to the @Concept.StreamConcept@ concept.
-..include:seqan/stream.h
- */
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Difference
-// ----------------------------------------------------------------------------
-
-template <>
-struct Difference< ::std::fstream>
-{
-    typedef ::std::fstream::pos_type Type;
-};
-
-template <>
-struct Difference< ::std::ifstream>
-{
-    typedef ::std::ifstream::pos_type Type;
-};
-
-template <>
-struct Difference< ::std::ofstream>
-{
-    typedef ::std::ofstream::pos_type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <>
-struct Size< ::std::fstream>
-{
-    typedef size_t Type;
-};
-
-template <>
-struct Size< ::std::ifstream>
-{
-    typedef size_t Type;
-};
-
-template <>
-struct Size< ::std::ofstream>
-{
-    typedef size_t Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <>
-struct Value< ::std::fstream>
-{
-    typedef ::std::fstream::char_type Type;
-};
-
-template <>
-struct Value< ::std::ifstream>
-{
-    typedef ::std::ifstream::char_type Type;
-};
-
-template <>
-struct Value< ::std::ofstream>
-{
-    typedef ::std::ofstream::char_type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::fstream, IsInput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ifstream, IsInput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ofstream, IsInput>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, IsOutput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::fstream, IsOutput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ifstream, IsOutput>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ofstream, IsOutput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, HasPeek>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::fstream, HasPeek>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ifstream, HasPeek>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ofstream, HasPeek>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, HasFilename>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::fstream, HasFilename>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ifstream, HasFilename>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ofstream, HasFilename>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, Seek<TSpec> >
-// ----------------------------------------------------------------------------
-
-template <typename TSpec>
-struct HasStreamFeature< ::std::fstream, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-template <typename TSpec>
-struct HasStreamFeature< ::std::ifstream, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-template <typename TSpec>
-struct HasStreamFeature< ::std::ofstream, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, Tell>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::fstream, Tell>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ifstream, Tell>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ofstream, Tell>
-{
-    typedef True Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function streamPeek()
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline int
-_streamPeekImplIOStream(char & c, TStream & stream)
-{
-    int x = stream.peek();
-    if (x == EOF)
-        return EOF;
-    c = x;
-    return 0;
-}
-
-inline int
-streamPeek(char & c, ::std::fstream & stream)
-{
-    return _streamPeekImplIOStream(c, stream);
-}
-
-inline int
-streamPeek(char & c, ::std::ifstream & stream)
-{
-    return _streamPeekImplIOStream(c, stream);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadChar()
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline int
-_streamReadCharImplIOStream(char & c, TStream & stream)
-{
-    int x = stream.get();
-    if (x == EOF)
-        return EOF;
-    c = x;
-    return 0;
-}
-
-inline int
-streamReadChar(char & c, ::std::fstream & stream)
-{
-    return _streamReadCharImplIOStream(c, stream);
-}
-
-inline int
-streamReadChar(char & c, ::std::ifstream & stream)
-{
-    return _streamReadCharImplIOStream(c, stream);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamEof()
-// ----------------------------------------------------------------------------
-
-inline bool
-streamEof(::std::fstream & stream)
-{
-    return stream.eof();
-}
-
-inline bool
-streamEof(::std::ifstream & stream)
-{
-    return stream.eof();
-}
-
-inline bool
-streamEof(::std::ofstream & stream)
-{
-    return stream.eof();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamError
-// ----------------------------------------------------------------------------
-
-inline int
-streamError(::std::fstream & stream)
-{
-    // If we read beyond the last char, then eof and fail will be
-    // set. Workaround to get the logic right.
-    if ((stream.rdstate() & ::std::ios_base::eofbit) != 0)
-        return 0;
-    return stream.rdstate();
-}
-
-inline int
-streamError(::std::ifstream & stream)
-{
-    // If we read beyond the last char, then eof and fail will be
-    // set. Workaround to get the logic right.
-    if ((stream.rdstate() & ::std::ios_base::eofbit) != 0)
-        return 0;
-    return stream.rdstate();
-}
-
-inline int
-streamError(::std::ofstream & stream)
-{
-    // If we read beyond the last char, then eof and fail will be
-    // set. Workaround to get the logic right.
-    if ((stream.rdstate() & ::std::ios_base::eofbit) != 0)
-        return 0;
-    return stream.rdstate();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadBlock()
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline size_t
-_streamReadBlockImplIOStream(char * target, TStream & stream, size_t maxLen)
-{
-    stream.read(target, maxLen);
-    return stream.gcount();
-}
-
-inline size_t
-streamReadBlock(char * target, ::std::fstream & stream, size_t maxLen)
-{
-    return _streamReadBlockImplIOStream(target, stream, maxLen);
-}
-
-inline size_t
-streamReadBlock(char * target, ::std::ifstream & stream, size_t maxLen)
-{
-    return _streamReadBlockImplIOStream(target, stream, maxLen);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteChar
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline int
-_streamWriteCharImplIOStream(TStream & stream, char const c)
-{
-    stream.put(c);
-    if (!stream.bad())
-        return 0;
-    if (stream.eof())
-        return EOF;
-    SEQAN_ASSERT(stream.fail());
-    return 1;
-}
-
-inline int
-streamWriteChar(::std::fstream & stream, char const c)
-{
-    return _streamWriteCharImplIOStream(stream, c);
-}
-
-inline int
-streamWriteChar(::std::ofstream & stream, char const c)
-{
-    return _streamWriteCharImplIOStream(stream, c);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteBlock()
-// ----------------------------------------------------------------------------
-
-template <typename TStream>
-inline size_t
-_streamWriteBlockImplIOStream(TStream & stream, char const * source, size_t count)
-{
-    stream.write(source, count);
-    return count; 
-}
-
-inline size_t
-streamWriteBlock(::std::fstream & stream, char const * source, size_t count)
-{
-    return _streamWriteBlockImplIOStream(stream, source, count);
-}
-
-inline size_t
-streamWriteBlock(::std::ofstream & stream, char const * source, size_t count)
-{
-    return _streamWriteBlockImplIOStream(stream, source, count);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamPut()
-// ----------------------------------------------------------------------------
-
-// fstream
-// --- characters
-
-inline int
-streamPut(::std::fstream & stream, char const c)
-{
-    return streamWriteChar(stream, c);
-}
-
-template <typename TValue, typename TSpec>
-inline int
-streamPut(::std::fstream & stream,
-          SimpleType<TValue, TSpec> const & c)
-{
-    return streamWriteChar(stream, convert<char>(c));
-}
-
-// --- strings
-
-inline int
-streamPut(::std::fstream & stream, char const * source)
-{
-    return (streamWriteBlock(stream, source, strlen(source))
-                == strlen(source) )  ?   0 : 1;
-}
-
-template <typename TSpec>
-inline int
-streamPut(::std::fstream & stream, String<char, TSpec> const & source)
-{
-    return (streamWriteBlock(stream, toCString(source), length(source))
-                == length(source))  ?   0 : 1;
-}
-
-template <typename TValue, typename TSpec, typename TSpec2>
-inline int
-streamPut(::std::fstream & stream,
-          String<SimpleType<TValue, TSpec>, TSpec2> const & source)
-{
-    String<char, CStyle> buf = source;
-    return (streamWriteBlock(stream, toCString(buf), length(buf))
-                == length(buf))  ?   0 : 1;
-}
-
-inline int
-streamPut(::std::fstream & stream, ::std::string const & source)
-{
-    return (streamWriteBlock(stream, source.data(), source.length()) == source.length())  ?   0 : 1;
-}
-
-inline int
-streamPut(::std::fstream & stream, ::std::stringstream const & source)
-{
-    stream << source.rdbuf();
-    return stream.fail();
-}
-
-// --- wildcard
-
-template <typename TSource>
-inline int
-streamPut(::std::fstream & stream, TSource const & source)
-{
-    stream << source;
-    return stream.fail();
-}
-
-// ofstream
-// --- characters
-
-inline int
-streamPut(::std::ofstream & stream, char const c)
-{
-    return streamWriteChar(stream, c);
-}
-
-template <typename TValue, typename TSpec>
-inline int
-streamPut(::std::ofstream & stream,
-          SimpleType<TValue, TSpec> const & c)
-{
-    return streamWriteChar(stream, convert<char>(c));
-}
-
-// --- strings
-
-inline int
-streamPut(::std::ofstream & stream, char const * source)
-{
-    return (streamWriteBlock(stream, source, strlen(source))
-                == strlen(source) )  ?   0 : 1;
-}
-
-template <typename TSpec>
-inline int
-streamPut(::std::ofstream & stream, String<char, TSpec> const & source)
-{
-    return (streamWriteBlock(stream, toCString(source), length(source))
-                == length(source))  ?   0 : 1;
-}
-
-inline int
-streamPut(::std::ofstream & stream, ::std::string const & source)
-{
-    return (streamWriteBlock(stream, source.data(), source.length()) == source.length())  ?   0 : 1;
-}
-
-inline int
-streamPut(::std::ofstream & stream, ::std::stringstream const & source)
-{
-    stream << source.rdbuf();
-    return stream.fail();
-}
-
-// --- wildcard
-
-template <typename TSource>
-inline int
-streamPut(::std::ofstream & stream, TSource const & source)
-{
-    stream << source;
-    return stream.fail();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamFlush()
-// ----------------------------------------------------------------------------
-
-inline int
-streamFlush(::std::fstream & stream)
-{
-    stream << std::flush;
-    return 0;
-}
-
-inline int
-streamFlush(::std::ofstream & stream)
-{
-    stream << std::flush;
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamSeek()
-// ----------------------------------------------------------------------------
-
-inline int
-streamSeek(::std::fstream & stream, long int delta, int origin)
-{
-    stream.clear();  // Reset fail flags before seek.
-    // For fstream, the input and output pointer are kept in sync.
-    if (origin == SEEK_SET) {
-        stream.seekg(delta, ::std::fstream::beg);
-    } else if (origin == SEEK_CUR) {
-        stream.seekg(delta, ::std::fstream::cur);
-    } else {
-        stream.seekg(delta, ::std::fstream::end);
-    }
-    int res = (stream.fail() || stream.bad());
-    stream.clear();  // Reset EOF flag.
-    return res;
-}
-
-inline int
-streamSeek(::std::ifstream & stream, long int delta, int origin)
-{
-    stream.clear();  // Reset fail flags before seek.
-    if (origin == SEEK_SET)
-        stream.seekg(delta, ::std::fstream::beg);
-    else if (origin == SEEK_CUR)
-        stream.seekg(delta, ::std::fstream::cur);
-    else
-        stream.seekg(delta, ::std::fstream::end);
-    int res = (stream.fail() || stream.bad());
-    stream.clear();  // Reset EOF flag.
-    return res;
-}
-
-inline int
-streamSeek(::std::ofstream & stream, long int delta, int origin)
-{
-    stream.clear();  // Reset fail flags before seek.
-    if (origin == SEEK_SET)
-        stream.seekp(delta, ::std::fstream::beg);
-    else if (origin == SEEK_CUR)
-        stream.seekp(delta, ::std::fstream::cur);
-    else
-        stream.seekp(delta, ::std::fstream::end);
-    int res = (stream.fail() || stream.bad());
-    stream.clear();  // Reset EOF flag.
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamTell()
-// ----------------------------------------------------------------------------
-
-inline Position< ::std::fstream>::Type
-streamTell(::std::fstream & stream)
-{
-    SEQAN_ASSERT_EQ(stream.tellp(), stream.tellg());
-    std::streampos x = stream.tellp();
-    return x;
-}
-
-inline Position< ::std::fstream>::Type
-streamTell(::std::ifstream & stream)
-{
-    std::streampos x = stream.tellg();
-    return x;
-}
-
-inline Position< ::std::fstream>::Type
-streamTell(::std::ofstream & stream)
-{
-    std::streampos x = stream.tellp();
-    return x;
-}
-
-// ----------------------------------------------------------------------------
-// Function open()
-// ----------------------------------------------------------------------------
-
-inline std::ios_base::openmode
-_getSTLStyleOpenMode(int openMode)
-{
-    std::ios_base::openmode flags = std::ios_base::binary;
-
-    if ((openMode & OPEN_MASK) == OPEN_RDONLY)
-        flags |= std::ios_base::in;
-    if ((openMode & OPEN_MASK) == OPEN_WRONLY)
-    {
-        flags |= std::ios_base::out;
-        if (openMode & OPEN_APPEND)
-            flags |= std::ios_base::app;
-        else
-            flags |= std::ios_base::trunc;
-    }
-    return flags;
-}
-
-inline bool
-open(std::fstream & stream, const char *fileName, int openMode)
-{
-    stream.open(fileName, _getSTLStyleOpenMode(openMode));
-    return stream.is_open();
-}
-
-// ----------------------------------------------------------------------------
-// Function close()
-// ----------------------------------------------------------------------------
-
-inline bool
-close(std::fstream & stream)
-{
-    stream.close();
-    return !stream.is_open();
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_ADAPT_FSTREAM_H_
diff --git a/seqan/stream/adapt_ios.h b/seqan/stream/adapt_ios.h
new file mode 100644
index 0000000..65f6864
--- /dev/null
+++ b/seqan/stream/adapt_ios.h
@@ -0,0 +1,402 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Adaptions for std::ios streams.
+// ==========================================================================
+
+#ifndef SEQAN_STREAM_ADAPT_IOS_H_
+#define SEQAN_STREAM_ADAPT_IOS_H_
+
+#define SEQAN_ASSERT_BADBIT(s) SEQAN_ASSERT_MSG(s.exceptions() | std::ios_base::badbit, \
+        "The badbit exception is not set in the stream. Call either std::exceptions() or streamInit() on the stream.")
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+// TODO(esiragusa): remove this when chunking goes into basic.
+
+template <typename TObject> struct Chunk;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits>
+struct Position<std::istreambuf_iterator<TValue, TTraits> >
+{
+    typedef typename std::istreambuf_iterator<TValue, TTraits>::difference_type Type;
+};
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_istream<TValue, TTraits> >
+{
+    typedef typename std::basic_istream<TValue, TTraits>::pos_type Type;
+};
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_ostream<TValue, TTraits> >
+{
+    typedef typename std::basic_ostream<TValue, TTraits>::pos_type Type;
+};
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_iostream<TValue, TTraits> >
+{
+    typedef typename std::basic_iostream<TValue, TTraits>::pos_type Type;
+};
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_fstream<TValue, TTraits> > :
+    Position<std::basic_iostream<TValue, TTraits> > {};
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_stringstream<TValue, TTraits> > :
+    Position<std::basic_iostream<TValue, TTraits> > {};
+
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_ifstream<TValue, TTraits> > :
+    Position<std::basic_istream<TValue, TTraits> > {};
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_istringstream<TValue, TTraits> > :
+    Position<std::basic_istream<TValue, TTraits> > {};
+
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_ofstream<TValue, TTraits> > :
+    Position<std::basic_ostream<TValue, TTraits> > {};
+
+template <typename TValue, typename TTraits>
+struct Position<std::basic_ostringstream<TValue, TTraits> > :
+    Position<std::basic_ostream<TValue, TTraits> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits>
+struct Value<std::istreambuf_iterator<TValue, TTraits> >
+{
+    typedef typename std::istreambuf_iterator<TValue, TTraits>::char_type Type;
+};
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_istream<TValue, TTraits> >
+{
+    typedef typename std::basic_istream<TValue, TTraits>::char_type Type;
+};
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_ostream<TValue, TTraits> >
+{
+    typedef typename std::basic_ostream<TValue, TTraits>::char_type Type;
+};
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_iostream<TValue, TTraits> >
+{
+    typedef typename std::basic_iostream<TValue, TTraits>::char_type Type;
+};
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_fstream<TValue, TTraits> > :
+    Value<std::basic_iostream<TValue, TTraits> > {};
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_stringstream<TValue, TTraits> > :
+    Value<std::basic_iostream<TValue, TTraits> > {};
+
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_ifstream<TValue, TTraits> > :
+    Value<std::basic_istream<TValue, TTraits> > {};
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_istringstream<TValue, TTraits> > :
+    Value<std::basic_istream<TValue, TTraits> > {};
+
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_ofstream<TValue, TTraits> > :
+    Value<std::basic_ostream<TValue, TTraits> > {};
+
+template <typename TValue, typename TTraits>
+struct Value<std::basic_ostringstream<TValue, TTraits> > :
+    Value<std::basic_ostream<TValue, TTraits> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Reference
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits>
+struct Reference<std::istreambuf_iterator<TValue, TTraits> >
+{
+    typedef typename std::istreambuf_iterator<TValue, TTraits>::char_type Type;
+//    typedef typename std::istreambuf_iterator<TValue, TTraits>::reference Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Chunk
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits>
+struct Chunk<std::basic_streambuf<TValue, TTraits> >
+{
+    typedef Range<TValue*> Type;
+};
+
+//template <typename TValue, typename TTraits>
+//struct Chunk<std::istreambuf_iterator<TValue, TTraits> >:
+//    Chunk<std::basic_streambuf<TValue, TTraits> > {};
+//
+//template <typename TValue, typename TTraits>
+//struct Chunk<std::ostreambuf_iterator<TValue, TTraits> >:
+//    Chunk<std::basic_streambuf<TValue, TTraits> > {};
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultOpenMode<std::>
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits, typename TDummy>
+struct DefaultOpenMode<std::basic_fstream<TValue, TTraits>, TDummy>
+{
+    enum { VALUE = OPEN_RDWR | OPEN_CREATE | OPEN_APPEND };
+};
+
+template <typename TValue, typename TTraits, typename TDummy>
+struct DefaultOpenMode<std::basic_ifstream<TValue, TTraits>, TDummy>
+{
+    enum { VALUE = OPEN_RDONLY };
+};
+
+template <typename TValue, typename TTraits, typename TDummy>
+struct DefaultOpenMode<std::basic_ofstream<TValue, TTraits>, TDummy>
+{
+    enum { VALUE = OPEN_WRONLY | OPEN_CREATE };
+};
+
+// ============================================================================
+// Concepts
+// ============================================================================
+
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_istream<TValue, TTraits>), (InputStreamConcept));
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_ifstream<TValue, TTraits>), (InputStreamConcept));
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_istringstream<TValue, TTraits>), (InputStreamConcept));
+
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_ostream<TValue, TTraits>), (OutputStreamConcept));
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_ofstream<TValue, TTraits>), (OutputStreamConcept));
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_ostringstream<TValue, TTraits>), (OutputStreamConcept));
+
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_iostream<TValue, TTraits>), (BidirectionalStreamConcept));
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_fstream<TValue, TTraits>), (BidirectionalStreamConcept));
+template <typename TValue, typename TTraits>
+SEQAN_CONCEPT_IMPL((std::basic_stringstream<TValue, TTraits>), (BidirectionalStreamConcept));
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _getSTLStyleOrigin()
+// ----------------------------------------------------------------------------
+
+template <typename TPos>
+inline std::ios_base::seekdir
+_getSTLStyleOrigin(TPos origin)
+{
+    switch (origin)
+    {
+    case SEEK_CUR:
+        return std::ios_base::cur;
+    case SEEK_END:
+        return std::ios_base::end;
+    case SEEK_SET:
+    default:
+        return std::ios_base::beg;
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function _getSTLStyleOpenMode()
+// ----------------------------------------------------------------------------
+
+inline std::ios_base::openmode
+_getSTLStyleOpenMode(int openMode)
+{
+    std::ios_base::openmode flags = std::ios_base::binary;
+
+    if (openMode & OPEN_RDONLY)
+        flags |= std::ios_base::in;
+    if (openMode & OPEN_WRONLY)
+    {
+        flags |= std::ios_base::out;
+        if (!(openMode & OPEN_APPEND))
+            flags |= std::ios_base::trunc;
+    }
+
+    return flags;
+}
+
+// ----------------------------------------------------------------------------
+// Function getChunk()
+// ----------------------------------------------------------------------------
+
+//template <typename TValue, typename TTraits, typename TDirection>
+//inline typename Chunk<std::basic_streambuf<TValue, TTraits> >::Type
+//getChunk(std::basic_streambuf<TValue, TTraits> const &buf, Tag<TDirection>)
+//{
+//    return getChunk(static_cast<StreamBuffer<TValue, TTraits> &>(buf), Tag<TDirection>());
+//}
+
+// ----------------------------------------------------------------------------
+// Function writeValue()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits, typename TValue2>
+inline void writeValue(std::ostreambuf_iterator<TValue, TTraits> &iter, TValue2 val)
+{
+    *iter = val;
+    ++iter;
+}
+
+template <typename TValue, typename TTraits, typename TValue2>
+inline void writeValue(std::basic_ostream<TValue, TTraits> &ostream, TValue2 val)
+{
+    ostream.put(val);
+}
+
+// ----------------------------------------------------------------------------
+// Function atEnd()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits>
+inline bool atEnd(std::istreambuf_iterator<TValue, TTraits> const &it)
+{
+    return it == std::istreambuf_iterator<TValue, TTraits>();
+}
+
+template <typename TValue, typename TTraits>
+inline bool atEnd(std::ostreambuf_iterator<TValue, TTraits> const &it)
+{
+    return it == std::ostreambuf_iterator<TValue, TTraits>();
+}
+
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits>
+inline bool open(std::basic_fstream<TValue, TTraits> & stream, const char *fileName, int openMode)
+{
+    stream.exceptions(std::ios_base::badbit);
+    stream.open(fileName, _getSTLStyleOpenMode(openMode));
+    return stream.is_open();
+}
+
+template <typename TValue, typename TTraits>
+inline bool open(std::basic_ifstream<TValue, TTraits> & stream, const char *fileName, int openMode)
+{
+    stream.exceptions(std::ios_base::badbit);
+    stream.open(fileName, _getSTLStyleOpenMode(openMode));
+    return stream.is_open();
+}
+
+template <typename TValue, typename TTraits>
+inline bool open(std::basic_ofstream<TValue, TTraits> & stream, const char *fileName, int openMode)
+{
+    stream.exceptions(std::ios_base::badbit);
+    stream.open(fileName, _getSTLStyleOpenMode(openMode));
+    return stream.is_open();
+}
+
+template <typename TValue, typename TTraits>
+inline bool open(std::basic_fstream<TValue, TTraits> & stream, const char *fileName)
+{
+    return open(stream, fileName, DefaultOpenMode<std::basic_fstream<TValue, TTraits> >::VALUE);
+}
+
+template <typename TValue, typename TTraits>
+inline bool open(std::basic_ifstream<TValue, TTraits> & stream, const char *fileName)
+{
+    return open(stream, fileName, DefaultOpenMode<std::basic_ifstream<TValue, TTraits> >::VALUE);
+}
+
+template <typename TValue, typename TTraits>
+inline bool open(std::basic_ofstream<TValue, TTraits> & stream, const char *fileName)
+{
+    return open(stream, fileName, DefaultOpenMode<std::basic_ofstream<TValue, TTraits> >::VALUE);
+}
+
+// ----------------------------------------------------------------------------
+// Function close()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TTraits>
+inline bool close(std::basic_fstream<TValue, TTraits> & stream)
+{
+    stream.close();
+    return !stream.is_open();
+}
+
+template <typename TValue, typename TTraits>
+inline bool close(std::basic_ifstream<TValue, TTraits> & stream)
+{
+    stream.close();
+    return !stream.is_open();
+}
+
+template <typename TValue, typename TTraits>
+inline bool close(std::basic_ofstream<TValue, TTraits> & stream)
+{
+    stream.close();
+    return !stream.is_open();
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_STREAM_ADAPT_IOS_H_
diff --git a/seqan/stream/adapt_iostream.h b/seqan/stream/adapt_iostream.h
deleted file mode 100644
index 7ebcec3..0000000
--- a/seqan/stream/adapt_iostream.h
+++ /dev/null
@@ -1,383 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Adaptions for <iostream> strams: std::istream, std::ostream like std::cin.
-// ==========================================================================
-
-#ifndef SEQAN_STREAM_ADAPT_IOSTREAM_H_
-#define SEQAN_STREAM_ADAPT_IOSTREAM_H_
-
-#include <iostream>
-
-namespace seqan {
-
-// TODO(holtgrew): Copied from adapt_fstream.h, not tested! Maybe specialize templates for basic_* streams?
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/**
-.Adaption.IO stream
-..summary:Adaption of standard C++ iostream objects.
-..cat:Input/Output
-..remarks:Also, adaption from $ostream$ and $istream$ to the @Concept.StreamConcept@ concept.
-..include:seqan/stream.h
- */
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Difference
-// ----------------------------------------------------------------------------
-
-template <>
-struct Difference< ::std::ostream>
-{
-    typedef ::std::ostream::pos_type Type;
-};
-
-template <>
-struct Difference< ::std::istream>
-{
-    typedef ::std::istream::pos_type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <>
-struct Size< ::std::ostream>
-{
-    typedef ::std::ostream::pos_type Type;
-};
-
-template <>
-struct Size< ::std::istream>
-{
-    typedef ::std::istream::pos_type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <>
-struct Value< ::std::ostream>
-{
-    typedef ::std::ostream::char_type Type;
-};
-
-template <>
-struct Value< ::std::istream>
-{
-    typedef ::std::istream::char_type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::ostream, IsInput>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istream, IsInput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, IsOutput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::ostream, IsOutput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istream, IsOutput>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, HasPeek>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::ostream, HasPeek>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istream, HasPeek>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, HasFilename>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::ostream, HasFilename>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istream, HasFilename>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, Seek<TSpec> >
-// ----------------------------------------------------------------------------
-
-template <typename TSpec>
-struct HasStreamFeature< ::std::ostream, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-template <typename TSpec>
-struct HasStreamFeature< ::std::istream, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, Tell>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::ostream, Tell>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istream, Tell>
-{
-    typedef False Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function streamPeek()
-// ----------------------------------------------------------------------------
-
-inline int
-streamPeek(char & c, ::std::istream & stream)
-{
-    return _streamPeekImplIOStream(c, stream);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadChar()
-// ----------------------------------------------------------------------------
-
-inline int
-streamReadChar(char & c, ::std::istream & stream)
-{
-    return _streamReadCharImplIOStream(c, stream);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamEof()
-// ----------------------------------------------------------------------------
-
-inline bool
-streamEof(::std::ostream & stream)
-{
-    return stream.eof();
-}
-
-inline bool
-streamEof(::std::istream & stream)
-{
-    return stream.eof();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamError
-// ----------------------------------------------------------------------------
-
-inline int
-streamError(::std::ostream & stream)
-{
-    // If we read beyond the last char, then eof and fail will be
-    // set. Workaround to get the logic right.
-    if ((stream.rdstate() & ::std::ios_base::eofbit) != 0)
-        return 0;
-    return stream.rdstate();
-}
-
-inline int
-streamError(::std::istream & stream)
-{
-    // If we read beyond the last char, then eof and fail will be
-    // set. Workaround to get the logic right.
-    if ((stream.rdstate() & ::std::ios_base::eofbit) != 0)
-        return 0;
-    return stream.rdstate();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamReadBlock(char * target, ::std::istream & stream, size_t maxLen)
-{
-    return _streamReadBlockImplIOStream(target, stream, maxLen);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteChar
-// ----------------------------------------------------------------------------
-
-inline int
-streamWriteChar(::std::ostream & stream, char const c)
-{
-    return _streamWriteCharImplIOStream(stream, c);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamWriteBlock(::std::ostream & stream, char const * source, size_t count)
-{
-    return _streamWriteBlockImplIOStream(stream, source, count);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamTell()
-// ----------------------------------------------------------------------------
-
-inline Position< ::std::istream>::Type
-streamTell(::std::istream & stream)
-{
-    std::streampos x = stream.tellg();
-    return x;
-}
-
-inline Position< ::std::ostream>::Type
-streamTell(::std::ostream & stream)
-{
-    std::streampos x = stream.tellp();
-    return x;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamPut()
-// ----------------------------------------------------------------------------
-
-// ostream
-// --- characters
-
-inline int
-streamPut(::std::ostream & stream, char const c)
-{
-    return streamWriteChar(stream, c);
-}
-
-template <typename TValue, typename TSpec>
-inline int
-streamPut(::std::ostream & stream,
-          SimpleType<TValue, TSpec> const & c)
-{
-    return streamWriteChar(stream, convert<char>(c));
-}
-
-// --- strings
-
-inline int
-streamPut(::std::ostream & stream, char const * source)
-{
-    return (streamWriteBlock(stream, source, strlen(source))
-                == strlen(source) )  ?   0 : 1;
-}
-
-template <typename TSpec>
-inline int
-streamPut(::std::ostream & stream, String<char, TSpec> const & source)
-{
-    return (streamWriteBlock(stream, toCString(source), length(source))
-                == length(source))  ?   0 : 1;
-}
-
-// --- wildcard
-
-template <typename TSource>
-inline int
-streamPut(::std::ostream & stream, TSource const & source)
-{
-    stream << source;
-    return stream.fail();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamFlush()
-// ----------------------------------------------------------------------------
-
-inline int
-streamFlush(::std::ostream & stream)
-{
-    stream << std::flush;
-    return 0;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_ADAPT_IOSTREAM_H_
diff --git a/seqan/stream/adapt_sstream.h b/seqan/stream/adapt_sstream.h
deleted file mode 100644
index c3fcd19..0000000
--- a/seqan/stream/adapt_sstream.h
+++ /dev/null
@@ -1,628 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Adaptions for the <sstream> streams: std::istringstream,
-// std::stringstream, std::ostringstream.
-// ==========================================================================
-
-#include <sstream>
-
-#ifndef SEQAN_STREAM_ADAPT_SSTREAM_H_
-#define SEQAN_STREAM_ADAPT_SSTREAM_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*
-.Adaption.String stream
-..cat:Input/Output
-..summary:Adaption from $fstream$, $ifstream$ and $ofstream$ to the @Concept.StreamConcept@ concept.
-..include:seqan/stream.h
- */
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Difference
-// ----------------------------------------------------------------------------
-
-template <>
-struct Difference< ::std::stringstream>
-{
-    typedef ::std::stringstream::pos_type Type;
-};
-
-template <>
-struct Difference< ::std::istringstream>
-{
-    typedef ::std::istringstream::pos_type Type;
-};
-
-template <>
-struct Difference< ::std::ostringstream>
-{
-    typedef ::std::ostringstream::pos_type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <>
-struct Size< ::std::stringstream>
-{
-    typedef ::std::stringstream::pos_type Type;
-};
-
-template <>
-struct Size< ::std::istringstream>
-{
-    typedef ::std::istringstream::pos_type Type;
-};
-
-template <>
-struct Size< ::std::ostringstream>
-{
-    typedef ::std::ostringstream::pos_type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <>
-struct Value< ::std::stringstream>
-{
-    typedef ::std::stringstream::char_type Type;
-};
-
-template <>
-struct Value< ::std::istringstream>
-{
-    typedef ::std::istringstream::char_type Type;
-};
-
-template <>
-struct Value< ::std::ostringstream>
-{
-    typedef ::std::ostringstream::char_type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::stringstream, IsInput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istringstream, IsInput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ostringstream, IsInput>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, IsOutput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::stringstream, IsOutput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istringstream, IsOutput>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ostringstream, IsOutput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, HasPeek>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::stringstream, HasPeek>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istringstream, HasPeek>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ostringstream, HasPeek>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, HasFilename>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::stringstream, HasFilename>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istringstream, HasFilename>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ostringstream, HasFilename>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, Seek<TSpec> >
-// ----------------------------------------------------------------------------
-
-template <typename TSpec>
-struct HasStreamFeature< ::std::stringstream, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-template <typename TSpec>
-struct HasStreamFeature< ::std::istringstream, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-template <typename TSpec>
-struct HasStreamFeature< ::std::ostringstream, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature< ::std::, Tell>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature< ::std::stringstream, Tell>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::istringstream, Tell>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature< ::std::ostringstream, Tell>
-{
-    typedef True Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function streamPeek()
-// ----------------------------------------------------------------------------
-
-inline int
-streamPeek(char & c, ::std::stringstream & stream)
-{
-    return _streamPeekImplIOStream(c, stream);
-}
-
-inline int
-streamPeek(char & c, ::std::istringstream & stream)
-{
-    return _streamPeekImplIOStream(c, stream);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadChar()
-// ----------------------------------------------------------------------------
-
-inline int
-streamReadChar(char & c, ::std::stringstream & stream)
-{
-    int res = _streamReadCharImplIOStream(c, stream);
-    stream.seekp(stream.tellg());
-    return res;
-}
-
-inline int
-streamReadChar(char & c, ::std::istringstream & stream)
-{
-    return _streamReadCharImplIOStream(c, stream);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamEof()
-// ----------------------------------------------------------------------------
-
-inline bool
-streamEof(::std::stringstream & stream)
-{
-    return stream.eof();
-}
-
-inline bool
-streamEof(::std::istringstream & stream)
-{
-    return stream.eof();
-}
-
-inline bool
-streamEof(::std::ostringstream & stream)
-{
-    return stream.eof();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamError
-// ----------------------------------------------------------------------------
-
-inline int
-streamError(::std::stringstream & stream)
-{
-    // If we read beyond the last char, then eof and fail will be
-    // set. Workaround to get the logic right.
-    if ((stream.rdstate() & ::std::ios_base::eofbit) != 0)
-        return 0;
-    return stream.rdstate();
-}
-
-inline int
-streamError(::std::istringstream & stream)
-{
-    // If we read beyond the last char, then eof and fail will be
-    // set. Workaround to get the logic right.
-    if ((stream.rdstate() & ::std::ios_base::eofbit) != 0)
-        return 0;
-    return stream.rdstate();
-}
-
-inline int
-streamError(::std::ostringstream & stream)
-{
-    // If we read beyond the last char, then eof and fail will be
-    // set. Workaround to get the logic right.
-    if ((stream.rdstate() & ::std::ios_base::eofbit) != 0)
-        return 0;
-    return stream.rdstate();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamReadBlock(char * target, ::std::stringstream & stream, size_t maxLen)
-{
-    int res = _streamReadBlockImplIOStream(target, stream, maxLen);
-    stream.seekp(stream.tellg());
-    return res;
-}
-
-inline size_t
-streamReadBlock(char * target, ::std::istringstream & stream, size_t maxLen)
-{
-    return _streamReadBlockImplIOStream(target, stream, maxLen);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteChar
-// ----------------------------------------------------------------------------
-
-inline int
-streamWriteChar(::std::stringstream & stream, char const c)
-{
-    int res = _streamWriteCharImplIOStream(stream, c);
-    stream.seekg(stream.tellp());
-    return res;
-}
-
-inline int
-streamWriteChar(::std::ostringstream & stream, char const c)
-{
-    return _streamWriteCharImplIOStream(stream, c);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamWriteBlock(::std::stringstream & stream, char const * source, size_t count)
-{
-    int res = _streamWriteBlockImplIOStream(stream, source, count);
-    stream.seekg(stream.tellp());
-    return res;
-}
-
-inline size_t
-streamWriteBlock(::std::ostringstream & stream, char const * source, size_t count)
-{
-    return _streamWriteBlockImplIOStream(stream, source, count);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamPut()
-// ----------------------------------------------------------------------------
-
-// sstream
-// --- characters
-
-inline int
-streamPut(::std::stringstream & stream, char const c)
-{
-    return streamWriteChar(stream, c);
-}
-
-template <typename TValue, typename TSpec>
-inline int
-streamPut(::std::stringstream & stream,
-          SimpleType<TValue, TSpec> const & c)
-{
-    return streamWriteChar(stream, convert<char>(c));
-}
-
-// --- strings
-
-inline int
-streamPut(::std::stringstream & stream, char const * source)
-{
-    return (streamWriteBlock(stream, source, strlen(source))
-                == strlen(source) )  ?   0 : 1;
-}
-
-template <typename TSpec>
-inline int
-streamPut(::std::stringstream & stream, String<char, TSpec> const & source)
-{
-    return (streamWriteBlock(stream, toCString(source), length(source))
-                == length(source))  ?   0 : 1;
-}
-
-template <typename TValue, typename TSpec, typename TSpec2>
-inline int
-streamPut(::std::stringstream & stream,
-          String<SimpleType<TValue, TSpec>, TSpec2> const & source)
-{
-    String<char, CStyle> buf = source;
-    return (streamWriteBlock(stream, toCString(buf), length(buf))
-                == length(buf))  ?   0 : 1;
-}
-
-inline int
-streamPut(::std::stringstream & stream, ::std::string const & source)
-{
-    return (streamWriteBlock(stream, source.data(), source.length()) == source.length())  ?   0 : 1;
-}
-
-inline int
-streamPut(::std::stringstream & stream, ::std::stringstream const & source)
-{
-    stream << source.rdbuf();
-    return stream.fail();
-}
-
-// --- wildcard
-
-template <typename TSource>
-inline int
-streamPut(::std::stringstream & stream, TSource const & source)
-{
-    stream << source;
-    return stream.fail();
-}
-
-// osstream
-// --- characters
-
-inline int
-streamPut(::std::ostringstream & stream, char const c)
-{
-    return streamWriteChar(stream, c);
-}
-
-template <typename TValue, typename TSpec>
-inline int
-streamPut(::std::ostringstream & stream,
-          SimpleType<TValue, TSpec> const & c)
-{
-    return streamWriteChar(stream, convert<char>(c));
-}
-
-// --- strings
-
-inline int
-streamPut(::std::ostringstream & stream, char const * source)
-{
-    return (streamWriteBlock(stream, source, strlen(source))
-                == strlen(source) )  ?   0 : 1;
-}
-
-template <typename TSpec>
-inline int
-streamPut(::std::ostringstream & stream, String<char, TSpec> const & source)
-{
-    return (streamWriteBlock(stream, toCString(source), length(source))
-                == length(source))  ?   0 : 1;
-}
-
-inline int
-streamPut(::std::ostringstream & stream, ::std::string const & source)
-{
-    return (streamWriteBlock(stream, source.data(), source.length()) == source.length())  ?   0 : 1;
-}
-
-inline int
-streamPut(::std::ostringstream & stream, ::std::stringstream const & source)
-{
-    stream << source.rdbuf();
-    return stream.fail();
-}
-
-// --- wildcard
-
-template <typename TSource>
-inline int
-streamPut(::std::ostringstream & stream, TSource const & source)
-{
-    stream << source;
-    return stream.fail();
-}
-
-// ----------------------------------------------------------------------------
-// Function streamFlush()
-// ----------------------------------------------------------------------------
-
-inline int
-streamFlush(::std::stringstream & stream)
-{
-    stream << std::flush;
-    return 0;
-}
-
-inline int
-streamFlush(::std::ostringstream & stream)
-{
-    stream << std::flush;
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamSeek()
-// ----------------------------------------------------------------------------
-
-inline int
-streamSeek(::std::stringstream & stream, long int delta, int origin)
-{
-    // For sstream, the input and output pointer are kept in sync.
-    if (origin == SEEK_SET) {
-        stream.seekg(delta, ::std::stringstream::beg);
-        stream.seekp(delta, ::std::stringstream::beg);
-    } else if (origin == SEEK_CUR) {
-        stream.seekg(delta, ::std::stringstream::cur);
-        stream.seekp(delta, ::std::stringstream::cur);
-    } else {
-        stream.seekg(delta, ::std::stringstream::end);
-        stream.seekp(delta, ::std::stringstream::end);
-    }
-    return (stream.fail() || stream.bad());
-}
-
-inline int
-streamSeek(::std::istringstream & stream, long int delta, int origin)
-{
-    if (origin == SEEK_SET)
-        stream.seekg(delta, ::std::stringstream::beg);
-    else if (origin == SEEK_CUR)
-        stream.seekg(delta, ::std::stringstream::cur);
-    else
-        stream.seekg(delta, ::std::stringstream::end);
-    return (stream.fail() || stream.bad());
-}
-
-inline int
-streamSeek(::std::ostringstream & stream, long int delta, int origin)
-{
-    if (origin == SEEK_SET)
-        stream.seekp(delta, ::std::stringstream::beg);
-    else if (origin == SEEK_CUR)
-        stream.seekp(delta, ::std::stringstream::cur);
-    else
-        stream.seekp(delta, ::std::stringstream::end);
-    return (stream.fail() || stream.bad());
-}
-
-// ----------------------------------------------------------------------------
-// Function streamTell()
-// ----------------------------------------------------------------------------
-
-inline Position< ::std::stringstream>::Type
-streamTell(::std::stringstream & stream)
-{
-    std::streampos x = stream.tellp();
-    return x;
-}
-
-inline Position< ::std::stringstream>::Type
-streamTell(::std::istringstream & stream)
-{
-    std::streampos x = stream.tellg();
-    return x;
-}
-
-inline Position< ::std::stringstream>::Type
-streamTell(::std::ostringstream & stream)
-{
-    std::streampos x = stream.tellp();
-    return x;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_ADAPT_SSTREAM_H_
diff --git a/seqan/stream/buffered_stream.h b/seqan/stream/buffered_stream.h
new file mode 100644
index 0000000..db96ba3
--- /dev/null
+++ b/seqan/stream/buffered_stream.h
@@ -0,0 +1,246 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_STREAM_BUFFERED_STREAM_
+#define SEQAN_STREAM_BUFFERED_STREAM_
+
+#include <cstdio>
+#include <cstring>
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TValue, typename TDirection, typename TTraits = std::char_traits<TValue> >
+class BufferedStreamBuf;
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class BufferedStream
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class BufferedStream
+ * @implements StreamConcept
+ * @headerfile <seqan/stream.h>
+ * @brief Adds a buffer to another @link StreamConcept stream @endlink.
+ *
+ * @signature template <typename TUnbufferedStream, TDirection>
+ *            class BufferedStream;
+ *
+ * @tparam TUnbufferedStream The type of the unbuffered @link StreamConcept stream @endlink to wrap.
+ * @tparam TDirection        The stream direction, one of @link DirectionTags @endlink.
+ */
+// TODO(esiragusa): @extends BasicStream::Type
+
+template <typename TUnbufferedStream, typename TDirection>
+class BufferedStream :
+    public BasicStream<
+        typename TUnbufferedStream::char_type,
+        TDirection,
+        typename TUnbufferedStream::traits_type>::Type
+{
+protected:
+    typedef typename TUnbufferedStream::char_type                   TValue;
+    typedef typename TUnbufferedStream::traits_type                 TTraits;
+    typedef typename BasicStream<TValue, TDirection, TTraits>::Type TBasicStream;
+    typedef std::basic_streambuf<TValue, TTraits>                   TStreamBuf;
+
+    BufferedStreamBuf<TValue, TDirection, TTraits> buf;
+
+public:
+
+    /*!
+     * @fn BufferedStream::BufferedStream
+     * @brief Default constructor and construction from to-be-wrapped unbuffered stream.
+     *
+     * @signature BufferedStream::BufferedStream();
+     * @signature BufferedStream::BufferedStream(unbufferedStream);
+     *
+     * @param[in] stream The to-be-wrapped stream.
+     */
+    BufferedStream() :
+        TBasicStream(&buf)
+    {}
+
+    explicit BufferedStream(TUnbufferedStream & stream) :
+        TBasicStream(&buf), buf(stream.rdbuf())
+    {}
+
+    /*!
+     * @fn BufferedStream::setStreamBuf
+     * @brief Set the stream buffer of the BufferedStream.
+     *
+     * @signature void BufferedStream::setStreamBuf(streamBuf);
+     *
+     * @param[in] streamBuf The <tt>std::basic_streambuf&lt;&gt;</tt> to use.
+     */
+    void setStreamBuf(TStreamBuf & streamBuf)
+    {
+        buf.setStreamBuf(streamBuf);
+    }
+
+    /*!
+     * @fn BufferedStream::setStream
+     * @brief Set the underlying stream to wrap.
+     *
+     * @signature void BufferedStream::setStream(stream);
+     *
+     * @param[in] stream The <tt>TUnbufferedStream</tt> to use.
+     */
+    void setStream(TUnbufferedStream & stream)
+    {
+        setStreamBuf(*stream.rdbuf());
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class BufferedStreamBuf
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TTraits>
+class BufferedStreamBuf :
+    public std::basic_streambuf<TValue, TTraits>
+{
+protected:
+    typedef std::basic_streambuf<TValue, TTraits>                   TStreamBuf;
+    typedef typename TTraits::int_type                              TInt;
+
+    static const size_t defaultBufferSize = 1024;   // size of the data buffer
+    static const size_t defaultPutbackSize = 256;   // size of the buffer that should be used as putback area
+    std::vector<TValue> buffer;                     // data buffer
+    size_t bufferSize;
+    size_t putbackSize;
+
+    using TStreamBuf::eback;
+    using TStreamBuf::gptr;
+    using TStreamBuf::egptr;
+    using TStreamBuf::setg;
+
+public:
+    TStreamBuf *streamBufPtr;
+
+    /* constructor
+     * - initialize empty data buffer
+     * - no putback area
+     * => force underflow()
+     */
+    BufferedStreamBuf(size_t bufferSize = defaultBufferSize,
+                      size_t putbackSize = defaultPutbackSize) :
+        bufferSize(bufferSize),
+        putbackSize(putbackSize),
+        streamBufPtr(NULL)
+    {
+        clear();
+    }
+
+    explicit
+    BufferedStreamBuf(TStreamBuf &streamBuf,
+                      size_t bufferSize = defaultBufferSize,
+                      size_t putbackSize = defaultPutbackSize) :
+        bufferSize(bufferSize),
+        putbackSize(putbackSize)
+    {
+        setStreamBuf(streamBuf);
+    }
+
+    void clear()
+    {
+        setg((TValue*)NULL,     // beginning of putback area
+             (TValue*)NULL,     // read position
+             (TValue*)NULL);    // end position
+    }
+
+    void setStreamBuf(TStreamBuf &streamBuf)
+    {
+        clear();
+        streamBufPtr = &streamBuf;
+    }
+
+protected:
+    // insert new characters into the buffer
+    virtual TInt underflow()
+    {
+        // is read position before end of buffer?
+        if (gptr() < egptr())
+            return TTraits::to_int_type(*gptr());
+
+        /* process size of putback area
+         * - use number of characters read
+         * - but at most four
+         */
+        size_t numPutback;
+        numPutback = gptr() - eback();
+        if (numPutback > putbackSize)
+            numPutback = putbackSize;
+
+        buffer.resize(bufferSize);
+
+        /* copy up to four characters previously read into
+         * the putback buffer (area of first four characters)
+         */
+        std::memmove(
+            &buffer[putbackSize - numPutback],
+            gptr() - numPutback,
+            numPutback * sizeof(TValue));
+
+        // read new characters
+		std::streamsize numRead = streamBufPtr->sgetn(
+                            &buffer[putbackSize],
+                            buffer.size() - putbackSize);
+
+        // reset buffer pointers
+        setg(&buffer[putbackSize - numPutback],     // beginning of putback area
+             &buffer[putbackSize],                  // read position
+             &buffer[putbackSize + static_cast<size_t>(numRead)]);       // end position
+
+        if (numRead <= 0)
+        {
+            // ERROR or EOF
+            return EOF;
+        }
+
+        // return next character
+        return TTraits::to_int_type(*gptr());
+    }
+};
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_STREAM_BUFFERED_STREAM_
diff --git a/seqan/stream/concept_stream.h b/seqan/stream/concept_stream.h
deleted file mode 100644
index 276a367..0000000
--- a/seqan/stream/concept_stream.h
+++ /dev/null
@@ -1,647 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Interface for the stream concept.
-// ==========================================================================
-
-#ifndef SEQAN_STREAM_CONCEPT_STREAM_H_
-#define SEQAN_STREAM_CONCEPT_STREAM_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @concept StreamConcept
- * @headerfile <seqan/stream.h>
- * @brief Concept for I/O streams.
- *
- * @signature concept StreamConcept;
- */
-
-/**
-.Concept.StreamConcept
-..summary:Concept for I/O streams.
- */
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-/*!
- * @defgroup StreamFeatureTags Stream Feature Tags
- * @brief Tags to select a given feature for querying in @link StreamConcept#HasStreamFeature @endlink.
- *
- *
- * @tag StreamFeatureTags#IsInput
- * @headerfile <seqan/stream.h>
- * @brief Query whether the stream supports @link StreamConcept#streamReadChar @endlink and @link
- *        StreamConcept#streamReadBlock @endlink.
- *
- * @signature typedef Tag<IsInput_> IsInput;
- *
- *
- * @tag StreamFeatureTags#IsOutput
- * @headerfile <seqan/stream.h>
- * @brief Query whether the stream supports @link StreamConcept#streamWriteChar @endlink and @link
- *        StreamConcept#streamWriteBlock @endlink.
- *
- * @signature typedef Tag<IsInput_> IsOutput;
- *
- *
- * @tag StreamFeatureTags#HasPeek
- * @headerfile <seqan/stream.h>
- * @brief Query whether the stream supports @link StreamConcept#streamPeek @endlink.
- *
- * @signature typedef Tag<HasPeek_> HasPeek;
- *
- *
- * @tag StreamFeatureTags#HasFilename
- * @headerfile <seqan/stream.h>
- * @brief Query whether the stream can have a file name.
- *
- * @signature typedef Tag<HasFilename_> HasFilename;
- *
- *
- * @tag StreamFeatureTags#SeekOriginBegin
- * @headerfile <seqan/stream.h>
- * @brief Query whether it is possible to @link StreamConcept#streamSeek @endlink with <tt>SEEK_SET</tt>.
- *
- * @signature typedef Tag<OriginBegin_> OriginBegin;
- *
- *
- * @tag StreamFeatureTags#SeekOriginCurrent
- * @headerfile <seqan/stream.h>
- * @brief Query whether it is possible to @link StreamConcept#streamSeek @endlink with <tt>SEEK_CUR</tt>.
- *
- * @signature typedef Tag<OriginCurrent_> OriginCurrent;
- *
- *
- * @tag StreamFeatureTags#SeekOriginEnd
- * @headerfile <seqan/stream.h>
- * @brief Query whether it is possible to @link StreamConcept#streamSeek @endlink with <tt>SEEK_END</tt>.
- *
- * @signature typedef Tag<OriginEnd_> OriginEnd;
- *
- *
- * @tag StreamFeatureTags#Tell
- * @headerfile <seqan/stream.h>
- * @brief Query whether the stream has a @link StreamConcept#streamTell @endlink function.
- *
- * @signature typedef Tag<Tell_> Tell;
- */
-
-/**
-.Tag.Stream Feature
-..cat:Input/Output
-..summary:Tag to select a given feature for querying in @Metafunction.HasStreamFeature@.
-..tag.IsInput:Query whether the stream supports @Function.streamReadChar@ and @Function.streamReadBlock@.
-..tag.IsOutput:Query whether the stream supports @Function.streamWriteChar@ and @Function.streamWriteBlock@.
-..tag.HasPeek:Query whether the stream supports @Function.streamPeek@.
-..tag.HasFilename:Query whether the stream has a file name.
-..tag.Seek<OriginBegin>:Query whether it is possible to @Function.streamSeek@ with $SEEK_SET$.
-..tag.Seek<OriginCurrent>:Query whether it is possible to @Function.streamSeek@ with $SEEK_CUR$.
-..tag.Seek<OriginEnd>:Query whether it is possible to @Function.streamSeek@ with $SEEK_END.
-..tag.Tell:Query whether the stream has a @Function.streamTell@ function.
-..include:seqan/stream.h
- */
-
-struct IsInput_;
-typedef Tag<IsInput_> IsInput;
-
-struct IsOutput_;
-typedef Tag<IsOutput_> IsOutput;
-
-struct HasPeek_;
-typedef Tag<HasPeek_> HasPeek;
-
-struct HasFilename_;
-typedef Tag<HasFilename_> HasFilename;
-
-struct OriginBegin_;
-typedef Tag<OriginBegin_> OriginBegin;
-
-struct OriginEnd_;
-typedef Tag<OriginEnd_> OriginEnd;
-
-struct OriginCurrent_;
-typedef Tag<OriginCurrent_> OriginCurrent;
-
-template <typename TSpec>
-struct Seek;
-
-struct Tell_;
-typedef Tag<Tell_> Tell;
-
-/*!
- * @mfn StreamConcept#HasStreamFeature
- * @brief Query features of a stream type.
- *
- * @signature HasStreamFeature<TStream, TTag>::Type;
- *
- * @tparam TStream The strema type to query the property of.
- * @tparam TTag    A tag to select a feature.
- *
- * @return Type Either <tt>True</tt> or <tt>False</tt>.
- *
- * @section Remarks
- *
- * Note that this only checks whether the type principally has this feature.  For example, if a stream wraps a Unix pipe
- * internally, seek might always fail.
- */
-
-/**
-.Metafunction.HasStreamFeature
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Query features of a stream type.
-..signature:HasStreamFeature<TStream, TFeatureTag>::Type
-..param.TStream:The stream type to query the property of.
-...type:Concept.StreamConcept
-..param.TFeatureTag:The feature tag.
-...type:Tag.Stream Feature
-..returns:Either $True$ or $False$.
-..remarks:Note that this only checks whether the type principally has this feature. For example, if a stream wraps a Unix PIPE internally, it might not support seek.
-..include:seqan/stream.h
- */
-
-template <typename TStream, typename TTag>
-struct HasStreamFeature;
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-/*!
- * @fn StreamConcept#streamSeek
- * @headerfile <seqan/stream.h>
- * @brief Perform a seek operation on the stream.
- * 
- * @signature int streamSeek(stream, delta, origin);
- * 
- * @param[in,out] stream The stream object to seek on.
- * @param[in]     delta  The (relative) position.  Type: <tt>__int64</tt>
- * @param[in]     origin Where to seek from, we use the integers from &lt;cstdio&gt;.  Possible values are
- *                <tt>SEEK_SET</tt>, <tt>SEEK_CUR</tt>, and <tt>SEEK_END</tt>. Type: <tt>int</tt>
- * 
- * @return int A status code, 0 on success, non-0 value on errors.
- *
- * @see StreamConcept#streamTell
- */
-
-/*!
- * @fn StreamConcept#streamPut
- * @headerfile <seqan/stream.h>
- * @brief Write different types to stream
- * 
- * @signature int streamPut(stream, source);
- * 
- * @param[in,out] stream The stream object to write to. Types: StreamConcept
- * @param[in]     source The data to write to the stream.
- *
- * @return int A status code, 0 on success, non-0 value on errors.
- * 
- * @section Remarks
- * 
- * Implementation note: for some specializations of @link StreamConcept @endlink certain conversions take place through
- * stringstream and a buffer of size 1023.  It follows that the result of the conversion cannot be longer.  However this
- * should only effect numericals right now.  If you still encounter truncated strings with another type, convert to
- * <tt>const char*</tt> manually before writing.
- * 
- * @see StreamConcept#streamWriteChar
- * @see StreamConcept#streamWriteBlock
- */
-
-/*!
- * @fn StreamConcept#streamWriteBlock
- * @headerfile <seqan/stream.h>
- * @brief Write a block of bytes from a buffer into a stream.
- * 
- * @signature TReturn streamWriteBlock(stream, source, count);
- * 
- * @param[in,out] stream The stream object to write to. Types: StreamConcept
- * @param[in]     source The data to write to the stream. Types: nolink:<tt>char *</tt>
- * @param[in]     count  The number of bytes to write to the stream.
- * 
- * @return TSize The number of successfully written objects.
- * 
- * @section Examples
- * 
- * Copying data from a std::fstream into another std::fstream using SeqAn's stream adaption.
- * 
- * @code{.cpp}
- * #include <fstream>
- * #include <seqan/sequence.h>
- * #include <seqan/stream.h>
- *  
- * int main()
- * {
- *     std::fstream in("in.txt", std::ios::binary | std::ios::in);
- *     std::fstream out("out.txt", std::ios::binary | std::ios::in);
- *  
- *     seqan::CharString buffer;
- *     resize(buffer, 1000);
- *  
- *     while (!seqan::atEnd(in) && seqan::streamError(in) == 0)
- *     {
- *         int num = seqan::streamReadBlock(&buffer[0], in, length(buffer));
- *         seqan::streamWriteBlock(out, &buffer[0], num);
- *     }
- *  
- *     return 0;
- * }
- * @endcode
- *
- * @see StreamConcept#streamWriteChar
- * @see StreamConcept#streamPut
- */
-
-/*!
- * @fn StreamConcept#streamPeek
- * @headerfile <seqan/stream.h>
- * @brief Read next character from stream without advancing current position.
- * 
- * @signature int streamPeek(c, stream);
- * 
- * @param[out]    c      The read character is written here. Type: <tt>char &amp;</tt>.
- * @param[in,out] stream The stream object to read from.
- * 
- * @return int 0 on success, otherwise the error value from the underlying string system.
- * 
- * @section Remarks
- * 
- * Note that this might involve two calls into the stream library, e.g. for cstdio streams, it involves a call to both
- * <tt>getc()</tt> and <tt>ungetc()</tt>.
- * 
- * @see StreamConcept#streamReadChar
- * @see StreamConcept#streamReadBlock
- */
-
-/*!
- * @fn StreamConcept#streamReadBlock
- * @headerfile <seqan/stream.h>
- * @brief Read a block of bytes into a buffer.
- * 
- * @signature TSize streamReadBlock(target, stream, maxLen)
- * 
- * @param maxLen maximal number of characters to read. Types:
- *               nolink:<tt>size_t</tt>
- * @param target The buffer to read into. There has to be enough space for
- *               <tt>maxLen</tt> bytes. Types: nolink:<tt>char *</tt>
- * @param stream The stream to read from. Types: StreamConcept
- * 
- * @return TSize Number of read bytes.
- * 
- * @section Examples
- * 
- * Copying data from a std::fstream into another std::fstream using SeqAn's stream adaption.
- * 
- * @code{.cpp}
- * #include <fstream>
- * #include <seqan/sequence.h>
- * #include <seqan/stream.h>
- *  
- * int main()
- * {
- *     std::fstream in("in.txt", std::ios::binary | std::ios::in);
- *     std::fstream out("out.txt", std::ios::binary | std::ios::in);
- *  
- *     seqan::CharString buffer;
- *     resize(buffer, 1000);
- *  
- *     while (!seqan::atEnd(in) && seqan::streamError(in) == 0)
- *     {
- *         int num = seqan::streamReadBlock(&buffer[0], in, length(buffer));
- *         seqan::streamWriteBlock(out, &buffer[0], num);
- *     }
- *  
- *     return 0;
- * }
- * @endcode
- *
- * @see StreamConcept#streamPeek
- * @see StreamConcept#streamReadChar
- */
-
-/*!
- * @fn StreamConcept#streamTell
- * @headerfile <seqan/stream.h>
- * @brief Get the position in the current stream.
- * 
- * @signature TPos streamTell(stream);
- * 
- * @param[in] stream The stream object to query the current position for.
- * 
- * @return TPos The position within the stream.
- * 
- * @see StreamConcept#streamSeek
- */
-
-/*!
- * @fn StreamConcept#streamError
- * @headerfile <seqan/stream.h>
- * @brief Return the stream's error code.
- *
- * @signature int streamError(stream);
- * 
- * @param[in] stream The stream object to query.
- * 
- * @return int An error code, 0 is used for "no errors."
- */
-
-/*!
- * @fn StreamConcept#streamWriteChar
- * @headerfile <seqan/stream.h>
- * @brief Write one character to the stream.
- * 
- * @signature int streamWriteChar(stream, c);
- * 
- * @param[in,out] stream The stream object to write to.
- * @param[in]     c      The character to write to the stream. Types: <tt>char</tt>
- * 
- * @return int Error code, 0 on success.
- * 
- * @see StreamConcept#streamWriteBlock
- * @see StreamConcept#streamPut
- */
-
-/*!
- * @fn StreamConcept#streamReadChar
- * @headerfile <seqan/stream.h>
- * @brief Read next character from stream and advance the current position.
- * 
- * @signature int streamReadChar(c, stream);
- * 
- * @param[out]    c      The read character is written here. Types: <tt>char &amp;</tt>
- * @param[in,out] stream The stream object to read from.
- * 
- * @return TReturn <tt>int</tt>, 0 on success, otherwise the error value from the underlying string system.
- * 
- * @see StreamConcept#streamPeek
- * @see StreamConcept#streamReadBlock
- */
-
-/*!
- * @fn StreamConcept#streamEof
- * @headerfile <seqan/stream.h>
- * @brief Check end-of-file state of a @link StreamConcept @endlink.
- * 
- * @signature bool streamEof(stream);
- * 
- * @param[in] stream The stream object to check.
- * 
- * @return bool true if the stream is in end-of-file state, false otherwise.
- * 
- * @section Remarks
- * 
- * Note that the exact behaviour depends on the underlying implementation. With <tt>FILE *</tt> streams, the stream can
- * be in the end-of-file state from the point where the last character was read or from the point where the user tried
- * to read beyond the end of the file.
- */
-
-/*!
- * @fn StreamConcept#streamFlush
- * @headerfile <seqan/stream.h>
- * @brief Flush the underlying stream.
- * 
- * @signature int streamFlush(stream);
- * 
- * @param[in,out] stream The stream object to flush.
- * 
- * @return int with an error code, 0 on success.
- */
-
-/**
-.Function.streamPeek
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Read next character from stream without advancing current position.
-..signature:streamPeek(c, stream)
-..param.c:The read character is written here.
-...type:nolink:$char &$
-..param.stream:The stream object to read from.
-...type:Concept.StreamConcept
-..returns:$int$, 0 on success, otherwise the error value from the underlying string system.
-..remarks:Note that this might involve two calls into the stream library, e.g. for cstdio streams, it involves a call to both $getc()$ and $ungetc()$.
-..see:Function.streamReadChar
-..see:Function.streamReadBlock
-..include:seqan/stream.h
-
-.Function.streamReadChar
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Read next character from stream and advance the current position.
-..signature:streamReadChar(c, stream)
-..param.c:The read character is written here.
-...type:nolink:$char &$
-..param.stream:The stream object to read from.
-...type:Concept.StreamConcept
-..returns:$int$, 0 on success, otherwise the error value from the underlying string system.
-..see:Function.streamPeek
-..see:Function.streamReadBlock
-..include:seqan/stream.h
-
-.Function.streamEof
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Check end-of-file state of a @Concept.StreamConcept@.
-..signature:streamReadChar(stream)
-..param.stream:The stream object to read from.
-...type:Concept.StreamConcept
-..returns:$bool$, true if the stream is in end-of-file state, false otherwise.
-..remarks:Note that the exact behaviour depends on the underlying implementation. With $FILE *$ streams, the stream can be in the end-of-file state from the point where the last character was read or from the point where the user tried to read beyond the end of the file.
-..include:seqan/stream.h
-
-.Function.streamReadBlock
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Read a block of bytes into a buffer.
-..signature:streamReadBlock(target, stream, maxLen)
-..param.target:The buffer to read into. There has to be enough space for $maxLen$ bytes.
-...type:nolink:$char *$
-..param.stream:The stream to read from.
-...type:Concept.StreamConcept
-..param.maxLen:maximal number of characters to read.
-...type:nolink:$size_t$
-..returns:Number of read bytes.
-..example.text:Copying data from a std::fstream into another std::fstream using SeqAn's stream adaption.
-..example.code:
-#include <fstream>
-#include <seqan/sequence.h>
-#include <seqan/stream.h>
-
-int main()
-{
-    std::fstream in("in.txt", std::ios::binary | std::ios::in);
-    std::fstream out("out.txt", std::ios::binary | std::ios::in);
-
-    seqan::CharString buffer;
-    resize(buffer, 1000);
-
-    while (!seqan::atEnd(in) && seqan::streamError(in) == 0)
-    {
-        int num = seqan::streamReadBlock(&buffer[0], in, length(buffer));
-        seqan::streamWriteBlock(out, &buffer[0], num);
-    }
-
-    return 0;
-}
-..see:Function.streamPeek
-..see:Function.streamReadChar
-..include:seqan/stream.h
-
-.Function.streamWriteChar
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Write one character to the stream.
-..signature:streamWriteChar(stream, c)
-..param.stream:The stream object to write to.
-...type:Concept.StreamConcept
-..param.c:The character to write to the stream.
-...type:nolink:$char$
-..returns:$int$ with error code, 0 on success.
-..see:Function.streamWriteBlock
-..include:seqan/stream.h
-
-.Function.streamWriteBlock
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Write a block of bytes from a buffer into a stream.
-..signature:streamWriteBlock(stream, source, count)
-..param.stream:The stream object to write to.
-...type:Concept.StreamConcept
-..param.source:The data to write to the stream.
-...type:nolink:$char *$
-..param.count:The number of bytes to write to the stream.
-...type:nolink:$size_t$
-..returns:$int$ with the number of successfully written objects. 
-..example.text:Copying data from a std::fstream into another std::fstream using SeqAn's stream adaption.
-..example.code:
-#include <fstream>
-#include <seqan/sequence.h>
-#include <seqan/stream.h>
-
-int main()
-{
-    std::fstream in("in.txt", std::ios::binary | std::ios::in);
-    std::fstream out("out.txt", std::ios::binary | std::ios::in);
-
-    seqan::CharString buffer;
-    resize(buffer, 1000);
-
-    while (!seqan::atEnd(in) && seqan::streamError(in) == 0)
-    {
-        int num = seqan::streamReadBlock(&buffer[0], in, length(buffer));
-        seqan::streamWriteBlock(out, &buffer[0], num);
-    }
-
-    return 0;
-}
-..see:Function.streamWriteChar
-..include:seqan/stream.h
-
-.Function.streamPut
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Write different types to stream
-..signature:streamPut(stream, source)
-..param.stream:The stream object to write to.
-...type:Concept.StreamConcept
-..param.source:The data to write to the stream.
-...type:nolink:$char *$ (must be 0-terminated!)
-...type:Shortcut.CharString
-...type:nolink:String<char, *>
-...type:nolink:numerical types ($int$, $double$ ...)
-..returns:$int$ with an error code, 0 on success.
-..remarks:Implementation note: for some specializations of @Concept.StreamConcept@ certain conversions take place through stringstream and a buffer of size 1023. It follows that the result of the conversion cannot be longer. However this should only effect numericals right now. If you still encounter truncated strings with another type, convert to $const char*$ manually before writing.
-..see:Function.streamWriteChar
-..see:Function.streamWriteBlock
-..include:seqan/stream.h
-
-.Function.streamFlush
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Flush the underlying stream.
-..signature:streamFlush(stream)
-..param.stream:The stream object to flush.
-...type:Concept.StreamConcept
-..returns:$int$ with an error code, 0 on success.
-..include:seqan/stream.h
-
-.Function.streamError
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Return the stream's error code.
-..signature:streamError(stream)
-..param.stream:The stream object to query.
-...type:Concept.StreamConcept
-..returns:$int$ with an error code, 0 is used for "no errors."
-..include:seqan/stream.h
-
-.Function.streamSeek
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Perform a seek operation on the stream.
-..signature:streamSeek(stream, delta, origin)
-..param.stream:The stream object to seek on.
-...type:Concept.StreamConcept
-..param.delta:The (relative) position.
-...type:nolink:$long int$
-..param.origin:Where to query from, we use the integers from <cstdio>.
-...type:nolink:$int$
-...remarks:Possible values are $SEEK_SET$, $SEEK_CUR$, and $SEEK_END$.
-..returns:$int$ with an error code, 0 is used for "no errors."
-..see:Function.streamTell
-..include:seqan/stream.h
-
-.Function.streamTell
-..concept:Concept.StreamConcept
-..cat:Input/Output
-..summary:Get the position in the current stream.
-..signature:streamTell(stream)
-..param.stream:The stream object to query the current position for.
-...type:Concept.StreamConcept
-..returns:The position within the stream, of type @Metafunction.Position@.
-..see:Function.streamSeek
-..include:seqan/stream.h
- */
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_CONCEPT_STREAM_H_
diff --git a/seqan/stream/file_stream.h b/seqan/stream/file_stream.h
old mode 100755
new mode 100644
index 5d16c72..c6f941c
--- a/seqan/stream/file_stream.h
+++ b/seqan/stream/file_stream.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -31,10 +31,16 @@
 // ==========================================================================
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
-// fast block-based file reader/writer with stream interfacce
+// fast block-based file reader/writer with buffer interface
 // supports async I/O / memory-mapping
 // ==========================================================================
 
+// TODO(weese):
+// * skip reading of a page frame when ptr is EMPTY and not ONDISK
+// * skip writing when page was not modified
+// * cancel writing and reading if page is locked while writing
+
+
 #ifndef SEQAN_FILE_FILE_STREAM_H_
 #define SEQAN_FILE_FILE_STREAM_H_
 
@@ -47,1120 +53,1255 @@ namespace seqan {
 // ============================================================================
 
 // ============================================================================
-// Tags, Classes, Enums
+// Functions
 // ============================================================================
 
-// ----------------------------------------------------------------------------
-// Class FileStream
-// ----------------------------------------------------------------------------
-
-//    template <typename TValue>
-//    struct Size<Stream<FileStream<TSpec, TValue> > >:
-//        public Size<typename Stream<FileStream<TSpec, TValue> >::TFile> {};
-//
-//    template <typename TValue>
-//    struct Position<Stream<FileStream<TSpec, TValue> > >:
-//        public Position<typename Stream<FileStream<TSpec, TValue> >::TFile> {};
-
-
-
-    // FileStream with async. file I/O
-/*
-template <typename TValue>
-class Stream<FileStream<FileWriter, TValue> >
+// template <typename TValue, typename TSpec>
+// inline void
+// free(Buffer<TValue, TSpec> & me)
+// {
+// #ifdef PLATFORM_WINDOWS
+//     VirtualFree(me.begin, 0, MEM_RELEASE);
+// #else
+//     ::free(me.begin);
+// #endif
+// }
+
+template <typename TValue, typename TSpec>
+inline void
+clear(Buffer<TValue, TSpec> & me)
 {
-public:
-    typedef File< Async<> >                             TFile;
-    typedef SimpleBuffer<TValue>                        TBuffer;
-    typedef PageFrame<TValue, TFile, Dynamic<> >        TPageFrame;
-    typedef PageChain<TPageFrame>                       TPageChain;
-    typedef	typename Iterator<TBuffer, Standard>::Type	TIterator;
-
-    static const unsigned pageSize = 4*1024*1024;      // 1M entries per page
-    static const unsigned numPages = 2;                // double-buffering
-
-    TFile       file;
-    TPageChain  chain;
-    unsigned    nextPageNo;
-    TIterator   it, itEnd;
+    me.begin = me.end = NULL;
+    _setCapacity(me, 0);
+}
 
-    Stream():
-        chain(numPages)
+template <typename TValue, typename TSpec, typename TSize>
+inline void
+reserve(Buffer<TValue, TSpec> & me, TSize newCapacity)
+{
+    typedef typename Size<Buffer<TValue, TSpec> >::Type TBufferSize;
+    if ((TBufferSize)newCapacity <= capacity(me))
+        return;
+
+    free(me);
+#ifdef PLATFORM_WINDOWS
+    me.begin = me.end = (TValue *) VirtualAlloc(NULL, newCapacity * sizeof(TValue), MEM_COMMIT, PAGE_READWRITE);
+#else
+    me.begin = me.end = (TValue *) valloc(newCapacity * sizeof(TValue));
+#endif
+    if (me.begin == NULL)
     {
-        _initialize();
+        _setCapacity(me, 0);
+        throw std::bad_alloc();
     }
 
-    ~Stream()
-    {
-        close(*this);
-    }
+    _setCapacity(me, newCapacity);
+}
 
-    inline void _initialize()
-    {
-        it = NULL;
-        itEnd = NULL;
-        nextPageNo = 0;
-    }
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
 
-    inline bool _advanceBuffer()
-    {
-        bool result = true;
+// ----------------------------------------------------------------------------
+// Class FilePage
+// ----------------------------------------------------------------------------
 
-        // write previously provided buffer to disk
-        if (nextPageNo != 0)
-            result &= _writeBuffer();
+enum PageCompletionState
+{
+    IS_READ = 1,            // raw buffer is in sync with disk
+    IS_PREPROCESSED = 2,    // data buffer is in sync (e.g. decompressed) with raw
+    IS_POSTPROCESSED = 4,   //
+    IS_WRITTEN = 8
+};
 
-        // step one buffer ahead
-        TPageFrame &pf = *chain.getReadyPage();
+template <typename TValue, typename TSpec>
+struct FilePage
+{
+    typedef File<Async<> >                          TFile;
+    typedef typename AsyncRequest<FilePage>::Type   TAsyncRequest;
+    typedef typename Position<TFile>::Type          TFilePos;
+    typedef typename Size<TFile>::Type              TFileSize;
+
+    FilePage                * next;
+    unsigned                lockCount;
+
+    Buffer<TValue>          raw;
+    Buffer<TValue>          data;
+    TAsyncRequest           request;
+
+    TFilePos                filePos;
+    TFileSize               size;
+    PageFrameState          state;
+    PageFrameState          targetState;
+    PageCompletionState     completionState;
+
+    FilePage() :
+        next(NULL),
+        lockCount(0),
+        filePos(0),
+        size(0),
+        state(UNUSED),
+        targetState(UNUSED),
+        completionState(IS_PREPROCESSED)
+    {}
+};
 
-        // allocate page memory if not done already
-        if (pf.begin == NULL)
-            allocPage(pf, pageSize, file);
+template <typename TValue, typename TSpec>
+struct AsyncRequest<FilePage<TValue, TSpec> >:
+    AsyncRequest<File<TSpec> > {};
 
-        // assign correct page number
-        pf.pageNo = nextPageNo++;
+template <typename TValue, typename TConfig>
+struct AsyncRequest<FilePage<TValue, MMap<TConfig> > >
+{
+    typedef AsyncDummyRequest Type;
+};
 
-        it = pf.begin;
-        itEnd = pf.end;
+// ============================================================================
+// Functions
+// ============================================================================
 
-        return result;
-    }
+template <typename TValue, typename TSpec>
+inline void
+clear(FilePage<TValue, TSpec> & me)
+{
+    free(me.raw);
+    free(me.data);
+    clear(me.raw);
+    clear(me.data);
+}
 
-    inline bool _stopWriting()
-    {
-        // has anything been written?
-        if (nextPageNo == 0)
-            return true;
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
 
-        // write previously provided buffer to disk
-        bool result = _writeBuffer();
+// ----------------------------------------------------------------------------
+// Class FilePager
+// ----------------------------------------------------------------------------
 
-        // wait for all outstanding operations to finish
-        result &= _flush();
+template <unsigned PAGESIZE = 4 * 1024>
+struct FixedPagingScheme
+{
+    enum { pageSize = PAGESIZE };
 
-        _initialize();
+    static void * EMPTY;
+    static void * ON_DISK;
 
-        return result;
-    }
+    String<void *> frameStart;
+};
 
-private:
+template <unsigned PAGESIZE>
+void * FixedPagingScheme<PAGESIZE>::EMPTY = NULL;
 
-    inline bool _writeBuffer()
-    {
-        // shrink buffer size if it was not fully written (like the last buffer)
-        if (it != itEnd)
-            resize(*chain.last, it - chain.last->begin);
-//            std::cout << chain.last->pageNo << '\t';
-//            std::cout << *chain.last << std::endl;
-        return writePage(*chain.last, file);
-    }
+template <unsigned PAGESIZE>
+void * FixedPagingScheme<PAGESIZE>::ON_DISK = (void *)-1;
 
-    inline bool _flush()
-    {
-        bool result = true;
-        TPageFrame *p = chain.first;
-        while (p != NULL)
-        {
-            result &= waitFor(*p);
-            freePage(*p, file);
-            p = p->next;
-        }
-result &= flush(file);
 
-        return result;
-    }
+template <typename TFilePageTable>
+struct PagingScheme
+{
+    typedef FixedPagingScheme<> Type;
 };
-*/
 
-template <typename TSpec = File<>, typename TValue = char>
-struct FileStream;
+template <typename TValue, typename TDirection, typename TSpec = Async<> >
+struct FilePageTable;
 
-// FileStream with memory mapping
 
-template <typename TSpec, typename TValue>
-class Stream<FileStream<TSpec, TValue> >
+template <typename TValue, typename TDirection, typename TSpec>
+struct Host<FilePageTable<TValue, TDirection, TSpec> >
 {
-public:
-    typedef File<Async<> >                              TFile;
-    typedef typename Size<TFile>::Type                  TSize;
-    typedef Buffer<TValue>                              TBuffer;
-    typedef Buffer<TValue, PageFrame<TFile, Dynamic> >  TPageFrame;
-    typedef PageChain<TPageFrame>                       TPageChain;
-//        typedef String<TPageFrame*>                         TPageChain;
-    typedef	typename Iterator<TBuffer, Standard>::Type	TIterator;
-
-    static const unsigned pageSize = 4*1024*1024;      // 1M entries per page
-//    static const unsigned pageSize = 4*1024;      // 1M entries per page
-    static const unsigned numPages = 2;                // double-buffering
+    typedef File<TSpec> Type;
+};
 
-    TFile       file;
-    TSize       fileSize;
-    TPageFrame  *framePtr;
-    TPageChain  inChain;
-    TPageChain  outChain;
+template <typename TValue, typename TDirection, typename TSpec>
+struct Host<FilePageTable<TValue, TDirection, MMap<TSpec> > >
+{
+    typedef FileMapping<TSpec> Type;
+};
 
-    unsigned    nextReadyPageNo;
-    unsigned    nextFetchPageNo;
-    int         lastPageNo;
 
-    bool        inChainNeedsHousekeeping;
-    bool        outChainNeedsHousekeeping;
+// incoming chain
+// cached chain
+// outgoing chain
 
-    // Iterators to the current position in the page, the end of the page and the end of the page as it is on the disk.
-    // itReadEnd is relevant if the file is opened in read+write mode on the last page.  itEnd can point behind the end
-    // of the file on the disk whereas itReadEnd points to the end of the file on the disk.  itReadEnd will be
-    // incremented if something is written on the last page.
-    TIterator   it, itEnd, itReadEnd;
+template <typename TValue, typename TDirection, typename TSpec>
+struct FilePageTable
+{
+    typedef typename Host<FilePageTable>::Type          TFile;
+    typedef typename Size<TFile>::Type                  TSize;
 
-    unsigned modeFlags;  // bitmask with open flags
-    bool eofFlag;  // whether we are at the end of the file
-    int errorFlag;  // error flag, 0 on no error
+    typedef FilePage<TValue, TSpec>                     TPageFrame;
+    typedef PageChain<TPageFrame>                       TPageChain;
+    typedef typename PagingScheme<FilePageTable>::Type  TPagingScheme;
+    typedef Buffer<TValue>                              TBuffer;
+    typedef typename Iterator<TBuffer, Standard>::Type  TIterator;
 
-    Stream()
-    {
-        _initialize();
-    }
+    typedef short int                                   TPageId;
+    typedef String<TPageId>                             TPageDir;
 
-    ~Stream()
-    {
-        close(*this);
-    }
+    static const unsigned numPages = 2;                // double-buffering
 
-    // Returns whether or not the stream was opened with reading enabled.
-    bool _isReadable() const
-    {
-        return modeFlags & OPEN_RDONLY;
-    }
+    TFile           file;
+    TSize           fileSize;
 
-    // Returns whether or not the stream was opened with writing enabled.
-    bool _isWriteable() const
-    {
-        return modeFlags & OPEN_WRONLY;
-    }
+    TPageChain      unused;
+    TPageChain      ready;
+    TPageChain      inProcess;
 
-    inline void _initialize()
-    {
-        fileSize = 0;
-        framePtr = NULL;
-        it = NULL;
-        itEnd = NULL;
-        itReadEnd = NULL;
-        nextReadyPageNo = 0;
-        nextFetchPageNo = 0;
-        lastPageNo = -1;
-        inChainNeedsHousekeeping = false;
-        outChainNeedsHousekeeping = false;
-        modeFlags = 0;
-        eofFlag = false;
-        errorFlag = 0;
-    }
+    TPagingScheme   table;
 
     inline void _printStats()
     {
-        std::cout << "in: " << inChain.size() << "\tout:" << outChain.size() << "\tframe:" << (__uint64)framePtr << std::endl;
-    }
-
-    inline int _getNextFetchPageNo()
-    {
-        return nextFetchPageNo++;
-    }
-
-    inline bool _injectUnusedBuffer(TPageFrame &frame)
-    {
-        bool inProgress;
-        frame.status = UNUSED;
-        if (!tryFetchBuffer(*this, frame, inProgress))
-            return false;
-
-        #ifdef SEQAN_DEBUG_FILESTREAM
-        std::cout << "ADDED INTO IN-CHAIN (" << inChain.frames << "):" << std::endl;
-        std::cout << frame << std::endl;
-        #endif
-        inChain.pushBack(frame);
-        inChainNeedsHousekeeping |= inProgress;
-        return true;
-    }
-
-    inline bool _houseKeeping()
-    {
-        bool inProgress;
-
-        if (outChainNeedsHousekeeping)
-        {
-            bool someAreInProgress = false;
-            for (TPageFrame *p = outChain.first; p != NULL;)
-            {
-                TPageFrame &page = *p;
-                p = p->next;
-
-                if (!tryReleaseBuffer(*this, page, inProgress))
-                    return false;
-
-                if (!inProgress)
-                {
-                    outChain.erase(page);
-                    _injectUnusedBuffer(page);
-                }
-                else
-                    someAreInProgress = true;
-            }
-            outChainNeedsHousekeeping = someAreInProgress;
-        }
-
-        if (inChainNeedsHousekeeping)
-        {
-            bool someAreInProgress = false;
-            for (TPageFrame *p = inChain.first; p != NULL; p = p->next)
-            {
-                if (!tryFetchBuffer(*this, *p, inProgress))
-                    return false;
-                someAreInProgress |= inProgress;
-            }
-            inChainNeedsHousekeeping = someAreInProgress;
-        }
-        return true;
-    }
-
-    // ,---, ,---, ,---, ,---, ,---,
-    // | 0 | | 1 | | 2 | | 3 | | 4 |
-    // '---' '---' '---' '---' '---'
-    //
-    //
-
-    inline bool _advanceBuffer()
-    {
-        bool result = true;
-        bool inProgress;
-
-        // release old buffer
-        if (framePtr != NULL)
-        {
-            // shrink current buffer size if it was not fully written (like the last buffer)
-            TPageFrame &oldFrame = *framePtr;
-            if (it != itEnd)
-                resize(oldFrame, it - oldFrame.begin);
-
-            // start to release the current buffer
-            result &= tryReleaseBuffer(*this, oldFrame, inProgress);
-            if (inProgress)
-            {
-                // writing is in progress
-                // -> we put the frame into the out-chain
-                #ifdef SEQAN_DEBUG_FILESTREAM
-                std::cout << "ADDED INTO OUT-CHAIN (" << outChain.frames << "):" << std::endl;
-                std::cout << oldFrame << std::endl;
-                #endif
-                outChain.pushBack(oldFrame);
-                outChainNeedsHousekeeping |= inProgress;
-            }
-            else
-                // writing finished immediately
-                // -> we reinject the now unused buffer into the in-chain
-                _injectUnusedBuffer(oldFrame);
-        }
-
-        // watch current progress
-        // initiate next asynchronous task for each buffer
-        // reinject written buffers for prefetching the next ones
-        _houseKeeping();
-
-        // fetch new buffer
-        if (inChain.empty())
-        {
-            // we need more incoming buffers
-            if (inChain.size() + outChain.size() < numPages)
-            {
-                // we can afford to create new buffers
-                _injectUnusedBuffer(*(new TPageFrame()));
-            }
-            else
-            {
-                // all out-chain buffers are in progress (otherwise in-chain would not be empty)
-                // so we take and wait for the first out-chain buffer
-                TPageFrame &anyOutChainBuffer = outChain.popFront();
-                tryReleaseBuffer(*this, anyOutChainBuffer, inProgress, true);
-                _injectUnusedBuffer(anyOutChainBuffer);
-            }
-        }
-
-        // we implicitly assume the front buffer
-        // to be the next in sequence nextReadyPageNo, nextReadyPageNo+1, ...
-        framePtr = &inChain.popFront();
-        SEQAN_ASSERT_EQ(framePtr->pageNo, nextReadyPageNo);
-        ++nextReadyPageNo;
-
-        // now fetch-and-wait for new buffer
-        result &= tryFetchBuffer(*this, *framePtr, inProgress, true);
-        it = framePtr->begin;
-        itEnd = framePtr->end;
-
-        // itEnd always points to the end of the page, whereas itReadEnd can point in the middle.
-        if (_isWriteable() && (unsigned)(itEnd - it) < pageSize)
-            itEnd = it + pageSize;
-
-        return result;
+        std::cout << "unused: " << unused.size() << "\tready:" << ready.size() << "\tinProcess:" << inProcess.size() << std::endl;
     }
 
-    // Flush everything to disk.  If preserveFileSize then the file size is preserved.
-    inline bool _stop(bool preserveFileSize = false)
+    ~FilePageTable()
     {
-        // has anything been written?
-        if (nextReadyPageNo == 0)
-            return true;
-
-        // shrink current buffer size if it was not fully written (like the last buffer)
-        TPageFrame &oldFrame = *framePtr;
-        resize(oldFrame, std::max(it, itReadEnd) - oldFrame.begin);
-
-        // start to release the current buffer
-        bool dummy;
-        bool result = tryReleaseBuffer(*this, oldFrame, dummy, true);
-        freePage(oldFrame, file);
-        delete &oldFrame;
-
-        while (!outChain.empty())
-        {
-            result &= tryReleaseBuffer(*this, outChain.front(), dummy, true);
-            freePage(outChain.front(), file);
-            delete &outChain.popFront();
-        }
-
-        while (!inChain.empty())
-        {
-            // cancel(inChain.front(), file);
-            freePage(inChain.front(), file);
-            delete &inChain.popFront();
-        }
-
-        TSize _fileSize = fileSize;
-        _initialize();
-        if (preserveFileSize)
-            fileSize = _fileSize;
-
-        return result;
+        flushAndFree(*this);
     }
 };
 
+
 // ============================================================================
-// Metafunctions
+// Functions
 // ============================================================================
 
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <typename TSpec, typename TValue>
-struct Value<Stream<FileStream<TSpec, TValue> > >
-{
-    typedef TValue Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Position
-// ----------------------------------------------------------------------------
-
-template <typename TSpec, typename TValue>
-struct Position<Stream<FileStream<TSpec, TValue> > >
-{
-    typedef Stream<FileStream<TSpec, TValue> > TStream_;
-    typedef typename TStream_::TFile TFile_;
-
-    typedef typename Position<TFile_>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <typename TSpec, typename TValue>
-struct Size<Stream<FileStream<TSpec, TValue> > >
-{
-    typedef Stream<FileStream<TSpec, TValue> > TStream_;
-    typedef typename TStream_::TFile TFile_;
-
-    typedef typename Size<TFile_>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
-// ----------------------------------------------------------------------------
-
-template <typename TSpec, typename TValue>
-struct HasStreamFeature<Stream<FileStream<TSpec, TValue> >, IsInput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsOutput>
-// ----------------------------------------------------------------------------
-
-template <typename TSpec, typename TValue>
-struct HasStreamFeature<Stream<FileStream<TSpec, TValue> >, IsOutput>
+template <typename TValue, typename TDirection, typename TSpec>
+inline void
+clear(FilePageTable<TValue, TDirection, TSpec> & pager)
 {
-    typedef True Type;
-};
+    pager.fileSize = 0;
+}
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasPeek>
+// Function _getPageOffsetAndLength()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-struct HasStreamFeature<Stream<FileStream<TSpec, TValue> >, HasPeek>
+template <unsigned PAGESIZE, typename TPos>
+inline Pair<__int64, unsigned>
+_getPageOffsetAndLength(FixedPagingScheme<PAGESIZE> const & scheme, TPos pos)
 {
-    typedef True Type;
-};
+    SEQAN_ASSERT_EQ(scheme.pageSize & (scheme.pageSize - 1), 0);  // pageSize must be a power of 2
+    return Pair<__int64, unsigned>((__int64)pos & ~(__int64)(scheme.pageSize - 1), scheme.pageSize);
+}
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasFilename>
+// Function _getFrameStart()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-struct HasStreamFeature<Stream<FileStream<TSpec, TValue> >, HasFilename>
+template <unsigned PAGESIZE, typename TFilePos, typename TSize>
+inline void *
+_getFrameStart(FixedPagingScheme<PAGESIZE> &table, TFilePos filePos, TSize)
 {
-    typedef False Type;
-};
+    unsigned pageNo = filePos / table.pageSize;
+    if (SEQAN_LIKELY(pageNo < length(table.frameStart)))
+        return table.frameStart[pageNo];
+    else
+        return table.EMPTY;
+}
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Seek<TSpec> >
+// Function _setFrameStart()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue, typename TSpec2>
-struct HasStreamFeature<Stream<FileStream<TSpec, TValue> >, Seek<TSpec2> >
+template <unsigned PAGESIZE, typename TFilePos, typename TSize>
+inline void
+_setFrameStart(FixedPagingScheme<PAGESIZE> &table, TFilePos filePos, TSize, void * frameStart)
 {
-    typedef True Type;
-};
+    unsigned pageNo = filePos / table.pageSize;
+    if (length(table.frameStart) <= pageNo)
+        resize(table.frameStart, pageNo + 1, table.EMPTY);
+    table.frameStart[pageNo] = frameStart;
+}
 
 // ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Tell>
+// Function _readFilePage()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-struct HasStreamFeature<Stream<FileStream<TSpec, TValue> >, Tell>
-{
-    typedef True Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// Variant for File<TFileSpec> (fallback if MMap<> not available as on Windows).
-template <typename TSpec, typename TValue, typename TPageFrame>
+// Variant for POSIX file access
+template <typename TValue, typename TDirection, typename TSpec, typename TFileSpec, typename TPageFrame>
 inline bool
-_readBuffer(Stream<FileStream<TSpec, TValue> > &stream, TPageFrame &pf)
+_readFilePage(FilePageTable<TValue, TDirection, TSpec> &pager, File<TFileSpec> & file, TPageFrame & page)
 {
-    // allocate page memory if not done already
-    if (pf.begin == NULL)
-        if (!allocPage(pf, stream.pageSize, stream.file))
-            SEQAN_FAIL("ERROR: Could not allocate page of size %u.", (unsigned)stream.pageSize);
+    // allocate required memory
+    reserve(page.raw, page.size);
 
-    // only read in read-mode
-    if (!stream._isReadable() || (int)pf.pageNo > stream.lastPageNo)
+    // do nothing in output-only mode or when there is nothing to read
+    if (IsSameType<TDirection, Output>::VALUE || page.filePos >= pager.fileSize)
     {
-        resize(pf, 0);
-        pf.status = READY;
-        return true;
+        // no valid data read and we return immediately
+        resize(page.raw, 0);
+        return true;    // true = reading completed
     }
 
-    // shrink buffer size at the end of file
-    if ((int)pf.pageNo < stream.lastPageNo)
-        resize(pf, stream.pageSize);
-    else
-        resize(pf, stream.fileSize - stream.lastPageNo * stream.pageSize);
-    stream.itReadEnd = pf.end;
+    // shrink read buffer size at the end of file
+    resize(page.raw, std::min(page.size, pager.fileSize - page.filePos));
 
-    // read next page into memory
-    return readPage(pf, stream.file);
+    // start asynchronous reading
+    bool success = asyncReadAt(file, begin(page.raw, Standard()), length(page.raw), page.filePos, page.request);
+
+    // if an error occurred, throw an I/O exception
+    if (!success)
+        throw IOError((std::string)_pageFrameStatusString(page.state) + " operation could not be initiated: \"" + strerror(errno) + '"');
+
+    return false;   // false = reading in process
 }
 
 #ifndef PLATFORM_WINDOWS
-template <typename TConfig, typename TValue, typename TPageFrame>
+template <typename TValue, typename TDirection, typename TSpec, typename TFileSpec, typename TPageFrame>
 inline bool
-_readBuffer(Stream<FileStream<MMap<TConfig>, TValue> > &stream, TPageFrame &pf)
+_readFilePage(FilePageTable<TValue, TDirection, TSpec> &, FileMapping<TFileSpec> & file, TPageFrame & page)
 {
-    typedef Stream<FileStream<MMap<TConfig>, TValue> >   TFileStream;
-    typedef typename TFileStream::TFile                         TFile;
-    typedef typename Size<TFile>::Type                          TSize;
+    typedef typename Size<FileMapping<TFileSpec> >::Type TSize;
 
-    _setCapacity(pf, stream.pageSize);
-    TSize size = stream.pageSize;
+    TSize endOfs = page.filePos + page.size;
+    TSize dataSize;
 
-    // Get the page size on the disk, adjusted for last page; required for setting itReadEnd.
-    unsigned pageSizeOnDisk = size;
+    // compute valid readable data
+    if (page.filePos >= length(file))
+        dataSize = 0;   // no valid data to read from behind the end of file
+    else
+        dataSize = std::min(page.size, length(file) - page.filePos);
 
     // how to handle pages crossing/beyond the end of file
-    if ((int)pf.pageNo >= stream.lastPageNo)
+    if (endOfs > length(file))
     {
-        if (stream._isWriteable())
+        if (!IsSameType<TDirection, Input>::VALUE)
         {
-            pageSizeOnDisk = stream.fileSize - pf.pageNo * stream.pageSize;
-
-            // 1. stream is writable:
-            //
-            // increase file size to next page boundary
-            // and map the whole page
-            stream.lastPageNo = pf.pageNo;
-            stream.fileSize = (TSize)(stream.lastPageNo + 1) * (TSize)stream.pageSize;
-            resize(stream.file, stream.fileSize);
+            // increase file size to next page boundary and map the whole page
+            resize(file, endOfs);
         }
         else
         {
-            // 2. stream is read-only:
-            //
-            // adapt buffer to file size
-            // map only the contents of the file
-            if ((int)pf.pageNo == stream.lastPageNo)
-            {
-                pageSizeOnDisk = size;
-                size = stream.fileSize - (TSize)stream.lastPageNo * (TSize)stream.pageSize;
-            }
-            else
-            {
-                pageSizeOnDisk = 0;
-                // don't try to read pages behind the end the file
-                resize(pf, 0);
-                pf.status = READY;
-                return true;
-            }
+            // adapt page size to file size and map only the contents of the file
+            page.size = dataSize;
         }
     }
 
-    bool res = false;
-    if (stream._isWriteable())
-        res = mapWritePage(pf, stream.file, size);
-    else
-        res = mapReadPage(pf, stream.file, size);
-    stream.itReadEnd = pf.begin + pageSizeOnDisk;
-    return res;
+    page.raw.begin = (TValue *) mapFileSegment(file, page.filePos, page.size);
+    _setCapacity(page.raw, page.size);
+    resize(page.raw, dataSize);
+    return true;    // true = reading completed
 }
+
 #endif
 
+// ----------------------------------------------------------------------------
+// Function _preprocessFilePage()
+// ----------------------------------------------------------------------------
 
-template <typename TValue, typename TSpec, typename TPageFrame>
+template <typename TValue, typename TDirection, typename TSpec, typename TPageFrame, typename TBool>
 inline bool
-_preprocessBuffer(Stream<FileStream<TSpec, TValue> > &, TPageFrame &pf, bool)
+_preprocessFilePage(FilePageTable<TValue, TDirection, TSpec> &, TPageFrame &page, TBool const &)
 {
     // not used yet, could be usefull for external sorters/mappers
-    pf.status = READY;
+    page.data = page.raw;
     return true;
 }
 
-template <typename TValue, typename TSpec, typename TPageFrame>
+// ----------------------------------------------------------------------------
+// Function _postprocessFilePage()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TSpec, typename TPageFrame, typename TBool>
 inline bool
-_postprocessBuffer(Stream<FileStream<TSpec, TValue> > &, TPageFrame &pf, bool)
+_postprocessFilePage(FilePageTable<TValue, TDirection, TSpec> &, TPageFrame &page, TBool const &)
 {
     // not used yet, could be usefull for external sorters/mappers
-    pf.status = POSTPROCESSED;
+    resize(page.raw, length(page.data));
+    clear(page.data);
     return true;
 }
 
+// ----------------------------------------------------------------------------
+// Function _writeFilePage()
+// ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue, typename TPageFrame>
+template <typename TValue, typename TDirection, typename TSpec, typename TFileSpec, typename TPageFrame>
 inline bool
-_writeBuffer(Stream<FileStream<TSpec, TValue> > &stream, TPageFrame &pf)
+_writeFilePage(FilePageTable<TValue, TDirection, TSpec> & pager, File<TFileSpec> & file, TPageFrame & page)
 {
+    typedef typename Size<File<TFileSpec> >::Type TSize;
+
     // only write in write-mode
-    if (!stream._isWriteable())
+    if (IsSameType<TDirection, Input>::VALUE)
     {
-        pf.status = UNUSED;
-        return true;
+        page.state = UNUSED;
+        return true;    // true = writing completed
     }
 
-    // shrink buffer size if it was not fully written (like the last buffer)
-    if (stream.it != stream.itEnd)
-        resize(pf, stream.it - pf.begin);
+    // start asynchronous writing
+    page.state = WRITING;
+    bool success = asyncWriteAt(file, begin(page.raw, Standard()), length(page.raw), page.filePos, page.request);
+
+    if (!IsSameType<TDirection, Input>::VALUE)
+        pager.fileSize = std::max(pager.fileSize, (TSize)page.filePos + (TSize)length(page.raw));
 
-    return writePage(pf, stream.file);
+    // if an error occurred, throw an I/O exception
+    if (!success)
+        throw IOError((std::string)_pageFrameStatusString(page.state) + " operation could not be initiated: \"" + strerror(errno) + '"');
+    return false;   // false = writing in process
 }
 
 #ifndef PLATFORM_WINDOWS
-template <typename TConfig, typename TValue, typename TPageFrame>
+template <typename TValue, typename TDirection, typename TSpec, typename TFileSpec, typename TPageFrame>
 inline bool
-_writeBuffer(Stream<FileStream<MMap<TConfig>, TValue> > &stream, TPageFrame &pf)
+_writeFilePage(FilePageTable<TValue, TDirection, TSpec> & pager, FileMapping<TFileSpec> & file, TPageFrame & page)
 {
-    typedef Stream<FileStream<MMap<TConfig>, TValue> >   TFileStream;
-    typedef typename TFileStream::TFile                         TFile;
-    typedef typename Size<TFile>::Type                          TSize;
+    typedef typename Size<FileMapping<TFileSpec> >::Type TSize;
 
-    TSize pageLen = length(pf);
-    pf.status = UNUSED;
-    unmapPage(pf, stream.file);
+    page.state = UNUSED;
+    unmapFileSegment(file, begin(page.raw, Standard()), capacity(page.raw));
 
-    if (stream._isWriteable() && (pageLen < stream.pageSize))
-    {
-        // shrink the file again, it was enlarged earlier (in _readBuffer)
-        stream.lastPageNo = pf.pageNo;
-        stream.fileSize = (TSize)pf.pageNo * (TSize)stream.pageSize + pageLen;
-        resize(stream.file, stream.fileSize);
-    }
-    return true;
+    if (!IsSameType<TDirection, Input>::VALUE)
+        pager.fileSize = std::max(pager.fileSize, (TSize)page.filePos + (TSize)length(page.raw));
+
+    clear(page.raw);
+    return true;    // true = writing completed
 }
+
 #endif
 
 // ----------------------------------------------------------------------------
-// Function tryFetchBuffer()
+// Function _processFilePage()
 // ----------------------------------------------------------------------------
 
-template <typename TValue, typename TSpec, typename TPageFrame>
+template <typename TValue, typename TDirection, typename TSpec, typename TPageFrame, typename TBool>
 inline bool
-tryFetchBuffer(Stream<FileStream<TSpec, TValue> > &stream, TPageFrame &pf, bool &inProgress, bool doWait = false)
+_processFilePage(FilePageTable<TValue, TDirection, TSpec> & pager, TPageFrame & page, TBool const & doWait)
 {
-    inProgress = true;
-    if (pf.status == UNUSED)
-    {
-        // buffer is idle, now read asynchronously
-        pf.pageNo = stream._getNextFetchPageNo();
-        if (!_readBuffer(stream, pf))
-            return false;
-    }
-
-    if (pf.status == READING)
+    bool inProgress;
+    while (page.state != page.targetState)
     {
-        bool inProgress = false;
-        if (doWait)
-        {
-            if (!waitFor(pf))
-                return false;
-        }
-        else
+        switch (page.state)
         {
-            if (!waitFor(pf, 0, inProgress))
+        case UNUSED:
+            // page is ready, start reading
+            page.state = (_readFilePage(pager, pager.file, page)) ? READING_DONE : READING;
+            break;
+
+        case READING:
+            inProgress = false;
+            if (doWait)
+                waitFor(page.request);
+            else
+                waitFor(page.request, 0, inProgress);
+
+            // still in operation?
+            if (inProgress)
                 return false;
-        }
 
-        // still in operation?
-        if (inProgress)
-            return true;
+            // was reading, now preprocessing
+            page.state = READING_DONE;
+            break;
 
-        // was reading, now preprocessing
-        pf.status = PREPROCESSING;
-        if (!_preprocessBuffer(stream, pf, doWait))
-            return false;
-    }
+        case READING_DONE:
+            page.state = (_preprocessFilePage(pager, page, doWait)) ? PREPROCESSING_DONE : PREPROCESSING;
+            break;
 
-    if (pf.status == PREPROCESSING)
-    {
-        // we get here only if doWait==false and the
-        // asynchronous postprocessing is in progress
-        SEQAN_ASSERT_NOT(doWait);
-        return true;
-    }
+        case PREPROCESSING:
+            // TODO: fill me
 
-    if (pf.status == READY)
-    {
-        // if in write mode, extend half-read buffer to page size
-        if (stream._isWriteable())
-            resize(pf, capacity(pf));
+            page.state = PREPROCESSING_DONE;
+            break;
 
-        // all done
-        inProgress = false;
-        return true;
-    }
+        case PREPROCESSING_DONE:
+            // TODO: put me into ready chain
+            page.state = READY;
+            break;
 
-    SEQAN_FAIL("PageFrame has inconsistent state.");
-    return false;
+        case READY:
+            // all done
+            page.state = (_postprocessFilePage(pager, page, doWait)) ? POSTPROCESSING_DONE : POSTPROCESSING;
+            break;
+
+        case POSTPROCESSING:
+            // TODO: fill me
+
+            page.state = PREPROCESSING_DONE;
+            break;
+
+        case POSTPROCESSING_DONE:
+            // page was postprocessed, now write asynchronously
+            page.state = (_writeFilePage(pager, pager.file, page)) ? WRITING_DONE : WRITING;
+            break;
+
+        case WRITING:
+            inProgress = false;
+            if (doWait)
+                waitFor(page.request);
+            else
+                waitFor(page.request, 0, inProgress);
+
+            // still in operation?
+            if (inProgress)
+                return false;
+
+            page.state = WRITING_DONE;
+            break;
+
+        case WRITING_DONE:
+            // TODO: put me into ready chain
+            page.state = UNUSED;
+            break;
+
+        default:
+            SEQAN_FAIL("Unknown page state: %i", page.state);
+        }
+    }
+    return true;
 }
 
 // ----------------------------------------------------------------------------
-// Function tryReleaseBuffer()
+// Function _houseKeeping()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue, typename TPageFrame>
+template <typename TValue, typename TDirection, typename TSpec>
 inline bool
-tryReleaseBuffer(Stream<FileStream<TSpec, TValue> > &stream, TPageFrame &pf, bool &inProgress, bool doWait = false)
+_houseKeeping(FilePageTable<TValue, TDirection, TSpec> & pager)
 {
-    inProgress = true;
-    #ifdef SEQAN_DEBUG_FILESTREAM
-    std::cout << "Release:" << std::endl;
-    #endif
-    if (pf.status == READY)
-    {
-        pf.status = POSTPROCESSING;
-        _postprocessBuffer(stream, pf, doWait);
-    }
+    typedef FilePageTable<TValue, TDirection, TSpec>    TFilePageTable;
+    typedef typename TFilePageTable::TPageFrame         TPageFrame;
 
-    if (pf.status == POSTPROCESSING)
+    if (!empty(pager.inProcess))
     {
-        #ifdef SEQAN_DEBUG_FILESTREAM
-        std::cout<<pf<<std::endl;
-        #endif
-        // we get here only if doWait==false and the
-        // asynchronous postprocessing is in progress
-        SEQAN_ASSERT_NOT(doWait);
-        return true;
-    }
+        for (TPageFrame * p = pager.inProcess.first; p != NULL; )
+        {
+            TPageFrame & page = *p;
+            p = p->next;
 
-    if (pf.status == POSTPROCESSED)
-    {
-        #ifdef SEQAN_DEBUG_FILESTREAM
-        std::cout<<pf<<std::endl;
-        #endif
-        // buffer was postprocessed, now write asynchronously
-        if (!_writeBuffer(stream, pf))
-            return false;
+            if (_processFilePage(pager, page, False()))
+            {
+                if (page.state == READY)
+                {
+                    erase(pager.inProcess, page);
+                    pushBack(pager.ready, page);
+                }
+                else if (page.state == UNUSED)
+                {
+                    erase(pager.inProcess, page);
+                    pushBack(pager.unused, page);
+                }
+            }
+        }
     }
+    return true;
+}
 
-    if (pf.status == WRITING)
-    {
-        #ifdef SEQAN_DEBUG_FILESTREAM
-        std::cout<<pf<<std::endl;
-        #endif
-        bool inProgress = false;
-        if (doWait)
-        {
-            if (!waitFor(pf))
-                return false;
-        }
-        else
-        {
-            if (!waitFor(pf, 0, inProgress))
-                return false;
-        }
+// ----------------------------------------------------------------------------
+// Function _swapOutFilePage()
+// ----------------------------------------------------------------------------
 
-        // still in operation?
-        if (inProgress)
-            return true;
-    }
+template <typename TValue, typename TDirection, typename TSpec>
+inline FilePage<TValue, TSpec> *
+_swapOutFilePage(FilePageTable<TValue, TDirection, TSpec> & pager)
+{
+    SEQAN_ASSERT_NOT(empty(pager.ready) && empty(pager.inProcess));
+
+    typedef FilePage<TValue, TSpec> TPage;
+
+    if (!empty(pager.ready))
+        for (TPage * p = pager.ready.first; p != NULL; p = p->next)
+            if (p->lockCount == 0)
+            {
+                p->targetState = UNUSED;
+                _processFilePage(pager, *p, True());
+                erase(pager.ready, *p);
+                return p;
+            }
+
+    if (!empty(pager.inProcess))
+        for (TPage * p = pager.inProcess.first; p != NULL; p = p->next)
+            if (p->lockCount == 0)
+            {
+                p->targetState = UNUSED;
+                _processFilePage(pager, *p, True());
+                erase(pager.inProcess, *p);
+                return p;
+            }
+    return NULL;
+}
+
+// ----------------------------------------------------------------------------
+// Function _flush()
+// ----------------------------------------------------------------------------
 
-    // transform ready after write into unused
-    if (pf.status == READY)
-        pf.status = UNUSED;
+template <typename TValue, typename TDirection, typename TSpec>
+inline void
+flush(FilePageTable<TValue, TDirection, TSpec> & pager)
+{
+    typedef FilePage<TValue, TSpec> TPage;
 
-    if (pf.status == UNUSED)
+    while (!empty(pager.ready))
     {
-        #ifdef SEQAN_DEBUG_FILESTREAM
-        std::cout<<pf<<std::endl;
-        #endif
-        // all done
-        inProgress = false;
-        return true;
+        TPage &page = popFront(pager.ready);
+        page.targetState = UNUSED;
+        _processFilePage(pager, page, True());
+        pushBack(pager.unused, page);
     }
 
-    SEQAN_FAIL("PageFrame has inconsistent state.");
-    return false;
+    while (!empty(pager.inProcess))
+    {
+        TPage &page = popFront(pager.inProcess);
+        page.targetState = UNUSED;
+        _processFilePage(pager, page, True());
+        pushBack(pager.unused, page);
+    }
+}
+
+template <typename TValue, typename TDirection, typename TSpec, typename TFilePage>
+inline void
+_freeFilePage(FilePageTable<TValue, TDirection, TSpec> & pager, TFilePage & page)
+{
+    _setFrameStart(pager.table, page.filePos, page.size, pager.table.ON_DISK);
+    clear(page);
+}
+
+template <typename TValue, typename TDirection, typename TSpec>
+inline void
+flushAndFree(FilePageTable<TValue, TDirection, TSpec> & pager)
+{
+    flush(pager);
+    while (!empty(pager.unused))
+        _freeFilePage(pager, popFront(pager.unused));
 }
 
 // ----------------------------------------------------------------------------
-// Function open()
+// Function _newFilePage()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue, typename TFilename, typename TFlags>
-inline int
-open(Stream<FileStream<TSpec, TValue> > & stream, TFilename const &filename, TFlags const &flags)
+template <typename TValue, typename TDirection, typename TSpec>
+inline FilePage<TValue, TSpec> *
+_newFilePage(FilePageTable<TValue, TDirection, TSpec> & pager)
 {
-    stream._initialize();
-    stream.modeFlags = flags;  // must be after _initialize()!
-    bool result = open(stream.file, filename, flags);
-    stream.fileSize = (result)? size(stream.file) / sizeof(TValue) : 0ul;
-    if (stream.fileSize != 0)
-        stream.lastPageNo = (stream.fileSize - 1) / stream.pageSize;
+    typedef FilePage<TValue, TSpec> TPage;
+
+    if (empty(pager.unused))
+        _houseKeeping(pager);
+
+    if (!empty(pager.unused))
+        return &popFront(pager.unused);
+
+    // fetch new page
+    if (length(pager.ready) + length(pager.inProcess) < pager.numPages)
+    {
+        // we can afford to create new buffers
+        return new TPage();
+    }
     else
-        stream.lastPageNo = -1;
-    return result;
+    {
+        // all out-chain buffers are in progress (otherwise in-chain would not be empty)
+        // so we take and wait for the first out-chain buffer
+        if (!empty(pager.inProcess))
+        {
+            for (TPage *p = pager.inProcess.first; p != NULL; p = p->next)
+            {
+                if (p->targetState == UNUSED)
+                {
+                    _processFilePage(pager, *p, True());
+                    erase(pager.inProcess, *p);
+                    return p;
+                }
+            }
+        }
+        TPage *p = _swapOutFilePage(pager);
+        if (p != NULL)
+            return p;
+        else
+            return new TPage(); // we can't swap out anything, so we have to allocate more pages
+    }
 }
 
 // ----------------------------------------------------------------------------
-// Function streamWriteChar()
+// Function _lockFilePage()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-inline int
-streamWriteChar(Stream<FileStream<TSpec, TValue> > & stream, TValue const &value)
+template <typename TValue, typename TDirection, typename TSpec, typename TFilePos, typename TSize>
+inline FilePage<TValue, TSpec> &
+_lockFilePage(FilePageTable<TValue, TDirection, TSpec> & pager, TFilePos filePos, TSize size, bool &newPage, bool /*readOnly*/)
 {
-    if (stream.it == stream.itEnd)
+    typedef FilePage<TValue, TSpec> TPage;
+    TPage * p;
+
+    SEQAN_OMP_PRAGMA(critical(lockPageTable))
     {
-        if (!stream._advanceBuffer())
+        p = static_cast<TPage *>(_getFrameStart(pager.table, filePos, size));
+        if (p == pager.table.EMPTY || p == pager.table.ON_DISK)
         {
-            stream.errorFlag = 1;
-            return 1;
+            p = _newFilePage(pager);
+            p->filePos = filePos;
+            p->size = size;
+            p->lockCount = 1;
+            _setFrameStart(pager.table, filePos, size, p);
+            newPage = true;
+        }
+        else
+        {
+            atomicInc(p->lockCount);
+            newPage = false;
         }
-
-        SEQAN_ASSERT_LT(stream.it, stream.itEnd);
     }
-    *(stream.it++) = value;
-    ++stream.itReadEnd;
-    return 0;
+    return *p;
 }
 
 // ----------------------------------------------------------------------------
-// Function streamWriteBlock()
+// Function fetchFilePage()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue, typename TSourceIter, typename TCount>
-inline TCount
-streamWriteBlock(Stream<FileStream<TSpec, TValue> > & stream, TSourceIter srcIter, TCount count)
+template <typename TValue, typename TDirection, typename TSpec, typename TFilePos, typename TSize>
+inline FilePage<TValue, TSpec> &
+fetchFilePage(FilePageTable<TValue, TDirection, TSpec> & pager, TFilePos filePos, TSize size, bool readOnly = false)
 {
-    typedef typename Size<Stream<FileStream<TSpec, TValue> > >::Type TSSize;
+    typedef FilePage<TValue, TSpec> TPage;
 
-    TSSize remaining = count;
-    while (remaining != 0)
+    bool notInList;
+    TPage & page = _lockFilePage(pager, filePos, size, notInList, readOnly);
+
+    // TODO(weese:) multithreading: the first should process, the others should suspend until page is READY
+    if (page.state != READY)
     {
-        // do we need a new buffer?
-        if (stream.it == stream.itEnd)
+        if (!notInList)
         {
-            if (!stream._advanceBuffer())
-                return count - remaining;
-
-            SEQAN_ASSERT_LT((void*)stream.it, (void*)stream.itEnd);
+            if (page.state == UNUSED)
+                erase(pager.unused, page);
+            else if (page.state != UNUSED)
+                erase(pager.inProcess, page);
+            notInList = true;
         }
+        page.targetState = READY;
+        _processFilePage(pager, page, True());
+        if (notInList)
+            pushBack(pager.ready, page);
+    }
+    return page;
+}
 
-        // how many values can we write into the buffer?
-        TSSize cnt = _min(remaining, (TSSize)(stream.itEnd - stream.it));
-        // write them
-        arrayCopyForward(srcIter, srcIter + cnt, stream.it);
+// ----------------------------------------------------------------------------
+// Function releaseFilePage()
+// ----------------------------------------------------------------------------
 
-        stream.it += cnt;
-        stream.itReadEnd = std::max(stream.it, stream.itReadEnd);
-        srcIter += cnt;
-        remaining -= cnt;
+template <typename TValue, typename TDirection, typename TSpec, typename TFilePage>
+inline void
+releaseFilePage(FilePageTable<TValue, TDirection, TSpec> &pager, TFilePage & page)
+{
+    // we automatically flush the page to disk here,
+    // to speed up the swap-out process
+    if (atomicDec(page.lockCount) == 0)
+    {
+        page.targetState = UNUSED;
+        erase(pager.ready, page);
+        if (_processFilePage(pager, page, False()))
+            pushBack(pager.unused, page);
+        else
+            pushBack(pager.inProcess, page);
     }
-    return count;
 }
 
 // ----------------------------------------------------------------------------
-// Function streamReadChar()
+// Class FileStreamBuffer
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-inline int
-streamReadChar(TValue &value, Stream<FileStream<TSpec, TValue> > & stream)
+template <typename TValue, typename TDirection, typename TSpec = Async<> >
+struct FileStreamBuffer :
+    public std::basic_streambuf<TValue>
 {
-    if (stream.it == stream.itReadEnd && stream.it != stream.itEnd)
+    typedef std::basic_streambuf<TValue>                TBase;
+    typedef std::char_traits<TValue>                    TTraits;
+
+    typedef FilePageTable<TValue, TDirection, TSpec>    TFilePageTable;
+    typedef typename TFilePageTable::TPageFrame         TPageFrame;
+    typedef typename TFilePageTable::TFile              TFile;
+
+    typedef typename Size<TFile>::Type                  TSize;
+    typedef typename TBase::int_type                    TIntValue;
+    typedef typename TBase::off_type                    TDifference;
+    typedef typename TBase::pos_type                    TPosition;
+
+    TFilePageTable  pager;
+    TPageFrame      *readPage;
+    TPageFrame      *writePage;
+
+    TPosition       readPagePos;
+    TPosition       writePagePos;
+
+    // Iterators to the current position in the page, the end of the page and the end of the page as it is on the disk.
+    // itReadEnd is relevant if the file is opened in read+write mode on the last page.  itEnd can point behind the end
+    // of the file on the disk whereas itReadEnd points to the end of the file on the disk.  itReadEnd will be
+    // incremented if something is written on the last page.
+
+    FileStreamBuffer()
     {
-        // On the end of the written part of the current page.  itEnd and itReadEnd can only deviate if open in
-        // read+write mode.
-        stream.eofFlag = true;
-        return EOF;
+        clear(*this);
     }
-    else if (stream.it == stream.itReadEnd)
+
+    ~FileStreamBuffer()
+    {
+        close(*this);
+    }
+
+    inline void _stop()
+    {
+        if (readPage != NULL)
+        {
+            releaseFilePage(pager, *readPage);
+            readPage = NULL;
+        }
+        if (writePage != NULL)
+        {
+            resize(writePage->data, std::max((TSize)length(writePage->data), (TSize)(this->pptr() - this->pbase())));
+            releaseFilePage(pager, *writePage);
+            writePage = NULL;
+        }
+        this->setg(NULL, NULL, NULL);
+        this->setp(NULL, NULL);
+    }
+
+    bool _nextReadPage()
+    {
+        if (readPage != NULL)
+        {
+            readPagePos += readPage->size;
+            releaseFilePage(pager, *readPage);
+            readPage = NULL;
+        }
+
+        if (pager.fileSize <= readPagePos)
+            return false;
+
+        Pair<__int64, unsigned> ol = _getPageOffsetAndLength(pager.table, readPagePos);
+        readPage = &fetchFilePage(pager, ol.i1, ol.i2);
+        this->setg(readPage->data.begin, readPage->data.begin, readPage->data.end);
+        return true;
+    }
+
+    bool _nextWritePage()
     {
-        // TODO(weese):
-        // Stop this horrible return value inconsistency,
-        // some stream functions return 1 on error and 0 on success
-        // or the number of transferred values :-/
-        //
-        // until this is fixed we return EOF in case of an error
+        if (writePage != NULL)
+        {
+            resize(writePage->data, std::max((TSize)length(writePage->data), (TSize)(this->pptr() - this->pbase())));
+            if (writePage->size >= 0)
+            {
+                writePagePos += writePage->size;
+                releaseFilePage(pager, *writePage);
+            }
+            else
+            {
+                // for BGZF files we know the block size on disk only after writing the page
+                int count = atomicDec(writePage->lockCount);
+                SEQAN_ASSERT_EQ(count, 0);
+                ignoreUnusedVariableWarning(count);
+                writePage->targetState = UNUSED;
+                erase(pager.ready, *writePage);
+                _processFilePage(pager, *writePage, True());
+                writePagePos += writePage->size;
+                pushBack(pager.unused, *writePage);
+            }
+            writePage = NULL;
+        }
 
-        // TODO(holtgrew): Still relevant?
+        Pair<__int64, unsigned> ol = _getPageOffsetAndLength(pager.table, writePagePos);
+        writePage = &fetchFilePage(pager, ol.i1, ol.i2);
+        this->setp(writePage->data.begin, writePage->data.begin + capacity(writePage->data));
+        return true;
+    }
 
-        // At the end of the file, we cannot read thus this is an error.
+    virtual TIntValue
+    overflow(TIntValue val)
+    {
+        if (SEQAN_UNLIKELY(!pager.file))
+            return TTraits::eof();
 
-        if (!stream._advanceBuffer())
+        if (SEQAN_UNLIKELY(this->pptr() >= this->epptr() && !_nextWritePage()))
         {
-            stream.eofFlag = true;
-            stream.errorFlag = 1;
-            return EOF;
+            this->setp(NULL, NULL);
+            return TTraits::eof();
         }
 
-        if (stream.it == stream.itReadEnd)
+        if (!TTraits::eq_int_type(val, TTraits::eof()))
         {
-            stream.eofFlag = true;
-            stream.errorFlag = 1;
-            return EOF;
+            *this->pptr() = TTraits::to_char_type(val);
+            this->pbump(1);
         }
+        return TTraits::not_eof(val);
     }
-    value = *(stream.it++);
-    return 0;
-}
 
-// ----------------------------------------------------------------------------
-// Function streamReadBlock()
-// ----------------------------------------------------------------------------
+    virtual TIntValue
+    underflow()
+    {
+        if (SEQAN_UNLIKELY(!pager.file))
+            return TTraits::eof();
 
-template <typename TDestIter, typename TSpec, typename TValue, typename TCount>
-inline TCount
-streamReadBlock(TDestIter dstIter, Stream<FileStream<TSpec, TValue> > & stream, TCount count)
-{
-    typedef typename Size<Stream<FileStream<TSpec, TValue> > >::Type TSSize;
+        if (SEQAN_UNLIKELY(this->gptr() >= this->egptr() && !_nextReadPage()))
+        {
+            this->setg(NULL, NULL, NULL);
+            return TTraits::eof();
+        }
 
-    TSSize remaining = count;
-    while (remaining != 0)
+        return TTraits::to_int_type(*this->gptr());
+    }
+
+    TValue * eback() const   { return TBase::eback(); }
+    TValue * gptr()  const   { return TBase::gptr();  }
+    TValue * egptr() const   { return TBase::egptr(); }
+
+    TValue * pbase() const   { return TBase::pbase(); }
+    TValue * pptr()  const   { return TBase::pptr();  }
+    TValue * epptr() const   { return TBase::epptr(); }
+
+    void setg(TValue * new_eback, TValue * new_gptr, TValue * new_egptr)
+    {
+        TBase::setg(new_eback, new_gptr, new_egptr);
+    }
+
+    void setp(TValue * new_pbase, TValue * new_epptr)
+    {
+        TBase::setp(new_pbase, new_epptr);
+    }
+
+    TPosition _tell(std::ios::openmode which)
     {
-        if (stream.it == stream.itReadEnd && stream.it != stream.itEnd)
+        if (SEQAN_LIKELY(pager.file))
+        {
+            if (which == std::ios::in)
+            {
+                if (SEQAN_LIKELY(readPage != NULL))
+                    return (TSize)readPagePos + (gptr() - eback());
+                else
+                    return 0;
+            }
+            else
+            {
+                if (SEQAN_LIKELY(writePage != NULL))
+                    return (TSize)writePagePos + (pptr() - pbase());
+                else
+                    return 0;
+            }
+        }
+        else
         {
-            // On the end of the written part of the current page.  itEnd and itReadEnd can only deviate if open in
-            // read+write mode.
-            stream.eofFlag = true;
-            return count - remaining;
+            return -1;
         }
-        else if (stream.it == stream.itEnd)
+    }
+
+    // on libc++ TFilePos is different from TPosition for some of our MMapConfig'ed files
+    TPosition _seek(typename TPageFrame::TFilePos pos, Input)
+    {
+        if (readPage != NULL)
         {
-            // We need a new buffer.
+            if (readPage->filePos <= pos && pos < readPage->filePos + readPage->size)
+            {
+                this->setg(readPage->data.begin, readPage->data.begin + (pos - readPage->filePos), readPage->data.end);
+                return pos;
+            }
+
+            // Release former page.
+            releaseFilePage(pager, *readPage);
+            readPage = NULL;
+        }
+
+        if (SEQAN_UNLIKELY(pos < (TPosition)0))
+            return -1;
+
 
-            // Reading a block of characters over the end is not a failure, we simply return the number of elements
-            // read.
+        // Fetch new page.
+        Pair<__int64, unsigned> ol = _getPageOffsetAndLength(pager.table, pos);
+        readPage = &fetchFilePage(pager, ol.i1, ol.i2);
+        readPagePos = readPage->filePos;
 
-            if (!stream._advanceBuffer())
-                return count - remaining;
+        // Seek to correct position in page.
+        this->setg(readPage->data.begin, readPage->data.begin + (pos - readPage->filePos), readPage->data.end);
 
-            if (stream.it == stream.itReadEnd)
+        return pos;
+    }
+
+    TPosition _seek(typename TPageFrame::TFilePos pos, Output)
+    {
+        if (writePage != NULL)
+        {
+            if (writePage->filePos <= pos && pos < writePage->filePos + writePage->size)
             {
-                stream.eofFlag = true;
-                return 0;
+                this->setg(writePage->data.begin, writePage->data.begin + (pos - writePage->filePos), writePage->data.end);
+                return pos;
             }
+
+            // Release former page.
+            releaseFilePage(pager, *writePage);
+            writePage = NULL;
         }
 
-        // how many values can we write into the buffer?
-        TSSize cnt = _min(remaining, (TSSize)(stream.itReadEnd - stream.it));
-        // write them
-        arrayCopyForward(stream.it, stream.it + cnt, dstIter);
+        if (SEQAN_UNLIKELY(pos < (TPosition)0))
+            return -1;
+
+
+        // Fetch new page.
+        Pair<__int64, unsigned> ol = _getPageOffsetAndLength(pager.table, pos);
+        writePage = &fetchFilePage(pager, ol.i1, ol.i2);
+        writePagePos = writePage->filePos;
+
+        // Seek to correct position in page.
+        this->setp(writePage->data.begin, writePage->data.begin + capacity(writePage->data));
+        this->pbump(pos - writePage->filePos);
+
+        return pos;
+    }
+
+    virtual TPosition
+    seekpos(
+        TPosition pos,
+        std::ios::openmode which)
+    {
+        SEQAN_ASSERT_NEQ((int)(which & IosOpenMode<TDirection>::VALUE), 0);
 
-        stream.it += cnt;
-        dstIter += cnt;
-        remaining -= cnt;
+        if (SEQAN_UNLIKELY(!pager.file))
+            return -1;
+
+        if (which == std::ios::in)
+            return _seek(pos, Input());
+        else
+            return _seek(pos, Output());
     }
-    return count;
+
+    virtual TPosition
+    seekoff(
+        TDifference off,
+        std::ios::seekdir dir,
+        std::ios::openmode which)
+    {
+        SEQAN_ASSERT_NEQ((int)(which & IosOpenMode<TDirection>::VALUE), 0);
+
+        if (SEQAN_UNLIKELY(!pager.file))
+            return -1;
+
+        TPosition pos;
+
+        if (dir == std::ios::beg)
+            pos = off;
+        else if (dir == std::ios::cur)
+            pos = _tell(which) + off;
+        else
+        {
+            if (IsSameType<TDirection, Input>::VALUE || writePage == NULL)
+                pos = pager.fileSize;
+            else
+                pos = std::max(pager.fileSize, writePage->filePos + (TSize)(pptr() - pbase()));
+            pos += off;
+        }
+
+        if (which == std::ios::in)
+            return _seek(pos, Input());
+        else
+            return _seek(pos, Output());
+    }
+
+};
+
+template <typename TValue, typename TDirection, typename TSpec>
+inline void
+clear(FileStreamBuffer<TValue, TDirection, TSpec> & buffer)
+{
+    buffer.setp(NULL, NULL);
+    buffer.setg(NULL, NULL, NULL);
+
+    buffer.readPage = NULL;
+    buffer.writePage = NULL;
+    buffer.readPagePos = 0;
+    buffer.writePagePos = 0;
 }
 
-// ----------------------------------------------------------------------------
-// Function close()
-// ----------------------------------------------------------------------------
+// --------------------------------------------------------------------------
+// Forwards
+// --------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-inline int
-close(Stream<FileStream<TSpec, TValue> > & stream)
+template <typename TValue, typename TDirection, typename TSpec>
+class FileStream;
+
+template <typename TValue, typename TDirection, typename TSpec>
+inline bool
+close(FileStream<TValue, TDirection, TSpec> & stream);
+
+// --------------------------------------------------------------------------
+// Metafunction DefaultOpenMode
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TSpec, typename TDummy>
+struct DefaultOpenMode<FilePageTable<TValue, TDirection, TSpec>, TDummy>:
+    DefaultOpenMode<typename Host<FilePageTable<TValue, TDirection, TSpec> >::Type, TDirection> {};
+
+template <typename TValue, typename TDirection, typename TSpec, typename TDummy>
+struct DefaultOpenMode<FileStream<TValue, TDirection, TSpec>, TDummy>:
+    DefaultOpenMode<FilePageTable<TValue, TDirection, TSpec>, TDummy> {};
+
+// --------------------------------------------------------------------------
+// Class FileStream
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TSpec>
+class FileStream :
+    public BasicStream<TValue, TDirection>::Type
 {
-    if (stream.file)
+public:
+    typedef FileStreamBuffer<TValue, TDirection, TSpec>     TStreamBuffer;
+    typedef typename BasicStream<TValue, TDirection>::Type  TBasicStream;
+
+    TStreamBuffer buffer;
+
+    FileStream() :
+        TBasicStream(&buffer)
+    {}
+
+    FileStream(const char * fileName, int openMode = DefaultOpenMode<FileStream>::VALUE) :
+        TBasicStream(&buffer)
     {
-        stream._stop();
-        return close(stream.file);
+        open(*this, fileName, openMode);
+    }
+
+    ~FileStream()
+    {
+        seqan::close(*this);
     }
-    return true;
-}
+
+    bool is_open()
+    {
+        return buffer.pager.file;
+    }
+
+    void close()
+    {
+        seqan::close(*this);
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function streamTell()
+// Metafunction Value
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-inline ptrdiff_t
-streamTell(Stream<FileStream<TSpec, TValue> > & stream)
+template <typename TValue, typename TDirection, typename TSpec>
+struct Value<FileStreamBuffer<TValue, TDirection, TSpec> >
 {
-    if (!stream.framePtr)
-        return 0;
-    else
-        return stream.framePtr->pageNo * stream.pageSize + (stream.it - stream.framePtr->begin);
-}
+    typedef TValue Type;
+};
+
+template <typename TValue, typename TDirection, typename TSpec>
+struct Value<FileStream<TValue, TDirection, TSpec> >:
+    Value<FileStreamBuffer<TValue, TDirection, TSpec> >{};
 
 // ----------------------------------------------------------------------------
-// Function streamSeek()
+// Metafunction Position
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-inline int
-streamSeek(Stream<FileStream<TSpec, TValue> > & stream,
-           __int64 delta,
-           int origin)
+template <typename TValue, typename TDirection, typename TSpec>
+struct Position<FileStreamBuffer<TValue, TDirection, TSpec> >
 {
-    __int64 currPos = streamTell(stream);
-
-    // Flush all pending read/write operations and reset to the same state as after open().
-    // TODO(holtgrew): Maybe add "bool isSeek" paramater to _stop()?
-    int lastPageNo = stream.lastPageNo;
-    unsigned modeFlags = stream.modeFlags;
-    stream._stop(true);
-    stream.lastPageNo = (stream.fileSize == 0) ? -1 : lastPageNo;
-    stream.modeFlags = modeFlags;
-
-    // Compute target position.
-    __int64 targetPos = delta;
-    if (origin == SEEK_END)
-        targetPos = stream.fileSize + delta;
-    else if (origin == SEEK_CUR)
-        targetPos = currPos + delta;
-
-    // Page id and offset on page that the target position lies on.
-    int pageID = targetPos / stream.pageSize;
-    int offset = targetPos % stream.pageSize;
-
-    // Fetch the given buffer and wait for this.
-    stream.nextFetchPageNo = pageID;
-    stream.nextReadyPageNo = pageID;
-    if (!stream._advanceBuffer())
-    {
-        stream.errorFlag = 1;
-        return 1;
-    }
+    typedef FileStreamBuffer<TValue, TDirection, TSpec> TStream_;
+    typedef typename TStream_::TFile TFile_;
 
-    // Seek to correct position in page.
-    stream.it += offset;
+    typedef typename Position<TFile_>::Type Type;
+};
 
-    return 0;
-}
+template <typename TValue, typename TDirection, typename TSpec>
+struct Position<FileStream<TValue, TDirection, TSpec> >:
+    Position<FileStreamBuffer<TValue, TDirection, TSpec> >{};
 
 // ----------------------------------------------------------------------------
-// Function streamTell()
+// Metafunction Size
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-inline void
-streamFlush(Stream<FileStream<TSpec, TValue> > & /*stream*/)
+template <typename TValue, typename TDirection, typename TSpec>
+struct Size<FileStreamBuffer<TValue, TDirection, TSpec> >
 {
-    // TODO(holtgrew): Implement.
-}
+    typedef FileStreamBuffer<TValue, TDirection, TSpec> TStream_;
+    typedef typename TStream_::TFile TFile_;
+
+    typedef typename Size<TFile_>::Type Type;
+};
+
+template <typename TValue, typename TDirection, typename TSpec>
+struct Size<FileStream<TValue, TDirection, TSpec> >:
+    Size<FileStreamBuffer<TValue, TDirection, TSpec> >{};
 
 // ----------------------------------------------------------------------------
-// Function streamEof()
+// Concepts
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
+template <typename TValue, typename TSpec>
+SEQAN_CONCEPT_IMPL((FileStream<TValue, Input, TSpec>), (InputStreamConcept));
+
+template <typename TValue, typename TSpec>
+SEQAN_CONCEPT_IMPL((FileStream<TValue, Output, TSpec>), (OutputStreamConcept));
+
+template <typename TValue, typename TSpec>
+SEQAN_CONCEPT_IMPL((FileStream<TValue, Bidirectional, TSpec>), (BidirectionalStreamConcept));
+
+
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TSpec>
 inline bool
-streamEof(Stream<FileStream<TSpec, TValue> > const & stream)
+open(FilePageTable<TValue, TDirection, TSpec> & pager, const char * fileName, int flags)
 {
-    return stream.eofFlag;
+    clear(pager);
+    if (IsSameType<TSpec, MMap<> >::VALUE && (flags & OPEN_WRONLY))
+        flags |= OPEN_RDWR;
+    bool result = open(pager.file, fileName, flags);
+    pager.fileSize = (result) ? length(pager.file) / sizeof(TValue) : 0ul;
+    return result;
+}
+
+template <typename TValue, typename TDirection, typename TSpec>
+inline bool
+open(FileStream<TValue, TDirection, TSpec> & stream, const char * fileName, int openMode = DefaultOpenMode<FileStream<TValue, TDirection, TSpec> >::VALUE)
+{
+    return open(stream.buffer.pager, fileName, openMode);
 }
 
 // ----------------------------------------------------------------------------
-// Function streamPeek()
+// Function close()
 // ----------------------------------------------------------------------------
 
-template <typename TSpec, typename TValue>
-inline int
-streamPeek(TValue & c, Stream<FileStream<TSpec, TValue> > & stream)
+template <typename TFile, typename TSize>
+inline void
+_updateFileSize(TFile &, TSize)
 {
-    if (stream.it == stream.itReadEnd && stream.it != stream.itEnd)
-    {
-        // On the end of the written part of the current page.  itEnd and itReadEnd can only deviate if open in
-        // read+write mode.
-        stream.eofFlag = true;
-        return EOF;
-    }
-    else if (stream.it == stream.itReadEnd)
-    {
-        // TODO(weese):
-        // Stop this horrible return value inconsistency,
-        // some stream functions return 1 on error and 0 on success
-        // or the number of transferred values :-/
-        //
-        // until this is fixed we return EOF in case of an error
-
-        if (!stream._advanceBuffer())
-        {
-            stream.errorFlag = 1;  // read behind end
-            return EOF;
-        }
+}
 
-        if (stream.it == stream.itReadEnd)
-        {
-            stream.errorFlag = 1;  // read behind end
-            return EOF;
-        }
-    }
+template <typename TFileSpec, typename TSize>
+inline void
+_updateFileSize(FileMapping<TFileSpec> & file, TSize size)
+{
+    resize(file, size);
+}
 
-    c = *stream.it;
-    return 0;
+template <typename TValue, typename TDirection, typename TSpec>
+inline void
+close(FilePageTable<TValue, TDirection, TSpec> & pager)
+{
+    if (pager.file)
+    {
+        flushAndFree(pager);
+        _updateFileSize(pager.file, pager.fileSize);
+        close(pager.file);
+    }
 }
 
-// ----------------------------------------------------------------------------
-// Function streamError()
-// ----------------------------------------------------------------------------
+template <typename TValue, typename TDirection, typename TSpec>
+inline void
+close(FileStreamBuffer<TValue, TDirection, TSpec> & buffer)
+{
+    buffer._stop();
+    close(buffer.pager);
+}
 
-template <typename TSpec, typename TValue>
-inline int
-streamError(Stream<FileStream<TSpec, TValue> > const & stream)
+template <typename TValue, typename TDirection, typename TSpec>
+inline bool
+close(FileStream<TValue, TDirection, TSpec> & stream)
 {
-    return stream.errorFlag;
+    close(stream.buffer);
+    return true;
 }
 
 } // namespace seqan
diff --git a/seqan/stream/formatted_file.h b/seqan/stream/formatted_file.h
new file mode 100644
index 0000000..71974f3
--- /dev/null
+++ b/seqan/stream/formatted_file.h
@@ -0,0 +1,936 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Base class for high level access to formatted files. It supports different
+// file formats, compression, auto detection from file extensions and content
+// as well as reading/writing from/to stdin/stdout.
+// ==========================================================================
+
+#ifndef SEQAN_STREAM_SMART_FILE_H_
+#define SEQAN_STREAM_SMART_FILE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+/*!
+ * @defgroup FileFormats File Formats
+ * @brief Tags for identifying file formats.
+ */
+
+/*!
+ * @mfn FormattedFile#FileFormat
+ * @brief Metafunction for retrieving the file format type of a formatted file.
+ *
+ * @signature FileFormat<TFormattedFile>::Type;
+ *
+ * @tparam TFormattedFile The formatted file type to query for its file format type.
+ * @return Type           The resulting @link FileFormats @endlink file formats type.
+ */
+
+template <typename TFormattedFile>
+struct FileFormat;
+
+template <typename TFormattedFile, typename TStorageSpec>
+struct FormattedFileContext;
+
+template <typename TObject, typename TStorageSpec>
+struct StorageSwitch;
+
+// ============================================================================
+// Concepts
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Concept FormattedFileHeaderConcept
+// ----------------------------------------------------------------------------
+
+/*!
+ * @concept FormattedFileHeaderConcept
+ * @extends DefaultConstructibleConcept
+ * @extends CopyConstructibleConcept
+ * @extends AssignableConcept
+ * @headerfile <seqan/stream.h>
+ * @brief Concept for header of formatted files.
+ * @signature concept FormattedFileHeaderConcept;
+ */
+
+// ----------------------------------------------------------------------------
+// Concept FormattedFileRecordConcept
+// ----------------------------------------------------------------------------
+
+/*!
+ * @concept FormattedFileRecordConcept
+ * @extends DefaultConstructibleConcept
+ * @extends CopyConstructibleConcept
+ * @extends AssignableConcept
+ * @headerfile <seqan/stream.h>
+ * @brief Concept for record of formatted files.
+ * @signature concept FormattedFileRecordConcept;
+ */
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class FormattedFile
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class FormattedFile
+ * @headerfile <seqan/stream.h>
+ * @brief Base class for formatted file I/O.
+ *
+ * @signature template <typename TFileFormat, typename TDirection[, typename TSpec]>
+ *            struct FormattedFile;
+ *
+ * @tparam TFileFormat  A type specifying the file format.
+ * @tparam TDirection The direction of the file, one of @link DirectionTags#Input Input
+ *                    @endlink or @link DirectionTags#Output @endlink.
+ * @tparam TSpec      A tag for the specialization, defauls to <tt>void</tt>.
+ *
+ * FormattedFile provides the following basic I/O operations on formatted files:
+ *
+ * <ul>
+ * <li>Open a file given its filename or attach to an existing stream like stdin/stdout.</li>
+ * <li>Guess the file format from the file content or filename extension.</li>
+ * <li>Set the file format manually.</li>
+ * <li>Access compressed or uncompressed files transparently.</li>
+ * </ul>
+ *
+ * FormattedFile encapsulates a VirtualStream and provides access to its @link StreamConcept#DirectionIterator @endlink.
+ * Each instance of FormattedFile keeps a @link FormattedFile#FormattedFileContext @endlink while reading or writing the formatted file.
+ */
+
+/*!
+ * @class FormattedFileIn
+ * @headerfile <seqan/stream.h>
+ * @brief Base class for reading formatted files.
+ * @signature typedef FormattedFile<TFileFormat, Input, TSpec> FormattedFileIn;
+ * @extends FormattedFile
+ *
+ * A formatted input file can write @link FormattedFileHeaderConcept Header @endlink
+ * and @link FormattedFileRecordConcept Records @endlink.
+ */
+
+/*!
+ * @fn FormattedFileIn#readHeader
+ * @brief Read one @link FormattedFileHeaderConcept @endlink from a @link FormattedFileIn @endlink object.
+ *
+ * @signature void readHeader(fileIn, header);
+ *
+ * @param[in,out] fileIn    The @link FormattedFileIn @endlink object to read from.
+ * @param[in]     header    The @link FormattedFileHeaderConcept @endlink to read.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+/*!
+ * @fn FormattedFileIn#readRecord
+ * @brief Read one @link FormattedFileRecordConcept @endlink from a @link FormattedFileIn @endlink object.
+ *
+ * @signature void readRecord(fileIn, record);
+ *
+ * @param[in,out] fileIn    The @link FormattedFileIn @endlink object to read from.
+ * @param[in]     record    The @link FormattedFileRecordConcept @endlink to read.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+/*!
+ * @class FormattedFileOut
+ * @headerfile <seqan/stream.h>
+ * @brief Base class for writing formatted files.
+ * @signature typedef FormattedFile<TFileFormat, Output, TSpec> FormattedFileOut;
+ * @extends FormattedFile
+ *
+ * A formatted output file can write @link FormattedFileHeaderConcept Header @endlink
+ * and @link FormattedFileRecordConcept Records @endlink.
+ */
+
+/*!
+ * @fn FormattedFileOut#writeHeader
+ * @brief Write one @link FormattedFileHeaderConcept @endlink to a @link FormattedFileOut @endlink object.
+ *
+ * @signature void writeHeader(fileOut, header);
+ *
+ * @param[in,out] fileOut   The @link FormattedFileOut @endlink object to write into.
+ * @param[in]     header    The @link FormattedFileHeaderConcept @endlink to write.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+/*!
+ * @fn FormattedFileOut#writeRecord
+ * @brief Write one @link FormattedFileRecordConcept @endlink to a @link FormattedFileOut @endlink object.
+ *
+ * @signature void writeRecord(fileOut, record);
+ *
+ * @param[in,out] fileOut   The @link FormattedFileOut @endlink object to write into.
+ * @param[in]     record    The @link FormattedFileRecordConcept @endlink to write.
+ *
+ * @throw IOError On low-level I/O errors.
+ * @throw ParseError On high-level file format errors.
+ */
+
+template <typename TFileFormat, typename TDirection, typename TSpec = void>
+struct FormattedFile
+{
+    typedef VirtualStream<char, TDirection>                                     TStream;
+    typedef typename Iterator<TStream, TDirection>::Type                        TIter;
+    typedef typename FileFormat<FormattedFile>::Type                            TFileFormats;
+    typedef typename FormattedFileContext<FormattedFile, Owner<> >::Type        TOwnerContext;
+    typedef typename FormattedFileContext<FormattedFile, Dependent<> >::Type    TDependentContext;
+
+    TStream             stream;
+    TIter               iter;
+    TFileFormats        format;
+    TOwnerContext       data_context;
+    TDependentContext   context;
+
+    /*!
+     * @fn FormattedFile#FormattedFile
+     * @brief Provides default construction.
+     *
+     * @signature FormattedFile::FormattedFile();
+     * @signature FormattedFile::FormattedFile(fileName[, openMode]);
+     * @signature FormattedFile::FormattedFile(stream);
+     * @signature FormattedFile::FormattedFile(other);
+     * @signature FormattedFile::FormattedFile(otherContext);
+     * @signature FormattedFile::FormattedFile(otherContext, fileName[, openMode]);
+     * @signature FormattedFile::FormattedFile(otherContext, stream);
+     *
+     * @param[in] fileName     Path to file to open, <tt>char const *</tt>.
+     * @param[in] openMode     Optionally, the file open mode, default obtained from <tt>TDirection</tt>.
+     * @param[in] stream       A <tt>std::basic_istream&lt;&gt;</tt> to read from or <tt>std::basic_ostream&lt;&gt;</tt>
+     *                         to write to, depending on <tt>TDirection</tt>.
+     * @param[in] other        A second FormattedFile, this FormattedFile's dependent context will depend on <tt>other</tt>'s
+     *                         dependent context.
+     * @param[in] otherContext The dependent context of another FormattedFile, this FormattedFile's dependent context will depend on <tt>otherContext</tt>.
+     *
+     * @throw IOError The variants that accept the <tt>fileName</tt> parameter throw an exception of this
+     *                type in case opening the file fails.
+     */
+    FormattedFile() : context(data_context)
+    {}
+
+    // filename based c'tors
+    explicit FormattedFile(const char * fileName, int openMode = DefaultOpenMode<FormattedFile>::VALUE) :
+        context(data_context)
+    {
+        _open(*this, fileName, openMode, True());
+    }
+
+    // stream based c'tors
+    template <typename TValue>
+    explicit
+    FormattedFile(std::basic_istream<TValue> &istream,
+              SEQAN_CTOR_ENABLE_IF(And<IsSameType<TDirection, Input>, IsSameType<TValue, char> >)) :
+        context(data_context)
+    {
+        _open(*this, istream, _mapFileFormatToCompressionFormat(format), True());
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    template <typename TValue, typename TFormat>
+    FormattedFile(std::basic_ostream<TValue> &ostream,
+              TFormat const &format,
+              SEQAN_CTOR_ENABLE_IF(And<IsSameType<TDirection, Output>, IsSameType<TValue, char> >)) :
+        context(data_context)
+    {
+        bool success = open(*this, ostream, format);
+        ignoreUnusedVariableWarning(dummy);
+        ignoreUnusedVariableWarning(success);
+        SEQAN_ASSERT(success);
+    }
+
+    // now everything given another context
+    explicit
+    FormattedFile(TDependentContext &otherCtx) :
+        context(otherCtx)
+    {}
+
+    explicit
+    FormattedFile(FormattedFile &other) :
+        context(other.context)
+    {}
+
+    FormattedFile(TDependentContext &otherCtx, const char *fileName, int openMode = DefaultOpenMode<FormattedFile>::VALUE) :
+        context(otherCtx)
+    {
+        _open(*this, fileName, openMode, True());
+    }
+
+    template <typename TValue>
+    explicit
+    FormattedFile(TDependentContext &otherCtx,
+              std::basic_istream<TValue> &istream,
+              SEQAN_CTOR_ENABLE_IF(And<IsSameType<TDirection, Input>, IsSameType<TValue, char> >)) :
+        context(otherCtx)
+    {
+        _open(*this, istream, _mapFileFormatToCompressionFormat(format), True());
+        ignoreUnusedVariableWarning(dummy);
+    }
+
+    template <typename TValue, typename TFormat>
+    FormattedFile(TDependentContext &otherCtx,
+              std::basic_ostream<TValue> &ostream,
+              TFormat const &format,
+              SEQAN_CTOR_ENABLE_IF(And<IsSameType<TDirection, Output>, IsSameType<TValue, char> >)) :
+        context(otherCtx)
+    {
+        bool success = open(*this, ostream, format);
+        ignoreUnusedVariableWarning(dummy);
+        ignoreUnusedVariableWarning(success);
+        SEQAN_ASSERT(success);
+    }
+
+    ~FormattedFile()
+    {
+        close(*this);
+    }
+
+    /*!
+     * @fn FormattedFile::operatorTDependentContext FormattedFile::operator TDependentContext
+     * @brief Allows conversion to a dependent context for the FormattedFile
+     * @signature TDependentContext & FormattedFile::operator TDependentContext();
+     *
+     * @return TDependentContext The dependent context of this FormattedFile.
+     */
+
+    operator TDependentContext & ()
+    {
+        return context;
+    }
+
+    /*!
+     * @fn FormattedFile::getFileExtensions
+     * @brief Static function that returns a list of allowed file format extension.
+     *
+     * @signature TExtensionVector getFileExtensions()
+     *
+     * @return TExtensionVector A <tt>std::vector&lt;std::string&gt;</tt> with the allowed file extensions.
+     */
+    static std::vector<std::string>
+    getFileExtensions()
+    {
+        std::vector<std::string> extensions;
+
+        _getCompressionExtensions(extensions,
+                                  TFileFormats(),
+                                  CompressedFileTypesWithoutBgzf_(),
+                                  false);
+        return extensions;
+    }
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction DirectionIterator
+// ----------------------------------------------------------------------------
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+struct DirectionIterator<FormattedFile<TFileFormat, TDirection, TSpec>, TDirection>
+{
+    typedef typename FormattedFile<TFileFormat, TDirection, TSpec>::TIter Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+// FormattedFile holds a Context either as owner or dependent (see StorageSwitch below).
+// Note that the FormattedFile class contains twice the context: both as owner and dependent.
+// NOTE(esiragusa): A statically-typed Holder should abstract this pattern.
+
+/*!
+ * @mfn FormattedFile#FormattedFileContext
+ * @brief Returns the context type for a FormattedFile.
+ *
+ * @signature FormattedFileContext<TFormattedFile, TStorageSpec>::Type
+ *
+ * @tparam TFormattedFile   The FormattedFile to query.
+ * @tparam TStorageSpec     The storage specification, passed as specialization to any @link StringSet @endlink
+ *                          contained in the context.
+ * @tparam Type             The resulting FormattedFile context type.
+ */
+
+template <typename TFormattedFile, typename TStorageSpec>
+struct FormattedFileContext
+{
+    typedef Nothing Type;
+};
+
+template <typename TFormattedFile, typename TStorageSpec>
+struct FormattedFileContext<TFormattedFile const, TStorageSpec>
+{
+    typedef typename FormattedFileContext<TFormattedFile, TStorageSpec>::Type const Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction StorageSwitch
+// ----------------------------------------------------------------------------
+// This metafunction is used to switch the relationship between the FormattedFile
+// and its Context among aggregation and composition.
+// NOTE(esiragusa): there was a more generic metafunction Member<> to do this.
+
+// Composition (owner).
+template <typename TObject, typename TStorageSpec>
+struct StorageSwitch
+{
+    typedef TObject Type;
+};
+
+// Aggregation (dependent).
+template <typename TObject, typename TSpec>
+struct StorageSwitch<TObject, Dependent<TSpec> >
+{
+    typedef TObject * Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+struct Value<FormattedFile<TFileFormat, TDirection, TSpec> > :
+    Value<typename FormattedFile<TFileFormat, TDirection, TSpec>::TStream> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+struct Position<FormattedFile<TFileFormat, TDirection, TSpec> > :
+    Position<typename FormattedFile<TFileFormat, TDirection, TSpec>::TStream> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction DefaultOpenMode
+// ----------------------------------------------------------------------------
+
+template <typename TFileFormat, typename TDirection, typename TSpec, typename TDummy>
+struct DefaultOpenMode<FormattedFile<TFileFormat, TDirection, TSpec>, TDummy> :
+    DefaultOpenMode<typename FormattedFile<TFileFormat, TDirection, TSpec>::TStream, TDummy> {};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Helper Function _throwIf().
+// ----------------------------------------------------------------------------
+// Helper functions that reduce number of "uncaught exception" false positives in static analysis tools.
+
+template <typename TException> void _throwIf(TException const & e, True const & /*tag*/) { SEQAN_THROW(e); }
+template <typename TException> void _throwIf(TException const & /*e*/, False const & /*tag*/) { /*nop*/ }
+
+// ----------------------------------------------------------------------------
+// Function directionIterator()
+// ----------------------------------------------------------------------------
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+inline typename FormattedFile<TFileFormat, TDirection, TSpec>::TIter &
+directionIterator(FormattedFile<TFileFormat, TDirection, TSpec> & file, TDirection const &)
+{
+    return file.iter;
+}
+
+// ----------------------------------------------------------------------------
+// Function format()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FormattedFile#format
+ * @brief Return the format of a FormattedFile.
+ *
+ * @signature TFormat format(file);
+ *
+ * @param[in] file The FormattedFile to check.
+ * @return TFormat The type as returned from @link FormattedFile#FileFormat @endlink.
+ */
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+inline typename FileFormat<FormattedFile<TFileFormat, TDirection, TSpec> >::Type &
+format(FormattedFile<TFileFormat, TDirection, TSpec> & file)
+{
+    return file.format;
+}
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+inline typename FileFormat<FormattedFile<TFileFormat, TDirection, TSpec> >::Type const &
+format(FormattedFile<TFileFormat, TDirection, TSpec> const & file)
+{
+    return file.format;
+}
+
+// ----------------------------------------------------------------------------
+// Function setFormat()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FormattedFile#setFormat
+ * @brief Set the format of a FormattedFile.
+ *
+ * @signature void setFormat(file, format);
+ *
+ * @param[in,out] file The FormattedFile to change.
+ * @param[in]     format The @link FormattedFile#FileFormat @endlink to set.
+ */
+
+template <typename TFileFormat, typename TDirection, typename TSpec, typename TFormat>
+inline void
+setFormat(FormattedFile<TFileFormat, TDirection, TSpec> & file, TFormat format)
+{
+    assign(file.format, format);
+}
+
+// ----------------------------------------------------------------------------
+// Function guessFormat()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FormattedFile#guessFormat
+ * @brief Guess the format of an open FormattedFile.
+ *
+ * @signature bool guessFormat(file);
+ *
+ * @param[in,out] file The open FormattedFile for which the format is to be guessed.
+ */
+
+template <typename TFileFormat, typename TSpec>
+inline bool guessFormat(FormattedFile<TFileFormat, Input, TSpec> & file)
+{
+    return guessFormatFromStream(file.stream, file.format);
+}
+
+template <typename TFileFormat, typename TSpec>
+inline bool guessFormat(FormattedFile<TFileFormat, Output, TSpec> &)
+{
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// _mapFileFormatToCompressionFormat
+// ----------------------------------------------------------------------------
+
+template <typename TFormat>
+inline Nothing
+_mapFileFormatToCompressionFormat(TFormat)
+{
+    return Nothing();
+}
+
+template <typename TCompressedFileTypes>
+inline void
+_mapFileFormatToCompressionFormat(TagSelector<TCompressedFileTypes> &,
+                                  TagSelector<void> const &)
+{}
+
+template <typename TCompressedFileTypes, typename TTagList>
+inline void
+_mapFileFormatToCompressionFormat(TagSelector<TCompressedFileTypes> & result,
+                                  TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+    typedef typename TagSelector<TTagList>::Base TBase;
+
+    if (isEqual(format, TFormat()))
+        assign(result, _mapFileFormatToCompressionFormat(TFormat()));
+    else
+        _mapFileFormatToCompressionFormat(result, static_cast<TBase const &>(format));
+}
+
+template <typename TFileFormatList>
+inline TagSelector<CompressedFileTypes>
+_mapFileFormatToCompressionFormat(TagSelector<TFileFormatList> format)
+{
+    TagSelector<CompressedFileTypes> compressionType;
+    _mapFileFormatToCompressionFormat(compressionType, format);
+    return compressionType;
+}
+
+
+template <typename TFormattedFile, typename TFormat>
+inline void
+_checkThatStreamOutputFormatIsSet(TFormattedFile const &, TFormat const &)
+{}
+
+template <typename TFileFormat, typename TSpec, typename TFileFormatList>
+inline void
+_checkThatStreamOutputFormatIsSet(FormattedFile<TFileFormat, Output, TSpec> const &, TagSelector<TFileFormatList> const &format)
+{
+    if (value(format) < 0)
+        SEQAN_FAIL("FormattedFile: File format not specified, use setFormat().");
+}
+
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FormattedFile#open
+ * @brief Open a FormattedFile.
+ *
+ * @signature bool open(file, fileName);
+ *
+ * @param[in,out] file The FormattedFile to open.
+ * @param[in]     fileName The name of the file open.
+ * @return bool <tt>true</tt> in the case of success, <tt>false</tt> otherwise.
+ */
+
+template <typename TFileFormat, typename TDirection, typename TSpec,
+          typename TStream, typename TCompressionFormat, typename TThrowExceptions>
+inline bool _open(FormattedFile<TFileFormat, TDirection, TSpec> & file,
+                  TStream &stream,
+                  TCompressionFormat const &compressionFormat,
+                  TThrowExceptions = True())
+{
+    if (!open(file.stream, stream, compressionFormat))
+    {
+        _throwIf(UnknownFileFormat(), TThrowExceptions());
+        return false;
+    }
+
+    if (!guessFormat(file))
+    {
+        _throwIf(UnknownFileFormat(), TThrowExceptions());
+        return false;
+    }
+
+    file.iter = directionIterator(file.stream, TDirection());
+
+    return true;
+}
+
+template <typename TFileFormat, typename TDirection, typename TSpec, typename TStream>
+inline SEQAN_FUNC_ENABLE_IF(Is<StreamConcept<TStream> >, bool)
+open(FormattedFile<TFileFormat, TDirection, TSpec> & file,
+     TStream &stream)
+{
+    return _open(file, stream, _mapFileFormatToCompressionFormat(file.format), False());
+}
+
+template <typename TFileFormat, typename TSpec, typename TStream, typename TFormat_>
+inline bool open(FormattedFile<TFileFormat, Output, TSpec> & file,
+                 TStream &stream,
+                 Tag<TFormat_> format)
+{
+    setFormat(file, format);
+    return _open(file, stream, _mapFileFormatToCompressionFormat(file.format), False());
+}
+
+template <typename TFileFormat, typename TSpec, typename TStream, typename TFormats>
+inline bool open(FormattedFile<TFileFormat, Output, TSpec> & file,
+                 TStream &stream,
+                 TagSelector<TFormats> format)
+{
+    setFormat(file, format);
+    return _open(file, stream, _mapFileFormatToCompressionFormat(file.format), False());
+}
+
+// ----------------------------------------------------------------------------
+// Function open(fileName)
+// ----------------------------------------------------------------------------
+
+template <typename TFileFormat, typename TDirection, typename TSpec, typename TThrowExceptions>
+inline bool _open(FormattedFile<TFileFormat, TDirection, TSpec> & file,
+                  const char *fileName,
+                  int openMode = DefaultOpenMode<FormattedFile<TFileFormat, TDirection, TSpec> >::VALUE,
+                  TThrowExceptions = True())
+{
+    if (!open(file.stream, fileName, openMode))
+    {
+        _throwIf(FileOpenError(fileName), TThrowExceptions());
+        return false;
+    }
+
+    if (IsSameType<TDirection, Input>::VALUE && _isPipe(fileName))
+    {
+        if (!guessFormat(file))
+        {
+            // read from a pipe (without file extension)
+            _throwIf(UnknownFileFormat(), TThrowExceptions());
+            return false;
+        }
+    }
+    else
+    {
+        Prefix<const char *>::Type basename = _getUncompressedBasename(fileName, format(file.stream));
+        if (!guessFormatFromFilename(basename, file.format))    // read/write from/to a file (with extension)
+        {
+            close(file.stream);
+            _throwIf(UnknownExtensionError(fileName), TThrowExceptions());
+            return false;
+        }
+    }
+
+    file.iter = directionIterator(file.stream, TDirection());
+    return true;
+}
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+inline bool open(FormattedFile<TFileFormat, TDirection, TSpec> & file,
+                 const char *fileName,
+                 int openMode = DefaultOpenMode<FormattedFile<TFileFormat, TDirection, TSpec> >::VALUE)
+{
+    return _open(file, fileName, openMode, False());
+}
+
+// ----------------------------------------------------------------------------
+// Function close()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FormattedFile#close
+ * @brief Close a FormattedFile.
+ *
+ * @signature bool close(file);
+ *
+ * @param[in,out] file The FormattedFile to close.
+ * @return bool <tt>true</tt> in the case of success, <tt>false</tt> otherwise.
+ */
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+inline bool close(FormattedFile<TFileFormat, TDirection, TSpec> & file)
+{
+    setFormat(file, typename FileFormat<FormattedFile<TFileFormat, TDirection, TSpec> >::Type());
+    file.iter = typename DirectionIterator<FormattedFile<TFileFormat, TDirection, TSpec>, TDirection>::Type();
+    return close(file.stream);
+}
+
+// ----------------------------------------------------------------------------
+// Function atEnd()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FormattedFile#atEnd
+ * @brief Determines whether a FormattedFile is at the end.
+ *
+ * @signature bool atEnd(file);
+ *
+ * @param[in,out] file The FormattedFile to check.
+ * @return bool <tt>true</tt> in the case of success, <tt>false</tt> otherwise.
+ *
+ * @datarace Not thread safe.
+ */
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+inline SEQAN_FUNC_ENABLE_IF(Is<InputStreamConcept<typename FormattedFile<TFileFormat, TDirection, TSpec>::TStream> >, bool)
+atEnd(FormattedFile<TFileFormat, TDirection, TSpec> const & file)
+{
+    return atEnd(file.iter);
+}
+
+// ----------------------------------------------------------------------------
+// Function position()
+// ----------------------------------------------------------------------------
+
+template <typename TFileFormat, typename TSpec>
+inline typename Position<FormattedFile<TFileFormat, Output, TSpec> >::Type
+position(FormattedFile<TFileFormat, Output, TSpec> & file)
+{
+    return file.stream.tellp();
+}
+
+template <typename TFileFormat, typename TSpec>
+inline typename Position<FormattedFile<TFileFormat, Input, TSpec> >::Type
+position(FormattedFile<TFileFormat, Input, TSpec> & file)
+{
+    return file.stream.tellg();
+}
+
+// ----------------------------------------------------------------------------
+// Function setPosition()
+// ----------------------------------------------------------------------------
+
+template <typename TFileFormat, typename TSpec, typename TPosition>
+inline bool
+setPosition(FormattedFile<TFileFormat, Output, TSpec> & file, TPosition pos)
+{
+    return (TPosition)file.stream.rdbuf()->pubseekpos(pos, std::ios_base::out) == pos;
+}
+
+template <typename TFileFormat, typename TSpec, typename TPosition>
+inline bool
+setPosition(FormattedFile<TFileFormat, Input, TSpec> & file, TPosition pos)
+{
+    return (TPosition)file.stream.rdbuf()->pubseekpos(pos, std::ios_base::in) == pos;
+}
+
+// ----------------------------------------------------------------------------
+// Function context()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FormattedFile#context
+ * @brief Return the FormattedFile's dependent context object.
+ *
+ * @signature TDependentContext & context(file);
+ *
+ * @param[in,out] file The FormattedFile to query for its context.
+ *
+ * @return TDependentContext The dependent context, type as returned from @link FormattedFile#FormattedFileContext @endlink.
+ */
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+inline typename FormattedFileContext<FormattedFile<TFileFormat, TDirection, TSpec>, Dependent<> >::Type &
+context(FormattedFile<TFileFormat, TDirection, TSpec> & file)
+{
+    return file.context;
+}
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+inline typename FormattedFileContext<FormattedFile<TFileFormat, TDirection, TSpec>, Dependent<> >::Type const &
+context(FormattedFile<TFileFormat, TDirection, TSpec> const & file)
+{
+    return file.context;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getCompressionFormatExtensions()
+// ----------------------------------------------------------------------------
+
+template <typename TStringSet, typename TFormat_, typename TCompressionFormats>
+inline void
+_getCompressionExtensions(
+    TStringSet &stringSet,
+    Tag<TFormat_> const & /*formatTag*/,
+    TCompressionFormats const & compress,
+    bool primaryExtensionOnly,
+    Nothing)
+{
+    typedef Tag<TFormat_> TFormat;
+
+    std::vector<std::string> compressionExtensions;
+    _getFileExtensions(compressionExtensions, compress, primaryExtensionOnly);
+
+    unsigned len = (primaryExtensionOnly)? 1 : sizeof(FileExtensions<TFormat>::VALUE) / sizeof(char*);
+    for (unsigned i = 0; i < len; ++i)
+        for (unsigned j = 0; j < compressionExtensions.size(); ++j)
+        {
+            size_t jj = (j == 0)? compressionExtensions.size() - 1 : j - 1;    // swap first and last compression extension
+            appendValue(stringSet, (std::string)FileExtensions<TFormat>::VALUE[i] + compressionExtensions[jj]);
+        }
+}
+
+template <typename TStringSet, typename TFormat_, typename TCompressionFormats, typename TCompression_>
+inline void
+_getCompressionExtensions(
+    TStringSet &stringSet,
+    Tag<TFormat_> const & formatTag,
+    TCompressionFormats const &,
+    bool primaryExtensionOnly,
+    Tag<TCompression_>)
+{
+    _getFileExtensions(stringSet, formatTag, primaryExtensionOnly);
+}
+
+template <typename TStringSet, typename TFormat_, typename TCompressionFormats>
+inline void
+_getCompressionExtensions(
+    TStringSet &stringSet,
+    Tag<TFormat_> const & formatTag,
+    TCompressionFormats const & compress,
+    bool primaryExtensionOnly)
+{
+    _getCompressionExtensions(stringSet, formatTag, compress, primaryExtensionOnly, _mapFileFormatToCompressionFormat(formatTag));
+}
+
+template <typename TStringSet, typename TTag, typename TCompressionFormats>
+inline void
+_getCompressionExtensions(
+    TStringSet &stringSet,
+    TagList<TTag, void> const & /*formatTag*/,
+    TCompressionFormats const & compress,
+    bool primaryExtensionOnly = false)
+{
+    _getCompressionExtensions(stringSet, TTag(), compress, primaryExtensionOnly);
+}
+
+template <typename TStringSet, typename TTag, typename TSubList, typename TCompressionFormats>
+inline void
+_getCompressionExtensions(
+    TStringSet &stringSet,
+    TagList<TTag, TSubList> const & /*formatTag*/,
+    TCompressionFormats const & compress,
+    bool primaryExtensionOnly = false)
+{
+    _getCompressionExtensions(stringSet, TTag(), compress, primaryExtensionOnly);
+    _getCompressionExtensions(stringSet, TSubList(), compress, primaryExtensionOnly);
+}
+
+template <typename TStringSet, typename TTagList, typename TCompressionFormats>
+inline void
+_getCompressionExtensions(
+    TStringSet &stringSet,
+    TagSelector<TTagList> const & /*formatTag*/,
+    TCompressionFormats const & compress,
+    bool primaryExtensionOnly = false)
+{
+    _getCompressionExtensions(stringSet, TTagList(), compress, primaryExtensionOnly);
+}
+
+// ----------------------------------------------------------------------------
+// Function getFileExtensions()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn FormattedFile#getFileExtensions
+ * @brief Static function that returns a list of allowed file format extension.
+ *
+ * @signature TExtensionVector getFileExtensions(file)
+ *
+ * @param[in] file The FormattedFile to query.
+ * @return TExtensionVector A <tt>std::vector&lt;std::string&gt;</tt> with the allowed file extensions.
+ *
+ * This is a shortcut to @link FormattedFile#getFileExtensions @endlink.
+ */
+
+template <typename TFileFormat, typename TDirection, typename TSpec>
+static std::vector<std::string>
+getFileExtensions(FormattedFile<TFileFormat, TDirection, TSpec> const & file)
+{
+    return file.getFileExtensions();
+}
+
+}  // namespace seqan
+
+#endif // SEQAN_STREAM_SMART_FILE_H_
diff --git a/seqan/stream/guess_format.h b/seqan/stream/guess_format.h
new file mode 100644
index 0000000..a4b3f38
--- /dev/null
+++ b/seqan/stream/guess_format.h
@@ -0,0 +1,224 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// TODO(esiragusa): tests
+
+#ifndef SEQAN_STREAM_GUESS_FORMAT_
+#define SEQAN_STREAM_GUESS_FORMAT_
+
+namespace seqan {
+
+// --------------------------------------------------------------------------
+// Class FileExtensions
+// --------------------------------------------------------------------------
+
+template <typename TFormat, typename T>
+struct FileExtensions;
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function guessFormatFromStream()
+// --------------------------------------------------------------------------
+// Base case: we get here if the file format could not be determined.
+
+template <typename TFileSeq>
+inline bool guessFormatFromStream(TFileSeq &, TagSelector<> &)
+{
+    return false;
+}
+
+// --------------------------------------------------------------------------
+// Function guessFormatFromStream(TagSelector)
+// --------------------------------------------------------------------------
+
+template <typename TFileSeq, typename TTagList>
+inline bool guessFormatFromStream(TFileSeq &seq, TagSelector<TTagList> &format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (value(format) == -1 || isEqual(format, TFormat()))
+    {
+        // if tagId is set to -1 (auto-detect) or the current format (TFormatTag) then test for TFormatTag format
+        if (guessFormatFromStream(seq, TFormat()))
+        {
+            assign(format, TFormat());
+            return true;
+        }
+    }
+    return guessFormatFromStream(seq, static_cast<typename TagSelector<TTagList>::Base &>(format));
+}
+
+// --------------------------------------------------------------------------
+// Function guessFormatFromFilename()
+// --------------------------------------------------------------------------
+// Base case: we get here if the file format could not be determined.
+
+template <typename TFilename>
+inline bool guessFormatFromFilename(TFilename const &, TagSelector<>)
+{
+    return false;
+}
+
+template <typename TFilename>
+inline typename Prefix<TFilename const>::Type
+getBasename(TFilename const & fname, TagSelector<> const &)
+{
+    return prefix(fname, length(fname));
+}
+
+// --------------------------------------------------------------------------
+// Function guessFormatFromFilename(TagSelector)
+// --------------------------------------------------------------------------
+
+template <typename TFilename, typename TTagList>
+inline bool guessFormatFromFilename(TFilename const &fname, TagSelector<TTagList> &format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (value(format) == -1 || isEqual(format, TFormat()))
+    {
+        // if tagId is set to -1 (auto-detect) or the current format (TFormatTag) then test for TFormatTag format
+        if (guessFormatFromFilename(fname, TFormat()))
+        {
+            assign(format, TFormat());
+            return true;
+        }
+    }
+    return guessFormatFromFilename(fname, static_cast<typename TagSelector<TTagList>::Base &>(format));
+}
+
+template <typename TFilename, typename TTagList>
+inline typename Prefix<TFilename const>::Type
+getBasename(TFilename const & fname, TagSelector<TTagList> const &format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        return getBasename(fname, TFormat());
+    else
+        return getBasename(fname, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+// --------------------------------------------------------------------------
+// Function guessFormatFromFilename(Tag)
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn guessFormatFromFilename
+ * @headerfile <seqan/file.h>
+ * @brief Guesses a file format from a sequence file name.
+ *
+ * @signature bool guessFormatFromFilename(fileName, formatTag);
+ *
+ * @param[in] fileName  A filename of a sequence file.
+ * @param[in] formatTag A file format tag.
+ *
+ * @return bool <tt>true</tt> if the format represented by <tt>formatTag</tt> was recognized in <tt>fileName</tt>.
+ */
+
+template <typename TFilename, typename TFormat_>
+inline bool guessFormatFromFilename(TFilename const & fileName, Tag<TFormat_> /*formatTag*/)
+{
+    typedef typename Value<TFilename>::Type                                     TValue;
+    typedef ModifiedString<TFilename const, ModView<FunctorLowcase<TValue> > >    TLowcase;
+    typedef Tag<TFormat_>                                                       TFormat;
+
+    TLowcase lowcaseFileName(fileName);
+    for (unsigned i = 0; i < sizeof(FileExtensions<TFormat>::VALUE) / sizeof(char*); ++i)
+        if (endsWith(lowcaseFileName, lowerString(FileExtensions<TFormat>::VALUE[i])))
+            return true;
+
+    return false;
+}
+
+template <typename TFilename, typename TFormat_>
+inline typename Prefix<TFilename const>::Type
+getBasename(TFilename const & fileName, Tag<TFormat_> const & /*formatTag*/)
+{
+    typedef typename Value<TFilename>::Type                                     TValue;
+    typedef ModifiedString<TFilename const, ModView<FunctorLowcase<TValue> > >    TLowcase;
+    typedef Tag<TFormat_>                                                       TFormat;
+
+    TLowcase lowcaseFileName(fileName);
+    for (unsigned i = 0; i < sizeof(FileExtensions<TFormat>::VALUE) / sizeof(char*); ++i)
+        if (endsWith(lowcaseFileName, lowerString(FileExtensions<TFormat>::VALUE[i])))
+            return prefix(fileName, length(fileName) - length(FileExtensions<TFormat>::VALUE[i]));
+
+    return prefix(fileName, length(fileName));
+}
+
+
+// --------------------------------------------------------------------------
+// Function _getFileExtensions()
+// --------------------------------------------------------------------------
+
+template <typename TStringSet, typename TFormat_>
+inline void _getFileExtensions(TStringSet &stringSet, Tag<TFormat_> /*formatTag*/, bool primaryExtensionOnly = false)
+{
+    typedef Tag<TFormat_> TFormat;
+    if (primaryExtensionOnly)
+    {
+        appendValue(stringSet, FileExtensions<TFormat>::VALUE[0]);    // first is primary
+    }
+    else
+    {
+        for (unsigned i = 0; i < sizeof(FileExtensions<TFormat>::VALUE) / sizeof(char*); ++i)
+            appendValue(stringSet, FileExtensions<TFormat>::VALUE[i]);
+    }
+}
+
+template <typename TStringSet, typename TTag>
+inline void _getFileExtensions(TStringSet &stringSet, TagList<TTag, void> const /*formatTag*/, bool primaryExtensionOnly = false)
+{
+    _getFileExtensions(stringSet, TTag(), primaryExtensionOnly);
+}
+
+template <typename TStringSet, typename TTag, typename TSubList>
+inline void _getFileExtensions(TStringSet &stringSet, TagList<TTag, TSubList> const /*formatTag*/, bool primaryExtensionOnly = false)
+{
+    _getFileExtensions(stringSet, TTag(), primaryExtensionOnly);
+    _getFileExtensions(stringSet, TSubList(), primaryExtensionOnly);
+}
+
+template <typename TStringSet, typename TTagList>
+inline void _getFileExtensions(TStringSet &stringSet, TagSelector<TTagList> const /*formatTag*/, bool primaryExtensionOnly = false)
+{
+    _getFileExtensions(stringSet, TTagList(), primaryExtensionOnly);
+}
+
+} // namespace seqan
+
+#endif  // #ifndef SEQAN_STREAM_GUESS_FORMAT_
diff --git a/seqan/stream/iostream_bgzf.h b/seqan/stream/iostream_bgzf.h
new file mode 100644
index 0000000..2ce0719
--- /dev/null
+++ b/seqan/stream/iostream_bgzf.h
@@ -0,0 +1,923 @@
+// zipstream Library License:
+// --------------------------
+//
+// The zlib/libpng License Copyright (c) 2003 Jonathan de Halleux.
+//
+// This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.
+//
+// Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:
+//
+// 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required.
+//
+// 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
+//
+// 3. This notice may not be removed or altered from any source distribution
+//
+//
+// Author: Jonathan de Halleux, dehalleux@pelikhan.com, 2003   (original zlib stream)
+// Author: David Weese, dave.weese@gmail.com, 2014             (extension to parallel block-wise compression in bgzf format)
+
+#ifndef INCLUDE_SEQAN_STREAM_IOSTREAM_BGZF_H_
+#define INCLUDE_SEQAN_STREAM_IOSTREAM_BGZF_H_
+
+namespace seqan {
+
+const unsigned BGZF_MAX_BLOCK_SIZE = 64 * 1024;
+const unsigned BGZF_BLOCK_HEADER_LENGTH = 18;
+const unsigned BGZF_BLOCK_FOOTER_LENGTH = 8;
+const unsigned ZLIB_BLOCK_OVERHEAD = 5; // 5 bytes block overhead (see 3.2.4. at http://www.gzip.org/zlib/rfc-deflate.html)
+
+// Reduce the maximal input size, such that the compressed data
+// always fits in one block even for level Z_NO_COMPRESSION.
+const unsigned BGZF_BLOCK_SIZE = BGZF_MAX_BLOCK_SIZE - BGZF_BLOCK_HEADER_LENGTH - BGZF_BLOCK_FOOTER_LENGTH - ZLIB_BLOCK_OVERHEAD;
+
+// ===========================================================================
+// Classes
+// ===========================================================================
+
+// --------------------------------------------------------------------------
+// Class basic_bgzf_streambuf
+// --------------------------------------------------------------------------
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bgzf_streambuf : public std::basic_streambuf<Elem, Tr>
+{
+public:
+    typedef std::basic_ostream<Elem, Tr>& ostream_reference;
+    typedef ElemA char_allocator_type;
+    typedef ByteT byte_type;
+    typedef ByteAT byte_allocator_type;
+    typedef byte_type* byte_buffer_type;
+    typedef typename Tr::char_type char_type;
+    typedef typename Tr::int_type int_type;
+
+    typedef ConcurrentQueue<size_t, Suspendable<Limit> > TJobQueue;
+
+    struct OutputBuffer
+    {
+        char    buffer[BGZF_MAX_BLOCK_SIZE];
+        size_t  size;
+    };
+
+    struct BufferWriter
+    {
+        ostream_reference ostream;
+
+        BufferWriter(ostream_reference ostream) :
+            ostream(ostream)
+        {}
+
+        bool operator() (OutputBuffer const & outputBuffer)
+        {
+            ostream.write(outputBuffer.buffer, outputBuffer.size);
+            return ostream.good();
+        }
+    };
+
+    struct CompressionJob
+    {
+        typedef std::vector<char_type, char_allocator_type> TBuffer;
+
+        TBuffer         buffer;
+        size_t          size;
+        OutputBuffer    *outputBuffer;
+
+        CompressionJob() :
+            buffer(BGZF_BLOCK_SIZE / sizeof(char_type), 0),
+            size(0),
+            outputBuffer(NULL)
+        {}
+    };
+
+    // string of recycable jobs
+    size_t                  numThreads;
+    size_t                  numJobs;
+    String<CompressionJob>  jobs;
+    TJobQueue               jobQueue;
+    TJobQueue               idleQueue;
+    Serializer<
+        OutputBuffer,
+        BufferWriter>       serializer;
+
+    size_t                  currentJobId;
+    bool                    currentJobAvail;
+
+
+    struct CompressionThread
+    {
+        basic_bgzf_streambuf            *streamBuf;
+        CompressionContext<BgzfFile>    compressionCtx;
+        size_t                          threadNum;
+
+        void operator()()
+        {
+            ScopedReadLock<TJobQueue> readLock(streamBuf->jobQueue);
+            ScopedWriteLock<TJobQueue> writeLock(streamBuf->idleQueue);
+
+            // wait for a new job to become available
+            bool success = true;
+            while (success)
+            {
+                size_t jobId = -1;
+                if (!popFront(jobId, streamBuf->jobQueue))
+                    return;
+
+                CompressionJob &job = streamBuf->jobs[jobId];
+
+                // compress block with zlib
+                job.outputBuffer->size = _compressBlock(
+                    job.outputBuffer->buffer, sizeof(job.outputBuffer->buffer),
+                    &job.buffer[0], job.size, compressionCtx);
+
+                success = releaseValue(streamBuf->serializer, job.outputBuffer);
+                appendValue(streamBuf->idleQueue, jobId);
+            }
+        }
+    };
+
+    // array of worker threads
+    Thread<CompressionThread>   *threads;
+
+    basic_bgzf_streambuf(ostream_reference ostream_,
+                         size_t numThreads = 16,
+                         size_t jobsPerThread = 8) :
+        numThreads(numThreads),
+        numJobs(numThreads * jobsPerThread),
+        jobQueue(numJobs),
+        idleQueue(numJobs),
+        serializer(ostream_, numThreads * jobsPerThread)
+    {
+        resize(jobs, numJobs, Exact());
+        currentJobId = 0;
+
+        lockWriting(jobQueue);
+        lockReading(idleQueue);
+        setReaderWriterCount(jobQueue, numThreads, 1);
+        setReaderWriterCount(idleQueue, 1, numThreads);
+
+        for (unsigned i = 0; i < numJobs; ++i)
+        {
+            bool success = appendValue(idleQueue, i);
+            ignoreUnusedVariableWarning(success);
+            SEQAN_ASSERT(success);
+        }
+
+        threads = new Thread<CompressionThread>[numThreads];
+        for (unsigned i = 0; i < numThreads; ++i)
+        {
+            threads[i].worker.streamBuf = this;
+            threads[i].worker.threadNum = i;
+            run(threads[i]);
+        }
+
+        currentJobAvail = popFront(currentJobId, idleQueue);
+        SEQAN_ASSERT(currentJobAvail);
+
+        CompressionJob &job = jobs[currentJobId];
+        job.outputBuffer = aquireValue(serializer);
+        this->setp(&job.buffer[0], &job.buffer[0] + (job.buffer.size() - 1));
+    }
+
+    ~basic_bgzf_streambuf()
+    {
+        // the buffer is now (after addFooter()) and flush will append the empty EOF marker
+        flush(true);
+
+        unlockWriting(jobQueue);
+        unlockReading(idleQueue);
+
+        for (unsigned i = 0; i < numThreads; ++i)
+            waitFor(threads[i]);
+        delete[] threads;
+    }
+
+    bool compressBuffer(size_t size)
+    {
+        // submit current job
+        if (currentJobAvail)
+        {
+            jobs[currentJobId].size = size;
+            appendValue(jobQueue, currentJobId);
+        }
+
+        // recycle existing idle job
+        if (!(currentJobAvail = popFront(currentJobId, idleQueue)))
+            return false;
+
+        jobs[currentJobId].outputBuffer = aquireValue(serializer);
+
+        return serializer;
+    }
+
+    int_type overflow(int_type c)
+    {
+        int w = static_cast<int>(this->pptr() - this->pbase());
+        if (c != EOF)
+        {
+            *this->pptr() = c;
+            ++w;
+        }
+        if (compressBuffer(w))
+        {
+            CompressionJob &job = jobs[currentJobId];
+            this->setp(&job.buffer[0], &job.buffer[0] + (job.buffer.size() - 1));
+            return c;
+        }
+        else
+        {
+            return EOF;
+        }
+    }
+
+    std::streamsize flush(bool flushEmptyBuffer = false)
+    {
+        int w = static_cast<int>(this->pptr() - this->pbase());
+        if ((w != 0 || flushEmptyBuffer) && compressBuffer(w))
+        {
+            CompressionJob &job = jobs[currentJobId];
+            this->setp(&job.buffer[0], &job.buffer[0] + (job.buffer.size() - 1));
+        }
+        else
+        {
+            w = 0;
+        }
+
+        // wait for running compressor threads
+        waitForMinSize(idleQueue, numJobs - 1);
+
+        serializer.worker.ostream.flush();
+        return w;
+    }
+
+    int sync()
+    {
+        if (this->pptr() != this->pbase())
+        {
+            int c = overflow(EOF);
+            if (c == EOF)
+                return -1;
+        }
+        return 0;
+    }
+
+    void addFooter()
+    {
+        // we flush the filled buffer here, so that an empty (EOF) buffer is flushed in the d'tor
+        if (this->pptr() != this->pbase())
+            overflow(EOF);
+    }
+
+    // returns a reference to the output stream
+    ostream_reference get_ostream() const    { return serializer.worker.ostream; };
+};
+
+// --------------------------------------------------------------------------
+// Class basic_unbgzf_streambuf
+// --------------------------------------------------------------------------
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_unbgzf_streambuf :
+    public std::basic_streambuf<Elem, Tr>
+{
+public:
+    typedef std::basic_istream<Elem, Tr>& istream_reference;
+    typedef ElemA char_allocator_type;
+    typedef ByteT byte_type;
+    typedef ByteAT byte_allocator_type;
+    typedef byte_type* byte_buffer_type;
+    typedef typename Tr::char_type char_type;
+    typedef typename Tr::int_type int_type;
+    typedef typename Tr::off_type off_type;
+    typedef typename Tr::pos_type pos_type;
+
+    typedef std::vector<char_type, char_allocator_type>     TBuffer;
+    typedef ConcurrentQueue<int, Suspendable<Limit> >       TJobQueue;
+
+    static const size_t MAX_PUTBACK = 4;
+
+    struct Serializer
+    {
+        istream_reference   istream;
+        Mutex               lock;
+        IOError             *error;
+        off_type            fileOfs;
+
+        Serializer(istream_reference istream) :
+            istream(istream),
+            lock(false),
+            error(NULL),
+            fileOfs(0u)
+        {}
+
+        ~Serializer()
+        {
+            delete error;
+        }
+    };
+
+    Serializer serializer;
+
+    struct DecompressionJob
+    {
+        typedef std::vector<byte_type, byte_allocator_type> TInputBuffer;
+
+        TInputBuffer    inputBuffer;
+        TBuffer         buffer;
+        off_type        fileOfs;
+        int             size;
+        unsigned        compressedSize;
+
+        CriticalSection cs;
+        Condition       readyEvent;
+        bool            ready;
+
+        DecompressionJob() :
+            inputBuffer(BGZF_MAX_BLOCK_SIZE, 0),
+            buffer(MAX_PUTBACK + BGZF_MAX_BLOCK_SIZE / sizeof(char_type), 0),
+            fileOfs(),
+            size(0),
+            readyEvent(cs),
+            ready(true)
+        {}
+
+        DecompressionJob(DecompressionJob const &other) :
+            inputBuffer(other.inputBuffer),
+            buffer(other.buffer),
+            fileOfs(other.fileOfs),
+            size(other.size),
+            readyEvent(cs),
+            ready(other.ready)
+        {}
+    };
+
+    // string of recycable jobs
+    size_t                      numThreads;
+    size_t                      numJobs;
+    String<DecompressionJob>    jobs;
+    TJobQueue                   runningQueue;
+    TJobQueue                   todoQueue;
+    int                         currentJobId;
+
+    struct DecompressionThread
+    {
+        basic_unbgzf_streambuf          *streamBuf;
+        CompressionContext<BgzfFile>    compressionCtx;
+
+        void operator()()
+        {
+            ScopedReadLock<TJobQueue> readLock(streamBuf->todoQueue);
+            ScopedWriteLock<TJobQueue> writeLock(streamBuf->runningQueue);
+
+            // wait for a new job to become available
+            while (true)
+            {
+                int jobId = -1;
+                if (!popFront(jobId, streamBuf->todoQueue))
+                    return;
+
+                DecompressionJob &job = streamBuf->jobs[jobId];
+                size_t tailLen = 0;
+
+                // typically the idle queue contains only ready jobs
+                // however, if seek() fast forwards running jobs into the todoQueue
+                // the caller defers the task of waiting to the decompression threads
+                if (!job.ready)
+                {
+                    ScopedLock<CriticalSection> lock(job.cs);
+                    if (!job.ready)
+                    {
+                        waitFor(job.readyEvent);
+                        job.ready = true;
+                    }
+                }
+
+                {
+                    ScopedLock<Mutex> scopedLock(streamBuf->serializer.lock);
+
+                    if (streamBuf->serializer.error != NULL)
+                        return;
+
+                    // remember start offset (for tellg later)
+                    job.fileOfs = streamBuf->serializer.fileOfs;
+                    job.size = -1;
+                    job.compressedSize = 0;
+
+                    // only load if not at EOF
+                    if (job.fileOfs != -1)
+                    {
+                        // read header
+                        streamBuf->serializer.istream.read(
+                            (char*)&job.inputBuffer[0],
+                            BGZF_BLOCK_HEADER_LENGTH);
+
+                        if (!streamBuf->serializer.istream.good())
+                        {
+                            streamBuf->serializer.fileOfs = -1;
+                            if (streamBuf->serializer.istream.eof())
+                                goto eofSkip;
+                            streamBuf->serializer.error = new IOError("Stream read error.");
+                            return;
+                        }
+
+                        // check header
+                        if (!_bgzfCheckHeader(&job.inputBuffer[0]))
+                        {
+                            streamBuf->serializer.fileOfs = -1;
+                            streamBuf->serializer.error = new IOError("Invalid BGZF block header.");
+                            return;
+                        }
+
+                        // extract length of compressed data
+                        tailLen = _bgzfUnpack16(&job.inputBuffer[0] + 16) + 1u - BGZF_BLOCK_HEADER_LENGTH;
+
+                        // read compressed data and tail
+                        streamBuf->serializer.istream.read(
+                            (char*)&job.inputBuffer[0] + BGZF_BLOCK_HEADER_LENGTH,
+                            tailLen);
+
+                        if (!streamBuf->serializer.istream.good())
+                        {
+                            streamBuf->serializer.fileOfs = -1;
+                            if (streamBuf->serializer.istream.eof())
+                                goto eofSkip;
+                            streamBuf->serializer.error = new IOError("Stream read error.");
+                            return;
+                        }
+
+                        job.compressedSize = BGZF_BLOCK_HEADER_LENGTH + tailLen;
+                        streamBuf->serializer.fileOfs += job.compressedSize;
+                        job.ready = false;
+
+                    eofSkip:
+                        streamBuf->serializer.istream.clear(
+                            streamBuf->serializer.istream.rdstate() & ~std::ios_base::failbit);
+                    }
+
+                    if (!appendValue(streamBuf->runningQueue, jobId))
+                    {
+                        // signal that job is ready
+                        {
+                            ScopedLock<CriticalSection> lock(job.cs);
+                            job.ready = true;
+                            signal(job.readyEvent);
+                        }
+                        return;
+                    }
+                }
+
+                if (!job.ready)
+                {
+                    // decompress block
+                    job.size = _decompressBlock(
+                        &job.buffer[0] + MAX_PUTBACK, capacity(job.buffer),
+                        &job.inputBuffer[0], job.compressedSize, compressionCtx);
+
+                    // signal that job is ready
+                    {
+                        ScopedLock<CriticalSection> lock(job.cs);
+                        job.ready = true;
+                        signal(job.readyEvent);
+                    }
+                }
+            }
+        }
+    };
+
+    // array of worker threads
+    Thread<DecompressionThread> *threads;
+    TBuffer                     putbackBuffer;
+
+    basic_unbgzf_streambuf(istream_reference istream_,
+                           size_t numThreads = 16,
+                           size_t jobsPerThread = 8) :
+        serializer(istream_),
+        numThreads(numThreads),
+        numJobs(numThreads * jobsPerThread),
+        runningQueue(numJobs),
+        todoQueue(numJobs),
+        putbackBuffer(MAX_PUTBACK)
+    {
+        resize(jobs, numJobs, Exact());
+        currentJobId = -1;
+
+        lockReading(runningQueue);
+        lockWriting(todoQueue);
+        setReaderWriterCount(runningQueue, 1, numThreads);
+        setReaderWriterCount(todoQueue, numThreads, 1);
+
+        for (unsigned i = 0; i < numJobs; ++i)
+        {
+            bool success = appendValue(todoQueue, i);
+            ignoreUnusedVariableWarning(success);
+            SEQAN_ASSERT(success);
+        }
+
+        threads = new Thread<DecompressionThread>[numThreads];
+        for (unsigned i = 0; i < numThreads; ++i)
+        {
+            threads[i].worker.streamBuf = this;
+            run(threads[i]);
+        }
+    }
+
+    ~basic_unbgzf_streambuf()
+    {
+        unlockWriting(todoQueue);
+        unlockReading(runningQueue);
+
+        for (unsigned i = 0; i < numThreads; ++i)
+            waitFor(threads[i]);
+        delete[] threads;
+    }
+
+    int_type underflow()
+    {
+        // no need to use the next buffer?
+        if (this->gptr() && this->gptr() < this->egptr())
+            return Tr::to_int_type(*this->gptr());
+
+        size_t putback = this->gptr() - this->eback();
+        if (putback > MAX_PUTBACK)
+            putback = MAX_PUTBACK;
+
+        // save at most MAX_PUTBACK characters from previous page to putback buffer
+        if (putback != 0)
+            std::copy(
+                this->gptr() - putback,
+                this->gptr(),
+                &putbackBuffer[0]);
+
+        if (currentJobId >= 0)
+            appendValue(todoQueue, currentJobId);
+
+        while (true)
+        {
+            if (!popFront(currentJobId, runningQueue))
+            {
+                currentJobId = -1;
+                SEQAN_ASSERT(serializer.error != NULL);
+                if (serializer.error != NULL)
+                    throw *serializer.error;
+                return EOF;
+            }
+
+            DecompressionJob &job = jobs[currentJobId];
+
+            // restore putback buffer
+            this->setp(&job.buffer[0], &job.buffer[0] + (job.buffer.size() - 1));
+            if (putback != 0)
+                std::copy(
+                    &putbackBuffer[0],
+                    &putbackBuffer[0] + putback,
+                    &job.buffer[0] + (MAX_PUTBACK - putback));
+
+            // wait for the end of decompression
+            {
+                ScopedLock<CriticalSection> lock(job.cs);
+                if (!job.ready)
+                    waitFor(job.readyEvent);
+            }
+
+            size_t size = (job.size != -1)? job.size : 0;
+
+            // reset buffer pointers
+            this->setg(
+                  &job.buffer[0] + (MAX_PUTBACK - putback),     // beginning of putback area
+                  &job.buffer[0] + MAX_PUTBACK,                 // read position
+                  &job.buffer[0] + (MAX_PUTBACK + size));       // end of buffer
+
+            if (job.size == -1)
+                return EOF;
+            else if (job.size > 0)
+                return Tr::to_int_type(*this->gptr());      // return next character
+        }
+    }
+
+    pos_type seekoff(off_type ofs, std::ios_base::seekdir dir, std::ios_base::openmode openMode)
+    {
+        if ((openMode & (std::ios_base::in | std::ios_base::out)) == std::ios_base::in)
+        {
+            if (dir == std::ios_base::cur && ofs >= 0)
+            {
+                // forward delta seek
+                while (currentJobId < 0 || this->egptr() - this->gptr() < ofs)
+                {
+                    ofs -= this->egptr() - this->gptr();
+                    if (this->underflow() == EOF)
+                        break;
+                }
+
+                if (currentJobId >= 0 && ofs <= this->egptr() - this->gptr())
+                {
+                    DecompressionJob &job = jobs[currentJobId];
+
+                    // reset buffer pointers
+                    this->setg(
+                          this->eback(),            // beginning of putback area
+                          this->gptr() + ofs,       // read position
+                          this->egptr());           // end of buffer
+
+                    if (this->gptr() != this->egptr())
+                        return pos_type((job.fileOfs << 16) + ((this->gptr() - &job.buffer[MAX_PUTBACK])));
+                    else
+                        return pos_type((job.fileOfs + job.compressedSize) << 16);
+                }
+
+            }
+            else if (dir == std::ios_base::beg)
+            {
+                // random seek
+                std::streampos destFileOfs = ofs >> 16;
+
+                // are we in the same block?
+                if (currentJobId >= 0 && jobs[currentJobId].fileOfs == (off_type)destFileOfs)
+                {
+                    DecompressionJob &job = jobs[currentJobId];
+
+                    // reset buffer pointers
+                    this->setg(
+                          this->eback(),                                        // beginning of putback area
+                          &job.buffer[0] + (MAX_PUTBACK + (ofs & 0xffff)),      // read position
+                          this->egptr());                                       // end of buffer
+                    return ofs;
+                }
+
+                // ok, different block
+                {
+                    ScopedLock<Mutex> scopedLock(serializer.lock);
+
+                    // remove all running jobs and put them in the idle queue unless we
+                    // find our seek target
+
+                    if (currentJobId >= 0)
+                        appendValue(todoQueue, currentJobId);
+
+                    // Note that if we are here the current job does not represent the sought block.
+                    // Hence if the running queue is empty we need to explicitly unset the jobId,
+                    // otherwise we would not update the serializers istream pointer to the correct position.
+                    if (empty(runningQueue))
+                        currentJobId = -1;
+
+                    // empty is thread-safe in serializer.lock
+                    while (!empty(runningQueue))
+                    {
+                        popFront(currentJobId, runningQueue);
+
+                        if (jobs[currentJobId].fileOfs == (off_type)destFileOfs)
+                            break;
+
+                        // push back useless job
+                        appendValue(todoQueue, currentJobId);
+                        currentJobId = -1;
+                    }
+
+                    if (currentJobId == -1)
+                    {
+                        SEQAN_ASSERT(empty(runningQueue));
+                        serializer.istream.clear(serializer.istream.rdstate() & ~std::ios_base::eofbit);
+                        if (serializer.istream.rdbuf()->pubseekpos(destFileOfs, std::ios_base::in) == destFileOfs)
+                            serializer.fileOfs = destFileOfs;
+                        else
+                            currentJobId = -2;      // temporarily signals a seek error
+                    }
+                }
+
+                // if our block wasn't in the running queue yet, it should now
+                // be the first that falls out after modifying serializer.fileOfs
+                if (currentJobId == -1)
+                    popFront(currentJobId, runningQueue);
+                else if (currentJobId == -2)
+                    currentJobId = -1;
+
+                if (currentJobId >= 0)
+                {
+                    // wait for the end of decompression
+                    DecompressionJob &job = jobs[currentJobId];
+                    {
+                        ScopedLock<CriticalSection> lock(job.cs);
+                        if (!job.ready)
+                            waitFor(job.readyEvent);
+                    }
+
+                    SEQAN_ASSERT_EQ(job.fileOfs, (off_type)destFileOfs);
+
+                    // reset buffer pointers
+                    this->setg(
+                          &job.buffer[0] + MAX_PUTBACK,                     // no putback area
+                          &job.buffer[0] + (MAX_PUTBACK + (ofs & 0xffff)),  // read position
+                          &job.buffer[0] + (MAX_PUTBACK + job.size));       // end of buffer
+                    return ofs;
+                }
+            }
+        }
+        return pos_type(off_type(-1));
+    }
+
+    pos_type seekpos(pos_type pos, std::ios_base::openmode openMode)
+    {
+        return seekoff(off_type(pos), std::ios_base::beg, openMode);
+    }
+
+    // returns the compressed input istream
+    istream_reference get_istream()    { return serializer.istream; };
+};
+
+// --------------------------------------------------------------------------
+// Class basic_bgzf_ostreambase
+// --------------------------------------------------------------------------
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bgzf_ostreambase : virtual public std::basic_ios<Elem,Tr>
+{
+public:
+    typedef std::basic_ostream<Elem, Tr>&                        ostream_reference;
+    typedef basic_bgzf_streambuf<Elem, Tr, ElemA, ByteT, ByteAT> bgzf_streambuf_type;
+
+    basic_bgzf_ostreambase(ostream_reference ostream_)
+        : m_buf(ostream_)
+    {
+        this->init(&m_buf );
+    };
+
+    // returns the underlying zip ostream object
+    bgzf_streambuf_type* rdbuf()            { return &m_buf; };
+    // returns the bgzf error state
+    int get_zerr() const                    { return m_buf.get_err(); };
+    // returns the uncompressed data crc
+    long get_crc() const                    { return m_buf.get_crc(); };
+    // returns the compressed data size
+    long get_out_size() const               { return m_buf.get_out_size(); };
+    // returns the uncompressed data size
+    long get_in_size() const                { return m_buf.get_in_size(); };
+
+private:
+    bgzf_streambuf_type m_buf;
+};
+
+// --------------------------------------------------------------------------
+// Class basic_bgzf_istreambase
+// --------------------------------------------------------------------------
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bgzf_istreambase : virtual public std::basic_ios<Elem,Tr>
+{
+public:
+    typedef std::basic_istream<Elem, Tr>&                           istream_reference;
+    typedef basic_unbgzf_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>  unbgzf_streambuf_type;
+
+    basic_bgzf_istreambase(istream_reference ostream_)
+        : m_buf(ostream_)
+    {
+        this->init(&m_buf );
+    };
+
+    // returns the underlying unzip istream object
+    unbgzf_streambuf_type* rdbuf() { return &m_buf; };
+
+    // returns the bgzf error state
+    int get_zerr() const                    { return m_buf.get_zerr(); };
+    // returns the uncompressed data crc
+    long get_crc() const                    { return m_buf.get_crc(); };
+    // returns the uncompressed data size
+    long get_out_size() const               { return m_buf.get_out_size(); };
+    // returns the compressed data size
+    long get_in_size() const                { return m_buf.get_in_size(); };
+
+private:
+    unbgzf_streambuf_type m_buf;
+};
+
+// --------------------------------------------------------------------------
+// Class basic_bgzf_ostream
+// --------------------------------------------------------------------------
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bgzf_ostream :
+    public basic_bgzf_ostreambase<Elem,Tr,ElemA,ByteT,ByteAT>,
+    public std::basic_ostream<Elem,Tr>
+{
+public:
+    typedef basic_bgzf_ostreambase<Elem,Tr,ElemA,ByteT,ByteAT> bgzf_ostreambase_type;
+    typedef std::basic_ostream<Elem,Tr>                        ostream_type;
+    typedef ostream_type&                                      ostream_reference;
+
+    basic_bgzf_ostream(ostream_reference ostream_) :
+        bgzf_ostreambase_type(ostream_),
+        ostream_type(bgzf_ostreambase_type::rdbuf())
+    {}
+
+    // flush inner buffer and zipper buffer
+    basic_bgzf_ostream<Elem,Tr>& zflush()
+    {
+        this->flush(); this->rdbuf()->flush(); return *this;
+    };
+
+    ~basic_bgzf_ostream()
+    {
+        this->rdbuf()->addFooter();
+    }
+
+private:
+    static void put_long(ostream_reference out_, unsigned long x_);
+#ifdef _WIN32
+    void _Add_vtordisp1() { } // Required to avoid VC++ warning C4250
+    void _Add_vtordisp2() { } // Required to avoid VC++ warning C4250
+#endif
+};
+
+// --------------------------------------------------------------------------
+// Class basic_bgzf_istream
+// --------------------------------------------------------------------------
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bgzf_istream :
+    public basic_bgzf_istreambase<Elem,Tr,ElemA,ByteT,ByteAT>,
+    public std::basic_istream<Elem,Tr>
+{
+public:
+    typedef basic_bgzf_istreambase<Elem,Tr,ElemA,ByteT,ByteAT> bgzf_istreambase_type;
+    typedef std::basic_istream<Elem,Tr>                        istream_type;
+    typedef istream_type &                                     istream_reference;
+    typedef char                                               byte_type;
+
+    basic_bgzf_istream(istream_reference istream_) :
+        bgzf_istreambase_type(istream_),
+        istream_type(bgzf_istreambase_type::rdbuf()),
+        m_is_gzip(false),
+        m_gbgzf_data_size(0)
+    {};
+
+    // returns true if it is a gzip file
+    bool is_gzip() const                { return m_is_gzip; };
+    // return data size check
+    bool check_data_size() const        { return this->get_out_size() == m_gbgzf_data_size; };
+
+    // return the data size in the file
+    long get_gbgzf_data_size() const    { return m_gbgzf_data_size; };
+
+protected:
+    static void read_long(istream_reference in_, unsigned long& x_);
+
+    int check_header();
+    bool m_is_gzip;
+    unsigned long m_gbgzf_data_size;
+
+#ifdef _WIN32
+private:
+    void _Add_vtordisp1() { } // Required to avoid VC++ warning C4250
+    void _Add_vtordisp2() { } // Required to avoid VC++ warning C4250
+#endif
+};
+
+// ===========================================================================
+// Typedefs
+// ===========================================================================
+
+// A typedef for basic_bgzf_ostream<char>
+typedef basic_bgzf_ostream<char> bgzf_ostream;
+// A typedef for basic_bgzf_ostream<wchar_t>
+typedef basic_bgzf_ostream<wchar_t> bgzf_wostream;
+// A typedef for basic_bgzf_istream<char>
+typedef basic_bgzf_istream<char> bgzf_istream;
+// A typedef for basic_bgzf_istream<wchart>
+typedef basic_bgzf_istream<wchar_t> bgzf_wistream;
+
+}  // namespace seqan
+
+#endif // INCLUDE_SEQAN_STREAM_IOSTREAM_BGZF_H_
diff --git a/seqan/stream/iostream_bzip2.h b/seqan/stream/iostream_bzip2.h
new file mode 100644
index 0000000..94f134b
--- /dev/null
+++ b/seqan/stream/iostream_bzip2.h
@@ -0,0 +1,302 @@
+// bzip2stream Library License:
+// --------------------------
+//
+// The zlib/libpng License Copyright (c) 2003 Jonathan de Halleux.
+//
+// This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.
+//
+// Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:
+//
+// 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required.
+//
+// 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
+//
+// 3. This notice may not be removed or altered from any source distribution
+//
+// Author: Jonathan de Halleux, dehalleux@pelikhan.com, 2003
+
+#ifndef INCLUDE_SEQAN_STREAM_IOSTREAM_BZIP2_H_
+#define INCLUDE_SEQAN_STREAM_IOSTREAM_BZIP2_H_
+
+#define BZ_NO_STDIO
+
+#include <bzlib.h>
+#include <vector>
+#include <iostream>
+#include <algorithm>
+
+namespace bzip2_stream{
+
+const size_t default_buffer_size = 4096;
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bzip2_streambuf :
+    public std::basic_streambuf<Elem, Tr>
+{
+public:
+    typedef std::basic_streambuf< Elem, Tr > basic_streambuf_type;
+    typedef std::basic_ostream<Elem, Tr>& ostream_reference;
+    typedef ElemA char_allocator_type;
+    typedef ByteT byte_type;
+    typedef ByteAT byte_allocator_type;
+    typedef byte_type* byte_buffer_type;
+    typedef typename Tr::char_type char_type;
+    typedef typename Tr::int_type int_type;
+    typedef std::vector<byte_type, byte_allocator_type > byte_vector_type;
+    typedef std::vector<char_type, char_allocator_type > char_vector_type;
+
+    using basic_streambuf_type::epptr;
+    using basic_streambuf_type::pbase;
+    using basic_streambuf_type::pptr;
+
+    basic_bzip2_streambuf(
+        ostream_reference ostream_,
+        size_t block_size_100k_ ,
+        size_t verbosity_ ,
+        size_t work_factor_,
+        size_t buffer_size_
+        );
+
+    ~basic_bzip2_streambuf();
+
+    int sync ();
+    int_type overflow (int_type c);
+
+    std::streamsize flush(int flush_mode);
+    int get_zerr() const
+    {    return m_err;};
+    __uint64 get_in_size() const
+    {
+        return ((__uint64)m_bzip2_stream.total_in_hi32 << 32)
+                + m_bzip2_stream.total_in_lo32;
+    }
+    __uint64 get_out_size() const
+    {
+        return ((__uint64)m_bzip2_stream.total_out_hi32 << 32)
+                + m_bzip2_stream.total_out_lo32;
+    }
+private:
+    bool bzip2_to_stream( char_type*, std::streamsize);
+    size_t fill_input_buffer();
+
+    ostream_reference m_ostream;
+    bz_stream m_bzip2_stream;
+    int m_err;
+    byte_vector_type m_output_buffer;
+    char_vector_type m_buffer;
+};
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_unbzip2_streambuf :
+    public std::basic_streambuf<Elem, Tr>
+{
+public:
+    typedef std::basic_istream<Elem, Tr>& istream_reference;
+    typedef ElemA char_allocator_type;
+    typedef ByteT byte_type;
+    typedef ByteAT byte_allocator_type;
+    typedef byte_type* byte_buffer_type;
+    typedef typename Tr::char_type char_type;
+    typedef typename Tr::int_type int_type;
+    typedef std::vector<byte_type, byte_allocator_type > byte_vector_type;
+    typedef std::vector<char_type, char_allocator_type > char_vector_type;
+
+    basic_unbzip2_streambuf(
+        istream_reference istream_,
+        size_t verbosity_,
+        bool small_,
+        size_t read_buffer_size_,
+        size_t input_buffer_size_
+        );
+
+    ~basic_unbzip2_streambuf();
+
+    int_type underflow();
+
+    istream_reference get_istream()        {    return m_istream;};
+    bz_stream& get_bzip2_stream()        {    return m_bzip2_stream;};
+    int get_zerr() const                {    return m_err;};
+private:
+    std::streamsize unbzip2_from_stream( char_type*, std::streamsize);
+    void put_back_from_bzip2_stream();
+    size_t fill_input_buffer();
+
+    istream_reference m_istream;
+    bz_stream m_bzip2_stream;
+    int m_err;
+    byte_vector_type m_input_buffer;
+    char_vector_type m_buffer;
+};
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bzip2_ostreambase : virtual public std::basic_ios<Elem,Tr>
+{
+public:
+    typedef std::basic_ostream<Elem, Tr>& ostream_reference;
+    typedef basic_bzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT> bzip2_streambuf_type;
+
+    basic_bzip2_ostreambase(
+        ostream_reference ostream_,
+        size_t block_size_100k_ ,
+        size_t verbosity_ ,
+        size_t work_factor_,
+        size_t buffer_size_
+        )
+        : m_buf(ostream_,block_size_100k_, verbosity_, work_factor_, buffer_size_)
+    {
+        this->init(&m_buf );
+    };
+
+    bzip2_streambuf_type* rdbuf() { return &m_buf; };
+
+private:
+    bzip2_streambuf_type m_buf;
+};
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bzip2_istreambase : virtual public std::basic_ios<Elem,Tr>
+{
+public:
+    typedef std::basic_istream<Elem, Tr>& istream_reference;
+    typedef basic_unbzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT> unbzip2_streambuf_type;
+
+    basic_bzip2_istreambase(
+        istream_reference ostream_,
+        size_t verbosity_,
+        bool small_,
+        size_t read_buffer_size_,
+        size_t input_buffer_size_
+        )
+        : m_buf(
+            ostream_,
+            verbosity_,
+            small_,
+            read_buffer_size_,
+            input_buffer_size_
+            )
+    {
+        this->init(&m_buf );
+    };
+
+    unbzip2_streambuf_type* rdbuf() { return &m_buf; };
+
+private:
+    unbzip2_streambuf_type m_buf;
+};
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bzip2_ostream :
+    public basic_bzip2_ostreambase<Elem,Tr,ElemA,ByteT,ByteAT>,
+    public std::basic_ostream<Elem,Tr>
+{
+public:
+    typedef basic_bzip2_ostreambase<
+        Elem,Tr,ElemA,ByteT,ByteAT> bzip2_ostreambase_type;
+    typedef std::basic_ostream<Elem,Tr> ostream_type;
+    typedef ostream_type& ostream_reference;
+
+    basic_bzip2_ostream(
+        ostream_reference ostream_,
+        size_t block_size_100k_ = 9,
+        size_t verbosity_ = 0,
+        size_t work_factor_ = 30,
+        size_t buffer_size_ = default_buffer_size
+        )
+    :
+        bzip2_ostreambase_type(ostream_,block_size_100k_, verbosity_, work_factor_,buffer_size_),
+        ostream_type(bzip2_ostreambase_type::rdbuf())
+    {
+
+    };
+
+    basic_bzip2_ostream& add_header();
+    basic_bzip2_ostream& zflush()
+    {
+        this->flush(); this->rdbuf()->flush(); return *this;
+    };
+
+#ifdef _WIN32
+private:
+    void _Add_vtordisp1() { } // Required to avoid VC++ warning C4250
+    void _Add_vtordisp2() { } // Required to avoid VC++ warning C4250
+#endif
+};
+
+template<
+    typename Elem,
+    typename Tr = std::char_traits<Elem>,
+    typename ElemA = std::allocator<Elem>,
+    typename ByteT = char,
+    typename ByteAT = std::allocator<ByteT>
+>
+class basic_bzip2_istream :
+    public basic_bzip2_istreambase<Elem,Tr,ElemA,ByteT,ByteAT>,
+    public std::basic_istream<Elem,Tr>
+{
+public:
+    typedef basic_bzip2_istreambase<
+        Elem,Tr,ElemA,ByteT,ByteAT> bzip2_istreambase_type;
+    typedef std::basic_istream<Elem,Tr> istream_type;
+    typedef istream_type& istream_reference;
+    typedef unsigned char byte_type;
+
+    basic_bzip2_istream(
+        istream_reference istream_,
+        size_t verbosity_ = 0,
+        bool small_ = false,
+        size_t read_buffer_size_ = default_buffer_size,
+        size_t input_buffer_size_ = default_buffer_size
+        )
+      :
+        bzip2_istreambase_type(istream_,verbosity_, small_, read_buffer_size_, input_buffer_size_),
+        istream_type(bzip2_istreambase_type::rdbuf())
+    {};
+#ifdef _WIN32
+private:
+    void _Add_vtordisp1() { } // Required to avoid VC++ warning C4250
+    void _Add_vtordisp2() { } // Required to avoid VC++ warning C4250
+#endif
+};
+
+typedef basic_bzip2_ostream<char> bzip2_ostream;
+typedef basic_bzip2_ostream<wchar_t> bzip2_wostream;
+typedef basic_bzip2_istream<char> bzip2_istream;
+typedef basic_bzip2_istream<wchar_t> bzip2_wistream;
+
+} // bzip2_stream
+
+#include "iostream_bzip2_impl.h"
+
+#endif // INCLUDE_SEQAN_STREAM_IOSTREAM_BZIP2_H_
diff --git a/seqan/stream/iostream_bzip2_impl.h b/seqan/stream/iostream_bzip2_impl.h
new file mode 100644
index 0000000..f0e5143
--- /dev/null
+++ b/seqan/stream/iostream_bzip2_impl.h
@@ -0,0 +1,429 @@
+// bzip2stream Library License:
+// --------------------------
+//
+// The zlib/libpng License Copyright (c) 2003 Jonathan de Halleux.
+//
+// This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.
+//
+// Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:
+//
+// 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required.
+//
+// 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
+//
+// 3. This notice may not be removed or altered from any source distribution
+//
+// Author: Jonathan de Halleux, dehalleux@pelikhan.com, 2003
+
+#ifndef INCLUDE_SEQAN_STREAM_IOSTREAM_BZIP2_IMPL_H_
+#define INCLUDE_SEQAN_STREAM_IOSTREAM_BZIP2_IMPL_H_
+
+#include "iostream_bzip2.h"
+
+namespace bzip2_stream{
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    basic_bzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >:: basic_bzip2_streambuf(
+        ostream_reference ostream_,
+        size_t block_size_100k_,
+        size_t verbosity_,
+        size_t work_factor_,
+        size_t buffer_size_
+        )
+    :
+        m_ostream(ostream_),
+        m_output_buffer(buffer_size_,0),
+        m_buffer(buffer_size_,0)
+    {
+        m_bzip2_stream.bzalloc=NULL;
+        m_bzip2_stream.bzfree=NULL;
+
+        m_bzip2_stream.next_in=NULL;
+        m_bzip2_stream.avail_in=0;
+        m_bzip2_stream.avail_out=0;
+        m_bzip2_stream.next_out=NULL;
+
+        m_err=BZ2_bzCompressInit(
+            &m_bzip2_stream,
+            std::min( 9, static_cast<int>(block_size_100k_) ),
+            std::min( 4, static_cast<int>(verbosity_) ),
+            std::min( 250, static_cast<int>(work_factor_) )
+            );
+
+        this->setp( &(m_buffer[0]), &(m_buffer[m_buffer.size()-1]));
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    basic_bzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::~basic_bzip2_streambuf()
+    {
+        flush(BZ_FINISH);
+        m_ostream.flush();
+        m_err=BZ2_bzCompressEnd(&m_bzip2_stream);
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    int basic_bzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::sync ()
+    {
+        if ( this->pptr() && this->pptr() > this->pbase())
+        {
+            int c = overflow( EOF);
+
+            if ( c == EOF)
+                return -1;
+        }
+
+        return 0;
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    typename basic_bzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::int_type
+            basic_bzip2_streambuf<
+                Elem,Tr,ElemA,ByteT,ByteAT
+                >::overflow (
+                    typename basic_bzip2_streambuf<
+                        Elem,Tr,ElemA,ByteT,ByteAT
+                        >::int_type c
+                    )
+    {
+        int w = static_cast<int>(this->pptr() - this->pbase());
+        if (c != EOF) {
+             *this->pptr() = c;
+             ++w;
+         }
+         if ( bzip2_to_stream( this->pbase(), w)) {
+             this->setp( this->pbase(), this->epptr());
+             return c;
+         } else
+             return EOF;
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    bool basic_bzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::bzip2_to_stream(
+            typename basic_bzip2_streambuf<
+                Elem,Tr,ElemA,ByteT,ByteAT
+                >::char_type* buffer_,
+            std::streamsize buffer_size_
+            )
+    {
+        std::streamsize written_byte_size=0, total_written_byte_size = 0;
+
+        m_bzip2_stream.next_in=(byte_buffer_type)buffer_;
+        m_bzip2_stream.avail_in=buffer_size_*sizeof(char_type);
+        m_bzip2_stream.avail_out=static_cast<unsigned int>(m_output_buffer.size());
+        m_bzip2_stream.next_out=&(m_output_buffer[0]);
+        size_t remainder=0;
+
+        do
+        {
+            m_err = BZ2_bzCompress (&m_bzip2_stream, BZ_RUN );
+
+            if (m_err == BZ_RUN_OK  || m_err == BZ_STREAM_END)
+            {
+                written_byte_size= static_cast<std::streamsize>(m_output_buffer.size()) - m_bzip2_stream.avail_out;
+                total_written_byte_size+=written_byte_size;
+                // ouput buffer is full, dumping to ostream
+                m_ostream.write(
+                    (const char_type*) &(m_output_buffer[0]),
+                    static_cast<std::streamsize>( written_byte_size/sizeof(char_type) )
+                    );
+
+                // checking if some bytes were not written.
+                if ( (remainder = written_byte_size%sizeof(char_type))!=0)
+                {
+                    // copy to the beginning of the stream
+                    std::memmove(
+                        &(m_output_buffer[0]),
+                        &(m_output_buffer[written_byte_size-remainder]),
+                        remainder);
+
+                }
+
+                m_bzip2_stream.avail_out=static_cast<unsigned int>(m_output_buffer.size()-remainder);
+                m_bzip2_stream.next_out=&m_output_buffer[remainder];
+            }
+        }
+        while (m_bzip2_stream.avail_in != 0 && m_err == BZ_RUN_OK);
+
+        return m_err == BZ_RUN_OK || m_err == BZ_FLUSH_OK;
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    std::streamsize basic_bzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::flush(int flush_mode)
+    {
+        std::streamsize written_byte_size=0, total_written_byte_size=0;
+
+        int const buffer_size = static_cast< int >( pptr() - pbase() ); // amount of data currently in buffer
+
+        m_bzip2_stream.next_in=(byte_buffer_type)pbase();
+        m_bzip2_stream.avail_in=static_cast< uInt >(buffer_size*sizeof(char_type));
+        m_bzip2_stream.avail_out=static_cast< uInt >(m_output_buffer.size());
+        m_bzip2_stream.next_out=&(m_output_buffer[0]);
+        size_t remainder=0;
+
+        do
+        {
+            m_err = BZ2_bzCompress (&m_bzip2_stream, flush_mode);
+            if (m_err == BZ_FINISH_OK || m_err == BZ_STREAM_END)
+            {
+                written_byte_size=
+                    static_cast<std::streamsize>(m_output_buffer.size())
+                    - m_bzip2_stream.avail_out;
+                total_written_byte_size+=written_byte_size;
+                // ouput buffer is full, dumping to ostream
+                m_ostream.write(
+                    (const char_type*) &(m_output_buffer[0]),
+                    static_cast<std::streamsize>( written_byte_size/sizeof(char_type)*sizeof(char) )
+                    );
+
+                // checking if some bytes were not written.
+                if ( (remainder = written_byte_size%sizeof(char_type))!=0)
+                {
+                    // copy to the beginning of the stream
+                    std::memmove(
+                        &(m_output_buffer[0]),
+                        &(m_output_buffer[written_byte_size-remainder]),
+                        remainder);
+
+                }
+
+                m_bzip2_stream.avail_out=static_cast<unsigned int>(m_output_buffer.size()-remainder);
+                m_bzip2_stream.next_out=&(m_output_buffer[remainder]);
+            }
+        } while (m_err == BZ_FINISH_OK);
+
+        m_ostream.flush();
+
+        return total_written_byte_size;
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    basic_unbzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::basic_unbzip2_streambuf(
+            istream_reference istream_,
+            size_t verbosity_,
+            bool small_,
+            size_t read_buffer_size_,
+            size_t input_buffer_size_
+    )
+    :
+        m_istream(istream_),
+        m_input_buffer(input_buffer_size_),
+        m_buffer(read_buffer_size_)
+    {
+        // setting zalloc, zfree and opaque
+        m_bzip2_stream.bzalloc=NULL;
+        m_bzip2_stream.bzfree=NULL;
+
+        m_bzip2_stream.next_in=NULL;
+        m_bzip2_stream.avail_in=0;
+        m_bzip2_stream.avail_out=0;
+        m_bzip2_stream.next_out=NULL;
+
+
+        m_err=BZ2_bzDecompressInit (
+            &m_bzip2_stream,
+            std::min(4, static_cast<int>(verbosity_)),
+            static_cast<int>(small_)
+        );
+
+        this->setg(
+            &(m_buffer[0])+4,     // beginning of putback area
+            &(m_buffer[0])+4,     // read position
+            &(m_buffer[0])+4);    // end position
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    size_t basic_unbzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::fill_input_buffer()
+    {
+        m_bzip2_stream.next_in=&(m_input_buffer[0]);
+        m_istream.read(
+            (char_type*)(&(m_input_buffer[0])),
+            static_cast<std::streamsize>(m_input_buffer.size()/sizeof(char_type))
+            );
+        return m_bzip2_stream.avail_in=m_istream.gcount()*sizeof(char_type);
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    void basic_unbzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::put_back_from_bzip2_stream()
+    {
+        if (m_bzip2_stream.avail_in==0)
+            return;
+
+        m_istream.clear( std::ios::goodbit );
+        m_istream.seekg(
+            -static_cast<int>(m_bzip2_stream.avail_in),
+            std::ios_base::cur
+            );
+
+        m_bzip2_stream.avail_in=0;
+    }
+
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    basic_unbzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::~basic_unbzip2_streambuf()
+    {
+        BZ2_bzDecompressEnd(&m_bzip2_stream);
+    }
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    typename basic_unbzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::int_type
+            basic_unbzip2_streambuf<
+                Elem,Tr,ElemA,ByteT,ByteAT
+                >::underflow()
+    {
+        if ( this->gptr() && ( this->gptr() < this->egptr()))
+            return * reinterpret_cast<unsigned char *>( this->gptr());
+
+       int n_putback = static_cast<int>(this->gptr() - this->eback());
+       if ( n_putback > 4)
+          n_putback = 4;
+       std::memmove(
+            &(m_buffer[0]) + (4 - n_putback),
+            this->gptr() - n_putback,
+            n_putback*sizeof(char_type)
+            );
+
+       int num = unbzip2_from_stream(
+           &(m_buffer[0])+4,
+           static_cast<std::streamsize>((m_buffer.size()-4)*sizeof(char_type))
+           );
+        if (num <= 0) // ERROR or EOF
+           return EOF;
+
+        // reset buffer pointers
+        this->setg(
+              &(m_buffer[0]) + (4 - n_putback),   // beginning of putback area
+              &(m_buffer[0]) + 4,                 // read position
+              &(m_buffer[0]) + 4 + num);          // end of buffer
+
+         // return next character
+         return* reinterpret_cast<unsigned char *>( this->gptr());
+     }
+
+
+    template<
+        typename Elem,
+        typename Tr,
+        typename ElemA,
+        typename ByteT,
+        typename ByteAT
+    >
+    std::streamsize basic_unbzip2_streambuf<
+        Elem,Tr,ElemA,ByteT,ByteAT
+        >::unbzip2_from_stream(
+            char_type* buffer_,
+            std::streamsize buffer_size_
+            )
+    {
+        m_bzip2_stream.next_out=(byte_buffer_type)buffer_;
+        m_bzip2_stream.avail_out=buffer_size_*sizeof(char_type);
+        size_t count =m_bzip2_stream.avail_in;
+
+        do
+        {
+            if (m_bzip2_stream.avail_in==0)
+                count=fill_input_buffer();
+
+            if (m_bzip2_stream.avail_in)
+            {
+                m_err = BZ2_bzDecompress( &m_bzip2_stream );
+            }
+        } while (m_err==BZ_OK && m_bzip2_stream.avail_out != 0 && count != 0);
+
+        if (m_err == BZ_STREAM_END)
+            put_back_from_bzip2_stream();
+
+        return buffer_size_ - m_bzip2_stream.avail_out/sizeof(char_type);
+    }
+
+
+} // zlib_sream
+
+#endif // INCLUDE_SEQAN_STREAM_IOSTREAM_BZIP2_IMPL_H_
diff --git a/seqan/stream/iostream_zip.h b/seqan/stream/iostream_zip.h
new file mode 100644
index 0000000..89fdf2e
--- /dev/null
+++ b/seqan/stream/iostream_zip.h
@@ -0,0 +1,383 @@
+// zipstream Library License:
+// --------------------------
+//
+// The zlib/libpng License Copyright (c) 2003 Jonathan de Halleux.
+//
+// This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.
+//
+// Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:
+//
+// 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required.
+//
+// 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
+//
+// 3. This notice may not be removed or altered from any source distribution
+//
+// Altered zipstream library header
+// Author: Jonathan de Halleux, dehalleux@pelikhan.com, 2003
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+
+#ifndef INCLUDE_SEQAN_STREAM_IOSTREAM_ZIP_H_
+#define INCLUDE_SEQAN_STREAM_IOSTREAM_ZIP_H_
+
+namespace zlib_stream {
+
+// Default gzip buffer size, change this to suite your needs.
+const size_t ZIP_DEFAULT_BUFFER_SIZE = 921600;
+
+// --------------------------------------------------------------------------
+// Enum EStrategy
+// --------------------------------------------------------------------------
+// Compression strategy, see zlib doc.
+
+enum EStrategy
+{
+    StrategyFiltered = 1,
+    StrategyHuffmanOnly = 2,
+    DefaultStrategy = 0
+};
+
+// ===========================================================================
+// Classes
+// ===========================================================================
+
+// --------------------------------------------------------------------------
+// Class basic_zip_streambuf
+// --------------------------------------------------------------------------
+// A stream decorator that takes raw input and zips it to a ostream.
+// The class wraps up the inflate method of the zlib library 1.1.4 http://www.gzip.org/zlib/
+
+template <typename Elem,
+          typename Tr = std::char_traits<Elem>,
+          typename ElemA = std::allocator<Elem>,
+          typename ByteT = unsigned char,
+          typename ByteAT = std::allocator<ByteT>
+          >
+class basic_zip_streambuf :
+    public std::basic_streambuf<Elem, Tr>
+{
+public:
+    typedef std::basic_ostream<Elem, Tr> &              ostream_reference;
+    typedef ElemA                                       char_allocator_type;
+    typedef ByteT                                       byte_type;
+    typedef ByteAT                                      byte_allocator_type;
+    typedef byte_type *                                 byte_buffer_type;
+    typedef Tr                                          traits_type;
+    typedef typename Tr::char_type                      char_type;
+    typedef typename Tr::int_type                       int_type;
+    typedef std::vector<byte_type, byte_allocator_type> byte_vector_type;
+    typedef std::vector<char_type, char_allocator_type> char_vector_type;
+
+    // Construct a zip stream
+    // More info on the following parameters can be found in the zlib documentation.
+    basic_zip_streambuf(ostream_reference ostream_,
+                        size_t level_,
+                        EStrategy strategy_,
+                        size_t window_size_,
+                        size_t memory_level_,
+                        size_t buffer_size_);
+
+    ~basic_zip_streambuf();
+
+    int sync();
+    int_type overflow(int_type c);
+
+    // flushes the zip buffer and output buffer.
+    // This method should be called at the end of the compression.
+    // Calling flush multiple times, will lower the compression ratio.
+    std::streamsize flush();
+
+    // flushes the zip buffer and output buffer and finalize the zip stream
+    // This method should be called at the end of the compression.
+    std::streamsize flush_finalize();
+
+
+private:
+    bool zip_to_stream(char_type *, std::streamsize);
+    size_t fill_input_buffer();
+    // flush the zip buffer using a particular mode and flush output buffer
+    std::streamsize flush(int flush_mode);
+
+    ostream_reference m_ostream;
+    z_stream m_zip_stream;
+    int m_err;
+    byte_vector_type m_output_buffer;
+    char_vector_type m_buffer;
+};
+
+// --------------------------------------------------------------------------
+// Class basic_unzip_streambuf
+// --------------------------------------------------------------------------
+// A stream decorator that takes compressed input and unzips it to a istream.
+// The class wraps up the deflate method of the zlib library 1.1.4 http://www.gzip.org/zlib/
+
+template <typename Elem,
+          typename Tr = std::char_traits<Elem>,
+          typename ElemA = std::allocator<Elem>,
+          typename ByteT = unsigned char,
+          typename ByteAT = std::allocator<ByteT>
+          >
+class basic_unzip_streambuf :
+    public std::basic_streambuf<Elem, Tr>
+{
+public:
+    typedef std::basic_istream<Elem, Tr> &              istream_reference;
+    typedef ElemA                                       char_allocator_type;
+    typedef ByteT                                       byte_type;
+    typedef ByteAT                                      byte_allocator_type;
+    typedef byte_type *                                 byte_buffer_type;
+    typedef Tr                                          traits_type;
+    typedef typename Tr::char_type                      char_type;
+    typedef typename Tr::int_type                       int_type;
+    typedef std::vector<byte_type, byte_allocator_type> byte_vector_type;
+    typedef std::vector<char_type, char_allocator_type> char_vector_type;
+
+    // Construct a unzip stream
+    // More info on the following parameters can be found in the zlib documentation.
+    basic_unzip_streambuf(istream_reference istream_,
+                          size_t window_size_,
+                          size_t read_buffer_size_,
+                          size_t input_buffer_size_);
+
+    ~basic_unzip_streambuf();
+
+    int_type underflow();
+
+    // returns the compressed input istream
+    istream_reference get_istream()  { return m_istream; }
+    // returns the zlib stream structure
+    z_stream & get_zip_stream()      { return m_zip_stream; }
+
+private:
+    void put_back_from_zip_stream();
+    std::streamsize unzip_from_stream(char_type *, std::streamsize);
+    size_t fill_input_buffer();
+
+    istream_reference m_istream;
+    z_stream m_zip_stream;
+    int m_err;
+    byte_vector_type m_input_buffer;
+    char_vector_type m_buffer;
+};
+
+// --------------------------------------------------------------------------
+// Class basic_zip_ostreambase
+// --------------------------------------------------------------------------
+// Base class for zip ostreams.
+// Contains a basic_zip_streambuf.
+
+template <typename Elem,
+          typename Tr = std::char_traits<Elem>,
+          typename ElemA = std::allocator<Elem>,
+          typename ByteT = unsigned char,
+          typename ByteAT = std::allocator<ByteT>
+          >
+class basic_zip_ostreambase :
+    virtual public std::basic_ios<Elem, Tr>
+{
+public:
+    typedef std::basic_ostream<Elem, Tr> &                      ostream_reference;
+    typedef basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT> zip_streambuf_type;
+
+    // Construct a zip stream
+    // More info on the following parameters can be found in the zlib documentation.
+    basic_zip_ostreambase(ostream_reference ostream_,
+                          size_t level_,
+                          EStrategy strategy_,
+                          size_t window_size_,
+                          size_t memory_level_,
+                          size_t buffer_size_) :
+        m_buf(ostream_, level_, strategy_, window_size_, memory_level_, buffer_size_)
+    {
+        this->init(&m_buf);
+    }
+
+    // returns the underlying zip ostream object
+    zip_streambuf_type * rdbuf() { return &m_buf; }
+
+private:
+    zip_streambuf_type m_buf;
+};
+
+// --------------------------------------------------------------------------
+// Class basic_zip_istreambase
+// --------------------------------------------------------------------------
+// Base class for unzip istreams
+// Contains a basic_unzip_streambuf.
+
+template <typename Elem,
+          typename Tr = std::char_traits<Elem>,
+          typename ElemA = std::allocator<Elem>,
+          typename ByteT = unsigned char,
+          typename ByteAT = std::allocator<ByteT>
+          >
+class basic_zip_istreambase :
+    virtual public std::basic_ios<Elem, Tr>
+{
+public:
+    typedef std::basic_istream<Elem, Tr> &                        istream_reference;
+    typedef basic_unzip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT> unzip_streambuf_type;
+
+    basic_zip_istreambase(istream_reference ostream_,
+                          size_t window_size_,
+                          size_t read_buffer_size_,
+                          size_t input_buffer_size_) :
+        m_buf(ostream_, window_size_, read_buffer_size_, input_buffer_size_)
+    {
+        this->init(&m_buf);
+    }
+
+    // returns the underlying unzip istream object
+    unzip_streambuf_type * rdbuf() { return &m_buf; }
+
+private:
+    unzip_streambuf_type m_buf;
+};
+
+// --------------------------------------------------------------------------
+// Class basic_zip_ostream
+// --------------------------------------------------------------------------
+// A zipper ostream
+//
+// This class is a ostream decorator that behaves 'almost' like any other ostream.
+// At construction, it takes any ostream that shall be used to output of the compressed data.
+// When finished, you need to call the special method zflush or call the destructor
+// to flush all the intermidiate streams.
+//
+// Example:
+//
+// // creating the target zip string, could be a fstream
+// ostringstream ostringstream_;
+// // creating the zip layer
+// zip_ostream zipper(ostringstream_);
+// // writing data
+// zipper<<f<<" "<<d<<" "<<ui<<" "<<ul<<" "<<us<<" "<<c<<" "<<dum;
+// // zip ostream needs special flushing...
+// zipper.zflush();
+
+template <typename Elem,
+          typename Tr = std::char_traits<Elem>,
+          typename ElemA = std::allocator<Elem>,
+          typename ByteT = unsigned char,
+          typename ByteAT = std::allocator<ByteT>
+          >
+class basic_zip_ostream :
+    public basic_zip_ostreambase<Elem, Tr, ElemA, ByteT, ByteAT>,
+    public std::basic_ostream<Elem, Tr>
+{
+public:
+    typedef basic_zip_ostreambase<Elem, Tr, ElemA, ByteT, ByteAT> zip_ostreambase_type;
+    typedef std::basic_ostream<Elem, Tr>                          ostream_type;
+    typedef ostream_type &                                        ostream_reference;
+
+    // Constructs a zipper ostream decorator
+    //
+    // ostream_ ostream where the compressed output is written
+    // is_gzip_ true if gzip header and footer have to be added
+    // level_ level of compression 0, bad and fast, 9, good and slower,
+    // strategy_ compression strategy
+    // window_size_ see zlib doc
+    // memory_level_ see zlib doc
+    // buffer_size_ the buffer size used to zip data
+
+    basic_zip_ostream(ostream_reference ostream_,
+                      size_t level_ = Z_DEFAULT_COMPRESSION,
+                      EStrategy strategy_ = DefaultStrategy,
+                      size_t window_size_ = 31, // 15 (size) + 16 (gzip header)
+                      size_t memory_level_ = 8,
+                      size_t buffer_size_ = ZIP_DEFAULT_BUFFER_SIZE) :
+        zip_ostreambase_type(ostream_, level_, strategy_, window_size_, memory_level_, buffer_size_),
+        ostream_type(this->rdbuf())
+    {}
+
+    ~basic_zip_ostream()
+    {
+        this->flush(); this->rdbuf()->flush_finalize();
+    }
+
+    // flush inner buffer and zipper buffer
+    basic_zip_ostream<Elem, Tr> & zflush()
+    {
+        this->flush(); this->rdbuf()->flush(); return *this;
+    }
+
+#ifdef _WIN32
+private:
+    void _Add_vtordisp1() {}  // Required to avoid VC++ warning C4250
+    void _Add_vtordisp2() {}  // Required to avoid VC++ warning C4250
+#endif
+};
+
+// --------------------------------------------------------------------------
+// Class basic_zip_istream
+// --------------------------------------------------------------------------
+// A zipper istream
+//
+// This class is a istream decorator that behaves 'almost' like any other ostream.
+// At construction, it takes any istream that shall be used to input of the compressed data.
+//
+// Simlpe example:
+//
+// // create a stream on zip string
+// istringstream istringstream_( ostringstream_.str());
+// // create unzipper istream
+// zip_istream unzipper( istringstream_);
+// // read and unzip
+// unzipper>>f_r>>d_r>>ui_r>>ul_r>>us_r>>c_r>>dum_r;
+
+template <typename Elem,
+          typename Tr = std::char_traits<Elem>,
+          typename ElemA = std::allocator<Elem>,
+          typename ByteT = unsigned char,
+          typename ByteAT = std::allocator<ByteT>
+          >
+class basic_zip_istream :
+    public basic_zip_istreambase<Elem, Tr, ElemA, ByteT, ByteAT>,
+    public std::basic_istream<Elem, Tr>
+{
+public:
+    typedef basic_zip_istreambase<Elem, Tr, ElemA, ByteT, ByteAT> zip_istreambase_type;
+    typedef std::basic_istream<Elem, Tr>                          istream_type;
+    typedef istream_type &                                        istream_reference;
+    typedef ByteT                                                 byte_type;
+    typedef Tr                                                    traits_type;
+
+    // Construct a unzipper stream
+    //
+    // istream_ input buffer
+    // window_size_
+    // read_buffer_size_
+    // input_buffer_size_
+
+    basic_zip_istream(istream_reference istream_,
+                      size_t window_size_ = 31, // 15 (size) + 16 (gzip header)
+                      size_t read_buffer_size_ = ZIP_DEFAULT_BUFFER_SIZE,
+                      size_t input_buffer_size_ = ZIP_DEFAULT_BUFFER_SIZE) :
+        zip_istreambase_type(istream_, window_size_, read_buffer_size_, input_buffer_size_),
+        istream_type(this->rdbuf())
+    {}
+
+#ifdef _WIN32
+private:
+    void _Add_vtordisp1() {}  // Required to avoid VC++ warning C4250
+    void _Add_vtordisp2() {}  // Required to avoid VC++ warning C4250
+#endif
+};
+
+// ===========================================================================
+// Typedefs
+// ===========================================================================
+
+// A typedef for basic_zip_ostream<char>
+typedef basic_zip_ostream<char>     zip_ostream;
+// A typedef for basic_zip_ostream<wchar_t>
+typedef basic_zip_ostream<wchar_t>  zip_wostream;
+// A typedef for basic_zip_istream<char>
+typedef basic_zip_istream<char>     zip_istream;
+// A typedef for basic_zip_istream<wchart>
+typedef basic_zip_istream<wchar_t>  zip_wistream;
+
+} // namespace zlib_stream
+
+#endif // INCLUDE_SEQAN_STREAM_IOSTREAM_ZIP_H_
diff --git a/seqan/stream/iostream_zip_impl.h b/seqan/stream/iostream_zip_impl.h
new file mode 100644
index 0000000..716986c
--- /dev/null
+++ b/seqan/stream/iostream_zip_impl.h
@@ -0,0 +1,386 @@
+// zipstream Library License:
+// --------------------------
+//
+// The zlib/libpng License Copyright (c) 2003 Jonathan de Halleux.
+//
+// This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.
+//
+// Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:
+//
+// 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required.
+//
+// 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software.
+//
+// 3. This notice may not be removed or altered from any source distribution
+//
+// Altered zipstream library header
+// Author: Jonathan de Halleux, dehalleux@pelikhan.com, 2003
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+
+#ifndef INCLUDE_SEQAN_STREAM_IOSTREAM_ZIP_IMPL_H_
+#define INCLUDE_SEQAN_STREAM_IOSTREAM_ZIP_IMPL_H_
+
+namespace zlib_stream {
+
+// --------------------------------------------------------------------------
+// Class basic_zip_streambuf
+// --------------------------------------------------------------------------
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::basic_zip_streambuf(
+    ostream_reference ostream_,
+    size_t level_,
+    EStrategy strategy_,
+    size_t window_size_,
+    size_t memory_level_,
+    size_t buffer_size_
+    ) :
+    m_ostream(ostream_),
+    m_output_buffer(buffer_size_, 0),
+    m_buffer(buffer_size_, 0)
+{
+    m_zip_stream.zalloc = (alloc_func)0;
+    m_zip_stream.zfree = (free_func)0;
+
+    m_zip_stream.next_in = NULL;
+    m_zip_stream.avail_in = 0;
+    m_zip_stream.avail_out = 0;
+    m_zip_stream.next_out = NULL;
+
+    m_err = deflateInit2(
+        &m_zip_stream,
+        std::min(9, static_cast<int>(level_)),
+        Z_DEFLATED,
+        static_cast<int>(window_size_),
+        std::min(9, static_cast<int>(memory_level_)),
+        static_cast<int>(strategy_)
+        );
+
+    this->setp(&(m_buffer[0]), &(m_buffer[m_buffer.size() - 1]));
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::~basic_zip_streambuf()
+{
+    flush_finalize();
+    m_ostream.flush();
+    m_err = deflateEnd(&m_zip_stream);
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+int basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::sync()
+{
+    if (this->pptr() && this->pptr() > this->pbase())
+    {
+        if (traits_type::eq_int_type(overflow(traits_type::eof()), traits_type::eof()))
+            return -1;
+    }
+
+    return 0;
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+typename basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::int_type
+basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::overflow(
+    typename basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::int_type c)
+{
+    int w = static_cast<int>(this->pptr() - this->pbase());
+
+    if (!traits_type::eq_int_type(c, traits_type::eof()))
+    {
+        *this->pptr() = c;
+        ++w;
+    }
+
+    if (zip_to_stream(this->pbase(), w))
+    {
+        this->setp(this->pbase(), this->epptr() - 1);
+        return c;
+    }
+    else
+    {
+        return traits_type::eof();
+    }
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+bool basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::zip_to_stream(
+    typename basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::char_type * buffer_,
+    std::streamsize buffer_size_)
+{
+    std::streamsize written_byte_size = 0, total_written_byte_size = 0;
+
+    m_zip_stream.next_in = (byte_buffer_type)buffer_;
+    m_zip_stream.avail_in = static_cast<uInt>(buffer_size_ * sizeof(char_type));
+    m_zip_stream.avail_out = static_cast<uInt>(m_output_buffer.size());
+    m_zip_stream.next_out = &(m_output_buffer[0]);
+    size_t remainder = 0;
+
+    do
+    {
+        m_err = deflate(&m_zip_stream, 0);
+
+        if (m_err == Z_OK  || m_err == Z_STREAM_END)
+        {
+            written_byte_size = static_cast<std::streamsize>(m_output_buffer.size()) - m_zip_stream.avail_out;
+            total_written_byte_size += written_byte_size;
+
+            // ouput buffer is full, dumping to ostream
+            m_ostream.write((const char_type *) &(m_output_buffer[0]),
+                            static_cast<std::streamsize>(written_byte_size / sizeof(char_type)));
+
+            // checking if some bytes were not written.
+            if ((remainder = written_byte_size % sizeof(char_type)) != 0)
+            {
+                // copy to the beginning of the stream
+                std::memmove(&(m_output_buffer[0]),
+                             &(m_output_buffer[written_byte_size - remainder]),
+                             remainder);
+            }
+
+            m_zip_stream.avail_out = static_cast<uInt>(m_output_buffer.size() - remainder);
+            m_zip_stream.next_out = &m_output_buffer[remainder];
+        }
+    }
+    while (m_zip_stream.avail_in != 0 && m_err == Z_OK);
+
+    return m_err == Z_OK;
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+std::streamsize basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::flush(int flush_mode)
+{
+    int const buffer_size = static_cast<int>(this->pptr() - this->pbase()); // amount of data currently in buffer
+
+    std::streamsize written_byte_size = 0, total_written_byte_size = 0;
+
+    m_zip_stream.next_in = (byte_buffer_type) this->pbase();
+    m_zip_stream.avail_in = static_cast<uInt>(buffer_size * sizeof(char_type));
+    m_zip_stream.avail_out = static_cast<uInt>(m_output_buffer.size());
+    m_zip_stream.next_out = &(m_output_buffer[0]);
+    size_t remainder = 0;
+
+    do
+    {
+        m_err = deflate(&m_zip_stream, flush_mode);
+        if (m_err == Z_OK || m_err == Z_STREAM_END)
+        {
+            written_byte_size = static_cast<std::streamsize>(m_output_buffer.size()) - m_zip_stream.avail_out;
+            total_written_byte_size += written_byte_size;
+
+            // ouput buffer is full, dumping to ostream
+            m_ostream.write((const char_type *) &(m_output_buffer[0]),
+                            static_cast<std::streamsize>(written_byte_size / sizeof(char_type) * sizeof(byte_type)));
+
+            // checking if some bytes were not written.
+            if ((remainder = written_byte_size % sizeof(char_type)) != 0)
+            {
+                // copy to the beginning of the stream
+                std::memmove(&(m_output_buffer[0]),
+                             &(m_output_buffer[written_byte_size - remainder]),
+                             remainder);
+            }
+
+            m_zip_stream.avail_out = static_cast<uInt>(m_output_buffer.size() - remainder);
+            m_zip_stream.next_out = &m_output_buffer[remainder];
+        }
+    }
+    while (m_err == Z_OK);
+
+    m_ostream.flush();
+
+    return total_written_byte_size;
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+std::streamsize basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::flush()
+{
+    return flush(Z_SYNC_FLUSH);
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+std::streamsize basic_zip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::flush_finalize()
+{
+    return flush(Z_FINISH);
+}
+
+// --------------------------------------------------------------------------
+// Class basic_unzip_streambuf
+// --------------------------------------------------------------------------
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+basic_unzip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::basic_unzip_streambuf(
+    istream_reference istream_,
+    size_t window_size_,
+    size_t read_buffer_size_,
+    size_t input_buffer_size_
+    ) :
+    m_istream(istream_),
+    m_input_buffer(input_buffer_size_),
+    m_buffer(read_buffer_size_)
+{
+    // setting zalloc, zfree and opaque
+    m_zip_stream.zalloc = (alloc_func)0;
+    m_zip_stream.zfree = (free_func)0;
+
+    m_zip_stream.next_in = NULL;
+    m_zip_stream.avail_in = 0;
+    m_zip_stream.avail_out = 0;
+    m_zip_stream.next_out = NULL;
+
+    m_err = inflateInit2(&m_zip_stream, static_cast<int>(window_size_));
+
+    this->setg(&(m_buffer[0]) + 4,  // beginning of putback area
+               &(m_buffer[0]) + 4,  // read position
+               &(m_buffer[0]) + 4); // end position
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+basic_unzip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::~basic_unzip_streambuf()
+{
+    inflateEnd(&m_zip_stream);
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+typename basic_unzip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::int_type
+basic_unzip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::underflow()
+{
+    if (this->gptr() && (this->gptr() < this->egptr()))
+        return *reinterpret_cast<unsigned char *>(this->gptr());
+
+    int n_putback = static_cast<int>(this->gptr() - this->eback());
+    if (n_putback > 4)
+        n_putback = 4;
+
+    std::memmove(&(m_buffer[0]) + (4 - n_putback), this->gptr() - n_putback, n_putback * sizeof(char_type));
+
+    int num = unzip_from_stream(&(m_buffer[0]) + 4,
+                                static_cast<std::streamsize>((m_buffer.size() - 4) * sizeof(char_type)));
+
+    if (num <= 0)     // ERROR or EOF
+        return traits_type::eof();
+
+    // reset buffer pointers
+    this->setg(&(m_buffer[0]) + (4 - n_putback),         // beginning of putback area
+               &(m_buffer[0]) + 4,                       // read position
+               &(m_buffer[0]) + 4 + num);                // end of buffer
+
+    // return next character
+    return *reinterpret_cast<unsigned char *>(this->gptr());
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+std::streamsize basic_unzip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::unzip_from_stream(
+    char_type * buffer_,
+    std::streamsize buffer_size_)
+{
+    m_zip_stream.next_out = (byte_buffer_type)buffer_;
+    m_zip_stream.avail_out = static_cast<uInt>(buffer_size_ * sizeof(char_type));
+    size_t count = m_zip_stream.avail_in;
+
+    do
+    {
+        if (m_zip_stream.avail_in == 0)
+            count = fill_input_buffer();
+
+        if (m_zip_stream.avail_in)
+            m_err = inflate(&m_zip_stream, Z_SYNC_FLUSH);
+
+        if (m_err == Z_STREAM_END)
+            inflateReset(&m_zip_stream);
+        else if (m_err < 0)
+            break;
+    }
+    while (m_zip_stream.avail_out > 0 && count > 0);
+
+    std::streamsize n_read = buffer_size_ - m_zip_stream.avail_out / sizeof(char_type);
+
+    // check if it is the end
+    if (m_zip_stream.avail_out > 0 && m_err == Z_STREAM_END)
+        put_back_from_zip_stream();
+
+    return n_read;
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+size_t basic_unzip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::fill_input_buffer()
+{
+    m_zip_stream.next_in = &(m_input_buffer[0]);
+    m_istream.read((char_type *)(&(m_input_buffer[0])),
+                   static_cast<std::streamsize>(m_input_buffer.size() / sizeof(char_type)));
+    return m_zip_stream.avail_in = m_istream.gcount() * sizeof(char_type);
+}
+
+template <typename Elem,
+          typename Tr,
+          typename ElemA,
+          typename ByteT,
+          typename ByteAT>
+void basic_unzip_streambuf<Elem, Tr, ElemA, ByteT, ByteAT>::put_back_from_zip_stream()
+{
+    if (m_zip_stream.avail_in == 0)
+        return;
+
+    m_istream.clear(std::ios::goodbit);
+    m_istream.seekg(-static_cast<int>(m_zip_stream.avail_in), std::ios_base::cur);
+
+    m_zip_stream.avail_in = 0;
+}
+
+} // namespace zlib_stream
+
+
+#endif // INCLUDE_SEQAN_STREAM_IOSTREAM_ZIP_IMPL_H_
diff --git a/seqan/stream/iostream_zutil.h b/seqan/stream/iostream_zutil.h
new file mode 100644
index 0000000..4d5ace9
--- /dev/null
+++ b/seqan/stream/iostream_zutil.h
@@ -0,0 +1,229 @@
+/* iostream_zutil.h -- internal interface and configuration of the compression library
+ * Copyright (C) 1995-2002 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+   part of the implementation of the compression library and is
+   subject to change. Applications should only use zlib.h.
+ */
+
+/* @(#) $Id: iostream_zutil.h,v 1.2 2003/06/28 15:03:05 pelikhan Exp $ */
+
+#ifndef INCLUDE_SEQAN_STREAM_IOSTREAM_ZUTIL_H_
+#define INCLUDE_SEQAN_STREAM_IOSTREAM_ZUTIL_H_
+
+//#include "zlib.h"
+
+#ifdef STDC
+#  include <stddef.h>
+#  include <string.h>
+#  include <stdlib.h>
+#endif
+
+//#define NO_ERRNO_H
+#ifdef NO_ERRNO_H
+    int errno;
+#else
+    #include <errno.h>
+#endif
+
+#ifndef local
+#  define local static
+#endif
+/* compile with -Dlocal if your debugger can't find static symbols */
+
+typedef unsigned char  uch;
+typedef uch FAR uchf;
+typedef unsigned short ush;
+typedef ush FAR ushf;
+typedef unsigned long  ulg;
+
+extern const char *z_errmsg[10]; /* indexed by 2-zlib_error */
+/* (size given to avoid silly warnings with Visual C++) */
+
+#define ERR_MSG(err) z_errmsg[Z_NEED_DICT-(err)]
+
+#define ERR_RETURN(strm,err) \
+  return (strm->msg = (char*)ERR_MSG(err), (err))
+/* To be used only when the state is known to be valid */
+
+        /* common constants */
+
+#ifndef DEF_WBITS
+#  define DEF_WBITS MAX_WBITS
+#endif
+/* default windowBits for decompression. MAX_WBITS is for compression only */
+
+#if MAX_MEM_LEVEL >= 8
+#  define DEF_MEM_LEVEL 8
+#else
+#  define DEF_MEM_LEVEL  MAX_MEM_LEVEL
+#endif
+/* default memLevel */
+
+#define STORED_BLOCK 0
+#define STATIC_TREES 1
+#define DYN_TREES    2
+/* The three kinds of block type */
+
+#define MIN_MATCH  3
+#define MAX_MATCH  258
+/* The minimum and maximum match lengths */
+
+#define PRESET_DICT 0x20 /* preset dictionary flag in zlib header */
+
+        /* target dependencies */
+
+#ifdef MSDOS
+#  define OS_CODE  0x00
+#  if defined(__TURBOC__) || defined(__BORLANDC__)
+#    if(__STDC__ == 1) && (defined(__LARGE__) || defined(__COMPACT__))
+       /* Allow compilation with ANSI keywords only enabled */
+       void _Cdecl farfree( void *block );
+       void *_Cdecl farmalloc( unsigned long nbytes );
+#    else
+#     include <alloc.h>
+#    endif
+#  else /* MSC or DJGPP */
+#    include <malloc.h>
+#  endif
+#endif
+
+#ifdef OS2
+#  define OS_CODE  0x06
+#endif
+
+#ifdef WIN32 /* Window 95 & Windows NT */
+#  define OS_CODE  0x0b
+#endif
+
+#if defined(VAXC) || defined(VMS)
+#  define OS_CODE  0x02
+#  define F_OPEN(name, mode) \
+     fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512")
+#endif
+
+#ifdef AMIGA
+#  define OS_CODE  0x01
+#endif
+
+#if defined(ATARI) || defined(atarist)
+#  define OS_CODE  0x05
+#endif
+
+#if defined(MACOS) || defined(TARGET_OS_MAC)
+#  define OS_CODE  0x07
+#  if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os
+#    include <unix.h> /* for fdopen */
+#  else
+#    ifndef fdopen
+#      define fdopen(fd,mode) NULL /* No fdopen() */
+#    endif
+#  endif
+#endif
+
+#ifdef __50SERIES /* Prime/PRIMOS */
+#  define OS_CODE  0x0F
+#endif
+
+#ifdef TOPS20
+#  define OS_CODE  0x0a
+#endif
+
+#if defined(_BEOS_) || defined(RISCOS)
+#  define fdopen(fd,mode) NULL /* No fdopen() */
+#endif
+
+#if (defined(_MSC_VER) && (_MSC_VER > 600))
+#  define fdopen(fd,type)  _fdopen(fd,type)
+#endif
+
+
+        /* Common defaults */
+
+#ifndef OS_CODE
+#  define OS_CODE  0x03  /* assume Unix */
+#endif
+
+#ifndef F_OPEN
+#  define F_OPEN(name, mode) fopen((name), (mode))
+#endif
+
+#ifndef OF
+#define OF(x) x
+#endif
+          /* functions */
+
+#ifdef HAVE_STRERROR
+   extern char *strerror OF((int));
+#  define zstrerror(errnum) strerror(errnum)
+#else
+#  define zstrerror(errnum) ""
+#endif
+
+#if defined(pyr)
+#  define NO_MEMCPY
+#endif
+#if defined(SMALL_MEDIUM) && !defined(_MSC_VER) && !defined(__SC__)
+ /* Use our own functions for small and medium model with MSC <= 5.0.
+  * You may have to use the same strategy for Borland C (untested).
+  * The __SC__ check is for Symantec.
+  */
+#  define NO_MEMCPY
+#endif
+#if defined(STDC) && !defined(HAVE_MEMCPY) && !defined(NO_MEMCPY)
+#  define HAVE_MEMCPY
+#endif
+#ifdef HAVE_MEMCPY
+#  ifdef SMALL_MEDIUM /* MSDOS small or medium model */
+#    define zmemcpy _fmemcpy
+#    define zmemcmp _fmemcmp
+#    define zmemzero(dest, len) _fmemset(dest, 0, len)
+#  else
+#    define zmemcpy memcpy
+#    define zmemcmp memcmp
+#    define zmemzero(dest, len) memset(dest, 0, len)
+#  endif
+#else
+   extern void zmemcpy  OF((Bytef* dest, const Bytef* source, uInt len));
+   extern int  zmemcmp  OF((const Bytef* s1, const Bytef* s2, uInt len));
+   extern void zmemzero OF((Bytef* dest, uInt len));
+#endif
+
+/* Diagnostic functions */
+#ifdef DEBUG
+#  include <stdio.h>
+   extern int z_verbose;
+   extern void z_error    OF((char *m));
+#  define Assert(cond,msg) {if(!(cond)) z_error(msg);}
+#  define Trace(x) {if (z_verbose>=0) fprintf x ;}
+#  define Tracev(x) {if (z_verbose>0) fprintf x ;}
+#  define Tracevv(x) {if (z_verbose>1) fprintf x ;}
+#  define Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;}
+#  define Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;}
+#else
+#  define Assert(cond,msg)
+#  define Trace(x)
+#  define Tracev(x)
+#  define Tracevv(x)
+#  define Tracec(c,x)
+#  define Tracecv(c,x)
+#endif
+
+
+typedef uLong (ZEXPORT *check_func) OF((uLong check, const Bytef *buf,
+                       uInt len));
+voidpf zcalloc OF((voidpf opaque, unsigned items, unsigned size));
+void   zcfree  OF((voidpf opaque, voidpf ptr));
+
+#define ZALLOC(strm, items, size) \
+           (*((strm)->zalloc))((strm)->opaque, (items), (size))
+#define ZFREE(strm, addr)  (*((strm)->zfree))((strm)->opaque, (voidpf)(addr))
+#define TRY_FREE(s, p) {if (p) ZFREE(s, p);}
+
+#ifdef local
+#undef local
+#endif
+
+#endif /* INCLUDE_SEQAN_STREAM_IOSTREAM_ZUTIL_H_ */
diff --git a/seqan/stream/is.h b/seqan/stream/is.h
deleted file mode 100644
index 0b5bd73..0000000
--- a/seqan/stream/is.h
+++ /dev/null
@@ -1,350 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
-// ==========================================================================
-// Collection of char checking functions
-// ==========================================================================
-
-#ifndef SEQAN_STREAM_IS_H_
-#define SEQAN_STREAM_IS_H_
-
-// ==========================================================================
-// We add documentation for cctype here for completeness.
-// ==========================================================================
-
-/*!
- * @fn isalnum
- * @headerfile <cctype>
- * @brief Check if character is alphanumeric.
- * 
- * @signature bool isalnum(c);
- * 
- * @param c The character to be checked. Type: <tt>int</tt>
- * 
- * @return bool <tt>true</tt> (non-zero) if <tt>c</tt> is alphanumeric.
- * 
- * @section Remarks
- * 
- * This is non-SeqAn, plain c and listed for completeness.
- * 
- * @see http://www.cplusplus.com/reference/clibrary/cctype/isalnum/
- * @see http://www.cppreference.com/wiki/string/character_classes
- * @see FileFormatTokenization#readAlphaNums
- * @see FileFormatTokenization#readIdentifier
- */
-
-/**
-.Function.isalnum:
-..summary:Check if character is alpha-numeric
-..cat:Input/Output
-..signature:isalnum(int c)
-..param.c:the character to be checked
-...type:nolink:$int$
-..returns:$true$(non-zero) if the check is successful and $false$ (zero) otherwise
-..remarks: This is non-seqan, plain c and listed for completeness
-..see:http://www.cplusplus.com/reference/clibrary/cctype/isalnum/
-..see:http://www.cppreference.com/wiki/string/character_classes
-..include:<cctype>
-*/
-
-/*!
- * @fn isalpha
- * @headerfile <cctype>
- * @brief Check if character is a upper or lowercase letter
- * 
- * @signature bool isalpha(c);
- * 
- * @param c The character to be checked. Type: <tt>int</tt>
- * 
- * @return bool <tt>true</tt> (non-zero) if <tt>c</tt> is a character.
- * 
- * @section Remarks
- * 
- * This is non-SeqAn, plain c and listed for completeness.
- * 
- * @see http://www.cplusplus.com/reference/clibrary/cctype/isalpha/
- * @see http://www.cppreference.com/wiki/string/character_classes
- * @see FileFormatTokenization#readLetters
- */
-
-/**
-.Function.isalpha:
-..summary:Check if character is a upper or lowercase letter
-..cat:Input/Output
-..signature:isalpha(int c)
-..param.c:the character to be checked
-...type:nolink:$int$
-..returns:$true$(non-zero) if the check is successful and $false$ (zero) otherwise
-..remarks: This is non-seqan, plain c and listed for completeness
-..see:http://www.cplusplus.com/reference/clibrary/cctype/isalpha/
-..see:http://www.cppreference.com/wiki/string/character_classes
-..include:<cctype>
-*/
-
-/*!
- * @fn isdigit
- * @headerfile <cctype>
- * @brief Check if character is a digit
- * 
- * @signature bool isdigit(c);
- * 
- * @param c The character to be checked. Type: <tt>int</tt>
- * 
- * @return bool <tt>true</tt> (non-zero) if <tt>c</tt> is a digit.
- * 
- * @section Remarks
- * 
- * This is non-SeqAn, plain c and listed for completeness.
- * 
- * @see http://www.cplusplus.com/reference/clibrary/cctype/isdigit/
- * @see http://www.cppreference.com/wiki/string/character_classes
- * @see FileFormatTokenization#readDigits
- * @see FileFormatTokenization#readFloat
- */
-
-/**
-.Function.isdigit:
-..summary:Check if character is a digit
-..cat:Input/Output
-..signature:isdigit(int c)
-..param.c:the character to be checked
-...type:nolink:$int$
-..returns:$true$(non-zero) if the check is successful and $false$ (zero) otherwise
-..remarks: This is non-seqan, plain c and listed for completeness
-..see:http://www.cplusplus.com/reference/clibrary/cctype/isdigit/
-..see:http://www.cppreference.com/wiki/string/character_classes
-..include:<cctype>
-*/
-
-/*!
- * @fn iscntrl
- * @headerfile <cctype>
- * @brief Check if character is a control character
- * 
- * @signature bool iscntrl(c);
- * 
- * @param c The character to be checked. Type: <tt>int</tt>
- * 
- * @return bool <tt>true</tt> (non-zero) if <tt>c</tt> is a control character.
- * 
- * @section Remarks
- * 
- * This is non-SeqAn, plain c and listed for completeness.
- * 
- * @see http://www.cplusplus.com/reference/clibrary/cctype/iscntrl/
- * @see http://www.cppreference.com/wiki/string/character_classes
- */
-
-/**
-.Function.iscntrl:
-..summary:Check if character is a control character
-..cat:Input/Output
-..signature:iscntrl(int c)
-..param.c:the character to be checked
-...type:nolink:$int$
-..returns:$true$(non-zero) if the check is successful and $false$ (zero) otherwise
-..remarks: This is non-seqan, plain c and listed for completeness
-..see:http://www.cplusplus.com/reference/clibrary/cctype/iscntrl/
-..see:http://www.cppreference.com/wiki/string/character_classes
-..include:<cctype>
-*/
-
-/*!
- * @fn isprint
- * @headerfile <cctype>
- * @brief Check if character is printable, i.e. not a control character
- * 
- * @signature bool isprint(c);
- * 
- * @param c The character to be checked. Type: <tt>int</tt>
- * 
- * @return bool <tt>true</tt> (non-zero) if <tt>c</tt> is a printable character.
- * 
- * @section Remarks
- * 
- * This is non-SeqAn, plain c and listed for completeness.
- * 
- * @see http://www.cplusplus.com/reference/clibrary/cctype/isprint/
- * @see http://www.cppreference.com/wiki/string/character_classes
- * @see isgraph
- */
-
-/**
-.Function.isprint:
-..summary:Check if character is printable, i.e. not a control character
-..cat:Input/Output
-..signature:isprint(int c)
-..param.c:the character to be checked
-...type:nolink:$int$
-..returns:$true$(non-zero) if the check is successful and $false$ (zero) otherwise
-..remarks: This is non-seqan, plain c and listed for completeness
-..see:http://www.cplusplus.com/reference/clibrary/cctype/isprint/
-..see:http://www.cppreference.com/wiki/string/character_classes
-..see:Function.isgraph
-..include:<cctype>
-*/
-
-/*!
- * @fn isgraph
- * @headerfile <cctype>
- * @brief Check if character is printable and not white space
- * 
- * @signature bool isgraph(c);
- * 
- * @param c The character to be checked. Type: <tt>int</tt>
- * 
- * @return bool <tt>true</tt> (non-zero) if <tt>c</tt> is a printable character.
- * 
- * @section Remarks
- * 
- * This is non-SeqAn, plain c and listed for completeness.
- * 
- * @see http://www.cplusplus.com/reference/clibrary/cctype/isgraph/
- * @see http://www.cppreference.com/wiki/string/character_classes
- * @see isprint
- * @see isspace
- * @see FileFormatTokenization#readGraphs
- * @see FileFormatTokenization#skipUntilGraph
- */
-
-/**
-.Function.isgraph:
-..summary:Check if character is printable and not white space
-..cat:Input/Output
-..signature:isgraph(int c)
-..param.c:the character to be checked
-...type:nolink:$int$
-..returns:$true$(non-zero) if the check is successful and $false$ (zero) otherwise
-..remarks: This is non-seqan, plain c and listed for completeness
-..see:http://www.cplusplus.com/reference/clibrary/cctype/isgraph/
-..see:http://www.cppreference.com/wiki/string/character_classes
-..see:Function.isprint
-..see:Function.isspace
-..include:<cctype>
-*/
-
-/*!
- * @fn isspace
- * @headerfile <cctype>
- * @brief Check if character is a white-space character
- * 
- * @signature bool isspace(c);
- * 
- * @param c The character to be checked. Type: <tt>int</tt>
- * 
- * @return bool <tt>true</tt> (non-zero) if <tt>c</tt> is a printable character.
- * 
- * @section Remarks
- * 
- * This is non-SeqAn, plain c and listed for completeness.
- * 
- * NOTE: White-Space contains more than space and tab characters, if you want to check for that, use Function.isblank
- * instead!
- * 
- * @see http://www.cplusplus.com/reference/clibrary/cctype/isspace/
- * @see http://www.cppreference.com/wiki/string/character_classes
- * @see isblank
- * @see FileFormatTokenization#readUntilWhitespace
- * @see FileFormatTokenization#skipUntilWhitespace
- * @see isgraph
- * @see FileFormatTokenization#readDna5IgnoringWhitespaces
- * @see FileFormatTokenization#skipWhitespaces
- */
-
-/**
-.Function.isspace:
-..summary:Check if character is a white-space character
-..cat:Input/Output
-..signature:isspace(int c)
-..param.c:the character to be checked
-...type:nolink:$int$
-..returns:$true$(non-zero) if the check is successful and $false$ (zero) otherwise
-..remarks: This is non-seqan, plain c and listed for completeness
-..remarks: NOTE: White-Space contains more than space and tab characters, if you want to check for that, use Function.isblank instead!
-..see:http://www.cplusplus.com/reference/clibrary/cctype/isspace/
-..see:http://www.cppreference.com/wiki/string/character_classes
-..see:Function.isblank
-..include:<cctype>
-*/
-
-/*!
- * @fn isblank
- * @headerfile seqan/stream.h
- * @brief Check if character is either ' ' or '\t'.
- * 
- * @signature bool isblank(c);
- * 
- * @param c The character to be checked. Type: <tt>int</tt>
- * 
- * @return bool <tt>true</tt> (non-zero) if <tt>c</tt> is a blank character.
- * 
- * @section Remarks
- * 
- * This is non-SeqAn, specified in POSIX and listed for completeness.
- * 
- * For visual studio, we define it ourselves.
- * 
- * @see http://www.opengroup.org/onlinepubs/009695399/functions/isblank.html
- * @see http://www.cppreference.com/wiki/string/character_classes
- * @see isspace
- * @see FileFormatTokenization#readLineStripTrailingBlanks
- * @see FileFormatTokenization#skipUntilBlank
- * @see FileFormatTokenization#skipBlanks
- * @see FileFormatTokenization#readUntilBlank
- */
-
-/**
-.Function.isblank:
-..summary:Check if character is either ' ' or '\t'
-..cat:Input/Output
-..signature:isblank(int c)
-..param.c:the character to be checked
-...type:nolink:$int$
-..returns:$true$(non-zero) if the check is successful and $false$ (zero) otherwise
-..remarks:This is non-seqan, specified in POSIX and listed for completeness.
-..remarks:For visual studio, we define it ourselves.
-..see:http://pubs.opengroup.org/onlinepubs/009695399/functions/isblank.html
-..see:http://www.cppreference.com/wiki/string/character_classes
-..see:Function.isspace
-..include:seqan/stream.h
-*/
-
-#ifdef PLATFORM_WINDOWS_VS
-// TODO(holtgrew): Adding basic/POSIX functions for OS that do not support them theirselves should go into platform.
-inline
-int isblank(int c)
-{
-    return (c == ' ') || (c == '\t');
-}
-#endif  // #ifdef PLATFORM_WINDOWS_VS
-
-#endif  // #ifndef SEQAN_STREAM_IS_H_
diff --git a/seqan/stream/iter_stream.h b/seqan/stream/iter_stream.h
new file mode 100644
index 0000000..aba25cf
--- /dev/null
+++ b/seqan/stream/iter_stream.h
@@ -0,0 +1,738 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// Our own implementation of a streambuf_iterator. We could not use the STL's
+// iterator as we need to have access to the underlying streambuf which is a
+// private member of the STL iterator.
+// ==========================================================================
+// TODO(esiragusa): tests
+
+#ifndef SEQAN_INCLUDE_SEQAN_STREAM_ITER_STREAM_H_
+#define SEQAN_INCLUDE_SEQAN_STREAM_ITER_STREAM_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags
+// ============================================================================
+
+template <typename TDirection>
+struct StreamIterator {};
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class StreamBuffer
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class StreamBuffer
+ * @headerfile <seqan/stream.h>
+ * @brief Buffer to use in stream.
+ *
+ * @signature template <typename TValue[, typenam TTraits]>
+ *            class StreamBuffer : public std::basic_streambuf<TValue, TTraits>;
+ *
+ * @tparam TValue  The value type of the stream buffer.
+ * @tparam TTraits The traits to use, defaults to <tt>std::char_traits&lt;TValue&gt;</tt>.
+ */
+
+// TODO(holtgrew): Add documentation for member functions.
+
+// Unfortunately some of the most useful members of basic_streambuf are
+// protected, so we define a subclass to cast and access them
+template <typename TValue, typename TTraits_ = std::char_traits<TValue> >
+class StreamBuffer : public std::basic_streambuf<TValue, TTraits_>
+{
+public:
+    typedef TTraits_ TTraits;
+    typedef std::basic_streambuf<TValue, TTraits_> TBase;
+
+    using TBase::eback;
+    using TBase::gptr;
+    using TBase::egptr;
+
+    using TBase::pbase;
+    using TBase::pptr;
+    using TBase::epptr;
+
+    size_t chunkSize(Input)
+    {
+        return egptr() - gptr();
+    }
+
+    size_t chunkSize(Output)
+    {
+        return epptr() - pptr();
+    }
+
+    template <typename TOffset>
+    void advanceChunk(TOffset ofs, Input)
+    {
+        this->gbump(ofs);
+    }
+
+    template <typename TOffset>
+    void advanceChunk(TOffset ofs, Output)
+    {
+        this->pbump(ofs);
+    }
+
+    void reserveChunk(Input)
+    {
+        if (gptr() == egptr())
+            this->underflow();
+    }
+
+    void reserveChunk(Output)
+    {
+        if (pptr() == epptr())
+            this->overflow(EOF);
+    }
+
+    template <typename TOffset>
+    typename std::streampos
+    seekoff(TOffset ofs, std::ios_base::seekdir way, std::ios_base::openmode which)
+    {
+        return TBase::seekoff(ofs, way, which);
+    }
+
+    template <typename TOffset, typename TDirection>
+    void goFurther(TOffset ofs, TDirection dir)
+    {
+        size_t left = chunkSize(dir);
+        if (SEQAN_LIKELY((size_t)ofs <= left))
+        {
+            advanceChunk(ofs, dir);
+            return;
+        }
+
+        while (true)
+        {
+            size_t adv = std::min((size_t)ofs, left);
+            advanceChunk(adv, dir);
+            ofs -= adv;
+            if (ofs == 0)
+                return;
+
+            if (IsSameType<TDirection, Input>::VALUE)
+                this->underflow();
+            else
+                this->overflow();
+            left = chunkSize(dir);
+
+            if (SEQAN_UNLIKELY(left == 0))
+            {
+                // if chunking isn't available try to seek
+                typename TTraits::pos_type res = seekoff(ofs,
+                                                         std::ios_base::cur,
+                                                         (IsSameType<TDirection, Input>::VALUE)? std::ios_base::in: std::ios_base::out);
+
+                // if seek doesn't work manually skip characters (when reading)
+                if (res == typename TTraits::pos_type(typename TTraits::off_type(-1)))
+                {
+                    if (IsSameType<TDirection, Input>::VALUE)
+                    {
+                        for (; ofs != 0; --ofs)
+                            this->sbumpc();
+                    }
+                    if (IsSameType<TDirection, Output>::VALUE)
+                    {
+                        for (; ofs != 0; --ofs)
+                            this->sputc('\0');
+                    }
+                }
+                return;
+            }
+        }
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Class StreamIterator
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class StreamIterator
+ * @extends Iter
+ * @brief Abstract base class for input and output stream iterators.
+ *
+ * @signature template <typename TStream, typename TDirection>
+ *            class Iter<TStream, StreamIterator<TDirection> >;
+ *
+ * @tparam TStream    The @link StreamConcept @endlink to iterate over.
+ * @tparam TDirection The iterator direction, one of the @link DirectionTags @endlink.
+ */
+
+// ----------------------------------------------------------------------------
+// Class Input StreamIterator
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class InputStreamIterator Input StreamIterator
+ * @extends StreamIterator
+ * @brief @link Iter @endlink specialiazion for reading from @link StreamConcept streams @endlink.
+ *
+ * @signature template <typename TStream>
+ *            class Iter<TStream, StreamIterator<Input> >;
+ *
+ * @tparam TStream    The @link StreamConcept @endlink to iterate over.
+ */
+
+template <typename TStream>
+class Iter<TStream, StreamIterator<Input> >
+{
+public:
+    typedef typename Value<TStream>::Type   TValue;
+    typedef std::basic_istream<TValue>      TIStream;
+    typedef std::basic_streambuf<TValue>    TBasicBuffer;
+    typedef StreamBuffer<TValue>            TStreamBuffer;
+
+    TStreamBuffer *streamBuf;
+
+    /*!
+     * @fn InputStreamIterator::Iter
+     * @brief The constructors.
+     *
+     * @signature Iter::Iter();
+     * @signature Iter::Iter(stream);
+     * @signature Iter::Iter(streamBuffer);
+     *
+     * @param[in] stream    The <tt>TStream</tt> to read from.
+     * @param[in] streamBuf A @link StreamBuffer @endlink to read from.
+     *
+     * Allows default construction, construction from stream, as well as from a @link StreamBuffer @endlink.
+     */
+    Iter() : streamBuf()
+    {}
+
+    Iter(TIStream & stream) :
+        streamBuf(static_cast<StreamBuffer<TValue> *>(stream.rdbuf()))
+    {
+        stream.exceptions(std::ios_base::badbit);
+    }
+
+    Iter(TStreamBuffer * buf) :
+        streamBuf(static_cast<StreamBuffer<TValue> *>(buf))
+    {}
+};
+
+// ----------------------------------------------------------------------------
+// Class StreamIterator
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class OutputStreamIterator Output StreamIterator
+ * @extends StreamIterator
+ * @brief @link Iter @endlink specialiazion for writing to @link StreamConcept streams @endlink.
+ *
+ * @signature template <typename TStream>
+ *            class Iter<TStream, StreamIterator<Output> >;
+ *
+ * @tparam TStream    The @link StreamConcept @endlink to iterate over.
+ */
+template <typename TStream>
+class Iter<TStream, StreamIterator<Output> >
+{
+public:
+    typedef typename Value<TStream>::Type   TValue;
+    typedef std::basic_ostream<TValue>      TOStream;
+    typedef std::basic_streambuf<TValue>    TBasicBuffer;
+    typedef StreamBuffer<TValue>            TStreamBuffer;
+
+    TStreamBuffer *streamBuf;
+
+    /*!
+     * @fn Iter::Iter
+     * @brief Constructor.
+     *
+     * @signature Iter::Iter()
+     * @signature Iter::Iter(stream)
+     * @signature Iter::Iter(streamBuf)
+     *
+     * @param[in] stream    The <tt>TStream</tt> to write to.
+     * @param[in] streamBuf A @link StreamBuffer @endlink to write to.
+     *
+     * Allows default construction, construction from stream, as well as from a @link StreamBuffer @endlink.
+     */
+    Iter() : streamBuf()
+    {}
+
+    Iter(TOStream & stream):
+        streamBuf(static_cast<StreamBuffer<TValue> *>(stream.rdbuf()))
+    {
+        stream.exceptions(std::ios_base::badbit);
+    }
+
+    Iter(TBasicBuffer *buf):
+        streamBuf(static_cast<StreamBuffer<TValue> *>(buf))
+    {}
+
+    template <typename TValue2>
+    TValue2 & operator=(TValue2 &val)
+    {
+        setValue(*this, val);
+        return val;
+    }
+
+    template <typename TValue2>
+    TValue2 const & operator=(TValue2 const &val)
+    {
+        setValue(*this, val);
+        return val;
+    }
+};
+
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction Chunk
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn StreamBuffer#Chunk
+ * @brief Return chunk type for StreamBuffer
+ *
+ * @signature Chunk<TStreamBuffer>::Type;
+ *
+ * @tparam TStreamBuffer The StreamBuffer to query for its chunk type.
+ * @return Type          The chunk type of the stream buffer.
+ */
+
+template <typename TValue, typename TTraits>
+struct Chunk<StreamBuffer<TValue, TTraits> >
+{
+    typedef Range<TValue*> Type;
+};
+
+template <typename TStream, typename TDirection>
+struct Chunk<Iter<TStream, StreamIterator<Tag<TDirection> > > >:
+    Chunk<typename Iter<TStream, StreamIterator<Tag<TDirection> > >::TStreamBuffer> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Reference
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn StreamBuffer#Reference
+ * @brief Return reference for StreamBuffer.
+ *
+ * @signature Reference<TStreamBuffer>::Type;
+ *
+ * @tparam TStreamBuffer The StreamBuffer to query for its reference type.
+ * @return Type          The reference type of the stream buffer.
+ */
+
+template <typename TStream>
+struct Reference<Iter<TStream, StreamIterator<Input> > >:
+    Value<Iter<TStream, StreamIterator<Input> > > {};
+
+template <typename TStream>
+struct Reference<Iter<TStream, StreamIterator<Input> > const>:
+    Value<Iter<TStream, StreamIterator<Input> > > {};
+
+template <typename TStream>
+struct Reference<Iter<TStream, StreamIterator<Output> > >
+{
+    typedef Iter<TStream, StreamIterator<Output> > Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction GetValue
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn StreamBuffer#GetValue
+ * @brief Return get value for StreamBuffer.
+ *
+ * @signature GetValue<TStreamBuffer>::Type;
+ *
+ * @tparam TStreamBuffer The StreamBuffer to query for its get value type.
+ * @return Type          The get value type of the stream buffer.
+ */
+
+template <typename TStream>
+struct GetValue<Iter<TStream, StreamIterator<Input> > >:
+    Reference<Iter<TStream, StreamIterator<Input> > const> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn StreamBuffer#Position
+ * @brief Return position for StreamBuffer.
+ *
+ * @signature Position<TStreamBuffer>::Type;
+ *
+ * @tparam TStreamBuffer The StreamBuffer to query for its position type.
+ * @return Type          The position type of the stream buffer.
+ */
+
+template <typename TStream, typename TDirection>
+struct Position<Iter<TStream, StreamIterator<TDirection> > > : Position<TStream> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Difference
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn StreamBuffer#Difference
+ * @brief Return difference for StreamBuffer.
+ *
+ * @signature Difference<TStreamBuffer>::Type;
+ *
+ * @tparam TStreamBuffer The StreamBuffer to query for its difference type.
+ * @return Type          The difference type of the stream buffer.
+ */
+
+template <typename TStream, typename TDirection>
+struct Difference<Iter<TStream, StreamIterator<TDirection> > > : Difference<TStream> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Size
+// ----------------------------------------------------------------------------
+
+/*!
+ * @mfn StreamBuffer#Size
+ * @brief Return size for StreamBuffer.
+ *
+ * @signature Size<TStreamBuffer>::Type;
+ *
+ * @tparam TStreamBuffer The StreamBuffer to query for its size type.
+ * @return Type          The size type of the stream buffer.
+ */
+
+template <typename TStream, typename TDirection>
+struct Size<Iter<TStream, StreamIterator<TDirection> > > : Size<TStream> {};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function directionIterator()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn StreamConcept#directionIterator
+ * @brief Returns direction iterator for Stream.
+ *
+ * @signature TDirIter directionIterator(stream, dirTag);
+ *
+ * @param[in] stream The @link StreamConcept @endlink object to compute iterator for.
+ * @param[in] dirTag Direction tag, one of the @link DirectionTags @endlink.
+ */
+
+template <typename TStream, typename TDirection>
+inline SEQAN_FUNC_ENABLE_IF(Is<StreamConcept<TStream> >, Iter<TStream, StreamIterator<TDirection> >)
+directionIterator(TStream &stream, TDirection const &)
+{
+    return Iter<TStream, StreamIterator<TDirection> >(stream);
+}
+
+/*!
+ * @fn ContainerConcept#directionIterator
+ * @brief Returns direction iterator for a container.
+ *
+ * @signature TDirIter directionIterator(streamBuf, dirTag);
+ *
+ * @param[in] streamBuf The @link ContainerConcept container @endlink object to compute iterator for.
+ * @param[in] dirTag    Direction tag, one of the @link DirectionTags @endlink.
+ *
+ * @return TDirIter The resulting @link ContainerConcept#DirectionIterator @endlink.
+ */
+
+template <typename TContainer, typename TDirection>
+inline SEQAN_FUNC_DISABLE_IF(Is<StreamConcept<TContainer> >, typename Iterator<TContainer, Rooted>::Type)
+directionIterator(TContainer &cont, TDirection const &)
+{
+    return begin(cont, Rooted());
+}
+
+// ----------------------------------------------------------------------------
+// Function reserveChunk()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn StreamIterator#reserveChunk
+ * @brief Reserve a chunk in the host of the StreamIterator
+ *
+ * @signature void reserveChunk(iter, len, dirTag);
+ *
+ * @param[in] iter   The @link StreamIterator @endlink object to reserve chunks for.
+ * @param[in] len    The length of the chunk to reserve.
+ * @param[in] dirTag Direction tag, one of @link DirectionTags#Input Input @endlink and @link
+ *                   DirectionTags#Input Output @endlink .
+ */
+
+template <typename TStream, typename TDirection, typename TSize>
+inline void reserveChunk(Iter<TStream, StreamIterator<TDirection> > &iter, TSize, Input dir)
+{
+    iter.streamBuf->reserveChunk(dir);
+}
+
+template <typename TStream, typename TDirection, typename TSize>
+inline void reserveChunk(Iter<TStream, StreamIterator<TDirection> > &iter, TSize, Output dir)
+{
+    iter.streamBuf->reserveChunk(dir);
+}
+
+// ----------------------------------------------------------------------------
+// Function advanceChunk()
+// ----------------------------------------------------------------------------
+
+// TODO(holtgrew): Documentation missing below here.
+
+template <typename TStream, typename TDirection, typename TSize>
+inline void advanceChunk(Iter<TStream, StreamIterator<TDirection> > &iter, TSize size)
+{
+    iter.streamBuf->advanceChunk(size, TDirection());
+}
+
+// ----------------------------------------------------------------------------
+// Function getChunk()
+// ----------------------------------------------------------------------------
+
+// StreamBuffer
+template <typename TChunk, typename TValue, typename TTraits>
+inline void
+getChunk(TChunk &result, StreamBuffer<TValue, TTraits> &buf, Input)
+{
+    return assignRange(result, buf.gptr(), buf.egptr());
+}
+
+template <typename TChunk, typename TValue, typename TTraits>
+inline void
+getChunk(TChunk &result, StreamBuffer<TValue, TTraits> &buf, Output)
+{
+    return assignRange(result, buf.pptr(), buf.epptr());
+}
+
+// StreamIterator
+template <typename TChunk, typename TStream, typename TDirection>
+inline void
+getChunk(TChunk &result, Iter<TStream, StreamIterator<Tag<TDirection> > > &iter, Tag<TDirection>)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    getChunk(result, *iter.streamBuf, Tag<TDirection>());
+}
+
+// ----------------------------------------------------------------------------
+// Function value() - Input
+// ----------------------------------------------------------------------------
+
+template <typename TStream>
+inline typename Reference<Iter<TStream, StreamIterator<Input> > >::Type
+value(Iter<TStream, StreamIterator<Input> > &iter)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    return iter.streamBuf->sgetc();
+}
+template <typename TStream>
+inline typename Reference<Iter<TStream, StreamIterator<Input> > const>::Type
+value(Iter<TStream, StreamIterator<Input> > const &iter)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    return iter.streamBuf->sgetc();
+}
+
+// ----------------------------------------------------------------------------
+// Function value() - Ouput
+// ----------------------------------------------------------------------------
+
+template <typename TStream>
+inline Iter<TStream, StreamIterator<Output> > &
+value(Iter<TStream, StreamIterator<Output> > & iter)
+{
+    return iter;
+}
+template <typename TStream>
+inline Iter<TStream, StreamIterator<Output> > const &
+value(Iter<TStream, StreamIterator<Output> > const & iter)
+{
+    return iter;
+}
+
+// ----------------------------------------------------------------------------
+// Function setValue()
+// ----------------------------------------------------------------------------
+
+template <typename TStream, typename TValue>
+inline void
+setValue(Iter<TStream, StreamIterator<Output> > & iter, TValue const &val)
+{
+    return setValue(const_cast<Iter<TStream, StreamIterator<Output> > const &>(iter), val);
+}
+template <typename TStream, typename TValue>
+inline void
+setValue(Iter<TStream, StreamIterator<Output> > const & iter, TValue const &val)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    iter.streamBuf->sputc((typename Value<Iter<TStream, StreamIterator<Output> > >::Type)val);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeValue()
+// ----------------------------------------------------------------------------
+
+// streams
+template <typename TContainer, typename TValue>
+inline void writeValue(Iter<TContainer, StreamIterator<Output> > &iter, TValue val)
+{
+    setValue(iter, val);
+    //goNext(iter);     // implicitly done by setValue above
+}
+
+// ----------------------------------------------------------------------------
+// Function goNext()
+// ----------------------------------------------------------------------------
+
+template <typename TStream>
+inline void
+goNext(Iter<TStream, StreamIterator<Input> > & iter)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    iter.streamBuf->sbumpc();
+}
+
+template <typename TStream>
+inline void
+goNext(Iter<TStream, StreamIterator<Output> > &)
+{
+    // We do nothing here, as the stream is advanced by sputc whenever you assign
+    // a value to the iterator with *iter= or setValue
+}
+
+// we intentionally don't return an iterator here, as the copied iterator wouldn't
+// point to the position before the increment.
+template <typename TContainer, typename TSpec>
+inline void
+operator++(Iter<TContainer, StreamIterator<Input> > & iter, int)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    iter.streamBuf->sbumpc();
+}
+
+// ----------------------------------------------------------------------------
+// Function goFurther()
+// ----------------------------------------------------------------------------
+
+template <typename TStream, typename TOffset, typename TDirection>
+inline void
+goFurther(Iter<TStream, StreamIterator<TDirection> > &iter, TOffset ofs)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    iter.streamBuf->goFurther(ofs, TDirection());
+}
+
+// ----------------------------------------------------------------------------
+// Function position()
+// ----------------------------------------------------------------------------
+
+template <typename TStream, typename TDirection>
+inline typename Position<Iter<TStream, StreamIterator<TDirection> > const>::Type
+position(Iter<TStream, StreamIterator<TDirection> > const & iter)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    return iter.streamBuf->pubseekoff(0, std::ios_base::cur,
+                                      (IsSameType<TDirection, Input>::VALUE)? std::ios_base::in: std::ios_base::out);
+}
+
+// ----------------------------------------------------------------------------
+// Function setPosition()
+// ----------------------------------------------------------------------------
+
+template <typename TStream, typename TDirection, typename TPosition>
+inline void
+setPosition(Iter<TStream, StreamIterator<TDirection> > const & iter, TPosition pos)
+{
+    SEQAN_ASSERT(iter.streamBuf != NULL);
+    iter.streamBuf->pubseekpos(pos, (IsSameType<TDirection, Input>::VALUE)? std::ios_base::in: std::ios_base::out);
+}
+
+// ----------------------------------------------------------------------------
+// Function atEnd()
+// ----------------------------------------------------------------------------
+
+template <typename TStream>
+inline bool
+atEnd(Iter<TStream, StreamIterator<Input> > const & iter)
+{
+    typedef typename Value<Iter<TStream, StreamIterator<Input> > >::Type TValue;
+    typedef StreamBuffer<TValue> TStreamBuffer;
+
+    if (SEQAN_UNLIKELY(iter.streamBuf == NULL))
+    {
+        return true;
+    }
+    else
+    {
+        TStreamBuffer *buf = static_cast<TStreamBuffer*>(iter.streamBuf);
+        if (SEQAN_LIKELY(buf->gptr() < buf->egptr()))
+            return false;
+        else
+            return TStreamBuffer::TTraits::eq_int_type(buf->sgetc(), TStreamBuffer::TTraits::eof());
+    }
+}
+
+template <typename TStream>
+inline bool
+atEnd(Iter<TStream, StreamIterator<Output> > const & iter)
+{
+    typedef typename Value<Iter<TStream, StreamIterator<Input> > >::Type TValue;
+    typedef StreamBuffer<TValue> TStreamBuffer;
+
+    if (SEQAN_UNLIKELY(iter.streamBuf == NULL))
+    {
+        return true;
+    }
+    else
+    {
+        TStreamBuffer *buf = static_cast<TStreamBuffer*>(iter.streamBuf);
+        if (SEQAN_LIKELY(buf->pptr() < buf->epptr()))
+            return false;
+        else
+            return TStreamBuffer::TTraits::eq_int_type(buf->overflow(), TStreamBuffer::TTraits::eof());
+    }
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_STREAM_ITER_STREAM_H_
diff --git a/seqan/stream/lexical_cast.h b/seqan/stream/lexical_cast.h
index 9a6d260..2ad58d4 100644
--- a/seqan/stream/lexical_cast.h
+++ b/seqan/stream/lexical_cast.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,193 +29,257 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
+// ==========================================================================
+// String => Numerical conversions
 // ==========================================================================
-// casts for reading different types from strings
-// ==========================================================================+
 
 #ifndef SEQAN_STREAM_LEXICAL_CAST_H
 #define SEQAN_STREAM_LEXICAL_CAST_H
 
 namespace seqan {
 
+// ============================================================================
+// Exceptions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Exception BadLexicalCast
+// ----------------------------------------------------------------------------
+
 /*!
- * @fn lexicalCast2
- * @headerfile seqan/stream.h
- * @brief Cast from a String-type to a numerical type
- * 
- * @signature bool lexicalCast2(target, source);
- * 
- * @param[out] target Object to hold result of cast.
- * @param[in]  source The string to be read from.  Type: @link SequenceConcept @endlink.
-
- * @return bool <tt>true</tt> if cast was successful, <tt>false</tt> otherwise.
- * 
- * @section Remarks
- * 
- * Uses istringstream internally, so right now "123foobar" will be succesfully cast to an int of 123.
- * 
- * @section Examples
- * 
- * Using lexicalCast2 is straightforward and we can detect errors.
- * 
- * @code{.cpp}
- * unsigned u = 0;
- * int i = 0;
- * double = 0;
- * bool success = false;
- *  
- * success = lexicalCast2(u, "3");      // => success is true, u is 3.
- * success = lexicalCast2(u, "-3");     // => success is false, u is undefined.
- * success = lexicalCast2(i, "-3");     // => success is true, i is -3.
- * success = lexicalCast2(d, "-3.99");  // => success is true, d is -3.99.
- * @endcode
+ * @class BadLexicalCast
+ * @extends ParseError
+ * @headerfile <seqan/stream.h>
+ * @brief Throw on bad lexical casts.
  *
- * @see lexicalCast
- */
-
-/**
-.Function.lexicalCast2
-..cat:Input/Output
-..summary:Cast from a String-type to a numerical type
-..signature:lexicalCast2(TTarget & target, TSource const & source)
-..signature:lexicalCast2(TTarget & target, String<TValue, TSpec> const & source)
-..param.target:Object to hold result of cast
-...type:nolink:$int$
-...type:nolink:$unsigned int$
-...type:nolink:$double$
-...type:nolink:or similar
-..param.source:The string to be read from
-...type:Shortcut.CharString
-...type:nolink:char[]
-...type:nolink:std::string
-...type:nolink:or similar
-..returns:$true$ if cast was successful, $false$ otherwise
-...type:nolink:$bool$
-..remarks:uses istringstream internally, so right now "123foobar" will be
-succesfully cast to an int of 123
-..include:seqan/stream.h
-..see:Function.lexicalCast
-..example.text:Using lexicalCast2 is straightforward and we can detect errors.
-..example.code:
-unsigned u = 0;
-int i = 0;
-double = 0;
-bool success = false;
-
-success = lexicalCast2(u, "3");      // => success is true, u is 3.
-success = lexicalCast2(u, "-3");     // => success is false, u is undefined.
-success = lexicalCast2(i, "-3");     // => success is true, i is -3.
-success = lexicalCast2(d, "-3.99");  // => success is true, d is -3.99.
+ * @signature struct BadLexicalCast : ParseError;
  */
 
-template < typename TTarget, typename TSource >
-inline bool
-lexicalCast2(TTarget & target, TSource const & source)
+struct BadLexicalCast : ParseError
 {
-    std::stringstream str;
-    str << source;
-    str.seekg(0);
-    return bool(str >> target);
-}
+    /*!
+     * @fn BadLexicalCast::BadLexicalCast
+     * @brief Constructor.
+     *
+     * @signature BadLexicalCast::BadLexicalCast(target, source);
+     *
+     * @param[in] target Target value, used as a tag only.
+     * @param[in] source Source value, a @link StringConcept sequence @endlink of <tt>char</tt>.
+     */
+    template <typename TTarget, typename TSource>
+    BadLexicalCast(TTarget const & target, TSource const & source) :
+        ParseError(std::string("Unable to convert '") +
+                   std::string(begin(source, Standard()), end(source, Standard())) +
+                   "' into " + toCString(Demangler<TTarget>(target)) + ".")
+    {}
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function lexicalCast()
+// ----------------------------------------------------------------------------
 
 /*!
  * @fn lexicalCast
  * @headerfile <seqan/stream.h>
- * @brief Cast from a String-type to a numerical type
- * 
- * @signature template <typename TTarget>
- *            TTarget lexicalCast<TTarget>(source);
- * 
- * @tparam TTarget Target type to cast to.
+ * @brief Interpret the character sequence in <tt>source</tt> as the numeric value and write to <tt>target</tt>.
+ *
+ * @signature bool lexicalCast(target, source);
+ * @signature TTarget lexicalCast<TTarge>(source)  // throws BadLexicalCast
+ *
+ * @param[out] target  A numeric value to write to.
+ * @param[in]  source  The source sequence of <tt>char</tt> to convert.
+ * @tparam     TTarget The type to use for lexical cast of <tt>source</tt>.
+ *
+ * @throw BadLexicalCast The second variant throws @link BadLexicalCast @endlink in the case that casting failed.
+ *
+ * @return bool <tt>true</tt> if successful and <tt>false</tt> if there was a problem with the cast.
  *
- * @param[in] source The string to be read from.  Type: @link SequenceConcept @endlink.
- * 
- * @return TTarget Value of Type TTarget with cast contents of source.
- * 
- * @section Remarks
- * 
- * Return value undefined if casting fails, see @link lexicalCast2 @endlink for a more robust variant.
- * 
- * This function uses <tt>std::istringstream</tt> internally, so right now "123foobar" will be succesfully cast to an
- * int of 123.
- * 
  * @section Examples
- * 
- * Using <tt>lexicalCast<>()</tt> is easy but not as robust as @link lexicalCast2 @endlink: We cannot detect parsing or
- * conversion errors.
- * 
- * @code{.cpp}
- * unsigned u = 0;
- * int i = 0;
- * double = 0;
- * bool success = false;
- *  
- * u = lexicalCast<unsigned>( "3");   // => u is 3.
- * u = lexicalCast<unsigned>("-3");   // => u is undefined.
- * i = lexicalCast<int>("-3");        // => i is -3.
- * d = lexicalCast<double>("-3.99");  // => d is -3.99.
- * @endcode
  *
- * @see lexicalCast2
+ * The following example shows some lexical cast from various sequence types to numbers.
+ *
+ * @include demos/dox/stream/lexical_cast.cpp
+ *
+ * @include demos/dox/stream/lexical_cast.cpp.stdout
  */
 
-/**
-.Function.lexicalCast
-..cat:Input/Output
-..summary:Cast from a String-type to a numerical type
-..signature:lexicalCast<TTarget>(TSource const & source)
-..signature:lexicalCast<TTarget>(String<TValue, TSpec> const & source)
-..param.source:The string to be read from
-...type:Shortcut.CharString
-...type:nolink:char[]
-...type:nolink:std::string
-...type:nolink:or similar
-..param.TTarget:Type to be casted to
-...type:nolink:$int$
-...type:nolink:$unsigned int$
-...type:nolink:$double$
-...type:nolink:or similar
-..returns:Value of Type TTarget with casted contents of source
-...type:nolink:TTarget
-..remarks:Return value undefined if casting fails, see @Function.lexicalCast2@ for a more robust variant.
-..remarks:This function uses $std::istringstream$ internally, so right now "123foobar" will be
-succesfully cast to an int of 123.
-..include:seqan/stream.h
-..see:Function.lexicalCast2
-..example.text:Using $lexicalCast<>()$ is easy but not as robust as @Function.lexicalCast2@: We cannot detect parsing or conversion errors.
-..example.code:
-unsigned u = 0;
-int i = 0;
-double = 0;
-bool success = false;
-
-u = lexicalCast<unsigned>( "3");   // => u is 3.
-u = lexicalCast<unsigned>("-3");   // => u is undefined.
-i = lexicalCast<int>("-3");        // => i is -3.
-d = lexicalCast<double>("-3.99");  // => d is -3.99.
- */
+// single char
+template <typename TSource>
+inline bool
+lexicalCast(char & target, TSource const & source)
+{
+    if (SEQAN_UNLIKELY(length(source) != 1))
+        return false;
+    target = getValue(begin(source, Standard()));
+    return true;
+}
+
+// (weese:) we have to implement our own cast functions as not all sources support toCString()
+
+// Generic version for unsigned integers.
+template <typename TInteger, typename TSource>
+inline SEQAN_FUNC_ENABLE_IF(Is<UnsignedIntegerConcept<TInteger> >, bool)
+lexicalCast(TInteger & target, TSource const & source)
+{
+    typedef typename Iterator<TSource const, Standard>::Type TIter;
+
+    TIter it = begin(source, Standard());
+    TIter itEnd = end(source, Standard());
+
+    if (SEQAN_UNLIKELY(it == itEnd))
+        return false;
+
+    TInteger val = 0;
+    do
+    {
+        unsigned char digit = *it++ - '0';
+
+        // invalid digit detection
+        if (SEQAN_UNLIKELY(digit > 9))
+            return false;
+
+        // overflow detection
+        if (SEQAN_UNLIKELY(val > MaxValue<TInteger>::VALUE / 10))
+            return false;
+        val *= 10;
+
+        // overflow detection
+        val += digit;
+        if (SEQAN_UNLIKELY(val < digit))
+            return false;
+    }
+    while (it != itEnd);
+    target = val;
+    return true;
+}
+
+// Generic version for signed integers.
+template <typename TInteger, typename TSource>
+inline SEQAN_FUNC_ENABLE_IF(Is<SignedIntegerConcept<TInteger> >, bool)
+lexicalCast(TInteger & target, TSource const & source)
+{
+    typedef typename Iterator<TSource const, Standard>::Type TIter;
+
+    TIter it = begin(source, Standard());
+    TIter itEnd = end(source, Standard());
+
+    if (SEQAN_UNLIKELY(it == itEnd))
+        return false;
+
+    TInteger val = 0;
+
+    if (*it != '-')
+    {
+        do
+        {
+            unsigned char digit = *it++ - '0';
+
+            // invalid digit detection
+            if (SEQAN_UNLIKELY(digit > 9))
+                return false;
+
+            // overflow detection
+            if (SEQAN_UNLIKELY(val > MaxValue<TInteger>::VALUE / 10))
+                return false;
+            val *= 10;
+
+            // overflow detection
+            val += digit;
+            if (SEQAN_UNLIKELY(val < digit))
+                return false;
+        }
+        while (it != itEnd);
+    }
+    else
+    {
+        if (SEQAN_UNLIKELY(++it == itEnd))
+            return false;
+        do
+        {
+            unsigned char digit = *it++ - '0';
+
+            // invalid digit detection
+            if (SEQAN_UNLIKELY(digit > 9))
+                return false;
+
+            // overflow detection
+            if (SEQAN_UNLIKELY(val < MinValue<TInteger>::VALUE / 10))
+                return false;
+            val *= 10;
+
+            // overflow detection
+            if (SEQAN_UNLIKELY(MinValue<TInteger>::VALUE - val > -(TInteger)digit))
+                return false;
+            val -= digit;
+        }
+        while (it != itEnd);
+    }
+    target = val;
+    return true;
+}
+
+// Specialization for float.
+
+template <typename TSource>
+inline bool lexicalCast(float & target, TSource const & source)
+{
+    int offset;
+    return (sscanf(toCString(source), "%g%n", &target, &offset) == 1) &&
+           (static_cast<typename Size<TSource>::Type>(offset) == length(source));
+}
+
+// Specialization for double
+template <typename TSource>
+inline bool lexicalCast(double & target, TSource const & source)
+{
+    int offset;
+    return (sscanf(toCString(source), "%lg%n", &target, &offset) == 1) &&
+           (static_cast<typename Size<TSource>::Type>(offset) == length(source));
+}
 
 template <typename TTarget, typename TSource>
-inline TTarget
-lexicalCast(TSource const & source)
+inline TTarget lexicalCast(TSource const & source)
 {
-    TTarget dest;
-    bool b = lexicalCast2(dest, source);
-    SEQAN_ASSERT(b);
-    (void)b;
-    return dest;
+    TTarget target;
+    if (!lexicalCast(target, source))
+        throw BadLexicalCast(target, source);
+    return target;
 }
 
-template < typename TTarget, typename TValue, typename TSpec>
-inline TTarget
-lexicalCast(String<TValue, TSpec> const & source)
+// ----------------------------------------------------------------------------
+// Function lexicalCastWithException()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn lexicalCastWithException
+ * @headerfile <seqan/stream.h>
+ * @brief Interpret the character sequence in <tt>source</tt> as the numeric value and write to <tt>target</tt>.
+ *
+ * @signature void lexicalCastWithException(target, source);
+ *
+ * @param[out] target  A numeric value to write to.
+ * @param[in]  source  The source sequence of <tt>char</tt> to convert.
+ *
+ * @throw BadLexicalCast in the case that casting failed
+ *
+ * See @link lexicalCast @endlink for examples.
+ */
+
+template <typename TTarget, typename TSource>
+inline void lexicalCastWithException(TTarget & target, TSource const & source)
 {
-    TTarget dest;
-    bool b = lexicalCast2(dest, source);
-    SEQAN_ASSERT(b);
-    (void)b;
-    return dest;
+    if (!lexicalCast(target, source))
+        throw BadLexicalCast(target, source);
 }
 
 }
diff --git a/seqan/stream/read.h b/seqan/stream/read.h
deleted file mode 100644
index b93e7a6..0000000
--- a/seqan/stream/read.h
+++ /dev/null
@@ -1,131 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
-// ==========================================================================
-// Main File for Record and Document-Reading. Contains only doc right now.
-// ==========================================================================
-
-
-#ifndef SEQAN_STREAM_READ_H_
-#define SEQAN_STREAM_READ_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// TODO(holtgrew): These functions do not really belong to the RecordReader concept.
-
-/*!
- * @fn RecordReader#readRecord
- * @brief Reads one records (e.g. a single DNA sequence and its meta data) from a @link StreamConcept @endlink by the
- *        means of a @link RecordReader @endlink.
- *
- * @signature int readRecord(OUTPUT, reader, tag);
- *
- * @param[out]    OUTPUT A format-specific value for one record, can also be multiple parameters.
- * @param[in,out] reader A @link RecordReader @endlink to read from.
- * @param[in]     tag    A format-specific tag.
- *
- * @return int A return code.  0 on success, non-0 value on error.
- *
- * @section Remarks
- *
- * If not noted otherwise, only a Single-Pass implementation is available for the given format.
- */
-
-/**
-.Function.readRecord
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:reads one record (e.g. a single DNA-sequence and its meta data) from a @Concept.StreamConcept@, by the means of @Class.RecordReader@
-..signature:readRecord(<format specific>, TRecordReader & reader, TTag const &)
-..param.<format specific>: possibly multiple fields (e.g. meta and sequence)
-..param.reader:The reader object to read from
-...type:Class.RecordReader
-..param.TTag:The file format tag
-..remarks: If not noted otherwise, only a Single-Pass implementation is available for a the given format
-..see:Function.read2
-..include:seqan/stream.h
-*/
-
-/*!
- * @fn RecordReader#read
- * @brief Reads an entire document from a @link StreamConcept @endlink by the means of a @link RecordReader @endlink.
- *
- * @signature int read2(OUTPUT, reader, tag);
- *
- * @param[out]    OUTPUT A format-specific value with records, can also be multiple parameters.
- * @param[in,out] reader A @link RecordReader @endlink to read from.
- * @param[in]     tag    A format-specific tag.
- *
- * @return int A return code.  0 on success, non-0 value on error.
- *
- * @section Remarks
- *
- * If not noted otherwise, only a Single-Pass implementation is available for the given format.
- */
-
-/**
-.Function.read2
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:reads an entire document from a @Concept.StreamConcept@, by the means of @Class.RecordReader@
-..signature:read2(<format specific>, TRecordReader & reader, TTag const &)
-..param.<format specific>: possibly multiple StringSets (e.g. of meta and sequences)
-..param.reader:The reader object to read from
-...type:Class.RecordReader
-..param.TTag:The file format tag
-..status:Should be renamed to "read" once the old IO-Code is removed
-..remarks: This is only supported for Double-Pass IO. If you cannot use Double-Pass IO (e.g. when you cannot seek on the stream), loop over @Function.readRecord@ instead.
-..remarks:If not noted otherwise an especially efficient version of the function is used if all StringSets are specialized as @Spec.ConcatDirect@ -StringSets.
-..include:seqan/stream.h
-..see:Class.RecordReader
-..see:Function.readRecord
-*/
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_READ_FASTA_FASTQ_H_
diff --git a/seqan/stream/read_auto_format.h b/seqan/stream/read_auto_format.h
deleted file mode 100644
index 5a5f561..0000000
--- a/seqan/stream/read_auto_format.h
+++ /dev/null
@@ -1,238 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// This header contains overloads for read2() and readRecord() that allow
-// them to be used for automatic format detection with sequence files.
-// ==========================================================================
-
-// (weese:)
-// Why did you introduce int i in every function?
-// That adds complexity and requires an additional _x() helper function
-// for each x() function. Please have a look at assignSeq() in file/file_format_mmap.h
-
-#ifndef SEQAN_STREAM_RECORD_READER_AUTO_FORMAT_H_
-#define SEQAN_STREAM_RECORD_READER_AUTO_FORMAT_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-enum ReadAutoFormatErrorCodes_
-{
-    IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT = 2049
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function read2
-// ----------------------------------------------------------------------------
-
-// For read2(metas, seqs, quals, reader, TTagSelector/AutoSeqStreamFormat).
-
-template <typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec, typename TQualString,
-          typename TQualSpec, typename TRecordReader>
-int _read2(StringSet<TIdString, TIdSpec> & /*metas*/,
-           StringSet<TSeqString, TSeqSpec> & /*seqs*/,
-           StringSet<TQualString, TQualSpec> & /*quals*/,
-           TRecordReader & /*reader*/,
-           TagSelector<void> const & /*tagSelector*/,
-           int i)
-{
-    SEQAN_ASSERT_EQ(i, -1);
-    (void)i;  // Only used for assertion.
-    return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-}
-
-template <typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec, typename TQualString,
-          typename TQualSpec, typename TRecordReader, typename TTagList>
-int _read2(StringSet<TIdString, TIdSpec> & metas,
-           StringSet<TSeqString, TSeqSpec> & seqs,
-           StringSet<TQualString, TQualSpec> & quals,
-           TRecordReader & reader,
-           TagSelector<TTagList> const & tagSelector,
-           int i)
-{
-    if (i == -1)
-        return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-    if (i != tagSelector.tagId)
-        return _read2(metas, seqs, quals, reader, static_cast<typename TagSelector<TTagList>::Base const &>(tagSelector), i - 1);
-
-    typedef typename TTagList::Type TFormat;
-    return read2(metas, seqs, quals, reader, TFormat());
-}
-
-template <typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec, typename TQualString,
-          typename TQualSpec, typename TRecordReader, typename TTagList>
-int read2(StringSet<TIdString, TIdSpec> & metas,
-          StringSet<TSeqString, TSeqSpec> & seqs,
-          StringSet<TQualString, TQualSpec> & quals,
-          TRecordReader & reader,
-          TagSelector<TTagList> & tagSelector)
-{
-    if (!guessStreamFormat(reader, tagSelector))
-        return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-
-    return _read2(metas, seqs, quals, reader, tagSelector, LENGTH<TTagList>::VALUE - 1);
-}
-
-// For read2(metas, seqs, reader, TTagSelector/AutoSeqStreamFormat).
-
-template <typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec,
-          typename TRecordReader>
-int _read2(StringSet<TIdString, TIdSpec> & /*metas*/,
-           StringSet<TSeqString, TSeqSpec> & /*seqs*/,
-           TRecordReader & /*reader*/,
-           TagSelector<void> const & /*tagSelector*/,
-           int i)
-{
-    SEQAN_ASSERT_EQ(i, -1);
-    (void)i;  // Only used for assertion.
-    return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-}
-
-template <typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec,
-          typename TRecordReader, typename TTagList>
-int _read2(StringSet<TIdString, TIdSpec> & metas,
-           StringSet<TSeqString, TSeqSpec> & seqs,
-           TRecordReader & reader,
-           TagSelector<TTagList> const & tagSelector,
-           int i)
-{
-    if (i == -1)
-        return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-    if (i != tagSelector.tagId)
-        return _read2(metas, seqs, reader, static_cast<typename TagSelector<TTagList>::Base const &>(tagSelector), i - 1);
-
-    typedef typename TTagList::Type TFormat;
-    return read2(metas, seqs, reader, TFormat());
-}
-
-template <typename TIdString, typename TIdSpec, typename TSeqString, typename TSeqSpec,
-          typename TRecordReader, typename TTagList>
-int read2(StringSet<TIdString, TIdSpec> & metas,
-          StringSet<TSeqString, TSeqSpec> & seqs,
-          TRecordReader & reader,
-          TagSelector<TTagList> & tagSelector)
-{
-    if (!guessStreamFormat(reader, tagSelector))
-        return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-
-    return _read2(metas, seqs, reader, tagSelector, LENGTH<TTagList>::VALUE - 1);
-}
-
-// ----------------------------------------------------------------------------
-// Function readRecord
-// ----------------------------------------------------------------------------
-
-// For readRecord(meta, seq, qual, reader, TTagSelector/AutoSeqStreamFormat).
-
-template <typename TIdString, typename TSeqString, typename TQualString, typename TRecordReader>
-int _readRecord(TIdString & /*meta*/, TSeqString & /*seq*/, TQualString & /*qual*/, TRecordReader & /*reader*/, TagSelector<void> const & /*tagSelector*/, int i)
-{
-    SEQAN_ASSERT_EQ(i, -1);
-    (void)i;  // only used for assertion.
-    return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-}
-
-template <typename TIdString, typename TSeqString, typename TQualString, typename TRecordReader, typename TTagList>
-int _readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TRecordReader & reader, TagSelector<TTagList> const & tagSelector, int i)
-{
-    if (i == -1)
-        return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-    if (i != tagSelector.tagId)
-        return _readRecord(meta, seq, qual, reader, static_cast<typename TagSelector<TTagList>::Base const &>(tagSelector), i - 1);
-
-    typedef typename TTagList::Type TFormat;
-    return readRecord(meta, seq, qual, reader, TFormat());
-}
-
-template <typename TIdString, typename TSeqString, typename TQualString, typename TRecordReader, typename TTagList>
-int readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TRecordReader & reader, TagSelector<TTagList> & tagSelector)
-{
-    if (value(tagSelector) == -1 && !guessStreamFormat(reader, tagSelector))
-        return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-
-    return _readRecord(meta, seq, qual, reader, tagSelector, LENGTH<TTagList>::VALUE - 1);
-}
-
-// For readRecord(meta, seq, reader, TTagSelector/AutoSeqStreamFormat).
-
-template <typename TIdString, typename TSeqString, typename TRecordReader>
-int _readRecord(TIdString & /*meta*/, TSeqString & /*seq*/, TRecordReader & /*reader*/, TagSelector<void> const & /*tagSelector*/, int i)
-{
-    (void)i;  // Only used in assertion.
-    SEQAN_ASSERT_EQ(i, -1);
-    return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-}
-
-template <typename TIdString, typename TSeqString, typename TRecordReader, typename TTagList>
-int _readRecord(TIdString & meta, TSeqString & seq, TRecordReader & reader, TagSelector<TTagList> const & tagSelector, int i)
-{
-    if (i == -1)
-        return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-    if (i != tagSelector.tagId)
-        return _readRecord(meta, seq, reader, static_cast<typename TagSelector<TTagList>::Base const &>(tagSelector), i - 1);
-
-    typedef typename TTagList::Type TFormat;
-    return readRecord(meta, seq, reader, TFormat());
-}
-
-// (weese:)
-// why is guessStreamFormat called insided readRecord?
-// guessStreamFormat should be called outside and only once, directly after opening a stream
-
-template <typename TIdString, typename TSeqString, typename TRecordReader, typename TTagList>
-int readRecord(TIdString & meta, TSeqString & seq, TRecordReader & reader, TagSelector<TTagList> & tagSelector)
-{
-    if (value(tagSelector) == -1 && !guessStreamFormat(reader, tagSelector))
-        return IOERR_READ_AUTO_FORMAT_UNKNOWN_FORMAT;
-
-    return _readRecord(meta, seq, reader, tagSelector, LENGTH<TTagList>::VALUE - 1);
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_RECORD_READER_AUTO_FORMAT_H_
diff --git a/seqan/stream/read_sam.h b/seqan/stream/read_sam.h
deleted file mode 100644
index c05cde6..0000000
--- a/seqan/stream/read_sam.h
+++ /dev/null
@@ -1,192 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Record I/O for SAM.  The FragmentStore uses this API for loading whole
-// SAM documents.  Only Single-Pass I/O is implemented.
-//
-// Usage:
-//
-// // Open file and record reader.
-// FILE * f = fopen("example.sam", "rb");
-// RecordReader<FILE *, SinglePass<TSpec> > reader(f);
-//
-// // Read all headers.
-// SamHeader header;
-// String<SamHeader> headers;
-// while (!atEnd(reader) && value(reader) == '@') {
-//     readRecord(header, reader, Sam());
-//     appendValue(headers, header);
-// }
-//
-// // Read all alignments.
-// SamAlignment alignment;
-// String<SamAlignment> alignments;
-// while (!atEnd(reader)) {
-//     readRecord(alignment, reader, Sam());
-//     appendValue(alignments, alignment);
-// }
-// ==========================================================================
-
-// TODO(holtgrew): Delete this, replaced by bam_io module.
-
-#ifndef SEQAN_STREAM_READ_SAM_H_
-#define SEQAN_STREAM_READ_SAM_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-struct SamHeader
-{
-    typedef String<char, Array<2> > TTag;
-
-    TTag recordType;
-    String<Pair<TTag, CharString> > dataFields;
-};
-
-enum SamFieldType
-{
-    SAM_CHAR,
-    SAM_INT_32,
-    SAM_FLOAT,
-    SAM_STRING,
-    SAM_HEX_STRING
-};
-
-struct SamAlignment
-{
-    typedef String<char, Array<2> > TTag;
-
-    CharString queryName;      //  1 QNAME
-    __int32 flag;              //  2 FLAG
-    CharString referenceName;  //  3 RNAME
-    __int32 pos;               //  4 POS
-    __int32 mappingQuality;    //  5 MAPQ
-    CharString cigarString;    //  6 CIGAR
-    CharString referenceNext;  //  7 RNEXT
-    __int32 positionNext;      //  8 PNEXT
-    __int32 templateLength;    //  9 TLEN
-    Dna5String sequence;       // 10 SEQ
-    CharString qualities;      // 11 QUAL
-    
-    String<Triple<TTag, SamFieldType, CharString> > optionalFields;
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function readRecord(SamHeader, );  Single-Pass.
-// ----------------------------------------------------------------------------
-
-inline
-bool isLineBreak(char c)
-{
-    return c == '\r' || c == '\n';
-}
-
-template <typename TIdString, typename TSeqString, typename TFile, typename TSpec>
-int readRecord(SamHeader & header,
-               RecordReader<TFile, SinglePass<TSpec> > & reader,
-               Sam const & /*tag*/)
-{
-    // Read record type.
-    SEQAN_ASSERT_NOT(atEnd(reader));
-    SEQAN_ASSERT_EQ(value(reader), '@');
-    goNext(reader);
-    SEQAN_ASSERT_NOT(atEnd(reader));
-    header.queryName[0] = value(reader);
-    goNext(reader);
-    SEQAN_ASSERT_NOT(atEnd(reader));
-    header.queryName[1] = value(reader);
-    goNext(reader);
-    SEQAN_ASSERT_NOT(atEnd(reader));
-
-    // Read all fields.
-    while (!atEnd(reader) && !isLineBreak(value(reader))) {
-        SEQAN_ASSERT_EQ(value(reader), '\t');
-        goNext(reader);
-
-        resize(header.dataFields, length(header.dataFields) + 1);
-        back(header.dataFields).i1[0] = value(reader);
-        goNext(reader);
-        back(header.dataFields).i1[1] = value(reader);
-        goNext(reader);
-        SEQAN_ASSERT_EQ(value(reader), ':');
-        goNext(reader);
-        for (; value(reader) != '\t' && !isLineBreak(value(reader)); goNext(reader))
-            appendValue(back(header.dataFields).i2, value(reader));
-    }
-    // Skip line break.
-    if (!atEnd(reader) && isLineBreak(value(reader))) {
-        goNext(reader);
-        if (value(reader) == '\n')
-            goNext(reader);
-    }
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function readRecord(SamHeader, );  Single-Pass.
-// ----------------------------------------------------------------------------
-
-template <typename TIdString, typename TSeqString, typename TFile, typename TSpec>
-int readRecord(SamAlignment & record,
-               RecordReader<TFile, SinglePass<TSpec> > & reader,
-               Sam const & /*tag*/)
-{
-    SEQAN_ASSERT_NEQ(value(reader), '@');
-
-    // Reading integers.
-    CharString buffer;
-    tokenizeTo(buffer, reader, '\t');
-    record.beginPos = ::seqan::lexical_cast<__int32>(buffer); // We should probably steal/port the boost code, with enforcing english locale.
-    goNext(reader);
-    
-    // ... etc.
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_READ_SAM_H_
diff --git a/seqan/stream/record_reader_base.h b/seqan/stream/record_reader_base.h
deleted file mode 100644
index b62aed8..0000000
--- a/seqan/stream/record_reader_base.h
+++ /dev/null
@@ -1,344 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-
-#ifndef SEQAN_STREAM_RECORD_READER_BASE_H_
-#define SEQAN_STREAM_RECORD_READER_BASE_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-struct StringReader_;
-typedef Tag<StringReader_> StringReader;
-
-template <typename TSpec = void>
-struct SinglePass {};
-
-template <typename TSpec = void>
-struct DoublePass {};
-
-/*!
- * @class RecordReader
- * @headerfile <seqan/stream.h>
- * @brief Buffer management when reading from @link StreamConcept streams @endlink.
- *
- * @signature template <typename TStream, typename TSpec>
- *            class RecordReader;
- *
- * @tparam TStream The @link ConceptStream @endlink to read from.
- * @tparam TSpec   The record reader specialization type.
- *
- * @section Examples
- *
- * @include demos/input_output/record_reader.cpp
- *
- * The output is as follows:
- *
- * @include demos/input_output/record_reader.cpp.stdout
- */
-
-/*!
- * @fn RecordReader::RecordReader
- * @brief Constructor.
- *
- * @signature RecordReader::RecordReader();
- * @signature RecordReader::RecordReader(stream[, bufferSize]);
- *
- * @param[in] stream     The @link StreamConcept @endlink to read from.
- * @param[in] bufferSize The size of the buffer to use.  Type: <tt>unsigned</tt>.
- */
-
-/**
-.Class.RecordReader
-..cat:Input/Output
-..summary:Buffer management for streams.
-..signature:RecordReader<TStream, TSpec>
-..param.TStream:The @Concept.StreamConcept@ type to work on.
-..param.TSpec:The record reader specialization to chose.
-..see:Concept.StreamConcept
-..example.file:demos/input_output/record_reader.cpp
-..include:seqan/stream.h
-
-.Memfunc.RecordReader#RecordReader
-..class:Class.RecordReader
-..summary:Constructor
-..signature:RecordReader()
-..signature:RecordReader(file[, bufferSize])
-..param.file:The file/String to use for reading.
-...type:nolink:The $TFile$ type of $RecordReader$.
-..param.bufferSize:The size of the buffer to use.
-...type:nolink:$unsigned$
- */
-
-template <typename TStream, typename TSpec>
-class RecordReader;
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafuction Position
-// ----------------------------------------------------------------------------
-
-/*!
- * @mfn RecordReader#Position
- * @brief Returns the position tpye to use in @link RecordReader#position @endlink and @link RecordReader#setPosition @endlink.
- *
- * @signature Position<TReader>::Type;
- *
- * @tparam TReader The RecordReader to query for its position type.
- *
- * @return Type The resulting position type.
- *
- * @see RecordReader#position
- * @see RecordReader#setPosition
- */
-
-/**
-.Metafunction.RecordReader#Position
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Returns the position type to use in @Function.RecordReader#position@ and @Function.RecordReader#setPosition@.
-..signature:Position<TReader>::Type
-..param.TReader:The @Class.RecordReader@ type to query for its position type.
-..returns:The position type related to the record reader type.
-..include:seqan/stream.h
-..see:Function.RecordReader#position
-..see:Function.RecordReader#setPosition
-*/
-
-template <typename TStream, typename TSpec>
-struct Position<RecordReader<TStream, TSpec> >
-{
-    typedef typename Position<TStream>::Type Type;
-};
-
-template <typename TStream, typename TSpec>
-struct Position<RecordReader<TStream, TSpec> const> :
-            Position<RecordReader<TStream, TSpec> >
-{};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-/*!
- * @fn RecordReader#resultCode
- * @brief Return current status code of the reader/underlying stream.
- *
- * @signature int resultCode(reader);
- *
- * @param[in] reader The RecordReader to query for its status code.
- *
- * @return int The status code, 0 for no errors, non-0 value for errors.
- */
-
-/*!
- * @fn RecordReader#value
- * @brief Return the current value (character) of the reader.
- *
- * This is undefined if the reader is at the end or an error occured.
- *
- * @signature char value(reader);
- *
- * @param[in] reader The RecordReader to read from.
- *
- * @return char The resulting character.
- */
-
-/*!
- * @fn RecordReader#goNext
- * @brief Advance to the next position in the stream.
- *
- * @signature bool goNext(reader);
- *
- * @param[in,out] reader The RecordReader to advance.
- *
- * @return bool <tt>true</tt> on success, <tt>false</tt> on failure.
- */
-
-/*!
- * @fn RecordReader#nextIs
- * @brief Query whether the next record is of a given type.
- * 
- * @signature bool nextIs(reader, tag)
- * 
- * @param[in,out] reader The @link RecordReader @endlink to peek into.  Remains unchanged.
- * @param[in]     tag    Tag to select the given record type.
- * 
- * @return bool Indicating whether the next record in <tt>reader</tt> is of type given by tag.
- * 
- * @section Remarks
- * 
- * The checks are mostly heuristic, mostly looking at one or few characters from reader.
- */
-
-/*!
- * @fn RecordReader#atEnd
- * @brief Returns <tt>true</tt> if there is no more data to be read.
- * 
- * @signature bool atEnd(reader);
- * 
- * @param reader The @link RecordReader @endlink to query the state of.
- * 
- * @return bool This function returns <tt>true</tt> if the file is at end or there was an error reading.  It returns
- *              <tt>false</tt> if there is more data to read.  In parsing functions, you can use @link
- *              RecordReader#resultCode @endlink to get the result to return from your parsing function.
- * 
- * @see RecordReader#value
- * @see RecordReader#resultCode
- */
-
-/*!
- * @fn RecordReader#position
- * @brief Returns the current position of the reader.
- *
- * @signature TPosition position(reader);
- *
- * @param[in] reader The RecordReader to query.
- *
- * @return TPosition The resulting position.  Use @link RecordReader#Position @endlink to retrieve.
- */
-
-/*!
- * @fn RecordReader#setPosition
- * @brief Sets the current position of the reader.
- *
- * @signature void setPosition(reader, pos);
- *
- * @param[in,out] reader The RecordReader to set the position of.
- * @param[in]     pos    The position to set.
- *
- * @section Remarks
- *
- * The underlying data source has to support setting the position.  For RecordReader objects reading from strings this
- * always works.  When reading from streams, setting the position must be supported by the underlying stream
- *
- * @see RecordReader#position
- */
-
-/**
-.Function.RecordReader#resultCode
-..cat:Input/Output
-..class:Class.RecordReader
-..signature:int resultCode(reader)
-..summary:Returns $int$ current status code for reader (0 on success).
-..param.reader:The @Class.RecordReader@ to query the state of.
-...type:Class.RecordReader
-..returns:$int$, zero if there was no error reading, non-zero value on errors. Note that zero is also returned on EOF.
-..include:seqan/stream.h
-
-.Function.RecordReader#value
-..summary:Returns the current value of the reader.
-..cat:Input/Output
-..class:Class.RecordReader
-..signature:char value(reader)
-..param.reader:The @Class.RecordReader@ to get the current value from.
-...type:Class.RecordReader
-..include:seqan/stream.h
-
-.Function.RecordReader#goNext
-..cat:Input/Output
-..class:Class.RecordReader
-..signature:bool goNext(recordReader)
-..summary:Advance record reader to next position.
-..param.recordReader:The @Class.RecordReader@ to advance the position in.
-...type:Class.RecordReader
-..include:seqan/stream.h
-
-.Function.RecordReader#nextIs
-..class:Class.RecordReader
-..cat:Input/Output
-..signature:bool nextIs(recordReader, tag)
-..summary:Query whether the next record is of a given type.
-..param.recordReader:The @Class.RecordReader@ to peek into.
-...type:Class.RecordReader
-...remarks:Stays unchanged.
-..param.tag:Tag to select the given record type.
-..returns:$bool$ indicating whether the next record in $recordReader$ is of type given by tag.
-..remarks:The checks are mostly heuristic, mostly looking at one or few characters from recordReader.
-..include:seqan/stream.h
-
-.Function.RecordReader#atEnd
-..cat:Input/Output
-..class:Class.RecordReader
-..summary:Returns $true$ if there is no more data to be read.
-..signature:bool atEnd(recordReader)
-..param.recordReader:The @Class.RecordReader@ to query the state of.
-...type:Class.RecordReader
-..returns:This function returns $true$ if the file is at end or there was an error reading. It returns $false$ if there is more data to read. In parsing functions, you can use @Function.RecordReader#resultCode@ to get the result to return from your parsing function.
-..see:Function.RecordReader#value
-..see:Function.RecordReader#resultCode
-..include:seqan/stream.h
-
-.Function.RecordReader#position
-..cat:Input/Output
-..class:Class.RecordReader
-..summary:Returns the current position of the reader.
-..signature:TPosition position(reader)
-..param.reader:The @Class.RecordReader@ to query for its position.
-...type:Class.RecordReader
-..param.TPosition:The @Metafunction.RecordReader#Position@ of the reader.
-..returns:The current position of the record reader.
-..see:Metafunction.RecordReader#Position
-..include:seqan/stream.h
-
-.Function.RecordReader#setPosition
-..cat:Input/Output
-..class:Class.RecordReader
-..summary:Returns the current position of the reader.
-..remarks:
-The underlying data source has to support setting the position.
-For String RecordReader objects, this works nicely, when reading from streams, setting the position of the record reader is supported if the underlying string supports it.
-..signature:void setPosition(reader, pos)
-..param.reader:The @Class.RecordReader@ to query for its position.
-...type:Class.RecordReader
-..param.pos:The position to set the reader to.
-...type:Metafunction.RecordReader#Position
-..returns:$void$
-..see:Metafunction.RecordReader#Position
-..see:Function.RecordReader#position
-..include:seqan/stream.h
- */
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_RECORD_READER_BASE_H_
diff --git a/seqan/stream/record_reader_double.h b/seqan/stream/record_reader_double.h
deleted file mode 100644
index 91add26..0000000
--- a/seqan/stream/record_reader_double.h
+++ /dev/null
@@ -1,454 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// The Double-Pass Record Reader specialization.  It works for all stream
-// types.
-// ==========================================================================
-
-#ifndef SEQAN_STREAM_RECORD_READER_DOUBLE_H_
-#define SEQAN_STREAM_RECORD_READER_DOUBLE_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class DoublePassRecordReader
- * @extends RecordReader
- * @headerfile <seqan/stream.h.
- * @brief Record reader specialization for double-pass reading.
- *
- * @signature template <typename TStream>
- *            class RecordReader<TStream, DoublePass>;
- *
- * @tparam TStream The @link StreamConcept @endlink type to use for reading.
- *
- * @section Remarks
- *
- * Not default or copy constructable.
- */
-
-/**
-.Spec.Double-Pass RecordReader
-..cat:Input/Output
-..general:Class.RecordReader
-..summary:Record reader specialization for double-pass reading.
-..signature:RecordReader<TStream, DoublePass>
-..param.TStream:The @Concept.StreamConcept@ type to work on.
-..remarks:Is not default or copy constructable.
-..include:seqan/stream.h
- */
-
-template <typename TFile>
-class RecordReader<TFile, DoublePass<> >
-{
-public:
-    TFile & _file;
-    unsigned _bufferSize;
-    // INVARIANT: No used buffer may be empty after reading into it!
-    String<CharString *> _usedBuffers;    // Buffers with relevant data.
-    // TODO(holtgrew): It is probably a bad idea to do our own pooling here!
-    String<CharString *> _unusedBuffers;  // Buffers without relevant data.
-    typedef typename Iterator<CharString, Standard>::Type TIter;
-    TIter _current, _end;
-    CharString * _currentBuffer;
-    unsigned _currentBuffNo;
-    int _resultCode;
-    int _passNo;
-    char * _beginInFirst;
-    bool _stayInOneBuffer; // needed for stream format detection
-    // In contrast to the SinglePass<> reader, we store the current position of the file in _position since it is more
-    // complex to do the computation otherwise.  This means more updates to _position, though.
-    typedef typename Position<TFile>::Type TPosition;
-    TPosition _position;  // Position in file.
-    TPosition _firstPassPos;  // Position of _firstPass call.
-
-    enum {
-        OK = 0,
-        INVALID_FORMAT
-    };
-
-    RecordReader(TFile & file)
-            : _file(file), _bufferSize(BUFSIZ), _current(0), _end(0),
-              _currentBuffer(0), _currentBuffNo(0), _resultCode(0),
-              _passNo(0), _beginInFirst(0), _stayInOneBuffer(false),
-              _position(0), _firstPassPos(0)
-    {
-        // resize(_buffer, _bufferSize);
-    }
-
-    RecordReader(TFile & file, unsigned bufferSize)
-            : _file(file), _bufferSize(bufferSize), _current(0), _end(0),
-              _currentBuffer(0), _currentBuffNo(0), _resultCode(0),
-              _passNo(0), _beginInFirst(0), _stayInOneBuffer(false),
-              _position(0), _firstPassPos(0)
-    {
-        // resize(_buffer, _bufferSize);
-    }
-
-    ~RecordReader()
-    {
-        for (unsigned i = 0; i < length(_usedBuffers); ++i)
-            delete _usedBuffers[i];
-        for (unsigned i = 0; i < length(_unusedBuffers); ++i)
-            delete _unusedBuffers[i];
-    }
-
-private:
-    // No default or copy constructor.
-    RecordReader(RecordReader const &other): _file(other._file) {}
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Helper Function _fillNextBuffer()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline bool
-_fillNextBuffer(RecordReader<TFile, DoublePass<> > & recordReader)
-{
-    if (recordReader._stayInOneBuffer && recordReader._end != 0)
-    // e.g. FileFormat Detection
-        return false;
-    // std::cerr << "REFILLING BUFFER" << std::endl;
-    if (streamEof(recordReader._file))
-        return false;
-    if (empty(recordReader._unusedBuffers)) {
-        recordReader._currentBuffer = new CharString();
-        appendValue(recordReader._usedBuffers, recordReader._currentBuffer);
-    } else {
-        recordReader._currentBuffer = back(recordReader._unusedBuffers);
-        eraseBack(recordReader._unusedBuffers);
-        appendValue(recordReader._usedBuffers, recordReader._currentBuffer);
-    }
-
-    resize(*recordReader._currentBuffer, recordReader._bufferSize);
-    recordReader._current = begin(*recordReader._currentBuffer, Standard());
-    // std::cerr << "recordReader._current = begin(...) == " << (void*)(recordReader._current) << " [fill next buffer]" << std::endl;
-    recordReader._currentBuffNo += 1;
-
-    if (recordReader._beginInFirst == NULL)
-        recordReader._beginInFirst = recordReader._current;
-
-    size_t bytesRead = streamReadBlock(recordReader._current, recordReader._file, recordReader._bufferSize);
-    if (bytesRead != recordReader._bufferSize) {
-        resize(*recordReader._currentBuffer, bytesRead);
-        // If we read fewer characters and the stream is not at its end then
-        // there was an error reading the file.
-        recordReader._resultCode = streamError(recordReader._file);
-        if (recordReader._resultCode) {
-            // std::cerr << "RESULT IS " << recordReader._resultCode << std::endl;
-            recordReader._end = recordReader._current;
-            return false;
-        }
-    }
-    recordReader._end = recordReader._current + bytesRead;
-    // std::cerr << "read " << bytesRead << " bytes" << std::endl;
-    // std::cerr << "ERROR? " << streamError(recordReader._file) << std::endl;
-    // std::cerr << "EOF? " << streamEof(recordReader._file) << std::endl;
-
-    return true;
-}
-
-// ----------------------------------------------------------------------------
-// Function startFirstPass()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn DoublePassRecordReader#startFirstPass
- * @brief Start the first reading pass.
- *
- * @signature void startFirstPass(reader);
- *
- * @param[in,out] reader The RecordReader to start the first pass with.
- *
- * @section Remarks
- *
- * Calling this function will memoize the current position in the buffer to return to in second pass.
- */
-
-/**
-.Function.startFirstPass
-..class:Spec.Double-Pass RecordReader
-..cat:Input/Output
-..signature:startFirstPass(recordReader)
-..summary:Start the first reading pass.
-..param.recordReader:RecordReader to start the first pass with.
-...type:Spec.Double-Pass RecordReader
-..remarks:This will memoize the current position in the buffer, to return to in second pass.
-..see:Function.startSecondPass
-..include:seqan/stream.h
- */
-
-template <typename TFile>
-void
-startFirstPass(RecordReader<TFile, DoublePass<> > & recordReader)
-{
-    // Store begin position of first pass.
-    recordReader._firstPassPos = recordReader._position;
-    recordReader._passNo = 1;
-    recordReader._beginInFirst = recordReader._current;
-    // TODO(holtgrew_): Add assertion that previous second pass ended at same position.
-    // What if is exactly at end of buffer?
-    if (length(recordReader._usedBuffers) > 1u) {
-        CharString * ptr = back(recordReader._usedBuffers);
-        eraseBack(recordReader._usedBuffers);
-        append(recordReader._unusedBuffers, recordReader._usedBuffers);
-        clear(recordReader._usedBuffers);
-        appendValue(recordReader._usedBuffers, ptr);
-    }
-
-    // Fill the next (or even: first) buffer if the current is empty.
-    if (recordReader._current == recordReader._end)
-        _fillNextBuffer(recordReader);
-    // std::cerr << "starting first pass from " << (void*)(recordReader._current) << std::endl;
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _jumpToNextBuffer()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-bool
-_jumpToNextBuffer(RecordReader<TFile, DoublePass<> > & recordReader)
-{
-    if (recordReader._stayInOneBuffer) // e.g. file format detection
-        return false;
-    SEQAN_ASSERT_EQ(recordReader._passNo, 2);
-    SEQAN_ASSERT(recordReader._current ==  recordReader._end);
-    if (recordReader._currentBuffNo + 1 >= length(recordReader._usedBuffers))
-        return false;
-    recordReader._currentBuffNo += 1;
-    recordReader._currentBuffer = recordReader._usedBuffers[recordReader._currentBuffNo];
-    recordReader._current = begin(*recordReader._currentBuffer, Standard());
-    // std::cerr << "recordReader._current = begin(...) == " << (void*)(recordReader._current) << " [jump to next]" << std::endl;
-    recordReader._end = end(*recordReader._currentBuffer, Standard());
-    return true;
-}
-
-// ----------------------------------------------------------------------------
-// Function startSecondPass()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn DoublePassRecordReader#startSecondPass
- * @brief Start the second reading pass.
- *
- * @signature void startSecondPass(reader);
- *
- * @param[in,out] reader The RecordReader to start the second pass with.
- *
- * @section Remarks
- *
- * This will reset the position in the buffer.
- */
-
-/**
-.Function.startSecondPass
-..class:Spec.Double-Pass RecordReader
-..cat:Input/Output
-..signature:startSecondPass(recordReader)
-..summary:Start the second reading pass.
-..param.recordReader:RecordReader to start the second pass with.
-...type:Spec.Double-Pass RecordReader
-..remarks:This will reset the position in the buffer
-..see:Function.startFirstPass
-..include:seqan/stream.h
- */
-
-template <typename TFile>
-void
-startSecondPass(RecordReader<TFile, DoublePass<> > & recordReader)
-{
-    // Set position back to first pass start position.
-    recordReader._position = recordReader._firstPassPos;
-    
-    SEQAN_ASSERT_EQ(recordReader._passNo, 1);
-    recordReader._passNo = 2;
-    recordReader._currentBuffNo = 0;
-    recordReader._currentBuffer = recordReader._usedBuffers[0];
-    recordReader._current = recordReader._beginInFirst;
-    // std::cerr << "recordReader._current = " << (void*)(recordReader._beginInFirst) << " [start second pass]" << std::endl;
-    recordReader._end = end(*recordReader._currentBuffer, Standard());
-}
-
-// ----------------------------------------------------------------------------
-// Function position()
-// ----------------------------------------------------------------------------
-
-// TODO(holtgrew): Document!
-template <typename TFile>
-inline typename Position<TFile>::Type
-position(RecordReader<TFile, DoublePass<void> > const & recordReader)
-{
-    return recordReader._position;
-}
-
-// ----------------------------------------------------------------------------
-// Function setPosition()
-// ----------------------------------------------------------------------------
-
-// This automatically starts the first pass at the position.
-template <typename TFile, typename TPosition>
-inline int
-setPosition(RecordReader<TFile, DoublePass<void> > & recordReader, TPosition pos)
-{
-    // Clear buffers, mark as unused.
-    append(recordReader._unusedBuffers, recordReader._usedBuffers);
-    clear(recordReader._usedBuffers);
-
-    // Seek to position in file.
-    int res = streamSeek(recordReader._file, pos, SEEK_SET);
-    if (res != 0)
-        return res;
-    recordReader._position = pos;
-    recordReader._current = recordReader._end = 0;
-    startFirstPass(recordReader);
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function atEnd()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline bool
-atEnd(RecordReader<TFile, DoublePass<> > & recordReader)
-{
-    // std::cerr << "HAS MORE " << __LINE__ << std::endl;
-    // There can be more data if the current buffer is not exhausted.
-    if (recordReader._current != recordReader._end)
-        return false;
-    // std::cerr << "HAS MORE " << __LINE__ << std::endl;
-    // There can be more data if the current buffer is not the last one.
-    if (recordReader._currentBuffNo + 1 < length(recordReader._usedBuffers))
-        return false;
-    // std::cerr << "HAS MORE " << __LINE__ << std::endl;
-
-    // There is no more data if the buffer is exhausted and the stream
-    // is at the end of the file or there previously was an error reading the
-    // file.
-
-    if (streamEof(recordReader._file) || recordReader._resultCode != 0)
-        return true;
-    // std::cerr << "HAS MORE " << __LINE__ << std::endl;
-
-    // std::cerr << "refilling in atEnd()" << std::endl;
-
-    // Otherwise, we can try to load some data.  This case only happens if
-    // atEnd() is called at the beginning of the file; Otherwise, goNext()
-    // will load data.
-    switch (recordReader._passNo) {
-        case 0:
-            return false;
-        case 1:
-            return !_fillNextBuffer(recordReader);
-        case 2:
-            if (!_jumpToNextBuffer(recordReader))
-                return !_fillNextBuffer(recordReader);
-            else
-                return false;
-        default:
-            SEQAN_ASSERT_FAIL("Invalid pass no: %d", recordReader._passNo);
-            return true;
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function resultCode()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline int
-resultCode(RecordReader<TFile, DoublePass<> > & recordReader)
-{
-    return recordReader._resultCode;
-}
-
-// ----------------------------------------------------------------------------
-// Function goNext()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline bool
-goNext(RecordReader<TFile, DoublePass<> > & recordReader)
-{
-    SEQAN_ASSERT(recordReader._current != recordReader._end);
-
-    // std::cerr << "recordReader._current += 1 == " << (void*)(recordReader._current) << std::endl;
-    recordReader._current += 1;
-    recordReader._position += 1;
-    // If there is more data in the buffer then we're done.
-    if (recordReader._current != recordReader._end)
-        return false;  // Has more data.
-
-    // std::cerr << "REFILLING IN goNext()" << std::endl;
-
-    SEQAN_ASSERT_GEQ(recordReader._passNo, 1);
-    SEQAN_ASSERT_LEQ(recordReader._passNo, 2);
-    if (recordReader._passNo == 1)
-        return !_fillNextBuffer(recordReader);
-    else
-        return !_jumpToNextBuffer(recordReader);
-}
-
-// ----------------------------------------------------------------------------
-// Function value()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline char
-value(RecordReader<TFile, DoublePass<> > & recordReader)
-{
-    SEQAN_ASSERT(recordReader._current != recordReader._end);
-    // std::cerr << "*recordReader._current == " << *recordReader._current << std::endl;
-    return *recordReader._current;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_RECORD_READER_DOUBLE_H_
diff --git a/seqan/stream/record_reader_double_mmap.h b/seqan/stream/record_reader_double_mmap.h
deleted file mode 100644
index dfebcaa..0000000
--- a/seqan/stream/record_reader_double_mmap.h
+++ /dev/null
@@ -1,235 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// The Double-Pass Record Reader using the Memory Mapped String
-// specialization.  It uses that data does not have to be read explicitely but
-// is automatically loaded by the OS on pagefaults.
-// ==========================================================================
-
-#ifndef SEQAN_STREAM_RECORD_READER_DOUBLE_MMAP_H_
-#define SEQAN_STREAM_RECORD_READER_DOUBLE_MMAP_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class StringDoublePassRecordReader
- * @extends DoublePassRecordReader
- * @headerfile <seqan/stream.h>
- * @brief RecordReader specialization for double-pass reading.
- *
- * @signature template <typename TString>
- *            class RecordReader<TString, DoublePass<StringReader> >;
- *
- * @tparam TString The @link String @endlink specialization to use for reading from.
- *
- * @section Remarks
- *
- * This RecordReader does not have any buffers but uses the string directly.
- *
- * Not default or copy constructable.
- */
-
-/**
-.Spec.Double-Pass String RecordReader
-..cat:Input/Output
-..general:Spec.Double-Pass RecordReader
-..summary:Record reader specialization for double-pass reading
-..signature:RecordReader<TString, DoublePass<StringReader> >
-..param.TString:The @Class.String@ type to work on.
-..remarks:This record reader does not have any buffers but uses the memory mapped string directly.
-..remarks:Is not default or copy constructable.
-..remarks:The buffer size is the granularity in which @Function.mmapAdvise@ will be called if $TString$ is a @Spec.MMap String@.
-..include:seqan/stream.h
- */
-
-template <typename TString>
-class RecordReader<TString, DoublePass<StringReader> >
-{
-public:
-    typedef typename Iterator<TString, Standard>::Type TIter;
-    typedef typename Size<TString>::Type TSize;
-
-    int _passNo;
-    TString & _string;
-    TIter _first, _current, _end;
-    TSize _bufferSize;
-
-    enum {
-        OK = 0,
-        INVALID_FORMAT
-    };
-
-    RecordReader(TString & string)
-            : _passNo(0), _string(string), _first(begin(string)),
-              _current(begin(string)), _end(end(string)), _bufferSize(BUFSIZ)
-    {}
-
-    RecordReader(TString & string, unsigned bufferSize)
-            : _passNo(0), _string(string), _first(begin(string)),
-              _current(begin(string)), _end(end(string)), _bufferSize(bufferSize)
-    {}
-
-private:
-    // No default or copy constructor.
-    RecordReader(RecordReader const &other): _string(other._string) {}
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function position()
-// ----------------------------------------------------------------------------
-
-// TODO(holtgrew): Document!
-template <typename TString>
-inline typename Position<TString>::Type
-position(RecordReader<TString, DoublePass<StringReader> > const & recordReader)
-{
-    return recordReader._current - begin(recordReader._string, Standard());
-}
-
-// ----------------------------------------------------------------------------
-// Function setPosition()
-// ----------------------------------------------------------------------------
-
-template <typename TString, typename TPosition>
-inline int
-setPosition(RecordReader<TString, DoublePass<StringReader> > & recordReader, TPosition pos)
-{
-    recordReader._current = iter(recordReader._string, pos, Standard());
-    startFirstPass(recordReader);
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function startFirstPass()
-// ----------------------------------------------------------------------------
-
-template <typename T>
-void _startFirstPassMMapAdvise(T const & /*x*/)
-{}
-
-template <typename TValue, typename TConfig>
-void _startFirstPassMMapAdvise(String<TValue, MMap<TConfig> > & s)
-{
-    mmapAdvise(s, MAP_SEQUENTIAL);
-    
-}
-
-template <typename TString>
-void
-startFirstPass(RecordReader<TString, DoublePass<StringReader> > & recordReader)
-{
-    _startFirstPassMMapAdvise(recordReader._string);
-    recordReader._passNo = 1;
-    recordReader._first = recordReader._current;
-}
-
-// ----------------------------------------------------------------------------
-// Function startSecondPass()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-void
-startSecondPass(RecordReader<TString, DoublePass<StringReader> > & recordReader)
-{
-    SEQAN_ASSERT_EQ(recordReader._passNo, 1);
-    recordReader._passNo = 2;
-    recordReader._current = recordReader._first;
-}
-
-// ----------------------------------------------------------------------------
-// Function atEnd()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline bool
-atEnd(RecordReader<TString, DoublePass<StringReader> > & recordReader)
-{
-    // There is more data if the current buffer is not exhausted.
-    return recordReader._current == recordReader._end;
-}
-
-// ----------------------------------------------------------------------------
-// Function resultCode()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline int
-resultCode(RecordReader<TString, DoublePass<StringReader> > & /*recordReader*/)
-{
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function goNext()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline bool
-goNext(RecordReader<TString, DoublePass<StringReader> > & recordReader)
-{
-    SEQAN_ASSERT(recordReader._current != recordReader._end);
-    recordReader._current += 1;
-    return recordReader._current == recordReader._end;
-}
-
-// ----------------------------------------------------------------------------
-// Function value()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline char
-value(RecordReader<TString, DoublePass<StringReader> > & recordReader)
-{
-    SEQAN_ASSERT(recordReader._current != recordReader._end);
-    return *recordReader._current;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_RECORD_READER_DOUBLE_MMAP_H_
diff --git a/seqan/stream/record_reader_single.h b/seqan/stream/record_reader_single.h
deleted file mode 100644
index 1708ae8..0000000
--- a/seqan/stream/record_reader_single.h
+++ /dev/null
@@ -1,270 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// The Single-Pass Record Reader specialization.  It works for all stream
-// types.
-// ==========================================================================
-
-#ifndef SEQAN_STREAM_RECORD_READER_SINGLE_H_
-#define SEQAN_STREAM_RECORD_READER_SINGLE_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-template <typename TFile>
-class RecordReader<TFile, SinglePass<void> >;
-
-template <typename TFile>
-inline bool
-_refillBuffer(RecordReader<TFile, SinglePass<void> > & recordReader);
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class SinglePassRecordReader
- * @extends RecordReader
- * @headerfile <seqan/stream.h>
- * @brief RecordReader specialization for single-pass reading.
- *
- * @signature template <typename TStream[, typename TSpec]>
- *            class RecordReader<TStream, TSpec>;
- *
- * @tparam TStream The @link StreamConcept @endlink to work on.
- * @tparam TSpec   Specializing type.  Defaults to <tt>void</tt>.
- *
- * @section Remarks
- *
- * Is neither default nor copy constructable.
- */
-
-/**
-.Spec.Single-Pass RecordReader
-..cat:Input/Output
-..general:Class.RecordReader
-..summary:Record reader specialization for single-pass reading.
-..signature:RecordReader<TStream, SinglePass<void> >
-..param.TStream:The @Concept.StreamConcept@ type to work on.
-..remarks:Is not default or copy constructable.
-..include:seqan/stream.h
- */
-
-template <typename TFile>
-class RecordReader<TFile, SinglePass<void> >
-{
-public:
-    TFile & _file;
-    unsigned _bufferSize;
-    CharString _buffer;
-    typedef typename Iterator<CharString, Standard>::Type TIter;
-    TIter _current, _end;
-    int _resultCode;
-    bool _stayInOneBuffer;
-    // We have to store the position of the end of the currently loaded block in the file separately because std streams
-    // cannot tell their position if at end and clearing the eofbit leads to problems with atEnd().
-    typedef typename Position<TFile>::Type TPosition;
-    TPosition _position;  // Position in file.
-
-    enum {
-        OK = 0,
-        INVALID_FORMAT
-    };
-
-    RecordReader(TFile & file)
-            : _file(file), _bufferSize(BUFSIZ), _current(0), _end(0),
-              _resultCode(0), _stayInOneBuffer(false), _position(0)
-    {
-        resize(_buffer, _bufferSize);
-        _refillBuffer(*this);
-    }
-
-    RecordReader(TFile & file, unsigned bufferSize)
-            : _file(file), _bufferSize(bufferSize), _current(0), _end(0),
-              _resultCode(0), _stayInOneBuffer(false), _position(0)
-    {
-        resize(_buffer, _bufferSize);
-        _refillBuffer(*this);
-    }
-
-private:
-    // No default or copy constructor.
-    RecordReader(RecordReader const &other): _file(other._file) {}
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Helper Function _refillBuffer()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline bool
-_refillBuffer(RecordReader<TFile, SinglePass<void> > & recordReader)
-{
-    if (recordReader._stayInOneBuffer && recordReader._end != 0)
-        // e.g. file format detection; if end==0 there hasnt yet been a buffer
-        return false;
-    // std::cerr << "REFILLING BUFFER" << std::endl;
-    if (streamEof(recordReader._file))
-        return false;
-    recordReader._current = begin(recordReader._buffer, Standard());
-    recordReader._position = streamTell(recordReader._file);
-    size_t bytesRead = streamReadBlock(recordReader._current, recordReader._file, recordReader._bufferSize);
-    recordReader._position += bytesRead;
-    if (bytesRead != recordReader._bufferSize) {
-        // If we read fewer characters and the stream is not at its end then
-        // there was an error reading the file.
-        recordReader._resultCode = streamError(recordReader._file);
-        if (recordReader._resultCode) {
-            // std::cerr << "RESULT IS " << recordReader._resultCode << std::endl;
-            recordReader._end = recordReader._current;
-            return false;
-        }
-    }
-    recordReader._end = recordReader._current + bytesRead;
-    // std::cerr << "read " << bytesRead << " bytes" << std::endl;
-    // std::cerr << "ERROR? " << streamError(recordReader._file) << std::endl;
-    // std::cerr << "EOF? " << streamEof(recordReader._file) << std::endl;
-
-    return true;
-}
-
-// ----------------------------------------------------------------------------
-// Function position()
-// ----------------------------------------------------------------------------
-
-// TODO(holtgrew): Document!
-template <typename TFile>
-inline typename Position<TFile>::Type
-position(RecordReader<TFile, SinglePass<void> > const & recordReader)
-{
-    typename Position<TFile>::Type bufferedUnread = recordReader._end - recordReader._current;
-    return recordReader._position - bufferedUnread;
-}
-
-// ----------------------------------------------------------------------------
-// Function setPosition()
-// ----------------------------------------------------------------------------
-
-template <typename TFile, typename TPosition>
-inline int
-setPosition(RecordReader<TFile, SinglePass<void> > & recordReader, TPosition pos)
-{
-    int res = streamSeek(recordReader._file, pos, SEEK_SET);
-    if (res != 0)
-        return res;
-    _refillBuffer(recordReader);
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function atEnd()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline bool
-atEnd(RecordReader<TFile, SinglePass<void> > & recordReader)
-{
-    // There is more data if the buffer is not exhausted.
-    if (recordReader._current != recordReader._end)
-        return false;
-    // There is no more data if the buffer is exhausted and there the stream
-    // is at the end of the file or there previously was an error reading the
-    // file.
-    
-    if (streamEof(recordReader._file) || recordReader._resultCode != 0)
-        return true;
-
-    // std::cerr << "refilling in atEnd()" << std::endl;
-
-    // Otherwise, we can try to load some data.  This case only happens if
-    // atEnd is called at the beginning of the file; Otherwise, goNext()
-    // will load data.
-    return !_refillBuffer(recordReader);
-}
-
-// ----------------------------------------------------------------------------
-// Function resultCode()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline int
-resultCode(RecordReader<TFile, SinglePass<void> > & recordReader)
-{
-    return recordReader._resultCode;
-}
-
-// ----------------------------------------------------------------------------
-// Function goNext()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline bool
-goNext(RecordReader<TFile, SinglePass<void> > & recordReader)
-{
-    SEQAN_ASSERT(recordReader._current != recordReader._end);
-
-    recordReader._current += 1;
-    // If there is more data in the buffer then we're done.
-    if (recordReader._current != recordReader._end)
-        return false;  // Has more data.
-
-    // Otherwise, try to load some data.
-    return !_refillBuffer(recordReader);
-}
-
-// ----------------------------------------------------------------------------
-// Function value()
-// ----------------------------------------------------------------------------
-
-template <typename TFile>
-inline char
-value(RecordReader<TFile, SinglePass<void> > & recordReader)
-{
-    SEQAN_ASSERT(recordReader._current != recordReader._end);
-    return *recordReader._current;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_RECORD_READER_SINGLE_H_
diff --git a/seqan/stream/record_reader_single_mmap.h b/seqan/stream/record_reader_single_mmap.h
deleted file mode 100644
index 10e5b05..0000000
--- a/seqan/stream/record_reader_single_mmap.h
+++ /dev/null
@@ -1,208 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// The Single-Pass Record Reader working on strings.  It uses that data does
-// not have to be read explicitely but is automatically loaded by the OS on
-// pagefaults.
-// ==========================================================================
-
-#ifndef SEQAN_STREAM_RECORD_READER_SINGLE_MMAP_H_
-#define SEQAN_STREAM_RECORD_READER_SINGLE_MMAP_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class StringSinglePassRecordReader
- * @extends SinglePassRecordReader
- * @headerfile <seqan/stream.h>
- * @brief RecordReader specializaton for single-pass reading from strings.
- *
- * @signature template <typename TString>
- *            class RecordReader<TString, SinglePass<StringReader> >;
- *
- * @tparam TMMapString The @link String @endlink to read from.
- *
- * @section Remarks
- *
- * This RecordReader does not have any buffers but uses the string directly.  You can use @link MMapString @endlink to
- * read from memory mapped files.
- *
- * Not default or copy constructable.
- */
-
-/**
-.Spec.Single-Pass String RecordReader
-..cat:Input/Output
-..general:Spec.Single-Pass RecordReader
-..summary:Record reader specialization for single-pass reading from memory mapped files.
-..signature:RecordReader<TStream, SinglePass<StringReader> >
-..param.TStream:The @Concept.StreamConcept@ type to work on.
-..remarks:This record reader does not have any buffers but uses the memory mapped string directly.
-..remarks:Is not default or copy constructable.
-..remarks:The buffer size is the granularity in which @Function.mmapAdvise@ will be called if $TString$ is an @Spec.MMap String@.
-..see:Class.String
-..include:seqan/stream.h
- */
-
-// TODO(holtgrew): Actually, this should work on sequences but is yet untested.
-
-template <typename TString>
-class RecordReader<TString, SinglePass<StringReader> >
-{
-public:
-    typedef typename Iterator<TString, Standard>::Type TIter;
-    typedef typename Size<TString>::Type TSize;
-
-    TString & _string;
-    TIter _current, _end;
-    TSize _bufferSize;
-
-    enum {
-        OK = 0,
-        INVALID_FORMAT
-    };
-
-    RecordReader(TString & string)
-            : _string(string), _current(begin(string)), _end(end(string)),
-              _bufferSize(BUFSIZ)
-    {}
-
-    RecordReader(TString & string, unsigned bufferSize)
-            : _string(string), _current(begin(string)), _end(end(string)),
-              _bufferSize(bufferSize)
-    {}
-
-private:
-    // No default or copy constructor.
-    RecordReader(RecordReader const &other): _string(other._string) {}
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function position()
-// ----------------------------------------------------------------------------
-
-// TODO(holtgrew): Document!
-template <typename TString>
-inline typename Position<TString>::Type
-position(RecordReader<TString, SinglePass<StringReader> > const & recordReader)
-{
-    return recordReader._current - begin(recordReader._string, Standard());
-}
-
-// ----------------------------------------------------------------------------
-// Function setPosition()
-// ----------------------------------------------------------------------------
-
-template <typename TString, typename TPosition>
-inline int
-setPosition(RecordReader<TString, SinglePass<StringReader> > & recordReader, TPosition pos)
-{
-    recordReader._current = iter(recordReader._string, pos, Standard());
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function atEnd()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline bool
-atEnd(RecordReader<TString, SinglePass<StringReader> > & recordReader)
-{
-    return recordReader._current == recordReader._end;
-}
-
-// TODO(holtgrew): We would rather have the const version only.
-
-template <typename TString>
-inline bool
-atEnd(RecordReader<TString, SinglePass<StringReader> > const & recordReader)
-{
-    return recordReader._current == recordReader._end;
-}
-
-// ----------------------------------------------------------------------------
-// Function resultCode()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline int
-resultCode(RecordReader<TString, SinglePass<StringReader> > & /*recordReader*/)
-{
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function goNext()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline bool
-goNext(RecordReader<TString, SinglePass<StringReader> > & recordReader)
-{
-    SEQAN_ASSERT(recordReader._current != recordReader._end);
-    recordReader._current += 1;
-    return false;
-}
-
-// ----------------------------------------------------------------------------
-// Function value()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline char
-value(RecordReader<TString, SinglePass<StringReader> > & recordReader)
-{
-    SEQAN_ASSERT(recordReader._current != recordReader._end);
-    return *recordReader._current;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_RECORD_READER_SINGLE_MMAP_H_
diff --git a/seqan/stream/stream_base.h b/seqan/stream/stream_base.h
index 5531d2d..04aaa0c 100644
--- a/seqan/stream/stream_base.h
+++ b/seqan/stream/stream_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,15 +29,13 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
-// Base class for streams.
-//
-// See header stream_put.h for the generic implementation of streamPut().
+// Basic definitions for the stream module
 // ==========================================================================
 
-#ifndef SEQAN_STREAM_STREAM_BASE_H_
-#define SEQAN_STREAM_STREAM_BASE_H_
+#ifndef SEQAN_STREAM_STREAM_BASE_
+#define SEQAN_STREAM_STREAM_BASE_
 
 namespace seqan {
 
@@ -46,96 +44,190 @@ namespace seqan {
 // ============================================================================
 
 // ============================================================================
-// Tags, Classes, Enums
+// Tags, Enums
 // ============================================================================
 
+// --------------------------------------------------------------------------
+// Compression Type Tags
+// --------------------------------------------------------------------------
+
 /*!
- * @class Stream
- * @implements StreamConcept
- * @headerfile <seqan/stream.h>
- * @brief Abstract base class to fulfill the @link StreamConcept stream concept @endlink.
- *
- * @signature template <typename TSpec>
- *            class Stream;
- *
- * @tparam TSpec The specializing type.
+ * @defgroup FileCompressionTags File Compression Tags
+ * @brief Tags for describing file compression formats.
  */
 
-/**
-.Class.Stream
-..cat:Input/Output
-..implements:Concept.StreamConcept
-..signature:Stream<TSpec>
-..summary:Abstract base class to fulfill the @Concept.StreamConcept@ concept.
-..concept:Concept.StreamConcept
-..include:seqan/stream.h
+/*!
+ * @tag FileCompressionTags#GZFile
+ * @headerfile <seqan/stream.h>
+ * @brief File compression using the popular <a href="http://gzip.org">gzip</a> format.
+ * @signature typedef Tag<GZFile_> GZFile;
  */
 
-template <typename TPointer = char *>
-struct CharArray;
-
-#if SEQAN_HAS_ZLIB  // Enable Stream<GZFile> if available.
 struct GZFile_;
 typedef Tag<GZFile_> GZFile;
-#endif  // #if SEQAN_HAS_ZLIB
-
-#if SEQAN_HAS_BZIP2  // Enable Stream<BZ2File> if available.
-struct BZ2File_;
-typedef Tag<BZ2File_> BZ2File;
-#endif  // #if SEQAN_HAS_ZLIB
-
-template <typename TSpec>
-class Stream;
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ============================================================================
-// Functions
-// ============================================================================
 
 /*!
- * @fn Stream#open
- * @brief Open a stream.
- *
- * @signature bool open(stream, fileName, mode);
+ * @tag FileCompressionTags#BgzFile
+ * @headerfile <seqan/stream.h>
+ * @signature typedef Tag<BgzfFile_> BgzfFile;
+ * @brief File compression using the BGZF (Block GZip Format).
  *
- * @param[in,out] stream   The stream to open.
- * @param[in]     fileName The path to the file to open.  Type: <tt>char const *</tt>.
- * @param[in]     mode     The mode for opening.
+ * The file format is described in the <a href="http://samtools.github.io/hts-specs/SAMv1.pdf">SAM file format
+ * description</a>.
  */
 
+struct BgzfFile_;
+typedef Tag<BgzfFile_> BgzfFile;
+
 /*!
- * @fn Stream#close
- * @brief Close a stream.
+ * @tag FileCompressionTags#BZ2File
+ * @headerfile <seqan/stream.h>
  *
- * @signature void close(stream);
+ * @brief File compression using the popular <a href="http://bzip.org">bzip2</a> format.
  *
- * @param[in,out] stream The Stream to close.
+ * @signature typedef Tag<BZ2File_> BZ2File;
  */
 
-// ----------------------------------------------------------------------------
-// Function atEnd()
-// ----------------------------------------------------------------------------
+struct BZ2File_;
+typedef Tag<BZ2File_> BZ2File;
+
+// --------------------------------------------------------------------------
+// MagicHeader
+// --------------------------------------------------------------------------
+
+template <typename T>
+struct MagicHeader<GZFile, T>
+{
+    static char const VALUE[3];
+};
 
-///.Function.atEnd.param.iterator.type:Class.Stream
-///.Function.atEnd.class:Class.Stream
+template <typename T>
+char const MagicHeader<GZFile, T>::VALUE[3] = { 0x1f, '\x8b', 0x08 };  // gzip's magic number
+
+
+template <typename T>
+struct MagicHeader<BZ2File, T>
+{
+    static char const VALUE[3];
+};
+
+template <typename T>
+char const MagicHeader<BZ2File, T>::VALUE[3] = { 0x42, 0x5a, 0x68 };  // bzip2's magic number
+
+// --------------------------------------------------------------------------
+// FileExtensions
+// --------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<GZFile, T>
+{
+    static char const * VALUE[1];
+};
+
+template <typename T>
+char const * FileExtensions<GZFile, T>::VALUE[1] =
+{
+    ".gz"      // default output extension
+};
+
+
+template <typename T>
+struct FileExtensions<BgzfFile, T>
+{
+    static char const * VALUE[4];
+};
+
+template <typename T>
+char const * FileExtensions<BgzfFile, T>::VALUE[4] =
+{
+    ".bgzf",      // default output extension
+    ".bam",       // BAM files are bgzf compressed
+    ".vcf.gz",    // Compressed and indexed VCF files are actually bgzf compressed
+    ".tbi"        // Tabix index files are bgzf compressed
+
+    // if you add extensions here, extend getBasename() below
+};
+
+
+template <typename T>
+struct FileExtensions<BZ2File, T>
+{
+    static char const * VALUE[1];
+};
+
+template <typename T>
+char const * FileExtensions<BZ2File, T>::VALUE[1] =
+{
+    ".bz2"      // default output extension
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function _isPipe()
+// --------------------------------------------------------------------------
 
-template <typename TSpec>
 inline bool
-atEnd(Stream<TSpec> & stream)
+_isPipe(const char * fileName)
 {
-    return streamEof(stream);
+#ifdef PLATFORM_WINDOWS
+    struct _stat buf;
+    if (_stat(fileName, &buf) == 0)
+        if ((buf.st_mode & _S_IFMT) == _S_IFCHR)
+            return true;
+#else
+    struct stat buf;
+    if (stat(fileName, &buf) == 0)
+        if ((buf.st_mode & S_IFMT) == S_IFIFO ||
+            (buf.st_mode & S_IFMT) == S_IFCHR)
+            return true;
+#endif
+    return false;
 }
 
-template <typename TSpec>
+// --------------------------------------------------------------------------
+// Function guessFormat()
+// --------------------------------------------------------------------------
+
+// read first bytes of a file/stream and compare with file format's magic header
+template <typename TStream, typename TFormat_>
 inline bool
-atEnd(Stream<TSpec> const & stream)
+guessFormatFromStream(TStream &istream, Tag<TFormat_>)
 {
-    return streamEof(stream);
+    typedef Tag<TFormat_> TFormat;
+
+    SEQAN_ASSERT(istream.good());
+
+    if ((char *)MagicHeader<TFormat>::VALUE == NULL)
+        return true;
+
+    bool match = true;
+
+    // check magic header
+    unsigned i;
+    for (i = 0; i != sizeof(MagicHeader<TFormat>::VALUE) / sizeof(char); ++i)
+    {
+        int c = (int)istream.get();
+        if (c != (unsigned char)MagicHeader<TFormat>::VALUE[i])
+        {
+            match = false;
+            if (c != EOF)
+                ++i;
+            break;
+        }
+    }
+
+    // unget all read characters
+    for (; i > 0; --i)
+        istream.unget();
+
+    SEQAN_ASSERT(istream.good());
+
+    return match;
 }
 
-}  // namespace seqean
+}  // namespace seqan
 
-#endif  // #ifndef SEQAN_STREAM_STREAM_BASE_H_
+#endif  // #ifndef SEQAN_STREAM_STREAM_BASE_
diff --git a/seqan/stream/stream_bgzf.h b/seqan/stream/stream_bgzf.h
deleted file mode 100644
index c72477c..0000000
--- a/seqan/stream/stream_bgzf.h
+++ /dev/null
@@ -1,1231 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// BGZF Stream Access.
-//
-// This code is based on the original code by the Broad institute at MIT.
-// The license for the original code is reproduced below.
-// ==========================================================================
-
-/* The MIT License
-
-   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
-
-   Permission is hereby granted, free of charge, to any person obtaining a copy
-   of this software and associated documentation files (the "Software"), to deal
-   in the Software without restriction, including without limitation the rights
-   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-   copies of the Software, and to permit persons to whom the Software is
-   furnished to do so, subject to the following conditions:
-
-   The above copyright notice and this permission notice shall be included in
-   all copies or substantial portions of the Software.
-
-   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-   THE SOFTWARE.
-*/
-
-#ifndef EXTRAS_INCLUDE_SEQAN_STREAM_STREAM_BGZF_H_
-#define EXTRAS_INCLUDE_SEQAN_STREAM_STREAM_BGZF_H_
-
-#include <map>
-
-#include <zlib.h>
-
-// TODO(holtgrew): Check file for truncation via function.
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-struct Bgzf_;
-typedef Tag<Bgzf_> Bgzf;
-template <> class Stream<Bgzf>;
-inline void close(Stream<Bgzf> & stream);
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// One entry in the BGZF cache.
-
-struct BgzfCacheEntry_
-{
-    int size;
-    String<char> block;
-    __int64 endOffset;
-};
-
-/*!
- * @class BgzfStream
- * @extends Stream
- * @headerfile <seqan/stream.h>
- * @brief Reading and writing of BGZF data.
- *
- * @section Remarks
- *
- * Not copy constructable, not assignable.
- *
- * BGZF is the Block GZip Format which is used as the underlying format for BAM and TABIX.  Data is written out
- * compressed with gzip but the uncompressed data is split into blocks with a maximum block size.  It is therefore
- * possible to jump to beginnings of blocks in the resulting files, decompress the block and then jump into the block
- * itself.
- *
- * @section Examples
- *
- * @code{.cpp}
- * Stream<Bgzf> stream;
- * if (!open(stream, "myfile.bam", "r"))
- *     return 1;  // error
- * // ... work
- * @endcode
- */
-
-/**
-.Spec.BGZF Stream
-..cat:Input/Output
-..signature:Stream<Bgzf>
-..general:Class.Stream
-..summary:Reading and writing of BGZF data.
-..remarks:Not copy constructable, not assignable.
-..remarks:
-BGZF is the Block GZip Format which is used as the underlying format for BAM and TABIX.
-Data is written out compressed with gzip but the uncompressed data is split into blocks with a maximum block size.
-It is therefore possible to jump to beginnings of blocks in the resulting files, decompress the block and then jump into the block itself.
-..include:seqan/stream.h
-..example.code:
-Stream<Bgzf> stream;
-if (!open(stream, "myfile.bam", "r"))
-    return 1;  // error
-// ... work
- */
-
-struct Bgzf_;
-typedef Tag<Bgzf_> Bgzf;
-
-template <>
-class Stream<Bgzf>
-{
-public:
-    typedef File<Sync<> > TFile;  // Type to use for reading/writing files.
-    typedef Position<TFile>::Type TPosition;
-
-    // The current error state, 0 for no error.
-    int _error;
-
-    // Flag that indicates whether we are at the end of the file.
-    bool _atEof;
-
-    // Mode of currently opened file.
-    int _openMode;  // TODO(holtgrew): Should go into File class.
-
-    // Current zlib compression level.
-    int _compressLevel;
-
-    // The file handle for the BGZF stream.
-    TFile _file;
-
-    // Buffer for uncompressed data.
-    String<char> _uncompressedBlock;
-
-    // Buffer for compressed data.
-    String<char> _compressedBlock;
-
-    // The address of the current block.
-    TPosition _blockPosition;
-
-    // Length of the current block.
-    __int32 _blockLength;
-
-    // Offset in the current block.
-    __int32 _blockOffset;
-
-    // Cache of decompressed blocks.
-    std::map<__int64, BgzfCacheEntry_ *> _cache;
-
-    // Number of bytes in cached blocks.
-    int _cacheSize;
-
-    // Maximum cache size, as number of bytes in cached blocks.
-    int _maxCacheSize;
-
-    // Whether or not the file is owned (i.e. opened with open()) or just attached to an already open file via POSIX
-    // file handle.
-    bool _fileOwned;
-
-    // Size of the file in bytes as it is on the disk.
-    __int64 _fileSize;
-
-    Stream() : _error(0), _atEof(false), _openMode(0), _compressLevel(Z_DEFAULT_COMPRESSION), _blockPosition(0),
-               _blockLength(0), _blockOffset(0), _cacheSize(0), _maxCacheSize(0), _fileOwned(false), _fileSize(0)
-    {}
-
-    ~Stream()
-    {
-        close(*this);
-    }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Difference
-// ----------------------------------------------------------------------------
-
-template <>
-struct Difference<Stream<Bgzf> >
-{
-    typedef __int64 Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Position
-// ----------------------------------------------------------------------------
-
-template <>
-struct Position<Stream<Bgzf> >
-{
-    typedef __int64 Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <>
-struct Size<Stream<Bgzf> >
-{
-    typedef __int64 Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <>
-struct Value<Stream<Bgzf> >
-{
-    typedef char Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<Bgzf>, IsInput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsOutput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<Bgzf>, IsOutput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasPeek>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<Bgzf>, HasPeek>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasFilename>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<Bgzf>, HasFilename>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Seek<TSpec> >
-// ----------------------------------------------------------------------------
-
-template <typename TSpec>
-struct HasStreamFeature<Stream<Bgzf>, Seek<TSpec> >
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature<Stream<Bgzf>, Seek<OriginBegin> >
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Tell>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<Bgzf>, Tell>
-{
-    typedef True Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function size()
-// ----------------------------------------------------------------------------
-
-// TODO(holtgrew): Do we want a trait for this? Only possible for random access streams and those that have an underlying file.
-///.Function.size.param.file.type:Spec.BGZF Stream
-///.Function.size.class:Spec.BGZF Stream
-
-// Just forward to underlying Class.File's size().
-
-/*
-inline typename Size<Stream<Bgzf> >::Type
-size(Stream<Bgzf> const & stream)
-{
-    return size(stream._file);
-}
-*/
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfUnpackInt16()
-// ----------------------------------------------------------------------------
-
-inline int
-_bgzfUnpackInt16(unsigned char const * buffer)
-{
-    return (buffer[0] | (buffer[1] << 8));
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfPackInt16()
-// ----------------------------------------------------------------------------
-
-inline
-void
-_bgzfPackInt16(unsigned char * buffer, __uint16 value)
-{
-    buffer[0] = value;
-    buffer[1] = value >> 8;
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfPackInt32()
-// ----------------------------------------------------------------------------
-
-inline void
-_bgzfPackInt32(unsigned char * buffer, __int32 value)
-{
-    buffer[0] = value;
-    buffer[1] = value >> 8;
-    buffer[2] = value >> 16;
-    buffer[3] = value >> 24;
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfCheckHeader()
-// ----------------------------------------------------------------------------
-
-inline int
-_bgzfCheckHeader(char const * header)
-{
-    const char GZIP_ID1 = 31;
-    const __uint8 GZIP_ID2 = 139;
-    const char FLG_FEXTRA = 4;
-    const char BGZF_ID1 = 66;  // 'B'
-    const char BGZF_ID2 = 67;  // 'C'
-    const char BGZF_LEN = 2;
-    const char BGZF_XLEN = 6;  // BGZF_LEN+4
-
-    return (header[0] == GZIP_ID1 &&
-            (__uint8)header[1] == (__uint8) GZIP_ID2 &&
-            header[2] == Z_DEFLATED &&
-            (header[3] & FLG_FEXTRA) != 0 &&
-            _bgzfUnpackInt16((unsigned char*)&header[10]) == BGZF_XLEN &&
-            header[12] == BGZF_ID1 &&
-            header[13] == BGZF_ID2 &&
-            _bgzfUnpackInt16((unsigned char*)&header[14]) == BGZF_LEN);
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfLoadBlockFromCache()
-// ----------------------------------------------------------------------------
-
-// Returns number of bytes loaded from cache, 0 if address could not be found.
-
-inline int
-_bgzfLoadBlockFromCache(Stream<Bgzf> & stream, __int64 blockAddress)
-{
-    // If there is no block in the cache with this address then return false.
-    std::map<__int64, BgzfCacheEntry_ *>::iterator it = stream._cache.find(blockAddress);
-    if (it == stream._cache.end())
-        return 0;
-
-    // Update fields of stream.
-    if (stream._blockLength != 0)
-        stream._blockOffset = 0;
-    stream._blockPosition = blockAddress;
-    stream._blockLength = it->second->size;
-
-    // Copy data from cache into uncompressed block buffer.
-    if (!empty(it->second->block))
-        memcpy(&stream._uncompressedBlock[0], &it->second->block[0], length(it->second->block));
-
-    // Seek to end of cached block in the underlying file.
-    seek(stream._file, it->second->endOffset, SEEK_SET);
-
-    return it->second->size;
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfCacheBlock()
-// ----------------------------------------------------------------------------
-
-inline bool
-_bgzfCacheBlock(Stream<Bgzf> & stream, size_t size)
-{
-    if (stream._blockLength > stream._maxCacheSize)
-        return false;  // Cannot cache this block.
-    if (stream._cache.find(stream._blockPosition) != stream._cache.end())
-        return true;  // Block is already cached.
-
-    // TODO(holtgrew): Implement LRU scheme?
-    
-    // Throw out blocks from cache until the new cache fits.  We simply remove the first block which should not make
-    // performance degrade much in practice.
-    while (stream._cacheSize + stream._blockLength > stream._maxCacheSize)
-    {
-        SEQAN_ASSERT_NOT(stream._cache.empty());
-        std::map<__int64, BgzfCacheEntry_ *>::iterator it = stream._cache.begin();
-        stream._cacheSize -= length(it->second->block);
-        delete it->second;
-        stream._cache.erase(it);
-    }
-
-    // Create new cache entry, copy out block data and put it into the cache.
-    BgzfCacheEntry_ * entry = new BgzfCacheEntry_();
-    entry->size = stream._blockLength;
-    entry->block = prefix(stream._uncompressedBlock, stream._blockLength);
-    entry->endOffset = stream._blockPosition + size;
-    stream._cache[stream._blockPosition] = entry;
-
-    stream._cacheSize += length(entry->block);
-    SEQAN_ASSERT_LEQ(stream._cacheSize, stream._maxCacheSize);
-
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfCacheBlock()
-// ----------------------------------------------------------------------------
-
-inline void
-_bgzfClearCache(Stream<Bgzf> & stream)
-{
-    typedef std::map<__int64, BgzfCacheEntry_ *>::iterator TIterator;
-    for (TIterator it = stream._cache.begin(); it != stream._cache.end(); ++it)
-        delete it->second;
-    stream._cacheSize = 0;
-    stream._cache.clear();
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfInflateBlock()
-// ----------------------------------------------------------------------------
-
-// Inflate from compression to decompression buffer.
-
-inline int
-_bgzfInflateBlock(Stream<Bgzf> & stream, size_t blockLength)
-{
-    int const GZIP_WINDOW_BITS = -15;  // no zlib header
-
-    z_stream zs;
-	int status;
-    zs.zalloc = NULL;
-    zs.zfree = NULL;
-    zs.next_in = static_cast<Bytef *>(static_cast<void *>(&stream._compressedBlock[0])) + 18;
-    zs.avail_in = blockLength - 16;
-    zs.next_out = static_cast<Bytef *>(static_cast<void *>(&stream._uncompressedBlock[0]));
-    zs.avail_out = length(stream._uncompressedBlock);
-
-    status = inflateInit2(&zs, GZIP_WINDOW_BITS);
-    if (status != Z_OK)
-        return -1;  // inflateInit2() has failed.
-
-    status = inflate(&zs, Z_FINISH);
-    if (status != Z_STREAM_END)
-    {
-        inflateEnd(&zs);
-        return -1;  // inflate() has failed.
-    }
-
-    status = inflateEnd(&zs);
-    if (status != Z_OK)
-        return -1;  // inflateEnd() failed.
-
-    return zs.total_out;
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfReadBlock()
-// ----------------------------------------------------------------------------
-
-// Returns 0 on success, -1 on error, -2 on eof.
-
-inline int
-_bgzfReadBlock(Stream<Bgzf> & stream)
-{
-    int const BLOCK_HEADER_LENGTH = 18;
-    // Make sure there is enough space in the buffer for compressed data.
-    unsigned const MAX_BLOCK_SIZE = 64 * 1024;
-    resize(stream._compressedBlock, MAX_BLOCK_SIZE);
-    resize(stream._uncompressedBlock, MAX_BLOCK_SIZE);
-
-    char header[BLOCK_HEADER_LENGTH];
-
-    // Get address from block and try to get cached block from this address.
-    __int64 blockAddress = tell(stream._file);
-    if (_bgzfLoadBlockFromCache(stream, blockAddress))
-        return 0;
-
-    // Try to read the heder.
-    __int64 posBefore = tell(stream._file);
-    // TODO(holtgrew): Complicated reading because File<> interface is not so good.
-    bool success = read(stream._file, &header[0], sizeof(header));
-    int count = tell(stream._file) - posBefore;
-    if (!success && count == 0)
-        return -2;  // EOF.
-    if (!success)  // Unnecessary, could go away when file interface changes.
-        return -1; // Could not read header.
-
-    // If no data could be read for the header then we are at the end of the file, this is no error.
-    // TODO(holtgrew): Correct with EOF?
-    if (count == 0)
-    {
-        stream._blockLength = 0;
-        return 0;
-    }
-
-    int size = count;
-
-    // Check that the header is valid.
-    if (count != sizeof(header))
-        return -1;  // Could not read the full header.
-    if (!_bgzfCheckHeader(header))
-        return -1;  // Header was invalid.
-
-    // Copy header into buffer for compressed data.
-    int blockLength = _bgzfUnpackInt16((unsigned char *)&header[16]) + 1;
-    char * compressedBlock = (char *)&stream._compressedBlock[0];
-    memcpy(compressedBlock, header, BLOCK_HEADER_LENGTH);
-    int remaining = blockLength - BLOCK_HEADER_LENGTH;
-
-    // Read remainder of block into buffer for compressed data.
-    // TODO(holtgrew): Complicated reading because File<> interface is not so good.
-    posBefore = tell(stream._file);
-    success = read(stream._file, &compressedBlock[BLOCK_HEADER_LENGTH], remaining);
-    if (!success)
-        return -1;
-    count = tell(stream._file) - posBefore;
-    if (count != remaining)
-        return -1;  // Read failed.
-
-    size += count;
-
-    // Decompress between compression and decompression buffer.
-    count = _bgzfInflateBlock(stream, blockLength);
-    if (count < 0)
-        return -1;  // Decompression failed.
-
-    if (stream._blockLength != 0)
-        stream._blockOffset = 0;  // Do not reset offset if this read follows a seek.
-
-    // Update block address and length in stream object and add block to cache.
-    stream._blockPosition = blockAddress;
-    stream._blockLength = count;
-    _bgzfCacheBlock(stream, size);
-
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Helper Function _bgzfDeflateBlock()
-// ----------------------------------------------------------------------------
-
-// Deflate from uncompressed block to compressed block.  Also add extra field that stores the compressed block length.
-
-inline int
-_bgzfDeflateBlock(Stream<Bgzf> & stream, int blockLength)
-{
-    const int BLOCK_HEADER_LENGTH = 18;
-    const int BLOCK_FOOTER_LENGTH = 8;
-
-    const char GZIP_ID1 = 31;
-    const __uint8 GZIP_ID2 = 139;
-    const char CM_DEFLATE = 8;
-    const char FLG_FEXTRA = 4;
-    const __uint8 OS_UNKNOWN = 255;
-    const char BGZF_ID1 = 66;  // 'B'
-    const char BGZF_ID2 = 67;  // 'C'
-    const char BGZF_LEN = 2;
-    const char BGZF_XLEN = 6;  // BGZF_LEN+4
-
-    const int GZIP_WINDOW_BITS = -15; // no zlib header
-    const int Z_DEFAULT_MEM_LEVEL = 8;
-
-    const int MAX_BLOCK_SIZE = 64 * 1024;
-
-    // Make sure there is enough space in the buffer for compressed and uncompressed data.
-    resize(stream._compressedBlock, MAX_BLOCK_SIZE);
-    resize(stream._uncompressedBlock, MAX_BLOCK_SIZE);
-
-    char * buffer = &stream._compressedBlock[0];
-    int bufferSize = length(stream._compressedBlock);
-
-    // Init gzip header
-    buffer[0] = GZIP_ID1;
-    buffer[1] = GZIP_ID2;
-    buffer[2] = CM_DEFLATE;
-    buffer[3] = FLG_FEXTRA;
-    buffer[4] = 0;  // mtime
-    buffer[5] = 0;
-    buffer[6] = 0;
-    buffer[7] = 0;
-    buffer[8] = 0;
-    buffer[9] = OS_UNKNOWN;
-    buffer[10] = BGZF_XLEN;
-    buffer[11] = 0;
-    buffer[12] = BGZF_ID1;
-    buffer[13] = BGZF_ID2;
-    buffer[14] = BGZF_LEN;
-    buffer[15] = 0;
-    buffer[16] = 0;  // Placeholder for block length.
-    buffer[17] = 0;
-
-    // Loop to retry for blocks that do not compress enough.
-    int inputLength = blockLength;
-    int compressedLength = 0;
-    while (true)
-    {
-        z_stream zs;
-        zs.zalloc = NULL;
-        zs.zfree = NULL;
-        zs.next_in = static_cast<Bytef *>(static_cast<void *>(&stream._uncompressedBlock[0]));
-        zs.avail_in = inputLength;
-        zs.next_out = static_cast<Bytef *>(static_cast<void *>(&buffer[BLOCK_HEADER_LENGTH]));
-        zs.avail_out = bufferSize - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
-
-        int status = deflateInit2(&zs, stream._compressLevel, Z_DEFLATED,
-                                  GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
-        if (status != Z_OK)
-            return -1;  // deflateInit2() failed.
-
-        status = deflate(&zs, Z_FINISH);
-        if (status != Z_STREAM_END)
-        {
-            status = deflateEnd(&zs);
-            if (status == Z_OK)
-            {
-                // Not enough space in buffer.  This can happen in the rare case the input doesn't compress enough.  We
-                // try to resolve this by reducing the amount of input until it fits.
-                inputLength -= 1024;
-                if (inputLength <= 0)
-                    return -1;  // Input reduction failed.
-                continue;
-            }
-            return -1;  // Deflate failed.
-        }
-
-        status = deflateEnd(&zs);
-        if (status != Z_OK)
-            return -1;  // Deflate end failed.
-
-        compressedLength = zs.total_out;
-        compressedLength += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
-        if (compressedLength > MAX_BLOCK_SIZE)
-            return -1;  // Deflate overflow, should never happen.
-
-        break;
-    }
-
-    // Set compressed length into buffer, compute CRC and write CRC into buffer.
-    _bgzfPackInt16((unsigned char*)&buffer[16], compressedLength - 1);
-    __uint32 crc = crc32(0L, NULL, 0L);
-    crc = crc32(crc, static_cast<Bytef *>(static_cast<void *>(&stream._uncompressedBlock[0])), inputLength);
-    _bgzfPackInt32((unsigned char*)&buffer[compressedLength - 8], crc);
-    _bgzfPackInt32((unsigned char*)&buffer[compressedLength - 4], inputLength);
-
-    // Copy data that did not fit into the compressed block forward in the uncompressed data buffer.
-    int remaining = blockLength - inputLength;
-    if (remaining > 0)
-    {
-        if (remaining > inputLength)
-            return -1;  // Remained too large.  Should never happen (checking here so we can use memcpy).
-        memcpy(&stream._uncompressedBlock[0],
-               &stream._uncompressedBlock[0] + inputLength,
-               remaining);
-    }
-    stream._blockOffset = remaining;
-
-    return compressedLength;
-}
-
-// ----------------------------------------------------------------------------
-// Function attachToFile
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BGZF Stream#attachToFile
- * @brief Attach to already open input/output POSIX file.
- *
- * @signature void attachToFile(stream, fileHandle, mode);
- * 
- * @param[in,out] stream     Stream to attach to file. Types: BGZF Stream
- * @param[in]     fileHandle The file handle to attach to.  Type: <tt>int</tt>
- * @param[in]     mode       The mode flag the file was opened with. Type: <tt>int</tt>
- * 
- * @section Remarks
- * 
- * A previously opened file is closed.
- */
-
-/**
-.Function.attachToFile
-..class:Spec.BGZF Stream
-..cat:Input/Output
-..summary:Attach to already open input / output file.
-..signature:attachToFile(stream, fileHandle, mode)
-..param.stream:Stream to attach to file.
-...type:Spec.BGZF Stream
-..param.fileHandle:The file handle to attach to.
-...type:nolink:$int$
-..param.mode:The mode flag the file was opened with.
-...type:nolink:$int$
-..remarks:A previously opened file is closed.
-..include:seqan/stream.
-*/
-
-inline void
-attachToFile(Stream<Bgzf> & stream, int fileHandle, int mode)
-{
-    close(stream);  // Close previously opened file.
-    stream._file.handle = fileHandle;
-    stream._openMode = mode;
-    stream._fileOwned = false;
-    // Set compression level.
-    if (mode & OPEN_WRONLY)
-        stream._compressLevel = Z_DEFAULT_COMPRESSION;
-}
-
-// ----------------------------------------------------------------------------
-// Function open()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BgzfStream#open
- * @brief Open a stream.
- *
- * @signature bool open(stream, fileName, mode);
- *
- * @param[in,out] stream   The stream to open.
- * @param[in]     fileName The path to the file to open.  Type: <tt>char const *</tt>.
- * @param[in]     mode     The mode for opening.
- *
- * @section Remarks
- *
- * You can append <tt>0-9</tt> or <tt>u</tt> or <tt>w</tt> in <tt>mode</tt>. for setting the compression level to 0-9 or
- * "no compression".
- */
-
-/**
-.Function.open
-..class:Spec.BGZF Stream
-..param.stream.type:Spec.BGZF Stream
-..param.mode.remarks:When opening $Stream<Bgzf>$ for writing, you can append $'0'$-$'9'$ or $'u'$ to $"w"$ for setting the compression level to 0-9 or "no compression".
- */
-
-inline bool
-open(Stream<Bgzf> & stream, char const * filename, char const * mode)
-{
-    // Reset stream state.
-    stream._error = 0;
-    stream._openMode = 0;
-    stream._blockPosition = 0;
-    stream._blockLength = 0;
-    stream._blockOffset = 0;
-    stream._fileSize = 0;
-
-    // Actually open files.
-    if (mode[0] == 'r' || mode[0] == 'R')  // Open for reading.
-    {
-        stream._openMode = OPEN_RDONLY;
-        open(stream._file, filename, stream._openMode);
-
-        // Determine file size.
-        if (seek(stream._file, 0, SEEK_END) == 0)
-        {
-            stream._error = -1;  // Seek from end of file failed.
-            return false;
-        }
-        stream._fileSize = tell(stream._file);
-        if (seek(stream._file, 0, SEEK_SET) != 0)
-        {
-            stream._error = -1;  // Seek from start of file failed.
-            return false;
-        }
-    }
-    else if (mode[0] == 'w' || mode[0] == 'W')  // Open for writing.
-    {
-        stream._compressLevel = Z_DEFAULT_COMPRESSION;
-
-        // Set compression level.
-        unsigned i;
-        for (i = 0; mode[i]; ++i)
-            if (mode[i] >= '0' && mode[i] <= '9') break;
-        if (mode[i])
-            stream._compressLevel = (int)mode[i] - '0';
-        if (strchr(mode, 'u'))
-            stream._compressLevel = 0;
-
-        stream._openMode = OPEN_WRONLY | OPEN_CREATE;
-        open(stream._file, filename, stream._openMode);
-    }
-
-    if (stream._file.handle != -1)  // TODO(holtgrew): File should provide isOpen().
-    {
-        stream._fileOwned = true;
-        return true;
-    }
-    return false;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamFlush()
-// ----------------------------------------------------------------------------
-
-inline int
-streamFlush(Stream<Bgzf> & stream)
-{
-    while (stream._blockOffset > 0)
-    {
-		int blockLength = _bgzfDeflateBlock(stream, stream._blockOffset);
-        if (blockLength < 0)
-            return -1;
-
-        typedef Position<Stream<Bgzf> >::Type TPos;
-        TPos posBefore = tell(stream._file);
-        if (!write(stream._file, &stream._compressedBlock[0], blockLength))
-            return -1;  // Could not write.
-        TPos posAfter = tell(stream._file);
-        int count = posAfter - posBefore;
-        if (count != blockLength)
-            return -1;  // Writing failed.
-
-        stream._blockPosition += blockLength;
-    }
-
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function close()
-// ----------------------------------------------------------------------------
-
-/**
-.Function.close
-..class:Spec.BGZF Stream
-..signature:close(stream)
-..param.stream:Stream to close.
-...type:Class.Stream
- */
-
-inline void
-close(Stream<Bgzf> & stream)
-{
-    if (stream._file.handle == -1)
-        return;   // Do nothing if file is not open.
-    if (!stream._fileOwned)
-        return;  // Do nothing if we do not own the file.
-
-    if (stream._openMode & OPEN_WRONLY)
-    {
-        // Flush stream, compressing and writing out any uncompressed data.
-        if (streamFlush(stream) != 0)
-        {
-            close(stream._file);
-            return;  // Could not flush.
-        }
-
-        // Write an empty block.
-        int blockLength = _bgzfDeflateBlock(stream, 0);
-        typedef Position<Stream<Bgzf> >::Type TPos;
-        TPos posBefore = tell(stream._file);
-        if (!write(stream._file, &stream._compressedBlock[0], blockLength))
-            return;  // Could not write
-        TPos posAfter = tell(stream._file);
-        int count = posAfter - posBefore;
-        // if (count != blockLength)
-        //     SEQAN_FAIL("Failed to write empty block at end of BGZF file.");
-        (void)count;
-        flush(stream._file);
-    }
-
-    // Clear the cache.
-    _bgzfClearCache(stream);
-
-    // Close file.
-    close(stream._file);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamPeek()
-// ----------------------------------------------------------------------------
-
-inline int
-streamPeek(char & c, Stream<Bgzf> & stream)
-{
-    // Read next block if at end of block.
-    if (stream._blockOffset >= stream._blockLength)
-    {
-        if (_bgzfReadBlock(stream) != 0)
-            return -2;  // Error.
-        if (stream._blockLength == 0)
-            return -1;  // EOF.
-    }
-
-    // Return next character from block without advancing stream.
-    SEQAN_ASSERT_LT(stream._blockOffset, stream._blockLength);
-	c = stream._uncompressedBlock[stream._blockOffset];
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadChar()
-// ----------------------------------------------------------------------------
-
-inline int
-streamReadChar(char & c, Stream<Bgzf> & stream)
-{
-    // Read next block if at end of block.
-    if (stream._blockOffset >= stream._blockLength)
-    {
-        if (_bgzfReadBlock(stream) != 0)
-            return -2;  // Error.
-        if (stream._blockLength == 0)
-            return -1;  // EOF.
-    }
-
-    // Return next address and advance stream, without reading next block yet.
-	c = stream._uncompressedBlock[stream._blockOffset++];
-    if (stream._blockOffset == stream._blockLength)
-    {
-        stream._blockPosition = tell(stream._file);
-        stream._blockOffset = 0;
-        stream._blockLength = 0;
-    }
-
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function checkEofIsValid()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn BgzfStream#checkEofIsValid
- * @brief Check that the EOF marker is present in BGZF (e.g. BAM) file.
- *
- * @signature bool checkEofIsValid(stream);
- *
- * @param[in] stream The BgzfStream to check.
- *
- * @return bool true if the marker is present and false otherwise.
- */
-
-/**
-.Function.checkEof
-..class:Spec.BGZF Stream
-..cat:Input/Output
-..summary:Check that the EOF marker is present in a BGZF(/BAM) file.
-..signature:streamEof(stream)
-..param.stream:The BGZF Stream to check.
-...type:Spec.BGZF Stream
-..remarks:This is NOT equivalent to @Function.streamEof@.
-..include:seqan/stream.h
-*/
-
-inline bool
-checkEofIsValid(Stream<Bgzf> & stream)
-{
-    // Setup magic number.
-	static char magic[28];
-    char const * MAGIC_INIT = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
-    memcpy(&magic[0], MAGIC_INIT, 28);
-
-    // Try to read magic number from end of file, then seek back to the current position.
-	uint8_t buf[28];
-    Position<Stream<Bgzf> >::Type offset = tell(stream._file);
-
-    if (!seek(stream._file, -28, SEEK_END))
-    {
-        stream._error = -1;  // Seek from end of file failed.
-        return false;
-    }
-
-    read(stream._file, &buf[0], 28);
-
-    if (!seek(stream._file, offset, SEEK_SET))
-    {
-        stream._error = -1;  // Seek to original position failed.
-        return false;
-    }
-
-    // Finally, compare read magic number with the expected one.
-	return (memcmp(magic, buf, 28) == 0) ? true : false;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamEof()
-// ----------------------------------------------------------------------------
-
-inline bool
-streamEof(Stream<Bgzf> & stream)
-{
-    if (stream._openMode & OPEN_WRONLY)
-        return true;  // Always EOF when writing.
-    if (stream._atEof)
-        return true;  // Two consecutive streamEof() calls.
-
-    // We are in read mode if we reach here.
-    if (stream._blockOffset < stream._blockLength)
-        return false;  // There is still stuff in the read buffer.
-    int res =_bgzfReadBlock(stream);
-    if (res == -2)
-        stream._atEof = true;
-    else if (res != 0)
-        SEQAN_FAIL("Error reading block in streamEof().");
-    else
-        stream._atEof = (stream._blockLength == 0);
-    return stream._atEof;
-}
-
-// TODO(holtgrew): We would rather have the const version only and then need to make some things in Stream<Bgzf> mutable.
-inline bool
-streamEof(Stream<Bgzf> const & stream)
-{
-    return streamEof(const_cast<Stream<Bgzf> &>(stream));
-}
-
-// ----------------------------------------------------------------------------
-// Function streamError
-// ----------------------------------------------------------------------------
-
-inline int
-streamError(Stream<Bgzf> & stream)
-{
-    if (stream._error == -1)
-        return 0;
-    return stream._error;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamReadBlock(char * target, Stream<Bgzf> & stream, size_t maxLen)
-{
-    if (!(stream._openMode & OPEN_RDONLY))
-        return 0;  // File not open for reading.
-
-    // Memoize number of read bytes and pointer into the buffer target.
-    size_t bytesRead = 0;
-    char * destPtr = target;
-
-    // Read at most maxLen characters, each loop iteration corresponds to reading the end of the first, the beginning of
-    // the last or the whole "middle" buffers.  Of course, the first and only iteration can also only read parts of the
-    // first buffer.
-    while (bytesRead < maxLen)
-    {
-        // If there are no more bytes left in the current block then read and decompress the next block.
-        int available = stream._blockLength - stream._blockOffset;
-        if (available <= 0)
-        {
-            if (_bgzfReadBlock(stream) != 0)
-                return -1;  // Could not read next block.
-            available = stream._blockLength - stream._blockOffset;
-            if (available <= 0)
-                break;
-        }
-
-        // Copy out the number of bytes to be read or the number of available bytes in the next buffer, whichever number
-        // is smaller.
-        int copyLength = std::min(static_cast<int>(maxLen - bytesRead), available);
-        char * buffer = &stream._uncompressedBlock[0];
-        memcpy(destPtr, buffer + stream._blockOffset, copyLength);
-
-        // Advance to next block.
-        stream._blockOffset += copyLength;
-        destPtr += copyLength;
-        bytesRead += copyLength;
-    }
-
-    // If we read to the end of the block above then switch the block address to the next block and mark it as unread.
-    if (stream._blockOffset == stream._blockLength)
-    {
-        stream._blockPosition = tell(stream._file);
-        stream._blockOffset = 0;
-        stream._blockLength = 0;
-    }
-
-    return bytesRead;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamWriteBlock(Stream<Bgzf> & stream, char const * source, size_t count)
-{
-    unsigned const MAX_BLOCK_SIZE = 64 * 1024;
-    unsigned const DEFAULT_BLOCK_SIZE = 64 * 1024;
-
-    if (!(stream._openMode & OPEN_WRONLY))
-        return -1;  // File is not open for writing.
-
-    // Allocate buffer for uncompressed data.
-    resize(stream._uncompressedBlock, MAX_BLOCK_SIZE);
-
-	char const * inPtr = source;
-    int blockLength = DEFAULT_BLOCK_SIZE;
-    unsigned bytesWritten = 0;
-
-    while (bytesWritten < count)
-    {
-        int copyLength = std::min(static_cast<int>(blockLength - stream._blockOffset),
-                                  static_cast<int>(count - bytesWritten));
-        char * buffer = &stream._uncompressedBlock[0];
-
-        memcpy(buffer + stream._blockOffset, inPtr, copyLength);
-
-        stream._blockOffset += copyLength;
-        inPtr += copyLength;
-        bytesWritten += copyLength;
-
-        if (stream._blockOffset == blockLength && streamFlush(stream) != 0)
-            break;
-    }
-
-    return bytesWritten;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteChar
-// ----------------------------------------------------------------------------
-
-inline int
-streamWriteChar(Stream<Bgzf> & stream, char const c)
-{
-    return streamWriteBlock(stream, &c, 1) != 1;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamSeek()
-// ----------------------------------------------------------------------------
-
-inline int
-streamSeek(Stream<Bgzf> & stream, __uint64 virtualPos, int origin)
-{
-    // Check whether seeking is feasible.
-    if (!(stream._openMode & OPEN_RDONLY))
-        return -1;  // Stream not open for reading.
-    if (origin != SEEK_SET)
-        return -1;  // Only seek set is implemented.
-
-    // Extract block offset and address within the block from the virtual position.
-    int blockOffset = virtualPos & 0xFFFF;
-    __int64 blockAddress = (virtualPos >> 16) & 0xFFFFFFFFFFFFLL;
-
-    // If EOF flag is set then check if we want to keep it.
-    if (stream._atEof)
-    {
-        __int64 currentPos = tell(stream._file);
-        if (currentPos != blockAddress)
-            stream._atEof = false;
-    }
-
-    // Actually perform the seek.
-    seek(stream._file, blockAddress, SEEK_SET);
-
-    // Set the stream state such that the address of the block and the offset in the block are set appropriately but the
-    // block is only loaded on the next read.
-    stream._blockLength = 0;  // Indicates that the current block is not loaded.
-    stream._blockPosition = blockAddress;
-    stream._blockOffset = blockOffset;
-
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamTell()
-// ----------------------------------------------------------------------------
-
-inline Position<Stream<Bgzf> >::Type
-streamTell(Stream<Bgzf> & stream)
-{
-    return (stream._blockPosition << 16) | (stream._blockOffset & 0xFFFF);
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef EXTRAS_INCLUDE_SEQAN_STREAM_STREAM_BGZF_H_
diff --git a/seqan/stream/stream_bz2_file.h b/seqan/stream/stream_bz2_file.h
deleted file mode 100644
index b1fa928..0000000
--- a/seqan/stream/stream_bz2_file.h
+++ /dev/null
@@ -1,453 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Wrapper to BZFILE * that fulfills the Stream concept.  Note that, different
-// from zlib, bzlib does not support seek, tell or position on BZFILE*.  We do
-// not emulate support for this either.  The main use case in SeqAn is
-// sequential reading and writing and we have full support for this.  We do
-// not support peek either, however.  There is no flush(), it is a null
-// implementation but should never be required for the use cases of bzlib in
-// SeqAn.
-// ==========================================================================
-
-#include <bzlib.h>
-
-#ifndef SEQAN_STREAM_BZ2_FILE_WRAPPER_H_
-#define SEQAN_STREAM_BZ2_FILE_WRAPPER_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-template <> class Stream<BZ2File>;
-inline void close(Stream<BZ2File> & stream);
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class BZ2FileStream
- * @extends Stream
- * @headerfile <seqan/stream.h>
- * @brief Wrapper for <tt>BZFILE *</tt> streams from bzlib.
- *
- * @signature template<>
- *            class Stream<BZ2File>;
- *
- * @section Remarks
- *
- * This is only available if @link SEQAN_HAS_BZIP2 @endlink is set to 1.
- *
- * Not copy constructable.
- *
- *
- * @fn BZ2FileStream::Stream();
- * @fn BZ2FileStream::Stream(bzFile);
- *
- * @param[in] bzFile The <tt>BZFILE *</tt> to open.
- *
- * The file <tt>bzFile</tt> must already be open when constructed with the second variant.  <tt>bzFile</tt> will
- * <b>not</b> be closed when the stream is destructed but has to be closed manually.
- */
-
-/**
-.Spec.BZ2 File Stream
-..cat:Input/Output
-..signature:Stream<BZ2File>
-..general:Class.Stream
-..summary:Wrapper for $BZFILE *$ streams from bzlib.
-..remarks:This is only available if @Macro.SEQAN_HAS_ZLIB@ is set to 1.
-..remarks:Not copy constructable.
-..remarks:Follows the RIIA pattern when the file is opened through @Function.open@ (and thus the underlying $BZFILE *$ and $FILE *$ are owned).
-..remarks:
-Can be used as a wrapper around a $BZFILE *$ or create such an object itself through @Function.open@.
-Also see @Memfunc.BZ2 File Stream#Stream|the constructor@.
-..include:seqan/stream.h
-..example.text:It is easy to open a BZ2 file via @Function.open@.
-..example.code:
-#include <seqan/stream.h>
-
-Stream<BZ2File> bzStream;
-open(bzStream, "/path/to/file.txt.bz2", "r");  // binary is implicit
-
-// Now, work with bzStream.  The object will close the file on destruction.
-..example.text:
-You can also use BZ2 File Stream as a wrapper around $BZFILE *$.
-In this case, we have to deal with the verbose code for opening $FILE *$ and $BZFILE *$ by hand.
-..example.code:
-#include <cstdio>
-#include <bzlib.h>
-#include <seqan/stream.h>
-
-// Open normal FILE *, BZFILE * above, and Stream<BZ2File> on top.
-FILE * f = fopen("/path/to/file.txt.bz2", "rb");
-SEQAN_ASSERT(f != NULL);
-int err = BZ_OK;
-BZFILE * f2 = BZ2_bzReadOpen(&err, f, 0, 0, NULL, 0);
-SEQAN_ASSERT_EQ(err, BZ_OK);
-Stream<BZ2File> bzStream(f2);
-
-// Now, you can work with the stream bzStream.
-
-// Note that you only have to close f2 and f, not bzStream.
-BZ2_bzReadClose(&err, f2);
-SEQAN_ASSERT_EQ(err, BZ_OK);
-fclose(f);
-
-.Memfunc.BZ2 File Stream#Stream
-..summary:Constructor
-..class:Spec.BZ2 File Stream
-..signature:Stream<BZ2File>()
-..signature:Stream<BZ2File>(file)
-..param.file:The $BZFILE *$ to wrap.
-...type:nolink:$BZFILE *$.
-..remarks:When $file$ is given then the BZ2 File Stream object does not own the underlying $BZFILE *$ object and will serve as a simple wrapper.
- */
-
-template <>
-class Stream<BZ2File>
-{
-public:
-    bool _fileOwned;
-    BZFILE * _file;
-    FILE * _underlyingFile;
-    int _error;
-    char _rw;
-
-    Stream() : _fileOwned(false), _file(0), _underlyingFile(0), _error(0), _rw('-')
-    {}
-
-    Stream(BZFILE * file) : _fileOwned(false), _file(file), _error(0), _rw('-')
-    {}
-
-    ~Stream()
-    {
-        if (this->_fileOwned)
-            close(*this);
-    }
-
-private:
-    // Disable default, copy construction and assignment.
-    Stream(Stream const & /*other*/) {}
-    Stream & operator=(Stream const & /*other*/) { return *this; }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Difference
-// ----------------------------------------------------------------------------
-
-template <>
-struct Difference<Stream<BZ2File> >
-{
-    // bzlib streams rely on FILE * streams
-    typedef Difference<Stream<FILE *> >::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Position
-// ----------------------------------------------------------------------------
-
-template <>
-struct Position<Stream<BZ2File> >
-{
-    // bzlib streams rely on FILE * streams
-    typedef Position<Stream<FILE *> >::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <>
-struct Size<Stream<BZ2File> >
-{
-    // bzlib streams rely on FILE * streams
-    typedef Size<Stream<FILE *> >::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <>
-struct Value<Stream<BZ2File> >
-{
-    // bzlib streams rely on FILE * streams
-    typedef Value<Stream<FILE *> >::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<BZ2File>, IsInput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsOutput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<BZ2File>, IsOutput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasPeek>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<BZ2File>, HasPeek>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasFilename>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<BZ2File>, HasFilename>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Seek<TSpec> >
-// ----------------------------------------------------------------------------
-
-template <typename TSpec>
-struct HasStreamFeature<Stream<BZ2File>, Seek<TSpec> >
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Tell>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<BZ2File>, Tell>
-{
-    typedef False Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function open()
-// ----------------------------------------------------------------------------
-
-inline bool
-open(Stream<BZ2File> & stream, char const * filename, char const * mode)
-{
-    if (stream._fileOwned)
-        close(stream);
-    CharString modeStr = mode;
-    if (length(modeStr) == 0u || (modeStr[0] != 'r' && modeStr[0] != 'w'))
-        return false;
-    if (modeStr == "r" || modeStr == "w")
-        appendValue(modeStr, 'b');
-    stream._rw = modeStr[0];
-    if (CharString(filename) == "-")
-    {
-        stream._fileOwned = false;
-        // TODO(holtgrew): Use constants instead of 0/1 for stdin/stdout.  A bit tricky to do such that it can be ported to Windows.
-        if (stream._rw == 'r')
-            stream._underlyingFile = stdin;
-        else
-            stream._underlyingFile = stdout;
-    }
-    else
-    {
-        stream._underlyingFile = fopen(filename, toCString(modeStr));
-        if (stream._underlyingFile == 0)
-            return false;
-        stream._fileOwned = true;
-    }
-    if (stream._rw == 'w')
-        stream._file = BZ2_bzWriteOpen(&stream._error, stream._underlyingFile, 7, 0, 0);
-    else
-        stream._file = BZ2_bzReadOpen(&stream._error, stream._underlyingFile, 0, 0, NULL, 0);
-    if (stream._file == 0 || stream._error != 0)
-    {
-        stream._file = 0;
-        stream._underlyingFile = 0;
-        stream._fileOwned = false;
-        return false;
-    }
-    return true;
-}
-
-// ----------------------------------------------------------------------------
-// Function close()
-// ----------------------------------------------------------------------------
-
-/**
-.Function.close
-..class:Class.Stream
-..signature:close(stream)
-..param.stream:Stream to close.
-...type:Class.Stream
- */
-
-inline void
-close(Stream<BZ2File> & stream)
-{
-    if (stream._file == 0 || stream._file == 0)
-        return;
-    if (stream._rw == 'w')
-        BZ2_bzWriteClose(&stream._error, stream._file, 0, NULL, NULL);
-    else
-        BZ2_bzReadClose(&stream._error, stream._file);
-    fclose(stream._underlyingFile);
-    stream._file = 0;
-    stream._underlyingFile = 0;
-    stream._rw = '-';
-    stream._fileOwned = false;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamEof()
-// ----------------------------------------------------------------------------
-
-inline bool
-streamEof(Stream<BZ2File> & stream)
-{
-    // std::cerr << "stream._error == " << stream._error << std::endl;
-    // std::cerr << "BZ_FINISH == " << BZ_STREAM_END << std::endl;
-    return stream._error == BZ_STREAM_END;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamTell()
-// ----------------------------------------------------------------------------
-
-// Always returns 0.
-
-inline Position<Stream<BZ2File> >::Type
-streamTell(Stream<BZ2File> const & /*stream*/)
-{
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadChar()
-// ----------------------------------------------------------------------------
-
-inline int
-streamReadChar(char & c, Stream<BZ2File> & stream)
-{
-    if (streamEof(stream))
-        return 1;
-    return BZ2_bzRead(&stream._error, stream._file, &c, 1) != 1;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamError
-// ----------------------------------------------------------------------------
-
-inline int
-streamError(Stream<BZ2File> & stream)
-{
-    // Anything >= means OK.
-    if (stream._error < 0)
-        return stream._error;
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamReadBlock(char * target, Stream<BZ2File> & stream, size_t maxLen)
-{
-    return BZ2_bzRead(&stream._error, stream._file, target, maxLen);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteChar
-// ----------------------------------------------------------------------------
-
-inline int
-streamWriteChar(Stream<BZ2File> & stream, char const c)
-{
-    BZ2_bzWrite(&stream._error, stream._file, const_cast<char *>(&c), 1);
-    return stream._error;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamWriteBlock(Stream<BZ2File> & stream, char const * source, size_t count)
-{
-    BZ2_bzWrite(&stream._error, stream._file, const_cast<char *>(source), count);
-    if (stream._error)
-        return 0;
-    else
-        return count;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamFlush()
-// ----------------------------------------------------------------------------
-
-///.Function.streamFlush.remarks:If the stream is of type @Spec.BZ2 File Stream@ then this function does nothing.
-
-inline int
-streamFlush(Stream<BZ2File> & /*stream*/)
-{
-    // Null implementation, function is not so important in the use cases for
-    // SeqAn anyway.
-    return 0;
-}
-
-}  // namespace seqean
-
-#endif  // #ifndef SEQAN_STREAM_BZ2_FILE_WRAPPER_H_
diff --git a/seqan/stream/stream_char_array.h b/seqan/stream/stream_char_array.h
deleted file mode 100644
index 729d151..0000000
--- a/seqan/stream/stream_char_array.h
+++ /dev/null
@@ -1,536 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// A Stream specialization that works on char arrays/char *.
-// ==========================================================================
-
-// TODO(holtgrew): Using the end pointer means that the used strings are bounded which might cost some performance, although the hope is that branches are mostly predicted.
-
-#ifndef SEQAN_STREAM_ADAPT_STREAM_CHAR_ARRAY_H_
-#define SEQAN_STREAM_ADAPT_STREAM_CHAR_ARRAY_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class CharArrayStream
- * @extends Stream
- * @headerfile <seqan/stream.h>
- * @brief Thin wrapper around <tt>char *</tt> to the @link StreamConcept @endlink concept.
- * 
- * @signature template <typename TPointer>
- *            class Stream<CharArray<TPointer> >;
- * 
- * @tparam TPointer Specification of the pointer type to work on.
- * 
- * @section Remarks
- * 
- * This class consists of the <tt>char *</tt>, another <tt>char *</tt> to the beginning of the array and a flag
- * signifying EOF.
- * 
- * Note that this is a bounded string variant and might have some performance problems.
- * 
- * @section Examples
- * 
- * Create a Char Array Stream from a @link CharString @endlink.
- * 
- * @code{.cpp}
- * CharString buffer = "This is a text.";
- * Stream<CharArray<char const *> > stream(&buffer[0], &buffer[0] + length(buffer));
- * @endcode
- *
- *
- * @fn CharArrayStream::Stream
- * 
- * @brief Constructor
- * 
- * @signature CharArrayStream(ptr, ptrEnd);
- * 
- * @param[in] ptrEnd The <tt>char *</tt> that works as the end of the stream.
- * @param[in] ptr    The <tt>char *</tt> that works as the beginning of the stream.
- */
-
-/**
-.Spec.Char Array Stream
-..cat:Input/Output
-..general:Class.Stream
-..summary:Thin wrapper around $char *$ to the @Concept.StreamConcept|Stream@ concept.
-..signature:Stream<CharArray<TPointer> >
-..param.TPointer:Specification of the pointer type to work on.
-...type:nolink:$char *$, $char const *$.
-..remarks:This class consists of the $char *$, another $char *$ to the beginning of the array and a flag signifying EOF.
-..remarks:Note that this is a bounded string variant and might have some performance problems.
-..remarks:One major use case for this is to create a @Class.RecordReader@ of a string for parsing.
-..include:seqan/stream.h
-..example.text:Create a Char Array Stream from a @Shortcut.CharString@.
-..example.code:
-CharString buffer = "This is a text.";
-Stream<CharArray<char const *> > stream(&buffer[0], &buffer[0] + length(buffer));
-
-.Memfunc.Char Array Stream#Stream
-..summary:Constructor
-..class:Spec.Char Array Stream
-..signature:CharArrayStream(ptr, ptrEnd)
-..param.ptr:The $char *$ that works as the "beginning" of the stream.
-..param.ptrEnd:The $char *$ that works as the "end" of the stream.
- */
-
-template <typename TPointer>
-class Stream<CharArray<TPointer> >
-{
-public:
-
-    // -----------------------------------------------------------------------
-    // Members
-    // -----------------------------------------------------------------------
-    TPointer _base;
-    TPointer _ptr;
-    TPointer _end;
-    bool _eof;
-
-    // -----------------------------------------------------------------------
-    // Constructors
-    // -----------------------------------------------------------------------
-
-    Stream() {}
-
-    Stream(TPointer p, TPointer e) : _base(p), _ptr(p), _end(e), _eof(false)
-    {}
-
-    Stream(Stream<CharArray<typename RemoveConst_<typename Value<TPointer>::Type>::Type *> > const & other)
-            : _base(other._base), _ptr(other._ptr), _end(other._end), _eof(other._eof)
-    {}
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Difference
-// ----------------------------------------------------------------------------
-
-template <>
-struct Difference<Stream<CharArray<char *> > >
-{
-    typedef Difference<char *>::Type Type;
-};
-
-template <>
-struct Difference<Stream<CharArray<char const *> > >
-{
-    typedef Difference<char const *>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Position
-// ----------------------------------------------------------------------------
-
-template <>
-struct Position<Stream<CharArray<char *> > >
-{
-    typedef Position<char *>::Type Type;
-};
-
-template <>
-struct Position<Stream<CharArray<char const *> > >
-{
-    typedef Position<char const *>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <>
-struct Size<Stream<CharArray<char *> > >
-{
-    typedef Size<char *>::Type Type;
-};
-
-template <>
-struct Size<Stream<CharArray<char const *> > >
-{
-    typedef Size<char const *>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <>
-struct Value<Stream<CharArray<char *> > >
-{
-    typedef Size<char *>::Type Type;
-};
-
-template <>
-struct Value<Stream<CharArray<char const *> > >
-{
-    typedef Value<char const *>::Type Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char *> >, IsInput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char const *> >, IsInput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsOutput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char *> >, IsOutput>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char const *> >, IsOutput>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasPeek>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char *> >, HasPeek>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char const *> >, HasPeek>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasFilename>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char *> >, HasFilename>
-{
-    typedef False Type;
-};
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char const *> >, HasFilename>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Seek<TSpec> >
-// ----------------------------------------------------------------------------
-
-template <typename TSpec>
-struct HasStreamFeature<Stream<CharArray<char *> >, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-template <typename TSpec>
-struct HasStreamFeature<Stream<CharArray<char const *> >, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Tell>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char *> >, Tell>
-{
-    typedef True Type;
-};
-
-template <>
-struct HasStreamFeature<Stream<CharArray<char const *> >, Tell>
-{
-    typedef True Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function streamPeek()
-// ----------------------------------------------------------------------------
-
-inline int
-_streamPeekImpl(char & c, char const * & ptr, char const * & end, bool & eof)
-{
-    if (ptr != end) {
-        c = *ptr;
-        return 0;
-    } else {
-        eof = true;
-        return EOF;
-    }
-}
-
-inline int
-streamPeek(char & c, Stream<CharArray<char const *> > & stream)
-{
-    return _streamPeekImpl(c, stream._ptr, stream._end, stream._eof);
-}
-
-inline int
-streamPeek(char & c, Stream<CharArray<char *> > & stream)
-{
-    return _streamPeekImpl(c, const_cast<char const *&>(stream._ptr), const_cast<char const *&>(stream._end), stream._eof);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadChar()
-// ----------------------------------------------------------------------------
-
-inline int
-_streamReadCharImpl(bool & eof, char & c, char const * & ptr, char const * & end)
-{
-    if (ptr != end) {
-        c = *ptr;
-        ++ptr;
-        return 0;
-    } else {
-        eof = true;
-        return EOF;
-    }
-}
-
-inline int
-streamReadChar(char & c, Stream<CharArray<char const *> > & stream)
-{
-    return _streamReadCharImpl(stream._eof, c, stream._ptr, stream._end);
-}
-
-inline int
-streamReadChar(char & c, Stream<CharArray<char *> > & stream)
-{
-    return _streamReadCharImpl(stream._eof, c, const_cast<char const *&>(stream._ptr), const_cast<char const *&>(stream._end));
-}
-
-// ----------------------------------------------------------------------------
-// Function streamEof()
-// ----------------------------------------------------------------------------
-
-inline bool
-streamEof(Stream<CharArray<char const *> > & stream)
-{
-    return stream._eof;
-}
-
-inline bool
-streamEof(Stream<CharArray<char *> > & stream)
-{
-    return stream._eof;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-_streamReadBlockImpl(bool & eof, char * target, char const * & ptr, char const * & end, size_t maxLen)
-{
-    char * targetPtr = target;
-    size_t valuesRead = 0;
-    for (size_t i = 0; i < maxLen; ++i) {
-        if (ptr != end) {
-            ++valuesRead;
-            *targetPtr++ = *ptr++;
-        } else {
-            eof = true;
-            break;
-        }
-    }
-    return valuesRead;
-}
-
-inline size_t
-streamReadBlock(char * target, Stream<CharArray<char const *> > & stream, size_t maxLen)
-{
-    return _streamReadBlockImpl(stream._eof, target, stream._ptr, stream._end, maxLen);
-}
-
-inline size_t
-streamReadBlock(char * target, Stream<CharArray<char *> > & stream, size_t maxLen)
-{
-    return _streamReadBlockImpl(stream._eof, target, const_cast<char const *&>(stream._ptr), const_cast<char const *&>(stream._end), maxLen);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteChar
-// ----------------------------------------------------------------------------
-
-inline int
-streamWriteChar(Stream<CharArray<char *> > & stream, char const c)
-{
-    if (stream._ptr != stream._end) {  // Const-sized stream.
-        *stream._ptr = c;
-        ++stream._ptr;
-        return 0;
-    } else {
-        stream._eof = true;
-        return EOF;
-    }
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamWriteBlock(Stream<CharArray<char *> > & stream, char const * source, size_t count)
-{
-    size_t charsWritten = 0;
-    for (; charsWritten < count && stream._ptr != stream._end; ++source, ++stream._ptr, ++charsWritten)
-        *stream._ptr = *source;
-    if (stream._ptr == stream._end)
-        stream._eof = true;
-    return charsWritten;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamFlush()
-// ----------------------------------------------------------------------------
-
-inline int
-streamFlush(Stream<CharArray<char *> > & /*stream*/)
-{
-    return 0;
-}
-
-inline int
-streamFlush(Stream<CharArray<char const *> > & /*stream*/)
-{
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamSeek()
-// ----------------------------------------------------------------------------
-
-inline int
-_streamSeekImpl(char const * & ptr, char const * base, char const * end, ptrdiff_t delta, int origin)
-{
-    switch (origin) {
-        case SEEK_SET:
-            if (base + delta > end)
-                return 1;
-            ptr = base + delta;
-            return 0;
-        case SEEK_CUR:
-            if (ptr + delta > end)
-                return 1;
-            ptr = ptr + delta;
-            return 0;
-        default:  // SEEK_END
-            if (delta > 0)
-                return 1;
-            ptr = end + delta;
-            return 0;
-    }
-}
-
-inline int
-streamSeek(Stream<CharArray<char const *> > & stream, ptrdiff_t delta, int origin)
-{
-    return _streamSeekImpl(stream._ptr, stream._base, stream._end, delta, origin);
-}
-
-inline int
-streamSeek(Stream<CharArray<char *> > & stream, ptrdiff_t delta, int origin)
-{
-    return _streamSeekImpl(const_cast<char const * &>(stream._ptr), stream._base, stream._end, delta, origin);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamTell()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamTell(Stream<CharArray<char *> > & stream)
-{
-    return stream._ptr - stream._base;
-}
-
-inline size_t
-streamTell(Stream<CharArray<char const *> > & stream)
-{
-    return stream._ptr - stream._base;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamError
-// ----------------------------------------------------------------------------
-
-inline int
-streamError(Stream<CharArray<char *> > & /*stream*/)
-{
-    return 0;
-}
-
-inline int
-streamError(Stream<CharArray<char const *> > & /*stream*/)
-{
-    return 0;
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef SEQAN_STREAM_ADAPT_STREAM_CHAR_ARRAY_H_
diff --git a/seqan/stream/stream_compressor.h b/seqan/stream/stream_compressor.h
new file mode 100644
index 0000000..51e5bb6
--- /dev/null
+++ b/seqan/stream/stream_compressor.h
@@ -0,0 +1,489 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_STREAM_STREAM_COMPRESSOR_H_
+#define SEQAN_STREAM_STREAM_COMPRESSOR_H_
+
+
+#if SEQAN_HAS_ZLIB
+// Zlib headers
+#include <zlib.h>
+#include "iostream_zutil.h"
+#endif
+
+#include <algorithm>    // copy
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TOutPager, typename TSpec>
+struct Pager;
+
+// ============================================================================
+// Tags, Enums
+// ============================================================================
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+template <typename TAlgTag>
+struct Compress;
+
+template <typename TAlgTag>
+struct CompressionContext {};
+
+template <typename TAlgTag>
+struct DefaultPageSize;
+
+#if SEQAN_HAS_ZLIB
+
+template <>
+struct CompressionContext<GZFile>
+{
+    z_stream strm;
+
+    CompressionContext()
+    {
+        memset(&strm, 0, sizeof(z_stream));
+    }
+};
+
+template <>
+struct CompressionContext<BgzfFile>:
+    CompressionContext<GZFile>
+{
+    enum { BLOCK_HEADER_LENGTH = 18 };
+    unsigned char headerPos;
+};
+
+template <typename T>
+struct MagicHeader<BgzfFile, T>
+{
+    static char const VALUE[18];
+};
+
+template <typename T>
+char const MagicHeader<BgzfFile, T>::VALUE[18] =
+{
+    MagicHeader<GZFile>::VALUE[0], MagicHeader<GZFile>::VALUE[1], MagicHeader<GZFile>::VALUE[2],
+    4, 0, 0, 0, 0, 0, '\xff', 6, 0, 'B', 'C', 2, 0, 0, 0
+};
+
+template <>
+struct DefaultPageSize<BgzfFile>
+{
+    static const unsigned MAX_BLOCK_SIZE = 64 * 1024;
+    static const unsigned BLOCK_FOOTER_LENGTH = 8;
+    // 5 bytes block overhead (see 3.2.4. at http://www.gzip.org/zlib/rfc-deflate.html)
+    static const unsigned ZLIB_BLOCK_OVERHEAD = 5;
+
+    // Reduce the maximal input size, such that the compressed data
+    // always fits in one block even for level Z_NO_COMPRESSION.
+    enum { BLOCK_HEADER_LENGTH = CompressionContext<BgzfFile>::BLOCK_HEADER_LENGTH };
+    static const unsigned VALUE = MAX_BLOCK_SIZE - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH - ZLIB_BLOCK_OVERHEAD;
+};
+
+
+/*
+template <typename TOutPager, typename TAlgTag>
+Pager<TOutPager, Compress<TAlgTag> >
+{
+    TOutPager outPager;             // outbound pager
+    PageTable<FixedSize> table;     // our page table
+
+    Pager():
+        table(DefaultPageSize<TAlgTag>::VALUE)
+    {}
+
+    Page & getPage (__int64 position)
+    {
+        Page *page;
+        {
+            ScopedReadLock(table.lock);
+
+            page = table[position];
+            if (posInPage(position, page))                      // does the page exist yet?
+                return page;
+        }
+        {
+            ScopedWriteLock(table.lock);
+
+            page = table[position];
+            if (posInPage(position, page))                      // does the page exist yet?
+                return page;
+
+            page = new Page(table.rangeForPos(position));       // create new page
+            reserve(page.data, table.pageSize);                 // allocate required memory
+            table.insertPage(page);                             // insert page
+            prevPage = prevPage(position);
+        }
+        return page;
+    }
+
+    void putPage (Page &page)
+    {
+        __int64 outPosition = 0;                                // compute start position in outbound pager
+        if (page.range.begin != 0)
+        {
+            PageRange range = getPageRange(beginPosition(page.range) - 1);
+            outPosition = endPosition(range);                   // wait for end position of the previous page
+        }
+
+        TCompressionContext ctx;
+        initCompressionContext(ctx);
+
+        Size<Page>::Type leftToCompress = length(page);
+        while (leftToCompress != 0)
+        {
+            Page &outPage = outPager.getPage(outPosition);
+
+            auto handle = std::async(std::launch::async,
+                                  parallel_sum<RAIter>, mid, end);
+            compress
+        }
+    }
+};
+*/
+// ============================================================================
+// Functions
+// ============================================================================
+
+inline void
+compressInit(CompressionContext<GZFile> & ctx)
+{
+    const int GZIP_WINDOW_BITS = -15;   // no zlib header
+    const int Z_DEFAULT_MEM_LEVEL = 8;
+
+    ctx.strm.zalloc = NULL;
+    ctx.strm.zfree = NULL;
+
+    // (weese:) We use Z_BEST_SPEED instead of Z_DEFAULT_COMPRESSION as it turned out
+    //          to be 2x faster and produces only 7% bigger output
+//    int status = deflateInit2(&ctx.strm, Z_DEFAULT_COMPRESSION, Z_DEFLATED,
+//                              GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
+    int status = deflateInit2(&ctx.strm, Z_BEST_SPEED, Z_DEFLATED,
+                              GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
+    if (status != Z_OK)
+        throw IOError("GZFile deflateInit2() failed.");
+}
+
+inline void
+compressInit(CompressionContext<BgzfFile> & ctx)
+{
+    compressInit(static_cast<CompressionContext<GZFile> &>(ctx));
+    ctx.headerPos = 0;
+}
+
+template <typename TTarget, typename TSourceIterator>
+inline typename Size<TTarget>::Type
+compress(TTarget & target, TSourceIterator & source, CompressionContext<BgzfFile> & ctx)
+{
+    typedef typename Chunk<TTarget>::Type           TTargetChunk;
+    typedef typename Chunk<TSourceIterator>::Type   TSourceChunk;
+    typedef typename Value<TSourceChunk>::Type      TSourceValue;
+
+    TTargetChunk tChunk;
+    TSourceChunk sChunk;
+
+    if (ctx.headerPos < sizeof(MagicHeader<BgzfFile>::VALUE))
+    {
+        size_t headerLeft = sizeof(MagicHeader<BgzfFile>::VALUE) - ctx.headerPos;
+        reserveChunk(target, headerLeft, Output());
+
+        tChunk = getChunk(target, Output());
+        size_t size = std::min(headerLeft, length(tChunk));
+        SEQAN_ASSERT_GT(size, 0u);
+
+        std::copy(tChunk.begin, sChunk.begin, size);
+
+        advanceChunk(target, size);
+        ctx.headerPos += size;
+        return size;
+    }
+    else
+    {
+        sChunk = getChunk(source, Input());
+        tChunk = getChunk(target, Output());
+
+        ctx.strm.next_in = static_cast<Bytef *>(sChunk.begin);
+        ctx.strm.next_out = static_cast<Bytef *>(tChunk.begin);
+        ctx.strm.avail_in = length(sChunk) * sizeof(TSourceValue);
+        ctx.strm.avail_out = length(tChunk);
+
+        SEQAN_ASSERT_GT(ctx.strm.avail_out, 0u);
+
+        int status = deflate(&ctx.strm, Z_NO_FLUSH);
+        if (status != Z_OK)
+            throw IOError("BgzfFile deflateInit2() failed.");
+
+        source += length(sChunk) - ctx.strm.avail_in;
+        size_t size = length(tChunk) - ctx.strm.avail_out;
+        advanceChunk(target, size);
+        return size;
+    }
+
+
+//    status = deflate(&zs, Z_FINISH);
+//    bool rawDataTooBig = (status != Z_STREAM_END);
+//
+//    status = deflateEnd(&zs);
+//    if (status != Z_OK)
+//        throw IOError("BgzfFile deflateEnd() failed.");
+//
+//    if (!rawDataTooBig)
+//    {
+//        resize(page.raw, zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH);
+//        break;
+//    }
+}
+
+// ----------------------------------------------------------------------------
+// Helper Function _bgzfUnpackXX()
+// ----------------------------------------------------------------------------
+
+inline unsigned short
+_bgzfUnpack16(char const * buffer)
+{
+    return *reinterpret_cast<unsigned short const *>(buffer);
+}
+
+inline unsigned
+_bgzfUnpack32(char const * buffer)
+{
+    return *reinterpret_cast<unsigned const *>(buffer);
+}
+
+// ----------------------------------------------------------------------------
+// Helper Function _bgzfPackXX()
+// ----------------------------------------------------------------------------
+
+inline void
+_bgzfPack16(char * buffer, unsigned short value)
+{
+    *reinterpret_cast<unsigned short *>(buffer) = value;
+}
+
+inline void
+_bgzfPack32(char * buffer, unsigned value)
+{
+    *reinterpret_cast<unsigned *>(buffer) = value;
+}
+
+
+template <typename TDestValue, typename TDestCapacity, typename TSourceValue, typename TSourceLength>
+inline TDestCapacity
+_compressBlock(TDestValue *dstBegin,   TDestCapacity dstCapacity,
+               TSourceValue *srcBegin, TSourceLength srcLength, CompressionContext<BgzfFile> & ctx)
+{
+    const size_t BLOCK_HEADER_LENGTH = DefaultPageSize<BgzfFile>::BLOCK_HEADER_LENGTH;
+    const size_t BLOCK_FOOTER_LENGTH = DefaultPageSize<BgzfFile>::BLOCK_FOOTER_LENGTH;
+
+    SEQAN_ASSERT_GT(dstCapacity, BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH);
+    SEQAN_ASSERT_EQ(sizeof(TDestValue), 1u);
+    SEQAN_ASSERT_EQ(sizeof(unsigned), 4u);
+
+    // 1. COPY HEADER
+
+    std::copy(&MagicHeader<BgzfFile>::VALUE[0], &MagicHeader<BgzfFile>::VALUE[BLOCK_HEADER_LENGTH], dstBegin);
+
+
+    // 2. COMPRESS
+
+    compressInit(ctx);
+    ctx.strm.next_in = (Bytef *)(srcBegin);
+    ctx.strm.next_out = (Bytef *)(dstBegin + BLOCK_HEADER_LENGTH);
+    ctx.strm.avail_in = srcLength * sizeof(TSourceValue);
+    ctx.strm.avail_out = dstCapacity - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
+
+    int status = deflate(&ctx.strm, Z_FINISH);
+    if (status != Z_STREAM_END)
+    {
+        deflateEnd(&ctx.strm);
+        throw IOError("Deflation failed. Compressed BGZF data is too big.");
+    }
+
+    status = deflateEnd(&ctx.strm);
+    if (status != Z_OK)
+        throw IOError("BGZF deflateEnd() failed.");
+
+
+    // 3. APPEND FOOTER
+
+    // Set compressed length into buffer, compute CRC and write CRC into buffer.
+
+    size_t len = dstCapacity - ctx.strm.avail_out;
+    _bgzfPack16(dstBegin + 16, len - 1);
+
+    dstBegin += len - BLOCK_FOOTER_LENGTH;
+    _bgzfPack32(dstBegin, crc32(crc32(0u, NULL, 0u), (Bytef *)(srcBegin), srcLength * sizeof(TSourceValue)));
+    _bgzfPack32(dstBegin + 4, srcLength * sizeof(TSourceValue));
+
+    return dstCapacity - ctx.strm.avail_out;
+}
+
+inline void
+decompressInit(CompressionContext<GZFile> & ctx)
+{
+    const int GZIP_WINDOW_BITS = -15;   // no zlib header
+
+    ctx.strm.zalloc = NULL;
+    ctx.strm.zfree = NULL;
+    int status = inflateInit2(&ctx.strm, GZIP_WINDOW_BITS);
+    if (status != Z_OK)
+        throw IOError("GZip inflateInit2() failed.");
+}
+
+inline void
+decompressInit(CompressionContext<BgzfFile> & ctx)
+{
+    decompressInit(static_cast<CompressionContext<GZFile> &>(ctx));
+    ctx.headerPos = 0;
+}
+
+inline bool
+_bgzfCheckHeader(char const * header)
+{
+    const char FLG_FEXTRA = 4;
+    const char BGZF_ID1 = 'B';
+    const char BGZF_ID2 = 'C';
+    const char BGZF_LEN = 2;
+    const char BGZF_XLEN = 6;  // BGZF_LEN+4
+
+    return (header[0] == (char)MagicHeader<GZFile>::VALUE[0] &&
+            header[1] == (char)MagicHeader<GZFile>::VALUE[1] &&
+            header[2] == (char)MagicHeader<GZFile>::VALUE[2] &&
+            (header[3] & FLG_FEXTRA) != 0 &&
+            _bgzfUnpack16(header + 10) == BGZF_XLEN &&
+            header[12] == BGZF_ID1 &&
+            header[13] == BGZF_ID2 &&
+            _bgzfUnpack16(header + 14) == BGZF_LEN);
+}
+
+// read first bytes of a file/stream and compare with file format's magic header
+template <typename TStream>
+inline bool
+guessFormatFromStream(TStream &istream, BgzfFile)
+{
+    char putbackBuf[18];
+    bool match = false;
+
+    SEQAN_ASSERT(istream.good());
+
+    // try to read and check header
+    size_t numRead = istream.readsome(&putbackBuf[0], sizeof(putbackBuf));
+    if (numRead == sizeof(putbackBuf) && _bgzfCheckHeader(putbackBuf))
+        match = true;
+
+    // unget all read characters
+    for (; numRead > 0; --numRead)
+        istream.unget();
+
+    SEQAN_ASSERT(istream.good());
+
+    return match;
+}
+
+// ----------------------------------------------------------------------------
+// Function _preprocessFilePage()
+// ----------------------------------------------------------------------------
+
+template <typename TDestValue, typename TDestCapacity, typename TSourceValue, typename TSourceLength>
+inline TDestCapacity
+_decompressBlock(TDestValue *dstBegin,   TDestCapacity dstCapacity,
+                 TSourceValue *srcBegin, TSourceLength srcLength, CompressionContext<BgzfFile> & ctx)
+{
+    const size_t BLOCK_HEADER_LENGTH = DefaultPageSize<BgzfFile>::BLOCK_HEADER_LENGTH;
+    const size_t BLOCK_FOOTER_LENGTH = DefaultPageSize<BgzfFile>::BLOCK_FOOTER_LENGTH;
+
+    SEQAN_ASSERT_EQ(sizeof(TSourceValue), 1u);
+    SEQAN_ASSERT_EQ(sizeof(unsigned), 4u);
+
+    // 1. CHECK HEADER
+
+    if (srcLength <= BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH)
+        throw IOError("BGZF block too short.");
+
+    if (!_bgzfCheckHeader(srcBegin))
+        throw IOError("Invalid BGZF block header.");
+
+    size_t compressedLen = _bgzfUnpack16(srcBegin + 16) + 1u;
+    if (compressedLen != srcLength)
+        throw IOError("BGZF compressed size mismatch.");
+
+
+    // 2. DECOMPRESS
+
+    decompressInit(ctx);
+    ctx.strm.next_in = (Bytef *)(srcBegin + BLOCK_HEADER_LENGTH);
+    ctx.strm.next_out = (Bytef *)(dstBegin);
+    ctx.strm.avail_in = srcLength - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
+    ctx.strm.avail_out = dstCapacity * sizeof(TDestValue);
+
+    int status = inflate(&ctx.strm, Z_FINISH);
+    if (status != Z_STREAM_END)
+    {
+        inflateEnd(&ctx.strm);
+        throw IOError("Inflation failed. Decompressed BGZF data is too big.");
+    }
+
+    status = inflateEnd(&ctx.strm);
+    if (status != Z_OK)
+        throw IOError("BGZF inflateEnd() failed.");
+
+
+    // 3. CHECK FOOTER
+
+    // Check compressed length in buffer, compute CRC and compare with CRC in buffer.
+
+    unsigned crc = crc32(crc32(0u, NULL, 0u), (Bytef *)(dstBegin), dstCapacity - ctx.strm.avail_out);
+
+    srcBegin += compressedLen - BLOCK_FOOTER_LENGTH;
+    if (_bgzfUnpack32(srcBegin) != crc)
+        throw IOError("BGZF wrong checksum.");
+
+    if (_bgzfUnpack32(srcBegin + 4) != dstCapacity - ctx.strm.avail_out)
+        throw IOError("BGZF size mismatch.");
+
+    return (dstCapacity - ctx.strm.avail_out) / sizeof(TDestValue);
+}
+
+#endif  // #if SEQAN_HAS_ZLIB
+
+}  // namespace seqan
+
+#endif  // SEQAN_STREAM_STREAM_COMPRESSOR_H_
diff --git a/seqan/stream/stream_gz_file.h b/seqan/stream/stream_gz_file.h
deleted file mode 100644
index b23a6ed..0000000
--- a/seqan/stream/stream_gz_file.h
+++ /dev/null
@@ -1,480 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// ==========================================================================
-// Wrapper for zlib streams.  We use a wrapper because gzFile is an alias
-// to void* which could be used in other places, too.
-// ==========================================================================
-
-#include <zlib.h>
-
-#ifndef SEQAN_STREAM_STREAM_GZ_FILE_H_
-#define SEQAN_STREAM_STREAM_GZ_FILE_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-template <> class Stream<GZFile>;
-inline void close(Stream<GZFile> & stream);
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-/*!
- * @class GzFileStream
- * @headerfile <seqan/stream.h>
- * @brief Allows to open gzip-compressed files.
- *
- * This is only available if @link SEQAN_HAS_ZLIB @endlink is set to 1.
- *
- * Not copy constructable.
- *
- *
- * @fn GzFileStream::Stream
- * @brief Constructor.
- *
- * @signature Stream::Stream();
- * @signature Stream::Stream(gzFile);
- *
- * @param[in] gzFile A <tt>gzFile</tt> to wrap.
- *
- * @section Remarks
- *
- * When <tt>gzFile</tt> is given then the GZFileStream object does nto own the underlying <tt>gzFile</tt> and will serve
- * as a simple wrapper.  The underlying file is not closed when the GzFileStream object is destroyed.
- */
-
-/**
-.Spec.GZ File Stream
-..cat:Input/Output
-..signature:Stream<GZFile>
-..general:Class.Stream
-..summary:Adaption from $gzFile$ of $<zlib.h>$ to streams.
-..remarks:This is only available if @Macro.SEQAN_HAS_ZLIB@ is set to 1.
-..remarks:Not copy constructable, not assignable.
-..remarks:Follows the RIIA pattern when the file is opened through @Function.open@ (and thus the underlying $gzFile$ is owned).
-..remarks:
-Can be used as a wrapper around a $gzFile$ or create such an object itself through @Function.open@.
-Also see @Memfunc.GZ File Stream#Stream|the constructor@.
-..include:seqan/stream.h
-..example.text:It is easy to open a GZ file via @Function.open@.
-..example.code:
-#include <seqan/stream.h>
-
-Stream<GZFile> gzStream;
-open(gzStream, "/path/to/file.txt.gz", "r");  // binary is implicit
-
-// Now, work with gzStream.  The object will close the file on destruction.
-..example.text:
-You can also use GZ File Stream as a wrapper around an $gzFile$ object.
-In this case, we have to deal with the verbose code for opening the $gzFile$ object.
-..example.code:
-#include <zlib.h>
-#include <seqan/stream.h>
-
-gzFile gzOut = gzopen("/path/to/file.txt.gz", "wb");
-SEQAN_ASSERT(gzOut != NULL);
-Stream<GZFile> gzStream(gzOut);
-
-// Now, you can work with the stream gzStream.
-
-// Note that you only have to close gzOut and not gzStream.
-int res = gzclose(gzOut);
-SEQAN_ASSERT_EQ(res, 0);
-
-.Memfunc.GZ File Stream#Stream
-..summary:Constructor
-..signature:Stream()
-..signature:Stream(gzFile)
-..param.gzFile:The $gzFile$ to wrap.
-...type:nolink:$gzFile$ (from zlib.h).
-..remarks:When $gzFile$ is given then the GZ File Stream object does not own the underlying $gzFile$ and will serve as a simple wrapper.
- */
-
-template <>
-class Stream<GZFile>
-{
-public:
-    bool _gzFileOwned;
-    gzFile _gzFile;
-
-    Stream() : _gzFileOwned(false), _gzFile(0) {}
-
-    Stream(gzFile & gzFile) : _gzFileOwned(false), _gzFile(gzFile) {}
-
-    ~Stream()
-    {
-        if (this->_gzFileOwned)
-            close(*this);
-    }
-};
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction Difference
-// ----------------------------------------------------------------------------
-
-template <>
-struct Difference<Stream<GZFile> >
-{
-    typedef z_off_t Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Position
-// ----------------------------------------------------------------------------
-
-template <>
-struct Position<Stream<GZFile> >
-{
-    typedef z_off_t Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Size
-// ----------------------------------------------------------------------------
-
-template <>
-struct Size<Stream<GZFile> >
-{
-    typedef z_off_t Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction Value
-// ----------------------------------------------------------------------------
-
-template <>
-struct Value<Stream<GZFile> >
-{
-    typedef char Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsInput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<GZFile>, IsInput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, IsOutput>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<GZFile>, IsOutput>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasPeek>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<GZFile>, HasPeek>
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, HasFilename>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<GZFile>, HasFilename>
-{
-    typedef False Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Seek<TSpec> >
-// ----------------------------------------------------------------------------
-
-template <typename TSpec>
-struct HasStreamFeature<Stream<GZFile>, Seek<TSpec> >
-{
-    typedef True Type;
-};
-
-// ----------------------------------------------------------------------------
-// Metafunction HasStreamFeature<, Tell>
-// ----------------------------------------------------------------------------
-
-template <>
-struct HasStreamFeature<Stream<GZFile>, Tell>
-{
-    typedef True Type;
-};
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function open()
-// ----------------------------------------------------------------------------
-
-/**
-.Function.open
-..class:Class.Stream
-..signature:open(stream, fileName, mode)
-..param.stream:Stream to open.
-...type:Class.Stream
-..param.mode:Mode string for opening the file, e.g. $"r"$, $"w"$.
-...remarks:Do not specify for @Spec.Char Array Stream@.
-...type:nolink:$char const *$
- */
-
-inline bool
-open(Stream<GZFile> & stream, char const * filename, char const * mode)
-{
-    if (stream._gzFileOwned)
-        close(stream);
-    // TODO(holtgrew): Use constants instead of 0/1 for stdin/stdout.  A bit tricky to do such that it can be ported to Windows.
-    if (CharString(filename) == "-")  // stdin/stdout
-    {
-        int fid = 0;  // stdin
-        for (char const * ptr = mode; *ptr != '\0'; ++ptr)
-            if (*ptr == 'w')
-                fid = 1;  // stdout
-        stream._gzFile = gzdopen(fid, mode);  // attach to stdout/stdin.
-    }
-    else
-    {
-        stream._gzFile = gzopen(filename, mode);
-        stream._gzFileOwned = true;
-    }
-    if (stream._gzFile == 0)
-    {
-        stream._gzFileOwned = false;
-        return false;
-    }
-    return true;
-}
-
-// ----------------------------------------------------------------------------
-// Function isDirect()
-// ----------------------------------------------------------------------------
-
-/*!
- * @fn GzFileStream#isDirect
- * @brief Query a GzFileStream for being "direct."
- *
- * @signature bool isDirect(gzStream);
- *
- * @param[in] gzStream The GzFileStream to query.
- *
- * @return bool <tt>true</tt> indicates that the file is opened uncompressed ("direct").
- *
- * @section Remarks
- *
- * GzFileStream objects can also open uncompressed files (at a possible performance cost).  Such functionality is
- * provided directly by zlib.
- */
-
-/**
-.Function.isDirect
-..class:Spec.GZ File Stream
-..cat:Input/Output
-..summary:Query a GZ File Stream for being "direct."
-..signature:isDirect(gzStream)
-..param.gzStream:GZ File Stream to query.
-...type:Spec.GZ File Stream
-..returns:$bool$, indicating whether the file is opened uncompressed ("direct").
-..remarks:
-GZ File Streams can also open uncompressed files (at a possible performance cost).
-This function returns whether the underlying file was not a compressed file and thus the file is read directly.
-..include:seqan/stream.h
- */
-
-inline bool
-isDirect(Stream<GZFile> & stream)
-{
-    return gzdirect(stream._gzFile);
-}
-
-// ----------------------------------------------------------------------------
-// Function close()
-// ----------------------------------------------------------------------------
-
-/**
-.Function.close
-..class:Class.Stream
-..signature:close(stream)
-..param.stream:Stream to close.
-...type:Class.Stream
- */
-
-inline void
-close(Stream<GZFile> & stream)
-{
-    if (stream._gzFile == 0)
-        return;
-    int res = gzclose(stream._gzFile);
-    (void) res;
-    stream._gzFile = 0;
-    return;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamPeek()
-// ----------------------------------------------------------------------------
-
-inline int
-streamPeek(char & c, Stream<GZFile> & stream)
-{
-    int x = gzgetc(stream._gzFile);
-    if (x < 0)
-        return x;
-    c = x;
-    gzungetc(c, stream._gzFile);
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadChar()
-// ----------------------------------------------------------------------------
-
-inline int
-streamReadChar(char & c, Stream<GZFile> & stream)
-{
-    int x = gzgetc(stream._gzFile);
-    if (x < 0)
-        return x;
-    c = x;
-    return 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamEof()
-// ----------------------------------------------------------------------------
-
-inline bool
-streamEof(Stream<GZFile> & stream)
-{
-    // std::cerr << "gzeof(stream._gzFile) == " << gzeof(stream._gzFile) << std::endl;
-    return gzeof(stream._gzFile) != 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamError
-// ----------------------------------------------------------------------------
-
-inline int
-streamError(Stream<GZFile> & stream)
-{
-    int result = 0;
-    gzerror(stream._gzFile, &result);
-    // Anything >= is OK/stream end etc.
-    return result < 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamReadBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamReadBlock(char * target, Stream<GZFile> & stream, size_t maxLen)
-{
-    int res = gzread(stream._gzFile, target, maxLen);
-    if (res < 0)
-        return 0;
-    return res;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteChar
-// ----------------------------------------------------------------------------
-
-inline int
-streamWriteChar(Stream<GZFile> & stream, char const c)
-{
-    return gzwrite(stream._gzFile, &c, 1) != 1;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamWriteBlock()
-// ----------------------------------------------------------------------------
-
-inline size_t
-streamWriteBlock(Stream<GZFile> & stream, char const * source, size_t count)
-{
-    return gzwrite(stream._gzFile, const_cast<char const *>(source), count);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamFlush()
-// ----------------------------------------------------------------------------
-
-///.Function.streamFlush.remarks:If the stream is of type @Spec.GZ File Stream@ then this function calls $gzflush()$ with $Z_SYNC_FLUSH$. Note that many flush calls to such compressed streams reduce the compression rate.
-
-inline int
-streamFlush(Stream<GZFile> & stream)
-{
-    return gzflush(stream._gzFile, Z_SYNC_FLUSH);
-}
-
-// ----------------------------------------------------------------------------
-// Function streamSeek()
-// ----------------------------------------------------------------------------
-
-inline int
-streamSeek(Stream<GZFile> & stream, long int delta, int origin)
-{
-    SEQAN_ASSERT_NEQ(origin, SEEK_END);  // Not supported.
-    return gzseek(stream._gzFile, delta, origin) < 0;
-}
-
-// ----------------------------------------------------------------------------
-// Function streamTell()
-// ----------------------------------------------------------------------------
-
-inline Position<Stream<GZFile> >::Type
-streamTell(Stream<GZFile> & stream)
-{
-    return gztell(stream._gzFile);
-}
-
-}  // namespace seqean
-
-#endif  // #ifndef SEQAN_STREAM_STREAM_GZ_FILE_H_
diff --git a/seqan/stream/stream_put.h b/seqan/stream/stream_put.h
deleted file mode 100644
index 7bc2477..0000000
--- a/seqan/stream/stream_put.h
+++ /dev/null
@@ -1,312 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
-// Author: David Weese <david.weese@fu-berlin.de>
-// ==========================================================================
-// Implementation of streamPut().
-//
-// We put this into its own header since the generic version requires some
-// metafunctions and more involved code.
-// ==========================================================================
-
-#ifndef CORE_INCLUDE_SEQAN_STREAM_STREAM_PUT_H_
-#define CORE_INCLUDE_SEQAN_STREAM_STREAM_PUT_H_
-
-namespace seqan {
-
-// ============================================================================
-// Forwards
-// ============================================================================
-
-// ============================================================================
-// Tags, Classes, Enums
-// ============================================================================
-
-// ============================================================================
-// Metafunctions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Metafunction IntegerFormatString_
-// ----------------------------------------------------------------------------
-
-// Return the format string for numbers.
-
-template <typename TUnsigned, unsigned SIZE, typename T = void>
-struct IntegerFormatString_;
-
-
-template <typename T>
-struct IntegerFormatString_<False, 1, T>
-{
-    static const char VALUE[];
-};
-template <typename T>
-const char IntegerFormatString_<False, 1, T>::VALUE[] = "%hhi";
-
-
-template <typename T>
-struct IntegerFormatString_<True, 1, T>
-{
-    static const char VALUE[];
-};
-template <typename T>
-const char IntegerFormatString_<True, 1, T>::VALUE[] = "%hhu";
-
-
-template <typename T>
-struct IntegerFormatString_<False, 2, T>
-{
-    static const char VALUE[];
-};
-template <typename T>
-const char IntegerFormatString_<False, 2, T>::VALUE[] = "%hi";
-
-
-template <typename T>
-struct IntegerFormatString_<True, 2, T>
-{
-    static const char VALUE[];
-};
-template <typename T>
-const char IntegerFormatString_<True, 2, T>::VALUE[] = "%hu";
-
-
-template <typename T>
-struct IntegerFormatString_<False, 4, T>
-{
-    static const char VALUE[];
-};
-template <typename T>
-const char IntegerFormatString_<False, 4, T>::VALUE[] = "%i";
-
-
-template <typename T>
-struct IntegerFormatString_<True, 4, T>
-{
-    static const char VALUE[];
-};
-template <typename T>
-const char IntegerFormatString_<True, 4, T>::VALUE[] = "%u";
-
-
-template <typename T>
-struct IntegerFormatString_<False, 8, T>
-{
-    static const char VALUE[];
-};
-template <typename T>
-const char IntegerFormatString_<False, 8, T>::VALUE[] = "%lli";
-
-
-template <typename T>
-struct IntegerFormatString_<True, 8, T>
-{
-    static const char VALUE[];
-};
-template <typename T>
-const char IntegerFormatString_<True, 8, T>::VALUE[] = "%llu";
-
-
-// ============================================================================
-// Functions
-// ============================================================================
-
-// ----------------------------------------------------------------------------
-// Function streamPut()
-// ----------------------------------------------------------------------------
-
-// Forward for generic case.
-
-template <typename TStream, typename TSource>
-inline int
-streamPut(TStream & stream, TSource const & source);
-
-// Important special case of char.
-
-template <typename TStreamSpec>
-inline int
-streamPut(Stream<TStreamSpec> & stream, char const c)
-{
-    return streamWriteChar(stream, c);
-}
-
-// Important special case of ::std::string.
-
-template <typename TStreamSpec>
-inline int
-streamPut(Stream<TStreamSpec> & stream, ::std::string const & source)
-{
-    return (streamWriteBlock(stream, source.data(), source.length()) == source.length())  ?   0 : 1;
-}
-
-// Important special case of ::std::stringstream.
-
-template <typename TStreamSpec>
-inline int
-streamPut(Stream<TStreamSpec> & stream, ::std::stringstream const & source)
-{
-    return streamPut(stream, source.str());
-}
-
-// Important special case of CharString.
-
-template <typename TStreamSpec, typename TSpec>
-inline int
-streamPut(Stream<TStreamSpec> & stream, String<char, TSpec> const & source)
-{
-    return (streamWriteBlock(stream, toCString(source), length(source)) == length(source))  ?   0 : 1;
-}
-
-// Special case for floats and doubles.
-
-template <typename TStream>
-int _streamPut(TStream & stream, float source, False const & /*tag*/)
-{
-    char buffer[32];
-    size_t len = snprintf(buffer, 32, "%g", source);
-    return (streamWriteBlock(stream, buffer, len) == len) ? 0 : 1;
-}
-
-template <typename TStream>
-int _streamPut(TStream & stream, double source, False const & /*tag*/)
-{
-    char buffer[32];
-    size_t len = snprintf(buffer, 32, "%g", source);
-    return (streamWriteBlock(stream, buffer, len) == len) ? 0 : 1;
-}
-
-// Generic version for integers.
-
-template <typename TStream, typename TInt>
-SEQAN_FUNC_ENABLE_IF(Is<IntegerConcept<TInt> >, int)
-_streamPut(TStream & stream, TInt i, False const & /*tag*/)
-{
-    // 1 byte has at most 3 decimal digits (plus 1 for the NULL character)
-    char buf[sizeof(TInt) * 3 + 2];
-    size_t len = snprintf(buf, sizeof(buf), IntegerFormatString_<typename Is<UnsignedIntegerConcept<TInt> >::Type,
-                          sizeof(TInt)>::VALUE, i);
-    return (streamWriteBlock(stream, buf, len) == len) ? 0 : 1;
-}
-
-template <typename TStream>
-int _streamPut(TStream & stream, unsigned long i, False const & /*tag*/)
-{
-    // 1 byte has at most 3 decimal digits (plus 1 for the NULL character)
-    char buf[sizeof(unsigned long) * 3 + 2];
-    size_t len = snprintf(buf, sizeof(buf), "%lu", i);
-    return (streamWriteBlock(stream, buf, len) == len) ? 0 : 1;
-}
-
-template <typename TStream>
-int _streamPut(TStream & stream, long i, False const & /*tag*/)
-{
-    // 1 byte has at most 3 decimal digits (plus 1 for the NULL character)
-    char buf[sizeof(long) * 3 + 2];
-    size_t len = snprintf(buf, sizeof(buf), "%li", i);
-    return (streamWriteBlock(stream, buf, len) == len) ? 0 : 1;
-}
-
-template <typename TStream>
-int _streamPut(TStream & stream, char c, False const & /*tag*/)
-{
-    return streamWriteChar(stream, c);
-}
-
-// Generic fallback version, based on stringstream.
-//
-// Parameters:
-// (1) stream The stream to write to.
-// (2) source The value to write to stream.
-// (3) tag    True if the type of source is a sequence and False otherwise.
-
-template <typename TStream, typename TSource>
-SEQAN_FUNC_DISABLE_IF(Is<IntegerConcept<TSource> >, int)
-_streamPut(TStream & stream, TSource const & source, False const & /*tag*/)
-{
-    ::std::stringstream s;
-
-    s << source;
-    if (s.fail())
-        return s.fail();
-
-    return streamPut(stream, s);
-}
-
-template <typename TStream, typename TSource>
-inline int
-_streamPut(TStream & target, TSource const & source, True const & /*tag*/)
-{
-    typename Iterator<TSource const, Standard>::Type it = begin(source, Standard());
-    typename Iterator<TSource const, Standard>::Type itEnd = end(source, Standard());
-    int res = 0;
-
-    for (; it != itEnd && res == 0; ++it)
-        res = streamPut(target, getValue(it));
-
-    return res;
-}
-
-// Case: Character arrays.
-
-template <typename TStream>
-inline int
-_streamPut(TStream & stream, char const * source, True const & /*tag*/)
-{
-    return (streamWriteBlock(stream, source, strlen(source)) == strlen(source)) ? 0 : 1;
-}
-
-// Case: Array.
-// TODO(holtgrew): Requires atEnd(it) <==> *it == 0. Remove?
-
-template <typename TStream, typename TSourceValue>
-inline int
-_streamPut(TStream & stream, TSourceValue const * source, True const & /*tag*/)
-{
-    int res = 0;
-    for (; !atEnd(source) && res == 0; ++source)
-        res = _streamWrite(stream, *source);
-    return res;
-}
-
-// Function entry for generic version.
-
-template <typename TStream, typename TSource>
-inline int
-streamPut(TStream & stream, TSource const & source)
-{
-    return _streamPut(stream, source, typename IsSequence<TSource const>::Type());
-}
-
-}  // namespace seqan
-
-#endif  // #ifndef CORE_INCLUDE_SEQAN_STREAM_STREAM_PUT_H_
diff --git a/seqan/stream/tokenization.h b/seqan/stream/tokenization.h
new file mode 100644
index 0000000..31d587d
--- /dev/null
+++ b/seqan/stream/tokenization.h
@@ -0,0 +1,677 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Tokenization.
+// ==========================================================================
+
+#ifndef SEQAN_STREAM_TOKENIZATION_H_
+#define SEQAN_STREAM_TOKENIZATION_H_
+
+namespace seqan {
+
+// ============================================================================
+// Functors
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Functor IsInAlphabet
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+struct IsInAlphabet
+{
+    template <typename TInValue>
+    bool operator() (TInValue const & inVal) const
+    {
+        TValue val = inVal;
+        return convert<TInValue>(val) == toUpperValue(inVal);
+    }
+
+    bool operator() (TValue const &) const
+    {
+        return true;
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Functor IsInRange
+// ----------------------------------------------------------------------------
+
+template <char FIRST_CHAR, char LAST_CHAR>
+struct IsInRange
+{
+    template <typename TValue>
+    bool operator() (TValue const & val) const
+    {
+        return FIRST_CHAR <= val && val <= LAST_CHAR;
+    }
+};
+
+template <char FIRST_CHAR, char LAST_CHAR, typename TContext>
+struct ExceptionMessage<IsInRange<FIRST_CHAR, LAST_CHAR>, TContext>
+{
+    static const std::string VALUE;
+};
+
+template <char FIRST_CHAR, char LAST_CHAR, typename TContext>
+const std::string ExceptionMessage<IsInRange<FIRST_CHAR, LAST_CHAR>, TContext>::VALUE =
+    std::string("Character in range'") + FIRST_CHAR + "' to '" + LAST_CHAR + "' expected.";
+
+// ----------------------------------------------------------------------------
+// Functor EqualsChar
+// ----------------------------------------------------------------------------
+
+template <char VALUE>
+struct EqualsChar
+{
+    template <typename TValue>
+    bool operator() (TValue const & val) const
+    {
+        return val == VALUE;
+    }
+};
+
+template <char CHAR, typename TContext>
+struct ExceptionMessage<EqualsChar<CHAR>, TContext>
+{
+    static const std::string VALUE;
+};
+
+template <char CHAR, typename TContext>
+const std::string ExceptionMessage<EqualsChar<CHAR>, TContext>::VALUE = std::string("Character '") + CHAR + "' expected.";
+
+// ----------------------------------------------------------------------------
+// Functor EqualsDynamicValue
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+struct EqualsDynamicValue
+{
+    TValue val;
+
+    EqualsDynamicValue(TValue const & val) :
+        val(val)
+    {}
+
+    template <typename TValue2>
+    bool operator() (TValue2 const & v) const
+    {
+        return v == val;
+    }
+};
+
+template <typename TValue, typename TContext>
+inline std::string const &
+getExceptionMessage(EqualsDynamicValue<TValue> const & func, TContext const &)
+{
+    return std::string("Character '") + func.val + "' expected.";
+}
+
+// ----------------------------------------------------------------------------
+// Composite Functors
+// ----------------------------------------------------------------------------
+// Don't use isblank() or isspace() as it they seem to be slower than our functors (due to inlining)
+
+typedef EqualsChar<'\t'>                                        IsTab;
+typedef EqualsChar<' '>                                         IsSpace;
+typedef OrFunctor<IsSpace, IsTab>                               IsBlank;
+typedef OrFunctor<EqualsChar<'\n'>, EqualsChar<'\r'> >          IsNewline;
+typedef OrFunctor<IsBlank, IsNewline>                           IsWhitespace;
+typedef IsInRange<'!', '~'>                                     IsGraph;
+typedef OrFunctor<IsInRange<'a', 'z'>, IsInRange<'A', 'Z'> >    IsAlpha;
+typedef IsInRange<'0', '9'>                                     IsDigit;
+typedef OrFunctor<IsAlpha, IsDigit>                             IsAlphaNum;
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _skipUntil(); Element-wise
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator, typename TStopFunctor, typename TChunk>
+inline void _skipUntil(TFwdIterator &iter, TStopFunctor &stopFunctor, TChunk)
+{
+    for (; !atEnd(iter) && !stopFunctor(*iter); ++iter) ;
+}
+
+// ----------------------------------------------------------------------------
+// Function _skipUntil(); Chunked
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator, typename TStopFunctor, typename TValue>
+inline void _skipUntil(TFwdIterator &iter, TStopFunctor &stopFunctor, Range<TValue*> *)
+{
+    typedef typename Value<TFwdIterator>::Type TIValue;
+
+    for (; !atEnd(iter); )
+    {
+        Range<TIValue const *> ichunk;
+        getChunk(ichunk, iter, Input());
+        SEQAN_ASSERT(!empty(ichunk));
+
+        const TIValue* SEQAN_RESTRICT ptr = ichunk.begin;
+
+        for (; ptr != ichunk.end; ++ptr)
+        {
+            if (SEQAN_UNLIKELY(stopFunctor(*ptr)))
+            {
+                iter += ptr - ichunk.begin;    // advance input iterator
+                return;
+            }
+        }
+
+        iter += ptr - ichunk.begin;            // advance input iterator
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function skipUntil()
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator, typename TStopFunctor>
+inline void skipUntil(TFwdIterator &iter, TStopFunctor &stopFunctor)
+{
+    typedef typename Chunk<TFwdIterator>::Type* TIChunk;
+
+    _skipUntil(iter, stopFunctor, TIChunk());
+}
+
+template <typename TFwdIterator, typename TStopFunctor>
+inline void skipUntil(TFwdIterator &iter, TStopFunctor const &stopFunctor)
+{
+    typedef typename Chunk<TFwdIterator>::Type* TIChunk;
+
+    TStopFunctor stopFunctor_ = stopFunctor;
+    _skipUntil(iter, stopFunctor_, TIChunk());
+}
+
+// ----------------------------------------------------------------------------
+// Function skipOne()
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator, typename TFunctor>
+inline void skipOne(TFwdIterator &iter, TFunctor &functor)
+{
+    AssertFunctor<TFunctor, ParseError> asserter(functor);
+
+    if (SEQAN_UNLIKELY(atEnd(iter)))
+        throw UnexpectedEnd();
+
+    asserter(*iter);
+    ++iter;
+}
+
+template <typename TFwdIterator, typename TFunctor>
+inline void skipOne(TFwdIterator &iter, TFunctor const &functor)
+{
+    TFunctor func(functor);
+    skipOne(iter, func);
+}
+
+template <typename TFwdIterator>
+inline void skipOne(TFwdIterator &iter)
+{
+    True func;
+    skipOne(iter, func);
+}
+
+// ----------------------------------------------------------------------------
+// Function _readUntil(); Element-wise
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator, typename TStopFunctor, typename TIgnoreFunctor, typename TIChunk, typename TOChunk>
+inline void
+_readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor &stopFunctor, TIgnoreFunctor &ignoreFunctor, TIChunk, TOChunk)
+{
+    typename RemoveConst<typename Value<TFwdIterator>::Type>::Type val;
+    for (; !atEnd(iter); ++iter)
+    {
+        if (SEQAN_UNLIKELY(stopFunctor(val = *iter)))
+            return;
+        if (SEQAN_LIKELY(!ignoreFunctor(val)))
+            writeValue(target, val);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function _readUntil(); Chunked
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator, typename TStopFunctor, typename TIgnoreFunctor, typename TIValue, typename TOValue>
+inline void _readUntil(TTarget &target,
+                       TFwdIterator &iter,
+                       TStopFunctor &stopFunctor,
+                       TIgnoreFunctor &ignoreFunctor,
+                       Range<TIValue*> *,
+                       Range<TOValue*> *)
+{
+    Range<TOValue*> ochunk(NULL, NULL);
+    TOValue* SEQAN_RESTRICT optr = NULL;
+
+    Range<TIValue*> ichunk;
+    for (; !atEnd(iter); )
+    {
+        getChunk(ichunk, iter, Input());
+        const TIValue* SEQAN_RESTRICT iptr = ichunk.begin;
+        SEQAN_ASSERT(iptr < ichunk.end);
+
+        for (; iptr != ichunk.end; ++iptr)
+        {
+            if (SEQAN_UNLIKELY(stopFunctor(*iptr)))
+            {
+                iter += iptr - ichunk.begin;               // advance input iterator
+                advanceChunk(target, optr - ochunk.begin); // extend target string size
+                return;
+            }
+
+            if (SEQAN_UNLIKELY(ignoreFunctor(*iptr)))
+                continue;
+
+            // construct values in reserved memory
+            if (SEQAN_UNLIKELY(optr == ochunk.end))
+            {
+                advanceChunk(target, optr - ochunk.begin);
+                // reserve memory for the worst-case
+                // TODO(weese):Document worst-case behavior
+                reserveChunk(target, length(ichunk), Output());
+                getChunk(ochunk, target, Output());
+                optr = ochunk.begin;
+                SEQAN_ASSERT(optr < ochunk.end);
+            }
+            *optr++ = *iptr;
+        }
+        iter += iptr - ichunk.begin;                       // advance input iterator
+    }
+    advanceChunk(target, optr - ochunk.begin);
+}
+
+// ----------------------------------------------------------------------------
+// Function readUntil()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator, typename TStopFunctor, typename TIgnoreFunctor>
+inline void readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor &stopFunctor, TIgnoreFunctor &ignoreFunctor)
+{
+    typedef typename Chunk<TFwdIterator>::Type*         TIChunk;
+    typedef typename Iterator<TTarget, Rooted>::Type    TTargetIter;
+    typedef typename Chunk<TTargetIter>::Type*          TOChunk;
+
+    _readUntil(target, iter, stopFunctor, ignoreFunctor, TIChunk(), TOChunk());
+}
+
+template <typename TTarget, typename TFwdIterator, typename TStopFunctor, typename TIgnoreFunctor>
+inline void
+readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor const &stopFunctor, TIgnoreFunctor const &ignoreFunctor)
+{
+    TStopFunctor stopFunctor_ = stopFunctor;
+    TIgnoreFunctor ignoreFunctor_ = ignoreFunctor;
+    readUntil(target, iter, stopFunctor_, ignoreFunctor_);
+}
+
+// ----------------------------------------------------------------------------
+// Function readUntil(); Not ignoring
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator, typename TStopFunctor>
+inline void readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor const &stopFunctor)
+{
+    readUntil(target, iter, stopFunctor, False());
+}
+
+template <typename TTarget, typename TFwdIterator, typename TStopFunctor>
+inline void readUntil(TTarget &target, TFwdIterator &iter, TStopFunctor &stopFunctor)
+{
+    False noAssertFunc;
+    readUntil(target, iter, stopFunctor, noAssertFunc);
+}
+
+// ----------------------------------------------------------------------------
+// Function readOne()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator, typename TFunctor>
+inline void readOne(TTarget & target, TFwdIterator &iter, TFunctor &functor)
+{
+    if (SEQAN_UNLIKELY(atEnd(iter)))
+        throw UnexpectedEnd();
+
+    AssertFunctor<TFunctor, ParseError> asserter(functor);
+
+    asserter(*iter);
+    target = *iter;
+    ++iter;
+}
+
+template <typename TTarget, typename TFwdIterator, typename TFunctor>
+inline void readOne(TTarget & target, TFwdIterator &iter, TFunctor const &functor)
+{
+    TFunctor func(functor);
+    readOne(target, iter, func);
+}
+
+template <typename TTarget, typename TFwdIterator>
+inline void readOne(TTarget & target, TFwdIterator &iter)
+{
+    if (SEQAN_UNLIKELY(atEnd(iter)))
+        throw UnexpectedEnd();
+
+    target = *iter;
+    ++iter;
+}
+
+// ----------------------------------------------------------------------------
+// Function readRawByte()
+// ----------------------------------------------------------------------------
+
+//TODO(singer) to be revised
+template <typename TValue, typename TFwdIterator>
+inline void readRawPod(TValue & value, TFwdIterator &srcIter)
+{
+    write((char*)&value, srcIter, sizeof(TValue));
+}
+
+// ----------------------------------------------------------------------------
+// Function readLine()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TFwdIterator>
+inline void readLine(TTarget &target, TFwdIterator &iter)
+{
+    readUntil(target, iter, IsNewline());
+
+    // consume "\r\n.", "\r[!\n]" or "\n."
+
+    if (SEQAN_UNLIKELY(atEnd(iter)))
+        return;
+
+    // If the current character is Line Feed ('\r') then this can be an ANSI or a Mac line ending.
+    if (*iter == '\r')
+    {
+        ++iter;     // consume the found newline
+        if (SEQAN_UNLIKELY(atEnd(iter)))
+            return;
+    }
+
+    // Unix Carriage Return ('\n') is the simplest case.
+    if (*iter == '\n')
+        ++iter;     // consume the found newline
+}
+
+// ----------------------------------------------------------------------------
+// Function skipLine()
+// ----------------------------------------------------------------------------
+
+template <typename TFwdIterator>
+inline void skipLine(TFwdIterator &iter)
+{
+    skipUntil(iter, IsNewline());
+
+    // consume "\r\n.", "\r[!\n]" or "\n."
+
+    if (SEQAN_UNLIKELY(atEnd(iter)))
+        return;
+
+    // If the current character is Line Feed ('\r') then this can be an ANSI or a Mac line ending.
+    if (*iter == '\r')
+    {
+        ++iter;     // consume the found newline
+        if (SEQAN_UNLIKELY(atEnd(iter)))
+            return;
+    }
+
+    // Unix Carriage Return ('\n') is the simplest case.
+    if (*iter == '\n')
+        ++iter;     // consume the found newline
+}
+
+// ----------------------------------------------------------------------------
+// Function writeWrappedString()
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TSequence, typename TSize>
+inline void writeWrappedString(TTarget & target, TSequence const & seq, TSize lineLength)
+{
+    typedef typename Size<TSequence>::Type TSeqSize;
+    typedef typename Iterator<TSequence const, Rooted>::Type TIter;
+
+    TIter iter = begin(seq, Rooted());
+    TSeqSize charsLeft = length(seq);
+    TSeqSize charsPerLine;
+    TSeqSize lineLength_ = (lineLength == 0)? maxValue<TSeqSize>() : lineLength;
+
+    do
+    {
+        charsPerLine = std::min(charsLeft, lineLength_);
+        write(target, iter, charsPerLine);
+        writeValue(target, '\n');
+        charsLeft -= charsPerLine;
+    }
+    while (charsLeft != 0);
+}
+
+// ----------------------------------------------------------------------------
+// Function findFirst()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline typename Position<TContainer>::Type
+findFirst(TContainer const &cont, TFunctor const &func)
+{
+    typename Iterator<TContainer const, Rooted>::Type iter = begin(cont, Rooted());
+    skipUntil(iter, func);
+    return iter - begin(cont, Rooted());
+}
+
+template <typename TContainer>
+inline typename Position<TContainer>::Type
+findFirst(TContainer const &cont, typename Value<TContainer>::Type const &val)
+{
+    EqualsDynamicValue<typename Value<TContainer>::Type> func(val);
+    return findFirst(cont, func);
+}
+
+// ----------------------------------------------------------------------------
+// Function findLast()
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline typename Position<TContainer>::Type
+findLast(TContainer const &cont, TFunctor const &func)
+{
+    typedef ModifiedString<TContainer const, ModReverse> TRevContainer;
+
+    SEQAN_CONCEPT_ASSERT((IntegerConcept<typename Position<TContainer>::Type>));
+
+    // search from back to front
+    TRevContainer rev(cont);
+    typename Iterator<TRevContainer, Rooted>::Type iter = begin(rev, Rooted());
+    skipUntil(iter, func);
+
+    if (atEnd(iter))
+        return -1;
+
+    return host(iter) - begin(cont, Rooted());
+}
+
+template <typename TContainer>
+inline typename Position<TContainer>::Type
+findLast(TContainer const &cont, typename Value<TContainer>::Type const &val)
+{
+    EqualsDynamicValue<typename Value<TContainer>::Type> func(val);
+    return findLast(cont, func);
+}
+
+// ----------------------------------------------------------------------------
+// Function cropAfterFirst(); crop after first occurrence (including it)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline void
+cropAfterFirst(TContainer &cont, TFunctor const &func)
+{
+    resize(cont, findFirst(cont, func));
+}
+
+// ----------------------------------------------------------------------------
+// Function cropAfterLast(); crop after last occurrence (excluding it)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline void
+cropAfterLast(TContainer &cont, TFunctor const &func)
+{
+    resize(cont, findLast(cont, func) + 1);
+}
+
+// ----------------------------------------------------------------------------
+// Function cropBeforeFirst(); crop before first occurrence (excluding it)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline void
+cropBeforeFirst(TContainer &cont, TFunctor const &func)
+{
+    erase(cont, 0, findFirst(cont, func));
+}
+
+// ----------------------------------------------------------------------------
+// Function cropBeforeLast(); crop before first occurrence (including it)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline void
+cropBeforeLast(TContainer &cont, TFunctor const &func)
+{
+    erase(cont, 0, findLast(cont, func) + 1);
+}
+// ----------------------------------------------------------------------------
+// Function cropOuter(); crop after last occurrence (excluding it)
+// ----------------------------------------------------------------------------
+
+template <typename TContainer, typename TFunctor>
+inline void
+cropOuter(TContainer &cont, TFunctor const &func)
+{
+    cropAfterLast(cont, NotFunctor<TFunctor>(func));
+    cropBeforeFirst(cont, NotFunctor<TFunctor>(func));
+}
+
+// --------------------------------------------------------------------------
+// Function strSplit()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn StringSet#strSplit
+ * @brief Append a list of the words in the string, using sep as the delimiter string @link StringSet @endlink.
+ *
+ * @signature void strSplit(result, sequence[, sep[, allowEmptyStrings[, maxSplit]]]);
+ *
+ * @param[out] result           The resulting string set.
+ * @param[in]  sequence         The sequence to split.
+ * @param[in]  sep              The splitter to use (default <tt>' '</tt>).
+ * @param[in]  allowEmptyString Whether or not to allow empty strings (<tt>bool</tt>, defaults to <tt>true</tt> iff
+ *                              <tt>sep</tt> is given).
+ * @param[in]  maxSplit         The maximal number of split operations to do if given.
+ */
+
+template <typename TString, typename TSpec, typename TSequence, typename TFunctor, typename TSize>
+inline void
+strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence, TFunctor const &sep, bool allowEmptyStrings, TSize maxSplit)
+{
+    typedef typename Iterator<TSequence const, Standard>::Type TIter;
+
+    TIter itBeg = begin(sequence, Standard());
+    TIter itEnd = end(sequence, Standard());
+    TIter itFrom = itBeg;
+
+    if (maxSplit == 0)
+    {
+        appendValue(result, sequence);
+        return;
+    }
+
+    for (TIter it = itBeg; it != itEnd; ++it)
+        if (sep(getValue(it)))
+        {
+            if (allowEmptyStrings || itFrom != it)
+            {
+                appendValue(result, infix(sequence, itFrom - itBeg, it - itBeg));
+                if (--maxSplit == 0)
+                {
+                    if (!allowEmptyStrings)
+                    {
+                        while (it != itEnd && sep(getValue(it)))
+                            ++it;
+                    }
+                    else
+                        ++it;
+
+                    if (it != itEnd)
+                        appendValue(result, infix(sequence, it - itBeg, itEnd - itBeg));
+
+                    return;
+                }
+            }
+            itFrom = it + 1;
+        }
+
+    if (allowEmptyStrings || itFrom != itEnd)
+        appendValue(result, infix(sequence, itFrom - itBeg, itEnd - itBeg));
+}
+
+template <typename TString, typename TSpec, typename TSequence, typename TFunctor>
+inline void
+strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence, TFunctor const &sep, bool allowEmptyStrings)
+{
+    strSplit(result, sequence, sep, allowEmptyStrings, maxValue<typename Size<TSequence>::Type>());
+}
+
+template <typename TString, typename TSpec, typename TSequence, typename TFunctor>
+inline void
+strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence, TFunctor const &sep)
+{
+    strSplit(result, sequence, sep, true);
+}
+
+template <typename TString, typename TSpec, typename TSequence>
+inline void
+strSplit(StringSet<TString, TSpec> & result, TSequence const &sequence)
+{
+    strSplit(result, sequence, EqualsChar<' '>(), false);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_STREAM_TOKENIZATION_H_
diff --git a/seqan/stream/tokenize.h b/seqan/stream/tokenize.h
deleted file mode 100644
index 8e51e6c..0000000
--- a/seqan/stream/tokenize.h
+++ /dev/null
@@ -1,2479 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
-// ==========================================================================
-// Functions for tokenizing streams
-// ==========================================================================
-
-// TODO(holtgrew): Some skip*, skipUntil* functions are missing.
-
-#ifndef SEQAN_STREAM_TOKENIZE_H
-#define SEQAN_STREAM_TOKENIZE_H
-
-#include <cctype>
-
-namespace seqan {
-
-// ==========================================================================
-// Forwards
-// ==========================================================================
-
-// ==========================================================================
-// Tags, Classes, Enums
-// ==========================================================================
-
-/*!
- * @enum TokenizeResult
- * @headerfile <seqan/stream.h>
- * @brief Enum with return values for Tokenization operations.
- *
- * @signature enum TokenizeResult;
- *
- * @var TokenizeResult SUCCESS = 0;
- * @brief Reading the specified data succeeded.
- *
- * @var TokenizeResult EOF_BEFORE_SUCCESS = 1024;
- * @brief End of file was reached before the read/skip operation succeeded.
- *
- * @var TokenizeResult NO_SUCCESS = 1025;
- * @brief The pattern was not found but we are not at EOF (may be returned when tokenizing on limited scope.
- */
-
-/**
-.Enum.TokenizeResult
-..cat:Input/Output
-..summary:Enum with return values for Tokenizing operations.
-..value.SUCCESS:Reading the specified data succeeded.
-..value.1-1023:File Error passed through
-..value.EOF_BEFORE_SUCCESS:End of file was reached before the pattern was found.
-..value.NO_SUCCESS:The pattern was not found, but we are not at EOF (may be returned when tokenizing on limited scope)
-..include:seqan/stream.h
- */
-
-enum TokenizeResult {
-    SUCCESS = 0,
-    EOF_BEFORE_SUCCESS = 1024,
-    NO_SUCCESS = 1025
-};
-
-// ----------------------- Helper structs / private tags -----------------------
-struct Whitespace__;
-struct Blank__;
-struct Char__;
-struct Digit__;
-struct Alpha__;
-struct AlphaNum__;
-struct UnixEOL__;
-struct BackslashR__;
-struct Graph__;
-struct TabOrLineBreak__;
-struct Identifier__;
-
-typedef Tag<Whitespace__> Whitespace_;
-typedef Tag<Blank__> Blank_;
-typedef Tag<Char__> Char_;
-typedef Tag<Digit__> Digit_;
-typedef Tag<Alpha__> Alpha_;
-typedef Tag<AlphaNum__> AlphaNum_;
-typedef Tag<UnixEOL__> UnixEOL_;
-typedef Tag<BackslashR__> BackslashR_;
-typedef Tag<Graph__> Graph_;
-typedef Tag<TabOrLineBreak__> TabOrLineBreak_;
-typedef Tag<Identifier__> Identifier_;
-
-// ==========================================================================
-// Metafunctions
-// ==========================================================================
-
-// ==========================================================================
-// Functions
-// ==========================================================================
-
-/*!
- * @defgroup FileFormatTokenization File Format Tokenization
- * @brief Helper code for tokenization when reading from @link RecordReader @endlink.
- */
-
-// ----------------------------------------------------------------------------
-// helper functions for tags
-// ----------------------------------------------------------------------------
-
-inline int
-_charCompare(int const c, Whitespace_ const & /* tag*/)
-{
-    return isspace(c);
-}
-
-inline int
-_charCompare(int const c, Blank_ const & /* tag*/)
-{
-#if defined(PLATFORM_WINDOWS_MINGW)
-    // MinGW 4.7.2 has problems in C++11 mode with isblank.
-    //return isblank(c);
-    return (c == ' ' || c == '\t');
-#else  // #if defined(PLATFORM_WINDOWS_MINGW)
-    return isblank(c);
-#endif  // #if defined(PLATFORM_WINDOWS_MINGW)
-}
-
-inline int
-_charCompare(int const c, Alpha_ const & /* tag*/)
-{
-    return isalpha(c);
-}
-
-inline int
-_charCompare(int const c, AlphaNum_ const & /* tag*/)
-{
-    return isalnum(c);
-}
-
-inline int
-_charCompare(int const c, Identifier_ const & /* tag*/)
-{
-    return isalnum(c) || c == '-' || c == '_';
-}
-
-inline int
-_charCompare(int const c, Digit_ const & /* tag*/)
-{
-    return isdigit(c);
-}
-
-inline int
-_charCompare(int const c, Graph_ const & /* tag*/)
-{
-    return isgraph(c);
-}
-
-inline int
-_charCompare(int const c, UnixEOL_ const & /* tag*/)
-{
-    return (c == '\n');
-}
-
-inline int
-_charCompare(int const c, BackslashR_ const & /* tag*/)
-{
-    return (c == '\r');
-}
-
-inline int
-_charCompare(int const c, Tag<AminoAcid_> const & /* tag*/)
-{
-    switch (c)
-    {
-        case '*':
-        case 'A':
-        case 'B':
-        case 'C':
-        case 'D':
-        case 'E':
-        case 'F':
-        case 'G':
-        case 'H':
-        case 'I':
-        case 'K':
-        case 'L':
-        case 'M':
-        case 'N':
-        case 'P':
-        case 'Q':
-        case 'R':
-        case 'S':
-        case 'T':
-        case 'V':
-        case 'W':
-        case 'X':
-        case 'Y':
-        case 'Z':
-        case 'a':
-        case 'b':
-        case 'c':
-        case 'd':
-        case 'e':
-        case 'f':
-        case 'g':
-        case 'h':
-        case 'i':
-        case 'k':
-        case 'l':
-        case 'm':
-        case 'n':
-        case 'p':
-        case 'q':
-        case 'r':
-        case 's':
-        case 't':
-        case 'v':
-        case 'w':
-        case 'x':
-        case 'y':
-        case 'z':
-            return true;
-    }
-    return false;
-}
-
-inline int
-_charCompare(int const c, Tag<Dna_> const & /* tag*/)
-{
-    switch (c)
-    {
-        case 'a':
-        case 'c':
-        case 'g':
-        case 't':
-        case 'A':
-        case 'C':
-        case 'G':
-        case 'T': return true;
-    }
-    return false;
-}
-
-inline int
-_charCompare(int const c, Tag<Rna_> const & /* tag*/)
-{
-    switch (c)
-    {
-        case 'a':
-        case 'c':
-        case 'g':
-        case 'u':
-        case 'A':
-        case 'C':
-        case 'G':
-        case 'U': return true;
-    }
-    return false;
-}
-
-inline int
-_charCompare(int const c, Tag<DnaQ_> const & /* tag*/)
-{
-    return _charCompare(c, Tag<Dna_>());
-}
-
-inline int
-_charCompare(int const c, Tag<Dna5_> const & /* tag*/)
-{
-    switch (c)
-    {
-        case 'a':
-        case 'c':
-        case 'g':
-        case 't':
-        case 'A':
-        case 'C':
-        case 'G':
-        case 'T':
-        case 'n':
-        case 'N':
-            return true;
-    }
-    return false;
-}
-
-inline int
-_charCompare(int const c, Tag<Rna5_> const & /* tag*/)
-{
-    switch (c)
-    {
-        case 'a':
-        case 'c':
-        case 'g':
-        case 'u':
-        case 'A':
-        case 'C':
-        case 'G':
-        case 'U':
-        case 'n':
-        case 'N':
-            return true;
-    }
-    return false;
-}
-
-inline int
-_charCompare(int const c, Tag<Dna5Q_> const & /* tag*/)
-{
-    return _charCompare(c, Tag<Dna5_>());
-}
-
-template <typename TSpec>
-inline int
-_charCompare(int const c,
-             Tag<SimpleType<unsigned char, TSpec> > const & /* tag */ )
-{
-    return _charCompare(c, Tag<TSpec>());
-}
-
-inline int
-_charCompare(int const c, TabOrLineBreak_ const & /* tag*/)
-{
-    return c == '\t' || c == '\r' || c == '\n';
-}
-
-//TODO(h4nn3s): add for AminoAcid and Rna-tags
-
-
-// ----------------------------------------------------------------------------
-// Function _readHelper() [other read functions use this]
-// ----------------------------------------------------------------------------
-
-// read chars from record reader depending on condition
-template <typename TTagSpec, // specialization of character comparison
-          typename TRecordReader, // record reader
-          typename TBuffer> // usually charstring, but maybe DnaString or so
-inline int
-_readHelper(TBuffer & buffer,
-            TRecordReader & reader,
-            Tag<TTagSpec> const & tag,
-            bool const desiredOutcomeOfComparison) 
-/*   desired behaviour of loop -> "readUntil()" or "readwhile()"  */
-{
-    typedef char TChar;
-
-    while (!atEnd(reader))
-    {
-        TChar c = value(reader);
-        if (bool( _charCompare(c, tag)) == desiredOutcomeOfComparison)
-            return 0;
-        appendValue(buffer, c, Generous());
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-template <typename TSpec, // specialization of character comparison
-          typename TRecordReader, // record reader
-          typename TBuffer> // usually charstring, but maybe DnaString or so
-inline int
-_readHelper(TBuffer & buffer,
-            TRecordReader & reader,
-            Tag<TSpec> const & tag)
-/*   default behaviour of loop is "readUntil()" */
-{
-    return _readHelper(buffer, reader, tag, true);
-}
-
-// same as above but allows for a second character type to be ignored
-template <typename TTagSpec,
-          typename TTagSpec2, // specialization of character class to be ignored
-          typename TRecordReader,
-          typename TBuffer>
-inline int
-_readHelper(TBuffer & buffer,
-            TRecordReader & reader,
-            Tag<TTagSpec> const & compTag,
-            Tag<TTagSpec2> const & skipTag,
-            bool const desiredOutcomeOfComparison)
-{
-    typedef char TChar;
-
-    while (!atEnd(reader))
-    {
-        TChar c = value(reader);
-        if (!_charCompare(c, skipTag))
-        {
-            if (bool (_charCompare(c, compTag)) == desiredOutcomeOfComparison)
-                return 0;
-            appendValue(buffer, c, Generous());
-        }
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-
-template <typename TTagSpec,
-          typename TTagSpec2, // specialization of character class to be ignored
-          typename TRecordReader,
-          typename TBuffer>
-inline int
-_readHelper(TBuffer & buffer,
-            TRecordReader & reader,
-            Tag<TTagSpec> const & compTag,
-            Tag<TTagSpec2> const & skipTag)
-
-{
-    return _readHelper(buffer, reader, compTag, skipTag, true);
-}
-
-
-// ----------------------------------------------------------------------------
-// Function _skipHelper() [other skip functions use this]
-// ----------------------------------------------------------------------------
-
-
-// same as above, just don't save characters read
-template <typename TTagSpec, typename TRecordReader>
-inline int
-_skipHelper(TRecordReader & reader,
-            Tag<TTagSpec> const & tag,
-            bool const desiredOutcomeOfComparison)
-{
-    typedef char TChar;
-
-    while (!atEnd(reader))
-    {
-        TChar c = value(reader);
-        if (bool(_charCompare(c, tag)) == desiredOutcomeOfComparison)
-            return 0;
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-
-template <typename TTagSpec, typename TRecordReader>
-inline int
-_skipHelper(TRecordReader & reader,
-            Tag<TTagSpec> const & tag)
-{
-    return _skipHelper(reader, tag, true);
-}
-
-// ----------------------------------------------------------------------------
-// Function _countHelper()
-// ----------------------------------------------------------------------------
-
-// same as skip, but count the characters read (for doublepass-io)
-template <typename TTagSpec, typename TRecordReader>
-inline int
-_countHelper(unsigned & count,
-            TRecordReader & reader,
-            Tag<TTagSpec> const & tag,
-            bool const desiredOutcomeOfComparison)
-{
-    typedef char TChar;
-    count = 0;
-
-    while (!atEnd(reader))
-    {
-        TChar c = value(reader);
-        count++;
-        if (bool(_charCompare(c, tag)) == desiredOutcomeOfComparison)
-            return 0;
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-template <typename TTagSpec, typename TRecordReader>
-inline int
-_countHelper(unsigned & count,
-            TRecordReader & reader,
-            Tag<TTagSpec> const & tag)
-{
-    return _countHelper(count, reader, tag);
-}
-
-// same as above but allows for a second character type to be ignored
-template <typename TTagSpec,
-          typename TTagSpec2, // specialization of character class to be ignored
-          typename TRecordReader>
-inline int
-_countHelper(unsigned & count,
-            TRecordReader & reader,
-            Tag<TTagSpec> const & compTag,
-            Tag<TTagSpec2> const & skipTag,
-            bool const desiredOutcomeOfComparison)
-{
-    count = 0;
-    typedef char TChar;
-
-    while (!atEnd(reader))
-    {
-        TChar c = value(reader);
-        if (!_charCompare(c, skipTag))
-        {
-            if (bool (_charCompare(c, compTag)) == desiredOutcomeOfComparison)
-                return 0;
-            ++count;
-        }
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-
-template <typename TTagSpec,
-          typename TTagSpec2, // specialization of character class to be ignored
-          typename TRecordReader>
-inline int
-_countHelper(unsigned & count,
-            TRecordReader & reader,
-            Tag<TTagSpec> const & compTag,
-            Tag<TTagSpec2> const & skipTag)
-
-{
-    return _countHelper(count, reader, compTag, skipTag, true);
-}
-
-
-
-
-// ----------------------------------------------------------------------------
-// Function _readAndCompareWithStr()
-// ----------------------------------------------------------------------------
-
-
-
-template <typename TRecordReader, typename TString>
-inline int
-_readAndCompareWithStr(TRecordReader & reader,
-                       TString const & str)
-{
-    bool win = false;
-    for (unsigned i = 0; i < length(str); ++i)
-    {
-        if (atEnd(reader))
-            return EOF_BEFORE_SUCCESS;
-        if (value(reader) != str[i]) //mismatch
-            break;
-        if (i == length(str)-1) // win
-            win = true;
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return win ? 0 : NO_SUCCESS;
-}
-
-
-
-// ----------------------- the real deal ------------------------------------
-
-/*!
- * @fn FileFormatTokenization#readUntilOneOf
- * @headerfile <seqan/stream.h>
- * @brief Read characters from RecordReader into buffer until one of the given character is encountered.
- *
- * @signature int readUntilOneOf(buffer, reader, c1[, c2[, c3[, c4[, c5]]]]);
- *
- * @param[in,out] buffer The buffer to write to.  Type: @link SequenceConcept @endlink.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     c1     One of the characters to look for.  Type: <tt>char</tt>.
- * @param[in]     c2     One of the characters to look for.  Type: <tt>char</tt>.
- * @param[in]     c3     One of the characters to look for.  Type: <tt>char</tt>.
- * @param[in]     c4     One of the characters to look for.  Type: <tt>char</tt>.
- * @param[in]     c5     One of the characters to look for.  Type: <tt>char</tt>.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops <b>on</b> the found character and the character itself is not written to the buffer.  Note that
- * even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF) occured.
- */
-
-/**
-.Function.readUntilOneOf
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream into buffer until one of the given characters is encountered
-..signature:readUntilOneOf(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader, c1[, c2[, c3[, c4[, c5]]])
-..param.buffer:The buffer to write to.
-...type:Shortcut.CharString
-...type:Shortcut.DnaString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *on* the found character. The character is not written to buffer.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
- */
-
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readUntilOneOf(TBuffer & buffer, RecordReader<TStream, TPass> & reader, char c1)
-{
-    while (!atEnd(reader))
-    {
-        char c = value(reader);
-        if (c == c1)
-            return 0;
-        appendValue(buffer, c, Generous());
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readUntilOneOf(TBuffer & buffer, RecordReader<TStream, TPass> & reader, char c1, char c2)
-{
-    while (!atEnd(reader))
-    {
-        char c = value(reader);
-        if (c == c1 || c == c2)
-            return 0;
-        appendValue(buffer, c, Generous());
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readUntilOneOf(TBuffer & buffer, RecordReader<TStream, TPass> & reader, char c1, char c2, char c3)
-{
-    while (!atEnd(reader))
-    {
-        char c = value(reader);
-        if (c == c1 || c == c2 || c == c3)
-            return 0;
-        appendValue(buffer, c, Generous());
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readUntilOneOf(TBuffer & buffer, RecordReader<TStream, TPass> & reader, char c1, char c2, char c3, char c4)
-{
-    while (!atEnd(reader))
-    {
-        char c = value(reader);
-        if (c == c1 || c == c2 || c == c3 || c == c4)
-            return 0;
-        appendValue(buffer, c, Generous());
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readUntilOneOf(TBuffer & buffer, RecordReader<TStream, TPass> & reader, char c1, char c2, char c3, char c4, char c5)
-{
-    while (!atEnd(reader))
-    {
-        char c = value(reader);
-        if (c == c1 || c == c2 || c == c3 || c == c4 || c == c5)
-            return 0;
-        appendValue(buffer, c, Generous());
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-/*!
- * @fn FileFormatTokenization#readUntilWhitespace
- * @headerfile <seqan/stream.h>
- * @brief Read characters from stream into buffer until a @link isspace whitespace @endlink is encountered.
- *
- * @signature int readUntilBlank(buffer, reader);
- *
- * @param[in,out] buffer The buffer to write to.  Type: @link SequenceConcept @endlink.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * Whitespace is more than <tt>' '</tt> and <tt>'\t'</tt>, see @link isspace @endlink.  Consider using @link
- * FileFormatTokenization#readUntilBlank @endlink for reading until space or tab.
- *
- * This function stops <b>on</b> the found character and the character itself is not written to the buffer.  Note that
- * even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF) occured.
- */
-
-/**
-.Function.readUntilWhitespace
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream into buffer until Whitespace is encountered
-..signature:readUntilWhitespace(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:Shortcut.DnaString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:Whitespace is more than '' and '\t', see @Function.isspace@
-..remarks:This function stops *on* the whitespace character. The whitespace is not written to buffer.
-..include:seqan/stream.h
-..see:Function.isspace
-..see:Function.skipUntilWhitespace
-..see:Enum.TokenizeResult
- */
-
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readUntilWhitespace(TBuffer & buffer,
-                    RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _readHelper(buffer,
-                       reader,
-                       Whitespace_());
-}
-
-/*!
- * @fn FileFormatTokenization#readUntilBlank
- * @headerfile <seqan/stream.h>
- * @brief Read characters from stream into buffer until a @link isblank blank @endlink is encountered.
- *
- * @signature int readUntilBlank(buffer, reader);
- *
- * @param[in,out] buffer The buffer to write to.  Type: @link SequenceConcept @endlink.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops <b>on</b> the found character and the character itself is not written to the buffer.  Note that
- * even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF) occured.
- */
-
-/**
-.Function.readUntilBlank
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream into buffer until Blank is encountered
-..signature:readUntilBlank(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:Shortcut.DnaString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:Blank is '' and '\t', see @Function.isblank@
-..remarks:This function stops *on* the blank character. The blank is not written to buffer.
-..include:seqan/stream.h
-..see:Function.isblank
-..see:Function.skipUntilBlank
-..see:Enum.TokenizeResult
- */
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readUntilBlank(TBuffer & buffer,
-               RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _readHelper(buffer,
-                       reader,
-                       Blank_());
-}
-
-/*!
- * @fn FileFormatTokenization#readUntilChar
- * @headerfile <seqan/stream.h>
- * @brief Read characters from stream into buffer until a given character is read.
- *
- * @signature int readUntilChar(buffer, reader, c);
- *
- * @param[in,out] buffer The buffer to write to.  Type: @link SequenceConcept @endlink.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     c      The <tt>char</tt> to look for.
- *
- * @return int 0 if there was no error and non-0 if there were errors.
- *             A special value is @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops <b>on</b> the found character and the character itself is not written to the buffer.  Note that
- * even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF) occured.
- */
-
-/**
-.Function.readUntilChar
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream into buffer until Char is encountered
-..signature:readUntilChar(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader, TChar const & x)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:Shortcut.DnaString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.x:The character to stop on
-...type:nolink:$char$ or similar
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *on* the character x. It is not written to buffer.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.skipUntilChar
- */
-template <typename TBuffer, typename TStream, typename TPass, typename TCharX>
-inline int
-readUntilChar(TBuffer & buffer,
-              RecordReader<TStream, TPass> & reader,
-              TCharX const & x)
-{
-    SEQAN_CHECKPOINT
-    typedef char TChar;
-
-    while (!atEnd(reader))
-    {
-        TChar c = value(reader);
-        if (c == x)
-            return 0;
-        appendValue(buffer, c, Generous());
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-/*!
- * @fn FileFormatTokenization#readNChars
- * @headerfile <seqan/stream.h>
- * @brief Read fixed number of characters from stream into buffer until a given character is read.
- *
- * @signature int readUntilChar(buffer, reader, n);
- *
- * @param[in,out] buffer The buffer to write to.  Type: @link SequenceConcept @endlink.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     n      The number of characters to read.  Type: <tt>unsigned</tt>.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops after <tt>n</tt> read characters.  Note that even when an error occurs, <tt>buffer</tt> will
- * contain the characters read until the error (or EOF) occured.
- */
-
-/**
-.Function.readNChars
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read exactly n characters from stream into buffer
-..signature:readNChars(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader, unsigned const n)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:Shortcut.DnaString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.n:The number of characters to read
-...type:nolink:$unsigned$
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
- */
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readNChars(TBuffer & buffer,
-           RecordReader<TStream, TPass> & reader,
-           unsigned const n)
-{
-    SEQAN_CHECKPOINT
-
-
-    reserve(buffer, n, Exact());
-
-    for (unsigned i = 0; i < n; ++i)
-    {
-        if (atEnd(reader))
-            return EOF_BEFORE_SUCCESS;
-        appendValue(buffer, value(reader));
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return 0;
-}
-
-/*!
- * @fn FileFormatTokenization#readNCharsIgnoringWhitespace
- * @headerfile <seqan/stream.h>
- * @brief Read fixed number of non-whitespace characters.
- *
- * @signature int readUntilChar(buffer, reader, n);
- *
- * @param[in,out] buffer The buffer to write to.  Type: @link SequenceConcept @endlink.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     n      The number of non-whitespace characters to read.  Type: <tt>unsigned</tt>.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * Whitespace is more than <tt>' '</tt> and <tt>'\t'</tt>, see @link isspace @endlink.
- *
- * This function stops after <tt>n</tt> read non-whitespace characters.  Note that even when an error occurs,
- * <tt>buffer</tt> will contain the characters read until the error (or EOF) occured.
- */
-
-/**
-.Function.readNCharsIgnoringWhitespace
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read n characters from stream into buffer, but skip certain Chars
-..signature:readNCharsIgnoringWhitespace(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader, unsigned const n)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:Shortcut.DnaString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.n:The number of characters to read
-...type:nolink:$unsigned$
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..include:seqan/stream.h
-..remarks:Whitespace characters are not counted
-..see:Enum.TokenizeResult
- */
-
-
-template <typename TBuffer, typename TStream, typename TPass,
-          typename TIgnoredType>
-inline int
-_readNCharsIgnoringType(TBuffer & buffer,
-                         RecordReader<TStream, TPass> & reader,
-                         unsigned const n,
-                         TIgnoredType /* tag */)
-{
-    SEQAN_CHECKPOINT
-
-
-    reserve(buffer, n, Exact());
-
-    for (unsigned i = 0; i < n; ++i)
-    {
-        if (atEnd(reader))
-            return EOF_BEFORE_SUCCESS;
-
-        if (_charCompare(value(reader), TIgnoredType()))
-            --i;
-        else
-            appendValue(buffer, value(reader));
-
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return 0;
-}
-
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readNCharsIgnoringWhitespace(TBuffer & buffer,
-                             RecordReader<TStream, TPass> & reader,
-                             unsigned const n)
-{
-    return _readNCharsIgnoringType(buffer, reader, n, Whitespace_());
-}
-
-/*!
- * @fn FileFormatTokenization#skipNChars
- * @headerfile <seqan/stream.h>
- * @brief Skip a fixed number of characters.
- *
- * @signature int skipNChars(reader, n);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     n      The number of characters to read.  Type: <tt>unsinged</tt>.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- */
-
-/**
-.Function.skipNChars
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip exactly n characters from stream
-..signature:skipNChars(RecordReader<TStream, TPass> & recordReader, unsigned const n)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.n:The number of characters to skip
-...type:nolink:$unsigned$
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
- */
-template <typename TStream, typename TPass>
-inline int
-skipNChars(RecordReader<TStream, TPass> & reader,
-           unsigned const n)
-{
-    SEQAN_CHECKPOINT
-
-    for (unsigned i = 0; i < n; ++i)
-    {
-        if (atEnd(reader))
-            return EOF_BEFORE_SUCCESS;
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return 0;
-}
-
-/*!
- * @fn FileFormatTokenization#skipNCharsIgnoringWhitespace
- * @headerfile <seqan/stream.h>
- * @brief Skip a fixed number of non-whitespace characters.
- *
- * @signature int skipNChars(reader, n);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     n      The number of characters to read.  Type: <tt>unsinged</tt>.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * Whitespace is more than <tt>' '</tt> and <tt>'\t'</tt>, see @link isspace @endlink.
- */
-
-
-/**
-.Function.skipNCharsIgnoringWhitespace
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip n characters from stream, not counting whitespaces
-..signature:skipNCharsIgnoringWhitespace(RecordReader<TStream, TPass> & recordReader, unsigned const n)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.n:The number of characters to skip
-...type:nolink:$unsigned$
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..include:seqan/stream.h
-..remarks:Whitespace characters are not counted towards n
-..see:Enum.TokenizeResult
-..see:Function.skipNChars
-..see:Function.readNCharsIgnoringWhitespace
- */
-template <typename TStream, typename TPass,
-          typename TIgnoredType>
-inline int
-_skipNCharsIgnoringType(RecordReader<TStream, TPass> & reader,
-                        unsigned const n,
-                        TIgnoredType const & /* tag */)
-{
-    for (unsigned i = 0; i < n; ++i)
-    {
-        if (atEnd(reader))
-            return EOF_BEFORE_SUCCESS;
-        if (_charCompare(value(reader), TIgnoredType()))
-            --i;
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return 0;
-}
-
-template <typename TStream, typename TPass>
-inline int
-skipNCharsIgnoringWhitespace(RecordReader<TStream, TPass> & reader,
-                             unsigned const n)
-{
-    return _skipNCharsIgnoringType(reader, n, Whitespace_());
-}
-
-/*!
- * @fn FileFormatTokenization#skipUntilWhitespace
- * @headerfile <seqan/stream.h>
- * @brief Skip until the first whitespace character is encountered.
- *
- * @signature int skipUntilWhitespace(reader);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * Whitespace is more than <tt>' '</tt> and <tt>'\t'</tt>, see @link isspace @endlink.  Consider using @link
- * FileFormatTokenization#skipUntilBlank @endlink for skipping until space or tab.
- *
- * The reader will stop <b>on</b> the first whitespace character.
- */
-
-/**
-.Function.skipUntilWhitespace
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip (i.e. read without saving) characters from stream until Whitespace is encountered
-..signature:skipUntilWhitespace(RecordReader<TStream, TPass> & recordReader)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:Whitespace is more than '' and '\t', see @Function.isspace@
-..remarks:This function stops *on* the whitespace character. The whitespace is not skipped.
-..include:seqan/stream.h
-..see:Function.isspace
-..see:Function.skipWhitespaces
-..see:Function.readUntilWhitespace
-..see:Enum.TokenizeResult
- */
-template <typename TStream, typename TPass>
-inline int
-skipUntilWhitespace(RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _skipHelper(reader, Whitespace_());
-}
-
-/*!
- * @fn FileFormatTokenization#skipUntilBlank
- * @headerfile <seqan/stream.h>
- * @brief Skip until the first blank character is encountered.
- *
- * @signature int skipUntilBlank(reader);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The reader will stop <b>on</b> the first blank character.
- */
-
-/**
-.Function.skipUntilBlank
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip (i.e. read without saving) characters from stream until Blank is encountered
-..signature:skipUntilBlank(RecordReader<TStream, TPass> & recordReader)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *on* the blank character. The blank is not skipped.
-..include:seqan/stream.h
-..see:Function.isblank
-..see:Enum.TokenizeResult
-..see:Function.readUntilBlank
- */
-
-template <typename TStream, typename TPass>
-inline int
-skipUntilBlank(RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _skipHelper(reader, Blank_());
-}
-
-/*!
- * @fn FileFormatTokenization#skipUntilGraph
- * @headerfile <seqan/stream.h>
- * @brief Skip until the first printable character is encountered.
- *
- * @signature int skipUntilGraph(reader);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The reader will stop <b>on</b> the first printable character.
- *
- * @see isgraph
- */
-
-/**
-.Function.skipUntilGraph
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip (i.e. read without saving) characters from stream until printable, non-' ' character is encountered
-..signature:skipUntilGraph(RecordReader<TStream, TPass> & recordReader)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *on* the graph character. The graph is not skipped.
-..remarks:See @Function.isgraph@ for details on the "graph"-group of characters
-..include:seqan/stream.h
-..see:Function.isgraph
-..see:Enum.TokenizeResult
- */
-template <typename TStream, typename TPass>
-inline int
-skipUntilGraph(RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _skipHelper(reader, Graph_());
-}
-
-/*!
- * @fn FileFormatTokenization#skipUntilChar
- * @headerfile <seqan/stream.h>
- * @brief Skip until the a given character is found.
- *
- * @signature int skipUntilChar(reader, c);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     c      The <tt>char</tt> to search for.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The reader will stop <b>on</b> the first found location of <tt>c</tt>.
- */
-
-/**
-.Function.skipUntilChar
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip (i.e. read without saving) characters from stream until Char is encountered
-..signature:skipUntilChar(RecordReader<TStream, TPass> & recordReader, TChar const & x)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.x:The character to stop on
-...type:nolink:$char$ or similar
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *on* the character x. x is not skipped.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.readUntilChar
- */
-template <typename TStream, typename TPass, typename TCharX>
-inline int
-skipUntilChar(RecordReader<TStream, TPass> & reader,
-              TCharX const & x)
-{
-    SEQAN_CHECKPOINT
-    typedef char TChar;
-
-    while (!atEnd(reader))
-    {
-        TChar c = value(reader);
-        if (c == x)
-            return 0;
-        goNext(reader);
-        if (resultCode(reader) != 0)
-            return resultCode(reader);
-    }
-    return EOF_BEFORE_SUCCESS;
-}
-
-/*!
- * @fn FileFormatTokenization#skipUntilString
- * @headerfile <seqan/stream.h>
- * @brief Skip until the a given string is found.
- *
- * @signature int skipUntilString(reader, str);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     str    The @link SequenceConcept @endlink to find.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The reader will stop <b>behind</b> the location of <tt>str</tt>.
- */
-
-/**
-.Function.skipUntilString
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip (i.e. read without saving) characters from stream until String is encountered
-..signature:skipUntilString(RecordReader<TStream, TPass> & recordReader, TString const & str)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.str:The string to stop on
-...type:nolink:f$char$ or similar
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *behind* the character string
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.skipUntilChar
- */
-// I think this function is stupid, but it is implemented in misc_parsing.h
-// so I offer replacement; with proper buffering shiftOr would be faster
-template <typename TStream, typename TPass, typename TString>
-inline int
-skipUntilString(RecordReader<TStream, TPass> & reader,
-                             TString const & str)
-{
-    SEQAN_CHECKPOINT
-    if (length(str) < 1)
-        return -1; //TODO some better error code
-    while(skipUntilChar(reader, str[0])==0)
-    {
-        switch(int r = _readAndCompareWithStr(reader, str))
-        {
-            case 0: return 0;
-            case NO_SUCCESS: break;
-            default: return r;
-        }
-    }
-    return EOF_BEFORE_SUCCESS;
-    /* NOTE I am not 100% sure this will get every pattern with repitions in it.
-     * it should be much better than the original, since it escapes on mismatch
-     * directly and doesnt read (and possibly discard) N charecters in a row,
-     * which definitely leads to misses. */
-}
-
-/*!
- * @fn FileFormatTokenization#skipTabOrLineBreak
- * @headerfile <seqan/stream.h>
- * @brief Skip over tab or line break characters (<tt>'\r' or '\n'</tt>).
- *
- * @signature int skipTabOrLineBreak(reader);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The reader will stop <b>behind</b> the (possibly empty) sequence of tab or line break characters (regex:
- * <tt>[\r\n\t]</tt>).
- */
-
-/**
-.Function.readUntilTabOrLineBreak
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream until a tab or line-break occurs.
-..signature:readUntilTabOrLineBreak(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to.
-...type:Shortcut.CharString
-...type:Shortcut.DnaString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *on* the tab or line-break character. This character is not written to buffer.
-..include:seqan/stream.h
- */
-
-template <typename TBuffer, typename TStream, typename TPass>
-inline int
-readUntilTabOrLineBreak(TBuffer & buffer,
-                        RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _readHelper(buffer,
-                       reader,
-                       TabOrLineBreak_());
-}
-
-// ---
-
-/*!
- * @fn FileFormatTokenization#readLetters
- * @headerfile <seqan/tokenize.h>
- * @brief Read from a RecordReader as long as the characters are letters (in @link isalpha alpha @endlink class).
- *
- * @signature int readLetters(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to read the data into.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The function will stop <b>after</b> the last read character.
- * 
- * Note that even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF)
- * occured.
- */
-
-/**
-.Function.readLetters
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream as long as characters are letters
-..signature:readLetters(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:Shortcut.DnaString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *behind* the last letter read.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.isalpha
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readLetters(TBuffer & buffer, RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _readHelper(buffer,
-                       reader,
-                       Alpha_(),
-                       false);
-}
-
-/*!
- * @fn FileFormatTokenization#readDigits
- * @headerfile <seqan/tokenize.h>
- * @brief Read from a RecordReader as long as the characters are digits (in @link isdigit digit @endlink class).
- *
- * @signature int readDigits(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to read the data into.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The function will stop <b>after</b> the last read character.
- * 
- * Note that even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF)
- * occured.
- */
-
-/**
-.Function.readDigits
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream as long as characters are digits
-..signature:readDigits(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *behind* the last letter read.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.isdigit
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readDigits(TBuffer & buffer, RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _readHelper(buffer,
-                       reader,
-                       Digit_(),
-                       false);
-}
-
-/*!
- * @fn FileFormatTokenization#readGraphs
- * @headerfile <seqan/tokenize.h>
- * @brief Read from a RecordReader as long as the characters are printable (in @link isgraph graph @endlink class).
- *
- * @signature int readGraphs(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to read the data into.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The function will stop <b>after</b> the last read character.
- * 
- * Note that even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF)
- * occured.
- */
-
-/**
-.Function.readGraphs
-..cat:Input/Output
-..summary:Read characters from stream as long as characters are graph characters.
-..signature:readGraphs(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *behind* the last letter read.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.isgraph
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readGraphs(TBuffer & buffer, RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _readHelper(buffer, reader, Graph_(), false);
-}
-
-/*!
- * @fn FileFormatTokenization#readFloat
- * @headerfile <seqan/tokenize.h>
- * @brief Read characters from @link RecordReader @endlink as long as the string is a valid floating point numbers.
- *
- * @signature int readFloat(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to read the data into.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The function will stop <b>after</b> the last read character.
- * 
- * Note that even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF)
- * occured.
- */
-
-/**
-.Function.readFloat
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream as long as the number is a valid floating point numbers.
-..description:Supports normal floating point numbers and scientific notation.
-..signature:readFloat(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *behind* the last letter read.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.isdigit
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readFloat(TBuffer & buffer, RecordReader<TStream, TPass> & reader)
-{
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-
-    // Read sign if any.
-    if (value(reader) == '+' || value(reader) == '-')
-        if (readNChars(buffer, reader, 1) != 0)
-            return 1;
-
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-
-    int res = 0;
-
-    // Either read [0-9]+(\.[0-9]*)? or \.[0-9]+.
-    if (value(reader) == '.')
-    {
-        res = readNChars(buffer, reader, 1);
-        if (res != 0)
-            return res;
-        if (atEnd(reader))
-            return EOF_BEFORE_SUCCESS;
-        if (!isdigit(value(reader)))
-            return 1;
-        if ((res = readDigits(buffer, reader)) != 0)
-            return res;
-    }
-    else
-    {
-        // A row of digits must follow.
-        if (!isdigit(value(reader)))
-            return 1;  // Invalid.
-        res = readDigits(buffer, reader);
-        // The input may end after these digits.
-        if (res == EOF_BEFORE_SUCCESS)
-            return 0;
-        if (res != 0)
-            return 1;
-        // Read \.[0-9]* block.
-        if (value(reader) == '.')
-        {
-            res = readNChars(buffer, reader, 1);
-            // The input may end after the dot.
-            if (res == EOF_BEFORE_SUCCESS)
-                return 0;
-            if (res != 0)
-                return 1;
-            if (isdigit(value(reader)))
-                if ((res = readDigits(buffer, reader)) != 0)
-                    return res;
-        }
-    }
-
-    if (value(reader) != 'e' && value(reader) != 'E')
-        return 0;
-    if ((res = readNChars(buffer, reader, 1)) != 0)
-        return res;
-    if (value(reader) == '+' || value(reader) == '-')
-        if ((res = readNChars(buffer, reader, 1)) != 0)
-            return res;
-    if (!isdigit(value(reader)))
-        return 1;
-    if ((res = readDigits(buffer, reader)) != 0)
-        return res;
-
-    return 0;
-}
-
-/*!
- * @fn FileFormatTokenization#readAlphaNums
- * @headerfile <seqan/tokenize.h>
- * @brief Read from a RecordReader as long as the characters are alphanumeric (in @link isalnum alnum @endlink class).
- *
- * @signature int readAlphaNums(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to read the data into.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The function will stop <b>after</b> the last read character.
- * 
- * Note that even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF)
- * occured.
- */
-
-/**
-.Function.readAlphaNums
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream as long as characters are letters
-..signature:readAlphaNums(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *behind* the last letter read.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.isalnum
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readAlphaNums(TBuffer & buffer, RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _readHelper(buffer,
-                       reader,
-                       AlphaNum_(),
-                       false);
-}
-
-/*!
- * @fn FileFormatTokenization#readIdentifier
- * @headerfile <seqan/tokenize.h>
- * @brief Read from a RecordReader as long as the characters form an identifier (alnum, <tt>'-'</tt>, <tt>'_'</tt>).
- *
- * @signature int readIdentifier(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to read the data into.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * The function will stop <b>after</b> the last read character.
- * 
- * Note that even when an error occurs, <tt>buffer</tt> will contain the characters read until the error (or EOF)
- * occured.
- */
-
-/**
-.Function.readIdentifier
-..cat:Input/Output
-..summary:Read characters from stream as long as characters are identifiers (alphanumeric, $'-'$, and $'_'$).
-..signature:readIdentifier(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *behind* the last letter read.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.isalnum
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readIdentifier(TBuffer & buffer, RecordReader<TStream, TPass> & reader)
-{
-    return _readHelper(buffer, reader, Identifier_(), false);
-}
-
-/*!
- * @fn FileFormatTokenization#skipWhitespaces
- * @headerfile <seqan/stream.h>
- * @brief Advance RecordReader until a whitespace occurs.
- *
- * @signature int skipWhitespaces(reader);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * Whitespace is more than <tt>' '</tt> and <tt>'\t'</tt>, see @link isspace @endlink.  Consider using @link
- * FileFormatTokenization#skipBlanks @endlink for skipping blanks.
- *
- * This function stops <b>after</b> the last skipped.
- */
-
-/**
-.Function.skipWhitespaces
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip (i.e. read without saving) characters from stream until non-Whitespace is encountered
-..signature:skipWhitespaces(RecordReader<TStream, TPass> & recordReader)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:Whitespace is more than '' and '\t', see @Function.isspace@
-..remarks:This function stops *behind* the last whitespace character.
-..include:seqan/stream.h
-..see:Function.isspace
-..see:Function.readUntilWhitespace
-..see:Function.skipUntilWhitespace
-..see:Enum.TokenizeResult
- */
-template <typename TStream, typename TPass>
-inline int
-skipWhitespaces(RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _skipHelper(reader, Whitespace_(), false);
-}
-
-/*!
- * @fn FileFormatTokenization#skipChar
- * @headerfile <seqan/stream.h>
- * @brief Skip one character that must be equal to a given one for this function to succeed.
- *
- * @signature int skipChar(reader, c);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     c      The <tt>char</tt> to skip.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- */
-
-/**
-.Function.skipChar
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip one character that must be equal to a given one for this function to succeed.
-..signature:skipChar(RecordReader<TStream, TPass> & recordReader, c)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.c:The character to skip.
-...type:nolink:$char$
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
- */
-template <typename TStream, typename TPass>
-inline int
-skipChar(RecordReader<TStream, TPass> & reader, char const c)
-{
-    SEQAN_CHECKPOINT;
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    if (value(reader) != c)
-        return 1;
-    goNext(reader);
-    return 0;
-}
-
-/*!
- * @fn FileFormatTokenization#skipBlanks
- * @headerfile <seqan/stream.h>
- * @brief Advance RecordReader until a blank occurs.
- *
- * @signature int skipBlanks(reader);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops <b>after</b> the last skipped.
- */
-
-/**
-.Function.skipBlanks
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip (i.e. read without saving) characters from stream until non-Blank is encountered
-..signature:skipBlanks(RecordReader<TStream, TPass> & recordReader)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops *behind* the last whitespace character.
-..include:seqan/stream.h
-..see:Function.isblank
-..see:Function.readUntilBlank
-..see:Function.skipUntilBlank
-..see:Enum.TokenizeResult
- */
-template <typename TStream, typename TPass>
-inline int
-skipBlanks(RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    return _skipHelper(reader, Blank_(), false);
-}
-
-/*!
- * @fn FileFormatTokenization#readLine
- * @headerfile <seqan/stream.h>
- * @brief Read a line from a RecordReader into a buffer.
- *
- * @signature int readLine(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to append the read data to.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops on the beginning of the next line (if there is any).  End of line characters are not written to
- * buffer.  Works on ANSI, Mac, and Unix EOL.
- */
-
-/**
-.Function.readLine
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read a line from stream and save it to buffer
-..signature:readLine(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops on the beginning of the next line, if there is a next line
-..remarks:End-line characters are not written to buffer.
-..remarks:Works on ANSI EOL, Mac EOL and on Unix EOL.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readLine(TBuffer & buffer, RecordReader<TStream, TPass> & reader)
-{
-    int r = 0;
-
-    // Loop over characters from stream, taking early exits on line breaks and errors.
-    while (!atEnd(reader))
-    {
-        char c = value(reader);
-
-        // Unix EOL is the simplest case.
-        if (c == '\n')
-        {
-            if (!atEnd(reader))
-                goNext(reader);
-            return resultCode(reader);
-        }
-
-        // If the current character is '\r' then this can be an ANSI or a Mac line ending.
-        if (c == '\r')
-        {
-            goNext(reader);
-            if ((r = resultCode(reader)) != 0)
-                return r;
-            if (atEnd(reader))
-                return 0;  // Assume Mac EOL at end of file.
-            if (value(reader) == '\n')
-            {
-                // Assume Windows EOL.
-                if (!atEnd(reader))
-                    goNext(reader);
-                return resultCode(reader);
-            }
-            return 0;  // Was Mac EOL, not at end of file.
-        }
-
-        appendValue(buffer, c);
-        goNext(reader);
-    }
-
-    return EOF_BEFORE_SUCCESS;
-}
-
-/*!
- * @fn FileFormatTokenization#readLineStripTrailingBlanks
- * @headerfile <seqan/stream.h>
- * @brief Read a line from a RecordReader into a buffer and remove trailing blanks.
- *
- * @signature int readLineStripTrailingBlanks(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to append the read data to.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops on the beginning of the next line (if there is any).  End of line characters and all trailing
- * whitespaces are not written to buffer.  Works on ANSI, Mac, and Unix EOL.
- */
-
-/**
-.Function.readLineStripTrailingBlanks
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read a line from stream and save it to buffer, remove trailing blanks
-..signature:readLineStripTrailingBlanks(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.CharString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops on the beginning of the next line, if there is a next line
-..remarks:End-line characters and all trailing blanks are not written to buffer.
-..remarks:Works on ANSI EOL and on Unix EOL.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.isblank
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readLineStripTrailingBlanks(TBuffer & buffer,
-                            RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    int r = readLine(buffer,reader);
-
-    if (r != 0)
-        return r;   // 1234567890
-
-    typename Size<TBuffer>::Type pos = length(buffer) -1;
-
-    if (pos < 0)
-        return 0;
-
-    while ((isblank(value(buffer, pos)) == 0) && (pos >= 0)) --pos;
-
-    if (pos + 1 != length(buffer))
-        resize(buffer, pos+1, Exact());
-    return 0;
-}
-
-/*!
- * @fn RecordReader#skipLine
- * @headerfile <seqan/stream.h>
- * @brief Skip a line in stream and go to beginning of next
- * 
- * @signature int skipLine(reader);
- * 
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * 
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- * 
- * @section Remarks
- * 
- * This function stops on the beginning of the next line, if there is a next line
- * 
- * Works on ANSI EOL and on Unix EOL.
- */
-
-/**
-.Function.skipLine
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip a line in stream and go to beginning of next
-..signature:skipLine(RecordReader<TStream, TPass> & recordReader)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops on the beginning of the next line, if there is a next line
-..remarks:Works on ANSI EOL and on Unix EOL.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.readLine
- */
-template <typename TStream, typename TPass>
-inline int
-skipLine(RecordReader<TStream, TPass> & reader)
-{
-    int r = _skipHelper(reader, UnixEOL_());
-
-    if (r != 0)
-        return r;
-
-    if (!atEnd(reader))
-        goNext(reader); // go to beginning of next line
-
-    return resultCode(reader);
-}
-
-/*!
- * @fn RecordReader#countLine
- * @headerfile <seqan/stream.h>
- * @brief Count characters in a line excluding <tt>'\r'</tt> and <tt>'\n'</tt>.
- * 
- * @signature int countLine(num, reader);
- *
- * @param[in,out] num    The <tt>unsigned</tt> to increment.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * 
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- * 
- * @section Remarks
- * 
- * This function stops on the beginning of the next line, if there is a next line (even though newline characters are
- * not counted).
- * 
- * Works on ANSI EOL and on Unix EOL.
- */
-
-/**
-.Function.countLine
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:count characters in a line not including \r and \n
-..signature:countLine(unsigned & count, RecordReader<TStream, TPass> & recordReader)
-..param.count:The variable to increment
-...type:nolink:unsigned int
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function stops on the beginning of the next line, if there is a next line (even though newline characters are not counted)
-..remarks:Works on ANSI EOL and on Unix EOL.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
- */
-template <typename TStream, typename TPass>
-inline int
-countLine(unsigned & count, RecordReader<TStream, TPass> & reader)
-{
-    SEQAN_CHECKPOINT
-    int r = _countHelper(count,
-                        reader,
-                        UnixEOL_(), // abort on Newline
-                        BackslashR_()); // just ignore carriage return
-    if (r != 0)
-        return r;
-
-    if (!atEnd(reader))
-        goNext(reader); // go to beginning of next line
-
-    return resultCode(reader);
-}
-
-/*!
- * @fn FileFormatTokenization#readDna5IgnoringWhitespaces
- * @headerfile <seqan/stream.h>
- * @brief Read characters from stream as long as they are DNA5 characters, skipping whitespaces.
- *
- * @signature int readDna5IgnoringWhitespaces(buffer, reader);
- *
- * @param[in,out] buffer The @link String @endlink to append the read data to.
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops <b>on</b> the first non-matching character, whitespaces such as newlines are discarded.
- */
-
-/**
-.Function.readDna5IgnoringWhitespaces
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Read characters from stream, as long as they are DNA5 characters. Skip over whitespaces.
-..signature:readDna5IgnoringWhitespaces(TBuffer & buffer, RecordReader<TStream, TPass> & recordReader)
-..param.buffer:The buffer to write to
-...type:Shortcut.Dna5String
-...type:Shortcut.CharString
-...type:nolink:or similar
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function read Dna5-Characters and simply discards whitespaces, including newlines.
-..remarks:It stops on the first character that is not Dna5 and not whitespace.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.isspace
-..see:Spec.Dna5
- */
-template <typename TStream, typename TPass, typename TBuffer>
-inline int
-readDna5IgnoringWhitespaces(TBuffer & buffer,
-                            RecordReader<TStream, TPass> & reader)
-{
-    return _readHelper(buffer, reader, Tag<Dna5_>(), Whitespace_(), false);
-} 
-// this would read a fasta or fastq sequence, since meta and qualities begin 
-// with special chars
-
-/*!
- * @fn FileFormatTokenization#sipUntilLineBeginsWithChar
- * @headerfile <seqan/stream.h>
- * @brief Skip input until the first graphical (see @link isgraph @endlink) character of a line is equal to c.
- *
- * @signature int skipUntilLineBeginsWithChar(reader, c);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     c      The <tt>char</tt> to look for.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops <b>on</b> the first occurence of <tt>c</tt> at the beginning of a line (ignoring leading
- * whitespace).
- */
-
-/**
-.Function.skipUntilLineBeginsWithChar
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip input until the first graphical(see @Function.isgraph@) character of a line is equal to c
-..signature:skipUntilLineBeginsWithChar(RecordReader<TStream, TPass> & recordReader, TChar const & c)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.c:The character to look for, must be in @Function.isgraph@
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function skips lines, and then non-graphical chars at the line beginnings,
-..remarks:until it finds a line where the first graph-character is c. It stops on c, not behind.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.skipUntilLineBeginsWithStr
- */
-// also skips non-graph characters at linestart, c must not be non-graph
-// NOTE that position is on c, like in old function
-// NOTE also, that we DO NOT reset in case of search failure as that would
-// require seek
-template <typename TStream, typename TPass, typename TChar>
-inline int
-skipUntilLineBeginsWithChar(RecordReader<TStream, TPass> & reader,
-                            TChar const & c )
-{
-    int r = 0;
-    while (!atEnd(reader) && (r = skipLine(reader)) == 0 )
-    {
-        r = skipUntilGraph(reader);
-        if (r != 0)
-            return r;
-        if (value(reader) == c)
-            return 0;
-    }
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    return r;
-}
-
-/*!
- * @fn FileFormatTokenization#sipUntilLineBeginsWithStr
- * @headerfile <seqan/stream.h>
- * @brief Skip input until a line begins with str (str itself must begin with a printable character).
- *
- * @signature int skipUntilLineBeginsWithChar(reader, str);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     c      The @link SequenceConcept @endlink to look for.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops <b>behind</b> the first occurence of <tt>str</tt> at the beginning of a line.  The function skips
- * over leading whitespace.
- */
-
-/**
-.Function.skipUntilLineBeginsWithStr
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip input until a line begins with str.
-..signature:skipUntilLineBeginsWithStr(RecordReader<TStream, TPass> & recordReader, TString const & str)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.str:The string to look for, must begin with a char in @Function.isgraph@
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function skips lines, and then non-graphical chars (see @Function.isgraph@) at the line beginnings,
-..remarks:until it finds a line where the first string beginning with graph-characters is equal to str.
-..remarks:It stops behaind the string.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.readLine
- */
-// also skips non-graph characters at linestart, str must not begin with non-graph
-// NOTE that position is behind str, like in old function, if a char behind
-// string exists. NOTE also, that we DO NOT reset in case of search failure
-// as that would require seek
-template <typename TStream, typename TPass, typename TString>
-inline int
-skipUntilLineBeginsWithStr(RecordReader<TStream, TPass> & reader,
-                           TString const & str )
-{
-    int r = 0;
-    while (!atEnd(reader) && (r = skipLine(reader)) == 0 )
-    {
-        r = skipUntilGraph(reader);
-        if (r != 0)
-            return r;
-        switch(r = _readAndCompareWithStr(reader, str))
-        {
-            case 0: return 0;
-            case NO_SUCCESS: break;
-            default: return r;
-        }
-    }
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    return r;
-}
-
-/*!
- * @fn FileFormatTokenization#sipUntilLineBeginsWithOneCharOfStr
- * @headerfile <seqan/stream.h>
- * @brief Skip input until a line begins with one of the character in str.
- *
- * @signature int skipUntilLineBeginsWithOneCharOfStr(reader, str);
- *
- * @param[in,out] reader The @link RecordReader @endlink to read from.
- * @param[in]     str    The @link SequenceConcept @endlink with the characters to look for.
- *
- * @return int 0 if there was no error on reading or non-0 if there were errors.  A special value is
- *             @link TokenizeResult EOF_BEFORE_SUCCESS @endlink.
- *
- * @section Remarks
- *
- * This function stops <b>on</b> the first found occurence.  All characters in <tt>str</tt> must be printable (see @link
- * isgraph @endlink).
- */
-
-/**
-.Function.skipUntilLineBeginsWithOneCharOfStr
-..class:Class.RecordReader
-..cat:Input/Output
-..summary:Skip input until a line begins with a one of the characters in str
-..signature:skipUntilLineBeginsWithOneCharOfStr(RecordReader<TStream, TPass> & recordReader, TString const & str)
-..param.recordReader:The @Class.RecordReader@ to read from.
-...type:Class.RecordReader
-..param.str:The set of characters to look for, must be in @Function.isgraph@
-..returns:0 if there was no error reading
-..returns:non-zero value on errors, especially EOF_BEFORE_SUCCESS
-...type:nolink:$int$
-...type:Enum.TokenizeResult
-..remarks:This function skips lines, and then non-graphical chars (see @Function.isgraph@) at the line beginnings,
-..remarks:until it finds a line where the first graph-char is one of the characters in str.
-..remarks:It stops on the char.
-..include:seqan/stream.h
-..see:Enum.TokenizeResult
-..see:Function.readLine
- */
-// also skips non-graph characters at linestart, c must not be non-graph
-// NOTE that position is on c, like in old function
-// NOTE also, that we DO NOT reset in case of search failure as that would
-// require seek
-template <typename TStream, typename TPass, typename TString>
-inline int
-skipUntilLineBeginsWithOneCharOfStr(RecordReader<TStream, TPass> & reader,
-                                    TString const & str )
-{
-
-    int r = 0;
-    while (!atEnd(reader) && (r = skipLine(reader)) == 0 )
-    {
-        r = skipUntilGraph(reader);
-        if (r != 0)
-            return r;
-        for (unsigned i = 0; i < length(str); ++i)
-        {
-            if (value(reader) == value(str,i))
-                return 0;
-        }
-
-    }
-    if (atEnd(reader))
-        return EOF_BEFORE_SUCCESS;
-    return r;
-}
-
-// TODO missing functions from misc_parsing.h:
-// _parseUntilBeginLine with max num lines
-//_parseUntilBeginLineOneOf(
-// all functions that require lexical_cast<>() which isnt there yet
-
-// TODO stuff from other files (shouldnt be that much and much is duplicate)
-
-}  // namespace seqan
-
-#endif // #ifdef SEQAN_STREAM_RECORD_READER_SINGLE_H_
diff --git a/seqan/stream/virtual_stream.h b/seqan/stream/virtual_stream.h
new file mode 100644
index 0000000..bf6b5dd
--- /dev/null
+++ b/seqan/stream/virtual_stream.h
@@ -0,0 +1,714 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Virtual stream class to automatically compress/decompress files/streams.
+// It adapts the zipstream and bzip2stream classes (Jonathan de Halleux, 2003)
+// http://www.codeproject.com/Articles/4457/zipstream-bzip2stream-iostream-wrappers-for-the-zl
+// and our own implementation of a parallel bgzfstream.
+// ==========================================================================
+
+#ifndef SEQAN_STREAM_VIRTUAL_STREAM_
+#define SEQAN_STREAM_VIRTUAL_STREAM_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+template <typename TStream>
+struct StreamFormat;
+
+// ============================================================================
+// Tags, Enums
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// TagList CompressedFileTypes
+// --------------------------------------------------------------------------
+
+typedef
+#if SEQAN_HAS_ZLIB
+    TagList<BgzfFile,
+    TagList<GZFile,
+#endif
+#if SEQAN_HAS_BZIP2
+    TagList<BZ2File,
+#endif
+    TagList<Nothing>
+#if SEQAN_HAS_BZIP2
+    >
+#endif
+#if SEQAN_HAS_ZLIB
+    >
+    >
+#endif
+    CompressedFileTypes;  // if TagSelector is set to -1, the file format is auto-detected
+
+// --------------------------------------------------------------------------
+// TagList CompressedFileTypes
+// --------------------------------------------------------------------------
+// NOTE(h-2): this currently lacks BGZF, so that we don't get .fasta.bam, .m8.bam ...
+// in the long term bgzf should just not contain .bam but that would require more changes
+
+typedef
+#if SEQAN_HAS_ZLIB
+    TagList<GZFile,
+#endif
+#if SEQAN_HAS_BZIP2
+    TagList<BZ2File,
+#endif
+    TagList<Nothing>
+#if SEQAN_HAS_BZIP2
+    >
+#endif
+#if SEQAN_HAS_ZLIB
+    >
+#endif
+    CompressedFileTypesWithoutBgzf_;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+#if SEQAN_HAS_ZLIB
+
+template <typename Elem, typename Tr, typename ElemA, typename ByteT, typename ByteAT>
+struct Value<basic_bgzf_istream<Elem, Tr, ElemA, ByteT, ByteAT> > :
+    Value<std::basic_istream<Elem, Tr> > {};
+
+template <typename Elem, typename Tr, typename ElemA, typename ByteT, typename ByteAT>
+struct Position<basic_bgzf_istream<Elem, Tr, ElemA, ByteT, ByteAT> > :
+    Position<std::basic_istream<Elem, Tr> > {};
+
+
+template <typename Elem, typename Tr, typename ElemA, typename ByteT, typename ByteAT>
+struct Value<basic_bgzf_ostream<Elem, Tr, ElemA, ByteT, ByteAT> > :
+    Value<std::basic_ostream<Elem, Tr> > {};
+
+template <typename Elem, typename Tr, typename ElemA, typename ByteT, typename ByteAT>
+struct Position<basic_bgzf_ostream<Elem, Tr, ElemA, ByteT, ByteAT> > :
+    Position<std::basic_ostream<Elem, Tr> > {};
+
+
+template <typename Elem, typename Tr, typename ElemA, typename ByteT, typename ByteAT>
+SEQAN_CONCEPT_IMPL((basic_bgzf_istream<Elem, Tr, ElemA, ByteT, ByteAT>), (InputStreamConcept));
+
+template <typename Elem, typename Tr, typename ElemA, typename ByteT, typename ByteAT>
+SEQAN_CONCEPT_IMPL((basic_bgzf_ostream<Elem, Tr, ElemA, ByteT, ByteAT>), (OutputStreamConcept));
+
+#endif
+
+// --------------------------------------------------------------------------
+// Metafunction VirtualStreamSwitch_
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TFormatTag>
+struct VirtualStreamSwitch_
+{
+    typedef Nothing Type;
+};
+
+#if SEQAN_HAS_ZLIB
+template <typename TValue>
+struct VirtualStreamSwitch_<TValue, Input, GZFile>
+{
+    typedef zlib_stream::basic_zip_istream<TValue> Type;
+};
+
+template <typename TValue>
+struct VirtualStreamSwitch_<TValue, Output, GZFile>
+{
+    typedef zlib_stream::basic_zip_ostream<TValue> Type;
+};
+
+template <typename TValue>
+struct VirtualStreamSwitch_<TValue, Input, BgzfFile>
+{
+    typedef basic_bgzf_istream<TValue> Type;
+};
+
+template <typename TValue>
+struct VirtualStreamSwitch_<TValue, Output, BgzfFile>
+{
+    typedef basic_bgzf_ostream<TValue> Type;
+};
+
+#endif
+
+#if SEQAN_HAS_BZIP2
+
+template <typename TValue>
+struct VirtualStreamSwitch_<TValue, Input, BZ2File>
+{
+    typedef bzip2_stream::basic_bzip2_istream<TValue> Type;
+};
+
+template <typename TValue>
+struct VirtualStreamSwitch_<TValue, Output, BZ2File>
+{
+    typedef bzip2_stream::basic_bzip2_ostream<TValue> Type;
+};
+#endif
+
+// ==========================================================================
+// Classes
+// ==========================================================================
+
+// --------------------------------------------------------------------------
+// Class VirtualStreamFactoryContext_
+// --------------------------------------------------------------------------
+
+template <typename TVirtualStream>
+struct VirtualStreamFactoryContext_;
+
+// --------------------------------------------------------------------------
+// Class VirtualStreamContext_
+// --------------------------------------------------------------------------
+
+// a compressed stream lives in the VirtualStreamContext_ and provides a basic_streambuf
+
+// base class
+template <typename TValue, typename TTraits>
+struct VirtualStreamContextBase_
+{
+    std::basic_streambuf<TValue, TTraits> *streamBuf;
+    VirtualStreamContextBase_(): streamBuf() {}
+    virtual ~VirtualStreamContextBase_() {}
+};
+
+// generic subclass with virtual destructor
+template <typename TValue, typename TDirection, typename TTraits, typename TFormatTag = void>
+struct VirtualStreamContext_:
+    VirtualStreamContextBase_<TValue, TTraits>
+{
+    typename VirtualStreamSwitch_<TValue, TDirection, TFormatTag>::Type stream;
+
+    template <typename TObject>
+    VirtualStreamContext_(TObject &object):
+        stream(object)
+    {
+        this->streamBuf = stream.rdbuf();
+    }
+};
+
+// special case: no compression, we simply forward the file stream
+template <typename TValue, typename TDirection, typename TTraits>
+struct VirtualStreamContext_<TValue, TDirection, TTraits, Nothing>:
+    VirtualStreamContextBase_<TValue, TTraits>
+{
+    template <typename TObject>
+    VirtualStreamContext_(TObject &object)
+    {
+        this->streamBuf = object.rdbuf();
+    }
+};
+
+// --------------------------------------------------------------------------
+// Class VirtualStream
+// --------------------------------------------------------------------------
+// The VirtualStream class auto-detects data compression from file name or stream.
+// It inherits from std::basic_Xstream to provide the convenient stream interface.
+// It accepts a file or stream.
+
+/*!
+ * @class VirtualStream
+ * @implements StreamConcept
+ * @headerfile <seqan/stream.h>
+ * @brief Provides seamless (de)compression for another @link StreamConcept stream @endlink.
+ *
+ * @signature template <typename TValue, typename TDirection, typename TTraits>
+ *            class VirtualStream;
+ *
+ * @tparam TValue       The stream value type, e.g. <tt>char</tt>.
+ * @tparam TDirection   The stream direction, one of @link DirectionTags @endlink.
+ * @tparam TTraits      The stream traits, defaults to <tt>std::char_traits&lt;TValue&gt;</tt>.
+ */
+
+template <typename TValue, typename TDirection, typename TTraits = std::char_traits<TValue> >
+class VirtualStream: public BasicStream<TValue, TDirection, TTraits>::Type
+{
+public:
+    typedef typename BasicStream<TValue, TDirection, TTraits>::Type TStream;                // the stream base class we expose
+    typedef std::basic_fstream<TValue, TTraits>                     TFile;                  // if a real file should be opened
+//    typedef FileStream<TValue, TDirection>                          TFile;                  // if a real file should be opened
+    typedef BufferedStream<TStream, TDirection>                     TBufferedStream;        // if input stream is not buffered
+    typedef std::basic_streambuf<TValue, TTraits>                   TStreamBuffer;          // the streambuf to use
+    typedef VirtualStreamContextBase_<TValue, TTraits>              TVirtualStreamContext;  // the owner of the streambuf
+    typedef typename StreamFormat<VirtualStream>::Type              TFormat;                // detected stream format
+
+    TFile                   file;
+    TBufferedStream         bufferedStream;
+    TStreamBuffer           *streamBuf;
+    TVirtualStreamContext   *context;
+    TFormat                 format;
+
+    /*!
+     * @fn VirtualStream::VirtualStream
+     * @brief Default constructor and construction from stream, stream buffer, or filename.
+     *
+     * @signature VirtualStream::VirtualStream();
+     * @signature VirtualStream::VirtualStream(stream);
+     * @signature VirtualStream::VirtualStream(streamBuf);
+     * @signature VirtualStream::VirtualStream(fileName, openMode);
+     *
+     * @param[in] stream    The @link StreamConcept stream @endlink to attach to.
+     * @param[in] streamBuf The @link StreamBuffer stream buffer @endlink to attach to.
+     * @param[in] fileName  Path to the file to open. Type: <tt>char const *</tt>.
+     * @param[in] openMode  The open mode. Type: <tt>int</tt>.
+     */
+    VirtualStream():
+        TStream(NULL),
+        streamBuf(),
+        context()
+    {}
+
+    VirtualStream(TStreamBuffer &streamBuf):
+        TStream(NULL),
+        streamBuf(streamBuf),
+        context()
+    {}
+
+    VirtualStream(TStream &stream):
+        TStream(NULL),
+        streamBuf(),
+        context()
+    {
+        open(*this, stream);
+    }
+
+    VirtualStream(const char *fileName,
+                  int openMode = DefaultOpenMode<VirtualStream>::VALUE):
+        TStream(NULL),
+        streamBuf(),
+        context()
+    {
+        open(*this, fileName, openMode);
+    }
+
+    ~VirtualStream()
+    {
+        close(*this);
+    }
+
+
+    operator TStreamBuffer*() const
+    {
+        return streamBuf;
+    }
+
+    operator bool() const
+    {
+        return streamBuf != NULL;
+    }
+
+    void _init()
+    {
+        this->init(streamBuf);
+    }
+
+    TStreamBuffer* rdbuf() const
+    {
+        return streamBuf;
+    }
+
+    /*!
+     * @fn VirtualStream::getFileExtensions
+     * @brief Static function that returns a list of allowed file format extension.
+     *
+     * @signature TExtensionVector getFileExtensions()
+     *
+     * @return TExtensionVector A <tt>std::vector&lt;std::string&gt;</tt> with the allowed file extensions.
+     */
+    static std::vector<std::string>
+    getFileExtensions()
+    {
+        std::vector<std::string> extensions;
+        _getFileExtensions(extensions, TFormat());
+        return extensions;
+    }
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction StreamFormat
+// ----------------------------------------------------------------------------
+
+/*!
+ * @defgroup StreamFormats Stream Formats
+ * @brief Tags for identifying stream formats.
+ */
+
+/*!
+ * @mfn VirtualStream#StreamFormat
+ * @brief Metafunction for retrieving the format type of a @link VirtualStream @endlink.
+ *
+ * @signature StreamFormat<TStream>::Type;
+ *
+ * @tparam TStream  The stream file type to query for its file format type.
+ * @return Type     The resulting @link VirtualStream @endlink file formats type.
+ */
+
+template <typename TValue, typename TDirection, typename TTraits>
+struct StreamFormat<VirtualStream<TValue, TDirection, TTraits> >
+{
+    typedef TagSelector<CompressedFileTypes> Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Value
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TTraits>
+struct Value<VirtualStream<TValue, TDirection, TTraits> >
+{
+    typedef TValue Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction Position
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TTraits>
+struct Position<VirtualStream<TValue, TDirection, TTraits> >:
+    Position<typename VirtualStream<TValue, TDirection, TTraits>::TFile> {};
+
+// ----------------------------------------------------------------------------
+// Metafunction Iterator<Standard>
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TTraits>
+struct Iterator<VirtualStream<TValue, TDirection, TTraits>, TDirection>
+{
+    typedef Iter<VirtualStream<TValue, TDirection, TTraits>, StreamIterator<TDirection> > Type;
+};
+
+// --------------------------------------------------------------------------
+// Metafunction DefaultOpenMode<Input>
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TDummy, typename TTraits>
+struct DefaultOpenMode<VirtualStream<TValue, Input, TTraits>, TDummy>
+{
+    enum { VALUE = OPEN_RDONLY };
+};
+
+// --------------------------------------------------------------------------
+// Metafunction DefaultOpenMode<Output>
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TDummy, typename TTraits>
+struct DefaultOpenMode<VirtualStream<TValue, Output, TTraits>, TDummy>
+{
+    enum { VALUE = OPEN_WRONLY | OPEN_CREATE };
+};
+
+// ----------------------------------------------------------------------------
+// Concepts
+// ----------------------------------------------------------------------------
+
+template <typename TValue>
+SEQAN_CONCEPT_IMPL((VirtualStream<TValue, Input>), (InputStreamConcept));
+
+template <typename TValue>
+SEQAN_CONCEPT_IMPL((VirtualStream<TValue, Output>), (OutputStreamConcept));
+
+template <typename TValue>
+SEQAN_CONCEPT_IMPL((VirtualStream<TValue, Bidirectional>), (BidirectionalStreamConcept));
+
+// --------------------------------------------------------------------------
+// Class VirtualStreamFactoryContext_
+// --------------------------------------------------------------------------
+
+template <typename TValue, typename TDirection, typename TTraits>
+struct VirtualStreamFactoryContext_<VirtualStream<TValue, TDirection, TTraits> >
+{
+    typedef VirtualStream<TValue, TDirection, TTraits>  TVirtualStream;
+    typedef typename TVirtualStream::TStream            TStream;
+
+    TStream &stream;
+    VirtualStreamFactoryContext_(TStream &stream):
+        stream(stream) {}
+};
+
+template <typename TVirtualStream>
+struct Value<VirtualStreamFactoryContext_<TVirtualStream> >
+{
+    typedef typename TVirtualStream::TVirtualStreamContext *Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function tagApply()
+// --------------------------------------------------------------------------
+// NOTE(esiragusa): private / impl.
+
+template <typename TValue, typename TDirection, typename TTraits, typename TFormat>
+inline VirtualStreamContextBase_<TValue, TTraits> *
+tagApply(VirtualStreamFactoryContext_<VirtualStream<TValue, TDirection, TTraits> > &ctx, Tag<TFormat>)
+{
+    return new VirtualStreamContext_<TValue, TDirection, TTraits, Tag<TFormat> >(ctx.stream);
+}
+
+// ----------------------------------------------------------------------------
+// _guessFormat wrapper
+// ----------------------------------------------------------------------------
+
+template <typename TValue, typename TStream, typename TCompressionType>
+inline bool _guessFormat(VirtualStream<TValue, Input> &, TStream &fileStream, TCompressionType &compressionType)
+{
+    // peek the first character to initialize the underlying streambuf
+    fileStream.rdbuf()->sgetc();
+    return guessFormatFromStream(fileStream, compressionType);
+}
+
+template <typename TValue, typename TStream, typename TCompressionType>
+inline bool _guessFormat(VirtualStream<TValue, Output> &, TStream &, TCompressionType &)
+{
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function _getUncompressedBasename()
+// ----------------------------------------------------------------------------
+
+// single format
+template <typename TFilename, typename TFormat>
+inline typename Prefix<TFilename const>::Type
+_getUncompressedBasename(TFilename const & fileName, TFormat const & format)
+{
+    return getBasename(fileName, format);
+}
+
+// make sure not to only cut the ".bgzf" extension and not ".bam"
+template <typename TFilename>
+inline typename Prefix<TFilename const>::Type
+_getUncompressedBasename(TFilename const & fileName, BgzfFile const &)
+{
+    typedef typename Value<TFilename>::Type                                     TValue;
+    typedef ModifiedString<TFilename const, ModView<FunctorLowcase<TValue> > >    TLowcase;
+
+    TLowcase lowcaseFileName(fileName);
+
+    if (endsWith(lowcaseFileName, ".bgzf"))
+        return prefix(fileName, length(fileName) - 5);
+
+    if (endsWith(lowcaseFileName, ".gz"))
+        return prefix(fileName, length(fileName) - 3);
+
+    return prefix(fileName, length(fileName));
+}
+
+// TagSelector
+template <typename TFilename>
+inline typename Prefix<TFilename const>::Type
+_getUncompressedBasename(TFilename const & fname, TagSelector<> const & format)
+{
+    return getBasename(fname, format);
+}
+
+template <typename TFilename, typename TTagList>
+inline typename Prefix<TFilename const>::Type
+_getUncompressedBasename(TFilename const & fname, TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        return _getUncompressedBasename(fname, TFormat());
+    else
+        return _getUncompressedBasename(fname, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+// --------------------------------------------------------------------------
+// Function open()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn VirtualStream#open
+ * @brief Open a VirtualStream.
+ *
+ * @signature bool open(stream, fileStream);
+ * @signature bool open(stream, fileName, openMode);
+ *
+ * @param[in,out] stream        The VirtualStream to open.
+ * @param[in,out  fileStream    File stream to attach to. Type: <tt>std::fstream</tt>.
+ * @param[in]     fileName      Path to the file to open. Type: <tt>char const *</tt>.
+ * @param[in]     openMode      The open mode. Type: <tt>int</tt>.
+ * @return bool <tt>true</tt> in the case of success, <tt>false</tt> otherwise.
+ */
+
+template <typename TValue, typename TDirection, typename TTraits, typename TStream, typename TCompressionType>
+inline SEQAN_FUNC_DISABLE_IF(IsPointer<TStream>, bool)
+open(VirtualStream<TValue, TDirection, TTraits> &stream, TStream &fileStream, TCompressionType & compressionType)
+{
+    SEQAN_ASSERT_MSG(stream.context == NULL, "VirtualStream: close() must be called before re-opening.");
+
+    typedef VirtualStream<TValue, TDirection, TTraits> TVirtualStream;
+    typedef typename TVirtualStream::TBufferedStream TBufferedStream;
+
+    // peek the first character to initialize the underlying streambuf (for in_avail)
+    if (IsSameType<TDirection, Input>::VALUE)  // Only getc if input stream.
+        fileStream.rdbuf()->sgetc();
+
+    if (IsSameType<TDirection, Input>::VALUE &&
+        !IsSameType<TStream, TBufferedStream>::VALUE &&
+        fileStream.rdbuf()->in_avail() < 2)
+    {
+        stream.bufferedStream.setStream(fileStream);
+        return open(stream, stream.bufferedStream, compressionType);
+    }
+
+    VirtualStreamFactoryContext_<TVirtualStream> ctx(fileStream);
+
+    // try to detect/verify format
+    if (!_guessFormat(stream, fileStream, compressionType))
+        return false;
+
+    // create a new (un)zipper buffer
+    stream.context = tagApply(ctx, compressionType);
+    if (stream.context == NULL)
+        return false;
+
+    SEQAN_ASSERT(stream.context->streamBuf != NULL);
+    stream.streamBuf = stream.context->streamBuf;
+
+    // reset our outer stream interface
+    stream._init();
+    return true;
+}
+
+template <typename TValue, typename TDirection, typename TTraits, typename TStream, typename TCompressionType>
+inline SEQAN_FUNC_DISABLE_IF(IsPointer<TStream>, bool)
+open(VirtualStream<TValue, TDirection, TTraits> &stream, TStream &fileStream, TCompressionType const & compressionType)
+{
+    assign(stream.format, compressionType);
+    return open(stream, fileStream, stream.format);
+}
+
+template <typename TValue, typename TStream>
+inline SEQAN_FUNC_DISABLE_IF(IsPointer<TStream>, bool)
+open(VirtualStream<TValue, Input> &stream, TStream &fileStream)
+{
+    // detect compression type from file extension
+    assign(stream.format, typename StreamFormat<VirtualStream<TValue, Input> >::Type());
+    return open(stream, fileStream, stream.format);
+}
+
+template <typename TValue, typename TDirection, typename TTraits>
+inline bool
+open(VirtualStream<TValue, TDirection, TTraits> &stream,
+     const char *fileName,
+     int openMode = DefaultOpenMode<VirtualStream<TValue, TDirection, TTraits> >::VALUE)
+{
+    SEQAN_ASSERT_MSG(stream.context == NULL, "VirtualStream: close() must be called before re-opening.");
+
+    typedef VirtualStream<TValue, TDirection, TTraits> TVirtualStream;
+
+    if (!open(stream.file, fileName, openMode))
+        return false;
+
+    // detect compression type from file extension
+    assign(stream.format, typename StreamFormat<TVirtualStream>::Type());
+
+    if (IsSameType<TDirection, Input>::VALUE && _isPipe(fileName))
+        open(stream, stream.file, stream.format);               // read from a pipe (without file extension)
+    else
+        guessFormatFromFilename(fileName, stream.format);       // read/write from/to a file (with extension)
+
+    VirtualStreamFactoryContext_<TVirtualStream> ctx(stream.file);
+
+    // create a new (un)zipper buffer
+    stream.context = tagApply(ctx, stream.format);
+    if (stream.context == NULL)
+    {
+        close(stream.file);
+        return false;
+    }
+    stream.streamBuf = stream.context->streamBuf;
+
+    // reset our outer stream interface
+    stream._init();
+    return true;
+}
+
+// --------------------------------------------------------------------------
+// Function close()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn VirtualStream#close
+ * @brief Close a VirtualStream.
+ *
+ * @signature bool close(stream);
+ *
+ * @param[in,out] stream The VirtualStream to close.
+ * @return bool <tt>true</tt> in the case of success, <tt>false</tt> otherwise.
+ */
+
+template <typename TValue, typename TDirection, typename TTraits>
+inline bool
+close(VirtualStream<TValue, TDirection, TTraits> &stream)
+{
+    delete stream.context;
+    stream.context = NULL;
+    stream.streamBuf = NULL;
+    assign(stream.format, typename StreamFormat<VirtualStream<TValue, TDirection, TTraits> >::Type());
+    return !stream.file.is_open() || close(stream.file);
+}
+
+// ----------------------------------------------------------------------------
+// Function format()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn VirtualStream#format
+ * @brief Return the format of a VirtualStream.
+ *
+ * @signature TFormat format(stream);
+ *
+ * @param[in] stream The VirtualStream to check.
+ * @return TFormat   The type as returned from @link VirtualStream#StreamFormat @endlink.
+ */
+
+template <typename TValue, typename TDirection, typename TTraits>
+inline typename StreamFormat<VirtualStream<TValue, TDirection, TTraits> >::Type &
+format(VirtualStream<TValue, TDirection, TTraits> &stream)
+{
+    return stream.format;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_STREAM_VIRTUAL_STREAM_
diff --git a/seqan/system.h b/seqan/system.h
index 53efc77..e8ef46f 100644
--- a/seqan/system.h
+++ b/seqan/system.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -77,8 +77,9 @@
 
 #include <seqan/system/system_base.h>
 #include <seqan/system/system_mutex.h>
-#include <seqan/system/system_sema.h>
 #include <seqan/system/system_event.h>
+#include <seqan/system/system_critical_section.h>
+#include <seqan/system/system_condition.h>
 #include <seqan/system/system_thread.h>
 
 //____________________________________________________________________________
diff --git a/seqan/system/INFO b/seqan/system/INFO
deleted file mode 100644
index 0642994..0000000
--- a/seqan/system/INFO
+++ /dev/null
@@ -1,9 +0,0 @@
-Name: seqan-system
-Author: David Weese <david.weese@fu-berlin.de>
-Maintainer: David Weese <david.weese@fu-berlin.de>
-License: BSD 3-clause
-Copyright: 2006-2013, FU Berlin
-Status: mature
-Description: Wrapper of operating system functionality.
- This module contains wrappers around threads and files for synchronous and
- asynchronous I/O.
diff --git a/seqan/system/file_async.h b/seqan/system/file_async.h
index bd8ccaf..28f3273 100644
--- a/seqan/system/file_async.h
+++ b/seqan/system/file_async.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -59,15 +59,15 @@
 namespace SEQAN_NAMESPACE_MAIN
 {
 
- 
-	template <typename TSpec /* = void */>
-	struct Async;
+
+    template <typename TSpec /* = void */>
+    struct Async {};
 
 
 #ifdef PLATFORM_WINDOWS
 
-	template <typename TSpec>
-	class File<Async<TSpec> >
+    template <typename TSpec>
+    class File<Async<TSpec> >
     {
 //IOREV _windows_
     public:
@@ -77,7 +77,7 @@ namespace SEQAN_NAMESPACE_MAIN
         typedef DWORD       SizeType_;
         typedef HANDLE      Handle;
 
-		Handle              handle, handleAsync;
+        Handle              handle, handleAsync;
         bool                noBuffering;
 
         File():
@@ -87,7 +87,7 @@ namespace SEQAN_NAMESPACE_MAIN
             handle(INVALID_HANDLE_VALUE) {}
 
         bool open(char const *fileName, int openMode = DefaultOpenMode<File>::VALUE) {
-			SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
+            SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
             noBuffering = (getExtraFlags(openMode | OPEN_ASYNC) & (FILE_FLAG_NO_BUFFERING | FILE_FLAG_OVERLAPPED)) != 0;
             handleAsync = CreateFileA(fileName,
                                 getFileAccess(openMode | OPEN_ASYNC),
@@ -98,13 +98,13 @@ namespace SEQAN_NAMESPACE_MAIN
                                 NULL);
 
             if (handleAsync == INVALID_HANDLE_VALUE) {
-				if (!(openMode & OPEN_QUIET))
-					std::cerr << "Open failed on file " << fileName << ". (ErrNo=" << GetLastError() << ")" << std::endl;
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "Open failed on file " << fileName << ". (ErrNo=" << GetLastError() << ")" << std::endl;
                 return false;
             }
             #ifdef SEQAN_VERBOSE
-				if (!(openMode & OPEN_QUIET))
-	                std::cerr << "file opened asynchronously " << fileName << " handle " << std::hex << handleAsync << std::dec << std::endl;
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "file opened asynchronously " << fileName << " handle " << std::hex << handleAsync << std::dec << std::endl;
             #endif
 
             if (noBuffering) {
@@ -116,13 +116,13 @@ namespace SEQAN_NAMESPACE_MAIN
                                 getExtraFlags(openMode & ~OPEN_ASYNC),
                                 NULL);
                 if (handle == INVALID_HANDLE_VALUE) {
-					if (!(openMode & OPEN_QUIET))
-	                	std::cerr << "Open failed on secondary file " << fileName << ". (ErrNo=" << GetLastError() << ")" << std::endl;
+                    if (!(openMode & OPEN_QUIET))
+                        std::cerr << "Open failed on secondary file " << fileName << ". (ErrNo=" << GetLastError() << ")" << std::endl;
                     return false;
                 }
-	            #ifdef SEQAN_VERBOSE
-					if (!(openMode & OPEN_QUIET))
-	                	std::cerr << "async file opened  " << fileName << " handle " << std::hex << handle << std::dec << std::endl;
+                #ifdef SEQAN_VERBOSE
+                    if (!(openMode & OPEN_QUIET))
+                        std::cerr << "async file opened  " << fileName << " handle " << std::hex << handle << std::dec << std::endl;
                 #endif
             } else
                 handle = handleAsync;
@@ -137,14 +137,14 @@ namespace SEQAN_NAMESPACE_MAIN
 #else
             char szTempPath[MAX_PATH];
             if (!GetTempPathA(MAX_PATH, szTempPath)) {
-				if (!(openMode & OPEN_QUIET))
-					std::cerr << "Couldn't get a temporary path name. (ErrNo=" << GetLastError() << ")" << std::endl;
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "Couldn't get a temporary path name. (ErrNo=" << GetLastError() << ")" << std::endl;
                 return false;
             }
 #endif
             if (!GetTempFileNameA(szTempPath, "GNDX", 0, szTempName)) {
-				if (!(openMode & OPEN_QUIET))
-					std::cerr << "Couldn't get a temporary file name. (ErrNo=" << GetLastError() << ")" << std::endl;
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "Couldn't get a temporary file name. (ErrNo=" << GetLastError() << ")" << std::endl;
                 return false;
             }
             return open(szTempName, openMode | OPEN_TEMPORARY);
@@ -160,15 +160,15 @@ namespace SEQAN_NAMESPACE_MAIN
             result &= CloseHandle(handle);
             handleAsync = INVALID_HANDLE_VALUE;
             handle = INVALID_HANDLE_VALUE;
-			SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
+            SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
             return result != FALSE;
         }
 
         inline DWORD read(void *memPtr, SizeType_ count) const {
             SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
             SEQAN_PROTIMESTART(tw);
-			DWORD _transferedBytes;
-		    ReadFile(handle, memPtr, count, &_transferedBytes, NULL);
+            DWORD _transferedBytes;
+            ReadFile(handle, memPtr, count, &_transferedBytes, NULL);
             SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
             return _transferedBytes;
         }
@@ -176,33 +176,33 @@ namespace SEQAN_NAMESPACE_MAIN
         inline DWORD write(void const *memPtr, SizeType_ count) const {
             SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
             SEQAN_PROTIMESTART(tw);
-			DWORD _transferedBytes;
-		    WriteFile(handle, memPtr, count, &_transferedBytes, NULL);
+            DWORD _transferedBytes;
+            WriteFile(handle, memPtr, count, &_transferedBytes, NULL);
             SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
             return _transferedBytes;
         }
 
-		inline FilePtr seek(FilePtr _pos, DWORD origin = FILE_BEGIN) {
+        inline FilePtr seek(FilePtr _pos, DWORD origin = FILE_BEGIN) {
 //          LARGE_INTEGER li = _pos;
-//			return SetFilePointer(handleAsync, li.LowPart, &li.HighPart, MoveMethod);
+//            return SetFilePointer(handleAsync, li.LowPart, &li.HighPart, MoveMethod);
             LARGE_INTEGER new_pos, pos;
             pos.QuadPart = _pos;
             SetFilePointerEx(handle, pos, &new_pos, origin);
 //            position = new_pos.QuadPart;
             return new_pos.QuadPart;
-		}
+        }
 
-		inline FilePtr tell() {
-			return seek(0, FILE_CURRENT);
+        inline FilePtr tell() {
+            return seek(0, FILE_CURRENT);
         }
 
-		inline FilePtr size() const {
+        inline FilePtr size() const {
             LARGE_INTEGER result;
             DWORD dwError, high;
             result.LowPart = GetFileSize(handle, &high);
             result.HighPart = high;
             if (result.LowPart == INVALID_FILE_SIZE && (dwError = GetLastError()) != NO_ERROR) {
-				std::cerr << "Couldn't get file size. (ErrNo=" << dwError << ")" << std::endl;
+                std::cerr << "Couldn't get file size. (ErrNo=" << dwError << ")" << std::endl;
                 return 0;
             }
             return result.QuadPart;
@@ -212,9 +212,9 @@ namespace SEQAN_NAMESPACE_MAIN
             return SetEndOfFile(handle) != FALSE;
         }
 
-		inline static DWORD error() {
-			return GetLastError();
-		}
+        inline static DWORD error() {
+            return GetLastError();
+        }
 
         operator bool () const {
             return (handle != INVALID_HANDLE_VALUE) && (handleAsync != INVALID_HANDLE_VALUE);
@@ -230,8 +230,8 @@ namespace SEQAN_NAMESPACE_MAIN
                     return GENERIC_WRITE;
                 case OPEN_RDWR:
                     return GENERIC_READ | GENERIC_WRITE;
-				default:
-					return 0;
+                default:
+                    return 0;
             }
         }
 
@@ -264,54 +264,77 @@ namespace SEQAN_NAMESPACE_MAIN
     // (SeqAn adaption)
     //////////////////////////////////////////////////////////////////////////////
 
-    struct aiocb_win32 {
+    struct aiocb_win32
+    {
         OVERLAPPED  overlapped;
         Event       xmitDone;
+
+        aiocb_win32()
+        {}
+
+        aiocb_win32(aiocb_win32 & other, Move) :
+            overlapped(other.overlapped),
+            xmitDone(other.xmitDone, Move())
+        {}
+
+#ifdef SEQAN_CXX11_STANDARD
+        aiocb_win32(aiocb_win32 && other) :
+            overlapped(other.overlapped),
+            xmitDone(other.xmitDone, Move())
+        {}
+#endif
+
+    private:
+        aiocb_win32(aiocb_win32 const &)
+        {}
     };
 
-	template <typename TSpec>
+    template <>
+    struct HasMoveConstructor<aiocb_win32> : True {};
+
+    template <typename TSpec>
     struct AsyncRequest<File<Async<TSpec> > >
     {
         typedef aiocb_win32 Type;
     };
 /*
-	template <typename TSpec>
+    template <typename TSpec>
     struct aEvent<File<Async<TSpec> > >
     {
         typedef Event Type;
     };
 
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct aQueue<File<Async<TSpec> > >
     {
         typedef IOQueue Type;
     };
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct aHint<File<Async<TSpec> > >
     {
         typedef typename aQueue<File<Async<TSpec> > >::Type::aHint Type;
     };
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct aCallback<File<Async<TSpec> > >
     {
         typedef typename aQueue<File<Async<TSpec> > >::Type::aCallback Type;
     };*/
 
 
-	template <typename TSpec>
-    inline typename Size<File<Async<TSpec> > >::Type size(File<Async<TSpec> > &me) {
+    template <typename TSpec>
+    inline typename Size<File<Async<TSpec> > >::Type length(File<Async<TSpec> > &me) {
         return me.size();
     }
 
-	template <typename TSpec>
+    template <typename TSpec>
     inline bool setEof(File<Async<TSpec> > &me) {
         return me.setEof();
     }
 
-	template <typename TSpec>
+    template <typename TSpec>
     inline unsigned sectorSize(File<Async<TSpec> > const &) {
         DWORD SpC, nofC, tnoC, aligning;
         if (GetDiskFreeSpace(NULL, &SpC, &aligning, &nofC, &tnoC) == 0)  {
@@ -335,8 +358,8 @@ namespace SEQAN_NAMESPACE_MAIN
         if (!request.xmitDone) open(request.xmitDone);
         request.overlapped.hEvent = request.xmitDone.hEvent;
         if (ReadFile(
-            me.handleAsync, 
-            memPtr, 
+            me.handleAsync,
+            memPtr,
             count * sizeof(TValue),
             &ofs.LowPart,
             &request.overlapped) || (me.error() == ERROR_IO_PENDING))
@@ -347,14 +370,14 @@ namespace SEQAN_NAMESPACE_MAIN
         }
         if (me.error() == ERROR_NO_SYSTEM_RESOURCES) {  // read synchronoulsy instead
             #if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
-            	std::cerr << "Warning: Falling back to sync. read. :( " << std::endl;
+                std::cerr << "Warning: Falling back to sync. read. :( " << std::endl;
             #endif
-			signal(request.xmitDone);
+            signal(request.xmitDone);
             return readAt(me, memPtr, count, fileOfs);
         }
         return false;
     }
-    
+
     template < typename TSpec, typename TValue, typename TSize, typename TPos >
     inline bool asyncWriteAt(File<Async<TSpec> > & me, TValue const *memPtr, TSize const count, TPos const fileOfs,
         aiocb_win32 &request)
@@ -368,8 +391,8 @@ namespace SEQAN_NAMESPACE_MAIN
         if (!request.xmitDone) open(request.xmitDone);
         request.overlapped.hEvent = request.xmitDone.hEvent;
         if (WriteFile(
-            me.handleAsync, 
-            memPtr, 
+            me.handleAsync,
+            memPtr,
             count * sizeof(TValue),
             &ofs.LowPart,
             &request.overlapped) || (me.error() == ERROR_IO_PENDING))
@@ -380,9 +403,9 @@ namespace SEQAN_NAMESPACE_MAIN
         }
         if (me.error() == ERROR_NO_SYSTEM_RESOURCES) {  // write synchronoulsy instead
             #if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
-            	std::cerr << "Warning: Falling back to sync. write. :( " << std::endl;
+                std::cerr << "Warning: Falling back to sync. write. :( " << std::endl;
             #endif
-			signal(request.xmitDone);
+            signal(request.xmitDone);
             return writeAt(me, memPtr, count, fileOfs);
         }
         return false;
@@ -392,28 +415,28 @@ namespace SEQAN_NAMESPACE_MAIN
     // queue specific functions
 
     inline bool waitFor(aiocb_win32 &request) {
-//IOREV _doc_ 
+//IOREV _doc_
         SEQAN_PROTIMESTART(tw);
-		bool inProgress;
-		bool waitResult = waitFor(request.xmitDone, 60000, inProgress);
-		if (inProgress)
+        bool inProgress;
+        bool waitResult = waitFor(request.xmitDone, 60000, inProgress);
+        if (inProgress)
             std::cerr << "waitFor timeout" << std::endl;
         SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
         return waitResult;
-	}
+    }
 
     template < typename TTime >
     inline bool waitFor(aiocb_win32 &request, TTime timeoutMilliSec, bool &inProgress) {
-//IOREV _doc_ 
+//IOREV _doc_
         SEQAN_PROTIMESTART(tw);
-		bool waitResult = waitFor(request.xmitDone, timeoutMilliSec, inProgress);
+        bool waitResult = waitFor(request.xmitDone, timeoutMilliSec, inProgress);
         SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
         return waitResult;
-	}
+    }
 
-	template < typename TSize >
-	inline int waitForAny(aiocb_win32 const * const contexts[], TSize count, DWORD timeoutMilliSec = Event::Infinite) {
-//IOREV _nodoc_ 
+    template < typename TSize >
+    inline int waitForAny(aiocb_win32 const * const contexts[], TSize count, DWORD timeoutMilliSec = Event::Infinite) {
+//IOREV _nodoc_
         Event::Handle *handles = new Event::Handle[count];
         for(TSize i = 0; i < count; ++i)
             handles[i] = contexts[i]->xmitDone.hEvent;
@@ -421,34 +444,34 @@ namespace SEQAN_NAMESPACE_MAIN
         SEQAN_PROTIMESTART(tw);
         DWORD result = WaitForMultipleObjects(count, handles, false, timeoutMilliSec);
         SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
-		delete[] handles;
+        delete[] handles;
         if (/*result >= WAIT_OBJECT_0 && */result < WAIT_OBJECT_0 + count)
-    		return result - WAIT_OBJECT_0;
+            return result - WAIT_OBJECT_0;
         return -1;
-	}
+    }
 
-	template <typename TSpec>
+    template <typename TSpec>
     inline bool cancel(File<Async<TSpec> > & me, aiocb_win32 const &request) {
-//IOREV _doc_ 
+//IOREV _doc_
         return CancelIo(me.handleAsync);
     }
 
-	template <typename TSpec>
+    template <typename TSpec>
     inline bool flush(File<Async<TSpec> > & me) {
-//IOREV _doc_ 
-		if (me.handle != me.handleAsync)	// in case of equality no direct access was done -> no flush needed
-        	return FlushFileBuffers(me.handle) != 0;
+//IOREV _doc_
+        if (me.handle != me.handleAsync)    // in case of equality no direct access was done -> no flush needed
+            return FlushFileBuffers(me.handle) != 0;
         else
             return true;
     }
 
     template < typename TSpec, typename AsyncRequest >
     inline void release(File<Async<TSpec> > & me, AsyncRequest & request) {
-//IOREV _nodoc_ 
+//IOREV _nodoc_
     }
 
 
-/*        
+/*
     //////////////////////////////////////////////////////////////////////
     // callback based read/write
 
@@ -459,7 +482,7 @@ namespace SEQAN_NAMESPACE_MAIN
         aCallback* cb, aHint* hint)
     {
         DWORD bsize = (DWORD)(count * sizeof(TValue));
-        typename AsyncRequest<File<Async<TSpec> > >::Type request = 
+        typename AsyncRequest<File<Async<TSpec> > >::Type request =
             me.queue->asyncReadAt(
                 me.handleAsync,
                 me.position,
@@ -470,7 +493,7 @@ namespace SEQAN_NAMESPACE_MAIN
         me.position += bsize;
         return request;
     }
-    
+
     template < typename TSpec, typename TValue, typename TSize,
                typename aCallback, typename aHint >
     inline typename AsyncRequest<File<Async<TSpec> > >::Type
@@ -478,7 +501,7 @@ namespace SEQAN_NAMESPACE_MAIN
         aCallback* cb, aHint* hint)
     {
         DWORD bsize = (DWORD)(count * sizeof(TValue));
-        typename AsyncRequest<File<Async<TSpec> > >::Type request = 
+        typename AsyncRequest<File<Async<TSpec> > >::Type request =
             me.queue->asyncWriteAt(
                 memPtr,
                 me.handleAsync,
@@ -505,7 +528,7 @@ namespace SEQAN_NAMESPACE_MAIN
             cb,
             hint);
     }
-    
+
     template < typename TSpec, typename TValue, typename TSize, typename TPos,
                typename aCallback, typename aHint >
     inline typename AsyncRequest<File<Async<TSpec> > >::Type
@@ -533,7 +556,7 @@ namespace SEQAN_NAMESPACE_MAIN
         aEvent &event)
     {
         DWORD bsize = (DWORD)(count * sizeof(TValue));
-        typename AsyncRequest<File<Async<TSpec> > >::Type request = 
+        typename AsyncRequest<File<Async<TSpec> > >::Type request =
             me.queue->asyncReadAt(
                 me.handleAsync,
                 me.position,
@@ -543,7 +566,7 @@ namespace SEQAN_NAMESPACE_MAIN
         me.position += bsize;
         return request;
     }
-    
+
     template < typename TSpec, typename TValue, typename TSize,
                typename aEvent >
     inline typename AsyncRequest<File<Async<TSpec> > >::Type
@@ -551,7 +574,7 @@ namespace SEQAN_NAMESPACE_MAIN
         aEvent &event)
     {
         DWORD bsize = (DWORD)(count * sizeof(TValue));
-        typename AsyncRequest<File<Async<TSpec> > >::Type request =  
+        typename AsyncRequest<File<Async<TSpec> > >::Type request =
             me.queue->asyncWriteAt(
                 memPtr,
                 me.handleAsync,
@@ -576,7 +599,7 @@ namespace SEQAN_NAMESPACE_MAIN
             bsize,
             event);
     }
-    
+
     template < typename TSpec, TValue, typename TSize, typename TPos,
                typename aEvent >
     inline typename AsyncRequest<File<Async<TSpec> > >::Type
@@ -596,7 +619,7 @@ namespace SEQAN_NAMESPACE_MAIN
     //////////////////////////////////////////////////////////////////////
     // queue specific functions
 
-	template <typename TSpec>
+    template <typename TSpec>
     inline void flush(File<Async<TSpec> > & me) {
         me.queue->flush();
     }
@@ -607,49 +630,49 @@ namespace SEQAN_NAMESPACE_MAIN
     }
 */
 
-	//////////////////////////////////////////////////////////////////////////////
-	// page aligned allocate for direct file io
+    //////////////////////////////////////////////////////////////////////////////
+    // page aligned allocate for direct file io
 
-    struct TagAllocateAligned_;	//< allocate page aligned memory for direct i/o access
+    struct TagAllocateAligned_;    //< allocate page aligned memory for direct i/o access
     typedef Tag<TagAllocateAligned_> const TagAllocateAligned;
 
-	template <typename T, typename TValue, typename TSize>
-	inline void
-	allocate(T const &, 
-			 TValue * & data,
-			 TSize count,
-			 TagAllocateAligned const)
-	{
-//IOREV _doc_ 
-		data = (TValue *) VirtualAlloc(NULL, count * sizeof(TValue), MEM_COMMIT, PAGE_READWRITE);
+    template <typename T, typename TValue, typename TSize>
+    inline void
+    allocate(T const &,
+             TValue * & data,
+             TSize count,
+             TagAllocateAligned const)
+    {
+//IOREV _doc_
+        data = (TValue *) VirtualAlloc(NULL, count * sizeof(TValue), MEM_COMMIT, PAGE_READWRITE);
         if (data)
             SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue));
         else
-			std::cerr << "AlignAllocator: Could not allocate memory of size " << std::hex << count * sizeof(TValue) << std::dec << ". (ErrNo=" << GetLastError() << ")" << std::endl;
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// page aligned deallocate for direct file io
-
-	template <typename T, typename TValue, typename TSize>
-	inline void 
-	deallocate( T const &,
-				TValue * data, 
-				TSize count,
-				TagAllocateAligned const)
-	{
-//IOREV _doc_ 
-		if (data) {
-			VirtualFree(data, 0, MEM_RELEASE);
-			if (count)	// .. to use count if SEQAN_PROFILE is not defined
-				SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue));
-		}
-	}
+            std::cerr << "AlignAllocator: Could not allocate memory of size " << std::hex << count * sizeof(TValue) << std::dec << ". (ErrNo=" << GetLastError() << ")" << std::endl;
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // page aligned deallocate for direct file io
+
+    template <typename T, typename TValue, typename TSize>
+    inline void
+    deallocate( T const &,
+                TValue * data,
+                TSize count,
+                TagAllocateAligned const)
+    {
+//IOREV _doc_
+        if (data) {
+            VirtualFree(data, 0, MEM_RELEASE);
+            if (count)    // .. to use count if SEQAN_PROFILE is not defined
+                SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue));
+        }
+    }
 
 #else
 
-    
-	template <typename TSpec>
+
+    template <typename TSpec>
     class File<Async<TSpec> > : public File<Sync<TSpec> >
     {
 //IOREV _nodoc_ members are not well documented
@@ -657,67 +680,67 @@ namespace SEQAN_NAMESPACE_MAIN
 
         typedef File<Sync<TSpec> >  Base;
 
-        typedef off_t			FilePtr;
-		typedef off_t           SizeType;   // type of file size
+        typedef off_t            FilePtr;
+        typedef off_t           SizeType;   // type of file size
         typedef size_t          SizeType_;  // type of transfer size (for read or write)
-		typedef int				Handle;
+        typedef int                Handle;
 
         Handle handleAsync;
-		using Base::handle;
+        using Base::handle;
 
-		File(void * = NULL): 	// to be compatible with the FILE*(NULL) constructor
-			handleAsync(-1) {}
+        File(void * = NULL):     // to be compatible with the FILE*(NULL) constructor
+            handleAsync(-1) {}
 
         virtual ~File() {}
-        
+
         bool open(char const *fileName, int openMode = DefaultOpenMode<File>::VALUE) {
             handle = ::open(fileName, Base::_getOFlag(openMode & ~OPEN_ASYNC), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
-			if (handle == -1) 
-			{
-				handleAsync = handle;
-				if (!(openMode & OPEN_QUIET))
-					std::cerr << "Open failed on file " << fileName << ": \"" << ::strerror(errno) << '"' << std::endl;
-				return false;
-			}
-
-			if (Base::_getOFlag(openMode | OPEN_ASYNC) & O_DIRECT) 
-			{
-				handleAsync = ::open(fileName, Base::_getOFlag(openMode | (OPEN_ASYNC & ~OPEN_CREATE)), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
-				if (handleAsync == -1 || errno == EINVAL) {	// fall back to cached access
-					#if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
-						if (!(openMode & OPEN_QUIET))
-							std::cerr << "Warning: Direct access openening failed. \"" << ::strerror(errno) << '"' << std::endl;
-					#endif
-					handleAsync = handle;
-				}
-				#if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
-				    else
-						if (!(openMode & OPEN_QUIET))
-							std::cerr << "Direct access successfully initiated" << std::endl;
-				#endif
-			} else
-				handleAsync = handle;
-
-			if (sizeof(FilePtr) < 8 && !(openMode & OPEN_QUIET))
-				// To remove this warning, you have to options:
-				// 1. include the following line before including anything in your application
-				//    #define _FILE_OFFSET_BITS 64
-				// 2. include <seqan/platform.h> or <seqan/sequence.h> before any other include
-				std::cerr << "WARNING: FilePtr is not 64bit wide" << std::endl;
-
-
-			SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
+            if (handle == -1)
+            {
+                handleAsync = handle;
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "Open failed on file " << fileName << ": \"" << ::strerror(errno) << '"' << std::endl;
+                return false;
+            }
+
+            if (Base::_getOFlag(openMode | OPEN_ASYNC) & O_DIRECT)
+            {
+                handleAsync = ::open(fileName, Base::_getOFlag(openMode | (OPEN_ASYNC & ~OPEN_CREATE)), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
+                if (handleAsync == -1 || errno == EINVAL) {    // fall back to cached access
+                    #if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
+                        if (!(openMode & OPEN_QUIET))
+                            std::cerr << "Warning: Direct access openening failed. \"" << ::strerror(errno) << '"' << std::endl;
+                    #endif
+                    handleAsync = handle;
+                }
+                #if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
+                    else
+                        if (!(openMode & OPEN_QUIET))
+                            std::cerr << "Direct access successfully initiated" << std::endl;
+                #endif
+            } else
+                handleAsync = handle;
+
+            if (sizeof(FilePtr) < 8 && !(openMode & OPEN_QUIET))
+                // To remove this warning, you have to options:
+                // 1. include the following line before including anything in your application
+                //    #define _FILE_OFFSET_BITS 64
+                // 2. include <seqan/platform.h> or <seqan/sequence.h> before any other include
+                std::cerr << "WARNING: FilePtr is not 64bit wide" << std::endl;
+
+
+            SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
             return true;
         }
 
-		bool close() {
-			bool result = true;
-			if (handleAsync != handle && handleAsync != -1)
-	            result &= (::close(handleAsync) == 0);
+        bool close() {
+            bool result = true;
+            if (handleAsync != handle && handleAsync != -1)
+                result &= (::close(handleAsync) == 0);
             result &= (::close(handle) == 0);
             handleAsync = -1;
             handle = -1;
-			SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
+            SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
             return result;
         }
     };
@@ -727,21 +750,45 @@ namespace SEQAN_NAMESPACE_MAIN
     // (SeqAn adaption)
     //////////////////////////////////////////////////////////////////////////////
 /*
-	template <typename TSpec>
+    template <typename TSpec>
     struct aQueue<File<Async<TSpec> > >
     {
         typedef void* Type;
     };
 */
 
-	template <typename TSpec>
+    struct AiocbWrapper : public aiocb
+    {
+        AiocbWrapper()
+        {}
+
+        AiocbWrapper(AiocbWrapper & other, Move) :
+            aiocb(other)
+        {}
+
+#ifdef SEQAN_CXX11_STANDARD
+        AiocbWrapper(AiocbWrapper && other) :
+            aiocb(other)
+        {}
+#endif
+
+    private:
+        AiocbWrapper(AiocbWrapper const &)
+        {}
+    };
+
+    template <>
+    struct HasMoveConstructor<AiocbWrapper> : True {};
+
+
+    template <typename TSpec>
     struct AsyncRequest<File<Async<TSpec> > >
     {
-//IOREV _doc_ 
-		typedef aiocb Type;
+//IOREV _doc_
+        typedef AiocbWrapper Type;
     };
 /*
-	template <typename TSpec>
+    template <typename TSpec>
     struct aEvent<File<Async<TSpec> > >
     {
         typedef aiocb Type;
@@ -753,29 +800,29 @@ namespace SEQAN_NAMESPACE_MAIN
 
 //    enum { AsyncIOSignal_ = SIGIO };
 
-	inline void printRequest(aiocb &request, const char *_hint)
+    inline void printRequest(AiocbWrapper &request, const char *_hint)
     {
 //IOREV _nodoc_ _notinlined_
-		std::cerr << std::hex;
-		if (_hint)
-			std::cerr << _hint << std::endl;
-		std::cerr << "fildes:  " << request.aio_fildes << std::endl;
-		std::cerr << "buffer:  " << (unsigned long)request.aio_buf << std::endl;
-		std::cerr << "offset:  " << request.aio_offset<< std::endl;
-		std::cerr << "nbytes:  " << request.aio_nbytes << std::endl;
-		std::cerr << "event:   " << request.aio_sigevent.sigev_notify << std::endl;
-		std::cerr << "Raddr:   " << &request << std::endl;
-		std::cerr << std::dec;
-	}
-
-    inline void printRequest(aiocb &request)
+        std::cerr << std::hex;
+        if (_hint)
+            std::cerr << _hint << std::endl;
+        std::cerr << "fildes:  " << request.aio_fildes << std::endl;
+        std::cerr << "buffer:  " << (unsigned long)request.aio_buf << std::endl;
+        std::cerr << "offset:  " << request.aio_offset<< std::endl;
+        std::cerr << "nbytes:  " << request.aio_nbytes << std::endl;
+        std::cerr << "event:   " << request.aio_sigevent.sigev_notify << std::endl;
+        std::cerr << "Raddr:   " << &request << std::endl;
+        std::cerr << std::dec;
+    }
+
+    inline void printRequest(AiocbWrapper &request)
     {
         printRequest(request, NULL);
     }
 
     template < typename TSpec, typename TValue, typename TSize, typename TPos >
     bool asyncReadAt(File<Async<TSpec> > & me, TValue *memPtr, TSize const count, TPos const fileOfs,
-        aiocb &request)
+        AiocbWrapper &request)
     {
 //IOREV _doc_ _notinlined_
         SEQAN_PROTIMESTART(tw);
@@ -789,38 +836,38 @@ namespace SEQAN_NAMESPACE_MAIN
 /*      request.aio_sigevent.sigev_notify = SIGEV_SIGNAL;
         request.aio_sigevent.sigev_signo = AsyncIOSignal_;
         request.aio_sigevent.sigev_value.sival_ptr = &request;
-		#ifdef SEQAN_VVERBOSE
-			printRequest(request, "aio_read():");
-		#endif
+        #ifdef SEQAN_VVERBOSE
+            printRequest(request, "aio_read():");
+        #endif
 */      if (request.aio_nbytes == 0) return true;
-		SEQAN_PROADD(SEQAN_PROIO, (request.aio_nbytes + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
-		int result = aio_read(&request);
+        SEQAN_PROADD(SEQAN_PROIO, (request.aio_nbytes + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
+        int result = aio_read(&request);
         SEQAN_PROADD(SEQAN_PROIWAIT, SEQAN_PROTIMEDIFF(tw));
         if (result != 0)
-		{
-			request.aio_nbytes = 0;
-			if (errno == EAGAIN) {  // read synchronoulsy instead
+        {
+            request.aio_nbytes = 0;
+            if (errno == EAGAIN) {  // read synchronoulsy instead
 #if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
-            	std::cerr << "Warning: Falling back to sync. read. :( " << std::endl;
+                std::cerr << "Warning: Falling back to sync. read. :( " << std::endl;
 #endif
-				bool success = readAt(me, memPtr, count, fileOfs);
+                bool success = readAt(me, memPtr, count, fileOfs);
                 if (!success)
                     SEQAN_FAIL(
                         "readAt(%d, %d, %d, %d) failed: \"%s\"",
                         me.handle, (size_t)memPtr, count, fileOfs, strerror(errno));
                 return success;
-			}
+            }
 #if SEQAN_ENABLE_DEBUG
-			else
-				std::cerr << "aio_read failed (asyncReadAt). \"" << ::strerror(errno) << '"' << std::endl;
+            else
+                std::cerr << "aio_read failed (asyncReadAt). \"" << ::strerror(errno) << '"' << std::endl;
 #endif
         }
-		return result == 0;
+        return result == 0;
     }
-    
+
     template < typename TSpec, typename TValue, typename TSize, typename TPos >
     bool asyncWriteAt(File<Async<TSpec> > & me, const TValue *memPtr, TSize const count, TPos const fileOfs,
-        aiocb &request)
+        AiocbWrapper &request)
     {
 //IOREV _doc_ _notinlined_
         SEQAN_PROTIMESTART(tw);
@@ -834,63 +881,63 @@ namespace SEQAN_NAMESPACE_MAIN
 /*      request.aio_sigevent.sigev_notify = SIGEV_SIGNAL;
         request.aio_sigevent.sigev_signo = AsyncIOSignal_;
         request.aio_sigevent.sigev_value.sival_ptr = &request;
-		#ifdef SEQAN_VVERBOSE
-			printRequest(request, "aio_write():");
-		#endif
+        #ifdef SEQAN_VVERBOSE
+            printRequest(request, "aio_write():");
+        #endif
 */      if (request.aio_nbytes == 0) return true;
-		SEQAN_PROADD(SEQAN_PROIO, (request.aio_nbytes + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
-		int result = aio_write(&request);
+        SEQAN_PROADD(SEQAN_PROIO, (request.aio_nbytes + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
+        int result = aio_write(&request);
         SEQAN_PROADD(SEQAN_PROIWAIT, SEQAN_PROTIMEDIFF(tw));
         if (result != 0)
-		{
-			request.aio_nbytes = 0;
+        {
+            request.aio_nbytes = 0;
             int errorNo = errno;
-			if (errorNo == EAGAIN)  // write synchronoulsy instead
+            if (errorNo == EAGAIN)  // write synchronoulsy instead
             {
 #if SEQAN_ENABLE_DEBUG || SEQAN_ENABLE_TESTING
-            	std::cerr << "Warning: Falling back to sync. write. :( " << std::endl;
+                std::cerr << "Warning: Falling back to sync. write. :( " << std::endl;
 #endif
-				bool success = writeAt(me, memPtr, count, fileOfs);
+                bool success = writeAt(me, memPtr, count, fileOfs);
                 if (!success)
                     SEQAN_FAIL(
                         "writeAt(%d, %d, %d, %d) failed: \"%s\"",
                         me.handle, (size_t)memPtr, count, fileOfs, strerror(errno));
                 return success;
-			}
+            }
 #if SEQAN_ENABLE_DEBUG
-			else
+            else
             {
-				std::cerr << "aio_write failed (asyncWriteAt): \"" << ::strerror(errno) << '"' << std::endl;
+                std::cerr << "aio_write failed (asyncWriteAt): \"" << ::strerror(errno) << '"' << std::endl;
             }
 #endif
         }
         return result == 0;
     }
 
-	template <typename TSpec>
+    template <typename TSpec>
     inline bool flush(File<Async<TSpec> > & me) {
-//IOREV _doc_ 
-		#if _POSIX_SYNCHRONIZED_IO > 0
-			return me.handle == me.handleAsync || fdatasync(me.handle) == 0;
-		#else
-			return me.handle == me.handleAsync || fsync(me.handle) == 0;
-		#endif
+//IOREV _doc_
+        #if _POSIX_SYNCHRONIZED_IO > 0
+            return me.handle == me.handleAsync || fdatasync(me.handle) == 0;
+        #else
+            return me.handle == me.handleAsync || fsync(me.handle) == 0;
+        #endif
     }
 
     //////////////////////////////////////////////////////////////////////
     // queue specific functions
 
-	inline bool waitFor(aiocb &request)
+    inline bool waitFor(AiocbWrapper &request)
     {
-//IOREV _doc_ 
-/*		#ifdef SEQAN_VVERBOSE
-			printRequest(request, "aio_suspend():");
-		#endif
+//IOREV _doc_
+/*        #ifdef SEQAN_VVERBOSE
+            printRequest(request, "aio_suspend():");
+        #endif
 */
-		if (request.aio_nbytes == 0) return true;
-		aiocb * cblist = &request;
+        if (request.aio_nbytes == 0) return true;
+        aiocb * cblist = &request;
         SEQAN_PROTIMESTART(tw);
-		int result = aio_suspend(&cblist, 1, NULL);
+        int result = aio_suspend(&cblist, 1, NULL);
         ssize_t nbytes = aio_return(&request);
         SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
 
@@ -902,44 +949,45 @@ namespace SEQAN_NAMESPACE_MAIN
             {
                 if (errorNo != ECANCELED)
                     errorNo = errno;
-				std::cerr << "Asynchronous I/O operation failed (waitFor): \"" << ::strerror(errorNo) << '"' << std::endl;
+                std::cerr << "Asynchronous I/O operation failed (waitFor): \"" << ::strerror(errorNo) << '"' << std::endl;
                 printRequest(request);
             }
         }
 //#endif
 
-		return (result == 0) && (nbytes == (ssize_t)request.aio_nbytes);
-	}
+        return (result == 0) && (nbytes == (ssize_t)request.aio_nbytes);
+    }
 
-	inline bool waitFor(aiocb &request, long timeoutMilliSec, bool &inProgress)
+    inline bool waitFor(AiocbWrapper &request, long timeoutMilliSec, bool &inProgress)
     {
-//IOREV _doc_ 
-/*		#ifdef SEQAN_VVERBOSE
-			printRequest(request, "aio_suspend_timeout():");
-		#endif
+//IOREV _doc_
+/*        #ifdef SEQAN_VVERBOSE
+            printRequest(request, "aio_suspend_timeout():");
+        #endif
 */
-		if (request.aio_nbytes == 0)
+        if (request.aio_nbytes == 0)
         {
             inProgress = false;
             return true;
         }
 
-		int result;
-		if (timeoutMilliSec != 0)
+        int result;
+        if (timeoutMilliSec != 0)
         {
-			aiocb * cblist = &request;
-			timespec ts;
-			ts.tv_sec = timeoutMilliSec / 1000;
-			ts.tv_nsec = (timeoutMilliSec % 1000) * 1000;
-			SEQAN_PROTIMESTART(tw);
-			result = aio_suspend(&cblist, 1, &ts);
-			SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
-		}
+            aiocb * cblist = &request;
+            timespec ts;
+            ts.tv_sec = timeoutMilliSec / 1000;
+            ts.tv_nsec = (timeoutMilliSec % 1000) * 1000;
+            SEQAN_PROTIMESTART(tw);
+            result = aio_suspend(&cblist, 1, &ts);
+            (void)result;  // never used
+            SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
+        }
 
         result = aio_error(&request);
         inProgress = (result == EINPROGRESS);
         ssize_t nbytes;
-        
+
         if (inProgress)
             result = 0;
         else
@@ -949,7 +997,7 @@ namespace SEQAN_NAMESPACE_MAIN
         }
 
         #if SEQAN_ENABLE_DEBUG
-			if (result != 0)
+            if (result != 0)
             {
                 int errorNo = aio_error(&request);
                 if (errorNo != EINPROGRESS)
@@ -959,54 +1007,54 @@ namespace SEQAN_NAMESPACE_MAIN
                     std::cerr << "Asynchronous I/O operation failed (waitFor with timeOut=" << timeoutMilliSec << "ms): \"" << ::strerror(errorNo) << '"' << std::endl;
                     printRequest(request);
                 }
-			}
-		#endif
+            }
+        #endif
         return result == 0;
-	}
+    }
 
-	template < typename TSize >
-	inline TSize waitForAny(aiocb const * const contexts[], TSize count) {
-//IOREV _nodoc_ 
+    template < typename TSize >
+    inline TSize waitForAny(AiocbWrapper const * const contexts[], TSize count) {
+//IOREV _nodoc_
         SEQAN_PROTIMESTART(tw);
-		bool result = aio_suspend(contexts, count, NULL);
+        bool result = aio_suspend(contexts, count, NULL);
         SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
         return result == 0;
-	}
+    }
 
-	template < typename TSize >
-	inline TSize waitForAny(aiocb const * const contexts[], TSize count, long timeoutMilliSec) {
-//IOREV _nodoc_ 
+    template < typename TSize >
+    inline TSize waitForAny(AiocbWrapper const * const contexts[], TSize count, long timeoutMilliSec) {
+//IOREV _nodoc_
         timespec ts;
         ts.tv_sec = timeoutMilliSec / 1000;
         ts.tv_nsec = (timeoutMilliSec % 1000) * 1000;
         SEQAN_PROTIMESTART(tw);
-		bool result = aio_suspend(contexts, count, &ts);
+        bool result = aio_suspend(contexts, count, &ts);
         SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
         return result == 0;
-	}
-
-	template <typename TSpec>
-    inline bool cancel(File<Async<TSpec> > & me, aiocb &request) {
-//IOREV _doc_ 
-/*		#ifdef SEQAN_VVERBOSE
-			printRequest(request, "aio_cancel():");
-		#endif
+    }
+
+    template <typename TSpec>
+    inline bool cancel(File<Async<TSpec> > & me, AiocbWrapper &request) {
+//IOREV _doc_
+/*        #ifdef SEQAN_VVERBOSE
+            printRequest(request, "aio_cancel():");
+        #endif
 */      return aio_cancel(me.handleAsync, &request) == 0;
     }
 
-    inline int error(aiocb const & request) {
-//IOREV _nodoc_ 
+    inline int error(AiocbWrapper const & request) {
+//IOREV _nodoc_
         return aio_error(&request);
     }
 
-    inline int _returnValue(aiocb & request) {
-//IOREV _nodoc_ 
+    inline int _returnValue(AiocbWrapper & request) {
+//IOREV _nodoc_
         return aio_return(&request);
     }
 
-	template <typename TSpec>
-    inline void release(File<Async<TSpec> > & /*me*/, aiocb const & /*request*/) {
-//IOREV _nodoc_ 
+    template <typename TSpec>
+    inline void release(File<Async<TSpec> > & /*me*/, AiocbWrapper const & /*request*/) {
+//IOREV _nodoc_
     }
 
 /*
@@ -1031,84 +1079,84 @@ namespace SEQAN_NAMESPACE_MAIN
         return oldSig.sa_handler;
     }
 */
-    
-	//////////////////////////////////////////////////////////////////////////////
-	// page aligned allocate for direct file io
 
-    struct TagAllocateAligned_;	//< allocate page aligned memory for direct i/o access
+    //////////////////////////////////////////////////////////////////////////////
+    // page aligned allocate for direct file io
+
+    struct TagAllocateAligned_;    //< allocate page aligned memory for direct i/o access
     typedef Tag<TagAllocateAligned_> const TagAllocateAligned;
 
-	template <typename T, typename TValue, typename TSize>
-	inline void
-	allocate(T const & /*me*/, 
-			 TValue * & data,
-			 TSize count,
-			 TagAllocateAligned const)
-	{
-//IOREV _doc_ 
-		data = (TValue *) ::valloc(count * sizeof(TValue));
-#ifdef SEQAN_PROFILE 
+    template <typename T, typename TValue, typename TSize>
+    inline void
+    allocate(T const & /*me*/,
+             TValue * & data,
+             TSize count,
+             TagAllocateAligned const)
+    {
+//IOREV _doc_
+        data = (TValue *) ::valloc(count * sizeof(TValue));
+#ifdef SEQAN_PROFILE
         if (data)
-			SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue));
-		else
-			std::cerr << "AlignAllocator: Could not allocate memory of size " << std::hex << 
-				count * sizeof(TValue) << " with page alignment. (ErrNo=" << std::dec <<
-				errno << ")" << std::endl;
+            SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue));
+        else
+            std::cerr << "AlignAllocator: Could not allocate memory of size " << std::hex <<
+                count * sizeof(TValue) << " with page alignment. (ErrNo=" << std::dec <<
+                errno << ")" << std::endl;
 #endif
-	}
-
-	//////////////////////////////////////////////////////////////////////////////
-	// page aligned deallocate for direct file io
-
-	template <typename T, typename TValue, typename TSize>
-	inline void 
-	deallocate( T const & /*me*/,
-				TValue * data,
-				TSize
-#ifdef SEQAN_PROFILE 
-					count
+    }
+
+    //////////////////////////////////////////////////////////////////////////////
+    // page aligned deallocate for direct file io
+
+    template <typename T, typename TValue, typename TSize>
+    inline void
+    deallocate( T const & /*me*/,
+                TValue * data,
+                TSize
+#ifdef SEQAN_PROFILE
+                    count
 #endif
-					,
-				TagAllocateAligned const)
-	{
-//IOREV _doc_ 
-#ifdef SEQAN_PROFILE 
-        if (data && count)	// .. to use count if SEQAN_PROFILE is not defined
-			SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue));
+                    ,
+                TagAllocateAligned const)
+    {
+//IOREV _doc_
+#ifdef SEQAN_PROFILE
+        if (data && count)    // .. to use count if SEQAN_PROFILE is not defined
+            SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue));
 #endif
-		::free(data);
-	}
+        ::free(data);
+    }
 
     template < typename TSpec, typename TSize >
     inline void resize(File<Async<TSpec> > &me, TSize new_length) {
-//IOREV _doc_ 
-		if (!me.resize(new_length))
+//IOREV _doc_
+        if (!me.resize(new_length))
             SEQAN_FAIL(
                 "resize(%d, %d) failed: \"%s\"",
                 me.handle, new_length, strerror(errno));
     }
-	
+
 
 #endif
 
     //////////////////////////////////////////////////////////////////////////////
     // global functions
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct Size< File<Async<TSpec> > >
     {
 //IOREV
         typedef typename File<Async<TSpec> >::SizeType Type;
     };
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct Position< File<Async<TSpec> > >
     {
 //IOREV
         typedef typename File<Async<TSpec> >::FilePtr Type;
     };
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct Difference< File<Async<TSpec> > >
     {
 //IOREV
@@ -1118,24 +1166,24 @@ namespace SEQAN_NAMESPACE_MAIN
 
 
     template < typename TSpec, typename TValue, typename TSize>
-	inline void
-	allocate( File<Async<TSpec> > const & me,
-			  TValue * & data, 
-			  TSize count)
-	{
-//IOREV _doc_ 
-		allocate(me, data, count, TagAllocateAligned());
-	}
+    inline void
+    allocate( File<Async<TSpec> > const & me,
+              TValue * & data,
+              TSize count)
+    {
+//IOREV _doc_
+        allocate(me, data, count, TagAllocateAligned());
+    }
 
     template <typename TSpec, typename TValue, typename TSize>
-	inline void
-	deallocate( File<Async<TSpec> > const & me,
-				TValue * data, 
-				TSize count)
-	{
-//IOREV _doc_ 
-		deallocate(me, data, count, TagAllocateAligned());
-	}
+    inline void
+    deallocate( File<Async<TSpec> > const & me,
+                TValue * data,
+                TSize count)
+    {
+//IOREV _doc_
+        deallocate(me, data, count, TagAllocateAligned());
+    }
 
 
 }
diff --git a/seqan/system/file_directory.h b/seqan/system/file_directory.h
index 49ce001..5a1603e 100644
--- a/seqan/system/file_directory.h
+++ b/seqan/system/file_directory.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -50,10 +50,10 @@
  * _tested_
  * _windows_
  *
- * 
+ *
  * used by file/file_format_mmap.h and some apps
  * no documentation at all
- * 
+ *
  */
 
 
@@ -68,246 +68,246 @@ namespace SEQAN_NAMESPACE_MAIN
     class Directory
     {
 //IOREV _nodoc_ _windows_
-	protected:
-	
-		intptr_t			handle;
-		struct _finddata_t	entry;
-		bool				_atEnd;
-
-		friend inline bool open(Directory &dir, char const *dirName);
-		friend inline bool close(Directory &dir);
-		friend inline char const * value(Directory &dir);
-		friend inline char const * value(Directory const &dir);
-		friend inline Directory & goNext(Directory &dir);
-		friend inline bool atEnd(Directory &dir);
-		friend inline bool atEnd(Directory const &dir);
-
-	public:
-
-		Directory()
-		{
-			handle = 0;
-			_atEnd = true;
-		}
-		
-		Directory(char const *dirName)
-		{
-			open(*this, dirName);
-		}
-		
-		~Directory()
-		{
-			close(*this);
-		}
-		
-		inline char const * operator* () const
-		{
-			return value(*this);
-		}
-
-		inline Directory & operator++ ()
-		{
-			return goNext(*this);
-		}
-		
-		inline operator bool () const
-		{
-			return !_atEnd;
-		}
-	};
-
-//////////////////////////////////////////////////////////////////////////////	
-
-	inline bool
-	open(Directory &dir, char const *dirName)
-	{
+    protected:
+
+        intptr_t            handle;
+        struct _finddata_t    entry;
+        bool                _atEnd;
+
+        friend inline bool open(Directory &dir, char const *dirName);
+        friend inline bool close(Directory &dir);
+        friend inline char const * value(Directory &dir);
+        friend inline char const * value(Directory const &dir);
+        friend inline Directory & goNext(Directory &dir);
+        friend inline bool atEnd(Directory &dir);
+        friend inline bool atEnd(Directory const &dir);
+
+    public:
+
+        Directory()
+        {
+            handle = 0;
+            _atEnd = true;
+        }
+
+        Directory(char const *dirName)
+        {
+            open(*this, dirName);
+        }
+
+        ~Directory()
+        {
+            close(*this);
+        }
+
+        inline char const * operator* () const
+        {
+            return value(*this);
+        }
+
+        inline Directory & operator++ ()
+        {
+            return goNext(*this);
+        }
+
+        inline operator bool () const
+        {
+            return !_atEnd;
+        }
+    };
+
+//////////////////////////////////////////////////////////////////////////////
+
+    inline bool
+    open(Directory &dir, char const *dirName)
+    {
 //IOREV _nodoc_
-		CharString selection = dirName;
-		append(selection, "\\*");
-		dir._atEnd = ((dir.handle = _findfirst(toCString(selection), &dir.entry)) == -1L);
-		return !dir._atEnd;
-	}
-
-	inline bool
-	close(Directory &dir)
-	{
+        CharString selection = dirName;
+        append(selection, "\\*");
+        dir._atEnd = ((dir.handle = _findfirst(toCString(selection), &dir.entry)) == -1L);
+        return !dir._atEnd;
+    }
+
+    inline bool
+    close(Directory &dir)
+    {
 //IOREV _nodoc_
         int result = 0;
-		if (dir.handle)
-			result = _findclose(dir.handle);
+        if (dir.handle)
+            result = _findclose(dir.handle);
 
-		dir._atEnd = true;
-		dir.handle = 0;
-		return result == 0;
-	}
+        dir._atEnd = true;
+        dir.handle = 0;
+        return result == 0;
+    }
 
-	inline char const *
-	value(Directory &dir)
-	{
+    inline char const *
+    value(Directory &dir)
+    {
 //IOREV _nodoc_
-		return dir.entry.name;
-	}
+        return dir.entry.name;
+    }
 
-	inline char const *
-	value(Directory const &dir)
-	{
+    inline char const *
+    value(Directory const &dir)
+    {
 //IOREV _nodoc_
         return dir.entry.name;
-	}
+    }
 
-	inline Directory &
-	goNext(Directory &dir)
-	{
+    inline Directory &
+    goNext(Directory &dir)
+    {
 //IOREV _nodoc_
         dir._atEnd = (_findnext(dir.handle, &dir.entry) != 0);
-		return dir;
-	}
+        return dir;
+    }
 
-	inline bool
-	atEnd(Directory &dir)
-	{
+    inline bool
+    atEnd(Directory &dir)
+    {
 //IOREV _nodoc_
-		return dir._atEnd;
-	}
-	
-	inline bool
-	atEnd(Directory const &dir)
-	{
+        return dir._atEnd;
+    }
+
+    inline bool
+    atEnd(Directory const &dir)
+    {
 //IOREV _nodoc_
-		return dir._atEnd;
-	}
-	
-//////////////////////////////////////////////////////////////////////////////	
-	
-	
+        return dir._atEnd;
+    }
+
+//////////////////////////////////////////////////////////////////////////////
+
+
 #else
 
 
-//////////////////////////////////////////////////////////////////////////////	
+//////////////////////////////////////////////////////////////////////////////
 
     class Directory
     {
 //IOREV _nodoc_
-	protected:
-	
-		DIR		*handle;
-		dirent	*it;
-		
-		friend inline bool open(Directory &dir, char const *dirName);
-		friend inline bool close(Directory &dir);
-		friend inline char const * value(Directory &dir);
-		friend inline char const * value(Directory const &dir);
-		friend inline Directory & goBegin(Directory &dir);
-		friend inline Directory & goNext(Directory &dir);
-		friend inline bool atEnd(Directory &dir);
-		friend inline bool atEnd(Directory const &dir);
-
-	public:
-
-		Directory()
-		{
-			handle = NULL;
-			it = NULL;
-		}
-		
-		Directory(char const *dirName)
-		{
-			open(*this, dirName);
-		}
-		
-		~Directory()
-		{
-			close(*this);
-		}
-		
-		inline char const * operator* () const
-		{
-			return value(*this);
-		}
-
-		inline Directory & operator++ ()
-		{
-			return goNext(*this);
-		}
-		
-		inline operator bool () const
-		{
-			return !atEnd(*this);
-		}
-	};
-	
-//////////////////////////////////////////////////////////////////////////////	
-	
-	inline bool
-	open(Directory &dir, char const *dirName)
-	{
+    protected:
+
+        DIR        *handle;
+        dirent    *it;
+
+        friend inline bool open(Directory &dir, char const *dirName);
+        friend inline bool close(Directory &dir);
+        friend inline char const * value(Directory &dir);
+        friend inline char const * value(Directory const &dir);
+        friend inline Directory & goBegin(Directory &dir);
+        friend inline Directory & goNext(Directory &dir);
+        friend inline bool atEnd(Directory &dir);
+        friend inline bool atEnd(Directory const &dir);
+
+    public:
+
+        Directory()
+        {
+            handle = NULL;
+            it = NULL;
+        }
+
+        Directory(char const *dirName)
+        {
+            open(*this, dirName);
+        }
+
+        ~Directory()
+        {
+            close(*this);
+        }
+
+        inline char const * operator* () const
+        {
+            return value(*this);
+        }
+
+        inline Directory & operator++ ()
+        {
+            return goNext(*this);
+        }
+
+        inline operator bool () const
+        {
+            return !atEnd(*this);
+        }
+    };
+
+//////////////////////////////////////////////////////////////////////////////
+
+    inline bool
+    open(Directory &dir, char const *dirName)
+    {
 //IOREV _nodoc_
-		if ((dir.handle = opendir(dirName)) != NULL)
-		{
-			goNext(dir);
-			return true;
-		}
-		dir.it = NULL;
-		return false;
-	}
-
-	inline bool
-	close(Directory &dir)
-	{
+        if ((dir.handle = opendir(dirName)) != NULL)
+        {
+            goNext(dir);
+            return true;
+        }
+        dir.it = NULL;
+        return false;
+    }
+
+    inline bool
+    close(Directory &dir)
+    {
 //IOREV _nodoc_
         int result = 0;
-		if (dir.handle != NULL)
-			result = closedir(dir.handle);
+        if (dir.handle != NULL)
+            result = closedir(dir.handle);
 
-		dir.handle = NULL;
-		dir.it = NULL;
-		return result == 0;
-	}
+        dir.handle = NULL;
+        dir.it = NULL;
+        return result == 0;
+    }
 
-	inline char const *
-	value(Directory &dir)
-	{
+    inline char const *
+    value(Directory &dir)
+    {
 //IOREV _nodoc_
         return dir.it->d_name;
-	}
+    }
 
-	inline char const *
-	value(Directory const &dir)
-	{
+    inline char const *
+    value(Directory const &dir)
+    {
 //IOREV _nodoc_
         return dir.it->d_name;
-	}
+    }
 
-	inline Directory &
-	goBegin(Directory &dir)
-	{
+    inline Directory &
+    goBegin(Directory &dir)
+    {
 //IOREV _nodoc_
         rewinddir(dir.handle);
-		return goNext(dir);
-	}
+        return goNext(dir);
+    }
 
-	inline Directory &
-	goNext(Directory &dir)
-	{
+    inline Directory &
+    goNext(Directory &dir)
+    {
 //IOREV _nodoc_
         dir.it = readdir(dir.handle);
-		return dir;
-	}
+        return dir;
+    }
 
-	inline bool
-	atEnd(Directory &dir)
-	{
+    inline bool
+    atEnd(Directory &dir)
+    {
 //IOREV _nodoc_
         return dir.it == NULL;
-	}
-	
-	inline bool
-	atEnd(Directory const &dir)
-	{
+    }
+
+    inline bool
+    atEnd(Directory const &dir)
+    {
 //IOREV _nodoc_
         return dir.it == NULL;
-	}
-	
+    }
+
 #endif
 
 }
diff --git a/seqan/system/file_forwards.h b/seqan/system/file_forwards.h
index 55dc26a..9d046aa 100644
--- a/seqan/system/file_forwards.h
+++ b/seqan/system/file_forwards.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_FILE_MANUAL_FORWARDS_H 
-#define SEQAN_HEADER_FILE_MANUAL_FORWARDS_H 
+#ifndef SEQAN_HEADER_FILE_MANUAL_FORWARDS_H
+#define SEQAN_HEADER_FILE_MANUAL_FORWARDS_H
 
 //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
 
@@ -46,8 +46,8 @@ namespace SEQAN_NAMESPACE_MAIN {
 //____________________________________________________________________________
 // TagAllocateAligned_
 
-struct TagAllocateAligned_;       	// "core/include/seqan/file/file_async.h"(283)
-//struct aiocb;
+struct TagAllocateAligned_;           // "include/seqan/file/file_async.h"(283)
+struct AiocbWrapper;
 
 //////////////////////////////////////////////////////////////////////////////
 // TYPEDEFS
@@ -56,12 +56,12 @@ struct TagAllocateAligned_;       	// "core/include/seqan/file/file_async.h"(283
 //____________________________________________________________________________
 // (*sighandler_t)(int)
 
-typedef void (*sighandler_t)(int);       	// "core/include/seqan/file/file_async.h"(258)
+typedef void (*sighandler_t)(int);           // "include/seqan/file/file_async.h"(258)
 
 //____________________________________________________________________________
 // TagAllocateAligned
 
-typedef Tag<TagAllocateAligned_> const TagAllocateAligned;       	// "core/include/seqan/file/file_async.h"(284)
+typedef Tag<TagAllocateAligned_> const TagAllocateAligned;           // "include/seqan/file/file_async.h"(284)
 
 
 //////////////////////////////////////////////////////////////////////////////
@@ -71,87 +71,87 @@ typedef Tag<TagAllocateAligned_> const TagAllocateAligned;       	// "core/inclu
 //____________________________________________________________________________
 // allocate
 
-template <typename T, typename TValue, typename TSize> inline void allocate(T const & me, TValue * & data, TSize count, TagAllocateAligned const);       	// "core/include/seqan/file/file_async.h"(292)
-template <typename TSpec, typename TValue, typename TSize> inline void allocate( File<Async<TSpec> > const & me, TValue * & data, TSize count);       	// "core/include/seqan/file/file_async.h"(351)
+template <typename T, typename TValue, typename TSize> inline void allocate(T const & me, TValue * & data, TSize count, TagAllocateAligned const);           // "include/seqan/file/file_async.h"(292)
+template <typename TSpec, typename TValue, typename TSize> inline void allocate( File<Async<TSpec> > const & me, TValue * & data, TSize count);           // "include/seqan/file/file_async.h"(351)
 
 //____________________________________________________________________________
 // asyncReadAt
 
-template <typename TSpec, typename TValue, typename TSize, typename TPos > bool asyncReadAt(File<Async<TSpec> > & me, TValue *memPtr, TSize const count, TPos const fileOfs, aiocb &request);       	// "core/include/seqan/file/file_async.h"(136)
+template <typename TSpec, typename TValue, typename TSize, typename TPos > bool asyncReadAt(File<Async<TSpec> > & me, TValue *memPtr, TSize const count, TPos const fileOfs, AiocbWrapper &request);           // "include/seqan/file/file_async.h"(136)
 
 //____________________________________________________________________________
 // asyncWriteAt
 
-template <typename TSpec, typename TValue, typename TSize, typename TPos > bool asyncWriteAt(File<Async<TSpec> > & me, const TValue *memPtr, TSize const count, TPos const fileOfs, aiocb &request);       	// "core/include/seqan/file/file_async.h"(160)
+template <typename TSpec, typename TValue, typename TSize, typename TPos > bool asyncWriteAt(File<Async<TSpec> > & me, const TValue *memPtr, TSize const count, TPos const fileOfs, AiocbWrapper &request);           // "include/seqan/file/file_async.h"(160)
 
 //____________________________________________________________________________
 // cancel
 
-template <typename TSpec> inline bool cancel(File<Async<TSpec> > & me, aiocb &request);       	// "core/include/seqan/file/file_async.h"(242)
+template <typename TSpec> inline bool cancel(File<Async<TSpec> > & me, AiocbWrapper &request);           // "include/seqan/file/file_async.h"(242)
 
 //____________________________________________________________________________
 // deallocate
 
-template <typename T, typename TValue, typename TSize> inline void deallocate( T const & me, TValue * data, TSize count, TagAllocateAligned const);       	// "core/include/seqan/file/file_async.h"(310)
-template <typename TSpec, typename TValue, typename TSize> inline void deallocate( File<Async<TSpec> > const & me, TValue * data, TSize count);       	// "core/include/seqan/file/file_async.h"(360)
+template <typename T, typename TValue, typename TSize> inline void deallocate( T const & me, TValue * data, TSize count, TagAllocateAligned const);           // "include/seqan/file/file_async.h"(310)
+template <typename TSpec, typename TValue, typename TSize> inline void deallocate( File<Async<TSpec> > const & me, TValue * data, TSize count);           // "include/seqan/file/file_async.h"(360)
 
 //____________________________________________________________________________
 // error
 
-inline int error(aiocb const &request);       	// "core/include/seqan/file/file_async.h"(246)
+inline int error(AiocbWrapper const &request);           // "include/seqan/file/file_async.h"(246)
 
 //____________________________________________________________________________
 // fileExists
 
-inline bool fileExists(const char *fileName);       	// "core/include/seqan/file/file_sync.h"(189)
+inline bool fileExists(const char *fileName);           // "include/seqan/file/file_sync.h"(189)
 
 //____________________________________________________________________________
 // fileUnlink
 
-inline bool fileUnlink(const char *fileName);       	// "core/include/seqan/file/file_sync.h"(194)
+inline bool fileUnlink(const char *fileName);           // "include/seqan/file/file_sync.h"(194)
 
 //____________________________________________________________________________
 // flush
 
-template <typename TSpec> inline bool flush(File<Async<TSpec> > & me);       	// "core/include/seqan/file/file_async.h"(182)
+template <typename TSpec> inline bool flush(File<Async<TSpec> > & me);           // "include/seqan/file/file_async.h"(182)
 
 //____________________________________________________________________________
 // printRequest
 
-inline void printRequest(aiocb &request, const char *_hint);       	// "core/include/seqan/file/file_async.h"(125)
-inline void printRequest(aiocb &request);       	// "core/include/seqan/file/file_async.h"(125)
+inline void printRequest(AiocbWrapper &request, const char *_hint);           // "include/seqan/file/file_async.h"(125)
+inline void printRequest(AiocbWrapper &request);           // "include/seqan/file/file_async.h"(125)
 
 //____________________________________________________________________________
 // read
 
-template <typename TSpec, typename TValue, typename TSize > inline bool read(File<Sync<TSpec> > & me, TValue *memPtr, TSize const count);       	// "core/include/seqan/file/file_sync.h"(226)
+template <typename TSpec, typename TValue, typename TSize > inline bool read(File<Sync<TSpec> > & me, TValue *memPtr, TSize const count);           // "include/seqan/file/file_sync.h"(226)
 
 //____________________________________________________________________________
 // release
 
-template <typename TSpec> inline void release(File<Async<TSpec> > & me, aiocb const &request);       	// "core/include/seqan/file/file_async.h"(255)
+template <typename TSpec> inline void release(File<Async<TSpec> > & me, AiocbWrapper const &request);           // "include/seqan/file/file_async.h"(255)
 
 //____________________________________________________________________________
 // _returnValue
 
-inline int _returnValue(aiocb &request);       	// "core/include/seqan/file/file_async.h"(250)
+inline int _returnValue(AiocbWrapper &request);           // "include/seqan/file/file_async.h"(250)
 
 //____________________________________________________________________________
 // waitFor
 
-inline bool waitFor(aiocb &request);       	// "core/include/seqan/file/file_async.h"(189)
-inline bool waitFor(aiocb &request, long timeoutMilliSec, bool &inProgress);       	// "core/include/seqan/file/file_async.h"(204)
+inline bool waitFor(AiocbWrapper &request);           // "include/seqan/file/file_async.h"(189)
+inline bool waitFor(AiocbWrapper &request, long timeoutMilliSec, bool &inProgress);           // "include/seqan/file/file_async.h"(204)
 
 //____________________________________________________________________________
 // waitForAny
 
-template <typename TSize > inline TSize waitForAny(aiocb const * const contexts[], TSize count);       	// "core/include/seqan/file/file_async.h"(223)
-template <typename TSize > inline TSize waitForAny(aiocb const * const contexts[], TSize count, long timeoutMilliSec);       	// "core/include/seqan/file/file_async.h"(231)
+template <typename TSize > inline TSize waitForAny(AiocbWrapper const * const contexts[], TSize count);           // "include/seqan/file/file_async.h"(223)
+template <typename TSize > inline TSize waitForAny(AiocbWrapper const * const contexts[], TSize count, long timeoutMilliSec);           // "include/seqan/file/file_async.h"(231)
 
 //____________________________________________________________________________
 // write
 
-template <typename TSpec, typename TValue, typename TSize > inline bool write(File<Sync<TSpec> > & me, TValue const *memPtr, TSize const count);       	// "core/include/seqan/file/file_sync.h"(231)
+template <typename TSpec, typename TValue, typename TSize > inline bool write(File<Sync<TSpec> > & me, TValue const *memPtr, TSize const count);           // "include/seqan/file/file_sync.h"(231)
 
 } //namespace SEQAN_NAMESPACE_MAIN
 
diff --git a/seqan/system/file_sync.h b/seqan/system/file_sync.h
index 6051ba0..2944a0a 100644
--- a/seqan/system/file_sync.h
+++ b/seqan/system/file_sync.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -38,7 +38,7 @@
 #define SEQAN_HEADER_FILE_SIMPLE_H
 
 #include <fcntl.h>          // O_CREAT ..
-#include <sys/stat.h>       // 
+#include <sys/stat.h>       //
 #include <cstdio>           // tmpnam(..)
 
 #ifdef PLATFORM_WINDOWS
@@ -76,237 +76,238 @@ namespace SEQAN_NAMESPACE_MAIN
 {
 
 
-	template <typename TSpec /* = void */>
-	struct Sync;
+    template <typename TSpec /* = void */>
+    struct Sync;
 
 
 #ifdef PLATFORM_WINDOWS
 
     //////////////////////////////////////////////////////////////////////////////
     // Windows rtl file access
-	template <typename TSpec>
-	class File<Sync<TSpec> >
+    template <typename TSpec>
+    class File<Sync<TSpec> >
     {
 //IOREV _windows_ _nodoc_
     public:
 
-		typedef __int64			FilePtr;
-		typedef __int64         SizeType;   // type of file size
+        typedef __int64            FilePtr;
+        typedef __int64         SizeType;   // type of file size
         typedef unsigned int    SizeType_;  // type of transfer size (for read or write)
-		typedef int				Handle;
+        typedef int                Handle;
 
         Handle handle;
 
         File(void * /*dummy*/ = NULL): // to be compatible with the FILE*(NULL) constructor
             handle(-1) {}
 
-	//File(int posixHandle) : handle(posixHandle) {}
+    //File(int posixHandle) : handle(posixHandle) {}
 
-        inline int _getOFlag(int openMode) const 
-		{
-			int result;
-			bool canWrite = false;
+        inline int _getOFlag(int openMode) const
+        {
+            int result;
+            bool canWrite = false;
 
-			switch (openMode & OPEN_MASK) {
+            switch (openMode & OPEN_MASK) {
                 case OPEN_RDONLY:
                     result = _O_RDONLY;
-					break;
+                    break;
                 case OPEN_WRONLY:
-					canWrite = true;
+                    canWrite = true;
                     result = _O_WRONLY;
-					break;
+                    break;
                 case OPEN_RDWR:
-				default:
-					canWrite = true;
+                default:
+                    canWrite = true;
                     result = _O_RDWR;
-					break;
-			}
+                    break;
+            }
 
-			if (openMode & OPEN_CREATE)     result |= _O_CREAT;
-			if (canWrite && !(openMode & OPEN_APPEND))	result |= _O_TRUNC;
+            if (openMode & OPEN_CREATE)     result |= _O_CREAT;
+            if (canWrite && !(openMode & OPEN_APPEND))    result |= _O_TRUNC;
             if (openMode & OPEN_TEMPORARY)  result |= _O_TEMPORARY;
-			return result | _O_BINARY;
+            return result | _O_BINARY;
         }
 
-        bool open(char const *fileName, int openMode = DefaultOpenMode<File>::VALUE) 
-		{
-            handle = _open(fileName, _getOFlag(openMode), _S_IREAD | _S_IWRITE);
-			if (handle == -1) {
-				if (!(openMode & OPEN_QUIET))
-					::std::cerr << "Open failed on file " << fileName << ". (" << ::strerror(errno) << ")" << ::std::endl;
-				return false;
-			}
-			SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
+        bool open(char const *fileName, int openMode = DefaultOpenMode<File>::VALUE)
+        {
+            handle = ::_open(fileName, _getOFlag(openMode), _S_IREAD | _S_IWRITE);
+            if (handle == -1) {
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "Open failed on file " << fileName << ". (" << ::strerror(errno) << ")" << std::endl;
+                return false;
+            }
+            SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
             return true;
         }
 
-        bool openTemp(int openMode = DefaultOpenTempMode<File>::VALUE) 
-		{
+        bool openTemp(int openMode = DefaultOpenTempMode<File>::VALUE)
+        {
 #ifdef PLATFORM_WINDOWS_MINGW
             char fileNameBuffer[L_tmpnam + 1];
             char * fileName = tmpnam(&fileNameBuffer[0]);
 #else // #ifdef PLATFORM_WINDOWS_MINGW
 # ifdef SEQAN_DEFAULT_TMPDIR
-			char *fileName = _tempnam(SEQAN_DEFAULT_TMPDIR, "SQN");
+            char *fileName = _tempnam(SEQAN_DEFAULT_TMPDIR, "SQN");
 # else  // #ifdef SEQAN_DEFAULT_TMPDIR
-			char *fileName = _tempnam(NULL, "SQN");
+            char *fileName = _tempnam(NULL, "SQN");
 # endif  // #ifdef SEQAN_DEFAULT_TMPDIR
 #endif // #ifdef PLATFORM_WINDOWS_MINGW
-			if (!fileName) {
-				if (!(openMode & OPEN_QUIET))
-					::std::cerr << "Cannot create a unique temporary filename" << ::std::endl;
-				return false;
-			}
+            if (!fileName) {
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "Cannot create a unique temporary filename" << std::endl;
+                return false;
+            }
             bool result = open(fileName, openMode | OPEN_TEMPORARY);
-			free(fileName);
-			return result;
+            ::free(fileName);
+            return result;
         }
 
-        inline bool close() 
-		{
+        inline bool close()
+        {
             if (_close(handle) != 0)
                 return false;
             handle = -1;
-			SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
+            SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
             return true;
         }
 
-		inline int read(void *buffer, SizeType_ count) const 
-		{
+        inline int read(void *buffer, SizeType_ count) const
+        {
             SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
             SEQAN_PROTIMESTART(tw);
-		    int result = _read(handle, buffer, count);
+            int result = ::_read(handle, buffer, count);
             SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
             return result;
-		}
+        }
 
-		inline int write(void const *buffer, SizeType_ count) const 
-		{
+        inline int write(void const *buffer, SizeType_ count) const
+        {
             SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
             SEQAN_PROTIMESTART(tw);
-		    int result = _write(handle, buffer, count);
+            int result = ::_write(handle, buffer, count);
             SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
             return result;
-		}
+        }
 
-		inline FilePtr seek(FilePtr pos, int origin = SEEK_SET) const 
-		{
-			return _lseeki64(handle, pos, origin);
-		}
+        inline FilePtr seek(FilePtr pos, int origin = SEEK_SET) const
+        {
+            return _lseeki64(handle, pos, origin);
+        }
 
-		inline FilePtr tell() const 
-		{
-			return _telli64(handle);
-		}
+        inline FilePtr tell() const
+        {
+            return _telli64(handle);
+        }
 
-		static int error() 
-		{
-			return errno;
-		}
+        static int error()
+        {
+            return errno;
+        }
 
-        operator bool () const 
-		{
+        operator bool () const
+        {
             return handle != -1;
         }
     };
 
-	inline bool fileExists(const char *fileName) 
-	{
+    inline bool fileExists(const char *fileName)
+    {
 //IOREV _windows_ _nodoc_
-		struct _stat buf;
-		return _stat(fileName, &buf) == 0;
-	}
+        struct _stat buf;
+        return _stat(fileName, &buf) == 0;
+    }
 
-	inline bool fileUnlink(const char *fileName) 
-	{
+    inline bool fileUnlink(const char *fileName)
+    {
 //IOREV _windows_ _nodoc_
-		return _unlink(fileName) == 0;
-	}
+        return _unlink(fileName) == 0;
+    }
 
 #else
 
     //////////////////////////////////////////////////////////////////////////////
     // Unix file access
-	template <typename TSpec>
-	class File<Sync<TSpec> >
+    template <typename TSpec>
+    class File<Sync<TSpec> >
     {
 //IOREV __nodoc_
     public:
 
-		typedef off_t			FilePtr;
-		typedef off_t           SizeType;   // type of file size
+        typedef off_t            FilePtr;
+        typedef off_t           SizeType;   // type of file size
         typedef size_t          SizeType_;  // type of transfer size (for read or write)
-		typedef int				Handle;
+        typedef int                Handle;
 
         Handle handle;
 
         File(void * /*dummy*/ = NULL): // to be compatible with the FILE*(NULL) constructor
             handle(-1) {}
 
-	///File(int posixHandle) : handle(posixHandle) {}
+    ///File(int posixHandle) : handle(posixHandle) {}
 
         virtual ~File() {}
-        
+
         inline int _getOFlag(int openMode) const {
-			int result = O_LARGEFILE;
+            int result = O_LARGEFILE;
 
-			switch (openMode & OPEN_MASK) {
+            switch (openMode & OPEN_MASK) {
                 case OPEN_RDONLY:
                     result |= O_RDONLY;
-					break;
+                    break;
                 case OPEN_WRONLY:
                     result |= O_WRONLY;
-					if (!(openMode & OPEN_APPEND))	result |= O_TRUNC;
-					break;
+                    if (!(openMode & OPEN_APPEND))    result |= O_TRUNC;
+                    break;
                 case OPEN_RDWR:
                     result |= O_RDWR;
-					if (!(openMode & OPEN_APPEND))	result |= O_TRUNC;
-					break;
-			}
+                    if (!(openMode & OPEN_APPEND))    result |= O_TRUNC;
+                    break;
+            }
 
-			if (openMode & OPEN_CREATE)     result |= O_CREAT;
-//			if (openMode & OPEN_TEMPORARY)  result |= O_TEMPORARY;
+            if (openMode & OPEN_CREATE)     result |= O_CREAT;
+//            if (openMode & OPEN_TEMPORARY)  result |= O_TEMPORARY;
         #ifdef SEQAN_DIRECTIO
-    		if (openMode & OPEN_ASYNC)		result |= O_DIRECT;
+            if (openMode & OPEN_ASYNC)        result |= O_DIRECT;
         #endif
-			return result;
+            return result;
         }
 
         virtual bool open(char const *fileName, int openMode = DefaultOpenMode<File>::VALUE) {
             handle = ::open(fileName, _getOFlag(openMode), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
-			if (handle == -1 && errno == EINVAL) {	// fall back to cached access
-	            #ifdef SEQAN_DEBUG_OR_TEST_
-					if (!(openMode & OPEN_QUIET))
-						::std::cerr << "Warning: Direct access openening failed: " << fileName << "." << ::std::endl;
-				#endif			
-          	    handle = ::open(fileName, _getOFlag(openMode & ~OPEN_ASYNC), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
-			}
-			
-			if (handle == -1) {
-				if (!(openMode & OPEN_QUIET))
-					::std::cerr << "Open failed on file " << fileName << ". (" << ::strerror(errno) << ")" << ::std::endl;
-				return false;
-			}
-
-			if (sizeof(FilePtr) < 8 && !(openMode & OPEN_QUIET))
-				// To remove this warning, you have to options:
-				// 1. include the following line before including anything in your application
-				//    #define _FILE_OFFSET_BITS 64
-				// 2. include <seqan/platform.h> or <seqan/sequence.h> before any other include
-				::std::cerr << "WARNING: FilePtr is not 64bit wide" << ::std::endl;
-
-			SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
+            if (handle == -1 && errno == EINVAL) {    // fall back to cached access
+                #ifdef SEQAN_DEBUG_OR_TEST_
+                    if (!(openMode & OPEN_QUIET))
+                        std::cerr << "Warning: Direct access openening failed: " << fileName << "." << std::endl;
+                #endif
+                  handle = ::open(fileName, _getOFlag(openMode & ~OPEN_ASYNC), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH);
+            }
+
+            if (handle == -1) {
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "Open failed on file " << fileName << ". (" << ::strerror(errno) << ")" << std::endl;
+                return false;
+            }
+
+            if (sizeof(FilePtr) < 8 && !(openMode & OPEN_QUIET))
+                // To remove this warning, you have to options:
+                // 1. include the following line before including anything in your application
+                //    #define _FILE_OFFSET_BITS 64
+                // 2. include <seqan/platform.h> or <seqan/sequence.h> before any other include
+                std::cerr << "WARNING: FilePtr is not 64bit wide" << std::endl;
+
+            SEQAN_PROADD(SEQAN_PROOPENFILES, 1);
             return true;
         }
 
-        bool openTemp(int openMode = DefaultOpenTempMode<File>::VALUE) {
+        bool openTemp(int openMode = DefaultOpenTempMode<File>::VALUE)
+        {
             // Construct the pattern for the temporary file.
             //
             // First, try to get the temporary directory from the environment
             // variables TMPDIR, TMP.
-            CharString tmpDir;
-            if ((getuid() == geteuid()) && (getgid() == getegid())) 
-			{
+            std::string tmpDir;
+            if ((getuid() == geteuid()) && (getgid() == getegid()))
+            {
                 char * res;
                 if ((res = getenv("TMPDIR")) != NULL)
                     tmpDir = res;
@@ -327,99 +328,100 @@ namespace SEQAN_NAMESPACE_MAIN
 
             // At this point, we have a temporary directory.  Now, we add the
             // file name template to get the full path template.
-            append(tmpDir, "/SQNXXXXXX");
+            tmpDir += "/SQNXXXXXX";
             // Open temporary file and unlink it immediately afterwards so the
             // memory is released when the program exits.
             int oldMode = umask(077);  // Create with restrictive permissions.
-			if ((handle = ::mkstemp(toCString(tmpDir))) == -1) {
-			    umask(oldMode);  // Reset umask mode.
-				if (!(openMode & OPEN_QUIET))
-					::std::cerr << "Couldn't create temporary file " << tmpDir << ". (" << ::strerror(errno) << ")" << ::std::endl;
-				return false;
-			}
-			if (!(close() && open(toCString(tmpDir), openMode))) 
-			{
-				umask(oldMode);  // Reset umask mode.
-			    return false;
+            if ((handle = ::mkstemp((char*)tmpDir.c_str())) == -1)
+            {
+                umask(oldMode);  // Reset umask mode.
+                if (!(openMode & OPEN_QUIET))
+                    std::cerr << "Couldn't create temporary file " << tmpDir << ". (" << ::strerror(errno) << ")" << std::endl;
+                return false;
+            }
+            if (!(close() && open(toCString(tmpDir), openMode)))
+            {
+                umask(oldMode);  // Reset umask mode.
+                return false;
             }
-			umask(oldMode);  // Reset umask mode.
+            umask(oldMode);  // Reset umask mode.
             #ifdef SEQAN_DEBUG
-				if (::unlink(toCString(tmpDir)) == -1 && !(openMode & OPEN_QUIET))
-					::std::cerr << "Couldn't unlink temporary file " << tmpDir << ". (" << ::strerror(errno) << ")" << ::std::endl;
+                if (::unlink(toCString(tmpDir)) == -1 && !(openMode & OPEN_QUIET))
+                    std::cerr << "Couldn't unlink temporary file " << tmpDir << ". (" << ::strerror(errno) << ")" << std::endl;
             #else
-				::unlink(toCString(tmpDir));
-			#endif
-			return true;
+                ::unlink(toCString(tmpDir));
+            #endif
+            return true;
         }
 
 
         virtual bool close() {
             if (::close(this->handle) == -1) return false;
             handle = -1;
-			SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
+            SEQAN_PROSUB(SEQAN_PROOPENFILES, 1);
             return true;
         }
 
-		inline ssize_t read(void *buffer, SizeType_ count) const {
+        inline ssize_t read(void *buffer, SizeType_ count) const {
             SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
             SEQAN_PROTIMESTART(tw);
-		    ssize_t result = ::read(handle, buffer, count);
+            ssize_t result = ::read(handle, buffer, count);
             SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
             return result;
-		}
+        }
 
-		inline ssize_t write(void const *buffer, SizeType_ count) const {
+        inline ssize_t write(void const *buffer, SizeType_ count) const {
             SEQAN_PROADD(SEQAN_PROIO, (count + SEQAN_PROPAGESIZE - 1) / SEQAN_PROPAGESIZE);
             SEQAN_PROTIMESTART(tw);
-		    ssize_t result = ::write(handle, buffer, count);
+            ssize_t result = ::write(handle, buffer, count);
             SEQAN_PROADD(SEQAN_PROCWAIT, SEQAN_PROTIMEDIFF(tw));
             return result;
-		}
+        }
 
-		inline FilePtr seek(FilePtr pos, int origin = SEEK_SET) const {
+        inline FilePtr seek(FilePtr pos, int origin = SEEK_SET) const {
             FilePtr result = ::lseek(handle, pos, origin);
-//			#ifdef SEQAN_DEBUG
-				if (result < 0)
-					::std::cerr << "lseek returned " << result << ". (" << ::strerror(errno) << ")" << ::std::endl;
-//			#endif
-			return result;
-		}
-
-		inline FilePtr tell() const {
+//            #ifdef SEQAN_DEBUG
+                if (result < 0)
+                    std::cerr << "lseek returned " << result << ". (" << ::strerror(errno) << ")" << std::endl;
+//            #endif
+            return result;
+        }
+
+        inline FilePtr tell() const {
             return seek(0, SEEK_CUR);
         }
 
-		inline bool resize(SizeType new_length) const {
-			return ftruncate(handle, new_length) == 0;
-		}
+        inline bool resize(SizeType new_length) const {
+            return ftruncate(handle, new_length) == 0;
+        }
 
-		static int error() {
+        static int error() {
             return errno;
-		}
+        }
 
         operator bool () const {
             return handle != -1;
         }
     };
 
-	inline bool fileExists(const char *fileName)
-	{
+    inline bool fileExists(const char *fileName)
+    {
 //IOREV _nodoc_
-		struct stat buf;
-		return stat(fileName, &buf) != -1;
-	}
+        struct stat buf;
+        return stat(fileName, &buf) != -1;
+    }
 
-	inline bool fileUnlink(const char *fileName)
-	{
+    inline bool fileUnlink(const char *fileName)
+    {
 //IOREV _noddoc_
-		return unlink(fileName) == 0;
-	}
+        return unlink(fileName) == 0;
+    }
 
     template < typename TSpec, typename TSize >
     inline void resize(File<Sync<TSpec> > &me, TSize new_length)
-	{
-//IOREV _doc_ 
-		if (!me.resize(new_length))
+    {
+//IOREV _doc_
+        if (!me.resize(new_length))
             SEQAN_FAIL(
                 "resize(%d, %d) failed: \"%s\"",
                 me.handle, new_length, strerror(errno));
@@ -430,21 +432,21 @@ namespace SEQAN_NAMESPACE_MAIN
     //////////////////////////////////////////////////////////////////////////////
     // global functions
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct Size< File<Sync<TSpec> > >
     {
 //IOREV
         typedef typename File<Sync<TSpec> >::SizeType Type;
     };
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct Position< File<Sync<TSpec> > >
     {
 //IOREV
         typedef typename File<Sync<TSpec> >::FilePtr Type;
     };
 
-	template <typename TSpec>
+    template <typename TSpec>
     struct Difference< File<Sync<TSpec> > >
     {
 //IOREV
@@ -452,15 +454,21 @@ namespace SEQAN_NAMESPACE_MAIN
     };
 
     template < typename TSpec, typename TValue, typename TSize >
-    inline bool read(File<Sync<TSpec> > & me, TValue *memPtr, TSize const count) {
-//IOREV
-		return (int) me.read(memPtr, count * sizeof(TValue)) == (int) (count * sizeof(TValue));
+    inline bool read(File<Sync<TSpec> > & me, TValue *memPtr, TSize const count)
+    {
+        return (size_t)me.read(memPtr, count * sizeof(TValue)) == (size_t)(count * sizeof(TValue));
+    }
+
+    template < typename TSpec, typename TValue, typename TSize >
+    inline bool write(File<Sync<TSpec> > & me, TValue *memPtr, TSize const count)
+    {
+        return (size_t)me.write(memPtr, count * sizeof(TValue)) == (size_t)(count * sizeof(TValue));
     }
-    
+
     template < typename TSpec, typename TValue, typename TSize >
-    inline bool write(File<Sync<TSpec> > & me, TValue const *memPtr, TSize const count) {
-//IOREV
-		return (int) me.write(memPtr, count * sizeof(TValue)) == (int) (count * sizeof(TValue));
+    inline bool write(File<Sync<TSpec> > & me, TValue const *memPtr, TSize const count)
+    {
+        return (size_t)me.write(memPtr, count * sizeof(TValue)) == (size_t)(count * sizeof(TValue));
     }
 
 }
diff --git a/seqan/system/system_base.h b/seqan/system/system_base.h
index 2be3290..0228062 100644
--- a/seqan/system/system_base.h
+++ b/seqan/system/system_base.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
diff --git a/seqan/system/system_condition.h b/seqan/system/system_condition.h
new file mode 100644
index 0000000..7aa4fbe
--- /dev/null
+++ b/seqan/system/system_condition.h
@@ -0,0 +1,147 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Condition class. In conjunction with a critical section (given in the
+// c'tor) this class allows to suspend a thread until another wakes it up via
+// signal().
+// ==========================================================================
+
+#ifndef SEQAN_HEADER_SYSTEM_CONDITION_H_
+#define SEQAN_HEADER_SYSTEM_CONDITION_H_
+
+namespace seqan {
+
+#ifdef PLATFORM_WINDOWS
+
+struct Condition
+{
+    enum { Infinite = INFINITE };
+
+    CONDITION_VARIABLE  data_cond;
+    CriticalSection     *csPtr;
+
+    explicit
+    Condition(CriticalSection &cs) :
+        csPtr(&cs)
+    {
+        InitializeConditionVariable(&data_cond);
+    }
+
+    ~Condition()
+    {
+        WakeAllConditionVariable(&data_cond);
+    }
+};
+
+#else
+
+struct Condition
+{
+    enum { Infinite = LONG_MAX };
+
+    pthread_cond_t      data_cond;
+    CriticalSection     *csPtr;
+
+    explicit
+    Condition(CriticalSection &cs) :
+        csPtr(&cs)
+    {
+        int result = pthread_cond_init(&data_cond, NULL);
+        ignoreUnusedVariableWarning(result);
+        SEQAN_ASSERT_EQ(result, 0);
+    }
+
+    ~Condition()
+    {
+        int result = pthread_cond_destroy(&data_cond);
+        ignoreUnusedVariableWarning(result);
+        SEQAN_ASSERT_EQ(result, 0);
+    }
+};
+
+#endif
+
+inline void
+waitFor(Condition &cond)
+{
+#ifdef PLATFORM_WINDOWS
+    BOOL success = SleepConditionVariableCS(&cond.data_cond, &cond.csPtr->data_cs, INFINITE);
+    ignoreUnusedVariableWarning(success);
+    SEQAN_ASSERT(success);
+#else
+    int result = pthread_cond_wait(&cond.data_cond, &cond.csPtr->data_cs);
+    ignoreUnusedVariableWarning(result);
+    SEQAN_ASSERT_EQ(result, 0);
+#endif
+}
+
+inline void
+waitFor(Condition &cond, long timeoutMilliSec, bool & inProgress)
+{
+#ifdef PLATFORM_WINDOWS
+    inProgress = (SleepConditionVariableCS(&cond.data_cond, &cond.csPtr->data_cs, timeoutMilliSec) == 0);
+    if (inProgress)
+        SEQAN_ASSERT_EQ(GetLastError(), ERROR_TIMEOUT);
+#else
+    if (timeoutMilliSec != Condition::Infinite)
+    {
+        timespec ts;
+        ts.tv_sec = timeoutMilliSec / 1000;
+        ts.tv_nsec = (timeoutMilliSec % 1000) * 1000;
+        int result = pthread_cond_timedwait(&cond.data_cond, &cond.csPtr->data_cs, &ts);
+        inProgress = (result == ETIMEDOUT);
+        SEQAN_ASSERT(result == 0 || inProgress);
+    }
+    else
+    {
+        inProgress = false;
+        waitFor(cond);
+    }
+#endif
+}
+
+inline void
+signal(Condition &cond)
+{
+#ifdef PLATFORM_WINDOWS
+    WakeAllConditionVariable(&cond.data_cond);
+#else
+    int result = pthread_cond_broadcast(&cond.data_cond);
+    ignoreUnusedVariableWarning(result);
+    SEQAN_ASSERT_EQ(result, 0);
+#endif
+}
+
+}
+
+#endif  // SEQAN_HEADER_SYSTEM_CONDITION_H_
diff --git a/seqan/system/system_critical_section.h b/seqan/system/system_critical_section.h
new file mode 100644
index 0000000..1efd145
--- /dev/null
+++ b/seqan/system/system_critical_section.h
@@ -0,0 +1,109 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Critical Section class. In conjunction with a condition object it allows
+// to suspend a thread until another wakes it up.
+// ==========================================================================
+
+#ifndef SEQAN_HEADER_SYSTEM_CRITICAL_SECTION_H_
+#define SEQAN_HEADER_SYSTEM_CRITICAL_SECTION_H_
+
+namespace seqan {
+
+#ifdef PLATFORM_WINDOWS
+
+struct CriticalSection
+{
+    CRITICAL_SECTION data_cs;
+
+    CriticalSection()
+    {
+        InitializeCriticalSection(&data_cs);
+    }
+
+    ~CriticalSection()
+    {
+        DeleteCriticalSection(&data_cs);
+    }
+};
+
+#else
+
+struct CriticalSection
+{
+    pthread_mutex_t data_cs;
+
+    CriticalSection()
+    {
+        int result = pthread_mutex_init(&data_cs, NULL);
+        ignoreUnusedVariableWarning(result);
+        SEQAN_ASSERT_EQ(result, 0);
+    }
+
+    ~CriticalSection()
+    {
+        int result = pthread_mutex_destroy(&data_cs);
+        ignoreUnusedVariableWarning(result);
+        SEQAN_ASSERT_EQ(result, 0);
+    }
+};
+
+#endif
+
+inline void
+lock(CriticalSection &cs)
+{
+#ifdef PLATFORM_WINDOWS
+    EnterCriticalSection(&cs.data_cs);
+#else
+    int result = pthread_mutex_lock(&cs.data_cs);
+    ignoreUnusedVariableWarning(result);
+    SEQAN_ASSERT_EQ(result, 0);
+#endif
+}
+
+inline void
+unlock(CriticalSection &cs)
+{
+#ifdef PLATFORM_WINDOWS
+    LeaveCriticalSection(&cs.data_cs);
+#else
+    int result = pthread_mutex_unlock(&cs.data_cs);
+    ignoreUnusedVariableWarning(result);
+    SEQAN_ASSERT_EQ(result, 0);
+#endif
+}
+
+}
+
+#endif  // SEQAN_HEADER_SYSTEM_CRITICAL_SECTION_H_
diff --git a/seqan/system/system_event.h b/seqan/system/system_event.h
index 8faf3f4..9772837 100644
--- a/seqan/system/system_event.h
+++ b/seqan/system/system_event.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -60,23 +60,24 @@ struct Event        // this class mustn't exceed the size of HANDLE (needed by w
         SEQAN_DO_SYS2(open(initial), "Could not create Event");
     }
 
-    ~Event()
+    // Move constructors
+    Event(Event & other, Move) :
+        hEvent(other.hEvent)
     {
-        if (*this) SEQAN_DO_SYS2(close(), "Could not destroy Event");
+        other.hEvent = NULL;
     }
 
-    // TODO(weese): Use rvalue refs instead
-    Event(Event const & origin)
+#ifdef SEQAN_CXX11_STANDARD
+    Event(Event && other) :
+        hEvent(other.hEvent)
     {
-        // resource sharing is not yet supported (performance reason)
-        // it needs a reference counting technique
-        if (origin)
-        {
-            hEvent = origin.hEvent;
-            const_cast<Event &>(origin).hEvent = NULL;
-        }
-        else
-            hEvent = NULL;
+        other.hEvent = NULL;
+    }
+#endif
+
+    ~Event()
+    {
+        if (*this) SEQAN_DO_SYS2(close(), "Could not destroy Event");
     }
 
     inline Event & operator=(Event const & origin)
@@ -138,6 +139,13 @@ struct Event        // this class mustn't exceed the size of HANDLE (needed by w
         return hEvent != NULL;
     }
 
+private:
+
+    Event(Event const &) :
+        hEvent(NULL)
+    {
+        // we only support move construction (no copy-construction)
+    }
 };
 
 
@@ -191,27 +199,26 @@ struct Event :
         SEQAN_DO_SYS(open(initial));
     }
 
-    ~Event()
+    // Move constructors
+    Event(Event & other, Move) :
+        Mutex(other, Move()),
+        hEvent(other.hEvent)
     {
-        if (*this)
-            SEQAN_DO_SYS(close());
+        other.hEvent = NULL;
     }
 
-    // TODO(weese): Change c'tor the rvalue refs
-    //Event(Event const &&origin):
-    Event(Event const & origin) :
-        Mutex()
+#ifdef SEQAN_CXX11_STANDARD
+    Event(Event && other) :
+        hEvent(other.hEvent)
     {
-        // resource sharing is not yet supported (performance reason)
-        // it needs a reference counting technique
-        if (origin)
-        {
-            data = origin.data;
-            const_cast<Event &>(origin).hEvent = NULL;
-            hEvent = &data;
-        }
-        else
-            hEvent = NULL;
+        other.hEvent = NULL;
+    }
+#endif
+
+    ~Event()
+    {
+        if (*this)
+            SEQAN_DO_SYS(close());
     }
 
     inline Event & operator=(Event const & origin)
@@ -254,7 +261,6 @@ struct Event :
     {
         if (!hEvent) return true;
 
-        Mutex::lock();
         return pthread_cond_wait(hEvent, Mutex::hMutex) == 0;
     }
 
@@ -265,7 +271,6 @@ struct Event :
             timespec ts;
             ts.tv_sec = timeoutMilliSec / 1000;
             ts.tv_nsec = (timeoutMilliSec % 1000) * 1000;
-            Mutex::lock();
             int result = pthread_cond_timedwait(hEvent, Mutex::hMutex, &ts);
             inProgress = (result == ETIMEDOUT);
             return result == 0 || inProgress;
@@ -287,10 +292,20 @@ struct Event :
         return hEvent != NULL;
     }
 
+private:
+
+    Event(Event const &) :
+        Mutex(),
+        hEvent(NULL)
+    {
+        // we only support move construction (no copy-construction)
+    }
 };
 
 #endif
 
+template <>
+struct HasMoveConstructor<Event> : True {};
 
 //////////////////////////////////////////////////////////////////////////////
 // global event functions
@@ -323,7 +338,7 @@ inline bool waitFor(Event & e, TTime timeoutMilliSec, bool & inProgress)
     bool b = e.wait(timeoutMilliSec, inProgress);
     double end = sysTime();
     if (begin != end)
-        ::std::cerr << "waitTime: " << end - begin << ::std::endl;
+        std::cerr << "waitTime: " << end - begin << std::endl;
     return b;
 
         #else
@@ -342,7 +357,7 @@ inline bool signal(Event & e)
     // emulate events in a singlethreaded environment
 
     struct DummyEvent {
-        typedef	void Handle;
+        typedef    void Handle;
         DummyEvent(bool initial = false) {}
         inline bool wait(unsigned timeOut = NULL) { return true; }
         inline void reset() {}
diff --git a/seqan/system/system_forwards.h b/seqan/system/system_forwards.h
index 495e84f..8ef970b 100644
--- a/seqan/system/system_forwards.h
+++ b/seqan/system/system_forwards.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -32,8 +32,8 @@
 // Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
 
-#ifndef SEQAN_HEADER_SYSTEM_MANUAL_FORWARDS_H 
-#define SEQAN_HEADER_SYSTEM_MANUAL_FORWARDS_H 
+#ifndef SEQAN_HEADER_SYSTEM_MANUAL_FORWARDS_H
+#define SEQAN_HEADER_SYSTEM_MANUAL_FORWARDS_H
 
 //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
 
@@ -46,22 +46,17 @@ namespace SEQAN_NAMESPACE_MAIN {
 //____________________________________________________________________________
 // Event
 
-struct Event;       	// "core/include/seqan/system/system_event.h"(18)
+struct Event;           // "include/seqan/system/system_event.h"(18)
 
 //____________________________________________________________________________
 // Mutex
 
-struct Mutex;       	// "core/include/seqan/system/system_mutex.h"(16)
-
-//____________________________________________________________________________
-// Semaphore
-
-struct Semaphore;       	// "core/include/seqan/system/system_sema.h"(16)
+struct Mutex;           // "include/seqan/system/system_mutex.h"(16)
 
 //____________________________________________________________________________
 // Thread
 
-template <typename Worker> struct Thread;       	// "core/include/seqan/system/system_thread.h"(18)
+template <typename Worker> struct Thread;           // "include/seqan/system/system_thread.h"(18)
 //IOREV _todo_
 
 
@@ -73,50 +68,50 @@ template <typename Worker> struct Thread;       	// "core/include/seqan/system/s
 //____________________________________________________________________________
 // close
 
-inline bool close(Event &e);       	// "core/include/seqan/system/system_event.h"(109)
-inline bool close(Mutex &m);       	// "core/include/seqan/system/system_mutex.h"(79)
-template <typename TWorker> inline bool close(Thread<TWorker> &m);       	// "core/include/seqan/system/system_thread.h"(97)
+inline bool close(Event &e);           // "include/seqan/system/system_event.h"(109)
+inline bool close(Mutex &m);           // "include/seqan/system/system_mutex.h"(79)
+template <typename TWorker> inline bool close(Thread<TWorker> &m);           // "include/seqan/system/system_thread.h"(97)
 
 //____________________________________________________________________________
 // kill
 
-template <typename TWorker> inline bool kill(Thread<TWorker> &m);       	// "core/include/seqan/system/system_thread.h"(102)
+template <typename TWorker> inline bool kill(Thread<TWorker> &m);           // "include/seqan/system/system_thread.h"(102)
 
 //____________________________________________________________________________
 // lock
 
-inline bool lock(Mutex &m);       	// "core/include/seqan/system/system_mutex.h"(83)
+inline bool lock(Mutex &m);           // "include/seqan/system/system_mutex.h"(83)
 
 //____________________________________________________________________________
 // open
 
-inline bool open(Event &e, bool initial);       	// "core/include/seqan/system/system_event.h"(101)
-inline bool open(Event &e);       	// "core/include/seqan/system/system_event.h"(105)
-inline bool open(Mutex &m, bool initial);       	// "core/include/seqan/system/system_mutex.h"(71)
-inline bool open(Mutex &m);       	// "core/include/seqan/system/system_mutex.h"(75)
-template <typename TWorker> inline bool open(Thread<TWorker> &m);       	// "core/include/seqan/system/system_thread.h"(87)
+inline bool open(Event &e, bool initial);           // "include/seqan/system/system_event.h"(101)
+inline bool open(Event &e);           // "include/seqan/system/system_event.h"(105)
+inline bool open(Mutex &m, bool initial);           // "include/seqan/system/system_mutex.h"(71)
+inline bool open(Mutex &m);           // "include/seqan/system/system_mutex.h"(75)
+template <typename TWorker> inline bool open(Thread<TWorker> &m);           // "include/seqan/system/system_thread.h"(87)
 
 //____________________________________________________________________________
 // run
 
-template <typename TWorker> inline bool run(Thread<TWorker> &m);       	// "core/include/seqan/system/system_thread.h"(92)
+template <typename TWorker> inline bool run(Thread<TWorker> &m);           // "include/seqan/system/system_thread.h"(92)
 
 //____________________________________________________________________________
 // signal
 
-inline bool signal(Event &e);       	// "core/include/seqan/system/system_event.h"(131)
+inline bool signal(Event &e);           // "include/seqan/system/system_event.h"(131)
 
 //____________________________________________________________________________
 // unlock
 
-inline bool unlock(Mutex &m);       	// "core/include/seqan/system/system_mutex.h"(87)
+inline bool unlock(Mutex &m);           // "include/seqan/system/system_mutex.h"(87)
 
 //____________________________________________________________________________
 // waitFor
 
-inline bool waitFor(Event &e);       	// "core/include/seqan/system/system_event.h"(113)
-template <typename TTime > inline bool waitFor(Event &e, TTime timeoutMilliSec, bool &inProgress);       	// "core/include/seqan/system/system_event.h"(118)
-template <typename TWorker> inline bool waitFor(Thread<TWorker> &m);       	// "core/include/seqan/system/system_thread.h"(107)
+inline bool waitFor(Event &e);           // "include/seqan/system/system_event.h"(113)
+template <typename TTime > inline bool waitFor(Event &e, TTime timeoutMilliSec, bool &inProgress);           // "include/seqan/system/system_event.h"(118)
+template <typename TWorker> inline bool waitFor(Thread<TWorker> &m);           // "include/seqan/system/system_thread.h"(107)
 
 } //namespace SEQAN_NAMESPACE_MAIN
 
diff --git a/seqan/system/system_mutex.h b/seqan/system/system_mutex.h
index 492fc84..96facd7 100644
--- a/seqan/system/system_mutex.h
+++ b/seqan/system/system_mutex.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -61,6 +61,21 @@ namespace SEQAN_NAMESPACE_MAIN
             SEQAN_DO_SYS2(open(initial), "Could not create Mutex");
         }
 
+        // Move constructors
+        Mutex(Mutex & other, Move) :
+            hMutex(other.hMutex)
+        {
+            other.hMutex = NULL;
+        }
+
+#ifdef SEQAN_CXX11_STANDARD
+        Mutex(Mutex && other) :
+            hMutex(other.hMutex)
+        {
+            other.hMutex = NULL;
+        }
+#endif
+
         ~Mutex() {
             if (*this)
                 SEQAN_DO_SYS2(close(), "Could not destroy Mutex");
@@ -72,8 +87,8 @@ namespace SEQAN_NAMESPACE_MAIN
 
         inline bool close() {
             bool success = CloseHandle(hMutex);
-			hMutex = NULL;
-			return success;
+            hMutex = NULL;
+            return success;
         }
 
         inline bool lock(DWORD timeoutMilliSec = INFINITE) {
@@ -90,27 +105,45 @@ namespace SEQAN_NAMESPACE_MAIN
 
     private:
 
-        Mutex(Mutex const &) {
-            // resource copying is not yet supported (performance reason)
-            // it needs a reference counting technique
+        Mutex(Mutex const &) :
+            hMutex(NULL)
+        {
+            // we only support move construction (no copy-construction)
         }
     };
-    
+
 #else
 
     struct Mutex
     {
         typedef pthread_mutex_t* Handle;
-        
+
         pthread_mutex_t data, *hMutex;
 
         Mutex():
-            hMutex(NULL) {}
+            hMutex(NULL)
+        {}
 
-        Mutex(bool initial) {
+        Mutex(bool initial)
+        {
             SEQAN_DO_SYS(open(initial));
         }
 
+        // Move constructors
+        Mutex(Mutex & other, Move) :
+            hMutex(other.hMutex)
+        {
+            other.hMutex = NULL;
+        }
+
+#ifdef SEQAN_CXX11_STANDARD
+        Mutex(Mutex && other) :
+            hMutex(other.hMutex)
+        {
+            other.hMutex = NULL;
+        }
+#endif
+
         ~Mutex() {
             if (*this)
                 SEQAN_DO_SYS(close());
@@ -126,9 +159,9 @@ namespace SEQAN_NAMESPACE_MAIN
         }
 
         inline bool close() {
-			bool success = (pthread_mutex_destroy(hMutex) == 0);
-			hMutex = NULL;
-			return success;
+            bool success = (pthread_mutex_destroy(hMutex) == 0);
+            hMutex = NULL;
+            return success;
         }
 
         inline bool lock() {
@@ -145,38 +178,41 @@ namespace SEQAN_NAMESPACE_MAIN
 
     private:
 
-        Mutex(Mutex const &) {
-            // resource copying is not yet supported (performance reason)
-            // it needs a reference counting technique
+        Mutex(Mutex const &) :
+            hMutex(NULL)
+        {
+            // we only support move construction (no copy-construction)
         }
 
     };
-    
+
 #endif
 
+    template <>
+    struct HasMoveConstructor<Mutex> : True {};
 
-	//////////////////////////////////////////////////////////////////////////////
-	// global mutex functions
+    //////////////////////////////////////////////////////////////////////////////
+    // global mutex functions
 
-	inline bool open(Mutex &m, bool initial) {
-		return m.open(initial);
-	}
+    inline bool open(Mutex &m, bool initial) {
+        return m.open(initial);
+    }
 
-	inline bool open(Mutex &m) {
-		return open(m, false);
-	}
+    inline bool open(Mutex &m) {
+        return open(m, false);
+    }
 
-	inline bool close(Mutex &m) {
-		return m.close();
-	}
+    inline bool close(Mutex &m) {
+        return m.close();
+    }
 
-	inline bool lock(Mutex &m) {
-		return m.lock();
-	}
+    inline bool lock(Mutex &m) {
+        return m.lock();
+    }
 
-	inline bool unlock(Mutex &m) {
-		return m.unlock();
-	}
+    inline bool unlock(Mutex &m) {
+        return m.unlock();
+    }
 
 }
 
diff --git a/seqan/system/system_sema.h b/seqan/system/system_sema.h
deleted file mode 100644
index 50be700..0000000
--- a/seqan/system/system_sema.h
+++ /dev/null
@@ -1,141 +0,0 @@
-// ==========================================================================
-//                 SeqAn - The Library for Sequence Analysis
-// ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above copyright
-//       notice, this list of conditions and the following disclaimer in the
-//       documentation and/or other materials provided with the distribution.
-//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
-//       its contributors may be used to endorse or promote products derived
-//       from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
-// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-// DAMAGE.
-//
-// ==========================================================================
-// Author: David Weese <david.weese@fu-berlin.de>
-// ==========================================================================
-
-//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
-
-#ifndef SEQAN_HEADER_SYSTEM_SEMAPHORE_H
-#define SEQAN_HEADER_SYSTEM_SEMAPHORE_H
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-#ifdef PLATFORM_WINDOWS
-
-    static SECURITY_ATTRIBUTES SemaphoreDefaultAttributes = {
-        sizeof(SECURITY_ATTRIBUTES),
-        NULL,
-        true
-    };
-
-    struct Semaphore
-    {
-        typedef LONG Type;
-        typedef HANDLE Handle;
-        enum { MAX_VALUE = MAXLONG };
-        
-        Handle hSemaphore;
-
-        Semaphore(Type init = 0, Type max = MAX_VALUE)
-        {
-            hSemaphore = CreateSemaphore(&SemaphoreDefaultAttributes, init, max, NULL);
-            SEQAN_ASSERT_MSG(hSemaphore != NULL, "Could not create Semaphore!");
-        }
-
-        ~Semaphore()
-        {
-            int res = CloseHandle(hSemaphore);
-            (void)res;  // Only used in assertion.
-            SEQAN_ASSERT_MSG(res != 0, "Could not destroy Semaphore!");
-        }
-
-        bool lock(DWORD timeoutMilliSec = INFINITE) {
-            return WaitForSingleObject(hSemaphore, timeoutMilliSec) != WAIT_TIMEOUT;
-        }
-
-        void unlock()
-        {
-            int res = ReleaseSemaphore(hSemaphore, 1, NULL);
-            (void)res;  // Only used in assertion.
-            SEQAN_ASSERT_MSG(res != 0, "Could not unlock Semaphore!");
-        }
-
-    private:
-
-        Semaphore(Semaphore const &) {
-            // resource copying is not yet supported (performance reason)
-            // it needs a reference counting technique
-        }
-
-    };
-
-#else
-
-    struct Semaphore
-    {
-        typedef unsigned int Type;
-        typedef sem_t* Handle;
-
-        sem_t data, *hSemaphore;
-
-        Semaphore(Type init = 0):
-            hSemaphore(&data)
-        {
-            bool res = !sem_init(hSemaphore, 0, init);
-            (void)res;  // Only used in assertion.
-            SEQAN_ASSERT(res);
-        }
-
-        ~Semaphore() {
-            bool res = sem_destroy(hSemaphore);
-            (void)res;  // Only used in assertion.
-            SEQAN_ASSERT(res);
-        }
-
-        void lock() {
-            bool res = !sem_wait(hSemaphore);
-            (void)res;  // Only used in assertion.
-            SEQAN_ASSERT(res);
-        }
-
-        void unlock() {
-            bool res = !sem_post(hSemaphore);
-            (void)res;  // Only used in assertion.
-            SEQAN_ASSERT(res);
-        }
-
-    private:
-
-        Semaphore(Semaphore const &) {
-            // resource copying is not yet supported (performance reason)
-            // it needs a reference counting technique
-        }
-
-    };
-
-
-#endif
-
-}
-
-#endif
diff --git a/seqan/system/system_thread.h b/seqan/system/system_thread.h
index 31c64d5..75717de 100644
--- a/seqan/system/system_thread.h
+++ b/seqan/system/system_thread.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -51,18 +51,27 @@ namespace SEQAN_NAMESPACE_MAIN
     template <typename Worker>
     struct Thread
     {
-//IOREV _notio_
         typedef HANDLE Handle;
 
         Handle hThread;
         DWORD  hThreadID;
         Worker worker;
 
-        Thread() {}
+        Thread() :
+            hThread()
+        {}
 
         template <typename TArg>
         Thread(TArg &arg):
-            worker(arg) {}
+            hThread(),
+            worker(arg)
+        {}
+
+        template <typename TArg>
+        Thread(TArg const &arg):
+            hThread(),
+            worker(arg)
+        {}
 
         ~Thread() {
             if (*this) {
@@ -73,18 +82,18 @@ namespace SEQAN_NAMESPACE_MAIN
 
         inline bool open(BOOL initital = false) {
             return hThread = CreateThread(
-                &ThreadDefaultAttributes,    // default security attributes 
-                0,                           // use default stack size  
-                &_start,                     // thread function 
-                this,                        // argument to thread function 
-                0,                           // use default creation flags 
-                &hThreadID);                 // returns the thread identifier 
+                &ThreadDefaultAttributes,    // default security attributes
+                0,                           // use default stack size
+                &_start,                     // thread function
+                this,                        // argument to thread function
+                0,                           // use default creation flags
+                &hThreadID);                 // returns the thread identifier
         }
 
         inline bool close() {
             if (CloseHandle(hThread)) return true;
-			hThread = NULL;
-			return false;
+            hThread = NULL;
+            return false;
         }
 
         inline bool cancel(DWORD exitCode = 0) {
@@ -107,45 +116,44 @@ namespace SEQAN_NAMESPACE_MAIN
         }
 
         static DWORD WINAPI _start(LPVOID _this) {
-            reinterpret_cast<Thread*>(_this)->worker.run(&reinterpret_cast<Thread*>(_this));
-			return 0;	// return value should indicate success/failure
+            reinterpret_cast<Thread*>(_this)->worker();
+            return 0;    // return value should indicate success/failure
         }
     };
-    
+
 #else
 
     template <typename Worker>
     struct Thread
     {
-//IOREV _notio_
-        typedef pthread_t* Handle;
+        pthread_t   data;
+        pthread_t   *hThread;
+        Worker      worker;
 
-        pthread_t data, *hThread;
-        Worker worker;
+        Thread() : data(), hThread(), worker()
+        {}
 
-        Thread() {}
+        template <typename TArg>
+        Thread(TArg & arg) : data(), hThread(), worker(arg)
+        {}
 
         template <typename TArg>
-        Thread(TArg &arg):
-            worker(arg) {}
+        Thread(TArg const & arg) : data(), hThread(), worker(arg)
+        {}
 
-        ~Thread() {
-            if (*this) {
-                cancel();
-                wait();
-            }
+        ~Thread()
+        {
+            if (*this)
+                close();
         }
 
         inline bool open()
         {
-            if (!pthread_create(&data, NULL, _start, this) && (hThread = &data)) {
-                return true;
-            } else
-                return false;
+            return !pthread_create(&data, NULL, _start, this) && (hThread = &data);
         }
 
         inline bool close() {
-            return cancel() && wait() && !(hThread == NULL);
+            return cancel() && wait() && !(hThread = NULL);
         }
 
         inline bool cancel() {
@@ -153,11 +161,11 @@ namespace SEQAN_NAMESPACE_MAIN
         }
 
         inline bool wait() {
-            return !(pthread_join(data, NULL));
+            return !(pthread_join(data, NULL)) && !(hThread = NULL);
         }
 
         inline bool wait(void* &retVal) {
-            return !(pthread_join(data, &retVal));
+            return !(pthread_join(data, &retVal)) && !(hThread = NULL);
         }
 
         inline bool detach() {
@@ -176,41 +184,41 @@ namespace SEQAN_NAMESPACE_MAIN
         }
 
         static void* _start(void* _this) {
-            reinterpret_cast<Thread*>(_this)->worker.run(&reinterpret_cast<Thread*>(_this));
-			return 0;
+            reinterpret_cast<Thread*>(_this)->worker();
+            return 0;
         }
     };
-    
+
 #endif
 
 
-	//////////////////////////////////////////////////////////////////////////////
-	// global thread functions
+    //////////////////////////////////////////////////////////////////////////////
+    // global thread functions
 
-	template <typename TWorker>
-	inline bool open(Thread<TWorker> &m) {
-		return m.open();
-	}
+    template <typename TWorker>
+    inline bool open(Thread<TWorker> &m) {
+        return m.open();
+    }
 
-	template <typename TWorker>
-	inline bool run(Thread<TWorker> &m) {
-		return m.open();
-	}
+    template <typename TWorker>
+    inline bool run(Thread<TWorker> &m) {
+        return m.open();
+    }
 
-	template <typename TWorker>
-	inline bool close(Thread<TWorker> &m) {
-		return m.close();
-	}
+    template <typename TWorker>
+    inline bool close(Thread<TWorker> &m) {
+        return m.close();
+    }
 
-	template <typename TWorker>
-	inline bool kill(Thread<TWorker> &m) {
-		return m.close();
-	}
+    template <typename TWorker>
+    inline bool kill(Thread<TWorker> &m) {
+        return m.close();
+    }
 
-	template <typename TWorker>
-	inline bool waitFor(Thread<TWorker> &m) {
-		return m.wait();
-	}
+    template <typename TWorker>
+    inline bool waitFor(Thread<TWorker> &m) {
+        return m.wait();
+    }
 
 }
 
diff --git a/seqan/tabix_io.h b/seqan/tabix_io.h
new file mode 100644
index 0000000..88f61da
--- /dev/null
+++ b/seqan/tabix_io.h
@@ -0,0 +1,59 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// Facade header for module tabix_io.
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_TABIX_IO_H_
+#define INCLUDE_SEQAN_TABIX_IO_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/basic.h>
+#include <seqan/file.h>
+#include <seqan/sequence.h>
+#include <seqan/stream.h>
+#include <seqan/misc/name_store_cache.h>
+
+// ===========================================================================
+// Tabix index
+// ===========================================================================
+
+// Tabix indices are only available when ZLIB is available.
+#if SEQAN_HAS_ZLIB
+#include <seqan/tabix_io/tabix_index_tbi.h>
+#endif  // #if SEQAN_HAS_ZLIB
+
+#endif  // INCLUDE_SEQAN_TABIX_IO_H_
diff --git a/seqan/tabix_io/tabix_index_tbi.h b/seqan/tabix_io/tabix_index_tbi.h
new file mode 100644
index 0000000..713e4f8
--- /dev/null
+++ b/seqan/tabix_io/tabix_index_tbi.h
@@ -0,0 +1,529 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+// (Read-only) Tabix index support.
+//
+// A Tabix index (Heng Li) allows to randomly seek in a tab-seperated genome
+// related file, e.g. VCF, GFF, SAM, BED, etc. The corresponding file only
+// needs to be sorted by chromosomal position in advance and optionally
+// compressed with 'bgzip'. The resulting file must be indexed with 'tabix'.
+//
+// TODOs:
+//  - clean jumpToRegion(), I simply adapted the one from bam_index.h
+//  - implement Tabix index creation (and BAM index creation as well)
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_TABIX_IO_TABIX_INDEX_TBI_H_
+#define INCLUDE_SEQAN_TABIX_IO_TABIX_INDEX_TBI_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+class TabixIndex;
+bool open(TabixIndex & index, char const * filename);
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Helper Class TabixIndexBinData_
+// ----------------------------------------------------------------------------
+
+// Store the information of a bin.
+
+struct TabixIndexBinData_
+{
+    String<Pair<__uint64, __uint64> > chunkBegEnds;
+};
+
+// ----------------------------------------------------------------------------
+// Helper Class TabixRecord_
+// ----------------------------------------------------------------------------
+
+struct TabixRecord_
+{
+    CharString refName;
+    __int32 posBeg;
+    __int32 posEnd;
+};
+
+// ----------------------------------------------------------------------------
+// Class TabixIndex
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class TabixIndex
+ * @headerfile <seqan/tabix_io.h>
+ * @brief Access to Tabix indexed files.
+ *
+ * @signature class TabixIndex;
+ */
+
+/*!
+ * @fn TabixIndex::TabixIndex
+ * @brief Constructor.
+ *
+ * @signature TabixIndex::TabixIndex();
+ *
+ * @section Remarks
+ *
+ * Only the default constructor is provided.
+ */
+
+class TabixIndex
+{
+public:
+    typedef std::map<__uint32, TabixIndexBinData_> TBinIndex_;
+    typedef String<__uint64> TLinearIndex_;
+    typedef StringSet<CharString, Owner<ConcatDirect<> > > TNameStore;
+
+    __int32 format;             // Format (0: generic; 1: SAM; 2: VCF)
+    __int32 colSeq;             // Column for the sequence name
+    __int32 colBeg;             // Column for the start of a region
+    __int32 colEnd;             // Column for the end of a region
+    __int32 meta;               // Leading character for comment lines
+    __int32 skip;               // # lines to skip at the beginning
+    __uint64 unalignedCount;    // # unmapped reads without coordinates set
+
+    // 1<<14 is the size of the minimum bin.
+    static const __int32 BAM_LIDX_SHIFT = 14;
+
+    String<TBinIndex_>          _binIndices;
+    String<TLinearIndex_>       _linearIndices;
+    TNameStore                  _nameStore;
+    NameStoreCache<TNameStore>  _nameStoreCache;
+
+    TabixIndex() :
+        format(0),
+        colSeq(1),
+        colBeg(2),
+        colEnd(3),
+        meta('#'),
+        skip(0),
+        unalignedCount(maxValue<__uint64>()),
+        _nameStoreCache(_nameStore)
+    {}
+
+    TabixIndex(char const * fileName) :
+        format(0),
+        colSeq(1),
+        colBeg(2),
+        colEnd(3),
+        meta('#'),
+        skip(0),
+        unalignedCount(maxValue<__uint64>()),
+        _nameStoreCache(_nameStore)
+    {
+        if (!open(*this, fileName))
+            SEQAN_THROW(FileOpenError(fileName));
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function _tbiReg2bins()
+// ----------------------------------------------------------------------------
+
+static inline void
+_tbiReg2bins(String<__uint16> & list, __uint32 beg, __uint32 end)
+{
+    unsigned k;
+    if (beg >= end) return;
+    if (end >= 1u<<29) end = 1u<<29;
+    --end;
+    appendValue(list, 0);
+    for (k =    1 + (beg>>26); k <=    1 + (end>>26); ++k) appendValue(list, k);
+    for (k =    9 + (beg>>23); k <=    9 + (end>>23); ++k) appendValue(list, k);
+    for (k =   73 + (beg>>20); k <=   73 + (end>>20); ++k) appendValue(list, k);
+    for (k =  585 + (beg>>17); k <=  585 + (end>>17); ++k) appendValue(list, k);
+    for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) appendValue(list, k);
+}
+
+// ----------------------------------------------------------------------------
+// Function _readTabixRecord()
+// ----------------------------------------------------------------------------
+
+template <typename TIter>
+bool _readTabixRecord(TabixRecord_ & record, CharString & buffer, TIter & iter, TabixIndex const & index)
+{
+    clear(record.refName);
+    record.posBeg = 0;
+    record.posEnd = 0;
+
+    // Skip comment lines.
+    while (!atEnd(iter) && *iter == (char)index.meta)
+        skipLine(iter);
+
+    if (atEnd(iter))
+        return false;
+    
+    // Extract columns.
+    __int32 maxCol = std::max(index.colSeq, std::max(index.colBeg, index.colEnd));
+    for (__int32 col = 1; col <= maxCol; ++col)
+    {
+        // Read column.
+        clear(buffer);
+        if (col < maxCol)
+        {
+            readUntil(buffer, iter, IsTab());
+            skipOne(iter, IsTab());
+        }
+        else
+        {
+            readUntil(buffer, iter, OrFunctor<IsTab, IsNewline>());
+        }
+        
+        if (col == index.colSeq)
+            record.refName = buffer;
+        else if (col == index.colBeg)
+            record.posBeg = lexicalCast<__int32>(buffer);
+        else if (col == index.colEnd)
+            record.posEnd = lexicalCast<__int32>(buffer);
+    }
+
+    if (index.colEnd == 0 || index.colEnd == index.colBeg)
+        record.posEnd = record.posBeg + 1;
+    
+    // all text-based file formats are 1-based (we use 0-based positions internally)
+    --record.posBeg;
+    --record.posEnd;
+    
+    // Go to next line.
+    skipLine(iter);
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function jumpToRegion()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn TabixIndex#jumpToRegion
+ * @brief Seek in a tab-separated genome related file using a Tabix index.
+ *
+ * You provide a region <tt>[posBeg, posEnd)</tt> on the contig <tt>refName</tt> that you want to jump to and the function
+ * jumps to the first entry in this region, if any.
+ *
+ * @signature bool jumpToRegion(fileIn, hasEntries, refName, posBeg, posEnd, index[, firstMatch]);
+ *
+ * @param[in,out] fileIn        The @link VcfFileIn @endlink, @link GffFileIn @endlink, or @link BedFileIn @endlink to jump with.
+ * @param[out]    hasEntries    A <tt>bool</tt> that is set true if the region <tt>[posBeg, posEnd)</tt> has any
+ *                              entries.
+ * @param[in]     refName       The reference name to jump to.
+ * @param[in]     posBeg        The begin of the region to jump to (<tt>__int32</tt>).
+ * @param[in]     posEnd        The end of the region to jump to (<tt>__int32</tt>).
+ * @param[in]     index         The @link TabixIndex @endlink to use for the jumping.
+ * @param[in]     firstMatch    A <tt>bool</tt>, if <tt>true</tt> (default) this function seeks to the first
+ *                              overlapping record. Otherwise, the function potentially stops before the first
+ *                              overlapping record.
+ *
+ * @return bool true if seeking was successful, false if not.
+ *
+ * @section Remarks
+ *
+ * This function fails if <tt>refName</tt>/<tt>pos</tt> wasn't found.
+ */
+
+template <typename TFileFormat, typename TSpec, typename TName>
+inline bool
+jumpToRegion(FormattedFile<TFileFormat, Input, TSpec> & fileIn,
+             bool & hasEntries,
+             TName const & refName,
+             __int32 posBeg,
+             __int32 posEnd,
+             TabixIndex const & index,
+             bool firstMatch = true)
+{
+    hasEntries = false;
+
+    // Get id of given contig name
+    unsigned refId = 0;
+    if (!getIdByName(refId, index._nameStoreCache, refName))
+        return false;
+
+    // ------------------------------------------------------------------------
+    // Compute offset in BGZF file.
+    // ------------------------------------------------------------------------
+    __uint64 offset = MaxValue<__uint64>::VALUE;
+
+    // Retrieve the candidate bin identifiers for [posBeg, posEnd).
+    String<__uint16> candidateBins;
+    _tbiReg2bins(candidateBins, posBeg, posEnd);
+
+    // Retrieve the smallest required offset from the linear index.
+    unsigned windowIdx = posBeg >> 14;  // Linear index consists of 16kb windows.
+    __uint64 linearMinOffset = 0;
+    if (windowIdx >= length(index._linearIndices[refId]))
+    {
+        // TODO(holtgrew): Can we simply always take case 1?
+
+        // This is the case were we want to jump in a non-existing window.
+        //
+        // If there are no linear indices for this reference then we use the linear min offset of the next
+        // reference that has an linear index.
+        if (empty(index._linearIndices[refId]))
+        {
+            for (unsigned i = refId; i < length(index._linearIndices); ++i)
+            {
+                if (!empty(index._linearIndices[i]))
+                {
+                    linearMinOffset = front(index._linearIndices[i]);
+                    if (linearMinOffset != 0u)
+                        break;
+                    for (unsigned j = 1; j < length(index._linearIndices[i]); ++j)
+                    {
+                        if (index._linearIndices[i][j] > linearMinOffset)
+                        {
+                            linearMinOffset = index._linearIndices[i][j];
+                            break;
+                        }
+                    }
+                    if (linearMinOffset != 0u)
+                        break;
+                }
+            }
+        }
+        else
+        {
+            linearMinOffset = back(index._linearIndices[refId]);
+        }
+    }
+    else
+    {
+        linearMinOffset = index._linearIndices[refId][windowIdx];
+    }
+
+    // Combine candidate bins and smallest required offset from linear index into candidate offset.
+    typedef std::set<__uint64> TOffsetCandidates;
+    TOffsetCandidates offsetCandidates;
+    typedef typename Iterator<String<__uint16>, Rooted>::Type TCandidateIter;
+    for (TCandidateIter it = begin(candidateBins, Rooted()); !atEnd(it); goNext(it))
+    {
+        typedef typename std::map<__uint32, TabixIndexBinData_>::const_iterator TMapIter;
+        TMapIter mIt = index._binIndices[refId].find(*it);
+        if (mIt == index._binIndices[refId].end())
+            continue;  // Candidate is not in index!
+
+        typedef typename Iterator<String<Pair<__uint64, __uint64> > const, Rooted>::Type TBegEndIter;
+        for (TBegEndIter it2 = begin(mIt->second.chunkBegEnds, Rooted()); !atEnd(it2); goNext(it2))
+            if (it2->i2 >= linearMinOffset)
+                offsetCandidates.insert(it2->i1);
+    }
+
+    // Search through candidate offsets, find rightmost possible.
+    //
+    // Note that it is not necessarily the first.
+    //
+    // TODO(holtgrew): Can this be optimized similar to how bamtools does it?
+    typedef typename TOffsetCandidates::const_iterator TOffsetCandidateIter;
+
+    CharString buffer;
+    TabixRecord_ record;
+    for (TOffsetCandidateIter candIt = offsetCandidates.begin(); candIt != offsetCandidates.end(); ++candIt)
+    {
+        setPosition(fileIn, *candIt);
+
+        if (!_readTabixRecord(record, buffer, fileIn.iter, index))
+            break;
+
+        if (record.refName != refName)
+            continue;  // Wrong contig.
+        
+        if (!hasEntries || record.posBeg <= posBeg)
+        {
+            // Found a valid record.
+            hasEntries = true;
+            offset = *candIt;
+        }
+
+        if (record.posBeg >= posEnd)
+            break;  // Cannot find overlapping any more.
+    }
+
+    if (offset != MaxValue<__uint64>::VALUE)
+    {
+        setPosition(fileIn, offset);
+        
+        if (firstMatch)
+        {
+            // skip to the first overlapping record
+            while (!atEnd(fileIn) && !(posBeg < record.posEnd && record.posBeg < posEnd))
+            {
+                offset = position(fileIn);
+                _readTabixRecord(record, buffer, fileIn.iter, index);
+                if (record.posBeg >= posEnd)
+                {
+                    hasEntries = false;
+                    return true;
+                }
+            }
+            setPosition(fileIn, offset);
+        }
+    }
+
+    // Finding no overlapping records is not an error, hasEntries is false.
+    return true;
+}
+
+// ----------------------------------------------------------------------------
+// Function getUnalignedCount()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn TabixIndex#getUnalignedCount
+ * @brief Query index for number of unaligned reads.
+ *
+ * @signature __uint64 getUnalignedCount(index);
+ *
+ * @param[in] index     Index to query.
+ * @return    __uint64  The number of unaligned reads.
+ */
+
+inline __uint64
+getUnalignedCount(TabixIndex const & index)
+{
+    return index.unalignedCount;
+}
+
+// ----------------------------------------------------------------------------
+// Function open()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn TabixIndex#open
+ * @brief Load a Tabix index from file.
+ * @signature bool open(index, filename);
+
+ * @param[in,out] index    Target data structure.
+ * @param[in]     filename Path to file to load. Types: char const *
+ *
+ * @return        bool     Returns <tt>true</tt> on success, false otherwise.
+ */
+
+inline bool
+open(TabixIndex & index, char const * filename)
+{
+    typedef VirtualStream<char, Input> TInStream;
+    
+    TInStream tbi;
+    if (!open(tbi, filename))
+        return false;  // Could not open file.
+
+    DirectionIterator<TInStream, Input>::Type iter = directionIterator(tbi, Input());
+
+    // Read magic header.
+    String<char, Array<4> > magic;
+    read(magic, iter, 4);
+    if (magic != "TBI\1")
+        SEQAN_THROW(ParseError("Not in TBI format."));
+
+    // Read parameters.
+    __int32 nRef = 0;
+    readRawPod(nRef, iter);
+    readRawPod(index.format, iter);
+    readRawPod(index.colSeq, iter);
+    readRawPod(index.colBeg, iter);
+    readRawPod(index.colEnd, iter);
+    readRawPod(index.meta, iter);
+    readRawPod(index.skip, iter);
+
+    // Read concatenated names.
+    __int32 lNm = 0;
+    CharString tmp;
+    readRawPod(lNm, iter);
+    read(tmp, iter, lNm);
+
+    // Split concatenated names at \0's.
+    clear(index._nameStore);
+    strSplit(index._nameStore, tmp, EqualsChar<'\0'>(), true, nRef - 1);
+    refresh(index._nameStoreCache);
+
+    clear(index._linearIndices);
+    clear(index._binIndices);
+    resize(index._linearIndices, nRef);
+    resize(index._binIndices, nRef);
+
+    TabixIndexBinData_ data;
+    for (int i = 0; i < nRef; ++i)  // For each reference.
+    {
+        // Read bin index.
+        __int32 nBin = 0;
+        readRawPod(nBin, iter);
+
+        for (int j = 0; j < nBin; ++j)  // For each bin.
+        {
+            __uint32 bin = 0;
+            __int32 nChunk = 0;
+            readRawPod(bin, iter);
+            readRawPod(nChunk, iter);
+
+            resize(data.chunkBegEnds, nChunk);
+            for (int k = 0; k < nChunk; ++k)  // For each chunk;
+            {
+                readRawPod(data.chunkBegEnds[k].i1, iter);
+                readRawPod(data.chunkBegEnds[k].i2, iter);
+            }
+
+            // Copy bin data into index.
+            index._binIndices[i][bin] = data;
+        }
+
+        // Read linear index.
+        __int32 nIntv = 0;
+        readRawPod(nIntv, iter);
+
+        resize(index._linearIndices[i], nIntv);
+        for (int j = 0; j < nIntv; ++j)
+            readRawPod(index._linearIndices[i][j], iter);
+    }
+
+
+    // Read (optional) number of alignments without coordinate.
+    if (!atEnd(iter))
+        readRawPod(index.unalignedCount, iter);
+    else
+        index.unalignedCount = maxValue<__uint64>();
+
+    return true;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef INCLUDE_SEQAN_TABIX_IO_TABIX_INDEX_TBI_H_
diff --git a/seqan/translation.h b/seqan/translation.h
new file mode 100644
index 0000000..9ae5202
--- /dev/null
+++ b/seqan/translation.h
@@ -0,0 +1,48 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// ==========================================================================
+// Code for Dna(5) to AminoAcid Translation
+// ==========================================================================
+
+
+#ifndef INCLUDE_SEQAN_TRANSLATION_H_
+#define INCLUDE_SEQAN_TRANSLATION_H_
+
+#include <seqan/basic.h>
+#include <seqan/sequence.h>
+#include <seqan/parallel.h>
+
+#include <seqan/translation/translation_tables.h>
+#include <seqan/translation/translation.h>
+
+#endif
diff --git a/seqan/translation/translation.h b/seqan/translation/translation.h
new file mode 100644
index 0000000..c1ee782
--- /dev/null
+++ b/seqan/translation/translation.h
@@ -0,0 +1,683 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// ==========================================================================
+// Code for Dna(5) to AminoAcid Translation
+// ==========================================================================
+
+
+#ifndef INCLUDE_SEQAN_TRANSLATION_TRANSLATION_H_
+#define INCLUDE_SEQAN_TRANSLATION_TRANSLATION_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Enum TranslationFrames
+// -----------------------------------------------------------------------
+
+/*!
+ * @enum TranslationFrames
+ * @headerfile <seqan/translation.h>
+ * @brief Class Enum with frames for @link translate @endlink()
+ *
+ * @signature enum class TranslationFrames : uint8_t { ... };
+ *
+ * Please not that this is part of the translation module which requires C++11.
+ *
+ * @val TranslationFrames SINGLE_FRAME = 0;
+ * @brief Translate the sequence(s) "as is", n input sequences result in n output sequences.
+ *
+ * @val TranslationFrames WITH_REVERSE_COMPLEMENT = 1;
+ * @brief Translate the sequence(s) as well as their reverse complements (n -> * 2n).
+ *
+ * @val TranslationFrames WITH_FRAME_SHIFTS = 2;
+ * @brief Translate the sequence(s) as well as their shifted frames (n -> 3n).
+ *
+ * @val TranslationFrames SIX_FRAME = 3;
+ * @brief Equals (WITH_REVERSE_COMPLEMENT | WITH_FRAME_SHIFTS); shifted frames of original and reverse complement are
+ *        translated (n -> 6n).
+ */
+
+enum TranslationFrames
+{
+    SINGLE_FRAME             = 0,
+    WITH_REVERSE_COMPLEMENT  = 1,
+    WITH_FRAME_SHIFTS        = 2,
+    SIX_FRAME                = 3
+};
+
+// -----------------------------------------------------------------------
+// Tag Frames_ (internal)
+// -----------------------------------------------------------------------
+
+template <uint8_t num>
+struct Frames_
+{};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// -----------------------------------------------------------------------
+// Metafunction ReverseComplement_
+// -----------------------------------------------------------------------
+
+// type of the reverse complement of a string, also works with infixes and
+// ModifiedStrings
+
+template <typename T>
+struct ReverseComplement_
+{
+    typedef ModifiedString<
+        ModifiedString<T, ModView<
+                           FunctorComplement<
+                               typename Value<T>::Type > > >, ModReverse> Type;
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// --------------------------------------------------------------------------
+// Function _ord()
+// --------------------------------------------------------------------------
+
+// returns ordValue of a DNA(5) or RNA(5) character
+// for everything else (e.g. char) the character is converted to Dna5 first
+
+template <typename T>
+inline typename ValueSize<T>::Type
+_ord(T const & c)
+{
+    return ordValue(Dna5(c));
+}
+
+inline ValueSize<Dna>::Type
+_ord(Dna const & c)
+{
+    return ordValue(c);
+}
+
+inline ValueSize<Dna5>::Type
+_ord(Dna5 const & c)
+{
+    return ordValue(c);
+}
+
+inline ValueSize<Rna>::Type
+_ord(Rna const & c)
+{
+    return ordValue(c);
+}
+
+inline ValueSize<Rna5>::Type
+_ord(Rna5 const & c)
+{
+    return ordValue(c);
+}
+
+// --------------------------------------------------------------------------
+// Function _translateTriplet()
+// --------------------------------------------------------------------------
+
+
+template <typename TOrd, GeneticCodeSpec CODE_SPEC>
+inline AminoAcid
+_translateTriplet(TOrd const & c1,
+                  TOrd const & c2,
+                  TOrd const & c3,
+                  GeneticCode<CODE_SPEC> const & /**/)
+{
+    return (( c1 > 3 ) || ( c2 > 3 ) || ( c3 > 3 ) )
+            ? 'X'
+            : TranslateTableDnaToAminoAcid_<
+                GeneticCode<CODE_SPEC> >::VALUE[c1][c2][c3];
+}
+
+// --------------------------------------------------------------------------
+// Function _translateString()
+// --------------------------------------------------------------------------
+
+template <typename TOutString, typename TInString, GeneticCodeSpec CODE_SPEC>
+inline void
+_translateString(TOutString & target,
+                 TInString const & source,
+                 GeneticCode<CODE_SPEC> const & /**/)
+{
+    SEQAN_ASSERT_EQ(length(source)/3, length(target));
+    typedef typename Position<TInString>::Type TPos;
+
+    for (TPos i = 0; i+2 < length(source); i+=3)
+    {
+        target[i/3] = _translateTriplet(_ord(value(source, i  )),
+                                        _ord(value(source, i+1)),
+                                        _ord(value(source, i+2)),
+                                        GeneticCode<CODE_SPEC>());
+    }
+}
+
+template <typename TOutString, typename TSpec, typename TInString, GeneticCodeSpec CODE_SPEC>
+inline void
+_translateString(Segment<TOutString, TSpec> SEQAN_FORWARD_RETURN target,
+                 TInString const & source,
+                 GeneticCode<CODE_SPEC> const & /**/)
+{
+    SEQAN_ASSERT_EQ(length(source)/3, length(target));
+    typedef typename Position<TInString>::Type TPos;
+
+    for (TPos i = 0; i+2 < length(source); i+=3)
+    {
+        target[i/3] = _translateTriplet(_ord(value(source, i  )),
+                                        _ord(value(source, i+1)),
+                                        _ord(value(source, i+2)),
+                                        GeneticCode<CODE_SPEC>());
+    }
+}
+
+// --------------------------------------------------------------------------
+// Function _translateImplLoop()
+// --------------------------------------------------------------------------
+
+// single frame
+template <typename TSpec1, typename TSpec2, typename TSpec3, typename TInString,
+          GeneticCodeSpec CODE_SPEC>
+inline void
+_translateImplLoop(StringSet<String<AminoAcid, TSpec1>, TSpec2> & target,
+                   unsigned const i,
+                   StringSet<TInString, TSpec3> const & source,
+                   GeneticCode<CODE_SPEC> const & /**/,
+                   Frames_<1u> const & /**/)
+{
+    typedef GeneticCode<CODE_SPEC> TCode;
+    _translateString(target[i], source[i], TCode());
+}
+
+// with reverse complement
+template <typename TSpec1, typename TSpec2, typename TSpec3, typename TInString,
+          GeneticCodeSpec CODE_SPEC>
+inline void
+_translateImplLoop(StringSet<String<AminoAcid, TSpec1>, TSpec2> & target,
+                   unsigned const i,
+                   StringSet<TInString, TSpec3> const & source,
+                   GeneticCode<CODE_SPEC> const & /**/,
+                   Frames_<2u> const & /**/)
+{
+    typedef typename Value<StringSet<TInString, TSpec3> const>::Type TVal;
+    typedef typename ReverseComplement_<TVal>::Type TRevComp;
+    typedef GeneticCode<CODE_SPEC> TCode;
+
+    if (i % 2)
+    {
+         TVal val(value(source, i/2));
+        _translateString(target[i], TRevComp(val), TCode());
+    }
+    else
+    {
+        _translateString(target[i], source[i/2], TCode());
+    }
+}
+
+// three frame
+template <typename TSpec1, typename TSpec2, typename TSpec3, typename TInString,
+          GeneticCodeSpec CODE_SPEC>
+inline void
+_translateImplLoop(StringSet<String<AminoAcid, TSpec1>, TSpec2> & target,
+                   unsigned const i,
+                   StringSet<TInString, TSpec3> const & source,
+                   GeneticCode<CODE_SPEC> const & /**/,
+                   Frames_<3u> const & /**/)
+{
+    typedef GeneticCode<CODE_SPEC> TCode;
+    _translateString(target[i], suffix(source[i/3], i % 3), TCode());
+}
+
+// six frame
+template <typename TSpec1, typename TSpec2, typename TSpec3, typename TInString,
+          GeneticCodeSpec CODE_SPEC>
+inline void
+_translateImplLoop(StringSet<String<AminoAcid, TSpec1>, TSpec2> & target,
+                   unsigned const i,
+                   StringSet<TInString, TSpec3> const & source,
+                   GeneticCode<CODE_SPEC> const & /**/,
+                   Frames_<6u> const & /**/)
+{
+    typedef typename Prefix<
+        typename Value<
+            StringSet<TInString, TSpec3> const>::Type>::Type TVal;
+    typedef typename ReverseComplement_<TVal>::Type TRevComp;
+    typedef GeneticCode<CODE_SPEC> TCode;
+
+    if ((i % 6) > 2)
+    {
+         TVal val(prefix(value(source, i/6), length(value(source,i/6)) - (i % 3)));
+        _translateString(target[i], TRevComp(val), TCode());
+    }
+    else
+    {
+        _translateString(target[i], suffix(source[i/6], i % 3), TCode());
+    }
+
+}
+
+// --------------------------------------------------------------------------
+// Function _translateImplLoopOMPWrapper()
+// --------------------------------------------------------------------------
+
+
+template <typename TSource, typename TTarget, uint8_t frames,
+          GeneticCodeSpec CODE_SPEC>
+inline void
+_translateImplLoopOMPWrapper(TTarget & target,
+                             TSource const & source,
+                             GeneticCode<CODE_SPEC> const & /**/,
+                             Frames_<frames> const & /**/,
+                             Parallel const & /**/)
+{
+    SEQAN_OMP_PRAGMA(parallel for schedule(dynamic))
+    for (int64_t i = 0; i < static_cast<int64_t>(length(target)); ++i)
+        _translateImplLoop(target, i, source, GeneticCode<CODE_SPEC>(),
+                           Frames_<frames>());
+}
+
+template <typename TSource, typename TTarget, uint8_t frames,
+          GeneticCodeSpec CODE_SPEC>
+inline void
+_translateImplLoopOMPWrapper(TTarget & target,
+                             TSource const & source,
+                             GeneticCode<CODE_SPEC> const & /**/,
+                             Frames_<frames> const & /**/,
+                             Serial const & /**/)
+{
+    typedef typename Size<TTarget>::Type TPos;
+    for (TPos i = 0; i < length(target); ++i)
+        _translateImplLoop(target, i, source, GeneticCode<CODE_SPEC>(),
+                           Frames_<frames>());
+}
+
+// --------------------------------------------------------------------------
+// Function _translateImpl()
+// --------------------------------------------------------------------------
+
+// general case
+template <typename TSpec1, typename TSpec2, typename TSpec3, typename TInString,
+          typename TParallelism, GeneticCodeSpec CODE_SPEC, unsigned char n>
+inline void
+_translateImpl(StringSet<String<AminoAcid, TSpec1>, TSpec2> & target,
+               StringSet<TInString, TSpec3> const & source,
+               GeneticCode<CODE_SPEC> const & /**/,
+               Frames_<n> const & /**/,
+               TParallelism const & /**/)
+{
+    typedef typename Position<StringSet<TInString, TSpec3> >::Type TPos;
+
+    resize(target, length(source) * n, Exact());
+    for (TPos i = 0; i < length(target); ++i)
+    {
+        // current dnastring's length / 3 (3DNA -> 1 AA)
+        TPos len = length(source[i/n]) / 3;
+        // shorten for shifted frames
+        if (( n > 2 ) && ( length(source[i/n]) % 3 ) < ( i%3 ))
+            --len;
+        resize(target[i], len, Exact());
+    }
+
+    _translateImplLoopOMPWrapper(target, source, GeneticCode<CODE_SPEC>(),
+                                 Frames_<n>(),
+                                 TParallelism());
+}
+
+// ConcatDirect specialization
+template <typename TSpec1, typename TSpec3, typename TInString,
+          typename TParallelism, GeneticCodeSpec CODE_SPEC, unsigned char n>
+inline void
+_translateImpl(StringSet<String<AminoAcid,
+                                TSpec1>, Owner<ConcatDirect<> > > & target,
+               StringSet<TInString, TSpec3> const & source,
+               GeneticCode<CODE_SPEC> const & /**/,
+               Frames_<n> const & /**/,
+               TParallelism const & /**/)
+{
+    typedef typename Position<StringSet<TInString, TSpec3> >::Type TPos;
+
+    resize(target.limits, length(source) * n + 1, Exact());
+    target.limits[0] = 0;
+    for (TPos i = 0; i+1 < length(target.limits); ++i)
+    {
+        // current dnastring's length / 3 (3DNA -> 1 AA)
+        TPos len = length(source[i/n]) / 3;
+        // shorten for shifted frames
+        if (( n > 2 ) && ( length(source[i/n]) % 3 ) < ( i%3 ))
+            --len;
+        target.limits[i+1] = target.limits[i] + len;
+    }
+
+    resize(target.concat, back(target.limits), Exact());
+
+    _translateImplLoopOMPWrapper(target, source, GeneticCode<CODE_SPEC>(),
+                                 Frames_<n>(),
+                                 TParallelism());
+}
+
+// --------------------------------------------------------------------------
+// Function _translateInputWrap()
+// --------------------------------------------------------------------------
+
+// stringset to stringset
+template <typename TSpec1, typename TSpec2, typename TSpec3, typename TInString,
+          typename TParallelism, GeneticCodeSpec CODE_SPEC, unsigned char n>
+inline void
+_translateInputWrap(StringSet<String<AminoAcid, TSpec1>, TSpec2> & target,
+                    StringSet<TInString, TSpec3> const & source,
+                    GeneticCode<CODE_SPEC> const & /**/,
+                    Frames_<n> const & /**/,
+                    TParallelism const & /**/)
+{
+    _translateImpl(target, source, GeneticCode<CODE_SPEC>(), Frames_<n>(),
+                   TParallelism());
+}
+
+// single string to stringset conversion
+template <typename TSpec1, typename TSpec2, typename TInString,
+          typename TParallelism, GeneticCodeSpec CODE_SPEC, unsigned char n>
+inline void
+_translateInputWrap(StringSet<String<AminoAcid, TSpec1>, TSpec2> & target,
+                    TInString const & source,
+                    GeneticCode<CODE_SPEC> const & /**/,
+                    Frames_<n> const & /**/,
+                    TParallelism const & /**/)
+{
+    StringSet<TInString, Dependent<> > set;
+    appendValue(set, source);
+    _translateImpl(target, set, GeneticCode<CODE_SPEC>(), Frames_<n>(),
+                   TParallelism());
+}
+
+//bail out because multiple frames don't fit in one string
+template <typename TSpec1, typename TInString, typename TParallelism,
+          GeneticCodeSpec CODE_SPEC, unsigned char n>
+inline void
+_translateInputWrap(String<AminoAcid, TSpec1> & /**/,
+                    TInString const & /**/,
+                    GeneticCode<CODE_SPEC> const & /**/,
+                    Frames_<n> const & /**/,
+                    TParallelism const & /**/)
+{
+    SEQAN_FAIL("Implementation error, multiple frames selected, but only a "
+               "singe target string.");
+}
+
+// single string to single string conversion
+template <typename TSpec1, typename TInString, typename TParallelism,
+          GeneticCodeSpec CODE_SPEC>
+inline void
+_translateInputWrap(String<AminoAcid, TSpec1> & target,
+                    TInString const & source,
+                    GeneticCode<CODE_SPEC> const & /**/,
+                    Frames_<1> const & /**/,
+                    TParallelism const & /**/)
+{
+    resize(target, length(source)/3, Exact());
+    _translateString(target, source, GeneticCode<CODE_SPEC>());
+}
+
+// --------------------------------------------------------------------------
+// Function translate()
+// --------------------------------------------------------------------------
+
+/*!
+ * @fn translate
+ * @headerfile <seqan/translation.h>
+ * @brief translate sequences of Dna or Rna into amino acid alphabet, optionally with frames
+ * @signature int translate(target, source[, frames][, geneticCode][, TParallelism])
+ * @signature int translate(target, source[, frames][, geneticCodeSpec][, TParallelism])
+ *
+ * @param[out]      target      The amino acid sequence(s).  @link StringSet @endlink of @link AminoAcid @endlink
+ *                              or @link String @endlink of @link AminoAcid @endlink if source is a single string
+ *                              and frames is <tt>SINGLE_FRAME</tt>.
+ * @param[in]       source      Source sequences @link String @endlink or @link StringSet @endlink.
+ *                              If the value type is not Dna, Dna5, Rna, Rna5 then it is converted
+ *                              to Dna5.
+ * @param[in]       frame       The @link TranslationFrames @endlink, defaults to SINGLE_FRAME.
+ * @param[in]       geneticCode The @link GeneticCode @endlink to use, defaults
+ *                              to <tt>GeneticCode&lt;CANONICAL&gt;</tt>
+ *                              (use to specify GeneticCode at compile-time)
+ * @param[in]       geneticCodeSpec The @link GeneticCodeSpec @endlink to use
+ *                              (use to specify GenetiCode at run-time)
+ * @param[in]       TParallelism Whether to use SMP or not, see @link ParallelismTags @endlink .
+ *
+ * @return int 0 on success, and -1 on incompatible parameters (e.g. multiple frames but target type not StringSet).
+ *
+ * If OpenMP is supported by platform and TParallelism is not specified as
+ * "Serial", translation will be parallelized. The only exception is when doing
+ * single-frame translation of a single string -- which is never parallelized.
+ *
+ * The translation process is fastest when using ConcatDirect-StringSets for
+ * both input and output StringSets and when not having to convert the alphabet
+ * of the source, i.e. feeding AminoAcid-Strings, not CharStrings (although
+ * the latter is possible).
+ *
+ * Please note that specifying the GeneticCode at compile time avoids having
+ * unrequired conversion tables in memory. The implementation profits slightly
+ * from having SEQAN_CXX11_STANDARD defined.
+ * @section Example
+ *
+ * @code{.cpp}
+ * StringSet<Dna5String> dnaSeqs;
+ *
+ * // do something that fills up dnaSeqs, e.g. read from file or assign
+ *
+ * StringSet<String<AminoAcid>, Owner<ConcatDirect<> > > aaSeqs;
+ *
+ * translate(aaSeqs, dnaSeqs, SIX_FRAME);
+ *
+ * // do something with the aaSeqs
+ * @endcode
+ *
+ * @see TranslationFrames
+ * @see GeneticCode
+ */
+
+template <typename TTarget, typename TSource, typename TParallelism,
+          GeneticCodeSpec CODE_SPEC>
+inline void
+translate(TTarget & target,
+          TSource const & source,
+          TranslationFrames const frames,
+          GeneticCode<CODE_SPEC> const & /**/,
+          TParallelism const & /**/)
+{
+    typedef GeneticCode<CODE_SPEC> TCode;
+    switch (frames)
+    {
+    case SINGLE_FRAME:
+        return _translateInputWrap(target, source, TCode(), Frames_<1>(),
+                                   TParallelism());
+    case WITH_REVERSE_COMPLEMENT:
+        return _translateInputWrap(target, source, TCode(), Frames_<2>(),
+                                   TParallelism());
+    case WITH_FRAME_SHIFTS:
+        return _translateInputWrap(target, source, TCode(), Frames_<3>(),
+                                   TParallelism());
+    case SIX_FRAME:
+        return _translateInputWrap(target, source, TCode(), Frames_<6>(),
+                                   TParallelism());
+    }
+}
+
+template <typename TTarget, typename TSource, GeneticCodeSpec CODE_SPEC>
+inline void
+translate(TTarget & target,
+          TSource const & source,
+          TranslationFrames const frames,
+          GeneticCode<CODE_SPEC> const & /**/)
+{
+    return translate(target, source, frames, GeneticCode<CODE_SPEC>(),
+                     Parallel());
+}
+
+template <typename TTarget, typename TSource, GeneticCodeSpec CODE_SPEC>
+inline void
+translate(TTarget & target,
+          TSource const & source,
+          GeneticCode<CODE_SPEC> const & /**/)
+{
+    return translate(target, source, SINGLE_FRAME,
+                     GeneticCode<CODE_SPEC>(), Parallel());
+}
+
+template <typename TTarget, typename TSource>
+inline void
+translate(TTarget & target,
+          TSource const & source,
+          TranslationFrames const frames)
+{
+    return translate(target, source, frames, GeneticCode<>(), Parallel());
+}
+
+template <typename TTarget, typename TSource>
+inline void
+translate(TTarget & target,
+          TSource const & source)
+{
+    return translate(target, source, SINGLE_FRAME,
+                     GeneticCode<>(), Parallel());
+}
+
+template <typename TTarget, typename TSource, typename TParallelism>
+inline void
+translate(TTarget & target,
+          TSource const & source,
+          TranslationFrames const frames,
+          TParallelism const & /**/)
+{
+    return translate(target, source, frames, GeneticCode<>(), TParallelism());
+}
+
+// -----------------------------------------------------------------------
+// Function translate() with run-time spec selection
+// -----------------------------------------------------------------------
+
+template <typename TTarget, typename TSource, typename TParallelism,
+          GeneticCodeSpec currentSpec, typename TRestList>
+inline void
+_translate(TTarget & /**/,
+           TSource const & /**/,
+           TranslationFrames const /**/,
+           GeneticCodeSpec const & /**/,
+           TagList<GeneticCode<currentSpec>, TRestList> const & /**/,
+           TParallelism const & /**/,
+           True const & /**/)
+{
+    SEQAN_FAIL("Invalid genetic code translation table selected.\n");
+}
+
+// forward declare because of double-recursion
+template <typename TTarget, typename TSource, typename TParallelism,
+          GeneticCodeSpec currentSpec, typename TRestList>
+inline void
+_translate(TTarget & target,
+           TSource const & source,
+           TranslationFrames const frames,
+           GeneticCodeSpec const & geneticCodeSpec,
+           TagList<GeneticCode<currentSpec>, TRestList> const & /**/,
+           TParallelism const & /**/);
+
+template <typename TTarget, typename TSource, typename TParallelism,
+          GeneticCodeSpec currentSpec, typename TRestList>
+inline void
+_translate(TTarget & target,
+           TSource const & source,
+           TranslationFrames const frames,
+           GeneticCodeSpec const & geneticCodeSpec,
+           TagList<GeneticCode<currentSpec>, TRestList> const & /**/,
+           TParallelism const & /**/,
+           False const & /**/)
+{
+    return _translate(target, source, frames, geneticCodeSpec, TRestList(),
+                      TParallelism());
+}
+
+template <typename TTarget, typename TSource, typename TParallelism,
+          GeneticCodeSpec currentSpec, typename TRestList>
+inline void
+_translate(TTarget & target,
+           TSource const & source,
+           TranslationFrames const frames,
+           GeneticCodeSpec const & geneticCodeSpec,
+           TagList<GeneticCode<currentSpec>, TRestList> const & /**/,
+           TParallelism const & /**/)
+{
+    typedef TagList<GeneticCode<currentSpec>, TRestList> TTagList;
+
+    if (geneticCodeSpec == currentSpec)
+        return translate(target, source, frames, GeneticCode<currentSpec>(),
+                         TParallelism());
+
+    return _translate(target, source, frames, geneticCodeSpec,
+                             TTagList(), TParallelism(),
+                             typename IsSameType<TRestList, void>::Type());
+}
+
+template <typename TTarget, typename TSource, typename TParallelism>
+inline void
+translate(TTarget & target,
+          TSource const & source,
+          TranslationFrames const frames,
+          GeneticCodeSpec const & geneticCodeSpec,
+          TParallelism const & /**/)
+{
+    return _translate(target, source, frames, geneticCodeSpec, GeneticCodes_(),
+                      TParallelism());
+}
+
+// convenience
+template <typename TTarget, typename TSource>
+inline void
+translate(TTarget & target,
+          TSource const & source,
+          TranslationFrames const frames,
+          GeneticCodeSpec const & geneticCode)
+{
+    return translate(target, source, frames, geneticCode, Parallel());
+}
+
+}
+
+#endif // INCLUDE_SEQAN_TRANSLATION_TRANSLATION_H_
diff --git a/seqan/translation/translation_tables.h b/seqan/translation/translation_tables.h
new file mode 100644
index 0000000..5cca538
--- /dev/null
+++ b/seqan/translation/translation_tables.h
@@ -0,0 +1,884 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
+// ==========================================================================
+// Code for Dna(5) to AminoAcid Translation - Conversion Tables
+// ==========================================================================
+
+#ifndef INCLUDE_SEQAN_TRANSLATION_TRANSLATION_TABLES_H_
+#define INCLUDE_SEQAN_TRANSLATION_TRANSLATION_TABLES_H_
+
+namespace seqan {
+
+// ============================================================================
+// Forwards
+// ============================================================================
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+/*!
+ * @enum GeneticCodeSpec GeneticCode Specs
+ * @brief Specialization values for @link GeneticCode @endlink
+ * @headerfile <seqan/translation.h>
+ *
+ * @signature enum class  GeneticCodeSpec : uint8_t { ...};
+ *
+ * @see translate
+ * @see GeneticCode
+ *
+ * The numeric values of the enums correspond to the genbank transl_table values
+ * (see <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi">http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi</a>).
+ * Some genetic codes have been deprecated, so not all numeric values are available.
+ *
+ * Please not that this is part of the translation module which requires C++11.
+ *
+ * @val GeneticCodeSpec CANONICAL = 1
+ * @brief The Standard Genetic Code
+ *
+ * @val GeneticCodeSpec VERT_MITOCHONDRIAL = 2
+ * @brief The Vertebrate Mitochondrial Code
+ *
+ * @val GeneticCodeSpec YEAST_MITOCHONDRIAL = 3
+ * @brief The Yeast Mitochondrial Code
+ *
+ * @val GeneticCodeSpec MOLD_MITOCHONDRIAL = 4
+ * @brief The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
+ *
+ * @val GeneticCodeSpec INVERT_MITOCHONDRIAL = 5
+ * @brief The Invertebrate Mitochondrial Code
+ *
+ * @val GeneticCodeSpec CILIATE = 6
+ * @brief The CILIATE, Dasycladacean and Hexamita Nuclear Code
+ *
+ * @val GeneticCodeSpec FLATWORM_MITOCHONDRIAL = 9
+ * @brief The Echinoderm and Flatworm Mitochondrial Code
+ *
+ * @val GeneticCodeSpec EUPLOTID = 10
+ * @brief The EUPLOTID Nuclear Code
+ *
+ * @val GeneticCodeSpec PROKARYOTE = 11
+ * @brief The Bacterial, Archaeal and Plant Plastid Code
+ *
+ * @val GeneticCodeSpec ALT_YEAST = 12
+ * @brief The Alternative Yeast Nuclear Code
+ *
+ * @val GeneticCodeSpec ASCIDIAN_MITOCHONDRIAL = 13
+ * @brief The Ascidian Mitochondrial Code
+ *
+ * @val GeneticCodeSpec ALT_FLATWORM_MITOCHONDRIAL = 14
+ * @brief The Alternative Flatworm Mitochondrial Code
+ *
+ * @val GeneticCodeSpec BLEPHARISMA = 15
+ * @brief BLEPHARISMA Nuclear Code
+ *
+ * @val GeneticCodeSpec CHLOROPHYCEAN_MITOCHONDRIAL = 16
+ * @brief Chlorophycean Mitochondrial Code
+ *
+ * @val GeneticCodeSpec TREMATODE_MITOCHONDRIAL = 21
+ * @brief Trematode Mitochondrial Code
+ *
+ * @val GeneticCodeSpec SCENEDESMUS_MITOCHONDRIAL = 22
+ * @brief Scenedesmus obliquus mitochondrial Code
+ *
+ * @val GeneticCodeSpec THRAUSTOCHYTRIUM_MITOCHONDRIAL = 23
+ * @brief Thraustochytrium Mitochondrial Code
+ *
+ * @val GeneticCodeSpec PTEROBRANCHIA_MITOCHONDRIAL = 24
+ * @brief Pterobranchia mitochondrial code
+ *
+ * @val GeneticCodeSpec GRACILIBACTERIA = 25
+ * @brief Candidate Division SR1 and GRACILIBACTERIA Code
+ */
+
+enum GeneticCodeSpec
+{
+    CANONICAL=1,
+    VERT_MITOCHONDRIAL,
+    YEAST_MITOCHONDRIAL,
+    MOLD_MITOCHONDRIAL,
+    INVERT_MITOCHONDRIAL,
+    CILIATE,
+    FLATWORM_MITOCHONDRIAL = 9,
+    EUPLOTID,
+    PROKARYOTE,
+    ALT_YEAST,
+    ASCIDIAN_MITOCHONDRIAL,
+    ALT_FLATWORM_MITOCHONDRIAL,
+    BLEPHARISMA,
+    CHLOROPHYCEAN_MITOCHONDRIAL,
+    TREMATODE_MITOCHONDRIAL = 21,
+    SCENEDESMUS_MITOCHONDRIAL,
+    THRAUSTOCHYTRIUM_MITOCHONDRIAL,
+    PTEROBRANCHIA_MITOCHONDRIAL,
+    GRACILIBACTERIA
+};
+// ALERT When modifying the above, also adapt GeneticCodes_ appropriately
+
+// -----------------------------------------------------------------------
+// Tag GeneticCode
+// -----------------------------------------------------------------------
+
+/*!
+ * @tag GeneticCode
+ * @brief DNA/RNA to AminoAcid translation code, needs to be spec'ed by one of @link GeneticCodeSpec @endlink.
+ * @headerfile <seqan/translation.h>
+ * @signature GeneticCode<value>
+ *
+ * @see translate
+ * @see GeneticCodeSpec
+ *
+ */
+
+template <GeneticCodeSpec spec = CANONICAL>
+struct GeneticCode
+{};
+
+// -----------------------------------------------------------------------
+// TagList GeneticCodes_
+// -----------------------------------------------------------------------
+
+typedef TagList<GeneticCode<CANONICAL>,
+        TagList<GeneticCode<VERT_MITOCHONDRIAL>,
+        TagList<GeneticCode<YEAST_MITOCHONDRIAL>,
+        TagList<GeneticCode<MOLD_MITOCHONDRIAL>,
+        TagList<GeneticCode<INVERT_MITOCHONDRIAL>,
+        TagList<GeneticCode<CILIATE>,
+        TagList<GeneticCode<FLATWORM_MITOCHONDRIAL>,
+        TagList<GeneticCode<EUPLOTID>,
+        TagList<GeneticCode<PROKARYOTE>,
+        TagList<GeneticCode<ALT_YEAST>,
+        TagList<GeneticCode<ASCIDIAN_MITOCHONDRIAL>,
+        TagList<GeneticCode<ALT_FLATWORM_MITOCHONDRIAL>,
+        TagList<GeneticCode<BLEPHARISMA>,
+        TagList<GeneticCode<CHLOROPHYCEAN_MITOCHONDRIAL>,
+        TagList<GeneticCode<TREMATODE_MITOCHONDRIAL>,
+        TagList<GeneticCode<SCENEDESMUS_MITOCHONDRIAL>,
+        TagList<GeneticCode<THRAUSTOCHYTRIUM_MITOCHONDRIAL>,
+        TagList<GeneticCode<PTEROBRANCHIA_MITOCHONDRIAL>,
+        TagList<GeneticCode<GRACILIBACTERIA>
+        > > > > > > > > > > > > > > > > > > >  GeneticCodes_;
+
+// -----------------------------------------------------------------------
+// struct TranslateTableDnaToAminoAcid_
+// -----------------------------------------------------------------------
+
+template <typename TCodeSpec = GeneticCode<CANONICAL>,
+          typename TVoidSpec = void>
+struct TranslateTableDnaToAminoAcid_
+{
+    static char const VALUE[4][4][4];
+};
+
+/* Tables according to:
+ * http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
+ */
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<CANONICAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        CANONICAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { '*', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<VERT_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        VERT_MITOCHONDRIAL>, TVoidSpec>::VALUE [4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { '*', 'S', '*', 'S' }, // ag?
+        { 'M', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<YEAST_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        YEAST_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'M', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'T', 'T', 'T', 'T' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<MOLD_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        MOLD_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<INVERT_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        INVERT_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'S', 'S', 'S', 'S' }, // ag?
+        { 'M', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<CILIATE>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        CILIATE>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { 'Q', 'Y', 'Q', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { '*', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<FLATWORM_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        FLATWORM_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'N', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'S', 'S', 'S', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<EUPLOTID>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        EUPLOTID>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'C', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<PROKARYOTE>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        PROKARYOTE>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { '*', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<ALT_YEAST>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        ALT_YEAST>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'S', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { '*', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<ASCIDIAN_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        ASCIDIAN_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'G', 'S', 'G', 'S' }, // ag?
+        { 'M', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<ALT_FLATWORM_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        ALT_FLATWORM_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'N', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'S', 'S', 'S', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { 'Y', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<BLEPHARISMA>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        BLEPHARISMA>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', 'Q', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { '*', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<CHLOROPHYCEAN_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        CHLOROPHYCEAN_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', 'L', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { '*', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<TREMATODE_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        TREMATODE_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'N', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'S', 'S', 'S', 'S' }, // ag?
+        { 'M', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<SCENEDESMUS_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        SCENEDESMUS_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', 'L', 'Y' }, // ua?
+        { '*', 'S', 'S', 'S' }, // uc?
+        { '*', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<THRAUSTOCHYTRIUM_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        THRAUSTOCHYTRIUM_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { '*', 'C', 'W', 'C' }, // ug?
+        { '*', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<PTEROBRANCHIA_MITOCHONDRIAL>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        PTEROBRANCHIA_MITOCHONDRIAL>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'S', 'S', 'K', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'W', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+template <typename TVoidSpec>
+struct TranslateTableDnaToAminoAcid_<GeneticCode<GRACILIBACTERIA>,
+                                     TVoidSpec>
+{
+    static char const VALUE[4][4][4];
+};
+
+template <typename TVoidSpec>
+char const TranslateTableDnaToAminoAcid_<
+    GeneticCode<
+        GRACILIBACTERIA>, TVoidSpec>::VALUE[4][4][4] =
+{
+    { // a??
+        { 'K', 'N', 'K', 'N' }, // aa?
+        { 'T', 'T', 'T', 'T' }, // ac?
+        { 'R', 'S', 'R', 'S' }, // ag?
+        { 'I', 'I', 'M', 'I' }  // au?
+    }, { // c??
+        { 'Q', 'H', 'Q', 'H' }, // ca?
+        { 'P', 'P', 'P', 'P' }, // cc?
+        { 'R', 'R', 'R', 'R' }, // cg?
+        { 'L', 'L', 'L', 'L' }  // cu?
+    }, { // g??
+        { 'E', 'D', 'E', 'D' }, // ga?
+        { 'A', 'A', 'A', 'A' }, // gc?
+        { 'G', 'G', 'G', 'G' }, // gg?
+        { 'V', 'V', 'V', 'V' }  // gu?
+    }, { // u??
+        { '*', 'Y', '*', 'Y' }, // ua?
+        { 'S', 'S', 'S', 'S' }, // uc?
+        { 'G', 'C', 'W', 'C' }, // ug?
+        { 'L', 'F', 'L', 'F' }  // uu?
+    }
+    //     a    c    g    u
+};
+
+}
+
+#endif // INCLUDE_SEQAN_TRANSLATION_TRANSLATION_TABLES_H_
diff --git a/seqan/misc/misc_cmdparser.h b/seqan/ucsc_io.h
similarity index 77%
rename from seqan/misc/misc_cmdparser.h
rename to seqan/ucsc_io.h
index 074dfea..a4f2a0f 100644
--- a/seqan/misc/misc_cmdparser.h
+++ b/seqan/ucsc_io.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,13 +29,17 @@
 // DAMAGE.
 //
 // ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for module ucsc_io.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_UCSC_IO_H_
+#define SEQAN_INCLUDE_SEQAN_UCSC_IO_H_
 
-#ifndef CORE_INCLUDE_SEQAN_MISC_CMDPARSER_H_
-#define CORE_INCLUDE_SEQAN_MISC_CMDPARSER_H_
+#include <seqan/ucsc_io/ucsc_record.h>
+#include <seqan/ucsc_io/ucsc_io.h>
+#include <seqan/ucsc_io/ucsc_file.h>
 
-#include <seqan/misc/cmdparser/cmdparser.h>
-#include <seqan/misc/cmdparser/cmdoption.h>
-#include <seqan/misc/cmdparser/cmdparser_ctd_support.h>
-#include <seqan/misc/cmdparser/cmdparser_parse.h>
+#endif  // SEQAN_INCLUDE_SEQAN_UCSC_IO_H_
 
-#endif  // CORE_INCLUDE_SEQAN_MISC_CMDPARSER_H_
diff --git a/seqan/ucsc_io/ucsc_file.h b/seqan/ucsc_io/ucsc_file.h
new file mode 100644
index 0000000..1d385bc
--- /dev/null
+++ b/seqan/ucsc_io/ucsc_file.h
@@ -0,0 +1,182 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Class for reading/writing files in UCSC format.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_UCSC_IO_UCSC_FILE_H_
+#define SEQAN_INCLUDE_SEQAN_UCSC_IO_UCSC_FILE_H_
+
+namespace seqan {
+
+// ============================================================================
+// Typedefs
+// ============================================================================
+
+typedef Tag<Ucsc_<> > Ucsc;
+
+
+// ----------------------------------------------------------------------------
+// Typedef UcscFileIn
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class UcscFileIn
+ * @signature typedef FormattedFile<Ucsc, Input> UcscFileIn;
+ * @extends FormattedFileIn
+ * @headerfile <seqan/ucsc_io.h>
+ * @brief Class for reading UCSC <tt>knownGenes.txt</tt> and <tt>knownIsoforms.txt</tt> files.
+ *
+ * @see UcscRecord
+ */
+
+typedef FormattedFile<Ucsc, Input>   UcscFileIn;
+
+// ----------------------------------------------------------------------------
+// Typedef UcscFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class UcscFileOut
+ * @signature typedef FormattedFile<Ucsc, Output> UcscFileOut;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/ucsc_io.h>
+ * @brief Class for writing UCSC <tt>knownGenes.txt</tt> and <tt>knownIsoforms.txt</tt> files.
+ *
+ * @see UcscRecord
+ */
+
+typedef FormattedFile<Ucsc, Output> UcscFileOut;
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction FormattedFileContext
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<Ucsc, TDirection, TSpec>, TStorageSpec>
+{
+    typedef UcscIOContext Type;
+};
+
+// ----------------------------------------------------------------------------
+// Metafunction FileFormats
+// ----------------------------------------------------------------------------
+
+template <typename TDirection, typename TSpec>
+struct FileFormat<FormattedFile<Ucsc, TDirection, TSpec> >
+{
+    typedef TagSelector<
+                TagList<UcscKnownGene,
+                TagList<UcscKnownIsoforms
+                > >
+            > Type;
+};
+
+// ----------------------------------------------------------------------------
+// Function readRecord(); UcscRecord
+// ----------------------------------------------------------------------------
+
+// support for dynamically chosen file formats
+template <typename TForwardIter>
+inline void
+readRecord(UcscRecord & /* record */,
+           UcscIOContext & /* context */,
+           TForwardIter & /* iter */,
+           TagSelector<> const & /* format */)
+{
+    SEQAN_FAIL("UcscFileIn: File format not specified.");
+}
+
+template <typename TForwardIter, typename TTagList>
+inline void
+readRecord(UcscRecord & record,
+           UcscIOContext & context,
+           TForwardIter & iter,
+           TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        readRecord(record, context, iter, TFormat());
+    else
+        readRecord(record, context, iter, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+template <typename TSpec>
+void readRecord(UcscRecord & record, FormattedFile<Ucsc, Input, TSpec> & file)
+{
+    readRecord(record, context(file), file.iter, file.format);
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord(); UcscRecord
+// ----------------------------------------------------------------------------
+
+// support for dynamically chosen file formats
+template <typename TTarget>
+inline void
+writeRecord(TTarget & /* target */,
+            UcscRecord const & /* record */,
+            TagSelector<> const & /* format */)
+{
+    SEQAN_FAIL("UcscFileOut: File format not specified.");
+}
+
+template <typename TTarget, typename TTagList>
+inline void
+writeRecord(TTarget & target,
+            UcscRecord const & record,
+            TagSelector<TTagList> const & format)
+{
+    typedef typename TTagList::Type TFormat;
+
+    if (isEqual(format, TFormat()))
+        writeRecord(target, record, TFormat());
+    else
+        writeRecord(target, record, static_cast<typename TagSelector<TTagList>::Base const &>(format));
+}
+
+template <typename TSpec>
+inline void
+writeRecord(FormattedFile<Ucsc, Output, TSpec> & file, UcscRecord const & record)
+{
+    writeRecord(file.iter, record, file.format);
+}
+
+}  // namespace seqan
+
+#endif // SEQAN_INCLUDE_SEQAN_UCSC_IO_UCSC_FILE_H_
diff --git a/seqan/ucsc_io/ucsc_io.h b/seqan/ucsc_io/ucsc_io.h
new file mode 100644
index 0000000..39a2a79
--- /dev/null
+++ b/seqan/ucsc_io/ucsc_io.h
@@ -0,0 +1,446 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: David Weese <david.weese@fu-berlin.de>
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_UCSC_UCSC_IO_H_
+#define SEQAN_INCLUDE_SEQAN_UCSC_UCSC_IO_H_
+
+namespace seqan
+{
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag Ucsc
+// ----------------------------------------------------------------------------
+
+/*!
+ * @tag FileFormats#Ucsc
+ * @headerfile <seqan/ucsc_io.h>
+ * @brief UCSC Genome browser annotation file (aka knownGene format).
+ *
+ * @signature typedef Tag<Ucsc_<UcscKnownGene_> > const Ucsc;
+ */
+
+template <typename TSpec = void>
+struct Ucsc_;
+
+struct UcscKnownGene_;
+typedef Tag<Ucsc_<UcscKnownGene_> > UcscKnownGene;
+
+// ----------------------------------------------------------------------------
+// Tag Ucsc
+// ----------------------------------------------------------------------------
+
+/*!
+ * @tag FileFormats#UcscIsoforms
+ * @headerfile <seqan/ucsc_io.h>
+ * @brief UCSC Genome browser isoform file (aka knownIsoforms format).
+ *
+ * @signature typedef Tag<Ucsc_<UcscIsoforms_> > const UcscIsoforms;
+ */
+
+struct UcscKnownIsoforms_;
+typedef Tag<Ucsc_<UcscKnownIsoforms_> > UcscKnownIsoforms;
+
+// ----------------------------------------------------------------------------
+// Class UcscIOContext
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class UcscIOContext
+ * @headerfile <sean/ucsc_io.h>
+ * @brief Context to use for UCSC file I/O.
+ *
+ * @signature struct UcscIOContext;
+ */
+struct UcscIOContext
+{
+    /*!
+     * @var CharString UcscIOContext::buffer
+     * @brief Buffer used during UCSC I/O.
+     */
+    CharString buffer;
+};
+
+// ============================================================================
+// Metafunctions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Metafunction FileExtensions
+// ----------------------------------------------------------------------------
+
+template <typename T>
+struct FileExtensions<UcscKnownGene, T>
+{
+    static char const * VALUE[1];  // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<UcscKnownGene, T>::VALUE[1] =
+{
+    "knownGene.txt"         // default output extension
+};
+
+
+template <typename T>
+struct FileExtensions<UcscKnownIsoforms, T>
+{
+    static char const * VALUE[1];  // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<UcscKnownIsoforms, T>::VALUE[1] =
+{
+    "knownIsoforms.txt"     // default output extension
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function guessFormatFromStream
+// ----------------------------------------------------------------------------
+
+template <typename TBuffer, typename TFormatSpec>
+inline bool
+_ucscCheckHeader(TBuffer const & header, Tag<Ucsc_<TFormatSpec> > /*format*/)
+{
+    // knownIsoforms files have 2 tab-separated columns
+    // knownGene files have 12
+
+    typename DirectionIterator<TBuffer const, Input>::Type reader = directionIterator(header, Input());
+
+    // skip comments
+    while (!atEnd(reader) && value(reader) == '#')
+        skipLine(reader);
+
+    unsigned columns = (IsSameType<TFormatSpec, UcscKnownIsoforms_>::VALUE)? 2 : 12;
+
+    for (unsigned i = 1; i != columns; ++i)
+    {
+        // skip to the i'th tab
+        skipUntil(reader, OrFunctor<IsNewline, IsTab>());
+
+        // check for premature end
+        if (atEnd(reader) || IsNewline()(value(reader)))
+            return false;
+
+        skipOne(reader);    // skip tab
+    }
+
+    // skip presumed last column
+    skipUntil(reader, OrFunctor<IsNewline, IsTab>());
+    return atEnd(reader) || IsNewline()(value(reader));
+}
+
+// read first bytes of a file/stream and compare with file format's magic header
+template <typename TStream, typename TFormatSpec>
+inline bool
+guessFormatFromStream(TStream &istream, Tag<Ucsc_<TFormatSpec> > const & format)
+{
+    String<char, Array<1000> > putbackBuf;
+    bool match = false;
+
+    SEQAN_ASSERT(istream.good());
+
+    // try to read and check header
+    size_t numRead = istream.readsome(&putbackBuf[0], capacity(putbackBuf));
+    _setLength(putbackBuf, numRead);
+    if (_ucscCheckHeader(putbackBuf, format))
+        match = true;
+
+    // unget all read characters
+    for (; numRead > 0; --numRead)
+        istream.unget();
+
+    SEQAN_ASSERT(istream.good());
+
+    return match;
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecod
+// ----------------------------------------------------------------------------
+
+template <typename TForwardIter>
+void readRecord(UcscRecord & record,
+                UcscIOContext & /*ucscIOContext*/,
+                TForwardIter & iter,
+                UcscKnownIsoforms const & /*tag*/)
+{
+    OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, UcscKnownIsoforms> > nextRecord;
+    OrFunctor<IsNewline, AssertFunctor<NotFunctor<IsTab>, ParseError, UcscKnownIsoforms> > lastRecord;
+
+    clear(record);
+
+    // skip comments
+    while (!atEnd(iter) && value(iter) == '#')
+        skipLine(iter);
+
+    // read column 1: gene name (stored in .transName)
+    readUntil(record.transName, iter, nextRecord);
+    if (empty(record.transName))
+        SEQAN_THROW(EmptyFieldError("clusterId"));
+    insert(record.transName, 0, "GENE");    // prepend "GENE" for compatibility reasons
+    skipOne(iter, IsTab());
+
+    // read column 2: transcript name (stored in .contigName)
+    readUntil(record.contigName, iter, lastRecord);
+    if (empty(record.contigName))
+        SEQAN_THROW(EmptyFieldError("transcript"));
+    skipLine(iter);
+}
+
+template <typename TForwardIter>
+void readRecord(UcscRecord & record,
+                UcscIOContext & ucscIOContext,
+                TForwardIter & iter,
+                UcscKnownGene const & /*tag*/)
+{
+    OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, UcscKnownGene> > nextRecord;
+    OrFunctor<IsNewline, AssertFunctor<NotFunctor<IsTab>, ParseError, UcscKnownGene> > lastRecord;
+
+    clear(record);
+
+    CharString & buffer = ucscIOContext.buffer;
+
+    // skip comments
+    while (!atEnd(iter) && value(iter) == '#')
+        skipLine(iter);
+
+    // read column 1: transcript name
+    readUntil(record.transName, iter, nextRecord);
+    if (empty(record.transName))
+        SEQAN_THROW(EmptyFieldError("name"));
+    skipOne(iter, IsTab());
+
+    // read column 2: contig name
+    readUntil(record.contigName, iter, nextRecord);
+    if (empty(record.contigName))
+        SEQAN_THROW(EmptyFieldError("chrom"));
+    skipOne(iter, IsTab());
+
+    // read column 3: orientation
+    char orientation;
+    readOne(orientation, iter, OrFunctor<EqualsChar<'+'>, EqualsChar<'-'> >());
+    skipOne(iter, IsTab());
+
+    // read column 4: transcript begin position
+    clear(buffer);
+    readUntil(buffer, iter, nextRecord);
+    record.annotationBeginPos = lexicalCast<__uint32>(buffer);
+    skipOne(iter, IsTab());
+
+    // read column 5: transcript end position
+    clear(buffer);
+    readUntil(buffer, iter, nextRecord);
+    record.annotationEndPos = lexicalCast<__uint32>(buffer);
+    skipOne(iter, IsTab());
+
+    // read column 6: CDS begin position
+    clear(buffer);
+    readUntil(buffer, iter, nextRecord);
+    record.cdsBegin = lexicalCast<__uint32>(buffer);
+    skipOne(iter, IsTab());
+
+    // read column 7: CDS end position
+    clear(buffer);
+    readUntil(buffer, iter, nextRecord);
+    record.cdsEnd = lexicalCast<__uint32>(buffer);
+    skipOne(iter, IsTab());
+
+    // read column 8: exon count
+    unsigned exons;
+    clear(buffer);
+    readUntil(buffer, iter, nextRecord);
+    lexicalCastWithException(exons, buffer);
+    skipOne(iter, IsTab());
+
+    // read column 9: exon begin positions
+    for (unsigned i = 0; i < exons; ++i)
+    {
+        clear(buffer);
+        readUntil(buffer, iter, OrFunctor<OrFunctor<EqualsChar<';'>, EqualsChar<','> >, AssertFunctor<NotFunctor<IsNewline>, ParseError, UcscKnownGene> >());
+
+        __int32 tempBegin;
+        lexicalCastWithException(tempBegin, buffer);
+        appendValue(record.exonBegin, tempBegin);
+        skipOne(iter);
+    }
+    skipOne(iter, IsTab());
+
+    // read column 10: exon end positions
+    for (unsigned int i = 0; i < exons; ++i)
+    {
+        clear(buffer);
+        readUntil(buffer, iter, OrFunctor<OrFunctor<EqualsChar<';'>, EqualsChar<','> >, AssertFunctor<NotFunctor<IsNewline>, ParseError, UcscKnownGene> >());
+
+        __int32 tempEnd;
+        lexicalCastWithException(tempEnd, buffer);
+        appendValue(record.exonEnds, tempEnd);
+        skipOne(iter);
+    }
+    skipOne(iter, IsTab());
+
+    // read column 11: protein name
+    readUntil(record.proteinName, iter, nextRecord);
+    skipOne(iter, IsTab());
+
+    // skip column 12: align id
+    skipUntil(iter, lastRecord);
+    skipLine(iter);
+
+    // adapt positions
+    if (orientation == '-')
+    {
+        std::swap(record.annotationBeginPos, record.annotationEndPos);
+        std::swap(record.cdsBegin, record.cdsEnd);
+        for (unsigned i = 0; i < exons; ++i)
+            std::swap(record.exonBegin[i], record.exonEnds[i]);
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord
+// ----------------------------------------------------------------------------
+
+template <typename TTarget>
+void writeRecord(TTarget & target,
+                 UcscRecord const & record,
+                 UcscKnownIsoforms const & /*tag*/)
+{
+    unsigned suf = 0;
+    if (length(record.transName) >= 4 && prefix(record.transName, 4) == "GENE")
+        suf = 4;
+
+    // write column 1: transcript name
+    // The letters until the first whitespace will be write.
+    // Then, we skip until we hit the first tab character.
+    write(target, suffix(record.transName, suf));
+    writeValue(target, '\t');
+
+    // write column 2: contig name
+    write(target, record.contigName);
+    writeValue(target, '\n');
+}
+
+template <typename TTarget>
+void writeRecord(TTarget & target,
+                 UcscRecord const & record,
+                 UcscKnownGene const & /*tag*/)
+{
+    // write column 1: transcript name
+    // The letters until the first whitespace will be write.
+    // Then, we skip until we hit the first tab character.
+    write(target, record.transName);
+    writeValue(target, '\t');
+
+    // write column 2: contig name
+    write(target, record.contigName);
+    writeValue(target, '\t');
+
+    // write column 3: orientation
+    __uint32 transBeginPos, transEndPos;
+    __uint32 cdsBeginPos, cdsEndPos;
+    if (record.annotationBeginPos < record.annotationEndPos)
+    {
+        writeValue(target, '+');
+        transBeginPos = record.annotationBeginPos;
+        transEndPos = record.annotationEndPos;
+        cdsBeginPos = record.cdsBegin;
+        cdsEndPos = record.cdsEnd;
+    }
+    else
+    {
+        writeValue(target, '-');
+        transEndPos = record.annotationBeginPos;
+        transBeginPos = record.annotationEndPos;
+        cdsEndPos = record.cdsBegin;
+        cdsBeginPos = record.cdsEnd;
+    }
+    writeValue(target, '\t');
+
+    // write column 4: transcript begin position
+    appendNumber(target, transBeginPos);
+    writeValue(target, '\t');
+
+    // write column 5: transcript end position
+    appendNumber(target, transEndPos);
+    writeValue(target, '\t');
+
+    // write column 6: CDS begin position
+    appendNumber(target, cdsBeginPos);
+    writeValue(target, '\t');
+
+    // write column 7: CDS end position
+    appendNumber(target, cdsEndPos);
+    writeValue(target, '\t');
+
+    // write column 8: exon count
+    appendNumber(target, length(record.exonBegin));
+    writeValue(target, '\t');
+
+    // write column 9: exon begin positions
+    for (unsigned i = 0; i < length(record.exonBegin); ++i)
+    {
+        appendNumber(target, std::min(record.exonBegin[i], record.exonEnds[i]));
+        writeValue(target, ',');
+    }
+    writeValue(target, '\t');
+
+    // write column 10: exon end positions
+    for (unsigned i = 0; i < length(record.exonBegin); ++i)
+    {
+        appendNumber(target, std::max(record.exonBegin[i], record.exonEnds[i]));
+        writeValue(target, ',');
+    }
+    writeValue(target, '\t');
+
+    // write column 11: protein name
+    write(target, record.proteinName);
+    writeValue(target, '\t');
+
+    // write column 12: align id
+    write(target, record.transName);
+    writeValue(target, '\n');
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_UCSC_UCSC_IO_H_
diff --git a/seqan/ucsc_io/ucsc_record.h b/seqan/ucsc_io/ucsc_record.h
new file mode 100644
index 0000000..7a3dcbd
--- /dev/null
+++ b/seqan/ucsc_io/ucsc_record.h
@@ -0,0 +1,163 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Jochen Singer <jochen.singer@fu-berlin.de>
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_UCSC_RECORD_H_
+#define SEQAN_INCLUDE_SEQAN_UCSC_RECORD_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class UcscRecord
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class UcscRecord
+ * @implements FormattedFileRecordConcept
+ * @headerfile <seqan/ucsc_io.h>
+ * @brief Represent the information for one UCSC gene annotation record.
+ *
+ * @signature class UcscRecord;
+ *
+ * The UCSC genome browser server allows the download of a set of the known genes and isoforms used in the browser.
+ * These files can be downloaded from the UCSC FTP's <tt>goldenPath</tt> folder, e.g. the one for <a
+ * href="http://hgdownload.cse.ucsc.edu/goldenpath/hg19/">hg19</a>.
+ *
+ * To load the annotations, you need to download both the <tt>knownGenes.txt.gz</tt> and the
+ * <tt>knownIsoforms.txt.gz</tt> files from the UCSC <tt>goldenPath</tt> database.  These files can then be read record
+ * by record into a <tt>UcscRecord</tt>.  This record type is capable of representing records from either file type.
+ */
+
+class UcscRecord
+{
+public:
+
+    /*!
+     * @var CharString UcscRecord::transName
+     * @brief Name of the transcript.
+     */
+    CharString transName;
+
+    /*!
+     * @var CharString UcscRecord::contigName
+     * @brief Name of the contig of the genomic location.
+     */
+    CharString contigName;
+
+    /*!
+     * @var __int32 UcscRecord::cdsBegin
+     * @brief Start of the coding region (<tt>0</tt>-based position, defaults to <tt>-1</tt>).
+     */
+    __int32 cdsBegin;
+
+    /*!
+     * @var __int32 UcscRecord::cdsEnd
+     * @brief End of the coding region, defaults to <tt>-1</tt>.
+     */
+    __int32 cdsEnd;
+
+    /*!
+     * @var CharString UcscRecord::exonBegin
+     * @brief Start of the exon (<tt>0</tt>-based position, defaults to <tt>-1</tt>).
+     */
+    String<__int32> exonBegin;
+
+    /*!
+     * @var CharString UcscRecord::exonEnds
+     * @brief End of the exon, defaults to <tt>-1</tt>.
+     */
+    String<__int32> exonEnds;
+
+    /*!
+     * @var CharString UcscRecord::proteinName
+     * @brief Name of the coded protein.
+     */
+    CharString proteinName;
+
+    /*!
+     * @var __uint32 UcscRecord::annotationBeginPos
+     * @brief Start of the annotation (<tt>0</tt>-based, defaults to <tt>-1</tt>).
+     */
+    __uint32 annotationBeginPos;
+
+    /*!
+     * @var CharString UcscRecord::annotationEndPos
+     * @brief End position of the annotation, defaults to <tt>-1</tt>.
+     */
+    __uint32 annotationEndPos;
+
+    UcscRecord() : cdsBegin(0), cdsEnd(0), annotationBeginPos(0), annotationEndPos(0)
+    {}
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn UcscRecord#clear
+ * @brief Clear UcscRecord.
+ *
+ * @signature void clear(record);
+ *
+ * @param record The UcscRecord to clear.
+ *
+ * Clears all strings and resets it to default initialization state.
+ */
+
+inline void clear(UcscRecord & record)
+{
+    clear(record.transName);
+    clear(record.contigName);
+    record.cdsBegin = -1;
+    record.cdsEnd = -1;
+    clear(record.exonBegin);
+    clear(record.exonEnds);
+    clear(record.proteinName);
+
+    record.annotationBeginPos = -1;
+    record.annotationEndPos = -1;
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_
diff --git a/seqan/vcf_io.h b/seqan/vcf_io.h
new file mode 100644
index 0000000..b6af0f4
--- /dev/null
+++ b/seqan/vcf_io.h
@@ -0,0 +1,67 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+// Facade header for module vcf_io.
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_VCF_IO_H_
+#define SEQAN_INCLUDE_SEQAN_VCF_IO_H_
+
+// ===========================================================================
+// Prerequisites.
+// ===========================================================================
+
+#include <seqan/basic.h>
+#include <seqan/file.h>
+#include <seqan/sequence.h>
+#include <seqan/misc/name_store_cache.h>
+#include <seqan/stream.h>
+
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h>
+#include <htslib/kseq.h>
+
+// ===========================================================================
+// First Header Group.
+// ===========================================================================
+
+#include <seqan/vcf_io/vcf_header_record.h>
+
+#include <seqan/vcf_io/tabix.h>
+#include <seqan/vcf_io/vcf_header.h>
+#include <seqan/vcf_io/vcf_record.h>
+#include <seqan/vcf_io/vcf_io_context.h>
+#include <seqan/vcf_io/read_vcf.h>
+#include <seqan/vcf_io/write_vcf.h>
+#include <seqan/vcf_io/vcf_file.h>
+#endif  // SEQAN_INCLUDE_SEQAN_VCF_IO_H_
diff --git a/seqan/vcf_io/read_vcf.h b/seqan/vcf_io/read_vcf.h
new file mode 100644
index 0000000..2c03204
--- /dev/null
+++ b/seqan/vcf_io/read_vcf.h
@@ -0,0 +1,262 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_VCF_READ_VCF_H_
+#define SEQAN_INCLUDE_SEQAN_VCF_READ_VCF_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Tag Vcf
+// ----------------------------------------------------------------------------
+
+/*!
+ * @tag FileFormats#Vcf
+ * @headerfile <seqan/vcf_io.h>
+ * @brief Variant callinf format file.
+ *
+ * @signature typedef Tag<Vcf_> Vcf;
+ */
+struct Vcf_;
+typedef Tag<Vcf_> Vcf;
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function readRecord()                                            [VcfHeader]
+// ----------------------------------------------------------------------------
+
+inline void
+_parseVcfContig(CharString & chromName, CharString const & headerValue)
+{
+    if (length(headerValue) < 3u)
+        return;
+
+    CharString tmp = infix(headerValue, 1, length(headerValue) - 2);
+    StringSet<CharString> tmp2;
+    strSplit(tmp2, tmp, EqualsChar<','>());
+    for (unsigned i = 0; i < length(tmp2); ++i)
+    {
+        if (!startsWith(tmp2[i], "ID="))
+            continue;
+        chromName = suffix(tmp2[i], 3);
+    }
+}
+
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readHeader(VcfHeader & header,
+           VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           Vcf const & /*tag*/)
+{
+    clear(header);
+    CharString buffer;
+    VcfHeaderRecord record;
+
+    while (!atEnd(iter) && value(iter) == '#')
+    {
+        skipOne(iter);
+        clear(buffer);
+
+        if (value(iter) == '#')
+        {
+            // Is header line.
+            skipOne(iter);
+            clear(record);
+
+            // Read header key.
+            readUntil(record.key, iter, OrFunctor<EqualsChar<'='>, AssertFunctor<NotFunctor<IsNewline>, ParseError, Vcf> >());
+
+            // Skip '='.
+            skipOne(iter);
+
+            // Read header value.
+            readLine(record.value, iter);
+            appendValue(header, record);
+
+            // Parse out name if headerRecord is a contig field.
+            if (record.key == "contig")
+            {
+                _parseVcfContig(buffer, record.value);
+                appendName(contigNamesCache(context), buffer);
+            }
+        }
+        else
+        {
+            // Is line "#CHROM\t...".
+            readLine(buffer, iter);
+            if (!startsWith(buffer, "CHROM"))
+                ParseError("Invalid line with samples.");
+
+            // Split line, get sample names.
+            //StringSet<CharString> fields;
+            //strSplit(fields, buffer, IsTab());
+            //if (length(fields) < 9u)
+                //ParseError("Not enough fields.");
+
+            // Get sample names.
+            //for (unsigned i = 9; i < length(fields); ++i)
+                //appendName(sampleNamesCache(context), fields[i]);
+        }
+    }
+}
+
+// ----------------------------------------------------------------------------
+// Function readRecord()                                            [VcfRecord]
+// ----------------------------------------------------------------------------
+// Read record, updating list of known sequences if new one occurs.
+
+template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+readRecord(VcfRecord & record,
+           VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+           TForwardIter & iter,
+           Vcf const & /*tag*/)
+{
+    typedef OrFunctor<IsTab, AssertFunctor<NotFunctor<IsNewline>, ParseError, Vcf> > NextEntry;
+
+    clear(record);
+    CharString &buffer = context.buffer;
+
+    // CHROM
+    clear(buffer);
+    readUntil(buffer, iter, NextEntry());
+    if (empty(buffer))
+        SEQAN_THROW(EmptyFieldError("CHROM"));
+    record.rID = nameToId(contigNamesCache(context), buffer);
+    skipOne(iter);
+
+    // POS
+    clear(buffer);
+    readUntil(buffer, iter, NextEntry());
+    if (empty(buffer))
+        SEQAN_THROW(EmptyFieldError("POS"));
+    record.beginPos = lexicalCast<__int32>(buffer) - 1; // Translate from 1-based to 0-based.
+    skipOne(iter);
+
+    // ID
+    readUntil(record.id, iter, NextEntry());
+    if (empty(record.id))
+        SEQAN_THROW(EmptyFieldError("ID"));
+    skipOne(iter);
+
+    // REF
+    readUntil(record.ref, iter, NextEntry());
+    if (empty(record.id))
+        SEQAN_THROW(EmptyFieldError("REF"));
+    skipOne(iter);
+
+    // ALT
+    readUntil(record.alt, iter, NextEntry());
+    if (empty(record.id))
+        SEQAN_THROW(EmptyFieldError("ALT"));
+    skipOne(iter);
+
+    // QUAL
+    clear(buffer);
+    readUntil(buffer, iter, NextEntry());
+    if (empty(buffer))
+        SEQAN_THROW(EmptyFieldError("QUAL"));
+
+    if (buffer == ".")
+        record.qual = VcfRecord::MISSING_QUAL();
+    else
+        lexicalCastWithException(record.qual, buffer);
+
+    skipOne(iter);
+
+    // FILTER
+    readUntil(record.filter, iter, NextEntry());
+    if (empty(record.filter))
+        SEQAN_THROW(EmptyFieldError("FILTER"));
+    skipOne(iter);
+
+    // INFO
+    readUntil(record.info, iter, OrFunctor<IsTab, IsNewline>());
+    if (empty(record.info))
+        SEQAN_THROW(EmptyFieldError("INFO"));
+
+    // the following columns are optional
+    if (atEnd(iter) || IsNewline()(value(iter)))
+    {
+        skipLine(iter);
+        return;
+    }
+    skipOne(iter);
+
+    // FORMAT
+    readUntil(record.format, iter, NextEntry());
+    if (empty(record.format))
+        SEQAN_THROW(EmptyFieldError("FORMAT"));
+    skipOne(iter);
+
+    // The samples.
+    unsigned numSamples = length(sampleNames(context));
+    for (unsigned i = 0; i < numSamples; ++i)
+    {
+        clear(buffer);
+        if (i + 1 != numSamples)
+        {
+            readUntil(buffer, iter, NextEntry());
+            skipOne(iter);
+        }
+        else
+        {
+            readUntil(buffer, iter, OrFunctor<IsTab, IsNewline>());
+        }
+
+        if (empty(buffer))
+        {
+            char buffer[30];    // == 9 (GENOTYPE_) + 20 (#digits in MIN_INT64) + 1 (trailing zero)
+            sprintf(buffer, "GENOTYPE_%u", i + 1);
+            SEQAN_THROW(EmptyFieldError(buffer));
+        }
+        appendValue(record.genotypeInfos, buffer);
+    }
+
+    // skip line break and optional additional columns
+    skipLine(iter);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_VCF_READ_VCF_H_
diff --git a/seqan/vcf_io/tabix.h b/seqan/vcf_io/tabix.h
new file mode 100644
index 0000000..f94d66b
--- /dev/null
+++ b/seqan/vcf_io/tabix.h
@@ -0,0 +1,358 @@
+#ifndef SEQAN_VCF_IO_TABIX_H_
+#define SEQAN_VCF_IO_TABIX_H_
+
+#include <cstdlib>
+#include <string>
+#include <sys/stat.h>
+#include <iostream>
+#include <cstring>
+#include <vector>
+
+#include <seqan/vcf_io/vcf_record.h>
+
+
+namespace seqan {
+
+
+class Tabix
+{
+ public:
+  htsFile* fp = nullptr;
+  tbx_t* tbx = nullptr;
+  hts_itr_t* hts_iter = nullptr;
+  const tbx_conf_t *idxconf;
+  String<String<char> > chroms;
+  unsigned rID = 0;
+  StringSet<CharString> samples;
+};
+
+
+inline void
+clear(Tabix & index)
+{
+    if (index.fp)
+    {
+        hts_close(index.fp);
+        index.fp = NULL;
+    }
+
+    if (index.hts_iter)
+    {
+        tbx_itr_destroy(index.hts_iter);
+        index.hts_iter = NULL;
+    }
+
+    if (index.tbx)
+    {
+        tbx_destroy(index.tbx);
+        index.tbx = NULL;
+    }
+
+    clear(index.chroms);
+    index.rID = 0;
+    clear(index.samples);
+}
+
+inline void
+getHeader(seqan::CharString& header_string, Tabix & index)
+{
+  // clear(header);
+  kstring_t str = {0,0,0};
+
+  while ( hts_getline(index.fp, KS_SEP_LINE, &str) >= 0 )
+  {
+    if ( !str.l || str.s[0] != index.tbx->conf.meta_char )
+    {
+      break;
+    }
+    else
+    {
+      if (length(str.s) > 5 && strncmp(str.s, "#CHROM", 6) == 0)
+      {
+        seqan::CharString h_line(str.s);
+        seqan::strSplit(index.samples, h_line, seqan::EqualsChar<'\t'>());
+        size_t end = 8;
+        if (length(index.samples) > 8 && index.samples[8] == "FORMAT") end = 9;
+        erase(index.samples, 0, end);
+      }
+      else
+      {
+        append(header_string, str.s);
+        append(header_string, "\n");
+      }
+    }
+  }
+
+  free(str.s);
+
+  //set back to start
+  // index.rID = 0;
+  //
+  // if (index.hts_iter)
+  // {
+  //   tbx_itr_destroy(index.hts_iter);
+  //   index.hts_iter = NULL;
+  // }
+  //
+  // index.hts_iter = tbx_itr_querys(index.tbx, toCString(index.chroms[rID]));
+}
+
+inline bool
+_onLastRId(Tabix & index)
+{
+  return index.rID == length(index.chroms) - 1;
+}
+
+inline void
+_nextRId(Tabix & index)
+{
+    ++index.rID;
+
+    if (index.hts_iter)
+    {
+        tbx_itr_destroy(index.hts_iter);
+        index.hts_iter = NULL;
+    }
+
+    index.hts_iter = tbx_itr_querys(index.tbx, toCString(index.chroms[index.rID]));
+}
+
+inline bool
+_extractLineOfThisRId(String<char> & line, Tabix & index)
+{
+  kstring_t str = {0,0,0};
+
+  if (index.hts_iter && tbx_itr_next(index.fp, index.tbx, index.hts_iter, &str) >= 0)
+  {
+    line = str.s;
+    free(str.s);
+    return true;
+  }
+
+  free(str.s);
+  return false;
+}
+
+inline bool
+_extractLineOfThisRId(std::string & line, Tabix & index)
+{
+  kstring_t str = {0,0,0};
+
+  if (index.hts_iter && tbx_itr_next(index.fp, index.tbx, index.hts_iter, &str) >= 0)
+  {
+    line = str.s;
+    free(str.s);
+    return true;
+  }
+
+  free(str.s);
+  return false;
+}
+
+inline void
+_insertDataToVcfRecord(VcfRecord & record, String<char> const & line, unsigned const & rID)
+{
+    seqan::StringSet< seqan::String<char> > splitted_line;
+    seqan::strSplit(splitted_line, line, seqan::EqualsChar<'\t'>());
+    record.rID = rID;
+    lexicalCast(record.beginPos, splitted_line[1]);
+    --record.beginPos; // Change from 1-based to 0-based indexing
+    record.id = splitted_line[2];
+    record.ref = splitted_line[3];
+    record.alt = splitted_line[4];
+    lexicalCast(record.qual, splitted_line[5]);
+    record.filter = splitted_line[6];
+    record.info = splitted_line[7];
+
+    if (length(splitted_line) > 8)
+    {
+        record.format = splitted_line[8];
+    }
+
+    if (length(splitted_line) > 9)
+    {
+        erase(splitted_line, 0, 9);
+        record.genotypeInfos = std::move(splitted_line);
+    }
+}
+
+/**
+ * @brief Reads a VCF record to a single string.
+ * @details [long description]
+ *
+ * @param[in,out] line [description]
+ * @param[in] index [description]
+ */
+inline bool
+readRawRecord(String<char> & line, Tabix & index)
+{
+  while (!_onLastRId(index))
+  {
+    if(_extractLineOfThisRId(line, index))
+    {
+      return true;
+    }
+
+    _nextRId(index);
+  }
+
+  // We are on the last rID.
+  if(_extractLineOfThisRId(line, index))
+  {
+    return true;
+  }
+
+  return false;
+}
+
+
+inline bool
+readRawRecord(std::string & line, Tabix & index)
+{
+  while (!_onLastRId(index))
+  {
+    if(_extractLineOfThisRId(line, index))
+    {
+      return true;
+    }
+
+    _nextRId(index);
+  }
+
+  // We are on the last rID.
+  if(_extractLineOfThisRId(line, index))
+  {
+    return true;
+  }
+
+  return false;
+}
+
+/**
+ * @brief Read a VCF record from a tabix file.
+ * @details The tabix file needs to have previously been opened. If no record can be read false is returned,
+ * this can happen either because we've reached the end of the specified region or end of the BCF file.
+ *
+ * @param record A VCF record.
+ * @param index Tabix index.
+ *
+ * @return True means a new record was read, false is returned otherwise.
+ */
+inline bool
+readRecord(VcfRecord & record, Tabix & index)
+{
+    seqan::String<char> line;
+    if (!seqan::readRawRecord(line, index))
+        return false;
+
+    _insertDataToVcfRecord(record, line, index.rID);
+    return true;
+}
+
+/**
+ * @brief Changes the region of the index.
+ * @details The
+ *
+ * @param[in,out] index Tabix index.
+ * @param[in] region The region to change to. It should be on the format chrX or chrX:Y-Z.
+ */
+inline void
+setRegion(Tabix & index, const char * region)
+{
+    if (index.hts_iter)
+    {
+        tbx_itr_destroy(index.hts_iter);
+        index.hts_iter = NULL;
+    }
+
+    index.hts_iter = tbx_itr_querys(index.tbx, region);
+}
+
+/**
+ * @brief Reads a region of a VCF file.
+ * @details Note: The records variable is not clear before adding VCF records, to allow extractions of multiple regions.
+ *
+ * @param[in,out] records A list of VCF records.
+ * @param index [description]
+ * @param region [description]
+ */
+inline void
+readRegion(seqan::String<VcfRecord> & records, Tabix & index, const char * region)
+{
+    setRegion(index, region);
+    seqan::String<char> line;
+
+    while(_extractLineOfThisRId(line, index))
+    {
+        VcfRecord record;
+        _insertDataToVcfRecord(record, line, index.rID);
+        append(records, record);
+    }
+}
+
+
+inline bool
+readRegion(VcfRecord & record, Tabix & index)
+{
+    seqan::String<char> line;
+
+    if (!_extractLineOfThisRId(line, index))
+        return false;
+
+    _insertDataToVcfRecord(record, line, index.rID);
+    return true;
+}
+
+
+inline void
+open(Tabix & index, char const * vcfFilename, const char * fileMode = "r")
+{
+  clear(index);
+  struct stat stat_tbi,stat_vcf;
+  char *fnidx = (char*) calloc(strlen(vcfFilename) + 5, 1);
+  strcat(strcpy(fnidx, vcfFilename), ".tbi");
+
+  if (bgzf_is_bgzf(vcfFilename)!=1 )
+  {
+    SEQAN_FAIL("File '%s' was not identified as bgzipped. Please use bgzip to compress the file.", vcfFilename);
+    std::free(fnidx);
+  }
+
+  // Common source of errors: new VCF is used with an old index
+  stat(fnidx, &stat_tbi);
+  stat(vcfFilename, &stat_vcf);
+
+  if (stat_vcf.st_mtime > stat_tbi.st_mtime )
+  {
+    SEQAN_FAIL("The index file is older than the bcf file. Please reindex the bcf file.");
+  }
+
+  std::free(fnidx);
+
+  if ((index.fp = hts_open(vcfFilename, fileMode)) == 0)
+    SEQAN_FAIL("Fail to open the VCF file.");
+
+  if ((index.tbx = tbx_index_load(vcfFilename)) == NULL)
+    SEQAN_FAIL("Failed to load the VCF index file.");
+
+  int nseq;
+  const char** seq = tbx_seqnames(index.tbx, &nseq);
+
+  for (int i = 0; i < nseq; ++i)
+  {
+    appendValue(index.chroms, seq[i]);
+  }
+
+  std::free(seq);
+  index.idxconf = &tbx_conf_vcf;
+
+  // set up the iterator, defaults to the beginning
+  index.rID = 0;
+
+  if (seqan::length(index.chroms) > 0)
+    index.hts_iter = tbx_itr_querys(index.tbx, toCString(index.chroms[0]));
+}
+
+}  // namespace seqan
+
+#endif  // SEQAN_VCF_IO_TABIX_H_
diff --git a/seqan/bam_io/bam_reader.h b/seqan/vcf_io/vcf_file.h
similarity index 53%
rename from seqan/bam_io/bam_reader.h
rename to seqan/vcf_io/vcf_file.h
index 17e4a64..4700ed7 100644
--- a/seqan/bam_io/bam_reader.h
+++ b/seqan/vcf_io/vcf_file.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,11 +29,14 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// Author: David Weese <david.weese@fu-berlin.de>
 // ==========================================================================
+// Class for reading/writing files in Vcf format.
+// ==========================================================================
+// TODO(weese:) add Bcf I/O and integrate it
 
-#ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_READER_H_
-#define CORE_INCLUDE_SEQAN_BAM_IO_BAM_READER_H_
+#ifndef SEQAN_VCF_IO_VCF_FILE_H_
+#define SEQAN_VCF_IO_VCF_FILE_H_
 
 namespace seqan {
 
@@ -41,166 +44,193 @@ namespace seqan {
 // Forwards
 // ============================================================================
 
+struct Vcf_;
+typedef Tag<Vcf_> Vcf;
+
+struct Bcf_;
+typedef Tag<Bcf_> Bcf;
+
 // ============================================================================
-// Tags, Classes, Enums
+// Typedefs
 // ============================================================================
 
-// Implementation of reading BAM files.
+// ----------------------------------------------------------------------------
+// Typedef VcfFileIn
+// ----------------------------------------------------------------------------
 
-class BamReader_ :
-    public XamReader_
-{
-public:
-    // The BGZF Stream to read from.
-    Stream<Bgzf> _stream;
-    // Flag indicating whether there was an error or not.
-    bool _isGood;
-    // Size of the underlying file in bytes as it is on the disk.
-    __int64 _fileSize;
-
-    BamReader_() :
-        XamReader_(), _isGood(true), _fileSize(0)
-    {}
-
-    BamReader_(CharString const & filename);
-
-    // XamReader_ interface.
-
-    virtual int open(CharString const & filename);
-    virtual bool isGood();
-    virtual bool atEnd();
-    virtual int readHeader(BamHeader & header, BamIOContext<StringSet<CharString> > & context);
-    virtual int readRecord(BamAlignmentRecord & record, BamIOContext<StringSet<CharString> > & context);
-    virtual int close();
-
-    virtual __int64 fileSize() const;
-    virtual __int64 positionInFile() const;
-
-    bool jumpToRegion(bool & hasAlignment, __int32 refId, __int32 pos, __int32 endPos, BamIndex<Bai> const & index, BamIOContext<StringSet<CharString> > & context);
-    bool jumpToOrphans(BamIndex<Bai> const & index, BamIOContext<StringSet<CharString> > & context);
-};
+/*!
+ * @class VcfFileIn
+ * @signature typedef FormattedFile<Vcf, Input> VcfFileIn;
+ * @extends FormattedFileIn
+ * @headerfile <seqan/vcf_io.h>
+ * @brief Class for reading VCF files.
+ *
+ * @see VcfHeader
+ * @see VcfRecord
+ */
 
-// ============================================================================
-// Metafunctions
-// ============================================================================
+typedef FormattedFile<Vcf, Input>   VcfFileIn;
+
+// ----------------------------------------------------------------------------
+// Typedef VcfFileOut
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class VcfFileOut
+ * @signature typedef FormattedFile<Vcf, Output> VcfFileOut;
+ * @extends FormattedFileOut
+ * @headerfile <seqan/vcf_io.h>
+ * @brief Class for writing VCF files.
+ *
+ * @see VcfHeader
+ * @see VcfRecord
+ */
+
+typedef FormattedFile<Vcf, Output>  VcfFileOut;
 
 // ============================================================================
-// Functions
+// Metafunctions
 // ============================================================================
 
 // ----------------------------------------------------------------------------
-// Member Function BamReader_::BamReader_()
+// Class MagicHeader
 // ----------------------------------------------------------------------------
 
-inline BamReader_::BamReader_(CharString const & filename) :
-    XamReader_(filename), _isGood(true)
+template <typename T>
+struct MagicHeader<Vcf, T>
 {
-    this->open(_filename);
-}
-
-// ----------------------------------------------------------------------------
-// Member Function BamReader_::open()
-// ----------------------------------------------------------------------------
+    static unsigned char const VALUE[16];
+};
 
-inline int BamReader_::open(CharString const & filename)
+template <typename T>
+unsigned char const MagicHeader<Vcf, T>::VALUE[16] =
 {
-    if (!seqan::open(this->_stream, toCString(filename), "r"))
-    {
-        _isGood = false;
-        return 1;
-    }
+    '#', '#', 'f', 'i', 'l', 'e', 'f', 'o', 'r', 'm', 'a', 't', '=', 'V', 'C', 'F'  // VCF's magic header
+};
 
-    // Get file size from BGZF stream.
-    this->_fileSize = this->_stream._fileSize;
+template <typename T>
+struct MagicHeader<Bcf, T>
+{
+    static unsigned char const VALUE[5];
+};
 
-    return 0;
-}
+template <typename T>
+unsigned char const MagicHeader<Bcf, T>::VALUE[5] = { 'B', 'C', 'F', '\2', '\1' };  // BCF2's magic header
 
 // ----------------------------------------------------------------------------
-// Member Function BamReader_::isGood()
+// Class FileExtensions
 // ----------------------------------------------------------------------------
 
-inline bool BamReader_::isGood()
+template <typename T>
+struct FileExtensions<Vcf, T>
 {
-    return this->_isGood;
-}
+    static char const * VALUE[1];    // default is one extension
+};
 
-// ----------------------------------------------------------------------------
-// Member Function BamReader_::atEnd()
-// ----------------------------------------------------------------------------
+template <typename T>
+char const * FileExtensions<Vcf, T>::VALUE[1] =
+{
+    ".vcf"     // default output extension
+};
 
-inline bool BamReader_::atEnd()
+template <typename T>
+struct FileExtensions<Bcf, T>
 {
-    return seqan::atEnd(this->_stream);
-}
+    static char const * VALUE[1];    // default is one extension
+};
+
+template <typename T>
+char const * FileExtensions<Bcf, T>::VALUE[1] =
+{
+    ".bcf"     // default output extension
+};
 
 // ----------------------------------------------------------------------------
-// Member Function BamReader_::readHeader()
+// Metafunction FormattedFileContext
 // ----------------------------------------------------------------------------
 
-inline int BamReader_::readHeader(BamHeader & header, BamIOContext<StringSet<CharString> > & context)
+template <typename TDirection, typename TSpec, typename TStorageSpec>
+struct FormattedFileContext<FormattedFile<Vcf, TDirection, TSpec>, TStorageSpec>
 {
-    return seqan::readRecord(header, context, this->_stream, Bam());
-}
+    typedef StringSet<CharString>                                   TNameStore;
+    typedef NameStoreCache<TNameStore>                              TNameStoreCache;
+    typedef VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> Type;
+};
 
 // ----------------------------------------------------------------------------
-// Member Function BamReader_::readRecord()
+// Metafunction FileFormats
 // ----------------------------------------------------------------------------
 
-inline int BamReader_::readRecord(BamAlignmentRecord & record, BamIOContext<StringSet<CharString> > & context)
+template <typename TDirection, typename TSpec>
+struct FileFormat<FormattedFile<Vcf, TDirection, TSpec> >
 {
-    return seqan::readRecord(record, context, this->_stream, Bam());
-}
+// TODO(weese:) Enable this, as soon as someone implements BCF
+
+//#if SEQAN_HAS_ZLIB
+//    typedef TagSelector<
+//                TagList<Bcf,
+//                TagList<Vcf
+//                > >
+//            > Type;
+//#else
+    typedef Vcf Type;
+//#endif
+};
 
-// ----------------------------------------------------------------------------
-// Member Function BamReader_::close()
-// ----------------------------------------------------------------------------
+// --------------------------------------------------------------------------
+// Function _mapBamFormatToCompressionFormat()
+// --------------------------------------------------------------------------
 
-inline int BamReader_::close()
+inline BgzfFile
+_mapFileFormatToCompressionFormat(Bcf)
 {
-    seqan::close(this->_stream);
-    return 0;
+    return BgzfFile();
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamReader_::fileSize()
+// Function readHeader(); VcfHeader
 // ----------------------------------------------------------------------------
 
-inline __int64 BamReader_::fileSize() const
+template <typename TSpec>
+inline void
+readHeader(VcfHeader & header, FormattedFile<Vcf, Input, TSpec> & file)
 {
-    return this->_fileSize;
+    readHeader(header, context(file), file.iter, file.format);
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamReader_::positionInFile()
+// Function readRecord(); VcfRecord
 // ----------------------------------------------------------------------------
 
-inline __int64 BamReader_::positionInFile() const
+template <typename TSpec>
+inline void
+readRecord(VcfRecord & record, FormattedFile<Vcf, Input, TSpec> & file)
 {
-    return this->_stream._blockPosition;
+    readRecord(record, context(file), file.iter, file.format);
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamReader_::jumpToRegion()
+// Function writeHeader(); VcfHeader
 // ----------------------------------------------------------------------------
 
-inline bool BamReader_::jumpToRegion(bool & hasAlignments, __int32 refId, __int32 pos, __int32 posEnd,
-                                     BamIndex<Bai> const & index, BamIOContext<StringSet<CharString> > & context)
+template <typename TSpec>
+inline void
+writeHeader(FormattedFile<Vcf, Output, TSpec> & file, VcfHeader & header)
 {
-    return seqan::jumpToRegion(this->_stream, hasAlignments, context, refId, pos, posEnd, index);
+    writeHeader(file.iter, header, context(file), file.format);
 }
 
 // ----------------------------------------------------------------------------
-// Member Function BamReader_::jumpToOrphans()
+// Function writeRecord(); VcfRecord
 // ----------------------------------------------------------------------------
 
-inline bool BamReader_::jumpToOrphans(BamIndex<Bai> const & index, BamIOContext<StringSet<CharString> > & context)
+template <typename TSpec>
+inline void
+writeRecord(FormattedFile<Vcf, Output, TSpec> & file, VcfRecord & record)
 {
-    bool hasAlignments = false;
-    (void) hasAlignments;
-    return seqan::jumpToOrphans(this->_stream, hasAlignments, context, index);
+    writeRecord(file.iter, record, context(file), file.format);
 }
 
 }  // namespace seqan
 
-#endif  // #ifndef CORE_INCLUDE_SEQAN_BAM_IO_BAM_READER_H_
+#endif // SEQAN_VCF_IO_VCF_FILE_H_
diff --git a/seqan/misc/cmdparser/cmdparser_type_support.h b/seqan/vcf_io/vcf_header.h
similarity index 69%
rename from seqan/misc/cmdparser/cmdparser_type_support.h
rename to seqan/vcf_io/vcf_header.h
index 9bf253d..f5b7f50 100644
--- a/seqan/misc/cmdparser/cmdparser_type_support.h
+++ b/seqan/vcf_io/vcf_header.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -29,40 +29,34 @@
 // DAMAGE.
 //
 // ==========================================================================
-// Author: Stephan Aiche <stephan.aiche@fu-berlin.de>
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
 // ==========================================================================
 
-#ifndef CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_TYPE_SUPPORT_H_
-#define CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_TYPE_SUPPORT_H_
+#ifndef SEQAN_INCLUDE_SEQAN_VCF_VCF_HEADER_H_
+#define SEQAN_INCLUDE_SEQAN_VCF_VCF_HEADER_H_
 
 namespace seqan {
 
-// ----------------------------------------------------------------------------
-// Function _isDouble()
-// ----------------------------------------------------------------------------
-
-template <typename TString>
-inline bool
-_isDouble(TString const s)
-{
-    double dst;
-    std::istringstream stream(toCString(s));
-    return (!(stream >> dst).fail()) && (stream.rdbuf()->in_avail() == 0);
-}
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
 
 // ----------------------------------------------------------------------------
-// Function _isInt()
+// Class VcfHeader
 // ----------------------------------------------------------------------------
 
-template <typename TString>
-inline bool
-_isInt(TString const s)
-{
-    int dst;
-    std::istringstream stream(toCString(s));
-    return (!(stream >> dst).fail()) && (stream.rdbuf()->in_avail() == 0);
-}
+/*!
+ * @class VcfHeader
+ * @implements FormattedFileHeaderConcept
+ * @headerfile <seqan/vcf_io.h>
+ * @brief Store VCF Header information.
+ *
+ * @signature typedef String<VcfHeaderRecord> VcfHeader;
+ */
+
+// Records for the meta information lines.
+typedef String<VcfHeaderRecord> VcfHeader;
 
-} // namespace seqan
+}  // namespace seqan
 
-#endif // CORE_INCLUDE_SEQAN_MISC_CMDPARSER_CMDPARSER_TYPE_SUPPORT_H_
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_VCF_VCF_HEADER_H_
diff --git a/seqan/vcf_io/vcf_header_record.h b/seqan/vcf_io/vcf_header_record.h
new file mode 100644
index 0000000..65fb712
--- /dev/null
+++ b/seqan/vcf_io/vcf_header_record.h
@@ -0,0 +1,114 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+// TODO(holtgrew): Parse more than just the key/value pair.
+
+#ifndef SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_HEADER_RECORD_H_
+#define SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_HEADER_RECORD_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class VcfHeaderRecord
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class VcfHeaderRecord
+ * @headerfile <seqan/vcf_io.h>
+ * @brief Store key/value pair for VCF header records.
+ *
+ * @signature class VcfHeaderRecord;
+ *
+ * @var CharString VcfHeaderRecord::key;
+ * @brief Key of the header record.
+ *
+ * @var CharString VcfHeaderRecord::value;
+ * @brief Value of the header record.
+ */
+
+/*!
+ * @fn VcfHeaderRecord::VcfHeaderRecord
+ * @brief Constructor
+ *
+ * @signature VcfHeaderRecord::VcfHeaderRecord();
+ * @signature VcfHeaderRecord::VcfHeaderRecord(key, value);
+ *
+ * @param[in] key   Key of the header record, @link CharString @endlink.
+ * @param[in] value Key of the header record, @link CharString @endlink.
+ */
+
+/*!
+ * @fn VcfHeaderRecord#clear
+ *
+ * @brief Clear a VcfHeaderRecord.
+ * @signature void clear(record);
+ *
+ * @param[in,out] record The VcfHeaderRecord to clear.
+ */
+
+class VcfHeaderRecord
+{
+public:
+    // Record's key.
+    CharString key;
+    // Record's value.
+    CharString value;
+
+    // Default constructor.
+    VcfHeaderRecord()
+    {}
+
+    // Construct directly with key/value.
+    VcfHeaderRecord(CharString const & key, CharString const & value) :
+            key(key), value(value)
+    {}
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+inline void clear(VcfHeaderRecord & record)
+{
+    clear(record.key);
+    clear(record.value);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_HEADER_RECORD_H_
diff --git a/seqan/vcf_io/vcf_io_context.h b/seqan/vcf_io/vcf_io_context.h
new file mode 100644
index 0000000..14012c3
--- /dev/null
+++ b/seqan/vcf_io/vcf_io_context.h
@@ -0,0 +1,226 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_IO_CONTEXT_H_
+#define SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_IO_CONTEXT_H_
+
+namespace seqan {
+
+// ============================================================================
+// Classes
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class VcfIOContext
+// ----------------------------------------------------------------------------
+
+/*!
+ * @class VcfIOContext
+ * @headerfile <seqan/vcf_io.h>
+ * @brief The I/O context to use for VCF I/O.
+ *
+ * @signature template <typename TNameStore[, typename TNameStoreCache]>
+ *            class VcfIOContext;
+ *
+ * @tparam TNameStore      The type used to represent the names.
+ * @tparam TNameStoreCache The type used to cache the names. Defaults to @link NameStoreCache @endlink &lt;TNameStore&gtl;.
+ */
+
+/*!
+ * @fn VcfIOContext::VcfIOContext
+ * @brief Constructor.
+ *
+ * @signature VcfIOContext::VcfIOContext();
+ * @signature VcfIOContext::VcfIOContext(contigNames, sampleNames);
+ *
+ * Default constructor or construction with references to contig and sample names.
+ */
+
+template <typename TNameStore_        = StringSet<CharString>,
+          typename TNameStoreCache_   = NameStoreCache<TNameStore_>,
+          typename TStorageSpec       = Owner<> >
+class VcfIOContext
+{
+public:
+    typedef TNameStore_ TNameStore;
+    typedef TNameStoreCache_ TNameStoreCache;
+
+    typedef typename StorageSwitch<TNameStore, TStorageSpec>::Type      TNameStoreMember;
+    typedef typename StorageSwitch<TNameStoreCache, TStorageSpec>::Type TNameStoreCacheMember;
+
+    // Cache for the sequence name lookup.
+    TNameStoreMember        _contigNames;
+    TNameStoreCacheMember   _contigNamesCache;
+
+    // Cache for the sample name lookup.
+    TNameStoreMember        _sampleNames;
+    TNameStoreCacheMember   _sampleNamesCache;
+
+    CharString              buffer;
+
+    VcfIOContext() :
+        _contigNames(TNameStoreMember()),
+        _contigNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 (TNameStoreCache*)NULL,
+                                 _contigNames)),
+        _sampleNames(TNameStoreMember()),
+        _sampleNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 (TNameStoreCache*)NULL,
+                                 _sampleNames))
+    {}
+
+    VcfIOContext(TNameStore & nameStore_, TNameStoreCache & nameStoreCache_) :
+        _contigNames(_referenceCast<typename Parameter_<TNameStoreMember>::Type>(nameStore_)),
+        _contigNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 &nameStoreCache_,
+                                 _contigNames)),
+        _sampleNames(TNameStoreMember()),
+        _sampleNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 (TNameStoreCache*)NULL,
+                                 _sampleNames))
+    {}
+
+    template <typename TOtherStorageSpec>
+    VcfIOContext(VcfIOContext<TNameStore, TNameStoreCache, TOtherStorageSpec> & other) :
+        _contigNames(_referenceCast<typename Parameter_<TNameStoreMember>::Type>(contigNames(other))),
+        _contigNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 &contigNamesCache(other),
+                                 _contigNames)),
+        _sampleNames(_referenceCast<typename Parameter_<TNameStoreMember>::Type>(sampleNames(other))),
+        _sampleNamesCache(ifSwitch(typename IsPointer<TNameStoreCacheMember>::Type(),
+                                 &sampleNamesCache(other),
+                                 _sampleNames))
+    {}
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function contigNames()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn VcfIOContext#contigNames
+ * @brief Return reference to the contig names from @link VcfIOContext @endlink.
+ *
+ * @signature TNameStoreRef contigNames(context);
+ *
+ * @param[in] context The @link VcfIOContext @endlink to query.
+ *
+ * @return TNameStoreRef A reference to the <tt>TNameStore</tt> of the context.
+ */
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStore &
+contigNames(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context)
+{
+    return _referenceCast<TNameStore &>(context._contigNames);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStore const &
+contigNames(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context)
+{
+    return _referenceCast<TNameStore &>(context._contigNames);
+}
+
+/*!
+ * @fn VcfIOContext#contigNamesCache
+ * @brief Return reference to contig names cache from @link VcfIOContext @endlink.
+ *
+ * @signature TNameStoreCacheRef contigNamesCache(context);
+ *
+ * @param[in] context The @link BamIOContext @endlink to query.
+ *
+ * @return TNameStoreCacheRef A reference to the <tt>TNameStoreCache</tt> of the context.
+ */
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStoreCache &
+contigNamesCache(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context)
+{
+    return _referenceCast<TNameStoreCache &>(context._contigNamesCache);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStoreCache const &
+contigNamesCache(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context)
+{
+    return _referenceCast<TNameStoreCache &>(context._contigNamesCache);
+}
+
+/*!
+ * @fn VcfIOContext#sampleNames
+ * @brief Return reference to the sample names from @link VcfIOContext @endlink.
+ *
+ * @signature TNameStoreRef sampleNames(context);
+ *
+ * @param[in] context The @link VcfIOContext @endlink to query.
+ *
+ * @return TNameStoreRef A reference to the <tt>TNameStore</tt> of the context.
+ */
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStore &
+sampleNames(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context)
+{
+    return _referenceCast<TNameStore &>(context._sampleNames);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStore const &
+sampleNames(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context)
+{
+    return _referenceCast<TNameStore &>(context._sampleNames);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStoreCache &
+sampleNamesCache(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context)
+{
+    return _referenceCast<TNameStoreCache &>(context._sampleNamesCache);
+}
+
+template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline TNameStoreCache const &
+sampleNamesCache(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context)
+{
+    return _referenceCast<TNameStoreCache &>(context._sampleNamesCache);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_IO_CONTEXT_H_
diff --git a/seqan/vcf_io/vcf_record.h b/seqan/vcf_io/vcf_record.h
new file mode 100644
index 0000000..27ff527
--- /dev/null
+++ b/seqan/vcf_io/vcf_record.h
@@ -0,0 +1,202 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+// TODO(holtgrew): Get out more than just strings...
+
+#ifndef SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_RECORD_H_
+#define SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_RECORD_H_
+
+namespace seqan {
+
+// ============================================================================
+// Tags, Classes, Enums
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Class VcfRecord
+// ----------------------------------------------------------------------------
+//
+/*!
+ * @class VcfRecord
+ * @implements FormattedFileRecordConcept
+ * @headerfile <seqan/vcf_io.h>
+ * @brief Information for one VCF record.
+ *
+ * @signature class VcfRecord;
+ *
+ * We store most information as strings and without structure since the VCF format's definition is quite loose.  We plan
+ * to provide classes for structured access to these strings later.
+ *
+ * @section Remarks
+ *
+ * Although all positions in the VCF text format are 1-based, they are stored 0-based in the @link VcfRecord @endlink.
+ * Positions in string members are stored verbatim in the @link VcfRecord @endlink's members, e.g. 1-based.
+ *
+ * Invalid qualities are stored as a float <tt>NaN</tt> (not a number).  To test a float quality <tt>q</tt> for being
+ * <tt>NaN</tt>, test for <tt>q != q</tt>.  Only <tt>NaN</tt> has the property that <tt>NaN != NaN</tt>.
+ */
+
+/*!
+ * @fn VcfRecord::MISSING_QUAL
+ * @brief Return IEEE <tt>NaN</tt> float value.
+ *
+ * @signature float VcfRecord::MISSING_QUAL();
+ *
+ * @section Remarks
+ *
+ * This cannot be implemented portably as a constant in a header-only library.  In C++11, there is a function
+ * <tt>std::nanf()</tt> that could be used instead.  For C++98, this is the best we can do.
+ */
+
+/*!
+ * @fn VcfRecord::VcfRecord
+ * @brief Default constructor.
+ *
+ * @signature VcfRecord::VcfRecord();
+ */
+
+/*!
+ * @var VariableType VcfRecord::ref
+ * @brief Bases in the reference (@link CharString @endlink).
+ *
+ * @var VariableType VcfRecord::genotypeInfos
+ * @brief Genotype information, as in VCF file (@link StringSet @endlink<@link CharString @endlink>).
+ *
+ * @var VariableType VcfRecord::info
+ * @brief Value of the INFO field, empty if "." in VCF file (@link CharString @endlink).
+ *
+ * @var VariableType VcfRecord::INVALID_REFID
+ * @brief Static member as marker for invalid reference (<tt>__int32</tt>)
+ *
+ * @var VariableType VcfRecord::format
+ * @brief Value of the VCF FORMAT field, empty if "." in VCF file (@link CharString @endlink).
+ *
+ * @var VariableType VcfRecord::alt
+ * @brief Alternative bases in the variants, comma-separated if multiple (@link CharString @endlink).
+ *
+ * @var VariableType VcfRecord::qual
+ * @brief Quality, <tt>NaN</tt> if invalid (<tt>float</tt>).
+ *
+ * @var VariableType VcfRecord::filter
+ * @brief Value of FILTER field, empty if "." in VCF file (@link CharString @endlink).
+ *
+ * @var VariableType VcfRecord::rID
+ * @brief Static member as marker for invalid reference (<tt>__int32</tt>)
+ *
+ * @var VariableType VcfRecord::beginPos
+ * @brief Position of the VCF record (<tt>__int32</tt>).
+ *
+ * @var VariableType VcfRecord::INVALID_POS
+ * @brief Static member as marker for invalid position (<tt>__int32</tt>)
+ *
+ * @var VariableType VcfRecord::id
+ * @brief Textual identifier of the variant (@link CharString @endlink).
+ */
+
+class VcfRecord
+{
+public:
+    // Constant for invalid reference id.
+    static const __int32 INVALID_REFID = -1;
+    // Constant for invalid position.
+    static const __int32 INVALID_POS = -1;
+
+    // Numeric id of the reference sequence.
+    __int32 rID;
+    // Position on the reference.
+    __int32 beginPos;
+    // Textual identifier of the variant.
+    CharString id;
+    // Bases in the reference.
+    CharString ref;
+    // Bases in the alternatives, comma-separated.
+    CharString alt;
+    // Quality
+    float qual;
+    // Value of FILTER field.
+    CharString filter;
+    // Value of INFO field.
+    CharString info;
+    // Value of FORMAT field.
+    CharString format;
+    // The genotype infos.
+    StringSet<CharString> genotypeInfos;
+
+    // Default constructor.
+    VcfRecord() : rID(INVALID_REFID), beginPos(INVALID_POS), qual(MISSING_QUAL())
+    {}
+
+    // Actually this is IEEE NaN.
+    static float MISSING_QUAL()
+    {
+        union {
+            __uint32 u;
+            float f;
+        } tmp;
+        tmp.u = 0x7F800001;
+        return tmp.f;
+    }
+};
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function clear()
+// ----------------------------------------------------------------------------
+
+/*!
+ * @fn VcfRecord#clear
+ * @brief Clear a VcfRecord.
+ *
+ * @signature void clear(record);
+ *
+ * @param[in,out] record The VcfRecord to clear.
+ */
+
+inline void clear(VcfRecord & record)
+{
+    clear(record.id);
+    clear(record.ref);
+    clear(record.alt);
+    clear(record.filter);
+    clear(record.info);
+    clear(record.format);
+    clear(record.genotypeInfos);
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_VCF_IO_VCF_RECORD_H_
diff --git a/seqan/vcf_io/write_vcf.h b/seqan/vcf_io/write_vcf.h
new file mode 100644
index 0000000..9513366
--- /dev/null
+++ b/seqan/vcf_io/write_vcf.h
@@ -0,0 +1,154 @@
+// ==========================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ==========================================================================
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+// ==========================================================================
+// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+// ==========================================================================
+
+#ifndef SEQAN_INCLUDE_SEQAN_VCF_WRITE_VCF_H_
+#define SEQAN_INCLUDE_SEQAN_VCF_WRITE_VCF_H_
+
+namespace seqan {
+
+// ============================================================================
+// Functions
+// ============================================================================
+
+// ----------------------------------------------------------------------------
+// Function writeHeader()                                           [VcfHeader]
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+writeHeader(TTarget & target,
+            VcfHeader const & header,
+            VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+            Vcf const & /*tag*/)
+{
+    for (unsigned i = 0; i < length(header); ++i)
+    {
+        write(target, "##");
+        write(target, header[i].key);
+        writeValue(target, '=');
+        write(target, header[i].value);
+        writeValue(target, '\n');
+    }
+
+    write(target, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
+    for (unsigned i = 0; i < length(sampleNames(context)); ++i)
+    {
+        writeValue(target, '\t');
+        write(target, sampleNames(context)[i]);
+    }
+    writeValue(target, '\n');
+}
+
+// ----------------------------------------------------------------------------
+// Function writeRecord()                                           [VcfRecord]
+// ----------------------------------------------------------------------------
+
+template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
+inline void
+writeRecord(TTarget & target,
+            VcfRecord const & record,
+            VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
+            Vcf const & /*tag*/)
+{
+    // CHROM
+    write(target, contigNames(context)[record.rID]);
+    writeValue(target, '\t');
+
+    // POS
+    appendNumber(target, record.beginPos + 1);
+    writeValue(target, '\t');
+
+    // ID
+    if (empty(record.id))
+        writeValue(target, '.');
+    else
+        write(target, record.id);
+    writeValue(target, '\t');
+
+    // REF
+    if (empty(record.ref))
+        writeValue(target, '.');
+    else
+        write(target, record.ref);
+    writeValue(target, '\t');
+
+    // ALT
+    if (empty(record.alt))
+        writeValue(target, '.');
+    else
+        write(target, record.alt);
+    writeValue(target, '\t');
+
+    // QUAL
+    if (record.qual != record.qual)  // only way to test for nan
+        writeValue(target, '.');
+    else
+        appendNumber(target, record.qual);
+
+    // FILTER
+    writeValue(target, '\t');
+    if (empty(record.filter))
+        writeValue(target, '.');
+    else
+        write(target, record.filter);
+    writeValue(target, '\t');
+
+    // INFO
+    if (empty(record.info))
+        writeValue(target, '.');
+    else
+        write(target, record.info);
+
+    // FORMAT
+    writeValue(target, '\t');
+    if (empty(record.format))
+        writeValue(target, '.');
+    else
+        write(target, record.format);
+
+    // The samples.
+    for (unsigned i = 0; i < length(record.genotypeInfos); ++i)
+    {
+        writeValue(target, '\t');
+        if (empty(record.genotypeInfos[i]))
+            writeValue(target, '.');
+        else
+            write(target, record.genotypeInfos[i]);
+    }
+    writeValue(target, '\n');
+}
+
+}  // namespace seqan
+
+#endif  // #ifndef SEQAN_INCLUDE_SEQAN_VCF_WRITE_VCF_H_
diff --git a/seqan/version.h b/seqan/version.h
index fdde278..8b95be7 100644
--- a/seqan/version.h
+++ b/seqan/version.h
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                 SeqAn - The Library for Sequence Analysis
 // ==========================================================================
-// Copyright (c) 2006-2013, Knut Reinert, FU Berlin
+// Copyright (c) 2006-2015, Knut Reinert, FU Berlin
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -37,40 +37,11 @@
 #ifndef SEQAN_VERSION_H_
 #define SEQAN_VERSION_H_
 
-/**
-.Macro.SEQAN_VERSION_MAJOR
-..cat:Versioning
-..summary:Major SeqAn revision number.
-..signature:SEQAN_VERSION_MAJOR
-..example:For SeqAn version "1.3", this value is $1$, for "2.5.4", it is $2$.
-..include:seqan/version.h
+#define SEQAN_VERSION_MAJOR 2
 
-.Macro.SEQAN_VERSION_MINOR
-..cat:Versioning
-..summary:Minor SeqAn revision number.
-..signature:SEQAN_VERSION_MINOR
-..example:For SeqAn version "1.3", this value is $3$, for "1.5.4", it is $5$.
-..include:seqan/version.h
+#define SEQAN_VERSION_MINOR 1
 
-.Macro.SEQAN_VERSION_PATCH
-..cat:Versioning
-..summary:SeqAn patch revision number.
-..signature:SEQAN_VERSION_PATCH
-..example:For SeqAn version "1.3", this value is $0$, for "1.3.4", it is $4$.
-..include:seqan/version.h
-
-.Macro.SEQAN_VERSION_PRE_RELEASE
-..cat:Versioning
-..summary:Flag ($0$/$1$) to indicate whether this is a pre-release (i.e. SVN version).
-..signature:SEQAN_VERSION_PRE_RELEASE
-..include:seqan/version.h
-*/
-
-#define SEQAN_VERSION_MAJOR 1
-
-#define SEQAN_VERSION_MINOR 4
-
-#define SEQAN_VERSION_PATCH 2
+#define SEQAN_VERSION_PATCH 0
 
 #define SEQAN_VERSION_PRE_RELEASE 0